RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy12964
(156 letters)
>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp
contractIle protein-transport protein complex; 24.00A
{Gallus gallus}
Length = 1080
Score = 81.3 bits (201), Expect = 7e-19
Identities = 24/73 (32%), Positives = 38/73 (52%)
Query: 57 QDKSDSSTVGLASQSRSQQTAATYFRYSLMELLQRIVSGTPQFVRCIKPNELGIPNSFDR 116
+ + ++T FR SL L++ + + TP +VRCIKPN+ P +FD
Sbjct: 616 TPVKPAKARPGQTSKEHKKTVGHQFRNSLHLLMETLNATTPHYVRCIKPNDFKFPFTFDE 675
Query: 117 CKVIKQLRYTGVL 129
+ ++QLR GVL
Sbjct: 676 KRAVQQLRACGVL 688
>4db1_A Myosin-7; S1DC, cardiac, beta isoform, MYH7, myhcb, MYHC-beta,
contractIle protein; HET: ANP; 2.60A {Homo sapiens} PDB:
2w4a_M 2w4g_M 2w4h_M 2mys_A* 1m8q_A* 1mvw_A* 1o18_A*
1o19_A* 1o1a_A* 1o1b_A* 1o1c_A* 1o1d_A* 1o1e_A* 1o1f_A*
1o1g_A*
Length = 783
Score = 78.5 bits (194), Expect = 8e-18
Identities = 29/84 (34%), Positives = 39/84 (46%)
Query: 46 FIHTIVLSPLLQDKSDSSTVGLASQSRSQQTAATYFRYSLMELLQRIVSGTPQFVRCIKP 105
+ T+ + D G A + S QT + R +L +L+ + S P FVRCI P
Sbjct: 616 LLSTLFANYAGADAPIEKGKGKAKKGSSFQTVSALHRENLNKLMTNLRSTHPHFVRCIIP 675
Query: 106 NELGIPNSFDRCKVIKQLRYTGVL 129
NE P D V+ QLR GVL
Sbjct: 676 NETKSPGVMDNPLVMHQLRCNGVL 699
>2v26_A Myosin VI; calmodulin-binding, nucleotide-binding, membrane,
vanadate, transport, PRE- powerstroke, transition state,
protein transport; HET: ADP; 1.75A {Sus scrofa} PDB:
2bki_A 2bkh_A 3l9i_A 2x51_A 2vb6_A* 2vas_A*
Length = 784
Score = 77.7 bits (192), Expect = 1e-17
Identities = 17/79 (21%), Positives = 38/79 (48%), Gaps = 1/79 (1%)
Query: 52 LSPLLQDKSDSSTVGLASQSRSQ-QTAATYFRYSLMELLQRIVSGTPQFVRCIKPNELGI 110
+ L + ++++ + + F+ L LL ++ S F+RCIKPN
Sbjct: 613 IRELFESSTNNNKDTKQKAGKLSFISVGNKFKTQLNLLLDKLRSTGASFIRCIKPNLKMT 672
Query: 111 PNSFDRCKVIKQLRYTGVL 129
+ F+ +++ QL+ +G++
Sbjct: 673 SHHFEGAQILSQLQCSGMV 691
>1g8x_A Myosin II heavy chain fused to alpha-actinin 3; motor, lever ARM,
protein engineering, structural protein; HET: ADP; 2.80A
{Dictyostelium discoideum} SCOP: k.1.1.1
Length = 1010
Score = 77.8 bits (192), Expect = 1e-17
Identities = 24/78 (30%), Positives = 38/78 (48%), Gaps = 3/78 (3%)
Query: 52 LSPLLQDKSDSSTVGLASQSRSQQTAATYFRYSLMELLQRIVSGTPQFVRCIKPNELGIP 111
++ L D + +S A + + T A ++ L L+ + + P FVRCI PN +P
Sbjct: 608 VTKLFNDPNIASR---AKKGANFITVAAQYKEQLASLMATLETTNPHFVRCIIPNNKQLP 664
Query: 112 NSFDRCKVIKQLRYTGVL 129
+ V+ QLR GVL
Sbjct: 665 AKLEDKVVLDQLRCNGVL 682
>1w9i_A Myosin II heavy chain; molecular motor, ATPase, motor domain,
mutant, muscle contraction; HET: ADP; 1.75A
{Dictyostelium discoideum} PDB: 1w9j_A* 1w9l_A* 1w9k_A*
1mma_A* 2aka_A 1d0x_A* 1d0y_A* 1d0z_A* 1d1a_A* 1d1b_A*
1d1c_A* 2xel_A* 1yv3_A* 3bz7_A* 3bz8_A* 3bz9_A* 1jwy_A*
1jx2_A* 3mjx_A* 2jhr_A* ...
Length = 770
Score = 76.9 bits (190), Expect = 2e-17
Identities = 24/78 (30%), Positives = 38/78 (48%), Gaps = 3/78 (3%)
Query: 52 LSPLLQDKSDSSTVGLASQSRSQQTAATYFRYSLMELLQRIVSGTPQFVRCIKPNELGIP 111
++ L D + +S A + + T A ++ L L+ + + P FVRCI PN +P
Sbjct: 608 VTKLFNDPNIASR---AKKGANFITVAAQYKEQLASLMATLETTNPHFVRCIIPNNKQLP 664
Query: 112 NSFDRCKVIKQLRYTGVL 129
+ V+ QLR GVL
Sbjct: 665 AKLEDKVVLDQLRCNGVL 682
>1i84_S Smooth muscle myosin heavy chain; muscle protein, myosin
subfragment 2, heavy meromyosin, essential light chain,
motor protein; HET: MLY; 20.00A {Gallus gallus} SCOP:
i.15.1.1 PDB: 3j04_A 3dtp_B 3dtp_A
Length = 1184
Score = 77.2 bits (190), Expect = 2e-17
Identities = 20/73 (27%), Positives = 32/73 (43%)
Query: 57 QDKSDSSTVGLASQSRSQQTAATYFRYSLMELLQRIVSGTPQFVRCIKPNELGIPNSFDR 116
+ S ++ +T ++ L +L+ + + P FVRCI PN D
Sbjct: 638 KMTESSLPSASKTKKGMFRTVGQLYKEQLTKLMTTLRNTNPNFVRCIIPNHEKRAGKLDA 697
Query: 117 CKVIKQLRYTGVL 129
V++QLR GVL
Sbjct: 698 HLVLEQLRCNGVL 710
>2ycu_A Non muscle myosin 2C, alpha-actinin; motor protein; HET: AOV; 2.25A
{Homo sapiens} PDB: 1br1_A* 1br4_A* 1br2_A*
Length = 995
Score = 76.6 bits (189), Expect = 3e-17
Identities = 20/77 (25%), Positives = 29/77 (37%)
Query: 53 SPLLQDKSDSSTVGLASQSRSQQTAATYFRYSLMELLQRIVSGTPQFVRCIKPNELGIPN 112
G + +T ++ SL L+ + + P FVRCI PN
Sbjct: 601 GLEQVSSLGDGPPGGRPRRGMFRTVGQLYKESLSRLMATLSNTNPSFVRCIVPNHEKRAG 660
Query: 113 SFDRCKVIKQLRYTGVL 129
+ V+ QLR GVL
Sbjct: 661 KLEPRLVLDQLRCNGVL 677
>1w7j_A Myosin VA; motor protein, unconventional myosin, myosin V, chicken,
molecular motor, ATPase, ELC, IQ motif, muscle protein,
ATP-binding; HET: ADP; 2A {Gallus gallus} SCOP: b.34.3.1
c.37.1.9 PDB: 1w7i_A* 1oe9_A* 1w8j_A
Length = 795
Score = 76.5 bits (189), Expect = 3e-17
Identities = 24/71 (33%), Positives = 38/71 (53%)
Query: 59 KSDSSTVGLASQSRSQQTAATYFRYSLMELLQRIVSGTPQFVRCIKPNELGIPNSFDRCK 118
+ + ++T FR SL L++ + + TP +VRCIKPN+ P +FD +
Sbjct: 618 VKPAKARPGQTSKEHKKTVGHQFRNSLHLLMETLNATTPHYVRCIKPNDFKFPFTFDEKR 677
Query: 119 VIKQLRYTGVL 129
++QLR GVL
Sbjct: 678 AVQQLRACGVL 688
>1lkx_A Myosin IE heavy chain; myosin motor domain, lever ARM, converter
domain, contractIle protein; HET: ADP; 3.00A
{Dictyostelium discoideum} SCOP: c.37.1.9
Length = 697
Score = 74.9 bits (185), Expect = 1e-16
Identities = 19/62 (30%), Positives = 34/62 (54%)
Query: 68 ASQSRSQQTAATYFRYSLMELLQRIVSGTPQFVRCIKPNELGIPNSFDRCKVIKQLRYTG 127
+ +TA + FR ++ L+ +++ +P +VRCIK N+ D +V Q+RY G
Sbjct: 553 EDSKKRPETAGSQFRNAMNALITTLLACSPHYVRCIKSNDNKQAGVIDEDRVRHQVRYLG 612
Query: 128 VL 129
+L
Sbjct: 613 LL 614
>1kk8_A Myosin heavy chain, striated muscle; actin-detached, mechanics of
motor, contractIle PROT; HET: ADP; 2.30A {Argopecten
irradians} SCOP: b.34.3.1 c.37.1.9 PDB: 1kk7_A* 1qvi_A*
1s5g_A* 1sr6_A 1b7t_A* 1kqm_A* 1kwo_A* 1l2o_A* 1dfl_A*
2w4t_C 2w4v_C 2w4w_C 1dfk_A 2ec6_A 2otg_A* 2os8_A*
2ovk_A 2ekv_A 2ekw_A 2oy6_A* ...
Length = 837
Score = 74.7 bits (184), Expect = 1e-16
Identities = 27/80 (33%), Positives = 42/80 (52%), Gaps = 2/80 (2%)
Query: 52 LSPLLQDKSDSSTVGLASQSR--SQQTAATYFRYSLMELLQRIVSGTPQFVRCIKPNELG 109
++ L + + + G + + + QT + R SL +L++ + S P FVRCI PNEL
Sbjct: 618 VAELFKAPEEPAGGGKKKKGKSSAFQTISAVHRESLNKLMKNLYSTHPHFVRCIIPNELK 677
Query: 110 IPNSFDRCKVIKQLRYTGVL 129
P D V+ QL+ GVL
Sbjct: 678 QPGLVDAELVLHQLQCNGVL 697
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl RED beta-ketoacyl
synthase, dehydratase; 4.00A {Saccharomyces cerevisiae}
Length = 2006
Score = 34.6 bits (79), Expect = 0.010
Identities = 29/155 (18%), Positives = 57/155 (36%), Gaps = 46/155 (29%)
Query: 34 RDV----DRRAVD-YGYFIHTIVLSPLLQDKSDSSTVGLASQSRSQQTAATYFRYSLMEL 88
+DV D D YG+ I IV + + T+ + + ++ YS M +
Sbjct: 1643 QDVWNRADNHFKDTYGFSILDIV-----INNPVNLTIHFGGE-KGKRIRE---NYSAM-I 1692
Query: 89 LQRIVSGTPQFVRCIKP-NELGIPNSF----DRCK---------------VIKQLRYTGV 128
+ IV G + + K NE +F + L+ G+
Sbjct: 1693 FETIVDGKLKTEKIFKEINEHSTSYTFRSEKGLLSATQFTQPALTLMEKAAFEDLKSKGL 1752
Query: 129 LACNASCLGHLS------LCA---ILSLK-LLRLL 153
+ +A+ GH S L + ++S++ L+ ++
Sbjct: 1753 IPADATFAGH-SLGEYAALASLADVMSIESLVEVV 1786
Score = 31.6 bits (71), Expect = 0.11
Identities = 25/115 (21%), Positives = 39/115 (33%), Gaps = 28/115 (24%)
Query: 45 YF-----IHTIVLSPLLQDKSDSSTVGLASQSRSQQTAATYFR--YSLMELLQRIVSGTP 97
YF ++ L+ D S L+ R+ A F +++E L+ P
Sbjct: 169 YFEELRDLYQT-YHVLVGDLIKFSAETLSELIRTTLDAEKVFTQGLNILEWLE-----NP 222
Query: 98 QFVRCIKPNE---LGIPNSFDRCKVIK--QL-RYTGVLACNASCLGHLSLCAILS 146
P++ L IP S C +I QL Y V+ L + L
Sbjct: 223 S----NTPDKDYLLSIPIS---CPLIGVIQLAHY--VVTAKLLGFTPGELRSYLK 268
Score = 30.8 bits (69), Expect = 0.21
Identities = 25/153 (16%), Positives = 44/153 (28%), Gaps = 65/153 (42%)
Query: 5 PSIHEMNLCCRGSVDGWTVQSTSID-VNRCRDVDRRAVDYGYFIH--------TIVLS-- 53
PS M L + VQ ++ N ++ + +V+S
Sbjct: 335 PS--PM-LSISN-LTQEQVQDY-VNKTNSHLPAGKQ-------VEISLVNGAKNLVVSGP 382
Query: 54 PLLQDKSDSSTVGLAS------------QSR---SQQTAATYFRY---------SLME-- 87
P S GL QSR S++ R+ L+
Sbjct: 383 P-------QSLYGLNLTLRKAKAPSGLDQSRIPFSERKLKFSNRFLPVASPFHSHLLVPA 435
Query: 88 ---LLQRIVSGTPQFVRCIKPNELGIP--NSFD 115
+ + +V F ++ IP ++FD
Sbjct: 436 SDLINKDLVKNNVSF----NAKDIQIPVYDTFD 464
Score = 30.0 bits (67), Expect = 0.39
Identities = 28/126 (22%), Positives = 45/126 (35%), Gaps = 40/126 (31%)
Query: 38 RRAVDYGYFI----H----TIVLSPLLQDKSDSSTVGLAS-------QSRSQ-QTAATYF 81
R+A+ +FI + L P + + S + G+ S ++ Q Q
Sbjct: 297 RKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPSPMLSISNLTQEQVQDYVNKT 356
Query: 82 RYSLME-------LL----QRIVSGTPQ-------FVRCIK-PNELG---IPNSFDRCKV 119
L L+ +VSG PQ +R K P+ L IP S +R K+
Sbjct: 357 NSHLPAGKQVEISLVNGAKNLVVSGPPQSLYGLNLTLRKAKAPSGLDQSRIPFS-ER-KL 414
Query: 120 IKQLRY 125
R+
Sbjct: 415 KFSNRF 420
Score = 29.2 bits (65), Expect = 0.56
Identities = 9/51 (17%), Positives = 18/51 (35%), Gaps = 15/51 (29%)
Query: 47 IHTIVLSPLLQDKSDSSTVGLASQSRSQQTAATYFRYSLMELLQRIVSGTP 97
IH + LLQ+ + ++++ Y RI++ P
Sbjct: 101 IHALAAK-LLQEND-------TTLVKTKELIKNYIT-------ARIMAKRP 136
>4djd_D C/Fe-SP, corrinoid/iron-sulfur protein small subunit; TIM barrel,
rossmann fold, B12-dependent methyltransferase; HET:
B12; 2.38A {Moorella thermoacetica} PDB: 4dje_D* 4djf_D*
Length = 323
Score = 28.1 bits (62), Expect = 1.1
Identities = 6/33 (18%), Positives = 16/33 (48%)
Query: 23 VQSTSIDVNRCRDVDRRAVDYGYFIHTIVLSPL 55
+ + +D+N C+ ++ + + IV+ P
Sbjct: 184 IARSPLDINICKQLNILINEMNLPLDHIVIDPS 216
>1gku_B Reverse gyrase, TOP-RG; topoisomerase, DNA supercoiling, archaea,
helicase; 2.7A {Archaeoglobus fulgidus} SCOP: c.37.1.16
c.37.1.16 e.10.1.1 PDB: 1gl9_B*
Length = 1054
Score = 28.1 bits (63), Expect = 1.5
Identities = 11/39 (28%), Positives = 15/39 (38%), Gaps = 14/39 (35%)
Query: 27 SIDVNRCRDVD----RRAVDY--GYFIHTIVLSPLLQDK 59
+D N V RR D G+ VLS L ++
Sbjct: 675 DVDENL---VKAQVVRRIEDRWIGF-----VLSQKLWER 705
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
programmed cell death; HET: DTP; 6.90A {Drosophila
melanogaster} PDB: 3iz8_A*
Length = 1221
Score = 27.9 bits (61), Expect = 1.7
Identities = 7/49 (14%), Positives = 20/49 (40%), Gaps = 6/49 (12%)
Query: 21 W---TVQSTSIDVNRCRD---VDRRAVDYGYFIHTIVLSPLLQDKSDSS 63
W + VN+ V+++ + I +I L ++ +++ +
Sbjct: 396 WFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYA 444
>2h9a_B CO dehydrogenase/acetyl-COA synthase, iron- sulfur protein;
heterodimer, beta-alpha-barrels, oxidoreductase; HET:
B12; 1.90A {Carboxydothermus hydrogenoformans} PDB:
2ycl_B*
Length = 310
Score = 27.7 bits (61), Expect = 1.8
Identities = 7/33 (21%), Positives = 17/33 (51%)
Query: 23 VQSTSIDVNRCRDVDRRAVDYGYFIHTIVLSPL 55
V S +D+N + ++ ++ + I++ PL
Sbjct: 177 VASAPLDINLSKQLNIMIMEMNLAPNRIIMDPL 209
>3r75_A Anthranilate/para-aminobenzoate synthases compone; ammonia channel,
chorismate, type 1 glutamine amidotransfera phenazine
biosynthesis, lyase; HET: CYG; 2.10A {Burkholderia SP}
PDB: 3r74_A* 3r76_A*
Length = 645
Score = 26.3 bits (58), Expect = 5.3
Identities = 13/49 (26%), Positives = 20/49 (40%), Gaps = 5/49 (10%)
Query: 109 GIPNSFDRCKVIKQLRYTGVLACN-----ASCLGHLSLCAILSLKLLRL 152
G P+ ++ + + L A CL H L AIL + L+R
Sbjct: 497 GDPSDAGDPRIARLYAWLRHLIDEGKPFMAVCLSHQILNAILGIPLVRR 545
>3l52_A Orotidine 5'-phosphate decarboxylase; TIM barrel, structural
genomics, PSI-2, protein structure initiative; 1.35A
{Streptomyces avermitilis}
Length = 284
Score = 25.9 bits (56), Expect = 6.1
Identities = 10/51 (19%), Positives = 15/51 (29%), Gaps = 5/51 (9%)
Query: 84 SLMELLQRIVSGTPQFVRCIKPN-----ELGIPNSFDRCKVIKQLRYTGVL 129
L + +V + V KP G K + + R G L
Sbjct: 47 GLERFSRTVVEALGEHVAVFKPQSAFFERFGSRGVAVLEKTVAEARAAGAL 97
>3r89_A Orotidine 5'-phosphate decarboxylase; PSI-biology, midwest center
for structural genomics, MCSG, O 5-phosphate
decarboxylase, lyase; 1.84A {Anaerococcus prevotii}
Length = 290
Score = 25.5 bits (55), Expect = 8.1
Identities = 9/51 (17%), Positives = 14/51 (27%), Gaps = 5/51 (9%)
Query: 84 SLMELLQRIVSGTPQFVRCIKPNE-----LGIPNSFDRCKVIKQLRYTGVL 129
+L + I+ T K GI + LR +L
Sbjct: 44 ALFSYNKEIIDQTYDVCAIYKLQIAYYESYGIEGMIAYRDTLSYLREKDLL 94
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.325 0.137 0.417
Gapped
Lambda K H
0.267 0.0542 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,249,583
Number of extensions: 115024
Number of successful extensions: 173
Number of sequences better than 10.0: 1
Number of HSP's gapped: 173
Number of HSP's successfully gapped: 22
Length of query: 156
Length of database: 6,701,793
Length adjustment: 86
Effective length of query: 70
Effective length of database: 4,300,587
Effective search space: 301041090
Effective search space used: 301041090
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 53 (24.6 bits)