RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy5133
(313 letters)
>1d4u_A Nucleotide excision repair protein XPA (XPA-MBD); DNA repair,
loop-rich domain, relaxation, DNA binding protein; NMR
{Homo sapiens} SCOP: a.6.1.2 g.39.1.5 PDB: 1xpa_A
Length = 111
Score = 145 bits (367), Expect = 5e-44
Identities = 62/110 (56%), Positives = 81/110 (73%)
Query: 128 LESEQPTCVECKKKFPQSFLYDKFGHSVCDSCRDGESKHCLVTRTDAKNEYLLKDCDLDK 187
+E + C EC K+F S+L D F CD CRD + KH L+T+T+AK EYLLKDCDL+K
Sbjct: 1 MEFDYVICEECGKEFMDSYLMDHFDLPTCDDCRDADDKHKLITKTEAKQEYLLKDCDLEK 60
Query: 188 REPVLRFLRAKNPHNKHWGDMKLYLSLQVEQRAIEVWGSEEELEQERERR 237
REP L+F+ KNPH+ WGDMKLYL LQ+ +R++EVWGS+E LE+ +E R
Sbjct: 61 REPPLKFIVKKNPHHSQWGDMKLYLKLQIVKRSLEVWGSQEALEEAKEVR 110
>2enk_A HUEL, solute carrier family 30 member 9; cation transporter,
cobalt, zinc, cadmium, protein of unknown function
DUF993, embryonic LUNG protein; NMR {Homo sapiens}
Length = 101
Score = 99.2 bits (247), Expect = 2e-26
Identities = 30/99 (30%), Positives = 51/99 (51%), Gaps = 6/99 (6%)
Query: 159 CRDGESKHCLVTRTDAKNEYLLKDCDLDKREPVLRFLRAKNPHNKHWGDMKLYLSLQVEQ 218
+++ +T A NE+ LK DL++ LR +R ++PH +YL VE
Sbjct: 5 SSGKYTQNNFITGVRAINEFCLKSSDLEQ----LRKIRRRSPHED-TESFTVYLRSDVEA 59
Query: 219 RAIEVWGSEEELEQERERRAEKASNSKLKQYNKKIKALR 257
+++EVWGS E L +E++ R E + + + + K LR
Sbjct: 60 KSLEVWGSPEALAREKKLRKEAEIEYRERLFRNQ-KILR 97
>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 = 68.2 bits (166), Expect = 9e-13
Identities = 69/346 (19%), Positives = 110/346 (31%), Gaps = 97/346 (28%)
Query: 17 ISLSAMQKEQIERNRQRAIQIQQTRTRD----LYDPYPNPVKAGVRQTASAPSSCP---- 68
I SA ++ R A ++ T+ + L +P P S P SCP
Sbjct: 188 IKFSAETLSELIRTTLDAEKVF-TQGLNILEWLENPSNTP---DKDYLLSIPISCPLIGV 243
Query: 69 -QSPNLRSTTRLGGARSPGTIRSIINAVGSKLFTDTGGGFLL--------DYDDKYE--E 117
Q + T +L G +PG +RS + T G + ++ +
Sbjct: 244 IQLAHYVVTAKLLG-FTPGELRSYLKGA-----TGHSQGLVTAVAIAETDSWESFFVSVR 297
Query: 118 KYIKQPAPLLLESEQPTCVECKKKFPQSFLYDKFGHSVCDSCRDGESKHCLVTRTDAKNE 177
K I +L V C + +P + L + DS + E
Sbjct: 298 KAIT----VLFFIG----VRCYEAYPNTSLPPSI---LEDSLENNEGVPS---------- 336
Query: 178 YLLKDCDLDKREPVLRFLRAKN---PHNKHWGDMKLYLSLQVEQRAIEVWGSEEELEQ-E 233
+L +L +E V ++ N P K + +SL + + V G + L
Sbjct: 337 PMLSISNLT-QEQVQDYVNKTNSHLPAGKQ-----VEISLVNGAKNLVVSGPPQSLYGLN 390
Query: 234 RERRAEKASNSKLKQYNKKIKALRMAVR-SSLFNKISTSPSSHSH--------------- 277
R KA S L Q +I ++ S+ F + SP HSH
Sbjct: 391 LTLRKAKAP-SGLDQ--SRIPFSERKLKFSNRFLPV-ASP-FHSHLLVPASDLINKDLVK 445
Query: 278 --------QFGMEVHNEEDDTYT----RKCSTCDFEETFEKIFRLH 311
+ V+ DT+ R S E + I RL
Sbjct: 446 NNVSFNAKDIQIPVY----DTFDGSDLRVLSGSISERIVDCIIRLP 487
>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 = 51.0 bits (121), Expect = 3e-07
Identities = 25/130 (19%), Positives = 45/130 (34%), Gaps = 17/130 (13%)
Query: 142 FPQSFLYDKFGHSVCDSCR----DGESKHCLVTRTDAKNEYLLKDCDLDKREP-VLRFLR 196
F +F+ + V D + E H ++++ L L K+E V +F+
Sbjct: 25 FEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQKFVE 84
Query: 197 AKNPHNKHWGDMKLYLSLQVEQRAIEVWGSEEELEQERERRAEKASNSKLKQYN----KK 252
N + L ++ EQR ++R+R N +YN +
Sbjct: 85 EVLRINYKF----LMSPIKTEQRQPS--MMTRMYIEQRDRLYN--DNQVFAKYNVSRLQP 136
Query: 253 IKALRMAVRS 262
LR A+
Sbjct: 137 YLKLRQALLE 146
Score = 40.6 bits (94), Expect = 5e-04
Identities = 32/164 (19%), Positives = 55/164 (33%), Gaps = 33/164 (20%)
Query: 89 RSIINAVGSKLFTDTGGGFLLDYDDKYEEKYIKQPAPLLLESEQPTCVECKKKFPQ---- 144
RSI++ D + Y D+Y +I L E P E F
Sbjct: 447 RSIVDHYNIPKTFD-SDDLIPPYLDQYFYSHI---GHHLKNIEHP---ERMTLFRMVFLD 499
Query: 145 -SFLYDKFGHSVCDSCRDGESKHCLVTRTDAKN--EYLLKDCDLDKR--EPVLRFLRAKN 199
FL K H G + L K Y+ + +R +L FL
Sbjct: 500 FRFLEQKIRHDSTAWNASGSILNTL---QQLKFYKPYICDNDPKYERLVNAILDFLPKIE 556
Query: 200 PH---NKHWGDMKLYLSLQVEQRAIEVWGSEEELEQERERRAEK 240
+ +K+ D+ L ++L E +E + +E ++ ++
Sbjct: 557 ENLICSKY-TDL-LRIALMAE---------DEAIFEEAHKQVQR 589
Score = 33.7 bits (76), Expect = 0.090
Identities = 35/246 (14%), Positives = 63/246 (25%), Gaps = 73/246 (29%)
Query: 76 TTRLGGARSPGTIRSIINAVGSKLFT-----DTGGGFLLDYDDKYEEKYIKQPA------ 124
TTR + + + + + T D KY+
Sbjct: 271 TTR---------FKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPRE 321
Query: 125 -----PLLLESEQPTCVECKKKFP------QSFLYDKFGHSVCDSCRD----GESKHCL- 168
P L E + + DK + +S + E +
Sbjct: 322 VLTTNPRRLS----IIAESIRDGLATWDNWKHVNCDKLTTII-ESSLNVLEPAEYRKMFD 376
Query: 169 ---VTRTDAK-NEYLLKD--CDLDKREP-------VLRFLRAKNPHNKHWGDMKLYLSLQ 215
V A LL D+ K + L K P +YL L+
Sbjct: 377 RLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELK 436
Query: 216 VEQRAIEVWGSEEELEQ---ERERRAEKA-SNSKLKQYNKK---------IKALRMAVRS 262
V+ +E L + + + S+ + Y + +K + R
Sbjct: 437 VKLE------NEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERM 490
Query: 263 SLFNKI 268
+LF +
Sbjct: 491 TLFRMV 496
>3k1f_M Transcription initiation factor IIB; RNA polymerase II, TFIIB,
transcription factor, DNA-binding, DNA-directed RNA
polymerase; 4.30A {Saccharomyces cerevisiae}
Length = 197
Score = 33.1 bits (75), Expect = 0.059
Identities = 10/31 (32%), Positives = 12/31 (38%), Gaps = 2/31 (6%)
Query: 130 SEQPTCVECKKKFPQSFLYD-KFGHSVCDSC 159
+ TC ECK P + G VC C
Sbjct: 19 NIVLTCPECKVY-PPKIVERFSEGDVVCALC 48
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 30.5 bits (68), Expect = 0.41
Identities = 8/62 (12%), Positives = 22/62 (35%), Gaps = 12/62 (19%)
Query: 214 LQVEQRAIEVWGSEEELEQERERRAEKASNSKLK------------QYNKKIKALRMAVR 261
L E +I W E+ + A K + + + +++++ ++ R
Sbjct: 80 LTQEPESIRKWREEQRKRLQELDAASKVMEQEWREKAKKDLEEWNQRQSEQVEKNKINNR 139
Query: 262 SS 263
+
Sbjct: 140 IA 141
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna; HET:
CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 29.9 bits (66), Expect = 0.67
Identities = 8/30 (26%), Positives = 17/30 (56%), Gaps = 1/30 (3%)
Query: 235 ERRAEKASNSKLKQYNKKIKALRMAVRSSL 264
E++A K + LK Y A +A+++++
Sbjct: 18 EKQALKKLQASLKLYADD-SAPALAIKATM 46
Score = 29.5 bits (65), Expect = 0.72
Identities = 7/38 (18%), Positives = 15/38 (39%), Gaps = 12/38 (31%)
Query: 23 QKEQIERNRQRAIQIQQTRTRDLYDPYPNP---VKAGV 57
+K+ +++ Q + LY P +KA +
Sbjct: 18 EKQALKK--------LQASLK-LYADDSAPALAIKATM 46
>2ogt_A Thermostable carboxylesterase EST50; alpha/beta hydrolase,
hydrolase; 1.58A {Geobacillus stearothermophilus} PDB:
2ogs_A
Length = 498
Score = 30.7 bits (70), Expect = 0.70
Identities = 10/38 (26%), Positives = 13/38 (34%), Gaps = 2/38 (5%)
Query: 50 PNPVKA--GVRQTASAPSSCPQSPNLRSTTRLGGARSP 85
P P A GVR+ S Q + + LG
Sbjct: 42 PEPPDAWDGVREATSFGPVVMQPSDPIFSGLLGRMSEA 79
>2hin_A GP39, repressor protein; transcription factor, dimer interface,
helix-turn-helix; 1.05A {Enterobacteria phage N15} PDB:
3qws_A
Length = 71
Score = 27.4 bits (60), Expect = 1.6
Identities = 13/46 (28%), Positives = 22/46 (47%), Gaps = 1/46 (2%)
Query: 203 KHWGDM-KLYLSLQVEQRAIEVWGSEEELEQERERRAEKASNSKLK 247
+H+GD+ K + + V A+ W E+ R+ E + KLK
Sbjct: 8 RHFGDVEKAAVGVGVTPGAVYQWLQAGEIPPLRQSDIEVRTAYKLK 53
>1x63_A Skeletal muscle LIM-protein 1; LIM domain, four and A half LIM
domains protein 1, structural genomics, NPPSFA; NMR
{Homo sapiens} SCOP: g.39.1.3 g.39.1.3
Length = 82
Score = 26.9 bits (60), Expect = 2.4
Identities = 7/26 (26%), Positives = 10/26 (38%)
Query: 134 TCVECKKKFPQSFLYDKFGHSVCDSC 159
TC CK+ + K C +C
Sbjct: 45 TCSNCKQVIGTGSFFPKGEDFYCVTC 70
>1fcq_A Hyaluronoglucosaminidase; 7-stranded (beta/alpha) TIM barrel,
glycosidase family 56, allergen, hydrolase; 1.60A {Apis
mellifera} SCOP: c.1.8.9 PDB: 1fcu_A 1fcv_A* 2j88_A
Length = 350
Score = 28.3 bits (63), Expect = 3.2
Identities = 17/55 (30%), Positives = 30/55 (54%), Gaps = 3/55 (5%)
Query: 205 WGDMKLY--LSLQVEQRAIEVWGSEEELEQERERRAEKASNSKLKQYNKKIKALR 257
W ++ Y LS++V +R W ++ +EQE +RR EK +++ K K +R
Sbjct: 123 WASLQPYKKLSVEVVRREHPFW-DDQRVEQEAKRRFEKYGQLFMEETLKAAKRMR 176
>2oln_A NIKD protein; flavoprotein, rossmann fold, oxidoreductase; HET:
FAD; 1.15A {Streptomyces tendae} PDB: 2olo_A* 3hzl_A*
2q6u_A*
Length = 397
Score = 28.2 bits (63), Expect = 3.5
Identities = 10/62 (16%), Positives = 21/62 (33%), Gaps = 4/62 (6%)
Query: 95 VGSKLFTDTGGGFLLDYDDKYEEKYIKQPAPLL----LESEQPTCVECKKKFPQSFLYDK 150
+L + G + D D E I A ++ + E + +++F L
Sbjct: 79 CERRLIHEIGSLWFGDTDVVTNEGQISGTAAMMDKLSVRYEWLKATDIERRFGFRGLPRD 138
Query: 151 FG 152
+
Sbjct: 139 YE 140
>2y69_K Cytochrome C oxidase polypeptide 7B; electron transport, complex
IV, proton pumps, membrane prote; HET: TPO HEA CHD PEK
PGV DMU; 1.95A {Bos taurus}
Length = 80
Score = 26.5 bits (58), Expect = 3.9
Identities = 14/39 (35%), Positives = 21/39 (53%), Gaps = 2/39 (5%)
Query: 18 SLSAMQKEQIERNRQRAIQIQQTRTRDLYDPYPNPVKAG 56
+LS ++ + I++ R QI Q R D +D Y N V A
Sbjct: 8 ALSRLRVQSIQQAVAR--QIHQKRAPDFHDKYGNAVLAS 44
>1v6g_A Actin binding LIM protein 2; LIM domain, zinc binding domain,
ablim2, structural genomics, riken structural
genomics/proteomics initiative, RSGI; NMR {Homo sapiens}
SCOP: g.39.1.3 g.39.1.3
Length = 81
Score = 26.3 bits (58), Expect = 4.8
Identities = 6/27 (22%), Positives = 9/27 (33%), Gaps = 1/27 (3%)
Query: 134 TCVECKKKFP-QSFLYDKFGHSVCDSC 159
C C+ FP + +C C
Sbjct: 43 VCAVCRLPFPPGDRVTFNGKECMCQKC 69
>1qe3_A PNB esterase, para-nitrobenzyl esterase; alpha-beta hydrolase
directed evolution; 1.50A {Bacillus subtilis} SCOP:
c.69.1.1 PDB: 1c7j_A 1c7i_A
Length = 489
Score = 28.0 bits (63), Expect = 4.9
Identities = 7/26 (26%), Positives = 10/26 (38%), Gaps = 2/26 (7%)
Query: 50 PNPVKA--GVRQTASAPSSCPQSPNL 73
P P + V + CPQ +L
Sbjct: 42 PEPPEVWEDVLDATAYGPICPQPSDL 67
>2p5i_A BH3822 protein; PFAM03099, structural genomics, PSI-2, protein
structure initiative, NEW YORK structural genomix
research consortium; 2.21A {Bacillus halodurans c-125}
SCOP: d.104.1.3
Length = 288
Score = 27.6 bits (61), Expect = 5.1
Identities = 6/26 (23%), Positives = 9/26 (34%)
Query: 174 AKNEYLLKDCDLDKREPVLRFLRAKN 199
A ++ L + P LR N
Sbjct: 34 AYDDTLCTSIGKSQSPPTLRAWVHHN 59
>2d8x_A Protein pinch; LIM domain, pinch protein, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens} SCOP: g.39.1.3
g.39.1.3
Length = 70
Score = 25.9 bits (57), Expect = 5.1
Identities = 5/26 (19%), Positives = 8/26 (30%)
Query: 134 TCVECKKKFPQSFLYDKFGHSVCDSC 159
C C++ G +C C
Sbjct: 33 RCDLCQEVLADIGFVKNAGRHLCRPC 58
>1mr1_C SKI oncogene, SKI, C-SKI; SMAD, cancer, TGF-B signaling, protein
interaction, signaling protein; 2.85A {Homo sapiens}
SCOP: d.217.1.2
Length = 99
Score = 26.4 bits (58), Expect = 5.7
Identities = 21/91 (23%), Positives = 32/91 (35%), Gaps = 22/91 (24%)
Query: 125 PLLLESEQPTCV---ECKKKF-PQSFLYDKFGHSVCDSCRDGESKHCLVTRTDAKN--EY 178
P L S C+ +C+ + P F V S + E++ C D+ N Y
Sbjct: 20 PELYSSPSAACIQCLDCRLMYPPHKF--------VVHSHKALENRTCHW-GFDSANWRAY 70
Query: 179 LLKDCDLDKREPVLRFLRAKNPHNKHWGDMK 209
+L D +E R R D+K
Sbjct: 71 ILLSQDYTGKEEQARLGRC-------LDDVK 94
>1ted_A PKS18; thiolase fold, substrate binding tunnel, transferase; HET:
MYR; 2.25A {Mycobacterium tuberculosis} SCOP: c.95.1.2
PDB: 1tee_A
Length = 393
Score = 27.7 bits (62), Expect = 5.9
Identities = 6/37 (16%), Positives = 13/37 (35%), Gaps = 3/37 (8%)
Query: 61 ASAPSSCPQSPNLRSTTRLGGARSPGTIRSIINAVGS 97
+ AP Q + +P T ++I + +
Sbjct: 7 SGAPRRAGQRHEVGLAQL---PPAPPTTVAVIEGLAT 40
>2p0l_A Lipoate-protein ligase A; PFAM, lopoate-protein ligase A, 10425H,
structural genomics, structure initiative, PSI-2; 2.04A
{Streptococcus agalactiae} SCOP: d.104.1.3
Length = 288
Score = 27.3 bits (60), Expect = 6.2
Identities = 4/26 (15%), Positives = 9/26 (34%)
Query: 174 AKNEYLLKDCDLDKREPVLRFLRAKN 199
E L++ + +E +L
Sbjct: 31 IWTEVFLREINRSNQEIILHIWPMTK 56
>2nsa_A Trigger factor, TF; chaperone; 1.70A {Thermotoga maritima}
Length = 170
Score = 26.6 bits (59), Expect = 7.3
Identities = 16/63 (25%), Positives = 30/63 (47%), Gaps = 6/63 (9%)
Query: 209 KLYLSLQ--VEQRAIEVWGSEEELEQERERRAE--KASNSKLKQYNKKIKALRMAVRSSL 264
K ++ +++ I V ++EELE+E E A S + K K + LR +R ++
Sbjct: 93 KRDRVIEVLAQEKGISV--NDEELEKEAEELAPFWGISPDRAKSLVKARQDLREELRWAI 150
Query: 265 FNK 267
+
Sbjct: 151 LKR 153
>1x61_A Thyroid receptor interacting protein 6; LIM domain, OPA-interacting
protein 1, zyxin related protein 1 (ZRP-1), structural
genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3
g.39.1.3
Length = 72
Score = 25.5 bits (56), Expect = 7.8
Identities = 5/26 (19%), Positives = 9/26 (34%)
Query: 134 TCVECKKKFPQSFLYDKFGHSVCDSC 159
C C+ + Y + C+ C
Sbjct: 35 VCSTCRAQLRGQHFYAVERRAYCEGC 60
>1x3h_A Leupaxin; paxillin family, protein-protein interaction, LIM domain,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
g.39.1.3 g.39.1.3
Length = 80
Score = 25.4 bits (56), Expect = 8.1
Identities = 5/26 (19%), Positives = 9/26 (34%)
Query: 134 TCVECKKKFPQSFLYDKFGHSVCDSC 159
C +C F ++ G C+
Sbjct: 43 VCGDCFTSFSTGSFFELDGRPFCELH 68
>1u5k_A Hypothetical protein; OBD-fold, Zn-binding,
recombination,replication; 2.00A {Deinococcus
radiodurans} SCOP: b.40.4.13 g.45.1.2 PDB: 1w3s_A 2v1c_C
Length = 244
Score = 26.7 bits (59), Expect = 8.2
Identities = 6/30 (20%), Positives = 8/30 (26%), Gaps = 1/30 (3%)
Query: 135 CVECKKKFPQSFLYDKFGHSVCDSCRDGES 164
C C P+ G +C C
Sbjct: 153 CARCGAPDPEHP-DPLGGQLLCSKCAALPP 181
>3bk6_A PH stomatin; archaea, trimer, coiled- coil, flotillin, SPFH,
membrane fusion, trafficking, transmembrane, membrane
protein; 3.20A {Pyrococcus horikoshii}
Length = 188
Score = 26.4 bits (59), Expect = 9.5
Identities = 12/38 (31%), Positives = 19/38 (50%), Gaps = 12/38 (31%)
Query: 218 QRAIEVWGSEEELEQERERRA-------EKASNSKLKQ 248
Q+A+ + E ERERRA E+ + KL++
Sbjct: 119 QKAMA-----RQAEAERERRARITLAEAERQAAEKLRE 151
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
0.315 0.130 0.380
Gapped
Lambda K H
0.267 0.0586 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 4,547,273
Number of extensions: 258073
Number of successful extensions: 935
Number of sequences better than 10.0: 1
Number of HSP's gapped: 915
Number of HSP's successfully gapped: 47
Length of query: 313
Length of database: 6,701,793
Length adjustment: 93
Effective length of query: 220
Effective length of database: 4,105,140
Effective search space: 903130800
Effective search space used: 903130800
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 57 (26.0 bits)