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= 029942
(185 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1Q7G|A Chain A, Homoserine Dehydrogenase In Complex With Suicide Inhibitor
Complex Nad-5-Hydroxy-4-Oxonorvaline
pdb|1Q7G|B Chain B, Homoserine Dehydrogenase In Complex With Suicide Inhibitor
Complex Nad-5-Hydroxy-4-Oxonorvaline
Length = 359
Score = 102 bits (255), Expect = 1e-22, Method: Compositional matrix adjust.
Identities = 58/138 (42%), Positives = 94/138 (68%), Gaps = 2/138 (1%)
Query: 45 QVIILARESGLKLEL-SDLPVRSFVPEPLKACASAEEFMKQLPQFDKELAKQRQEAEDAG 103
+V I+ R SG+++E + PV+S +P+PL++ SA+EF+++L +DK+L + ++EA
Sbjct: 223 KVTIVGRISGVEVESPTSFPVQSLIPKPLESVKSADEFLEKLSDYDKDLTQLKKEAATEN 282
Query: 104 EVLRYVGVVDAINKEGRVELRRYKRDHPFAQLSGSDNIIAFTTKRYKEQPLIVRGPGAGA 163
+VLR++G VD K V + +Y HPFA L GSDN+I+ TKRY P++++G GAGA
Sbjct: 283 KVLRFIGKVDVATKSVSVGIEKYDYSHPFASLKGSDNVISIKTKRY-TNPVVIQGAGAGA 341
Query: 164 QVTAGGIFSDILRLASYL 181
VTA G+ D++++A L
Sbjct: 342 AVTAAGVLGDVIKIAQRL 359
>pdb|1EBF|A Chain A, Homoserine Dehydrogenase From S. Cerevisiae Complex With
Nad+
pdb|1EBF|B Chain B, Homoserine Dehydrogenase From S. Cerevisiae Complex With
Nad+
pdb|1EBU|A Chain A, Homoserine Dehydrogenase Complex With Nad Analogue And L-
Homoserine
pdb|1EBU|B Chain B, Homoserine Dehydrogenase Complex With Nad Analogue And L-
Homoserine
pdb|1EBU|C Chain C, Homoserine Dehydrogenase Complex With Nad Analogue And L-
Homoserine
pdb|1EBU|D Chain D, Homoserine Dehydrogenase Complex With Nad Analogue And L-
Homoserine
pdb|1TVE|A Chain A, Homoserine Dehydrogenase In Complex With 4-(4-Hydroxy-3-
Isopropylphenylthio)-2-Isopropylphenol
pdb|1TVE|B Chain B, Homoserine Dehydrogenase In Complex With 4-(4-Hydroxy-3-
Isopropylphenylthio)-2-Isopropylphenol
Length = 358
Score = 102 bits (254), Expect = 1e-22, Method: Compositional matrix adjust.
Identities = 58/138 (42%), Positives = 94/138 (68%), Gaps = 2/138 (1%)
Query: 45 QVIILARESGLKLEL-SDLPVRSFVPEPLKACASAEEFMKQLPQFDKELAKQRQEAEDAG 103
+V I+ R SG+++E + PV+S +P+PL++ SA+EF+++L +DK+L + ++EA
Sbjct: 222 KVTIVGRISGVEVESPTSFPVQSLIPKPLESVKSADEFLEKLSDYDKDLTQLKKEAATEN 281
Query: 104 EVLRYVGVVDAINKEGRVELRRYKRDHPFAQLSGSDNIIAFTTKRYKEQPLIVRGPGAGA 163
+VLR++G VD K V + +Y HPFA L GSDN+I+ TKRY P++++G GAGA
Sbjct: 282 KVLRFIGKVDVATKSVSVGIEKYDYSHPFASLKGSDNVISIKTKRY-TNPVVIQGAGAGA 340
Query: 164 QVTAGGIFSDILRLASYL 181
VTA G+ D++++A L
Sbjct: 341 AVTAAGVLGDVIKIAQRL 358
>pdb|2FU4|A Chain A, Crystal Structure Of The Dna Binding Domain Of E.Coli Fur
(Ferric Uptake Regulator)
pdb|2FU4|B Chain B, Crystal Structure Of The Dna Binding Domain Of E.Coli Fur
(Ferric Uptake Regulator)
Length = 83
Score = 28.9 bits (63), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 18/63 (28%), Positives = 32/63 (50%), Gaps = 5/63 (7%)
Query: 51 RESGLKLELSDLPVRSFVPEPLKACASAEEFMKQLPQFDKELA-----KQRQEAEDAGEV 105
+++GLK+ L L + + EP SAE+ K+L +E+ + + +DAG V
Sbjct: 9 KKAGLKVTLPRLKILEVLQEPDNHHVSAEDLYKRLIDMGEEIGLATVYRVLNQFDDAGIV 68
Query: 106 LRY 108
R+
Sbjct: 69 TRH 71
>pdb|2P90|A Chain A, The Crystal Structure Of A Protein Of Unknown Function
From Corynebacterium Glutamicum Atcc 13032
pdb|2P90|B Chain B, The Crystal Structure Of A Protein Of Unknown Function
From Corynebacterium Glutamicum Atcc 13032
pdb|2P90|C Chain C, The Crystal Structure Of A Protein Of Unknown Function
From Corynebacterium Glutamicum Atcc 13032
Length = 319
Score = 28.1 bits (61), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 14/41 (34%), Positives = 24/41 (58%), Gaps = 3/41 (7%)
Query: 97 QEAEDAGEVLRYVGVVDAINKEGRVELRRYKRDHPFAQLSG 137
++ E++ E+ R VG A+ ++ EL RY+ HP A + G
Sbjct: 247 EQTEESSEIQRVVG---ALEQQYDSELERYRNRHPQAVMPG 284
>pdb|3DO5|A Chain A, Crystal Structure Of Putative Homoserine Dehydrogenase
(Np_069768.1) From Archaeoglobus Fulgidus At 2.20 A
Resolution
Length = 327
Score = 27.7 bits (60), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 17/48 (35%), Positives = 23/48 (47%), Gaps = 3/48 (6%)
Query: 130 HPFAQLSGSDNIIAFTTKRYKEQPLIVRGPGAGAQVTAGGIFSDILRL 177
HP A + G+ N F T + V G GAG + TA I SD+ +
Sbjct: 278 HPLA-IKGTXNAAXFKTD--TAGSIFVAGRGAGKEETASAILSDLYEI 322
>pdb|1DOS|A Chain A, Structure Of Fructose-Bisphosphate Aldolase
pdb|1DOS|B Chain B, Structure Of Fructose-Bisphosphate Aldolase
Length = 358
Score = 27.3 bits (59), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 21/57 (36%), Positives = 30/57 (52%), Gaps = 2/57 (3%)
Query: 131 PFAQLSGSDNIIA-FTTKRYKEQPLIVRGPGAGAQVTAG-GIFSDILRLASYLGAPS 185
P G+D+I A T + P+IV+ GA AG G+ SD+ + A+ LGA S
Sbjct: 32 PAVNCVGTDSINAVLETAAKVKAPVIVQFSNGGASFIAGKGVKSDVPQGAAILGAIS 88
>pdb|1B57|A Chain A, Class Ii Fructose-1,6-Bisphosphate Aldolase In Complex
With Phosphoglycolohydroxamate
pdb|1B57|B Chain B, Class Ii Fructose-1,6-Bisphosphate Aldolase In Complex
With Phosphoglycolohydroxamate
pdb|1GYN|A Chain A, Class Ii Fructose 1,6-Bisphosphate Aldolase With Cadmium
(Not Zinc) In The Active Site
pdb|1ZEN|A Chain A, Class Ii Fructose-1,6-Bisphosphate Aldolase
Length = 358
Score = 26.9 bits (58), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 21/57 (36%), Positives = 30/57 (52%), Gaps = 2/57 (3%)
Query: 131 PFAQLSGSDNIIA-FTTKRYKEQPLIVRGPGAGAQVTAG-GIFSDILRLASYLGAPS 185
P G+D+I A T + P+IV+ GA AG G+ SD+ + A+ LGA S
Sbjct: 32 PAVNCVGTDSINAVLETAAKVKAPVIVQFSNGGASFIAGKGVKSDVPQGAAILGAIS 88
>pdb|2RFG|A Chain A, Crystal Structure Of Dihydrodipicolinate Synthase From
Hahella Chejuensis At 1.5a Resolution
pdb|2RFG|B Chain B, Crystal Structure Of Dihydrodipicolinate Synthase From
Hahella Chejuensis At 1.5a Resolution
pdb|2RFG|C Chain C, Crystal Structure Of Dihydrodipicolinate Synthase From
Hahella Chejuensis At 1.5a Resolution
pdb|2RFG|D Chain D, Crystal Structure Of Dihydrodipicolinate Synthase From
Hahella Chejuensis At 1.5a Resolution
Length = 297
Score = 26.9 bits (58), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 14/33 (42%), Positives = 17/33 (51%)
Query: 107 RYVGVVDAINKEGRVELRRYKRDHPFAQLSGSD 139
R VGV DA R+ R + PF+ LSG D
Sbjct: 155 RIVGVKDATTDLARISRERMLINKPFSFLSGDD 187
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 0.137 0.390
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,975,466
Number of Sequences: 62578
Number of extensions: 186679
Number of successful extensions: 473
Number of sequences better than 100.0: 18
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 12
Number of HSP's that attempted gapping in prelim test: 465
Number of HSP's gapped (non-prelim): 18
length of query: 185
length of database: 14,973,337
effective HSP length: 93
effective length of query: 92
effective length of database: 9,153,583
effective search space: 842129636
effective search space used: 842129636
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: 48 (23.1 bits)