RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6275
(391 letters)
>gnl|CDD|226947 COG4581, COG4581, Superfamily II RNA helicase [DNA replication,
recombination, and repair].
Length = 1041
Score = 462 bits (1190), Expect = e-154
Identities = 186/387 (48%), Positives = 252/387 (65%), Gaps = 19/387 (4%)
Query: 9 RESKTKACMKVIVVETLEACLHEVALPPDLEYQPLAQSKEK---PAREYPFVLDPFQKEA 65
E ++ + V L +VA+P D + P A+S PAREYPF LDPFQ+EA
Sbjct: 68 SEIESLNVGMRLDVRLSSKELSDVAVPDDYDMVPDAESPFDLAPPAREYPFELDPFQQEA 127
Query: 66 ILCIENNQSVLVSAHTSAGKTVVAEYAIASSLKQSQRVIYTTPIKALSNQKYREFEEQFK 125
I +E +SVLV A TS+GKTVVAEYAIA +L+ QRVIYT+PIKALSNQKYR+ +F
Sbjct: 128 IAILERGESVLVCAPTSSGKTVVAEYAIALALRDGQRVIYTSPIKALSNQKYRDLLAKFG 187
Query: 126 DV----GLITGDVTINPSSSCLIMTTEILRNMLYRGSEITREVGWVIFDEIHYMRDKERG 181
DV GL+TGDV+INP + CL+MTTEILRNMLYRGSE R++ WV+FDE+HY+ D+ERG
Sbjct: 188 DVADMVGLMTGDVSINPDAPCLVMTTEILRNMLYRGSESLRDIEWVVFDEVHYIGDRERG 247
Query: 182 YVWEETLILLSDNVRFVFLSATIPNASQFAQWVSHLHHQPCHVVYTDYRPTPLQHYLFPN 241
VWEE +ILL D+VRFVFLSAT+PNA +FA+W+ +H QP HVV T++RP PL+H+++
Sbjct: 248 VVWEEVIILLPDHVRFVFLSATVPNAEEFAEWIQRVHSQPIHVVSTEHRPVPLEHFVYV- 306
Query: 242 GGDGIHLIVDDNK-FKEHNYQVAMNVLAN-AGDAAKAGDHKGGRKGGPKGGVQTNC---- 295
G G+ +VD+ K F N+ A L+ + + D GR ++ +
Sbjct: 307 -GKGLFDLVDEKKKFNAENFPSANRSLSCFSEKVRETDDGDVGRYARRTKALRGSAKGPA 365
Query: 296 --FKIVKMIMERNLAPVIVFSFSKKDCEIYAMQMAKLNFNETEEVKL-VDDVFSNAMDVL 352
+IV + + NL P IVFSFS++ CE A ++ L+ TEE + + ++ +A+ L
Sbjct: 366 GRPEIVNKLDKDNLLPAIVFSFSRRGCEEAAQILSTLDLVLTEEKERAIREIIDHAIGDL 425
Query: 353 SEEDRKLP-QIENILPLLRRGIGIHHG 378
+EEDR+LP QI I LL RGI +HH
Sbjct: 426 AEEDRELPLQILEISALLLRGIAVHHA 452
>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 = 126 bits (319), Expect = 5e-35
Identities = 47/162 (29%), Positives = 75/162 (46%), Gaps = 16/162 (9%)
Query: 60 PFQKEAILCIENNQSVLVSAHTSAGKTVVAEYAIASSL---KQSQRVIYTTPIKALSNQK 116
P Q +AI I + + VLV A T +GKT+ I +L K + + P + L+ Q
Sbjct: 2 PIQAQAIPAILSGKDVLVQAPTGSGKTLAFLLPILQALLPKKGGPQALVLAPTRELAEQI 61
Query: 117 YREFEEQFK----DVGLITGDVTINPSSS--------CLIMTTEILRNMLYRGSEIT-RE 163
Y E ++ FK V L+TG ++ + L+ T L ++L RG +
Sbjct: 62 YEELKKLFKILGLRVALLTGGTSLKEQARKLKKGKADILVGTPGRLLDLLRRGKLKLLKN 121
Query: 164 VGWVIFDEIHYMRDKERGYVWEETLILLSDNVRFVFLSATIP 205
+ ++ DE H + D G EE L L + + + LSAT+P
Sbjct: 122 LKLLVLDEAHRLLDMGFGDDLEEILSRLPPDRQILLLSATLP 163
>gnl|CDD|214692 smart00487, DEXDc, DEAD-like helicases superfamily.
Length = 201
Score = 121 bits (304), Expect = 1e-32
Identities = 52/198 (26%), Positives = 83/198 (41%), Gaps = 17/198 (8%)
Query: 55 PFVLDPFQKEAILCI-ENNQSVLVSAHTSAGKTVVAEYAIASSLKQSQ--RVIYTTPIKA 111
L P+QKEAI + + V+++A T +GKT+ A +LK+ + RV+ P +
Sbjct: 6 FEPLRPYQKEAIEALLSGLRDVILAAPTGSGKTLAALLPALEALKRGKGGRVLVLVPTRE 65
Query: 112 LSNQKYREFEEQFKD-----VGLITGDVT-------INPSSSCLIMTTEILRNMLYRGSE 159
L+ Q E ++ VGL GD + + L+ T L ++L
Sbjct: 66 LAEQWAEELKKLGPSLGLKVVGLYGGDSKREQLRKLESGKTDILVTTPGRLLDLLENDKL 125
Query: 160 ITREVGWVIFDEIHYMRDKERGYVWEETLILLSDNVRFVFLSATIPNASQFAQWVSHLHH 219
V VI DE H + D G E+ L LL NV+ + LSAT P + +
Sbjct: 126 SLSNVDLVILDEAHRLLDGGFGDQLEKLLKLLPKNVQLLLLSATPPEEIENLLE--LFLN 183
Query: 220 QPCHVVYTDYRPTPLQHY 237
P + P++ +
Sbjct: 184 DPVFIDVGFTPLEPIEQF 201
>gnl|CDD|224125 COG1204, COG1204, Superfamily II helicase [General function
prediction only].
Length = 766
Score = 127 bits (320), Expect = 7e-32
Identities = 86/324 (26%), Positives = 143/324 (44%), Gaps = 59/324 (18%)
Query: 69 IENNQSVLVSAHTSAGKTVVAEYAIASSLKQSQ-RVIYTTPIKALSNQKYREFE--EQFK 125
+ ++++VL+SA T +GKT++A AI S+L + +V+Y P+KAL+ +KY EF E+
Sbjct: 44 LLSDENVLISAPTGSGKTLIALLAILSTLLEGGGKVVYIVPLKALAEEKYEEFSRLEELG 103
Query: 126 D-VGLITGDVTINPS----SSCLIMTTEILRNMLYRGSEITREVGWVIFDEIHYMRDKER 180
VG+ TGD ++ ++ T E L ++ + EV V+ DEIH + D+ R
Sbjct: 104 IRVGISTGDYDLDDERLARYDVIVTTPEKLDSLTRKRPSWIEEVDLVVIDEIHLLGDRTR 163
Query: 181 GYVWEETLI---LLSDNVRFVFLSATIPNASQFAQWVSHLHHQPCHVVYTDYRPTPLQHY 237
G V E + L++ +R V LSAT+PNA + A W++ +V +D+RP PL+
Sbjct: 164 GPVLESIVARMRRLNELIRIVGLSATLPNAEEVADWLN------AKLVESDWRPVPLRRG 217
Query: 238 LFPNGGDGIHLIVDDNKFKEHNYQVAMNVLANAGDAAKAGDHKGGRKGGPKGGVQTNCFK 297
+ G + D K K ++ LA
Sbjct: 218 VPYVG----AFLGADGKKKTWPL--LIDNLALE--------------------------L 245
Query: 298 IVKMIMERNLAPVIVFSFSKKDCEIYAMQMAKLNFNETEEVKLVDDVFSNAMDVLSEEDR 357
+++ + V+VF S+K+ A + AK L DD + S
Sbjct: 246 VLESL--AEGGQVLVFVHSRKE----AEKTAK-KLRIKMSATLSDDEKIVLDEGASPILI 298
Query: 358 KLP---QIENILPLLRRGIGIHHG 378
+ E + L+ RG+ HH
Sbjct: 299 PETPTSEDEELAELVLRGVAFHHA 322
>gnl|CDD|100801 PRK01172, PRK01172, ski2-like helicase; Provisional.
Length = 674
Score = 106 bits (265), Expect = 8e-25
Identities = 81/334 (24%), Positives = 149/334 (44%), Gaps = 74/334 (22%)
Query: 56 FVLDPFQKEAILCIENNQSVLVSAHTSAGKTVVAEYAIASSLKQSQRVIYTTPIKALSNQ 115
F L Q+ AI + ++V+VS T+AGKT++A AI + + IY P+++L+ +
Sbjct: 21 FELYDHQRMAIEQLRKGENVIVSVPTAAGKTLIAYSAIYETFLAGLKSIYIVPLRSLAME 80
Query: 116 KYREFEEQFKDVGL-IT---GDVTINPS----SSCLIMTTEILRNMLYRGSEITREVGWV 167
KY E + + +G+ + GD P +I+T+E ++++ I +VG +
Sbjct: 81 KYEEL-SRLRSLGMRVKISIGDYDDPPDFIKRYDVVILTSEKADSLIHHDPYIINDVGLI 139
Query: 168 IFDEIHYMRDKERGYVWEETLI---LLSDNVRFVFLSATIPNASQFAQWVSHLHHQPCHV 224
+ DEIH + D++RG E L ++ + R + LSAT+ NA++ AQW++ +
Sbjct: 140 VADEIHIIGDEDRGPTLETVLSSARYVNPDARILALSATVSNANELAQWLN------ASL 193
Query: 225 VYTDYRPTPLQ-HYLFPNGGDGIHLIVDDNKFKEHNYQVAMNVLANAGDAAKAGDHKGGR 283
+ +++RP PL+ L+ LI+D
Sbjct: 194 IKSNFRPVPLKLGILYRK-----RLILD-------------------------------- 216
Query: 284 KGGPKGGVQTNCFKIVKMIMERNLAPVIVFSFSKKDCEIYAMQMAKLNFNETEEVKLVDD 343
G + V N ++K + V+VF S+K+ E YA + + F E + K+ +
Sbjct: 217 -GYERSQVDIN--SLIKETVNDG-GQVLVFVSSRKNAEDYAEMLIQH-FPEFNDFKVSSE 271
Query: 344 VFSNAMDVLSEEDRKLPQIENILPLLRRGIGIHH 377
+N D +++ +L G+ HH
Sbjct: 272 N-NNVYD------------DSLNEMLPHGVAFHH 292
>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 = 94.7 bits (236), Expect = 2e-23
Identities = 36/144 (25%), Positives = 66/144 (45%), Gaps = 12/144 (8%)
Query: 73 QSVLVSAHTSAGKTVVAEYAIASSLKQSQ--RVIYTTPIKALSNQKYREFEEQFK---DV 127
+ VL++A T +GKT+ A I L + +V+ P + L+NQ +E F V
Sbjct: 1 RDVLLAAPTGSGKTLAALLPILELLDSLKGGQVLVLAPTRELANQVAERLKELFGEGIKV 60
Query: 128 GLITGDVTINPS-------SSCLIMTTEILRNMLYRGSEITREVGWVIFDEIHYMRDKER 180
G + G +I + ++ T L + L R +++ +I DE H + ++
Sbjct: 61 GYLIGGTSIKQQEKLLSGKTDIVVGTPGRLLDELERLKLSLKKLDLLILDEAHRLLNQGF 120
Query: 181 GYVWEETLILLSDNVRFVFLSATI 204
G + + L+ L + + + LSAT
Sbjct: 121 GLLGLKILLKLPKDRQVLLLSATP 144
>gnl|CDD|234702 PRK00254, PRK00254, ski2-like helicase; Provisional.
Length = 720
Score = 89.9 bits (223), Expect = 2e-19
Identities = 59/194 (30%), Positives = 103/194 (53%), Gaps = 15/194 (7%)
Query: 58 LDPFQKEAILC-IENNQSVLVSAHTSAGKTVVAEYAIASS-LKQSQRVIYTTPIKALSNQ 115
L P Q EA+ + ++++++ T++GKT+VAE + + L++ + +Y P+KAL+ +
Sbjct: 24 LYPPQAEALKSGVLEGKNLVLAIPTASGKTLVAEIVMVNKLLREGGKAVYLVPLKALAEE 83
Query: 116 KYREFEEQFK---DVGLITGDVTINPS----SSCLIMTTEILRNMLYRGSEITREVGWVI 168
KYREF++ K V + TGD +I T E ++L GS ++V V+
Sbjct: 84 KYREFKDWEKLGLRVAMTTGDYDSTDEWLGKYDIIIATAEKFDSLLRHGSSWIKDVKLVV 143
Query: 169 FDEIHYMRDKERGYVWEETLILLSDNVRFVFLSATIPNASQFAQWVSHLHHQPCHVVYTD 228
DEIH + +RG E L + + + LSAT+ NA + A+W++ +V +D
Sbjct: 144 ADEIHLIGSYDRGATLEMILTHMLGRAQILGLSATVGNAEELAEWLN------AELVVSD 197
Query: 229 YRPTPLQHYLFPNG 242
+RP L+ +F G
Sbjct: 198 WRPVKLRKGVFYQG 211
>gnl|CDD|235032 PRK02362, PRK02362, ski2-like helicase; Provisional.
Length = 737
Score = 88.9 bits (221), Expect = 4e-19
Identities = 60/213 (28%), Positives = 108/213 (50%), Gaps = 41/213 (19%)
Query: 58 LDPFQKEAILCIE----NNQSVLVSAHTSAGKTVVAEYAIASSLKQSQRVIYTTPIKALS 113
L P Q E +E + +++L + T++GKT++AE A+ ++ + + +Y P++AL+
Sbjct: 24 LYPPQAE---AVEAGLLDGKNLLAAIPTASGKTLIAELAMLKAIARGGKALYIVPLRALA 80
Query: 114 NQKYREFEEQFKDVGLITGDVTINPSSS--------CLIMTTE----ILRNMLYRGSEIT 161
++K+ EFE F+++G+ G T + S ++ T+E +LRN G+
Sbjct: 81 SEKFEEFER-FEELGVRVGISTGDYDSRDEWLGDNDIIVATSEKVDSLLRN----GAPWL 135
Query: 162 REVGWVIFDEIHYMRDKERGYVWEETLILL---SDNVRFVFLSATIPNASQFAQWVSHLH 218
++ V+ DE+H + RG E TL L + +++ V LSATI NA + A W+
Sbjct: 136 DDITCVVVDEVHLIDSANRGPTLEVTLAKLRRLNPDLQVVALSATIGNADELADWLD--- 192
Query: 219 HQPCHVVYTDYRPTPLQ---HYLFPNGGDGIHL 248
+V +++RP L+ Y G IH
Sbjct: 193 ---AELVDSEWRPIDLREGVFY-----GGAIHF 217
>gnl|CDD|224123 COG1202, COG1202, Superfamily II helicase, archaea-specific
[General function prediction only].
Length = 830
Score = 85.6 bits (212), Expect = 6e-18
Identities = 68/235 (28%), Positives = 111/235 (47%), Gaps = 45/235 (19%)
Query: 29 LHEVALPPDLEYQPLAQSKEKPAREYPFVLDPFQKEAILCIEN------NQSVLVSAHTS 82
+ E+ +P K RE L P Q +L +E N V VSA T+
Sbjct: 196 VDELDIPEKF--------KRMLKREGIEELLPVQ---VLAVEAGLLEGENLLV-VSA-TA 242
Query: 83 AGKTVVAEYA-IASSLKQSQRVIYTTPIKALSNQKYREFEEQFKDVGLITG--------- 132
+GKT++ E A I L +++++ P+ AL+NQKY +F+E++ +GL
Sbjct: 243 SGKTLIGELAGIPRLLSGGKKMLFLVPLVALANQKYEDFKERYSKLGLKVAIRVGMSRIK 302
Query: 133 ------DVTINPSSSCLIMTTEILRNMLYRGSEITREVGWVIFDEIHYMRDKERGYVWE- 185
V +P + ++ T E + +L R + ++G V+ DEIH + D+ERG +
Sbjct: 303 TREEPVVVDTSPDADIIVGTYEGIDYLL-RTGKDLGDIGTVVIDEIHTLEDEERGPRLDG 361
Query: 186 --ETLILLSDNVRFVFLSATIPNASQFAQWVSHLHHQPCHVVYTDYRPTPLQHYL 238
L L +F++LSAT+ N + A L + V+Y D RP PL+ +L
Sbjct: 362 LIGRLRYLFPGAQFIYLSATVGNPEELA---KKLGAKL--VLY-DERPVPLERHL 410
>gnl|CDD|224122 COG1201, Lhr, Lhr-like helicases [General function prediction
only].
Length = 814
Score = 73.1 bits (180), Expect = 6e-14
Identities = 53/181 (29%), Positives = 88/181 (48%), Gaps = 26/181 (14%)
Query: 60 PFQKEAILCIENNQSVLVSAHTSAGKTVVAEYAIASSL--------KQSQRVIYTTPIKA 111
P Q+ AI I + ++VL+ A T +GKT A + + L + +Y +P+KA
Sbjct: 25 PPQRYAIPEIHSGENVLIIAPTGSGKTEAAFLPVINELLSLGKGKLEDGIYALYISPLKA 84
Query: 112 LSNQKYREFEEQFKDVGLI----TGDVT--------INPSSSCLIMTTEILRNML--YRG 157
L+N R EE +++G+ GD NP LI T E L +L +
Sbjct: 85 LNNDIRRRLEEPLRELGIEVAVRHGDTPQSEKQKMLKNP-PHILITTPESLAILLNSPKF 143
Query: 158 SEITREVGWVIFDEIHYMRDKERGY---VWEETLILLSDNVRFVFLSATIPNASQFAQWV 214
E+ R+V +VI DEIH + + +RG + E L L+ + + + LSAT+ + A+++
Sbjct: 144 RELLRDVRYVIVDEIHALAESKRGVQLALSLERLRELAGDFQRIGLSATVGPPEEVAKFL 203
Query: 215 S 215
Sbjct: 204 V 204
>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 = 63.7 bits (156), Expect = 6e-11
Identities = 51/195 (26%), Positives = 82/195 (42%), Gaps = 34/195 (17%)
Query: 60 PFQKEAILCIENNQSVLVSAHTSAGKT------VVAEYAIASSLKQSQRVIYTTPIKALS 113
PFQ E +S L+ A T +GKT + + A K+ +Y TP++AL+
Sbjct: 16 PFQLEMWAAALEGRSGLLIAPTGSGKTLAGFLPSLIDLAGPEKPKKGLHTLYITPLRALA 75
Query: 114 NQKYREFEEQFKDVGLI------TGDVTINPSS----------SCLIMTTEILRNML-YR 156
R + +++GL TGD SS L+ T E L +L Y
Sbjct: 76 VDIARNLQAPIEELGLPIRVETRTGDT---SSSERARQRKKPPDILLTTPESLALLLSYP 132
Query: 157 GSE-ITREVGWVIFDEIHYMRDKERGYVWEETLIL-----LSDNVRFVFLSATIPNASQF 210
+ + +++ V+ DE H + +RG E L L L+ +R LSATI N +
Sbjct: 133 DAARLFKDLRCVVVDEWHELAGSKRGDQLE--LALARLRRLAPGLRRWGLSATIGNLEEA 190
Query: 211 AQWVSHLHHQPCHVV 225
+ + + P +V
Sbjct: 191 RRVLLGVGGAPAVLV 205
>gnl|CDD|237497 PRK13767, PRK13767, ATP-dependent helicase; Provisional.
Length = 876
Score = 61.8 bits (151), Expect = 3e-10
Identities = 47/156 (30%), Positives = 69/156 (44%), Gaps = 34/156 (21%)
Query: 60 PFQKEAILCIENNQSVLVSAHTSAGKTVVAEYAIASSLKQSQR---------VIYTTPIK 110
P Q+ AI I ++VL+S+ T +GKT+ A AI L + R +Y +P++
Sbjct: 35 PPQRYAIPLIHEGKNVLISSPTGSGKTLAAFLAIIDELFRLGREGELEDKVYCLYVSPLR 94
Query: 111 ALSNQKYREFEEQFK-----------DVGLI-----TGDVTINPSSS-------CLIMTT 147
AL+N +R EE ++ I TGD + LI T
Sbjct: 95 ALNNDIHRNLEEPLTEIREIAKERGEELPEIRVAIRTGDTSSYEKQKMLKKPPHILITTP 154
Query: 148 EILRNMLY--RGSEITREVGWVIFDEIHYMRDKERG 181
E L +L + E R V WVI DEIH + + +RG
Sbjct: 155 ESLAILLNSPKFREKLRTVKWVIVDEIHSLAENKRG 190
>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 = 58.6 bits (142), Expect = 3e-09
Identities = 43/184 (23%), Positives = 73/184 (39%), Gaps = 27/184 (14%)
Query: 55 PFVLDPFQKEAILCIENNQSVLVSAHTSAGKTVVAEYAI-ASSLKQSQ-RVIYTTPIKAL 112
L Q +A+ I ++V+V+ T +GKT I L+ R + P AL
Sbjct: 68 IERLYSHQVDALRLIREGRNVVVTTGTGSGKTESFLLPILDHLLRDPSARALLLYPTNAL 127
Query: 113 SN---QKYREFEEQFK---DVGLITGDV--------TINPSSSCLIMTTEILRNMLYRGS 158
+N ++ RE G TGD NP L+ ++L +L R
Sbjct: 128 ANDQAERLRELISDLPGKVTFGRYTGDTPPEERRAIIRNP-PDILLTNPDMLHYLLLRNH 186
Query: 159 E----ITREVGWVIFDEIHYMRD---KERGYVWEETLILL---SDNVRFVFLSATIPNAS 208
+ + R + +++ DE+H R E + L L ++ + SAT+ N
Sbjct: 187 DAWLWLLRNLKYLVVDELHTYRGVQGSEVALLLRRLLRRLRRYGSPLQIICTSATLANPG 246
Query: 209 QFAQ 212
+FA+
Sbjct: 247 EFAE 250
>gnl|CDD|224124 COG1203, COG1203, CRISPR-associated helicase Cas3 [Defense
mechanisms].
Length = 733
Score = 52.1 bits (125), Expect = 3e-07
Identities = 37/186 (19%), Positives = 60/186 (32%), Gaps = 38/186 (20%)
Query: 60 PFQKEAILCIENNQS----VLVSAHTSAGKTVV----AEYAIASSLKQSQRVIYTTPIKA 111
Q++A+ I + V++ A T GKT A + +K RVIY P +
Sbjct: 198 ELQEKALELILRLEKRSLLVVLEAPTGYGKTEASLILALALLDEKIKLKSRVIYVLPFRT 257
Query: 112 LSNQKYREFEEQFKDVGLITGDVTINPSSSCL----IMTTEILRNM-----LYRGSEITR 162
+ YR +E F +I + + L L L +
Sbjct: 258 IIEDMYRRAKEIFGLFSVIGKSLHSSSKEPLLLEPDQDILLTLTTNDSYKKLLLALIVVT 317
Query: 163 EVGW--------------------VIFDEIHYMRDKERGYVWEETLILLSDN-VRFVFLS 201
+ VI DE+H D+ L L++ V + +S
Sbjct: 318 PIQILIFSVKGFKFEFLALLLTSLVILDEVHLYADETMLAALLALLEALAEAGVPVLLMS 377
Query: 202 ATIPNA 207
AT+P
Sbjct: 378 ATLPPF 383
>gnl|CDD|223989 COG1061, SSL2, DNA or RNA helicases of superfamily II
[Transcription / DNA replication, recombination, and
repair].
Length = 442
Score = 47.8 bits (114), Expect = 5e-06
Identities = 33/129 (25%), Positives = 54/129 (41%), Gaps = 18/129 (13%)
Query: 56 FVLDPFQKEAI----LCIENNQSVLVSAHTSAGKTVVAEYAIASSLKQSQRVIYTTPIKA 111
F L P+Q+EA+ + ++ T AGKTVVA AIA + + + P K
Sbjct: 35 FELRPYQEEALDALVKNRRTERRGVIVLPTGAGKTVVAAEAIA---ELKRSTLVLVPTKE 91
Query: 112 LSNQKYREFEEQF---KDVGLITGDVTINPSSSCLIMTTEILRNMLYRGSEI----TREV 164
L +Q ++ ++G+ G + + + T L R + E
Sbjct: 92 LLDQWAEALKKFLLLNDEIGIYGGG-EKELEPAKVTVATV---QTLARRQLLDEFLGNEF 147
Query: 165 GWVIFDEIH 173
G +IFDE+H
Sbjct: 148 GLIIFDEVH 156
>gnl|CDD|137505 PRK09751, PRK09751, putative ATP-dependent helicase Lhr;
Provisional.
Length = 1490
Score = 47.2 bits (112), Expect = 1e-05
Identities = 52/179 (29%), Positives = 73/179 (40%), Gaps = 41/179 (22%)
Query: 77 VSAHTSAGKTVVA-EYAIASSLKQ------------SQRVIYTTPIKALSNQKYREFEEQ 123
V A T +GKT+ A YA+ ++ + R++Y +PIKAL R +
Sbjct: 1 VIAPTGSGKTLAAFLYALDRLFREGGEDTREAHKRKTSRILYISPIKALGTDVQRNLQIP 60
Query: 124 FK----------------DVGLITGDVTINPSS-------SCLIMTTEILRNMLY-RGSE 159
K VG+ TGD S LI T E L ML R E
Sbjct: 61 LKGIADERRRRGETEVNLRVGIRTGDTPAQERSKLTRNPPDILITTPESLYLMLTSRARE 120
Query: 160 ITREVGWVIFDEIHYMRDKERG----YVWEETLILLSDNVRFVFLSATIPNASQFAQWV 214
R V VI DE+H + +RG E LL + + + LSAT+ +AS A ++
Sbjct: 121 TLRGVETVIIDEVHAVAGSKRGAHLALSLERLDALLHTSAQRIGLSATVRSASDVAAFL 179
>gnl|CDD|224557 COG1643, HrpA, HrpA-like helicases [DNA replication, recombination,
and repair].
Length = 845
Score = 45.8 bits (109), Expect = 4e-05
Identities = 46/194 (23%), Positives = 83/194 (42%), Gaps = 29/194 (14%)
Query: 69 IENNQSVLVSAHTSAGKTV-VAEYAIASSLKQSQRVIYTTP--IKALSNQKY--REF-EE 122
IE NQ V++ T +GKT + ++ + L + ++ T P + A S + E E+
Sbjct: 62 IEQNQVVIIVGETGSGKTTQLPQFLLEEGLGIAGKIGCTQPRRLAARSVAERVAEELGEK 121
Query: 123 QFKDVG-LITGDVTINPSSSCLIMTTEILRNMLYRGSEITREVGWVIFDEIHYMRDKER- 180
+ VG I + ++P + +MT IL + + VI DE H ER
Sbjct: 122 LGETVGYSIRFESKVSPRTRIKVMTDGILLREIQNDPLL-SGYSVVIIDEAH-----ERS 175
Query: 181 -------GYVWEETLILLSDNVRFVFLSATIPNASQFAQWVSHLHHQPCHVVYTDYRPTP 233
G + + L D+++ + +SAT+ +A +F+ + V+ + R P
Sbjct: 176 LNTDILLGLLKDL-LARRRDDLKLIIMSATL-DAERFSA-----YFGNAPVIEIEGRTYP 228
Query: 234 LQ-HYLFPNGGDGI 246
++ YL D I
Sbjct: 229 VEIRYLPEAEADYI 242
>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 = 44.0 bits (104), Expect = 1e-04
Identities = 39/188 (20%), Positives = 71/188 (37%), Gaps = 22/188 (11%)
Query: 69 IENNQSVLVSAHTSAGKTVVAEYAIASSLKQSQRVIYTTP--IKALSNQKY--REFEEQF 124
+ + V++ A AGK+ A+ + ++I P + A S + + E
Sbjct: 14 LAAHPQVVLEAPPGAGKSTAVPLALLDAPGIGGKIIMLEPRRLAARSAAQRLASQLGEAV 73
Query: 125 KD-VGL-ITGDVTINPSSSCLIMTTEILRNMLYRGSEITREVGWVIFDEIHYMRDKERGY 182
VG + G+ ++ + ++T IL M+ E+ VG +IFDE H ER
Sbjct: 74 GQTVGYRVRGENKVSRRTRLEVVTEGILTRMIQDDPELDG-VGALIFDEFH-----ERSL 127
Query: 183 VWEETLIL-------LSDNVRFVFLSATIPNA--SQFAQWVSHLHHQ-PCHVVYTDYRPT 232
+ L L L ++++ + +SAT+ S + + V Y P
Sbjct: 128 DADLGLALALDVQSSLREDLKILAMSATLDGERLSSLLPDAPVVESEGRSFPVEIRYLPL 187
Query: 233 PLQHYLFP 240
L
Sbjct: 188 RGDQRLED 195
>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 = 43.6 bits (103), Expect = 1e-04
Identities = 38/166 (22%), Positives = 59/166 (35%), Gaps = 35/166 (21%)
Query: 75 VLVSAHTSAGKTVVAEYAIASSLKQSQ--RVIYTTPIKALSNQKYREFEEQFKDVGLI-- 130
+++ A T GKT A SLK + RVI P +A N YR +E F + GL
Sbjct: 2 LVIEAPTGYGKTEAALLWALHSLKSQKADRVIIALPTRATINAMYRRAKEAFGETGLYHS 61
Query: 131 ---TGDVTINPSSS----CLIMTTEILRNMLYRG----------SEITREVGW------- 166
+ + S + + + E G
Sbjct: 62 SILSSRIKEMGDSEEFEHLFPLYIHSNDTLFLDPITVCTIDQVLKSVFGEFGHYEFTLAS 121
Query: 167 -----VIFDEIHYMRDKERGYVWEETLILLSDN-VRFVFLSATIPN 206
+IFDE+H+ + + L +L DN V + +SAT+P
Sbjct: 122 IANSLLIFDEVHFYDEYTLALI-LAVLEVLKDNDVPILLMSATLPK 166
>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 = 42.4 bits (100), Expect = 2e-04
Identities = 38/168 (22%), Positives = 56/168 (33%), Gaps = 38/168 (22%)
Query: 75 VLVSAHTSAGKTVVAEYAIASSLKQSQ---RVIYTTPIKALSNQKYREFEEQFKD--VGL 129
+++ A T GKT A A +SQ RVI P +A N YR +E F L
Sbjct: 2 LVIEAPTGYGKTEAA-LLWALHSIKSQKADRVIIALPTRATINAMYRRAKELFGSNLGLL 60
Query: 130 ITGDVTINPSSSCLIMTTEILRNMLYRG------------------SEITREVGW----- 166
+ E L + + E G
Sbjct: 61 HSSSSFKRIKEMGDSEEFEHLFPLYIHSNDKLFLDPITVCTIDQVLKSVFGEFGHYEFTL 120
Query: 167 -------VIFDEIHYMRDKERGYVWEETLILLSDN-VRFVFLSATIPN 206
+IFDE+H+ + + L +L DN V + +SAT+P
Sbjct: 121 ASIANSLLIFDEVHFYDEYTLALI-LAVLEVLKDNDVPILLMSATLPK 167
>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 = 41.7 bits (98), Expect = 5e-04
Identities = 39/192 (20%), Positives = 71/192 (36%), Gaps = 37/192 (19%)
Query: 59 DPFQKEAILCIENNQSVLVSAHTSAGKTVVAEYAIA-------SSLKQSQRVIYTTPIKA 111
P Q AI I + VL A T GKT A + + S ++ + P +
Sbjct: 53 TPIQLAAIPLILAGRDVLGQAQTGTGKT--AAFLLPLLQKILKSVERKYVSALILAPTRE 110
Query: 112 LSNQKYREFEE------QFKDVGLITGDVTINP-----SSSC--LIMTTEILRNMLYRGS 158
L+ Q E + + V ++ G V+I ++ T L +++ RG
Sbjct: 111 LAVQIAEELRKLGKNLGGLR-VAVVYGGVSIRKQIEALKRGVDIVVATPGRLLDLIKRGK 169
Query: 159 EITREVGWVIFDEIHYMRDK--ERGYVWEETL--IL--LSDNVRFVFLSATIPNASQFAQ 212
V ++ DE D+ + G + + + IL L + + + SAT+P +
Sbjct: 170 LDLSGVETLVLDEA----DRMLDMG--FIDDIEKILKALPPDRQTLLFSATMP--DDIRE 221
Query: 213 WVSHLHHQPCHV 224
+ P +
Sbjct: 222 LARRYLNDPVEI 233
>gnl|CDD|218292 pfam04851, ResIII, Type III restriction enzyme, res subunit.
Length = 100
Score = 37.6 bits (88), Expect = 0.001
Identities = 25/87 (28%), Positives = 39/87 (44%), Gaps = 16/87 (18%)
Query: 56 FVLDPFQKEAILCIENNQSVLVSAHTSAGKTVVAEYAIASSLKQSQRVIYTTPIKAL--- 112
L P+Q+EAI + + L+ T +GKT+ A IA K ++V++ P K L
Sbjct: 2 LELRPYQEEAIERLLEKKRGLIVMATGSGKTLTAAALIARLAKGKKKVLFVVPRKDLLEQ 61
Query: 113 -------------SNQKYREFEEQFKD 126
+ KYR+ E+FK
Sbjct: 62 ALVIIIDEAHHSSAKTKYRKILEKFKP 88
>gnl|CDD|224036 COG1111, MPH1, ERCC4-like helicases [DNA replication,
recombination, and repair].
Length = 542
Score = 40.0 bits (94), Expect = 0.002
Identities = 28/112 (25%), Positives = 46/112 (41%), Gaps = 11/112 (9%)
Query: 73 QSVLVSAHTSAGKTVVAEYAIASSLKQSQR-VIYTTPIKALSNQKYREFEEQFK----DV 127
++ LV T GKT +A IA+ L+ V++ P K L Q + ++
Sbjct: 30 KNTLVVLPTGLGKTFIAAMVIANRLRWFGGKVLFLAPTKPLVLQHAEFCRKVTGIPEDEI 89
Query: 128 GLITGDVTINP------SSSCLIMTTEILRNMLYRGSEITREVGWVIFDEIH 173
+TG+V + T +++ N L G +V +IFDE H
Sbjct: 90 AALTGEVRPEEREELWAKKKVFVATPQVVENDLKAGRIDLDDVSLLIFDEAH 141
>gnl|CDD|233032 TIGR00580, mfd, transcription-repair coupling factor (mfd). All
proteins in this family for which functions are known
are DNA-dependent ATPases that function in the process
of transcription-coupled DNA repair in which the repair
of the transcribed strand of actively transcribed genes
is repaired at a higher rate than the repair of
non-transcribed regions of the genome and than the
non-transcribed strand of the same gene. This family is
based on the phylogenomic analysis of JA Eisen (1999,
Ph.D. Thesis, Stanford University). This family is
closely related to the RecG and UvrB families [DNA
metabolism, DNA replication, recombination, and repair].
Length = 926
Score = 36.9 bits (86), Expect = 0.020
Identities = 50/204 (24%), Positives = 81/204 (39%), Gaps = 56/204 (27%)
Query: 33 ALPPDLEYQPLAQSKEKPAREYPFVLDPFQKEAI------LCIENNQSVLVSAHTSAGKT 86
A PPDLE+Q + +PF P Q +AI + LV GKT
Sbjct: 433 AFPPDLEWQQEFED------SFPFEETPDQLKAIEEIKADMESPRPMDRLVCGDVGFGKT 486
Query: 87 VVAEYAIASSLKQSQRVIYTTPIKALSNQKYREFEEQFKD----VGLIT----------- 131
VA A ++ ++V P L+ Q + F+E+F + + L++
Sbjct: 487 EVAMRAAFKAVLDGKQVAVLVPTTLLAQQHFETFKERFANFPVTIELLSRFRSAKEQNEI 546
Query: 132 ------GDVTINPSSSCLIMTTEILRNMLYRGSEIT-REVGWVIFDEIHY--MRDKERGY 182
G + I LI T ++L ++ +++G +I DE ++ KE+
Sbjct: 547 LKELASGKIDI------LIGTHKLL------QKDVKFKDLGLLIIDEEQRFGVKQKEK-- 592
Query: 183 VWEETLILLSDNVRFVFLSAT-IP 205
L L +V + LSAT IP
Sbjct: 593 -----LKELRTSVDVLTLSATPIP 611
>gnl|CDD|233069 TIGR00643, recG, ATP-dependent DNA helicase RecG. [DNA metabolism,
DNA replication, recombination, and repair].
Length = 630
Score = 36.2 bits (84), Expect = 0.029
Identities = 23/91 (25%), Positives = 37/91 (40%), Gaps = 10/91 (10%)
Query: 55 PFVLDPFQKEAILCIEN--NQSV----LVSAHTSAGKTVVAEYAIASSLKQSQRVIYTTP 108
PF L QK + I V L+ +GKT+VA A+ ++++ +V P
Sbjct: 233 PFKLTRAQKRVVKEILQDLKSDVPMNRLLQGDVGSGKTLVAALAMLAAIEAGYQVALMAP 292
Query: 109 IKALSNQKYREFEEQFKD----VGLITGDVT 135
+ L+ Q Y V L+TG +
Sbjct: 293 TEILAEQHYNSLRNLLAPLGIEVALLTGSLK 323
>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 = 35.5 bits (82), Expect = 0.053
Identities = 45/183 (24%), Positives = 69/183 (37%), Gaps = 26/183 (14%)
Query: 73 QSVLVSAHTSAGKTVVAEYAIASSLKQSQR--VIYTTPIKALSNQKYREFEE-QFKDVGL 129
+ V+V+ T++GK++ + + S+L R +Y P KAL+ + R E + V
Sbjct: 52 RHVVVATGTASGKSLAYQLPVLSALADDPRATALYLAPTKALAADQLRAVRELTLRGVRP 111
Query: 130 ITGDVTINPSSSCLI--MTTEILRN--MLYRG--------SEITREVGWVIFDEIHYMRD 177
T D +L N ML+RG + R + +V+ DE H R
Sbjct: 112 ATYDGDTPTEERRWAREHARYVLTNPDMLHRGILPSHARWARFLRRLRYVVIDECHSYRG 171
Query: 178 KERGYVWEETLILL-------SDNVRFVFLSATIPNASQFAQWVSHLHHQPCHVVYTDYR 230
+V L + V FV SAT + + A S L P V D
Sbjct: 172 VFGSHVALVLRRLRRLCARYGASPV-FVLASATTADPAAAA---SRLIGAPVVAVTEDGS 227
Query: 231 PTP 233
P
Sbjct: 228 PRG 230
>gnl|CDD|214640 smart00382, AAA, ATPases associated with a variety of cellular
activities. AAA - ATPases associated with a variety of
cellular activities. This profile/alignment only detects
a fraction of this vast family. The poorly conserved
N-terminal helix is missing from the alignment.
Length = 148
Score = 33.1 bits (75), Expect = 0.088
Identities = 15/109 (13%), Positives = 29/109 (26%), Gaps = 15/109 (13%)
Query: 72 NQSVLVSAHTSAGKTVVAEYAIASSLKQSQRVIYTTPIKALSNQKYREFEEQFKDVGLIT 131
+ +L+ +GKT +A VIY L +
Sbjct: 2 GEVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKASG 61
Query: 132 GDVTINPSSSCLIMTTEILRNMLYRGSEITREVGWVIFDEIHYMRDKER 180
+ + + + + +I DEI + D E+
Sbjct: 62 SG----------ELRLRLALALARK-----LKPDVLILDEITSLLDAEQ 95
>gnl|CDD|238071 cd00124, MYSc, Myosin motor domain. 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 = 679
Score = 34.5 bits (80), Expect = 0.097
Identities = 13/54 (24%), Positives = 26/54 (48%), Gaps = 9/54 (16%)
Query: 72 NQSVLVSAHTSAGKTVVAEYAI--------ASSLKQSQRVIYTTPI-KALSNQK 116
NQS+++S + AGKT + + ++ ++++ PI +A N K
Sbjct: 86 NQSIIISGESGAGKTENTKLIMKYLASLAGSNDTGIEEKILAANPILEAFGNAK 139
>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 = 34.4 bits (79), Expect = 0.099
Identities = 17/89 (19%), Positives = 32/89 (35%), Gaps = 4/89 (4%)
Query: 31 EVALPPDLEYQPLAQSKEKPAREYPFVLDPFQ----KEAILCIENNQSVLVSAHTSAGKT 86
+ P+ Y L+ K P Q + + + +++ L+ A T GKT
Sbjct: 219 VASKKPETNYNTLSSLFSKNIDRLGLEYRPEQLKLAELVLDQLTHSEKSLIEAPTGTGKT 278
Query: 87 VVAEYAIASSLKQSQRVIYTTPIKALSNQ 115
+ + V+ +T K L +Q
Sbjct: 279 LGYLLPALYYAITEKPVVISTNTKVLQSQ 307
>gnl|CDD|237496 PRK13766, PRK13766, Hef nuclease; Provisional.
Length = 773
Score = 34.1 bits (79), Expect = 0.12
Identities = 29/115 (25%), Positives = 49/115 (42%), Gaps = 15/115 (13%)
Query: 72 NQSVLVSAHTSAGKTVVAEYAIASSLKQSQ-RVIYTTPIKALSNQKYREFEEQFK----D 126
++ LV T GKT +A IA L + +V+ P K L Q F +
Sbjct: 29 KKNTLVVLPTGLGKTAIALLVIAERLHKKGGKVLILAPTKPLVEQHAEFFRKFLNIPEEK 88
Query: 127 VGLITGDVTINP--------SSSCLIMTTEILRNMLYRGSEITREVGWVIFDEIH 173
+ + TG+ ++P + ++ T +++ N L G +V +IFDE H
Sbjct: 89 IVVFTGE--VSPEKRAELWEKAKVIVATPQVIENDLIAGRISLEDVSLLIFDEAH 141
>gnl|CDD|238676 cd01380, MYSc_type_V, Myosin motor domain, type V myosins. Myosins
V transport a variety of intracellular cargo
processively along actin filaments, such as membraneous
organelles and mRNA. 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 = 691
Score = 34.2 bits (79), Expect = 0.13
Identities = 20/61 (32%), Positives = 32/61 (52%), Gaps = 14/61 (22%)
Query: 70 ENNQSVLVSAHTSAGKTVVAEYAI-------ASSLKQS------QRVIYTTPI-KALSNQ 115
E NQS++VS + AGKTV A+Y + S ++ ++V+ + PI +A N
Sbjct: 84 EKNQSIIVSGESGAGKTVSAKYIMRYFASVGGSDSREVSETQVEEKVLASNPIMEAFGNA 143
Query: 116 K 116
K
Sbjct: 144 K 144
>gnl|CDD|226583 COG4098, comFA, Superfamily II DNA/RNA helicase required for DNA
uptake (late competence protein) [DNA replication,
recombination, and repair].
Length = 441
Score = 33.2 bits (76), Expect = 0.20
Identities = 20/55 (36%), Positives = 27/55 (49%), Gaps = 4/55 (7%)
Query: 58 LDPFQKEA----ILCIENNQSVLVSAHTSAGKTVVAEYAIASSLKQSQRVIYTTP 108
L P QK+A + I+ + LV A T AGKT + I +L Q RV +P
Sbjct: 98 LSPGQKKASNQLVQYIKQKEDTLVWAVTGAGKTEMIFQGIEQALNQGGRVCIASP 152
>gnl|CDD|226581 COG4096, HsdR, Type I site-specific restriction-modification
system, R (restriction) subunit and related helicases
[Defense mechanisms].
Length = 875
Score = 33.6 bits (77), Expect = 0.22
Identities = 21/73 (28%), Positives = 28/73 (38%), Gaps = 9/73 (12%)
Query: 57 VLDPFQKEAILCIE-----NNQSVLVSAHTSAGKTVVAEYAIASSLKQSQ---RVIYTTP 108
+Q AI + L+ T GKT A AI L +S RV++
Sbjct: 165 GPRYYQIIAIRRVIEAFSKGQNRALLVMATGTGKTRTA-IAIIDRLIKSGWVKRVLFLAD 223
Query: 109 IKALSNQKYREFE 121
AL +Q Y FE
Sbjct: 224 RNALVDQAYGAFE 236
>gnl|CDD|224120 COG1199, DinG, Rad3-related DNA helicases [Transcription / DNA
replication, recombination, and repair].
Length = 654
Score = 33.2 bits (76), Expect = 0.26
Identities = 20/71 (28%), Positives = 34/71 (47%), Gaps = 5/71 (7%)
Query: 55 PFVLDPFQKEAI----LCIENNQSVLVSAHTSAGKTVVA-EYAIASSLKQSQRVIYTTPI 109
F P Q+E ++ + +L+ A T GKT+ A+A + ++ ++VI +T
Sbjct: 13 GFEPRPEQREMAEAVAEALKGGEGLLIEAPTGTGKTLAYLLPALAYAREEGKKVIISTRT 72
Query: 110 KALSNQKYREF 120
KAL Q E
Sbjct: 73 KALQEQLLEED 83
>gnl|CDD|227910 COG5623, CLP1, Predicted GTPase subunit of the pre-mRNA cleavage
complex [Translation, ribosomal structure and
biogenesis].
Length = 424
Score = 32.6 bits (74), Expect = 0.33
Identities = 19/83 (22%), Positives = 33/83 (39%), Gaps = 4/83 (4%)
Query: 24 TLEACLHEVALPPDLEYQPLAQSKEKPAREYPFVLDPFQKEAILCIENNQSVLVSAHTSA 83
T C +V DL+Y S P + +K + E +V+V +
Sbjct: 55 TFSGCKLKVEGACDLQYV----SDTTPMPLIFNLHFFLEKRRMFNYEKGPTVMVVGGSQN 110
Query: 84 GKTVVAEYAIASSLKQSQRVIYT 106
GKT I+ +LK ++ ++T
Sbjct: 111 GKTSFCFTLISYALKLGKKPLFT 133
>gnl|CDD|215103 PLN00206, PLN00206, DEAD-box ATP-dependent RNA helicase;
Provisional.
Length = 518
Score = 32.5 bits (74), Expect = 0.42
Identities = 23/71 (32%), Positives = 32/71 (45%), Gaps = 10/71 (14%)
Query: 23 ETLEACLH-EVALPPDLEY------QPLAQSKEKPAREYPFVLDPFQKEAILCIENNQSV 75
LE + E PP L + L + E E+P P Q +AI + +S+
Sbjct: 105 RKLEIHVKGEAVPPPILSFSSCGLPPKLLLNLETAGYEFP---TPIQMQAIPAALSGRSL 161
Query: 76 LVSAHTSAGKT 86
LVSA T +GKT
Sbjct: 162 LVSADTGSGKT 172
>gnl|CDD|236877 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional.
Length = 434
Score = 32.2 bits (74), Expect = 0.42
Identities = 36/134 (26%), Positives = 53/134 (39%), Gaps = 18/134 (13%)
Query: 62 QKEAILCIENNQSVLVSAHTSAGKTV-----VAEYAIASSLKQS--QRVIYTTPIKALSN 114
Q EAI + + VL SA T GKT ++ + ++S R++ TP + L+
Sbjct: 28 QAEAIPPALDGRDVLGSAPTGTGKTAAFLLPALQHLLDFPRRKSGPPRILILTPTRELAM 87
Query: 115 QKYREFEEQFKDVGL----ITGDVTINPSSSCLIMTTEIL-----RNMLYRGSEI--TRE 163
Q + E K L ITG V + +I+ R + Y E R
Sbjct: 88 QVADQARELAKHTHLDIATITGGVAYMNHAEVFSENQDIVVATPGRLLQYIKEENFDCRA 147
Query: 164 VGWVIFDEIHYMRD 177
V +I DE M D
Sbjct: 148 VETLILDEADRMLD 161
>gnl|CDD|224121 COG1200, RecG, RecG-like helicase [DNA replication, recombination,
and repair / Transcription].
Length = 677
Score = 31.8 bits (73), Expect = 0.71
Identities = 23/91 (25%), Positives = 39/91 (42%), Gaps = 10/91 (10%)
Query: 55 PFVLDPFQKEAILCIENNQSV------LVSAHTSAGKTVVAEYAIASSLKQSQRVIYTTP 108
PF L QK I I + + L+ +GKTVVA A+ ++++ + P
Sbjct: 260 PFKLTNAQKRVIKEILADLASPVPMNRLLQGDVGSGKTVVALLAMLAAIEAGYQAALMAP 319
Query: 109 IKALSNQKYREFEEQFKD----VGLITGDVT 135
+ L+ Q Y + + V L+TG +
Sbjct: 320 TEILAEQHYESLRKWLEPLGIRVALLTGSLK 350
>gnl|CDD|222005 pfam13245, AAA_19, Part of AAA domain.
Length = 73
Score = 28.9 bits (65), Expect = 0.84
Identities = 18/76 (23%), Positives = 29/76 (38%), Gaps = 10/76 (13%)
Query: 64 EAILCIENNQSVLV---SAHTSAGKTVVAEYAIASSLKQSQRVIYTTPIKALSNQKYREF 120
EA+ + +S+ V T GKT A IA L + V+ P + + R
Sbjct: 1 EAVEAAASGRSLFVVDGGPGT--GKTATAAAIIARLLAAGRSVLVVAP----TGRAARRL 54
Query: 121 EEQFKDVGLITGDVTI 136
E+ + L T+
Sbjct: 55 RERLAALDL-ADASTL 69
>gnl|CDD|182986 PRK11131, PRK11131, ATP-dependent RNA helicase HrpA; Provisional.
Length = 1294
Score = 31.6 bits (72), Expect = 0.88
Identities = 21/73 (28%), Positives = 34/73 (46%), Gaps = 3/73 (4%)
Query: 17 MKVIVVETLEACLHEVALPPDLEYQPLAQSKE-KPAREYPFVLDPFQK-EAIL-CIENNQ 73
K+ + +A E+A Q + + +P YP L QK + IL I ++Q
Sbjct: 31 KKIKNPDAQQAIFQEIAKEIAQAAQRVLLREAARPEITYPENLPVSQKKQDILEAIRDHQ 90
Query: 74 SVLVSAHTSAGKT 86
V+V+ T +GKT
Sbjct: 91 VVIVAGETGSGKT 103
>gnl|CDD|236950 PRK11664, PRK11664, ATP-dependent RNA helicase HrpB; Provisional.
Length = 812
Score = 31.4 bits (72), Expect = 0.89
Identities = 23/71 (32%), Positives = 35/71 (49%), Gaps = 13/71 (18%)
Query: 144 IMTTEILRNMLYRGSEITREVGWVIFDEIHYMRDKERGYVWEETLIL-------LSDNVR 196
++T IL M+ R E++ VG VI DE H ER + L L L D+++
Sbjct: 98 VVTEGILTRMIQRDPELS-GVGLVILDEFH-----ERSLQADLALALLLDVQQGLRDDLK 151
Query: 197 FVFLSATIPNA 207
+ +SAT+ N
Sbjct: 152 LLIMSATLDND 162
>gnl|CDD|214580 smart00242, MYSc, Myosin. Large ATPases. ATPase; molecular motor.
Muscle contraction consists of a cyclical interaction
between myosin and actin. The core of the myosin
structure is similar in fold to that of kinesin.
Length = 677
Score = 31.0 bits (71), Expect = 1.1
Identities = 20/90 (22%), Positives = 34/90 (37%), Gaps = 25/90 (27%)
Query: 71 NNQSVLVSAHTSAGKTVVAEY------AIASSLKQ----SQRVIYTTPI-------KALS 113
NQS+++S + AGKT + +++ S + +++ + PI K L
Sbjct: 91 ENQSIIISGESGAGKTENTKKIMQYLASVSGSNTEVGSVEDQILESNPILEAFGNAKTLR 150
Query: 114 NQ------KYREFEEQFKDVGLITGDVTIN 137
N K+ E F G I G
Sbjct: 151 NNNSSRFGKF--IEIHFDAKGKIIGAKIET 178
>gnl|CDD|238547 cd01127, TrwB, Bacterial conjugation protein TrwB, ATP binding
domain. TrwB is a homohexamer encoded by conjugative
plasmids in Gram-negative bacteria. TrwB also has an all
alpha domain which has been hypothesized to be
responsible for DNA binding. TrwB is a component of Type
IV secretion and is responsible for the horizontal
transfer of DNA between bacteria.
Length = 410
Score = 30.8 bits (70), Expect = 1.2
Identities = 20/101 (19%), Positives = 31/101 (30%), Gaps = 31/101 (30%)
Query: 72 NQSVLVSAHTSAGKTVVAEYAIASSLKQSQRVIYTTPIKALSNQKYREFEEQFKDVGLIT 131
++ T GKT +AS + R I P ++ YR
Sbjct: 42 EAHTMIIGTTGTGKTTQIRELLASIRARGDRAIIYDPNGGFVSKFYRP-----------A 90
Query: 132 GDVTINPSSSCLIMTTEILRNMLYRGSEITREVGWVIFDEI 172
D+ +NP + R GW +F+EI
Sbjct: 91 TDIILNPFDA--------------------RCAGWSLFNEI 111
>gnl|CDD|233063 TIGR00631, uvrb, excinuclease ABC, B subunit. All proteins in this
family for wich functions are known are DNA helicases
that function in the nucleotide excision repair and are
endonucleases that make the 3' incision next to DNA
damage. They are part of a pathway requiring UvrA, UvrB,
UvrC, and UvrD homologs. This family is based on the
phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis,
Stanford University) [DNA metabolism, DNA replication,
recombination, and repair].
Length = 655
Score = 31.1 bits (71), Expect = 1.3
Identities = 25/85 (29%), Positives = 36/85 (42%), Gaps = 22/85 (25%)
Query: 55 PFVLD-PF-----QKEAILCIENNQS------VLVSAHTSAGKTVVAEYAIASSLKQSQR 102
F L PF Q +AI + + L+ T +GKT + +A+ + Q R
Sbjct: 1 LFKLHSPFQPAGDQPKAIAKLVEGLTDGEKHQTLLGV-TGSGKT----FTMANVIAQVNR 55
Query: 103 ---VIYTTPIKALSNQKYREFEEQF 124
VI K L+ Q Y EF+E F
Sbjct: 56 PTLVI--AHNKTLAAQLYNEFKEFF 78
>gnl|CDD|227355 COG5022, COG5022, Myosin heavy chain [Cytoskeleton].
Length = 1463
Score = 30.8 bits (70), Expect = 1.6
Identities = 12/52 (23%), Positives = 23/52 (44%), Gaps = 10/52 (19%)
Query: 72 NQSVLVSAHTSAGKTVVAEYAIASSLKQSQRVIYTTPIKALSNQKYREFEEQ 123
NQ++++S + AGKT A+ + Y + + S + E+Q
Sbjct: 152 NQTIIISGESGAGKTENAKRIMQ----------YLASVTSSSTVEISSIEKQ 193
>gnl|CDD|233040 TIGR00595, priA, primosomal protein N'. All proteins in this
family for which functions are known are components of
the primosome which is involved in replication, repair,
and recombination.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 = 505
Score = 30.4 bits (69), Expect = 1.7
Identities = 15/45 (33%), Positives = 22/45 (48%)
Query: 81 TSAGKTVVAEYAIASSLKQSQRVIYTTPIKALSNQKYREFEEQFK 125
T +GKT V AI L + V+ P AL+ Q + F+ +F
Sbjct: 6 TGSGKTEVYLQAIEKVLALGKSVLVLVPEIALTPQMIQRFKYRFG 50
>gnl|CDD|238550 cd01130, VirB11-like_ATPase, Type IV secretory pathway component
VirB11, and related ATPases. The homohexamer, VirB11 is
one of eleven Vir proteins, which are required for
T-pilus biogenesis and virulence in the transfer of
T-DNA from the Ti (tumor-inducing) plasmid of bacterial
to plant cells. The pilus is a fibrous cell surface
organelle, which mediates adhesion between bacteria
during conjugative transfer or between bacteria and host
eukaryotic cells during infection. VirB11- related
ATPases include the archaeal flagella biosynthesis
protein and the pilus assembly proteins CpaF/TadA and
TrbB. This alignment contains the C-terminal domain,
which is the ATPase.
Length = 186
Score = 29.6 bits (67), Expect = 1.8
Identities = 13/48 (27%), Positives = 26/48 (54%), Gaps = 2/48 (4%)
Query: 58 LDPFQKEAI-LCIENNQSVLVSAHTSAGKTVVAEYAIASSLKQSQRVI 104
P Q + L +E +++L+S T +GKT + A+ + + +R+I
Sbjct: 10 FSPLQAAYLWLAVEARKNILISGGTGSGKTTLLN-ALLAFIPPDERII 56
>gnl|CDD|215687 pfam00063, Myosin_head, Myosin head (motor domain).
Length = 679
Score = 30.3 bits (69), Expect = 1.8
Identities = 13/57 (22%), Positives = 26/57 (45%), Gaps = 12/57 (21%)
Query: 72 NQSVLVSAHTSAGKTVVAEY------AIASSLKQ-----SQRVIYTTPI-KALSNQK 116
NQ +++S + AGKT + +++ S +++ + PI +A N K
Sbjct: 85 NQCIVISGESGAGKTENTKKLMQYLASVSGSTPSAVGPLEDQILQSNPILEAFGNAK 141
>gnl|CDD|236912 PRK11448, hsdR, type I restriction enzyme EcoKI subunit R;
Provisional.
Length = 1123
Score = 30.3 bits (69), Expect = 2.0
Identities = 13/56 (23%), Positives = 23/56 (41%), Gaps = 12/56 (21%)
Query: 43 LAQSKEKPAR-------EYPFVLDPFQKEAILCIEN-----NQSVLVSAHTSAGKT 86
L E + +Y L +Q++AI +E + +L++ T GKT
Sbjct: 392 LESDIEAANQWLADEPFDYGLGLRYYQEDAIQAVEKAIVEGQREILLAMATGTGKT 447
>gnl|CDD|216004 pfam00580, UvrD-helicase, UvrD/REP helicase N-terminal domain.
The Rep family helicases are composed of four
structural domains. The Rep family function as dimers.
REP helicases catalyze ATP dependent unwinding of
double stranded DNA to single stranded DNA. Some
members have large insertions near to the
carboxy-terminus relative to other members of the
family.
Length = 267
Score = 29.9 bits (68), Expect = 2.3
Identities = 13/42 (30%), Positives = 22/42 (52%), Gaps = 2/42 (4%)
Query: 58 LDPFQKEAILCIENNQSVLVSAHTSAGKTVVAEYAIASSLKQ 99
L+P Q++A+ + +LV A +GKT V IA + +
Sbjct: 1 LNPEQRKAVTHL--GGPLLVLAGAGSGKTRVLTERIAYLILE 40
>gnl|CDD|236722 PRK10590, PRK10590, ATP-dependent RNA helicase RhlE; Provisional.
Length = 456
Score = 30.2 bits (68), Expect = 2.3
Identities = 23/92 (25%), Positives = 38/92 (41%), Gaps = 13/92 (14%)
Query: 60 PFQKEAILCIENNQSVLVSAHTSAGKTVVAEYAIASSLKQSQ---------RVIYTTPIK 110
P Q++AI + + ++ SA T GKT + L Q R + TP +
Sbjct: 26 PIQQQAIPAVLEGRDLMASAQTGTGKTAGFTLPLLQHLITRQPHAKGRRPVRALILTPTR 85
Query: 111 ALSNQKYREFEEQFKDVGL----ITGDVTINP 138
L+ Q + K + + + G V+INP
Sbjct: 86 ELAAQIGENVRDYSKYLNIRSLVVFGGVSINP 117
>gnl|CDD|238677 cd01381, MYSc_type_VII, Myosin motor domain, type VII myosins.
Myosins in this group have been associated with
functions in sensory systems such as vision and 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 = 671
Score = 29.7 bits (67), Expect = 2.7
Identities = 18/53 (33%), Positives = 29/53 (54%), Gaps = 8/53 (15%)
Query: 72 NQSVLVSAHTSAGKT----VVAEYAIASSLKQS---QRVIYTTPI-KALSNQK 116
NQ +++S + AGKT ++ +Y A S K S Q+++ PI +A N K
Sbjct: 86 NQCIIISGESGAGKTESTKLILQYLAAISGKHSWIEQQILEANPILEAFGNAK 138
>gnl|CDD|223288 COG0210, UvrD, Superfamily I DNA and RNA helicases [DNA
replication, recombination, and repair].
Length = 655
Score = 29.8 bits (67), Expect = 2.8
Identities = 15/37 (40%), Positives = 21/37 (56%), Gaps = 2/37 (5%)
Query: 58 LDPFQKEAILCIENNQSVLVSAHTSAGKTVVAEYAIA 94
L+P Q+EA+L + +LV A +GKT V IA
Sbjct: 3 LNPEQREAVLHPDGP--LLVLAGAGSGKTRVLTERIA 37
>gnl|CDD|216619 pfam01637, Arch_ATPase, Archaeal ATPase. This family contain a
conserved P-loop motif that is involved in binding ATP.
This family is almost exclusively found in
archaebacteria and particularly in Methanococcus
jannaschii that encodes sixteen members of this family.
Length = 223
Score = 29.2 bits (66), Expect = 3.4
Identities = 24/107 (22%), Positives = 41/107 (38%), Gaps = 10/107 (9%)
Query: 84 GKTVVAEYAIASSLKQSQRVIYTTPIKALSNQKYREFEEQ---FKDVGLITGDVTINPSS 140
GKT + + + RVIY P++ +K FEE + +G + I S
Sbjct: 32 GKTALLREFLEELRELGYRVIYYDPLRREFEEKLDRFEEAKRLAEALGDALPKIGIAKSK 91
Query: 141 SCLIMTTEILRNMLYRGSEITREVGWVIFDEIHYMR--DKERGYVWE 185
+ T + + +G +I +I DE+ Y + YV
Sbjct: 92 LAFLSLTLLFELLKRKGKKIA-----IIIDEVQYAIGLNGAESYVKL 133
>gnl|CDD|236461 PRK09302, PRK09302, circadian clock protein KaiC; Reviewed.
Length = 509
Score = 29.5 bits (67), Expect = 3.8
Identities = 9/32 (28%), Positives = 18/32 (56%)
Query: 74 SVLVSAHTSAGKTVVAEYAIASSLKQSQRVIY 105
+LVS T GKT++A ++ ++ +R +
Sbjct: 275 IILVSGATGTGKTLLASKFAEAACRRGERCLL 306
>gnl|CDD|238679 cd01383, MYSc_type_VIII, Myosin motor domain, plant-specific type
VIII myosins, a subgroup which has been associated with
endocytosis, cytokinesis, cell-to-cell coupling and
gating at plasmodesmata. 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 = 29.4 bits (66), Expect = 4.1
Identities = 24/80 (30%), Positives = 35/80 (43%), Gaps = 17/80 (21%)
Query: 70 ENNQSVLVSAHTSAGKTVVAEYAIA--SSLKQSQ----RVIYTTPI-------KALSNQK 116
E NQS+++S + AGKT A+ A+ +SL ++ T PI K N
Sbjct: 90 EVNQSIIISGESGAGKTETAKIAMQYLASLGGGSGIEYEILQTNPILEAFGNAKTSRNDN 149
Query: 117 YREF----EEQFKDVGLITG 132
F E F + G I+G
Sbjct: 150 SSRFGKLIEIHFSETGKISG 169
>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 = 28.6 bits (65), Expect = 4.1
Identities = 39/172 (22%), Positives = 71/172 (41%), Gaps = 32/172 (18%)
Query: 60 PFQKEAILCIENNQSVLVSAHTSAGKTVVAEYAI-------ASSLKQSQRVIYTTPIKAL 112
P Q AI + + + V+ A T +GKT A + I S K + + P + L
Sbjct: 24 PIQARAIPPLLSGRDVIGQAQTGSGKT--AAFLIPILEKLDPSPKKDGPQALILAPTREL 81
Query: 113 SNQKYREFEE--QFKD--VGLITGDVTINPSSSCLIMTTEIL-----R--NMLYRGSEIT 161
+ Q + + + V +I G +I+ L I+ R ++L RG
Sbjct: 82 ALQIAEVARKLGKHTNLKVVVIYGGTSIDKQIRKLKRGPHIVVATPGRLLDLLERGKLDL 141
Query: 162 REVGWVIFDEIHYMRDK--ERGYVWEETLI----LLSDNVRFVFLSATIPNA 207
+V +++ DE D+ + G+ E+ + LL + + + SAT+P
Sbjct: 142 SKVKYLVLDEA----DRMLDMGF--EDQIREILKLLPKDRQTLLFSATMPKE 187
>gnl|CDD|224118 COG1197, Mfd, Transcription-repair coupling factor (superfamily II
helicase) [DNA replication, recombination, and repair /
Transcription].
Length = 1139
Score = 29.5 bits (67), Expect = 4.2
Identities = 29/103 (28%), Positives = 41/103 (39%), Gaps = 18/103 (17%)
Query: 33 ALPPDLEYQPLAQSKEKPAREYPFVLDPFQKEAILCIENN--QSV----LVSAHTSAGKT 86
A PPD E+Q E+ +P+ P Q +AI ++ + L+ GKT
Sbjct: 576 AFPPDTEWQ------EEFEASFPYEETPDQLKAIEEVKRDMESGKPMDRLICGDVGFGKT 629
Query: 87 VVAEYAI---ASSLKQSQRVIYTTPIKALSNQKYREFEEQFKD 126
VA A KQ V P L+ Q Y F+E+F
Sbjct: 630 EVAMRAAFKAVMDGKQ---VAVLVPTTLLAQQHYETFKERFAG 669
>gnl|CDD|238540 cd01120, RecA-like_NTPases, RecA-like NTPases. This family includes
the NTP binding domain of F1 and V1 H+ATPases, DnaB and
related helicases as well as bacterial RecA and related
eukaryotic and archaeal recombinases. This group also
includes bacterial conjugation proteins and related DNA
transfer proteins involved in type II and type IV
secretion.
Length = 165
Score = 28.2 bits (63), Expect = 4.4
Identities = 21/109 (19%), Positives = 41/109 (37%), Gaps = 11/109 (10%)
Query: 75 VLVSAHTSAGKTVVAEYAIASSLKQSQRVIYTTPIKALSN--QKYREFEEQFKDVGLITG 132
+LV T +GKT +A + + +V+Y + + ++ + LI
Sbjct: 2 ILVFGPTGSGKTTLALQLALNIATKGGKVVYVDIEEEIEELTERLIGESLKGALDNLIIV 61
Query: 133 DVTIN-PSSSCLIMTTEILRNMLYRGSEITREVGWVIFDEIHYMRDKER 180
T + P+++ L+ E LR +I DE+ + R
Sbjct: 62 FATADDPAAARLLSKAERLRERGGD--------DLIILDELTRLVRALR 102
>gnl|CDD|99813 cd06217, FNR_iron_sulfur_binding_3, Iron-sulfur binding ferredoxin
reductase (FNR) proteins combine the FAD and NAD(P)
binding regions of FNR with an iron-sulfur binding
cluster domain. Ferredoxin-NADP+ (oxido)reductase is an
FAD-containing enzyme that catalyzes the reversible
electron transfer between NADP(H) and electron carrier
proteins such as ferredoxin and flavodoxin. Isoforms of
these flavoproteins (i.e. having a non-covalently bound
FAD as a prosthetic group) are present in chloroplasts,
mitochondria, and bacteria in which they participate in
a wide variety of redox metabolic pathways. The
C-terminal domain contains most of the NADP(H) binding
residues and the N-terminal domain interacts
non-covalently with the isoalloxazine rings of the
flavin molecule which lies largely in a large gap
between the two domains. Ferredoxin-NADP+ reductase
first accepts one electron from reduced ferredoxin to
form a flavin semiquinone intermediate. The enzyme then
accepts a second electron to form FADH2 which then
transfers two electrons and a proton to NADP+ to form
NADPH.
Length = 235
Score = 28.8 bits (65), Expect = 4.9
Identities = 12/31 (38%), Positives = 14/31 (45%)
Query: 73 QSVLVSAHTSAGKTVVAEYAIASSLKQSQRV 103
Q V + G T Y+IASS Q RV
Sbjct: 35 QHVDLRLTAIDGYTAQRSYSIASSPTQRGRV 65
>gnl|CDD|222875 PHA02558, uvsW, UvsW helicase; Provisional.
Length = 501
Score = 28.8 bits (65), Expect = 5.4
Identities = 16/65 (24%), Positives = 34/65 (52%), Gaps = 5/65 (7%)
Query: 61 FQKEAI-LCIENNQSVLVSAHTSAGKTVVAEYAIASSLKQ--SQRVIYTTPIKALSNQKY 117
+Q +A+ ++NN+ +L TSAGK+++ Y ++ + +V+ P +L Q
Sbjct: 118 YQYDAVYEGLKNNRRLLNLP-TSAGKSLIQ-YLLSRYYLENYEGKVLIIVPTTSLVTQMI 175
Query: 118 REFEE 122
+F +
Sbjct: 176 DDFVD 180
>gnl|CDD|182649 PRK10689, PRK10689, transcription-repair coupling factor;
Provisional.
Length = 1147
Score = 28.9 bits (65), Expect = 5.9
Identities = 25/92 (27%), Positives = 37/92 (40%), Gaps = 13/92 (14%)
Query: 39 EYQPLAQSKEKPAREYPFVLDPFQKEAI------LCIENNQSVLVSAHTSAGKTVVAEYA 92
+YQ S +PF P Q +AI +C LV GKT VA A
Sbjct: 589 QYQLFCDS-------FPFETTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRA 641
Query: 93 IASSLKQSQRVIYTTPIKALSNQKYREFEEQF 124
+++ ++V P L+ Q Y F ++F
Sbjct: 642 AFLAVENHKQVAVLVPTTLLAQQHYDNFRDRF 673
>gnl|CDD|221970 pfam13191, AAA_16, AAA ATPase domain. This family of domains
contain a P-loop motif that is characteristic of the AAA
superfamily.
Length = 154
Score = 27.9 bits (62), Expect = 6.0
Identities = 22/136 (16%), Positives = 45/136 (33%), Gaps = 16/136 (11%)
Query: 73 QSVLVSAHTSAGKTVVAEYAIASSLKQSQRVIY---------TTPIKALSNQKYREFEEQ 123
SVL++ + GKT + + L + + + ++ L Q RE +
Sbjct: 25 PSVLLTGPSGTGKTSLLRELLEGLLVAAGKCDQAERNPPYAFSQALRELLRQLLRELAAE 84
Query: 124 FKDVGLITGDVTINPSSSCLIMTTEILRNMLYRGSEITREVGWVIFDEIHYMRDKERGYV 183
+ L E+L +L R + ++ D++ + D+E +
Sbjct: 85 LLLLREALLAALGAELIEGLQDLVELLERLLARARPLV-----LVLDDLQWA-DEESLDL 138
Query: 184 WEETLILLSD-NVRFV 198
L L + V
Sbjct: 139 LAALLRRLERLPLLVV 154
>gnl|CDD|221758 pfam12762, DDE_Tnp_IS1595, ISXO2-like transposase domain. This
domain probably functions as an integrase that is found
in a wide variety of transposases, including ISXO2.
Length = 151
Score = 27.6 bits (62), Expect = 6.4
Identities = 9/24 (37%), Positives = 13/24 (54%), Gaps = 1/24 (4%)
Query: 359 LPQIENILPLLRRGI-GIHHGVKP 381
+E+ L+R I G +HGV P
Sbjct: 113 TNWVESFFSNLKRWILGTYHGVSP 136
>gnl|CDD|215422 PLN02788, PLN02788, phenylalanine-tRNA synthetase.
Length = 402
Score = 28.6 bits (64), Expect = 7.1
Identities = 15/41 (36%), Positives = 21/41 (51%), Gaps = 10/41 (24%)
Query: 287 PKGGVQTNCFKIVKMIMERNLAPVIVFSFSKKDCEIYAMQM 327
PK G ++C++IV MER+L D EI A+Q
Sbjct: 357 PKKGKTSHCYRIVYRSMERSLT----------DEEINALQD 387
>gnl|CDD|227780 COG5493, COG5493, Uncharacterized conserved protein containing a
coiled-coil domain [Function unknown].
Length = 231
Score = 27.9 bits (62), Expect = 8.3
Identities = 13/29 (44%), Positives = 19/29 (65%), Gaps = 3/29 (10%)
Query: 158 SEITREVGWVIFDEIHYMRDKERGYVWEE 186
EI REVG+V+ ++Y DKE G+V+
Sbjct: 124 REILREVGYVVERWLYY--DKE-GHVYGH 149
>gnl|CDD|182349 PRK10271, thiK, thiamine kinase; Provisional.
Length = 188
Score = 27.8 bits (62), Expect = 8.7
Identities = 7/20 (35%), Positives = 12/20 (60%)
Query: 203 TIPNASQFAQWVSHLHHQPC 222
+P+ ++ A + HLH QP
Sbjct: 13 YLPDTNELAGLLYHLHQQPR 32
>gnl|CDD|184733 PRK14540, PRK14540, nucleoside diphosphate kinase; Provisional.
Length = 134
Score = 27.1 bits (60), Expect = 8.8
Identities = 14/35 (40%), Positives = 17/35 (48%)
Query: 303 MERNLAPVIVFSFSKKDCEIYAMQMAKLNFNETEE 337
+ER L I+ F K EI M+M KL EE
Sbjct: 14 VERKLIGKIIQRFENKGFEIVEMKMLKLTREMAEE 48
>gnl|CDD|172499 PRK13998, PRK13998, potassium-transporting ATPase subunit C;
Provisional.
Length = 186
Score = 27.4 bits (60), Expect = 9.8
Identities = 15/63 (23%), Positives = 31/63 (49%), Gaps = 3/63 (4%)
Query: 71 NNQSVLVSAHTSAGKTVVAEYAIASSLKQSQRVIYTTPIKALSNQKYREFEEQFKDVGLI 130
N +V + A TS+G + + ++LKQ+ R+ + +S + + + K G++
Sbjct: 111 GNSNVTIDAATSSGSGLDPHITVENALKQAPRI---ADARHVSTSRVADLIQHRKQRGVL 167
Query: 131 TGD 133
T D
Sbjct: 168 TND 170
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 0.136 0.408
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: 19,930,725
Number of extensions: 1918687
Number of successful extensions: 1815
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1767
Number of HSP's successfully gapped: 82
Length of query: 391
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 292
Effective length of database: 6,546,556
Effective search space: 1911594352
Effective search space used: 1911594352
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: 60 (27.1 bits)