RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy2760
(333 letters)
>4a4z_A Antiviral helicase SKI2; hydrolase, ATPase, mRNA degradation,
exosome; HET: ANP; 2.40A {Saccharomyces cerevisiae} PDB:
4a4k_A
Length = 997
Score = 159 bits (403), Expect = 1e-43
Identities = 62/106 (58%), Positives = 84/106 (79%), Gaps = 2/106 (1%)
Query: 164 QTEWAEMLDVSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKT 223
+ EWA ++D++ + +FD +P A +WPFELD FQK+A+ LE+ + VFV AHTSAGKT
Sbjct: 9 KKEWAHVVDLNHKIENFDELIPNPARSWPFELDTFQKEAVYHLEQGDSVFVAAHTSAGKT 68
Query: 224 VIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETF--QDVGLI 267
V+AEYAIA++ + T+TIYTSPIKALSNQK+RDF+ETF ++GLI
Sbjct: 69 VVAEYAIAMAHRNMTKTIYTSPIKALSNQKFRDFKETFDDVNIGLI 114
>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 = 157 bits (397), Expect = 8e-43
Identities = 56/172 (32%), Positives = 78/172 (45%), Gaps = 7/172 (4%)
Query: 103 ENASKFEQGLWESHEVISGDAKEEQEKATVFPSNEEENNVIPQEVDIPILKISNTLPKHV 162
E+ + + K ++ V + E+ + + +
Sbjct: 86 EHEENNSENKKIKSNKSKTEDKNKKVVVPVLADSFEQEASREVDASKGLTNSETLQVEQD 145
Query: 163 TQTEWAEMLDVSKPVLDFDAKVPI-------MAHTWPFELDVFQKQAIIKLEEHNHVFVT 215
+ + + + PI A T+PF LD FQ AI ++ V V+
Sbjct: 146 GKVRLSHQVRHQVALPPNYDYTPIAEHKRVNEARTYPFTLDPFQDTAISCIDRGESVLVS 205
Query: 216 AHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQDVGLI 267
AHTSAGKTV+AEYAIA S +K R IYTSPIKALSNQKYR+ F DVGL+
Sbjct: 206 AHTSAGKTVVAEYAIAQSLKNKQRVIYTSPIKALSNQKYRELLAEFGDVGLM 257
>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 = 156 bits (395), Expect = 1e-42
Identities = 57/159 (35%), Positives = 78/159 (49%), Gaps = 8/159 (5%)
Query: 116 HEVISGDAKEEQEKATVFPSNEEEN-------NVIPQEVDIPILKISNTLPKHVTQTEWA 168
H + + + + S E+E + + + + H + + A
Sbjct: 2 HHHHHENLYFQGAASMLADSFEQEASREVDASKGLTNSETLQVEQDGKVRLSHQVRHQVA 61
Query: 169 EMLDVSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEY 228
+ + K A T+PF LD FQ AI ++ V V+AHTSAGKTV+AEY
Sbjct: 62 LPPNY-DYTPIAEHKRVNEARTYPFTLDPFQDTAISCIDRGESVLVSAHTSAGKTVVAEY 120
Query: 229 AIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQDVGLI 267
AIA S +K R IYTSPIKALSNQKYR+ F DVGL+
Sbjct: 121 AIAQSLKNKQRVIYTSPIKALSNQKYRELLAEFGDVGLM 159
>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-bindin
nucleotide-binding; 2.30A {Sulfolobus solfataricus}
Length = 715
Score = 86.3 bits (214), Expect = 9e-19
Identities = 27/85 (31%), Positives = 51/85 (60%), Gaps = 3/85 (3%)
Query: 184 VPIMAHTWPFELDVFQKQAIIK-LEEHNHVFVTAHTSAGKTVIAEYAI-ALSQNHKTRTI 241
+ I+ +L+ Q +A+ K L E N + +T+ T +GKT+IAE I + + + I
Sbjct: 20 IEIIKKRGIKKLNPPQTEAVKKGLLEGNRLLLTSPTGSGKTLIAEMGIISFLLKNGGKAI 79
Query: 242 YTSPIKALSNQKYRDFRETFQDVGL 266
Y +P++AL+N+KY F++ ++ +G
Sbjct: 80 YVTPLRALTNEKYLTFKD-WELIGF 103
>2p6r_A Afuhel308 helicase; protein-DNA complex, SF2 helicase, archaeal
helicase, DNA repair,, DNA binding protein/DNA complex;
3.00A {Archaeoglobus fulgidus} SCOP: a.4.5.43 a.289.1.2
c.37.1.19 c.37.1.19 PDB: 2p6u_A
Length = 702
Score = 66.4 bits (162), Expect = 3e-12
Identities = 22/73 (30%), Positives = 44/73 (60%), Gaps = 1/73 (1%)
Query: 194 ELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQK 253
EL Q +A+ K+ ++ + T+AGKT++AE A+ +++Y P++AL+ +K
Sbjct: 25 ELFPPQAEAVEKVFSGKNLLLAMPTAAGKTLLAEMAMVREAIKGGKSLYVVPLRALAGEK 84
Query: 254 YRDFRETFQDVGL 266
Y F++ ++ +GL
Sbjct: 85 YESFKK-WEKIGL 96
>2zj8_A DNA helicase, putative SKI2-type helicase; RECA fold, ATP-binding,
hydrolase, nucleotide- binding; 2.00A {Pyrococcus
furiosus} PDB: 2zj5_A* 2zj2_A 2zja_A*
Length = 720
Score = 62.6 bits (152), Expect = 5e-11
Identities = 23/92 (25%), Positives = 48/92 (52%), Gaps = 4/92 (4%)
Query: 178 LDFDAKVPIMAHTWPFE-LDVFQKQAI-IKLEEHNHVFVTAHTSAGKTVIAEYAIA-LSQ 234
L D ++ E Q +A+ + E + ++ T++GKT+IAE A+
Sbjct: 6 LRVDERIKSTLKERGIESFYPPQAEALKSGILEGKNALISIPTASGKTLIAEIAMVHRIL 65
Query: 235 NHKTRTIYTSPIKALSNQKYRDFRETFQDVGL 266
+ +Y P+KAL+ +K+++F++ ++ +GL
Sbjct: 66 TQGGKAVYIVPLKALAEEKFQEFQD-WEKIGL 96
>3b6e_A Interferon-induced helicase C domain-containing P; DECH, DEXD/H
RNA-binding helicase, innate immunity, IFIH1, S
genomics; 1.60A {Homo sapiens}
Length = 216
Score = 51.7 bits (124), Expect = 6e-08
Identities = 16/98 (16%), Positives = 31/98 (31%), Gaps = 10/98 (10%)
Query: 174 SKPVLDFDAKVPIMAHTW----PFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYA 229
+ D+ +A +L +Q + E ++ + T +GKT +A Y
Sbjct: 9 DSGTMGSDSDEENVAARASPEPELQLRPYQMEVAQPALEGKNIIICLPTGSGKTRVAVYI 68
Query: 230 IA------LSQNHKTRTIYTSPIKALSNQKYRDFRETF 261
+ + I L Q +R + F
Sbjct: 69 AKDHLDKKKKASEPGKVIVLVNKVLLVEQLFRKEFQPF 106
>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 = 48.9 bits (116), Expect = 2e-06
Identities = 69/420 (16%), Positives = 114/420 (27%), Gaps = 159/420 (37%)
Query: 3 LHKVTESSIKIYVDHRALIIPRGG-----LFWD---TLYE-YDVITILDPGPRIDDLPPV 53
V E + ++ A+ GG +++ LY+ Y + DL
Sbjct: 146 FRAVGEGNAQLV----AIF---GGQGNTDDYFEELRDLYQTY--------HVLVGDL--- 187
Query: 54 FPDVEKLLEDLNIGGLDELSIHDFNKHLKFW------KPKVQLVAGI------INLIQLG 101
+ L +L LD + ++ W P + I I +IQL
Sbjct: 188 IKFSAETLSELIRTTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSIPISCPLIGVIQLA 247
Query: 102 -------------GENASKFE------QGL-----------WESHEVISGDA-------- 123
GE S + QGL WES V A
Sbjct: 248 HYVVTAKLLGFTPGELRSYLKGATGHSQGLVTAVAIAETDSWESFFVSVRKAITVLFFIG 307
Query: 124 KEEQEKATVFPSNEEENNVIPQEVDIPILKISNTLPKHVTQTEWAEMLDVSKPVLDFDAK 183
E +P N +P + L+ + +P ML +S
Sbjct: 308 VRCYE---AYP-----NTSLPPSILEDSLENNEGVPSP--------MLSIS--------- 342
Query: 184 VPIMAHTWPFELDVFQKQAIIK-----LEEHNHVFVTAHTSAGKTVIAEYAIAL-SQNHK 237
L Q Q + L V ++ A V++ +L N
Sbjct: 343 ----------NLTQEQVQDYVNKTNSHLPAGKQVEISLVNGAKNLVVSGPPQSLYGLNLT 392
Query: 238 TRTIYTSPIKALS--NQKYRDFRE---TFQDVGLIDDLPPVF---------PDVEKLLED 283
R KA S +Q F E F + L PV P + + +D
Sbjct: 393 LRK-----AKAPSGLDQSRIPFSERKLKFSNRFL-----PVASPFHSHLLVPASDLINKD 442
Query: 284 LNIGGLD----ELSIHDFN----KHLKFWKPKVQLDDLFD--------WTMASDATTLEI 327
L + ++ I ++ L+ + + + D W + I
Sbjct: 443 LVKNNVSFNAKDIQIPVYDTFDGSDLRVLSGSI-SERIVDCIIRLPVKWETTTQFKATHI 501
>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 = 48.7 bits (115), Expect = 2e-06
Identities = 50/321 (15%), Positives = 93/321 (28%), Gaps = 73/321 (22%)
Query: 6 VTESSIKIYVDHRALIIPRGGLFWDTLYEYDVITILDPGPRIDDLPPVFPDVEKLLEDLN 65
VT+ H +L L T E + + R DLP +
Sbjct: 277 VTDFLSAATTTHISLDHHSMTL---TPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSI- 332
Query: 66 IGGLDELSIHDFNKHLKFWKPKVQLVAGIINLIQLGGENASKFEQGLWESHEVIS-GDAK 124
I SI D WK + N K + S V+ + +
Sbjct: 333 IA----ESIRDGLATWDNWK---HV-------------NCDKLTTIIESSLNVLEPAEYR 372
Query: 125 EEQEKATVFPSNEEENNVIPQEVDIPILKISNTLPKHVTQTEWAEML-DVSKPVLDFDAK 183
+ ++ +VFP + IP + W +++ V++ K
Sbjct: 373 KMFDRLSVFPPS----------AHIPT---------ILLSLIWFDVIKSDVMVVVNKLHK 413
Query: 184 VPIMAHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAI--ALSQNHKTRT- 240
+ P E + ++L+ H ++++ Y I +
Sbjct: 414 YS-LVEKQPKESTISIPSIYLELKVKLENEYALH----RSIVDHYNIPKTFDSDDLIPPY 468
Query: 241 ----IYTSPI-----KALSNQKYRDFRETFQDVGLIDDLPPVFPDVEKLLEDLNIGGLDE 291
Y S I ++ FR F D ++ +K+ D
Sbjct: 469 LDQYFY-SHIGHHLKNIEHPERMTLFRMVFLDFRFLE---------QKIRHDSTAWNASG 518
Query: 292 LSIHDFNKHLKFWKPKVQLDD 312
++ + LKF+KP + +D
Sbjct: 519 SILNTLQQ-LKFYKPYICDND 538
Score = 46.4 bits (109), Expect = 9e-06
Identities = 40/296 (13%), Positives = 101/296 (34%), Gaps = 69/296 (23%)
Query: 49 DLPPVFPDVEKLLEDLNIGGLDE-----LSIHDFNKHLKFWKPKVQLVAGIINLIQLGGE 103
D+ VF + +++ + + + LS + H+ K V + + E
Sbjct: 20 DILSVF--EDAFVDNFDCKDVQDMPKSILSKEEI-DHIIMSKDAVSGTLRLFWTLLSKQE 76
Query: 104 NASK--FEQGLWESHE-VISGDAKEEQEKATVFPSNEEENNVIPQEVDIPILKISNTLPK 160
+ E+ L +++ ++S E+++ + + E+ + + D +
Sbjct: 77 EMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYN--DNQVFA-----KY 129
Query: 161 HVTQTEWAEMLDVSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSA 220
+V++ + P L +L +QA+++L +V + +
Sbjct: 130 NVSRLQ---------PYL---------------KL----RQALLELRPAKNVLIDGVLGS 161
Query: 221 GKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQDVGLIDDLPPVFPDVEKL 280
GKT + A+ + ++K + I L+ + +++ L + ++
Sbjct: 162 GKTWV---ALDVCLSYKVQCKMDFKIFWLN------LKNCNSPETVLEMLQKLLYQIDPN 212
Query: 281 LEDLNIGGLD-ELSIHDFNKHLK---FWKPKVQ----LDDLFDWTMASDATTLEIF 328
+ + +L IH L+ KP L ++ +A F
Sbjct: 213 WTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNV--Q----NAKAWNAF 262
Score = 36.4 bits (83), Expect = 0.015
Identities = 47/290 (16%), Positives = 93/290 (32%), Gaps = 90/290 (31%)
Query: 1 MELHKVTESSIKIY--VDHRAL-----I------IPRG--GLFWDTLYEYDVITILDPGP 45
+L + ESS+ + ++R + + IP L W + + DV+ +++
Sbjct: 353 DKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVN--- 409
Query: 46 RIDDLPPVFPDVEKLLEDLNIGGLDE-LSIHDFNKHLKFWKPKVQLVAGIINLIQLGGEN 104
+ L + + +SI +L+ K K++ N L
Sbjct: 410 ---------KLHKYSL--VEKQPKESTISIPSI--YLEL-KVKLE------NEYAL---- 445
Query: 105 ASKFEQGLWESHEVISGDAKEEQEKATVFPSNEEENNVIPQEVDIPILKISNTLPKHVTQ 164
H I + P + +++IP +D + + H+
Sbjct: 446 -----------HRSIV-----DHYN---IPKTFDSDDLIPPYLDQYFY---SHIGHHLKN 483
Query: 165 TEWAEMLDVSKPV-LDF---DAKVPIMAHTWPFE---LDVFQ-----KQAIIKLEEHNHV 212
E E + + + V LDF + K+ + W L+ Q K I +
Sbjct: 484 IEHPERMTLFRMVFLDFRFLEQKIRHDSTAWNASGSILNTLQQLKFYKPYICDNDPKYER 543
Query: 213 FVTA-----HTSAGKTVIAEYA----IALSQNHKTRTIYTSPIKALSNQK 253
V A + ++Y IAL + I+ K + Q+
Sbjct: 544 LVNAILDFLPKIEENLICSKYTDLLRIAL--MAEDEAIFEEAHKQV--QR 589
>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate
immunity; 2.50A {Homo sapiens} PDB: 3tmi_A*
Length = 696
Score = 41.1 bits (95), Expect = 4e-04
Identities = 14/83 (16%), Positives = 31/83 (37%), Gaps = 8/83 (9%)
Query: 187 MAHTW---PFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIA-----LSQNHKT 238
++ T PF+ +Q + + + + + A T GKT ++ Q K
Sbjct: 3 VSDTNLYSPFKPRNYQLELALPAMKGKNTIICAPTGCGKTFVSLLICEHHLKKFPQGQKG 62
Query: 239 RTIYTSPIKALSNQKYRDFRETF 261
+ ++ + + Q F + F
Sbjct: 63 KVVFFANQIPVYEQNKSVFSKYF 85
>3rc3_A ATP-dependent RNA helicase SUPV3L1, mitochondrial; SUV3, nucleus,
hydrolase; HET: ANP; 2.08A {Homo sapiens} PDB: 3rc8_A
Length = 677
Score = 40.7 bits (94), Expect = 5e-04
Identities = 11/58 (18%), Positives = 24/58 (41%), Gaps = 4/58 (6%)
Query: 210 NHVFVTAHTSAGKTVIAEYAIALSQNHKTRTIYTSPIKALSNQKYRDFRETFQDVGLI 267
+F + T++GKT A ++ +Y P+K L+++ + L+
Sbjct: 156 KIIFHSGPTNSGKTYHAIQKYFSAK----SGVYCGPLKLLAHEIFEKSNAAGVPCDLV 209
>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 = 38.1 bits (89), Expect = 0.002
Identities = 20/92 (21%), Positives = 33/92 (35%), Gaps = 4/92 (4%)
Query: 177 VLDFDAKVPIMAHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNH 236
V + +P L +Q++A+ + + T +GKT +A AI
Sbjct: 76 VDNAADPIPTPYFDAEISLRDYQEKALERWLVDKRGCIVLPTGSGKTHVAMAAIN---EL 132
Query: 237 KTRTIYTSPIKALSNQKYRDFRE-TFQDVGLI 267
T T+ P AL+ Q + VG
Sbjct: 133 STPTLIVVPTLALAEQWKERLGIFGEEYVGEF 164
>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 = 38.7 bits (90), Expect = 0.002
Identities = 20/92 (21%), Positives = 33/92 (35%), Gaps = 4/92 (4%)
Query: 177 VLDFDAKVPIMAHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQNH 236
V + +P L +Q++A+ + + T +GKT +A AI
Sbjct: 76 VDNAADPIPTPYFDAEISLRDYQEKALERWLVDKRGCIVLPTGSGKTHVAMAAIN---EL 132
Query: 237 KTRTIYTSPIKALSNQKYRDFRE-TFQDVGLI 267
T T+ P AL+ Q + VG
Sbjct: 133 STPTLIVVPTLALAEQWKERLGIFGEEYVGEF 164
>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET:
ANP; 2.14A {Mus musculus}
Length = 555
Score = 36.4 bits (83), Expect = 0.011
Identities = 12/80 (15%), Positives = 30/80 (37%), Gaps = 5/80 (6%)
Query: 192 PFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIA-----LSQNHKTRTIYTSPI 246
P + +Q + + ++ + + A T GKT ++ K + ++ +
Sbjct: 2 PLKPRNYQLELALPAKKGKNTIICAPTGCGKTFVSLLICEHHLKKFPCGQKGKVVFFANQ 61
Query: 247 KALSNQKYRDFRETFQDVGL 266
+ Q+ F F+ +G
Sbjct: 62 IPVYEQQATVFSRYFERLGY 81
>4a2q_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2
RNA helicase, ATP and dsRNA binding antiviral signalling
pathway; 3.40A {Anas platyrhynchos}
Length = 797
Score = 35.7 bits (81), Expect = 0.018
Identities = 15/146 (10%), Positives = 41/146 (28%), Gaps = 10/146 (6%)
Query: 125 EEQEKATVFPSNEEENNVIPQEVDIPILKISNTLPKHVTQTEWAEMLDVSKPVLDFDAKV 184
+ + ++VD + S + D + + +
Sbjct: 176 LDTTGYYRASELWDIREDNAKDVDSEMTDASEDCLEASMTYSEEAEPDDNLS-ENLGSAA 234
Query: 185 PIMAHTWP----FELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIA-----LSQN 235
+ P + +Q + + + A T +GKT ++ +
Sbjct: 235 EGIGKPPPVYETKKARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPAG 294
Query: 236 HKTRTIYTSPIKALSNQKYRDFRETF 261
K + ++ + + Q+ F+ F
Sbjct: 295 RKAKVVFLATKVPVYEQQKNVFKHHF 320
>4a2w_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2
RNA helicase, ATP and dsRNA binding antiviral signalling
pathway; 3.70A {Anas platyrhynchos}
Length = 936
Score = 34.9 bits (79), Expect = 0.036
Identities = 15/146 (10%), Positives = 41/146 (28%), Gaps = 10/146 (6%)
Query: 125 EEQEKATVFPSNEEENNVIPQEVDIPILKISNTLPKHVTQTEWAEMLDVSKPVLDFDAKV 184
+ + ++VD + S + D + + +
Sbjct: 176 LDTTGYYRASELWDIREDNAKDVDSEMTDASEDCLEASMTYSEEAEPDDNLS-ENLGSAA 234
Query: 185 PIMAHTWP----FELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIA-----LSQN 235
+ P + +Q + + + A T +GKT ++ +
Sbjct: 235 EGIGKPPPVYETKKARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPAG 294
Query: 236 HKTRTIYTSPIKALSNQKYRDFRETF 261
K + ++ + + Q+ F+ F
Sbjct: 295 RKAKVVFLATKVPVYEQQKNVFKHHF 320
>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 = 33.4 bits (75), Expect = 0.040
Identities = 8/22 (36%), Positives = 13/22 (59%), Gaps = 4/22 (18%)
Query: 2 ELHKVTESSIKIYVDHRALIIP 23
L K+ ++S+K+Y D A P
Sbjct: 21 ALKKL-QASLKLYADDSA---P 38
Score = 30.7 bits (68), Expect = 0.37
Identities = 9/37 (24%), Positives = 16/37 (43%), Gaps = 11/37 (29%)
Query: 199 QKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIALSQN 235
+KQA+ KL+ ++ K + A AL+
Sbjct: 18 EKQALKKLQ-----------ASLKLYADDSAPALAIK 43
>4a2p_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2
RNA helicase, ATP and dsRNA binding antiviral signalling
pathway; 3.00A {Anas platyrhynchos} PDB: 4a36_A*
Length = 556
Score = 32.6 bits (73), Expect = 0.20
Identities = 10/61 (16%), Positives = 23/61 (37%), Gaps = 6/61 (9%)
Query: 206 LEEHNHVFVTAHTSAGKTVIAEYAIA-----LSQNHKTRTIYTSPIKALSNQKYRDFRET 260
+ N + A T +GKT ++ + K + ++ + + Q+ F+
Sbjct: 20 INGKN-ALICAPTGSGKTFVSILICEHHFQNMPAGRKAKVVFLATKVPVYEQQKNVFKHH 78
Query: 261 F 261
F
Sbjct: 79 F 79
>3e1s_A Exodeoxyribonuclease V, subunit RECD; alpha and beta protein,
ATP-binding, nucleotide-binding, HYD; 2.20A {Deinococcus
radiodurans} PDB: 3gp8_A 3gpl_A*
Length = 574
Score = 30.8 bits (70), Expect = 0.59
Identities = 12/76 (15%), Positives = 23/76 (30%)
Query: 170 MLDVSKPVLDFDAKVPIMAHTWPFELDVFQKQAIIKLEEHNHVFVTAHTSAGKTVIAEYA 229
L + P + L Q + +L H V +T GK+ +
Sbjct: 165 TLLATPPADGAGNDDWAVPKKARKGLSEEQASVLDQLAGHRLVVLTGGPGTGKSTTTKAV 224
Query: 230 IALSQNHKTRTIYTSP 245
L+++ +P
Sbjct: 225 ADLAESLGLEVGLCAP 240
>1t7l_A 5-methyltetrahydropteroyltriglutamate-- homocysteine
methyltransferase; TIM barrel, methyltetrahydrofolate,
zinc; 2.00A {Thermotoga maritima} PDB: 3bq5_A 3bq6_A
1xdj_A 1xr2_A* 1xpg_A*
Length = 766
Score = 30.9 bits (70), Expect = 0.62
Identities = 15/75 (20%), Positives = 30/75 (40%), Gaps = 5/75 (6%)
Query: 224 VIAEYAIALSQNHKTRTIYTSPIK--ALSNQKYRDFRETFQDVGLIDDLPPVFPDVEKLL 281
+ +Y S+ +T P LS + R Q L++ L V+ +++
Sbjct: 161 PLEDYLFFKSKGIETAPWVIGPFTFLYLSKRNGEWIRRPNQMEKLLESLVSVY---KEVF 217
Query: 282 EDLNIGGLDELSIHD 296
E L G E+ +++
Sbjct: 218 EKLVENGCKEILVNE 232
>1l8q_A Chromosomal replication initiator protein DNAA; AAA+,
helix-turn-helix, nucleotide-binding, DNA binding, REP
initiation, DNA binding protein; HET: ADP; 2.70A
{Aquifex aeolicus} SCOP: a.4.12.2 c.37.1.20 PDB: 3r8f_A*
2hcb_A*
Length = 324
Score = 29.8 bits (68), Expect = 1.1
Identities = 15/62 (24%), Positives = 24/62 (38%), Gaps = 17/62 (27%)
Query: 221 GKT----VIAEYAIALSQNHKTRTIYTSP-------IKALSNQKYRDFRETFQ--DVGLI 267
GKT A + R IY+S ++ L +FR ++ D+ L+
Sbjct: 49 GKTHLLQAAGNEA----KKRGYRVIYSSADDFAQAMVEHLKKGTINEFRNMYKSVDLLLL 104
Query: 268 DD 269
DD
Sbjct: 105 DD 106
>1wp9_A ATP-dependent RNA helicase, putative; ATPase, DNA replication, DNA
repair, DNA recombina hydrolase; 2.90A {Pyrococcus
furiosus} SCOP: c.37.1.19 c.37.1.19
Length = 494
Score = 29.8 bits (66), Expect = 1.5
Identities = 17/65 (26%), Positives = 25/65 (38%), Gaps = 2/65 (3%)
Query: 199 QKQAIIKLEEHNHVFVTAHTSAGKTVIAEYAIA-LSQNHKTRTIYTSPIKALSNQKYRDF 257
Q+ K +E N + T GKT+IA + + + +P K L Q F
Sbjct: 14 QEVIYAKCKETN-CLIVLPTGLGKTLIAMMIAEYRLTKYGGKVLMLAPTKPLVLQHAESF 72
Query: 258 RETFQ 262
R F
Sbjct: 73 RRLFN 77
>2wjy_A Regulator of nonsense transcripts 1; nonsense mediated decay,
zinc-finger, ATP-binding, metal-BIN UPF2, UPF1,
helicase, hydrolase; 2.50A {Homo sapiens} PDB: 2wjv_A
2iyk_A
Length = 800
Score = 29.9 bits (67), Expect = 1.5
Identities = 11/77 (14%), Positives = 24/77 (31%), Gaps = 2/77 (2%)
Query: 171 LDVSKPVLDFDAKVPIMAHTWPF-ELDVFQKQAIIKLEEHNHVFVTAHTSAGKT-VIAEY 228
L + ++P +L+ Q A+ + + + GKT A
Sbjct: 332 LGHEVEDVIIKCQLPKRFTAQGLPDLNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSATI 391
Query: 229 AIALSQNHKTRTIYTSP 245
L++ + +P
Sbjct: 392 VYHLARQGNGPVLVCAP 408
>2z4s_A Chromosomal replication initiator protein DNAA; AAA+ ATPase, domain
III (ATPase domain), ATP-binding, cytoplasm, DNA
replication; HET: ADP; 3.00A {Thermotoga maritima} PDB:
2z4r_A*
Length = 440
Score = 29.2 bits (66), Expect = 1.8
Identities = 16/63 (25%), Positives = 26/63 (41%), Gaps = 16/63 (25%)
Query: 221 GKT----VIAEYAIALSQNHKTRTIYTSP-------IKALSNQKYRDFRETFQ---DVGL 266
GKT I Y + R +Y + + ++ K +FRE ++ D+ L
Sbjct: 142 GKTHLLQSIGNYV--VQNEPDLRVMYITSEKFLNDLVDSMKEGKLNEFREKYRKKVDILL 199
Query: 267 IDD 269
IDD
Sbjct: 200 IDD 202
>2wf7_A Beta-PGM, beta-phosphoglucomutase; transition state analogue,
haloacid dehalogenase superfamily, isomerase,
phosphotransferase; HET: G7P; 1.05A {Lactococcus lactis}
PDB: 1o03_A* 1z4n_A* 1z4o_A* 1zol_A 2wf5_A* 2wf6_A*
1o08_A* 2wf8_A* 2wf9_A* 2wfa_A 2whe_A 1lvh_A* 3fm9_A
Length = 221
Score = 28.3 bits (64), Expect = 3.0
Identities = 12/39 (30%), Positives = 21/39 (53%), Gaps = 4/39 (10%)
Query: 246 IKALSNQKYRDFRETFQDVGLIDDLPPVFPDVEKLLEDL 284
K L+ +K ++ + QDV V+P + +LL+DL
Sbjct: 69 FKELAKRKNDNYVKMIQDVSPA----DVYPGILQLLKDL 103
>3v4v_A Integrin alpha-4; cell adhesion, madcam-1, membrane; HET: NAG BMA
MAN 0DU; 3.10A {Homo sapiens} PDB: 3v4p_A*
Length = 597
Score = 28.3 bits (62), Expect = 4.8
Identities = 12/48 (25%), Positives = 18/48 (37%), Gaps = 1/48 (2%)
Query: 150 PI-LKISNTLPKHVTQTEWAEMLDVSKPVLDFDAKVPIMAHTWPFELD 196
PI ++ + L HV E +P+L + IM T F
Sbjct: 541 PIQIEAAYHLGPHVISKASTEEFPPLQPILQQKKEKDIMKKTINFART 588
>2go7_A Hydrolase, haloacid dehalogenase-like family; structural genomics,
joint center for structural genomics, J protein
structure initiative; 2.10A {Streptococcus pneumoniae}
SCOP: c.108.1.6
Length = 207
Score = 27.2 bits (61), Expect = 6.5
Identities = 10/82 (12%), Positives = 25/82 (30%), Gaps = 12/82 (14%)
Query: 245 PIKALSNQKYRDFRETFQDVGLIDDLPPVFPDVEKLLEDLNIGGLDELSI-----HDFNK 299
+ L + R + + P ++L + G+ + I ++
Sbjct: 60 EDRNLDVEVLNQVRAQSLAEK--NAQVVLMPGAREVLAWADESGI-QQFIYTHKGNNAFT 116
Query: 300 HLKFWKPKVQLDDLFDWTMASD 321
LK + ++ F + S
Sbjct: 117 ILK----DLGVESYFTEILTSQ 134
>2gk6_A Regulator of nonsense transcripts 1; UPF1, helicase, NMD,
hydrolase; HET: ADP; 2.40A {Homo sapiens} PDB: 2gjk_A*
2gk7_A 2xzo_A* 2xzp_A
Length = 624
Score = 27.5 bits (61), Expect = 7.1
Identities = 12/77 (15%), Positives = 25/77 (32%), Gaps = 2/77 (2%)
Query: 171 LDVSKPVLDFDAKVPIMAHTWPF-ELDVFQKQAIIKLEEHNHVFVTAHTSAGKTV-IAEY 228
L + ++P +L+ Q A+ + + + GKTV A
Sbjct: 156 LGHEVEDVIIKCQLPKRFTAQGLPDLNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSATI 215
Query: 229 AIALSQNHKTRTIYTSP 245
L++ + +P
Sbjct: 216 VYHLARQGNGPVLVCAP 232
>3dhf_A Nicotinamide phosphoribosyltransferase; NMPRTASE, NAMPRTASE,
visfatin, beryllium fluoride, nicotinamide
D-ribonucleotide, pyrophosphate; HET: NMN; 1.80A {Homo
sapiens} PDB: 3dgr_A* 3dhd_A* 3dkj_A* 3dkl_A* 2gvj_A*
2gvg_A* 2e5b_A 2e5c_A* 2e5d_A 2h3d_A* 2gvl_A 2h3b_A
2g95_A 2g96_A* 2g97_A* 3g8e_A*
Length = 484
Score = 27.4 bits (60), Expect = 8.3
Identities = 17/105 (16%), Positives = 33/105 (31%), Gaps = 15/105 (14%)
Query: 68 GLDELSIHDFNKHLKFWKPKVQLVAGIINLIQLGGENASKFEQGLWESHE-VISGDAKEE 126
GL + ++ + K K K+Q + K + E ++ + + K
Sbjct: 61 GLQYI-LNKYLKGKVVTKEKIQEAKDVYKEHFQDDVFNEKGWNYILEKYDGHLPIEIKAV 119
Query: 127 QEKATVFPSNEEENNVIPQEVDIPILKISNTLPKHVTQTEWAEML 171
E + N + + NT P+ T W E +
Sbjct: 120 PEGFVIPRGN-------------VLFTVENTDPECYWLTNWIETI 151
>3u0g_A Putative branched-chain amino acid aminotransfera; structural
genomics, seattle structural genomics center for
infectious disease; 1.90A {Burkholderia pseudomallei}
Length = 328
Score = 27.2 bits (61), Expect = 8.6
Identities = 12/39 (30%), Positives = 19/39 (48%), Gaps = 10/39 (25%)
Query: 181 DAKVPIMAHTWPFELDVF----------QKQAIIKLEEH 209
DAK+ ++ HT + + VF AI +L+EH
Sbjct: 42 DAKIHVLTHTLHYGMGVFEGVRAYKTADGGTAIFRLKEH 80
>2eiy_A ILVE, branched-chain amino acid aminotransferase; PLP-dependent
enzyme; HET: PLP; 1.35A {Thermus thermophilus} PDB:
1wrv_A* 2ej0_A* 2ej2_A* 2ej3_A*
Length = 308
Score = 27.2 bits (61), Expect = 8.6
Identities = 10/38 (26%), Positives = 18/38 (47%), Gaps = 9/38 (23%)
Query: 181 DAKVPIMAHTWPFELDVF---------QKQAIIKLEEH 209
+AK +++H + VF + AI +L+EH
Sbjct: 19 EAKTSVLSHALHYGTSVFEGIRAYETAKGPAIFRLKEH 56
>1iye_A Branched-chain amino acid aminotransferase; hexamer, PLP; HET: PGU;
1.82A {Escherichia coli} SCOP: e.17.1.1 PDB: 1i1l_A*
1i1m_A* 1iyd_A* 1i1k_A* 1a3g_A*
Length = 309
Score = 26.8 bits (60), Expect = 9.4
Identities = 10/38 (26%), Positives = 16/38 (42%), Gaps = 9/38 (23%)
Query: 181 DAKVPIMAHTWPFELDVF---------QKQAIIKLEEH 209
DAKV +M+H + VF + + + EH
Sbjct: 20 DAKVHVMSHALHYGTSVFEGIRCYDSHKGPVVFRHREH 57
>3tnd_B Antitoxin VAPB; PIN domain, spovt/ABRB-like domain, ribonuclease,
DNA-bindin translation; 2.70A {Shigella flexneri}
Length = 81
Score = 25.2 bits (55), Expect = 9.4
Identities = 14/64 (21%), Positives = 22/64 (34%), Gaps = 7/64 (10%)
Query: 124 KEEQEKATVFPSNEEENNVIPQEVDIP-------ILKISNTLPKHVTQTEWAEMLDVSKP 176
+ TVF SN + +P+ V +P ++ + T W E D
Sbjct: 3 HHHHHETTVFLSNRSQAVRLPKAVALPENVKRVEVIAVGRTRIITPAGETWDEWFDGHSV 62
Query: 177 VLDF 180
DF
Sbjct: 63 STDF 66
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
0.318 0.137 0.411
Gapped
Lambda K H
0.267 0.0515 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 5,302,218
Number of extensions: 326427
Number of successful extensions: 866
Number of sequences better than 10.0: 1
Number of HSP's gapped: 858
Number of HSP's successfully gapped: 51
Length of query: 333
Length of database: 6,701,793
Length adjustment: 94
Effective length of query: 239
Effective length of database: 4,077,219
Effective search space: 974455341
Effective search space used: 974455341
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 (21.7 bits)
S2: 57 (26.2 bits)