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= psy280
(156 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3DZD|A Chain A, Crystal Structure Of Sigma54 Activator Ntrc4 In The
Inactive State
pdb|3DZD|B Chain B, Crystal Structure Of Sigma54 Activator Ntrc4 In The
Inactive State
Length = 368
Score = 30.0 bits (66), Expect = 0.62, Method: Compositional matrix adjust.
Identities = 16/45 (35%), Positives = 26/45 (57%), Gaps = 8/45 (17%)
Query: 23 LVDEISEIIKQVQA--------VDFTKLPNDKKIEADLLVLYAIN 59
+DE+ E+ ++VQA FT+L ++KIE D+ V+ A N
Sbjct: 227 FLDEVGELDQRVQAKLLRVLETGSFTRLGGNQKIEVDIRVISATN 271
>pdb|1NM5|A Chain A, R. Rubrum Transhydrogenase (Di.Q132n)2(Diii)1 Asymmetric
Complex
pdb|1NM5|B Chain B, R. Rubrum Transhydrogenase (Di.Q132n)2(Diii)1 Asymmetric
Complex
Length = 384
Score = 28.9 bits (63), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 22/75 (29%), Positives = 35/75 (46%), Gaps = 5/75 (6%)
Query: 34 VQAVDFTKLPNDKKIEADLLVLYAINSLYFINLRIKHVDSDFVKVELKRIQETMKKFKQT 93
V+ V T +P+ ++ AD L+A N L F+ HVD D + +K ET+ T
Sbjct: 315 VKIVGHTNVPS--RVAADASPLFAKNLLNFLT---PHVDKDTKTLVMKLEDETVSGTCVT 369
Query: 94 KDKLTIMPRLDKDAS 108
+D + P L +
Sbjct: 370 RDGAIVHPALTGQGA 384
>pdb|2FRD|A Chain A, Structure Of Transhydrogenase
(di.s138a.nadh)2(diii.nadph)1 Asymmetric Complex
pdb|2FRD|B Chain B, Structure Of Transhydrogenase
(di.s138a.nadh)2(diii.nadph)1 Asymmetric Complex
Length = 384
Score = 28.9 bits (63), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 22/75 (29%), Positives = 35/75 (46%), Gaps = 5/75 (6%)
Query: 34 VQAVDFTKLPNDKKIEADLLVLYAINSLYFINLRIKHVDSDFVKVELKRIQETMKKFKQT 93
V+ V T +P+ ++ AD L+A N L F+ HVD D + +K ET+ T
Sbjct: 315 VKIVGHTNVPS--RVAADASPLFAKNLLNFLT---PHVDKDTKTLVMKLEDETVSGTCVT 369
Query: 94 KDKLTIMPRLDKDAS 108
+D + P L +
Sbjct: 370 RDGAIVHPALTGQGA 384
>pdb|1HZZ|A Chain A, The Asymmetric Complex Of The Two Nucleotide-Binding
Components (Di, Diii) Of Proton-Translocating
Transhydrogenase
pdb|1HZZ|B Chain B, The Asymmetric Complex Of The Two Nucleotide-Binding
Components (Di, Diii) Of Proton-Translocating
Transhydrogenase
pdb|1L7D|A Chain A, Crystal Structure Of R. Rubrum Transhydrogenase Domain I
Without Bound Nad(H)
pdb|1L7D|C Chain C, Crystal Structure Of R. Rubrum Transhydrogenase Domain I
Without Bound Nad(H)
pdb|1L7D|D Chain D, Crystal Structure Of R. Rubrum Transhydrogenase Domain I
Without Bound Nad(H)
pdb|1L7E|A Chain A, Crystal Structure Of R. Rubrum Transhydrogenase Domain I
With Bound Nadh
pdb|1L7E|B Chain B, Crystal Structure Of R. Rubrum Transhydrogenase Domain I
With Bound Nadh
pdb|1L7E|C Chain C, Crystal Structure Of R. Rubrum Transhydrogenase Domain I
With Bound Nadh
pdb|1L7E|D Chain D, Crystal Structure Of R. Rubrum Transhydrogenase Domain I
With Bound Nadh
pdb|1U28|A Chain A, R. Rubrum Transhydrogenase Asymmetric Complex
(Di.Nad+)2(Diii.Nadp+)1
pdb|1U28|B Chain B, R. Rubrum Transhydrogenase Asymmetric Complex
(Di.Nad+)2(Diii.Nadp+)1
pdb|1U2D|A Chain A, Structre Of Transhydrogenaes (Di.Nadh)2(Diii.Nadph)1
Asymmetric Complex
pdb|1U2D|B Chain B, Structre Of Transhydrogenaes (Di.Nadh)2(Diii.Nadph)1
Asymmetric Complex
pdb|1U2G|A Chain A, Transhydrogenase (Di.Adpr)2(Diii.Nadph)1 Asymmetric
Complex
pdb|1U2G|B Chain B, Transhydrogenase (Di.Adpr)2(Diii.Nadph)1 Asymmetric
Complex
pdb|1XLT|A Chain A, Crystal Structure Of Transhydrogenase [(Domain I)2:domain
Iii] Heterotrimer Complex
pdb|1XLT|B Chain B, Crystal Structure Of Transhydrogenase [(Domain I)2:domain
Iii] Heterotrimer Complex
pdb|1XLT|D Chain D, Crystal Structure Of Transhydrogenase [(Domain I)2:domain
Iii] Heterotrimer Complex
pdb|1XLT|E Chain E, Crystal Structure Of Transhydrogenase [(Domain I)2:domain
Iii] Heterotrimer Complex
pdb|1XLT|G Chain G, Crystal Structure Of Transhydrogenase [(Domain I)2:domain
Iii] Heterotrimer Complex
pdb|1XLT|H Chain H, Crystal Structure Of Transhydrogenase [(Domain I)2:domain
Iii] Heterotrimer Complex
pdb|2OO5|A Chain A, Structure Of Transhydrogenase (Di.H2nadh)2(Diii.Nadp+)1
Asymmetric Complex
pdb|2OO5|B Chain B, Structure Of Transhydrogenase (Di.H2nadh)2(Diii.Nadp+)1
Asymmetric Complex
pdb|2OOR|A Chain A, Structure Of Transhydrogenase (Di.Nad+)2(Diii.H2nadph)1
Asymmetric Complex
pdb|2OOR|B Chain B, Structure Of Transhydrogenase (Di.Nad+)2(Diii.H2nadph)1
Asymmetric Complex
Length = 384
Score = 28.9 bits (63), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 22/75 (29%), Positives = 35/75 (46%), Gaps = 5/75 (6%)
Query: 34 VQAVDFTKLPNDKKIEADLLVLYAINSLYFINLRIKHVDSDFVKVELKRIQETMKKFKQT 93
V+ V T +P+ ++ AD L+A N L F+ HVD D + +K ET+ T
Sbjct: 315 VKIVGHTNVPS--RVAADASPLFAKNLLNFLT---PHVDKDTKTLVMKLEDETVSGTCVT 369
Query: 94 KDKLTIMPRLDKDAS 108
+D + P L +
Sbjct: 370 RDGAIVHPALTGQGA 384
>pdb|2FSV|A Chain A, Structure Of Transhydrogenase
(Di.D135n.Nad+)2(Diii.E155w.Nadp+)1 Asymmetric Complex
pdb|2FSV|B Chain B, Structure Of Transhydrogenase
(Di.D135n.Nad+)2(Diii.E155w.Nadp+)1 Asymmetric Complex
Length = 384
Score = 28.9 bits (63), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 22/75 (29%), Positives = 35/75 (46%), Gaps = 5/75 (6%)
Query: 34 VQAVDFTKLPNDKKIEADLLVLYAINSLYFINLRIKHVDSDFVKVELKRIQETMKKFKQT 93
V+ V T +P+ ++ AD L+A N L F+ HVD D + +K ET+ T
Sbjct: 315 VKIVGHTNVPS--RVAADASPLFAKNLLNFLT---PHVDKDTKTLVMKLEDETVSGTCVT 369
Query: 94 KDKLTIMPRLDKDAS 108
+D + P L +
Sbjct: 370 RDGAIVHPALTGQGA 384
>pdb|2FR8|A Chain A, Structure Of Transhydrogenase
(Di.R127a.Nad+)2(Diii.Nadp+)1 Asymmetric Complex
pdb|2FR8|B Chain B, Structure Of Transhydrogenase
(Di.R127a.Nad+)2(Diii.Nadp+)1 Asymmetric Complex
Length = 384
Score = 28.9 bits (63), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 22/75 (29%), Positives = 35/75 (46%), Gaps = 5/75 (6%)
Query: 34 VQAVDFTKLPNDKKIEADLLVLYAINSLYFINLRIKHVDSDFVKVELKRIQETMKKFKQT 93
V+ V T +P+ ++ AD L+A N L F+ HVD D + +K ET+ T
Sbjct: 315 VKIVGHTNVPS--RVAADASPLFAKNLLNFLT---PHVDKDTKTLVMKLEDETVSGTCVT 369
Query: 94 KDKLTIMPRLDKDAS 108
+D + P L +
Sbjct: 370 RDGAIVHPALTGQGA 384
>pdb|1L7D|B Chain B, Crystal Structure Of R. Rubrum Transhydrogenase Domain I
Without Bound Nad(H)
Length = 384
Score = 28.9 bits (63), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 22/75 (29%), Positives = 35/75 (46%), Gaps = 5/75 (6%)
Query: 34 VQAVDFTKLPNDKKIEADLLVLYAINSLYFINLRIKHVDSDFVKVELKRIQETMKKFKQT 93
V+ V T +P+ ++ AD L+A N L F+ HVD D + +K ET+ T
Sbjct: 315 VKIVGHTNVPS--RVAADASPLFAKNLLNFLT---PHVDKDTKTLVMKLEDETVSGTCVT 369
Query: 94 KDKLTIMPRLDKDAS 108
+D + P L +
Sbjct: 370 RDGAIVHPALTGQGA 384
>pdb|1PTJ|A Chain A, Crystal Structure Analysis Of The Di And Diii Complex Of
Transhydrogenase With A Thio-Nicotinamide Nucleotide
Analogue
pdb|1PTJ|B Chain B, Crystal Structure Analysis Of The Di And Diii Complex Of
Transhydrogenase With A Thio-Nicotinamide Nucleotide
Analogue
Length = 381
Score = 28.1 bits (61), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 34/70 (48%), Gaps = 5/70 (7%)
Query: 34 VQAVDFTKLPNDKKIEADLLVLYAINSLYFINLRIKHVDSDFVKVELKRIQETMKKFKQT 93
V+ V T +P+ ++ AD L+A N L F+ HVD D + +K ET+ T
Sbjct: 315 VKIVGHTNVPS--RVAADASPLFAKNLLNFLT---PHVDKDTKTLVMKLEDETVSGTCVT 369
Query: 94 KDKLTIMPRL 103
+D + P L
Sbjct: 370 RDGAIVHPAL 379
>pdb|3KYH|C Chain C, Saccharomyces Cerevisiae Cet1-Ceg1 Capping Apparatus
pdb|3KYH|D Chain D, Saccharomyces Cerevisiae Cet1-Ceg1 Capping Apparatus
Length = 461
Score = 27.7 bits (60), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 12/41 (29%), Positives = 21/41 (51%)
Query: 52 LLVLYAINSLYFINLRIKHVDSDFVKVELKRIQETMKKFKQ 92
+ LY +N R+KH D F + E + ++ T +KF +
Sbjct: 291 VFSLYVWQGGADVNSRLKHFDQPFDRKEFEILERTYRKFAE 331
>pdb|1F8G|A Chain A, The X-Ray Structure Of Nicotinamide Nucleotide
Transhydrogenase From Rhodospirillum Rubrum Complexed
With Nad+
pdb|1F8G|B Chain B, The X-Ray Structure Of Nicotinamide Nucleotide
Transhydrogenase From Rhodospirillum Rubrum Complexed
With Nad+
pdb|1F8G|C Chain C, The X-Ray Structure Of Nicotinamide Nucleotide
Transhydrogenase From Rhodospirillum Rubrum Complexed
With Nad+
pdb|1F8G|D Chain D, The X-Ray Structure Of Nicotinamide Nucleotide
Transhydrogenase From Rhodospirillum Rubrum Complexed
With Nad+
Length = 384
Score = 27.7 bits (60), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 22/75 (29%), Positives = 34/75 (45%), Gaps = 5/75 (6%)
Query: 34 VQAVDFTKLPNDKKIEADLLVLYAINSLYFINLRIKHVDSDFVKVELKRIQETMKKFKQT 93
V+ V T +P+ ++ AD L+A N L F+ HVD D + K ET+ T
Sbjct: 315 VKIVGHTNVPS--RVAADASPLFAKNLLNFLT---PHVDKDTKTLVXKLEDETVSGTCVT 369
Query: 94 KDKLTIMPRLDKDAS 108
+D + P L +
Sbjct: 370 RDGAIVHPALTGQGA 384
>pdb|1SZ7|A Chain A, Crystal Structure Of Human Bet3
Length = 200
Score = 27.3 bits (59), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 25/99 (25%), Positives = 46/99 (46%), Gaps = 13/99 (13%)
Query: 25 DEISEIIKQVQAVDFTKLPNDKK--IEADLLVLYAINSLYFINLRIKHVDSDFVKVELKR 82
DE S I++ VDF +LP++ I ++LL +L + + VE K
Sbjct: 110 DEFSLILENNPLVDFVELPDNHSSLIYSNLLCGVLRGALEMVQM----------AVEAKF 159
Query: 83 IQETMKKFKQTKDKLTIMPRLDKDASKRFVRNALWTPPE 121
+Q+T+K T+ ++ + R++ D A W+ P+
Sbjct: 160 VQDTLKGDGVTEIRMRFIRRIE-DNLPAGEEAAAWSHPQ 197
>pdb|3OIS|A Chain A, Crystal Structure Xylellain, A Cysteine Protease From
Xylella Fastidiosa
pdb|3OIS|B Chain B, Crystal Structure Xylellain, A Cysteine Protease From
Xylella Fastidiosa
pdb|3OIS|C Chain C, Crystal Structure Xylellain, A Cysteine Protease From
Xylella Fastidiosa
pdb|3OIS|D Chain D, Crystal Structure Xylellain, A Cysteine Protease From
Xylella Fastidiosa
Length = 291
Score = 26.9 bits (58), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 10/26 (38%), Positives = 16/26 (61%)
Query: 120 PESDTPCDKKTKDIPPVSKKTKFDAD 145
P DTP D +T++ PP + +K +D
Sbjct: 145 PYGDTPADPRTEEFPPGAPASKKPSD 170
>pdb|3A5X|A Chain A, L-Type Straight Flagellar Filament Made Of Full-Length
Flagellin
Length = 494
Score = 26.6 bits (57), Expect = 5.9, Method: Composition-based stats.
Identities = 19/77 (24%), Positives = 38/77 (49%), Gaps = 3/77 (3%)
Query: 15 NSQHDLESLVDEISEIIKQVQAVDFTKLPNDKKIEAD---LLVLYAINSLYFINLRIKHV 71
NSQ DL+S+ EI++ + ++ V N K+ A L + N I++ +K +
Sbjct: 103 NSQSDLDSIQAEITQRLNEIDRVSGQTQFNGVKVLAQDNTLTIQVGANDGETIDIDLKQI 162
Query: 72 DSDFVKVELKRIQETMK 88
+S + ++ +Q+ K
Sbjct: 163 NSQTLGLDTLNVQQKYK 179
>pdb|1UCU|A Chain A, R-type Straight Flagellar Filament Made Of Full-length
Flagellin
Length = 494
Score = 26.6 bits (57), Expect = 6.0, Method: Composition-based stats.
Identities = 19/77 (24%), Positives = 38/77 (49%), Gaps = 3/77 (3%)
Query: 15 NSQHDLESLVDEISEIIKQVQAVDFTKLPNDKKIEAD---LLVLYAINSLYFINLRIKHV 71
NSQ DL+S+ EI++ + ++ V N K+ A L + N I++ +K +
Sbjct: 103 NSQSDLDSIQAEITQRLNEIDRVSGQTQFNGVKVLAQDNTLTIQVGANDGETIDIDLKQI 162
Query: 72 DSDFVKVELKRIQETMK 88
+S + ++ +Q+ K
Sbjct: 163 NSQTLGLDTLNVQQKYK 179
>pdb|1IO1|A Chain A, Crystal Structure Of F41 Fragment Of Flagellin
Length = 398
Score = 26.6 bits (57), Expect = 6.4, Method: Compositional matrix adjust.
Identities = 22/93 (23%), Positives = 44/93 (47%), Gaps = 6/93 (6%)
Query: 15 NSQHDLESLVDEISEIIKQVQAVDFTKLPNDKKIEAD---LLVLYAINSLYFINLRIKHV 71
NSQ DL+S+ EI++ + ++ V N K+ A L + N I++ +K +
Sbjct: 51 NSQSDLDSIQAEITQRLNEIDRVSGQTQFNGVKVLAQDNTLTIQVGANDGETIDIDLKQI 110
Query: 72 DSDFVKVELKRIQETMKKFKQTKDKLTIMPRLD 104
+S + ++ +Q+ K+K + T+ D
Sbjct: 111 NSQTLGLDTLNVQQ---KYKVSDTAATVTGYAD 140
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
0.317 0.135 0.372
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,172,392
Number of Sequences: 62578
Number of extensions: 154808
Number of successful extensions: 500
Number of sequences better than 100.0: 22
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 18
Number of HSP's that attempted gapping in prelim test: 496
Number of HSP's gapped (non-prelim): 22
length of query: 156
length of database: 14,973,337
effective HSP length: 91
effective length of query: 65
effective length of database: 9,278,739
effective search space: 603118035
effective search space used: 603118035
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 47 (22.7 bits)