Nr search
BLASTX 2.2.2 [Dec-14-2001]
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.
Query= KMC004613A_C01 KMC004613A_c01
(530 letters)
Database: nr
1,393,205 sequences; 448,689,247 total letters
Searching..................................................done
Score E
Sequences producing significant alignments: (bits) Value
ref|NP_172201.1| hypothetical protein; protein id: At1g07210.1, ... 136 2e-31
gb|AAM93681.1| putative ribosomal protein [Oryza sativa (japonic... 123 1e-27
pdb|1I94|R Chain R, Crystal Structures Of The Small Ribosomal Su... 53 3e-06
sp|P80382|RS18_THETH 30S ribosomal protein S18 gi|10120581|pdb|1... 53 3e-06
ref|NP_230022.1| ribosomal protein S18 [Vibrio cholerae] gi|1138... 52 4e-06
>ref|NP_172201.1| hypothetical protein; protein id: At1g07210.1, supported by cDNA:
gi_12083223 [Arabidopsis thaliana]
gi|25406963|pir||C86207 hypothetical protein [imported]
- Arabidopsis thaliana
gi|8954025|gb|AAF82199.1|AC067971_7 Contains similarity
to a ribosomal protein S18 - Chlamydomonas reinhardtii
chloroplast (fragment) from Chlamydomonas reinhardtii
gb|Y16473. It contains a ribosomal protein S18 domain
PF|01084. EST gb|AI997380 comes from this gene.
[Arabidopsis thaliana]
gi|12083224|gb|AAG48771.1|AF332408_1 unknown protein
[Arabidopsis thaliana]
Length = 261
Score = 136 bits (342), Expect = 2e-31
Identities = 68/84 (80%), Positives = 74/84 (87%)
Frame = -2
Query: 511 KVTTKEVLSQADFRNVRFLANFITEAGILKKRSMTKISAKAQRKVAREIKTARAFGLMPF 332
+VTT+EVL ADFRNVRFLANFITEAGI+ KR T ISAKAQRK+AREIKTARAFGLMPF
Sbjct: 165 EVTTEEVLKNADFRNVRFLANFITEAGIIIKRKQTGISAKAQRKIAREIKTARAFGLMPF 224
Query: 331 TTMGTKSFAFGKTMENLDADFAYK 260
TTMGTK+F FGKTMEN D DF Y+
Sbjct: 225 TTMGTKAFQFGKTMENRDQDFEYE 248
>gb|AAM93681.1| putative ribosomal protein [Oryza sativa (japonica cultivar-group)]
Length = 274
Score = 123 bits (309), Expect = 1e-27
Identities = 65/102 (63%), Positives = 81/102 (78%), Gaps = 2/102 (1%)
Frame = -2
Query: 529 PIRPEFKVTTKEVLSQADFRNVRFLANFITEAGILKKRSMTKISAKAQRKVAREIKTARA 350
P RP+F+ TT+EVL +ADFRNVRFLANF+TEAGI+ KRS T+ISAKAQRKVAREIKTARA
Sbjct: 154 PPRPQFQTTTEEVLKKADFRNVRFLANFLTEAGIIIKRSQTRISAKAQRKVAREIKTARA 213
Query: 349 FGLMPFTTMGTKSFAFGKTME-NL-DADFAYKSDVRNVHELD 230
GL+PFTTMG + F +G+++E NL + ++ Y R E D
Sbjct: 214 LGLLPFTTMGQRPFIYGRSVEVNLSEEEYGYDFVDRRAGEPD 255
>pdb|1I94|R Chain R, Crystal Structures Of The Small Ribosomal Subunit With
Tetracycline, Edeine And If3 gi|14278568|pdb|1I95|R
Chain R, Crystal Structure Of The 30s Ribosomal Subunit
From Thermus Thermophilus In Complex With Edeine
gi|14278589|pdb|1I96|R Chain R, Crystal Structure Of The
30s Ribosomal Subunit From Thermus Thermophilus In
Complex With The Translation Initiation Factor If3
(C-Terminal Domain) gi|14278611|pdb|1I97|R Chain R,
Crystal Structure Of The 30s Ribosomal Subunit From
Thermus Thermophilus In Complex With Tetracycline
Length = 87
Score = 52.8 bits (125), Expect = 3e-06
Identities = 29/68 (42%), Positives = 38/68 (55%), Gaps = 3/68 (4%)
Frame = -2
Query: 523 RPEFKVTTKEVLSQ---ADFRNVRFLANFITEAGILKKRSMTKISAKAQRKVAREIKTAR 353
RP K K L + D+RNV L F++E G + R T +S K QR +A+ IK AR
Sbjct: 14 RPSRKAKVKATLGEFDLRDYRNVEVLKRFLSETGKILPRRRTGLSGKEQRILAKTIKRAR 73
Query: 352 AFGLMPFT 329
GL+PFT
Sbjct: 74 ILGLLPFT 81
>sp|P80382|RS18_THETH 30S ribosomal protein S18 gi|10120581|pdb|1FKA|R Chain R, Structure
Of Functionally Activated Small Ribosomal Subunit At 3.3
A Resolution gi|10835602|pdb|1FJG|R Chain R, Structure
Of The Thermus Thermophilus 30s Ribosomal Subunit In
Complex With The Antibiotics Streptomycin, Spectinomycin
And Paromomycin gi|11514244|pdb|1G1X|C Chain C,
Structure Of Ribosomal Proteins S15, S6, S18, And 16s
Ribosomal Rna gi|11514249|pdb|1G1X|H Chain H, Structure
Of Ribosomal Proteins S15, S6, S18, And 16s Ribosomal
Rna gi|13096411|pdb|1HR0|R Chain R, Crystal Structure Of
Initiation Factor If1 Bound To The 30s Ribosomal Subunit
gi|13399809|pdb|1HNW|R Chain R, Structure Of The Thermus
Thermophilus 30s Ribosomal Subunit In Complex With
Tetracycline gi|13399831|pdb|1HNX|R Chain R, Structure
Of The Thermus Thermophilus 30s Ribosomal Subunit In
Complex With Pactamycin gi|13399853|pdb|1HNZ|R Chain R,
Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit In Complex With Hygromycin B
gi|14278027|pdb|1GIX|U Chain U, Crystal Structure Of The
Ribosome At 5.5 A Resolution. This File, 1gix, Contains
The 30s Ribosome Subunit, Three Trna, And Mrna
Molecules. 50s Ribosome Subunit Is In The File 1giy
gi|14278073|pdb|1IBK|R Chain R, Structure Of The Thermus
Thermophilus 30s Ribosomal Subunit In Complex With The
Antibiotic Paromomycin gi|14278094|pdb|1IBL|R Chain R,
Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit In Complex With A Messenger Rna Fragment And
Cognate Transfer Rna Anticodon Stem-Loop Bound At The A
Site And With The Antibiotic Paromomycin
gi|14278118|pdb|1IBM|R Chain R, Structure Of The Thermus
Thermophilus 30s Ribosomal Subunit In Complex With A
Messenger Rna Fragment And Cognate Transfer Rna
Anticodon Stem-Loop Bound At The A Site
gi|15826137|pdb|1JGO|U Chain U, The Path Of Messenger
Rna Through The Ribosome. This File, 1jgo, Contains The
30s Ribosome Subunit, Three Trna, And Mrna Molecules.
50s Ribosome Subunit Is In The File 1giy
gi|15826162|pdb|1JGP|U Chain U, The Path Of Messenger
Rna Through The Ribosome. This File, 1jgp, Contains The
30s Ribosome Subunit, Three Trna, And Mrna Molecules.
50s Ribosome Subunit Is In The File 1giy
gi|15826187|pdb|1JGQ|U Chain U, The Path Of Messenger
Rna Through The Ribosome. This File, 1jgq, Contains The
30s Ribosome Subunit, Three Trna, And Mrna Molecules.
50s Ribosome Subunit Is In The File 1giy
gi|20663903|pdb|1J5E|R Chain R, Structure Of The Thermus
Thermophilus 30s Ribosomal Subunit
gi|27065893|pdb|1N32|R Chain R, Structure Of The Thermus
Thermophilus 30s Ribosomal Subunit Bound To Codon And
Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched
At The First Codon Position At The A Site With
Paromomycin gi|27065920|pdb|1N33|R Chain R, Structure Of
The Thermus Thermophilus 30s Ribosomal Subunit Bound To
Codon And Near-Cognate Transfer Rna Anticodon Stem-Loop
Mismatched At The Second Codon Position At The A Site
With Paromomycin gi|27065947|pdb|1N34|R Chain R,
Structure Of The Thermus Thermophilus 30s Ribosomal
Subunit In The Presence Of Codon And
Crystallographically Disordered Near-Cognate Transfer
Rna Anticodon Stem-Loop Mismatched At The First Codon
Position gi|27065973|pdb|1N36|R Chain R, Structure Of
The Thermus Thermophilus 30s Ribosomal Subunit In The
Presence Of Crystallographically Disordered Codon And
Near-Cognate Transfer Rna Anticodon Stem-Loop Mismatched
At The Second Codon Position gi|28373716|pdb|1ML5|U
Chain U, Structure Of The E. Coli Ribosomal Termination
Complex With Release Factor 2
gi|6739549|gb|AAF27297.1|AF146075_3 ribosomal protein
S18 [Thermus thermophilus]
Length = 88
Score = 52.8 bits (125), Expect = 3e-06
Identities = 29/68 (42%), Positives = 38/68 (55%), Gaps = 3/68 (4%)
Frame = -2
Query: 523 RPEFKVTTKEVLSQ---ADFRNVRFLANFITEAGILKKRSMTKISAKAQRKVAREIKTAR 353
RP K K L + D+RNV L F++E G + R T +S K QR +A+ IK AR
Sbjct: 15 RPSRKAKVKATLGEFDLRDYRNVEVLKRFLSETGKILPRRRTGLSGKEQRILAKTIKRAR 74
Query: 352 AFGLMPFT 329
GL+PFT
Sbjct: 75 ILGLLPFT 82
>ref|NP_230022.1| ribosomal protein S18 [Vibrio cholerae]
gi|11387102|sp|Q9KUZ0|RS18_VIBCH 30S ribosomal protein
S18 gi|11356096|pir||B82333 ribosomal protein S18 VC0368
[imported] - Vibrio cholerae (strain N16961 serogroup
O1) gi|9654785|gb|AAF93541.1| ribosomal protein S18
[Vibrio cholerae]
Length = 75
Score = 52.0 bits (123), Expect = 4e-06
Identities = 28/65 (43%), Positives = 41/65 (63%)
Frame = -2
Query: 523 RPEFKVTTKEVLSQADFRNVRFLANFITEAGILKKRSMTKISAKAQRKVAREIKTARAFG 344
R +F T E + + D+++V L N+ITEAG + +T SAK QR++AR IK AR
Sbjct: 7 RRKFCRFTAEGVQEIDYKDVATLKNYITEAGKIVPSRITGTSAKYQRQLARAIKRARYLA 66
Query: 343 LMPFT 329
L+P+T
Sbjct: 67 LLPYT 71
Database: nr
Posted date: Apr 1, 2003 2:05 AM
Number of letters in database: 448,689,247
Number of sequences in database: 1,393,205
Lambda K H
0.318 0.135 0.401
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 411,617,545
Number of Sequences: 1393205
Number of extensions: 8073539
Number of successful extensions: 17959
Number of sequences better than 10.0: 107
Number of HSP's better than 10.0 without gapping: 17664
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 0
Number of HSP's gapped (non-prelim): 17953
length of database: 448,689,247
effective HSP length: 115
effective length of database: 288,470,672
effective search space used: 17596710992
frameshift window, decay const: 50, 0.1
T: 12
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
