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= 039855
(198 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1NI7|A Chain A, Northeast Structural Genomic Consortium Target Er75
Length = 155
Score = 65.1 bits (157), Expect = 3e-11, Method: Compositional matrix adjust.
Identities = 35/106 (33%), Positives = 57/106 (53%), Gaps = 5/106 (4%)
Query: 51 NPE----PIATTSTKLQLLVSEFDSLTEPIDRVKRLLDYAAVLPGLDESGRVQAKKVAGC 106
NP+ P TT T + L + F LT+ D+ ++L+ LP L + + QAK++AGC
Sbjct: 3 NPQFAGHPFGTTVTA-ETLRNTFAPLTQWEDKYRQLIMLGKQLPALPDELKAQAKEIAGC 61
Query: 107 ATQVWLEVVMDERGRMRFRADSDSEISKGFCSCLIMVLDGAEPEEV 152
+VWL + E G+M F DS+ I +G + L+ ++G E+
Sbjct: 62 ENRVWLGYTVAENGKMHFFGDSEGRIVRGLLAVLLTAVEGKTAAEL 107
>pdb|1MZG|A Chain A, X-Ray Structure Of Sufe From E.Coli Northeast Structural
Genomics (Nesg) Consortium Target Er30
pdb|1MZG|B Chain B, X-Ray Structure Of Sufe From E.Coli Northeast Structural
Genomics (Nesg) Consortium Target Er30
Length = 146
Score = 47.0 bits (110), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 19/67 (28%), Positives = 36/67 (53%)
Query: 89 LPGLDESGRVQAKKVAGCATQVWLEVVMDERGRMRFRADSDSEISKGFCSCLIMVLDGAE 148
LP L + R + GC +QVW+ + +G + + DSD+ I KG + + ++ D
Sbjct: 34 LPELRDEDRSPQNSIQGCQSQVWIVXRQNAQGIIELQGDSDAAIVKGLIAVVFILYDQXT 93
Query: 149 PEEVLGF 155
P++++ F
Sbjct: 94 PQDIVNF 100
>pdb|3G0M|A Chain A, Crystal Structure Of Cysteine Desulfuration Protein Sufe
From Salmonella Typhimurium Lt2
Length = 141
Score = 37.0 bits (84), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 16/67 (23%), Positives = 33/67 (49%)
Query: 89 LPGLDESGRVQAKKVAGCATQVWLEVVMDERGRMRFRADSDSEISKGFCSCLIMVLDGAE 148
L L+ R + GC +QVW+ + + G + + DSD+ I KG + + ++
Sbjct: 37 LAELNPQDRNPQNTIHGCQSQVWIVMRRNANGIIELQGDSDAAIVKGLMAVVFILYHQMT 96
Query: 149 PEEVLGF 155
++++ F
Sbjct: 97 AQDIVHF 103
>pdb|1WLO|A Chain A, Solution Structure Of The Hypothetical Protein From
Thermus Thermophilus Hb8
Length = 136
Score = 33.1 bits (74), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 28/97 (28%), Positives = 45/97 (46%), Gaps = 4/97 (4%)
Query: 58 TSTKLQLLVSEFDSLTEPIDRVKRLLDYAAVLPGLDESGRVQAKKVAGCATQVWLEV-VM 116
KL+ + F SL + + R + LL+YAA +P V+ ++V C T ++ V
Sbjct: 2 VPPKLKQALELFKSLPKEL-RSQVLLEYAAKVP--PPPPGVELERVHECQTPFFVHADVE 58
Query: 117 DERGRMRFRADSDSEISKGFCSCLIMVLDGAEPEEVL 153
+ R+ F ++ K F L L+G PE VL
Sbjct: 59 GGKVRLYFHVPDEAPTVKAFAGLLREGLEGESPEAVL 95
>pdb|2IS1|A Chain A, Crystal Structure Of Uvrd-Dna-So4 Complex
pdb|2IS1|B Chain B, Crystal Structure Of Uvrd-Dna-So4 Complex
pdb|2IS2|A Chain A, Crystal Structure Of Uvrd-Dna Binary Complex
pdb|2IS2|B Chain B, Crystal Structure Of Uvrd-Dna Binary Complex
pdb|2IS4|A Chain A, Crystal Structure Of Uvrd-Dna-Adpnp Ternary Complex
pdb|2IS4|B Chain B, Crystal Structure Of Uvrd-Dna-Adpnp Ternary Complex
pdb|2IS6|A Chain A, Crystal Structure Of Uvrd-Dna-Adpmgf3 Ternary Complex
pdb|2IS6|B Chain B, Crystal Structure Of Uvrd-Dna-Adpmgf3 Ternary Complex
Length = 680
Score = 28.1 bits (61), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 11/39 (28%), Positives = 20/39 (51%)
Query: 153 LGFKTEDLTEMNVGVGVSHVGIKAGASRVNTWQNVLLAM 191
+ ED M + +SH ++AG + +TWQ+ + M
Sbjct: 519 FSYNEEDEDLMPLQAFLSHAALEAGEGQADTWQDAVQLM 557
>pdb|1Z7M|A Chain A, Atp Phosphoribosyl Transferase (hiszg Atp-prtase) From
Lactococcus Lactis
pdb|1Z7M|B Chain B, Atp Phosphoribosyl Transferase (hiszg Atp-prtase) From
Lactococcus Lactis
pdb|1Z7M|C Chain C, Atp Phosphoribosyl Transferase (hiszg Atp-prtase) From
Lactococcus Lactis
pdb|1Z7M|D Chain D, Atp Phosphoribosyl Transferase (hiszg Atp-prtase) From
Lactococcus Lactis
pdb|1Z7N|A Chain A, Atp Phosphoribosyl Transferase (Hiszg Atp-Prtase) From
Lactococcus Lactis With Bound Prpp Substrate
pdb|1Z7N|B Chain B, Atp Phosphoribosyl Transferase (Hiszg Atp-Prtase) From
Lactococcus Lactis With Bound Prpp Substrate
pdb|1Z7N|C Chain C, Atp Phosphoribosyl Transferase (Hiszg Atp-Prtase) From
Lactococcus Lactis With Bound Prpp Substrate
pdb|1Z7N|D Chain D, Atp Phosphoribosyl Transferase (Hiszg Atp-Prtase) From
Lactococcus Lactis With Bound Prpp Substrate
Length = 344
Score = 27.3 bits (59), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 23/98 (23%), Positives = 46/98 (46%), Gaps = 6/98 (6%)
Query: 58 TSTKLQLLVSEFDSL---TEPIDRVKRLLDYAAVLPGLDESGRVQAKKVAGCATQVWLEV 114
T+TK +L+S FD L +E + +K ++ ++P +D + K + A Q L
Sbjct: 245 TNTKDDVLISSFDQLKEFSEKLSMIKPIIIDLGMVPKMDYYTDLMFKAYSSAANQPILSG 304
Query: 115 VMDERGRMRFRADSDSEISKGFCSCLIMVLDGAEPEEV 152
++ F+ ++ + GFC + +L E +E+
Sbjct: 305 GRYDQLLSNFQEEA---FAIGFCCHMDTILKALERQEL 339
>pdb|1U7L|A Chain A, Crystal Structure Of Subunit C (Vma5p) Of The Yeast
V-Atpase
Length = 392
Score = 27.3 bits (59), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 18/61 (29%), Positives = 34/61 (55%), Gaps = 3/61 (4%)
Query: 47 VHERNPEPIATTSTKLQLLVSEFDSLTEPIDRVKRLLDYAAVLPGLDESGRVQAKKVAGC 106
+ ++N + T + + + + EF+ E ID++K+ D AA L++S RVQ ++A
Sbjct: 238 LFKKNVQEFTTAAREKKFIPREFNYSEELIDQLKKEHDSAA---SLEQSLRVQLVRLAKT 294
Query: 107 A 107
A
Sbjct: 295 A 295
>pdb|2I9E|A Chain A, Structure Of Triosephosphate Isomerase Of Tenebrio Molitor
pdb|2I9E|B Chain B, Structure Of Triosephosphate Isomerase Of Tenebrio Molitor
pdb|2I9E|C Chain C, Structure Of Triosephosphate Isomerase Of Tenebrio Molitor
pdb|2I9E|D Chain D, Structure Of Triosephosphate Isomerase Of Tenebrio Molitor
Length = 259
Score = 26.9 bits (58), Expect = 7.2, Method: Compositional matrix adjust.
Identities = 22/84 (26%), Positives = 37/84 (44%), Gaps = 14/84 (16%)
Query: 114 VVMDERGRMRFRADSDSEISKGFCSCL-----IMVLDGAEPEEVLGFKTEDLTEMNVGVG 168
V++ R + +SD I++ C L ++ G EE KTE++
Sbjct: 90 VILGHSERRQIFGESDELIAEKVCHALESGLKVIACIGETLEEREAGKTEEVVFRQT--- 146
Query: 169 VSHVGIKAGASRVNTWQNVLLAMQ 192
KA A++VN W NV++A +
Sbjct: 147 ------KAIAAKVNDWSNVVIAYE 164
>pdb|3LFU|A Chain A, Crystal Structure Of E. Coli Uvrd
Length = 647
Score = 26.9 bits (58), Expect = 7.7, Method: Composition-based stats.
Identities = 11/39 (28%), Positives = 20/39 (51%)
Query: 153 LGFKTEDLTEMNVGVGVSHVGIKAGASRVNTWQNVLLAM 191
+ ED M + +SH ++AG + +TWQ+ + M
Sbjct: 519 FSYNEEDEDLMPLQAFLSHAALEAGEGQADTWQDAVQLM 557
>pdb|3VMA|A Chain A, Crystal Structure Of The Full-Length Transglycosylase
Pbp1b From Escherichia Coli
Length = 768
Score = 26.6 bits (57), Expect = 9.3, Method: Compositional matrix adjust.
Identities = 24/83 (28%), Positives = 36/83 (43%), Gaps = 16/83 (19%)
Query: 112 LEVVMDERGRMRFRADSDSEISKGFCSCLIMVLDGAEPEEVLGFKTEDLTEMNVGVGVSH 171
LE+ M+E + D+EI +GF + P E L + L
Sbjct: 271 LELYMNE---VYLGQSGDNEI-RGFPLASLYYF--GRPVEELSLDQQALL---------- 314
Query: 172 VGIKAGASRVNTWQNVLLAMQKR 194
VG+ GAS N W+N LA+++R
Sbjct: 315 VGMVKGASIYNPWRNPKLALERR 337
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
0.318 0.132 0.380
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,793,100
Number of Sequences: 62578
Number of extensions: 172362
Number of successful extensions: 382
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 375
Number of HSP's gapped (non-prelim): 13
length of query: 198
length of database: 14,973,337
effective HSP length: 94
effective length of query: 104
effective length of database: 9,091,005
effective search space: 945464520
effective search space used: 945464520
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 bits)