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= psy12858
(131 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1PJ5|A Chain A, Crystal Structure Of Dimethylglycine Oxidase Of
Arthrobacter Globiformis In Complex With Acetate
pdb|1PJ6|A Chain A, Crystal Structure Of Dimethylglycine Oxidase Of
Arthrobacter Globiformis In Complex With Folic Acid
pdb|1PJ7|A Chain A, Structure Of Dimethylglycine Oxidase Of Arthrobacter
Globiformis In Complex With Folinic Acid
Length = 830
Score = 48.1 bits (113), Expect = 1e-06, Method: Composition-based stats.
Identities = 25/72 (34%), Positives = 40/72 (55%), Gaps = 4/72 (5%)
Query: 5 KDYFIGKAALQRQKDQGVQKRLVMFVAEDLDPDTDVWLWGSEPIYRNDQFVGTITSAGYG 64
K+ FIGK AL+ + ++ +RL +D + G EP++ +Q VG +TSA YG
Sbjct: 725 KESFIGKGALEGRTEEASARRLRCLTIDD----GRSIVLGKEPVFYKEQAVGYVTSAAYG 780
Query: 65 FTMKKLIGLGYI 76
+T+ K I Y+
Sbjct: 781 YTVAKPIAYSYL 792
>pdb|3GSI|A Chain A, Crystal Structure Of D552a Dimethylglycine Oxidase Mutant
Of Arthrobacter Globiformis In Complex With
Tetrahydrofolate
Length = 827
Score = 48.1 bits (113), Expect = 1e-06, Method: Composition-based stats.
Identities = 25/72 (34%), Positives = 40/72 (55%), Gaps = 4/72 (5%)
Query: 5 KDYFIGKAALQRQKDQGVQKRLVMFVAEDLDPDTDVWLWGSEPIYRNDQFVGTITSAGYG 64
K+ FIGK AL+ + ++ +RL +D + G EP++ +Q VG +TSA YG
Sbjct: 722 KESFIGKGALEGRTEEASARRLRCLTIDD----GRSIVLGKEPVFYKEQAVGYVTSAAYG 777
Query: 65 FTMKKLIGLGYI 76
+T+ K I Y+
Sbjct: 778 YTVAKPIAYSYL 789
>pdb|1V5V|A Chain A, Crystal Structure Of A Component Of Glycine Cleavage
System: T-Protein From Pyrococcus Horikoshii Ot3 At 1.5
A Resolution
pdb|1V5V|B Chain B, Crystal Structure Of A Component Of Glycine Cleavage
System: T-Protein From Pyrococcus Horikoshii Ot3 At 1.5
A Resolution
Length = 401
Score = 36.2 bits (82), Expect = 0.006, Method: Composition-based stats.
Identities = 21/70 (30%), Positives = 37/70 (52%), Gaps = 5/70 (7%)
Query: 8 FIGKAALQRQKDQGVQKRLVMFVAEDLDPDTDVWLWGSEPIYRNDQFVGTITSAGYGFTM 67
FIGK AL +QK++GV ++LV F D + + +Y N + +G +TS +
Sbjct: 297 FIGKDALLKQKERGVGRKLVHFKMIDKGIPREGY-----KVYANGEMIGEVTSGTLSPLL 351
Query: 68 KKLIGLGYIR 77
IG+ +++
Sbjct: 352 NVGIGIAFVK 361
>pdb|1YX2|A Chain A, Crystal Structure Of The Probable Aminomethyltransferase
From Bacillus Subtilis
pdb|1YX2|B Chain B, Crystal Structure Of The Probable Aminomethyltransferase
From Bacillus Subtilis
Length = 365
Score = 30.4 bits (67), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 20/75 (26%), Positives = 37/75 (49%), Gaps = 5/75 (6%)
Query: 8 FIGKAALQRQKDQGVQKRLVMFVAEDLDPDTDVWLWGSEPIYRNDQFVGTITSAGYGFTM 67
F GK+ L QK+ G +++LV + + G E +++N + VG +T+ T+
Sbjct: 270 FFGKSVLSEQKENGAKRKLVGLEX----IEKGIPRHGYE-VFQNGKSVGKVTTGTQSPTL 324
Query: 68 KKLIGLGYIRHPSEQ 82
K +GL I + +
Sbjct: 325 GKNVGLALIDSETSE 339
>pdb|3TFH|A Chain A, Dmsp-Dependent Demethylase From P. Ubique - Apo
pdb|3TFH|B Chain B, Dmsp-Dependent Demethylase From P. Ubique - Apo
pdb|3TFI|A Chain A, Dmsp-Dependent Demethylase From P. Ubique - With Substrate
Dmsp
pdb|3TFI|B Chain B, Dmsp-Dependent Demethylase From P. Ubique - With Substrate
Dmsp
pdb|3TFJ|A Chain A, Dmsp-Dependent Demethylase From P. Ubique - With Cofactor
Thf
pdb|3TFJ|B Chain B, Dmsp-Dependent Demethylase From P. Ubique - With Cofactor
Thf
Length = 369
Score = 28.1 bits (61), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 25/71 (35%), Positives = 40/71 (56%), Gaps = 5/71 (7%)
Query: 8 FIGKAALQRQKDQGVQKRLVMFVAEDLDPDTDVWLWGSEPIY-RNDQFVGTITSAGYGFT 66
F+GK L+ K +G QK+L V D+ ++ L GS+ IY N+ +G + SA Y
Sbjct: 274 FLGKEKLKEIKLKGPQKKL-RGVKIDI---KEISLTGSKNIYDENNNVIGELRSACYSPH 329
Query: 67 MKKLIGLGYIR 77
+K+IG+ I+
Sbjct: 330 FQKVIGIAMIK 340
>pdb|3E1T|A Chain A, Structure And Action Of The Myxobacterial Chondrochloren
Halogenase Cndh, A New Variant Of Fad-Dependent
Halogenases
Length = 512
Score = 27.3 bits (59), Expect = 2.1, Method: Composition-based stats.
Identities = 17/59 (28%), Positives = 27/59 (45%), Gaps = 7/59 (11%)
Query: 33 DLDPDTDVWLWGSEPIYRNDQFVGTITSAGYGFTMKKLIGLGYIRHPSEQNVTNDFVTE 91
D++ DTD + W + I + T A F ++ + G + P Q+V DF TE
Sbjct: 367 DMNQDTDSYFWSARKI------INTEERANEAF-VRLIAGRSNLDEPVFQSVAKDFFTE 418
>pdb|3PQU|A Chain A, The Crystal Structures Of Porcine Pathogen Ash57_tbpb
pdb|3PQU|B Chain B, The Crystal Structures Of Porcine Pathogen Ash57_tbpb
Length = 570
Score = 26.9 bits (58), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 18/47 (38%), Positives = 21/47 (44%), Gaps = 8/47 (17%)
Query: 65 FTMKKLIGL----GYIRHPSEQNVTNDFVTEGTYTLDVAGNRFQASA 107
F KKL G GYI Q VT + E D+ GNRF+ A
Sbjct: 237 FDNKKLTGSLYRNGYINRNKAQEVTKRYSIE----ADITGNRFRGKA 279
>pdb|3BC9|A Chain A, Alpha-Amylase B In Complex With Acarbose
pdb|3BCD|A Chain A, Alpha-Amylase B In Complex With Maltotetraose And
Alpha-Cyclodextrin
pdb|3BCF|A Chain A, Alpha-Amylase B From Halothermothrix Orenii
Length = 599
Score = 26.2 bits (56), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 16/53 (30%), Positives = 24/53 (45%), Gaps = 7/53 (13%)
Query: 64 GFTMKKLIGLGYIRHPSEQNVTNDFVT-------EGTYTLDVAGNRFQASAHI 109
G M L G + P +N FV EG+YT+ + ++QA A+I
Sbjct: 418 GAYMADLRNAGLVNSPGYENRAVTFVDNHDTDRDEGSYTVSIYSRKYQAYAYI 470
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 0.138 0.417
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,036,678
Number of Sequences: 62578
Number of extensions: 165631
Number of successful extensions: 330
Number of sequences better than 100.0: 24
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 21
Number of HSP's that attempted gapping in prelim test: 324
Number of HSP's gapped (non-prelim): 24
length of query: 131
length of database: 14,973,337
effective HSP length: 88
effective length of query: 43
effective length of database: 9,466,473
effective search space: 407058339
effective search space used: 407058339
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: 46 (22.3 bits)