RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14500
(938 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 = 1122 bits (2905), Expect = 0.0
Identities = 418/661 (63%), Positives = 547/661 (82%), Gaps = 5/661 (0%)
Query: 14 LKKYTIDLTEKARLGKLDPVIGRDDEIRRAIQVLQRRSKNNPVLIGEPGVGKTAIVEGLA 73
L+KY DLTE+AR GKLDPVIGRD+EIRR IQVL RR+KNNPVLIGEPGVGKTAIVEGLA
Sbjct: 156 LEKYARDLTERAREGKLDPVIGRDEEIRRTIQVLSRRTKNNPVLIGEPGVGKTAIVEGLA 215
Query: 74 QRIINGEVPNSLLSKKILLLDIALLLAGTKYRGEFEDRLKKILKEISNNQKDIIIFIDEL 133
QRI+NG+VP SL +K++L LD+ L+AG KYRGEFE+RLK +L E++ ++ II+FIDEL
Sbjct: 216 QRIVNGDVPESLKNKRLLALDMGALIAGAKYRGEFEERLKAVLNEVTKSEGQIILFIDEL 275
Query: 134 HTMIGTGKVEGSIDAGNMLKPELSRGELHCIGATTLNEYRQYIEKDAAFERRFQKILVEE 193
HT++G GK EG++DAGNMLKP L+RGELHCIGATTL+EYR+YIEKDAA ERRFQ + V+E
Sbjct: 276 HTLVGAGKAEGAMDAGNMLKPALARGELHCIGATTLDEYRKYIEKDAALERRFQPVFVDE 335
Query: 194 PDIEETISILRGLQKKYEVHHGVEITDPAIVAASELSYRYISDRFMPDKAIDLIDEAAAK 253
P +E+TISILRGL+++YEVHHGV ITDPAIVAA+ LS+RYI+DRF+PDKAIDLIDEAAA+
Sbjct: 336 PTVEDTISILRGLKERYEVHHGVRITDPAIVAAATLSHRYITDRFLPDKAIDLIDEAAAR 395
Query: 254 IKIEIDSKPEIMDKLERRLIQLKIEHEAIKREYDESSKKRLLLIKKEINKLEIKYANLEK 313
I++EIDSKPE +D+L+RR+IQL+IE EA+K+E DE+SK+RL ++KE+ +LE +YA+LE+
Sbjct: 396 IRMEIDSKPEELDELDRRIIQLEIEREALKKEKDEASKERLEDLEKELAELEEEYADLEE 455
Query: 314 IWKYEKTLIKDSQQIKEEIEKVRLKINKATRKSDWQTVSKLKYGELNKLERILKEKSQKD 373
WK EK I+ QQIKEEIE+VRL++ +A R+ D ++L+YG+L +LE+ L+ K
Sbjct: 456 QWKAEKAAIQGIQQIKEEIEQVRLELEQAEREGDLAKAAELQYGKLPELEKRLQAAEAKL 515
Query: 374 IQLPNNANKFTLLKTKVGSEEIAEIVSRTTGIPVSKIVQVEREKLLNIENLLCKRVVGQD 433
+ LL+ +V +EEIAE+VSR TGIPVSK+++ EREKLL++E +L +RVVGQD
Sbjct: 516 GEETKPR----LLREEVTAEEIAEVVSRWTGIPVSKMLEGEREKLLHMEEVLHERVVGQD 571
Query: 434 EAISAVSNAIRRSRSGLSDAKRPYGSFMFLGPTGVGKTELCKTLSACIFNNEESIIRIDM 493
EA+ AVS+AIRRSR+GLSD RP GSF+FLGPTGVGKTEL K L+ +F++E++++RIDM
Sbjct: 572 EAVEAVSDAIRRSRAGLSDPNRPIGSFLFLGPTGVGKTELAKALAEFLFDDEDAMVRIDM 631
Query: 494 SEFIEKHSISRLIGAPPGYIGYEEGGYLTEIVRRKPYSLILLDEIEKANSDVFNILLQIL 553
SE++EKHS++RLIGAPPGY+GYEEGG LTE VRRKPYS++L DE+EKA+ DVFN+LLQ+L
Sbjct: 632 SEYMEKHSVARLIGAPPGYVGYEEGGQLTEAVRRKPYSVVLFDEVEKAHPDVFNVLLQVL 691
Query: 554 DDGRLTDNRGRTINFRNTIIVMTSNLGSDKIKEM-EKGDKEIIKLAVMNEVKIYFRPEFI 612
DDGRLTD +GRT++FRNT+I+MTSNLGS I+E+ D E ++ AVM ++ +FRPEF+
Sbjct: 692 DDGRLTDGQGRTVDFRNTVIIMTSNLGSQFIQELAGGDDYEEMREAVMEVLRAHFRPEFL 751
Query: 613 NRIDDIIVFRYLNRKNILSIANIQLNILKNKLLKMNMDLKISKAALKKISNIGFDLIYGA 672
NRID+I+VF L R+ I I IQL L+ +L + + L++S AAL ++ G+D +YGA
Sbjct: 752 NRIDEIVVFHPLGREQIARIVEIQLGRLRKRLAERKITLELSDAALDFLAEAGYDPVYGA 811
Query: 673 R 673
R
Sbjct: 812 R 812
>gnl|CDD|182791 PRK10865, PRK10865, protein disaggregation chaperone; Provisional.
Length = 857
Score = 928 bits (2400), Expect = 0.0
Identities = 412/701 (58%), Positives = 550/701 (78%), Gaps = 15/701 (2%)
Query: 14 LKKYTIDLTEKARLGKLDPVIGRDDEIRRAIQVLQRRSKNNPVLIGEPGVGKTAIVEGLA 73
LKKYTIDLTE+A GKLDPVIGRD+EIRR IQVLQRR+KNNPVLIGEPGVGKTAIVEGLA
Sbjct: 161 LKKYTIDLTERAEQGKLDPVIGRDEEIRRTIQVLQRRTKNNPVLIGEPGVGKTAIVEGLA 220
Query: 74 QRIINGEVPNSLLSKKILLLDIALLLAGTKYRGEFEDRLKKILKEISNNQKDIIIFIDEL 133
QRIINGEVP L +++L LD+ L+AG KYRGEFE+RLK +L +++ + ++I+FIDEL
Sbjct: 221 QRIINGEVPEGLKGRRVLALDMGALVAGAKYRGEFEERLKGVLNDLAKQEGNVILFIDEL 280
Query: 134 HTMIGTGKVEGSIDAGNMLKPELSRGELHCIGATTLNEYRQYIEKDAAFERRFQKILVEE 193
HTM+G GK +G++DAGNMLKP L+RGELHC+GATTL+EYRQYIEKDAA ERRFQK+ V E
Sbjct: 281 HTMVGAGKADGAMDAGNMLKPALARGELHCVGATTLDEYRQYIEKDAALERRFQKVFVAE 340
Query: 194 PDIEETISILRGLQKKYEVHHGVEITDPAIVAASELSYRYISDRFMPDKAIDLIDEAAAK 253
P +E+TI+ILRGL+++YE+HH V+ITDPAIVAA+ LS+RYI+DR +PDKAIDLIDEAA+
Sbjct: 341 PSVEDTIAILRGLKERYELHHHVQITDPAIVAAATLSHRYIADRQLPDKAIDLIDEAASS 400
Query: 254 IKIEIDSKPEIMDKLERRLIQLKIEHEAIKREYDESSKKRLLLIKKEINKLEIKYANLEK 313
I+++IDSKPE +D+L+RR+IQLK+E +A+ +E DE+SKKRL ++ +E++ E +Y+ LE+
Sbjct: 401 IRMQIDSKPEELDRLDRRIIQLKLEQQALMKESDEASKKRLDMLNEELSDKERQYSELEE 460
Query: 314 IWKYEKTLIKDSQQIKEEIEKVRLKINKATRKSDWQTVSKLKYGELNKLERILKEKSQKD 373
WK EK + +Q IK E+E+ ++ I +A R D +S+L+YG++ +LE+ L +Q +
Sbjct: 461 EWKAEKASLSGTQTIKAELEQAKIAIEQARRVGDLARMSELQYGKIPELEKQLAAATQLE 520
Query: 374 IQLPNNANKFTLLKTKVGSEEIAEIVSRTTGIPVSKIVQVEREKLLNIENLLCKRVVGQD 433
LL+ KV EIAE+++R TGIPVS++++ EREKLL +E L RV+GQ+
Sbjct: 521 ------GKTMRLLRNKVTDAEIAEVLARWTGIPVSRMLESEREKLLRMEQELHHRVIGQN 574
Query: 434 EAISAVSNAIRRSRSGLSDAKRPYGSFMFLGPTGVGKTELCKTLSACIFNNEESIIRIDM 493
EA+ AVSNAIRRSR+GLSD RP GSF+FLGPTGVGKTELCK L+ +F+++++++RIDM
Sbjct: 575 EAVEAVSNAIRRSRAGLSDPNRPIGSFLFLGPTGVGKTELCKALANFMFDSDDAMVRIDM 634
Query: 494 SEFIEKHSISRLIGAPPGYIGYEEGGYLTEIVRRKPYSLILLDEIEKANSDVFNILLQIL 553
SEF+EKHS+SRL+GAPPGY+GYEEGGYLTE VRR+PYS+ILLDE+EKA+ DVFNILLQ+L
Sbjct: 635 SEFMEKHSVSRLVGAPPGYVGYEEGGYLTEAVRRRPYSVILLDEVEKAHPDVFNILLQVL 694
Query: 554 DDGRLTDNRGRTINFRNTIIVMTSNLGSDKIKE-MEKGDKEIIKLAVMNEVKIYFRPEFI 612
DDGRLTD +GRT++FRNT+++MTSNLGSD I+E + D +K V+ V FRPEFI
Sbjct: 695 DDGRLTDGQGRTVDFRNTVVIMTSNLGSDLIQERFGELDYAHMKELVLGVVSHNFRPEFI 754
Query: 613 NRIDDIIVFRYLNRKNILSIANIQLNILKNKLLKMNMDLKISKAALKKISNIGFDLIYGA 672
NRID+++VF L ++I SIA IQL L +L + ++ IS ALK +S G+D +YGA
Sbjct: 755 NRIDEVVVFHPLGEQHIASIAQIQLQRLYKRLEERGYEIHISDEALKLLSENGYDPVYGA 814
Query: 673 RDVHGCKKSLSILLKKIHKKSPEANFIFLGDLINKGPQSLD 713
R + K+++ + ++P A I G+L+ L+
Sbjct: 815 RPL---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 = 856 bits (2214), Expect = 0.0
Identities = 374/672 (55%), Positives = 486/672 (72%), Gaps = 81/672 (12%)
Query: 7 DEEHIGYLKKYTIDLTEKARLGKLDPVIGRDDEIRRAIQVLQRRSKNNPVLIGEPGVGKT 66
EE L+KYT DLTE AR GKLDPVIGRD+EIRR IQ+L RR+KNNPVL+GEPGVGKT
Sbjct: 146 AEEDQDALEKYTRDLTELAREGKLDPVIGRDEEIRRTIQILSRRTKNNPVLVGEPGVGKT 205
Query: 67 AIVEGLAQRIINGEVPNSLLSKKILLLDIALLLAGTKYRGEFEDRLKKILKEISNNQKDI 126
AIVEGLAQRI+NG+VP SL K+I LD+ L+AG KYRGEFE+RLK +LKE+ + K++
Sbjct: 206 AIVEGLAQRIVNGDVPESLKDKRIYSLDLGSLVAGAKYRGEFEERLKAVLKEVEKS-KNV 264
Query: 127 IIFIDELHTMIGTGKVEG-SIDAGNMLKPELSRGELHCIGATTLNEYRQYIEKDAAFERR 185
I+FIDE+HT++G G EG ++DA N+LKP L+RGEL CIGATTL+EYR+YIEKDAA ERR
Sbjct: 265 ILFIDEIHTIVGAGATEGGAMDAANLLKPALARGELRCIGATTLDEYRKYIEKDAALERR 324
Query: 186 FQKILVEEPDIEETISILRGLQKKYEVHHGVEITDPAIVAASELSYRYISDRFMPDKAID 245
FQK+LV+EP +E+TI+ILRGL+++YE HHGV ITD A+VAA LS RYI DRF+PDKAID
Sbjct: 325 FQKVLVDEPSVEDTIAILRGLKERYEAHHGVRITDEALVAAVTLSDRYIPDRFLPDKAID 384
Query: 246 LIDEAAAKIKIEIDSKPEIMDKLERRLIQLKIEHEAIKREYDESSKKRLLLIKKEINKLE 305
L+DEA A++++EID KPE +D+LER L QL+IE EA++
Sbjct: 385 LLDEAGARVRLEID-KPEELDELERELAQLEIEKEALE---------------------- 421
Query: 306 IKYANLEKIWKYEKTLIKDSQQIKEEIEKVRLKINKATRKSDWQTVSKLKYGELNKLERI 365
+E+ EK + I++ + KLK G + +LE+
Sbjct: 422 -----------------------REQDEKEKKLIDE---------IIKLKEGRIPELEKE 449
Query: 366 LKEKSQKDIQLPNNANKFTLLKTKVGSEEIAEIVSRTTGIPVSKIVQVEREKLLNIENLL 425
L+ + V ++IAE+V+R TGIPV+K+++ E+EKLLN+E L
Sbjct: 450 LEAE--------------------VDEDDIAEVVARWTGIPVAKLLEDEKEKLLNLERRL 489
Query: 426 CKRVVGQDEAISAVSNAIRRSRSGLSDAKRPYGSFMFLGPTGVGKTELCKTLSACIFNNE 485
KRV+GQDEA+ AVS+AIRR+R+GL D RP GSF+FLGPTGVGKTEL K L+ +F +E
Sbjct: 490 KKRVIGQDEAVEAVSDAIRRARAGLGDPNRPIGSFLFLGPTGVGKTELAKALAEALFGDE 549
Query: 486 ESIIRIDMSEFIEKHSISRLIGAPPGYIGYEEGGYLTEIVRRKPYSLILLDEIEKANSDV 545
+++IRIDMSE++EKHS+SRLIGAPPGY+GYEEGG LTE VRRKPYS+ILLDEIEKA+ DV
Sbjct: 550 QALIRIDMSEYMEKHSVSRLIGAPPGYVGYEEGGQLTEAVRRKPYSVILLDEIEKAHPDV 609
Query: 546 FNILLQILDDGRLTDNRGRTINFRNTIIVMTSNLGSDKIKEMEKGD----KEIIKLAVMN 601
FN+LLQ+LDDGRLTD +GRT++FRNTII+MTSN GS++I GD KE +K AVM
Sbjct: 610 FNLLLQVLDDGRLTDGQGRTVDFRNTIIIMTSNAGSEEILRDADGDDFADKEALKEAVME 669
Query: 602 EVKIYFRPEFINRIDDIIVFRYLNRKNILSIANIQLNILKNKLLKMNMDLKISKAALKKI 661
E+K +FRPEF+NRID+II F L+++ + I ++QLN L +L + + L++S A +
Sbjct: 670 ELKKHFRPEFLNRIDEIIPFNPLSKEVLERIVDLQLNRLAKRLAERGITLELSDEAKDFL 729
Query: 662 SNIGFDLIYGAR 673
+ G+D YGAR
Sbjct: 730 AEKGYDPEYGAR 741
>gnl|CDD|214361 CHL00095, clpC, Clp protease ATP binding subunit.
Length = 821
Score = 682 bits (1761), Expect = 0.0
Identities = 318/673 (47%), Positives = 444/673 (65%), Gaps = 79/673 (11%)
Query: 14 LKKYTIDLTEKARLGKLDPVIGRDDEIRRAIQVLQRRSKNNPVLIGEPGVGKTAIVEGLA 73
L+++ +LT++A G LDPVIGR+ EI R IQ+L RR+KNNP+LIGEPGVGKTAI EGLA
Sbjct: 162 LEEFGTNLTKEAIDGNLDPVIGREKEIERVIQILGRRTKNNPILIGEPGVGKTAIAEGLA 221
Query: 74 QRIINGEVPNSLLSKKILLLDIALLLAGTKYRGEFEDRLKKILKEISNNQKDIIIFIDEL 133
QRI+N +VP+ L K ++ LDI LLLAGTKYRGEFE+RLK+I EI N +II+ IDE+
Sbjct: 222 QRIVNRDVPDILEDKLVITLDIGLLLAGTKYRGEFEERLKRIFDEIQEN-NNIILVIDEV 280
Query: 134 HTMIGTGKVEGSIDAGNMLKPELSRGELHCIGATTLNEYRQYIEKDAAFERRFQKILVEE 193
HT+IG G EG+IDA N+LKP L+RGEL CIGATTL+EYR++IEKD A ERRFQ + V E
Sbjct: 281 HTLIGAGAAEGAIDAANILKPALARGELQCIGATTLDEYRKHIEKDPALERRFQPVYVGE 340
Query: 194 PDIEETISILRGLQKKYEVHHGVEITDPAIVAASELSYRYISDRFMPDKAIDLIDEAAAK 253
P +EETI IL GL+ +YE HH + I+D A+ AA++LS +YI+DRF+PDKAIDL+DEA ++
Sbjct: 341 PSVEETIEILFGLRSRYEKHHNLSISDKALEAAAKLSDQYIADRFLPDKAIDLLDEAGSR 400
Query: 254 IKIEIDSKPEIMDKLERRLIQLKIEHEAIKREYDESSKKRLLLIKKEINKLEIKYANLEK 313
+++ P +L++ L ++ + + RE D + K+L + E+
Sbjct: 401 VRLINSRLPPAARELDKELREILKDKDEAIREQDFETAKQLRDREMEV------------ 448
Query: 314 IWKYEKTLIKDSQQIKEEIEKVRLKINKATRKSDWQTVSKLKYGELNKLERILKEKSQKD 373
+ + I S++ +EE + +++D
Sbjct: 449 --RAQIAAIIQSKKTEEEKRLEVPVV------------------------------TEED 476
Query: 374 IQLPNNANKFTLLKTKVGSEEIAEIVSRTTGIPVSKIVQVEREKLLNIENLLCKRVVGQD 433
I AEIVS TGIPV+K+ + E EKLL++E L KR++GQD
Sbjct: 477 I---------------------AEIVSAWTGIPVNKLTKSESEKLLHMEETLHKRIIGQD 515
Query: 434 EAISAVSNAIRRSRSGLSDAKRPYGSFMFLGPTGVGKTELCKTLSACIFNNEESIIRIDM 493
EA+ AVS AIRR+R GL + RP SF+F GPTGVGKTEL K L++ F +E+++IR+DM
Sbjct: 516 EAVVAVSKAIRRARVGLKNPNRPIASFLFSGPTGVGKTELTKALASYFFGSEDAMIRLDM 575
Query: 494 SEFIEKHSISRLIGAPPGYIGYEEGGYLTEIVRRKPYSLILLDEIEKANSDVFNILLQIL 553
SE++EKH++S+LIG+PPGY+GY EGG LTE VR+KPY+++L DEIEKA+ D+FN+LLQIL
Sbjct: 576 SEYMEKHTVSKLIGSPPGYVGYNEGGQLTEAVRKKPYTVVLFDEIEKAHPDIFNLLLQIL 635
Query: 554 DDGRLTDNRGRTINFRNTIIVMTSNLGSDKI----------KEMEKGDK---EIIKLAVM 600
DDGRLTD++GRTI+F+NT+I+MTSNLGS I + + + + V
Sbjct: 636 DDGRLTDSKGRTIDFKNTLIIMTSNLGSKVIETNSGGLGFELSENQLSEKQYKRLSNLVN 695
Query: 601 NEVKIYFRPEFINRIDDIIVFRYLNRKNILSIANIQLNILKNKLLKMNMDLKISKAALKK 660
E+K +FRPEF+NR+D+IIVFR L + ++ IA I L L +L + + L++++
Sbjct: 696 EELKQFFRPEFLNRLDEIIVFRQLTKNDVWEIAEIMLKNLFKRLNEQGIQLEVTERIKTL 755
Query: 661 ISNIGFDLIYGAR 673
+ G++ +YGAR
Sbjct: 756 LIEEGYNPLYGAR 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 = 666 bits (1720), Expect = 0.0
Identities = 282/656 (42%), Positives = 416/656 (63%), Gaps = 28/656 (4%)
Query: 14 LKKYTIDLTEKARLGKLDPVIGRDDEIRRAIQVLQRRSKNNPVLIGEPGVGKTAIVEGLA 73
L +YT DLT +AR GK+DPV+GRDDEIR+ I +L RR +NNP+L GE GVGKTA+VEGLA
Sbjct: 170 LDQYTTDLTAQAREGKIDPVLGRDDEIRQMIDILLRRRQNNPILTGEAGVGKTAVVEGLA 229
Query: 74 QRIINGEVPNSLLSKKILLLDIALLLAGTKYRGEFEDRLKKILKEISNNQKDIIIFIDEL 133
RI G+VP +L + ++L LD+ LL AG +GEFE+RLK ++ E+ + + II+FIDE
Sbjct: 230 LRIAAGDVPPALRNVRLLSLDLGLLQAGASVKGEFENRLKSVIDEVKASPQPIILFIDEA 289
Query: 134 HTMIGTGKVEGSIDAGNMLKPELSRGELHCIGATTLNEYRQYIEKDAAFERRFQKILVEE 193
HT+IG G G DA N+LKP L+RGEL I ATT EY++Y EKD A RRFQ + VEE
Sbjct: 290 HTLIGAGGQAGQGDAANLLKPALARGELRTIAATTWAEYKKYFEKDPALTRRFQVVKVEE 349
Query: 194 PDIEETISILRGLQKKYEVHHGVEITDPAIVAASELSYRYISDRFMPDKAIDLIDEAAAK 253
PD E I +LRGL E HHGV I D A+VAA ELS+RYI R +PDKA+ L+D A A+
Sbjct: 350 PDEETAIRMLRGLAPVLEKHHGVLILDEAVVAAVELSHRYIPGRQLPDKAVSLLDTACAR 409
Query: 254 IKIEIDSKPEIMDKLERRLIQLKIEHEAIKRE--YDESSKKRLLLIKKEINKLEIKYANL 311
+ + ++ P ++ L RR+ L++E +A++RE +RL ++ E+ LE + A L
Sbjct: 410 VALSQNATPAALEDLRRRIAALELELDALEREAALGADHDERLAELRAELAALEAELAAL 469
Query: 312 EKIWKYEKTLIKDSQQIKEEIEKVRLKINKATRKSDWQTVSKLKYGELNKLERILKEKSQ 371
E W+ EK L++ ++ E+E +L +LE L +Q
Sbjct: 470 EARWQQEKELVEAILALRAELE---------ADADAPADDDAALRAQLAELEAALAS-AQ 519
Query: 372 KDIQLPNNANKFTLLKTKVGSEEIAEIVSRTTGIPVSKIVQVEREKLLNIENLLCKRVVG 431
+ P L+ +V ++ +AE+V+ TGIPV ++V+ E E +L++ + L +RV+G
Sbjct: 520 GE--EP-------LVFPEVDAQAVAEVVADWTGIPVGRMVRDEIEAVLSLPDRLAERVIG 570
Query: 432 QDEAISAVSNAIRRSRSGLSDAKRPYGSFMFLGPTGVGKTELCKTLSACIFNNEESIIRI 491
QD A+ A++ IR +R+GL D ++P G F+ +GP+GVGKTE L+ ++ E+++I I
Sbjct: 571 QDHALEAIAERIRTARAGLEDPRKPLGVFLLVGPSGVGKTETALALAELLYGGEQNLITI 630
Query: 492 DMSEFIEKHSISRLIGAPPGYIGYEEGGYLTEIVRRKPYSLILLDEIEKANSDVFNILLQ 551
+MSEF E H++SRL G+PPGY+GY EGG LTE VRRKPYS++LLDE+EKA+ DV + Q
Sbjct: 631 NMSEFQEAHTVSRLKGSPPGYVGYGEGGVLTEAVRRKPYSVVLLDEVEKAHPDVLELFYQ 690
Query: 552 ILDDGRLTDNRGRTINFRNTIIVMTSNLGSDKIKEM-----EKGDKEIIKLAVMNEVKIY 606
+ D G + D GR I+F+NT+I++TSN GSD I + D E + A+ E+
Sbjct: 691 VFDKGVMEDGEGREIDFKNTVILLTSNAGSDLIMALCADPETAPDPEALLEALRPELLKV 750
Query: 607 FRPEFINRIDDIIVFRYLNRKNILSIANIQLNILKNKLLK-MNMDLKISKAALKKI 661
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: 13 YLKKYTIDLTEKARLGKLDPVIGRDDEIRRAIQVLQRRSKNNPVLIGEPGVGKTAIVEGL 72
L+KYT+DLTEKA+ GK+DP+IGR+DE+ R IQVL RR KNNP+L+GEPGVGKTAIVEGL
Sbjct: 163 ALEKYTVDLTEKAKNGKIDPLIGREDELERTIQVLCRRKKNNPLLVGEPGVGKTAIVEGL 222
Query: 73 AQRIINGEVPNSLLSKKILLLDIALLLAGTKYRGEFEDRLKKILKEISNNQKDIIIFIDE 132
A RI G+VP L + KI LD+ LLAGTKYRG+FE+RLK ++ EI + + I+FIDE
Sbjct: 223 ALRIAEGKVPERLKNAKIYSLDMGTLLAGTKYRGDFEERLKAVVSEIEK-EPNAILFIDE 281
Query: 133 LHTMIGTGKV-EGSIDAGNMLKPELSRGELHCIGATTLNEYRQYIEKDAAFERRFQKILV 191
+HT++G G GS+DA N+LKP LS G++ CIG+TT EY+ + EKD A RRFQKI V
Sbjct: 282 IHTIVGAGATSGGSMDASNLLKPALSSGKIRCIGSTTYEEYKNHFEKDRALSRRFQKIDV 341
Query: 192 EEPDIEETISILRGLQKKYEVHHGVEITDPAIVAASELSYRYISDRFMPDKAIDLIDEAA 251
EP IEET+ IL+GL+++YE H V+ +D A+ AA ELS RYI+DRF+PDKAID+IDEA
Sbjct: 342 GEPSIEETVKILKGLKEQYEEFHHVKYSDEALEAAVELSARYINDRFLPDKAIDVIDEAG 401
Query: 252 AKIKIEIDSKP 262
A ++ +K
Sbjct: 402 AAFRLRPKAKK 412
Score = 314 bits (806), Expect = 1e-94
Identities = 130/291 (44%), Positives = 192/291 (65%), Gaps = 10/291 (3%)
Query: 387 KTKVGSEEIAEIVSRTTGIPVSKIVQVEREKLLNIENLLCKRVVGQDEAISAVSNAIRRS 446
K V ++I +V++ IPV + +RE+L N+E L ++ GQDEAI + +AI+RS
Sbjct: 413 KANVNVKDIENVVAKMAKIPVKTVSSDDREQLKNLEKNLKAKIFGQDEAIDQLVSAIKRS 472
Query: 447 RSGLSDAKRPYGSFMFLGPTGVGKTELCKTLSACIFNNEESIIRIDMSEFIEKHSISRLI 506
R+GL D +P GSF+F+GPTGVGKTEL K L A ++R DMSE++EKH++SRLI
Sbjct: 473 RAGLGDPNKPVGSFLFVGPTGVGKTELAKQL-AEELGVH--LLRFDMSEYMEKHTVSRLI 529
Query: 507 GAPPGYIGYEEGGYLTEIVRRKPYSLILLDEIEKANSDVFNILLQILDDGRLTDNRGRTI 566
G+PPGY+G+E+GG LT+ VR+ P+ ++LLDEIEKA+ D++NILLQ++D LTDN GR
Sbjct: 530 GSPPGYVGFEQGGLLTDAVRKHPHCVLLLDEIEKAHPDIYNILLQVMDYATLTDNNGRKA 589
Query: 567 NFRNTIIVMTSNLGSDKIKEMEKGD----KEIIKLAVMNEVKIYFRPEFINRIDDIIVFR 622
+FRN I++MTSN G+ EM K E + + +K F PEF NR+D II F
Sbjct: 590 DFRNVILIMTSNAGA---SEMSKPPIGFGGENSESKSLKAIKKLFSPEFRNRLDAIIHFN 646
Query: 623 YLNRKNILSIANIQLNILKNKLLKMNMDLKISKAALKKISNIGFDLIYGAR 673
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 (853), Expect = e-107
Identities = 113/266 (42%), Positives = 156/266 (58%), Gaps = 9/266 (3%)
Query: 674 DVHGCKKSLSILLKKIHKKSPEANFIFLGDLINKGPQSLDTLRMVYSMRNYAKIVLGNHE 733
D+ GC L LL+KI + +GDL+N+GP SL+ LR V S+ + A VLGNH+
Sbjct: 8 DIQGCYDELQRLLEKIDFDPAKDTLWLVGDLVNRGPDSLEVLRFVKSLGDSAVTVLGNHD 67
Query: 734 IHLLDVLININKKSKLDTFDDILDAPDKKKLVSWLRTQPLAIYY--KKYLMIHAGVAKQW 791
+HLL V I + K DT D IL+APD+ +L+ WLR QPL +M+HAG+ QW
Sbjct: 68 LHLLAVAAGIKRNKKKDTLDPILEAPDRDELLDWLRHQPLLHVDEELGLVMVHAGIPPQW 127
Query: 792 TAQQTIKLSHQVEKILRTSYWKNLFFKLYNHNSINWDNHLHTIHLNTIDKLQFIINTLTR 851
+ L+ +VE +LR+ +++ +Y + W L +++L++IIN TR
Sbjct: 128 DLATALALAREVEAVLRSDDYRDFLANMYGNEPDRWSP-----DLTGLERLRYIINAFTR 182
Query: 852 TRFCKIDGTIEFIKKNIKNNNFQNNYIPWFDLPNRKTIDITVLFGHWSTL-GLIMKPNII 910
RFC DG ++F K + PWF++P RKT D T++FGHW+ L GL PNII
Sbjct: 183 MRFCTPDGRLDFKCKGPPDEA-PAGLKPWFEVPGRKTRDYTIVFGHWAALEGLTTPPNII 241
Query: 911 CLDTGCVWGNKLTALCLEDRSIIQVN 936
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 (823), Expect = e-103
Identities = 118/259 (45%), Positives = 159/259 (61%), Gaps = 11/259 (4%)
Query: 674 DVHGCKKSLSILLKKIHKKSPEANFIFLGDLINKGPQSLDTLRMVYSMRNYAKIVLGNHE 733
D+ GC L LL+KI+ + +GDL+N+GP SL+TLR V S+ + AK VLGNH+
Sbjct: 6 DIQGCYDELQRLLEKINFDPAKDRLWLVGDLVNRGPDSLETLRFVKSLGDSAKTVLGNHD 65
Query: 734 IHLLDVLININKKSKLDTFDDILDAPDKKKLVSWLRTQPLAIY--YKKYLMIHAGVAKQW 791
+HLL V I K K DT DDIL+APD+ +L+ WLR QPL LM+HAG+ QW
Sbjct: 66 LHLLAVAAGIKKPKKKDTLDDILNAPDRDELLDWLRHQPLLHRDPELGILMVHAGIPPQW 125
Query: 792 TAQQTIKLSHQVEKILRTSYWKNLFFKLYNHNSINWDNHLHTIHLNTIDKLQFIINTLTR 851
+ +Q +KL+ +VE LR ++ +Y + W + L ID+L++I+N TR
Sbjct: 126 SIEQALKLAREVEAALRGPNYREFLKNMYGNEPDRWSD-----DLTGIDRLRYIVNAFTR 180
Query: 852 TRFCKIDGTIEF-IKKNIKNNNFQNNYIPWFDLPNRKTIDITVLFGHWSTLGLIMKP-NI 909
RFC DG ++F K ++ PWF+LPNRKT D T++FGHW+ LG +P NI
Sbjct: 181 MRFCTPDGRLDFSSKGAPEDAP--KGLKPWFELPNRKTDDYTIVFGHWAALGGKTRPNNI 238
Query: 910 ICLDTGCVWGNKLTALCLE 928
I LDTGCVWG KLTAL LE
Sbjct: 239 IALDTGCVWGGKLTALRLE 257
>gnl|CDD|236828 PRK11034, clpA, ATP-dependent Clp protease ATP-binding subunit;
Provisional.
Length = 758
Score = 296 bits (759), Expect = 1e-87
Identities = 133/249 (53%), Positives = 176/249 (70%), Gaps = 2/249 (0%)
Query: 14 LKKYTIDLTEKARLGKLDPVIGRDDEIRRAIQVLQRRSKNNPVLIGEPGVGKTAIVEGLA 73
++ +T +L + AR+G +DP+IGR+ E+ RAIQVL RR KNNP+L+GE GVGKTAI EGLA
Sbjct: 169 MENFTTNLNQLARVGGIDPLIGREKELERAIQVLCRRRKNNPLLVGESGVGKTAIAEGLA 228
Query: 74 QRIINGEVPNSLLSKKILLLDIALLLAGTKYRGEFEDRLKKILKEISNNQKDIIIFIDEL 133
RI+ G+VP + I LDI LLAGTKYRG+FE R K +LK++ + I+FIDE+
Sbjct: 229 WRIVQGDVPEVMADCTIYSLDIGSLLAGTKYRGDFEKRFKALLKQLE-QDTNSILFIDEI 287
Query: 134 HTMIGTGKVE-GSIDAGNMLKPELSRGELHCIGATTLNEYRQYIEKDAAFERRFQKILVE 192
HT+IG G G +DA N++KP LS G++ IG+TT E+ EKD A RRFQKI +
Sbjct: 288 HTIIGAGAASGGQVDAANLIKPLLSSGKIRVIGSTTYQEFSNIFEKDRALARRFQKIDIT 347
Query: 193 EPDIEETISILRGLQKKYEVHHGVEITDPAIVAASELSYRYISDRFMPDKAIDLIDEAAA 252
EP IEET+ I+ GL+ KYE HH V T A+ AA EL+ +YI+DR +PDKAID+IDEA A
Sbjct: 348 EPSIEETVQIINGLKPKYEAHHDVRYTAKAVRAAVELAVKYINDRHLPDKAIDVIDEAGA 407
Query: 253 KIKIEIDSK 261
+ ++ SK
Sbjct: 408 RARLMPVSK 416
Score = 248 bits (635), Expect = 2e-70
Identities = 133/326 (40%), Positives = 204/326 (62%), Gaps = 18/326 (5%)
Query: 387 KTKVGSEEIAEIVSRTTGIPVSKIVQVEREKLLNIENLLCKRVVGQDEAISAVSNAIRRS 446
K V +I +V+R IP + Q +R+ L N+ + L V GQD+AI A++ AI+ S
Sbjct: 418 KKTVNVADIESVVARIARIPEKSVSQSDRDTLKNLGDRLKMLVFGQDKAIEALTEAIKMS 477
Query: 447 RSGLSDAKRPYGSFMFLGPTGVGKTELCKTLSACIFNNEESIIRIDMSEFIEKHSISRLI 506
R+GL +P GSF+F GPTGVGKTE+ LS + ++R DMSE++E+H++SRLI
Sbjct: 478 RAGLGHEHKPVGSFLFAGPTGVGKTEVTVQLSKAL---GIELLRFDMSEYMERHTVSRLI 534
Query: 507 GAPPGYIGYEEGGYLTEIVRRKPYSLILLDEIEKANSDVFNILLQILDDGRLTDNRGRTI 566
GAPPGY+G+++GG LT+ V + P++++LLDEIEKA+ DVFN+LLQ++D+G LTDN GR
Sbjct: 535 GAPPGYVGFDQGGLLTDAVIKHPHAVLLLDEIEKAHPDVFNLLLQVMDNGTLTDNNGRKA 594
Query: 567 NFRNTIIVMTSNLGSDKIKEMEKGDKEIIK----LAVMNEVKIYFRPEFINRIDDIIVFR 622
+FRN ++VMT+N G ++E E+ +I M E+K F PEF NR+D+II F
Sbjct: 595 DFRNVVLVMTTNAG---VRETERKSIGLIHQDNSTDAMEEIKKIFTPEFRNRLDNIIWFD 651
Query: 623 YLNRKNILSIANIQLNILKNKLLKMNMDLKISKAALKKISNIGFDLIYGARDVHGCKKSL 682
+L+ I + + + L+ +L + + L++S+ A ++ G+D GAR + + +
Sbjct: 652 HLSTDVIHQVVDKFIVELQAQLDQKGVSLEVSQEARDWLAEKGYDRAMGARPM---ARVI 708
Query: 683 SILLKKIHKKSPEANFIFLGDLINKG 708
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: 455 RPYGSFMFLGPTGVGKTELCKTLSACIFNNEESIIRIDMSEFIEKHSISRLIGAPPGYIG 514
RP GSF+FLGPTGVGKTEL K L+ +F +E ++IRIDMSE++E+HS+SRLIGAPPGY+G
Sbjct: 1 RPIGSFLFLGPTGVGKTELAKALAELLFGDERALIRIDMSEYMEEHSVSRLIGAPPGYVG 60
Query: 515 YEEGGYLTEIVRRKPYSLILLDEIEKANSDVFNILLQILDDGRLTDNRGRTINFRNTIIV 574
YEEGG LTE VRRKPYS++L+DEIEKA+ V N LLQIL+ G LTD +GR ++FRNT+ +
Sbjct: 61 YEEGGQLTEAVRRKPYSIVLIDEIEKAHPGVQNDLLQILEGGTLTDKQGRKVDFRNTLFI 120
Query: 575 MTSNLGSDKIKEMEKG----DKEIIKLAVMNEVKIYFRPEFINRIDDI 618
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 (515), Expect = 8e-59
Identities = 91/261 (34%), Positives = 139/261 (53%), Gaps = 11/261 (4%)
Query: 674 DVHGCKKSLSILLKKIHKKSPEANFIFLGDLINKGPQSLDTLRMVYSMRNYAKIVLGNHE 733
D+HGC L LL+++ + GDL+ +GP SL+ LR V S+ + ++VLGNH+
Sbjct: 8 DLHGCYDELQALLERVEFDPGQDTLWLTGDLVARGPGSLEVLRYVKSLGDAVRLVLGNHD 67
Query: 734 IHLLDVLININKKSKLDTFDDILDAPDKKKLVSWLRTQPLAIY--YKKYLMIHAGVAKQW 791
+HLL V I++ D D +L+APD +L++WLR QPL + KK +M HAG+ QW
Sbjct: 68 LHLLAVFAGISRNKPKDRLDPLLEAPDADELLNWLRRQPLLQHDEEKKLVMAHAGITPQW 127
Query: 792 TAQQTIKLSHQVEKILRTSYWKNLFFKLYNHNSINWDNHLHTIHLNTIDKLQFIINTLTR 851
Q + + VE +L + + +Y W L + +L+FIIN TR
Sbjct: 128 DLQTAKECARDVEAVLSSDSYPFFLDAMYGDMPNRWSPELQ-----GLARLRFIINAFTR 182
Query: 852 TRFCKIDGTIEFI-KKNIKNNNFQNNYIPWFDLPNRKTIDITVLFGHWSTL-GLIMKPNI 909
RFC +G ++ K++ ++ PWF +P + ++ FGHW++L G I
Sbjct: 183 MRFCFPNGQLDMYSKESPEDA--PAPLKPWFAIPGPVYEEYSIAFGHWASLEGEGTPEGI 240
Query: 910 ICLDTGCVWGNKLTALCLEDR 930
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: 674 DVHGCKKSLSILLKKIHKKSPEANFIFLGDLINKGPQSLDTLRMVYSM---RNYAKIVLG 730
D+HGC L LL+KI P IFLGD +++GP S++ + ++ ++ + ++ G
Sbjct: 5 DIHGCLDDLLRLLEKIGF-PPNDKLIFLGDYVDRGPDSVEVIDLLLALKILPDNVILLRG 63
Query: 731 NHEIHLLDVLININKKSKLDTFDDI----LDAPDKKKLVSWLRTQPLAIYY--KKYLMIH 784
NHE LL+ L + + L ++ PLA KK L +H
Sbjct: 64 NHEDMLLNFLYGFYDEDEWIGGTLRLLKKLGEDLWEEFNDVFFYLPLAALIETKKVLCVH 123
Query: 785 AGVAKQWTAQQTIKLSHQVEKILRTSYWKNLFFKLYNHNSINWDNHLHTIHLNTIDKLQF 844
G++ ++ IK +
Sbjct: 124 GGLSPGLPLEEQIKEEPE----------------------------------------DQ 143
Query: 845 IINTLTRTRFCKIDGTIEFIKKNIKNNNFQNNYIPWFDLPNRKTIDITVLFGHWSTLGLI 904
+ L + ++ G ++ + + WF N ++ GH
Sbjct: 144 LPEDLLWSDPLELPGGFGSSRRGGG-----PDAVEWFLKKNG---LKLIVRGHTPVEEGY 195
Query: 905 M---KPNIICLDTGCVW----GNKLTALCL 927
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 = 82.6 bits (204), Expect = 2e-18
Identities = 38/163 (23%), Positives = 65/163 (39%), Gaps = 14/163 (8%)
Query: 34 IGRDDEIRRAIQVLQRRSKNNPVLIGEPGVGKTAIVEGLAQRIINGEVPNSLLSKKILLL 93
+G+++ I + L+ N +L G PG GKT + +A + P L L
Sbjct: 1 VGQEEAIEALREALELPPPKNLLLYGPPGTGKTTLARAIANELFRPGAP-------FLYL 53
Query: 94 DIALLLAGTKYRGEFEDRLKKILKEISNNQKDIIIFIDELHTMIG--TGKVEGSIDAGNM 151
+ + LL G F L ++L E++ K ++FIDE+ ++ + ++ N
Sbjct: 54 NASDLLEGLVVAELFGHFLVRLLFELAEKAKPGVLFIDEIDSLSRGAQNALLRVLETLND 113
Query: 152 LKPELSRGELHCIGATTLNEYRQYIEKDAAFERRFQKILVEEP 194
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: 430 VGQDEAISAVSNAIRRSRSGLSDAKRPYGSFMFLGPTGVGKTELCKTLSACIFNNEESII 489
VGQ+EAI A+ A+ P + + GP G GKT L + ++ +F +
Sbjct: 1 VGQEEAIEALREALEL---------PPPKNLLLYGPPGTGKTTLARAIANELFRPGAPFL 51
Query: 490 RIDMSEFIEKHSISRLIGAPPGYIGYEEGGYLTEIVRRKPYSLILLDEIEKANSDVFNIL 549
++ S+ +E ++ L G + L E+ + ++ +DEI+ + N L
Sbjct: 52 YLNASDLLEGLVVAELFGHFLVRL-------LFELAEKAKPGVLFIDEIDSLSRGAQNAL 104
Query: 550 LQILDDGRLTDNRGRTINFRNTIIVMTSNLGSDKIKEMEKGDKEIIKLAVMNEVKIYFRP 609
L++L+ I+ N ++ +N
Sbjct: 105 LRVLETLNDL-----RIDRENVRVIGATNRPLLGD----------------------LDR 137
Query: 610 EFINRIDDIIVFRY 623
+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 = 3e-12
Identities = 40/140 (28%), Positives = 64/140 (45%), Gaps = 33/140 (23%)
Query: 674 DVHGCKKSLSILLKKI----------HKKSPEANFIFLGDLINKGPQSLDTLRMVYSM-- 721
D+HG + L +LL K+ H PE +FLGDLI++GP+ + L +V SM
Sbjct: 6 DIHGHAEKLVVLLHKLGYQELSGVYRH---PERQVVFLGDLIDRGPEIRELLEIVKSMVD 62
Query: 722 RNYAKIVLGNHEI-----HLLDVLI----------NINK-KSKLDTFDDILDAPDKKKLV 765
+A V+GNHE H D N+ + ++ L+ F + + K +
Sbjct: 63 AGHALAVMGNHEFNAIAWHTKDPSGGEWLRAHSKKNLRQHQAFLEQF--REHSEEHKDWL 120
Query: 766 SWLRTQPLAIYYKKYLMIHA 785
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 = 5e-12
Identities = 30/134 (22%), Positives = 53/134 (39%), Gaps = 7/134 (5%)
Query: 456 PYGSFMFLGPTGVGKTELCKTLSACIFNNEESIIRIDMSEFIEKHSISRLIGAPPGYIGY 515
P + +GP G GKT L + L+ + +I ID + +E+ L+ G
Sbjct: 1 PGEVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKAS 60
Query: 516 EEGGY----LTEIVRRKPYSLILLDEIEKANSDVFNILLQILDDGRLTDNRGRTINFRNT 571
G + R+ +++LDEI LL +L++ RL +N
Sbjct: 61 GSGELRLRLALALARKLKPDVLILDEITSLLDAEQEALLLLLEELRLLLLLKS---EKNL 117
Query: 572 IIVMTSNLGSDKIK 585
+++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: 51 SKNNPVLIGEPGVGKTAIVEGLAQRI---------INGEVPNSLLSKKILLLDIALLLAG 101
+++G PG GKT + LA+ + I+GE + ++LL+ + G
Sbjct: 1 PGEVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIV----GG 56
Query: 102 TKYRGEFEDRLKKILKEISNNQKDIIIFIDELHTMIG--TGKVEGSIDAGNMLKPELSRG 159
K G E RL+ L + D ++ +DE+ +++ + ++ +L S
Sbjct: 57 KKASGSGELRLRLALALARKLKPD-VLILDEITSLLDAEQEALLLLLEELRLLLLLKSEK 115
Query: 160 ELHCIGATTLNEYRQYIEKDAAFERRFQKILVEEP 194
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 = 63.1 bits (154), Expect = 8e-12
Identities = 36/136 (26%), Positives = 56/136 (41%), Gaps = 16/136 (11%)
Query: 459 SFMFLGPTGVGKTELCKTLSACIFNNEESIIRI--DMSEFIEKHSISRLIGA--PPGYIG 514
+ +GP G GK+EL + L+A + N +++ D +E L G
Sbjct: 1 GVLLVGPPGTGKSELAERLAAALSNRPVFYVQLTRDTTE-------EDLKGRRNIDPGGA 53
Query: 515 YEEGGYLTEIVRRKPYSLILLDEIEKANSDVFNILLQILDDGRLTDNRGRTI---NFRNT 571
G L R + +LDEI +AN DV N LL +LD+ RL G +
Sbjct: 54 SWVDGPLVRAAREG--EIAVLDEINRANPDVLNSLLSLLDERRLLLPEGGELVKAAPDGF 111
Query: 572 IIVMTSNLGSDKIKEM 587
++ T N + E+
Sbjct: 112 RLIATMNPLDRGLNEL 127
Score = 36.1 bits (84), Expect = 0.021
Identities = 28/140 (20%), Positives = 45/140 (32%), Gaps = 16/140 (11%)
Query: 56 VLIGEPGVGKTAIVEGLAQRIINGEVPNSLLSKKILLLDIALLLAGTKYRGEFEDRLKKI 115
+L+G PG GK+ + E LA + N V L++ L +
Sbjct: 3 LLVGPPGTGKSELAERLAAALSNRPVFYVQLTRD---TTEEDLKGRRNIDPGGASWVDGP 59
Query: 116 LKEISNNQKDIIIFIDELHTMIGT---GKVEGSIDAGNMLKPELSRGELHC------IGA 166
L + + I +DE+ + +D +L PE + + A
Sbjct: 60 LVRAAREGE--IAVLDEI-NRANPDVLNSLLSLLDERRLLLPEG-GELVKAAPDGFRLIA 115
Query: 167 TTLNEYRQYIEKDAAFERRF 186
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: 57 LIGEPGVGKTAIVEGLAQRIINGEVPNSLLSKKILLLDIALLLAGTKYRGEFEDRLKKIL 116
L G PG GKT + + +A+ + ++I+ +KY GE E RL+++
Sbjct: 3 LYGPPGTGKTTLAKAVAKEL------------GAPFIEISGSELVSKYVGESEKRLRELF 50
Query: 117 KEISNNQKDIIIFIDELHTMIGTGKVEGSIDAG---NMLKPEL-----SRGELHCIGATT 168
+ +IFIDE+ + G+ G ++ N L EL S ++ I AT
Sbjct: 51 EAAKKLAPC-VIFIDEIDALAGSRGSGGDSESRRVVNQLLTELDGFTSSLSKVIVIAATN 109
Query: 169 LNEYRQYIEK-DAAFER-RFQKIL 190
+K D A R RF +I+
Sbjct: 110 ------RPDKLDPALLRGRFDRII 127
Score = 42.6 bits (101), Expect = 1e-04
Identities = 29/129 (22%), Positives = 46/129 (35%), Gaps = 32/129 (24%)
Query: 461 MFLGPTGVGKTELCKTLSACIFNNEESIIRIDMSEFIEKHSISRLIGAPPGYIGYEEGGY 520
+ GP G GKT L K ++ + I I SE + K+ +G +
Sbjct: 2 LLYGPPGTGKTTLAKAVAKELGAP---FIEISGSELVSKY-----VGESEKRL----REL 49
Query: 521 LTEIVRRKPYSLILLDEIEK-----------ANSDVFNILLQILDDGRLTDNRGRTINFR 569
+ P +I +DEI+ + V N LL LD G T +
Sbjct: 50 FEAAKKLAP-CVIFIDEIDALAGSRGSGGDSESRRVVNQLLTELD--------GFTSSLS 100
Query: 570 NTIIVMTSN 578
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 = 60.7 bits (148), Expect = 4e-10
Identities = 41/142 (28%), Positives = 66/142 (46%), Gaps = 25/142 (17%)
Query: 666 FDLIYGARDVHGCKKSLSILL-------KKIHKKSPEAN--FIFLGDLINKGPQSLDTLR 716
FD+I DVHGC L LL K++ + +F+GDL+++GP S + LR
Sbjct: 3 FDII---GDVHGCYDELEELLEKLGYRIKRVGTVTHPEGRRAVFVGDLVDRGPDSPEVLR 59
Query: 717 MVYSM--RNYAKIVLGNHEIHLLDVLININKKSK--LD-TFDDILDAPD--KKKLVSWLR 769
+V SM A V GNH+ L L N K L+ T + + K++++ +
Sbjct: 60 LVMSMVAAGAALCVPGNHDNKLYRKLQGRNVKITHGLEETVAQLEAESEEFKEEVIEFYE 119
Query: 770 TQPLAIYY----KKYLMIHAGV 787
+ 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: 890 DITVLFGHWSTLGLIMKPNIICLDTGCVWGNKLTALCLEDRSIIQV 935
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 = 60.9 bits (148), Expect = 8e-10
Identities = 46/172 (26%), Positives = 69/172 (40%), Gaps = 23/172 (13%)
Query: 412 QVEREKLLNIENLLCKRVVGQDEAISAVSNAIRRSRSGLSDAKRPYGSFMFLGPTGVGKT 471
+ E L I + L K VVG +E I A+ A + GP GVGKT
Sbjct: 9 ERVAEILGKIRSELEKVVVGDEEVIELALLALL--------AGGH---VLLEGPPGVGKT 57
Query: 472 ELCKTLSACIFNNEESIIRIDMSEFIEKHSISRLIGAPPGYIGYEEGGYLTEIVRRK--- 528
L + L+ + +RI + + S L+G E G V
Sbjct: 58 LLARALARALGLP---FVRIQCTPDLLP---SDLLGTYAYAALLLEPGE-FRFVPGPLFA 110
Query: 529 -PYSLILLDEIEKANSDVFNILLQILDDGRLTDNRGRTINFRN-TIIVMTSN 578
++LLDEI +A +V N LL+ L++ ++T TI I++ T N
Sbjct: 111 AVRVILLLDEINRAPPEVQNALLEALEERQVTVPGLTTIRLPPPFIVIATQN 162
Score = 39.3 bits (92), Expect = 0.006
Identities = 17/54 (31%), Positives = 27/54 (50%), Gaps = 2/54 (3%)
Query: 23 EKARLGKLDPVIGRDDEIRRAIQVLQRRSKNNPVLIGEPGVGKTAIVEGLAQRI 76
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 = 51.2 bits (124), Expect = 3e-08
Identities = 15/50 (30%), Positives = 31/50 (62%)
Query: 624 LNRKNILSIANIQLNILKNKLLKMNMDLKISKAALKKISNIGFDLIYGAR 673
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: 666 FDLIYGARDVHGCKKSLSILLKKI--------HKKSPEAN------FIFLGDLINKGPQS 711
FD+I G DVHGC+ L LL+++ + + +F+GDL+++GP S
Sbjct: 182 FDII-G--DVHGCRDELETLLEELGYQIERDEGGRPVDVTHPEGRKAVFVGDLVDRGPDS 238
Query: 712 LDTLRMVYSMRN--YAKIVLGNHEIHLLDVL 740
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: 892 TVLFGHWSTLGLIMKPNIICLDTGCVWGNKLTALCLEDRSIIQV 935
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 = 49.5 bits (118), Expect = 6e-07
Identities = 28/129 (21%), Positives = 54/129 (41%), Gaps = 26/129 (20%)
Query: 32 PVIGRDDEIRRAIQVLQRRSKNNP---VLIGEPGVGKTAIVEGLAQR---------IING 79
++GR++E+ R + L+R P +L G G GKT+++ L +
Sbjct: 1 RLVGREEELERLLDALRRARSGGPPSVLLTGPSGTGKTSLLRELLEGLLVAAGKCDQAER 60
Query: 80 EVPNSL--------------LSKKILLLDIALLLAGTKYRGEFEDRLKKILKEISNNQKD 125
P + L+ ++LLL ALL A E L ++L+ + +
Sbjct: 61 NPPYAFSQALRELLRQLLRELAAELLLLREALLAALGAELIEGLQDLVELLERLLARARP 120
Query: 126 IIIFIDELH 134
+++ +D+L
Sbjct: 121 LVLVLDDLQ 129
Score = 40.6 bits (95), Expect = 8e-04
Identities = 29/153 (18%), Positives = 62/153 (40%), Gaps = 29/153 (18%)
Query: 428 RVVGQDEAISAVSNAIRRSRSGLSDAKRPYGSFMFLGPTGVGKTELCKTLS--------- 478
R+VG++E + + +A+RR+RSG S + GP+G GKT L + L
Sbjct: 1 RLVGREEELERLLDALRRARSG------GPPSVLLTGPSGTGKTSLLRELLEGLLVAAGK 54
Query: 479 -----ACIFNNEESIIRIDMSEFIEKH---------SISRLIGAPPGYIGYEEGGYLTEI 524
+R + + + + ++ +GA + L +
Sbjct: 55 CDQAERNPPYAFSQALRELLRQLLRELAAELLLLREALLAALGAELIEGLQDLVELLERL 114
Query: 525 VRRKPYSLILLDEIEKANSDVFNILLQILDDGR 557
+ 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 = 45.9 bits (110), Expect = 3e-06
Identities = 15/50 (30%), Positives = 32/50 (64%)
Query: 624 LNRKNILSIANIQLNILKNKLLKMNMDLKISKAALKKISNIGFDLIYGAR 673
L++++++ I ++ LN L+ +L + + L+ + AL ++ G+D YGAR
Sbjct: 1 LDKEDLVRIVDLPLNALQKRLAEKGITLEFTDEALDWLAEKGYDPKYGAR 50
>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: 674 DVHGCKKSLSILLKKIHKKSPEAN-FIFLGDLINKGPQSLDTLRM-----VYSMRNYAKI 727
D+HG L L + P + I +GDLI++GP+SL L + ++
Sbjct: 8 DIHGHYSLLQKALDAVGF-DPARDRLISVGDLIDRGPESLACLELLLEPWFHA------- 59
Query: 728 VLGNHEIHLLDVLININKKSKL------DTFDDILDAPDKKKLVSWLRTQPLAI 775
V GNHE +D L + + F D+ D ++ L L PLAI
Sbjct: 60 VRGNHEQMAIDALRAEPLDAVRWLANGGEWFLDLPDEELRRWLALKLEQLPLAI 113
Score = 30.3 bits (69), Expect = 3.8
Identities = 12/36 (33%), Positives = 18/36 (50%)
Query: 892 TVLFGHWSTLGLIMKPNIICLDTGCVWGNKLTALCL 927
V+ GH + N++ +DTG V+ LT L L
Sbjct: 171 AVVHGHTPVKRPLRLGNVLYIDTGAVFDGNLTLLDL 206
>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 = 49.5 bits (118), Expect = 7e-06
Identities = 68/252 (26%), Positives = 101/252 (40%), Gaps = 59/252 (23%)
Query: 56 VLIGEPGVGKTAIVEGLAQRI------INGEVPNSLLSKKILLLDIALLLAGTKYRGEFE 109
+L G PG GKT + + +A ING P + +KY GE E
Sbjct: 216 LLYGPPGTGKTLLAKAVANEAGAYFISING--PEIM----------------SKYYGESE 257
Query: 110 DRLKKILKEISNNQKDIIIFIDELHTMI-----GTGKVEGSIDAG--NMLKPELSRGELH 162
+RL++I KE N IIFIDE+ + TG+VE + A ++ RG +
Sbjct: 258 ERLREIFKEAEENAPS-IIFIDEIDAIAPKREEVTGEVEKRVVAQLLTLMDGLKGRGRVI 316
Query: 163 CIGATTLNEYRQYIEKDAAFER--RFQK-ILVEEPDIEETISILR------------GLQ 207
IGAT + D A R RF + I++ PD IL+ L
Sbjct: 317 VIGATNRPD-----ALDPALRRPGRFDREIVIRVPDKRARKEILKVHTRNMPLAEDVDLD 371
Query: 208 KKYEVHHGVEITDPAIVAASELSYRYISDRFMPDKAIDLIDEAAAK-----IKIEIDSKP 262
K EV HG D A + A E + + RF+ + I+ E +K+ +
Sbjct: 372 KLAEVTHGFVGADLAAL-AKEAAMAALR-RFIREGKINFEAEEIPAEVLKELKVTMKDFM 429
Query: 263 EIMDKLERRLIQ 274
E + +E I+
Sbjct: 430 EALKMVEPSAIR 441
>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: 674 DVHGCKKSLSI--LLKKIHKKSPEANFIFLGDLINKGPQSLDTLRMVYSMRNYAKI---- 727
D+HG L + LL ++ + +FLGDL+++GP SL+ L ++++++ A
Sbjct: 7 DLHGGLDDLDLLLLLLELLGEPKPDLVLFLGDLVDRGPPSLEVLALLFALKLKAPGPVYL 66
Query: 728 VLGNHEIHLLD 738
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: 674 DVHGCKKSLSILLKKIHKK--SPEANF-IFLGDLINKGPQSLDTLRMVYSMRNYAKIVLG 730
D+HGC L++K+ P + I +GDLI++GPQSL L+++ ++ + V G
Sbjct: 24 DIHGC---FEQLMRKLRHCRFDPWRDLLISVGDLIDRGPQSLRCLQLLE--EHWVRAVRG 78
Query: 731 NHEIHLLDVLIN 742
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: 674 DVHGCKKSLSILLKKIHKKSPEANF-IFLGDLINKGPQSLDTLRMVYSMRNYAKI----V 728
D+HG ++L +L+ + + +F + LGDL+ GP + L ++ I V
Sbjct: 5 DIHGNLEALEAVLEAALAAAEKPDFVLVLGDLVGDGPDPEEVLAAALALLLLLGIPVYVV 64
Query: 729 LGNHEIHL 736
GNH+I L
Sbjct: 65 PGNHDILL 72
>gnl|CDD|222104 pfam13401, AAA_22, AAA domain.
Length = 124
Score = 44.2 bits (105), Expect = 3e-05
Identities = 20/105 (19%), Positives = 42/105 (40%), Gaps = 7/105 (6%)
Query: 458 GSFMFLGPTGVGKTELCKTLSACIFNNEESIIRIDMSEFIEKHSISRLI----GAPPGYI 513
G + G +G GKT L + L+ + N ++ ++ + R I G P
Sbjct: 5 GIGVLTGESGSGKTTLLRRLARQLPNRR--VVYVEAPSLGTPKDLLRKILRALGLPLSGG 62
Query: 514 GYEEG-GYLTEIVRRKPYSLILLDEIEKANSDVFNILLQILDDGR 557
E + + ++R+ L+++DE + + + L + D
Sbjct: 63 TTAELLEAILDALKRRGRPLLIIDEAQHLSLEALEELRDLYDLSE 107
Score = 43.0 bits (102), Expect = 6e-05
Identities = 27/90 (30%), Positives = 39/90 (43%), Gaps = 5/90 (5%)
Query: 49 RRSKNNPVLIGEPGVGKTAIVEGLAQRIINGEV----PNSLLSKKILLLDIALLLAGTKY 104
RR VL GE G GKT ++ LA+++ N V SL + K LL I L G
Sbjct: 1 RRGAGIGVLTGESGSGKTTLLRRLARQLPNRRVVYVEAPSLGTPKDLLRKILRAL-GLPL 59
Query: 105 RGEFEDRLKKILKEISNNQKDIIIFIDELH 134
G L + + + + ++ IDE
Sbjct: 60 SGGTTAELLEAILDALKRRGRPLLIIDEAQ 89
>gnl|CDD|184187 PRK13625, PRK13625, bis(5'-nucleosyl)-tetraphosphatase PrpE;
Provisional.
Length = 245
Score = 46.2 bits (110), Expect = 3e-05
Identities = 24/80 (30%), Positives = 39/80 (48%), Gaps = 19/80 (23%)
Query: 666 FDLIYGARDVHGCKKSLSILLKK----------IHKKSPEA-NFIFLGDLINKGPQSLDT 714
+D+I D+HGC + L +K +H P+ F+GDL ++GP SL
Sbjct: 3 YDII---GDIHGCYQEFQALTEKLGYNWSSGLPVH---PDQRKLAFVGDLTDRGPHSLRM 56
Query: 715 LRMVYSM--RNYAKIVLGNH 732
+ +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: 908 NIICLDTGCVWGNKLTAL 925
+ + +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: 669 IYGARDVHG-CKKSLSILLKKIHKKSPEANFIFLGDLINKGPQSLDTLRMVYS-MRNYAK 726
IY D+HG +K L+I+ K +++ PE +FLGD +++G +S D + ++ M N
Sbjct: 3 IYVVPDIHGEYQKLLTIMDKINNERKPEETIVFLGDYVDRGKRSKDVVNYIFDLMSNDDN 62
Query: 727 IV--LGNHEIHLLDVLININKKSKLD 750
+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: 659 KKISNIGFDLIYGARDVHGCKKSLSILLKKIHKKS--PEANF-IFLGDLINKGPQSLDTL 715
+KI+ + I+ D+HG +L ++H+ S PE + I +GD I++GP+SL+ L
Sbjct: 7 QKINAHHYRHIWVVGDIHGE---YQLLQSRLHQLSFCPETDLLISVGDNIDRGPESLNVL 63
Query: 716 RMVYSMRNYAKIVLGNHEIHLLDVLI----NINKKSKLDTFDDILDAPDKKKLVSWLRTQ 771
R++ + + V GNHE LD N+ S D F D+ D+ ++ L+
Sbjct: 64 RLLN--QPWFISVKGNHEAMALDAFETGDGNMWLASGGDWFFDLNDSEQQEATDLLLKFH 121
Query: 772 --PLAIYYK----KYLMIHA 785
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: 674 DVHGCKKSLSILLKKIHKKSPEANFIFLGDLINKGPQSLDTLRMVYSM--RNYAKIVL-- 729
D+HG L L K + PE N++FLGD +++GP S++ + +++++ +IVL
Sbjct: 35 DIHGQFDDLLRLFDKN-GQPPETNYVFLGDYVDRGPFSIEVILLLFALKILYPNRIVLLR 93
Query: 730 GNHE 733
GNHE
Sbjct: 94 GNHE 97
>gnl|CDD|226415 COG3899, COG3899, Predicted ATPase [General function prediction
only].
Length = 849
Score = 42.0 bits (99), Expect = 0.002
Identities = 30/143 (20%), Positives = 53/143 (37%), Gaps = 24/143 (16%)
Query: 32 PVIGRDDEIRRAIQVLQRRSKNNPVLI---GEPGVGKTAIVEGLAQRIINGEVPNSLLSK 88
P+ GR+ E+ + + R SK ++ GE G+GK+A+V + + I +
Sbjct: 1 PLYGRETELAQLLAAFDRVSKGRGEVVLVAGESGIGKSALVNEVHKPITQQR--GYFIKG 58
Query: 89 KILLL--DIALL--------LAG---TKYRGEFEDRLKKILKEISNNQKDIIIFIDELHT 135
K +I L L G ++ ++L + N + II I EL
Sbjct: 59 KFDQFERNIPLSPLVQAFRDLMGQLLSESDTRILSWRARLLAALGENGQVIIDVIPEL-- 116
Query: 136 MIGTGKVEGSIDAGNMLKPELSR 158
+ 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: 461 MFLGPTGVGKTELCKTLSACIFNNEESIIRIDMSEFIE-KHSISRLIGAPPGYIGYEEGG 519
G G GK+ L L + I+ I + E + K I PG + +G
Sbjct: 153 YLEGGRGSGKSFLISELCD---EGGQRIVEIHLREITDAKVLIGTYTSPKPGDFEWMKGV 209
Query: 520 YLTEIVRRKPYSLILLDEIEKANSDVFNILLQILDDGRLT-DNRGRTI----NFRNTIIV 574
+ +V IL I+KA V + LL +L+ RL +RG T+ NF+ I
Sbjct: 210 LIEAVVSGD---WILFKRIDKAPHGVLSYLLTLLEKRRLLIPSRGETVLAHDNFQ---IF 263
Query: 575 MTSNLGSDKIKEMEKGDKEIIKLAVMNEVKIYFRPEF 611
TS S K K + + +I+ L +E R +
Sbjct: 264 FTS---SMKTKILGQRLWQILDLTQPDECVEVVRFDM 297
Score = 37.3 bits (86), Expect = 0.045
Identities = 30/95 (31%), Positives = 47/95 (49%), Gaps = 7/95 (7%)
Query: 464 GPTGVGKTELCKTLSACIFNNEESIIRIDMSEFIE-KHSISRLIGAPPGYIGYEEGGYLT 522
GPT GKT + L+ +RI+ E + + I + G + ++EG L
Sbjct: 895 GPTSSGKTSMILYLAR---ETGHKFVRINNHEHTDLQEYIGTYVTDDDGSLSFKEG-VLV 950
Query: 523 EIVRRKPYSLILLDEIEKANSDVFNILLQILDDGR 557
E +RR + I+LDE+ A +DV L ++LDD R
Sbjct: 951 EALRRGYW--IVLDELNLAPTDVLEALNRLLDDNR 983
Score = 31.9 bits (72), Expect = 2.5
Identities = 26/96 (27%), Positives = 46/96 (47%), Gaps = 11/96 (11%)
Query: 40 IRRAIQVLQRRSKNNPVLI-GEPGVGKTAIVEGLAQRIINGEVPNSLLSKKILLLDIALL 98
+ RA+QV + P+L+ G PGVGKT+++ LA R ++ LS++ L D+
Sbjct: 1536 VLRAMQVGK------PILLEGSPGVGKTSLITALA-RKTGKKLIRINLSEQTDLCDLFGS 1588
Query: 99 LAGTKYRGEFEDRLKKILKEISNNQKDIIIFIDELH 134
+ 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: 241 DKAIDLIDEAAAKIKIEIDSKPEIMDKLERRLIQLKIEHEAIKREYDESSKKRLLLIKKE 300
K ++ ++E ++++ E++ E +++ E+ + +LK E E ++ E +E + LL +K+E
Sbjct: 238 RKELEELEEELSRLEEELEELQEELEEAEKEIEELKSELEELREELEELQ-EELLELKEE 296
Query: 301 INKLEIKYANLEKIWKYEKTLIKDSQQIKEEIEKVRLKI-NKATRKSDWQTVSKLKYGEL 359
I +LE + + L + + L + ++++E +E+++ KI + +T+ + L
Sbjct: 297 IEELEGEISLLRER---LEELENELEELEERLEELKEKIEALKEELEERETLLEELEQLL 353
Query: 360 NKLERILKEKSQK 372
+LE +E +K
Sbjct: 354 AELEEAKEELEEK 366
Score = 36.2 bits (84), Expect = 0.088
Identities = 24/155 (15%), Positives = 70/155 (45%), Gaps = 15/155 (9%)
Query: 242 KAIDLIDEAAAKIKIEIDSKPEIMDKLERRLIQLKIEHEAIKREYDESSKKRLLLIKKEI 301
+ ++ ++E + + +D+ ++ LE+R +L+ E E ++ E +E +++L +++E+
Sbjct: 793 EELEELEEELEEAERRLDALERELESLEQRRERLEQEIEELEEEIEEL-EEKLDELEEEL 851
Query: 302 NKLEIKYANL--------EKIWKYEKTLIKDSQQIKE---EIEKVRLKINKATRKSDWQT 350
+LE + L + + E L + ++ +E E+ ++ ++ + + +
Sbjct: 852 EELEKELEELKEELEELEAEKEELEDELKELEEEKEELEEELRELESELAELKEEIEKLR 911
Query: 351 VSKLKYGELNKLERILKEKSQKDIQLPNNANKFTL 385
+ EL L+ + + + + TL
Sbjct: 912 E---RLEELEAKLERLEVELPELEEELEEEYEDTL 943
Score = 35.1 bits (81), Expect = 0.23
Identities = 37/208 (17%), Positives = 95/208 (45%), Gaps = 14/208 (6%)
Query: 179 DAAFERRFQKILVEEPDIEETISILRGLQKKYEVH--HGVEITDPAIVAASELSYRYISD 236
+ A LV + D+E+ + R L+ KY + G + + + R
Sbjct: 606 EPAVRFVLGDTLVVD-DLEQARRLARKLRIKYRIVTLDGDLVEPSGSITGGSRNKRSSLA 664
Query: 237 RF----MPDKAIDLIDEAAAKIKIEIDSKPEIMDKLERRLIQLKIEHEAIKREYDESSKK 292
+ ++ + ++ K++ E+ S + LE L +L+ + E ++R+ +E K+
Sbjct: 665 QKRELKELEEELAELEAQLEKLEEELKSLKNELRSLEDLLEELRRQLEELERQLEE-LKR 723
Query: 293 RLLLIKKEINKLEIKYANLEK----IWKYEKTLIKDSQQIKEEIEKVRLKINKATRKSDW 348
L +++E+ +L+ + LE+ + + + L + ++++EE+E + + K K +
Sbjct: 724 ELAALEEELEQLQSRLEELEEELEELEEELEELQERLEELEEELESLEEALAK--LKEEI 781
Query: 349 QTVSKLKYGELNKLERILKEKSQKDIQL 376
+ + + + +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: 258 IDSKPEIMDKLERRLIQLKIEHEAIKREYDESSKKRLL---LIKKEINKLEIKYANLEKI 314
++ +++++LE++L +L+ + E +R + ++ R L L+ ++ +L + LE+
Sbjct: 188 LERLEDLLEELEKQLEKLERQAEKAERYQELKAELRELELALLLAKLKELRKELEELEEE 247
Query: 315 WKYEKTLIKDSQQ----IKEEIEKVRLKINKATRKSDWQTVSKLKYGELNKLERILKEKS 370
+ +++ Q+ ++EIE+++ ++ + + + + + ++E + E S
Sbjct: 248 LSRLEEELEELQEELEEAEKEIEELKSELEELREE--LEELQEELLELKEEIEELEGEIS 305
Query: 371 QKDIQLPNNANKFTLLKTKVGSEEIAEIVSRTTGIPVSKIVQVEREKLLNIENLLCKRVV 430
+L N+ L+ ++ E +I + + + + E E+LL + +
Sbjct: 306 LLRERLEELENELEELEERL-EELKEKIEALKEELEERETLLEELEQLLAELEEAKEELE 364
Query: 431 G-QDEAISAVSNAIRRSRSGLSDAKR 455
+ + R L++ +
Sbjct: 365 EKLSALLEELEELFEALREELAELEA 390
Score = 31.2 bits (71), Expect = 3.2
Identities = 26/117 (22%), Positives = 58/117 (49%), Gaps = 12/117 (10%)
Query: 241 DKAIDLIDEAAAKIKIEIDSKPEIMDKLERRLIQLKIEHEAIKREY-DESSKKRLLLIKK 299
++ + ++ A++K EI+ E +++LE +L +L++E ++ E +E +++
Sbjct: 890 EEELRELESELAELKEEIEKLRERLEELEAKLERLEVELPELEEELEEEYEDTLETELER 949
Query: 300 EINKLEIKYA-----NLEKIWKYEKT------LIKDSQQIKEEIEKVRLKINKATRK 345
EI +LE + NL I +YE+ L + ++E EK+ I + ++
Sbjct: 950 EIERLEEEIEALGPVNLRAIEEYEEVEERYEELKSQREDLEEAKEKLLEVIEELDKE 1006
Score = 30.5 bits (69), Expect = 5.5
Identities = 34/201 (16%), Positives = 89/201 (44%), Gaps = 23/201 (11%)
Query: 183 ERRFQKILVEEPDIEETISILRGLQKKYEVHHGVEITDPAIVAASELSYRYISDRFMP-D 241
E + + + +IEE + LQ++ E + A E + R +
Sbjct: 768 ESLEEALAKLKEEIEELEEKRQALQEELEELEEELEEAERRLDALERELESLEQRRERLE 827
Query: 242 KAIDLIDEAAAKIKIEIDSKPEIMDKLERRLIQLKIEHEAIKREYDESS------KKRLL 295
+ I+ ++E +++ ++D E +++LE+ L +LK E E ++ E +E ++
Sbjct: 828 QEIEELEEEIEELEEKLDELEEELEELEKELEELKEELEELEAEKEELEDELKELEEEKE 887
Query: 296 LIKKEINKLE-----IKYANLEKIWKYEKTLIKDSQQIKEEIEKVRLKIN---KATRKSD 347
+++E+ +LE +K + + E L ++++ E+ ++ ++ + T +++
Sbjct: 888 ELEEELRELESELAELKEEIEKLRERLE-ELEAKLERLEVELPELEEELEEEYEDTLETE 946
Query: 348 WQTVSKLKYGELNKLERILKE 368
+ 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 = 40.0 bits (94), Expect = 0.003
Identities = 24/67 (35%), Positives = 39/67 (58%), Gaps = 11/67 (16%)
Query: 674 DVHGCKKSLSILLKKIHKKS--PEANFIFLGDLINKGPQSLDT--LRMVYSMRNYAK--- 726
D+HG LL+ PE+N++FLGD +++G QSL+T L + Y ++ Y +
Sbjct: 57 DIHG---QYYDLLRLFEYGGFPPESNYLFLGDYVDRGKQSLETICLLLAYKIK-YPENFF 112
Query: 727 IVLGNHE 733
++ 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 = 40.5 bits (95), Expect = 0.004
Identities = 59/212 (27%), Positives = 88/212 (41%), Gaps = 52/212 (24%)
Query: 25 ARLGKLDPVIGRDDEIRRAIQV------LQRRSKNNP----VLIGEPGVGKT----AIVE 70
A +G L I + IR A+++ L R P +L G PG GKT A+
Sbjct: 182 ADIGGLGSQIEQ---IRDAVELPFLHPELYREYGLKPPKGVLLYGPPGCGKTLIAKAVAN 238
Query: 71 GLAQRI-INGEVPNSLLS-KKILLLDIALLLAGTKYRGEFEDRLKKIL---KEISNNQKD 125
LA RI G + L+ K LL+ KY GE E +++ I +E ++ +
Sbjct: 239 SLAARIGAEGGGKSYFLNIKGPELLN--------KYVGETERQIRLIFQRAREKASEGRP 290
Query: 126 IIIFIDELHTMI---GTGKVEGSIDAGNMLKPEL--------SRGELHCIGATTLNEYRQ 174
+I+F DE+ ++ G+G S D + P+L S + IGA+ +
Sbjct: 291 VIVFFDEMDSLFRTRGSGV---SSDVETTVVPQLLAEIDGVESLDNVIVIGASNREDM-- 345
Query: 175 YIEKDAAFER--RFQ-KILVEEPDIEETISIL 203
D A R R KI +E PD E I
Sbjct: 346 ---IDPAILRPGRLDVKIRIERPDAEAAADIF 374
>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: 459 SFMFLGPTGVGKTELCKTLSACIFNNEESIIRIDMSEFIEKHSISRLIGAPPGYIGYEEG 518
+ + LGP GVGKT L A NE I + +S+L A ++EG
Sbjct: 107 NLVLLGPPGVGKTHL-----AIAIGNELLKAGISVLFITAPDLLSKLKAA------FDEG 155
Query: 519 GYLTEIVRR-KPYSLILLDEI--EKANSDVFNILLQILDDGRLTDNRGRTINFRNTIIVM 575
+++R K L+++D+I E + + ++L Q++ I +
Sbjct: 156 RLEEKLLRELKKVDLLIIDDIGYEPFSQEEADLLFQLISRRY---ESRSLI--------I 204
Query: 576 TSNLGSDKIKEM---EKGDKEIIKLAVMNEVKIYFR 608
TSNL + E+ + + ++ + + I +
Sbjct: 205 TSNLSFGEWDELFGDDALTEALLDRILHHSHVIVIK 240
Score = 29.7 bits (67), Expect = 7.5
Identities = 21/102 (20%), Positives = 43/102 (42%), Gaps = 15/102 (14%)
Query: 37 DDEIRRAIQVLQRRSKNNP-----VLIGEPGVGKTAIVEGLAQRIINGEVPNSLLSKKIL 91
++A++ L + VL+G PGVGKT + + ++ + ++ L
Sbjct: 85 PGIDKKALEDLASLVEFFERGENLVLLGPPGVGKTHLAIAIGNELLKAGISVLFITAPDL 144
Query: 92 LLDIALLLAGTKYRGEFEDRLKKILKEISNNQKDIIIFIDEL 133
L L G E++L + LK++ ++ ID++
Sbjct: 145 LSK----LKAAFDEGRLEEKLLRELKKVD------LLIIDDI 176
>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 = 40.2 bits (94), Expect = 0.005
Identities = 35/155 (22%), Positives = 68/155 (43%), Gaps = 18/155 (11%)
Query: 42 RAIQVLQRRSKNNPVLIGEPGVGKTAIVEGLAQRIINGEVPNSLLSKKILLLDIALLLAG 101
R + V Q N+ + G PG GKT I +A +I G + +K L+ +++
Sbjct: 304 RGLPVAQT--SNHMLFAGPPGTGKTTIARVVA-KIYCGLG----VLRKPLVREVSR---- 352
Query: 102 TKYRGEFEDRLKKILKEISNNQKDIIIFIDELHTMIGTGKVEGSIDAGN------MLKPE 155
G++ + EI ++ ++F+DE +T++ TG + G + + E
Sbjct: 353 ADLIGQYIGESEAKTNEIIDSALGGVLFLDEAYTLVETGYGQKD-PFGLEAIDTLLARME 411
Query: 156 LSRGELHCIGATTLNEYRQYIEKDAAFERRFQKIL 190
R L IGA + +++E + RF +++
Sbjct: 412 NDRDRLVVIGAGYRKDLDKFLEVNEGLRSRFTRVI 446
Score = 30.6 bits (69), Expect = 4.5
Identities = 23/93 (24%), Positives = 40/93 (43%), Gaps = 7/93 (7%)
Query: 413 VEREKLLNIENLLCKRVVGQDEAI-SAVSNAIRRSRSGLSDAKRPYGSFMFLGPTGVGKT 471
E E L E + +RV Q A+ S+ + A+ R+ GL A+ +F GP G GKT
Sbjct: 269 AEAEAELA-EQIGLERVKRQVAALKSSTAMALARAERGLPVAQTSN-HMLFAGPPGTGKT 326
Query: 472 E----LCKTLSACIFNNEESIIRIDMSEFIEKH 500
+ K + + + ++ I ++
Sbjct: 327 TIARVVAKIYCGLGVLRKPLVREVSRADLIGQY 359
>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: 252 AKIKIEIDSKPEIMDKLERRLIQLKIEHEAIKREYDESSKK-------RLLLIKKEINKL 304
I+ ++ S E ++KL + +L+ E I++ +E +KK L +K++I +L
Sbjct: 240 EAIERQLASLEEELEKLTEEISELEKRLEEIEQLLEELNKKIKDLGEEEQLRVKEKIGEL 299
Query: 305 EIKYANLEKIWKYEKTLIKDSQ----QIKEEIEKVRLKI--------NKATRKSDWQTVS 352
E + A+LE+ ++ ++D++ +++ EI+K+ +I + R+
Sbjct: 300 EAEIASLERSIAEKERELEDAEERLAKLEAEIDKLLAEIEELEREIEEERKRRDKLTEEY 359
Query: 353 KLKYGELNKLERILKEKSQK 372
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: 248 DEAAAKIKIEIDSKPEIMDKLERRLIQLKIEHEAIKREYDESSKKRLLLIKKEINKLEIK 307
+E AK++ EID +++LER + + + + + EY E K+E+ L
Sbjct: 321 EERLAKLEAEIDKLLAEIEELEREIEEERKRRDKLTEEYAEL--------KEELEDLR-- 370
Query: 308 YANLEKIWKYEKTLIKDSQQIKEEIEKVRLKINKATRKSDWQTVSKLKYGELNKLERILK 367
A LE++ K + + +E++EK++ +IN+ R+ D R+ +
Sbjct: 371 -AELEEVDKEFAETRDELKDYREKLEKLKREINELKRELD----------------RLQE 413
Query: 368 EKSQKDIQLPNNANKFTLLKTKVGSEEIAEIVSRTTGIPVSKIVQVEREKLLNIENLLCK 427
E + +L + ++ +I E+ +I + E + +L
Sbjct: 414 ELQRLSEELADLNAAIAGIE-----AKINELEEEKEDK-ALEIKKQEWKLEQLAADL--- 464
Query: 428 RVVGQDEAISAVSNAIRRSRSGLSDAKRPY 457
++ + + R LS +R
Sbjct: 465 --SKYEQELYDLKEEYDRVEKELSKLQREL 492
Score = 34.3 bits (79), Expect = 0.40
Identities = 34/160 (21%), Positives = 72/160 (45%), Gaps = 14/160 (8%)
Query: 253 KIKIEIDSKPEIMDKLERRLIQLKIEHEAIKREYDESSKKRLLLIKKEINKLEIKYANLE 312
+K E+ S + ++E RL +L E R+ E K + +++E KL+ + LE
Sbjct: 685 GLKRELSSLQSELRRIENRLDELSQELSDASRKIGEIE-KEIEQLEQEEEKLKERLEELE 743
Query: 313 --------KIWKYE---KTLIKDSQQIKEEIEKVRLKINKATRKSDWQTVSKLKYGELNK 361
+I + K L ++++E++ K+ +N + + +++ EL+K
Sbjct: 744 EDLSSLEQEIENVKSELKELEARIEELEEDLHKLEEALNDLEARLSHSRIPEIQ-AELSK 802
Query: 362 LERILKEKSQKDIQLPNNANKFTLLKTKVGSEEIAEIVSR 401
LE + + ++ N+ TL K + +EI E+ +
Sbjct: 803 LEEEVSRIEARLREIEQKLNRLTLEK-EYLEKEIQELQEQ 841
Score = 31.2 bits (71), Expect = 3.0
Identities = 30/138 (21%), Positives = 64/138 (46%), Gaps = 13/138 (9%)
Query: 244 IDLIDEAAAKIKIEIDSKPEIMDKLERRLIQLKIEHEAIKREYDESSKKRLLL------I 297
I I +K++ E+ + ++E++L +L +E E +++E E ++R+ L I
Sbjct: 793 IPEIQAELSKLEEEVSRIEARLREIEQKLNRLTLEKEYLEKEIQELQEQRIDLKEQIKSI 852
Query: 298 KKEINKLEIKYANL----EKIWKYEKTLIKDSQQIKEEIEKVRLKINKATRKSDWQTVSK 353
+KEI L K L E++ + L +K+E +++ ++ + RK + +
Sbjct: 853 EKEIENLNGKKEELEEELEELEAALRDLESRLGDLKKERDELEAQLRELERKIEEL---E 909
Query: 354 LKYGELNKLERILKEKSQ 371
+ + K LK K +
Sbjct: 910 AQIEKKRKRLSELKAKLE 927
>gnl|CDD|237090 PRK12402, PRK12402, replication factor C small subunit 2;
Reviewed.
Length = 337
Score = 38.8 bits (91), Expect = 0.009
Identities = 18/55 (32%), Positives = 32/55 (58%)
Query: 22 TEKARLGKLDPVIGRDDEIRRAIQVLQRRSKNNPVLIGEPGVGKTAIVEGLAQRI 76
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: 674 DVHGCKKSLSILLKKIHKKSPEANFIFLGDLINKGPQSLDT--LRMVYSMRNYAKIVL-- 729
DVHG L + L + PE+N++FLGD +++G QSL+T L + Y ++ L
Sbjct: 66 DVHGQYFDL-LRLFEYGGYPPESNYLFLGDYVDRGKQSLETICLLLAYKIKYPENFFLLR 124
Query: 730 GNHE 733
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: 242 KAIDLIDEAAAKIKIEIDSKPEIMDKLER--------------RLIQL-KIEHEAIKREY 286
KAI IDE I+ ++K ++++LE+ RL +L K+E E + +E
Sbjct: 355 KAILNIDEVINLIRSSDEAKKALIEELEKLGFSEIQADAILDMRLRRLTKLEREKLLKEL 414
Query: 287 DESSKKRLLLIKKEINKLEIKYANLEKIWKYEKTLIKDSQQIKEEIEKV 335
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: 270 RRLIQLKIEHEAIKREYDESSKKRLLLIKKEINKLEIKYANLEKIWKYEKT-----LIKD 324
L +L+++ + E +E +K ++ N+ A+L K+ K +
Sbjct: 20 NSLYELRLDLARLLLENEELKQKVEEALEGATNEDGKLAADLLKLEVARKKERLNQIRAR 79
Query: 325 SQQIKEEIEKVRLKINK-----ATRKSDWQTVSKLKYGELNKLERILKEKSQKDIQ 375
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 = 0.014
Identities = 35/134 (26%), Positives = 59/134 (44%), Gaps = 31/134 (23%)
Query: 674 DVHGCKKSLSILLKKIHKKSPEANFIFLGDLINKGPQSLD------TLRMVYSMRNYAKI 727
D+HG L ++ K SPE ++F GD +++G +S++ +VY + +
Sbjct: 58 DLHGKLDDLFLIFYKNGLPSPENPYVFNGDFVDRGKRSIEILIILFAFFLVYPNEVH--L 115
Query: 728 VLGNHEIHLLDVLININK----------KSKLDTFDDILDAPDKKKLVSWLRTQPLA-IY 776
GNHE H++++ K K L +D+ SWL PLA I
Sbjct: 116 NRGNHEDHIMNLRYGFTKEVMSKYKLHGKKILRLLEDVF---------SWL---PLATII 163
Query: 777 YKKYLMIHAGVAKQ 790
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: 698 FIFLGDLINKGPQSLDTLRMVYSMRNYAK-------IVLGNHEI-HLLDVLININKKSKL 749
+ LGD+ ++GP ++ L ++Y + A +LGNHE+ +L ++ K
Sbjct: 36 LVQLGDIFDRGPDVIEILWLLYKLEQEAAKAGGKVHFLLGNHELMNLCGDFRYVHPKY-F 94
Query: 750 DTFDDILDA-----PDKKKLVSWLRTQPLAIYYKKYLMIHAGVAKQWT 792
+ 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 = 0.017
Identities = 49/166 (29%), Positives = 71/166 (42%), Gaps = 48/166 (28%)
Query: 21 LTEKARLGKLDPVIGRDDEI------RRAIQVLQRRSKNNPVLIGEPGVGKTAIVEGLAQ 74
L ++ R L+ +G+D + RRAI+ + + +L G PGVGKT LA
Sbjct: 18 LADRLRPRTLEEFVGQDHILGEGRLLRRAIKADRV---GSLILYGPPGVGKTT----LA- 69
Query: 75 RII----NGEVPNSLLSKKILLLDIALLLAGTK-YRGEFE---DRLKKILKEISNNQKDI 126
RII + +LAG K R E + +RL++ + K
Sbjct: 70 RIIANHTRAHF-----------SSLNAVLAGVKDLRAEVDRAKERLER-------HGKRT 111
Query: 127 IIFIDELHTMIGTGKVEGSIDAGNMLKPELSRGELHCIGATTLNEY 172
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: 16 KYTIDLTEKARLGKLDPVIGRDDEIRRAIQVLQRRSKN--NPVLIGEPGVGKTAIVEGLA 73
+ T ++ RL +D VIG+++ A++++++ +K N +LIGEPGVGK+ + + +A
Sbjct: 5 ETTEEIPVPERL--IDQVIGQEE----AVEIIKKAAKQKRNVLLIGEPGVGKSMLAKAMA 58
Query: 74 QRIINGEVPNSLLSKKILLLD---IALLLAGTKYRGEFEDRLKKILKE 118
+ + + 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 = 0.030
Identities = 39/163 (23%), Positives = 66/163 (40%), Gaps = 43/163 (26%)
Query: 21 LTEKARLGKLDPVIG------RDDEIRRAIQVLQRRSKNNPVLI--GEPGVGKTAIVEGL 72
L E+ R LD V+G +RRA++ + + +I G PG GKT + +
Sbjct: 14 LAERLRPKSLDEVVGQEHLLGEGKPLRRAVE-----AGHLHSMILWGPPGTGKTTLARLI 68
Query: 73 AQRIINGEVPNSLLSKKILLLDIALLLAGTKYRGEFEDRLKKILKEISNNQ---KDIIIF 129
A N ++ + +G K L++I++E N+ + I+F
Sbjct: 69 AGT-TNAAF-----------EALSAVTSGVK-------DLREIIEEARKNRLLGRRTILF 109
Query: 130 IDELHTMIGTGKVEGSIDAGNMLKPELSRGELHCIGATTLNEY 172
+DE+H + + L P + G + IGATT N
Sbjct: 110 LDEIHRF--------NKAQQDALLPHVENGTIILIGATTENPS 144
Score = 29.9 bits (68), Expect = 7.3
Identities = 34/142 (23%), Positives = 54/142 (38%), Gaps = 44/142 (30%)
Query: 429 VVGQDEAISAVSNAIRRSRSGLSDAKRPYGSFMFLGPTGVGKTELCK-----------TL 477
VVGQ+ + +RR +A S + GP G GKT L + L
Sbjct: 26 VVGQEHLLGE-GKPLRR----AVEAGHL-HSMILWGPPGTGKTTLARLIAGTTNAAFEAL 79
Query: 478 SACIFNNEESIIRIDMSEFIEKHSISRLIGAPPGYIGYEEGGYLTEIVRRKPYSLILLDE 537
SA + D+ E IE+ +RL+G R+ ++ LDE
Sbjct: 80 SAVTSGVK------DLREIIEEARKNRLLG-------------------RRT--ILFLDE 112
Query: 538 IEKANSDVFNILLQILDDGRLT 559
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: 674 DVHGCKKSLSILLKKIHKKSPEANFIFLGDLINKGPQSLDTLRMVYSMR-NY-AKIVL-- 729
D+HG L L K+ P AN+IF+GD +++G S++T+ + ++ Y I L
Sbjct: 50 DIHGQFYDLQALFKE-GGDIPNANYIFIGDFVDRGYNSVETMEYLLCLKVKYPGNITLLR 108
Query: 730 GNHE 733
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 = 0.030
Identities = 29/80 (36%), Positives = 43/80 (53%), Gaps = 10/80 (12%)
Query: 425 LCKRVVGQDEAISAVS----NAIRRSR--SGLSDAKRPYGSFMFLGPTGVGKTELCKTLS 478
L K ++GQDEA +V+ N RRS+ L D P M +GPTGVGKTE+ + L+
Sbjct: 10 LDKYIIGQDEAKKSVAIALRNRYRRSQLPEELKDEVTPKNILM-IGPTGVGKTEIARRLA 68
Query: 479 ACIFNNEESIIRIDMSEFIE 498
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 = 0.038
Identities = 27/117 (23%), Positives = 49/117 (41%), Gaps = 5/117 (4%)
Query: 185 RFQKILVEEPDIEETISILRGLQKKYEVHHGVEITDPAIVAASELSYRYISDRFMPDKAI 244
R +LV+ + EE IL L ++Y T + E + ++ + P+K
Sbjct: 370 RHLAVLVQIANAEEE-DILEILIRRYLPDA-DPDTIEDLDERIEYAINWL-RDYAPEKVK 426
Query: 245 DLIDEAAAKIKIEIDSKPEIMDKLERRL--IQLKIEHEAIKREYDESSKKRLLLIKK 299
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 = 0.038
Identities = 79/337 (23%), Positives = 132/337 (39%), Gaps = 85/337 (25%)
Query: 407 VSKIVQVEREKLLN-------IENLLCKRVVGQDEAIS----AVSNAIRRSRSGLSDAKR 455
+ + E E L+ I+ L + V+GQ++A AV N +R +
Sbjct: 50 RKESKEYEEEFELSYLPTPKEIKAHLDEYVIGQEQAKKVLSVAVYNHYKRLNFEKNKKSD 109
Query: 456 PY-----GSFMFLGPTGVGKTELCKTLSACIFNNEESIIRIDMSEFIEKHSISRLIGAPP 510
+ + +GPTG GKT L +TL A I N +I D + E
Sbjct: 110 NGVELSKSNILLIGPTGSGKTLLAQTL-ARILNVPFAI--ADATTLTEA----------- 155
Query: 511 GYIGYEEGGYLTEIVRRKPYS-------LILLDEIEK--------------ANSDVFNIL 549
GY+G + L ++++ Y +I +DEI+K + V L
Sbjct: 156 GYVGEDVENILLKLLQAADYDVEKAQKGIIYIDEIDKISRKSENPSITRDVSGEGVQQAL 215
Query: 550 LQILDDGRLTD---NRGRTINFRNTIIVMTSNL---------GSDKI------------- 584
L+I+ +G + + GR ++ I + TSN+ G +KI
Sbjct: 216 LKII-EGTVANVPPQGGRKHPYQEFIQIDTSNILFICGGAFVGLEKIIKKRTGKSSIGFG 274
Query: 585 ---KEMEKGDKEIIKLAVMNE-VKIYFRPEFINRIDDIIVFRYLNRKNILSIANIQLNIL 640
K+ K ++++ + VK PEFI R+ I L+ + +++I N L
Sbjct: 275 AEVKKKSKEKADLLRQVEPEDLVKFGLIPEFIGRLPVIATLEKLDEEALIAILTKPKNAL 334
Query: 641 KN---KLLKM-NMDLKISKAALKKISNIGFDLIYGAR 673
L KM N++L + ALK I+ + GAR
Sbjct: 335 VKQYQALFKMDNVELDFEEEALKAIAKKALERKTGAR 371
Score = 29.7 bits (67), Expect = 7.2
Identities = 31/88 (35%), Positives = 45/88 (51%), Gaps = 17/88 (19%)
Query: 51 SKNNPVLIGEPGVGKTAIVEGLAQRIINGEVPNSLLSKKILLLDIALLLAGTKYRGE-FE 109
SK+N +LIG G GKT + + LA+ + VP + D A L Y GE E
Sbjct: 115 SKSNILLIGPTGSGKTLLAQTLARIL---NVP-------FAIAD-ATTLTEAGYVGEDVE 163
Query: 110 DRLKKILK----EISNNQKDIIIFIDEL 133
+ L K+L+ ++ QK II+IDE+
Sbjct: 164 NILLKLLQAADYDVEKAQKG-IIYIDEI 190
>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 = 0.042
Identities = 35/112 (31%), Positives = 47/112 (41%), Gaps = 30/112 (26%)
Query: 247 IDEAAAKIKIEIDSKPEIMDK-----------LERRLIQL-KIEHEAIKREYDESSKKRL 294
IDE I+ E + K +M++ L RL L K+E AI E E K+R
Sbjct: 382 IDEVIEIIREEDEPKTILMERFKLSAIQAEAILNLRLRHLAKLEEHAIIDEQSELEKER- 440
Query: 295 LLIKKEINKLEIKYANLEKIWKYEKTLIKDSQQIKEEIEKVRLKINKATRKS 346
A LEKI K E+ L +Q +K+EI+ K A R S
Sbjct: 441 --------------AILEKILKSEREL---NQLVKKEIQADATKYGLARRSS 475
>gnl|CDD|225288 COG2433, COG2433, Uncharacterized conserved protein [Function
unknown].
Length = 652
Score = 37.4 bits (87), Expect = 0.044
Identities = 23/117 (19%), Positives = 55/117 (47%), Gaps = 14/117 (11%)
Query: 249 EAAAKIKIEIDSKPEIMDKLERRLIQLKIEHEAIKREYDESSKKRLLLIKKEINKLEIKY 308
+ + EI + + KLE + +L+ E+ +KRE +E +K+EI KLE +
Sbjct: 408 GTEEEERREITVYEKRIKKLEETVERLEEENSELKRELEE--------LKREIEKLESEL 459
Query: 309 ANLEKIWKYEKTLIKDSQQIKEEIEKVRLKINKATRKSDWQTVSKLKYGELNKLERI 365
+ + + ++ + IE++ ++ + ++ V +L+ +L +L ++
Sbjct: 460 ERFRREVRDKVRKDREIRARDRRIERLEKELEEKKKR-----VEELE-RKLAELRKM 510
>gnl|CDD|184922 PRK14958, PRK14958, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 509
Score = 37.0 bits (85), Expect = 0.045
Identities = 36/146 (24%), Positives = 64/146 (43%), Gaps = 33/146 (22%)
Query: 427 KRVVGQDEAISAVSNAIRRSRSGLSDAKRPYGSFMFLGPTGVGKTELCKTLSACI----- 481
+ V+GQ + A+SNA+ D + + +++F G GVGKT + + L+ C+
Sbjct: 16 QEVIGQAPVVRALSNAL--------DQQYLHHAYLFTGTRGVGKTTISRILAKCLNCEKG 67
Query: 482 -----FNNEESIIRIDMSEF---IEKHSISRLIGAPPGYIGYEEGGYLTEIVRRKP---- 529
N+ E+ ID F E + SR E+ L + + P
Sbjct: 68 VSANPCNDCENCREIDEGRFPDLFEVDAASR--------TKVEDTRELLDNIPYAPTKGR 119
Query: 530 YSLILLDEIEKANSDVFNILLQILDD 555
+ + 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 = 0.045
Identities = 24/57 (42%), Positives = 33/57 (57%), Gaps = 4/57 (7%)
Query: 23 EKARLGKLDPVIGRDDEIRRAIQVLQRRSKNNPVLI--GEPGVGKTAIVEGLAQRII 77
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 = 0.051
Identities = 14/46 (30%), Positives = 24/46 (52%), Gaps = 6/46 (13%)
Query: 33 VIGRDDEIRRAIQVLQRRSKNN-PVLI-GEPGVGKTAIVEGLAQRI 76
+IG ++ +++ +R + + VLI GE G GK E A+ I
Sbjct: 1 LIGESPAMQEVLELAKRVAPTDATVLITGESGTGK----ELFARAI 42
>gnl|CDD|184921 PRK14957, PRK14957, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 546
Score = 37.0 bits (85), Expect = 0.052
Identities = 34/141 (24%), Positives = 66/141 (46%), Gaps = 27/141 (19%)
Query: 429 VVGQDEAISAVSNAIRRSRSGLSDAKRPYGSFMFLGPTGVGKTELCKTLSACI------- 481
V GQ A++++ +A+ + ++ + +++F G GVGKT L + L+ C+
Sbjct: 18 VAGQQHALNSLVHAL--------ETQKVHHAYLFTGTRGVGKTTLGRLLAKCLNCKTGVT 69
Query: 482 ---FNNEESIIRIDMSEFIEKHSISRLIGAPPGYIGYEEGGYLTEIVRRKP----YSLIL 534
N E+ + I+ + FI+ I G EE + + ++ P Y + L
Sbjct: 70 AEPCNKCENCVAINNNSFIDLIEID-----AASRTGVEETKEILDNIQYMPSQGRYKVYL 124
Query: 535 LDEIEKANSDVFNILLQILDD 555
+DE+ + FN LL+ L++
Sbjct: 125 IDEVHMLSKQSFNALLKTLEE 145
>gnl|CDD|183088 PRK11331, PRK11331, 5-methylcytosine-specific restriction enzyme
subunit McrB; Provisional.
Length = 459
Score = 36.6 bits (84), Expect = 0.054
Identities = 29/106 (27%), Positives = 58/106 (54%), Gaps = 9/106 (8%)
Query: 464 GPTGVGKTELCKTLSACIFNNEESIIRIDMSEFIEKHSISRLI-GAPPGYIGY--EEGGY 520
GP GVGKT + + L A + E++ R++M +F + +S I G P +G+ ++G +
Sbjct: 201 GPPGVGKTFVARRL-AYLLTGEKAPQRVNMVQFHQSYSYEDFIQGYRPNGVGFRRKDGIF 259
Query: 521 --LTEIVRRKPYS--LILLDEIEKAN-SDVFNILLQILDDGRLTDN 561
+ + +P + ++DEI +AN S VF ++ +++ + +N
Sbjct: 260 YNFCQQAKEQPEKKYVFIIDEINRANLSKVFGEVMMLMEHDKRGEN 305
>gnl|CDD|235364 PRK05201, hslU, ATP-dependent protease ATP-binding subunit HslU;
Provisional.
Length = 443
Score = 36.6 bits (86), Expect = 0.067
Identities = 24/53 (45%), Positives = 31/53 (58%), Gaps = 9/53 (16%)
Query: 427 KRVVGQDEAISAVSNAIR---RSRSGLSDAKR----PYGSFMFLGPTGVGKTE 472
K ++GQD+A AV+ A+R R R L + R P M +GPTGVGKTE
Sbjct: 15 KYIIGQDDAKRAVAIALRNRWR-RMQLPEELRDEVTPKNILM-IGPTGVGKTE 65
>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 = 0.068
Identities = 52/230 (22%), Positives = 87/230 (37%), Gaps = 42/230 (18%)
Query: 414 EREKLLNIENLLCKRVVGQDEAISAVSNAIRRSRSGLSDAKRPYGSFMFL-GPTGVGKT- 471
LL + + R+V +DE I ++ A+R G RP S +F+ G TG GKT
Sbjct: 3 RNRDLLEPDYVP-DRIVHRDEQIEELAKALRPILRG----SRP--SNVFIYGKTGTGKTA 55
Query: 472 ---ELCKTLSACIFNNEE--SIIRID----------MSEFIEKHSISRLIGAPPGYIGYE 516
+ K L + + + ++ + E + R G G
Sbjct: 56 VTKYVMKELEEAAEDRDVRVVTVYVNCQILDTLYQVLVELANQ---LRGSGEEVPTTGLS 112
Query: 517 EGGYL----TEIVRRKPYSLILLDEIEKANSDVFNILLQILDDGRLTDNRGRTINFRNTI 572
E+ R +I+LDEI+ D ++L Q+ R N G N + +
Sbjct: 113 TSEVFRRLYKELNERGDSLIIVLDEIDYLVGDDDDLLYQLS---RARSN-GDLDNAKVGV 168
Query: 573 IVMTSNLGSDKIKEMEKGDKEIIKLAVMNEVKIYFRPEFINRIDDIIVFR 622
I + S+ +K E D + + + E +I F P + DI+ R
Sbjct: 169 IGI-----SNDLKFRENLDPRV--KSSLCEEEIIFPPYDAEELRDILENR 211
Score = 34.1 bits (79), Expect = 0.32
Identities = 29/134 (21%), Positives = 64/134 (47%), Gaps = 27/134 (20%)
Query: 31 DPVIGRDDEI---RRAIQVLQRRSKNNPVLI-GEPGVGKTAIVEGLAQRI---------- 76
D ++ RD++I +A++ + R S+ + V I G+ G GKTA+ + + + +
Sbjct: 15 DRIVHRDEQIEELAKALRPILRGSRPSNVFIYGKTGTGKTAVTKYVMKELEEAAEDRDVR 74
Query: 77 -----INGEVPNSLLSKKILLLDIALLLAGTK----YRGEFEDRLKKILKEISNNQKDII 127
+N ++ ++L +L+++A L G+ G + + L + N + D +
Sbjct: 75 VVTVYVNCQILDTLYQ---VLVELANQLRGSGEEVPTTGLSTSEVFRRLYKELNERGDSL 131
Query: 128 IFI-DELHTMIGTG 140
I + DE+ ++G
Sbjct: 132 IIVLDEIDYLVGDD 145
>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: 453 AKRPYGSFMFLGPTGVGKTELCKTLSACIFNNEESIIRI 491
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 = 0.082
Identities = 25/60 (41%), Positives = 34/60 (56%), Gaps = 7/60 (11%)
Query: 425 LCKRVVGQDEAISAVS----NAIRRSR--SGLSDAKRPYGSFMFLGPTGVGKTELCKTLS 478
L + ++GQDEA AV+ N RR + L D P M +GPTGVGKTE+ + L+
Sbjct: 13 LDRYIIGQDEAKKAVAIALRNRWRRMQLEEELRDEVTPKNILM-IGPTGVGKTEIARRLA 71
>gnl|CDD|184934 PRK14970, PRK14970, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 367
Score = 36.0 bits (83), Expect = 0.088
Identities = 36/133 (27%), Positives = 56/133 (42%), Gaps = 19/133 (14%)
Query: 427 KRVVGQDEAISAVSNAIRRSRSGLSDAKRPYGSFMFLGPTGVGKTELCKTLSACIFNNEE 486
VVGQ + + NAI + L+ A +F GP GVGKT + L+ I N+
Sbjct: 17 DDVVGQSHITNTLLNAIENNH--LAQA------LLFCGPRGVGKTTCARILARKI--NQP 66
Query: 487 SIIRIDMSEFIEKHSISRLIGAPPGYIGYEEGGYLTEIVRRKP----YSLILLDEIEKAN 542
D +I L A ++ L + VR P Y + ++DE+ +
Sbjct: 67 G---YDDPNEDFSFNIFELDAASNN--SVDDIRNLIDQVRIPPQTGKYKIYIIDEVHMLS 121
Query: 543 SDVFNILLQILDD 555
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: 674 DVHGCKKSLSILLKKIHKKSPEANFIFLGDLINKGPQSLDT--LRMVYSMRNYAKIVL-- 729
D+HG L L + + P+ N++FLGD +++G S++T L + +R +I L
Sbjct: 49 DIHGQFYDLLELFR-VGGDPPDTNYLFLGDYVDRGYYSVETFLLLLALKVRYPDRITLLR 107
Query: 730 GNHE 733
GNHE
Sbjct: 108 GNHE 111
>gnl|CDD|224144 COG1223, COG1223, Predicted ATPase (AAA+ superfamily) [General
function prediction only].
Length = 368
Score = 35.6 bits (82), Expect = 0.10
Identities = 68/261 (26%), Positives = 104/261 (39%), Gaps = 49/261 (18%)
Query: 21 LTEKARLGKLDPVIGRDDEIRRAIQVLQRRSKN----------NPVLIGEPGVGKTAIVE 70
E LD VIG++ E +R +++ +N N + G PG GKT + +
Sbjct: 111 DREIISDITLDDVIGQE-EAKRKCRLIMEYLENPERFGDWAPKNVLFYGPPGTGKTMMAK 169
Query: 71 GLAQRIINGEVPNSLLSKKILLLDIALLLAGTKYRGEFEDRLKKILKEISNNQKDIIIFI 130
LA E LL K A L G ++ G+ R+ + L E + I+FI
Sbjct: 170 ALA-----NEAKVPLLLVK------ATELIG-EHVGDGARRIHE-LYERARKAAPCIVFI 216
Query: 131 DELHTMIG--------TGKVEGSIDAGNMLKPELSR---GELHC-IGATTLNEYRQYIEK 178
DEL I G V ++A L EL E I AT E
Sbjct: 217 DELDA-IALDRRYQELRGDVSEIVNA---LLTELDGIKENEGVVTIAATNRPELL----- 267
Query: 179 DAAFERRFQ-KILVEEPDIEETISILRGLQKKYEVHHGVEITDPAIVAASE-LSYRYISD 236
D A RF+ +I + P+ EE + IL KK+ + V+ + A ++ +S R I +
Sbjct: 268 DPAIRSRFEEEIEFKLPNDEERLEILEYYAKKFPLP--VDADLRYLAAKTKGMSGRDIKE 325
Query: 237 RFMPDKAIDLIDEAAAKIKIE 257
+ + I E K++ E
Sbjct: 326 KVLKTALHRAIAEDREKVERE 346
>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: 19 IDLTEKARLGKLDPVIGRDDEIRRAIQVLQRRSKNNP----VLIGEPGVGKTAIVEGLA 73
+ 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 = 0.12
Identities = 49/219 (22%), Positives = 88/219 (40%), Gaps = 47/219 (21%)
Query: 608 RPEFINRIDDIIVFRYLNRKNILSIANIQLNILKNK--LLKMNMDLKISKAALKKISNIG 665
+P D F N IL + + +I K + +L++ +KI
Sbjct: 7 KPRIWKPPTDRRFF--FNWNEILELCDAAEDIFKQEPMVLRLRAPIKI------------ 52
Query: 666 FDLIYGARDVHGCKKSLSILLKKIHKKSPEA-------NFIFLGDLINKGPQSLDTLRMV 718
+G D+HG L L + EA +++FLGD +++G SL+T+ ++
Sbjct: 53 ----FG--DIHGQFGDLMRLFDEYGSPVTEAAGDIEYIDYLFLGDYVDRGSNSLETICLL 106
Query: 719 YSMR----NYAKIVLGNHEIHLLDVL----ININKKSKLDTFDDILDAPDKKKLVSWLRT 770
+++ N ++ GNHE ++ L ++ D D +L WL
Sbjct: 107 LALKVKYPNQIHLIRGNHEDRDINALFGFREECKERLGEDPNDGDSVWRRINRLFEWL-- 164
Query: 771 QPL-AIYYKKYLMIHAGVAKQWTAQQTIKLSHQVEKILR 808
PL AI K L +H G+ + +I ++E + R
Sbjct: 165 -PLAAIIEDKILCMHGGIGR------SINHVSEIEDLKR 196
>gnl|CDD|227355 COG5022, COG5022, Myosin heavy chain [Cytoskeleton].
Length = 1463
Score = 35.8 bits (83), Expect = 0.15
Identities = 25/128 (19%), Positives = 53/128 (41%), Gaps = 11/128 (8%)
Query: 263 EIMDKLERRLIQLKIEHEAIKREYDESSK--KRLLLIKKEINKLEIK--YANLEKIWKYE 318
+ ++ ER+L +LKI+ ++I + + ++ +KK ++ I+ E I + +
Sbjct: 875 QRVELAERQLQELKIDVKSISSLKLVNLELESEIIELKKSLSSDLIENLEFKTELIARLK 934
Query: 319 KTL----IKDSQQIKEEIEKVRLKINKATRKSDWQTVSKLKYGELNKLERILKEKSQKDI 374
K L +++ I+ K++ +S + S+ L K IL + K
Sbjct: 935 KLLNNIDLEEGPSIEYVKLPELNKLH--EVESKLKETSEEYEDLLKKST-ILVREGNKAN 991
Query: 375 QLPNNANK 382
N K
Sbjct: 992 SELKNFKK 999
>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: 247 IDEAAAKIKIEIDSKPEIMDKLERRLIQLKIEHEAIKREYDE---------SSKKRLLLI 297
I+E + + E++ ++++ L +L+ E E +++E E +K L +
Sbjct: 191 IEELIKEKEKELEEVLREINEISSELPELREELEKLEKEVKELEELKEEIEELEKELESL 250
Query: 298 KKEINKLEIKYANLEKIWKYEKTLIKDSQQIKEEIEKVRLKINKATRKSDWQTVSKLKYG 357
+ KLE K LE+ + K I++ ++ +E+++++ K ++ +S+
Sbjct: 251 EGSKRKLEEKIRELEERIEELKKEIEELEEKVKELKELKEK------AEEYIKLSEFYEE 304
Query: 358 ELNKLERILKEKS 370
L++L I K S
Sbjct: 305 YLDELREIEKRLS 317
Score = 35.4 bits (82), Expect = 0.19
Identities = 60/277 (21%), Positives = 131/277 (47%), Gaps = 27/277 (9%)
Query: 102 TKYRGEFEDRLKKILKEISNNQKDIIIFIDELHTMIGTGKVEGSIDAGNMLKPELSRGEL 161
+ G ++L+K L+E+ +++I I ++ IG K E + + + ++G+
Sbjct: 379 KRLTGLTPEKLEKELEELEKAKEEIEEEISKITARIGELKKEIKELKKAIEELKKAKGKC 438
Query: 162 HCIGATTLNEYRQYIEKDAAFERRFQKILVEEPDIEETISILRGLQKKYEVHHGVEITDP 221
G E+R+ + ++ + ++I E +IEE LR ++ E
Sbjct: 439 PVCGRELTEEHRKELLEE--YTAELKRIEKELKEIEEKERKLRKELRELEK--------- 487
Query: 222 AIVAASELSYRYISDRFMPDKAIDLIDEAAAKIKI----EIDSKPEIMDKLERRLIQLKI 277
+ SEL + + + E K+K E++ K E +KL+ +LI+LK
Sbjct: 488 VLKKESELIKLK--------ELAEQLKELEEKLKKYNLEELEKKAEEYEKLKEKLIKLKG 539
Query: 278 EHEAIKREYDESS--KKRLLLIKKEINKLEIKYANLEKIWKYEKTLIKDSQQIKEEIEKV 335
E +++K+E ++ KK+L ++K++++LE + A L K + E+ + ++++E ++++
Sbjct: 540 EIKSLKKELEKLEELKKKLAELEKKLDELEEELAELLK--ELEELGFESVEELEERLKEL 597
Query: 336 RLKINKATRKSDWQTVSKLKYGELNKLERILKEKSQK 372
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: 252 AKIKIEIDSKPEIMDKLERRLIQLKIEHEAIKREYDESS----KKRLLLIKKEINKLEIK 307
K++ E+D E + + E+RL +L+ E E ++++Y E ++ L + +E+ L +
Sbjct: 622 KKLEEELDKAFEELAETEKRLEELRKELEELEKKYSEEEYEELREEYLELSRELAGLRAE 681
Query: 308 YANLEKIWKYEKTLIKDSQQIKEEIEKVRLKINK 341
LEK + K ++ ++ EE EK + ++ K
Sbjct: 682 LEELEKRREEIKKTLEKLKEELEEREKAKKELEK 715
Score = 30.0 bits (68), Expect = 7.9
Identities = 23/91 (25%), Positives = 50/91 (54%), Gaps = 7/91 (7%)
Query: 257 EIDSKPEIMDKLERRLIQLKIEHEAIKREYDESSKKRLLL-----IKKEINKLEIKYANL 311
I+ + + +++ E RL +LK + + +++ +E ++ L K+E+ +L+ + L
Sbjct: 325 GIEERIKELEEKEERLEELKKKLKELEKRLEELEERHELYEEAKAKKEELERLKKRLTGL 384
Query: 312 --EKIWKYEKTLIKDSQQIKEEIEKVRLKIN 340
EK+ K + L K ++I+EEI K+ +I
Sbjct: 385 TPEKLEKELEELEKAKEEIEEEISKITARIG 415
>gnl|CDD|223540 COG0464, SpoVK, ATPases of the AAA+ class [Posttranslational
modification, protein turnover, chaperones].
Length = 494
Score = 35.2 bits (81), Expect = 0.15
Identities = 40/158 (25%), Positives = 66/158 (41%), Gaps = 28/158 (17%)
Query: 57 LIGEPGVGKTAIVEGLAQRIINGEVPNSLLSKKILLLDIALLLAGTKYRGEFEDRLKKIL 116
L G PG GKT + + +A + + + + LL +K+ GE E ++++
Sbjct: 281 LYGPPGTGKTLLAKAVAL----------ESRSRFISVKGSELL--SKWVGESEKNIRELF 328
Query: 117 KEISNNQKDIIIFIDELHTMI---GTGKVEGSIDAGNMLKPELSRGE----LHCIGATTL 169
++ + IIFIDE+ ++ G + L EL E + I AT
Sbjct: 329 EK-ARKLAPSIIFIDEIDSLASGRGPSEDGSGRRVVGQLLTELDGIEKAEGVLVIAAT-- 385
Query: 170 NEYRQYIEKDAAFER--RFQK-ILVEEPDIEETISILR 204
+ D A R RF + I V PD+EE + I +
Sbjct: 386 -NRPDDL--DPALLRPGRFDRLIYVPLPDLEERLEIFK 420
Score = 35.2 bits (81), Expect = 0.18
Identities = 69/445 (15%), Positives = 134/445 (30%), Gaps = 94/445 (21%)
Query: 248 DEAAAKIKIEIDSKPEIMDK------LERRLIQLKIEHEA----IKREYDESSKKRLLLI 297
A + + PEI+ K L R + + E A E D + KR
Sbjct: 37 ALANEGAEFLSINGPEILSKYVGESELRLRELFEEAEKLAPSIIFIDEIDALAPKRSSDQ 96
Query: 298 KKEINKLEIKYANLEKIWKYEKTLIKDSQQIKEEIEKVRLKINKATRKSDWQTVSKLKYG 357
+ ++ + L K + ++ + + ++ + + + R+ +
Sbjct: 97 GEVERRVVAQLLALMDGLKRGQVIVIGATNRPDGLDPAKRRPGRFDREIEVNLPD----- 151
Query: 358 ELNKLERILKEKSQKDIQLPNNANKFTLLKTK---------VGSEEIAEIVSRTTGIPVS 408
IL+ ++ P K +T + E + R +
Sbjct: 152 -EAGRLEILQIHTRLMFLGPPGTGKTLAARTVGKSGADLGALAKEAALRELRRAIDLVGE 210
Query: 409 KIVQVEREKLLNIENLLCKRVV-------------GQDEAIS----AVSNAIRRSRSGLS 451
I E + ++ +L R V G +EA A+ ++R
Sbjct: 211 YIGVTEDDFEEALKKVLPSRGVLFEDEDVTLDDIGGLEEAKEELKEAIETPLKRPELFRK 270
Query: 452 DAKRPYGSFMFLGPTGVGKTELCKTLSACIFNNEES-IIRIDMSEFIEKHSISRLIGAPP 510
RP + GP G GKT L+ + S I + SE + K
Sbjct: 271 LGLRPPKGVLLYGPPGTGKT----LLAKAVALESRSRFISVKGSELLSK----------- 315
Query: 511 GYIGYEEGGYLTEIVRRKPYSL----ILLDEIEK-----------ANSDVFNILLQILDD 555
++G E + K L I +DEI+ + V LL LD
Sbjct: 316 -WVG--ESEKNIRELFEKARKLAPSIIFIDEIDSLASGRGPSEDGSGRRVVGQLLTELDG 372
Query: 556 GRLTDNRGRTINFRNTIIVMTSNLGSDKIKEMEKGDKEIIKLAVMNEVKIYFRPEFINRI 615
+ +++ +N + D +++ + + P+ R+
Sbjct: 373 IEKAEGV---------LVIAATN-------RPDDLDPALLRPGRFDRLIYVPLPDLEERL 416
Query: 616 DDIIVFRYLNRKNILSIANIQLNIL 640
+ I +L K ++ L L
Sbjct: 417 E--IFKIHLRDKKPPLAEDVDLEEL 439
Score = 31.3 bits (71), Expect = 2.4
Identities = 51/172 (29%), Positives = 71/172 (41%), Gaps = 28/172 (16%)
Query: 44 IQVLQRRSKNNPVLIGEPGVGKTAIVEGLAQRIINGEVPNSLLSKKILLLDIALLLAGTK 103
+ L +L G PG GKT + LA G S+ +IL +K
Sbjct: 10 FKKLGIEPPKGVLLHGPPGTGKTLLARALANE---GAEFLSINGPEIL----------SK 56
Query: 104 YRGEFEDRLKKILKEISNNQKDIIIFIDELHTMIG-----TGKVEGSIDAG-NMLKPELS 157
Y GE E RL+++ +E IIFIDE+ + G+VE + A L L
Sbjct: 57 YVGESELRLRELFEEAEKLAP-SIIFIDEIDALAPKRSSDQGEVERRVVAQLLALMDGLK 115
Query: 158 RGELHCIGATTLNEYRQYIEKDAAFER--RFQK-ILVEEPDIEETISILRGL 206
RG++ IGAT + D A R RF + I V PD + IL+
Sbjct: 116 RGQVIVIGAT-----NRPDGLDPAKRRPGRFDREIEVNLPDEAGRLEILQIH 162
>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 = 0.15
Identities = 15/53 (28%), Positives = 28/53 (52%), Gaps = 8/53 (15%)
Query: 429 VVGQDEAISAVSNAIRRSRSGLSDAKRPYGSFMFLGPTGVGKTELCKTLSACI 481
V+GQ+ + + NAI+ R ++ A ++F GP G GKT + + + +
Sbjct: 16 VIGQEHIVQTLKNAIKNGR--IAHA------YLFSGPRGTGKTSIARIFAKAL 60
>gnl|CDD|237177 PRK12704, PRK12704, phosphodiesterase; Provisional.
Length = 520
Score = 35.1 bits (82), Expect = 0.16
Identities = 27/121 (22%), Positives = 59/121 (48%), Gaps = 14/121 (11%)
Query: 249 EAAAKIKIEIDSKPEIMDKLERRLIQLKIEHEAIKREYDESSKKRLLLIKKEINKLEIKY 308
E AK +E ++K E + L++ K E ++ E+++ ++R ++K +L K
Sbjct: 37 EEEAKRILE-EAKKEAEAIKKEALLEAKEEIHKLRNEFEKELRERRNELQKLEKRLLQKE 95
Query: 309 ANLEK----IWKYEKTLIKDSQQIKEEIEKVRLKINKATRKSDWQTVSKLKYGELNKLER 364
NL++ + K E+ L K ++++++ +++ K + + Q L +LER
Sbjct: 96 ENLDRKLELLEKREEELEKKEKELEQKQQELEKKEEELEELIEEQ---------LQELER 146
Query: 365 I 365
I
Sbjct: 147 I 147
Score = 31.7 bits (73), Expect = 2.1
Identities = 21/96 (21%), Positives = 50/96 (52%), Gaps = 9/96 (9%)
Query: 258 IDSKPEIMDKLERRLIQLKIEHEAIKREYDESSKKRLLLIKKEINKLEIKYANLEK---- 313
+D K E+++K E L + + E E ++E ++ ++ LI++++ +LE + + L
Sbjct: 98 LDRKLELLEKREEELEKKEKELEQKQQELEKKEEELEELIEEQLQELE-RISGLTAEEAK 156
Query: 314 ---IWKYEKTLIKD-SQQIKEEIEKVRLKINKATRK 345
+ K E+ + + IKE E+ + + +K ++
Sbjct: 157 EILLEKVEEEARHEAAVLIKEIEEEAKEEADKKAKE 192
>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 = 0.16
Identities = 30/170 (17%), Positives = 70/170 (41%), Gaps = 23/170 (13%)
Query: 242 KAIDLIDEAAAKIKIEIDSKPEIMDKLERRLIQLKIEHEAIKREYDESSKKRLLLIKKEI 301
K + + E +I+ +I+ + + KLE ++ QL+ E E + E +++ K L K++
Sbjct: 81 KGVFTLGEENIEIEAQIEELKKELKKLEEKIEQLEAEIEKKEEELEKAKNKFLDKAWKKL 140
Query: 302 NKLEIKYANLEKIWKYEKTLIKDSQQIKEEIEKVRLKINKATRKSDWQTVSKLKYGELNK 361
K NL + K +++ +E++ V +N ++ S EL
Sbjct: 141 AKKYDS--NLSEALKGLNYKKNFKEKLLKELKSV--ILNASSLLSL---------EELKA 187
Query: 362 LERILKEKSQKDIQLPN-------NANKFTLLKTKV---GSEEIAEIVSR 401
+ L ++ ++ L + +L+ + I+E+++
Sbjct: 188 KIKTLFSSNKPELALLTLSVIDFDEIEQAEILEKSIIGSSDVPISELINN 237
>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: 31 DPVIGRD---DEIRRAIQVLQRRSKNNPVLIGEPGVGKTAIVEGLAQ 74
D VIG++ + I++A + QRR + ++IG PG GK+ + + +A+
Sbjct: 31 DQVIGQEHAVEVIKKAAK--QRR---HVMMIGSPGTGKSMLAKAMAE 72
>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 = 0.23
Identities = 17/65 (26%), Positives = 25/65 (38%), Gaps = 16/65 (24%)
Query: 21 LTEKARLGKLDPVIGRDDEIRR-------AIQVLQRRSKNNP---------VLIGEPGVG 64
L A KL + EIR A+ +L+R ++IG PG G
Sbjct: 64 LAALAAPTKLKADAAAEAEIRELRARFNEALALLKRSRLGGRRYLYDLPWYLVIGPPGSG 123
Query: 65 KTAIV 69
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: 333 EKVRLKINKATRKSDWQTVSKLKYGELNKLERILKEKSQKDIQLPNNANKFTLLKTKVGS 392
EK R K+ + ++S + + +LK +K+E+ + A+KF LK +
Sbjct: 2 EKYRSKLLQKAKESGLEFIERLKKALKDKIEKKEFSAKKPPTGPSKQASKFKTLKPPKPA 61
Query: 393 EEIAEIVSRTTGI-PVSKIVQVEREKLLNIENL 424
++ P+S I+ VE+ K L+ E +
Sbjct: 62 DKKK---PFDKPFKPLSSILDVEKIKDLSAEEI 91
>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 = 0.25
Identities = 18/52 (34%), Positives = 29/52 (55%)
Query: 16 KYTIDLTEKARLGKLDPVIGRDDEIRRAIQVLQRRSKNNPVLIGEPGVGKTA 67
+ T L+EK R D +IG+++ I+ L + + ++ G PGVGKTA
Sbjct: 50 RLTEPLSEKTRPKSFDEIIGQEEGIKALKAALCGPNPQHVIIYGPPGVGKTA 101
Score = 30.5 bits (69), Expect = 4.9
Identities = 40/147 (27%), Positives = 63/147 (42%), Gaps = 28/147 (19%)
Query: 427 KRVVGQDEAISAVSNAIRRSRSGLSDAKRPYGSFMFLGPTGVGKT-------ELCKTLSA 479
++GQ+E I A+ A+ P ++ GP GVGKT E K A
Sbjct: 65 DEIIGQEEGIKALKAALC--------GPNPQHVIIY-GPPGVGKTAAARLVLEEAKKNPA 115
Query: 480 CIFNNEESIIRIDMS--EFIEKHSISRLIGA--PPGYIGYEEGGYLTEIVRRKPYS---- 531
F + + ID + F E+ LIG+ P Y G G + I + KP +
Sbjct: 116 SPFKEGAAFVEIDATTARFDERGIADPLIGSVHDPIYQGAGPLG-IAGIPQPKPGAVTRA 174
Query: 532 ---LILLDEIEKANSDVFNILLQILDD 555
++ +DEI + + N LL++L+D
Sbjct: 175 HGGVLFIDEIGELHPVQMNKLLKVLED 201
>gnl|CDD|184920 PRK14956, PRK14956, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 484
Score = 34.5 bits (79), Expect = 0.26
Identities = 39/137 (28%), Positives = 62/137 (45%), Gaps = 19/137 (13%)
Query: 429 VVGQDEAISAVSNAIRRSRSGLSDAKRPYGSFMFLGPTGVGKTELCKTLSACIFNNEESI 488
V+ QD AI A+ NA++ + G +++F GP GVGKT + + L A N E I
Sbjct: 20 VIHQDLAIGALQNALKSGKIG--------HAYIFFGPRGVGKTTIARIL-AKRLNCENPI 70
Query: 489 IRIDMSEFIEKHSISRLIGAPPGYI------GYEEGGYLTEIVRRKP----YSLILLDEI 538
+E I++ I + I G E L + V+ P Y + ++DE+
Sbjct: 71 GNEPCNECTSCLEITKGISSDVLEIDAASNRGIENIRELRDNVKFAPMGGKYKVYIIDEV 130
Query: 539 EKANSDVFNILLQILDD 555
FN LL+ L++
Sbjct: 131 HMLTDQSFNALLKTLEE 147
>gnl|CDD|236333 PRK08691, PRK08691, DNA polymerase III subunits gamma and tau;
Validated.
Length = 709
Score = 34.7 bits (79), Expect = 0.28
Identities = 32/140 (22%), Positives = 59/140 (42%), Gaps = 25/140 (17%)
Query: 429 VVGQDEAISAVSNAIRRSRSGLSDAKRPYGSFMFLGPTGVGKTELCKTLSACIFNNE--- 485
+VGQ+ + A+ NA+ D R + +++ G GVGKT + + L+ + N E
Sbjct: 18 LVGQEHVVKALQNAL--------DEGRLHHAYLLTGTRGVGKTTIARILAKSL-NCENAQ 68
Query: 486 --------ESIIRIDMSEFIEKHSISRLIGAPPGYIG--YEEGGYLTEIVRRKPYSLILL 535
+S +ID +++ I I E Y + K Y ++
Sbjct: 69 HGEPCGVCQSCTQIDAGRYVDLLEIDAASNTGIDNIREVLENAQYAPTAGKYKVY---II 125
Query: 536 DEIEKANSDVFNILLQILDD 555
DE+ + FN +L+ L++
Sbjct: 126 DEVHMLSKSAFNAMLKTLEE 145
>gnl|CDD|237057 PRK12323, PRK12323, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 700
Score = 34.5 bits (79), Expect = 0.29
Identities = 15/49 (30%), Positives = 29/49 (59%), Gaps = 8/49 (16%)
Query: 430 VGQDEAISAVSNAIRRSRSGLSDAKRPYGSFMFLGPTGVGKTELCKTLS 478
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 = 0.29
Identities = 22/113 (19%), Positives = 43/113 (38%), Gaps = 41/113 (36%)
Query: 33 VIGRDDEIRRAIQVLQRRSKNNPVLI--GEPGVGKTAIVEGLAQ------RIINGEVPNS 84
++G +RR I+ + +I G PG GKT + +A ++
Sbjct: 20 LLGPGKPLRRMIE-----AGRLSSMILWGPPGTGKTTLARIIAGATDAPFEALSA----- 69
Query: 85 LLSKKILLLDIALLLAGTKYRGEFEDRLKKILKEISNNQ---KDIIIFIDELH 134
+ +G K L+++++E + + I+FIDE+H
Sbjct: 70 -------------VTSGVK-------DLREVIEEARQRRSAGRRTILFIDEIH 102
>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: 271 RLIQLKIEHEAIKREYDESSKKRLLLIKK---EINKLEIKYANLEKIW-----KYEKTLI 322
+L L + K+ Y E ++ KK E+ KL+ +Y L + + K+E+ ++
Sbjct: 95 KLTLLIKDKRKAKKAYQEERQQIDEQYKKLTDEVEKLKSEYQKLLEDYKAAKSKFEEAVV 154
Query: 323 KDSQQIKEEIEKVRLKINKATRK 345
K + +++K R K KA RK
Sbjct: 155 K-GGRGGRKLDKARDKYQKACRK 176
>gnl|CDD|234763 PRK00440, rfc, replication factor C small subunit; Reviewed.
Length = 319
Score = 34.1 bits (79), Expect = 0.30
Identities = 20/56 (35%), Positives = 29/56 (51%), Gaps = 8/56 (14%)
Query: 22 TEKARLGKLDPVIGRDDEIRRAIQVLQR--RSKNNPVLI--GEPGVGKTAIVEGLA 73
EK R LD ++G+++ + R L+ + KN P L+ G PG GKT LA
Sbjct: 8 VEKYRPRTLDEIVGQEEIVER----LKSYVKEKNMPHLLFAGPPGTGKTTAALALA 59
>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 = 0.38
Identities = 28/88 (31%), Positives = 40/88 (45%), Gaps = 22/88 (25%)
Query: 456 PYGSFMFLGPTGVGKTELCKTLSACIFNNEESIIRIDMSEFIEKHSISRLIGAPPGYIGY 515
P G ++ GP G GKT L K ++ + IR+ SE + K YIG
Sbjct: 156 PKGVLLY-GPPGTGKTLLAKAVAH---ETNATFIRVVGSELVRK------------YIG- 198
Query: 516 EEGGYLT----EIVRRKPYSLILLDEIE 539
EG L E+ + K S+I +DEI+
Sbjct: 199 -EGARLVREIFELAKEKAPSIIFIDEID 225
>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: 107 EFEDRLKKILKEISNNQKDIIIFIDELHTMIGTGKVEGSIDAGNMLKPELSRGELHCIGA 166
E E+ L ++L+ ++++ +++L ++ + LK EL + E
Sbjct: 512 ELEEELIELLELEEALKEELEEKLEKLENLLEELEELKEKLQLQQLKEELRQLEDRLQEL 571
Query: 167 TTLNEY----RQYIEKDAAFERRFQKILVEEPDIEETISILRGLQKKYEVHHGVEITDPA 222
L E R E+ R +++ + ++EE +S L L + E+ + A
Sbjct: 572 KELLEELRLLRTRKEELEELRERLKELKKKLKELEERLSQLEELLQSLELSEAENELEEA 631
Query: 223 IVAASELSYRYISDRFMPDKAIDLIDEAAAKIKIEIDSKPEIMDKLERRLIQLKIEHEAI 282
++ ++ A ++ + E+ +K+E +++ E + I
Sbjct: 632 EEELESE--------------LEKLNLQAELEELLQAALEELEEKVEELEAEIRRELQRI 677
Query: 283 KREYDESSKKRLLLIKKEINKLEIKYANLEKIWKYEKTLIKDSQQIKEEIEKVRLKINKA 342
+ E E +++L +++ +LE LE++ K + + ++++ ++ +
Sbjct: 678 ENE--EQLEEKLEELEQLEEELEQLREELEELLKKLGEIEQLIEELESRKAELEELKKEL 735
Query: 343 TRKSDWQTVSKLKYGELNKLERILKEKSQKDIQLPNNANKFTLL 386
+ 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: 244 IDLIDEAAAKIKIEIDSKPEIMDKLERRLIQLKIEHEAIKREYDESSKKRLLLIKKEINK 303
++ ++ + +K + E K+E QL E I+ + ++ L K E +
Sbjct: 166 LEKYEKLSELLK---EVIKEAKAKIEELEGQLSELLEDIEDLLEALEEELKELKKLEEIQ 222
Query: 304 LEIKYANLEKIWKYEKTLIKDSQQIKEEIEKVRLKINKATRKSDWQTVSKLKYGELNKLE 363
E + LE+ + + + + ++ KE +E+++ ++ +S K++ EL +LE
Sbjct: 223 EEQEEEELEQEIEALEERLAELEEEKERLEELKARL--LEIESLELEALKIREEELRELE 280
Query: 364 RILKEKSQKDIQLPNNANKFTLLK 387
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: 248 DEAAAKIKIEIDSKPEIMDKLERRLIQLKIEHEAIKREYDESSKKRLLLIKKEINKLEIK 307
E + + E ++KLE L +L+ E ++ + + ++L +E+ +L +
Sbjct: 518 IELLELEEALKEELEEKLEKLENLLEELEELKEKLQLQQLKEELRQLEDRLQELKELLEE 577
Query: 308 YANLEKIWKYEKTLIKDSQQIKEEIEKVRLKINKATRKSDWQTVSKLKYGELNKLERILK 367
L + + L + +++K++++++ ++++ +S+ + E +
Sbjct: 578 LRLLRTRKEELEELRERLKELKKKLKELEERLSQLEELLQSLELSEAENELEEAEEELES 637
Query: 368 EKSQKDIQLPNNANKFTLLKTKVGSEE 394
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: 241 DKAIDLIDEAAAKIKIEIDSKPEIMDKLERRLIQLKIEHEAIKREYDESSKKRLLLIKKE 300
+ + ++EA ++K E+ +++++ L +L+ E E ++RE +E ++ + ++++
Sbjct: 381 LERLKQLEEAIQELKEELAELSAALEEIQEELEELEKELEELERELEEL-EEEIKKLEEQ 439
Query: 301 INKLEIKYANLEKIWK-----------------------YEKTLIKDSQQIKEEIEKVRL 337
IN+LE K + ++ YE L + +++ E E+ L
Sbjct: 440 INQLESKELMIAELAGAGEKCPVCGQELPEEHEKELLELYELELEELEEELSREKEEAEL 499
Query: 338 KINKATRKSDWQTVSKLKYGELNKLERILKEKSQKDIQLPNNANKFTLLKTKVGSEEIAE 397
+ + + + + + L E + +E +K +L N + LK K+ +++ E
Sbjct: 500 REEIEELEKELRELEEELIELLELEEALKEELEEKLEKLENLLEELEELKEKLQLQQLKE 559
>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 = 34.0 bits (78), Expect = 0.41
Identities = 16/55 (29%), Positives = 29/55 (52%), Gaps = 7/55 (12%)
Query: 27 LGKLDPVIGRDDEI----RRAIQVLQRRSKNNPVLI-GEPGVGKTAIVEGLAQRI 76
G P++GR E+ RR + R + +L+ GE G+GK+ +V L +++
Sbjct: 476 GGTTTPLVGRSRELEALRRRWRDTVAGRGR--AILVVGEAGIGKSRLVHELVEKV 528
>gnl|CDD|223250 COG0172, SerS, Seryl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 429
Score = 33.7 bits (78), Expect = 0.42
Identities = 16/73 (21%), Positives = 37/73 (50%)
Query: 267 KLERRLIQLKIEHEAIKREYDESSKKRLLLIKKEINKLEIKYANLEKIWKYEKTLIKDSQ 326
+L+ +L E E ++ E +E SK+ +K+ + E A ++++ + K L
Sbjct: 33 ELDEERRKLLRELEELQAERNELSKEIGRALKRGEDDAEELIAEVKELKEKLKELEAALD 92
Query: 327 QIKEEIEKVRLKI 339
+++ E++ + L I
Sbjct: 93 ELEAELDTLLLTI 105
>gnl|CDD|235871 PRK06835, PRK06835, DNA replication protein DnaC; Validated.
Length = 329
Score = 33.7 bits (78), Expect = 0.42
Identities = 21/84 (25%), Positives = 40/84 (47%), Gaps = 12/84 (14%)
Query: 263 EIMDKLERRLIQLKIEHEAIKREYDESSK-KRLLLIKKEINKLEIKYANLEKIWKYEKTL 321
EI+ + E+R + K E E R+ + K + I EI KL IK + + +
Sbjct: 8 EILKEYEKR--RDKEELELKNRKEEVYKKIPEIAEIDDEIAKLGIKLS---------RAI 56
Query: 322 IKDSQQIKEEIEKVRLKINKATRK 345
+K+ + +E +++++ KI K
Sbjct: 57 LKNPDKKEETLKELKEKITDLRVK 80
>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: 280 EAIKREYDESSKKRLLLIKKEINKLEIKYANLEKIWKYEKTLIKDSQQIKEEIEKVRLKI 339
+ RE K +L ++ + K + + + + + E L + +++++ E +
Sbjct: 60 NPVLREEKRKPAKSILSLQALLEKRPSRTNSQDALLQAENALPEWKKELEKPSEPKEEEP 119
Query: 340 NK-ATRKSDWQTVSKLKYGELNKLERILKEKSQKDIQL----PNNANKFTLLKTKVG-SE 393
A K + + +L+ EL +L+ +L+++ Q+ P A + LK + G S
Sbjct: 120 KAAAESKVVQKELDELR-DELKELKNLLEDQLSGLRQVERIPPEFAELYKRLK-RSGLSP 177
Query: 394 EIAEIVSRTTGIPVSKIVQVEREKLLNIENLLCKRVVGQDEAISAVSNAIRRSRSGLSDA 453
EIAE + + + + LL LL + + E I +
Sbjct: 178 EIAEKLLKLLLEHMPPRERTAWRYLLE---LLANMIPVRVEDILKQGGVV---------- 224
Query: 454 KRPYGSFMFLGPTGVGKT 471
+GPTGVGKT
Sbjct: 225 -------ALVGPTGVGKT 235
>gnl|CDD|237865 PRK14951, PRK14951, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 618
Score = 33.9 bits (78), Expect = 0.46
Identities = 17/48 (35%), Positives = 27/48 (56%), Gaps = 8/48 (16%)
Query: 430 VGQDEAISAVSNAIRRSRSGLSDAKRPYGSFMFLGPTGVGKTELCKTL 477
VGQ+ + A++NA+ + R L A ++F G GVGKT + + L
Sbjct: 19 VGQEHVVQALTNALTQQR--LHHA------YLFTGTRGVGKTTVSRIL 58
>gnl|CDD|235503 PRK05561, PRK05561, DNA topoisomerase IV subunit A; Validated.
Length = 742
Score = 33.9 bits (79), Expect = 0.47
Identities = 29/107 (27%), Positives = 42/107 (39%), Gaps = 30/107 (28%)
Query: 242 KAIDLIDEAAAKIKIEIDSKPEIMDK-----------LERRLIQL-KIEHEAIKREYDES 289
A IDE I+ + K +M + LE RL +L K+E I++E DE
Sbjct: 390 IAFLNIDEVIRIIRESDEPKANLMARFDLSEIQAEAILELRLRRLAKLEEIEIRKEQDEL 449
Query: 290 SKKRLLLIKKEINKLEIKYANLEKIWKYEKTLIKDSQQIKEEIEKVR 336
K+ A LE I E+ L K IK+E++
Sbjct: 450 RKEI---------------AELEAILASERKLRK---LIKKELKADA 478
>gnl|CDD|140271 PTZ00244, PTZ00244, serine/threonine-protein phosphatase PP1;
Provisional.
Length = 294
Score = 33.3 bits (76), Expect = 0.47
Identities = 27/113 (23%), Positives = 57/113 (50%), Gaps = 18/113 (15%)
Query: 694 PEANFIFLGDLINKGPQSLDTLRMVYSMR-----NYAKIVLGNHEIHLLDVLININKKSK 748
P +N++FLGD +++G S++T+ + + + N+ ++ GNHE +INK
Sbjct: 78 PYSNYLFLGDYVDRGKHSVETITLQFCYKIVYPENFF-LLRGNHEC------ASINKMYG 130
Query: 749 LDTFDDILDAPDKKKLVSW---LRTQPL-AIYYKKYLMIHAGVAKQWTAQQTI 797
FDD+ + K ++ T P+ + +K + +H G++ T+ ++
Sbjct: 131 F--FDDVKRRYNIKLFKAFTDVFNTMPVCCVISEKIICMHGGLSPDLTSLASV 181
>gnl|CDD|226400 COG3883, COG3883, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 265
Score = 33.2 bits (76), Expect = 0.49
Identities = 29/171 (16%), Positives = 69/171 (40%), Gaps = 23/171 (13%)
Query: 242 KAIDLIDEAAAKIKIEIDSKPEIMDKLERRLIQLKIEHEAIK---REYDESSKKRL---- 294
I+ +D +I+ +ID + +D+ + + +L+ E +K E E KKR
Sbjct: 52 NEIESLDNQIEEIQSKIDELQKEIDQSKAEIKKLQKEIAELKENIVERQELLKKRARAMQ 111
Query: 295 -----------LLIKKEINKLEIKYANLEKIWKYEKTLIKDSQQIKEEIEKVRLKINKAT 343
+L K + L + + I +K +++ ++ K+ +E+ + +
Sbjct: 112 VNGTATSYIDVILNSKSFSDLISRVTAISVIVDADKKILEQQKEDKKSLEEKQAALEDKL 171
Query: 344 RKSDWQTVSKLKYGELNKLERILKEKSQKDIQLPNNANKFTLLKTKVGSEE 394
+T+ L+ +L + +K++K+ + A K + + E
Sbjct: 172 -----ETLVALQNELETQLNSLNSQKAEKNALIAALAAKEASALGEKAALE 217
>gnl|CDD|237868 PRK14960, PRK14960, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 702
Score = 33.9 bits (77), Expect = 0.50
Identities = 17/53 (32%), Positives = 30/53 (56%), Gaps = 8/53 (15%)
Query: 429 VVGQDEAISAVSNAIRRSRSGLSDAKRPYGSFMFLGPTGVGKTELCKTLSACI 481
+VGQ+ A+S+A+ R R + +++F G GVGKT + + L+ C+
Sbjct: 17 LVGQNHVSRALSSALERGRL--------HHAYLFTGTRGVGKTTIARILAKCL 61
>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: 23 EKARLGKLDPVIGRDDEIRRAIQVLQRRSKNNPVLIGEPGVGKTAIVEGLAQRIINGEV 81
EK R +LD ++G++ ++R ++ S + + G PGVGK + G + I NGE+
Sbjct: 11 EKYRPQRLDDIVGQEHIVKRLKHYVKTGSMPHLLFAGPPGVGKC--LTGDTKVIANGEL 67
>gnl|CDD|184697 PRK14475, PRK14475, F0F1 ATP synthase subunit B; Provisional.
Length = 167
Score = 32.2 bits (73), Expect = 0.60
Identities = 12/39 (30%), Positives = 22/39 (56%)
Query: 247 IDEAAAKIKIEIDSKPEIMDKLERRLIQLKIEHEAIKRE 285
+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 = 33.2 bits (76), Expect = 0.62
Identities = 34/149 (22%), Positives = 55/149 (36%), Gaps = 42/149 (28%)
Query: 429 VVGQDEAISAVSNAIRRSRSGLSDAKRPYGSFMFLGPTGVGKT----------------- 471
+VGQ+ + + NAI R +++F GP GVGKT
Sbjct: 18 LVGQEHVVQTLRNAIAEGRVA--------HAYLFTGPRGVGKTSTARILAKAVNCTTNDP 69
Query: 472 --ELCKTLSACIFNNEES---IIRIDMSEFIEKHSISRLIGAPPGYIGYEEGGYLTEIVR 526
C T C E S +I +D + +I E + + R
Sbjct: 70 KGRPCGTCEMCRAIAEGSAVDVIEMDAASHTSVDDAREII---------ERVQFRPALAR 120
Query: 527 RKPYSLILLDEIEKANSDVFNILLQILDD 555
K Y ++DE+ ++ FN LL+ L++
Sbjct: 121 YKVY---IIDEVHMLSTAAFNALLKTLEE 146
>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 = 0.65
Identities = 37/176 (21%), Positives = 67/176 (38%), Gaps = 25/176 (14%)
Query: 242 KAIDLIDEAAAKIKIEIDSKPEIMDKLERRLIQLKIEHEAIKREYDESSKKRLLLIKKEI 301
A+ IDE I+ KPE ++L R + + EAI + +RL E
Sbjct: 384 IALLNIDEVIEIIRES-KDKPEAKEELMARFGLSEKQAEAIL----DLRLRRLT--GLEE 436
Query: 302 NKLEIKYANLEKIWKYEKTLI----KDSQQIKEEIEKVRLKINKATRKSDWQTVSKLKYG 357
K+E + LEK + ++ + IK+E+ +++ K R + + +
Sbjct: 437 EKIEKELKELEKEIADLEKILASEERLLDIIKKELLEIKKKFGDERR----TEIVEEEED 492
Query: 358 ELNKLERILKE-----KSQK--DIQLPN---NANKFTLLKTKVGSEEIAEIVSRTT 403
E+ + I +E S K ++P A + + L K G + T
Sbjct: 493 EIEDEDLIAEEDVVVTLSHKGYIKRVPLKGYEAQRVSGLGLKEGDFLERLFEANTH 548
>gnl|CDD|184927 PRK14963, PRK14963, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 504
Score = 33.3 bits (76), Expect = 0.65
Identities = 16/43 (37%), Positives = 23/43 (53%), Gaps = 8/43 (18%)
Query: 429 VVGQDEAISAVSNAIRRSRSGLSDAKRPYGSFMFLGPTGVGKT 471
VVGQ+ + A+R+ R G +++F GP GVGKT
Sbjct: 16 VVGQEHVKEVLLAALRQGRLG--------HAYLFSGPRGVGKT 50
>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 = 32.3 bits (74), Expect = 0.76
Identities = 19/71 (26%), Positives = 36/71 (50%), Gaps = 5/71 (7%)
Query: 294 LLLIKKEINKLEIKYANLEKIWKYEKTLIKDSQQIKEEIEKVRLKINKATRKSDWQTVSK 353
+ E++K K A LEK+ + KT + + E+E+ + ++ K +++ VS+
Sbjct: 117 WQSAESELSK---KKAQLEKLKRQGKTQQEKLNSLLSELEEAERRASEL--KKEFEEVSE 171
Query: 354 LKYGELNKLER 364
L EL + ER
Sbjct: 172 LIKSELERFER 182
>gnl|CDD|225369 COG2812, DnaX, DNA polymerase III, gamma/tau subunits [DNA
replication, recombination, and repair].
Length = 515
Score = 33.1 bits (76), Expect = 0.81
Identities = 35/140 (25%), Positives = 61/140 (43%), Gaps = 29/140 (20%)
Query: 429 VVGQDEAISAVSNAIRRSRSGLSDAKRPYGSFMFLGPTGVGKTELCKTLSACIFNNEESI 488
VVGQ+ + +SNA+ + R +++F GP GVGKT + + L+ + N E
Sbjct: 18 VVGQEHVVKTLSNAL--------ENGRIAHAYLFSGPRGVGKTTIARILAKAL-NCENGP 68
Query: 489 -----IRIDMSEFIEKHSISRLIGAPPGYI------GYEEGGYLTEIVRRKP----YSLI 533
+ + I + S+ +I I G ++ + E V P Y +
Sbjct: 69 TAEPCGKCISCKEINEGSLIDVI-----EIDAASNTGVDDIREIIEKVNYAPSEGRYKVY 123
Query: 534 LLDEIEKANSDVFNILLQIL 553
++DE+ + FN LL+ L
Sbjct: 124 IIDEVHMLSKQAFNALLKTL 143
>gnl|CDD|224337 COG1419, FlhF, Flagellar GTP-binding protein [Cell motility and
secretion].
Length = 407
Score = 32.7 bits (75), Expect = 0.86
Identities = 34/217 (15%), Positives = 72/217 (33%), Gaps = 29/217 (13%)
Query: 282 IKREYDESSKKRLLLIKKE-------INKLEIKYANLEKIWKYEKTL--IKDSQQIKEEI 332
IK+ ES ++ + I+KE ++ IK + KT + + E+
Sbjct: 3 IKKFTAESMREAIEKIRKELGEDAVILSNRRIK-KGGFLGLLFSKTAVEVTKLAAVDSEL 61
Query: 333 EKVRLKINKATRKSDWQTVSKLKYGELNKLERILKE-----KSQKDIQLPNNANKFTLLK 387
K + + + ++ Q + + + + K+ S + + + +
Sbjct: 62 RKFQTREAAKVKDAEAQLLKDPA-EKKREERKAAKKIERSTPSLIERKTQEVKDSGEEIA 120
Query: 388 TKVGSEE--IAEIVSRTTGIPVSKIVQVEREKLLNIENLLCKR-VVGQDEAISAVSNAIR 444
+ E+ I E+ +++ LN+ N L + + + + S
Sbjct: 121 EMMRDEKVPIRELEEIPPEFVALYKQEIQSPTRLNLINELLRAGLELEILDMKDESYEDL 180
Query: 445 RSRSGL----------SDAKRPYGSFMFLGPTGVGKT 471
R S + +GPTGVGKT
Sbjct: 181 RYFSEKLRKLLLSLIENLIVEQKRVIALVGPTGVGKT 217
>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 = 0.87
Identities = 25/159 (15%), Positives = 63/159 (39%), Gaps = 20/159 (12%)
Query: 169 LNEYRQYIEKDAAFERRF---QKILVEEPDIEETISILRGLQKKYEVHHGVEITDPAIVA 225
+E E +A++ RF + +LV +PD+ +R K+++ + I+
Sbjct: 159 ADELGTLEEDPSAYQIRFGGYKGVLVVDPDLPGNEIHIRPSMLKFDLLGDAAVNSLEIIR 218
Query: 226 ASELSYRYISDRFM--------PDKA-IDLIDEAAAKIKIEIDS--------KPEIMDKL 268
+S+ + Y++ + + PD+ I+L+ EA ++ + + + +
Sbjct: 219 SSKPTPAYLNRQLITVLSTLGVPDEVFIELLREALKELAEALTDWDQALDLLRKQADEND 278
Query: 269 ERRLIQLKIEHEAIKREYDESSKKRLLLIKKEINKLEIK 307
++ + 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: 245 DLIDEAAAK-IKIEIDSKPEIMDKL-----ERRLIQLKIEHEAIKREYDESSKKRLLLIK 298
DL E + +K+ K + ++ + ER+ + + E A K ++E+ + LL+
Sbjct: 557 DLAREEFQRRVKLLQLQKEKQLEDIQDCREERKSLSERAEKLAEK--FEEAKYNQELLVN 614
Query: 299 KEINKLEIKYANLEKIWKYEKTLIKDSQQIKEEIEKVRLKINKATRKSDWQTVSKLKYGE 358
+ L+ + L + E+ + K+ Q+I ++++ + I + +K ++Q
Sbjct: 615 RCKRLLQSANSQLPVLSDSERDMSKELQRINKQLQHLANGIKQVKKKKNYQRYHMASQES 674
Query: 359 LNKLERILKEKSQKDIQLPNNANKFTLLKTKVGSEEIAEIVSRTTGI 405
K L EK K I +LK E I ++ + I
Sbjct: 675 PKKSSYTLPEKQHKTIT--------EILKEL--GEHIDRMIKQIKRI 711
>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: 588 EKGDKEIIKLAVMNEVKIYFRPEFINRID 616
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 = 1.2
Identities = 25/122 (20%), Positives = 47/122 (38%), Gaps = 14/122 (11%)
Query: 42 RAIQVLQRRSKNNPVLIGEPGVGKTAIVEGLAQRIINGEVPNSLLSKKILLLDIALLLAG 101
+AI++L R ++ PV++G+ + + LA RIIN ++ + ALL+
Sbjct: 850 KAIEILSRLCRDQPVVLGDLIANASKCISSLADRIINSSSL------EVKIGGTALLICA 903
Query: 102 TKYRGEFEDRLKKILKEISNNQKDIIIFIDELHTMIGTGKVEGSIDAGNMLKPELSRGEL 161
K E R + E + + + I L M+ + S+ + P
Sbjct: 904 AK-----EHRQLVM--EALDESGYLKLLIQALVDMLKQNSKKESLSIE-IQTPRGFLESN 955
Query: 162 HC 163
Sbjct: 956 LF 957
>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: 429 VVGQDEA---IS-AVSNAIRRSRSGLSD------AKRPYGS-FMFLGPTGVGKTELCKTL 477
V+GQ+ A +S AV N +R R G K S + +GPTG GKT L +TL
Sbjct: 73 VIGQERAKKVLSVAVYNHYKRLRHGDKKDDDVELQK----SNILLIGPTGSGKTLLAQTL 128
Query: 478 S 478
+
Sbjct: 129 A 129
>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 = 1.3
Identities = 34/107 (31%), Positives = 51/107 (47%), Gaps = 12/107 (11%)
Query: 241 DKAIDLIDEAAAKIKIEIDSKPEIMDKLERRLIQLKIE-----HEAIKR-EYDESSKKRL 294
D D ++AA + + PE +D+ RL+ L ++ EAI+ E S RL
Sbjct: 90 DDIADAAEDAAKLLLLRKPFIPEELDEEFLRLVDLSLKAAELLAEAIELLEDLLESADRL 149
Query: 295 LLIKKEINKLE-----IKYANLEKIWKYEKTL-IKDSQQIKEEIEKV 335
L I KEI LE I+ L+K++ E + D +KE IEK+
Sbjct: 150 LEIIKEIEALEHECDDIQRELLKKLFSLETEINPIDVIILKEIIEKI 196
>gnl|CDD|237576 PRK13979, PRK13979, DNA topoisomerase IV subunit A; Provisional.
Length = 957
Score = 32.4 bits (74), Expect = 1.3
Identities = 37/120 (30%), Positives = 54/120 (45%), Gaps = 33/120 (27%)
Query: 242 KAIDLIDEAAAKI---KIEIDSKPEIMDK-----------LERRLIQLK-IEHEAIKREY 286
KAI ++DE I K + D+ +++K LE L +L +E A ++EY
Sbjct: 396 KAIGIMDEIIKTIRSSKSKKDASENLIEKFGFTDEQAEAILELMLYRLTGLEIVAFEKEY 455
Query: 287 DESSKKRLLLIKKEINKLEIKYANLEKIWKYEKTLIKDSQQIKEEIEKVRLKINKATRKS 346
E K LIKK L KI EK L+K IK+E+++V+ K R S
Sbjct: 456 KELEK----LIKK-----------LTKILSSEKELLK---VIKKELKEVKEKYGDERRTS 497
>gnl|CDD|226859 COG4452, CreD, Inner membrane protein involved in colicin E2
resistance [Defense mechanisms].
Length = 443
Score = 32.0 bits (73), Expect = 1.4
Identities = 25/77 (32%), Positives = 36/77 (46%), Gaps = 7/77 (9%)
Query: 26 RLGKLDPVIGRDDEIRRAIQVLQRRSKNNPVLIGEPGVGKTAIVEGLAQRIINGEVPNSL 85
LGK V+ D R I V++ S N L EPG+ +G ++ +P S
Sbjct: 139 TLGKPFLVLSIGDA--RGIGVVKAPSVNGTALTFEPGIRLEQSGQG-----VHIPLPESD 191
Query: 86 LSKKILLLDIALLLAGT 102
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 = 1.4
Identities = 16/49 (32%), Positives = 29/49 (59%), Gaps = 8/49 (16%)
Query: 430 VGQDEAISAVSNAIRRSRSGLSDAKRPYGSFMFLGPTGVGKTELCKTLS 478
VGQ+ + A++NA+ + +R + +++F G GVGKT L + L+
Sbjct: 19 VGQEHVVRALTNALEQ--------QRLHHAYLFTGTRGVGKTTLARILA 59
>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 = 1.4
Identities = 53/272 (19%), Positives = 102/272 (37%), Gaps = 38/272 (13%)
Query: 108 FEDRLKKILKEISNNQKDIIIFIDELHTMIGTGKVEGSIDAGNMLKPELSRGELHCIGAT 167
F +K I +S ++ ++ DEL GT EGS A ++L+ L + + T
Sbjct: 386 FSGHMKNISAILSKTTENSLVLFDELGA--GTDPDEGSALAISILE-YLLKQNAQVLITT 442
Query: 168 TLNEYRQYIEKDAAFERRFQKILVEEPDIEETISILRGLQKKYEVHHGVEITDPAIVAAS 227
E + + + E D E L Y++ G+ P A
Sbjct: 443 HYKELKALMYNNEGVEN-----ASVLFDEET-------LSPTYKLLKGI----PGESYAF 486
Query: 228 ELSYRYISDRFMPDKAIDL-------IDEAAAKIKIEIDSKPEIMDKLERRLIQLKIEHE 280
E++ RY F+ ++A I+ K+ + + LE+ L + + +
Sbjct: 487 EIAQRYGIPHFIIEQAKTFYGEFKEEINVLIEKLSALEKELEQKNEHLEKLLKEQEKLKK 546
Query: 281 AIKREYDESSKKRLLLIKKEINKLEIKYANLEKIWKYEKTLIKDSQQIKEEIEKVRLKIN 340
+++E +E L ++ K A + K L K+ + I E++ KI+
Sbjct: 547 ELEQEMEE-----LKERERNKKLELEKEAQ-----EALKALKKEVESIIRELK--EKKIH 594
Query: 341 KATRKSDWQTVSKLKYGELNKLERILKEKSQK 372
KA + + KLK + ++ ++ K
Sbjct: 595 KAKEIKSIEDLVKLKETKQKIPQKPTNFQADK 626
>gnl|CDD|237874 PRK14971, PRK14971, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 614
Score = 32.4 bits (74), Expect = 1.4
Identities = 39/153 (25%), Positives = 60/153 (39%), Gaps = 50/153 (32%)
Query: 429 VVGQDEAISAVSNAIRRSRSGLSDAKRPYGSFMFLGPTGVGKT----------------- 471
VVGQ+ + + NAI ++ L+ A ++F GP GVGKT
Sbjct: 19 VVGQEALTTTLKNAIATNK--LAHA------YLFCGPRGVGKTTCARIFAKTINCQNLTA 70
Query: 472 --ELCKTLSACI-FNNEES--IIRIDMSEFIEKHSISRLIGAPPGYIGYEEGGYLTEIVR 526
E C +C+ FN + S I +D + I LI E VR
Sbjct: 71 DGEACNECESCVAFNEQRSYNIHELDAASNNSVDDIRNLI----------------EQVR 114
Query: 527 RKP----YSLILLDEIEKANSDVFNILLQILDD 555
P Y + ++DE+ + FN L+ L++
Sbjct: 115 IPPQIGKYKIYIIDEVHMLSQAAFNAFLKTLEE 147
>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 = 1.6
Identities = 27/141 (19%), Positives = 51/141 (36%), Gaps = 23/141 (16%)
Query: 432 QDEAISAVSNAIRRSRSGLSDAKRPYGSFMFLGPTGVGKTELCKTLSAC-------IFNN 484
+ +A+ V+ R+ L + P GP G GKT L ++ I +
Sbjct: 3 ETDAVKRVT---SRALRYL-KSGYP---VHLRGPAGTGKTTLAMHVARKRDRPVMLINGD 55
Query: 485 EESIIRIDMSEFIEKHSISRLIGAPPGYIGYEE-------GGYLTEIVRRKPYSLILLDE 537
E + + + E+ LT V R+ ++L+ DE
Sbjct: 56 AELTTSDLVGSYAGYTRKKVHDQFIHNVVKLEDIVRQNWVDNRLTLAV-REGFTLV-YDE 113
Query: 538 IEKANSDVFNILLQILDDGRL 558
++ + N+LL + ++G L
Sbjct: 114 FTRSKPETNNVLLSVFEEGVL 134
>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: 692 KSPEAN-FIFLGDLINKGPQSLDTLRMVYSMR-NYAKIVL---GNHEIHLLDVLININK- 745
SP ++FLGD +++G S++ + +++++ Y K + GNHE L +
Sbjct: 66 GSPANTRYLFLGDYVDRGYFSIECVLYLWALKILYPKTLFLLRGNHECRHLTEYFTFKQE 125
Query: 746 ---KSKLDTFDDILDAPDKKKLVSWLRTQPLA-IYYKKYLMIHAGV 787
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: 429 VVGQDEA---IS-AVSNAIRRSRSGLSDAKRPYG--SFMFLGPTGVGKTELCKTLS 478
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: 263 EIMDKLERRLIQLKIEHEAIKREYDE---------SSKKRLLLIKKEINKLEIKY-ANLE 312
E +D L+ L QL I E E + + +L + +E K + + L
Sbjct: 161 ERIDALKATLKQLAAVRAEIAAEQAELTTLLSEQRAQQAKLAQLLEERKKTLAQLNSELS 220
Query: 313 KIWKYEKTLIKDSQQIKEEIEKVRLKINKATRK 345
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 = 1.7
Identities = 25/126 (19%), Positives = 49/126 (38%), Gaps = 20/126 (15%)
Query: 268 LERRLIQLKIEHEAIKREYDESSKKRLLLIKKEINKLEIKYANLEKIWKYEKTLIKDSQQ 327
L+ +L+ L A+KR D + +L+ K KLEI + L + + L K Q+
Sbjct: 158 LQDKLLLLD---AAVKRH-DGNVITAVLIFLKRTLKLEILFQELAERQTALRHLSKHLQE 213
Query: 328 IKEEIEKVRLKINKATRKSDWQTVSKLKYGELNKLERILKEKSQKDIQLPNNANKFTLLK 387
E + ++L + + + +Y ++K+ + +Q + LK
Sbjct: 214 EGELQQLLKL----LRAEGESEKQELQQY----------RQKAHRILQSKE--KRINFLK 257
Query: 388 TKVGSE 393
E
Sbjct: 258 EGCLFE 263
>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: 252 AKIKIEIDSKPEIMDKLERRLIQLKIEHEAIKREYDESSKKRLLLIKKEINKLEIKYANL 311
AK K+E+ + + +D+ ++ + + + + + ++E++E SK IKKEI + E
Sbjct: 138 AKAKLELSGRTDKLDQAQQEIKEWEAKVDRGQKEFEEISK----TIKKEIERFEKNRVKD 193
Query: 312 EK--IWKYEKTLIKDSQQIKEEIEK 334
K I KY ++L+ QQ+ + E
Sbjct: 194 FKDIIIKYLESLLNTQQQLIKYWEA 218
>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: 430 VGQDEAISAVSNAIRRSRSGLSDAKRPYGSFMFLGPTGVGKT 471
GQ+ + NAI D R +F+F G GVGKT
Sbjct: 19 TGQEHVSRTLQNAI--------DTGRVAHAFLFTGARGVGKT 52
>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: 460 FMFLGPTGVGKTELCKTLSACIFNN-EESIIRIDMSEFIEKHSISRLIGAPPGYIGYEEG 518
+ G G GKT L+ACI N E + + F + ++R+ +E
Sbjct: 117 LLLWGSVGTGKT----YLAACIANELIEKGVPVIFVNFPQ--LLNRIKSTYKSSGKEDE- 169
Query: 519 GYLTEIVRR-KPYSLILLDE--IEKANS----DVFNILLQILDDGRLTDNRGRTINFRNT 571
EI+R L++LD+ E+ V+NI+ D+R R T
Sbjct: 170 ---NEIIRSLVNADLLILDDLGAERDTEWAREKVYNII----------DSRYR--KGLPT 214
Query: 572 IIVMTSNLGSDKIKE 586
I+ T+NL +++K
Sbjct: 215 IV--TTNLSLEELKN 227
>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 = 2.1
Identities = 32/160 (20%), Positives = 67/160 (41%), Gaps = 36/160 (22%)
Query: 177 EKDAAFERRFQKILVEEPDIEETISILRGLQKKYEVHHGVEITDPAIVAASELSYRYISD 236
+ A R Q+I+ EE + I L G SY Y+
Sbjct: 341 DFSARIARNTQQIIQEESGVTRVIDPLGG------------------------SY-YV-- 373
Query: 237 RFMPDKAIDLIDEAAAKIKIEIDSKPEIMDKLERRLIQLKIEHEAIKREYDESSKKRLLL 296
+ D I E A K EI+ + +ER + +L+IE A + + S +++++
Sbjct: 374 ----EWLTDDIYERAWKYIQEIEEMGGMAKAIERGIPKLRIEEAAARTQARIDSGRQVIV 429
Query: 297 IKKEINKLEIKYANLEKIWKYEKTLIKDSQQIKEEIEKVR 336
+NK +++ + ++ K + + +++ Q +++K+R
Sbjct: 430 ---GVNKYQLEEEDEVEVLKVDNSSVREEQ--IAKLKKLR 464
>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 = 2.1
Identities = 22/88 (25%), Positives = 37/88 (42%), Gaps = 15/88 (17%)
Query: 511 GYIGYEEGGYLTEIVRRKPYSLILLDEIEKANSDVFNILLQILDDGRLTDNRGRTINFRN 570
G + Y G Y+TE+ Y+ V+N L+ + DG D +G T N ++
Sbjct: 34 GTVAYVNGEYITEL----NYNF----------RSVYNATLKAIQDGNTFDVKGNTYNSKD 79
Query: 571 TIIVMTSNLGSDKIK-EMEKGDKEIIKL 597
I ++ + SD +EK K+
Sbjct: 80 ATITASNKIDSDSFSIRIEKLTDNATKV 107
>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: 429 VVGQDEAISAVSNAIRRSRSGLSDAKRPYGSFMFLGPTGVGKTELCKTLSACI 481
VVGQ+ +S+A+ DA R +++F GP G GKT + L+ +
Sbjct: 15 VVGQEHVTEPLSSAL--------DAGRINHAYLFSGPRGCGKTSSARILARSL 59
>gnl|CDD|172375 PRK13851, PRK13851, type IV secretion system protein VirB11;
Provisional.
Length = 344
Score = 31.4 bits (71), Expect = 2.2
Identities = 29/85 (34%), Positives = 40/85 (47%), Gaps = 8/85 (9%)
Query: 459 SFMFLGPTGVGKTELCKTLSACIFNNEESIIRIDMSEFIEKH-SISRLI----GAPPGYI 513
+ + GPTG GKT + KTL + I E I D E + H + RL+ GA G +
Sbjct: 164 TMLLCGPTGSGKTTMSKTLISAIPPQERLITIEDTLELVIPHENHVRLLYSKNGAGLGAV 223
Query: 514 GYEEGGYLTEIVRRKPYSLILLDEI 538
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 = 31.4 bits (72), Expect = 2.2
Identities = 24/107 (22%), Positives = 48/107 (44%), Gaps = 13/107 (12%)
Query: 242 KAIDLIDEA-----AAKIKIEIDSKPEIMDKLERRLIQLKIEHEAIKREYDESSKKRLLL 296
A +I+EA K + +++K E+ ++ ++E E +R + +R LL
Sbjct: 33 LAKRIIEEAKKEAETLKKEALLEAKEEVHK------LRAELERELKERRNELQRLERRLL 86
Query: 297 IKKEI--NKLEIKYANLEKIWKYEKTLIKDSQQIKEEIEKVRLKINK 341
++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: 582 DKIKEMEKGDKEIIKLAVMNEVKIYFRPEFINR 614
+K +++ K +KL +++ + +FR E++ R
Sbjct: 180 EKAEDLIKELNNPVKLLIVDSLTSHFRAEYVGR 212
>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: 182 FERRFQKILVEEPDIEETISILRGLQKKYEVHHGVEITDPAIVAASELSYRYISDRFMPD 241
E R K + E E I + + ++ E+T+ IV +E+ + IS +F D
Sbjct: 370 IEERIYKEIEEAETWEAVIEAIDKGLEPFKKQFIREVTEDDIVRLTEIKIKRIS-KFDSD 428
Query: 242 KAIDLIDEAAAKIKIEIDSKPEIMDKLERRLIQLKIEH-EAIKREY 286
KA +LI A+I E+ L L I + +K++Y
Sbjct: 429 KADELIARLEAEIA-------EVKHHLA-HLTDYAIAYFTNLKKKY 466
>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: 461 MFLGPTGVGKTELCKTLS 478
M +G +G GKT L + L+
Sbjct: 5 MLIGRSGCGKTTLTQALN 22
>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: 266 DKLERRLIQLKIEHEAIKREYDESSKKRLLLIKKEINKLEIKYANLEKIWK-YEKTLIKD 324
DK R L + + E E + + +E + RL ++ + A + ++ + L +
Sbjct: 1 DKAARNLAEAQQELEQAEEKLEELQQYRLEYRQQLSGSGQGISAAELRNYQAFISALDEA 60
Query: 325 SQQIKEEIEKVRLKINKATRKSDWQTVSKLKYGELNKLERILKEKSQKDIQL 376
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 = 2.4
Identities = 17/51 (33%), Positives = 30/51 (58%), Gaps = 2/51 (3%)
Query: 44 IQVLQRRSKNNPVLIGEPGVGKTAIVEGLAQRIINGEVPNSLLSKKILLLD 94
I+ L + N ++IG P VGKT ++ +A+ + +G N L KK+ ++D
Sbjct: 129 IKDLYQNGWLNTLIIGPPQVGKTTLLRDIARLLSDGI--NQFLPKKVGIID 177
>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 = 2.4
Identities = 11/32 (34%), Positives = 19/32 (59%), Gaps = 4/32 (12%)
Query: 56 VLIGEPGVGKTAIVEGLAQRIINGEVPNSLLS 87
VLIG+ GVGKT+++ R ++ + + S
Sbjct: 4 VLIGDSGVGKTSLL----LRFVDNKFSENYKS 31
>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 = 2.6
Identities = 19/87 (21%), Positives = 38/87 (43%), Gaps = 11/87 (12%)
Query: 56 VLIGEPGVGKTAIVEGLAQRIINGE---VPNSLLSKKILLLDIALLLAGTKYRGEFEDRL 112
+L G PG GK+ + LA + G P + ++L LD ++ RL
Sbjct: 37 LLAGAPGTGKSTLALDLAAAVATGRPFLGPFPVEPGRVLYLD----GEDSEAG--LRRRL 90
Query: 113 KKILKEISNNQKDI-IIFIDELHTMIG 138
+ + + + + ++ ID L +++G
Sbjct: 91 RALGEAL-EEIEGPDLVVIDPLASLLG 116
>gnl|CDD|234232 TIGR03499, FlhF, flagellar biosynthetic protein FlhF. [Cellular
processes, Chemotaxis and motility].
Length = 283
Score = 30.8 bits (70), Expect = 2.8
Identities = 9/20 (45%), Positives = 10/20 (50%)
Query: 452 DAKRPYGSFMFLGPTGVGKT 471
G +GPTGVGKT
Sbjct: 190 PILERGGVIALVGPTGVGKT 209
>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: 113 KKILKEISNNQKDIIIFIDELHTMIGTGKVEGSIDAGNMLKPELSRGELHCIGATTLNEY 172
KI + +S KD I+ DE H + + L ELSR L + +Y
Sbjct: 225 PKIRQALSIELKDSIVIFDEAHNLDNV--------CISALSSELSRRSL-ERAHKNIKKY 275
Query: 173 RQYIEKD 179
+ IEK
Sbjct: 276 FERIEKI 282
>gnl|CDD|225224 COG2348, COG2348, Peptidoglycan interpeptide bridge formation
enzyme [Cell wall/membrane/envelope biogenesis].
Length = 418
Score = 31.2 bits (71), Expect = 2.8
Identities = 26/141 (18%), Positives = 49/141 (34%), Gaps = 14/141 (9%)
Query: 258 IDSKPEIMDKLERRLI-----QLKIEHEAIKREYDESSKKRLLLIKKEINKLE-IKYANL 311
D EI++ I L +H + D+S + R + +K E +
Sbjct: 115 FDLGGEIIENYNNLAIIKLLKDLGYKHSGFTKGLDDSIQPRWHSVLDLKDKTEDQLLKSF 174
Query: 312 EKIWKY-----EKTLIKDSQQIKEEIEKVRLKINKATRKSDWQTVSKLKYGELNKLERIL 366
K + EK +K +++ E + ++ K T + T L Y E I
Sbjct: 175 SKKTRRNIKKAEKKGVKV-RRLSREELDLFSELMKKTSERKGFTDRSLSYYE--NFYDIY 231
Query: 367 KEKSQKDIQLPNNANKFTLLK 387
K+K++ + + L
Sbjct: 232 KDKAELPLAYLDLDEYLKKLN 252
>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: 53 NNPVLIGEPGVGKTAIVEGLAQRIINGEVPNSLLSKKILLLD 94
N ++I P GKT ++ LA+ + G L KK+ ++D
Sbjct: 112 LNTLIISPPQCGKTTLLRDLARILSTGISQLGLRGKKVGIVD 153
>gnl|CDD|100796 PRK01156, PRK01156, chromosome segregation protein; Provisional.
Length = 895
Score = 31.4 bits (71), Expect = 2.9
Identities = 35/152 (23%), Positives = 65/152 (42%), Gaps = 6/152 (3%)
Query: 244 IDLIDEAAAKIKIEIDS-KPEI--MDKLERRLIQLKIEHEAIKREYDESSKKRLLLIKKE 300
I+ ++ K+K ID + EI +D LE +L +E E IK++ + K + KE
Sbjct: 161 INSLERNYDKLKDVIDMLRAEISNIDYLEEKLKSSNLELENIKKQIADDEKS-HSITLKE 219
Query: 301 INKLEIKYANLEKIWKYEKTLIKDSQQIKEEIEKVRLKINKATRKSDWQTVSKLKYGELN 360
I +L I+Y N + K+ + + +++ + +I A + Y EL
Sbjct: 220 IERLSIEYNNAMDDYNNLKSALNELSSLEDMKNRYESEIKTAESDLSMELEKNNYYKELE 279
Query: 361 KLERILKEKSQKDIQLPNNANKFTLLKTKVGS 392
ER +K + + N N + K + +
Sbjct: 280 --ERHMKIINDPVYKNRNYINDYFKYKNDIEN 309
>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: 461 MFLGPTGVGKTELCKTLSACIFN-NEESIIRIDMSEF 496
M +G GVGKT LCK L F+ +E S I++ ++
Sbjct: 5 MLVGQGGVGKTSLCKQLIGEKFDGDESSTHGINVQDW 41
>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 = 31.1 bits (71), Expect = 3.0
Identities = 32/104 (30%), Positives = 49/104 (47%), Gaps = 23/104 (22%)
Query: 462 FLGPTGVGKTELCKTLSACIFNNEESIIRI------DMSEFIEKHSISRLIGAPPGYIGY 515
+GP GVGKT L K+++ + +R D +E I H + +GA PG I
Sbjct: 352 LVGPPGVGKTSLGKSIAKAL---NRKFVRFSLGGVRDEAE-IRGHRRT-YVGAMPGRI-- 404
Query: 516 EEGGYLTEIVRRKPYS-LILLDEIEKANSDV----FNILLQILD 554
+ + + K + L LLDEI+K S + LL++LD
Sbjct: 405 -----IQGLKKAKTKNPLFLLDEIDKIGSSFRGDPASALLEVLD 443
>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 = 3.1
Identities = 22/112 (19%), Positives = 37/112 (33%), Gaps = 18/112 (16%)
Query: 57 LIGEPGVGKTAIVEGLAQRI-----------INGEVPN-----SLLSKKILLLDIALLLA 100
+ G G GKT + LA I I E+ S K L ++ ++ A
Sbjct: 4 VFGPTGSGKTTLALQLALNIATKGGKVVYVDIEEEIEELTERLIGESLKGALDNLIIVFA 63
Query: 101 GTKYRGEFEDRLKKILKEISNNQKDIIIFIDELHTMIGTGKVEGSIDAGNML 152
RL + + D +I +DEL ++ + G +
Sbjct: 64 TAD--DPAAARLLSKAERLRERGGDDLIILDELTRLVRALREIREGYPGELD 113
Score = 29.8 bits (67), Expect = 4.3
Identities = 25/89 (28%), Positives = 33/89 (37%), Gaps = 14/89 (15%)
Query: 464 GPTGVGKTELCKTLSACIFNNEESIIRIDMSEFIE----KHSISRLIGAPPGYIGYEEGG 519
GPTG GKT L L+ I ++ +D+ E IE + L GA I
Sbjct: 6 GPTGSGKTTLALQLALNIATKGGKVVYVDIEEEIEELTERLIGESLKGALDNLIIVFATA 65
Query: 520 YLTEIVR----------RKPYSLILLDEI 538
R R LI+LDE+
Sbjct: 66 DDPAAARLLSKAERLRERGGDDLIILDEL 94
>gnl|CDD|237862 PRK14948, PRK14948, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 620
Score = 31.1 bits (71), Expect = 3.3
Identities = 20/55 (36%), Positives = 29/55 (52%), Gaps = 15/55 (27%)
Query: 429 VVGQDEAISA-VSNAIRRSRSGLSDAKRPYGSFMFLGPTGVGKTELCKTLSACIF 482
+VGQ EAI+ + NA+ +R ++ A ++F GP G GKT SA I
Sbjct: 18 LVGQ-EAIATTLKNALISNR--IAPA------YLFTGPRGTGKTS-----SARIL 58
>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 = 3.3
Identities = 23/84 (27%), Positives = 36/84 (42%), Gaps = 4/84 (4%)
Query: 274 QLKIEHEAIKREYDESSKKRLLLIKKEINKLEIKYANLEKIWKYEK--TLIKDSQQIKEE 331
+++E I EYD S K L +K + + + E + + L D Q K+E
Sbjct: 9 DSVLDNERIYLEYDSSQKSFLGALKTNATQSDGEKLTDETLSLQRQINQLNSDLQLQKQE 68
Query: 332 IEKVRL--KINKATRKSDWQTVSK 353
EK+R K KA +S + K
Sbjct: 69 NEKLRKLNKTQKALLESKLSSKKK 92
>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: 427 KRVVGQDEAISAVSNAIRRSRSGLSDAKRPYGSFMFLGPTGVGKTELCKTLS 478
K V+GQ+ + + NA++ R +S A ++F GP G GKT + + L+
Sbjct: 16 KEVIGQEIVVRILKNAVKLQR--VSHA------YIFAGPRGTGKTTIARILA 59
>gnl|CDD|182043 PRK09716, PRK09716, hypothetical protein; Provisional.
Length = 395
Score = 30.8 bits (69), Expect = 3.5
Identities = 25/80 (31%), Positives = 39/80 (48%), Gaps = 8/80 (10%)
Query: 264 IMDKLERRLIQLKIEHEAIKREYDESSKKRLLLIKKEINKL---EIKYANLEKIWKYEKT 320
I+ + R + K+E+E K Y SSK I +N++ E+ + EKI Y
Sbjct: 256 IIKSIPRATLTDKLENELTKEIYKSSSK-----INNCLNRIKLPEMIDFSSEKIHDYIDI 310
Query: 321 LIKDSQQIKEEIEKVRLKIN 340
+I+D + IKE V +IN
Sbjct: 311 IIEDYENIKENAYLVIPQIN 330
>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: 453 AKRPYGSFMFLGPTGVGKTELCKTLSACI 481
++P+G + GPTG GKT TL + +
Sbjct: 76 LEKPHGIILVTGPTGSGKT---TTLYSAL 101
>gnl|CDD|183702 PRK12723, PRK12723, flagellar biosynthesis regulator FlhF;
Provisional.
Length = 388
Score = 30.6 bits (69), Expect = 3.5
Identities = 30/99 (30%), Positives = 45/99 (45%), Gaps = 12/99 (12%)
Query: 460 FMFLGPTGVGKTELCKTLSACIFNNEES------IIRIDMSEFIEKHSISR---LIGAPP 510
F+ +GPTGVGKT L+A N + II ID K I ++G P
Sbjct: 177 FILVGPTGVGKTTTIAKLAAIYGINSDDKSLNIKIITIDNYRIGAKKQIQTYGDIMGIPV 236
Query: 511 GYI-GYEEGGYLTEIVRRKPYSLILLDEIEKANSDVFNI 548
I +++ EI + K + L+L+D I K+ D +
Sbjct: 237 KAIESFKD--LKEEITQSKDFDLVLVDTIGKSPKDFMKL 273
>gnl|CDD|222194 pfam13521, AAA_28, AAA domain.
Length = 162
Score = 29.8 bits (68), Expect = 3.7
Identities = 10/20 (50%), Positives = 13/20 (65%)
Query: 56 VLIGEPGVGKTAIVEGLAQR 75
V+ G P GKT ++E LA R
Sbjct: 3 VITGGPSTGKTTLLEALAAR 22
>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: 21 LTEKARLGKLDPVI----GRDDEIRRAIQVLQRRSKNNPVLIGEPGVGKTAIVEGLAQRI 76
L E+AR K I G ++ + RA QVL + P+L+G P + + L +
Sbjct: 5 LFERAR--KAPKRIVLPEGEEERVLRAAQVLAKEGLAKPILVGRPEEIEEVA-KALGLDL 61
Query: 77 INGEVPNSLLSKKILLLDIALLLAGTKYRGEFEDRLKKILKE 118
E+ N L + + L K +G + +++++E
Sbjct: 62 DGIEIINPELDPERFEEYVDRLYELRKRKGVTPEDAQELVRE 103
>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 = 3.9
Identities = 31/206 (15%), Positives = 69/206 (33%), Gaps = 14/206 (6%)
Query: 242 KAIDLIDEAAAKIKIEIDSKPEIMDKLERRLIQLKIEHEAIKREYDESSKKRLLLIKKEI 301
+ +E K++ E ++ + + + E + S+K L ++KE+
Sbjct: 272 LKENKEEEKEKKLQEEELKLLAKEEEELKSELLKLERRKVDDEEKLKESEKELKKLEKEL 331
Query: 302 NKLEIKYANLEKIWKYEKTLIKDSQQIKEEIEKVRLKINKATRKSDWQTVSKLKYGELNK 361
K + + LEK K L + +EE E++ K + + K E
Sbjct: 332 KKEKEEIEELEKE---LKELEIKREAEEEEEEQLEKLQEKLEQLEEELLAKKKLESERLS 388
Query: 362 LERILKEK-----------SQKDIQLPNNANKFTLLKTKVGSEEIAEIVSRTTGIPVSKI 410
LKE+ ++ ++L + K + + E+
Sbjct: 389 SAAKLKEEELELKNEEEKEAKLLLELSEQEEDLLKEEKKEELKIVEELEESLETKQGKLT 448
Query: 411 VQVEREKLLNIENLLCKRVVGQDEAI 436
+ E + ++ L K + + E +
Sbjct: 449 EEKEELEKQALKLLKDKLELKKSEDL 474
Score = 30.7 bits (69), Expect = 4.8
Identities = 34/206 (16%), Positives = 80/206 (38%), Gaps = 16/206 (7%)
Query: 167 TTLNEYRQYIEKDAAFERRFQKILVEEPDIEETISILRGLQKKYEVHHGVEITDPAIVAA 226
L +++ A + ++ + EE + L Y + I +
Sbjct: 194 EELKLQELKLKEQAKKALEYYQLKEKLELEEENL-----LYLDYLKLNEERIDLLQELLR 248
Query: 227 SELSYRYISDRFMPDKAIDLIDEAAAKIKIEIDSKPEIMDKLERRLIQLKIEHEAIKREY 286
E S + +K +++ + + K E K KL+ ++L + E +
Sbjct: 249 DEQE-EIESSKQELEKEEEILAQVLKENKEEEKEK-----KLQEEELKLLAKEEEELKSE 302
Query: 287 DESSKKRLLLIKKEINKLEIKYANLEKIWKYEKTLIKDSQQIKEEIEKVRLKINKATRKS 346
++R + ++++ + E + LEK K EK I++ ++ +E L+I + +
Sbjct: 303 LLKLERRKVDDEEKLKESEKELKKLEKELKKEKEEIEELEKELKE-----LEIKREAEEE 357
Query: 347 DWQTVSKLKYGELNKLERILKEKSQK 372
+ + + KL+ E +L +K +
Sbjct: 358 EEEQLEKLQEKLEQLEEELLAKKKLE 383
>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 = 29.1 bits (66), Expect = 4.1
Identities = 33/137 (24%), Positives = 57/137 (41%), Gaps = 30/137 (21%)
Query: 464 GPTGVGKTELCKTLSACIFNNEESIIRIDMSEF-IEKHSISRLIGAPPGYIGYEEGGYLT 522
GP VGKT L + + E+I+ I++ + + ++ L+ +L
Sbjct: 9 GPRQVGKTTLLLQFLKELLS--ENILYINLDDPRFLRLALLDLLEE-----------FLK 55
Query: 523 EIVRRKPYSLILLDEIEKANSDVFNILLQILDDGRLTDNRGRTINFRNTIIVMTSNLG-- 580
++ K Y + LDEI+K D + L ++ DDGR II+ S+
Sbjct: 56 LLLPGKKY--LFLDEIQKVP-DWEDALKRLYDDGRNLR-----------IILTGSSSLLL 101
Query: 581 SDKIKEMEKGDKEIIKL 597
S +I G E ++L
Sbjct: 102 SKEIATSLAGRAEELEL 118
Score = 29.1 bits (66), Expect = 5.3
Identities = 17/79 (21%), Positives = 32/79 (40%), Gaps = 14/79 (17%)
Query: 56 VLIGEPGVGKTAIVEGLAQRIINGEVPNSLLSKKILLLDIALLLAGTKYRGEFEDRLKKI 115
V+ G VGKT ++ + LLS+ IL ++ L ++ L +
Sbjct: 6 VITGPRQVGKTTLLLQFLK---------ELLSENILYIN----LDDPRFLRLALLDLLEE 52
Query: 116 LKEISNNQKDIIIFIDELH 134
++ K +F+DE+
Sbjct: 53 FLKLLLPGKK-YLFLDEIQ 70
>gnl|CDD|240423 PTZ00454, PTZ00454, 26S protease regulatory subunit 6B-like
protein; Provisional.
Length = 398
Score = 30.5 bits (69), Expect = 4.1
Identities = 35/118 (29%), Positives = 53/118 (44%), Gaps = 35/118 (29%)
Query: 456 PYGSFMFLGPTGVGKTELCKTLSACIFNNEESIIRIDMSEFIEKHSISRLIGAPPGYIGY 515
P G ++ GP G GKT L K A + + IR+ SEF++K Y+G
Sbjct: 179 PRGVLLY-GPPGTGKTMLAK---AVAHHTTATFIRVVGSEFVQK------------YLG- 221
Query: 516 EEGGYLTEIV----RRKPYSLILLDEIEK-----------ANSDVFNILLQILD--DG 556
EG + V R S+I +DE++ A+ +V ILL++L+ DG
Sbjct: 222 -EGPRMVRDVFRLARENAPSIIFIDEVDSIATKRFDAQTGADREVQRILLELLNQMDG 278
>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 = 4.1
Identities = 19/72 (26%), Positives = 29/72 (40%), Gaps = 9/72 (12%)
Query: 152 LKPELSRGELHCIGATTLNEYRQYIEKDAAFER-RFQKILVEEPDIEETISILRGLQKK- 209
++P L E+ G T R+ A+F+ R K EE +E +K+
Sbjct: 221 VRPSL-VAEVEYAGITRDGILRE-----ASFKGLREDKP-AEEVTLETPQRHAAAKRKRS 273
Query: 210 YEVHHGVEITDP 221
+ GV IT P
Sbjct: 274 AALVAGVRITHP 285
>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 = 4.1
Identities = 20/79 (25%), Positives = 31/79 (39%), Gaps = 1/79 (1%)
Query: 291 KKRLLLIKKEINKLEIKYANLEKIWKYEKTLIKDSQQIKEEIEKVRLKINKATRKSDWQT 350
K LL ++ K E K A I + + L + ++K E+E L D
Sbjct: 2 LKDLLKQLGKLTKEETKPALGALINEVKIELQDELTKLKPELESAGLWSKLKFETYDVSL 61
Query: 351 VSKLKY-GELNKLERILKE 368
Y G L+ L R++ E
Sbjct: 62 PGTKIYPGSLHPLTRVIDE 80
>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 = 4.3
Identities = 24/98 (24%), Positives = 41/98 (41%), Gaps = 15/98 (15%)
Query: 40 IRRAIQVLQR----RSKNNPVLIGEPGVGKTAIVEGLAQRIINGEVPNSLLSKKILLLDI 95
RR I L N +L+G PGVGKT + L + +L
Sbjct: 31 DRRLIAELAGLDWIEQAENLLLLGPPGVGKTHLACALGHQACR-------AGYSVLFTRT 83
Query: 96 ALLLAGTKYRGEFEDRLKKILKEISNNQKDIIIFIDEL 133
L+ K R + RL + L+ ++ + D++I +D++
Sbjct: 84 PDLVEQLK-RARGDGRLARTLQRLA--KADLLI-LDDI 117
>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: 302 NKLEIKYANLEKIWKYEKTLIKDSQQIKEEIEKVRLKINKATRKSDWQTVSKLKYGELNK 361
L K A L K+ K+ QQ K+E+++ K+ +A ++ ++ +S+ EL +
Sbjct: 142 QDLSKKRAQLAKLKGAGKSRQDKLQQAKKEVDEAERKVQQAKKE--FEDISETIKKELER 199
Query: 362 LER 364
E
Sbjct: 200 FET 202
Score = 29.2 bits (66), Expect = 9.6
Identities = 12/57 (21%), Positives = 31/57 (54%), Gaps = 4/57 (7%)
Query: 249 EAAAKIKIEIDSKPEIMDKLERRLIQLKIEHEAIKREYDESSKKRLLLIKKEINKLE 305
AK+K S+ + + + ++ + + + + + K+E+++ S+ IKKE+ + E
Sbjct: 149 AQLAKLKGAGKSRQDKLQQAKKEVDEAERKVQQAKKEFEDISET----IKKELERFE 201
>gnl|CDD|180607 PRK06526, PRK06526, transposase; Provisional.
Length = 254
Score = 30.2 bits (68), Expect = 5.1
Identities = 31/113 (27%), Positives = 42/113 (37%), Gaps = 33/113 (29%)
Query: 7 DEEHIGYLKKYTIDLTEKARLGKLDPVIGRDDEIRRAIQVLQRRSKNNPVLIGEPGVGKT 66
D +H LK+ TI A LG LD V G++ N V +G PG GKT
Sbjct: 74 DFDHQRSLKRDTI-----AHLGTLDFVTGKE----------------NVVFLGPPGTGKT 112
Query: 67 AIVEGLAQRIINGEVPNSLLSKKILLLDIAL----LLAGTKYRGEFEDRLKKI 115
+ GL R + +L A LA + G + L K+
Sbjct: 113 HLAIGLGIRACQ--------AGHRVLFATAAQWVARLAAAHHAGRLQAELVKL 157
>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: 464 GPTGVGKTELCKTLSACIFNNEESIIRI 491
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 = 5.2
Identities = 9/17 (52%), Positives = 11/17 (64%)
Query: 461 MFLGPTGVGKTELCKTL 477
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 = 5.2
Identities = 16/49 (32%), Positives = 23/49 (46%), Gaps = 3/49 (6%)
Query: 429 VVGQDEAISAVSNAIRRSRSGLSDAKRPYGSFMFLGPTGVGKTELCKTL 477
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: 56 VLI-GEPGVGK-TAIVEGLAQRIINGEVPNSLLSKKILLLDIALLLAGTKYR-----GEF 108
VLI G+PG+GK T LLL +A LA + GE
Sbjct: 83 VLIGGDPGIGKST------------------------LLLQVAARLAAAGGKVLYVSGE- 117
Query: 109 E---------DRLK---------------KILKEISNNQKDIIIFIDELHTM 136
E +RL IL I + D+++ ID + TM
Sbjct: 118 ESASQIKLRAERLGLPSDNLYLLAETNLEAILATIEEEKPDLVV-IDSIQTM 168
>gnl|CDD|181459 PRK08533, PRK08533, flagellar accessory protein FlaH; Reviewed.
Length = 230
Score = 29.7 bits (67), Expect = 6.0
Identities = 18/57 (31%), Positives = 32/57 (56%), Gaps = 4/57 (7%)
Query: 81 VPNSLLSKKILLLDIALLLAGTKYRGEFEDRLKKILKEISNNQKDIIIFIDELHTMI 137
+ L+S K+L + + LL+G + +F LKK++ +KD+II D L ++I
Sbjct: 78 INKKLISGKLLYIPVYPLLSGNSEKRKF---LKKLMNTRRFYEKDVIII-DSLSSLI 130
>gnl|CDD|223775 COG0703, AroK, Shikimate kinase [Amino acid transport and
metabolism].
Length = 172
Score = 29.1 bits (66), Expect = 6.2
Identities = 11/25 (44%), Positives = 13/25 (52%)
Query: 51 SKNNPVLIGEPGVGKTAIVEGLAQR 75
N VLIG G GK+ I LA+
Sbjct: 1 RNMNIVLIGFMGAGKSTIGRALAKA 25
>gnl|CDD|182730 PRK10787, PRK10787, DNA-binding ATP-dependent protease La;
Provisional.
Length = 784
Score = 30.3 bits (68), Expect = 6.4
Identities = 29/100 (29%), Positives = 50/100 (50%), Gaps = 15/100 (15%)
Query: 462 FLGPTGVGKTELCKTLSACIFNNEESIIRIDMSEFIEKHSISRLIGAPPGYIGYEEGGYL 521
+GP GVGKT L ++++ +R+ + ++ I G YIG G +
Sbjct: 354 LVGPPGVGKTSLGQSIAKA---TGRKYVRMALGGVRDEAEIR---GHRRTYIGSMPGKLI 407
Query: 522 TEIVR---RKPYSLILLDEIEKANSDV----FNILLQILD 554
++ + + P L LLDEI+K +SD+ + LL++LD
Sbjct: 408 QKMAKVGVKNP--LFLLDEIDKMSSDMRGDPASALLEVLD 445
>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 = 6.4
Identities = 12/50 (24%), Positives = 23/50 (46%), Gaps = 4/50 (8%)
Query: 33 VIGRDDEIRRAIQVLQRRSKN----NPVLIGEPGVGKTAIVEGLAQRIIN 78
+ R++EI + L + N ++ G G GKTA V+ + + +
Sbjct: 19 LPHREEEINQLASFLAPALRGERPSNIIIYGPTGTGKTATVKFVMEELEE 68
>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: 56 VLIGEPGVGKTAIVEGLAQRIINGEVP 82
VLIG+ GVGK++++ L VP
Sbjct: 6 VLIGDEGVGKSSLIMSLVSEEFPENVP 32
>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: 360 NKLERILKEKSQKDIQLPNNANKFTLLKTKVGSEEIAEIVSRTTGIPVSKIVQVEREKLL 419
K+E ++E+ K ++ + +LK + G E + +T + ++ ++E++KL
Sbjct: 92 RKVETRMQERQNKYLE----EIRLQVLKEEKGPE------NSSTLKKLERLEKLEKKKLH 141
Query: 420 -NIENLLCKR----VVGQDEAISAVSNAIRRSRSGLSDAKRPYGSFMFL-GPTGVGKT-- 471
+ ++LL R +VGQ+ AI A+ L+ P+ + L GP GVGKT
Sbjct: 142 KSAQSLLRPRAFSEIVGQERAIKAL----------LAKVASPFPQHIILYGPPGVGKTTA 191
Query: 472 -----ELCKTLSACIFNNEESIIRID 492
E K L F + + +D
Sbjct: 192 ARLALEEAKKLKHTPFAEDAPFVEVD 217
>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 = 6.7
Identities = 25/111 (22%), Positives = 51/111 (45%), Gaps = 10/111 (9%)
Query: 262 PEIMDKLERRLIQLKIEHEAIKREYDE-SSKKRLLLIKKEINKLEIK----YANLEKIWK 316
E +++E+ LK + K+ + +K+ L KK + ++ K L+KI +
Sbjct: 163 VETAEEIEK---SLKAMQQKWKKRKKDLPNKQDLEEYKKRLEAIKKKDIKNPLELQKIKE 219
Query: 317 YEKTLIKDSQQIKEEIEKVR--LKINKATRKSDWQTVSKLKYGELNKLERI 365
L K+ + K++I+ + L+ +K K+D + K +L +LE
Sbjct: 220 EFDKLKKEGKADKQKIKSAKNDLQNDKKQLKADLAELKKAPQNDLKRLENK 270
>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 = 29.5 bits (67), Expect = 6.7
Identities = 15/42 (35%), Positives = 21/42 (50%)
Query: 450 LSDAKRPYGSFMFLGPTGVGKTELCKTLSACIFNNEESIIRI 491
L A + G+ + G TG GKT L L I ++E I+ I
Sbjct: 122 LRQAVQARGNILVSGGTGSGKTTLLYALLNEINTDDERIVTI 163
>gnl|CDD|237551 PRK13902, alaS, alanyl-tRNA synthetase; Provisional.
Length = 900
Score = 30.2 bits (69), Expect = 6.8
Identities = 14/68 (20%), Positives = 33/68 (48%)
Query: 245 DLIDEAAAKIKIEIDSKPEIMDKLERRLIQLKIEHEAIKREYDESSKKRLLLIKKEINKL 304
DL+ EAA + + + P+ +++ + K E E +++E E LL +E+ +
Sbjct: 743 DLLKEAAEILGVPPEQLPKTVERFFEEWKEQKKEIEKLRKELAELLASELLSKAEEVGGV 802
Query: 305 EIKYANLE 312
++ ++
Sbjct: 803 KVVVEEVD 810
>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: 56 VLIGEPGVGKTAIV 69
V++G GVGK+A+
Sbjct: 3 VVLGAGGVGKSALT 16
>gnl|CDD|223637 COG0563, Adk, Adenylate kinase and related kinases [Nucleotide
transport and metabolism].
Length = 178
Score = 29.2 bits (66), Expect = 7.1
Identities = 9/22 (40%), Positives = 13/22 (59%)
Query: 460 FMFLGPTGVGKTELCKTLSACI 481
+ LGP G GK+ L K L+ +
Sbjct: 3 ILILGPPGAGKSTLAKKLAKKL 24
>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 = 7.5
Identities = 27/123 (21%), Positives = 54/123 (43%), Gaps = 18/123 (14%)
Query: 261 KPEIMDKLERRLIQLKIEHEAIKREYDESSKKRLLLIKKEINKLEIKYANLEKIWKYEKT 320
KP +++KLE L +E ++ S ++ + ++ KL +Y+ LE+I +
Sbjct: 2 KPSLLEKLES----LLERYEELEALL---SDPEVISDQDKLRKLSKEYSQLEEIVDCYRE 54
Query: 321 LIKDSQQIKEEIEKVRLKINKATRKSDWQTVSKLKYGELNKLERILKEKSQ--KDIQLPN 378
+ + IKE K + + ++ EL +LE ++E + K + LP
Sbjct: 55 YQQAQEDIKE---------AKEILEESDPEMREMAKEELEELEEKIEELEEQLKVLLLPK 105
Query: 379 NAN 381
+ 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: 464 GPTGVGKTELCKTLSACIFNNEESIIRIDMSEFIEKHSISRLIGAPPGYIGYEEGGYLT- 522
GP G GKT L K A + + IR+ SE ++K YIG EG L
Sbjct: 192 GPPGTGKTLLAK---AVANQTDATFIRVVGSELVQK------------YIG--EGARLVR 234
Query: 523 ---EIVRRKPYSLILLDEI 538
E+ R K S+I +DEI
Sbjct: 235 ELFELAREKAPSIIFIDEI 253
>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 = 7.8
Identities = 31/124 (25%), Positives = 51/124 (41%), Gaps = 27/124 (21%)
Query: 238 FMPDKAIDLIDEAAAKIKIEIDSKPEIMDKLERRLIQLKIEHEAIKREYDE--------- 288
F+ D I+E +K D E ++L+R L +K + +K + E
Sbjct: 56 FLDDYREKEIEELEKALKKTKD--SEEKEELKRTLQSMKSRLKTLKNKDREREILKEHKK 113
Query: 289 -------SSKKRLLLIKKEINKLEIKYANLEKIWKYEKTLIKDSQQIKEEIEKVRLKINK 341
KK L K EI KL +K K+++ +K S+Q+ + +EK R K
Sbjct: 114 QEKELIKEGKKPYYLKKSEIKKLVLK-------KKFDE--LKKSKQLDKALEKKRKKNAG 164
Query: 342 ATRK 345
+K
Sbjct: 165 KEKK 168
>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: 265 MDKLERRLIQLKIEHEAIKREYDESSKKRLLLIKKEINKLEIKYANLEKIW-KYEKTLIK 323
+++L++R+ +L+ + E +K+ +E+ ++ LL +E+ +LE + L+ KYEK +
Sbjct: 78 LEELKQRIAELQAQIEKLKKGREETEERTELL--EELKQLEKELKKLKAELEKYEKNDPE 135
Query: 324 DSQQIKEEIEKVRLKINKAT 343
+++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: 458 GSFMFLGPTGVGKT 471
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 = 8.3
Identities = 7/12 (58%), Positives = 9/12 (75%)
Query: 460 FMFLGPTGVGKT 471
+ +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 = 8.7
Identities = 13/48 (27%), Positives = 22/48 (45%), Gaps = 5/48 (10%)
Query: 35 GRDDEIRRAIQVLQRRSKN--NPVLIG---EPGVGKTAIVEGLAQRII 77
R D A ++L+ N +IG PG GK+ ++E L + +
Sbjct: 29 RRPDHRALARELLRALYPRTGNAHVIGITGVPGAGKSTLIEALGRELR 76
>gnl|CDD|183703 PRK12724, PRK12724, flagellar biosynthesis regulator FlhF;
Provisional.
Length = 432
Score = 29.5 bits (66), Expect = 9.6
Identities = 33/121 (27%), Positives = 61/121 (50%), Gaps = 9/121 (7%)
Query: 253 KIKIEIDSKPEIMDKLERRLIQLKIEHEAIK-REYDESSKKRLLLIKKEINK-LEIKYAN 310
+I+I I K +K+ER+L LK E +K + Y E +K+ L K +++ LE K +
Sbjct: 51 EIQIGIPEKQASREKIERKLQDLK---ELLKQKSYTEPERKKTLQTLKPLSERLEEKESA 107
Query: 311 LEKI--WKYEKTLIKDSQQIKEEIEKVRLKINKATRKSDWQTVSKLKYGELNKL-ERILK 367
+ +I ++ E+ + + + + EK + N + V K K L +L ER+++
Sbjct: 108 IYEIESFELEEVITEPERPVGLSFEKELFEKNSFLES-ETTIVRKEKDSPLQRLGERLVR 166
Query: 368 E 368
E
Sbjct: 167 E 167
>gnl|CDD|212683 cd11733, HSPA9-like_NBD, Nucleotide-binding domain of human HSPA9,
Escherichia coli DnaK, and similar proteins. This
subgroup includes human mitochondrial HSPA9 (also known
as 70-kDa heat shock protein 9, CSA; MOT; MOT2; GRP75;
PBP74; GRP-75; HSPA9B; MTHSP75; the gene encoding HSPA9
maps to 5q31.1), Escherichia coli DnaK, and
Saccharomyces cerevisiae Stress-Seventy subfamily
C/Ssc1p (also called mtHSP70, Endonuclease SceI 75 kDa
subunit). It belongs to the heat shock protein 70
(HSP70) family of chaperones that assist in protein
folding and assembly, and can direct incompetent
"client" proteins towards degradation. Typically, HSP70s
have a nucleotide-binding domain (NBD) and a
substrate-binding domain (SBD). The nucleotide sits in a
deep cleft formed between the two lobes of the NBD. The
two subdomains of each lobe change conformation between
ATP-bound, ADP-bound, and nucleotide-free states. ATP
binding opens up the substrate-binding site;
substrate-binding increases the rate of ATP hydrolysis.
Hsp70 chaperone activity is regulated by various
co-chaperones: J-domain proteins and nucleotide exchange
factors (NEFs); for Escherichia coli DnaK, these are the
DnaJ and GrpE, respectively. HSPA9 is involved in
multiple processses including mitochondrial import,
antigen processing, control of cellular proliferation
and differentiation, and regulation of glucose
responses. During glucose deprivation-induced cellular
stress, HSPA9 plays an important role in the suppression
of apoptosis by inhibiting a conformational change in
Bax that allow the release of cytochrome c. DnaK
modulates the heat shock response in Escherichia coli.
It protects E. coli from protein carbonylation, an
irreversible oxidative modification that increases
during organism aging and bacterial growth arrest. Under
severe thermal stress, it functions as part of a
bi-chaperone system: the DnaK system and the
ring-forming AAA+ chaperone ClpB (Hsp104) system, to
promote cell survival. DnaK has also been shown to
cooperate with GroEL and the ribosome-associated
Escherichia coli Trigger Factor in the proper folding of
cytosolic proteins. S. cerevisiae Ssc1p is the major
HSP70 chaperone of the mitochondrial matrix, promoting
translocation of proteins from the cytosol, across the
inner membrane, to the matrix, and their subsequent
folding. Ssc1p interacts with Tim44, a peripheral inner
membrane protein associated with the TIM23 protein
translocase. It is also a subunit of the endoSceI
site-specific endoDNase and is required for full
endoSceI activity. Ssc1p plays roles in the import of
Yfh1p, a nucleus-encoded mitochondrial protein involved
in iron homeostasis (and a homolog of human frataxin,
implicated in the neurodegenerative disease,
Friedreich's ataxia). Ssc1 also participates in
translational regulation of cytochrome c oxidase (COX)
biogenesis by interacting with Mss51 and
Mss51-containing complexes.
Length = 377
Score = 29.3 bits (66), Expect = 9.8
Identities = 23/80 (28%), Positives = 34/80 (42%), Gaps = 23/80 (28%)
Query: 200 ISILRGLQKKYEV-------HHGVEITDPAIVAASELSYRYISDRFMPDKAIDL------ 246
ISIL + +EV G E D A++ R++ F ++ IDL
Sbjct: 201 ISILEIQKGVFEVKSTNGDTFLGGEDFDNALL-------RHLVKEFKKEQGIDLTKDNMA 253
Query: 247 ---IDEAAAKIKIEIDSKPE 263
+ EAA K KIE+ S +
Sbjct: 254 LQRLREAAEKAKIELSSSLQ 273
>gnl|CDD|240271 PTZ00108, PTZ00108, DNA topoisomerase 2-like protein; Provisional.
Length = 1388
Score = 29.6 bits (67), Expect = 9.8
Identities = 19/113 (16%), Positives = 45/113 (39%), Gaps = 12/113 (10%)
Query: 263 EIMDKLERRLIQLKIEHEAIKREYDESSKKRLLLIKKEINKLEIKYANLEKIWKYEKTLI 322
E ++KL L + + E E +K + + ++++K E E + + E+
Sbjct: 1102 EKVEKLNAELEKKEKELEKLK------NTTPKDMWLEDLDKFE------EALEEQEEVEE 1149
Query: 323 KDSQQIKEEIEKVRLKINKATRKSDWQTVSKLKYGELNKLERILKEKSQKDIQ 375
K+ + + K + K +K + + K K +K ++ + K +
Sbjct: 1150 KEIAKEQRLKSKTKGKASKLRKPKLKKKEKKKKKSSADKSKKASVVGNSKRVD 1202
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 0.390
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: 49,042,056
Number of extensions: 5168652
Number of successful extensions: 8487
Number of sequences better than 10.0: 1
Number of HSP's gapped: 8114
Number of HSP's successfully gapped: 557
Length of query: 938
Length of database: 10,937,602
Length adjustment: 106
Effective length of query: 832
Effective length of database: 6,236,078
Effective search space: 5188416896
Effective search space used: 5188416896
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)