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= 029365
(194 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2KMF|A Chain A, Solution Structure Of Psb27 From Cyanobacterial
Photosystem Ii
Length = 115
Score = 54.7 bits (130), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 31/104 (29%), Positives = 58/104 (55%), Gaps = 2/104 (1%)
Query: 89 SGKVLPKAYLKSARELVKTLRESLKEDPKDIANFRRNADSAKESIRDYLSNWRGQKTVAG 148
SG L Y + ++ TLRE++ + P+D N + D+A+ I DY+S +R + G
Sbjct: 8 SGTGLTGNYSQDTLTVIATLREAI-DLPQDAPNRQEVQDTARGQINDYISRYRRKGDAGG 66
Query: 149 EESYVELEKAIRSLASFYSKAGPSAPLPGEVKSEILNDLDTAEK 192
+S+ ++ A+ SLA +Y+ G + P+P ++K + + AE+
Sbjct: 67 LKSFTTMQTALNSLAGYYTSYG-ARPIPEKLKKRLQLEFTQAER 109
>pdb|2KND|A Chain A, Psb27 Structure From Synechocystis
Length = 110
Score = 54.7 bits (130), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 31/104 (29%), Positives = 58/104 (55%), Gaps = 2/104 (1%)
Query: 89 SGKVLPKAYLKSARELVKTLRESLKEDPKDIANFRRNADSAKESIRDYLSNWRGQKTVAG 148
SG L Y + ++ TLRE++ + P+D N + D+A+ I DY+S +R + G
Sbjct: 3 SGTGLTGNYSQDTLTVIATLREAI-DLPQDAPNRQEVQDTARGQINDYISRYRRKGDAGG 61
Query: 149 EESYVELEKAIRSLASFYSKAGPSAPLPGEVKSEILNDLDTAEK 192
+S+ ++ A+ SLA +Y+ G + P+P ++K + + AE+
Sbjct: 62 LKSFTTMQTALNSLAGYYTSYG-ARPIPEKLKKRLQLEFTQAER 104
>pdb|2Y6X|A Chain A, Structure Of Psb27 From Thermosynechococcus Elongatus
Length = 113
Score = 36.2 bits (82), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 22/88 (25%), Positives = 49/88 (55%), Gaps = 2/88 (2%)
Query: 104 LVKTLRESLKEDPKDIANFRRNADSAKESIRDYLSNWRGQKTVAGEESYVELEKAIRSLA 163
L+ +LRE++ P++ N + A++ + D+ + +R ++ S++ ++ A+ SLA
Sbjct: 19 LISSLREAIAL-PENDPNKKAAQAEARKKLNDFFALYRRDDSLRSLSSFMTMQTALNSLA 77
Query: 164 SFYSKAGPSAPLPGEVKSEILNDLDTAE 191
YS + P+ PLP ++K+ + + E
Sbjct: 78 GHYS-SYPNRPLPEKLKARLEQEFKQVE 104
>pdb|2ZW9|A Chain A, Crystal Structure Of Trna Wybutosine Synthesizing Enzyme
Tyw4
pdb|2ZW9|B Chain B, Crystal Structure Of Trna Wybutosine Synthesizing Enzyme
Tyw4
pdb|2ZWA|A Chain A, Crystal Structure Of Trna Wybutosine Synthesizing Enzyme
Tyw4
pdb|2ZWA|B Chain B, Crystal Structure Of Trna Wybutosine Synthesizing Enzyme
Tyw4
pdb|2ZZK|A Chain A, Crystal Structure Of Trna Wybutosine Synthesizing Enzyme
Tyw4
pdb|2ZZK|B Chain B, Crystal Structure Of Trna Wybutosine Synthesizing Enzyme
Tyw4
Length = 695
Score = 30.4 bits (67), Expect = 0.60, Method: Compositional matrix adjust.
Identities = 31/124 (25%), Positives = 47/124 (37%), Gaps = 20/124 (16%)
Query: 17 LSRLSWQTLKAASSRRHVI--SCSSTALVAILTFNCGLAPLPVQAEDMSNGQDEKEEGVV 74
++R W L A SR + I + ++ CG PLP Q D +N Q ++ V
Sbjct: 81 INRGYWLRLFAIRSRLNSIIEQTPQDKKIVVVNLGCGYDPLPFQLLDTNNIQSQQYHDRV 140
Query: 75 GAIKSLFDPNEKTKSGKVLPKAYLKSARELVKTLRESLKEDPKDIANFRRNADSAKESIR 134
I + LK EL+KT+ E K I + D +S
Sbjct: 141 SFIDIDY-------------SDLLKIKIELIKTIPELSK-----IIGLSEDKDYVDDSNV 182
Query: 135 DYLS 138
D+L+
Sbjct: 183 DFLT 186
>pdb|3LWB|A Chain A, Crystal Structure Of Apo D-Alanine:d-Alanine Ligase (Ddl)
From Mycobacterium Tuberculosis
pdb|3LWB|B Chain B, Crystal Structure Of Apo D-Alanine:d-Alanine Ligase (Ddl)
From Mycobacterium Tuberculosis
Length = 373
Score = 26.9 bits (58), Expect = 7.4, Method: Compositional matrix adjust.
Identities = 28/99 (28%), Positives = 42/99 (42%), Gaps = 13/99 (13%)
Query: 9 SRQSSTLPLSRLS-WQTLKAA--SSRRHVISCSSTALVAILTFNCGLAPLPVQAEDMSNG 65
+R S++ +SR+S W L AA +RRH A ++ CG+ +P + S
Sbjct: 196 ARGGSSIGVSRVSSWDQLPAAVARARRHDPKVIVEAAISGRELECGVLEMPDGTLEASTL 255
Query: 66 QDEKEEGVVGAIKSLFDPNEKTKSGKVLPKAYLKSAREL 104
+ + GV G S +D K YL A EL
Sbjct: 256 GEIRVAGVRGREDSFYDFATK----------YLDDAAEL 284
>pdb|2UXT|A Chain A, Sufi Protein From Escherichia Coli
pdb|2UXT|B Chain B, Sufi Protein From Escherichia Coli
pdb|2UXV|A Chain A, Sufi Protein From Escherichia Coli
pdb|2UXV|B Chain B, Sufi Protein From Escherichia Coli
Length = 451
Score = 26.6 bits (57), Expect = 8.6, Method: Compositional matrix adjust.
Identities = 21/88 (23%), Positives = 38/88 (43%), Gaps = 19/88 (21%)
Query: 25 LKAASSRRHVISCSSTALVAILTFNCGLAPLPVQAE--------------DMSNGQD--- 67
L A++SRR+ + + + +++ + G P PV + DMSNG +
Sbjct: 207 LNASNSRRYQLQMNDGRPLHVISGDQGFLPAPVSVKQLSLAPGERREILVDMSNGDEVSI 266
Query: 68 --EKEEGVVGAIKSLFDPNEKTKSGKVL 93
+ +V I+ F+P+ S VL
Sbjct: 267 TCGEAASIVDRIRGFFEPSSILVSTLVL 294
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
0.310 0.126 0.342
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,237,176
Number of Sequences: 62578
Number of extensions: 196770
Number of successful extensions: 522
Number of sequences better than 100.0: 23
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 15
Number of HSP's that attempted gapping in prelim test: 514
Number of HSP's gapped (non-prelim): 23
length of query: 194
length of database: 14,973,337
effective HSP length: 94
effective length of query: 100
effective length of database: 9,091,005
effective search space: 909100500
effective search space used: 909100500
T: 11
A: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 49 (23.5 bits)