RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780334|ref|YP_003064747.1| DNA repair protein RadA
[Candidatus Liberibacter asiaticus str. psy62]
(479 letters)
>gnl|CDD|31265 COG1066, Sms, Predicted ATP-dependent serine protease
[Posttranslational modification, protein turnover,
chaperones].
Length = 456
Score = 586 bits (1511), Expect = e-168
Identities = 237/460 (51%), Positives = 320/460 (69%), Gaps = 10/460 (2%)
Query: 1 MVKIRSQYFCQSCGEIHSRWIGKCDSCNAWNTIIED---SSRKESDQRFSKTIKQGHSIS 57
M K ++ + CQ CG + +W+GKC +C AWNT++E+ +S + +
Sbjct: 1 MAKKKTAFVCQECGYVSPKWLGKCPACGAWNTLVEEVLAASPGGAPNKRRSGKAGSEPSK 60
Query: 58 LFMLSEESIEEESRIQTHIDELDRVTGGGFVRGSVILVGGDPGIGKSTLLMQTAASLAYK 117
+ LS+ +EEE RI T I+ELDRV GGG V GSVIL+GGDPGIGKSTLL+Q AA LA K
Sbjct: 61 VLKLSDIELEEEPRISTGIEELDRVLGGGLVPGSVILIGGDPGIGKSTLLLQVAARLA-K 119
Query: 118 KHRITYVSGEEAIGQIRLRAQRLNTINSSVYIAIETNVEDIIATLITNEKPDLVIIDSIQ 177
+ ++ YVSGEE++ QI+LRA RL +++Y+ ETN+EDIIA + EKPDLV+IDSIQ
Sbjct: 120 RGKVLYVSGEESLQQIKLRADRLGLPTNNLYLLAETNLEDIIAE-LEQEKPDLVVIDSIQ 178
Query: 178 TLWSQTAESSPGTVIQVRTSVQAMIQYAKKNGVAMVLVGHVTKEGQIAGPRVIEHMVDAV 237
TL+S+ S+PG+V QVR +++ AK +A+ +VGHVTKEG IAGPRV+EHMVD V
Sbjct: 179 TLYSEEITSAPGSVSQVREVAAELMRLAKTKNIAIFIVGHVTKEGAIAGPRVLEHMVDTV 238
Query: 238 LYFEGGTRNTQYDYRILRSVKNRFGPTDEIGVFEMSDKGLQEVSDPSKIFLSDRDSTSPG 297
LYFEG + YRILRSVKNRFG T+E+GVFEM++ GL+EVS+PS +FLS+R +PG
Sbjct: 239 LYFEG---DRHSRYRILRSVKNRFGATNELGVFEMTENGLREVSNPSALFLSERGEQTPG 295
Query: 298 TAVFAGIEGTRALLVEIQSLVVPTSLGMPRRTVVGWDSSRLAMILAVLEARCNIKFGNHD 357
+AV +EGTR LLVEIQ+LV P+S G PRR VG D +RLAM+LAVLE R + G+ D
Sbjct: 296 SAVVVVMEGTRPLLVEIQALVSPSSFGNPRRVAVGLDQNRLAMLLAVLEKRLGLPLGDQD 355
Query: 358 VHLNIAGGYRISEPAADVAVAAALISSILSIPLPSDFVYFGEVSLSGSVRAVGHMQQRLK 417
V++N+AGG +++EPAAD+AVA AL+SS + PLP D V FGEV LSG +R V ++RLK
Sbjct: 356 VYVNVAGGVKVTEPAADLAVALALVSSFRNRPLPQDTVVFGEVGLSGEIRPVPRGERRLK 415
Query: 418 EAEKIGFLSGVFPESAKGECKIGMLDRQYIKNLSDLVKKI 457
EA K+GF + P+ + + L++ ++ +
Sbjct: 416 EAAKLGFKRAIVPKGNIP--LPEGIKVIGVSTLAEALEVV 453
>gnl|CDD|29987 cd01121, Sms, Sms (bacterial radA) DNA repair protein. This protein
is not related to archael radA any more than is to other
RecA-like NTPases. Sms has a role in recombination and
recombinational repair and is responsible for the
stabilization or processing of branched DNA molecules..
Length = 372
Score = 488 bits (1259), Expect = e-138
Identities = 203/377 (53%), Positives = 270/377 (71%), Gaps = 5/377 (1%)
Query: 8 YFCQSCGEIHSRWIGKCDSCNAWNTIIEDSSRKESDQRFSKTIKQGHSISLFMLSEESIE 67
Y C CG + +W+GKC C WNT++E+ S ++ S + LS+ E
Sbjct: 1 YVCSECGYVSPKWLGKCPECGEWNTLVEEIEPSSSSGSGGRSSGGSAS-KVIPLSDIEAE 59
Query: 68 EESRIQTHIDELDRVTGGGFVRGSVILVGGDPGIGKSTLLMQTAASLAYKKHRITYVSGE 127
EE RI T I+ELDRV GGG V GSVIL+GGDPGIGKSTLL+Q AA LA + ++ YVSGE
Sbjct: 60 EEERIPTGIEELDRVLGGGLVPGSVILIGGDPGIGKSTLLLQVAARLAKRGGKVLYVSGE 119
Query: 128 EAIGQIRLRAQRLNTINSSVYIAIETNVEDIIATLITNEKPDLVIIDSIQTLWSQTAESS 187
E+ QI+LRA RL ++Y+ ETN+EDI+A+ I KPDLVIIDSIQT++S S+
Sbjct: 120 ESPEQIKLRADRLGISTENLYLLAETNLEDILAS-IEELKPDLVIIDSIQTVYSSELTSA 178
Query: 188 PGTVIQVRTSVQAMIQYAKKNGVAMVLVGHVTKEGQIAGPRVIEHMVDAVLYFEGGTRNT 247
PG+V QVR ++++AK+ + + +VGHVTKEG IAGP+V+EHMVD VLYFEG +
Sbjct: 179 PGSVSQVRECTAELMRFAKERNIPIFIVGHVTKEGSIAGPKVLEHMVDTVLYFEGDRHS- 237
Query: 248 QYDYRILRSVKNRFGPTDEIGVFEMSDKGLQEVSDPSKIFLSDRDSTSPGTAVFAGIEGT 307
+YRILRSVKNRFG T+E+GVFEM + GL+EVS+PS++FLS+R+ PG+AV +EG+
Sbjct: 238 --EYRILRSVKNRFGSTNELGVFEMRENGLREVSNPSELFLSEREEDVPGSAVTVVMEGS 295
Query: 308 RALLVEIQSLVVPTSLGMPRRTVVGWDSSRLAMILAVLEARCNIKFGNHDVHLNIAGGYR 367
R LLVE+Q+LV PTS PRR VG+D +RL+M+LAVLE R + + DV +N+AGG +
Sbjct: 296 RPLLVEVQALVSPTSYANPRRVAVGFDPNRLSMLLAVLEKRLGLPLADQDVFVNVAGGLK 355
Query: 368 ISEPAADVAVAAALISS 384
I+EPAAD+AVA A++SS
Sbjct: 356 ITEPAADLAVALAIVSS 372
>gnl|CDD|29986 cd01120, RecA-like_NTPases, RecA-like NTPases. This family includes
the NTP binding domain of F1 and V1 H+ATPases, DnaB and
related helicases as well as bacterial RecA and related
eukaryotic and archaeal recombinases. This group also
includes bacterial conjugation proteins and related DNA
transfer proteins involved in type II and type IV
secretion..
Length = 165
Score = 73.6 bits (180), Expect = 1e-13
Identities = 39/165 (23%), Positives = 69/165 (41%), Gaps = 14/165 (8%)
Query: 92 VILVGGDPGIGKSTLLMQTAASLAYKKHRITYVSGEEAIGQIRLRAQRLNT--INSSVYI 149
+ILV G G GK+TL +Q A ++A K ++ YV EE I ++ R + ++ I
Sbjct: 1 LILVFGPTGSGKTTLALQLALNIATKGGKVVYVDIEEEIEELTERLIGESLKGALDNLII 60
Query: 150 AIETNVEDIIAT-------LITNEKPDLVIIDSIQTLWSQTAESSPGTVIQVRTSVQAMI 202
T + A L DL+I+D + L E G ++ ++ ++
Sbjct: 61 VFATADDPAAARLLSKAERLRERGGDDLIILDELTRLVRALREIREGYPGELDEELRELL 120
Query: 203 QYAKKNGVAMVLVGHV-----TKEGQIAGPRVIEHMVDAVLYFEG 242
+ A+K GV ++ V G + +E + D V+
Sbjct: 121 ERARKGGVTVIFTLQVPSGDKGDPRLTRGAQNLEDIADTVIVLSR 165
>gnl|CDD|30816 COG0468, RecA, RecA/RadA recombinase [DNA replication,
recombination, and repair].
Length = 279
Score = 69.2 bits (169), Expect = 3e-12
Identities = 51/250 (20%), Positives = 95/250 (38%), Gaps = 22/250 (8%)
Query: 53 GHSISLFMLSEESIEEESRIQTHIDELDRVTGGGFVRGSVILVGGDPGIGKSTLLMQTAA 112
SI + + +E E+ I T LD GGG RG + + G GK+TL +Q A
Sbjct: 24 KGSI-MALGGDERREDIEAISTGSLALDEALGGGLPRGRITEIYGPESSGKTTLALQLVA 82
Query: 113 SLAYKKHRITYVSGEEAIGQIRLRAQRLNTINSSVYIAIETNVED---IIATLITN--EK 167
+ + ++ E A+ R + ++ + ++ ++ E I L + EK
Sbjct: 83 NAQKPGGKAAFIDTEHALDPERAKQLGVDLL-DNLLVSQPDTGEQQLEIAEKLARSGAEK 141
Query: 168 PDLVIIDSIQTLWSQTAESSPGTVI--QVRTSVQA--MIQYAKKNGVAMVLVGHV-TKEG 222
DL+++DS+ L + E G + S + + A K A++ V K G
Sbjct: 142 IDLLVVDSVAALV-RAEEIEDGHLGLRARLLSKALRKLTRLANKYNTAVIFTNQVRAKIG 200
Query: 223 -------QIAGPRVIEHMVDAVLYFEGGTRNTQY--DYRILRSVKNRFGPTDEIGVFEMS 273
G ++ L + + R ++ VKN+ P + F+++
Sbjct: 201 VMFGDPETTTGGNALKFYASVRLDLRRIESLKEDVGNKRRVKVVKNKVAPPFKEAEFDIT 260
Query: 274 DKGLQEVSDP 283
G +
Sbjct: 261 YGGGIDREGE 270
>gnl|CDD|30815 COG0467, RAD55, RecA-superfamily ATPases implicated in signal
transduction [Signal transduction mechanisms].
Length = 260
Score = 69.0 bits (168), Expect = 3e-12
Identities = 62/249 (24%), Positives = 98/249 (39%), Gaps = 31/249 (12%)
Query: 70 SRIQTHIDELDRVTGGGFVRGSVILVGGDPGIGKSTLLMQTAASLAYKKHRITYVSGEE- 128
RI T I LD + GGG RGSV+L+ G PG GK+ +Q A + + YVS EE
Sbjct: 3 ERIPTGIPGLDEILGGGLPRGSVVLITGPPGTGKTIFALQFLYEGAREGEPVLYVSTEES 62
Query: 129 -------------------AIGQIRLRAQRLNTINSSVYIAIETN----VEDIIATLITN 165
G++ + L+ + + + D I ++
Sbjct: 63 PEELLENARSFGWDLEVYIEKGKLAILDAFLSEKGLVSIVVGDPLDLEELLDRIREIVEK 122
Query: 166 EKPDLVIIDSIQTLWSQTAESSPGTVIQVRTSVQAMIQYAKKNGVAMVLVGHVTKEGQIA 225
E D V+IDSI L + VR + + ++ KK GV +L +
Sbjct: 123 EGADRVVIDSITELTLYLNDP-----ALVRRILLLLKRFLKKLGVTSLLT-TEAPVEERG 176
Query: 226 GPRVIEHMVDAVLYFEGGTRNTQYDYRILRSVKNR-FGPTDEIGVFEMSDKGLQEVSDPS 284
V E++VD V+ + D R LR +K R + ++ FE++D V
Sbjct: 177 ESGVEEYIVDGVIRLDLKEIEGGGDRRYLRILKMRGTPHSLKVIPFEITDGEGIVVYPEG 236
Query: 285 KIFLSDRDS 293
+I L +
Sbjct: 237 RIRLEEERV 245
>gnl|CDD|30003 cd01393, recA_like, RecA is a bacterial enzyme which has roles in
homologous recombination, DNA repair, and the induction
of the SOS response. RecA couples ATP hydrolysis to DNA
strand exchange. While prokaryotes have a single RecA
protein, eukaryotes have multiple RecA homologs such as
Rad51, DMC1 and Rad55/57. Archaea have the RecA-like
homologs radA and radB..
Length = 226
Score = 59.8 bits (145), Expect = 1e-09
Identities = 50/227 (22%), Positives = 87/227 (38%), Gaps = 34/227 (14%)
Query: 72 IQTHIDELDRVTGGGFVRGSVILVGGDPGIGKSTLLMQTAASLAYKKH------RITYVS 125
I T LD + GGG G + + G+ G GK+ L +Q A ++ Y+
Sbjct: 1 ISTGSKALDELLGGGIPTGRITEIFGEFGSGKTQLCLQLAVEAQLPGELGGLEGKVVYID 60
Query: 126 GEEAIGQIRLRA------QRLNTINSSVYIAIETNVE------DIIATLITNEKPDLVII 173
E A RL + ++Y+A N E + + ++++ + DLV++
Sbjct: 61 TEGAFRPERLVQLAVRFGLDPEEVLDNIYVARPYNGEQQLEIVEELERIMSSGRVDLVVV 120
Query: 174 DSIQTLWSQTAESSPGTVIQVRTS-----VQAMIQYAKKNGVAMVLVGHVT--------K 220
DS+ L+ + E ++ R ++ +++ A K VA+V V
Sbjct: 121 DSVAALFRK--EFIGRGMLAERARLLSQALRKLLRLADKFNVAVVFTNQVRAKVDVMFGD 178
Query: 221 EGQIAGPRVIEHMVDAVLYFEGGTRNTQYDYRILRSVKNRFGPTDEI 267
AG + H L G R + RI + VK+ P E
Sbjct: 179 PETPAGGNALAHASTTRLDLRKG-RGIIGERRIAKVVKSPALPEAEA 224
>gnl|CDD|30004 cd01394, radB, RadB. The archaeal protein radB shares similarity
radA, the archaeal functional homologue to the bacterial
RecA. The precise function of radB is unclear..
Length = 218
Score = 58.0 bits (140), Expect = 5e-09
Identities = 58/219 (26%), Positives = 93/219 (42%), Gaps = 27/219 (12%)
Query: 79 LDRVTGGGFVRGSVILVGGDPGIGKSTLLMQTAASLAYKKHRITYVSGE----EAIGQI- 133
LD + GGG RG+V V G PG GK+ + +Q A A + ++ Y+ E E QI
Sbjct: 8 LDELLGGGVERGTVTQVYGPPGTGKTNIAIQLAVETAGQGKKVAYIDTEGLSSERFRQIA 67
Query: 134 RLRAQRL--NTINSSVYIAIETNVEDIIATLITNEKPDLVIIDSIQTLWSQTAESSPGTV 191
R +R + I E +EK DLV++DS L+ T+
Sbjct: 68 GDRPERAASSIIVFEPMDFNEQGRAIQETETFADEKVDLVVVDSATALYRLELGDDDTTI 127
Query: 192 ---IQVRTSVQAMIQYAKKNGVAMVLVGHVTKEGQ------IAGPRVIEHMVDAVLYFE- 241
++ + ++ A+K+ VA+V+ V + + G +EH +L E
Sbjct: 128 KNYRELAKQLTFLLWLARKHDVAVVITNQVYSDVGSGSVRPLGGH-TLEHWSKVILRLEK 186
Query: 242 --GGTRNTQYDYRILRSVKNRFGPTDEIGVFEMSDKGLQ 278
GTR +L K+RF P F ++DKG++
Sbjct: 187 LRVGTR-----RAVLE--KHRFRPEGSSVYFRITDKGIE 218
>gnl|CDD|29989 cd01123, Rad51_DMC1_radA, Rad51_DMC1_radA,B. This group of
recombinases includes the eukaryotic proteins RAD51,
RAD55/57 and the meiosis-specific protein DMC1, and the
archaeal proteins radA and radB. They are closely
related to the bacterial RecA group. Rad51 proteins
catalyze a similiar recombination reaction as RecA,
using ATP-dependent DNA binding activity and a
DNA-dependent ATPase. However, this reaction is less
efficient and requires accessory proteins such as
RAD55/57 ..
Length = 235
Score = 56.0 bits (135), Expect = 2e-08
Identities = 54/241 (22%), Positives = 92/241 (38%), Gaps = 42/241 (17%)
Query: 72 IQTHIDELDRVTGGGFVRGSVILVGGDPGIGKSTLLMQTAASLAYKKH------RITYVS 125
+ T LD + GGG GS+ + G+ G GK+ L Q A ++ + Y+
Sbjct: 1 LTTGSKALDELLGGGIETGSITEIFGEFGSGKTQLCHQLAVTVQLPIELGGLEGKAVYID 60
Query: 126 GEEAIGQIRLRA------QRLNTINSSVYIAIETNVEDII-------ATLITNEKPDLVI 172
E RL + ++Y+A N + + A LI + + LVI
Sbjct: 61 TEGTFRPERLVQIAERFGLDPEEVLDNIYVARAYNSDHQLQLLEELEAILIESSRIKLVI 120
Query: 173 IDSIQTLWSQTAESSPGTVIQVRTS-----VQAMIQYAKKNGVAMVLVGHVT-------- 219
+DS+ L+ AE + R ++ + + A + VA+V+ VT
Sbjct: 121 VDSVTALFR--AEFDGRGELAERQQHLAKLLRTLKRLADEFNVAVVITNQVTARPDGAAM 178
Query: 220 ---KEGQIAGPRVIEHMVDAVLYFEGGTRNTQYDYRILRSVKNRFGPTDEIGVFEMSDKG 276
+ AG + H LY G RI + V + P E VF ++++G
Sbjct: 179 FGGDPKKPAGGNIWAHASTTRLYLRKGRGEE----RIAKIVDSPHLPEGEA-VFAITEEG 233
Query: 277 L 277
+
Sbjct: 234 I 234
>gnl|CDD|29990 cd01124, KaiC, KaiC is a circadian clock protein primarily found in
cyanobacteria KaiC is a RecA-like ATPase, having both
Walker A and Walker B motifs. A related protein is found
in archaea..
Length = 187
Score = 54.9 bits (132), Expect = 5e-08
Identities = 43/197 (21%), Positives = 71/197 (36%), Gaps = 34/197 (17%)
Query: 92 VILVGGDPGIGKSTLLMQTAASLAYKKHRITYVSGEEAIGQIRLRAQRL----------- 140
L+ G PG GK+T +Q + + YV+ EE+ ++ A+ L
Sbjct: 1 STLLSGGPGTGKTTFALQFLYAGLARGEPGLYVTLEESPEELIENAESLGWDLERLEDEG 60
Query: 141 -------NTINSSVYIA-IETNVEDIIATLITNEKPDLVIIDSIQTLWSQTAESSPGTVI 192
+ + + + + I K V+IDS+ L
Sbjct: 61 LLAIVDADPDEIGPAESSLRLELIQRLKDAIEEFKAKRVVIDSVSGLLLMEQS------- 113
Query: 193 QVRTSVQAMIQYAKKNGV-AMVLVGHVTKEGQIAGPRVIEHMVDAVL---YFEGGTRNTQ 248
R ++ ++ K+ GV ++ EG G +E++VD V+ E G R
Sbjct: 114 TARLEIRRLLFALKRFGVTTLLTSEQSGLEGTGFGGGDVEYLVDGVIRLRLDEEGGRLR- 172
Query: 249 YDYRILRSVKNRFGPTD 265
R L VK R GP D
Sbjct: 173 ---RSLSVVKMRGGPHD 186
>gnl|CDD|31266 COG1067, LonB, Predicted ATP-dependent protease [Posttranslational
modification, protein turnover, chaperones].
Length = 647
Score = 48.8 bits (116), Expect = 3e-06
Identities = 20/82 (24%), Positives = 35/82 (42%), Gaps = 11/82 (13%)
Query: 336 SRLAMILAVLEARCNIKFGNHDVHLNIAGGYRISE-------PAADVAVAAALISSILSI 388
++ MI + N+D+H+ + + +A +A A ALIS++ I
Sbjct: 477 NKGMMIKQA----FLMSILNYDIHIPFSASLVFEQSYGEVDGDSASLAEACALISALSKI 532
Query: 389 PLPSDFVYFGEVSLSGSVRAVG 410
P+ D G + G V+ VG
Sbjct: 533 PVDQDIAITGSIDQFGEVQPVG 554
>gnl|CDD|32701 COG2874, FlaH, Predicted ATPases involved in biogenesis of archaeal
flagella [Cell motility and secretion / Intracellular
trafficking and secretion].
Length = 235
Score = 47.5 bits (113), Expect = 7e-06
Identities = 41/128 (32%), Positives = 61/128 (47%), Gaps = 18/128 (14%)
Query: 67 EEESRIQTHIDELDRVTGGGFVRGSVILVGGDPGIGKSTLLMQTAASLAYKKHRITYVSG 126
E + I++ DELD+ GGG GS+IL+ GD G GKS L + A +R+TYVS
Sbjct: 5 ELKKIIKSGNDELDKRLGGGIPVGSLILIEGDNGTGKSVLSQRFAYGFLMNGYRVTYVST 64
Query: 127 E----EAIGQIR-LRAQRLNTINSSVYIAIETNVE-------------DIIATLITNEKP 168
E E I Q+ L + + S + N+E D++ I +
Sbjct: 65 ELTVREFIKQMESLSYDVSDFLLSGRLLFFPVNLEPVNWGRRSARKLLDLLLEFIKRWEK 124
Query: 169 DLVIIDSI 176
D++IIDS+
Sbjct: 125 DVIIIDSL 132
>gnl|CDD|37215 KOG2004, KOG2004, KOG2004, Mitochondrial ATP-dependent protease
PIM1/LON [Posttranslational modification, protein
turnover, chaperones].
Length = 906
Score = 46.5 bits (110), Expect = 2e-05
Identities = 50/178 (28%), Positives = 81/178 (45%), Gaps = 19/178 (10%)
Query: 270 FEMSDKGLQEVSDPSKIFLSDR--DSTSPGTAVFAGIE--GTRALLVEIQSLVVPTSLGM 325
E+ + LQ++ P +F S+R + T PG + G L VE SL+ G
Sbjct: 692 IEIDESNLQDILGP-PVFTSERMYEVTPPGVVMGLAWTAMGGSTLYVE-TSLMRGLGDGS 749
Query: 326 PRRT----VVGWDSSRLAMILAVLEARCNIK------FGNHDVHLNI-AGGYRISEPAAD 374
T V +S+++A A + K N D+HL++ G P+A
Sbjct: 750 LEITGQLGDVMKESAQIA--YTWARAFLSKKEPENKFLENSDIHLHVPEGATPKDGPSAG 807
Query: 375 VAVAAALISSILSIPLPSDFVYFGEVSLSGSVRAVGHMQQRLKEAEKIGFLSGVFPES 432
V + AL+S L P+ D GEV+L+G V VG ++++ A + G + +FPE+
Sbjct: 808 VTMVTALLSLALGKPVRQDLAMTGEVTLTGKVLPVGGIKEKTIAARRSGVKTIIFPEA 865
Score = 28.8 bits (64), Expect = 3.8
Identities = 15/49 (30%), Positives = 27/49 (55%), Gaps = 1/49 (2%)
Query: 86 GFVRGSVILVGGDPGIGKSTLLMQTAASLAYKKHRITYVSGEEAIGQIR 134
G V+G ++ G PG+GK+++ A +L K R + V G + +I+
Sbjct: 434 GSVQGKILCFVGPPGVGKTSIAKSIARALNRKFFRFS-VGGMTDVAEIK 481
>gnl|CDD|30653 COG0305, DnaB, Replicative DNA helicase [DNA replication,
recombination, and repair].
Length = 435
Score = 46.0 bits (109), Expect = 2e-05
Identities = 30/150 (20%), Positives = 67/150 (44%), Gaps = 20/150 (13%)
Query: 72 IQTHIDELDRVTGGGFVRGSVILVGGDPGIGKSTLLMQTAASLAYKKHR-ITYVSGEEAI 130
+ T +LD +T G F G +I+V PG+GK+ L + A + A + + S E +
Sbjct: 179 VPTGFTDLDEITSG-FRPGDLIIVAARPGMGKTALALNIALNAAADGRKPVAIFSLEMSE 237
Query: 131 GQIRLRAQRLNTINSSVYIAIETNVE-DIIATLITNEKPDLVIIDSIQTL--WSQTAESS 187
Q+ +R ++ E+ +E + T ++ +I + L + +
Sbjct: 238 EQLVMRL-----------LSSESGIESSKLRTGRLSDDEWERLIKAASELSEAPIFIDDT 286
Query: 188 PG-TVIQVRTSVQAMIQYAKKNGVAMVLVG 216
PG T+ ++R+ + + K+ + ++++
Sbjct: 287 PGLTITEIRSKARRL---KLKHNLGLIVID 313
>gnl|CDD|30814 COG0466, Lon, ATP-dependent Lon protease, bacterial type
[Posttranslational modification, protein turnover,
chaperones].
Length = 782
Score = 44.4 bits (105), Expect = 6e-05
Identities = 22/80 (27%), Positives = 45/80 (56%), Gaps = 1/80 (1%)
Query: 353 FGNHDVHLNIAGGYRISE-PAADVAVAAALISSILSIPLPSDFVYFGEVSLSGSVRAVGH 411
F D+H+++ G + P+A + +A AL+S + P+ +D GE++L G V +G
Sbjct: 661 FEKRDIHIHVPEGATPKDGPSAGITMATALVSLLTGKPVRADVAMTGEITLRGRVLPIGG 720
Query: 412 MQQRLKEAEKIGFLSGVFPE 431
++++L A + G + + P+
Sbjct: 721 LKEKLLAAHRGGIKTVIIPK 740
>gnl|CDD|146436 pfam03796, DnaB_C, DnaB-like helicase C terminal domain. The
hexameric helicase DnaB unwinds the DNA duplex at the
Escherichia coli chromosome replication fork. Although
the mechanism by which DnaB both couples ATP hydrolysis
to translocation along DNA and denatures the duplex is
unknown, a change in the quaternary structure of the
protein involving dimerization of the N-terminal domain
has been observed and may occur during the enzymatic
cycle. This C-terminal domain contains an ATP-binding
site and is therefore probably the site of ATP
hydrolysis.
Length = 186
Score = 44.5 bits (106), Expect = 6e-05
Identities = 14/49 (28%), Positives = 28/49 (57%), Gaps = 1/49 (2%)
Query: 72 IQTHIDELDRVTGGGFVRGSVILVGGDPGIGKSTLLMQTAASLAYKKHR 120
+ T +LD++TGG +G +I++ P +GK+ + A + A K+ +
Sbjct: 2 LPTGFTDLDQLTGG-LQKGDLIIIAARPSMGKTAFALNIARNAALKQDK 49
>gnl|CDD|36646 KOG1433, KOG1433, KOG1433, DNA repair protein RAD51/RHP55
[Replication, recombination and repair].
Length = 326
Score = 43.9 bits (103), Expect = 1e-04
Identities = 50/238 (21%), Positives = 91/238 (38%), Gaps = 33/238 (13%)
Query: 72 IQTHIDELDRVTGGGFVRGSVILVGGDPGIGKSTLLMQTAASLAYKKHRITYVSGEEAIG 131
+ T LD++ GGG GS+ + G PG GK+ L A + + ++ Y+ E
Sbjct: 93 LSTGSKALDKLLGGGIETGSLTELVGPPGSGKTQLCHTLAVTCGGGEGKVLYIDTESTFR 152
Query: 132 QIRL------RAQRLNTINSSVYIAIETNVEDIIATLITNE------KPDLVIIDSIQTL 179
RL R S++ +A N++ + + E + L+I+DS L
Sbjct: 153 LERLTEIAGRSGLRGRDTLSNLMLARAYNLDHQLQLIQEAEIMINQSRVKLLIVDSATAL 212
Query: 180 WSQT---AESSPGTVIQVRTSVQAMIQYAKKNGVAMVLVGHVT------------KEGQI 224
+ T + + ++++ + A + GVA+V+ VT + I
Sbjct: 213 YRTTFKGRGELSARQMLLAKFLRSLKKLADEFGVAVVITNQVTAQVDGAIMFGSDPKKPI 272
Query: 225 AGPRVIEHMVDAVLYFEGGTRNTQYDYRILRSVKNRFGPTDEIGVFEMSDKGLQEVSD 282
G H V L G RI + + P E VF +++ G+ + +
Sbjct: 273 GGNI-WAHAVTTRLGLRKGKGER----RICKIADSPCLPEAE-AVFAITEDGISDQRE 324
>gnl|CDD|29988 cd01122, GP4d_helicase, GP4d_helicase is a homohexameric 5'-3'
helicases. Helicases couple NTP hydrolysis to the
unwinding of nucleic acid duplexes into their component
strands..
Length = 271
Score = 43.0 bits (101), Expect = 2e-04
Identities = 47/237 (19%), Positives = 86/237 (36%), Gaps = 57/237 (24%)
Query: 77 DELDRVTGGGFVRGSVILVGGDPGIGKSTLLMQTAASLAYK-KHRITYVSGEEA------ 129
L+++T G +G +I++ G+GK+T L + A L + R+ +S EE
Sbjct: 18 PVLNKLTKG-LRKGELIILTAGTGVGKTTFLREYALDLITQHGVRVGTISLEEPVVRTAR 76
Query: 130 --IGQI---RLRAQRLNTINSS-----------------VYIAIETN----VEDIIATLI 163
+GQ RL I + +Y + V + + +
Sbjct: 77 RLLGQYAGKRLHLPDTVFIYTLEEFDAAFDEFEGTGRLFMYDSFGEYSMDSVLEKVRYMA 136
Query: 164 TNEKPDLVIIDSIQTLWSQTAESSPGTVIQVRTSVQAMIQYAKKNGVAMVLVGHVTKE-- 221
+ +IID++ + S S + + + +A ++G+ + LV H+ +
Sbjct: 137 VSHGIQHIIIDNLSIMVSDERASG-DERKALDEIMTKLRGFATEHGIHITLVSHLRRPDG 195
Query: 222 ------------GQIAGPRVIEHMVDAVLYFEGGTRNTQYDYRI-----LRSVKNRF 261
G I + D V+ E RN Q + LR +KNRF
Sbjct: 196 DKTHEEGGEVSLSDFRGSAAIGQLADNVIALE---RNQQAELDERNTTYLRILKNRF 249
>gnl|CDD|29984 cd00983, recA, RecA is a bacterial enzyme which has roles in
homologous recombination, DNA repair, and the induction
of the SOS response. RecA couples ATP hydrolysis to DNA
strand exchange..
Length = 325
Score = 42.5 bits (100), Expect = 3e-04
Identities = 39/172 (22%), Positives = 77/172 (44%), Gaps = 21/172 (12%)
Query: 40 KESDQRFSKTIKQGHSISLFMLSEESIEEESRIQTHIDELDRVTG-GGFVRGSVILVGGD 98
K+ +++F K S+ L ++++++ I T LD G GG+ +G +I + G
Sbjct: 11 KQIEKKFGKG-------SIMKLGDDAVQDVEVIPTGSLSLDIALGIGGYPKGRIIEIYGP 63
Query: 99 PGIGKSTLLMQTAASLAYKKHRITYVSGEEAIGQIRLRAQRLNTINSSVYIAIETNVE-- 156
GK+TL + A + ++ E A+ + A++L ++ I+ E
Sbjct: 64 ESSGKTTLALHAIAEAQKLGGTVAFIDAEHALD--PVYAKKLGVDLDNLLISQPDTGEQA 121
Query: 157 -DIIATLITNEKPDLVIIDSIQTLWSQT------AESSPGTVIQVRTSVQAM 201
+I +L+ + DL+++DS+ L + +S G Q R QA+
Sbjct: 122 LEIADSLVRSGAVDLIVVDSVAALVPKAEIEGEMGDSHVGL--QARLMSQAL 171
>gnl|CDD|99707 cd00009, AAA, The AAA+ (ATPases Associated with a wide variety of
cellular Activities) superfamily represents an ancient
group of ATPases belonging to the ASCE (for additional
strand, catalytic E) division of the P-loop NTPase fold.
The ASCE division also includes ABC, RecA-like,
VirD4-like, PilT-like, and SF1/2 helicases. Members of
the AAA+ ATPases function as molecular chaperons, ATPase
subunits of proteases, helicases, or nucleic-acid
stimulated ATPases. The AAA+ proteins contain several
distinct features in addition to the conserved
alpha-beta-alpha core domain structure and the Walker A
and B motifs of the P-loop NTPases..
Length = 151
Score = 42.1 bits (99), Expect = 4e-04
Identities = 18/91 (19%), Positives = 34/91 (37%), Gaps = 13/91 (14%)
Query: 89 RGSVILVGGDPGIGKSTLLMQTAASLAYKKHRITYVSGEEAIGQIRLRAQRLNTINSSVY 148
+++L G PG GK+TL A L Y++ + + + +
Sbjct: 19 PKNLLLYG-PPGTGKTTLARAIANELFRPGAPFLYLNASDLLEGLVVA------------ 65
Query: 149 IAIETNVEDIIATLITNEKPDLVIIDSIQTL 179
+ ++ L KP ++ ID I +L
Sbjct: 66 ELFGHFLVRLLFELAEKAKPGVLFIDEIDSL 96
>gnl|CDD|36647 KOG1434, KOG1434, KOG1434, Meiotic recombination protein Dmc1
[Energy production and conversion, Replication,
recombination and repair].
Length = 335
Score = 40.7 bits (95), Expect = 8e-04
Identities = 40/200 (20%), Positives = 74/200 (37%), Gaps = 34/200 (17%)
Query: 47 SKTIKQGHSISLFMLSEESIEEESRIQTHIDELDRVTGGGFVRGSVILVGGDPGIGKSTL 106
+K+I G +L +L + + I T LD + GGG S+ + G+ GK+ L
Sbjct: 74 NKSISHGFCTALELLEQR--KTVGSITTGSSALDDILGGGIPSMSITEIFGEFRCGKTQL 131
Query: 107 LMQTAAS------LAYKKHRITYVSGEEAIGQIRLR--AQRLN--------------TIN 144
+ + + ++ E R++ A+R N
Sbjct: 132 SHTLCVTVQLPREMGGVGGKAIFIDTEGTFRPDRIKDIAERFKVDPDFTLDNILYFRAYN 191
Query: 145 SSVYIAIETNVEDIIATLITNEKPDLVIIDSIQTLWSQTAESSPGTVIQVRTSV-----Q 199
S + + + D ++ + K LVI+DSI L+ + + R Q
Sbjct: 192 SEEQMELVYLLGDFLS---EHGKYRLVIVDSIMALFRV--DYDGRGELSERQQKLNQMLQ 246
Query: 200 AMIQYAKKNGVAMVLVGHVT 219
+ + A++ VA+ L VT
Sbjct: 247 KLNKLAEEFNVAVFLTNQVT 266
>gnl|CDD|29985 cd00984, DnaB_C, DnaB helicase C terminal domain. The hexameric
helicase DnaB unwinds the DNA duplex at the chromosome
replication fork. Although the mechanism by which DnaB
both couples ATP hydrolysis to translocation along DNA
and denatures the duplex is unknown, a change in the
quaternary structure of the protein involving
dimerization of the N-terminal domain has been observed
and may occur during the enzymatic cycle. This
C-terminal domain contains an ATP-binding site and is
therefore probably the site of ATP hydrolysis..
Length = 242
Score = 39.8 bits (93), Expect = 0.002
Identities = 30/134 (22%), Positives = 53/134 (39%), Gaps = 34/134 (25%)
Query: 77 DELDRVTGGGFVRGSVILVGGDPGIGKSTLLMQTAASLAYK-KHRITYVSGEEAIGQIRL 135
+LD +TGG G +I++ P +GK+ + A ++A K + + S E + Q+
Sbjct: 1 TDLDNLTGG-LQPGDLIIIAARPSMGKTAFALNIAENIAKKQGKPVLFFSLEMSKEQLLQ 59
Query: 136 R---------AQRLNTINSS------------------VYIAIETN--VEDIIAT---LI 163
R +L T + S +YI ++ V DI + L
Sbjct: 60 RLLASESGISLSKLRTGSLSDEDWERLAEAIGELKELPIYIDDSSSLTVSDIRSRARRLK 119
Query: 164 TNEKPDLVIIDSIQ 177
L++ID +Q
Sbjct: 120 KEHGLGLIVIDYLQ 133
>gnl|CDD|114104 pfam05362, Lon_C, Lon protease (S16) C-terminal proteolytic domain.
The Lon serine proteases must hydrolyse ATP to degrade
protein substrates. In Escherichia coli, these proteases
are involved in turnover of intracellular proteins,
including abnormal proteins following heat-shock. The
active site for protease activity resides in a
C-terminal domain. The Lon proteases are classified as
family S16 in Merops.
Length = 205
Score = 39.1 bits (92), Expect = 0.003
Identities = 24/80 (30%), Positives = 45/80 (56%), Gaps = 1/80 (1%)
Query: 353 FGNHDVHLNI-AGGYRISEPAADVAVAAALISSILSIPLPSDFVYFGEVSLSGSVRAVGH 411
F D+H+++ G P+A V +A AL+S++ IP+ D GE++L G V +G
Sbjct: 91 FEKKDIHIHVPEGATPKDGPSAGVTMATALVSALTGIPVRKDVAMTGEITLRGRVLPIGG 150
Query: 412 MQQRLKEAEKIGFLSGVFPE 431
++++L A + G + + P+
Sbjct: 151 LKEKLLAAHRAGIKTVIIPK 170
>gnl|CDD|30951 COG0606, COG0606, Predicted ATPase with chaperone activity
[Posttranslational modification, protein turnover,
chaperones].
Length = 490
Score = 35.6 bits (82), Expect = 0.029
Identities = 36/160 (22%), Positives = 66/160 (41%), Gaps = 22/160 (13%)
Query: 309 ALLVEIQSLVVPTSLGMPRRTVVGWDSSRLAMILAVLEAR---------CNIKFGNHDVH 359
A VE++ + S G+P T+VG + AV E+R +F +
Sbjct: 2 APPVEVEVDI---SNGLPGFTIVGLPDT------AVKESRERVRAALTNSGFEFPAKRIT 52
Query: 360 LNIA-GGYRISEPAADVAVAAALISSILSIPLP--SDFVYFGEVSLSGSVRAVGHMQQRL 416
+N+A D+ +A ++++ +P + + GE+SL G +R VG +
Sbjct: 53 INLAPADLPKEGSRFDLPIALGILAASGQLPADALILYEFLGELSLDGLLRPVGGVLPAA 112
Query: 417 KEAEKIGFLSGVFPESAKGECK-IGMLDRQYIKNLSDLVK 455
A++ G + P+ E IG L + L ++V
Sbjct: 113 LAAKEKGKRGLIVPKENAEEASLIGGLPVYGARYLEEVVN 152
>gnl|CDD|144183 pfam00493, MCM, MCM2/3/5 family.
Length = 327
Score = 34.8 bits (81), Expect = 0.052
Identities = 19/47 (40%), Positives = 25/47 (53%), Gaps = 5/47 (10%)
Query: 81 RVTGGGFVRGSV-ILVGGDPGIGKSTLLMQTAASLAYKKHRITYVSG 126
+ G +RG + +L+ GDPG KS LL + A LA R Y SG
Sbjct: 47 NLPDGTRLRGDINVLLVGDPGTAKSQLL-KYVAKLA---PRAVYTSG 89
>gnl|CDD|33687 COG3899, COG3899, Predicted ATPase [General function prediction
only].
Length = 849
Score = 35.0 bits (80), Expect = 0.052
Identities = 17/57 (29%), Positives = 28/57 (49%), Gaps = 3/57 (5%)
Query: 66 IEEESRIQTHIDELDRVTGGGFVRGSVILVGGDPGIGKSTLLMQTAASLAYKKHRIT 122
E+ + + DRV+ G RG V+LV G+ GIGKS L+ + + ++
Sbjct: 3 YGRETELAQLLAAFDRVSKG---RGEVVLVAGESGIGKSALVNEVHKPITQQRGYFI 56
>gnl|CDD|29991 cd01125, repA, Hexameric Replicative Helicase RepA. RepA is
encoded by a plasmid, which is found in most Gram
negative bacteria. RepA is a 5'-3' DNA helicase which
can utilize ATP, GTP and CTP to a lesser extent..
Length = 239
Score = 34.9 bits (80), Expect = 0.053
Identities = 43/165 (26%), Positives = 74/165 (44%), Gaps = 39/165 (23%)
Query: 90 GSVILVGGDPGIGKSTLLMQTAASLAYKKH------------RITYVSGEEAIGQI--RL 135
G V + G GKS+LL+ A ++A K+ R+ Y+S E+ +I RL
Sbjct: 1 GYVSALVAPGGTGKSSLLLVLALAMALGKNLFGGGLKVTEPGRVVYLSAEDPREEIHRRL 60
Query: 136 RA--QRLNTINSSVYIAIET------------------NVEDIIATLITNEKPDLVIIDS 175
A Q L ++ + I++ E II L+ + DLV+ID
Sbjct: 61 EAILQHLEPDDAGDRLFIDSGRIQPISIAREGRIIVVPEFERIIEQLLI-RRIDLVVIDP 119
Query: 176 IQTLWSQTAESSPGTVIQVRTSVQAMIQYAKKNGVAMVLVGHVTK 220
+ + + +E+ G + V ++A+ + A + G A++LV HV K
Sbjct: 120 LVS-FHGVSENDNGAMDAV---IKALRRIAAQTGAAILLVHHVRK 160
>gnl|CDD|33398 COG3598, RepA, RecA-family ATPase [DNA replication, recombination,
and repair].
Length = 402
Score = 34.6 bits (79), Expect = 0.060
Identities = 36/165 (21%), Positives = 70/165 (42%), Gaps = 32/165 (19%)
Query: 87 FVRGSVILVGGDPGIGKSTLLMQTAASLAYKKH----------RITYVSGE----EAIGQ 132
F +G V ++ GD G+GK+TLL+ +LA K+ ++ YVS E + + +
Sbjct: 86 FRKGYVSILYGDSGVGKTTLLLYLCIALAAGKNLFGNKVKEPGKVLYVSLELYREDILER 145
Query: 133 IRLRAQRLNTINSSVYIAIETNVE------DIIA------TLITNE--KPDLVIIDSIQT 178
+ R+ + V T+V D+++ E +PD V+ID
Sbjct: 146 LEPVRARMGLSPADVRNMDLTDVSGAADESDVLSPKLYRRFEKILEQKRPDFVVIDPFVA 205
Query: 179 LWSQTAESSPGTVIQVRTSVQAMIQYAKKNGVAMVLVGHVTKEGQ 223
+ + S +QV+ ++ + A+ A++ + H +K
Sbjct: 206 FYEGKSISD----VQVKEFIKKTRKLARNLECAIIYIHHTSKSSG 246
>gnl|CDD|36777 KOG1564, KOG1564, KOG1564, DNA repair protein RHP57 [Replication,
recombination and repair].
Length = 351
Score = 34.6 bits (79), Expect = 0.066
Identities = 36/182 (19%), Positives = 61/182 (33%), Gaps = 32/182 (17%)
Query: 70 SRIQTHIDELDRVTGGGFVRGSVILVGGDPGIGKSTLLMQTAASLAYKKH------RITY 123
S++ T LD GG + + G+ G GK+ LL+Q + + + Y
Sbjct: 82 SKLTTGCVALDECLRGGIPTDGITEICGESGCGKTQLLLQLSLCVQLPRSHGGLGGGAVY 141
Query: 124 VSGEEAIGQIRLR----------------------AQRLNTINSSVYIAIETNVEDIIAT 161
+ E RL + N + V +
Sbjct: 142 ICTESPFPTRRLHQLSHTLPQRPNPEKELNYNDNPGDHIFVENVHDVDHLLHIVNRQLPI 201
Query: 162 LITNEKPDLVIIDSIQTLWSQTAESSPGTVI----QVRTSVQAMIQYAKKNGVAMVLVGH 217
L+ +K LVIIDS+ L+ + +P + + + Q A K +A+V
Sbjct: 202 LLNRKKIKLVIIDSVAALFRSEFDYNPSDLKKRARHLFRLAGKLRQLASKFDLAVVCANQ 261
Query: 218 VT 219
VT
Sbjct: 262 VT 263
>gnl|CDD|31936 COG1750, COG1750, Archaeal serine proteases [General function
prediction only].
Length = 579
Score = 33.8 bits (77), Expect = 0.12
Identities = 27/142 (19%), Positives = 60/142 (42%), Gaps = 10/142 (7%)
Query: 302 AGIEGTRALLVEIQSLVVPTS-------LGMPRRTVVGWDSSRLAMILAVLEARCNIKFG 354
+ + + V I V T P + S+R+A +A+ A +
Sbjct: 40 SVTSQGQGVGVPINISVTVTPGDGRVYVATFPYTQIDMQGSARVAAGVALRLA--GVDMS 97
Query: 355 NHDVHLNI-AGGYRISEPAADVAVAAALISSILSIPLPSDFVYFGEVSLSGSVRAVGHMQ 413
++DV++ + A + P+A + A+ ++++ + D + G ++ GS+ VG +
Sbjct: 98 SYDVYIAVEADSPVVGGPSAGGYMTVAIYAALMGWSIRKDVMMTGMINPDGSIGPVGGIL 157
Query: 414 QRLKEAEKIGFLSGVFPESAKG 435
++L+ A K G + P +
Sbjct: 158 EKLEAAAKAGAKIFLIPVGQRI 179
>gnl|CDD|72971 cd00267, ABC_ATPase, ABC (ATP-binding cassette) transporter
nucleotide-binding domain; ABC transporters are a large
family of proteins involved in the transport of a wide
variety of different compounds, like sugars, ions,
peptides, and more complex organic molecules. The
nucleotide-binding domain shows the highest similarity
between all members of the family. ABC transporters are
a subset of nucleotide hydrolases that contain a
signature motif, Q-loop, and H-loop/switch region, in
addition to, the Walker A motif/P-loop and Walker B
motif commonly found in a number of ATP- and GTP-binding
and hydrolyzing proteins..
Length = 157
Score = 33.3 bits (76), Expect = 0.13
Identities = 31/142 (21%), Positives = 55/142 (38%), Gaps = 14/142 (9%)
Query: 89 RGSVILVGGDPGIGKSTLLMQTAASLAYKKHRITYVSGEEAIGQIRLRAQRLNTINSSVY 148
G ++ + G G GKSTLL A L I + I ++ L R
Sbjct: 24 AGEIVALVGPNGSGKSTLLRAIAGLLKPTSGEILI--DGKDIAKLPLEELRRRIGYVPQL 81
Query: 149 IAIETNVEDIIATLITNEKPDLVIIDSIQTLWSQTAESSPGTVIQVRTSVQAMIQYAKKN 208
+ + L+ N PDL+++D E + G R + +++ +
Sbjct: 82 SGGQRQRVALARALLLN--PDLLLLD----------EPTSGLDPASRERLLELLRELAEE 129
Query: 209 GVAMVLVGHVTKEGQIAGPRVI 230
G +++V H + ++A RVI
Sbjct: 130 GRTVIIVTHDPELAELAADRVI 151
>gnl|CDD|147726 pfam05729, NACHT, NACHT domain. This NTPase domain is found in
apoptosis proteins as well as those involved in MHC
transcription activation. This family is closely related
to pfam00931.
Length = 165
Score = 33.4 bits (77), Expect = 0.14
Identities = 17/98 (17%), Positives = 36/98 (36%), Gaps = 22/98 (22%)
Query: 91 SVILVGGDPGIGKSTLLMQTAASLA----YKKHRITYVSGEEAIGQIRLRAQRLNTIN-- 144
+++ G+ G GK+TLL + A A + + L + L+
Sbjct: 1 RTVILQGEAGSGKTTLLQKLALLWAQGKLPQDFDFVFF----------LPCRELSRSGEA 50
Query: 145 ------SSVYIAIETNVEDIIATLITNEKPDLVIIDSI 176
S + V ++ A ++ + L+I+D +
Sbjct: 51 SLADLLFSQWPEPAAPVSEVWAVILELPERVLLILDGL 88
>gnl|CDD|31058 COG0714, COG0714, MoxR-like ATPases [General function prediction
only].
Length = 329
Score = 33.2 bits (75), Expect = 0.15
Identities = 12/36 (33%), Positives = 18/36 (50%)
Query: 86 GFVRGSVILVGGDPGIGKSTLLMQTAASLAYKKHRI 121
+ G +L+ G PG+GK+ L A +L RI
Sbjct: 39 ALLAGGHVLLEGPPGVGKTLLARALARALGLPFVRI 74
>gnl|CDD|31673 COG1484, DnaC, DNA replication protein [DNA replication,
recombination, and repair].
Length = 254
Score = 32.7 bits (74), Expect = 0.23
Identities = 24/176 (13%), Positives = 60/176 (34%), Gaps = 32/176 (18%)
Query: 4 IRSQYFCQSCGEIHSRWIGKCDSCNAWNTIIEDSSRKESDQRFSKTIKQGHSISLF---M 60
+ C+ G ++ ++ + +RK + S + + F
Sbjct: 30 LEQAADCKEWG--YAEFLEYLLEEE----KLAREARKIERRLRSASFPAKKTFEEFDFEF 83
Query: 61 LSEESIEEESRIQTHIDELDRVTGGGFVRGSVILVGGDPGIGKSTLLMQTAASLAYKKHR 120
+ + + ++ +R +++ G PG+GK+ L + L
Sbjct: 84 QPGIDKKALEDLASLVEFFERGEN--------LVLLGPPGVGKTHLAIAIGNELLKAGIS 135
Query: 121 ITYVSGEEAIGQIRLRAQRLNTINSSVYIAIETNVEDIIATLITNEKPDLVIIDSI 176
+ +++ + + +++ A + E ++ L K DL+IID I
Sbjct: 136 VLFITAPDLLSKLK-AAFDEGRLE-----------EKLLRELK---KVDLLIIDDI 176
>gnl|CDD|146080 pfam03266, DUF265, Protein of unknown function, DUF265.
Length = 168
Score = 32.6 bits (75), Expect = 0.25
Identities = 25/107 (23%), Positives = 36/107 (33%), Gaps = 25/107 (23%)
Query: 92 VILVGGDPGIGKSTLLMQTAASLAY---------------KKHRI-----TYVSGEEAIG 131
I + G PG+GK+TL+ + L RI SGE
Sbjct: 1 RIFITGPPGVGKTTLVKKVIELLKSEGVKVGGFYTPEVREGGRRIGFDIVDLASGERGP- 59
Query: 132 QIRLRAQRLNTINSSVYIAIETNVEDIIATLITN--EKPDLVIIDSI 176
R+ Y+ E+I + E+ DL+IID I
Sbjct: 60 LARVGGVS--GPRVGKYVVNLEEFEEIALPALRRALEEADLIIIDEI 104
>gnl|CDD|31438 COG1245, COG1245, Predicted ATPase, RNase L inhibitor (RLI) homolog
[General function prediction only].
Length = 591
Score = 31.7 bits (72), Expect = 0.41
Identities = 14/64 (21%), Positives = 22/64 (34%), Gaps = 8/64 (12%)
Query: 59 FMLSEESIEEESRIQTHIDELDR--------VTGGGFVRGSVILVGGDPGIGKSTLLMQT 110
F ++ +L + V G G VI + G GIGK+T +
Sbjct: 328 FEEKPPRDDKARDTLVEYPDLKKTYGDFKLEVEEGEIYDGEVIGILGPNGIGKTTFVKLL 387
Query: 111 AASL 114
A +
Sbjct: 388 AGVI 391
>gnl|CDD|35288 KOG0065, KOG0065, KOG0065, Pleiotropic drug resistance proteins
(PDR1-15), ABC superfamily [Secondary metabolites
biosynthesis, transport and catabolism].
Length = 1391
Score = 31.8 bits (72), Expect = 0.43
Identities = 16/37 (43%), Positives = 18/37 (48%), Gaps = 3/37 (8%)
Query: 90 GSVILVGGDPGIGKSTLLMQTAASL---AYKKHRITY 123
G + LV G PG GK+TLL A L ITY
Sbjct: 141 GEMTLVLGPPGSGKTTLLKALAGKLDNFLKSSGEITY 177
>gnl|CDD|35701 KOG0480, KOG0480, KOG0480, DNA replication licensing factor, MCM6
component [Replication, recombination and repair].
Length = 764
Score = 31.8 bits (72), Expect = 0.43
Identities = 15/40 (37%), Positives = 19/40 (47%), Gaps = 5/40 (12%)
Query: 88 VRGSV-ILVGGDPGIGKSTLLMQTAASLAYKKHRITYVSG 126
+RG + + + GDPG GKS L A R Y SG
Sbjct: 375 LRGDINVCIVGDPGTGKSQFLKAVCAFSP----RSVYTSG 410
>gnl|CDD|32257 COG2074, COG2074, 2-phosphoglycerate kinase [Carbohydrate transport
and metabolism].
Length = 299
Score = 31.4 bits (71), Expect = 0.57
Identities = 27/94 (28%), Positives = 45/94 (47%), Gaps = 15/94 (15%)
Query: 92 VILVGGDPGIGKSTLLMQTAASLAYKKHRITYVSGEEAIGQIRLRA----QRLNTINSSV 147
+IL+GG G+GKST+ + A L I V ++I ++ LR + L T+++S
Sbjct: 91 IILIGGASGVGKSTIAGELARRLG-----IRSVISTDSIREV-LRKIISPELLPTLHTSS 144
Query: 148 YIA-----IETNVEDIIATLITNEKPDLVIIDSI 176
Y A T+ IIA +V I+++
Sbjct: 145 YDAWKALRDPTDENPIIAGFEDQASAVMVGIEAV 178
>gnl|CDD|39152 KOG3949, KOG3949, KOG3949, RNA polymerase II elongator complex,
subunit ELP4 [Chromatin structure and dynamics,
Transcription].
Length = 360
Score = 31.1 bits (70), Expect = 0.60
Identities = 13/65 (20%), Positives = 31/65 (47%)
Query: 72 IQTHIDELDRVTGGGFVRGSVILVGGDPGIGKSTLLMQTAASLAYKKHRITYVSGEEAIG 131
+ I +LD++ GGG GS +L+ D + ++L++ + + ++ +
Sbjct: 29 TSSGIADLDQILGGGLPLGSSVLIEEDRSMIYHSVLLKYFLAEGLVNNHTLLLASPKKDP 88
Query: 132 QIRLR 136
++ LR
Sbjct: 89 KMFLR 93
>gnl|CDD|31434 COG1241, MCM2, Predicted ATPase involved in replication control,
Cdc46/Mcm family [DNA replication, recombination, and
repair].
Length = 682
Score = 31.1 bits (70), Expect = 0.61
Identities = 18/44 (40%), Positives = 22/44 (50%), Gaps = 5/44 (11%)
Query: 85 GGFVRGSV-ILVGGDPGIGKSTLLMQTAASLAYKKHRITYVSGE 127
G +RG + IL+ GDPG KS LL A R Y SG+
Sbjct: 313 GTRIRGDIHILLVGDPGTAKSQLLKYVAKLA----PRGVYTSGK 352
>gnl|CDD|147666 pfam05625, PAXNEB, PAXNEB protein. PAXNEB or PAX6 neighbour is
found in several eukaryotic organisms. PAXNED is an RNA
polymerase II Elongator protein subunit. It is part of
the HAP subcomplex of Elongator, which is a six-subunit
component of the RNA polymerase II holoenzyme. The HAP
subcomplex is required for Elongator structural
integrity and histone acetyltransferase activity. This
protein family has a P-loop motif. However its sequence
has degraded in many members of the family.
Length = 353
Score = 31.1 bits (71), Expect = 0.66
Identities = 24/100 (24%), Positives = 46/100 (46%), Gaps = 2/100 (2%)
Query: 144 NSSVYIAIETNVEDIIATLITNEKPDL-VIIDSI-QTLWSQTAESSPGTVIQVRTSVQAM 201
N S Y ++ ++ +IA + N L ++I S+ LW S P ++ S++A+
Sbjct: 170 NESPYASLLKQIQSLIAKSLFNPNNVLRIVIPSLLSPLWYPPECSQPTELLPFLHSLRAL 229
Query: 202 IQYAKKNGVAMVLVGHVTKEGQIAGPRVIEHMVDAVLYFE 241
++ N VA++ + + R IE + D V+ E
Sbjct: 230 LRKYSSNLVAIITLPLSLYPRSSSLVRWIELLADGVIELE 269
>gnl|CDD|35699 KOG0478, KOG0478, KOG0478, DNA replication licensing factor, MCM4
component [Replication, recombination and repair].
Length = 804
Score = 31.1 bits (70), Expect = 0.69
Identities = 18/44 (40%), Positives = 19/44 (43%), Gaps = 4/44 (9%)
Query: 83 TGGGFVRGSVILVGGDPGIGKSTLLMQTAASLAYKKHRITYVSG 126
G F IL+ GDPG KS LL Q L R Y SG
Sbjct: 455 KSGRFRGDINILLVGDPGTSKSQLL-QYCHRLL---PRGVYTSG 494
>gnl|CDD|58499 cd01822, Lysophospholipase_L1_like, Lysophospholipase L1-like
subgroup of SGNH-hydrolases. The best characterized
member in this family is TesA, an E. coli periplasmic
protein with thioesterase, esterase, arylesterase,
protease and lysophospholipase activity..
Length = 177
Score = 30.9 bits (70), Expect = 0.76
Identities = 18/63 (28%), Positives = 31/63 (49%), Gaps = 15/63 (23%)
Query: 159 IATLITNEKPDLVII-----DSIQTLWSQTAESSPGTVIQVRTSVQAMIQYAKKNGVAMV 213
+ L+ KPDLVI+ D ++ + P Q R +++ MI+ A+ G ++
Sbjct: 56 LPALLAQHKPDLVILELGGNDGLRGI-------PPD---QTRANLRQMIETAQARGAPVL 105
Query: 214 LVG 216
LVG
Sbjct: 106 LVG 108
>gnl|CDD|73290 cd01983, Fer4_NifH, The Fer4_NifH superfamily contains a variety of
proteins which share a common ATP-binding domain.
Functionally, proteins in this superfamily use the
energy from hydrolysis of NTP to transfer electron or
ion..
Length = 99
Score = 30.8 bits (69), Expect = 0.83
Identities = 14/33 (42%), Positives = 21/33 (63%)
Query: 92 VILVGGDPGIGKSTLLMQTAASLAYKKHRITYV 124
VI+V G G+GK+TL AA+LA + R+ +
Sbjct: 1 VIVVTGKGGVGKTTLAANLAAALAKRGKRVLLI 33
>gnl|CDD|73298 cd02035, ArsA, ArsA ATPase functionas as an efflux pump located on
the inner membrane of the cell. This ATP-driven oxyanion
pump catalyzes the extrusion of arsenite, antimonite and
arsenate. Maintenance of a low intracellular
concentration of oxyanion produces resistance to the
toxic agents. The pump is composed of two subunits, the
catalytic ArsA subunit and the membrane subunit ArsB,
which are encoded by arsA and arsB genes respectively.
Arsenic efflux in bacteria is catalyzed by either ArsB
alone or by ArsAB complex. The ATP-coupled pump,
however, is more efficient. ArsA is composed of two
homologous halves, A1 and A2, connected by a short
linker sequence..
Length = 217
Score = 30.6 bits (69), Expect = 0.96
Identities = 17/63 (26%), Positives = 25/63 (39%)
Query: 92 VILVGGDPGIGKSTLLMQTAASLAYKKHRITYVSGEEAIGQIRLRAQRLNTINSSVYIAI 151
VI G G+GK+T+ TA LA + ++ VS + A L+ I
Sbjct: 1 VIFFTGKGGVGKTTIAAATAVRLAEEGKKVLLVSTDPAHNLSDKGLPNLSDAFIVEDPEI 60
Query: 152 ETN 154
N
Sbjct: 61 APN 63
>gnl|CDD|33845 COG4088, COG4088, Predicted nucleotide kinase [Nucleotide transport
and metabolism].
Length = 261
Score = 30.7 bits (69), Expect = 0.99
Identities = 26/126 (20%), Positives = 52/126 (41%), Gaps = 13/126 (10%)
Query: 92 VILVGGDPGIGKSTLLMQTAASLAYKKHRITYVSGEEAIGQIRLRAQRLNTINSSVYIAI 151
+I++ G PG GK+T + A L + R+ ++ + G + I VY
Sbjct: 3 LIILTGYPGSGKTTFAKELAKELRQEIWRVIHLEKDYLRG---ILWDESLPILKEVY--R 57
Query: 152 ETNVEDIIATLITNEKPDLVIIDSIQTLWSQTAE--------SSPGTVIQVRTSVQAMIQ 203
E+ ++ + L + K LVI+D S + + +I +RT + ++
Sbjct: 58 ESFLKSVERLLDSALKNYLVIVDDTNYYKSMRRQLACEAKERKTTWCIIYLRTPLDTCLR 117
Query: 204 YAKKNG 209
++ G
Sbjct: 118 RNRERG 123
>gnl|CDD|143922 pfam00154, RecA, recA bacterial DNA recombination protein. RecA is
a DNA-dependent ATPase and functions in DNA repair
systems. RecA protein catalyses an ATP-dependent DNA
strand-exchange reaction that is the central step in the
repair of dsDNA breaks by homologous recombination.
Length = 322
Score = 30.3 bits (69), Expect = 1.1
Identities = 29/127 (22%), Positives = 57/127 (44%), Gaps = 6/127 (4%)
Query: 57 SLFMLSEESIEEESRIQTHIDELDRVTG-GGFVRGSVILVGGDPGIGKSTLLMQTAASLA 115
S+ L ++++E+ I T LD G GG +G +I + G GK+TL + A
Sbjct: 18 SIMRLGDKTVEDVEVISTGSLGLDIALGIGGLPKGRIIEIYGPESSGKTTLALHAIAEAQ 77
Query: 116 YKKHRITYVSGEEAIGQIRLRAQRLNTINSSVYIAIETNVE---DIIATLITNEKPDLVI 172
++ E A+ + + ++ N + ++ E +I L+ + DL++
Sbjct: 78 KAGGTAAFIDAEHALDPVYAKKLGVDIDN--LLVSQPDTGEQALEIADMLVRSGAVDLIV 135
Query: 173 IDSIQTL 179
+DS+ L
Sbjct: 136 VDSVAAL 142
>gnl|CDD|32776 COG2956, COG2956, Predicted N-acetylglucosaminyl transferase
[Carbohydrate transport and metabolism].
Length = 389
Score = 30.3 bits (68), Expect = 1.1
Identities = 12/32 (37%), Positives = 17/32 (53%)
Query: 2 VKIRSQYFCQSCGEIHSRWIGKCDSCNAWNTI 33
++ + +Y CQ+CG C SC AW TI
Sbjct: 349 LRRKPRYRCQNCGFTAHTLYWHCPSCRAWETI 380
>gnl|CDD|110677 pfam01695, IstB, IstB-like ATP binding protein. This protein
contains an ATP/GTP binding P-loop motif. It is found
associated with IS21 family insertion sequences. The
function of this protein is unknown, but it may perform
a transposase function.
Length = 178
Score = 30.3 bits (69), Expect = 1.2
Identities = 21/98 (21%), Positives = 42/98 (42%), Gaps = 25/98 (25%)
Query: 84 GGGFV-RGSVILVGGDPGIGKSTLLMQTAASLAYKK----HRITYVSGEEAIGQIRLRAQ 138
G ++ + +L+ G PG+GK+ L A +L ++ + + + + + Q++ RA+
Sbjct: 40 GLDWIEQAENLLLLGPPGVGKTHL----ACALGHQACRAGYSVLFTRTPDLVEQLK-RAR 94
Query: 139 RLNTINSSVYIAIETNVEDIIATLITNEKPDLVIIDSI 176
+ TL K DL+I+D I
Sbjct: 95 GDGRLAR---------------TLQRLAKADLLILDDI 117
>gnl|CDD|73214 cd00550, ArsA_ATPase, Oxyanion-translocating ATPase (ArsA). This
ATPase is involved in transport of arsenite, antimonite
or other oxyanions across biological membranes in all
three kingdoms of life. ArsA contains a highly
conserved AAA motif present in the AAA+ ATPase
superfamily associated with a variety of cellular
activities. To form a functional ATP-driven pump, ArsA
interacts with the permease ArsB, which is a
channel-forming integral membrane protein. One of the
most interesting features of ArsA is the allosteric
activation by its transport substrates. A divalent
cation, typically Mg2+, is required for its enzymatic
activity..
Length = 254
Score = 30.2 bits (68), Expect = 1.2
Identities = 14/38 (36%), Positives = 21/38 (55%)
Query: 92 VILVGGDPGIGKSTLLMQTAASLAYKKHRITYVSGEEA 129
I GG G+GK+T+ TA LA + ++ VS + A
Sbjct: 2 YIFFGGKGGVGKTTISAATAVRLAEQGKKVLLVSTDPA 39
>gnl|CDD|72996 cd03237, ABC_RNaseL_inhibitor_domain2, The ATPase domain 2 of RNase
L inhibitor. The ABC ATPase, RNase L inhibitor (RLI),
is a key enzyme in ribosomal biogenesis, formation of
translation preinitiation complexes, and assembly of HIV
capsids. RLI's are not transport proteins and thus
cluster with a group of soluble proteins that lack the
transmembrane components commonly found in other members
of the family. Structurally, RLI's have an N-terminal
Fe-S domain and two nucleotide-binding domains which are
arranged to form two composite active sites in their
interface cleft. RLI is one of the most conserved
enzymes between archaea and eukaryotes with a sequence
identity of more than 48%. The high degree of
evolutionary conservation suggests that RLI performs a
central role in archaeal and eukaryotic physiology..
Length = 246
Score = 30.3 bits (68), Expect = 1.3
Identities = 13/33 (39%), Positives = 16/33 (48%)
Query: 82 VTGGGFVRGSVILVGGDPGIGKSTLLMQTAASL 114
V GG VI + G GIGK+T + A L
Sbjct: 17 VEGGSISESEVIGILGPNGIGKTTFIKMLAGVL 49
>gnl|CDD|48371 cd02117, NifH_like, This family contains the NifH (iron protein) of
nitrogenase, L subunit (BchL/ChlL) of the
protochlorophyllide reductase and the BchX subunit of
the Chlorophyllide reductase. Members of this family use
energey from ATP hydrolysis and transfer electrons
through a Fe4-S4 cluster to other subunit for reduction
of substrate..
Length = 212
Score = 29.8 bits (67), Expect = 1.8
Identities = 11/30 (36%), Positives = 16/30 (53%)
Query: 92 VILVGGDPGIGKSTLLMQTAASLAYKKHRI 121
I + G GIGKST +A+LA ++
Sbjct: 2 QIAIYGKGGIGKSTTSQNLSAALAEMGKKV 31
>gnl|CDD|143913 pfam00142, Fer4_NifH, 4Fe-4S iron sulfur cluster binding proteins,
NifH/frxC family.
Length = 269
Score = 29.6 bits (67), Expect = 1.9
Identities = 12/30 (40%), Positives = 17/30 (56%)
Query: 92 VILVGGDPGIGKSTLLMQTAASLAYKKHRI 121
I + G GIGKST T+A+LA ++
Sbjct: 2 KIAIYGKGGIGKSTTSQNTSAALAEMGKKV 31
>gnl|CDD|32733 COG2909, MalT, ATP-dependent transcriptional regulator
[Transcription].
Length = 894
Score = 29.5 bits (66), Expect = 2.0
Identities = 21/114 (18%), Positives = 40/114 (35%), Gaps = 20/114 (17%)
Query: 76 IDELDRVTGGGFVRGSVILVGGDPGIGKSTLLMQTAASLAYKKHRITYVSGEEAIGQIRL 135
+D L R +IL+ G GK+TLL Q A E R
Sbjct: 28 LDRLRRAN-----DYRLILISAPAGFGKTTLLAQWRELAADGAAVAWLSLDESDNDPARF 82
Query: 136 RAQRLNTINSSV---------------YIAIETNVEDIIATLITNEKPDLVIID 174
+ + + + Y+++E+ + ++ L + E P +++D
Sbjct: 83 LSYLIAALQQATPTLGDEAQTLLQKHQYVSLESLLSSLLNELASYEGPLYLVLD 136
>gnl|CDD|144046 pfam00308, Bac_DnaA, Bacterial dnaA protein.
Length = 219
Score = 29.6 bits (67), Expect = 2.0
Identities = 23/86 (26%), Positives = 37/86 (43%), Gaps = 20/86 (23%)
Query: 97 GDPGIGKSTLLMQTAASLAYKKH---RITYVSGEEAIGQIRLRAQRLNTINSSVYIAIET 153
G G+GK T L+ + A + R+ Y++ EE + A R N I A +
Sbjct: 41 GGVGLGK-THLLHAIGNYALRNFPNLRVVYLTSEE-FLNDFVDALRDNKIE-----AFKK 93
Query: 154 NVEDIIATLITNEKPDLVIIDSIQTL 179
+ ++ DL++ID IQ L
Sbjct: 94 SYRNV----------DLLLIDDIQFL 109
>gnl|CDD|48369 cd02040, NifH, NifH gene encodes component II (iron protein) of
nitrogenase. Nitrogenase is responsible for the
biological nitrogen fixation, i.e. reduction of
molecular nitrogen to ammonia. NifH consists of two
oxygen-sensitive metallosulfur proteins: the
mollybdenum-iron (alternatively, vanadium-iron or
iron-iron) protein (commonly referred to as component
1), and the iron protein (commonly referred to as
component 2). The iron protein is a homodimer, with an
Fe4S4 cluster bound between the subunits and two
ATP-binding domains. It supplies energy by ATP
hydrolysis, and transfers electrons from reduced
ferredoxin or flavodoxin to component 1 for the
reduction of molecular nitrogen to ammonia..
Length = 270
Score = 29.4 bits (66), Expect = 2.1
Identities = 12/32 (37%), Positives = 17/32 (53%)
Query: 93 ILVGGDPGIGKSTLLMQTAASLAYKKHRITYV 124
I + G GIGKST +A+LA ++ V
Sbjct: 4 IAIYGKGGIGKSTTTQNLSAALAEMGKKVMIV 35
>gnl|CDD|145008 pfam01637, Arch_ATPase, Archaeal ATPase. This family contain a
conserved P-loop motif that is involved in binding ATP.
This family is almost exclusively found in
archaebacteria and particularly in Methanococcus
jannaschii that encodes sixteen members of this family.
Length = 223
Score = 29.2 bits (66), Expect = 2.3
Identities = 21/102 (20%), Positives = 35/102 (34%), Gaps = 14/102 (13%)
Query: 91 SVILVGGDPGIGKSTLLMQTAASLAYKKHRITYVS--GEEAIGQIRLR------AQRLNT 142
+I+V G GK+ LL + L +R+ Y E ++ A+ L
Sbjct: 21 PIIVVYGPRRCGKTALLREFLEELRELGYRVIYYDPLRREFEEKLDRFEEAKRLAEALGD 80
Query: 143 INSSVYIAIETNVEDIIATLI-----TNEKPDLVIIDSIQTL 179
+ IA + L +K +IID +Q
Sbjct: 81 ALPKIGIAKSKLAFLSLTLLFELLKRKGKKI-AIIIDEVQYA 121
>gnl|CDD|36919 KOG1707, KOG1707, KOG1707, Predicted Ras related/Rac-GTP binding
protein [Defense mechanisms].
Length = 625
Score = 29.2 bits (65), Expect = 2.4
Identities = 19/67 (28%), Positives = 29/67 (43%), Gaps = 5/67 (7%)
Query: 32 TIIEDSSRKESDQRFSKTIKQGHSISLFML--SEESIEEESRIQTHIDELDRVTGGGFVR 89
+I++ SS + K I++ I L E +++ RI T L R G +
Sbjct: 59 SIVDTSSDSDDRLCLRKEIRKADVICLVYAVDDESTVD---RISTKWLPLIRQLFGDYHE 115
Query: 90 GSVILVG 96
VILVG
Sbjct: 116 TPVILVG 122
>gnl|CDD|31539 COG1348, NifH, Nitrogenase subunit NifH (ATPase) [Inorganic ion
transport and metabolism].
Length = 278
Score = 29.4 bits (66), Expect = 2.5
Identities = 13/32 (40%), Positives = 17/32 (53%)
Query: 93 ILVGGDPGIGKSTLLMQTAASLAYKKHRITYV 124
I + G GIGKST AA+LA ++ V
Sbjct: 4 IAIYGKGGIGKSTTSQNLAAALAELGKKVLIV 35
>gnl|CDD|111283 pfam02374, ArsA_ATPase, Anion-transporting ATPase. This Pfam
family represents a conserved domain, which is sometimes
repeated, in an anion-transporting ATPase. The ATPase is
involved in the removal of arsenate, antimonite, and
arsenate from the cell.
Length = 304
Score = 29.2 bits (66), Expect = 2.6
Identities = 13/38 (34%), Positives = 21/38 (55%)
Query: 92 VILVGGDPGIGKSTLLMQTAASLAYKKHRITYVSGEEA 129
I GG G+GK+T+ TA L+ + ++ VS + A
Sbjct: 3 WIFFGGKGGVGKTTVSCATAVRLSEQGKKVLLVSTDPA 40
>gnl|CDD|143799 pfam00006, ATP-synt_ab, ATP synthase alpha/beta family,
nucleotide-binding domain. This family includes the ATP
synthase alpha and beta subunits, the ATP synthase
associated with flagella and the termination factor Rho.
Length = 213
Score = 29.3 bits (67), Expect = 2.6
Identities = 9/24 (37%), Positives = 12/24 (50%)
Query: 88 VRGSVILVGGDPGIGKSTLLMQTA 111
+G I + G G GK+ LL A
Sbjct: 13 GKGQRIGIFGGSGTGKTVLLGMIA 36
>gnl|CDD|48379 cd03115, SRP, The signal recognition particle (SRP) mediates the
transport to or across the plasma membrane in bacteria
and the endoplasmic reticulum in eukaryotes. SRP
recognizes N-terminal sighnal sequences of newly
synthesized polypeptides at the ribosome. The
SRP-polypeptide complex is then targeted to the membrane
by an interaction between SRP and its cognated receptor
(SR). In mammals, SRP consists of six protein subunits
and a 7SL RNA. One of these subunits is a 54 kd protein
(SRP54), which is a GTP-binding protein that interacts
with the signal sequence when it emerges from the
ribosome. SRP54 is a multidomain protein that consists
of an N-terminal domain, followed by a central G
(GTPase) domain and a C-terminal M domain..
Length = 173
Score = 29.3 bits (66), Expect = 2.7
Identities = 23/92 (25%), Positives = 41/92 (44%), Gaps = 9/92 (9%)
Query: 91 SVILVGGDPGIGKSTLLMQTAASLAYKKHRITYVSGE----EAIGQIRLRAQRLNTINSS 146
+VIL+ G G+GK+T + A L K ++ V+ + AI Q+R+ +++
Sbjct: 1 TVILLVGLQGVGKTTTAAKLALYLKKKGKKVLLVAADTYRPAAIEQLRVLGEQVGV--PV 58
Query: 147 VYIAIETNVEDIIATLIT---NEKPDLVIIDS 175
+ I I E D+VI+D+
Sbjct: 59 FEEGEGKDPVSIAKRAIEHAREENFDVVIVDT 90
>gnl|CDD|144508 pfam00931, NB-ARC, NB-ARC domain.
Length = 285
Score = 29.2 bits (66), Expect = 2.7
Identities = 24/119 (20%), Positives = 42/119 (35%), Gaps = 24/119 (20%)
Query: 72 IQTHIDEL-DRVTGGGFVRGSVILVGGDPGIGKSTLLMQTAASLAYKKHRIT-------- 122
+ I+ L +++ G V +VG G+GK+TL A Y +
Sbjct: 1 REDMIEALIEKLLEMSENLGVVGIVGM-GGVGKTTL-----AKQIYNDDSVGGHFDSVAW 54
Query: 123 -YVSGEEAIGQI-RLRAQRLNTINSSVYIAIETNVEDIIATLITN---EKPDLVIIDSI 176
VS ++ + Q L +S E +A I K L+++D +
Sbjct: 55 VVVSKTYTEFRLQKDILQELGLDDSDWV----EKNESELAVKIKEALLRKRFLLVLDDV 109
>gnl|CDD|30898 COG0552, FtsY, Signal recognition particle GTPase [Intracellular
trafficking and secretion].
Length = 340
Score = 29.1 bits (65), Expect = 3.0
Identities = 20/82 (24%), Positives = 36/82 (43%), Gaps = 6/82 (7%)
Query: 64 ESIEEESRIQTHIDELDRVTGGGFVRGSVILVGGDPGIGKSTLLMQTAASLAYKKHRITY 123
E++ E R +D + + VIL G G+GK+T + + A L + +
Sbjct: 115 EALIEILRPVDKVDLPLEIPKEK--KPFVILFVGVNGVGKTTTIAKLAKYLKQQGKSVLL 172
Query: 124 VSGEE----AIGQIRLRAQRLN 141
+G+ AI Q+ + +RL
Sbjct: 173 AAGDTFRAAAIEQLEVWGERLG 194
>gnl|CDD|34201 COG4559, COG4559, ABC-type hemin transport system, ATPase component
[Inorganic ion transport and metabolism].
Length = 259
Score = 29.1 bits (65), Expect = 3.0
Identities = 15/70 (21%), Positives = 28/70 (40%)
Query: 90 GSVILVGGDPGIGKSTLLMQTAASLAYKKHRITYVSGEEAIGQIRLRAQRLNTINSSVYI 149
G V+ + G G GKSTLL + L+ +T A+ + + +
Sbjct: 27 GEVLAILGPNGAGKSTLLKALSGELSPDSGEVTLNGVPLNSWPPEELARHRAVLPQNSSL 86
Query: 150 AIETNVEDII 159
A V++++
Sbjct: 87 AFPFTVQEVV 96
>gnl|CDD|72992 cd03233, ABC_PDR_domain1, The pleiotropic drug resistance (PDR)
family of ATP-binding cassette (ABC) transporters. PDR
is a well-described phenomenon occurring in fungi and
shares several similarities with processes in bacteria
and higher eukaryotes. This PDR subfamily represents
domain I of its (ABC-IM)2 organization. ABC
transporters are a large family of proteins involved in
the transport of a wide variety of different compounds
including sugars, ions, peptides, and more complex
organic molecules. The nucleotide-binding domain shows
the highest similarity between all members of the
family. ABC transporters are a subset of nucleotide
hydrolases that contain a signature motif, Q-loop, and
H-loop/switch region, in addition to, the Walker A
motif/P-loop and Walker B motif commonly found in a
number of ATP- and GTP-binding and hydrolyzing
proteins..
Length = 202
Score = 29.0 bits (65), Expect = 3.2
Identities = 13/24 (54%), Positives = 16/24 (66%), Gaps = 1/24 (4%)
Query: 86 GFVR-GSVILVGGDPGIGKSTLLM 108
G V+ G ++LV G PG G STLL
Sbjct: 28 GVVKPGEMVLVLGRPGSGCSTLLK 51
>gnl|CDD|36000 KOG0781, KOG0781, KOG0781, Signal recognition particle receptor,
alpha subunit [Intracellular trafficking, secretion, and
vesicular transport].
Length = 587
Score = 28.4 bits (63), Expect = 4.0
Identities = 21/61 (34%), Positives = 32/61 (52%), Gaps = 8/61 (13%)
Query: 92 VILVGGDPGIGKSTLLMQTAASLAYKKHRI------TYVSGEEAIGQIRLRAQRLNTINS 145
VI G G+GKST L + A L K R+ T+ SG A+ Q+R +RL+ ++
Sbjct: 380 VISFVGVNGVGKSTNLAKIAYWLLQNKFRVLIAACDTFRSG--AVEQLRTHVERLSALHG 437
Query: 146 S 146
+
Sbjct: 438 T 438
>gnl|CDD|37891 KOG2680, KOG2680, KOG2680, DNA helicase TIP49, TBP-interacting
protein [Transcription].
Length = 454
Score = 28.4 bits (63), Expect = 4.0
Identities = 16/43 (37%), Positives = 22/43 (51%), Gaps = 1/43 (2%)
Query: 86 GFVRGSVILVGGDPGIGKSTLLMQTAASLAYKKHRITYVSGEE 128
G + G IL+ G PG GK+ + M + SL T +SG E
Sbjct: 62 GKIAGRAILIAGQPGTGKTAIAMGMSKSLGDDTPF-TSISGSE 103
>gnl|CDD|38557 KOG3347, KOG3347, KOG3347, Predicted nucleotide kinase/nuclear
protein involved oxidative stress response [Nucleotide
transport and metabolism].
Length = 176
Score = 28.3 bits (63), Expect = 4.2
Identities = 12/25 (48%), Positives = 14/25 (56%)
Query: 93 ILVGGDPGIGKSTLLMQTAASLAYK 117
ILV G PG GKSTL + A +
Sbjct: 10 ILVTGTPGTGKSTLAERLAEKTGLE 34
>gnl|CDD|35844 KOG0625, KOG0625, KOG0625, Phosphoglucomutase [Carbohydrate
transport and metabolism].
Length = 558
Score = 28.3 bits (63), Expect = 4.6
Identities = 23/94 (24%), Positives = 42/94 (44%), Gaps = 13/94 (13%)
Query: 195 RTSVQAMIQYAKKNGVAMVLVGHVTKEGQIAGPRVIEHMVDAVLYFEGGTRNTQYDYRIL 254
+ ++Q + + A NGV ++VG + G ++ P V ++ + GG IL
Sbjct: 68 KEAIQIIAKIAAANGVGRLIVG---QNGILSTPAV-SCIIRKYIKAGGGI--------IL 115
Query: 255 RSVKNRFGPTDEIGV-FEMSDKGLQEVSDPSKIF 287
+ N GP + G+ F + + G S KI+
Sbjct: 116 TASHNPGGPEGDFGIKFNLENGGPAPESVTDKIY 149
>gnl|CDD|48378 cd03114, ArgK-like, The function of this protein family is unkown.
The protein sequences are similar to the ArgK protein in
E. coli. ArgK protein is a membrane ATPase which is
required for transporting arginine, ornithine and lysine
into the cells by the arginine and ornithine (AO system)
and lysine, arginine and ornithine (LAO) transport
systems..
Length = 148
Score = 28.3 bits (63), Expect = 5.1
Identities = 20/66 (30%), Positives = 32/66 (48%), Gaps = 10/66 (15%)
Query: 92 VILVGGDPGIGKSTLLMQTAASLAYKKHRITYV--------SGEEAIGQIRLRAQRLNTI 143
VI + G PG GKSTL+ +L + R+ + SG +G R+R +R +
Sbjct: 1 VIGITGVPGAGKSTLIDALITALRARGKRVAVLAIDPSSPFSGGAILGD-RIRMERHAS- 58
Query: 144 NSSVYI 149
+ V+I
Sbjct: 59 DPGVFI 64
>gnl|CDD|34868 COG5271, MDN1, AAA ATPase containing von Willebrand factor type A
(vWA) domain [General function prediction only].
Length = 4600
Score = 28.1 bits (62), Expect = 5.4
Identities = 16/57 (28%), Positives = 24/57 (42%), Gaps = 14/57 (24%)
Query: 93 ILVGGDPGIGKSTLLMQTAASLAYKKHRI-------------TYVSGEEAIGQIRLR 136
IL+ G PG+GK++L+ A K RI + + EE G+ R
Sbjct: 1546 ILLEGSPGVGKTSLITALARKTGKKLIRINLSEQTDLCDLFGSDLPVEEG-GEFRWM 1601
>gnl|CDD|133282 cd01882, BMS1, Bms1. Bms1 is an essential, evolutionarily
conserved, nucleolar protein. Its depletion interferes
with processing of the 35S pre-rRNA at sites A0, A1, and
A2, and the formation of 40S subunits. Bms1, the
putative endonuclease Rc11, and the essential U3 small
nucleolar RNA form a stable subcomplex that is believed
to control an early step in the formation of the 40S
subumit. The C-terminal domain of Bms1 contains a
GTPase-activating protein (GAP) that functions
intramolecularly. It is believed that Rc11 activates
Bms1 by acting as a guanine-nucleotide exchange factor
(GEF) to promote GDP/GTP exchange, and that activated
(GTP-bound) Bms1 delivers Rc11 to the preribosomes.
Length = 225
Score = 28.0 bits (63), Expect = 5.4
Identities = 27/80 (33%), Positives = 39/80 (48%), Gaps = 17/80 (21%)
Query: 92 VILVGGDPGIGKSTLLMQTAASLA--YKKHRITYVSGEEAIGQIRLRAQRL------NTI 143
V+ V G PG+GK+TL+ SL Y K I+ + G + + R RL N I
Sbjct: 41 VVAVVGPPGVGKTTLI----KSLVKNYTKQNISDIKGPITVVTGKKR--RLTFIECPNDI 94
Query: 144 NSSVYIAIETNVEDIIATLI 163
N+ + IA V D++ LI
Sbjct: 95 NAMIDIA---KVADLVLLLI 111
>gnl|CDD|144975 pfam01580, FtsK_SpoIIIE, FtsK/SpoIIIE family. FtsK has extensive
sequence similarity to wide variety of proteins from
prokaryotes and plasmids, termed the FtsK/SpoIIIE
family. This domain contains a putative ATP binding
P-loop motif. It is found in the FtsK cell division
protein from E. coli and the stage III sporulation
protein E SpoIIIE which has roles in regulation of
prespore specific gene expression in B. subtilis. A
mutation in FtsK causes a temperature sensitive block in
cell division and it is involved in peptidoglycan
synthesis or modification. The SpoIIIE protein is
implicated in intercellular chromosomal DNA transfer.
Length = 202
Score = 28.1 bits (63), Expect = 5.5
Identities = 11/27 (40%), Positives = 14/27 (51%)
Query: 93 ILVGGDPGIGKSTLLMQTAASLAYKKH 119
+L+ G G GKST L SLA +
Sbjct: 41 LLIAGATGSGKSTFLNTLILSLAARHS 67
>gnl|CDD|30352 COG0003, ArsA, Predicted ATPase involved in chromosome partitioning
[Cell division and chromosome partitioning].
Length = 322
Score = 28.0 bits (62), Expect = 6.1
Identities = 12/38 (31%), Positives = 20/38 (52%)
Query: 92 VILVGGDPGIGKSTLLMQTAASLAYKKHRITYVSGEEA 129
++ G G+GK+T+ TA LA ++ VS + A
Sbjct: 4 IVFFTGKGGVGKTTIAAATAVKLAESGKKVLLVSTDPA 41
>gnl|CDD|30727 COG0378, HypB, Ni2+-binding GTPase involved in regulation of
expression and maturation of urease and hydrogenase
[Posttranslational modification, protein turnover,
chaperones / Transcription].
Length = 202
Score = 27.9 bits (62), Expect = 6.1
Identities = 13/36 (36%), Positives = 23/36 (63%), Gaps = 1/36 (2%)
Query: 92 VILVGGDPGIGKSTLLMQTAASLAYKKHRITYVSGE 127
I VGG PG GK+ L+ +T +L +++I ++G+
Sbjct: 15 RIGVGGPPGSGKTALIEKTLRALK-DEYKIAVITGD 49
>gnl|CDD|34242 COG4619, COG4619, ABC-type uncharacterized transport system, ATPase
component [General function prediction only].
Length = 223
Score = 28.0 bits (62), Expect = 6.1
Identities = 22/88 (25%), Positives = 34/88 (38%), Gaps = 13/88 (14%)
Query: 89 RGSVILVGGDPGIGKSTLLMQ-------TAASLAYKKHRITYVSGEEAIGQIRLRAQRLN 141
G I + G G GKSTLL T+ +L ++ ++ + E Q+ AQ
Sbjct: 28 AGEFIAITGPSGCGKSTLLKIVASLISPTSGTLLFEGEDVSTLKPEAYRQQVSYCAQTPA 87
Query: 142 TINSSVYIAIETNVEDIIATLITNEKPD 169
+V + I I N +PD
Sbjct: 88 LFGDTVEDNL------IFPWQIRNRRPD 109
>gnl|CDD|112137 pfam03308, ArgK, ArgK protein. The ArgK protein acts as an ATPase
enzyme and as a kinase, and phosphorylates periplasmic
binding proteins involved in the LAO (lysine, arginine,
ornithine)/AO transport systems.
Length = 267
Score = 27.7 bits (62), Expect = 6.4
Identities = 26/87 (29%), Positives = 37/87 (42%), Gaps = 15/87 (17%)
Query: 64 ESIEEESRIQTHIDELDRVTGGGFVRGSVILVGGDPGIGKSTLLMQTAASLAYKKHRITY 123
ES E+R + L +TG R + + G PG GKSTL+ L + HR+
Sbjct: 9 ESRRPEAR--ELLRRLMPLTG----RAHRVGITGVPGAGKSTLIEALGMELRRRGHRVAV 62
Query: 124 V--------SGEEAIGQIRLRAQRLNT 142
+ +G +G R R QRL
Sbjct: 63 LAVDPSSPFTGGSILGD-RTRMQRLAV 88
>gnl|CDD|73302 cd02042, ParA, ParA and ParB of Caulobacter crescentus belong to a
conserved family of bacterial proteins implicated in
chromosome segregation. ParB binds to DNA sequences
adjacent to the origin of replication and localizes to
opposite cell poles shortly following the initiation of
DNA replication. ParB regulates the ParA ATPase activity
by promoting nucleotide exchange in a fashion
reminiscent of the exchange factors of eukaryotic G
proteins. ADP-bound ParA binds single-stranded DNA,
whereas the ATP-bound form dissociates ParB from its DNA
binding sites. Increasing the fraction of ParA-ADP in
the cell inhibits cell division, suggesting that this
simple nucleotide switch may regulate cytokinesis. ParA
shares sequence similarity to a conserved and widespread
family of ATPases which includes the repA protein of the
repABC operon in R. etli Sym plasmid. This operon is
involved in the plasmid replication and partition..
Length = 104
Score = 27.9 bits (62), Expect = 6.9
Identities = 9/22 (40%), Positives = 15/22 (68%)
Query: 100 GIGKSTLLMQTAASLAYKKHRI 121
G+GK+T + AA+LA + R+
Sbjct: 10 GVGKTTTAVNLAAALARRGKRV 31
>gnl|CDD|35194 COG5635, COG5635, Predicted NTPase (NACHT family) [Signal
transduction mechanisms].
Length = 824
Score = 27.8 bits (61), Expect = 7.1
Identities = 23/109 (21%), Positives = 42/109 (38%), Gaps = 8/109 (7%)
Query: 13 CGEIHSRWIGKCDSCNAWNTIIEDSSRKESDQRFSKTIKQGHSISLFM---LSEESIEEE 69
G + I + + +I+ + +E S+ K+ ++ EE + E
Sbjct: 147 AGTLLELLI--ARGVQSQDKLIDVNILEEVPLA-SQRSKRIFDLNTKGEKRFDEEFLLEL 203
Query: 70 SRIQTHIDELDRVTGGGFVRGSVILVGGDPGIGKSTLLMQTAASLAYKK 118
++ D L + +IL G PG GK+T L + A LA +
Sbjct: 204 TQSADDQDALPGLEALEKYAKLLIL--GAPGSGKTTFLQRLALWLAQRT 250
>gnl|CDD|34265 COG4646, COG4646, DNA methylase [Transcription / DNA replication,
recombination, and repair].
Length = 637
Score = 27.7 bits (61), Expect = 7.5
Identities = 14/55 (25%), Positives = 22/55 (40%), Gaps = 4/55 (7%)
Query: 424 FLSGVFPESAKGECKIGMLDRQYIKNLSDLVKKITALQKKDKKTVHKTRSLNSPW 478
+LSG + K LD + +N+ L +Q D + T L +PW
Sbjct: 292 YLSGQVRDKLKAAKAAAALDPVFERNVRAL----VEVQPADLRPSDITARLGAPW 342
>gnl|CDD|133251 cd00157, Rho, Rho (Ras homology) family. Members of the Rho family
include RhoA, Cdc42, Rac, Rnd, Wrch1, RhoBTB, and Rop.
There are 22 human Rho family members identified
currently. These proteins are all involved in the
reorganization of the actin cytoskeleton in response to
external stimuli. They also have roles in cell
transformation by Ras in cytokinesis, in focal adhesion
formation and in the stimulation of stress-activated
kinase. These various functions are controlled through
distinct effector proteins and mediated through a
GTP-binding/GTPase cycle involving three classes of
regulating proteins: GAPs (GTPase-activating proteins),
GEFs (guanine nucleotide exchange factors), and GDIs
(guanine nucleotide dissociation inhibitors). Most Rho
proteins contain a lipid modification site at the
C-terminus, with a typical sequence motif CaaX, where a
= an aliphatic amino acid and X = any amino acid. Lipid
binding is essential for membrane attachment, a key
feature of most Rho proteins. Since crystal structures
often lack C-terminal residues, this feature is not
available for annotation in many of the CDs in the
hierarchy.
Length = 171
Score = 27.5 bits (62), Expect = 7.5
Identities = 11/35 (31%), Positives = 17/35 (48%), Gaps = 13/35 (37%)
Query: 93 ILVGGDPGIGKSTLLMQTAASLAYKKHRITYVSGE 127
I+V GD +GK+ LL I+Y +G+
Sbjct: 3 IVVVGDGAVGKTCLL-------------ISYTTGK 24
>gnl|CDD|33644 COG3854, SpoIIIAA, ncharacterized protein conserved in bacteria
[Function unknown].
Length = 308
Score = 27.6 bits (61), Expect = 7.7
Identities = 22/96 (22%), Positives = 39/96 (40%), Gaps = 12/96 (12%)
Query: 91 SVILVGGDPGIGKSTLLMQTAASLAYKKHRITYVSGEEAIGQIRLRAQRLNTINS--SVY 148
L+ G P +GK+TLL A L+ ++ +G I R++ +N
Sbjct: 138 LNTLIIGPPQVGKTTLLRDIARLLSDGINQFLPKK----VGIIDERSEIAGCLNGVPQHG 193
Query: 149 IAIETNVED------IIATLITNEKPDLVIIDSIQT 178
+V D + I + P+++I+D I T
Sbjct: 194 RGRRMDVLDPCPKAEGMMMAIRSMSPEVIIVDEIGT 229
>gnl|CDD|30605 COG0256, RplR, Ribosomal protein L18 [Translation, ribosomal
structure and biogenesis].
Length = 125
Score = 27.5 bits (61), Expect = 7.7
Identities = 17/85 (20%), Positives = 41/85 (48%), Gaps = 3/85 (3%)
Query: 162 LITNEKPDLVIIDSIQTLWSQTAESSPGTVIQVRTSVQAMIQ-YAKKNGVAMVLVGHVTK 220
L T+ +P LV+ S + +++Q + G + +++ ++ Y KK G ++
Sbjct: 24 LGTSGRPRLVVRRSNRHIYAQIIDDVKGGTLASASTLSKELRKYGKKGGGGNTEAAYLV- 82
Query: 221 EGQIAGPRVIEHMVDAVLYFEGGTR 245
G++ R + ++ V++ GG +
Sbjct: 83 -GKLIAERALAKGIEEVVFDRGGYK 106
>gnl|CDD|133293 cd01893, Miro1, Miro1 subfamily. Miro (mitochondrial Rho) proteins
have tandem GTP-binding domains separated by a linker
region containing putative calcium-binding EF hand
motifs. Genes encoding Miro-like proteins were found in
several eukaryotic organisms. This CD represents the
N-terminal GTPase domain of Miro proteins. These
atypical Rho GTPases have roles in mitochondrial
homeostasis and apoptosis. Most Rho proteins contain a
lipid modification site at the C-terminus; however, Miro
is one of few Rho subfamilies that lack this feature.
Length = 166
Score = 27.7 bits (62), Expect = 8.3
Identities = 9/16 (56%), Positives = 14/16 (87%)
Query: 93 ILVGGDPGIGKSTLLM 108
I++ GD G+GKS+L+M
Sbjct: 3 IVLIGDEGVGKSSLIM 18
>gnl|CDD|31805 COG1618, COG1618, Predicted nucleotide kinase [Nucleotide transport
and metabolism].
Length = 179
Score = 27.5 bits (61), Expect = 8.9
Identities = 11/29 (37%), Positives = 20/29 (68%)
Query: 93 ILVGGDPGIGKSTLLMQTAASLAYKKHRI 121
I + G PG+GK+TL+++ A L K +++
Sbjct: 8 IFITGRPGVGKTTLVLKIAEKLREKGYKV 36
>gnl|CDD|145449 pfam02301, HORMA, HORMA domain. The HORMA (for Hop1p, Rev7p and
MAD2) domain has been suggested to recognize chromatin
states that result from DNA adducts, double stranded
breaks or non-attachment to the spindle and acts as an
adaptor that recruits other proteins. MAD2 is a spindle
checkpoint protein which prevents progression of the
cell cycle upon detection of a defect in mitotic spindle
integrity.
Length = 189
Score = 27.3 bits (61), Expect = 9.1
Identities = 13/56 (23%), Positives = 23/56 (41%), Gaps = 11/56 (19%)
Query: 422 IGFLSGVFPESAKGECKIGMLD---------RQYIKNLSDLVKKITALQKKDKKTV 468
I +L G++PE + + K L Y++ + V AL+K K +
Sbjct: 20 ILYLRGIYPEESFEDRKKYNLPVLVSEDPQLIDYLEKVLSGVFD--ALEKGYLKKL 73
>gnl|CDD|31385 COG1192, Soj, ATPases involved in chromosome partitioning [Cell
division and chromosome partitioning].
Length = 259
Score = 27.5 bits (60), Expect = 9.4
Identities = 16/81 (19%), Positives = 34/81 (41%), Gaps = 14/81 (17%)
Query: 100 GIGKSTLLMQTAASLA-YKKHRITYVSGEEAIGQIRLRAQRLNTINSSVYIAIETNVEDI 158
G+GK+T + AA+LA ++ I L Q + + ++ + ++E
Sbjct: 13 GVGKTTTAVNLAAALAKRGGKKVLL---------IDLDPQG----SLTSWLGLRPDLEGD 59
Query: 159 IATLITNEKPDLVIIDSIQTL 179
+ L++ K I+D +
Sbjct: 60 LYNLLSGLKERPDILDYTVVI 80
>gnl|CDD|163626 cd07383, MPP_Dcr2, Saccharomyces cerevisiae DCR2 phosphatase and
related proteins, metallophosphatase domain. DCR2
phosphatase (Dosage-dependent Cell Cycle Regulator 2)
functions together with DCR1 (Gid8) in a common pathway
to accelerate initiation of DNA replication in
Saccharomyces cerevisiae. Genetic analysis suggests that
DCR1 functions upstream of DCR2. DCR2 interacts with
and dephosphorylates Sic1, an inhibitor of mitotic
cyclin/cyclin-dependent kinase complexes, which may
serve to trigger the initiation of cell division. DCR2
belongs to the metallophosphatase (MPP) superfamily.
MPPs are functionally diverse, but all share a conserved
domain with an active site consisting of two metal ions
(usually manganese, iron, or zinc) coordinated with
octahedral geometry by a cage of histidine, aspartate,
and asparagine residues. The MPP superfamily includes:
Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat
debranching enzymes, YfcE-like phosphodiesterases,
purple acid phosphatases (PAPs), YbbF-like
UDP-2,3-diacylglucosamine hydrolases, and acid
sphingomyelinases (ASMases). The conserved domain is a
double beta-sheet sandwich with a di-metal active site
made up of residues located at the C-terminal side of
the sheets. This domain is thought to allow for
productive metal coordination.
Length = 199
Score = 27.2 bits (61), Expect = 9.5
Identities = 11/60 (18%), Positives = 21/60 (35%), Gaps = 13/60 (21%)
Query: 159 IATLITNEKPDLVII--DSIQTLWSQTAESSPGTVIQVRTSVQAMIQYAKKNGV--AMVL 214
I ++ EKPDLV++ D I + T +++ + + A
Sbjct: 33 IERVLDAEKPDLVVLTGDLI---------TGENTNDNSTSALDKAVSPMIDRKIPWAATF 83
>gnl|CDD|110632 pfam01645, Glu_synthase, Conserved region in glutamate synthase.
This family represents a region of the glutamate
synthase protein. This region is expressed as a separate
subunit in the glutamate synthase alpha subunit from
archaebacteria, or part of a large multidomain enzyme in
other organisms. The aligned region of these proteins
contains a putative FMN binding site and Fe-S cluster.
Length = 367
Score = 27.3 bits (61), Expect = 9.5
Identities = 18/47 (38%), Positives = 20/47 (42%), Gaps = 12/47 (25%)
Query: 356 HDVHLNIAGGYRISEPAADVAVAAALISSILSIPLPSDFVYFGEVSL 402
V L GG R ADVA AAA L +D VY G +L
Sbjct: 272 DRVSLIADGGLRTG---ADVAKAAA---------LGADAVYIGTAAL 306
>gnl|CDD|34522 COG4913, COG4913, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 1104
Score = 27.3 bits (60), Expect = 9.6
Identities = 23/117 (19%), Positives = 40/117 (34%), Gaps = 35/117 (29%)
Query: 93 ILVGGDPGIGKSTL------LMQTAASLAY---------KKHRITYVSG------EEAIG 131
ILV G G GKSTL ++ L + ++ +TY+ G +
Sbjct: 40 ILVTGGSGSGKSTLIDAITAVLLPQGKLRFNSAAQANTPRRSLVTYIRGAWRAQEDPLQD 99
Query: 132 QIRLRAQRLNTINSSVYIAIETNVEDIIATLITNEKPDLVIIDSIQTLWSQTAESSP 188
QI R S+ +N E + TL + + ++++ S
Sbjct: 100 QIVSTYLR-PRATYSLVGLTYSNGEGVEHTL-------------VAIFYLKSSDISS 142
>gnl|CDD|73300 cd02037, MRP-like, MRP (Multiple Resistance and pH adaptation) is a
homologue of the Fer4_NifH superfamily. Like the other
members of the superfamily, MRP contains a ATP-binding
domain at the N-termini. It is found in bacteria as a
membrane-spanning protein and functions as a Na+/H+
antiporter..
Length = 169
Score = 27.4 bits (61), Expect = 9.6
Identities = 12/31 (38%), Positives = 19/31 (61%), Gaps = 1/31 (3%)
Query: 92 VILVG-GDPGIGKSTLLMQTAASLAYKKHRI 121
VI V G G+GKST+ + A +LA +++
Sbjct: 1 VIAVMSGKGGVGKSTVAVNLALALAKLGYKV 31
>gnl|CDD|144961 pfam01561, Hanta_G2, Hantavirus glycoprotein G2. The medium (M)
genome segment of hantaviruses (family Bunyaviridae)
encodes the two virion glycoproteins. G1 and G2, as a
precursor protein in the complementary sense RNA.
Length = 486
Score = 27.5 bits (61), Expect = 9.6
Identities = 15/52 (28%), Positives = 19/52 (36%)
Query: 51 KQGHSISLFMLSEESIEEESRIQTHIDELDRVTGGGFVRGSVILVGGDPGIG 102
K GHS S F + + LDRVTG + + G P G
Sbjct: 386 KGGHSGSKFKCCHGTDCSSEGLTAAAPHLDRVTGYNEIDSDKVYDDGAPECG 437
>gnl|CDD|72981 cd03222, ABC_RNaseL_inhibitor, The ABC ATPase RNase L inhibitor
(RLI) is a key enzyme in ribosomal biogenesis, formation
of translation preinitiation complexes, and assembly of
HIV capsids. RLI's are not transport proteins, and thus
cluster with a group of soluble proteins that lack the
transmembrane components commonly found in other members
of the family. Structurally, RLI's have an N-terminal
Fe-S domain and two nucleotide-binding domains, which
are arranged to form two composite active sites in their
interface cleft. RLI is one of the most conserved
enzymes between archaea and eukaryotes with a sequence
identity more than 48%. The high degree of evolutionary
conservation suggests that RLI performs a central role
in archaeal and eukaryotic physiology..
Length = 177
Score = 27.3 bits (60), Expect = 9.8
Identities = 31/128 (24%), Positives = 41/128 (32%), Gaps = 21/128 (16%)
Query: 66 IEEESRIQTHIDELDRVTGGGFVRGSVILVGGDPGIGKSTLLMQTAASL----------- 114
++ + V G G VI + G G GK+T + A L
Sbjct: 1 QLYPDCVKRYGVFFLLVELGVVKEGEVIGIVGPNGTGKTTAVKILAGQLIPNGDNDEWDG 60
Query: 115 ---AYKKHRITYVSGE---EAIGQIRLRAQRLNTINS-SVYIAIET--NVEDIIATLIT- 164
YK I GE AI LR + S Y+ IE N I L
Sbjct: 61 ITPVYKPQYIDLSGGELQRVAIAAALLRNATFYLFDEPSAYLDIEQRLNAARAIRRLSEE 120
Query: 165 NEKPDLVI 172
+K LV+
Sbjct: 121 GKKTALVV 128
>gnl|CDD|39108 KOG3905, KOG3905, KOG3905, Dynein light intermediate chain [Cell
motility].
Length = 473
Score = 27.3 bits (60), Expect = 9.8
Identities = 12/31 (38%), Positives = 17/31 (54%)
Query: 90 GSVILVGGDPGIGKSTLLMQTAASLAYKKHR 120
G +LV GD G GK++L+ + S KK
Sbjct: 52 GKNVLVLGDNGSGKTSLISKLQGSETVKKGS 82
>gnl|CDD|72862 cd04760, BAH_Dnmt1_I, BAH, or Bromo Adjacent Homology domain, first
copy present in DNA (Cytosine-5)-methyltransferases from
Bilateria, Dnmt1 and similar proteins. DNA methylation,
or the covalent addition of a methyl group to cytosine
within the context of the CpG dinucleotide, has profound
effects on the genome. These effects include
transcriptional repression via inhibition of
transcription factor binding, the recruitment of
methyl-binding proteins and their associated chromatin
remodeling factors, X chromosome inactivation,
imprinting, and the suppression of parasitic DNA
sequences. DNA methylation is also essential for proper
embryonic development and is an important player in both
DNA repair and genome stability. BAH domains are found
in a variety of proteins playing roles in
transcriptional silencing and the remodeling of
chromatin. It is assumed that in most or all of these
instances the BAH domain mediates protein-protein
interactions..
Length = 124
Score = 27.2 bits (60), Expect = 9.8
Identities = 10/19 (52%), Positives = 12/19 (63%)
Query: 273 SDKGLQEVSDPSKIFLSDR 291
SD L E SDP ++FL D
Sbjct: 48 SDTVLGETSDPLELFLVDE 66
>gnl|CDD|38036 KOG2825, KOG2825, KOG2825, Putative arsenite-translocating ATPase
[Inorganic ion transport and metabolism].
Length = 323
Score = 27.3 bits (60), Expect = 9.9
Identities = 13/37 (35%), Positives = 19/37 (51%)
Query: 93 ILVGGDPGIGKSTLLMQTAASLAYKKHRITYVSGEEA 129
I VGG G+GK+T A LA + + +S + A
Sbjct: 22 IFVGGKGGVGKTTCSCSLAVQLAKVRESVLIISTDPA 58
>gnl|CDD|31889 COG1703, ArgK, Putative periplasmic protein kinase ArgK and related
GTPases of G3E family [Amino acid transport and
metabolism].
Length = 323
Score = 27.2 bits (60), Expect = 9.9
Identities = 20/62 (32%), Positives = 28/62 (45%), Gaps = 9/62 (14%)
Query: 89 RGSVILVGGDPGIGKSTLLMQTAASLAYKKHRITYV--------SGEEAIGQIRLRAQRL 140
VI + G PG GKSTL+ L + HR+ + +G +G R+R QRL
Sbjct: 50 NAHVIGITGVPGAGKSTLIEALGRELRERGHRVAVLAVDPSSPFTGGSILGD-RIRMQRL 108
Query: 141 NT 142
Sbjct: 109 AV 110
Database: CddA
Posted date: Feb 4, 2011 9:38 PM
Number of letters in database: 6,263,737
Number of sequences in database: 21,609
Lambda K H
0.317 0.133 0.378
Gapped
Lambda K H
0.267 0.0724 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 5,419,556
Number of extensions: 282818
Number of successful extensions: 1312
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1290
Number of HSP's successfully gapped: 130
Length of query: 479
Length of database: 6,263,737
Length adjustment: 97
Effective length of query: 382
Effective length of database: 4,167,664
Effective search space: 1592047648
Effective search space used: 1592047648
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 (26.5 bits)