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= 038188
(384 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2IMR|A Chain A, Crystal Structure Of Amidohydrolase Dr_0824 From
Deinococcus Radiodurans
Length = 420
Score = 30.8 bits (68), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 18/67 (26%), Positives = 32/67 (47%), Gaps = 6/67 (8%)
Query: 200 GNIKWIPYVFESYYNNANLNGVFYWFVSRA-GDFHSKLILLFRISDEEFQEIQRPCI--- 255
G+I W P V ++ +L+G Y+ V D ++ R E ++ ++RP +
Sbjct: 150 GDIVWAPEVMDALLAREDLSGTLYFEVLNPFPDKADEVFAAARTHLERWRRLERPGLRLG 209
Query: 256 --PYTPF 260
P+TPF
Sbjct: 210 LSPHTPF 216
>pdb|1RVU|A Chain A, E75q Mutant Of Rabbit Cytosolic Serine
Hydroxymethyltransferase
pdb|1RVU|B Chain B, E75q Mutant Of Rabbit Cytosolic Serine
Hydroxymethyltransferase
pdb|1RVY|A Chain A, E75q Mutant Of Rabbit Cytosolic Serine
Hydroxymethyltransferase, Complex With Glycine
pdb|1RVY|B Chain B, E75q Mutant Of Rabbit Cytosolic Serine
Hydroxymethyltransferase, Complex With Glycine
Length = 483
Score = 29.6 bits (65), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 11/39 (28%), Positives = 21/39 (53%)
Query: 67 ISYQVYDDNGPNSVTSLFKDKTLADLSYENIHRPISREL 105
++ Q+ DD GP + FK+K D ++ R + +E+
Sbjct: 430 LTVQIQDDTGPRATLKEFKEKLAGDEKHQRAVRALRQEV 468
>pdb|1RV3|A Chain A, E75l Mutant Of Rabbit Cytosolic Serine
Hydroxymethyltransferase, Complex With Glycine
pdb|1RV4|A Chain A, E75l Mutant Of Rabbit Cytosolic Serine
Hydroxymethyltransferase
pdb|1RV4|B Chain B, E75l Mutant Of Rabbit Cytosolic Serine
Hydroxymethyltransferase
pdb|1RV3|B Chain B, E75l Mutant Of Rabbit Cytosolic Serine
Hydroxymethyltransferase, Complex With Glycine
Length = 483
Score = 29.6 bits (65), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 11/39 (28%), Positives = 21/39 (53%)
Query: 67 ISYQVYDDNGPNSVTSLFKDKTLADLSYENIHRPISREL 105
++ Q+ DD GP + FK+K D ++ R + +E+
Sbjct: 430 LTVQIQDDTGPRATLKEFKEKLAGDEKHQRAVRALRQEV 468
>pdb|1CJ0|A Chain A, Crystal Structure Of Rabbit Cytosolic Serine
Hydroxymethyltransferase At 2.8 Angstrom Resolution
pdb|1CJ0|B Chain B, Crystal Structure Of Rabbit Cytosolic Serine
Hydroxymethyltransferase At 2.8 Angstrom Resolution
Length = 470
Score = 29.6 bits (65), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 11/39 (28%), Positives = 21/39 (53%)
Query: 67 ISYQVYDDNGPNSVTSLFKDKTLADLSYENIHRPISREL 105
++ Q+ DD GP + FK+K D ++ R + +E+
Sbjct: 417 LTVQIQDDTGPRATLKEFKEKLAGDEKHQRAVRALRQEV 455
>pdb|1LS3|B Chain B, Crystal Structure Of The Complex Between Rabbit Cytosolic
Serine Hydroxymethyltransferase And
Triglu-5-Formyl-Tetrahydrofolate
pdb|1LS3|D Chain D, Crystal Structure Of The Complex Between Rabbit Cytosolic
Serine Hydroxymethyltransferase And
Triglu-5-Formyl-Tetrahydrofolate
pdb|1LS3|A Chain A, Crystal Structure Of The Complex Between Rabbit Cytosolic
Serine Hydroxymethyltransferase And
Triglu-5-Formyl-Tetrahydrofolate
pdb|1LS3|C Chain C, Crystal Structure Of The Complex Between Rabbit Cytosolic
Serine Hydroxymethyltransferase And
Triglu-5-Formyl-Tetrahydrofolate
Length = 483
Score = 29.6 bits (65), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 11/39 (28%), Positives = 21/39 (53%)
Query: 67 ISYQVYDDNGPNSVTSLFKDKTLADLSYENIHRPISREL 105
++ Q+ DD GP + FK+K D ++ R + +E+
Sbjct: 430 LTVQIQDDTGPRATLKEFKEKLAGDEKHQRAVRALRQEV 468
>pdb|2WAO|A Chain A, Structure Of A Family Two Carbohydrate Esterase From
Clostridium Thermocellum In Complex With Cellohexaose
Length = 341
Score = 29.6 bits (65), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 26/93 (27%), Positives = 37/93 (39%), Gaps = 20/93 (21%)
Query: 76 GPNSVTSLFKDKTLADLSYENIHRPISRELLGPYDGIFCLCDGGLITLWNPATKECRTLP 135
G N ++ F DKT +Y+N+ + R P IFC C G + LW CR+
Sbjct: 222 GTNDFSTSFADKTKFVTAYKNLISEVRRNY--PDAHIFC-CVGPM--LWGTGLDLCRSY- 275
Query: 136 NYKKNLPALATFLKRNAIFGLCDASGDYKVVFI 168
+ C+ SGD KV F+
Sbjct: 276 --------------VTEVVNDCNRSGDLKVYFV 294
>pdb|2WAB|A Chain A, Structure Of An Active Site Mutant Of A Family Two
Carbohydrate Esterase From Clostridium Thermocellum In
Complex With Celluohexase
Length = 341
Score = 29.3 bits (64), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 26/93 (27%), Positives = 37/93 (39%), Gaps = 20/93 (21%)
Query: 76 GPNSVTSLFKDKTLADLSYENIHRPISRELLGPYDGIFCLCDGGLITLWNPATKECRTLP 135
G N ++ F DKT +Y+N+ + R P IFC C G + LW CR+
Sbjct: 222 GTNDFSTSFADKTKFVTAYKNLISEVRRNY--PDAHIFC-CVGPM--LWGTGLDLCRSY- 275
Query: 136 NYKKNLPALATFLKRNAIFGLCDASGDYKVVFI 168
+ C+ SGD KV F+
Sbjct: 276 --------------VTEVVNDCNRSGDLKVYFV 294
>pdb|3IKL|A Chain A, Crystal Structure Of Pol Gb Delta-I4.
pdb|3IKL|B Chain B, Crystal Structure Of Pol Gb Delta-I4
Length = 459
Score = 28.5 bits (62), Expect = 7.2, Method: Compositional matrix adjust.
Identities = 8/23 (34%), Positives = 17/23 (73%)
Query: 278 SNQYIEIWVMNEMNWIQQFAIGP 300
SNQ+++ W+ + + W ++FA+ P
Sbjct: 216 SNQWLDFWLRHRLQWWRKFAMSP 238
>pdb|3IKM|B Chain B, Crystal Structure Of Human Mitochondrial Dna Polymerase
Holoenzyme
pdb|3IKM|C Chain C, Crystal Structure Of Human Mitochondrial Dna Polymerase
Holoenzyme
pdb|3IKM|E Chain E, Crystal Structure Of Human Mitochondrial Dna Polymerase
Holoenzyme
pdb|3IKM|F Chain F, Crystal Structure Of Human Mitochondrial Dna Polymerase
Holoenzyme
Length = 427
Score = 28.5 bits (62), Expect = 7.4, Method: Compositional matrix adjust.
Identities = 8/23 (34%), Positives = 17/23 (73%)
Query: 278 SNQYIEIWVMNEMNWIQQFAIGP 300
SNQ+++ W+ + + W ++FA+ P
Sbjct: 190 SNQWLDFWLRHRLQWWRKFAMSP 212
>pdb|2G4C|A Chain A, Crystal Structure Of Human Dna Polymerase Gamma Accessory
Subunit
pdb|2G4C|B Chain B, Crystal Structure Of Human Dna Polymerase Gamma Accessory
Subunit
pdb|2G4C|C Chain C, Crystal Structure Of Human Dna Polymerase Gamma Accessory
Subunit
pdb|2G4C|D Chain D, Crystal Structure Of Human Dna Polymerase Gamma Accessory
Subunit
Length = 474
Score = 28.1 bits (61), Expect = 7.6, Method: Compositional matrix adjust.
Identities = 8/23 (34%), Positives = 17/23 (73%)
Query: 278 SNQYIEIWVMNEMNWIQQFAIGP 300
SNQ+++ W+ + + W ++FA+ P
Sbjct: 237 SNQWLDFWLRHRLQWWRKFAMSP 259
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
0.322 0.138 0.435
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,997,207
Number of Sequences: 62578
Number of extensions: 508669
Number of successful extensions: 1101
Number of sequences better than 100.0: 26
Number of HSP's better than 100.0 without gapping: 16
Number of HSP's successfully gapped in prelim test: 10
Number of HSP's that attempted gapping in prelim test: 1085
Number of HSP's gapped (non-prelim): 32
length of query: 384
length of database: 14,973,337
effective HSP length: 101
effective length of query: 283
effective length of database: 8,652,959
effective search space: 2448787397
effective search space used: 2448787397
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: 52 (24.6 bits)