RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 total letters
Searching..................................................done
Query= gi|254780334|ref|YP_003064747.1| DNA repair protein RadA
[Candidatus Liberibacter asiaticus str. psy62]
(479 letters)
>gnl|CDD|183326 PRK11823, PRK11823, DNA repair protein RadA; Provisional.
Length = 446
Score = 716 bits (1852), Expect = 0.0
Identities = 242/457 (52%), Positives = 320/457 (70%), Gaps = 14/457 (3%)
Query: 1 MVKIRSQYFCQSCGEIHSRWIGKCDSCNAWNTIIEDSSRKESDQRFSKTIKQGHSISLFM 60
M K ++ Y CQ CG +W+G+C C AWNT++E K G S +
Sbjct: 1 MAKKKTAYVCQECGAESPKWLGRCPECGAWNTLVE----------EVAASKAGSSKPVQP 50
Query: 61 LSEESIEEESRIQTHIDELDRVTGGGFVRGSVILVGGDPGIGKSTLLMQTAASLAYKKHR 120
LS+ EEE RI T I ELDRV GGG V GSV+L+GGDPGIGKSTLL+Q AA LA +
Sbjct: 51 LSDIEAEEEPRISTGIGELDRVLGGGLVPGSVVLIGGDPGIGKSTLLLQVAARLAAAGGK 110
Query: 121 ITYVSGEEAIGQIRLRAQRLNTINSSVYIAIETNVEDIIATLITNEKPDLVIIDSIQTLW 180
+ YVSGEE+ QI+LRA+RL + ++Y+ ETN+E I+AT I EKPDLV+IDSIQT++
Sbjct: 111 VLYVSGEESASQIKLRAERLGLPSDNLYLLAETNLEAILAT-IEEEKPDLVVIDSIQTMY 169
Query: 181 SQTAESSPGTVIQVRTSVQAMIQYAKKNGVAMVLVGHVTKEGQIAGPRVIEHMVDAVLYF 240
S ES+PG+V QVR +++ AK+ G+A+ LVGHVTKEG IAGPRV+EHMVD VLYF
Sbjct: 170 SPELESAPGSVSQVRECAAELMRLAKQRGIAVFLVGHVTKEGAIAGPRVLEHMVDTVLYF 229
Query: 241 EGGTRNTQYDYRILRSVKNRFGPTDEIGVFEMSDKGLQEVSDPSKIFLSDRDSTSPGTAV 300
EG + YRILR+VKNRFG T+EIGVFEM+++GL+EVS+PS++FLS+RD PG+AV
Sbjct: 230 EG---DRHSRYRILRAVKNRFGATNEIGVFEMTEQGLREVSNPSELFLSERDENVPGSAV 286
Query: 301 FAGIEGTRALLVEIQSLVVPTSLGMPRRTVVGWDSSRLAMILAVLEARCNIKFGNHDVHL 360
+EGTR LLVEIQ+LV PTS G PRRT VG DS+RLAM+LAVLE R + G+ DV++
Sbjct: 287 TVTMEGTRPLLVEIQALVSPTSFGNPRRTAVGLDSNRLAMLLAVLEKRLGLPLGDQDVYV 346
Query: 361 NIAGGYRISEPAADVAVAAALISSILSIPLPSDFVYFGEVSLSGSVRAVGHMQQRLKEAE 420
N+ GG +I+EPAAD+AVA A+ SS+ PLP D V FGEV L+G +R V +++RLKEA
Sbjct: 347 NVVGGLKITEPAADLAVALAIASSLRDRPLPPDTVVFGEVGLTGEIRPVPRIERRLKEAA 406
Query: 421 KIGFLSGVFPESAKGECKIGMLDRQYIKNLSDLVKKI 457
K+GF + P+ + ++ +K L++ ++ +
Sbjct: 407 KLGFKRAIVPKGNLPKKPPKGIEVIGVKTLAEALELL 443
>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 = 487 bits (1256), Expect = e-138
Identities = 217/460 (47%), Positives = 295/460 (64%), Gaps = 12/460 (2%)
Query: 1 MVKIRSQYFCQSCGEIHSRWIGKCDSCNAWNTIIED------SSRKESDQRFSKTIKQGH 54
M K +S++ CQ CG +W GKC +C+AWNTI E+ ++K I Q
Sbjct: 1 MAKAKSKFVCQHCGADSPKWQGKCPACHAWNTITEERLHRSLGAQKNRRNSGKAGIPQAQ 60
Query: 55 SISLFMLSEESIEEESRIQTHIDELDRVTGGGFVRGSVILVGGDPGIGKSTLLMQTAASL 114
+S +EE R + ELDRV GGG V GS+IL+GGDPGIGKSTLL+Q A L
Sbjct: 61 KSQ--TISAIELEEVPRFSSGFGELDRVLGGGIVPGSLILIGGDPGIGKSTLLLQVACQL 118
Query: 115 AYKKHRITYVSGEEAIGQIRLRAQRLNTINSSVYIAIETNVEDIIATLITNEKPDLVIID 174
A + ++ YVSGEE++ QI++RA RL ++Y+ ETN E I A I E P +ID
Sbjct: 119 AKNQMKVLYVSGEESLQQIKMRAIRLGLPEPNLYVLSETNWEQICA-NIEEENPQACVID 177
Query: 175 SIQTLWSQTAESSPGTVIQVRTSVQAMIQYAKKNGVAMVLVGHVTKEGQIAGPRVIEHMV 234
SIQTL+S S+PG+V QVR +++ AK G+A+ +VGHVTKEG IAGP+V+EHMV
Sbjct: 178 SIQTLYSPDISSAPGSVSQVRECTAELMRLAKTRGIAIFIVGHVTKEGSIAGPKVLEHMV 237
Query: 235 DAVLYFEGGTRNTQYDYRILRSVKNRFGPTDEIGVFEMSDKGLQEVSDPSKIFLSDRDST 294
D VLYFEG + +RILRSVKNRFG T+EIG+FEM+++GL+EV +PS IFLS R+
Sbjct: 238 DTVLYFEGDRDSR---FRILRSVKNRFGATNEIGIFEMTEQGLREVLNPSAIFLSRREEP 294
Query: 295 SPGTAVFAGIEGTRALLVEIQSLVVPTSLGMPRRTVVGWDSSRLAMILAVLEARCNIKFG 354
G+++ EGTR LLVEIQ+LV PTS PRR G D +RLA++LAVLE R +
Sbjct: 295 MSGSSITVTWEGTRPLLVEIQALVSPTSFANPRRVATGLDQNRLALLLAVLEKRLGLPLA 354
Query: 355 NHDVHLNIAGGYRISEPAADVAVAAALISSILSIPLPSDFVYFGEVSLSGSVRAVGHMQQ 414
+ DV LN+AGG ++SEPAAD+A+ A++SS PL D V+ GEV L+G +R V +++
Sbjct: 355 DQDVFLNVAGGVKVSEPAADLALLIAIVSSFRDRPLDPDLVFLGEVGLAGEIRPVPSLEE 414
Query: 415 RLKEAEKIGFLSGVFPESAKGECKIGMLDRQYIKNLSDLV 454
RLKEA K+GF + P++ + + +K + D +
Sbjct: 415 RLKEAAKLGFKRAIVPKANSPKTAPEGIKVIGVKKVGDAL 454
>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 = 69.4 bits (170), Expect = 2e-12
Identities = 35/114 (30%), Positives = 65/114 (57%), Gaps = 2/114 (1%)
Query: 312 VEIQSLVVPTSLGMPRRTVVGWDSSRLAM--ILAVLEARCNIKFGNHDVHLNIAGGYRIS 369
+ + ++ +G ++V S+R ++ +LAVL + I N+D+H+N GG +
Sbjct: 381 INVTGIIEEEEIGGSGKSVRRKSSARGSVENVLAVLRSVFGINPQNYDIHINFPGGIPVD 440
Query: 370 EPAADVAVAAALISSILSIPLPSDFVYFGEVSLSGSVRAVGHMQQRLKEAEKIG 423
P+A VA+A A+ S+I P+ + GE+SL+G V+ VG + +++ A+K G
Sbjct: 441 GPSAGVAIAVAIYSAIFKCPIDNKVAMTGEISLNGLVKPVGGVPSKIEAAKKAG 494
>gnl|CDD|181771 PRK09302, PRK09302, circadian clock protein KaiC; Reviewed.
Length = 509
Score = 68.0 bits (167), Expect = 4e-12
Identities = 46/176 (26%), Positives = 75/176 (42%), Gaps = 26/176 (14%)
Query: 54 HSISLFMLSEESIEEES---RIQTHIDELDRVTGGGFVRGSVILVGGDPGIGKSTLLMQT 110
IS+ L+ + + S RI + + +LD + GGGF RGS+ILV G G GK+ L +
Sbjct: 234 DGISVLPLTAMRLTQRSSNERISSGVPDLDEMLGGGFFRGSIILVSGATGTGKTLLASKF 293
Query: 111 AASLAYKKHRITYVSGEEAIGQI------------RLRAQRLNTINSSVYIAIETNVED- 157
A + + R + EE+ Q+ ++ + L I + +ED
Sbjct: 294 AEAACRRGERCLLFAFEESRAQLIRNARSWGIDLEKMEEKGLLKIICAR--PESYGLEDH 351
Query: 158 --IIATLITNEKPDLVIIDSIQTLWSQTAESSPGTVIQVRTSVQAMIQYAKKNGVA 211
II I KP V ID + +A + G++ + R V + Y K +
Sbjct: 352 LIIIKREIEEFKPSRVAIDPL------SALARGGSLNEFRQFVIRLTDYLKSEEIT 401
Score = 46.4 bits (111), Expect = 1e-05
Identities = 50/227 (22%), Positives = 83/227 (36%), Gaps = 35/227 (15%)
Query: 60 MLSEESIEEESRIQTHIDELDRVTGGGFVRGSVILVGGDPGIGKSTLLMQ-TAASLAYKK 118
M + ++ T I+ D +T GG +G LV G G GK+ +Q +
Sbjct: 1 MNQPSASPGIEKLPTGIEGFDDITHGGLPKGRPTLVSGTAGTGKTLFALQFLVNGIKRFD 60
Query: 119 HRITYVSGEEAIGQIRLRAQRLN------------------TINSSVYIAIETNVEDIIA 160
+V+ EE+ I S A E ++E +
Sbjct: 61 EPGVFVTFEESPEDIIRNVASFGWDLQKLIDEGKLFILDASPDPSEQEEAGEYDLEALFI 120
Query: 161 TL---ITNEKPDLVIIDSIQTLWSQTAESSPGTVIQVRTSVQAMIQYAKKNGVAMVLVGH 217
+ I V++DSI+ L+S + + VR ++ + + K+ GV V+ G
Sbjct: 121 RIEYAIDKIGAKRVVLDSIEALFSGFSNEAV-----VRRELRRLFAWLKQKGVTAVITGE 175
Query: 218 VTKE-GQIAGPRVIEHMVDAVLYFEGGTRNT---QYDYRILRSVKNR 260
E G + V E + D V+ RN + R LR +K R
Sbjct: 176 RGDEYGPLTRYGVEEFVSDCVIIL----RNRLEGEKRTRTLRILKYR 218
>gnl|CDD|148381 pfam06745, KaiC, KaiC. This family represents a conserved region
within bacterial and archaeal proteins, most of which
are hypothetical. More than one copy is sometimes found
in each protein. This family includes KaiC, which is one
of the Kai proteins among which direct protein-protein
association may be a critical process in the generation
of circadian rhythms in cyanobacteria.
Length = 231
Score = 63.4 bits (155), Expect = 1e-10
Identities = 59/234 (25%), Positives = 94/234 (40%), Gaps = 38/234 (16%)
Query: 72 IQTHIDELDRVTGGGFVRGSVILVGGDPGIGKSTLLMQTAASLAYKKHRIT-YVSGEEAI 130
++T I LD + GG G V+L+ G PG GK+ +Q + A + YV+ EE
Sbjct: 1 VKTGIPGLDEILKGGIPEGRVVLITGGPGTGKTIFGLQFLYNGALEYGEPGVYVTLEEPP 60
Query: 131 GQIRLRAQRLN----TINSSVYIAI---------------ETNVEDIIATL---ITNEKP 168
+R A+ + +AI ++E++I L I
Sbjct: 61 EDLRENAKSFGWDLEKLEEEGKLAIIDASTSGIGIAEVKGRFDLEELIERLREAIREIGA 120
Query: 169 DLVIIDSIQTLWSQTAESSPGTVIQVRTSVQAMIQYAKKNGVAMVLVGHVTK-EGQIAGP 227
V+IDSI TL P R ++ + + KK GV + EG I G
Sbjct: 121 KRVVIDSITTL---FYLLKPA---MAREILRRLKRVLKKLGVTAIFTSEKPSGEGGIGGY 174
Query: 228 RVIEHMVDAVLYFEGGTRNTQYDYRILRS---VKNRFGPTD-EIGVFEMSDKGL 277
V E +VD V+ + + ++R+ VK R P + FE++D G+
Sbjct: 175 GVEEFVVDGVIRL----DLKEIEGELVRTIEIVKMRGTPHSMKRYPFEITDNGI 224
>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 = 62.9 bits (153), Expect = 2e-10
Identities = 31/106 (29%), Positives = 60/106 (56%), Gaps = 2/106 (1%)
Query: 355 NHDVHLNIAGGYRISEPAADVAVAAALISSILSIPLPSDFVYFGEVSLSGSVRAVGHMQQ 414
N+D+H+N+ GG RI P+A A+ +IS+IL P+ D GE+SL G ++ VG + +
Sbjct: 510 NYDIHVNVIGGGRIDGPSAGAAITLCMISAILGKPIRQDVAITGEISLRGKIKPVGGIFE 569
Query: 415 RLKEAEKIGFLSGVFPESAKGECKIGMLDRQ--YIKNLSDLVKKIT 458
++ A++ G + V PE + G+ + ++ + +L++ +
Sbjct: 570 KIYGAKQAGIKTVVIPEENLKDVPQGLPGIEVKFVSTIEELMRIVF 615
>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 = 59.7 bits (144), Expect = 2e-09
Identities = 31/153 (20%), Positives = 65/153 (42%), Gaps = 8/153 (5%)
Query: 89 RGSVILVGGDPGIGKSTLLMQTAASLAYKKHRITYVSGEEAIGQIRLRAQRLNTINSSVY 148
G VIL+ G PG GK+TL A L + Y+ GE+ + ++ + +
Sbjct: 1 PGEVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKAS 60
Query: 149 IAIETNVEDIIATLITNEKPDLVIIDSIQTLWSQTAESSPGTVIQVRTSVQAMIQYAKKN 208
+ E + +A L KPD++I+D I +L ++ ++ + ++ ++ +
Sbjct: 61 GSGELRLRLALA-LARKLKPDVLILDEITSL----LDAEQEALLLLLEELRLLLLLKSEK 115
Query: 209 GVAMVLVGHVTKEGQIAGPRVIEHMVDAVLYFE 241
+ ++L + K GP ++ D +
Sbjct: 116 NLTVILTTNDEK---DLGPALLRRRFDRRIVLL 145
>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 = 59.7 bits (145), Expect = 2e-09
Identities = 50/216 (23%), Positives = 94/216 (43%), Gaps = 25/216 (11%)
Query: 79 LDRVTGGGFVRGSVILVGGDPGIGKSTLLMQTAASLAYKKHRITYVSGE----EAIGQI- 133
+D + GGG RG++ + G PG GK+ + M A + A + ++ Y+ E E QI
Sbjct: 1 IDELLGGGVERGTITQIYGPPGSGKTNICMILAVNAARQGKKVVYIDTEGLSPERFKQIA 60
Query: 134 RLRAQRLNTINSSVYIAIETNVEDII----ATLITNEKPDLVIIDSIQTLW-SQTAESSP 188
R +R + N V+ + + + + + I + LV++DS L+ + ++
Sbjct: 61 EDRPERALS-NFIVFEVFDFDEQGVAIQKTSKFIDRDSASLVVVDSFTALYRLELSDDRI 119
Query: 189 GTVIQVRTSVQAMIQYAKKNGVAMVLVGHV---TKEGQIA--GPRVIEHMVDAVLYFE-- 241
++ + ++ A+K +A+V+ V G + G ++EH +L E
Sbjct: 120 SRNRELARQLTLLLSLARKKNLAVVITNQVYTDVNNGTLRPLGGHLLEHWSKVILRLEKF 179
Query: 242 GGTRNTQYDYRILRSVKNRFGPTDEIGVFEMSDKGL 277
G R L K+R P E F ++D G+
Sbjct: 180 RGRRLA-----TLE--KHRSRPEGESVYFRITDDGI 208
>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 = 56.0 bits (135), Expect = 2e-08
Identities = 28/124 (22%), Positives = 62/124 (50%), Gaps = 6/124 (4%)
Query: 355 NHDVHLNIAGGY-RISEPAADVAVAAALISSILSIPLPSDFVYFGEVSLSGSVRAVGHMQ 413
N+D+H+ Y + +A ++VA A+IS++ IP+ D G +S+ G V VG +
Sbjct: 484 NYDIHIQFLQTYEGVEGDSASISVATAVISALEEIPVDQDVAMTGSLSVRGEVLPVGGVT 543
Query: 414 QRLKEAEKIGFLSGVFPESAKGECKI-----GMLDRQYIKNLSDLVKKITALQKKDKKTV 468
++++ A + G + P+S + + G ++ ++ L ++++ + L KK +
Sbjct: 544 EKIEAAIEAGIKKVIIPKSNMIDVILEKETEGKIEIIPVETLDEVLEHVLDLDKKKGSLI 603
Query: 469 HKTR 472
+
Sbjct: 604 ERFN 607
>gnl|CDD|181799 PRK09361, radB, DNA repair and recombination protein RadB;
Provisional.
Length = 225
Score = 54.5 bits (132), Expect = 6e-08
Identities = 52/237 (21%), Positives = 97/237 (40%), Gaps = 35/237 (14%)
Query: 68 EESRIQTHIDELDRVTGGGFVRGSVILVGGDPGIGKSTLLMQTAASLAYKKHRITYVSGE 127
+ R+ T LD + GGGF RG++ + G PG GK+ + +Q A A ++ Y+ E
Sbjct: 1 MDERLPTGCKMLDELLGGGFERGTITQIYGPPGSGKTNICLQLAVEAAKNGKKVIYIDTE 60
Query: 128 ----EAIGQIRLRAQRLNTINSSVYI-----------AIETNVEDIIATLITNEKPDLVI 172
E QI + + S++ I AI E + E L++
Sbjct: 61 GLSPERFKQI--AGEDFEELLSNIIIFEPSSFEEQSEAIR-KAEKLAK-----ENVGLIV 112
Query: 173 IDSIQTLW---SQTAESSPGTVIQVRTSVQAMIQYAKKNGVAMVLVGHV---TKEGQI-- 224
+DS +L+ + E + ++ + +++ A+K+ +A+V+ V +
Sbjct: 113 LDSATSLYRLELEDEEDNSKLNRELGRQLTHLLKLARKHDLAVVITNQVYSDIDSDGLRP 172
Query: 225 AGPRVIEHMVDAVLYFEGGTRNTQYDYRILRSVKNRFGPTDEIGVFEMSDKGLQEVS 281
G +EH +L E R K+R P E F ++D+G++ +
Sbjct: 173 LGGHTLEHWSKTILRLEKFRNGK----RRATLEKHRSRPEGESAEFRITDRGIEIID 225
>gnl|CDD|163593 TIGR03881, KaiC_arch_4, KaiC domain protein, PAE1156 family.
Members of this protein family are archaeal
single-domain KaiC_related proteins, homologous to the
Cyanobacterial circadian clock cycle protein KaiC, an
autokinase/autophosphorylase that has two copies of the
domain.
Length = 229
Score = 49.7 bits (119), Expect = 2e-06
Identities = 32/141 (22%), Positives = 57/141 (40%), Gaps = 20/141 (14%)
Query: 71 RIQTHIDELDRVTGGGFVRGSVILVGGDPGIGKSTLLMQTAASLAYKKHRITYVSGEEAI 130
R+ T ++ LD++ GG RG + V G+PG GK+ + A + YV+ EE+
Sbjct: 1 RLSTGVEGLDKLLEGGIPRGFFVAVTGEPGTGKTIFCLHFAYKGLRDGDPVIYVTTEESR 60
Query: 131 GQIRLRAQRLNTINSSVYIAIETNVEDIIATLITNEKPDLVIIDSIQTLWSQTAESSPGT 190
I +A + ++ I E+ LVIID+ L + +
Sbjct: 61 ESIIRQAAQFG-MDFEKAI----------------EEGKLVIIDA---LMKEKEDEWSLR 100
Query: 191 VIQVRTSVQAMIQYAKKNGVA 211
+ + + +I+ K G
Sbjct: 101 ELSIEELLNKVIEAKKYLGYG 121
>gnl|CDD|181459 PRK08533, PRK08533, flagellar accessory protein FlaH; Reviewed.
Length = 230
Score = 49.7 bits (119), Expect = 2e-06
Identities = 40/135 (29%), Positives = 61/135 (45%), Gaps = 16/135 (11%)
Query: 67 EEESRIQTHIDELDRVTGGGFVRGSVILVGGDPGIGKSTLLMQTAASLAYKKHRITYVSG 126
E ++I+ DEL + GGG GS+IL+ GD GKS L + A + ++YVS
Sbjct: 1 MELAKIELSRDELHKRLGGGIPAGSLILIEGDESTGKSILSQRLAYGFLQNGYSVSYVST 60
Query: 127 E----EAIGQIR-LRAQRLNTINS------SVYIAIETNVE--DIIATLITNEK---PDL 170
+ E I Q+ L + S VY + N E + L+ + D+
Sbjct: 61 QLTTTEFIKQMMSLGYDINKKLISGKLLYIPVYPLLSGNSEKRKFLKKLMNTRRFYEKDV 120
Query: 171 VIIDSIQTLWSQTAE 185
+IIDS+ +L S A
Sbjct: 121 IIIDSLSSLISNDAS 135
>gnl|CDD|163590 TIGR03878, thermo_KaiC_2, KaiC domain protein, AF_0795 family.
This KaiC domain-containing protein family occurs
sporadically across a broad taxonomic range
(Euryarchaeota, Aquificae, Dictyoglomi,
Epsilonproteobacteria, and Firmicutes), but exclusively
in thermophiles.
Length = 259
Score = 46.6 bits (111), Expect = 1e-05
Identities = 52/238 (21%), Positives = 92/238 (38%), Gaps = 42/238 (17%)
Query: 81 RVTGGGFVRGSVILVGGDPGIGKSTLLMQTAASLAYKKHRITYVSGEE----AIGQIRLR 136
R GG SVI + G GKS ++ Q A + A + + + +V+ E ++ R
Sbjct: 27 RKPLGGIPAYSVINITGVSDTGKSLMVEQFAVTQASRGNPVLFVTVESPANFVYTSLKER 86
Query: 137 AQRLNT----INSSVYI-------AIETNVEDIIATL---ITNEKPDLVIIDSIQTLWSQ 182
A+ + I ++ + + NV +++ATL I K +IDSI L+
Sbjct: 87 AKAMGVDFDKIEENIILIDAASSTELRENVPNLLATLAYAIKEYKVKNTVIDSITGLYE- 145
Query: 183 TAESSPGTVIQVRTSVQAMIQYAKKNGVAMVLV-----GHVTKEGQIAGPRVIEHMVDAV 237
+ R V+ + + KK + V GH + AG + H+VD
Sbjct: 146 ------AKEMMAREIVRQLFNFMKKWYQTALFVSQKRSGHEELSAEAAGGYAVSHIVDGT 199
Query: 238 LYFEGGTRNTQYD-----------YRILRSVKNRFGPTD-EIGVFEMSDKGLQEVSDP 283
+ +++D R+ R R D + V E+ + GL ++ P
Sbjct: 200 IVLAKQLIMSRFDASLYKKPIGEIVRLFRIDGCRMCGHDTKTHVLEIDETGLVKIGPP 257
>gnl|CDD|132639 TIGR03600, phage_DnaB, phage replicative helicase, DnaB family,
HK022 subfamily. Members of this family are phage (or
prophage-region) homologs of the bacterial homohexameric
replicative helicase DnaB. Some phage may rely on host
DnaB, while others encode their own verions. This model
describes the largest phage-specific clade among the
close homologs of DnaB, but there are, or course, other
DnaB homologs from phage that fall outside the scope of
this model.
Length = 421
Score = 45.1 bits (107), Expect = 4e-05
Identities = 43/193 (22%), Positives = 86/193 (44%), Gaps = 36/193 (18%)
Query: 72 IQTHIDELDRVTGGGFVRGSVILVGGDPGIGKSTLLMQTAASLAYKK-HRITYVSGEEAI 130
+ T + +LDR+T G V+G +I++G P +GK+TL + A ++A ++ + + S E +
Sbjct: 177 LSTGLPKLDRLTNG-LVKGDLIVIGARPSMGKTTLALNIAENVALREGKPVLFFSLEMSA 235
Query: 131 GQI--RLRAQRLNTINSSVYIAIETNVE--DIIATLITNEKPDLVIIDSIQTLWSQTAES 186
Q+ RL A + ++ + + ++ + + DL I D+
Sbjct: 236 EQLGERLLASKSGINTGNIRTGRFNDSDFNRLLNAVDRLSEKDLYIDDTGGL-------- 287
Query: 187 SPGTVIQVRTSVQAMIQYAKKNGVAMVLVGHVTKEGQIAGPRVIEHMVDAVLYFEGGTRN 246
TV Q+R+ + + + KK G+ +++V ++ +A R G RN
Sbjct: 288 ---TVAQIRSIARRIKR--KKGGLDLIVVDYIQL---MAPTR-------------GRDRN 326
Query: 247 TQYDYRILRSVKN 259
+ I R +K
Sbjct: 327 EELGG-ISRGLKA 338
>gnl|CDD|184312 PRK13765, PRK13765, ATP-dependent protease Lon; Provisional.
Length = 637
Score = 44.6 bits (106), Expect = 6e-05
Identities = 28/129 (21%), Positives = 63/129 (48%), Gaps = 12/129 (9%)
Query: 355 NHDVHLNIAGGYRISE-PAADVAVAAALISSILSIPLPSDFVYFGEVSLSGSVRAVGHMQ 413
N+D+H+ Y E +A ++VA A+IS++ +IP+ G +S+ G V VG +
Sbjct: 493 NYDIHIQFVQTYEGVEGDSASISVATAVISALENIPVDQSVAMTGSLSVRGDVLPVGGVT 552
Query: 414 QRLKEAEKIGFLSGVFPESAKGECKIGMLDRQY--------IKNLSDLVKKITALQKKDK 465
+++ A + G + P+S + + M++ +Y + +S++++ +
Sbjct: 553 YKIEAAAEAGIKKVIIPKSNEQDV---MIEDEYEDKIEIIPVSTISEVLEHALVGGPEKD 609
Query: 466 KTVHKTRSL 474
+ K +S+
Sbjct: 610 SLLDKLKSI 618
>gnl|CDD|131703 TIGR02655, circ_KaiC, circadian clock protein KaiC. Members of
this family are the circadian clock protein KaiC, part
of the kaiABC operon that controls circadian rhythm. It
may be universal in Cyanobacteria. Each member has two
copies of the KaiC domain (Pfam model pfam06745), which
is also found in other proteins. KaiC performs
autophosphorylation and acts as its own transcriptional
repressor.
Length = 484
Score = 44.6 bits (105), Expect = 6e-05
Identities = 37/142 (26%), Positives = 62/142 (43%), Gaps = 16/142 (11%)
Query: 54 HSISLFMLSEESIEEES---RIQTHIDELDRVTGGGFVRGSVILVGGDPGIGKSTLLMQT 110
H I++F L + + S R+ + + LD + GGGF + S+IL G G GK+ L+ +
Sbjct: 224 HGINIFPLGAMRLTQRSSNVRVSSGVVRLDEMCGGGFFKDSIILATGATGTGKTLLVSKF 283
Query: 111 AASLAYKKHRITYVSGEEAIGQIRLRA----------QRLNTINSSVYIAIETNVED--- 157
+ K R + EE+ Q+ A ++ + +ED
Sbjct: 284 LENACANKERAILFAYEESRAQLLRNAYSWGIDFEEMEQQGLLKIICAYPESAGLEDHLQ 343
Query: 158 IIATLITNEKPDLVIIDSIQTL 179
II + I + KP + IDS+ L
Sbjct: 344 IIKSEIADFKPARIAIDSLSAL 365
Score = 28.8 bits (64), Expect = 3.7
Identities = 14/40 (35%), Positives = 22/40 (55%)
Query: 70 SRIQTHIDELDRVTGGGFVRGSVILVGGDPGIGKSTLLMQ 109
++I+T I+ D ++ GG G LV G G GK+ +Q
Sbjct: 1 AKIRTMIEGFDDISHGGLPIGRSTLVSGTSGTGKTLFSIQ 40
>gnl|CDD|163592 TIGR03880, KaiC_arch_3, KaiC domain protein, AF_0351 family. This
model represents a rather narrowly distributed archaeal
protein family in which members have a single copy of
the KaiC domain. This stands in contrast to the
circadian clock protein KaiC itself, with two copies of
the domain. Members are expected to have weak ATPase
activity, by homology to the
autokinase/autophosphorylase KaiC itself.
Length = 224
Score = 43.9 bits (104), Expect = 9e-05
Identities = 63/223 (28%), Positives = 98/223 (43%), Gaps = 30/223 (13%)
Query: 76 IDELDRVTGGGFVRGSVILVGGDPGIGKSTLLMQTAASLAYKKHRITYVSGEEAIGQIRL 135
I LD + GGGF G VI+V G+ G GK+T +Q + Y+S EE +I
Sbjct: 2 IPGLDEMLGGGFPEGHVIVVIGEYGTGKTTFSLQFLYQGLKNGEKAMYISLEEREERILG 61
Query: 136 RAQRL-----NTINSSVYIAIETNVEDIIATL--ITNEKPDL--------VIIDSI---Q 177
A+ + I+ S+YI + + D +L I NE P L V+ID I +
Sbjct: 62 YAKSKGWDLEDYIDKSLYI-VRLDPSDFKTSLNRIKNELPILIKELGASRVVIDPISLLE 120
Query: 178 TLWSQTAESSPGTVIQVRTSVQAMIQYAKKNGVAMVLVGHVTKEGQIAGPR-VIEHMVDA 236
TL+ AE RT + ++ GV +L K A +IE++ D
Sbjct: 121 TLFDDDAER--------RTELFRFYSSLRETGVTTILTSEADKTNVFASKYGLIEYLADG 172
Query: 237 VLYFEGGTRNTQYDYRI-LRSVKNRFGP-TDEIGVFEMSDKGL 277
V+ + + D R+ + VK R + EI +E++D G+
Sbjct: 173 VIILKYVRNSDLRDVRLAVEVVKMRRSKHSREIKPYEITDSGI 215
>gnl|CDD|180381 PRK06067, PRK06067, flagellar accessory protein FlaH; Validated.
Length = 234
Score = 43.8 bits (104), Expect = 1e-04
Identities = 32/141 (22%), Positives = 56/141 (39%), Gaps = 23/141 (16%)
Query: 72 IQTHIDELDRVTGGGFVRGSVILVGGDPGIGKSTLLMQTAASLAYKKHRITYVSGEEAIG 131
I T +ELDR GGG S+IL+ GD G GKS L Q + ++ ++ E
Sbjct: 7 ISTGNEELDRKLGGGIPFPSLILIEGDHGTGKSVLSQQFVYGALKQGKKVYVITTENTSK 66
Query: 132 QIRLRAQRLNTINSSVYIAI------ETNVE-------------DIIATLITNEKPDLVI 172
+ + + I+ S + N E ++I I +++ D++I
Sbjct: 67 SYLKQMESV-KIDISDFFLWGYLRIFPLNTEGFEWNSTLANKLLELIIEFIKSKREDVII 125
Query: 173 IDSIQTLWSQTAESSPGTVIQ 193
IDS+ + ++
Sbjct: 126 IDSLTIF---ATYAEEDDILN 143
>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 = 42.7 bits (101), Expect = 2e-04
Identities = 23/81 (28%), Positives = 42/81 (51%), Gaps = 1/81 (1%)
Query: 353 FGNHDVHLNI-AGGYRISEPAADVAVAAALISSILSIPLPSDFVYFGEVSLSGSVRAVGH 411
F D+HL++ G P+A + +A AL+S P+ D GE++L G V +G
Sbjct: 663 FEKADIHLHVPEGATPKDGPSAGITMATALLSLATGKPVRPDVAMTGEITLRGKVLPIGG 722
Query: 412 MQQRLKEAEKIGFLSGVFPES 432
++++ A++ G + + PE
Sbjct: 723 LKEKTIAAKRAGIKTIILPEK 743
>gnl|CDD|182730 PRK10787, PRK10787, DNA-binding ATP-dependent protease La;
Provisional.
Length = 784
Score = 42.2 bits (99), Expect = 3e-04
Identities = 32/127 (25%), Positives = 62/127 (48%), Gaps = 15/127 (11%)
Query: 342 LAVLEARCNIKFG-------NHDVHLNIAGGYRISE-PAADVAVAAALISSILSIPLPSD 393
L V+ AR K G D+H+++ G + P+A +A+ AL+S + P+ +D
Sbjct: 642 LTVVRARAE-KLGINPDFYEKRDIHVHVPEGATPKDGPSAGIAMCTALVSCLTGNPVRAD 700
Query: 394 FVYFGEVSLSGSVRAVGHMQQRLKEAEKIGFLSGVFPESAKGECK------IGMLDRQYI 447
GE++L G V +G ++++L A + G + + P K + + I LD +
Sbjct: 701 VAMTGEITLRGQVLPIGGLKEKLLAAHRGGIKTVLIPFENKRDLEEIPDNVIADLDIHPV 760
Query: 448 KNLSDLV 454
K + +++
Sbjct: 761 KRIEEVL 767
>gnl|CDD|168322 PRK05973, PRK05973, replicative DNA helicase; Provisional.
Length = 237
Score = 40.4 bits (95), Expect = 0.001
Identities = 36/142 (25%), Positives = 62/142 (43%), Gaps = 20/142 (14%)
Query: 87 FVRGSVILVGGDPGIGKSTLLMQTAASLAYKKHRITYVSGE----------EAIGQIRLR 136
G ++L+G PG GK+ L ++ A + + E A+G R +
Sbjct: 61 LKPGDLVLLGARPGHGKTLLGLELAVEAMKSGRTGVFFTLEYTEQDVRDRLRALGADRAQ 120
Query: 137 AQRLNTINSSVYIAIETNVEDIIATLITNEKPDLVIIDSIQTLWSQTAESSPGTVIQVRT 196
L ++S I + IIA L + + LV+ID +Q L Q E +V QVR
Sbjct: 121 FADLFEFDTSDAIC----ADYIIARLASAPRGTLVVIDYLQLL-DQRREKPDLSV-QVR- 173
Query: 197 SVQAMIQYAKKNGVAMVLVGHV 218
A+ +A++ G+ +V + +
Sbjct: 174 ---ALKSFARERGLIIVFISQI 192
>gnl|CDD|181111 PRK07773, PRK07773, replicative DNA helicase; Validated.
Length = 886
Score = 39.3 bits (92), Expect = 0.002
Identities = 21/65 (32%), Positives = 32/65 (49%), Gaps = 7/65 (10%)
Query: 78 ELDRVTGGGFVRGSVILVGGDPGIGKSTLLMQTAASLAYKKHRITYV--SGEEAIGQIRL 135
ELD +T G G +I+V P +GK+T + A + A +HR+ S E + Q+
Sbjct: 206 ELDAMTNG-LHPGQLIIVAARPSMGKTTFGLDFARNCA-IRHRLAVAIFSLEMSKEQL-- 261
Query: 136 RAQRL 140
RL
Sbjct: 262 -VMRL 265
>gnl|CDD|161985 TIGR00665, DnaB, replicative DNA helicase. This model describes
the helicase DnaB, a homohexameric protein required for
DNA replication. The homohexamer can form a ring around
a single strand of DNA near a replication fork. An
intein of > 400 residues is found at a conserved
location in DnaB of Synechocystis PCC6803, Rhodothermus
marinus (both experimentally confirmed), and
Mycobacterium tuberculosis. The intein removes itself by
a self-splicing reaction. The seed alignment contains
inteins so that the model built from the seed alignment
will model a low cost at common intein insertion sites.
Length = 434
Score = 38.9 bits (92), Expect = 0.003
Identities = 12/47 (25%), Positives = 24/47 (51%), Gaps = 1/47 (2%)
Query: 72 IQTHIDELDRVTGGGFVRGSVILVGGDPGIGKSTLLMQTAASLAYKK 118
+ T +LD++T G +I++ P +GK+ + A + A K+
Sbjct: 178 VPTGFTDLDKLTSG-LQPSDLIILAARPSMGKTAFALNIAENAAIKE 223
>gnl|CDD|162659 TIGR02012, tigrfam_recA, protein RecA. This model describes
orthologs of the recA protein. RecA promotes
hybridization of homolgous regions of DNA. A segment of
ssDNA can be hybridized to another ssDNA region, or to a
dsDNA region. ATP is hydrolyzed in the process. Part of
the SOS respones, it is regulated by LexA via
autocatalytic cleavage.
Length = 321
Score = 35.8 bits (83), Expect = 0.026
Identities = 38/155 (24%), Positives = 67/155 (43%), Gaps = 14/155 (9%)
Query: 57 SLFMLSEESIEEESRIQTHIDELDRVTG-GGFVRGSVILVGGDPGIGKSTLLMQTAASLA 115
S+ L E+S+ + I T LD G GG RG +I + G GK+TL + A
Sbjct: 21 SIMRLGEKSVMDVETISTGSLSLDLALGVGGLPRGRIIEIYGPESSGKTTLALHAIAEAQ 80
Query: 116 YKKHRITYVSGEEAIGQIRLRAQRLNTINSSVYIAIETNVE---DIIATLITNEKPDLVI 172
++ E A+ + R ++ N + ++ E +I TL+ + D+++
Sbjct: 81 KAGGTAAFIDAEHALDPVYARKLGVDIDN--LLVSQPDTGEQALEIAETLVRSGAVDIIV 138
Query: 173 IDSIQTLWSQT------AESSPGTVIQVRTSVQAM 201
+DS+ L + +S G +Q R QA+
Sbjct: 139 VDSVAALVPKAEIEGEMGDSHVG--LQARLMSQAL 171
>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 = 35.2 bits (81), Expect = 0.037
Identities = 23/88 (26%), Positives = 39/88 (44%), Gaps = 3/88 (3%)
Query: 351 IKFGNHDVHLNIAG--GYRISEPAADVAVAAALISSILSIPLPSDFVYFGEVSLSGSVRA 408
KF HD HL++ S A+ +A AL S++L P+ V G +++ G +
Sbjct: 558 AKFSEHDYHLHVVDLHNTGPSTEAS-LAALIALCSALLKRPVQEQMVILGSMTIGGVINP 616
Query: 409 VGHMQQRLKEAEKIGFLSGVFPESAKGE 436
V + L+ A G + P S+ +
Sbjct: 617 VQDLAGSLQLAMDSGAKRVLIPMSSARD 644
>gnl|CDD|181451 PRK08506, PRK08506, replicative DNA helicase; Provisional.
Length = 472
Score = 35.0 bits (81), Expect = 0.043
Identities = 22/97 (22%), Positives = 43/97 (44%), Gaps = 7/97 (7%)
Query: 47 SKTIKQGHSI--SLFMLSEESIEEESRIQTHID----ELDRVTGGGFVRGSVILVGGDPG 100
S+ K + S ++ ++ +D EL+++T G F +G +I++ P
Sbjct: 144 SEDFKDSKEVIESTMEHIKKQKRLGNKDIIGLDTGFVELNKMTKG-FNKGDLIIIAARPS 202
Query: 101 IGKSTLLMQTAASLAYKKHRITYVSGEEAIGQIRLRA 137
+GK+TL + A + + + S E Q+ LR
Sbjct: 203 MGKTTLCLNMALKALNQDKGVAFFSLEMPAEQLMLRM 239
>gnl|CDD|77219 PRK09519, recA, DNA recombination protein RecA; Reviewed.
Length = 790
Score = 34.3 bits (78), Expect = 0.078
Identities = 35/127 (27%), Positives = 57/127 (44%), Gaps = 6/127 (4%)
Query: 57 SLFMLSEESIEEESRIQTHIDELDRVTG-GGFVRGSVILVGGDPGIGKSTLLMQTAASLA 115
S+ L +E+ + S I T LD G GG RG VI + G GK+T+ + A+
Sbjct: 26 SVMRLGDEARQPISVIPTGSIALDVALGIGGLPRGRVIEIYGPESSGKTTVALHAVANAQ 85
Query: 116 YKKHRITYVSGEEAIGQIRLRAQRLNTINSSVYIAIETNVE---DIIATLITNEKPDLVI 172
++ E A+ A++L S+ ++ E +I LI + D+V+
Sbjct: 86 AAGGVAAFIDAEHALDPD--YAKKLGVDTDSLLVSQPDTGEQALEIADMLIRSGALDIVV 143
Query: 173 IDSIQTL 179
IDS+ L
Sbjct: 144 IDSVAAL 150
>gnl|CDD|179826 PRK04328, PRK04328, hypothetical protein; Provisional.
Length = 249
Score = 33.5 bits (77), Expect = 0.11
Identities = 15/39 (38%), Positives = 22/39 (56%)
Query: 71 RIQTHIDELDRVTGGGFVRGSVILVGGDPGIGKSTLLMQ 109
R++T I +D + GG +V+L+ G PG GKS Q
Sbjct: 4 RVKTGIPGMDEILYGGIPERNVVLLSGGPGTGKSIFSQQ 42
>gnl|CDD|183452 PRK12337, PRK12337, 2-phosphoglycerate kinase; Provisional.
Length = 475
Score = 33.6 bits (77), Expect = 0.11
Identities = 19/50 (38%), Positives = 30/50 (60%), Gaps = 6/50 (12%)
Query: 88 VRGSVILVGGDPGIGKSTLLMQTAASLAYKKHRITYVSGEEAIGQIRLRA 137
R +L+GG G+GKS L A++LAY+ IT + +A+ ++ LRA
Sbjct: 253 PRPLHVLIGGVSGVGKSVL----ASALAYRLG-ITRIVSTDAVREV-LRA 296
>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.
Length = 310
Score = 33.2 bits (76), Expect = 0.14
Identities = 33/129 (25%), Positives = 55/129 (42%), Gaps = 26/129 (20%)
Query: 71 RIQTHIDELDRVTGGGFVRGSVILVGGDPGIGKSTLLMQTAASLAYKKHR------ITYV 124
+I T ELD + GGG ++ V G+ G GK+ + Q A ++ + + Y+
Sbjct: 76 KITTGSKELDELLGGGIETQAITEVFGEFGSGKTQICHQLAVNVQLPEEKGGLGGKAVYI 135
Query: 125 SGE-----EAIGQIRLRAQRLN------------TINSSVYIAIETNVEDIIATLITNEK 167
E E I Q+ A+ L+ NS+ + + ED+I L K
Sbjct: 136 DTENTFRPERIMQM-AEARGLDPDEVLKNIYVARAYNSNHQMLLVEKAEDLIKELNNPVK 194
Query: 168 PDLVIIDSI 176
L+I+DS+
Sbjct: 195 --LLIVDSL 201
>gnl|CDD|163589 TIGR03877, thermo_KaiC_1, KaiC domain protein, Ph0284 family.
Members of this family contain a single copy of the KaiC
domain (pfam06745) that occurs in two copies of the
circadian clock protein kinase KaiC itself. Members
occur primarily in thermophilic archaea and in
Thermotoga.
Length = 237
Score = 33.2 bits (76), Expect = 0.15
Identities = 15/39 (38%), Positives = 22/39 (56%)
Query: 71 RIQTHIDELDRVTGGGFVRGSVILVGGDPGIGKSTLLMQ 109
R++T I +D + GG +V+L+ G PG GKS Q
Sbjct: 2 RVKTGIPGMDEILHGGIPERNVVLLSGGPGTGKSIFSQQ 40
>gnl|CDD|129465 TIGR00368, TIGR00368, Mg chelatase-related protein. The N-terminal
end matches very strongly a pfam Mg_chelatase domain.
Length = 499
Score = 32.1 bits (73), Expect = 0.36
Identities = 30/137 (21%), Positives = 55/137 (40%), Gaps = 21/137 (15%)
Query: 306 GTRALLVEIQSLVVPTSLGMPRRTVVGWDSSRLAMILAVLEAR---------CNIKFGNH 356
G A L+ I+ V S G+P T+VG + V E+R F
Sbjct: 8 GVEAPLITIE---VDISKGLPGITIVGLPET------TVKESRERVKSAIKNSGFHFPAK 58
Query: 357 DVHLNIA-GGYRISEPAADVAVAAALI--SSILSIPLPSDFVYFGEVSLSGSVRAVGHMQ 413
+ +N+A D+ +A ++ S L ++++ GE++L G +R + +
Sbjct: 59 RITINLAPADLPKEGGRFDLPIAIGILAASEQLDAKNLGEYLFLGELALDGKLRGIKGVL 118
Query: 414 QRLKEAEKIGFLSGVFP 430
+ A+K G + P
Sbjct: 119 PAIALAQKSGRKFIIVP 135
>gnl|CDD|177377 PHA02542, 41, 41 helicase; Provisional.
Length = 473
Score = 31.6 bits (72), Expect = 0.42
Identities = 20/76 (26%), Positives = 39/76 (51%), Gaps = 4/76 (5%)
Query: 69 ESRIQTHIDELDRVTGGGFVRGSVILVGGDPGIGKSTLLMQTAASLAYKKHRITYVS--- 125
++I ++ L+++T GG R ++ ++ +GKS L AA + + + Y+S
Sbjct: 169 ANKIPFKLEILNKITKGGAERKTLNVLLAGVNVGKSLGLCSLAADYLQQGYNVLYISMEM 228
Query: 126 GEEAIGQIRLRAQRLN 141
EE I + R+ A L+
Sbjct: 229 AEEVIAK-RIDANLLD 243
>gnl|CDD|180232 PRK05748, PRK05748, replicative DNA helicase; Provisional.
Length = 448
Score = 31.5 bits (72), Expect = 0.48
Identities = 14/49 (28%), Positives = 25/49 (51%), Gaps = 1/49 (2%)
Query: 72 IQTHIDELDRVTGGGFVRGSVILVGGDPGIGKSTLLMQTAASLAYKKHR 120
I T +LD++T G +I+V P +GK+ + A ++A K +
Sbjct: 186 IPTGFTDLDKMTSG-LQPNDLIIVAARPSVGKTAFALNIAQNVATKTDK 233
>gnl|CDD|183314 PRK11788, PRK11788, tetratricopeptide repeat protein; Provisional.
Length = 389
Score = 31.3 bits (72), Expect = 0.51
Identities = 13/34 (38%), Positives = 19/34 (55%), Gaps = 4/34 (11%)
Query: 2 VKIRSQYFCQSCG-EIHSR-WIGKCDSCNAWNTI 33
+K + +Y C++CG + W C SC AW TI
Sbjct: 349 LKRKPRYRCRNCGFTARTLYW--HCPSCKAWETI 380
>gnl|CDD|150510 pfam09848, DUF2075, Uncharacterized conserved protein (DUF2075).
This domain, found in various prokaryotic proteins
(including putative ATP/GTP binding proteins), has no
known function.
Length = 348
Score = 31.0 bits (71), Expect = 0.65
Identities = 24/102 (23%), Positives = 40/102 (39%), Gaps = 19/102 (18%)
Query: 91 SVILVGGDPGIGKSTLLMQTAASLAYKKHRIT--YVSGEEAIGQIRLR---AQRLNTINS 145
+V LV G PG GK+ + + A L+ T ++SG + + L A L
Sbjct: 2 AVFLVTGGPGTGKTVVALNLFAELSDSDLGRTAVFLSGNHPLVLV-LYEALAGDLKVRKK 60
Query: 146 SVYIAIETNVEDIIATLITNEKP-----DLVIIDSIQTLWSQ 182
++ + I N D+VI+D LW++
Sbjct: 61 KLFRK--------PTSFINNLHKAPPHEDVVIVDEAHRLWTK 94
>gnl|CDD|183905 PRK13233, nifH, nitrogenase reductase; Reviewed.
Length = 275
Score = 30.9 bits (70), Expect = 0.81
Identities = 14/34 (41%), Positives = 20/34 (58%)
Query: 93 ILVGGDPGIGKSTLLMQTAASLAYKKHRITYVSG 126
I + G GIGKST TAA++AY + ++ G
Sbjct: 5 IAIYGKGGIGKSTTTQNTAAAMAYFHDKKVFIHG 38
>gnl|CDD|180177 PRK05636, PRK05636, replicative DNA helicase; Provisional.
Length = 505
Score = 30.6 bits (69), Expect = 0.91
Identities = 18/49 (36%), Positives = 26/49 (53%), Gaps = 1/49 (2%)
Query: 69 ESRIQTHIDELDRVTGGGFVRGSVILVGGDPGIGKSTLLMQTAASLAYK 117
+ I T +LD +T G G +I+V PG+GKSTL + S + K
Sbjct: 245 ATGIPTGFKDLDDLTNG-LRGGQMIIVAARPGVGKSTLALDFMRSASIK 292
>gnl|CDD|181547 PRK08760, PRK08760, replicative DNA helicase; Provisional.
Length = 476
Score = 30.3 bits (68), Expect = 1.2
Identities = 22/81 (27%), Positives = 36/81 (44%), Gaps = 11/81 (13%)
Query: 72 IQTHIDELDRVTGGGFVRGSVILVGGDPGIGKSTLLMQTAASLAYK-KHRITYVSGEEAI 130
+ T ++ D +T G +I++ P +GK+T + A A K K + S E +
Sbjct: 212 LPTGYNDFDAMTAG-LQPTDLIILAARPAMGKTTFALNIAEYAAIKSKKGVAVFSMEMSA 270
Query: 131 GQIRLR---------AQRLNT 142
Q+ +R AQRL T
Sbjct: 271 SQLAMRLISSNGRINAQRLRT 291
>gnl|CDD|184251 PRK13695, PRK13695, putative NTPase; Provisional.
Length = 174
Score = 30.3 bits (69), Expect = 1.2
Identities = 10/29 (34%), Positives = 20/29 (68%)
Query: 93 ILVGGDPGIGKSTLLMQTAASLAYKKHRI 121
I + G PG+GK+TL+++ A L + +++
Sbjct: 3 IGITGPPGVGKTTLVLKIAELLKEEGYKV 31
>gnl|CDD|117696 pfam09140, MipZ, ATPase MipZ. MipZ is an ATPase that forms a
complex with the chromosome partitioning protein ParB
near the chromosomal origin of replication. It is
responsible for the temporal and spatial regulation of
FtsZ ring formation.
Length = 261
Score = 30.4 bits (69), Expect = 1.2
Identities = 13/31 (41%), Positives = 18/31 (58%), Gaps = 1/31 (3%)
Query: 92 VILVGGDPG-IGKSTLLMQTAASLAYKKHRI 121
VI+VG + G GKST + A +L Y R+
Sbjct: 2 VIVVGNEKGGSGKSTTAVHVAVALLYLGARV 32
>gnl|CDD|139909 PRK13849, PRK13849, putative crown gall tumor protein VirC1;
Provisional.
Length = 231
Score = 30.2 bits (68), Expect = 1.3
Identities = 19/57 (33%), Positives = 28/57 (49%), Gaps = 4/57 (7%)
Query: 100 GIGKSTLLMQTAASLAYKKHRITYVSGEE--AIGQIRLRAQRLNTINSS--VYIAIE 152
G GK+T LM A+LA R+ +E + + + A R NT + + VY A E
Sbjct: 12 GAGKTTALMGLCAALASDGKRVALFEADENRPLTRWKENALRSNTWDPACEVYAADE 68
>gnl|CDD|148602 pfam07088, GvpD, GvpD gas vesicle protein. This family consists of
several archaeal GvpD gas vesicle proteins. GvpD is
thought to be involved in the regulation of gas vesicle
formation.
Length = 484
Score = 29.9 bits (67), Expect = 1.4
Identities = 10/28 (35%), Positives = 18/28 (64%)
Query: 68 EESRIQTHIDELDRVTGGGFVRGSVILV 95
+++ T I +LD++ GG RGSV+ +
Sbjct: 236 DKAEFSTGIGDLDKILSGGTNRGSVVHL 263
>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 = 30.0 bits (68), Expect = 1.4
Identities = 18/69 (26%), Positives = 28/69 (40%), Gaps = 9/69 (13%)
Query: 91 SVILVGGDPGIGKSTLLMQTAASLAYKKHRITYVSG------EEAIGQIRLRAQRLNTIN 144
V+LVG PG GKS L + AA A + YV E+ G+ + + ++
Sbjct: 1 GVLLVG-PPGTGKSELAERLAA--ALSNRPVFYVQLTRDTTEEDLKGRRNIANGTTSWVD 57
Query: 145 SSVYIAIET 153
+ A
Sbjct: 58 GPLVRAARE 66
>gnl|CDD|162286 TIGR01287, nifH, nitrogenase iron protein. This model describes
nitrogenase (EC 1.18.6.1) iron protein, also called
nitrogenase reductase or nitrogenase component II. This
model includes molybdenum-iron nitrogenase reductase
(nifH), vanadium-iron nitrogenase reductase (vnfH), and
iron-iron nitrogenase reductase (anfH). The model
excludes the homologous protein from the
light-independent protochlorophyllide reductase.
Length = 275
Score = 29.7 bits (67), Expect = 1.8
Identities = 13/32 (40%), Positives = 17/32 (53%)
Query: 93 ILVGGDPGIGKSTLLMQTAASLAYKKHRITYV 124
I + G GIGKST AA+LA ++ V
Sbjct: 3 IAIYGKGGIGKSTTTQNIAAALAEMGKKVMIV 34
>gnl|CDD|179154 PRK00885, PRK00885, phosphoribosylamine--glycine ligase;
Provisional.
Length = 420
Score = 29.6 bits (68), Expect = 1.8
Identities = 7/21 (33%), Positives = 16/21 (76%)
Query: 196 TSVQAMIQYAKKNGVAMVLVG 216
T ++A++ +AK+ G+ + +VG
Sbjct: 49 TDIEALVAFAKEEGIDLTVVG 69
>gnl|CDD|162131 TIGR00956, 3a01205, Pleiotropic Drug Resistance (PDR) Family
protein.
Length = 1394
Score = 29.3 bits (66), Expect = 2.0
Identities = 23/72 (31%), Positives = 30/72 (41%), Gaps = 16/72 (22%)
Query: 90 GSVILVGGDPGIGKSTLLMQTAA----SLAYKKHRITY--VSGEEAIGQIRLRAQRLNTI 143
G + +V G PG G STLL A+ + ITY ++ EE R
Sbjct: 87 GELTVVLGRPGSGCSTLLKTIASNTDGFHIGVEGVITYDGITPEEIKKHYR--------- 137
Query: 144 NSSVYIAIETNV 155
VY A ET+V
Sbjct: 138 GDVVYNA-ETDV 148
>gnl|CDD|181894 PRK09480, slmA, division inhibitor protein; Provisional.
Length = 194
Score = 29.0 bits (66), Expect = 2.7
Identities = 11/47 (23%), Positives = 25/47 (53%), Gaps = 1/47 (2%)
Query: 172 IIDSIQTLWSQTAESSPGTVIQVRTSVQAMIQYAKKN-GVAMVLVGH 217
I +S+ + +Q + T+ + R + ++ +A++N G+ VL G
Sbjct: 65 IEESLFSRINQILKDEKDTLARARLILLLLLGFAERNPGMTRVLTGD 111
>gnl|CDD|147840 pfam05907, DUF866, Eukaryotic protein of unknown function
(DUF866). This family consists of a number of
hypothetical eukaryotic proteins of unknown function
with an average length of around 165 residues.
Length = 161
Score = 28.9 bits (65), Expect = 2.9
Identities = 18/66 (27%), Positives = 24/66 (36%), Gaps = 26/66 (39%)
Query: 10 CQSCGEIHSRWIG--------------------KCDSCNAWNTI--IEDSSRK---ESDQ 44
C +CGE+ +WI KC C+ N+I I S E
Sbjct: 33 CSNCGEVSDKWIYITLSETVPLPGGKGTANLVQKCKLCSRENSIDIIPGSGSPYTAEDSG 92
Query: 45 RFSKTI 50
+F KTI
Sbjct: 93 KF-KTI 97
>gnl|CDD|179771 PRK04182, PRK04182, cytidylate kinase; Provisional.
Length = 180
Score = 28.6 bits (65), Expect = 3.2
Identities = 13/35 (37%), Positives = 20/35 (57%), Gaps = 5/35 (14%)
Query: 92 VILVGGDPGIGKSTLLMQTAASLAYKKHRITYVSG 126
+I + G PG GK+T+ A LA +K + +VS
Sbjct: 2 IITISGPPGSGKTTV----ARLLA-EKLGLKHVSA 31
>gnl|CDD|149060 pfam07786, DUF1624, Protein of unknown function (DUF1624). These
sequences are found in hypothetical proteins of unknown
function expressed by bacterial and archaeal species.
The region in question is approximately 230 residues
long.
Length = 222
Score = 28.7 bits (65), Expect = 3.3
Identities = 10/24 (41%), Positives = 14/24 (58%)
Query: 375 VAVAAALISSILSIPLPSDFVYFG 398
+ AA LI++ I P F+YFG
Sbjct: 79 IFAAALLITAATYIVFPDSFIYFG 102
>gnl|CDD|148565 pfam07015, VirC1, VirC1 protein. This family consists of several
bacterial VirC1 proteins. In Agrobacterium tumefaciens,
a cis-active 24-base-pair sequence adjacent to the right
border of the T-DNA, called overdrive, stimulates tumour
formation by increasing the level of T-DNA processing.
It is thought that the virC operon which enhances T-DNA
processing probably does so because the VirC1 protein
interacts with overdrive. It has now been shown that the
virC1 gene product binds to overdrive but not to the
right border of T-DNA.
Length = 231
Score = 28.7 bits (64), Expect = 3.8
Identities = 16/57 (28%), Positives = 26/57 (45%), Gaps = 4/57 (7%)
Query: 100 GIGKSTLLMQTAASLAYKKHRITYVSGEE--AIGQIRLRAQRLNTINS--SVYIAIE 152
G GK+T LM ++LA R+ +E + + R A R T + ++ A E
Sbjct: 12 GAGKTTALMGLCSALASDGKRVALFEADENRPLTKWRENALRKGTWDPACEIFNADE 68
>gnl|CDD|179814 PRK04301, radA, DNA repair and recombination protein RadA;
Validated.
Length = 317
Score = 28.7 bits (65), Expect = 3.9
Identities = 15/41 (36%), Positives = 21/41 (51%)
Query: 71 RIQTHIDELDRVTGGGFVRGSVILVGGDPGIGKSTLLMQTA 111
+I T ELD + GGG S+ G+ G GK+ + Q A
Sbjct: 83 KITTGSKELDELLGGGIETQSITEFYGEFGSGKTQICHQLA 123
>gnl|CDD|163585 TIGR03873, F420-0_ABC_ATP, proposed F420-0 ABC transporter,
ATP-binding protein. This small clade of ABC-type
transporter ATP-binding protein components is found as a
three gene cassette along with a periplasmic
substrate-binding protein (TIGR03868) and a permease
(TIGR03869). The organisms containing this cassette are
all Actinobacteria and all contain numerous genes
requiring the coenzyme F420. This model was defined
based on five such organisms, four of which are lacking
all F420 biosynthetic capability save the final
side-chain polyglutamate attachment step (via the gene
cofE: TIGR01916). In Jonesia denitrificans DSM 20603 and
marine actinobacterium PHSC20C1 this cassette is in an
apparent operon with the cofE gene and, in PHSC20C1,
also with a F420-dependent glucose-6-phosphate
dehydrogenase (TIGR03554). Based on these observations
we propose that this ATP-binding protein is a component
of an F420-0 (that is, F420 lacking only the
polyglutamate tail) transporter.
Length = 256
Score = 28.6 bits (64), Expect = 3.9
Identities = 20/71 (28%), Positives = 31/71 (43%)
Query: 90 GSVILVGGDPGIGKSTLLMQTAASLAYKKHRITYVSGEEAIGQIRLRAQRLNTINSSVYI 149
GS+ + G G GKSTLL A +L + + R RA+R+ +
Sbjct: 27 GSLTGLLGPNGSGKSTLLRLLAGALRPDAGTVDLAGVDLHGLSRRARARRVALVEQDSDT 86
Query: 150 AIETNVEDIIA 160
A+ V D++A
Sbjct: 87 AVPLTVRDVVA 97
>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 = 28.4 bits (64), Expect = 4.2
Identities = 20/86 (23%), Positives = 40/86 (46%), Gaps = 14/86 (16%)
Query: 93 ILVGGDPGIGKSTLLMQTAASLAYKKHRITYVSGEEAIGQIR---LRAQRLNTINSSVYI 149
I++ G P GKST + A L K + + +S +E++G +++ + S+
Sbjct: 2 IILTGLPSSGKSTRAKELAKYLEEKGYDVIVIS-DESLGIESDDYKDSKKEKFLRGSLRS 60
Query: 150 AIETNVEDIIATLITNEKPDLVIIDS 175
A++ ++ K +VI+DS
Sbjct: 61 AVKRDL----------SKNTIVIVDS 76
>gnl|CDD|136670 PRK08181, PRK08181, transposase; Validated.
Length = 269
Score = 28.4 bits (63), Expect = 4.4
Identities = 26/99 (26%), Positives = 47/99 (47%), Gaps = 16/99 (16%)
Query: 89 RGSVILVGGDPGIGKSTLLMQTAASLAYKKHRITYVSGEEAIGQIRLRAQRLNTINSSVY 148
+G+ +L+ G PG GKS L +L R+ + + + ++++ A+R
Sbjct: 105 KGANLLLFGPPGGGKSHLAAAIGLALIENGWRVLFTRTTDLVQKLQV-ARR--------- 154
Query: 149 IAIETNVEDIIATLITNEKPDLVIIDSIQTLWSQTAESS 187
E +E IA L +K DL+I+D + + AE+S
Sbjct: 155 ---ELQLESAIAKL---DKFDLLILDDLAYVTKDQAETS 187
>gnl|CDD|163451 TIGR03739, PRTRC_D, PRTRC system protein D. A novel genetic system
characterized by six major proteins, included a ParB
homolog and a ThiF homolog, is designated PRTRC, or
ParB-Related,ThiF-Related Cassette. It is often found on
plasmids. This protein family is designated PRTRC system
protein D. The gray zone, between trusted and noise,
includes proteins found in the same genomes as other
proteins of the PRTRC systems, but not in the same
contiguous gene region.
Length = 320
Score = 28.2 bits (63), Expect = 4.4
Identities = 14/53 (26%), Positives = 22/53 (41%), Gaps = 6/53 (11%)
Query: 69 ESRIQTHIDELDRVTGGGFVRGSVILVGGDPGIGKSTLLMQTAASLAYKKHRI 121
E+ Q + + G +++LVGG L + A A+ KHRI
Sbjct: 254 ETVAQQAVSTMMTWIGAPESIQNIVLVGG------GAFLFKKAVKAAFPKHRI 300
>gnl|CDD|183453 PRK12338, PRK12338, hypothetical protein; Provisional.
Length = 319
Score = 28.2 bits (63), Expect = 4.8
Identities = 13/26 (50%), Positives = 17/26 (65%)
Query: 92 VILVGGDPGIGKSTLLMQTAASLAYK 117
VIL+G GIGKST+ + A +L K
Sbjct: 6 VILIGSASGIGKSTIASELARTLNIK 31
>gnl|CDD|147929 pfam06032, DUF917, Protein of unknown function (DUF917). This
family consists of hypothetical bacterial and archaeal
proteins of unknown function.
Length = 352
Score = 28.3 bits (64), Expect = 4.8
Identities = 11/35 (31%), Positives = 17/35 (48%)
Query: 75 HIDELDRVTGGGFVRGSVILVGGDPGIGKSTLLMQ 109
I +++R T GGF G V + G + T+ Q
Sbjct: 241 KIVDVERRTRGGFDVGEVTIEGLEYLGRTLTIPFQ 275
>gnl|CDD|128644 smart00350, MCM, minichromosome maintenance proteins.
Length = 509
Score = 28.4 bits (64), Expect = 4.8
Identities = 13/28 (46%), Positives = 17/28 (60%), Gaps = 1/28 (3%)
Query: 81 RVTGGGFVRGSV-ILVGGDPGIGKSTLL 107
+ G +RG + IL+ GDPG KS LL
Sbjct: 226 NLPDGMKIRGDINILLLGDPGTAKSQLL 253
>gnl|CDD|163179 TIGR03185, DNA_S_dndD, DNA sulfur modification protein DndD. This
model describes the DndB protein encoded by an operon
associated with a sulfur-containing modification to DNA.
The operon is sporadically distributed in bacteria, much
like some restriction enzyme operons. DndD is described
as a putative ATPase. The small number of examples known
so far include species from among the Firmicutes,
Actinomycetes, Proteobacteria, and Cyanobacteria.
Length = 650
Score = 28.1 bits (63), Expect = 5.4
Identities = 17/42 (40%), Positives = 23/42 (54%), Gaps = 3/42 (7%)
Query: 92 VILVGGDPGIGKSTLLMQTAASLA-YKKHRITYVSGEEAIGQ 132
+IL+GG G GK+TLL A LA Y K + G ++ Q
Sbjct: 30 IILIGGLNGAGKTTLL--DAIQLALYGKRALCSGRGNKSYEQ 69
>gnl|CDD|184311 PRK13764, PRK13764, ATPase; Provisional.
Length = 602
Score = 27.9 bits (63), Expect = 6.4
Identities = 12/23 (52%), Positives = 14/23 (60%), Gaps = 4/23 (17%)
Query: 93 ILVGGDPGIGKSTLLMQTAASLA 115
IL+ G PG GKST A +LA
Sbjct: 260 ILIAGAPGAGKSTF----AQALA 278
>gnl|CDD|105560 PRK12339, PRK12339, 2-phosphoglycerate kinase; Provisional.
Length = 197
Score = 27.8 bits (62), Expect = 6.6
Identities = 15/61 (24%), Positives = 28/61 (45%), Gaps = 4/61 (6%)
Query: 92 VILVGGDPGIGKSTLLMQTAASLAYKKHRITYVSGEEAIGQIRLRAQRLNTINSSVYIAI 151
+ +GG PG+GK+++ + +A + +SG+ +R + SVY A
Sbjct: 5 IHFIGGIPGVGKTSI----SGYIARHRAIDIVLSGDYLREFLRPYVDDEPVLAKSVYDAW 60
Query: 152 E 152
E
Sbjct: 61 E 61
>gnl|CDD|162807 TIGR02323, CP_lyasePhnK, phosphonate C-P lyase system protein PhnK.
Members of this family are the PhnK protein of C-P
lyase systems for utilization of phosphonates. These
systems resemble phosphonatase-based systems in having a
three component ABC transporter, where TIGR01097 is the
permease, TIGR01098 is the phosphonates binding protein,
and TIGR02315 is the ATP-binding cassette (ABC) protein.
They differ, however, in having, typically, ten or more
additional genes, many of which are believed to form a
membrane-associated complex. This protein (PhnK) and the
adjacent-encoded PhnL resemble transporter ATP-binding
proteins but are suggested, based on mutatgenesis
studies, to be part of this complex rather than part of
a transporter per se.
Length = 253
Score = 27.5 bits (61), Expect = 7.1
Identities = 15/36 (41%), Positives = 19/36 (52%)
Query: 90 GSVILVGGDPGIGKSTLLMQTAASLAYKKHRITYVS 125
G V+ + G+ G GKSTLL A LA TY+
Sbjct: 29 GEVLGIVGESGSGKSTLLGCLAGRLAPDHGTATYIM 64
>gnl|CDD|184129 PRK13543, PRK13543, cytochrome c biogenesis protein CcmA;
Provisional.
Length = 214
Score = 27.5 bits (61), Expect = 8.2
Identities = 11/18 (61%), Positives = 13/18 (72%)
Query: 90 GSVILVGGDPGIGKSTLL 107
G +LV GD G GK+TLL
Sbjct: 37 GEALLVQGDNGAGKTTLL 54
>gnl|CDD|181676 PRK09165, PRK09165, replicative DNA helicase; Provisional.
Length = 497
Score = 27.5 bits (62), Expect = 8.3
Identities = 15/47 (31%), Positives = 25/47 (53%), Gaps = 5/47 (10%)
Query: 70 SRIQTHIDELDRVTGGGFVRGSVILVGGDPGIGKSTLLMQTAASLAY 116
S I T + +LD GG +I++ G P +GK+ L A ++A+
Sbjct: 198 SGISTGLRDLDSKLGG-LHPSDLIILAGRPSMGKTAL----ATNIAF 239
>gnl|CDD|150847 pfam10236, DAP3, Mitochondrial ribosomal death-associated protein
3. This is a family of conserved proteins which were
originally described as death-associated-protein-3
(DAP-3). The proteins carry a P-loop DNA-binding motif,
and induce apoptosis. DAP3 has been shown to be a
pro-apoptotic factor in the mitochondrial matrix and to
be crucial for mitochondrial biogenesis and so has also
been designated as MRP-S29 (mitochondrial ribosomal
protein subunit 29).
Length = 274
Score = 27.2 bits (61), Expect = 8.7
Identities = 9/20 (45%), Positives = 12/20 (60%)
Query: 93 ILVGGDPGIGKSTLLMQTAA 112
++ G+ G GKS LL Q A
Sbjct: 26 FVLTGERGSGKSVLLAQAMA 45
>gnl|CDD|180157 PRK05595, PRK05595, replicative DNA helicase; Provisional.
Length = 444
Score = 27.1 bits (60), Expect = 9.5
Identities = 14/34 (41%), Positives = 20/34 (58%), Gaps = 1/34 (2%)
Query: 78 ELDRVTGGGFVRGSVILVGGDPGIGKSTLLMQTA 111
ELD T G F +G +IL+ P +GK+T + A
Sbjct: 190 ELDAKTSG-FQKGDMILIAARPSMGKTTFALNIA 222
>gnl|CDD|180538 PRK06349, PRK06349, homoserine dehydrogenase; Provisional.
Length = 426
Score = 27.4 bits (62), Expect = 9.5
Identities = 8/30 (26%), Positives = 16/30 (53%), Gaps = 1/30 (3%)
Query: 197 SVQAMIQYAKKNGVA-MVLVGHVTKEGQIA 225
S+++++Q A +V+V H T E +
Sbjct: 375 SIESILQKGAGGEGAEIVIVTHETSEAALR 404
>gnl|CDD|178352 PLN02751, PLN02751, glutamyl-tRNA(Gln) amidotransferase.
Length = 544
Score = 27.1 bits (60), Expect = 9.7
Identities = 10/16 (62%), Positives = 11/16 (68%)
Query: 223 QIAGPRVIEHMVDAVL 238
QI+ P IE MVD VL
Sbjct: 480 QISDPAEIEAMVDKVL 495
>gnl|CDD|148176 pfam06414, Zeta_toxin, Zeta toxin. This family consists of several
bacterial zeta toxin proteins. Zeta toxin is thought to
be part of a postregulational killing system in
bacteria. It relies on antitoxin/toxin systems that
secure stable inheritance of low and medium copy number
plasmids during cell division and kill cells that have
lost the plasmid.
Length = 191
Score = 27.2 bits (61), Expect = 10.0
Identities = 9/25 (36%), Positives = 12/25 (48%)
Query: 92 VILVGGDPGIGKSTLLMQTAASLAY 116
+L+GG PG GK+ L L
Sbjct: 14 AVLLGGQPGAGKTELARALLEELGG 38
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 0.133 0.378
Gapped
Lambda K H
0.267 0.0669 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 7,575,960
Number of extensions: 495210
Number of successful extensions: 1478
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1458
Number of HSP's successfully gapped: 96
Length of query: 479
Length of database: 5,994,473
Length adjustment: 97
Effective length of query: 382
Effective length of database: 3,898,497
Effective search space: 1489225854
Effective search space used: 1489225854
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: 59 (26.6 bits)