RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy14273
(115 letters)
>4a15_A XPD helicase, ATP-dependent DNA helicase TA0057; hydrolase,
nucleotide excision repair,; 2.20A {Thermoplasma
acidophilum} PDB: 2vsf_A*
Length = 620
Score = 58.2 bits (141), Expect = 2e-11
Identities = 16/74 (21%), Positives = 31/74 (41%), Gaps = 9/74 (12%)
Query: 29 FDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKW---------YSDHKI 79
++ Q + L +L S ESPTG+GK++ + L++ Y
Sbjct: 2 YENRQYQVEAIDFLRSSLQKSYGVALESPTGSGKTIMALKSALQYSSERKLKVLYLVRTN 61
Query: 80 AGLEKIEAEIKDLE 93
+ E++ E++ L
Sbjct: 62 SQEEQVIKELRSLS 75
>2vl7_A XPD; helicase, unknown function; 2.25A {Sulfolobus tokodaii}
Length = 540
Score = 53.8 bits (129), Expect = 6e-10
Identities = 10/82 (12%), Positives = 25/82 (30%), Gaps = 5/82 (6%)
Query: 27 FPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKW-----YSDHKIAG 81
Q+ + L + K + + G GK++ + ++ +
Sbjct: 4 LKLQLRQWQAEKLGEAINALKHGKTLLLNAKPGLGKTVFVEVLGMQLKKKVLIFTRTHSQ 63
Query: 82 LEKIEAEIKDLEISKNETVSED 103
L+ I K L + + +
Sbjct: 64 LDSIYKNAKLLGLKTGFLIGKS 85
>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 = 45.4 bits (107), Expect = 7e-07
Identities = 12/66 (18%), Positives = 23/66 (34%), Gaps = 5/66 (7%)
Query: 32 YDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKW-----YSDHKIAGLEKIE 86
D Q + L N+ +PTG+GK+L + L+ + I
Sbjct: 5 RDWQEKLKDKVIEGLRNNFLVALNAPTGSGKTLFSLLVSLEVKPKVLFVVRTHNEFYPIY 64
Query: 87 AEIKDL 92
++ +
Sbjct: 65 RDLTKI 70
>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 = 32.9 bits (75), Expect = 0.014
Identities = 12/62 (19%), Positives = 19/62 (30%), Gaps = 12/62 (19%)
Query: 7 NEDKEFKEQRPLAEVPSEFPFPFDAYDIQ----SNFMKNLYYTLDNSKFGIFESPTGTGK 62
+ EF + F D Q ++ + K G PTG+GK
Sbjct: 70 SNGIEFVDNAADPIPTPYFDAEISLRDYQEKALERWLVD--------KRGCIVLPTGSGK 121
Query: 63 SL 64
+
Sbjct: 122 TH 123
>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 = 28.5 bits (64), Expect = 0.43
Identities = 13/69 (18%), Positives = 21/69 (30%), Gaps = 15/69 (21%)
Query: 7 NEDKEFKEQRPLAEVPSEFPFPFDAYDIQ----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
>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 = 28.3 bits (62), Expect = 0.53
Identities = 12/63 (19%), Positives = 21/63 (33%), 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 YSD 76
Sbjct: 101 LWR 103
>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 = 26.7 bits (58), Expect = 1.8
Identities = 17/111 (15%), Positives = 40/111 (36%), Gaps = 10/111 (9%)
Query: 3 SKTPNED-KEFKEQR-PLAEVPSEFPFPFDAYDIQS-NFMKNLYYTLDNSKFGIFESPTG 59
+ P+ + + EQR L F ++ +Q ++ L +K + + G
Sbjct: 102 QRQPSMMTRMYIEQRDRLYNDNQVFA-KYNVSRLQPYLKLRQALLELRPAKNVLIDGVLG 160
Query: 60 TGKSLSLICGILKWYSDHKIAGLEKIEAEIKDLEISKNETVSEDWIEQQSF 110
+GK+ + + +K+ K++ +I L + + Q
Sbjct: 161 SGKT-WVALDVCL---SYKV--QCKMDFKIFWLNLKNCNSPETVLEMLQKL 205
>2xgj_A ATP-dependent RNA helicase DOB1; hydrolase-RNA complex, hydrolase,
tramp, exosome, DEAD, nucleotide-binding; HET: ADP;
2.90A {Saccharomyces cerevisiae}
Length = 1010
Score = 26.7 bits (58), Expect = 2.4
Identities = 11/59 (18%), Positives = 19/59 (32%), Gaps = 6/59 (10%)
Query: 6 PNEDKEFKEQRPLAEVPSEFPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSL 64
PN D + +PF D F +D + + + T GK++
Sbjct: 64 PNYDYTPIAEHKRVNEARTYPFTLD------PFQDTAISCIDRGESVLVSAHTSAGKTV 116
>2p32_A Heat shock 70 kDa protein A; three-helix bundle, chaperone; 3.20A
{Caenorhabditis elegans}
Length = 120
Score = 25.7 bits (56), Expect = 2.5
Identities = 17/55 (30%), Positives = 25/55 (45%), Gaps = 3/55 (5%)
Query: 39 MKNLYYTLDNSKFGIFESPTGTGKSLSLICGILKWYSDHKIAGLEKIEAEIKDLE 93
+K T+++ K SP K ILKW ++ A E+ E + KDLE
Sbjct: 30 LKQ---TIEDEKLKDKISPEDKKKIEDKCDEILKWLDSNQTAEKEEFEHQQKDLE 81
>3l9o_A ATP-dependent RNA helicase DOB1; REC-A fold,
winged-helix-turn-helix, antiparallel-coiled-COI domain,
ATP-binding, helicase, hydrolase; 3.39A {Saccharomyces
cerevisiae}
Length = 1108
Score = 26.0 bits (56), Expect = 3.3
Identities = 11/60 (18%), Positives = 19/60 (31%), Gaps = 6/60 (10%)
Query: 5 TPNEDKEFKEQRPLAEVPSEFPFPFDAYDIQSNFMKNLYYTLDNSKFGIFESPTGTGKSL 64
PN D + +PF D F +D + + + T GK++
Sbjct: 161 PPNYDYTPIAEHKRVNEARTYPFTLD------PFQDTAISCIDRGESVLVSAHTSAGKTV 214
>2z83_A Helicase/nucleoside triphosphatase; hydrolase, membrane,
nucleotide-binding, RNA replication, transmembrane,
viral protein; 1.80A {Japanese encephalitis virus} PDB:
2v8o_A 2qeq_A
Length = 459
Score = 25.9 bits (57), Expect = 3.7
Identities = 6/40 (15%), Positives = 13/40 (32%), Gaps = 2/40 (5%)
Query: 46 LDNSKFGIFESPTGTGKS--LSLICGILKWYSDHKIAGLE 83
L + + + G+GK+ + + A L
Sbjct: 18 LRKRQMTVLDLHPGSGKTRKILPQIIKDAIQQRLRTAVLA 57
>1tj7_A Argininosuccinate lyase; crystallin, E. coli, fumarase, ASPA lyase;
2.44A {Escherichia coli} SCOP: a.127.1.1
Length = 457
Score = 24.8 bits (55), Expect = 9.3
Identities = 8/45 (17%), Positives = 19/45 (42%), Gaps = 4/45 (8%)
Query: 68 CGILKWYSDHKI-AGLEKIEAEIKDLEISKNETVSED---WIEQQ 108
G+L ++ L + +++ E+ +ED W+E +
Sbjct: 47 VGVLTAEEQAQLEEALNVLLEDVRARPQQILESDAEDIHSWVEGK 91
>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 = 24.5 bits (52), Expect = 10.0
Identities = 8/27 (29%), Positives = 13/27 (48%), Gaps = 10/27 (37%)
Query: 82 LEKIEAEIK----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
0.313 0.133 0.387
Gapped
Lambda K H
0.267 0.0457 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,706,750
Number of extensions: 87713
Number of successful extensions: 178
Number of sequences better than 10.0: 1
Number of HSP's gapped: 178
Number of HSP's successfully gapped: 27
Length of query: 115
Length of database: 6,701,793
Length adjustment: 78
Effective length of query: 37
Effective length of database: 4,523,955
Effective search space: 167386335
Effective search space used: 167386335
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 51 (24.1 bits)