RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4493
(323 letters)
>gnl|CDD|129701 TIGR00614, recQ_fam, ATP-dependent DNA helicase, RecQ family. All
proteins in this family for which functions are known
are 3'-5' DNA-DNA helicases. These proteins are used for
recombination, recombinational repair, and possibly
maintenance of chromosome stability. This family is
based on the phylogenomic analysis of JA Eisen (1999,
Ph.D. Thesis, Stanford University) [DNA metabolism, DNA
replication, recombination, and repair].
Length = 470
Score = 273 bits (699), Expect = 9e-89
Identities = 121/323 (37%), Positives = 177/323 (54%), Gaps = 39/323 (12%)
Query: 13 SVLKSKFNLTDFRPNQLAAINIALLKKDAIIIMPT--------DYP--WSDRVRSVLKSK 62
S+LK+ F L+ FRP QL IN LL +D ++MPT P SD + V+
Sbjct: 1 SILKTVFGLSSFRPVQLEVINAVLLGRDCFVVMPTGGGKSLCYQLPALCSDGITLVISPL 60
Query: 63 FNLTDFRPNQLAAINIALLKKDAIIIMPTGKLLKKKKICLMTESSSLKLLYVSPEKLAKS 122
+L + + QL A I A + + ++K + + +KLLYV+PEK + S
Sbjct: 61 ISLMEDQVLQLKASGIP-----ATFLNSSQSKEQQKNVLTDLKDGKIKLLYVTPEKCSAS 115
Query: 123 KSFMTKLQKMYKAGCLARIAIDEVHCCSSWGHDFRPDYQYLSILKTMFPDVPILGLTATA 182
+ L++ + IA+DE HC S WGHDFRPDY+ L LK FP+VPI+ LTATA
Sbjct: 116 NRLLQTLEERKG---ITLIAVDEAHCISQWGHDFRPDYKALGSLKQKFPNVPIMALTATA 172
Query: 183 TTKVMLDVQKMLQIEDCVVIKAPFNRPNLFYEVRIKPAAQKDCLDELADLMSRRFRNQSG 242
+ V D+ + L +++ + F+RPNL+YEVR K L++L + + F+ +SG
Sbjct: 173 SPSVREDILRQLNLKNPQIFCTSFDRPNLYYEVRRKTP---KILEDLLRFIRKEFKGKSG 229
Query: 243 IIYTTSIKECEDLREELRNRGLRVSAYHAKLESNV------------------SIAFGLG 284
IIY S K+ E + L+N G+ AYHA LE + ++AFG+G
Sbjct: 230 IIYCPSRKKSEQVTASLQNLGIAAGAYHAGLEISARDDVHHKFQRDEIQVVVATVAFGMG 289
Query: 285 IDKPNVRFVIHHCLSKSMENFYQ 307
I+KP+VRFVIH+ L KSME++YQ
Sbjct: 290 INKPDVRFVIHYSLPKSMESYYQ 312
>gnl|CDD|223588 COG0514, RecQ, Superfamily II DNA helicase [DNA replication,
recombination, and repair].
Length = 590
Score = 234 bits (599), Expect = 1e-72
Identities = 112/326 (34%), Positives = 158/326 (48%), Gaps = 83/326 (25%)
Query: 53 DRVRSVLKSKFNLTDFRPNQLAAINIALLKKDAIIIMPTGKLLKKKKIC----------- 101
+ + VLK F FRP Q I+ L KD +++MPTG K +C
Sbjct: 3 EEAQQVLKQVFGYASFRPGQQEIIDALLSGKDTLVVMPTG---GGKSLCYQIPALLLEGL 59
Query: 102 ---------LM---------------TESSSL-----------------KLLYVSPEKLA 120
LM +S+L KLLY+SPE+L
Sbjct: 60 TLVVSPLISLMKDQVDQLEAAGIRAAYLNSTLSREERQQVLNQLKSGQLKLLYISPERLM 119
Query: 121 KSKSFMTKLQKMYKAGCLARIAIDEVHCCSSWGHDFRPDYQYLSILKTMFPDVPILGLTA 180
S F+ L K ++ +AIDE HC S WGHDFRPDY+ L L+ P+ P+L LTA
Sbjct: 120 -SPRFLELL----KRLPISLVAIDEAHCISQWGHDFRPDYRRLGRLRAGLPNPPVLALTA 174
Query: 181 TATTKVMLDVQKMLQIEDCVVIKAPFNRPNLFYEVRIKPAAQKDCLDELADLMSR-RFRN 239
TAT +V D+++ L ++D + + F+RPNL +V K + D+LA L + +
Sbjct: 175 TATPRVRDDIREQLGLQDANIFRGSFDRPNLALKVVEKG----EPSDQLAFLATVLPQLS 230
Query: 240 QSGIIYTTSIKECEDLREELRNRGLRVSAYHAKLESNV------------------SIAF 281
+SGIIY + K+ E+L E LR G+ AYHA L + + AF
Sbjct: 231 KSGIIYCLTRKKVEELAEWLRKNGISAGAYHAGLSNEERERVQQAFLNDEIKVMVATNAF 290
Query: 282 GLGIDKPNVRFVIHHCLSKSMENFYQ 307
G+GIDKP+VRFVIH+ L S+E++YQ
Sbjct: 291 GMGIDKPDVRFVIHYDLPGSIESYYQ 316
>gnl|CDD|215597 PLN03137, PLN03137, ATP-dependent DNA helicase; Q4-like;
Provisional.
Length = 1195
Score = 223 bits (570), Expect = 7e-66
Identities = 131/342 (38%), Positives = 180/342 (52%), Gaps = 54/342 (15%)
Query: 4 NYPWSDRVRSVLKSKFNLTDFRPNQLAAINIALLKKDAIIIMPTDYPWSDRVRSVLKSKF 63
N+PW+ ++ K F FRPNQ IN + D ++MPT S
Sbjct: 441 NFPWTKKLEVNNKKVFGNHSFRPNQREIINATMSGYDVFVLMPTGGGKS----------- 489
Query: 64 NLTDFRPNQLAAINIAL-------LKKDAIIIM-----PTGKL------LKKKKIC--LM 103
LT P + I L L +D I+ + P L ++ +I L
Sbjct: 490 -LTYQLPALICP-GITLVISPLVSLIQDQIMNLLQANIPAASLSAGMEWAEQLEILQELS 547
Query: 104 TESSSLKLLYVSPEKLAKSKSFMTKLQKMYKAGCLARIAIDEVHCCSSWGHDFRPDYQYL 163
+E S KLLYV+PEK+AKS S + L+ + G LAR IDE HC S WGHDFRPDYQ L
Sbjct: 548 SEYSKYKLLYVTPEKVAKSDSLLRHLENLNSRGLLARFVIDEAHCVSQWGHDFRPDYQGL 607
Query: 164 SILKTMFPDVPILGLTATATTKVMLDVQKMLQIEDCVVIKAPFNRPNLFYEVRIKPAAQK 223
ILK FP++P+L LTATAT V DV + L + +CVV + FNRPNL+Y V K K
Sbjct: 608 GILKQKFPNIPVLALTATATASVKEDVVQALGLVNCVVFRQSFNRPNLWYSVVPK---TK 664
Query: 224 DCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYH------------- 270
CL+++ + ++ GIIY S +CE + E L+ G + + YH
Sbjct: 665 KCLEDIDKFIKENHFDECGIIYCLSRMDCEKVAERLQEFGHKAAFYHGSMDPAQRAFVQK 724
Query: 271 --AKLESNV---SIAFGLGIDKPNVRFVIHHCLSKSMENFYQ 307
+K E N+ ++AFG+GI+KP+VRFVIHH L KS+E ++Q
Sbjct: 725 QWSKDEINIICATVAFGMGINKPDVRFVIHHSLPKSIEGYHQ 766
Score = 39.5 bits (92), Expect = 0.002
Identities = 16/46 (34%), Positives = 24/46 (52%)
Query: 47 TDYPWSDRVRSVLKSKFNLTDFRPNQLAAINIALLKKDAIIIMPTG 92
++PW+ ++ K F FRPNQ IN + D ++MPTG
Sbjct: 440 RNFPWTKKLEVNNKKVFGNHSFRPNQREIINATMSGYDVFVLMPTG 485
>gnl|CDD|130456 TIGR01389, recQ, ATP-dependent DNA helicase RecQ. The
ATP-dependent DNA helicase RecQ of E. coli is about 600
residues long. This model represents bacterial proteins
with a high degree of similarity in domain architecture
and in primary sequence to E. coli RecQ. The model
excludes eukaryotic and archaeal proteins with RecQ-like
regions, as well as more distantly related bacterial
helicases related to RecQ [DNA metabolism, DNA
replication, recombination, and repair].
Length = 591
Score = 199 bits (508), Expect = 3e-59
Identities = 114/319 (35%), Positives = 159/319 (49%), Gaps = 77/319 (24%)
Query: 56 RSVLKSKFNLTDFRPNQLAAINIALLKKDAIIIMPTG----------KLLKKKK------ 99
+ VLK F DFRP Q I+ L +D +++MPTG LL K
Sbjct: 2 QQVLKRTFGYDDFRPGQEEIISHVLDGRDVLVVMPTGGGKSLCYQVPALLLKGLTVVISP 61
Query: 100 -ICLMTE--------------------------------SSSLKLLYVSPEKLAKSKSFM 126
I LM + + LKLLYV+PE+L + F+
Sbjct: 62 LISLMKDQVDQLRAAGVAAAYLNSTLSAKEQQDIEKALVNGELKLLYVAPERL-EQDYFL 120
Query: 127 TKLQKMYKAGCLARIAIDEVHCCSSWGHDFRPDYQYLSILKTMFPDVPILGLTATATTKV 186
LQ++ +A +A+DE HC S WGHDFRP+YQ L L FP VP + LTATA +
Sbjct: 121 NMLQRIP----IALVAVDEAHCVSQWGHDFRPEYQRLGSLAERFPQVPRIALTATADAET 176
Query: 187 MLDVQKMLQIEDCVVIKAPFNRPNLFYEVRIKPAAQKDCLDELADLMSRRFRNQSGIIYT 246
D++++L++ D F+RPNL + V K QK LD L ++ R QSGIIY
Sbjct: 177 RQDIRELLRLADANEFITSFDRPNLRFSVVKKNNKQKFLLDYL-----KKHRGQSGIIYA 231
Query: 247 TSIKECEDLREELRNRGLRVSAYHAKLESNV------------------SIAFGLGIDKP 288
+S K+ E+L E L ++G+ AYHA L + V + AFG+GIDKP
Sbjct: 232 SSRKKVEELAERLESQGISALAYHAGLSNKVRAENQEDFLYDDVKVMVATNAFGMGIDKP 291
Query: 289 NVRFVIHHCLSKSMENFYQ 307
NVRFVIH+ + ++E++YQ
Sbjct: 292 NVRFVIHYDMPGNLESYYQ 310
>gnl|CDD|182933 PRK11057, PRK11057, ATP-dependent DNA helicase RecQ; Provisional.
Length = 607
Score = 191 bits (487), Expect = 4e-56
Identities = 100/323 (30%), Positives = 154/323 (47%), Gaps = 89/323 (27%)
Query: 58 VLKSKFNLTDFRPNQLAAINIALLKKDAIIIMPTG-----------------KLLKKKKI 100
VL+ F FRP Q I+ L +D +++MPTG L+ I
Sbjct: 16 VLQETFGYQQFRPGQQEIIDAVLSGRDCLVVMPTGGGKSLCYQIPALVLDGLTLVVSPLI 75
Query: 101 CLMTE--------------------------------SSSLKLLYVSPEKLAKSKSFMTK 128
LM + + +KLLY++PE+L +F+
Sbjct: 76 SLMKDQVDQLLANGVAAACLNSTQTREQQLEVMAGCRTGQIKLLYIAPERLM-MDNFLEH 134
Query: 129 LQKMYKAGCLARIAIDEVHCCSSWGHDFRPDYQYLSILKTMFPDVPILGLTATATTKVML 188
L A +A+DE HC S WGHDFRP+Y L L+ FP +P + LTATA
Sbjct: 135 LAHWN----PALLAVDEAHCISQWGHDFRPEYAALGQLRQRFPTLPFMALTATADDTTRQ 190
Query: 189 DVQKMLQIEDCVVIKAPFNRPNLFYEV--RIKPAAQKDCLDELADLMSRRF----RNQSG 242
D+ ++L + D ++ + F+RPN+ Y + + KP LD+L R+ R +SG
Sbjct: 191 DIVRLLGLNDPLIQISSFDRPNIRYTLVEKFKP------LDQLM-----RYVQEQRGKSG 239
Query: 243 IIYTTSIKECEDLREELRNRGLRVSAYHAKLESNV------------------SIAFGLG 284
IIY S + ED L++RG+ +AYHA L+++V ++AFG+G
Sbjct: 240 IIYCNSRAKVEDTAARLQSRGISAAAYHAGLDNDVRADVQEAFQRDDLQIVVATVAFGMG 299
Query: 285 IDKPNVRFVIHHCLSKSMENFYQ 307
I+KPNVRFV+H + +++E++YQ
Sbjct: 300 INKPNVRFVVHFDIPRNIESYYQ 322
>gnl|CDD|238034 cd00079, HELICc, Helicase superfamily c-terminal domain; associated
with DEXDc-, DEAD-, and DEAH-box proteins, yeast
initiation factor 4A, Ski2p, and Hepatitis C virus NS3
helicases; this domain is found in a wide variety of
helicases and helicase related proteins; may not be an
autonomously folding unit, but an integral part of the
helicase; 4 helicase superfamilies at present according
to the organization of their signature motifs; all
helicases share the ability to unwind nucleic acid
duplexes with a distinct directional polarity; they
utilize the free energy from nucleoside triphosphate
hydrolysis to fuel their translocation along DNA,
unwinding the duplex in the process.
Length = 131
Score = 64.2 bits (157), Expect = 7e-13
Identities = 30/116 (25%), Positives = 46/116 (39%), Gaps = 20/116 (17%)
Query: 210 NLFYEVRIKPAAQKDCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAY 269
+ V + + L EL L + +I+ S K ++L E LR G++V+A
Sbjct: 1 PIKQYVLPVEDEKLEALLEL--LKEHLKKGGKVLIFCPSKKMLDELAELLRKPGIKVAAL 58
Query: 270 HAKL---------------ESNVSIA---FGLGIDKPNVRFVIHHCLSKSMENFYQ 307
H E V +A GID PNV VI++ L S ++ Q
Sbjct: 59 HGDGSQEEREEVLKDFREGEIVVLVATDVIARGIDLPNVSVVINYDLPWSPSSYLQ 114
>gnl|CDD|215832 pfam00270, DEAD, DEAD/DEAH box helicase. Members of this family
include the DEAD and DEAH box helicases. Helicases are
involved in unwinding nucleic acids. The DEAD box
helicases are involved in various aspects of RNA
metabolism, including nuclear transcription, pre mRNA
splicing, ribosome biogenesis, nucleocytoplasmic
transport, translation, RNA decay and organellar gene
expression.
Length = 169
Score = 58.8 bits (143), Expect = 1e-10
Identities = 46/192 (23%), Positives = 69/192 (35%), Gaps = 54/192 (28%)
Query: 25 RPNQLAAINIALLKKDAIIIMPTDYPWSDRVRSVLKSK-FNLTDFRPNQLAAINIALLKK 83
P Q AI L KD ++ PT K+ F L + L KK
Sbjct: 1 TPIQAQAIPAILSGKDVLVQAPTGSG---------KTLAF--------LLPILQALLPKK 43
Query: 84 D---AIIIMPT-----------GKLLKKK--KICLMTESSSLK------------LLYVS 115
A+++ PT KL K ++ L+T +SLK +L +
Sbjct: 44 GGPQALVLAPTRELAEQIYEELKKLFKILGLRVALLTGGTSLKEQARKLKKGKADILVGT 103
Query: 116 PEKLAKSKSFMTKLQKMYKAGCLARIAIDEVHCCSSWGHDFRPDYQYLSILKTMFPDVPI 175
P +L + + K+ L + +DE H G F D + IL + PD I
Sbjct: 104 PGRLLD----LLRRGKLKLLKNLKLLVLDEAHRLLDMG--FGDDLE--EILSRLPPDRQI 155
Query: 176 LGLTATATTKVM 187
L L+AT +
Sbjct: 156 LLLSATLPRNLE 167
>gnl|CDD|214692 smart00487, DEXDc, DEAD-like helicases superfamily.
Length = 201
Score = 48.6 bits (116), Expect = 8e-07
Identities = 44/217 (20%), Positives = 68/217 (31%), Gaps = 34/217 (15%)
Query: 17 SKFNLTDFRPNQLAAINIAL-LKKDAIIIMPT------DYPWSDRVRSVLKSKFNLTDFR 69
KF RP Q AI L +D I+ PT L++ R
Sbjct: 2 EKFGFEPLRPYQKEAIEALLSGLRDVILAAPTGSGKTLAAL-----LPALEALKRGKGGR 56
Query: 70 -----PNQLAAINIA-----LLKKDAIIIMPTGKLLKKKKICLMTESSSLKLLYVSPEKL 119
P + A A L + ++ K++ ES +L +P +L
Sbjct: 57 VLVLVPTRELAEQWAEELKKLGPSLGLKVVGLYGGDSKREQLRKLESGKTDILVTTPGRL 116
Query: 120 AKSKSFMTKLQKMYKAGCLARIAIDEVHCCSSWGHDFRPDYQYLSILKTMFPDVPILGLT 179
+ +DE H G F Q +LK + +V +L L+
Sbjct: 117 LDLLENDKLSLSNVD-----LVILDEAHRLLDGG--FGD--QLEKLLKLLPKNVQLLLLS 167
Query: 180 ATATTKVMLDVQKMLQIEDCVVIKAPFNRPNLFYEVR 216
AT ++ ++ L D V I F P E
Sbjct: 168 ATPPEEIENLLELFLN--DPVFIDVGF-TPLEPIEQF 201
>gnl|CDD|197757 smart00490, HELICc, helicase superfamily c-terminal domain.
Length = 82
Score = 44.1 bits (105), Expect = 3e-06
Identities = 18/73 (24%), Positives = 28/73 (38%), Gaps = 18/73 (24%)
Query: 253 EDLREELRNRGLRVSAYHAKLESN-----------------VSI-AFGLGIDKPNVRFVI 294
E+L E L+ G++V+ H L V+ G+D P V VI
Sbjct: 1 EELAELLKELGIKVARLHGGLSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVI 60
Query: 295 HHCLSKSMENFYQ 307
+ L S ++ Q
Sbjct: 61 IYDLPWSPASYIQ 73
>gnl|CDD|201125 pfam00271, Helicase_C, Helicase conserved C-terminal domain. The
Prosite family is restricted to DEAD/H helicases,
whereas this domain family is found in a wide variety of
helicases and helicase related proteins. It may be that
this is not an autonomously folding unit, but an
integral part of the helicase.
Length = 78
Score = 44.0 bits (105), Expect = 3e-06
Identities = 17/69 (24%), Positives = 28/69 (40%), Gaps = 18/69 (26%)
Query: 257 EELRNRGLRVSAYHAKLESN-----------------VSI-AFGLGIDKPNVRFVIHHCL 298
+ LR G++V+ H L V+ G GID P+V VI++ L
Sbjct: 1 KLLRKPGIKVARLHGGLSQEEREEILEDFRNGKSKVLVATDVAGRGIDLPDVNLVINYDL 60
Query: 299 SKSMENFYQ 307
+ ++ Q
Sbjct: 61 PWNPASYIQ 69
>gnl|CDD|224123 COG1202, COG1202, Superfamily II helicase, archaea-specific
[General function prediction only].
Length = 830
Score = 43.2 bits (102), Expect = 1e-04
Identities = 32/145 (22%), Positives = 63/145 (43%), Gaps = 22/145 (15%)
Query: 141 IAIDEVHCCSSWGHDFRPDYQYLSILKTMFPDVPILGLTATATT----------KVMLDV 190
+ IDE+H R D + L+ +FP + L+AT K++L
Sbjct: 342 VVIDEIHTLEDEERGPRLD-GLIGRLRYLFPGAQFIYLSATVGNPEELAKKLGAKLVLYD 400
Query: 191 QKMLQIEDCVVI-KAPFNRPNLFYEVRIKPAAQKDCLDELADLMSRRFRNQSGIIYTTSI 249
++ + +E +V + + ++ + E + S+ +R Q+ I++T S
Sbjct: 401 ERPVPLERHLVFARNESEKWDIIARL---------VKREFSTESSKGYRGQT-IVFTYSR 450
Query: 250 KECEDLREELRNRGLRVSAYHAKLE 274
+ C +L + L +GL+ + YHA L
Sbjct: 451 RRCHELADALTGKGLKAAPYHAGLP 475
>gnl|CDD|238005 cd00046, DEXDc, DEAD-like helicases superfamily. A diverse family
of proteins involved in ATP-dependent RNA or DNA
unwinding. This domain contains the ATP-binding region.
Length = 144
Score = 40.0 bits (94), Expect = 3e-04
Identities = 23/117 (19%), Positives = 43/117 (36%), Gaps = 16/117 (13%)
Query: 70 PNQLAAINIA-----LLKKDAIIIMPTGKLLKKKKICLMTESSSLKLLYVSPEKLAKSKS 124
P + A +A L + + G K++ L++ + ++ +P +L
Sbjct: 38 PTRELANQVAERLKELFGEGIKVGYLIGGTSIKQQEKLLSGKT--DIVVGTPGRLLDE-- 93
Query: 125 FMTKLQKMYKAGCLARIAIDEVHCCSSWGHDFRPDYQYLSILKTMFPDVPILGLTAT 181
+ K L + +DE H + G L IL + D +L L+AT
Sbjct: 94 LERLKLSLKK---LDLLILDEAHRLLNQGFGLLG----LKILLKLPKDRQVLLLSAT 143
>gnl|CDD|223587 COG0513, SrmB, Superfamily II DNA and RNA helicases [DNA
replication, recombination, and repair / Transcription /
Translation, ribosomal structure and biogenesis].
Length = 513
Score = 39.0 bits (91), Expect = 0.002
Identities = 26/112 (23%), Positives = 47/112 (41%), Gaps = 23/112 (20%)
Query: 213 YEVRIKPAAQK-DCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHA 271
+ + ++ +K + L +L I++ + + E+L E LR RG +V+A H
Sbjct: 250 FYLEVESEEEKLELLLKLLKDE----DEGRVIVFVRTKRLVEELAESLRKRGFKVAALHG 305
Query: 272 KL---------------ESNVSIA---FGLGIDKPNVRFVIHHCLSKSMENF 305
L E V +A G+D P+V VI++ L E++
Sbjct: 306 DLPQEERDRALEKFKDGELRVLVATDVAARGLDIPDVSHVINYDLPLDPEDY 357
>gnl|CDD|218292 pfam04851, ResIII, Type III restriction enzyme, res subunit.
Length = 100
Score = 33.3 bits (77), Expect = 0.034
Identities = 35/116 (30%), Positives = 44/116 (37%), Gaps = 24/116 (20%)
Query: 68 FRPNQLAAINIALLKKDAIIIMPT--GKLLKKKKICLMTESSSLKLLYVSPEKLAKSKSF 125
RP Q AI L KK +I+M T GK L + K+L+V P K +
Sbjct: 4 LRPYQEEAIERLLEKKRGLIVMATGSGKTLTAAALIARLAKGKKKVLFVVPRKDLLEQ-- 61
Query: 126 MTKLQKMYKAGCLARIAIDEVHCCSSWGHDFRPDYQYLSILKTMFPDVPILGLTAT 181
+ I IDE H H Y IL+ F +LGLTAT
Sbjct: 62 -ALV-----------IIIDEAH------HSSAKTK-YRKILE-KFKPAFLLGLTAT 97
>gnl|CDD|185609 PTZ00424, PTZ00424, helicase 45; Provisional.
Length = 401
Score = 34.8 bits (80), Expect = 0.057
Identities = 44/170 (25%), Positives = 71/170 (41%), Gaps = 33/170 (19%)
Query: 161 QYLSILKTMFPDVPILGLTATA-------TTKVMLDVQKMLQIEDCVVIKAPFNRPNLFY 213
Q + K + PDV + +AT TTK M D +++L +D + ++ FY
Sbjct: 190 QIYDVFKKLPPDVQVALFSATMPNEILELTTKFMRDPKRILVKKDELTLEGI----RQFY 245
Query: 214 EVRIKPAAQKDCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAKL 273
V ++ K D L DL Q+ IIY + ++ + L +++ R VS H +
Sbjct: 246 -VAVEKEEWK--FDTLCDLYETLTITQA-IIYCNTRRKVDYLTKKMHERDFTVSCMHGDM 301
Query: 274 E---------------SNVSIAFGL---GIDKPNVRFVIHHCLSKSMENF 305
+ + V I L GID V VI++ L S EN+
Sbjct: 302 DQKDRDLIMREFRSGSTRVLITTDLLARGIDVQQVSLVINYDLPASPENY 351
>gnl|CDD|236977 PRK11776, PRK11776, ATP-dependent RNA helicase DbpA; Provisional.
Length = 460
Score = 34.0 bits (79), Expect = 0.10
Identities = 17/63 (26%), Positives = 31/63 (49%), Gaps = 6/63 (9%)
Query: 212 FYEVRIKPAAQKDCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHA 271
FYEV + + L L L+ + +S +++ + KEC+++ + L +G A H
Sbjct: 221 FYEV-----SPDERLPALQRLLLH-HQPESCVVFCNTKKECQEVADALNAQGFSALALHG 274
Query: 272 KLE 274
LE
Sbjct: 275 DLE 277
>gnl|CDD|224122 COG1201, Lhr, Lhr-like helicases [General function prediction
only].
Length = 814
Score = 33.8 bits (78), Expect = 0.12
Identities = 16/41 (39%), Positives = 19/41 (46%), Gaps = 2/41 (4%)
Query: 52 SDRVRSVLKSKFNLTDFRPNQLAAINIALLKKDAIIIMPTG 92
RVR K KF T P Q AI ++ +II PTG
Sbjct: 9 DPRVREWFKRKF--TSLTPPQRYAIPEIHSGENVLIIAPTG 47
Score = 31.5 bits (72), Expect = 0.78
Identities = 15/40 (37%), Positives = 18/40 (45%), Gaps = 2/40 (5%)
Query: 8 SDRVRSVLKSKFNLTDFRPNQLAAINIALLKKDAIIIMPT 47
RVR K KF T P Q AI ++ +II PT
Sbjct: 9 DPRVREWFKRKF--TSLTPPQRYAIPEIHSGENVLIIAPT 46
>gnl|CDD|234506 TIGR04221, SecA2_Mycobac, accessory Sec system translocase SecA2,
Actinobacterial type. Members of this family are the
SecA2 subunit of the Mycobacterial type of accessory
secretory system. This family is quite different SecA2
of the Staph/Strep type (TIGR03714).
Length = 762
Score = 33.6 bits (77), Expect = 0.13
Identities = 28/109 (25%), Positives = 50/109 (45%), Gaps = 14/109 (12%)
Query: 169 MFPDVPILGLTATATTKVMLDVQKMLQIEDCVVIKAPFNRPNLFYE----VRIKPAAQKD 224
+P V G+T TA + +++ Q D V P N PN+ ++ V A + D
Sbjct: 359 RYPTV--CGMTGTA----VAAGEQLRQFYDLGVSVIPPNTPNIRFDEADRVYATAAEKND 412
Query: 225 CL-DELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAK 272
+ +E+A++ Q ++ T + E E+L E L G+ + +AK
Sbjct: 413 AIVEEIAEVHKT---GQPVLVGTQDVAESEELAEALLEAGVPCNVLNAK 458
>gnl|CDD|233063 TIGR00631, uvrb, excinuclease ABC, B subunit. All proteins in this
family for wich functions are known are DNA helicases
that function in the nucleotide excision repair and are
endonucleases that make the 3' incision next to DNA
damage. They are part of a pathway requiring UvrA, UvrB,
UvrC, and UvrD homologs. This family is based on the
phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis,
Stanford University) [DNA metabolism, DNA replication,
recombination, and repair].
Length = 655
Score = 32.7 bits (75), Expect = 0.27
Identities = 19/67 (28%), Positives = 36/67 (53%), Gaps = 11/67 (16%)
Query: 214 EVRIKPAA-QKDCLDELADLMS----RRFRNQSGIIYTTSIKECEDLREELRNRGLRVSA 268
E+ ++P Q D DL+S R RN+ ++ T + K EDL + L+ G++V
Sbjct: 418 EIEVRPTDGQVD------DLLSEIRQRVARNERVLVTTLTKKMAEDLTDYLKELGIKVRY 471
Query: 269 YHAKLES 275
H+++++
Sbjct: 472 LHSEIDT 478
>gnl|CDD|234874 PRK00955, PRK00955, hypothetical protein; Provisional.
Length = 620
Score = 31.8 bits (73), Expect = 0.47
Identities = 10/26 (38%), Positives = 14/26 (53%), Gaps = 3/26 (11%)
Query: 154 HDFRPDYQ---YLSILKTMFPDVPIL 176
RPD Y + +K +PDVPI+
Sbjct: 102 MGLRPDRATIVYCNKIKEAYPDVPII 127
>gnl|CDD|235910 PRK07024, PRK07024, short chain dehydrogenase; Provisional.
Length = 257
Score = 31.4 bits (72), Expect = 0.55
Identities = 17/40 (42%), Positives = 19/40 (47%), Gaps = 11/40 (27%)
Query: 249 IKECEDLREELRNRGLRVSAYHAKLESNVSIAFGLGIDKP 288
IK E LR ELR G+RV V+IA G I P
Sbjct: 159 IKYLESLRVELRPAGVRV----------VTIAPGY-IRTP 187
>gnl|CDD|234594 PRK00047, glpK, glycerol kinase; Provisional.
Length = 498
Score = 30.9 bits (71), Expect = 0.98
Identities = 11/32 (34%), Positives = 15/32 (46%), Gaps = 1/32 (3%)
Query: 3 PNYPWSDRVRSVLKSKFNLTDFRPNQLAAINI 34
PN W+ SV+ P+Q+AAI I
Sbjct: 50 PNEIWA-SQLSVIAEALAKAGISPDQIAAIGI 80
Score = 30.2 bits (69), Expect = 1.8
Identities = 9/28 (32%), Positives = 13/28 (46%), Gaps = 1/28 (3%)
Query: 51 WSDRVRSVLKSKFNLTDFRPNQLAAINI 78
W+ SV+ P+Q+AAI I
Sbjct: 54 WA-SQLSVIAEALAKAGISPDQIAAIGI 80
>gnl|CDD|203656 pfam07503, zf-HYPF, HypF finger. The HypF family of proteins are
involved in the maturation and regulation of
hydrogenase. In the N-terminus they appear to have two
Zinc finger domains, as modelled by this family.
Length = 35
Score = 27.4 bits (62), Expect = 1.0
Identities = 10/30 (33%), Positives = 13/30 (43%), Gaps = 5/30 (16%)
Query: 223 KDCLDELADLMSRRFRNQSGIIYTTSIKEC 252
+CL E D ++RRF Q S C
Sbjct: 3 PECLKEYFDPLNRRFHAQ-----FISCTNC 27
>gnl|CDD|185771 cd09248, BRO1_Rhophilin_1, Protein-interacting Bro1-like domain of
RhoA-binding protein Rhophilin-1. This subfamily
contains the Bro1-like domain of the RhoA-binding
protein, Rhophilin-1. It belongs to the BRO1_Alix_like
superfamily which also includes the Bro1-like domains of
mammalian Alix (apoptosis-linked gene-2 interacting
protein X), His-Domain type N23 protein tyrosine
phosphatase (HD-PTP, also known as PTPN23), RhoA-binding
protein Rhophilin-2, Brox, Bro1 and Rim20 (also known as
PalA) from Saccharomyces cerevisiae, Ustilago maydis
Rim23 (also known as PalC), and related domains.
Rhophilin-1 binds both GDP- and GTP-bound RhoA.
Bro1-like domains are boomerang-shaped, and part of the
domain is a tetratricopeptide repeat (TPR)-like
structure. In addition to this Bro1-like domain,
Rhophilin-1 contains an N-terminal Rho-binding domain
and a C-terminal PDZ (PS.D.-95, Disc-large, ZO-1)
domain. The Drosophila knockout of the Rhophilin-1 is
embryonic lethal, suggesting an essential role in
embryonic development. The isolated Bro1-like domain of
Rhophilin-1 binds human immunodeficiency virus type 1
(HIV-1) nucleocapsid. Rhophilin-1 lacks the V-shaped (V)
domain found in many members of the BRO1_Alix_ like
superfamily.
Length = 384
Score = 30.2 bits (68), Expect = 1.3
Identities = 15/44 (34%), Positives = 23/44 (52%), Gaps = 1/44 (2%)
Query: 217 IKPAAQKDCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELR 260
+K + D L +L+S F + G Y I+E EDLR+ +R
Sbjct: 6 LKETKELDLPTPLKELISEHF-GEDGTSYEAEIRELEDLRQAMR 48
>gnl|CDD|224035 COG1110, COG1110, Reverse gyrase [DNA replication, recombination,
and repair].
Length = 1187
Score = 29.3 bits (66), Expect = 3.1
Identities = 17/74 (22%), Positives = 32/74 (43%), Gaps = 21/74 (28%)
Query: 242 GIIYTTS---IKECEDLREELRNRGLRVSAYHAKLESN--------VSIAFGL------- 283
G+I+ ++ E+L E LR+ G+ HA+ E V + G+
Sbjct: 338 GLIFVPIDYGREKAEELAEYLRSHGINAELIHAEKEEALEDFEEGEVDVLVGVASYYGVL 397
Query: 284 --GIDKPN-VRFVI 294
G+D P+ +R+ +
Sbjct: 398 VRGLDLPHRIRYAV 411
>gnl|CDD|222108 pfam13407, Peripla_BP_4, Periplasmic binding protein domain.
This domain is found in a variety of bacterial
periplasmic binding proteins.
Length = 258
Score = 28.8 bits (65), Expect = 3.3
Identities = 12/34 (35%), Positives = 17/34 (50%), Gaps = 4/34 (11%)
Query: 28 QLAAINIALLKK-DAIIIMPTDYPWSDRVRSVLK 60
Q+A I A+ + DAII+ P D + LK
Sbjct: 44 QVAQIENAIAQGVDAIIVAPVD---PTALAPALK 74
>gnl|CDD|223120 COG0042, COG0042, tRNA-dihydrouridine synthase [Translation,
ribosomal structure and biogenesis].
Length = 323
Score = 28.8 bits (65), Expect = 3.4
Identities = 20/106 (18%), Positives = 39/106 (36%), Gaps = 9/106 (8%)
Query: 139 ARIAIDEVHCCSSW-GHDFRPDYQYLSILKTMFPDVPILGLTATATTKVMLDVQKMLQIE 197
A VH + G+ D+ Y+ LK P +P++ + + D ++ML+
Sbjct: 164 AGADALTVHGRTRAQGYLGPADWDYIKELKEAVPSIPVIANGDIKSLE---DAKEMLEYT 220
Query: 198 DC--VVIK-APFNRPNLFYEVRIKPAAQKDCLD--ELADLMSRRFR 238
V+I P LF ++ + E+ D++
Sbjct: 221 GADGVMIGRGALGNPWLFRQIDYLETGELLPPTLAEVLDILREHLE 266
>gnl|CDD|223630 COG0556, UvrB, Helicase subunit of the DNA excision repair complex
[DNA replication, recombination, and repair].
Length = 663
Score = 29.1 bits (66), Expect = 4.0
Identities = 18/63 (28%), Positives = 36/63 (57%), Gaps = 3/63 (4%)
Query: 214 EVRIKPAA-QKDCLDELADLMSRRFRNQSGIIYTTSIKECEDLREELRNRGLRVSAYHAK 272
E+ ++P Q D D L+++ R +N+ ++ T + K EDL E L+ G++V H+
Sbjct: 422 EIEVRPTKGQVD--DLLSEIRKRVAKNERVLVTTLTKKMAEDLTEYLKELGIKVRYLHSD 479
Query: 273 LES 275
+++
Sbjct: 480 IDT 482
>gnl|CDD|236949 PRK11655, ubiC, chorismate pyruvate lyase; Provisional.
Length = 169
Score = 28.0 bits (63), Expect = 4.9
Identities = 14/41 (34%), Positives = 20/41 (48%), Gaps = 1/41 (2%)
Query: 219 PAAQKDCLDELADLMSRRFRNQSGIIYTTSIKECEDLREEL 259
P D L E D M++RF Q + T I+E ++EL
Sbjct: 22 PPQLLDWLMEE-DSMTKRFEQQCKRVSVTLIREGFVTQDEL 61
>gnl|CDD|233290 TIGR01141, hisC, histidinol-phosphate aminotransferase. Alternate
names: histidinol-phosphate transaminase; imidazole
acetol-phosphate transaminase Histidinol-phosphate
aminotransferase is a pyridoxal-phosphate dependent
enzyme [Amino acid biosynthesis, Histidine family].
Length = 346
Score = 28.4 bits (64), Expect = 5.4
Identities = 30/134 (22%), Positives = 51/134 (38%), Gaps = 24/134 (17%)
Query: 2 LPNYPWSD--RVRSVLKSKFNLTDFRPNQLAAIN----------IALLK-KDAIIIMP-- 46
L YP D ++ L + + P Q+ N A L+ DA+++ P
Sbjct: 48 LHRYPDPDPAELKQALADYYGVD---PEQILLGNGSDEIIELLIRAFLEPGDAVLVPPPT 104
Query: 47 -TDYPWSDRVRSVLKSKFNLTDFRPNQLAAINIALLKKDAIIIM-----PTGKLLKKKKI 100
+ Y S ++ K L + L I +A+ K ++ + PTG LL + I
Sbjct: 105 YSMYEISAKIHGAEVVKVPLDEDGQLDLEDILVAIDDKPKLVFLCSPNNPTGNLLSRSDI 164
Query: 101 CLMTESSSLKLLYV 114
+ E + L V
Sbjct: 165 EAVLERTPEDALVV 178
>gnl|CDD|212139 cd11532, NTP-PPase_COG4997, Nucleoside Triphosphate
Pyrophosphohydrolase (EC 3.6.1.8) MazG-like domain found
in a group of uncharacterized proteins from archaea and
bacteria. The family includes some uncharacterized
hypothetical proteins from archaea and bacteria.
Although their biological roles remain unclear, the
family members show significant sequence similarity to
the dimeric 2-deoxyuridine 5'-triphosphate
nucleotidohydrolase (dUTP pyrophosphatase or dUTPase)
and NTP-PPase MazG proteins. However, unlike typical
tandem-domain MazG proteins, the family contains a
single MazG-like domain.
Length = 95
Score = 26.7 bits (60), Expect = 5.5
Identities = 17/47 (36%), Positives = 24/47 (51%), Gaps = 7/47 (14%)
Query: 220 AAQKDCLDELADLMS--RRFRNQSGIIYTTSIKECEDLREE-LRNRG 263
A +D L+ELADL+ GI S++E E +RE+ RG
Sbjct: 48 AKTEDSLEELADLLEVIYAIAEAHGI----SLEELEKVREKKREERG 90
>gnl|CDD|234478 TIGR04121, DEXH_lig_assoc, DEXH box helicase, DNA
ligase-associated. Members of this protein family are
DEAD/DEAH box helicases found associated with a
bacterial ATP-dependent DNA ligase, part of a four-gene
system that occurs in about 12 % of prokaryotic
reference genomes. The actual motif in this family is
DE[VILW]H.
Length = 803
Score = 28.3 bits (64), Expect = 6.0
Identities = 18/67 (26%), Positives = 25/67 (37%), Gaps = 19/67 (28%)
Query: 69 RPNQLAAINIALLKKDAIIIMPTG-------------KLLKKKKICLMTESSSLKLLYVS 115
RP QL AL + ++I PTG L +K L LY++
Sbjct: 15 RPFQLEMWAAALEGRSGLLIAPTGSGKTLAGFLPSLIDLAGPEK-----PKKGLHTLYIT 69
Query: 116 PEK-LAK 121
P + LA
Sbjct: 70 PLRALAV 76
>gnl|CDD|218981 pfam06307, Herpes_IR6, Herpesvirus IR6 protein. This family
consists of several Herpesvirus IR6 proteins. The equine
herpesvirus 1 (EHV-1) IR6 protein forms typical rod-like
structures in infected cells, influences virus growth at
elevated temperatures, and determines the virulence of
EHV-1 Rac strains.
Length = 214
Score = 27.6 bits (61), Expect = 8.2
Identities = 11/35 (31%), Positives = 20/35 (57%)
Query: 189 DVQKMLQIEDCVVIKAPFNRPNLFYEVRIKPAAQK 223
+V+ Q+ D ++ PF P+ +YE I+P A +
Sbjct: 74 EVRFFKQLYDGTFVRLPFLYPDEYYEDEIEPLADR 108
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.324 0.137 0.405
Gapped
Lambda K H
0.267 0.0781 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 16,354,196
Number of extensions: 1573292
Number of successful extensions: 2202
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2174
Number of HSP's successfully gapped: 66
Length of query: 323
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 226
Effective length of database: 6,635,264
Effective search space: 1499569664
Effective search space used: 1499569664
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 59 (26.4 bits)