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= 022962
(289 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1XDZ|A Chain A, Crystal Structure Of Gram_positive Bacillus Subtilis
Glucose Inhibited Division Protein B (Gidb), Structural
Genomics, Mcsg
Length = 240
Score = 174 bits (440), Expect = 6e-44, Method: Compositional matrix adjust.
Identities = 93/232 (40%), Positives = 127/232 (54%), Gaps = 10/232 (4%)
Query: 58 TLNTRQQEQIHLYVDALLQWNRKMNLTAVKDVNEVMERHIDDSLAIIPPIKNSYTSHCDS 117
+L+ RQ EQ LY D L++WN K+NLT++ + EV +H DS+ T+
Sbjct: 17 SLSPRQLEQFELYYDMLVEWNEKINLTSITEKKEVYLKHFYDSI----------TAAFYV 66
Query: 118 SCNSNLKLVDVGTGAGLPGLVLAIACPDWKVTLLESMNKRCVFLEHAVSLTQLLNVQIVR 177
N + DVG GAG P L + I P VT+++S+NKR FLE QL N
Sbjct: 67 DFNQVNTICDVGAGAGFPSLPIKICFPHLHVTIVDSLNKRITFLEKLSEALQLENTTFCH 126
Query: 178 GRAETLGKDVSFREQYDVAVARAVAEMRILAEYCLPLVRVGGLFVAAKGHDPQEEVKNSE 237
RAET G+ RE YD+ ARAVA + +L+E CLPLV+ GLFVA K +EE+ +
Sbjct: 127 DRAETFGQRKDVRESYDIVTARAVARLSVLSELCLPLVKKNGLFVALKAASAEEELNAGK 186
Query: 238 RAVQLMGASLLQLCSVESQSPFGQRTAVVCLKSRRTPKKYPRDPGTPAKVPL 289
+A+ +G L + S + R +V K + TPKKYPR PGTP K P+
Sbjct: 187 KAITTLGGELENIHSFKLPIEESDRNIMVIRKIKNTPKKYPRKPGTPNKSPI 238
>pdb|3G88|A Chain A, T. Thermophilus 16s Rrna G527 Methyltransferase In Complex
With Adomet In Space Group P61
pdb|3G88|B Chain B, T. Thermophilus 16s Rrna G527 Methyltransferase In Complex
With Adomet In Space Group P61
pdb|3G89|A Chain A, T. Thermophilus 16s Rrna G527 Methyltransferase In Complex
With Adomet And Amp In Space Group P61
pdb|3G89|B Chain B, T. Thermophilus 16s Rrna G527 Methyltransferase In Complex
With Adomet And Amp In Space Group P61
pdb|3G8A|A Chain A, T. Thermophilus 16s Rrna G527 Methyltransferase In Complex
With Adohcy In Space Group P61
pdb|3G8A|B Chain B, T. Thermophilus 16s Rrna G527 Methyltransferase In Complex
With Adohcy In Space Group P61
pdb|3G8A|C Chain C, T. Thermophilus 16s Rrna G527 Methyltransferase In Complex
With Adohcy In Space Group P61
pdb|3G8A|D Chain D, T. Thermophilus 16s Rrna G527 Methyltransferase In Complex
With Adohcy In Space Group P61
pdb|3G8A|E Chain E, T. Thermophilus 16s Rrna G527 Methyltransferase In Complex
With Adohcy In Space Group P61
pdb|3G8A|F Chain F, T. Thermophilus 16s Rrna G527 Methyltransferase In Complex
With Adohcy In Space Group P61
pdb|3G8B|A Chain A, T. Thermophilus 16s Rrna G527 Methyltransferase In Complex
With Adomet In Space Group I222
pdb|3G8B|B Chain B, T. Thermophilus 16s Rrna G527 Methyltransferase In Complex
With Adomet In Space Group I222
Length = 249
Score = 109 bits (272), Expect = 2e-24, Method: Compositional matrix adjust.
Identities = 79/218 (36%), Positives = 121/218 (55%), Gaps = 11/218 (5%)
Query: 73 ALLQ-WNRKMNLTAVKDVNEVMERHIDDSLAIIPPIKNSYTSHCDSSCNSNLKLVDVGTG 131
ALLQ + K+NLTA++ EV+ +H DSL ++ L+++D+GTG
Sbjct: 41 ALLQEASGKVNLTALRGEEEVVVKHFLDSLTLL----------RLPLWQGPLRVLDLGTG 90
Query: 132 AGLPGLVLAIACPDWKVTLLESMNKRCVFLEHAVSLTQLLNVQIVRGRAETLGKDVSFRE 191
AG PGL L I P+ ++ L+++ K+ F+E A+ + L + + GRAE L ++ RE
Sbjct: 91 AGFPGLPLKIVRPELELVLVDATRKKVAFVERAIEVLGLKGARALWGRAEVLAREAGHRE 150
Query: 192 QYDVAVARAVAEMRILAEYCLPLVRVGGLFVAAKGHDPQEEVKNSERAVQLMGASLLQLC 251
Y AVARAVA + +L+E LP + VGG VA KG +EE+ A++ +G L ++
Sbjct: 151 AYARAVARAVAPLCVLSELLLPFLEVGGAAVAMKGPRVEEELAPLPPALERLGGRLGEVL 210
Query: 252 SVESQSPFGQRTAVVCLKSRRTPKKYPRDPGTPAKVPL 289
+++ R VV K+ TP YPR PG P + PL
Sbjct: 211 ALQLPLSGEARHLVVLEKTAPTPPAYPRRPGVPERHPL 248
>pdb|1JSX|A Chain A, Crystal Structure Of The Escherichia Coli
Glucose-Inhibited Division Protein B (Gidb)
Length = 207
Score = 107 bits (267), Expect = 9e-24, Method: Compositional matrix adjust.
Identities = 67/210 (31%), Positives = 107/210 (50%), Gaps = 22/210 (10%)
Query: 58 TLNTRQQEQIHLYVDALLQWNRKMNLTAVKDVNEVMERHIDDSLAIIPPIKNSYTSHCDS 117
+L Q+ Q+ YV+ L +WN+ NLT+V+D NE++ RHI DS+ + P ++
Sbjct: 15 SLTDHQKNQLIAYVNMLHKWNKAYNLTSVRDPNEMLVRHILDSIVVAPYLQGE------- 67
Query: 118 SCNSNLKLVDVGTGAGLPGLVLAIACPDWKVTLLESMNKRCVFLEHAVSLTQLLNVQIVR 177
+ +DVGTG GLPG+ L+I P+ TLL+S+ KR FL +L N++ V+
Sbjct: 68 ------RFIDVGTGPGLPGIPLSIVRPEAHFTLLDSLGKRVRFLRQVQHELKLENIEPVQ 121
Query: 178 GRAETLGKDVSFREQYDVAVARAVAEMRILAEYCLPLVRVGGLFVAAKGHDPQEEVKNSE 237
R E + F D ++RA A + + +C L G F A KG P++E+
Sbjct: 122 SRVEEFPSEPPF----DGVISRAFASLNDMVSWCHHLPGEQGRFYALKGQMPEDEIALLP 177
Query: 238 RAVQLMGASLLQLCSVESQSPFGQRTAVVC 267
Q+ LQ+ +++ G+R VV
Sbjct: 178 EEYQVESVVKLQVPALD-----GERHLVVI 202
>pdb|4DZR|A Chain A, The Crystal Structure Of Protein-(Glutamine-N5)
Methyltransferase (Release Factor-Specific) From
Alicyclobacillus Acidocaldarius Subsp. Acidocaldarius
Dsm 446
Length = 215
Score = 31.2 bits (69), Expect = 0.76, Method: Compositional matrix adjust.
Identities = 13/32 (40%), Positives = 22/32 (68%)
Query: 121 SNLKLVDVGTGAGLPGLVLAIACPDWKVTLLE 152
S +++DVGTG+G + +A+ACP VT ++
Sbjct: 30 SGTRVIDVGTGSGCIAVSIALACPGVSVTAVD 61
>pdb|1JNN|H Chain H, Crystal Structure Of Fab-Estradiol Complexes
Length = 214
Score = 29.3 bits (64), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 21/73 (28%), Positives = 33/73 (45%), Gaps = 13/73 (17%)
Query: 227 HDPQEEVKNSERAVQLMGASLLQL------------CSVESQSPFGQRTAVVCLKSRRTP 274
+DP+ + K + A + LQL C++E P+GQ T V ++ TP
Sbjct: 60 YDPRFQGKATLTADTSSNTAYLQLDNLTSEDTAVYYCAIEKDLPWGQGTLVTVSVAKTTP 119
Query: 275 KK-YPRDPGTPAK 286
YP PG+ A+
Sbjct: 120 PSVYPLAPGSAAQ 132
>pdb|2YXD|A Chain A, Crystal Structure Of Cobalamin Biosynthesis Precorrin 8w
Decarboxylase (Cbit)
pdb|2YXD|B Chain B, Crystal Structure Of Cobalamin Biosynthesis Precorrin 8w
Decarboxylase (Cbit)
Length = 183
Score = 29.3 bits (64), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 25/89 (28%), Positives = 41/89 (46%), Gaps = 28/89 (31%)
Query: 118 SCNSNLKLVDVGTGAGLPGLVLAIACPDWKVTLLESMNKRCVF------LEHAVSLTQ-- 169
+ N + +VDVG G+G G + IA KRC F L+ A+ +T+
Sbjct: 32 NLNKDDVVVDVGCGSG--GXTVEIA-------------KRCKFVYAIDYLDGAIEVTKQN 76
Query: 170 -----LLNVQIVRGRAETLGKDVSFREQY 193
+ N QI++GRAE + + F + +
Sbjct: 77 LAKFNIKNCQIIKGRAEDVLDKLEFNKAF 105
>pdb|1JNL|H Chain H, Crystal Structure Of Fab-Estradiol Complexes
Length = 216
Score = 29.3 bits (64), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 21/73 (28%), Positives = 33/73 (45%), Gaps = 13/73 (17%)
Query: 227 HDPQEEVKNSERAVQLMGASLLQL------------CSVESQSPFGQRTAVVCLKSRRTP 274
+DP+ + K + A + LQL C++E P+GQ T V ++ TP
Sbjct: 60 YDPRFQGKATLTADTSSNTAYLQLDNLTSEDTAVYYCAIEKDLPWGQGTLVTVSVAKTTP 119
Query: 275 KK-YPRDPGTPAK 286
YP PG+ A+
Sbjct: 120 PSVYPLAPGSAAQ 132
>pdb|2GSI|B Chain B, Crystal Structure Of A Murine Fab In Complex With An 11
Residue Peptide Derived From Staphylococcal Nuclease
pdb|2GSI|D Chain D, Crystal Structure Of A Murine Fab In Complex With An 11
Residue Peptide Derived From Staphylococcal Nuclease
pdb|2GSI|F Chain F, Crystal Structure Of A Murine Fab In Complex With An 11
Residue Peptide Derived From Staphylococcal Nuclease
pdb|2GSI|H Chain H, Crystal Structure Of A Murine Fab In Complex With An 11
Residue Peptide Derived From Staphylococcal Nuclease
Length = 221
Score = 28.5 bits (62), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 15/57 (26%), Positives = 27/57 (47%), Gaps = 1/57 (1%)
Query: 231 EEVKNSERAVQLMGASLLQLCSVESQSPFGQRTAVVCLKSRRTPKK-YPRDPGTPAK 286
+ + + AV A ++ + ++ +GQ T V ++ TP YP PGT A+
Sbjct: 83 SSLTSEDTAVYYCNAGVITMMGYQAMDYWGQGTTVTTSSAKTTPPSVYPLAPGTAAQ 139
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
0.321 0.133 0.399
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,899,942
Number of Sequences: 62578
Number of extensions: 280084
Number of successful extensions: 644
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 634
Number of HSP's gapped (non-prelim): 11
length of query: 289
length of database: 14,973,337
effective HSP length: 98
effective length of query: 191
effective length of database: 8,840,693
effective search space: 1688572363
effective search space used: 1688572363
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 51 (24.3 bits)