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= psy9563
(192 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4AI6|A Chain A, Dynein Motor Domain - Adp Complex
pdb|4AI6|B Chain B, Dynein Motor Domain - Adp Complex
pdb|4AKG|A Chain A, Dynein Motor Domain - Atp Complex
pdb|4AKG|B Chain B, Dynein Motor Domain - Atp Complex
pdb|4AKH|A Chain A, Dynein Motor Domain - Amppnp Complex
pdb|4AKH|B Chain B, Dynein Motor Domain - Amppnp Complex
pdb|4AKI|A Chain A, Dynein Motor Domain - Luac Derivative
pdb|4AKI|B Chain B, Dynein Motor Domain - Luac Derivative
Length = 2695
Score = 54.7 bits (130), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 44/178 (24%), Positives = 85/178 (47%), Gaps = 8/178 (4%)
Query: 1 MNMKGFYSLEKPGEFTTLIDVQFVAAMAQPGG-GRNDIPSRLKRQFCIFNCVLPSDKAID 59
M +GF+ + ++ T+ + V A P GR + R R I PS K++
Sbjct: 1366 MEKQGFWKTPE-NKWVTIERIHIVGACNPPTDPGRIPMSERFTRHAAILYLGYPSGKSLS 1424
Query: 60 NIFSVIGEGHYNAKRGFPIEVRNLVKQLIPLTRLLWKSTRAQLLPTPAKFHYVFSLRDLS 119
I+ + +Y A E R+ + + L+ +A+ T + HY+FS R+L+
Sbjct: 1425 QIYEI----YYKAIFKLVPEFRSYTEPFARASVHLYNECKARY-STGLQSHYLFSPRELT 1479
Query: 120 RIWQGMVGTLST-VIDSEKVLMLLWKHEVTRVFSDRFTIMSDKHWFDDEVLNLVEQNL 176
R+ +G+ ++T + + L+ LW +E R+F+DR + +K+ F+ + V++ L
Sbjct: 1480 RLVRGVYTAINTGPRQTLRSLIRLWAYEAWRIFADRLVGVKEKNSFEQLLYETVDKYL 1537
Score = 27.3 bits (59), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 33/149 (22%), Positives = 62/149 (41%), Gaps = 33/149 (22%)
Query: 30 PG-GGRNDIPSRLKRQFCIFNCVLPSDKAIDNIFSVIGEGHYNAKRGFPIEVRNLVKQLI 88
PG GR+++P LK+ F F+ P I + I GF + ++L +++
Sbjct: 756 PGYNGRSELPENLKKSFREFSMKSPQSGTIAEMILQI--------MGFE-DSKSLASKIV 806
Query: 89 PLTRLLWKSTRAQLLPTPAKFHYVFSLRDLSRIWQGMVGTLSTVIDSEKVLM-------- 140
LL S++ + HY F LR L + + +S + EK ++
Sbjct: 807 HFLELL--SSKCSSMN-----HYHFGLRTLKGVLRNCSPLISEFGEGEKTVVESLKRVIL 859
Query: 141 --------LLWKHEVTRVFSDRFTIMSDK 161
L++K E++++F T ++ K
Sbjct: 860 PSLGDTDELVFKDELSKIFDSAGTPLNSK 888
>pdb|3QMZ|A Chain A, Crystal Structure Of The Cytoplasmic Dynein Heavy Chain
Motor Domain
pdb|3QMZ|B Chain B, Crystal Structure Of The Cytoplasmic Dynein Heavy Chain
Motor Domain
Length = 2486
Score = 54.3 bits (129), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 44/178 (24%), Positives = 85/178 (47%), Gaps = 8/178 (4%)
Query: 1 MNMKGFYSLEKPGEFTTLIDVQFVAAMAQPGG-GRNDIPSRLKRQFCIFNCVLPSDKAID 59
M +GF+ + ++ T+ + V A P GR + R R I PS K++
Sbjct: 1147 MEKQGFWKTPE-NKWVTIERIHIVGACNPPTDPGRIPMSERFTRHAAILYLGYPSGKSLS 1205
Query: 60 NIFSVIGEGHYNAKRGFPIEVRNLVKQLIPLTRLLWKSTRAQLLPTPAKFHYVFSLRDLS 119
I+ + +Y A E R+ + + L+ +A+ T + HY+FS R+L+
Sbjct: 1206 QIYEI----YYKAIFKLVPEFRSYTEPFARASVHLYNECKARY-STGLQSHYLFSPRELT 1260
Query: 120 RIWQGMVGTLST-VIDSEKVLMLLWKHEVTRVFSDRFTIMSDKHWFDDEVLNLVEQNL 176
R+ +G+ ++T + + L+ LW +E R+F+DR + +K+ F+ + V++ L
Sbjct: 1261 RLVRGVYTAINTGPRQTLRSLIRLWAYEAWRIFADRLVGVKEKNSFEQLLYETVDKYL 1318
Score = 27.3 bits (59), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 35/149 (23%), Positives = 65/149 (43%), Gaps = 33/149 (22%)
Query: 30 PG-GGRNDIPSRLKRQFCIFNCVLPSDKAIDNIFSVIGEGHYNAKRGFPIEVRNLVKQLI 88
PG GR+++P LK+ F F+ P I + I GF + ++L +++
Sbjct: 537 PGYNGRSELPENLKKSFREFSMKSPQSGTIAEMILQI--------MGFE-DSKSLASKIV 587
Query: 89 PLTRLLWKSTRAQLLPTPAKFHYVFSLRDLSRIWQGMVGTLS-------TVIDSEKVLM- 140
LL S++ + HY F LR L + + +S TV++S K ++
Sbjct: 588 HFLELL--SSKCSSMN-----HYHFGLRTLKGVLRNCSPLISEFGEGEKTVVESLKRVIL 640
Query: 141 --------LLWKHEVTRVFSDRFTIMSDK 161
L++K E++++F T ++ K
Sbjct: 641 PSLGDTDELVFKDELSKIFDSAGTPLNSK 669
>pdb|3VKH|A Chain A, X-Ray Structure Of A Functional Full-Length Dynein Motor
Domain
pdb|3VKH|B Chain B, X-Ray Structure Of A Functional Full-Length Dynein Motor
Domain
Length = 3367
Score = 50.4 bits (119), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 39/151 (25%), Positives = 66/151 (43%), Gaps = 9/151 (5%)
Query: 21 VQFVAAMAQP-GGGRNDIPSRLKRQFCIFNCVLPSDKAIDNIFSVIGEGHYN-AKRGFPI 78
+QFV A P GR + R R I PS ++ I+ G +N A
Sbjct: 1423 IQFVGACNPPTDAGRVQLTHRFLRHAPILLVDFPSTSSLTQIY-----GTFNRALMKLLP 1477
Query: 79 EVRNLVKQLIPLTRLLWKSTRAQLLPTPAKFHYVFSLRDLSRIWQGMVGTLSTVIDSE-K 137
+R+ L + ++ + P + HY++S R+LSR + ++ + T+ +
Sbjct: 1478 NLRSFADNLTDAMVEFYSESQKRFTPD-IQAHYIYSPRELSRWDRALLEAIQTMDGCTLE 1536
Query: 138 VLMLLWKHEVTRVFSDRFTIMSDKHWFDDEV 168
L+ LW HE R+F DR +K W D ++
Sbjct: 1537 GLVRLWAHEALRLFQDRLVETEEKEWTDKKI 1567
>pdb|3VKG|A Chain A, X-Ray Structure Of An Mtbd Truncation Mutant Of Dynein Motor
Domain
pdb|3VKG|B Chain B, X-Ray Structure Of An Mtbd Truncation Mutant Of Dynein Motor
Domain
Length = 3245
Score = 50.1 bits (118), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 39/151 (25%), Positives = 66/151 (43%), Gaps = 9/151 (5%)
Query: 21 VQFVAAMAQP-GGGRNDIPSRLKRQFCIFNCVLPSDKAIDNIFSVIGEGHYN-AKRGFPI 78
+QFV A P GR + R R I PS ++ I+ G +N A
Sbjct: 1423 IQFVGACNPPTDAGRVQLTHRFLRHAPILLVDFPSTSSLTQIY-----GTFNRALMKLLP 1477
Query: 79 EVRNLVKQLIPLTRLLWKSTRAQLLPTPAKFHYVFSLRDLSRIWQGMVGTLSTVIDSE-K 137
+R+ L + ++ + P + HY++S R+LSR + ++ + T+ +
Sbjct: 1478 NLRSFADNLTDAMVEFYSESQKRFTPD-IQAHYIYSPRELSRWDRALLEAIQTMDGCTLE 1536
Query: 138 VLMLLWKHEVTRVFSDRFTIMSDKHWFDDEV 168
L+ LW HE R+F DR +K W D ++
Sbjct: 1537 GLVRLWAHEALRLFQDRLVETEEKEWTDKKI 1567
>pdb|2Q5E|A Chain A, Crystal Structure Of Human Carboxy-Terminal Domain Rna
Polymerase Ii Polypeptide A Small Phosphatase 2
pdb|2Q5E|B Chain B, Crystal Structure Of Human Carboxy-Terminal Domain Rna
Polymerase Ii Polypeptide A Small Phosphatase 2
pdb|2Q5E|C Chain C, Crystal Structure Of Human Carboxy-Terminal Domain Rna
Polymerase Ii Polypeptide A Small Phosphatase 2
pdb|2Q5E|D Chain D, Crystal Structure Of Human Carboxy-Terminal Domain Rna
Polymerase Ii Polypeptide A Small Phosphatase 2
pdb|2Q5E|E Chain E, Crystal Structure Of Human Carboxy-Terminal Domain Rna
Polymerase Ii Polypeptide A Small Phosphatase 2
pdb|2Q5E|F Chain F, Crystal Structure Of Human Carboxy-Terminal Domain Rna
Polymerase Ii Polypeptide A Small Phosphatase 2
pdb|2Q5E|G Chain G, Crystal Structure Of Human Carboxy-Terminal Domain Rna
Polymerase Ii Polypeptide A Small Phosphatase 2
pdb|2Q5E|H Chain H, Crystal Structure Of Human Carboxy-Terminal Domain Rna
Polymerase Ii Polypeptide A Small Phosphatase 2
Length = 187
Score = 30.8 bits (68), Expect = 0.52, Method: Compositional matrix adjust.
Identities = 30/115 (26%), Positives = 51/115 (44%), Gaps = 23/115 (20%)
Query: 82 NLVKQLIPLTRLLWKST--RAQLLPTPAKFHYVFSLRDLSRIWQGMVGTLSTVIDSEKVL 139
+L K P+T LL + RA+L FH ++DLSR+ + + TL ++D+
Sbjct: 81 SLAKYADPVTDLLDRCGVFRARLFRESCVFHQGCYVKDLSRLGRDLRKTL--ILDNSPAS 138
Query: 140 MLLWKHEVTRVFSDRFTIMSDKHWFDD----EVLNLVEQNLGVKYREMAGTDPVF 190
+ V + WFDD E+LNL+ + E++G + V+
Sbjct: 139 YIFHPENAVPV----------QSWFDDMADTELLNLIP-----IFEELSGAEDVY 178
>pdb|2G36|A Chain A, Crystal Structure Of Tryptophanyl-Trna Synthetase (Ec
6.1.1.2) (Tryptophan-Trna Ligase)(Trprs) (Tm0492) From
Thermotoga Maritima At 2.50 A Resolution
Length = 340
Score = 30.0 bits (66), Expect = 0.86, Method: Compositional matrix adjust.
Identities = 16/78 (20%), Positives = 36/78 (46%), Gaps = 2/78 (2%)
Query: 108 KFHYVFSLRDLSR--IWQGMVGTLSTVIDSEKVLMLLWKHEVTRVFSDRFTIMSDKHWFD 165
K+H F + + +W+G +D +K+L+ K ++ ++ + I D H+ D
Sbjct: 252 KYHQAFDISEEESKWVWEGCTTASIGCVDCKKLLLKNMKRKLAPIWENFRKIDEDPHYVD 311
Query: 166 DEVLNLVEQNLGVKYREM 183
D ++ ++ V + M
Sbjct: 312 DVIMEGTKKAREVAAKTM 329
>pdb|1ZN0|B Chain B, Coordinates Of Rrf And Ef-G Fitted Into Cryo-Em Map Of The
50s Subunit Bound With Both Ef-G (Gdpnp) And Rrf
Length = 655
Score = 27.3 bits (59), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 19/97 (19%), Positives = 39/97 (40%), Gaps = 8/97 (8%)
Query: 88 IPLTRLLWKSTRAQLLPTPAKFHYVFSLRDLSRIWQGMVGTLSTVIDSEKVLMLLW---- 143
I +T WK R ++ TP + + R+ G + + E +W
Sbjct: 34 IAVTTCFWKDHRINIIDTPGHVDFTIEVERSMRVLDGAIVVFDSSQGVEPQSETVWRQAE 93
Query: 144 KHEVTRV-FSDRFTIMSDKHWFDDEVLNLVEQNLGVK 179
K++V R+ F+++ W V+ +++ LG +
Sbjct: 94 KYKVPRIAFANKMDKTGADLWL---VIRTMQERLGAR 127
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
0.325 0.140 0.431
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,872,372
Number of Sequences: 62578
Number of extensions: 230942
Number of successful extensions: 542
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 529
Number of HSP's gapped (non-prelim): 11
length of query: 192
length of database: 14,973,337
effective HSP length: 93
effective length of query: 99
effective length of database: 9,153,583
effective search space: 906204717
effective search space used: 906204717
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 49 (23.5 bits)