RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14504
(951 letters)
>gnl|CDD|234173 TIGR03346, chaperone_ClpB, ATP-dependent chaperone ClpB. Members
of this protein family are the bacterial ATP-dependent
chaperone ClpB. This protein belongs to the AAA family,
ATPases associated with various cellular activities
(pfam00004). This molecular chaperone does not act as a
protease, but rather serves to disaggregate misfolded
and aggregated proteins [Protein fate, Protein folding
and stabilization].
Length = 852
Score = 1127 bits (2917), Expect = 0.0
Identities = 421/676 (62%), Positives = 553/676 (81%), Gaps = 5/676 (0%)
Query: 12 GKNILSQQDEEHIGYLKKYTIDLTEKARLGKLDPVIGRDDEIRRAIQVLQRRSKNNPVLI 71
G+ + S E+ L+KY DLTE+AR GKLDPVIGRD+EIRR IQVL RR+KNNPVLI
Sbjct: 141 GQKVTSANAEDQYEALEKYARDLTERAREGKLDPVIGRDEEIRRTIQVLSRRTKNNPVLI 200
Query: 72 GEPGVGKTAIVEGLAQRIINGEVPNSLLSKKILLLDIALLLAGTKYRGEFEDRLKKILKE 131
GEPGVGKTAIVEGLAQRI+NG+VP SL +K++L LD+ L+AG KYRGEFE+RLK +L E
Sbjct: 201 GEPGVGKTAIVEGLAQRIVNGDVPESLKNKRLLALDMGALIAGAKYRGEFEERLKAVLNE 260
Query: 132 ISNNQKDIIIFIDELHTMIGTGKVEGSIDAGNMLKPELSRGELHCIGATTLNEYRQYIEK 191
++ ++ II+FIDELHT++G GK EG++DAGNMLKP L+RGELHCIGATTL+EYR+YIEK
Sbjct: 261 VTKSEGQIILFIDELHTLVGAGKAEGAMDAGNMLKPALARGELHCIGATTLDEYRKYIEK 320
Query: 192 DAAFERRFQKILVEEPDIEETISILRGLQKKYEVHHGVEITDPAIVAASELSYRYISDRF 251
DAA ERRFQ + V+EP +E+TISILRGL+++YEVHHGV ITDPAIVAA+ LS+RYI+DRF
Sbjct: 321 DAALERRFQPVFVDEPTVEDTISILRGLKERYEVHHGVRITDPAIVAAATLSHRYITDRF 380
Query: 252 MPDKAIDLIDEAAAKIKIEIDSKPEIMDKLERRLIQLKIEHEAIKREYDESSKKRLLLIK 311
+PDKAIDLIDEAAA+I++EIDSKPE +D+L+RR+IQL+IE EA+K+E DE+SK+RL ++
Sbjct: 381 LPDKAIDLIDEAAARIRMEIDSKPEELDELDRRIIQLEIEREALKKEKDEASKERLEDLE 440
Query: 312 KEINKLEIKYANLEKIWKYEKTLIKDSQQIKEEIEKVRLKINKATRKSDWQTVSKLKYGE 371
KE+ +LE +YA+LE+ WK EK I+ QQIKEEIE+VRL++ +A R+ D ++L+YG+
Sbjct: 441 KELAELEEEYADLEEQWKAEKAAIQGIQQIKEEIEQVRLELEQAEREGDLAKAAELQYGK 500
Query: 372 LNKLERILKEKSQKDIQLPNNANKFTLLKTKVGSEEIAEIVSRTTGIPVSKIVQVEREKL 431
L +LE+ L+ K + LL+ +V +EEIAE+VSR TGIPVSK+++ EREKL
Sbjct: 501 LPELEKRLQAAEAKLGEETKPR----LLREEVTAEEIAEVVSRWTGIPVSKMLEGEREKL 556
Query: 432 LNIENLLCKRVVGQDEAISAVSNAIRRSRSGLSDAKRPYGSFMFLGPTGVGKTELCKTLS 491
L++E +L +RVVGQDEA+ AVS+AIRRSR+GLSD RP GSF+FLGPTGVGKTEL K L+
Sbjct: 557 LHMEEVLHERVVGQDEAVEAVSDAIRRSRAGLSDPNRPIGSFLFLGPTGVGKTELAKALA 616
Query: 492 ACIFNNEESIIRIDMSEFIEKHSISRLIGAPPGYIGYEEGGYLTEIVRRKPYSLILLDEI 551
+F++E++++RIDMSE++EKHS++RLIGAPPGY+GYEEGG LTE VRRKPYS++L DE+
Sbjct: 617 EFLFDDEDAMVRIDMSEYMEKHSVARLIGAPPGYVGYEEGGQLTEAVRRKPYSVVLFDEV 676
Query: 552 EKANSDVFNILLQILDDGRLTDNRGRTINFRNTIIVMTSNLGSDKIKEM-EKGDKEIIKL 610
EKA+ DVFN+LLQ+LDDGRLTD +GRT++FRNT+I+MTSNLGS I+E+ D E ++
Sbjct: 677 EKAHPDVFNVLLQVLDDGRLTDGQGRTVDFRNTVIIMTSNLGSQFIQELAGGDDYEEMRE 736
Query: 611 AVMNEVKIYFRPEFINRIDDIIVFRYLNRKNILSIANIQLNILKNKLLKMNMDLKISKAA 670
AVM ++ +FRPEF+NRID+I+VF L R+ I I IQL L+ +L + + L++S AA
Sbjct: 737 AVMEVLRAHFRPEFLNRIDEIVVFHPLGREQIARIVEIQLGRLRKRLAERKITLELSDAA 796
Query: 671 LKKISNIGFDLIYGAR 686
L ++ G+D +YGAR
Sbjct: 797 LDFLAEAGYDPVYGAR 812
>gnl|CDD|182791 PRK10865, PRK10865, protein disaggregation chaperone; Provisional.
Length = 857
Score = 931 bits (2409), Expect = 0.0
Identities = 415/716 (57%), Positives = 557/716 (77%), Gaps = 15/716 (2%)
Query: 12 GKNILSQQDEEHIGYLKKYTIDLTEKARLGKLDPVIGRDDEIRRAIQVLQRRSKNNPVLI 71
G+++ Q E+ LKKYTIDLTE+A GKLDPVIGRD+EIRR IQVLQRR+KNNPVLI
Sbjct: 146 GESVNDQGAEDQRQALKKYTIDLTERAEQGKLDPVIGRDEEIRRTIQVLQRRTKNNPVLI 205
Query: 72 GEPGVGKTAIVEGLAQRIINGEVPNSLLSKKILLLDIALLLAGTKYRGEFEDRLKKILKE 131
GEPGVGKTAIVEGLAQRIINGEVP L +++L LD+ L+AG KYRGEFE+RLK +L +
Sbjct: 206 GEPGVGKTAIVEGLAQRIINGEVPEGLKGRRVLALDMGALVAGAKYRGEFEERLKGVLND 265
Query: 132 ISNNQKDIIIFIDELHTMIGTGKVEGSIDAGNMLKPELSRGELHCIGATTLNEYRQYIEK 191
++ + ++I+FIDELHTM+G GK +G++DAGNMLKP L+RGELHC+GATTL+EYRQYIEK
Sbjct: 266 LAKQEGNVILFIDELHTMVGAGKADGAMDAGNMLKPALARGELHCVGATTLDEYRQYIEK 325
Query: 192 DAAFERRFQKILVEEPDIEETISILRGLQKKYEVHHGVEITDPAIVAASELSYRYISDRF 251
DAA ERRFQK+ V EP +E+TI+ILRGL+++YE+HH V+ITDPAIVAA+ LS+RYI+DR
Sbjct: 326 DAALERRFQKVFVAEPSVEDTIAILRGLKERYELHHHVQITDPAIVAAATLSHRYIADRQ 385
Query: 252 MPDKAIDLIDEAAAKIKIEIDSKPEIMDKLERRLIQLKIEHEAIKREYDESSKKRLLLIK 311
+PDKAIDLIDEAA+ I+++IDSKPE +D+L+RR+IQLK+E +A+ +E DE+SKKRL ++
Sbjct: 386 LPDKAIDLIDEAASSIRMQIDSKPEELDRLDRRIIQLKLEQQALMKESDEASKKRLDMLN 445
Query: 312 KEINKLEIKYANLEKIWKYEKTLIKDSQQIKEEIEKVRLKINKATRKSDWQTVSKLKYGE 371
+E++ E +Y+ LE+ WK EK + +Q IK E+E+ ++ I +A R D +S+L+YG+
Sbjct: 446 EELSDKERQYSELEEEWKAEKASLSGTQTIKAELEQAKIAIEQARRVGDLARMSELQYGK 505
Query: 372 LNKLERILKEKSQKDIQLPNNANKFTLLKTKVGSEEIAEIVSRTTGIPVSKIVQVEREKL 431
+ +LE+ L +Q + LL+ KV EIAE+++R TGIPVS++++ EREKL
Sbjct: 506 IPELEKQLAAATQLE------GKTMRLLRNKVTDAEIAEVLARWTGIPVSRMLESEREKL 559
Query: 432 LNIENLLCKRVVGQDEAISAVSNAIRRSRSGLSDAKRPYGSFMFLGPTGVGKTELCKTLS 491
L +E L RV+GQ+EA+ AVSNAIRRSR+GLSD RP GSF+FLGPTGVGKTELCK L+
Sbjct: 560 LRMEQELHHRVIGQNEAVEAVSNAIRRSRAGLSDPNRPIGSFLFLGPTGVGKTELCKALA 619
Query: 492 ACIFNNEESIIRIDMSEFIEKHSISRLIGAPPGYIGYEEGGYLTEIVRRKPYSLILLDEI 551
+F+++++++RIDMSEF+EKHS+SRL+GAPPGY+GYEEGGYLTE VRR+PYS+ILLDE+
Sbjct: 620 NFMFDSDDAMVRIDMSEFMEKHSVSRLVGAPPGYVGYEEGGYLTEAVRRRPYSVILLDEV 679
Query: 552 EKANSDVFNILLQILDDGRLTDNRGRTINFRNTIIVMTSNLGSDKIKE-MEKGDKEIIKL 610
EKA+ DVFNILLQ+LDDGRLTD +GRT++FRNT+++MTSNLGSD I+E + D +K
Sbjct: 680 EKAHPDVFNILLQVLDDGRLTDGQGRTVDFRNTVVIMTSNLGSDLIQERFGELDYAHMKE 739
Query: 611 AVMNEVKIYFRPEFINRIDDIIVFRYLNRKNILSIANIQLNILKNKLLKMNMDLKISKAA 670
V+ V FRPEFINRID+++VF L ++I SIA IQL L +L + ++ IS A
Sbjct: 740 LVLGVVSHNFRPEFINRIDEVVVFHPLGEQHIASIAQIQLQRLYKRLEERGYEIHISDEA 799
Query: 671 LKKISNIGFDLIYGARDVHGCKKSLSILLKKIHKKSPEANFIFLGDLINKGPQSLD 726
LK +S G+D +YGAR + K+++ + ++P A I G+L+ L+
Sbjct: 800 LKLLSENGYDPVYGARPL---KRAIQQQI-----ENPLAQQILSGELVPGKVIRLE 847
>gnl|CDD|223616 COG0542, clpA, ATP-binding subunits of Clp protease and DnaK/DnaJ
chaperones [Posttranslational modification, protein
turnover, chaperones].
Length = 786
Score = 860 bits (2225), Expect = 0.0
Identities = 376/681 (55%), Positives = 490/681 (71%), Gaps = 81/681 (11%)
Query: 11 NGKNILSQQDEEHIGYLKKYTIDLTEKARLGKLDPVIGRDDEIRRAIQVLQRRSKNNPVL 70
G + S+ EE L+KYT DLTE AR GKLDPVIGRD+EIRR IQ+L RR+KNNPVL
Sbjct: 137 GGNEVDSKNAEEDQDALEKYTRDLTELAREGKLDPVIGRDEEIRRTIQILSRRTKNNPVL 196
Query: 71 IGEPGVGKTAIVEGLAQRIINGEVPNSLLSKKILLLDIALLLAGTKYRGEFEDRLKKILK 130
+GEPGVGKTAIVEGLAQRI+NG+VP SL K+I LD+ L+AG KYRGEFE+RLK +LK
Sbjct: 197 VGEPGVGKTAIVEGLAQRIVNGDVPESLKDKRIYSLDLGSLVAGAKYRGEFEERLKAVLK 256
Query: 131 EISNNQKDIIIFIDELHTMIGTGKVEG-SIDAGNMLKPELSRGELHCIGATTLNEYRQYI 189
E+ + K++I+FIDE+HT++G G EG ++DA N+LKP L+RGEL CIGATTL+EYR+YI
Sbjct: 257 EVEKS-KNVILFIDEIHTIVGAGATEGGAMDAANLLKPALARGELRCIGATTLDEYRKYI 315
Query: 190 EKDAAFERRFQKILVEEPDIEETISILRGLQKKYEVHHGVEITDPAIVAASELSYRYISD 249
EKDAA ERRFQK+LV+EP +E+TI+ILRGL+++YE HHGV ITD A+VAA LS RYI D
Sbjct: 316 EKDAALERRFQKVLVDEPSVEDTIAILRGLKERYEAHHGVRITDEALVAAVTLSDRYIPD 375
Query: 250 RFMPDKAIDLIDEAAAKIKIEIDSKPEIMDKLERRLIQLKIEHEAIKREYDESSKKRLLL 309
RF+PDKAIDL+DEA A++++EID KPE +D+LER L QL+IE EA++
Sbjct: 376 RFLPDKAIDLLDEAGARVRLEID-KPEELDELERELAQLEIEKEALE------------- 421
Query: 310 IKKEINKLEIKYANLEKIWKYEKTLIKDSQQIKEEIEKVRLKINKATRKSDWQTVSKLKY 369
+E+ EK + I++ + KLK
Sbjct: 422 --------------------------------REQDEKEKKLIDE---------IIKLKE 440
Query: 370 GELNKLERILKEKSQKDIQLPNNANKFTLLKTKVGSEEIAEIVSRTTGIPVSKIVQVERE 429
G + +LE+ L+ + V ++IAE+V+R TGIPV+K+++ E+E
Sbjct: 441 GRIPELEKELEAE--------------------VDEDDIAEVVARWTGIPVAKLLEDEKE 480
Query: 430 KLLNIENLLCKRVVGQDEAISAVSNAIRRSRSGLSDAKRPYGSFMFLGPTGVGKTELCKT 489
KLLN+E L KRV+GQDEA+ AVS+AIRR+R+GL D RP GSF+FLGPTGVGKTEL K
Sbjct: 481 KLLNLERRLKKRVIGQDEAVEAVSDAIRRARAGLGDPNRPIGSFLFLGPTGVGKTELAKA 540
Query: 490 LSACIFNNEESIIRIDMSEFIEKHSISRLIGAPPGYIGYEEGGYLTEIVRRKPYSLILLD 549
L+ +F +E+++IRIDMSE++EKHS+SRLIGAPPGY+GYEEGG LTE VRRKPYS+ILLD
Sbjct: 541 LAEALFGDEQALIRIDMSEYMEKHSVSRLIGAPPGYVGYEEGGQLTEAVRRKPYSVILLD 600
Query: 550 EIEKANSDVFNILLQILDDGRLTDNRGRTINFRNTIIVMTSNLGSDKIKEMEKGD----K 605
EIEKA+ DVFN+LLQ+LDDGRLTD +GRT++FRNTII+MTSN GS++I GD K
Sbjct: 601 EIEKAHPDVFNLLLQVLDDGRLTDGQGRTVDFRNTIIIMTSNAGSEEILRDADGDDFADK 660
Query: 606 EIIKLAVMNEVKIYFRPEFINRIDDIIVFRYLNRKNILSIANIQLNILKNKLLKMNMDLK 665
E +K AVM E+K +FRPEF+NRID+II F L+++ + I ++QLN L +L + + L+
Sbjct: 661 EALKEAVMEELKKHFRPEFLNRIDEIIPFNPLSKEVLERIVDLQLNRLAKRLAERGITLE 720
Query: 666 ISKAALKKISNIGFDLIYGAR 686
+S A ++ G+D YGAR
Sbjct: 721 LSDEAKDFLAEKGYDPEYGAR 741
>gnl|CDD|214361 CHL00095, clpC, Clp protease ATP binding subunit.
Length = 821
Score = 682 bits (1761), Expect = 0.0
Identities = 324/701 (46%), Positives = 455/701 (64%), Gaps = 83/701 (11%)
Query: 3 IKNNSLNVNGKNILSQQDEEHIGY----LKKYTIDLTEKARLGKLDPVIGRDDEIRRAIQ 58
I++ LN+ G+ I + E L+++ +LT++A G LDPVIGR+ EI R IQ
Sbjct: 134 IRSLILNLIGEIIEAILGAEQSRSKTPTLEEFGTNLTKEAIDGNLDPVIGREKEIERVIQ 193
Query: 59 VLQRRSKNNPVLIGEPGVGKTAIVEGLAQRIINGEVPNSLLSKKILLLDIALLLAGTKYR 118
+L RR+KNNP+LIGEPGVGKTAI EGLAQRI+N +VP+ L K ++ LDI LLLAGTKYR
Sbjct: 194 ILGRRTKNNPILIGEPGVGKTAIAEGLAQRIVNRDVPDILEDKLVITLDIGLLLAGTKYR 253
Query: 119 GEFEDRLKKILKEISNNQKDIIIFIDELHTMIGTGKVEGSIDAGNMLKPELSRGELHCIG 178
GEFE+RLK+I EI N +II+ IDE+HT+IG G EG+IDA N+LKP L+RGEL CIG
Sbjct: 254 GEFEERLKRIFDEIQEN-NNIILVIDEVHTLIGAGAAEGAIDAANILKPALARGELQCIG 312
Query: 179 ATTLNEYRQYIEKDAAFERRFQKILVEEPDIEETISILRGLQKKYEVHHGVEITDPAIVA 238
ATTL+EYR++IEKD A ERRFQ + V EP +EETI IL GL+ +YE HH + I+D A+ A
Sbjct: 313 ATTLDEYRKHIEKDPALERRFQPVYVGEPSVEETIEILFGLRSRYEKHHNLSISDKALEA 372
Query: 239 ASELSYRYISDRFMPDKAIDLIDEAAAKIKIEIDSKPEIMDKLERRLIQLKIEHEAIKRE 298
A++LS +YI+DRF+PDKAIDL+DEA +++++ P +L++ L ++ + + RE
Sbjct: 373 AAKLSDQYIADRFLPDKAIDLLDEAGSRVRLINSRLPPAARELDKELREILKDKDEAIRE 432
Query: 299 YDESSKKRLLLIKKEINKLEIKYANLEKIWKYEKTLIKDSQQIKEEIEKVRLKINKATRK 358
D + K+L + E+ + + I S++ +EE +
Sbjct: 433 QDFETAKQLRDREMEV--------------RAQIAAIIQSKKTEEEKRLEVPVV------ 472
Query: 359 SDWQTVSKLKYGELNKLERILKEKSQKDIQLPNNANKFTLLKTKVGSEEIAEIVSRTTGI 418
+++DI AEIVS TGI
Sbjct: 473 ------------------------TEEDI---------------------AEIVSAWTGI 487
Query: 419 PVSKIVQVEREKLLNIENLLCKRVVGQDEAISAVSNAIRRSRSGLSDAKRPYGSFMFLGP 478
PV+K+ + E EKLL++E L KR++GQDEA+ AVS AIRR+R GL + RP SF+F GP
Sbjct: 488 PVNKLTKSESEKLLHMEETLHKRIIGQDEAVVAVSKAIRRARVGLKNPNRPIASFLFSGP 547
Query: 479 TGVGKTELCKTLSACIFNNEESIIRIDMSEFIEKHSISRLIGAPPGYIGYEEGGYLTEIV 538
TGVGKTEL K L++ F +E+++IR+DMSE++EKH++S+LIG+PPGY+GY EGG LTE V
Sbjct: 548 TGVGKTELTKALASYFFGSEDAMIRLDMSEYMEKHTVSKLIGSPPGYVGYNEGGQLTEAV 607
Query: 539 RRKPYSLILLDEIEKANSDVFNILLQILDDGRLTDNRGRTINFRNTIIVMTSNLGSDKI- 597
R+KPY+++L DEIEKA+ D+FN+LLQILDDGRLTD++GRTI+F+NT+I+MTSNLGS I
Sbjct: 608 RKKPYTVVLFDEIEKAHPDIFNLLLQILDDGRLTDSKGRTIDFKNTLIIMTSNLGSKVIE 667
Query: 598 ---------KEMEKGDK---EIIKLAVMNEVKIYFRPEFINRIDDIIVFRYLNRKNILSI 645
+ + + + V E+K +FRPEF+NR+D+IIVFR L + ++ I
Sbjct: 668 TNSGGLGFELSENQLSEKQYKRLSNLVNEELKQFFRPEFLNRLDEIIVFRQLTKNDVWEI 727
Query: 646 ANIQLNILKNKLLKMNMDLKISKAALKKISNIGFDLIYGAR 686
A I L L +L + + L++++ + G++ +YGAR
Sbjct: 728 AEIMLKNLFKRLNEQGIQLEVTERIKTLLIEEGYNPLYGAR 768
>gnl|CDD|234172 TIGR03345, VI_ClpV1, type VI secretion ATPase, ClpV1 family.
Members of this protein family are homologs of ClpB, an
ATPase associated with chaperone-related functions.
These ClpB homologs, designated ClpV1, are a key
component of the bacterial pathogenicity-associated type
VI secretion system [Protein fate, Protein and peptide
secretion and trafficking, Cellular processes,
Pathogenesis].
Length = 852
Score = 667 bits (1723), Expect = 0.0
Identities = 282/656 (42%), Positives = 416/656 (63%), Gaps = 28/656 (4%)
Query: 27 LKKYTIDLTEKARLGKLDPVIGRDDEIRRAIQVLQRRSKNNPVLIGEPGVGKTAIVEGLA 86
L +YT DLT +AR GK+DPV+GRDDEIR+ I +L RR +NNP+L GE GVGKTA+VEGLA
Sbjct: 170 LDQYTTDLTAQAREGKIDPVLGRDDEIRQMIDILLRRRQNNPILTGEAGVGKTAVVEGLA 229
Query: 87 QRIINGEVPNSLLSKKILLLDIALLLAGTKYRGEFEDRLKKILKEISNNQKDIIIFIDEL 146
RI G+VP +L + ++L LD+ LL AG +GEFE+RLK ++ E+ + + II+FIDE
Sbjct: 230 LRIAAGDVPPALRNVRLLSLDLGLLQAGASVKGEFENRLKSVIDEVKASPQPIILFIDEA 289
Query: 147 HTMIGTGKVEGSIDAGNMLKPELSRGELHCIGATTLNEYRQYIEKDAAFERRFQKILVEE 206
HT+IG G G DA N+LKP L+RGEL I ATT EY++Y EKD A RRFQ + VEE
Sbjct: 290 HTLIGAGGQAGQGDAANLLKPALARGELRTIAATTWAEYKKYFEKDPALTRRFQVVKVEE 349
Query: 207 PDIEETISILRGLQKKYEVHHGVEITDPAIVAASELSYRYISDRFMPDKAIDLIDEAAAK 266
PD E I +LRGL E HHGV I D A+VAA ELS+RYI R +PDKA+ L+D A A+
Sbjct: 350 PDEETAIRMLRGLAPVLEKHHGVLILDEAVVAAVELSHRYIPGRQLPDKAVSLLDTACAR 409
Query: 267 IKIEIDSKPEIMDKLERRLIQLKIEHEAIKRE--YDESSKKRLLLIKKEINKLEIKYANL 324
+ + ++ P ++ L RR+ L++E +A++RE +RL ++ E+ LE + A L
Sbjct: 410 VALSQNATPAALEDLRRRIAALELELDALEREAALGADHDERLAELRAELAALEAELAAL 469
Query: 325 EKIWKYEKTLIKDSQQIKEEIEKVRLKINKATRKSDWQTVSKLKYGELNKLERILKEKSQ 384
E W+ EK L++ ++ E+E +L +LE L +Q
Sbjct: 470 EARWQQEKELVEAILALRAELE---------ADADAPADDDAALRAQLAELEAALAS-AQ 519
Query: 385 KDIQLPNNANKFTLLKTKVGSEEIAEIVSRTTGIPVSKIVQVEREKLLNIENLLCKRVVG 444
+ P L+ +V ++ +AE+V+ TGIPV ++V+ E E +L++ + L +RV+G
Sbjct: 520 GE--EP-------LVFPEVDAQAVAEVVADWTGIPVGRMVRDEIEAVLSLPDRLAERVIG 570
Query: 445 QDEAISAVSNAIRRSRSGLSDAKRPYGSFMFLGPTGVGKTELCKTLSACIFNNEESIIRI 504
QD A+ A++ IR +R+GL D ++P G F+ +GP+GVGKTE L+ ++ E+++I I
Sbjct: 571 QDHALEAIAERIRTARAGLEDPRKPLGVFLLVGPSGVGKTETALALAELLYGGEQNLITI 630
Query: 505 DMSEFIEKHSISRLIGAPPGYIGYEEGGYLTEIVRRKPYSLILLDEIEKANSDVFNILLQ 564
+MSEF E H++SRL G+PPGY+GY EGG LTE VRRKPYS++LLDE+EKA+ DV + Q
Sbjct: 631 NMSEFQEAHTVSRLKGSPPGYVGYGEGGVLTEAVRRKPYSVVLLDEVEKAHPDVLELFYQ 690
Query: 565 ILDDGRLTDNRGRTINFRNTIIVMTSNLGSDKIKEM-----EKGDKEIIKLAVMNEVKIY 619
+ D G + D GR I+F+NT+I++TSN GSD I + D E + A+ E+
Sbjct: 691 VFDKGVMEDGEGREIDFKNTVILLTSNAGSDLIMALCADPETAPDPEALLEALRPELLKV 750
Query: 620 FRPEFINRIDDIIVFRYLNRKNILSIANIQLNILKNKLLK-MNMDLKISKAALKKI 674
F+P F+ R+ +I + L+ + +I ++L+ + +L + +L S+A ++ I
Sbjct: 751 FKPAFLGRM-TVIPYLPLDDDVLAAIVRLKLDRIARRLKENHGAELVYSEALVEHI 805
>gnl|CDD|233959 TIGR02639, ClpA, ATP-dependent Clp protease ATP-binding subunit
clpA. [Protein fate, Degradation of proteins, peptides,
and glycopeptides].
Length = 730
Score = 358 bits (921), Expect = e-111
Identities = 149/251 (59%), Positives = 192/251 (76%), Gaps = 2/251 (0%)
Query: 26 YLKKYTIDLTEKARLGKLDPVIGRDDEIRRAIQVLQRRSKNNPVLIGEPGVGKTAIVEGL 85
L+KYT+DLTEKA+ GK+DP+IGR+DE+ R IQVL RR KNNP+L+GEPGVGKTAIVEGL
Sbjct: 163 ALEKYTVDLTEKAKNGKIDPLIGREDELERTIQVLCRRKKNNPLLVGEPGVGKTAIVEGL 222
Query: 86 AQRIINGEVPNSLLSKKILLLDIALLLAGTKYRGEFEDRLKKILKEISNNQKDIIIFIDE 145
A RI G+VP L + KI LD+ LLAGTKYRG+FE+RLK ++ EI + + I+FIDE
Sbjct: 223 ALRIAEGKVPERLKNAKIYSLDMGTLLAGTKYRGDFEERLKAVVSEIEK-EPNAILFIDE 281
Query: 146 LHTMIGTGKV-EGSIDAGNMLKPELSRGELHCIGATTLNEYRQYIEKDAAFERRFQKILV 204
+HT++G G GS+DA N+LKP LS G++ CIG+TT EY+ + EKD A RRFQKI V
Sbjct: 282 IHTIVGAGATSGGSMDASNLLKPALSSGKIRCIGSTTYEEYKNHFEKDRALSRRFQKIDV 341
Query: 205 EEPDIEETISILRGLQKKYEVHHGVEITDPAIVAASELSYRYISDRFMPDKAIDLIDEAA 264
EP IEET+ IL+GL+++YE H V+ +D A+ AA ELS RYI+DRF+PDKAID+IDEA
Sbjct: 342 GEPSIEETVKILKGLKEQYEEFHHVKYSDEALEAAVELSARYINDRFLPDKAIDVIDEAG 401
Query: 265 AKIKIEIDSKP 275
A ++ +K
Sbjct: 402 AAFRLRPKAKK 412
Score = 314 bits (806), Expect = 2e-94
Identities = 130/291 (44%), Positives = 192/291 (65%), Gaps = 10/291 (3%)
Query: 400 KTKVGSEEIAEIVSRTTGIPVSKIVQVEREKLLNIENLLCKRVVGQDEAISAVSNAIRRS 459
K V ++I +V++ IPV + +RE+L N+E L ++ GQDEAI + +AI+RS
Sbjct: 413 KANVNVKDIENVVAKMAKIPVKTVSSDDREQLKNLEKNLKAKIFGQDEAIDQLVSAIKRS 472
Query: 460 RSGLSDAKRPYGSFMFLGPTGVGKTELCKTLSACIFNNEESIIRIDMSEFIEKHSISRLI 519
R+GL D +P GSF+F+GPTGVGKTEL K L A ++R DMSE++EKH++SRLI
Sbjct: 473 RAGLGDPNKPVGSFLFVGPTGVGKTELAKQL-AEELGVH--LLRFDMSEYMEKHTVSRLI 529
Query: 520 GAPPGYIGYEEGGYLTEIVRRKPYSLILLDEIEKANSDVFNILLQILDDGRLTDNRGRTI 579
G+PPGY+G+E+GG LT+ VR+ P+ ++LLDEIEKA+ D++NILLQ++D LTDN GR
Sbjct: 530 GSPPGYVGFEQGGLLTDAVRKHPHCVLLLDEIEKAHPDIYNILLQVMDYATLTDNNGRKA 589
Query: 580 NFRNTIIVMTSNLGSDKIKEMEKGD----KEIIKLAVMNEVKIYFRPEFINRIDDIIVFR 635
+FRN I++MTSN G+ EM K E + + +K F PEF NR+D II F
Sbjct: 590 DFRNVILIMTSNAGA---SEMSKPPIGFGGENSESKSLKAIKKLFSPEFRNRLDAIIHFN 646
Query: 636 YLNRKNILSIANIQLNILKNKLLKMNMDLKISKAALKKISNIGFDLIYGAR 686
L+ + I L+ L+++L + N++L+++ A K ++ G+D +GAR
Sbjct: 647 DLSEEMAEKIVKKFLDELQDQLNEKNIELELTDDAKKYLAEKGYDEEFGAR 697
>gnl|CDD|234673 PRK00166, apaH, diadenosine tetraphosphatase; Reviewed.
Length = 275
Score = 332 bits (854), Expect = e-107
Identities = 113/266 (42%), Positives = 156/266 (58%), Gaps = 9/266 (3%)
Query: 687 DVHGCKKSLSILLKKIHKKSPEANFIFLGDLINKGPQSLDTLRMVYSMRNYAKIVLGNHE 746
D+ GC L LL+KI + +GDL+N+GP SL+ LR V S+ + A VLGNH+
Sbjct: 8 DIQGCYDELQRLLEKIDFDPAKDTLWLVGDLVNRGPDSLEVLRFVKSLGDSAVTVLGNHD 67
Query: 747 IHLLDVLININKKSKLDTFDDILDAPDKKKLVSWLRTQPLAIYY--KKYLMIHAGVAKQW 804
+HLL V I + K DT D IL+APD+ +L+ WLR QPL +M+HAG+ QW
Sbjct: 68 LHLLAVAAGIKRNKKKDTLDPILEAPDRDELLDWLRHQPLLHVDEELGLVMVHAGIPPQW 127
Query: 805 TAQQTIKLSHQVEKILRTSYWKNLFFKLYNHNSINWDNHLHTIHLNTIDKLQFIINTLTR 864
+ L+ +VE +LR+ +++ +Y + W L +++L++IIN TR
Sbjct: 128 DLATALALAREVEAVLRSDDYRDFLANMYGNEPDRWSP-----DLTGLERLRYIINAFTR 182
Query: 865 TRFCKIDGTIEFIKKNIKNNNFQNNYIPWFDLPNRKTIDITVLFGHWSTL-GLIMKPNII 923
RFC DG ++F K + PWF++P RKT D T++FGHW+ L GL PNII
Sbjct: 183 MRFCTPDGRLDFKCKGPPDEA-PAGLKPWFEVPGRKTRDYTIVFGHWAALEGLTTPPNII 241
Query: 924 CLDTGCVWGNKLTALCLEDRSIIQVN 949
LDTGCVWG KLTAL LED+ I QV
Sbjct: 242 ALDTGCVWGGKLTALRLEDKQIFQVP 267
>gnl|CDD|163665 cd07422, MPP_ApaH, Escherichia coli ApaH and related proteins,
metallophosphatase domain. ApaH (also known as
symmetrically cleaving Ap4A hydrolase and
bis(5'nucleosyl)-tetraphosphatase) is a bacterial member
of the PPP (phosphoprotein phosphatase) family of
serine/threonine phosphatases that hydrolyzes the
nucleotide-signaling molecule diadenosine tetraphosphate
(Ap(4)A) into two ADP and also hydrolyzes Ap(5)A,
Gp(4)G, and other extending compounds. Null mutations
in apaH result in high intracellular levels of Ap(4)A
which correlate with multiple phenotypes, including a
decreased expression of catabolite-repressible genes, a
reduction in the expression of flagellar operons, and an
increased sensitivity to UV and heat. Ap4A hydrolase
is important in responding to heat shock and oxidative
stress via regulating the concentration of Ap4A in
bacteria. Ap4A hydrolase is also thought to play a role
in siderophore production, but the mechanism by which
ApaH interacts with siderophore pathways in unknown.
The PPP (phosphoprotein phosphatase) family, to which
ApaH belongs, is one of two known protein phosphatase
families specific for serine and threonine. The PPP
family also includes: PP1, PP2A, PP2B (calcineurin),
PP4, PP5, PP6, PP7, Bsu1, RdgC, PrpE, and PrpA/PrpB. The
PPP catalytic domain is defined by three conserved
motifs (-GDXHG-, -GDXVDRG- and -GNHE-). The PPP enzyme
family is ancient with members found in all eukaryotes,
and in most bacterial and archeal genomes.
Dephosphorylation of phosphoserines and
phosphothreonines on target proteins plays a central
role in the regulation of many cellular processes. PPPs
belong to the metallophosphatase (MPP) superfamily.
MPPs are functionally diverse, but all share a conserved
domain with an active site consisting of two metal ions
(usually manganese, iron, or zinc) coordinated with
octahedral geometry by a cage of histidine, aspartate,
and asparagine residues. The MPP superfamily includes:
Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat
debranching enzymes, YfcE-like phosphodiesterases,
purple acid phosphatases (PAPs), YbbF-like
UDP-2,3-diacylglucosamine hydrolases, and acid
sphingomyelinases (ASMases). The conserved domain is a
double beta-sheet sandwich with a di-metal active site
made up of residues located at the C-terminal side of
the sheets. This domain is thought to allow for
productive metal coordination.
Length = 257
Score = 320 bits (824), Expect = e-103
Identities = 118/259 (45%), Positives = 159/259 (61%), Gaps = 11/259 (4%)
Query: 687 DVHGCKKSLSILLKKIHKKSPEANFIFLGDLINKGPQSLDTLRMVYSMRNYAKIVLGNHE 746
D+ GC L LL+KI+ + +GDL+N+GP SL+TLR V S+ + AK VLGNH+
Sbjct: 6 DIQGCYDELQRLLEKINFDPAKDRLWLVGDLVNRGPDSLETLRFVKSLGDSAKTVLGNHD 65
Query: 747 IHLLDVLININKKSKLDTFDDILDAPDKKKLVSWLRTQPLAIY--YKKYLMIHAGVAKQW 804
+HLL V I K K DT DDIL+APD+ +L+ WLR QPL LM+HAG+ QW
Sbjct: 66 LHLLAVAAGIKKPKKKDTLDDILNAPDRDELLDWLRHQPLLHRDPELGILMVHAGIPPQW 125
Query: 805 TAQQTIKLSHQVEKILRTSYWKNLFFKLYNHNSINWDNHLHTIHLNTIDKLQFIINTLTR 864
+ +Q +KL+ +VE LR ++ +Y + W + L ID+L++I+N TR
Sbjct: 126 SIEQALKLAREVEAALRGPNYREFLKNMYGNEPDRWSD-----DLTGIDRLRYIVNAFTR 180
Query: 865 TRFCKIDGTIEF-IKKNIKNNNFQNNYIPWFDLPNRKTIDITVLFGHWSTLGLIMKP-NI 922
RFC DG ++F K ++ PWF+LPNRKT D T++FGHW+ LG +P NI
Sbjct: 181 MRFCTPDGRLDFSSKGAPEDAP--KGLKPWFELPNRKTDDYTIVFGHWAALGGKTRPNNI 238
Query: 923 ICLDTGCVWGNKLTALCLE 941
I LDTGCVWG KLTAL LE
Sbjct: 239 IALDTGCVWGGKLTALRLE 257
>gnl|CDD|236828 PRK11034, clpA, ATP-dependent Clp protease ATP-binding subunit;
Provisional.
Length = 758
Score = 297 bits (761), Expect = 6e-88
Identities = 137/277 (49%), Positives = 184/277 (66%), Gaps = 5/277 (1%)
Query: 2 GIKNNSLNVNGKNILSQQDEEHIG---YLKKYTIDLTEKARLGKLDPVIGRDDEIRRAIQ 58
G + + + + EE G ++ +T +L + AR+G +DP+IGR+ E+ RAIQ
Sbjct: 141 GTRKDEPSQSSDPGSQPNSEEQAGGEERMENFTTNLNQLARVGGIDPLIGREKELERAIQ 200
Query: 59 VLQRRSKNNPVLIGEPGVGKTAIVEGLAQRIINGEVPNSLLSKKILLLDIALLLAGTKYR 118
VL RR KNNP+L+GE GVGKTAI EGLA RI+ G+VP + I LDI LLAGTKYR
Sbjct: 201 VLCRRRKNNPLLVGESGVGKTAIAEGLAWRIVQGDVPEVMADCTIYSLDIGSLLAGTKYR 260
Query: 119 GEFEDRLKKILKEISNNQKDIIIFIDELHTMIGTGKVE-GSIDAGNMLKPELSRGELHCI 177
G+FE R K +LK++ + I+FIDE+HT+IG G G +DA N++KP LS G++ I
Sbjct: 261 GDFEKRFKALLKQLE-QDTNSILFIDEIHTIIGAGAASGGQVDAANLIKPLLSSGKIRVI 319
Query: 178 GATTLNEYRQYIEKDAAFERRFQKILVEEPDIEETISILRGLQKKYEVHHGVEITDPAIV 237
G+TT E+ EKD A RRFQKI + EP IEET+ I+ GL+ KYE HH V T A+
Sbjct: 320 GSTTYQEFSNIFEKDRALARRFQKIDITEPSIEETVQIINGLKPKYEAHHDVRYTAKAVR 379
Query: 238 AASELSYRYISDRFMPDKAIDLIDEAAAKIKIEIDSK 274
AA EL+ +YI+DR +PDKAID+IDEA A+ ++ SK
Sbjct: 380 AAVELAVKYINDRHLPDKAIDVIDEAGARARLMPVSK 416
Score = 248 bits (635), Expect = 2e-70
Identities = 133/326 (40%), Positives = 204/326 (62%), Gaps = 18/326 (5%)
Query: 400 KTKVGSEEIAEIVSRTTGIPVSKIVQVEREKLLNIENLLCKRVVGQDEAISAVSNAIRRS 459
K V +I +V+R IP + Q +R+ L N+ + L V GQD+AI A++ AI+ S
Sbjct: 418 KKTVNVADIESVVARIARIPEKSVSQSDRDTLKNLGDRLKMLVFGQDKAIEALTEAIKMS 477
Query: 460 RSGLSDAKRPYGSFMFLGPTGVGKTELCKTLSACIFNNEESIIRIDMSEFIEKHSISRLI 519
R+GL +P GSF+F GPTGVGKTE+ LS + ++R DMSE++E+H++SRLI
Sbjct: 478 RAGLGHEHKPVGSFLFAGPTGVGKTEVTVQLSKAL---GIELLRFDMSEYMERHTVSRLI 534
Query: 520 GAPPGYIGYEEGGYLTEIVRRKPYSLILLDEIEKANSDVFNILLQILDDGRLTDNRGRTI 579
GAPPGY+G+++GG LT+ V + P++++LLDEIEKA+ DVFN+LLQ++D+G LTDN GR
Sbjct: 535 GAPPGYVGFDQGGLLTDAVIKHPHAVLLLDEIEKAHPDVFNLLLQVMDNGTLTDNNGRKA 594
Query: 580 NFRNTIIVMTSNLGSDKIKEMEKGDKEIIK----LAVMNEVKIYFRPEFINRIDDIIVFR 635
+FRN ++VMT+N G ++E E+ +I M E+K F PEF NR+D+II F
Sbjct: 595 DFRNVVLVMTTNAG---VRETERKSIGLIHQDNSTDAMEEIKKIFTPEFRNRLDNIIWFD 651
Query: 636 YLNRKNILSIANIQLNILKNKLLKMNMDLKISKAALKKISNIGFDLIYGARDVHGCKKSL 695
+L+ I + + + L+ +L + + L++S+ A ++ G+D GAR + + +
Sbjct: 652 HLSTDVIHQVVDKFIVELQAQLDQKGVSLEVSQEARDWLAEKGYDRAMGARPM---ARVI 708
Query: 696 SILLKKIHKKSPEANFIFLGDLINKG 721
LKK P AN + G L++ G
Sbjct: 709 QDNLKK-----PLANELLFGSLVDGG 729
>gnl|CDD|219536 pfam07724, AAA_2, AAA domain (Cdc48 subfamily). This Pfam entry
includes some of the AAA proteins not detected by the
pfam00004 model.
Length = 168
Score = 259 bits (663), Expect = 5e-81
Identities = 100/168 (59%), Positives = 130/168 (77%), Gaps = 4/168 (2%)
Query: 468 RPYGSFMFLGPTGVGKTELCKTLSACIFNNEESIIRIDMSEFIEKHSISRLIGAPPGYIG 527
RP GSF+FLGPTGVGKTEL K L+ +F +E ++IRIDMSE++E+HS+SRLIGAPPGY+G
Sbjct: 1 RPIGSFLFLGPTGVGKTELAKALAELLFGDERALIRIDMSEYMEEHSVSRLIGAPPGYVG 60
Query: 528 YEEGGYLTEIVRRKPYSLILLDEIEKANSDVFNILLQILDDGRLTDNRGRTINFRNTIIV 587
YEEGG LTE VRRKPYS++L+DEIEKA+ V N LLQIL+ G LTD +GR ++FRNT+ +
Sbjct: 61 YEEGGQLTEAVRRKPYSIVLIDEIEKAHPGVQNDLLQILEGGTLTDKQGRKVDFRNTLFI 120
Query: 588 MTSNLGSDKIKEMEKG----DKEIIKLAVMNEVKIYFRPEFINRIDDI 631
MT N GS+KI + + D E++K VM+ +K F PEF+ R+ I
Sbjct: 121 MTGNFGSEKISDASRLGDSPDYELLKELVMDLLKKGFIPEFLGRLPII 168
>gnl|CDD|233082 TIGR00668, apaH, bis(5'-nucleosyl)-tetraphosphatase (symmetrical).
Diadenosine 5',5"'-P1,P4-tetraphosphate (Ap4A) is a
regulatory metabolite of stress conditions. It is
hydrolyzed to two ADP by this enzyme. Alternate names
include diadenosine-tetraphosphatase and Ap4A hydrolase
[Cellular processes, Adaptations to atypical
conditions].
Length = 279
Score = 202 bits (516), Expect = 7e-59
Identities = 91/261 (34%), Positives = 139/261 (53%), Gaps = 11/261 (4%)
Query: 687 DVHGCKKSLSILLKKIHKKSPEANFIFLGDLINKGPQSLDTLRMVYSMRNYAKIVLGNHE 746
D+HGC L LL+++ + GDL+ +GP SL+ LR V S+ + ++VLGNH+
Sbjct: 8 DLHGCYDELQALLERVEFDPGQDTLWLTGDLVARGPGSLEVLRYVKSLGDAVRLVLGNHD 67
Query: 747 IHLLDVLININKKSKLDTFDDILDAPDKKKLVSWLRTQPLAIY--YKKYLMIHAGVAKQW 804
+HLL V I++ D D +L+APD +L++WLR QPL + KK +M HAG+ QW
Sbjct: 68 LHLLAVFAGISRNKPKDRLDPLLEAPDADELLNWLRRQPLLQHDEEKKLVMAHAGITPQW 127
Query: 805 TAQQTIKLSHQVEKILRTSYWKNLFFKLYNHNSINWDNHLHTIHLNTIDKLQFIINTLTR 864
Q + + VE +L + + +Y W L + +L+FIIN TR
Sbjct: 128 DLQTAKECARDVEAVLSSDSYPFFLDAMYGDMPNRWSPELQ-----GLARLRFIINAFTR 182
Query: 865 TRFCKIDGTIEFI-KKNIKNNNFQNNYIPWFDLPNRKTIDITVLFGHWSTL-GLIMKPNI 922
RFC +G ++ K++ ++ PWF +P + ++ FGHW++L G I
Sbjct: 183 MRFCFPNGQLDMYSKESPEDA--PAPLKPWFAIPGPVYEEYSIAFGHWASLEGEGTPEGI 240
Query: 923 ICLDTGCVWGNKLTALCLEDR 943
LDTGC WG +LT L ED+
Sbjct: 241 YALDTGCCWGGRLTCLRWEDK 261
>gnl|CDD|163613 cd00144, MPP_PPP_family, phosphoprotein phosphatases of the
metallophosphatase superfamily, metallophosphatase
domain. The PPP (phosphoprotein phosphatase) family is
one of two known protein phosphatase families specific
for serine and threonine. This family includes: PP1,
PP2A, PP2B (calcineurin), PP4, PP5, PP6, PP7, Bsu1,
RdgC, PrpE, PrpA/PrpB, and ApA4 hydrolase. The PPP
catalytic domain is defined by three conserved motifs
(-GDXHG-, -GDXVDRG- and -GNHE-). The PPP enzyme family
is ancient with members found in all eukaryotes, and in
most bacterial and archeal genomes. Dephosphorylation
of phosphoserines and phosphothreonines on target
proteins plays a central role in the regulation of many
cellular processes. PPPs belong to the
metallophosphatase (MPP) superfamily. MPPs are
functionally diverse, but all share a conserved domain
with an active site consisting of two metal ions
(usually manganese, iron, or zinc) coordinated with
octahedral geometry by a cage of histidine, aspartate,
and asparagine residues. The MPP superfamily includes:
Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat
debranching enzymes, YfcE-like phosphodiesterases,
purple acid phosphatases (PAPs), YbbF-like
UDP-2,3-diacylglucosamine hydrolases, and acid
sphingomyelinases (ASMases). The conserved domain is a
double beta-sheet sandwich with a di-metal active site
made up of residues located at the C-terminal side of
the sheets. This domain is thought to allow for
productive metal coordination.
Length = 225
Score = 98.7 bits (246), Expect = 4e-23
Identities = 55/270 (20%), Positives = 95/270 (35%), Gaps = 65/270 (24%)
Query: 687 DVHGCKKSLSILLKKIHKKSPEANFIFLGDLINKGPQSLDTLRMVYSM---RNYAKIVLG 743
D+HGC L LL+KI P IFLGD +++GP S++ + ++ ++ + ++ G
Sbjct: 5 DIHGCLDDLLRLLEKIGF-PPNDKLIFLGDYVDRGPDSVEVIDLLLALKILPDNVILLRG 63
Query: 744 NHEIHLLDVLININKKSKLDTFDDI----LDAPDKKKLVSWLRTQPLAIYY--KKYLMIH 797
NHE LL+ L + + L ++ PLA KK L +H
Sbjct: 64 NHEDMLLNFLYGFYDEDEWIGGTLRLLKKLGEDLWEEFNDVFFYLPLAALIETKKVLCVH 123
Query: 798 AGVAKQWTAQQTIKLSHQVEKILRTSYWKNLFFKLYNHNSINWDNHLHTIHLNTIDKLQF 857
G++ ++ IK +
Sbjct: 124 GGLSPGLPLEEQIKEEPE----------------------------------------DQ 143
Query: 858 IINTLTRTRFCKIDGTIEFIKKNIKNNNFQNNYIPWFDLPNRKTIDITVLFGHWSTLGLI 917
+ L + ++ G ++ + + WF N ++ GH
Sbjct: 144 LPEDLLWSDPLELPGGFGSSRRGGG-----PDAVEWFLKKNG---LKLIVRGHTPVEEGY 195
Query: 918 M---KPNIICLDTGCVW----GNKLTALCL 940
N+I +D+GC + GNKL AL L
Sbjct: 196 EFGHDGNLITIDSGCNYCGGGGNKLAALVL 225
>gnl|CDD|99707 cd00009, AAA, The AAA+ (ATPases Associated with a wide variety of
cellular Activities) superfamily represents an ancient
group of ATPases belonging to the ASCE (for additional
strand, catalytic E) division of the P-loop NTPase fold.
The ASCE division also includes ABC, RecA-like,
VirD4-like, PilT-like, and SF1/2 helicases. Members of
the AAA+ ATPases function as molecular chaperons, ATPase
subunits of proteases, helicases, or nucleic-acid
stimulated ATPases. The AAA+ proteins contain several
distinct features in addition to the conserved
alpha-beta-alpha core domain structure and the Walker A
and B motifs of the P-loop NTPases.
Length = 151
Score = 83.0 bits (205), Expect = 2e-18
Identities = 38/163 (23%), Positives = 65/163 (39%), Gaps = 14/163 (8%)
Query: 47 IGRDDEIRRAIQVLQRRSKNNPVLIGEPGVGKTAIVEGLAQRIINGEVPNSLLSKKILLL 106
+G+++ I + L+ N +L G PG GKT + +A + P L L
Sbjct: 1 VGQEEAIEALREALELPPPKNLLLYGPPGTGKTTLARAIANELFRPGAP-------FLYL 53
Query: 107 DIALLLAGTKYRGEFEDRLKKILKEISNNQKDIIIFIDELHTMIG--TGKVEGSIDAGNM 164
+ + LL G F L ++L E++ K ++FIDE+ ++ + ++ N
Sbjct: 54 NASDLLEGLVVAELFGHFLVRLLFELAEKAKPGVLFIDEIDSLSRGAQNALLRVLETLND 113
Query: 165 LKPELSRGELHCIGATTLNEYRQYIEKDAAFERRFQKILVEEP 207
L+ R + IGAT D A R +V
Sbjct: 114 LRI--DRENVRVIGATNRPLLGD---LDRALYDRLDIRIVIPL 151
Score = 79.1 bits (195), Expect = 4e-17
Identities = 37/194 (19%), Positives = 70/194 (36%), Gaps = 43/194 (22%)
Query: 443 VGQDEAISAVSNAIRRSRSGLSDAKRPYGSFMFLGPTGVGKTELCKTLSACIFNNEESII 502
VGQ+EAI A+ A+ P + + GP G GKT L + ++ +F +
Sbjct: 1 VGQEEAIEALREALEL---------PPPKNLLLYGPPGTGKTTLARAIANELFRPGAPFL 51
Query: 503 RIDMSEFIEKHSISRLIGAPPGYIGYEEGGYLTEIVRRKPYSLILLDEIEKANSDVFNIL 562
++ S+ +E ++ L G + L E+ + ++ +DEI+ + N L
Sbjct: 52 YLNASDLLEGLVVAELFGHFLVRL-------LFELAEKAKPGVLFIDEIDSLSRGAQNAL 104
Query: 563 LQILDDGRLTDNRGRTINFRNTIIVMTSNLGSDKIKEMEKGDKEIIKLAVMNEVKIYFRP 622
L++L+ I+ N ++ +N
Sbjct: 105 LRVLETLNDL-----RIDRENVRVIGATNRPLLGD----------------------LDR 137
Query: 623 EFINRIDDIIVFRY 636
+R+D IV
Sbjct: 138 ALYDRLDIRIVIPL 151
>gnl|CDD|163656 cd07413, MPP_PA3087, Pseudomonas aeruginosa PA3087 and related
proteins, metallophosphatase domain. PA3087 is an
uncharacterized protein from Pseudomonas aeruginosa with
a metallophosphatase domain that belongs to the
phosphoprotein phosphatase (PPP) family. The PPP family
also includes: PP1, PP2A, PP2B (calcineurin), PP4, PP5,
PP6, PP7, Bsu1, RdgC, PrpE, PrpA/PrpB, and ApA4
hydrolase. The PPP catalytic domain is defined by three
conserved motifs (-GDXHG-, -GDXVDRG- and -GNHE-). The
PPP enzyme family is ancient with members found in all
eukaryotes, and in most bacterial and archeal genomes.
Dephosphorylation of phosphoserines and
phosphothreonines on target proteins plays a central
role in the regulation of many cellular processes. PPPs
belong to the metallophosphatase (MPP) superfamily.
MPPs are functionally diverse, but all share a conserved
domain with an active site consisting of two metal ions
(usually manganese, iron, or zinc) coordinated with
octahedral geometry by a cage of histidine, aspartate,
and asparagine residues. The MPP superfamily includes:
Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat
debranching enzymes, YfcE-like phosphodiesterases,
purple acid phosphatases (PAPs), YbbF-like
UDP-2,3-diacylglucosamine hydrolases, and acid
sphingomyelinases (ASMases). The conserved domain is a
double beta-sheet sandwich with a di-metal active site
made up of residues located at the C-terminal side of
the sheets. This domain is thought to allow for
productive metal coordination.
Length = 222
Score = 66.9 bits (164), Expect = 2e-12
Identities = 40/140 (28%), Positives = 64/140 (45%), Gaps = 33/140 (23%)
Query: 687 DVHGCKKSLSILLKKI----------HKKSPEANFIFLGDLINKGPQSLDTLRMVYSM-- 734
D+HG + L +LL K+ H PE +FLGDLI++GP+ + L +V SM
Sbjct: 6 DIHGHAEKLVVLLHKLGYQELSGVYRH---PERQVVFLGDLIDRGPEIRELLEIVKSMVD 62
Query: 735 RNYAKIVLGNHEI-----HLLDVLI----------NINK-KSKLDTFDDILDAPDKKKLV 778
+A V+GNHE H D N+ + ++ L+ F + + K +
Sbjct: 63 AGHALAVMGNHEFNAIAWHTKDPSGGEWLRAHSKKNLRQHQAFLEQF--REHSEEHKDWL 120
Query: 779 SWLRTQPLAIYYKKYLMIHA 798
W +T PL + ++HA
Sbjct: 121 EWFKTLPLFLDLGGVRVVHA 140
>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 = 64.3 bits (156), Expect = 4e-12
Identities = 30/134 (22%), Positives = 53/134 (39%), Gaps = 7/134 (5%)
Query: 469 PYGSFMFLGPTGVGKTELCKTLSACIFNNEESIIRIDMSEFIEKHSISRLIGAPPGYIGY 528
P + +GP G GKT L + L+ + +I ID + +E+ L+ G
Sbjct: 1 PGEVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKAS 60
Query: 529 EEGGY----LTEIVRRKPYSLILLDEIEKANSDVFNILLQILDDGRLTDNRGRTINFRNT 584
G + R+ +++LDEI LL +L++ RL +N
Sbjct: 61 GSGELRLRLALALARKLKPDVLILDEITSLLDAEQEALLLLLEELRLLLLLKS---EKNL 117
Query: 585 IIVMTSNLGSDKIK 598
+++T+N D
Sbjct: 118 TVILTTNDEKDLGP 131
Score = 48.9 bits (116), Expect = 1e-06
Identities = 33/155 (21%), Positives = 61/155 (39%), Gaps = 20/155 (12%)
Query: 64 SKNNPVLIGEPGVGKTAIVEGLAQRI---------INGEVPNSLLSKKILLLDIALLLAG 114
+++G PG GKT + LA+ + I+GE + ++LL+ + G
Sbjct: 1 PGEVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIV----GG 56
Query: 115 TKYRGEFEDRLKKILKEISNNQKDIIIFIDELHTMIG--TGKVEGSIDAGNMLKPELSRG 172
K G E RL+ L + D ++ +DE+ +++ + ++ +L S
Sbjct: 57 KKASGSGELRLRLALALARKLKPD-VLILDEITSLLDAEQEALLLLLEELRLLLLLKSEK 115
Query: 173 ELHCIGATTLNEYRQYIEKDAAFERRFQKILVEEP 207
L I T + A RRF + +V
Sbjct: 116 NLTVILTTNDEK----DLGPALLRRRFDRRIVLLL 146
>gnl|CDD|219538 pfam07728, AAA_5, AAA domain (dynein-related subfamily). This Pfam
entry includes some of the AAA proteins not detected by
the pfam00004 model.
Length = 135
Score = 63.5 bits (155), Expect = 8e-12
Identities = 36/136 (26%), Positives = 56/136 (41%), Gaps = 16/136 (11%)
Query: 472 SFMFLGPTGVGKTELCKTLSACIFNNEESIIRI--DMSEFIEKHSISRLIGA--PPGYIG 527
+ +GP G GK+EL + L+A + N +++ D +E L G
Sbjct: 1 GVLLVGPPGTGKSELAERLAAALSNRPVFYVQLTRDTTE-------EDLKGRRNIDPGGA 53
Query: 528 YEEGGYLTEIVRRKPYSLILLDEIEKANSDVFNILLQILDDGRLTDNRGRTI---NFRNT 584
G L R + +LDEI +AN DV N LL +LD+ RL G +
Sbjct: 54 SWVDGPLVRAAREG--EIAVLDEINRANPDVLNSLLSLLDERRLLLPEGGELVKAAPDGF 111
Query: 585 IIVMTSNLGSDKIKEM 600
++ T N + E+
Sbjct: 112 RLIATMNPLDRGLNEL 127
Score = 36.1 bits (84), Expect = 0.020
Identities = 28/140 (20%), Positives = 45/140 (32%), Gaps = 16/140 (11%)
Query: 69 VLIGEPGVGKTAIVEGLAQRIINGEVPNSLLSKKILLLDIALLLAGTKYRGEFEDRLKKI 128
+L+G PG GK+ + E LA + N V L++ L +
Sbjct: 3 LLVGPPGTGKSELAERLAAALSNRPVFYVQLTRD---TTEEDLKGRRNIDPGGASWVDGP 59
Query: 129 LKEISNNQKDIIIFIDELHTMIGT---GKVEGSIDAGNMLKPELSRGELHC------IGA 179
L + + I +DE+ + +D +L PE + + A
Sbjct: 60 LVRAAREGE--IAVLDEI-NRANPDVLNSLLSLLDERRLLLPEG-GELVKAAPDGFRLIA 115
Query: 180 TTLNEYRQYIEKDAAFERRF 199
T R E A RF
Sbjct: 116 TMNPLDRGLNELSPALRSRF 135
>gnl|CDD|215649 pfam00004, AAA, ATPase family associated with various cellular
activities (AAA). AAA family proteins often perform
chaperone-like functions that assist in the assembly,
operation, or disassembly of protein complexes.
Length = 131
Score = 59.2 bits (144), Expect = 2e-10
Identities = 38/144 (26%), Positives = 62/144 (43%), Gaps = 29/144 (20%)
Query: 70 LIGEPGVGKTAIVEGLAQRIINGEVPNSLLSKKILLLDIALLLAGTKYRGEFEDRLKKIL 129
L G PG GKT + + +A+ + ++I+ +KY GE E RL+++
Sbjct: 3 LYGPPGTGKTTLAKAVAKEL------------GAPFIEISGSELVSKYVGESEKRLRELF 50
Query: 130 KEISNNQKDIIIFIDELHTMIGTGKVEGSIDAG---NMLKPEL-----SRGELHCIGATT 181
+ +IFIDE+ + G+ G ++ N L EL S ++ I AT
Sbjct: 51 EAAKKLAPC-VIFIDEIDALAGSRGSGGDSESRRVVNQLLTELDGFTSSLSKVIVIAATN 109
Query: 182 LNEYRQYIEK-DAAFER-RFQKIL 203
+K D A R RF +I+
Sbjct: 110 ------RPDKLDPALLRGRFDRII 127
Score = 43.0 bits (102), Expect = 9e-05
Identities = 29/129 (22%), Positives = 46/129 (35%), Gaps = 32/129 (24%)
Query: 474 MFLGPTGVGKTELCKTLSACIFNNEESIIRIDMSEFIEKHSISRLIGAPPGYIGYEEGGY 533
+ GP G GKT L K ++ + I I SE + K+ +G +
Sbjct: 2 LLYGPPGTGKTTLAKAVAKELGAP---FIEISGSELVSKY-----VGESEKRL----REL 49
Query: 534 LTEIVRRKPYSLILLDEIEK-----------ANSDVFNILLQILDDGRLTDNRGRTINFR 582
+ P +I +DEI+ + V N LL LD G T +
Sbjct: 50 FEAAKKLAP-CVIFIDEIDALAGSRGSGGDSESRRVVNQLLTELD--------GFTSSLS 100
Query: 583 NTIIVMTSN 591
I++ +N
Sbjct: 101 KVIVIAATN 109
>gnl|CDD|163666 cd07423, MPP_PrpE, Bacillus subtilis PrpE and related proteins,
metallophosphatase domain. PrpE (protein phosphatase E)
is a bacterial member of the PPP (phosphoprotein
phosphatase) family of serine/threonine phosphatases and
a key signal transduction pathway component controlling
the expression of spore germination receptors GerA and
GerK in Bacillus subtilis. PrpE is closely related to
ApaH (also known symmetrical Ap(4)A hydrolase and
bis(5'nucleosyl)-tetraphosphatase). PrpE has
specificity for phosphotyrosine only, unlike the
serine/threonine phosphatases to which it is related.
The Bacilli members of this family are single domain
proteins while the other members have N- and C-terminal
domains in addition to this phosphatase domain. The PPP
(phosphoprotein phosphatase) family, to which PrpE
belongs, is one of two known protein phosphatase
families specific for serine and threonine. The PPP
family also includes: PP1, PP2A, PP2B (calcineurin),
PP4, PP5, PP6, PP7, Bsu1, RdgC, PrpA/PrpB, and ApA4
hydrolase. The PPP catalytic domain is defined by three
conserved motifs (-GDXHG-, -GDXVDRG- and -GNHE-). The
PPP enzyme family is ancient with members found in all
eukaryotes, and in most bacterial and archeal genomes.
Dephosphorylation of phosphoserines and
phosphothreonines on target proteins plays a central
role in the regulation of many cellular processes. PPPs
belong to the metallophosphatase (MPP) superfamily.
MPPs are functionally diverse, but all share a conserved
domain with an active site consisting of two metal ions
(usually manganese, iron, or zinc) coordinated with
octahedral geometry by a cage of histidine, aspartate,
and asparagine residues. The MPP superfamily includes:
Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat
debranching enzymes, YfcE-like phosphodiesterases,
purple acid phosphatases (PAPs), YbbF-like
UDP-2,3-diacylglucosamine hydrolases, and acid
sphingomyelinases (ASMases). The conserved domain is a
double beta-sheet sandwich with a di-metal active site
made up of residues located at the C-terminal side of
the sheets. This domain is thought to allow for
productive metal coordination.
Length = 234
Score = 61.1 bits (149), Expect = 3e-10
Identities = 41/142 (28%), Positives = 66/142 (46%), Gaps = 25/142 (17%)
Query: 679 FDLIYGARDVHGCKKSLSILL-------KKIHKKSPEAN--FIFLGDLINKGPQSLDTLR 729
FD+I DVHGC L LL K++ + +F+GDL+++GP S + LR
Sbjct: 3 FDII---GDVHGCYDELEELLEKLGYRIKRVGTVTHPEGRRAVFVGDLVDRGPDSPEVLR 59
Query: 730 MVYSM--RNYAKIVLGNHEIHLLDVLININKKSK--LD-TFDDILDAPD--KKKLVSWLR 782
+V SM A V GNH+ L L N K L+ T + + K++++ +
Sbjct: 60 LVMSMVAAGAALCVPGNHDNKLYRKLQGRNVKITHGLEETVAQLEAESEEFKEEVIEFYE 119
Query: 783 TQPLAIYY----KKYLMIHAGV 800
+ P + K ++ HAG+
Sbjct: 120 SLPS--HLVLDEGKLVVAHAGI 139
Score = 43.0 bits (102), Expect = 3e-04
Identities = 20/46 (43%), Positives = 26/46 (56%)
Query: 903 DITVLFGHWSTLGLIMKPNIICLDTGCVWGNKLTALCLEDRSIIQV 948
D V++GH N I +DTGCV+G KLTAL +R I+ V
Sbjct: 182 DALVVYGHTPVPEPRWLNNTINIDTGCVFGGKLTALRYPEREIVSV 227
>gnl|CDD|223786 COG0714, COG0714, MoxR-like ATPases [General function prediction
only].
Length = 329
Score = 61.3 bits (149), Expect = 6e-10
Identities = 46/172 (26%), Positives = 69/172 (40%), Gaps = 23/172 (13%)
Query: 425 QVEREKLLNIENLLCKRVVGQDEAISAVSNAIRRSRSGLSDAKRPYGSFMFLGPTGVGKT 484
+ E L I + L K VVG +E I A+ A + GP GVGKT
Sbjct: 9 ERVAEILGKIRSELEKVVVGDEEVIELALLALL--------AGGH---VLLEGPPGVGKT 57
Query: 485 ELCKTLSACIFNNEESIIRIDMSEFIEKHSISRLIGAPPGYIGYEEGGYLTEIVRRK--- 541
L + L+ + +RI + + S L+G E G V
Sbjct: 58 LLARALARALGLP---FVRIQCTPDLLP---SDLLGTYAYAALLLEPGE-FRFVPGPLFA 110
Query: 542 -PYSLILLDEIEKANSDVFNILLQILDDGRLTDNRGRTINFRN-TIIVMTSN 591
++LLDEI +A +V N LL+ L++ ++T TI I++ T N
Sbjct: 111 AVRVILLLDEINRAPPEVQNALLEALEERQVTVPGLTTIRLPPPFIVIATQN 162
Score = 39.7 bits (93), Expect = 0.006
Identities = 17/54 (31%), Positives = 27/54 (50%), Gaps = 2/54 (3%)
Query: 36 EKARLGKLDPVIGRDDEIRRAIQVLQRRSKNNPVLIGEPGVGKTAIVEGLAQRI 89
K R V+G ++ I A+ L + + +L G PGVGKT + LA+ +
Sbjct: 16 GKIRSELEKVVVGDEEVIELAL--LALLAGGHVLLEGPPGVGKTLLARALARAL 67
>gnl|CDD|204486 pfam10431, ClpB_D2-small, C-terminal, D2-small domain, of ClpB
protein. This is the C-terminal domain of ClpB protein,
referred to as the D2-small domain, and is a mixed
alpha-beta structure. Compared with the D1-small domain
(included in AAA, pfam00004) it lacks the long
coiled-coil insertion, and instead of helix C4 contains
a beta-strand (e3) that is part of a three stranded
beta-pleated sheet. In Thermophilus the whole protein
forms a hexamer with the D1-small and D2-small domains
located on the outside of the hexamer, with the long
coiled-coil being exposed on the surface. The D2-small
domain is essential for oligomerisation, forming a tight
interface with the D2-large domain of a neighboring
subunit and thereby providing enough binding energy to
stabilise the functional assembly. The domain is
associated with two Clp_N, pfam02861, at the N-terminus
as well as AAA, pfam00004 and AAA_2, pfam07724.
Length = 81
Score = 51.6 bits (125), Expect = 2e-08
Identities = 15/50 (30%), Positives = 31/50 (62%)
Query: 637 LNRKNILSIANIQLNILKNKLLKMNMDLKISKAALKKISNIGFDLIYGAR 686
L+++ + I ++QL L+ +L + + L+++ AA ++ G+D YGAR
Sbjct: 1 LSKEELRQIVDLQLKRLQKRLAERGITLELTDAAKDWLAEKGYDPEYGAR 50
>gnl|CDD|234457 TIGR04075, bacter_Pnkp, polynucleotide kinase-phosphatase. Members
of this protein family are the bacterial polynucleotide
kinase-phosphatase (Pnkp) whose genes occur paired with
genes for the 3' terminal RNA ribose
2'-O-methyltransferase Hen1. All members of the seed
alignment belong to a cassette with the Hen1. The pair
acts in bacterial RNA repair. This enzyme performs
end-healing reactions on broken RNA, preparing from the
RNA ligase to close the break. The working hypothesis is
that the combination of Pnkp (RNA repair) and Hen1 (RNA
modification) serves to first repair RNA damage from
ribotoxins and then perform a modification that prevents
the damage from recurring [Transcription, RNA
processing].
Length = 851
Score = 57.3 bits (139), Expect = 3e-08
Identities = 31/91 (34%), Positives = 46/91 (50%), Gaps = 19/91 (20%)
Query: 679 FDLIYGARDVHGCKKSLSILLKKI--------HKKSPEAN------FIFLGDLINKGPQS 724
FD+I G DVHGC+ L LL+++ + + +F+GDL+++GP S
Sbjct: 182 FDII-G--DVHGCRDELETLLEELGYQIERDEGGRPVDVTHPEGRKAVFVGDLVDRGPDS 238
Query: 725 LDTLRMVYSMRN--YAKIVLGNHEIHLLDVL 753
LR+V M A V GNH++ LL L
Sbjct: 239 PGVLRLVMGMVAAGTALCVPGNHDVKLLRAL 269
Score = 46.1 bits (110), Expect = 9e-05
Identities = 19/44 (43%), Positives = 26/44 (59%)
Query: 905 TVLFGHWSTLGLIMKPNIICLDTGCVWGNKLTALCLEDRSIIQV 948
V++GH N IC+DTGCV+G KLTAL +R ++ V
Sbjct: 368 MVVYGHTPVPEAEWVNNTICIDTGCVFGGKLTALRYPERELVSV 411
>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 = 49.9 bits (119), Expect = 5e-07
Identities = 28/129 (21%), Positives = 54/129 (41%), Gaps = 26/129 (20%)
Query: 45 PVIGRDDEIRRAIQVLQRRSKNNP---VLIGEPGVGKTAIVEGLAQR---------IING 92
++GR++E+ R + L+R P +L G G GKT+++ L +
Sbjct: 1 RLVGREEELERLLDALRRARSGGPPSVLLTGPSGTGKTSLLRELLEGLLVAAGKCDQAER 60
Query: 93 EVPNSL--------------LSKKILLLDIALLLAGTKYRGEFEDRLKKILKEISNNQKD 138
P + L+ ++LLL ALL A E L ++L+ + +
Sbjct: 61 NPPYAFSQALRELLRQLLRELAAELLLLREALLAALGAELIEGLQDLVELLERLLARARP 120
Query: 139 IIIFIDELH 147
+++ +D+L
Sbjct: 121 LVLVLDDLQ 129
Score = 41.0 bits (96), Expect = 6e-04
Identities = 29/153 (18%), Positives = 62/153 (40%), Gaps = 29/153 (18%)
Query: 441 RVVGQDEAISAVSNAIRRSRSGLSDAKRPYGSFMFLGPTGVGKTELCKTLS--------- 491
R+VG++E + + +A+RR+RSG S + GP+G GKT L + L
Sbjct: 1 RLVGREEELERLLDALRRARSG------GPPSVLLTGPSGTGKTSLLRELLEGLLVAAGK 54
Query: 492 -----ACIFNNEESIIRIDMSEFIEKH---------SISRLIGAPPGYIGYEEGGYLTEI 537
+R + + + + ++ +GA + L +
Sbjct: 55 CDQAERNPPYAFSQALRELLRQLLRELAAELLLLREALLAALGAELIEGLQDLVELLERL 114
Query: 538 VRRKPYSLILLDEIEKANSDVFNILLQILDDGR 570
+ R +++LD+++ A+ + ++L +L
Sbjct: 115 LARARPLVLVLDDLQWADEESLDLLAALLRRLE 147
>gnl|CDD|198154 smart01086, ClpB_D2-small, C-terminal, D2-small domain, of ClpB
protein. This is the C-terminal domain of ClpB protein,
referred to as the D2-small domain, and is a mixed
alpha-beta structure. Compared with the D1-small domain
(included in AAA) it lacks the long coiled-coil
insertion, and instead of helix C4 contains a
beta-strand (e3) that is part of a three stranded
beta-pleated sheet. In Thermophilus the whole protein
forms a hexamer with the D1-small and D2-small domains
located on the outside of the hexamer, with the long
coiled-coil being exposed on the surface. The D2-small
domain is essential for oligomerisation, forming a tight
interface with the D2-large domain of a neighbouring
subunit and thereby providing enough binding energy to
stabilise the functional assembly. The domain is
associated with two Clp_N at the N-terminus as well as
AAA and AAA_2.
Length = 90
Score = 46.3 bits (111), Expect = 3e-06
Identities = 15/50 (30%), Positives = 32/50 (64%)
Query: 637 LNRKNILSIANIQLNILKNKLLKMNMDLKISKAALKKISNIGFDLIYGAR 686
L++++++ I ++ LN L+ +L + + L+ + AL ++ G+D YGAR
Sbjct: 1 LDKEDLVRIVDLPLNALQKRLAEKGITLEFTDEALDWLAEKGYDPKYGAR 50
>gnl|CDD|233328 TIGR01243, CDC48, AAA family ATPase, CDC48 subfamily. This
subfamily of the AAA family ATPases includes two members
each from three archaeal species. It also includes yeast
CDC48 (cell division control protein 48) and the human
ortholog, transitional endoplasmic reticulum ATPase
(valosin-containing protein). These proteins in
eukaryotes are involved in the budding and transfer of
membrane from the transitional endoplasmic reticulum to
the Golgi apparatus.
Length = 733
Score = 49.9 bits (119), Expect = 6e-06
Identities = 68/252 (26%), Positives = 101/252 (40%), Gaps = 59/252 (23%)
Query: 69 VLIGEPGVGKTAIVEGLAQRI------INGEVPNSLLSKKILLLDIALLLAGTKYRGEFE 122
+L G PG GKT + + +A ING P + +KY GE E
Sbjct: 216 LLYGPPGTGKTLLAKAVANEAGAYFISING--PEIM----------------SKYYGESE 257
Query: 123 DRLKKILKEISNNQKDIIIFIDELHTMI-----GTGKVEGSIDAG--NMLKPELSRGELH 175
+RL++I KE N IIFIDE+ + TG+VE + A ++ RG +
Sbjct: 258 ERLREIFKEAEENAPS-IIFIDEIDAIAPKREEVTGEVEKRVVAQLLTLMDGLKGRGRVI 316
Query: 176 CIGATTLNEYRQYIEKDAAFER--RFQK-ILVEEPDIEETISILR------------GLQ 220
IGAT + D A R RF + I++ PD IL+ L
Sbjct: 317 VIGATNRPD-----ALDPALRRPGRFDREIVIRVPDKRARKEILKVHTRNMPLAEDVDLD 371
Query: 221 KKYEVHHGVEITDPAIVAASELSYRYISDRFMPDKAIDLIDEAAAK-----IKIEIDSKP 275
K EV HG D A + A E + + RF+ + I+ E +K+ +
Sbjct: 372 KLAEVTHGFVGADLAAL-AKEAAMAALR-RFIREGKINFEAEEIPAEVLKELKVTMKDFM 429
Query: 276 EIMDKLERRLIQ 287
E + +E I+
Sbjct: 430 EALKMVEPSAIR 441
>gnl|CDD|163667 cd07424, MPP_PrpA_PrpB, PrpA and PrpB, metallophosphatase domain.
PrpA and PrpB are bacterial type I serine/threonine and
tyrosine phosphatases thought to modulate the expression
of proteins that protect the cell upon accumulation of
misfolded proteins in the periplasm. The PPP
(phosphoprotein phosphatase) family, to which PrpA and
PrpB belong, is one of two known protein phosphatase
families specific for serine and threonine. This family
also includes: PP1, PP2A, PP2B (calcineurin), PP4, PP5,
PP6, PP7, Bsu1, RdgC, PrpE, and ApA4 hydrolase. The PPP
catalytic domain is defined by three conserved motifs
(-GDXHG-, -GDXVDRG- and -GNHE-). The PPP enzyme family
is ancient with members found in all eukaryotes, and in
most bacterial and archeal genomes. Dephosphorylation
of phosphoserines and phosphothreonines on target
proteins plays a central role in the regulation of many
cellular processes. PPPs belong to the
metallophosphatase (MPP) superfamily. MPPs are
functionally diverse, but all share a conserved domain
with an active site consisting of two metal ions
(usually manganese, iron, or zinc) coordinated with
octahedral geometry by a cage of histidine, aspartate,
and asparagine residues. The MPP superfamily includes:
Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat
debranching enzymes, YfcE-like phosphodiesterases,
purple acid phosphatases (PAPs), YbbF-like
UDP-2,3-diacylglucosamine hydrolases, and acid
sphingomyelinases (ASMases). The conserved domain is a
double beta-sheet sandwich with a di-metal active site
made up of residues located at the C-terminal side of
the sheets. This domain is thought to allow for
productive metal coordination.
Length = 207
Score = 47.6 bits (114), Expect = 6e-06
Identities = 32/114 (28%), Positives = 48/114 (42%), Gaps = 20/114 (17%)
Query: 687 DVHGCKKSLSILLKKIHKKSPEAN-FIFLGDLINKGPQSLDTLRM-----VYSMRNYAKI 740
D+HG L L + P + I +GDLI++GP+SL L + ++
Sbjct: 8 DIHGHYSLLQKALDAVGF-DPARDRLISVGDLIDRGPESLACLELLLEPWFHA------- 59
Query: 741 VLGNHEIHLLDVLININKKSKL------DTFDDILDAPDKKKLVSWLRTQPLAI 788
V GNHE +D L + + F D+ D ++ L L PLAI
Sbjct: 60 VRGNHEQMAIDALRAEPLDAVRWLANGGEWFLDLPDEELRRWLALKLEQLPLAI 113
Score = 30.3 bits (69), Expect = 3.7
Identities = 12/36 (33%), Positives = 18/36 (50%)
Query: 905 TVLFGHWSTLGLIMKPNIICLDTGCVWGNKLTALCL 940
V+ GH + N++ +DTG V+ LT L L
Sbjct: 171 AVVHGHTPVKRPLRLGNVLYIDTGAVFDGNLTLLDL 206
>gnl|CDD|215750 pfam00149, Metallophos, Calcineurin-like phosphoesterase. This
family includes a diverse range of phosphoesterases,
including protein phosphoserine phosphatases,
nucleotidases, sphingomyelin phosphodiesterases and
2'-3' cAMP phosphodiesterases as well as nucleases such
as bacterial SbcD or yeast MRE11. The most conserved
regions in this superfamily centre around the metal
chelating residues.
Length = 185
Score = 47.1 bits (111), Expect = 9e-06
Identities = 21/71 (29%), Positives = 39/71 (54%), Gaps = 6/71 (8%)
Query: 687 DVHGCKKSLSI--LLKKIHKKSPEANFIFLGDLINKGPQSLDTLRMVYSMRNYAKI---- 740
D+HG L + LL ++ + +FLGDL+++GP SL+ L ++++++ A
Sbjct: 7 DLHGGLDDLDLLLLLLELLGEPKPDLVLFLGDLVDRGPPSLEVLALLFALKLKAPGPVYL 66
Query: 741 VLGNHEIHLLD 751
V GNH+ +
Sbjct: 67 VRGNHDFDSGN 77
>gnl|CDD|236911 PRK11439, pphA, serine/threonine protein phosphatase 1;
Provisional.
Length = 218
Score = 46.7 bits (111), Expect = 2e-05
Identities = 26/72 (36%), Positives = 41/72 (56%), Gaps = 8/72 (11%)
Query: 687 DVHGCKKSLSILLKKIHKK--SPEANF-IFLGDLINKGPQSLDTLRMVYSMRNYAKIVLG 743
D+HGC L++K+ P + I +GDLI++GPQSL L+++ ++ + V G
Sbjct: 24 DIHGC---FEQLMRKLRHCRFDPWRDLLISVGDLIDRGPQSLRCLQLLE--EHWVRAVRG 78
Query: 744 NHEIHLLDVLIN 755
NHE LD L +
Sbjct: 79 NHEQMALDALAS 90
>gnl|CDD|163614 cd00838, MPP_superfamily, metallophosphatase superfamily,
metallophosphatase domain. Metallophosphatases (MPPs),
also known as metallophosphoesterases,
phosphodiesterases (PDEs), binuclear
metallophosphoesterases, and dimetal-containing
phosphoesterases (DMPs), represent a diverse superfamily
of enzymes with a conserved domain containing an active
site consisting of two metal ions (usually manganese,
iron, or zinc) coordinated with octahedral geometry by a
cage of histidine, aspartate, and asparagine residues.
This superfamily includes: the phosphoprotein
phosphatases (PPPs), Mre11/SbcD-like exonucleases,
Dbr1-like RNA lariat debranching enzymes, YfcE-like
phosphodiesterases, purple acid phosphatases (PAPs),
YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid
sphingomyelinases (ASMases). The conserved domain is a
double beta-sheet sandwich with a di-metal active site
made up of residues located at the C-terminal side of
the sheets. This domain is thought to allow for
productive metal coordination.
Length = 131
Score = 45.0 bits (106), Expect = 2e-05
Identities = 20/68 (29%), Positives = 34/68 (50%), Gaps = 5/68 (7%)
Query: 687 DVHGCKKSLSILLKKIHKKSPEANF-IFLGDLINKGPQSLDTLRMVYSMRNYAKI----V 741
D+HG ++L +L+ + + +F + LGDL+ GP + L ++ I V
Sbjct: 5 DIHGNLEALEAVLEAALAAAEKPDFVLVLGDLVGDGPDPEEVLAAALALLLLLGIPVYVV 64
Query: 742 LGNHEIHL 749
GNH+I L
Sbjct: 65 PGNHDILL 72
>gnl|CDD|222104 pfam13401, AAA_22, AAA domain.
Length = 124
Score = 44.2 bits (105), Expect = 2e-05
Identities = 20/105 (19%), Positives = 42/105 (40%), Gaps = 7/105 (6%)
Query: 471 GSFMFLGPTGVGKTELCKTLSACIFNNEESIIRIDMSEFIEKHSISRLI----GAPPGYI 526
G + G +G GKT L + L+ + N ++ ++ + R I G P
Sbjct: 5 GIGVLTGESGSGKTTLLRRLARQLPNRR--VVYVEAPSLGTPKDLLRKILRALGLPLSGG 62
Query: 527 GYEEG-GYLTEIVRRKPYSLILLDEIEKANSDVFNILLQILDDGR 570
E + + ++R+ L+++DE + + + L + D
Sbjct: 63 TTAELLEAILDALKRRGRPLLIIDEAQHLSLEALEELRDLYDLSE 107
Score = 43.4 bits (103), Expect = 6e-05
Identities = 27/90 (30%), Positives = 39/90 (43%), Gaps = 5/90 (5%)
Query: 62 RRSKNNPVLIGEPGVGKTAIVEGLAQRIINGEV----PNSLLSKKILLLDIALLLAGTKY 117
RR VL GE G GKT ++ LA+++ N V SL + K LL I L G
Sbjct: 1 RRGAGIGVLTGESGSGKTTLLRRLARQLPNRRVVYVEAPSLGTPKDLLRKILRAL-GLPL 59
Query: 118 RGEFEDRLKKILKEISNNQKDIIIFIDELH 147
G L + + + + ++ IDE
Sbjct: 60 SGGTTAELLEAILDALKRRGRPLLIIDEAQ 89
>gnl|CDD|184187 PRK13625, PRK13625, bis(5'-nucleosyl)-tetraphosphatase PrpE;
Provisional.
Length = 245
Score = 46.6 bits (111), Expect = 3e-05
Identities = 24/80 (30%), Positives = 39/80 (48%), Gaps = 19/80 (23%)
Query: 679 FDLIYGARDVHGCKKSLSILLKK----------IHKKSPEA-NFIFLGDLINKGPQSLDT 727
+D+I D+HGC + L +K +H P+ F+GDL ++GP SL
Sbjct: 3 YDII---GDIHGCYQEFQALTEKLGYNWSSGLPVH---PDQRKLAFVGDLTDRGPHSLRM 56
Query: 728 LRMVYSM--RNYAKIVLGNH 745
+ +V+ + + A V GNH
Sbjct: 57 IEIVWELVEKKAAYYVPGNH 76
Score = 31.2 bits (71), Expect = 2.3
Identities = 10/18 (55%), Positives = 15/18 (83%)
Query: 921 NIICLDTGCVWGNKLTAL 938
+ + +DTGCV+G +LTAL
Sbjct: 203 HTVNIDTGCVFGGRLTAL 220
>gnl|CDD|107154 PHA02239, PHA02239, putative protein phosphatase.
Length = 235
Score = 45.8 bits (108), Expect = 4e-05
Identities = 28/86 (32%), Positives = 51/86 (59%), Gaps = 4/86 (4%)
Query: 682 IYGARDVHG-CKKSLSILLKKIHKKSPEANFIFLGDLINKGPQSLDTLRMVYS-MRNYAK 739
IY D+HG +K L+I+ K +++ PE +FLGD +++G +S D + ++ M N
Sbjct: 3 IYVVPDIHGEYQKLLTIMDKINNERKPEETIVFLGDYVDRGKRSKDVVNYIFDLMSNDDN 62
Query: 740 IV--LGNHEIHLLDVLININKKSKLD 763
+V LGNH+ +++ N+++ S D
Sbjct: 63 VVTLLGNHDDEFYNIMENVDRLSIYD 88
>gnl|CDD|182173 PRK09968, PRK09968, serine/threonine-specific protein phosphatase
2; Provisional.
Length = 218
Score = 45.7 bits (108), Expect = 4e-05
Identities = 41/140 (29%), Positives = 68/140 (48%), Gaps = 18/140 (12%)
Query: 672 KKISNIGFDLIYGARDVHGCKKSLSILLKKIHKKS--PEANF-IFLGDLINKGPQSLDTL 728
+KI+ + I+ D+HG +L ++H+ S PE + I +GD I++GP+SL+ L
Sbjct: 7 QKINAHHYRHIWVVGDIHGE---YQLLQSRLHQLSFCPETDLLISVGDNIDRGPESLNVL 63
Query: 729 RMVYSMRNYAKIVLGNHEIHLLDVLI----NINKKSKLDTFDDILDAPDKKKLVSWLRTQ 784
R++ + + V GNHE LD N+ S D F D+ D+ ++ L+
Sbjct: 64 RLLN--QPWFISVKGNHEAMALDAFETGDGNMWLASGGDWFFDLNDSEQQEATDLLLKFH 121
Query: 785 --PLAIYYK----KYLMIHA 798
P I KY++ HA
Sbjct: 122 HLPHIIEITNDNIKYVIAHA 141
>gnl|CDD|197547 smart00156, PP2Ac, Protein phosphatase 2A homologues, catalytic
domain. Large family of serine/threonine phosphatases,
that includes PP1, PP2A and PP2B (calcineurin) family
members.
Length = 271
Score = 42.6 bits (101), Expect = 5e-04
Identities = 23/64 (35%), Positives = 39/64 (60%), Gaps = 5/64 (7%)
Query: 687 DVHGCKKSLSILLKKIHKKSPEANFIFLGDLINKGPQSLDTLRMVYSM--RNYAKIVL-- 742
D+HG L L K + PE N++FLGD +++GP S++ + +++++ +IVL
Sbjct: 35 DIHGQFDDLLRLFDKN-GQPPETNYVFLGDYVDRGPFSIEVILLLFALKILYPNRIVLLR 93
Query: 743 GNHE 746
GNHE
Sbjct: 94 GNHE 97
>gnl|CDD|226415 COG3899, COG3899, Predicted ATPase [General function prediction
only].
Length = 849
Score = 42.0 bits (99), Expect = 0.001
Identities = 30/143 (20%), Positives = 53/143 (37%), Gaps = 24/143 (16%)
Query: 45 PVIGRDDEIRRAIQVLQRRSKNNPVLI---GEPGVGKTAIVEGLAQRIINGEVPNSLLSK 101
P+ GR+ E+ + + R SK ++ GE G+GK+A+V + + I +
Sbjct: 1 PLYGRETELAQLLAAFDRVSKGRGEVVLVAGESGIGKSALVNEVHKPITQQR--GYFIKG 58
Query: 102 KILLL--DIALL--------LAG---TKYRGEFEDRLKKILKEISNNQKDIIIFIDELHT 148
K +I L L G ++ ++L + N + II I EL
Sbjct: 59 KFDQFERNIPLSPLVQAFRDLMGQLLSESDTRILSWRARLLAALGENGQVIIDVIPEL-- 116
Query: 149 MIGTGKVEGSIDAGNMLKPELSR 171
+ G L P ++
Sbjct: 117 ----ELIIGKRPPALELSPTAAQ 135
>gnl|CDD|227596 COG5271, MDN1, AAA ATPase containing von Willebrand factor type A
(vWA) domain [General function prediction only].
Length = 4600
Score = 41.9 bits (98), Expect = 0.002
Identities = 41/157 (26%), Positives = 63/157 (40%), Gaps = 18/157 (11%)
Query: 474 MFLGPTGVGKTELCKTLSACIFNNEESIIRIDMSEFIE-KHSISRLIGAPPGYIGYEEGG 532
G G GK+ L L + I+ I + E + K I PG + +G
Sbjct: 153 YLEGGRGSGKSFLISELCD---EGGQRIVEIHLREITDAKVLIGTYTSPKPGDFEWMKGV 209
Query: 533 YLTEIVRRKPYSLILLDEIEKANSDVFNILLQILDDGRLT-DNRGRTI----NFRNTIIV 587
+ +V IL I+KA V + LL +L+ RL +RG T+ NF+ I
Sbjct: 210 LIEAVVSGD---WILFKRIDKAPHGVLSYLLTLLEKRRLLIPSRGETVLAHDNFQ---IF 263
Query: 588 MTSNLGSDKIKEMEKGDKEIIKLAVMNEVKIYFRPEF 624
TS S K K + + +I+ L +E R +
Sbjct: 264 FTS---SMKTKILGQRLWQILDLTQPDECVEVVRFDM 297
Score = 37.3 bits (86), Expect = 0.047
Identities = 30/95 (31%), Positives = 47/95 (49%), Gaps = 7/95 (7%)
Query: 477 GPTGVGKTELCKTLSACIFNNEESIIRIDMSEFIE-KHSISRLIGAPPGYIGYEEGGYLT 535
GPT GKT + L+ +RI+ E + + I + G + ++EG L
Sbjct: 895 GPTSSGKTSMILYLAR---ETGHKFVRINNHEHTDLQEYIGTYVTDDDGSLSFKEG-VLV 950
Query: 536 EIVRRKPYSLILLDEIEKANSDVFNILLQILDDGR 570
E +RR + I+LDE+ A +DV L ++LDD R
Sbjct: 951 EALRRGYW--IVLDELNLAPTDVLEALNRLLDDNR 983
Score = 31.5 bits (71), Expect = 2.6
Identities = 26/96 (27%), Positives = 46/96 (47%), Gaps = 11/96 (11%)
Query: 53 IRRAIQVLQRRSKNNPVLI-GEPGVGKTAIVEGLAQRIINGEVPNSLLSKKILLLDIALL 111
+ RA+QV + P+L+ G PGVGKT+++ LA R ++ LS++ L D+
Sbjct: 1536 VLRAMQVGK------PILLEGSPGVGKTSLITALA-RKTGKKLIRINLSEQTDLCDLFGS 1588
Query: 112 LAGTKYRGEFEDRLKKILKEISNNQKDIIIFIDELH 147
+ GEF L + + + +DE++
Sbjct: 1589 DLPVEEGGEFRWMDAPFLHAMRDGG---WVLLDEIN 1621
>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and
chromosome partitioning].
Length = 1163
Score = 41.2 bits (97), Expect = 0.003
Identities = 30/133 (22%), Positives = 73/133 (54%), Gaps = 5/133 (3%)
Query: 254 DKAIDLIDEAAAKIKIEIDSKPEIMDKLERRLIQLKIEHEAIKREYDESSKKRLLLIKKE 313
K ++ ++E ++++ E++ E +++ E+ + +LK E E ++ E +E + LL +K+E
Sbjct: 238 RKELEELEEELSRLEEELEELQEELEEAEKEIEELKSELEELREELEELQ-EELLELKEE 296
Query: 314 INKLEIKYANLEKIWKYEKTLIKDSQQIKEEIEKVRLKI-NKATRKSDWQTVSKLKYGEL 372
I +LE + + L + + L + ++++E +E+++ KI + +T+ + L
Sbjct: 297 IEELEGEISLLRER---LEELENELEELEERLEELKEKIEALKEELEERETLLEELEQLL 353
Query: 373 NKLERILKEKSQK 385
+LE +E +K
Sbjct: 354 AELEEAKEELEEK 366
Score = 36.2 bits (84), Expect = 0.090
Identities = 24/155 (15%), Positives = 70/155 (45%), Gaps = 15/155 (9%)
Query: 255 KAIDLIDEAAAKIKIEIDSKPEIMDKLERRLIQLKIEHEAIKREYDESSKKRLLLIKKEI 314
+ ++ ++E + + +D+ ++ LE+R +L+ E E ++ E +E +++L +++E+
Sbjct: 793 EELEELEEELEEAERRLDALERELESLEQRRERLEQEIEELEEEIEEL-EEKLDELEEEL 851
Query: 315 NKLEIKYANL--------EKIWKYEKTLIKDSQQIKE---EIEKVRLKINKATRKSDWQT 363
+LE + L + + E L + ++ +E E+ ++ ++ + + +
Sbjct: 852 EELEKELEELKEELEELEAEKEELEDELKELEEEKEELEEELRELESELAELKEEIEKLR 911
Query: 364 VSKLKYGELNKLERILKEKSQKDIQLPNNANKFTL 398
+ EL L+ + + + + TL
Sbjct: 912 E---RLEELEAKLERLEVELPELEEELEEEYEDTL 943
Score = 35.1 bits (81), Expect = 0.24
Identities = 37/208 (17%), Positives = 95/208 (45%), Gaps = 14/208 (6%)
Query: 192 DAAFERRFQKILVEEPDIEETISILRGLQKKYEVH--HGVEITDPAIVAASELSYRYISD 249
+ A LV + D+E+ + R L+ KY + G + + + R
Sbjct: 606 EPAVRFVLGDTLVVD-DLEQARRLARKLRIKYRIVTLDGDLVEPSGSITGGSRNKRSSLA 664
Query: 250 RF----MPDKAIDLIDEAAAKIKIEIDSKPEIMDKLERRLIQLKIEHEAIKREYDESSKK 305
+ ++ + ++ K++ E+ S + LE L +L+ + E ++R+ +E K+
Sbjct: 665 QKRELKELEEELAELEAQLEKLEEELKSLKNELRSLEDLLEELRRQLEELERQLEE-LKR 723
Query: 306 RLLLIKKEINKLEIKYANLEK----IWKYEKTLIKDSQQIKEEIEKVRLKINKATRKSDW 361
L +++E+ +L+ + LE+ + + + L + ++++EE+E + + K K +
Sbjct: 724 ELAALEEELEQLQSRLEELEEELEELEEELEELQERLEELEEELESLEEALAK--LKEEI 781
Query: 362 QTVSKLKYGELNKLERILKEKSQKDIQL 389
+ + + + +LE + +E + + +L
Sbjct: 782 EELEEKRQALQEELEELEEELEEAERRL 809
Score = 32.4 bits (74), Expect = 1.4
Identities = 30/206 (14%), Positives = 90/206 (43%), Gaps = 11/206 (5%)
Query: 271 IDSKPEIMDKLERRLIQLKIEHEAIKREYDESSKKRLL---LIKKEINKLEIKYANLEKI 327
++ +++++LE++L +L+ + E +R + ++ R L L+ ++ +L + LE+
Sbjct: 188 LERLEDLLEELEKQLEKLERQAEKAERYQELKAELRELELALLLAKLKELRKELEELEEE 247
Query: 328 WKYEKTLIKDSQQ----IKEEIEKVRLKINKATRKSDWQTVSKLKYGELNKLERILKEKS 383
+ +++ Q+ ++EIE+++ ++ + + + + + ++E + E S
Sbjct: 248 LSRLEEELEELQEELEEAEKEIEELKSELEELREE--LEELQEELLELKEEIEELEGEIS 305
Query: 384 QKDIQLPNNANKFTLLKTKVGSEEIAEIVSRTTGIPVSKIVQVEREKLLNIENLLCKRVV 443
+L N+ L+ ++ E +I + + + + E E+LL + +
Sbjct: 306 LLRERLEELENELEELEERL-EELKEKIEALKEELEERETLLEELEQLLAELEEAKEELE 364
Query: 444 G-QDEAISAVSNAIRRSRSGLSDAKR 468
+ + R L++ +
Sbjct: 365 EKLSALLEELEELFEALREELAELEA 390
Score = 31.2 bits (71), Expect = 3.3
Identities = 26/117 (22%), Positives = 58/117 (49%), Gaps = 12/117 (10%)
Query: 254 DKAIDLIDEAAAKIKIEIDSKPEIMDKLERRLIQLKIEHEAIKREY-DESSKKRLLLIKK 312
++ + ++ A++K EI+ E +++LE +L +L++E ++ E +E +++
Sbjct: 890 EEELRELESELAELKEEIEKLRERLEELEAKLERLEVELPELEEELEEEYEDTLETELER 949
Query: 313 EINKLEIKYA-----NLEKIWKYEKT------LIKDSQQIKEEIEKVRLKINKATRK 358
EI +LE + NL I +YE+ L + ++E EK+ I + ++
Sbjct: 950 EIERLEEEIEALGPVNLRAIEEYEEVEERYEELKSQREDLEEAKEKLLEVIEELDKE 1006
Score = 30.5 bits (69), Expect = 5.7
Identities = 34/201 (16%), Positives = 89/201 (44%), Gaps = 23/201 (11%)
Query: 196 ERRFQKILVEEPDIEETISILRGLQKKYEVHHGVEITDPAIVAASELSYRYISDRFMP-D 254
E + + + +IEE + LQ++ E + A E + R +
Sbjct: 768 ESLEEALAKLKEEIEELEEKRQALQEELEELEEELEEAERRLDALERELESLEQRRERLE 827
Query: 255 KAIDLIDEAAAKIKIEIDSKPEIMDKLERRLIQLKIEHEAIKREYDESS------KKRLL 308
+ I+ ++E +++ ++D E +++LE+ L +LK E E ++ E +E ++
Sbjct: 828 QEIEELEEEIEELEEKLDELEEELEELEKELEELKEELEELEAEKEELEDELKELEEEKE 887
Query: 309 LIKKEINKLE-----IKYANLEKIWKYEKTLIKDSQQIKEEIEKVRLKIN---KATRKSD 360
+++E+ +LE +K + + E L ++++ E+ ++ ++ + T +++
Sbjct: 888 ELEEELRELESELAELKEEIEKLRERLE-ELEAKLERLEVELPELEEELEEEYEDTLETE 946
Query: 361 WQTVSKLKYGELNKLERILKE 381
+ E+ +LE ++
Sbjct: 947 LER-------EIERLEEEIEA 960
>gnl|CDD|163657 cd07414, MPP_PP1_PPKL, PP1, PPKL (PP1 and kelch-like) enzymes, and
related proteins, metallophosphatase domain. PP1
(protein phosphatase type 1) is a serine/threonine
phosphatase that regulates many cellular processes
including: cell-cycle progression, protein synthesis,
muscle contraction, carbohydrate metabolism,
transcription and neuronal signaling, through its
interaction with at least 180 known targeting proteins.
PP1 occurs in all tissues and regulates many pathways,
ranging from cell-cycle progression to carbohydrate
metabolism. Also included here are the PPKL (PP1 and
kelch-like) enzymes including the PPQ, PPZ1, and PPZ2
fungal phosphatases. These PPKLs have a large
N-terminal kelch repeat in addition to a C-terminal
phosphoesterase domain. The PPP (phosphoprotein
phosphatase) family, to which PP1 belongs, is one of two
known protein phosphatase families specific for serine
and threonine. The PPP family also includes: PP2A, PP2B
(calcineurin), PP4, PP5, PP6, PP7, Bsu1, RdgC, PrpE,
PrpA/PrpB, and ApA4 hydrolase. The PPP catalytic domain
is defined by three conserved motifs (-GDXHG-, -GDXVDRG-
and -GNHE-). The PPP enzyme family is ancient with
members found in all eukaryotes, and in most bacterial
and archeal genomes. Dephosphorylation of
phosphoserines and phosphothreonines on target proteins
plays a central role in the regulation of many cellular
processes. PPPs belong to the metallophosphatase (MPP)
superfamily. MPPs are functionally diverse, but all
share a conserved domain with an active site consisting
of two metal ions (usually manganese, iron, or zinc)
coordinated with octahedral geometry by a cage of
histidine, aspartate, and asparagine residues. The MPP
superfamily includes: Mre11/SbcD-like exonucleases,
Dbr1-like RNA lariat debranching enzymes, YfcE-like
phosphodiesterases, purple acid phosphatases (PAPs),
YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid
sphingomyelinases (ASMases). The conserved domain is a
double beta-sheet sandwich with a di-metal active site
made up of residues located at the C-terminal side of
the sheets. This domain is thought to allow for
productive metal coordination.
Length = 293
Score = 40.4 bits (95), Expect = 0.003
Identities = 24/67 (35%), Positives = 39/67 (58%), Gaps = 11/67 (16%)
Query: 687 DVHGCKKSLSILLKKIHKKS--PEANFIFLGDLINKGPQSLDT--LRMVYSMRNYAK--- 739
D+HG LL+ PE+N++FLGD +++G QSL+T L + Y ++ Y +
Sbjct: 57 DIHG---QYYDLLRLFEYGGFPPESNYLFLGDYVDRGKQSLETICLLLAYKIK-YPENFF 112
Query: 740 IVLGNHE 746
++ GNHE
Sbjct: 113 LLRGNHE 119
>gnl|CDD|200312 TIGR03689, pup_AAA, proteasome ATPase. In the Actinobacteria, as
shown for Mycobacterium tuberculosis, some proteins are
modified by ligation between an epsilon-amino group of a
lysine side chain and the C-terminal carboxylate of the
ubiquitin-like protein Pup. This modification leads to
protein degradation by the archaeal-like proteasome
found in the Actinobacteria. Members of this protein
family belong to the AAA family of ATPases and tend to
be clustered with the genes for Pup, the Pup ligase
PafA, and structural components of the proteasome. This
protein forms hexameric rings with ATPase activity
[Protein fate, Degradation of proteins, peptides, and
glycopeptides].
Length = 512
Score = 40.8 bits (96), Expect = 0.003
Identities = 59/212 (27%), Positives = 88/212 (41%), Gaps = 52/212 (24%)
Query: 38 ARLGKLDPVIGRDDEIRRAIQV------LQRRSKNNP----VLIGEPGVGKT----AIVE 83
A +G L I + IR A+++ L R P +L G PG GKT A+
Sbjct: 182 ADIGGLGSQIEQ---IRDAVELPFLHPELYREYGLKPPKGVLLYGPPGCGKTLIAKAVAN 238
Query: 84 GLAQRI-INGEVPNSLLS-KKILLLDIALLLAGTKYRGEFEDRLKKIL---KEISNNQKD 138
LA RI G + L+ K LL+ KY GE E +++ I +E ++ +
Sbjct: 239 SLAARIGAEGGGKSYFLNIKGPELLN--------KYVGETERQIRLIFQRAREKASEGRP 290
Query: 139 IIIFIDELHTMI---GTGKVEGSIDAGNMLKPEL--------SRGELHCIGATTLNEYRQ 187
+I+F DE+ ++ G+G S D + P+L S + IGA+ +
Sbjct: 291 VIVFFDEMDSLFRTRGSGV---SSDVETTVVPQLLAEIDGVESLDNVIVIGASNREDM-- 345
Query: 188 YIEKDAAFER--RFQ-KILVEEPDIEETISIL 216
D A R R KI +E PD E I
Sbjct: 346 ---IDPAILRPGRLDVKIRIERPDAEAAADIF 374
>gnl|CDD|188437 TIGR03922, T7SS_EccA, type VII secretion AAA-ATPase EccA. This
model represents the AAA family ATPase, EccA, of the
actinobacterial flavor of type VII secretion systems.
Species such as Mycobacterium tuberculosis have several
instances of this system per genome, designated EccA1,
EccA2, etc [Protein fate, Protein and peptide secretion
and trafficking].
Length = 557
Score = 40.6 bits (95), Expect = 0.004
Identities = 35/155 (22%), Positives = 68/155 (43%), Gaps = 18/155 (11%)
Query: 55 RAIQVLQRRSKNNPVLIGEPGVGKTAIVEGLAQRIINGEVPNSLLSKKILLLDIALLLAG 114
R + V Q N+ + G PG GKT I +A +I G + +K L+ +++
Sbjct: 304 RGLPVAQT--SNHMLFAGPPGTGKTTIARVVA-KIYCGLG----VLRKPLVREVSR---- 352
Query: 115 TKYRGEFEDRLKKILKEISNNQKDIIIFIDELHTMIGTGKVEGSIDAGN------MLKPE 168
G++ + EI ++ ++F+DE +T++ TG + G + + E
Sbjct: 353 ADLIGQYIGESEAKTNEIIDSALGGVLFLDEAYTLVETGYGQKD-PFGLEAIDTLLARME 411
Query: 169 LSRGELHCIGATTLNEYRQYIEKDAAFERRFQKIL 203
R L IGA + +++E + RF +++
Sbjct: 412 NDRDRLVVIGAGYRKDLDKFLEVNEGLRSRFTRVI 446
Score = 30.6 bits (69), Expect = 4.2
Identities = 23/93 (24%), Positives = 40/93 (43%), Gaps = 7/93 (7%)
Query: 426 VEREKLLNIENLLCKRVVGQDEAI-SAVSNAIRRSRSGLSDAKRPYGSFMFLGPTGVGKT 484
E E L E + +RV Q A+ S+ + A+ R+ GL A+ +F GP G GKT
Sbjct: 269 AEAEAELA-EQIGLERVKRQVAALKSSTAMALARAERGLPVAQTSN-HMLFAGPPGTGKT 326
Query: 485 E----LCKTLSACIFNNEESIIRIDMSEFIEKH 513
+ K + + + ++ I ++
Sbjct: 327 TIARVVAKIYCGLGVLRKPLVREVSRADLIGQY 359
>gnl|CDD|224401 COG1484, DnaC, DNA replication protein [DNA replication,
recombination, and repair].
Length = 254
Score = 39.7 bits (93), Expect = 0.005
Identities = 33/156 (21%), Positives = 63/156 (40%), Gaps = 28/156 (17%)
Query: 472 SFMFLGPTGVGKTELCKTLSACIFNNEESIIRIDMSEFIEKHSISRLIGAPPGYIGYEEG 531
+ + LGP GVGKT L A NE I + +S+L A ++EG
Sbjct: 107 NLVLLGPPGVGKTHL-----AIAIGNELLKAGISVLFITAPDLLSKLKAA------FDEG 155
Query: 532 GYLTEIVRR-KPYSLILLDEI--EKANSDVFNILLQILDDGRLTDNRGRTINFRNTIIVM 588
+++R K L+++D+I E + + ++L Q++ I +
Sbjct: 156 RLEEKLLRELKKVDLLIIDDIGYEPFSQEEADLLFQLISRRY---ESRSLI--------I 204
Query: 589 TSNLGSDKIKEM---EKGDKEIIKLAVMNEVKIYFR 621
TSNL + E+ + + ++ + + I +
Sbjct: 205 TSNLSFGEWDELFGDDALTEALLDRILHHSHVIVIK 240
Score = 29.3 bits (66), Expect = 7.6
Identities = 21/102 (20%), Positives = 43/102 (42%), Gaps = 15/102 (14%)
Query: 50 DDEIRRAIQVLQRRSKNNP-----VLIGEPGVGKTAIVEGLAQRIINGEVPNSLLSKKIL 104
++A++ L + VL+G PGVGKT + + ++ + ++ L
Sbjct: 85 PGIDKKALEDLASLVEFFERGENLVLLGPPGVGKTHLAIAIGNELLKAGISVLFITAPDL 144
Query: 105 LLDIALLLAGTKYRGEFEDRLKKILKEISNNQKDIIIFIDEL 146
L L G E++L + LK++ ++ ID++
Sbjct: 145 LSK----LKAAFDEGRLEEKLLRELKKVD------LLIIDDI 176
>gnl|CDD|233758 TIGR02169, SMC_prok_A, chromosome segregation protein SMC,
primarily archaeal type. SMC (structural maintenance of
chromosomes) proteins bind DNA and act in organizing and
segregating chromosomes for partition. SMC proteins are
found in bacteria, archaea, and eukaryotes. It is found
in a single copy and is homodimeric in prokaryotes, but
six paralogs (excluded from this family) are found in
eukarotes, where SMC proteins are heterodimeric. This
family represents the SMC protein of archaea and a few
bacteria (Aquifex, Synechocystis, etc); the SMC of other
bacteria is described by TIGR02168. The N- and
C-terminal domains of this protein are well conserved,
but the central hinge region is skewed in composition
and highly divergent [Cellular processes, Cell division,
DNA metabolism, Chromosome-associated proteins].
Length = 1164
Score = 40.1 bits (94), Expect = 0.007
Identities = 30/140 (21%), Positives = 66/140 (47%), Gaps = 19/140 (13%)
Query: 265 AKIKIEIDSKPEIMDKLERRLIQLKIEHEAIKREYDESSKK-------RLLLIKKEINKL 317
I+ ++ S E ++KL + +L+ E I++ +E +KK L +K++I +L
Sbjct: 240 EAIERQLASLEEELEKLTEEISELEKRLEEIEQLLEELNKKIKDLGEEEQLRVKEKIGEL 299
Query: 318 EIKYANLEKIWKYEKTLIKDSQ----QIKEEIEKVRLKI--------NKATRKSDWQTVS 365
E + A+LE+ ++ ++D++ +++ EI+K+ +I + R+
Sbjct: 300 EAEIASLERSIAEKERELEDAEERLAKLEAEIDKLLAEIEELEREIEEERKRRDKLTEEY 359
Query: 366 KLKYGELNKLERILKEKSQK 385
EL L L+E ++
Sbjct: 360 AELKEELEDLRAELEEVDKE 379
Score = 39.3 bits (92), Expect = 0.011
Identities = 38/210 (18%), Positives = 81/210 (38%), Gaps = 38/210 (18%)
Query: 261 DEAAAKIKIEIDSKPEIMDKLERRLIQLKIEHEAIKREYDESSKKRLLLIKKEINKLEIK 320
+E AK++ EID +++LER + + + + + EY E K+E+ L
Sbjct: 321 EERLAKLEAEIDKLLAEIEELEREIEEERKRRDKLTEEYAEL--------KEELEDLR-- 370
Query: 321 YANLEKIWKYEKTLIKDSQQIKEEIEKVRLKINKATRKSDWQTVSKLKYGELNKLERILK 380
A LE++ K + + +E++EK++ +IN+ R+ D R+ +
Sbjct: 371 -AELEEVDKEFAETRDELKDYREKLEKLKREINELKRELD----------------RLQE 413
Query: 381 EKSQKDIQLPNNANKFTLLKTKVGSEEIAEIVSRTTGIPVSKIVQVEREKLLNIENLLCK 440
E + +L + ++ +I E+ +I + E + +L
Sbjct: 414 ELQRLSEELADLNAAIAGIE-----AKINELEEEKEDK-ALEIKKQEWKLEQLAADL--- 464
Query: 441 RVVGQDEAISAVSNAIRRSRSGLSDAKRPY 470
++ + + R LS +R
Sbjct: 465 --SKYEQELYDLKEEYDRVEKELSKLQREL 492
Score = 34.3 bits (79), Expect = 0.38
Identities = 34/160 (21%), Positives = 72/160 (45%), Gaps = 14/160 (8%)
Query: 266 KIKIEIDSKPEIMDKLERRLIQLKIEHEAIKREYDESSKKRLLLIKKEINKLEIKYANLE 325
+K E+ S + ++E RL +L E R+ E K + +++E KL+ + LE
Sbjct: 685 GLKRELSSLQSELRRIENRLDELSQELSDASRKIGEIE-KEIEQLEQEEEKLKERLEELE 743
Query: 326 --------KIWKYE---KTLIKDSQQIKEEIEKVRLKINKATRKSDWQTVSKLKYGELNK 374
+I + K L ++++E++ K+ +N + + +++ EL+K
Sbjct: 744 EDLSSLEQEIENVKSELKELEARIEELEEDLHKLEEALNDLEARLSHSRIPEIQ-AELSK 802
Query: 375 LERILKEKSQKDIQLPNNANKFTLLKTKVGSEEIAEIVSR 414
LE + + ++ N+ TL K + +EI E+ +
Sbjct: 803 LEEEVSRIEARLREIEQKLNRLTLEK-EYLEKEIQELQEQ 841
Score = 31.6 bits (72), Expect = 3.0
Identities = 30/138 (21%), Positives = 64/138 (46%), Gaps = 13/138 (9%)
Query: 257 IDLIDEAAAKIKIEIDSKPEIMDKLERRLIQLKIEHEAIKREYDESSKKRLLL------I 310
I I +K++ E+ + ++E++L +L +E E +++E E ++R+ L I
Sbjct: 793 IPEIQAELSKLEEEVSRIEARLREIEQKLNRLTLEKEYLEKEIQELQEQRIDLKEQIKSI 852
Query: 311 KKEINKLEIKYANL----EKIWKYEKTLIKDSQQIKEEIEKVRLKINKATRKSDWQTVSK 366
+KEI L K L E++ + L +K+E +++ ++ + RK + +
Sbjct: 853 EKEIENLNGKKEELEEELEELEAALRDLESRLGDLKKERDELEAQLRELERKIEEL---E 909
Query: 367 LKYGELNKLERILKEKSQ 384
+ + K LK K +
Sbjct: 910 AQIEKKRKRLSELKAKLE 927
>gnl|CDD|237090 PRK12402, PRK12402, replication factor C small subunit 2;
Reviewed.
Length = 337
Score = 39.2 bits (92), Expect = 0.009
Identities = 18/55 (32%), Positives = 32/55 (58%)
Query: 35 TEKARLGKLDPVIGRDDEIRRAIQVLQRRSKNNPVLIGEPGVGKTAIVEGLAQRI 89
TEK R L+ ++G+D+ + R + + + + ++ G PG GKTA V LA+ +
Sbjct: 6 TEKYRPALLEDILGQDEVVERLSRAVDSPNLPHLLVQGPPGSGKTAAVRALAREL 60
>gnl|CDD|185658 PTZ00480, PTZ00480, serine/threonine-protein phosphatase;
Provisional.
Length = 320
Score = 38.9 bits (90), Expect = 0.009
Identities = 25/64 (39%), Positives = 37/64 (57%), Gaps = 5/64 (7%)
Query: 687 DVHGCKKSLSILLKKIHKKSPEANFIFLGDLINKGPQSLDT--LRMVYSMRNYAKIVL-- 742
DVHG L + L + PE+N++FLGD +++G QSL+T L + Y ++ L
Sbjct: 66 DVHGQYFDL-LRLFEYGGYPPESNYLFLGDYVDRGKQSLETICLLLAYKIKYPENFFLLR 124
Query: 743 GNHE 746
GNHE
Sbjct: 125 GNHE 128
>gnl|CDD|238111 cd00187, TOP4c, DNA Topoisomerase, subtype IIA; domain A';
bacterial DNA topoisomerase IV (C subunit, ParC),
bacterial DNA gyrases (A subunit, GyrA),mammalian DNA
toposiomerases II. DNA topoisomerases are essential
enzymes that regulate the conformational changes in DNA
topology by catalysing the concerted breakage and
rejoining of DNA strands during normal cellular growth.
Length = 445
Score = 38.7 bits (91), Expect = 0.013
Identities = 27/109 (24%), Positives = 46/109 (42%), Gaps = 33/109 (30%)
Query: 255 KAIDLIDEAAAKIKIEIDSKPEIMDKLER--------------RLIQL-KIEHEAIKREY 299
KAI IDE I+ ++K ++++LE+ RL +L K+E E + +E
Sbjct: 355 KAILNIDEVINLIRSSDEAKKALIEELEKLGFSEIQADAILDMRLRRLTKLEREKLLKEL 414
Query: 300 DESSKKRLLLIKKEINKLEIKYANLEKIWKYEKTLIKDSQQIKEEIEKV 348
E ++ EI LE A+ E+ KEE+++
Sbjct: 415 KE--------LEAEIEDLEKILASEERPKDL----------WKEELDEF 445
>gnl|CDD|220623 pfam10186, Atg14, UV radiation resistance protein and
autophagy-related subunit 14. The Atg14 or Apg14
proteins are hydrophilic proteins with a predicted
molecular mass of 40.5 kDa, and have a coiled-coil motif
at the N terminus region. Yeast cells with mutant Atg14
are defective not only in autophagy but also in sorting
of carboxypeptidase Y (CPY), a vacuolar-soluble
hydrolase, to the vacuole. Subcellular fractionation
indicate that Apg14p and Apg6p are peripherally
associated with a membrane structure(s). Apg14p was
co-immunoprecipitated with Apg6p, suggesting that they
form a stable protein complex. These results imply that
Apg6/Vps30p has two distinct functions: in the
autophagic process and in the vacuolar protein sorting
pathway. Apg14p may be a component specifically required
for the function of Apg6/Vps30p through the autophagic
pathway. There are 17 auto-phagosomal component proteins
which are categorized into six functional units, one of
which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The
AS-PI3K complex and the Atg2-Atg18 complex are essential
for nucleation, and the specific function of the AS-PI3K
apparently is to produce phosphatidylinositol
3-phosphate (PtdIns(3)P) at the pre-autophagosomal
structure (PAS). The localisation of this complex at the
PAS is controlled by Atg14. Autophagy mediates the
cellular response to nutrient deprivation, protein
aggregation, and pathogen invasion in humans, and
malfunction of autophagy has been implicated in multiple
human diseases including cancer. This effect seems to be
mediated through direct interaction of the human Atg14
with Beclin 1 in the human phosphatidylinositol 3-kinase
class III complex.
Length = 307
Score = 38.5 bits (90), Expect = 0.014
Identities = 29/116 (25%), Positives = 51/116 (43%), Gaps = 14/116 (12%)
Query: 283 RRLIQLKIEHEAIKREYDESSKKRLLLIKKEINKLEIKYANLEKIWKYEKT-----LIKD 337
L +L+++ + E +E +K ++ N+ A+L K+ K +
Sbjct: 20 NSLYELRLDLARLLLENEELKQKVEEALEGATNEDGKLAADLLKLEVARKKERLNQIRAR 79
Query: 338 SQQIKEEIEKVRLKINK-----ATRKSDWQTVSKLKYGELNKLERILKEKSQKDIQ 388
Q+KEEIE+ R +I + A R+SD +S Y + L EK Q +I+
Sbjct: 80 ISQLKEEIEQKRERIEELKRALAQRRSD---LSSASYQLEKRRASQL-EKLQDEIK 131
>gnl|CDD|163663 cd07420, MPP_RdgC, Drosophila melanogaster RdgC and related
proteins, metallophosphatase domain. RdgC (retinal
degeneration C) is a vertebrate serine-threonine protein
phosphatase that is required to prevent light-induced
retinal degeneration. In addition to its catalytic
domain, RdgC has two C-terminal EF hands. Homologs of
RdgC include the human phosphatases protein phosphatase
with EF hands 1 and -2 (PPEF-1 and -2). PPEF-1
transcripts are present at low levels in the retina,
PPEF-2 transcripts and PPEF-2 protein are present at
high levels in photoreceptors. The PPP (phosphoprotein
phosphatase) family, to which RdgC belongs, is one of
two known protein phosphatase families specific for
serine and threonine. The PPP family also includes:
PP1, PP2A, PP2B (calcineurin), PP4, PP5, PP6, PP7, Bsu1,
PrpE, PrpA/PrpB, and ApA4 hydrolase. The PPP catalytic
domain is defined by three conserved motifs (-GDXHG-,
-GDXVDRG- and -GNHE-). The PPP enzyme family is ancient
with members found in all eukaryotes, and in most
bacterial and archeal genomes. Dephosphorylation of
phosphoserines and phosphothreonines on target proteins
plays a central role in the regulation of many cellular
processes. PPPs belong to the metallophosphatase (MPP)
superfamily. MPPs are functionally diverse, but all
share a conserved domain with an active site consisting
of two metal ions (usually manganese, iron, or zinc)
coordinated with octahedral geometry by a cage of
histidine, aspartate, and asparagine residues. The MPP
superfamily includes: Mre11/SbcD-like exonucleases,
Dbr1-like RNA lariat debranching enzymes, YfcE-like
phosphodiesterases, purple acid phosphatases (PAPs),
YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid
sphingomyelinases (ASMases). The conserved domain is a
double beta-sheet sandwich with a di-metal active site
made up of residues located at the C-terminal side of
the sheets. This domain is thought to allow for
productive metal coordination.
Length = 321
Score = 38.1 bits (89), Expect = 0.015
Identities = 35/134 (26%), Positives = 59/134 (44%), Gaps = 31/134 (23%)
Query: 687 DVHGCKKSLSILLKKIHKKSPEANFIFLGDLINKGPQSLD------TLRMVYSMRNYAKI 740
D+HG L ++ K SPE ++F GD +++G +S++ +VY + +
Sbjct: 58 DLHGKLDDLFLIFYKNGLPSPENPYVFNGDFVDRGKRSIEILIILFAFFLVYPNEVH--L 115
Query: 741 VLGNHEIHLLDVLININK----------KSKLDTFDDILDAPDKKKLVSWLRTQPLA-IY 789
GNHE H++++ K K L +D+ SWL PLA I
Sbjct: 116 NRGNHEDHIMNLRYGFTKEVMSKYKLHGKKILRLLEDVF---------SWL---PLATII 163
Query: 790 YKKYLMIHAGVAKQ 803
K L++H G++
Sbjct: 164 DNKILVVHGGISDS 177
>gnl|CDD|163668 cd07425, MPP_Shelphs, Shewanella-like phosphatases,
metallophosphatase domain. This family includes
bacterial, eukaryotic, and archeal proteins orthologous
to the Shewanella cold-active protein-tyrosine
phosphatase, CAPTPase. CAPTPase is an uncharacterized
protein that belongs to the Shelph (Shewanella-like
phosphatase) family of PPP (phosphoprotein
phosphatases). The PPP family is one of two known
protein phosphatase families specific for serine and
threonine. In addition to Shelps, the PPP family also
includes: PP1, PP2A, PP2B (calcineurin), PP4, PP5, PP6,
PP7, Bsu1, RdgC, PrpE, PrpA/PrpB, and ApA4 hydrolase.
The PPP catalytic domain is defined by three conserved
motifs (-GDXHG-, -GDXVDRG- and -GNHE-). The PPP enzyme
family is ancient with members found in all eukaryotes,
and in most bacterial and archeal genomes.
Dephosphorylation of phosphoserines and
phosphothreonines on target proteins plays a central
role in the regulation of many cellular processes. PPPs
belong to the metallophosphatase (MPP) superfamily.
MPPs are functionally diverse, but all share a conserved
domain with an active site consisting of two metal ions
(usually manganese, iron, or zinc) coordinated with
octahedral geometry by a cage of histidine, aspartate,
and asparagine residues. The MPP superfamily includes:
Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat
debranching enzymes, YfcE-like phosphodiesterases,
purple acid phosphatases (PAPs), YbbF-like
UDP-2,3-diacylglucosamine hydrolases, and acid
sphingomyelinases (ASMases). The conserved domain is a
double beta-sheet sandwich with a di-metal active site
made up of residues located at the C-terminal side of
the sheets. This domain is thought to allow for
productive metal coordination.
Length = 208
Score = 37.6 bits (88), Expect = 0.015
Identities = 25/108 (23%), Positives = 48/108 (44%), Gaps = 14/108 (12%)
Query: 711 FIFLGDLINKGPQSLDTLRMVYSMRNYAK-------IVLGNHEI-HLLDVLININKKSKL 762
+ LGD+ ++GP ++ L ++Y + A +LGNHE+ +L ++ K
Sbjct: 36 LVQLGDIFDRGPDVIEILWLLYKLEQEAAKAGGKVHFLLGNHELMNLCGDFRYVHPKY-F 94
Query: 763 DTFDDILDA-----PDKKKLVSWLRTQPLAIYYKKYLMIHAGVAKQWT 805
+ F + +L WLR++P+ + L +H G+ W
Sbjct: 95 NEFGGLAMRRRELFSPGGELGRWLRSKPVIVKVNDTLFVHGGLGPLWY 142
>gnl|CDD|237354 PRK13341, PRK13341, recombination factor protein RarA/unknown
domain fusion protein; Reviewed.
Length = 725
Score = 38.5 bits (90), Expect = 0.016
Identities = 49/166 (29%), Positives = 71/166 (42%), Gaps = 48/166 (28%)
Query: 34 LTEKARLGKLDPVIGRDDEI------RRAIQVLQRRSKNNPVLIGEPGVGKTAIVEGLAQ 87
L ++ R L+ +G+D + RRAI+ + + +L G PGVGKT LA
Sbjct: 18 LADRLRPRTLEEFVGQDHILGEGRLLRRAIKADRV---GSLILYGPPGVGKTT----LA- 69
Query: 88 RII----NGEVPNSLLSKKILLLDIALLLAGTK-YRGEFE---DRLKKILKEISNNQKDI 139
RII + +LAG K R E + +RL++ + K
Sbjct: 70 RIIANHTRAHF-----------SSLNAVLAGVKDLRAEVDRAKERLER-------HGKRT 111
Query: 140 IIFIDELHTMIGTGKVEGSIDAGNMLKPELSRGELHCIGATTLNEY 185
I+FIDE+H + DA L P + G + IGATT N Y
Sbjct: 112 ILFIDEVHRFNKAQQ-----DA---LLPWVENGTITLIGATTENPY 149
>gnl|CDD|233120 TIGR00764, lon_rel, lon-related putative ATP-dependent protease.
This model represents a set of proteins with extensive
C-terminal homology to the ATP-dependent protease La,
product of the lon gene of E. coli. The model is based
on a seed alignment containing only archaeal members,
but several bacterial proteins match the model well.
Because several species, including Thermotoga maritima
and Treponema pallidum, contain both a close homolog of
the lon protease and nearly full-length homolog of the
members of this family, we suggest there may also be a
functional division between the two families. Members of
this family from Pyrococcus horikoshii and Pyrococcus
abyssi each contain a predicted intein [Protein fate,
Degradation of proteins, peptides, and glycopeptides].
Length = 608
Score = 38.3 bits (89), Expect = 0.020
Identities = 31/108 (28%), Positives = 60/108 (55%), Gaps = 12/108 (11%)
Query: 29 KYTIDLTEKARLGKLDPVIGRDDEIRRAIQVLQRRSKN--NPVLIGEPGVGKTAIVEGLA 86
+ T ++ RL +D VIG+++ A++++++ +K N +LIGEPGVGK+ + + +A
Sbjct: 5 ETTEEIPVPERL--IDQVIGQEE----AVEIIKKAAKQKRNVLLIGEPGVGKSMLAKAMA 58
Query: 87 QRIINGEVPNSLLSKKILLLD---IALLLAGTKYRGEFEDRLKKILKE 131
+ + + E+ + L+ + I + AG + R ED KK K+
Sbjct: 59 ELLPDEELEDILVYPNPEDPNMPRIVEVPAG-EGREIVEDYKKKAFKQ 105
>gnl|CDD|225165 COG2256, MGS1, ATPase related to the helicase subunit of the
Holliday junction resolvase [DNA replication,
recombination, and repair].
Length = 436
Score = 37.6 bits (88), Expect = 0.028
Identities = 39/163 (23%), Positives = 66/163 (40%), Gaps = 43/163 (26%)
Query: 34 LTEKARLGKLDPVIG------RDDEIRRAIQVLQRRSKNNPVLI--GEPGVGKTAIVEGL 85
L E+ R LD V+G +RRA++ + + +I G PG GKT + +
Sbjct: 14 LAERLRPKSLDEVVGQEHLLGEGKPLRRAVE-----AGHLHSMILWGPPGTGKTTLARLI 68
Query: 86 AQRIINGEVPNSLLSKKILLLDIALLLAGTKYRGEFEDRLKKILKEISNNQ---KDIIIF 142
A N ++ + +G K L++I++E N+ + I+F
Sbjct: 69 AGT-TNAAF-----------EALSAVTSGVK-------DLREIIEEARKNRLLGRRTILF 109
Query: 143 IDELHTMIGTGKVEGSIDAGNMLKPELSRGELHCIGATTLNEY 185
+DE+H + + L P + G + IGATT N
Sbjct: 110 LDEIHRF--------NKAQQDALLPHVENGTIILIGATTENPS 144
Score = 29.9 bits (68), Expect = 7.2
Identities = 34/142 (23%), Positives = 54/142 (38%), Gaps = 44/142 (30%)
Query: 442 VVGQDEAISAVSNAIRRSRSGLSDAKRPYGSFMFLGPTGVGKTELCK-----------TL 490
VVGQ+ + +RR +A S + GP G GKT L + L
Sbjct: 26 VVGQEHLLGE-GKPLRR----AVEAGHL-HSMILWGPPGTGKTTLARLIAGTTNAAFEAL 79
Query: 491 SACIFNNEESIIRIDMSEFIEKHSISRLIGAPPGYIGYEEGGYLTEIVRRKPYSLILLDE 550
SA + D+ E IE+ +RL+G R+ ++ LDE
Sbjct: 80 SAVTSGVK------DLREIIEEARKNRLLG-------------------RRT--ILFLDE 112
Query: 551 IEKANSDVFNILLQILDDGRLT 572
I + N + LL +++G +
Sbjct: 113 IHRFNKAQQDALLPHVENGTII 134
>gnl|CDD|173488 PTZ00239, PTZ00239, serine/threonine protein phosphatase 2A;
Provisional.
Length = 303
Score = 37.1 bits (86), Expect = 0.030
Identities = 23/64 (35%), Positives = 36/64 (56%), Gaps = 5/64 (7%)
Query: 687 DVHGCKKSLSILLKKIHKKSPEANFIFLGDLINKGPQSLDTLRMVYSMR-NY-AKIVL-- 742
D+HG L L K+ P AN+IF+GD +++G S++T+ + ++ Y I L
Sbjct: 50 DIHGQFYDLQALFKE-GGDIPNANYIFIGDFVDRGYNSVETMEYLLCLKVKYPGNITLLR 108
Query: 743 GNHE 746
GNHE
Sbjct: 109 GNHE 112
>gnl|CDD|213527 TIGR00390, hslU, ATP-dependent protease HslVU, ATPase subunit.
This model represents the ATPase subunit of HslVU, while
the proteasome-related peptidase subunit is HslV.
Residues 54-61 of the model contain a P-loop ATP-binding
motif. Cys-287 of E. coli (position 308 in the seed
alignment), studied in MEDLINE:98389714, is Ser in other
members of the seed alignment [Protein fate, Protein
folding and stabilization].
Length = 441
Score = 37.5 bits (87), Expect = 0.031
Identities = 29/80 (36%), Positives = 43/80 (53%), Gaps = 10/80 (12%)
Query: 438 LCKRVVGQDEAISAVS----NAIRRSR--SGLSDAKRPYGSFMFLGPTGVGKTELCKTLS 491
L K ++GQDEA +V+ N RRS+ L D P M +GPTGVGKTE+ + L+
Sbjct: 10 LDKYIIGQDEAKKSVAIALRNRYRRSQLPEELKDEVTPKNILM-IGPTGVGKTEIARRLA 68
Query: 492 ACIFNNEESIIRIDMSEFIE 511
I+++ ++F E
Sbjct: 69 KLA---NAPFIKVEATKFTE 85
>gnl|CDD|224302 COG1384, LysS, Lysyl-tRNA synthetase (class I) [Translation,
ribosomal structure and biogenesis].
Length = 521
Score = 37.3 bits (87), Expect = 0.034
Identities = 27/117 (23%), Positives = 49/117 (41%), Gaps = 5/117 (4%)
Query: 198 RFQKILVEEPDIEETISILRGLQKKYEVHHGVEITDPAIVAASELSYRYISDRFMPDKAI 257
R +LV+ + EE IL L ++Y T + E + ++ + P+K
Sbjct: 370 RHLAVLVQIANAEEE-DILEILIRRYLPDA-DPDTIEDLDERIEYAINWL-RDYAPEKVK 426
Query: 258 DLIDEAAAKIKIEIDSKPEIMDKLERRL--IQLKIEHEAIKREYDESSKKRLLLIKK 312
I E + ++ D+K E ++ L L IQ + E E +KK+ +L +
Sbjct: 427 FSILEKPPEAELSEDAKLEALEDLAEFLESIQKASLEVELHNEVYEVAKKKGILPRA 483
>gnl|CDD|232949 TIGR00382, clpX, endopeptidase Clp ATP-binding regulatory subunit
(clpX). A member of the ATP-dependent proteases, ClpX
has ATP-dependent chaperone activity and is required for
specific ATP-dependent proteolytic activities expressed
by ClpPX. The gene is also found to be involved in
stress tolerance in Bacillus subtilis and is essential
for the efficient acquisition of genes specifying type
IA and IB restriction [Protein fate, Protein folding and
stabilization, Protein fate, Degradation of proteins,
peptides, and glycopeptides].
Length = 413
Score = 37.1 bits (86), Expect = 0.039
Identities = 79/337 (23%), Positives = 132/337 (39%), Gaps = 85/337 (25%)
Query: 420 VSKIVQVEREKLLN-------IENLLCKRVVGQDEAIS----AVSNAIRRSRSGLSDAKR 468
+ + E E L+ I+ L + V+GQ++A AV N +R +
Sbjct: 50 RKESKEYEEEFELSYLPTPKEIKAHLDEYVIGQEQAKKVLSVAVYNHYKRLNFEKNKKSD 109
Query: 469 PY-----GSFMFLGPTGVGKTELCKTLSACIFNNEESIIRIDMSEFIEKHSISRLIGAPP 523
+ + +GPTG GKT L +TL A I N +I D + E
Sbjct: 110 NGVELSKSNILLIGPTGSGKTLLAQTL-ARILNVPFAI--ADATTLTEA----------- 155
Query: 524 GYIGYEEGGYLTEIVRRKPYS-------LILLDEIEK--------------ANSDVFNIL 562
GY+G + L ++++ Y +I +DEI+K + V L
Sbjct: 156 GYVGEDVENILLKLLQAADYDVEKAQKGIIYIDEIDKISRKSENPSITRDVSGEGVQQAL 215
Query: 563 LQILDDGRLTD---NRGRTINFRNTIIVMTSNL---------GSDKI------------- 597
L+I+ +G + + GR ++ I + TSN+ G +KI
Sbjct: 216 LKII-EGTVANVPPQGGRKHPYQEFIQIDTSNILFICGGAFVGLEKIIKKRTGKSSIGFG 274
Query: 598 ---KEMEKGDKEIIKLAVMNE-VKIYFRPEFINRIDDIIVFRYLNRKNILSIANIQLNIL 653
K+ K ++++ + VK PEFI R+ I L+ + +++I N L
Sbjct: 275 AEVKKKSKEKADLLRQVEPEDLVKFGLIPEFIGRLPVIATLEKLDEEALIAILTKPKNAL 334
Query: 654 KN---KLLKM-NMDLKISKAALKKISNIGFDLIYGAR 686
L KM N++L + ALK I+ + GAR
Sbjct: 335 VKQYQALFKMDNVELDFEEEALKAIAKKALERKTGAR 371
Score = 29.7 bits (67), Expect = 7.3
Identities = 31/88 (35%), Positives = 45/88 (51%), Gaps = 17/88 (19%)
Query: 64 SKNNPVLIGEPGVGKTAIVEGLAQRIINGEVPNSLLSKKILLLDIALLLAGTKYRGE-FE 122
SK+N +LIG G GKT + + LA+ + VP + D A L Y GE E
Sbjct: 115 SKSNILLIGPTGSGKTLLAQTLARIL---NVP-------FAIAD-ATTLTEAGYVGEDVE 163
Query: 123 DRLKKILK----EISNNQKDIIIFIDEL 146
+ L K+L+ ++ QK II+IDE+
Sbjct: 164 NILLKLLQAADYDVEKAQKG-IIYIDEI 190
>gnl|CDD|225288 COG2433, COG2433, Uncharacterized conserved protein [Function
unknown].
Length = 652
Score = 37.4 bits (87), Expect = 0.041
Identities = 23/117 (19%), Positives = 55/117 (47%), Gaps = 14/117 (11%)
Query: 262 EAAAKIKIEIDSKPEIMDKLERRLIQLKIEHEAIKREYDESSKKRLLLIKKEINKLEIKY 321
+ + EI + + KLE + +L+ E+ +KRE +E +K+EI KLE +
Sbjct: 408 GTEEEERREITVYEKRIKKLEETVERLEEENSELKRELEE--------LKREIEKLESEL 459
Query: 322 ANLEKIWKYEKTLIKDSQQIKEEIEKVRLKINKATRKSDWQTVSKLKYGELNKLERI 378
+ + + ++ + IE++ ++ + ++ V +L+ +L +L ++
Sbjct: 460 ERFRREVRDKVRKDREIRARDRRIERLEKELEEKKKR-----VEELE-RKLAELRKM 510
>gnl|CDD|130134 TIGR01062, parC_Gneg, DNA topoisomerase IV, A subunit,
proteobacterial. Operationally, topoisomerase IV is a
type II topoisomerase required for the decatenation of
chromosome segregation. Not every bacterium has both a
topo II and a topo IV. The topo IV families of the
Gram-positive bacteria and the Gram-negative bacteria
appear not to represent a single clade among the type II
topoisomerases, and are represented by separate models
for this reason [DNA metabolism, DNA replication,
recombination, and repair].
Length = 735
Score = 37.2 bits (86), Expect = 0.043
Identities = 35/112 (31%), Positives = 47/112 (41%), Gaps = 30/112 (26%)
Query: 260 IDEAAAKIKIEIDSKPEIMDK-----------LERRLIQL-KIEHEAIKREYDESSKKRL 307
IDE I+ E + K +M++ L RL L K+E AI E E K+R
Sbjct: 382 IDEVIEIIREEDEPKTILMERFKLSAIQAEAILNLRLRHLAKLEEHAIIDEQSELEKER- 440
Query: 308 LLIKKEINKLEIKYANLEKIWKYEKTLIKDSQQIKEEIEKVRLKINKATRKS 359
A LEKI K E+ L +Q +K+EI+ K A R S
Sbjct: 441 --------------AILEKILKSEREL---NQLVKKEIQADATKYGLARRSS 475
>gnl|CDD|184922 PRK14958, PRK14958, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 509
Score = 37.0 bits (85), Expect = 0.044
Identities = 36/146 (24%), Positives = 64/146 (43%), Gaps = 33/146 (22%)
Query: 440 KRVVGQDEAISAVSNAIRRSRSGLSDAKRPYGSFMFLGPTGVGKTELCKTLSACI----- 494
+ V+GQ + A+SNA+ D + + +++F G GVGKT + + L+ C+
Sbjct: 16 QEVIGQAPVVRALSNAL--------DQQYLHHAYLFTGTRGVGKTTISRILAKCLNCEKG 67
Query: 495 -----FNNEESIIRIDMSEF---IEKHSISRLIGAPPGYIGYEEGGYLTEIVRRKP---- 542
N+ E+ ID F E + SR E+ L + + P
Sbjct: 68 VSANPCNDCENCREIDEGRFPDLFEVDAASR--------TKVEDTRELLDNIPYAPTKGR 119
Query: 543 YSLILLDEIEKANSDVFNILLQILDD 568
+ + L+DE+ + FN LL+ L++
Sbjct: 120 FKVYLIDEVHMLSGHSFNALLKTLEE 145
>gnl|CDD|178596 PLN03025, PLN03025, replication factor C subunit; Provisional.
Length = 319
Score = 36.6 bits (85), Expect = 0.046
Identities = 24/57 (42%), Positives = 33/57 (57%), Gaps = 4/57 (7%)
Query: 36 EKARLGKLDPVIGRDDEIRRAIQVLQRRSKNNPVLI--GEPGVGKTAIVEGLAQRII 90
EK R KLD ++G +D + R +QV+ R N P LI G PG GKT + LA ++
Sbjct: 5 EKYRPTKLDDIVGNEDAVSR-LQVIAR-DGNMPNLILSGPPGTGKTTSILALAHELL 59
>gnl|CDD|215758 pfam00158, Sigma54_activat, Sigma-54 interaction domain.
Length = 168
Score = 35.4 bits (83), Expect = 0.050
Identities = 14/46 (30%), Positives = 24/46 (52%), Gaps = 6/46 (13%)
Query: 46 VIGRDDEIRRAIQVLQRRSKNN-PVLI-GEPGVGKTAIVEGLAQRI 89
+IG ++ +++ +R + + VLI GE G GK E A+ I
Sbjct: 1 LIGESPAMQEVLELAKRVAPTDATVLITGESGTGK----ELFARAI 42
>gnl|CDD|183088 PRK11331, PRK11331, 5-methylcytosine-specific restriction enzyme
subunit McrB; Provisional.
Length = 459
Score = 37.0 bits (85), Expect = 0.052
Identities = 29/106 (27%), Positives = 58/106 (54%), Gaps = 9/106 (8%)
Query: 477 GPTGVGKTELCKTLSACIFNNEESIIRIDMSEFIEKHSISRLI-GAPPGYIGY--EEGGY 533
GP GVGKT + + L A + E++ R++M +F + +S I G P +G+ ++G +
Sbjct: 201 GPPGVGKTFVARRL-AYLLTGEKAPQRVNMVQFHQSYSYEDFIQGYRPNGVGFRRKDGIF 259
Query: 534 --LTEIVRRKPYS--LILLDEIEKAN-SDVFNILLQILDDGRLTDN 574
+ + +P + ++DEI +AN S VF ++ +++ + +N
Sbjct: 260 YNFCQQAKEQPEKKYVFIIDEINRANLSKVFGEVMMLMEHDKRGEN 305
>gnl|CDD|184921 PRK14957, PRK14957, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 546
Score = 36.6 bits (84), Expect = 0.059
Identities = 34/141 (24%), Positives = 66/141 (46%), Gaps = 27/141 (19%)
Query: 442 VVGQDEAISAVSNAIRRSRSGLSDAKRPYGSFMFLGPTGVGKTELCKTLSACI------- 494
V GQ A++++ +A+ + ++ + +++F G GVGKT L + L+ C+
Sbjct: 18 VAGQQHALNSLVHAL--------ETQKVHHAYLFTGTRGVGKTTLGRLLAKCLNCKTGVT 69
Query: 495 ---FNNEESIIRIDMSEFIEKHSISRLIGAPPGYIGYEEGGYLTEIVRRKP----YSLIL 547
N E+ + I+ + FI+ I G EE + + ++ P Y + L
Sbjct: 70 AEPCNKCENCVAINNNSFIDLIEID-----AASRTGVEETKEILDNIQYMPSQGRYKVYL 124
Query: 548 LDEIEKANSDVFNILLQILDD 568
+DE+ + FN LL+ L++
Sbjct: 125 IDEVHMLSKQSFNALLKTLEE 145
>gnl|CDD|234063 TIGR02928, TIGR02928, orc1/cdc6 family replication initiation
protein. Members of this protein family are found
exclusively in the archaea. This set of DNA binding
proteins shows homology to the origin recognition
complex subunit 1/cell division control protein 6 family
in eukaryotes. Several members may be found in genome
and interact with each other [DNA metabolism, DNA
replication, recombination, and repair].
Length = 365
Score = 36.5 bits (85), Expect = 0.062
Identities = 52/230 (22%), Positives = 87/230 (37%), Gaps = 42/230 (18%)
Query: 427 EREKLLNIENLLCKRVVGQDEAISAVSNAIRRSRSGLSDAKRPYGSFMFL-GPTGVGKT- 484
LL + + R+V +DE I ++ A+R G RP S +F+ G TG GKT
Sbjct: 3 RNRDLLEPDYVP-DRIVHRDEQIEELAKALRPILRG----SRP--SNVFIYGKTGTGKTA 55
Query: 485 ---ELCKTLSACIFNNEE--SIIRID----------MSEFIEKHSISRLIGAPPGYIGYE 529
+ K L + + + ++ + E + R G G
Sbjct: 56 VTKYVMKELEEAAEDRDVRVVTVYVNCQILDTLYQVLVELANQ---LRGSGEEVPTTGLS 112
Query: 530 EGGYL----TEIVRRKPYSLILLDEIEKANSDVFNILLQILDDGRLTDNRGRTINFRNTI 585
E+ R +I+LDEI+ D ++L Q+ R N G N + +
Sbjct: 113 TSEVFRRLYKELNERGDSLIIVLDEIDYLVGDDDDLLYQLS---RARSN-GDLDNAKVGV 168
Query: 586 IVMTSNLGSDKIKEMEKGDKEIIKLAVMNEVKIYFRPEFINRIDDIIVFR 635
I + S+ +K E D + + + E +I F P + DI+ R
Sbjct: 169 IGI-----SNDLKFRENLDPRV--KSSLCEEEIIFPPYDAEELRDILENR 211
Score = 34.1 bits (79), Expect = 0.31
Identities = 29/134 (21%), Positives = 64/134 (47%), Gaps = 27/134 (20%)
Query: 44 DPVIGRDDEI---RRAIQVLQRRSKNNPVLI-GEPGVGKTAIVEGLAQRI---------- 89
D ++ RD++I +A++ + R S+ + V I G+ G GKTA+ + + + +
Sbjct: 15 DRIVHRDEQIEELAKALRPILRGSRPSNVFIYGKTGTGKTAVTKYVMKELEEAAEDRDVR 74
Query: 90 -----INGEVPNSLLSKKILLLDIALLLAGTK----YRGEFEDRLKKILKEISNNQKDII 140
+N ++ ++L +L+++A L G+ G + + L + N + D +
Sbjct: 75 VVTVYVNCQILDTLYQ---VLVELANQLRGSGEEVPTTGLSTSEVFRRLYKELNERGDSL 131
Query: 141 IFI-DELHTMIGTG 153
I + DE+ ++G
Sbjct: 132 IIVLDEIDYLVGDD 145
>gnl|CDD|235364 PRK05201, hslU, ATP-dependent protease ATP-binding subunit HslU;
Provisional.
Length = 443
Score = 36.6 bits (86), Expect = 0.066
Identities = 24/53 (45%), Positives = 31/53 (58%), Gaps = 9/53 (16%)
Query: 440 KRVVGQDEAISAVSNAIR---RSRSGLSDAKR----PYGSFMFLGPTGVGKTE 485
K ++GQD+A AV+ A+R R R L + R P M +GPTGVGKTE
Sbjct: 15 KYIIGQDDAKRAVAIALRNRWR-RMQLPEELRDEVTPKNILM-IGPTGVGKTE 65
>gnl|CDD|225363 COG2804, PulE, Type II secretory pathway, ATPase PulE/Tfp pilus
assembly pathway, ATPase PilB [Cell motility and
secretion / Intracellular trafficking and secretion].
Length = 500
Score = 36.5 bits (85), Expect = 0.071
Identities = 14/39 (35%), Positives = 18/39 (46%)
Query: 466 AKRPYGSFMFLGPTGVGKTELCKTLSACIFNNEESIIRI 504
RP G + GPTG GKT + + E +II I
Sbjct: 254 LNRPQGLILVTGPTGSGKTTTLYAALSELNTPERNIITI 292
>gnl|CDD|224141 COG1220, HslU, ATP-dependent protease HslVU (ClpYQ), ATPase subunit
[Posttranslational modification, protein turnover,
chaperones].
Length = 444
Score = 36.1 bits (84), Expect = 0.081
Identities = 25/60 (41%), Positives = 34/60 (56%), Gaps = 7/60 (11%)
Query: 438 LCKRVVGQDEAISAVS----NAIRRSR--SGLSDAKRPYGSFMFLGPTGVGKTELCKTLS 491
L + ++GQDEA AV+ N RR + L D P M +GPTGVGKTE+ + L+
Sbjct: 13 LDRYIIGQDEAKKAVAIALRNRWRRMQLEEELRDEVTPKNILM-IGPTGVGKTEIARRLA 71
>gnl|CDD|224144 COG1223, COG1223, Predicted ATPase (AAA+ superfamily) [General
function prediction only].
Length = 368
Score = 35.9 bits (83), Expect = 0.089
Identities = 68/261 (26%), Positives = 104/261 (39%), Gaps = 49/261 (18%)
Query: 34 LTEKARLGKLDPVIGRDDEIRRAIQVLQRRSKN----------NPVLIGEPGVGKTAIVE 83
E LD VIG++ E +R +++ +N N + G PG GKT + +
Sbjct: 111 DREIISDITLDDVIGQE-EAKRKCRLIMEYLENPERFGDWAPKNVLFYGPPGTGKTMMAK 169
Query: 84 GLAQRIINGEVPNSLLSKKILLLDIALLLAGTKYRGEFEDRLKKILKEISNNQKDIIIFI 143
LA E LL K A L G ++ G+ R+ + L E + I+FI
Sbjct: 170 ALA-----NEAKVPLLLVK------ATELIG-EHVGDGARRIHE-LYERARKAAPCIVFI 216
Query: 144 DELHTMIG--------TGKVEGSIDAGNMLKPELSR---GELHC-IGATTLNEYRQYIEK 191
DEL I G V ++A L EL E I AT E
Sbjct: 217 DELDA-IALDRRYQELRGDVSEIVNA---LLTELDGIKENEGVVTIAATNRPELL----- 267
Query: 192 DAAFERRFQ-KILVEEPDIEETISILRGLQKKYEVHHGVEITDPAIVAASE-LSYRYISD 249
D A RF+ +I + P+ EE + IL KK+ + V+ + A ++ +S R I +
Sbjct: 268 DPAIRSRFEEEIEFKLPNDEERLEILEYYAKKFPLP--VDADLRYLAAKTKGMSGRDIKE 325
Query: 250 RFMPDKAIDLIDEAAAKIKIE 270
+ + I E K++ E
Sbjct: 326 KVLKTALHRAIAEDREKVERE 346
>gnl|CDD|184934 PRK14970, PRK14970, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 367
Score = 36.0 bits (83), Expect = 0.093
Identities = 36/133 (27%), Positives = 56/133 (42%), Gaps = 19/133 (14%)
Query: 440 KRVVGQDEAISAVSNAIRRSRSGLSDAKRPYGSFMFLGPTGVGKTELCKTLSACIFNNEE 499
VVGQ + + NAI + L+ A +F GP GVGKT + L+ I N+
Sbjct: 17 DDVVGQSHITNTLLNAIENNH--LAQA------LLFCGPRGVGKTTCARILARKI--NQP 66
Query: 500 SIIRIDMSEFIEKHSISRLIGAPPGYIGYEEGGYLTEIVRRKP----YSLILLDEIEKAN 555
D +I L A ++ L + VR P Y + ++DE+ +
Sbjct: 67 G---YDDPNEDFSFNIFELDAASNN--SVDDIRNLIDQVRIPPQTGKYKIYIIDEVHMLS 121
Query: 556 SDVFNILLQILDD 568
S FN L+ L++
Sbjct: 122 SAAFNAFLKTLEE 134
>gnl|CDD|163658 cd07415, MPP_PP2A_PP4_PP6, PP2A, PP4, and PP6 phosphoprotein
phosphatases, metallophosphatase domain. PP2A-like
family of phosphoprotein phosphatases (PPP's) including
PP4 and PP6. PP2A (Protein phosphatase 2A) is a
critical regulator of many cellular activities. PP2A
comprises about 1% of total cellular proteins. PP2A,
together with protein phosphatase 1 (PP1), accounts for
more than 90% of all serine/threonine phosphatase
activities in most cells and tissues. The PP2A subunit
in addition to having a catalytic domain homologous to
PP1, has a unique C-terminal tail, containing a motif
that is conserved in the catalytic subunits of all
PP2A-like phosphatases including PP4 and PP6, and has an
important role in PP2A regulation. The PP2A-like family
of phosphatases all share a similar heterotrimeric
architecture, that includes: a 65kDa scaffolding subunit
(A), a 36kDa catalytic subunit (C), and one of 18
regulatory subunits (B). The PPP (phosphoprotein
phosphatase) family, to which PP2A belongs, is one of
two known protein phosphatase families specific for
serine and threonine. The PPP family also includes:
PP1, PP2B (calcineurin), PP4, PP5, PP6, PP7, Bsu1, RdgC,
PrpE, PrpA/PrpB, and ApA4 hydrolase. The PPP catalytic
domain is defined by three conserved motifs (-GDXHG-,
-GDXVDRG- and -GNHE-). The PPP enzyme family is ancient
with members found in all eukaryotes, and in most
bacterial and archeal genomes. Dephosphorylation of
phosphoserines and phosphothreonines on target proteins
plays a central role in the regulation of many cellular
processes. PPPs belong to the metallophosphatase (MPP)
superfamily. MPPs are functionally diverse, but all
share a conserved domain with an active site consisting
of two metal ions (usually manganese, iron, or zinc)
coordinated with octahedral geometry by a cage of
histidine, aspartate, and asparagine residues. The MPP
superfamily includes: Mre11/SbcD-like exonucleases,
Dbr1-like RNA lariat debranching enzymes, YfcE-like
phosphodiesterases, purple acid phosphatases (PAPs),
YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid
sphingomyelinases (ASMases). The conserved domain is a
double beta-sheet sandwich with a di-metal active site
made up of residues located at the C-terminal side of
the sheets. This domain is thought to allow for
productive metal coordination.
Length = 285
Score = 35.7 bits (83), Expect = 0.10
Identities = 22/64 (34%), Positives = 36/64 (56%), Gaps = 5/64 (7%)
Query: 687 DVHGCKKSLSILLKKIHKKSPEANFIFLGDLINKGPQSLDT--LRMVYSMRNYAKIVL-- 742
D+HG L L + + P+ N++FLGD +++G S++T L + +R +I L
Sbjct: 49 DIHGQFYDLLELFR-VGGDPPDTNYLFLGDYVDRGYYSVETFLLLLALKVRYPDRITLLR 107
Query: 743 GNHE 746
GNHE
Sbjct: 108 GNHE 111
>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit;
Provisional.
Length = 482
Score = 35.7 bits (83), Expect = 0.12
Identities = 18/59 (30%), Positives = 28/59 (47%), Gaps = 4/59 (6%)
Query: 32 IDLTEKARLGKLDPVIGRDDEIRRAIQVLQRRSKNNP----VLIGEPGVGKTAIVEGLA 86
+ EK R L V+G + + + ++ K P +L G PGVGKT++ LA
Sbjct: 2 MPWVEKYRPKTLSDVVGNEKAKEQLREWIESWLKGKPKKALLLYGPPGVGKTSLAHALA 60
>gnl|CDD|163662 cd07419, MPP_Bsu1_C, Arabidopsis thaliana Bsu1 phosphatase and
related proteins, C-terminal metallophosphatase domain.
Bsu1 encodes a nuclear serine-threonine protein
phosphatase found in plants and protozoans. Bsu1 has a
C-terminal phosphatase domain and an N-terminal
Kelch-repeat domain. Bsu1 is preferentially expressed
in elongating plant cells. It modulates the
phosphorylation state of Bes1, a transcriptional
regulator phosphorylated by the glycogen synthase kinase
Bin2, as part of a steroid hormone signal transduction
pathway. The PPP (phosphoprotein phosphatase) family,
to which Bsu1 belongs, is one of two known protein
phosphatase families specific for serine and threonine.
The PPP family also includes: PP1, PP2A, PP2B
(calcineurin), PP4, PP5, PP6, PP7, Bsu1, RdgC, PrpE,
PrpA/PrpB, and ApA4 hydrolase. The PPP catalytic domain
is defined by three conserved motifs (-GDXHG-, -GDXVDRG-
and -GNHE-). The PPP enzyme family is ancient with
members found in all eukaryotes, and in most bacterial
and archeal genomes. Dephosphorylation of
phosphoserines and phosphothreonines on target proteins
plays a central role in the regulation of many cellular
processes. PPPs belong to the metallophosphatase (MPP)
superfamily. MPPs are functionally diverse, but all
share a conserved domain with an active site consisting
of two metal ions (usually manganese, iron, or zinc)
coordinated with octahedral geometry by a cage of
histidine, aspartate, and asparagine residues. The MPP
superfamily includes: Mre11/SbcD-like exonucleases,
Dbr1-like RNA lariat debranching enzymes, YfcE-like
phosphodiesterases, purple acid phosphatases (PAPs),
YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid
sphingomyelinases (ASMases). The conserved domain is a
double beta-sheet sandwich with a di-metal active site
made up of residues located at the C-terminal side of
the sheets. This domain is thought to allow for
productive metal coordination.
Length = 311
Score = 35.5 bits (82), Expect = 0.13
Identities = 49/219 (22%), Positives = 88/219 (40%), Gaps = 47/219 (21%)
Query: 621 RPEFINRIDDIIVFRYLNRKNILSIANIQLNILKNK--LLKMNMDLKISKAALKKISNIG 678
+P D F N IL + + +I K + +L++ +KI
Sbjct: 7 KPRIWKPPTDRRFF--FNWNEILELCDAAEDIFKQEPMVLRLRAPIKI------------ 52
Query: 679 FDLIYGARDVHGCKKSLSILLKKIHKKSPEA-------NFIFLGDLINKGPQSLDTLRMV 731
+G D+HG L L + EA +++FLGD +++G SL+T+ ++
Sbjct: 53 ----FG--DIHGQFGDLMRLFDEYGSPVTEAAGDIEYIDYLFLGDYVDRGSNSLETICLL 106
Query: 732 YSMR----NYAKIVLGNHEIHLLDVL----ININKKSKLDTFDDILDAPDKKKLVSWLRT 783
+++ N ++ GNHE ++ L ++ D D +L WL
Sbjct: 107 LALKVKYPNQIHLIRGNHEDRDINALFGFREECKERLGEDPNDGDSVWRRINRLFEWL-- 164
Query: 784 QPL-AIYYKKYLMIHAGVAKQWTAQQTIKLSHQVEKILR 821
PL AI K L +H G+ + +I ++E + R
Sbjct: 165 -PLAAIIEDKILCMHGGIGR------SINHVSEIEDLKR 196
>gnl|CDD|223540 COG0464, SpoVK, ATPases of the AAA+ class [Posttranslational
modification, protein turnover, chaperones].
Length = 494
Score = 35.6 bits (82), Expect = 0.14
Identities = 40/158 (25%), Positives = 66/158 (41%), Gaps = 28/158 (17%)
Query: 70 LIGEPGVGKTAIVEGLAQRIINGEVPNSLLSKKILLLDIALLLAGTKYRGEFEDRLKKIL 129
L G PG GKT + + +A + + + + LL +K+ GE E ++++
Sbjct: 281 LYGPPGTGKTLLAKAVAL----------ESRSRFISVKGSELL--SKWVGESEKNIRELF 328
Query: 130 KEISNNQKDIIIFIDELHTMI---GTGKVEGSIDAGNMLKPELSRGE----LHCIGATTL 182
++ + IIFIDE+ ++ G + L EL E + I AT
Sbjct: 329 EK-ARKLAPSIIFIDEIDSLASGRGPSEDGSGRRVVGQLLTELDGIEKAEGVLVIAAT-- 385
Query: 183 NEYRQYIEKDAAFER--RFQK-ILVEEPDIEETISILR 217
+ D A R RF + I V PD+EE + I +
Sbjct: 386 -NRPDDL--DPALLRPGRFDRLIYVPLPDLEERLEIFK 420
Score = 35.6 bits (82), Expect = 0.15
Identities = 69/445 (15%), Positives = 134/445 (30%), Gaps = 94/445 (21%)
Query: 261 DEAAAKIKIEIDSKPEIMDK------LERRLIQLKIEHEA----IKREYDESSKKRLLLI 310
A + + PEI+ K L R + + E A E D + KR
Sbjct: 37 ALANEGAEFLSINGPEILSKYVGESELRLRELFEEAEKLAPSIIFIDEIDALAPKRSSDQ 96
Query: 311 KKEINKLEIKYANLEKIWKYEKTLIKDSQQIKEEIEKVRLKINKATRKSDWQTVSKLKYG 370
+ ++ + L K + ++ + + ++ + + + R+ +
Sbjct: 97 GEVERRVVAQLLALMDGLKRGQVIVIGATNRPDGLDPAKRRPGRFDREIEVNLPD----- 151
Query: 371 ELNKLERILKEKSQKDIQLPNNANKFTLLKTK---------VGSEEIAEIVSRTTGIPVS 421
IL+ ++ P K +T + E + R +
Sbjct: 152 -EAGRLEILQIHTRLMFLGPPGTGKTLAARTVGKSGADLGALAKEAALRELRRAIDLVGE 210
Query: 422 KIVQVEREKLLNIENLLCKRVV-------------GQDEAIS----AVSNAIRRSRSGLS 464
I E + ++ +L R V G +EA A+ ++R
Sbjct: 211 YIGVTEDDFEEALKKVLPSRGVLFEDEDVTLDDIGGLEEAKEELKEAIETPLKRPELFRK 270
Query: 465 DAKRPYGSFMFLGPTGVGKTELCKTLSACIFNNEES-IIRIDMSEFIEKHSISRLIGAPP 523
RP + GP G GKT L+ + S I + SE + K
Sbjct: 271 LGLRPPKGVLLYGPPGTGKT----LLAKAVALESRSRFISVKGSELLSK----------- 315
Query: 524 GYIGYEEGGYLTEIVRRKPYSL----ILLDEIEK-----------ANSDVFNILLQILDD 568
++G E + K L I +DEI+ + V LL LD
Sbjct: 316 -WVG--ESEKNIRELFEKARKLAPSIIFIDEIDSLASGRGPSEDGSGRRVVGQLLTELDG 372
Query: 569 GRLTDNRGRTINFRNTIIVMTSNLGSDKIKEMEKGDKEIIKLAVMNEVKIYFRPEFINRI 628
+ +++ +N + D +++ + + P+ R+
Sbjct: 373 IEKAEGV---------LVIAATN-------RPDDLDPALLRPGRFDRLIYVPLPDLEERL 416
Query: 629 DDIIVFRYLNRKNILSIANIQLNIL 653
+ I +L K ++ L L
Sbjct: 417 E--IFKIHLRDKKPPLAEDVDLEEL 439
Score = 31.7 bits (72), Expect = 2.1
Identities = 51/172 (29%), Positives = 71/172 (41%), Gaps = 28/172 (16%)
Query: 57 IQVLQRRSKNNPVLIGEPGVGKTAIVEGLAQRIINGEVPNSLLSKKILLLDIALLLAGTK 116
+ L +L G PG GKT + LA G S+ +IL +K
Sbjct: 10 FKKLGIEPPKGVLLHGPPGTGKTLLARALANE---GAEFLSINGPEIL----------SK 56
Query: 117 YRGEFEDRLKKILKEISNNQKDIIIFIDELHTMIG-----TGKVEGSIDAG-NMLKPELS 170
Y GE E RL+++ +E IIFIDE+ + G+VE + A L L
Sbjct: 57 YVGESELRLRELFEEAEKLAP-SIIFIDEIDALAPKRSSDQGEVERRVVAQLLALMDGLK 115
Query: 171 RGELHCIGATTLNEYRQYIEKDAAFER--RFQK-ILVEEPDIEETISILRGL 219
RG++ IGAT + D A R RF + I V PD + IL+
Sbjct: 116 RGQVIVIGAT-----NRPDGLDPAKRRPGRFDREIEVNLPDEAGRLEILQIH 162
>gnl|CDD|235175 PRK03918, PRK03918, chromosome segregation protein; Provisional.
Length = 880
Score = 35.4 bits (82), Expect = 0.15
Identities = 27/133 (20%), Positives = 62/133 (46%), Gaps = 15/133 (11%)
Query: 260 IDEAAAKIKIEIDSKPEIMDKLERRLIQLKIEHEAIKREYDE---------SSKKRLLLI 310
I+E + + E++ ++++ L +L+ E E +++E E +K L +
Sbjct: 191 IEELIKEKEKELEEVLREINEISSELPELREELEKLEKEVKELEELKEEIEELEKELESL 250
Query: 311 KKEINKLEIKYANLEKIWKYEKTLIKDSQQIKEEIEKVRLKINKATRKSDWQTVSKLKYG 370
+ KLE K LE+ + K I++ ++ +E+++++ K ++ +S+
Sbjct: 251 EGSKRKLEEKIRELEERIEELKKEIEELEEKVKELKELKEK------AEEYIKLSEFYEE 304
Query: 371 ELNKLERILKEKS 383
L++L I K S
Sbjct: 305 YLDELREIEKRLS 317
Score = 35.4 bits (82), Expect = 0.18
Identities = 60/277 (21%), Positives = 131/277 (47%), Gaps = 27/277 (9%)
Query: 115 TKYRGEFEDRLKKILKEISNNQKDIIIFIDELHTMIGTGKVEGSIDAGNMLKPELSRGEL 174
+ G ++L+K L+E+ +++I I ++ IG K E + + + ++G+
Sbjct: 379 KRLTGLTPEKLEKELEELEKAKEEIEEEISKITARIGELKKEIKELKKAIEELKKAKGKC 438
Query: 175 HCIGATTLNEYRQYIEKDAAFERRFQKILVEEPDIEETISILRGLQKKYEVHHGVEITDP 234
G E+R+ + ++ + ++I E +IEE LR ++ E
Sbjct: 439 PVCGRELTEEHRKELLEE--YTAELKRIEKELKEIEEKERKLRKELRELEK--------- 487
Query: 235 AIVAASELSYRYISDRFMPDKAIDLIDEAAAKIKI----EIDSKPEIMDKLERRLIQLKI 290
+ SEL + + + E K+K E++ K E +KL+ +LI+LK
Sbjct: 488 VLKKESELIKLK--------ELAEQLKELEEKLKKYNLEELEKKAEEYEKLKEKLIKLKG 539
Query: 291 EHEAIKREYDESS--KKRLLLIKKEINKLEIKYANLEKIWKYEKTLIKDSQQIKEEIEKV 348
E +++K+E ++ KK+L ++K++++LE + A L K + E+ + ++++E ++++
Sbjct: 540 EIKSLKKELEKLEELKKKLAELEKKLDELEEELAELLK--ELEELGFESVEELEERLKEL 597
Query: 349 RLKINKATRKSDWQTVSKLKYGELNKLERILKEKSQK 385
N+ D + + + EL KLE L + ++
Sbjct: 598 EPFYNEYLELKDAEKELEREEKELKKLEEELDKAFEE 634
Score = 32.3 bits (74), Expect = 1.4
Identities = 24/94 (25%), Positives = 50/94 (53%), Gaps = 4/94 (4%)
Query: 265 AKIKIEIDSKPEIMDKLERRLIQLKIEHEAIKREYDESS----KKRLLLIKKEINKLEIK 320
K++ E+D E + + E+RL +L+ E E ++++Y E ++ L + +E+ L +
Sbjct: 622 KKLEEELDKAFEELAETEKRLEELRKELEELEKKYSEEEYEELREEYLELSRELAGLRAE 681
Query: 321 YANLEKIWKYEKTLIKDSQQIKEEIEKVRLKINK 354
LEK + K ++ ++ EE EK + ++ K
Sbjct: 682 LEELEKRREEIKKTLEKLKEELEEREKAKKELEK 715
Score = 30.0 bits (68), Expect = 7.7
Identities = 23/91 (25%), Positives = 50/91 (54%), Gaps = 7/91 (7%)
Query: 270 EIDSKPEIMDKLERRLIQLKIEHEAIKREYDESSKKRLLL-----IKKEINKLEIKYANL 324
I+ + + +++ E RL +LK + + +++ +E ++ L K+E+ +L+ + L
Sbjct: 325 GIEERIKELEEKEERLEELKKKLKELEKRLEELEERHELYEEAKAKKEELERLKKRLTGL 384
Query: 325 --EKIWKYEKTLIKDSQQIKEEIEKVRLKIN 353
EK+ K + L K ++I+EEI K+ +I
Sbjct: 385 TPEKLEKELEELEKAKEEIEEEISKITARIG 415
>gnl|CDD|237177 PRK12704, PRK12704, phosphodiesterase; Provisional.
Length = 520
Score = 35.5 bits (83), Expect = 0.15
Identities = 27/121 (22%), Positives = 59/121 (48%), Gaps = 14/121 (11%)
Query: 262 EAAAKIKIEIDSKPEIMDKLERRLIQLKIEHEAIKREYDESSKKRLLLIKKEINKLEIKY 321
E AK +E ++K E + L++ K E ++ E+++ ++R ++K +L K
Sbjct: 37 EEEAKRILE-EAKKEAEAIKKEALLEAKEEIHKLRNEFEKELRERRNELQKLEKRLLQKE 95
Query: 322 ANLEK----IWKYEKTLIKDSQQIKEEIEKVRLKINKATRKSDWQTVSKLKYGELNKLER 377
NL++ + K E+ L K ++++++ +++ K + + Q L +LER
Sbjct: 96 ENLDRKLELLEKREEELEKKEKELEQKQQELEKKEEELEELIEEQ---------LQELER 146
Query: 378 I 378
I
Sbjct: 147 I 147
Score = 31.7 bits (73), Expect = 2.0
Identities = 21/96 (21%), Positives = 50/96 (52%), Gaps = 9/96 (9%)
Query: 271 IDSKPEIMDKLERRLIQLKIEHEAIKREYDESSKKRLLLIKKEINKLEIKYANLEK---- 326
+D K E+++K E L + + E E ++E ++ ++ LI++++ +LE + + L
Sbjct: 98 LDRKLELLEKREEELEKKEKELEQKQQELEKKEEELEELIEEQLQELE-RISGLTAEEAK 156
Query: 327 ---IWKYEKTLIKD-SQQIKEEIEKVRLKINKATRK 358
+ K E+ + + IKE E+ + + +K ++
Sbjct: 157 EILLEKVEEEARHEAAVLIKEIEEEAKEEADKKAKE 192
>gnl|CDD|233847 TIGR02397, dnaX_nterm, DNA polymerase III, subunit gamma and tau.
This model represents the well-conserved first ~ 365
amino acids of the translation of the dnaX gene. The
full-length product of the dnaX gene in the model
bacterium E. coli is the DNA polymerase III tau subunit.
A translational frameshift leads to early termination
and a truncated protein subunit gamma, about 1/3 shorter
than tau and present in roughly equal amounts. This
frameshift mechanism is not necessarily universal for
species with DNA polymerase III but appears conserved in
the exterme thermophile Thermus thermophilis [DNA
metabolism, DNA replication, recombination, and repair].
Length = 355
Score = 35.2 bits (82), Expect = 0.16
Identities = 15/53 (28%), Positives = 28/53 (52%), Gaps = 8/53 (15%)
Query: 442 VVGQDEAISAVSNAIRRSRSGLSDAKRPYGSFMFLGPTGVGKTELCKTLSACI 494
V+GQ+ + + NAI+ R ++ A ++F GP G GKT + + + +
Sbjct: 16 VIGQEHIVQTLKNAIKNGR--IAHA------YLFSGPRGTGKTSIARIFAKAL 60
>gnl|CDD|227355 COG5022, COG5022, Myosin heavy chain [Cytoskeleton].
Length = 1463
Score = 35.4 bits (82), Expect = 0.16
Identities = 25/128 (19%), Positives = 53/128 (41%), Gaps = 11/128 (8%)
Query: 276 EIMDKLERRLIQLKIEHEAIKREYDESSK--KRLLLIKKEINKLEIK--YANLEKIWKYE 331
+ ++ ER+L +LKI+ ++I + + ++ +KK ++ I+ E I + +
Sbjct: 875 QRVELAERQLQELKIDVKSISSLKLVNLELESEIIELKKSLSSDLIENLEFKTELIARLK 934
Query: 332 KTL----IKDSQQIKEEIEKVRLKINKATRKSDWQTVSKLKYGELNKLERILKEKSQKDI 387
K L +++ I+ K++ +S + S+ L K IL + K
Sbjct: 935 KLLNNIDLEEGPSIEYVKLPELNKLH--EVESKLKETSEEYEDLLKKST-ILVREGNKAN 991
Query: 388 QLPNNANK 395
N K
Sbjct: 992 SELKNFKK 999
>gnl|CDD|221952 pfam13166, AAA_13, AAA domain. This family of domains contain a
P-loop motif that is characteristic of the AAA
superfamily. Many of the proteins in this family are
conjugative transfer proteins. This family includes the
PrrC protein that is thought to be the active component
of the anticodon nuclease.
Length = 713
Score = 35.4 bits (82), Expect = 0.17
Identities = 30/170 (17%), Positives = 70/170 (41%), Gaps = 23/170 (13%)
Query: 255 KAIDLIDEAAAKIKIEIDSKPEIMDKLERRLIQLKIEHEAIKREYDESSKKRLLLIKKEI 314
K + + E +I+ +I+ + + KLE ++ QL+ E E + E +++ K L K++
Sbjct: 81 KGVFTLGEENIEIEAQIEELKKELKKLEEKIEQLEAEIEKKEEELEKAKNKFLDKAWKKL 140
Query: 315 NKLEIKYANLEKIWKYEKTLIKDSQQIKEEIEKVRLKINKATRKSDWQTVSKLKYGELNK 374
K NL + K +++ +E++ V +N ++ S EL
Sbjct: 141 AKKYDS--NLSEALKGLNYKKNFKEKLLKELKSV--ILNASSLLSL---------EELKA 187
Query: 375 LERILKEKSQKDIQLPN-------NANKFTLLKTKV---GSEEIAEIVSR 414
+ L ++ ++ L + +L+ + I+E+++
Sbjct: 188 KIKTLFSSNKPELALLTLSVIDFDEIEQAEILEKSIIGSSDVPISELINN 237
>gnl|CDD|234175 TIGR03348, VI_IcmF, type VI secretion protein IcmF. Members of
this protein family are IcmF homologs and tend to be
associated with type VI secretion systems [Cellular
processes, Pathogenesis].
Length = 1169
Score = 35.0 bits (81), Expect = 0.22
Identities = 17/65 (26%), Positives = 25/65 (38%), Gaps = 16/65 (24%)
Query: 34 LTEKARLGKLDPVIGRDDEIRR-------AIQVLQRRSKNNP---------VLIGEPGVG 77
L A KL + EIR A+ +L+R ++IG PG G
Sbjct: 64 LAALAAPTKLKADAAAEAEIRELRARFNEALALLKRSRLGGRRYLYDLPWYLVIGPPGSG 123
Query: 78 KTAIV 82
KT ++
Sbjct: 124 KTTLL 128
>gnl|CDD|203489 pfam06644, ATP11, ATP11 protein. This family consists of several
eukaryotic ATP11 proteins. In Saccharomyces cerevisiae,
expression of functional F1-ATPase requires two proteins
encoded by the ATP11 and ATP12 genes. Atp11p is a
molecular chaperone of the mitochondrial matrix that
participates in the biogenesis pathway to form F1, the
catalytic unit of the ATP synthase.
Length = 250
Score = 34.3 bits (79), Expect = 0.23
Identities = 22/93 (23%), Positives = 42/93 (45%), Gaps = 4/93 (4%)
Query: 346 EKVRLKINKATRKSDWQTVSKLKYGELNKLERILKEKSQKDIQLPNNANKFTLLKTKVGS 405
EK R K+ + ++S + + +LK +K+E+ + A+KF LK +
Sbjct: 2 EKYRSKLLQKAKESGLEFIERLKKALKDKIEKKEFSAKKPPTGPSKQASKFKTLKPPKPA 61
Query: 406 EEIAEIVSRTTGI-PVSKIVQVEREKLLNIENL 437
++ P+S I+ VE+ K L+ E +
Sbjct: 62 DKKK---PFDKPFKPLSSILDVEKIKDLSAEEI 91
>gnl|CDD|237495 PRK13765, PRK13765, ATP-dependent protease Lon; Provisional.
Length = 637
Score = 35.0 bits (81), Expect = 0.23
Identities = 16/47 (34%), Positives = 30/47 (63%), Gaps = 8/47 (17%)
Query: 44 DPVIGRD---DEIRRAIQVLQRRSKNNPVLIGEPGVGKTAIVEGLAQ 87
D VIG++ + I++A + QRR + ++IG PG GK+ + + +A+
Sbjct: 31 DQVIGQEHAVEVIKKAAK--QRR---HVMMIGSPGTGKSMLAKAMAE 72
>gnl|CDD|131948 TIGR02902, spore_lonB, ATP-dependent protease LonB. Members of
this protein are LonB, a paralog of the ATP-dependent
protease La (LonA, TIGR00763). LonB proteins are found
strictly, and almost universally, in endospore-forming
bacteria. This protease was shown, in Bacillus subtilis,
to be expressed specifically in the forespore, during
sporulation, under control of sigma(F). The lonB gene,
despite location immediately upstream of lonA, was shown
to be monocistronic. LonB appears able to act on
sigma(H) for post-translation control, but lonB mutation
did not produce an obvious sporulation defect under the
conditions tested. Note that additional paralogs of LonA
and LonB occur in the Clostridium lineage and this model
selects only one per species as the protein that
corresponds to LonB in B. subtilis [Protein fate,
Degradation of proteins, peptides, and glycopeptides,
Cellular processes, Sporulation and germination].
Length = 531
Score = 34.7 bits (80), Expect = 0.26
Identities = 18/52 (34%), Positives = 29/52 (55%)
Query: 29 KYTIDLTEKARLGKLDPVIGRDDEIRRAIQVLQRRSKNNPVLIGEPGVGKTA 80
+ T L+EK R D +IG+++ I+ L + + ++ G PGVGKTA
Sbjct: 50 RLTEPLSEKTRPKSFDEIIGQEEGIKALKAALCGPNPQHVIIYGPPGVGKTA 101
Score = 30.5 bits (69), Expect = 5.3
Identities = 40/147 (27%), Positives = 63/147 (42%), Gaps = 28/147 (19%)
Query: 440 KRVVGQDEAISAVSNAIRRSRSGLSDAKRPYGSFMFLGPTGVGKT-------ELCKTLSA 492
++GQ+E I A+ A+ P ++ GP GVGKT E K A
Sbjct: 65 DEIIGQEEGIKALKAALC--------GPNPQHVIIY-GPPGVGKTAAARLVLEEAKKNPA 115
Query: 493 CIFNNEESIIRIDMS--EFIEKHSISRLIGA--PPGYIGYEEGGYLTEIVRRKPYS---- 544
F + + ID + F E+ LIG+ P Y G G + I + KP +
Sbjct: 116 SPFKEGAAFVEIDATTARFDERGIADPLIGSVHDPIYQGAGPLG-IAGIPQPKPGAVTRA 174
Query: 545 ---LILLDEIEKANSDVFNILLQILDD 568
++ +DEI + + N LL++L+D
Sbjct: 175 HGGVLFIDEIGELHPVQMNKLLKVLED 201
>gnl|CDD|236333 PRK08691, PRK08691, DNA polymerase III subunits gamma and tau;
Validated.
Length = 709
Score = 34.7 bits (79), Expect = 0.27
Identities = 32/140 (22%), Positives = 59/140 (42%), Gaps = 25/140 (17%)
Query: 442 VVGQDEAISAVSNAIRRSRSGLSDAKRPYGSFMFLGPTGVGKTELCKTLSACIFNNE--- 498
+VGQ+ + A+ NA+ D R + +++ G GVGKT + + L+ + N E
Sbjct: 18 LVGQEHVVKALQNAL--------DEGRLHHAYLLTGTRGVGKTTIARILAKSL-NCENAQ 68
Query: 499 --------ESIIRIDMSEFIEKHSISRLIGAPPGYIG--YEEGGYLTEIVRRKPYSLILL 548
+S +ID +++ I I E Y + K Y ++
Sbjct: 69 HGEPCGVCQSCTQIDAGRYVDLLEIDAASNTGIDNIREVLENAQYAPTAGKYKVY---II 125
Query: 549 DEIEKANSDVFNILLQILDD 568
DE+ + FN +L+ L++
Sbjct: 126 DEVHMLSKSAFNAMLKTLEE 145
>gnl|CDD|184920 PRK14956, PRK14956, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 484
Score = 34.5 bits (79), Expect = 0.27
Identities = 39/137 (28%), Positives = 62/137 (45%), Gaps = 19/137 (13%)
Query: 442 VVGQDEAISAVSNAIRRSRSGLSDAKRPYGSFMFLGPTGVGKTELCKTLSACIFNNEESI 501
V+ QD AI A+ NA++ + G +++F GP GVGKT + + L A N E I
Sbjct: 20 VIHQDLAIGALQNALKSGKIG--------HAYIFFGPRGVGKTTIARIL-AKRLNCENPI 70
Query: 502 IRIDMSEFIEKHSISRLIGAPPGYI------GYEEGGYLTEIVRRKP----YSLILLDEI 551
+E I++ I + I G E L + V+ P Y + ++DE+
Sbjct: 71 GNEPCNECTSCLEITKGISSDVLEIDAASNRGIENIRELRDNVKFAPMGGKYKVYIIDEV 130
Query: 552 EKANSDVFNILLQILDD 568
FN LL+ L++
Sbjct: 131 HMLTDQSFNALLKTLEE 147
>gnl|CDD|237057 PRK12323, PRK12323, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 700
Score = 34.9 bits (80), Expect = 0.28
Identities = 15/49 (30%), Positives = 29/49 (59%), Gaps = 8/49 (16%)
Query: 443 VGQDEAISAVSNAIRRSRSGLSDAKRPYGSFMFLGPTGVGKTELCKTLS 491
VGQ+ + A+++A+ + +R + +++F G GVGKT L + L+
Sbjct: 19 VGQEHVVRALTHAL--------EQQRLHHAYLFTGTRGVGKTTLSRILA 59
>gnl|CDD|237355 PRK13342, PRK13342, recombination factor protein RarA; Reviewed.
Length = 413
Score = 34.3 bits (80), Expect = 0.28
Identities = 22/113 (19%), Positives = 43/113 (38%), Gaps = 41/113 (36%)
Query: 46 VIGRDDEIRRAIQVLQRRSKNNPVLI--GEPGVGKTAIVEGLAQ------RIINGEVPNS 97
++G +RR I+ + +I G PG GKT + +A ++
Sbjct: 20 LLGPGKPLRRMIE-----AGRLSSMILWGPPGTGKTTLARIIAGATDAPFEALSA----- 69
Query: 98 LLSKKILLLDIALLLAGTKYRGEFEDRLKKILKEISNNQ---KDIIIFIDELH 147
+ +G K L+++++E + + I+FIDE+H
Sbjct: 70 -------------VTSGVK-------DLREVIEEARQRRSAGRRTILFIDEIH 102
Score = 29.3 bits (67), Expect = 9.6
Identities = 35/142 (24%), Positives = 55/142 (38%), Gaps = 44/142 (30%)
Query: 442 VVGQDEAISAVSNAIRRSRSGLSDAKRPYGSFMFLGPTGVGKTELCK-----------TL 490
VVGQ+ + +RR + +A R S + GP G GKT L + L
Sbjct: 14 VVGQEHLLGPGK-PLRR----MIEAGRL-SSMILWGPPGTGKTTLARIIAGATDAPFEAL 67
Query: 491 SACIFNNEESIIRIDMSEFIEKHSISRLIGAPPGYIGYEEGGYLTEIVRRKPYSLILLDE 550
SA ++ +R E IE+ R G R+ ++ +DE
Sbjct: 68 SAVTSGVKD--LR----EVIEEARQRRSAG-------------------RRT--ILFIDE 100
Query: 551 IEKANSDVFNILLQILDDGRLT 572
I + N + LL ++DG +T
Sbjct: 101 IHRFNKAQQDALLPHVEDGTIT 122
>gnl|CDD|234763 PRK00440, rfc, replication factor C small subunit; Reviewed.
Length = 319
Score = 34.1 bits (79), Expect = 0.29
Identities = 20/56 (35%), Positives = 29/56 (51%), Gaps = 8/56 (14%)
Query: 35 TEKARLGKLDPVIGRDDEIRRAIQVLQR--RSKNNPVLI--GEPGVGKTAIVEGLA 86
EK R LD ++G+++ + R L+ + KN P L+ G PG GKT LA
Sbjct: 8 VEKYRPRTLDEIVGQEEIVER----LKSYVKEKNMPHLLFAGPPGTGKTTAALALA 59
>gnl|CDD|153341 cd07657, F-BAR_Fes_Fer, The F-BAR (FES-CIP4 Homology and
Bin/Amphiphysin/Rvs) domain of Fes (feline sarcoma) and
Fer (Fes related) tyrosine kinases. F-BAR domains are
dimerization modules that bind and bend membranes and
are found in proteins involved in membrane dynamics and
actin reorganization. Fes (feline sarcoma), also called
Fps (Fujinami poultry sarcoma), and Fer (Fes related)
are cytoplasmic (or nonreceptor) tyrosine kinases that
play roles in haematopoiesis, inflammation and immunity,
growth factor signaling, cytoskeletal regulation, cell
migration and adhesion, and the regulation of cell-cell
interactions. Although Fes and Fer show redundancy in
their biological functions, they show differences in
their expression patterns. Fer is ubiquitously expressed
while Fes is expressed predominantly in myeloid and
endothelial cells. Fes and Fer contain an N-terminal
F-BAR domain, an SH2 domain, and a C-terminal catalytic
kinase domain. F-BAR domains form banana-shaped dimers
with a positively-charged concave surface that binds to
negatively-charged lipid membranes. They can induce
membrane deformation in the form of long tubules. The
F-BAR domain of Fes is critical in its role in
microtubule nucleation and bundling.
Length = 237
Score = 33.9 bits (78), Expect = 0.29
Identities = 22/83 (26%), Positives = 40/83 (48%), Gaps = 9/83 (10%)
Query: 284 RLIQLKIEHEAIKREYDESSKKRLLLIKK---EINKLEIKYANLEKIW-----KYEKTLI 335
+L L + K+ Y E ++ KK E+ KL+ +Y L + + K+E+ ++
Sbjct: 95 KLTLLIKDKRKAKKAYQEERQQIDEQYKKLTDEVEKLKSEYQKLLEDYKAAKSKFEEAVV 154
Query: 336 KDSQQIKEEIEKVRLKINKATRK 358
K + +++K R K KA RK
Sbjct: 155 K-GGRGGRKLDKARDKYQKACRK 176
>gnl|CDD|130309 TIGR01242, 26Sp45, 26S proteasome subunit P45 family. Many
proteins may score above the trusted cutoff because an
internal.
Length = 364
Score = 34.0 bits (78), Expect = 0.36
Identities = 28/88 (31%), Positives = 40/88 (45%), Gaps = 22/88 (25%)
Query: 469 PYGSFMFLGPTGVGKTELCKTLSACIFNNEESIIRIDMSEFIEKHSISRLIGAPPGYIGY 528
P G ++ GP G GKT L K ++ + IR+ SE + K YIG
Sbjct: 156 PKGVLLY-GPPGTGKTLLAKAVAH---ETNATFIRVVGSELVRK------------YIG- 198
Query: 529 EEGGYLT----EIVRRKPYSLILLDEIE 552
EG L E+ + K S+I +DEI+
Sbjct: 199 -EGARLVREIFELAKEKAPSIIFIDEID 225
>gnl|CDD|234389 TIGR03903, TOMM_kin_cyc, TOMM system kinase/cyclase fusion protein.
This model represents proteins of 1350 in length, in
multiple species of Burkholderia, in Acidovorax avenae
subsp. citrulli AAC00-1 and Delftia acidovorans SPH-1,
and in multiple copies in Sorangium cellulosum, in
genomic neighborhoods that include a
cyclodehydratase/docking scaffold fusion protein
(TIGR03882) and a member of the thiazole/oxazole
modified metabolite (TOMM) precursor family TIGR03795.
It has a kinase domain in the N-terminal 300 amino
acids, followed by a cyclase homology domain, followed
by regions without named domain definitions. It is a
probable bacteriocin-like metabolite biosynthesis
protein [Cellular processes, Toxin production and
resistance].
Length = 1266
Score = 34.4 bits (79), Expect = 0.37
Identities = 16/55 (29%), Positives = 29/55 (52%), Gaps = 7/55 (12%)
Query: 40 LGKLDPVIGRDDEI----RRAIQVLQRRSKNNPVLI-GEPGVGKTAIVEGLAQRI 89
G P++GR E+ RR + R + +L+ GE G+GK+ +V L +++
Sbjct: 476 GGTTTPLVGRSRELEALRRRWRDTVAGRGR--AILVVGEAGIGKSRLVHELVEKV 528
>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication,
recombination, and repair].
Length = 908
Score = 34.4 bits (79), Expect = 0.40
Identities = 41/284 (14%), Positives = 105/284 (36%), Gaps = 27/284 (9%)
Query: 120 EFEDRLKKILKEISNNQKDIIIFIDELHTMIGTGKVEGSIDAGNMLKPELSRGELHCIGA 179
E E+ L ++L+ ++++ +++L ++ + LK EL + E
Sbjct: 512 ELEEELIELLELEEALKEELEEKLEKLENLLEELEELKEKLQLQQLKEELRQLEDRLQEL 571
Query: 180 TTLNEY----RQYIEKDAAFERRFQKILVEEPDIEETISILRGLQKKYEVHHGVEITDPA 235
L E R E+ R +++ + ++EE +S L L + E+ + A
Sbjct: 572 KELLEELRLLRTRKEELEELRERLKELKKKLKELEERLSQLEELLQSLELSEAENELEEA 631
Query: 236 IVAASELSYRYISDRFMPDKAIDLIDEAAAKIKIEIDSKPEIMDKLERRLIQLKIEHEAI 295
++ ++ A ++ + E+ +K+E +++ E + I
Sbjct: 632 EEELESE--------------LEKLNLQAELEELLQAALEELEEKVEELEAEIRRELQRI 677
Query: 296 KREYDESSKKRLLLIKKEINKLEIKYANLEKIWKYEKTLIKDSQQIKEEIEKVRLKINKA 355
+ E E +++L +++ +LE LE++ K + + ++++ ++ +
Sbjct: 678 ENE--EQLEEKLEELEQLEEELEQLREELEELLKKLGEIEQLIEELESRKAELEELKKEL 735
Query: 356 TRKSDWQTVSKLKYGELNKLERILKEKSQKDIQLPNNANKFTLL 399
+ L +L L + + L N +
Sbjct: 736 EKLEK-------ALELLEELREKLGKAGLRADILRNLLAQIEAE 772
Score = 34.0 bits (78), Expect = 0.50
Identities = 29/144 (20%), Positives = 66/144 (45%), Gaps = 5/144 (3%)
Query: 257 IDLIDEAAAKIKIEIDSKPEIMDKLERRLIQLKIEHEAIKREYDESSKKRLLLIKKEINK 316
++ ++ + +K + E K+E QL E I+ + ++ L K E +
Sbjct: 166 LEKYEKLSELLK---EVIKEAKAKIEELEGQLSELLEDIEDLLEALEEELKELKKLEEIQ 222
Query: 317 LEIKYANLEKIWKYEKTLIKDSQQIKEEIEKVRLKINKATRKSDWQTVSKLKYGELNKLE 376
E + LE+ + + + + ++ KE +E+++ ++ +S K++ EL +LE
Sbjct: 223 EEQEEEELEQEIEALEERLAELEEEKERLEELKARL--LEIESLELEALKIREEELRELE 280
Query: 377 RILKEKSQKDIQLPNNANKFTLLK 400
R+L+E +K +L + L+
Sbjct: 281 RLLEELEEKIERLEELEREIEELE 304
Score = 32.0 bits (73), Expect = 1.8
Identities = 20/147 (13%), Positives = 60/147 (40%)
Query: 261 DEAAAKIKIEIDSKPEIMDKLERRLIQLKIEHEAIKREYDESSKKRLLLIKKEINKLEIK 320
E + + E ++KLE L +L+ E ++ + + ++L +E+ +L +
Sbjct: 518 IELLELEEALKEELEEKLEKLENLLEELEELKEKLQLQQLKEELRQLEDRLQELKELLEE 577
Query: 321 YANLEKIWKYEKTLIKDSQQIKEEIEKVRLKINKATRKSDWQTVSKLKYGELNKLERILK 380
L + + L + +++K++++++ ++++ +S+ + E +
Sbjct: 578 LRLLRTRKEELEELRERLKELKKKLKELEERLSQLEELLQSLELSEAENELEEAEEELES 637
Query: 381 EKSQKDIQLPNNANKFTLLKTKVGSEE 407
E + ++Q L+ E
Sbjct: 638 ELEKLNLQAELEELLQAALEELEEKVE 664
Score = 31.7 bits (72), Expect = 2.6
Identities = 32/180 (17%), Positives = 80/180 (44%), Gaps = 24/180 (13%)
Query: 254 DKAIDLIDEAAAKIKIEIDSKPEIMDKLERRLIQLKIEHEAIKREYDESSKKRLLLIKKE 313
+ + ++EA ++K E+ +++++ L +L+ E E ++RE +E ++ + ++++
Sbjct: 381 LERLKQLEEAIQELKEELAELSAALEEIQEELEELEKELEELERELEEL-EEEIKKLEEQ 439
Query: 314 INKLEIKYANLEKIWK-----------------------YEKTLIKDSQQIKEEIEKVRL 350
IN+LE K + ++ YE L + +++ E E+ L
Sbjct: 440 INQLESKELMIAELAGAGEKCPVCGQELPEEHEKELLELYELELEELEEELSREKEEAEL 499
Query: 351 KINKATRKSDWQTVSKLKYGELNKLERILKEKSQKDIQLPNNANKFTLLKTKVGSEEIAE 410
+ + + + + + L E + +E +K +L N + LK K+ +++ E
Sbjct: 500 REEIEELEKELRELEEELIELLELEEALKEELEEKLEKLENLLEELEELKEKLQLQQLKE 559
>gnl|CDD|223250 COG0172, SerS, Seryl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 429
Score = 33.7 bits (78), Expect = 0.41
Identities = 16/73 (21%), Positives = 37/73 (50%)
Query: 280 KLERRLIQLKIEHEAIKREYDESSKKRLLLIKKEINKLEIKYANLEKIWKYEKTLIKDSQ 339
+L+ +L E E ++ E +E SK+ +K+ + E A ++++ + K L
Sbjct: 33 ELDEERRKLLRELEELQAERNELSKEIGRALKRGEDDAEELIAEVKELKEKLKELEAALD 92
Query: 340 QIKEEIEKVRLKI 352
+++ E++ + L I
Sbjct: 93 ELEAELDTLLLTI 105
>gnl|CDD|235570 PRK05703, flhF, flagellar biosynthesis regulator FlhF; Validated.
Length = 424
Score = 33.7 bits (78), Expect = 0.44
Identities = 40/198 (20%), Positives = 78/198 (39%), Gaps = 28/198 (14%)
Query: 293 EAIKREYDESSKKRLLLIKKEINKLEIKYANLEKIWKYEKTLIKDSQQIKEEIEKVRLKI 352
+ RE K +L ++ + K + + + + + E L + +++++ E +
Sbjct: 60 NPVLREEKRKPAKSILSLQALLEKRPSRTNSQDALLQAENALPEWKKELEKPSEPKEEEP 119
Query: 353 NK-ATRKSDWQTVSKLKYGELNKLERILKEKSQKDIQL----PNNANKFTLLKTKVG-SE 406
A K + + +L+ EL +L+ +L+++ Q+ P A + LK + G S
Sbjct: 120 KAAAESKVVQKELDELR-DELKELKNLLEDQLSGLRQVERIPPEFAELYKRLK-RSGLSP 177
Query: 407 EIAEIVSRTTGIPVSKIVQVEREKLLNIENLLCKRVVGQDEAISAVSNAIRRSRSGLSDA 466
EIAE + + + + LL LL + + E I +
Sbjct: 178 EIAEKLLKLLLEHMPPRERTAWRYLLE---LLANMIPVRVEDILKQGGVV---------- 224
Query: 467 KRPYGSFMFLGPTGVGKT 484
+GPTGVGKT
Sbjct: 225 -------ALVGPTGVGKT 235
>gnl|CDD|235871 PRK06835, PRK06835, DNA replication protein DnaC; Validated.
Length = 329
Score = 33.7 bits (78), Expect = 0.44
Identities = 21/84 (25%), Positives = 40/84 (47%), Gaps = 12/84 (14%)
Query: 276 EIMDKLERRLIQLKIEHEAIKREYDESSK-KRLLLIKKEINKLEIKYANLEKIWKYEKTL 334
EI+ + E+R + K E E R+ + K + I EI KL IK + + +
Sbjct: 8 EILKEYEKR--RDKEELELKNRKEEVYKKIPEIAEIDDEIAKLGIKLS---------RAI 56
Query: 335 IKDSQQIKEEIEKVRLKINKATRK 358
+K+ + +E +++++ KI K
Sbjct: 57 LKNPDKKEETLKELKEKITDLRVK 80
>gnl|CDD|237865 PRK14951, PRK14951, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 618
Score = 33.9 bits (78), Expect = 0.44
Identities = 17/48 (35%), Positives = 27/48 (56%), Gaps = 8/48 (16%)
Query: 443 VGQDEAISAVSNAIRRSRSGLSDAKRPYGSFMFLGPTGVGKTELCKTL 490
VGQ+ + A++NA+ + R L A ++F G GVGKT + + L
Sbjct: 19 VGQEHVVQALTNALTQQR--LHHA------YLFTGTRGVGKTTVSRIL 58
>gnl|CDD|140271 PTZ00244, PTZ00244, serine/threonine-protein phosphatase PP1;
Provisional.
Length = 294
Score = 33.7 bits (77), Expect = 0.44
Identities = 27/113 (23%), Positives = 57/113 (50%), Gaps = 18/113 (15%)
Query: 707 PEANFIFLGDLINKGPQSLDTLRMVYSMR-----NYAKIVLGNHEIHLLDVLININKKSK 761
P +N++FLGD +++G S++T+ + + + N+ ++ GNHE +INK
Sbjct: 78 PYSNYLFLGDYVDRGKHSVETITLQFCYKIVYPENFF-LLRGNHEC------ASINKMYG 130
Query: 762 LDTFDDILDAPDKKKLVSW---LRTQPL-AIYYKKYLMIHAGVAKQWTAQQTI 810
FDD+ + K ++ T P+ + +K + +H G++ T+ ++
Sbjct: 131 F--FDDVKRRYNIKLFKAFTDVFNTMPVCCVISEKIICMHGGLSPDLTSLASV 181
>gnl|CDD|235503 PRK05561, PRK05561, DNA topoisomerase IV subunit A; Validated.
Length = 742
Score = 33.9 bits (79), Expect = 0.45
Identities = 29/107 (27%), Positives = 42/107 (39%), Gaps = 30/107 (28%)
Query: 255 KAIDLIDEAAAKIKIEIDSKPEIMDK-----------LERRLIQL-KIEHEAIKREYDES 302
A IDE I+ + K +M + LE RL +L K+E I++E DE
Sbjct: 390 IAFLNIDEVIRIIRESDEPKANLMARFDLSEIQAEAILELRLRRLAKLEEIEIRKEQDEL 449
Query: 303 SKKRLLLIKKEINKLEIKYANLEKIWKYEKTLIKDSQQIKEEIEKVR 349
K+ A LE I E+ L K IK+E++
Sbjct: 450 RKEI---------------AELEAILASERKLRK---LIKKELKADA 478
>gnl|CDD|237868 PRK14960, PRK14960, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 702
Score = 33.9 bits (77), Expect = 0.49
Identities = 17/53 (32%), Positives = 30/53 (56%), Gaps = 8/53 (15%)
Query: 442 VVGQDEAISAVSNAIRRSRSGLSDAKRPYGSFMFLGPTGVGKTELCKTLSACI 494
+VGQ+ A+S+A+ R R + +++F G GVGKT + + L+ C+
Sbjct: 17 LVGQNHVSRALSSALERGRL--------HHAYLFTGTRGVGKTTIARILAKCL 61
>gnl|CDD|184697 PRK14475, PRK14475, F0F1 ATP synthase subunit B; Provisional.
Length = 167
Score = 32.2 bits (73), Expect = 0.57
Identities = 12/39 (30%), Positives = 22/39 (56%)
Query: 260 IDEAAAKIKIEIDSKPEIMDKLERRLIQLKIEHEAIKRE 298
+D AAKI+ E+D + ++ + L +K E E +R+
Sbjct: 39 LDAYAAKIQAELDEAQRLREEAQALLADVKAEREEAERQ 77
>gnl|CDD|237864 PRK14950, PRK14950, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 585
Score = 33.6 bits (77), Expect = 0.60
Identities = 34/149 (22%), Positives = 55/149 (36%), Gaps = 42/149 (28%)
Query: 442 VVGQDEAISAVSNAIRRSRSGLSDAKRPYGSFMFLGPTGVGKT----------------- 484
+VGQ+ + + NAI R +++F GP GVGKT
Sbjct: 18 LVGQEHVVQTLRNAIAEGRVA--------HAYLFTGPRGVGKTSTARILAKAVNCTTNDP 69
Query: 485 --ELCKTLSACIFNNEES---IIRIDMSEFIEKHSISRLIGAPPGYIGYEEGGYLTEIVR 539
C T C E S +I +D + +I E + + R
Sbjct: 70 KGRPCGTCEMCRAIAEGSAVDVIEMDAASHTSVDDAREII---------ERVQFRPALAR 120
Query: 540 RKPYSLILLDEIEKANSDVFNILLQILDD 568
K Y ++DE+ ++ FN LL+ L++
Sbjct: 121 YKVY---IIDEVHMLSTAAFNALLKTLEE 146
>gnl|CDD|235223 PRK04132, PRK04132, replication factor C small subunit;
Provisional.
Length = 846
Score = 33.7 bits (77), Expect = 0.60
Identities = 19/59 (32%), Positives = 33/59 (55%), Gaps = 2/59 (3%)
Query: 36 EKARLGKLDPVIGRDDEIRRAIQVLQRRSKNNPVLIGEPGVGKTAIVEGLAQRIINGEV 94
EK R +LD ++G++ ++R ++ S + + G PGVGK + G + I NGE+
Sbjct: 11 EKYRPQRLDDIVGQEHIVKRLKHYVKTGSMPHLLFAGPPGVGKC--LTGDTKVIANGEL 67
>gnl|CDD|226400 COG3883, COG3883, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 265
Score = 33.2 bits (76), Expect = 0.62
Identities = 29/171 (16%), Positives = 69/171 (40%), Gaps = 23/171 (13%)
Query: 255 KAIDLIDEAAAKIKIEIDSKPEIMDKLERRLIQLKIEHEAIK---REYDESSKKRL---- 307
I+ +D +I+ +ID + +D+ + + +L+ E +K E E KKR
Sbjct: 52 NEIESLDNQIEEIQSKIDELQKEIDQSKAEIKKLQKEIAELKENIVERQELLKKRARAMQ 111
Query: 308 -----------LLIKKEINKLEIKYANLEKIWKYEKTLIKDSQQIKEEIEKVRLKINKAT 356
+L K + L + + I +K +++ ++ K+ +E+ + +
Sbjct: 112 VNGTATSYIDVILNSKSFSDLISRVTAISVIVDADKKILEQQKEDKKSLEEKQAALEDKL 171
Query: 357 RKSDWQTVSKLKYGELNKLERILKEKSQKDIQLPNNANKFTLLKTKVGSEE 407
+T+ L+ +L + +K++K+ + A K + + E
Sbjct: 172 -----ETLVALQNELETQLNSLNSQKAEKNALIAALAAKEASALGEKAALE 217
>gnl|CDD|184927 PRK14963, PRK14963, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 504
Score = 33.3 bits (76), Expect = 0.62
Identities = 16/43 (37%), Positives = 23/43 (53%), Gaps = 8/43 (18%)
Query: 442 VVGQDEAISAVSNAIRRSRSGLSDAKRPYGSFMFLGPTGVGKT 484
VVGQ+ + A+R+ R G +++F GP GVGKT
Sbjct: 16 VVGQEHVKEVLLAALRQGRLG--------HAYLFSGPRGVGKT 50
>gnl|CDD|223266 COG0188, GyrA, Type IIA topoisomerase (DNA gyrase/topo II,
topoisomerase IV), A subunit [DNA replication,
recombination, and repair].
Length = 804
Score = 33.4 bits (77), Expect = 0.66
Identities = 37/176 (21%), Positives = 67/176 (38%), Gaps = 25/176 (14%)
Query: 255 KAIDLIDEAAAKIKIEIDSKPEIMDKLERRLIQLKIEHEAIKREYDESSKKRLLLIKKEI 314
A+ IDE I+ KPE ++L R + + EAI + +RL E
Sbjct: 384 IALLNIDEVIEIIRES-KDKPEAKEELMARFGLSEKQAEAIL----DLRLRRLT--GLEE 436
Query: 315 NKLEIKYANLEKIWKYEKTLI----KDSQQIKEEIEKVRLKINKATRKSDWQTVSKLKYG 370
K+E + LEK + ++ + IK+E+ +++ K R + + +
Sbjct: 437 EKIEKELKELEKEIADLEKILASEERLLDIIKKELLEIKKKFGDERR----TEIVEEEED 492
Query: 371 ELNKLERILKE-----KSQK--DIQLPN---NANKFTLLKTKVGSEEIAEIVSRTT 416
E+ + I +E S K ++P A + + L K G + T
Sbjct: 493 EIEDEDLIAEEDVVVTLSHKGYIKRVPLKGYEAQRVSGLGLKEGDFLERLFEANTH 548
>gnl|CDD|153311 cd07627, BAR_Vps5p, The Bin/Amphiphysin/Rvs (BAR) domain of yeast
Sorting Nexin Vps5p. BAR domains are dimerization,
lipid binding and curvature sensing modules found in
many different proteins with diverse functions. Sorting
nexins (SNXs) are Phox homology (PX) domain containing
proteins that are involved in regulating membrane
traffic and protein sorting in the endosomal system.
SNXs differ from each other in their lipid-binding
specificity, subcellular localization and specific
function in the endocytic pathway. A subset of SNXs also
contain BAR domains. The PX-BAR structural unit
determines the specific membrane targeting of SNXs.
Vsp5p is the yeast counterpart of human SNX1 and is part
of the retromer complex, which functions in the
endosome-to-Golgi retrieval of vacuolar protein sorting
receptor Vps10p, the Golgi-resident membrane protein
A-ALP, and endopeptidase Kex2. BAR domains form dimers
that bind to membranes, induce membrane bending and
curvature, and may also be involved in protein-protein
interactions.
Length = 216
Score = 32.7 bits (75), Expect = 0.73
Identities = 19/71 (26%), Positives = 36/71 (50%), Gaps = 5/71 (7%)
Query: 307 LLLIKKEINKLEIKYANLEKIWKYEKTLIKDSQQIKEEIEKVRLKINKATRKSDWQTVSK 366
+ E++K K A LEK+ + KT + + E+E+ + ++ K +++ VS+
Sbjct: 117 WQSAESELSK---KKAQLEKLKRQGKTQQEKLNSLLSELEEAERRASEL--KKEFEEVSE 171
Query: 367 LKYGELNKLER 377
L EL + ER
Sbjct: 172 LIKSELERFER 182
>gnl|CDD|224337 COG1419, FlhF, Flagellar GTP-binding protein [Cell motility and
secretion].
Length = 407
Score = 33.1 bits (76), Expect = 0.80
Identities = 34/217 (15%), Positives = 72/217 (33%), Gaps = 29/217 (13%)
Query: 295 IKREYDESSKKRLLLIKKE-------INKLEIKYANLEKIWKYEKTL--IKDSQQIKEEI 345
IK+ ES ++ + I+KE ++ IK + KT + + E+
Sbjct: 3 IKKFTAESMREAIEKIRKELGEDAVILSNRRIK-KGGFLGLLFSKTAVEVTKLAAVDSEL 61
Query: 346 EKVRLKINKATRKSDWQTVSKLKYGELNKLERILKE-----KSQKDIQLPNNANKFTLLK 400
K + + + ++ Q + + + + K+ S + + + +
Sbjct: 62 RKFQTREAAKVKDAEAQLLKDPA-EKKREERKAAKKIERSTPSLIERKTQEVKDSGEEIA 120
Query: 401 TKVGSEE--IAEIVSRTTGIPVSKIVQVEREKLLNIENLLCKR-VVGQDEAISAVSNAIR 457
+ E+ I E+ +++ LN+ N L + + + + S
Sbjct: 121 EMMRDEKVPIRELEEIPPEFVALYKQEIQSPTRLNLINELLRAGLELEILDMKDESYEDL 180
Query: 458 RSRSGL----------SDAKRPYGSFMFLGPTGVGKT 484
R S + +GPTGVGKT
Sbjct: 181 RYFSEKLRKLLLSLIENLIVEQKRVIALVGPTGVGKT 217
>gnl|CDD|225369 COG2812, DnaX, DNA polymerase III, gamma/tau subunits [DNA
replication, recombination, and repair].
Length = 515
Score = 33.1 bits (76), Expect = 0.84
Identities = 35/140 (25%), Positives = 61/140 (43%), Gaps = 29/140 (20%)
Query: 442 VVGQDEAISAVSNAIRRSRSGLSDAKRPYGSFMFLGPTGVGKTELCKTLSACIFNNEESI 501
VVGQ+ + +SNA+ + R +++F GP GVGKT + + L+ + N E
Sbjct: 18 VVGQEHVVKTLSNAL--------ENGRIAHAYLFSGPRGVGKTTIARILAKAL-NCENGP 68
Query: 502 -----IRIDMSEFIEKHSISRLIGAPPGYI------GYEEGGYLTEIVRRKP----YSLI 546
+ + I + S+ +I I G ++ + E V P Y +
Sbjct: 69 TAEPCGKCISCKEINEGSLIDVI-----EIDAASNTGVDDIREIIEKVNYAPSEGRYKVY 123
Query: 547 LLDEIEKANSDVFNILLQIL 566
++DE+ + FN LL+ L
Sbjct: 124 IIDEVHMLSKQAFNALLKTL 143
>gnl|CDD|218483 pfam05183, RdRP, RNA dependent RNA polymerase. This family of
proteins are eukaryotic RNA dependent RNA polymerases.
These proteins are involved in post transcriptional gene
silencing where they are thought to amplify dsRNA
templates.
Length = 508
Score = 32.9 bits (75), Expect = 0.86
Identities = 25/159 (15%), Positives = 63/159 (39%), Gaps = 20/159 (12%)
Query: 182 LNEYRQYIEKDAAFERRF---QKILVEEPDIEETISILRGLQKKYEVHHGVEITDPAIVA 238
+E E +A++ RF + +LV +PD+ +R K+++ + I+
Sbjct: 159 ADELGTLEEDPSAYQIRFGGYKGVLVVDPDLPGNEIHIRPSMLKFDLLGDAAVNSLEIIR 218
Query: 239 ASELSYRYISDRFM--------PDKA-IDLIDEAAAKIKIEIDS--------KPEIMDKL 281
+S+ + Y++ + + PD+ I+L+ EA ++ + + + +
Sbjct: 219 SSKPTPAYLNRQLITVLSTLGVPDEVFIELLREALKELAEALTDWDQALDLLRKQADEND 278
Query: 282 ERRLIQLKIEHEAIKREYDESSKKRLLLIKKEINKLEIK 320
++ + R+ + K L KE ++ +
Sbjct: 279 FTLTLRFMPSEDPFLRKLLRALVKHTLKKLKEKLRIPVP 317
>gnl|CDD|118696 pfam10168, Nup88, Nuclear pore component. Nup88 can be divided
into two structural domains; the N-terminal two-thirds
of the protein has no obvious structural motifs but is
the region for binding to Nup98, one of the components
of the nuclear pore. the C-terminal end is a predicted
coiled-coil domain. Nup88 is overexpressed in tumour
cells.
Length = 717
Score = 32.9 bits (75), Expect = 0.91
Identities = 33/167 (19%), Positives = 69/167 (41%), Gaps = 18/167 (10%)
Query: 258 DLIDEAAAK-IKIEIDSKPEIMDKL-----ERRLIQLKIEHEAIKREYDESSKKRLLLIK 311
DL E + +K+ K + ++ + ER+ + + E A K ++E+ + LL+
Sbjct: 557 DLAREEFQRRVKLLQLQKEKQLEDIQDCREERKSLSERAEKLAEK--FEEAKYNQELLVN 614
Query: 312 KEINKLEIKYANLEKIWKYEKTLIKDSQQIKEEIEKVRLKINKATRKSDWQTVSKLKYGE 371
+ L+ + L + E+ + K+ Q+I ++++ + I + +K ++Q
Sbjct: 615 RCKRLLQSANSQLPVLSDSERDMSKELQRINKQLQHLANGIKQVKKKKNYQRYHMASQES 674
Query: 372 LNKLERILKEKSQKDIQLPNNANKFTLLKTKVGSEEIAEIVSRTTGI 418
K L EK K I +LK E I ++ + I
Sbjct: 675 PKKSSYTLPEKQHKTIT--------EILKEL--GEHIDRMIKQIKRI 711
>gnl|CDD|224310 COG1392, COG1392, Phosphate transport regulator (distant homolog of
PhoU) [Inorganic ion transport and metabolism].
Length = 217
Score = 31.9 bits (73), Expect = 1.2
Identities = 34/107 (31%), Positives = 51/107 (47%), Gaps = 12/107 (11%)
Query: 254 DKAIDLIDEAAAKIKIEIDSKPEIMDKLERRLIQLKIE-----HEAIKR-EYDESSKKRL 307
D D ++AA + + PE +D+ RL+ L ++ EAI+ E S RL
Sbjct: 90 DDIADAAEDAAKLLLLRKPFIPEELDEEFLRLVDLSLKAAELLAEAIELLEDLLESADRL 149
Query: 308 LLIKKEINKLE-----IKYANLEKIWKYEKTL-IKDSQQIKEEIEKV 348
L I KEI LE I+ L+K++ E + D +KE IEK+
Sbjct: 150 LEIIKEIEALEHECDDIQRELLKKLFSLETEINPIDVIILKEIIEKI 196
>gnl|CDD|235422 PRK05342, clpX, ATP-dependent protease ATP-binding subunit ClpX;
Provisional.
Length = 412
Score = 32.4 bits (75), Expect = 1.2
Identities = 23/61 (37%), Positives = 31/61 (50%), Gaps = 15/61 (24%)
Query: 442 VVGQDEA---IS-AVSNAIRRSRSGLSD------AKRPYGS-FMFLGPTGVGKTELCKTL 490
V+GQ+ A +S AV N +R R G K S + +GPTG GKT L +TL
Sbjct: 73 VIGQERAKKVLSVAVYNHYKRLRHGDKKDDDVELQK----SNILLIGPTGSGKTLLAQTL 128
Query: 491 S 491
+
Sbjct: 129 A 129
>gnl|CDD|185140 PRK15218, PRK15218, fimbrial chaperone protein PegB; Provisional.
Length = 226
Score = 31.9 bits (72), Expect = 1.2
Identities = 12/29 (41%), Positives = 19/29 (65%)
Query: 601 EKGDKEIIKLAVMNEVKIYFRPEFINRID 629
E DK IIK A+ N +K+ +RP + ++D
Sbjct: 117 ENKDKNIIKFALQNRIKLIYRPPGVQKVD 145
>gnl|CDD|215629 PLN03200, PLN03200, cellulose synthase-interactive protein;
Provisional.
Length = 2102
Score = 32.8 bits (75), Expect = 1.3
Identities = 25/122 (20%), Positives = 47/122 (38%), Gaps = 14/122 (11%)
Query: 55 RAIQVLQRRSKNNPVLIGEPGVGKTAIVEGLAQRIINGEVPNSLLSKKILLLDIALLLAG 114
+AI++L R ++ PV++G+ + + LA RIIN ++ + ALL+
Sbjct: 850 KAIEILSRLCRDQPVVLGDLIANASKCISSLADRIINSSSL------EVKIGGTALLICA 903
Query: 115 TKYRGEFEDRLKKILKEISNNQKDIIIFIDELHTMIGTGKVEGSIDAGNMLKPELSRGEL 174
K E R + E + + + I L M+ + S+ + P
Sbjct: 904 AK-----EHRQLVM--EALDESGYLKLLIQALVDMLKQNSKKESLSIE-IQTPRGFLESN 955
Query: 175 HC 176
Sbjct: 956 LF 957
>gnl|CDD|226859 COG4452, CreD, Inner membrane protein involved in colicin E2
resistance [Defense mechanisms].
Length = 443
Score = 32.4 bits (74), Expect = 1.3
Identities = 25/77 (32%), Positives = 36/77 (46%), Gaps = 7/77 (9%)
Query: 39 RLGKLDPVIGRDDEIRRAIQVLQRRSKNNPVLIGEPGVGKTAIVEGLAQRIINGEVPNSL 98
LGK V+ D R I V++ S N L EPG+ +G ++ +P S
Sbjct: 139 TLGKPFLVLSIGDA--RGIGVVKAPSVNGTALTFEPGIRLEQSGQG-----VHIPLPESD 191
Query: 99 LSKKILLLDIALLLAGT 115
K+ L DIAL L+G+
Sbjct: 192 WRKQKLDFDIALSLSGS 208
>gnl|CDD|237873 PRK14969, PRK14969, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 527
Score = 32.4 bits (74), Expect = 1.3
Identities = 16/49 (32%), Positives = 29/49 (59%), Gaps = 8/49 (16%)
Query: 443 VGQDEAISAVSNAIRRSRSGLSDAKRPYGSFMFLGPTGVGKTELCKTLS 491
VGQ+ + A++NA+ + +R + +++F G GVGKT L + L+
Sbjct: 19 VGQEHVVRALTNALEQ--------QRLHHAYLFTGTRGVGKTTLARILA 59
>gnl|CDD|237576 PRK13979, PRK13979, DNA topoisomerase IV subunit A; Provisional.
Length = 957
Score = 32.4 bits (74), Expect = 1.4
Identities = 37/120 (30%), Positives = 54/120 (45%), Gaps = 33/120 (27%)
Query: 255 KAIDLIDEAAAKI---KIEIDSKPEIMDK-----------LERRLIQLK-IEHEAIKREY 299
KAI ++DE I K + D+ +++K LE L +L +E A ++EY
Sbjct: 396 KAIGIMDEIIKTIRSSKSKKDASENLIEKFGFTDEQAEAILELMLYRLTGLEIVAFEKEY 455
Query: 300 DESSKKRLLLIKKEINKLEIKYANLEKIWKYEKTLIKDSQQIKEEIEKVRLKINKATRKS 359
E K LIKK L KI EK L+K IK+E+++V+ K R S
Sbjct: 456 KELEK----LIKK-----------LTKILSSEKELLK---VIKKELKEVKEKYGDERRTS 497
>gnl|CDD|131688 TIGR02640, gas_vesic_GvpN, gas vesicle protein GvpN. Members of
this family are the GvpN protein associated with the
production of gas vesicles produced in some prokaryotes
to give cells buoyancy. This family belongs to a larger
family of ATPases (pfam07728) [Cellular processes,
Other].
Length = 262
Score = 31.7 bits (72), Expect = 1.5
Identities = 27/141 (19%), Positives = 51/141 (36%), Gaps = 23/141 (16%)
Query: 445 QDEAISAVSNAIRRSRSGLSDAKRPYGSFMFLGPTGVGKTELCKTLSAC-------IFNN 497
+ +A+ V+ R+ L + P GP G GKT L ++ I +
Sbjct: 3 ETDAVKRVT---SRALRYL-KSGYP---VHLRGPAGTGKTTLAMHVARKRDRPVMLINGD 55
Query: 498 EESIIRIDMSEFIEKHSISRLIGAPPGYIGYEE-------GGYLTEIVRRKPYSLILLDE 550
E + + + E+ LT V R+ ++L+ DE
Sbjct: 56 AELTTSDLVGSYAGYTRKKVHDQFIHNVVKLEDIVRQNWVDNRLTLAV-REGFTLV-YDE 113
Query: 551 IEKANSDVFNILLQILDDGRL 571
++ + N+LL + ++G L
Sbjct: 114 FTRSKPETNNVLLSVFEEGVL 134
>gnl|CDD|130141 TIGR01069, mutS2, MutS2 family protein. Function of MutS2 is
unknown. It should not be considered a DNA mismatch
repair protein. It is likely a DNA mismatch binding
protein of unknown cellular function [DNA metabolism,
Other].
Length = 771
Score = 32.5 bits (74), Expect = 1.5
Identities = 53/272 (19%), Positives = 102/272 (37%), Gaps = 38/272 (13%)
Query: 121 FEDRLKKILKEISNNQKDIIIFIDELHTMIGTGKVEGSIDAGNMLKPELSRGELHCIGAT 180
F +K I +S ++ ++ DEL GT EGS A ++L+ L + + T
Sbjct: 386 FSGHMKNISAILSKTTENSLVLFDELGA--GTDPDEGSALAISILE-YLLKQNAQVLITT 442
Query: 181 TLNEYRQYIEKDAAFERRFQKILVEEPDIEETISILRGLQKKYEVHHGVEITDPAIVAAS 240
E + + + E D E L Y++ G+ P A
Sbjct: 443 HYKELKALMYNNEGVEN-----ASVLFDEET-------LSPTYKLLKGI----PGESYAF 486
Query: 241 ELSYRYISDRFMPDKAIDL-------IDEAAAKIKIEIDSKPEIMDKLERRLIQLKIEHE 293
E++ RY F+ ++A I+ K+ + + LE+ L + + +
Sbjct: 487 EIAQRYGIPHFIIEQAKTFYGEFKEEINVLIEKLSALEKELEQKNEHLEKLLKEQEKLKK 546
Query: 294 AIKREYDESSKKRLLLIKKEINKLEIKYANLEKIWKYEKTLIKDSQQIKEEIEKVRLKIN 353
+++E +E L ++ K A + K L K+ + I E++ KI+
Sbjct: 547 ELEQEMEE-----LKERERNKKLELEKEAQ-----EALKALKKEVESIIRELK--EKKIH 594
Query: 354 KATRKSDWQTVSKLKYGELNKLERILKEKSQK 385
KA + + KLK + ++ ++ K
Sbjct: 595 KAKEIKSIEDLVKLKETKQKIPQKPTNFQADK 626
>gnl|CDD|237874 PRK14971, PRK14971, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 614
Score = 32.1 bits (73), Expect = 1.5
Identities = 39/153 (25%), Positives = 60/153 (39%), Gaps = 50/153 (32%)
Query: 442 VVGQDEAISAVSNAIRRSRSGLSDAKRPYGSFMFLGPTGVGKT----------------- 484
VVGQ+ + + NAI ++ L+ A ++F GP GVGKT
Sbjct: 19 VVGQEALTTTLKNAIATNK--LAHA------YLFCGPRGVGKTTCARIFAKTINCQNLTA 70
Query: 485 --ELCKTLSACI-FNNEES--IIRIDMSEFIEKHSISRLIGAPPGYIGYEEGGYLTEIVR 539
E C +C+ FN + S I +D + I LI E VR
Sbjct: 71 DGEACNECESCVAFNEQRSYNIHELDAASNNSVDDIRNLI----------------EQVR 114
Query: 540 RKP----YSLILLDEIEKANSDVFNILLQILDD 568
P Y + ++DE+ + FN L+ L++
Sbjct: 115 IPPQIGKYKIYIIDEVHMLSQAAFNAFLKTLEE 147
>gnl|CDD|163659 cd07416, MPP_PP2B, PP2B, metallophosphatase domain. PP2B
(calcineurin) is a unique serine/threonine protein
phosphatase in its regulation by a second messenger
(calcium and calmodulin). PP2B is involved in many
biological processes including immune responses, the
second messenger cAMP pathway, sodium/potassium ion
transport in the nephron, cell cycle progression in
lower eukaryotes, cardiac hypertrophy, and memory
formation. PP2B is highly conserved from yeast to
humans, but is absent from plants. PP2B is a
heterodimer consisting of a catalytic subunit (CnA) and
a regulatory subunit (CnB); CnB contains four Ca2+
binding motifs referred to as EF hands. The PPP
(phosphoprotein phosphatase) family, to which PP2B
belongs, is one of two known protein phosphatase
families specific for serine and threonine. The PPP
family also includes: PP1, PP2A, PP4, PP5, PP6, PP7,
Bsu1, RdgC, PrpE, PrpA/PrpB, and ApA4 hydrolase. The PPP
catalytic domain is defined by three conserved motifs
(-GDXHG-, -GDXVDRG- and -GNHE-). The PPP enzyme family
is ancient with members found in all eukaryotes, and in
most bacterial and archeal genomes. Dephosphorylation
of phosphoserines and phosphothreonines on target
proteins plays a central role in the regulation of many
cellular processes. PPPs belong to the
metallophosphatase (MPP) superfamily. MPPs are
functionally diverse, but all share a conserved domain
with an active site consisting of two metal ions
(usually manganese, iron, or zinc) coordinated with
octahedral geometry by a cage of histidine, aspartate,
and asparagine residues. The MPP superfamily includes:
Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat
debranching enzymes, YfcE-like phosphodiesterases,
purple acid phosphatases (PAPs), YbbF-like
UDP-2,3-diacylglucosamine hydrolases, and acid
sphingomyelinases (ASMases). The conserved domain is a
double beta-sheet sandwich with a di-metal active site
made up of residues located at the C-terminal side of
the sheets. This domain is thought to allow for
productive metal coordination.
Length = 305
Score = 31.9 bits (73), Expect = 1.6
Identities = 25/106 (23%), Positives = 49/106 (46%), Gaps = 19/106 (17%)
Query: 705 KSPEAN-FIFLGDLINKGPQSLDTLRMVYSMR-NYAKIVL---GNHEIHLLDVLININK- 758
SP ++FLGD +++G S++ + +++++ Y K + GNHE L +
Sbjct: 66 GSPANTRYLFLGDYVDRGYFSIECVLYLWALKILYPKTLFLLRGNHECRHLTEYFTFKQE 125
Query: 759 ---KSKLDTFDDILDAPDKKKLVSWLRTQPLA-IYYKKYLMIHAGV 800
K +D ++A D PLA + +++L +H G+
Sbjct: 126 CKIKYSERVYDACMEAFD---------CLPLAALMNQQFLCVHGGL 162
>gnl|CDD|224140 COG1219, ClpX, ATP-dependent protease Clp, ATPase subunit
[Posttranslational modification, protein turnover,
chaperones].
Length = 408
Score = 31.8 bits (73), Expect = 1.6
Identities = 19/56 (33%), Positives = 31/56 (55%), Gaps = 6/56 (10%)
Query: 442 VVGQDEA---IS-AVSNAIRRSRSGLSDAKRPYG--SFMFLGPTGVGKTELCKTLS 491
V+GQ++A +S AV N +R + + + + +GPTG GKT L +TL+
Sbjct: 63 VIGQEQAKKVLSVAVYNHYKRLNNKEDNDDVELSKSNILLIGPTGSGKTLLAQTLA 118
>gnl|CDD|227278 COG4942, COG4942, Membrane-bound metallopeptidase [Cell division
and chromosome partitioning].
Length = 420
Score = 32.0 bits (73), Expect = 1.7
Identities = 20/93 (21%), Positives = 33/93 (35%), Gaps = 10/93 (10%)
Query: 276 EIMDKLERRLIQLKIEHEAIKREYDE---------SSKKRLLLIKKEINKLEIKY-ANLE 325
E +D L+ L QL I E E + + +L + +E K + + L
Sbjct: 161 ERIDALKATLKQLAAVRAEIAAEQAELTTLLSEQRAQQAKLAQLLEERKKTLAQLNSELS 220
Query: 326 KIWKYEKTLIKDSQQIKEEIEKVRLKINKATRK 358
K + L + ++K EI KA
Sbjct: 221 ADQKKLEELRANESRLKNEIASAEAAAAKAREA 253
>gnl|CDD|220402 pfam09787, Golgin_A5, Golgin subfamily A member 5. Members of this
family of proteins are involved in maintaining Golgi
structure. They stimulate the formation of Golgi stacks
and ribbons, and are involved in intra-Golgi retrograde
transport. Two main interactions have been
characterized: one with RAB1A that has been activated by
GTP-binding and another with isoform CASP of CUTL1.
Length = 509
Score = 32.1 bits (73), Expect = 1.8
Identities = 25/126 (19%), Positives = 49/126 (38%), Gaps = 20/126 (15%)
Query: 281 LERRLIQLKIEHEAIKREYDESSKKRLLLIKKEINKLEIKYANLEKIWKYEKTLIKDSQQ 340
L+ +L+ L A+KR D + +L+ K KLEI + L + + L K Q+
Sbjct: 158 LQDKLLLLD---AAVKRH-DGNVITAVLIFLKRTLKLEILFQELAERQTALRHLSKHLQE 213
Query: 341 IKEEIEKVRLKINKATRKSDWQTVSKLKYGELNKLERILKEKSQKDIQLPNNANKFTLLK 400
E + ++L + + + +Y ++K+ + +Q + LK
Sbjct: 214 EGELQQLLKL----LRAEGESEKQELQQY----------RQKAHRILQSKE--KRINFLK 257
Query: 401 TKVGSE 406
E
Sbjct: 258 EGCLFE 263
>gnl|CDD|237871 PRK14965, PRK14965, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 576
Score = 32.0 bits (73), Expect = 1.8
Identities = 15/42 (35%), Positives = 19/42 (45%), Gaps = 8/42 (19%)
Query: 443 VGQDEAISAVSNAIRRSRSGLSDAKRPYGSFMFLGPTGVGKT 484
GQ+ + NAI D R +F+F G GVGKT
Sbjct: 19 TGQEHVSRTLQNAI--------DTGRVAHAFLFTGARGVGKT 52
>gnl|CDD|153307 cd07623, BAR_SNX1_2, The Bin/Amphiphysin/Rvs (BAR) domain of
Sorting Nexins 1 and 2. BAR domains are dimerization,
lipid binding and curvature sensing modules found in
many different proteins with diverse functions. Sorting
nexins (SNXs) are Phox homology (PX) domain containing
proteins that are involved in regulating membrane
traffic and protein sorting in the endosomal system.
SNXs differ from each other in their lipid-binding
specificity, subcellular localization and specific
function in the endocytic pathway. A subset of SNXs also
contain BAR domains. The PX-BAR structural unit
determines the specific membrane targeting of SNXs. This
subfamily consists of SNX1, SNX2, and similar proteins.
SNX1 and SNX2 are components of the retromer complex, a
membrane coat multimeric complex required for endosomal
retrieval of lysosomal hydrolase receptors to the Golgi.
The retromer consists of a cargo-recognition subcomplex
and a subcomplex formed by a dimer of sorting nexins
(SNX1 and/or SNX2), which ensures efficient cargo
sorting by facilitating proper membrane localization of
the cargo-recognition subcomplex. BAR domains form
dimers that bind to membranes, induce membrane bending
and curvature, and may also be involved in
protein-protein interactions.
Length = 224
Score = 31.5 bits (72), Expect = 1.8
Identities = 23/85 (27%), Positives = 46/85 (54%), Gaps = 6/85 (7%)
Query: 265 AKIKIEIDSKPEIMDKLERRLIQLKIEHEAIKREYDESSKKRLLLIKKEINKLEIKYANL 324
AK K+E+ + + +D+ ++ + + + + + ++E++E SK IKKEI + E
Sbjct: 138 AKAKLELSGRTDKLDQAQQEIKEWEAKVDRGQKEFEEISK----TIKKEIERFEKNRVKD 193
Query: 325 EK--IWKYEKTLIKDSQQIKEEIEK 347
K I KY ++L+ QQ+ + E
Sbjct: 194 FKDIIIKYLESLLNTQQQLIKYWEA 218
>gnl|CDD|233067 TIGR00641, acid_CoA_mut_N, methylmalonyl-CoA mutase N-terminal
domain. Methylmalonyl-CoA mutase (EC 5.4.99.2)
catalyzes a reversible isomerization between
L-methylmalonyl-CoA and succinyl-CoA. The enzyme uses an
adenosylcobalamin cofactor. It may be a homodimer, as in
mitochondrion, or a heterodimer with partially
homologous beta chain that does not bind the
adenosylcobalamin cofactor, as in Propionibacterium
freudenreichii. The most similar archaeal sequences are
separate chains, such as AF2215 abd AF2219 of
Archaeoglobus fulgidus, that correspond roughly to the
first 500 and last 130 residues, respectively of known
methylmalonyl-CoA mutases. This model describes the
N-terminal domain subfamily. In a neighbor-joining tree,
AF2215 branches with a bacterial isobutyryl-CoA mutase,
which is also the same length. Scoring between the noise
and trusted cutoffs are the non-catalytic, partially
homologous beta chains from certain heterodimeric
examples of 5.4.99.2.
Length = 524
Score = 31.7 bits (72), Expect = 2.0
Identities = 32/160 (20%), Positives = 67/160 (41%), Gaps = 36/160 (22%)
Query: 190 EKDAAFERRFQKILVEEPDIEETISILRGLQKKYEVHHGVEITDPAIVAASELSYRYISD 249
+ A R Q+I+ EE + I L G SY Y+
Sbjct: 341 DFSARIARNTQQIIQEESGVTRVIDPLGG------------------------SY-YV-- 373
Query: 250 RFMPDKAIDLIDEAAAKIKIEIDSKPEIMDKLERRLIQLKIEHEAIKREYDESSKKRLLL 309
+ D I E A K EI+ + +ER + +L+IE A + + S +++++
Sbjct: 374 ----EWLTDDIYERAWKYIQEIEEMGGMAKAIERGIPKLRIEEAAARTQARIDSGRQVIV 429
Query: 310 IKKEINKLEIKYANLEKIWKYEKTLIKDSQQIKEEIEKVR 349
+NK +++ + ++ K + + +++ Q +++K+R
Sbjct: 430 ---GVNKYQLEEEDEVEVLKVDNSSVREEQ--IAKLKKLR 464
>gnl|CDD|237866 PRK14952, PRK14952, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 584
Score = 31.8 bits (72), Expect = 2.1
Identities = 17/53 (32%), Positives = 27/53 (50%), Gaps = 8/53 (15%)
Query: 442 VVGQDEAISAVSNAIRRSRSGLSDAKRPYGSFMFLGPTGVGKTELCKTLSACI 494
VVGQ+ +S+A+ DA R +++F GP G GKT + L+ +
Sbjct: 15 VVGQEHVTEPLSSAL--------DAGRINHAYLFSGPRGCGKTSSARILARSL 59
>gnl|CDD|236153 PRK08116, PRK08116, hypothetical protein; Validated.
Length = 268
Score = 31.1 bits (71), Expect = 2.1
Identities = 33/135 (24%), Positives = 55/135 (40%), Gaps = 32/135 (23%)
Query: 473 FMFLGPTGVGKTELCKTLSACIFNN-EESIIRIDMSEFIEKHSISRLIGAPPGYIGYEEG 531
+ G G GKT L+ACI N E + + F + ++R+ +E
Sbjct: 117 LLLWGSVGTGKT----YLAACIANELIEKGVPVIFVNFPQ--LLNRIKSTYKSSGKEDE- 169
Query: 532 GYLTEIVRR-KPYSLILLDE--IEKANS----DVFNILLQILDDGRLTDNRGRTINFRNT 584
EI+R L++LD+ E+ V+NI+ D+R R T
Sbjct: 170 ---NEIIRSLVNADLLILDDLGAERDTEWAREKVYNII----------DSRYR--KGLPT 214
Query: 585 IIVMTSNLGSDKIKE 599
I+ T+NL +++K
Sbjct: 215 IV--TTNLSLEELKN 227
>gnl|CDD|172375 PRK13851, PRK13851, type IV secretion system protein VirB11;
Provisional.
Length = 344
Score = 31.4 bits (71), Expect = 2.1
Identities = 29/85 (34%), Positives = 40/85 (47%), Gaps = 8/85 (9%)
Query: 472 SFMFLGPTGVGKTELCKTLSACIFNNEESIIRIDMSEFIEKH-SISRLI----GAPPGYI 526
+ + GPTG GKT + KTL + I E I D E + H + RL+ GA G +
Sbjct: 164 TMLLCGPTGSGKTTMSKTLISAIPPQERLITIEDTLELVIPHENHVRLLYSKNGAGLGAV 223
Query: 527 GYEEGGYLTEIVRRKPYSLILLDEI 551
E L +R +P ILL E+
Sbjct: 224 TAEH--LLQASLRMRP-DRILLGEM 245
>gnl|CDD|188306 TIGR03319, RNase_Y, ribonuclease Y. Members of this family are
RNase Y, an endoribonuclease. The member from Bacillus
subtilis, YmdA, has been shown to be involved in
turnover of yitJ riboswitch [Transcription, Degradation
of RNA].
Length = 514
Score = 31.8 bits (73), Expect = 2.2
Identities = 24/107 (22%), Positives = 48/107 (44%), Gaps = 13/107 (12%)
Query: 255 KAIDLIDEA-----AAKIKIEIDSKPEIMDKLERRLIQLKIEHEAIKREYDESSKKRLLL 309
A +I+EA K + +++K E+ ++ ++E E +R + +R LL
Sbjct: 33 LAKRIIEEAKKEAETLKKEALLEAKEEVHK------LRAELERELKERRNELQRLERRLL 86
Query: 310 IKKEI--NKLEIKYANLEKIWKYEKTLIKDSQQIKEEIEKVRLKINK 354
++E K+E E + K EK L + + E+ E++ I +
Sbjct: 87 QREETLDRKMESLDKKEENLEKKEKELSNKEKNLDEKEEELEELIAE 133
>gnl|CDD|131290 TIGR02236, recomb_radA, DNA repair and recombination protein RadA.
This family consists exclusively of archaeal RadA
protein, a homolog of bacterial RecA (TIGR02012),
eukaryotic RAD51 (TIGR02239), and archaeal RadB
(TIGR02237). This protein is involved in DNA repair and
recombination. The member from Pyrococcus horikoshii
contains an intein [DNA metabolism, DNA replication,
recombination, and repair].
Length = 310
Score = 31.3 bits (71), Expect = 2.3
Identities = 8/33 (24%), Positives = 20/33 (60%)
Query: 595 DKIKEMEKGDKEIIKLAVMNEVKIYFRPEFINR 627
+K +++ K +KL +++ + +FR E++ R
Sbjct: 180 EKAEDLIKELNNPVKLLIVDSLTSHFRAEYVGR 212
>gnl|CDD|151168 pfam10662, PduV-EutP, Ethanolamine utilisation - propanediol
utilisation. Members of this family function in
ethanolamine and propanediol degradation pathways,
however the exact roles of these proteins is poorly
understood.
Length = 143
Score = 30.3 bits (69), Expect = 2.3
Identities = 8/18 (44%), Positives = 12/18 (66%)
Query: 474 MFLGPTGVGKTELCKTLS 491
M +G +G GKT L + L+
Sbjct: 5 MLIGRSGCGKTTLTQALN 22
>gnl|CDD|237192 PRK12758, PRK12758, DNA topoisomerase IV subunit A; Provisional.
Length = 869
Score = 31.5 bits (72), Expect = 2.3
Identities = 27/106 (25%), Positives = 45/106 (42%), Gaps = 10/106 (9%)
Query: 195 FERRFQKILVEEPDIEETISILRGLQKKYEVHHGVEITDPAIVAASELSYRYISDRFMPD 254
E R K + E E I + + ++ E+T+ IV +E+ + IS +F D
Sbjct: 370 IEERIYKEIEEAETWEAVIEAIDKGLEPFKKQFIREVTEDDIVRLTEIKIKRIS-KFDSD 428
Query: 255 KAIDLIDEAAAKIKIEIDSKPEIMDKLERRLIQLKIEH-EAIKREY 299
KA +LI A+I E+ L L I + +K++Y
Sbjct: 429 KADELIARLEAEIA-------EVKHHLA-HLTDYAIAYFTNLKKKY 466
>gnl|CDD|221417 pfam12092, DUF3568, Protein of unknown function (DUF3568). This
family of proteins is functionally uncharacterized. This
protein is found in bacteria. Proteins in this family
are about 130 amino acids in length.
Length = 131
Score = 30.1 bits (68), Expect = 2.4
Identities = 22/88 (25%), Positives = 37/88 (42%), Gaps = 15/88 (17%)
Query: 524 GYIGYEEGGYLTEIVRRKPYSLILLDEIEKANSDVFNILLQILDDGRLTDNRGRTINFRN 583
G + Y G Y+TE+ Y+ V+N L+ + DG D +G T N ++
Sbjct: 34 GTVAYVNGEYITEL----NYNF----------RSVYNATLKAIQDGNTFDVKGNTYNSKD 79
Query: 584 TIIVMTSNLGSDKIK-EMEKGDKEIIKL 610
I ++ + SD +EK K+
Sbjct: 80 ATITASNKIDSDSFSIRIEKLTDNATKV 107
>gnl|CDD|202101 pfam02050, FliJ, Flagellar FliJ protein.
Length = 122
Score = 29.9 bits (68), Expect = 2.4
Identities = 25/112 (22%), Positives = 49/112 (43%), Gaps = 8/112 (7%)
Query: 279 DKLERRLIQLKIEHEAIKREYDESSKKRLLLIKKEINKLEIKYANLEKIWK-YEKTLIKD 337
DK R L + + E E + + +E + RL ++ + A + ++ + L +
Sbjct: 1 DKAARNLAEAQQELEQAEEKLEELQQYRLEYRQQLSGSGQGISAAELRNYQAFISALDEA 60
Query: 338 SQQIKEEIEKVRLKINKATRKSDWQTVSKLKYGELNKLERILKEKSQKDIQL 389
Q ++E+E+ ++ +A + WQ E KLE L E+ +K Q
Sbjct: 61 IAQQQQELEQAEKQVEQA--REQWQ----EANQERKKLE-KLLEREKKKEQK 105
>gnl|CDD|226372 COG3854, SpoIIIAA, ncharacterized protein conserved in bacteria
[Function unknown].
Length = 308
Score = 31.3 bits (71), Expect = 2.5
Identities = 17/51 (33%), Positives = 30/51 (58%), Gaps = 2/51 (3%)
Query: 57 IQVLQRRSKNNPVLIGEPGVGKTAIVEGLAQRIINGEVPNSLLSKKILLLD 107
I+ L + N ++IG P VGKT ++ +A+ + +G N L KK+ ++D
Sbjct: 129 IKDLYQNGWLNTLIIGPPQVGKTTLLRDIARLLSDGI--NQFLPKKVGIID 177
>gnl|CDD|222165 pfam13481, AAA_25, AAA domain. This AAA domain is found in a wide
variety of presumed DNA repair proteins.
Length = 154
Score = 30.3 bits (69), Expect = 2.5
Identities = 19/87 (21%), Positives = 38/87 (43%), Gaps = 11/87 (12%)
Query: 69 VLIGEPGVGKTAIVEGLAQRIINGE---VPNSLLSKKILLLDIALLLAGTKYRGEFEDRL 125
+L G PG GK+ + LA + G P + ++L LD ++ RL
Sbjct: 37 LLAGAPGTGKSTLALDLAAAVATGRPFLGPFPVEPGRVLYLD----GEDSEAG--LRRRL 90
Query: 126 KKILKEISNNQKDI-IIFIDELHTMIG 151
+ + + + + ++ ID L +++G
Sbjct: 91 RALGEAL-EEIEGPDLVVIDPLASLLG 116
>gnl|CDD|206640 cd00154, Rab, Ras-related in brain (Rab) family of small guanosine
triphosphatases (GTPases). Rab GTPases form the largest
family within the Ras superfamily. There are at least 60
Rab genes in the human genome, and a number of Rab
GTPases are conserved from yeast to humans. Rab GTPases
are small, monomeric proteins that function as molecular
switches to regulate vesicle trafficking pathways. The
different Rab GTPases are localized to the cytosolic
face of specific intracellular membranes, where they
regulate distinct steps in membrane traffic pathways. In
the GTP-bound form, Rab GTPases recruit specific sets of
effector proteins onto membranes. Through their
effectors, Rab GTPases regulate vesicle formation,
actin- and tubulin-dependent vesicle movement, and
membrane fusion. GTPase activating proteins (GAPs)
interact with GTP-bound Rab and accelerate the
hydrolysis of GTP to GDP. Guanine nucleotide exchange
factors (GEFs) interact with GDP-bound Rabs to promote
the formation of the GTP-bound state. Rabs are further
regulated by guanine nucleotide dissociation inhibitors
(GDIs), which mask C-terminal lipid binding and promote
cytosolic localization. While most unicellular organisms
possess 5-20 Rab members, several have been found to
possess 60 or more Rabs; for many of these Rab isoforms,
homologous proteins are not found in other organisms.
Most Rab GTPases contain a lipid modification site at
the C-terminus, with sequence motifs CC, CXC, or CCX.
Lipid binding is essential for membrane attachment, a
key feature of most Rab proteins. Since crystal
structures often lack C-terminal residues, the lipid
modification site is not available for annotation in
many of the CDs in the hierarchy, but is included where
possible.
Length = 159
Score = 30.5 bits (70), Expect = 2.5
Identities = 11/32 (34%), Positives = 19/32 (59%), Gaps = 4/32 (12%)
Query: 69 VLIGEPGVGKTAIVEGLAQRIINGEVPNSLLS 100
VLIG+ GVGKT+++ R ++ + + S
Sbjct: 4 VLIGDSGVGKTSLL----LRFVDNKFSENYKS 31
>gnl|CDD|234232 TIGR03499, FlhF, flagellar biosynthetic protein FlhF. [Cellular
processes, Chemotaxis and motility].
Length = 283
Score = 31.1 bits (71), Expect = 2.7
Identities = 9/20 (45%), Positives = 10/20 (50%)
Query: 465 DAKRPYGSFMFLGPTGVGKT 484
G +GPTGVGKT
Sbjct: 190 PILERGGVIALVGPTGVGKT 209
>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 = 30.2 bits (68), Expect = 2.7
Identities = 22/112 (19%), Positives = 37/112 (33%), Gaps = 18/112 (16%)
Query: 70 LIGEPGVGKTAIVEGLAQRI-----------INGEVPN-----SLLSKKILLLDIALLLA 113
+ G G GKT + LA I I E+ S K L ++ ++ A
Sbjct: 4 VFGPTGSGKTTLALQLALNIATKGGKVVYVDIEEEIEELTERLIGESLKGALDNLIIVFA 63
Query: 114 GTKYRGEFEDRLKKILKEISNNQKDIIIFIDELHTMIGTGKVEGSIDAGNML 165
RL + + D +I +DEL ++ + G +
Sbjct: 64 TAD--DPAAARLLSKAERLRERGGDDLIILDELTRLVRALREIREGYPGELD 113
Score = 29.8 bits (67), Expect = 3.9
Identities = 25/89 (28%), Positives = 33/89 (37%), Gaps = 14/89 (15%)
Query: 477 GPTGVGKTELCKTLSACIFNNEESIIRIDMSEFIE----KHSISRLIGAPPGYIGYEEGG 532
GPTG GKT L L+ I ++ +D+ E IE + L GA I
Sbjct: 6 GPTGSGKTTLALQLALNIATKGGKVVYVDIEEEIEELTERLIGESLKGALDNLIIVFATA 65
Query: 533 YLTEIVR----------RKPYSLILLDEI 551
R R LI+LDE+
Sbjct: 66 DDPAAARLLSKAERLRERGGDDLIILDEL 94
>gnl|CDD|225224 COG2348, COG2348, Peptidoglycan interpeptide bridge formation
enzyme [Cell wall/membrane/envelope biogenesis].
Length = 418
Score = 31.2 bits (71), Expect = 2.7
Identities = 26/141 (18%), Positives = 49/141 (34%), Gaps = 14/141 (9%)
Query: 271 IDSKPEIMDKLERRLI-----QLKIEHEAIKREYDESSKKRLLLIKKEINKLE-IKYANL 324
D EI++ I L +H + D+S + R + +K E +
Sbjct: 115 FDLGGEIIENYNNLAIIKLLKDLGYKHSGFTKGLDDSIQPRWHSVLDLKDKTEDQLLKSF 174
Query: 325 EKIWKY-----EKTLIKDSQQIKEEIEKVRLKINKATRKSDWQTVSKLKYGELNKLERIL 379
K + EK +K +++ E + ++ K T + T L Y E I
Sbjct: 175 SKKTRRNIKKAEKKGVKV-RRLSREELDLFSELMKKTSERKGFTDRSLSYYE--NFYDIY 231
Query: 380 KEKSQKDIQLPNNANKFTLLK 400
K+K++ + + L
Sbjct: 232 KDKAELPLAYLDLDEYLKKLN 252
>gnl|CDD|214693 smart00488, DEXDc2, DEAD-like helicases superfamily.
Length = 289
Score = 30.8 bits (70), Expect = 2.8
Identities = 19/67 (28%), Positives = 27/67 (40%), Gaps = 9/67 (13%)
Query: 126 KKILKEISNNQKDIIIFIDELHTMIGTGKVEGSIDAGNMLKPELSRGELHCIGATTLNEY 185
KI + +S KD I+ DE H + + L ELSR L + +Y
Sbjct: 225 PKIRQALSIELKDSIVIFDEAHNLDNV--------CISALSSELSRRSL-ERAHKNIKKY 275
Query: 186 RQYIEKD 192
+ IEK
Sbjct: 276 FERIEKI 282
>gnl|CDD|234034 TIGR02858, spore_III_AA, stage III sporulation protein AA. Members
of this protein are the stage III sporulation protein
AA, encoded by one of several genes in the spoIIIA
locus. It seems that this protein is found in a species
if and only if that species is capable of endospore
formation [Cellular processes, Sporulation and
germination].
Length = 270
Score = 30.8 bits (70), Expect = 2.9
Identities = 13/42 (30%), Positives = 22/42 (52%)
Query: 66 NNPVLIGEPGVGKTAIVEGLAQRIINGEVPNSLLSKKILLLD 107
N ++I P GKT ++ LA+ + G L KK+ ++D
Sbjct: 112 LNTLIISPPQCGKTTLLRDLARILSTGISQLGLRGKKVGIVD 153
>gnl|CDD|233119 TIGR00763, lon, ATP-dependent protease La. This protein is induced
by heat shock and other stresses in E. coli, B.
subtilis, and other species. The yeast member,
designated PIM1, is located in the mitochondrial matrix,
required for mitochondrial function, and also induced by
heat shock [Protein fate, Degradation of proteins,
peptides, and glycopeptides].
Length = 775
Score = 31.5 bits (72), Expect = 2.9
Identities = 32/104 (30%), Positives = 49/104 (47%), Gaps = 23/104 (22%)
Query: 475 FLGPTGVGKTELCKTLSACIFNNEESIIRI------DMSEFIEKHSISRLIGAPPGYIGY 528
+GP GVGKT L K+++ + +R D +E I H + +GA PG I
Sbjct: 352 LVGPPGVGKTSLGKSIAKAL---NRKFVRFSLGGVRDEAE-IRGHRRT-YVGAMPGRI-- 404
Query: 529 EEGGYLTEIVRRKPYS-LILLDEIEKANSDV----FNILLQILD 567
+ + + K + L LLDEI+K S + LL++LD
Sbjct: 405 -----IQGLKKAKTKNPLFLLDEIDKIGSSFRGDPASALLEVLD 443
>gnl|CDD|206741 cd09914, RocCOR, Ras of complex proteins (Roc) C-terminal of Roc
(COR) domain family. RocCOR (or Roco) protein family is
characterized by a superdomain containing a Ras-like
GTPase domain, called Roc (Ras of complex proteins), and
a characteristic second domain called COR (C-terminal of
Roc). A kinase domain and diverse regulatory domains are
also often found in Roco proteins. Their functions are
diverse; in Dictyostelium discoideum, which encodes 11
Roco proteins, they are involved in cell division,
chemotaxis and development, while in human, where 4 Roco
proteins (LRRK1, LRRK2, DAPK1, and MFHAS1) are encoded,
these proteins are involved in epilepsy and cancer.
Mutations in LRRK2 (leucine-rich repeat kinase 2) are
known to cause familial Parkinson's disease.
Length = 161
Score = 30.0 bits (68), Expect = 3.0
Identities = 15/37 (40%), Positives = 22/37 (59%), Gaps = 1/37 (2%)
Query: 474 MFLGPTGVGKTELCKTLSACIFN-NEESIIRIDMSEF 509
M +G GVGKT LCK L F+ +E S I++ ++
Sbjct: 5 MLVGQGGVGKTSLCKQLIGEKFDGDESSTHGINVQDW 41
>gnl|CDD|100796 PRK01156, PRK01156, chromosome segregation protein; Provisional.
Length = 895
Score = 31.4 bits (71), Expect = 3.2
Identities = 35/152 (23%), Positives = 65/152 (42%), Gaps = 6/152 (3%)
Query: 257 IDLIDEAAAKIKIEIDS-KPEI--MDKLERRLIQLKIEHEAIKREYDESSKKRLLLIKKE 313
I+ ++ K+K ID + EI +D LE +L +E E IK++ + K + KE
Sbjct: 161 INSLERNYDKLKDVIDMLRAEISNIDYLEEKLKSSNLELENIKKQIADDEKS-HSITLKE 219
Query: 314 INKLEIKYANLEKIWKYEKTLIKDSQQIKEEIEKVRLKINKATRKSDWQTVSKLKYGELN 373
I +L I+Y N + K+ + + +++ + +I A + Y EL
Sbjct: 220 IERLSIEYNNAMDDYNNLKSALNELSSLEDMKNRYESEIKTAESDLSMELEKNNYYKELE 279
Query: 374 KLERILKEKSQKDIQLPNNANKFTLLKTKVGS 405
ER +K + + N N + K + +
Sbjct: 280 --ERHMKIINDPVYKNRNYINDYFKYKNDIEN 309
>gnl|CDD|237867 PRK14953, PRK14953, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 486
Score = 30.9 bits (70), Expect = 3.4
Identities = 17/52 (32%), Positives = 29/52 (55%), Gaps = 8/52 (15%)
Query: 440 KRVVGQDEAISAVSNAIRRSRSGLSDAKRPYGSFMFLGPTGVGKTELCKTLS 491
K V+GQ+ + + NA++ R +S A ++F GP G GKT + + L+
Sbjct: 16 KEVIGQEIVVRILKNAVKLQR--VSHA------YIFAGPRGTGKTTIARILA 59
>gnl|CDD|222194 pfam13521, AAA_28, AAA domain.
Length = 162
Score = 29.8 bits (68), Expect = 3.4
Identities = 10/20 (50%), Positives = 13/20 (65%)
Query: 69 VLIGEPGVGKTAIVEGLAQR 88
V+ G P GKT ++E LA R
Sbjct: 3 VITGGPSTGKTTLLEALAAR 22
>gnl|CDD|237862 PRK14948, PRK14948, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 620
Score = 31.1 bits (71), Expect = 3.5
Identities = 20/55 (36%), Positives = 29/55 (52%), Gaps = 15/55 (27%)
Query: 442 VVGQDEAISA-VSNAIRRSRSGLSDAKRPYGSFMFLGPTGVGKTELCKTLSACIF 495
+VGQ EAI+ + NA+ +R ++ A ++F GP G GKT SA I
Sbjct: 18 LVGQ-EAIATTLKNALISNR--IAPA------YLFTGPRGTGKTS-----SARIL 58
>gnl|CDD|183702 PRK12723, PRK12723, flagellar biosynthesis regulator FlhF;
Provisional.
Length = 388
Score = 31.0 bits (70), Expect = 3.5
Identities = 30/99 (30%), Positives = 45/99 (45%), Gaps = 12/99 (12%)
Query: 473 FMFLGPTGVGKTELCKTLSACIFNNEES------IIRIDMSEFIEKHSISR---LIGAPP 523
F+ +GPTGVGKT L+A N + II ID K I ++G P
Sbjct: 177 FILVGPTGVGKTTTIAKLAAIYGINSDDKSLNIKIITIDNYRIGAKKQIQTYGDIMGIPV 236
Query: 524 GYI-GYEEGGYLTEIVRRKPYSLILLDEIEKANSDVFNI 561
I +++ EI + K + L+L+D I K+ D +
Sbjct: 237 KAIESFKD--LKEEITQSKDFDLVLVDTIGKSPKDFMKL 273
>gnl|CDD|238549 cd01129, PulE-GspE, PulE/GspE The type II secretory pathway is the
main terminal branch of the general secretory pathway
(GSP). It is responsible for the export the majority of
Gram-negative bacterial exoenzymes and toxins. PulE is a
cytoplasmic protein of the GSP, which contains an ATP
binding site and a tetracysteine motif. This subgroup
also includes PillB and HofB.
Length = 264
Score = 30.7 bits (70), Expect = 3.5
Identities = 11/29 (37%), Positives = 17/29 (58%), Gaps = 3/29 (10%)
Query: 466 AKRPYGSFMFLGPTGVGKTELCKTLSACI 494
++P+G + GPTG GKT TL + +
Sbjct: 76 LEKPHGIILVTGPTGSGKT---TTLYSAL 101
>gnl|CDD|221955 pfam13173, AAA_14, AAA domain. This family of domains contain a
P-loop motif that is characteristic of the AAA
superfamily.
Length = 127
Score = 29.4 bits (67), Expect = 3.6
Identities = 33/137 (24%), Positives = 57/137 (41%), Gaps = 30/137 (21%)
Query: 477 GPTGVGKTELCKTLSACIFNNEESIIRIDMSEF-IEKHSISRLIGAPPGYIGYEEGGYLT 535
GP VGKT L + + E+I+ I++ + + ++ L+ +L
Sbjct: 9 GPRQVGKTTLLLQFLKELLS--ENILYINLDDPRFLRLALLDLLEE-----------FLK 55
Query: 536 EIVRRKPYSLILLDEIEKANSDVFNILLQILDDGRLTDNRGRTINFRNTIIVMTSNLG-- 593
++ K Y + LDEI+K D + L ++ DDGR II+ S+
Sbjct: 56 LLLPGKKY--LFLDEIQKVP-DWEDALKRLYDDGRNLR-----------IILTGSSSLLL 101
Query: 594 SDKIKEMEKGDKEIIKL 610
S +I G E ++L
Sbjct: 102 SKEIATSLAGRAEELEL 118
Score = 29.1 bits (66), Expect = 5.0
Identities = 17/79 (21%), Positives = 32/79 (40%), Gaps = 14/79 (17%)
Query: 69 VLIGEPGVGKTAIVEGLAQRIINGEVPNSLLSKKILLLDIALLLAGTKYRGEFEDRLKKI 128
V+ G VGKT ++ + LLS+ IL ++ L ++ L +
Sbjct: 6 VITGPRQVGKTTLLLQFLK---------ELLSENILYIN----LDDPRFLRLALLDLLEE 52
Query: 129 LKEISNNQKDIIIFIDELH 147
++ K +F+DE+
Sbjct: 53 FLKLLLPGKK-YLFLDEIQ 70
>gnl|CDD|240274 PTZ00112, PTZ00112, origin recognition complex 1 protein;
Provisional.
Length = 1164
Score = 31.1 bits (70), Expect = 3.7
Identities = 31/96 (32%), Positives = 49/96 (51%), Gaps = 10/96 (10%)
Query: 2 GIKNNSLNVNGKNILSQQDEEHIGYLKKYTIDLTEKA-RLGKLDPVIG----RDDEIRRA 56
K++ NV+ K+ + Q E + L + D T+KA R+ +LD V R+ EI+
Sbjct: 708 KKKSDPHNVDFKSFIKQDQENYYVNLLRNITDPTDKAIRMMQLDVVPKYLPCREKEIKEV 767
Query: 57 IQVLQ---RRSKNNPVLI--GEPGVGKTAIVEGLAQ 87
L+ ++S +N +L G PG GKTA V + Q
Sbjct: 768 HGFLESGIKQSGSNQILYISGMPGTGKTATVYSVIQ 803
>gnl|CDD|220745 pfam10422, LRS4, Monopolin complex subunit LRS4. Monopolin is a
protein complex, originally identified in Saccharomyces
cerevisiae, that is required for the segregation of
homologous centromeres to opposite poles of a dividing
cell during meiosis I. The orthologous complex in
Schizosaccharomyces pombe is not required for meiosis I
chromosome segregation, but is proposed to play a
similar physiological role in clamping microtubule
binding sites. In S.cerevisiae this subunit is called
LRS4, and in S. pombe it is known as Mde4.
Length = 211
Score = 30.4 bits (68), Expect = 3.8
Identities = 23/84 (27%), Positives = 36/84 (42%), Gaps = 4/84 (4%)
Query: 287 QLKIEHEAIKREYDESSKKRLLLIKKEINKLEIKYANLEKIWKYEK--TLIKDSQQIKEE 344
+++E I EYD S K L +K + + + E + + L D Q K+E
Sbjct: 9 DSVLDNERIYLEYDSSQKSFLGALKTNATQSDGEKLTDETLSLQRQINQLNSDLQLQKQE 68
Query: 345 IEKVRL--KINKATRKSDWQTVSK 366
EK+R K KA +S + K
Sbjct: 69 NEKLRKLNKTQKALLESKLSSKKK 92
>gnl|CDD|234007 TIGR02776, NHEJ_ligase_prk, DNA ligase D. Members of this protein
family are DNA ligases involved in the repair of DNA
double-stranded breaks by non-homologous end joining
(NHEJ). The system of the bacterial Ku protein
(TIGR02772) plus this DNA ligase is seen in about 20 %
of bacterial genomes to date and at least one archaeon
(Archeoglobus fulgidus). This model describes a central
and a C-terminal domain. These two domains may be
permuted, as in genus Mycobacterium, or divided into
tandem ORFs, and therefore not be identified by This
model. An additional N-terminal 3'-phosphoesterase (PE)
domain present in some but not all examples of this
ligase is not included in the seed alignment for this
model; This model models only the central ATP-dependent
ligase domain and the C-terminal polymerase domain. Most
examples of genes for this ligase are adjacent to the
gene for Ku [DNA metabolism, DNA replication,
recombination, and repair].
Length = 552
Score = 30.7 bits (70), Expect = 3.8
Identities = 19/72 (26%), Positives = 29/72 (40%), Gaps = 9/72 (12%)
Query: 165 LKPELSRGELHCIGATTLNEYRQYIEKDAAFER-RFQKILVEEPDIEETISILRGLQKK- 222
++P L E+ G T R+ A+F+ R K EE +E +K+
Sbjct: 221 VRPSL-VAEVEYAGITRDGILRE-----ASFKGLREDKP-AEEVTLETPQRHAAAKRKRS 273
Query: 223 YEVHHGVEITDP 234
+ GV IT P
Sbjct: 274 AALVAGVRITHP 285
>gnl|CDD|223357 COG0280, Pta, Phosphotransacetylase [Energy production and
conversion].
Length = 327
Score = 30.7 bits (70), Expect = 3.8
Identities = 24/102 (23%), Positives = 44/102 (43%), Gaps = 7/102 (6%)
Query: 34 LTEKARLGKLDPVI----GRDDEIRRAIQVLQRRSKNNPVLIGEPGVGKTAIVEGLAQRI 89
L E+AR K I G ++ + RA QVL + P+L+G P + + L +
Sbjct: 5 LFERAR--KAPKRIVLPEGEEERVLRAAQVLAKEGLAKPILVGRPEEIEEVA-KALGLDL 61
Query: 90 INGEVPNSLLSKKILLLDIALLLAGTKYRGEFEDRLKKILKE 131
E+ N L + + L K +G + +++++E
Sbjct: 62 DGIEIINPELDPERFEEYVDRLYELRKRKGVTPEDAQELVRE 103
>gnl|CDD|182043 PRK09716, PRK09716, hypothetical protein; Provisional.
Length = 395
Score = 30.8 bits (69), Expect = 3.9
Identities = 25/80 (31%), Positives = 39/80 (48%), Gaps = 8/80 (10%)
Query: 277 IMDKLERRLIQLKIEHEAIKREYDESSKKRLLLIKKEINKL---EIKYANLEKIWKYEKT 333
I+ + R + K+E+E K Y SSK I +N++ E+ + EKI Y
Sbjct: 256 IIKSIPRATLTDKLENELTKEIYKSSSK-----INNCLNRIKLPEMIDFSSEKIHDYIDI 310
Query: 334 LIKDSQQIKEEIEKVRLKIN 353
+I+D + IKE V +IN
Sbjct: 311 IIEDYENIKENAYLVIPQIN 330
>gnl|CDD|110677 pfam01695, IstB_IS21, IstB-like ATP binding protein. This protein
contains an ATP/GTP binding P-loop motif. It is found
associated with IS21 family insertion sequences. The
function of this protein is unknown, but it may perform
a transposase function.
Length = 178
Score = 29.9 bits (68), Expect = 3.9
Identities = 24/98 (24%), Positives = 41/98 (41%), Gaps = 15/98 (15%)
Query: 53 IRRAIQVLQR----RSKNNPVLIGEPGVGKTAIVEGLAQRIINGEVPNSLLSKKILLLDI 108
RR I L N +L+G PGVGKT + L + +L
Sbjct: 31 DRRLIAELAGLDWIEQAENLLLLGPPGVGKTHLACALGHQACR-------AGYSVLFTRT 83
Query: 109 ALLLAGTKYRGEFEDRLKKILKEISNNQKDIIIFIDEL 146
L+ K R + RL + L+ ++ + D++I +D++
Sbjct: 84 PDLVEQLK-RARGDGRLARTLQRLA--KADLLI-LDDI 117
>gnl|CDD|180607 PRK06526, PRK06526, transposase; Provisional.
Length = 254
Score = 30.2 bits (68), Expect = 4.0
Identities = 32/117 (27%), Positives = 44/117 (37%), Gaps = 33/117 (28%)
Query: 16 LSQQDEEHIGYLKKYTIDLTEKARLGKLDPVIGRDDEIRRAIQVLQRRSKNNPVLIGEPG 75
L + D +H LK+ TI A LG LD V G++ N V +G PG
Sbjct: 70 LEEFDFDHQRSLKRDTI-----AHLGTLDFVTGKE----------------NVVFLGPPG 108
Query: 76 VGKTAIVEGLAQRIINGEVPNSLLSKKILLLDIAL----LLAGTKYRGEFEDRLKKI 128
GKT + GL R + +L A LA + G + L K+
Sbjct: 109 TGKTHLAIGLGIRACQ--------AGHRVLFATAAQWVARLAAAHHAGRLQAELVKL 157
>gnl|CDD|232988 TIGR00468, pheS, phenylalanyl-tRNA synthetase, alpha subunit. Most
phenylalanyl-tRNA synthetases are heterodimeric, with 2
alpha (pheS) and 2 beta (pheT) subunits. This model
describes the alpha subunit, which shows some similarity
to class II aminoacyl-tRNA ligases. Mitochondrial
phenylalanyl-tRNA synthetase is a single polypeptide
chain, active as a monomer, and similar to this chain
rather than to the beta chain, but excluded from this
model. An interesting feature of the alignment of all
sequences captured by this model is a deep split between
non-spirochete bacterial examples and all other
examples; supporting this split is a relative deletion
of about 50 residues in the former set between two
motifs well conserved throughout the alignment [Protein
synthesis, tRNA aminoacylation].
Length = 293
Score = 30.4 bits (69), Expect = 4.0
Identities = 20/79 (25%), Positives = 31/79 (39%), Gaps = 1/79 (1%)
Query: 304 KKRLLLIKKEINKLEIKYANLEKIWKYEKTLIKDSQQIKEEIEKVRLKINKATRKSDWQT 363
K LL ++ K E K A I + + L + ++K E+E L D
Sbjct: 2 LKDLLKQLGKLTKEETKPALGALINEVKIELQDELTKLKPELESAGLWSKLKFETYDVSL 61
Query: 364 VSKLKY-GELNKLERILKE 381
Y G L+ L R++ E
Sbjct: 62 PGTKIYPGSLHPLTRVIDE 80
>gnl|CDD|240423 PTZ00454, PTZ00454, 26S protease regulatory subunit 6B-like
protein; Provisional.
Length = 398
Score = 30.5 bits (69), Expect = 4.0
Identities = 35/118 (29%), Positives = 53/118 (44%), Gaps = 35/118 (29%)
Query: 469 PYGSFMFLGPTGVGKTELCKTLSACIFNNEESIIRIDMSEFIEKHSISRLIGAPPGYIGY 528
P G ++ GP G GKT L K A + + IR+ SEF++K Y+G
Sbjct: 179 PRGVLLY-GPPGTGKTMLAK---AVAHHTTATFIRVVGSEFVQK------------YLG- 221
Query: 529 EEGGYLTEIV----RRKPYSLILLDEIEK-----------ANSDVFNILLQILD--DG 569
EG + V R S+I +DE++ A+ +V ILL++L+ DG
Sbjct: 222 -EGPRMVRDVFRLARENAPSIIFIDEVDSIATKRFDAQTGADREVQRILLELLNQMDG 278
>gnl|CDD|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain. This domain is
found at the N terminus of SMC proteins. The SMC
(structural maintenance of chromosomes) superfamily
proteins have ATP-binding domains at the N- and
C-termini, and two extended coiled-coil domains
separated by a hinge in the middle. The eukaryotic SMC
proteins form two kind of heterodimers: the SMC1/SMC3
and the SMC2/SMC4 types. These heterodimers constitute
an essential part of higher order complexes, which are
involved in chromatin and DNA dynamics. This family also
includes the RecF and RecN proteins that are involved in
DNA metabolism and recombination.
Length = 1162
Score = 31.1 bits (70), Expect = 4.2
Identities = 31/206 (15%), Positives = 69/206 (33%), Gaps = 14/206 (6%)
Query: 255 KAIDLIDEAAAKIKIEIDSKPEIMDKLERRLIQLKIEHEAIKREYDESSKKRLLLIKKEI 314
+ +E K++ E ++ + + + E + S+K L ++KE+
Sbjct: 272 LKENKEEEKEKKLQEEELKLLAKEEEELKSELLKLERRKVDDEEKLKESEKELKKLEKEL 331
Query: 315 NKLEIKYANLEKIWKYEKTLIKDSQQIKEEIEKVRLKINKATRKSDWQTVSKLKYGELNK 374
K + + LEK K L + +EE E++ K + + K E
Sbjct: 332 KKEKEEIEELEKE---LKELEIKREAEEEEEEQLEKLQEKLEQLEEELLAKKKLESERLS 388
Query: 375 LERILKEK-----------SQKDIQLPNNANKFTLLKTKVGSEEIAEIVSRTTGIPVSKI 423
LKE+ ++ ++L + K + + E+
Sbjct: 389 SAAKLKEEELELKNEEEKEAKLLLELSEQEEDLLKEEKKEELKIVEELEESLETKQGKLT 448
Query: 424 VQVEREKLLNIENLLCKRVVGQDEAI 449
+ E + ++ L K + + E +
Sbjct: 449 EEKEELEKQALKLLKDKLELKKSEDL 474
Score = 30.7 bits (69), Expect = 5.3
Identities = 34/206 (16%), Positives = 80/206 (38%), Gaps = 16/206 (7%)
Query: 180 TTLNEYRQYIEKDAAFERRFQKILVEEPDIEETISILRGLQKKYEVHHGVEITDPAIVAA 239
L +++ A + ++ + EE + L Y + I +
Sbjct: 194 EELKLQELKLKEQAKKALEYYQLKEKLELEEENL-----LYLDYLKLNEERIDLLQELLR 248
Query: 240 SELSYRYISDRFMPDKAIDLIDEAAAKIKIEIDSKPEIMDKLERRLIQLKIEHEAIKREY 299
E S + +K +++ + + K E K KL+ ++L + E +
Sbjct: 249 DEQE-EIESSKQELEKEEEILAQVLKENKEEEKEK-----KLQEEELKLLAKEEEELKSE 302
Query: 300 DESSKKRLLLIKKEINKLEIKYANLEKIWKYEKTLIKDSQQIKEEIEKVRLKINKATRKS 359
++R + ++++ + E + LEK K EK I++ ++ +E L+I + +
Sbjct: 303 LLKLERRKVDDEEKLKESEKELKKLEKELKKEKEEIEELEKELKE-----LEIKREAEEE 357
Query: 360 DWQTVSKLKYGELNKLERILKEKSQK 385
+ + + KL+ E +L +K +
Sbjct: 358 EEEQLEKLQEKLEQLEEELLAKKKLE 383
>gnl|CDD|220180 pfam09325, Vps5, Vps5 C terminal like. Vps5 is a sorting nexin
that functions in membrane trafficking. This is the C
terminal dimerisation domain.
Length = 236
Score = 29.9 bits (68), Expect = 5.0
Identities = 16/63 (25%), Positives = 31/63 (49%), Gaps = 2/63 (3%)
Query: 315 NKLEIKYANLEKIWKYEKTLIKDSQQIKEEIEKVRLKINKATRKSDWQTVSKLKYGELNK 374
L K A L K+ K+ QQ K+E+++ K+ +A ++ ++ +S+ EL +
Sbjct: 142 QDLSKKRAQLAKLKGAGKSRQDKLQQAKKEVDEAERKVQQAKKE--FEDISETIKKELER 199
Query: 375 LER 377
E
Sbjct: 200 FET 202
Score = 29.2 bits (66), Expect = 9.5
Identities = 12/57 (21%), Positives = 31/57 (54%), Gaps = 4/57 (7%)
Query: 262 EAAAKIKIEIDSKPEIMDKLERRLIQLKIEHEAIKREYDESSKKRLLLIKKEINKLE 318
AK+K S+ + + + ++ + + + + + K+E+++ S+ IKKE+ + E
Sbjct: 149 AQLAKLKGAGKSRQDKLQQAKKEVDEAERKVQQAKKEFEDISET----IKKELERFE 201
>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 = 5.1
Identities = 14/28 (50%), Positives = 15/28 (53%), Gaps = 1/28 (3%)
Query: 477 GPTGVGKTELCKTLSACIFNNEESIIRI 504
G TG GKT L L A I +E II I
Sbjct: 32 GGTGSGKTTLLNALLAFI-PPDERIITI 58
>gnl|CDD|131580 TIGR02528, EutP, ethanolamine utilization protein, EutP. This
protein is found within operons which code for
polyhedral organelles containing the enzyme ethanolamine
ammonia lyase. The function of this gene is unknown,
although the presence of an N-terminal GxxGxGK motif
implies a GTP-binding site [Energy metabolism, Amino
acids and amines].
Length = 142
Score = 29.3 bits (66), Expect = 5.1
Identities = 9/17 (52%), Positives = 11/17 (64%)
Query: 474 MFLGPTGVGKTELCKTL 490
MF+G G GKT L + L
Sbjct: 4 MFIGSVGCGKTTLTQAL 20
>gnl|CDD|214810 smart00763, AAA_PrkA, PrkA AAA domain. This is a family of PrkA
bacterial and archaeal serine kinases approximately 630
residues long. This is the N-terminal AAA domain.
Length = 361
Score = 30.3 bits (69), Expect = 5.1
Identities = 16/49 (32%), Positives = 23/49 (46%), Gaps = 3/49 (6%)
Query: 442 VVGQDEAISAVSNAIRRSRSGLSDAKRPYGSFMFLGPTGVGKTELCKTL 490
G +EAI N + + GL + K+ LGP G GK+ L + L
Sbjct: 53 FFGMEEAIERFVNYFKSAAQGLEERKQ---ILYLLGPVGGGKSSLVECL 98
>gnl|CDD|236994 PRK11823, PRK11823, DNA repair protein RadA; Provisional.
Length = 446
Score = 30.4 bits (70), Expect = 5.4
Identities = 28/112 (25%), Positives = 38/112 (33%), Gaps = 57/112 (50%)
Query: 69 VLI-GEPGVGK-TAIVEGLAQRIINGEVPNSLLSKKILLLDIALLLAGTKYR-----GEF 121
VLI G+PG+GK T LLL +A LA + GE
Sbjct: 83 VLIGGDPGIGKST------------------------LLLQVAARLAAAGGKVLYVSGE- 117
Query: 122 E---------DRLK---------------KILKEISNNQKDIIIFIDELHTM 149
E +RL IL I + D+++ ID + TM
Sbjct: 118 ESASQIKLRAERLGLPSDNLYLLAETNLEAILATIEEEKPDLVV-IDSIQTM 168
>gnl|CDD|223775 COG0703, AroK, Shikimate kinase [Amino acid transport and
metabolism].
Length = 172
Score = 29.5 bits (67), Expect = 6.0
Identities = 11/25 (44%), Positives = 13/25 (52%)
Query: 64 SKNNPVLIGEPGVGKTAIVEGLAQR 88
N VLIG G GK+ I LA+
Sbjct: 1 RNMNIVLIGFMGAGKSTIGRALAKA 25
>gnl|CDD|181459 PRK08533, PRK08533, flagellar accessory protein FlaH; Reviewed.
Length = 230
Score = 29.7 bits (67), Expect = 6.1
Identities = 18/57 (31%), Positives = 32/57 (56%), Gaps = 4/57 (7%)
Query: 94 VPNSLLSKKILLLDIALLLAGTKYRGEFEDRLKKILKEISNNQKDIIIFIDELHTMI 150
+ L+S K+L + + LL+G + +F LKK++ +KD+II D L ++I
Sbjct: 78 INKKLISGKLLYIPVYPLLSGNSEKRKF---LKKLMNTRRFYEKDVIII-DSLSSLI 130
>gnl|CDD|224391 COG1474, CDC6, Cdc6-related protein, AAA superfamily ATPase [DNA
replication, recombination, and repair /
Posttranslational modification, protein turnover,
chaperones].
Length = 366
Score = 30.0 bits (68), Expect = 6.3
Identities = 12/50 (24%), Positives = 23/50 (46%), Gaps = 4/50 (8%)
Query: 46 VIGRDDEIRRAIQVLQRRSKN----NPVLIGEPGVGKTAIVEGLAQRIIN 91
+ R++EI + L + N ++ G G GKTA V+ + + +
Sbjct: 19 LPHREEEINQLASFLAPALRGERPSNIIIYGPTGTGKTATVKFVMEELEE 68
>gnl|CDD|182730 PRK10787, PRK10787, DNA-binding ATP-dependent protease La;
Provisional.
Length = 784
Score = 30.3 bits (68), Expect = 6.3
Identities = 29/100 (29%), Positives = 50/100 (50%), Gaps = 15/100 (15%)
Query: 475 FLGPTGVGKTELCKTLSACIFNNEESIIRIDMSEFIEKHSISRLIGAPPGYIGYEEGGYL 534
+GP GVGKT L ++++ +R+ + ++ I G YIG G +
Sbjct: 354 LVGPPGVGKTSLGQSIAKA---TGRKYVRMALGGVRDEAEIR---GHRRTYIGSMPGKLI 407
Query: 535 TEIVR---RKPYSLILLDEIEKANSDV----FNILLQILD 567
++ + + P L LLDEI+K +SD+ + LL++LD
Sbjct: 408 QKMAKVGVKNP--LFLLDEIDKMSSDMRGDPASALLEVLD 445
>gnl|CDD|206680 cd01893, Miro1, Mitochondrial Rho family 1 (Miro1), N-terminal.
Miro1 subfamily. Miro (mitochondrial Rho) proteins have
tandem GTP-binding domains separated by a linker region
containing putative calcium-binding EF hand motifs.
Genes encoding Miro-like proteins were found in several
eukaryotic organisms. This CD represents the N-terminal
GTPase domain of Miro proteins. These atypical Rho
GTPases have roles in mitochondrial homeostasis and
apoptosis. Most Rho proteins contain a lipid
modification site at the C-terminus; however, Miro is
one of few Rho subfamilies that lack this feature.
Length = 168
Score = 29.2 bits (66), Expect = 6.4
Identities = 11/27 (40%), Positives = 16/27 (59%)
Query: 69 VLIGEPGVGKTAIVEGLAQRIINGEVP 95
VLIG+ GVGK++++ L VP
Sbjct: 6 VLIGDEGVGKSSLIMSLVSEEFPENVP 32
>gnl|CDD|237551 PRK13902, alaS, alanyl-tRNA synthetase; Provisional.
Length = 900
Score = 30.2 bits (69), Expect = 6.5
Identities = 14/68 (20%), Positives = 33/68 (48%)
Query: 258 DLIDEAAAKIKIEIDSKPEIMDKLERRLIQLKIEHEAIKREYDESSKKRLLLIKKEINKL 317
DL+ EAA + + + P+ +++ + K E E +++E E LL +E+ +
Sbjct: 743 DLLKEAAEILGVPPEQLPKTVERFFEEWKEQKKEIEKLRKELAELLASELLSKAEEVGGV 802
Query: 318 EIKYANLE 325
++ ++
Sbjct: 803 KVVVEEVD 810
>gnl|CDD|234053 TIGR02903, spore_lon_C, ATP-dependent protease, Lon family.
Members of this protein family resemble the widely
distributed ATP-dependent protease La, also called Lon
and LonA. It resembles even more closely LonB, which is
a LonA paralog found in genomes if and only if the
species is capable of endospore formation (as in
Bacillus subtilis, Clostridium tetani, and select other
members of the Firmicutes) and expressed specifically in
the forespore compartment. Members of this family are
restricted to a subset of spore-forming species, and are
very likely to participate in the program of endospore
formation. We propose the designation LonC [Protein
fate, Degradation of proteins, peptides, and
glycopeptides, Cellular processes, Sporulation and
germination].
Length = 615
Score = 30.2 bits (68), Expect = 6.6
Identities = 36/146 (24%), Positives = 66/146 (45%), Gaps = 33/146 (22%)
Query: 373 NKLERILKEKSQKDIQLPNNANKFTLLKTKVGSEEIAEIVSRTTGIPVSKIVQVEREKLL 432
K+E ++E+ K ++ + +LK + G E + +T + ++ ++E++KL
Sbjct: 92 RKVETRMQERQNKYLE----EIRLQVLKEEKGPE------NSSTLKKLERLEKLEKKKLH 141
Query: 433 -NIENLLCKR----VVGQDEAISAVSNAIRRSRSGLSDAKRPYGSFMFL-GPTGVGKT-- 484
+ ++LL R +VGQ+ AI A+ L+ P+ + L GP GVGKT
Sbjct: 142 KSAQSLLRPRAFSEIVGQERAIKAL----------LAKVASPFPQHIILYGPPGVGKTTA 191
Query: 485 -----ELCKTLSACIFNNEESIIRID 505
E K L F + + +D
Sbjct: 192 ARLALEEAKKLKHTPFAEDAPFVEVD 217
>gnl|CDD|215920 pfam00437, T2SE, Type II/IV secretion system protein. This family
contains both type II and type IV pathway secretion
proteins from bacteria. VirB11 ATPase is a subunit of
the Agrobacterium tumefaciens transfer DNA (T-DNA)
transfer system, a type IV secretion pathway required
for delivery of T-DNA and effector proteins to plant
cells during infection.
Length = 273
Score = 29.9 bits (68), Expect = 6.6
Identities = 15/42 (35%), Positives = 21/42 (50%)
Query: 463 LSDAKRPYGSFMFLGPTGVGKTELCKTLSACIFNNEESIIRI 504
L A + G+ + G TG GKT L L I ++E I+ I
Sbjct: 122 LRQAVQARGNILVSGGTGSGKTTLLYALLNEINTDDERIVTI 163
>gnl|CDD|223637 COG0563, Adk, Adenylate kinase and related kinases [Nucleotide
transport and metabolism].
Length = 178
Score = 29.2 bits (66), Expect = 6.9
Identities = 9/22 (40%), Positives = 13/22 (59%)
Query: 473 FMFLGPTGVGKTELCKTLSACI 494
+ LGP G GK+ L K L+ +
Sbjct: 3 ILILGPPGAGKSTLAKKLAKKL 24
>gnl|CDD|206642 cd00876, Ras, Rat sarcoma (Ras) family of small guanosine
triphosphatases (GTPases). The Ras family of the Ras
superfamily includes classical N-Ras, H-Ras, and K-Ras,
as well as R-Ras, Rap, Ral, Rheb, Rhes, ARHI, RERG,
Rin/Rit, RSR1, RRP22, Ras2, Ras-dva, and RGK proteins.
Ras proteins regulate cell growth, proliferation and
differentiation. Ras is activated by guanine nucleotide
exchange factors (GEFs) that release GDP and allow GTP
binding. Many RasGEFs have been identified. These are
sequestered in the cytosol until activation by growth
factors triggers recruitment to the plasma membrane or
Golgi, where the GEF colocalizes with Ras. Active
GTP-bound Ras interacts with several effector proteins:
among the best characterized are the Raf kinases,
phosphatidylinositol 3-kinase (PI3K), RalGEFs and
NORE/MST1. Most Ras proteins contain a lipid
modification site at the C-terminus, with a typical
sequence motif CaaX, where a = an aliphatic amino acid
and X = any amino acid. Lipid binding is essential for
membrane attachment, a key feature of most Ras
proteins. Due to the presence of truncated sequences in
this CD, the lipid modification site is not available
for annotation.
Length = 160
Score = 29.0 bits (66), Expect = 7.1
Identities = 7/14 (50%), Positives = 11/14 (78%)
Query: 69 VLIGEPGVGKTAIV 82
V++G GVGK+A+
Sbjct: 3 VVLGAGGVGKSALT 16
>gnl|CDD|234252 TIGR03545, TIGR03545, TIGR03545 family protein. This model
represents a relatively rare but broadly distributed
uncharacterized protein family, distributed in 1-2
percent of bacterial genomes, all of which have outer
membranes. In many of these genomes, it is part of a
two-gene pair.
Length = 555
Score = 30.1 bits (68), Expect = 7.2
Identities = 25/111 (22%), Positives = 51/111 (45%), Gaps = 10/111 (9%)
Query: 275 PEIMDKLERRLIQLKIEHEAIKREYDE-SSKKRLLLIKKEINKLEIK----YANLEKIWK 329
E +++E+ LK + K+ + +K+ L KK + ++ K L+KI +
Sbjct: 163 VETAEEIEK---SLKAMQQKWKKRKKDLPNKQDLEEYKKRLEAIKKKDIKNPLELQKIKE 219
Query: 330 YEKTLIKDSQQIKEEIEKVR--LKINKATRKSDWQTVSKLKYGELNKLERI 378
L K+ + K++I+ + L+ +K K+D + K +L +LE
Sbjct: 220 EFDKLKKEGKADKQKIKSAKNDLQNDKKQLKADLAELKKAPQNDLKRLENK 270
>gnl|CDD|129130 TIGR00019, prfA, peptide chain release factor 1. This model
describes peptide chain release factor 1 (PrfA, RF-1),
and excludes the related peptide chain release factor 2
(PrfB, RF-2). RF-1 helps recognize and terminate
translation at UAA and UAG stop codons. The
mitochondrial release factors are prfA-like, although
not included above the trusted cutoff for this model.
RF-1 does not have a translational frameshift [Protein
synthesis, Translation factors].
Length = 360
Score = 29.7 bits (67), Expect = 7.6
Identities = 27/123 (21%), Positives = 54/123 (43%), Gaps = 18/123 (14%)
Query: 274 KPEIMDKLERRLIQLKIEHEAIKREYDESSKKRLLLIKKEINKLEIKYANLEKIWKYEKT 333
KP +++KLE L +E ++ S ++ + ++ KL +Y+ LE+I +
Sbjct: 2 KPSLLEKLES----LLERYEELEALL---SDPEVISDQDKLRKLSKEYSQLEEIVDCYRE 54
Query: 334 LIKDSQQIKEEIEKVRLKINKATRKSDWQTVSKLKYGELNKLERILKEKSQ--KDIQLPN 391
+ + IKE K + + ++ EL +LE ++E + K + LP
Sbjct: 55 YQQAQEDIKE---------AKEILEESDPEMREMAKEELEELEEKIEELEEQLKVLLLPK 105
Query: 392 NAN 394
+ N
Sbjct: 106 DPN 108
>gnl|CDD|224143 COG1222, RPT1, ATP-dependent 26S proteasome regulatory subunit
[Posttranslational modification, protein turnover,
chaperones].
Length = 406
Score = 29.9 bits (68), Expect = 7.7
Identities = 28/79 (35%), Positives = 36/79 (45%), Gaps = 21/79 (26%)
Query: 477 GPTGVGKTELCKTLSACIFNNEESIIRIDMSEFIEKHSISRLIGAPPGYIGYEEGGYLT- 535
GP G GKT L K A + + IR+ SE ++K YIG EG L
Sbjct: 192 GPPGTGKTLLAK---AVANQTDATFIRVVGSELVQK------------YIG--EGARLVR 234
Query: 536 ---EIVRRKPYSLILLDEI 551
E+ R K S+I +DEI
Sbjct: 235 ELFELAREKAPSIIFIDEI 253
>gnl|CDD|202833 pfam03962, Mnd1, Mnd1 family. This family of proteins includes
MND1 from S. cerevisiae. The mnd1 protein forms a
complex with hop2 to promote homologous chromosome
pairing and meiotic double-strand break repair.
Length = 188
Score = 29.1 bits (66), Expect = 7.9
Identities = 21/80 (26%), Positives = 48/80 (60%), Gaps = 3/80 (3%)
Query: 278 MDKLERRLIQLKIEHEAIKREYDESSKKRLLLIKKEINKLEIKYANLEKIW-KYEKTLIK 336
+++L++R+ +L+ + E +K+ +E+ ++ LL +E+ +LE + L+ KYEK +
Sbjct: 78 LEELKQRIAELQAQIEKLKKGREETEERTELL--EELKQLEKELKKLKAELEKYEKNDPE 135
Query: 337 DSQQIKEEIEKVRLKINKAT 356
+++KEE + + N+ T
Sbjct: 136 RIEKLKEETKVAKEAANRWT 155
>gnl|CDD|235904 PRK06995, flhF, flagellar biosynthesis regulator FlhF; Validated.
Length = 484
Score = 29.9 bits (68), Expect = 8.1
Identities = 10/14 (71%), Positives = 11/14 (78%)
Query: 471 GSFMFLGPTGVGKT 484
G F +GPTGVGKT
Sbjct: 257 GVFALMGPTGVGKT 270
>gnl|CDD|214940 smart00962, SRP54, SRP54-type protein, GTPase domain. This entry
represents the GTPase domain of the 54 kDa SRP54
component, a GTP-binding protein that interacts with the
signal sequence when it emerges from the ribosome. SRP54
of the signal recognition particle has a three-domain
structure: an N-terminal helical bundle domain, a GTPase
domain, and the M-domain that binds the 7s RNA and also
binds the signal sequence. The extreme C-terminal region
is glycine-rich and lower in complexity and poorly
conserved between species. The GTPase domain is
evolutionary related to P-loop NTPase domains found in a
variety of other proteins.
Length = 197
Score = 28.9 bits (66), Expect = 8.2
Identities = 7/12 (58%), Positives = 9/12 (75%)
Query: 473 FMFLGPTGVGKT 484
+ +GP GVGKT
Sbjct: 4 ILLVGPNGVGKT 15
>gnl|CDD|224617 COG1703, ArgK, Putative periplasmic protein kinase ArgK and
related GTPases of G3E family [Amino acid transport and
metabolism].
Length = 323
Score = 29.6 bits (67), Expect = 8.4
Identities = 13/48 (27%), Positives = 22/48 (45%), Gaps = 5/48 (10%)
Query: 48 GRDDEIRRAIQVLQRRSKN--NPVLIG---EPGVGKTAIVEGLAQRII 90
R D A ++L+ N +IG PG GK+ ++E L + +
Sbjct: 29 RRPDHRALARELLRALYPRTGNAHVIGITGVPGAGKSTLIEALGRELR 76
>gnl|CDD|218899 pfam06102, DUF947, Domain of unknown function (DUF947). Family of
eukaryotic proteins with unknown function.
Length = 168
Score = 28.8 bits (65), Expect = 8.6
Identities = 25/107 (23%), Positives = 44/107 (41%), Gaps = 25/107 (23%)
Query: 268 KIEIDSKPEIMDKLERRLIQLKIEHEAIKREYDE----------------SSKKRLLLIK 311
++ E ++L+R L +K + +K + E KK L K
Sbjct: 71 ALKKTKDSEEKEELKRTLQSMKSRLKTLKNKDREREILKEHKKQEKELIKEGKKPYYLKK 130
Query: 312 KEINKLEIKYANLEKIWKYEKTLIKDSQQIKEEIEKVRLKINKATRK 358
EI KL +K K+++ +K S+Q+ + +EK R K +K
Sbjct: 131 SEIKKLVLK-------KKFDE--LKKSKQLDKALEKKRKKNAGKEKK 168
>gnl|CDD|183703 PRK12724, PRK12724, flagellar biosynthesis regulator FlhF;
Provisional.
Length = 432
Score = 29.5 bits (66), Expect = 9.2
Identities = 33/121 (27%), Positives = 61/121 (50%), Gaps = 9/121 (7%)
Query: 266 KIKIEIDSKPEIMDKLERRLIQLKIEHEAIK-REYDESSKKRLLLIKKEINK-LEIKYAN 323
+I+I I K +K+ER+L LK E +K + Y E +K+ L K +++ LE K +
Sbjct: 51 EIQIGIPEKQASREKIERKLQDLK---ELLKQKSYTEPERKKTLQTLKPLSERLEEKESA 107
Query: 324 LEKI--WKYEKTLIKDSQQIKEEIEKVRLKINKATRKSDWQTVSKLKYGELNKL-ERILK 380
+ +I ++ E+ + + + + EK + N + V K K L +L ER+++
Sbjct: 108 IYEIESFELEEVITEPERPVGLSFEKELFEKNSFLES-ETTIVRKEKDSPLQRLGERLVR 166
Query: 381 E 381
E
Sbjct: 167 E 167
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
0.319 0.138 0.389
Gapped
Lambda K H
0.267 0.0868 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 49,580,072
Number of extensions: 5228423
Number of successful extensions: 8545
Number of sequences better than 10.0: 1
Number of HSP's gapped: 8171
Number of HSP's successfully gapped: 555
Length of query: 951
Length of database: 10,937,602
Length adjustment: 106
Effective length of query: 845
Effective length of database: 6,236,078
Effective search space: 5269485910
Effective search space used: 5269485910
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 (21.7 bits)
S2: 64 (28.2 bits)