RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11867
(399 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 = 254 bits (650), Expect = 8e-80
Identities = 107/305 (35%), Positives = 173/305 (56%), Gaps = 13/305 (4%)
Query: 101 SVKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFT 160
+ F +L L PELL+ + ++GF P+ IQ A+P +LA +++ Q+Q+GTGKTAAF
Sbjct: 27 TPPEFASLGLSPELLQALKDLGFEEPTPIQLAAIPLILAG--RDVLGQAQTGTGKTAAFL 84
Query: 161 LTMLSRVN--PSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLE-RN 217
L +L ++ + L LAPT ELA+QI E + K+GK++ L V G ++ +
Sbjct: 85 LPLLQKILKSVERKYVSALILAPTRELAVQIAEELRKLGKNLGGLRVAVVYGGVSIRKQI 144
Query: 218 KKITE--QIIIGTPGKVLDWGLKYR-FFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKR 274
+ + I++ TPG++LD L R DLS ++ VLDEAD + G D +I K
Sbjct: 145 EALKRGVDIVVATPGRLLD--LIKRGKLDLSGVETLVLDEAD-RMLDMGFIDDIEKILKA 201
Query: 275 LPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKRE--EESLDNIKQHYVMCKNIDEKF 332
LP D Q +LFSAT ++ E A+ + +P+ I++ E E +L IKQ Y+ ++ +EK
Sbjct: 202 LPPDRQTLLFSATMPDDIRELARRYLNDPVEIEVSVEKLERTLKKIKQFYLEVESEEEKL 261
Query: 333 EAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFRE 392
E + + G+ ++F T++ LAE + K G V L G+L E+R L++F++
Sbjct: 262 ELLLKLLKDEDEGRVIVFVRTKRLVEELAESLRKRGFKVAALHGDLPQEERDRALEKFKD 321
Query: 393 GEFKI 397
GE ++
Sbjct: 322 GELRV 326
>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 = 231 bits (592), Expect = 4e-75
Identities = 93/208 (44%), Positives = 131/208 (62%), Gaps = 10/208 (4%)
Query: 105 FEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTML 164
FE L L PELL+G+Y +GF P+ IQ A+P LL+ ++I Q+Q+G+GKTAAF + +L
Sbjct: 1 FEELGLSPELLRGIYALGFEKPTPIQARAIPPLLS--GRDVIGQAQTGSGKTAAFLIPIL 58
Query: 165 SRVN--PSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENL-ERNKKIT 221
+++ P PQ L LAPT ELA+QI EV K+GKH T+L V G ++ ++ +K+
Sbjct: 59 EKLDPSPKKDGPQALILAPTRELALQIAEVARKLGKH-TNLKVVVIYGGTSIDKQIRKLK 117
Query: 222 E--QIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDC 279
I++ TPG++LD L+ DLSK+K VLDEAD M+ G +D I K LP D
Sbjct: 118 RGPHIVVATPGRLLDL-LERGKLDLSKVKYLVLDEADRML-DMGFEDQIREILKLLPKDR 175
Query: 280 QIMLFSATYDKEVMEFAQDMVPNPLIIK 307
Q +LFSAT KEV + A+ + NP+ I
Sbjct: 176 QTLLFSATMPKEVRDLARKFLRNPVRIL 203
>gnl|CDD|185609 PTZ00424, PTZ00424, helicase 45; Provisional.
Length = 401
Score = 209 bits (533), Expect = 1e-63
Identities = 107/301 (35%), Positives = 175/301 (58%), Gaps = 12/301 (3%)
Query: 102 VKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTL 161
V +F+AL L +LL+G+Y GF PS IQ+ + +L ++ I Q+QSGTGKTA F +
Sbjct: 27 VDSFDALKLNEDLLRGIYSYGFEKPSAIQQRGIKPILDG--YDTIGQAQSGTGKTATFVI 84
Query: 162 TMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVR-YAVRGENLERNK-- 218
L ++ + Q L LAPT ELA QI +VV +G + L VR +A G + R+
Sbjct: 85 AALQLIDYDLNACQALILAPTRELAQQIQKVVLALGDY---LKVRCHACVGGTVVRDDIN 141
Query: 219 --KITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLP 276
K +++GTPG+V D + R + +K+F+LDEAD M+ ++G + + K+LP
Sbjct: 142 KLKAGVHMVVGTPGRVYDM-IDKRHLRVDDLKLFILDEADEML-SRGFKGQIYDVFKKLP 199
Query: 277 SDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKNIDEKFEAVS 336
D Q+ LFSAT E++E + +P I +K++E +L+ I+Q YV + + KF+ +
Sbjct: 200 PDVQVALFSATMPNEILELTTKFMRDPKRILVKKDELTLEGIRQFYVAVEKEEWKFDTLC 259
Query: 337 NIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFK 396
++Y +TI QA+I+C+TR+ +L +KM + V + G++ + R I+ FR G +
Sbjct: 260 DLYETLTITQAIIYCNTRRKVDYLTKKMHERDFTVSCMHGDMDQKDRDLIMREFRSGSTR 319
Query: 397 I 397
+
Sbjct: 320 V 320
>gnl|CDD|236977 PRK11776, PRK11776, ATP-dependent RNA helicase DbpA; Provisional.
Length = 460
Score = 153 bits (389), Expect = 3e-42
Identities = 95/302 (31%), Positives = 149/302 (49%), Gaps = 43/302 (14%)
Query: 101 SVKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFT 160
S+ F L L P LL + E+G+ + IQ +LP +LA ++IAQ+++G+GKTAAF
Sbjct: 2 SMTAFSTLPLPPALLANLNELGYTEMTPIQAQSLPAILAG--KDVIAQAKTGSGKTAAFG 59
Query: 161 LTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERNKKI 220
L +L +++ Q L L PT ELA Q VAK +R R N K+
Sbjct: 60 LGLLQKLDVKRFRVQALVLCPTRELADQ----VAK--------EIRRLARFI---PNIKV 104
Query: 221 TE------------------QIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQ 262
II+GTPG++LD L+ DL + VLDEAD M+
Sbjct: 105 LTLCGGVPMGPQIDSLEHGAHIIVGTPGRILDH-LRKGTLDLDALNTLVLDEADRML-DM 162
Query: 263 GHQDFSIR-IQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQH 321
G QD +I I ++ P+ Q +LFSATY + + +Q +P+ +K++ L I+Q
Sbjct: 163 GFQD-AIDAIIRQAPARRQTLLFSATYPEGIAAISQRFQRDPVEVKVE-STHDLPAIEQR 220
Query: 322 YVMCKNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVE 381
+ DE+ A+ + ++FC+T+K +A+ ++ +G + L G+L E
Sbjct: 221 FYEVSP-DERLPALQRLLLHHQPESCVVFCNTKKECQEVADALNAQGFSALALHGDL--E 277
Query: 382 QR 383
QR
Sbjct: 278 QR 279
>gnl|CDD|234938 PRK01297, PRK01297, ATP-dependent RNA helicase RhlB; Provisional.
Length = 475
Score = 151 bits (382), Expect = 4e-41
Identities = 102/379 (26%), Positives = 191/379 (50%), Gaps = 27/379 (7%)
Query: 32 KQADTPSPTEDAKPAPSSPDSSAPGNKDEEDKPLSVAEKSLLQKIVRRGLIESKQELEIQ 91
A P AP++ ++ +KP +K ++ + + ++ ++
Sbjct: 24 PAAAPAPPPPAKTAAPATKAAAPAAAAPRAEKP--KKDKPRRERKPKPASLWKLEDFVVE 81
Query: 92 RKDPHSPLYSVKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQS 151
P F +L PEL+ ++++GF + IQ L LA H+ I ++Q+
Sbjct: 82 ------PQEGKTRFHDFNLAPELMHAIHDLGFPYCTPIQAQVLGYTLAG--HDAIGRAQT 133
Query: 152 GTGKTAAFTLTMLSRV--NPS-----IQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLS 204
GTGKTAAF +++++++ P + EP+ L +APT EL +QI + A + K+ T L+
Sbjct: 134 GTGKTAAFLISIINQLLQTPPPKERYMGEPRALIIAPTRELVVQIAKDAAALTKY-TGLN 192
Query: 205 VRYAVRGENLERNKKITEQ----IIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIA 260
V V G + ++ K E I++ TPG++LD+ + L ++V VLDEAD M+
Sbjct: 193 VMTFVGGMDFDKQLKQLEARFCDILVATPGRLLDFNQRGEVH-LDMVEVMVLDEADRML- 250
Query: 261 TQGHQDFSIRIQKRLP--SDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNI 318
G +I ++ P + Q +LFSAT+ +VM A+ +P I++++ E + D +
Sbjct: 251 DMGFIPQVRQIIRQTPRKEERQTLLFSATFTDDVMNLAKQWTTDPAIVEIEPENVASDTV 310
Query: 319 KQHYVMCKNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGEL 378
+QH D K++ + N+ + M+F + + + E++ K+G+N LSG++
Sbjct: 311 EQHVYAVAGSD-KYKLLYNLVTQNPWERVMVFANRKDEVRRIEERLVKDGINAAQLSGDV 369
Query: 379 TVEQRLSILDRFREGEFKI 397
+R+ L+ FREG+ ++
Sbjct: 370 PQHKRIKTLEGFREGKIRV 388
>gnl|CDD|236941 PRK11634, PRK11634, ATP-dependent RNA helicase DeaD; Provisional.
Length = 629
Score = 152 bits (385), Expect = 9e-41
Identities = 96/301 (31%), Positives = 156/301 (51%), Gaps = 16/301 (5%)
Query: 104 TFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTM 163
TF L LK +L+ + ++G+ PS IQ +P LL +++ +Q+G+GKTAAF+L +
Sbjct: 7 TFADLGLKAPILEALNDLGYEKPSPIQAECIPHLLNG--RDVLGMAQTGSGKTAAFSLPL 64
Query: 164 LSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSV-------RYAVRGENLER 216
L ++P ++ PQ+L LAPT ELA+Q+ E + KH+ ++V RY V+ L +
Sbjct: 65 LHNLDPELKAPQILVLAPTRELAVQVAEAMTDFSKHMRGVNVVALYGGQRYDVQLRALRQ 124
Query: 217 NKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLP 276
QI++GTPG++LD LK DLSK+ VLDEAD M+ +D I ++P
Sbjct: 125 GP----QIVVGTPGRLLD-HLKRGTLDLSKLSGLVLDEADEMLRMGFIEDVE-TIMAQIP 178
Query: 277 SDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKNIDEKFEAVS 336
Q LFSAT + + + + P ++++ + +I Q Y + K EA+
Sbjct: 179 EGHQTALFSATMPEAIRRITRRFMKEPQEVRIQSSVTTRPDISQSYWTVWGM-RKNEALV 237
Query: 337 NIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFK 396
A+IF T+ +AE + + G N L+G++ R L+R ++G
Sbjct: 238 RFLEAEDFDAAIIFVRTKNATLEVAEALERNGYNSAALNGDMNQALREQTLERLKDGRLD 297
Query: 397 I 397
I
Sbjct: 298 I 298
>gnl|CDD|236722 PRK10590, PRK10590, ATP-dependent RNA helicase RhlE; Provisional.
Length = 456
Score = 148 bits (375), Expect = 3e-40
Identities = 94/306 (30%), Positives = 164/306 (53%), Gaps = 21/306 (6%)
Query: 104 TFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTM 163
+F++L L P++L+ V E G+ P+ IQ+ A+P +L +++A +Q+GTGKTA FTL +
Sbjct: 2 SFDSLGLSPDILRAVAEQGYREPTPIQQQAIPAVLEG--RDLMASAQTGTGKTAGFTLPL 59
Query: 164 LSRVNPSIQEPQ------VLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLERN 217
L + + L L PT ELA QIGE V K+ L++R V + N
Sbjct: 60 LQHLITRQPHAKGRRPVRALILTPTRELAAQIGENVRDYSKY---LNIRSLVVFGGVSIN 116
Query: 218 KKITE-----QIIIGTPGKVLDWGLKY-RFFDLSKIKVFVLDEADVMIATQGHQDFSIRI 271
++ + +++ TPG++LD L++ L ++++ VLDEAD M+ D R+
Sbjct: 117 PQMMKLRGGVDVLVATPGRLLD--LEHQNAVKLDQVEILVLDEADRMLDMGFIHDIR-RV 173
Query: 272 QKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKNIDEK 331
+LP+ Q +LFSAT+ ++ A+ ++ NPL I++ R + + + QH V + K
Sbjct: 174 LAKLPAKRQNLLFSATFSDDIKALAEKLLHNPLEIEVARRNTASEQVTQH-VHFVDKKRK 232
Query: 332 FEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFR 391
E +S + G Q ++F T+ A LAE+++K+G+ + G + R L F+
Sbjct: 233 RELLSQMIGKGNWQQVLVFTRTKHGANHLAEQLNKDGIRSAAIHGNKSQGARTRALADFK 292
Query: 392 EGEFKI 397
G+ ++
Sbjct: 293 SGDIRV 298
>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 = 139 bits (352), Expect = 9e-40
Identities = 61/173 (35%), Positives = 93/173 (53%), Gaps = 8/173 (4%)
Query: 127 SKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELA 186
+ IQ A+P +L+ +++ Q+ +G+GKT AF L +L + P PQ L LAPT ELA
Sbjct: 1 TPIQAQAIPAILSG--KDVLVQAPTGSGKTLAFLLPILQALLPKKGGPQALVLAPTRELA 58
Query: 187 IQIGEVVAKMGKHITDLSVRYAVRGENLERNKKITE----QIIIGTPGKVLDWGLKYRFF 242
QI E + K+ K L V G +L+ + + I++GTPG++LD + +
Sbjct: 59 EQIYEELKKLFKI-LGLRVALLTGGTSLKEQARKLKKGKADILVGTPGRLLDLLRRGKLK 117
Query: 243 DLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEF 295
L +K+ VLDEA ++ G D I RLP D QI+L SAT + + +
Sbjct: 118 LLKNLKLLVLDEAHRLL-DMGFGDDLEEILSRLPPDRQILLLSATLPRNLEDL 169
>gnl|CDD|235307 PRK04537, PRK04537, ATP-dependent RNA helicase RhlB; Provisional.
Length = 572
Score = 140 bits (353), Expect = 1e-36
Identities = 97/315 (30%), Positives = 170/315 (53%), Gaps = 24/315 (7%)
Query: 98 PLYSVKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTA 157
PL + TF + L P LL G+ GF + IQ LP L P ++ Q+Q+GTGKT
Sbjct: 5 PLTDL-TFSSFDLHPALLAGLESAGFTRCTPIQALTLPVAL--PGGDVAGQAQTGTGKTL 61
Query: 158 AFTLTMLSR-------VNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAV- 209
AF + +++R + ++P+ L LAPT ELAIQI + K G DL +R+A+
Sbjct: 62 AFLVAVMNRLLSRPALADRKPEDPRALILAPTRELAIQIHKDAVKFG---ADLGLRFALV 118
Query: 210 -RGENLERNKKITEQ---IIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQ 265
G + ++ +++ +Q +II TPG+++D+ +++ L ++ VLDEAD M +
Sbjct: 119 YGGVDYDKQRELLQQGVDVIIATPGRLIDYVKQHKVVSLHACEICVLDEADRMFDLGFIK 178
Query: 266 DFSIR-IQKRLPSDC--QIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHY 322
D IR + +R+P Q +LFSAT V+E A + + P + ++ E + ++Q
Sbjct: 179 D--IRFLLRRMPERGTRQTLLFSATLSHRVLELAYEHMNEPEKLVVETETITAARVRQRI 236
Query: 323 VMCKNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQ 382
+ +EK + + + M+F +T+ +A + + G VG+LSG++ ++
Sbjct: 237 YFPAD-EEKQTLLLGLLSRSEGARTMVFVNTKAFVERVARTLERHGYRVGVLSGDVPQKK 295
Query: 383 RLSILDRFREGEFKI 397
R S+L+RF++G+ +I
Sbjct: 296 RESLLNRFQKGQLEI 310
>gnl|CDD|236877 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional.
Length = 434
Score = 137 bits (347), Expect = 2e-36
Identities = 90/323 (27%), Positives = 151/323 (46%), Gaps = 53/323 (16%)
Query: 103 KTFEALHLKPELLKGVYEMGFYAPSKIQETALP------TLLADPPHNMIAQSQSGTGKT 156
TF L L LL+ + + G+ P+ IQ A+P +L P +GTGKT
Sbjct: 1 TTFSELELDESLLEALQDKGYTRPTAIQAEAIPPALDGRDVLGSAP--------TGTGKT 52
Query: 157 AAFTLTMLSRVNPSIQ-----------EPQVLCLAPTYELAIQIGEVVAKMGKHITDLS- 204
AAF L P++Q P++L L PT ELA+Q+ + ++ KH T L
Sbjct: 53 AAFLL-------PALQHLLDFPRRKSGPPRILILTPTRELAMQVADQARELAKH-THLDI 104
Query: 205 ------VRYAVRGENLERNKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVM 258
V Y E N + I++ TPG++L + +K FD ++ +LDEAD M
Sbjct: 105 ATITGGVAYMNHAEVFSEN----QDIVVATPGRLLQY-IKEENFDCRAVETLILDEADRM 159
Query: 259 IATQGHQDF-SIRIQKRLPSDCQIMLFSATYDKE-VMEFAQDMVPNPLIIKLK--REEES 314
+ QD +I + R Q +LFSAT + + V +FA+ ++ +P+ ++ + R E
Sbjct: 160 LDMGFAQDIETIAAETRWRK--QTLLFSATLEGDAVQDFAERLLNDPVEVEAEPSRRERK 217
Query: 315 LDNIKQHYVMCKNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLL 374
I Q Y +++ K + ++ + ++++F TR+ LA + K G+N L
Sbjct: 218 --KIHQWYYRADDLEHKTALLCHLLKQPEVTRSIVFVRTRERVHELAGWLRKAGINCCYL 275
Query: 375 SGELTVEQRLSILDRFREGEFKI 397
GE+ +R + R +G +
Sbjct: 276 EGEMVQAKRNEAIKRLTDGRVNV 298
>gnl|CDD|214692 smart00487, DEXDc, DEAD-like helicases superfamily.
Length = 201
Score = 130 bits (329), Expect = 4e-36
Identities = 57/207 (27%), Positives = 98/207 (47%), Gaps = 9/207 (4%)
Query: 118 VYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVL 177
+ + GF Q+ A+ LL+ ++I + +G+GKT A L L + + +VL
Sbjct: 1 IEKFGFEPLRPYQKEAIEALLSGL-RDVILAAPTGSGKTLAALLPALEALKRG-KGGRVL 58
Query: 178 CLAPTYELAIQIGEVVAKMGKHITDLSVRY---AVRGENLERNKKITEQIIIGTPGKVLD 234
L PT ELA Q E + K+G + V + E L + + I++ TPG++LD
Sbjct: 59 VLVPTRELAEQWAEELKKLGPSLGLKVVGLYGGDSKREQLRKLESGKTDILVTTPGRLLD 118
Query: 235 WGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVME 294
LS + + +LDEA ++ G D ++ K LP + Q++L SAT +E+
Sbjct: 119 LLEN-DKLSLSNVDLVILDEAHRLLD-GGFGDQLEKLLKLLPKNVQLLLLSATPPEEIEN 176
Query: 295 FAQDMVPNPLIIKLKREEESLDNIKQH 321
+ + +P+ I L+ I+Q
Sbjct: 177 LLELFLNDPVFI--DVGFTPLEPIEQF 201
>gnl|CDD|235314 PRK04837, PRK04837, ATP-dependent RNA helicase RhlB; Provisional.
Length = 423
Score = 135 bits (342), Expect = 8e-36
Identities = 101/313 (32%), Positives = 164/313 (52%), Gaps = 30/313 (9%)
Query: 103 KTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLT 162
+ F L P++++ + + GF+ + IQ ALP LA ++ Q+Q+GTGKT AF LT
Sbjct: 8 QKFSDFALHPQVVEALEKKGFHNCTPIQALALPLTLAG--RDVAGQAQTGTGKTMAF-LT 64
Query: 163 -----MLSRVNP---SIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENL 214
+LS P + +P+ L +APT ELA+QI + + T L + A G+
Sbjct: 65 ATFHYLLSHPAPEDRKVNQPRALIMAPTRELAVQIHADAEPLAQA-TGLKLGLAYGGDGY 123
Query: 215 ERNKKITEQ---IIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIR- 270
++ K+ E I+IGT G+++D+ K +L I+V VLDEAD M +D IR
Sbjct: 124 DKQLKVLESGVDILIGTTGRLIDY-AKQNHINLGAIQVVVLDEADRMFDLGFIKD--IRW 180
Query: 271 IQKRLPSDCQ--IMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKNI 328
+ +R+P Q MLFSAT V E A + + NP ++++ E+++ IK+ N
Sbjct: 181 LFRRMPPANQRLNMLFSATLSYRVRELAFEHMNNPEYVEVEPEQKTGHRIKEELFYPSN- 239
Query: 329 DEKFEAVSNIYGVVTIGQAMIFCHTR----KTAAWLAEKMSKEGLNVGLLSGELTVEQRL 384
+EK + + +A+IF +T+ + LA +G VGLL+G++ ++RL
Sbjct: 240 EEKMRLLQTLIEEEWPDRAIIFANTKHRCEEIWGHLA----ADGHRVGLLTGDVAQKKRL 295
Query: 385 SILDRFREGEFKI 397
IL+ F G+ I
Sbjct: 296 RILEEFTRGDLDI 308
>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 = 117 bits (294), Expect = 1e-31
Identities = 48/148 (32%), Positives = 81/148 (54%), Gaps = 8/148 (5%)
Query: 143 HNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITD 202
+++ + +G+GKT A L +L ++ + QVL LAPT ELA Q+ E + ++
Sbjct: 1 RDVLLAAPTGSGKTLAALLPILELLDSL-KGGQVLVLAPTRELANQVAERLKELFGE--G 57
Query: 203 LSVRYAVRGEN---LERNKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMI 259
+ V Y + G + E+ I++GTPG++LD L+ L K+ + +LDEA ++
Sbjct: 58 IKVGYLIGGTSIKQQEKLLSGKTDIVVGTPGRLLD-ELERLKLSLKKLDLLILDEAHRLL 116
Query: 260 ATQGHQDFSIRIQKRLPSDCQIMLFSAT 287
QG ++I +LP D Q++L SAT
Sbjct: 117 N-QGFGLLGLKILLKLPKDRQVLLLSAT 143
Score = 30.8 bits (70), Expect = 0.64
Identities = 14/48 (29%), Positives = 27/48 (56%), Gaps = 3/48 (6%)
Query: 345 GQAMIFCHTRKTAAWLAEKMSKE---GLNVGLLSGELTVEQRLSILDR 389
GQ ++ TR+ A +AE++ + G+ VG L G +++Q+ +L
Sbjct: 31 GQVLVLAPTRELANQVAERLKELFGEGIKVGYLIGGTSIKQQEKLLSG 78
>gnl|CDD|215103 PLN00206, PLN00206, DEAD-box ATP-dependent RNA helicase;
Provisional.
Length = 518
Score = 114 bits (286), Expect = 1e-27
Identities = 99/356 (27%), Positives = 175/356 (49%), Gaps = 43/356 (12%)
Query: 58 KDEEDK-PLSVAEKSLLQKIVRRGLIESKQELEIQRKDPHSPLYSVKTFEALHLKPELLK 116
+D LS ++ LL RR L E+ ++ + P+ S F + L P+LL
Sbjct: 87 RDPGSTSGLSSSQAELL----RRKL-----EIHVKGEAVPPPILS---FSSCGLPPKLLL 134
Query: 117 GVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRV------NPS 170
+ G+ P+ IQ A+P L+ +++ + +G+GKTA+F + ++SR +PS
Sbjct: 135 NLETAGYEFPTPIQMQAIPAALSG--RSLLVSADTGSGKTASFLVPIISRCCTIRSGHPS 192
Query: 171 IQE-PQVLCLAPTYELAIQIGEVVAKMGKHI---TDLSVRYAVRGENLERNKKITEQIII 226
Q P + L PT EL +Q+ + +GK + T L V + L R ++ E +I+
Sbjct: 193 EQRNPLAMVLTPTRELCVQVEDQAKVLGKGLPFKTALVVGGDAMPQQLYRIQQGVE-LIV 251
Query: 227 GTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFSA 286
GTPG+++D K+ +L + V VLDE D M+ +G +D ++I + L Q++LFSA
Sbjct: 252 GTPGRLIDLLSKHDI-ELDNVSVLVLDEVDCML-ERGFRDQVMQIFQALSQP-QVLLFSA 308
Query: 287 TYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQH--YVMCKNIDEKFEAVSNIYGVVTI 344
T EV +FA + + ++I + +KQ +V K +K ++ ++
Sbjct: 309 TVSPEVEKFASSLAKDIILISIGNPNRPNKAVKQLAIWVETKQKKQK------LFDILKS 362
Query: 345 GQ-----AMIFCHTRKTAAWLAEKMSK-EGLNVGLLSGELTVEQRLSILDRFREGE 394
Q A++F +R A LA ++ GL + GE ++++R ++ F GE
Sbjct: 363 KQHFKPPAVVFVSSRLGADLLANAITVVTGLKALSIHGEKSMKERREVMKSFLVGE 418
>gnl|CDD|240273 PTZ00110, PTZ00110, helicase; Provisional.
Length = 545
Score = 109 bits (274), Expect = 5e-26
Identities = 95/322 (29%), Positives = 152/322 (47%), Gaps = 46/322 (14%)
Query: 102 VKTFEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKTAAFTL 161
V +FE +LK + GF P+ IQ P L+ +MI +++G+GKT AF L
Sbjct: 129 VVSFEYTSFPDYILKSLKNAGFTEPTPIQVQGWPIALSG--RDMIGIAETGSGKTLAFLL 186
Query: 162 TMLSRVN--PSIQE---PQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRGENLER 216
+ +N P ++ P VL LAPT ELA QI E K G +R V + +
Sbjct: 187 PAIVHINAQPLLRYGDGPIVLVLAPTRELAEQIREQCNKFG---ASSKIRNTVAYGGVPK 243
Query: 217 NKKITE-----QIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRI 271
+I +I+I PG+++D+ L+ +L ++ VLDEAD M+ F +I
Sbjct: 244 RGQIYALRRGVEILIACPGRLIDF-LESNVTNLRRVTYLVLDEADRML----DMGFEPQI 298
Query: 272 QK---RLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEE------SLD-----N 317
+K ++ D Q +++SAT+ KEV A+D L +EE SLD N
Sbjct: 299 RKIVSQIRPDRQTLMWSATWPKEVQSLARD---------LCKEEPVHVNVGSLDLTACHN 349
Query: 318 IKQHYVMCKNIDEKFEAVSNIYGVVTI--GQAMIFCHTRKTAAWLAEKMSKEGLNVGLLS 375
IKQ V EK + + + + +IF T+K A +L +++ +G +
Sbjct: 350 IKQ-EVFVVEEHEKRGKLKMLLQRIMRDGDKILIFVETKKGADFLTKELRLDGWPALCIH 408
Query: 376 GELTVEQRLSILDRFREGEFKI 397
G+ E+R +L+ F+ G+ I
Sbjct: 409 GDKKQEERTWVLNEFKTGKSPI 430
>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 = 65.0 bits (159), Expect = 6e-13
Identities = 29/83 (34%), Positives = 46/83 (55%), Gaps = 4/83 (4%)
Query: 317 NIKQHYVMCKNIDEKFEAVSNIY--GVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLL 374
IKQ+ + + DEK EA+ + + G+ +IFC ++K LAE + K G+ V L
Sbjct: 1 PIKQYVLPVE--DEKLEALLELLKEHLKKGGKVLIFCPSKKMLDELAELLRKPGIKVAAL 58
Query: 375 SGELTVEQRLSILDRFREGEFKI 397
G+ + E+R +L FREGE +
Sbjct: 59 HGDGSQEEREEVLKDFREGEIVV 81
>gnl|CDD|223588 COG0514, RecQ, Superfamily II DNA helicase [DNA replication,
recombination, and repair].
Length = 590
Score = 48.8 bits (117), Expect = 3e-06
Identities = 38/174 (21%), Positives = 71/174 (40%), Gaps = 28/174 (16%)
Query: 240 RFFD-LSKIKV--FVLDEADVMIATQGHQDFS------IRIQKRLPSDCQIMLFSATYDK 290
RF + L ++ + +DEA I+ GH DF R++ LP + ++ +AT
Sbjct: 122 RFLELLKRLPISLVAIDEAHC-ISQWGH-DFRPDYRRLGRLRAGLP-NPPVLALTATATP 178
Query: 291 EVMEFAQDMV-------PNPLIIKLKREEESLDNIKQHYVMCKNIDEKFEAVSNIYGVVT 343
V D+ N R +L +++ ++ ++ + ++
Sbjct: 179 RV---RDDIREQLGLQDANIFRGSFDRPNLALKVVEKGEPS-----DQLAFLATVLPQLS 230
Query: 344 IGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKI 397
+I+C TRK LAE + K G++ G L+ E+R + F E K+
Sbjct: 231 -KSGIIYCLTRKKVEELAEWLRKNGISAGAYHAGLSNEERERVQQAFLNDEIKV 283
>gnl|CDD|197757 smart00490, HELICc, helicase superfamily c-terminal domain.
Length = 82
Score = 42.6 bits (101), Expect = 1e-05
Identities = 16/39 (41%), Positives = 24/39 (61%)
Query: 359 WLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKI 397
LAE + + G+ V L G L+ E+R ILD+F G+ K+
Sbjct: 2 ELAELLKELGIKVARLHGGLSQEEREEILDKFNNGKIKV 40
>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 = 39.0 bits (92), Expect = 3e-04
Identities = 14/36 (38%), Positives = 22/36 (61%)
Query: 362 EKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKI 397
+ + K G+ V L G L+ E+R IL+ FR G+ K+
Sbjct: 1 KLLRKPGIKVARLHGGLSQEEREEILEDFRNGKSKV 36
>gnl|CDD|224125 COG1204, COG1204, Superfamily II helicase [General function
prediction only].
Length = 766
Score = 41.6 bits (98), Expect = 6e-04
Identities = 56/262 (21%), Positives = 91/262 (34%), Gaps = 66/262 (25%)
Query: 144 NMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDL 203
N++ + +G+GKT L +LS + +V+ + P LA E + + + +L
Sbjct: 49 NVLISAPTGSGKTLIALLAILSTLLEG--GGKVVYIVPLKALA---EEKYEEFSR-LEEL 102
Query: 204 SVRYAV-------RGENLERNKKITEQIIIGTPGKVLDWGLKYRFFD--LSKIKVFVLDE 254
+R + E L R +I+ TP K LD R + ++ + V+DE
Sbjct: 103 GIRVGISTGDYDLDDERLARY-----DVIVTTPEK-LDSLT--RKRPSWIEEVDLVVIDE 154
Query: 255 ADVMIATQGHQ-DFSIR------IQKRLP---SDCQIMLFSATYDKEVMEFAQDMVPNPL 304
H R I R+ +I+ SAT E A D + L
Sbjct: 155 I--------HLLGDRTRGPVLESIVARMRRLNELIRIVGLSATL-PNAEEVA-DWLNAKL 204
Query: 305 IIKLKREEESLDNIKQHYVMCK----NIDEKFEAVSNIYGVVTI----------GQAMIF 350
+ R V D K + + + + GQ ++F
Sbjct: 205 VESDWRPVPLR-----RGVPYVGAFLGADGKKKTWPLLIDNLALELVLESLAEGGQVLVF 259
Query: 351 CHTRK----TAAWLAEKMSKEG 368
H+RK TA L KMS
Sbjct: 260 VHSRKEAEKTAKKLRIKMSATL 281
>gnl|CDD|224123 COG1202, COG1202, Superfamily II helicase, archaea-specific
[General function prediction only].
Length = 830
Score = 38.2 bits (89), Expect = 0.008
Identities = 40/169 (23%), Positives = 64/169 (37%), Gaps = 30/169 (17%)
Query: 243 DLSKIKVFVLDEADVMIA--TQGHQ-DFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDM 299
DL I V+DE + +G + D I + L Q + SAT
Sbjct: 335 DLGDIGTVVIDEIH-TLEDEERGPRLDGLIGRLRYLFPGAQFIYLSAT------------ 381
Query: 300 VPNP------LIIKLKREEESLDNIKQHYVMCKNIDEKF--------EAVSNIYGVVTIG 345
V NP L KL +E +++H V +N EK+ S G
Sbjct: 382 VGNPEELAKKLGAKLVLYDERPVPLERHLVFARNESEKWDIIARLVKREFSTESSKGYRG 441
Query: 346 QAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGE 394
Q ++F ++R+ LA+ ++ +GL L ++R S+ F E
Sbjct: 442 QTIVFTYSRRRCHELADALTGKGLKAAPYHAGLPYKERKSVERAFAAQE 490
>gnl|CDD|233069 TIGR00643, recG, ATP-dependent DNA helicase RecG. [DNA metabolism,
DNA replication, recombination, and repair].
Length = 630
Score = 37.7 bits (88), Expect = 0.011
Identities = 73/336 (21%), Positives = 120/336 (35%), Gaps = 88/336 (26%)
Query: 108 LHLKPELLKGVYEMGFYAPSKIQETALPTLLAD----PPHNMIAQSQSGTGKTAAFTLTM 163
+ ELL + ++ Q+ + +L D P N + Q G+GKT L M
Sbjct: 218 ANPSEELLTKFLASLPFKLTRAQKRVVKEILQDLKSDVPMNRLLQGDVGSGKTLVAALAM 277
Query: 164 LSRVNPSIQEPQVLCLAPTYELAIQ----IGEVVAKMGKHITDL--SVRYAVRGENLERN 217
L+ + QV +APT LA Q + ++A +G + L S++ R E LE
Sbjct: 278 LAAIE---AGYQVALMAPTEILAEQHYNSLRNLLAPLGIEVALLTGSLKGKRRKELLETI 334
Query: 218 KKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEAD--------------------- 256
+++GT + + K F L+ + ++DE
Sbjct: 335 ASGQIHLVVGTHALIQE---KVEFKRLALV---IIDEQHRFGVEQRKKLREKGQGGFTPH 388
Query: 257 --VMIAT--------QGHQDFSIRIQKRLPSDCQIM---LFSATYDKEVMEFAQDMVPNP 303
VM AT + D I LP + + L V EF
Sbjct: 389 VLVMSATPIPRTLALTVYGDLDTSIIDELPPGRKPITTVLIKHDEKDIVYEFI------- 441
Query: 304 LIIKLKREEESLDNIKQHYVMCKNID--EKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLA 361
EE + +Q YV+ I+ EK + + A +
Sbjct: 442 --------EEEIAKGRQAYVVYPLIEESEKLDLKAAE------------------ALYER 475
Query: 362 EKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKI 397
K + NVGLL G + +++ ++++ FREGE I
Sbjct: 476 LKKAFPKYNVGLLHGRMKSDEKEAVMEEFREGEVDI 511
>gnl|CDD|223989 COG1061, SSL2, DNA or RNA helicases of superfamily II
[Transcription / DNA replication, recombination, and
repair].
Length = 442
Score = 37.4 bits (87), Expect = 0.012
Identities = 21/74 (28%), Positives = 35/74 (47%), Gaps = 2/74 (2%)
Query: 325 CKNIDEKFEAVSNIYGVVTIG-QAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQR 383
+ K AV + G + +IF + A +A+ G+ V ++GE E+R
Sbjct: 263 AIASERKIAAVRGLLLKHARGDKTLIFASDVEHAYEIAKLFLAPGI-VEAITGETPKEER 321
Query: 384 LSILDRFREGEFKI 397
+IL+RFR G K+
Sbjct: 322 EAILERFRTGGIKV 335
>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 = 37.4 bits (87), Expect = 0.013
Identities = 48/191 (25%), Positives = 84/191 (43%), Gaps = 34/191 (17%)
Query: 130 QETALPTLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEP--QVLCLAPTYELAI 187
Q AL + N++ + +G+GKT +F L +L + +++P + L L PT LA
Sbjct: 75 QVDALRLIREG--RNVVVTTGTGSGKTESFLLPILDHL---LRDPSARALLLYPTNALAN 129
Query: 188 ----QIGEVVAKMGKHITDLSVRY--AVRGENLERNKKITEQ--IIIGTPGKVLDWGL-- 237
++ E+++ + +T RY E ER I I++ P +L + L
Sbjct: 130 DQAERLRELISDLPGKVT--FGRYTGDTPPE--ERRAIIRNPPDILLTNP-DMLHYLLLR 184
Query: 238 ---KYRFFDLSKIKVFVLDEADVMIATQGHQDFSI------RIQKRLPSDCQIMLFSATY 288
+ + L +K V+DE QG + ++ R +R S QI+ SAT
Sbjct: 185 NHDAWLWL-LRNLKYLVVDELHTYRGVQG-SEVALLLRRLLRRLRRYGSPLQIICTSATL 242
Query: 289 DKEVMEFAQDM 299
EFA+++
Sbjct: 243 -ANPGEFAEEL 252
>gnl|CDD|224122 COG1201, Lhr, Lhr-like helicases [General function prediction
only].
Length = 814
Score = 36.5 bits (85), Expect = 0.028
Identities = 74/319 (23%), Positives = 133/319 (41%), Gaps = 42/319 (13%)
Query: 105 FEALHLKPELLKGVYEMGFYAPSKIQETALPTLLADPPHNMIAQSQSGTGKT-AAF--TL 161
F L P + + F + + Q A+P + + N++ + +G+GKT AAF +
Sbjct: 5 FNILD--PRVREWFKR-KFTSLTPPQRYAIPEIHSG--ENVLIIAPTGSGKTEAAFLPVI 59
Query: 162 TMLSRVNPSIQEPQVLCL--APTYELAIQIGEVVAKMGKHITDLSVRYAVR-GE--NLER 216
L + E + L +P L I + + + + + V AVR G+ E+
Sbjct: 60 NELLSLGKGKLEDGIYALYISPLKALNNDIRRRLEEPLREL-GIEV--AVRHGDTPQSEK 116
Query: 217 NKKITE--QIIIGTP---GKVLDWGLKYRFFDLSKIKVFVLDEA-DVMIATQGHQDFSIR 270
K + I+I TP +L+ L ++ ++DE + + +G Q ++
Sbjct: 117 QKMLKNPPHILITTPESLAILLNSPKFREL--LRDVRYVIVDEIHALAESKRGVQ-LALS 173
Query: 271 IQ--KRLPSDCQIMLFSATYDKEVMEFAQDMVP--NPLIIKLKREEESLDNIKQHYVMCK 326
++ + L D Q + SAT E A+ +V +P I + L+ IK V+
Sbjct: 174 LERLRELAGDFQRIGLSATV-GPPEEVAKFLVGFGDPCEIVDVSAAKKLE-IK---VISP 228
Query: 327 NIDEKFEAVSNIYGVVTIGQ-------AMIFCHTRKTAAWLAEKMSKEG-LNVGLLSGEL 378
D ++ I + +IF +TR A LA ++ K G + + G L
Sbjct: 229 VEDLIYDEELWAALYERIAELVKKHRTTLIFTNTRSGAERLAFRLKKLGPDIIEVHHGSL 288
Query: 379 TVEQRLSILDRFREGEFKI 397
+ E RL + +R +EGE K
Sbjct: 289 SRELRLEVEERLKEGELKA 307
>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 = 35.8 bits (83), Expect = 0.040
Identities = 40/180 (22%), Positives = 66/180 (36%), Gaps = 31/180 (17%)
Query: 232 VLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFS------IRIQKRLPSDCQIMLFS 285
D+ L I + +DEA ++ GH DF + +R P + +
Sbjct: 115 EQDYFL--NMLQRIPIALVAVDEAHC-VSQWGH-DFRPEYQRLGSLAERFPQV-PRIALT 169
Query: 286 ATYDKEVMEFAQDMV-------PNPLIIKLKREEESLDNIKQHYVMCKNIDEKFEAVSNI 338
AT D E QD+ N I R V+ KN +KF
Sbjct: 170 ATADAET---RQDIRELLRLADANEFITSFDRPNLRFS------VVKKNNKQKFLLD--- 217
Query: 339 YGVVTIGQA-MIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKI 397
Y GQ+ +I+ +RK LAE++ +G++ L+ + R + F + K+
Sbjct: 218 YLKKHRGQSGIIYASSRKKVEELAERLESQGISALAYHAGLSNKVRAENQEDFLYDDVKV 277
>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 = 33.9 bits (78), Expect = 0.14
Identities = 35/182 (19%), Positives = 60/182 (32%), Gaps = 38/182 (20%)
Query: 223 QIIIGTPGKVL---DWGLKYRFFDLSKI--KVFVLDEADVMIA-TQGHQDFSIRIQKRLP 276
I + T +VL + F L+ I + + DE T + + K
Sbjct: 95 PITVCTIDQVLKSVFGEFGHYEFTLASIANSLLIFDEVHFYDEYTLALILAVLEVLKDN- 153
Query: 277 SDCQIMLFSATYDKEVMEFAQDM-------VPNPLIIKL----KREEESLDNIKQHYVMC 325
D I+L SAT K + E+A+ + + + K E + + I +
Sbjct: 154 -DVPILLMSATLPKFLKEYAEKIGYVEENEPLDLKPNERAPFIKIESDKVGEISSLERLL 212
Query: 326 KNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTA----AWLAEKMSKEGLNVGLLSGELTVE 381
+ I + G I +T A L EK +E + L+ T +
Sbjct: 213 EFIKKG-------------GSVAIIVNTVDRAQEFYQQLKEKGPEE--EIMLIHSRFTEK 257
Query: 382 QR 383
R
Sbjct: 258 DR 259
>gnl|CDD|178207 PLN02597, PLN02597, phosphoenolpyruvate carboxykinase [ATP].
Length = 555
Score = 34.0 bits (78), Expect = 0.15
Identities = 20/47 (42%), Positives = 24/47 (51%), Gaps = 5/47 (10%)
Query: 345 GQAMIFCHTRKTAAWLAEKMSKEG-----LNVGLLSGELTVEQRLSI 386
G A I H K AA LAEKM K G +N G G V +R+S+
Sbjct: 415 GAAFIMLHPTKYAAMLAEKMQKHGATAWLVNTGWSGGSYGVGKRMSL 461
>gnl|CDD|233483 TIGR01587, cas3_core, CRISPR-associated helicase Cas3. This model
represents the highly conserved core region of an
alignment of Cas3, a protein found in association with
CRISPR repeat elements in a broad range of bacteria and
archaea. Cas3 appears to be a helicase, with regions
found by pfam00270 (DEAD/DEAH box helicase) and
pfam00271 (Helicase conserved C-terminal domain). Some
but not all members have an N-terminal HD domain region
(pfam01966) that is not included within this model
[Mobile and extrachromosomal element functions, Other].
Length = 358
Score = 33.6 bits (77), Expect = 0.16
Identities = 39/189 (20%), Positives = 69/189 (36%), Gaps = 23/189 (12%)
Query: 223 QIIIGTPGKVL---DWGLKYRFFDLSKI--KVFVLDEADVMIA-TQGHQDFSIRIQKRLP 276
I + T +VL + F L+ I + + DE T + + K
Sbjct: 96 PITVCTIDQVLKSVFGEFGHYEFTLASIANSLLIFDEVHFYDEYTLALILAVLEVLKDN- 154
Query: 277 SDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKNIDEKFEAVS 336
D I+L SAT K + E+A+ + L +EE ++H + D+ E S
Sbjct: 155 -DVPILLMSATLPKFLKEYAEKIGYVEFNEPLDLKEE--RRFERHRFIKIESDKVGEISS 211
Query: 337 ---NIYGVVTIGQAMIFCHTRKTA----AWLAEKMSKEGLNVGLLSGELT----VEQRLS 385
+ + G+ I +T A L E +E + LL T ++
Sbjct: 212 LERLLEFIKKGGKIAIIVNTVDRAQEFYQQLKENAPEE--EIMLLHSRFTEKDRAKKEAE 269
Query: 386 ILDRFREGE 394
+L+ ++ E
Sbjct: 270 LLEEMKKNE 278
>gnl|CDD|182933 PRK11057, PRK11057, ATP-dependent DNA helicase RecQ; Provisional.
Length = 607
Score = 32.4 bits (74), Expect = 0.45
Identities = 39/162 (24%), Positives = 66/162 (40%), Gaps = 35/162 (21%)
Query: 253 DEADVMIATQGHQDFSI------RIQKRLPSDCQIMLFSATYDKEVMEFAQDMV-----P 301
DEA I+ GH DF ++++R P M +AT D QD+V
Sbjct: 146 DEAHC-ISQWGH-DFRPEYAALGQLRQRFP-TLPFMALTATADDTTR---QDIVRLLGLN 199
Query: 302 NPLIIKLKREEESLD--NIKQHYVMCKNIDEKFEAVSNIYGVVTIGQ----AMIFCHTRK 355
+PLI + S D NI+ V EKF+ + + V Q +I+C++R
Sbjct: 200 DPLI-----QISSFDRPNIRYTLV------EKFKPLDQLMRYVQ-EQRGKSGIIYCNSRA 247
Query: 356 TAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKI 397
A ++ G++ L + R + + F+ + +I
Sbjct: 248 KVEDTAARLQSRGISAAAYHAGLDNDVRADVQEAFQRDDLQI 289
>gnl|CDD|224124 COG1203, COG1203, CRISPR-associated helicase Cas3 [Defense
mechanisms].
Length = 733
Score = 32.4 bits (74), Expect = 0.47
Identities = 24/157 (15%), Positives = 54/157 (34%), Gaps = 22/157 (14%)
Query: 249 VFVLDEADVM---------IATQGHQDFSIRIQKRLPSDCQIMLFSATYDKEVMEFAQDM 299
+ +LDE + +A + ++L SAT + E +
Sbjct: 341 LVILDEVHLYADETMLAALLAL-------LEALAEA--GVPVLLMSATLPPFLKEKLKKA 391
Query: 300 VPNPLII----KLKREEESLDNIKQHYVMCKNIDEKFEAVSNIYGVVTIGQAMIFCHTRK 355
+ + K +E+ ++ V ++ ++ V + ++ +T
Sbjct: 392 LGKGREVVENAKFCPKEDEPGLKRKERVDVEDGPQEELIELISEEVKEGKKVLVIVNTVD 451
Query: 356 TAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFRE 392
A L EK+ ++G V LL T++ R ++
Sbjct: 452 RAIELYEKLKEKGPKVLLLHSRFTLKDREEKERELKK 488
>gnl|CDD|236794 PRK10917, PRK10917, ATP-dependent DNA helicase RecG; Provisional.
Length = 681
Score = 32.4 bits (75), Expect = 0.47
Identities = 12/45 (26%), Positives = 24/45 (53%), Gaps = 2/45 (4%)
Query: 355 KTAAWLAEKMSKE--GLNVGLLSGELTVEQRLSILDRFREGEFKI 397
++A E++ + L VGLL G + ++ +++ F+ GE I
Sbjct: 490 QSAEETYEELQEAFPELRVGLLHGRMKPAEKDAVMAAFKAGEIDI 534
Score = 30.9 bits (71), Expect = 1.3
Identities = 14/46 (30%), Positives = 19/46 (41%), Gaps = 4/46 (8%)
Query: 352 HTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKI 397
H L G+ V LL+G L ++R IL+ GE I
Sbjct: 326 HYENLKKLLE----PLGIRVALLTGSLKGKERREILEAIASGEADI 367
>gnl|CDD|224557 COG1643, HrpA, HrpA-like helicases [DNA replication, recombination,
and repair].
Length = 845
Score = 32.3 bits (74), Expect = 0.48
Identities = 56/270 (20%), Positives = 105/270 (38%), Gaps = 52/270 (19%)
Query: 152 GTGKTAAFTLTMLS--RVNPSIQEPQVLCLAPTYELAIQIGEVVAK-MGKHITDLSVRYA 208
G+GKT +L ++ C P A + E VA+ +G+ + + V Y+
Sbjct: 75 GSGKTTQLPQFLLEEGLGIAG----KIGCTQPRRLAARSVAERVAEELGEKLGET-VGYS 129
Query: 209 VRGENLERNKKITEQIIIGTPGKVLDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQ--- 265
+R E+ + +I + T G +L LS V ++DEA H+
Sbjct: 130 IRFESKVSPR---TRIKVMTDGILLREIQNDPL--LSGYSVVIIDEA--------HERSL 176
Query: 266 --DFSI----RIQKRLPSDCQIMLFSATYDKEVMEFAQDMVPNPLIIKL-KR-------- 310
D + + R D ++++ SAT D E F+ N +I++ R
Sbjct: 177 NTDILLGLLKDLLARRRDDLKLIIMSATLDAE--RFSA-YFGNAPVIEIEGRTYPVEIRY 233
Query: 311 EEESLDNIKQHYVMCKNIDEKFEAVSNIYGVVTI---GQAMIFCHTRKTAAWLAEKMSKE 367
E+ + + +D + G + + GQ I +TA WL + +
Sbjct: 234 LPEAEADYILLDAIVAAVD---IHLREGSGSILVFLPGQREI----ERTAEWLEKAELGD 286
Query: 368 GLNVGLLSGELTVEQRLSILDRFREGEFKI 397
L + L G L+ E+++ + + G+ K+
Sbjct: 287 DLEILPLYGALSAEEQVRVFEPAPGGKRKV 316
>gnl|CDD|224121 COG1200, RecG, RecG-like helicase [DNA replication, recombination,
and repair / Transcription].
Length = 677
Score = 31.8 bits (73), Expect = 0.74
Identities = 15/46 (32%), Positives = 20/46 (43%), Gaps = 4/46 (8%)
Query: 352 HTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGEFKI 397
H WL G+ V LL+G L + R IL++ GE I
Sbjct: 327 HYESLRKWLE----PLGIRVALLTGSLKGKARKEILEQLASGEIDI 368
Score = 31.0 bits (71), Expect = 1.3
Identities = 13/45 (28%), Positives = 25/45 (55%), Gaps = 2/45 (4%)
Query: 355 KTAAWLAEKMSK--EGLNVGLLSGELTVEQRLSILDRFREGEFKI 397
+ A L E++ L VGL+ G + ++ ++++ F+EGE I
Sbjct: 492 QAAEELYEELKSFLPELKVGLVHGRMKPAEKDAVMEAFKEGEIDI 536
Score = 28.3 bits (64), Expect = 8.0
Identities = 24/83 (28%), Positives = 38/83 (45%), Gaps = 9/83 (10%)
Query: 152 GTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQ----IGEVVAKMGKHITDL--SV 205
G+GKT L ML+ + Q +APT LA Q + + + +G + L S+
Sbjct: 293 GSGKTVVALLAMLAAIE---AGYQAALMAPTEILAEQHYESLRKWLEPLGIRVALLTGSL 349
Query: 206 RYAVRGENLERNKKITEQIIIGT 228
+ R E LE+ I++GT
Sbjct: 350 KGKARKEILEQLASGEIDIVVGT 372
>gnl|CDD|131210 TIGR02155, PA_CoA_ligase, phenylacetate-CoA ligase.
Phenylacetate-CoA ligase (PA-CoA ligase) catalyzes the
first step in aromatic catabolism of phenylacetic acid
(PA) into phenylacetyl-CoA (PA-CoA). Often located in a
conserved gene cluster with enzymes involved in
phenylacetic acid activation (paaG/H/I/J),
phenylacetate-CoA ligase has been found among the
proteobacteria as well as in gram positive prokaryotes.
In the B-subclass proteobacterium Azoarcus evansii,
phenylacetate-CoA ligase has been shown to be induced
under aerobic and anaerobic growth conditions. It
remains unclear however, whether this induction is due
to the same enzyme or to another isoenzyme restricted to
specific anaerobic growth conditions [Energy metabolism,
Other].
Length = 422
Score = 30.9 bits (70), Expect = 1.0
Identities = 9/39 (23%), Positives = 20/39 (51%), Gaps = 2/39 (5%)
Query: 173 EPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRG 211
+P ++ + P+Y L + E + +MG S++ + G
Sbjct: 167 KPDIIMVTPSYMLN--LLEELKRMGIDPAQTSLQVGIFG 203
>gnl|CDD|233660 TIGR01970, DEAH_box_HrpB, ATP-dependent helicase HrpB. This model
represents HrpB, one of two related but uncharacterized
DEAH-box ATP-dependent helicases in many Proteobacteria,
but also in a few species of other lineages. The member
from Rhizobium meliloti has been designated HelO. HrpB
is typically about 800 residues in length, while its
paralog HrpA (TIGR01967), also uncharacterized, is about
1300 amino acids long. Related characterized eukarotic
proteins are RNA helicases associated with pre-mRNA
processing [Unknown function, Enzymes of unknown
specificity].
Length = 819
Score = 31.3 bits (71), Expect = 1.1
Identities = 69/293 (23%), Positives = 113/293 (38%), Gaps = 76/293 (25%)
Query: 131 ETALPTLLA--DPPHNMIAQSQSGTGKTAAFTLTMLSR--VNPSI--QEPQVLCL-APTY 183
LP L ++ ++ G GK+ A L +L + I EP+ L +
Sbjct: 4 HAVLPALRDALAAHPQVVLEAPPGAGKSTAVPLALLDAPGIGGKIIMLEPRRLAARSAAQ 63
Query: 184 ELAIQIGEVVAKMGKHITDLSVRYAVRGEN-LERNKKI---TEQI----IIGTPGKVLDW 235
LA Q+GE V + +V Y VRGEN + R ++ TE I I P
Sbjct: 64 RLASQLGEAVGQ--------TVGYRVRGENKVSRRTRLEVVTEGILTRMIQDDPE----- 110
Query: 236 GLKYRFFDLSKIKVFVLDE-------ADVMIATQGHQDFSIRIQKRLPSDCQIMLFSATY 288
L + + DE AD+ +A ++ +Q L D +I+ SAT
Sbjct: 111 --------LDGVGALIFDEFHERSLDADLGLA------LALDVQSSLREDLKILAMSATL 156
Query: 289 DKE----------VMEFAQDMVPNPLIIKLKREEESLDNIKQHYVMCKNIDEKFEAVSNI 338
D E V+E P + R ++ L++ V A+++
Sbjct: 157 DGERLSSLLPDAPVVESEGRSFPVEIRYLPLRGDQRLEDAVSRAVE--------HALASE 208
Query: 339 YGVVTI---GQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVE-QRLSIL 387
G + + GQA I R+ LAE++ + + + L GEL++ Q +I
Sbjct: 209 TGSILVFLPGQAEI----RRVQEQLAERLDSD-VLICPLYGELSLAAQDRAIK 256
>gnl|CDD|224036 COG1111, MPH1, ERCC4-like helicases [DNA replication,
recombination, and repair].
Length = 542
Score = 31.2 bits (71), Expect = 1.2
Identities = 12/60 (20%), Positives = 28/60 (46%), Gaps = 9/60 (15%)
Query: 347 AMIFCHTRKTAAWLAEKMSKEGLNVGLL---------SGELTVEQRLSILDRFREGEFKI 397
++F R TA + + K G+ + ++ +++ I+D+FR+GE+ +
Sbjct: 369 VIVFTEYRDTAEEIVNFLKKIGIKARVRFIGQASREGDKGMSQKEQKEIIDQFRKGEYNV 428
>gnl|CDD|184207 PRK13648, cbiO, cobalt transporter ATP-binding subunit;
Provisional.
Length = 269
Score = 30.1 bits (68), Expect = 1.6
Identities = 17/55 (30%), Positives = 29/55 (52%), Gaps = 2/55 (3%)
Query: 249 VFVLDEADVMIATQGHQDFSIRIQKRLPSDCQIMLFSATYD-KEVMEFAQDMVPN 302
V +LDEA M+ Q+ + + +++ S+ I + S T+D E ME +V N
Sbjct: 163 VIILDEATSMLDPDARQNL-LDLVRKVKSEHNITIISITHDLSEAMEADHVIVMN 216
>gnl|CDD|224035 COG1110, COG1110, Reverse gyrase [DNA replication, recombination,
and repair].
Length = 1187
Score = 30.8 bits (70), Expect = 1.7
Identities = 31/119 (26%), Positives = 50/119 (42%), Gaps = 20/119 (16%)
Query: 152 GTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKMGKHITDLSVRYAVRG 211
G GKT T +L + + + +V + PT L Q+ E + K + L V
Sbjct: 107 GVGKT---TFGLLMSLYLAKKGKRVYIIVPTTTLVRQVYERLKKFAEDAGSLDVLVVYHS 163
Query: 212 ENLERNKK-ITEQ-------IIIGTPGKVLDWGLKYRFFDLSKIK---VFVLDEADVMI 259
+ K+ E+ I+I T L RF +LSK+K +FV D+ D ++
Sbjct: 164 ALPTKEKEEALERIESGDFDILITTSQF-----LSKRFEELSKLKFDFIFV-DDVDAIL 216
>gnl|CDD|237496 PRK13766, PRK13766, Hef nuclease; Provisional.
Length = 773
Score = 30.6 bits (70), Expect = 1.8
Identities = 18/59 (30%), Positives = 33/59 (55%), Gaps = 8/59 (13%)
Query: 347 AMIFCHTRKTAAWLAEKMSKEGLN----VGLLSGE----LTVEQRLSILDRFREGEFKI 397
++F R TA + + + KEG+ VG S + ++ ++++ ILD+FR GEF +
Sbjct: 368 IIVFTQYRDTAEKIVDLLEKEGIKAVRFVGQASKDGDKGMSQKEQIEILDKFRAGEFNV 426
>gnl|CDD|180702 PRK06802, flgC, flagellar basal body rod protein FlgC; Reviewed.
Length = 141
Score = 29.0 bits (65), Expect = 2.5
Identities = 15/71 (21%), Positives = 30/71 (42%), Gaps = 8/71 (11%)
Query: 30 NLKQADTPSPTEDAKPAPSSPDSSAPGNKDEEDKPLSVAEKSL-LQKIVRRGLIESKQEL 88
NL A++P+ + SP +A + P V + + +V+ G
Sbjct: 27 NLANAESPAASAATAYKARSPVFAAVYSARTLADPRGVQGAQVQVLDVVQVG-------G 79
Query: 89 EIQRKDPHSPL 99
++R +P++PL
Sbjct: 80 SVKRYEPNNPL 90
>gnl|CDD|233494 TIGR01616, nitro_assoc, nitrogenase-associated protein. This
model describes a small family of uncharacterized
proteins found so far in alpha and gamma proteobacteria
and in Nostoc sp. PCC 7120, a cyanobacterium. The gene
for this protein is associated with nitrogenase genes.
This family shows sequence similarity to TIGR00014, a
glutaredoxin-dependent arsenate reductase that converts
arsentate to arsenite for disposal. This family is one
of several included in pfam03960 [Unknown function,
General].
Length = 126
Score = 28.0 bits (62), Expect = 4.0
Identities = 20/60 (33%), Positives = 26/60 (43%), Gaps = 6/60 (10%)
Query: 33 QADTPSPTEDAKPAPSSPDSSAPGNKDEEDKPLSVAEKSLLQKIV------RRGLIESKQ 86
ADT P KP S + +AP K E P S+ E S L +V RR L++
Sbjct: 39 HADTLRPYFGNKPVGSWFNRAAPRVKSGEVNPDSIDEASALALMVSDPLLIRRPLMDLGG 98
>gnl|CDD|238683 cd01387, MYSc_type_XV, Myosin motor domain, type XV myosins. In
vertebrates, myosin XV appears to be expressed in
sensory tissue and play a role in hearing. This
catalytic (head) domain has ATPase activity and belongs
to the larger group of P-loop NTPases. Myosins are
actin-dependent molecular motors that play important
roles in muscle contraction, cell motility, and
organelle transport. The head domain is a molecular
motor, which utilizes ATP hydrolysis to generate
directed movement toward the plus end along actin
filaments. A cyclical interaction between myosin and
actin provides the driving force. Rates of ATP
hydrolysis and consequently the speed of movement along
actin filaments vary widely, from about 0.04 micrometer
per second for myosin I to 4.5 micrometer per second for
myosin II in skeletal muscle. Myosin II moves in
discrete steps about 5-10 nm long and generates 1-5
piconewtons of force. Upon ATP binding, the myosin head
dissociates from an actin filament. ATP hydrolysis
causes the head to pivot and associate with a new actin
subunit. The release of Pi causes the head to pivot and
move the filament (power stroke). Release of ADP
completes the cycle.
Length = 677
Score = 29.1 bits (65), Expect = 4.5
Identities = 24/91 (26%), Positives = 38/91 (41%), Gaps = 25/91 (27%)
Query: 119 YEM-GFYAPSKIQETALPTLLADPPH-------------------NMIAQSQSGTGKTAA 158
Y+M Y P ++Q+ A L +PPH +I +SG+GKT A
Sbjct: 44 YKMFPIYGPEQVQQYAGRALGENPPHLFAIANLAFAKMLDAKQNQCVIISGESGSGKTEA 103
Query: 159 FTLTM--LSRVNP---SIQEPQVLCLAPTYE 184
L + L+ +N ++ Q+L P E
Sbjct: 104 TKLILRYLAAMNQGGSAVITEQILEATPLLE 134
>gnl|CDD|219205 pfam06862, DUF1253, Protein of unknown function (DUF1253). This
family represents the C-terminal portion (approximately
500 residues) of several hypothetical eukaryotic
proteins of unknown function.
Length = 436
Score = 28.7 bits (65), Expect = 5.5
Identities = 14/37 (37%), Positives = 22/37 (59%), Gaps = 7/37 (18%)
Query: 223 QIIIGTPGKVLDWGLKYRFFD-LSKIKVFVLDEADVM 258
++II K K R +D LS I+V ++D+ADV+
Sbjct: 138 RMIIENEDK------KKRDYDFLSSIEVLIVDQADVI 168
>gnl|CDD|224969 COG2058, RPP1A, Ribosomal protein L12E/L44/L45/RPP1/RPP2
[Translation, ribosomal structure and biogenesis].
Length = 109
Score = 27.4 bits (61), Expect = 6.0
Identities = 13/57 (22%), Positives = 25/57 (43%)
Query: 15 SALKPDDLIDVLSNVNLKQADTPSPTEDAKPAPSSPDSSAPGNKDEEDKPLSVAEKS 71
+AL+ D+ +V+ N A + A A + ++ +EE+K E+S
Sbjct: 43 AALEGVDIDEVIKNAAEAPAAAAAAGAAAAAAAGAEAAAEADEAEEEEKEEEAEEES 99
>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 = 28.6 bits (64), Expect = 6.9
Identities = 36/183 (19%), Positives = 70/183 (38%), Gaps = 14/183 (7%)
Query: 223 QIIIGTPGKV-LDWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDF-----SIRIQKRLP 276
+++ TP K L + I + +DEA I+ GH DF ++ K+
Sbjct: 103 KLLYVTPEKCSASNRLLQTLEERKGITLIAVDEAHC-ISQWGH-DFRPDYKALGSLKQKF 160
Query: 277 SDCQIMLFSATYDKEVMEFAQDMVPNPLIIKLKREEESLD--NIKQHYVMCKNIDEKFEA 334
+ IM +AT V +D++ + + S D N+ + V K +
Sbjct: 161 PNVPIMALTATASPSVR---EDILRQLNLKNPQIFCTSFDRPNLY-YEVRRKTPKILEDL 216
Query: 335 VSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQRLSILDRFREGE 394
+ I +I+C +RK + + + G+ G L + R + +F+ E
Sbjct: 217 LRFIRKEFKGKSGIIYCPSRKKSEQVTASLQNLGIAAGAYHAGLEISARDDVHHKFQRDE 276
Query: 395 FKI 397
++
Sbjct: 277 IQV 279
>gnl|CDD|180905 PRK07246, PRK07246, bifunctional ATP-dependent DNA helicase/DNA
polymerase III subunit epsilon; Validated.
Length = 820
Score = 28.5 bits (64), Expect = 6.9
Identities = 19/67 (28%), Positives = 34/67 (50%), Gaps = 8/67 (11%)
Query: 137 LLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAKM 196
D P + I ++Q+G GKT + L +L++ + Q++ PT L QI +A+
Sbjct: 260 DFHDGPASFI-EAQTGIGKTYGYLLPLLAQS----DQRQIIVSVPTKILQDQI---MAEE 311
Query: 197 GKHITDL 203
K I ++
Sbjct: 312 VKAIQEV 318
>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 = 28.6 bits (64), Expect = 7.2
Identities = 18/74 (24%), Positives = 31/74 (41%), Gaps = 4/74 (5%)
Query: 136 TLLADPPHNMIAQSQSGTGKTAAFTLTMLSRVNPSIQEPQVLCLAPTYELAIQIGEVVAK 195
L ++I ++ +GTGKT + L L +I E V+ T L Q+ E
Sbjct: 259 DQLTHSEKSLI-EAPTGTGKTLGYLLPALYY---AITEKPVVISTNTKVLQSQLLEKDIP 314
Query: 196 MGKHITDLSVRYAV 209
+ I + + A+
Sbjct: 315 LLNEILNFKINAAL 328
>gnl|CDD|223420 COG0343, Tgt, Queuine/archaeosine tRNA-ribosyltransferase
[Translation, ribosomal structure and biogenesis].
Length = 372
Score = 28.4 bits (64), Expect = 7.7
Identities = 26/126 (20%), Positives = 46/126 (36%), Gaps = 29/126 (23%)
Query: 268 SIRIQKRLPSDCQIML-----FSATYDKEVMEFAQDMVPNPLIIKLKREEESLDNIKQHY 322
S+ IQK L SD ++L A + + L+ E SL+ K+
Sbjct: 125 SMEIQKDLGSDIIMILDECTPPPADREY---------AEKSVERTLRWAERSLEAHKRLN 175
Query: 323 VMCKNIDEKFEAVSNIYGVVTIGQAMIFCHTRKTAAWLAEKMSKEGLNVGLLSGELTVEQ 382
++G+V Q + R+ +A ++ +G +G LS E
Sbjct: 176 DQ------------ALFGIV---QGGTYEDLRRRSAEELNELDFDGYAIGGLSVGEPKED 220
Query: 383 RLSILD 388
+ IL+
Sbjct: 221 MVRILE 226
>gnl|CDD|234000 TIGR02760, TraI_TIGR, conjugative transfer relaxase protein TraI.
This protein is a component of the relaxosome complex. In
the process of conjugative plasmid transfer the
realaxosome binds to the plasmid at the oriT (origin of
transfer) site. The relaxase protein TraI mediates the
single-strand nicking and ATP-dependent unwinding
(relaxation, helicase activity) of the plasmid molecule.
These two activities reside in separate domains of the
protein.
Length = 1960
Score = 28.3 bits (63), Expect = 9.5
Identities = 13/39 (33%), Positives = 19/39 (48%), Gaps = 3/39 (7%)
Query: 148 QSQSGTGKTAAFTLTMLSRVN--PSIQEPQVLCLAPTYE 184
Q +G GKT + V ++ QV+ LAPT+E
Sbjct: 1042 QGLAGVGKTT-MLESRYKPVLQAFESEQLQVIGLAPTHE 1079
>gnl|CDD|224120 COG1199, DinG, Rad3-related DNA helicases [Transcription / DNA
replication, recombination, and repair].
Length = 654
Score = 28.2 bits (63), Expect = 9.8
Identities = 22/111 (19%), Positives = 36/111 (32%), Gaps = 22/111 (19%)
Query: 216 RNKKITEQIIIGTPGKVL-DWGLKYRFFDLSKIKVFVLDEADVMIATQGHQDFSIRIQKR 274
R + +++ +L D L+ L + V V DEA H
Sbjct: 189 RKEAENADLVVTNHALLLADVALEESRILLPENDVVVFDEA--------HN--------- 231
Query: 275 LPSDCQIMLFSATYDKEVMEFAQDMVP---NPLIIKLKREEESLDNIKQHY 322
LP D S + +E + L LKR E+ D +++
Sbjct: 232 LP-DIARSALSIRLSERTLERLLKEIQALGETLEKDLKRLEDLADRLEKAL 281
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
0.316 0.133 0.374
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: 20,288,483
Number of extensions: 1984304
Number of successful extensions: 2221
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2137
Number of HSP's successfully gapped: 82
Length of query: 399
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 300
Effective length of database: 6,546,556
Effective search space: 1963966800
Effective search space used: 1963966800
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 60 (26.8 bits)