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= psy17389
(259 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3HXT|A Chain A, Structure Of Human Mthfs
pdb|3HY3|A Chain A, Structure Of Human Mthfs With 10-Formyltetrahydrofolate
pdb|3HY4|A Chain A, Structure Of Human Mthfs With N5-Iminium Phosphate
pdb|3HY6|A Chain A, Structure Of Human Mthfs With Adp
Length = 203
Score = 109 bits (273), Expect = 1e-24, Method: Compositional matrix adjust.
Identities = 65/182 (35%), Positives = 99/182 (54%), Gaps = 24/182 (13%)
Query: 80 LKHPVYEQSKRISIYVDRDDEISTRKIIQHICSSGKECFIPRYDKTEMTMRIFRQTWSGE 139
+ H Y++SKRISI++ DEI T +II+ I GK CFIPRY M + R
Sbjct: 41 IAHSEYQKSKRISIFLSMQDEIETEEIIKDIFQRGKICFIPRYRFQSNHMDMVR------ 94
Query: 140 ATXXXXXXXXXXXXXXYEDLDNLIKNKENILQHSQTEPTEDAMKTGGLDLVVVPGRAFTE 199
E++ L K NI Q + + E+A+ TGGLDL+ +PG F +
Sbjct: 95 -------------IESPEEISLLPKTSWNIPQPGEGDVREEALSTGGLDLIFMPGLGFDK 141
Query: 200 TGKRMGRGKGYYDTYLS---ELKRISPHCKTIGLAFSCQMVEDLPMSDHDVPLDYVIHPL 256
G R+GRGKGYYD YL + + + P+ T+ LAF Q+ +P++++D+ +D V++
Sbjct: 142 HGNRLGRGKGYYDAYLKRCLQHQEVKPY--TLALAFKEQICLQVPVNENDMKVDEVLYED 199
Query: 257 ST 258
S+
Sbjct: 200 SS 201
Score = 45.8 bits (107), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 22/62 (35%), Positives = 35/62 (56%)
Query: 5 RYDKTEMTMLKLHRYEDLDNLIKNKENILQHSQTEPTEDAMKTGGLDLVVVPGRAFTETG 64
R+ M M+++ E++ L K NI Q + + E+A+ TGGLDL+ +PG F + G
Sbjct: 84 RFQSNHMDMVRIESPEEISLLPKTSWNIPQPGEGDVREEALSTGGLDLIFMPGLGFDKHG 143
Query: 65 KR 66
R
Sbjct: 144 NR 145
>pdb|1YDM|A Chain A, X-ray Structure Of Northeast Structural Genomics Target
Sr44
pdb|1YDM|B Chain B, X-ray Structure Of Northeast Structural Genomics Target
Sr44
pdb|1YDM|C Chain C, X-ray Structure Of Northeast Structural Genomics Target
Sr44
Length = 187
Score = 63.5 bits (153), Expect = 9e-11, Method: Compositional matrix adjust.
Identities = 48/173 (27%), Positives = 73/173 (42%), Gaps = 33/173 (19%)
Query: 83 PVYEQSKRISIYVDRDDEISTRKIIQHICSSGKECFIPRY--DKTEMTMRIFRQTWSGEA 140
P ++ + I++ + R EI TR +I+ GK+ IP+ D + R ++ E
Sbjct: 36 PEWQNAGTIAVTISRGLEIPTRPVIEQAWEEGKQVCIPKCHPDTKKXQFRTYQTDDQLET 95
Query: 141 TXXXXXXXXXXXXXXYEDLDNLIKNKENILQHSQTEPTEDAMKTGGLDLVVVPGRAFTET 200
Y L + K + SQ +DL +VPG F
Sbjct: 96 V--------------YAGLLEPVIEKTKEVNPSQ------------IDLXIVPGVCFDVN 129
Query: 201 GKRMGRGKGYYDTYLSELKRISPHCKTIGLAFSCQMVEDLPMSDHDVPLDYVI 253
G R+G G GYYD YLSE + KT+ L CQ+ +P HD+P+ +I
Sbjct: 130 GFRVGFGGGYYDRYLSEYEG-----KTVSLLLECQLFAHVPRLPHDIPVHKLI 177
>pdb|2JCB|A Chain A, The Crystal Structure Of 5-Formyl-Tetrahydrofolate
Cycloligase From Bacillus Anthracis (Ba4489)
pdb|2JCB|B Chain B, The Crystal Structure Of 5-Formyl-Tetrahydrofolate
Cycloligase From Bacillus Anthracis (Ba4489)
Length = 200
Score = 58.5 bits (140), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 52/169 (30%), Positives = 83/169 (49%), Gaps = 29/169 (17%)
Query: 85 YEQSKRISIYVDRDDEISTRKIIQHICSSGKECFIPRYDKTEMTMRIFRQTWSGEATXXX 144
+ ++K I I + ++E++T II+ GK +P+ +K TM FRQ
Sbjct: 49 WAEAKTIGITLSMENEVNTYPIIEKAWKEGKRVVVPKCNKETRTMS-FRQI--------- 98
Query: 145 XXXXXXXXXXXYEDLDNLIKNKENILQHSQTEPTEDAMKTGGLDLVVVPGRAFTETGKRM 204
++ L+ + N L+ TE+ + +DL +VPG A+TE G+R+
Sbjct: 99 ---------SNFDQLETVYMN----LREPIPALTEE-VNADEIDLQIVPGVAYTERGERI 144
Query: 205 GRGKGYYDTYLSELKRISPHCKTIGLAFSCQMVEDLPMSDHDVPLDYVI 253
G G GYYD YL K KT+ LA+S QMVE +P+ D ++ +I
Sbjct: 145 GYGGGYYDRYLVHYK-----GKTLSLAYSFQMVEHIPVEPFDKNVEKII 188
>pdb|1SOU|A Chain A, Nmr Structure Of Aquifex Aeolicus 5,10-
Methenyltetrahydrofolate Synthetase: Northeast
Structural Genomics Consortium Target Qr46
Length = 194
Score = 57.0 bits (136), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 30/79 (37%), Positives = 45/79 (56%), Gaps = 6/79 (7%)
Query: 176 EPTE-DAMKTGGLDLVVVPGRAFTETGKRMGRGKGYYDTYLSELKRISPHCKTIGLAFSC 234
EP E + + +D + VPG AF G R+G GKGYYD L +K + +G+A+S
Sbjct: 100 EPVEGERVNPEDVDFIAVPGVAFDLEGYRLGFGKGYYDRLLKRVKGLK-----VGVAYSF 154
Query: 235 QMVEDLPMSDHDVPLDYVI 253
Q+ E LP D+P+D ++
Sbjct: 155 QVFERLPRDAWDIPVDVLV 173
>pdb|1WKC|A Chain A, Crystal Structure Of A 5-Formyltetrahydrofolate
Cycloligase-Related Protein From Thermus Thermophilus
Hb8
Length = 184
Score = 56.6 bits (135), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 31/78 (39%), Positives = 43/78 (55%), Gaps = 8/78 (10%)
Query: 175 TEPTEDAMKTGGLDLVVVPGRAFTETGKRMGRGKGYYDTYLSELKRISPHCKTIGLAFSC 234
T P ED LDLVVVPG AF G R+G G+G+YD +L E++ T+G+
Sbjct: 94 TTPPEDPRV---LDLVVVPGLAFDREGYRLGHGQGFYDRFLKEVR-----AATVGVVPQA 145
Query: 235 QMVEDLPMSDHDVPLDYV 252
+ LP DVP+D++
Sbjct: 146 LLFPALPRDPWDVPVDHL 163
>pdb|1SBQ|A Chain A, Crystal Structure Of Methenyltetrahydrofolate Synthetase
From Mycoplasma Pneumoniae At 2.2 Resolution
pdb|1SBQ|B Chain B, Crystal Structure Of Methenyltetrahydrofolate Synthetase
From Mycoplasma Pneumoniae At 2.2 Resolution
pdb|1U3F|A Chain A, Structural And Functional Characterization Of A 5,10-
Methenyltetrahydrofolate Synthetase From Mycoplasma
Pneumoniae (Gi: 13508087)
pdb|1U3F|B Chain B, Structural And Functional Characterization Of A 5,10-
Methenyltetrahydrofolate Synthetase From Mycoplasma
Pneumoniae (Gi: 13508087)
pdb|1U3G|A Chain A, Structural And Functional Characterization Of A 5,10-
Methenyltetrahydrofolate Synthetase From Mycoplasma
Pneumoniae (gi: 13508087)
Length = 189
Score = 47.8 bits (112), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 27/75 (36%), Positives = 39/75 (52%), Gaps = 4/75 (5%)
Query: 180 DAMKTGGLDLVVVPGRAFTETGKRMGRGKGYYDTYLSELKRISPHCKTIGLAFSCQMVED 239
+ + +D ++P F + R+G GKGYYD YL +L R P IG+A+S Q D
Sbjct: 117 NTFEPNQIDCFLIPLVGFNKDNYRLGFGKGYYDRYLMQLTRQQPK---IGIAYSFQK-GD 172
Query: 240 LPMSDHDVPLDYVIH 254
DV LD +I+
Sbjct: 173 FLADPWDVQLDLIIN 187
>pdb|3IYD|C Chain C, Three-Dimensional Em Structure Of An Intact
Activator-Dependent Transcription Initiation Complex
pdb|4IGC|C Chain C, X-ray Crystal Structure Of Escherichia Coli Sigma70
Holoenzyme
pdb|4IGC|H Chain H, X-ray Crystal Structure Of Escherichia Coli Sigma70
Holoenzyme
Length = 1342
Score = 32.7 bits (73), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 16/53 (30%), Positives = 26/53 (49%), Gaps = 6/53 (11%)
Query: 213 TYLSELKRISPHCKTIG------LAFSCQMVEDLPMSDHDVPLDYVIHPLSTP 259
YL+ +RI P K G + +ED+P ++ P+D V++PL P
Sbjct: 1052 VYLAVKRRIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVP 1104
>pdb|3LU0|C Chain C, Molecular Model Of Escherichia Coli Core Rna Polymerase
Length = 1342
Score = 32.7 bits (73), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 16/53 (30%), Positives = 26/53 (49%), Gaps = 6/53 (11%)
Query: 213 TYLSELKRISPHCKTIG------LAFSCQMVEDLPMSDHDVPLDYVIHPLSTP 259
YL+ +RI P K G + +ED+P ++ P+D V++PL P
Sbjct: 1052 VYLAVKRRIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVP 1104
>pdb|4EBA|G Chain G, Crystal Structure Of The Rna14-Rna15 Complex
pdb|4EBA|I Chain I, Crystal Structure Of The Rna14-Rna15 Complex
pdb|4EBA|H Chain H, Crystal Structure Of The Rna14-Rna15 Complex
Length = 174
Score = 28.5 bits (62), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 15/60 (25%), Positives = 28/60 (46%), Gaps = 3/60 (5%)
Query: 69 VSFSWPYIGCFLKHPVYEQSKRISI---YVDRDDEISTRKIIQHICSSGKECFIPRYDKT 125
V F W +G + + + IS + +D +++ K+IQH C KE F+ ++
Sbjct: 25 VKFPWLPVGVDVNINMTTPAMCISSELGKLQKDQQMALLKVIQHFCKDDKETFVALLEEA 84
>pdb|1ZD8|A Chain A, Structure Of Human Adenylate Kinase 3 Like 1
Length = 227
Score = 26.9 bits (58), Expect = 10.0, Method: Compositional matrix adjust.
Identities = 24/87 (27%), Positives = 38/87 (43%), Gaps = 25/87 (28%)
Query: 7 DKTEMTMLKLHRYEDLDNLIKNKENILQHSQTEPTEDAMKTGGLDLVVVPGRAFTETGKR 66
DK E + +L YED QT+P + + G V+ + TET K
Sbjct: 164 DKPETVIKRLKAYED---------------QTKPVLEYYQKKG----VLETFSGTETNK- 203
Query: 67 CTVSFSWPYIGCFLKHPVYEQSKRISI 93
WPY+ FL+ V ++S++ S+
Sbjct: 204 -----IWPYVYAFLQTKVPQRSQKASV 225
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 0.135 0.407
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,663,595
Number of Sequences: 62578
Number of extensions: 299587
Number of successful extensions: 809
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 790
Number of HSP's gapped (non-prelim): 14
length of query: 259
length of database: 14,973,337
effective HSP length: 97
effective length of query: 162
effective length of database: 8,903,271
effective search space: 1442329902
effective search space used: 1442329902
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: 50 (23.9 bits)