BLASTP 2.2.26 [Sep-21-2011]
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= 031985
(149 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2J5A|A Chain A, Folding Of S6 Structures With Divergent Amino-Acid
Composition: Pathway Flexibility Within Partly
Overlapping Foldons
Length = 110
Score = 35.4 bits (80), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 25/105 (23%), Positives = 53/105 (50%), Gaps = 6/105 (5%)
Query: 4 YDCMLLLKPHVRKESLMELVARVGKHVYGRNGVLTDITSFGTVQLGYGIKKL-DGRYYQG 62
Y+ + +KP + +E + + +V + + + G + +G QL Y I+K + RY+
Sbjct: 10 YETVFAVKPTLSEEEMKKKFEQVKEFIKQKGGEILYEEDWGMRQLAYPIQKFNNARYF-- 67
Query: 63 QLMQMTMMSTPNINKELQY-LNKEDRLLRWLLVKHRGMKNGKEAR 106
L+Q P + EL + L ++ ++RWL ++ + + K A+
Sbjct: 68 -LVQFK-TENPQLPNELDFQLKIDEDVIRWLNIQIKESEVKKNAQ 110
>pdb|1VMB|A Chain A, Crystal Structure Of 30s Ribosomal Protein S6 (tm0603)
From Thermotoga Maritima At 1.70 A Resolution
Length = 140
Score = 33.5 bits (75), Expect = 0.047, Method: Compositional matrix adjust.
Identities = 17/55 (30%), Positives = 28/55 (50%), Gaps = 1/55 (1%)
Query: 3 LYDCMLLLKPHVRKESLMELVARVGKHVYGR-NGVLTDITSFGTVQLGYGIKKLD 56
+Y+ M ++ P+V +E LV RV K + R G + + G + Y IKK +
Sbjct: 20 IYESMFIIAPNVPEEERENLVERVKKIIEERVKGKIDKVERMGMRKFAYEIKKFN 74
>pdb|3R3T|A Chain A, Crystal Structure Of 30s Ribosomal Protein S From
Bacillus Anthracis
pdb|3R3T|B Chain B, Crystal Structure Of 30s Ribosomal Protein S From
Bacillus Anthracis
Length = 99
Score = 28.9 bits (63), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 23/100 (23%), Positives = 41/100 (41%), Gaps = 17/100 (17%)
Query: 4 YDCMLLLKPHVRKESLMELVARVGKHVYGRNGVLTDITSFGTVQLGYGIKKLDGRYYQGQ 63
Y+ +++P V +E+ LV R + + + +G +L Y I L +Y
Sbjct: 7 YEIXYIIRPGVEEEAQKALVERFAGVLTNNGAEIINTKEWGKRRLAYEINDLREGFY--- 63
Query: 64 LMQMTMMSTPNINKELQYLNKEDRL-------LRWLLVKH 96
N+N + +N+ DRL LR ++VK
Sbjct: 64 -------XILNVNANAEAINEFDRLAKINEDILRHIVVKE 96
>pdb|4D93|A Chain A, Crystal Structure Of Tep1s
pdb|4D93|B Chain B, Crystal Structure Of Tep1s
pdb|4D93|C Chain C, Crystal Structure Of Tep1s
Length = 1323
Score = 27.3 bits (59), Expect = 3.3, Method: Composition-based stats.
Identities = 14/52 (26%), Positives = 29/52 (55%)
Query: 42 SFGTVQLGYGIKKLDGRYYQGQLMQMTMMSTPNINKELQYLNKEDRLLRWLL 93
S GT QLG +DG ++ + ++ ++ I EL+ K ++L+R+++
Sbjct: 371 SEGTEQLGINFNAVDGFFFYEDVNKVETVTDAYIKLELKSPIKRNKLMRFMV 422
>pdb|3F2B|A Chain A, Dna Polymerase Polc From Geobacillus Kaustophilus Complex
With Dna, Dgtp, Mg And Zn
pdb|3F2C|A Chain A, Dna Polymerase Polc From Geobacillus Kaustophilus Complex
With Dna, Dgtp And Mn
pdb|3F2D|A Chain A, Dna Polymerase Polc From Geobacillus Kaustophilus Complex
With Dna, Dgtp, Mn And Zn
Length = 1041
Score = 26.2 bits (56), Expect = 6.9, Method: Composition-based stats.
Identities = 12/40 (30%), Positives = 25/40 (62%), Gaps = 4/40 (10%)
Query: 62 GQLMQMTMMSTPNINKELQYLNKEDRLLRWLLVKHRGMKN 101
G+ + + +++T N++ YLN ED++ R +L+ +G N
Sbjct: 317 GEKLDIPVVATGNVH----YLNPEDKIYRKILIHSQGGAN 352
>pdb|3BBN|F Chain F, Homology Model For The Spinach Chloroplast 30s Subunit
Fitted To 9.4a Cryo-Em Map Of The 70s Chlororibosome
Length = 168
Score = 26.2 bits (56), Expect = 7.9, Method: Compositional matrix adjust.
Identities = 21/103 (20%), Positives = 44/103 (42%), Gaps = 6/103 (5%)
Query: 4 YDCMLLLKPHVRKESLMELVARVGKHVYGRNGVLTDITSFGTVQLGYGIKKLD-----GR 58
Y+ M +L+P + ++ + L + + + + ++ + G + L Y IK+ +
Sbjct: 65 YETMAVLRPDMTEDERLTLTQKYEELLVAGGAMYVEVFNRGVIPLAYSIKRKNKAGETNN 124
Query: 59 YYQGQLMQMTMMSTPNINKELQ-YLNKEDRLLRWLLVKHRGMK 100
Y G + T + P L+ L +D ++R K R K
Sbjct: 125 YLDGIYLLFTYFTKPESISPLEAALVTDDDVIRSSSFKIRKRK 167
>pdb|3KHK|A Chain A, Crystal Structure Of Type-I Restriction-Modification
System Methylation Subunit (Mm_0429) From
Methanosarchina Mazei.
pdb|3KHK|B Chain B, Crystal Structure Of Type-I Restriction-Modification
System Methylation Subunit (Mm_0429) From
Methanosarchina Mazei
Length = 544
Score = 25.8 bits (55), Expect = 9.6, Method: Composition-based stats.
Identities = 11/29 (37%), Positives = 14/29 (48%)
Query: 91 WLLVKHRGMKNGKEARYAETSEADLKKYG 119
W L K + KNGK R + D +K G
Sbjct: 441 WFLTKDKNAKNGKRDRRGQVLFIDARKLG 469
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.320 0.137 0.404
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,729,965
Number of Sequences: 62578
Number of extensions: 138700
Number of successful extensions: 216
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 210
Number of HSP's gapped (non-prelim): 9
length of query: 149
length of database: 14,973,337
effective HSP length: 90
effective length of query: 59
effective length of database: 9,341,317
effective search space: 551137703
effective search space used: 551137703
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 47 (22.7 bits)