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= psy5568
(685 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 = 176 bits (445), Expect = 5e-44, Method: Compositional matrix adjust.
Identities = 101/268 (37%), Positives = 143/268 (53%), Gaps = 9/268 (3%)
Query: 184 SICQSIQLHSCAESFYDRMTECVYSSPLTS---FNHGIKPDPWFYVDVMGKGKVALQEVN 240
S + Q A +DRM E V+SS + F H +P P VD++G+G+ AL + N
Sbjct: 125 STLTAEQWRQVAAELHDRMMETVFSSLTDAEKLFIHH-QPAPVSSVDLLGEGRQALIDAN 183
Query: 241 QKLGLAFDEWDLEYYTDIFRNKLKRNPTSVECFDLAQSNSEHSRHWFFKGKMIVDGIESD 300
+LGLA E +++Y + F KL RNP +E + AQ+NSEH RH F I+DG
Sbjct: 184 LRLGLALAEDEIDYLQEAF-TKLGRNPNDIELYMFAQANSEHCRHKIFNADWIIDGKPQP 242
Query: 301 KCLFEMIMDTTKHSNQNNVIKFNDNSSAIQGYRDLPAITPTNPGAPGPYTITNQDLDIIF 360
K LF+MI +T + + + + DN++ ++G N G Y + I+
Sbjct: 243 KSLFKMIKNTFETTPDYVLSAYKDNAAVMEGSAVGRYFADHNTGR---YDFHQEPAHILM 299
Query: 361 TAETHNFPTGVSPFSGATTGTGGRIRDVQAVGRGGNCIAGTAGYCVGNLNIPGYKLPWED 420
ETHN PT +SP+ GA TG+GG IRD A GRG AG G+ V NL IPG++ PWE
Sbjct: 300 KVETHNHPTAISPWPGAATGSGGEIRDEGATGRGAKPKAGLVGFSVSNLRIPGFEQPWE- 358
Query: 421 EQYGYPNNFATPLNILIEASNGASDYGN 448
E +G P T L+I+ E G + + N
Sbjct: 359 EDFGKPERIVTALDIMTEGPLGGAAFNN 386
Score = 126 bits (316), Expect = 5e-29, Method: Compositional matrix adjust.
Identities = 84/217 (38%), Positives = 119/217 (54%), Gaps = 19/217 (8%)
Query: 459 ATSIGEQPIKGLVDPKRGARMAVAEALTNLVFAKISDLKDVKCSGNWMWAAKLPGEGAAL 518
A SIGE+ L+D AR+AV EALTN+ +I D+K +K S NWM AA PGE A L
Sbjct: 702 AMSIGERAPVALLDFAASARLAVGEALTNIAATQIGDIKRIKLSANWMAAAGHPGEDAGL 761
Query: 519 FDACQAMSWVLPARMGNTRREWIKPIMFSGGIGTMK------HELKEKASPNVGSLVIST 572
+DA +A+ L ++G T I +MK +E +E SP SLVIS
Sbjct: 762 YDAVKAVGEELCPQLGLT-------IPVGKDSMSMKTRWQEGNEQREMTSPL--SLVISA 812
Query: 573 YAPCPDIRQVVTPDIKSPRLGYSSSLLWIDLSCGQHRVGGSALSQVLAEVRGPSPDVEDA 632
+A D+R +TP + + ++LL IDL G + +G +AL+QV ++ DV D
Sbjct: 813 FARVEDVRHTLTPQLSTE----DNALLLIDLGKGHNALGATALAQVYRQLGDKPADVRDV 868
Query: 633 AALVRAFNVTQRLIQDGQVLSGHDISDGGLLICLLEM 669
A L ++ Q L+ ++L+ HD SDGGLL+ L EM
Sbjct: 869 AQLKGFYDAMQALVAARKLLAWHDRSDGGLLVTLAEM 905
Score = 62.4 bits (150), Expect = 9e-10, Method: Compositional matrix adjust.
Identities = 30/84 (35%), Positives = 48/84 (57%), Gaps = 5/84 (5%)
Query: 1 YKLPWEDEQYGYPNNFATPLNILIEASNGASDYGNKFGEPLILGFARSYGQHCNG----E 56
++ PWE E +G P T L+I+ E G + + N+FG P + G+ R+Y + N E
Sbjct: 353 FEQPWE-EDFGKPERIVTALDIMTEGPLGGAAFNNEFGRPALTGYFRTYEEKVNSHNGEE 411
Query: 57 RREWIKPIMFSGGIGTMKHELKEK 80
R + KPIM +GGIG ++ + +K
Sbjct: 412 LRGYHKPIMLAGGIGNIRADHVQK 435
Score = 32.0 bits (71), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 16/46 (34%), Positives = 25/46 (54%)
Query: 534 GNTRREWIKPIMFSGGIGTMKHELKEKASPNVGSLVISTYAPCPDI 579
G R + KPIM +GGIG ++ + +K VG+ +I P +I
Sbjct: 409 GEELRGYHKPIMLAGGIGNIRADHVQKGEIVVGAKLIVLGGPAMNI 454
>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 = 176 bits (445), Expect = 5e-44, Method: Compositional matrix adjust.
Identities = 101/268 (37%), Positives = 143/268 (53%), Gaps = 9/268 (3%)
Query: 184 SICQSIQLHSCAESFYDRMTECVYSSPLTS---FNHGIKPDPWFYVDVMGKGKVALQEVN 240
S + Q A +DRM E V+SS + F H +P P VD++G+G+ AL + N
Sbjct: 125 STLTAEQWRQVAAELHDRMMETVFSSLTDAEKLFIHH-QPAPVSSVDLLGEGRQALIDAN 183
Query: 241 QKLGLAFDEWDLEYYTDIFRNKLKRNPTSVECFDLAQSNSEHSRHWFFKGKMIVDGIESD 300
+LGLA E +++Y + F KL RNP +E + AQ+NSEH RH F I+DG
Sbjct: 184 LRLGLALAEDEIDYLQEAF-TKLGRNPNDIELYMFAQANSEHCRHKIFNADWIIDGKPQP 242
Query: 301 KCLFEMIMDTTKHSNQNNVIKFNDNSSAIQGYRDLPAITPTNPGAPGPYTITNQDLDIIF 360
K LF+MI +T + + + + DN++ ++G N G Y + I+
Sbjct: 243 KSLFKMIKNTFETTPDYVLSAYKDNAAVMEGSAVGRYFADHNTGR---YDFHQEPAHILM 299
Query: 361 TAETHNFPTGVSPFSGATTGTGGRIRDVQAVGRGGNCIAGTAGYCVGNLNIPGYKLPWED 420
ETHN PT +SP+ GA TG+GG IRD A GRG AG G+ V NL IPG++ PWE
Sbjct: 300 KVETHNHPTAISPWPGAATGSGGEIRDEGATGRGAKPKAGLVGFSVSNLRIPGFEQPWE- 358
Query: 421 EQYGYPNNFATPLNILIEASNGASDYGN 448
E +G P T L+I+ E G + + N
Sbjct: 359 EDFGKPERIVTALDIMTEGPLGGAAFNN 386
Score = 126 bits (316), Expect = 5e-29, Method: Compositional matrix adjust.
Identities = 84/217 (38%), Positives = 119/217 (54%), Gaps = 19/217 (8%)
Query: 459 ATSIGEQPIKGLVDPKRGARMAVAEALTNLVFAKISDLKDVKCSGNWMWAAKLPGEGAAL 518
A SIGE+ L+D AR+AV EALTN+ +I D+K +K S NWM AA PGE A L
Sbjct: 702 AMSIGERAPVALLDFAASARLAVGEALTNIAATQIGDIKRIKLSANWMAAAGHPGEDAGL 761
Query: 519 FDACQAMSWVLPARMGNTRREWIKPIMFSGGIGTMK------HELKEKASPNVGSLVIST 572
+DA +A+ L ++G T I +MK +E +E SP SLVIS
Sbjct: 762 YDAVKAVGEELCPQLGLT-------IPVGKDSMSMKTRWQEGNEQREMTSPL--SLVISA 812
Query: 573 YAPCPDIRQVVTPDIKSPRLGYSSSLLWIDLSCGQHRVGGSALSQVLAEVRGPSPDVEDA 632
+A D+R +TP + + ++LL IDL G + +G +AL+QV ++ DV D
Sbjct: 813 FARVEDVRHTLTPQLSTE----DNALLLIDLGKGHNALGATALAQVYRQLGDKPADVRDV 868
Query: 633 AALVRAFNVTQRLIQDGQVLSGHDISDGGLLICLLEM 669
A L ++ Q L+ ++L+ HD SDGGLL+ L EM
Sbjct: 869 AQLKGFYDAMQALVAARKLLAWHDRSDGGLLVTLAEM 905
Score = 62.4 bits (150), Expect = 8e-10, Method: Compositional matrix adjust.
Identities = 30/84 (35%), Positives = 48/84 (57%), Gaps = 5/84 (5%)
Query: 1 YKLPWEDEQYGYPNNFATPLNILIEASNGASDYGNKFGEPLILGFARSYGQHCNG----E 56
++ PWE E +G P T L+I+ E G + + N+FG P + G+ R+Y + N E
Sbjct: 353 FEQPWE-EDFGKPERIVTALDIMTEGPLGGAAFNNEFGRPALTGYFRTYEEKVNSHNGEE 411
Query: 57 RREWIKPIMFSGGIGTMKHELKEK 80
R + KPIM +GGIG ++ + +K
Sbjct: 412 LRGYHKPIMLAGGIGNIRADHVQK 435
Score = 32.0 bits (71), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 16/46 (34%), Positives = 25/46 (54%)
Query: 534 GNTRREWIKPIMFSGGIGTMKHELKEKASPNVGSLVISTYAPCPDI 579
G R + KPIM +GGIG ++ + +K VG+ +I P +I
Sbjct: 409 GEELRGYHKPIMLAGGIGNIRADHVQKGEIVVGAKLIVLGGPAMNI 454
>pdb|3D54|A Chain A, Stucture Of Purlqs From Thermotoga Maritima
pdb|3D54|E Chain E, Stucture Of Purlqs From Thermotoga Maritima
pdb|3D54|I Chain I, Stucture Of Purlqs From Thermotoga Maritima
Length = 629
Score = 45.4 bits (106), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 22/51 (43%), Positives = 30/51 (58%), Gaps = 2/51 (3%)
Query: 344 GAPGPYTITNQD--LDIIFTAETHNFPTGVSPFSGATTGTGGRIRDVQAVG 392
G G + N D + F E+HN P+ + P++GA TG GG IRDV A+G
Sbjct: 75 GFEGNAGVVNLDDYYSVAFKIESHNHPSAIEPYNGAATGVGGIIRDVLAMG 125
>pdb|2HS0|A Chain A, T. Maritima Purl Complexed With Atp
pdb|2HS3|A Chain A, T. Maritima Purl Complexed With Fgar
pdb|2HS4|A Chain A, T. Maritima Purl Complexed With Fgar And Amppcp
Length = 603
Score = 45.4 bits (106), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 18/35 (51%), Positives = 25/35 (71%)
Query: 358 IIFTAETHNFPTGVSPFSGATTGTGGRIRDVQAVG 392
+ F E+HN P+ + P++GA TG GG IRDV A+G
Sbjct: 65 VAFKIESHNHPSAIEPYNGAATGVGGIIRDVLAMG 99
>pdb|1VK3|A Chain A, Crystal Structure Of Phosphoribosylformylglycinamidine
Synthase Ii (Tm1246) From Thermotoga Maritima At 2.15 A
Resolution
Length = 615
Score = 44.3 bits (103), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 18/35 (51%), Positives = 24/35 (68%)
Query: 358 IIFTAETHNFPTGVSPFSGATTGTGGRIRDVQAVG 392
+ F E+HN P+ + P++GA TG GG IRDV A G
Sbjct: 77 VAFKIESHNHPSAIEPYNGAATGVGGIIRDVLAXG 111
>pdb|3VIU|A Chain A, Crystal Structure Of Purl From Thermus Thermophilus
Length = 725
Score = 44.3 bits (103), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 17/35 (48%), Positives = 23/35 (65%)
Query: 358 IIFTAETHNFPTGVSPFSGATTGTGGRIRDVQAVG 392
+ F E+HN P+ V PF GA TG GG +RD+ + G
Sbjct: 80 VAFKIESHNHPSAVEPFQGAATGVGGILRDIXSXG 114
Score = 30.4 bits (67), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 12/24 (50%), Positives = 17/24 (70%)
Query: 645 LIQDGQVLSGHDISDGGLLICLLE 668
LIQ G + HD+++GGLL+ L E
Sbjct: 609 LIQRGLTRTAHDVAEGGLLLALAE 632
>pdb|2HRU|A Chain A, T. Maritima Purl Complexed With Adp
pdb|2HRY|A Chain A, T. Maritima Purl Complexed With Amppcp
Length = 603
Score = 41.6 bits (96), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 17/35 (48%), Positives = 24/35 (68%)
Query: 358 IIFTAETHNFPTGVSPFSGATTGTGGRIRDVQAVG 392
+ F E+ N P+ + P++GA TG GG IRDV A+G
Sbjct: 65 VAFKIESANHPSAIEPYNGAATGVGGIIRDVLAMG 99
>pdb|1S05|A Chain A, Nmr-Validated Structural Model For Oxidized R.Palustris
Cytochrome C556
Length = 129
Score = 31.6 bits (70), Expect = 1.5, Method: Composition-based stats.
Identities = 21/77 (27%), Positives = 32/77 (41%), Gaps = 1/77 (1%)
Query: 333 RDLPAITPTNPGAPGPYTITNQDLDIIFTAETHNFPTGVSPFSGATTGTGGRIRDVQAVG 392
+DLP + P + P+ I+ AE F T ++ F+ A G G+I+DV +
Sbjct: 49 KDLPKLFPDSVKGLKPFDSKYSSSPKIW-AERAKFDTEIADFAKAVDGAKGKIKDVDTLK 107
Query: 393 RGGNCIAGTAGYCVGNL 409
I G C N
Sbjct: 108 AAMQPIGKACGNCHENF 124
>pdb|1EO9|A Chain A, Crystal Structure Of Acinetobacter Sp. Adp1
Protocatechuate 3,4- Dioxygenase At Ph < 7.0
Length = 209
Score = 28.9 bits (63), Expect = 9.5, Method: Composition-based stats.
Identities = 23/92 (25%), Positives = 38/92 (41%), Gaps = 1/92 (1%)
Query: 465 QPIKGLVDPKRGARMAVAEALTNLVFAKISDLKDVKCSGNWM-WAAKLPGEGAALFDACQ 523
Q GL P R + + +A TN V+ +D + + N++ W G +
Sbjct: 58 QVFDGLSLPLRDVLIEIWQADTNGVYPSQADTQGKQVDPNFLGWGRTGADFGTGFWSFNT 117
Query: 524 AMSWVLPARMGNTRREWIKPIMFSGGIGTMKH 555
+P R G+T+ I I+F+ GI H
Sbjct: 118 IKPGAVPGRKGSTQAPHISLIIFARGINIGLH 149
>pdb|1S58|A Chain A, The Structure Of B19 Parvovirus Capsid
Length = 554
Score = 28.9 bits (63), Expect = 9.6, Method: Compositional matrix adjust.
Identities = 25/78 (32%), Positives = 36/78 (46%), Gaps = 13/78 (16%)
Query: 411 IPGYKLPWEDEQYGYPNNFATPLNI--LIEASNGASDYGNIEPCSNDRAIATSIGEQPIK 468
I GY PW + N F +PL LIE +YG+I P A+ +I E +K
Sbjct: 80 IMGYSTPWRYLDFNALNLFFSPLEFQHLIE------NYGSIAP----DALTVTISEIAVK 129
Query: 469 GLVDPKRGARMAVAEALT 486
+ D K G + V ++ T
Sbjct: 130 DVTD-KTGGGVQVTDSAT 146
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 0.136 0.419
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 22,415,294
Number of Sequences: 62578
Number of extensions: 986451
Number of successful extensions: 1989
Number of sequences better than 100.0: 16
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 1951
Number of HSP's gapped (non-prelim): 32
length of query: 685
length of database: 14,973,337
effective HSP length: 105
effective length of query: 580
effective length of database: 8,402,647
effective search space: 4873535260
effective search space used: 4873535260
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)