RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy14956
(147 letters)
>4dck_A Sodium channel protein type 5 subunit alpha; IQ-motif, EF-hand,
voltage-gated sodium channel regulation, CTD binds to
FGF13 and CAM. CAM binds to Ca2+.; 2.20A {Homo sapiens}
PDB: 2kbi_A
Length = 168
Score = 78.2 bits (192), Expect = 3e-19
Identities = 23/72 (31%), Positives = 36/72 (50%), Gaps = 1/72 (1%)
Query: 1 MFCVDILDALTKDFFARKGNPIEETGDLVAEV-NTRPDEAGYDPVSSTLWRQREEYCARL 59
+ C+DIL A TK G + + P + Y+P+++TL R+ EE A +
Sbjct: 76 IHCMDILFAFTKRVLGESGEMDALKIQMEEKFMAANPSKISYEPITTTLRRKHEEVSAMV 135
Query: 60 IQHAWRKHKQCR 71
IQ A+R+H R
Sbjct: 136 IQRAFRRHLLQR 147
>2i87_A D-alanine-D-alanine ligase; APO; 2.00A {Staphylococcus aureus
subsp} PDB: 2i8c_A* 3n8d_A* 2i80_A*
Length = 364
Score = 33.7 bits (78), Expect = 0.015
Identities = 16/64 (25%), Positives = 23/64 (35%), Gaps = 16/64 (25%)
Query: 13 DFFARKGNPIEETGDLVA-EVNTRPDEAGYDPVS--STLWRQR----EEYCARLIQHAWR 65
DFF + E + E N P G+ S LW E +LI+ A
Sbjct: 293 DFF------VTEDNQIYINETNAMP---GFTAFSMYPKLWENMGLSYPELITKLIELAKE 343
Query: 66 KHKQ 69
+H+
Sbjct: 344 RHQD 347
>3tqt_A D-alanine--D-alanine ligase; cell envelope; 1.88A {Coxiella
burnetii}
Length = 372
Score = 33.4 bits (77), Expect = 0.017
Identities = 14/64 (21%), Positives = 26/64 (40%), Gaps = 16/64 (25%)
Query: 13 DFFARKGNPIEETGDLVA-EVNTRPDEAGYDPVS--STLWRQR----EEYCARLIQHAWR 65
DFF + ++ E+NT P G+ +S +W +LI+ A
Sbjct: 303 DFF------VTPNNKVLVNEINTIP---GFTNISMYPKMWEASGLPCPNLLDQLIELAID 353
Query: 66 KHKQ 69
+H++
Sbjct: 354 RHQE 357
>1ehi_A LMDDL2, D-alanine:D-lactate ligase; ATP-binding. grAsp motif for
ATP.; HET: ADP PHY; 2.38A {Leuconostoc mesenteroides}
SCOP: c.30.1.2 d.142.1.1
Length = 377
Score = 33.4 bits (77), Expect = 0.018
Identities = 14/64 (21%), Positives = 21/64 (32%), Gaps = 16/64 (25%)
Query: 13 DFFARKGNPIEETGDLVA-EVNTRPDEAGYDPVS--STLWRQR----EEYCARLIQHAWR 65
DF ++E E NT P G+ +S LW + LI + +
Sbjct: 303 DFL------LDENNVPYLGEPNTLP---GFTNMSLFKRLWDYSDINNAKLVDMLIDYGFE 353
Query: 66 KHKQ 69
Q
Sbjct: 354 DFAQ 357
>3i12_A D-alanine-D-alanine ligase A; D-alanyl-alanine synthetase A, ADP
binding protein, csgid, A binding, cell shape; HET: ADP;
2.20A {Salmonella typhimurium} PDB: 3q1k_A*
Length = 364
Score = 33.0 bits (76), Expect = 0.027
Identities = 16/64 (25%), Positives = 27/64 (42%), Gaps = 16/64 (25%)
Query: 13 DFFARKGNPIEETGDLVA-EVNTRPDEAGYDPVS--STLWRQR----EEYCARLIQHAWR 65
D F + ++V E+NT P G+ +S LW+ + +RLI+ A
Sbjct: 302 DVF------LTADNEVVINEINTLP---GFTNISMYPKLWQASGLGYTDLISRLIELALE 352
Query: 66 KHKQ 69
+H
Sbjct: 353 RHTA 356
>3e5n_A D-alanine-D-alanine ligase A; bacterial blight; 2.00A {Xanthomonas
oryzae PV} PDB: 3r5f_A* 3rfc_A*
Length = 386
Score = 32.2 bits (74), Expect = 0.043
Identities = 18/64 (28%), Positives = 25/64 (39%), Gaps = 16/64 (25%)
Query: 13 DFFARKGNPIEETGDLVA-EVNTRPDEAGYDPVS--STLWRQR----EEYCARLIQHAWR 65
D F + G +V EVNT P G+ +S LW+ RLI+ A
Sbjct: 321 DVF------LCADGRIVINEVNTLP---GFTRISVYPKLWQASGLDYRGLITRLIELALE 371
Query: 66 KHKQ 69
+H
Sbjct: 372 RHTD 375
>3k3p_A D-alanine--D-alanine ligase; D-alanyl-alanine synthetase,
ATP-binding, cell shape, cell W biogenesis/degradation,
magnesium, manganese; 2.23A {Streptococcus mutans}
Length = 383
Score = 31.8 bits (73), Expect = 0.055
Identities = 15/64 (23%), Positives = 21/64 (32%), Gaps = 16/64 (25%)
Query: 13 DFFARKGNPIEETGDLVA-EVNTRPDEAGYDPVS--STLWRQR----EEYCARLIQHAWR 65
DFF + E G + E+NT P G+ S LW L+ A
Sbjct: 323 DFF------LTEDGKVYLNELNTMP---GFTQWSMYPLLWENMGLSYSVLIEELVSLAKE 373
Query: 66 KHKQ 69
+
Sbjct: 374 MFDK 377
>3lwb_A D-alanine--D-alanine ligase; DDL, D-alanyl--D-alanine ligase
RV2981C, structural genomics, TB structural GENO
consortium, TBSGC; 2.10A {Mycobacterium tuberculosis}
Length = 373
Score = 30.7 bits (70), Expect = 0.13
Identities = 13/61 (21%), Positives = 24/61 (39%), Gaps = 15/61 (24%)
Query: 13 DFFARKGNPIEETGDLVAEVNTRPDEAGYDPVS--STLWRQR----EEYCARLIQHAWRK 66
DFF + + G ++ E+NT P G+ +S +W A +I+ +
Sbjct: 318 DFF------LTDDGPVINEINTMP---GFTTISMYPRMWAASGVDYPTLLATMIETTLAR 368
Query: 67 H 67
Sbjct: 369 G 369
>3se7_A VANA; alpha-beta structure, D-alanine-D-lactate ligase, ligase;
HET: ATP; 3.07A {}
Length = 346
Score = 30.6 bits (70), Expect = 0.15
Identities = 15/64 (23%), Positives = 21/64 (32%), Gaps = 16/64 (25%)
Query: 13 DFFARKGNPIEETGDLVA-EVNTRPDEAGYDPVS--STLWRQR----EEYCARLIQHAWR 65
D F + E G +V EVNT P G S + + RL+ A
Sbjct: 292 DLF------LTEDGKVVLNEVNTFP---GMTSYSRYPRMMTAAGLSRADVIDRLVSLALA 342
Query: 66 KHKQ 69
+
Sbjct: 343 GKSR 346
>2vns_A Metalloreductase steap3; metal-binding, transmembrane, rossmann
fold, transport, cell cycle, transferrin, flavoprotein,
alternative splicing; HET: CIT; 2.0A {Homo sapiens} PDB:
2vq3_A*
Length = 215
Score = 28.4 bits (63), Expect = 0.66
Identities = 8/22 (36%), Positives = 15/22 (68%)
Query: 99 IKNGHRVVIHSRSPSQTSRSAE 120
+ +G +VV+ SR+P +T+R
Sbjct: 48 VGSGFKVVVGSRNPKRTARLFP 69
>1zwx_A SMCL, sphingomyelinase-C; dnase1-like fold, beta-hairpin,
hydrolase; 1.90A {Listeria ivanovii} SCOP: d.151.1.3
Length = 301
Score = 28.5 bits (63), Expect = 0.85
Identities = 22/127 (17%), Positives = 39/127 (30%), Gaps = 10/127 (7%)
Query: 4 VDILDALTKDFFARKGNPIEETGDLVAEVNTRPDEAGYDPVSSTLWRQREEYCARLIQHA 63
+ + K I GDL N Y + L
Sbjct: 172 MQEIQTFIAKKNIPKDEIIFIGGDL----NVNYGTDEYHDMLKLLNVSSPANFNG-QMAT 226
Query: 64 WRKHKQCRAGGTEPGSPGSPDGR-DTAVLVESDGFSIKNGHRVVIHSRSPSQTSRSAECL 122
W + P + D + VE+ + H V+H++SP + +S
Sbjct: 227 WDPTTNSMLKESYPKAAPE---YLDY-IFVENGHARPHSWHNKVLHTKSPQWSVKSWFKT 282
Query: 123 FSFKDFS 129
++++DFS
Sbjct: 283 YTYQDFS 289
>2kxw_B Sodium channel protein type 2 subunit alpha; action potential,
amino acid motifs, animals, autism, biomol brain
chemistry; NMR {Rattus norvegicus}
Length = 27
Score = 25.7 bits (56), Expect = 0.90
Identities = 8/23 (34%), Positives = 15/23 (65%)
Query: 50 RQREEYCARLIQHAWRKHKQCRA 72
R++EE A +IQ A+R++ +
Sbjct: 2 RKQEEVSAIVIQRAYRRYLLKQK 24
>3dtt_A NADP oxidoreductase; structural genomics, joint center for
structural genomics, J protein structure initiative,
PSI-2; HET: NAP; 1.70A {Arthrobacter SP}
Length = 245
Score = 28.1 bits (62), Expect = 0.99
Identities = 9/22 (40%), Positives = 10/22 (45%)
Query: 99 IKNGHRVVIHSRSPSQTSRSAE 120
GH V I +R P T AE
Sbjct: 39 ADLGHEVTIGTRDPKATLARAE 60
>2rb7_A Peptidase, M20/M25/M40 family; YP_387682.1, CO-catalytic
metallopeptidase, peptidase family M20/M25/M40,
structural genomics; HET: MSE PGE PG4; 1.60A
{Desulfovibrio desulfuricans subsp}
Length = 364
Score = 27.6 bits (62), Expect = 1.5
Identities = 5/29 (17%), Positives = 10/29 (34%)
Query: 20 NPIEETGDLVAEVNTRPDEAGYDPVSSTL 48
N ++ + + T E D T+
Sbjct: 199 NAVDLLMEDYTRLKTLFAEENEDHWHRTV 227
>3h4r_A Exodeoxyribonuclease 8; exonuclease, recombination, hydrolase;
2.80A {Escherichia coli}
Length = 265
Score = 27.6 bits (60), Expect = 1.6
Identities = 5/47 (10%), Positives = 11/47 (23%)
Query: 32 VNTRPDEAGYDPVSSTLWRQREEYCARLIQHAWRKHKQCRAGGTEPG 78
+T + Y + + + + R C P
Sbjct: 203 ASTTIECGRYPVEIFMMGEEAKLAGQQEYHRNLRTLSDCLNTDEWPA 249
>2yjz_A Metalloreductase steap4; oxidoreductase, metabolic syndrome; HET:
NAP; 2.20A {Rattus norvegicus}
Length = 201
Score = 27.3 bits (60), Expect = 1.7
Identities = 7/22 (31%), Positives = 12/22 (54%)
Query: 99 IKNGHRVVIHSRSPSQTSRSAE 120
++ G+ VV SR+P +S
Sbjct: 39 LQCGYSVVFGSRNPQVSSLLPR 60
>1r9w_A Replication protein E1; HPV-18, DNA-binding domain, viral
replication, initiator protein; 1.80A {Human
papillomavirus type 18} SCOP: d.89.1.2
Length = 145
Score = 26.9 bits (60), Expect = 2.0
Identities = 10/31 (32%), Positives = 13/31 (41%), Gaps = 5/31 (16%)
Query: 121 CLFSFKDFSMGKWAYLCLL-----CGKNRET 146
L++ KW L L CGK+R T
Sbjct: 57 ILYAHIQCLDCKWGVLILALLRYKCGKSRLT 87
>1f08_A Replication protein E1; DNA-binding domain, initiator protein,
helicase; 1.90A {Bovine papillomavirus} SCOP: d.89.1.2
PDB: 1ksx_A 1ksy_A
Length = 148
Score = 26.6 bits (59), Expect = 2.5
Identities = 6/31 (19%), Positives = 9/31 (29%), Gaps = 5/31 (16%)
Query: 121 CLFSFKDFSMGKWAYLCLL-----CGKNRET 146
C F + + K+RET
Sbjct: 60 CSFLQMQKRSHEGGTCAVYLICFNTAKSRET 90
>2l53_B CAM, voltage-gated sodium channel type V alpha isoform variant;
calmodulin, IQ motif, complex, Ca-binding protein; NMR
{Homo sapiens}
Length = 31
Score = 24.6 bits (53), Expect = 3.0
Identities = 9/20 (45%), Positives = 13/20 (65%)
Query: 53 EEYCARLIQHAWRKHKQCRA 72
EE A +IQ A+R+H R+
Sbjct: 5 EEVSAMVIQRAFRRHLLQRS 24
>2kav_A Sodium channel protein type 2 subunit alpha; voltage-gated sodium
channel, alternative splicing, disease epilepsy,
glycoprotein, ION transport; NMR {Homo sapiens} PDB:
2kbi_A
Length = 129
Score = 25.9 bits (57), Expect = 3.5
Identities = 8/20 (40%), Positives = 10/20 (50%)
Query: 1 MFCVDILDALTKDFFARKGN 20
+ C+DIL A TK G
Sbjct: 99 IHCLDILFAFTKRVLGESGE 118
>3bqa_A Sensor protein PHOQ; histidine kinase sensor domain, ATP-binding,
inner membrane, magnesium, membrane, metal-binding,
nucleotide-binding; 2.00A {Escherichia coli} PDB:
3bq8_A 1yax_A
Length = 148
Score = 26.0 bits (57), Expect = 3.6
Identities = 10/27 (37%), Positives = 14/27 (51%), Gaps = 1/27 (3%)
Query: 41 YDPVSSTLWRQRE-EYCARLIQHAWRK 66
YD LW QR+ + ++IQ W K
Sbjct: 47 YDENGQLLWAQRDVPWLMKMIQPDWLK 73
>1yae_A Glutamate receptor, ionotropic kainate 2; kainate receptor,
membrane protein; HET: NAG FUC DOQ; 3.11A {Rattus
norvegicus} SCOP: c.94.1.1
Length = 312
Score = 26.3 bits (57), Expect = 4.5
Identities = 11/64 (17%), Positives = 24/64 (37%), Gaps = 13/64 (20%)
Query: 2 FCVDILDALTKDF----------FARKGNPIEETG---DLVAEVNTRPDEAGYDPVSSTL 48
+C+D+L L+ + G + G +V E+ + P++ T
Sbjct: 44 YCIDLLRELSTILGFTYEIRLVEDGKYGAQDDVNGQWNGMVRELIDHKADLAVAPLAITY 103
Query: 49 WRQR 52
R++
Sbjct: 104 VREK 107
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT,
cytoplasmic vesicle, membrane, Ca structural protein;
7.94A {Bos taurus}
Length = 190
Score = 25.9 bits (56), Expect = 4.6
Identities = 9/26 (34%), Positives = 11/26 (42%), Gaps = 2/26 (7%)
Query: 34 TRPDEAGYDPVSSTLWRQREEYCARL 59
+ D +P S W REE RL
Sbjct: 75 AQADRLTQEPESIRKW--REEQRKRL 98
>2v3u_A Glutamate receptor delta-2 subunit; postsynaptic membrane,
ionotropic glutamate receptors, transmembrane, membrane
protein; 1.74A {Rattus norvegicus} PDB: 2v3t_A
Length = 265
Score = 26.2 bits (57), Expect = 4.7
Identities = 6/12 (50%), Positives = 9/12 (75%)
Query: 2 FCVDILDALTKD 13
F +D+LDAL+
Sbjct: 32 FSIDVLDALSNY 43
>4dvk_A E(RNS) glycoprotein; T2 ribonuclease, virus envelope
glycoprotein, viral protein; HET: NAG BMA MAN; 2.21A
{Bovine viral diarrhea virus} PDB: 4dw5_A* 4dvl_A*
4dvn_A* 4dw3_A* 4dw4_A* 4dwc_A* 4dwa_A* 4dw7_A*
Length = 165
Score = 25.9 bits (56), Expect = 5.4
Identities = 10/22 (45%), Positives = 11/22 (50%)
Query: 56 CARLIQHAWRKHKQCRAGGTEP 77
C RL +H W KH C EP
Sbjct: 68 CCRLQRHEWNKHGWCNWYNIEP 89
>3g3k_A Glutamate receptor, ionotropic kainate 2; membrane protein, cell
junction, cell membrane, glycoprotein, ION transport,
ionic channel, membrane; HET: GLU IPA; 1.24A {Rattus
norvegicus} PDB: 3g3j_A* 3g3i_A* 2i0b_A* 3g3h_A*
3g3g_A* 3g3f_A* 1s7y_A* 1s9t_A* 1sd3_A* 1tt1_A* 1s50_A*
2xxr_A* 2xxt_A* 2xxx_A* 2xxw_A* 2xxy_A* 2xxu_A* 2xxv_A*
3qxm_A* 2i0c_A* ...
Length = 259
Score = 25.7 bits (56), Expect = 5.8
Identities = 4/12 (33%), Positives = 8/12 (66%)
Query: 2 FCVDILDALTKD 13
+C+D+L L+
Sbjct: 35 YCIDLLRELSTH 46
>2a5s_A N-methyl-D-aspartate receptor nmdar2A subunit, NMDA receptor
nmdar2A; protein-ligand complex, metal
transport,membrane protein; HET: GLU; 1.70A {Rattus
norvegicus} SCOP: c.94.1.1 PDB: 2a5t_B* 3oen_A* 3oel_A*
3oem_A* 3oek_A*
Length = 284
Score = 25.8 bits (56), Expect = 6.7
Identities = 6/12 (50%), Positives = 9/12 (75%)
Query: 2 FCVDILDALTKD 13
FC+DIL L++
Sbjct: 60 FCIDILKKLSRT 71
>2ix7_C Myosin-5A; contractIle protein/metal binding, actin-binding, UBL
conjugation, Ca2+ regulation, myosin, calcium, IQ
motif, acetylation; 2.5A {Mus musculus}
Length = 58
Score = 24.1 bits (53), Expect = 6.8
Identities = 6/28 (21%), Positives = 10/28 (35%), Gaps = 5/28 (17%)
Query: 49 WRQREEY-----CARLIQHAWRKHKQCR 71
W R+ Y A +Q R ++
Sbjct: 18 WLLRKRYLCMQRAAITVQRYVRGYQARC 45
>1mqi_A Glutamate receptor 2; GLUR2, ligand binding core, S1S2, partial
agonist, WILLARDIINES, fluoro-WILLARDIINE, membrane
protein; HET: FWD; 1.35A {Rattus norvegicus} SCOP:
c.94.1.1 PDB: 1ftj_A* 1ftl_A* 1fto_A 1fw0_A* 1m5b_A*
1ftm_A* 1m5c_A* 1mm6_A* 1mm7_A* 1mqg_A* 1m5e_A* 1mqj_A*
1ms7_A* 1mxu_A* 1mxv_A 1mxw_A 1mxx_A 1mxy_A 1mxz_A
1my0_A ...
Length = 263
Score = 25.4 bits (55), Expect = 7.7
Identities = 4/12 (33%), Positives = 7/12 (58%)
Query: 2 FCVDILDALTKD 13
+CVD+ + K
Sbjct: 35 YCVDLAAEIAKH 46
>1pb7_A N-methyl-D-aspartate receptor subunit 1; ligand binding receptor,
NR1, ligand binding protein; 1.35A {Rattus norvegicus}
SCOP: c.94.1.1 PDB: 1pbq_A* 1y1m_A 1y1z_A 1y20_A
2a5t_A* 1pb8_A 1pb9_A
Length = 292
Score = 25.4 bits (55), Expect = 8.4
Identities = 5/12 (41%), Positives = 8/12 (66%)
Query: 2 FCVDILDALTKD 13
FC+D+L L +
Sbjct: 66 FCIDLLIKLART 77
>4e21_A 6-phosphogluconate dehydrogenase (decarboxylating; structural
genomics, PSI-biology, NEW YORK structural genomi
research consortium; 2.30A {Geobacter metallireducens}
Length = 358
Score = 25.4 bits (56), Expect = 8.8
Identities = 4/22 (18%), Positives = 8/22 (36%)
Query: 99 IKNGHRVVIHSRSPSQTSRSAE 120
K GH V++ + +
Sbjct: 42 RKGGHECVVYDLNVNAVQALER 63
>3sxu_A DNA polymerase III subunit CHI; DNA replication, CHI binds to SSB
and PSI, transferase; HET: DNA; 1.85A {Escherichia coli}
PDB: 1em8_A*
Length = 150
Score = 24.9 bits (54), Expect = 9.1
Identities = 9/33 (27%), Positives = 14/33 (42%)
Query: 98 SIKNGHRVVIHSRSPSQTSRSAECLFSFKDFSM 130
++G RV+I Q R E L++ S
Sbjct: 35 RWRSGKRVLIACEDEKQAYRLDEALWARPAESF 67
>3cmg_A Putative beta-galactosidase; structural genomics, PSI-2, Pro
structure initiative, NEW YORK SGX research center for
STRU genomics, nysgxrc; 1.90A {Bacteroides fragilis}
Length = 667
Score = 25.4 bits (56), Expect = 9.7
Identities = 10/74 (13%), Positives = 17/74 (22%), Gaps = 14/74 (18%)
Query: 24 ETGDLVAEVNTRPDEAGYDPVSSTLWRQREEYCARLIQHAW---RKHKQCRAG------- 73
E G A + + S++ W E + W +
Sbjct: 476 EYG---AGASIYHQQDSLKQPSASGWWHPENWQTYYHMENWKIIAERPFVWGTFVWNMFD 532
Query: 74 -GTEPGSPGSPDGR 86
G + G G
Sbjct: 533 FGAAHRTEGDRPGI 546
>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 = 25.4 bits (55), Expect = 9.8
Identities = 13/84 (15%), Positives = 24/84 (28%), Gaps = 25/84 (29%)
Query: 5 DILDALTKDFFARKGNPIEETG-DLVA---EVNTRPDEAGY---DPVS---STLWRQREE 54
+ L L + + G +++ + PD+ Y P+S + Q
Sbjct: 193 ETLSELIRT--TLDAEKVFTQGLNILEWLENPSNTPDKD-YLLSIPISCPLIGVI-QLAH 248
Query: 55 YCARLIQHAWRKHKQCRAGGTEPG 78
Y + G PG
Sbjct: 249 YVV-----------TAKLLGFTPG 261
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 0.134 0.425
Gapped
Lambda K H
0.267 0.0715 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,332,611
Number of extensions: 130572
Number of successful extensions: 366
Number of sequences better than 10.0: 1
Number of HSP's gapped: 365
Number of HSP's successfully gapped: 41
Length of query: 147
Length of database: 6,701,793
Length adjustment: 85
Effective length of query: 62
Effective length of database: 4,328,508
Effective search space: 268367496
Effective search space used: 268367496
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: 53 (24.2 bits)