RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1548
(448 letters)
>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 = 247 bits (633), Expect = 9e-77
Identities = 96/270 (35%), Positives = 168/270 (62%), Gaps = 8/270 (2%)
Query: 149 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYV--LVMCHTRELAFQISKEYERFSKY 206
G D+L QA++G GKTA F+L LQ++ + YV L++ TRELA QI++E + K
Sbjct: 66 GRDVLGQAQTGTGKTAAFLLPLLQKILKSVERKYVSALILAPTRELAVQIAEELRKLGKN 125
Query: 207 MSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECD 266
+ ++V V +GG+ I+K E LK IVV TPGR+L L++ KL+LS ++ +LDE D
Sbjct: 126 LGGLRVAVVYGGVSIRKQIEALKR-GVDIVVATPGRLLDLIKRGKLDLSGVETLVLDEAD 184
Query: 267 KMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDEA-KLT 325
+ML+ + D+++I ++ P +Q ++FSAT+ +IR + +++++DP+E+ V E + T
Sbjct: 185 RMLD-MGFIDDIEKILKALPPDRQTLLFSATMPDDIRELARRYLNDPVEIEVSVEKLERT 243
Query: 326 LHGLQQHYVKLK-ENEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSI 384
L ++Q Y++++ E EK + L +LL + +V++FV++ L+ L ++ F ++
Sbjct: 244 LKKIKQFYLEVESEEEKLELLLKLLKDEDEGRVIVFVRTKRLVEELAESLRKRGFKVAAL 303
Query: 385 HRGMTQEERLKKYQEFKDFHKGLAITFASD 414
H + QEER + ++FKD L + A+D
Sbjct: 304 HGDLPQEERDRALEKFKD--GELRVLVATD 331
Score = 71.0 bits (174), Expect = 4e-13
Identities = 24/46 (52%), Positives = 33/46 (71%)
Query: 100 RILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTK 145
R+LVAT++ RG+DI V+ V NYD+P D + Y+HR+ R GR G K
Sbjct: 325 RVLVATDVAARGLDIPDVSHVINYDLPLDPEDYVHRIGRTGRAGRK 370
>gnl|CDD|238167 cd00268, DEADc, DEAD-box helicases. A diverse family of proteins
involved in ATP-dependent RNA unwinding, needed in a
variety of cellular processes including splicing,
ribosome biogenesis and RNA degradation. The name
derives from the sequence of the Walker B motif (motif
II). This domain contains the ATP- binding region.
Length = 203
Score = 210 bits (536), Expect = 4e-66
Identities = 66/170 (38%), Positives = 106/170 (62%), Gaps = 5/170 (2%)
Query: 149 GMDILCQAKSGMGKTAVFVLATLQQLETTDSN--VYVLVMCHTRELAFQISKEYERFSKY 206
G D++ QA++G GKTA F++ L++L+ + L++ TRELA QI++ + K+
Sbjct: 36 GRDVIGQAQTGSGKTAAFLIPILEKLDPSPKKDGPQALILAPTRELALQIAEVARKLGKH 95
Query: 207 MSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECD 266
N+KV V +GG I K LK P IVV TPGR+L L+ KL+LS +K+ +LDE D
Sbjct: 96 T-NLKVVVIYGGTSIDKQIRKLK-RGPHIVVATPGRLLDLLERGKLDLSKVKYLVLDEAD 153
Query: 267 KMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEV 316
+ML+ ++EI + P +Q ++FSAT+ KE+R + +KF+ +P+ +
Sbjct: 154 RMLDM-GFEDQIREILKLLPKDRQTLLFSATMPKEVRDLARKFLRNPVRI 202
>gnl|CDD|236977 PRK11776, PRK11776, ATP-dependent RNA helicase DbpA; Provisional.
Length = 460
Score = 174 bits (444), Expect = 2e-49
Identities = 88/247 (35%), Positives = 140/247 (56%), Gaps = 8/247 (3%)
Query: 149 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMS 208
G D++ QAK+G GKTA F L LQ+L+ V LV+C TRELA Q++KE R ++++
Sbjct: 41 GKDVIAQAKTGSGKTAAFGLGLLQKLDVKRFRVQALVLCPTRELADQVAKEIRRLARFIP 100
Query: 209 NIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKM 268
NIKV GG+P+ + L+ H I+VGTPGRIL +R L+L L +LDE D+M
Sbjct: 101 NIKVLTLCGGVPMGPQIDSLE-HGAHIIVGTPGRILDHLRKGTLDLDALNTLVLDEADRM 159
Query: 269 LEQLEM--RRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDEAKLTL 326
L+M + + I R +P +Q ++FSAT + I + ++F DP+EV V+ L
Sbjct: 160 ---LDMGFQDAIDAIIRQAPARRQTLLFSATYPEGIAAISQRFQRDPVEVKVESTHDLP- 215
Query: 327 HGLQQHYVKLKENEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHR 386
++Q + ++ +E+ L LL + V+F + C ++ L+ Q F A+++H
Sbjct: 216 -AIEQRFYEVSPDERLPALQRLLLHHQPESCVVFCNTKKECQEVADALNAQGFSALALHG 274
Query: 387 GMTQEER 393
+ Q +R
Sbjct: 275 DLEQRDR 281
Score = 58.7 bits (143), Expect = 3e-09
Identities = 19/46 (41%), Positives = 32/46 (69%)
Query: 100 RILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTK 145
+LVAT++ RG+DI+ + V NY++ D + ++HR+ R GR G+K
Sbjct: 294 SVLVATDVAARGLDIKALEAVINYELARDPEVHVHRIGRTGRAGSK 339
>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 = 150 bits (381), Expect = 1e-43
Identities = 58/156 (37%), Positives = 87/156 (55%), Gaps = 3/156 (1%)
Query: 149 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMS 208
G D+L QA +G GKT F+L LQ L LV+ TRELA QI +E ++ K +
Sbjct: 14 GKDVLVQAPTGSGKTLAFLLPILQALLPKKGGPQALVLAPTRELAEQIYEELKKLFKIL- 72
Query: 209 NIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLS-LLKHFILDECDK 267
++V + GG +++ LK I+VGTPGR+L L+R KL L LK +LDE +
Sbjct: 73 GLRVALLTGGTSLKEQARKLKKGKADILVGTPGRLLDLLRRGKLKLLKNLKLLVLDEAHR 132
Query: 268 MLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIR 303
+L+ D++EI P +Q+++ SATL + +
Sbjct: 133 LLDM-GFGDDLEEILSRLPPDRQILLLSATLPRNLE 167
>gnl|CDD|185609 PTZ00424, PTZ00424, helicase 45; Provisional.
Length = 401
Score = 150 bits (380), Expect = 6e-41
Identities = 91/261 (34%), Positives = 142/261 (54%), Gaps = 6/261 (2%)
Query: 143 GTKAVL-GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYE 201
G K +L G D + QA+SG GKTA FV+A LQ ++ + L++ TRELA QI K
Sbjct: 58 GIKPILDGYDTIGQAQSGTGKTATFVIAALQLIDYDLNACQALILAPTRELAQQIQKVVL 117
Query: 202 RFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFI 261
Y+ ++ GG ++ D LK +VVGTPGR+ ++ + L + LK FI
Sbjct: 118 ALGDYL-KVRCHACVGGTVVRDDINKLKA-GVHMVVGTPGRVYDMIDKRHLRVDDLKLFI 175
Query: 262 LDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDE 321
LDE D+ML + + + ++F+ P QV +FSAT+ EI + KFM DP + V +
Sbjct: 176 LDEADEMLSR-GFKGQIYDVFKKLPPDVQVALFSATMPNEILELTTKFMRDPKRILVKKD 234
Query: 322 AKLTLHGLQQHYVKL-KENEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFP 380
+LTL G++Q YV + KE K L +L + L Q +I+ + + L+ + E++F
Sbjct: 235 -ELTLEGIRQFYVAVEKEEWKFDTLCDLYETLTITQAIIYCNTRRKVDYLTKKMHERDFT 293
Query: 381 AVSIHRGMTQEERLKKYQEFK 401
+H M Q++R +EF+
Sbjct: 294 VSCMHGDMDQKDRDLIMREFR 314
Score = 67.9 bits (166), Expect = 2e-12
Identities = 23/48 (47%), Positives = 37/48 (77%)
Query: 100 RILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAV 147
R+L+ T+L RG+D+++V++V NYD+P + Y+HR+ R+GRFG K V
Sbjct: 319 RVLITTDLLARGIDVQQVSLVINYDLPASPENYIHRIGRSGRFGRKGV 366
>gnl|CDD|214692 smart00487, DEXDc, DEAD-like helicases superfamily.
Length = 201
Score = 138 bits (349), Expect = 1e-38
Identities = 55/183 (30%), Positives = 98/183 (53%), Gaps = 6/183 (3%)
Query: 150 MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSN 209
D++ A +G GKT +L L+ L+ VLV+ TRELA Q ++E ++ +
Sbjct: 25 RDVILAAPTGSGKTLAALLPALEALKR-GKGGRVLVLVPTRELAEQWAEELKKLGPSLGL 83
Query: 210 IKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKML 269
VG++ GG ++ L++ I+V TPGR+L L+ N KL+LS + ILDE ++L
Sbjct: 84 KVVGLY-GGDSKREQLRKLESGKTDILVTTPGRLLDLLENDKLSLSNVDLVILDEAHRLL 142
Query: 270 EQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDEAKLTLHGL 329
+ ++++ + P Q+++ SAT +EI + + F++DP+ + V L +
Sbjct: 143 DG-GFGDQLEKLLKLLPKNVQLLLLSATPPEEIENLLELFLNDPVFIDVGF---TPLEPI 198
Query: 330 QQH 332
+Q
Sbjct: 199 EQF 201
>gnl|CDD|236941 PRK11634, PRK11634, ATP-dependent RNA helicase DeaD; Provisional.
Length = 629
Score = 142 bits (359), Expect = 8e-37
Identities = 88/268 (32%), Positives = 140/268 (52%), Gaps = 9/268 (3%)
Query: 149 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMS 208
G D+L A++G GKTA F L L L+ +LV+ TRELA Q+++ FSK+M
Sbjct: 43 GRDVLGMAQTGSGKTAAFSLPLLHNLDPELKAPQILVLAPTRELAVQVAEAMTDFSKHMR 102
Query: 209 NIKVGVFFGGLPIQKDEEYLKT--HNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECD 266
+ V +GG Q+ + L+ PQIVVGTPGR+L ++ L+LS L +LDE D
Sbjct: 103 GVNVVALYGG---QRYDVQLRALRQGPQIVVGTPGRLLDHLKRGTLDLSKLSGLVLDEAD 159
Query: 267 KMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDEAKLTL 326
+ML ++ DV+ I P Q +FSAT+ + IR + ++FM +P EV + T
Sbjct: 160 EML-RMGFIEDVETIMAQIPEGHQTALFSATMPEAIRRITRRFMKEPQEVRIQSSVT-TR 217
Query: 327 HGLQQHYVKLKENEKNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHR 386
+ Q Y + KN+ L L+ +F+ +IFV++ + ++ L + + +++
Sbjct: 218 PDISQSYWTVWGMRKNEALVRFLEAEDFDAAIIFVRTKNATLEVAEALERNGYNSAALNG 277
Query: 387 GMTQEERLKKYQEFKDFHKGLAITFASD 414
M Q R + + KD L I A+D
Sbjct: 278 DMNQALREQTLERLKDGR--LDILIATD 303
Score = 63.3 bits (154), Expect = 1e-10
Identities = 23/43 (53%), Positives = 36/43 (83%)
Query: 101 ILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFG 143
IL+AT++ RG+D+ER+++V NYD+P DS++Y+HR+ R GR G
Sbjct: 298 ILIATDVAARGLDVERISLVVNYDIPMDSESYVHRIGRTGRAG 340
>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 = 122 bits (307), Expect = 3e-33
Identities = 55/149 (36%), Positives = 77/149 (51%), Gaps = 5/149 (3%)
Query: 150 MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSN 209
D+L A +G GKT +L L+ L++ VLV+ TRELA Q+++ +
Sbjct: 1 RDVLLAAPTGSGKTLAALLPILELLDSLK-GGQVLVLAPTRELANQVAERLKELFGE--G 57
Query: 210 IKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDECDKML 269
IKVG GG I K +E L + IVVGTPGR+L + KL+L L ILDE ++L
Sbjct: 58 IKVGYLIGGTSI-KQQEKLLSGKTDIVVGTPGRLLDELERLKLSLKKLDLLILDEAHRLL 116
Query: 270 EQLEMRRDVQEIFRSSPHTKQVMMFSATL 298
Q +I P +QV++ SAT
Sbjct: 117 NQ-GFGLLGLKILLKLPKDRQVLLLSATP 144
>gnl|CDD|236722 PRK10590, PRK10590, ATP-dependent RNA helicase RhlE; Provisional.
Length = 456
Score = 121 bits (304), Expect = 4e-30
Identities = 87/281 (30%), Positives = 142/281 (50%), Gaps = 45/281 (16%)
Query: 146 AVL-GMDILCQAKSGMGKTAVFVLATLQQLETTDSN------VYVLVMCHTRELAFQISK 198
AVL G D++ A++G GKTA F L LQ L T + V L++ TRELA QI +
Sbjct: 34 AVLEGRDLMASAQTGTGKTAGFTLPLLQHLITRQPHAKGRRPVRALILTPTRELAAQIGE 93
Query: 199 EYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQ---------IVVGTPGRILALVRN 249
+SKY+ NI+ V FGG+ I NPQ ++V TPGR+L L
Sbjct: 94 NVRDYSKYL-NIRSLVVFGGVSI----------NPQMMKLRGGVDVLVATPGRLLDLEHQ 142
Query: 250 KKLNLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKF 309
+ L ++ +LDE D+ML+ + D++ + P +Q ++FSAT S +I+ + +K
Sbjct: 143 NAVKLDQVEILVLDEADRMLD-MGFIHDIRRVLAKLPAKRQNLLFSATFSDDIKALAEKL 201
Query: 310 MHDPMEVYV----DDEAKLTLHGLQQHYVKLKENEKNKKLFELLDVL----EFNQVVIFV 361
+H+P+E+ V ++T H H+V +K +K ELL + + QV++F
Sbjct: 202 LHNPLEIEVARRNTASEQVTQH---VHFV-----DKKRKR-ELLSQMIGKGNWQQVLVFT 252
Query: 362 KSVTRCIALSTLLSEQNFPAVSIHRGMTQEERLKKYQEFKD 402
++ L+ L++ + +IH +Q R + +FK
Sbjct: 253 RTKHGANHLAEQLNKDGIRSAAIHGNKSQGARTRALADFKS 293
Score = 52.5 bits (126), Expect = 2e-07
Identities = 20/42 (47%), Positives = 30/42 (71%)
Query: 100 RILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGR 141
R+LVAT++ RG+DIE + V NY++P + Y+HR+ R GR
Sbjct: 297 RVLVATDIAARGLDIEELPHVVNYELPNVPEDYVHRIGRTGR 338
>gnl|CDD|234938 PRK01297, PRK01297, ATP-dependent RNA helicase RhlB; Provisional.
Length = 475
Score = 113 bits (285), Expect = 2e-27
Identities = 83/332 (25%), Positives = 155/332 (46%), Gaps = 44/332 (13%)
Query: 80 SGFRDFLLKPEILRAIVDCWRILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARA 139
+ F DF L PE++ AI D + F Y P + + +A
Sbjct: 87 TRFHDFNLAPELMHAIHD---------------------LGFPYCTPIQAQVLGYTLA-- 123
Query: 140 GRFGTKAVLGMDILCQAKSGMGKTAVFVLATLQQLETTD-------SNVYVLVMCHTREL 192
G D + +A++G GKTA F+++ + QL T L++ TREL
Sbjct: 124 ---------GHDAIGRAQTGTGKTAAFLISIINQLLQTPPPKERYMGEPRALIIAPTREL 174
Query: 193 AFQISKEYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKL 252
QI+K+ +KY + + V F GG+ K + L+ I+V TPGR+L + ++
Sbjct: 175 VVQIAKDAAALTKY-TGLNVMTFVGGMDFDKQLKQLEARFCDILVATPGRLLDFNQRGEV 233
Query: 253 NLSLLKHFILDECDKMLEQLEMRRDVQEIFRSSPHT--KQVMMFSATLSKEIRPVCKKFM 310
+L +++ +LDE D+ML+ + V++I R +P +Q ++FSAT + ++ + K++
Sbjct: 234 HLDMVEVMVLDEADRMLD-MGFIPQVRQIIRQTPRKEERQTLLFSATFTDDVMNLAKQWT 292
Query: 311 HDPMEVYVDDEAKLTLHGLQQHYVKLKENEKNKKLFELLDVLEFNQVVIFVKSVTRCIAL 370
DP V ++ E ++QH + ++K K L+ L+ + +V++F +
Sbjct: 293 TDPAIVEIEPENV-ASDTVEQHVYAVAGSDKYKLLYNLVTQNPWERVMVFANRKDEVRRI 351
Query: 371 STLLSEQNFPAVSIHRGMTQEERLKKYQEFKD 402
L + A + + Q +R+K + F++
Sbjct: 352 EERLVKDGINAAQLSGDVPQHKRIKTLEGFRE 383
Score = 60.3 bits (146), Expect = 9e-10
Identities = 23/48 (47%), Positives = 34/48 (70%)
Query: 100 RILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAV 147
R+LVAT++ GRG+ I+ ++ V N+ +PED D Y+HR+ R GR G V
Sbjct: 387 RVLVATDVAGRGIHIDGISHVINFTLPEDPDDYVHRIGRTGRAGASGV 434
>gnl|CDD|236877 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional.
Length = 434
Score = 108 bits (273), Expect = 5e-26
Identities = 73/267 (27%), Positives = 128/267 (47%), Gaps = 18/267 (6%)
Query: 146 AVLGMDILCQAKSGMGKTAVFVLATLQQL----ETTDSNVYVLVMCHTRELAFQISKEYE 201
A+ G D+L A +G GKTA F+L LQ L +L++ TRELA Q++ +
Sbjct: 35 ALDGRDVLGSAPTGTGKTAAFLLPALQHLLDFPRRKSGPPRILILTPTRELAMQVADQAR 94
Query: 202 RFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFI 261
+K+ +++ + GG+ E N IVV TPGR+L ++ + + ++ I
Sbjct: 95 ELAKH-THLDIATITGGVAYMNHAEVFSE-NQDIVVATPGRLLQYIKEENFDCRAVETLI 152
Query: 262 LDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATL-SKEIRPVCKKFMHDPMEVYVD- 319
LDE D+ML + +D++ I + KQ ++FSATL ++ ++ ++DP+EV +
Sbjct: 153 LDEADRML-DMGFAQDIETIAAETRWRKQTLLFSATLEGDAVQDFAERLLNDPVEVEAEP 211
Query: 320 ---DEAKLTLHGLQQHYVKLKENE-KNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLS 375
+ K + Q Y + + E K L LL E + ++FV++ R L+ L
Sbjct: 212 SRRERKK-----IHQWYYRADDLEHKTALLCHLLKQPEVTRSIVFVRTRERVHELAGWLR 266
Query: 376 EQNFPAVSIHRGMTQEERLKKYQEFKD 402
+ + M Q +R + + D
Sbjct: 267 KAGINCCYLEGEMVQAKRNEAIKRLTD 293
Score = 65.7 bits (161), Expect = 1e-11
Identities = 25/45 (55%), Positives = 34/45 (75%)
Query: 101 ILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTK 145
+LVAT++ RG+DI+ V+ V N+DMP +DTYLHR+ R GR G K
Sbjct: 298 VLVATDVAARGIDIDDVSHVINFDMPRSADTYLHRIGRTGRAGRK 342
>gnl|CDD|240273 PTZ00110, PTZ00110, helicase; Provisional.
Length = 545
Score = 110 bits (276), Expect = 6e-26
Identities = 84/270 (31%), Positives = 141/270 (52%), Gaps = 23/270 (8%)
Query: 146 AVLGMDILCQAKSGMGKTAVFVLATL-----QQLETTDSNVYVLVMCHTRELAFQISKEY 200
A+ G D++ A++G GKT F+L + Q L VLV+ TRELA QI ++
Sbjct: 164 ALSGRDMIGIAETGSGKTLAFLLPAIVHINAQPLLRYGDGPIVLVLAPTRELAEQIREQC 223
Query: 201 ERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHF 260
+F S I+ V +GG+P ++ + Y +I++ PGR++ + + NL + +
Sbjct: 224 NKFGA-SSKIRNTVAYGGVP-KRGQIYALRRGVEILIACPGRLIDFLESNVTNLRRVTYL 281
Query: 261 ILDECDKMLE---QLEMRRDVQEIFRSSPHTKQVMMFSATLSKEI----RPVCKKFMHDP 313
+LDE D+ML+ + ++R+ V +I P +Q +M+SAT KE+ R +CK +P
Sbjct: 282 VLDEADRMLDMGFEPQIRKIVSQI---RP-DRQTLMWSATWPKEVQSLARDLCK---EEP 334
Query: 314 MEVYVDDEAKLTLHGLQQHYVKLKENEKNKKLFELLDVL--EFNQVVIFVKSVTRCIALS 371
+ V V H ++Q ++E+EK KL LL + + ++++IFV++ L+
Sbjct: 335 VHVNVGSLDLTACHNIKQEVFVVEEHEKRGKLKMLLQRIMRDGDKILIFVETKKGADFLT 394
Query: 372 TLLSEQNFPAVSIHRGMTQEERLKKYQEFK 401
L +PA+ IH QEER EFK
Sbjct: 395 KELRLDGWPALCIHGDKKQEERTWVLNEFK 424
Score = 56.3 bits (136), Expect = 1e-08
Identities = 19/47 (40%), Positives = 30/47 (63%)
Query: 101 ILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAV 147
I++AT++ RG+D++ V V N+D P + Y+HR+ R GR G K
Sbjct: 430 IMIATDVASRGLDVKDVKYVINFDFPNQIEDYVHRIGRTGRAGAKGA 476
>gnl|CDD|235314 PRK04837, PRK04837, ATP-dependent RNA helicase RhlB; Provisional.
Length = 423
Score = 101 bits (254), Expect = 2e-23
Identities = 62/192 (32%), Positives = 105/192 (54%), Gaps = 13/192 (6%)
Query: 149 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVY-------VLVMCHTRELAFQISKEYE 201
G D+ QA++G GKT F+ AT L + + L+M TRELA QI + E
Sbjct: 45 GRDVAGQAQTGTGKTMAFLTATFHYLLSHPAPEDRKVNQPRALIMAPTRELAVQIHADAE 104
Query: 202 RFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFI 261
++ + +K+G+ +GG K + L++ I++GT GR++ + +NL ++ +
Sbjct: 105 PLAQ-ATGLKLGLAYGGDGYDKQLKVLES-GVDILIGTTGRLIDYAKQNHINLGAIQVVV 162
Query: 262 LDECDKMLEQLEMRRDVQEIFRSSPHTKQ--VMMFSATLSKEIRPVCKKFMHDPMEVYVD 319
LDE D+M + L +D++ +FR P Q M+FSATLS +R + + M++P V V+
Sbjct: 163 LDEADRMFD-LGFIKDIRWLFRRMPPANQRLNMLFSATLSYRVRELAFEHMNNPEYVEVE 221
Query: 320 DEAKLTLHGLQQ 331
E K T H +++
Sbjct: 222 PEQK-TGHRIKE 232
Score = 59.2 bits (144), Expect = 1e-09
Identities = 23/47 (48%), Positives = 31/47 (65%)
Query: 101 ILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAV 147
ILVAT++ RG+ I V VFNYD+P+D + Y+HR+ R GR G
Sbjct: 308 ILVATDVAARGLHIPAVTHVFNYDLPDDCEDYVHRIGRTGRAGASGH 354
>gnl|CDD|215103 PLN00206, PLN00206, DEAD-box ATP-dependent RNA helicase;
Provisional.
Length = 518
Score = 93.3 bits (232), Expect = 2e-20
Identities = 70/263 (26%), Positives = 128/263 (48%), Gaps = 25/263 (9%)
Query: 146 AVLGMDILCQAKSGMGKTAVFVL------ATLQQLETTDS-NVYVLVMCHTRELAFQISK 198
A+ G +L A +G GKTA F++ T++ ++ N +V+ TREL Q+
Sbjct: 155 ALSGRSLLVSADTGSGKTASFLVPIISRCCTIRSGHPSEQRNPLAMVLTPTRELCVQVED 214
Query: 199 EYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLK 258
+ + K + K + GG + + + Y +++VGTPGR++ L+ + L +
Sbjct: 215 QAKVLGKGLP-FKTALVVGGDAMPQ-QLYRIQQGVELIVGTPGRLIDLLSKHDIELDNVS 272
Query: 259 HFILDECDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYV 318
+LDE D MLE+ R V +IF++ QV++FSAT+S E+ D + + +
Sbjct: 273 VLVLDEVDCMLER-GFRDQVMQIFQALS-QPQVLLFSATVSPEVEKFASSLAKDIILISI 330
Query: 319 DDEAKLTLHGLQQHYVKLKENEKNKKLFELLDVLEFNQ--VVIFVKS------VTRCIAL 370
+ + ++Q + ++ +K +KLF++L + + V+FV S + I +
Sbjct: 331 GNPNRPN-KAVKQLAIWVETKQKKQKLFDILKSKQHFKPPAVVFVSSRLGADLLANAITV 389
Query: 371 STLLSEQNFPAVSIHRGMTQEER 393
T L A+SIH + +ER
Sbjct: 390 VTGLK-----ALSIHGEKSMKER 407
Score = 49.0 bits (117), Expect = 3e-06
Identities = 29/88 (32%), Positives = 49/88 (55%), Gaps = 5/88 (5%)
Query: 57 ADGAGDALAKQKEVKGAYVSIHSSGFRDFLLKPEILRA-IVDCWRILVATNLFGRGMDIE 115
AD +A+ +K +SIH G + + E++++ +V ++VAT + GRG+D+
Sbjct: 380 ADLLANAITVVTGLKA--LSIH--GEKSMKERREVMKSFLVGEVPVIVATGVLGRGVDLL 435
Query: 116 RVNIVFNYDMPEDSDTYLHRVARAGRFG 143
RV V +DMP Y+H++ RA R G
Sbjct: 436 RVRQVIIFDMPNTIKEYIHQIGRASRMG 463
>gnl|CDD|235307 PRK04537, PRK04537, ATP-dependent RNA helicase RhlB; Provisional.
Length = 572
Score = 91.6 bits (227), Expect = 8e-20
Identities = 65/228 (28%), Positives = 119/228 (52%), Gaps = 14/228 (6%)
Query: 146 AVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNV-------YVLVMCHTRELAFQISK 198
A+ G D+ QA++G GKT F++A + +L + + L++ TRELA QI K
Sbjct: 43 ALPGGDVAGQAQTGTGKTLAFLVAVMNRLLSRPALADRKPEDPRALILAPTRELAIQIHK 102
Query: 199 EYERFSKYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKL-NLSLL 257
+ +F + ++ + +GG+ K E L+ +++ TPGR++ V+ K+ +L
Sbjct: 103 DAVKFGADLG-LRFALVYGGVDYDKQRELLQ-QGVDVIIATPGRLIDYVKQHKVVSLHAC 160
Query: 258 KHFILDECDKMLEQLEMRRDVQEIFRSSPH--TKQVMMFSATLSKEIRPVCKKFMHDPME 315
+ +LDE D+M + L +D++ + R P T+Q ++FSATLS + + + M++P +
Sbjct: 161 EICVLDEADRMFD-LGFIKDIRFLLRRMPERGTRQTLLFSATLSHRVLELAYEHMNEPEK 219
Query: 316 VYVDDEAKLTLHGLQQHYVKLKENEKNKKLFELLDVLEFNQVVIFVKS 363
+ V+ E Q+ Y + EK L LL E + ++FV +
Sbjct: 220 LVVETETITAARVRQRIYFP-ADEEKQTLLLGLLSRSEGARTMVFVNT 266
Score = 56.1 bits (135), Expect = 2e-08
Identities = 21/43 (48%), Positives = 31/43 (72%)
Query: 101 ILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFG 143
ILVAT++ RG+ I+ V V+NYD+P D++ Y+HR+ R R G
Sbjct: 310 ILVATDVAARGLHIDGVKYVYNYDLPFDAEDYVHRIGRTARLG 352
>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 = 68.3 bits (168), Expect = 1e-14
Identities = 27/75 (36%), Positives = 42/75 (56%), Gaps = 11/75 (14%)
Query: 74 YVSIHSSGFRDFLLKPEILRAIVDCWR-----ILVATNLFGRGMDIERVNIVFNYDMPED 128
+H L E I++ +R +LVAT++ GRG+D+ VN+V NYD+P +
Sbjct: 10 VARLHGG------LSQEEREEILEDFRNGKSKVLVATDVAGRGIDLPDVNLVINYDLPWN 63
Query: 129 SDTYLHRVARAGRFG 143
+Y+ R+ RAGR G
Sbjct: 64 PASYIQRIGRAGRAG 78
Score = 33.3 bits (77), Expect = 0.028
Identities = 9/30 (30%), Positives = 18/30 (60%)
Query: 373 LLSEQNFPAVSIHRGMTQEERLKKYQEFKD 402
LL + +H G++QEER + ++F++
Sbjct: 2 LLRKPGIKVARLHGGLSQEEREEILEDFRN 31
>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 = 68.8 bits (169), Expect = 4e-14
Identities = 22/47 (46%), Positives = 32/47 (68%)
Query: 100 RILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKA 146
+LVAT++ RG+D+ V++V NYD+P +YL R+ RAGR G K
Sbjct: 80 VVLVATDVIARGIDLPNVSVVINYDLPWSPSSYLQRIGRAGRAGQKG 126
Score = 53.8 bits (130), Expect = 6e-09
Identities = 22/74 (29%), Positives = 39/74 (52%), Gaps = 2/74 (2%)
Query: 331 QHYVKLKENEKNKKLFELLD--VLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGM 388
+ YV E+EK + L ELL + + +V+IF S L+ LL + ++H
Sbjct: 3 KQYVLPVEDEKLEALLELLKEHLKKGGKVLIFCPSKKMLDELAELLRKPGIKVAALHGDG 62
Query: 389 TQEERLKKYQEFKD 402
+QEER + ++F++
Sbjct: 63 SQEEREEVLKDFRE 76
>gnl|CDD|197757 smart00490, HELICc, helicase superfamily c-terminal domain.
Length = 82
Score = 64.9 bits (159), Expect = 2e-13
Identities = 24/75 (32%), Positives = 38/75 (50%), Gaps = 11/75 (14%)
Query: 74 YVSIHSSGFRDFLLKPEILRAIVDCWR-----ILVATNLFGRGMDIERVNIVFNYDMPED 128
+H L E I+D + +LVAT++ RG+D+ V++V YD+P
Sbjct: 14 VARLHGG------LSQEEREEILDKFNNGKIKVLVATDVAERGLDLPGVDLVIIYDLPWS 67
Query: 129 SDTYLHRVARAGRFG 143
+Y+ R+ RAGR G
Sbjct: 68 PASYIQRIGRAGRAG 82
Score = 34.1 bits (79), Expect = 0.017
Identities = 11/33 (33%), Positives = 18/33 (54%)
Query: 370 LSTLLSEQNFPAVSIHRGMTQEERLKKYQEFKD 402
L+ LL E +H G++QEER + +F +
Sbjct: 3 LAELLKELGIKVARLHGGLSQEEREEILDKFNN 35
>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 = 46.6 bits (111), Expect = 2e-05
Identities = 21/46 (45%), Positives = 28/46 (60%)
Query: 101 ILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKA 146
++VATN FG G+D V V +YDMP + ++Y RAGR G A
Sbjct: 277 VMVATNAFGMGIDKPNVRFVIHYDMPGNLESYYQEAGRAGRDGLPA 322
>gnl|CDD|224125 COG1204, COG1204, Superfamily II helicase [General function
prediction only].
Length = 766
Score = 44.7 bits (106), Expect = 9e-05
Identities = 28/115 (24%), Positives = 53/115 (46%), Gaps = 10/115 (8%)
Query: 151 DILCQAKSGMGKTAVFVLATLQQL-ETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSN 209
++L A +G GKT + +LA L L E VY+ + LA + +E+ R +
Sbjct: 49 NVLISAPTGSGKTLIALLAILSTLLEGGGKVVYI---VPLKALAEEKYEEFSRLEEL--G 103
Query: 210 IKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDE 264
I+VG+ G + + ++V TP ++ +L R + + + ++DE
Sbjct: 104 IRVGISTGDYDLDDERLA----RYDVIVTTPEKLDSLTRKRPSWIEEVDLVVIDE 154
>gnl|CDD|223989 COG1061, SSL2, DNA or RNA helicases of superfamily II
[Transcription / DNA replication, recombination, and
repair].
Length = 442
Score = 43.6 bits (103), Expect = 2e-04
Identities = 30/120 (25%), Positives = 50/120 (41%), Gaps = 22/120 (18%)
Query: 149 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMS 208
+ +G GKT V A + LV+ T+EL Q ++ ++F +
Sbjct: 55 ERRGVIVLPTGAGKTVVAAEAI------AELKRSTLVLVPTKELLDQWAEALKKF--LLL 106
Query: 209 NIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHF---ILDEC 265
N ++G++ GG +K+ E K + V T + L R + L+ L F I DE
Sbjct: 107 NDEIGIYGGG---EKELEPAK-----VTVAT---VQTLARRQLLDEFLGNEFGLIIFDEV 155
>gnl|CDD|223588 COG0514, RecQ, Superfamily II DNA helicase [DNA replication,
recombination, and repair].
Length = 590
Score = 41.9 bits (99), Expect = 6e-04
Identities = 20/48 (41%), Positives = 28/48 (58%)
Query: 100 RILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKAV 147
+++VATN FG G+D V V +YD+P ++Y RAGR G A
Sbjct: 282 KVMVATNAFGMGIDKPDVRFVIHYDLPGSIESYYQETGRAGRDGLPAE 329
>gnl|CDD|224126 COG1205, COG1205, Distinct helicase family with a unique C-terminal
domain including a metal-binding cysteine cluster
[General function prediction only].
Length = 851
Score = 41.2 bits (97), Expect = 0.001
Identities = 70/302 (23%), Positives = 117/302 (38%), Gaps = 51/302 (16%)
Query: 149 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMS 208
G +++ +G GKT F+L L L S +L+ T LA + ER + +S
Sbjct: 85 GRNVVVTTGTGSGKTESFLLPILDHLLRDPSARALLLY-PTNALAND---QAERLRELIS 140
Query: 209 N----IKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRI-LALVRNKKLNLSL---LKHF 260
+ + G + G P ++ + + P I++ P + L+RN L L LK+
Sbjct: 141 DLPGKVTFGRYTGDTP-PEERRAIIRNPPDILLTNPDMLHYLLLRNHDAWLWLLRNLKYL 199
Query: 261 ILDECD----------KMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLS--KEIRPVCKK 308
++DE +L +RR + R Q++ SATL+ E ++
Sbjct: 200 VVDELHTYRGVQGSEVALL----LRR-LLRRLRRYGSPLQIICTSATLANPGEF---AEE 251
Query: 309 FMHDPMEVYVDD----EAKLTLHGLQQHYVKLKENEKNKKLFEL-----LDVLEFNQVVI 359
EV VD+ + +L E+ + L EL L V Q ++
Sbjct: 252 LFGRDFEVPVDEDGSPRGLRYFVRREPPIRELAESIRRSALAELATLAALLVRNGIQTLV 311
Query: 360 FVKS-------VTRCIALSTLLSEQNFPAVSIHR-GMTQEERLKKYQEFKDFH-KGLAIT 410
F +S + AVS +R G+ +EER + EFK+ G+ T
Sbjct: 312 FFRSRKQVELLYLSPRRRLVREGGKLLDAVSTYRAGLHREERRRIEAEFKEGELLGVIAT 371
Query: 411 FA 412
A
Sbjct: 372 NA 373
>gnl|CDD|224036 COG1111, MPH1, ERCC4-like helicases [DNA replication,
recombination, and repair].
Length = 542
Score = 38.9 bits (91), Expect = 0.005
Identities = 22/121 (18%), Positives = 49/121 (40%), Gaps = 5/121 (4%)
Query: 145 KAVLGMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFS 204
L + L +G+GKT + + +L VL + T+ L Q ++ + +
Sbjct: 25 AKALFKNTLVVLPTGLGKTFIAAMVIANRLRWFGG--KVLFLAPTKPLVLQHAEFCRKVT 82
Query: 205 KYMSNIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDE 264
+ ++ G + ++ EE ++ V TP + ++ +++L + I DE
Sbjct: 83 G-IPEDEIAALTGEVRPEEREELWAKK--KVFVATPQVVENDLKAGRIDLDDVSLLIFDE 139
Query: 265 C 265
Sbjct: 140 A 140
>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 = 38.6 bits (90), Expect = 0.005
Identities = 16/46 (34%), Positives = 26/46 (56%)
Query: 101 ILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKA 146
++VAT FG G++ V V +Y +P+ ++Y RAGR G +
Sbjct: 279 VVVATVAFGMGINKPDVRFVIHYSLPKSMESYYQESGRAGRDGLPS 324
>gnl|CDD|224124 COG1203, COG1203, CRISPR-associated helicase Cas3 [Defense
mechanisms].
Length = 733
Score = 39.0 bits (91), Expect = 0.006
Identities = 37/160 (23%), Positives = 63/160 (39%), Gaps = 22/160 (13%)
Query: 259 HFILDE-----CDKMLEQLEMRRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDP 313
ILDE + ML L + V++ SATL ++ KK +
Sbjct: 341 LVILDEVHLYADETMLAALLALLEALAEAGVP-----VLLMSATLPPFLKEKLKKALGKG 395
Query: 314 MEVYV-------DDEAKLTLHGLQQHYVKLKENE-KNKKLFELLDVLEFNQVVIFVKSVT 365
EV +DE L ++ V +++ + +V E +V++ V +V
Sbjct: 396 REVVENAKFCPKEDEPGLK----RKERVDVEDGPQEELIELISEEVKEGKKVLVIVNTVD 451
Query: 366 RCIALSTLLSEQNFPAVSIHRGMTQEERLKKYQEFKDFHK 405
R I L L E+ + +H T ++R +K +E K K
Sbjct: 452 RAIELYEKLKEKGPKVLLLHSRFTLKDREEKERELKKLFK 491
>gnl|CDD|187770 cd09639, Cas3_I, CRISPR/Cas system-associated protein Cas3. CRISPR
(Clustered Regularly Interspaced Short Palindromic
Repeats) and associated Cas proteins comprise a system
for heritable host defense by prokaryotic cells against
phage and other foreign DNA; DEAD/DEAH box helicase DNA
helicase cas3'; Often but not always is fused to HD
nuclease domain; signature gene for Type I.
Length = 353
Score = 37.4 bits (87), Expect = 0.011
Identities = 32/130 (24%), Positives = 56/130 (43%), Gaps = 16/130 (12%)
Query: 291 VMMFSATLSKEIRPVCKKFMHDPMEVYVDDEAKLTLHGLQQHYVKLKENEKNKKLFELLD 350
+++ SATL K ++ +K + ++E L L ++ E++K ++ L
Sbjct: 157 ILLMSATLPKFLKEYAEK-----IGYVEENEP-LDLKPNERAPFIKIESDKVGEISSLER 210
Query: 351 VLEF----NQVVIFVKSVTRCIALSTLLSEQN--FPAVSIHRGMTQEERLKKYQE----F 400
+LEF V I V +V R L E+ + IH T+++R KK E F
Sbjct: 211 LLEFIKKGGSVAIIVNTVDRAQEFYQQLKEKGPEEEIMLIHSRFTEKDRAKKEAELLLEF 270
Query: 401 KDFHKGLAIT 410
K K + +
Sbjct: 271 KKSEKFVIVA 280
>gnl|CDD|233069 TIGR00643, recG, ATP-dependent DNA helicase RecG. [DNA metabolism,
DNA replication, recombination, and repair].
Length = 630
Score = 37.3 bits (87), Expect = 0.015
Identities = 44/155 (28%), Positives = 71/155 (45%), Gaps = 23/155 (14%)
Query: 150 MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMS- 208
M+ L Q G GKT V LA L ++ V +M T LA Q Y ++
Sbjct: 257 MNRLLQGDVGSGKTLVAALAMLA---AIEAGYQVALMAPTEILAEQ---HYNSLRNLLAP 310
Query: 209 -NIKVGVFFGGL-PIQKDE--EYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDE 264
I+V + G L ++ E E + + +VVGT AL++ +K+ L I+DE
Sbjct: 311 LGIEVALLTGSLKGKRRKELLETIASGQIHLVVGTH----ALIQ-EKVEFKRLALVIIDE 365
Query: 265 CDK--MLEQLEMRRDVQEIFRSSPHTKQVMMFSAT 297
+ + ++ ++R Q F +PH V++ SAT
Sbjct: 366 QHRFGVEQRKKLREKGQGGF--TPH---VLVMSAT 395
>gnl|CDD|182933 PRK11057, PRK11057, ATP-dependent DNA helicase RecQ; Provisional.
Length = 607
Score = 37.0 bits (86), Expect = 0.020
Identities = 18/47 (38%), Positives = 28/47 (59%)
Query: 100 RILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKA 146
+I+VAT FG G++ V V ++D+P + ++Y RAGR G A
Sbjct: 288 QIVVATVAFGMGINKPNVRFVVHFDIPRNIESYYQETGRAGRDGLPA 334
>gnl|CDD|224123 COG1202, COG1202, Superfamily II helicase, archaea-specific
[General function prediction only].
Length = 830
Score = 36.7 bits (85), Expect = 0.029
Identities = 69/276 (25%), Positives = 113/276 (40%), Gaps = 41/276 (14%)
Query: 149 GMDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEY-ERFSKYM 207
G ++L + + GKT + LA + +L + + LV LA Q +++ ER+SK
Sbjct: 232 GENLLVVSATASGKTLIGELAGIPRLLSGGKKMLFLV--PLVALANQKYEDFKERYSKL- 288
Query: 208 SNIKVGVFFGGLPIQKDEEYLKTHNP---QIVVGTPGRILALVRNKKLNLSLLKHFILDE 264
+KV + G I+ EE + I+VGT I L+R K +L + ++DE
Sbjct: 289 -GLKVAIRVGMSRIKTREEPVVVDTSPDADIIVGTYEGIDYLLRTGK-DLGDIGTVVIDE 346
Query: 265 CDKMLEQLEM--RRD--VQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDD 320
LE E R D + + P Q + SAT+ +P E+
Sbjct: 347 I-HTLEDEERGPRLDGLIGRLRYLFPGA-QFIYLSATVG------------NPEELAKKL 392
Query: 321 EAKLTLHG-----LQQHYVKLKENEKNKKLFELLDVLEFN---------QVVIFVKSVTR 366
AKL L+ L++H V + + + L EF+ Q ++F S R
Sbjct: 393 GAKLVLYDERPVPLERHLVFARNESEKWDIIARLVKREFSTESSKGYRGQTIVFTYSRRR 452
Query: 367 CIALSTLLSEQNFPAVSIHRGMTQEERLKKYQEFKD 402
C L+ L+ + A H G+ +ER + F
Sbjct: 453 CHELADALTGKGLKAAPYHAGLPYKERKSVERAFAA 488
>gnl|CDD|237496 PRK13766, PRK13766, Hef nuclease; Provisional.
Length = 773
Score = 36.4 bits (85), Expect = 0.036
Identities = 32/116 (27%), Positives = 55/116 (47%), Gaps = 11/116 (9%)
Query: 153 LCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMSNI-- 210
L +G+GKTA+ +L ++L VL++ T+ L Q E F K++ NI
Sbjct: 33 LVVLPTGLGKTAIALLVIAERLHKKGGK--VLILAPTKPLVEQ---HAEFFRKFL-NIPE 86
Query: 211 -KVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDEC 265
K+ VF G + +K E + +++V TP I + +++L + I DE
Sbjct: 87 EKIVVFTGEVSPEKRAELWE--KAKVIVATPQVIENDLIAGRISLEDVSLLIFDEA 140
>gnl|CDD|236709 PRK10531, PRK10531, acyl-CoA thioesterase; Provisional.
Length = 422
Score = 35.1 bits (81), Expect = 0.073
Identities = 25/124 (20%), Positives = 39/124 (31%), Gaps = 18/124 (14%)
Query: 56 VADGAGDALAKQKEVKGAY---VSIHSSGFRDFLLKPEILRAIVDCWRILVATN-----L 107
V AG V+ A ++ ++ + + P + V V L
Sbjct: 83 VVGPAGTQGVTHTTVQAAVDAAIAKRTNKRQYIAVMPGTYQGTV-----YVPAAAPPITL 137
Query: 108 FGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRF-GTKAVLGMDILCQAKS----GMGK 162
+G G V I D + V G++ K M CQ+K G
Sbjct: 138 YGTGEKPIDVKIGLALDGEMSPADWRANVNPRGKYMPGKPAWYMYDSCQSKRAATIGTLC 197
Query: 163 TAVF 166
+AVF
Sbjct: 198 SAVF 201
>gnl|CDD|233656 TIGR01957, nuoB_fam, NADH-quinone oxidoreductase, B subunit. This
model describes the B chain of complexes that resemble
NADH-quinone oxidoreductases. The electron acceptor is a
quinone, ubiquinone, in mitochondria and most bacteria,
including Escherichia coli, where the recommended gene
symbol is nuoB. The quinone is plastoquinone in
Synechocystis (where the chain is designated K) and in
chloroplast, where NADH may be replaced by NADPH. In the
methanogenic archaeal genus Methanosarcina, NADH is
replaced by F420H2 [Energy metabolism, Electron
transport].
Length = 145
Score = 31.6 bits (72), Expect = 0.40
Identities = 12/37 (32%), Positives = 23/37 (62%), Gaps = 3/37 (8%)
Query: 280 EIFRSSPHTKQVMMFSATLSKEIRPVCKKF---MHDP 313
E+FR+SP VM+ + T++K++ P ++ M +P
Sbjct: 49 EVFRASPRQADVMIVAGTVTKKMAPALRRLYDQMPEP 85
>gnl|CDD|215932 pfam00465, Fe-ADH, Iron-containing alcohol dehydrogenase.
Length = 323
Score = 31.0 bits (71), Expect = 1.2
Identities = 17/50 (34%), Positives = 22/50 (44%), Gaps = 4/50 (8%)
Query: 55 IVADGAGDALAKQKEVKGAYVSIHSSGFRDFLLKPEILRAIVDCWRILVA 104
+ A DALA E AYVS ++ D L E +R I + VA
Sbjct: 177 LTAATGMDALAHAIE---AYVSKGANPLTDALAL-EAIRLIAENLPRAVA 222
>gnl|CDD|177443 PHA02653, PHA02653, RNA helicase NPH-II; Provisional.
Length = 675
Score = 30.7 bits (70), Expect = 2.1
Identities = 39/154 (25%), Positives = 62/154 (40%), Gaps = 41/154 (26%)
Query: 291 VMMFSATLSKEIRPVCKKFMHDPMEVYVDDEAKLTLHGLQQHYVKLKENEKNKKLF---E 347
+M +ATL + R K+F +P V++ TL + + YVK K N KNK+ + E
Sbjct: 325 FLM-TATLEDD-RDRIKEFFPNPAFVHIPGG---TLFPISEVYVKNKYNPKNKRAYIEEE 379
Query: 348 LLDVLEFNQ---------VVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEERLKKYQ 398
+++ + ++FV SV++C L E+RL Y
Sbjct: 380 KKNIVTALKKYTPPKGSSGIVFVASVSQCEEYKKYL----------------EKRLPIY- 422
Query: 399 EFKDFHKGLAITFASDENDAKILNNVQDRFDVSI 432
DF+ I N +IL V + SI
Sbjct: 423 ---DFY----IIHGKVPNIDEILEKVYSSKNPSI 449
>gnl|CDD|224121 COG1200, RecG, RecG-like helicase [DNA replication, recombination,
and repair / Transcription].
Length = 677
Score = 30.6 bits (70), Expect = 2.1
Identities = 46/157 (29%), Positives = 65/157 (41%), Gaps = 29/157 (18%)
Query: 150 MDILCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQISKEYERFSKYMS- 208
M+ L Q G GKT V +LA L ++ +M T LA Q YE K++
Sbjct: 284 MNRLLQGDVGSGKTVVALLAMLA---AIEAGYQAALMAPTEILAEQ---HYESLRKWLEP 337
Query: 209 -NIKVGVFFGGL-PIQKDE--EYLKTHNPQIVVGTPGRILALVRNKKLNLSLLKHFILDE 264
I+V + G L + E E L + IVVGT I V L L I+D
Sbjct: 338 LGIRVALLTGSLKGKARKEILEQLASGEIDIVVGTHALIQDKVEFHNLGLV-----IID- 391
Query: 265 CDKMLEQ----LEMRRDVQEIFRSSPHTKQVMMFSAT 297
EQ + R ++E +PH V++ +AT
Sbjct: 392 -----EQHRFGVHQRLALREKGEQNPH---VLVMTAT 420
>gnl|CDD|223779 COG0707, MurG, UDP-N-acetylglucosamine:LPS N-acetylglucosamine
transferase [Cell envelope biogenesis, outer membrane].
Length = 357
Score = 30.4 bits (69), Expect = 2.2
Identities = 23/107 (21%), Positives = 36/107 (33%), Gaps = 16/107 (14%)
Query: 153 LCQAKSGMGKTAVFVLATLQQLETTDSNVYVLVMCHTRELAFQ-ISKEYERFSKYMSNIK 211
L + + G V VL T LE Y + F+ I R + +K
Sbjct: 20 LAEELAKRGWEQVIVLGTGDGLEAFLVKQY--------GIEFELIPSGGLRRKGSLKLLK 71
Query: 212 VGVFFGGLPIQKDEEYLKTHNPQIVVGT------PGRILALVRNKKL 252
F + + + LK P +V+GT P I A + +
Sbjct: 72 -APFKLLKGVLQARKILKKLKPDVVIGTGGYVSGPVGIAAKLLGIPV 117
>gnl|CDD|236794 PRK10917, PRK10917, ATP-dependent DNA helicase RecG; Provisional.
Length = 681
Score = 30.5 bits (70), Expect = 2.3
Identities = 27/87 (31%), Positives = 37/87 (42%), Gaps = 13/87 (14%)
Query: 159 GMGKTAVFVLATLQQLETTDSNVY-VLVMCHTRELAFQISKEYERFSKYMS--NIKVGVF 215
G GKT V LA L +E Y +M T LA Q YE K + I+V +
Sbjct: 292 GSGKTVVAALAALAAIE----AGYQAALMAPTEILAEQH---YENLKKLLEPLGIRVALL 344
Query: 216 FGGLPI-QKDEEY--LKTHNPQIVVGT 239
G L ++ E + + IV+GT
Sbjct: 345 TGSLKGKERREILEAIASGEADIVIGT 371
>gnl|CDD|99709 cd05826, Sortase_B_2, Sortase B (SrtB) or subfamily-2 sortases are
membrane cysteine transpeptidases found in gram-positive
bacteria that anchor surface proteins to peptidoglycans
of the bacterial cell wall envelope. This involves a
transpeptidation reaction in which the surface protein
substrate is cleaved at a conserved cell wall sorting
signal and covalently linked to peptidoglycan for
display on the bacterial surface. Sortases are grouped
into different classes and subfamilies based on
sequence, membrane topology, genomic positioning, and
cleavage site preference. Sortase B cleaves surface
protein precursors between threonine and asparagine at a
conserved NPQTN motif with subsequent covalent linkage
to peptidoglycan. It is required for anchoring the
heme-iron binding surface protein IsdC to the cell wall
envelope and the gene encoding Sortase B is located
within the isd locus in S. aureus and B. anthracis. It
may also play a role in pathogenesis. Sortase B contains
an N-terminal region that functions as both a signal
peptide for secretion and a stop-transfer signal for
membrane anchoring. At the C-terminus, it contains the
catalytic TLXTC signature sequence, where X is usually a
serine. Genes encoding SrtB and its targets are
generally clustered in the same locus.
Length = 209
Score = 29.5 bits (67), Expect = 2.5
Identities = 15/36 (41%), Positives = 19/36 (52%), Gaps = 1/36 (2%)
Query: 209 NIKVGVFFGGLPIQKDEEYLKTHNPQIVVGTPGRIL 244
N+K G FG L KD+E+ K H P I TP +
Sbjct: 102 NMKNGSMFGDLDKYKDKEFFKKH-PYIYFYTPDKKY 136
>gnl|CDD|237822 PRK14819, PRK14819, NADH dehydrogenase subunit B; Provisional.
Length = 264
Score = 30.0 bits (67), Expect = 2.7
Identities = 13/40 (32%), Positives = 24/40 (60%), Gaps = 1/40 (2%)
Query: 280 EIFRSSPHTKQVMMFSATLSKEIRP-VCKKFMHDPMEVYV 318
E+FR+SP +M+ + T++K++ P V + + P YV
Sbjct: 63 ELFRASPRQADLMIVAGTVTKKMAPQVVRLYNQMPEPRYV 102
>gnl|CDD|237253 PRK12898, secA, preprotein translocase subunit SecA; Reviewed.
Length = 656
Score = 29.6 bits (67), Expect = 3.5
Identities = 11/15 (73%), Positives = 12/15 (80%)
Query: 100 RILVATNLFGRGMDI 114
RI VATN+ GRG DI
Sbjct: 523 RITVATNMAGRGTDI 537
>gnl|CDD|130152 TIGR01080, rplX_A_E, ribosomal protein L24p/L26e,
archaeal/eukaryotic. This model represents the archaeal
and eukaryotic branch of the ribosomal protein L24p/L26e
family. Bacterial and organellar forms are represented
by related model TIGR01079 [Protein synthesis, Ribosomal
proteins: synthesis and modification].
Length = 114
Score = 28.2 bits (63), Expect = 4.0
Identities = 14/50 (28%), Positives = 28/50 (56%), Gaps = 4/50 (8%)
Query: 275 RRDVQEIFRSSPHTKQVMMFSATLSKEIRPVCKKFMHDPMEVYVDDEAKL 324
R+ + +F + H ++ +M SA LSKE+R +K+ + V D+ ++
Sbjct: 5 RKQRKALFTAPLHVRRKLM-SAPLSKELR---EKYGKRALPVRKGDKVRI 50
>gnl|CDD|215597 PLN03137, PLN03137, ATP-dependent DNA helicase; Q4-like;
Provisional.
Length = 1195
Score = 29.5 bits (66), Expect = 4.4
Identities = 15/46 (32%), Positives = 25/46 (54%)
Query: 101 ILVATNLFGRGMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKA 146
I+ AT FG G++ V V ++ +P+ + Y RAGR G ++
Sbjct: 733 IICATVAFGMGINKPDVRFVIHHSLPKSIEGYHQECGRAGRDGQRS 778
>gnl|CDD|214516 smart00102, ADF, Actin depolymerisation factor/cofilin -like
domains. Severs actin filaments and binds to actin
monomers.
Length = 127
Score = 27.6 bits (62), Expect = 5.9
Identities = 12/51 (23%), Positives = 22/51 (43%), Gaps = 2/51 (3%)
Query: 391 EERLKKYQEFKDFHKGLAITFA-SDENDAKILNNVQDRFDVSISELPDEID 440
E+ + + E K K AI F +N+ ++ V + S E +E+
Sbjct: 1 EDCKEAFNELKKKRKHSAIIFKIDKDNEEIVVEEVGST-EDSYDEFVEELP 50
>gnl|CDD|217811 pfam03951, Gln-synt_N, Glutamine synthetase, beta-Grasp domain.
Length = 84
Score = 26.7 bits (60), Expect = 6.4
Identities = 9/27 (33%), Positives = 14/27 (51%), Gaps = 3/27 (11%)
Query: 74 YVSIHSSGFRDFLLKPEILRAIVDCWR 100
+ I+ S D LKP+ A +D +R
Sbjct: 45 FAPINES---DMYLKPDPSTAYIDPFR 68
>gnl|CDD|222681 pfam14324, PINIT, PINIT domain. The PINIT domain is a protein
domain that is found in PIAS proteins. The PINIT domain
is about 180 amino acids in length.
Length = 144
Score = 27.6 bits (62), Expect = 8.8
Identities = 17/75 (22%), Positives = 29/75 (38%), Gaps = 15/75 (20%)
Query: 283 RSSPHTKQVMMFSATLSKEIRPVCKKFMHDP--MEVYVDD-EAKLTLHGLQQH------- 332
++S T QV +F C++ + P +EV V+ + K L GL+
Sbjct: 51 KNSRPTVQVYLFCGAFCLLDTS-CEQDIEFPPQIEVKVNGKQVKANLRGLKNKPGTARPV 109
Query: 333 ----YVKLKENEKNK 343
Y++L N
Sbjct: 110 DITDYIRLSATVPNT 124
>gnl|CDD|220447 pfam09861, DUF2088, Domain of unknown function (DUF2088). This
domain, found in various hypothetical prokaryotic
proteins, has no known function.
Length = 203
Score = 27.9 bits (63), Expect = 9.9
Identities = 17/59 (28%), Positives = 24/59 (40%), Gaps = 13/59 (22%)
Query: 341 KNKKLFELLDVLEFNQVVIFVKSVTRCIALSTLLSEQNFPAVSIHRGMTQEERLKKYQE 399
+ + LL + E N V I + +T +A T HR MT+EE K E
Sbjct: 69 PSDIILPLL-LEELNAVGIPDEDITILVATGT------------HRPMTEEELKKILGE 114
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
0.321 0.136 0.388
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: 23,038,115
Number of extensions: 2302584
Number of successful extensions: 2405
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2352
Number of HSP's successfully gapped: 74
Length of query: 448
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 348
Effective length of database: 6,502,202
Effective search space: 2262766296
Effective search space used: 2262766296
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 61 (27.2 bits)