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= psy7376
(180 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1IXK|A Chain A, Crystal Structure Analysis Of Methyltransferase Homolog
Protein From Pyrococcus Horikoshii
Length = 315
Score = 42.4 bits (98), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 27/102 (26%), Positives = 46/102 (45%), Gaps = 9/102 (8%)
Query: 65 FSYNEFLMERIMQIFPLDELMSFLEASETQRPLTIRTNTLKTRRRDLAQALVNRGVNLDP 124
Y++ +R Q++ + + EA E P R NTLK +DL + L +G
Sbjct: 14 LGYSKLFADRYFQLWG-ERAIRIAEAXEKPLPRCFRVNTLKISVQDLVKRLNKKGFQFKR 72
Query: 125 IGKWSKVGLVIYNSTVPIGATPEYLGAALMKNTGVLFANDVS 166
+ W+K G + I +TPE+L TG+++ + S
Sbjct: 73 V-PWAKEGFCLTREPFSITSTPEFL-------TGLIYIQEAS 106
>pdb|3A4T|A Chain A, Crystal Structure Of Atrm4 From M.Jannaschii With
Sinefungin
pdb|3A4T|B Chain B, Crystal Structure Of Atrm4 From M.Jannaschii With
Sinefungin
pdb|3AJD|A Chain A, Crystal Structure Of Atrm4
Length = 274
Score = 39.7 bits (91), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 34/121 (28%), Positives = 47/121 (38%), Gaps = 41/121 (33%)
Query: 99 IRTNTLKTRRRDLAQALVNRGVNLDPIGKWSKVGLVIYNSTVPIGATPEYLG-------- 150
IR NTLK L + L N+GV L+ + + S IG+TPEYL
Sbjct: 13 IRVNTLKINPEVLKKRLENKGVVLEKT--FLDYAFEVKKSPFSIGSTPEYLFGYYMPQSI 70
Query: 151 -------------------------------AALMKNTGVLFANDVSKERSKAIVGNFHR 179
A LMKN G + A ++SK R+KA+ N +R
Sbjct: 71 SSMIPPIVLNPREDDFILDMCAAPGGKTTHLAQLMKNKGTIVAVEISKTRTKALKSNINR 130
Query: 180 L 180
+
Sbjct: 131 M 131
>pdb|2FRX|A Chain A, Crystal Structure Of Yebu, A M5c Rna Methyltransferase
From E.Coli
pdb|2FRX|B Chain B, Crystal Structure Of Yebu, A M5c Rna Methyltransferase
From E.Coli
pdb|2FRX|C Chain C, Crystal Structure Of Yebu, A M5c Rna Methyltransferase
From E.Coli
pdb|2FRX|D Chain D, Crystal Structure Of Yebu, A M5c Rna Methyltransferase
From E.Coli
Length = 479
Score = 35.4 bits (80), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 27/68 (39%), Positives = 33/68 (48%), Gaps = 8/68 (11%)
Query: 87 FLEASETQRPL--TIRTNTLKTRRRDLAQALVNRGVNLDPIGKWSKVGLVIY---NSTVP 141
FL A QRPL +IR NTLK D Q G L PI W + G I +P
Sbjct: 29 FLAA--CQRPLRRSIRVNTLKISVADFLQLTAPYGWTLTPI-PWCEEGFWIERDNEDALP 85
Query: 142 IGATPEYL 149
+G+T E+L
Sbjct: 86 LGSTAEHL 93
>pdb|3EPM|A Chain A, Crystal Structure Of Caulobacter Crescentus Thic
pdb|3EPM|B Chain B, Crystal Structure Of Caulobacter Crescentus Thic
Length = 612
Score = 28.1 bits (61), Expect = 2.7, Method: Composition-based stats.
Identities = 21/53 (39%), Positives = 28/53 (52%), Gaps = 9/53 (16%)
Query: 116 VNRGVNLDPIGKWSKVGLVIYNSTVPIGATPEYLGAALMKNTGVLFANDVSKE 168
++ G N+ I W +I NS+VPIG P Y AL K GV A D++ E
Sbjct: 250 LSTGRNIHNIRDW-----IIRNSSVPIGTVPIY--QALEKVNGV--AEDLNWE 293
>pdb|3QX3|A Chain A, Human Topoisomerase Iibeta In Complex With Dna And
Etoposide
pdb|3QX3|B Chain B, Human Topoisomerase Iibeta In Complex With Dna And
Etoposide
Length = 803
Score = 28.1 bits (61), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 12/30 (40%), Positives = 18/30 (60%), Gaps = 1/30 (3%)
Query: 103 TLKTR-RRDLAQALVNRGVNLDPIGKWSKV 131
T++ R ++DL Q LV RG DP+ W +
Sbjct: 662 TIENRSKKDLIQMLVQRGYESDPVKAWKEA 691
>pdb|3EPN|A Chain A, Crystal Structure Of Caulobacter Crescentus Thic Complexed
With Imidazole Ribonucleotide
pdb|3EPN|B Chain B, Crystal Structure Of Caulobacter Crescentus Thic Complexed
With Imidazole Ribonucleotide
pdb|3EPO|A Chain A, Crystal Structure Of Caulobacter Crescentus Thic Complexed
With Hmp-P
pdb|3EPO|B Chain B, Crystal Structure Of Caulobacter Crescentus Thic Complexed
With Hmp-P
Length = 612
Score = 26.9 bits (58), Expect = 6.2, Method: Compositional matrix adjust.
Identities = 21/53 (39%), Positives = 28/53 (52%), Gaps = 9/53 (16%)
Query: 116 VNRGVNLDPIGKWSKVGLVIYNSTVPIGATPEYLGAALMKNTGVLFANDVSKE 168
++ G N+ I W +I NS+VPIG P Y AL K GV A D++ E
Sbjct: 250 LSTGRNIHNIRDW-----IIRNSSVPIGTVPIY--QALEKVNGV--AEDLNWE 293
>pdb|1WA3|A Chain A, Mechanism Of The Class I Kdpg Aldolase
pdb|1WA3|B Chain B, Mechanism Of The Class I Kdpg Aldolase
pdb|1WA3|C Chain C, Mechanism Of The Class I Kdpg Aldolase
pdb|1WA3|D Chain D, Mechanism Of The Class I Kdpg Aldolase
pdb|1WA3|E Chain E, Mechanism Of The Class I Kdpg Aldolase
pdb|1WA3|F Chain F, Mechanism Of The Class I Kdpg Aldolase
Length = 205
Score = 26.9 bits (58), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 18/56 (32%), Positives = 28/56 (50%), Gaps = 16/56 (28%)
Query: 119 GVNLDPIGKWSKVGLVIYNSTVPIGATPEYLGAALMKNTGVLFANDVSKERSKAIV 174
GVNLD + +W K G++ +G+AL+K T D +E++KA V
Sbjct: 158 GVNLDNVCEWFKAGVLAVG-----------VGSALVKGT-----PDEVREKAKAFV 197
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 26.9 bits (58), Expect = 6.5, Method: Compositional matrix adjust.
Identities = 8/25 (32%), Positives = 20/25 (80%)
Query: 11 FPSEEEADKVLSIPDVEQRIKDVLM 35
FP++EEAD+ + + ++E R+++ ++
Sbjct: 9 FPAQEEADRTVFVGNLEARVREEIL 33
>pdb|1VLW|A Chain A, Crystal Structure Of 2-Dehydro-3-Deoxyphosphogluconate
Aldolase4- Hydroxy-2-Oxoglutarate Aldolase (Tm0066) From
Thermotoga Maritima At 2.30 A Resolution
pdb|1VLW|B Chain B, Crystal Structure Of 2-Dehydro-3-Deoxyphosphogluconate
Aldolase4- Hydroxy-2-Oxoglutarate Aldolase (Tm0066) From
Thermotoga Maritima At 2.30 A Resolution
pdb|1VLW|C Chain C, Crystal Structure Of 2-Dehydro-3-Deoxyphosphogluconate
Aldolase4- Hydroxy-2-Oxoglutarate Aldolase (Tm0066) From
Thermotoga Maritima At 2.30 A Resolution
Length = 217
Score = 26.9 bits (58), Expect = 6.8, Method: Compositional matrix adjust.
Identities = 18/56 (32%), Positives = 28/56 (50%), Gaps = 16/56 (28%)
Query: 119 GVNLDPIGKWSKVGLVIYNSTVPIGATPEYLGAALMKNTGVLFANDVSKERSKAIV 174
GVNLD + +W K G++ +G+AL+K T D +E++KA V
Sbjct: 170 GVNLDNVCEWFKAGVLAVG-----------VGSALVKGT-----PDEVREKAKAFV 209
>pdb|3EFY|A Chain A, Structure Of The Cyclomodulin Cif From Pathogenic
Escherichia Coli
pdb|3EFY|B Chain B, Structure Of The Cyclomodulin Cif From Pathogenic
Escherichia Coli
Length = 195
Score = 26.6 bits (57), Expect = 9.2, Method: Compositional matrix adjust.
Identities = 15/44 (34%), Positives = 23/44 (52%), Gaps = 3/44 (6%)
Query: 54 TSLLLKDLCTYFSY---NEFLMERIMQIFPLDELMSFLEASETQ 94
T +LL D+C YFS N+ +E+I +F +D + L Q
Sbjct: 109 TPILLDDICNYFSCMSQNKTDLEQIATLFDIDGNVKMLRKENIQ 152
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 0.136 0.391
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,905,284
Number of Sequences: 62578
Number of extensions: 181389
Number of successful extensions: 436
Number of sequences better than 100.0: 12
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 426
Number of HSP's gapped (non-prelim): 15
length of query: 180
length of database: 14,973,337
effective HSP length: 93
effective length of query: 87
effective length of database: 9,153,583
effective search space: 796361721
effective search space used: 796361721
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)