RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12758
(308 letters)
>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 = 265 bits (679), Expect = 2e-89
Identities = 102/246 (41%), Positives = 142/246 (57%), Gaps = 57/246 (23%)
Query: 63 FDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQ 122
F+++ ++ + I ++KPTP+Q AIP ++SGRDV+ AQTGSGKTAAFL+PIL +
Sbjct: 1 FEELGLSPELLRGIYALGFEKPTPIQARAIPPLLSGRDVIGQAQTGSGKTAAFLIPILEK 60
Query: 123 MYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVVRKK 182
+ P A
Sbjct: 61 LDPSPKKDGPQA------------------------------------------------ 72
Query: 183 VFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVVYGGSNVGDQMRDLDRGCHLLVATP 242
L+LAPTRELA QI + A+K + L+ V+YGG+++ Q+R L RG H++VATP
Sbjct: 73 -----LILAPTRELALQIAEVARKLGKHTNLKVVVIYGGTSIDKQIRKLKRGPHIVVATP 127
Query: 243 GRLVDMLERGKIGLANCRFLVLDEADRMLDMGFEPQIRCIVQENGMPRTGDRQTLMFSAT 302
GRL+D+LERGK+ L+ ++LVLDEADRMLDMGFE QIR I++ +P+ DRQTL+FSAT
Sbjct: 128 GRLLDLLERGKLDLSKVKYLVLDEADRMLDMGFEDQIREILKL--LPK--DRQTLLFSAT 183
Query: 303 FPKEIQ 308
PKE++
Sbjct: 184 MPKEVR 189
>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 = 240 bits (615), Expect = 6e-76
Identities = 93/251 (37%), Positives = 133/251 (52%), Gaps = 56/251 (22%)
Query: 58 PLPPQFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLV 117
PP+F + ++ + + +++PTP+Q AIP+I++GRDV+ AQTG+GKTAAFL+
Sbjct: 26 KTPPEFASLGLSPELLQALKDLGFEEPTPIQLAAIPLILAGRDVLGQAQTGTGKTAAFLL 85
Query: 118 PILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPC 177
P+L ++ + A L+LAPTRELA QI +E +K
Sbjct: 86 PLLQKILKSVERKYVSA--------------LILAPTRELAVQIAEELRKLG-------- 123
Query: 178 VVRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVVYGGSNVGDQMRDLDRGCHL 237
LR VVYGG ++ Q+ L RG +
Sbjct: 124 ------------------------------KNLGGLRVAVVYGGVSIRKQIEALKRGVDI 153
Query: 238 LVATPGRLVDMLERGKIGLANCRFLVLDEADRMLDMGFEPQIRCIVQENGMPRTGDRQTL 297
+VATPGRL+D+++RGK+ L+ LVLDEADRMLDMGF I I++ +P DRQTL
Sbjct: 154 VVATPGRLLDLIKRGKLDLSGVETLVLDEADRMLDMGFIDDIEKILKA--LPP--DRQTL 209
Query: 298 MFSATFPKEIQ 308
+FSAT P +I+
Sbjct: 210 LFSATMPDDIR 220
>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 = 174 bits (444), Expect = 2e-54
Identities = 86/226 (38%), Positives = 112/226 (49%), Gaps = 61/226 (26%)
Query: 85 TPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKV 144
TP+Q AIP I+SG+DV+ A TGSGKT AFL+PIL + KK
Sbjct: 1 TPIQAQAIPAILSGKDVLVQAPTGSGKTLAFLLPILQALLP----------------KKG 44
Query: 145 FPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVVRKKVFPLGLVLAPTRELATQIYDEA 204
P LVL APTRELA QIY+E
Sbjct: 45 GPQALVL---------------------------------------APTRELAEQIYEEL 65
Query: 205 KKFAYRSQLRPCVVYGGSNVGDQMRDLDRG-CHLLVATPGRLVDMLERGKIGL-ANCRFL 262
KK LR ++ GG+++ +Q R L +G +LV TPGRL+D+L RGK+ L N + L
Sbjct: 66 KKLFKILGLRVALLTGGTSLKEQARKLKKGKADILVGTPGRLLDLLRRGKLKLLKNLKLL 125
Query: 263 VLDEADRMLDMGFEPQIRCIVQENGMPRTGDRQTLMFSATFPKEIQ 308
VLDEA R+LDMGF + I+ DRQ L+ SAT P+ ++
Sbjct: 126 VLDEAHRLLDMGFGDDLEEILSR----LPPDRQILLLSATLPRNLE 167
>gnl|CDD|240273 PTZ00110, PTZ00110, helicase; Provisional.
Length = 545
Score = 174 bits (442), Expect = 2e-50
Identities = 102/257 (39%), Positives = 128/257 (49%), Gaps = 63/257 (24%)
Query: 57 LPLP-PQFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAF 115
+P P F+ + I ++ A + +PTP+Q P+ +SGRD++ A+TGSGKT AF
Sbjct: 125 VPKPVVSFEYTSFPDYILKSLKNAGFTEPTPIQVQGWPIALSGRDMIGIAETGSGKTLAF 184
Query: 116 LVP----ILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYR 171
L+P I Q PL G P+ LVLAPTRELA QI
Sbjct: 185 LLPAIVHINAQ-----PLLRYGDG----------PIVLVLAPTRELAEQI---------- 219
Query: 172 SQLRPCVVRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVVYGGSNVGDQMRDL 231
RE + KF S++R V YGG Q+ L
Sbjct: 220 ----------------------RE-------QCNKFGASSKIRNTVAYGGVPKRGQIYAL 250
Query: 232 DRGCHLLVATPGRLVDMLERGKIGLANCRFLVLDEADRMLDMGFEPQIRCIVQENGMPRT 291
RG +L+A PGRL+D LE L +LVLDEADRMLDMGFEPQIR IV R
Sbjct: 251 RRGVEILIACPGRLIDFLESNVTNLRRVTYLVLDEADRMLDMGFEPQIRKIV---SQIRP 307
Query: 292 GDRQTLMFSATFPKEIQ 308
DRQTLM+SAT+PKE+Q
Sbjct: 308 -DRQTLMWSATWPKEVQ 323
>gnl|CDD|214692 smart00487, DEXDc, DEAD-like helicases superfamily.
Length = 201
Score = 155 bits (393), Expect = 2e-46
Identities = 74/235 (31%), Positives = 104/235 (44%), Gaps = 62/235 (26%)
Query: 76 IALARYDKPTPVQKYAIPVIISG-RDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPA 134
I ++ P QK AI ++SG RDV+ A TGSGKT A L+P L +
Sbjct: 1 IEKFGFEPLRPYQKEAIEALLSGLRDVILAAPTGSGKTLAALLPALEALKRGKGGRV--- 57
Query: 135 GRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVVRKKVFPLGLVLAPTR 194
LVL PTR
Sbjct: 58 --------------LVL---------------------------------------VPTR 64
Query: 195 ELATQIYDEAKKFAYRSQLRPCVVYGGSNVGDQMRDLDRGC-HLLVATPGRLVDMLERGK 253
ELA Q +E KK L+ +YGG + +Q+R L+ G +LV TPGRL+D+LE K
Sbjct: 65 ELAEQWAEELKKLGPSLGLKVVGLYGGDSKREQLRKLESGKTDILVTTPGRLLDLLENDK 124
Query: 254 IGLANCRFLVLDEADRMLDMGFEPQIRCIVQENGMPRTGDRQTLMFSATFPKEIQ 308
+ L+N ++LDEA R+LD GF Q+ +++ + Q L+ SAT P+EI+
Sbjct: 125 LSLSNVDLVILDEAHRLLDGGFGDQLEKLLKL----LPKNVQLLLLSATPPEEIE 175
>gnl|CDD|236977 PRK11776, PRK11776, ATP-dependent RNA helicase DbpA; Provisional.
Length = 460
Score = 161 bits (409), Expect = 5e-46
Identities = 87/256 (33%), Positives = 125/256 (48%), Gaps = 75/256 (29%)
Query: 57 LPLPPQFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFL 116
LPLPP ++ N L Y + TP+Q ++P I++G+DV+A A+TGSGKTAAF
Sbjct: 9 LPLPP--------ALLANLNELG-YTEMTPIQAQSLPAILAGKDVIAQAKTGSGKTAAFG 59
Query: 117 VPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRP 176
+ +L ++ + K+F ++
Sbjct: 60 LGLLQKL----------------------------------------DVKRFRVQA---- 75
Query: 177 CVVRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQ----LRPCVVYGGSNVGDQMRDLD 232
LVL PTRELA Q+ E ++ A L C GG +G Q+ L+
Sbjct: 76 -----------LVLCPTRELADQVAKEIRRLARFIPNIKVLTLC---GGVPMGPQIDSLE 121
Query: 233 RGCHLLVATPGRLVDMLERGKIGLANCRFLVLDEADRMLDMGFEPQIRCIVQENGMPRTG 292
G H++V TPGR++D L +G + L LVLDEADRMLDMGF+ I I+++ P
Sbjct: 122 HGAHIIVGTPGRILDHLRKGTLDLDALNTLVLDEADRMLDMGFQDAIDAIIRQ--APA-- 177
Query: 293 DRQTLMFSATFPKEIQ 308
RQTL+FSAT+P+ I
Sbjct: 178 RRQTLLFSATYPEGIA 193
>gnl|CDD|236722 PRK10590, PRK10590, ATP-dependent RNA helicase RhlE; Provisional.
Length = 456
Score = 158 bits (400), Expect = 7e-45
Identities = 91/246 (36%), Positives = 125/246 (50%), Gaps = 53/246 (21%)
Query: 63 FDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQ 122
FD + ++ I +A Y +PTP+Q+ AIP ++ GRD+MA AQTG+GKTA F +P+L
Sbjct: 3 FDSLGLSPDILRAVAEQGYREPTPIQQQAIPAVLEGRDLMASAQTGTGKTAGFTLPLLQH 62
Query: 123 MYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVVRKK 182
+ R P GR RP VR
Sbjct: 63 LITRQP---HAKGR--------------------------------------RP--VR-- 77
Query: 183 VFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVVYGGSNVGDQMRDLDRGCHLLVATP 242
L+L PTRELA QI + + ++ +R VV+GG ++ QM L G +LVATP
Sbjct: 78 ----ALILTPTRELAAQIGENVRDYSKYLNIRSLVVFGGVSINPQMMKLRGGVDVLVATP 133
Query: 243 GRLVDMLERGKIGLANCRFLVLDEADRMLDMGFEPQIRCIVQENGMPRTGDRQTLMFSAT 302
GRL+D+ + + L LVLDEADRMLDMGF IR ++ +P RQ L+FSAT
Sbjct: 134 GRLLDLEHQNAVKLDQVEILVLDEADRMLDMGFIHDIRRVL--AKLP--AKRQNLLFSAT 189
Query: 303 FPKEIQ 308
F +I+
Sbjct: 190 FSDDIK 195
>gnl|CDD|236877 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional.
Length = 434
Score = 143 bits (363), Expect = 1e-39
Identities = 79/245 (32%), Positives = 109/245 (44%), Gaps = 61/245 (24%)
Query: 61 PQFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPIL 120
F ++++ E + + Y +PT +Q AIP + GRDV+ A TG+GKTAAFL+P L
Sbjct: 1 TTFSELELDESLLEALQDKGYTRPTAIQAEAIPPALDGRDVLGSAPTGTGKTAAFLLPAL 60
Query: 121 NQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVVR 180
+ + +P RK P L+L PTRELA Q+ D+A
Sbjct: 61 QHLLD------------FPRRKSGPPRILILTPTRELAMQVADQA--------------- 93
Query: 181 KKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVVYGGSNVGDQMRDLDRGCHLLVA 240
RELA + L + GG + ++VA
Sbjct: 94 -------------RELAK-----------HTHLDIATITGGVAYMNHAEVFSENQDIVVA 129
Query: 241 TPGRLVDMLERGKIGLANCR---FLVLDEADRMLDMGFEPQIRCIVQENGMPRTGDRQTL 297
TPGRL+ ++ +CR L+LDEADRMLDMGF I I E +QTL
Sbjct: 130 TPGRLLQYIKEENF---DCRAVETLILDEADRMLDMGFAQDIETIAAET----RWRKQTL 182
Query: 298 MFSAT 302
+FSAT
Sbjct: 183 LFSAT 187
>gnl|CDD|215103 PLN00206, PLN00206, DEAD-box ATP-dependent RNA helicase;
Provisional.
Length = 518
Score = 142 bits (360), Expect = 8e-39
Identities = 83/256 (32%), Positives = 116/256 (45%), Gaps = 59/256 (23%)
Query: 57 LPLPP--QFDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAA 114
PP F + + N+ A Y+ PTP+Q AIP +SGR ++ A TGSGKTA+
Sbjct: 115 AVPPPILSFSSCGLPPKLLLNLETAGYEFPTPIQMQAIPAALSGRSLLVSADTGSGKTAS 174
Query: 115 FLVPILNQ--MYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRS 172
FLVPI+++ G ++ PL +VL PTREL Q+ D+AK
Sbjct: 175 FLVPIISRCCTIRSG---------HPSEQRN--PLAMVLTPTRELCVQVEDQAKVL---- 219
Query: 173 QLRPCVVRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVVYGGSNVGDQMRDLD 232
K +++ L V GG + Q+ +
Sbjct: 220 -------------------------------GKGLPFKTAL----VVGGDAMPQQLYRIQ 244
Query: 233 RGCHLLVATPGRLVDMLERGKIGLANCRFLVLDEADRMLDMGFEPQIRCIVQENGMPRTG 292
+G L+V TPGRL+D+L + I L N LVLDE D ML+ GF Q+ I Q P
Sbjct: 245 QGVELIVGTPGRLIDLLSKHDIELDNVSVLVLDEVDCMLERGFRDQVMQIFQALSQP--- 301
Query: 293 DRQTLMFSATFPKEIQ 308
Q L+FSAT E++
Sbjct: 302 --QVLLFSATVSPEVE 315
>gnl|CDD|234938 PRK01297, PRK01297, ATP-dependent RNA helicase RhlB; Provisional.
Length = 475
Score = 141 bits (358), Expect = 9e-39
Identities = 83/224 (37%), Positives = 115/224 (51%), Gaps = 51/224 (22%)
Query: 85 TPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKV 144
TP+Q + ++G D + AQTG+GKTAAFL+ I+NQ+ L TPP
Sbjct: 111 TPIQAQVLGYTLAGHDAIGRAQTGTGKTAAFLISIINQL-----LQTPP----------- 154
Query: 145 FPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVVRKKVFPLGLVLAPTRELATQIYDEA 204
K Y + P L++APTREL QI +A
Sbjct: 155 ---------------------PKERYMGE-----------PRALIIAPTRELVVQIAKDA 182
Query: 205 KKFAYRSQLRPCVVYGGSNVGDQMRDLD-RGCHLLVATPGRLVDMLERGKIGLANCRFLV 263
+ L GG + Q++ L+ R C +LVATPGRL+D +RG++ L +V
Sbjct: 183 AALTKYTGLNVMTFVGGMDFDKQLKQLEARFCDILVATPGRLLDFNQRGEVHLDMVEVMV 242
Query: 264 LDEADRMLDMGFEPQIRCIVQENGMPRTGDRQTLMFSATFPKEI 307
LDEADRMLDMGF PQ+R I+++ PR +RQTL+FSATF ++
Sbjct: 243 LDEADRMLDMGFIPQVRQIIRQT--PRKEERQTLLFSATFTDDV 284
>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 = 130 bits (328), Expect = 2e-37
Identities = 62/205 (30%), Positives = 85/205 (41%), Gaps = 61/205 (29%)
Query: 99 RDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELA 158
RDV+ A TGSGKT A L+PIL + LVLAPTRELA
Sbjct: 1 RDVLLAAPTGSGKTLAALLPILELLDSLKGGQV-----------------LVLAPTRELA 43
Query: 159 TQIYDEAKKFAYRSQLRPCVVRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVV 218
Q+ + K+ F G ++ +
Sbjct: 44 NQVAERLKEL---------------FGEG-------------------------IKVGYL 63
Query: 219 YGGSNVGDQMRDLDRGCHLLVATPGRLVDMLERGKIGLANCRFLVLDEADRMLDMGFEPQ 278
GG+++ Q + L ++V TPGRL+D LER K+ L L+LDEA R+L+ GF
Sbjct: 64 IGGTSIKQQEKLLSGKTDIVVGTPGRLLDELERLKLSLKKLDLLILDEAHRLLNQGFGLL 123
Query: 279 IRCIVQENGMPRTGDRQTLMFSATF 303
I+ + DRQ L+ SAT
Sbjct: 124 GLKILLKLP----KDRQVLLLSATP 144
>gnl|CDD|235314 PRK04837, PRK04837, ATP-dependent RNA helicase RhlB; Provisional.
Length = 423
Score = 135 bits (341), Expect = 1e-36
Identities = 72/218 (33%), Positives = 103/218 (47%), Gaps = 50/218 (22%)
Query: 85 TPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKV 144
TP+Q A+P+ ++GRDV AQTG+GKT AFL + L + PA
Sbjct: 32 TPIQALALPLTLAGRDVAGQAQTGTGKTMAFLTATFHY------LLSHPAPED------- 78
Query: 145 FPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVVRKKVFPLGLVLAPTRELATQIYDEA 204
RK P L++APTRELA QI+ +A
Sbjct: 79 -----------------------------------RKVNQPRALIMAPTRELAVQIHADA 103
Query: 205 KKFAYRSQLRPCVVYGGSNVGDQMRDLDRGCHLLVATPGRLVDMLERGKIGLANCRFLVL 264
+ A + L+ + YGG Q++ L+ G +L+ T GRL+D ++ I L + +VL
Sbjct: 104 EPLAQATGLKLGLAYGGDGYDKQLKVLESGVDILIGTTGRLIDYAKQNHINLGAIQVVVL 163
Query: 265 DEADRMLDMGFEPQIRCIVQENGMPRTGDRQTLMFSAT 302
DEADRM D+GF IR + + MP R ++FSAT
Sbjct: 164 DEADRMFDLGFIKDIRWLFRR--MPPANQRLNMLFSAT 199
>gnl|CDD|235307 PRK04537, PRK04537, ATP-dependent RNA helicase RhlB; Provisional.
Length = 572
Score = 133 bits (336), Expect = 3e-35
Identities = 83/226 (36%), Positives = 112/226 (49%), Gaps = 51/226 (22%)
Query: 79 ARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGY 138
A + + TP+Q +PV + G DV AQTG+GKT AFLV ++N++ R L
Sbjct: 27 AGFTRCTPIQALTLPVALPGGDVAGQAQTGTGKTLAFLVAVMNRLLSRPAL--------- 77
Query: 139 PSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVVRKKVFPLGLVLAPTRELAT 198
RK P L+LAPTRELA
Sbjct: 78 ---------------------------------------ADRKPEDPRALILAPTRELAI 98
Query: 199 QIYDEAKKFAYRSQLRPCVVYGGSNVGDQMRDLDRGCHLLVATPGRLVDMLERGK-IGLA 257
QI+ +A KF LR +VYGG + Q L +G +++ATPGRL+D +++ K + L
Sbjct: 99 QIHKDAVKFGADLGLRFALVYGGVDYDKQRELLQQGVDVIIATPGRLIDYVKQHKVVSLH 158
Query: 258 NCRFLVLDEADRMLDMGFEPQIRCIVQENGMPRTGDRQTLMFSATF 303
C VLDEADRM D+GF IR +++ MP G RQTL+FSAT
Sbjct: 159 ACEICVLDEADRMFDLGFIKDIRFLLRR--MPERGTRQTLLFSATL 202
>gnl|CDD|236941 PRK11634, PRK11634, ATP-dependent RNA helicase DeaD; Provisional.
Length = 629
Score = 128 bits (324), Expect = 2e-33
Identities = 84/246 (34%), Positives = 120/246 (48%), Gaps = 58/246 (23%)
Query: 63 FDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQ 122
F D+ + I + Y+KP+P+Q IP +++GRDV+ AQTGSGKTAAF +P+L+
Sbjct: 8 FADLGLKAPILEALNDLGYEKPSPIQAECIPHLLNGRDVLGMAQTGSGKTAAFSLPLLHN 67
Query: 123 MYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVVRKK 182
+ P K P LVLAPTRELA Q+ + F+ K
Sbjct: 68 L--------------DPELKA--PQILVLAPTRELAVQVAEAMTDFS-----------KH 100
Query: 183 VFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVVYGGSNVGDQMRDLDRGCHLLVATP 242
+ + +V +YGG Q+R L +G ++V TP
Sbjct: 101 MRGVNVV---------------------------ALYGGQRYDVQLRALRQGPQIVVGTP 133
Query: 243 GRLVDMLERGKIGLANCRFLVLDEADRMLDMGFEPQIRCIVQENGMPRTGDRQTLMFSAT 302
GRL+D L+RG + L+ LVLDEAD ML MGF + I+ + +P QT +FSAT
Sbjct: 134 GRLLDHLKRGTLDLSKLSGLVLDEADEMLRMGFIEDVETIMAQ--IP--EGHQTALFSAT 189
Query: 303 FPKEIQ 308
P+ I+
Sbjct: 190 MPEAIR 195
>gnl|CDD|185609 PTZ00424, PTZ00424, helicase 45; Provisional.
Length = 401
Score = 117 bits (294), Expect = 5e-30
Identities = 71/245 (28%), Positives = 109/245 (44%), Gaps = 59/245 (24%)
Query: 63 FDDIQMTEIITNNIALARYDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQ 122
FD +++ E + I ++KP+ +Q+ I I+ G D + AQ+G+GKTA F++
Sbjct: 30 FDALKLNEDLLRGIYSYGFEKPSAIQQRGIKPILDGYDTIGQAQSGTGKTATFVIA---- 85
Query: 123 MYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVVRKK 182
A Q+ D L C
Sbjct: 86 -----------------------------------ALQLID--------YDLNACQA--- 99
Query: 183 VFPLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVVYGGSNVGDQMRDLDRGCHLLVATP 242
L+LAPTRELA QI ++R GG+ V D + L G H++V TP
Sbjct: 100 -----LILAPTRELAQQIQKVVLALGDYLKVRCHACVGGTVVRDDINKLKAGVHMVVGTP 154
Query: 243 GRLVDMLERGKIGLANCRFLVLDEADRMLDMGFEPQIRCIVQENGMPRTGDRQTLMFSAT 302
GR+ DM+++ + + + + +LDEAD ML GF+ QI + ++ +P D Q +FSAT
Sbjct: 155 GRVYDMIDKRHLRVDDLKLFILDEADEMLSRGFKGQIYDVFKK--LPP--DVQVALFSAT 210
Query: 303 FPKEI 307
P EI
Sbjct: 211 MPNEI 215
>gnl|CDD|224122 COG1201, Lhr, Lhr-like helicases [General function prediction
only].
Length = 814
Score = 68.4 bits (168), Expect = 8e-13
Identities = 25/56 (44%), Positives = 34/56 (60%), Gaps = 2/56 (3%)
Query: 80 RYDKPTPVQKYAIPVIISGRDVMACAQTGSGKT-AAFLVPILNQMYERGPLPTPPA 134
++ TP Q+YAIP I SG +V+ A TGSGKT AAFL P++N++ G
Sbjct: 19 KFTSLTPPQRYAIPEIHSGENVLIIAPTGSGKTEAAFL-PVINELLSLGKGKLEDG 73
>gnl|CDD|237497 PRK13767, PRK13767, ATP-dependent helicase; Provisional.
Length = 876
Score = 59.1 bits (144), Expect = 1e-09
Identities = 22/49 (44%), Positives = 35/49 (71%), Gaps = 2/49 (4%)
Query: 80 RYDKPTPVQKYAIPVIISGRDVMACAQTGSGKT-AAFLVPILNQMYERG 127
++ TP Q+YAIP+I G++V+ + TGSGKT AAFL I+++++ G
Sbjct: 29 KFGTFTPPQRYAIPLIHEGKNVLISSPTGSGKTLAAFLA-IIDELFRLG 76
>gnl|CDD|224125 COG1204, COG1204, Superfamily II helicase [General function
prediction only].
Length = 766
Score = 52.0 bits (125), Expect = 2e-07
Identities = 39/184 (21%), Positives = 63/184 (34%), Gaps = 65/184 (35%)
Query: 86 PVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVF 145
P Q+ ++S +V+ A TGSGKT L+ IL+ + E G K V+
Sbjct: 35 PQQEAVEKGLLSDENVLISAPTGSGKTLIALLAILSTLLEGG-------------GKVVY 81
Query: 146 PLGLVLAPTRELATQIYDEAKKFAYRSQLRPCVVRKKVFPLGLVLAP-TRELATQIYDEA 204
+ P + LA + Y+E + LG+ + T + YD
Sbjct: 82 -----IVPLKALAEEKYEEFSRLE---------------ELGIRVGISTGD-----YDLD 116
Query: 205 KKFAYRSQLRPCVVYGGSNVGDQMRDLDRGCHLLVATPGRLVDMLERGKIGLAN-CRFLV 263
+ R ++V TP +L D L R + +V
Sbjct: 117 DERLAR------------------------YDVIVTTPEKL-DSLTRKRPSWIEEVDLVV 151
Query: 264 LDEA 267
+DE
Sbjct: 152 IDEI 155
>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 = 50.1 bits (120), Expect = 8e-07
Identities = 49/222 (22%), Positives = 74/222 (33%), Gaps = 85/222 (38%)
Query: 88 QKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPL 147
Q A+ +I GR+V+ TGSGKT +FL+PIL+ + PS +
Sbjct: 75 QVDALRLIREGRNVVVTTGTGSGKTESFLLPILDHLLRD------------PSAR----- 117
Query: 148 GLVLAPTRELATQIYDEAKKFAYRSQLRPCVVRKKVFPLGLVLAPTRELATQIYDEAKKF 207
L+L PT LA D+A++ REL + + +
Sbjct: 118 ALLLYPTNALAN---DQAERL-------------------------RELISDLPGKVTFG 149
Query: 208 AYRSQLRPCVVYGGSNVGDQMRDLDRGCHLLVATPGRLVDMLE--------RGKIGLANC 259
Y P ++ + +L+ P DML L N
Sbjct: 150 RYTGDTPP---------EERRAIIRNPPDILLTNP----DMLHYLLLRNHDAWLWLLRNL 196
Query: 260 RFLVLDEA---------------DRMLDM----GFEPQIRCI 282
++LV+DE R+L G QI C
Sbjct: 197 KYLVVDELHTYRGVQGSEVALLLRRLLRRLRRYGSPLQIICT 238
>gnl|CDD|218292 pfam04851, ResIII, Type III restriction enzyme, res subunit.
Length = 100
Score = 38.0 bits (89), Expect = 8e-04
Identities = 31/113 (27%), Positives = 49/113 (43%), Gaps = 28/113 (24%)
Query: 83 KPTPVQKYAIPVIISGRDVMACAQTGSGKT--AAFLVPILNQMYERGPLPTPPAGRGYPS 140
+ P Q+ AI ++ + + TGSGKT AA L+ L +
Sbjct: 3 ELRPYQEEAIERLLEKKRGLIVMATGSGKTLTAAALIARLAK-----------------G 45
Query: 141 RKKVFPLGLVLAPTRELATQ----IYDEAKKFAYRSQLRPCVVR-KKVFPLGL 188
+KKV L + P ++L Q I DEA + +++ R + + K F LGL
Sbjct: 46 KKKV----LFVVPRKDLLEQALVIIIDEAHHSSAKTKYRKILEKFKPAFLLGL 94
>gnl|CDD|238061 cd00113, PLAT, PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin)
domain or LH2 (Lipoxygenase homology 2) domain. It
consists of an eight stranded beta-barrel. The domain
can be found in various domain architectures, in case
of lipoxygenases, alpha toxin, lipases and polycystin,
but also as a single domain or as repeats.The putative
function of this domain is to facilitate access to
sequestered membrane or micelle bound substrates.
Length = 116
Score = 35.0 bits (81), Expect = 0.010
Identities = 12/33 (36%), Positives = 14/33 (42%)
Query: 39 PHLRNQPSGGRNSTDTFLLPLPPQFDDIQMTEI 71
P L S R STDTF + L DI +
Sbjct: 36 PILDGPGSFERGSTDTFQIDLKLDIGDITKVYL 68
>gnl|CDD|223989 COG1061, SSL2, DNA or RNA helicases of superfamily II
[Transcription / DNA replication, recombination, and
repair].
Length = 442
Score = 37.0 bits (86), Expect = 0.011
Identities = 26/112 (23%), Positives = 42/112 (37%), Gaps = 30/112 (26%)
Query: 63 FDDIQMTEIITNNIALARYDKPTPVQKYAIPVIIS----GRDVMACAQTGSGKT--AAFL 116
D + E + + +A + P Q+ A+ ++ R + TG+GKT AA
Sbjct: 16 LADYVLDEGLPLKLIVAFEFELRPYQEEALDALVKNRRTERRGVIVLPTGAGKTVVAAEA 75
Query: 117 VPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKKF 168
+ E ++ LVL PT+EL Q + KKF
Sbjct: 76 ------IAEL--------------KRST----LVLVPTKELLDQWAEALKKF 103
Score = 30.5 bits (69), Expect = 1.3
Identities = 11/20 (55%), Positives = 13/20 (65%)
Query: 188 LVLAPTRELATQIYDEAKKF 207
LVL PT+EL Q + KKF
Sbjct: 84 LVLVPTKELLDQWAEALKKF 103
>gnl|CDD|226947 COG4581, COG4581, Superfamily II RNA helicase [DNA replication,
recombination, and repair].
Length = 1041
Score = 34.7 bits (80), Expect = 0.074
Identities = 18/93 (19%), Positives = 28/93 (30%), Gaps = 10/93 (10%)
Query: 20 DLSAKKESAPGSNPRVYVPPHLRNQPSGGRNSTDTFLLPLPPQFDDIQMTEIITNNIALA 79
S + G V + + + + P A
Sbjct: 66 KHSEIESLNVGMRLDVRLSSKELSDVAVPDDYDMVPDAESPFDLAPP----------ARE 115
Query: 80 RYDKPTPVQKYAIPVIISGRDVMACAQTGSGKT 112
+ P Q+ AI ++ G V+ CA T SGKT
Sbjct: 116 YPFELDPFQQEAIAILERGESVLVCAPTSSGKT 148
>gnl|CDD|224124 COG1203, COG1203, CRISPR-associated helicase Cas3 [Defense
mechanisms].
Length = 733
Score = 34.4 bits (79), Expect = 0.087
Identities = 20/94 (21%), Positives = 35/94 (37%), Gaps = 19/94 (20%)
Query: 82 DKPTPVQKYAIPVIISGR----DVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRG 137
+ +Q+ A+ +I+ V+ A TG GKT A L+ L + E+ L
Sbjct: 194 HEGYELQEKALELILRLEKRSLLVVLEAPTGYGKTEASLILALALLDEKIKL-------- 245
Query: 138 YPSRKKVFPLGLVLAPTRELATQIYDEAKKFAYR 171
+ + P R + +Y AK+
Sbjct: 246 -------KSRVIYVLPFRTIIEDMYRRAKEIFGL 272
>gnl|CDD|234468 TIGR04095, dnd_restrict_1, DNA phosphorothioation system
restriction enzyme. The DNA phosphorothioate
modification system dnd (DNA instability during
electrophoresis) recently has been shown to provide a
modification essential to a restriction system. This
protein family was detected by Partial Phylogenetic
Profiling as linked to dnd, and its members usually are
clustered with the dndABCDE genes.
Length = 451
Score = 32.7 bits (75), Expect = 0.26
Identities = 21/73 (28%), Positives = 29/73 (39%), Gaps = 22/73 (30%)
Query: 98 GRDVMACAQTGSGKT--AAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTR 155
GR ++ A TG+GKT A L + + G L LV+ P +
Sbjct: 25 GRGILKMA-TGTGKTLTALAAASKLYE--KIGLLVL-----------------LVVCPYQ 64
Query: 156 ELATQIYDEAKKF 168
L Q EA+KF
Sbjct: 65 HLVDQWAREAEKF 77
Score = 28.5 bits (64), Expect = 5.1
Identities = 12/36 (33%), Positives = 17/36 (47%), Gaps = 4/36 (11%)
Query: 188 LVLAPTRELATQIYDEAKKFAYRSQLRPCVVYGGSN 223
LV+ P + L Q EA+KF L P + Y +
Sbjct: 58 LVVCPYQHLVDQWAREAEKFG----LNPILCYESVS 89
>gnl|CDD|224120 COG1199, DinG, Rad3-related DNA helicases [Transcription / DNA
replication, recombination, and repair].
Length = 654
Score = 31.3 bits (71), Expect = 0.79
Identities = 16/49 (32%), Positives = 24/49 (48%), Gaps = 4/49 (8%)
Query: 83 KPTPVQKYAI----PVIISGRDVMACAQTGSGKTAAFLVPILNQMYERG 127
+P P Q+ + G ++ A TG+GKT A+L+P L E G
Sbjct: 15 EPRPEQREMAEAVAEALKGGEGLLIEAPTGTGKTLAYLLPALAYAREEG 63
>gnl|CDD|224123 COG1202, COG1202, Superfamily II helicase, archaea-specific
[General function prediction only].
Length = 830
Score = 30.5 bits (69), Expect = 1.3
Identities = 23/90 (25%), Positives = 36/90 (40%), Gaps = 30/90 (33%)
Query: 57 LPLPPQFDDIQMTEIITNNIALARYDKPTPVQKYAIPV-IISGRDVMACAQTGSGKTAA- 114
L +P +F + E I + PVQ A+ ++ G +++ + T SGKT
Sbjct: 199 LDIPEKFKRMLKREGIE---------ELLPVQVLAVEAGLLEGENLLVVSATASGKTLIG 249
Query: 115 ----------------FLVPIL---NQMYE 125
FLVP++ NQ YE
Sbjct: 250 ELAGIPRLLSGGKKMLFLVPLVALANQKYE 279
>gnl|CDD|234365 TIGR03817, DECH_helic, helicase/secretion neighborhood putative
DEAH-box helicase. A conserved gene neighborhood widely
spread in the Actinobacteria contains this
uncharacterized DEAH-box family helicase encoded
convergently towards an operon of genes for protein
homologous to type II secretion and pilus formation
proteins. The context suggests that this helicase may
play a role in conjugal transfer of DNA.
Length = 742
Score = 30.5 bits (69), Expect = 1.5
Identities = 19/61 (31%), Positives = 27/61 (44%), Gaps = 17/61 (27%)
Query: 98 GRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTREL 157
GR V+ T SGK+ A+ +P+L+ + P T L LAPT+ L
Sbjct: 51 GRHVVVATGTASGKSLAYQLPVLSAL-ADDPRAT----------------ALYLAPTKAL 93
Query: 158 A 158
A
Sbjct: 94 A 94
>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 = 29.7 bits (67), Expect = 2.0
Identities = 16/40 (40%), Positives = 22/40 (55%)
Query: 81 YDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPIL 120
YD P Q+ I ++ GRDV+ TG GK+ + VP L
Sbjct: 11 YDDFRPGQEEIISHVLDGRDVLVVMPTGGGKSLCYQVPAL 50
>gnl|CDD|237496 PRK13766, PRK13766, Hef nuclease; Provisional.
Length = 773
Score = 29.8 bits (68), Expect = 2.1
Identities = 22/68 (32%), Positives = 32/68 (47%), Gaps = 20/68 (29%)
Query: 102 MACAQTGSGKTA-AFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQ 160
+ TG GKTA A LV I +++++G KV L+LAPT+ L Q
Sbjct: 33 LVVLPTGLGKTAIALLV-IAERLHKKG--------------GKV----LILAPTKPLVEQ 73
Query: 161 IYDEAKKF 168
+ +KF
Sbjct: 74 HAEFFRKF 81
Score = 27.9 bits (63), Expect = 8.0
Identities = 26/86 (30%), Positives = 45/86 (52%), Gaps = 9/86 (10%)
Query: 188 LVLAPTRELATQIYDEAKKFAYRSQLRP--CVVYGGSNVGDQMRDLDRGCHLLVATPGRL 245
L+LAPT+ L Q + +KF + VV+ G ++ +L ++VATP ++
Sbjct: 62 LILAPTKPLVEQHAEFFRKF---LNIPEEKIVVFTGEVSPEKRAELWEKAKVIVATP-QV 117
Query: 246 V--DMLERGKIGLANCRFLVLDEADR 269
+ D++ G+I L + L+ DEA R
Sbjct: 118 IENDLIA-GRISLEDVSLLIFDEAHR 142
>gnl|CDD|223630 COG0556, UvrB, Helicase subunit of the DNA excision repair complex
[DNA replication, recombination, and repair].
Length = 663
Score = 29.9 bits (68), Expect = 2.2
Identities = 25/91 (27%), Positives = 34/91 (37%), Gaps = 27/91 (29%)
Query: 83 KPTPVQKYAIPVIISG-----RDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRG 137
KP Q AI ++ G + TGSGKT + + + PT
Sbjct: 12 KPAGDQPEAIAELVEGIENGLKHQTLLGVTGSGKTFT-----MANVIAKVQRPT------ 60
Query: 138 YPSRKKVFPLGLVLAPTRELATQIYDEAKKF 168
LVLA + LA Q+Y E K+F
Sbjct: 61 -----------LVLAHNKTLAAQLYSEFKEF 80
Score = 28.3 bits (64), Expect = 5.5
Identities = 11/20 (55%), Positives = 14/20 (70%)
Query: 188 LVLAPTRELATQIYDEAKKF 207
LVLA + LA Q+Y E K+F
Sbjct: 61 LVLAHNKTLAAQLYSEFKEF 80
>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 = 29.7 bits (67), Expect = 2.3
Identities = 13/35 (37%), Positives = 18/35 (51%)
Query: 86 PVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPIL 120
PVQ I ++ GRD TG GK+ + +P L
Sbjct: 14 PVQLEVINAVLLGRDCFVVMPTGGGKSLCYQLPAL 48
>gnl|CDD|180905 PRK07246, PRK07246, bifunctional ATP-dependent DNA helicase/DNA
polymerase III subunit epsilon; Validated.
Length = 820
Score = 29.7 bits (67), Expect = 2.4
Identities = 12/22 (54%), Positives = 16/22 (72%)
Query: 105 AQTGSGKTAAFLVPILNQMYER 126
AQTG GKT +L+P+L Q +R
Sbjct: 271 AQTGIGKTYGYLLPLLAQSDQR 292
>gnl|CDD|104071 PRK09629, PRK09629, bifunctional thiosulfate
sulfurtransferase/phosphatidylserine decarboxylase;
Provisional.
Length = 610
Score = 29.3 bits (65), Expect = 2.7
Identities = 17/43 (39%), Positives = 21/43 (48%)
Query: 125 ERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKK 167
ERGP+ G + + GLV P REL T YDEA +
Sbjct: 515 ERGPMAVVLVGAMIVASVETVWAGLVTPPKRELKTFSYDEAAR 557
>gnl|CDD|213255 cd03288, ABCC_SUR2, ATP-binding cassette domain 2 of the
sulfonylurea receptor SUR. The SUR domain 2. The
sulfonylurea receptor SUR is an ATP binding cassette
(ABC) protein of the ABCC/MRP family. Unlike other ABC
proteins, it has no intrinsic transport function,
neither active nor passive, but associates with the
potassium channel proteins Kir6.1 or Kir6.2 to form the
ATP-sensitive potassium (K(ATP)) channel. Within the
channel complex, SUR serves as a regulatory subunit that
fine-tunes the gating of Kir6.x in response to
alterations in cellular metabolism. It constitutes a
major pharmaceutical target as it binds numerous drugs,
K(ATP) channel openers and blockers, capable of up- or
down-regulating channel activity.
Length = 257
Score = 28.7 bits (64), Expect = 3.6
Identities = 16/45 (35%), Positives = 26/45 (57%), Gaps = 2/45 (4%)
Query: 70 EIITNNIALARYDKP-TPVQKYAIPVIISGRDVMACAQTGSGKTA 113
EI +++ + RY+ PV K+ I G+ V C +TGSGK++
Sbjct: 19 EIKIHDLCV-RYENNLKPVLKHVKAYIKPGQKVGICGRTGSGKSS 62
>gnl|CDD|203709 pfam07652, Flavi_DEAD, Flavivirus DEAD domain.
Length = 146
Score = 28.1 bits (63), Expect = 3.8
Identities = 18/76 (23%), Positives = 29/76 (38%), Gaps = 19/76 (25%)
Query: 108 GSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPLGLVLAPTRELATQIYDEAKK 167
G+GKT L ++ + +R L T LVLAPTR + ++ + +
Sbjct: 12 GAGKTRKVLPELVRECIDRR-LRT-----------------LVLAPTRVVLAEMEEALRG 53
Query: 168 FAYRSQLRPCVVRKKV 183
R P V +
Sbjct: 54 LPIRYH-TPAVSSEHT 68
>gnl|CDD|183426 PRK12309, PRK12309, transaldolase/EF-hand domain-containing
protein; Provisional.
Length = 391
Score = 28.9 bits (65), Expect = 3.8
Identities = 25/96 (26%), Positives = 36/96 (37%), Gaps = 33/96 (34%)
Query: 198 TQIYDEAKKFAYRSQLRPCVVYGGSNVGDQMRDLDR-----GCHLLVATPGRLVDM---- 248
TQIY+ KKF Y+++ V G S R++ GC LL +P L +
Sbjct: 211 TQIYNYYKKFGYKTE-----VMGAS-----FRNIGEIIELAGCDLLTISPKLLEQLRSTE 260
Query: 249 --------------LERGKIGLANCRFLVLDEADRM 270
+E KI + F + DRM
Sbjct: 261 AELPRKLDPANAAGMEIEKIHMDRATFDKMHAEDRM 296
>gnl|CDD|148673 pfam07209, DUF1415, Protein of unknown function (DUF1415). This
family consists of several hypothetical bacterial
proteins of around 180 residues in length. The function
of this family is unknown.
Length = 174
Score = 28.3 bits (64), Expect = 4.2
Identities = 23/86 (26%), Positives = 34/86 (39%), Gaps = 23/86 (26%)
Query: 204 AKKFAYRSQLRPCVVYGGSNVGDQMRDLDRGCHLLVATPGRLVD--------MLERGKIG 255
AK+ + Q+R VV ++V D + DL LL ++ LE
Sbjct: 25 AKREVVKGQIR-YVVSEATDVEDLLEDLLAELQLLDQDDAEEIETTLLILPNGLE----- 78
Query: 256 LANCRFL----VLDEADRML-DMGFE 276
FL LD AD +L ++G E
Sbjct: 79 ----DFLDYNDFLDIADALLEELGLE 100
>gnl|CDD|223588 COG0514, RecQ, Superfamily II DNA helicase [DNA replication,
recombination, and repair].
Length = 590
Score = 28.8 bits (65), Expect = 4.5
Identities = 13/40 (32%), Positives = 21/40 (52%)
Query: 81 YDKPTPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPIL 120
Y P Q+ I ++SG+D + TG GK+ + +P L
Sbjct: 15 YASFRPGQQEIIDALLSGKDTLVVMPTGGGKSLCYQIPAL 54
>gnl|CDD|212669 cd10227, ParM_like, Plasmid segregation protein ParM and similar
proteins. ParM is a plasmid-encoded bacterial homolog
of actin, which polymerizes into filaments similar to
F-actin, and plays a vital role in plasmid segregation.
ParM filaments segregate plasmids paired at midcell into
the individual daughter cells. This subfamily also
contains Thermoplasma acidophilum Ta0583, an active
ATPase at physiological temperatures, which has a
propensity to form filaments.
Length = 312
Score = 28.2 bits (63), Expect = 5.7
Identities = 18/94 (19%), Positives = 32/94 (34%), Gaps = 8/94 (8%)
Query: 136 RGYPSRKKVFPLGL-VLAPTRELATQIYDEAKKFAYRSQLRPCVVRKKVFPLGL------ 188
G P L L V +A ++ E ++ + K+ G
Sbjct: 186 NGKPVESSSGSLELGVSDLYEAIAKELNKEYGIDLSDEEIEEILRNGKIKNYGKEEDITE 245
Query: 189 -VLAPTRELATQIYDEAKKFAYRSQLRPCVVYGG 221
+ E A +I +E K+F S + ++ GG
Sbjct: 246 IIEEAAEEYAEKILNELKEFLGLSDVDKVILVGG 279
>gnl|CDD|223703 COG0630, VirB11, Type IV secretory pathway, VirB11 components, and
related ATPases involved in archaeal flagella
biosynthesis [Cell motility and secretion /
Intracellular trafficking and secretion].
Length = 312
Score = 28.1 bits (63), Expect = 6.1
Identities = 15/44 (34%), Positives = 20/44 (45%), Gaps = 2/44 (4%)
Query: 70 EIITNNIALARYDKPTPVQ-KYAIPVIISGRDVMACAQTGSGKT 112
E IT L Y +P Q Y I + + ++ C T SGKT
Sbjct: 115 EPITP-EDLIEYGTISPEQAAYLWLAIEARKSIIICGGTASGKT 157
>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 = 6.5
Identities = 16/47 (34%), Positives = 21/47 (44%), Gaps = 1/47 (2%)
Query: 83 KPTPVQKYAIPVIISGRDVMACAQTGSGKT-AAFLVPILNQMYERGP 128
P P Q + GR + A TGSGKT A FL +++ P
Sbjct: 13 TPRPFQLEMWAAALEGRSGLLIAPTGSGKTLAGFLPSLIDLAGPEKP 59
>gnl|CDD|236498 PRK09401, PRK09401, reverse gyrase; Reviewed.
Length = 1176
Score = 28.4 bits (64), Expect = 7.2
Identities = 22/93 (23%), Positives = 35/93 (37%), Gaps = 31/93 (33%)
Query: 83 KPTPVQKYAIPVIISGRDVMACAQTGSGKT------AAFLVPILNQMYERGPLPTPPAGR 136
KP +Q+ ++ G A TG GKT + +L A +
Sbjct: 80 KPWSLQRTWAKRLLLGESFAIIAPTGVGKTTFGLVMSLYL-----------------AKK 122
Query: 137 GYPSRKKVFPLGLVLAPTRELATQIYDEAKKFA 169
G KK ++ PTR L Q+ ++ +KF
Sbjct: 123 G----KKS----YIIFPTRLLVEQVVEKLEKFG 147
>gnl|CDD|234013 TIGR02785, addA_Gpos, helicase-exonuclease AddAB, AddA subunit,
Firmicutes type. AddAB, also called RexAB, substitutes
for RecBCD in several bacterial lineages. These DNA
recombination proteins act before synapse and are
particularly important for DNA repair of double-stranded
breaks by homologous recombination. The term AddAB is
used broadly, with AddA homologous between the
Firmicutes (as modeled here) and the
alphaproteobacteria, while the partner AddB proteins
show no strong homology across the two groups of species
[DNA metabolism, DNA replication, recombination, and
repair].
Length = 1230
Score = 28.1 bits (63), Expect = 7.7
Identities = 14/38 (36%), Positives = 20/38 (52%), Gaps = 2/38 (5%)
Query: 85 TPVQKYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQ 122
T Q AI G+D++ A GSGKTA + I+ +
Sbjct: 3 TDEQWQAI--YTRGQDILVSASAGSGKTAVLVERIIRK 38
>gnl|CDD|219079 pfam06542, PHA-1, Regulator protein PHA-1. This family represents
the protein product of the gene pha-1 which coordinates
with lin-35 Rb during animal development. The protein is
expressed during embryonic development and functions in
the cytoplasm. PHA-1 acts in a parallel pathway with
UBC-18 to regulate the activity of a common cellular
target.
Length = 389
Score = 27.9 bits (62), Expect = 7.9
Identities = 13/39 (33%), Positives = 20/39 (51%)
Query: 57 LPLPPQFDDIQMTEIITNNIALARYDKPTPVQKYAIPVI 95
L FD++ +T+ + IAL +PT V+KY I
Sbjct: 149 LREKHHFDELIVTDRLLAEIALQNVKQPTLVEKYINSNI 187
>gnl|CDD|233824 TIGR02342, chap_CCT_delta, T-complex protein 1, delta subunit.
Members of this family, all eukaryotic, are part of the
group II chaperonin complex called CCT (chaperonin
containing TCP-1) or TRiC. The archaeal equivalent group
II chaperonin is often called the thermosome. Both are
somewhat related to the group I chaperonin of bacterial,
GroEL/GroES. This family consists exclusively of the CCT
delta chain (part of a paralogous family) from animals,
plants, fungi, and other eukaryotes.
Length = 517
Score = 27.8 bits (62), Expect = 8.5
Identities = 17/50 (34%), Positives = 28/50 (56%), Gaps = 7/50 (14%)
Query: 239 VATPGRLVDMLERGKIGLANCRFLVLDEADRMLDMGFEPQIRCIVQENGM 288
+ G+ V ++ RG +N LV+DEA+R L IRC+V++ G+
Sbjct: 357 IQNAGKTVTVVVRG----SNK--LVIDEAERSLHDAL-CVIRCLVKKRGL 399
>gnl|CDD|233090 TIGR00682, lpxK, tetraacyldisaccharide 4'-kinase. Also called
lipid-A 4'-kinase. This essential gene encodes an enzyme
in the pathway of lipid A biosynthesis in Gram-negative
organisms. A single copy of this protein is found in
Gram-negative bacteria. PSI-BLAST converges on this set
of apparent orthologs without identifying any other
homologs [Cell envelope, Biosynthesis and degradation of
surface polysaccharides and lipopolysaccharides].
Length = 311
Score = 27.4 bits (61), Expect = 8.7
Identities = 18/59 (30%), Positives = 29/59 (49%), Gaps = 6/59 (10%)
Query: 89 KYAIPVIISGRDVMACAQTGSGKTAAFLVPILNQMYERGPLPTPPAGRGYPSRKKVFPL 147
+ +PV+I G + G+GKT +V + + +RG L RGY S+ K + L
Sbjct: 25 RAPVPVVIVGN----LSVGGTGKTP-VVVWLAELLKDRG-LRVGVLSRGYGSKTKKYTL 77
>gnl|CDD|233398 TIGR01407, dinG_rel, DnaQ family exonuclease/DinG family helicase,
putative. This model represents a family of proteins in
Gram-positive bacteria. The N-terminal region of about
200 amino acids resembles the epsilon subunit of E. coli
DNA polymerase III and the homologous region of the
Gram-positive type DNA polymerase III alpha subunit. The
epsilon subunit contains an exonuclease domain. The
remainder of this protein family resembles a predicted
ATP-dependent helicase, the DNA damage-inducible protein
DinG of E. coli [DNA metabolism, DNA replication,
recombination, and repair].
Length = 850
Score = 27.8 bits (62), Expect = 9.3
Identities = 9/23 (39%), Positives = 13/23 (56%)
Query: 100 DVMACAQTGSGKTAAFLVPILNQ 122
+ A TG+GKT +L+P L
Sbjct: 266 KSLIEAPTGTGKTLGYLLPALYY 288
>gnl|CDD|131338 TIGR02285, TIGR02285, conserved hypothetical protein. Members of
this family are found in several Proteobacteria,
including Pseudomonas putida KT2440, Bdellovibrio
bacteriovorus HD100 (three members), Aeromonas
hydrophila, and Chromobacterium violaceum ATCC 12472.
The function is unknown [Hypothetical proteins,
Conserved].
Length = 268
Score = 27.4 bits (61), Expect = 9.6
Identities = 27/105 (25%), Positives = 40/105 (38%), Gaps = 19/105 (18%)
Query: 164 EAKKFAYRSQLRPCVVRKKVFPLGLVLAPTRELATQIYDEA------KKFAYRSQLRPCV 217
E +KF S P + P+GLV +EL + DE KK + R V
Sbjct: 89 EREKFLIFS--DPTLR---ALPVGLV--LRKELTAGVRDEQDGDVDLKKLLASKKKRLGV 141
Query: 218 VYG---GSNVGDQMRDLDRG---CHLLVATPGRLVDMLERGKIGL 256
+ G + D + D + A G L MLE+G++
Sbjct: 142 IASRSYGQQIDDILSDSGYQHNTRIIGNAAMGNLFKMLEKGRVNY 186
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
0.320 0.138 0.411
Gapped
Lambda K H
0.267 0.0643 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 16,142,825
Number of extensions: 1575776
Number of successful extensions: 1521
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1469
Number of HSP's successfully gapped: 85
Length of query: 308
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 211
Effective length of database: 6,635,264
Effective search space: 1400040704
Effective search space used: 1400040704
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 (21.8 bits)
S2: 59 (26.7 bits)