RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3143
(337 letters)
>gnl|CDD|238167 cd00268, DEADc, DEAD-box helicases. A diverse family of proteins
involved in ATP-dependent RNA unwinding, needed in a
variety of cellular processes including splicing,
ribosome biogenesis and RNA degradation. The name
derives from the sequence of the Walker B motif (motif
II). This domain contains the ATP- binding region.
Length = 203
Score = 274 bits (703), Expect = 1e-92
Identities = 100/205 (48%), Positives = 134/205 (65%), Gaps = 2/205 (0%)
Query: 93 FHQMNLSRPLLKAIGALNYIYPTPIQAATIPVALLGRDICGCAATGTGKTAAFMLPILER 152
F ++ LS LL+ I AL + PTPIQA IP L GRD+ G A TG+GKTAAF++PILE+
Sbjct: 1 FEELGLSPELLRGIYALGFEKPTPIQARAIPPLLSGRDVIGQAQTGSGKTAAFLIPILEK 60
Query: 153 LLYKPRDDQNTRVLVLVPTRELGVQVYQVTRQLAQFTSVEVALSVGGLEVKVQESVLRKC 212
L P+ D + L+L PTREL +Q+ +V R+L + T+++V + GG + Q L++
Sbjct: 61 LDPSPKKDG-PQALILAPTRELALQIAEVARKLGKHTNLKVVVIYGGTSIDKQIRKLKRG 119
Query: 213 PDIVIATPGRLLDHLHNTPSFSLSDIEVLVLDEADRMLDEHFASQMKEIIRLCSRTRQTM 272
P IV+ATPGRLLD L LS ++ LVLDEADRMLD F Q++EI++L + RQT+
Sbjct: 120 PHIVVATPGRLLDLLERG-KLDLSKVKYLVLDEADRMLDMGFEDQIREILKLLPKDRQTL 178
Query: 273 LFSATMTDAVNDLVSVSLTRPVRVF 297
LFSATM V DL L PVR+
Sbjct: 179 LFSATMPKEVRDLARKFLRNPVRIL 203
>gnl|CDD|223587 COG0513, SrmB, Superfamily II DNA and RNA helicases [DNA
replication, recombination, and repair / Transcription /
Translation, ribosomal structure and biogenesis].
Length = 513
Score = 247 bits (632), Expect = 5e-78
Identities = 94/226 (41%), Positives = 134/226 (59%), Gaps = 5/226 (2%)
Query: 91 SSFHQMNLSRPLLKAIGALNYIYPTPIQAATIPVALLGRDICGCAATGTGKTAAFMLPIL 150
F + LS LL+A+ L + PTPIQ A IP+ L GRD+ G A TGTGKTAAF+LP+L
Sbjct: 29 PEFASLGLSPELLQALKDLGFEEPTPIQLAAIPLILAGRDVLGQAQTGTGKTAAFLLPLL 88
Query: 151 ERLLYKPRDDQNTRVLVLVPTRELGVQVYQVTRQLAQFTS-VEVALSVGGLEVKVQESVL 209
+++L L+L PTREL VQ+ + R+L + + VA+ GG+ ++ Q L
Sbjct: 89 QKILKSVERKYV-SALILAPTRELAVQIAEELRKLGKNLGGLRVAVVYGGVSIRKQIEAL 147
Query: 210 RKCPDIVIATPGRLLDHLHNTPSFSLSDIEVLVLDEADRMLDEHFASQMKEIIRLCSRTR 269
++ DIV+ATPGRLLD + LS +E LVLDEADRMLD F +++I++ R
Sbjct: 148 KRGVDIVVATPGRLLDLIKRG-KLDLSGVETLVLDEADRMLDMGFIDDIEKILKALPPDR 206
Query: 270 QTMLFSATMTDAVNDLVSVSLTRP--VRVFVDNNHEVALNLRQEFV 313
QT+LFSATM D + +L L P + V V+ ++Q ++
Sbjct: 207 QTLLFSATMPDDIRELARRYLNDPVEIEVSVEKLERTLKKIKQFYL 252
>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 = 196 bits (500), Expect = 1e-62
Identities = 76/172 (44%), Positives = 103/172 (59%), Gaps = 4/172 (2%)
Query: 115 TPIQAATIPVALLGRDICGCAATGTGKTAAFMLPILERLLYKPRDDQNTRVLVLVPTREL 174
TPIQA IP L G+D+ A TG+GKT AF+LPIL+ LL K + LVL PTREL
Sbjct: 1 TPIQAQAIPAILSGKDVLVQAPTGSGKTLAFLLPILQALLPKKGG---PQALVLAPTREL 57
Query: 175 GVQVYQVTRQLAQFTSVEVALSVGGLEVKVQESVLRK-CPDIVIATPGRLLDHLHNTPSF 233
Q+Y+ ++L + + VAL GG +K Q L+K DI++ TPGRLLD L
Sbjct: 58 AEQIYEELKKLFKILGLRVALLTGGTSLKEQARKLKKGKADILVGTPGRLLDLLRRGKLK 117
Query: 234 SLSDIEVLVLDEADRMLDEHFASQMKEIIRLCSRTRQTMLFSATMTDAVNDL 285
L ++++LVLDEA R+LD F ++EI+ RQ +L SAT+ + DL
Sbjct: 118 LLKNLKLLVLDEAHRLLDMGFGDDLEEILSRLPPDRQILLLSATLPRNLEDL 169
>gnl|CDD|236877 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional.
Length = 434
Score = 196 bits (501), Expect = 2e-59
Identities = 94/209 (44%), Positives = 123/209 (58%), Gaps = 3/209 (1%)
Query: 93 FHQMNLSRPLLKAIGALNYIYPTPIQAATIPVALLGRDICGCAATGTGKTAAFMLPILER 152
F ++ L LL+A+ Y PT IQA IP AL GRD+ G A TGTGKTAAF+LP L+
Sbjct: 3 FSELELDESLLEALQDKGYTRPTAIQAEAIPPALDGRDVLGSAPTGTGKTAAFLLPALQH 62
Query: 153 LLYKPRDDQN-TRVLVLVPTRELGVQVYQVTRQLAQFTSVEVALSVGGLEVKVQESVLRK 211
LL PR R+L+L PTREL +QV R+LA+ T +++A GG+ V +
Sbjct: 63 LLDFPRRKSGPPRILILTPTRELAMQVADQARELAKHTHLDIATITGGVAYMNHAEVFSE 122
Query: 212 CPDIVIATPGRLLDHLHNTPSFSLSDIEVLVLDEADRMLDEHFASQMKEIIRLCSRTRQT 271
DIV+ATPGRLL ++ +F +E L+LDEADRMLD FA ++ I +QT
Sbjct: 123 NQDIVVATPGRLLQYIKEE-NFDCRAVETLILDEADRMLDMGFAQDIETIAAETRWRKQT 181
Query: 272 MLFSATMT-DAVNDLVSVSLTRPVRVFVD 299
+LFSAT+ DAV D L PV V +
Sbjct: 182 LLFSATLEGDAVQDFAERLLNDPVEVEAE 210
>gnl|CDD|236977 PRK11776, PRK11776, ATP-dependent RNA helicase DbpA; Provisional.
Length = 460
Score = 189 bits (483), Expect = 2e-56
Identities = 97/254 (38%), Positives = 136/254 (53%), Gaps = 16/254 (6%)
Query: 90 NSSFHQMNLSRPLLKAIGALNYIYPTPIQAATIPVALLGRDICGCAATGTGKTAAFMLPI 149
++F + L LL + L Y TPIQA ++P L G+D+ A TG+GKTAAF L +
Sbjct: 3 MTAFSTLPLPPALLANLNELGYTEMTPIQAQSLPAILAGKDVIAQAKTGSGKTAAFGLGL 62
Query: 150 LERLLYKPRDDQNTRV--LVLVPTRELGVQVYQVTRQLAQFT-SVEVALSVGGLEVKVQE 206
L++L D + RV LVL PTREL QV + R+LA+F +++V GG+ + Q
Sbjct: 63 LQKL-----DVKRFRVQALVLCPTRELADQVAKEIRRLARFIPNIKVLTLCGGVPMGPQI 117
Query: 207 SVLRKCPDIVIATPGRLLDHLHNTPSFSLSDIEVLVLDEADRMLDEHFASQMKEIIRLCS 266
L I++ TPGR+LDHL + L + LVLDEADRMLD F + IIR
Sbjct: 118 DSLEHGAHIIVGTPGRILDHLRKG-TLDLDALNTLVLDEADRMLDMGFQDAIDAIIRQAP 176
Query: 267 RTRQTMLFSATMTDAVNDLVSVSLTRPVRVFVDNNHEVALNLRQEFVSFSNIDEVRLYNV 326
RQT+LFSAT + + + PV V V++ H+ + Q F S + RL
Sbjct: 177 ARRQTLLFSATYPEGIAAISQRFQRDPVEVKVESTHD-LPAIEQRFYEVSPDE--RL-PA 232
Query: 327 LGLMLLR---ENCL 337
L +LL E+C+
Sbjct: 233 LQRLLLHHQPESCV 246
>gnl|CDD|234938 PRK01297, PRK01297, ATP-dependent RNA helicase RhlB; Provisional.
Length = 475
Score = 171 bits (434), Expect = 2e-49
Identities = 102/251 (40%), Positives = 142/251 (56%), Gaps = 11/251 (4%)
Query: 86 PVEENSSFHQMNLSRPLLKAIGALNYIYPTPIQAATIPVALLGRDICGCAATGTGKTAAF 145
P E + FH NL+ L+ AI L + Y TPIQA + L G D G A TGTGKTAAF
Sbjct: 82 PQEGKTRFHDFNLAPELMHAIHDLGFPYCTPIQAQVLGYTLAGHDAIGRAQTGTGKTAAF 141
Query: 146 MLPILERLLYKPRDDQ----NTRVLVLVPTRELGVQVYQVTRQLAQFTSVEVALSVGGLE 201
++ I+ +LL P + R L++ PTREL VQ+ + L ++T + V VGG++
Sbjct: 142 LISIINQLLQTPPPKERYMGEPRALIIAPTRELVVQIAKDAAALTKYTGLNVMTFVGGMD 201
Query: 202 VKVQESVL--RKCPDIVIATPGRLLDHLHNTPSFSLSDIEVLVLDEADRMLDEHFASQMK 259
Q L R C DI++ATPGRLLD + L +EV+VLDEADRMLD F Q++
Sbjct: 202 FDKQLKQLEARFC-DILVATPGRLLD-FNQRGEVHLDMVEVMVLDEADRMLDMGFIPQVR 259
Query: 260 EIIRLCSRT--RQTMLFSATMTDAVNDLVSVSLTRPVRVFVDNNHEVALNLRQEFVSFSN 317
+IIR R RQT+LFSAT TD V +L T P V ++ + + + Q + +
Sbjct: 260 QIIRQTPRKEERQTLLFSATFTDDVMNLAKQWTTDPAIVEIEPENVASDTVEQHVYAVAG 319
Query: 318 IDEVR-LYNVL 327
D+ + LYN++
Sbjct: 320 SDKYKLLYNLV 330
>gnl|CDD|214692 smart00487, DEXDc, DEAD-like helicases superfamily.
Length = 201
Score = 162 bits (411), Expect = 7e-49
Identities = 70/185 (37%), Positives = 102/185 (55%), Gaps = 7/185 (3%)
Query: 114 PTPIQAATIPVALLG-RDICGCAATGTGKTAAFMLPILERLLYKPRDDQNTRVLVLVPTR 172
P Q I L G RD+ A TG+GKT A +LP LE L RVLVLVPTR
Sbjct: 9 LRPYQKEAIEALLSGLRDVILAAPTGSGKTLAALLPALEALKRGK----GGRVLVLVPTR 64
Query: 173 ELGVQVYQVTRQLAQFTSVEVALSVGGLEVKVQESVLRK-CPDIVIATPGRLLDHLHNTP 231
EL Q + ++L ++V GG + Q L DI++ TPGRLLD L N
Sbjct: 65 ELAEQWAEELKKLGPSLGLKVVGLYGGDSKREQLRKLESGKTDILVTTPGRLLDLLENDK 124
Query: 232 SFSLSDIEVLVLDEADRMLDEHFASQMKEIIRLCSRTRQTMLFSATMTDAVNDLVSVSLT 291
SLS++++++LDEA R+LD F Q++++++L + Q +L SAT + + +L+ + L
Sbjct: 125 -LSLSNVDLVILDEAHRLLDGGFGDQLEKLLKLLPKNVQLLLLSATPPEEIENLLELFLN 183
Query: 292 RPVRV 296
PV +
Sbjct: 184 DPVFI 188
>gnl|CDD|236722 PRK10590, PRK10590, ATP-dependent RNA helicase RhlE; Provisional.
Length = 456
Score = 163 bits (415), Expect = 9e-47
Identities = 90/247 (36%), Positives = 135/247 (54%), Gaps = 7/247 (2%)
Query: 92 SFHQMNLSRPLLKAIGALNYIYPTPIQAATIPVALLGRDICGCAATGTGKTAAFMLPILE 151
SF + LS +L+A+ Y PTPIQ IP L GRD+ A TGTGKTA F LP+L+
Sbjct: 2 SFDSLGLSPDILRAVAEQGYREPTPIQQQAIPAVLEGRDLMASAQTGTGKTAGFTLPLLQ 61
Query: 152 RLLYK---PRDDQNTRVLVLVPTRELGVQVYQVTRQLAQFTSVEVALSVGGLEVKVQESV 208
L+ + + + R L+L PTREL Q+ + R +++ ++ + GG+ + Q
Sbjct: 62 HLITRQPHAKGRRPVRALILTPTRELAAQIGENVRDYSKYLNIRSLVVFGGVSINPQMMK 121
Query: 209 LRKCPDIVIATPGRLLDHLHNTPSFSLSDIEVLVLDEADRMLDEHFASQMKEIIRLCSRT 268
LR D+++ATPGRLLD H + L +E+LVLDEADRMLD F ++ ++
Sbjct: 122 LRGGVDVLVATPGRLLDLEHQN-AVKLDQVEILVLDEADRMLDMGFIHDIRRVLAKLPAK 180
Query: 269 RQTMLFSATMTDAVNDLVSVSLTRPVRVFVDNNHEVALNLRQEFVSFSNIDEVRLYNVLG 328
RQ +LFSAT +D + L L P+ + V + + + Q V F +D+ R +L
Sbjct: 181 RQNLLFSATFSDDIKALAEKLLHNPLEIEVARRNTASEQVTQ-HVHF--VDKKRKRELLS 237
Query: 329 LMLLREN 335
M+ + N
Sbjct: 238 QMIGKGN 244
>gnl|CDD|235314 PRK04837, PRK04837, ATP-dependent RNA helicase RhlB; Provisional.
Length = 423
Score = 157 bits (400), Expect = 1e-44
Identities = 85/237 (35%), Positives = 124/237 (52%), Gaps = 7/237 (2%)
Query: 93 FHQMNLSRPLLKAIGALNYIYPTPIQAATIPVALLGRDICGCAATGTGKTAAFMLPILER 152
F L +++A+ + TPIQA +P+ L GRD+ G A TGTGKT AF+
Sbjct: 10 FSDFALHPQVVEALEKKGFHNCTPIQALALPLTLAGRDVAGQAQTGTGKTMAFLTATFHY 69
Query: 153 LLYKP----RDDQNTRVLVLVPTRELGVQVYQVTRQLAQFTSVEVALSVGGLEVKVQESV 208
LL P R R L++ PTREL VQ++ LAQ T +++ L+ GG Q V
Sbjct: 70 LLSHPAPEDRKVNQPRALIMAPTRELAVQIHADAEPLAQATGLKLGLAYGGDGYDKQLKV 129
Query: 209 LRKCPDIVIATPGRLLDHLHNTPSFSLSDIEVLVLDEADRMLDEHFASQMKEIIRLC--S 266
L DI+I T GRL+D+ +L I+V+VLDEADRM D F ++ + R +
Sbjct: 130 LESGVDILIGTTGRLIDYAKQN-HINLGAIQVVVLDEADRMFDLGFIKDIRWLFRRMPPA 188
Query: 267 RTRQTMLFSATMTDAVNDLVSVSLTRPVRVFVDNNHEVALNLRQEFVSFSNIDEVRL 323
R MLFSAT++ V +L + P V V+ + +++E SN +++RL
Sbjct: 189 NQRLNMLFSATLSYRVRELAFEHMNNPEYVEVEPEQKTGHRIKEELFYPSNEEKMRL 245
>gnl|CDD|235307 PRK04537, PRK04537, ATP-dependent RNA helicase RhlB; Provisional.
Length = 572
Score = 159 bits (403), Expect = 3e-44
Identities = 91/247 (36%), Positives = 142/247 (57%), Gaps = 8/247 (3%)
Query: 90 NSSFHQMNLSRPLLKAIGALNYIYPTPIQAATIPVALLGRDICGCAATGTGKTAAFMLPI 149
+ +F +L LL + + + TPIQA T+PVAL G D+ G A TGTGKT AF++ +
Sbjct: 8 DLTFSSFDLHPALLAGLESAGFTRCTPIQALTLPVALPGGDVAGQAQTGTGKTLAFLVAV 67
Query: 150 LERLLYKP----RDDQNTRVLVLVPTRELGVQVYQVTRQLAQFTSVEVALSVGGLEVKVQ 205
+ RLL +P R ++ R L+L PTREL +Q+++ + + AL GG++ Q
Sbjct: 68 MNRLLSRPALADRKPEDPRALILAPTRELAIQIHKDAVKFGADLGLRFALVYGGVDYDKQ 127
Query: 206 ESVLRKCPDIVIATPGRLLDHLHNTPSFSLSDIEVLVLDEADRMLDEHFASQMKEII-RL 264
+L++ D++IATPGRL+D++ SL E+ VLDEADRM D F ++ ++ R+
Sbjct: 128 RELLQQGVDVIIATPGRLIDYVKQHKVVSLHACEICVLDEADRMFDLGFIKDIRFLLRRM 187
Query: 265 CSR-TRQTMLFSATMTDAVNDLVSVSLTRPVRVFVDNNHEVALNLRQEFVSFSNIDEVRL 323
R TRQT+LFSAT++ V +L + P ++ V+ A +RQ + DE +
Sbjct: 188 PERGTRQTLLFSATLSHRVLELAYEHMNEPEKLVVETETITAARVRQRI--YFPADEEKQ 245
Query: 324 YNVLGLM 330
+LGL+
Sbjct: 246 TLLLGLL 252
>gnl|CDD|236941 PRK11634, PRK11634, ATP-dependent RNA helicase DeaD; Provisional.
Length = 629
Score = 153 bits (387), Expect = 1e-41
Identities = 92/218 (42%), Positives = 117/218 (53%), Gaps = 13/218 (5%)
Query: 88 EENSSFHQMNLSRPLLKAIGALNYIYPTPIQAATIPVALLGRDICGCAATGTGKTAAFML 147
E ++F + L P+L+A+ L Y P+PIQA IP L GRD+ G A TG+GKTAAF L
Sbjct: 3 EFETTFADLGLKAPILEALNDLGYEKPSPIQAECIPHLLNGRDVLGMAQTGSGKTAAFSL 62
Query: 148 PILERLLYKPRDDQNTRVLVLVPTRELGVQVYQVTRQLA-QFTSVEVALSVGGLEVKVQE 206
P+L L + + Q +LVL PTREL VQV + + V V GG VQ
Sbjct: 63 PLLHNLDPELKAPQ---ILVLAPTRELAVQVAEAMTDFSKHMRGVNVVALYGGQRYDVQL 119
Query: 207 SVLRKCPDIVIATPGRLLDHLHNTPSFSLSDIEVLVLDEADRMLDEHFASQMKEIIRLCS 266
LR+ P IV+ TPGRLLDHL + LS + LVLDEAD ML F ++ I+
Sbjct: 120 RALRQGPQIVVGTPGRLLDHL-KRGTLDLSKLSGLVLDEADEMLRMGFIEDVETIMAQIP 178
Query: 267 RTRQTMLFSATMTDAVNDLVSVSLTRPVRVFVDNNHEV 304
QT LFSATM +A+ R R F+ EV
Sbjct: 179 EGHQTALFSATMPEAIR--------RITRRFMKEPQEV 208
>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 = 139 bits (353), Expect = 6e-41
Identities = 62/150 (41%), Positives = 87/150 (58%), Gaps = 6/150 (4%)
Query: 129 RDICGCAATGTGKTAAFMLPILERLLYKPRDDQNTRVLVLVPTRELGVQVYQVTRQLAQF 188
RD+ A TG+GKT A +LPILE L + +VLVL PTREL QV + ++L
Sbjct: 1 RDVLLAAPTGSGKTLAALLPILELL----DSLKGGQVLVLAPTRELANQVAERLKELFGE 56
Query: 189 TSVEVALSVGGLEVKVQESVLRKCPDIVIATPGRLLDHLHNTPSFSLSDIEVLVLDEADR 248
++V +GG +K QE +L DIV+ TPGRLLD L SL +++L+LDEA R
Sbjct: 57 -GIKVGYLIGGTSIKQQEKLLSGKTDIVVGTPGRLLDELER-LKLSLKKLDLLILDEAHR 114
Query: 249 MLDEHFASQMKEIIRLCSRTRQTMLFSATM 278
+L++ F +I+ + RQ +L SAT
Sbjct: 115 LLNQGFGLLGLKILLKLPKDRQVLLLSATP 144
>gnl|CDD|240273 PTZ00110, PTZ00110, helicase; Provisional.
Length = 545
Score = 142 bits (360), Expect = 3e-38
Identities = 85/224 (37%), Positives = 123/224 (54%), Gaps = 14/224 (6%)
Query: 82 EDAP-PVEENSSFHQMNLSRPLLKAIGALNYIYPTPIQAATIPVALLGRDICGCAATGTG 140
E+ P PV SF + +LK++ + PTPIQ P+AL GRD+ G A TG+G
Sbjct: 123 ENVPKPVV---SFEYTSFPDYILKSLKNAGFTEPTPIQVQGWPIALSGRDMIGIAETGSG 179
Query: 141 KTAAFMLP----ILERLLYKPRDDQNTRVLVLVPTRELGVQVYQVTRQLAQFTSVEVALS 196
KT AF+LP I + L + D VLVL PTREL Q+ + + + + ++
Sbjct: 180 KTLAFLLPAIVHINAQPLLRYGD--GPIVLVLAPTRELAEQIREQCNKFGASSKIRNTVA 237
Query: 197 VGGLEVKVQESVLRKCPDIVIATPGRLLDHLHNTPSFSLSDIEVLVLDEADRMLDEHFAS 256
GG+ + Q LR+ +I+IA PGRL+D L + + +L + LVLDEADRMLD F
Sbjct: 238 YGGVPKRGQIYALRRGVEILIACPGRLIDFLESNVT-NLRRVTYLVLDEADRMLDMGFEP 296
Query: 257 QMKEIIRLCSRTRQTMLFSATMTDAVNDLVSVSLTR--PVRVFV 298
Q+++I+ RQT+++SAT V L + L + PV V V
Sbjct: 297 QIRKIVSQIRPDRQTLMWSATWPKEVQSL-ARDLCKEEPVHVNV 339
>gnl|CDD|215103 PLN00206, PLN00206, DEAD-box ATP-dependent RNA helicase;
Provisional.
Length = 518
Score = 136 bits (345), Expect = 2e-36
Identities = 80/218 (36%), Positives = 117/218 (53%), Gaps = 18/218 (8%)
Query: 92 SFHQMNLSRPLLKAIGALNYIYPTPIQAATIPVALLGRDICGCAATGTGKTAAFMLPILE 151
SF L LL + Y +PTPIQ IP AL GR + A TG+GKTA+F++PI+
Sbjct: 122 SFSSCGLPPKLLLNLETAGYEFPTPIQMQAIPAALSGRSLLVSADTGSGKTASFLVPIIS 181
Query: 152 RL----LYKPRDDQNTRVLVLVPTRELGVQVYQVTRQLAQFTSVEVALSVGGLEVKVQES 207
R P + +N +VL PTREL VQV + L + + AL VGG + Q
Sbjct: 182 RCCTIRSGHPSEQRNPLAMVLTPTRELCVQVEDQAKVLGKGLPFKTALVVGGDAMPQQLY 241
Query: 208 VLRKCPDIVIATPGRLLDHL--HNTPSFSLSDIEVLVLDEADRMLDEHFASQMKEIIRLC 265
+++ ++++ TPGRL+D L H+ L ++ VLVLDE D ML+ F Q+ +I +
Sbjct: 242 RIQQGVELIVGTPGRLIDLLSKHD---IELDNVSVLVLDEVDCMLERGFRDQVMQIFQAL 298
Query: 266 SRTRQTMLFSATMTDAV--------NDLVSVSLTRPVR 295
S Q +LFSAT++ V D++ +S+ P R
Sbjct: 299 S-QPQVLLFSATVSPEVEKFASSLAKDIILISIGNPNR 335
>gnl|CDD|185609 PTZ00424, PTZ00424, helicase 45; Provisional.
Length = 401
Score = 126 bits (318), Expect = 3e-33
Identities = 70/222 (31%), Positives = 112/222 (50%), Gaps = 4/222 (1%)
Query: 92 SFHQMNLSRPLLKAIGALNYIYPTPIQAATIPVALLGRDICGCAATGTGKTAAFMLPILE 151
SF + L+ LL+ I + + P+ IQ I L G D G A +GTGKTA F++ L+
Sbjct: 29 SFDALKLNEDLLRGIYSYGFEKPSAIQQRGIKPILDGYDTIGQAQSGTGKTATFVIAALQ 88
Query: 152 RLLYKPRDDQNTRVLVLVPTRELGVQVYQVTRQLAQFTSVEVALSVGGLEVKVQESVLRK 211
+ Y + L+L PTREL Q+ +V L + V VGG V+ + L+
Sbjct: 89 LIDYDLN---ACQALILAPTRELAQQIQKVVLALGDYLKVRCHACVGGTVVRDDINKLKA 145
Query: 212 CPDIVIATPGRLLDHLHNTPSFSLSDIEVLVLDEADRMLDEHFASQMKEIIRLCSRTRQT 271
+V+ TPGR+ D + + + D+++ +LDEAD ML F Q+ ++ + Q
Sbjct: 146 GVHMVVGTPGRVYDMI-DKRHLRVDDLKLFILDEADEMLSRGFKGQIYDVFKKLPPDVQV 204
Query: 272 MLFSATMTDAVNDLVSVSLTRPVRVFVDNNHEVALNLRQEFV 313
LFSATM + + +L + + P R+ V + +RQ +V
Sbjct: 205 ALFSATMPNEILELTTKFMRDPKRILVKKDELTLEGIRQFYV 246
>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 = 61.7 bits (150), Expect = 2e-10
Identities = 61/243 (25%), Positives = 99/243 (40%), Gaps = 43/243 (17%)
Query: 59 KEGKLKQVEAEEYEENEGGKEFFEDAPPV--EENSSFHQMNLSRPLLKA-IGALNYIYPT 115
E + + E +E ++ +A P E +L L+KA I L Y +
Sbjct: 18 TEYLEDEFKDAEGQEGSILRDPEIEARPGKTSEFPELRDESLKSALVKAGIERL-YSH-- 74
Query: 116 PIQAATIPVALLGRDICGCAATGTGKTAAFMLPILERLLYKPRDDQNTRVLVLVPTRELG 175
Q + + GR++ TG+GKT +F+LPIL+ LL P R L+L PT L
Sbjct: 75 --QVDALRLIREGRNVVVTTGTGSGKTESFLLPILDHLLRDPSA----RALLLYPTNALA 128
Query: 176 VQVYQVTRQLAQFTS-----VEVALSVGGLEVKVQESVLRKCPDIVIATPGRLLDHL--- 227
Q R L + S V G + + +++R PDI++ P +L +L
Sbjct: 129 ND--QAER-LRELISDLPGKVTFGRYTGDTPPEERRAIIRNPPDILLTNP-DMLHYLLLR 184
Query: 228 -HNTPSFSLSDIEVLVLDEADRMLDEH-----FASQM-------KEIIRLCSRTRQTMLF 274
H+ + L +++ LV+DE H S++ +R Q +
Sbjct: 185 NHDAWLWLLRNLKYLVVDEL------HTYRGVQGSEVALLLRRLLRRLRRYGSPLQIICT 238
Query: 275 SAT 277
SAT
Sbjct: 239 SAT 241
>gnl|CDD|224125 COG1204, COG1204, Superfamily II helicase [General function
prediction only].
Length = 766
Score = 57.4 bits (139), Expect = 5e-09
Identities = 35/138 (25%), Positives = 67/138 (48%), Gaps = 10/138 (7%)
Query: 116 PIQAATIPVALLGRDICGCAATGTGKTAAFMLPILERLLYKPRDDQNTRVLVLVPTRELG 175
P Q A L ++ A TG+GKT +L IL LL + +V+ +VP + L
Sbjct: 35 PQQEAVEKGLLSDENVLISAPTGSGKTLIALLAILSTLL-----EGGGKVVYIVPLKALA 89
Query: 176 VQVYQVTRQLAQFTSVEVALSVGGLEVKVQESVLRKCPDIVIATPGRLLDHLHNTPSFSL 235
+ Y+ +L + + V +S G ++ + L + D+++ TP +L PS+ +
Sbjct: 90 EEKYEEFSRLEEL-GIRVGISTGDYDLDDER--LARY-DVIVTTPEKLDSLTRKRPSW-I 144
Query: 236 SDIEVLVLDEADRMLDEH 253
+++++V+DE + D
Sbjct: 145 EEVDLVVIDEIHLLGDRT 162
>gnl|CDD|224122 COG1201, Lhr, Lhr-like helicases [General function prediction
only].
Length = 814
Score = 56.9 bits (138), Expect = 6e-09
Identities = 46/188 (24%), Positives = 79/188 (42%), Gaps = 11/188 (5%)
Query: 98 LSRPLLKAIGALNYIYPTPIQAATIPVALLGRDICGCAATGTGKTAAFMLPILERLLYKP 157
L + + + TP Q IP G ++ A TG+GKT A LP++ LL
Sbjct: 8 LDPRVREWF-KRKFTSLTPPQRYAIPEIHSGENVLIIAPTGSGKTEAAFLPVINELLSLG 66
Query: 158 RDDQNTRVLVL--VPTRELGVQVYQVTRQLAQFTSVEVALSVGGLEVKVQESVLRKCPDI 215
+ + L P + L + + + + +EVA+ G ++ +L+ P I
Sbjct: 67 KGKLEDGIYALYISPLKALNNDIRRRLEEPLRELGIEVAVRHGDTPQSEKQKMLKNPPHI 126
Query: 216 VIATPGRLLDHLHNTPSFS--LSDIEVLVLDEADRMLDE----HFASQMKEIIRLCSRTR 269
+I TP L L N+P F L D+ +++DE + + A ++ + L
Sbjct: 127 LITTPESLAILL-NSPKFRELLRDVRYVIVDEIHALAESKRGVQLALSLERLRELAGDF- 184
Query: 270 QTMLFSAT 277
Q + SAT
Sbjct: 185 QRIGLSAT 192
>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 = 53.2 bits (128), Expect = 1e-07
Identities = 51/193 (26%), Positives = 78/193 (40%), Gaps = 23/193 (11%)
Query: 102 LLKAIGALNYIYPTPIQAATIPVALLGRDICGCAATGTGKTAAFMLPILERLLYKPRDDQ 161
++ A+ A P QA +A GR + T +GK+ A+ LP+L L PR
Sbjct: 25 VVAALEAAGIHRPWQHQARAAELAHAGRHVVVATGTASGKSLAYQLPVLSALADDPR--- 81
Query: 162 NTRVLVLVPTRELGVQVYQVTRQLAQFTSVEVALSVGGLEVKVQESVLRKCPDIVIATPG 221
L L PT+ L + R+L V A G + + R+ V+ P
Sbjct: 82 -ATALYLAPTKALAADQLRAVRELTL-RGVRPATYDGDTPTEERRWA-REHARYVLTNP- 137
Query: 222 RLLDHLHNT--PSFS-----LSDIEVLVLDEADR---MLDEHFASQMKEIIRLCSRTRQT 271
D LH PS + L + +V+DE + H A ++ + RLC+R +
Sbjct: 138 ---DMLHRGILPSHARWARFLRRLRYVVIDECHSYRGVFGSHVALVLRRLRRLCARYGAS 194
Query: 272 ---MLFSATMTDA 281
+L SAT D
Sbjct: 195 PVFVLASATTADP 207
>gnl|CDD|137505 PRK09751, PRK09751, putative ATP-dependent helicase Lhr;
Provisional.
Length = 1490
Score = 49.5 bits (118), Expect = 2e-06
Identities = 48/185 (25%), Positives = 77/185 (41%), Gaps = 23/185 (12%)
Query: 135 AATGTGKTAAFMLPILERLLYK-------PRDDQNTRVLVLVPTRELGVQVYQ------- 180
A TG+GKT A L L+RL + + +R+L + P + LG V +
Sbjct: 3 APTGSGKTLAAFLYALDRLFREGGEDTREAHKRKTSRILYISPIKALGTDVQRNLQIPLK 62
Query: 181 ---VTRQLAQFTSVE--VALSVGGLEVKVQESVLRKCPDIVIATPGRLLDHLHNTPSFSL 235
R+ T V V + G + + + R PDI+I TP L L + +L
Sbjct: 63 GIADERRRRGETEVNLRVGIRTGDTPAQERSKLTRNPPDILITTPESLYLMLTSRARETL 122
Query: 236 SDIEVLVLDE----ADRMLDEHFASQMKEIIRLCSRTRQTMLFSATMTDAVNDLVSVSLT 291
+E +++DE A H A ++ + L + Q + SAT+ A + +
Sbjct: 123 RGVETVIIDEVHAVAGSKRGAHLALSLERLDALLHTSAQRIGLSATVRSASDVAAFLGGD 182
Query: 292 RPVRV 296
RPV V
Sbjct: 183 RPVTV 187
>gnl|CDD|224036 COG1111, MPH1, ERCC4-like helicases [DNA replication,
recombination, and repair].
Length = 542
Score = 44.6 bits (106), Expect = 4e-05
Identities = 39/146 (26%), Positives = 60/146 (41%), Gaps = 13/146 (8%)
Query: 108 ALNYIYPTPIQA----ATIPVALLGRDICGCAATGTGKTAAFMLPILERLLYKPRDDQNT 163
A I P I+ I L ++ TG GKT + I RL +
Sbjct: 5 AHPLIKPNTIEPRLYQLNIAAKALFKNTLVVLPTGLGKTFIAAMVIANRLRWFGG----- 59
Query: 164 RVLVLVPTRELGVQVYQVTRQLAQFTSVEVALSVGGLEVKVQESVLR-KCPDIVIATPGR 222
+VL L PT+ L +Q + R++ E+A G EV+ +E + +ATP
Sbjct: 60 KVLFLAPTKPLVLQHAEFCRKVTGIPEDEIAALTG--EVRPEEREELWAKKKVFVATPQV 117
Query: 223 LLDHLHNTPSFSLSDIEVLVLDEADR 248
+ + L L D+ +L+ DEA R
Sbjct: 118 VENDL-KAGRIDLDDVSLLIFDEAHR 142
>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 = 42.2 bits (100), Expect = 3e-04
Identities = 41/158 (25%), Positives = 62/158 (39%), Gaps = 56/158 (35%)
Query: 214 DIVIATP-----------GRLLDHLHNTPSFSLSDIEVLVLDEADRMLD---EHFASQMK 259
DI+IA+P + D+ F LS IEVL++D+AD +L EH + K
Sbjct: 128 DIIIASPLGLRMIIENEDKKKRDY-----DF-LSSIEVLIVDQADVILMQNWEHVLTVFK 181
Query: 260 EIIRL--------CSRT------------RQTMLFSATMTDAVNDLVS---------VSL 290
+ ++ SR RQT+LFS+ +T +N L + V L
Sbjct: 182 HLNKIPKKSHGADFSRVRMWYLDGQAKYYRQTILFSSYITPEINSLFNSKCVNYRGKVKL 241
Query: 291 TRPVRVFVDNNHEVALNLRQEFVSFS-----NIDEVRL 323
+ V V L +RQ F F + + R
Sbjct: 242 KPIYKSGVIGQ--VGLKVRQVFQRFDASSIVDDPDARF 277
>gnl|CDD|237496 PRK13766, PRK13766, Hef nuclease; Provisional.
Length = 773
Score = 42.2 bits (100), Expect = 3e-04
Identities = 35/124 (28%), Positives = 55/124 (44%), Gaps = 25/124 (20%)
Query: 134 CAATGTGKTAAFMLPILERLLYKPRDDQNTRVLVLVPTRELGVQVYQVTRQLAQFTSVEV 193
TG GKTA +L I ERL K +VL+L PT+ L Q + R+ ++
Sbjct: 35 VLPTGLGKTAIALLVIAERLHKK-----GGKVLILAPTKPLVEQHAEFFRKFLNIPEEKI 89
Query: 194 ALSVGGLEVKVQESVLRKCPDIVIATP---------GRLLDHLHNTPSFSLSDIEVLVLD 244
+ G + + + + K +++ATP GR+ SL D+ +L+ D
Sbjct: 90 VVFTGEVSPEKRAELWEKA-KVIVATPQVIENDLIAGRI----------SLEDVSLLIFD 138
Query: 245 EADR 248
EA R
Sbjct: 139 EAHR 142
>gnl|CDD|223989 COG1061, SSL2, DNA or RNA helicases of superfamily II
[Transcription / DNA replication, recombination, and
repair].
Length = 442
Score = 40.1 bits (94), Expect = 0.001
Identities = 34/154 (22%), Positives = 51/154 (33%), Gaps = 30/154 (19%)
Query: 128 GRDICGCAATGTGKTAAFMLPILERLLYKPRDDQNTRVLVLVPTRELGVQVYQVTRQLAQ 187
R TG GKT I E LVLVPT+EL + Q L +
Sbjct: 55 ERRGVIVLPTGAGKTVVAAEAIAEL---------KRSTLVLVPTKEL---LDQWAEALKK 102
Query: 188 FTSVEVALSVGGLEVKVQESVLRKCPDIVIAT----PGRLLDHLHNTPSFSLSDIEVLVL 243
F + + + G K + + +AT R L F L ++
Sbjct: 103 FLLLNDEIGIYGGGEK-----ELEPAKVTVATVQTLARRQLLDEFLGNEFGL-----IIF 152
Query: 244 DEADRMLDEHFASQMKEIIRLCSRTRQTMLFSAT 277
DE + + + I+ L S + +AT
Sbjct: 153 DEVHHLPAPSY----RRILELLSAAYPRLGLTAT 182
>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 = 40.6 bits (96), Expect = 0.001
Identities = 39/146 (26%), Positives = 59/146 (40%), Gaps = 25/146 (17%)
Query: 114 PTPIQAATIPVALLGRDICGCAATGTGKTAAFMLPILERLLYKPRDDQNTRVLVLVPTRE 173
P P Q AL GR A TG+GKT A LP L L + + L + P R
Sbjct: 14 PRPFQLEMWAAALEGRSGLLIAPTGSGKTLAGFLPSLIDLAGPEKPKKGLHTLYITPLRA 73
Query: 174 LGVQVYQVTRQLAQFTSVEVALSVGGLEVKV-----------QESVLRKCPDIVIATPGR 222
L V + + +++ + GL ++V + +K PDI++ TP
Sbjct: 74 LAVDIAR---------NLQAPIEELGLPIRVETRTGDTSSSERARQRKKPPDILLTTPES 124
Query: 223 L---LDHLHNTPSFSLSDIEVLVLDE 245
L L + F D+ +V+DE
Sbjct: 125 LALLLSYPDAARLF--KDLRCVVVDE 148
>gnl|CDD|224123 COG1202, COG1202, Superfamily II helicase, archaea-specific
[General function prediction only].
Length = 830
Score = 39.0 bits (91), Expect = 0.003
Identities = 55/213 (25%), Positives = 87/213 (40%), Gaps = 43/213 (20%)
Query: 115 TPIQAATIPVALL-GRDICGCAATGTGKTAAFMLPILERLLYKPRDDQNTRVLVLVPTRE 173
P+Q + LL G ++ +AT +GKT L + RLL ++L LVP
Sbjct: 218 LPVQVLAVEAGLLEGENLLVVSATASGKTLIGELAGIPRLL-----SGGKKMLFLVPLVA 272
Query: 174 LGVQVYQVTRQLAQFTSVEVALSVGGLEVKVQESVLR----KCPDIVIAT-PGRLLDHLH 228
L Q Y+ ++ ++VA+ VG +K +E + DI++ T G +D+L
Sbjct: 273 LANQKYEDFKERYSKLGLKVAIRVGMSRIKTREEPVVVDTSPDADIIVGTYEG--IDYLL 330
Query: 229 NTPSFSLSDIEVLVLDEADRMLDEHFASQMKEIIRLCSRTR------QTMLFSATMTDAV 282
T L DI +V+DE + DE ++ +I R R Q + SAT
Sbjct: 331 RTGKD-LGDIGTVVIDEIHTLEDEERGPRLDGLI---GRLRYLFPGAQFIYLSAT----- 381
Query: 283 NDLVSVSLTRPVRVFVDNNHEVALNLRQEFVSF 315
V N E+A L + V +
Sbjct: 382 ---------------VGNPEELAKKLGAKLVLY 399
>gnl|CDD|237497 PRK13767, PRK13767, ATP-dependent helicase; Provisional.
Length = 876
Score = 38.3 bits (90), Expect = 0.006
Identities = 40/152 (26%), Positives = 69/152 (45%), Gaps = 26/152 (17%)
Query: 115 TPIQAATIPVALLGRDICGCAATGTGKTAAFMLPILERLLYKPRDDQ-NTRVLVLV--PT 171
TP Q IP+ G+++ + TG+GKT A L I++ L R+ + +V L P
Sbjct: 34 TPPQRYAIPLIHEGKNVLISSPTGSGKTLAAFLAIIDELFRLGREGELEDKVYCLYVSPL 93
Query: 172 RELGVQVY-------QVTRQLAQFTSVEVALSVGGLEVKVQES---------VLRKCPDI 215
R L ++ R++A+ E + + V ++ +L+K P I
Sbjct: 94 RALNNDIHRNLEEPLTEIREIAKERGEE----LPEIRVAIRTGDTSSYEKQKMLKKPPHI 149
Query: 216 VIATPGRLLDHLHNTPSFS--LSDIEVLVLDE 245
+I TP L L N+P F L ++ +++DE
Sbjct: 150 LITTPESLAILL-NSPKFREKLRTVKWVIVDE 180
>gnl|CDD|218292 pfam04851, ResIII, Type III restriction enzyme, res subunit.
Length = 100
Score = 34.9 bits (81), Expect = 0.009
Identities = 16/45 (35%), Positives = 24/45 (53%), Gaps = 10/45 (22%)
Query: 135 AATGTGKT--AAFMLPILERLLYKPRDDQNTRVLVLVPTRELGVQ 177
ATG+GKT AA ++ RL + +VL +VP ++L Q
Sbjct: 25 MATGSGKTLTAAA---LIARLAKGKK-----KVLFVVPRKDLLEQ 61
>gnl|CDD|236498 PRK09401, PRK09401, reverse gyrase; Reviewed.
Length = 1176
Score = 37.2 bits (87), Expect = 0.012
Identities = 45/194 (23%), Positives = 67/194 (34%), Gaps = 51/194 (26%)
Query: 57 LAKEGKLKQVEA-----EEYEENEGGKEFFEDAPPVEENSSFHQMNLSRPLLKAIGALNY 111
L + G LK+ E EEY+E E +FF+ K G+
Sbjct: 47 LKENGTLKEYEELYNLEEEYKEFE---KFFK---------------------KKTGSK-- 80
Query: 112 IYPTPIQAATIPVALLGRDICGCAATGTGKTA--AFMLPILERLLYKPRDDQNTRVLVLV 169
P +Q LLG A TG GKT M LY + + + ++
Sbjct: 81 --PWSLQRTWAKRLLLGESFAIIAPTGVGKTTFGLVMS------LYLAK--KGKKSYIIF 130
Query: 170 PTRELGVQVYQVTRQLAQFTSVEVALSV--GGLEVKVQESVLRKCP----DIVIATPGRL 223
PTR L QV + + + V + L+ K +E L + DI++ T L
Sbjct: 131 PTRLLVEQVVEKLEKFGEKVGCGVKILYYHSSLKKKEKEEFLERLKEGDFDILVTTSQFL 190
Query: 224 LDHLHNTPS--FSL 235
+ P F
Sbjct: 191 SKNFDELPKKKFDF 204
>gnl|CDD|221175 pfam11705, RNA_pol_3_Rpc31, DNA-directed RNA polymerase III subunit
Rpc31. RNA polymerase III contains seventeen subunits
in yeasts and in human cells. Twelve of these are akin
to RNA polymerase I or II and the other five are RNA pol
III-specific, and form the functionally distinct groups
(i) Rpc31-Rpc34-Rpc82, and (ii) Rpc37-Rpc53. Rpc31,
Rpc34 and Rpc82 form a cluster of enzyme-specific
subunits that contribute to transcription initiation in
S.cerevisiae and H.sapiens. There is evidence that these
subunits are anchored at or near the N-terminal Zn-fold
of Rpc1, itself prolonged by a highly conserved but RNA
polymerase III-specific domain.
Length = 221
Score = 33.6 bits (77), Expect = 0.084
Identities = 12/40 (30%), Positives = 23/40 (57%), Gaps = 4/40 (10%)
Query: 1 DDSSDEEGNKEDKEDNEGSEEDDVDAEEDFALPDDEMKHD 40
+ +E +++D+E+ E EE+D D ++D DD+ D
Sbjct: 164 EAEDVDEEDEKDEEEEEEEEEEDEDFDDD----DDDDDDD 199
Score = 32.0 bits (73), Expect = 0.33
Identities = 14/43 (32%), Positives = 23/43 (53%), Gaps = 6/43 (13%)
Query: 1 DDSSDEEGNKEDKEDNEGSEEDDVDAE------EDFALPDDEM 37
++ +EE ED +D++ ++DD +AE ED DDE
Sbjct: 177 EEEEEEEEEDEDFDDDDDDDDDDYNAENYFDNGEDDDYDDDEA 219
>gnl|CDD|227596 COG5271, MDN1, AAA ATPase containing von Willebrand factor type A
(vWA) domain [General function prediction only].
Length = 4600
Score = 34.6 bits (79), Expect = 0.084
Identities = 19/99 (19%), Positives = 39/99 (39%), Gaps = 7/99 (7%)
Query: 1 DDSSDEEGNKEDKEDNEGSEEDDVDAEEDFALPDDEMKHDN-------IKNRQKLIGKKK 53
D DE ED + + ++D+ ++ L +D+ K + +N + K
Sbjct: 4024 DAEKDEPMQDEDPLEENNTLDEDIQQDDFSDLAEDDEKMNEDGFEENVQENEESTEDGVK 4083
Query: 54 QKRLAKEGKLKQVEAEEYEENEGGKEFFEDAPPVEENSS 92
++G++ + +A + K F A EEN+
Sbjct: 4084 SDEELEQGEVPEDQAIDNHPKMDAKSTFASAEADEENTD 4122
Score = 30.7 bits (69), Expect = 1.3
Identities = 21/104 (20%), Positives = 47/104 (45%), Gaps = 3/104 (2%)
Query: 1 DDSSDEEGNKEDKEDNEGSEEDDVDAEEDFALPD---DEMKHDNIKNRQKLIGKKKQKRL 57
++S EE N++ E+ ED ++ + + +++ K+ ++ + +
Sbjct: 3877 ENSDSEEENQDLDEEVNDIPEDLSNSLNEKLWDEPNEEDLLETEQKSNEQSAANNESDLV 3936
Query: 58 AKEGKLKQVEAEEYEENEGGKEFFEDAPPVEENSSFHQMNLSRP 101
+KE K +E ++ +E E +E +D +E Q N S+P
Sbjct: 3937 SKEDDNKALEDKDRQEKEDEEEMSDDVGIDDEIQPDIQENNSQP 3980
Score = 28.8 bits (64), Expect = 4.9
Identities = 24/99 (24%), Positives = 51/99 (51%), Gaps = 11/99 (11%)
Query: 1 DDSSDEEGNKEDKEDNEGSEEDDV--------DAEEDFALPDDEMKHDNIKNRQKLIGKK 52
D+ + E+ ++++KED E DDV D +E+ + P E + ++ KL +
Sbjct: 3941 DNKALEDKDRQEKED-EEEMSDDVGIDDEIQPDIQENNSQPPPENEDLDLPEDLKL--DE 3997
Query: 53 KQKRLAKEGKLKQVEAEEYEENEGGKEFFEDAPPVEENS 91
K+ ++K+ L+ ++ E +EN+ + +D P +E+
Sbjct: 3998 KEGDVSKDSDLEDMDMEAADENKEEADAEKDEPMQDEDP 4036
>gnl|CDD|240246 PTZ00053, PTZ00053, methionine aminopeptidase 2; Provisional.
Length = 470
Score = 33.9 bits (78), Expect = 0.11
Identities = 28/123 (22%), Positives = 46/123 (37%), Gaps = 17/123 (13%)
Query: 2 DSSDEEGNKEDKEDNEGSEEDDVDAEEDFALPDDEMKHDNIKNRQKLIGKKKQKRLAKEG 61
+ K K+ N+ S++D +D E+ +N + K KKK+K+ K+
Sbjct: 12 QQKQQNKQKGTKKKNKKSKKD----VDDDDAFLAELISENQEAENKQNNKKKKKKKKKKK 67
Query: 62 KLKQVEAEEYEENEGGKEFFEDAPPVEENSSFHQMNLSRPLLKAIGALNYIYPTPIQAAT 121
K +N G PV +S+ Q N ++ +G Q T
Sbjct: 68 K----------KNLGEAYDLAYDLPVVWSSAAFQDN---SHIRKLGNWPEQEWKQTQPPT 114
Query: 122 IPV 124
IPV
Sbjct: 115 IPV 117
>gnl|CDD|213179 cd00267, ABC_ATPase, ATP-binding cassette transporter
nucleotide-binding domain. ABC transporters are a large
family of proteins involved in the transport of a wide
variety of different compounds, like sugars, ions,
peptides, and more complex organic molecules. The
nucleotide-binding domain shows the highest similarity
between all members of the family. ABC transporters are
a subset of nucleotide hydrolases that contain a
signature motif, Q-loop, and H-loop/switch region, in
addition to, the Walker A motif/P-loop and Walker B
motif commonly found in a number of ATP- and GTP-binding
and hydrolyzing proteins.
Length = 157
Score = 32.6 bits (75), Expect = 0.11
Identities = 10/41 (24%), Positives = 22/41 (53%)
Query: 235 LSDIEVLVLDEADRMLDEHFASQMKEIIRLCSRTRQTMLFS 275
L + ++L+LDE LD ++ E++R + +T++
Sbjct: 96 LLNPDLLLLDEPTSGLDPASRERLLELLRELAEEGRTVIIV 136
>gnl|CDD|218752 pfam05793, TFIIF_alpha, Transcription initiation factor IIF, alpha
subunit (TFIIF-alpha). Transcription initiation factor
IIF, alpha subunit (TFIIF-alpha) or RNA polymerase
II-associating protein 74 (RAP74) is the large subunit
of transcription factor IIF (TFIIF), which is essential
for accurate initiation and stimulates elongation by RNA
polymerase II.
Length = 528
Score = 33.8 bits (77), Expect = 0.13
Identities = 23/76 (30%), Positives = 34/76 (44%), Gaps = 11/76 (14%)
Query: 4 SDEEGNKEDKEDNEGSEEDDVDAEEDFALPDDEMKHDNIKNRQKLIGKKKQKRLAKEGKL 63
D EG+ ED D +D D E + K KN++KL KK KR +
Sbjct: 216 KDLEGDDEDDGDESDKGGEDGDEE-----KSKKKKKKLAKNKKKLDDDKKGKRGGDD--- 267
Query: 64 KQVEAEEYEENEGGKE 79
+A+EY+ ++G E
Sbjct: 268 ---DADEYDSDDGDDE 280
Score = 31.1 bits (70), Expect = 0.83
Identities = 16/90 (17%), Positives = 38/90 (42%), Gaps = 2/90 (2%)
Query: 2 DSSDEEGNKEDKEDNEGSEEDDVDAEEDFALPDDEMKHDNIKNRQKLIGKKKQKRLAKEG 61
D D+EG +ED + + +D + ED P+ K + ++ + ++++ +EG
Sbjct: 275 DDGDDEGREEDYISDSSASGNDPEEREDKLSPEIPAKPEIEQDEDS--EESEEEKNEEEG 332
Query: 62 KLKQVEAEEYEENEGGKEFFEDAPPVEENS 91
L + + + +D ++S
Sbjct: 333 GLSKKGKKLKKLKGKKNGLDKDDSDSGDDS 362
>gnl|CDD|219563 pfam07767, Nop53, Nop53 (60S ribosomal biogenesis). This nucleolar
family of proteins are involved in 60S ribosomal
biogenesis. They are specifically involved in the
processing beyond the 27S stage of 25S rRNA maturation.
This family contains sequences that bear similarity to
the glioma tumour suppressor candidate region gene 2
protein (p60). This protein has been found to interact
with herpes simplex type 1 regulatory proteins.
Length = 387
Score = 33.5 bits (77), Expect = 0.13
Identities = 24/68 (35%), Positives = 33/68 (48%), Gaps = 6/68 (8%)
Query: 6 EEGNKEDKEDNEGSEEDDVDAEEDFALPDDEMKHDNIKNRQKLIGKKKQKRLAKEGKLKQ 65
EG E+ +D+ E DD A E F + E + N R K K K +R KE + K+
Sbjct: 238 SEGLLEESDDDGEEESDDESAWEGF---ESEYEPINKPVRPKR--KTKAQR-NKEKRRKE 291
Query: 66 VEAEEYEE 73
+E E EE
Sbjct: 292 LEREAKEE 299
Score = 29.3 bits (66), Expect = 3.4
Identities = 14/71 (19%), Positives = 33/71 (46%), Gaps = 3/71 (4%)
Query: 1 DDSSDEEGNKEDKEDNEGSEEDDVDAEEDFALPDDEMKHDNIKNRQKLIGKKKQKRLAKE 60
++S D+ +E+ +D E + + E + K +N++K K+ ++ +E
Sbjct: 243 EESDDDG--EEESDDESAWEGFESEYEPINKPVRPKRKTKAQRNKEKR-RKELEREAKEE 299
Query: 61 GKLKQVEAEEY 71
+LK+ A+
Sbjct: 300 KQLKKKLAQLA 310
>gnl|CDD|218177 pfam04615, Utp14, Utp14 protein. This protein is found to be part
of a large ribonucleoprotein complex containing the U3
snoRNA. Depletion of the Utp proteins impedes production
of the 18S rRNA, indicating that they are part of the
active pre-rRNA processing complex. This large RNP
complex has been termed the small subunit (SSU)
processome.
Length = 728
Score = 33.9 bits (78), Expect = 0.13
Identities = 21/74 (28%), Positives = 30/74 (40%), Gaps = 10/74 (13%)
Query: 11 EDKEDNEGSEEDDVDAEEDFALPDDEMKHDNIKNRQKLIGKKKQKRLAKEGKLKQVEAEE 70
E K +E E++D D+EE+ DDE D K GKLK+ E +E
Sbjct: 319 EGKSVSEEDEDEDSDSEEED-EDDDEDDDDGENPW---------MLRKKLGKLKEGEDDE 368
Query: 71 YEENEGGKEFFEDA 84
+F + A
Sbjct: 369 ENSGLLSMKFMQRA 382
Score = 29.6 bits (67), Expect = 3.0
Identities = 16/57 (28%), Positives = 25/57 (43%), Gaps = 7/57 (12%)
Query: 19 SEEDDVDAEEDFALPDDEMKHDNIKNRQKLIGKKKQKRLAKEGKLKQVEAEEYEENE 75
S++D+ D E+D DDE KH + I ++ E K E +E+E
Sbjct: 2 SDDDESDEEDD----DDEDKHSKL---LSAISSLGGEKKKDEKKKADRSEESGKESE 51
>gnl|CDD|240433 PTZ00482, PTZ00482, membrane-attack complex/perforin (MACPF)
Superfamily; Provisional.
Length = 844
Score = 33.7 bits (77), Expect = 0.13
Identities = 18/93 (19%), Positives = 33/93 (35%), Gaps = 2/93 (2%)
Query: 1 DDSSDEEGNKEDKEDNEGSEEDDVDAEEDFALPDDEMKHD-NIKNRQKLIGKKKQKRLAK 59
+ D + N D + + D +K N+ + +KLI +KK +
Sbjct: 120 LLELPDRDEDADTQANNDQTNDFDQDDSSNSQTDQGLKQSVNLSSAEKLIEEKKGQTENT 179
Query: 60 EGKLKQV-EAEEYEENEGGKEFFEDAPPVEENS 91
+ EE +GGK D P+ ++
Sbjct: 180 FKFYNFGNDGEEAAAKDGGKSKSSDPGPLNDSD 212
>gnl|CDD|233251 TIGR01054, rgy, reverse gyrase. This model describes reverse
gyrase, found in both archaeal and bacterial
thermophiles. This enzyme, a fusion of a type I
topoisomerase domain and a helicase domain, introduces
positive supercoiling to increase the melting
temperature of DNA double strands. Generally, these
gyrases are encoded as a single polypeptide. An
exception was found in Methanopyrus kandleri, where
enzyme is split within the topoisomerase domain,
yielding a heterodimer of gene products designated RgyB
and RgyA [DNA metabolism, DNA replication,
recombination, and repair].
Length = 1171
Score = 33.3 bits (76), Expect = 0.20
Identities = 29/122 (23%), Positives = 43/122 (35%), Gaps = 16/122 (13%)
Query: 126 LLGRDICGCAATGTGKTAAFMLPILERLLYKPRDDQNTRVLVLVPTRELGVQVYQVTRQL 185
L G A TG GKT + L + R +++PT L +QV + L
Sbjct: 91 LRGDSFAIIAPTGVGKTT---FGLAMSLFLAK---KGKRCYIILPTTLLVIQVAEKISSL 144
Query: 186 AQFTSV---EVALSVGGLEVKVQESVLRKCP----DIVIATPGRL---LDHLHNTPSFSL 235
A+ V + L K ++ + + DI+I T L D L F
Sbjct: 145 AEKAGVGTVNIGAYHSRLPTKEKKEFMERIENGDFDILITTTMFLSKNYDELGPKFDFIF 204
Query: 236 SD 237
D
Sbjct: 205 VD 206
>gnl|CDD|220271 pfam09507, CDC27, DNA polymerase subunit Cdc27. This protein forms
the C subunit of DNA polymerase delta. It carries the
essential residues for binding to the Pol1 subunit of
polymerase alpha, from residues 293-332, which are
characterized by the motif D--G--VT, referred to as the
DPIM motif. The first 160 residues of the protein form
the minimal domain for binding to the B subunit, Cdc1,
of polymerase delta, the final 10 C-terminal residues,
362-372, being the DNA sliding clamp, PCNA, binding
motif.
Length = 427
Score = 32.5 bits (74), Expect = 0.32
Identities = 23/91 (25%), Positives = 46/91 (50%), Gaps = 8/91 (8%)
Query: 1 DDSSDEEGNKEDKEDNEGSEEDDVDAEEDFALPDDEMKHDNIKNRQKLIGKKKQKRLAKE 60
++S +E G ++ ++E +E +D +ED P + + ++ K+K+KR
Sbjct: 242 EESEEESGKRDVILEDESAEPTGLDEDEDEDEPKPSGE--RSDSEEETEEKEKEKRK--- 296
Query: 61 GKLKQVEAEEYEENEGGKEFFEDAPPVEENS 91
+LK++ +E E+ E E ++P EE S
Sbjct: 297 -RLKKMMEDEDEDEE--MEIVPESPVEEEES 324
>gnl|CDD|217203 pfam02724, CDC45, CDC45-like protein. CDC45 is an essential gene
required for initiation of DNA replication in S.
cerevisiae, forming a complex with MCM5/CDC46.
Homologues of CDC45 have been identified in human, mouse
and smut fungus among others.
Length = 583
Score = 32.3 bits (74), Expect = 0.35
Identities = 15/73 (20%), Positives = 35/73 (47%), Gaps = 7/73 (9%)
Query: 1 DDSSDEEGNKEDKEDNEGSEEDDVDAEEDFALPDDEMKHDNIKNRQKLIGKKKQKRLAKE 60
D D++ ++E E++E S + + D ++D DD+ D + L +++++R E
Sbjct: 122 DLEEDDDDDEESDEEDEESSKSEDDEDDD----DDDDDDDIATRERSL--ERRRRRREWE 175
Query: 61 GKLKQVEAEEYEE 73
+ + Y +
Sbjct: 176 -EKRAELEFYYYQ 187
>gnl|CDD|99783 cd06186, NOX_Duox_like_FAD_NADP, NADPH oxidase (NOX) catalyzes the
generation of reactive oxygen species (ROS) such as
superoxide and hydrogen peroxide. ROS were originally
identified as bactericidal agents in phagocytes, but are
now also implicated in cell signaling and metabolism.
NOX has a 6-alpha helix heme-binding transmembrane
domain fused to a flavoprotein with the nucleotide
binding domain located in the cytoplasm. Duox enzymes
link a peroxidase domain to the NOX domain via a single
transmembrane and EF-hand Ca2+ binding sites. The
flavoprotein module has a ferredoxin like FAD/NADPH
binding domain. In classical phagocytic NOX2, electron
transfer occurs from NADPH to FAD to the heme of cytb to
oxygen leading to superoxide formation.
Length = 210
Score = 31.5 bits (72), Expect = 0.40
Identities = 14/34 (41%), Positives = 18/34 (52%), Gaps = 2/34 (5%)
Query: 136 ATGTGKTAAFMLPILERLLYKPRDDQNTRVLVLV 169
A G+G F+LPIL LL + TR + LV
Sbjct: 113 AGGSG--ITFVLPILRDLLRRSSKTSRTRRVKLV 144
>gnl|CDD|224120 COG1199, DinG, Rad3-related DNA helicases [Transcription / DNA
replication, recombination, and repair].
Length = 654
Score = 32.1 bits (73), Expect = 0.44
Identities = 15/46 (32%), Positives = 25/46 (54%), Gaps = 5/46 (10%)
Query: 135 AATGTGKTAAFMLPILERLLYKPRDDQNTRVLVLVPTRELGVQVYQ 180
A TGTGKT A++LP L + + +V++ T+ L Q+ +
Sbjct: 41 APTGTGKTLAYLLPALAYAREEGK-----KVIISTRTKALQEQLLE 81
>gnl|CDD|217840 pfam04006, Mpp10, Mpp10 protein. This family includes proteins
related to Mpp10 (M phase phosphoprotein 10). The U3
small nucleolar ribonucleoprotein (snoRNP) is required
for three cleavage events that generate the mature 18S
rRNA from the pre-rRNA. In Saccharomyces cerevisiae,
depletion of Mpp10, a U3 snoRNP-specific protein, halts
18S rRNA production and impairs cleavage at the three U3
snoRNP-dependent sites.
Length = 613
Score = 31.9 bits (72), Expect = 0.52
Identities = 19/93 (20%), Positives = 29/93 (31%), Gaps = 9/93 (9%)
Query: 1 DDSSDEEGNKEDKEDNEGSEEDDVDAEEDFALPDDEMKHDNIKNRQKLIGKKKQKRLAKE 60
D S + + ED D+E EE+D E++ +DE N
Sbjct: 102 DGSDGSDMDSEDSADDEEEEEEDESLEDEMIDDEDEADLFNESE---------SSLEDLS 152
Query: 61 GKLKQVEAEEYEENEGGKEFFEDAPPVEENSSF 93
+ + E+ E E E E F
Sbjct: 153 DDETEDDEEKKMEEEEAGEEKESVEQATREKKF 185
>gnl|CDD|217861 pfam04050, Upf2, Up-frameshift suppressor 2. Transcripts
harbouring premature signals for translation
termination are recognised and rapidly degraded by
eukaryotic cells through a pathway known as
nonsense-mediated mRNA decay. In Saccharomyces
cerevisiae, three trans-acting factors (Upf1 to Upf3)
are required for nonsense-mediated mRNA decay.
Length = 171
Score = 30.8 bits (70), Expect = 0.61
Identities = 13/47 (27%), Positives = 27/47 (57%)
Query: 1 DDSSDEEGNKEDKEDNEGSEEDDVDAEEDFALPDDEMKHDNIKNRQK 47
DD ++E E+ ED+E S+E++VD +D + + + + I ++
Sbjct: 8 DDGEEDEELPEEDEDDESSDEEEVDLPDDEQDEESDSEEEQIFVTRQ 54
>gnl|CDD|221185 pfam11719, Drc1-Sld2, DNA replication and checkpoint protein.
Genome duplication is precisely regulated by
cyclin-dependent kinases CDKs, which bring about the
onset of S phase by activating replication origins and
then prevent relicensing of origins until mitosis is
completed. The optimum sequence motif for CDK
phosphorylation is S/T-P-K/R-K/R, and Drc1-Sld2 is found
to have at least 11 potential phosphorylation sites.
Drc1 is required for DNA synthesis and S-M replication
checkpoint control. Drc1 associates with Cdc2 and is
phosphorylated at the onset of S phase when Cdc2 is
activated. Thus Cdc2 promotes DNA replication by
phosphorylating Drc1 and regulating its association with
Cut5. Sld2 and Sld3 represent the minimal set of S-CDK
substrates required for DNA replication.
Length = 397
Score = 31.3 bits (71), Expect = 0.69
Identities = 15/68 (22%), Positives = 29/68 (42%), Gaps = 7/68 (10%)
Query: 13 KEDNEGSEEDDVDAEEDFALPDDEMKHDNIKNRQ-------KLIGKKKQKRLAKEGKLKQ 65
+E+ +E DV E + + + + Q ++ KK QKR + K++
Sbjct: 241 QEEESIDDELDVLREIEAEEAGIGPIEEEVVDSQAANDEPRRVFKKKGQKRTTRRVKMRP 300
Query: 66 VEAEEYEE 73
V A+ +E
Sbjct: 301 VRAKPSDE 308
>gnl|CDD|222104 pfam13401, AAA_22, AAA domain.
Length = 124
Score = 29.9 bits (68), Expect = 0.74
Identities = 26/143 (18%), Positives = 46/143 (32%), Gaps = 41/143 (28%)
Query: 131 ICGCAATGTGKTAAFMLPILERLLYKPRDDQNTRVLVLVPTRELGVQVYQVTRQLAQFTS 190
+ G + G+GKT L RL R N RV+ + + + R++ +
Sbjct: 9 LTGES--GSGKTTL-----LRRLA---RQLPNRRVVYVEAPSLGTPK--DLLRKILR--- 53
Query: 191 VEVALSVGGLEVKVQESVLRKCPDIVIATPGRLLDHLHNTPSFSLSDIEVLVLDEADRML 250
AL + E + +LD L +L++DEA +
Sbjct: 54 ---ALGLPLSGGTTAELL------------EAILDALKRR------GRPLLIIDEAQHLS 92
Query: 251 DEHFASQMKEIIRLCSRTRQTML 273
E E +R + +
Sbjct: 93 LEAL-----EELRDLYDLSEKGI 110
>gnl|CDD|220440 pfam09848, DUF2075, Uncharacterized conserved protein (DUF2075).
This domain, found in various prokaryotic proteins
(including putative ATP/GTP binding proteins), has no
known function.
Length = 348
Score = 31.0 bits (71), Expect = 0.82
Identities = 30/133 (22%), Positives = 50/133 (37%), Gaps = 38/133 (28%)
Query: 138 GTGKTAAFMLPILERLLYKPRDDQNTRVLVLVPTRELGVQVYQVTRQLAQFTSVEVALSV 197
GTGKT L + L D T V + V V LA
Sbjct: 11 GTGKTVV-ALNLFAELSDS--DLGRTAVFLSGNHPL--VLVLY--EALA----------- 52
Query: 198 GGLEVKVQESVLRKCPDIVIATPGRLLDHLHNTPSFSLSDIEVLVLDEADRMLD-----E 252
G L+V+ ++ + P +++LH P +V+++DEA R+
Sbjct: 53 GDLKVRKKKLFRK---------PTSFINNLHKAPP----HEDVVIVDEAHRLWTKSDLYF 99
Query: 253 HF--ASQMKEIIR 263
+F +Q+ EI++
Sbjct: 100 NFSGPNQLDEIMK 112
>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 = 31.3 bits (71), Expect = 0.85
Identities = 15/35 (42%), Positives = 18/35 (51%)
Query: 116 PIQAATIPVALLGRDICGCAATGTGKTAAFMLPIL 150
P+Q I LLGRD TG GK+ + LP L
Sbjct: 14 PVQLEVINAVLLGRDCFVVMPTGGGKSLCYQLPAL 48
>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 = 0.87
Identities = 27/114 (23%), Positives = 47/114 (41%), Gaps = 19/114 (16%)
Query: 135 AATGTGKTAAFMLPILERLLYKPRDDQNTRVLVLVPTRELGVQVYQVTRQLAQFTSVEVA 194
A G GK+ A L +L+ ++++L P R R AQ + ++
Sbjct: 24 APPGAGKSTAVPLALLDAPGI------GGKIIMLEPRR-------LAARSAAQRLASQLG 70
Query: 195 LSVG---GLEVKVQESVLRKCPDIVIATPGRLLDHLHNTPSFSLSDIEVLVLDE 245
+VG G V+ + V R+ + + T G L + + P L + L+ DE
Sbjct: 71 EAVGQTVGYRVRGENKVSRRT-RLEVVTEGILTRMIQDDP--ELDGVGALIFDE 121
>gnl|CDD|224054 COG1131, CcmA, ABC-type multidrug transport system, ATPase
component [Defense mechanisms].
Length = 293
Score = 30.7 bits (70), Expect = 1.0
Identities = 15/42 (35%), Positives = 22/42 (52%), Gaps = 1/42 (2%)
Query: 235 LSDIEVLVLDEADRMLDEHFASQMKEIIR-LCSRTRQTMLFS 275
L D E+L+LDE LD ++ E++R L T+L S
Sbjct: 152 LHDPELLILDEPTSGLDPESRREIWELLRELAKEGGVTILLS 193
>gnl|CDD|213260 cd03293, ABC_NrtD_SsuB_transporters, ATP-binding cassette domain of
the nitrate and sulfonate transporters. NrtD and SsuB
are the ATP-binding subunits of the bacterial ABC-type
nitrate and sulfonate transport systems, respectively.
ABC transporters are a large family of proteins involved
in the transport of a wide variety of different
compounds, like sugars, ions, peptides, and more complex
organic molecules. The nucleotide binding domain shows
the highest similarity between all members of the
family. ABC transporters are a subset of nucleotide
hydrolases that contain a signature motif, Q-loop, and
H-loop/switch region, in addition to, the Walker A
motif/P-loop and Walker B motif commonly found in a
number of ATP- and GTP-binding and hydrolyzing proteins.
Length = 220
Score = 30.5 bits (70), Expect = 1.0
Identities = 12/37 (32%), Positives = 21/37 (56%), Gaps = 1/37 (2%)
Query: 239 EVLVLDEADRMLDEHFASQMK-EIIRLCSRTRQTMLF 274
+VL+LDE LD Q++ E++ + T +T+L
Sbjct: 151 DVLLLDEPFSALDALTREQLQEELLDIWRETGKTVLL 187
>gnl|CDD|227012 COG4666, COG4666, TRAP-type uncharacterized transport system, fused
permease components [General function prediction only].
Length = 642
Score = 30.7 bits (70), Expect = 1.1
Identities = 14/54 (25%), Positives = 23/54 (42%), Gaps = 1/54 (1%)
Query: 105 AIGALNYIYPTPIQAATIPVALLGRDICGCAATGTGKTAAFMLPILERLLYKPR 158
A P + A + L+G I G + T T +F +P+++R Y P
Sbjct: 215 AFALAGLRRGGPAKVAVVSSGLMGM-ISGSSVANTVTTGSFTIPLMKRAGYPPE 267
>gnl|CDD|217943 pfam04180, LTV, Low temperature viability protein. The
low-temperature viability protein LTV1 is involved in
ribosome biogenesis 40S subunit production.
Length = 426
Score = 30.4 bits (68), Expect = 1.5
Identities = 10/104 (9%), Positives = 33/104 (31%)
Query: 7 EGNKEDKEDNEGSEEDDVDAEEDFALPDDEMKHDNIKNRQKLIGKKKQKRLAKEGKLKQV 66
D+ ++ + +A + ++E + N + + ++ + + +
Sbjct: 200 SAGFLDEFEDLSAPGSPQEAMKKHLFVEEETESRNTEYSETSEVMRRNEDWTLHFERFKK 259
Query: 67 EAEEYEENEGGKEFFEDAPPVEENSSFHQMNLSRPLLKAIGALN 110
++ ++ E G + E S + K A +
Sbjct: 260 FEKKNDDVEIGAADNSELEGSIEVDSNRLQEVLNDYYKTEKAKS 303
>gnl|CDD|224035 COG1110, COG1110, Reverse gyrase [DNA replication, recombination,
and repair].
Length = 1187
Score = 30.4 bits (69), Expect = 1.5
Identities = 21/74 (28%), Positives = 31/74 (41%), Gaps = 10/74 (13%)
Query: 135 AATGTGKTA--AFMLPILERLLYKPRDDQNTRVLVLVPTRELGVQVYQVTRQLAQFTSVE 192
A TG GKT M L + + RV ++VPT L QVY+ ++ A+
Sbjct: 104 APTGVGKTTFGLLMSLYLAK--------KGKRVYIIVPTTTLVRQVYERLKKFAEDAGSL 155
Query: 193 VALSVGGLEVKVQE 206
L V + +E
Sbjct: 156 DVLVVYHSALPTKE 169
>gnl|CDD|218312 pfam04889, Cwf_Cwc_15, Cwf15/Cwc15 cell cycle control protein.
This family represents Cwf15/Cwc15 (from
Schizosaccharomyces pombe and Saccharomyces cerevisiae
respectively) and their homologues. The function of
these proteins is unknown, but they form part of the
spliceosome and are thus thought to be involved in mRNA
splicing.
Length = 241
Score = 30.1 bits (68), Expect = 1.5
Identities = 21/78 (26%), Positives = 38/78 (48%), Gaps = 4/78 (5%)
Query: 1 DDSSDEEGNKEDKEDNEGSEEDDVDAEEDFALPDDEMKHDNIKNRQKLI----GKKKQKR 56
DD DE K +ED S+ DD D+ D DD+ D+ ++ + K K++R
Sbjct: 99 DDEEDEIKRKRIEEDARNSDADDSDSSSDSDSSDDDSDDDDSEDETAALLRELEKIKKER 158
Query: 57 LAKEGKLKQVEAEEYEEN 74
++ + ++ +A E E+
Sbjct: 159 AEEKEREEEEKAAEEEKA 176
Score = 29.3 bits (66), Expect = 2.4
Identities = 13/69 (18%), Positives = 28/69 (40%), Gaps = 8/69 (11%)
Query: 1 DDSSDEEGNKEDKEDNEGSEEDDVDAEEDFALPDDEMKHDNIKNRQKLIGKKKQKRLAKE 60
DDS + +D++ + +D A L + IK +++ K++++
Sbjct: 120 DDSDSSSDSDSSDDDSDDDDSEDETAALLREL-------EKIK-KERAEEKEREEEEKAA 171
Query: 61 GKLKQVEAE 69
+ K E E
Sbjct: 172 EEEKAREEE 180
>gnl|CDD|213192 cd03225, ABC_cobalt_CbiO_domain1, First domain of the ATP-binding
cassette component of cobalt transport system. Domain I
of the ABC component of a cobalt transport family found
in bacteria, archaea, and eukaryota. The transition
metal cobalt is an essential component of many enzymes
and must be transported into cells in appropriate
amounts when needed. This ABC transport system of the
CbiMNQO family is involved in cobalt transport in
association with the cobalamin (vitamin B12)
biosynthetic pathways. Most of cobalt (Cbi) transport
systems possess a separate CbiN component, the
cobalt-binding periplasmic protein, and they are encoded
by the conserved gene cluster cbiMNQO. Both the CbiM and
CbiQ proteins are integral cytoplasmic membrane
proteins, and the CbiO protein has the linker peptide
and the Walker A and B motifs commonly found in the
ATPase components of the ABC-type transport systems.
Length = 211
Score = 29.7 bits (68), Expect = 1.7
Identities = 14/67 (20%), Positives = 28/67 (41%), Gaps = 15/67 (22%)
Query: 224 LDHLHNTPSFSLS---------------DIEVLVLDEADRMLDEHFASQMKEIIRLCSRT 268
L+ L + F+LS D ++L+LDE LD ++ E+++
Sbjct: 124 LEGLRDRSPFTLSGGQKQRVAIAGVLAMDPDILLLDEPTAGLDPAGRRELLELLKKLKAE 183
Query: 269 RQTMLFS 275
+T++
Sbjct: 184 GKTIIIV 190
>gnl|CDD|145067 pfam01718, Orbi_NS1, Orbivirus non-structural protein NS1, or
hydrophobic tubular protein. This family consists of
orbivirus non-structural protein NS1, or hydrophobic
tubular protein. NS1 has no specific function in virus
replication, it is however thought to play a role in
transport of mature virus particles from virus inclusion
bodies to the cell membrane. Orbivirus are part of the
larger reoviridae which have a dsRNA genome of at least
10 segments encoding at least 10 viral proteins;
orbivirus found in this family include bluetongue virus,
and African horsesickness virus.
Length = 546
Score = 30.1 bits (68), Expect = 1.9
Identities = 14/60 (23%), Positives = 23/60 (38%), Gaps = 6/60 (10%)
Query: 242 VLDEADRMLDEHFASQMKEIIRLCSRTRQTMLFSATMTDAVNDLVSVSLTRPVRVFVDNN 301
VL ADR + E A +M+E ++ S + P RV+ D++
Sbjct: 85 VLKSADRPVSEDLAEEMQETLQALYD---AYSHSGMREEVQG---FRKRNDPARVYTDDS 138
>gnl|CDD|218737 pfam05764, YL1, YL1 nuclear protein. The proteins in this family
are designated YL1. These proteins have been shown to be
DNA-binding and may be a transcription factor.
Length = 238
Score = 29.7 bits (67), Expect = 2.0
Identities = 21/71 (29%), Positives = 37/71 (52%), Gaps = 7/71 (9%)
Query: 6 EEGNKEDKEDNEGSEEDDVDA-----EEDFALPDDEMKHDNIKNRQKLIGKKKQKR--LA 58
EE + E+ E E EE++VD+ E+D DDE + + R++ + KKK+ +
Sbjct: 36 EEEDDEEFEIEEEEEEEEVDSDFDDSEDDEPESDDEEEGEKELQREERLKKKKRVKTKAY 95
Query: 59 KEGKLKQVEAE 69
KE K+ + +
Sbjct: 96 KEPTKKKKKKD 106
>gnl|CDD|184207 PRK13648, cbiO, cobalt transporter ATP-binding subunit;
Provisional.
Length = 269
Score = 29.7 bits (67), Expect = 2.0
Identities = 12/46 (26%), Positives = 23/46 (50%), Gaps = 2/46 (4%)
Query: 239 EVLVLDEADRMLDEHFASQMKEIIRLCSRTRQTMLFSAT--MTDAV 282
V++LDEA MLD + +++R + S T +++A+
Sbjct: 162 SVIILDEATSMLDPDARQNLLDLVRKVKSEHNITIISITHDLSEAM 207
>gnl|CDD|226581 COG4096, HsdR, Type I site-specific restriction-modification
system, R (restriction) subunit and related helicases
[Defense mechanisms].
Length = 875
Score = 29.7 bits (67), Expect = 2.3
Identities = 29/118 (24%), Positives = 42/118 (35%), Gaps = 19/118 (16%)
Query: 136 ATGTGKT-AAFMLPILERLLYKPRDDQNTRVLVLVPTRELGVQVYQVTR----QLAQFTS 190
ATGTGKT A I++RL+ + RVL L L Q Y +
Sbjct: 193 ATGTGKTRTAIA--IIDRLI---KSGWVKRVLFLADRNALVDQAYGAFEDFLPFGTKMNK 247
Query: 191 VEVALSVGGLEVKVQESVLRKCPDIVIATPGRLLDHLHNTPSFSLSDIEVLVLDEADR 248
+E E+ L + GR+ F +++V+DEA R
Sbjct: 248 IEDKKGDTSSEI-----YLSTYQTMT----GRIEQKEDEYRRFGPGFFDLIVIDEAHR 296
>gnl|CDD|221641 pfam12569, NARP1, NMDA receptor-regulated protein 1. This domain
family is found in eukaryotes, and is approximately 40
amino acids in length. The family is found in
association with pfam07719, pfam00515. There is a single
completely conserved residue L that may be functionally
important. NARP1 is the mammalian homologue of a yeast
N-terminal acetyltransferase that regulates entry into
the G(0) phase of the cell cycle.
Length = 516
Score = 29.5 bits (67), Expect = 2.6
Identities = 18/79 (22%), Positives = 29/79 (36%), Gaps = 10/79 (12%)
Query: 12 DKEDNEGSEEDDVDAEEDFALPDDEMKHDNIKNRQKLIGKKKQKRLAKEGKLKQVEAEEY 71
DK EE++ + L E K K R+K +K +K+ KE K ++
Sbjct: 389 DKPLLAEGEEEEGENG---NLSPAERK----KLRKKQ--RKAEKKAEKEEAEKAAAKKKA 439
Query: 72 EENEG-GKEFFEDAPPVEE 89
E K + V+
Sbjct: 440 EAAAKKAKGPDGETKKVDP 458
>gnl|CDD|184733 PRK14540, PRK14540, nucleoside diphosphate kinase; Provisional.
Length = 134
Score = 28.6 bits (64), Expect = 2.7
Identities = 20/47 (42%), Positives = 24/47 (51%), Gaps = 10/47 (21%)
Query: 45 RQKLIGKKKQKRLAKEG---------KLKQVEAEEYEENEGGKEFFE 82
+KLIGK Q R +G KL + AEEY E GKEF+E
Sbjct: 15 ERKLIGKIIQ-RFENKGFEIVEMKMLKLTREMAEEYYEEHKGKEFYE 60
>gnl|CDD|232933 TIGR00348, hsdR, type I site-specific deoxyribonuclease, HsdR
family. This gene is part of the type I restriction and
modification system which is composed of three
polypeptides R (restriction endonuclease), M
(modification) and S (specificity). This group of
enzymes recognize specific short DNA sequences and have
an absolute requirement for ATP (or dATP) and
S-adenosyl-L-methionine. They also catalyse the
reactions of EC 2.1.1.72 and EC 2.1.1.73, with similar
site specificity.(J. Mol. Biol. 271 (3), 342-348
(1997)). Members of this family are assumed to differ
from each other in DNA site specificity [DNA metabolism,
Restriction/modification].
Length = 667
Score = 29.7 bits (67), Expect = 2.8
Identities = 30/133 (22%), Positives = 52/133 (39%), Gaps = 17/133 (12%)
Query: 136 ATGTGKTAAFMLPILERLLYKPRDDQNTRVLVLVPTRELGVQVYQVTRQLAQFTSVEVAL 195
G+GKT + R + +N +V +V REL Q+ + + L Q E
Sbjct: 271 TQGSGKT--LTMLFAARKALE--LLKNPKVFFVVDRRELDYQLMKEFQSL-QKDCAERIE 325
Query: 196 SVGGLEVKVQESVLRKCPDIVIAT-----PGRLLDHLHNTPSFSLSDIEVLVLDEADRML 250
S+ L + +L K +I T +L + P ++ V+ DEA R
Sbjct: 326 SIAEL-----KELLEKDDGGIIITTIQKFDKKLKEEEEKFPVD-RKEVVVIF-DEAHRSQ 378
Query: 251 DEHFASQMKEIIR 263
A +K+ ++
Sbjct: 379 YGELAKNLKKALK 391
>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional.
Length = 2084
Score = 29.7 bits (66), Expect = 3.1
Identities = 21/84 (25%), Positives = 39/84 (46%), Gaps = 3/84 (3%)
Query: 6 EEGNKEDKEDNEGSEEDDVDAEEDFALPDDEMKHDNIKNRQKLIGKKKQKRLAKEGKLKQ 65
+E K+ +ED + ++E A + + K + K + K ++ + A E K K
Sbjct: 1394 DEAKKKAEEDKKKADELKKAAAAKKKADEAKKKAEEKKKADEAKKKAEEAKKADEAKKK- 1452
Query: 66 VEAEEYEENEGGKEFFEDAPPVEE 89
AEE ++ E K+ E+A +E
Sbjct: 1453 --AEEAKKAEEAKKKAEEAKKADE 1474
>gnl|CDD|240412 PTZ00420, PTZ00420, coronin; Provisional.
Length = 568
Score = 29.1 bits (65), Expect = 3.4
Identities = 17/82 (20%), Positives = 31/82 (37%), Gaps = 8/82 (9%)
Query: 13 KEDNEGSEEDDVDAEEDFALPDDEMKHDNIKNRQKLIGKKKQKRLAKEGKLKQVEAEEYE 72
E N+G D E F P ++L+ +K + + L++ E+Y
Sbjct: 438 GEHNDGFSSVDSFKESVFIYPKS-------FKEKELLTEKGGAQFSSANSLERGADEDYL 490
Query: 73 E-NEGGKEFFEDAPPVEENSSF 93
N + + E+ EN +F
Sbjct: 491 IVNGTNEPYEEEVIKTNENENF 512
>gnl|CDD|218538 pfam05285, SDA1, SDA1. This family consists of several SDA1
protein homologues. SDA1 is a Saccharomyces cerevisiae
protein which is involved in the control of the actin
cytoskeleton. The protein is essential for cell
viability and is localised in the nucleus.
Length = 317
Score = 29.2 bits (66), Expect = 3.4
Identities = 22/76 (28%), Positives = 35/76 (46%), Gaps = 5/76 (6%)
Query: 1 DDSSDEEGNKEDKEDNEGSEEDD-VDAEEDFALPDDEMKHDNIKNRQKLIGKKKQKRLAK 59
DD DEE E +ED + +E + +D E D + + + + K+ KK K +
Sbjct: 95 DDDDDEEEEWEVEEDEDSDDEGEWIDVESDKEIESSDSEDEEEKDE----AAKKAKEDSD 150
Query: 60 EGKLKQVEAEEYEENE 75
E ++ E E EE E
Sbjct: 151 EELSEEDEEEAAEEEE 166
>gnl|CDD|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger. [Transport and
binding proteins, Cations and iron carrying compounds].
Length = 1096
Score = 29.2 bits (65), Expect = 3.7
Identities = 12/32 (37%), Positives = 21/32 (65%)
Query: 2 DSSDEEGNKEDKEDNEGSEEDDVDAEEDFALP 33
DS +EE +E++E+ E EE++ + EE+ P
Sbjct: 862 DSEEEEEEEEEEEEEEEEEEEEEEEEEENEEP 893
>gnl|CDD|220759 pfam10446, DUF2457, Protein of unknown function (DUF2457). This
is a family of uncharacterized proteins.
Length = 449
Score = 28.8 bits (64), Expect = 4.0
Identities = 11/35 (31%), Positives = 21/35 (60%)
Query: 1 DDSSDEEGNKEDKEDNEGSEEDDVDAEEDFALPDD 35
++ D+E + +D +D + ++DD D E+D DD
Sbjct: 51 EEEDDDEEDDDDDDDEDEDDDDDDDDEDDEDEDDD 85
>gnl|CDD|234487 TIGR04157, glyco_rSAM_CFB, glycosyltransferase, GG-Bacteroidales
peptide system. Members of this protein family are
predicted glycosyltransferases that occur in conserved
gene neighborhoods in various members of the
Bacteroidales. These neighborhoods feature a radical SAM
enzyme predicted to act in peptide modification (family
TIGR04148), peptides from family TIGR04149 with a
characteristic GG cleavage motif, and several other
proteins.
Length = 406
Score = 28.8 bits (65), Expect = 4.1
Identities = 12/46 (26%), Positives = 21/46 (45%), Gaps = 7/46 (15%)
Query: 37 MKHDNIKNRQKLIGKKKQKRLAKEGKLKQVEAEEYEENEGGKEFFE 82
N+ + ++ K++ KR E +K EE+E KE F+
Sbjct: 130 KLKGNVSLLRSILRKEETKRSELEKLIK----EEFERE---KEMFQ 168
>gnl|CDD|235640 PRK05901, PRK05901, RNA polymerase sigma factor; Provisional.
Length = 509
Score = 28.8 bits (65), Expect = 4.1
Identities = 9/36 (25%), Positives = 16/36 (44%)
Query: 1 DDSSDEEGNKEDKEDNEGSEEDDVDAEEDFALPDDE 36
DD D++ + D ED E E +++ D +
Sbjct: 155 DDDEDDDDDDVDDEDEEKKEAKELEKLSDDDDFVWD 190
>gnl|CDD|217927 pfam04147, Nop14, Nop14-like family. Emg1 and Nop14 are novel
proteins whose interaction is required for the
maturation of the 18S rRNA and for 40S ribosome
production.
Length = 809
Score = 28.8 bits (65), Expect = 4.5
Identities = 12/36 (33%), Positives = 24/36 (66%)
Query: 1 DDSSDEEGNKEDKEDNEGSEEDDVDAEEDFALPDDE 36
D+ D++ +E++ED + S+E++ + +ED DDE
Sbjct: 334 DEEDDDDDLEEEEEDVDLSDEEEDEEDEDSDDEDDE 369
Score = 28.4 bits (64), Expect = 7.2
Identities = 11/36 (30%), Positives = 22/36 (61%), Gaps = 1/36 (2%)
Query: 1 DDSSDEEGNKEDKEDNEGSEEDDVDAEEDFALPDDE 36
+D +EE +D+++ + ++D + EED L D+E
Sbjct: 321 EDEEEEEDGVDDEDEED-DDDDLEEEEEDVDLSDEE 355
>gnl|CDD|185378 PRK15481, PRK15481, transcriptional regulatory protein PtsJ;
Provisional.
Length = 431
Score = 28.9 bits (65), Expect = 4.5
Identities = 22/83 (26%), Positives = 34/83 (40%), Gaps = 24/83 (28%)
Query: 186 AQFTSVEVALSVGGLEVKVQESVLRKCPDIVIATPGRLLDHLHNTPSFSLSDI------- 238
A F++ V++ G++ + E L + VI TP HN SLS
Sbjct: 185 AGFSASPVSVDAEGMQPEKLERALAQGARAVILTP-----RAHNPTGCSLSARRAAALRN 239
Query: 239 ------EVLVLDEADRMLDEHFA 255
+VLV+ +D+HFA
Sbjct: 240 LLARYPQVLVI------IDDHFA 256
>gnl|CDD|180970 PRK07417, PRK07417, arogenate dehydrogenase; Reviewed.
Length = 279
Score = 28.7 bits (65), Expect = 4.7
Identities = 19/56 (33%), Positives = 29/56 (51%), Gaps = 4/56 (7%)
Query: 172 RELGVQVYQVTRQLAQFTSVEVALSVGGL-EVKVQESVLRKCPDIVIATPGRLLDH 226
R LG VY V+R+ + T E A+ G + E S+L+ C +++A P LL
Sbjct: 20 RSLGHTVYGVSRR--EST-CERAIERGLVDEASTDLSLLKDCDLVILALPIGLLLP 72
>gnl|CDD|234113 TIGR03117, cas_csf4, CRISPR type AFERR-associated DEAD/DEAH-box
helicase Csf4. Members of this family show up near
CRISPR repeats in Acidithiobacillus ferrooxidans ATCC
23270, Azoarcus sp. EbN1, and Rhodoferax ferrireducens
DSM 15236. In the latter two species, the CRISPR/cas
locus is found on a plasmid. This family is one of
several characteristic of a type of CRISPR-associated
(cas) gene cluster we designate Aferr after A.
ferrooxidans, where it is both chromosomal and the only
type of cas gene cluster found. The gene is designated
csf4 (CRISPR/cas Subtype as in A. ferrooxidans protein
1), as it lies farthest (fourth closest) from the
repeats in the A. ferrooxidans genome [Mobile and
extrachromosomal element functions, Other].
Length = 636
Score = 28.8 bits (64), Expect = 4.7
Identities = 15/51 (29%), Positives = 27/51 (52%), Gaps = 4/51 (7%)
Query: 135 AATGTGKTAAFMLPILERLLYKPRDDQNTRVLVLVPTRELGVQVYQVTRQL 185
A+TG GKT A ++ L L ++ + ++ + VPT L Q++ +L
Sbjct: 23 ASTGVGKTLAMIMAALTML----KERPDQKIAIAVPTLALMGQLWSELERL 69
>gnl|CDD|180905 PRK07246, PRK07246, bifunctional ATP-dependent DNA helicase/DNA
polymerase III subunit epsilon; Validated.
Length = 820
Score = 28.9 bits (65), Expect = 4.9
Identities = 15/44 (34%), Positives = 24/44 (54%), Gaps = 7/44 (15%)
Query: 135 AATGTGKTAAFMLPILERLLYKPRDDQNTRVLVLVPTRELGVQV 178
A TG GKT ++LP+L + +++V VPT+ L Q+
Sbjct: 271 AQTGIGKTYGYLLPLLAQ-------SDQRQIIVSVPTKILQDQI 307
>gnl|CDD|218274 pfam04801, Sin_N, Sin-like protein conserved region. Family of
higher eukaryotic proteins. SIN was identified as a
protein that interacts specifically with SXL (sex
lethal) in a yeast two-hybrid assay. The interaction is
mediated by one of the SXL RNA binding domains.
Length = 422
Score = 28.6 bits (64), Expect = 5.0
Identities = 19/64 (29%), Positives = 32/64 (50%), Gaps = 7/64 (10%)
Query: 11 EDKEDNEGSEEDDVDAEEDFALPDDEMKHDN----IKNRQKLIGKKKQKRLAKEGKLKQV 66
DK+D EED D +ED PD+E + + +K + K++++R L++
Sbjct: 139 LDKKDKRKKEEDTADEDED---PDEEAEEELKQVTVKFSRPETEKQRKRREQSYNFLQKK 195
Query: 67 EAEE 70
AEE
Sbjct: 196 IAEE 199
>gnl|CDD|187839 cd09708, Csf4_U, CRISPR/Cas system-associated DinG family helicase
Csf4. 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;
DinG family DNA helicase.
Length = 632
Score = 28.8 bits (64), Expect = 5.0
Identities = 15/51 (29%), Positives = 27/51 (52%), Gaps = 4/51 (7%)
Query: 135 AATGTGKTAAFMLPILERLLYKPRDDQNTRVLVLVPTRELGVQVYQVTRQL 185
A+TG GKT A ++ L L ++ + ++ + VPT L Q++ +L
Sbjct: 23 ASTGVGKTLAMIMAALTML----KERPDQKIAIAVPTLALMGQLWSELERL 69
>gnl|CDD|215601 PLN03142, PLN03142, Probable chromatin-remodeling complex ATPase
chain; Provisional.
Length = 1033
Score = 29.0 bits (65), Expect = 5.1
Identities = 18/81 (22%), Positives = 38/81 (46%), Gaps = 6/81 (7%)
Query: 1 DDSSDEEGNKEDKEDNE------GSEEDDVDAEEDFALPDDEMKHDNIKNRQKLIGKKKQ 54
+ + + +ED+E+ E GS+ DD + + D+E + + I K+++
Sbjct: 3 EQVNTQANEEEDEEELEAVARSAGSDSDDDEVPAEDEDEDEEDDEEAESPAKAEISKREK 62
Query: 55 KRLAKEGKLKQVEAEEYEENE 75
RL + K K+ E ++ E +
Sbjct: 63 ARLKELKKQKKQEIQKILEQQ 83
>gnl|CDD|219069 pfam06512, Na_trans_assoc, Sodium ion transport-associated.
Members of this family contain a region found
exclusively in eukaryotic sodium channels or their
subunits, many of which are voltage-gated. Members very
often also contain between one and four copies of
pfam00520 and, less often, one copy of pfam00612.
Length = 230
Score = 28.1 bits (63), Expect = 5.4
Identities = 14/35 (40%), Positives = 19/35 (54%)
Query: 1 DDSSDEEGNKEDKEDNEGSEEDDVDAEEDFALPDD 35
DSS EG+ D E E EE+ + EE+ P+D
Sbjct: 147 KDSSSSEGSTVDLEPPEEEEEEIAEEEEEVKEPED 181
>gnl|CDD|224041 COG1116, TauB, ABC-type nitrate/sulfonate/bicarbonate transport
system, ATPase component [Inorganic ion transport and
metabolism].
Length = 248
Score = 28.3 bits (64), Expect = 5.4
Identities = 13/37 (35%), Positives = 22/37 (59%), Gaps = 1/37 (2%)
Query: 239 EVLVLDEADRMLDEHFASQM-KEIIRLCSRTRQTMLF 274
++L+LDE LD ++ E++RL TR+T+L
Sbjct: 150 KLLLLDEPFGALDALTREELQDELLRLWEETRKTVLL 186
>gnl|CDD|240329 PTZ00248, PTZ00248, eukaryotic translation initiation factor 2
subunit 1; Provisional.
Length = 319
Score = 28.5 bits (64), Expect = 5.5
Identities = 11/39 (28%), Positives = 22/39 (56%), Gaps = 3/39 (7%)
Query: 2 DSSDEEGNKEDKEDNEGSEEDDVDAEEDFALPDDEMKHD 40
+ ++EE ++D ++E +E+D D EE+ DD+
Sbjct: 284 EKAEEEEEEDDYSESEDEDEEDEDEEEE---EDDDEGDK 319
>gnl|CDD|220102 pfam09073, BUD22, BUD22. BUD22 has been shown in yeast to be a
nuclear protein involved in bud-site selection. It plays
a role in positioning the proximal bud pole signal. More
recently it has been shown to be involved in ribosome
biogenesis.
Length = 424
Score = 28.6 bits (64), Expect = 5.6
Identities = 21/97 (21%), Positives = 36/97 (37%), Gaps = 9/97 (9%)
Query: 2 DSSDEEG-----NKEDKEDNEGSEEDDVDAEEDFALPDDEMKHDNIKNRQKLIGKKKQKR 56
DSSDEE + ED SE D+ D+E + + + ++ +K KK
Sbjct: 213 DSSDEEEGEEAPSINYNEDTSESESDESDSEISESRSVSDSE-ESSPPSKKPKEKKTSST 271
Query: 57 LAKE---GKLKQVEAEEYEENEGGKEFFEDAPPVEEN 90
G E E+ ++ + + P +N
Sbjct: 272 FLPSLMGGYFSGSEDEDDDDEDIDPDQVVKKPVKRKN 308
Score = 27.9 bits (62), Expect = 9.9
Identities = 11/36 (30%), Positives = 20/36 (55%)
Query: 2 DSSDEEGNKEDKEDNEGSEEDDVDAEEDFALPDDEM 37
+S DE ++E ED+ EE++ ED++ D +
Sbjct: 176 ESEDESKSEESAEDDSDDEEEEDSDSEDYSQYDGML 211
>gnl|CDD|218333 pfam04931, DNA_pol_phi, DNA polymerase phi. This family includes
the fifth essential DNA polymerase in yeast EC:2.7.7.7.
Pol5p is localised exclusively to the nucleolus and
binds near or at the enhancer region of rRNA-encoding
DNA repeating units.
Length = 784
Score = 28.7 bits (64), Expect = 5.6
Identities = 16/79 (20%), Positives = 23/79 (29%), Gaps = 5/79 (6%)
Query: 1 DDSSDEEGNKEDKEDNEGSEEDDVDAEEDFALPDDEMKHDNIKNRQKLIGKKKQKRLAKE 60
DD DE + ++ SE D D EED D E N ++
Sbjct: 659 DDDEDEC--EAIEDSESESESDGEDGEEDEQEDDAE---ANEGVVPIDKAVRRALPKVLN 713
Query: 61 GKLKQVEAEEYEENEGGKE 79
+ +E E
Sbjct: 714 LPDALDGGDSEDEEGMDDE 732
>gnl|CDD|234011 TIGR02782, TrbB_P, P-type conjugative transfer ATPase TrbB. The
TrbB protein is found in the trb locus of Agrobacterium
Ti plasmids where it is involved in the type IV
secretion system for plasmid conjugative transfer. TrbB
is a homolog of the vir system VirB11 ATPase , and the
Flp pilus sytem ATPase TadA [Cellular processes,
Conjugation].
Length = 299
Score = 28.2 bits (63), Expect = 6.0
Identities = 30/112 (26%), Positives = 44/112 (39%), Gaps = 17/112 (15%)
Query: 70 EYEENEGGKEFFEDAPPVEENSSFHQMNLSRPLLKAIGALNYIYP---TPIQAATIPVAL 126
E E G F PPV SF + + + +Y+ T Q + A+
Sbjct: 73 EGELPLDGSRFEGLIPPVVAAPSF---AIRKKAVAVFTLDDYVEAGIMTAAQRDVLREAV 129
Query: 127 LGR-DICGCAATGTGKTA---AFMLPILERLLYKPRDDQNTRVLVLVPTREL 174
L R +I TG+GKT A + I + D RV+++ TREL
Sbjct: 130 LARKNILVVGGTGSGKTTLANALLAEIAKN-------DPTDRVVIIEDTREL 174
>gnl|CDD|203444 pfam06424, PRP1_N, PRP1 splicing factor, N-terminal. This domain
is specific to the N-terminal part of the prp1 splicing
factor, which is involved in mRNA splicing (and possibly
also poly(A)+ RNA nuclear export and cell cycle
progression). This domain is specific to the N terminus
of the RNA splicing factor encoded by prp1. It is
involved in mRNA splicing and possibly also poly(A)and
RNA nuclear export and cell cycle progression.
Length = 131
Score = 27.3 bits (61), Expect = 6.0
Identities = 17/71 (23%), Positives = 34/71 (47%), Gaps = 6/71 (8%)
Query: 1 DDSSDEEGNKEDKEDNEG------SEEDDVDAEEDFALPDDEMKHDNIKNRQKLIGKKKQ 54
DD DE+ + DNEG +++D +A+ + D+ M K R++ ++ +
Sbjct: 32 DDEEDEDPKRYQDGDNEGLFSDGKYDDEDEEADRIYESIDERMDERRKKRREQKEKEEIE 91
Query: 55 KRLAKEGKLKQ 65
K + K++Q
Sbjct: 92 KYREENPKIQQ 102
>gnl|CDD|219124 pfam06658, DUF1168, Protein of unknown function (DUF1168). This
family consists of several hypothetical eukaryotic
proteins of unknown function.
Length = 142
Score = 27.3 bits (61), Expect = 6.2
Identities = 26/96 (27%), Positives = 35/96 (36%), Gaps = 17/96 (17%)
Query: 6 EEGNKEDKEDNEGS---EEDDVDAEEDFALPDDEMKHDNIKN---RQKLIGKKKQKRLAK 59
+E K++ ED E EE EE A K RQK KKK+K+ AK
Sbjct: 56 DEKWKKETEDEEFQQKREEKKRKDEEKTA-----------KKRAKRQKKKQKKKKKKKAK 104
Query: 60 EGKLKQVEAEEYEENEGGKEFFEDAPPVEENSSFHQ 95
+G K+ + E E E +E
Sbjct: 105 KGNKKEEKEGSKSSEESSDEEEEGEEDKQEEPVEIM 140
>gnl|CDD|219256 pfam06991, Prp19_bind, Splicing factor, Prp19-binding domain.
This family represents the C-terminus (approximately
300 residues) of proteins that are involved as binding
partners for Prp19 as part of the nuclear pore complex.
The family in Drosophila is necessary for pre-mRNA
splicing, and the human protein has been found in
purifications of the spliceosome. In the past this
family was thought, erroneously, to be associated with
microfibrillin.
Length = 277
Score = 28.0 bits (62), Expect = 6.3
Identities = 20/68 (29%), Positives = 33/68 (48%), Gaps = 3/68 (4%)
Query: 3 SSDEEGNKEDKEDNEGSEEDDVDAEEDFAL---PDDEMKHDNIKNRQKLIGKKKQKRLAK 59
+EE ++E+ E EE++ D+E+D P K D I +++ K+K L +
Sbjct: 6 ELEEEDESGEEEEEESEEEEETDSEDDMEPRLKPVFTRKKDRITIQEREREAAKEKALEE 65
Query: 60 EGKLKQVE 67
E K K E
Sbjct: 66 EAKRKAEE 73
>gnl|CDD|215774 pfam00183, HSP90, Hsp90 protein.
Length = 529
Score = 28.2 bits (63), Expect = 6.5
Identities = 13/65 (20%), Positives = 28/65 (43%), Gaps = 5/65 (7%)
Query: 1 DDSSDEEGNKEDKEDNEGSEEDDVDAEEDFALP-----DDEMKHDNIKNRQKLIGKKKQK 55
++ EE +E+++ + EE D + E++ + + N+ K I + K
Sbjct: 40 EEEEKEEKKEEEEKTTDKEEEVDEEEEKEEKKKKTKKVKETTTEWELLNKTKPIWTRNPK 99
Query: 56 RLAKE 60
+ KE
Sbjct: 100 DVTKE 104
>gnl|CDD|115196 pfam06524, NOA36, NOA36 protein. This family consists of several
NOA36 proteins which contain 29 highly conserved
cysteine residues. The function of this protein is
unknown.
Length = 314
Score = 28.0 bits (62), Expect = 6.6
Identities = 9/27 (33%), Positives = 15/27 (55%)
Query: 3 SSDEEGNKEDKEDNEGSEEDDVDAEED 29
S D+EG+ + D E +DD + + D
Sbjct: 273 SDDDEGSSSNDYDEEEDGDDDDNEDND 299
>gnl|CDD|223683 COG0610, COG0610, Type I site-specific restriction-modification
system, R (restriction) subunit and related helicases
[Defense mechanisms].
Length = 962
Score = 28.5 bits (64), Expect = 6.7
Identities = 41/190 (21%), Positives = 70/190 (36%), Gaps = 34/190 (17%)
Query: 137 TGTGKTAAFMLPILERLLYKPRDDQNTRVLVLVPTRELGVQVYQVTRQLAQFTSVEV--- 193
G+GKT M + LL +N +VL +V ++L Q + + F V
Sbjct: 282 QGSGKTLT-MFKLARLLL---ELPKNPKVLFVVDRKDL---DDQTSDEFQSFGKVAFNDP 334
Query: 194 -ALSVGGLEVKVQESVLRKCPDIVIATPGRLLDHLHNTPSFSLSDIEVLVL-DEADRMLD 251
A S L ++ E K I++ T + + L V+V+ DEA R
Sbjct: 335 KAESTSEL-KELLEDGKGK---IIVTTIQKFNKAVKEDELELLKRKNVVVIIDEAHRSQY 390
Query: 252 EHFASQMKEIIRLC---------------SRTRQT---MLFSATMTDAVNDLVSVSLTRP 293
A +K+ ++ T+ L + T+TDA+ D + +
Sbjct: 391 GELAKLLKKALKKAIFIGFTGTPIFKEDKDTTKDVFGDYLHTYTITDAIRDGAVLPVYYE 450
Query: 294 VRVFVDNNHE 303
RV ++ E
Sbjct: 451 NRVELELIEE 460
>gnl|CDD|223588 COG0514, RecQ, Superfamily II DNA helicase [DNA replication,
recombination, and repair].
Length = 590
Score = 28.4 bits (64), Expect = 6.7
Identities = 41/189 (21%), Positives = 65/189 (34%), Gaps = 38/189 (20%)
Query: 118 QAATIPVALLGRDICGCAATGTGKTAAFMLPILERLLYKPRDDQNTRVLVLVPTREL-GV 176
Q I L G+D TG GK+ + +P LL LV+ P L
Sbjct: 22 QQEIIDALLSGKDTLVVMPTGGGKSLCYQIP--ALLLEGL-------TLVVSPLISLMKD 72
Query: 177 QVYQVTRQLAQFTSVEVALSVGGLEVKVQESVLRKCP----DIVIATPGRLL-DHLHNTP 231
QV Q+ + A L + ++ VL + ++ +P RL+
Sbjct: 73 QVDQLEAA-----GIRAAYLNSTLSREERQQVLNQLKSGQLKLLYISPERLMSPRFLEL- 126
Query: 232 SFSLSDIEVLVLDEADRMLDEHFASQM--------KEIIRLCSRTRQT--MLFSATMTDA 281
I ++ +DEA H SQ + + RL + + +AT T
Sbjct: 127 -LKRLPISLVAIDEA------HCISQWGHDFRPDYRRLGRLRAGLPNPPVLALTATATPR 179
Query: 282 VNDLVSVSL 290
V D + L
Sbjct: 180 VRDDIREQL 188
>gnl|CDD|221490 pfam12253, CAF1A, Chromatin assembly factor 1 subunit A. The
CAF-1 or chromatin assembly factor-1 consists of three
subunits, and this is the first, or A. The A domain is
uniquely required for the progression of S phase in
mouse cells, independent of its ability to promote
histone deposition but dependent on its ability to
interact with HP1 - heterochromatin protein 1-rich
heterochromatin domains next to centromeres that are
crucial for chromosome segregation during mitosis. This
HP1-CAF-1 interaction module functions as a built-in
replication control for heterochromatin, which, like a
control barrier, has an impact on S-phase progression
in addition to DNA-based checkpoints.
Length = 76
Score = 26.0 bits (58), Expect = 7.4
Identities = 12/26 (46%), Positives = 15/26 (57%)
Query: 5 DEEGNKEDKEDNEGSEEDDVDAEEDF 30
+EEG + ED E EEDD D + F
Sbjct: 51 EEEGEDLESEDEEDEEEDDDDDMDGF 76
>gnl|CDD|237538 PRK13876, PRK13876, conjugal transfer coupling protein TraG;
Provisional.
Length = 663
Score = 28.4 bits (64), Expect = 7.5
Identities = 12/51 (23%), Positives = 20/51 (39%), Gaps = 5/51 (9%)
Query: 1 DDSSDEEGNKEDKEDNEGSEEDDVD-----AEEDFALPDDEMKHDNIKNRQ 46
D + N + E E +++ E +F L DD+ D + RQ
Sbjct: 591 GDDDGDPDNGGIRRQPELPEHEEIVPEPRPPENEFDLLDDDDDDDAARPRQ 641
>gnl|CDD|184292 PRK13740, PRK13740, conjugal transfer protein TraY; Provisional.
Length = 70
Score = 25.9 bits (57), Expect = 7.5
Identities = 11/26 (42%), Positives = 14/26 (53%)
Query: 222 RLLDHLHNTPSFSLSDIEVLVLDEAD 247
RL DHL P F S+I V +E +
Sbjct: 44 RLRDHLKRFPDFYNSEIFREVAEETE 69
>gnl|CDD|219924 pfam08597, eIF3_subunit, Translation initiation factor eIF3
subunit. This is a family of proteins which are
subunits of the eukaryotic translation initiation
factor 3 (eIF3). In yeast it is called Hcr1. The
Saccharomyces cerevisiae protein eIF3j (HCR1) has been
shown to be required for processing of 20S pre-rRNA and
binds to 18S rRNA and eIF3 subunits Rpg1p and Prt1p.
Length = 242
Score = 27.7 bits (62), Expect = 7.6
Identities = 21/89 (23%), Positives = 42/89 (47%), Gaps = 10/89 (11%)
Query: 1 DDSSDEEGNKE----DKEDNEGSEEDDVDAEEDFALPDDEMKHDNIKNRQKLIGKKKQKR 56
++ + DK D+E ++D D+ ++ +DE K + + K+ K K K+
Sbjct: 7 EEFEPPAPPAKAVVKDKWDDEDEDDDVKDSWDE---EEDEEKE---EEKAKVAAKAKAKK 60
Query: 57 LAKEGKLKQVEAEEYEENEGGKEFFEDAP 85
K ++ +A+ +E +G +E ED P
Sbjct: 61 ALKAKIEEKEKAKREKEEKGLRELEEDTP 89
>gnl|CDD|145949 pfam03066, Nucleoplasmin, Nucleoplasmin. Nucleoplasmins are also
known as chromatin decondensation proteins. They bind to
core histones and transfer DNA to them in a reaction
that requires ATP. This is thought to play a role in the
assembly of regular nucleosomal arrays.
Length = 146
Score = 27.3 bits (61), Expect = 7.7
Identities = 14/38 (36%), Positives = 23/38 (60%), Gaps = 3/38 (7%)
Query: 1 DDSSDEEGNKEDKEDNEGSEEDDVDAEEDFALPDDEMK 38
D+S D+E ED+E+ + E+DD D E+ P ++K
Sbjct: 112 DESDDDE---EDEEEEDDEEDDDEDESEEEESPVKKVK 146
>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 = 28.2 bits (63), Expect = 8.0
Identities = 10/16 (62%), Positives = 12/16 (75%)
Query: 135 AATGTGKTAAFMLPIL 150
A TGTGKT ++LP L
Sbjct: 271 APTGTGKTLGYLLPAL 286
>gnl|CDD|215595 PLN03130, PLN03130, ABC transporter C family member; Provisional.
Length = 1622
Score = 28.2 bits (63), Expect = 8.0
Identities = 16/61 (26%), Positives = 26/61 (42%), Gaps = 6/61 (9%)
Query: 15 DNEGSEEDDVDAEEDFALPDDE---MKHDNIKNRQKLIGKKKQKRLAKEGKLKQVEAEEY 71
+N G E+ V+ + + + N N +K KK+ KEGK ++ EE
Sbjct: 838 ENAGKMEEYVEENGEEEDDQTSSKPVANGNANNLKKDSSSKKKS---KEGKSVLIKQEER 894
Query: 72 E 72
E
Sbjct: 895 E 895
>gnl|CDD|217392 pfam03153, TFIIA, Transcription factor IIA, alpha/beta subunit.
Transcription initiation factor IIA (TFIIA) is a
heterotrimer, the three subunits being known as alpha,
beta, and gamma, in order of molecular weight. The N and
C-terminal domains of the gamma subunit are represented
in pfam02268 and pfam02751, respectively. This family
represents the precursor that yields both the alpha and
beta subunits. The TFIIA heterotrimer is an essential
general transcription initiation factor for the
expression of genes transcribed by RNA polymerase II.
Together with TFIID, TFIIA binds to the promoter region;
this is the first step in the formation of a
pre-initiation complex (PIC). Binding of the rest of the
transcription machinery follows this step. After
initiation, the PIC does not completely dissociate from
the promoter. Some components, including TFIIA, remain
attached and re-initiate a subsequent round of
transcription.
Length = 332
Score = 27.8 bits (62), Expect = 8.1
Identities = 9/41 (21%), Positives = 19/41 (46%), Gaps = 5/41 (12%)
Query: 1 DDSSDEEGNKEDKEDNEGSEE-----DDVDAEEDFALPDDE 36
D + +G+ +D +++ + DDV E+ L D +
Sbjct: 248 DSDDEGDGSDDDDDEDAIESDLDDSDDDVSDEDGEDLFDTD 288
>gnl|CDD|235321 PRK04946, PRK04946, hypothetical protein; Provisional.
Length = 181
Score = 27.6 bits (62), Expect = 8.1
Identities = 21/72 (29%), Positives = 31/72 (43%), Gaps = 12/72 (16%)
Query: 22 DDVDAEEDFALPDDE------MKHDNI--KNRQKLIGKKKQKRLAKEGKLKQVEAEEYEE 73
D +E+D AL +K D I + +K I KK +KRL +E Q +A Y
Sbjct: 4 KDSLSEDDLALFRQLIKGTKKIKQDTIVHRPPRKKIKKKPEKRLLQE----QADASHYFS 59
Query: 74 NEGGKEFFEDAP 85
+E + P
Sbjct: 60 DEFQPLLNTEGP 71
>gnl|CDD|227504 COG5177, COG5177, Uncharacterized conserved protein [Function
unknown].
Length = 769
Score = 28.1 bits (62), Expect = 8.1
Identities = 12/82 (14%), Positives = 38/82 (46%), Gaps = 14/82 (17%)
Query: 1 DDSSDEEGNKE------DKEDNEGSEEDDVDAEEDFALPDDEMKHDNIKNRQKLIGKKKQ 54
++ + ++E D +D + ++ ++V +E+ A+ D+E + + +++
Sbjct: 397 EEEDGQCNDEESTMSAIDDDDPKENDNEEVAGDEESAIDDNEGFEE--------LSPEEE 448
Query: 55 KRLAKEGKLKQVEAEEYEENEG 76
+R +E + + E E+ +
Sbjct: 449 ERQLREFRDMEKEDREFPDEAE 470
>gnl|CDD|234033 TIGR02857, CydD, thiol reductant ABC exporter, CydD subunit. The
gene pair cydCD encodes an ABC-family transporter in
which each gene contains an N-terminal membrane-spanning
domain (pfam00664) and a C-terminal ATP-binding domain
(pfam00005). In E. coli these genes were discovered as
mutants which caused the terminal heme-copper oxidase
complex cytochrome bd to fail to assemble. Recent work
has shown that the transporter is involved in export of
redox-active thiol compounds such as cysteine and
glutathione. The linkage to assembly of the cytochrome
bd complex is further supported by the conserved operon
structure found outside the gammaproteobacteria
(cydABCD) containing both the transporter and oxidase
genes components. The genes used as the seed members for
this model are all either found in the
gammproteobacterial context or the CydABCD context. All
members of this family scoring above trusted at the time
of its creation were from genomes which encode a
cytochrome bd complex. Unfortunately, the gene symbol
nomenclature adopted based on this operon in B. subtilis
assigns cydC to the third gene in the operon where this
gene is actually homologous to the E. coli cydD gene. We
have chosen to name all homologs in this family in
accordance with the precedence of publication of the E.
coli name, CydD.
Length = 529
Score = 28.0 bits (63), Expect = 8.1
Identities = 12/39 (30%), Positives = 21/39 (53%)
Query: 235 LSDIEVLVLDEADRMLDEHFASQMKEIIRLCSRTRQTML 273
L D +L+LDE LD +++ E +R ++ R +L
Sbjct: 474 LRDAPLLLLDEPTAHLDAETEAEVLEALRALAQGRTVLL 512
>gnl|CDD|239286 cd02988, Phd_like_VIAF, Phosducin (Phd)-like family, Viral
inhibitor of apoptosis (IAP)-associated factor (VIAF)
subfamily; VIAF is a Phd-like protein that functions in
caspase activation during apoptosis. It was identified
as an IAP binding protein through a screen of a human
B-cell library using a prototype IAP. VIAF lacks a
consensus IAP binding motif and while it does not
function as an IAP antagonist, it still plays a
regulatory role in the complete activation of caspases.
VIAF itself is a substrate for IAP-mediated
ubiquitination, suggesting that it may be a target of
IAPs in the prevention of cell death. The similarity of
VIAF to Phd points to a potential role distinct from
apoptosis regulation. Phd functions as a cytosolic
regulator of G protein by specifically binding to G
protein betagamma (Gbg)-subunits. The C-terminal domain
of Phd adopts a thioredoxin fold, but it does not
contain a CXXC motif. Phd interacts with G protein beta
mostly through the N-terminal helical domain.
Length = 192
Score = 27.6 bits (62), Expect = 8.5
Identities = 20/78 (25%), Positives = 34/78 (43%), Gaps = 11/78 (14%)
Query: 6 EEGNKEDKEDNEGSEEDDVDAEEDFALPDDEMKHDNIKNRQKLIGKKKQKRLAKEGKLKQ 65
E E K +E EE D + E+D L E + R++L K +K G++ +
Sbjct: 36 HENALEKKLLDELDEELD-EEEDDRFL---EE----YR-RKRLAEMKALAEKSKFGEVYE 86
Query: 66 VEAEEY--EENEGGKEFF 81
+ +Y E E K+ +
Sbjct: 87 ISKPDYVREVTEASKDTW 104
>gnl|CDD|219922 pfam08595, RXT2_N, RXT2-like, N-terminal. The family represents
the N-terminal region of RXT2-like proteins. In S.
cerevisiae, RXT2 has been demonstrated to be involved
in conjugation with cellular fusion (mating) and
invasive growth. A high throughput localisation study
has localised RXT2 to the nucleus.
Length = 141
Score = 27.0 bits (60), Expect = 9.0
Identities = 9/26 (34%), Positives = 17/26 (65%)
Query: 4 SDEEGNKEDKEDNEGSEEDDVDAEED 29
DE+G D +D + ++++ DAE+D
Sbjct: 47 IDEDGGDIDDDDEDDEDDEEADAEDD 72
>gnl|CDD|220284 pfam09538, FYDLN_acid, Protein of unknown function (FYDLN_acid).
Members of this family are bacterial proteins with a
conserved motif [KR]FYDLN, sometimes flanked by a pair
of CXXC motifs, followed by a long region of low
complexity sequence in which roughly half the residues
are Asp and Glu, including multiple runs of five or more
acidic residues. The function of members of this family
is unknown.
Length = 104
Score = 26.5 bits (59), Expect = 9.1
Identities = 12/38 (31%), Positives = 22/38 (57%), Gaps = 2/38 (5%)
Query: 1 DDSSDEEGNKEDKEDNEGSEEDDVDAEE--DFALPDDE 36
D D++ + +D +D ++DDVD ++ D L DD+
Sbjct: 65 DVVLDDDDDDDDDDDLPDLDDDDVDLDDDDDDFLEDDD 102
>gnl|CDD|233069 TIGR00643, recG, ATP-dependent DNA helicase RecG. [DNA metabolism,
DNA replication, recombination, and repair].
Length = 630
Score = 28.1 bits (63), Expect = 9.2
Identities = 22/72 (30%), Positives = 34/72 (47%), Gaps = 6/72 (8%)
Query: 138 GTGKTAAFMLPILERLLYKPRDDQNTRVLVLVPTRELGVQVYQVTRQLAQFTSVEVALSV 197
G+GKT L +L + + +V ++ PT L Q Y R L +EVAL
Sbjct: 266 GSGKTLVAALAMLAAI------EAGYQVALMAPTEILAEQHYNSLRNLLAPLGIEVALLT 319
Query: 198 GGLEVKVQESVL 209
G L+ K ++ +L
Sbjct: 320 GSLKGKRRKELL 331
>gnl|CDD|235249 PRK04194, PRK04194, hypothetical protein; Provisional.
Length = 392
Score = 27.8 bits (63), Expect = 9.8
Identities = 11/31 (35%), Positives = 15/31 (48%)
Query: 174 LGVQVYQVTRQLAQFTSVEVALSVGGLEVKV 204
LGV+ Y V R + + V G + VKV
Sbjct: 317 LGVREYPVERWVLERRIETVETPYGEVRVKV 347
>gnl|CDD|221333 pfam11942, Spt5_N, Spt5 transcription elongation factor, acidic
N-terminal. This is the very acidic N-terminal region
of the early transcription elongation factor Spt5. The
Spt5-Spt4 complex regulates early transcription
elongation by RNA polymerase II and has an imputed role
in pre-mRNA processing via its physical association
with mRNA capping enzymes. The actual function of this
N-terminal domain is not known although it is
dispensable for binding to Spt4.
Length = 92
Score = 26.3 bits (58), Expect = 9.8
Identities = 16/85 (18%), Positives = 41/85 (48%), Gaps = 1/85 (1%)
Query: 1 DDSSDEEGNKEDKEDNEGSEEDDVDAEEDFALPDDEMKHDNIKNRQKLIGKKKQKRLAKE 60
+ D+E +E++E+++ + D D D A +D+ +H + R++ ++ + LA+
Sbjct: 5 EAEVDDEEEEEEEEEDDLEDLSDEDEFIDEAEAEDDRRHRRLDRRREKEEEEDAEELAEY 64
Query: 61 GKLK-QVEAEEYEENEGGKEFFEDA 84
+ + EA+ ++ E +
Sbjct: 65 LRKRYGDEADADADDSDSDEVPQRL 89
>gnl|CDD|225664 COG3122, COG3122, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 215
Score = 27.2 bits (60), Expect = 10.0
Identities = 17/66 (25%), Positives = 35/66 (53%), Gaps = 1/66 (1%)
Query: 3 SSDEEGNKEDKEDNEGSEEDDVDAEEDFALPDDEMKHDNIKNRQKLIGKKKQKRLAKEGK 62
+ +K+ + +++ VDA E + + +E K + ++ ++L ++KQ LAKE K
Sbjct: 51 KAGLVTSKKRAKVQRLAKKSRVDAREAYRIAAEENKAEQLERDKQLSEQQKQAALAKEYK 110
Query: 63 LKQVEA 68
QV+
Sbjct: 111 -AQVKQ 115
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 0.134 0.372
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: 17,417,325
Number of extensions: 1734244
Number of successful extensions: 3299
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2925
Number of HSP's successfully gapped: 241
Length of query: 337
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 240
Effective length of database: 6,635,264
Effective search space: 1592463360
Effective search space used: 1592463360
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: 59 (26.7 bits)