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= psy1354
(118 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2WJV|A Chain A, Crystal Structure Of The Complex Between Human Nonsense
Mediated Decay Factors Upf1 And Upf2
pdb|2WJV|B Chain B, Crystal Structure Of The Complex Between Human Nonsense
Mediated Decay Factors Upf1 And Upf2
pdb|2WJY|A Chain A, Crystal Structure Of The Complex Between Human Nonsense
Mediated Decay Factors Upf1 And Upf2 Orthorhombic Form
Length = 800
Score = 56.6 bits (135), Expect = 3e-09, Method: Composition-based stats.
Identities = 31/95 (32%), Positives = 50/95 (52%), Gaps = 10/95 (10%)
Query: 3 LISGIPTDHIGVIATYRNQVSLLKRLLD----------KDIEINTVDQYQGRDKSIILYX 52
L +G D IG+I Y Q S L + + +++EI +VD +QGR+K I+
Sbjct: 667 LKAGAKPDQIGIITPYEGQRSYLVQYMQFSGSLHTKLYQEVEIASVDAFQGREKDFIILS 726
Query: 53 XXXXXXXXXXXILNDRKRLTVAISRAKHKLIILGD 87
LND +RL VA++RA++ +II+G+
Sbjct: 727 CVRANEHQGIGFLNDPRRLNVALTRARYGVIIVGN 761
>pdb|2XZO|A Chain A, Upf1 Helicase - Rna Complex
pdb|2XZP|A Chain A, Upf1 Helicase
Length = 623
Score = 55.8 bits (133), Expect = 6e-09, Method: Composition-based stats.
Identities = 31/95 (32%), Positives = 50/95 (52%), Gaps = 10/95 (10%)
Query: 3 LISGIPTDHIGVIATYRNQVSLLKRLLD----------KDIEINTVDQYQGRDKSIILYX 52
L +G D IG+I Y Q S L + + +++EI +VD +QGR+K I+
Sbjct: 490 LKAGAKPDQIGIITPYEGQRSYLVQYMQFSGSLHTKLYQEVEIASVDAFQGREKDFIILS 549
Query: 53 XXXXXXXXXXXILNDRKRLTVAISRAKHKLIILGD 87
LND +RL VA++RA++ +II+G+
Sbjct: 550 CVRANEHQGIGFLNDPRRLNVALTRARYGVIIVGN 584
>pdb|2GJK|A Chain A, Structural And Functional Insights Into The Human Upf1
Helicase Core
pdb|2GK6|A Chain A, Structural And Functional Insights Into The Human Upf1
Helicase Core
pdb|2GK6|B Chain B, Structural And Functional Insights Into The Human Upf1
Helicase Core
pdb|2GK7|A Chain A, Structural And Functional Insights Into The Human Upf1
Helicase Core
Length = 624
Score = 55.8 bits (133), Expect = 6e-09, Method: Composition-based stats.
Identities = 31/95 (32%), Positives = 50/95 (52%), Gaps = 10/95 (10%)
Query: 3 LISGIPTDHIGVIATYRNQVSLLKRLLD----------KDIEINTVDQYQGRDKSIILYX 52
L +G D IG+I Y Q S L + + +++EI +VD +QGR+K I+
Sbjct: 491 LKAGAKPDQIGIITPYEGQRSYLVQYMQFSGSLHTKLYQEVEIASVDAFQGREKDFIILS 550
Query: 53 XXXXXXXXXXXILNDRKRLTVAISRAKHKLIILGD 87
LND +RL VA++RA++ +II+G+
Sbjct: 551 CVRANEHQGIGFLNDPRRLNVALTRARYGVIIVGN 585
>pdb|2XZL|A Chain A, Upf1-Rna Complex
Length = 802
Score = 53.9 bits (128), Expect = 2e-08, Method: Composition-based stats.
Identities = 31/92 (33%), Positives = 48/92 (52%), Gaps = 10/92 (10%)
Query: 6 GIPTDHIGVIATYRNQVSLLKRL------LDKD----IEINTVDQYQGRDKSIILYXXXX 55
G+ + IGVI Y Q + + + LDKD +E+ +VD +QGR+K I+
Sbjct: 672 GVKPEQIGVITPYEGQRAYILQYMQMNGSLDKDLYIKVEVASVDAFQGREKDYIILSCVR 731
Query: 56 XXXXXXXXILNDRKRLTVAISRAKHKLIILGD 87
L D +RL V ++RAK+ L+ILG+
Sbjct: 732 ANEQQAIGFLRDPRRLNVGLTRAKYGLVILGN 763
>pdb|4B3G|A Chain A, Crystal Structure Of Ighmbp2 Helicase In Complex With Rna
pdb|4B3G|B Chain B, Crystal Structure Of Ighmbp2 Helicase In Complex With Rna
Length = 646
Score = 50.4 bits (119), Expect = 3e-07, Method: Composition-based stats.
Identities = 25/90 (27%), Positives = 49/90 (54%), Gaps = 3/90 (3%)
Query: 5 SGIPTDHIGVIATYRNQVSLLKRLL---DKDIEINTVDQYQGRDKSIILYXXXXXXXXXX 61
+G+P I V++ Y QV LL++ L ++EI +VD +QGR+K ++
Sbjct: 526 AGVPARDIAVVSPYNLQVDLLRQSLVHRHPELEIKSVDGFQGREKEAVILSFVRSNRKGE 585
Query: 62 XXILNDRKRLTVAISRAKHKLIILGDLQVI 91
L + +R+ VA++RA+ + ++ D + +
Sbjct: 586 VGFLAEDRRINVAVTRARRHVAVICDSRTV 615
>pdb|4B3F|X Chain X, Crystal Structure Of 1ghmbp2 Helicase
Length = 646
Score = 50.1 bits (118), Expect = 3e-07, Method: Composition-based stats.
Identities = 25/90 (27%), Positives = 49/90 (54%), Gaps = 3/90 (3%)
Query: 5 SGIPTDHIGVIATYRNQVSLLKRLL---DKDIEINTVDQYQGRDKSIILYXXXXXXXXXX 61
+G+P I V++ Y QV LL++ L ++EI +VD +QGR+K ++
Sbjct: 526 AGVPARDIAVVSPYNLQVDLLRQSLVHRHPELEIKSVDGFQGREKEAVILSFVRSNRKGE 585
Query: 62 XXILNDRKRLTVAISRAKHKLIILGDLQVI 91
L + +R+ VA++RA+ + ++ D + +
Sbjct: 586 VGFLAEDRRINVAVTRARRHVAVICDSRTV 615
>pdb|1G61|A Chain A, Crystal Structure Of M.Jannaschii Eif6
pdb|1G61|B Chain B, Crystal Structure Of M.Jannaschii Eif6
Length = 228
Score = 30.0 bits (66), Expect = 0.38, Method: Compositional matrix adjust.
Identities = 17/37 (45%), Positives = 24/37 (64%), Gaps = 3/37 (8%)
Query: 4 ISGIPTDHIGVIATYRNQVSLLKRLLDKDIEINTVDQ 40
SGIPT IGV+A +++LL LDKD ++N V +
Sbjct: 9 FSGIPT--IGVLALTTEEITLLPIFLDKD-DVNEVSE 42
>pdb|1XQB|A Chain A, X-Ray Structure Of Yaeb From Haemophilus Influenzae.
Northeast Structural Genomics Research Consortium
(Nesgc) Target Ir47.
pdb|1XQB|B Chain B, X-Ray Structure Of Yaeb From Haemophilus Influenzae.
Northeast Structural Genomics Research Consortium
(Nesgc) Target Ir47
Length = 247
Score = 25.8 bits (55), Expect = 7.2, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 25/50 (50%)
Query: 65 LNDRKRLTVAISRAKHKLIILGDLQVIIAIVNCPNTGRYGNLGQIPGTDG 114
L +R+ V SRA H+ LG +V + V C N + +LG + DG
Sbjct: 80 LGGNQRVGVFASRATHRPNPLGXSKVELRQVECINGNIFLHLGAVDLVDG 129
>pdb|2GO1|A Chain A, Nad-Dependent Formate Dehydrogenase From Pseudomonas
Sp.101
Length = 401
Score = 25.4 bits (54), Expect = 8.4, Method: Composition-based stats.
Identities = 9/32 (28%), Positives = 21/32 (65%)
Query: 11 HIGVIATYRNQVSLLKRLLDKDIEINTVDQYQ 42
H+G +A R +++L+RL D+ ++ D+++
Sbjct: 194 HVGTVAAGRIGLAVLRRLAPFDVHLHYTDRHR 225
>pdb|2GUG|A Chain A, Nad-dependent Formate Dehydrogenase From Pseudomonas
Sp.101 In Complex With Formate
pdb|2GUG|B Chain B, Nad-dependent Formate Dehydrogenase From Pseudomonas
Sp.101 In Complex With Formate
pdb|2GUG|C Chain C, Nad-dependent Formate Dehydrogenase From Pseudomonas
Sp.101 In Complex With Formate
pdb|2GUG|D Chain D, Nad-dependent Formate Dehydrogenase From Pseudomonas
Sp.101 In Complex With Formate
Length = 401
Score = 25.4 bits (54), Expect = 8.4, Method: Composition-based stats.
Identities = 9/32 (28%), Positives = 21/32 (65%)
Query: 11 HIGVIATYRNQVSLLKRLLDKDIEINTVDQYQ 42
H+G +A R +++L+RL D+ ++ D+++
Sbjct: 194 HVGTVAAGRIGLAVLRRLAPFDVHLHYTDRHR 225
>pdb|2NAC|A Chain A, High Resolution Structures Of Holo And Apo Formate
Dehydrogenase
pdb|2NAC|B Chain B, High Resolution Structures Of Holo And Apo Formate
Dehydrogenase
pdb|2NAD|A Chain A, High Resolution Structures Of Holo And Apo Formate
Dehydrogenase
pdb|2NAD|B Chain B, High Resolution Structures Of Holo And Apo Formate
Dehydrogenase
Length = 393
Score = 25.4 bits (54), Expect = 8.4, Method: Composition-based stats.
Identities = 9/32 (28%), Positives = 21/32 (65%)
Query: 11 HIGVIATYRNQVSLLKRLLDKDIEINTVDQYQ 42
H+G +A R +++L+RL D+ ++ D+++
Sbjct: 193 HVGTVAAGRIGLAVLRRLAPFDVHLHYTDRHR 224
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 0.142 0.400
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,936,261
Number of Sequences: 62578
Number of extensions: 88530
Number of successful extensions: 150
Number of sequences better than 100.0: 16
Number of HSP's better than 100.0 without gapping: 15
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 135
Number of HSP's gapped (non-prelim): 16
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 (21.8 bits)
S2: 45 (21.9 bits)