Miyakogusa Predicted Gene
- Lj0g3v0206989.2
BLASTP 2.2.25 [Feb-01-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= Lj0g3v0206989.2 tr|B9IDF9|B9IDF9_POPTR DNA-directed RNA
polymerase (Fragment) OS=Populus trichocarpa
GN=POPTRDRAFT_9,75.51,0,beta and beta-prime subunits of DNA dependent
RNA-polymerase,NULL; seg,NULL; RNA_pol_Rpb2_1,RNA poly,CUFF.13386.2
(486 letters)
Database: Medicago_aa4.0v1
62,319 sequences; 21,947,249 total letters
Searching..................................................done
Score E
Sequences producing significant alignments: (bits) Value
Medtr8g023445.1 | DNA-directed RNA polymerase | LC | chr8:845866... 742 0.0
Medtr1g023500.1 | DNA-directed RNA polymerase subunit beta | HC ... 249 5e-66
Medtr1g022135.1 | DNA-directed RNA polymerase | HC | chr1:686549... 226 3e-59
Medtr3g105990.1 | DNA-directed RNA polymerase subunit beta | HC ... 155 6e-38
Medtr0189s0050.1 | DNA-directed RNA polymerase | HC | scaffold01... 91 3e-18
Medtr8g023440.1 | RNA polymerase Rpb2 domain 3 protein | HC | ch... 79 1e-14
Medtr4g124030.1 | DNA-directed RNA polymerase | HC | chr4:511718... 69 2e-11
>Medtr8g023445.1 | DNA-directed RNA polymerase | LC |
chr8:8458667-8488921 | 20130731
Length = 2002
Score = 742 bits (1915), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 361/487 (74%), Positives = 410/487 (84%), Gaps = 5/487 (1%)
Query: 1 MPVMLRSCRCVLYEKDEAELAKLGECPLDPGGYFVIKGNEKVILIQEQLSKNRIIIVMDK 60
+P+MLRSC CVL +DEAELAKLGECPLDPGGYFV+KGNEKVILIQEQLSKNRIII DK
Sbjct: 1000 LPIMLRSCCCVLSNRDEAELAKLGECPLDPGGYFVVKGNEKVILIQEQLSKNRIIIDTDK 1059
Query: 61 NRNIXXXXXXXXXXXXXXXDIVMEKEKMWLKLNRFAKQVPLMVVMKAMGMESDQEVVQMV 120
+NI I+MEKEK+WL+LN+F K+VPLMVVMKAMGME DQEVVQ++
Sbjct: 1060 KKNITASVTSSTDKVKTKTTILMEKEKLWLELNQFPKKVPLMVVMKAMGMEHDQEVVQLI 1119
Query: 121 GRDPRYSLLLLPSFEECAQNGVYTQEQALAHLDSK-VKRSMFSNISSEKEGRGSPALKVL 179
GRDPRYS LL+PS EEC + G++TQ QAL ++DSK VKR + N+ KE + A +L
Sbjct: 1120 GRDPRYSFLLMPSIEECTKIGIFTQAQALDYVDSKAVKRHVPGNMQPPKERQ---AFNIL 1176
Query: 180 EEEFLSNIPVHQGNFRLKCIYAAVMMRRIMDAILNKDAMDDKDYVGNKRLELSGQLISLL 239
E FL+N+PVH NFR KCIY AVM+RRIMDAILNKDAMDDKDYVGNKRLELSGQ+ISLL
Sbjct: 1177 RETFLANVPVHGYNFRPKCIYVAVMIRRIMDAILNKDAMDDKDYVGNKRLELSGQVISLL 1236
Query: 240 FEDRFKTMGEQVRNSSDKLLDKPDKANRFDISSVLARHQDLITHGLESTLSTGNFEIRRF 299
FED FK+M +++ + DKLLDKPDKA +FD + L ++D IT GLE TLSTGNF+++RF
Sbjct: 1237 FEDLFKSMTTEIKFAVDKLLDKPDKARKFDFLTQLI-NRDCITPGLERTLSTGNFDVKRF 1295
Query: 300 RMERKGMTQVLQRLSFIGFLGQMTRVSPQFEKSRKVSGPRALQPSQWGMLCPCDTPEGEA 359
+M + G+TQVLQRLSFI LGQMTRV PQFEKSRKVSGPRALQPSQWGMLCPCDTPEGE+
Sbjct: 1296 KMHKSGVTQVLQRLSFISALGQMTRVQPQFEKSRKVSGPRALQPSQWGMLCPCDTPEGES 1355
Query: 360 CGLVKNLALMTHVTTDEEEAPLISLCYYLGVEDMEYLSGEELHTPDSFLVIFNGLILGKH 419
CGLVKNLALMTHVTTDEEE PLISLCY LGVE+ME+LSGEELHTP+SFLVIFNG+ILGKH
Sbjct: 1356 CGLVKNLALMTHVTTDEEEGPLISLCYLLGVENMEHLSGEELHTPNSFLVIFNGMILGKH 1415
Query: 420 RRPRGFVTAMRKLRRAGKIGEFVSVYVNEKQGCVYLASDGGRVCRPLVIADNGISRIKEY 479
RRP+ F TAMRKLRRA IGEFVSVYVNEKQ CVYLASDGGRVCRPLVIADNGISR+K +
Sbjct: 1416 RRPQRFATAMRKLRRACLIGEFVSVYVNEKQCCVYLASDGGRVCRPLVIADNGISRVKAH 1475
Query: 480 HMKELMD 486
HMKEL D
Sbjct: 1476 HMKELKD 1482
>Medtr1g023500.1 | DNA-directed RNA polymerase subunit beta | HC |
chr1:7523400-7533496 | 20130731
Length = 1195
Score = 249 bits (636), Expect = 5e-66, Method: Compositional matrix adjust.
Identities = 158/489 (32%), Positives = 248/489 (50%), Gaps = 33/489 (6%)
Query: 1 MPVMLRSCRCVLYEKDEAELAKLGECPLDPGGYFVIKGNEKVILIQEQLSKNRIIIV--- 57
+P+MLRS C LY+ E +L +LGECP D GGYF+I G+EKV++ QE++S N + +
Sbjct: 161 VPIMLRSSYCTLYQNSEKDLTELGECPYDQGGYFIINGSEKVLIAQEKMSTNHVYVFKKR 220
Query: 58 -------------MDKNRNIXXXXXXXXXXXXXXXDIVMEKEKMWLKLNRFAKQVPLMVV 104
M +++N + + L ++P+++V
Sbjct: 221 QPNKYAYVGEVRSMAESQNRPPSTMFVRMLSRASAKGGSSGQYIRATLPYIRTEIPIIIV 280
Query: 105 MKAMGMESDQEVVQMVG---RDPRYSLLLLPSFEECAQNGVYTQEQALAHLDSKVKRSMF 161
+A+G +D+++++ + D + LL PS EE Q Q +A LD KR
Sbjct: 281 FRALGFVADKDILEHICYDFADTQMMELLRPSLEEA----FVIQNQQVA-LDYIGKRG-- 333
Query: 162 SNISSEKEGRGSPALKVLEEEFLSNIPVHQGNFRLKCIYAAVMMRRIMDAILNKDAMDDK 221
S + KE R A +L++E L ++ V + K Y ++ R++ L + A DD+
Sbjct: 334 STVGVTKEKRIKYAKDILQKEMLPHVGVGEYCETKKAYYFGYIIHRLLLCALGRRAEDDR 393
Query: 222 DYVGNKRLELSGQLISLLFEDRFKTMGEQVRNSSDKLLDKPDKANRFDISSVLARHQDLI 281
D+ GNKRL+L+G L+ LF F+ + VR K +D N D++ A I
Sbjct: 394 DHYGNKRLDLAGPLLGGLFRMLFRKLTRDVRGYVQKCVD-----NGKDVNLQFAIKAKTI 448
Query: 282 THGLESTLSTGNFEIRRFRMERKGMTQVLQRLSFIGFLGQMTRVSPQFEKSRKVSGPRAL 341
T GL+ +L+TGN+ R G++QVL RL++ L + R++ + K++ PR L
Sbjct: 449 TSGLKYSLATGNWGQANAAGTRAGVSQVLNRLTYASTLSHLRRLNSPIGREGKLAKPRQL 508
Query: 342 QPSQWGMLCPCDTPEGEACGLVKNLALMTHVTTDEEEAPLISLCYYLGVEDMEYLSGEEL 401
SQWGM+CP +TPEG+ACGLVKNLALM ++T P++ G E+ E +S +
Sbjct: 509 HNSQWGMMCPAETPEGQACGLVKNLALMVYITVGSAAYPILEFLEEWGTENFEEISPAVI 568
Query: 402 HTPDSFLVIFNGLILGKHRRPRGFVTAMRKLRRAGKIGEFVSVYVNEKQGCVYLASDGGR 461
P + + NG +G HR P V +RKLRR + V V + + + + +D GR
Sbjct: 569 --PQATKIFVNGCWMGIHRDPDMLVRTLRKLRRRVDVNTEVGVVRDIRLKELRIYTDYGR 626
Query: 462 VCRPLVIAD 470
RPL I D
Sbjct: 627 CSRPLFIVD 635
>Medtr1g022135.1 | DNA-directed RNA polymerase | HC |
chr1:6865496-6872581 | 20130731
Length = 299
Score = 226 bits (577), Expect = 3e-59, Method: Compositional matrix adjust.
Identities = 125/222 (56%), Positives = 146/222 (65%), Gaps = 36/222 (16%)
Query: 1 MPVMLRSCRCVLYEKDEAELAKLGECPLDPGGYFVIKGNEKVILI-QEQLSKNRIIIVMD 59
MP+MLRSC CVL +DE ELAKLGECPLDPGGYF+IKGNEK I +Q +N
Sbjct: 52 MPIMLRSCCCVLNNRDEDELAKLGECPLDPGGYFIIKGNEKHYCICYKQYREN------- 104
Query: 60 KNRNIXXXXXXXXXXXXXXXDIVMEKEKMWLKLNRFAKQVPLMVVMKAMGMESDQEVVQM 119
KN+N + VPLMVVMKAMGME DQEVVQ+
Sbjct: 105 KNKNYHFD-------------------------GKGEDVVPLMVVMKAMGMEIDQEVVQL 139
Query: 120 VGRDPRYSLLLLPSFEECAQNGVYTQEQALAHLDSKVKRSMFSNISSEKEGRGSPALKVL 179
+GRDPRYS LL+PS EE V+TQ QAL +LDSK K FSN+++EK+GR A +L
Sbjct: 140 IGRDPRYSFLLMPSIEEYINCRVFTQAQALEYLDSKAKGPRFSNMAAEKDGR---AFNIL 196
Query: 180 EEEFLSNIPVHQGNFRLKCIYAAVMMRRIMDAILNKDAMDDK 221
+ EFL+N+P+H NFR KCIY AVMMRRIMDAILNKDAMDDK
Sbjct: 197 KNEFLANVPMHGDNFRPKCIYLAVMMRRIMDAILNKDAMDDK 238
>Medtr3g105990.1 | DNA-directed RNA polymerase subunit beta | HC |
chr3:48883860-48876376 | 20130731
Length = 1188
Score = 155 bits (393), Expect = 6e-38, Method: Compositional matrix adjust.
Identities = 138/495 (27%), Positives = 227/495 (45%), Gaps = 63/495 (12%)
Query: 1 MPVMLRSCRCVLYEKDEAELAKLGECPLDPGGYFVIKGNEKVILIQEQLSKNRIIIV--- 57
+PVM++S C + E A+ G+C D GGYF+IKG EK+ + QEQ+ R+ +
Sbjct: 191 LPVMVKSDLCWMSE------AEKGDCEFDHGGYFLIKGAEKIFIAQEQIFLKRLWVSNIP 244
Query: 58 ---------MDKNRNIXXXXXXXXXXXXXXXDIVMEKEKMWLKLNRFAKQVPLMVVMKAM 108
M +NR + + + EK+ L + + ++P+ ++ A+
Sbjct: 245 YWAVAFKSQMKRNRMVVKLVEGST-------EGITNGEKL-LTVYFLSVEIPVWILFFAL 296
Query: 109 GMESDQEVVQMVG---RDPRYSLLLLPSFEECAQN--GVYTQEQALAHLDSKVKRSMFSN 163
G+ SD+E+V ++ + R +L S E + AL L+ +VK F
Sbjct: 297 GVTSDKEIVDLIDYGEANGRIENILFASIREADDKCEAFRRGKNALLFLEERVKGVQF-- 354
Query: 164 ISSEKEGRGSPALKVLEEEFLSNIPVHQGNFRLKCIYAAVMMRRIMDAILNKDAMDDKDY 223
P + ++E F + + + K Y A M++ ++ A + D++D
Sbjct: 355 ----------PPAESIDECFNMYVFPNVKGLKRKARYLAYMVKVLLLAYTGRRKTDNRDD 404
Query: 224 VGNKRLELSGQL----ISLLFEDRFKTMGEQVRNSSDKLLDKPDKANRFDISSVLARHQD 279
NKRLEL+G+L I + F K MG+ ++ + + D S
Sbjct: 405 FRNKRLELAGELLEREIKVHFAHARKRMGKALQRDLYGEREVRQIEHYLDAS-------- 456
Query: 280 LITHGLESTLSTGNFEIRRFRMER-KGMTQVLQRLSFIGFLGQMTRVSPQFEKSRKVSGP 338
+IT+GL+ STG + RMER G+ L R + + + ++ R Q + + KV
Sbjct: 457 IITNGLQRAFSTGAWTHPFKRMERISGVVATLGRTNPLQTMAELRRTRQQVQYTGKVGDA 516
Query: 339 RALQPSQWGMLCPCDTPEGEACGLVKNLALMTHVTTDEEEA--PLISLCYYLGVEDMEYL 396
R PS WG +C TP+GE CGLVKNLA+ V+TD E+ P +S C G+E++
Sbjct: 517 RYPHPSHWGKVCFLSTPDGENCGLVKNLAVTGVVSTDVTESILPQLSDC---GMEELVDD 573
Query: 397 SGEELHTPDSFLVIFNGLILGKHRRPRGFVTAMRKLRRAGKIGEFVSVYVNEKQGCVYLA 456
+ L D V NG +G FV +R RR ++ V + ++ Q V +
Sbjct: 574 TTTVLGKKDK--VFLNGDWVGVCSDSISFVAELRTRRRRNELPHQVEIKRDQCQQEVRIL 631
Query: 457 SDGGRVCRPLVIADN 471
SD GR+ RPL++ N
Sbjct: 632 SDAGRILRPLLVVSN 646
>Medtr0189s0050.1 | DNA-directed RNA polymerase | HC |
scaffold0189:29521-32643 | 20130731
Length = 517
Score = 90.9 bits (224), Expect = 3e-18, Method: Compositional matrix adjust.
Identities = 91/358 (25%), Positives = 157/358 (43%), Gaps = 50/358 (13%)
Query: 1 MPVMLRSCRCVLYEKDEAELAKLGECPLDPGGYFVIKGNEKVILIQEQLSKNRIIIV--- 57
+PVM++S C + E A+ G+C D GGYF+IKG EK+ + QEQ+ R+ +
Sbjct: 189 LPVMVKSDLCWMSE------AEKGDCEFDHGGYFLIKGAEKIFIAQEQVFLKRLWVSNIP 242
Query: 58 ---------MDKNRNIXXXXXXXXXXXXXXXDIVMEKEKMWLKLNRFAKQVPLMVVMKAM 108
M +NR + + + EK+ L + + ++P+ ++ A+
Sbjct: 243 YWAVAFKSQMKRNRMV-------VKLVEGSTEGITNGEKL-LTVYFLSVEIPVWILFFAL 294
Query: 109 GMESDQEVVQMVG---RDPRYSLLLLPSFEECAQN--GVYTQEQALAHLDSKVKRSMFSN 163
G+ SD+E+V ++ D R +L S E + AL L+ +VK F
Sbjct: 295 GVTSDKEIVDLIDYGESDGRIENILFASIREADDKCEAFRRGKNALLFLEERVKGVQF-- 352
Query: 164 ISSEKEGRGSPALKVLEEEFLSNIPVHQGNFRLKCIYAAVMMRRIMDAILNKDAMDDKDY 223
P + ++E F + + + K Y A M++ ++ A + D++D
Sbjct: 353 ----------PPAESIDECFNMYVFPNIKGLKRKARYLAYMVKVLLLAYTGRRKTDNRDD 402
Query: 224 VGNKRLELSGQLISLLFEDRFKTMGEQVRNSSDKLLDKPDKANRFDISSVLAR-HQDLIT 282
NKRLEL+G+L+ E K R K L + +R D+ + +IT
Sbjct: 403 FRNKRLELAGELL----EREIKVHFAHARKRMGKALQRDLYGDR-DVRQIEHYLDASIIT 457
Query: 283 HGLESTLSTGNFEIRRFRMER-KGMTQVLQRLSFIGFLGQMTRVSPQFEKSRKVSGPR 339
+GL+ STG + RMER G+ L R + + + ++ R Q + + KV R
Sbjct: 458 NGLQRAFSTGAWTHPFKRMERISGVVATLGRTNPLQTIAELRRTRQQVQYTGKVGDAR 515
>Medtr8g023440.1 | RNA polymerase Rpb2 domain 3 protein | HC |
chr8:8454247-8456089 | 20130731
Length = 181
Score = 79.0 bits (193), Expect = 1e-14, Method: Compositional matrix adjust.
Identities = 35/37 (94%), Positives = 35/37 (94%)
Query: 348 MLCPCDTPEGEACGLVKNLALMTHVTTDEEEAPLISL 384
MLCPCDTPEGE CGLVKNLALMTHVT DEEEAPLISL
Sbjct: 102 MLCPCDTPEGEYCGLVKNLALMTHVTADEEEAPLISL 138
>Medtr4g124030.1 | DNA-directed RNA polymerase | HC |
chr4:51171803-51193467 | 20130731
Length = 1191
Score = 68.6 bits (166), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 92/432 (21%), Positives = 166/432 (38%), Gaps = 82/432 (18%)
Query: 1 MPVMLRSCRCVLYEKDEAELAKLGECPLDPGGYFVIKGNEKVILIQEQLSKNRIIIVMDK 60
P+ML+S RC L + +L E + GGYF++ G E+ I R II+ +
Sbjct: 132 FPIMLQSKRCNLRDFPPRKLVSYKEEASEMGGYFIVNGLERCI---------RPIILPKR 182
Query: 61 NRNIXXXXXXXXXXXXXXXD-------IVMEKEKMWLKLNRFAK--------------QV 99
N + D + ++ + +KL +
Sbjct: 183 NYPMSTVRSSFSERREGYTDKAVVIRCVRADQTSLTVKLYHLRNGSARLGFWIHGREYML 242
Query: 100 PLMVVMKAMGMESDQEV--------------------VQMVGRDPRYSLLLLPSFEECAQ 139
P+ +++KA+ +D+E+ Q+VG R ++L E C
Sbjct: 243 PVGILLKALIDTTDREIYANLTSCYSEKYEKGKGVVGTQLVGE--RAKIILD---EVCEV 297
Query: 140 NGVYTQEQALAHLDSKVKRSMFSNISSEKEGRGSPALKVLEEEFLSNIPVHQGNFRLKCI 199
+ +T+ + L ++ + M E R V ++ + I VH N K
Sbjct: 298 SKKFTRLECLEYIGEHFQPIM-------HELRNESHYTVADDVLKNYIFVHLENNFDKFN 350
Query: 200 YAAVMMRRIMDAILNKDAMDDKDYVGNKRLELSGQLISLLFEDRFKTMGEQVRNSSDKLL 259
M++++ + D+ D + N+ + L G LI++ + + + E + LL
Sbjct: 351 LLIFMLQKLFSLVDQTSVPDNPDSLQNQEVLLPGHLITIYLKAKLE---EWLAKGKTLLL 407
Query: 260 DKPDKANR-------FD------ISSVLAR-HQDLITHGLESTLSTGNF--EIRRFRMER 303
D+ + + FD + VL + H + +ES L+TG I +
Sbjct: 408 DEIKRGGKIGKIGEKFDFRKFHHVKKVLEKNHASGVGKAIESMLTTGRLATSIPLDLPQT 467
Query: 304 KGMTQVLQRLSFIGFLGQMTRVS-PQFEKSRKVSGPRALQPSQWGMLCPCDTPEGEACGL 362
G+T +RL+F+ FL V + + R L P WG LCP TP+G CGL
Sbjct: 468 SGLTLQAERLNFLRFLSHFRHVHRGALFAGLRTTTVRKLLPESWGFLCPVHTPDGGPCGL 527
Query: 363 VKNLALMTHVTT 374
+ ++ +T+
Sbjct: 528 LNHMTHTCRITS 539