RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy14272
(194 letters)
>4a15_A XPD helicase, ATP-dependent DNA helicase TA0057; hydrolase,
nucleotide excision repair,; 2.20A {Thermoplasma
acidophilum} PDB: 2vsf_A*
Length = 620
Score = 53.9 bits (130), Expect = 5e-09
Identities = 15/74 (20%), Positives = 30/74 (40%), Gaps = 9/74 (12%)
Query: 29 FDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKW---------YYDHKI 79
++ Q + L +L S ESPTG+GK++ + L++ Y
Sbjct: 2 YENRQYQVEAIDFLRSSLQKSYGVALESPTGSGKTIMALKSALQYSSERKLKVLYLVRTN 61
Query: 80 VGLEKIEAKIKDLE 93
E++ +++ L
Sbjct: 62 SQEEQVIKELRSLS 75
>2vl7_A XPD; helicase, unknown function; 2.25A {Sulfolobus tokodaii}
Length = 540
Score = 50.7 bits (121), Expect = 7e-08
Identities = 8/54 (14%), Positives = 18/54 (33%), Gaps = 2/54 (3%)
Query: 27 FPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDHKIV 80
Q+ + L + K + + G GK++ + L K++
Sbjct: 4 LKLQLRQWQAEKLGEAINALKHGKTLLLNAKPGLGKTVFVEV--LGMQLKKKVL 55
>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 = 50.2 bits (119), Expect = 1e-07
Identities = 30/213 (14%), Positives = 72/213 (33%), Gaps = 33/213 (15%)
Query: 3 SKTPNED-KEFNEQR-PLAEVPSEFPFPFDAYDIQS-NFMKNLYYTLDNSKFGIFESPTG 59
+ P+ + + EQR L F ++ +Q ++ L +K + + G
Sbjct: 102 QRQPSMMTRMYIEQRDRLYNDNQVFA-KYNVSRLQPYLKLRQALLELRPAKNVLIDGVLG 160
Query: 60 TGKSLSLICGILKWYYDHKIVGLEKIEAKIKDLEISKNETVSEDWIEQQSFELKMRNQID 119
+GK+ + + +K+ K++ KI L + + Q ++
Sbjct: 161 SGKT-WVALDVCL---SYKV--QCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWT 214
Query: 120 ALKDALKSQK-TYDELIENIRK--QNEKRKKSL---RN--DQEVKVHA--------LTYR 163
+ D + K + +R+ +++ + L N + + +A LT R
Sbjct: 215 SRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKA-WNAFNLSCKILLTTR 273
Query: 164 NR-----MDEKNSKEKRKEEERDGL-ENETQEL 190
+ + + + L +E + L
Sbjct: 274 FKQVTDFLSAATTTHISLDHHSMTLTPDEVKSL 306
Score = 37.1 bits (85), Expect = 0.002
Identities = 22/123 (17%), Positives = 46/123 (37%), Gaps = 25/123 (20%)
Query: 91 DLEISKNETVSEDWIE--QQSF--ELKMRNQIDALKDALKSQKTYDELIEN--------- 137
D E +++ +D + + +F ++ D K L ++ D +I +
Sbjct: 8 DFETGEHQYQYKDILSVFEDAFVDNFDCKDVQDMPKSILSKEE-IDHIIMSKDAVSGTLR 66
Query: 138 -----IRKQNEKRKK----SLRNDQEVKVHALTYRNRMDEKNSKEKRKEEERDGLENETQ 188
+ KQ E +K LR + + + + R + + + E+RD L N+ Q
Sbjct: 67 LFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQR--QPSMMTRMYIEQRDRLYNDNQ 124
Query: 189 ELD 191
Sbjct: 125 VFA 127
Score = 26.7 bits (58), Expect = 5.8
Identities = 10/55 (18%), Positives = 23/55 (41%), Gaps = 11/55 (20%)
Query: 103 DWIEQQSFELKMR------NQIDALKDALKSQKTYDELIENIRKQNEKRKKSLRN 151
++EQ K+R N ++ + L+ K Y I + + E+ ++ +
Sbjct: 501 RFLEQ-----KIRHDSTAWNASGSILNTLQQLKFYKPYICDNDPKYERLVNAILD 550
Score = 26.7 bits (58), Expect = 6.7
Identities = 21/127 (16%), Positives = 42/127 (33%), Gaps = 23/127 (18%)
Query: 18 LAEVPSEFPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYYDH 77
E + F F D F++ + + + +G L+ + LK+Y +
Sbjct: 486 HPERMTLFRMVF--LDF--RFLEQ---KIRHDST----AWNASGSILNTL-QQLKFYKPY 533
Query: 78 KIVGLEKIEAKIKDLEISKNETVSEDWIEQQSFELKMRNQIDALKDALKSQKTYDELIEN 137
K E + + D++ + L D L+ AL + + E
Sbjct: 534 ICDNDPKYERLVNAI---------LDFLPKIEENLICSKYTDLLRIAL--MAEDEAIFEE 582
Query: 138 IRKQNEK 144
KQ ++
Sbjct: 583 AHKQVQR 589
>3crv_A XPD/RAD3 related DNA helicase; XPD helicase DNA repair cancer
aging, hydrolase; HET: FLC; 2.00A {Sulfolobus
acidocaldarius} PDB: 3crw_1*
Length = 551
Score = 41.5 bits (97), Expect = 9e-05
Identities = 11/42 (26%), Positives = 18/42 (42%)
Query: 32 YDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKW 73
D Q + L N+ +PTG+GK+L + L+
Sbjct: 5 RDWQEKLKDKVIEGLRNNFLVALNAPTGSGKTLFSLLVSLEV 46
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 38.6 bits (89), Expect = 4e-04
Identities = 17/91 (18%), Positives = 38/91 (41%), Gaps = 18/91 (19%)
Query: 94 ISKNETVSED------WIEQQSFELKMRNQIDALKDALKSQKTYDELIENIRKQNEKRKK 147
I++ + ++++ W E+Q L+ DA S+ E E +K E+ +
Sbjct: 74 IAQADRLTQEPESIRKWREEQRKRLQE-------LDA-ASKVMEQEWREKAKKDLEEWNQ 125
Query: 148 SLRNDQEVKVHALTYRNRMDEKNSKEKRKEE 178
+++Q K NR+ +K ++ +
Sbjct: 126 R-QSEQVEKNKI---NNRIADKAFYQQPDAD 152
Score = 32.8 bits (74), Expect = 0.041
Identities = 14/57 (24%), Positives = 25/57 (43%), Gaps = 19/57 (33%)
Query: 136 ENIRKQNEKRKKSLRNDQEVKVHALTYRNRMDEKNSKEKRKEEERDGLENETQELDE 192
E+IRK E+++K R+ E ++ K E+E E ++L+E
Sbjct: 85 ESIRKWREEQRK-----------------RLQELDAASKVMEQEW--REKAKKDLEE 122
>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 = 33.5 bits (76), Expect = 0.043
Identities = 18/93 (19%), Positives = 34/93 (36%), Gaps = 13/93 (13%)
Query: 89 IKDLEISKNETVSEDWIEQQS-FELKMR--NQIDALKDALKSQKTYDELIENIRKQNEKR 145
K L ++D E + EL + + +L + +D+++ + E
Sbjct: 38 NKILPEPTEGFAADD--EPTTPAELVGKFLGYVSSLVEP-SKVGQFDQVLNLCLTEFENC 94
Query: 146 KKSLR-NDQEVKVHALTYRNRMDEKNSKEKRKE 177
L ND +HAL + + + K KE
Sbjct: 95 --YLEGND----IHALAAKLLQENDTTLVKTKE 121
Score = 28.9 bits (64), Expect = 1.2
Identities = 8/53 (15%), Positives = 22/53 (41%), Gaps = 14/53 (26%)
Query: 59 GTGKSLSLICGILKWYYDHKIVGLEKIEAKIKDLEISK-NETVSEDWIEQQSF 110
G ++L + +L K++ ++I + +++S + +E F
Sbjct: 1857 GDLRALDTVTNVLN-------------FIKLQKIDIIELQKSLSLEEVEGHLF 1896
>2dq0_A Seryl-tRNA synthetase; coiled-coil, homodimer, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; HET: SSA; 2.60A {Pyrococcus
horikoshii} PDB: 2dq1_A* 2dq2_A 2zr2_A* 2zr3_A
Length = 455
Score = 31.8 bits (73), Expect = 0.11
Identities = 14/81 (17%), Positives = 38/81 (46%), Gaps = 6/81 (7%)
Query: 114 MRNQIDALKDALKS--QKTYDELIENIRKQNEKRKKSLRNDQEVKVHALTYRNRMDEKNS 171
+R + +K+ L + + ++ I K + + + L+ ++ RN++ +
Sbjct: 7 IRENPELVKNDLIKRGELEKVKWVDEILKLDTEWRTKLKEINRLR----HERNKIAVEIG 62
Query: 172 KEKRKEEERDGLENETQELDE 192
K ++K E D L +++E+ +
Sbjct: 63 KRRKKGEPVDELLAKSREIVK 83
>4aw6_A CAAX prenyl protease 1 homolog; hydrolase, M48 peptidase, integral
membrane protein, prelami processing, ageing, progeria;
HET: PC1; 3.40A {Homo sapiens}
Length = 482
Score = 31.0 bits (69), Expect = 0.26
Identities = 12/63 (19%), Positives = 22/63 (34%), Gaps = 1/63 (1%)
Query: 15 QRPLAEVPSEFPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLS-LICGILKW 73
QR + + + P F K+ Y LD S F + + L+ G + +
Sbjct: 41 QRRIYKTTTHVPPELGQIMDSETFEKSRLYQLDKSTFSFWSGLYSETEGTLILLFGGIPY 100
Query: 74 YYD 76
+
Sbjct: 101 LWR 103
>2fwr_A DNA repair protein RAD25; DNA unwinding, XPB, DNA binding protein;
HET: DNA; 2.60A {Archaeoglobus fulgidus} SCOP: c.37.1.19
c.37.1.19 PDB: 2fzl_A*
Length = 472
Score = 30.6 bits (69), Expect = 0.31
Identities = 12/62 (19%), Positives = 19/62 (30%), Gaps = 12/62 (19%)
Query: 7 NEDKEFNEQRPLAEVPSEFPFPFDAYDIQ----SNFMKNLYYTLDNSKFGIFESPTGTGK 62
+ EF + F D Q ++ + K G PTG+GK
Sbjct: 70 SNGIEFVDNAADPIPTPYFDAEISLRDYQEKALERWLVD--------KRGCIVLPTGSGK 121
Query: 63 SL 64
+
Sbjct: 122 TH 123
>3qne_A Seryl-tRNA synthetase, cytoplasmic; amino acid biosynthesis,
CTG-clade, codon ambiguity, pathoge II aminoacyl-tRNA
synthetase family; 2.00A {Candida albicans} PDB: 3qo7_A*
3qo8_A* 3qo5_A
Length = 485
Score = 29.1 bits (66), Expect = 1.0
Identities = 13/74 (17%), Positives = 31/74 (41%), Gaps = 4/74 (5%)
Query: 119 DALKDALKSQKTYDELIENIRKQNEKRKKSLRNDQEVKVHALTYRNRMDEKNSKEKRKEE 178
+ +K + K + EL++ I + ++ K + E N + ++ K + +E
Sbjct: 16 EIIKASQKKRGDSVELVDEIIAEYKEWVKLRFDLDEHN----KKLNSVQKEIGKRFKAKE 71
Query: 179 ERDGLENETQELDE 192
+ L E ++L
Sbjct: 72 DAKDLIAEKEKLSN 85
>2dfs_A Myosin-5A; myosin-V, inhibited state, cryoelectron tomograp
contractIle protein-transport protein complex; 24.00A
{Gallus gallus}
Length = 1080
Score = 28.2 bits (63), Expect = 2.0
Identities = 18/111 (16%), Positives = 42/111 (37%), Gaps = 2/111 (1%)
Query: 82 LEKIEAKIKDLEISKNETVSEDWIEQQSFELKMRNQIDALKDALKSQKTYDELIENIRKQ 141
+ I L+ +++ +++ E + + L L+++ +L I +Q
Sbjct: 883 YHRTLKAIVYLQCCYRRMMAKRELKKLKIEARSVERYKKLHIGLENKIM--QLQRKIDEQ 940
Query: 142 NEKRKKSLRNDQEVKVHALTYRNRMDEKNSKEKRKEEERDGLENETQELDE 192
N++ K L +++ T ++ + + EEE N L E
Sbjct: 941 NKEYKSLLEKMNNLEITYSTETEKLRSDVERLRMSEEEAKNATNRVLSLQE 991
>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 = 27.9 bits (62), Expect = 2.5
Identities = 15/109 (13%), Positives = 46/109 (42%), Gaps = 21/109 (19%)
Query: 82 LEKIEAKIKDLEISKNETVSEDWIEQQSFELKMRNQIDALKDALKSQKTYDELIENIRKQ 141
+K EA++K+LE + E + Q+ + + +A +E+ + +
Sbjct: 873 QQKAEAELKELEQKHTQLCEEKNLLQEKLQAETELYAEA-----------EEMRVRLAAK 921
Query: 142 NEKRKKSLRNDQEVKVHALTYRNRMDEKNSKEKRKEEERDGLENETQEL 190
++ ++ L + R++E+ + ++ + E+ ++ + +L
Sbjct: 922 KQELEEILHEMEA----------RIEEEEERSQQLQAEKKKMQQQMLDL 960
Score = 27.1 bits (60), Expect = 5.0
Identities = 21/112 (18%), Positives = 50/112 (44%), Gaps = 16/112 (14%)
Query: 82 LEKIEAKIKDLEISKNETVSEDWIEQQSFELKMRNQIDALKDALKSQKTYDELIENIRKQ 141
L ++EA+I++ E + +E + KM+ Q+ L++ L+ ++ + ++ +
Sbjct: 929 LHEMEARIEEEEERSQQLQAE--------KKKMQQQMLDLEEQLEEEEAARQKLQLEKVT 980
Query: 142 NEKRKKSLRNDQEVKVHALTYRNRMDEKNSKEKRK-EEERDGLENETQELDE 192
+ + K + +D + + K +KE++ EE L E +E
Sbjct: 981 ADGKIKKMEDDILIM-------EDQNNKLTKERKLLEERVSDLTTNLAEEEE 1025
>3err_A Fusion protein of microtubule binding domain from mouse cytoplasmic
dynein and seryl-tRNA...; coiled coil, ligase; HET: AMP;
2.27A {Mus musculus}
Length = 536
Score = 27.7 bits (62), Expect = 3.0
Identities = 8/85 (9%), Positives = 23/85 (27%), Gaps = 7/85 (8%)
Query: 114 MRNQIDALKDALKSQKTYDELIENIRKQN------EKRKKSLRNDQEVKVHALTYRNRMD 167
++ + ++ + I N + EK KK+ ++ + +
Sbjct: 104 STTDWKQIRSIIM-RENFIPTIVNFSAEEISDAIREKMKKNYMSNPSYNYEIVNRASLAA 162
Query: 168 EKNSKEKRKEEERDGLENETQELDE 192
K + + + L
Sbjct: 163 GPMVKWAIAQLNYADMLKRVEPLRN 187
>2fz4_A DNA repair protein RAD25; RECA-like domain, DNA damage recognition
domain, DNA binding; HET: DNA; 2.40A {Archaeoglobus
fulgidus} SCOP: c.37.1.19
Length = 237
Score = 27.3 bits (61), Expect = 3.2
Identities = 13/69 (18%), Positives = 21/69 (30%), Gaps = 15/69 (21%)
Query: 7 NEDKEFNEQRPLAEVPSEFPFPFDAYDIQ----SNFMKNLYYTLDNSKFGIFESPTGTGK 62
+ EF + F D Q ++ + K G PTG+GK
Sbjct: 70 SNGIEFVDNAADPIPTPYFDAEISLRDYQEKALERWLVD--------KRGCIVLPTGSGK 121
Query: 63 SL---SLIC 68
+ + I
Sbjct: 122 THVAMAAIN 130
>3haj_A Human pacsin2 F-BAR; pacsin,syndapin,FAP52,F-BAR, alternative
splicing, coiled coil, cytoplasmic vesicle, endocytosis,
phosphoprotein, polymorphism; 2.78A {Homo sapiens}
Length = 486
Score = 27.0 bits (58), Expect = 4.5
Identities = 16/111 (14%), Positives = 41/111 (36%), Gaps = 3/111 (2%)
Query: 84 KIEAKIKDLEISKNETVSEDWIEQQSFELKMRNQIDALKDALKSQKTYDELIENIRKQNE 143
+ E + + + + E +++ + + A+ S+ E ++K +
Sbjct: 133 EAEDGFRKAQKPWAKKLKEVEAAKKAHHAACKEEKLAISREANSKADPSLNPEQLKKLQD 192
Query: 144 KRKKSLRNDQEVKVHALTYRNRMDEKNSKEKRKEEERDGLENETQELDESR 194
K +K Q+V Y + E + + E + + + Q+ +E R
Sbjct: 193 KIEKC---KQDVLKTKEKYEKSLKELDQGTPQYMENMEQVFEQCQQFEEKR 240
>1mqm_B Hemagglutinin HA2 chain; influenza virus, viral protein; HET: NAG
BMA MAN SIA GAL; 2.60A {Influenza a virus} SCOP: h.3.1.1
PDB: 1mql_B* 1mqn_B* 2l4g_A
Length = 221
Score = 26.5 bits (58), Expect = 4.8
Identities = 19/73 (26%), Positives = 31/73 (42%), Gaps = 11/73 (15%)
Query: 82 LEKIEAKIKDLEISKNETVSEDWIEQQSFELKMRNQIDALKDALKSQKTYDELIENIRKQ 141
++E +I+DLE +T + W L AL++Q T D + K
Sbjct: 70 FSEVEGRIQDLEKYVEDTKIDLWSYNAE-----------LLVALENQHTIDLADSEMNKL 118
Query: 142 NEKRKKSLRNDQE 154
EK ++ LR + E
Sbjct: 119 FEKTRRQLRENAE 131
>3haz_A Proline dehydrogenase; proline utilization A, PUTA, flavoenzyme,
1-pyrroline-5-carboxylate dehydrogenase, oxidoreductase;
HET: FAD NAD; 2.10A {Bradyrhizobium japonicum usda 110}
Length = 1001
Score = 26.6 bits (59), Expect = 6.4
Identities = 13/54 (24%), Positives = 17/54 (31%), Gaps = 1/54 (1%)
Query: 122 KDALKSQKTYDELIENIRKQNEKRKKSLRNDQEVKVHALTYR-NRMDEKNSKEK 174
DA + Y IE I K R VK+ AL R + +
Sbjct: 205 ADARRYFDAYASAIETIGKAAGNHALPDRPGISVKLSALHPRFEAISRARVMVE 258
>2wr1_A Hemagglutinin; glycoprotein, lipoprotein, envelope protein, viral
protein; HET: SIA GAL NAG BMA MAN; 2.10A {Unidentified
influenza virus} PDB: 2wr0_A* 2wr2_A* 2wr3_A* 2wr4_A*
2wr5_A 2wrf_A* 2wr7_A* 2wrb_A* 2wrc_A 2wrd_A 2wre_A*
3gbm_A* 2fk0_A* 3s11_A* 3s13_A* 3s12_A* 3fku_A*
Length = 509
Score = 26.6 bits (58), Expect = 6.7
Identities = 10/72 (13%), Positives = 29/72 (40%), Gaps = 11/72 (15%)
Query: 83 EKIEAKIKDLEISKNETVSEDWIEQQSFELKMRNQIDALKDALKSQKTYDELIENIRKQN 142
+E ++++L + + W L +++++T D N++
Sbjct: 411 SNLERRLENLNKKMEDGFLDVWTYNAE-----------LLVLMENERTLDFHDSNVKNLY 459
Query: 143 EKRKKSLRNDQE 154
+K + LR++ +
Sbjct: 460 DKVRMQLRDNVK 471
>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 = 25.3 bits (54), Expect = 10.0
Identities = 8/27 (29%), Positives = 13/27 (48%), Gaps = 10/27 (37%)
Query: 82 LEKIEAKIK----D----LEISKNETV 100
L+K++A +K D L I T+
Sbjct: 22 LKKLQASLKLYADDSAPALAI--KATM 46
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
0.310 0.129 0.356
Gapped
Lambda K H
0.267 0.0765 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,801,451
Number of extensions: 157705
Number of successful extensions: 572
Number of sequences better than 10.0: 1
Number of HSP's gapped: 560
Number of HSP's successfully gapped: 118
Length of query: 194
Length of database: 6,701,793
Length adjustment: 88
Effective length of query: 106
Effective length of database: 4,244,745
Effective search space: 449942970
Effective search space used: 449942970
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.7 bits)
S2: 55 (24.9 bits)