RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy879
(317 letters)
>gnl|CDD|178596 PLN03025, PLN03025, replication factor C subunit; Provisional.
Length = 319
Score = 541 bits (1395), Expect = 0.0
Identities = 208/315 (66%), Positives = 255/315 (80%)
Query: 1 IEKYRPQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSF 60
+EKYRP DIVGNED V RL+V + GN+PN+I+SGPPG GKTT+IL LA LLGP++
Sbjct: 4 VEKYRPTKLDDIVGNEDAVSRLQVIARDGNMPNLILSGPPGTGKTTSILALAHELLGPNY 63
Query: 61 KDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTM 120
K+AVLELNAS+DRGID VRNKIKMFAQ+KVTLPPGRHKIVILDEADSMT GAQQALRRTM
Sbjct: 64 KEAVLELNASDDRGIDVVRNKIKMFAQKKVTLPPGRHKIVILDEADSMTSGAQQALRRTM 123
Query: 121 EIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGL 180
EIYSNTTRFALACN S KIIEPIQSRCA++R+++L+D ++L +++++ E E + + +GL
Sbjct: 124 EIYSNTTRFALACNTSSKIIEPIQSRCAIVRFSRLSDQEILGRLMKVVEAEKVPYVPEGL 183
Query: 181 EAIVFTAQGDMRQALNNLQSTHNGFGHVTAEYVFKVCDEPHPLAVKEMLLNCVEGNMKDS 240
EAI+FTA GDMRQALNNLQ+TH+GFG V E VFKVCD+PHPL VK ++ NC++G D+
Sbjct: 184 EAIIFTADGDMRQALNNLQATHSGFGFVNQENVFKVCDQPHPLHVKNIVRNCLKGKFDDA 243
Query: 241 YKIIHHLYKLGYAPEDIIGNIFRVAKTLDIPEPLKLSIIQEIGNVHLRISEGVNSLLQLS 300
+ LY LGY+P DII +FRV K D+PE LKL ++EIG H+RI +GV SLLQLS
Sbjct: 244 CDGLKQLYDLGYSPTDIITTLFRVVKNYDMPEFLKLEYLREIGFAHMRICDGVGSLLQLS 303
Query: 301 GLLARLCIVGSKNKK 315
GLLA+LC+V K
Sbjct: 304 GLLAKLCLVRETAKA 318
>gnl|CDD|234763 PRK00440, rfc, replication factor C small subunit; Reviewed.
Length = 319
Score = 369 bits (950), Expect = e-128
Identities = 148/315 (46%), Positives = 204/315 (64%), Gaps = 6/315 (1%)
Query: 1 IEKYRPQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSF 60
+EKYRP+T +IVG E+ VERLK + N+P+++ +GPPG GKTT L LAR L G +
Sbjct: 8 VEKYRPRTLDEIVGQEEIVERLKSYVKEKNMPHLLFAGPPGTGKTTAALALARELYGEDW 67
Query: 61 KDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPG--RHKIVILDEADSMTDGAQQALRR 118
++ LELNAS++RGID +RNKIK FA+ T P G KI+ LDEAD++T AQQALRR
Sbjct: 68 RENFLELNASDERGIDVIRNKIKEFAR---TAPVGGAPFKIIFLDEADNLTSDAQQALRR 124
Query: 119 TMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTND 178
TME+YS TRF L+CN S KII+PIQSRCA+ R++ L + ++ I E E I T+D
Sbjct: 125 TMEMYSQNTRFILSCNYSSKIIDPIQSRCAVFRFSPLKKEAVAERLRYIAENEGIEITDD 184
Query: 179 GLEAIVFTAQGDMRQALNNLQSTHNGFGHVTAEYVFKVCDEPHPLAVKEMLLNCVEGNMK 238
LEAI + ++GDMR+A+N LQ+ VT E V+K+ P ++EM+ + G+
Sbjct: 185 ALEAIYYVSEGDMRKAINALQAAAATGKEVTEEAVYKITGTARPEEIREMIELALNGDFT 244
Query: 239 DSYKIIHHL-YKLGYAPEDIIGNIFRVAKTLDIPEPLKLSIIQEIGNVHLRISEGVNSLL 297
++ + + L G + EDII I R +LDIPE LK+ +I IG RI+EG N +
Sbjct: 245 EAREKLRDLMIDYGLSGEDIIKQIHREVWSLDIPEELKVELIDAIGEADFRITEGANERI 304
Query: 298 QLSGLLARLCIVGSK 312
QL LLA+L ++G K
Sbjct: 305 QLEALLAKLALLGKK 319
>gnl|CDD|235223 PRK04132, PRK04132, replication factor C small subunit;
Provisional.
Length = 846
Score = 246 bits (629), Expect = 4e-75
Identities = 120/286 (41%), Positives = 175/286 (61%), Gaps = 13/286 (4%)
Query: 28 SGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKIKMFAQ 87
GN+P + + TT L LAR L G +++ LELNAS++RGI+ +R K+K FA+
Sbjct: 570 GGNLPTV-------LHNTTAALALARELFGENWRHNFLELNASDERGINVIREKVKEFAR 622
Query: 88 QKVTLPPG--RHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQS 145
K P G KI+ LDEAD++T AQQALRRTME++S+ RF L+CN S KIIEPIQS
Sbjct: 623 TK---PIGGASFKIIFLDEADALTQDAQQALRRTMEMFSSNVRFILSCNYSSKIIEPIQS 679
Query: 146 RCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHNGF 205
RCA+ R+ L D + ++ I E E + T +GL+AI++ A+GDMR+A+N LQ+
Sbjct: 680 RCAIFRFRPLRDEDIAKRLRYIAENEGLELTEEGLQAILYIAEGDMRRAINILQAAAALD 739
Query: 206 GHVTAEYVFKVCDEPHPLAVKEMLLNCVEGN-MKDSYKIIHHLYKLGYAPEDIIGNIFRV 264
+T E VF V P ++EM+L ++GN +K K+ L K G + ED++ + R
Sbjct: 740 DKITDENVFLVASRARPEDIREMMLLALKGNFLKAREKLREILLKQGLSGEDVLVQMHRE 799
Query: 265 AKTLDIPEPLKLSIIQEIGNVHLRISEGVNSLLQLSGLLARLCIVG 310
L I EP K+ + +IG + R+ EG N ++QL LLA+ ++G
Sbjct: 800 VFNLPIDEPKKVELADKIGEYNFRLVEGANEMIQLEALLAQFTLMG 845
Score = 63.7 bits (155), Expect = 3e-11
Identities = 25/47 (53%), Positives = 35/47 (74%)
Query: 1 IEKYRPQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTT 47
+EKYRPQ DIVG E V+RLK + +G++P+++ +GPPGVGK T
Sbjct: 10 VEKYRPQRLDDIVGQEHIVKRLKHYVKTGSMPHLLFAGPPGVGKCLT 56
>gnl|CDD|237090 PRK12402, PRK12402, replication factor C small subunit 2; Reviewed.
Length = 337
Score = 214 bits (547), Expect = 1e-67
Identities = 104/332 (31%), Positives = 169/332 (50%), Gaps = 27/332 (8%)
Query: 1 IEKYRPQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSF 60
EKYRP DI+G ++ VERL S N+P++++ GPPG GKT + LAR L G +
Sbjct: 6 TEKYRPALLEDILGQDEVVERLSRAVDSPNLPHLLVQGPPGSGKTAAVRALARELYGDPW 65
Query: 61 KDAVLELNASN--DRG-------------IDTVRN----KIKMFAQ---QKVTLPP--GR 96
++ E N ++ D+G + T + KI F + + P
Sbjct: 66 ENNFTEFNVADFFDQGKKYLVEDPRFAHFLGTDKRIRSSKIDNFKHVLKEYASYRPLSAD 125
Query: 97 HKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLT 156
+K ++LD A+++ + AQQALRR ME YS T RF +A K+I PI+SRC L + T
Sbjct: 126 YKTILLDNAEALREDAQQALRRIMEQYSRTCRFIIATRQPSKLIPPIRSRCLPLFFRAPT 185
Query: 157 DAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHNGFGHVTAEYVFKV 216
D +L+ + I E E + + +DGLE I + A GD+R+A+ LQ+ G +T E ++
Sbjct: 186 DDELVDVLESIAEAEGVDYDDDGLELIAYYAGGDLRKAILTLQTAALAAGEITMEAAYEA 245
Query: 217 C-DEPHPLAVKEMLLNCVEGNMKDSYKIIHHL-YKLGYAPEDIIGNIFRVAKTLDIPEPL 274
D ++ +L G+ D+ K + L G + +++ + RVA++ + L
Sbjct: 246 LGDVGTDEVIESLLDAAEAGDFTDARKTLDDLLIDEGLSGGEVLEELLRVARSRYRGDNL 305
Query: 275 KLSIIQEIGNVHLRISEGVNSLLQLSGLLARL 306
+ + + R+++G N +QL LLA L
Sbjct: 306 AR-LHRLAADADARLTDGANDRIQLEALLAEL 336
>gnl|CDD|222866 PHA02544, 44, clamp loader, small subunit; Provisional.
Length = 316
Score = 141 bits (358), Expect = 8e-40
Identities = 70/209 (33%), Positives = 100/209 (47%), Gaps = 19/209 (9%)
Query: 2 EKYRPQTFSDIVGNEDTVERLKVFSSSGNVPNIII-SGPPGVGKTTTILCLARILLGPSF 60
+KYRP T + + E K G +PN+++ S PG GKTT L +
Sbjct: 13 QKYRPSTIDECILPAADKETFKSIVKKGRIPNMLLHSPSPGTGKTTVAKALCNEV----- 67
Query: 61 KDA-VLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEAD-SMTDGAQQALRR 118
A VL +N S+ R ID VRN++ FA V+L G K++I+DE D AQ+ LR
Sbjct: 68 -GAEVLFVNGSDCR-IDFVRNRLTRFAST-VSLTGG-GKVIIIDEFDRLGLADAQRHLRS 123
Query: 119 TMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDA-------QLLSKVIEICEKE 171
ME YS F + NN IIEP++SRC ++ + T Q++ + I E E
Sbjct: 124 FMEAYSKNCSFIITANNKNGIIEPLRSRCRVIDFGVPTKEEQIEMMKQMIVRCKGILEAE 183
Query: 172 NISHTNDGLEAIVFTAQGDMRQALNNLQS 200
+ L A+V D R+ +N LQ
Sbjct: 184 GVEVDMKVLAALVKKNFPDFRRTINELQR 212
>gnl|CDD|225369 COG2812, DnaX, DNA polymerase III, gamma/tau subunits [DNA
replication, recombination, and repair].
Length = 515
Score = 124 bits (314), Expect = 4e-32
Identities = 88/310 (28%), Positives = 146/310 (47%), Gaps = 37/310 (11%)
Query: 3 KYRPQTFSDIVGNEDTVERLKVFSSSGNVPN-IIISGPPGVGKTT-------TILCLARI 54
KYRP+TF D+VG E V+ L +G + + + SGP GVGKTT + C
Sbjct: 9 KYRPKTFDDVVGQEHVVKTLSNALENGRIAHAYLFSGPRGVGKTTIARILAKALNCENGP 68
Query: 55 LLGP-------------SFKDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPP--GRHKI 99
P S D V+E++A+++ G+D +R I +KV P GR+K+
Sbjct: 69 TAEPCGKCISCKEINEGSLID-VIEIDAASNTGVDDIREII-----EKVNYAPSEGRYKV 122
Query: 100 VILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQ 159
I+DE ++ A AL +T+E + +F LA +KI I SRC + +L +
Sbjct: 123 YIIDEVHMLSKQAFNALLKTLEEPPSHVKFILATTEPQKIPNTILSRCQRFDFKRLDLEE 182
Query: 160 LLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNL-QSTHNGFGHVTAEYVFKVCD 218
+ + I +KE I+ D L I A+G +R AL+ L Q+ G G +T E V +
Sbjct: 183 IAKHLAAILDKEGINIEEDALSLIARAAEGSLRDALSLLDQAIAFGEGEITLESVRDMLG 242
Query: 219 EPHPLAVKEMLLNCVEGNMKDSYKIIHHLYKLGYAPEDIIGNIFR-------VAKTLDIP 271
+ +L ++G+ K++ ++I+ L + G PE + ++ +T+
Sbjct: 243 LTDIEKLLSLLEAILKGDAKEALRLINELIEEGKDPEAFLEDLLNFLRDLLLFKQTVPNE 302
Query: 272 EPLKLSIIQE 281
L + I+E
Sbjct: 303 LQLNTTEIEE 312
>gnl|CDD|237867 PRK14953, PRK14953, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 486
Score = 121 bits (305), Expect = 3e-31
Identities = 95/334 (28%), Positives = 159/334 (47%), Gaps = 43/334 (12%)
Query: 3 KYRPQTFSDIVGNEDTVERLKVFSSSGNVPNI-IISGPPGVGKTTTILCLARIL--LGP- 58
KYRP+ F +++G E V LK V + I +GP G GKTT LA++L L P
Sbjct: 9 KYRPKFFKEVIGQEIVVRILKNAVKLQRVSHAYIFAGPRGTGKTTIARILAKVLNCLNPQ 68
Query: 59 -----------------SFKDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPP--GRHKI 99
SF D + E++A+++RGID +R + V+ P G++K+
Sbjct: 69 EGEPCGKCENCVEIDKGSFPDLI-EIDAASNRGIDDIRA-----LRDAVSYTPIKGKYKV 122
Query: 100 VILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQ 159
I+DEA +T A AL +T+E T F L +KI I SRC ++K T Q
Sbjct: 123 YIIDEAHMLTKEAFNALLKTLEEPPPRTIFILCTTEYDKIPPTILSRCQRFIFSKPTKEQ 182
Query: 160 LLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNL-QSTHNGFGHVTAEYVFKVCD 218
+ + IC +E I + L+ + ++G MR A + L Q++ G G VT + V +
Sbjct: 183 IKEYLKRICNEEKIEYEEKALDLLAQASEGGMRDAASLLDQASTYGEGKVTIKVVEEFLG 242
Query: 219 EPHPLAVKEMLLNCVEGNMKDSYKIIHHLYKLGY-------APEDIIGNIFRVAKTLDIP 271
+V++ L +E ++ ++ K + L + GY E+ I NI + K+L P
Sbjct: 243 IVSQESVRKFLNLLLESDVDEAIKFLRTLEEKGYNLNKFWKQLEEEIRNIL-LNKSLKNP 301
Query: 272 EPLKLSIIQEIGNVHLRISEGVNSLLQLSGLLAR 305
E + Q + + ++ + + +LL L ++ +
Sbjct: 302 E----EVFQV-EDFYRKLEKPLEALLYLEDVINK 330
>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit;
Provisional.
Length = 482
Score = 118 bits (298), Expect = 4e-30
Identities = 69/222 (31%), Positives = 115/222 (51%), Gaps = 17/222 (7%)
Query: 1 IEKYRPQTFSDIVGNEDTVERLKVFSSS---GNVPN-IIISGPPGVGKTTTILCLARILL 56
+EKYRP+T SD+VGNE E+L+ + S G +++ GPPGVGKT+ LA
Sbjct: 5 VEKYRPKTLSDVVGNEKAKEQLREWIESWLKGKPKKALLLYGPPGVGKTSLAHALAN--- 61
Query: 57 GPSFKDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSM---TD-GA 112
+ V+ELNAS+ R D + A +L R K+++LDE D + D G
Sbjct: 62 --DYGWEVIELNASDQRTADVIERVAGEAATSG-SLFGARRKLILLDEVDGIHGNEDRGG 118
Query: 113 QQALRRTMEIYSNTTRFALACNNS-EKIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEKE 171
+A+ ++ L N+ + + +++ C M+ + +L+ ++ + IC KE
Sbjct: 119 ARAILELIKKAKQP--IILTANDPYDPSLRELRNACLMIEFKRLSTRSIVPVLKRICRKE 176
Query: 172 NISHTNDGLEAIVFTAQGDMRQALNNLQSTHNGFGHVTAEYV 213
I ++ L+ I + GD+R A+N+LQ+ G+G +T E V
Sbjct: 177 GIECDDEALKEIAERSGGDLRSAINDLQAIAEGYGKLTLEDV 218
>gnl|CDD|233847 TIGR02397, dnaX_nterm, DNA polymerase III, subunit gamma and tau.
This model represents the well-conserved first ~ 365
amino acids of the translation of the dnaX gene. The
full-length product of the dnaX gene in the model
bacterium E. coli is the DNA polymerase III tau subunit.
A translational frameshift leads to early termination
and a truncated protein subunit gamma, about 1/3 shorter
than tau and present in roughly equal amounts. This
frameshift mechanism is not necessarily universal for
species with DNA polymerase III but appears conserved in
the exterme thermophile Thermus thermophilis [DNA
metabolism, DNA replication, recombination, and repair].
Length = 355
Score = 115 bits (291), Expect = 8e-30
Identities = 81/289 (28%), Positives = 137/289 (47%), Gaps = 42/289 (14%)
Query: 3 KYRPQTFSDIVGNEDTVERLKVFSSSGNVPN-IIISGPPGVGKTTTILCLARIL------ 55
KYRPQTF D++G E V+ LK +G + + + SGP G GKT+ ARI
Sbjct: 7 KYRPQTFEDVIGQEHIVQTLKNAIKNGRIAHAYLFSGPRGTGKTSI----ARIFAKALNC 62
Query: 56 -LGPSFK-----------------DAVLELNASNDRGIDTVRNKIKMFAQQKVTLPP--G 95
GP + D V+E++A+++ G+D +R + V P G
Sbjct: 63 QNGPDGEPCNECESCKEINSGSSLD-VIEIDAASNNGVDDIREILD-----NVKYAPSSG 116
Query: 96 RHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYN-- 153
++K+ I+DE ++ A AL +T+E F LA KI I SRC R++
Sbjct: 117 KYKVYIIDEVHMLSKSAFNALLKTLEEPPEHVVFILATTEPHKIPATILSRC--QRFDFK 174
Query: 154 KLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNL-QSTHNGFGHVTAEY 212
++ ++ ++ +I +KE I ++ LE I A G +R AL+ L Q G G++T E
Sbjct: 175 RIPLEDIVERLKKILDKEGIKIEDEALELIARAADGSLRDALSLLDQLISFGNGNITYED 234
Query: 213 VFKVCDEPHPLAVKEMLLNCVEGNMKDSYKIIHHLYKLGYAPEDIIGNI 261
V ++ + E+L + + ++ KI+ + + G PE + ++
Sbjct: 235 VNELLGLVDDEKLIELLEAILNKDTAEALKILDEILESGVDPEKFLEDL 283
>gnl|CDD|237869 PRK14962, PRK14962, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 472
Score = 112 bits (282), Expect = 5e-28
Identities = 86/285 (30%), Positives = 141/285 (49%), Gaps = 40/285 (14%)
Query: 3 KYRPQTFSDIVGNEDTVERLKVFSSSGNVPN--IIISGPPGVGKTTTILCLARIL----- 55
KYRP+TFS++VG +D V++L + + N + I +GP G GKTT LA+ L
Sbjct: 7 KYRPKTFSEVVG-QDHVKKLIINALKKNSISHAYIFAGPRGTGKTTVARILAKSLNCENR 65
Query: 56 --LGP-------------SFKDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPP--GRHK 98
+ P +F D V+EL+A+++RGID +R KI+ V P G++K
Sbjct: 66 KGVEPCNECRACRSIDEGTFMD-VIELDAASNRGIDEIR-KIR----DAVGYRPMEGKYK 119
Query: 99 IVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDA 158
+ I+DE +T A AL +T+E + F LA N EK+ I SRC ++ + ++D
Sbjct: 120 VYIIDEVHMLTKEAFNALLKTLEEPPSHVVFVLATTNLEKVPPTIISRCQVIEFRNISDE 179
Query: 159 QLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHN-GFGHVTAEYVFK-- 215
++ ++ E+ E E I + L I A G +R AL L+ G +T E V +
Sbjct: 180 LIIKRLQEVAEAEGIEIDREALSFIAKRASGGLRDALTMLEQVWKFSEGKITLETVHEAL 239
Query: 216 --VCDEPHPLAVKEMLLNCVEGNMKDSYKIIHHLYKLGYAPEDII 258
+ E V++ + G++K + ++ +Y G E +I
Sbjct: 240 GLIPIE----VVRDYINAIFNGDVKRVFTVLDDVYYSGKDYEVLI 280
>gnl|CDD|184927 PRK14963, PRK14963, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 504
Score = 105 bits (264), Expect = 2e-25
Identities = 77/282 (27%), Positives = 126/282 (44%), Gaps = 34/282 (12%)
Query: 2 EKYRPQTFSDIVGNEDTVERLKVFSSSGNVPNI-IISGPPGVGKTTTILCLARIL----- 55
++ RP TF ++VG E E L G + + + SGP GVGKTTT AR++
Sbjct: 6 QRARPITFDEVVGQEHVKEVLLAALRQGRLGHAYLFSGPRGVGKTTT----ARLIAMAVN 61
Query: 56 -LGPSFKDA----------------VLELNASNDRGIDTVRNKIKMFAQQKVTLPP--GR 96
G K VLE++A+++ ++ VR+ ++KV L P G
Sbjct: 62 CSGEDPKPCGECESCLAVRRGAHPDVLEIDAASNNSVEDVRD-----LREKVLLAPLRGG 116
Query: 97 HKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLT 156
K+ ILDEA M+ A AL +T+E F LA EK+ I SR R+ +LT
Sbjct: 117 RKVYILDEAHMMSKSAFNALLKTLEEPPEHVIFILATTEPEKMPPTILSRTQHFRFRRLT 176
Query: 157 DAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHNGFGHVTAEYVFKV 216
+ ++ K+ + E E + L+ + A G MR A + L+ VT + V +
Sbjct: 177 EEEIAGKLRRLLEAEGREAEPEALQLVARLADGAMRDAESLLERLLALGTPVTRKQVEEA 236
Query: 217 CDEPHPLAVKEMLLNCVEGNMKDSYKIIHHLYKLGYAPEDII 258
P ++ + +G+ ++ LY+ G+A ++
Sbjct: 237 LGLPPQERLRGIAAALAQGDAAEALSGAAQLYRDGFAARTLV 278
>gnl|CDD|184934 PRK14970, PRK14970, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 367
Score = 103 bits (259), Expect = 3e-25
Identities = 67/204 (32%), Positives = 100/204 (49%), Gaps = 15/204 (7%)
Query: 3 KYRPQTFSDIVGNEDTVERLKVFSSSGNVPN-IIISGPPGVGKTTTILCLARILLGPSFK 61
KYRPQTF D+VG L + ++ ++ GP GVGKTT LAR + P +
Sbjct: 10 KYRPQTFDDVVGQSHITNTLLNAIENNHLAQALLFCGPRGVGKTTCARILARKINQPGYD 69
Query: 62 DA-------VLELNASNDRGIDTVRNKIKMFAQQKVTLPP--GRHKIVILDEADSMTDGA 112
D + EL+A+++ +D +RN I +V +PP G++KI I+DE ++ A
Sbjct: 70 DPNEDFSFNIFELDAASNNSVDDIRNLI-----DQVRIPPQTGKYKIYIIDEVHMLSSAA 124
Query: 113 QQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEKEN 172
A +T+E F LA KII I SRC + + ++T + + I KE
Sbjct: 125 FNAFLKTLEEPPAHAIFILATTEKHKIIPTILSRCQIFDFKRITIKDIKEHLAGIAVKEG 184
Query: 173 ISHTNDGLEAIVFTAQGDMRQALN 196
I +D L I A G +R AL+
Sbjct: 185 IKFEDDALHIIAQKADGALRDALS 208
>gnl|CDD|203973 pfam08542, Rep_fac_C, Replication factor C C-terminal domain. This
is the C-terminal domain of RFC (replication factor-C)
protein of the clamp loader complex which binds to the
DNA sliding clamp (proliferating cell nuclear antigen,
PCNA). The five modules of RFC assemble into a
right-handed spiral, which results in only three of the
five RFC subunits (RFC-A, RFC-B and RFC-C) making
contact with PCNA, leaving a wedge-shaped gap between
RFC-E and the PCNA clamp-loader complex. The C-terminal
is vital for the correct orientation of RFC-E with
respect to RFC-A.
Length = 89
Score = 96.0 bits (240), Expect = 4e-25
Identities = 29/89 (32%), Positives = 53/89 (59%)
Query: 218 DEPHPLAVKEMLLNCVEGNMKDSYKIIHHLYKLGYAPEDIIGNIFRVAKTLDIPEPLKLS 277
P P +KE+L + ++G+ ++ + ++ L G + EDI+ + V LDIP+ LKL
Sbjct: 1 GWPPPEDIKEILDSILKGDFDEARETLYELLVEGISAEDILKQLHEVLIRLDIPDSLKLE 60
Query: 278 IIQEIGNVHLRISEGVNSLLQLSGLLARL 306
II+E+ + R+S+G ++QL L+A+
Sbjct: 61 IIKELAEIEHRLSDGAKEIIQLEALIAKF 89
>gnl|CDD|237355 PRK13342, PRK13342, recombination factor protein RarA; Reviewed.
Length = 413
Score = 99.8 bits (250), Expect = 1e-23
Identities = 61/223 (27%), Positives = 102/223 (45%), Gaps = 25/223 (11%)
Query: 2 EKYRPQTFSDIVGNEDTVERLKVFSS---SGNVPNIIISGPPGVGKTTTILCLARILLGP 58
E+ RP+T ++VG E + K +G + ++I+ GPPG GKTT LARI+ G
Sbjct: 4 ERMRPKTLDEVVGQEHLLGPGKPLRRMIEAGRLSSMILWGPPGTGKTT----LARIIAG- 58
Query: 59 SFKDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQAL-- 116
+ L+A G+ +R ++ + + GR I+ +DE Q AL
Sbjct: 59 ATDAPFEALSAVTS-GVKDLR---EVIEEARQRRSAGRRTILFIDEIHRFNKAQQDALLP 114
Query: 117 ---RRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDA---QLLSKVIEICEK 170
T+ + TT N S ++ + SR + L++ QLL + +E E+
Sbjct: 115 HVEDGTITLIGATTE-----NPSFEVNPALLSRAQVFELKPLSEEDIEQLLKRALEDKER 169
Query: 171 ENISHTNDGLEAIVFTAQGDMRQALNNLQSTHNGFGHVTAEYV 213
+ ++ L+A+ A GD R+ALN L+ G +T E +
Sbjct: 170 GLVELDDEALDALARLANGDARRALNLLELAALGVDSITLELL 212
>gnl|CDD|237870 PRK14964, PRK14964, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 491
Score = 96.4 bits (240), Expect = 3e-22
Identities = 65/218 (29%), Positives = 105/218 (48%), Gaps = 33/218 (15%)
Query: 3 KYRPQTFSDIVGNEDTVERLKVFSSSGNVPN-IIISGPPGVGKTTTILCLARIL------ 55
KYRP +F D+VG + V L+ + +P I++ G GVGKTT ARI+
Sbjct: 6 KYRPSSFKDLVGQDVLVRILRNAFTLNKIPQSILLVGASGVGKTTC----ARIISLCLNC 61
Query: 56 -LGPSFKDA----------------VLELNASNDRGIDTVRNKIKMFAQQKVTLP-PGRH 97
GP+ V+E++A+++ +D IK+ + LP +
Sbjct: 62 SNGPTSDPCGTCHNCISIKNSNHPDVIEIDAASNTSVD----DIKVILENSCYLPISSKF 117
Query: 98 KIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTD 157
K+ I+DE +++ A AL +T+E + +F LA +KI I SRC K+
Sbjct: 118 KVYIIDEVHMLSNSAFNALLKTLEEPAPHVKFILATTEVKKIPVTIISRCQRFDLQKIPT 177
Query: 158 AQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQAL 195
+L+ +++I +KENI H + L+ I + G MR AL
Sbjct: 178 DKLVEHLVDIAKKENIEHDEESLKLIAENSSGSMRNAL 215
>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 = 89.1 bits (221), Expect = 1e-21
Identities = 39/145 (26%), Positives = 58/145 (40%), Gaps = 12/145 (8%)
Query: 13 VGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASND 72
VG E+ +E L+ N+++ GPPG GKTT +A L P L LNAS+
Sbjct: 1 VGQEEAIEALREALELPPPKNLLLYGPPGTGKTTLARAIANELFRPGAP--FLYLNASDL 58
Query: 73 RGIDTVRNKIKMFA--QQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTT--- 127
V F + ++ +DE DS++ GAQ AL R +E ++
Sbjct: 59 LEGLVVAELFGHFLVRLLFELAEKAKPGVLFIDEIDSLSRGAQNALLRVLETLNDLRIDR 118
Query: 128 ---RFALACNNSE--KIIEPIQSRC 147
R A N + + R
Sbjct: 119 ENVRVIGATNRPLLGDLDRALYDRL 143
>gnl|CDD|237864 PRK14950, PRK14950, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 585
Score = 93.0 bits (231), Expect = 6e-21
Identities = 67/226 (29%), Positives = 103/226 (45%), Gaps = 36/226 (15%)
Query: 3 KYRPQTFSDIVGNEDTVERLKVFSSSGNVPNI-IISGPPGVGKTTTILCLARIL------ 55
K+R QTF+++VG E V+ L+ + G V + + +GP GVGKT+T ARIL
Sbjct: 9 KWRSQTFAELVGQEHVVQTLRNAIAEGRVAHAYLFTGPRGVGKTST----ARILAKAVNC 64
Query: 56 LGPSFKDA------------------VLELNASNDRGIDTVRNKIKMFAQQKVTLPPG-- 95
K V+E++A++ +D R I ++V P
Sbjct: 65 TTNDPKGRPCGTCEMCRAIAEGSAVDVIEMDAASHTSVDDAREII-----ERVQFRPALA 119
Query: 96 RHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKL 155
R+K+ I+DE ++ A AL +T+E F LA K+ I SRC +++
Sbjct: 120 RYKVYIIDEVHMLSTAAFNALLKTLEEPPPHAIFILATTEVHKVPATILSRCQRFDFHRH 179
Query: 156 TDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQST 201
+ A + + + +I E I+ LEAI A G MR A N LQ
Sbjct: 180 SVADMAAHLRKIAAAEGINLEPGALEAIARAATGSMRDAENLLQQL 225
>gnl|CDD|223546 COG0470, HolB, ATPase involved in DNA replication [DNA replication,
recombination, and repair].
Length = 230
Score = 88.2 bits (218), Expect = 2e-20
Identities = 51/200 (25%), Positives = 83/200 (41%), Gaps = 21/200 (10%)
Query: 121 EIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGL 180
TRF L N+ KI+ I+SRC +R+ + I E + GL
Sbjct: 39 TAPPKNTRFILITNDPSKILPTIRSRCQRIRFKPPSRL------EAIAWLE-----DQGL 87
Query: 181 EAIVFTAQGDMRQALNNLQSTHNGFGHVTAEYVFKVCDEPHP-----LAVKEMLLNCVEG 235
E I A+GD R+A+N LQ+ + E +++ P LA E+L
Sbjct: 88 EEIAAVAEGDARKAINPLQALA--ALEIGEESIYEALLLALPESLAQLAALELLKLAENK 145
Query: 236 NMKDSYKIIHHLYKLGYAPEDIIGNIFRVAKTLD---IPEPLKLSIIQEIGNVHLRISEG 292
++ K+ L G ED++ + R LD I E ++ + R+ +G
Sbjct: 146 FLEALEKLWLLLLLEGLLGEDLLDQLQRELLKLDKALIQEEKAAELLDALAQARRRLLDG 205
Query: 293 VNSLLQLSGLLARLCIVGSK 312
+ +L+QL LLA L ++
Sbjct: 206 LLALIQLENLLAELLLLQLL 225
Score = 32.3 bits (73), Expect = 0.21
Identities = 17/39 (43%), Positives = 26/39 (66%), Gaps = 2/39 (5%)
Query: 10 SDIVGNEDTVERLKVFS-SSGNVP-NIIISGPPGVGKTT 46
++V ++ V+RL V + SG +P ++ GPPGVGKTT
Sbjct: 1 DELVPWQEAVKRLLVQALESGRLPHALLFYGPPGVGKTT 39
>gnl|CDD|237871 PRK14965, PRK14965, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 576
Score = 91.0 bits (226), Expect = 2e-20
Identities = 61/220 (27%), Positives = 102/220 (46%), Gaps = 31/220 (14%)
Query: 3 KYRPQTFSDIVGNEDTVERLKVFSSSGNVPN-IIISGPPGVGKTTTILCLARIL---LGP 58
KYRPQTFSD+ G E L+ +G V + + +G GVGKT+T LA+ L G
Sbjct: 9 KYRPQTFSDLTGQEHVSRTLQNAIDTGRVAHAFLFTGARGVGKTSTARILAKALNCEQGL 68
Query: 59 SFKDA----------------VLELNASNDRGIDTVR---NKIKMFAQQKVTLPP-GRHK 98
+ + V E++ +++ G+D +R +K LP R+K
Sbjct: 69 TAEPCNVCPPCVEITEGRSVDVFEIDGASNTGVDDIRELRENVKY-------LPSRSRYK 121
Query: 99 IVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDA 158
I I+DE ++ A AL +T+E +F A K+ I SRC + ++
Sbjct: 122 IFIIDEVHMLSTNAFNALLKTLEEPPPHVKFIFATTEPHKVPITILSRCQRFDFRRIPLQ 181
Query: 159 QLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNL 198
+++ ++ I ++E IS ++ L + G MR +L+ L
Sbjct: 182 KIVDRLRYIADQEGISISDAALALVARKGDGSMRDSLSTL 221
>gnl|CDD|235943 PRK07133, PRK07133, DNA polymerase III subunits gamma and tau;
Validated.
Length = 725
Score = 89.1 bits (221), Expect = 1e-19
Identities = 81/314 (25%), Positives = 146/314 (46%), Gaps = 44/314 (14%)
Query: 3 KYRPQTFSDIVGNEDTVERLKVFSSSGNVPN-IIISGPPGVGKT-------TTILCLARI 54
KYRP+TF DIVG + V+ LK S + + + SGP G GKT + C +
Sbjct: 11 KYRPKTFDDIVGQDHIVQTLKNIIKSNKISHAYLFSGPRGTGKTSVAKIFANALNCSHKT 70
Query: 55 -LLGP------SFKDA--VLELNASNDRGIDTVRN---KIKMFAQQKVTLPPGRHKIVIL 102
LL P + ++ ++E++A+++ G+D +R +K Q ++KI I+
Sbjct: 71 DLLEPCQECIENVNNSLDIIEMDAASNNGVDEIRELIENVKNLPTQ------SKYKIYII 124
Query: 103 DEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQLLS 162
DE ++ A AL +T+E F LA KI I SR + ++++ +++S
Sbjct: 125 DEVHMLSKSAFNALLKTLEEPPKHVIFILATTEVHKIPLTILSRVQRFNFRRISEDEIVS 184
Query: 163 KVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQSTHN-GFGHVTAEYVFKVCDEPH 221
++ I EKENIS+ + L+ I + G +R AL+ + G +T + V +E
Sbjct: 185 RLEFILEKENISYEKNALKLIAKLSSGSLRDALSIAEQVSIFGNNKITLKNV----EELF 240
Query: 222 PLAVKEMLLNCVE----GNMKDSYKIIHHLYKLGYAPE-------DIIGN--IFRVAKTL 268
L E L+N + ++K+ I++ + + G PE +++ IF K
Sbjct: 241 GLVSNENLINLLNLLYSKDIKEVLNILNQIKEQGIDPELLLISLINLVKEFIIFNKTKDN 300
Query: 269 DIPEPLKLSIIQEI 282
+ E ++++
Sbjct: 301 SLLEYYSEEDLEKL 314
>gnl|CDD|180523 PRK06305, PRK06305, DNA polymerase III subunits gamma and tau;
Validated.
Length = 451
Score = 84.8 bits (210), Expect = 2e-18
Identities = 68/223 (30%), Positives = 102/223 (45%), Gaps = 44/223 (19%)
Query: 3 KYRPQTFSDIVGNEDTVERLK---VFSSSGNVPNIIISGPPGVGKTTTILCLARIL---- 55
KYRPQTFS+I+G + V LK F+ + + + SG G GKTT LARI
Sbjct: 10 KYRPQTFSEILGQDAVVAVLKNALRFNRAAHA--YLFSGIRGTGKTT----LARIFAKAL 63
Query: 56 ----------------------LGPSFKDAVLELNASNDRGIDTVR--NKIKMFAQQKVT 91
G S VLE++ ++ RGI+ +R N+ +F K
Sbjct: 64 NCQNPTEDQEPCNQCASCKEISSGTSLD--VLEIDGASHRGIEDIRQINETVLFTPSK-- 119
Query: 92 LPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLR 151
R+KI I+DE +T A +L +T+E +F LA KI I SRC +
Sbjct: 120 ---SRYKIYIIDEVHMLTKEAFNSLLKTLEEPPQHVKFFLATTEIHKIPGTILSRCQKMH 176
Query: 152 YNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQA 194
++ + ++ K+ I ++E I + + L I AQG +R A
Sbjct: 177 LKRIPEETIIDKLALIAKQEGIETSREALLPIARAAQGSLRDA 219
>gnl|CDD|236333 PRK08691, PRK08691, DNA polymerase III subunits gamma and tau;
Validated.
Length = 709
Score = 83.2 bits (205), Expect = 1e-17
Identities = 65/232 (28%), Positives = 112/232 (48%), Gaps = 24/232 (10%)
Query: 3 KYRPQTFSDIVGNEDTVERLKVFSSSGNVPNI-IISGPPGVGKTTTILCLARILLGPSFK 61
K+RP+TF+D+VG E V+ L+ G + + +++G GVGKTT LA+ L + +
Sbjct: 9 KWRPKTFADLVGQEHVVKALQNALDEGRLHHAYLLTGTRGVGKTTIARILAKSLNCENAQ 68
Query: 62 DA-------------------VLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVIL 102
+LE++A+++ GID +R ++ AQ T G++K+ I+
Sbjct: 69 HGEPCGVCQSCTQIDAGRYVDLLEIDAASNTGIDNIREVLEN-AQYAPTA--GKYKVYII 125
Query: 103 DEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQLLS 162
DE ++ A A+ +T+E +F LA + K+ + SRC +T Q+
Sbjct: 126 DEVHMLSKSAFNAMLKTLEEPPEHVKFILATTDPHKVPVTVLSRCLQFVLRNMTAQQVAD 185
Query: 163 KVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNL-QSTHNGFGHVTAEYV 213
+ + + E I++ L+ + A G MR AL+ L Q+ G G V V
Sbjct: 186 HLAHVLDSEKIAYEPPALQLLGRAAAGSMRDALSLLDQAIALGSGKVAENDV 237
>gnl|CDD|184920 PRK14956, PRK14956, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 484
Score = 82.7 bits (204), Expect = 1e-17
Identities = 64/216 (29%), Positives = 100/216 (46%), Gaps = 27/216 (12%)
Query: 3 KYRPQTFSDIVGNEDTVERLKVFSSSGNVPNI-IISGPPGVGKTTTILCLARIL------ 55
KYRPQ F D++ + + L+ SG + + I GP GVGKTT LA+ L
Sbjct: 11 KYRPQFFRDVIHQDLAIGALQNALKSGKIGHAYIFFGPRGVGKTTIARILAKRLNCENPI 70
Query: 56 -------------LGPSFKDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPP--GRHKIV 100
+ VLE++A+++RGI+ +R + V P G++K+
Sbjct: 71 GNEPCNECTSCLEITKGISSDVLEIDAASNRGIENIRE-----LRDNVKFAPMGGKYKVY 125
Query: 101 ILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQL 160
I+DE +TD + AL +T+E F LA KI E I SRC + K+ + L
Sbjct: 126 IIDEVHMLTDQSFNALLKTLEEPPAHIVFILATTEFHKIPETILSRCQDFIFKKVPLSVL 185
Query: 161 LSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALN 196
++C+ EN+ + +GL I G +R L+
Sbjct: 186 QDYSEKLCKIENVQYDQEGLFWIAKKGDGSVRDMLS 221
>gnl|CDD|237874 PRK14971, PRK14971, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 614
Score = 81.7 bits (202), Expect = 3e-17
Identities = 66/216 (30%), Positives = 104/216 (48%), Gaps = 28/216 (12%)
Query: 3 KYRPQTFSDIVGNEDTVERLKVFSSSGNVPN-IIISGPPGVGKTT-------TILCLARI 54
KYRP TF +VG E LK ++ + + + GP GVGKTT TI C
Sbjct: 10 KYRPSTFESVVGQEALTTTLKNAIATNKLAHAYLFCGPRGVGKTTCARIFAKTINCQNLT 69
Query: 55 LLGP---------SFKDA----VLELNASNDRGIDTVRNKIKMFAQQKVTLPP--GRHKI 99
G +F + + EL+A+++ +D +RN I ++V +PP G++KI
Sbjct: 70 ADGEACNECESCVAFNEQRSYNIHELDAASNNSVDDIRNLI-----EQVRIPPQIGKYKI 124
Query: 100 VILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQ 159
I+DE ++ A A +T+E + F LA KI+ I SRC + +N++ A
Sbjct: 125 YIIDEVHMLSQAAFNAFLKTLEEPPSYAIFILATTEKHKILPTILSRCQIFDFNRIQVAD 184
Query: 160 LLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQAL 195
+++ + + KE I+ + L I A G MR AL
Sbjct: 185 IVNHLQYVASKEGITAEPEALNVIAQKADGGMRDAL 220
>gnl|CDD|235845 PRK06647, PRK06647, DNA polymerase III subunits gamma and tau;
Validated.
Length = 563
Score = 79.8 bits (197), Expect = 1e-16
Identities = 59/214 (27%), Positives = 105/214 (49%), Gaps = 27/214 (12%)
Query: 3 KYRPQTFSDIVGNEDTVERLKVFSSSGNVPNI-IISGPPGVGKTTTILCLARIL---LGP 58
K RP+ F+ + G + VE LK S + N I SGP GVGKT++ AR L GP
Sbjct: 9 KRRPRDFNSLEGQDFVVETLKHSIESNKIANAYIFSGPRGVGKTSSARAFARCLNCVNGP 68
Query: 59 ---------SFKDA-------VLELNASNDRGIDTVRNKIKMFAQQKVTLPP--GRHKIV 100
S K V+E++ +++ + VR +IK +++ PP R+++
Sbjct: 69 TPMPCGECSSCKSIDNDNSLDVIEIDGASNTSVQDVR-QIK----EEIMFPPASSRYRVY 123
Query: 101 ILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQL 160
I+DE +++ A AL +T+E F A K+ I+SRC + L+ ++
Sbjct: 124 IIDEVHMLSNSAFNALLKTIEEPPPYIVFIFATTEVHKLPATIKSRCQHFNFRLLSLEKI 183
Query: 161 LSKVIEICEKENISHTNDGLEAIVFTAQGDMRQA 194
+ + ++C ++ I + ++ L+ I + + G +R A
Sbjct: 184 YNMLKKVCLEDQIKYEDEALKWIAYKSTGSVRDA 217
>gnl|CDD|225165 COG2256, MGS1, ATPase related to the helicase subunit of the
Holliday junction resolvase [DNA replication,
recombination, and repair].
Length = 436
Score = 79.2 bits (196), Expect = 2e-16
Identities = 56/207 (27%), Positives = 95/207 (45%), Gaps = 19/207 (9%)
Query: 2 EKYRPQTFSDIVGNEDTVERLKVFS---SSGNVPNIIISGPPGVGKTTTILCLARILLGP 58
E+ RP++ ++VG E + K +G++ ++I+ GPPG GKTT LAR++ G
Sbjct: 16 ERLRPKSLDEVVGQEHLLGEGKPLRRAVEAGHLHSMILWGPPGTGKTT----LARLIAG- 70
Query: 59 SFKDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRR 118
+ A L+A G+ +R I+ + + GR I+ LDE Q AL
Sbjct: 71 TTNAAFEALSAVTS-GVKDLREIIE---EARKNRLLGRRTILFLDEIHRFNKAQQDALLP 126
Query: 119 TMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDA---QLLSKVIEICEK----E 171
+E + A N S ++ + SR + L+ +LL + + E+ +
Sbjct: 127 HVENGTIILIGATTENPSFELNPALLSRARVFELKPLSSEDIKKLLKRALLDEERGLGGQ 186
Query: 172 NISHTNDGLEAIVFTAQGDMRQALNNL 198
I + L+ +V + GD R+ALN L
Sbjct: 187 IIVLDEEALDYLVRLSNGDARRALNLL 213
>gnl|CDD|184923 PRK14959, PRK14959, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 624
Score = 77.8 bits (191), Expect = 6e-16
Identities = 60/219 (27%), Positives = 104/219 (47%), Gaps = 29/219 (13%)
Query: 3 KYRPQTFSDIVGNEDTVERLKVFSSSGN--VPNIIISGPPGVGKTTTILCLARIL---LG 57
+YRPQTF+++ G E TV+ + ++ N P + SG GVGKTT A+ L
Sbjct: 9 RYRPQTFAEVAGQE-TVKAILSRAAQENRVAPAYLFSGTRGVGKTTIARIFAKALNCETA 67
Query: 58 PSFKDA----------------VLELNASNDRGIDTVRNKIKMFAQQKVTLPP--GRHKI 99
P+ + V+E++ +++RGID + ++ + P GR+K+
Sbjct: 68 PTGEPCNTCEQCRKVTQGMHVDVVEIDGASNRGIDDAKR-----LKEAIGYAPMEGRYKV 122
Query: 100 VILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQ 159
I+DEA +T A AL +T+E F LA K I SRC + +L++A
Sbjct: 123 FIIDEAHMLTREAFNALLKTLEEPPARVTFVLATTEPHKFPVTIVSRCQHFTFTRLSEAG 182
Query: 160 LLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNL 198
L + + ++ +E + + + I A G +R +++ L
Sbjct: 183 LEAHLTKVLGREGVDYDPAAVRLIARRAAGSVRDSMSLL 221
>gnl|CDD|236267 PRK08451, PRK08451, DNA polymerase III subunits gamma and tau;
Validated.
Length = 535
Score = 77.4 bits (191), Expect = 1e-15
Identities = 65/232 (28%), Positives = 109/232 (46%), Gaps = 24/232 (10%)
Query: 3 KYRPQTFSDIVGNEDTVERLKVFSSSGNVPNI-IISGPPGVGKTTTILCLARILL---GP 58
KYRP+ F +++G E + L + + + + + SG G GKT++ AR L+ GP
Sbjct: 7 KYRPKHFDELIGQESVSKTLSLALDNNRLAHAYLFSGLRGSGKTSSARIFARALVCEQGP 66
Query: 59 SFKDA----------------VLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVIL 102
S ++E++A+++RGID +R I+ Q K R KI I+
Sbjct: 67 SSTPCDTCIQCQSALENRHIDIIEMDAASNRGIDDIRELIE---QTKYKPSMARFKIFII 123
Query: 103 DEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQLLS 162
DE +T A AL +T+E + +F LA + K+ I SR R+ ++ ++S
Sbjct: 124 DEVHMLTKEAFNALLKTLEEPPSYVKFILATTDPLKLPATILSRTQHFRFKQIPQNSIIS 183
Query: 163 KVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNL-QSTHNGFGHVTAEYV 213
+ I EKE +S+ + LE + + G +R L L Q+ +T V
Sbjct: 184 HLKTILEKEGVSYEPEALEILARSGNGSLRDTLTLLDQAIIYCKNAITESKV 235
>gnl|CDD|235638 PRK05896, PRK05896, DNA polymerase III subunits gamma and tau;
Validated.
Length = 605
Score = 77.2 bits (190), Expect = 1e-15
Identities = 61/218 (27%), Positives = 99/218 (45%), Gaps = 23/218 (10%)
Query: 2 EKYRPQTFSDIVGNEDTVERLKVFSSSGNVPN-IIISGPPGVGKTTTILCLARIL--LGP 58
KYRP F I+G E + L + + + I SGP G+GKT+ A+ + L P
Sbjct: 8 RKYRPHNFKQIIGQELIKKILVNAILNNKLTHAYIFSGPRGIGKTSIAKIFAKAINCLNP 67
Query: 59 SFKDA-----------------VLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVI 101
D ++EL+A+++ G+D +RN I T ++K+ I
Sbjct: 68 KDGDCCNSCSVCESINTNQSVDIVELDAASNNGVDEIRNIIDNINYLPTTF---KYKVYI 124
Query: 102 LDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQLL 161
+DEA ++ A AL +T+E F A +KI I SRC + KL +++L
Sbjct: 125 IDEAHMLSTSAWNALLKTLEEPPKHVVFIFATTEFQKIPLTIISRCQRYNFKKLNNSELQ 184
Query: 162 SKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQ 199
+ I +KE I ++ ++ I A G +R L+ L
Sbjct: 185 ELLKSIAKKEKIKIEDNAIDKIADLADGSLRDGLSILD 222
>gnl|CDD|235505 PRK05563, PRK05563, DNA polymerase III subunits gamma and tau;
Validated.
Length = 559
Score = 76.8 bits (190), Expect = 1e-15
Identities = 78/297 (26%), Positives = 126/297 (42%), Gaps = 86/297 (28%)
Query: 3 KYRPQTFSDIVGNEDTVERLKVFSSSGNVPNIII----------SGPPGVGKTTTILCLA 52
K+RPQTF D+VG E + LK N I SGP G GKT+ A
Sbjct: 9 KWRPQTFEDVVGQEHITKTLK---------NAIKQGKISHAYLFSGPRGTGKTSAAKIFA 59
Query: 53 RILLGPSFKDA-------------------VLELNASNDRGIDTVRNKIKMFAQQKVTLP 93
+ + + D V+E++A+++ G+D +R+ KV
Sbjct: 60 KAVNCLNPPDGEPCNECEICKAITNGSLMDVIEIDAASNNGVDEIRDIR-----DKVKYA 114
Query: 94 P--GRHKIVILDEADSMTDGAQQALRRTME------IYSNTTRFALACNNSEKIIEPIQS 145
P ++K+ I+DE ++ GA AL +T+E I F LA KI I S
Sbjct: 115 PSEAKYKVYIIDEVHMLSTGAFNALLKTLEEPPAHVI------FILATTEPHKIPATILS 168
Query: 146 RCAMLRYN--KLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNL-Q--S 200
RC R++ +++ ++ ++ I +KE I + ++ L I A+G MR AL+ L Q S
Sbjct: 169 RCQ--RFDFKRISVEDIVERLKYILDKEGIEYEDEALRLIARAAEGGMRDALSILDQAIS 226
Query: 201 THNGF----------GHVTAEYVFKVCDEPHPLAVKEMLLNCVEGNMKDSYKIIHHL 247
+G G V+ E + ++ VEG++ + KI+ L
Sbjct: 227 FGDGKVTYEDALEVTGSVSQEALDD------------LVDAIVEGDVAKALKILEEL 271
>gnl|CDD|184925 PRK14961, PRK14961, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 363
Score = 74.8 bits (184), Expect = 4e-15
Identities = 71/273 (26%), Positives = 125/273 (45%), Gaps = 35/273 (12%)
Query: 3 KYRPQTFSDIVGNEDTVERLKVFSSSGNVPNI-IISGPPGVGKTTTILCLAR-------I 54
K+RPQ F DI+G + V + S G + + ++SG GVGKTT LA+ I
Sbjct: 9 KWRPQYFRDIIGQKHIVTAISNGLSLGRIHHAWLLSGTRGVGKTTIARLLAKSLNCQNGI 68
Query: 55 LLGP-------------SFKDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVI 101
P D ++E++A++ ++ +R ++ + R K+ +
Sbjct: 69 TSNPCRKCIICKEIEKGLCLD-LIEIDAASRTKVEEMR---EILDNIYYSPSKSRFKVYL 124
Query: 102 LDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQLL 161
+DE ++ + AL +T+E +F LA + EKI + I SRC + +++ ++
Sbjct: 125 IDEVHMLSRHSFNALLKTLEEPPQHIKFILATTDVEKIPKTILSRCLQFKLKIISEEKIF 184
Query: 162 SKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNL-QSTHNGFGHVTAEYVFK---VC 217
+ + I KE+I L+ I + A G MR ALN L + + G G++ + V +
Sbjct: 185 NFLKYILIKESIDTDEYALKLIAYHAHGSMRDALNLLEHAINLGKGNINIKNVTDMLGLL 244
Query: 218 DEPHPLAVKEMLLNCVEGNMKDSYKIIHHLYKL 250
+E + + LL KDS K + L K+
Sbjct: 245 NEKQSFLLTDALLK------KDSKKTMLLLNKI 271
>gnl|CDD|237057 PRK12323, PRK12323, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 700
Score = 73.8 bits (181), Expect = 2e-14
Identities = 61/224 (27%), Positives = 101/224 (45%), Gaps = 40/224 (17%)
Query: 3 KYRPQTFSDIVGNEDTVERLKVFSSSGNVPNI-IISGPPGVGKTTTILCLARIL------ 55
K+RP+ F+ +VG E V L + + + +G GVGKTT L+RIL
Sbjct: 9 KWRPRDFTTLVGQEHVVRALTHALEQQRLHHAYLFTGTRGVGKTT----LSRILAKSLNC 64
Query: 56 LGPS-----------------------FKDAVLELNASNDRGIDTVRNKIKMFAQQKVTL 92
G F D +E++A+++RG+D ++ + V
Sbjct: 65 TGADGEGGITAQPCGQCRACTEIDAGRFVD-YIEMDAASNRGVD----EMAQLLDKAVYA 119
Query: 93 P-PGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLR 151
P GR K+ ++DE +T+ A A+ +T+E +F LA + +KI + SRC
Sbjct: 120 PTAGRFKVYMIDEVHMLTNHAFNAMLKTLEEPPEHVKFILATTDPQKIPVTVLSRCLQFN 179
Query: 152 YNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQAL 195
++ ++S + I +E I+H + L + AQG MR AL
Sbjct: 180 LKQMPPGHIVSHLDAILGEEGIAHEVNALRLLAQAAQGSMRDAL 223
>gnl|CDD|237866 PRK14952, PRK14952, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 584
Score = 73.0 bits (179), Expect = 2e-14
Identities = 65/237 (27%), Positives = 104/237 (43%), Gaps = 35/237 (14%)
Query: 3 KYRPQTFSDIVGNEDTVERLKVFSSSGNVPNI-IISGPPGVGKTTTILCLARIL------ 55
KYRP TF+++VG E E L +G + + + SGP G GKT++ LAR L
Sbjct: 6 KYRPATFAEVVGQEHVTEPLSSALDAGRINHAYLFSGPRGCGKTSSARILARSLNCAQGP 65
Query: 56 -------------LGPSFKDA--VLELNASNDRGIDTVRNKIKMFAQQKVTLPPG--RHK 98
L P+ + V+EL+A++ G+D R + + P R++
Sbjct: 66 TATPCGVCESCVALAPNGPGSIDVVELDAASHGGVDDTRE-----LRDRAFYAPAQSRYR 120
Query: 99 IVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDA 158
I I+DEA +T AL + +E F A EK++ I+SR + L
Sbjct: 121 IFIVDEAHMVTTAGFNALLKIVEEPPEHLIFIFATTEPEKVLPTIRSRTHHYPFRLLPPR 180
Query: 159 QLLSKVIEICEKENISHTNDGLEAIVFTAQG----DMRQALNNLQSTHNGFGHVTAE 211
+ + + ICE+E + +D + +V A G D L+ L + HVT +
Sbjct: 181 TMRALIARICEQEGVV-VDDAVYPLVIRAGGGSPRDTLSVLDQLLAGAAD-THVTYQ 235
>gnl|CDD|184921 PRK14957, PRK14957, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 546
Score = 71.7 bits (175), Expect = 7e-14
Identities = 61/220 (27%), Positives = 104/220 (47%), Gaps = 31/220 (14%)
Query: 3 KYRPQTFSDIVGNEDTVERLKVFSSSGNVPNI-IISGPPGVGKTTTILCLARILL----- 56
KYRPQ+F+++ G + + L + V + + +G GVGKTT LA+ L
Sbjct: 9 KYRPQSFAEVAGQQHALNSLVHALETQKVHHAYLFTGTRGVGKTTLGRLLAKCLNCKTGV 68
Query: 57 ---------------GPSFKDAVLELNASNDRGIDTVR---NKIKMFAQQKVTLPPGRHK 98
SF D ++E++A++ G++ + + I+ Q GR+K
Sbjct: 69 TAEPCNKCENCVAINNNSFID-LIEIDAASRTGVEETKEILDNIQYMPSQ------GRYK 121
Query: 99 IVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDA 158
+ ++DE ++ + AL +T+E +F LA + KI I SRC L ++ A
Sbjct: 122 VYLIDEVHMLSKQSFNALLKTLEEPPEYVKFILATTDYHKIPVTILSRCIQLHLKHISQA 181
Query: 159 QLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNL 198
+ ++ I KENI+ LE I + A+G +R AL+ L
Sbjct: 182 DIKDQLKIILAKENINSDEQSLEYIAYHAKGSLRDALSLL 221
>gnl|CDD|237873 PRK14969, PRK14969, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 527
Score = 70.2 bits (172), Expect = 2e-13
Identities = 62/218 (28%), Positives = 100/218 (45%), Gaps = 33/218 (15%)
Query: 3 KYRPQTFSDIVGNEDTVERLKVFSSSGNVPNI-IISGPPGVGKTTTILCLARILL----- 56
K+RP++FS++VG E V L + + + +G GVGKTT LARIL
Sbjct: 9 KWRPKSFSELVGQEHVVRALTNALEQQRLHHAYLFTGTRGVGKTT----LARILAKSLNC 64
Query: 57 -------------------GPSFKDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRH 97
F D ++E++A+++ +D +R + AQ T GR
Sbjct: 65 ETGVTATPCGVCSACLEIDSGRFVD-LIEVDAASNTQVDAMRELLDN-AQYAPTR--GRF 120
Query: 98 KIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTD 157
K+ I+DE ++ A A+ +T+E +F LA + +KI + SRC ++
Sbjct: 121 KVYIIDEVHMLSKSAFNAMLKTLEEPPEHVKFILATTDPQKIPVTVLSRCLQFNLKQMPP 180
Query: 158 AQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQAL 195
++S + I E+ENI L+ + A G MR AL
Sbjct: 181 PLIVSHLQHILEQENIPFDATALQLLARAAAGSMRDAL 218
>gnl|CDD|184918 PRK14954, PRK14954, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 620
Score = 70.0 bits (171), Expect = 3e-13
Identities = 63/223 (28%), Positives = 91/223 (40%), Gaps = 37/223 (16%)
Query: 3 KYRPQTFSDIVGNEDTVERLKVFSSSGNVPN-IIISGPPGVGKTTTILCLA------RIL 55
KYRP F+DI E ++ V + I SG GVGKTT A R++
Sbjct: 9 KYRPSKFADITAQEHITHTIQNSLRMDRVGHGYIFSGLRGVGKTTAARVFAKAVNCQRMI 68
Query: 56 LGPSFKDAVLE----------------LN------ASNDR--GIDTVRNKIKMFAQQKVT 91
P + V E LN ASN+ I +R ++ + QK
Sbjct: 69 DDPVYLQEVTEPCGECESCRDFDAGTSLNISEFDAASNNSVDDIRQLRENVR-YGPQK-- 125
Query: 92 LPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLR 151
GR+++ I+DE ++ A A +T+E F A KI I SRC
Sbjct: 126 ---GRYRVYIIDEVHMLSTAAFNAFLKTLEEPPPHAIFIFATTELHKIPATIASRCQRFN 182
Query: 152 YNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQA 194
+ ++ ++ S++ IC E I D L+ I AQG MR A
Sbjct: 183 FKRIPLDEIQSQLQMICRAEGIQIDADALQLIARKAQGSMRDA 225
>gnl|CDD|184919 PRK14955, PRK14955, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 397
Score = 69.5 bits (170), Expect = 3e-13
Identities = 60/225 (26%), Positives = 93/225 (41%), Gaps = 41/225 (18%)
Query: 3 KYRPQTFSDIVGNEDTVERLKVFSSSGNVPN-IIISGPPGVGKTTTILCLARIL------ 55
KYRP+ F+DI E ++ G V + I SG GVGKTT A+ +
Sbjct: 9 KYRPKKFADITAQEHITRTIQNSLRMGRVGHGYIFSGLRGVGKTTAARVFAKAVNCQRMI 68
Query: 56 -----------------------LGPSFKDAVLELNASNDRGID---TVRNKIKMFAQQK 89
G S + E +A+++ +D +R ++ + QK
Sbjct: 69 DDADYLQEVTEPCGECESCRDFDAGTSLN--ISEFDAASNNSVDDIRLLRENVR-YGPQK 125
Query: 90 VTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAM 149
GR+++ I+DE ++ A A +T+E F A KI I SRC
Sbjct: 126 -----GRYRVYIIDEVHMLSIAAFNAFLKTLEEPPPHAIFIFATTELHKIPATIASRCQR 180
Query: 150 LRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQA 194
+ ++ ++ ++ ICE E IS D L+ I AQG MR A
Sbjct: 181 FNFKRIPLEEIQQQLQGICEAEGISVDADALQLIGRKAQGSMRDA 225
>gnl|CDD|180643 PRK06645, PRK06645, DNA polymerase III subunits gamma and tau;
Validated.
Length = 507
Score = 69.1 bits (169), Expect = 5e-13
Identities = 58/221 (26%), Positives = 100/221 (45%), Gaps = 27/221 (12%)
Query: 3 KYRPQTFSDIVGNEDTVERLKVFSSSGNVPN-IIISGPPGVGKTT-------TILCLARI 54
KYRP F+++ G E V+ L + + +++G GVGKTT + C A I
Sbjct: 14 KYRPSNFAELQGQEVLVKVLSYTILNDRLAGGYLLTGIRGVGKTTSARIIAKAVNCSALI 73
Query: 55 LLGPSFKDA----------------VLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHK 98
+ K ++E++A++ +D +R I+ A+ K G+HK
Sbjct: 74 TENTTIKTCEQCTNCISFNNHNHPDIIEIDAASKTSVDDIRRIIES-AEYKPLQ--GKHK 130
Query: 99 IVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDA 158
I I+DE ++ GA AL +T+E F A +KI I SRC +L+
Sbjct: 131 IFIIDEVHMLSKGAFNALLKTLEEPPPHIIFIFATTEVQKIPATIISRCQRYDLRRLSFE 190
Query: 159 QLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQ 199
++ + I ++EN+ + L I + ++G R A++ L
Sbjct: 191 EIFKLLEYITKQENLKTDIEALRIIAYKSEGSARDAVSILD 231
>gnl|CDD|236382 PRK09111, PRK09111, DNA polymerase III subunits gamma and tau;
Validated.
Length = 598
Score = 68.4 bits (168), Expect = 8e-13
Identities = 79/263 (30%), Positives = 121/263 (46%), Gaps = 61/263 (23%)
Query: 3 KYRPQTFSDIVGNEDTVERLKVFSSSGNVPN-IIISGPPGVGKTTTILCLARIL------ 55
KYRPQTF D++G E V L +G + +++G GVGKTTT ARIL
Sbjct: 17 KYRPQTFDDLIGQEAMVRTLTNAFETGRIAQAFMLTGVRGVGKTTT----ARILARALNY 72
Query: 56 ------LGPSFK--------DA--------VLELNASNDRGIDTVRNKIKMFAQQKVTLP 93
GP+ A VLE++A++ G+D +R I + V
Sbjct: 73 EGPDGDGGPTIDLCGVGEHCQAIMEGRHVDVLEMDAASHTGVDDIREII-----ESVRYR 127
Query: 94 P--GRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQ--SRCAM 149
P R+K+ I+DE ++ A AL +T+E +F A K+ P+ SRC
Sbjct: 128 PVSARYKVYIIDEVHMLSTAAFNALLKTLEEPPPHVKFIFATTEIRKV--PVTVLSRCQ- 184
Query: 150 LRYN-KLTDAQLLSKVIE-ICEKENISHTNDGLEAIVFTAQGDMRQALNNL-QSTHNGFG 206
R++ + +A +L+ + I KE + ++ L I A+G +R L+ L Q+ +G G
Sbjct: 185 -RFDLRRIEADVLAAHLSRIAAKEGVEVEDEALALIARAAEGSVRDGLSLLDQAIAHGAG 243
Query: 207 HVTAEYVFKVCDEPHPLAVKEML 229
VTAE AV++ML
Sbjct: 244 EVTAE------------AVRDML 254
>gnl|CDD|235906 PRK07003, PRK07003, DNA polymerase III subunits gamma and tau;
Validated.
Length = 830
Score = 66.4 bits (162), Expect = 4e-12
Identities = 61/221 (27%), Positives = 99/221 (44%), Gaps = 39/221 (17%)
Query: 3 KYRPQTFSDIVGNEDTVERLKVFSSSGNVPNI-IISGPPGVGKTTTILCLARILLGP--- 58
K+RP+ F+ +VG E V L G + + + +G GVGKTT L+RI
Sbjct: 9 KWRPKDFASLVGQEHVVRALTHALDGGRLHHAYLFTGTRGVGKTT----LSRIFAKALNC 64
Query: 59 ---------------------SFKDAVLELNASNDRGIDTVRNKIKMFA--QQKVTLP-P 94
F D V E++A+++RG+D +M A ++ V P
Sbjct: 65 ETGVTSQPCGVCRACREIDEGRFVDYV-EMDAASNRGVD------EMAALLERAVYAPVD 117
Query: 95 GRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNK 154
R K+ ++DE +T+ A A+ +T+E +F LA + +KI + SRC +
Sbjct: 118 ARFKVYMIDEVHMLTNHAFNAMLKTLEEPPPHVKFILATTDPQKIPVTVLSRCLQFNLKQ 177
Query: 155 LTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQAL 195
+ ++S + I +E I+ L + AQG MR AL
Sbjct: 178 MPAGHIVSHLERILGEERIAFEPQALRLLARAAQGSMRDAL 218
>gnl|CDD|237354 PRK13341, PRK13341, recombination factor protein RarA/unknown
domain fusion protein; Reviewed.
Length = 725
Score = 66.2 bits (162), Expect = 5e-12
Identities = 57/218 (26%), Positives = 95/218 (43%), Gaps = 38/218 (17%)
Query: 2 EKYRPQTFSDIVGN-----EDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILL 56
++ RP+T + VG E + R + + V ++I+ GPPGVGKTT LARI+
Sbjct: 20 DRLRPRTLEEFVGQDHILGEGRLLRRAI--KADRVGSLILYGPPGVGKTT----LARIIA 73
Query: 57 GPSFKDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRH---KIVILDEADSMTDGAQ 113
+ LNA G+ +R ++ A++++ RH I+ +DE Q
Sbjct: 74 N-HTRAHFSSLNAVL-AGVKDLRAEVDR-AKERL----ERHGKRTILFIDEVHRFNKAQQ 126
Query: 114 QAL-----RRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDA---QLLSKVI 165
AL T+ + TT N ++ + + SR + R L+D QLL + +
Sbjct: 127 DALLPWVENGTITLIGATTE-----NPYFEVNKALVSRSRLFRLKSLSDEDLHQLLKRAL 181
Query: 166 EICE----KENISHTNDGLEAIVFTAQGDMRQALNNLQ 199
+ E + + + +V A GD R LN L+
Sbjct: 182 QDKERGYGDRKVDLEPEAEKHLVDVANGDARSLLNALE 219
>gnl|CDD|221959 pfam13177, DNA_pol3_delta2, DNA polymerase III, delta subunit. DNA
polymerase III, delta subunit (EC 2.7.7.7) is required
for, along with delta' subunit, the assembly of the
processivity factor beta(2) onto primed DNA in the DNA
polymerase III holoenzyme-catalyzed reaction. The delta
subunit is also known as HolA.
Length = 161
Score = 62.6 bits (153), Expect = 6e-12
Identities = 39/164 (23%), Positives = 69/164 (42%), Gaps = 24/164 (14%)
Query: 14 GNEDTVERLKVFSSSGNVPN-IIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASND 72
G ++ LK + + + SGP GVGK L A+ L + +D +
Sbjct: 1 GQPKVIKLLKNSIKKNKLSHAYLFSGPDGVGKLELALEFAKALFCENPQDDEPCGECKSC 60
Query: 73 R--------------------GIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGA 112
+ ID +R + +K G+ K+ I+++A+ MT+ A
Sbjct: 61 KRIENGNHPDVIIIEPEGKSIKIDQIRE-LIEEFSKKPFE--GKKKVYIIEDAEKMTESA 117
Query: 113 QQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLT 156
AL +T+E T F L +N K++ I+SRC ++ + L+
Sbjct: 118 ANALLKTLEEPPENTYFILLTSNPNKLLPTIRSRCQVINFKPLS 161
>gnl|CDD|184922 PRK14958, PRK14958, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 509
Score = 65.1 bits (158), Expect = 8e-12
Identities = 75/310 (24%), Positives = 127/310 (40%), Gaps = 43/310 (13%)
Query: 3 KYRPQTFSDIVGNEDTVERLKVFSSSGNVPNI-IISGPPGVGKTTTILCLARILLGPSFK 61
K+RP+ F +++G V L + + + +G GVGKTT LA+ L
Sbjct: 9 KWRPRCFQEVIGQAPVVRALSNALDQQYLHHAYLFTGTRGVGKTTISRILAKCLNCEKGV 68
Query: 62 DAVLELNASNDRGID------------TVRNKIKMFAQQKVTLP----PGRHKIVILDEA 105
A + N R ID R K++ + +P GR K+ ++DE
Sbjct: 69 SANPCNDCENCREIDEGRFPDLFEVDAASRTKVEDTRELLDNIPYAPTKGRFKVYLIDEV 128
Query: 106 DSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQLLSKVI 165
++ + AL +T+E + +F LA + K+ + SRC +L Q+ +
Sbjct: 129 HMLSGHSFNALLKTLEEPPSHVKFILATTDHHKLPVTVLSRCLQFHLAQLPPLQIAAHCQ 188
Query: 166 EICEKENISHTNDGLEAIVFTAQGDMRQALNNL-QSTHNGFGHVTAEYVFKVCDEPHPLA 224
+ ++EN+ N L+ + A G +R AL+ L QS G G V V + PL
Sbjct: 189 HLLKEENVEFENAALDLLARAANGSVRDALSLLDQSIAYGNGKVLIADVKTMLGTIEPLL 248
Query: 225 VKEM-----------LLNCV----------EGNMKDSYKIIHHLYKLGYAPEDIIGN--- 260
+ ++ LL CV + D ++H + + PE +I N
Sbjct: 249 LFDILEALAAKAGDRLLGCVTRLVEQGVDFSNALADLLSLLHQIAIIQTVPEALIENDSE 308
Query: 261 -IFRVAKTLD 269
+ ++AK LD
Sbjct: 309 QLRQLAKLLD 318
>gnl|CDD|233087 TIGR00678, holB, DNA polymerase III, delta' subunit. This model
describes the N-terminal half of the delta' subunit of
DNA polymerase III. Delta' is homologous to the gamma
and tau subunits, which form an outgroup for
phylogenetic comparison. The gamma/tau branch of the
tree is much more tighly conserved than the delta'
branch, and some members of that branch score more
highly against this model than some proteins
classisified as delta'. The noise cutoff is set to
detect weakly scoring delta' subunits rather than to
exclude gamma/tau subunits. At position 126-127 of the
seed alignment, this family lacks the HM motif of
gamma/tau; at 132 it has a near-invariant A vs. an
invariant F in gamma/tau [DNA metabolism, DNA
replication, recombination, and repair].
Length = 188
Score = 61.1 bits (149), Expect = 3e-11
Identities = 37/147 (25%), Positives = 63/147 (42%), Gaps = 23/147 (15%)
Query: 35 IISGPPGVGKTTTILCLARILLGPSFKDA-------------------VLELNASNDR-G 74
+ +GP GVGK L LA+ LL + L
Sbjct: 18 LFAGPEGVGKELLALALAKALLCEQPGGGEPCGECPSCRLIEAGNHPDLHRLEPEGQSIK 77
Query: 75 IDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACN 134
+D VR ++ ++ ++VI+++A+ M + A AL +T+E T F L
Sbjct: 78 VDQVRELVEFLSRTPQE---SGRRVVIIEDAERMNEAAANALLKTLEEPPPNTLFILITP 134
Query: 135 NSEKIIEPIQSRCAMLRYNKLTDAQLL 161
+ EK++ I+SRC +L + L++ LL
Sbjct: 135 SPEKLLPTIRSRCQVLPFPPLSEEALL 161
>gnl|CDD|237865 PRK14951, PRK14951, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 618
Score = 63.2 bits (154), Expect = 4e-11
Identities = 70/261 (26%), Positives = 119/261 (45%), Gaps = 57/261 (21%)
Query: 3 KYRPQTFSDIVGNEDTVERLKVFSSSGNVPNI-IISGPPGVGKTTTILCLARIL------ 55
KYRP++FS++VG E V+ L + + + + +G GVGKTT ++RIL
Sbjct: 9 KYRPRSFSEMVGQEHVVQALTNALTQQRLHHAYLFTGTRGVGKTT----VSRILAKSLNC 64
Query: 56 LGPS-----------------------FKDAVLELNASNDRGIDTVRNKIKMFAQQKVTL 92
GP F D EL+A+++RG+D +++ +Q V
Sbjct: 65 QGPDGQGGITATPCGVCQACRDIDSGRFVDYT-ELDAASNRGVD----EVQQLLEQAVYK 119
Query: 93 P-PGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLR 151
P GR K+ ++DE +T+ A A+ +T+E +F LA + +K+ + SRC L+
Sbjct: 120 PVQGRFKVFMIDEVHMLTNTAFNAMLKTLEEPPEYLKFVLATTDPQKVPVTVLSRC--LQ 177
Query: 152 YN--KLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALN-NLQSTHNGFGHV 208
+N + +L + ++ EN+ L + A+G MR AL+ Q+ G G +
Sbjct: 178 FNLRPMAPETVLEHLTQVLAAENVPAEPQALRLLARAARGSMRDALSLTDQAIAFGSGQL 237
Query: 209 TAEYVFKVCDEPHPLAVKEML 229
AV++ML
Sbjct: 238 QEA------------AVRQML 246
>gnl|CDD|237868 PRK14960, PRK14960, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 702
Score = 62.4 bits (151), Expect = 1e-10
Identities = 85/332 (25%), Positives = 146/332 (43%), Gaps = 49/332 (14%)
Query: 3 KYRPQTFSDIVGNEDTVERLKVFSSSGNVPNI-IISGPPGVGKTTTILCLARIL-----L 56
KYRP+ F+++VG L G + + + +G GVGKTT LA+ L +
Sbjct: 8 KYRPRNFNELVGQNHVSRALSSALERGRLHHAYLFTGTRGVGKTTIARILAKCLNCETGV 67
Query: 57 GPSFKDAVLELNASND-RGIDTV------RNKIKMFAQQKVTLP----PGRHKIVILDEA 105
+ + A N+ R ID + R K++ + +P GR K+ ++DE
Sbjct: 68 TSTPCEVCATCKAVNEGRFIDLIEIDAASRTKVEDTRELLDNVPYAPTQGRFKVYLIDEV 127
Query: 106 DSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQLLSKVI 165
++ + AL +T+E +F A + +K+ + SRC L ++ +
Sbjct: 128 HMLSTHSFNALLKTLEEPPEHVKFLFATTDPQKLPITVISRCLQFTLRPLAVDEITKHLG 187
Query: 166 EICEKENISHTNDGLEAIVFTAQGDMRQALN-NLQSTHNGFGHVTAEYVFKVCDEPHPLA 224
I EKE I+ D + I +AQG +R AL+ Q+ G G V H
Sbjct: 188 AILEKEQIAADQDAIWQIAESAQGSLRDALSLTDQAIAYGQGAV------------HHQD 235
Query: 225 VKEM-----------LLNCVEGNMKDSYKIIHHLYKLGYAPEDIIGNIFRVAKTLDIPEP 273
VKEM L+ V N ++ K+ L + Y D+ + ++ TL
Sbjct: 236 VKEMLGLIDRTIIYDLILAVHQNQRE--KVSQLLLQFRYQALDVSLVLDQLISTLH---- 289
Query: 274 LKLSIIQEIGNVHLRISEGVNS-LLQLSGLLA 304
+L+++Q + + L+ SE +N+ +LQLS L++
Sbjct: 290 -ELALLQYLPELGLKYSEEINAKILQLSKLIS 320
>gnl|CDD|214640 smart00382, AAA, ATPases associated with a variety of cellular
activities. AAA - ATPases associated with a variety of
cellular activities. This profile/alignment only detects
a fraction of this vast family. The poorly conserved
N-terminal helix is missing from the alignment.
Length = 148
Score = 57.0 bits (137), Expect = 4e-10
Identities = 29/132 (21%), Positives = 49/132 (37%), Gaps = 23/132 (17%)
Query: 33 NIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKIKMFAQQKVTL 92
I+I GPPG GKTT LAR L P V+ ++ + + + + +K +
Sbjct: 4 VILIVGPPGSGKTTLARALARELGPPGGG--VIYIDGEDILEEVLDQLLLIIVGGKKASG 61
Query: 93 PPG-------------RHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFA--------L 131
+ ++ILDE S+ D Q+AL +E L
Sbjct: 62 SGELRLRLALALARKLKPDVLILDEITSLLDAEQEALLLLLEELRLLLLLKSEKNLTVIL 121
Query: 132 ACNNSEKIIEPI 143
N+ + + +
Sbjct: 122 TTNDEKDLGPAL 133
>gnl|CDD|180132 PRK05564, PRK05564, DNA polymerase III subunit delta'; Validated.
Length = 313
Score = 59.3 bits (144), Expect = 5e-10
Identities = 46/155 (29%), Positives = 78/155 (50%), Gaps = 13/155 (8%)
Query: 9 FSDIVGNEDTVERLKVFSSSGNVPN-IIISGPPGVGKTTTILCLARILLG-PSFKDAV-- 64
F I+G+E+ R+K + II G G+GK+ +A +LG ++ V
Sbjct: 3 FHTIIGHENIKNRIKNSIIKNRFSHAHIIVGEDGIGKSLLAKEIALKILGKSQQREYVDI 62
Query: 65 LELNASNDR--GIDTVRNKIKMFAQQKVTLPP--GRHKIVILDEADSMTDGAQQALRRTM 120
+E N + G+D +RN I+ +V P G K++I+ ++ MT+ AQ A +T+
Sbjct: 63 IEFKPINKKSIGVDDIRNIIE-----EVNKKPYEGDKKVIIIYNSEKMTEQAQNAFLKTI 117
Query: 121 EIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKL 155
E L C N E+I++ I+SRC + + N+L
Sbjct: 118 EEPPKGVFIILLCENLEQILDTIKSRCQIYKLNRL 152
>gnl|CDD|215649 pfam00004, AAA, ATPase family associated with various cellular
activities (AAA). AAA family proteins often perform
chaperone-like functions that assist in the assembly,
operation, or disassembly of protein complexes.
Length = 131
Score = 55.7 bits (135), Expect = 9e-10
Identities = 23/137 (16%), Positives = 53/137 (38%), Gaps = 27/137 (19%)
Query: 34 IIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRG---IDTVRNKIKMFAQQKV 90
+++ GPPG GKTT +A+ L +E++ S ++ + ++F K
Sbjct: 1 LLLYGPPGTGKTTLAKAVAKEL-----GAPFIEISGSELVSKYVGESEKRLRELFEAAKK 55
Query: 91 TLPPGRHKIVILDEADSM-----------TDGAQQALRRTMEIYSNTTR---FALACNNS 136
P ++ +DE D++ + L ++ ++++ A N
Sbjct: 56 LAPC----VIFIDEIDALAGSRGSGGDSESRRVVNQLLTELDGFTSSLSKVIVIAATNRP 111
Query: 137 EKIIEPI-QSRCAMLRY 152
+K+ + + R +
Sbjct: 112 DKLDPALLRGRFDRIIE 128
>gnl|CDD|237862 PRK14948, PRK14948, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 620
Score = 57.3 bits (139), Expect = 4e-09
Identities = 59/218 (27%), Positives = 100/218 (45%), Gaps = 33/218 (15%)
Query: 3 KYRPQTFSDIVGNEDTVERLKVFSSSGNV-PNIIISGPPGVGKTTTILCLARILLGPSFK 61
KYRPQ F ++VG E LK S + P + +GP G GKT++ LA+ L +
Sbjct: 9 KYRPQRFDELVGQEAIATTLKNALISNRIAPAYLFTGPRGTGKTSSARILAKSLNCLNSD 68
Query: 62 DA---------------------VLELNASNDRGIDTVRNKIK--MFAQQKVTLPP--GR 96
V+E++A+++ G+D +R I+ FA P R
Sbjct: 69 KPTPEPCGKCELCRAIAAGNALDVIEIDAASNTGVDNIRELIERAQFA-------PVQAR 121
Query: 97 HKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLT 156
K+ ++DE ++ A AL +T+E F LA + ++++ I SRC + ++
Sbjct: 122 WKVYVIDECHMLSTAAFNALLKTLEEPPPRVVFVLATTDPQRVLPTIISRCQRFDFRRIP 181
Query: 157 DAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQA 194
++ + EI EKE+I + L + +QG +R A
Sbjct: 182 LEAMVQHLSEIAEKESIEIEPEALTLVAQRSQGGLRDA 219
>gnl|CDD|169667 PRK09112, PRK09112, DNA polymerase III subunit delta'; Validated.
Length = 351
Score = 53.9 bits (130), Expect = 4e-08
Identities = 51/225 (22%), Positives = 89/225 (39%), Gaps = 40/225 (17%)
Query: 6 PQTFSDIVGNEDTVERLKVFSSSGNVPN-IIISGPPGVGKTTTILCLA-RILLGPSFKDA 63
P + + G+E+ L G + + ++ GP G+GK T LA IL P +A
Sbjct: 19 PSENTRLFGHEEAEAFLAQAYREGKLHHALLFEGPEGIGKATLAFHLANHILSHPDPAEA 78
Query: 64 ------------------------VLELNASNDRG---------IDTVRNKIKMFAQQKV 90
+L + D +D +R +Q
Sbjct: 79 PETLADPDPASPVWRQIAQGAHPNLLHITRPFDEKTGKFKTAITVDEIRRVGHFLSQ--- 135
Query: 91 TLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAML 150
T G +IVI+D AD M A A+ +T+E F L ++S +++ I+SRC +
Sbjct: 136 TSGDGNWRIVIIDPADDMNRNAANAILKTLEEPPARALFILISHSSGRLLPTIRSRCQPI 195
Query: 151 RYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQAL 195
L D +L + + + + EA++ ++G +R+AL
Sbjct: 196 SLKPLDDDELKKALSHLGSSQGS--DGEITEALLQRSKGSVRKAL 238
>gnl|CDD|131948 TIGR02902, spore_lonB, ATP-dependent protease LonB. Members of
this protein are LonB, a paralog of the ATP-dependent
protease La (LonA, TIGR00763). LonB proteins are found
strictly, and almost universally, in endospore-forming
bacteria. This protease was shown, in Bacillus subtilis,
to be expressed specifically in the forespore, during
sporulation, under control of sigma(F). The lonB gene,
despite location immediately upstream of lonA, was shown
to be monocistronic. LonB appears able to act on
sigma(H) for post-translation control, but lonB mutation
did not produce an obvious sporulation defect under the
conditions tested. Note that additional paralogs of LonA
and LonB occur in the Clostridium lineage and this model
selects only one per species as the protein that
corresponds to LonB in B. subtilis [Protein fate,
Degradation of proteins, peptides, and glycopeptides,
Cellular processes, Sporulation and germination].
Length = 531
Score = 54.0 bits (130), Expect = 5e-08
Identities = 32/87 (36%), Positives = 50/87 (57%), Gaps = 17/87 (19%)
Query: 2 EKYRPQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILL----- 56
EK RP++F +I+G E+ ++ LK N ++II GPPGVGKT AR++L
Sbjct: 57 EKTRPKSFDEIIGQEEGIKALKAALCGPNPQHVIIYGPPGVGKTAA----ARLVLEEAKK 112
Query: 57 --GPSFKD--AVLELNAS----NDRGI 75
FK+ A +E++A+ ++RGI
Sbjct: 113 NPASPFKEGAAFVEIDATTARFDERGI 139
>gnl|CDD|236011 PRK07399, PRK07399, DNA polymerase III subunit delta'; Validated.
Length = 314
Score = 52.2 bits (126), Expect = 1e-07
Identities = 52/228 (22%), Positives = 95/228 (41%), Gaps = 44/228 (19%)
Query: 9 FSDIVGNEDTVERLKVFSSSGNV-PNIIISGPPGVGKTTTILCLA--------------- 52
F++++G +E L + P + +GP GVG+ LC
Sbjct: 3 FANLIGQPLAIELLTAAIKQNRIAPAYLFAGPEGVGRKLAALCFIEGLLSQGSPSKNIRR 62
Query: 53 RILLG---------PSF-------KDAVLELNASNDRG-----IDTVRNKIKMFAQQKVT 91
R+ G P++ + E + ++ +R IK F +
Sbjct: 63 RLEEGNHPDLLWVEPTYQHQGKLITASEAEEAGLKRKAPPQIRLEQIRE-IKRFLSRP-P 120
Query: 92 LPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLR 151
L R K+V++++A++M + A AL +T+E N T L + E ++ I SRC ++
Sbjct: 121 LEAPR-KVVVIEDAETMNEAAANALLKTLEEPGNGT-LILIAPSPESLLPTIVSRCQIIP 178
Query: 152 YNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQALNNLQ 199
+ +L+D QL V++ E I N ++ AQG A+ N++
Sbjct: 179 FYRLSDEQLEQ-VLKRLGDEEIL--NINFPELLALAQGSPGAAIANIE 223
>gnl|CDD|236022 PRK07471, PRK07471, DNA polymerase III subunit delta'; Validated.
Length = 365
Score = 52.3 bits (126), Expect = 1e-07
Identities = 41/165 (24%), Positives = 62/165 (37%), Gaps = 41/165 (24%)
Query: 36 ISGPPGVGKTTTILCLARILL------GPSFKDAV--LELNAS----------------- 70
I GP G+GK T +AR LL G L ++
Sbjct: 46 IGGPQGIGKATLAYRMARFLLATPPPGGDGAVPPPTSLAIDPDHPVARRIAAGAHGGLLT 105
Query: 71 -----NDRG--------IDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALR 117
N++G +D VR I F +T G ++VI+D AD M A AL
Sbjct: 106 LERSWNEKGKRLRTVITVDEVRELISFFG---LTAAEGGWRVVIVDTADEMNANAANALL 162
Query: 118 RTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTDAQLLS 162
+ +E + F L + +++ I+SRC LR L ++
Sbjct: 163 KVLEEPPARSLFLLVSHAPARLLPTIRSRCRKLRLRPLAPEDVID 207
>gnl|CDD|234619 PRK00080, ruvB, Holliday junction DNA helicase RuvB; Reviewed.
Length = 328
Score = 49.4 bits (119), Expect = 8e-07
Identities = 20/56 (35%), Positives = 32/56 (57%), Gaps = 9/56 (16%)
Query: 5 RPQTFSDIVGNEDTVERLKVFSSS----GNVPN-IIISGPPGVGKTTTILCLARIL 55
RP++ + +G E E LK+F + G + +++ GPPG+GKTT LA I+
Sbjct: 20 RPKSLDEFIGQEKVKENLKIFIEAAKKRGEALDHVLLYGPPGLGKTT----LANII 71
>gnl|CDD|180738 PRK06871, PRK06871, DNA polymerase III subunit delta'; Validated.
Length = 325
Score = 48.6 bits (116), Expect = 2e-06
Identities = 27/79 (34%), Positives = 40/79 (50%), Gaps = 9/79 (11%)
Query: 72 DRGIDTVRN---KIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTR 128
D G+D VR K+ AQQ G +K+V + A+ +T+ A AL +T+E T
Sbjct: 86 DIGVDQVREINEKVSQHAQQ------GGNKVVYIQGAERLTEAAANALLKTLEEPRPNTY 139
Query: 129 FALACNNSEKIIEPIQSRC 147
F L + S ++ I SRC
Sbjct: 140 FLLQADLSAALLPTIYSRC 158
>gnl|CDD|225164 COG2255, RuvB, Holliday junction resolvasome, helicase subunit
[DNA replication, recombination, and repair].
Length = 332
Score = 47.6 bits (114), Expect = 4e-06
Identities = 23/65 (35%), Positives = 37/65 (56%), Gaps = 12/65 (18%)
Query: 5 RPQTFSDIVGNEDTVERLKVFSSS----GNVPN-IIISGPPGVGKTTTILCLARIL---L 56
RP+T + +G E E+L++F + G + +++ GPPG+GKTT LA I+ L
Sbjct: 21 RPKTLDEFIGQEKVKEQLQIFIKAAKKRGEALDHVLLFGPPGLGKTT----LAHIIANEL 76
Query: 57 GPSFK 61
G + K
Sbjct: 77 GVNLK 81
>gnl|CDD|236090 PRK07764, PRK07764, DNA polymerase III subunits gamma and tau;
Validated.
Length = 824
Score = 47.7 bits (114), Expect = 5e-06
Identities = 43/136 (31%), Positives = 61/136 (44%), Gaps = 47/136 (34%)
Query: 3 KYRPQTFSDIVGNEDTVERLKVFSSSGNVPN--IIISGPPGVGKTTTILCLARIL----- 55
+YRP TF++++G E E L SG + N + SGP G GKT++ ARIL
Sbjct: 8 RYRPATFAEVIGQEHVTEPLSTALDSGRI-NHAYLFSGPRGCGKTSS----ARILARSLN 62
Query: 56 ------------------L---GPSFKDAVLELNASNDRGID---TVRNKIKMFAQQKVT 91
L GP D V E++A++ G+D +R + FA
Sbjct: 63 CVEGPTSTPCGECDSCVALAPGGPGSLD-VTEIDAASHGGVDDARELRER-AFFA----- 115
Query: 92 LPPG--RHKIVILDEA 105
P R+KI I+DEA
Sbjct: 116 --PAESRYKIFIIDEA 129
>gnl|CDD|129690 TIGR00602, rad24, checkpoint protein rad24. All proteins in this
family for which functions are known are involved in DNA
damage tolerance (likely cell cycle checkpoints).This
family is based on the phylogenomic analysis of JA Eisen
(1999, Ph.D. Thesis, Stanford University) [DNA
metabolism, DNA replication, recombination, and repair].
Length = 637
Score = 47.3 bits (112), Expect = 6e-06
Identities = 45/252 (17%), Positives = 93/252 (36%), Gaps = 54/252 (21%)
Query: 1 IEKYRPQTFSDIVGNEDTVERLKVFSSSGNVPN-----IIISGPPGVGKTTTILCLARIL 55
+EKY+P+T ++ ++ +E ++ + + + N ++I+GP G GK+TTI L++
Sbjct: 75 VEKYKPETQHELAVHKKKIEEVETWLKAQVLENAPKRILLITGPSGCGKSTTIKILSKE- 133
Query: 56 LGPSFKDAVLELN---ASND-RGIDTVRNKIKMFAQQKVTLPP----------------- 94
LG ++ ND + ++ + F Q
Sbjct: 134 LGIQVQEWSNPTLPDFQKNDHKVTLSLESCFSNFQSQIEVFSEFLLRATNKLQMLGDDLM 193
Query: 95 GRHKIVILDEADSMTDGAQQALRRTME-IYSNTTRFALAC---------NNSEKIIEP-- 142
KI+++++ + +AL + Y + R L NN +++ P
Sbjct: 194 TDKKIILVEDLPNQFYRDTRALHEILRWKYVSIGRCPLVFIITESLEGDNNQRRLLFPAE 253
Query: 143 ------IQSRCAM--LRYNKLTDAQLLSKVIEICEKE-------NISHTNDGLEAIVFTA 187
I + + +N + + + I E +E +
Sbjct: 254 TIMNKEILEEPRVSNISFNPIAPTIMKKFLNRIVTIEAKKNGEKIKVPKKTSVELLCQGC 313
Query: 188 QGDMRQALNNLQ 199
GD+R A+N+LQ
Sbjct: 314 SGDIRSAINSLQ 325
>gnl|CDD|217429 pfam03215, Rad17, Rad17 cell cycle checkpoint protein.
Length = 490
Score = 46.6 bits (110), Expect = 9e-06
Identities = 44/246 (17%), Positives = 95/246 (38%), Gaps = 48/246 (19%)
Query: 2 EKYRPQTFSDIVGNEDTVERLK-----VFSSSGNVPNIIISGPPGVGKTTTILCLARILL 56
EKY+P+ ++ ++ + + VF S ++++GP G GK+TT+ L++ L
Sbjct: 11 EKYKPRRRDELAIHKKKIAEVDHWLKAVFLESNKQLILLLTGPSGCGKSTTVKVLSKELG 70
Query: 57 --------GPSFKDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRH----------K 98
+ E + RG V + +M ++ L R+ K
Sbjct: 71 IEIIEWSNPEYLHNPDNECQKPDFRGDCIVNSLSQMEQFREFLLRGARYGSLQGGGLKKK 130
Query: 99 IVILDE----ADSMTDGAQQALRRTME-------IYSNTTRFALACNNSEKIIEP----- 142
+++++E S + ++ +R ++ I+ T +L +N++
Sbjct: 131 LILVEELPNQFYSDAEKFREVIREVLQSIWHLPLIFCLTECNSLEGDNNQDRFGIDAETI 190
Query: 143 ------IQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIVFTAQ---GDMRQ 193
I R + +N + + ++ I +E + + Q GD+R
Sbjct: 191 MTKDILIMPRIDTITFNPIAPTFMKKALVRISVQEGKLKSPKSDSKLEVICQEAGGDLRS 250
Query: 194 ALNNLQ 199
A+N+LQ
Sbjct: 251 AINSLQ 256
>gnl|CDD|234053 TIGR02903, spore_lon_C, ATP-dependent protease, Lon family.
Members of this protein family resemble the widely
distributed ATP-dependent protease La, also called Lon
and LonA. It resembles even more closely LonB, which is
a LonA paralog found in genomes if and only if the
species is capable of endospore formation (as in
Bacillus subtilis, Clostridium tetani, and select other
members of the Firmicutes) and expressed specifically in
the forespore compartment. Members of this family are
restricted to a subset of spore-forming species, and are
very likely to participate in the program of endospore
formation. We propose the designation LonC [Protein
fate, Degradation of proteins, peptides, and
glycopeptides, Cellular processes, Sporulation and
germination].
Length = 615
Score = 46.7 bits (111), Expect = 9e-06
Identities = 24/52 (46%), Positives = 32/52 (61%), Gaps = 4/52 (7%)
Query: 5 RPQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILL 56
RP+ FS+IVG E ++ L +S +II+ GPPGVGKTT AR+ L
Sbjct: 149 RPRAFSEIVGQERAIKALLAKVASPFPQHIILYGPPGVGKTTA----ARLAL 196
Score = 28.6 bits (64), Expect = 5.0
Identities = 21/64 (32%), Positives = 36/64 (56%), Gaps = 5/64 (7%)
Query: 137 EKIIEPIQSRCAMLRYNKLTDAQLLSKVIEICEKENISHTNDGLEAIV--FTAQGDMRQA 194
E+I ++SRCA + + LT + V+ EK N+ H G+E ++ +T +G R+A
Sbjct: 335 EEINPALRSRCAEVFFEPLTPEDIALIVLNAAEKINV-HLAAGVEELIARYTIEG--RKA 391
Query: 195 LNNL 198
+N L
Sbjct: 392 VNIL 395
>gnl|CDD|203260 pfam05496, RuvB_N, Holliday junction DNA helicase ruvB
N-terminus. The RuvB protein makes up part of the
RuvABC revolvasome which catalyzes the resolution of
Holliday junctions that arise during genetic
recombination and DNA repair. Branch migration is
catalyzed by the RuvB protein that is targeted to the
Holliday junction by the structure specific RuvA
protein. This family contains the N-terminal region of
the protein.
Length = 231
Score = 45.5 bits (109), Expect = 1e-05
Identities = 20/65 (30%), Positives = 34/65 (52%), Gaps = 12/65 (18%)
Query: 5 RPQTFSDIVGNEDTVERLKVF---SSSGNVP--NIIISGPPGVGKTTTILCLARIL---L 56
RP+ + +G E E LK+F + ++++ GPPG+GKTT LA I+ +
Sbjct: 19 RPRRLDEYIGQEKVKENLKIFIEAAKKRGEALDHVLLYGPPGLGKTT----LANIIANEM 74
Query: 57 GPSFK 61
G + +
Sbjct: 75 GVNIR 79
>gnl|CDD|180394 PRK06090, PRK06090, DNA polymerase III subunit delta'; Validated.
Length = 319
Score = 45.2 bits (107), Expect = 2e-05
Identities = 31/152 (20%), Positives = 67/152 (44%), Gaps = 29/152 (19%)
Query: 20 ERLKVFSSSGNVPN-IIISGPPGVGKTTTILCLARILLGPSFKDAVL------ELNASND 72
+ K +G +P +++ G+G + + +R LL +++ EL S +
Sbjct: 13 QNWKAGLDAGRIPGALLLQSDEGLGVESLVELFSRALLCQNYQSEACGFCHSCELMQSGN 72
Query: 73 R---------------GIDTVR--NKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQA 115
++ +R N++ AQ+ L +++ +++ AD+M + A A
Sbjct: 73 HPDLHVIKPEKEGKSITVEQIRQCNRL---AQESSQL--NGYRLFVIEPADAMNESASNA 127
Query: 116 LRRTMEIYSNTTRFALACNNSEKIIEPIQSRC 147
L +T+E + F L +N ++++ I SRC
Sbjct: 128 LLKTLEEPAPNCLFLLVTHNQKRLLPTIVSRC 159
>gnl|CDD|181190 PRK07993, PRK07993, DNA polymerase III subunit delta'; Validated.
Length = 334
Score = 45.1 bits (107), Expect = 2e-05
Identities = 26/77 (33%), Positives = 39/77 (50%), Gaps = 9/77 (11%)
Query: 74 GIDTVRN---KIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFA 130
G+D VR K+ A+ G K+V L +A +TD A AL +T+E T F
Sbjct: 89 GVDAVREVTEKLYEHARL------GGAKVVWLPDAALLTDAAANALLKTLEEPPENTWFF 142
Query: 131 LACNNSEKIIEPIQSRC 147
LAC +++ ++SRC
Sbjct: 143 LACREPARLLATLRSRC 159
>gnl|CDD|222104 pfam13401, AAA_22, AAA domain.
Length = 124
Score = 42.6 bits (101), Expect = 3e-05
Identities = 21/111 (18%), Positives = 38/111 (34%), Gaps = 14/111 (12%)
Query: 34 IIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDR-----------GIDTVRNKI 82
+++G G GKTT + LAR L +E + G+
Sbjct: 7 GVLTGESGSGKTTLLRRLARQLPNRRV--VYVEAPSLGTPKDLLRKILRALGLPLSGGTT 64
Query: 83 K-MFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALA 132
+ L ++I+DEA ++ A + LR ++ + L
Sbjct: 65 AELLEAILDALKRRGRPLLIIDEAQHLSLEALEELRDLYDLSEKGIQVILV 115
>gnl|CDD|236134 PRK07940, PRK07940, DNA polymerase III subunit delta'; Validated.
Length = 394
Score = 44.9 bits (107), Expect = 3e-05
Identities = 44/169 (26%), Positives = 72/169 (42%), Gaps = 34/169 (20%)
Query: 9 FSDIVGNEDTVERLK----------VFSSSGNVPNIIISGPPGVGKTTTILCLARILLGP 58
+ D+VG E V L+ + SG + +GPPG G++ A L
Sbjct: 4 WDDLVGQEAVVAELRAAARAARADVAAAGSGMTHAWLFTGPPGSGRSVAARAFAAALQCT 63
Query: 59 SFKD----------AVLELNASNDR---------GIDTVRNKIKMFAQQKVTLPPGRHKI 99
+ VL + R G+D VR + + A++ T GR +I
Sbjct: 64 DPDEPGCGECRACRTVLAGTHPDVRVVAPEGLSIGVDEVRELVTIAARRPST---GRWRI 120
Query: 100 VILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNS-EKIIEPIQSRC 147
V++++AD +T+ A AL + +E T + L C S E ++ I+SRC
Sbjct: 121 VVIEDADRLTERAANALLKAVEEPPPRTVWLL-CAPSPEDVLPTIRSRC 168
>gnl|CDD|221970 pfam13191, AAA_16, AAA ATPase domain. This family of domains
contain a P-loop motif that is characteristic of the
AAA superfamily.
Length = 154
Score = 41.0 bits (96), Expect = 2e-04
Identities = 21/60 (35%), Positives = 33/60 (55%), Gaps = 3/60 (5%)
Query: 12 IVGNEDTVERLKVF---SSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELN 68
+VG E+ +ERL + SG P+++++GP G GKT+ + L LL + K E N
Sbjct: 2 LVGREEELERLLDALRRARSGGPPSVLLTGPSGTGKTSLLRELLEGLLVAAGKCDQAERN 61
>gnl|CDD|181551 PRK08769, PRK08769, DNA polymerase III subunit delta'; Validated.
Length = 319
Score = 41.1 bits (96), Expect = 4e-04
Identities = 40/146 (27%), Positives = 60/146 (41%), Gaps = 32/146 (21%)
Query: 34 IIISGPPGVGKTTTILCLARILLGPSFKDAV---------------LEL-----NASNDR 73
++I GP G+GK L LA +L A L+L N + D+
Sbjct: 29 LLICGPEGLGKRAVALALAEHVLASGPDPAAAQRTRQLIAAGTHPDLQLVSFIPNRTGDK 88
Query: 74 -----GIDTVRNKIKMFAQQKVTLPP--GRHKIVILDEADSMTDGAQQALRRTMEIYSNT 126
I+ VR QK+ L P G ++VI+D AD++ A AL +T+E S
Sbjct: 89 LRTEIVIEQVRE-----ISQKLALTPQYGIAQVVIVDPADAINRAACNALLKTLEEPSPG 143
Query: 127 TRFALACNNSEKIIEPIQSRCAMLRY 152
L ++ I+SRC L +
Sbjct: 144 RYLWLISAQPARLPATIRSRCQRLEF 169
>gnl|CDD|181214 PRK08058, PRK08058, DNA polymerase III subunit delta'; Validated.
Length = 329
Score = 41.1 bits (97), Expect = 4e-04
Identities = 25/81 (30%), Positives = 40/81 (49%), Gaps = 6/81 (7%)
Query: 98 KIVILDEADSMTDGAQQALRRTMEIYS-NTTRFALACNNSEKIIEPIQSRCAMLRYNKLT 156
K+ I++ AD MT A +L + +E S TT L N +I+ I SRC ++ + L
Sbjct: 112 KVYIIEHADKMTASAANSLLKFLEEPSGGTTAILLT-ENKHQILPTILSRCQVVEFRPLP 170
Query: 157 DAQLLSKVIEICEKENISHTN 177
L+ ++ E E IS +
Sbjct: 171 PESLIQRLQE----EGISESL 187
>gnl|CDD|221955 pfam13173, AAA_14, AAA domain. This family of domains contain a
P-loop motif that is characteristic of the AAA
superfamily.
Length = 127
Score = 39.1 bits (92), Expect = 5e-04
Identities = 24/94 (25%), Positives = 39/94 (41%), Gaps = 8/94 (8%)
Query: 32 PNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKIKMFAQQKVT 91
I+I+GP VGKTT L L + +L +N + R +R + ++ +
Sbjct: 3 KIIVITGPRQVGKTT----LLLQFLKELLSENILYINLDDPR---FLRLALLDLLEEFLK 55
Query: 92 LPPGRHKIVILDEADSMTDGAQQALRRTMEIYSN 125
L K + LDE + AL+R + N
Sbjct: 56 LLLPGKKYLFLDEI-QKVPDWEDALKRLYDDGRN 88
>gnl|CDD|213179 cd00267, ABC_ATPase, 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 = 39.5 bits (93), Expect = 6e-04
Identities = 28/132 (21%), Positives = 56/132 (42%), Gaps = 19/132 (14%)
Query: 34 IIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKIKMFAQ------ 87
+ + GP G GK+T + +A LL P+ + +++ ++ +R +I Q
Sbjct: 28 VALVGPNGSGKSTLLRAIAG-LLKPTSGEILIDGKDIAKLPLEELRRRIGYVPQLSGGQR 86
Query: 88 QKVTL-------PPGRHKIVILDEADSMTDGA-QQALRRTMEIYSNTTRFALACNNSEKI 139
Q+V L P +++LDE S D A ++ L + + R + + ++
Sbjct: 87 QRVALARALLLNPD----LLLLDEPTSGLDPASRERLLELLRELAEEGRTVIIVTHDPEL 142
Query: 140 IEPIQSRCAMLR 151
E R +L+
Sbjct: 143 AELAADRVIVLK 154
>gnl|CDD|237475 PRK13695, PRK13695, putative NTPase; Provisional.
Length = 174
Score = 39.1 bits (92), Expect = 0.001
Identities = 15/29 (51%), Positives = 20/29 (68%)
Query: 33 NIIISGPPGVGKTTTILCLARILLGPSFK 61
I I+GPPGVGKTT +L +A +L +K
Sbjct: 2 KIGITGPPGVGKTTLVLKIAELLKEEGYK 30
>gnl|CDD|224391 COG1474, CDC6, Cdc6-related protein, AAA superfamily ATPase [DNA
replication, recombination, and repair /
Posttranslational modification, protein turnover,
chaperones].
Length = 366
Score = 39.6 bits (93), Expect = 0.001
Identities = 32/109 (29%), Positives = 43/109 (39%), Gaps = 23/109 (21%)
Query: 28 SGNVP-NIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKIKMFA 86
G P NIII GP G GKT T+ + L S V+ +N R V +KI
Sbjct: 38 RGERPSNIIIYGPTGTGKTATVKFVMEELEESSANVEVVYINCLELRTPYQVLSKI---L 94
Query: 87 QQKVTLPP-------------------GRHKIVILDEADSMTDGAQQAL 116
+ +P G+ IVILDE D++ D + L
Sbjct: 95 NKLGKVPLTGDSSLEILKRLYDNLSKKGKTVIVILDEVDALVDKDGEVL 143
>gnl|CDD|129721 TIGR00635, ruvB, Holliday junction DNA helicase, RuvB subunit.
All proteins in this family for which functions are
known are 5'-3' DNA helicases that, as part of a
complex with RuvA homologs serve as a 5'-3' Holliday
junction helicase. RuvA specifically binds Holliday
junctions as a sandwich of two tetramers and maintains
the configuration of the junction. It forms a complex
with two hexameric rings of RuvB, the subunit that
contains helicase activity. The complex drives
ATP-dependent branch migration of the Holliday junction
recombination intermediate. The endonuclease RuvC
resolves junctions [DNA metabolism, DNA replication,
recombination, and repair].
Length = 305
Score = 38.4 bits (90), Expect = 0.003
Identities = 16/54 (29%), Positives = 32/54 (59%), Gaps = 9/54 (16%)
Query: 7 QTFSDIVGNEDTVERLKVF--SSSGN---VPNIIISGPPGVGKTTTILCLARIL 55
+ ++ +G E E+L++F ++ + ++++ GPPG+GKTT LA I+
Sbjct: 1 KLLAEFIGQEKVKEQLQLFIEAAKMRQEALDHLLLYGPPGLGKTT----LAHII 50
>gnl|CDD|216506 pfam01443, Viral_helicase1, Viral (Superfamily 1) RNA helicase.
Helicase activity for this family has been demonstrated
and NTPase activity. This helicase has multiple roles at
different stages of viral RNA replication, as dissected
by mutational analysis.
Length = 226
Score = 37.4 bits (87), Expect = 0.004
Identities = 18/72 (25%), Positives = 26/72 (36%), Gaps = 4/72 (5%)
Query: 34 IIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKIKMFAQQKVTLP 93
I++ G PG GK+T I L R + D ++ + L
Sbjct: 1 IVVHGVPGCGKSTLIRKLLR----TDLTVIRPTAELRTEGKPDLPNLNVRTVDTFLMALL 56
Query: 94 PGRHKIVILDEA 105
KI+ILDE
Sbjct: 57 KPTGKILILDEY 68
>gnl|CDD|222000 pfam13238, AAA_18, AAA domain.
Length = 128
Score = 35.9 bits (83), Expect = 0.007
Identities = 16/38 (42%), Positives = 20/38 (52%), Gaps = 7/38 (18%)
Query: 34 IIISGPPGVGKTTTILCLARIL---LGPSFKDAVLELN 68
I+I+G PG GKTT LA+ L LG +D E
Sbjct: 1 ILITGTPGSGKTT----LAKELAERLGDVLRDLAKENG 34
>gnl|CDD|129465 TIGR00368, TIGR00368, Mg chelatase-related protein. The N-terminal
end matches very strongly a pfam Mg_chelatase domain
[Unknown function, General].
Length = 499
Score = 37.5 bits (87), Expect = 0.007
Identities = 24/91 (26%), Positives = 40/91 (43%), Gaps = 10/91 (10%)
Query: 1 IEKYRPQT--FSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGP 58
I K DI G + L++ ++ G+ N+++ GPPG GKT L IL
Sbjct: 181 INKSYIIDLDLKDIKGQQHAKRALEIAAAGGH--NLLLFGPPGSGKTMLASRLQGILPPL 238
Query: 59 SFKDAVLELNASNDRGIDTVRNKIKMFAQQK 89
+ ++A +E I ++ K+ Q K
Sbjct: 239 TNEEA-IETAR-----IWSLVGKLIDRKQIK 263
>gnl|CDD|217465 pfam03266, NTPase_1, NTPase. This domain is found across all
species from bacteria to human, and the function was
determined first in a hyperthermophilic bacterium to be
an NTPase. The structure of one member-sequence
represents a variation of the RecA fold, and implies
that the function might be that of a DNA/RNA modifying
enzyme. The sequence carries both a Walker A and Walker
B motif which together are characteristic of ATPases or
GTPases. The protein exhibits an increased expression
profile in human liver cholangiocarcinoma when compared
to normal tissue.
Length = 168
Score = 36.0 bits (84), Expect = 0.008
Identities = 13/29 (44%), Positives = 17/29 (58%)
Query: 33 NIIISGPPGVGKTTTILCLARILLGPSFK 61
I I+GPPGVGKTT + + +L K
Sbjct: 1 RIFITGPPGVGKTTLVKKVIELLKSEGVK 29
>gnl|CDD|144608 pfam01078, Mg_chelatase, Magnesium chelatase, subunit ChlI.
Magnesium-chelatase is a three-component enzyme that
catalyzes the insertion of Mg2+ into protoporphyrin IX.
This is the first unique step in the synthesis of
(bacterio)chlorophyll. Due to this, it is thought that
Mg-chelatase has an important role in channelling
inter- mediates into the (bacterio)chlorophyll branch
in response to conditions suitable for photosynthetic
growth. ChlI and BchD have molecular weight between
38-42 kDa.
Length = 207
Score = 36.3 bits (85), Expect = 0.009
Identities = 20/61 (32%), Positives = 34/61 (55%), Gaps = 3/61 (4%)
Query: 9 FSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELN 68
+D+ G E L++ ++ G+ N+++ GPPG GKT L IL + ++A LE+
Sbjct: 2 LADVKGQEQAKRALEIAAAGGH--NLLMIGPPGSGKTMLAKRLPGILPPLTEQEA-LEVT 58
Query: 69 A 69
A
Sbjct: 59 A 59
>gnl|CDD|223786 COG0714, COG0714, MoxR-like ATPases [General function prediction
only].
Length = 329
Score = 36.6 bits (85), Expect = 0.011
Identities = 31/119 (26%), Positives = 50/119 (42%), Gaps = 15/119 (12%)
Query: 1 IEKYRPQTFSDIVGNEDTVERLKV-FSSSGNVPNIIISGPPGVGKTTTILCLARILLGPS 59
+ K R + +VG+E+ +E + + G+V ++ GPPGVGKT LAR LG
Sbjct: 15 LGKIRSELEKVVVGDEEVIELALLALLAGGHV---LLEGPPGVGKTLLARALAR-ALGLP 70
Query: 60 FKDAVL---ELNASNDRGIDTVRNKIKMFAQQKVT---LPPGRHKIVILDE---ADSMT 109
F + +L S+ G + + + L I++LDE A
Sbjct: 71 FVR-IQCTPDLLPSDLLGTYAYAALLLEPGEFRFVPGPLFAAVRVILLLDEINRAPPEV 128
>gnl|CDD|223540 COG0464, SpoVK, ATPases of the AAA+ class [Posttranslational
modification, protein turnover, chaperones].
Length = 494
Score = 36.7 bits (85), Expect = 0.012
Identities = 33/139 (23%), Positives = 53/139 (38%), Gaps = 23/139 (16%)
Query: 8 TFSDIVGNEDTVERLK-----------VFSSSGNVPN--IIISGPPGVGKTTTILCLARI 54
T DI G E+ E LK +F G P +++ GPPG GKT +A
Sbjct: 240 TLDDIGGLEEAKEELKEAIETPLKRPELFRKLGLRPPKGVLLYGPPGTGKTLLAKAVALE 299
Query: 55 LLGP--SFKDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGA 112
S K + L + ++ +N ++F + + L P I+ +DE DS+ G
Sbjct: 300 SRSRFISVKGSEL----LSKWVGESEKNIRELFEKAR-KLAPS---IIFIDEIDSLASGR 351
Query: 113 QQALRRTMEIYSNTTRFAL 131
+ + L
Sbjct: 352 GPSEDGSGRRVVGQLLTEL 370
>gnl|CDD|234063 TIGR02928, TIGR02928, orc1/cdc6 family replication initiation
protein. Members of this protein family are found
exclusively in the archaea. This set of DNA binding
proteins shows homology to the origin recognition
complex subunit 1/cell division control protein 6
family in eukaryotes. Several members may be found in
genome and interact with each other [DNA metabolism,
DNA replication, recombination, and repair].
Length = 365
Score = 36.5 bits (85), Expect = 0.014
Identities = 16/58 (27%), Positives = 23/58 (39%), Gaps = 7/58 (12%)
Query: 2 EKYRPQTFSDIVGNEDTVERLKVFSSS---GNVP-NIIISGPPGVGKTTTILCLARIL 55
Y P IV ++ +E L G+ P N+ I G G GKT + + L
Sbjct: 10 PDYVP---DRIVHRDEQIEELAKALRPILRGSRPSNVFIYGKTGTGKTAVTKYVMKEL 64
>gnl|CDD|221983 pfam13207, AAA_17, AAA domain.
Length = 114
Score = 34.2 bits (78), Expect = 0.022
Identities = 12/22 (54%), Positives = 16/22 (72%), Gaps = 4/22 (18%)
Query: 34 IIISGPPGVGKTTTILCLARIL 55
I+I+GPPG GK+T LA+ L
Sbjct: 2 ILITGPPGSGKST----LAKKL 19
>gnl|CDD|221912 pfam13086, AAA_11, AAA domain. This family of domains contain a
P-loop motif that is characteristic of the AAA
superfamily. Many of the proteins in this family are
conjugative transfer proteins.
Length = 220
Score = 35.4 bits (82), Expect = 0.024
Identities = 17/37 (45%), Positives = 22/37 (59%)
Query: 35 IISGPPGVGKTTTILCLARILLGPSFKDAVLELNASN 71
+I GPPG GKTTTI+ + + LL + VL SN
Sbjct: 21 LIQGPPGTGKTTTIVEIIKQLLSNAPGKKVLVCAPSN 57
>gnl|CDD|222258 pfam13604, AAA_30, AAA domain. This family of domains contain a
P-loop motif that is characteristic of the AAA
superfamily. Many of the proteins in this family are
conjugative transfer proteins. There is a Walker A and
Walker B.
Length = 195
Score = 34.9 bits (81), Expect = 0.029
Identities = 25/97 (25%), Positives = 42/97 (43%), Gaps = 19/97 (19%)
Query: 34 IIISGPPGVGKTTTILCLAR----------ILLGPSFKDAVLELNASNDRGID--TVRNK 81
++ GP G GKTT+ L AR I L P+ K A L + GI+ T+ +
Sbjct: 21 AVVQGPAGTGKTTS-LKAAREAWEAAGYRVIGLAPTGK-AAKVL--GEELGIEARTLASL 76
Query: 82 IKMFAQQKVTLPP-GRHKIVILDEADSMTDGAQQALR 117
+ + + + ++++DEA M +Q R
Sbjct: 77 LHRWDKGEDPGRVLDAGTLLVVDEA-GMVG-TRQMAR 111
>gnl|CDD|222005 pfam13245, AAA_19, Part of AAA domain.
Length = 73
Score = 32.7 bits (75), Expect = 0.034
Identities = 11/37 (29%), Positives = 19/37 (51%), Gaps = 2/37 (5%)
Query: 20 ERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILL 56
E ++ +S ++ ++ G PG GKT T + LL
Sbjct: 1 EAVEAAASGRSL--FVVDGGPGTGKTATAAAIIARLL 35
>gnl|CDD|180215 PRK05707, PRK05707, DNA polymerase III subunit delta'; Validated.
Length = 328
Score = 35.1 bits (81), Expect = 0.038
Identities = 37/136 (27%), Positives = 60/136 (44%), Gaps = 25/136 (18%)
Query: 34 IIISGPPGVGK-------TTTILCLA-------------RILLGPSFKDA-VLE-LNASN 71
++ GP G+GK +LC A ++L S D VLE A
Sbjct: 25 YLLHGPAGIGKRALAERLAAALLCEAPQGGGACGSCKGCQLLRAGSHPDNFVLEPEEADK 84
Query: 72 DRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFAL 131
+D VR ++ F Q L G K+V+++ A++M A AL +++E S T L
Sbjct: 85 TIKVDQVR-ELVSFVVQTAQL--GGRKVVLIEPAEAMNRNAANALLKSLEEPSGDTVLLL 141
Query: 132 ACNNSEKIIEPIQSRC 147
+ +++ I+SRC
Sbjct: 142 ISHQPSRLLPTIKSRC 157
>gnl|CDD|234654 PRK00131, aroK, shikimate kinase; Reviewed.
Length = 175
Score = 34.4 bits (80), Expect = 0.038
Identities = 14/31 (45%), Positives = 18/31 (58%), Gaps = 1/31 (3%)
Query: 32 PNIIISGPPGVGKTTTILCLARILLGPSFKD 62
PNI++ G G GK+T LA+ LG F D
Sbjct: 5 PNIVLIGFMGAGKSTIGRLLAK-RLGYDFID 34
>gnl|CDD|236138 PRK07994, PRK07994, DNA polymerase III subunits gamma and tau;
Validated.
Length = 647
Score = 35.2 bits (82), Expect = 0.039
Identities = 23/65 (35%), Positives = 31/65 (47%), Gaps = 27/65 (41%)
Query: 3 KYRPQTFSDIVGNEDTV---------ERLK---VFSSSGNVPNIIISGPPGVGKTTTILC 50
K+RPQTF+++VG E + RL +F SG GVGKTT
Sbjct: 9 KWRPQTFAEVVGQEHVLTALANALDLGRLHHAYLF-----------SGTRGVGKTT---- 53
Query: 51 LARIL 55
+AR+L
Sbjct: 54 IARLL 58
>gnl|CDD|224533 COG1618, COG1618, Predicted nucleotide kinase [Nucleotide
transport and metabolism].
Length = 179
Score = 34.2 bits (79), Expect = 0.040
Identities = 14/29 (48%), Positives = 18/29 (62%)
Query: 33 NIIISGPPGVGKTTTILCLARILLGPSFK 61
I I+G PGVGKTT +L +A L +K
Sbjct: 7 KIFITGRPGVGKTTLVLKIAEKLREKGYK 35
>gnl|CDD|180855 PRK07132, PRK07132, DNA polymerase III subunit delta'; Validated.
Length = 299
Score = 34.7 bits (80), Expect = 0.044
Identities = 18/69 (26%), Positives = 34/69 (49%)
Query: 98 KIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRCAMLRYNKLTD 157
KI+I+ + ++ AL +T+E T F L N K++ I SRC + +
Sbjct: 92 KILIIKNIEKTSNSLLNALLKTIEEPPKDTYFLLTTKNINKVLPTIVSRCQVFNVKEPDQ 151
Query: 158 AQLLSKVIE 166
++L+K++
Sbjct: 152 QKILAKLLS 160
>gnl|CDD|224847 COG1936, COG1936, Predicted nucleotide kinase (related to CMP and
AMP kinases) [Nucleotide transport and metabolism].
Length = 180
Score = 34.2 bits (79), Expect = 0.045
Identities = 10/16 (62%), Positives = 11/16 (68%)
Query: 32 PNIIISGPPGVGKTTT 47
I I+G PGVGKTT
Sbjct: 1 MLIAITGTPGVGKTTV 16
>gnl|CDD|238941 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 = 32.8 bits (75), Expect = 0.049
Identities = 11/32 (34%), Positives = 17/32 (53%)
Query: 34 IIISGPPGVGKTTTILCLARILLGPSFKDAVL 65
I+++G GVGKTT LA L + ++
Sbjct: 2 IVVTGKGGVGKTTLAANLAAALAKRGKRVLLI 33
>gnl|CDD|214940 smart00962, SRP54, SRP54-type protein, GTPase domain. This entry
represents the GTPase domain of the 54 kDa SRP54
component, a GTP-binding protein that interacts with
the signal sequence when it emerges from the ribosome.
SRP54 of the signal recognition particle has a
three-domain structure: an N-terminal helical bundle
domain, a GTPase domain, and the M-domain that binds
the 7s RNA and also binds the signal sequence. The
extreme C-terminal region is glycine-rich and lower in
complexity and poorly conserved between species. The
GTPase domain is evolutionary related to P-loop NTPase
domains found in a variety of other proteins.
Length = 197
Score = 33.9 bits (79), Expect = 0.052
Identities = 15/25 (60%), Positives = 17/25 (68%), Gaps = 1/25 (4%)
Query: 32 PNII-ISGPPGVGKTTTILCLARIL 55
P +I + GP GVGKTTTI LA L
Sbjct: 1 PGVILLVGPNGVGKTTTIAKLAARL 25
>gnl|CDD|234751 PRK00411, cdc6, cell division control protein 6; Reviewed.
Length = 394
Score = 34.4 bits (80), Expect = 0.060
Identities = 11/17 (64%), Positives = 14/17 (82%)
Query: 32 PNIIISGPPGVGKTTTI 48
N++I GPPG GKTTT+
Sbjct: 56 LNVLIYGPPGTGKTTTV 72
>gnl|CDD|222194 pfam13521, AAA_28, AAA domain.
Length = 162
Score = 33.3 bits (77), Expect = 0.066
Identities = 10/20 (50%), Positives = 13/20 (65%)
Query: 34 IIISGPPGVGKTTTILCLAR 53
I+I+G P GKTT + LA
Sbjct: 2 IVITGGPSTGKTTLLEALAA 21
>gnl|CDD|116340 pfam07726, AAA_3, ATPase family associated with various cellular
activities (AAA). This Pfam entry includes some of the
AAA proteins not detected by the pfam00004 model.
Length = 131
Score = 32.5 bits (75), Expect = 0.095
Identities = 11/28 (39%), Positives = 16/28 (57%), Gaps = 1/28 (3%)
Query: 34 IIISGPPGVGKTTTILCLARILLGPSFK 61
+++ G PG+ KT LAR LG F+
Sbjct: 2 VLLEGVPGLAKTLLARTLARS-LGLDFR 28
>gnl|CDD|222165 pfam13481, AAA_25, AAA domain. This AAA domain is found in a wide
variety of presumed DNA repair proteins.
Length = 154
Score = 32.6 bits (75), Expect = 0.11
Identities = 19/86 (22%), Positives = 36/86 (41%), Gaps = 12/86 (13%)
Query: 34 IIISGPPGVGKTTTILCLA-RILLGPSFKD-------AVLELNASNDRGIDTVRNKIKMF 85
+++G PG GK+T L LA + G F VL L+ + +R +++
Sbjct: 36 TLLAGAPGTGKSTLALDLAAAVATGRPFLGPFPVEPGRVLYLDG--EDSEAGLRRRLRAL 93
Query: 86 AQQKVTLPPGRHKIVILDEADSMTDG 111
+ + +V++D S+ G
Sbjct: 94 GEALEEIEGPD--LVVIDPLASLLGG 117
>gnl|CDD|182120 PRK09862, PRK09862, putative ATP-dependent protease; Provisional.
Length = 506
Score = 33.4 bits (76), Expect = 0.15
Identities = 14/40 (35%), Positives = 24/40 (60%), Gaps = 2/40 (5%)
Query: 6 PQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKT 45
SD++G E L++ ++ G+ N+++ GPPG GKT
Sbjct: 187 QHDLSDVIGQEQGKRGLEITAAGGH--NLLLIGPPGTGKT 224
>gnl|CDD|215451 PLN02840, PLN02840, tRNA dimethylallyltransferase.
Length = 421
Score = 33.3 bits (76), Expect = 0.15
Identities = 30/98 (30%), Positives = 45/98 (45%), Gaps = 18/98 (18%)
Query: 34 IIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASND----RGIDTVRNKIKMFAQQK 89
I+ISGP G GK+ L LA+ L G E+ +++ RG+D K ++
Sbjct: 24 IVISGPTGAGKSRLALELAKRLNG--------EIISADSVQVYRGLDV--GSAKPSLSER 73
Query: 90 VTLPPGRHKIVILDEADSMTDGA--QQALRRTMEIYSN 125
+P H I IL +D + GA A R T +I +
Sbjct: 74 KEVP--HHLIDILHPSDDYSVGAFFDDARRATQDILNR 109
>gnl|CDD|233761 TIGR02173, cyt_kin_arch, cytidylate kinase, putative. Proteins
in this family are believed to be cytidylate kinase.
Members of this family are found in the archaea and in
spirochaetes, and differ considerably from the common
bacterial form of cytidylate kinase described by
TIGR00017.
Length = 171
Score = 32.4 bits (74), Expect = 0.16
Identities = 14/22 (63%), Positives = 14/22 (63%)
Query: 34 IIISGPPGVGKTTTILCLARIL 55
I ISGPPG GKTT LA L
Sbjct: 3 ITISGPPGSGKTTVAKILAEKL 24
>gnl|CDD|130254 TIGR01186, proV, glycine betaine/L-proline transport ATP binding
subunit. This model describes the glycine
betaine/L-proline ATP binding subunit in bacteria and
its equivalents in archaea. This transport system
belong to the larger ATP-Binding Cassette (ABC)
transporter superfamily. The characteristic feature of
these transporter is the obligatory coupling of ATP
hydrolysis to substrate translocation. The minimal
configuration of bacterial ABC transport system: an
ATPase or ATP binding subunit; An integral membrane
protein; a hydrophilic polypetpide, which likely
functions as substrate binding protein. Functionally,
this transport system is involved in osmoregulation.
Under conditions of stress, the organism recruits these
transport system to accumulate glycine betaine and
other solutes which offer osmo-protection. It has been
demonstrated that glycine betaine uptake is accompanied
by symport with sodium ions. The locus has been named
variously as proU or opuA. A gene library from L.lactis
functionally complements an E.coli proU mutant. The
comlementing locus is similar to a opuA locus in
B.sutlis. This clarifies the differences in
nomenclature [Transport and binding proteins, Amino
acids, peptides and amines].
Length = 363
Score = 33.3 bits (76), Expect = 0.17
Identities = 21/64 (32%), Positives = 28/64 (43%), Gaps = 5/64 (7%)
Query: 34 IIISGPPGVGKTTTILCLARILLGPS----FKDAVLELNASNDRGIDTVRNKIKMFAQQK 89
+I G G GK+TT+ L R L+ P+ F D + S + R KI M QQ
Sbjct: 22 FVIMGLSGSGKSTTVRMLNR-LIEPTAGQIFIDGENIMKQSPVELREVRRKKIGMVFQQF 80
Query: 90 VTLP 93
P
Sbjct: 81 ALFP 84
>gnl|CDD|206669 cd01882, BMS1, Bms1, an essential GTPase, promotes assembly of
preribosomal RNA processing complexes. 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 = 231
Score = 32.7 bits (75), Expect = 0.18
Identities = 10/20 (50%), Positives = 15/20 (75%)
Query: 34 IIISGPPGVGKTTTILCLAR 53
+++ GPPGVGK+T I L +
Sbjct: 42 VVVVGPPGVGKSTLIRSLIK 61
>gnl|CDD|129694 TIGR00606, rad50, rad50. All proteins in this family for which
functions are known are involvedin recombination,
recombinational repair, and/or non-homologous end
joining.They are components of an exonuclease complex
with MRE11 homologs. This family is distantly related
to the SbcC family of bacterial proteins.This family is
based on the phylogenomic analysis of JA Eisen (1999,
Ph.D. Thesis, Stanford University).
Length = 1311
Score = 33.5 bits (76), Expect = 0.18
Identities = 19/45 (42%), Positives = 23/45 (51%), Gaps = 4/45 (8%)
Query: 13 VGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLG 57
G ED +++ F S P I+ GP G GKTT I CL I G
Sbjct: 14 FGIEDKDKQIIDFFS----PLTILVGPNGAGKTTIIECLKYICTG 54
>gnl|CDD|234232 TIGR03499, FlhF, flagellar biosynthetic protein FlhF. [Cellular
processes, Chemotaxis and motility].
Length = 283
Score = 32.7 bits (75), Expect = 0.19
Identities = 11/15 (73%), Positives = 12/15 (80%)
Query: 38 GPPGVGKTTTILCLA 52
GP GVGKTTT+ LA
Sbjct: 202 GPTGVGKTTTLAKLA 216
>gnl|CDD|221803 pfam12846, AAA_10, AAA-like domain. This family of domains
contain a P-loop motif that is characteristic of the
AAA superfamily. Many of the proteins in this family
are conjugative transfer proteins.
Length = 316
Score = 32.8 bits (75), Expect = 0.19
Identities = 12/29 (41%), Positives = 17/29 (58%), Gaps = 2/29 (6%)
Query: 32 PNIIISGPPGVGKTTTI--LCLARILLGP 58
PN++I GP G GK+T + L L + G
Sbjct: 2 PNMLIVGPSGSGKSTLLKLLALRLLARGG 30
>gnl|CDD|219839 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 = 32.6 bits (75), Expect = 0.21
Identities = 19/78 (24%), Positives = 37/78 (47%), Gaps = 12/78 (15%)
Query: 34 IIISGPPGVGKTTTILCLARILLGPSFKDAVLE---LNASNDRGIDT-----VRNKIKMF 85
II++G P GK+T LA+ L + V+ L +D D+ +R ++
Sbjct: 2 IILTGLPSSGKSTRAKELAKYLEEKGYDVIVISDESLGIESDDYKDSKKEKFLRGSLRSA 61
Query: 86 AQQKVTLPPGRHKIVILD 103
++ ++ ++ IVI+D
Sbjct: 62 VKRDLS----KNTIVIVD 75
>gnl|CDD|216202 pfam00931, NB-ARC, NB-ARC domain.
Length = 285
Score = 32.7 bits (75), Expect = 0.21
Identities = 15/35 (42%), Positives = 19/35 (54%), Gaps = 2/35 (5%)
Query: 15 NEDTVERL--KVFSSSGNVPNIIISGPPGVGKTTT 47
ED +E L K+ S N+ + I G GVGKTT
Sbjct: 1 REDMIEALIEKLLEMSDNLGVVGIVGMGGVGKTTL 35
>gnl|CDD|224292 COG1373, COG1373, Predicted ATPase (AAA+ superfamily) [General
function prediction only].
Length = 398
Score = 32.8 bits (75), Expect = 0.22
Identities = 22/89 (24%), Positives = 35/89 (39%), Gaps = 9/89 (10%)
Query: 19 VERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTV 78
+ RL I+I GP VGKTT + L + LL +L +D +
Sbjct: 26 LPRLIKKLDLRP-FIILILGPRQVGKTTLLKLLIKGLLEEIIYINFDDLRLDRIELLDLL 84
Query: 79 RNKIKMFAQQKVTLPPGRHKIVILDEADS 107
R I++ ++K + LDE +
Sbjct: 85 RAYIELKEREK--------SYIFLDEIQN 105
>gnl|CDD|234719 PRK00300, gmk, guanylate kinase; Provisional.
Length = 205
Score = 32.4 bits (75), Expect = 0.22
Identities = 11/23 (47%), Positives = 15/23 (65%), Gaps = 4/23 (17%)
Query: 34 IIISGPPGVGKTTTILCLARILL 56
I++SGP G GK+T L + LL
Sbjct: 8 IVLSGPSGAGKST----LVKALL 26
>gnl|CDD|235244 PRK04182, PRK04182, cytidylate kinase; Provisional.
Length = 180
Score = 32.1 bits (74), Expect = 0.22
Identities = 14/22 (63%), Positives = 16/22 (72%), Gaps = 4/22 (18%)
Query: 34 IIISGPPGVGKTTTILCLARIL 55
I ISGPPG GKTT +AR+L
Sbjct: 3 ITISGPPGSGKTT----VARLL 20
>gnl|CDD|223679 COG0606, COG0606, Predicted ATPase with chaperone activity
[Posttranslational modification, protein turnover,
chaperones].
Length = 490
Score = 33.0 bits (76), Expect = 0.22
Identities = 16/48 (33%), Positives = 26/48 (54%), Gaps = 2/48 (4%)
Query: 8 TFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARIL 55
F D+ G E L++ ++ G+ N+++ GPPG GKT L +L
Sbjct: 177 DFKDVKGQEQAKRALEIAAAGGH--NLLLVGPPGTGKTMLASRLPGLL 222
>gnl|CDD|234203 TIGR03420, DnaA_homol_Hda, DnaA regulatory inactivator Hda.
Members of this protein family are Hda (Homologous to
DnaA). These proteins are about half the length of DnaA
and homologous over length of Hda. In the model species
Escherichia coli, the initiation of DNA replication
requires DnaA bound to ATP rather than ADP; Hda helps
facilitate the conversion of DnaA-ATP to DnaA-ADP [DNA
metabolism, DNA replication, recombination, and
repair].
Length = 226
Score = 32.2 bits (74), Expect = 0.25
Identities = 9/42 (21%), Positives = 18/42 (42%), Gaps = 2/42 (4%)
Query: 6 PQTFSDIV--GNEDTVERLKVFSSSGNVPNIIISGPPGVGKT 45
TF + GN + + L+ ++ + + G G GK+
Sbjct: 11 DPTFDNFYAGGNAELLAALRQLAAGKGDRFLYLWGESGSGKS 52
>gnl|CDD|223637 COG0563, Adk, Adenylate kinase and related kinases [Nucleotide
transport and metabolism].
Length = 178
Score = 31.5 bits (72), Expect = 0.30
Identities = 12/23 (52%), Positives = 15/23 (65%), Gaps = 4/23 (17%)
Query: 33 NIIISGPPGVGKTTTILCLARIL 55
I+I GPPG GK+T LA+ L
Sbjct: 2 RILILGPPGAGKST----LAKKL 20
>gnl|CDD|236783 PRK10875, recD, exonuclease V subunit alpha; Provisional.
Length = 615
Score = 32.6 bits (75), Expect = 0.30
Identities = 12/21 (57%), Positives = 16/21 (76%), Gaps = 3/21 (14%)
Query: 35 IISGPPGVGKTTTILCLARIL 55
+ISG PG GKTTT+ A++L
Sbjct: 171 VISGGPGTGKTTTV---AKLL 188
>gnl|CDD|188437 TIGR03922, T7SS_EccA, type VII secretion AAA-ATPase EccA. This
model represents the AAA family ATPase, EccA, of the
actinobacterial flavor of type VII secretion systems.
Species such as Mycobacterium tuberculosis have several
instances of this system per genome, designated EccA1,
EccA2, etc [Protein fate, Protein and peptide secretion
and trafficking].
Length = 557
Score = 32.5 bits (74), Expect = 0.30
Identities = 11/24 (45%), Positives = 16/24 (66%)
Query: 34 IIISGPPGVGKTTTILCLARILLG 57
++ +GPPG GKTT +A+I G
Sbjct: 315 MLFAGPPGTGKTTIARVVAKIYCG 338
>gnl|CDD|226372 COG3854, SpoIIIAA, ncharacterized protein conserved in bacteria
[Function unknown].
Length = 308
Score = 32.1 bits (73), Expect = 0.31
Identities = 13/23 (56%), Positives = 17/23 (73%)
Query: 33 NIIISGPPGVGKTTTILCLARIL 55
N +I GPP VGKTT + +AR+L
Sbjct: 139 NTLIIGPPQVGKTTLLRDIARLL 161
>gnl|CDD|224617 COG1703, ArgK, Putative periplasmic protein kinase ArgK and
related GTPases of G3E family [Amino acid transport and
metabolism].
Length = 323
Score = 32.3 bits (74), Expect = 0.32
Identities = 18/48 (37%), Positives = 26/48 (54%)
Query: 23 KVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNAS 70
++ +GN I I+G PG GK+T I L R L + AVL ++ S
Sbjct: 43 ALYPRTGNAHVIGITGVPGAGKSTLIEALGRELRERGHRVAVLAVDPS 90
>gnl|CDD|181538 PRK08699, PRK08699, DNA polymerase III subunit delta'; Validated.
Length = 325
Score = 32.1 bits (73), Expect = 0.35
Identities = 20/73 (27%), Positives = 36/73 (49%), Gaps = 3/73 (4%)
Query: 75 IDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACN 134
ID VR I +T G +++++ A+SM A +L + +E F L +
Sbjct: 95 IDAVREIID-NVY--LTSVRGGLRVILIHPAESMNLQAANSLLKVLEEPPPQVVFLLVSH 151
Query: 135 NSEKIIEPIQSRC 147
++K++ I+SRC
Sbjct: 152 AADKVLPTIKSRC 164
>gnl|CDD|235570 PRK05703, flhF, flagellar biosynthesis regulator FlhF; Validated.
Length = 424
Score = 32.2 bits (74), Expect = 0.37
Identities = 11/15 (73%), Positives = 12/15 (80%)
Query: 38 GPPGVGKTTTILCLA 52
GP GVGKTTT+ LA
Sbjct: 228 GPTGVGKTTTLAKLA 242
>gnl|CDD|219536 pfam07724, AAA_2, AAA domain (Cdc48 subfamily). This Pfam entry
includes some of the AAA proteins not detected by the
pfam00004 model.
Length = 168
Score = 31.4 bits (72), Expect = 0.37
Identities = 13/38 (34%), Positives = 21/38 (55%), Gaps = 2/38 (5%)
Query: 33 NIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNAS 70
+ + GP GVGKT LA +L G + A++ ++ S
Sbjct: 5 SFLFLGPTGVGKTELAKALAELLFG--DERALIRIDMS 40
>gnl|CDD|183088 PRK11331, PRK11331, 5-methylcytosine-specific restriction enzyme
subunit McrB; Provisional.
Length = 459
Score = 32.0 bits (72), Expect = 0.39
Identities = 15/25 (60%), Positives = 17/25 (68%)
Query: 33 NIIISGPPGVGKTTTILCLARILLG 57
NII+ GPPGVGKT LA +L G
Sbjct: 196 NIILQGPPGVGKTFVARRLAYLLTG 220
>gnl|CDD|238978 cd02020, CMPK, Cytidine monophosphate kinase (CMPK) catalyzes the
reversible phosphorylation of cytidine monophosphate
(CMP) to produce cytidine diphosphate (CDP), using ATP
as the preferred phosphoryl donor.
Length = 147
Score = 30.9 bits (71), Expect = 0.42
Identities = 11/22 (50%), Positives = 13/22 (59%)
Query: 34 IIISGPPGVGKTTTILCLARIL 55
I I GP G GK+T LA+ L
Sbjct: 2 IAIDGPAGSGKSTVAKLLAKKL 23
>gnl|CDD|238540 cd01120, RecA-like_NTPases, RecA-like NTPases. This family includes
the NTP binding domain of F1 and V1 H+ATPases, DnaB and
related helicases as well as bacterial RecA and related
eukaryotic and archaeal recombinases. This group also
includes bacterial conjugation proteins and related DNA
transfer proteins involved in type II and type IV
secretion.
Length = 165
Score = 30.9 bits (70), Expect = 0.47
Identities = 19/97 (19%), Positives = 29/97 (29%), Gaps = 21/97 (21%)
Query: 33 NIIISGPPGVGKTTTILCLARILLGP-------SFKDAVLELNASNDRGIDTVRNKIKMF 85
I++ GP G GKTT L LA + ++ + EL +
Sbjct: 1 LILVFGPTGSGKTTLALQLALNIATKGGKVVYVDIEEEIEELTERLIGESLKGALDNLII 60
Query: 86 AQQKVTLPP--------------GRHKIVILDEADSM 108
P G ++ILDE +
Sbjct: 61 VFATADDPAAARLLSKAERLRERGGDDLIILDELTRL 97
>gnl|CDD|226573 COG4088, COG4088, Predicted nucleotide kinase [Nucleotide
transport and metabolism].
Length = 261
Score = 31.4 bits (71), Expect = 0.47
Identities = 13/25 (52%), Positives = 17/25 (68%)
Query: 31 VPNIIISGPPGVGKTTTILCLARIL 55
+P II++G PG GKTT LA+ L
Sbjct: 1 MPLIILTGYPGSGKTTFAKELAKEL 25
>gnl|CDD|232804 TIGR00064, ftsY, signal recognition particle-docking protein
FtsY. There is a weak division between FtsY and SRP54;
both are GTPases. In E.coli, ftsY is an essential gene
located in an operon with cell division genes ftsE and
ftsX, but its apparent function is as the signal
recognition particle docking protein [Protein fate,
Protein and peptide secretion and trafficking].
Length = 272
Score = 31.4 bits (72), Expect = 0.48
Identities = 16/32 (50%), Positives = 17/32 (53%), Gaps = 1/32 (3%)
Query: 25 FSSSGNVPNII-ISGPPGVGKTTTILCLARIL 55
N PN+I G GVGKTTTI LA L
Sbjct: 65 LIVEENKPNVILFVGVNGVGKTTTIAKLANKL 96
>gnl|CDD|224027 COG1102, Cmk, Cytidylate kinase [Nucleotide transport and
metabolism].
Length = 179
Score = 30.8 bits (70), Expect = 0.53
Identities = 13/22 (59%), Positives = 13/22 (59%)
Query: 34 IIISGPPGVGKTTTILCLARIL 55
I ISG PG GKTT LA L
Sbjct: 3 ITISGLPGSGKTTVARELAEHL 24
>gnl|CDD|223775 COG0703, AroK, Shikimate kinase [Amino acid transport and
metabolism].
Length = 172
Score = 30.6 bits (70), Expect = 0.57
Identities = 12/35 (34%), Positives = 16/35 (45%), Gaps = 7/35 (20%)
Query: 32 PNIIISGPPGVGKTTTILCLARIL---LGPSFKDA 63
NI++ G G GK+T + R L L F D
Sbjct: 3 MNIVLIGFMGAGKST----IGRALAKALNLPFIDT 33
>gnl|CDD|236515 PRK09435, PRK09435, membrane ATPase/protein kinase; Provisional.
Length = 332
Score = 31.3 bits (72), Expect = 0.58
Identities = 18/38 (47%), Positives = 22/38 (57%)
Query: 28 SGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVL 65
+GN I I+G PGVGK+T I L L+ K AVL
Sbjct: 53 TGNALRIGITGVPGVGKSTFIEALGMHLIEQGHKVAVL 90
>gnl|CDD|238026 cd00071, GMPK, Guanosine monophosphate kinase (GMPK, EC 2.7.4.8),
also known as guanylate kinase (GKase), catalyzes the
reversible phosphoryl transfer from adenosine
triphosphate (ATP) to guanosine monophosphate (GMP) to
yield adenosine diphosphate (ADP) and guanosine
diphosphate (GDP). It plays an essential role in the
biosynthesis of guanosine triphosphate (GTP). This
enzyme is also important for the activation of some
antiviral and anticancer agents, such as acyclovir,
ganciclovir, carbovir, and thiopurines.
Length = 137
Score = 30.2 bits (69), Expect = 0.58
Identities = 9/13 (69%), Positives = 12/13 (92%)
Query: 34 IIISGPPGVGKTT 46
I++SGP GVGK+T
Sbjct: 2 IVLSGPSGVGKST 14
>gnl|CDD|129833 TIGR00750, lao, LAO/AO transport system ATPase. In E. coli,
mutation of this kinase blocks phosphorylation of two
transporter system periplasmic binding proteins and
consequently inhibits those transporters. This kinase
is also found in Gram-positive bacteria, archaea, and
the roundworm C. elegans. It may have a more general,
but still unknown function. Mutations have also been
found that do not phosphorylate the periplasmic binding
proteins, yet still allow transport. The ATPase
activity of this protein seems to be necessary, however
[Transport and binding proteins, Amino acids, peptides
and amines, Regulatory functions, Protein
interactions].
Length = 300
Score = 31.3 bits (71), Expect = 0.58
Identities = 14/49 (28%), Positives = 25/49 (51%)
Query: 22 LKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNAS 70
++ +GN + I+G PG GK+T + L L + AV+ ++ S
Sbjct: 25 DRIMPYTGNAHRVGITGTPGAGKSTLLEALGMELRRRGLRVAVIAVDPS 73
>gnl|CDD|233417 TIGR01447, recD, exodeoxyribonuclease V, alpha subunit. This
family describes the exodeoxyribonuclease V alpha
subunit, RecD. RecD is part of a RecBCD complex. A
related family in the Gram-positive bacteria separates
in a phylogenetic tree, has an additional N-terminal
extension of about 200 residues, and is not supported as
a member of a RecBCD complex by neighboring genes. The
related family is consequently described by a different
model [DNA metabolism, DNA replication, recombination,
and repair].
Length = 586
Score = 31.7 bits (72), Expect = 0.58
Identities = 14/33 (42%), Positives = 19/33 (57%)
Query: 35 IISGPPGVGKTTTILCLARILLGPSFKDAVLEL 67
+I+G PG GKTTT+ L L+ S K L +
Sbjct: 164 LITGGPGTGKTTTVARLLLALVKQSPKQGKLRI 196
>gnl|CDD|223563 COG0489, Mrp, ATPases involved in chromosome partitioning [Cell
division and chromosome partitioning].
Length = 265
Score = 31.2 bits (71), Expect = 0.62
Identities = 13/30 (43%), Positives = 16/30 (53%), Gaps = 2/30 (6%)
Query: 28 SGNVPNII--ISGPPGVGKTTTILCLARIL 55
V N+I SG GVGK+T + LA L
Sbjct: 53 RKGVKNVIAVTSGKGGVGKSTVAVNLAAAL 82
>gnl|CDD|227922 COG5635, COG5635, Predicted NTPase (NACHT family) [Signal
transduction mechanisms].
Length = 824
Score = 31.7 bits (72), Expect = 0.62
Identities = 12/48 (25%), Positives = 21/48 (43%)
Query: 5 RPQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLA 52
+ ++ + D + L + ++I G PG GKTT + LA
Sbjct: 196 DEEFLLELTQSADDQDALPGLEALEKYAKLLILGAPGSGKTTFLQRLA 243
>gnl|CDD|238550 cd01130, VirB11-like_ATPase, Type IV secretory pathway component
VirB11, and related ATPases. The homohexamer, VirB11 is
one of eleven Vir proteins, which are required for
T-pilus biogenesis and virulence in the transfer of
T-DNA from the Ti (tumor-inducing) plasmid of bacterial
to plant cells. The pilus is a fibrous cell surface
organelle, which mediates adhesion between bacteria
during conjugative transfer or between bacteria and
host eukaryotic cells during infection. VirB11- related
ATPases include the archaeal flagella biosynthesis
protein and the pilus assembly proteins CpaF/TadA and
TrbB. This alignment contains the C-terminal domain,
which is the ATPase.
Length = 186
Score = 30.7 bits (70), Expect = 0.62
Identities = 11/20 (55%), Positives = 13/20 (65%)
Query: 33 NIIISGPPGVGKTTTILCLA 52
NI+ISG G GKTT + L
Sbjct: 27 NILISGGTGSGKTTLLNALL 46
>gnl|CDD|213788 TIGR03263, guanyl_kin, guanylate kinase. Members of this family
are the enzyme guanylate kinase, also called GMP
kinase. This enzyme transfers a phosphate from ATP to
GMP, yielding ADP and GDP [Purines, pyrimidines,
nucleosides, and nucleotides, Nucleotide and nucleoside
interconversions].
Length = 179
Score = 30.5 bits (70), Expect = 0.63
Identities = 9/13 (69%), Positives = 11/13 (84%)
Query: 34 IIISGPPGVGKTT 46
I+ISGP G GK+T
Sbjct: 3 IVISGPSGAGKST 15
>gnl|CDD|224768 COG1855, COG1855, ATPase (PilT family) [General function prediction
only].
Length = 604
Score = 31.6 bits (72), Expect = 0.67
Identities = 14/42 (33%), Positives = 21/42 (50%), Gaps = 5/42 (11%)
Query: 15 NEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILL 56
++ ERL+ + G I+I+G PG GK+T LA
Sbjct: 252 SDKLKERLEE-RAEG----ILIAGAPGAGKSTFAQALAEFYA 288
>gnl|CDD|222307 pfam13671, AAA_33, AAA domain. This family of domains contain only
a P-loop motif, that is characteristic of the AAA
superfamily. Many of the proteins in this family are
just short fragments so there is no Walker B motif.
Length = 143
Score = 30.4 bits (69), Expect = 0.70
Identities = 22/85 (25%), Positives = 38/85 (44%), Gaps = 17/85 (20%)
Query: 34 IIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKIKMFAQQKVTLP 93
I++ G PG GK+T AR LL AV+ L++ DT+R +++ ++
Sbjct: 2 ILMVGLPGSGKST----FARRLLRE--LGAVV-LSS------DTLRKRLRGDGPPDISYY 48
Query: 94 PGRHKIVILDEADSMTDGAQQALRR 118
V + + A++ALR
Sbjct: 49 ARASGRV----YQRLLELAREALRA 69
>gnl|CDD|224337 COG1419, FlhF, Flagellar GTP-binding protein [Cell motility and
secretion].
Length = 407
Score = 31.2 bits (71), Expect = 0.72
Identities = 14/32 (43%), Positives = 17/32 (53%)
Query: 33 NIIISGPPGVGKTTTILCLARILLGPSFKDAV 64
I + GP GVGKTTT+ LA + K V
Sbjct: 205 VIALVGPTGVGKTTTLAKLAARYVMLKKKKKV 236
>gnl|CDD|238713 cd01428, ADK, Adenylate kinase (ADK) catalyzes the reversible
phosphoryl transfer from adenosine triphosphates (ATP)
to adenosine monophosphates (AMP) and to yield
adenosine diphosphates (ADP). This enzyme is required
for the biosynthesis of ADP and is essential for
homeostasis of adenosine phosphates.
Length = 194
Score = 30.7 bits (70), Expect = 0.73
Identities = 8/14 (57%), Positives = 10/14 (71%)
Query: 33 NIIISGPPGVGKTT 46
I++ GPPG GK T
Sbjct: 1 RILLLGPPGSGKGT 14
>gnl|CDD|238260 cd00464, SK, Shikimate kinase (SK) is the fifth enzyme in the
shikimate pathway, a seven-step biosynthetic pathway
which converts erythrose-4-phosphate to chorismic acid,
found in bacteria, fungi and plants. Chorismic acid is
a important intermediate in the synthesis of aromatic
compounds, such as aromatic amino acids, p-aminobenzoic
acid, folate and ubiquinone. Shikimate kinase catalyses
the phosphorylation of the 3-hydroxyl group of shikimic
acid using ATP.
Length = 154
Score = 30.2 bits (69), Expect = 0.74
Identities = 14/34 (41%), Positives = 18/34 (52%), Gaps = 7/34 (20%)
Query: 33 NIIISGPPGVGKTTTILCLARIL---LGPSFKDA 63
NI++ G G GKTT + R+L LG F D
Sbjct: 1 NIVLIGMMGAGKTT----VGRLLAKALGLPFVDL 30
>gnl|CDD|183617 PRK12600, PRK12600, putative monovalent cation/H+ antiporter
subunit F; Reviewed.
Length = 94
Score = 29.1 bits (66), Expect = 0.78
Identities = 13/37 (35%), Positives = 22/37 (59%)
Query: 33 NIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNA 69
NII+S + + +L L R++ GP+ D V+ L+A
Sbjct: 3 NIILSIALIIVAISMLLMLIRVIKGPTLADRVVALDA 39
>gnl|CDD|184311 PRK13764, PRK13764, ATPase; Provisional.
Length = 602
Score = 31.3 bits (72), Expect = 0.79
Identities = 8/13 (61%), Positives = 11/13 (84%)
Query: 34 IIISGPPGVGKTT 46
I+I+G PG GK+T
Sbjct: 260 ILIAGAPGAGKST 272
>gnl|CDD|215925 pfam00448, SRP54, SRP54-type protein, GTPase domain. This family
includes relatives of the G-domain of the SRP54 family
of proteins.
Length = 196
Score = 30.2 bits (69), Expect = 0.85
Identities = 14/25 (56%), Positives = 16/25 (64%), Gaps = 1/25 (4%)
Query: 32 PNII-ISGPPGVGKTTTILCLARIL 55
PN+I + G G GKTTTI LA L
Sbjct: 1 PNVILLVGLQGSGKTTTIAKLAAYL 25
>gnl|CDD|216186 pfam00910, RNA_helicase, RNA helicase. This family includes RNA
helicases thought to be involved in duplex unwinding
during viral RNA replication. Members of this family
are found in a variety of single stranded RNA viruses.
Length = 105
Score = 29.5 bits (67), Expect = 0.85
Identities = 13/23 (56%), Positives = 15/23 (65%)
Query: 34 IIISGPPGVGKTTTILCLARILL 56
I + GPPG GK+T LAR LL
Sbjct: 1 IWLYGPPGCGKSTLAKYLARALL 23
>gnl|CDD|153287 cd07603, BAR_ACAPs, The Bin/Amphiphysin/Rvs (BAR) domain of ArfGAP
with Coiled-coil, ANK repeat and PH domain containing
proteins. BAR domains are dimerization, lipid binding
and curvature sensing modules found in many different
proteins with diverse functions. This subfamily is
composed of ACAPs (ArfGAP with Coiled-coil, ANK repeat
and PH domain containing proteins), which are Arf GTPase
activating proteins (GAPs) containing an N-terminal BAR
domain, followed by a Pleckstrin homology (PH) domain,
an Arf GAP domain, and C-terminal ankyrin (ANK) repeats.
Vertebrates contain at least three members, ACAP1,
ACAP2, and ACAP3. ACAP1 and ACAP2 are Arf6-specific
GAPs, involved in the regulation of endocytosis,
phagocytosis, cell adhesion and migration, by mediating
Arf6 signaling. BAR domains form dimers that bind to
membranes, induce membrane bending and curvature, and
may also be involved in protein-protein interactions.
Length = 200
Score = 30.3 bits (69), Expect = 0.90
Identities = 17/53 (32%), Positives = 26/53 (49%), Gaps = 10/53 (18%)
Query: 171 ENISHTNDGLE-AIVFTAQG------DMRQALNNLQSTHNGFGHVTAEYVFKV 216
E IS D L+ A+V AQ + +A N L +T + F H +YV ++
Sbjct: 111 EKIS---DDLDNALVKNAQAPRSKPQEAEEATNILTATRSCFRHTALDYVLQI 160
>gnl|CDD|213213 cd03246, ABCC_Protease_Secretion, ATP-binding cassette domain of
PrtD, subfamily C. This family represents the ABC
component of the protease secretion system PrtD, a
60-kDa integral membrane protein sharing 37% identity
with HlyB, the ABC component of the alpha-hemolysin
secretion pathway, in the C-terminal domain. They export
degradative enzymes by using a type I protein secretion
system and lack an N-terminal signal peptide, but
contain a C-terminal secretion signal. The Type I
secretion apparatus is made up of three components, an
ABC transporter, a membrane fusion protein (MFP), and an
outer membrane protein (OMP). For the HlyA transporter
complex, HlyB (ABC transporter) and HlyD (MFP) reside in
the inner membrane of E. coli. The OMP component is
TolC, which is thought to interact with the MFP to form
a continuous channel across the periplasm from the
cytoplasm to the exterior. HlyB belongs to the family of
ABC transporters, which are ubiquitous, ATP-dependent
transmembrane pumps or channels. The spectrum of
transport substrates ranges from inorganic ions,
nutrients such as amino acids, sugars, or peptides,
hydrophobic drugs, to large polypeptides, such as HlyA.
Length = 173
Score = 29.9 bits (68), Expect = 0.97
Identities = 28/114 (24%), Positives = 49/114 (42%), Gaps = 36/114 (31%)
Query: 36 ISGPPGVGKTTTILCLARILLG---PSFKDAVL----ELN--ASNDRG--IDTVRNKIKM 84
I GP G GK+T LAR++LG P+ V +++ N+ G + + ++
Sbjct: 33 IIGPSGSGKST----LARLILGLLRPT-SGRVRLDGADISQWDPNELGDHVGYLPQDDEL 87
Query: 85 FA------------QQKVTLPP---GRHKIVILDEADSMTDGA-----QQALRR 118
F+ +Q++ L G +I++LDE +S D QA+
Sbjct: 88 FSGSIAENILSGGQRQRLGLARALYGNPRILVLDEPNSHLDVEGERALNQAIAA 141
>gnl|CDD|224144 COG1223, COG1223, Predicted ATPase (AAA+ superfamily) [General
function prediction only].
Length = 368
Score = 30.6 bits (69), Expect = 1.0
Identities = 16/60 (26%), Positives = 24/60 (40%), Gaps = 9/60 (15%)
Query: 2 EKYRPQTFSDIVGNEDTVERLKVFSSSGNVP---------NIIISGPPGVGKTTTILCLA 52
E T D++G E+ + ++ P N++ GPPG GKT LA
Sbjct: 113 EIISDITLDDVIGQEEAKRKCRLIMEYLENPERFGDWAPKNVLFYGPPGTGKTMMAKALA 172
>gnl|CDD|132613 TIGR03574, selen_PSTK, L-seryl-tRNA(Sec) kinase, archaeal.
Members of this protein are L-seryl-tRNA(Sec) kinase.
This enzyme is part of a two-step pathway in Eukaryota
and Archaea for performing selenocysteine biosynthesis
by changing serine misacylated on selenocysteine-tRNA
to selenocysteine. This enzyme performs the first step,
phosphorylation of the OH group of the serine side
chain. This family represents archaeal proteins with
this activity [Protein synthesis, tRNA aminoacylation].
Length = 249
Score = 30.5 bits (69), Expect = 1.0
Identities = 13/36 (36%), Positives = 20/36 (55%)
Query: 34 IIISGPPGVGKTTTILCLARILLGPSFKDAVLELNA 69
II++G PGVGK+T LA+ L + +L +
Sbjct: 2 IILTGLPGVGKSTFSKELAKKLSEKNIDVIILGTDL 37
>gnl|CDD|223455 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 = 30.3 bits (69), Expect = 1.1
Identities = 14/33 (42%), Positives = 17/33 (51%), Gaps = 1/33 (3%)
Query: 34 IIISGPPGVGKTTTILCLARILLGPSFKDAVLE 66
I + GPPG GKT I R L +K AV+
Sbjct: 16 IGVGGPPGSGKTALIEKTLRALKD-EYKIAVIT 47
>gnl|CDD|237875 PRK14974, PRK14974, cell division protein FtsY; Provisional.
Length = 336
Score = 30.3 bits (69), Expect = 1.1
Identities = 15/45 (33%), Positives = 22/45 (48%)
Query: 11 DIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARIL 55
+++ D + ++ S G I+ G G GKTTTI LA L
Sbjct: 120 EVLSVGDLFDLIEEIKSKGKPVVIVFVGVNGTGKTTTIAKLAYYL 164
>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 = 30.4 bits (69), Expect = 1.1
Identities = 15/51 (29%), Positives = 25/51 (49%)
Query: 23 KVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDR 73
++ +G + I+G PG GK+T I L L + AVL ++ S+
Sbjct: 21 RLMPLTGRAHRVGITGVPGAGKSTLIEALGMELRRRGHRVAVLAVDPSSPF 71
>gnl|CDD|222163 pfam13479, AAA_24, AAA domain. This AAA domain is found in a wide
variety of presumed phage proteins.
Length = 201
Score = 29.9 bits (68), Expect = 1.2
Identities = 19/84 (22%), Positives = 32/84 (38%), Gaps = 13/84 (15%)
Query: 33 NIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASN---DRGIDTVR-NKIKMFAQQ 88
++I GPPG+GKT+ LA+ L K L+L+A D V +
Sbjct: 5 KVLIYGPPGIGKTS----LAKTLPP---KTLFLDLDAGTTKVLSRGDNVDIRSWQDLRDF 57
Query: 89 KVTLP--PGRHKIVILDEADSMTD 110
L + +++D +
Sbjct: 58 LDELAEDLAEYDTLVIDTITKLER 81
>gnl|CDD|110677 pfam01695, IstB_IS21, IstB-like ATP binding protein. This
protein contains an ATP/GTP binding P-loop motif. It is
found associated with IS21 family insertion sequences.
The function of this protein is unknown, but it may
perform a transposase function.
Length = 178
Score = 29.9 bits (68), Expect = 1.2
Identities = 9/13 (69%), Positives = 12/13 (92%)
Query: 33 NIIISGPPGVGKT 45
N+++ GPPGVGKT
Sbjct: 49 NLLLLGPPGVGKT 61
>gnl|CDD|215920 pfam00437, T2SE, Type II/IV secretion system protein. This family
contains both type II and type IV pathway secretion
proteins from bacteria. VirB11 ATPase is a subunit of
the Agrobacterium tumefaciens transfer DNA (T-DNA)
transfer system, a type IV secretion pathway required
for delivery of T-DNA and effector proteins to plant
cells during infection.
Length = 273
Score = 30.3 bits (69), Expect = 1.3
Identities = 20/88 (22%), Positives = 38/88 (43%), Gaps = 22/88 (25%)
Query: 33 NIIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKIKMFAQQKVTL 92
NI++SG G GKTT + + E+N ++R I T+ + ++
Sbjct: 131 NILVSGGTGSGKTTLL------------YALLNEINTDDER-IVTIEDPVE-------IQ 170
Query: 93 PPGRHKIVILDEADSMT--DGAQQALRR 118
G +++ + +T D + ALR+
Sbjct: 171 LEGPNQVQLNTRLAGVTFADLLRAALRQ 198
>gnl|CDD|234172 TIGR03345, VI_ClpV1, type VI secretion ATPase, ClpV1 family.
Members of this protein family are homologs of ClpB, an
ATPase associated with chaperone-related functions.
These ClpB homologs, designated ClpV1, are a key
component of the bacterial pathogenicity-associated type
VI secretion system [Protein fate, Protein and peptide
secretion and trafficking, Cellular processes,
Pathogenesis].
Length = 852
Score = 30.7 bits (70), Expect = 1.3
Identities = 13/20 (65%), Positives = 14/20 (70%)
Query: 38 GPPGVGKTTTILCLARILLG 57
GP GVGKT T L LA +L G
Sbjct: 603 GPSGVGKTETALALAELLYG 622
>gnl|CDD|236442 PRK09270, PRK09270, nucleoside triphosphate hydrolase
domain-containing protein; Reviewed.
Length = 229
Score = 29.9 bits (68), Expect = 1.3
Identities = 10/20 (50%), Positives = 13/20 (65%)
Query: 36 ISGPPGVGKTTTILCLARIL 55
I+GPPG GK+T L +L
Sbjct: 38 IAGPPGAGKSTLAEFLEALL 57
>gnl|CDD|224009 COG1084, COG1084, Predicted GTPase [General function prediction
only].
Length = 346
Score = 30.3 bits (69), Expect = 1.3
Identities = 8/24 (33%), Positives = 16/24 (66%)
Query: 30 NVPNIIISGPPGVGKTTTILCLAR 53
++P I+++G P VGK++ + L
Sbjct: 167 DLPTIVVAGYPNVGKSSLVRKLTT 190
>gnl|CDD|234711 PRK00279, adk, adenylate kinase; Reviewed.
Length = 215
Score = 29.7 bits (68), Expect = 1.3
Identities = 8/14 (57%), Positives = 10/14 (71%)
Query: 33 NIIISGPPGVGKTT 46
+I+ GPPG GK T
Sbjct: 2 RLILLGPPGAGKGT 15
>gnl|CDD|234034 TIGR02858, spore_III_AA, stage III sporulation protein AA. Members
of this protein are the stage III sporulation protein
AA, encoded by one of several genes in the spoIIIA
locus. It seems that this protein is found in a species
if and only if that species is capable of endospore
formation [Cellular processes, Sporulation and
germination].
Length = 270
Score = 30.0 bits (68), Expect = 1.3
Identities = 14/28 (50%), Positives = 17/28 (60%)
Query: 28 SGNVPNIIISGPPGVGKTTTILCLARIL 55
+ V N +I PP GKTT + LARIL
Sbjct: 108 NNRVLNTLIISPPQCGKTTLLRDLARIL 135
>gnl|CDD|223626 COG0552, FtsY, Signal recognition particle GTPase [Intracellular
trafficking and secretion].
Length = 340
Score = 29.9 bits (68), Expect = 1.5
Identities = 14/35 (40%), Positives = 16/35 (45%), Gaps = 1/35 (2%)
Query: 28 SGNVPNII-ISGPPGVGKTTTILCLARILLGPSFK 61
P +I G GVGKTTTI LA+ L
Sbjct: 135 KEKKPFVILFVGVNGVGKTTTIAKLAKYLKQQGKS 169
>gnl|CDD|223998 COG1072, CoaA, Panthothenate kinase [Coenzyme metabolism].
Length = 283
Score = 29.9 bits (68), Expect = 1.5
Identities = 15/42 (35%), Positives = 20/42 (47%), Gaps = 7/42 (16%)
Query: 15 NEDTVERLKVFSSSGNVPNII-ISGPPGVGKTTTILCLARIL 55
+ + L + P II I+G VGK+TT ARIL
Sbjct: 67 FAELLRFLGTNNQQR--PFIIGIAGSVAVGKSTT----ARIL 102
>gnl|CDD|183702 PRK12723, PRK12723, flagellar biosynthesis regulator FlhF;
Provisional.
Length = 388
Score = 30.3 bits (68), Expect = 1.6
Identities = 14/21 (66%), Positives = 15/21 (71%)
Query: 34 IIISGPPGVGKTTTILCLARI 54
I+ GP GVGKTTTI LA I
Sbjct: 177 FILVGPTGVGKTTTIAKLAAI 197
>gnl|CDD|183044 PRK11231, fecE, iron-dicitrate transporter ATP-binding subunit;
Provisional.
Length = 255
Score = 30.0 bits (68), Expect = 1.6
Identities = 14/42 (33%), Positives = 23/42 (54%), Gaps = 2/42 (4%)
Query: 14 GNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARIL 55
G + + L + +G + +I GP G GK+T + C AR+L
Sbjct: 13 GTKRILNDLSLSLPTGKITALI--GPNGCGKSTLLKCFARLL 52
>gnl|CDD|215633 PLN03210, PLN03210, Resistant to P. syringae 6; Provisional.
Length = 1153
Score = 30.2 bits (68), Expect = 1.6
Identities = 18/49 (36%), Positives = 24/49 (48%), Gaps = 6/49 (12%)
Query: 9 FSDIVGNEDTVERLKVFS--SSGNVPNIIISGPPGVGKTTTILCLARIL 55
F D VG ED + ++ S V + I G G+GKTT +AR L
Sbjct: 183 FEDFVGIEDHIAKMSSLLHLESEEVRMVGIWGSSGIGKTT----IARAL 227
>gnl|CDD|235904 PRK06995, flhF, flagellar biosynthesis regulator FlhF; Validated.
Length = 484
Score = 30.3 bits (69), Expect = 1.6
Identities = 11/15 (73%), Positives = 11/15 (73%)
Query: 38 GPPGVGKTTTILCLA 52
GP GVGKTTT LA
Sbjct: 263 GPTGVGKTTTTAKLA 277
>gnl|CDD|224557 COG1643, HrpA, HrpA-like helicases [DNA replication,
recombination, and repair].
Length = 845
Score = 30.0 bits (68), Expect = 1.7
Identities = 10/28 (35%), Positives = 12/28 (42%), Gaps = 2/28 (7%)
Query: 34 IIISGPPGVGKTTTI--LCLARILLGPS 59
+II G G GKTT + L L
Sbjct: 68 VIIVGETGSGKTTQLPQFLLEEGLGIAG 95
>gnl|CDD|219538 pfam07728, AAA_5, AAA domain (dynein-related subfamily). This
Pfam entry includes some of the AAA proteins not
detected by the pfam00004 model.
Length = 135
Score = 28.8 bits (65), Expect = 1.8
Identities = 9/25 (36%), Positives = 13/25 (52%)
Query: 33 NIIISGPPGVGKTTTILCLARILLG 57
+++ GPPG GK+ LA L
Sbjct: 1 GVLLVGPPGTGKSELAERLAAALSN 25
>gnl|CDD|213229 cd03262, ABC_HisP_GlnQ, ATP-binding cassette domain of the
histidine and glutamine transporters. HisP and GlnQ
are the ATP-binding components of the bacterial
periplasmic histidine and glutamine permeases,
respectively. Histidine permease is a multi-subunit
complex containing the HisQ and HisM integral membrane
subunits and two copies of HisP. HisP has properties
intermediate between those of integral and peripheral
membrane proteins and is accessible from both sides of
the membrane, presumably by its interaction with HisQ
and HisM. The two HisP subunits form a homodimer within
the complex. The domain structure of the amino acid
uptake systems is typical for prokaryotic extracellular
solute binding protein-dependent uptake systems. All of
the amino acid uptake systems also have at least one,
and in a few cases, two extracellular solute binding
proteins located in the periplasm of Gram-negative
bacteria, or attached to the cell membrane of
Gram-positive bacteria. The best-studied member of the
PAAT (polar amino acid transport) family is the HisJQMP
system of S. typhimurium, where HisJ is the
extracellular solute binding proteins and HisP is the
ABC protein.
Length = 213
Score = 29.4 bits (67), Expect = 1.8
Identities = 17/58 (29%), Positives = 29/58 (50%), Gaps = 5/58 (8%)
Query: 34 IIISGPPGVGKTTTILCLARILLGPSFKDAVLE---LNASNDRGIDTVRNKIKMFAQQ 88
++I GP G GK+T + C+ L P +++ L + I+ +R K+ M QQ
Sbjct: 29 VVIIGPSGSGKSTLLRCINL-LEEPDSGTIIIDGLKLTDD-KKNINELRQKVGMVFQQ 84
>gnl|CDD|223272 COG0194, Gmk, Guanylate kinase [Nucleotide transport and
metabolism].
Length = 191
Score = 29.4 bits (67), Expect = 1.8
Identities = 10/18 (55%), Positives = 14/18 (77%)
Query: 34 IIISGPPGVGKTTTILCL 51
I++SGP GVGK+T + L
Sbjct: 7 IVLSGPSGVGKSTLVKAL 24
>gnl|CDD|213223 cd03256, ABC_PhnC_transporter, ATP-binding cassette domain of the
binding protein-dependent phosphonate transport system.
Phosphonates are a class of organophosphorus compounds
characterized by a chemically stable
carbon-to-phosphorus (C-P) bond. Phosphonates are
widespread among naturally occurring compounds in all
kingdoms of wildlife, but only prokaryotic
microorganisms are able to cleave this bond. Certain
bacteria such as E. coli can use alkylphosphonates as a
phosphorus source. 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 = 241
Score = 29.5 bits (67), Expect = 1.8
Identities = 16/60 (26%), Positives = 28/60 (46%), Gaps = 8/60 (13%)
Query: 34 IIISGPPGVGKTTTILCLARILLGPS-----FKDAVLELNASNDRGIDTVRNKIKMFAQQ 88
+ + GP G GK+T + CL L+ P+ ++N + + +R +I M QQ
Sbjct: 30 VALIGPSGAGKSTLLRCLNG-LVEPTSGSVLIDG--TDINKLKGKALRQLRRQIGMIFQQ 86
>gnl|CDD|213232 cd03265, ABC_DrrA, Daunorubicin/doxorubicin resistance
ATP-binding protein. DrrA is the ATP-binding protein
component of a bacterial exporter complex that confers
resistance to the antibiotics daunorubicin and
doxorubicin. In addition to DrrA, the complex includes
an integral membrane protein called DrrB. DrrA belongs
to the ABC family of transporters and shares sequence
and functional similarities with a protein found in
cancer cells called P-glycoprotein. 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 = 220
Score = 29.6 bits (67), Expect = 1.9
Identities = 17/51 (33%), Positives = 23/51 (45%), Gaps = 2/51 (3%)
Query: 38 GPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKIKMFAQQ 88
GP G GKTTTI L +L S + V + + VR +I + Q
Sbjct: 33 GPNGAGKTTTIKMLTTLLKPTSGRATVAGHDVVREP--REVRRRIGIVFQD 81
>gnl|CDD|240274 PTZ00112, PTZ00112, origin recognition complex 1 protein;
Provisional.
Length = 1164
Score = 30.0 bits (67), Expect = 1.9
Identities = 58/208 (27%), Positives = 89/208 (42%), Gaps = 46/208 (22%)
Query: 28 SGNVPNIIISGPPGVGKTTTILCLARIL-------LGPSFKDAVLELNASN--------- 71
SG+ + ISG PG GKT T+ + ++L L PSF V E+N N
Sbjct: 778 SGSNQILYISGMPGTGKTATVYSVIQLLQHKTKQKLLPSFN--VFEINGMNVVHPNAAYQ 835
Query: 72 -------DRGIDTVRNKIKM----FAQQKVTLPPGRH-KIVILDEADSMTDGAQQALRRT 119
++ N K+ F Q K R+ I+I+DE D + Q+ L
Sbjct: 836 VLYKQLFNKKPPNALNSFKILDRLFNQNK---KDNRNVSILIIDEIDYLITKTQKVLFTL 892
Query: 120 MEIYS--NTTRFALACNNS----EKIIEPIQSRCAMLR-----YNKLTDAQLLSKVIEIC 168
+ + N+ +A +N+ E++I +SR A R Y +++ + +E C
Sbjct: 893 FDWPTKINSKLVLIAISNTMDLPERLIPRCRSRLAFGRLVFSPYKGDEIEKIIKERLENC 952
Query: 169 EKENISHTNDGLEA-IVFTAQGDMRQAL 195
KE I HT L A V GD+R+AL
Sbjct: 953 -KEIIDHTAIQLCARKVANVSGDIRKAL 979
>gnl|CDD|234896 PRK01077, PRK01077, cobyrinic acid a,c-diamide synthase;
Validated.
Length = 451
Score = 29.7 bits (68), Expect = 2.0
Identities = 12/27 (44%), Positives = 16/27 (59%), Gaps = 1/27 (3%)
Query: 30 NVPNIIISGP-PGVGKTTTILCLARIL 55
+P ++I+ P G GKTT L L R L
Sbjct: 2 RMPALVIAAPASGSGKTTVTLGLMRAL 28
>gnl|CDD|238991 cd02034, CooC, The accessory protein CooC, which contains a
nucleotide-binding domain (P-loop) near the N-terminus,
participates in the maturation of the nickel center of
carbon monoxide dehydrogenase (CODH). CODH from
Rhodospirillum rubrum catalyzes the reversible
oxidation of CO to CO2. CODH contains a
nickel-iron-sulfur cluster (C-center) and an
iron-sulfur cluster (B-center). CO oxidation occurs at
the C-center. Three accessory proteins encoded by
cooCTJ genes are involved in nickel incorporation into
a nickel site. CooC functions as a nickel insertase
that mobilizes nickel to apoCODH using energy released
from ATP hydrolysis. CooC is a homodimer and has NTPase
activities. Mutation at the P-loop abolishs its
function.
Length = 116
Score = 28.4 bits (64), Expect = 2.0
Identities = 13/25 (52%), Positives = 14/25 (56%)
Query: 33 NIIISGPPGVGKTTTILCLARILLG 57
I I+G GVGKTT LAR L
Sbjct: 1 KIAITGKGGVGKTTIAALLARYLAE 25
>gnl|CDD|205733 pfam13555, AAA_29, P-loop containing region of AAA domain.
Length = 60
Score = 27.1 bits (61), Expect = 2.2
Identities = 8/27 (29%), Positives = 15/27 (55%)
Query: 33 NIIISGPPGVGKTTTILCLARILLGPS 59
+++GP G GK+T I + +L+
Sbjct: 23 GTLLTGPSGSGKSTLIDAIQTLLVPAK 49
>gnl|CDD|233327 TIGR01241, FtsH_fam, ATP-dependent metalloprotease FtsH.
HflB(FtsH) is a pleiotropic protein required for correct
cell division in bacteria. It has ATP-dependent zinc
metalloprotease activity. It was formerly designated
cell division protein FtsH [Cellular processes, Cell
division, Protein fate, Degradation of proteins,
peptides, and glycopeptides].
Length = 495
Score = 29.6 bits (67), Expect = 2.2
Identities = 15/50 (30%), Positives = 22/50 (44%), Gaps = 12/50 (24%)
Query: 8 TFSDIVGNEDTVERL-----------KVFSSSGNVPN-IIISGPPGVGKT 45
TF D+ G ++ E L K +P +++ GPPG GKT
Sbjct: 53 TFKDVAGIDEAKEELMEIVDFLKNPSKFTKLGAKIPKGVLLVGPPGTGKT 102
>gnl|CDD|181681 PRK09183, PRK09183, transposase/IS protein; Provisional.
Length = 259
Score = 29.3 bits (66), Expect = 2.3
Identities = 23/90 (25%), Positives = 42/90 (46%), Gaps = 17/90 (18%)
Query: 33 NIIISGPPGVGKTTTILCLARILLGPSFK-------DAVLELNASNDRGIDTVRNKIKMF 85
NI++ GP GVGKT + L + K D +L+L+ + +G R K +
Sbjct: 104 NIVLLGPSGVGKTHLAIALGYEAVRAGIKVRFTTAADLLLQLSTAQRQG----RYKTTL- 158
Query: 86 AQQKVTLPPGRHKIVILDEADSMTDGAQQA 115
Q+ + P +++I+DE + ++A
Sbjct: 159 --QRGVMAP---RLLIIDEIGYLPFSQEEA 183
>gnl|CDD|226426 COG3911, COG3911, Predicted ATPase [General function prediction
only].
Length = 183
Score = 29.1 bits (65), Expect = 2.4
Identities = 11/19 (57%), Positives = 14/19 (73%)
Query: 35 IISGPPGVGKTTTILCLAR 53
I++G PG GKTT + LAR
Sbjct: 13 ILTGGPGAGKTTLLAALAR 31
>gnl|CDD|105560 PRK12339, PRK12339, 2-phosphoglycerate kinase; Provisional.
Length = 197
Score = 29.0 bits (65), Expect = 2.4
Identities = 24/108 (22%), Positives = 36/108 (33%), Gaps = 38/108 (35%)
Query: 34 IIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTV------RNKIKMFAQ 87
I G PGVGKT+ +AR R ID V R ++ +
Sbjct: 6 HFIGGIPGVGKTSISGYIAR------------------HRAIDIVLSGDYLREFLRPYVD 47
Query: 88 QKVTL------------PPGRHKIV--ILDEADSMTDGAQQALRRTME 121
+ L IV LD+A ++ G + +RR +
Sbjct: 48 DEPVLAKSVYDAWEFYGSMTDENIVKGYLDQARAIMPGINRVIRRALL 95
>gnl|CDD|227596 COG5271, MDN1, AAA ATPase containing von Willebrand factor type A
(vWA) domain [General function prediction only].
Length = 4600
Score = 30.0 bits (67), Expect = 2.4
Identities = 12/21 (57%), Positives = 15/21 (71%)
Query: 34 IIISGPPGVGKTTTILCLARI 54
I++ G PGVGKT+ I LAR
Sbjct: 1546 ILLEGSPGVGKTSLITALARK 1566
>gnl|CDD|213227 cd03260, ABC_PstB_phosphate_transporter, ATP-binding cassette
domain of the phosphate transport system. Phosphate
uptake is of fundamental importance in the cell
physiology of bacteria because phosphate is required as
a nutrient. The Pst system of E. coli comprises four
distinct subunits encoded by the pstS, pstA, pstB, and
pstC genes. The PstS protein is a phosphate-binding
protein located in the periplasmic space. PstA and PstC
are hydrophobic and they form the transmembrane portion
of the Pst system. PstB is the catalytic subunit, which
couples the energy of ATP hydrolysis to the import of
phosphate across cellular membranes through the Pst
system, often referred as ABC-protein. PstB belongs to
one of the largest superfamilies of proteins
characterized by a highly conserved adenosine
triphosphate (ATP) binding cassette (ABC), which is
also a nucleotide binding domain (NBD).
Length = 227
Score = 29.1 bits (66), Expect = 2.5
Identities = 16/57 (28%), Positives = 26/57 (45%), Gaps = 6/57 (10%)
Query: 38 GPPGVGKTTTILCLAR-ILLGPSFKDA-VLELNASNDRGIDT----VRNKIKMFAQQ 88
GP G GK+T + L R L P D + L+ + +D +R ++ M Q+
Sbjct: 33 GPSGCGKSTLLRLLNRLNDLIPGAPDEGEVLLDGKDIYDLDVDVLELRRRVGMVFQK 89
>gnl|CDD|232945 TIGR00376, TIGR00376, DNA helicase, putative. The gene product may
represent a DNA helicase. Eukaryotic members of this
family have been characterized as binding certain
single-stranded G-rich DNA sequences (GGGGT and GGGCT).
A number of related proteins are characterized as
helicases [DNA metabolism, DNA replication,
recombination, and repair].
Length = 637
Score = 29.4 bits (66), Expect = 2.6
Identities = 12/22 (54%), Positives = 16/22 (72%)
Query: 35 IISGPPGVGKTTTILCLARILL 56
+I GPPG GKT T++ L R L+
Sbjct: 177 LIHGPPGTGKTRTLVELIRQLV 198
>gnl|CDD|223993 COG1066, Sms, Predicted ATP-dependent serine protease
[Posttranslational modification, protein turnover,
chaperones].
Length = 456
Score = 29.5 bits (67), Expect = 2.6
Identities = 13/26 (50%), Positives = 18/26 (69%), Gaps = 2/26 (7%)
Query: 29 GNVPN--IIISGPPGVGKTTTILCLA 52
G VP I+I G PG+GK+T +L +A
Sbjct: 89 GLVPGSVILIGGDPGIGKSTLLLQVA 114
>gnl|CDD|224048 COG1123, COG1123, ATPase components of various ABC-type transport
systems, contain duplicated ATPase [General function
prediction only].
Length = 539
Score = 29.5 bits (67), Expect = 2.6
Identities = 24/73 (32%), Positives = 32/73 (43%), Gaps = 17/73 (23%)
Query: 36 ISGPPGVGKTTTILCLARILLG---PS-----FKDAVLELNASNDRGIDTVRNKIKM-FA 86
+ G G GK+T LARIL G PS F L+L R + R +I+M F
Sbjct: 322 LVGESGSGKST----LARILAGLLPPSSGSIIFDGQDLDLTGGELRRL---RRRIQMVFQ 374
Query: 87 QQKVTLPPGRHKI 99
+L P R +
Sbjct: 375 DPYSSLNP-RMTV 386
>gnl|CDD|222178 pfam13500, AAA_26, AAA domain. This domain is found in a number
of proteins involved in cofactor biosynthesis such as
dethiobiotin synthase and cobyric acid synthase. This
domain contains a P-loop motif.
Length = 197
Score = 28.7 bits (65), Expect = 2.6
Identities = 11/25 (44%), Positives = 13/25 (52%), Gaps = 1/25 (4%)
Query: 34 IIISGP-PGVGKTTTILCLARILLG 57
I ++G GVGKT L L R L
Sbjct: 3 IFVTGTDTGVGKTVVSLGLVRALKR 27
>gnl|CDD|214692 smart00487, DEXDc, DEAD-like helicases superfamily.
Length = 201
Score = 29.0 bits (65), Expect = 2.7
Identities = 11/36 (30%), Positives = 16/36 (44%)
Query: 30 NVPNIIISGPPGVGKTTTILCLARILLGPSFKDAVL 65
+ ++I++ P G GKT L A L VL
Sbjct: 23 GLRDVILAAPTGSGKTLAALLPALEALKRGKGGRVL 58
>gnl|CDD|237148 PRK12599, PRK12599, putative monovalent cation/H+ antiporter
subunit F; Reviewed.
Length = 91
Score = 27.6 bits (62), Expect = 2.8
Identities = 11/24 (45%), Positives = 16/24 (66%)
Query: 48 ILCLARILLGPSFKDAVLELNASN 71
IL L R++LGP+ D V+ L+ N
Sbjct: 20 ILSLYRVILGPTLPDRVVALDTLN 43
>gnl|CDD|224054 COG1131, CcmA, ABC-type multidrug transport system, ATPase
component [Defense mechanisms].
Length = 293
Score = 29.2 bits (66), Expect = 2.8
Identities = 10/18 (55%), Positives = 12/18 (66%)
Query: 38 GPPGVGKTTTILCLARIL 55
GP G GKTT + LA +L
Sbjct: 38 GPNGAGKTTLLKILAGLL 55
>gnl|CDD|225887 COG3351, FlaD, Putative archaeal flagellar protein D/E [Cell
motility and secretion].
Length = 214
Score = 29.0 bits (65), Expect = 2.9
Identities = 14/74 (18%), Positives = 32/74 (43%), Gaps = 8/74 (10%)
Query: 232 CVEGNMKDSYKIIHHLYKLGYAPEDIIGNIFRVAKTLDIPEPLKLSIIQEIGNVHLRISE 291
G K++ ++ + +G+ E ++ + + AK + QE ++ L + +
Sbjct: 119 LDRGGPKNTLDVLDYYESIGWISEKVLEQLLKFAKGTKVMNDD-----QEEKSIKLTMQD 173
Query: 292 GVNSLL---QLSGL 302
+ SLL +L G
Sbjct: 174 HIISLLFIERLRGE 187
>gnl|CDD|235898 PRK06964, PRK06964, DNA polymerase III subunit delta'; Validated.
Length = 342
Score = 29.3 bits (66), Expect = 3.0
Identities = 15/50 (30%), Positives = 27/50 (54%)
Query: 98 KIVILDEADSMTDGAQQALRRTMEIYSNTTRFALACNNSEKIIEPIQSRC 147
++V+L A+++ A AL +T+E T F L ++++ I SRC
Sbjct: 134 RVVVLYPAEALNVAAANALLKTLEEPPPGTVFLLVSARIDRLLPTILSRC 183
>gnl|CDD|220642 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 = 29.1 bits (66), Expect = 3.0
Identities = 9/37 (24%), Positives = 17/37 (45%), Gaps = 3/37 (8%)
Query: 16 EDTVERLKVFSSSGN---VPNIIISGPPGVGKTTTIL 49
E+T+E K + V +++G G GK+ +
Sbjct: 5 EETLELTKKLKEADASKKVVRFVLTGERGSGKSVLLA 41
>gnl|CDD|233120 TIGR00764, lon_rel, lon-related putative ATP-dependent protease.
This model represents a set of proteins with extensive
C-terminal homology to the ATP-dependent protease La,
product of the lon gene of E. coli. The model is based
on a seed alignment containing only archaeal members,
but several bacterial proteins match the model well.
Because several species, including Thermotoga maritima
and Treponema pallidum, contain both a close homolog of
the lon protease and nearly full-length homolog of the
members of this family, we suggest there may also be a
functional division between the two families. Members
of this family from Pyrococcus horikoshii and
Pyrococcus abyssi each contain a predicted intein
[Protein fate, Degradation of proteins, peptides, and
glycopeptides].
Length = 608
Score = 29.4 bits (66), Expect = 3.1
Identities = 15/51 (29%), Positives = 28/51 (54%), Gaps = 2/51 (3%)
Query: 12 IVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSFKD 62
++G E+ VE +K ++ N+++ G PGVGK+ +A +L +D
Sbjct: 20 VIGQEEAVEIIK--KAAKQKRNVLLIGEPGVGKSMLAKAMAELLPDEELED 68
>gnl|CDD|224045 COG1120, FepC, ABC-type cobalamin/Fe3+-siderophores transport
systems, ATPase components [Inorganic ion transport and
metabolism / Coenzyme metabolism].
Length = 258
Score = 29.1 bits (66), Expect = 3.1
Identities = 11/22 (50%), Positives = 14/22 (63%)
Query: 34 IIISGPPGVGKTTTILCLARIL 55
I GP G GK+T + CLA +L
Sbjct: 31 TGILGPNGSGKSTLLKCLAGLL 52
>gnl|CDD|238835 cd01672, TMPK, Thymidine monophosphate kinase (TMPK), also known
as thymidylate kinase, catalyzes the phosphorylation of
thymidine monophosphate (TMP) to thymidine diphosphate
(TDP) utilizing ATP as its preferred phophoryl donor.
TMPK represents the rate-limiting step in either de
novo or salvage biosynthesis of thymidine triphosphate
(TTP).
Length = 200
Score = 28.8 bits (65), Expect = 3.2
Identities = 11/22 (50%), Positives = 12/22 (54%)
Query: 34 IIISGPPGVGKTTTILCLARIL 55
I+ G G GKTT I LA L
Sbjct: 3 IVFEGIDGAGKTTLIELLAERL 24
>gnl|CDD|201078 pfam00202, Aminotran_3, Aminotransferase class-III.
Length = 338
Score = 29.2 bits (66), Expect = 3.2
Identities = 31/158 (19%), Positives = 47/158 (29%), Gaps = 44/158 (27%)
Query: 51 LARILLG--PSFKDAVLELNASNDRGIDTVRNKIKM-FAQQKVTLPPGRHKIVILDEA-D 106
LA L P D V +N+ G + IK+ K G+ KI+
Sbjct: 64 LAEKLAQLTPGGLDRVFFMNS----GSEANETAIKLARQYAKKKGATGKTKIIAFSGGFH 119
Query: 107 SMTDGAQQALRRTMEIYSN-----------------TTRFALAC----NNSEK------- 138
T GA ++ + LAC K
Sbjct: 120 GRTLGAL-SVTGSSGYKKGFGPSLPGVYFLPYPDLEAAEEELACADEALRLIKAVHDDNI 178
Query: 139 ---IIEPIQSRCAMLRYNKLTDAQLLSKVIEICEKENI 173
I+EPIQ ++ L+ + EIC+K +
Sbjct: 179 AAVIVEPIQGEGGVVPP----PPGFLAGLREICKKHGV 212
>gnl|CDD|234041 TIGR02868, CydC, thiol reductant ABC exporter, CydC subunit. The
gene pair cydCD encodes an ABC-family transporter in
which each gene contains an N-terminal membrane-spanning
domain (pfam00664) and a C-terminal ATP-binding domain
(pfam00005). In E. coli these genes were discovered as
mutants which caused the terminal heme-copper oxidase
complex cytochrome bd to fail to assemble. Recent work
has shown that the transporter is involved in export of
redox-active thiol compounds such as cysteine and
glutathione. The linkage to assembly of the cytochrome
bd complex is further supported by the conserved operon
structure found outside the gammaproteobacteria
(cydABCD) containing both the transporter and oxidase
genes components. The genes used as the seed members for
this model are all either found in the
gammproteobacterial context or the CydABCD context. All
members of this family scoring above trusted at the time
of its creation were from genomes which encode a
cytochrome bd complex.
Length = 530
Score = 29.3 bits (66), Expect = 3.2
Identities = 18/55 (32%), Positives = 27/55 (49%), Gaps = 1/55 (1%)
Query: 34 IIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKIKMFAQQ 88
+ I GP G GK+T + LA LL P + L+ + D VR ++ + AQ
Sbjct: 364 VAILGPSGSGKSTLLATLAG-LLDPLQGEVTLDGVPVSSLDQDEVRRRVSVCAQD 417
>gnl|CDD|239388 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 = 28.4 bits (64), Expect = 3.3
Identities = 17/50 (34%), Positives = 27/50 (54%), Gaps = 1/50 (2%)
Query: 36 ISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDR-GIDTVRNKIKM 84
I+G PG GK+T I L L + AVL ++ S+ G + ++I+M
Sbjct: 4 ITGVPGAGKSTLIDALITALRARGKRVAVLAIDPSSPFSGGAILGDRIRM 53
>gnl|CDD|223703 COG0630, VirB11, Type IV secretory pathway, VirB11 components, and
related ATPases involved in archaeal flagella
biosynthesis [Cell motility and secretion /
Intracellular trafficking and secretion].
Length = 312
Score = 28.9 bits (65), Expect = 3.3
Identities = 11/34 (32%), Positives = 16/34 (47%), Gaps = 1/34 (2%)
Query: 33 NIIISGPPGVGKTTTILCLARILLGPSFKDAVLE 66
+III G GKTT + L + P + +E
Sbjct: 145 SIIICGGTASGKTTLLNALLD-FIPPEERIVTIE 177
>gnl|CDD|238977 cd02019, NK, Nucleoside/nucleotide kinase (NK) is a protein
superfamily consisting of multiple families of enzymes
that share structural similarity and are functionally
related to the catalysis of the reversible phosphate
group transfer from nucleoside triphosphates to
nucleosides/nucleotides, nucleoside monophosphates, or
sugars. Members of this family play a wide variety of
essential roles in nucleotide metabolism, the
biosynthesis of coenzymes and aromatic compounds, as
well as the metabolism of sugar and sulfate.
Length = 69
Score = 26.9 bits (60), Expect = 3.4
Identities = 12/27 (44%), Positives = 14/27 (51%)
Query: 34 IIISGPPGVGKTTTILCLARILLGPSF 60
I I+G G GK+T LA L G S
Sbjct: 2 IAITGGSGSGKSTVAKKLAEQLGGRSV 28
>gnl|CDD|233870 TIGR02442, Cob-chelat-sub, cobaltochelatase subunit.
Cobaltochelatase is responsible for the insertion of
cobalt into the corrin ring of coenzyme B12 during its
biosynthesis. Two versions have been well described.
CbiK/CbiX is a monomeric, anaerobic version which acts
early in the biosynthesis (pfam06180). CobNST is a
trimeric, ATP-dependent, aerobic version which acts
late in the biosynthesis
(TIGR02257/TIGR01650/TIGR01651). A number of genomes
(actinobacteria, cyanobacteria, betaproteobacteria and
pseudomonads) which apparently biosynthesize B12,
encode a cobN gene but are demonstrably lacking cobS
and cobT. These genomes do, however contain a homolog
(modelled here) of the magnesium chelatase subunits
BchI/BchD family. Aside from the cyanobacteria (which
have a separate magnesium chelatase trimer), these
species do not make chlorins, so do not have any use
for a magnesium chelatase. Furthermore, in nearly all
cases the members of this family are proximal to either
CobN itself or other genes involved in cobalt transport
or B12 biosynthesis.
Length = 633
Score = 29.3 bits (66), Expect = 3.4
Identities = 15/47 (31%), Positives = 23/47 (48%)
Query: 9 FSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARIL 55
F+ IVG ED L + + + ++I G G K+T LA +L
Sbjct: 3 FTAIVGQEDLKLALLLNAVDPRIGGVLIRGEKGTAKSTAARGLAALL 49
>gnl|CDD|216619 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 = 28.4 bits (64), Expect = 3.8
Identities = 19/114 (16%), Positives = 37/114 (32%), Gaps = 24/114 (21%)
Query: 16 EDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLGPSF-----------KDAV 64
E ++ L+ ++ G P I++ GP GKT + L + +
Sbjct: 5 EKELKELEEWAERGTYPIIVVYGPRRCGKTALLREFLEELRELGYRVIYYDPLRREFEEK 64
Query: 65 LELNASNDRGIDTVRNKIKMFAQQKVTLPP-------------GRHKIVILDEA 105
L+ R + + + + K L G+ +I+DE
Sbjct: 65 LDRFEEAKRLAEALGDALPKIGIAKSKLAFLSLTLLFELLKRKGKKIAIIIDEV 118
>gnl|CDD|237802 PRK14723, flhF, flagellar biosynthesis regulator FlhF; Provisional.
Length = 767
Score = 29.0 bits (65), Expect = 3.9
Identities = 11/15 (73%), Positives = 11/15 (73%)
Query: 38 GPPGVGKTTTILCLA 52
GP GVGKTTT LA
Sbjct: 192 GPTGVGKTTTTAKLA 206
>gnl|CDD|184036 PRK13407, bchI, magnesium chelatase subunit I; Provisional.
Length = 334
Score = 28.7 bits (64), Expect = 3.9
Identities = 15/50 (30%), Positives = 27/50 (54%)
Query: 6 PQTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARIL 55
P FS IVG E+ + + + + + +++ G G GK+T + LA +L
Sbjct: 4 PFPFSAIVGQEEMKQAMVLTAIDPGIGGVLVFGDRGTGKSTAVRALAALL 53
>gnl|CDD|213233 cd03266, ABC_NatA_sodium_exporter, ATP-binding cassette domain of
the Na+ transporter. NatA is the ATPase component of a
bacterial ABC-type Na+ transport system called NatAB,
which catalyzes ATP-dependent electrogenic Na+
extrusion without mechanically coupled proton or K+
uptake. NatB possess six putative membrane spanning
regions at its C-terminus. In B. subtilis, NatAB is
inducible by agents such as ethanol and protonophores,
which lower the proton-motive force across the
membrane. The closest sequence similarity to NatA is
exhibited by DrrA of the two-component daunorubicin-
and doxorubicin-efflux system. Hence, the functional
NatAB is presumably assembled with two copies of a
single ATP-binding protein and a single integral
membrane protein.
Length = 218
Score = 28.5 bits (64), Expect = 4.1
Identities = 21/79 (26%), Positives = 32/79 (40%), Gaps = 16/79 (20%)
Query: 7 QTFSDIVGNEDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARILLG---PSFKDA 63
+ F D+ V+ + G V ++ GP G GKTTT+ R+L G P A
Sbjct: 9 KRFRDVKKTVQAVDGVSFTVKPGEVTGLL--GPNGAGKTTTL----RMLAGLLEPDAGFA 62
Query: 64 VLELNASNDRGIDTVRNKI 82
++ G D V+
Sbjct: 63 TVD-------GFDVVKEPA 74
>gnl|CDD|238997 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 = 27.2 bits (61), Expect = 4.4
Identities = 10/15 (66%), Positives = 11/15 (73%)
Query: 41 GVGKTTTILCLARIL 55
GVGKTTT + LA L
Sbjct: 10 GVGKTTTAVNLAAAL 24
>gnl|CDD|233369 TIGR01351, adk, adenylate kinase. Adenylate kinase (EC 2.7.4.3)
converts ATP + AMP to ADP + ADP, that is, uses ATP as a
phosphate donor for AMP. Most members of this family
are known or believed to be adenylate kinase. However,
some members accept other nucleotide triphosphates as
donors, may be unable to use ATP, and may fail to
complement adenylate kinase mutants. An example of a
nucleoside-triphosphate--adenylate kinase (EC 2.7.4.10)
is a GTP:AMP phosphotransferase. This family is
designated subfamily rather than equivalog for this
reason [Purines, pyrimidines, nucleosides, and
nucleotides, Nucleotide and nucleoside
interconversions].
Length = 210
Score = 28.3 bits (64), Expect = 4.4
Identities = 7/14 (50%), Positives = 10/14 (71%)
Query: 33 NIIISGPPGVGKTT 46
+++ GPPG GK T
Sbjct: 1 RLVLLGPPGSGKGT 14
>gnl|CDD|215957 pfam00506, Flu_NP, Influenza virus nucleoprotein.
Length = 506
Score = 28.8 bits (64), Expect = 4.4
Identities = 28/168 (16%), Positives = 51/168 (30%), Gaps = 18/168 (10%)
Query: 89 KVTLPPGRHKIVILDEADSMTDGAQQALRRTMEIYSNTTRFAL--ACNNSEKIIEPIQSR 146
K LP + + + D +G + +N F+L ++ E + +
Sbjct: 278 KSCLPACVYGLAVASGYDFEREGYSLVGIDAFRLLNNAQVFSLIRPNDDPEDKSQLVWMA 337
Query: 147 CAMLRYNKLT------------DAQLLSKVIEICEKENISHTNDGLEAIVFTAQGDMRQA 194
C Y L QL ++ ++ EN+ + L + ++
Sbjct: 338 CFGAAYEDLRVSSAIRGTRVKPRGQLKTRGFQVASNENVETMDSSLLELRSRYWAIRTRS 397
Query: 195 LNNLQSTHNGFGHVTAEYVFKVCDEPHPL---AVKEMLLNCVEGNMKD 239
N G ++ VF V + P V L EG D
Sbjct: 398 GGNTNQQRASAGQISVSPVFAV-ERNIPFERQTVMAALNGNTEGRTSD 444
>gnl|CDD|222290 pfam13654, AAA_32, AAA domain. This family includes a wide
variety of AAA domains including some that have lost
essential nucleotide binding residues in the P-loop.
Length = 509
Score = 28.6 bits (65), Expect = 4.6
Identities = 8/17 (47%), Positives = 11/17 (64%)
Query: 33 NIIISGPPGVGKTTTIL 49
NI + G PG G+TT +
Sbjct: 32 NIFVLGEPGTGRTTLVR 48
>gnl|CDD|236492 PRK09382, ispDF, bifunctional 2-C-methyl-D-erythritol 4-phosphate
cytidylyltransferase/2-C-methyl-D-erythritol
2,4-cyclodiphosphate synthase protein; Provisional.
Length = 378
Score = 28.7 bits (65), Expect = 4.7
Identities = 13/58 (22%), Positives = 23/58 (39%), Gaps = 6/58 (10%)
Query: 178 DGLEAIVFTAQGDMRQALNNLQSTHNGFGHVTAEYVFKVCDEPHPLAVKEMLLNCVEG 235
++ + G RQ +S N + +EYV + D P KE++ +E
Sbjct: 69 PEIKFVTLVTGGATRQ-----ESVRNALEALDSEYVL-IHDAARPFVPKELIDRLIEA 120
>gnl|CDD|185575 PTZ00361, PTZ00361, 26 proteosome regulatory subunit 4-like
protein; Provisional.
Length = 438
Score = 28.6 bits (64), Expect = 4.7
Identities = 16/58 (27%), Positives = 29/58 (50%), Gaps = 13/58 (22%)
Query: 1 IEKYRPQTFSDIVGNEDTVERLK-----------VFSSSGNVP--NIIISGPPGVGKT 45
++K ++++DI G E ++ +K ++ G P +I+ GPPG GKT
Sbjct: 174 VDKAPLESYADIGGLEQQIQEIKEAVELPLTHPELYDDIGIKPPKGVILYGPPGTGKT 231
>gnl|CDD|224401 COG1484, DnaC, DNA replication protein [DNA replication,
recombination, and repair].
Length = 254
Score = 28.5 bits (64), Expect = 4.7
Identities = 9/20 (45%), Positives = 14/20 (70%)
Query: 33 NIIISGPPGVGKTTTILCLA 52
N+++ GPPGVGKT + +
Sbjct: 107 NLVLLGPPGVGKTHLAIAIG 126
>gnl|CDD|217066 pfam02492, cobW, CobW/HypB/UreG, nucleotide-binding domain. This
domain is found in HypB, a hydrogenase expression /
formation protein, and UreG a urease accessory protein.
Both these proteins contain a P-loop nucleotide binding
motif. HypB has GTPase activity and is a guanine
nucleotide binding protein. It is not known whether
UreG binds GTP or some other nucleotide. Both enzymes
are involved in nickel binding. HypB can store nickel
and is required for nickel dependent hydrogenase
expression. UreG is required for functional
incorporation of the urease nickel metallocenter. GTP
hydrolysis may required by these proteins for nickel
incorporation into other nickel proteins. This family
of domains also contains P47K, a Pseudomonas
chlororaphis protein needed for nitrile hydratase
expression, and the cobW gene product, which may be
involved in cobalamin biosynthesis in Pseudomonas
denitrificans.
Length = 178
Score = 28.0 bits (63), Expect = 4.8
Identities = 11/35 (31%), Positives = 16/35 (45%), Gaps = 1/35 (2%)
Query: 32 PNIIISGPPGVGKTTTILCLARILLGPSFKDAVLE 66
P +++G G GKTT + L K AV+
Sbjct: 1 PVTVLTGFLGSGKTTLLEHLLE-KNREGLKIAVIV 34
>gnl|CDD|131368 TIGR02315, ABC_phnC, phosphonate ABC transporter, ATP-binding
protein. Phosphonates are a class of
phosphorus-containing organic compound with a stable
direct C-P bond rather than a C-O-P linkage. A number
of bacterial species have operons, typically about 14
genes in size, with genes for ATP-dependent transport
of phosphonates, degradation, and regulation of the
expression of the system. Members of this protein
family are the ATP-binding cassette component of
tripartite ABC transporters of phosphonates [Transport
and binding proteins, Anions].
Length = 243
Score = 28.4 bits (64), Expect = 4.9
Identities = 18/58 (31%), Positives = 29/58 (50%), Gaps = 4/58 (6%)
Query: 34 IIISGPPGVGKTTTILCLARILLGPSFKDAVLE---LNASNDRGIDTVRNKIKMFAQQ 88
+ I GP G GK+T + C+ R L+ PS +LE + + + +R +I M Q
Sbjct: 31 VAIIGPSGAGKSTLLRCINR-LVEPSSGSILLEGTDITKLRGKKLRKLRRRIGMIFQH 87
>gnl|CDD|223401 COG0324, MiaA, tRNA delta(2)-isopentenylpyrophosphate transferase
[Translation, ribosomal structure and biogenesis].
Length = 308
Score = 28.4 bits (64), Expect = 5.0
Identities = 11/25 (44%), Positives = 15/25 (60%)
Query: 34 IIISGPPGVGKTTTILCLARILLGP 58
I+I+GP GKT + LA+ L G
Sbjct: 6 IVIAGPTASGKTALAIALAKRLGGE 30
>gnl|CDD|237420 PRK13537, PRK13537, nodulation ABC transporter NodI; Provisional.
Length = 306
Score = 28.2 bits (63), Expect = 5.1
Identities = 14/26 (53%), Positives = 17/26 (65%), Gaps = 4/26 (15%)
Query: 38 GPPGVGKTTTILCLARILLGPSFKDA 63
GP G GKTTT+ R+LLG + DA
Sbjct: 40 GPNGAGKTTTL----RMLLGLTHPDA 61
>gnl|CDD|236686 PRK10416, PRK10416, signal recognition particle-docking protein
FtsY; Provisional.
Length = 318
Score = 28.5 bits (65), Expect = 5.1
Identities = 14/34 (41%), Positives = 17/34 (50%), Gaps = 1/34 (2%)
Query: 23 KVFSSSGNVPNII-ISGPPGVGKTTTILCLARIL 55
K + P +I + G GVGKTTTI LA
Sbjct: 105 KPLNIEEKKPFVILVVGVNGVGKTTTIGKLAHKY 138
>gnl|CDD|222264 pfam13614, AAA_31, AAA domain. This family includes a wide
variety of AAA domains including some that have lost
essential nucleotide binding residues in the P-loop.
Length = 145
Score = 27.6 bits (62), Expect = 5.3
Identities = 13/37 (35%), Positives = 17/37 (45%)
Query: 35 IISGPPGVGKTTTILCLARILLGPSFKDAVLELNASN 71
+ S G GKTT L LA+ L K L+L +
Sbjct: 5 VYSPVGGEGKTTFALNLAQSLAEEGPKVLYLDLEEYS 41
>gnl|CDD|217445 pfam03237, Terminase_6, Terminase-like family. This family
represents a group of terminase proteins.
Length = 380
Score = 28.5 bits (64), Expect = 5.3
Identities = 13/72 (18%), Positives = 25/72 (34%), Gaps = 2/72 (2%)
Query: 35 IISGPPGVGKTTTILC-LARILLGPSFKDAVLELNASNDRGIDTVRNKIKMFAQQ-KVTL 92
I G GKT R LG K+ ++ + ++ + I++ ++T
Sbjct: 1 NILGSRQSGKTFAFAREALRHALGNGPKNQIILSASKAQARLEFKKGIIEIAGDLLEITF 60
Query: 93 PPGRHKIVILDE 104
+IL
Sbjct: 61 EEKNGNPIILPN 72
>gnl|CDD|224710 COG1797, CobB, Cobyrinic acid a,c-diamide synthase [Coenzyme
metabolism].
Length = 451
Score = 28.3 bits (64), Expect = 5.3
Identities = 12/25 (48%), Positives = 15/25 (60%), Gaps = 1/25 (4%)
Query: 32 PNIIISGP-PGVGKTTTILCLARIL 55
P ++I+G G GKTT L L R L
Sbjct: 1 PAVVIAGTSSGSGKTTVTLGLMRAL 25
>gnl|CDD|172748 PRK14260, PRK14260, phosphate ABC transporter ATP-binding protein;
Provisional.
Length = 259
Score = 28.1 bits (62), Expect = 5.4
Identities = 23/64 (35%), Positives = 32/64 (50%), Gaps = 6/64 (9%)
Query: 36 ISGPPGVGKTTTILCLARI--LLGPSFKDAVLEL---NASNDR-GIDTVRNKIKMFAQQK 89
I GP G GK+T I L RI L GP + V++ N + R I+ +R +I M Q+
Sbjct: 38 IIGPSGCGKSTFIKTLNRISELEGPVKVEGVVDFFGQNIYDPRININRLRRQIGMVFQRP 97
Query: 90 VTLP 93
P
Sbjct: 98 NPFP 101
>gnl|CDD|235466 PRK05439, PRK05439, pantothenate kinase; Provisional.
Length = 311
Score = 28.2 bits (64), Expect = 5.4
Identities = 14/30 (46%), Positives = 18/30 (60%), Gaps = 5/30 (16%)
Query: 27 SSGNVPNII-ISGPPGVGKTTTILCLARIL 55
+ VP II I+G VGK+TT AR+L
Sbjct: 81 NGQKVPFIIGIAGSVAVGKSTT----ARLL 106
>gnl|CDD|215414 PLN02772, PLN02772, guanylate kinase.
Length = 398
Score = 28.3 bits (63), Expect = 5.6
Identities = 11/15 (73%), Positives = 12/15 (80%)
Query: 34 IIISGPPGVGKTTTI 48
I+ISGP GVGK T I
Sbjct: 138 IVISGPSGVGKGTLI 152
>gnl|CDD|234015 TIGR02788, VirB11, P-type DNA transfer ATPase VirB11. The VirB11
protein is found in the vir locus of Agrobacterium Ti
plasmids where it is involved in the type IV secretion
system for DNA transfer. VirB11 is believed to be an
ATPase. VirB11 is a homolog of the P-like conjugation
system TrbB protein and the Flp pilus sytem protein
TadA.
Length = 308
Score = 28.1 bits (63), Expect = 5.6
Identities = 11/14 (78%), Positives = 11/14 (78%)
Query: 33 NIIISGPPGVGKTT 46
NIIISG G GKTT
Sbjct: 146 NIIISGGTGSGKTT 159
>gnl|CDD|238836 cd01673, dNK, Deoxyribonucleoside kinase (dNK) catalyzes the
phosphorylation of deoxyribonucleosides to yield
corresponding monophosphates (dNMPs). This family
consists of various deoxynucleoside kinases including
deoxyribo- cytidine (EC 2.7.1.74), guanosine (EC
2.7.1.113), adenosine (EC 2.7.1.76), and thymidine (EC
2.7.1.21) kinases. They are key enzymes in the salvage
of deoxyribonucleosides originating from extra- or
intracellular breakdown of DNA.
Length = 193
Score = 28.0 bits (63), Expect = 5.7
Identities = 9/22 (40%), Positives = 13/22 (59%), Gaps = 4/22 (18%)
Query: 34 IIISGPPGVGKTTTILCLARIL 55
I++ G G GK+T LA+ L
Sbjct: 2 IVVEGNIGAGKST----LAKEL 19
>gnl|CDD|217424 pfam03205, MobB, Molybdopterin guanine dinucleotide synthesis
protein B. This protein contains a P-loop.
Length = 126
Score = 27.4 bits (61), Expect = 5.7
Identities = 12/34 (35%), Positives = 18/34 (52%)
Query: 32 PNIIISGPPGVGKTTTILCLARILLGPSFKDAVL 65
P +++ GP GKTT I L L ++ AV+
Sbjct: 1 PIVLVVGPKDSGKTTLIRKLLNYLKRRGYRVAVV 34
>gnl|CDD|235210 PRK04040, PRK04040, adenylate kinase; Provisional.
Length = 188
Score = 27.9 bits (63), Expect = 5.7
Identities = 12/28 (42%), Positives = 18/28 (64%), Gaps = 1/28 (3%)
Query: 34 IIISGPPGVGKTTTILCLARILLGPSFK 61
++++G PGVGK TT+L A L +K
Sbjct: 5 VVVTGVPGVGK-TTVLNKALEKLKEDYK 31
>gnl|CDD|237182 PRK12727, PRK12727, flagellar biosynthesis regulator FlhF;
Provisional.
Length = 559
Score = 28.4 bits (63), Expect = 5.8
Identities = 25/88 (28%), Positives = 33/88 (37%), Gaps = 18/88 (20%)
Query: 34 IIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGI---DTVRNKIKMFAQQKV 90
I + GP G GKTTTI LA+ +A D + DT R ++
Sbjct: 353 IALVGPTGAGKTTTIAKLAQRF---------AAQHAPRDVALVTTDTQR-----VGGREQ 398
Query: 91 TLPPGRHKIVILDEADSMTDGAQQALRR 118
GR + + EADS L R
Sbjct: 399 LHSYGRQLGIAVHEADSAES-LLDLLER 425
>gnl|CDD|224142 COG1221, PspF, Transcriptional regulators containing an AAA-type
ATPase domain and a DNA-binding domain [Transcription /
Signal transduction mechanisms].
Length = 403
Score = 28.1 bits (63), Expect = 5.8
Identities = 11/51 (21%), Positives = 23/51 (45%), Gaps = 6/51 (11%)
Query: 8 TFSDIVGN----EDTVERLKVFSSSGNVPNIIISGPPGVGKTTTILCLARI 54
D++G ++ E++K ++ SG ++I G G GK + +
Sbjct: 76 ALDDLIGESPSLQELREQIKAYAPSGL--PVLIIGETGTGKELFARLIHAL 124
>gnl|CDD|213221 cd03254, ABCC_Glucan_exporter_like, ATP-binding cassette domain of
glucan transporter and related proteins, subfamily C.
Glucan exporter ATP-binding protein. In A. tumefaciens
cyclic beta-1, 2-glucan must be transported into the
periplasmic space to exert its action as a virulence
factor. This subfamily belongs to the MRP-like family
and is involved in drug, peptide, and lipid export. The
MRP-like family, similar to all ABC proteins, have a
common four-domain core structure constituted by two
membrane-spanning domains each composed of six
transmembrane (TM) helices and two nucleotide-binding
domains (NBD). 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 = 229
Score = 28.0 bits (63), Expect = 5.9
Identities = 15/40 (37%), Positives = 22/40 (55%), Gaps = 8/40 (20%)
Query: 98 KIVILDEA----DSMTDGA-QQALRRTMEIYSNTTRFALA 132
KI+ILDEA D+ T+ Q+AL + M+ T +A
Sbjct: 159 KILILDEATSNIDTETEKLIQEALEKLMK---GRTSIIIA 195
>gnl|CDD|182733 PRK10790, PRK10790, putative multidrug transporter
membrane\ATP-binding components; Provisional.
Length = 592
Score = 28.5 bits (64), Expect = 6.0
Identities = 17/40 (42%), Positives = 23/40 (57%), Gaps = 8/40 (20%)
Query: 98 KIVILDEA----DSMTDGA-QQALRRTMEIYSNTTRFALA 132
+I+ILDEA DS T+ A QQAL + +TT +A
Sbjct: 496 QILILDEATANIDSGTEQAIQQALA---AVREHTTLVVIA 532
>gnl|CDD|217733 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 dimerisation 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 = 260
Score = 27.9 bits (63), Expect = 6.1
Identities = 10/22 (45%), Positives = 14/22 (63%)
Query: 34 IIISGPPGVGKTTTILCLARIL 55
III+ P +GKT L +AR +
Sbjct: 22 IIIAARPSMGKTAFALNIARNI 43
>gnl|CDD|237809 PRK14738, gmk, guanylate kinase; Provisional.
Length = 206
Score = 27.8 bits (62), Expect = 6.1
Identities = 8/15 (53%), Positives = 11/15 (73%)
Query: 34 IIISGPPGVGKTTTI 48
++ISGP GVGK +
Sbjct: 16 VVISGPSGVGKDAVL 30
>gnl|CDD|227297 COG4962, CpaF, Flp pilus assembly protein, ATPase CpaF
[Intracellular trafficking and secretion].
Length = 355
Score = 28.1 bits (63), Expect = 6.2
Identities = 11/19 (57%), Positives = 13/19 (68%)
Query: 33 NIIISGPPGVGKTTTILCL 51
NI+ISG G GKTT + L
Sbjct: 175 NILISGGTGSGKTTLLNAL 193
>gnl|CDD|213193 cd03226, ABC_cobalt_CbiO_domain2, Second domain of the
ATP-binding cassette component of cobalt transport
system. Domain II of the ABC component of a cobalt
transport family found in bacteria, archaea, and
eukaryota. The transition metal cobalt is an essential
component of many enzymes and must be transported into
cells in appropriate amounts when needed. The CbiMNQO
family ABC transport system is involved in cobalt
transport in association with the cobalamin (vitamin
B12) biosynthetic pathways. Most cobalt (Cbi) transport
systems possess a separate CbiN component, the
cobalt-binding periplasmic protein, and they are
encoded by the conserved gene cluster cbiMNQO. Both the
CbiM and CbiQ proteins are integral cytoplasmic
membrane proteins, and the CbiO protein has the linker
peptide and the Walker A and B motifs commonly found in
the ATPase components of the ABC-type transport
systems.
Length = 205
Score = 28.0 bits (63), Expect = 6.2
Identities = 12/24 (50%), Positives = 15/24 (62%), Gaps = 4/24 (16%)
Query: 34 IIISGPPGVGKTTTILCLARILLG 57
I ++G G GKTT LA+IL G
Sbjct: 29 IALTGKNGAGKTT----LAKILAG 48
>gnl|CDD|180682 PRK06761, PRK06761, hypothetical protein; Provisional.
Length = 282
Score = 28.2 bits (63), Expect = 6.3
Identities = 13/22 (59%), Positives = 14/22 (63%)
Query: 34 IIISGPPGVGKTTTILCLARIL 55
III G PG GK+TT L IL
Sbjct: 6 IIIEGLPGFGKSTTAKMLNDIL 27
>gnl|CDD|182683 PRK10733, hflB, ATP-dependent metalloprotease; Reviewed.
Length = 644
Score = 28.5 bits (63), Expect = 6.4
Identities = 34/119 (28%), Positives = 54/119 (45%), Gaps = 30/119 (25%)
Query: 8 TFSDIVGNEDT-------VERLKVFSS----SGNVPN-IIISGPPGVGKTTTILCLARIL 55
TF+D+ G ++ VE L+ S G +P +++ GPPG GKT LA+ +
Sbjct: 150 TFADVAGCDEAKEEVAELVEYLREPSRFQKLGGKIPKGVLMVGPPGTGKTL----LAKAI 205
Query: 56 LGPSFKDAVLELNASN------DRGIDTVRNKIKMFAQQKVTLPPGRHKIVILDEADSM 108
G + K ++ S+ G VR+ MF Q K P I+ +DE D++
Sbjct: 206 AGEA-KVPFFTISGSDFVEMFVGVGASRVRD---MFEQAKKAAPC----IIFIDEIDAV 256
>gnl|CDD|206684 cd01897, NOG, Nucleolar GTP-binding protein (NOG). NOG1 is a
nucleolar GTP-binding protein present in eukaryotes
ranging from trypanosomes to humans. NOG1 is
functionally linked to ribosome biogenesis and found in
association with the nuclear pore complexes and
identified in many preribosomal complexes. Thus,
defects in NOG1 can lead to defects in 60S biogenesis.
The S. cerevisiae NOG1 gene is essential for cell
viability, and mutations in the predicted G motifs
abrogate function. It is a member of the ODN family of
GTP-binding proteins that also includes the bacterial
Obg and DRG proteins.
Length = 167
Score = 27.5 bits (62), Expect = 6.5
Identities = 8/22 (36%), Positives = 14/22 (63%)
Query: 32 PNIIISGPPGVGKTTTILCLAR 53
++I+G P VGK++ + L R
Sbjct: 1 RTLVIAGYPNVGKSSLVNKLTR 22
>gnl|CDD|213207 cd03240, ABC_Rad50, ATP-binding cassette domain of Rad50. The
catalytic domains of Rad50 are similar to the
ATP-binding cassette of ABC transporters, but are not
associated with membrane-spanning domains. The
conserved ATP-binding motifs common to Rad50 and the
ABC transporter family include the Walker A and Walker
B motifs, the Q loop, a histidine residue in the switch
region, a D-loop, and a conserved LSGG sequence. This
conserved sequence, LSGG, is the most specific and
characteristic motif of this family and is thus known
as the ABC signature sequence.
Length = 204
Score = 27.6 bits (62), Expect = 7.0
Identities = 17/69 (24%), Positives = 23/69 (33%), Gaps = 18/69 (26%)
Query: 35 IISGPPGVGKTTTILCLARILLG------------PSF-----KDAVLELNASNDRGID- 76
+I G G GKTT I L L G P A ++L N G
Sbjct: 26 LIVGQNGAGKTTIIEALKYALTGELPPNSKGGAHDPKLIREGEVRAQVKLAFENANGKKY 85
Query: 77 TVRNKIKMF 85
T+ + +
Sbjct: 86 TITRSLAIL 94
>gnl|CDD|236093 PRK07773, PRK07773, replicative DNA helicase; Validated.
Length = 886
Score = 28.2 bits (63), Expect = 7.1
Identities = 10/20 (50%), Positives = 13/20 (65%)
Query: 34 IIISGPPGVGKTTTILCLAR 53
II++ P +GKTT L AR
Sbjct: 220 IIVAARPSMGKTTFGLDFAR 239
>gnl|CDD|236539 PRK09490, metH, B12-dependent methionine synthase; Provisional.
Length = 1229
Score = 28.2 bits (64), Expect = 7.1
Identities = 13/28 (46%), Positives = 18/28 (64%), Gaps = 4/28 (14%)
Query: 240 SYKIIHHLYKLGYAPEDII--GNIFRVA 265
+Y I+ ++G+ PEDII NIF VA
Sbjct: 507 AYDILTE--EVGFPPEDIIFDPNIFAVA 532
>gnl|CDD|224160 COG1239, ChlI, Mg-chelatase subunit ChlI [Coenzyme metabolism].
Length = 423
Score = 28.1 bits (63), Expect = 7.3
Identities = 8/23 (34%), Positives = 12/23 (52%)
Query: 33 NIIISGPPGVGKTTTILCLARIL 55
+I+G G K+T LA +L
Sbjct: 40 GALIAGEKGTAKSTLARALADLL 62
>gnl|CDD|224025 COG1100, COG1100, GTPase SAR1 and related small G proteins [General
function prediction only].
Length = 219
Score = 27.6 bits (61), Expect = 7.4
Identities = 18/90 (20%), Positives = 28/90 (31%), Gaps = 23/90 (25%)
Query: 34 IIISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKIKMFAQQKVTLP 93
I++ G GVGKTT + L + + L+ + R IK+
Sbjct: 8 IVVLGDGGVGKTTLLNRLVGDEFPEGYPPTIGNLDPAKTIEPY--RRNIKL--------- 56
Query: 94 PGRHKIVILDEADSMTDGAQQALRRTMEIY 123
+ D A Q+ R Y
Sbjct: 57 ------QLWDTAG------QEEYRSLRPEY 74
>gnl|CDD|238544 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 = 27.3 bits (61), Expect = 7.4
Identities = 8/14 (57%), Positives = 11/14 (78%)
Query: 33 NIIISGPPGVGKTT 46
+ ++SG PG GKTT
Sbjct: 1 STLLSGGPGTGKTT 14
>gnl|CDD|213965 TIGR04352, HprK_rel_A, HprK-related kinase A. A number of protein
families resemble HPr kinase (see TIGR00679) but do not
belong to that system. They include this family, which
appears instead to be the marker for a different type of
gene neighborhood, in which one of the conserved
neighboring proteins resembles (but is distinct from)
PqqD.
Length = 280
Score = 27.7 bits (62), Expect = 7.7
Identities = 12/24 (50%), Positives = 15/24 (62%), Gaps = 2/24 (8%)
Query: 34 IIISGPPGVGKTTTILCLARILLG 57
+I+ PPG GK+T LC A L G
Sbjct: 111 LILPAPPGSGKST--LCAALALRG 132
>gnl|CDD|213211 cd03244, ABCC_MRP_domain2, ATP-binding cassette domain 2 of
multidrug resistance-associated protein. The ABC
subfamily C is also known as MRP (multidrug
resistance-associated protein). Some of the MRP members
have five additional transmembrane segments in their
N-terminus, but the function of these additional
membrane-spanning domains is not clear. The MRP was
found in the multidrug-resistance lung cancer cell in
which p-glycoprotein was not overexpressed. MRP exports
glutathione by drug stimulation, as well as, certain
substrates in conjugated forms with anions, such as
glutathione, glucuronate, and sulfate.
Length = 221
Score = 27.5 bits (62), Expect = 7.9
Identities = 13/42 (30%), Positives = 20/42 (47%), Gaps = 8/42 (19%)
Query: 96 RHKIVILDEA----DSMTDGA-QQALRRTMEIYSNTTRFALA 132
+ KI++LDEA D TD Q+ +R + T +A
Sbjct: 157 KSKILVLDEATASVDPETDALIQKTIREAF---KDCTVLTIA 195
>gnl|CDD|213197 cd03230, ABC_DR_subfamily_A, ATP-binding cassette domain of the
drug resistance transporter and related proteins,
subfamily A. This family of ATP-binding proteins
belongs to a multi-subunit transporter involved in drug
resistance (BcrA and DrrA), nodulation, lipid
transport, and lantibiotic immunity. In bacteria and
archaea, these transporters usually include an
ATP-binding protein and one or two integral membrane
proteins. Eukaryotic systems of the ABCA subfamily
display ABC domains that are quite similar to this
family. The ATP-binding domain shows the highest
similarity between all members of the ABC transporter
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 = 173
Score = 27.4 bits (62), Expect = 8.1
Identities = 11/20 (55%), Positives = 13/20 (65%), Gaps = 4/20 (20%)
Query: 38 GPPGVGKTTTILCLARILLG 57
GP G GKTT I +I+LG
Sbjct: 33 GPNGAGKTTLI----KIILG 48
>gnl|CDD|165867 PLN02223, PLN02223, phosphoinositide phospholipase C.
Length = 537
Score = 28.1 bits (62), Expect = 8.4
Identities = 15/35 (42%), Positives = 20/35 (57%), Gaps = 1/35 (2%)
Query: 7 QTFSDIVGNEDTVERLKVFSSSGNVPN-IIISGPP 40
QTF D+V +ED L+ F S + N I+IS P
Sbjct: 219 QTFGDMVYHEDPQHSLEEFPSPAELQNKILISRRP 253
>gnl|CDD|226031 COG3500, COG3500, Phage protein D [General function prediction
only].
Length = 350
Score = 27.8 bits (62), Expect = 8.4
Identities = 12/92 (13%), Positives = 24/92 (26%), Gaps = 14/92 (15%)
Query: 35 IISGPPGVGKTTTILCLARILLGPSFKDAVLELNASNDRGIDTVRNKIKMFAQQKVTLPP 94
+I G + T L + L S + A ++
Sbjct: 177 LIFKRLGESGSATGRRLPPVNLLREEIA-------SLRVTYADREAYGWVVAYYQLVRAA 229
Query: 95 GRHKIVILDEADS-------MTDGAQQALRRT 119
R ++V ++ D A + L +
Sbjct: 230 AREEVVSGKDSLGERLPAAAAADSAARLLLHS 261
>gnl|CDD|235029 PRK02308, uvsE, putative UV damage endonuclease; Provisional.
Length = 303
Score = 27.6 bits (62), Expect = 8.6
Identities = 12/50 (24%), Positives = 20/50 (40%), Gaps = 4/50 (8%)
Query: 128 RFALACNNSEKIIEPIQSRCAML-RYNKLTDAQLLSKVIEICEKENISHT 176
R C + SR L ++ KL+D + K+ EI N+ +
Sbjct: 4 RLGYVCMTVT--LNASPSRTMTLKQFQKLSDREREEKLEEIA-LSNLENL 50
>gnl|CDD|184125 PRK13538, PRK13538, cytochrome c biogenesis protein CcmA;
Provisional.
Length = 204
Score = 27.5 bits (62), Expect = 8.7
Identities = 12/22 (54%), Positives = 13/22 (59%), Gaps = 4/22 (18%)
Query: 36 ISGPPGVGKTTTILCLARILLG 57
I GP G GKT+ L RIL G
Sbjct: 32 IEGPNGAGKTS----LLRILAG 49
>gnl|CDD|213236 cd03269, ABC_putative_ATPase, ATP-binding cassette domain of an
uncharacterized transporter. This subgroup is related
to the subfamily A transporters involved in drug
resistance, nodulation, lipid transport, and
bacteriocin and lantibiotic immunity. In eubacteria and
archaea, the typical organization consists of one ABC
and one or two integral membranes. 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 = 210
Score = 27.2 bits (61), Expect = 9.0
Identities = 11/19 (57%), Positives = 13/19 (68%)
Query: 38 GPPGVGKTTTILCLARILL 56
GP G GKTTTI + I+L
Sbjct: 33 GPNGAGKTTTIRMILGIIL 51
>gnl|CDD|233959 TIGR02639, ClpA, ATP-dependent Clp protease ATP-binding subunit
clpA. [Protein fate, Degradation of proteins, peptides,
and glycopeptides].
Length = 730
Score = 27.7 bits (62), Expect = 9.2
Identities = 19/54 (35%), Positives = 28/54 (51%), Gaps = 4/54 (7%)
Query: 2 EKYRPQTFSDIVGNEDTVER-LKVFS-SSGNVPNIIISGPPGVGKTTTILCLAR 53
EK + ++G ED +ER ++V N P ++ G PGVGKT + LA
Sbjct: 173 EKAKNGKIDPLIGREDELERTIQVLCRRKKNNP--LLVGEPGVGKTAIVEGLAL 224
>gnl|CDD|172744 PRK14256, PRK14256, phosphate ABC transporter ATP-binding
protein; Provisional.
Length = 252
Score = 27.3 bits (60), Expect = 9.2
Identities = 20/64 (31%), Positives = 33/64 (51%), Gaps = 6/64 (9%)
Query: 36 ISGPPGVGKTTTILCLARIL-LGPSFK---DAVLELNASNDRGID--TVRNKIKMFAQQK 89
I GP G GK+T + + R+ L PS + +L+ DRG+D ++R ++ M Q+
Sbjct: 35 IIGPSGCGKSTVLRSINRMHDLVPSARVTGKILLDDTDIYDRGVDPVSIRRRVGMVFQKP 94
Query: 90 VTLP 93
P
Sbjct: 95 NPFP 98
>gnl|CDD|215651 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 = 27.4 bits (62), Expect = 9.5
Identities = 9/20 (45%), Positives = 11/20 (55%)
Query: 34 IIISGPPGVGKTTTILCLAR 53
I I G G GKT + +AR
Sbjct: 18 IGIFGGSGTGKTVLLGMIAR 37
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.318 0.136 0.386
Gapped
Lambda K H
0.267 0.0889 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 15,963,083
Number of extensions: 1535353
Number of successful extensions: 2579
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2452
Number of HSP's successfully gapped: 374
Length of query: 317
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 220
Effective length of database: 6,635,264
Effective search space: 1459758080
Effective search space used: 1459758080
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 59 (26.2 bits)