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= psy2354
(749 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1T3T|A Chain A, Structure Of Formylglycinamide Synthetase
pdb|3UJN|A Chain A, Formyl Glycinamide Ribonucleotide Amidotransferase From
Salmonella Typhimurium : Role Of The Atp Complexation
And Glutaminase Domain In Catalytic Coupling
pdb|3UMM|A Chain A, Formylglycinamide Ribonucleotide Amidotransferase From
Salmonella Typhimurium: Role Of The Atp Complexation And
Glutaminase Domain In Catalytic Coupling
Length = 1303
Score = 83.6 bits (205), Expect = 4e-16, Method: Compositional matrix adjust.
Identities = 56/180 (31%), Positives = 86/180 (47%), Gaps = 14/180 (7%)
Query: 220 PVQFVGVVTG--SNKVQGDNAADLDFDAVQRGDPEMGQKLNRVIRACIELPNNLNPIESI 277
P +G+ G S+ G + ADLDF +VQR +PEM ++ VI C +L + NPI I
Sbjct: 450 PAMNIGLGGGAASSMASGQSDADLDFASVQRDNPEMERRCQEVIDRCWQL-GDANPILFI 508
Query: 278 HDQGAGGNGNVLKEIVEP--VGAVVFTESFLLGDPSISTLELWGAEYQENNALLCKPLHC 335
HD GAGG N + E+V G L +P +S LE+W E QE L
Sbjct: 509 HDVGAGGLSNAMPELVSDGGRGGKFELRDILSDEPGMSPLEIWCNESQERYVLAVAADQL 568
Query: 336 KTLRMISAREKCPVQFVGVVTGSNKIVLAEDKAKYYSNPSSPLQHPVDIQMELICGKMPQ 395
+ RE+ P +G T + L ++ ++ N P+D+ ++++ GK P+
Sbjct: 569 PLFDELCKRERAPYAVIGDATEEQHLSLHDN---HFDN------QPIDLPLDVLLGKTPK 619
Score = 79.7 bits (195), Expect = 6e-15, Method: Compositional matrix adjust.
Identities = 43/93 (46%), Positives = 59/93 (63%), Gaps = 1/93 (1%)
Query: 649 GAATSIGEQPIKGLVDPKRGARMAVAEALTNLVFAKISDLKDVKCSGNWMWAAKLPGEGA 708
G A SIGE+ L+D AR+AV EALTN+ +I D+K +K S NWM AA PGE A
Sbjct: 700 GEAMSIGERAPVALLDFAASARLAVGEALTNIAATQIGDIKRIKLSANWMAAAGHPGEDA 759
Query: 709 ALFDACQAMC-DIMGEFGIAVDGGKDSLSMAAR 740
L+DA +A+ ++ + G+ + GKDS+SM R
Sbjct: 760 GLYDAVKAVGEELCPQLGLTIPVGKDSMSMKTR 792
Score = 77.8 bits (190), Expect = 2e-14, Method: Compositional matrix adjust.
Identities = 37/107 (34%), Positives = 62/107 (57%), Gaps = 6/107 (5%)
Query: 538 DALGSAKGWAASLLLNEGIKTQLNKFIARSDTFSFGVCNGCQLMNLLGWFSVSTQDKNNL 597
D LG+ +GWA S+L N ++ + F R T + GV NGCQ+M+ L ++
Sbjct: 1106 DVLGAGEGWAKSILFNHRVRDEFETFFHRPQTLALGVXNGCQMMSNLRELIPGSELWPRF 1165
Query: 598 VTDVMLSHNNSERFECRYSTVKIMKSPAIMLRNLENSVLGVWVAHGE 644
V N+S+RFE R+S V++ +SP+++L+ + S + + V+HGE
Sbjct: 1166 V------RNHSDRFEARFSLVEVTQSPSLLLQGMVGSQMPIAVSHGE 1206
Score = 55.8 bits (133), Expect = 8e-08, Method: Compositional matrix adjust.
Identities = 38/126 (30%), Positives = 66/126 (52%), Gaps = 9/126 (7%)
Query: 396 KMAFAGLSGMTVDIPSDVTTSEVLELLFAEELGWLLEVTNENEAFV---LEQFKAANVSC 452
+MAFAG G+ VDI + + L LF EELG +++V E+ V L Q+ A+
Sbjct: 904 EMAFAGHCGVQVDIAA--LGDDHLAALFNEELGGVIQVRAEDRDAVEALLAQYGLADC-V 960
Query: 453 KKIGVCDAFGMNAKISVAVNNEPVLNEDLGTLFLIWERTSYELEKLQMNARCADEEYNSL 512
+G A + + N++ V +E TL + W T++++++L+ N +CAD+E+ +
Sbjct: 961 HYLGQALA---GDRFVITANDQTVFSESRTTLRVWWAETTWQMQRLRDNPQCADQEHEAK 1017
Query: 513 VTRIGP 518
P
Sbjct: 1018 ANDTDP 1023
>pdb|3UGJ|A Chain A, Formyl Glycinamide Ribonucletide Amidotransferase From
Salmonella Typhimurum: Role Of The Atp Complexation And
Glutaminase Domain In Catalytic Coupling
Length = 1303
Score = 83.6 bits (205), Expect = 4e-16, Method: Compositional matrix adjust.
Identities = 56/180 (31%), Positives = 86/180 (47%), Gaps = 14/180 (7%)
Query: 220 PVQFVGVVTG--SNKVQGDNAADLDFDAVQRGDPEMGQKLNRVIRACIELPNNLNPIESI 277
P +G+ G S+ G + ADLDF +VQR +PEM ++ VI C +L + NPI I
Sbjct: 450 PAMNIGLGGGAASSMASGQSDADLDFASVQRDNPEMERRCQEVIDRCWQL-GDANPILFI 508
Query: 278 HDQGAGGNGNVLKEIVEP--VGAVVFTESFLLGDPSISTLELWGAEYQENNALLCKPLHC 335
HD GAGG N + E+V G L +P +S LE+W E QE L
Sbjct: 509 HDVGAGGLSNAMPELVSDGGRGGKFELRDILSDEPGMSPLEIWCNESQERYVLAVAADQL 568
Query: 336 KTLRMISAREKCPVQFVGVVTGSNKIVLAEDKAKYYSNPSSPLQHPVDIQMELICGKMPQ 395
+ RE+ P +G T + L ++ ++ N P+D+ ++++ GK P+
Sbjct: 569 PLFDELCKRERAPYAVIGDATEEQHLSLHDN---HFDN------QPIDLPLDVLLGKTPK 619
Score = 82.0 bits (201), Expect = 1e-15, Method: Compositional matrix adjust.
Identities = 38/107 (35%), Positives = 63/107 (58%), Gaps = 6/107 (5%)
Query: 538 DALGSAKGWAASLLLNEGIKTQLNKFIARSDTFSFGVCNGCQLMNLLGWFSVSTQDKNNL 597
D LG+ +GWA S+L N ++ + F R T + GVCNGCQ+M+ L ++
Sbjct: 1106 DVLGAGEGWAKSILFNHRVRDEFETFFHRPQTLALGVCNGCQMMSNLRELIPGSELWPRF 1165
Query: 598 VTDVMLSHNNSERFECRYSTVKIMKSPAIMLRNLENSVLGVWVAHGE 644
V N+S+RFE R+S V++ +SP+++L+ + S + + V+HGE
Sbjct: 1166 V------RNHSDRFEARFSLVEVTQSPSLLLQGMVGSQMPIAVSHGE 1206
Score = 79.7 bits (195), Expect = 6e-15, Method: Compositional matrix adjust.
Identities = 43/93 (46%), Positives = 59/93 (63%), Gaps = 1/93 (1%)
Query: 649 GAATSIGEQPIKGLVDPKRGARMAVAEALTNLVFAKISDLKDVKCSGNWMWAAKLPGEGA 708
G A SIGE+ L+D AR+AV EALTN+ +I D+K +K S NWM AA PGE A
Sbjct: 700 GEAMSIGERAPVALLDFAASARLAVGEALTNIAATQIGDIKRIKLSANWMAAAGHPGEDA 759
Query: 709 ALFDACQAMC-DIMGEFGIAVDGGKDSLSMAAR 740
L+DA +A+ ++ + G+ + GKDS+SM R
Sbjct: 760 GLYDAVKAVGEELCPQLGLTIPVGKDSMSMKTR 792
Score = 55.8 bits (133), Expect = 8e-08, Method: Compositional matrix adjust.
Identities = 38/126 (30%), Positives = 66/126 (52%), Gaps = 9/126 (7%)
Query: 396 KMAFAGLSGMTVDIPSDVTTSEVLELLFAEELGWLLEVTNENEAFV---LEQFKAANVSC 452
+MAFAG G+ VDI + + L LF EELG +++V E+ V L Q+ A+
Sbjct: 904 EMAFAGHCGVQVDIAA--LGDDHLAALFNEELGGVIQVRAEDRDAVEALLAQYGLADC-V 960
Query: 453 KKIGVCDAFGMNAKISVAVNNEPVLNEDLGTLFLIWERTSYELEKLQMNARCADEEYNSL 512
+G A + + N++ V +E TL + W T++++++L+ N +CAD+E+ +
Sbjct: 961 HYLGQALA---GDRFVITANDQTVFSESRTTLRVWWAETTWQMQRLRDNPQCADQEHEAK 1017
Query: 513 VTRIGP 518
P
Sbjct: 1018 ANDTDP 1023
>pdb|3VIU|A Chain A, Crystal Structure Of Purl From Thermus Thermophilus
Length = 725
Score = 38.5 bits (88), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 48/179 (26%), Positives = 72/179 (40%), Gaps = 17/179 (9%)
Query: 179 LGDPSISTLELWGAEYQEN---NALLCKPLHCKTLRMISAREKCPVQFVGVVTGSNKVQG 235
+G P++ + Y+EN NA L + L+ A P+ + G TG + + G
Sbjct: 152 IGVPTVGGDLYFHEGYRENPLVNAXCLGLLREEHLKRSRASLGRPIYYAGAKTGRDGIGG 211
Query: 236 DNAADL--------DFDAVQRGDPEMGQKLNRVIRACIELPNNLNPIESIHDQGAGGNGN 287
A D AVQ GDP +G+ L IE L+ +E + D GA G +
Sbjct: 212 AAFASRELKEEKAEDRPAVQVGDPFLGKLLXEATLEAIE----LDLVEGVQDXGAAGLTS 267
Query: 288 VLKEIVEPVGAVVFTESFLLG--DPSISTLELWGAEYQENNALLCKPLHCKTLRMISAR 344
L E+ G V L+ + + EL +E QE L+ K K L + R
Sbjct: 268 SLSELAHKSGLGVELHLDLVPTREEGXTPEELLLSESQERXVLVPKEGKEKALEEVFGR 326
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 0.134 0.396
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 21,524,213
Number of Sequences: 62578
Number of extensions: 890682
Number of successful extensions: 3262
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 3238
Number of HSP's gapped (non-prelim): 14
length of query: 749
length of database: 14,973,337
effective HSP length: 106
effective length of query: 643
effective length of database: 8,340,069
effective search space: 5362664367
effective search space used: 5362664367
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: 55 (25.8 bits)