RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2887
(899 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 = 1044 bits (2701), Expect = 0.0
Identities = 387/621 (62%), Positives = 512/621 (82%), Gaps = 5/621 (0%)
Query: 15 NPVLIGEPGVGKTAIVEGLAQRIINGEVPNSLLSKKILLLDIALLLAGTKYRGEFEDRLK 74
NPVLIGEPGVGKTAIVEGLAQRI+NG+VP SL +K++L LD+ L+AG KYRGEFE+RLK
Sbjct: 196 NPVLIGEPGVGKTAIVEGLAQRIVNGDVPESLKNKRLLALDMGALIAGAKYRGEFEERLK 255
Query: 75 KILKEISNNQKDIIIFIDELHTMIGTGKVEGSIDAGNMLKPELSRGELHCIGATTLNEYR 134
+L E++ ++ II+FIDELHT++G GK EG++DAGNMLKP L+RGELHCIGATTL+EYR
Sbjct: 256 AVLNEVTKSEGQIILFIDELHTLVGAGKAEGAMDAGNMLKPALARGELHCIGATTLDEYR 315
Query: 135 QYIEKDAAFERRFQKILVEEPDIEETISILRGLQKKYEVHHGVEITDPAIVAASELSYRY 194
+YIEKDAA ERRFQ + V+EP +E+TISILRGL+++YEVHHGV ITDPAIVAA+ LS+RY
Sbjct: 316 KYIEKDAALERRFQPVFVDEPTVEDTISILRGLKERYEVHHGVRITDPAIVAAATLSHRY 375
Query: 195 ISDRFMPDKAIDLIDEAAAKIKIEIDSKPEIMDKLERRLIQLKIEHEAIKREYDESSKKR 254
I+DRF+PDKAIDLIDEAAA+I++EIDSKPE +D+L+RR+IQL+IE EA+K+E DE+SK+R
Sbjct: 376 ITDRFLPDKAIDLIDEAAARIRMEIDSKPEELDELDRRIIQLEIEREALKKEKDEASKER 435
Query: 255 LLLIKKEINKLEIKYANLEKIWKYEKTLIKDSQQIKEEIEKVRLKINKATRKSDWQTVSK 314
L ++KE+ +LE +YA+LE+ WK EK I+ QQIKEEIE+VRL++ +A R+ D ++
Sbjct: 436 LEDLEKELAELEEEYADLEEQWKAEKAAIQGIQQIKEEIEQVRLELEQAEREGDLAKAAE 495
Query: 315 LKYGELNKLERILKEKSQKDIQLPNNANKFTLLKTKVGSEEIAEIVSRTTGIPVSKIVQV 374
L+YG+L +LE+ L+ K + LL+ +V +EEIAE+VSR TGIPVSK+++
Sbjct: 496 LQYGKLPELEKRLQAAEAKLGEETKPR----LLREEVTAEEIAEVVSRWTGIPVSKMLEG 551
Query: 375 EREKLLNIENLLCKRVVGQDEAISAVSNAIRRSRSGLSDAKRPYGSFMFLGPTGVGKTEL 434
EREKLL++E +L +RVVGQDEA+ AVS+AIRRSR+GLSD RP GSF+FLGPTGVGKTEL
Sbjct: 552 EREKLLHMEEVLHERVVGQDEAVEAVSDAIRRSRAGLSDPNRPIGSFLFLGPTGVGKTEL 611
Query: 435 CKTLSACIFNNEESIIRIDMSEFIEKHSISRLIGAPPGYIGYEEGGYLTEIVRRKPYSLI 494
K L+ +F++E++++RIDMSE++EKHS++RLIGAPPGY+GYEEGG LTE VRRKPYS++
Sbjct: 612 AKALAEFLFDDEDAMVRIDMSEYMEKHSVARLIGAPPGYVGYEEGGQLTEAVRRKPYSVV 671
Query: 495 LLDEIEKANSDVFNILLQILDDGRLTDNRGRTINFRNTIIVMTSNLGSDKIKEM-EKGDK 553
L DE+EKA+ DVFN+LLQ+LDDGRLTD +GRT++FRNT+I+MTSNLGS I+E+ D
Sbjct: 672 LFDEVEKAHPDVFNVLLQVLDDGRLTDGQGRTVDFRNTVIIMTSNLGSQFIQELAGGDDY 731
Query: 554 EIIKLAVMNEVKIYFRPEFINRIDDIIVFRYLNRKNILSIANIQLNILKNKLLKMNMDLK 613
E ++ AVM ++ +FRPEF+NRID+I+VF L R+ I I IQL L+ +L + + L+
Sbjct: 732 EEMREAVMEVLRAHFRPEFLNRIDEIVVFHPLGREQIARIVEIQLGRLRKRLAERKITLE 791
Query: 614 ISKAALKKISNIGFDLIYGAR 634
+S AAL ++ G+D +YGAR
Sbjct: 792 LSDAALDFLAEAGYDPVYGAR 812
>gnl|CDD|182791 PRK10865, PRK10865, protein disaggregation chaperone; Provisional.
Length = 857
Score = 857 bits (2216), Expect = 0.0
Identities = 378/662 (57%), Positives = 514/662 (77%), Gaps = 15/662 (2%)
Query: 14 SNPVLIGEPGVGKTAIVEGLAQRIINGEVPNSLLSKKILLLDIALLLAGTKYRGEFEDRL 73
+NPVLIGEPGVGKTAIVEGLAQRIINGEVP L +++L LD+ L+AG KYRGEFE+RL
Sbjct: 200 NNPVLIGEPGVGKTAIVEGLAQRIINGEVPEGLKGRRVLALDMGALVAGAKYRGEFEERL 259
Query: 74 KKILKEISNNQKDIIIFIDELHTMIGTGKVEGSIDAGNMLKPELSRGELHCIGATTLNEY 133
K +L +++ + ++I+FIDELHTM+G GK +G++DAGNMLKP L+RGELHC+GATTL+EY
Sbjct: 260 KGVLNDLAKQEGNVILFIDELHTMVGAGKADGAMDAGNMLKPALARGELHCVGATTLDEY 319
Query: 134 RQYIEKDAAFERRFQKILVEEPDIEETISILRGLQKKYEVHHGVEITDPAIVAASELSYR 193
RQYIEKDAA ERRFQK+ V EP +E+TI+ILRGL+++YE+HH V+ITDPAIVAA+ LS+R
Sbjct: 320 RQYIEKDAALERRFQKVFVAEPSVEDTIAILRGLKERYELHHHVQITDPAIVAAATLSHR 379
Query: 194 YISDRFMPDKAIDLIDEAAAKIKIEIDSKPEIMDKLERRLIQLKIEHEAIKREYDESSKK 253
YI+DR +PDKAIDLIDEAA+ I+++IDSKPE +D+L+RR+IQLK+E +A+ +E DE+SKK
Sbjct: 380 YIADRQLPDKAIDLIDEAASSIRMQIDSKPEELDRLDRRIIQLKLEQQALMKESDEASKK 439
Query: 254 RLLLIKKEINKLEIKYANLEKIWKYEKTLIKDSQQIKEEIEKVRLKINKATRKSDWQTVS 313
RL ++ +E++ E +Y+ LE+ WK EK + +Q IK E+E+ ++ I +A R D +S
Sbjct: 440 RLDMLNEELSDKERQYSELEEEWKAEKASLSGTQTIKAELEQAKIAIEQARRVGDLARMS 499
Query: 314 KLKYGELNKLERILKEKSQKDIQLPNNANKFTLLKTKVGSEEIAEIVSRTTGIPVSKIVQ 373
+L+YG++ +LE+ L +Q + LL+ KV EIAE+++R TGIPVS++++
Sbjct: 500 ELQYGKIPELEKQLAAATQLE------GKTMRLLRNKVTDAEIAEVLARWTGIPVSRMLE 553
Query: 374 VEREKLLNIENLLCKRVVGQDEAISAVSNAIRRSRSGLSDAKRPYGSFMFLGPTGVGKTE 433
EREKLL +E L RV+GQ+EA+ AVSNAIRRSR+GLSD RP GSF+FLGPTGVGKTE
Sbjct: 554 SEREKLLRMEQELHHRVIGQNEAVEAVSNAIRRSRAGLSDPNRPIGSFLFLGPTGVGKTE 613
Query: 434 LCKTLSACIFNNEESIIRIDMSEFIEKHSISRLIGAPPGYIGYEEGGYLTEIVRRKPYSL 493
LCK L+ +F+++++++RIDMSEF+EKHS+SRL+GAPPGY+GYEEGGYLTE VRR+PYS+
Sbjct: 614 LCKALANFMFDSDDAMVRIDMSEFMEKHSVSRLVGAPPGYVGYEEGGYLTEAVRRRPYSV 673
Query: 494 ILLDEIEKANSDVFNILLQILDDGRLTDNRGRTINFRNTIIVMTSNLGSDKIKE-MEKGD 552
ILLDE+EKA+ DVFNILLQ+LDDGRLTD +GRT++FRNT+++MTSNLGSD I+E + D
Sbjct: 674 ILLDEVEKAHPDVFNILLQVLDDGRLTDGQGRTVDFRNTVVIMTSNLGSDLIQERFGELD 733
Query: 553 KEIIKLAVMNEVKIYFRPEFINRIDDIIVFRYLNRKNILSIANIQLNILKNKLLKMNMDL 612
+K V+ V FRPEFINRID+++VF L ++I SIA IQL L +L + ++
Sbjct: 734 YAHMKELVLGVVSHNFRPEFINRIDEVVVFHPLGEQHIASIAQIQLQRLYKRLEERGYEI 793
Query: 613 KISKAALKKISNIGFDLIYGARDVHGCKKSLSILLKKIHKKSPEANFIFLGDLINKGPQS 672
IS ALK +S G+D +YGAR + K+++ + ++P A I G+L+
Sbjct: 794 HISDEALKLLSENGYDPVYGARPL---KRAIQQQI-----ENPLAQQILSGELVPGKVIR 845
Query: 673 LD 674
L+
Sbjct: 846 LE 847
>gnl|CDD|223616 COG0542, clpA, ATP-binding subunits of Clp protease and DnaK/DnaJ
chaperones [Posttranslational modification, protein
turnover, chaperones].
Length = 786
Score = 785 bits (2030), Expect = 0.0
Identities = 341/626 (54%), Positives = 450/626 (71%), Gaps = 81/626 (12%)
Query: 14 SNPVLIGEPGVGKTAIVEGLAQRIINGEVPNSLLSKKILLLDIALLLAGTKYRGEFEDRL 73
+NPVL+GEPGVGKTAIVEGLAQRI+NG+VP SL K+I LD+ L+AG KYRGEFE+RL
Sbjct: 192 NNPVLVGEPGVGKTAIVEGLAQRIVNGDVPESLKDKRIYSLDLGSLVAGAKYRGEFEERL 251
Query: 74 KKILKEISNNQKDIIIFIDELHTMIGTGKVEG-SIDAGNMLKPELSRGELHCIGATTLNE 132
K +LKE+ + K++I+FIDE+HT++G G EG ++DA N+LKP L+RGEL CIGATTL+E
Sbjct: 252 KAVLKEVEKS-KNVILFIDEIHTIVGAGATEGGAMDAANLLKPALARGELRCIGATTLDE 310
Query: 133 YRQYIEKDAAFERRFQKILVEEPDIEETISILRGLQKKYEVHHGVEITDPAIVAASELSY 192
YR+YIEKDAA ERRFQK+LV+EP +E+TI+ILRGL+++YE HHGV ITD A+VAA LS
Sbjct: 311 YRKYIEKDAALERRFQKVLVDEPSVEDTIAILRGLKERYEAHHGVRITDEALVAAVTLSD 370
Query: 193 RYISDRFMPDKAIDLIDEAAAKIKIEIDSKPEIMDKLERRLIQLKIEHEAIKREYDESSK 252
RYI DRF+PDKAIDL+DEA A++++EID KPE +D+LER L QL+IE EA++
Sbjct: 371 RYIPDRFLPDKAIDLLDEAGARVRLEID-KPEELDELERELAQLEIEKEALE-------- 421
Query: 253 KRLLLIKKEINKLEIKYANLEKIWKYEKTLIKDSQQIKEEIEKVRLKINKATRKSDWQTV 312
+E+ EK + I++ +
Sbjct: 422 -------------------------------------REQDEKEKKLIDE---------I 435
Query: 313 SKLKYGELNKLERILKEKSQKDIQLPNNANKFTLLKTKVGSEEIAEIVSRTTGIPVSKIV 372
KLK G + +LE+ L+ + V ++IAE+V+R TGIPV+K++
Sbjct: 436 IKLKEGRIPELEKELEAE--------------------VDEDDIAEVVARWTGIPVAKLL 475
Query: 373 QVEREKLLNIENLLCKRVVGQDEAISAVSNAIRRSRSGLSDAKRPYGSFMFLGPTGVGKT 432
+ E+EKLLN+E L KRV+GQDEA+ AVS+AIRR+R+GL D RP GSF+FLGPTGVGKT
Sbjct: 476 EDEKEKLLNLERRLKKRVIGQDEAVEAVSDAIRRARAGLGDPNRPIGSFLFLGPTGVGKT 535
Query: 433 ELCKTLSACIFNNEESIIRIDMSEFIEKHSISRLIGAPPGYIGYEEGGYLTEIVRRKPYS 492
EL K L+ +F +E+++IRIDMSE++EKHS+SRLIGAPPGY+GYEEGG LTE VRRKPYS
Sbjct: 536 ELAKALAEALFGDEQALIRIDMSEYMEKHSVSRLIGAPPGYVGYEEGGQLTEAVRRKPYS 595
Query: 493 LILLDEIEKANSDVFNILLQILDDGRLTDNRGRTINFRNTIIVMTSNLGSDKIKEMEKGD 552
+ILLDEIEKA+ DVFN+LLQ+LDDGRLTD +GRT++FRNTII+MTSN GS++I GD
Sbjct: 596 VILLDEIEKAHPDVFNLLLQVLDDGRLTDGQGRTVDFRNTIIIMTSNAGSEEILRDADGD 655
Query: 553 ----KEIIKLAVMNEVKIYFRPEFINRIDDIIVFRYLNRKNILSIANIQLNILKNKLLKM 608
KE +K AVM E+K +FRPEF+NRID+II F L+++ + I ++QLN L +L +
Sbjct: 656 DFADKEALKEAVMEELKKHFRPEFLNRIDEIIPFNPLSKEVLERIVDLQLNRLAKRLAER 715
Query: 609 NMDLKISKAALKKISNIGFDLIYGAR 634
+ L++S A ++ G+D YGAR
Sbjct: 716 GITLELSDEAKDFLAEKGYDPEYGAR 741
>gnl|CDD|214361 CHL00095, clpC, Clp protease ATP binding subunit.
Length = 821
Score = 632 bits (1633), Expect = 0.0
Identities = 296/633 (46%), Positives = 413/633 (65%), Gaps = 79/633 (12%)
Query: 15 NPVLIGEPGVGKTAIVEGLAQRIINGEVPNSLLSKKILLLDIALLLAGTKYRGEFEDRLK 74
NP+LIGEPGVGKTAI EGLAQRI+N +VP+ L K ++ LDI LLLAGTKYRGEFE+RLK
Sbjct: 202 NPILIGEPGVGKTAIAEGLAQRIVNRDVPDILEDKLVITLDIGLLLAGTKYRGEFEERLK 261
Query: 75 KILKEISNNQKDIIIFIDELHTMIGTGKVEGSIDAGNMLKPELSRGELHCIGATTLNEYR 134
+I EI N +II+ IDE+HT+IG G EG+IDA N+LKP L+RGEL CIGATTL+EYR
Sbjct: 262 RIFDEIQEN-NNIILVIDEVHTLIGAGAAEGAIDAANILKPALARGELQCIGATTLDEYR 320
Query: 135 QYIEKDAAFERRFQKILVEEPDIEETISILRGLQKKYEVHHGVEITDPAIVAASELSYRY 194
++IEKD A ERRFQ + V EP +EETI IL GL+ +YE HH + I+D A+ AA++LS +Y
Sbjct: 321 KHIEKDPALERRFQPVYVGEPSVEETIEILFGLRSRYEKHHNLSISDKALEAAAKLSDQY 380
Query: 195 ISDRFMPDKAIDLIDEAAAKIKIEIDSKPEIMDKLERRLIQLKIEHEAIKREYDESSKKR 254
I+DRF+PDKAIDL+DEA +++++ P +L++ L ++ + + RE D + K+
Sbjct: 381 IADRFLPDKAIDLLDEAGSRVRLINSRLPPAARELDKELREILKDKDEAIREQDFETAKQ 440
Query: 255 LLLIKKEINKLEIKYANLEKIWKYEKTLIKDSQQIKEEIEKVRLKINKATRKSDWQTVSK 314
L + E+ + + I S++ +EE +
Sbjct: 441 LRDREMEV--------------RAQIAAIIQSKKTEEEKRLEVPVV-------------- 472
Query: 315 LKYGELNKLERILKEKSQKDIQLPNNANKFTLLKTKVGSEEIAEIVSRTTGIPVSKIVQV 374
+++DI AEIVS TGIPV+K+ +
Sbjct: 473 ----------------TEEDI---------------------AEIVSAWTGIPVNKLTKS 495
Query: 375 EREKLLNIENLLCKRVVGQDEAISAVSNAIRRSRSGLSDAKRPYGSFMFLGPTGVGKTEL 434
E EKLL++E L KR++GQDEA+ AVS AIRR+R GL + RP SF+F GPTGVGKTEL
Sbjct: 496 ESEKLLHMEETLHKRIIGQDEAVVAVSKAIRRARVGLKNPNRPIASFLFSGPTGVGKTEL 555
Query: 435 CKTLSACIFNNEESIIRIDMSEFIEKHSISRLIGAPPGYIGYEEGGYLTEIVRRKPYSLI 494
K L++ F +E+++IR+DMSE++EKH++S+LIG+PPGY+GY EGG LTE VR+KPY+++
Sbjct: 556 TKALASYFFGSEDAMIRLDMSEYMEKHTVSKLIGSPPGYVGYNEGGQLTEAVRKKPYTVV 615
Query: 495 LLDEIEKANSDVFNILLQILDDGRLTDNRGRTINFRNTIIVMTSNLGSDKI--------- 545
L DEIEKA+ D+FN+LLQILDDGRLTD++GRTI+F+NT+I+MTSNLGS I
Sbjct: 616 LFDEIEKAHPDIFNLLLQILDDGRLTDSKGRTIDFKNTLIIMTSNLGSKVIETNSGGLGF 675
Query: 546 -KEMEKGDK---EIIKLAVMNEVKIYFRPEFINRIDDIIVFRYLNRKNILSIANIQLNIL 601
+ + + + V E+K +FRPEF+NR+D+IIVFR L + ++ IA I L L
Sbjct: 676 ELSENQLSEKQYKRLSNLVNEELKQFFRPEFLNRLDEIIVFRQLTKNDVWEIAEIMLKNL 735
Query: 602 KNKLLKMNMDLKISKAALKKISNIGFDLIYGAR 634
+L + + L++++ + G++ +YGAR
Sbjct: 736 FKRLNEQGIQLEVTERIKTLLIEEGYNPLYGAR 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 = 601 bits (1551), Expect = 0.0
Identities = 257/616 (41%), Positives = 384/616 (62%), Gaps = 28/616 (4%)
Query: 15 NPVLIGEPGVGKTAIVEGLAQRIINGEVPNSLLSKKILLLDIALLLAGTKYRGEFEDRLK 74
NP+L GE GVGKTA+VEGLA RI G+VP +L + ++L LD+ LL AG +GEFE+RLK
Sbjct: 210 NPILTGEAGVGKTAVVEGLALRIAAGDVPPALRNVRLLSLDLGLLQAGASVKGEFENRLK 269
Query: 75 KILKEISNNQKDIIIFIDELHTMIGTGKVEGSIDAGNMLKPELSRGELHCIGATTLNEYR 134
++ E+ + + II+FIDE HT+IG G G DA N+LKP L+RGEL I ATT EY+
Sbjct: 270 SVIDEVKASPQPIILFIDEAHTLIGAGGQAGQGDAANLLKPALARGELRTIAATTWAEYK 329
Query: 135 QYIEKDAAFERRFQKILVEEPDIEETISILRGLQKKYEVHHGVEITDPAIVAASELSYRY 194
+Y EKD A RRFQ + VEEPD E I +LRGL E HHGV I D A+VAA ELS+RY
Sbjct: 330 KYFEKDPALTRRFQVVKVEEPDEETAIRMLRGLAPVLEKHHGVLILDEAVVAAVELSHRY 389
Query: 195 ISDRFMPDKAIDLIDEAAAKIKIEIDSKPEIMDKLERRLIQLKIEHEAIKRE--YDESSK 252
I R +PDKA+ L+D A A++ + ++ P ++ L RR+ L++E +A++RE
Sbjct: 390 IPGRQLPDKAVSLLDTACARVALSQNATPAALEDLRRRIAALELELDALEREAALGADHD 449
Query: 253 KRLLLIKKEINKLEIKYANLEKIWKYEKTLIKDSQQIKEEIEKVRLKINKATRKSDWQTV 312
+RL ++ E+ LE + A LE W+ EK L++ ++ E+E
Sbjct: 450 ERLAELRAELAALEAELAALEARWQQEKELVEAILALRAELE---------ADADAPADD 500
Query: 313 SKLKYGELNKLERILKEKSQKDIQLPNNANKFTLLKTKVGSEEIAEIVSRTTGIPVSKIV 372
+L +LE L +Q + P L+ +V ++ +AE+V+ TGIPV ++V
Sbjct: 501 DAALRAQLAELEAALAS-AQGE--EP-------LVFPEVDAQAVAEVVADWTGIPVGRMV 550
Query: 373 QVEREKLLNIENLLCKRVVGQDEAISAVSNAIRRSRSGLSDAKRPYGSFMFLGPTGVGKT 432
+ E E +L++ + L +RV+GQD A+ A++ IR +R+GL D ++P G F+ +GP+GVGKT
Sbjct: 551 RDEIEAVLSLPDRLAERVIGQDHALEAIAERIRTARAGLEDPRKPLGVFLLVGPSGVGKT 610
Query: 433 ELCKTLSACIFNNEESIIRIDMSEFIEKHSISRLIGAPPGYIGYEEGGYLTEIVRRKPYS 492
E L+ ++ E+++I I+MSEF E H++SRL G+PPGY+GY EGG LTE VRRKPYS
Sbjct: 611 ETALALAELLYGGEQNLITINMSEFQEAHTVSRLKGSPPGYVGYGEGGVLTEAVRRKPYS 670
Query: 493 LILLDEIEKANSDVFNILLQILDDGRLTDNRGRTINFRNTIIVMTSNLGSDKIKEM---- 548
++LLDE+EKA+ DV + Q+ D G + D GR I+F+NT+I++TSN GSD I +
Sbjct: 671 VVLLDEVEKAHPDVLELFYQVFDKGVMEDGEGREIDFKNTVILLTSNAGSDLIMALCADP 730
Query: 549 -EKGDKEIIKLAVMNEVKIYFRPEFINRIDDIIVFRYLNRKNILSIANIQLNILKNKLLK 607
D E + A+ E+ F+P F+ R+ +I + L+ + +I ++L+ + +L +
Sbjct: 731 ETAPDPEALLEALRPELLKVFKPAFLGRM-TVIPYLPLDDDVLAAIVRLKLDRIARRLKE 789
Query: 608 -MNMDLKISKAALKKI 622
+L S+A ++ I
Sbjct: 790 NHGAELVYSEALVEHI 805
>gnl|CDD|234673 PRK00166, apaH, diadenosine tetraphosphatase; Reviewed.
Length = 275
Score = 332 bits (855), Expect = e-107
Identities = 113/266 (42%), Positives = 156/266 (58%), Gaps = 9/266 (3%)
Query: 635 DVHGCKKSLSILLKKIHKKSPEANFIFLGDLINKGPQSLDTLRMVYSMRNYAKIVLGNHE 694
D+ GC L LL+KI + +GDL+N+GP SL+ LR V S+ + A VLGNH+
Sbjct: 8 DIQGCYDELQRLLEKIDFDPAKDTLWLVGDLVNRGPDSLEVLRFVKSLGDSAVTVLGNHD 67
Query: 695 IHLLDVLININKKSKLDTFDDILDAPDKKKLVSWLRTQPLAIYY--KKYLMIHAGVAKQW 752
+HLL V I + K DT D IL+APD+ +L+ WLR QPL +M+HAG+ QW
Sbjct: 68 LHLLAVAAGIKRNKKKDTLDPILEAPDRDELLDWLRHQPLLHVDEELGLVMVHAGIPPQW 127
Query: 753 TAQQTIKLSHQVEKILRTSYWKNLFFKLYNHNSINWDNHLHTIHLNTIDKLQFIINTLTR 812
+ L+ +VE +LR+ +++ +Y + W L +++L++IIN TR
Sbjct: 128 DLATALALAREVEAVLRSDDYRDFLANMYGNEPDRWSP-----DLTGLERLRYIINAFTR 182
Query: 813 TRFCKIDGTIEFIKKNIKNNNFQNNYIPWFDLPNRKTIDITVLFGHWSTL-GLIMKPNII 871
RFC DG ++F K + PWF++P RKT D T++FGHW+ L GL PNII
Sbjct: 183 MRFCTPDGRLDFKCKGPPDEA-PAGLKPWFEVPGRKTRDYTIVFGHWAALEGLTTPPNII 241
Query: 872 CLDTGCVWGNKLTALCLEDRSIIQVN 897
LDTGCVWG KLTAL LED+ I QV
Sbjct: 242 ALDTGCVWGGKLTALRLEDKQIFQVP 267
>gnl|CDD|163665 cd07422, MPP_ApaH, Escherichia coli ApaH and related proteins,
metallophosphatase domain. ApaH (also known as
symmetrically cleaving Ap4A hydrolase and
bis(5'nucleosyl)-tetraphosphatase) is a bacterial member
of the PPP (phosphoprotein phosphatase) family of
serine/threonine phosphatases that hydrolyzes the
nucleotide-signaling molecule diadenosine tetraphosphate
(Ap(4)A) into two ADP and also hydrolyzes Ap(5)A,
Gp(4)G, and other extending compounds. Null mutations
in apaH result in high intracellular levels of Ap(4)A
which correlate with multiple phenotypes, including a
decreased expression of catabolite-repressible genes, a
reduction in the expression of flagellar operons, and an
increased sensitivity to UV and heat. Ap4A hydrolase
is important in responding to heat shock and oxidative
stress via regulating the concentration of Ap4A in
bacteria. Ap4A hydrolase is also thought to play a role
in siderophore production, but the mechanism by which
ApaH interacts with siderophore pathways in unknown.
The PPP (phosphoprotein phosphatase) family, to which
ApaH belongs, is one of two known protein phosphatase
families specific for serine and threonine. The PPP
family also includes: PP1, PP2A, PP2B (calcineurin),
PP4, PP5, PP6, PP7, Bsu1, RdgC, PrpE, and PrpA/PrpB. The
PPP catalytic domain is defined by three conserved
motifs (-GDXHG-, -GDXVDRG- and -GNHE-). The PPP enzyme
family is ancient with members found in all eukaryotes,
and in most bacterial and archeal genomes.
Dephosphorylation of phosphoserines and
phosphothreonines on target proteins plays a central
role in the regulation of many cellular processes. PPPs
belong to the metallophosphatase (MPP) superfamily.
MPPs are functionally diverse, but all share a conserved
domain with an active site consisting of two metal ions
(usually manganese, iron, or zinc) coordinated with
octahedral geometry by a cage of histidine, aspartate,
and asparagine residues. The MPP superfamily includes:
Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat
debranching enzymes, YfcE-like phosphodiesterases,
purple acid phosphatases (PAPs), YbbF-like
UDP-2,3-diacylglucosamine hydrolases, and acid
sphingomyelinases (ASMases). The conserved domain is a
double beta-sheet sandwich with a di-metal active site
made up of residues located at the C-terminal side of
the sheets. This domain is thought to allow for
productive metal coordination.
Length = 257
Score = 320 bits (824), Expect = e-103
Identities = 118/259 (45%), Positives = 159/259 (61%), Gaps = 11/259 (4%)
Query: 635 DVHGCKKSLSILLKKIHKKSPEANFIFLGDLINKGPQSLDTLRMVYSMRNYAKIVLGNHE 694
D+ GC L LL+KI+ + +GDL+N+GP SL+TLR V S+ + AK VLGNH+
Sbjct: 6 DIQGCYDELQRLLEKINFDPAKDRLWLVGDLVNRGPDSLETLRFVKSLGDSAKTVLGNHD 65
Query: 695 IHLLDVLININKKSKLDTFDDILDAPDKKKLVSWLRTQPLAIY--YKKYLMIHAGVAKQW 752
+HLL V I K K DT DDIL+APD+ +L+ WLR QPL LM+HAG+ QW
Sbjct: 66 LHLLAVAAGIKKPKKKDTLDDILNAPDRDELLDWLRHQPLLHRDPELGILMVHAGIPPQW 125
Query: 753 TAQQTIKLSHQVEKILRTSYWKNLFFKLYNHNSINWDNHLHTIHLNTIDKLQFIINTLTR 812
+ +Q +KL+ +VE LR ++ +Y + W + L ID+L++I+N TR
Sbjct: 126 SIEQALKLAREVEAALRGPNYREFLKNMYGNEPDRWSD-----DLTGIDRLRYIVNAFTR 180
Query: 813 TRFCKIDGTIEF-IKKNIKNNNFQNNYIPWFDLPNRKTIDITVLFGHWSTLGLIMKP-NI 870
RFC DG ++F K ++ PWF+LPNRKT D T++FGHW+ LG +P NI
Sbjct: 181 MRFCTPDGRLDFSSKGAPEDAP--KGLKPWFELPNRKTDDYTIVFGHWAALGGKTRPNNI 238
Query: 871 ICLDTGCVWGNKLTALCLE 889
I LDTGCVWG KLTAL LE
Sbjct: 239 IALDTGCVWGGKLTALRLE 257
>gnl|CDD|233959 TIGR02639, ClpA, ATP-dependent Clp protease ATP-binding subunit
clpA. [Protein fate, Degradation of proteins, peptides,
and glycopeptides].
Length = 730
Score = 315 bits (809), Expect = 3e-95
Identities = 130/291 (44%), Positives = 192/291 (65%), Gaps = 10/291 (3%)
Query: 348 KTKVGSEEIAEIVSRTTGIPVSKIVQVEREKLLNIENLLCKRVVGQDEAISAVSNAIRRS 407
K V ++I +V++ IPV + +RE+L N+E L ++ GQDEAI + +AI+RS
Sbjct: 413 KANVNVKDIENVVAKMAKIPVKTVSSDDREQLKNLEKNLKAKIFGQDEAIDQLVSAIKRS 472
Query: 408 RSGLSDAKRPYGSFMFLGPTGVGKTELCKTLSACIFNNEESIIRIDMSEFIEKHSISRLI 467
R+GL D +P GSF+F+GPTGVGKTEL K L A ++R DMSE++EKH++SRLI
Sbjct: 473 RAGLGDPNKPVGSFLFVGPTGVGKTELAKQL-AEELGVH--LLRFDMSEYMEKHTVSRLI 529
Query: 468 GAPPGYIGYEEGGYLTEIVRRKPYSLILLDEIEKANSDVFNILLQILDDGRLTDNRGRTI 527
G+PPGY+G+E+GG LT+ VR+ P+ ++LLDEIEKA+ D++NILLQ++D LTDN GR
Sbjct: 530 GSPPGYVGFEQGGLLTDAVRKHPHCVLLLDEIEKAHPDIYNILLQVMDYATLTDNNGRKA 589
Query: 528 NFRNTIIVMTSNLGSDKIKEMEKGD----KEIIKLAVMNEVKIYFRPEFINRIDDIIVFR 583
+FRN I++MTSN G+ EM K E + + +K F PEF NR+D II F
Sbjct: 590 DFRNVILIMTSNAGA---SEMSKPPIGFGGENSESKSLKAIKKLFSPEFRNRLDAIIHFN 646
Query: 584 YLNRKNILSIANIQLNILKNKLLKMNMDLKISKAALKKISNIGFDLIYGAR 634
L+ + I L+ L+++L + N++L+++ A K ++ G+D +GAR
Sbjct: 647 DLSEEMAEKIVKKFLDELQDQLNEKNIELELTDDAKKYLAEKGYDEEFGAR 697
Score = 295 bits (757), Expect = 7e-88
Identities = 121/210 (57%), Positives = 157/210 (74%), Gaps = 2/210 (0%)
Query: 15 NPVLIGEPGVGKTAIVEGLAQRIINGEVPNSLLSKKILLLDIALLLAGTKYRGEFEDRLK 74
NP+L+GEPGVGKTAIVEGLA RI G+VP L + KI LD+ LLAGTKYRG+FE+RLK
Sbjct: 204 NPLLVGEPGVGKTAIVEGLALRIAEGKVPERLKNAKIYSLDMGTLLAGTKYRGDFEERLK 263
Query: 75 KILKEISNNQKDIIIFIDELHTMIGTGKV-EGSIDAGNMLKPELSRGELHCIGATTLNEY 133
++ EI + + I+FIDE+HT++G G GS+DA N+LKP LS G++ CIG+TT EY
Sbjct: 264 AVVSEIEK-EPNAILFIDEIHTIVGAGATSGGSMDASNLLKPALSSGKIRCIGSTTYEEY 322
Query: 134 RQYIEKDAAFERRFQKILVEEPDIEETISILRGLQKKYEVHHGVEITDPAIVAASELSYR 193
+ + EKD A RRFQKI V EP IEET+ IL+GL+++YE H V+ +D A+ AA ELS R
Sbjct: 323 KNHFEKDRALSRRFQKIDVGEPSIEETVKILKGLKEQYEEFHHVKYSDEALEAAVELSAR 382
Query: 194 YISDRFMPDKAIDLIDEAAAKIKIEIDSKP 223
YI+DRF+PDKAID+IDEA A ++ +K
Sbjct: 383 YINDRFLPDKAIDVIDEAGAAFRLRPKAKK 412
>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 (664), Expect = 2e-81
Identities = 100/168 (59%), Positives = 130/168 (77%), Gaps = 4/168 (2%)
Query: 416 RPYGSFMFLGPTGVGKTELCKTLSACIFNNEESIIRIDMSEFIEKHSISRLIGAPPGYIG 475
RP GSF+FLGPTGVGKTEL K L+ +F +E ++IRIDMSE++E+HS+SRLIGAPPGY+G
Sbjct: 1 RPIGSFLFLGPTGVGKTELAKALAELLFGDERALIRIDMSEYMEEHSVSRLIGAPPGYVG 60
Query: 476 YEEGGYLTEIVRRKPYSLILLDEIEKANSDVFNILLQILDDGRLTDNRGRTINFRNTIIV 535
YEEGG LTE VRRKPYS++L+DEIEKA+ V N LLQIL+ G LTD +GR ++FRNT+ +
Sbjct: 61 YEEGGQLTEAVRRKPYSIVLIDEIEKAHPGVQNDLLQILEGGTLTDKQGRKVDFRNTLFI 120
Query: 536 MTSNLGSDKIKEMEKG----DKEIIKLAVMNEVKIYFRPEFINRIDDI 579
MT N GS+KI + + D E++K VM+ +K F PEF+ R+ I
Sbjct: 121 MTGNFGSEKISDASRLGDSPDYELLKELVMDLLKKGFIPEFLGRLPII 168
>gnl|CDD|236828 PRK11034, clpA, ATP-dependent Clp protease ATP-binding subunit;
Provisional.
Length = 758
Score = 249 bits (638), Expect = 5e-71
Identities = 133/326 (40%), Positives = 204/326 (62%), Gaps = 18/326 (5%)
Query: 348 KTKVGSEEIAEIVSRTTGIPVSKIVQVEREKLLNIENLLCKRVVGQDEAISAVSNAIRRS 407
K V +I +V+R IP + Q +R+ L N+ + L V GQD+AI A++ AI+ S
Sbjct: 418 KKTVNVADIESVVARIARIPEKSVSQSDRDTLKNLGDRLKMLVFGQDKAIEALTEAIKMS 477
Query: 408 RSGLSDAKRPYGSFMFLGPTGVGKTELCKTLSACIFNNEESIIRIDMSEFIEKHSISRLI 467
R+GL +P GSF+F GPTGVGKTE+ LS + ++R DMSE++E+H++SRLI
Sbjct: 478 RAGLGHEHKPVGSFLFAGPTGVGKTEVTVQLSKAL---GIELLRFDMSEYMERHTVSRLI 534
Query: 468 GAPPGYIGYEEGGYLTEIVRRKPYSLILLDEIEKANSDVFNILLQILDDGRLTDNRGRTI 527
GAPPGY+G+++GG LT+ V + P++++LLDEIEKA+ DVFN+LLQ++D+G LTDN GR
Sbjct: 535 GAPPGYVGFDQGGLLTDAVIKHPHAVLLLDEIEKAHPDVFNLLLQVMDNGTLTDNNGRKA 594
Query: 528 NFRNTIIVMTSNLGSDKIKEMEKGDKEIIK----LAVMNEVKIYFRPEFINRIDDIIVFR 583
+FRN ++VMT+N G ++E E+ +I M E+K F PEF NR+D+II F
Sbjct: 595 DFRNVVLVMTTNAG---VRETERKSIGLIHQDNSTDAMEEIKKIFTPEFRNRLDNIIWFD 651
Query: 584 YLNRKNILSIANIQLNILKNKLLKMNMDLKISKAALKKISNIGFDLIYGARDVHGCKKSL 643
+L+ I + + + L+ +L + + L++S+ A ++ G+D GAR + + +
Sbjct: 652 HLSTDVIHQVVDKFIVELQAQLDQKGVSLEVSQEARDWLAEKGYDRAMGARPM---ARVI 708
Query: 644 SILLKKIHKKSPEANFIFLGDLINKG 669
LKK P AN + G L++ G
Sbjct: 709 QDNLKK-----PLANELLFGSLVDGG 729
Score = 248 bits (635), Expect = 1e-70
Identities = 112/210 (53%), Positives = 146/210 (69%), Gaps = 2/210 (0%)
Query: 14 SNPVLIGEPGVGKTAIVEGLAQRIINGEVPNSLLSKKILLLDIALLLAGTKYRGEFEDRL 73
+NP+L+GE GVGKTAI EGLA RI+ G+VP + I LDI LLAGTKYRG+FE R
Sbjct: 208 NNPLLVGESGVGKTAIAEGLAWRIVQGDVPEVMADCTIYSLDIGSLLAGTKYRGDFEKRF 267
Query: 74 KKILKEISNNQKDIIIFIDELHTMIGTGKVEG-SIDAGNMLKPELSRGELHCIGATTLNE 132
K +LK++ + I+FIDE+HT+IG G G +DA N++KP LS G++ IG+TT E
Sbjct: 268 KALLKQLEQ-DTNSILFIDEIHTIIGAGAASGGQVDAANLIKPLLSSGKIRVIGSTTYQE 326
Query: 133 YRQYIEKDAAFERRFQKILVEEPDIEETISILRGLQKKYEVHHGVEITDPAIVAASELSY 192
+ EKD A RRFQKI + EP IEET+ I+ GL+ KYE HH V T A+ AA EL+
Sbjct: 327 FSNIFEKDRALARRFQKIDITEPSIEETVQIINGLKPKYEAHHDVRYTAKAVRAAVELAV 386
Query: 193 RYISDRFMPDKAIDLIDEAAAKIKIEIDSK 222
+YI+DR +PDKAID+IDEA A+ ++ SK
Sbjct: 387 KYINDRHLPDKAIDVIDEAGARARLMPVSK 416
>gnl|CDD|233082 TIGR00668, apaH, bis(5'-nucleosyl)-tetraphosphatase (symmetrical).
Diadenosine 5',5"'-P1,P4-tetraphosphate (Ap4A) is a
regulatory metabolite of stress conditions. It is
hydrolyzed to two ADP by this enzyme. Alternate names
include diadenosine-tetraphosphatase and Ap4A hydrolase
[Cellular processes, Adaptations to atypical
conditions].
Length = 279
Score = 202 bits (516), Expect = 5e-59
Identities = 91/261 (34%), Positives = 139/261 (53%), Gaps = 11/261 (4%)
Query: 635 DVHGCKKSLSILLKKIHKKSPEANFIFLGDLINKGPQSLDTLRMVYSMRNYAKIVLGNHE 694
D+HGC L LL+++ + GDL+ +GP SL+ LR V S+ + ++VLGNH+
Sbjct: 8 DLHGCYDELQALLERVEFDPGQDTLWLTGDLVARGPGSLEVLRYVKSLGDAVRLVLGNHD 67
Query: 695 IHLLDVLININKKSKLDTFDDILDAPDKKKLVSWLRTQPLAIY--YKKYLMIHAGVAKQW 752
+HLL V I++ D D +L+APD +L++WLR QPL + KK +M HAG+ QW
Sbjct: 68 LHLLAVFAGISRNKPKDRLDPLLEAPDADELLNWLRRQPLLQHDEEKKLVMAHAGITPQW 127
Query: 753 TAQQTIKLSHQVEKILRTSYWKNLFFKLYNHNSINWDNHLHTIHLNTIDKLQFIINTLTR 812
Q + + VE +L + + +Y W L + +L+FIIN TR
Sbjct: 128 DLQTAKECARDVEAVLSSDSYPFFLDAMYGDMPNRWSPELQ-----GLARLRFIINAFTR 182
Query: 813 TRFCKIDGTIEFI-KKNIKNNNFQNNYIPWFDLPNRKTIDITVLFGHWSTL-GLIMKPNI 870
RFC +G ++ K++ ++ PWF +P + ++ FGHW++L G I
Sbjct: 183 MRFCFPNGQLDMYSKESPEDA--PAPLKPWFAIPGPVYEEYSIAFGHWASLEGEGTPEGI 240
Query: 871 ICLDTGCVWGNKLTALCLEDR 891
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 = 98.3 bits (245), Expect = 4e-23
Identities = 55/270 (20%), Positives = 95/270 (35%), Gaps = 65/270 (24%)
Query: 635 DVHGCKKSLSILLKKIHKKSPEANFIFLGDLINKGPQSLDTLRMVYSM---RNYAKIVLG 691
D+HGC L LL+KI P IFLGD +++GP S++ + ++ ++ + ++ G
Sbjct: 5 DIHGCLDDLLRLLEKIGF-PPNDKLIFLGDYVDRGPDSVEVIDLLLALKILPDNVILLRG 63
Query: 692 NHEIHLLDVLININKKSKLDTFDDI----LDAPDKKKLVSWLRTQPLAIYY--KKYLMIH 745
NHE LL+ L + + L ++ PLA KK L +H
Sbjct: 64 NHEDMLLNFLYGFYDEDEWIGGTLRLLKKLGEDLWEEFNDVFFYLPLAALIETKKVLCVH 123
Query: 746 AGVAKQWTAQQTIKLSHQVEKILRTSYWKNLFFKLYNHNSINWDNHLHTIHLNTIDKLQF 805
G++ ++ IK +
Sbjct: 124 GGLSPGLPLEEQIKEEPE----------------------------------------DQ 143
Query: 806 IINTLTRTRFCKIDGTIEFIKKNIKNNNFQNNYIPWFDLPNRKTIDITVLFGHWSTLGLI 865
+ L + ++ G ++ + + WF N ++ GH
Sbjct: 144 LPEDLLWSDPLELPGGFGSSRRGGG-----PDAVEWFLKKNG---LKLIVRGHTPVEEGY 195
Query: 866 M---KPNIICLDTGCVW----GNKLTALCL 888
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 = 79.5 bits (196), Expect = 3e-17
Identities = 37/194 (19%), Positives = 70/194 (36%), Gaps = 43/194 (22%)
Query: 391 VGQDEAISAVSNAIRRSRSGLSDAKRPYGSFMFLGPTGVGKTELCKTLSACIFNNEESII 450
VGQ+EAI A+ A+ P + + GP G GKT L + ++ +F +
Sbjct: 1 VGQEEAIEALREALEL---------PPPKNLLLYGPPGTGKTTLARAIANELFRPGAPFL 51
Query: 451 RIDMSEFIEKHSISRLIGAPPGYIGYEEGGYLTEIVRRKPYSLILLDEIEKANSDVFNIL 510
++ S+ +E ++ L G + L E+ + ++ +DEI+ + N L
Sbjct: 52 YLNASDLLEGLVVAELFGHFLVRL-------LFELAEKAKPGVLFIDEIDSLSRGAQNAL 104
Query: 511 LQILDDGRLTDNRGRTINFRNTIIVMTSNLGSDKIKEMEKGDKEIIKLAVMNEVKIYFRP 570
L++L+ I+ N ++ +N
Sbjct: 105 LRVLETLNDL-----RIDRENVRVIGATNRPLLGD----------------------LDR 137
Query: 571 EFINRIDDIIVFRY 584
+R+D IV
Sbjct: 138 ALYDRLDIRIVIPL 151
Score = 67.6 bits (165), Expect = 3e-13
Identities = 35/144 (24%), Positives = 56/144 (38%), Gaps = 14/144 (9%)
Query: 14 SNPVLIGEPGVGKTAIVEGLAQRIINGEVPNSLLSKKILLLDIALLLAGTKYRGEFEDRL 73
N +L G PG GKT + +A + P L L+ + LL G F L
Sbjct: 20 KNLLLYGPPGTGKTTLARAIANELFRPGAP-------FLYLNASDLLEGLVVAELFGHFL 72
Query: 74 KKILKEISNNQKDIIIFIDELHTMIG--TGKVEGSIDAGNMLKPELSRGELHCIGATTLN 131
++L E++ K ++FIDE+ ++ + ++ N L+ R + IGAT
Sbjct: 73 VRLLFELAEKAKPGVLFIDEIDSLSRGAQNALLRVLETLNDLRI--DRENVRVIGATNRP 130
Query: 132 EYRQYIEKDAAFERRFQKILVEEP 155
D A R +V
Sbjct: 131 LLGD---LDRALYDRLDIRIVIPL 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: 635 DVHGCKKSLSILLKKI----------HKKSPEANFIFLGDLINKGPQSLDTLRMVYSM-- 682
D+HG + L +LL K+ H PE +FLGDLI++GP+ + L +V SM
Sbjct: 6 DIHGHAEKLVVLLHKLGYQELSGVYRH---PERQVVFLGDLIDRGPEIRELLEIVKSMVD 62
Query: 683 RNYAKIVLGNHEI-----HLLDVLI----------NINK-KSKLDTFDDILDAPDKKKLV 726
+A V+GNHE H D N+ + ++ L+ F + + K +
Sbjct: 63 AGHALAVMGNHEFNAIAWHTKDPSGGEWLRAHSKKNLRQHQAFLEQF--REHSEEHKDWL 120
Query: 727 SWLRTQPLAIYYKKYLMIHA 746
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 = 64.7 bits (157), Expect = 3e-12
Identities = 30/134 (22%), Positives = 53/134 (39%), Gaps = 7/134 (5%)
Query: 417 PYGSFMFLGPTGVGKTELCKTLSACIFNNEESIIRIDMSEFIEKHSISRLIGAPPGYIGY 476
P + +GP G GKT L + L+ + +I ID + +E+ L+ G
Sbjct: 1 PGEVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKAS 60
Query: 477 EEGGY----LTEIVRRKPYSLILLDEIEKANSDVFNILLQILDDGRLTDNRGRTINFRNT 532
G + R+ +++LDEI LL +L++ RL +N
Sbjct: 61 GSGELRLRLALALARKLKPDVLILDEITSLLDAEQEALLLLLEELRLLLLLKS---EKNL 117
Query: 533 IIVMTSNLGSDKIK 546
+++T+N D
Sbjct: 118 TVILTTNDEKDLGP 131
Score = 48.9 bits (116), Expect = 1e-06
Identities = 33/149 (22%), Positives = 60/149 (40%), Gaps = 20/149 (13%)
Query: 18 LIGEPGVGKTAIVEGLAQRI---------INGEVPNSLLSKKILLLDIALLLAGTKYRGE 68
++G PG GKT + LA+ + I+GE + ++LL+ + G K G
Sbjct: 7 IVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIV----GGKKASGS 62
Query: 69 FEDRLKKILKEISNNQKDIIIFIDELHTMIG--TGKVEGSIDAGNMLKPELSRGELHCIG 126
E RL+ L + D ++ +DE+ +++ + ++ +L S L I
Sbjct: 63 GELRLRLALALARKLKPD-VLILDEITSLLDAEQEALLLLLEELRLLLLLKSEKNLTVIL 121
Query: 127 ATTLNEYRQYIEKDAAFERRFQKILVEEP 155
T + A RRF + +V
Sbjct: 122 TTNDEK----DLGPALLRRRFDRRIVLLL 146
>gnl|CDD|219538 pfam07728, AAA_5, AAA domain (dynein-related subfamily). This Pfam
entry includes some of the AAA proteins not detected by
the pfam00004 model.
Length = 135
Score = 63.5 bits (155), Expect = 6e-12
Identities = 36/136 (26%), Positives = 56/136 (41%), Gaps = 16/136 (11%)
Query: 420 SFMFLGPTGVGKTELCKTLSACIFNNEESIIRI--DMSEFIEKHSISRLIGA--PPGYIG 475
+ +GP G GK+EL + L+A + N +++ D +E L G
Sbjct: 1 GVLLVGPPGTGKSELAERLAAALSNRPVFYVQLTRDTTE-------EDLKGRRNIDPGGA 53
Query: 476 YEEGGYLTEIVRRKPYSLILLDEIEKANSDVFNILLQILDDGRLTDNRGRTI---NFRNT 532
G L R + +LDEI +AN DV N LL +LD+ RL G +
Sbjct: 54 SWVDGPLVRAAREG--EIAVLDEINRANPDVLNSLLSLLDERRLLLPEGGELVKAAPDGF 111
Query: 533 IIVMTSNLGSDKIKEM 548
++ T N + E+
Sbjct: 112 RLIATMNPLDRGLNEL 127
Score = 36.5 bits (85), Expect = 0.016
Identities = 28/140 (20%), Positives = 45/140 (32%), Gaps = 16/140 (11%)
Query: 17 VLIGEPGVGKTAIVEGLAQRIINGEVPNSLLSKKILLLDIALLLAGTKYRGEFEDRLKKI 76
+L+G PG GK+ + E LA + N V L++ L +
Sbjct: 3 LLVGPPGTGKSELAERLAAALSNRPVFYVQLTRD---TTEEDLKGRRNIDPGGASWVDGP 59
Query: 77 LKEISNNQKDIIIFIDELHTMIGT---GKVEGSIDAGNMLKPELSRGELHC------IGA 127
L + + I +DE+ + +D +L PE + + A
Sbjct: 60 LVRAAREGE--IAVLDEI-NRANPDVLNSLLSLLDERRLLLPEG-GELVKAAPDGFRLIA 115
Query: 128 TTLNEYRQYIEKDAAFERRF 147
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 = 59.5 bits (145), Expect = 1e-10
Identities = 38/144 (26%), Positives = 62/144 (43%), Gaps = 29/144 (20%)
Query: 18 LIGEPGVGKTAIVEGLAQRIINGEVPNSLLSKKILLLDIALLLAGTKYRGEFEDRLKKIL 77
L G PG GKT + + +A+ + ++I+ +KY GE E RL+++
Sbjct: 3 LYGPPGTGKTTLAKAVAKEL------------GAPFIEISGSELVSKYVGESEKRLRELF 50
Query: 78 KEISNNQKDIIIFIDELHTMIGTGKVEGSIDAG---NMLKPEL-----SRGELHCIGATT 129
+ +IFIDE+ + G+ G ++ N L EL S ++ I AT
Sbjct: 51 EAAKKLAPC-VIFIDEIDALAGSRGSGGDSESRRVVNQLLTELDGFTSSLSKVIVIAATN 109
Query: 130 LNEYRQYIEK-DAAFER-RFQKIL 151
+K D A R RF +I+
Sbjct: 110 ------RPDKLDPALLRGRFDRII 127
Score = 43.0 bits (102), Expect = 8e-05
Identities = 29/129 (22%), Positives = 46/129 (35%), Gaps = 32/129 (24%)
Query: 422 MFLGPTGVGKTELCKTLSACIFNNEESIIRIDMSEFIEKHSISRLIGAPPGYIGYEEGGY 481
+ GP G GKT L K ++ + I I SE + K+ +G +
Sbjct: 2 LLYGPPGTGKTTLAKAVAKELGAP---FIEISGSELVSKY-----VGESEKRL----REL 49
Query: 482 LTEIVRRKPYSLILLDEIEK-----------ANSDVFNILLQILDDGRLTDNRGRTINFR 530
+ P +I +DEI+ + V N LL LD G T +
Sbjct: 50 FEAAKKLAP-CVIFIDEIDALAGSRGSGGDSESRRVVNQLLTELD--------GFTSSLS 100
Query: 531 NTIIVMTSN 539
I++ +N
Sbjct: 101 KVIVIAATN 109
>gnl|CDD|163666 cd07423, MPP_PrpE, Bacillus subtilis PrpE and related proteins,
metallophosphatase domain. PrpE (protein phosphatase E)
is a bacterial member of the PPP (phosphoprotein
phosphatase) family of serine/threonine phosphatases and
a key signal transduction pathway component controlling
the expression of spore germination receptors GerA and
GerK in Bacillus subtilis. PrpE is closely related to
ApaH (also known symmetrical Ap(4)A hydrolase and
bis(5'nucleosyl)-tetraphosphatase). PrpE has
specificity for phosphotyrosine only, unlike the
serine/threonine phosphatases to which it is related.
The Bacilli members of this family are single domain
proteins while the other members have N- and C-terminal
domains in addition to this phosphatase domain. The PPP
(phosphoprotein phosphatase) family, to which PrpE
belongs, is one of two known protein phosphatase
families specific for serine and threonine. The PPP
family also includes: PP1, PP2A, PP2B (calcineurin),
PP4, PP5, PP6, PP7, Bsu1, RdgC, PrpA/PrpB, and ApA4
hydrolase. The PPP catalytic domain is defined by three
conserved motifs (-GDXHG-, -GDXVDRG- and -GNHE-). The
PPP enzyme family is ancient with members found in all
eukaryotes, and in most bacterial and archeal genomes.
Dephosphorylation of phosphoserines and
phosphothreonines on target proteins plays a central
role in the regulation of many cellular processes. PPPs
belong to the metallophosphatase (MPP) superfamily.
MPPs are functionally diverse, but all share a conserved
domain with an active site consisting of two metal ions
(usually manganese, iron, or zinc) coordinated with
octahedral geometry by a cage of histidine, aspartate,
and asparagine residues. The MPP superfamily includes:
Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat
debranching enzymes, YfcE-like phosphodiesterases,
purple acid phosphatases (PAPs), YbbF-like
UDP-2,3-diacylglucosamine hydrolases, and acid
sphingomyelinases (ASMases). The conserved domain is a
double beta-sheet sandwich with a di-metal active site
made up of residues located at the C-terminal side of
the sheets. This domain is thought to allow for
productive metal coordination.
Length = 234
Score = 61.1 bits (149), Expect = 3e-10
Identities = 41/142 (28%), Positives = 66/142 (46%), Gaps = 25/142 (17%)
Query: 627 FDLIYGARDVHGCKKSLSILL-------KKIHKKSPEAN--FIFLGDLINKGPQSLDTLR 677
FD+I DVHGC L LL K++ + +F+GDL+++GP S + LR
Sbjct: 3 FDII---GDVHGCYDELEELLEKLGYRIKRVGTVTHPEGRRAVFVGDLVDRGPDSPEVLR 59
Query: 678 MVYSM--RNYAKIVLGNHEIHLLDVLININKKSK--LD-TFDDILDAPD--KKKLVSWLR 730
+V SM A V GNH+ L L N K L+ T + + K++++ +
Sbjct: 60 LVMSMVAAGAALCVPGNHDNKLYRKLQGRNVKITHGLEETVAQLEAESEEFKEEVIEFYE 119
Query: 731 TQPLAIYY----KKYLMIHAGV 748
+ 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: 851 DITVLFGHWSTLGLIMKPNIICLDTGCVWGNKLTALCLEDRSIIQV 896
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 = 62.1 bits (151), Expect = 4e-10
Identities = 46/172 (26%), Positives = 69/172 (40%), Gaps = 23/172 (13%)
Query: 373 QVEREKLLNIENLLCKRVVGQDEAISAVSNAIRRSRSGLSDAKRPYGSFMFLGPTGVGKT 432
+ E L I + L K VVG +E I A+ A + GP GVGKT
Sbjct: 9 ERVAEILGKIRSELEKVVVGDEEVIELALLALL--------AGGH---VLLEGPPGVGKT 57
Query: 433 ELCKTLSACIFNNEESIIRIDMSEFIEKHSISRLIGAPPGYIGYEEGGYLTEIVRRK--- 489
L + L+ + +RI + + S L+G E G V
Sbjct: 58 LLARALARALGLP---FVRIQCTPDLLP---SDLLGTYAYAALLLEPGE-FRFVPGPLFA 110
Query: 490 -PYSLILLDEIEKANSDVFNILLQILDDGRLTDNRGRTINFRN-TIIVMTSN 539
++LLDEI +A +V N LL+ L++ ++T TI I++ T N
Sbjct: 111 AVRVILLLDEINRAPPEVQNALLEALEERQVTVPGLTTIRLPPPFIVIATQN 162
Score = 32.8 bits (75), Expect = 0.86
Identities = 10/20 (50%), Positives = 13/20 (65%)
Query: 18 LIGEPGVGKTAIVEGLAQRI 37
L G PGVGKT + LA+ +
Sbjct: 48 LEGPPGVGKTLLARALARAL 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 = 52.0 bits (126), Expect = 2e-08
Identities = 15/50 (30%), Positives = 31/50 (62%)
Query: 585 LNRKNILSIANIQLNILKNKLLKMNMDLKISKAALKKISNIGFDLIYGAR 634
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 = 57.7 bits (140), Expect = 2e-08
Identities = 31/91 (34%), Positives = 46/91 (50%), Gaps = 19/91 (20%)
Query: 627 FDLIYGARDVHGCKKSLSILLKKI--------HKKSPEAN------FIFLGDLINKGPQS 672
FD+I G DVHGC+ L LL+++ + + +F+GDL+++GP S
Sbjct: 182 FDII-G--DVHGCRDELETLLEELGYQIERDEGGRPVDVTHPEGRKAVFVGDLVDRGPDS 238
Query: 673 LDTLRMVYSMRN--YAKIVLGNHEIHLLDVL 701
LR+V M A V GNH++ LL L
Sbjct: 239 PGVLRLVMGMVAAGTALCVPGNHDVKLLRAL 269
Score = 46.1 bits (110), Expect = 8e-05
Identities = 19/44 (43%), Positives = 26/44 (59%)
Query: 853 TVLFGHWSTLGLIMKPNIICLDTGCVWGNKLTALCLEDRSIIQV 896
V++GH N IC+DTGCV+G KLTAL +R ++ V
Sbjct: 368 MVVYGHTPVPEAEWVNNTICIDTGCVFGGKLTALRYPERELVSV 411
>gnl|CDD|198154 smart01086, ClpB_D2-small, C-terminal, D2-small domain, of ClpB
protein. This is the C-terminal domain of ClpB protein,
referred to as the D2-small domain, and is a mixed
alpha-beta structure. Compared with the D1-small domain
(included in AAA) it lacks the long coiled-coil
insertion, and instead of helix C4 contains a
beta-strand (e3) that is part of a three stranded
beta-pleated sheet. In Thermophilus the whole protein
forms a hexamer with the D1-small and D2-small domains
located on the outside of the hexamer, with the long
coiled-coil being exposed on the surface. The D2-small
domain is essential for oligomerisation, forming a tight
interface with the D2-large domain of a neighbouring
subunit and thereby providing enough binding energy to
stabilise the functional assembly. The domain is
associated with two Clp_N at the N-terminus as well as
AAA and AAA_2.
Length = 90
Score = 46.7 bits (112), Expect = 2e-06
Identities = 15/50 (30%), Positives = 32/50 (64%)
Query: 585 LNRKNILSIANIQLNILKNKLLKMNMDLKISKAALKKISNIGFDLIYGAR 634
L++++++ I ++ LN L+ +L + + L+ + AL ++ G+D YGAR
Sbjct: 1 LDKEDLVRIVDLPLNALQKRLAEKGITLEFTDEALDWLAEKGYDPKYGAR 50
>gnl|CDD|233328 TIGR01243, CDC48, AAA family ATPase, CDC48 subfamily. This
subfamily of the AAA family ATPases includes two members
each from three archaeal species. It also includes yeast
CDC48 (cell division control protein 48) and the human
ortholog, transitional endoplasmic reticulum ATPase
(valosin-containing protein). These proteins in
eukaryotes are involved in the budding and transfer of
membrane from the transitional endoplasmic reticulum to
the Golgi apparatus.
Length = 733
Score = 50.7 bits (121), Expect = 3e-06
Identities = 68/252 (26%), Positives = 101/252 (40%), Gaps = 59/252 (23%)
Query: 17 VLIGEPGVGKTAIVEGLAQRI------INGEVPNSLLSKKILLLDIALLLAGTKYRGEFE 70
+L G PG GKT + + +A ING P + +KY GE E
Sbjct: 216 LLYGPPGTGKTLLAKAVANEAGAYFISING--PEIM----------------SKYYGESE 257
Query: 71 DRLKKILKEISNNQKDIIIFIDELHTMI-----GTGKVEGSIDAG--NMLKPELSRGELH 123
+RL++I KE N IIFIDE+ + TG+VE + A ++ RG +
Sbjct: 258 ERLREIFKEAEENAPS-IIFIDEIDAIAPKREEVTGEVEKRVVAQLLTLMDGLKGRGRVI 316
Query: 124 CIGATTLNEYRQYIEKDAAFER--RFQK-ILVEEPDIEETISILR------------GLQ 168
IGAT + D A R RF + I++ PD IL+ L
Sbjct: 317 VIGATNRPD-----ALDPALRRPGRFDREIVIRVPDKRARKEILKVHTRNMPLAEDVDLD 371
Query: 169 KKYEVHHGVEITDPAIVAASELSYRYISDRFMPDKAIDLIDEAAAK-----IKIEIDSKP 223
K EV HG D A + A E + + RF+ + I+ E +K+ +
Sbjct: 372 KLAEVTHGFVGADLAAL-AKEAAMAALR-RFIREGKINFEAEEIPAEVLKELKVTMKDFM 429
Query: 224 EIMDKLERRLIQ 235
E + +E I+
Sbjct: 430 EALKMVEPSAIR 441
>gnl|CDD|163667 cd07424, MPP_PrpA_PrpB, PrpA and PrpB, metallophosphatase domain.
PrpA and PrpB are bacterial type I serine/threonine and
tyrosine phosphatases thought to modulate the expression
of proteins that protect the cell upon accumulation of
misfolded proteins in the periplasm. The PPP
(phosphoprotein phosphatase) family, to which PrpA and
PrpB belong, is one of two known protein phosphatase
families specific for serine and threonine. This family
also includes: PP1, PP2A, PP2B (calcineurin), PP4, PP5,
PP6, PP7, Bsu1, RdgC, PrpE, and ApA4 hydrolase. The PPP
catalytic domain is defined by three conserved motifs
(-GDXHG-, -GDXVDRG- and -GNHE-). The PPP enzyme family
is ancient with members found in all eukaryotes, and in
most bacterial and archeal genomes. Dephosphorylation
of phosphoserines and phosphothreonines on target
proteins plays a central role in the regulation of many
cellular processes. PPPs belong to the
metallophosphatase (MPP) superfamily. MPPs are
functionally diverse, but all share a conserved domain
with an active site consisting of two metal ions
(usually manganese, iron, or zinc) coordinated with
octahedral geometry by a cage of histidine, aspartate,
and asparagine residues. The MPP superfamily includes:
Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat
debranching enzymes, YfcE-like phosphodiesterases,
purple acid phosphatases (PAPs), YbbF-like
UDP-2,3-diacylglucosamine hydrolases, and acid
sphingomyelinases (ASMases). The conserved domain is a
double beta-sheet sandwich with a di-metal active site
made up of residues located at the C-terminal side of
the sheets. This domain is thought to allow for
productive metal coordination.
Length = 207
Score = 48.0 bits (115), Expect = 5e-06
Identities = 32/114 (28%), Positives = 48/114 (42%), Gaps = 20/114 (17%)
Query: 635 DVHGCKKSLSILLKKIHKKSPEAN-FIFLGDLINKGPQSLDTLRM-----VYSMRNYAKI 688
D+HG L L + P + I +GDLI++GP+SL L + ++
Sbjct: 8 DIHGHYSLLQKALDAVGF-DPARDRLISVGDLIDRGPESLACLELLLEPWFHA------- 59
Query: 689 VLGNHEIHLLDVLININKKSKL------DTFDDILDAPDKKKLVSWLRTQPLAI 736
V GNHE +D L + + F D+ D ++ L L PLAI
Sbjct: 60 VRGNHEQMAIDALRAEPLDAVRWLANGGEWFLDLPDEELRRWLALKLEQLPLAI 113
Score = 30.3 bits (69), Expect = 3.4
Identities = 12/36 (33%), Positives = 18/36 (50%)
Query: 853 TVLFGHWSTLGLIMKPNIICLDTGCVWGNKLTALCL 888
V+ GH + N++ +DTG V+ LT L L
Sbjct: 171 AVVHGHTPVKRPLRLGNVLYIDTGAVFDGNLTLLDL 206
>gnl|CDD|215750 pfam00149, Metallophos, Calcineurin-like phosphoesterase. This
family includes a diverse range of phosphoesterases,
including protein phosphoserine phosphatases,
nucleotidases, sphingomyelin phosphodiesterases and
2'-3' cAMP phosphodiesterases as well as nucleases such
as bacterial SbcD or yeast MRE11. The most conserved
regions in this superfamily centre around the metal
chelating residues.
Length = 185
Score = 46.7 bits (110), Expect = 1e-05
Identities = 21/71 (29%), Positives = 39/71 (54%), Gaps = 6/71 (8%)
Query: 635 DVHGCKKSLSI--LLKKIHKKSPEANFIFLGDLINKGPQSLDTLRMVYSMRNYAKI---- 688
D+HG L + LL ++ + +FLGDL+++GP SL+ L ++++++ A
Sbjct: 7 DLHGGLDDLDLLLLLLELLGEPKPDLVLFLGDLVDRGPPSLEVLALLFALKLKAPGPVYL 66
Query: 689 VLGNHEIHLLD 699
V GNH+ +
Sbjct: 67 VRGNHDFDSGN 77
>gnl|CDD|236911 PRK11439, pphA, serine/threonine protein phosphatase 1;
Provisional.
Length = 218
Score = 47.1 bits (112), Expect = 1e-05
Identities = 26/72 (36%), Positives = 41/72 (56%), Gaps = 8/72 (11%)
Query: 635 DVHGCKKSLSILLKKIHKK--SPEANF-IFLGDLINKGPQSLDTLRMVYSMRNYAKIVLG 691
D+HGC L++K+ P + I +GDLI++GPQSL L+++ ++ + V G
Sbjct: 24 DIHGC---FEQLMRKLRHCRFDPWRDLLISVGDLIDRGPQSLRCLQLLE--EHWVRAVRG 78
Query: 692 NHEIHLLDVLIN 703
NHE LD L +
Sbjct: 79 NHEQMALDALAS 90
>gnl|CDD|222104 pfam13401, AAA_22, AAA domain.
Length = 124
Score = 44.6 bits (106), Expect = 2e-05
Identities = 20/105 (19%), Positives = 42/105 (40%), Gaps = 7/105 (6%)
Query: 419 GSFMFLGPTGVGKTELCKTLSACIFNNEESIIRIDMSEFIEKHSISRLI----GAPPGYI 474
G + G +G GKT L + L+ + N ++ ++ + R I G P
Sbjct: 5 GIGVLTGESGSGKTTLLRRLARQLPNRR--VVYVEAPSLGTPKDLLRKILRALGLPLSGG 62
Query: 475 GYEEG-GYLTEIVRRKPYSLILLDEIEKANSDVFNILLQILDDGR 518
E + + ++R+ L+++DE + + + L + D
Sbjct: 63 TTAELLEAILDALKRRGRPLLIIDEAQHLSLEALEELRDLYDLSE 107
Score = 42.3 bits (100), Expect = 1e-04
Identities = 25/83 (30%), Positives = 37/83 (44%), Gaps = 5/83 (6%)
Query: 17 VLIGEPGVGKTAIVEGLAQRIINGEV----PNSLLSKKILLLDIALLLAGTKYRGEFEDR 72
VL GE G GKT ++ LA+++ N V SL + K LL I L G G
Sbjct: 8 VLTGESGSGKTTLLRRLARQLPNRRVVYVEAPSLGTPKDLLRKILRAL-GLPLSGGTTAE 66
Query: 73 LKKILKEISNNQKDIIIFIDELH 95
L + + + + ++ IDE
Sbjct: 67 LLEAILDALKRRGRPLLIIDEAQ 89
>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: 635 DVHGCKKSLSILLKKIHKKSPEANF-IFLGDLINKGPQSLDTLRMVYSMRNYAKI----V 689
D+HG ++L +L+ + + +F + LGDL+ GP + L ++ I V
Sbjct: 5 DIHGNLEALEAVLEAALAAAEKPDFVLVLGDLVGDGPDPEEVLAAALALLLLLGIPVYVV 64
Query: 690 LGNHEIHL 697
GNH+I L
Sbjct: 65 PGNHDILL 72
>gnl|CDD|184187 PRK13625, PRK13625, bis(5'-nucleosyl)-tetraphosphatase PrpE;
Provisional.
Length = 245
Score = 46.2 bits (110), Expect = 2e-05
Identities = 24/80 (30%), Positives = 39/80 (48%), Gaps = 19/80 (23%)
Query: 627 FDLIYGARDVHGCKKSLSILLKK----------IHKKSPEA-NFIFLGDLINKGPQSLDT 675
+D+I D+HGC + L +K +H P+ F+GDL ++GP SL
Sbjct: 3 YDII---GDIHGCYQEFQALTEKLGYNWSSGLPVH---PDQRKLAFVGDLTDRGPHSLRM 56
Query: 676 LRMVYSM--RNYAKIVLGNH 693
+ +V+ + + A V GNH
Sbjct: 57 IEIVWELVEKKAAYYVPGNH 76
Score = 31.2 bits (71), Expect = 2.2
Identities = 10/18 (55%), Positives = 15/18 (83%)
Query: 869 NIICLDTGCVWGNKLTAL 886
+ + +DTGCV+G +LTAL
Sbjct: 203 HTVNIDTGCVFGGRLTAL 220
>gnl|CDD|107154 PHA02239, PHA02239, putative protein phosphatase.
Length = 235
Score = 46.1 bits (109), Expect = 3e-05
Identities = 28/86 (32%), Positives = 51/86 (59%), Gaps = 4/86 (4%)
Query: 630 IYGARDVHG-CKKSLSILLKKIHKKSPEANFIFLGDLINKGPQSLDTLRMVYS-MRNYAK 687
IY D+HG +K L+I+ K +++ PE +FLGD +++G +S D + ++ M N
Sbjct: 3 IYVVPDIHGEYQKLLTIMDKINNERKPEETIVFLGDYVDRGKRSKDVVNYIFDLMSNDDN 62
Query: 688 IV--LGNHEIHLLDVLININKKSKLD 711
+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: 620 KKISNIGFDLIYGARDVHGCKKSLSILLKKIHKKS--PEANF-IFLGDLINKGPQSLDTL 676
+KI+ + I+ D+HG +L ++H+ S PE + I +GD I++GP+SL+ L
Sbjct: 7 QKINAHHYRHIWVVGDIHGE---YQLLQSRLHQLSFCPETDLLISVGDNIDRGPESLNVL 63
Query: 677 RMVYSMRNYAKIVLGNHEIHLLDVLI----NINKKSKLDTFDDILDAPDKKKLVSWLRTQ 732
R++ + + V GNHE LD N+ S D F D+ D+ ++ L+
Sbjct: 64 RLLN--QPWFISVKGNHEAMALDAFETGDGNMWLASGGDWFFDLNDSEQQEATDLLLKFH 121
Query: 733 --PLAIYYK----KYLMIHA 746
P I KY++ HA
Sbjct: 122 HLPHIIEITNDNIKYVIAHA 141
>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 = 41.4 bits (97), Expect = 4e-04
Identities = 29/153 (18%), Positives = 62/153 (40%), Gaps = 29/153 (18%)
Query: 389 RVVGQDEAISAVSNAIRRSRSGLSDAKRPYGSFMFLGPTGVGKTELCKTLS--------- 439
R+VG++E + + +A+RR+RSG S + GP+G GKT L + L
Sbjct: 1 RLVGREEELERLLDALRRARSG------GPPSVLLTGPSGTGKTSLLRELLEGLLVAAGK 54
Query: 440 -----ACIFNNEESIIRIDMSEFIEKH---------SISRLIGAPPGYIGYEEGGYLTEI 485
+R + + + + ++ +GA + L +
Sbjct: 55 CDQAERNPPYAFSQALRELLRQLLRELAAELLLLREALLAALGAELIEGLQDLVELLERL 114
Query: 486 VRRKPYSLILLDEIEKANSDVFNILLQILDDGR 518
+ R +++LD+++ A+ + ++L +L
Sbjct: 115 LARARPLVLVLDDLQWADEESLDLLAALLRRLE 147
Score = 36.4 bits (84), Expect = 0.018
Identities = 21/102 (20%), Positives = 40/102 (39%), Gaps = 23/102 (22%)
Query: 17 VLIGEPGVGKTAIVEGLAQR---------IINGEVPNSL--------------LSKKILL 53
+L G G GKT+++ L + P + L+ ++LL
Sbjct: 28 LLTGPSGTGKTSLLRELLEGLLVAAGKCDQAERNPPYAFSQALRELLRQLLRELAAELLL 87
Query: 54 LDIALLLAGTKYRGEFEDRLKKILKEISNNQKDIIIFIDELH 95
L ALL A E L ++L+ + + +++ +D+L
Sbjct: 88 LREALLAALGAELIEGLQDLVELLERLLARARPLVLVLDDLQ 129
>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: 635 DVHGCKKSLSILLKKIHKKSPEANFIFLGDLINKGPQSLDTLRMVYSM--RNYAKIVL-- 690
D+HG L L K + PE N++FLGD +++GP S++ + +++++ +IVL
Sbjct: 35 DIHGQFDDLLRLFDKN-GQPPETNYVFLGDYVDRGPFSIEVILLLFALKILYPNRIVLLR 93
Query: 691 GNHE 694
GNHE
Sbjct: 94 GNHE 97
>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and
chromosome partitioning].
Length = 1163
Score = 42.0 bits (99), Expect = 0.002
Identities = 30/133 (22%), Positives = 73/133 (54%), Gaps = 5/133 (3%)
Query: 202 DKAIDLIDEAAAKIKIEIDSKPEIMDKLERRLIQLKIEHEAIKREYDESSKKRLLLIKKE 261
K ++ ++E ++++ E++ E +++ E+ + +LK E E ++ E +E + LL +K+E
Sbjct: 238 RKELEELEEELSRLEEELEELQEELEEAEKEIEELKSELEELREELEELQ-EELLELKEE 296
Query: 262 INKLEIKYANLEKIWKYEKTLIKDSQQIKEEIEKVRLKI-NKATRKSDWQTVSKLKYGEL 320
I +LE + + L + + L + ++++E +E+++ KI + +T+ + L
Sbjct: 297 IEELEGEISLLRER---LEELENELEELEERLEELKEKIEALKEELEERETLLEELEQLL 353
Query: 321 NKLERILKEKSQK 333
+LE +E +K
Sbjct: 354 AELEEAKEELEEK 366
Score = 37.0 bits (86), Expect = 0.057
Identities = 24/155 (15%), Positives = 70/155 (45%), Gaps = 15/155 (9%)
Query: 203 KAIDLIDEAAAKIKIEIDSKPEIMDKLERRLIQLKIEHEAIKREYDESSKKRLLLIKKEI 262
+ ++ ++E + + +D+ ++ LE+R +L+ E E ++ E +E +++L +++E+
Sbjct: 793 EELEELEEELEEAERRLDALERELESLEQRRERLEQEIEELEEEIEEL-EEKLDELEEEL 851
Query: 263 NKLEIKYANL--------EKIWKYEKTLIKDSQQIKE---EIEKVRLKINKATRKSDWQT 311
+LE + L + + E L + ++ +E E+ ++ ++ + + +
Sbjct: 852 EELEKELEELKEELEELEAEKEELEDELKELEEEKEELEEELRELESELAELKEEIEKLR 911
Query: 312 VSKLKYGELNKLERILKEKSQKDIQLPNNANKFTL 346
+ EL L+ + + + + TL
Sbjct: 912 E---RLEELEAKLERLEVELPELEEELEEEYEDTL 943
Score = 35.5 bits (82), Expect = 0.14
Identities = 37/208 (17%), Positives = 95/208 (45%), Gaps = 14/208 (6%)
Query: 140 DAAFERRFQKILVEEPDIEETISILRGLQKKYEVH--HGVEITDPAIVAASELSYRYISD 197
+ A LV + D+E+ + R L+ KY + G + + + R
Sbjct: 606 EPAVRFVLGDTLVVD-DLEQARRLARKLRIKYRIVTLDGDLVEPSGSITGGSRNKRSSLA 664
Query: 198 RF----MPDKAIDLIDEAAAKIKIEIDSKPEIMDKLERRLIQLKIEHEAIKREYDESSKK 253
+ ++ + ++ K++ E+ S + LE L +L+ + E ++R+ +E K+
Sbjct: 665 QKRELKELEEELAELEAQLEKLEEELKSLKNELRSLEDLLEELRRQLEELERQLEE-LKR 723
Query: 254 RLLLIKKEINKLEIKYANLEK----IWKYEKTLIKDSQQIKEEIEKVRLKINKATRKSDW 309
L +++E+ +L+ + LE+ + + + L + ++++EE+E + + K K +
Sbjct: 724 ELAALEEELEQLQSRLEELEEELEELEEELEELQERLEELEEELESLEEALAK--LKEEI 781
Query: 310 QTVSKLKYGELNKLERILKEKSQKDIQL 337
+ + + + +LE + +E + + +L
Sbjct: 782 EELEEKRQALQEELEELEEELEEAERRL 809
Score = 33.1 bits (76), Expect = 0.92
Identities = 30/206 (14%), Positives = 90/206 (43%), Gaps = 11/206 (5%)
Query: 219 IDSKPEIMDKLERRLIQLKIEHEAIKREYDESSKKRLL---LIKKEINKLEIKYANLEKI 275
++ +++++LE++L +L+ + E +R + ++ R L L+ ++ +L + LE+
Sbjct: 188 LERLEDLLEELEKQLEKLERQAEKAERYQELKAELRELELALLLAKLKELRKELEELEEE 247
Query: 276 WKYEKTLIKDSQQ----IKEEIEKVRLKINKATRKSDWQTVSKLKYGELNKLERILKEKS 331
+ +++ Q+ ++EIE+++ ++ + + + + + ++E + E S
Sbjct: 248 LSRLEEELEELQEELEEAEKEIEELKSELEELREE--LEELQEELLELKEEIEELEGEIS 305
Query: 332 QKDIQLPNNANKFTLLKTKVGSEEIAEIVSRTTGIPVSKIVQVEREKLLNIENLLCKRVV 391
+L N+ L+ ++ E +I + + + + E E+LL + +
Sbjct: 306 LLRERLEELENELEELEERL-EELKEKIEALKEELEERETLLEELEQLLAELEEAKEELE 364
Query: 392 G-QDEAISAVSNAIRRSRSGLSDAKR 416
+ + R L++ +
Sbjct: 365 EKLSALLEELEELFEALREELAELEA 390
Score = 31.6 bits (72), Expect = 2.3
Identities = 26/117 (22%), Positives = 58/117 (49%), Gaps = 12/117 (10%)
Query: 202 DKAIDLIDEAAAKIKIEIDSKPEIMDKLERRLIQLKIEHEAIKREY-DESSKKRLLLIKK 260
++ + ++ A++K EI+ E +++LE +L +L++E ++ E +E +++
Sbjct: 890 EEELRELESELAELKEEIEKLRERLEELEAKLERLEVELPELEEELEEEYEDTLETELER 949
Query: 261 EINKLEIKYA-----NLEKIWKYEKT------LIKDSQQIKEEIEKVRLKINKATRK 306
EI +LE + NL I +YE+ L + ++E EK+ I + ++
Sbjct: 950 EIERLEEEIEALGPVNLRAIEEYEEVEERYEELKSQREDLEEAKEKLLEVIEELDKE 1006
Score = 31.2 bits (71), Expect = 3.4
Identities = 34/201 (16%), Positives = 89/201 (44%), Gaps = 23/201 (11%)
Query: 144 ERRFQKILVEEPDIEETISILRGLQKKYEVHHGVEITDPAIVAASELSYRYISDRFMP-D 202
E + + + +IEE + LQ++ E + A E + R +
Sbjct: 768 ESLEEALAKLKEEIEELEEKRQALQEELEELEEELEEAERRLDALERELESLEQRRERLE 827
Query: 203 KAIDLIDEAAAKIKIEIDSKPEIMDKLERRLIQLKIEHEAIKREYDESS------KKRLL 256
+ I+ ++E +++ ++D E +++LE+ L +LK E E ++ E +E ++
Sbjct: 828 QEIEELEEEIEELEEKLDELEEELEELEKELEELKEELEELEAEKEELEDELKELEEEKE 887
Query: 257 LIKKEINKLE-----IKYANLEKIWKYEKTLIKDSQQIKEEIEKVRLKIN---KATRKSD 308
+++E+ +LE +K + + E L ++++ E+ ++ ++ + T +++
Sbjct: 888 ELEEELRELESELAELKEEIEKLRERLE-ELEAKLERLEVELPELEEELEEEYEDTLETE 946
Query: 309 WQTVSKLKYGELNKLERILKE 329
+ E+ +LE ++
Sbjct: 947 LER-------EIERLEEEIEA 960
>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: 422 MFLGPTGVGKTELCKTLSACIFNNEESIIRIDMSEFIE-KHSISRLIGAPPGYIGYEEGG 480
G G GK+ L L + I+ I + E + K I PG + +G
Sbjct: 153 YLEGGRGSGKSFLISELCD---EGGQRIVEIHLREITDAKVLIGTYTSPKPGDFEWMKGV 209
Query: 481 YLTEIVRRKPYSLILLDEIEKANSDVFNILLQILDDGRLT-DNRGRTI----NFRNTIIV 535
+ +V IL I+KA V + LL +L+ RL +RG T+ NF+ I
Sbjct: 210 LIEAVVSGD---WILFKRIDKAPHGVLSYLLTLLEKRRLLIPSRGETVLAHDNFQ---IF 263
Query: 536 MTSNLGSDKIKEMEKGDKEIIKLAVMNEVKIYFRPEF 572
TS S K K + + +I+ L +E R +
Sbjct: 264 FTS---SMKTKILGQRLWQILDLTQPDECVEVVRFDM 297
Score = 37.7 bits (87), Expect = 0.042
Identities = 30/95 (31%), Positives = 47/95 (49%), Gaps = 7/95 (7%)
Query: 425 GPTGVGKTELCKTLSACIFNNEESIIRIDMSEFIE-KHSISRLIGAPPGYIGYEEGGYLT 483
GPT GKT + L+ +RI+ E + + I + G + ++EG L
Sbjct: 895 GPTSSGKTSMILYLAR---ETGHKFVRINNHEHTDLQEYIGTYVTDDDGSLSFKEG-VLV 950
Query: 484 EIVRRKPYSLILLDEIEKANSDVFNILLQILDDGR 518
E +RR + I+LDE+ A +DV L ++LDD R
Sbjct: 951 EALRRGYW--IVLDELNLAPTDVLEALNRLLDDNR 983
>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: 635 DVHGCKKSLSILLKKIHKKS--PEANFIFLGDLINKGPQSLDT--LRMVYSMRNYAK--- 687
D+HG LL+ PE+N++FLGD +++G QSL+T L + Y ++ Y +
Sbjct: 57 DIHG---QYYDLLRLFEYGGFPPESNYLFLGDYVDRGKQSLETICLLLAYKIK-YPENFF 112
Query: 688 IVLGNHE 694
++ GNHE
Sbjct: 113 LLRGNHE 119
>gnl|CDD|224401 COG1484, DnaC, DNA replication protein [DNA replication,
recombination, and repair].
Length = 254
Score = 39.7 bits (93), Expect = 0.004
Identities = 33/156 (21%), Positives = 63/156 (40%), Gaps = 28/156 (17%)
Query: 420 SFMFLGPTGVGKTELCKTLSACIFNNEESIIRIDMSEFIEKHSISRLIGAPPGYIGYEEG 479
+ + LGP GVGKT L A NE I + +S+L A ++EG
Sbjct: 107 NLVLLGPPGVGKTHL-----AIAIGNELLKAGISVLFITAPDLLSKLKAA------FDEG 155
Query: 480 GYLTEIVRR-KPYSLILLDEI--EKANSDVFNILLQILDDGRLTDNRGRTINFRNTIIVM 536
+++R K L+++D+I E + + ++L Q++ I +
Sbjct: 156 RLEEKLLRELKKVDLLIIDDIGYEPFSQEEADLLFQLISRRY---ESRSLI--------I 204
Query: 537 TSNLGSDKIKEM---EKGDKEIIKLAVMNEVKIYFR 569
TSNL + E+ + + ++ + + I +
Sbjct: 205 TSNLSFGEWDELFGDDALTEALLDRILHHSHVIVIK 240
>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 = 40.4 bits (95), Expect = 0.004
Identities = 30/140 (21%), Positives = 66/140 (47%), Gaps = 19/140 (13%)
Query: 213 AKIKIEIDSKPEIMDKLERRLIQLKIEHEAIKREYDESSKK-------RLLLIKKEINKL 265
I+ ++ S E ++KL + +L+ E I++ +E +KK L +K++I +L
Sbjct: 240 EAIERQLASLEEELEKLTEEISELEKRLEEIEQLLEELNKKIKDLGEEEQLRVKEKIGEL 299
Query: 266 EIKYANLEKIWKYEKTLIKDSQ----QIKEEIEKVRLKI--------NKATRKSDWQTVS 313
E + A+LE+ ++ ++D++ +++ EI+K+ +I + R+
Sbjct: 300 EAEIASLERSIAEKERELEDAEERLAKLEAEIDKLLAEIEELEREIEEERKRRDKLTEEY 359
Query: 314 KLKYGELNKLERILKEKSQK 333
EL L L+E ++
Sbjct: 360 AELKEELEDLRAELEEVDKE 379
Score = 40.1 bits (94), Expect = 0.006
Identities = 38/210 (18%), Positives = 81/210 (38%), Gaps = 38/210 (18%)
Query: 209 DEAAAKIKIEIDSKPEIMDKLERRLIQLKIEHEAIKREYDESSKKRLLLIKKEINKLEIK 268
+E AK++ EID +++LER + + + + + EY E K+E+ L
Sbjct: 321 EERLAKLEAEIDKLLAEIEELEREIEEERKRRDKLTEEYAEL--------KEELEDLR-- 370
Query: 269 YANLEKIWKYEKTLIKDSQQIKEEIEKVRLKINKATRKSDWQTVSKLKYGELNKLERILK 328
A LE++ K + + +E++EK++ +IN+ R+ D R+ +
Sbjct: 371 -AELEEVDKEFAETRDELKDYREKLEKLKREINELKRELD----------------RLQE 413
Query: 329 EKSQKDIQLPNNANKFTLLKTKVGSEEIAEIVSRTTGIPVSKIVQVEREKLLNIENLLCK 388
E + +L + ++ +I E+ +I + E + +L
Sbjct: 414 ELQRLSEELADLNAAIAGIE-----AKINELEEEKEDK-ALEIKKQEWKLEQLAADL--- 464
Query: 389 RVVGQDEAISAVSNAIRRSRSGLSDAKRPY 418
++ + + R LS +R
Sbjct: 465 --SKYEQELYDLKEEYDRVEKELSKLQREL 492
Score = 34.7 bits (80), Expect = 0.25
Identities = 34/160 (21%), Positives = 72/160 (45%), Gaps = 14/160 (8%)
Query: 214 KIKIEIDSKPEIMDKLERRLIQLKIEHEAIKREYDESSKKRLLLIKKEINKLEIKYANLE 273
+K E+ S + ++E RL +L E R+ E K + +++E KL+ + LE
Sbjct: 685 GLKRELSSLQSELRRIENRLDELSQELSDASRKIGEIE-KEIEQLEQEEEKLKERLEELE 743
Query: 274 --------KIWKYE---KTLIKDSQQIKEEIEKVRLKINKATRKSDWQTVSKLKYGELNK 322
+I + K L ++++E++ K+ +N + + +++ EL+K
Sbjct: 744 EDLSSLEQEIENVKSELKELEARIEELEEDLHKLEEALNDLEARLSHSRIPEIQ-AELSK 802
Query: 323 LERILKEKSQKDIQLPNNANKFTLLKTKVGSEEIAEIVSR 362
LE + + ++ N+ TL K + +EI E+ +
Sbjct: 803 LEEEVSRIEARLREIEQKLNRLTLEK-EYLEKEIQELQEQ 841
Score = 32.0 bits (73), Expect = 2.1
Identities = 30/138 (21%), Positives = 64/138 (46%), Gaps = 13/138 (9%)
Query: 205 IDLIDEAAAKIKIEIDSKPEIMDKLERRLIQLKIEHEAIKREYDESSKKRLLL------I 258
I I +K++ E+ + ++E++L +L +E E +++E E ++R+ L I
Sbjct: 793 IPEIQAELSKLEEEVSRIEARLREIEQKLNRLTLEKEYLEKEIQELQEQRIDLKEQIKSI 852
Query: 259 KKEINKLEIKYANL----EKIWKYEKTLIKDSQQIKEEIEKVRLKINKATRKSDWQTVSK 314
+KEI L K L E++ + L +K+E +++ ++ + RK + +
Sbjct: 853 EKEIENLNGKKEELEEELEELEAALRDLESRLGDLKKERDELEAQLRELERKIEEL---E 909
Query: 315 LKYGELNKLERILKEKSQ 332
+ + K LK K +
Sbjct: 910 AQIEKKRKRLSELKAKLE 927
>gnl|CDD|185658 PTZ00480, PTZ00480, serine/threonine-protein phosphatase;
Provisional.
Length = 320
Score = 38.9 bits (90), Expect = 0.008
Identities = 25/64 (39%), Positives = 37/64 (57%), Gaps = 5/64 (7%)
Query: 635 DVHGCKKSLSILLKKIHKKSPEANFIFLGDLINKGPQSLDT--LRMVYSMRNYAKIVL-- 690
DVHG L + L + PE+N++FLGD +++G QSL+T L + Y ++ L
Sbjct: 66 DVHGQYFDL-LRLFEYGGYPPESNYLFLGDYVDRGKQSLETICLLLAYKIKYPENFFLLR 124
Query: 691 GNHE 694
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 = 39.1 bits (92), Expect = 0.010
Identities = 27/109 (24%), Positives = 46/109 (42%), Gaps = 33/109 (30%)
Query: 203 KAIDLIDEAAAKIKIEIDSKPEIMDKLER--------------RLIQL-KIEHEAIKREY 247
KAI IDE I+ ++K ++++LE+ RL +L K+E E + +E
Sbjct: 355 KAILNIDEVINLIRSSDEAKKALIEELEKLGFSEIQADAILDMRLRRLTKLEREKLLKEL 414
Query: 248 DESSKKRLLLIKKEINKLEIKYANLEKIWKYEKTLIKDSQQIKEEIEKV 296
E ++ EI LE A+ E+ KEE+++
Sbjct: 415 KE--------LEAEIEDLEKILASEERPKDL----------WKEELDEF 445
>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 = 39.1 bits (91), Expect = 0.010
Identities = 31/141 (21%), Positives = 62/141 (43%), Gaps = 16/141 (11%)
Query: 17 VLIGEPGVGKTAIVEGLAQRIINGEVPNSLLSKKILLLDIALLLAGTKYRGEFEDRLKKI 76
+ G PG GKT I +A +I G + +K L+ +++ G++ +
Sbjct: 316 LFAGPPGTGKTTIARVVA-KIYCGLG----VLRKPLVREVSR----ADLIGQYIGESEAK 366
Query: 77 LKEISNNQKDIIIFIDELHTMIGTGKVEGSIDAGN------MLKPELSRGELHCIGATTL 130
EI ++ ++F+DE +T++ TG + G + + E R L IGA
Sbjct: 367 TNEIIDSALGGVLFLDEAYTLVETGYGQKD-PFGLEAIDTLLARMENDRDRLVVIGAGYR 425
Query: 131 NEYRQYIEKDAAFERRFQKIL 151
+ +++E + RF +++
Sbjct: 426 KDLDKFLEVNEGLRSRFTRVI 446
Score = 31.0 bits (70), Expect = 3.5
Identities = 23/93 (24%), Positives = 40/93 (43%), Gaps = 7/93 (7%)
Query: 374 VEREKLLNIENLLCKRVVGQDEAI-SAVSNAIRRSRSGLSDAKRPYGSFMFLGPTGVGKT 432
E E L E + +RV Q A+ S+ + A+ R+ GL A+ +F GP G GKT
Sbjct: 269 AEAEAELA-EQIGLERVKRQVAALKSSTAMALARAERGLPVAQTSN-HMLFAGPPGTGKT 326
Query: 433 E----LCKTLSACIFNNEESIIRIDMSEFIEKH 461
+ K + + + ++ I ++
Sbjct: 327 TIARVVAKIYCGLGVLRKPLVREVSRADLIGQY 359
>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 = 0.011
Identities = 29/116 (25%), Positives = 51/116 (43%), Gaps = 14/116 (12%)
Query: 231 RRLIQLKIEHEAIKREYDESSKKRLLLIKKEINKLEIKYANLEKIWKYEKT-----LIKD 285
L +L+++ + E +E +K ++ N+ A+L K+ K +
Sbjct: 20 NSLYELRLDLARLLLENEELKQKVEEALEGATNEDGKLAADLLKLEVARKKERLNQIRAR 79
Query: 286 SQQIKEEIEKVRLKINK-----ATRKSDWQTVSKLKYGELNKLERILKEKSQKDIQ 336
Q+KEEIE+ R +I + A R+SD +S Y + L EK Q +I+
Sbjct: 80 ISQLKEEIEQKRERIEELKRALAQRRSD---LSSASYQLEKRRASQL-EKLQDEIK 131
>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 = 0.013
Identities = 25/108 (23%), Positives = 48/108 (44%), Gaps = 14/108 (12%)
Query: 659 FIFLGDLINKGPQSLDTLRMVYSMRNYAK-------IVLGNHEI-HLLDVLININKKSKL 710
+ LGD+ ++GP ++ L ++Y + A +LGNHE+ +L ++ K
Sbjct: 36 LVQLGDIFDRGPDVIEILWLLYKLEQEAAKAGGKVHFLLGNHELMNLCGDFRYVHPKY-F 94
Query: 711 DTFDDILDA-----PDKKKLVSWLRTQPLAIYYKKYLMIHAGVAKQWT 753
+ F + +L WLR++P+ + L +H G+ W
Sbjct: 95 NEFGGLAMRRRELFSPGGELGRWLRSKPVIVKVNDTLFVHGGLGPLWY 142
>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: 635 DVHGCKKSLSILLKKIHKKSPEANFIFLGDLINKGPQSLD------TLRMVYSMRNYAKI 688
D+HG L ++ K SPE ++F GD +++G +S++ +VY + +
Sbjct: 58 DLHGKLDDLFLIFYKNGLPSPENPYVFNGDFVDRGKRSIEILIILFAFFLVYPNEVH--L 115
Query: 689 VLGNHEIHLLDVLININK----------KSKLDTFDDILDAPDKKKLVSWLRTQPLA-IY 737
GNHE H++++ K K L +D+ SWL PLA I
Sbjct: 116 NRGNHEDHIMNLRYGFTKEVMSKYKLHGKKILRLLEDVF---------SWL---PLATII 163
Query: 738 YKKYLMIHAGVAKQ 751
K L++H G++
Sbjct: 164 DNKILVVHGGISDS 177
>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 = 37.9 bits (88), Expect = 0.024
Identities = 29/80 (36%), Positives = 43/80 (53%), Gaps = 10/80 (12%)
Query: 386 LCKRVVGQDEAISAVS----NAIRRSR--SGLSDAKRPYGSFMFLGPTGVGKTELCKTLS 439
L K ++GQDEA +V+ N RRS+ L D P M +GPTGVGKTE+ + L+
Sbjct: 10 LDKYIIGQDEAKKSVAIALRNRYRRSQLPEELKDEVTPKNILM-IGPTGVGKTEIARRLA 68
Query: 440 ACIFNNEESIIRIDMSEFIE 459
I+++ ++F E
Sbjct: 69 KLA---NAPFIKVEATKFTE 85
>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 = 37.8 bits (88), Expect = 0.025
Identities = 79/337 (23%), Positives = 132/337 (39%), Gaps = 85/337 (25%)
Query: 368 VSKIVQVEREKLLN-------IENLLCKRVVGQDEAIS----AVSNAIRRSRSGLSDAKR 416
+ + E E L+ I+ L + V+GQ++A AV N +R +
Sbjct: 50 RKESKEYEEEFELSYLPTPKEIKAHLDEYVIGQEQAKKVLSVAVYNHYKRLNFEKNKKSD 109
Query: 417 PY-----GSFMFLGPTGVGKTELCKTLSACIFNNEESIIRIDMSEFIEKHSISRLIGAPP 471
+ + +GPTG GKT L +TL A I N +I D + E
Sbjct: 110 NGVELSKSNILLIGPTGSGKTLLAQTL-ARILNVPFAI--ADATTLTEA----------- 155
Query: 472 GYIGYEEGGYLTEIVRRKPYS-------LILLDEIEK--------------ANSDVFNIL 510
GY+G + L ++++ Y +I +DEI+K + V L
Sbjct: 156 GYVGEDVENILLKLLQAADYDVEKAQKGIIYIDEIDKISRKSENPSITRDVSGEGVQQAL 215
Query: 511 LQILDDGRLTD---NRGRTINFRNTIIVMTSNL---------GSDKI------------- 545
L+I+ +G + + GR ++ I + TSN+ G +KI
Sbjct: 216 LKII-EGTVANVPPQGGRKHPYQEFIQIDTSNILFICGGAFVGLEKIIKKRTGKSSIGFG 274
Query: 546 ---KEMEKGDKEIIKLAVMNE-VKIYFRPEFINRIDDIIVFRYLNRKNILSIANIQLNIL 601
K+ K ++++ + VK PEFI R+ I L+ + +++I N L
Sbjct: 275 AEVKKKSKEKADLLRQVEPEDLVKFGLIPEFIGRLPVIATLEKLDEEALIAILTKPKNAL 334
Query: 602 KN---KLLKM-NMDLKISKAALKKISNIGFDLIYGAR 634
L KM N++L + ALK I+ + GAR
Sbjct: 335 VKQYQALFKMDNVELDFEEEALKAIAKKALERKTGAR 371
>gnl|CDD|225288 COG2433, COG2433, Uncharacterized conserved protein [Function
unknown].
Length = 652
Score = 37.8 bits (88), Expect = 0.027
Identities = 23/117 (19%), Positives = 55/117 (47%), Gaps = 14/117 (11%)
Query: 210 EAAAKIKIEIDSKPEIMDKLERRLIQLKIEHEAIKREYDESSKKRLLLIKKEINKLEIKY 269
+ + EI + + KLE + +L+ E+ +KRE +E +K+EI KLE +
Sbjct: 408 GTEEEERREITVYEKRIKKLEETVERLEEENSELKRELEE--------LKREIEKLESEL 459
Query: 270 ANLEKIWKYEKTLIKDSQQIKEEIEKVRLKINKATRKSDWQTVSKLKYGELNKLERI 326
+ + + ++ + IE++ ++ + ++ V +L+ +L +L ++
Sbjct: 460 ERFRREVRDKVRKDREIRARDRRIERLEKELEEKKKR-----VEELE-RKLAELRKM 510
>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 = 37.8 bits (88), Expect = 0.029
Identities = 49/170 (28%), Positives = 72/170 (42%), Gaps = 39/170 (22%)
Query: 18 LIGEPGVGKT----AIVEGLAQRI-INGEVPNSLLS-KKILLLDIALLLAGTKYRGEFED 71
L G PG GKT A+ LA RI G + L+ K LL+ KY GE E
Sbjct: 221 LYGPPGCGKTLIAKAVANSLAARIGAEGGGKSYFLNIKGPELLN--------KYVGETER 272
Query: 72 RLKKIL---KEISNNQKDIIIFIDELHTMI---GTGKVEGSIDAGNMLKPEL-------- 117
+++ I +E ++ + +I+F DE+ ++ G+G S D + P+L
Sbjct: 273 QIRLIFQRAREKASEGRPVIVFFDEMDSLFRTRGSGV---SSDVETTVVPQLLAEIDGVE 329
Query: 118 SRGELHCIGATTLNEYRQYIEKDAAFER--RFQ-KILVEEPDIEETISIL 164
S + IGA+ + D A R R KI +E PD E I
Sbjct: 330 SLDNVIVIGASNREDM-----IDPAILRPGRLDVKIRIERPDAEAAADIF 374
>gnl|CDD|173488 PTZ00239, PTZ00239, serine/threonine protein phosphatase 2A;
Provisional.
Length = 303
Score = 37.1 bits (86), Expect = 0.029
Identities = 23/64 (35%), Positives = 36/64 (56%), Gaps = 5/64 (7%)
Query: 635 DVHGCKKSLSILLKKIHKKSPEANFIFLGDLINKGPQSLDTLRMVYSMR-NY-AKIVL-- 690
D+HG L L K+ P AN+IF+GD +++G S++T+ + ++ Y I L
Sbjct: 50 DIHGQFYDLQALFKE-GGDIPNANYIFIGDFVDRGYNSVETMEYLLCLKVKYPGNITLLR 108
Query: 691 GNHE 694
GNHE
Sbjct: 109 GNHE 112
>gnl|CDD|224302 COG1384, LysS, Lysyl-tRNA synthetase (class I) [Translation,
ribosomal structure and biogenesis].
Length = 521
Score = 37.3 bits (87), Expect = 0.032
Identities = 27/117 (23%), Positives = 49/117 (41%), Gaps = 5/117 (4%)
Query: 146 RFQKILVEEPDIEETISILRGLQKKYEVHHGVEITDPAIVAASELSYRYISDRFMPDKAI 205
R +LV+ + EE IL L ++Y T + E + ++ + P+K
Sbjct: 370 RHLAVLVQIANAEEE-DILEILIRRYLPDA-DPDTIEDLDERIEYAINWL-RDYAPEKVK 426
Query: 206 DLIDEAAAKIKIEIDSKPEIMDKLERRL--IQLKIEHEAIKREYDESSKKRLLLIKK 260
I E + ++ D+K E ++ L L IQ + E E +KK+ +L +
Sbjct: 427 FSILEKPPEAELSEDAKLEALEDLAEFLESIQKASLEVELHNEVYEVAKKKGILPRA 483
>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 = 37.6 bits (87), Expect = 0.033
Identities = 35/112 (31%), Positives = 47/112 (41%), Gaps = 30/112 (26%)
Query: 208 IDEAAAKIKIEIDSKPEIMDK-----------LERRLIQL-KIEHEAIKREYDESSKKRL 255
IDE I+ E + K +M++ L RL L K+E AI E E K+R
Sbjct: 382 IDEVIEIIREEDEPKTILMERFKLSAIQAEAILNLRLRHLAKLEEHAIIDEQSELEKER- 440
Query: 256 LLIKKEINKLEIKYANLEKIWKYEKTLIKDSQQIKEEIEKVRLKINKATRKS 307
A LEKI K E+ L +Q +K+EI+ K A R S
Sbjct: 441 --------------AILEKILKSEREL---NQLVKKEIQADATKYGLARRSS 475
>gnl|CDD|184922 PRK14958, PRK14958, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 509
Score = 37.4 bits (86), Expect = 0.038
Identities = 36/146 (24%), Positives = 64/146 (43%), Gaps = 33/146 (22%)
Query: 388 KRVVGQDEAISAVSNAIRRSRSGLSDAKRPYGSFMFLGPTGVGKTELCKTLSACI----- 442
+ V+GQ + A+SNA+ D + + +++F G GVGKT + + L+ C+
Sbjct: 16 QEVIGQAPVVRALSNAL--------DQQYLHHAYLFTGTRGVGKTTISRILAKCLNCEKG 67
Query: 443 -----FNNEESIIRIDMSEF---IEKHSISRLIGAPPGYIGYEEGGYLTEIVRRKP---- 490
N+ E+ ID F E + SR E+ L + + P
Sbjct: 68 VSANPCNDCENCREIDEGRFPDLFEVDAASR--------TKVEDTRELLDNIPYAPTKGR 119
Query: 491 YSLILLDEIEKANSDVFNILLQILDD 516
+ + L+DE+ + FN LL+ L++
Sbjct: 120 FKVYLIDEVHMLSGHSFNALLKTLEE 145
>gnl|CDD|234063 TIGR02928, TIGR02928, orc1/cdc6 family replication initiation
protein. Members of this protein family are found
exclusively in the archaea. This set of DNA binding
proteins shows homology to the origin recognition
complex subunit 1/cell division control protein 6 family
in eukaryotes. Several members may be found in genome
and interact with each other [DNA metabolism, DNA
replication, recombination, and repair].
Length = 365
Score = 36.8 bits (86), Expect = 0.041
Identities = 52/230 (22%), Positives = 87/230 (37%), Gaps = 42/230 (18%)
Query: 375 EREKLLNIENLLCKRVVGQDEAISAVSNAIRRSRSGLSDAKRPYGSFMFL-GPTGVGKT- 432
LL + + R+V +DE I ++ A+R G RP S +F+ G TG GKT
Sbjct: 3 RNRDLLEPDYVP-DRIVHRDEQIEELAKALRPILRG----SRP--SNVFIYGKTGTGKTA 55
Query: 433 ---ELCKTLSACIFNNEE--SIIRID----------MSEFIEKHSISRLIGAPPGYIGYE 477
+ K L + + + ++ + E + R G G
Sbjct: 56 VTKYVMKELEEAAEDRDVRVVTVYVNCQILDTLYQVLVELANQ---LRGSGEEVPTTGLS 112
Query: 478 EGGYL----TEIVRRKPYSLILLDEIEKANSDVFNILLQILDDGRLTDNRGRTINFRNTI 533
E+ R +I+LDEI+ D ++L Q+ R N G N + +
Sbjct: 113 TSEVFRRLYKELNERGDSLIIVLDEIDYLVGDDDDLLYQLS---RARSN-GDLDNAKVGV 168
Query: 534 IVMTSNLGSDKIKEMEKGDKEIIKLAVMNEVKIYFRPEFINRIDDIIVFR 583
I + S+ +K E D + + + E +I F P + DI+ R
Sbjct: 169 IGI-----SNDLKFRENLDPRV--KSSLCEEEIIFPPYDAEELRDILENR 211
>gnl|CDD|184921 PRK14957, PRK14957, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 546
Score = 37.0 bits (85), Expect = 0.050
Identities = 34/141 (24%), Positives = 66/141 (46%), Gaps = 27/141 (19%)
Query: 390 VVGQDEAISAVSNAIRRSRSGLSDAKRPYGSFMFLGPTGVGKTELCKTLSACI------- 442
V GQ A++++ +A+ + ++ + +++F G GVGKT L + L+ C+
Sbjct: 18 VAGQQHALNSLVHAL--------ETQKVHHAYLFTGTRGVGKTTLGRLLAKCLNCKTGVT 69
Query: 443 ---FNNEESIIRIDMSEFIEKHSISRLIGAPPGYIGYEEGGYLTEIVRRKP----YSLIL 495
N E+ + I+ + FI+ I G EE + + ++ P Y + L
Sbjct: 70 AEPCNKCENCVAINNNSFIDLIEID-----AASRTGVEETKEILDNIQYMPSQGRYKVYL 124
Query: 496 LDEIEKANSDVFNILLQILDD 516
+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 = 0.052
Identities = 29/106 (27%), Positives = 58/106 (54%), Gaps = 9/106 (8%)
Query: 425 GPTGVGKTELCKTLSACIFNNEESIIRIDMSEFIEKHSISRLI-GAPPGYIGY--EEGGY 481
GP GVGKT + + L A + E++ R++M +F + +S I G P +G+ ++G +
Sbjct: 201 GPPGVGKTFVARRL-AYLLTGEKAPQRVNMVQFHQSYSYEDFIQGYRPNGVGFRRKDGIF 259
Query: 482 --LTEIVRRKPYS--LILLDEIEKAN-SDVFNILLQILDDGRLTDN 522
+ + +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 = 0.052
Identities = 24/53 (45%), Positives = 31/53 (58%), Gaps = 9/53 (16%)
Query: 388 KRVVGQDEAISAVSNAIR---RSRSGLSDAKR----PYGSFMFLGPTGVGKTE 433
K ++GQD+A AV+ A+R R R L + R P M +GPTGVGKTE
Sbjct: 15 KYIIGQDDAKRAVAIALRNRWR-RMQLPEELRDEVTPKNILM-IGPTGVGKTE 65
>gnl|CDD|225363 COG2804, PulE, Type II secretory pathway, ATPase PulE/Tfp pilus
assembly pathway, ATPase PilB [Cell motility and
secretion / Intracellular trafficking and secretion].
Length = 500
Score = 36.5 bits (85), Expect = 0.060
Identities = 14/39 (35%), Positives = 18/39 (46%)
Query: 414 AKRPYGSFMFLGPTGVGKTELCKTLSACIFNNEESIIRI 452
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 = 36.5 bits (85), Expect = 0.063
Identities = 25/60 (41%), Positives = 34/60 (56%), Gaps = 7/60 (11%)
Query: 386 LCKRVVGQDEAISAVS----NAIRRSR--SGLSDAKRPYGSFMFLGPTGVGKTELCKTLS 439
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: 388 KRVVGQDEAISAVSNAIRRSRSGLSDAKRPYGSFMFLGPTGVGKTELCKTLSACIFNNEE 447
VVGQ + + NAI + L+ A +F GP GVGKT + L+ I N+
Sbjct: 17 DDVVGQSHITNTLLNAIENNH--LAQA------LLFCGPRGVGKTTCARILARKI--NQP 66
Query: 448 SIIRIDMSEFIEKHSISRLIGAPPGYIGYEEGGYLTEIVRRKP----YSLILLDEIEKAN 503
D +I L A ++ L + VR P Y + ++DE+ +
Sbjct: 67 G---YDDPNEDFSFNIFELDAASNN--SVDDIRNLIDQVRIPPQTGKYKIYIIDEVHMLS 121
Query: 504 SDVFNILLQILDD 516
S FN L+ L++
Sbjct: 122 SAAFNAFLKTLEE 134
>gnl|CDD|223540 COG0464, SpoVK, ATPases of the AAA+ class [Posttranslational
modification, protein turnover, chaperones].
Length = 494
Score = 36.0 bits (83), Expect = 0.089
Identities = 69/445 (15%), Positives = 134/445 (30%), Gaps = 94/445 (21%)
Query: 209 DEAAAKIKIEIDSKPEIMDK------LERRLIQLKIEHEA----IKREYDESSKKRLLLI 258
A + + PEI+ K L R + + E A E D + KR
Sbjct: 37 ALANEGAEFLSINGPEILSKYVGESELRLRELFEEAEKLAPSIIFIDEIDALAPKRSSDQ 96
Query: 259 KKEINKLEIKYANLEKIWKYEKTLIKDSQQIKEEIEKVRLKINKATRKSDWQTVSKLKYG 318
+ ++ + L K + ++ + + ++ + + + R+ +
Sbjct: 97 GEVERRVVAQLLALMDGLKRGQVIVIGATNRPDGLDPAKRRPGRFDREIEVNLPD----- 151
Query: 319 ELNKLERILKEKSQKDIQLPNNANKFTLLKTK---------VGSEEIAEIVSRTTGIPVS 369
IL+ ++ P K +T + E + R +
Sbjct: 152 -EAGRLEILQIHTRLMFLGPPGTGKTLAARTVGKSGADLGALAKEAALRELRRAIDLVGE 210
Query: 370 KIVQVEREKLLNIENLLCKRVV-------------GQDEAIS----AVSNAIRRSRSGLS 412
I E + ++ +L R V G +EA A+ ++R
Sbjct: 211 YIGVTEDDFEEALKKVLPSRGVLFEDEDVTLDDIGGLEEAKEELKEAIETPLKRPELFRK 270
Query: 413 DAKRPYGSFMFLGPTGVGKTELCKTLSACIFNNEES-IIRIDMSEFIEKHSISRLIGAPP 471
RP + GP G GKT L+ + S I + SE + K
Sbjct: 271 LGLRPPKGVLLYGPPGTGKT----LLAKAVALESRSRFISVKGSELLSK----------- 315
Query: 472 GYIGYEEGGYLTEIVRRKPYSL----ILLDEIEK-----------ANSDVFNILLQILDD 516
++G E + K L I +DEI+ + V LL LD
Sbjct: 316 -WVG--ESEKNIRELFEKARKLAPSIIFIDEIDSLASGRGPSEDGSGRRVVGQLLTELDG 372
Query: 517 GRLTDNRGRTINFRNTIIVMTSNLGSDKIKEMEKGDKEIIKLAVMNEVKIYFRPEFINRI 576
+ +++ +N + D +++ + + P+ R+
Sbjct: 373 IEKAEGV---------LVIAATN-------RPDDLDPALLRPGRFDRLIYVPLPDLEERL 416
Query: 577 DDIIVFRYLNRKNILSIANIQLNIL 601
+ I +L K ++ L L
Sbjct: 417 E--IFKIHLRDKKPPLAEDVDLEEL 439
Score = 36.0 bits (83), Expect = 0.100
Identities = 48/205 (23%), Positives = 82/205 (40%), Gaps = 36/205 (17%)
Query: 18 LIGEPGVGKTAIVEGLAQRIINGEVPNSLLSKKILLLDIALLLAGTKYRGEFEDRLKKIL 77
L G PG GKT + + +A + + + + LL +K+ GE E ++++
Sbjct: 281 LYGPPGTGKTLLAKAVAL----------ESRSRFISVKGSELL--SKWVGESEKNIRELF 328
Query: 78 KEISNNQKDIIIFIDELHTMI---GTGKVEGSIDAGNMLKPELSRGE----LHCIGATTL 130
++ + IIFIDE+ ++ G + L EL E + I AT
Sbjct: 329 EK-ARKLAPSIIFIDEIDSLASGRGPSEDGSGRRVVGQLLTELDGIEKAEGVLVIAAT-- 385
Query: 131 NEYRQYIEKDAAFER--RFQK-ILVEEPDIEETISILRGLQKKYEVHHGVEITDPAIVAA 187
+ D A R RF + I V PD+EE + I + + + + E D +A
Sbjct: 386 -NRPDDL--DPALLRPGRFDRLIYVPLPDLEERLEIFK-IHLRDKKPPLAEDVDLEELA- 440
Query: 188 SELSYRYISDRFMPDKAIDLIDEAA 212
I++ + L+ EAA
Sbjct: 441 ------EITEGYSGADIAALVREAA 459
Score = 32.1 bits (73), Expect = 1.5
Identities = 50/164 (30%), Positives = 69/164 (42%), Gaps = 28/164 (17%)
Query: 13 TSNPVLIGEPGVGKTAIVEGLAQRIINGEVPNSLLSKKILLLDIALLLAGTKYRGEFEDR 72
+L G PG GKT + LA G S+ +IL +KY GE E R
Sbjct: 18 PKGVLLHGPPGTGKTLLARALANE---GAEFLSINGPEIL----------SKYVGESELR 64
Query: 73 LKKILKEISNNQKDIIIFIDELHTMIG-----TGKVEGSIDAG-NMLKPELSRGELHCIG 126
L+++ +E IIFIDE+ + G+VE + A L L RG++ IG
Sbjct: 65 LRELFEEAEKLAP-SIIFIDEIDALAPKRSSDQGEVERRVVAQLLALMDGLKRGQVIVIG 123
Query: 127 ATTLNEYRQYIEKDAAFER--RFQK-ILVEEPDIEETISILRGL 167
AT + D A R RF + I V PD + IL+
Sbjct: 124 AT-----NRPDGLDPAKRRPGRFDREIEVNLPDEAGRLEILQIH 162
>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 = 35.3 bits (82), Expect = 0.098
Identities = 22/64 (34%), Positives = 36/64 (56%), Gaps = 5/64 (7%)
Query: 635 DVHGCKKSLSILLKKIHKKSPEANFIFLGDLINKGPQSLDT--LRMVYSMRNYAKIVL-- 690
D+HG L L + + P+ N++FLGD +++G S++T L + +R +I L
Sbjct: 49 DIHGQFYDLLELFR-VGGDPPDTNYLFLGDYVDRGYYSVETFLLLLALKVRYPDRITLLR 107
Query: 691 GNHE 694
GNHE
Sbjct: 108 GNHE 111
>gnl|CDD|235175 PRK03918, PRK03918, chromosome segregation protein; Provisional.
Length = 880
Score = 35.8 bits (83), Expect = 0.11
Identities = 27/133 (20%), Positives = 62/133 (46%), Gaps = 15/133 (11%)
Query: 208 IDEAAAKIKIEIDSKPEIMDKLERRLIQLKIEHEAIKREYDE---------SSKKRLLLI 258
I+E + + E++ ++++ L +L+ E E +++E E +K L +
Sbjct: 191 IEELIKEKEKELEEVLREINEISSELPELREELEKLEKEVKELEELKEEIEELEKELESL 250
Query: 259 KKEINKLEIKYANLEKIWKYEKTLIKDSQQIKEEIEKVRLKINKATRKSDWQTVSKLKYG 318
+ KLE K LE+ + K I++ ++ +E+++++ K ++ +S+
Sbjct: 251 EGSKRKLEEKIRELEERIEELKKEIEELEEKVKELKELKEK------AEEYIKLSEFYEE 304
Query: 319 ELNKLERILKEKS 331
L++L I K S
Sbjct: 305 YLDELREIEKRLS 317
Score = 35.8 bits (83), Expect = 0.11
Identities = 60/277 (21%), Positives = 131/277 (47%), Gaps = 27/277 (9%)
Query: 63 TKYRGEFEDRLKKILKEISNNQKDIIIFIDELHTMIGTGKVEGSIDAGNMLKPELSRGEL 122
+ G ++L+K L+E+ +++I I ++ IG K E + + + ++G+
Sbjct: 379 KRLTGLTPEKLEKELEELEKAKEEIEEEISKITARIGELKKEIKELKKAIEELKKAKGKC 438
Query: 123 HCIGATTLNEYRQYIEKDAAFERRFQKILVEEPDIEETISILRGLQKKYEVHHGVEITDP 182
G E+R+ + ++ + ++I E +IEE LR ++ E
Sbjct: 439 PVCGRELTEEHRKELLEE--YTAELKRIEKELKEIEEKERKLRKELRELEK--------- 487
Query: 183 AIVAASELSYRYISDRFMPDKAIDLIDEAAAKIKI----EIDSKPEIMDKLERRLIQLKI 238
+ SEL + + + E K+K E++ K E +KL+ +LI+LK
Sbjct: 488 VLKKESELIKLK--------ELAEQLKELEEKLKKYNLEELEKKAEEYEKLKEKLIKLKG 539
Query: 239 EHEAIKREYDESS--KKRLLLIKKEINKLEIKYANLEKIWKYEKTLIKDSQQIKEEIEKV 296
E +++K+E ++ KK+L ++K++++LE + A L K + E+ + ++++E ++++
Sbjct: 540 EIKSLKKELEKLEELKKKLAELEKKLDELEEELAELLK--ELEELGFESVEELEERLKEL 597
Query: 297 RLKINKATRKSDWQTVSKLKYGELNKLERILKEKSQK 333
N+ D + + + EL KLE L + ++
Sbjct: 598 EPFYNEYLELKDAEKELEREEKELKKLEEELDKAFEE 634
Score = 32.7 bits (75), Expect = 1.1
Identities = 24/94 (25%), Positives = 50/94 (53%), Gaps = 4/94 (4%)
Query: 213 AKIKIEIDSKPEIMDKLERRLIQLKIEHEAIKREYDESS----KKRLLLIKKEINKLEIK 268
K++ E+D E + + E+RL +L+ E E ++++Y E ++ L + +E+ L +
Sbjct: 622 KKLEEELDKAFEELAETEKRLEELRKELEELEKKYSEEEYEELREEYLELSRELAGLRAE 681
Query: 269 YANLEKIWKYEKTLIKDSQQIKEEIEKVRLKINK 302
LEK + K ++ ++ EE EK + ++ K
Sbjct: 682 LEELEKRREEIKKTLEKLKEELEEREKAKKELEK 715
Score = 30.4 bits (69), Expect = 5.9
Identities = 23/91 (25%), Positives = 50/91 (54%), Gaps = 7/91 (7%)
Query: 218 EIDSKPEIMDKLERRLIQLKIEHEAIKREYDESSKKRLLL-----IKKEINKLEIKYANL 272
I+ + + +++ E RL +LK + + +++ +E ++ L K+E+ +L+ + L
Sbjct: 325 GIEERIKELEEKEERLEELKKKLKELEKRLEELEERHELYEEAKAKKEELERLKKRLTGL 384
Query: 273 --EKIWKYEKTLIKDSQQIKEEIEKVRLKIN 301
EK+ K + L K ++I+EEI K+ +I
Sbjct: 385 TPEKLEKELEELEKAKEEIEEEISKITARIG 415
>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: 569 RPEFINRIDDIIVFRYLNRKNILSIANIQLNILKNK--LLKMNMDLKISKAALKKISNIG 626
+P D F N IL + + +I K + +L++ +KI
Sbjct: 7 KPRIWKPPTDRRFF--FNWNEILELCDAAEDIFKQEPMVLRLRAPIKI------------ 52
Query: 627 FDLIYGARDVHGCKKSLSILLKKIHKKSPEA-------NFIFLGDLINKGPQSLDTLRMV 679
+G D+HG L L + EA +++FLGD +++G SL+T+ ++
Sbjct: 53 ----FG--DIHGQFGDLMRLFDEYGSPVTEAAGDIEYIDYLFLGDYVDRGSNSLETICLL 106
Query: 680 YSMR----NYAKIVLGNHEIHLLDVL----ININKKSKLDTFDDILDAPDKKKLVSWLRT 731
+++ N ++ GNHE ++ L ++ D D +L WL
Sbjct: 107 LALKVKYPNQIHLIRGNHEDRDINALFGFREECKERLGEDPNDGDSVWRRINRLFEWL-- 164
Query: 732 QPL-AIYYKKYLMIHAGVAKQWTAQQTIKLSHQVEKILR 769
PL AI K L +H G+ + +I ++E + R
Sbjct: 165 -PLAAIIEDKILCMHGGIGR------SINHVSEIEDLKR 196
>gnl|CDD|237177 PRK12704, PRK12704, phosphodiesterase; Provisional.
Length = 520
Score = 35.5 bits (83), Expect = 0.12
Identities = 27/121 (22%), Positives = 59/121 (48%), Gaps = 14/121 (11%)
Query: 210 EAAAKIKIEIDSKPEIMDKLERRLIQLKIEHEAIKREYDESSKKRLLLIKKEINKLEIKY 269
E AK +E ++K E + L++ K E ++ E+++ ++R ++K +L K
Sbjct: 37 EEEAKRILE-EAKKEAEAIKKEALLEAKEEIHKLRNEFEKELRERRNELQKLEKRLLQKE 95
Query: 270 ANLEK----IWKYEKTLIKDSQQIKEEIEKVRLKINKATRKSDWQTVSKLKYGELNKLER 325
NL++ + K E+ L K ++++++ +++ K + + Q L +LER
Sbjct: 96 ENLDRKLELLEKREEELEKKEKELEQKQQELEKKEEELEELIEEQ---------LQELER 146
Query: 326 I 326
I
Sbjct: 147 I 147
Score = 32.1 bits (74), Expect = 1.6
Identities = 21/96 (21%), Positives = 50/96 (52%), Gaps = 9/96 (9%)
Query: 219 IDSKPEIMDKLERRLIQLKIEHEAIKREYDESSKKRLLLIKKEINKLEIKYANLEK---- 274
+D K E+++K E L + + E E ++E ++ ++ LI++++ +LE + + L
Sbjct: 98 LDRKLELLEKREEELEKKEKELEQKQQELEKKEEELEELIEEQLQELE-RISGLTAEEAK 156
Query: 275 ---IWKYEKTLIKD-SQQIKEEIEKVRLKINKATRK 306
+ K E+ + + IKE E+ + + +K ++
Sbjct: 157 EILLEKVEEEARHEAAVLIKEIEEEAKEEADKKAKE 192
>gnl|CDD|227355 COG5022, COG5022, Myosin heavy chain [Cytoskeleton].
Length = 1463
Score = 35.8 bits (83), Expect = 0.14
Identities = 25/128 (19%), Positives = 53/128 (41%), Gaps = 11/128 (8%)
Query: 224 EIMDKLERRLIQLKIEHEAIKREYDESSK--KRLLLIKKEINKLEIK--YANLEKIWKYE 279
+ ++ ER+L +LKI+ ++I + + ++ +KK ++ I+ E I + +
Sbjct: 875 QRVELAERQLQELKIDVKSISSLKLVNLELESEIIELKKSLSSDLIENLEFKTELIARLK 934
Query: 280 KTL----IKDSQQIKEEIEKVRLKINKATRKSDWQTVSKLKYGELNKLERILKEKSQKDI 335
K L +++ I+ K++ +S + S+ L K IL + K
Sbjct: 935 KLLNNIDLEEGPSIEYVKLPELNKLH--EVESKLKETSEEYEDLLKKST-ILVREGNKAN 991
Query: 336 QLPNNANK 343
N K
Sbjct: 992 SELKNFKK 999
>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 = 0.14
Identities = 15/53 (28%), Positives = 28/53 (52%), Gaps = 8/53 (15%)
Query: 390 VVGQDEAISAVSNAIRRSRSGLSDAKRPYGSFMFLGPTGVGKTELCKTLSACI 442
V+GQ+ + + NAI+ R ++ A ++F GP G GKT + + + +
Sbjct: 16 VIGQEHIVQTLKNAIKNGR--IAHA------YLFSGPRGTGKTSIARIFAKAL 60
>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: 203 KAIDLIDEAAAKIKIEIDSKPEIMDKLERRLIQLKIEHEAIKREYDESSKKRLLLIKKEI 262
K + + E +I+ +I+ + + KLE ++ QL+ E E + E +++ K L K++
Sbjct: 81 KGVFTLGEENIEIEAQIEELKKELKKLEEKIEQLEAEIEKKEEELEKAKNKFLDKAWKKL 140
Query: 263 NKLEIKYANLEKIWKYEKTLIKDSQQIKEEIEKVRLKINKATRKSDWQTVSKLKYGELNK 322
K NL + K +++ +E++ V +N ++ S EL
Sbjct: 141 AKKYDS--NLSEALKGLNYKKNFKEKLLKELKSV--ILNASSLLSL---------EELKA 187
Query: 323 LERILKEKSQKDIQLPN-------NANKFTLLKTKV---GSEEIAEIVSR 362
+ L ++ ++ L + +L+ + I+E+++
Sbjct: 188 KIKTLFSSNKPELALLTLSVIDFDEIEQAEILEKSIIGSSDVPISELINN 237
>gnl|CDD|237354 PRK13341, PRK13341, recombination factor protein RarA/unknown
domain fusion protein; Reviewed.
Length = 725
Score = 35.4 bits (82), Expect = 0.17
Identities = 40/128 (31%), Positives = 54/128 (42%), Gaps = 39/128 (30%)
Query: 14 SNPVLIGEPGVGKTAIVEGLAQRII----NGEVPNSLLSKKILLLDIALLLAGTK-YRGE 68
+ +L G PGVGKT LA RII + +LAG K R E
Sbjct: 53 GSLILYGPPGVGKTT----LA-RIIANHTRAHF-----------SSLNAVLAGVKDLRAE 96
Query: 69 FE---DRLKKILKEISNNQKDIIIFIDELHTMIGTGKVEGSIDAGNMLKPELSRGELHCI 125
+ +RL++ + K I+FIDE+H + DA L P + G + I
Sbjct: 97 VDRAKERLER-------HGKRTILFIDEVHRFNKAQQ-----DA---LLPWVENGTITLI 141
Query: 126 GATTLNEY 133
GATT N Y
Sbjct: 142 GATTENPY 149
>gnl|CDD|236333 PRK08691, PRK08691, DNA polymerase III subunits gamma and tau;
Validated.
Length = 709
Score = 35.1 bits (80), Expect = 0.22
Identities = 32/140 (22%), Positives = 59/140 (42%), Gaps = 25/140 (17%)
Query: 390 VVGQDEAISAVSNAIRRSRSGLSDAKRPYGSFMFLGPTGVGKTELCKTLSACIFNNE--- 446
+VGQ+ + A+ NA+ D R + +++ G GVGKT + + L+ + N E
Sbjct: 18 LVGQEHVVKALQNAL--------DEGRLHHAYLLTGTRGVGKTTIARILAKSL-NCENAQ 68
Query: 447 --------ESIIRIDMSEFIEKHSISRLIGAPPGYIG--YEEGGYLTEIVRRKPYSLILL 496
+S +ID +++ I I E Y + K Y ++
Sbjct: 69 HGEPCGVCQSCTQIDAGRYVDLLEIDAASNTGIDNIREVLENAQYAPTAGKYKVY---II 125
Query: 497 DEIEKANSDVFNILLQILDD 516
DE+ + FN +L+ L++
Sbjct: 126 DEVHMLSKSAFNAMLKTLEE 145
>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 = 0.22
Identities = 22/93 (23%), Positives = 42/93 (45%), Gaps = 4/93 (4%)
Query: 294 EKVRLKINKATRKSDWQTVSKLKYGELNKLERILKEKSQKDIQLPNNANKFTLLKTKVGS 353
EK R K+ + ++S + + +LK +K+E+ + A+KF LK +
Sbjct: 2 EKYRSKLLQKAKESGLEFIERLKKALKDKIEKKEFSAKKPPTGPSKQASKFKTLKPPKPA 61
Query: 354 EEIAEIVSRTTGI-PVSKIVQVEREKLLNIENL 385
++ P+S I+ VE+ K L+ E +
Sbjct: 62 DKKK---PFDKPFKPLSSILDVEKIKDLSAEEI 91
>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication,
recombination, and repair].
Length = 908
Score = 35.1 bits (81), Expect = 0.22
Identities = 41/284 (14%), Positives = 105/284 (36%), Gaps = 27/284 (9%)
Query: 68 EFEDRLKKILKEISNNQKDIIIFIDELHTMIGTGKVEGSIDAGNMLKPELSRGELHCIGA 127
E E+ L ++L+ ++++ +++L ++ + LK EL + E
Sbjct: 512 ELEEELIELLELEEALKEELEEKLEKLENLLEELEELKEKLQLQQLKEELRQLEDRLQEL 571
Query: 128 TTLNEY----RQYIEKDAAFERRFQKILVEEPDIEETISILRGLQKKYEVHHGVEITDPA 183
L E R E+ R +++ + ++EE +S L L + E+ + A
Sbjct: 572 KELLEELRLLRTRKEELEELRERLKELKKKLKELEERLSQLEELLQSLELSEAENELEEA 631
Query: 184 IVAASELSYRYISDRFMPDKAIDLIDEAAAKIKIEIDSKPEIMDKLERRLIQLKIEHEAI 243
++ ++ A ++ + E+ +K+E +++ E + I
Sbjct: 632 EEELESE--------------LEKLNLQAELEELLQAALEELEEKVEELEAEIRRELQRI 677
Query: 244 KREYDESSKKRLLLIKKEINKLEIKYANLEKIWKYEKTLIKDSQQIKEEIEKVRLKINKA 303
+ E E +++L +++ +LE LE++ K + + ++++ ++ +
Sbjct: 678 ENE--EQLEEKLEELEQLEEELEQLREELEELLKKLGEIEQLIEELESRKAELEELKKEL 735
Query: 304 TRKSDWQTVSKLKYGELNKLERILKEKSQKDIQLPNNANKFTLL 347
+ L +L L + + L N +
Sbjct: 736 EKLEK-------ALELLEELREKLGKAGLRADILRNLLAQIEAE 772
Score = 34.4 bits (79), Expect = 0.33
Identities = 29/144 (20%), Positives = 66/144 (45%), Gaps = 5/144 (3%)
Query: 205 IDLIDEAAAKIKIEIDSKPEIMDKLERRLIQLKIEHEAIKREYDESSKKRLLLIKKEINK 264
++ ++ + +K + E K+E QL E I+ + ++ L K E +
Sbjct: 166 LEKYEKLSELLK---EVIKEAKAKIEELEGQLSELLEDIEDLLEALEEELKELKKLEEIQ 222
Query: 265 LEIKYANLEKIWKYEKTLIKDSQQIKEEIEKVRLKINKATRKSDWQTVSKLKYGELNKLE 324
E + LE+ + + + + ++ KE +E+++ ++ +S K++ EL +LE
Sbjct: 223 EEQEEEELEQEIEALEERLAELEEEKERLEELKARL--LEIESLELEALKIREEELRELE 280
Query: 325 RILKEKSQKDIQLPNNANKFTLLK 348
R+L+E +K +L + L+
Sbjct: 281 RLLEELEEKIERLEELEREIEELE 304
Score = 32.4 bits (74), Expect = 1.3
Identities = 26/154 (16%), Positives = 57/154 (37%), Gaps = 14/154 (9%)
Query: 209 DEAAAKIKIEIDSKPEIMDKLERRLIQLKIEHE-----AIKREYD--ESSKKRLLLIKKE 261
E + + E ++KLE L +L+ E +K E E + L + +E
Sbjct: 518 IELLELEEALKEELEEKLEKLENLLEELEELKEKLQLQQLKEELRQLEDRLQELKELLEE 577
Query: 262 INKLEIKYANLEKIWKYEKTLIKDSQQIKEEIEKVRLKINKATRKSDWQTVSKLKYGELN 321
+ L + LE++ + K L K ++++E + ++ + ++L+
Sbjct: 578 LRLLRTRKEELEELRERLKELKKKLKELEERLSQLEELLQSLELSEAE---NELE----E 630
Query: 322 KLERILKEKSQKDIQLPNNANKFTLLKTKVGSEE 355
E + E + ++Q L+ E
Sbjct: 631 AEEELESELEKLNLQAELEELLQAALEELEEKVE 664
Score = 32.0 bits (73), Expect = 1.6
Identities = 32/180 (17%), Positives = 80/180 (44%), Gaps = 24/180 (13%)
Query: 202 DKAIDLIDEAAAKIKIEIDSKPEIMDKLERRLIQLKIEHEAIKREYDESSKKRLLLIKKE 261
+ + ++EA ++K E+ +++++ L +L+ E E ++RE +E ++ + ++++
Sbjct: 381 LERLKQLEEAIQELKEELAELSAALEEIQEELEELEKELEELERELEEL-EEEIKKLEEQ 439
Query: 262 INKLEIKYANLEKIWK-----------------------YEKTLIKDSQQIKEEIEKVRL 298
IN+LE K + ++ YE L + +++ E E+ L
Sbjct: 440 INQLESKELMIAELAGAGEKCPVCGQELPEEHEKELLELYELELEELEEELSREKEEAEL 499
Query: 299 KINKATRKSDWQTVSKLKYGELNKLERILKEKSQKDIQLPNNANKFTLLKTKVGSEEIAE 358
+ + + + + + L E + +E +K +L N + LK K+ +++ E
Sbjct: 500 REEIEELEKELRELEEELIELLELEEALKEELEEKLEKLENLLEELEELKEKLQLQQLKE 559
>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 = 0.23
Identities = 22/83 (26%), Positives = 40/83 (48%), Gaps = 9/83 (10%)
Query: 232 RLIQLKIEHEAIKREYDESSKKRLLLIKK---EINKLEIKYANLEKIW-----KYEKTLI 283
+L L + K+ Y E ++ KK E+ KL+ +Y L + + K+E+ ++
Sbjct: 95 KLTLLIKDKRKAKKAYQEERQQIDEQYKKLTDEVEKLKSEYQKLLEDYKAAKSKFEEAVV 154
Query: 284 KDSQQIKEEIEKVRLKINKATRK 306
K + +++K R K KA RK
Sbjct: 155 K-GGRGGRKLDKARDKYQKACRK 176
>gnl|CDD|237057 PRK12323, PRK12323, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 700
Score = 34.9 bits (80), Expect = 0.24
Identities = 15/49 (30%), Positives = 29/49 (59%), Gaps = 8/49 (16%)
Query: 391 VGQDEAISAVSNAIRRSRSGLSDAKRPYGSFMFLGPTGVGKTELCKTLS 439
VGQ+ + A+++A+ + +R + +++F G GVGKT L + L+
Sbjct: 19 VGQEHVVRALTHAL--------EQQRLHHAYLFTGTRGVGKTTLSRILA 59
>gnl|CDD|184920 PRK14956, PRK14956, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 484
Score = 34.5 bits (79), Expect = 0.25
Identities = 39/137 (28%), Positives = 62/137 (45%), Gaps = 19/137 (13%)
Query: 390 VVGQDEAISAVSNAIRRSRSGLSDAKRPYGSFMFLGPTGVGKTELCKTLSACIFNNEESI 449
V+ QD AI A+ NA++ + G +++F GP GVGKT + + L A N E I
Sbjct: 20 VIHQDLAIGALQNALKSGKIG--------HAYIFFGPRGVGKTTIARIL-AKRLNCENPI 70
Query: 450 IRIDMSEFIEKHSISRLIGAPPGYI------GYEEGGYLTEIVRRKP----YSLILLDEI 499
+E I++ I + I G E L + V+ P Y + ++DE+
Sbjct: 71 GNEPCNECTSCLEITKGISSDVLEIDAASNRGIENIRELRDNVKFAPMGGKYKVYIIDEV 130
Query: 500 EKANSDVFNILLQILDD 516
FN LL+ L++
Sbjct: 131 HMLTDQSFNALLKTLEE 147
>gnl|CDD|130309 TIGR01242, 26Sp45, 26S proteasome subunit P45 family. Many
proteins may score above the trusted cutoff because an
internal.
Length = 364
Score = 34.4 bits (79), Expect = 0.27
Identities = 28/88 (31%), Positives = 40/88 (45%), Gaps = 22/88 (25%)
Query: 417 PYGSFMFLGPTGVGKTELCKTLSACIFNNEESIIRIDMSEFIEKHSISRLIGAPPGYIGY 476
P G ++ GP G GKT L K ++ + IR+ SE + K YIG
Sbjct: 156 PKGVLLY-GPPGTGKTLLAKAVAH---ETNATFIRVVGSELVRK------------YIG- 198
Query: 477 EEGGYLT----EIVRRKPYSLILLDEIE 500
EG L E+ + K S+I +DEI+
Sbjct: 199 -EGARLVREIFELAKEKAPSIIFIDEID 225
>gnl|CDD|235570 PRK05703, flhF, flagellar biosynthesis regulator FlhF; Validated.
Length = 424
Score = 34.1 bits (79), Expect = 0.34
Identities = 40/198 (20%), Positives = 78/198 (39%), Gaps = 28/198 (14%)
Query: 241 EAIKREYDESSKKRLLLIKKEINKLEIKYANLEKIWKYEKTLIKDSQQIKEEIEKVRLKI 300
+ RE K +L ++ + K + + + + + E L + +++++ E +
Sbjct: 60 NPVLREEKRKPAKSILSLQALLEKRPSRTNSQDALLQAENALPEWKKELEKPSEPKEEEP 119
Query: 301 NK-ATRKSDWQTVSKLKYGELNKLERILKEKSQKDIQL----PNNANKFTLLKTKVG-SE 354
A K + + +L+ EL +L+ +L+++ Q+ P A + LK + G S
Sbjct: 120 KAAAESKVVQKELDELR-DELKELKNLLEDQLSGLRQVERIPPEFAELYKRLK-RSGLSP 177
Query: 355 EIAEIVSRTTGIPVSKIVQVEREKLLNIENLLCKRVVGQDEAISAVSNAIRRSRSGLSDA 414
EIAE + + + + LL LL + + E I +
Sbjct: 178 EIAEKLLKLLLEHMPPRERTAWRYLLE---LLANMIPVRVEDILKQGGVV---------- 224
Query: 415 KRPYGSFMFLGPTGVGKT 432
+GPTGVGKT
Sbjct: 225 -------ALVGPTGVGKT 235
>gnl|CDD|235503 PRK05561, PRK05561, DNA topoisomerase IV subunit A; Validated.
Length = 742
Score = 34.3 bits (80), Expect = 0.36
Identities = 29/107 (27%), Positives = 42/107 (39%), Gaps = 30/107 (28%)
Query: 203 KAIDLIDEAAAKIKIEIDSKPEIMDK-----------LERRLIQL-KIEHEAIKREYDES 250
A IDE I+ + K +M + LE RL +L K+E I++E DE
Sbjct: 390 IAFLNIDEVIRIIRESDEPKANLMARFDLSEIQAEAILELRLRRLAKLEEIEIRKEQDEL 449
Query: 251 SKKRLLLIKKEINKLEIKYANLEKIWKYEKTLIKDSQQIKEEIEKVR 297
K+ A LE I E+ L K IK+E++
Sbjct: 450 RKEI---------------AELEAILASERKLRK---LIKKELKADA 478
>gnl|CDD|223250 COG0172, SerS, Seryl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 429
Score = 34.1 bits (79), Expect = 0.37
Identities = 16/73 (21%), Positives = 37/73 (50%)
Query: 228 KLERRLIQLKIEHEAIKREYDESSKKRLLLIKKEINKLEIKYANLEKIWKYEKTLIKDSQ 287
+L+ +L E E ++ E +E SK+ +K+ + E A ++++ + K L
Sbjct: 33 ELDEERRKLLRELEELQAERNELSKEIGRALKRGEDDAEELIAEVKELKEKLKELEAALD 92
Query: 288 QIKEEIEKVRLKI 300
+++ E++ + L I
Sbjct: 93 ELEAELDTLLLTI 105
>gnl|CDD|237865 PRK14951, PRK14951, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 618
Score = 33.9 bits (78), Expect = 0.38
Identities = 17/48 (35%), Positives = 27/48 (56%), Gaps = 8/48 (16%)
Query: 391 VGQDEAISAVSNAIRRSRSGLSDAKRPYGSFMFLGPTGVGKTELCKTL 438
VGQ+ + A++NA+ + R L A ++F G GVGKT + + L
Sbjct: 19 VGQEHVVQALTNALTQQR--LHHA------YLFTGTRGVGKTTVSRIL 58
>gnl|CDD|226400 COG3883, COG3883, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 265
Score = 33.5 bits (77), Expect = 0.39
Identities = 29/171 (16%), Positives = 69/171 (40%), Gaps = 23/171 (13%)
Query: 203 KAIDLIDEAAAKIKIEIDSKPEIMDKLERRLIQLKIEHEAIK---REYDESSKKRL---- 255
I+ +D +I+ +ID + +D+ + + +L+ E +K E E KKR
Sbjct: 52 NEIESLDNQIEEIQSKIDELQKEIDQSKAEIKKLQKEIAELKENIVERQELLKKRARAMQ 111
Query: 256 -----------LLIKKEINKLEIKYANLEKIWKYEKTLIKDSQQIKEEIEKVRLKINKAT 304
+L K + L + + I +K +++ ++ K+ +E+ + +
Sbjct: 112 VNGTATSYIDVILNSKSFSDLISRVTAISVIVDADKKILEQQKEDKKSLEEKQAALEDKL 171
Query: 305 RKSDWQTVSKLKYGELNKLERILKEKSQKDIQLPNNANKFTLLKTKVGSEE 355
+T+ L+ +L + +K++K+ + A K + + E
Sbjct: 172 -----ETLVALQNELETQLNSLNSQKAEKNALIAALAAKEASALGEKAALE 217
>gnl|CDD|235871 PRK06835, PRK06835, DNA replication protein DnaC; Validated.
Length = 329
Score = 33.7 bits (78), Expect = 0.40
Identities = 21/84 (25%), Positives = 40/84 (47%), Gaps = 12/84 (14%)
Query: 224 EIMDKLERRLIQLKIEHEAIKREYDESSK-KRLLLIKKEINKLEIKYANLEKIWKYEKTL 282
EI+ + E+R + K E E R+ + K + I EI KL IK + + +
Sbjct: 8 EILKEYEKR--RDKEELELKNRKEEVYKKIPEIAEIDDEIAKLGIKLS---------RAI 56
Query: 283 IKDSQQIKEEIEKVRLKINKATRK 306
+K+ + +E +++++ KI K
Sbjct: 57 LKNPDKKEETLKELKEKITDLRVK 80
>gnl|CDD|140271 PTZ00244, PTZ00244, serine/threonine-protein phosphatase PP1;
Provisional.
Length = 294
Score = 33.3 bits (76), Expect = 0.43
Identities = 27/113 (23%), Positives = 57/113 (50%), Gaps = 18/113 (15%)
Query: 655 PEANFIFLGDLINKGPQSLDTLRMVYSMR-----NYAKIVLGNHEIHLLDVLININKKSK 709
P +N++FLGD +++G S++T+ + + + N+ ++ GNHE +INK
Sbjct: 78 PYSNYLFLGDYVDRGKHSVETITLQFCYKIVYPENFF-LLRGNHEC------ASINKMYG 130
Query: 710 LDTFDDILDAPDKKKLVSW---LRTQPL-AIYYKKYLMIHAGVAKQWTAQQTI 758
FDD+ + K ++ T P+ + +K + +H G++ T+ ++
Sbjct: 131 F--FDDVKRRYNIKLFKAFTDVFNTMPVCCVISEKIICMHGGLSPDLTSLASV 181
>gnl|CDD|237868 PRK14960, PRK14960, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 702
Score = 33.9 bits (77), Expect = 0.44
Identities = 17/53 (32%), Positives = 30/53 (56%), Gaps = 8/53 (15%)
Query: 390 VVGQDEAISAVSNAIRRSRSGLSDAKRPYGSFMFLGPTGVGKTELCKTLSACI 442
+VGQ+ A+S+A+ R R + +++F G GVGKT + + L+ C+
Sbjct: 17 LVGQNHVSRALSSALERGRL--------HHAYLFTGTRGVGKTTIARILAKCL 61
>gnl|CDD|184697 PRK14475, PRK14475, F0F1 ATP synthase subunit B; Provisional.
Length = 167
Score = 32.6 bits (74), Expect = 0.46
Identities = 12/39 (30%), Positives = 22/39 (56%)
Query: 208 IDEAAAKIKIEIDSKPEIMDKLERRLIQLKIEHEAIKRE 246
+D AAKI+ E+D + ++ + L +K E E +R+
Sbjct: 39 LDAYAAKIQAELDEAQRLREEAQALLADVKAEREEAERQ 77
>gnl|CDD|237864 PRK14950, PRK14950, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 585
Score = 33.6 bits (77), Expect = 0.47
Identities = 34/149 (22%), Positives = 55/149 (36%), Gaps = 42/149 (28%)
Query: 390 VVGQDEAISAVSNAIRRSRSGLSDAKRPYGSFMFLGPTGVGKT----------------- 432
+VGQ+ + + NAI R +++F GP GVGKT
Sbjct: 18 LVGQEHVVQTLRNAIAEGRVA--------HAYLFTGPRGVGKTSTARILAKAVNCTTNDP 69
Query: 433 --ELCKTLSACIFNNEES---IIRIDMSEFIEKHSISRLIGAPPGYIGYEEGGYLTEIVR 487
C T C E S +I +D + +I E + + R
Sbjct: 70 KGRPCGTCEMCRAIAEGSAVDVIEMDAASHTSVDDAREII---------ERVQFRPALAR 120
Query: 488 RKPYSLILLDEIEKANSDVFNILLQILDD 516
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 = 33.8 bits (78), Expect = 0.47
Identities = 37/176 (21%), Positives = 67/176 (38%), Gaps = 25/176 (14%)
Query: 203 KAIDLIDEAAAKIKIEIDSKPEIMDKLERRLIQLKIEHEAIKREYDESSKKRLLLIKKEI 262
A+ IDE I+ KPE ++L R + + EAI + +RL E
Sbjct: 384 IALLNIDEVIEIIRES-KDKPEAKEELMARFGLSEKQAEAIL----DLRLRRLT--GLEE 436
Query: 263 NKLEIKYANLEKIWKYEKTLI----KDSQQIKEEIEKVRLKINKATRKSDWQTVSKLKYG 318
K+E + LEK + ++ + IK+E+ +++ K R + + +
Sbjct: 437 EKIEKELKELEKEIADLEKILASEERLLDIIKKELLEIKKKFGDERR----TEIVEEEED 492
Query: 319 ELNKLERILKE-----KSQK--DIQLPN---NANKFTLLKTKVGSEEIAEIVSRTT 364
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 = 33.7 bits (77), Expect = 0.53
Identities = 16/43 (37%), Positives = 23/43 (53%), Gaps = 8/43 (18%)
Query: 390 VVGQDEAISAVSNAIRRSRSGLSDAKRPYGSFMFLGPTGVGKT 432
VVGQ+ + A+R+ R G +++F GP GVGKT
Sbjct: 16 VVGQEHVKEVLLAALRQGRLG--------HAYLFSGPRGVGKT 50
>gnl|CDD|224337 COG1419, FlhF, Flagellar GTP-binding protein [Cell motility and
secretion].
Length = 407
Score = 33.1 bits (76), Expect = 0.65
Identities = 34/217 (15%), Positives = 72/217 (33%), Gaps = 29/217 (13%)
Query: 243 IKREYDESSKKRLLLIKKE-------INKLEIKYANLEKIWKYEKTL--IKDSQQIKEEI 293
IK+ ES ++ + I+KE ++ IK + KT + + E+
Sbjct: 3 IKKFTAESMREAIEKIRKELGEDAVILSNRRIK-KGGFLGLLFSKTAVEVTKLAAVDSEL 61
Query: 294 EKVRLKINKATRKSDWQTVSKLKYGELNKLERILKE-----KSQKDIQLPNNANKFTLLK 348
K + + + ++ Q + + + + K+ S + + + +
Sbjct: 62 RKFQTREAAKVKDAEAQLLKDPA-EKKREERKAAKKIERSTPSLIERKTQEVKDSGEEIA 120
Query: 349 TKVGSEE--IAEIVSRTTGIPVSKIVQVEREKLLNIENLLCKR-VVGQDEAISAVSNAIR 405
+ E+ I E+ +++ LN+ N L + + + + S
Sbjct: 121 EMMRDEKVPIRELEEIPPEFVALYKQEIQSPTRLNLINELLRAGLELEILDMKDESYEDL 180
Query: 406 RSRSGL----------SDAKRPYGSFMFLGPTGVGKT 432
R S + +GPTGVGKT
Sbjct: 181 RYFSEKLRKLLLSLIENLIVEQKRVIALVGPTGVGKT 217
>gnl|CDD|153311 cd07627, BAR_Vps5p, The Bin/Amphiphysin/Rvs (BAR) domain of yeast
Sorting Nexin Vps5p. BAR domains are dimerization,
lipid binding and curvature sensing modules found in
many different proteins with diverse functions. Sorting
nexins (SNXs) are Phox homology (PX) domain containing
proteins that are involved in regulating membrane
traffic and protein sorting in the endosomal system.
SNXs differ from each other in their lipid-binding
specificity, subcellular localization and specific
function in the endocytic pathway. A subset of SNXs also
contain BAR domains. The PX-BAR structural unit
determines the specific membrane targeting of SNXs.
Vsp5p is the yeast counterpart of human SNX1 and is part
of the retromer complex, which functions in the
endosome-to-Golgi retrieval of vacuolar protein sorting
receptor Vps10p, the Golgi-resident membrane protein
A-ALP, and endopeptidase Kex2. BAR domains form dimers
that bind to membranes, induce membrane bending and
curvature, and may also be involved in protein-protein
interactions.
Length = 216
Score = 32.7 bits (75), Expect = 0.65
Identities = 19/71 (26%), Positives = 36/71 (50%), Gaps = 5/71 (7%)
Query: 255 LLLIKKEINKLEIKYANLEKIWKYEKTLIKDSQQIKEEIEKVRLKINKATRKSDWQTVSK 314
+ E++K K A LEK+ + KT + + E+E+ + ++ K +++ VS+
Sbjct: 117 WQSAESELSK---KKAQLEKLKRQGKTQQEKLNSLLSELEEAERRASEL--KKEFEEVSE 171
Query: 315 LKYGELNKLER 325
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 = 0.73
Identities = 35/140 (25%), Positives = 61/140 (43%), Gaps = 29/140 (20%)
Query: 390 VVGQDEAISAVSNAIRRSRSGLSDAKRPYGSFMFLGPTGVGKTELCKTLSACIFNNEESI 449
VVGQ+ + +SNA+ + R +++F GP GVGKT + + L+ + N E
Sbjct: 18 VVGQEHVVKTLSNAL--------ENGRIAHAYLFSGPRGVGKTTIARILAKAL-NCENGP 68
Query: 450 -----IRIDMSEFIEKHSISRLIGAPPGYI------GYEEGGYLTEIVRRKP----YSLI 494
+ + I + S+ +I I G ++ + E V P Y +
Sbjct: 69 TAEPCGKCISCKEINEGSLIDVI-----EIDAASNTGVDDIREIIEKVNYAPSEGRYKVY 123
Query: 495 LLDEIEKANSDVFNILLQIL 514
++DE+ + FN LL+ L
Sbjct: 124 IIDEVHMLSKQAFNALLKTL 143
>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 = 0.78
Identities = 33/167 (19%), Positives = 69/167 (41%), Gaps = 18/167 (10%)
Query: 206 DLIDEAAAK-IKIEIDSKPEIMDKL-----ERRLIQLKIEHEAIKREYDESSKKRLLLIK 259
DL E + +K+ K + ++ + ER+ + + E A K ++E+ + LL+
Sbjct: 557 DLAREEFQRRVKLLQLQKEKQLEDIQDCREERKSLSERAEKLAEK--FEEAKYNQELLVN 614
Query: 260 KEINKLEIKYANLEKIWKYEKTLIKDSQQIKEEIEKVRLKINKATRKSDWQTVSKLKYGE 319
+ L+ + L + E+ + K+ Q+I ++++ + I + +K ++Q
Sbjct: 615 RCKRLLQSANSQLPVLSDSERDMSKELQRINKQLQHLANGIKQVKKKKNYQRYHMASQES 674
Query: 320 LNKLERILKEKSQKDIQLPNNANKFTLLKTKVGSEEIAEIVSRTTGI 366
K L EK K I +LK E I ++ + I
Sbjct: 675 PKKSSYTLPEKQHKTIT--------EILKEL--GEHIDRMIKQIKRI 711
>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 = 0.78
Identities = 25/159 (15%), Positives = 63/159 (39%), Gaps = 20/159 (12%)
Query: 130 LNEYRQYIEKDAAFERRF---QKILVEEPDIEETISILRGLQKKYEVHHGVEITDPAIVA 186
+E E +A++ RF + +LV +PD+ +R K+++ + I+
Sbjct: 159 ADELGTLEEDPSAYQIRFGGYKGVLVVDPDLPGNEIHIRPSMLKFDLLGDAAVNSLEIIR 218
Query: 187 ASELSYRYISDRFM--------PDKA-IDLIDEAAAKIKIEIDS--------KPEIMDKL 229
+S+ + Y++ + + PD+ I+L+ EA ++ + + + +
Sbjct: 219 SSKPTPAYLNRQLITVLSTLGVPDEVFIELLREALKELAEALTDWDQALDLLRKQADEND 278
Query: 230 ERRLIQLKIEHEAIKREYDESSKKRLLLIKKEINKLEIK 268
++ + R+ + K L KE ++ +
Sbjct: 279 FTLTLRFMPSEDPFLRKLLRALVKHTLKKLKEKLRIPVP 317
>gnl|CDD|235422 PRK05342, clpX, ATP-dependent protease ATP-binding subunit ClpX;
Provisional.
Length = 412
Score = 32.4 bits (75), Expect = 0.98
Identities = 23/61 (37%), Positives = 31/61 (50%), Gaps = 15/61 (24%)
Query: 390 VVGQDEA---IS-AVSNAIRRSRSGLSD------AKRPYGS-FMFLGPTGVGKTELCKTL 438
V+GQ+ A +S AV N +R R G K S + +GPTG GKT L +TL
Sbjct: 73 VIGQERAKKVLSVAVYNHYKRLRHGDKKDDDVELQK----SNILLIGPTGSGKTLLAQTL 128
Query: 439 S 439
+
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 = 0.99
Identities = 34/107 (31%), Positives = 51/107 (47%), Gaps = 12/107 (11%)
Query: 202 DKAIDLIDEAAAKIKIEIDSKPEIMDKLERRLIQLKIE-----HEAIKR-EYDESSKKRL 255
D D ++AA + + PE +D+ RL+ L ++ EAI+ E S RL
Sbjct: 90 DDIADAAEDAAKLLLLRKPFIPEELDEEFLRLVDLSLKAAELLAEAIELLEDLLESADRL 149
Query: 256 LLIKKEINKLE-----IKYANLEKIWKYEKTL-IKDSQQIKEEIEKV 296
L I KEI LE I+ L+K++ E + D +KE IEK+
Sbjct: 150 LEIIKEIEALEHECDDIQRELLKKLFSLETEINPIDVIILKEIIEKI 196
>gnl|CDD|227278 COG4942, COG4942, Membrane-bound metallopeptidase [Cell division
and chromosome partitioning].
Length = 420
Score = 32.4 bits (74), Expect = 1.1
Identities = 20/93 (21%), Positives = 33/93 (35%), Gaps = 10/93 (10%)
Query: 224 EIMDKLERRLIQLKIEHEAIKREYDE---------SSKKRLLLIKKEINKLEIKY-ANLE 273
E +D L+ L QL I E E + + +L + +E K + + L
Sbjct: 161 ERIDALKATLKQLAAVRAEIAAEQAELTTLLSEQRAQQAKLAQLLEERKKTLAQLNSELS 220
Query: 274 KIWKYEKTLIKDSQQIKEEIEKVRLKINKATRK 306
K + L + ++K EI KA
Sbjct: 221 ADQKKLEELRANESRLKNEIASAEAAAAKAREA 253
>gnl|CDD|185140 PRK15218, PRK15218, fimbrial chaperone protein PegB; Provisional.
Length = 226
Score = 31.9 bits (72), Expect = 1.1
Identities = 12/29 (41%), Positives = 19/29 (65%)
Query: 549 EKGDKEIIKLAVMNEVKIYFRPEFINRID 577
E DK IIK A+ N +K+ +RP + ++D
Sbjct: 117 ENKDKNIIKFALQNRIKLIYRPPGVQKVD 145
>gnl|CDD|225165 COG2256, MGS1, ATPase related to the helicase subunit of the
Holliday junction resolvase [DNA replication,
recombination, and repair].
Length = 436
Score = 32.2 bits (74), Expect = 1.2
Identities = 29/123 (23%), Positives = 50/123 (40%), Gaps = 30/123 (24%)
Query: 14 SNPVLIGEPGVGKTAIVEGLAQRIINGEVPNSLLSKKILLLDIALLLAGTKYRGEFEDRL 73
+ +L G PG GKT + +A N ++ + +G K L
Sbjct: 49 HSMILWGPPGTGKTTLARLIAGT-TNAAF-----------EALSAVTSGVK-------DL 89
Query: 74 KKILKEISNNQ---KDIIIFIDELHTMIGTGKVEGSIDAGNMLKPELSRGELHCIGATTL 130
++I++E N+ + I+F+DE+H + + L P + G + IGATT
Sbjct: 90 REIIEEARKNRLLGRRTILFLDEIHRF--------NKAQQDALLPHVENGTIILIGATTE 141
Query: 131 NEY 133
N
Sbjct: 142 NPS 144
Score = 30.3 bits (69), Expect = 5.7
Identities = 34/142 (23%), Positives = 54/142 (38%), Gaps = 44/142 (30%)
Query: 390 VVGQDEAISAVSNAIRRSRSGLSDAKRPYGSFMFLGPTGVGKTELCK-----------TL 438
VVGQ+ + +RR +A S + GP G GKT L + L
Sbjct: 26 VVGQEHLLGE-GKPLRR----AVEAGHL-HSMILWGPPGTGKTTLARLIAGTTNAAFEAL 79
Query: 439 SACIFNNEESIIRIDMSEFIEKHSISRLIGAPPGYIGYEEGGYLTEIVRRKPYSLILLDE 498
SA + D+ E IE+ +RL+G R+ ++ LDE
Sbjct: 80 SAVTSGVK------DLREIIEEARKNRLLG-------------------RRT--ILFLDE 112
Query: 499 IEKANSDVFNILLQILDDGRLT 520
I + N + LL +++G +
Sbjct: 113 IHRFNKAQQDALLPHVENGTII 134
>gnl|CDD|237576 PRK13979, PRK13979, DNA topoisomerase IV subunit A; Provisional.
Length = 957
Score = 32.4 bits (74), Expect = 1.2
Identities = 37/120 (30%), Positives = 54/120 (45%), Gaps = 33/120 (27%)
Query: 203 KAIDLIDEAAAKI---KIEIDSKPEIMDK-----------LERRLIQLK-IEHEAIKREY 247
KAI ++DE I K + D+ +++K LE L +L +E A ++EY
Sbjct: 396 KAIGIMDEIIKTIRSSKSKKDASENLIEKFGFTDEQAEAILELMLYRLTGLEIVAFEKEY 455
Query: 248 DESSKKRLLLIKKEINKLEIKYANLEKIWKYEKTLIKDSQQIKEEIEKVRLKINKATRKS 307
E K LIKK L KI EK L+K IK+E+++V+ K R S
Sbjct: 456 KELEK----LIKK-----------LTKILSSEKELLK---VIKKELKEVKEKYGDERRTS 497
>gnl|CDD|237873 PRK14969, PRK14969, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 527
Score = 32.4 bits (74), Expect = 1.2
Identities = 16/49 (32%), Positives = 29/49 (59%), Gaps = 8/49 (16%)
Query: 391 VGQDEAISAVSNAIRRSRSGLSDAKRPYGSFMFLGPTGVGKTELCKTLS 439
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 = 1.2
Identities = 53/272 (19%), Positives = 102/272 (37%), Gaps = 38/272 (13%)
Query: 69 FEDRLKKILKEISNNQKDIIIFIDELHTMIGTGKVEGSIDAGNMLKPELSRGELHCIGAT 128
F +K I +S ++ ++ DEL GT EGS A ++L+ L + + T
Sbjct: 386 FSGHMKNISAILSKTTENSLVLFDELGA--GTDPDEGSALAISILE-YLLKQNAQVLITT 442
Query: 129 TLNEYRQYIEKDAAFERRFQKILVEEPDIEETISILRGLQKKYEVHHGVEITDPAIVAAS 188
E + + + E D E L Y++ G+ P A
Sbjct: 443 HYKELKALMYNNEGVEN-----ASVLFDEET-------LSPTYKLLKGI----PGESYAF 486
Query: 189 ELSYRYISDRFMPDKAIDL-------IDEAAAKIKIEIDSKPEIMDKLERRLIQLKIEHE 241
E++ RY F+ ++A I+ K+ + + LE+ L + + +
Sbjct: 487 EIAQRYGIPHFIIEQAKTFYGEFKEEINVLIEKLSALEKELEQKNEHLEKLLKEQEKLKK 546
Query: 242 AIKREYDESSKKRLLLIKKEINKLEIKYANLEKIWKYEKTLIKDSQQIKEEIEKVRLKIN 301
+++E +E L ++ K A + K L K+ + I E++ KI+
Sbjct: 547 ELEQEMEE-----LKERERNKKLELEKEAQ-----EALKALKKEVESIIRELK--EKKIH 594
Query: 302 KATRKSDWQTVSKLKYGELNKLERILKEKSQK 333
KA + + KLK + ++ ++ K
Sbjct: 595 KAKEIKSIEDLVKLKETKQKIPQKPTNFQADK 626
>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 = 32.1 bits (73), Expect = 1.2
Identities = 27/141 (19%), Positives = 51/141 (36%), Gaps = 23/141 (16%)
Query: 393 QDEAISAVSNAIRRSRSGLSDAKRPYGSFMFLGPTGVGKTELCKTLSAC-------IFNN 445
+ +A+ V+ R+ L + P GP G GKT L ++ I +
Sbjct: 3 ETDAVKRVT---SRALRYL-KSGYP---VHLRGPAGTGKTTLAMHVARKRDRPVMLINGD 55
Query: 446 EESIIRIDMSEFIEKHSISRLIGAPPGYIGYEE-------GGYLTEIVRRKPYSLILLDE 498
E + + + E+ LT V R+ ++L+ DE
Sbjct: 56 AELTTSDLVGSYAGYTRKKVHDQFIHNVVKLEDIVRQNWVDNRLTLAV-REGFTLV-YDE 113
Query: 499 IEKANSDVFNILLQILDDGRL 519
++ + N+LL + ++G L
Sbjct: 114 FTRSKPETNNVLLSVFEEGVL 134
>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 = 32.5 bits (74), Expect = 1.3
Identities = 25/126 (19%), Positives = 49/126 (38%), Gaps = 20/126 (15%)
Query: 229 LERRLIQLKIEHEAIKREYDESSKKRLLLIKKEINKLEIKYANLEKIWKYEKTLIKDSQQ 288
L+ +L+ L A+KR D + +L+ K KLEI + L + + L K Q+
Sbjct: 158 LQDKLLLLD---AAVKRH-DGNVITAVLIFLKRTLKLEILFQELAERQTALRHLSKHLQE 213
Query: 289 IKEEIEKVRLKINKATRKSDWQTVSKLKYGELNKLERILKEKSQKDIQLPNNANKFTLLK 348
E + ++L + + + +Y ++K+ + +Q + LK
Sbjct: 214 EGELQQLLKL----LRAEGESEKQELQQY----------RQKAHRILQSKE--KRINFLK 257
Query: 349 TKVGSE 354
E
Sbjct: 258 EGCLFE 263
>gnl|CDD|202101 pfam02050, FliJ, Flagellar FliJ protein.
Length = 122
Score = 30.7 bits (70), Expect = 1.3
Identities = 25/112 (22%), Positives = 49/112 (43%), Gaps = 8/112 (7%)
Query: 227 DKLERRLIQLKIEHEAIKREYDESSKKRLLLIKKEINKLEIKYANLEKIWK-YEKTLIKD 285
DK R L + + E E + + +E + RL ++ + A + ++ + L +
Sbjct: 1 DKAARNLAEAQQELEQAEEKLEELQQYRLEYRQQLSGSGQGISAAELRNYQAFISALDEA 60
Query: 286 SQQIKEEIEKVRLKINKATRKSDWQTVSKLKYGELNKLERILKEKSQKDIQL 337
Q ++E+E+ ++ +A + WQ E KLE L E+ +K Q
Sbjct: 61 IAQQQQELEQAEKQVEQA--REQWQ----EANQERKKLE-KLLEREKKKEQK 105
>gnl|CDD|237874 PRK14971, PRK14971, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 614
Score = 32.4 bits (74), Expect = 1.3
Identities = 39/153 (25%), Positives = 60/153 (39%), Gaps = 50/153 (32%)
Query: 390 VVGQDEAISAVSNAIRRSRSGLSDAKRPYGSFMFLGPTGVGKT----------------- 432
VVGQ+ + + NAI ++ L+ A ++F GP GVGKT
Sbjct: 19 VVGQEALTTTLKNAIATNK--LAHA------YLFCGPRGVGKTTCARIFAKTINCQNLTA 70
Query: 433 --ELCKTLSACI-FNNEES--IIRIDMSEFIEKHSISRLIGAPPGYIGYEEGGYLTEIVR 487
E C +C+ FN + S I +D + I LI E VR
Sbjct: 71 DGEACNECESCVAFNEQRSYNIHELDAASNNSVDDIRNLI----------------EQVR 114
Query: 488 RKP----YSLILLDEIEKANSDVFNILLQILDD 516
P Y + ++DE+ + FN L+ L++
Sbjct: 115 IPPQIGKYKIYIIDEVHMLSQAAFNAFLKTLEE 147
>gnl|CDD|224140 COG1219, ClpX, ATP-dependent protease Clp, ATPase subunit
[Posttranslational modification, protein turnover,
chaperones].
Length = 408
Score = 32.2 bits (74), Expect = 1.4
Identities = 19/56 (33%), Positives = 31/56 (55%), Gaps = 6/56 (10%)
Query: 390 VVGQDEA---IS-AVSNAIRRSRSGLSDAKRPYG--SFMFLGPTGVGKTELCKTLS 439
V+GQ++A +S AV N +R + + + + +GPTG GKT L +TL+
Sbjct: 63 VIGQEQAKKVLSVAVYNHYKRLNNKEDNDDVELSKSNILLIGPTGSGKTLLAQTLA 118
>gnl|CDD|224144 COG1223, COG1223, Predicted ATPase (AAA+ superfamily) [General
function prediction only].
Length = 368
Score = 32.1 bits (73), Expect = 1.4
Identities = 59/218 (27%), Positives = 88/218 (40%), Gaps = 38/218 (17%)
Query: 15 NPVLIGEPGVGKTAIVEGLAQRIINGEVPNSLLSKKILLLDIALLLAGTKYRGEFEDRLK 74
N + G PG GKT + + LA E LL K A L G ++ G+ R+
Sbjct: 153 NVLFYGPPGTGKTMMAKALA-----NEAKVPLLLVK------ATELIG-EHVGDGARRIH 200
Query: 75 KILKEISNNQKDIIIFIDELHTMIG--------TGKVEGSIDAGNMLKPELSR---GELH 123
+ L E + I+FIDEL I G V ++A L EL E
Sbjct: 201 E-LYERARKAAPCIVFIDELDA-IALDRRYQELRGDVSEIVNA---LLTELDGIKENEGV 255
Query: 124 C-IGATTLNEYRQYIEKDAAFERRFQ-KILVEEPDIEETISILRGLQKKYEVHHGVEITD 181
I AT E D A RF+ +I + P+ EE + IL KK+ + V+
Sbjct: 256 VTIAATNRPELL-----DPAIRSRFEEEIEFKLPNDEERLEILEYYAKKFPLP--VDADL 308
Query: 182 PAIVAASE-LSYRYISDRFMPDKAIDLIDEAAAKIKIE 218
+ A ++ +S R I ++ + I E K++ E
Sbjct: 309 RYLAAKTKGMSGRDIKEKVLKTALHRAIAEDREKVERE 346
>gnl|CDD|237871 PRK14965, PRK14965, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 576
Score = 32.0 bits (73), Expect = 1.5
Identities = 15/42 (35%), Positives = 19/42 (45%), Gaps = 8/42 (19%)
Query: 391 VGQDEAISAVSNAIRRSRSGLSDAKRPYGSFMFLGPTGVGKT 432
GQ+ + NAI D R +F+F G GVGKT
Sbjct: 19 TGQEHVSRTLQNAI--------DTGRVAHAFLFTGARGVGKT 52
>gnl|CDD|153307 cd07623, BAR_SNX1_2, The Bin/Amphiphysin/Rvs (BAR) domain of
Sorting Nexins 1 and 2. BAR domains are dimerization,
lipid binding and curvature sensing modules found in
many different proteins with diverse functions. Sorting
nexins (SNXs) are Phox homology (PX) domain containing
proteins that are involved in regulating membrane
traffic and protein sorting in the endosomal system.
SNXs differ from each other in their lipid-binding
specificity, subcellular localization and specific
function in the endocytic pathway. A subset of SNXs also
contain BAR domains. The PX-BAR structural unit
determines the specific membrane targeting of SNXs. This
subfamily consists of SNX1, SNX2, and similar proteins.
SNX1 and SNX2 are components of the retromer complex, a
membrane coat multimeric complex required for endosomal
retrieval of lysosomal hydrolase receptors to the Golgi.
The retromer consists of a cargo-recognition subcomplex
and a subcomplex formed by a dimer of sorting nexins
(SNX1 and/or SNX2), which ensures efficient cargo
sorting by facilitating proper membrane localization of
the cargo-recognition subcomplex. BAR domains form
dimers that bind to membranes, induce membrane bending
and curvature, and may also be involved in
protein-protein interactions.
Length = 224
Score = 31.5 bits (72), Expect = 1.6
Identities = 23/85 (27%), Positives = 46/85 (54%), Gaps = 6/85 (7%)
Query: 213 AKIKIEIDSKPEIMDKLERRLIQLKIEHEAIKREYDESSKKRLLLIKKEINKLEIKYANL 272
AK K+E+ + + +D+ ++ + + + + + ++E++E SK IKKEI + E
Sbjct: 138 AKAKLELSGRTDKLDQAQQEIKEWEAKVDRGQKEFEEISK----TIKKEIERFEKNRVKD 193
Query: 273 EK--IWKYEKTLIKDSQQIKEEIEK 295
K I KY ++L+ QQ+ + E
Sbjct: 194 FKDIIIKYLESLLNTQQQLIKYWEA 218
>gnl|CDD|236153 PRK08116, PRK08116, hypothetical protein; Validated.
Length = 268
Score = 31.5 bits (72), Expect = 1.6
Identities = 33/135 (24%), Positives = 55/135 (40%), Gaps = 32/135 (23%)
Query: 421 FMFLGPTGVGKTELCKTLSACIFNN-EESIIRIDMSEFIEKHSISRLIGAPPGYIGYEEG 479
+ G G GKT L+ACI N E + + F + ++R+ +E
Sbjct: 117 LLLWGSVGTGKT----YLAACIANELIEKGVPVIFVNFPQ--LLNRIKSTYKSSGKEDE- 169
Query: 480 GYLTEIVRR-KPYSLILLDE--IEKANS----DVFNILLQILDDGRLTDNRGRTINFRNT 532
EI+R L++LD+ E+ V+NI+ D+R R T
Sbjct: 170 ---NEIIRSLVNADLLILDDLGAERDTEWAREKVYNII----------DSRYR--KGLPT 214
Query: 533 IIVMTSNLGSDKIKE 547
I+ T+NL +++K
Sbjct: 215 IV--TTNLSLEELKN 227
>gnl|CDD|188306 TIGR03319, RNase_Y, ribonuclease Y. Members of this family are
RNase Y, an endoribonuclease. The member from Bacillus
subtilis, YmdA, has been shown to be involved in
turnover of yitJ riboswitch [Transcription, Degradation
of RNA].
Length = 514
Score = 31.8 bits (73), Expect = 1.7
Identities = 24/107 (22%), Positives = 48/107 (44%), Gaps = 13/107 (12%)
Query: 203 KAIDLIDEA-----AAKIKIEIDSKPEIMDKLERRLIQLKIEHEAIKREYDESSKKRLLL 257
A +I+EA K + +++K E+ ++ ++E E +R + +R LL
Sbjct: 33 LAKRIIEEAKKEAETLKKEALLEAKEEVHK------LRAELERELKERRNELQRLERRLL 86
Query: 258 IKKEI--NKLEIKYANLEKIWKYEKTLIKDSQQIKEEIEKVRLKINK 302
++E K+E E + K EK L + + E+ E++ I +
Sbjct: 87 QREETLDRKMESLDKKEENLEKKEKELSNKEKNLDEKEEELEELIAE 133
>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 = 32.1 bits (73), Expect = 1.7
Identities = 32/160 (20%), Positives = 67/160 (41%), Gaps = 36/160 (22%)
Query: 138 EKDAAFERRFQKILVEEPDIEETISILRGLQKKYEVHHGVEITDPAIVAASELSYRYISD 197
+ A R Q+I+ EE + I L G SY Y+
Sbjct: 341 DFSARIARNTQQIIQEESGVTRVIDPLGG------------------------SY-YV-- 373
Query: 198 RFMPDKAIDLIDEAAAKIKIEIDSKPEIMDKLERRLIQLKIEHEAIKREYDESSKKRLLL 257
+ D I E A K EI+ + +ER + +L+IE A + + S +++++
Sbjct: 374 ----EWLTDDIYERAWKYIQEIEEMGGMAKAIERGIPKLRIEEAAARTQARIDSGRQVIV 429
Query: 258 IKKEINKLEIKYANLEKIWKYEKTLIKDSQQIKEEIEKVR 297
+NK +++ + ++ K + + +++ Q +++K+R
Sbjct: 430 ---GVNKYQLEEEDEVEVLKVDNSSVREEQ--IAKLKKLR 464
>gnl|CDD|172375 PRK13851, PRK13851, type IV secretion system protein VirB11;
Provisional.
Length = 344
Score = 31.8 bits (72), Expect = 1.7
Identities = 29/85 (34%), Positives = 40/85 (47%), Gaps = 8/85 (9%)
Query: 420 SFMFLGPTGVGKTELCKTLSACIFNNEESIIRIDMSEFIEKH-SISRLI----GAPPGYI 474
+ + GPTG GKT + KTL + I E I D E + H + RL+ GA G +
Sbjct: 164 TMLLCGPTGSGKTTMSKTLISAIPPQERLITIEDTLELVIPHENHVRLLYSKNGAGLGAV 223
Query: 475 GYEEGGYLTEIVRRKPYSLILLDEI 499
E L +R +P ILL E+
Sbjct: 224 TAEH--LLQASLRMRP-DRILLGEM 245
>gnl|CDD|237866 PRK14952, PRK14952, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 584
Score = 31.8 bits (72), Expect = 1.8
Identities = 17/53 (32%), Positives = 27/53 (50%), Gaps = 8/53 (15%)
Query: 390 VVGQDEAISAVSNAIRRSRSGLSDAKRPYGSFMFLGPTGVGKTELCKTLSACI 442
VVGQ+ +S+A+ DA R +++F GP G GKT + L+ +
Sbjct: 15 VVGQEHVTEPLSSAL--------DAGRINHAYLFSGPRGCGKTSSARILARSL 59
>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 = 31.5 bits (72), Expect = 1.8
Identities = 28/123 (22%), Positives = 55/123 (44%), Gaps = 19/123 (15%)
Query: 635 DVHGCKKSLSILLKKIHKKSPEANFIFLGDLINKGPQSLDTLRMVYSMR-NYAKIVL--- 690
D+HG L L + + ++FLGD +++G S++ + +++++ Y K +
Sbjct: 50 DIHGQFYDLLKLFE-VGGSPANTRYLFLGDYVDRGYFSIECVLYLWALKILYPKTLFLLR 108
Query: 691 GNHEIHLLDVLININK----KSKLDTFDDILDAPDKKKLVSWLRTQPLA-IYYKKYLMIH 745
GNHE L + K +D ++A D PLA + +++L +H
Sbjct: 109 GNHECRHLTEYFTFKQECKIKYSERVYDACMEAFD---------CLPLAALMNQQFLCVH 159
Query: 746 AGV 748
G+
Sbjct: 160 GGL 162
>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 = 2.0
Identities = 22/88 (25%), Positives = 37/88 (42%), Gaps = 15/88 (17%)
Query: 472 GYIGYEEGGYLTEIVRRKPYSLILLDEIEKANSDVFNILLQILDDGRLTDNRGRTINFRN 531
G + Y G Y+TE+ Y+ V+N L+ + DG D +G T N ++
Sbjct: 34 GTVAYVNGEYITEL----NYNF----------RSVYNATLKAIQDGNTFDVKGNTYNSKD 79
Query: 532 TIIVMTSNLGSDKIK-EMEKGDKEIIKL 558
I ++ + SD +EK K+
Sbjct: 80 ATITASNKIDSDSFSIRIEKLTDNATKV 107
>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 = 2.0
Identities = 8/33 (24%), Positives = 20/33 (60%)
Query: 543 DKIKEMEKGDKEIIKLAVMNEVKIYFRPEFINR 575
+K +++ K +KL +++ + +FR E++ R
Sbjct: 180 EKAEDLIKELNNPVKLLIVDSLTSHFRAEYVGR 212
>gnl|CDD|237192 PRK12758, PRK12758, DNA topoisomerase IV subunit A; Provisional.
Length = 869
Score = 31.9 bits (73), Expect = 2.0
Identities = 27/106 (25%), Positives = 45/106 (42%), Gaps = 10/106 (9%)
Query: 143 FERRFQKILVEEPDIEETISILRGLQKKYEVHHGVEITDPAIVAASELSYRYISDRFMPD 202
E R K + E E I + + ++ E+T+ IV +E+ + IS +F D
Sbjct: 370 IEERIYKEIEEAETWEAVIEAIDKGLEPFKKQFIREVTEDDIVRLTEIKIKRIS-KFDSD 428
Query: 203 KAIDLIDEAAAKIKIEIDSKPEIMDKLERRLIQLKIEH-EAIKREY 247
KA +LI A+I E+ L L I + +K++Y
Sbjct: 429 KADELIARLEAEIA-------EVKHHLA-HLTDYAIAYFTNLKKKY 466
>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 = 2.1
Identities = 19/87 (21%), Positives = 38/87 (43%), Gaps = 11/87 (12%)
Query: 17 VLIGEPGVGKTAIVEGLAQRIINGE---VPNSLLSKKILLLDIALLLAGTKYRGEFEDRL 73
+L G PG GK+ + LA + G P + ++L LD ++ RL
Sbjct: 37 LLAGAPGTGKSTLALDLAAAVATGRPFLGPFPVEPGRVLYLD----GEDSEAG--LRRRL 90
Query: 74 KKILKEISNNQKDI-IIFIDELHTMIG 99
+ + + + + ++ ID L +++G
Sbjct: 91 RALGEAL-EEIEGPDLVVIDPLASLLG 116
>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 = 30.5 bits (69), Expect = 2.1
Identities = 26/128 (20%), Positives = 42/128 (32%), Gaps = 21/128 (16%)
Query: 18 LIGEPGVGKTAIVEGLAQRI-----------INGEVPN-----SLLSKKILLLDIALLLA 61
+ G G GKT + LA I I E+ S K L ++ ++ A
Sbjct: 4 VFGPTGSGKTTLALQLALNIATKGGKVVYVDIEEEIEELTERLIGESLKGALDNLIIVFA 63
Query: 62 GTKYRGEFEDRLKKILKEISNNQKDIIIFIDELHTMIGTGKVEGSIDAGNMLKPELSRGE 121
RL + + D +I +DEL ++ + G + + EL E
Sbjct: 64 TAD--DPAAARLLSKAERLRERGGDDLIILDELTRLVRALREIREGYPGELDE-EL--RE 118
Query: 122 LHCIGATT 129
L
Sbjct: 119 LLERARKG 126
Score = 30.2 bits (68), Expect = 3.1
Identities = 25/89 (28%), Positives = 33/89 (37%), Gaps = 14/89 (15%)
Query: 425 GPTGVGKTELCKTLSACIFNNEESIIRIDMSEFIE----KHSISRLIGAPPGYIGYEEGG 480
GPTG GKT L L+ I ++ +D+ E IE + L GA I
Sbjct: 6 GPTGSGKTTLALQLALNIATKGGKVVYVDIEEEIEELTERLIGESLKGALDNLIIVFATA 65
Query: 481 YLTEIVR----------RKPYSLILLDEI 499
R R LI+LDE+
Sbjct: 66 DDPAAARLLSKAERLRERGGDDLIILDEL 94
>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 = 2.2
Identities = 8/18 (44%), Positives = 12/18 (66%)
Query: 422 MFLGPTGVGKTELCKTLS 439
M +G +G GKT L + L+
Sbjct: 5 MLIGRSGCGKTTLTQALN 22
>gnl|CDD|100796 PRK01156, PRK01156, chromosome segregation protein; Provisional.
Length = 895
Score = 31.8 bits (72), Expect = 2.2
Identities = 35/152 (23%), Positives = 65/152 (42%), Gaps = 6/152 (3%)
Query: 205 IDLIDEAAAKIKIEIDS-KPEI--MDKLERRLIQLKIEHEAIKREYDESSKKRLLLIKKE 261
I+ ++ K+K ID + EI +D LE +L +E E IK++ + K + KE
Sbjct: 161 INSLERNYDKLKDVIDMLRAEISNIDYLEEKLKSSNLELENIKKQIADDEKS-HSITLKE 219
Query: 262 INKLEIKYANLEKIWKYEKTLIKDSQQIKEEIEKVRLKINKATRKSDWQTVSKLKYGELN 321
I +L I+Y N + K+ + + +++ + +I A + Y EL
Sbjct: 220 IERLSIEYNNAMDDYNNLKSALNELSSLEDMKNRYESEIKTAESDLSMELEKNNYYKELE 279
Query: 322 KLERILKEKSQKDIQLPNNANKFTLLKTKVGS 353
ER +K + + N N + K + +
Sbjct: 280 --ERHMKIINDPVYKNRNYINDYFKYKNDIEN 309
>gnl|CDD|234232 TIGR03499, FlhF, flagellar biosynthetic protein FlhF. [Cellular
processes, Chemotaxis and motility].
Length = 283
Score = 31.1 bits (71), Expect = 2.3
Identities = 9/20 (45%), Positives = 10/20 (50%)
Query: 413 DAKRPYGSFMFLGPTGVGKT 432
G +GPTGVGKT
Sbjct: 190 PILERGGVIALVGPTGVGKT 209
>gnl|CDD|233119 TIGR00763, lon, ATP-dependent protease La. This protein is induced
by heat shock and other stresses in E. coli, B.
subtilis, and other species. The yeast member,
designated PIM1, is located in the mitochondrial matrix,
required for mitochondrial function, and also induced by
heat shock [Protein fate, Degradation of proteins,
peptides, and glycopeptides].
Length = 775
Score = 31.5 bits (72), Expect = 2.3
Identities = 32/104 (30%), Positives = 49/104 (47%), Gaps = 23/104 (22%)
Query: 423 FLGPTGVGKTELCKTLSACIFNNEESIIRI------DMSEFIEKHSISRLIGAPPGYIGY 476
+GP GVGKT L K+++ + +R D +E I H + +GA PG I
Sbjct: 352 LVGPPGVGKTSLGKSIAKAL---NRKFVRFSLGGVRDEAE-IRGHRRT-YVGAMPGRI-- 404
Query: 477 EEGGYLTEIVRRKPYS-LILLDEIEKANSDV----FNILLQILD 515
+ + + K + L LLDEI+K S + LL++LD
Sbjct: 405 -----IQGLKKAKTKNPLFLLDEIDKIGSSFRGDPASALLEVLD 443
>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: 17 VLIGEPGVGKTAIVEGLAQRIINGEVPNSLLS 48
VLIG+ GVGKT+++ R ++ + + S
Sbjct: 4 VLIGDSGVGKTSLL----LRFVDNKFSENYKS 31
>gnl|CDD|214693 smart00488, DEXDc2, DEAD-like helicases superfamily.
Length = 289
Score = 31.2 bits (71), Expect = 2.5
Identities = 19/67 (28%), Positives = 27/67 (40%), Gaps = 9/67 (13%)
Query: 74 KKILKEISNNQKDIIIFIDELHTMIGTGKVEGSIDAGNMLKPELSRGELHCIGATTLNEY 133
KI + +S KD I+ DE H + + L ELSR L + +Y
Sbjct: 225 PKIRQALSIELKDSIVIFDEAHNLDNV--------CISALSSELSRRSL-ERAHKNIKKY 275
Query: 134 RQYIEKD 140
+ IEK
Sbjct: 276 FERIEKI 282
>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 = 30.8 bits (69), Expect = 2.7
Identities = 23/84 (27%), Positives = 36/84 (42%), Gaps = 4/84 (4%)
Query: 235 QLKIEHEAIKREYDESSKKRLLLIKKEINKLEIKYANLEKIWKYEK--TLIKDSQQIKEE 292
+++E I EYD S K L +K + + + E + + L D Q K+E
Sbjct: 9 DSVLDNERIYLEYDSSQKSFLGALKTNATQSDGEKLTDETLSLQRQINQLNSDLQLQKQE 68
Query: 293 IEKVRL--KINKATRKSDWQTVSK 314
EK+R K KA +S + K
Sbjct: 69 NEKLRKLNKTQKALLESKLSSKKK 92
>gnl|CDD|225224 COG2348, COG2348, Peptidoglycan interpeptide bridge formation
enzyme [Cell wall/membrane/envelope biogenesis].
Length = 418
Score = 31.2 bits (71), Expect = 2.7
Identities = 26/141 (18%), Positives = 49/141 (34%), Gaps = 14/141 (9%)
Query: 219 IDSKPEIMDKLERRLI-----QLKIEHEAIKREYDESSKKRLLLIKKEINKLE-IKYANL 272
D EI++ I L +H + D+S + R + +K E +
Sbjct: 115 FDLGGEIIENYNNLAIIKLLKDLGYKHSGFTKGLDDSIQPRWHSVLDLKDKTEDQLLKSF 174
Query: 273 EKIWKY-----EKTLIKDSQQIKEEIEKVRLKINKATRKSDWQTVSKLKYGELNKLERIL 327
K + EK +K +++ E + ++ K T + T L Y E I
Sbjct: 175 SKKTRRNIKKAEKKGVKV-RRLSREELDLFSELMKKTSERKGFTDRSLSYYE--NFYDIY 231
Query: 328 KEKSQKDIQLPNNANKFTLLK 348
K+K++ + + L
Sbjct: 232 KDKAELPLAYLDLDEYLKKLN 252
>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 = 31.5 bits (71), Expect = 2.8
Identities = 31/206 (15%), Positives = 69/206 (33%), Gaps = 14/206 (6%)
Query: 203 KAIDLIDEAAAKIKIEIDSKPEIMDKLERRLIQLKIEHEAIKREYDESSKKRLLLIKKEI 262
+ +E K++ E ++ + + + E + S+K L ++KE+
Sbjct: 272 LKENKEEEKEKKLQEEELKLLAKEEEELKSELLKLERRKVDDEEKLKESEKELKKLEKEL 331
Query: 263 NKLEIKYANLEKIWKYEKTLIKDSQQIKEEIEKVRLKINKATRKSDWQTVSKLKYGELNK 322
K + + LEK K L + +EE E++ K + + K E
Sbjct: 332 KKEKEEIEELEKE---LKELEIKREAEEEEEEQLEKLQEKLEQLEEELLAKKKLESERLS 388
Query: 323 LERILKEK-----------SQKDIQLPNNANKFTLLKTKVGSEEIAEIVSRTTGIPVSKI 371
LKE+ ++ ++L + K + + E+
Sbjct: 389 SAAKLKEEELELKNEEEKEAKLLLELSEQEEDLLKEEKKEELKIVEELEESLETKQGKLT 448
Query: 372 VQVEREKLLNIENLLCKRVVGQDEAI 397
+ E + ++ L K + + E +
Sbjct: 449 EEKEELEKQALKLLKDKLELKKSEDL 474
Score = 31.1 bits (70), Expect = 3.2
Identities = 34/206 (16%), Positives = 80/206 (38%), Gaps = 16/206 (7%)
Query: 128 TTLNEYRQYIEKDAAFERRFQKILVEEPDIEETISILRGLQKKYEVHHGVEITDPAIVAA 187
L +++ A + ++ + EE + L Y + I +
Sbjct: 194 EELKLQELKLKEQAKKALEYYQLKEKLELEEENL-----LYLDYLKLNEERIDLLQELLR 248
Query: 188 SELSYRYISDRFMPDKAIDLIDEAAAKIKIEIDSKPEIMDKLERRLIQLKIEHEAIKREY 247
E S + +K +++ + + K E K KL+ ++L + E +
Sbjct: 249 DEQE-EIESSKQELEKEEEILAQVLKENKEEEKEK-----KLQEEELKLLAKEEEELKSE 302
Query: 248 DESSKKRLLLIKKEINKLEIKYANLEKIWKYEKTLIKDSQQIKEEIEKVRLKINKATRKS 307
++R + ++++ + E + LEK K EK I++ ++ +E L+I + +
Sbjct: 303 LLKLERRKVDDEEKLKESEKELKKLEKELKKEKEEIEELEKELKE-----LEIKREAEEE 357
Query: 308 DWQTVSKLKYGELNKLERILKEKSQK 333
+ + + KL+ E +L +K +
Sbjct: 358 EEEQLEKLQEKLEQLEEELLAKKKLE 383
>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 = 2.9
Identities = 15/37 (40%), Positives = 22/37 (59%), Gaps = 1/37 (2%)
Query: 422 MFLGPTGVGKTELCKTLSACIFN-NEESIIRIDMSEF 457
M +G GVGKT LCK L F+ +E S I++ ++
Sbjct: 5 MLVGQGGVGKTSLCKQLIGEKFDGDESSTHGINVQDW 41
>gnl|CDD|237862 PRK14948, PRK14948, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 620
Score = 31.1 bits (71), Expect = 2.9
Identities = 20/55 (36%), Positives = 29/55 (52%), Gaps = 15/55 (27%)
Query: 390 VVGQDEAISA-VSNAIRRSRSGLSDAKRPYGSFMFLGPTGVGKTELCKTLSACIF 443
+VGQ EAI+ + NA+ +R ++ A ++F GP G GKT SA I
Sbjct: 18 LVGQ-EAIATTLKNALISNR--IAPA------YLFTGPRGTGKTS-----SARIL 58
>gnl|CDD|183702 PRK12723, PRK12723, flagellar biosynthesis regulator FlhF;
Provisional.
Length = 388
Score = 31.0 bits (70), Expect = 2.9
Identities = 30/99 (30%), Positives = 45/99 (45%), Gaps = 12/99 (12%)
Query: 421 FMFLGPTGVGKTELCKTLSACIFNNEES------IIRIDMSEFIEKHSISR---LIGAPP 471
F+ +GPTGVGKT L+A N + II ID K I ++G P
Sbjct: 177 FILVGPTGVGKTTTIAKLAAIYGINSDDKSLNIKIITIDNYRIGAKKQIQTYGDIMGIPV 236
Query: 472 GYI-GYEEGGYLTEIVRRKPYSLILLDEIEKANSDVFNI 509
I +++ EI + K + L+L+D I K+ D +
Sbjct: 237 KAIESFKD--LKEEITQSKDFDLVLVDTIGKSPKDFMKL 273
>gnl|CDD|237867 PRK14953, PRK14953, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 486
Score = 30.9 bits (70), Expect = 3.0
Identities = 17/52 (32%), Positives = 29/52 (55%), Gaps = 8/52 (15%)
Query: 388 KRVVGQDEAISAVSNAIRRSRSGLSDAKRPYGSFMFLGPTGVGKTELCKTLS 439
K V+GQ+ + + NA++ R +S A ++F GP G GKT + + L+
Sbjct: 16 KEVIGQEIVVRILKNAVKLQR--VSHA------YIFAGPRGTGKTTIARILA 59
>gnl|CDD|240423 PTZ00454, PTZ00454, 26S protease regulatory subunit 6B-like
protein; Provisional.
Length = 398
Score = 30.9 bits (70), Expect = 3.0
Identities = 35/118 (29%), Positives = 53/118 (44%), Gaps = 35/118 (29%)
Query: 417 PYGSFMFLGPTGVGKTELCKTLSACIFNNEESIIRIDMSEFIEKHSISRLIGAPPGYIGY 476
P G ++ GP G GKT L K A + + IR+ SEF++K Y+G
Sbjct: 179 PRGVLLY-GPPGTGKTMLAK---AVAHHTTATFIRVVGSEFVQK------------YLG- 221
Query: 477 EEGGYLTEIV----RRKPYSLILLDEIEK-----------ANSDVFNILLQILD--DG 517
EG + V R S+I +DE++ A+ +V ILL++L+ DG
Sbjct: 222 -EGPRMVRDVFRLARENAPSIIFIDEVDSIATKRFDAQTGADREVQRILLELLNQMDG 278
>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 = 3.0
Identities = 11/29 (37%), Positives = 17/29 (58%), Gaps = 3/29 (10%)
Query: 414 AKRPYGSFMFLGPTGVGKTELCKTLSACI 442
++P+G + GPTG GKT TL + +
Sbjct: 76 LEKPHGIILVTGPTGSGKT---TTLYSAL 101
>gnl|CDD|222194 pfam13521, AAA_28, AAA domain.
Length = 162
Score = 29.8 bits (68), Expect = 3.1
Identities = 10/20 (50%), Positives = 13/20 (65%)
Query: 17 VLIGEPGVGKTAIVEGLAQR 36
V+ G P GKT ++E LA R
Sbjct: 3 VITGGPSTGKTTLLEALAAR 22
>gnl|CDD|234007 TIGR02776, NHEJ_ligase_prk, DNA ligase D. Members of this protein
family are DNA ligases involved in the repair of DNA
double-stranded breaks by non-homologous end joining
(NHEJ). The system of the bacterial Ku protein
(TIGR02772) plus this DNA ligase is seen in about 20 %
of bacterial genomes to date and at least one archaeon
(Archeoglobus fulgidus). This model describes a central
and a C-terminal domain. These two domains may be
permuted, as in genus Mycobacterium, or divided into
tandem ORFs, and therefore not be identified by This
model. An additional N-terminal 3'-phosphoesterase (PE)
domain present in some but not all examples of this
ligase is not included in the seed alignment for this
model; This model models only the central ATP-dependent
ligase domain and the C-terminal polymerase domain. Most
examples of genes for this ligase are adjacent to the
gene for Ku [DNA metabolism, DNA replication,
recombination, and repair].
Length = 552
Score = 30.7 bits (70), Expect = 3.5
Identities = 19/72 (26%), Positives = 29/72 (40%), Gaps = 9/72 (12%)
Query: 113 LKPELSRGELHCIGATTLNEYRQYIEKDAAFER-RFQKILVEEPDIEETISILRGLQKK- 170
++P L E+ G T R+ A+F+ R K EE +E +K+
Sbjct: 221 VRPSL-VAEVEYAGITRDGILRE-----ASFKGLREDKP-AEEVTLETPQRHAAAKRKRS 273
Query: 171 YEVHHGVEITDP 182
+ GV IT P
Sbjct: 274 AALVAGVRITHP 285
>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: 225 IMDKLERRLIQLKIEHEAIKREYDESSKKRLLLIKKEINKL---EIKYANLEKIWKYEKT 281
I+ + R + K+E+E K Y SSK I +N++ E+ + EKI Y
Sbjct: 256 IIKSIPRATLTDKLENELTKEIYKSSSK-----INNCLNRIKLPEMIDFSSEKIHDYIDI 310
Query: 282 LIKDSQQIKEEIEKVRLKIN 301
+I+D + IKE V +IN
Sbjct: 311 IIEDYENIKENAYLVIPQIN 330
>gnl|CDD|221955 pfam13173, AAA_14, AAA domain. This family of domains contain a
P-loop motif that is characteristic of the AAA
superfamily.
Length = 127
Score = 29.4 bits (67), Expect = 3.7
Identities = 33/137 (24%), Positives = 57/137 (41%), Gaps = 30/137 (21%)
Query: 425 GPTGVGKTELCKTLSACIFNNEESIIRIDMSEF-IEKHSISRLIGAPPGYIGYEEGGYLT 483
GP VGKT L + + E+I+ I++ + + ++ L+ +L
Sbjct: 9 GPRQVGKTTLLLQFLKELLS--ENILYINLDDPRFLRLALLDLLEE-----------FLK 55
Query: 484 EIVRRKPYSLILLDEIEKANSDVFNILLQILDDGRLTDNRGRTINFRNTIIVMTSNLG-- 541
++ K Y + LDEI+K D + L ++ DDGR II+ S+
Sbjct: 56 LLLPGKKY--LFLDEIQKVP-DWEDALKRLYDDGRNLR-----------IILTGSSSLLL 101
Query: 542 SDKIKEMEKGDKEIIKL 558
S +I G E ++L
Sbjct: 102 SKEIATSLAGRAEELEL 118
Score = 29.1 bits (66), Expect = 4.9
Identities = 17/79 (21%), Positives = 32/79 (40%), Gaps = 14/79 (17%)
Query: 17 VLIGEPGVGKTAIVEGLAQRIINGEVPNSLLSKKILLLDIALLLAGTKYRGEFEDRLKKI 76
V+ G VGKT ++ + LLS+ IL ++ L ++ L +
Sbjct: 6 VITGPRQVGKTTLLLQFLK---------ELLSENILYIN----LDDPRFLRLALLDLLEE 52
Query: 77 LKEISNNQKDIIIFIDELH 95
++ K +F+DE+
Sbjct: 53 FLKLLLPGKK-YLFLDEIQ 70
>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: 252 KKRLLLIKKEINKLEIKYANLEKIWKYEKTLIKDSQQIKEEIEKVRLKINKATRKSDWQT 311
K LL ++ K E K A I + + L + ++K E+E L D
Sbjct: 2 LKDLLKQLGKLTKEETKPALGALINEVKIELQDELTKLKPELESAGLWSKLKFETYDVSL 61
Query: 312 VSKLKY-GELNKLERILKE 329
Y G L+ L R++ E
Sbjct: 62 PGTKIYPGSLHPLTRVIDE 80
>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 = 30.4 bits (69), Expect = 4.1
Identities = 13/41 (31%), Positives = 22/41 (53%)
Query: 15 NPVLIGEPGVGKTAIVEGLAQRIINGEVPNSLLSKKILLLD 55
N ++I P GKT ++ LA+ + G L KK+ ++D
Sbjct: 113 NTLIISPPQCGKTTLLRDLARILSTGISQLGLRGKKVGIVD 153
>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 = 30.5 bits (69), Expect = 4.2
Identities = 40/147 (27%), Positives = 63/147 (42%), Gaps = 28/147 (19%)
Query: 388 KRVVGQDEAISAVSNAIRRSRSGLSDAKRPYGSFMFLGPTGVGKT-------ELCKTLSA 440
++GQ+E I A+ A+ P ++ GP GVGKT E K A
Sbjct: 65 DEIIGQEEGIKALKAALC--------GPNPQHVIIY-GPPGVGKTAAARLVLEEAKKNPA 115
Query: 441 CIFNNEESIIRIDMS--EFIEKHSISRLIGA--PPGYIGYEEGGYLTEIVRRKPYS---- 492
F + + ID + F E+ LIG+ P Y G G + I + KP +
Sbjct: 116 SPFKEGAAFVEIDATTARFDERGIADPLIGSVHDPIYQGAGPLG-IAGIPQPKPGAVTRA 174
Query: 493 ---LILLDEIEKANSDVFNILLQILDD 516
++ +DEI + + N LL++L+D
Sbjct: 175 HGGVLFIDEIGELHPVQMNKLLKVLED 201
>gnl|CDD|236994 PRK11823, PRK11823, DNA repair protein RadA; Provisional.
Length = 446
Score = 30.4 bits (70), Expect = 4.3
Identities = 28/112 (25%), Positives = 38/112 (33%), Gaps = 57/112 (50%)
Query: 17 VLI-GEPGVGK-TAIVEGLAQRIINGEVPNSLLSKKILLLDIALLLAGTKYR-----GEF 69
VLI G+PG+GK T LLL +A LA + GE
Sbjct: 83 VLIGGDPGIGKST------------------------LLLQVAARLAAAGGKVLYVSGE- 117
Query: 70 E---------DRLK---------------KILKEISNNQKDIIIFIDELHTM 97
E +RL IL I + D+++ ID + TM
Sbjct: 118 ESASQIKLRAERLGLPSDNLYLLAETNLEAILATIEEEKPDLVV-IDSIQTM 168
>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 = 29.9 bits (68), Expect = 4.4
Identities = 14/28 (50%), Positives = 15/28 (53%), Gaps = 1/28 (3%)
Query: 425 GPTGVGKTELCKTLSACIFNNEESIIRI 452
G TG GKT L L A I +E II I
Sbjct: 32 GGTGSGKTTLLNALLAFI-PPDERIITI 58
>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 = 4.6
Identities = 16/63 (25%), Positives = 31/63 (49%), Gaps = 2/63 (3%)
Query: 263 NKLEIKYANLEKIWKYEKTLIKDSQQIKEEIEKVRLKINKATRKSDWQTVSKLKYGELNK 322
L K A L K+ K+ QQ K+E+++ K+ +A ++ ++ +S+ EL +
Sbjct: 142 QDLSKKRAQLAKLKGAGKSRQDKLQQAKKEVDEAERKVQQAKKE--FEDISETIKKELER 199
Query: 323 LER 325
E
Sbjct: 200 FET 202
Score = 29.2 bits (66), Expect = 8.6
Identities = 12/57 (21%), Positives = 31/57 (54%), Gaps = 4/57 (7%)
Query: 210 EAAAKIKIEIDSKPEIMDKLERRLIQLKIEHEAIKREYDESSKKRLLLIKKEINKLE 266
AK+K S+ + + + ++ + + + + + K+E+++ S+ IKKE+ + E
Sbjct: 149 AQLAKLKGAGKSRQDKLQQAKKEVDEAERKVQQAKKEFEDISET----IKKELERFE 201
>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 = 4.7
Identities = 16/49 (32%), Positives = 23/49 (46%), Gaps = 3/49 (6%)
Query: 390 VVGQDEAISAVSNAIRRSRSGLSDAKRPYGSFMFLGPTGVGKTELCKTL 438
G +EAI N + + GL + K+ LGP G GK+ L + L
Sbjct: 53 FFGMEEAIERFVNYFKSAAQGLEERKQ---ILYLLGPVGGGKSSLVECL 98
>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 = 4.7
Identities = 9/17 (52%), Positives = 11/17 (64%)
Query: 422 MFLGPTGVGKTELCKTL 438
MF+G G GKT L + L
Sbjct: 4 MFIGSVGCGKTTLTQAL 20
>gnl|CDD|182730 PRK10787, PRK10787, DNA-binding ATP-dependent protease La;
Provisional.
Length = 784
Score = 30.7 bits (69), Expect = 4.8
Identities = 29/100 (29%), Positives = 50/100 (50%), Gaps = 15/100 (15%)
Query: 423 FLGPTGVGKTELCKTLSACIFNNEESIIRIDMSEFIEKHSISRLIGAPPGYIGYEEGGYL 482
+GP GVGKT L ++++ +R+ + ++ I G YIG G +
Sbjct: 354 LVGPPGVGKTSLGQSIAKA---TGRKYVRMALGGVRDEAEIR---GHRRTYIGSMPGKLI 407
Query: 483 TEIVR---RKPYSLILLDEIEKANSDV----FNILLQILD 515
++ + + P L LLDEI+K +SD+ + LL++LD
Sbjct: 408 QKMAKVGVKNP--LFLLDEIDKMSSDMRGDPASALLEVLD 445
>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 = 30.5 bits (69), Expect = 4.9
Identities = 36/146 (24%), Positives = 66/146 (45%), Gaps = 33/146 (22%)
Query: 321 NKLERILKEKSQKDIQLPNNANKFTLLKTKVGSEEIAEIVSRTTGIPVSKIVQVEREKLL 380
K+E ++E+ K ++ + +LK + G E + +T + ++ ++E++KL
Sbjct: 92 RKVETRMQERQNKYLE----EIRLQVLKEEKGPE------NSSTLKKLERLEKLEKKKLH 141
Query: 381 -NIENLLCKR----VVGQDEAISAVSNAIRRSRSGLSDAKRPYGSFMFL-GPTGVGKT-- 432
+ ++LL R +VGQ+ AI A+ L+ P+ + L GP GVGKT
Sbjct: 142 KSAQSLLRPRAFSEIVGQERAIKAL----------LAKVASPFPQHIILYGPPGVGKTTA 191
Query: 433 -----ELCKTLSACIFNNEESIIRID 453
E K L F + + +D
Sbjct: 192 ARLALEEAKKLKHTPFAEDAPFVEVD 217
>gnl|CDD|215920 pfam00437, T2SE, Type II/IV secretion system protein. This family
contains both type II and type IV pathway secretion
proteins from bacteria. VirB11 ATPase is a subunit of
the Agrobacterium tumefaciens transfer DNA (T-DNA)
transfer system, a type IV secretion pathway required
for delivery of T-DNA and effector proteins to plant
cells during infection.
Length = 273
Score = 29.9 bits (68), Expect = 5.5
Identities = 15/42 (35%), Positives = 21/42 (50%)
Query: 411 LSDAKRPYGSFMFLGPTGVGKTELCKTLSACIFNNEESIIRI 452
L A + G+ + G TG GKT L L I ++E I+ I
Sbjct: 122 LRQAVQARGNILVSGGTGSGKTTLLYALLNEINTDDERIVTI 163
>gnl|CDD|181459 PRK08533, PRK08533, flagellar accessory protein FlaH; Reviewed.
Length = 230
Score = 29.7 bits (67), Expect = 5.6
Identities = 18/57 (31%), Positives = 32/57 (56%), Gaps = 4/57 (7%)
Query: 42 VPNSLLSKKILLLDIALLLAGTKYRGEFEDRLKKILKEISNNQKDIIIFIDELHTMI 98
+ L+S K+L + + LL+G + +F LKK++ +KD+II D L ++I
Sbjct: 78 INKKLISGKLLYIPVYPLLSGNSEKRKF---LKKLMNTRRFYEKDVIII-DSLSSLI 130
>gnl|CDD|218899 pfam06102, DUF947, Domain of unknown function (DUF947). Family of
eukaryotic proteins with unknown function.
Length = 168
Score = 29.2 bits (66), Expect = 5.6
Identities = 31/124 (25%), Positives = 51/124 (41%), Gaps = 27/124 (21%)
Query: 199 FMPDKAIDLIDEAAAKIKIEIDSKPEIMDKLERRLIQLKIEHEAIKREYDE--------- 249
F+ D I+E +K D E ++L+R L +K + +K + E
Sbjct: 56 FLDDYREKEIEELEKALKKTKD--SEEKEELKRTLQSMKSRLKTLKNKDREREILKEHKK 113
Query: 250 -------SSKKRLLLIKKEINKLEIKYANLEKIWKYEKTLIKDSQQIKEEIEKVRLKINK 302
KK L K EI KL +K K+++ +K S+Q+ + +EK R K
Sbjct: 114 QEKELIKEGKKPYYLKKSEIKKLVLK-------KKFDE--LKKSKQLDKALEKKRKKNAG 164
Query: 303 ATRK 306
+K
Sbjct: 165 KEKK 168
>gnl|CDD|224143 COG1222, RPT1, ATP-dependent 26S proteasome regulatory subunit
[Posttranslational modification, protein turnover,
chaperones].
Length = 406
Score = 29.9 bits (68), Expect = 5.8
Identities = 28/79 (35%), Positives = 36/79 (45%), Gaps = 21/79 (26%)
Query: 425 GPTGVGKTELCKTLSACIFNNEESIIRIDMSEFIEKHSISRLIGAPPGYIGYEEGGYLT- 483
GP G GKT L K A + + IR+ SE ++K YIG EG L
Sbjct: 192 GPPGTGKTLLAK---AVANQTDATFIRVVGSELVQK------------YIG--EGARLVR 234
Query: 484 ---EIVRRKPYSLILLDEI 499
E+ R K S+I +DEI
Sbjct: 235 ELFELAREKAPSIIFIDEI 253
>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 = 5.8
Identities = 25/111 (22%), Positives = 51/111 (45%), Gaps = 10/111 (9%)
Query: 223 PEIMDKLERRLIQLKIEHEAIKREYDE-SSKKRLLLIKKEINKLEIK----YANLEKIWK 277
E +++E+ LK + K+ + +K+ L KK + ++ K L+KI +
Sbjct: 163 VETAEEIEK---SLKAMQQKWKKRKKDLPNKQDLEEYKKRLEAIKKKDIKNPLELQKIKE 219
Query: 278 YEKTLIKDSQQIKEEIEKVR--LKINKATRKSDWQTVSKLKYGELNKLERI 326
L K+ + K++I+ + L+ +K K+D + K +L +LE
Sbjct: 220 EFDKLKKEGKADKQKIKSAKNDLQNDKKQLKADLAELKKAPQNDLKRLENK 270
>gnl|CDD|223637 COG0563, Adk, Adenylate kinase and related kinases [Nucleotide
transport and metabolism].
Length = 178
Score = 29.2 bits (66), Expect = 5.8
Identities = 9/22 (40%), Positives = 13/22 (59%)
Query: 421 FMFLGPTGVGKTELCKTLSACI 442
+ 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 = 30.0 bits (68), Expect = 5.8
Identities = 27/123 (21%), Positives = 54/123 (43%), Gaps = 18/123 (14%)
Query: 222 KPEIMDKLERRLIQLKIEHEAIKREYDESSKKRLLLIKKEINKLEIKYANLEKIWKYEKT 281
KP +++KLE L +E ++ S ++ + ++ KL +Y+ LE+I +
Sbjct: 2 KPSLLEKLES----LLERYEELEALL---SDPEVISDQDKLRKLSKEYSQLEEIVDCYRE 54
Query: 282 LIKDSQQIKEEIEKVRLKINKATRKSDWQTVSKLKYGELNKLERILKEKSQ--KDIQLPN 339
+ + IKE K + + ++ EL +LE ++E + K + LP
Sbjct: 55 YQQAQEDIKE---------AKEILEESDPEMREMAKEELEELEEKIEELEEQLKVLLLPK 105
Query: 340 NAN 342
+ N
Sbjct: 106 DPN 108
>gnl|CDD|237551 PRK13902, alaS, alanyl-tRNA synthetase; Provisional.
Length = 900
Score = 30.2 bits (69), Expect = 5.9
Identities = 14/68 (20%), Positives = 33/68 (48%)
Query: 206 DLIDEAAAKIKIEIDSKPEIMDKLERRLIQLKIEHEAIKREYDESSKKRLLLIKKEINKL 265
DL+ EAA + + + P+ +++ + K E E +++E E LL +E+ +
Sbjct: 743 DLLKEAAEILGVPPEQLPKTVERFFEEWKEQKKEIEKLRKELAELLASELLSKAEEVGGV 802
Query: 266 EIKYANLE 273
++ ++
Sbjct: 803 KVVVEEVD 810
>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 = 5.9
Identities = 11/27 (40%), Positives = 16/27 (59%)
Query: 17 VLIGEPGVGKTAIVEGLAQRIINGEVP 43
VLIG+ GVGK++++ L VP
Sbjct: 6 VLIGDEGVGKSSLIMSLVSEEFPENVP 32
>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 = 6.6
Identities = 7/14 (50%), Positives = 11/14 (78%)
Query: 17 VLIGEPGVGKTAIV 30
V++G GVGK+A+
Sbjct: 3 VVLGAGGVGKSALT 16
>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 = 6.7
Identities = 21/80 (26%), Positives = 48/80 (60%), Gaps = 3/80 (3%)
Query: 226 MDKLERRLIQLKIEHEAIKREYDESSKKRLLLIKKEINKLEIKYANLEKIW-KYEKTLIK 284
+++L++R+ +L+ + E +K+ +E+ ++ LL +E+ +LE + L+ KYEK +
Sbjct: 78 LEELKQRIAELQAQIEKLKKGREETEERTELL--EELKQLEKELKKLKAELEKYEKNDPE 135
Query: 285 DSQQIKEEIEKVRLKINKAT 304
+++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 = 7.0
Identities = 10/14 (71%), Positives = 11/14 (78%)
Query: 419 GSFMFLGPTGVGKT 432
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 = 29.3 bits (67), Expect = 7.3
Identities = 7/12 (58%), Positives = 9/12 (75%)
Query: 421 FMFLGPTGVGKT 432
+ +GP GVGKT
Sbjct: 4 ILLVGPNGVGKT 15
>gnl|CDD|226415 COG3899, COG3899, Predicted ATPase [General function prediction
only].
Length = 849
Score = 30.1 bits (68), Expect = 7.6
Identities = 23/115 (20%), Positives = 40/115 (34%), Gaps = 21/115 (18%)
Query: 18 LIGEPGVGKTAIVEGLAQRIINGEVPNSLLSKKILLL--DIALL--------LAG---TK 64
+ GE G+GK+A+V + + I + K +I L L G ++
Sbjct: 29 VAGESGIGKSALVNEVHKPITQQR--GYFIKGKFDQFERNIPLSPLVQAFRDLMGQLLSE 86
Query: 65 YRGEFEDRLKKILKEISNNQKDIIIFIDELHTMIGTGKVEGSIDAGNMLKPELSR 119
++L + N + II I EL + G L P ++
Sbjct: 87 SDTRILSWRARLLAALGENGQVIIDVIPEL------ELIIGKRPPALELSPTAAQ 135
>gnl|CDD|237355 PRK13342, PRK13342, recombination factor protein RarA; Reviewed.
Length = 413
Score = 29.7 bits (68), Expect = 8.0
Identities = 35/142 (24%), Positives = 55/142 (38%), Gaps = 44/142 (30%)
Query: 390 VVGQDEAISAVSNAIRRSRSGLSDAKRPYGSFMFLGPTGVGKTELCK-----------TL 438
VVGQ+ + +RR + +A R S + GP G GKT L + L
Sbjct: 14 VVGQEHLLGPGK-PLRR----MIEAGRL-SSMILWGPPGTGKTTLARIIAGATDAPFEAL 67
Query: 439 SACIFNNEESIIRIDMSEFIEKHSISRLIGAPPGYIGYEEGGYLTEIVRRKPYSLILLDE 498
SA ++ +R E IE+ R G R+ ++ +DE
Sbjct: 68 SAVTSGVKD--LR----EVIEEARQRRSAG-------------------RRT--ILFIDE 100
Query: 499 IEKANSDVFNILLQILDDGRLT 520
I + N + LL ++DG +T
Sbjct: 101 IHRFNKAQQDALLPHVEDGTIT 122
>gnl|CDD|226372 COG3854, SpoIIIAA, ncharacterized protein conserved in bacteria
[Function unknown].
Length = 308
Score = 29.4 bits (66), Expect = 8.1
Identities = 15/42 (35%), Positives = 26/42 (61%), Gaps = 2/42 (4%)
Query: 14 SNPVLIGEPGVGKTAIVEGLAQRIINGEVPNSLLSKKILLLD 55
N ++IG P VGKT ++ +A+ + +G N L KK+ ++D
Sbjct: 138 LNTLIIGPPQVGKTTLLRDIARLLSDGI--NQFLPKKVGIID 177
>gnl|CDD|217417 pfam03194, LUC7, LUC7 N_terminus. This family contains the N
terminal region of several LUC7 protein homologues and
only contains eukaryotic proteins. LUC7 has been shown
to be a U1 snRNA associated protein with a role in
splice site recognition. The family also contains human
and mouse LUC7 like (LUC7L) proteins and human cisplatin
resistance-associated overexpressed protein (CROP).
Length = 252
Score = 29.3 bits (66), Expect = 8.1
Identities = 18/96 (18%), Positives = 44/96 (45%), Gaps = 10/96 (10%)
Query: 209 DEAAAKIKIEIDSKPEIMDKLERRLIQLKIEHEAIKREYDESSKKRLLLIKKEINKLEIK 268
EA ++ + +DK ++RL ++ E + +S + L + +EI KL
Sbjct: 82 VEALEILERFVHDCDRKIDKAKQRL---ELTQEEQTKIAADSKAEELAELDEEIGKL--- 135
Query: 269 YANLEKIWKY-EKTLIKDSQQIKEEIEKVRLKINKA 303
L + E+ + ++ ++ +E+E+++ K +
Sbjct: 136 ---LAEAEALGEEGKVDEAMKLMKEVEELKAKKKEL 168
>gnl|CDD|183703 PRK12724, PRK12724, flagellar biosynthesis regulator FlhF;
Provisional.
Length = 432
Score = 29.5 bits (66), Expect = 8.2
Identities = 33/121 (27%), Positives = 61/121 (50%), Gaps = 9/121 (7%)
Query: 214 KIKIEIDSKPEIMDKLERRLIQLKIEHEAIK-REYDESSKKRLLLIKKEINK-LEIKYAN 271
+I+I I K +K+ER+L LK E +K + Y E +K+ L K +++ LE K +
Sbjct: 51 EIQIGIPEKQASREKIERKLQDLK---ELLKQKSYTEPERKKTLQTLKPLSERLEEKESA 107
Query: 272 LEKI--WKYEKTLIKDSQQIKEEIEKVRLKINKATRKSDWQTVSKLKYGELNKL-ERILK 328
+ +I ++ E+ + + + + EK + N + V K K L +L ER+++
Sbjct: 108 IYEIESFELEEVITEPERPVGLSFEKELFEKNSFLES-ETTIVRKEKDSPLQRLGERLVR 166
Query: 329 E 329
E
Sbjct: 167 E 167
>gnl|CDD|225114 COG2204, AtoC, Response regulator containing CheY-like receiver,
AAA-type ATPase, and DNA-binding domains [Signal
transduction mechanisms].
Length = 464
Score = 29.6 bits (67), Expect = 8.3
Identities = 33/166 (19%), Positives = 68/166 (40%), Gaps = 25/166 (15%)
Query: 391 VGQDEAISAVSNAIRRSRSGLSDAKRPYGSFMFLGPTGVGKTELCKTLSACIFNNEESII 450
VG+ A+ + I + SDA S + G +G GK + + + + I
Sbjct: 144 VGESPAMQQLRRLIAKV--APSDA-----SVLITGESGTGKELVARAIHQASPRAKGPFI 196
Query: 451 RIDMSEFIEKHSISRLIGAPPGYIGYEEGGYLTEIVRRKPY------SLILLDEIEKANS 504
++ + I ++ + + G+E+G + I RR + LDEI +
Sbjct: 197 AVNCAA-IPENLLESEL------FGHEKGAFTGAITRRIGRFEQANGGTLFLDEIGEMPL 249
Query: 505 DVFNILLQILDDG---RLTDNRGRTINFRNTIIVMTSNLGSDKIKE 547
++ LL++L + R+ N+ ++ R II T+ +++
Sbjct: 250 ELQVKLLRVLQEREFERVGGNKPIKVDVR--IIAATNRDLEEEVAA 293
>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 = 29.7 bits (67), Expect = 8.4
Identities = 23/80 (28%), Positives = 34/80 (42%), Gaps = 23/80 (28%)
Query: 161 ISILRGLQKKYEV-------HHGVEITDPAIVAASELSYRYISDRFMPDKAIDL------ 207
ISIL + +EV G E D A++ R++ F ++ IDL
Sbjct: 201 ISILEIQKGVFEVKSTNGDTFLGGEDFDNALL-------RHLVKEFKKEQGIDLTKDNMA 253
Query: 208 ---IDEAAAKIKIEIDSKPE 224
+ EAA K KIE+ S +
Sbjct: 254 LQRLREAAEKAKIELSSSLQ 273
>gnl|CDD|234654 PRK00131, aroK, shikimate kinase; Reviewed.
Length = 175
Score = 28.6 bits (65), Expect = 8.8
Identities = 12/23 (52%), Positives = 14/23 (60%)
Query: 14 SNPVLIGEPGVGKTAIVEGLAQR 36
N VLIG G GK+ I LA+R
Sbjct: 5 PNIVLIGFMGAGKSTIGRLLAKR 27
>gnl|CDD|222426 pfam13870, DUF4201, Domain of unknown function (DUF4201). This is
a family of coiled-coil proteins from eukaryotes. The
function is not known.
Length = 177
Score = 28.7 bits (65), Expect = 9.1
Identities = 18/91 (19%), Positives = 43/91 (47%), Gaps = 13/91 (14%)
Query: 216 KIEIDSKPEIMDKLERRLIQLKIEHEAIKREYDESSKKRLLLIKKEINKLEIKYANLEKI 275
K E+ K E + KL + L ++K+E + ++++ + ++ LL +
Sbjct: 97 KKELKEKEERLAKLRKELYKVKLERDKLRKQNKKLRQQGGLLHVPALLY----------- 145
Query: 276 WKYEKTLIKDSQQIKEEIEKVRLKINKATRK 306
Y+KT+ + ++ ++ +EK+R K +
Sbjct: 146 -DYDKTV-EKVEEKRKSVEKLRRKHKILEMR 174
>gnl|CDD|240271 PTZ00108, PTZ00108, DNA topoisomerase 2-like protein; Provisional.
Length = 1388
Score = 29.6 bits (67), Expect = 9.2
Identities = 19/113 (16%), Positives = 45/113 (39%), Gaps = 12/113 (10%)
Query: 224 EIMDKLERRLIQLKIEHEAIKREYDESSKKRLLLIKKEINKLEIKYANLEKIWKYEKTLI 283
E ++KL L + + E E +K + + ++++K E E + + E+
Sbjct: 1102 EKVEKLNAELEKKEKELEKLK------NTTPKDMWLEDLDKFE------EALEEQEEVEE 1149
Query: 284 KDSQQIKEEIEKVRLKINKATRKSDWQTVSKLKYGELNKLERILKEKSQKDIQ 336
K+ + + K + K +K + + K K +K ++ + K +
Sbjct: 1150 KEIAKEQRLKSKTKGKASKLRKPKLKKKEKKKKKSSADKSKKASVVGNSKRVD 1202
>gnl|CDD|236011 PRK07399, PRK07399, DNA polymerase III subunit delta'; Validated.
Length = 314
Score = 29.1 bits (66), Expect = 9.2
Identities = 14/44 (31%), Positives = 26/44 (59%), Gaps = 8/44 (18%)
Query: 388 KRVVGQDEAISAVSNAIRRSRSGLSDAKRPYGSFMFLGPTGVGK 431
++GQ AI ++ AI+++R ++ A ++F GP GVG+
Sbjct: 4 ANLIGQPLAIELLTAAIKQNR--IAPA------YLFAGPEGVGR 39
>gnl|CDD|235223 PRK04132, PRK04132, replication factor C small subunit;
Provisional.
Length = 846
Score = 29.8 bits (67), Expect = 9.2
Identities = 42/187 (22%), Positives = 78/187 (41%), Gaps = 25/187 (13%)
Query: 215 IKIEIDSKPEIM----DKLERRLIQLKIEHEAIKREYDESSKKRLLLIKKEINKLEIKYA 270
I ++ K ++ + L+R L ++ E E +K L LIKKE L+
Sbjct: 300 IIAKLREKYHVIISGSENLKRFLDEIGFSQE-------EKLEKALKLIKKENPNLDGLTI 352
Query: 271 NLEKIWKYEKTLIKDSQQIKEEIEKVRLKINKATRKSDWQTVSKLKY--GELNKLERILK 328
+ E I + ++D ++K +K KA R+ W+ + ++ Y EL +L++ L
Sbjct: 353 DKELI-----SYVRDRLKLKFTRDKRNWSYRKA-REISWELMKEIYYRLEELERLKKALS 406
Query: 329 EKSQKDIQLPNNANKFTLLKTKVGSEEIAEIV------SRTTGIPVSKIVQVEREKLLNI 382
E D K KT + ++ I E + S I ++K + + EK +
Sbjct: 407 ESILIDWNEVAKRRKEIAEKTGIRADRILEYIKGKRKPSLKNYIKIAKALGINLEKTIEA 466
Query: 383 ENLLCKR 389
+ K+
Sbjct: 467 MRIFAKK 473
>gnl|CDD|223626 COG0552, FtsY, Signal recognition particle GTPase [Intracellular
trafficking and secretion].
Length = 340
Score = 29.1 bits (66), Expect = 9.4
Identities = 33/169 (19%), Positives = 70/169 (41%), Gaps = 30/169 (17%)
Query: 277 KYEKTLIKDSQQIKEEIEKVRLKINKATRKSDW----QTVSKLKYGELNKLERI-LKEKS 331
+ + L ++ ++++ E EK+ + + ++ + Q +SK K ++ + LK+
Sbjct: 2 GFFEKLEEELEELEAEKEKIEEEDEEEEKEGWFERLKQGLSKTKKNFGKGIKGLFLKKIK 61
Query: 332 QKDIQLPNNANKFTLLKTKVG-------SEEIAEIVSRTTGIPVSKIVQ-VEREKLLNIE 383
+K + + L++ VG EE+ + + I + V+ RE L+ I
Sbjct: 62 EKLDEDLLEELEELLIEADVGVETAEEIIEELRKREGKKKKIKDEETVKEALREALIEI- 120
Query: 384 NLLCKRVVGQDEAISAVSNAIRRSRSGLSDAKRPYGSFMFLGPTGVGKT 432
R V + + + K+P+ +F+G GVGKT
Sbjct: 121 ----LRPVDKVDLPLEIPKE-----------KKPF-VILFVGVNGVGKT 153
>gnl|CDD|153328 cd07644, I-BAR_IMD_BAIAP2L2, Inverse (I)-BAR, also known as the
IRSp53/MIM homology Domain (IMD), of Brain-specific
Angiogenesis Inhibitor 1-Associated Protein 2-Like 2.
The IMD domain, also called Inverse-Bin/Amphiphysin/Rvs
(I-BAR) domain, is a dimerization and lipid-binding
module that bends membranes and induces membrane
protrusions. This group is composed of uncharacterized
proteins known as BAIAP2L2 (Brain-specific Angiogenesis
Inhibitor 1-Associated Protein 2-Like 2). They contain
an N-terminal IMD, an SH3 domain, and a WASP homology 2
(WH2) actin-binding motif at the C-terminus. The related
proteins, BAIAP2L1 and IRSp53, function as regulators of
membrane dynamics and the actin cytoskeleton. The IMD
domain binds and bundles actin filaments, binds
membranes and produces membrane protrusions, and
interacts with the small GTPase Rac.
Length = 215
Score = 29.1 bits (65), Expect = 9.6
Identities = 16/66 (24%), Positives = 36/66 (54%), Gaps = 8/66 (12%)
Query: 240 HEAIKREYDESSKKRLLLIKKEINKLEIKY----ANLEK----IWKYEKTLIKDSQQIKE 291
H + + D+++K + I+ E++Y ANLEK +W+ E+ ++ +++KE
Sbjct: 92 HVDLLQHMDKNTKLDMQFIEDSRRVYELEYRHRAANLEKCMSELWRMERQRDRNVREMKE 151
Query: 292 EIEKVR 297
+ ++R
Sbjct: 152 NVNRLR 157
>gnl|CDD|223775 COG0703, AroK, Shikimate kinase [Amino acid transport and
metabolism].
Length = 172
Score = 28.7 bits (65), Expect = 9.6
Identities = 11/24 (45%), Positives = 13/24 (54%)
Query: 13 TSNPVLIGEPGVGKTAIVEGLAQR 36
N VLIG G GK+ I LA+
Sbjct: 2 NMNIVLIGFMGAGKSTIGRALAKA 25
>gnl|CDD|233406 TIGR01420, pilT_fam, pilus retraction protein PilT. This model
represents the PilT subfamily of proteins related to
GspE, a protein involved in type II secretion (also
called the General Secretion Pathway). PilT is an
apparent cytosolic ATPase associated with type IV pilus
systems. It is not required for pilin biogenesis, but is
required for twitching motility and social gliding
behaviors, shown in some species, powered by pilus
retraction. Members of this family may be found in some
species that type IV pili but have related structures
for DNA uptake and natural transformation [Cell
envelope, Surface structures, Cellular processes,
Chemotaxis and motility].
Length = 343
Score = 29.2 bits (66), Expect = 10.0
Identities = 20/53 (37%), Positives = 30/53 (56%), Gaps = 8/53 (15%)
Query: 414 AKRPYGSFMFLGPTGVGKTELCKTLSACI-FNNEES---IIRI-DMSEFIEKH 461
A+RP G + GPTG GK+ TL++ I + N+ II I D E++ K+
Sbjct: 118 AERPRGLILVTGPTGSGKS---TTLASMIDYINKNKAYHIITIEDPIEYVHKN 167
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.319 0.138 0.391
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: 46,755,353
Number of extensions: 4904001
Number of successful extensions: 8131
Number of sequences better than 10.0: 1
Number of HSP's gapped: 7766
Number of HSP's successfully gapped: 534
Length of query: 899
Length of database: 10,937,602
Length adjustment: 106
Effective length of query: 793
Effective length of database: 6,236,078
Effective search space: 4945209854
Effective search space used: 4945209854
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 64 (28.2 bits)