RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy5308
(137 letters)
>2a20_A Regulating synaptic membrane exocytosis protein 2; zinc-finger
domain, metal binding protein; NMR {Rattus norvegicus}
PDB: 2cjs_C
Length = 62
Score = 70.2 bits (171), Expect = 2e-17
Identities = 29/42 (69%), Positives = 33/42 (78%)
Query: 80 DATCHICLKTKFADGVGHMCNYCNIRCCARCGGKVTLRSNKV 121
TC IC KTKFADG GH C+YC + CARCGG+V+LRSNKV
Sbjct: 9 APTCGICHKTKFADGCGHNCSYCQTKFCARCGGRVSLRSNKV 50
>1zbd_B Rabphilin-3A; G protein, effector, RABCDR, synaptic exocytosis, RAB
protein, RAB3A; HET: GTP; 2.60A {Rattus norvegicus}
SCOP: g.50.1.1
Length = 134
Score = 69.6 bits (169), Expect = 2e-16
Identities = 21/103 (20%), Positives = 39/103 (37%), Gaps = 11/103 (10%)
Query: 20 PDLSHLTLEERQIIESVMMRQKQEEERELEIMRRKQDEVHLLEQSIRQRSEQQKKAGVEL 79
LT EE++II V+ R ++ E E E + R D + + +++ +
Sbjct: 5 RKQEELTDEEKEIINRVIARAEKMETMEQERIGRLVDRLETMRKNVAGDGVNR------- 57
Query: 80 DATCHICLKTKFADGV-GHMCNYCNIRCCARCGGKVTLRSNKV 121
C +C + G +C C C +CG + +
Sbjct: 58 ---CILCGEQLGMLGSASVVCEDCKKNVCTKCGVETSNNRPHP 97
>2zet_C Melanophilin; complex, GTP-binding protein, GTPase, G-protein, RAB,
RAB27B, effector, SLP homology domain, acetylation,
lipoprotein, membrane; HET: GTP; 3.00A {Mus musculus}
Length = 153
Score = 60.0 bits (144), Expect = 1e-12
Identities = 21/93 (22%), Positives = 36/93 (38%), Gaps = 5/93 (5%)
Query: 20 PDLSHLTLEERQIIESVMMRQKQEEERELEIMRRKQDEVHLLEQSIRQRSEQQKKAGVEL 79
DLS LT EE + + +V+ R RE E ++ + ++ Q + E
Sbjct: 12 LDLSTLTDEEAEHVWAVVQRDFDLRRREEERLQGLKGKI----QKESSKRELLSDTAHLN 67
Query: 80 DATCHICLKT-KFADGVGHMCNYCNIRCCARCG 111
+ C CL+ + C C++ C C
Sbjct: 68 ETHCARCLQPYRLLLNSRRQCLECSLFVCKSCS 100
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 34.4 bits (78), Expect = 0.005
Identities = 12/53 (22%), Positives = 22/53 (41%), Gaps = 8/53 (15%)
Query: 28 EERQIIESVMMRQKQEEERELEIMRRKQDEVHLLEQSIRQRSEQQKKAGVELD 80
+R E +R K EE+ + ++ D S E ++KA +L+
Sbjct: 77 ADRLTQEPESIR-KWREEQRKRL--QELDA-----ASKVMEQEWREKAKKDLE 121
Score = 33.2 bits (75), Expect = 0.013
Identities = 10/49 (20%), Positives = 23/49 (46%), Gaps = 7/49 (14%)
Query: 28 EERQI-IESVMMRQKQEEERELEIMRRKQDEVHLLEQSIRQRSEQQKKA 75
EE++ ++ + E E + + + LE+ +++SEQ +K
Sbjct: 92 EEQRKRLQE---LDAASKVMEQEWREKAKKD---LEEWNQRQSEQVEKN 134
Score = 32.4 bits (73), Expect = 0.026
Identities = 12/56 (21%), Positives = 27/56 (48%), Gaps = 3/56 (5%)
Query: 27 LEERQIIESVMMRQ-KQEEERELEIMRRKQDEVHLLEQSIRQRSEQQKKAGVELDA 81
L+E VM ++ +++ +++LE ++Q E +E++ K + DA
Sbjct: 98 LQELDAASKVMEQEWREKAKKDLEEWNQRQSE--QVEKNKINNRIADKAFYQQPDA 151
Score = 28.2 bits (62), Expect = 0.81
Identities = 5/42 (11%), Positives = 15/42 (35%), Gaps = 4/42 (9%)
Query: 40 QKQEEERELEIMRRKQDEVHLLEQSIRQRSEQQKKAGVELDA 81
+ +E + R +Q + L++ + + + A
Sbjct: 79 RLTQEPESIRKWREEQRK--RLQE--LDAASKVMEQEWREKA 116
>3opc_A Uncharacterized protein; structural genomics, PSI-2, protein
structure initiative, MI center for structural
genomics, MCSG, chaperone; HET: MSE; 2.09A {Bordetella
pertussis}
Length = 154
Score = 27.8 bits (61), Expect = 0.87
Identities = 10/70 (14%), Positives = 23/70 (32%), Gaps = 5/70 (7%)
Query: 13 QTNADIIPDLSHLTLEERQIIESVMMRQKQEEERELEIMRRKQDEVHLLEQSIRQRSEQQ 72
+ ++ + H E + + ++ E ++RK+ L Q +R
Sbjct: 14 ERENALVVEFLHALEAETEALM-----DRRAHESLQAAVQRKETLADDLAQLGAERDALL 68
Query: 73 KKAGVELDAT 82
AG+
Sbjct: 69 SGAGLASGPA 78
>2zuo_A MVP, major vault protein; repeat domains, protein-protein complex,
cytoplasm, ribonucleoprotein, structural protein; 3.50A
{Rattus norvegicus} PDB: 2zv4_N 2zv5_a 2qzv_A
Length = 861
Score = 28.2 bits (62), Expect = 0.98
Identities = 8/48 (16%), Positives = 21/48 (43%)
Query: 28 EERQIIESVMMRQKQEEERELEIMRRKQDEVHLLEQSIRQRSEQQKKA 75
E R +E + + E E+ + + + +E + ++E + +A
Sbjct: 683 EARGRLERQKILDQSEAEKARKELLELEAMSMAVESTGNAKAEAESRA 730
Score = 25.9 bits (56), Expect = 5.0
Identities = 12/49 (24%), Positives = 17/49 (34%)
Query: 27 LEERQIIESVMMRQKQEEERELEIMRRKQDEVHLLEQSIRQRSEQQKKA 75
+++R Q E + E LEQ R R E+QK
Sbjct: 646 VDQRTRDALQRSVQLAIEITTNSQEAAAKHEAQRLEQEARGRLERQKIL 694
>3dmq_A RNA polymerase-associated protein RAPA; SWF2/SNF2, transcription
factor, RNA polymerase recycling, activator,
ATP-binding, DNA-binding; 3.20A {Escherichia coli K12}
Length = 968
Score = 28.1 bits (62), Expect = 1.1
Identities = 17/60 (28%), Positives = 28/60 (46%), Gaps = 8/60 (13%)
Query: 30 RQIIESVM--MRQKQEEERE-LEIMRR-----KQDEVHLLEQSIRQRSEQQKKAGVELDA 81
R +I++ +K E LE +R + DE+ +E + +Q E +AG LDA
Sbjct: 900 RALIDAARNEADEKLSAELSRLEALRAVNPNIRDDELTAIESNRQQVMESLDQAGWRLDA 959
>3k35_A NAD-dependent deacetylase sirtuin-6; rossmann fold, Zn-binding
domain, structural genomics, struc genomics consortium,
SGC, ADP-ribosylation; HET: APR; 2.00A {Homo sapiens}
Length = 318
Score = 27.7 bits (62), Expect = 1.3
Identities = 8/43 (18%), Positives = 12/43 (27%), Gaps = 9/43 (20%)
Query: 81 ATCHIC---------LKTKFADGVGHMCNYCNIRCCARCGGKV 114
C C + T G +C R C G++
Sbjct: 139 EECAKCKTQYVRDTVVGTMGLKATGRLCTVAKARGLRACRGEL 181
>2fup_A Hypothetical protein PA3352; structural genomics, joint center
for structural genomics, J protein structure
initiative, PSI-2; 1.48A {Pseudomonas aeruginosa} SCOP:
a.47.5.1
Length = 157
Score = 27.3 bits (60), Expect = 1.4
Identities = 19/61 (31%), Positives = 31/61 (50%), Gaps = 6/61 (9%)
Query: 22 LSHLTLEERQIIESVMMRQKQEEERELEIMRRKQDEVHLLEQSIRQRSEQQKKAGVELDA 81
L L EE Q +E ++E +++ KQ + LE++ R R+E ++AGV LD
Sbjct: 22 LLQLVDEEFQALE------RRELPVLQQLLGAKQPLMQQLERNGRARAEILREAGVSLDR 75
Query: 82 T 82
Sbjct: 76 E 76
>3pki_A NAD-dependent deacetylase sirtuin-6; ADP ribose, structural
genomics, structural genomics consortium, SGC,
hydrolase; HET: AR6; 2.04A {Homo sapiens} PDB: 3pkj_A*
Length = 355
Score = 27.4 bits (61), Expect = 1.7
Identities = 8/43 (18%), Positives = 12/43 (27%), Gaps = 9/43 (20%)
Query: 81 ATCHIC---------LKTKFADGVGHMCNYCNIRCCARCGGKV 114
C C + T G +C R C G++
Sbjct: 139 EECAKCKTQYVRDTVVGTMGLKATGRLCTVAKARGLRACRGEL 181
>4ask_A Lysine-specific demethylase 6B; oxidoreductase, KDM6B, GSK-J1,
inhibitor, lysine specific HI demethylase; HET: K0I;
1.86A {Homo sapiens} PDB: 2xue_A*
Length = 510
Score = 27.5 bits (60), Expect = 1.8
Identities = 11/84 (13%), Positives = 31/84 (36%)
Query: 31 QIIESVMMRQKQEEERELEIMRRKQDEVHLLEQSIRQRSEQQKKAGVELDATCHICLKTK 90
++I+ +++ + + + E + R ++ + + + + VE+ + +
Sbjct: 395 KMIKFCLLQSMKHCQVQRESLVRAGKKIAYQGRVKDEPAYYCNECDVEVFNILFVTSENG 454
Query: 91 FADGVGHMCNYCNIRCCARCGGKV 114
+ C C R A G V
Sbjct: 455 SRNTYLVHCEGCARRRSAGLQGVV 478
>3mpx_A FYVE, rhogef and PH domain-containing protein 5; structural
genomics consortium, DH domain, SGC, L binding protein;
2.80A {Homo sapiens}
Length = 434
Score = 26.9 bits (59), Expect = 2.9
Identities = 14/89 (15%), Positives = 21/89 (23%)
Query: 22 LSHLTLEERQIIESVMMRQKQEEERELEIMRRKQDEVHLLEQSIRQRSEQQKKAGVELDA 81
LS + ER + R E+ + + + V
Sbjct: 317 LSASSCAERDEWYGCLSRALPEDYKAQALAAFHHSVEIRERLGVSLGERPPTLVPVTHVM 376
Query: 82 TCHICLKTKFADGVGHMCNYCNIRCCARC 110
C C H C+ C C C
Sbjct: 377 MCMNCGCDFSLTLRRHHCHACGKIVCRNC 405
>2qag_B Septin-6, protein NEDD5; cell cycle, cell division, GTP-binding,
nucleotide-binding, phosphorylation, acetylation,
alternative splicing, coiled coil; HET: GDP GTP; 4.00A
{Homo sapiens}
Length = 427
Score = 26.2 bits (57), Expect = 4.7
Identities = 10/49 (20%), Positives = 22/49 (44%), Gaps = 1/49 (2%)
Query: 28 EERQIIESVMMRQKQEEERELEIMRRK-QDEVHLLEQSIRQRSEQQKKA 75
+E + + Q+E+++LE ++ DEV+ +Q Q +
Sbjct: 362 KELHEKFDRLKKLHQDEKKKLEDKKKSLDDEVNAFKQRKTAAELLQSQG 410
>1zun_A Sulfate adenylyltransferase subunit 2; beta barrel, switch domain,
heterodimer, pyrophosphate, G protein; HET: GDP AGS;
2.70A {Pseudomonas syringae} SCOP: c.26.2.2
Length = 325
Score = 25.9 bits (56), Expect = 4.7
Identities = 12/44 (27%), Positives = 18/44 (40%), Gaps = 6/44 (13%)
Query: 6 GMVTSMAQTNADIIPDLSHLTLEERQ------IIESVMMRQKQE 43
G V S A + DII ++ ERQ M +K++
Sbjct: 279 GAVESEATSLTDIIQEMLLTRTSERQGRVIDHDGAGSMEEKKRQ 322
>2vrw_B P95VAV, VAV1, proto-oncogene VAV; lipoprotein, GTP-binding,
metal-binding, phosphoprotein, exchange factor, RAC,
GTPase, membrane domain; 1.85A {Mus musculus} PDB:
3bji_A 1f5x_A
Length = 406
Score = 25.9 bits (57), Expect = 5.1
Identities = 18/116 (15%), Positives = 33/116 (28%), Gaps = 7/116 (6%)
Query: 3 LTEGMVTSMAQTNADIIPDLSHLTLEERQIIESVMMRQKQEEERE--LEIMRRKQDEVHL 60
L V + D L E Q + + K E ++ +E ++
Sbjct: 280 LHSFQVRDDSSGERDNKKWSHMFLLIEDQGAQGYELFFKTRELKKKWMEQFEMAISNIY- 338
Query: 61 LEQSIRQRSEQQKKAGVELDATCHICLKTKFADGV--GHMCNYCNIRCCARCGGKV 114
++ + E +C C + G+ C C C G+V
Sbjct: 339 -PENATANGHDFQMFSFEETTSCKAC-QMLLRGTFYQGYRCYRCRAPAHKECLGRV 392
>1xu2_R Tumor necrosis factor receptor superfamily member; TNFSF, cytokine,
CRD, jelly-roll, cysteine-rich, H growth factor receptor
complex; 2.35A {Homo sapiens} SCOP: g.24.1.2 PDB:
2kn1_A* 1oqd_K
Length = 47
Score = 24.0 bits (51), Expect = 6.6
Identities = 11/44 (25%), Positives = 19/44 (43%)
Query: 86 CLKTKFADGVGHMCNYCNIRCCARCGGKVTLRSNKVSVEVTTRG 129
C + ++ D + H C C +RC + R SV + +G
Sbjct: 4 CSQNEYFDSLLHACIPCQLRCSSNTPPLTCQRYCNASVTNSVKG 47
>2o30_A Nuclear movement protein; MCSG, structural genomics, PSI-2,
structure initiative; 1.66A {Encephalitozoon cuniculi}
Length = 131
Score = 25.2 bits (55), Expect = 6.7
Identities = 7/25 (28%), Positives = 14/25 (56%)
Query: 21 DLSHLTLEERQIIESVMMRQKQEEE 45
D+S L E R+++E +M ++
Sbjct: 106 DMSMLDAEAREVVEKMMHNTSGKDS 130
>3ky9_A Proto-oncogene VAV; calponin homology domain, DBL homology domain,
pleckst homology domain, C1 domain, guanine-nucleotide
releasing FA metal-binding; 2.73A {Homo sapiens} PDB:
2d86_A
Length = 587
Score = 25.4 bits (55), Expect = 7.4
Identities = 18/115 (15%), Positives = 36/115 (31%), Gaps = 5/115 (4%)
Query: 3 LTEGMVTSMAQTNADIIPDLSHLTLEERQIIESVMMRQKQEEERE--LEIMRRKQDEVHL 60
L V + + D L E Q + + K E ++ +E ++
Sbjct: 452 LHSFQVRDDSSGDRDNKKWSHMFLLIEDQGAQGYELFFKTRELKKKWMEQFEMAISNIY- 510
Query: 61 LEQSIRQRSEQQKKAGVELDATCHIC-LKTKFADGVGHMCNYCNIRCCARCGGKV 114
++ + E +C C + + G+ C+ C C G+V
Sbjct: 511 -PENATANGHDFQMFSFEETTSCKACQMLLRGTFYQGYRCHRCRASAHKECLGRV 564
>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 = 25.6 bits (56), Expect = 8.1
Identities = 11/49 (22%), Positives = 24/49 (48%)
Query: 27 LEERQIIESVMMRQKQEEERELEIMRRKQDEVHLLEQSIRQRSEQQKKA 75
+E R E +Q Q E+++++ +E E++ RQ+ + +K
Sbjct: 932 MEARIEEEEERSQQLQAEKKKMQQQMLDLEEQLEEEEAARQKLQLEKVT 980
>4f3n_A Uncharacterized ACR, COG1565 superfamily; structural genomics,
niaid, national institute of allergy AN infectious
diseases; 1.75A {Burkholderia thailandensis}
Length = 432
Score = 25.2 bits (55), Expect = 8.4
Identities = 6/29 (20%), Positives = 14/29 (48%)
Query: 46 RELEIMRRKQDEVHLLEQSIRQRSEQQKK 74
L + + DE +++ S R+ Q++
Sbjct: 157 TALAALGVELDEYAIVDLSGELRARQRET 185
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
0.319 0.131 0.379
Gapped
Lambda K H
0.267 0.0439 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,960,971
Number of extensions: 106380
Number of successful extensions: 488
Number of sequences better than 10.0: 1
Number of HSP's gapped: 474
Number of HSP's successfully gapped: 84
Length of query: 137
Length of database: 6,701,793
Length adjustment: 84
Effective length of query: 53
Effective length of database: 4,356,429
Effective search space: 230890737
Effective search space used: 230890737
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 52 (24.5 bits)