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= psy13666
(278 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2BH7|A Chain A, Crystal Structure Of A Semet Derivative Of Amid At 2.2
Angstroms
Length = 261
Score = 149 bits (377), Expect = 1e-36, Method: Compositional matrix adjust.
Identities = 97/249 (38%), Positives = 127/249 (51%), Gaps = 22/249 (8%)
Query: 34 VKYLILHYTVYNFAHIITAFTSNRAHNLHSSHYVISEKEGKYLPGGKVIQIVPDNMRAWH 93
+K L++HYT +F + T + SSHY++ +Y ++ Q+VP+ AWH
Sbjct: 29 IKVLVIHYTADDFDSSLATLTDKQV----SSHYLVPAVPPRYNGKPRIWQLVPEQELAWH 84
Query: 94 AGIGKWRRDRNLNSMSIGIHLVNGGVVGEKFRSTNYY-PFDENQIHTLGLLGKDIVSQFK 152
AGI WR LN SIGI L N G +K Y+ PF+ QI L L KDI++++
Sbjct: 85 AGISAWRGATRLNDTSIGIELENRG--WQKSAGVKYFAPFEPAQIQALIPLAKDIIARYH 142
Query: 153 IKPQYVLGHTDIAPGSKMDPGPLFPWGKLYLDYGIGAWLSPDEMTVEAIVRKFKPARPYP 212
IKP+ V+ H DIAP K DPGPLFPW +L GIGAW PD V + P P
Sbjct: 143 IKPENVVAHADIAPQRKDDPGPLFPWQQL-AQQGIGAW--PDAQRVNFYLAGRAPHTP-- 197
Query: 213 RKLDRGIFLELLKAYGYNV----TITNKRSVIRAFKTHFSANQNPERIYADITTEDMFWA 268
+D LELL YGY+V T +R VI AF+ HF P + E A
Sbjct: 198 --VDTASLLELLARYGYDVKPDXTPREQRRVIXAFQXHF----RPTLYNGEADAETQAIA 251
Query: 269 WALVAKYGS 277
AL+ KYG
Sbjct: 252 EALLEKYGQ 260
>pdb|3D2Y|A Chain A, Complex Of The N-Acetylmuramyl-L-Alanine Amidase Amid From
E.Coli With The Substrate Anhydro-N-Acetylmuramic
Acid-L-Ala-D-Gamma-Glu-L-Lys
pdb|3D2Z|A Chain A, Complex Of The N-Acetylmuramyl-L-Alanine Amidase Amid From
E.Coli With The Product L-Ala-D-Gamma-Glu-L-Lys
pdb|2WKX|A Chain A, Crystal Structure Of The Native E. Coli Zinc Amidase Amid
Length = 261
Score = 149 bits (377), Expect = 1e-36, Method: Compositional matrix adjust.
Identities = 97/249 (38%), Positives = 127/249 (51%), Gaps = 22/249 (8%)
Query: 34 VKYLILHYTVYNFAHIITAFTSNRAHNLHSSHYVISEKEGKYLPGGKVIQIVPDNMRAWH 93
+K L++HYT +F + T + SSHY++ +Y ++ Q+VP+ AWH
Sbjct: 29 IKVLVIHYTADDFDSSLATLTDKQV----SSHYLVPAVPPRYNGKPRIWQLVPEQELAWH 84
Query: 94 AGIGKWRRDRNLNSMSIGIHLVNGGVVGEKFRSTNYY-PFDENQIHTLGLLGKDIVSQFK 152
AGI WR LN SIGI L N G +K Y+ PF+ QI L L KDI++++
Sbjct: 85 AGISAWRGATRLNDTSIGIELENRG--WQKSAGVKYFAPFEPAQIQALIPLAKDIIARYH 142
Query: 153 IKPQYVLGHTDIAPGSKMDPGPLFPWGKLYLDYGIGAWLSPDEMTVEAIVRKFKPARPYP 212
IKP+ V+ H DIAP K DPGPLFPW +L GIGAW PD V + P P
Sbjct: 143 IKPENVVAHADIAPQRKDDPGPLFPWQQL-AQQGIGAW--PDAQRVNFYLAGRAPHTP-- 197
Query: 213 RKLDRGIFLELLKAYGYNV----TITNKRSVIRAFKTHFSANQNPERIYADITTEDMFWA 268
+D LELL YGY+V T +R VI AF+ HF P + E A
Sbjct: 198 --VDTASLLELLARYGYDVKPDMTPREQRRVIMAFQMHF----RPTLYNGEADAETQAIA 251
Query: 269 WALVAKYGS 277
AL+ KYG
Sbjct: 252 EALLEKYGQ 260
>pdb|2Y2B|A Chain A, Crystal Structure Of Ampd In Complex With Reaction
Products
pdb|2Y2B|B Chain B, Crystal Structure Of Ampd In Complex With Reaction
Products
pdb|2Y2B|C Chain C, Crystal Structure Of Ampd In Complex With Reaction
Products
pdb|2Y2C|A Chain A, Crystal Structure Of Ampd Apoenzyme
pdb|2Y2C|B Chain B, Crystal Structure Of Ampd Apoenzyme
pdb|2Y2C|C Chain C, Crystal Structure Of Ampd Apoenzyme
pdb|2Y2D|A Chain A, Crystal Structure Of Ampd Holoenzyme
pdb|2Y2D|B Chain B, Crystal Structure Of Ampd Holoenzyme
pdb|2Y2D|C Chain C, Crystal Structure Of Ampd Holoenzyme
pdb|2Y2E|A Chain A, Crystal Structure Of Ampd Grown At Ph 5.5
pdb|2Y2E|B Chain B, Crystal Structure Of Ampd Grown At Ph 5.5
pdb|2Y2E|C Chain C, Crystal Structure Of Ampd Grown At Ph 5.5
pdb|1J3G|A Chain A, Solution Structure Of Citrobacter Freundii Ampd
Length = 187
Score = 64.7 bits (156), Expect = 5e-11, Method: Compositional matrix adjust.
Identities = 36/124 (29%), Positives = 57/124 (45%), Gaps = 17/124 (13%)
Query: 58 AHNLHSSHYVISEKEGKYLPGGKVIQIVPDNMRAWHAGIGKWRRDRNLNSMSIGIHLVNG 117
AH S+H +I G+++Q VP + RAWHAG+ ++ N SIGI L
Sbjct: 68 AHLRVSAHCLIRRD-------GEIVQYVPFDKRAWHAGVSSYQGRERCNDFSIGIEL--- 117
Query: 118 GVVGEKFRSTNYYPFDENQIHTLGLLGKDIVSQFKIKPQYVLGHTDIAPGSKMDPGPLFP 177
T+ + + Q L + +++++ + GH +IAP K DPGP F
Sbjct: 118 -------EGTDTLAYTDAQYQQLAAVTNALITRYPAIANNMTGHCNIAPERKTDPGPSFD 170
Query: 178 WGKL 181
W +
Sbjct: 171 WARF 174
>pdb|2Y28|A Chain A, Crystal Structure Of Se-Met Ampd Derivative
pdb|2Y28|B Chain B, Crystal Structure Of Se-Met Ampd Derivative
pdb|2Y28|C Chain C, Crystal Structure Of Se-Met Ampd Derivative
Length = 187
Score = 64.3 bits (155), Expect = 8e-11, Method: Compositional matrix adjust.
Identities = 36/124 (29%), Positives = 56/124 (45%), Gaps = 17/124 (13%)
Query: 58 AHNLHSSHYVISEKEGKYLPGGKVIQIVPDNMRAWHAGIGKWRRDRNLNSMSIGIHLVNG 117
AH S+H +I G+++Q VP + RAWHAG+ ++ N SIGI L
Sbjct: 68 AHLRVSAHCLIRRD-------GEIVQYVPFDKRAWHAGVSSYQGRERCNDFSIGIEL--- 117
Query: 118 GVVGEKFRSTNYYPFDENQIHTLGLLGKDIVSQFKIKPQYVLGHTDIAPGSKMDPGPLFP 177
T+ + + Q L + +++++ GH +IAP K DPGP F
Sbjct: 118 -------EGTDTLAYTDAQYQQLAAVTNALITRYPAIANNXTGHCNIAPERKTDPGPSFD 170
Query: 178 WGKL 181
W +
Sbjct: 171 WARF 174
>pdb|2C2Q|A Chain A, The Crystal Structure Of Mismatch Specific Uracil-Dna
Glycosylase (Mug) From Deinococcus Radiodurans. Inactive
Mutant Asp93ala
Length = 199
Score = 33.5 bits (75), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 21/57 (36%), Positives = 29/57 (50%), Gaps = 5/57 (8%)
Query: 114 LVNGGVVGEKFRSTNYYPFDENQ----IHTLGLLGKDIVSQ-FKIKPQYVLGHTDIA 165
LV G R+ YY EN+ +H +GL + +V Q + PQY LG TD+A
Sbjct: 30 LVGTAPSGISARARAYYANPENKFWRTLHAVGLTPRQLVPQEYATLPQYGLGLTDVA 86
>pdb|2C2P|A Chain A, The Crystal Structure Of Mismatch Specific Uracil-Dna
Glycosylase (Mug) From Deinococcus Radiodurans
Length = 199
Score = 33.5 bits (75), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 21/57 (36%), Positives = 29/57 (50%), Gaps = 5/57 (8%)
Query: 114 LVNGGVVGEKFRSTNYYPFDENQ----IHTLGLLGKDIVSQ-FKIKPQYVLGHTDIA 165
LV G R+ YY EN+ +H +GL + +V Q + PQY LG TD+A
Sbjct: 30 LVGTAPSGISARARAYYANPENKFWRTLHAVGLTPRQLVPQEYATLPQYGLGLTDVA 86
>pdb|2CJL|A Chain A, Crystal Structure And Enzymatic Properties Of A Bacterial
Family 19 Chitinase Reveal Differences With Plant
Enzymes
pdb|2CJL|B Chain B, Crystal Structure And Enzymatic Properties Of A Bacterial
Family 19 Chitinase Reveal Differences With Plant
Enzymes
Length = 204
Score = 27.7 bits (60), Expect = 8.2, Method: Compositional matrix adjust.
Identities = 14/42 (33%), Positives = 19/42 (45%)
Query: 87 DNMRAWHAGIGKWRRDRNLNSMSIGIHLVNGGVVGEKFRSTN 128
D+ AW G+ W +M+ +VNG GE RS N
Sbjct: 126 DSAVAWKTGLWYWNTQTGPGTMTPHDAMVNGAGFGETIRSIN 167
>pdb|3T66|A Chain A, Crystal Structure Of Nickel Abc Transporter From Bacillus
Halodurans
Length = 496
Score = 27.3 bits (59), Expect = 9.6, Method: Compositional matrix adjust.
Identities = 19/70 (27%), Positives = 30/70 (42%), Gaps = 4/70 (5%)
Query: 195 EMTVEAIVRKFKPARPYPRKLDRGIFLELLKAYGYNVTITNKRSVIRAFKTHFSANQNPE 254
EM EA+ + A ++ + ++ ++A GY + IT K F S NP
Sbjct: 86 EMDAEAVKASLERALDESVAIENALKIDEIEADGYTLHITTK----EPFPEFISELVNPN 141
Query: 255 RIYADITTED 264
D+T ED
Sbjct: 142 VSIIDVTEED 151
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 0.139 0.442
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,685,854
Number of Sequences: 62578
Number of extensions: 428103
Number of successful extensions: 868
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 854
Number of HSP's gapped (non-prelim): 13
length of query: 278
length of database: 14,973,337
effective HSP length: 98
effective length of query: 180
effective length of database: 8,840,693
effective search space: 1591324740
effective search space used: 1591324740
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: 51 (24.3 bits)