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= psy9412
(118 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2APN|A Chain A, Hi1723 Solution Structure
Length = 114
Score = 122 bits (307), Expect = 4e-29, Method: Compositional matrix adjust.
Identities = 55/107 (51%), Positives = 71/107 (66%)
Query: 9 ISITLTEVAIKKVSHXXXXXXXXXXXXRVFIQGGGCSGFQYGFMFDEHTNKDDIIFKKNG 68
+ +T T+ A KV RV+I GGGCSGFQYGF FDE N D+ +K+G
Sbjct: 7 VPLTFTDAAANKVKSLISEEENTDLKLRVYITGGGCSGFQYGFTFDEKVNDGDLTIEKSG 66
Query: 69 IQLLIDSVSYQYLIGSEIDYKDDLDGSKFVIKNPNAVTTCGCGSSFS 115
+QL+ID +S QYLIG +DY + L+GS+F + NPNA +TCGCGSSFS
Sbjct: 67 VQLVIDPMSLQYLIGGTVDYTEGLEGSRFTVNNPNATSTCGCGSSFS 113
>pdb|1NWB|A Chain A, Solution Nmr Structure Of Protein Aq_1857 From Aquifex
Aeolicus: Northeast Structural Genomics Consortium
Target Qr6
Length = 124
Score = 87.0 bits (214), Expect = 2e-18, Method: Compositional matrix adjust.
Identities = 40/103 (38%), Positives = 62/103 (60%)
Query: 13 LTEVAIKKVSHXXXXXXXXXXXXRVFIQGGGCSGFQYGFMFDEHTNKDDIIFKKNGIQLL 72
+T+ A++++ R+ + GGCSGFQY FD+ + D +F+ +G++++
Sbjct: 12 VTDKAVEEIKKVAQENNIENPILRIRVVPGGCSGFQYAMGFDDTVEEGDHVFEYDGVKVV 71
Query: 73 IDSVSYQYLIGSEIDYKDDLDGSKFVIKNPNAVTTCGCGSSFS 115
ID S Y+ G+E+DY D G F I+NPNA +CGCGSSFS
Sbjct: 72 IDPFSMPYVNGAELDYVVDFMGGGFTIRNPNATGSCGCGSSFS 114
>pdb|1R94|A Chain A, Crystal Structure Of Isca (mercury Derivative)
pdb|1R94|B Chain B, Crystal Structure Of Isca (mercury Derivative)
pdb|1R95|A Chain A, Crystal Structure Of Isca (Native)
pdb|1R95|B Chain B, Crystal Structure Of Isca (Native)
Length = 118
Score = 63.9 bits (154), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 33/106 (31%), Positives = 56/106 (52%), Gaps = 1/106 (0%)
Query: 9 ISITLTEVAIKKVSHXXXXXXXXXXXXRVFIQGGGCSGFQYGFMFDEHTNKDDIIFKKNG 68
+SITL++ A +V + R+ ++ GCSG Y F + +DI+F+ G
Sbjct: 1 MSITLSDSAAARV-NTFLANRGKGFGLRLGVRTSGCSGMAYVLEFVDEPTPEDIVFEDKG 59
Query: 69 IQLLIDSVSYQYLIGSEIDYKDDLDGSKFVIKNPNAVTTCGCGSSF 114
+++++D S Q+L G+++D+ + F NPN CGCG SF
Sbjct: 60 VKVVVDGKSLQFLDGTQLDFVKEGLNEGFKFTNPNVKDECGCGESF 105
>pdb|1S98|A Chain A, E.Coli Isca Crystal Structure To 2.3 A
pdb|1S98|B Chain B, E.Coli Isca Crystal Structure To 2.3 A
Length = 107
Score = 63.9 bits (154), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 33/106 (31%), Positives = 56/106 (52%), Gaps = 1/106 (0%)
Query: 9 ISITLTEVAIKKVSHXXXXXXXXXXXXRVFIQGGGCSGFQYGFMFDEHTNKDDIIFKKNG 68
+SITL++ A +V + R+ ++ GCSG Y F + +DI+F+ G
Sbjct: 1 MSITLSDSAAARV-NTFLANRGKGFGLRLGVRTSGCSGMAYVLEFVDEPTPEDIVFEDKG 59
Query: 69 IQLLIDSVSYQYLIGSEIDYKDDLDGSKFVIKNPNAVTTCGCGSSF 114
+++++D S Q+L G+++D+ + F NPN CGCG SF
Sbjct: 60 VKVVVDGKSMQFLDGTQLDFVKEGLNEGFKFTNPNVKDECGCGESF 105
>pdb|2D2A|A Chain A, Crystal Structure Of Escherichia Coli Sufa Involved In
Biosynthesis Of Iron-Sulfur Clusters
pdb|2D2A|B Chain B, Crystal Structure Of Escherichia Coli Sufa Involved In
Biosynthesis Of Iron-Sulfur Clusters
Length = 145
Score = 53.9 bits (128), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 25/79 (31%), Positives = 43/79 (54%)
Query: 36 RVFIQGGGCSGFQYGFMFDEHTNKDDIIFKKNGIQLLIDSVSYQYLIGSEIDYKDDLDGS 95
R+ ++ GC+GF Y +KDD++F+ +G +L + + ++ G+E+D+ +
Sbjct: 65 RLGVKQTGCAGFGYVLDSVSEPDKDDLLFEHDGAKLFVPLQAMPFIDGTEVDFVREGLNQ 124
Query: 96 KFVIKNPNAVTTCGCGSSF 114
F NP A CGCG SF
Sbjct: 125 IFKFHNPKAQNECGCGESF 143
>pdb|1X0G|A Chain A, Crystal Structure Of Isca With The [2fe-2s] Cluster
pdb|1X0G|B Chain B, Crystal Structure Of Isca With The [2fe-2s] Cluster
pdb|1X0G|C Chain C, Crystal Structure Of Isca With The [2fe-2s] Cluster
pdb|1X0G|D Chain D, Crystal Structure Of Isca With The [2fe-2s] Cluster
Length = 112
Score = 51.2 bits (121), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 29/110 (26%), Positives = 48/110 (43%), Gaps = 2/110 (1%)
Query: 11 ITLTEVAIKKVSHXXX--XXXXXXXXXRVFIQGGGCSGFQYGFMFDEHTNKDDIIFKKNG 68
+ LT AI+++ R+ +Q C ++Y D++ + G
Sbjct: 2 VELTPAAIQELERLQTHGVRRGQAAILRIQVQPSECGDWRYDLALVAEPKPTDLLTQSQG 61
Query: 69 IQLLIDSVSYQYLIGSEIDYKDDLDGSKFVIKNPNAVTTCGCGSSFSTYK 118
+ I + + + L G +DY +DL G F NPNA TCGCG +F +
Sbjct: 62 WTIAIAAEAAELLRGLRVDYIEDLMGGAFRFHNPNASQTCGCGMAFRVSR 111
>pdb|1U6I|A Chain A, The Structure Of Native Coenzyme F420-Dependent
Methylenetetrahydromethanopterin Dehydrogenase At 2.2a
Resolution
pdb|1U6I|B Chain B, The Structure Of Native Coenzyme F420-Dependent
Methylenetetrahydromethanopterin Dehydrogenase At 2.2a
Resolution
pdb|1U6I|C Chain C, The Structure Of Native Coenzyme F420-Dependent
Methylenetetrahydromethanopterin Dehydrogenase At 2.2a
Resolution
pdb|1U6I|D Chain D, The Structure Of Native Coenzyme F420-Dependent
Methylenetetrahydromethanopterin Dehydrogenase At 2.2a
Resolution
pdb|1U6I|E Chain E, The Structure Of Native Coenzyme F420-Dependent
Methylenetetrahydromethanopterin Dehydrogenase At 2.2a
Resolution
pdb|1U6I|F Chain F, The Structure Of Native Coenzyme F420-Dependent
Methylenetetrahydromethanopterin Dehydrogenase At 2.2a
Resolution
pdb|1U6I|G Chain G, The Structure Of Native Coenzyme F420-Dependent
Methylenetetrahydromethanopterin Dehydrogenase At 2.2a
Resolution
pdb|1U6I|H Chain H, The Structure Of Native Coenzyme F420-Dependent
Methylenetetrahydromethanopterin Dehydrogenase At 2.2a
Resolution
pdb|1U6I|I Chain I, The Structure Of Native Coenzyme F420-Dependent
Methylenetetrahydromethanopterin Dehydrogenase At 2.2a
Resolution
pdb|1U6I|J Chain J, The Structure Of Native Coenzyme F420-Dependent
Methylenetetrahydromethanopterin Dehydrogenase At 2.2a
Resolution
pdb|1U6I|K Chain K, The Structure Of Native Coenzyme F420-Dependent
Methylenetetrahydromethanopterin Dehydrogenase At 2.2a
Resolution
pdb|1U6I|L Chain L, The Structure Of Native Coenzyme F420-Dependent
Methylenetetrahydromethanopterin Dehydrogenase At 2.2a
Resolution
pdb|1U6J|A Chain A, The Structure Of Native Coenzyme F420-Dependent
Methylenetetrahydromethanopterin Dehydrogenase At 2.4a
Resolution
pdb|1U6J|B Chain B, The Structure Of Native Coenzyme F420-Dependent
Methylenetetrahydromethanopterin Dehydrogenase At 2.4a
Resolution
pdb|1U6J|C Chain C, The Structure Of Native Coenzyme F420-Dependent
Methylenetetrahydromethanopterin Dehydrogenase At 2.4a
Resolution
pdb|1U6J|D Chain D, The Structure Of Native Coenzyme F420-Dependent
Methylenetetrahydromethanopterin Dehydrogenase At 2.4a
Resolution
pdb|1U6J|E Chain E, The Structure Of Native Coenzyme F420-Dependent
Methylenetetrahydromethanopterin Dehydrogenase At 2.4a
Resolution
pdb|1U6J|F Chain F, The Structure Of Native Coenzyme F420-Dependent
Methylenetetrahydromethanopterin Dehydrogenase At 2.4a
Resolution
pdb|1U6J|G Chain G, The Structure Of Native Coenzyme F420-Dependent
Methylenetetrahydromethanopterin Dehydrogenase At 2.4a
Resolution
pdb|1U6J|H Chain H, The Structure Of Native Coenzyme F420-Dependent
Methylenetetrahydromethanopterin Dehydrogenase At 2.4a
Resolution
pdb|1U6J|I Chain I, The Structure Of Native Coenzyme F420-Dependent
Methylenetetrahydromethanopterin Dehydrogenase At 2.4a
Resolution
pdb|1U6J|J Chain J, The Structure Of Native Coenzyme F420-Dependent
Methylenetetrahydromethanopterin Dehydrogenase At 2.4a
Resolution
pdb|1U6J|K Chain K, The Structure Of Native Coenzyme F420-Dependent
Methylenetetrahydromethanopterin Dehydrogenase At 2.4a
Resolution
pdb|1U6J|L Chain L, The Structure Of Native Coenzyme F420-Dependent
Methylenetetrahydromethanopterin Dehydrogenase At 2.4a
Resolution
pdb|3IQE|A Chain A, Structure Of F420 Dependent
Methylene-Tetrahydromethanopterin Dehydrogenase In
Complex With Methylene-Tetrahydromethanopterin And
Coenzyme F420
pdb|3IQE|B Chain B, Structure Of F420 Dependent
Methylene-Tetrahydromethanopterin Dehydrogenase In
Complex With Methylene-Tetrahydromethanopterin And
Coenzyme F420
pdb|3IQE|C Chain C, Structure Of F420 Dependent
Methylene-Tetrahydromethanopterin Dehydrogenase In
Complex With Methylene-Tetrahydromethanopterin And
Coenzyme F420
pdb|3IQE|D Chain D, Structure Of F420 Dependent
Methylene-Tetrahydromethanopterin Dehydrogenase In
Complex With Methylene-Tetrahydromethanopterin And
Coenzyme F420
pdb|3IQE|E Chain E, Structure Of F420 Dependent
Methylene-Tetrahydromethanopterin Dehydrogenase In
Complex With Methylene-Tetrahydromethanopterin And
Coenzyme F420
pdb|3IQE|F Chain F, Structure Of F420 Dependent
Methylene-Tetrahydromethanopterin Dehydrogenase In
Complex With Methylene-Tetrahydromethanopterin And
Coenzyme F420
pdb|3IQF|A Chain A, Structure Of F420 Dependent
Methylene-Tetrahydromethanopterin Dehydrogenase In
Complex With Methenyl-Tetrahydromethanopterin
pdb|3IQF|B Chain B, Structure Of F420 Dependent
Methylene-Tetrahydromethanopterin Dehydrogenase In
Complex With Methenyl-Tetrahydromethanopterin
pdb|3IQF|C Chain C, Structure Of F420 Dependent
Methylene-Tetrahydromethanopterin Dehydrogenase In
Complex With Methenyl-Tetrahydromethanopterin
pdb|3IQF|D Chain D, Structure Of F420 Dependent
Methylene-Tetrahydromethanopterin Dehydrogenase In
Complex With Methenyl-Tetrahydromethanopterin
pdb|3IQF|E Chain E, Structure Of F420 Dependent
Methylene-Tetrahydromethanopterin Dehydrogenase In
Complex With Methenyl-Tetrahydromethanopterin
pdb|3IQF|F Chain F, Structure Of F420 Dependent
Methylene-Tetrahydromethanopterin Dehydrogenase In
Complex With Methenyl-Tetrahydromethanopterin
pdb|3IQF|G Chain G, Structure Of F420 Dependent
Methylene-Tetrahydromethanopterin Dehydrogenase In
Complex With Methenyl-Tetrahydromethanopterin
pdb|3IQF|H Chain H, Structure Of F420 Dependent
Methylene-Tetrahydromethanopterin Dehydrogenase In
Complex With Methenyl-Tetrahydromethanopterin
pdb|3IQF|I Chain I, Structure Of F420 Dependent
Methylene-Tetrahydromethanopterin Dehydrogenase In
Complex With Methenyl-Tetrahydromethanopterin
pdb|3IQF|J Chain J, Structure Of F420 Dependent
Methylene-Tetrahydromethanopterin Dehydrogenase In
Complex With Methenyl-Tetrahydromethanopterin
pdb|3IQF|K Chain K, Structure Of F420 Dependent
Methylene-Tetrahydromethanopterin Dehydrogenase In
Complex With Methenyl-Tetrahydromethanopterin
pdb|3IQF|L Chain L, Structure Of F420 Dependent
Methylene-Tetrahydromethanopterin Dehydrogenase In
Complex With Methenyl-Tetrahydromethanopterin
pdb|3IQZ|A Chain A, Structure Of F420 Dependent
Methylene-tetrahydromethanopterin Dehydrogenase In
Complex With Methylene-tetrahydromethanopterin
pdb|3IQZ|B Chain B, Structure Of F420 Dependent
Methylene-tetrahydromethanopterin Dehydrogenase In
Complex With Methylene-tetrahydromethanopterin
pdb|3IQZ|C Chain C, Structure Of F420 Dependent
Methylene-tetrahydromethanopterin Dehydrogenase In
Complex With Methylene-tetrahydromethanopterin
pdb|3IQZ|D Chain D, Structure Of F420 Dependent
Methylene-tetrahydromethanopterin Dehydrogenase In
Complex With Methylene-tetrahydromethanopterin
pdb|3IQZ|E Chain E, Structure Of F420 Dependent
Methylene-tetrahydromethanopterin Dehydrogenase In
Complex With Methylene-tetrahydromethanopterin
pdb|3IQZ|F Chain F, Structure Of F420 Dependent
Methylene-tetrahydromethanopterin Dehydrogenase In
Complex With Methylene-tetrahydromethanopterin
Length = 283
Score = 27.7 bits (60), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 14/72 (19%), Positives = 30/72 (41%), Gaps = 1/72 (1%)
Query: 37 VFIQGGGC-SGFQYGFMFDEHTNKDDIIFKKNGIQLLIDSVSYQYLIGSEIDYKDDLDGS 95
+FI+ G + + DE +++D+ F+ G + +D + + +D +D +
Sbjct: 7 IFIKCGNLGTSMMMDMLLDERADREDVEFRVVGTSVKMDPECVEAAVEMALDIAEDFEPD 66
Query: 96 KFVIKNPNAVTT 107
V PN
Sbjct: 67 FIVYGGPNPAAP 78
>pdb|1QB2|A Chain A, Crystal Structure Of The Conserved Subdomain Of Human
Protein Srp54m At 2.1a Resolution: Evidence For The
Mechanism Of Signal Peptide Binding
pdb|1QB2|B Chain B, Crystal Structure Of The Conserved Subdomain Of Human
Protein Srp54m At 2.1a Resolution: Evidence For The
Mechanism Of Signal Peptide Binding
pdb|1RY1|W Chain W, Structure Of The Signal Recognition Particle Interacting
With The Elongation-Arrested Ribosome
pdb|2GO5|W Chain W, Structure Of Signal Recognition Particle Receptor (Sr) In
Complex With Signal Recognition Particle (Srp) And
Ribosome Nascent Chain Complex
Length = 109
Score = 25.4 bits (54), Expect = 8.6, Method: Compositional matrix adjust.
Identities = 20/75 (26%), Positives = 31/75 (41%), Gaps = 10/75 (13%)
Query: 42 GGCSGFQYGFMFDEHTNKDDIIFKKNGIQLLIDSVSYQYLIGSEIDYKDDLDGSKFVIKN 101
G GF FM N+ + + + + ++DS++ Q L D DG+K K
Sbjct: 25 GMIPGFGTDFM--SKGNEQESMARLKKLMTIMDSMNDQEL--------DSTDGAKVFSKQ 74
Query: 102 PNAVTTCGCGSSFST 116
P + GS ST
Sbjct: 75 PGRIQRVARGSGVST 89
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
0.319 0.138 0.402
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,257,169
Number of Sequences: 62578
Number of extensions: 117547
Number of successful extensions: 218
Number of sequences better than 100.0: 12
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 209
Number of HSP's gapped (non-prelim): 12
length of query: 118
length of database: 14,973,337
effective HSP length: 81
effective length of query: 37
effective length of database: 9,904,519
effective search space: 366467203
effective search space used: 366467203
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 45 (21.9 bits)