RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 total letters
Searching..................................................done
Query= gi|254780270|ref|YP_003064683.1| ATP-dependent protease La
[Candidatus Liberibacter asiaticus str. psy62]
(820 letters)
>gnl|CDD|162028 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.
Length = 775
Score = 960 bits (2484), Expect = 0.0
Identities = 385/775 (49%), Positives = 534/775 (68%), Gaps = 16/775 (2%)
Query: 29 PLLPLRDIVVFPYMIVPLFVGREKSVRALDEAMNSHKKII-LVTQMNSNDENPIASSVYR 87
PLLPLR +FP MI P+ VGREKS++ + EA+ + + L Q + ++E P +Y
Sbjct: 1 PLLPLRRRPLFPGMIKPIDVGREKSIKLIKEALRLKQPYLGLFLQKDDDNEEPEEDDIYS 60
Query: 88 IGTIVDIVQILRLPD---GTVKILVEGSVRARIVEYIEREDFLEAITQVLPD--PTEDPV 142
+G + I+++L LP T K++VEG R RI E ++ +L L + +D
Sbjct: 61 VGVVAQILEMLPLPSSGTATYKVVVEGLRRIRIKELSDKGGYLVVRVDNLKEEPFDKDDE 120
Query: 143 ELEALSRSVIAEFSNYIKLNK--KISPEVIGITSQIEGFSKLADVIAANLSIK-VAERQK 199
E++AL+R + F I L+K + P ++ I+ +LAD +AA+L +K E Q+
Sbjct: 121 EIKALTREIKETFRELISLSKLFREQPALLSALEDIDEPGRLADFVAASLQLKEKDELQE 180
Query: 200 ILEAVSVKERLEMLLVFMESEISVLQVEKRIRSRVKRQMEKTQREYYLHEQMKAIQKELD 259
+LE V++++RL+ L ++ E+ +L+++ +I +V+ +MEKTQREYYL EQ+KAI+KEL
Sbjct: 181 VLETVNIEKRLKKALELLKKELELLKLQNKITKKVEEKMEKTQREYYLREQLKAIKKELG 240
Query: 260 NGEEGRDEISDFEARISKIRLSKEAREKALSELQKLRQMNPLSAESSVVRNYLDWLLGVP 319
++ +DE+ + ++ +++L +E ++ EL KL + P S+E +V RNYLDWL +P
Sbjct: 241 IEKDDKDELEKLKEKLEELKLPEEVKKVIEKELTKLSLLEPSSSEFTVTRNYLDWLTDLP 300
Query: 320 WDKKSKTKKNLDFAIRILDQDHFGLEKVKERIIEYLAVQMRVIKNKGLILCFVGPPGVGK 379
W K SK +L A ILD+DH+GL+KVKERI+EYLAVQ K KG ILC VGPPGVGK
Sbjct: 301 WGKYSKENLDLKRAKEILDEDHYGLKKVKERILEYLAVQKLRGKMKGPILCLVGPPGVGK 360
Query: 380 TSLAQSIAKATGRQYVRMSLGGVYDEADIRGHRRTYIGSMPGRIIQSLKRAKRSNPLLLL 439
TSL +SIAKA R++VR SLGGV DEA+IRGHRRTY+G+MPGRIIQ LK+AK NPL LL
Sbjct: 361 TSLGKSIAKALNRKFVRFSLGGVRDEAEIRGHRRTYVGAMPGRIIQGLKKAKTKNPLFLL 420
Query: 440 DEIDKMGSDLRGDPSAALLEVLDPAQNSSFVDHYLEVEYDLSDVMFIMTANTLN-IPLPL 498
DEIDK+GS RGDP++ALLEVLDP QN++F DHYL+V +DLS V+FI TAN+++ IP PL
Sbjct: 421 DEIDKIGSSFRGDPASALLEVLDPEQNNAFSDHYLDVPFDLSKVIFIATANSIDTIPRPL 480
Query: 499 MDRMEIIRIAGYTEEEKLQIAKNHLVKKVLTEHALKQEECCISDGVLLDIIRLFTHEAGV 558
+DRME+I ++GYTEEEKL+IAK +L+ K L +H LK +E I+D LL +I+ +T EAGV
Sbjct: 481 LDRMEVIELSGYTEEEKLEIAKKYLIPKALEDHGLKPDELKITDEALLLLIKYYTREAGV 540
Query: 559 RSFERALMKIARKAVTKIVK------NSDTTVSINENNLQDYLGVPRYKYGKIEGEDQVG 612
R+ ER + KI RKA K+V+ + +V I +NL+ YLG P + Y + G
Sbjct: 541 RNLERQIEKICRKAAVKLVEQGEKKKSEAESVVITPDNLKKYLGKPVFTYERAYEVTPPG 600
Query: 613 IVTGLAWTEVGGEILTVEGVIMPGKGEITITGNLKEIMKESILAASSYVRSKATTFGIIP 672
+V GLAWT +GG+ L +E + GKG + +TG L ++MKES A +YVRS A GI P
Sbjct: 601 VVMGLAWTPMGGDTLFIETTKVAGKGSLELTGQLGDVMKESAQIALTYVRSIAADLGISP 660
Query: 673 SAFNEINIHVHVPEGATPKDGPSAGIAMATAIVSIMTCIPVYKNVAMTGELTLRGRVLPI 732
+ F + +IH+HVPEGATPKDGPSAGI MATA++S+ T PV +VAMTGE+TLRG+VLPI
Sbjct: 661 NFFEKADIHLHVPEGATPKDGPSAGITMATALLSLATGKPVRPDVAMTGEITLRGKVLPI 720
Query: 733 GGLKEKLLAALRAGVTKVLIPEENIKDLMDIPENVKNGLEIIPVSFMGEVLKHAL 787
GGLKEK +AA RAG+ +++PE+N +DL ++PENVK GLEI V EVLK A
Sbjct: 721 GGLKEKTIAAKRAGIKTIILPEKNRRDLEELPENVKEGLEIHFVKHYDEVLKKAF 775
>gnl|CDD|182730 PRK10787, PRK10787, DNA-binding ATP-dependent protease La;
Provisional.
Length = 784
Score = 947 bits (2450), Expect = 0.0
Identities = 449/764 (58%), Positives = 586/764 (76%), Gaps = 1/764 (0%)
Query: 29 PLLPLRDIVVFPYMIVPLFVGREKSVRALDEAMNSHKKIILVTQMNSNDENPIASSVYRI 88
P+LPLRD+VV+P+M++PLFVGREKS+R L+ AM+ KKI+LV Q ++ + P + ++ +
Sbjct: 12 PVLPLRDVVVYPHMVIPLFVGREKSIRCLEAAMDHDKKIMLVAQKEASTDEPGVNDLFTV 71
Query: 89 GTIVDIVQILRLPDGTVKILVEGSVRARIVEYIEREDFLEAITQVLPDPTEDPVELEALS 148
GT+ I+Q+L+LPDGTVK+LVEG RARI + + A + L PT D E E L
Sbjct: 72 GTVASILQMLKLPDGTVKVLVEGLQRARISALSDNGEHFSAKAEYLESPTIDEREQEVLV 131
Query: 149 RSVIAEFSNYIKLNKKISPEVIGITSQIEGFSKLADVIAANLSIKVAERQKILEAVSVKE 208
R+ I++F YIKLNKKI PEV+ + I+ ++LAD IAA++ +K+A++Q +LE V E
Sbjct: 132 RTAISQFEGYIKLNKKIPPEVLTSLNSIDDPARLADTIAAHMPLKLADKQSVLEMSDVNE 191
Query: 209 RLEMLLVFMESEISVLQVEKRIRSRVKRQMEKTQREYYLHEQMKAIQKELDNGEEGRDEI 268
RLE L+ MESEI +LQVEKRIR+RVK+QMEK+QREYYL+EQMKAIQKEL ++ DE
Sbjct: 192 RLEYLMAMMESEIDLLQVEKRIRNRVKKQMEKSQREYYLNEQMKAIQKELGEMDDAPDEN 251
Query: 269 SDFEARISKIRLSKEAREKALSELQKLRQMNPLSAESSVVRNYLDWLLGVPWDKKSKTKK 328
+ +I ++ KEA+EKA +ELQKL+ M+P+SAE++VVR Y+DW++ VPW+ +SK KK
Sbjct: 252 EALKRKIDAAKMPKEAKEKAEAELQKLKMMSPMSAEATVVRGYIDWMVQVPWNARSKVKK 311
Query: 329 NLDFAIRILDQDHFGLEKVKERIIEYLAVQMRVIKNKGLILCFVGPPGVGKTSLAQSIAK 388
+L A ILD DH+GLE+VK+RI+EYLAVQ RV K KG ILC VGPPGVGKTSL QSIAK
Sbjct: 312 DLRQAQEILDTDHYGLERVKDRILEYLAVQSRVNKIKGPILCLVGPPGVGKTSLGQSIAK 371
Query: 389 ATGRQYVRMSLGGVYDEADIRGHRRTYIGSMPGRIIQSLKRAKRSNPLLLLDEIDKMGSD 448
ATGR+YVRM+LGGV DEA+IRGHRRTYIGSMPG++IQ + + NPL LLDEIDKM SD
Sbjct: 372 ATGRKYVRMALGGVRDEAEIRGHRRTYIGSMPGKLIQKMAKVGVKNPLFLLDEIDKMSSD 431
Query: 449 LRGDPSAALLEVLDPAQNSSFVDHYLEVEYDLSDVMFIMTANTLNIPLPLMDRMEIIRIA 508
+RGDP++ALLEVLDP QN +F DHYLEV+YDLSDVMF+ T+N++NIP PL+DRME+IR++
Sbjct: 432 MRGDPASALLEVLDPEQNVAFSDHYLEVDYDLSDVMFVATSNSMNIPAPLLDRMEVIRLS 491
Query: 509 GYTEEEKLQIAKNHLVKKVLTEHALKQEECCISDGVLLDIIRLFTHEAGVRSFERALMKI 568
GYTE+EKL IAK HL+ K + +ALK+ E + D ++ IIR +T EAGVRS ER + K+
Sbjct: 492 GYTEDEKLNIAKRHLLPKQIERNALKKGELTVDDSAIIGIIRYYTREAGVRSLEREISKL 551
Query: 569 ARKAVTKIVKNSDTT-VSINENNLQDYLGVPRYKYGKIEGEDQVGIVTGLAWTEVGGEIL 627
RKAV +++ + + IN +NL DYLGV R+ YG+ + E++VG VTGLAWTEVGG++L
Sbjct: 552 CRKAVKQLLLDKSLKHIEINGDNLHDYLGVQRFDYGRADNENRVGQVTGLAWTEVGGDLL 611
Query: 628 TVEGVIMPGKGEITITGNLKEIMKESILAASSYVRSKATTFGIIPSAFNEINIHVHVPEG 687
T+E +PGKG++T TG+L E+M+ESI AA + VR++A GI P + + +IHVHVPEG
Sbjct: 612 TIETACVPGKGKLTYTGSLGEVMQESIQAALTVVRARAEKLGINPDFYEKRDIHVHVPEG 671
Query: 688 ATPKDGPSAGIAMATAIVSIMTCIPVYKNVAMTGELTLRGRVLPIGGLKEKLLAALRAGV 747
ATPKDGPSAGIAM TA+VS +T PV +VAMTGE+TLRG+VLPIGGLKEKLLAA R G+
Sbjct: 672 ATPKDGPSAGIAMCTALVSCLTGNPVRADVAMTGEITLRGQVLPIGGLKEKLLAAHRGGI 731
Query: 748 TKVLIPEENIKDLMDIPENVKNGLEIIPVSFMGEVLKHALLRMP 791
VLIP EN +DL +IP+NV L+I PV + EVL AL P
Sbjct: 732 KTVLIPFENKRDLEEIPDNVIADLDIHPVKRIEEVLTLALQNEP 775
>gnl|CDD|184312 PRK13765, PRK13765, ATP-dependent protease Lon; Provisional.
Length = 637
Score = 137 bits (346), Expect = 2e-32
Identities = 78/199 (39%), Positives = 121/199 (60%), Gaps = 13/199 (6%)
Query: 599 RYKYGKIEGEDQVGIVTGLAWT-EVGGEILTVEGVIMPG----KGEITITGNLKEIMKES 653
Y+ EG +VG V GLA E G +L + + P +G++ TG LKEI KE+
Sbjct: 417 DYELFVTEGG-EVGRVNGLAVMGEDSGIVLPIMAEVTPAQSKEEGKVIATGKLKEIAKEA 475
Query: 654 ILAASSYVRSKATTFGIIPSAFNEINIHVHVPEGATPKDGPSAGIAMATAIVSIMTCIPV 713
+ S+ ++ K T I + +IH+ + +G SA I++ATA++S + IPV
Sbjct: 476 VQNVSAIIK-KFTGKDI-----SNYDIHIQFVQTYEGVEGDSASISVATAVISALENIPV 529
Query: 714 YKNVAMTGELTLRGRVLPIGGLKEKLLAALRAGVTKVLIPEENIKDLMDIPENVKNGLEI 773
++VAMTG L++RG VLP+GG+ K+ AA AG+ KV+IP+ N +D+M I + ++ +EI
Sbjct: 530 DQSVAMTGSLSVRGDVLPVGGVTYKIEAAAEAGIKKVIIPKSNEQDVM-IEDEYEDKIEI 588
Query: 774 IPVSFMGEVLKHALLRMPD 792
IPVS + EVL+HAL+ P+
Sbjct: 589 IPVSTISEVLEHALVGGPE 607
>gnl|CDD|162029 TIGR00764, lon_rel, lon-related putative ATP-dependent protease.
Members of this family from Pyrococcus horikoshii and
Pyrococcus abyssi each contain a predicted intein.
Length = 608
Score = 126 bits (317), Expect = 3e-29
Identities = 74/194 (38%), Positives = 114/194 (58%), Gaps = 13/194 (6%)
Query: 599 RYKYGKIEGEDQVGIVTGLAWT-EVGGEILTVEGVIMPG----KGEITITGNLKEIMKES 653
RYK EG +VG V GLA E G +L ++ ++ P +G I TG L EI KE+
Sbjct: 408 RYKVIVNEG-GEVGRVNGLAVIGEASGIVLPIKAIVAPAESKEEGRIIATGKLGEIAKEA 466
Query: 654 ILAASSYVRSKATTFGIIPSAFNEINIHVHVPEGATPKDGPSAGIAMATAIVSIMTCIPV 713
+ S+ ++ + +IH+ + +G SA I++ATA++S + IPV
Sbjct: 467 VTNVSALIKKYTGE------DISNYDIHIQFLQTYEGVEGDSASISVATAVISALEEIPV 520
Query: 714 YKNVAMTGELTLRGRVLPIGGLKEKLLAALRAGVTKVLIPEENIKDLMDIPENVKNGLEI 773
++VAMTG L++RG VLP+GG+ EK+ AA+ AG+ KV+IP+ N+ D++ E + +EI
Sbjct: 521 DQDVAMTGSLSVRGEVLPVGGVTEKIEAAIEAGIKKVIIPKSNMIDVILEKET-EGKIEI 579
Query: 774 IPVSFMGEVLKHAL 787
IPV + EVL+H L
Sbjct: 580 IPVETLDEVLEHVL 593
>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.
Length = 531
Score = 116 bits (291), Expect = 3e-26
Identities = 99/317 (31%), Positives = 141/317 (44%), Gaps = 43/317 (13%)
Query: 488 TANTLNIPLPLMDRMEIIRIAGYTEEEKLQIAKNHLVK--KVLTEHALKQEECCISDGVL 545
T N IP L R I +EE +IAKN K L +HAL+ S+G
Sbjct: 241 TRNPEEIPPALRSRCVEIFFRPLLDEEIKEIAKNAAEKIGINLEKHALELIVKYASNG-- 298
Query: 546 LDIIRLFTHEAGVRSFERALMKIARKAVTKIVKNSDTTVSINENNLQDYLGVPRYKYGKI 605
+ + + AG+ E RK + D N P+ K+
Sbjct: 299 REAVNIVQLAAGIALGE------GRKRILA----EDIEWVAENGNYH-----PKP-EIKL 342
Query: 606 EGEDQVGIVTGLAWTEVG-GEILTVEGVIMP---GKGEITITGNLKEIMKESILAASSYV 661
E Q+G V GLA G +L VE G I +TG ++E E I + V
Sbjct: 343 SSEPQIGRVNGLAVYGPNSGAVLEVEATAERAENLPGSINVTGIIEE---EEIGGSGKSV 399
Query: 662 RSKAT-------TFGIIPSAFNE----INIHVHVPEGATPKDGPSAGIAMATAIVSIMTC 710
R K++ ++ S F +IH++ P G P DGPSAG+A+A AI S +
Sbjct: 400 RRKSSARGSVENVLAVLRSVFGINPQNYDIHINFP-GGIPVDGPSAGVAIAVAIYSAIFK 458
Query: 711 IPVYKNVAMTGELTLRGRVLPIGGLKEKLLAALRAGVTKVLIPEENIKDLMDIPENVKNG 770
P+ VAMTGE++L G V P+GG+ K+ AA +AG KV+IP EN ++ +
Sbjct: 459 CPIDNKVAMTGEISLNGLVKPVGGVPSKIEAAKKAGAKKVIIPYENWQESFGSISGIN-- 516
Query: 771 LEIIPVSFMGEVLKHAL 787
+IPV + E L +AL
Sbjct: 517 --VIPVKNIDEALNYAL 531
>gnl|CDD|163066 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.
Length = 615
Score = 108 bits (271), Expect = 7e-24
Identities = 71/208 (34%), Positives = 121/208 (58%), Gaps = 18/208 (8%)
Query: 584 VSINENNLQDYLGVPRYK-YGKIEGED--QVGIVTGLAWTEVGGEILTVEGVIM----PG 636
V+I ++++ + + + R Y K + +VG V GL + G +L +E V PG
Sbjct: 416 VTITQDDVYEVIQISRLSPYEKRKASPTYEVGHVFGLGVSGFVGSVLEIEAVAFEAKEPG 475
Query: 637 KGEITITGNLKEIMKESILAASSYVRSKATTFGIIPSAFNEINIHVHVPEGATPKDGPSA 696
KG + + K+S+ A+S +R K T G S ++ IHV+V G DGPSA
Sbjct: 476 KGTVRFNDTAGSMAKDSVFNAASVIR-KIT--GKDLSNYD---IHVNVIGGGR-IDGPSA 528
Query: 697 GIAMATAIVSIMTCIPVYKNVAMTGELTLRGRVLPIGGLKEKLLAALRAGVTKVLIPEEN 756
G A+ ++S + P+ ++VA+TGE++LRG++ P+GG+ EK+ A +AG+ V+IPEEN
Sbjct: 529 GAAITLCMISAILGKPIRQDVAITGEISLRGKIKPVGGIFEKIYGAKQAGIKTVVIPEEN 588
Query: 757 IKDLMDIPENVKNGLEIIPVSFMGEVLK 784
+K D+P+ + G+E+ VS + E+++
Sbjct: 589 LK---DVPQGLP-GIEVKFVSTIEELMR 612
>gnl|CDD|131701 TIGR02653, Lon_rel_chp, conserved hypothetical protein. This model
describes a protein family of unknown function, about
690 residues in length, in which some members show
C-terminal sequence similarity to Pfam model pfam05362,
which is the Lon protease C-terminal proteolytic domain,
from MEROPS family S16. However, the annotated catalytic
sites of E. coli Lon protease are not conserved in
members of this family. Members have a motif
GP[RK][GS]TGKS, similar to the ATP-binding P-loop motif
GxxGxGK[ST].
Length = 675
Score = 70.3 bits (172), Expect = 2e-12
Identities = 45/182 (24%), Positives = 82/182 (45%), Gaps = 5/182 (2%)
Query: 587 NENNLQDYLGVPRYKYGKI--EGEDQVGIVTGLAWTEVGG-EILTVEGVIMPGKGEITIT 643
NE+ + ++ VP K+ G + G+V + E G + E + G G+ +++
Sbjct: 469 NESLEEFFVSVPEQGGSKLIPAGPPKPGVVYAVTQNESGKVGLYRFEVQVSAGSGKHSVS 528
Query: 644 GNLKEI-MKESILAASSYVRSKATTFGIIPSAFNEINIHVHVPEGATPKDGPSAGIAMAT 702
G KESI A Y + + F+E + H+HV + A +A
Sbjct: 529 GLGSNTTAKESIRVAFDYFKGNLVRISA-SAKFSEHDYHLHVVDLHNTGPSTEASLAALI 587
Query: 703 AIVSIMTCIPVYKNVAMTGELTLRGRVLPIGGLKEKLLAALRAGVTKVLIPEENIKDLMD 762
A+ S + PV + + + G +T+ G + P+ L L A+ +G +VLIP + +D+
Sbjct: 588 ALCSALLKRPVQEQMVILGSMTIGGVINPVQDLAGSLQLAMDSGAKRVLIPMSSARDIPT 647
Query: 763 IP 764
+P
Sbjct: 648 VP 649
>gnl|CDD|183326 PRK11823, PRK11823, DNA repair protein RadA; Provisional.
Length = 446
Score = 58.2 bits (142), Expect = 9e-09
Identities = 25/94 (26%), Positives = 49/94 (52%), Gaps = 6/94 (6%)
Query: 694 PSAGIAMATAIVSIMTCIPVYKNVAMTGELTLRGRVLPIGGLKEKLLAALRAGVTKVLIP 753
P+A +A+A AI S + P+ + + GE+ L G + P+ ++ +L A + G + ++P
Sbjct: 357 PAADLAVALAIASSLRDRPLPPDTVVFGEVGLTGEIRPVPRIERRLKEAAKLGFKRAIVP 416
Query: 754 EENIKDLMDIPENVKNGLEIIPVSFMGEVLKHAL 787
+ N +P+ G+E+I V + E L+
Sbjct: 417 KGN------LPKKPPKGIEVIGVKTLAEALELLF 444
>gnl|CDD|183986 PRK13342, PRK13342, recombination factor protein RarA; Reviewed.
Length = 413
Score = 57.8 bits (141), Expect = 1e-08
Identities = 26/88 (29%), Positives = 42/88 (47%), Gaps = 20/88 (22%)
Query: 360 RVIKNKGLI-LCFVGPPGVGKTSLAQSIAKATGRQYVRMS--LGGVYDEADIRGHRRTYI 416
R+I+ L + GPPG GKT+LA+ IA AT + +S GV D+R
Sbjct: 29 RMIEAGRLSSMILWGPPGTGKTTLARIIAGATDAPFEALSAVTSGV---KDLR------- 78
Query: 417 GSMPGRIIQSLKRAKRS--NPLLLLDEI 442
+I+ ++ + + +L +DEI
Sbjct: 79 -----EVIEEARQRRSAGRRTILFIDEI 101
>gnl|CDD|149019 pfam07728, AAA_5, AAA domain (dynein-related subfamily). This Pfam
entry includes some of the AAA proteins not detected by
the pfam00004 model.
Length = 139
Score = 57.7 bits (140), Expect = 1e-08
Identities = 36/143 (25%), Positives = 55/143 (38%), Gaps = 14/143 (9%)
Query: 369 LCFVGPPGVGKTSLAQSIAKAT-GRQYVRMSLGGVYDEADIRGHRRTYIGSMPGRIIQSL 427
+ VGPPG GK+ LA+ +A A R + L E D++G R + L
Sbjct: 2 VLLVGPPGTGKSELAERLAAALSNRPVFYVQLTRDTTEEDLKGRRN-IANGTTSWVDGPL 60
Query: 428 KRAKRSNPLLLLDEIDKMGSDLRGDPSAALLEVLDPA---QNSSFVDHYLEVEYDLSDVM 484
RA R + +LDEI++ D+ +LL +LD + +
Sbjct: 61 VRAAREGEIAVLDEINRANPDVLN----SLLSLLDERRLLLPEGGELVKVAPDDFAKRFR 116
Query: 485 FIMTANTLN-----IPLPLMDRM 502
I T N L+ + L R
Sbjct: 117 LIATMNPLDRGLNELSPALRSRF 139
>gnl|CDD|162958 TIGR02639, ClpA, ATP-dependent Clp protease ATP-binding subunit
clpA.
Length = 731
Score = 52.4 bits (126), Expect = 5e-07
Identities = 44/130 (33%), Positives = 63/130 (48%), Gaps = 24/130 (18%)
Query: 371 FVGPPGVGKTSLAQSIAKATGRQYVRMSLGGVYDEADIRGHRRT---YIGSMPGRIIQS- 426
F GP GVGKT LA+ +A+A G R + Y E + T IG+ PG +
Sbjct: 489 FTGPTGVGKTELAKQLAEALGVHLERFDMSE-YME------KHTVSRLIGAPPGYVGFEQ 541
Query: 427 ---LKRAKRSNP--LLLLDEIDKMGSDLRGDPSAALLEVLDPAQNSSFVDHYLEVEYDLS 481
L A R +P +LLLDEI+K D+ LL+V+D ++ D+ D
Sbjct: 542 GGLLTEAVRKHPHCVLLLDEIEKAHPDI----YNILLQVMD---YATLTDNNGRKA-DFR 593
Query: 482 DVMFIMTANT 491
+V+ IMT+N
Sbjct: 594 NVILIMTSNA 603
Score = 33.5 bits (77), Expect = 0.21
Identities = 32/105 (30%), Positives = 47/105 (44%), Gaps = 12/105 (11%)
Query: 343 GLEKVKERIIEYLAVQMRVIKNKGLILCFVGPPGVGKTSLAQSIAKATGRQYVRMSLGG- 401
G E ER I+ L R KN L VG PGVGKT++A+ +A V +L
Sbjct: 186 GREDELERTIQVLC---RRKKNNPL---LVGEPGVGKTAIAEGLALRIAEGKVPENLKNA 239
Query: 402 -VY--DEADIRGHRRTYIGSMPGRIIQSLKRAKR-SNPLLLLDEI 442
+Y D + + Y G R+ + ++ N +L +DEI
Sbjct: 240 KIYSLDMGSLLAGTK-YRGDFEERLKAVVSEIEKEPNAILFIDEI 283
>gnl|CDD|128665 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 = 51.2 bits (122), Expect = 9e-07
Identities = 34/147 (23%), Positives = 58/147 (39%), Gaps = 20/147 (13%)
Query: 365 KGLILCFVGPPGVGKTSLAQSIAKATGRQYVRM-------SLGGVYDEADIRGHRRTYIG 417
G ++ VGPPG GKT+LA+++A+ G + L V D+ +
Sbjct: 1 PGEVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKAS 60
Query: 418 SMPGRII-QSLKRAKRSNP-LLLLDEIDKMGSDLRGDPSAALLEVLDPAQNSSFVDHYLE 475
+ +L A++ P +L+LDEI + ALL +L+ L
Sbjct: 61 GSGELRLRLALALARKLKPDVLILDEITSLLDAE----QEALLLLLE-------ELRLLL 109
Query: 476 VEYDLSDVMFIMTANTLNIPLPLMDRM 502
+ ++ I+T N P + R
Sbjct: 110 LLKSEKNLTVILTTNDEKDLGPALLRR 136
>gnl|CDD|163222 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.
Length = 852
Score = 49.9 bits (120), Expect = 2e-06
Identities = 73/289 (25%), Positives = 116/289 (40%), Gaps = 50/289 (17%)
Query: 176 IEGFSKLADVIAANLSIKVAERQKILEAVSVKERLEMLLVFMESEISVLQVE-KRIRSRV 234
+E + + L E + ERL L +E++ L+ E + +R
Sbjct: 421 LEDLRRRIAALELELDALEREAALGAD---HDERLAEL----RAELAALEAELAALEARW 473
Query: 235 KRQMEKTQREYYLHEQMKAIQKELDNGEEGRDEISDFEARISKIRLSKEAREKALSELQK 294
+++ E L E + A++ EL+ + D A +++ E AL+ Q
Sbjct: 474 QQEKE-------LVEAILALRAELEADAD--APADDDAALRAQLA----ELEAALASAQG 520
Query: 295 -LRQMNPLSAESSVVRNYLDWLLGVPWDK--KSKTKKNLDFAI----RILDQDHFGLEKV 347
+ P +V DW G+P + + + + L R++ QDH LE +
Sbjct: 521 EEPLVFPEVDAQAVAEVVADWT-GIPVGRMVRDEIEAVLSLPDRLAERVIGQDH-ALEAI 578
Query: 348 KERIIEYLAVQMRVIKNKGLILCFVGPPGVGKTSLAQSIAKAT--GRQY---VRMSLGGV 402
ERI A K G+ L VGP GVGKT A ++A+ G Q + MS
Sbjct: 579 AERIRTARAGLEDPRKPLGVFL-LVGPSGVGKTETALALAELLYGGEQNLITINMS---E 634
Query: 403 YDEADIRGHR-RTYIGSMPGRIIQS----LKRAKRSNP--LLLLDEIDK 444
+ EA H GS PG + L A R P ++LLDE++K
Sbjct: 635 FQEA----HTVSRLKGSPPGYVGYGEGGVLTEAVRRKPYSVVLLDEVEK 679
>gnl|CDD|162266 TIGR01241, FtsH_fam, ATP-dependent metalloprotease FtsH.
HflB(FtsH) is a pleiotropic protein required for correct
cell division in bacteria. It has ATP-dependent zinc
metalloprotease activity. It was formerly designated
cell division protein FtsH.
Length = 495
Score = 46.9 bits (112), Expect = 2e-05
Identities = 39/134 (29%), Positives = 69/134 (51%), Gaps = 20/134 (14%)
Query: 323 KSKTKKNLDFAIRILDQDHFGLEKVKER---IIEYLAVQMRVIK-----NKGLILCFVGP 374
KSK K + ++ +D G+++ KE I+++L + K KG++L VGP
Sbjct: 39 KSKAKLLNEEKPKVTFKDVAGIDEAKEELMEIVDFLKNPSKFTKLGAKIPKGVLL--VGP 96
Query: 375 PGVGKTSLAQSIAKATGRQYVRMSLGGVYDEADIRGHRRTYIGSMPGRIIQSLKRAKRSN 434
PG GKT LA+++A G + +S G + E ++G R+ ++AK++
Sbjct: 97 PGTGKTLLAKAVAGEAGVPFFSIS-GSDFVE--------MFVGVGASRVRDLFEQAKKNA 147
Query: 435 P-LLLLDEIDKMGS 447
P ++ +DEID +G
Sbjct: 148 PCIIFIDEIDAVGR 161
>gnl|CDD|128740 smart00464, LON, Found in ATP-dependent protease La (LON).
N-terminal domain of the ATP-dependent protease La
(LON), present also in other bacterial ORFs.
Length = 92
Score = 46.7 bits (111), Expect = 3e-05
Identities = 19/57 (33%), Positives = 31/57 (54%), Gaps = 2/57 (3%)
Query: 29 PLLPLRDIVVFPYMIVPLFVGREKSVRALDEAMNSHKK--IILVTQMNSNDENPIAS 83
PLLP+R +FP ++P+ V R KSV A+ EA+ + I+ + Q + + S
Sbjct: 3 PLLPIRRRPLFPGFVLPIPVKRPKSVAAIKEALRRSQPYVIVFLLQDDPTETPEPLS 59
>gnl|CDD|116338 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 = 46.4 bits (111), Expect = 3e-05
Identities = 41/174 (23%), Positives = 68/174 (39%), Gaps = 40/174 (22%)
Query: 371 FVGPPGVGKTSLAQSIAKATGRQYVRMSLGGVYDEADIRGHRRTY---------IGSMPG 421
F+GP GVGKT LA+++A+ L + A IR Y IG+ PG
Sbjct: 8 FLGPTGVGKTELAKALAE----------LLFGDERALIRIDMSEYMEEHSVSRLIGAPPG 57
Query: 422 RI------IQSLKRAKRSNPLLLLDEIDKMGSD-LRGDPSAALLEVLDPAQNSSFVDHYL 474
+ + ++ ++L+DEI+K LL++L+ + D
Sbjct: 58 YVGYEEGGQLTEAVRRKPYSIVLIDEIEKAHPGVQN-----DLLQILE---GGTLTDKQ- 108
Query: 475 EVEYDLSDVMFIMTANTLNIPLPLMDRMEIIRIAGYTEEEKLQIAKNHLVKKVL 528
+ D + +FIMT N + R+ + E L+ L+KK
Sbjct: 109 GRKVDFRNTLFIMTGN-----FGSEKISDASRLGKSPDYELLKELVMDLLKKGF 157
>gnl|CDD|179778 PRK04195, PRK04195, replication factor C large subunit;
Provisional.
Length = 482
Score = 44.9 bits (107), Expect = 9e-05
Identities = 41/132 (31%), Positives = 65/132 (49%), Gaps = 30/132 (22%)
Query: 345 EKVKERIIEYLAVQMRVIKNKGLILCFVGPPGVGKTSLAQSIAKATGRQYVRM--SLGGV 402
EK KE++ E++ ++ K L+L GPPGVGKTSLA ++A G + + + S
Sbjct: 20 EKAKEQLREWIESWLKGKPKKALLL--YGPPGVGKTSLAHALANDYGWEVIELNAS---- 73
Query: 403 YDEADIRGHRRTYIGSMPGRIIQSLKRAKRSNPL-------LLLDEIDKM-GSDLRGDPS 454
D+ RT I + A S L +LLDE+D + G++ RG +
Sbjct: 74 -DQ-------RTA-----DVIERVAGEAATSGSLFGARRKLILLDEVDGIHGNEDRGG-A 119
Query: 455 AALLEVLDPAQN 466
A+LE++ A+
Sbjct: 120 RAILELIKKAKQ 131
>gnl|CDD|161868 TIGR00416, sms, DNA repair protein RadA. The gene protuct codes
for a probable ATP-dependent protease involved in both
DNA repair and degradation of proteins, peptides,
glycopeptides. Also known as sms. Residues 11-28 of the
SEED alignment contain a putative Zn binding domain.
Residues 110-117 of the seed contain a putative ATP
binding site both documented in Haemophilus and in
Listeria monocytogenes. for E.coli see ( J. BACTERIOL.
178:5045-5048(1996)).
Length = 454
Score = 44.0 bits (104), Expect = 1e-04
Identities = 26/92 (28%), Positives = 48/92 (52%), Gaps = 6/92 (6%)
Query: 692 DGPSAGIAMATAIVSIMTCIPVYKNVAMTGELTLRGRVLPIGGLKEKLLAALRAGVTKVL 751
P+A +A+ AIVS P+ ++ GE+ L G + P+ L+E+L A + G + +
Sbjct: 369 SEPAADLALLIAIVSSFRDRPLDPDLVFLGEVGLAGEIRPVPSLEERLKEAAKLGFKRAI 428
Query: 752 IPEENIKDLMDIPENVKNGLEIIPVSFMGEVL 783
+P+ N P+ G+++I V +G+ L
Sbjct: 429 VPKAN------SPKTAPEGIKVIGVKKVGDAL 454
>gnl|CDD|182683 PRK10733, hflB, ATP-dependent metalloprotease; Reviewed.
Length = 644
Score = 43.9 bits (103), Expect = 2e-04
Identities = 40/131 (30%), Positives = 64/131 (48%), Gaps = 16/131 (12%)
Query: 323 KSKTKKNLDFAIRILDQDHFGLEKVKERI---IEYLAVQMRVIKNKGLI---LCFVGPPG 376
KSK + + I+ D G ++ KE + +EYL R K G I + VGPPG
Sbjct: 136 KSKARMLTEDQIKTTFADVAGCDEAKEEVAELVEYLREPSRFQKLGGKIPKGVLMVGPPG 195
Query: 377 VGKTSLAQSIAKATGRQYVRMSLGGVYDEADIRGHRRTYIGSMPGRIIQSLKRAKRSNP- 435
GKT LA++IA + +S G + E ++G R+ ++AK++ P
Sbjct: 196 TGKTLLAKAIAGEAKVPFFTIS-GSDFVE--------MFVGVGASRVRDMFEQAKKAAPC 246
Query: 436 LLLLDEIDKMG 446
++ +DEID +G
Sbjct: 247 IIFIDEIDAVG 257
>gnl|CDD|183985 PRK13341, PRK13341, recombination factor protein RarA/unknown
domain fusion protein; Reviewed.
Length = 725
Score = 42.4 bits (100), Expect = 5e-04
Identities = 27/77 (35%), Positives = 40/77 (51%), Gaps = 16/77 (20%)
Query: 369 LCFVGPPGVGKTSLAQSIAKATGRQYVRMS--LGGVYDEADIRGHRRTYIGSMPGRIIQS 426
L GPPGVGKT+LA+ IA T + ++ L GV D+R + R +
Sbjct: 55 LILYGPPGVGKTTLARIIANHTRAHFSSLNAVLAGV---KDLR--------AEVDRAKER 103
Query: 427 LKR-AKRSNPLLLLDEI 442
L+R KR+ +L +DE+
Sbjct: 104 LERHGKRT--ILFIDEV 118
>gnl|CDD|129002 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 = 41.1 bits (97), Expect = 0.001
Identities = 21/69 (30%), Positives = 35/69 (50%), Gaps = 1/69 (1%)
Query: 335 RILDQDHFGLEKVKERIIEYLAVQMRVIKNKGLILCFVGPPGVGKTSLAQSIAKATGRQY 394
R D D FG+E+ ER + Y + ++ + IL +GP G GK+SL + + + +Y
Sbjct: 47 RFFDHDFFGMEEAIERFVNYFKSAAQGLEERKQILYLLGPVGGGKSSLVECLKRGL-EEY 105
Query: 395 VRMSLGGVY 403
+ G Y
Sbjct: 106 SKTPEGRRY 114
>gnl|CDD|131926 TIGR02880, cbbX_cfxQ, probable Rubsico expression protein CbbX.
Proteins in this family are now designated CbbX. Some
previously were CfxQ (carbon fixation Q). Its gene is
often found immmediately downstream of the Rubisco large
and small chain genes, and it is suggested to be
necessary for Rubisco expression. CbbX has been shown to
be necessary for photoautotrophic growth. This protein
belongs to the larger family of pfam00004, ATPase family
Associated with various cellular Activities. Within that
larger family, members of this family are most closely
related to the stage V sporulation protein K, or SpoVK,
in endospore-forming bacteria such as Bacillus subtilis.
Length = 284
Score = 41.0 bits (96), Expect = 0.001
Identities = 37/115 (32%), Positives = 53/115 (46%), Gaps = 15/115 (13%)
Query: 337 LDQDHFGLEKVKERIIEYLAV----QMR-----VIKNKGLILCFVGPPGVGKTSLAQSIA 387
LD++ GL+ VK RI E A+ ++R L + F G PG GKT++A +A
Sbjct: 20 LDRELIGLKPVKTRIREIAALLLVERLRQRLGLASAAPTLHMSFTGNPGTGKTTVALRMA 79
Query: 388 KATGR-QYVRMSLGGVYDEADIRGHRRTYIGSMPGRIIQSLKRAKRSNPLLLLDE 441
+ R YVR D+ G YIG + + LKRA +L +DE
Sbjct: 80 QILHRLGYVRKGHLVSVTRDDLVGQ---YIGHTAPKTKEILKRAM--GGVLFIDE 129
>gnl|CDD|177379 PHA02544, 44, clamp loader, small subunit; Provisional.
Length = 316
Score = 39.6 bits (93), Expect = 0.003
Identities = 47/200 (23%), Positives = 84/200 (42%), Gaps = 43/200 (21%)
Query: 359 MRVIKNKGLI--LCFVGP-PGVGKTSLAQSIAKATGRQY--VRMSLGGVYDEADIRGHRR 413
+ I KG I + P PG GKT++A+++ G + V S + +R
Sbjct: 33 FKSIVKKGRIPNMLLHSPSPGTGKTTVAKALCNEVGAEVLFVNGSDCRI---DFVRNRLT 89
Query: 414 TYIGSMPGRIIQSLKRAKRSNPLLLLDEIDKMGSDLRGDPSAALLEVLDPAQNS--SFVD 471
+ ++ SL ++++DE D++G L AQ SF++
Sbjct: 90 RFASTV------SLT-GGGK--VIIIDEFDRLG--------------LADAQRHLRSFME 126
Query: 472 HYLEVEYDLSDVMFIMTANTLN-IPLPLMDRMEIIRIAGYTEEEKLQIAKNHLVKKVLTE 530
Y + FI+TAN N I PL R +I T+EE++++ K +V+ +
Sbjct: 127 AY------SKNCSFIITANNKNGIIEPLRSRCRVIDFGVPTKEEQIEMMKQMIVR---CK 177
Query: 531 HALKQEECCISDGVLLDIIR 550
L+ E + VL +++
Sbjct: 178 GILEAEGVEVDMKVLAALVK 197
>gnl|CDD|182917 PRK11034, clpA, ATP-dependent Clp protease ATP-binding subunit;
Provisional.
Length = 758
Score = 39.4 bits (92), Expect = 0.004
Identities = 39/129 (30%), Positives = 63/129 (48%), Gaps = 24/129 (18%)
Query: 371 FVGPPGVGKTSLAQSIAKATGRQYVRMSLGGVYDEADIRGHRRT---YIGSMPGRI---- 423
F GP GVGKT + ++KA G + +R +D ++ R T IG+ PG +
Sbjct: 493 FAGPTGVGKTEVTVQLSKALGIELLR------FDMSEY-MERHTVSRLIGAPPGYVGFDQ 545
Query: 424 --IQSLKRAKRSNPLLLLDEIDKMGSDLRGDPSAALLEVLDPAQNSSFVDHYLEVEYDLS 481
+ + K + +LLLDEI+K D+ LL+V+D N + D+ + D
Sbjct: 546 GGLLTDAVIKHPHAVLLLDEIEKAHPDVFN----LLLQVMD---NGTLTDNNGR-KADFR 597
Query: 482 DVMFIMTAN 490
+V+ +MT N
Sbjct: 598 NVVLVMTTN 606
>gnl|CDD|116881 pfam08298, 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 = 358
Score = 39.4 bits (92), Expect = 0.004
Identities = 19/50 (38%), Positives = 30/50 (60%)
Query: 340 DHFGLEKVKERIIEYLAVQMRVIKNKGLILCFVGPPGVGKTSLAQSIAKA 389
D FG+E+ ERI+ Y + ++ + IL +GP G GK+SLA+ + K
Sbjct: 59 DFFGMEETIERIVNYFRHAAQGLEERKQILYLLGPVGGGKSSLAERLKKL 108
>gnl|CDD|178847 PRK00080, ruvB, Holliday junction DNA helicase RuvB; Reviewed.
Length = 328
Score = 38.2 bits (90), Expect = 0.008
Identities = 24/54 (44%), Positives = 30/54 (55%), Gaps = 11/54 (20%)
Query: 343 GLEKVKERI---IEYLAVQMRVIKNKGL--ILCFVGPPGVGKTSLAQSIAKATG 391
G EKVKE + IE A + R + L +L GPPG+GKT+LA IA G
Sbjct: 29 GQEKVKENLKIFIE--AAKKR---GEALDHVL-LYGPPGLGKTTLANIIANEMG 76
>gnl|CDD|181233 PRK08116, PRK08116, hypothetical protein; Validated.
Length = 268
Score = 38.1 bits (89), Expect = 0.010
Identities = 24/83 (28%), Positives = 38/83 (45%), Gaps = 11/83 (13%)
Query: 363 KNKGLILCFVGPPGVGKTSLAQSIAKATGRQYVR---MSLGGVYDEADIRGHRRTYIGSM 419
+N GL+L G G GKT LA IA + V ++ + + I+ ++
Sbjct: 113 ENVGLLLW--GSVGTGKTYLAACIANELIEKGVPVIFVNFPQLLNR--IKSTYKSSGKED 168
Query: 420 PGRIIQSLKRAKRSNPLLLLDEI 442
II+SL A LL+LD++
Sbjct: 169 ENEIIRSLVNA----DLLILDDL 187
>gnl|CDD|179026 PRK00440, rfc, replication factor C small subunit; Reviewed.
Length = 319
Score = 37.9 bits (89), Expect = 0.010
Identities = 18/47 (38%), Positives = 27/47 (57%), Gaps = 8/47 (17%)
Query: 343 GLEKVKERIIEYLAVQMRVIKNKGLI-LCFVGPPGVGKTSLAQSIAK 388
G E++ ER+ Y +K K + L F GPPG GKT+ A ++A+
Sbjct: 21 GQEEIVERLKSY-------VKEKNMPHLLFAGPPGTGKTTAALALAR 60
>gnl|CDD|162267 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 = 38.0 bits (88), Expect = 0.011
Identities = 50/204 (24%), Positives = 90/204 (44%), Gaps = 34/204 (16%)
Query: 343 GLEKVKERIIEYLAVQ-----------MRVIKNKGLILCFVGPPGVGKTSLAQSIAKATG 391
GLE+VK+ + E AV+ M + KG++L GPPG GKT LA+++A +G
Sbjct: 457 GLEEVKQELRE--AVEWPLKHPEIFEKMGIRPPKGVLL--FGPPGTGKTLLAKAVATESG 512
Query: 392 RQYVRMSLGGVYDEADIRGHRRTYIGSMPGRIIQSLKRAKRSNP-LLLLDEIDKMGSDLR 450
++ + + + ++G I + ++A+++ P ++ DEID +
Sbjct: 513 ANFIAVRGPEILSK---------WVGESEKAIREIFRKARQAAPAIIFFDEIDAIAPARG 563
Query: 451 GDPSAALLEVLDPAQNSSFVDHYLEVEYDLSDVMFIMTANTLNIPLPLMDRM----EIIR 506
+ V D N + ++ +LS+V+ I N +I P + R +I
Sbjct: 564 ARFDTS---VTDRIVNQLLTE--MDGIQELSNVVVIAATNRPDILDPALLRPGRFDRLIL 618
Query: 507 IAGYTEEEKLQIAKNHLVKKVLTE 530
+ EE + +I K H L E
Sbjct: 619 VPPPDEEARKEIFKIHTRSMPLAE 642
Score = 36.8 bits (85), Expect = 0.020
Identities = 32/115 (27%), Positives = 58/115 (50%), Gaps = 21/115 (18%)
Query: 339 QDHFGLEKVKERIIEYLAVQMR---------VIKNKGLILCFVGPPGVGKTSLAQSIAKA 389
+D GL++ KE+I E + + M+ + KG++L GPPG GKT LA+++A
Sbjct: 178 EDIGGLKEAKEKIREMVELPMKHPELFEHLGIEPPKGVLL--YGPPGTGKTLLAKAVANE 235
Query: 390 TGRQYVRMSLGGVYDEADIRGHRRTYIGSMPGRIIQSLKRAKRSNP-LLLLDEID 443
G ++ ++ + + Y G R+ + K A+ + P ++ +DEID
Sbjct: 236 AGAYFISINGPEIMSK---------YYGESEERLREIFKEAEENAPSIIFIDEID 281
>gnl|CDD|130309 TIGR01242, 26Sp45, 26S proteasome subunit P45 family. Many
proteins may score above the trusted cutoff because an
internal.
Length = 364
Score = 37.9 bits (88), Expect = 0.011
Identities = 56/223 (25%), Positives = 95/223 (42%), Gaps = 27/223 (12%)
Query: 365 KGLILCFVGPPGVGKTSLAQSIAKATGRQYVRMSLGGVYDEADIRGHRRTYIGSMPGRII 424
KG++L GPPG GKT LA+++A T ++R+ V E R YIG +
Sbjct: 157 KGVLL--YGPPGTGKTLLAKAVAHETNATFIRV----VGSEL-----VRKYIGEGARLVR 205
Query: 425 QSLKRAKRSNP-LLLLDEIDKMGSDLRGDPSAALLEVLDPAQNSSFVDHYLEVE-YD-LS 481
+ + AK P ++ +DEID + + ++ EV + + E++ +D
Sbjct: 206 EIFELAKEKAPSIIFIDEIDAIAAKRTDSGTSGDREV-----QRTLMQLLAELDGFDPRG 260
Query: 482 DVMFIMTANTLNIPLPLMDRM----EIIRIAGYTEEEKLQIAKNHLVKKVLTEHALKQEE 537
+V I N +I P + R II + E +L+I K H K L E +
Sbjct: 261 NVKVIAATNRPDILDPALLRPGRFDRIIEVPLPDFEGRLEILKIHTRKMKLAEDVDLEAI 320
Query: 538 CCISDGVLLDIIRLFTHEAGVRSFERALMKIA----RKAVTKI 576
+++G ++ EAG+ + + KAV K+
Sbjct: 321 AKMTEGASGADLKAICTEAGMFAIREERDYVTMDDFIKAVEKV 363
>gnl|CDD|163294 TIGR03499, FlhF, flagellar biosynthetic protein FlhF.
Length = 282
Score = 37.3 bits (87), Expect = 0.017
Identities = 37/192 (19%), Positives = 68/192 (35%), Gaps = 30/192 (15%)
Query: 207 KERLEMLLVFMESEISVLQVEKRIRSRVKRQMEKTQREYYLHEQMKAIQKELDNGEEGRD 266
K+ +E+ E E++ E+ + ++ ++ A +E
Sbjct: 42 KKFVEVTAAIDEEEVATASTEEEAKKALEPADPAKLSATAEPLELPAPLEEPAAPAAQAA 101
Query: 267 EISDFEARISKIRLSKEAREKALSELQKLRQMNPLSAESSVVRNYLDWLL--GVPWDKKS 324
E E ++ +E E+ L+ L L+ L+ LL GV +
Sbjct: 102 EPLLPEELRKELEALRELLERLLAGLAWLQ-------RDPEGAKLLERLLRAGVSPE--- 151
Query: 325 KTKKNLDFAIRILD--QDHFGLEKVKERIIEYLAVQMRV------IKNKGLILCFVGPPG 376
A +L+ + E + E L + V I +G ++ VGP G
Sbjct: 152 -------LARELLEKLPERADAEDAWRWLREALEKMLPVKPEEDEILEQGGVIALVGPTG 204
Query: 377 VGKTSLAQSIAK 388
VGKT+ ++AK
Sbjct: 205 VGKTT---TLAK 213
>gnl|CDD|129401 TIGR00300, TIGR00300, conserved hypothetical protein TIGR00300.
All members of the family come from genome projects. A
partial length search brings in two plant
lysine-ketoglutarate reductase/saccharopine
dehydrogenase bifunctional enzymes hitting the
N-terminal region of the family.
Length = 407
Score = 37.1 bits (86), Expect = 0.019
Identities = 20/57 (35%), Positives = 29/57 (50%)
Query: 345 EKVKERIIEYLAVQMRVIKNKGLILCFVGPPGVGKTSLAQSIAKATGRQYVRMSLGG 401
E+ E +IE +A +M I++KG + V P V T AQ++A YV L G
Sbjct: 180 ERPVETLIEQIAWEMYEIRDKGGKIGVVAGPAVIHTGAAQALAHLIREGYVDALLAG 236
>gnl|CDD|180607 PRK06526, PRK06526, transposase; Provisional.
Length = 254
Score = 36.4 bits (84), Expect = 0.029
Identities = 28/105 (26%), Positives = 42/105 (40%), Gaps = 10/105 (9%)
Query: 338 DQDHFGLEKVKERIIEYLAVQMRVIKNKGLILCFVGPPGVGKTSLAQSIAKATGRQYVRM 397
D DH +K I +L V + ++ F+GPPG GKT LA + + R+
Sbjct: 74 DFDH--QRSLKRDTIAHLGTLDFVTGKENVV--FLGPPGTGKTHLAIGLGIRACQAGHRV 129
Query: 398 SLGGVYDEADIRGHRRTYIGSMPGRIIQSLKRAKRSNPLLLLDEI 442
R GR+ L + R PLL++DE+
Sbjct: 130 LFATAAQWVA-----RLAAAHHAGRLQAELVKLGRY-PLLIVDEV 168
>gnl|CDD|185575 PTZ00361, PTZ00361, 26 proteosome regulatory subunit 4-like
protein; Provisional.
Length = 438
Score = 35.5 bits (82), Expect = 0.052
Identities = 28/84 (33%), Positives = 47/84 (55%), Gaps = 12/84 (14%)
Query: 365 KGLILCFVGPPGVGKTSLAQSIAKATGRQYVRMSLGGVYDEADIRGHRRTYIGSMPGRII 424
KG+IL GPPG GKT LA+++A T ++R+ V E + Y+G P +
Sbjct: 218 KGVIL--YGPPGTGKTLLAKAVANETSATFLRV----VGSEL-----IQKYLGDGPKLVR 266
Query: 425 QSLKRAKRSNP-LLLLDEIDKMGS 447
+ + A+ + P ++ +DEID +G+
Sbjct: 267 ELFRVAEENAPSIVFIDEIDAIGT 290
>gnl|CDD|129721 TIGR00635, ruvB, Holliday junction DNA helicase, RuvB subunit.
RuvA specifically binds Holliday junctions as a sandwich
of two tetramers and maintains the configuration of the
junction. It forms a complex with two hexameric rings of
RuvB, the subunit that contains helicase activity. The
complex drives ATP-dependent branch migration of the
Holliday junction recombination intermediate. The
endonuclease RuvC resolves junctions.
Length = 305
Score = 35.4 bits (82), Expect = 0.063
Identities = 21/54 (38%), Positives = 33/54 (61%), Gaps = 5/54 (9%)
Query: 340 DHFGLEKVKERIIEYLAVQMRVIKNKGL--ILCFVGPPGVGKTSLAQSIAKATG 391
+ G EKVKE++ L ++ ++ + L +L + GPPG+GKT+LA IA G
Sbjct: 5 EFIGQEKVKEQL--QLFIEAAKMRQEALDHLLLY-GPPGLGKTTLAHIIANEMG 55
>gnl|CDD|179675 PRK03918, PRK03918, chromosome segregation protein; Provisional.
Length = 880
Score = 35.4 bits (82), Expect = 0.064
Identities = 40/189 (21%), Positives = 80/189 (42%), Gaps = 14/189 (7%)
Query: 114 RARIVEYIEREDFLEAITQVLPDPTEDPVELEALSRSVIAEFSNYIKLNKKISPEVIGIT 173
RI E + + LE + L + E E LS + Y+ ++I + +
Sbjct: 265 EERIEELKKEIEELEEKVKELKELKEKAEEYIKLSE----FYEEYLDELREIEKRLSRLE 320
Query: 174 SQIEGFSKLADVIAANLSIKVAERQKILEAVS-VKERLEMLLVFMESEISVLQVEKRIRS 232
+I G + L K +++ + + +++RLE L E ++ +
Sbjct: 321 EEINGIEERIK----ELEEKEERLEELKKKLKELEKRLEELEERHELYEEAKAKKEELER 376
Query: 233 RVKRQMEKTQREYYLHEQMKAIQKELDNGEEGRDEISDFEARISKIRLSKEAREKALSEL 292
KR T + L ++++ ++K EE +EIS ARI +++ + +KA+ EL
Sbjct: 377 LKKRLTGLTPEK--LEKELEELEKA---KEEIEEEISKITARIGELKKEIKELKKAIEEL 431
Query: 293 QKLRQMNPL 301
+K + P+
Sbjct: 432 KKAKGKCPV 440
Score = 30.0 bits (68), Expect = 2.6
Identities = 23/90 (25%), Positives = 44/90 (48%), Gaps = 3/90 (3%)
Query: 207 KERLEMLLVFMESEISVL--QVEKRIRSRVKRQMEKTQREYYLHEQMKAIQKELDNGEEG 264
ERLE + I L + EK + ++ E + L E+++ ++KE+ EE
Sbjct: 178 IERLEKFIK-RTENIEELIKEKEKELEEVLREINEISSELPELREELEKLEKEVKELEEL 236
Query: 265 RDEISDFEARISKIRLSKEAREKALSELQK 294
++EI + E + + SK E+ + EL++
Sbjct: 237 KEEIEELEKELESLEGSKRKLEEKIRELEE 266
>gnl|CDD|185633 PTZ00454, PTZ00454, 26S protease regulatory subunit 6B-like
protein; Provisional.
Length = 398
Score = 34.4 bits (79), Expect = 0.12
Identities = 23/73 (31%), Positives = 41/73 (56%), Gaps = 12/73 (16%)
Query: 373 GPPGVGKTSLAQSIAKATGRQYVRMSLGGVYDEADIRGHRRTYIGSMPGRIIQSLKRAKR 432
GPPG GKT LA+++A T ++R+ +G + + Y+G P R+++ + R R
Sbjct: 186 GPPGTGKTMLAKAVAHHTTATFIRV-VGSEFVQ--------KYLGEGP-RMVRDVFRLAR 235
Query: 433 SN--PLLLLDEID 443
N ++ +DE+D
Sbjct: 236 ENAPSIIFIDEVD 248
>gnl|CDD|163057 TIGR02881, spore_V_K, stage V sporulation protein K. Members of
this protein family are the stage V sporulation protein
K (SpoVK), a close homolog of the Rubisco expression
protein CbbX (TIGR02880) and a members of the ATPase
family associated with various cellular activities
(pfam00004). Members are strictly limited to bacterial
endospore-forming species, but are not universal in this
group and are missing from the Clostridium group.
Length = 261
Score = 34.3 bits (79), Expect = 0.14
Identities = 30/110 (27%), Positives = 53/110 (48%), Gaps = 17/110 (15%)
Query: 343 GLEKVKERIIE---YLAVQMRVIK------NKGLILCFVGPPGVGKTSLAQSIAKATGRQ 393
GL++VK I E ++ + + + + L + F G PG GKT++A+ + K
Sbjct: 10 GLDEVKALIKEIYAWIQINEKRKEEGLKTSKQVLHMIFKGNPGTGKTTVARILGKLFKEM 69
Query: 394 YVRMSLGGVY--DEADIRGHRRTYIGSMPGRIIQSLKRAKRSNPLLLLDE 441
V +S G + + AD+ G YIG + + +K+A +L +DE
Sbjct: 70 NV-LSKGHLIEVERADLVGE---YIGHTAQKTREVIKKA--LGGVLFIDE 113
>gnl|CDD|116340 pfam07726, AAA_3, ATPase family associated with various cellular
activities (AAA). This Pfam entry includes some of the
AAA proteins not detected by the pfam00004 model.
Length = 131
Score = 34.1 bits (79), Expect = 0.17
Identities = 10/24 (41%), Positives = 17/24 (70%)
Query: 373 GPPGVGKTSLAQSIAKATGRQYVR 396
G PG+ KT LA+++A++ G + R
Sbjct: 6 GVPGLAKTLLARTLARSLGLDFRR 29
>gnl|CDD|179385 PRK02224, PRK02224, chromosome segregation protein; Provisional.
Length = 880
Score = 33.9 bits (78), Expect = 0.17
Identities = 53/214 (24%), Positives = 85/214 (39%), Gaps = 51/214 (23%)
Query: 124 EDFLEAITQVLPDPTEDPVELEALSRSV---IAEFSNYIKLNK--------KISPEVIGI 172
EDFLE + + + E ELEA R+ + E ++ K + SP V I
Sbjct: 411 EDFLEELREERDELREREAELEATLRTARERVEEAEALLEAGKCPECGQPVEGSPHVETI 470
Query: 173 TSQIEGFSKLADVIAANLSIKVAERQKILEAVS-VKERLEML--LVFMESEISVLQ---- 225
E +L AE + + E V V+ERLE LV E I L+
Sbjct: 471 EEDRERVEELE-----------AELEDLEEEVEEVEERLERAEDLVEAEDRIERLEERRE 519
Query: 226 -VEKRIRSRVKRQMEKTQREYYLHEQM-----------KAIQKELDNGEEGRDEISDFEA 273
+E+ I R + EK +R L E+ +A + + EE R+E+++ +
Sbjct: 520 DLEELIAERRETIEEKRERAEELRERAAELEAEAEEKREAAAEAEEEAEEAREEVAELNS 579
Query: 274 ----------RISKIRLSKEAREKALSELQKLRQ 297
+ +IR A A E+++LR+
Sbjct: 580 KLAELKERIESLERIRTLLAAIADAEDEIERLRE 613
>gnl|CDD|185352 PRK15455, PRK15455, PrkA family serine protein kinase; Provisional.
Length = 644
Score = 33.8 bits (78), Expect = 0.20
Identities = 16/45 (35%), Positives = 28/45 (62%)
Query: 340 DHFGLEKVKERIIEYLAVQMRVIKNKGLILCFVGPPGVGKTSLAQ 384
+ +G+E+ E+I+ Y + ++ K IL +GP G GK+SLA+
Sbjct: 77 EFYGMEEAIEQIVSYFRHAAQGLEEKKQILYLLGPVGGGKSSLAE 121
>gnl|CDD|161686 TIGR00064, ftsY, signal recognition particle-docking protein FtsY.
There is a weak division between FtsY and SRP54; both
are GTPases. In E.coli, ftsY is an essential gene
located in an operon with cell division genes ftsE and
ftsX, but its apparent function is as the signal
recognition particle docking protein.
Length = 272
Score = 33.4 bits (77), Expect = 0.24
Identities = 20/51 (39%), Positives = 28/51 (54%), Gaps = 10/51 (19%)
Query: 345 EKVKERIIEYLAVQ-------MRVIKNKGLILCFVGPPGVGKTSLAQSIAK 388
E +KE + EYL + V +NK ++ FVG GVGKT+ +IAK
Sbjct: 44 ELLKEILKEYLKEILKETDLELIVEENKPNVILFVGVNGVGKTT---TIAK 91
>gnl|CDD|180213 PRK05703, flhF, flagellar biosynthesis regulator FlhF; Validated.
Length = 424
Score = 33.3 bits (77), Expect = 0.24
Identities = 15/48 (31%), Positives = 26/48 (54%), Gaps = 3/48 (6%)
Query: 345 EKVKERIIEYLAVQMRVIKNKGLILCFVGPPGVGKTSLAQSIAKATGR 392
+ E + + V++ I +G ++ VGP GVGKT+ ++AK R
Sbjct: 200 RYLLELLANMIPVRVEDILKQGGVVALVGPTGVGKTT---TLAKLAAR 244
>gnl|CDD|179699 PRK03992, PRK03992, proteasome-activating nucleotidase;
Provisional.
Length = 389
Score = 33.3 bits (77), Expect = 0.25
Identities = 22/67 (32%), Positives = 35/67 (52%), Gaps = 15/67 (22%)
Query: 343 GLEKVKERIIEYLAVQMRVIKN-----------KGLILCFVGPPGVGKTSLAQSIAKATG 391
GLE+ + E AV++ + K KG++L GPPG GKT LA+++A T
Sbjct: 135 GLEEQIREVRE--AVELPLKKPELFEEVGIEPPKGVLL--YGPPGTGKTLLAKAVAHETN 190
Query: 392 RQYVRMS 398
++R+
Sbjct: 191 ATFIRVV 197
>gnl|CDD|129690 TIGR00602, rad24, checkpoint protein rad24. This family is based
on the phylogenomic analysis of JA Eisen (1999, Ph.D.
Thesis, Stanford University).
Length = 637
Score = 33.4 bits (76), Expect = 0.26
Identities = 40/198 (20%), Positives = 74/198 (37%), Gaps = 17/198 (8%)
Query: 268 ISDFEARISKIRLSKEAREKALSELQKLRQMNPLSAE--SSVVRNYLDWLLGVPWDKKSK 325
IS S R+ + S R+ LS E + + + + PW +K K
Sbjct: 20 ISTITKWSLSRPTSSHRRKNSPSTDIHARKRGFLSLEQDTGLELSSENLDGNEPWVEKYK 79
Query: 326 TKKNLDFAIRILDQDHFGLEKVKERIIEYLAVQMRVIKNKGLILCFVGPPGVGKTSLAQS 385
+ + A+ +E+V+ + A + + L++ GP G GK++ +
Sbjct: 80 PETQHELAVH-----KKKIEEVETWL---KAQVLENAPKRILLIT--GPSGCGKSTTIKI 129
Query: 386 IAKATGRQYVRMSLGGVYDEADIRGHRRTYIGSMPGRIIQSLKRAKRSNPLLLLD--EID 443
++K G Q S + D H+ T S+ + + + LL ++
Sbjct: 130 LSKELGIQVQEWSNPTLPDFQK-NDHKVTL--SLESCFSNFQSQIEVFSEFLLRATNKLQ 186
Query: 444 KMGSDLRGDPSAALLEVL 461
+G DL D L+E L
Sbjct: 187 MLGDDLMTDKKIILVEDL 204
>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).
Length = 262
Score = 33.2 bits (76), Expect = 0.27
Identities = 14/64 (21%), Positives = 27/64 (42%)
Query: 352 IEYLAVQMRVIKNKGLILCFVGPPGVGKTSLAQSIAKATGRQYVRMSLGGVYDEADIRGH 411
++ + + G + GP G GKT+LA +A+ R + ++ +D+ G
Sbjct: 7 VKRVTSRALRYLKSGYPVHLRGPAGTGKTTLAMHVARKRDRPVMLINGDAELTTSDLVGS 66
Query: 412 RRTY 415
Y
Sbjct: 67 YAGY 70
>gnl|CDD|163196 TIGR03265, PhnT2, putative 2-aminoethylphosphonate ABC transporter,
ATP-binding protein. This ABC transporter ATP-binding
protein is found in a number of genomes in operon-like
contexts strongly suggesting a substrate specificity for
2-aminoethylphosphonate (2-AEP). The characterized
PhnSTUV system is absent in the genomes in which this
system is found. These genomes encode systems for the
catabolism of 2-AEP, making the need for a
2-AEP-specific transporter likely.
Length = 353
Score = 32.3 bits (74), Expect = 0.46
Identities = 12/23 (52%), Positives = 16/23 (69%)
Query: 365 KGLILCFVGPPGVGKTSLAQSIA 387
KG +C +GP G GKT+L + IA
Sbjct: 29 KGEFVCLLGPSGCGKTTLLRIIA 51
>gnl|CDD|107157 PHA02244, PHA02244, ATPase-like protein.
Length = 383
Score = 32.4 bits (73), Expect = 0.46
Identities = 30/120 (25%), Positives = 48/120 (40%), Gaps = 14/120 (11%)
Query: 373 GPPGVGKTSLAQSIAKATGRQYVRMSLGGVYDEADIRGHRRTYIGSMPGRIIQSLKRAKR 432
G G GK +A+ IA+A + M+ + DE +++G +I + A +
Sbjct: 126 GGAGSGKNHIAEQIAEALDLDFYFMN--AIMDEFELKG----FIDANGKFHETPFYEAFK 179
Query: 433 SNPLLLLDEIDKMGSDLRGDPSAALLEVLDPAQNSSFVDHYLEVEYDLSDVMFIMTANTL 492
L +DEID P A ++ ++ A + F D E D I NTL
Sbjct: 180 KGGLFFIDEIDA------SIPEALII--INSAIANKFFDFADERVTAHEDFRVISAGNTL 231
>gnl|CDD|184311 PRK13764, PRK13764, ATPase; Provisional.
Length = 602
Score = 32.5 bits (75), Expect = 0.48
Identities = 17/55 (30%), Positives = 31/55 (56%), Gaps = 12/55 (21%)
Query: 334 IRILDQDHFGL-EKVKERIIEYLAVQMRVIKNKGLILCFVGPPGVGKTSLAQSIA 387
+ L + + L EK+KER+ E + +G+++ G PG GK++ AQ++A
Sbjct: 235 VVKLSLEDYNLSEKLKERLEE---------RAEGILI--AGAPGAGKSTFAQALA 278
>gnl|CDD|178887 PRK00131, aroK, shikimate kinase; Reviewed.
Length = 175
Score = 32.1 bits (74), Expect = 0.56
Identities = 7/25 (28%), Positives = 15/25 (60%)
Query: 371 FVGPPGVGKTSLAQSIAKATGRQYV 395
+G G GK+++ + +AK G ++
Sbjct: 9 LIGFMGAGKSTIGRLLAKRLGYDFI 33
>gnl|CDD|173184 PRK14721, flhF, flagellar biosynthesis regulator FlhF; Provisional.
Length = 420
Score = 31.8 bits (72), Expect = 0.72
Identities = 26/90 (28%), Positives = 41/90 (45%), Gaps = 13/90 (14%)
Query: 349 ERIIEYLAVQMRVIKN-----KGLILCFVGPPGVGKTSLAQSIAKATGRQYVRMSLGGV- 402
++ I L + +R I +G + +GP GVGKT+ + AK R +R V
Sbjct: 169 KKTISLLTLNLRTIGGDEIIEQGGVYALIGPTGVGKTT---TTAKLAARAVIRHGADKVA 225
Query: 403 ---YDEADIRGHRRTYI-GSMPGRIIQSLK 428
D I GH + I G + G ++S+K
Sbjct: 226 LLTTDSYRIGGHEQLRIYGKLLGVSVRSIK 255
>gnl|CDD|180719 PRK06835, PRK06835, DNA replication protein DnaC; Validated.
Length = 329
Score = 31.8 bits (73), Expect = 0.77
Identities = 14/45 (31%), Positives = 19/45 (42%), Gaps = 4/45 (8%)
Query: 345 EKVKERIIEYLAVQMRVIKNKGLILCFVGPPGVGKTSLAQSIAKA 389
EK+ E+ ++ L F G G GKT L+ IAK
Sbjct: 166 EKILEKCKNFIEN----FDKNNENLLFYGNTGTGKTFLSNCIAKE 206
>gnl|CDD|183703 PRK12724, PRK12724, flagellar biosynthesis regulator FlhF;
Provisional.
Length = 432
Score = 31.9 bits (72), Expect = 0.80
Identities = 52/207 (25%), Positives = 93/207 (44%), Gaps = 35/207 (16%)
Query: 220 EISVLQVEKRI-RSRVKRQMEK-----TQREYYLHEQMKAIQ------KELDNGEEGRDE 267
EI + EK+ R +++R+++ Q+ Y E+ K +Q + L+ E E
Sbjct: 51 EIQIGIPEKQASREKIERKLQDLKELLKQKSYTEPERKKTLQTLKPLSERLEEKESAIYE 110
Query: 268 ISDFEARISKIRLSKEAREKALSELQKLRQMNPLS-AESSVVRNYLD---WLLGVPWDKK 323
I FE + ++ E R LS ++L + N +E+++VR D LG ++
Sbjct: 111 IESFE--LEEVITEPE-RPVGLSFEKELFEKNSFLESETTIVRKEKDSPLQRLGERLVRE 167
Query: 324 SKTKKNLDFAIRILDQ-----DHFGLEKVKERIIEYLAVQMRVI--------KNKGLILC 370
++ ++ L++ D V ER + YL ++ V KN+ ++
Sbjct: 168 GMSQSYVEEMASKLEERLSPVDQGRNHNVTERAVTYLEERVSVDSDLFSGTGKNQRKVVF 227
Query: 371 FVGPPGVGKTSLAQSIAKATGRQYVRM 397
FVGP G GKT+ SIAK + ++ M
Sbjct: 228 FVGPTGSGKTT---SIAKLAAKYFLHM 251
>gnl|CDD|147949 pfam06068, TIP49, TIP49 C-terminus. This family consists of the
C-terminal region of several eukaryotic and archaeal
RuvB-like 1 (Pontin or TIP49a) and RuvB-like 2 (Reptin
or TIP49b) proteins. The N-terminal domain contains the
pfam00004 domain. In zebrafish, the liebeskummer (lik)
mutation, causes development of hyperplastic embryonic
hearts. lik encodes Reptin, a component of a
DNA-stimulated ATPase complex. Beta-catenin and Pontin,
a DNA-stimulated ATPase that is often part of complexes
with Reptin, are in the same genetic pathways. The
Reptin/Pontin ratio serves to regulate heart growth
during development, at least in part via the
beta-catenin pathway. TBP-interacting protein 49 (TIP49)
was originally identified as a TBP-binding protein, and
two related proteins are encoded by individual genes,
tip49a and b. Although the function of this gene family
has not been elucidated, they are supposed to play a
critical role in nuclear events because they interact
with various kinds of nuclear factors and have DNA
helicase activities.TIP49a has been suggested to act as
an autoantigen in some patients with autoimmune
diseases.
Length = 395
Score = 31.5 bits (72), Expect = 0.82
Identities = 19/53 (35%), Positives = 27/53 (50%), Gaps = 5/53 (9%)
Query: 356 AVQMRVIKNK---GLILCFVGPPGVGKTSLAQSIAKATGRQ--YVRMSLGGVY 403
V + +IK G + GPPG GKT+LA +I+K G + +S VY
Sbjct: 37 GVIVEMIKEGKIAGRAVLIAGPPGTGKTALAIAISKELGEDTPFCPISGSEVY 89
Score = 30.4 bits (69), Expect = 1.9
Identities = 14/27 (51%), Positives = 17/27 (62%)
Query: 494 IPLPLMDRMEIIRIAGYTEEEKLQIAK 520
IPL L+DR+ II YT EE QI +
Sbjct: 329 IPLDLLDRLLIITTEPYTREEIKQILE 355
>gnl|CDD|162839 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.
Length = 355
Score = 31.4 bits (72), Expect = 0.86
Identities = 12/19 (63%), Positives = 14/19 (73%)
Query: 371 FVGPPGVGKTSLAQSIAKA 389
F GP G GKTS+A+ AKA
Sbjct: 41 FSGPRGTGKTSIARIFAKA 59
>gnl|CDD|161993 TIGR00678, holB, DNA polymerase III, delta' subunit. At position
126-127 of the seed alignment, this family lacks the HM
motif of gamma/tau; at 132 it has a near-invariant A vs.
an invariant F in gamma/tau.
Length = 188
Score = 31.4 bits (72), Expect = 0.88
Identities = 12/19 (63%), Positives = 14/19 (73%)
Query: 371 FVGPPGVGKTSLAQSIAKA 389
F GP GVGK LA ++AKA
Sbjct: 19 FAGPEGVGKELLALALAKA 37
>gnl|CDD|162740 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.
Length = 1164
Score = 31.2 bits (71), Expect = 1.0
Identities = 32/125 (25%), Positives = 57/125 (45%), Gaps = 26/125 (20%)
Query: 194 VAERQKILEAVSVKERLEML---LVFMESEISVLQVEK-RIRSRV--------------- 234
A R IL + S L+ L L ++ E+S LQ E RI +R+
Sbjct: 660 RAPRGGILFSRSEPAELQRLRERLEGLKRELSSLQSELRRIENRLDELSQELSDASRKIG 719
Query: 235 ---KRQMEKTQREYYLHEQMKAIQKELDNGEEG----RDEISDFEARISKIRLSKEAREK 287
K + Q E L E+++ ++++L + E+ + E+ + EARI ++ E+
Sbjct: 720 EIEKEIEQLEQEEEKLKERLEELEEDLSSLEQEIENVKSELKELEARIEELEEDLHKLEE 779
Query: 288 ALSEL 292
AL++L
Sbjct: 780 ALNDL 784
Score = 29.3 bits (66), Expect = 3.7
Identities = 16/68 (23%), Positives = 34/68 (50%), Gaps = 3/68 (4%)
Query: 227 EKRIRSRVKRQMEKTQREYYLHEQMKAIQKELDNGEEGRDEISDFEARISKIRLSKEARE 286
E R+R ++ T + YL ++++ +Q++ + +++I E I + KE E
Sbjct: 811 EARLREIEQKLNRLTLEKEYLEKEIQELQEQRI---DLKEQIKSIEKEIENLNGKKEELE 867
Query: 287 KALSELQK 294
+ L EL+
Sbjct: 868 EELEELEA 875
Score = 28.5 bits (64), Expect = 6.7
Identities = 24/102 (23%), Positives = 44/102 (43%), Gaps = 5/102 (4%)
Query: 201 LEAVSVK-ERLEMLLVFMESEISVLQVEKRIRSRVKR-QMEKTQREYYLHEQMKAIQKEL 258
LE V ERL++++ ++ L+ E+ R + EK + E Y +K +
Sbjct: 179 LEEVEENIERLDLIIDEKRQQLERLRREREKAERYQALLKEKREYEGYEL--LKEKEALE 236
Query: 259 DNGEEGRDEISDFEARISKIRLSKEAREKALSEL-QKLRQMN 299
E +++ E + K+ EK L E+ Q L ++N
Sbjct: 237 RQKEAIERQLASLEEELEKLTEEISELEKRLEEIEQLLEELN 278
>gnl|CDD|181681 PRK09183, PRK09183, transposase/IS protein; Provisional.
Length = 259
Score = 31.2 bits (71), Expect = 1.2
Identities = 30/117 (25%), Positives = 54/117 (46%), Gaps = 20/117 (17%)
Query: 333 AIRILDQDHFGLEK-VKERIIEYLAVQMRVIKNKGLILCFVGPPGVGKTSLAQSIAKATG 391
A++ ++ F ++ ++ L + +N+ ++L +GP GVGKT L A A G
Sbjct: 70 AVKTFEEYDFTFATGAPQKQLQSLRSLSFIERNENIVL--LGPSGVGKTHL----AIALG 123
Query: 392 RQYVRMSLGGVY-DEADI-----RGHRRTYIGSMPGRIIQSLKRAKRSNPLLLLDEI 442
+ VR + + AD+ R+ GR +L+R + LL++DEI
Sbjct: 124 YEAVRAGIKVRFTTAADLLLQLSTAQRQ-------GRYKTTLQRGVMAPRLLIIDEI 173
>gnl|CDD|184914 PRK14950, PRK14950, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 585
Score = 30.9 bits (70), Expect = 1.2
Identities = 13/19 (68%), Positives = 15/19 (78%)
Query: 371 FVGPPGVGKTSLAQSIAKA 389
F GP GVGKTS A+ +AKA
Sbjct: 43 FTGPRGVGKTSTARILAKA 61
>gnl|CDD|181797 PRK09358, PRK09358, adenosine deaminase; Provisional.
Length = 340
Score = 30.9 bits (71), Expect = 1.2
Identities = 10/35 (28%), Positives = 14/35 (40%)
Query: 540 ISDGVLLDIIRLFTHEAGVRSFERALMKIARKAVT 574
IS ++L +R F EA R E + V
Sbjct: 134 ISVRLILCFMRHFGEEAAARELEALAARYRDDGVV 168
>gnl|CDD|100796 PRK01156, PRK01156, chromosome segregation protein; Provisional.
Length = 895
Score = 31.0 bits (70), Expect = 1.4
Identities = 40/205 (19%), Positives = 72/205 (35%), Gaps = 16/205 (7%)
Query: 163 KKISPEVIGITSQIEGFSKLADVI---AANLS----IKVAERQKILEAVSVKERLEMLLV 215
KKI E++ I S + KL DVI A +S ++ + LE ++K+++
Sbjct: 152 KKILDEILEINSLERNYDKLKDVIDMLRAEISNIDYLEEKLKSSNLELENIKKQIADD-- 209
Query: 216 FMESEISVLQVEKRIRSRVKRQMEKTQREYYLHEQMKAIQKELDNGEEGRDEISDFEARI 275
E S+ E S L + + D EI E+ +
Sbjct: 210 --EKSHSITLKEIERLSIEYNNAMD--DYNNLKSALNELSSLEDMKNRYESEIKTAESDL 265
Query: 276 SKIRLSKEAREKALSELQKLRQMNPLSAESSVVRNYLDWLLGVPWDKKSKTKKNLDFAIR 335
S L K K L E +P+ + + +Y + + K + N+D I
Sbjct: 266 SME-LEKNNYYKELEERHMKIINDPVYKNRNYINDY--FKYKNDIENKKQILSNIDAEIN 322
Query: 336 ILDQDHFGLEKVKERIIEYLAVQMR 360
L +++ +Y+ + R
Sbjct: 323 KYHAIIKKLSVLQKDYNDYIKKKSR 347
>gnl|CDD|184929 PRK14965, PRK14965, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 576
Score = 30.9 bits (70), Expect = 1.4
Identities = 12/19 (63%), Positives = 14/19 (73%)
Query: 371 FVGPPGVGKTSLAQSIAKA 389
F G GVGKTS A+ +AKA
Sbjct: 43 FTGARGVGKTSTARILAKA 61
>gnl|CDD|128712 smart00435, TOPEUc, DNA Topoisomerase I (eukaryota). DNA
Topoisomerase I (eukaryota), DNA topoisomerase V,
Vaccina virus topoisomerase, Variola virus
topoisomerase, Shope fibroma virus topoisomeras.
Length = 391
Score = 30.8 bits (70), Expect = 1.4
Identities = 32/131 (24%), Positives = 60/131 (45%), Gaps = 22/131 (16%)
Query: 193 KVAERQKILEAVSVKERLEMLLVFMESEISVLQVEKRIRSRVKRQMEKTQREYYLHEQMK 252
K+ E+ K L+ + + +LL M S++ +++++S+ +R EK L ++K
Sbjct: 281 KLQEKIKALKYQLKRLKKMILLFEMISDL-----KRKLKSKFERDNEK------LDAEVK 329
Query: 253 AIQKELDNGEEGRDEISDFEARISKIRLSKEAREKALSELQKLRQMNPLSAESSVVRNYL 312
+KE E+ + +I E RI K+ + +E+ N A + NY+
Sbjct: 330 EKKKEKKKEEKKKKQIERLEERIEKLEVQATDKEE-----------NKTVALGTSKINYI 378
Query: 313 DWLLGVPWDKK 323
D + V W KK
Sbjct: 379 DPRITVAWCKK 389
>gnl|CDD|179009 PRK00409, PRK00409, recombination and DNA strand exchange inhibitor
protein; Reviewed.
Length = 782
Score = 30.9 bits (71), Expect = 1.5
Identities = 23/122 (18%), Positives = 49/122 (40%), Gaps = 19/122 (15%)
Query: 181 KLADVIAANLSIKVAERQKILEAVSVKERLEMLLVFMESEISVLQVEKRIRSRVKRQMEK 240
KL ++IA+ ++ QK EA ++ + E +++ ++ + EK
Sbjct: 517 KLNELIASLEELERELEQKAEEAEALLKEAE-----------------KLKEELEEKKEK 559
Query: 241 TQREYY--LHEQMKAIQKELDNGEEGRDEISDFEARISKIRLSKEAREKALSELQKLRQM 298
Q E L E K Q+ + ++ DEI ++ K + + + ++L +
Sbjct: 560 LQEEEDKLLEEAEKEAQQAIKEAKKEADEIIKELRQLQKGGYASVKAHELIEARKRLNKA 619
Query: 299 NP 300
N
Sbjct: 620 NE 621
>gnl|CDD|182791 PRK10865, PRK10865, protein disaggregation chaperone; Provisional.
Length = 857
Score = 30.6 bits (69), Expect = 1.6
Identities = 29/98 (29%), Positives = 48/98 (48%), Gaps = 11/98 (11%)
Query: 371 FVGPPGVGKTSLAQSIAK---ATGRQYVRMSLGGVYDEADIR---GHRRTYIGSMPGRII 424
F+GP GVGKT L +++A + VR+ + ++ + G Y+G G +
Sbjct: 603 FLGPTGVGKTELCKALANFMFDSDDAMVRIDMSEFMEKHSVSRLVGAPPGYVGYEEGGYL 662
Query: 425 QSLKRAKRSNPLLLLDEIDKMGSDLRGDPSAALLEVLD 462
R +R ++LLDE++K D+ LL+VLD
Sbjct: 663 TEAVR-RRPYSVILLDEVEKAHPDVFN----ILLQVLD 695
>gnl|CDD|184726 PRK14527, PRK14527, adenylate kinase; Provisional.
Length = 191
Score = 30.5 bits (69), Expect = 2.0
Identities = 18/52 (34%), Positives = 28/52 (53%), Gaps = 4/52 (7%)
Query: 359 MRVIKNKGLILCFVGPPGVGKTSLAQSIAKATGRQYVRMSLGGVYDEADIRG 410
M KNK +I F+GPPG GK + A+ +A+ ++S G + + RG
Sbjct: 1 MTQTKNKVVI--FLGPPGAGKGTQAERLAQE--LGLKKLSTGDILRDHVARG 48
>gnl|CDD|131325 TIGR02272, gentisate_1_2, gentisate 1,2-dioxygenase. This family
consists of gentisate 1,2-dioxygenases. This
ring-opening enzyme acts in salicylate degradation that
goes via gentisate rather than via catechol. It converts
gentisate to maleylpyruvate. Some putative gentisate
1,2-dioxygenases are excluded by a relatively high
trusted cutoff score because they are too closely
related to known examples of 1-hydroxy-2-naphthoate
dioxygenase. Therefore some homologs may be bona fide
gentisate 1,2-dioxygenases even if they score below the
given cutoffs.
Length = 335
Score = 30.1 bits (68), Expect = 2.1
Identities = 27/88 (30%), Positives = 39/88 (44%), Gaps = 14/88 (15%)
Query: 79 NPIASSVYRIGTIVDIVQIL---------RLPDGTVKILVEGSVRARIVEYIEREDFLEA 129
NP A+ Y + TI +Q+L R D TV +VEG + RI + F +
Sbjct: 239 NP-ATGGYPMPTIGAFIQLLPKGFRTATYRSTDATVFCVVEGRGQVRIGD----AVFRFS 293
Query: 130 ITQVLPDPTEDPVELEALSRSVIAEFSN 157
V P+ PV EA +V+ FS+
Sbjct: 294 PKDVFVVPSWHPVRFEASDDAVLFSFSD 321
>gnl|CDD|179771 PRK04182, PRK04182, cytidylate kinase; Provisional.
Length = 180
Score = 30.2 bits (69), Expect = 2.1
Identities = 11/23 (47%), Positives = 18/23 (78%)
Query: 373 GPPGVGKTSLAQSIAKATGRQYV 395
GPPG GKT++A+ +A+ G ++V
Sbjct: 7 GPPGSGKTTVARLLAEKLGLKHV 29
>gnl|CDD|181809 PRK09376, rho, transcription termination factor Rho; Provisional.
Length = 416
Score = 30.1 bits (69), Expect = 2.1
Identities = 13/29 (44%), Positives = 16/29 (55%), Gaps = 3/29 (10%)
Query: 366 GLILCFVGPPGVGKTSLAQSIAKATGRQY 394
GLI V PP GKT L Q+IA + +
Sbjct: 172 GLI---VAPPKAGKTVLLQNIANSITTNH 197
>gnl|CDD|184927 PRK14963, PRK14963, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 504
Score = 30.2 bits (68), Expect = 2.1
Identities = 21/49 (42%), Positives = 26/49 (53%), Gaps = 5/49 (10%)
Query: 343 GLEKVKERIIEYLAVQMRVIKNKGLILCFVGPPGVGKTSLAQSIAKATG 391
G E VKE ++ L Q R+ G F GP GVGKT+ A+ IA A
Sbjct: 18 GQEHVKEVLLAALR-QGRL----GHAYLFSGPRGVGKTTTARLIAMAVN 61
>gnl|CDD|178435 PLN02842, PLN02842, nucleotide kinase.
Length = 505
Score = 30.2 bits (68), Expect = 2.5
Identities = 16/33 (48%), Positives = 25/33 (75%), Gaps = 4/33 (12%)
Query: 85 VYRIGTIVDIVQILRLP---DGT-VKILVEGSV 113
VYRIGT++++V++L L DG VK+ V+GS+
Sbjct: 277 VYRIGTLMELVRVLALSFADDGKRVKVCVQGSM 309
>gnl|CDD|177370 PHA02530, pseT, polynucleotide kinase; Provisional.
Length = 300
Score = 30.0 bits (68), Expect = 2.5
Identities = 14/41 (34%), Positives = 19/41 (46%), Gaps = 6/41 (14%)
Query: 368 ILCFVGPPGVGKTSLAQSIAKATG------RQYVRMSLGGV 402
I+ VG PG GK++ A+ A R +R SL G
Sbjct: 4 IILTVGVPGSGKSTWAREFAAKNPKAVNVNRDDLRQSLFGH 44
>gnl|CDD|169983 PRK09579, PRK09579, multidrug efflux protein; Reviewed.
Length = 1017
Score = 29.8 bits (67), Expect = 2.8
Identities = 25/65 (38%), Positives = 31/65 (47%), Gaps = 14/65 (21%)
Query: 679 NIHVHVPEGATPKDGPSAGIAMATAIVSIMTCIPVYKNVAMTGELTLRGRVLPIGGLKEK 738
NIH H+ EG +P D A + A I +PV V+MT +TL PIG L
Sbjct: 408 NIHRHIEEGKSPFD---AALEGAREI-----AMPV---VSMT--ITLAAVYAPIGFL-TG 453
Query: 739 LLAAL 743
L AL
Sbjct: 454 LTGAL 458
>gnl|CDD|181799 PRK09361, radB, DNA repair and recombination protein RadB;
Provisional.
Length = 225
Score = 29.8 bits (68), Expect = 2.9
Identities = 10/30 (33%), Positives = 15/30 (50%)
Query: 364 NKGLILCFVGPPGVGKTSLAQSIAKATGRQ 393
+G I GPPG GKT++ +A +
Sbjct: 21 ERGTITQIYGPPGSGKTNICLQLAVEAAKN 50
>gnl|CDD|185327 PRK15429, PRK15429, formate hydrogenlyase transcriptional activator
FhlA; Provisional.
Length = 686
Score = 29.8 bits (67), Expect = 3.0
Identities = 34/104 (32%), Positives = 49/104 (47%), Gaps = 21/104 (20%)
Query: 367 LILCFVGPPGVGKTSLAQSIAKATGRQYVRM------SLGGVYDEADIRGHRRTYIGSMP 420
LIL G G GK +A++I +GR RM ++ E+D+ GH R G+
Sbjct: 403 LIL---GETGTGKELIARAIHNLSGRNNRRMVKMNCAAMPAGLLESDLFGHER---GAFT 456
Query: 421 GRIIQSLKR---AKRSNPLLLLDEIDKMGSDLRGDPSAALLEVL 461
G Q + R A +S+ L LDE+ M +L+ LL VL
Sbjct: 457 GASAQRIGRFELADKSS--LFLDEVGDMPLELQ----PKLLRVL 494
>gnl|CDD|180029 PRK05342, clpX, ATP-dependent protease ATP-binding subunit ClpX;
Provisional.
Length = 412
Score = 29.7 bits (68), Expect = 3.1
Identities = 10/17 (58%), Positives = 14/17 (82%)
Query: 372 VGPPGVGKTSLAQSIAK 388
+GP G GKT LAQ++A+
Sbjct: 114 IGPTGSGKTLLAQTLAR 130
>gnl|CDD|183622 PRK12608, PRK12608, transcription termination factor Rho;
Provisional.
Length = 380
Score = 29.7 bits (67), Expect = 3.1
Identities = 14/30 (46%), Positives = 16/30 (53%), Gaps = 3/30 (10%)
Query: 365 KGLILCFVGPPGVGKTSLAQSIAKATGRQY 394
+GLI V PP GKT L Q IA A +
Sbjct: 135 RGLI---VAPPRAGKTVLLQQIAAAVAANH 161
>gnl|CDD|184913 PRK14949, PRK14949, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 944
Score = 29.7 bits (67), Expect = 3.1
Identities = 12/18 (66%), Positives = 13/18 (72%)
Query: 371 FVGPPGVGKTSLAQSIAK 388
F G GVGKTSLA+ AK
Sbjct: 43 FTGTRGVGKTSLARLFAK 60
>gnl|CDD|178968 PRK00300, gmk, guanylate kinase; Provisional.
Length = 205
Score = 29.7 bits (68), Expect = 3.2
Identities = 8/23 (34%), Positives = 15/23 (65%)
Query: 362 IKNKGLILCFVGPPGVGKTSLAQ 384
+ +GL++ GP G GK++L +
Sbjct: 1 MMRRGLLIVLSGPSGAGKSTLVK 23
>gnl|CDD|180615 PRK06547, PRK06547, hypothetical protein; Provisional.
Length = 172
Score = 29.7 bits (67), Expect = 3.2
Identities = 12/25 (48%), Positives = 16/25 (64%)
Query: 373 GPPGVGKTSLAQSIAKATGRQYVRM 397
G G GKT+LA ++A TG Q V +
Sbjct: 22 GRSGSGKTTLAGALAARTGFQLVHL 46
>gnl|CDD|180345 PRK05995, PRK05995, enoyl-CoA hydratase; Provisional.
Length = 262
Score = 29.5 bits (67), Expect = 3.2
Identities = 12/27 (44%), Positives = 19/27 (70%)
Query: 268 ISDFEARISKIRLSKEAREKALSELQK 294
I+D +RI+ IR ++EARE + L+K
Sbjct: 228 IADTASRIALIRATEEAREGVAAFLEK 254
>gnl|CDD|178078 PLN02459, PLN02459, probable adenylate kinase.
Length = 261
Score = 29.8 bits (67), Expect = 3.3
Identities = 11/29 (37%), Positives = 17/29 (58%)
Query: 363 KNKGLILCFVGPPGVGKTSLAQSIAKATG 391
K + + F+G PGVGK + A ++K G
Sbjct: 26 KGRNVNWVFLGCPGVGKGTYASRLSKLLG 54
>gnl|CDD|183713 PRK12740, PRK12740, elongation factor G; Reviewed.
Length = 668
Score = 29.7 bits (68), Expect = 3.3
Identities = 10/21 (47%), Positives = 13/21 (61%)
Query: 372 VGPPGVGKTSLAQSIAKATGR 392
VG G GKT+L ++I TG
Sbjct: 1 VGHSGAGKTTLTEAILFYTGA 21
>gnl|CDD|184937 PRK14974, PRK14974, cell division protein FtsY; Provisional.
Length = 336
Score = 29.6 bits (67), Expect = 3.3
Identities = 36/170 (21%), Positives = 73/170 (42%), Gaps = 29/170 (17%)
Query: 228 KRIRSRVKRQMEKTQREYYLHEQMKAIQKELDNGEEGRDEISDFEARISKIRLSKEAREK 287
+ +V+ ++E+ + E + + +++ EE + E F + + ++ E
Sbjct: 10 SKFVEKVEEKIEEEEEEEAPEAEEEEEEED----EEEKKEKPGFFDKAKITEIKEKDIED 65
Query: 288 ALSELQKLRQMNPLSA--ESSVVRNYLDWLLGVPWDKKSKTKKNLDFAIRILDQDHFGLE 345
L EL+ + L + V L+ L KK K ++++ ++
Sbjct: 66 LLEELE----LELLESDVALEVAEEILESLKEKLVGKKVKRGEDVEEIVK---------N 112
Query: 346 KVKERIIEYLAV--QMRVI-----KNKGLILCFVGPPGVGKTSLAQSIAK 388
+KE ++E L+V +I K K +++ FVG G GKT+ +IAK
Sbjct: 113 ALKEALLEVLSVGDLFDLIEEIKSKGKPVVIVFVGVNGTGKTT---TIAK 159
>gnl|CDD|180644 PRK06647, PRK06647, DNA polymerase III subunits gamma and tau;
Validated.
Length = 563
Score = 29.7 bits (67), Expect = 3.4
Identities = 11/19 (57%), Positives = 14/19 (73%)
Query: 371 FVGPPGVGKTSLAQSIAKA 389
F GP GVGKTS A++ A+
Sbjct: 43 FSGPRGVGKTSSARAFARC 61
>gnl|CDD|162777 TIGR02237, recomb_radB, DNA repair and recombination protein RadB.
This family consists exclusively of archaeal RadB
protein, a homolog of bacterial RecA (TIGR02012),
eukaryotic RAD51 (TIGR02239) and DMC1 (TIGR02238), and
archaeal RadA (TIGR02236).
Length = 209
Score = 29.7 bits (67), Expect = 3.5
Identities = 12/29 (41%), Positives = 16/29 (55%)
Query: 365 KGLILCFVGPPGVGKTSLAQSIAKATGRQ 393
+G I GPPG GKT++ +A RQ
Sbjct: 11 RGTITQIYGPPGSGKTNICMILAVNAARQ 39
>gnl|CDD|184935 PRK14971, PRK14971, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 614
Score = 29.4 bits (66), Expect = 3.6
Identities = 11/19 (57%), Positives = 13/19 (68%)
Query: 371 FVGPPGVGKTSLAQSIAKA 389
F GP GVGKT+ A+ AK
Sbjct: 44 FCGPRGVGKTTCARIFAKT 62
>gnl|CDD|162744 TIGR02173, cyt_kin_arch, cytidylate kinase, putative. Proteins in
this family are believed to be cytidylate kinase.
Members of this family are found in the archaea and in
spirochaetes, and differ considerably from the common
bacterial form of cytidylate kinase described by
TIGR00017.
Length = 171
Score = 29.3 bits (66), Expect = 3.9
Identities = 21/79 (26%), Positives = 36/79 (45%), Gaps = 17/79 (21%)
Query: 367 LILCFVGPPGVGKTSLAQSIAKATGRQYVRMSLGGVYDEADIRGHRRTYIGSMPGRIIQS 426
+I+ GPPG GKT++A+ +A+ + + S G ++ R M +I+
Sbjct: 1 MIITISGPPGSGKTTVAKILAEKLSLKLI--SAGDIF---------RELAAKMGLDLIEF 49
Query: 427 LKRAKRSNPLLLLDEIDKM 445
L A+ + EIDK
Sbjct: 50 LNYAEENP------EIDKK 62
>gnl|CDD|184251 PRK13695, PRK13695, putative NTPase; Provisional.
Length = 174
Score = 29.5 bits (67), Expect = 3.9
Identities = 31/106 (29%), Positives = 45/106 (42%), Gaps = 37/106 (34%)
Query: 373 GPPGVGKTSLAQSIAKATGRQYVRMSLGGVYDEADIR--GHR-----------------R 413
GPPGVGKT+L IA+ + + +GG Y E ++R G R R
Sbjct: 7 GPPGVGKTTLVLKIAELLKEEGYK--VGGFYTE-EVREGGKRIGFKIIDLDTGEEGILAR 63
Query: 414 TYIGSMPGRI--------------IQSLKRAKRSNPLLLLDEIDKM 445
S P R+ I +L+RA ++++DEI KM
Sbjct: 64 VGFPSRP-RVGKYVVNLEDLERIGIPALERALEEADVIIIDEIGKM 108
>gnl|CDD|149480 pfam08433, KTI12, Chromatin associated protein KTI12. This is a
family of chromatin associated proteins which interact
with the Elongator complex, a component of the
elongating form of RNA polymerase II. The Elongator
complex has histone acetyltransferase activity.
Length = 266
Score = 29.2 bits (66), Expect = 4.1
Identities = 18/82 (21%), Positives = 34/82 (41%), Gaps = 16/82 (19%)
Query: 367 LILCFVGPPGVGKTSLAQSIAK---ATGRQYVRMSLGGVYDEADIRGHRRTYIGS----- 418
+IL G P GK++ A+ +AK G + V + + Y S
Sbjct: 2 IILT--GLPSSGKSTRAKELAKYLEEKGYDVI------VISDESLGIESDDYKDSKKEKF 53
Query: 419 MPGRIIQSLKRAKRSNPLLLLD 440
+ G + ++KR N ++++D
Sbjct: 54 LRGSLRSAVKRDLSKNTIVIVD 75
>gnl|CDD|162243 TIGR01189, ccmA, heme ABC exporter, ATP-binding protein CcmA. This
model describes the cyt c biogenesis protein encoded by
ccmA in bacteria. An exception is, an arabidopsis
protein. Quite likely this is encoded by an organelle.
Bacterial c-type cytocromes are located on the
periplasmic side of the cytoplasmic membrane. Several
gene products encoded in a locus designated as 'ccm' are
implicated in the transport and assembly of the
functional cytochrome C. This cluster includes genes:
ccmA;B;C;D;E;F;G and H. The posttranslational pathway
includes the transport of heme moiety, the secretion of
the apoprotein and the covalent attachment of the heme
with the apoprotein. The proteins ccmA and B represent
an ABC transporter; ccmC and D participate in heme
transfer to ccmE, which function as a periplasmic heme
chaperone. The presence of ccmF, G and H is suggested to
be obligatory for the final functional assembly of
cytochrome c.
Length = 198
Score = 29.3 bits (66), Expect = 4.2
Identities = 19/62 (30%), Positives = 30/62 (48%), Gaps = 6/62 (9%)
Query: 364 NKGLILCFVGPPGVGKTSLAQSIA----KATGRQYVRMSLGGVYDEADIRGHRRTYIGSM 419
N G L GP G+GKT+L + +A +G VR + + ++ D Y+G +
Sbjct: 24 NAGEALQVTGPNGIGKTTLLRILAGLLRPDSGE--VRWNGTALAEQRDEPHRNILYLGHL 81
Query: 420 PG 421
PG
Sbjct: 82 PG 83
>gnl|CDD|183088 PRK11331, PRK11331, 5-methylcytosine-specific restriction enzyme
subunit McrB; Provisional.
Length = 459
Score = 29.3 bits (65), Expect = 4.4
Identities = 31/109 (28%), Positives = 49/109 (44%), Gaps = 15/109 (13%)
Query: 347 VKERIIEYLAVQMRVIKNKGLILCFVGPPGVGKTSLAQSIAK-ATGR---QYVRM-SLGG 401
+ E IE + ++ + KN + GPPGVGKT +A+ +A TG Q V M
Sbjct: 179 IPETTIETILKRLTIKKN----IILQGPPGVGKTFVARRLAYLLTGEKAPQRVNMVQFHQ 234
Query: 402 VYDEAD-IRGHRRTYIG-----SMPGRIIQSLKRAKRSNPLLLLDEIDK 444
Y D I+G+R +G + Q K + ++DEI++
Sbjct: 235 SYSYEDFIQGYRPNGVGFRRKDGIFYNFCQQAKEQPEKKYVFIIDEINR 283
>gnl|CDD|178179 PLN02566, PLN02566, amine oxidase (copper-containing).
Length = 646
Score = 29.1 bits (65), Expect = 4.7
Identities = 23/97 (23%), Positives = 39/97 (40%), Gaps = 20/97 (20%)
Query: 455 AALLEVLDP------------AQNSSFVD------HYLEV-EYDLSDVMFIMTANTLNIP 495
A+L LDP Q S + H+L++ E + DV+ +++N N
Sbjct: 18 ASLYHPLDPLNPQEINKIRLIVQKSHLGNLPNLTFHFLDLEEPEKRDVLKWLSSNPSNKS 77
Query: 496 LPLMDRMEIIRIAGYTEEEKLQIAKNHLV-KKVLTEH 531
P ++R G T E + +A + +V T H
Sbjct: 78 PPPRRAKVVVRAGGETYELIVDLATGSITSSRVYTGH 114
>gnl|CDD|178856 PRK00091, miaA, tRNA delta(2)-isopentenylpyrophosphate transferase;
Reviewed.
Length = 307
Score = 28.9 bits (66), Expect = 4.8
Identities = 15/49 (30%), Positives = 19/49 (38%), Gaps = 16/49 (32%)
Query: 368 ILCFVGPPGVGKTSLAQSIAKATG--------RQYVRMSLGGVYDEADI 408
++ VGP GKT+LA +AK Q VY DI
Sbjct: 6 VIVIVGPTASGKTALAIELAKRLNGEIISADSMQ--------VYRGMDI 46
>gnl|CDD|183675 PRK12678, PRK12678, transcription termination factor Rho;
Provisional.
Length = 672
Score = 29.1 bits (66), Expect = 4.8
Identities = 13/24 (54%), Positives = 16/24 (66%), Gaps = 3/24 (12%)
Query: 366 GLILCFVGPPGVGKTSLAQSIAKA 389
GLI V PP GKT++ Q+IA A
Sbjct: 419 GLI---VSPPKAGKTTILQNIANA 439
>gnl|CDD|163223 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.
Length = 852
Score = 29.2 bits (66), Expect = 5.0
Identities = 11/17 (64%), Positives = 15/17 (88%)
Query: 371 FVGPPGVGKTSLAQSIA 387
F+GP GVGKT LA+++A
Sbjct: 600 FLGPTGVGKTELAKALA 616
>gnl|CDD|162135 TIGR00963, secA, preprotein translocase, SecA subunit. The
proteins SecA-F and SecY, not all of which are
necessary, comprise the standard prokaryotic protein
translocation apparatus. Other, specialized
translocation systems also exist but are not as broadly
distributed. This model describes SecA, an essential
member of the apparatus.
Length = 745
Score = 28.8 bits (65), Expect = 5.4
Identities = 27/122 (22%), Positives = 50/122 (40%), Gaps = 12/122 (9%)
Query: 195 AERQKILEAVSVKER-LEMLLVFMESEISVLQVEKRIRSRVKRQ--MEKTQREYYLHEQM 251
AER++ILE+ + E L+ML ++ + E++ + +EK + + L
Sbjct: 587 AERRRILESEDLSELILQMLESTLDEIVDAYINEQKPSEEWDLEGLIEKLKTLFLLDG-- 644
Query: 252 KAIQKELDNGEEGRDEISDFEARISKIRLSKEAREKALSELQKLRQMNPLSAESSVVRNY 311
+ E E E + KIR + + +E L E ++ M E V+
Sbjct: 645 -DLTPEDL---ENLTSEDLKELLLEKIRAAYDEKEAEL-ESERPGLMR--EFERYVLLQS 697
Query: 312 LD 313
+D
Sbjct: 698 ID 699
>gnl|CDD|180504 PRK06277, PRK06277, hydrogenase subunit F; Validated.
Length = 478
Score = 28.8 bits (65), Expect = 5.7
Identities = 13/32 (40%), Positives = 19/32 (59%), Gaps = 5/32 (15%)
Query: 29 PLLPLRDIVVFPY---MIVPLFVGREKSVRAL 57
LLPL +VVFP +I L G++K ++ L
Sbjct: 2 NLLPL--MVVFPMICAIIFNLLHGKDKLIKYL 31
>gnl|CDD|148114 pfam06309, Torsin, Torsin. This family consists of several
eukaryotic torsin proteins. Torsion dystonia is an
autosomal dominant movement disorder characterized by
involuntary, repetitive muscle contractions and twisted
postures. The most severe early-onset form of dystonia
has been linked to mutations in the human DYT1 (TOR1A)
gene encoding a protein termed torsinA. While causative
genetic alterations have been identified, the function
of torsin proteins and the molecular mechanism
underlying dystonia remain unknown. Phylogenetic
analysis of the torsin protein family indicates these
proteins share distant sequence similarity with the
large and diverse family of (pfam00004) proteins. It has
been suggested that torsins play a role in effectively
managing protein folding and that possible breakdown in
a neuroprotective mechanism that is, in part, mediated
by torsins may be responsible for the neuronal
dysfunction associated with dystonia.
Length = 127
Score = 28.9 bits (65), Expect = 5.8
Identities = 14/41 (34%), Positives = 18/41 (43%), Gaps = 5/41 (12%)
Query: 365 KGLILCFVGPPGVGKTSLAQSIAKATGRQ-----YVRMSLG 400
K L+L F G G GK +A+ IA R YV +
Sbjct: 52 KPLVLSFHGWTGTGKNFVAEIIADNLYRDGLRSPYVHHFVA 92
>gnl|CDD|163043 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.
Length = 270
Score = 28.8 bits (65), Expect = 5.8
Identities = 23/83 (27%), Positives = 37/83 (44%), Gaps = 10/83 (12%)
Query: 321 DKKSKTKKNL-DFAIRILDQDHFGLEKVKERIIEYLAVQMRVIKNKGLILCFVGPPGVGK 379
+ K KT KN+ IRI + ++++ YL RV LI + PP GK
Sbjct: 74 NGKVKTIKNVSSLNIRIARE----KLGAADKLLPYLVRNNRV--LNTLI---ISPPQCGK 124
Query: 380 TSLAQSIAKATGRQYVRMSLGGV 402
T+L + +A+ ++ L G
Sbjct: 125 TTLLRDLARILSTGISQLGLRGK 147
>gnl|CDD|180308 PRK05896, PRK05896, DNA polymerase III subunits gamma and tau;
Validated.
Length = 605
Score = 28.7 bits (64), Expect = 5.8
Identities = 12/19 (63%), Positives = 15/19 (78%)
Query: 371 FVGPPGVGKTSLAQSIAKA 389
F GP G+GKTS+A+ AKA
Sbjct: 43 FSGPRGIGKTSIAKIFAKA 61
>gnl|CDD|163553 TIGR03841, F420_Rv3093c, probable F420-dependent oxidoreductase,
Rv3093c family. This model describes a small family of
enzymes in the bacterial luciferase-like monooxygenase
family, which includes F420-dependent enzymes such as
N5,N10-methylenetetrahydromethanopterin reductase as
well as FMN-dependent enzymes. All members of this
family are from species that produce coenzyme F420;
SIMBAL analysis suggests that members of this family
bind F420 rather than FMN.
Length = 301
Score = 28.6 bits (64), Expect = 6.1
Identities = 8/41 (19%), Positives = 17/41 (41%)
Query: 387 AKATGRQYVRMSLGGVYDEADIRGHRRTYIGSMPGRIIQSL 427
A G + + G V A RR + ++P ++ ++
Sbjct: 231 APGYGEMFAWLGFGEVLRLARAAADRRELLAAVPDEVVDAV 271
>gnl|CDD|178596 PLN03025, PLN03025, replication factor C subunit; Provisional.
Length = 319
Score = 28.5 bits (64), Expect = 6.4
Identities = 32/107 (29%), Positives = 46/107 (42%), Gaps = 32/107 (29%)
Query: 357 VQMRVIKNKG----LILCFVGPPGVGKTSLAQSIAKATGRQYVRMSLGGVYDEA------ 406
+++VI G LIL GPPG GKT+ ++A LG Y EA
Sbjct: 23 SRLQVIARDGNMPNLILS--GPPGTGKTTSILALA--------HELLGPNYKEAVLELNA 72
Query: 407 -DIRGHRRTYIGSMPGRIIQSLKRAKRSNP-----LLLLDEIDKMGS 447
D RG I + + I+ + K + P +++LDE D M S
Sbjct: 73 SDDRG-----IDVVRNK-IKMFAQKKVTLPPGRHKIVILDEADSMTS 113
>gnl|CDD|129661 TIGR00570, cdk7, CDK-activating kinase assembly factor MAT1. All
proteins in this family for which functions are known
are cyclin dependent protein kinases that are components
of TFIIH, a complex that is involved in nucleotide
excision repair and transcription initiation. Also known
as MAT1 (menage a trois 1). This family is based on the
phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis,
Stanford University).
Length = 309
Score = 28.6 bits (64), Expect = 6.9
Identities = 18/64 (28%), Positives = 30/64 (46%), Gaps = 5/64 (7%)
Query: 238 MEKTQR--EYYLHEQMKAIQKELDNGEEGRDEISDFEARISKIRLSKEAREKALSELQKL 295
+E T++ E Y E IQK N E+ E + E + + +E R L + ++
Sbjct: 115 LENTKKKIETYQKENKDVIQK---NKEKSTREQEELEEALEFEKEEEEQRRLLLQKEEEE 171
Query: 296 RQMN 299
+QMN
Sbjct: 172 QQMN 175
>gnl|CDD|184920 PRK14956, PRK14956, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 484
Score = 28.4 bits (63), Expect = 7.1
Identities = 11/18 (61%), Positives = 15/18 (83%)
Query: 371 FVGPPGVGKTSLAQSIAK 388
F GP GVGKT++A+ +AK
Sbjct: 45 FFGPRGVGKTTIARILAK 62
>gnl|CDD|179996 PRK05291, trmE, tRNA modification GTPase TrmE; Reviewed.
Length = 449
Score = 28.5 bits (65), Expect = 7.2
Identities = 18/60 (30%), Positives = 27/60 (45%), Gaps = 6/60 (10%)
Query: 329 NLDFA---IRILDQDHF--GLEKVKERIIEYLA-VQMRVIKNKGLILCFVGPPGVGKTSL 382
+DF I L + LE++ + LA + I +GL + G P VGK+SL
Sbjct: 172 AIDFPEEDIEFLSDEKILEKLEELIAELEALLASARQGEILREGLKVVIAGRPNVGKSSL 231
>gnl|CDD|162030 TIGR00767, rho, transcription termination factor Rho. Members of
this family differ in the specificity of RNA binding.
Length = 415
Score = 28.5 bits (64), Expect = 7.2
Identities = 15/30 (50%), Positives = 18/30 (60%), Gaps = 3/30 (10%)
Query: 365 KGLILCFVGPPGVGKTSLAQSIAKATGRQY 394
+GLI V PP GKT L Q IA+A R +
Sbjct: 170 RGLI---VAPPKAGKTVLLQKIAQAITRNH 196
>gnl|CDD|163254 TIGR03420, DnaA_homol_Hda, DnaA regulatory inactivator Hda.
Members of this protein family are Hda (Homologous to
DnaA). These proteins are about half the length of DnaA
and homologous over length of Hda. In the model species
Escherichia coli, the initiation of DNA replication
requires DnaA bound to ATP rather than ADP; Hda helps
facilitate the conversion of DnaA-ATP to DnaA-ADP.
Length = 226
Score = 28.3 bits (64), Expect = 7.3
Identities = 15/83 (18%), Positives = 32/83 (38%), Gaps = 21/83 (25%)
Query: 369 LCFVGPPGVGKTSLAQSI---AKATGRQYVRMSLGGVYDEADIRGHRRTYIGSMPGRIIQ 425
L G G GK+ L Q+ A+ G+ + + L + +++
Sbjct: 41 LYLWGESGSGKSHLLQAACAAAEERGKSAIYLPLAE--------------LAQADPEVLE 86
Query: 426 SLKRAKRSNPLLLLDEIDKMGSD 448
L++A L+ LD+++ +
Sbjct: 87 GLEQA----DLVCLDDVEAIAGQ 105
>gnl|CDD|162313 TIGR01351, adk, adenylate kinases. Adenylate kinase (EC 2.7.4.3)
converts ATP + AMP to ADP + ADP, that is, uses ATP as a
phosphate donor for AMP. Most members of this family are
known or believed to be adenylate kinase. However, some
members accept other nucleotide triphosphates as donors,
may be unable to use ATP, and may fail to complement
adenylate kinase mutants. An example of a
nucleoside-triphosphate--adenylate kinase (EC 2.7.4.10)
is a GTP:AMP phosphotransferase. This family is
designated subfamily rather than equivalog for this
reason.
Length = 210
Score = 28.3 bits (64), Expect = 7.6
Identities = 10/25 (40%), Positives = 16/25 (64%)
Query: 371 FVGPPGVGKTSLAQSIAKATGRQYV 395
+GPPG GK + A+ IA+ G ++
Sbjct: 4 LLGPPGSGKGTQAKRIAEKYGLPHI 28
>gnl|CDD|184933 PRK14969, PRK14969, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 527
Score = 28.2 bits (63), Expect = 8.1
Identities = 11/19 (57%), Positives = 15/19 (78%)
Query: 371 FVGPPGVGKTSLAQSIAKA 389
F G GVGKT+LA+ +AK+
Sbjct: 43 FTGTRGVGKTTLARILAKS 61
>gnl|CDD|162618 TIGR01947, rnfG, electron transport complex, RnfABCDGE type, G
subunit. The six subunit complex RnfABCDGE in
Rhodobacter capsulatus encodes an apparent NADH
oxidoreductase responsible for electron transport to
nitrogenase, necessary for nitrogen fixation. A closely
related complex in E. coli, RsxABCDGE (Reducer of SoxR),
reduces the 2Fe-2S-containing superoxide sensor SoxR,
active as a transcription factor when oxidized. This
family of putative NADH oxidoreductase complexes exists
in many of the same species as the related NQR, a
Na(+)-translocating NADH-quinone reductase, but is
distinct. This model describes the A subunit.
Length = 186
Score = 28.5 bits (64), Expect = 8.3
Identities = 18/88 (20%), Positives = 26/88 (29%), Gaps = 7/88 (7%)
Query: 107 ILVEGSVRARIVEYIEREDFLEAITQVLP------DPTEDPVELEALSRSVIAEFSNYIK 160
LV + I E E + LEA+ QVLP D E V +
Sbjct: 16 ALVNQFTKEVIAE-AEAKQQLEALKQVLPQGLYDNDLLESTVPEVDEDLLGLGTILPVYG 74
Query: 161 LNKKISPEVIGITSQIEGFSKLADVIAA 188
K + G+S ++
Sbjct: 75 AKKGGQVVAYVLEVSAPGYSGPIQLLVG 102
>gnl|CDD|179397 PRK02256, PRK02256, putative aminopeptidase 1; Provisional.
Length = 462
Score = 28.3 bits (64), Expect = 8.5
Identities = 10/18 (55%), Positives = 14/18 (77%)
Query: 801 SIPLSVEGIVVGKDGRSV 818
+IPL++ G+VV KDG V
Sbjct: 138 AIPLALHGVVVKKDGTKV 155
>gnl|CDD|130254 TIGR01186, proV, glycine betaine/L-proline transport ATP binding
subunit. This model describes the glycine
betaine/L-proline ATP binding subunit in bacteria and
its equivalents in archaea. This transport system belong
to the larger ATP-Binding Cassette (ABC) transporter
superfamily. The characteristic feature of these
transporter is the obligatory coupling of ATP hydrolysis
to substrate translocation. The minimal configuration of
bacterial ABC transport system: an ATPase or ATP binding
subunit; An integral membrane protein; a hydrophilic
polypetpide, which likely functions as substrate binding
protein. Functionally, this transport system is involved
in osmoregulation. Under conditions of stress, the
organism recruits these transport system to accumulate
glycine betaine and other solutes which offer
osmo-protection. It has been demonstrated that glycine
betaine uptake is accompanied by symport with sodium
ions. The locus has been named variously as proU or
opuA. A gene library from L.lactis functionally
complements an E.coli proU mutant. The comlementing
locus is similar to a opuA locus in B.sutlis. This
clarifies the differences in nomenclature.
Length = 363
Score = 28.3 bits (63), Expect = 9.3
Identities = 13/57 (22%), Positives = 24/57 (42%), Gaps = 4/57 (7%)
Query: 365 KGLILCFVGPPGVGKTSLAQSIAK----ATGRQYVRMSLGGVYDEADIRGHRRTYIG 417
KG I +G G GK++ + + + G+ ++ ++R RR IG
Sbjct: 18 KGEIFVIMGLSGSGKSTTVRMLNRLIEPTAGQIFIDGENIMKQSPVELREVRRKKIG 74
>gnl|CDD|178393 PLN02796, PLN02796, D-glycerate 3-kinase.
Length = 347
Score = 28.2 bits (63), Expect = 9.5
Identities = 23/105 (21%), Positives = 46/105 (43%), Gaps = 19/105 (18%)
Query: 367 LILCFVGPPGVGKTSLAQSIA---KATGRQYVRMSLGGVY----DEADI----------- 408
L++ P G GKT+L ++ ATGR+ +S+ Y D+A +
Sbjct: 101 LVIGISAPQGCGKTTLVFALVYLFNATGRRAASLSIDDFYLTAADQAKLAEANPGNALLE 160
Query: 409 -RGHRRTYIGSMPGRIIQSLKRAKRSNPLLLLDEIDKMGSDLRGD 452
RG+ ++ ++ +++L++ + + + DK RGD
Sbjct: 161 LRGNAGSHDLALGVETLEALRKLNKEGSKMKVPRYDKSAYGGRGD 205
>gnl|CDD|149775 pfam08822, DUF1804, Protein of unknown function (DUF1804). This
family of bacterial protein is uncharacterized.
Length = 165
Score = 28.1 bits (63), Expect = 9.8
Identities = 21/92 (22%), Positives = 40/92 (43%), Gaps = 8/92 (8%)
Query: 99 RLPDGTVKILVEGSVRARIVEYIEREDFLEAITQVLPDPTEDPVE-LEALSRSVIAEFSN 157
L G ++ L + +V+Y D L+ + P D + L +L+ S FS
Sbjct: 58 TLAGGGIEDLARQMLTGFVVQYQATMDELQEDEDL---PPSDKAKLLASLADS----FSK 110
Query: 158 YIKLNKKISPEVIGITSQIEGFSKLADVIAAN 189
+ +K++ PE + + +E +LAD +
Sbjct: 111 TVAASKRVLPETSKLATALEVLQRLADFVQER 142
>gnl|CDD|150839 pfam10228, DUF2228, Uncharacterized conserved protein (DUF2228).
This is a family of conserved proteins of approximately
700 residues found from worms to humans.
Length = 253
Score = 28.2 bits (63), Expect = 9.8
Identities = 25/86 (29%), Positives = 41/86 (47%), Gaps = 14/86 (16%)
Query: 217 MESEISVLQVEKRIRSRVKRQMEKTQREYYLHEQMKAIQKELDN-GEEGRDEISDFEARI 275
E +S+ Q K ++ R K+ + KT H+ + +DN + G +S+ +A +
Sbjct: 121 KELGLSLEQKTKVMKQRKKKVVTKT-----FHKGG--LVVPVDNKTDVGYRPLSESDANL 173
Query: 276 SKI------RLSKEAREKALSELQKL 295
KI KE R+KA ELQ+L
Sbjct: 174 KKILKTIEEAEDKEERDKAFDELQEL 199
>gnl|CDD|172750 PRK14262, PRK14262, phosphate ABC transporter ATP-binding protein;
Provisional.
Length = 250
Score = 28.0 bits (62), Expect = 9.9
Identities = 14/32 (43%), Positives = 21/32 (65%), Gaps = 2/32 (6%)
Query: 357 VQMRVIKNKGLILCFVGPPGVGKTSLAQSIAK 388
V M++ KN+ I +GP G GKT+L +SI +
Sbjct: 22 VTMKIFKNQ--ITAIIGPSGCGKTTLLRSINR 51
Database: CddB
Posted date: Feb 4, 2011 9:54 PM
Number of letters in database: 5,994,473
Number of sequences in database: 21,608
Lambda K H
0.317 0.136 0.374
Gapped
Lambda K H
0.267 0.0636 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 13,534,825
Number of extensions: 936636
Number of successful extensions: 2852
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2811
Number of HSP's successfully gapped: 226
Length of query: 820
Length of database: 5,994,473
Length adjustment: 101
Effective length of query: 719
Effective length of database: 3,812,065
Effective search space: 2740874735
Effective search space used: 2740874735
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 61 (27.5 bits)