RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4285
(533 letters)
>gnl|CDD|234763 PRK00440, rfc, replication factor C small subunit; Reviewed.
Length = 319
Score = 198 bits (507), Expect = 2e-59
Identities = 75/144 (52%), Positives = 98/144 (68%), Gaps = 3/144 (2%)
Query: 299 RFIDENELPHLLFYGPPGTGKTTTILACARKLYTKA-QFNAMVLELNASDDRGIGIVRDQ 357
++ E +PHLLF GPPGTGKTT LA AR+LY + + N LELNASD+RGI ++R++
Sbjct: 31 SYVKEKNMPHLLFAGPPGTGKTTAALALARELYGEDWREN--FLELNASDERGIDVIRNK 88
Query: 358 IFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPA 417
I +FA T + + +K+I LDEAD +T+DAQ ALRR +E ++ N RF + CNY SKI
Sbjct: 89 IKEFARTAPVGGAPFKIIFLDEADNLTSDAQQALRRTMEMYSQNTRFILSCNYSSKIIDP 148
Query: 418 IQSRCTRFRFGPLDSSLIMSRLDY 441
IQSRC FRF PL + RL Y
Sbjct: 149 IQSRCAVFRFSPLKKEAVAERLRY 172
Score = 147 bits (374), Expect = 3e-40
Identities = 67/188 (35%), Positives = 100/188 (53%), Gaps = 28/188 (14%)
Query: 2 EKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGK 61
E ++ N RF + CNY SKI IQSRC FRF PL + RL Y+ E E + +T D
Sbjct: 127 EMYSQNTRFILSCNYSSKIIDPIQSRCAVFRFSPLKKEAVAERLRYIAENEGIEITDDAL 186
Query: 62 KAIIDLSDGDMRKVLNILQSAATAHADEVNEDTIFTLL-VSRVEKYRP------------ 108
+AI +S+GDMRK +N LQ+AA EV E+ ++ + +R E+ R
Sbjct: 187 EAIYYVSEGDMRKAINALQAAAAT-GKEVTEEAVYKITGTARPEEIREMIELALNGDFTE 245
Query: 109 --STLDEL-----VSHQDIISTI-------EIPESMLVDLVLKMSDIEYRLAAGTSEKIQ 154
L +L +S +DII I +IPE + V+L+ + + ++R+ G +E+IQ
Sbjct: 246 AREKLRDLMIDYGLSGEDIIKQIHREVWSLDIPEELKVELIDAIGEADFRITEGANERIQ 305
Query: 155 LSALIAAF 162
L AL+A
Sbjct: 306 LEALLAKL 313
Score = 131 bits (333), Expect = 2e-34
Identities = 78/251 (31%), Positives = 110/251 (43%), Gaps = 83/251 (33%)
Query: 103 VEKYRPSTLDELVSHQDIISTIEIPESMLVDLVLKMSDIEYRLAAG------TSEKIQLS 156
VEKYRP TLDE+V ++I+ L V K ++ + L AG T+
Sbjct: 8 VEKYRPRTLDEIVGQEEIVER-------LKSYV-KEKNMPHLLFAGPPGTGKTT------ 53
Query: 157 ALIAAFNSARD------KLEVLELNASDDRGIGIVRDQIFQFASTKTMHKSSYKLIILDE 210
AA AR+ + LELNASD+RGI ++R++I +FA T + + +K+I LDE
Sbjct: 54 ---AALALARELYGEDWRENFLELNASDERGIDVIRNKIKEFARTAPVGGAPFKIIFLDE 110
Query: 211 ADAMTNDAQNALRR---------------------------------------------- 224
AD +T+DAQ ALRR
Sbjct: 111 ADNLTSDAQQALRRTMEMYSQNTRFILSCNYSSKIIDPIQSRCAVFRFSPLKKEAVAERL 170
Query: 225 -------KLPVTPDGKKAIIDLSDGDMRKVLNILQSAATAHADEVNEDTVYNSVGYPTKT 277
+ +T D +AI +S+GDMRK +N LQ+AA EV E+ VY G
Sbjct: 171 RYIAENEGIEITDDALEAIYYVSEGDMRKAINALQAAAAT-GKEVTEEAVYKITGTARPE 229
Query: 278 EITNILRWLLN 288
EI ++ LN
Sbjct: 230 EIREMIELALN 240
Score = 55.3 bits (134), Expect = 3e-08
Identities = 23/65 (35%), Positives = 43/65 (66%)
Query: 455 KIQEIKIEKGLALTDILTEISLLVHRLEIPESMLVDLVLKMSDIEYRLAAGTSEKIQLSA 514
K++++ I+ GL+ DI+ +I V L+IPE + V+L+ + + ++R+ G +E+IQL A
Sbjct: 249 KLRDLMIDYGLSGEDIIKQIHREVWSLDIPEELKVELIDAIGEADFRITEGANERIQLEA 308
Query: 515 LIAAF 519
L+A
Sbjct: 309 LLAKL 313
>gnl|CDD|178596 PLN03025, PLN03025, replication factor C subunit; Provisional.
Length = 319
Score = 150 bits (380), Expect = 3e-41
Identities = 70/135 (51%), Positives = 89/135 (65%), Gaps = 2/135 (1%)
Query: 306 LPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFASTK 365
+P+L+ GPPGTGKTT+ILA A +L A VLELNASDDRGI +VR++I FA K
Sbjct: 34 MPNLILSGPPGTGKTTSILALAHELLGPNYKEA-VLELNASDDRGIDVVRNKIKMFAQKK 92
Query: 366 -TMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTR 424
T+ +K++ILDEAD+MT+ AQ ALRR +E ++ RF + CN SKI IQSRC
Sbjct: 93 VTLPPGRHKIVILDEADSMTSGAQQALRRTMEIYSNTTRFALACNTSSKIIEPIQSRCAI 152
Query: 425 FRFGPLDSSLIMSRL 439
RF L I+ RL
Sbjct: 153 VRFSRLSDQEILGRL 167
Score = 105 bits (263), Expect = 5e-25
Identities = 77/248 (31%), Positives = 110/248 (44%), Gaps = 62/248 (25%)
Query: 103 VEKYRPSTLDELVSHQDIISTIE-IPESMLVDLVLKMSDIEYRLAAGTSEKIQLSALIAA 161
VEKYRP+ LD++V ++D +S ++ I M ++ GT + + AL
Sbjct: 4 VEKYRPTKLDDIVGNEDAVSRLQVIARDG------NMPNLILSGPPGTGKTTSILALAHE 57
Query: 162 FNSARDKLEVLELNASDDRGIGIVRDQIFQFASTK-TMHKSSYKLIILDEADAMTNDAQN 220
K VLELNASDDRGI +VR++I FA K T+ +K++ILDEAD+MT+ AQ
Sbjct: 58 LLGPNYKEAVLELNASDDRGIDVVRNKIKMFAQKKVTLPPGRHKIVILDEADSMTSGAQQ 117
Query: 221 ALRR-----------------------------------------------------KLP 227
ALRR K+P
Sbjct: 118 ALRRTMEIYSNTTRFALACNTSSKIIEPIQSRCAIVRFSRLSDQEILGRLMKVVEAEKVP 177
Query: 228 VTPDGKKAIIDLSDGDMRKVLNILQSAATAHADEVNEDTVYNSVGYPTKTEITNILRWLL 287
P+G +AII +DGDMR+ LN LQ+ + VN++ V+ P + NI+R L
Sbjct: 178 YVPEGLEAIIFTADGDMRQALNNLQATHSGFG-FVNQENVFKVCDQPHPLHVKNIVRNCL 236
Query: 288 NESMDLCY 295
D
Sbjct: 237 KGKFDDAC 244
Score = 89.4 bits (222), Expect = 1e-19
Identities = 58/194 (29%), Positives = 90/194 (46%), Gaps = 27/194 (13%)
Query: 1 IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDG 60
+E ++ RF + CN SKI IQSRC RF L I+ RL V+E EKV P+G
Sbjct: 123 MEIYSNTTRFALACNTSSKIIEPIQSRCAIVRFSRLSDQEILGRLMKVVEAEKVPYVPEG 182
Query: 61 KKAIIDLSDGDMRKVLNILQSAATAHADEVNEDTIFT--------LLVSRVEKYRPSTLD 112
+AII +DGDMR+ LN LQ+ + VN++ +F + + V D
Sbjct: 183 LEAIIFTADGDMRQALNNLQATHSGFG-FVNQENVFKVCDQPHPLHVKNIVRNCLKGKFD 241
Query: 113 ELV-----------SHQDIISTI-------EIPESMLVDLVLKMSDIEYRLAAGTSEKIQ 154
+ S DII+T+ ++PE + ++ + ++ R+ G +Q
Sbjct: 242 DACDGLKQLYDLGYSPTDIITTLFRVVKNYDMPEFLKLEYLREIGFAHMRICDGVGSLLQ 301
Query: 155 LSALIAAFNSARDK 168
LS L+A R+
Sbjct: 302 LSGLLAKLCLVRET 315
Score = 28.9 bits (65), Expect = 6.8
Identities = 18/66 (27%), Positives = 35/66 (53%)
Query: 464 GLALTDILTEISLLVHRLEIPESMLVDLVLKMSDIEYRLAAGTSEKIQLSALIAAFNSAR 523
G + TDI+T + +V ++PE + ++ + ++ R+ G +QLS L+A R
Sbjct: 254 GYSPTDIITTLFRVVKNYDMPEFLKLEYLREIGFAHMRICDGVGSLLQLSGLLAKLCLVR 313
Query: 524 DKLEAP 529
+ +AP
Sbjct: 314 ETAKAP 319
>gnl|CDD|235223 PRK04132, PRK04132, replication factor C small subunit;
Provisional.
Length = 846
Score = 136 bits (344), Expect = 7e-34
Identities = 65/122 (53%), Positives = 85/122 (69%), Gaps = 1/122 (0%)
Query: 320 TTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFASTKTMHKSSYKLIILDE 379
TT LA AR+L+ + + LELNASD+RGI ++R+++ +FA TK + +S+K+I LDE
Sbjct: 580 TTAALALARELFGE-NWRHNFLELNASDERGINVIREKVKEFARTKPIGGASFKIIFLDE 638
Query: 380 ADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTRFRFGPLDSSLIMSRL 439
ADA+T DAQ ALRR +E F++NVRF + CNY SKI IQSRC FRF PL I RL
Sbjct: 639 ADALTQDAQQALRRTMEMFSSNVRFILSCNYSSKIIEPIQSRCAIFRFRPLRDEDIAKRL 698
Query: 440 DY 441
Y
Sbjct: 699 RY 700
Score = 123 bits (310), Expect = 1e-29
Identities = 69/190 (36%), Positives = 99/190 (52%), Gaps = 30/190 (15%)
Query: 1 IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDG 60
+E F++NVRF + CNY SKI IQSRC FRF PL I RL Y+ E E + +T +G
Sbjct: 654 MEMFSSNVRFILSCNYSSKIIEPIQSRCAIFRFRPLRDEDIAKRLRYIAENEGLELTEEG 713
Query: 61 KKAIIDLSDGDMRKVLNILQSAATAHADEVNEDTIFTLLVSRV----------------- 103
+AI+ +++GDMR+ +NILQ+AA D+ D L+ SR
Sbjct: 714 LQAILYIAEGDMRRAINILQAAAA--LDDKITDENVFLVASRARPEDIREMMLLALKGNF 771
Query: 104 ----EKYRPSTLDELVSHQDI-------ISTIEIPESMLVDLVLKMSDIEYRLAAGTSEK 152
EK R L + +S +D+ + + I E V+L K+ + +RL G +E
Sbjct: 772 LKAREKLREILLKQGLSGEDVLVQMHREVFNLPIDEPKKVELADKIGEYNFRLVEGANEM 831
Query: 153 IQLSALIAAF 162
IQL AL+A F
Sbjct: 832 IQLEALLAQF 841
Score = 76.0 bits (187), Expect = 2e-14
Identities = 32/55 (58%), Positives = 45/55 (81%)
Query: 172 LELNASDDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRKL 226
LELNASD+RGI ++R+++ +FA TK + +S+K+I LDEADA+T DAQ ALRR +
Sbjct: 600 LELNASDERGINVIREKVKEFARTKPIGGASFKIIFLDEADALTQDAQQALRRTM 654
Score = 50.2 bits (120), Expect = 2e-06
Identities = 25/65 (38%), Positives = 40/65 (61%)
Query: 455 KIQEIKIEKGLALTDILTEISLLVHRLEIPESMLVDLVLKMSDIEYRLAAGTSEKIQLSA 514
K++EI +++GL+ D+L ++ V L I E V+L K+ + +RL G +E IQL A
Sbjct: 777 KLREILLKQGLSGEDVLVQMHREVFNLPIDEPKKVELADKIGEYNFRLVEGANEMIQLEA 836
Query: 515 LIAAF 519
L+A F
Sbjct: 837 LLAQF 841
Score = 34.8 bits (80), Expect = 0.14
Identities = 12/27 (44%), Positives = 17/27 (62%)
Query: 296 KINRFIDENELPHLLFYGPPGTGKTTT 322
++ ++ +PHLLF GPPG GK T
Sbjct: 30 RLKHYVKTGSMPHLLFAGPPGVGKCLT 56
Score = 30.2 bits (68), Expect = 3.4
Identities = 10/19 (52%), Positives = 14/19 (73%)
Query: 103 VEKYRPSTLDELVSHQDII 121
VEKYRP LD++V + I+
Sbjct: 10 VEKYRPQRLDDIVGQEHIV 28
>gnl|CDD|222866 PHA02544, 44, clamp loader, small subunit; Provisional.
Length = 316
Score = 119 bits (300), Expect = 5e-30
Identities = 47/131 (35%), Positives = 69/131 (52%), Gaps = 10/131 (7%)
Query: 300 FIDENELPHLLFYGP-PGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQI 358
+ + +P++L + P PGTGKTT A + A VL +N SD R I VR+++
Sbjct: 36 IVKKGRIPNMLLHSPSPGTGKTTVAKALC------NEVGAEVLFVNGSDCR-IDFVRNRL 88
Query: 359 FQFASTKTMHKSSYKLIILDEAD-AMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPA 417
+FAST ++ K+II+DE D DAQ LR +E ++ N F I N + I
Sbjct: 89 TRFASTVSL-TGGGKVIIIDEFDRLGLADAQRHLRSFMEAYSKNCSFIITANNKNGIIEP 147
Query: 418 IQSRCTRFRFG 428
++SRC FG
Sbjct: 148 LRSRCRVIDFG 158
Score = 62.3 bits (152), Expect = 1e-10
Identities = 42/129 (32%), Positives = 63/129 (48%), Gaps = 26/129 (20%)
Query: 103 VEKYRPSTLDELV-------SHQDIISTIEIPESMLVDLVLKMSDIEYRLAAGTSEKIQL 155
+KYRPST+DE + + + I+ IP +ML+ + + GT +
Sbjct: 12 EQKYRPSTIDECILPAADKETFKSIVKKGRIP-NMLL----------HSPSPGTGKTTVA 60
Query: 156 SALIAAFNSARDKLEVLELNASDDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEAD-AM 214
AL + EVL +N SD R I VR+++ +FAST ++ K+II+DE D
Sbjct: 61 KALCNEVGA-----EVLFVNGSDCR-IDFVRNRLTRFASTVSL-TGGGKVIIIDEFDRLG 113
Query: 215 TNDAQNALR 223
DAQ LR
Sbjct: 114 LADAQRHLR 122
Score = 57.3 bits (139), Expect = 6e-09
Identities = 23/91 (25%), Positives = 39/91 (42%), Gaps = 7/91 (7%)
Query: 1 IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDS-------SLIMSRLDYVIEQEK 53
+E ++ N F I N + I ++SRC FG ++ R ++E E
Sbjct: 125 MEAYSKNCSFIITANNKNGIIEPLRSRCRVIDFGVPTKEEQIEMMKQMIVRCKGILEAEG 184
Query: 54 VNVTPDGKKAIIDLSDGDMRKVLNILQSAAT 84
V V A++ + D R+ +N LQ A+
Sbjct: 185 VEVDMKVLAALVKKNFPDFRRTINELQRYAS 215
>gnl|CDD|237090 PRK12402, PRK12402, replication factor C small subunit 2; Reviewed.
Length = 337
Score = 115 bits (290), Expect = 2e-28
Identities = 59/166 (35%), Positives = 79/166 (47%), Gaps = 26/166 (15%)
Query: 299 RFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASD--DRG-IGIVR 355
R +D LPHLL GPPG+GKT + A AR+LY + E N +D D+G +V
Sbjct: 29 RAVDSPNLPHLLVQGPPGSGKTAAVRALARELYGD-PWENNFTEFNVADFFDQGKKYLVE 87
Query: 356 DQIF-QFASTKTMHKSS---------------------YKLIILDEADAMTNDAQNALRR 393
D F F T +SS YK I+LD A+A+ DAQ ALRR
Sbjct: 88 DPRFAHFLGTDKRIRSSKIDNFKHVLKEYASYRPLSADYKTILLDNAEALREDAQQALRR 147
Query: 394 IIEKFTTNVRFCIICNYLSKIPPAIQSRCTRFRFGPLDSSLIMSRL 439
I+E+++ RF I SK+ P I+SRC F ++ L
Sbjct: 148 IMEQYSRTCRFIIATRQPSKLIPPIRSRCLPLFFRAPTDDELVDVL 193
Score = 91.6 bits (228), Expect = 3e-20
Identities = 46/191 (24%), Positives = 77/191 (40%), Gaps = 34/191 (17%)
Query: 2 EKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGK 61
E+++ RF I SK+ P I+SRC F ++ L+ + E E V+ DG
Sbjct: 150 EQYSRTCRFIIATRQPSKLIPPIRSRCLPLFFRAPTDDELVDVLESIAEAEGVDYDDDGL 209
Query: 62 KAIIDLSDGDMRKVLNILQSAATAHADEVNEDTIFTLLVSRVEKYRPSTLDELVS---HQ 118
+ I + GD+RK + LQ+AA A E+ + + L V ++ L+
Sbjct: 210 ELIAYYAGGDLRKAILTLQTAAL-AAGEITMEAAYEAL-GDVG--TDEVIESLLDAAEAG 265
Query: 119 DIISTIEIPESMLVD---------------------------LVLKMSDIEYRLAAGTSE 151
D + + +L+D L +D + RL G ++
Sbjct: 266 DFTDARKTLDDLLIDEGLSGGEVLEELLRVARSRYRGDNLARLHRLAADADARLTDGAND 325
Query: 152 KIQLSALIAAF 162
+IQL AL+A
Sbjct: 326 RIQLEALLAEL 336
Score = 53.1 bits (128), Expect = 1e-07
Identities = 55/261 (21%), Positives = 91/261 (34%), Gaps = 89/261 (34%)
Query: 104 EKYRPSTLDELVSHQDIISTIE--IPESMLVDLVLKMSDIEYRLAAGTSEKIQLSALIAA 161
EKYRP+ L++++ +++ + + L L+++ G+ + + AL
Sbjct: 7 EKYRPALLEDILGQDEVVERLSRAVDSPNLPHLLVQGP-------PGSGKTAAVRALARE 59
Query: 162 FNSARDKLEVLELNASD--DRG-IGIVRDQIF-QFASTKTMHKSS--------------- 202
+ E N +D D+G +V D F F T +SS
Sbjct: 60 LYGDPWENNFTEFNVADFFDQGKKYLVEDPRFAHFLGTDKRIRSSKIDNFKHVLKEYASY 119
Query: 203 ------YKLIILDEADAMTNDAQNALRR-------------------------------- 224
YK I+LD A+A+ DAQ ALRR
Sbjct: 120 RPLSADYKTILLDNAEALREDAQQALRRIMEQYSRTCRFIIATRQPSKLIPPIRSRCLPL 179
Query: 225 ---------------------KLPVTPDGKKAIIDLSDGDMRKVLNILQSAATAHADEVN 263
+ DG + I + GD+RK + LQ+AA A E+
Sbjct: 180 FFRAPTDDELVDVLESIAEAEGVDYDDDGLELIAYYAGGDLRKAILTLQTAAL-AAGEIT 238
Query: 264 EDTVYNSVG-YPTKTEITNIL 283
+ Y ++G T I ++L
Sbjct: 239 MEAAYEALGDVGTDEVIESLL 259
Score = 45.4 bits (108), Expect = 4e-05
Identities = 17/64 (26%), Positives = 35/64 (54%), Gaps = 1/64 (1%)
Query: 456 IQEIKIEKGLALTDILTEISLLVHRLEIPESMLVDLVLKMSDIEYRLAAGTSEKIQLSAL 515
+ ++ I++GL+ ++L E+ + ++ L L +D + RL G +++IQL AL
Sbjct: 274 LDDLLIDEGLSGGEVLEELLRVARSRYRGDN-LARLHRLAADADARLTDGANDRIQLEAL 332
Query: 516 IAAF 519
+A
Sbjct: 333 LAEL 336
>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 = 86.8 bits (215), Expect = 4e-20
Identities = 42/146 (28%), Positives = 62/146 (42%), Gaps = 15/146 (10%)
Query: 296 KINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVR 355
+ ++ +LL YGPPGTGKTT A A +L+ A L LNASD +V
Sbjct: 9 ALREALELPPPKNLLLYGPPGTGKTTLARAIANELFRP---GAPFLYLNASDLLEGLVVA 65
Query: 356 DQI---FQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTT------NVRFCI 406
+ + K+ ++ +DE D+++ AQNAL R++E NVR
Sbjct: 66 ELFGHFLVRLLFELAEKAKPGVLFIDEIDSLSRGAQNALLRVLETLNDLRIDRENVRVIG 125
Query: 407 ICNY--LSKIPPAIQSRC-TRFRFGP 429
N L + A+ R R
Sbjct: 126 ATNRPLLGDLDRALYDRLDIRIVIPL 151
Score = 38.7 bits (90), Expect = 0.002
Identities = 18/65 (27%), Positives = 28/65 (43%), Gaps = 3/65 (4%)
Query: 163 NSARDKLEVLELNASDDRGIGIVRDQI---FQFASTKTMHKSSYKLIILDEADAMTNDAQ 219
R L LNASD +V + + K+ ++ +DE D+++ AQ
Sbjct: 42 ELFRPGAPFLYLNASDLLEGLVVAELFGHFLVRLLFELAEKAKPGVLFIDEIDSLSRGAQ 101
Query: 220 NALRR 224
NAL R
Sbjct: 102 NALLR 106
>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 = 82.3 bits (204), Expect = 3e-18
Identities = 41/160 (25%), Positives = 65/160 (40%), Gaps = 24/160 (15%)
Query: 301 IDENELPH-LLFYGPPGTGKTTTILACARKLYTKAQFNA--------------------M 339
+++ L H LF GP G GK LA A+ L +
Sbjct: 8 LEKGRLAHAYLFAGPEGVGKELLALALAKALLCEQPGGGEPCGECPSCRLIEAGNHPDLH 67
Query: 340 VLELNASDDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFT 399
LE + VR+ + +F S S +++I+++A+ M A NAL + +E+
Sbjct: 68 RLEPEG-QSIKVDQVRE-LVEFLSRTPQE-SGRRVVIIEDAERMNEAAANALLKTLEEPP 124
Query: 400 TNVRFCIICNYLSKIPPAIQSRCTRFRFGPLDSSLIMSRL 439
N F +I K+ P I+SRC F PL ++ L
Sbjct: 125 PNTLFILITPSPEKLLPTIRSRCQVLPFPPLSEEALLQWL 164
Score = 38.4 bits (90), Expect = 0.003
Identities = 13/43 (30%), Positives = 24/43 (55%), Gaps = 4/43 (9%)
Query: 182 IGI--VRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNAL 222
I + VR+ + +F S S +++I+++A+ M A NAL
Sbjct: 76 IKVDQVRE-LVEFLSRTPQE-SGRRVVIIEDAERMNEAAANAL 116
Score = 32.2 bits (74), Expect = 0.42
Identities = 13/39 (33%), Positives = 18/39 (46%)
Query: 7 NVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRL 45
N F +I K+ P I+SRC F PL ++ L
Sbjct: 126 NTLFILITPSPEKLLPTIRSRCQVLPFPPLSEEALLQWL 164
>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 = 74.6 bits (184), Expect = 5e-16
Identities = 40/143 (27%), Positives = 63/143 (44%), Gaps = 33/143 (23%)
Query: 309 LLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGI------VRDQIFQFA 362
LL YGPPGTGKTT A A++L A +E++ S+ + +R ++F+ A
Sbjct: 1 LLLYGPPGTGKTTLAKAVAKEL------GAPFIEISGSELVSKYVGESEKRLR-ELFEAA 53
Query: 363 STKTMHKSSYKLIILDEADAM-----------TNDAQNALRRIIEKFTTN---VRFCIIC 408
K + +I +DE DA+ + N L ++ FT++ V
Sbjct: 54 K-----KLAPCVIFIDEIDALAGSRGSGGDSESRRVVNQLLTELDGFTSSLSKVIVIAAT 108
Query: 409 NYLSKIPPAI-QSRCTRFRFGPL 430
N K+ PA+ + R R PL
Sbjct: 109 NRPDKLDPALLRGRFDRIIEFPL 131
>gnl|CDD|225369 COG2812, DnaX, DNA polymerase III, gamma/tau subunits [DNA
replication, recombination, and repair].
Length = 515
Score = 74.4 bits (183), Expect = 4e-14
Identities = 47/162 (29%), Positives = 72/162 (44%), Gaps = 25/162 (15%)
Query: 301 IDENELPH-LLFYGPPGTGKTTT--ILA----------------CARKLYTKAQFNAMVL 341
++ + H LF GP G GKTT ILA C V+
Sbjct: 32 LENGRIAHAYLFSGPRGVGKTTIARILAKALNCENGPTAEPCGKCISCKEINEGSLIDVI 91
Query: 342 ELNASDDRGIGIVRDQI--FQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFT 399
E++A+ + G+ +R+ I +A ++ YK+ I+DE ++ A NAL + +E+
Sbjct: 92 EIDAASNTGVDDIREIIEKVNYAPSE----GRYKVYIIDEVHMLSKQAFNALLKTLEEPP 147
Query: 400 TNVRFCIICNYLSKIPPAIQSRCTRFRFGPLDSSLIMSRLDY 441
++V+F + KIP I SRC RF F LD I L
Sbjct: 148 SHVKFILATTEPQKIPNTILSRCQRFDFKRLDLEEIAKHLAA 189
Score = 55.5 bits (134), Expect = 4e-08
Identities = 26/95 (27%), Positives = 47/95 (49%)
Query: 1 IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDG 60
+E+ ++V+F + KI I SRC RF F LD I L ++++E +N+ D
Sbjct: 143 LEEPPSHVKFILATTEPQKIPNTILSRCQRFDFKRLDLEEIAKHLAAILDKEGINIEEDA 202
Query: 61 KKAIIDLSDGDMRKVLNILQSAATAHADEVNEDTI 95
I ++G +R L++L A E+ +++
Sbjct: 203 LSLIARAAEGSLRDALSLLDQAIAFGEGEITLESV 237
Score = 36.2 bits (84), Expect = 0.043
Identities = 16/54 (29%), Positives = 31/54 (57%), Gaps = 6/54 (11%)
Query: 171 VLELNASDDRGIGIVRDQI--FQFASTKTMHKSSYKLIILDEADAMTNDAQNAL 222
V+E++A+ + G+ +R+ I +A ++ YK+ I+DE ++ A NAL
Sbjct: 90 VIEIDAASNTGVDDIREIIEKVNYAPSE----GRYKVYIIDEVHMLSKQAFNAL 139
>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 = 69.2 bits (170), Expect = 6e-14
Identities = 41/151 (27%), Positives = 69/151 (45%), Gaps = 22/151 (14%)
Query: 301 IDENELPH-LLFYGPPGTGKTTTILACARKLYTKAQFNA----------MVLELN----- 344
I +N+L H LF GP G GK L A+ L+ + + + N
Sbjct: 13 IKKNKLSHAYLFSGPDGVGKLELALEFAKALFCENPQDDEPCGECKSCKRIENGNHPDVI 72
Query: 345 --ASDDRGIGI--VRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTT 400
+ + I I +R+ + + S K + K+ I+++A+ MT A NAL + +E+
Sbjct: 73 IIEPEGKSIKIDQIRE-LIEEFSKKPF-EGKKKVYIIEDAEKMTESAANALLKTLEEPPE 130
Query: 401 NVRFCIICNYLSKIPPAIQSRCTRFRFGPLD 431
N F ++ + +K+ P I+SRC F PL
Sbjct: 131 NTYFILLTSNPNKLLPTIRSRCQVINFKPLS 161
Score = 35.3 bits (82), Expect = 0.027
Identities = 14/49 (28%), Positives = 26/49 (53%), Gaps = 4/49 (8%)
Query: 176 ASDDRGIGI--VRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNAL 222
+ + I I +R+ + + S K + K+ I+++A+ MT A NAL
Sbjct: 75 EPEGKSIKIDQIRE-LIEEFSKKPF-EGKKKVYIIEDAEKMTESAANAL 121
>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 = 71.1 bits (175), Expect = 2e-13
Identities = 46/163 (28%), Positives = 72/163 (44%), Gaps = 27/163 (16%)
Query: 301 IDENELPH-LLFYGPPGTGKTTT--ILA----------------CARKLYTKAQFNAMVL 341
I + H LF GP GTGKT+ I A C + + V+
Sbjct: 30 IKNGRIAHAYLFSGPRGTGKTSIARIFAKALNCQNGPDGEPCNECESCKEINSGSSLDVI 89
Query: 342 ELNASDDRGIGIVR---DQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKF 398
E++A+ + G+ +R D + ++A + YK+ I+DE ++ A NAL + +E+
Sbjct: 90 EIDAASNNGVDDIREILDNV-KYAPSSGK----YKVYIIDEVHMLSKSAFNALLKTLEEP 144
Query: 399 TTNVRFCIICNYLSKIPPAIQSRCTRFRFGPLDSSLIMSRLDY 441
+V F + KIP I SRC RF F + I+ RL
Sbjct: 145 PEHVVFILATTEPHKIPATILSRCQRFDFKRIPLEDIVERLKK 187
Score = 61.4 bits (150), Expect = 4e-10
Identities = 40/166 (24%), Positives = 73/166 (43%), Gaps = 8/166 (4%)
Query: 19 KITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNI 78
KI I SRC RF F + I+ RL ++++E + + + + I +DG +R L++
Sbjct: 159 KIPATILSRCQRFDFKRIPLEDIVERLKKILDKEGIKIEDEALELIARAADGSLRDALSL 218
Query: 79 LQSAATAHADEVNEDTIFTLL--VSRVEKYRPSTLDELVSHQDIISTIEIPESML---VD 133
L + + + + LL V + L E + ++D ++I + +L VD
Sbjct: 219 LDQLISFGNGNITYEDVNELLGLVDDEKLIE---LLEAILNKDTAEALKILDEILESGVD 275
Query: 134 LVLKMSDIEYRLAAGTSEKIQLSALIAAFNSARDKLEVLELNASDD 179
+ D+ L K S L+A S ++ L+ L L S +
Sbjct: 276 PEKFLEDLIEILRDLLLIKKTPSNLLAVLESEQEFLKELALKLSLE 321
>gnl|CDD|237867 PRK14953, PRK14953, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 486
Score = 71.0 bits (174), Expect = 4e-13
Identities = 47/151 (31%), Positives = 66/151 (43%), Gaps = 22/151 (14%)
Query: 310 LFYGPPGTGKTTTILACARKL-------------------YTKAQFNAMVLELNASDDRG 350
+F GP GTGKTT A+ L K F ++ E++A+ +RG
Sbjct: 42 IFAGPRGTGKTTIARILAKVLNCLNPQEGEPCGKCENCVEIDKGSFPDLI-EIDAASNRG 100
Query: 351 IGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNY 410
I +R + S + K YK+ I+DEA +T +A NAL + +E+ F +
Sbjct: 101 IDDIR-ALRDAVSYTPI-KGKYKVYIIDEAHMLTKEAFNALLKTLEEPPPRTIFILCTTE 158
Query: 411 LSKIPPAIQSRCTRFRFGPLDSSLIMSRLDY 441
KIPP I SRC RF F I L
Sbjct: 159 YDKIPPTILSRCQRFIFSKPTKEQIKEYLKR 189
Score = 57.9 bits (140), Expect = 7e-09
Identities = 23/83 (27%), Positives = 33/83 (39%)
Query: 17 LSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVL 76
KI P I SRC RF F I L + +EK+ + S+G MR
Sbjct: 159 YDKIPPTILSRCQRFIFSKPTKEQIKEYLKRICNEEKIEYEEKALDLLAQASEGGMRDAA 218
Query: 77 NILQSAATAHADEVNEDTIFTLL 99
++L A+T +V + L
Sbjct: 219 SLLDQASTYGEGKVTIKVVEEFL 241
Score = 36.7 bits (85), Expect = 0.031
Identities = 41/187 (21%), Positives = 70/187 (37%), Gaps = 55/187 (29%)
Query: 170 EVLELNASDDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRR----- 224
+++E++A+ +RGI +R + S + K YK+ I+DEA +T +A NAL +
Sbjct: 89 DLIEIDAASNRGIDDIR-ALRDAVSYTPI-KGKYKVYIIDEAHMLTKEAFNALLKTLEEP 146
Query: 225 --------------KLPVT-----------PDGKKAII---------------------- 237
K+P T K+ I
Sbjct: 147 PPRTIFILCTTEYDKIPPTILSRCQRFIFSKPTKEQIKEYLKRICNEEKIEYEEKALDLL 206
Query: 238 -DLSDGDMRKVLNILQSAATAHADEVNEDTVYNSVGYPTKTEITNILRWLLNESMDLCYK 296
S+G MR ++L A+T +V V +G ++ + L LL +D K
Sbjct: 207 AQASEGGMRDAASLLDQASTYGEGKVTIKVVEEFLGIVSQESVRKFLNLLLESDVDEAIK 266
Query: 297 INRFIDE 303
R ++E
Sbjct: 267 FLRTLEE 273
>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit;
Provisional.
Length = 482
Score = 70.7 bits (174), Expect = 5e-13
Identities = 32/93 (34%), Positives = 48/93 (51%), Gaps = 10/93 (10%)
Query: 309 LLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFASTKTMH 368
LL YGPPG GKT+ A A + V+ELNASD R ++ + A++ ++
Sbjct: 42 LLLYGPPGVGKTSLAHALAN------DYGWEVIELNASDQRTADVIERVAGEAATSGSLF 95
Query: 369 KSSYKLIILDEADAM--TNDA--QNALRRIIEK 397
+ KLI+LDE D + D A+ +I+K
Sbjct: 96 GARRKLILLDEVDGIHGNEDRGGARAILELIKK 128
Score = 58.0 bits (141), Expect = 6e-09
Identities = 51/250 (20%), Positives = 81/250 (32%), Gaps = 87/250 (34%)
Query: 103 VEKYRPSTLDELVSHQDIISTIEIPESMLVDLVLKMSDIEYRLAAGTSEKIQLSALI--- 159
VEKYRP TL ++V ++ + IE G +K AL+
Sbjct: 5 VEKYRPKTLSDVVGNEKAKEQLR-------------EWIE-SWLKGKPKK----ALLLYG 46
Query: 160 --------AAFNSARD-KLEVLELNASDDRGIGIVRDQIFQFASTKTMHKSSYKLIILDE 210
A A D EV+ELNASD R ++ + A++ ++ + KLI+LDE
Sbjct: 47 PPGVGKTSLAHALANDYGWEVIELNASDQRTADVIERVAGEAATSGSLFGARRKLILLDE 106
Query: 211 ADAM---------------------------------------------------TNDAQ 219
D + T
Sbjct: 107 VDGIHGNEDRGGARAILELIKKAKQPIILTANDPYDPSLRELRNACLMIEFKRLSTRSIV 166
Query: 220 NALRR-----KLPVTPDGKKAIIDLSDGDMRKVLNILQSAATAHADEVNEDTVYNSVGYP 274
L+R + + K I + S GD+R +N LQ+ A ++ + V
Sbjct: 167 PVLKRICRKEGIECDDEALKEIAERSGGDLRSAINDLQAIAEG-YGKLTLEDVKTLGRRD 225
Query: 275 TKTEITNILR 284
+ I + L
Sbjct: 226 REESIFDALD 235
Score = 39.1 bits (92), Expect = 0.006
Identities = 18/76 (23%), Positives = 35/76 (46%), Gaps = 1/76 (1%)
Query: 24 IQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNILQSAA 83
+++ C F L + I+ L + +E + + K I + S GD+R +N LQ+ A
Sbjct: 148 LRNACLMIEFKRLSTRSIVPVLKRICRKEGIECDDEALKEIAERSGGDLRSAINDLQAIA 207
Query: 84 TAHADEVNEDTIFTLL 99
++ + + TL
Sbjct: 208 EG-YGKLTLEDVKTLG 222
>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 = 64.1 bits (157), Expect = 6e-13
Identities = 25/67 (37%), Positives = 47/67 (70%), Gaps = 1/67 (1%)
Query: 453 YIKIQEIKIEKGLALTDILTEISLLVHRLEIPESMLVDLVLKMSDIEYRLAAGTSEKIQL 512
+ E+ +E G++ DIL ++ ++ RL+IP+S+ ++++ ++++IE+RL+ G E IQL
Sbjct: 24 RETLYELLVE-GISAEDILKQLHEVLIRLDIPDSLKLEIIKELAEIEHRLSDGAKEIIQL 82
Query: 513 SALIAAF 519
ALIA F
Sbjct: 83 EALIAKF 89
Score = 52.1 bits (126), Expect = 1e-08
Identities = 23/65 (35%), Positives = 40/65 (61%), Gaps = 11/65 (16%)
Query: 109 STLDELVSH----QDIISTI-------EIPESMLVDLVLKMSDIEYRLAAGTSEKIQLSA 157
TL EL+ +DI+ + +IP+S+ ++++ ++++IE+RL+ G E IQL A
Sbjct: 25 ETLYELLVEGISAEDILKQLHEVLIRLDIPDSLKLEIIKELAEIEHRLSDGAKEIIQLEA 84
Query: 158 LIAAF 162
LIA F
Sbjct: 85 LIAKF 89
>gnl|CDD|237869 PRK14962, PRK14962, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 472
Score = 69.8 bits (171), Expect = 1e-12
Identities = 50/158 (31%), Positives = 77/158 (48%), Gaps = 21/158 (13%)
Query: 301 IDENELPH-LLFYGPPGTGKTTTILACARKLY-TKAQF----------------NAM-VL 341
+ +N + H +F GP GTGKTT A+ L + M V+
Sbjct: 30 LKKNSISHAYIFAGPRGTGKTTVARILAKSLNCENRKGVEPCNECRACRSIDEGTFMDVI 89
Query: 342 ELNASDDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTN 401
EL+A+ +RGI +R +I + M + YK+ I+DE +T +A NAL + +E+ ++
Sbjct: 90 ELDAASNRGIDEIR-KIRDAVGYRPM-EGKYKVYIIDEVHMLTKEAFNALLKTLEEPPSH 147
Query: 402 VRFCIICNYLSKIPPAIQSRCTRFRFGPLDSSLIMSRL 439
V F + L K+PP I SRC F + LI+ RL
Sbjct: 148 VVFVLATTNLEKVPPTIISRCQVIEFRNISDELIIKRL 185
Score = 46.7 bits (111), Expect = 2e-05
Identities = 24/95 (25%), Positives = 43/95 (45%)
Query: 1 IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDG 60
+E+ ++V F + L K+ P I SRC F + LI+ RL V E E + + +
Sbjct: 141 LEEPPSHVVFVLATTNLEKVPPTIISRCQVIEFRNISDELIIKRLQEVAEAEGIEIDREA 200
Query: 61 KKAIIDLSDGDMRKVLNILQSAATAHADEVNEDTI 95
I + G +R L +L+ ++ +T+
Sbjct: 201 LSFIAKRASGGLRDALTMLEQVWKFSEGKITLETV 235
Score = 38.6 bits (90), Expect = 0.007
Identities = 22/62 (35%), Positives = 37/62 (59%), Gaps = 2/62 (3%)
Query: 169 LEVLELNASDDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRKLPV 228
++V+EL+A+ +RGI +R +I + M + YK+ I+DE +T +A NAL + L
Sbjct: 86 MDVIELDAASNRGIDEIR-KIRDAVGYRPM-EGKYKVYIIDEVHMLTKEAFNALLKTLEE 143
Query: 229 TP 230
P
Sbjct: 144 PP 145
>gnl|CDD|235638 PRK05896, PRK05896, DNA polymerase III subunits gamma and tau;
Validated.
Length = 605
Score = 64.5 bits (157), Expect = 6e-11
Identities = 53/185 (28%), Positives = 80/185 (43%), Gaps = 38/185 (20%)
Query: 301 IDENELPH-LLFYGPPGTGKTT--TILACARKLYTKAQFNAM----------------VL 341
I N+L H +F GP G GKT+ I A A + ++
Sbjct: 32 ILNNKLTHAYIFSGPRGIGKTSIAKIFAKAINCLNPKDGDCCNSCSVCESINTNQSVDIV 91
Query: 342 ELNASDDRGIGIVR---DQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKF 398
EL+A+ + G+ +R D I +T YK+ I+DEA ++ A NAL + +E+
Sbjct: 92 ELDAASNNGVDEIRNIIDNINYLPTT-----FKYKVYIIDEAHMLSTSAWNALLKTLEEP 146
Query: 399 TTNVRFCIICNYLSKIPPAIQSRCTRFRFGPLDSSLIMSRLDYDDISFFNIIIWYIKIQE 458
+V F KIP I SRC R+ F L++S + L +I K ++
Sbjct: 147 PKHVVFIFATTEFQKIPLTIISRCQRYNFKKLNNSELQELLK-------SI----AKKEK 195
Query: 459 IKIEK 463
IKIE
Sbjct: 196 IKIED 200
Score = 56.0 bits (135), Expect = 3e-08
Identities = 33/109 (30%), Positives = 52/109 (47%), Gaps = 5/109 (4%)
Query: 19 KITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNI 78
KI I SRC R+ F L++S + L + ++EK+ + + I DL+DG +R L+I
Sbjct: 161 KIPLTIISRCQRYNFKKLNNSELQELLKSIAKKEKIKIEDNAIDKIADLADGSLRDGLSI 220
Query: 79 LQSAATAHADEVNEDTIFTL--LVSRVEKYRPSTLDELVSHQDIISTIE 125
L +T E++ + I LV +K L EL+ DI
Sbjct: 221 LDQLSTFKNSEIDIEDINKTFGLVDNNKKI---NLIELIQKNDIEELRN 266
Score = 32.5 bits (74), Expect = 0.68
Identities = 40/206 (19%), Positives = 76/206 (36%), Gaps = 67/206 (32%)
Query: 163 NSARDKLEVLELNASDDRGIGIVR---DQIFQFASTKTMHKSSYKLIILDEADAMTNDAQ 219
N + D ++EL+A+ + G+ +R D I +T YK+ I+DEA ++ A
Sbjct: 85 NQSVD---IVELDAASNNGVDEIRNIIDNINYLPTT-----FKYKVYIIDEAHMLSTSAW 136
Query: 220 NALRR-------------------KLPVT------------------------------- 229
NAL + K+P+T
Sbjct: 137 NALLKTLEEPPKHVVFIFATTEFQKIPLTIISRCQRYNFKKLNNSELQELLKSIAKKEKI 196
Query: 230 ---PDGKKAIIDLSDGDMRKVLNILQSAATAHADEVNEDTVYNSVGYPTKTEITNILRWL 286
+ I DL+DG +R L+IL +T E++ + + + G + N++ +
Sbjct: 197 KIEDNAIDKIADLADGSLRDGLSILDQLSTFKNSEIDIEDINKTFGLVDNNKKINLIELI 256
Query: 287 LNESMDLCYKINRFIDENELPHLLFY 312
++ ++ I+E E + F
Sbjct: 257 QKNDIE---ELRNLINELESKGINFE 279
>gnl|CDD|184927 PRK14963, PRK14963, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 504
Score = 62.9 bits (153), Expect = 2e-10
Identities = 47/149 (31%), Positives = 67/149 (44%), Gaps = 23/149 (15%)
Query: 310 LFYGPPGTGKTTT--ILA---------------CARKLYTKAQFNAMVLELNASDDRGIG 352
LF GP G GKTTT ++A C L + + VLE++A+ + +
Sbjct: 40 LFSGPRGVGKTTTARLIAMAVNCSGEDPKPCGECESCLAVRRGAHPDVLEIDAASNNSVE 99
Query: 353 IVRD--QIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNY 410
VRD + A + K+ ILDEA M+ A NAL + +E+ +V F +
Sbjct: 100 DVRDLREKVLLAPLR----GGRKVYILDEAHMMSKSAFNALLKTLEEPPEHVIFILATTE 155
Query: 411 LSKIPPAIQSRCTRFRFGPLDSSLIMSRL 439
K+PP I SR FRF L I +L
Sbjct: 156 PEKMPPTILSRTQHFRFRRLTEEEIAGKL 184
Score = 41.7 bits (98), Expect = 7e-04
Identities = 19/55 (34%), Positives = 27/55 (49%)
Query: 19 KITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMR 73
K+ P I SR FRF L I +L ++E E P+ + + L+DG MR
Sbjct: 158 KMPPTILSRTQHFRFRRLTEEEIAGKLRRLLEAEGREAEPEALQLVARLADGAMR 212
Score = 31.3 bits (71), Expect = 1.4
Identities = 21/65 (32%), Positives = 33/65 (50%), Gaps = 6/65 (9%)
Query: 170 EVLELNASDDRGIGIVRD--QIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRKLP 227
+VLE++A+ + + VRD + A + K+ ILDEA M+ A NAL + L
Sbjct: 86 DVLEIDAASNNSVEDVRDLREKVLLAPLR----GGRKVYILDEAHMMSKSAFNALLKTLE 141
Query: 228 VTPDG 232
P+
Sbjct: 142 EPPEH 146
>gnl|CDD|223546 COG0470, HolB, ATPase involved in DNA replication [DNA replication,
recombination, and repair].
Length = 230
Score = 60.0 bits (145), Expect = 3e-10
Identities = 50/200 (25%), Positives = 76/200 (38%), Gaps = 42/200 (21%)
Query: 4 FTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKA 63
N RF +I N SKI P I+SRC R RF P SRL+ + E G +
Sbjct: 41 PPKNTRFILITNDPSKILPTIRSRCQRIRFKPP------SRLEAIAWLED-----QGLEE 89
Query: 64 IIDLSDGDMRKVLNILQSAATAHADEVNE---------------------DTIFTLLVSR 102
I +++GD RK +N LQ+ A E + +
Sbjct: 90 IAAVAEGDARKAINPLQALAALEIGEESIYEALLLALPESLAQLAALELLKLAENKFLEA 149
Query: 103 VEKYRPSTLDELVSHQDIISTIE----------IPESMLVDLVLKMSDIEYRLAAGTSEK 152
+EK L E + +D++ ++ I E +L+ ++ RL G
Sbjct: 150 LEKLWLLLLLEGLLGEDLLDQLQRELLKLDKALIQEEKAAELLDALAQARRRLLDGLLAL 209
Query: 153 IQLSALIAAFNSARDKLEVL 172
IQL L+A + LE +
Sbjct: 210 IQLENLLAELLLLQLLLEGV 229
Score = 43.1 bits (101), Expect = 1e-04
Identities = 17/34 (50%), Positives = 19/34 (55%)
Query: 398 FTTNVRFCIICNYLSKIPPAIQSRCTRFRFGPLD 431
N RF +I N SKI P I+SRC R RF P
Sbjct: 41 PPKNTRFILITNDPSKILPTIRSRCQRIRFKPPS 74
Score = 28.8 bits (64), Expect = 6.6
Identities = 12/42 (28%), Positives = 20/42 (47%)
Query: 220 NALRRKLPVTPDGKKAIIDLSDGDMRKVLNILQSAATAHADE 261
+ L + G + I +++GD RK +N LQ+ A E
Sbjct: 74 SRLEAIAWLEDQGLEEIAAVAEGDARKAINPLQALAALEIGE 115
>gnl|CDD|237871 PRK14965, PRK14965, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 576
Score = 61.3 bits (149), Expect = 7e-10
Identities = 46/160 (28%), Positives = 75/160 (46%), Gaps = 21/160 (13%)
Query: 301 IDENELPH-LLFYGPPGTGKTTT--ILA----CARKLYTK-----------AQFNAM-VL 341
ID + H LF G G GKT+T ILA C + L + + ++ V
Sbjct: 32 IDTGRVAHAFLFTGARGVGKTSTARILAKALNCEQGLTAEPCNVCPPCVEITEGRSVDVF 91
Query: 342 ELNASDDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTN 401
E++ + + G+ +R+ + +S YK+ I+DE ++ +A NAL + +E+ +
Sbjct: 92 EIDGASNTGVDDIRE--LRENVKYLPSRSRYKIFIIDEVHMLSTNAFNALLKTLEEPPPH 149
Query: 402 VRFCIICNYLSKIPPAIQSRCTRFRFGPLDSSLIMSRLDY 441
V+F K+P I SRC RF F + I+ RL Y
Sbjct: 150 VKFIFATTEPHKVPITILSRCQRFDFRRIPLQKIVDRLRY 189
Score = 50.1 bits (120), Expect = 2e-06
Identities = 25/81 (30%), Positives = 38/81 (46%)
Query: 19 KITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNI 78
K+ I SRC RF F + I+ RL Y+ +QE ++++ + DG MR L+
Sbjct: 161 KVPITILSRCQRFDFRRIPLQKIVDRLRYIADQEGISISDAALALVARKGDGSMRDSLST 220
Query: 79 LQSAATAHADEVNEDTIFTLL 99
L D V +D + LL
Sbjct: 221 LDQVLAFCGDAVGDDDVAELL 241
Score = 29.7 bits (67), Expect = 4.6
Identities = 20/78 (25%), Positives = 37/78 (47%), Gaps = 6/78 (7%)
Query: 159 IAAFNSARDKLEVLELNASDDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDA 218
I S ++V E++ + + G+ +R+ + +S YK+ I+DE ++ +A
Sbjct: 82 ITEGRS----VDVFEIDGASNTGVDDIRE--LRENVKYLPSRSRYKIFIIDEVHMLSTNA 135
Query: 219 QNALRRKLPVTPDGKKAI 236
NAL + L P K I
Sbjct: 136 FNALLKTLEEPPPHVKFI 153
>gnl|CDD|237355 PRK13342, PRK13342, recombination factor protein RarA; Reviewed.
Length = 413
Score = 59.7 bits (146), Expect = 1e-09
Identities = 40/153 (26%), Positives = 61/153 (39%), Gaps = 27/153 (17%)
Query: 297 INRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRD 356
+ R I+ L ++ +GPPGTGKTT A T A F L+A G+ +R
Sbjct: 27 LRRMIEAGRLSSMILWGPPGTGKTTLARIIAG--ATDAPF----EALSAVTS-GVKDLR- 78
Query: 357 QIFQFASTKTMHKSSYK-LIILDEADAMTNDAQNALRRIIEKF-------TT-NVRFCII 407
++ + A + + + ++ +DE Q+AL +E TT N F +
Sbjct: 79 EVIEEA--RQRRSAGRRTILFIDEIHRFNKAQQDALLPHVEDGTITLIGATTENPSFEVN 136
Query: 408 CNYLSKIPPAIQSRCTRFRFGPLDSSLIMSRLD 440
PA+ SR F PL I L
Sbjct: 137 --------PALLSRAQVFELKPLSEEDIEQLLK 161
Score = 58.9 bits (144), Expect = 2e-09
Identities = 31/106 (29%), Positives = 49/106 (46%), Gaps = 8/106 (7%)
Query: 20 ITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEK---VNVTPDGKKAIIDLSDGDMRKVL 76
+ PA+ SR F PL I L +E ++ V + + A+ L++GD R+ L
Sbjct: 135 VNPALLSRAQVFELKPLSEEDIEQLLKRALEDKERGLVELDDEALDALARLANGDARRAL 194
Query: 77 NILQSAATAHADEVNEDTIFTLLVSRVEKYRPSTLDELVSHQDIIS 122
N+L+ AA D + + + L R +Y DE H D+IS
Sbjct: 195 NLLELAALGV-DSITLELLEEALQKRAARYD-KDGDE---HYDLIS 235
Score = 41.6 bits (99), Expect = 9e-04
Identities = 12/54 (22%), Positives = 28/54 (51%), Gaps = 1/54 (1%)
Query: 219 QNALRRKLPVTPDGKKAIIDLSDGDMRKVLNILQSAATAHADEVNEDTVYNSVG 272
++ R + + + A+ L++GD R+ LN+L+ AA D + + + ++
Sbjct: 165 EDKERGLVELDDEALDALARLANGDARRALNLLELAALGV-DSITLELLEEALQ 217
>gnl|CDD|237864 PRK14950, PRK14950, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 585
Score = 59.1 bits (143), Expect = 3e-09
Identities = 46/149 (30%), Positives = 69/149 (46%), Gaps = 26/149 (17%)
Query: 301 IDENELPH-LLFYGPPGTGKTTT--ILACARKLYTK----------------AQFNAM-V 340
I E + H LF GP G GKT+T ILA A T A+ +A+ V
Sbjct: 32 IAEGRVAHAYLFTGPRGVGKTSTARILAKAVNCTTNDPKGRPCGTCEMCRAIAEGSAVDV 91
Query: 341 LELNASDDRGIGIVRDQI--FQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKF 398
+E++A+ + R+ I QF + YK+ I+DE ++ A NAL + +E+
Sbjct: 92 IEMDAASHTSVDDAREIIERVQFRPAL----ARYKVYIIDEVHMLSTAAFNALLKTLEEP 147
Query: 399 TTNVRFCIICNYLSKIPPAIQSRCTRFRF 427
+ F + + K+P I SRC RF F
Sbjct: 148 PPHAIFILATTEVHKVPATILSRCQRFDF 176
Score = 51.0 bits (122), Expect = 1e-06
Identities = 23/72 (31%), Positives = 35/72 (48%)
Query: 19 KITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNI 78
K+ I SRC RF F + + + L + E +N+ P +AI + G MR N+
Sbjct: 162 KVPATILSRCQRFDFHRHSVADMAAHLRKIAAAEGINLEPGALEAIARAATGSMRDAENL 221
Query: 79 LQSAATAHADEV 90
LQ AT + E+
Sbjct: 222 LQQLATTYGGEI 233
Score = 31.7 bits (72), Expect = 1.2
Identities = 17/62 (27%), Positives = 29/62 (46%)
Query: 228 VTPDGKKAIIDLSDGDMRKVLNILQSAATAHADEVNEDTVYNSVGYPTKTEITNILRWLL 287
+ P +AI + G MR N+LQ AT + E++ V + +G E+ + LL
Sbjct: 199 LEPGALEAIARAATGSMRDAENLLQQLATTYGGEISLSQVQSLLGISGDEEVKALAEALL 258
Query: 288 NE 289
+
Sbjct: 259 AK 260
Score = 30.2 bits (68), Expect = 3.2
Identities = 23/82 (28%), Positives = 40/82 (48%), Gaps = 8/82 (9%)
Query: 169 LEVLELNASDDRGIGIVRDQI--FQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRKL 226
++V+E++A+ + R+ I QF + YK+ I+DE ++ A NAL + L
Sbjct: 89 VDVIEMDAASHTSVDDAREIIERVQFRPAL----ARYKVYIIDEVHMLSTAAFNALLKTL 144
Query: 227 PVTPDGKKAIIDLSDGDMRKVL 248
P AI L+ ++ KV
Sbjct: 145 EEPPP--HAIFILATTEVHKVP 164
>gnl|CDD|225165 COG2256, MGS1, ATPase related to the helicase subunit of the
Holliday junction resolvase [DNA replication,
recombination, and repair].
Length = 436
Score = 57.6 bits (140), Expect = 6e-09
Identities = 28/112 (25%), Positives = 50/112 (44%), Gaps = 13/112 (11%)
Query: 20 ITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEK-------VNVTPDGKKAIIDLSDGDM 72
+ PA+ SR F PL S I L + E+ + + + ++ LS+GD
Sbjct: 147 LNPALLSRARVFELKPLSSEDIKKLLKRALLDEERGLGGQIIVLDEEALDYLVRLSNGDA 206
Query: 73 RKVLNILQSAATAH--ADEVNEDTIFTLLVSRVEKYRPSTLDELVSHQDIIS 122
R+ LN+L+ AA + + + + + +L R ++ D H D+IS
Sbjct: 207 RRALNLLELAALSAEPDEVLILELLEEILQRRSARFDKDG-DA---HYDLIS 254
Score = 57.6 bits (140), Expect = 7e-09
Identities = 41/153 (26%), Positives = 59/153 (38%), Gaps = 27/153 (17%)
Query: 297 INRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRD 356
+ R ++ L ++ +GPPGTGKTT LA T A F L+A G+ +R+
Sbjct: 39 LRRAVEAGHLHSMILWGPPGTGKTT--LARLIAGTTNAAF----EALSAVTS-GVKDLRE 91
Query: 357 QIFQFASTKTMHKSSYKLII-LDEADAMTNDAQNALRRIIEK--------FTTNVRFCII 407
+ + I+ LDE Q+AL +E T N F
Sbjct: 92 ---IIEEARKNRLLGRRTILFLDEIHRFNKAQQDALLPHVENGTIILIGATTENPSF--- 145
Query: 408 CNYLSKIPPAIQSRCTRFRFGPLDSSLIMSRLD 440
++ PA+ SR F PL S I L
Sbjct: 146 -----ELNPALLSRARVFELKPLSSEDIKKLLK 173
Score = 34.9 bits (81), Expect = 0.11
Identities = 17/96 (17%), Positives = 34/96 (35%), Gaps = 22/96 (22%)
Query: 186 RDQIFQFASTKTMHKSSYKLIILDEADAMT--NDAQNALRRKLP-----VTPDGKKAIID 238
R ++F+ L D A R L + + ++
Sbjct: 154 RARVFELKP-------------LSSEDIKKLLKRALLDEERGLGGQIIVLDEEALDYLVR 200
Query: 239 LSDGDMRKVLNILQSAATAH--ADEVNEDTVYNSVG 272
LS+GD R+ LN+L+ AA + + + + + +
Sbjct: 201 LSNGDARRALNLLELAALSAEPDEVLILELLEEILQ 236
>gnl|CDD|180523 PRK06305, PRK06305, DNA polymerase III subunits gamma and tau;
Validated.
Length = 451
Score = 57.5 bits (139), Expect = 8e-09
Identities = 44/151 (29%), Positives = 66/151 (43%), Gaps = 25/151 (16%)
Query: 310 LFYGPPGTGKTTTILACARKLYTKAQFNAM-------------------VLELNASDDRG 350
LF G GTGKTT A+ L + VLE++ + RG
Sbjct: 43 LFSGIRGTGKTTLARIFAKALNCQNPTEDQEPCNQCASCKEISSGTSLDVLEIDGASHRG 102
Query: 351 IGIVRDQIFQFASTK--TMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIIC 408
I + I Q T T KS YK+ I+DE +T +A N+L + +E+ +V+F +
Sbjct: 103 I----EDIRQINETVLFTPSKSRYKIYIIDEVHMLTKEAFNSLLKTLEEPPQHVKFFLAT 158
Query: 409 NYLSKIPPAIQSRCTRFRFGPLDSSLIMSRL 439
+ KIP I SRC + + I+ +L
Sbjct: 159 TEIHKIPGTILSRCQKMHLKRIPEETIIDKL 189
Score = 35.9 bits (83), Expect = 0.055
Identities = 33/107 (30%), Positives = 52/107 (48%), Gaps = 9/107 (8%)
Query: 164 SARDKLEVLELNASDDRGIGIVRDQIFQFASTK--TMHKSSYKLIILDEADAMTNDAQNA 221
S+ L+VLE++ + RGI + I Q T T KS YK+ I+DE +T +A N+
Sbjct: 85 SSGTSLDVLEIDGASHRGI----EDIRQINETVLFTPSKSRYKIYIIDEVHMLTKEAFNS 140
Query: 222 LRRKLPVTPDGKKAIIDLSDGDMRKVLN-ILQSAATAHADEVNEDTV 267
L + L P K L+ ++ K+ IL H + E+T+
Sbjct: 141 LLKTLEEPPQHVKFF--LATTEIHKIPGTILSRCQKMHLKRIPEETI 185
Score = 30.5 bits (69), Expect = 2.4
Identities = 15/66 (22%), Positives = 29/66 (43%)
Query: 8 VRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDL 67
V+F + + KI I SRC + + I+ +L + +QE + + + I
Sbjct: 152 VKFFLATTEIHKIPGTILSRCQKMHLKRIPEETIIDKLALIAKQEGIETSREALLPIARA 211
Query: 68 SDGDMR 73
+ G +R
Sbjct: 212 AQGSLR 217
>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 = 53.9 bits (129), Expect = 9e-09
Identities = 31/142 (21%), Positives = 51/142 (35%), Gaps = 25/142 (17%)
Query: 308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFASTKT- 366
+L GPPG+GKTT A AR+L V+ ++ D + + + K
Sbjct: 4 VILIVGPPGSGKTTLARALARELGPP---GGGVIYIDGEDILEEVLDQLLLIIVGGKKAS 60
Query: 367 -------------MHKSSYKLIILDEADAMTNDAQNALRR--------IIEKFTTNVRFC 405
K ++ILDE ++ + Q AL ++ K N+
Sbjct: 61 GSGELRLRLALALARKLKPDVLILDEITSLLDAEQEALLLLLEELRLLLLLKSEKNLTVI 120
Query: 406 IICNYLSKIPPAIQSRCTRFRF 427
+ N + PA+ R R
Sbjct: 121 LTTNDEKDLGPALLRRRFDRRI 142
>gnl|CDD|184934 PRK14970, PRK14970, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 367
Score = 55.3 bits (133), Expect = 4e-08
Identities = 44/134 (32%), Positives = 64/134 (47%), Gaps = 9/134 (6%)
Query: 301 IDENELPH-LLFYGPPGTGKTTTILACARKL----YTKAQ--FNAMVLELNASDDRGIGI 353
I+ N L LLF GP G GKTT ARK+ Y F+ + EL+A+ + +
Sbjct: 33 IENNHLAQALLFCGPRGVGKTTCARILARKINQPGYDDPNEDFSFNIFELDAASNNSVDD 92
Query: 354 VRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSK 413
+R+ I Q K YK+ I+DE +++ A NA + +E+ + F + K
Sbjct: 93 IRNLIDQVRIPPQTGK--YKIYIIDEVHMLSSAAFNAFLKTLEEPPAHAIFILATTEKHK 150
Query: 414 IPPAIQSRCTRFRF 427
I P I SRC F F
Sbjct: 151 IIPTILSRCQIFDF 164
Score = 34.1 bits (78), Expect = 0.18
Identities = 29/114 (25%), Positives = 43/114 (37%), Gaps = 9/114 (7%)
Query: 19 KITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNI 78
KI P I SRC F F + I L + +E + D I +DG +R L+I
Sbjct: 150 KIIPTILSRCQIFDFKRITIKDIKEHLAGIAVKEGIKFEDDALHIIAQKADGALRDALSI 209
Query: 79 LQSAATAHADEVN-EDTIFTLLVSRVEKYRPSTLDELVSHQDIISTIEIPESML 131
T + + L + + Y T D+I +IPE +L
Sbjct: 210 FDRVVTFCGKNITRQAVTENLNILDYDTYINVT--------DLILENKIPELLL 255
Score = 33.3 bits (76), Expect = 0.27
Identities = 37/150 (24%), Positives = 62/150 (41%), Gaps = 13/150 (8%)
Query: 105 KYRPSTLDELVSHQDIISTIE--IPESMLVDLVLKMSDIEYRLAAGTSEKIQLSALIAAF 162
KYRP T D++V I +T+ I + L +L R T+ L+ I
Sbjct: 10 KYRPQTFDDVVGQSHITNTLLNAIENNHLAQALLFCGP---RGVGKTTCARILARKINQP 66
Query: 163 NSARDK----LEVLELNASDDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDA 218
+ EL+A+ + + +R+ I Q K YK+ I+DE +++ A
Sbjct: 67 GYDDPNEDFSFNIFELDAASNNSVDDIRNLIDQVRIPPQTGK--YKIYIIDEVHMLSSAA 124
Query: 219 QNALRRKLPVTPDGKKAIIDLSDGDMRKVL 248
NA + L P AI L+ + K++
Sbjct: 125 FNAFLKTLEEPP--AHAIFILATTEKHKII 152
>gnl|CDD|180394 PRK06090, PRK06090, DNA polymerase III subunit delta'; Validated.
Length = 319
Score = 54.4 bits (131), Expect = 4e-08
Identities = 28/94 (29%), Positives = 47/94 (50%), Gaps = 6/94 (6%)
Query: 350 GIGIVRDQIFQFASTKTMHKSS----YKLIILDEADAMTNDAQNALRRIIEKFTTNVRFC 405
G I +QI Q + +SS Y+L +++ ADAM A NAL + +E+ N F
Sbjct: 85 GKSITVEQIRQ--CNRLAQESSQLNGYRLFVIEPADAMNESASNALLKTLEEPAPNCLFL 142
Query: 406 IICNYLSKIPPAIQSRCTRFRFGPLDSSLIMSRL 439
++ + ++ P I SRC ++ P ++ M L
Sbjct: 143 LVTHNQKRLLPTIVSRCQQWVVTPPSTAQAMQWL 176
Score = 34.4 bits (79), Expect = 0.12
Identities = 18/50 (36%), Positives = 26/50 (52%), Gaps = 6/50 (12%)
Query: 181 GIGIVRDQIFQFASTKTMHKSS----YKLIILDEADAMTNDAQNALRRKL 226
G I +QI Q + +SS Y+L +++ ADAM A NAL + L
Sbjct: 85 GKSITVEQIRQ--CNRLAQESSQLNGYRLFVIEPADAMNESASNALLKTL 132
>gnl|CDD|236011 PRK07399, PRK07399, DNA polymerase III subunit delta'; Validated.
Length = 314
Score = 53.0 bits (128), Expect = 1e-07
Identities = 36/177 (20%), Positives = 62/177 (35%), Gaps = 37/177 (20%)
Query: 310 LFYGPPGTGKTTTILACARKLYTKAQFNAMVLE-----------------------LNAS 346
LF GP G G+ L L ++ + + + AS
Sbjct: 30 LFAGPEGVGRKLAALCFIEGLLSQGSPSKNIRRRLEEGNHPDLLWVEPTYQHQGKLITAS 89
Query: 347 D-------DRGIGIVR-DQI---FQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRII 395
+ + +R +QI +F S + + K++++++A+ M A NAL + +
Sbjct: 90 EAEEAGLKRKAPPQIRLEQIREIKRFLSRPPLE-APRKVVVIEDAETMNEAAANALLKTL 148
Query: 396 EKFTTNVRFCIICNYLSKIPPAIQSRCTRFRFGPLDSSLIMSRL-DYDDISFFNIII 451
E+ N +I + P I SRC F L + L D NI
Sbjct: 149 EE-PGNGTLILIAPSPESLLPTIVSRCQIIPFYRLSDEQLEQVLKRLGDEEILNINF 204
Score = 30.6 bits (70), Expect = 1.9
Identities = 11/38 (28%), Positives = 23/38 (60%), Gaps = 2/38 (5%)
Query: 185 VRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNAL 222
+R+ I +F S + + K++++++A+ M A NAL
Sbjct: 109 IRE-IKRFLSRPPLE-APRKVVVIEDAETMNEAAANAL 144
>gnl|CDD|184920 PRK14956, PRK14956, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 484
Score = 53.8 bits (129), Expect = 1e-07
Identities = 40/138 (28%), Positives = 64/138 (46%), Gaps = 24/138 (17%)
Query: 310 LFYGPPGTGKTTTILACARKLYTKAQFN------------------AMVLELNASDDRGI 351
+F+GP G GKTT A++L + + VLE++A+ +RGI
Sbjct: 44 IFFGPRGVGKTTIARILAKRLNCENPIGNEPCNECTSCLEITKGISSDVLEIDAASNRGI 103
Query: 352 GIVRD--QIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICN 409
+R+ +FA YK+ I+DE +T+ + NAL + +E+ ++ F +
Sbjct: 104 ENIRELRDNVKFAPMG----GKYKVYIIDEVHMLTDQSFNALLKTLEEPPAHIVFILATT 159
Query: 410 YLSKIPPAIQSRCTRFRF 427
KIP I SRC F F
Sbjct: 160 EFHKIPETILSRCQDFIF 177
Score = 31.1 bits (70), Expect = 1.8
Identities = 21/63 (33%), Positives = 35/63 (55%), Gaps = 6/63 (9%)
Query: 170 EVLELNASDDRGIGIVRD--QIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRKLP 227
+VLE++A+ +RGI +R+ +FA YK+ I+DE +T+ + NAL + L
Sbjct: 91 DVLEIDAASNRGIENIRELRDNVKFAPMG----GKYKVYIIDEVHMLTDQSFNALLKTLE 146
Query: 228 VTP 230
P
Sbjct: 147 EPP 149
>gnl|CDD|180215 PRK05707, PRK05707, DNA polymerase III subunit delta'; Validated.
Length = 328
Score = 52.8 bits (127), Expect = 2e-07
Identities = 40/151 (26%), Positives = 67/151 (44%), Gaps = 27/151 (17%)
Query: 306 LPH-LLFYGPPGTGKTTTILACARKLYTKAQ--------------FNA------MVLELN 344
PH L +GP G GK A L +A A VLE
Sbjct: 21 HPHAYLLHGPAGIGKRALAERLAAALLCEAPQGGGACGSCKGCQLLRAGSHPDNFVLEPE 80
Query: 345 ASDDRGIGIVRDQIFQFAS--TKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNV 402
+D + I + DQ+ + S +T K+++++ A+AM +A NAL + +E+ + +
Sbjct: 81 EAD-KTIKV--DQVRELVSFVVQTAQLGGRKVVLIEPAEAMNRNAANALLKSLEEPSGDT 137
Query: 403 RFCIICNYLSKIPPAIQSRCTRFRFGPLDSS 433
+I + S++ P I+SRC + PL S+
Sbjct: 138 VLLLISHQPSRLLPTIKSRCQQQAC-PLPSN 167
Score = 32.8 bits (75), Expect = 0.38
Identities = 16/57 (28%), Positives = 30/57 (52%), Gaps = 3/57 (5%)
Query: 187 DQIFQFAS--TKTMHKSSYKLIILDEADAMTNDAQNALRRKLPVTPDGKKAIIDLSD 241
DQ+ + S +T K+++++ A+AM +A NAL + L P G ++ +S
Sbjct: 89 DQVRELVSFVVQTAQLGGRKVVLIEPAEAMNRNAANALLKSLE-EPSGDTVLLLISH 144
>gnl|CDD|235845 PRK06647, PRK06647, DNA polymerase III subunits gamma and tau;
Validated.
Length = 563
Score = 53.2 bits (128), Expect = 2e-07
Identities = 45/162 (27%), Positives = 74/162 (45%), Gaps = 29/162 (17%)
Query: 301 IDENELPH-LLFYGPPGTGKTTTILACARKLYTKAQFNAM------------------VL 341
I+ N++ + +F GP G GKT++ A AR L M V+
Sbjct: 32 IESNKIANAYIFSGPRGVGKTSSARAFARCLNCVNGPTPMPCGECSSCKSIDNDNSLDVI 91
Query: 342 ELNASDDRGIGIVR---DQI-FQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEK 397
E++ + + + VR ++I F AS++ Y++ I+DE ++N A NAL + IE+
Sbjct: 92 EIDGASNTSVQDVRQIKEEIMFPPASSR------YRVYIIDEVHMLSNSAFNALLKTIEE 145
Query: 398 FTTNVRFCIICNYLSKIPPAIQSRCTRFRFGPLDSSLIMSRL 439
+ F + K+P I+SRC F F L I + L
Sbjct: 146 PPPYIVFIFATTEVHKLPATIKSRCQHFNFRLLSLEKIYNML 187
Score = 28.6 bits (64), Expect = 9.5
Identities = 18/59 (30%), Positives = 34/59 (57%), Gaps = 10/59 (16%)
Query: 168 KLEVLELNASDDRGIGIVR---DQI-FQFASTKTMHKSSYKLIILDEADAMTNDAQNAL 222
L+V+E++ + + + VR ++I F AS++ Y++ I+DE ++N A NAL
Sbjct: 87 SLDVIEIDGASNTSVQDVRQIKEEIMFPPASSR------YRVYIIDEVHMLSNSAFNAL 139
>gnl|CDD|235505 PRK05563, PRK05563, DNA polymerase III subunits gamma and tau;
Validated.
Length = 559
Score = 52.6 bits (127), Expect = 3e-07
Identities = 23/75 (30%), Positives = 38/75 (50%)
Query: 19 KITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNI 78
KI I SRC RF F + I+ RL Y++++E + + + I ++G MR L+I
Sbjct: 161 KIPATILSRCQRFDFKRISVEDIVERLKYILDKEGIEYEDEALRLIARAAEGGMRDALSI 220
Query: 79 LQSAATAHADEVNED 93
L A + +V +
Sbjct: 221 LDQAISFGDGKVTYE 235
Score = 51.4 bits (124), Expect = 8e-07
Identities = 47/159 (29%), Positives = 72/159 (45%), Gaps = 38/159 (23%)
Query: 310 LFYGPPGTGKTTT--ILACARKLYTKA----------------------QFNAM-VLELN 344
LF GP GTGKT+ I A KA + M V+E++
Sbjct: 42 LFSGPRGTGKTSAAKIFA-------KAVNCLNPPDGEPCNECEICKAITNGSLMDVIEID 94
Query: 345 ASDDRGIGIVRDQI--FQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNV 402
A+ + G+ +RD ++A ++ + YK+ I+DE ++ A NAL + +E+ +V
Sbjct: 95 AASNNGVDEIRDIRDKVKYAPSE----AKYKVYIIDEVHMLSTGAFNALLKTLEEPPAHV 150
Query: 403 RFCIICNYLSKIPPAIQSRCTRFRFGPLDSSLIMSRLDY 441
F + KIP I SRC RF F + I+ RL Y
Sbjct: 151 IFILATTEPHKIPATILSRCQRFDFKRISVEDIVERLKY 189
>gnl|CDD|237870 PRK14964, PRK14964, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 491
Score = 52.1 bits (125), Expect = 4e-07
Identities = 39/155 (25%), Positives = 71/155 (45%), Gaps = 21/155 (13%)
Query: 304 NELPH-LLFYGPPGTGKTTT--ILA----------------CARKLYTKAQFNAMVLELN 344
N++P +L G G GKTT I++ C + K + V+E++
Sbjct: 32 NKIPQSILLVGASGVGKTTCARIISLCLNCSNGPTSDPCGTCHNCISIKNSNHPDVIEID 91
Query: 345 ASDDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRF 404
A+ + + ++ + S S +K+ I+DE ++N A NAL + +E+ +V+F
Sbjct: 92 AASNTSVDDIK--VILENSCYLPISSKFKVYIIDEVHMLSNSAFNALLKTLEEPAPHVKF 149
Query: 405 CIICNYLSKIPPAIQSRCTRFRFGPLDSSLIMSRL 439
+ + KIP I SRC RF + + ++ L
Sbjct: 150 ILATTEVKKIPVTIISRCQRFDLQKIPTDKLVEHL 184
Score = 43.6 bits (103), Expect = 2e-04
Identities = 25/92 (27%), Positives = 46/92 (50%)
Query: 8 VRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDL 67
V+F + + KI I SRC RF + + ++ L + ++E + + K I +
Sbjct: 147 VKFILATTEVKKIPVTIISRCQRFDLQKIPTDKLVEHLVDIAKKENIEHDEESLKLIAEN 206
Query: 68 SDGDMRKVLNILQSAATAHADEVNEDTIFTLL 99
S G MR L +L+ AA ++++E ++ LL
Sbjct: 207 SSGSMRNALFLLEQAAIYSNNKISEKSVRDLL 238
>gnl|CDD|180132 PRK05564, PRK05564, DNA polymerase III subunit delta'; Validated.
Length = 313
Score = 51.2 bits (123), Expect = 5e-07
Identities = 43/156 (27%), Positives = 71/156 (45%), Gaps = 9/156 (5%)
Query: 297 INRFIDENELPHL-LFYGPPGTGKTTTILACARKLYTKAQFNAMV--LELNASDDRGIGI 353
I I +N H + G G GK+ A K+ K+Q V +E + + IG+
Sbjct: 16 IKNSIIKNRFSHAHIIVGEDGIGKSLLAKEIALKILGKSQQREYVDIIEFKPINKKSIGV 75
Query: 354 --VRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYL 411
+R+ I + K ++ K+II+ ++ MT AQNA + IE+ V ++C L
Sbjct: 76 DDIRNIIEEV--NKKPYEGDKKVIIIYNSEKMTEQAQNAFLKTIEEPPKGVFIILLCENL 133
Query: 412 SKIPPAIQSRCTRFRFGPLDSSLIMSRLD--YDDIS 445
+I I+SRC ++ L I + Y+DI
Sbjct: 134 EQILDTIKSRCQIYKLNRLSKEEIEKFISYKYNDIK 169
Score = 30.8 bits (70), Expect = 1.6
Identities = 19/70 (27%), Positives = 31/70 (44%), Gaps = 4/70 (5%)
Query: 1 IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDG 60
IE+ V ++C L +I I+SRC ++ L I I + ++ +
Sbjct: 117 IEEPPKGVFIILLCENLEQILDTIKSRCQIYKLNRLSKEEIEK----FISYKYNDIKEEE 172
Query: 61 KKAIIDLSDG 70
KK+ I SDG
Sbjct: 173 KKSAIAFSDG 182
>gnl|CDD|184923 PRK14959, PRK14959, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 624
Score = 52.0 bits (124), Expect = 5e-07
Identities = 46/155 (29%), Positives = 67/155 (43%), Gaps = 25/155 (16%)
Query: 297 INRFIDENEL-PHLLFYGPPGTGKTTT--ILA----CA--------------RKLYTKAQ 335
++R EN + P LF G G GKTT I A C RK+
Sbjct: 28 LSRAAQENRVAPAYLFSGTRGVGKTTIARIFAKALNCETAPTGEPCNTCEQCRKVTQGMH 87
Query: 336 FNAMVLELNASDDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRII 395
+ V+E++ + +RGI + + A + YK+ I+DEA +T +A NAL + +
Sbjct: 88 VD--VVEIDGASNRGIDDAKR--LKEAIGYAPMEGRYKVFIIDEAHMLTREAFNALLKTL 143
Query: 396 EKFTTNVRFCIICNYLSKIPPAIQSRCTRFRFGPL 430
E+ V F + K P I SRC F F L
Sbjct: 144 EEPPARVTFVLATTEPHKFPVTIVSRCQHFTFTRL 178
Score = 32.7 bits (74), Expect = 0.51
Identities = 19/62 (30%), Positives = 34/62 (54%), Gaps = 2/62 (3%)
Query: 169 LEVLELNASDDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRKLPV 228
++V+E++ + +RGI + + A + YK+ I+DEA +T +A NAL + L
Sbjct: 88 VDVVEIDGASNRGIDDAKR--LKEAIGYAPMEGRYKVFIIDEAHMLTREAFNALLKTLEE 145
Query: 229 TP 230
P
Sbjct: 146 PP 147
>gnl|CDD|222104 pfam13401, AAA_22, AAA domain.
Length = 124
Score = 48.4 bits (116), Expect = 5e-07
Identities = 21/115 (18%), Positives = 39/115 (33%), Gaps = 20/115 (17%)
Query: 308 HLLFYGPPGTGKTT-------------TILACARKLYTKAQFNAMVL-ELNASDDRG-IG 352
+ G G+GKTT + A L T +L L G
Sbjct: 6 IGVLTGESGSGKTTLLRRLARQLPNRRVVYVEAPSLGTPKDLLRKILRALGLPLSGGTTA 65
Query: 353 IVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCII 407
+ + I + L+I+DEA ++ +A LR + + ++ ++
Sbjct: 66 ELLEAILDALKRRGR-----PLLIIDEAQHLSLEALEELRDLYDLSEKGIQVILV 115
Score = 28.0 bits (63), Expect = 6.6
Identities = 8/21 (38%), Positives = 13/21 (61%)
Query: 204 KLIILDEADAMTNDAQNALRR 224
L+I+DEA ++ +A LR
Sbjct: 81 PLLIIDEAQHLSLEALEELRD 101
>gnl|CDD|235943 PRK07133, PRK07133, DNA polymerase III subunits gamma and tau;
Validated.
Length = 725
Score = 51.0 bits (122), Expect = 1e-06
Identities = 51/174 (29%), Positives = 84/174 (48%), Gaps = 22/174 (12%)
Query: 301 IDENELPH-LLFYGPPGTGKTTT--ILACARKLYTKAQF-------------NAMVLELN 344
I N++ H LF GP GTGKT+ I A A K + ++E++
Sbjct: 34 IKSNKISHAYLFSGPRGTGKTSVAKIFANALNCSHKTDLLEPCQECIENVNNSLDIIEMD 93
Query: 345 ASDDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRF 404
A+ + G+ +R+ I + T +S YK+ I+DE ++ A NAL + +E+ +V F
Sbjct: 94 AASNNGVDEIRELIENVKNLPT--QSKYKIYIIDEVHMLSKSAFNALLKTLEEPPKHVIF 151
Query: 405 CIICNYLSKIPPAIQSRCTRFRFGPLDSSLIMSRLDY----DDISFFNIIIWYI 454
+ + KIP I SR RF F + I+SRL++ ++IS+ + I
Sbjct: 152 ILATTEVHKIPLTILSRVQRFNFRRISEDEIVSRLEFILEKENISYEKNALKLI 205
Score = 45.2 bits (107), Expect = 8e-05
Identities = 23/80 (28%), Positives = 41/80 (51%)
Query: 19 KITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNI 78
KI I SR RF F + I+SRL++++E+E ++ + K I LS G +R L+I
Sbjct: 160 KIPLTILSRVQRFNFRRISEDEIVSRLEFILEKENISYEKNALKLIAKLSSGSLRDALSI 219
Query: 79 LQSAATAHADEVNEDTIFTL 98
+ + +++ + L
Sbjct: 220 AEQVSIFGNNKITLKNVEEL 239
Score = 30.6 bits (69), Expect = 2.5
Identities = 45/171 (26%), Positives = 78/171 (45%), Gaps = 39/171 (22%)
Query: 105 KYRPSTLDELVSHQDIISTIEIPESMLVDLVLKMSDIEYR-LAAG-------TSEKIQLS 156
KYRP T D++V I+ T+ ++K + I + L +G + KI +
Sbjct: 11 KYRPKTFDDIVGQDHIVQTL--------KNIIKSNKISHAYLFSGPRGTGKTSVAKIFAN 62
Query: 157 AL---------------IAAFNSARDKLEVLELNASDDRGIGIVRDQIFQFASTKTMHKS 201
AL I N + L+++E++A+ + G+ +R+ I + T +S
Sbjct: 63 ALNCSHKTDLLEPCQECIENVN---NSLDIIEMDAASNNGVDEIRELIENVKNLPT--QS 117
Query: 202 SYKLIILDEADAMTNDAQNALRRKLPVTPDGKKAIIDLSDGDMRKV-LNIL 251
YK+ I+DE ++ A NAL + L P K I L+ ++ K+ L IL
Sbjct: 118 KYKIYIIDEVHMLSKSAFNALLKTLEEPP--KHVIFILATTEVHKIPLTIL 166
>gnl|CDD|181214 PRK08058, PRK08058, DNA polymerase III subunit delta'; Validated.
Length = 329
Score = 49.5 bits (119), Expect = 2e-06
Identities = 47/163 (28%), Positives = 72/163 (44%), Gaps = 18/163 (11%)
Query: 301 IDENELPH-LLFYGPPGTGKTTTILACARKLYTKAQFNAM----------VLELNASDDR 349
I +N L H LF G GTGK T L A+ L+ + + N D
Sbjct: 22 IAKNRLSHAYLFEGAKGTGKKATALWLAKSLFCLERNGVEPCGTCTNCKRIDSGNHPDVH 81
Query: 350 -----GIGIVRDQI--FQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNV 402
G I +DQI + +K+ +S+ K+ I++ AD MT A N+L + +E+ +
Sbjct: 82 LVAPDGQSIKKDQIRYLKEEFSKSGVESNKKVYIIEHADKMTASAANSLLKFLEEPSGGT 141
Query: 403 RFCIICNYLSKIPPAIQSRCTRFRFGPLDSSLIMSRLDYDDIS 445
++ +I P I SRC F PL ++ RL + IS
Sbjct: 142 TAILLTENKHQILPTILSRCQVVEFRPLPPESLIQRLQEEGIS 184
Score = 28.7 bits (65), Expect = 8.7
Identities = 11/28 (39%), Positives = 19/28 (67%)
Query: 195 TKTMHKSSYKLIILDEADAMTNDAQNAL 222
+K+ +S+ K+ I++ AD MT A N+L
Sbjct: 103 SKSGVESNKKVYIIEHADKMTASAANSL 130
>gnl|CDD|184925 PRK14961, PRK14961, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 363
Score = 49.4 bits (118), Expect = 3e-06
Identities = 35/145 (24%), Positives = 66/145 (45%), Gaps = 11/145 (7%)
Query: 1 IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDG 60
+E+ +++F + + KI I SRC +F+ + I + L Y++ +E ++
Sbjct: 143 LEEPPQHIKFILATTDVEKIPKTILSRCLQFKLKIISEEKIFNFLKYILIKESIDTDEYA 202
Query: 61 KKAIIDLSDGDMRKVLNILQSAATAHADEVNEDTIFTLLVSRVEKYRPSTLDELVSHQDI 120
K I + G MR LN+L+ A +N + +L EK D L+ +D
Sbjct: 203 LKLIAYHAHGSMRDALNLLEHAINLGKGNINIKNVTDMLGLLNEKQSFLLTDALLK-KDS 261
Query: 121 ---------ISTIEIP-ESMLVDLV 135
IS+I I E++L++++
Sbjct: 262 KKTMLLLNKISSIGIEWENILIEML 286
Score = 43.3 bits (102), Expect = 2e-04
Identities = 21/73 (28%), Positives = 40/73 (54%)
Query: 369 KSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTRFRFG 428
KS +K+ ++DE ++ + NAL + +E+ +++F + + KIP I SRC +F+
Sbjct: 117 KSRFKVYLIDEVHMLSRHSFNALLKTLEEPPQHIKFILATTDVEKIPKTILSRCLQFKLK 176
Query: 429 PLDSSLIMSRLDY 441
+ I + L Y
Sbjct: 177 IISEEKIFNFLKY 189
>gnl|CDD|236022 PRK07471, PRK07471, DNA polymerase III subunit delta'; Validated.
Length = 365
Score = 49.3 bits (118), Expect = 3e-06
Identities = 19/55 (34%), Positives = 33/55 (60%)
Query: 376 ILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTRFRFGPL 430
I+D AD M +A NAL +++E+ F ++ + +++ P I+SRC + R PL
Sbjct: 146 IVDTADEMNANAANALLKVLEEPPARSLFLLVSHAPARLLPTIRSRCRKLRLRPL 200
Score = 32.3 bits (74), Expect = 0.64
Identities = 9/27 (33%), Positives = 17/27 (62%)
Query: 10 FCIICNYLSKITPAIQSRCTRFRFGPL 36
F ++ + +++ P I+SRC + R PL
Sbjct: 174 FLLVSHAPARLLPTIRSRCRKLRLRPL 200
>gnl|CDD|236267 PRK08451, PRK08451, DNA polymerase III subunits gamma and tau;
Validated.
Length = 535
Score = 49.3 bits (118), Expect = 4e-06
Identities = 48/161 (29%), Positives = 79/161 (49%), Gaps = 27/161 (16%)
Query: 301 IDENELPH-LLFYGPPGTGKTTTILACARKLYTKAQFNAM------------------VL 341
+D N L H LF G G+GKT++ AR L + ++ ++
Sbjct: 30 LDNNRLAHAYLFSGLRGSGKTSSARIFARALVCEQGPSSTPCDTCIQCQSALENRHIDII 89
Query: 342 ELNASDDRGIGIVRDQIFQFASTKTMHKSS---YKLIILDEADAMTNDAQNALRRIIEKF 398
E++A+ +RGI +R+ I Q T +K S +K+ I+DE +T +A NAL + +E+
Sbjct: 90 EMDAASNRGIDDIRELIEQ-----TKYKPSMARFKIFIIDEVHMLTKEAFNALLKTLEEP 144
Query: 399 TTNVRFCIICNYLSKIPPAIQSRCTRFRFGPLDSSLIMSRL 439
+ V+F + K+P I SR FRF + + I+S L
Sbjct: 145 PSYVKFILATTDPLKLPATILSRTQHFRFKQIPQNSIISHL 185
Score = 32.3 bits (74), Expect = 0.63
Identities = 25/76 (32%), Positives = 44/76 (57%), Gaps = 8/76 (10%)
Query: 169 LEVLELNASDDRGIGIVRDQIFQFASTKTMHKSS---YKLIILDEADAMTNDAQNALRRK 225
++++E++A+ +RGI +R+ I Q T +K S +K+ I+DE +T +A NAL +
Sbjct: 86 IDIIEMDAASNRGIDDIRELIEQ-----TKYKPSMARFKIFIIDEVHMLTKEAFNALLKT 140
Query: 226 LPVTPDGKKAIIDLSD 241
L P K I+ +D
Sbjct: 141 LEEPPSYVKFILATTD 156
Score = 28.8 bits (65), Expect = 8.2
Identities = 22/79 (27%), Positives = 39/79 (49%), Gaps = 1/79 (1%)
Query: 22 PA-IQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNILQ 80
PA I SR FRF + + I+S L ++E+E V+ P+ + + +G +R L +L
Sbjct: 161 PATILSRTQHFRFKQIPQNSIISHLKTILEKEGVSYEPEALEILARSGNGSLRDTLTLLD 220
Query: 81 SAATAHADEVNEDTIFTLL 99
A + + E + +L
Sbjct: 221 QAIIYCKNAITESKVADML 239
>gnl|CDD|237873 PRK14969, PRK14969, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 527
Score = 49.0 bits (117), Expect = 5e-06
Identities = 42/160 (26%), Positives = 75/160 (46%), Gaps = 25/160 (15%)
Query: 301 IDENELPH-LLFYGPPGTGKTTT--ILA----CARKLYTK--AQFNAMV----------L 341
+++ L H LF G G GKTT ILA C + +A + +
Sbjct: 32 LEQQRLHHAYLFTGTRGVGKTTLARILAKSLNCETGVTATPCGVCSACLEIDSGRFVDLI 91
Query: 342 ELNASDDRGIGIVRDQI--FQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFT 399
E++A+ + + +R+ + Q+A T+ +K+ I+DE ++ A NA+ + +E+
Sbjct: 92 EVDAASNTQVDAMRELLDNAQYAPTR----GRFKVYIIDEVHMLSKSAFNAMLKTLEEPP 147
Query: 400 TNVRFCIICNYLSKIPPAIQSRCTRFRFGPLDSSLIMSRL 439
+V+F + KIP + SRC +F + LI+S L
Sbjct: 148 EHVKFILATTDPQKIPVTVLSRCLQFNLKQMPPPLIVSHL 187
Score = 45.5 bits (108), Expect = 5e-05
Identities = 30/112 (26%), Positives = 55/112 (49%), Gaps = 1/112 (0%)
Query: 19 KITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNI 78
KI + SRC +F + LI+S L +++EQE + + + + G MR L++
Sbjct: 161 KIPVTVLSRCLQFNLKQMPPPLIVSHLQHILEQENIPFDATALQLLARAAAGSMRDALSL 220
Query: 79 LQSAATAHADEVNEDTIFTLLVSRVEKYRPSTLDELVSHQDIISTIEIPESM 130
L A VNE + +L + + Y + L+ L++ QD + + I ++M
Sbjct: 221 LDQAIAYGGGTVNESEVRAMLGAIDQDYLFALLEALLA-QDGAALLAIADAM 271
>gnl|CDD|169667 PRK09112, PRK09112, DNA polymerase III subunit delta'; Validated.
Length = 351
Score = 48.1 bits (115), Expect = 7e-06
Identities = 20/68 (29%), Positives = 38/68 (55%)
Query: 364 TKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCT 423
++T +++++I+D AD M +A NA+ + +E+ F +I + ++ P I+SRC
Sbjct: 134 SQTSGDGNWRIVIIDPADDMNRNAANAILKTLEEPPARALFILISHSSGRLLPTIRSRCQ 193
Query: 424 RFRFGPLD 431
PLD
Sbjct: 194 PISLKPLD 201
Score = 35.4 bits (82), Expect = 0.071
Identities = 20/73 (27%), Positives = 35/73 (47%), Gaps = 6/73 (8%)
Query: 10 FCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGK--KAIIDL 67
F +I + ++ P I+SRC PLD + L ++ + DG+ +A++
Sbjct: 174 FILISHSSGRLLPTIRSRCQPISLKPLDDDELKKALSHLG----SSQGSDGEITEALLQR 229
Query: 68 SDGDMRKVLNILQ 80
S G +RK L +L
Sbjct: 230 SKGSVRKALLLLN 242
>gnl|CDD|237866 PRK14952, PRK14952, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 584
Score = 47.2 bits (112), Expect = 2e-05
Identities = 44/151 (29%), Positives = 70/151 (46%), Gaps = 29/151 (19%)
Query: 301 IDENELPH-LLFYGPPGTGKTTT--ILA----CAR--------------KLYTKAQFNAM 339
+D + H LF GP G GKT++ ILA CA+ L +
Sbjct: 29 LDAGRINHAYLFSGPRGCGKTSSARILARSLNCAQGPTATPCGVCESCVALAPNGPGSID 88
Query: 340 VLELNASDDRGIG---IVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIE 396
V+EL+A+ G+ +RD+ F +A + S Y++ I+DEA +T NAL +I+E
Sbjct: 89 VVELDAASHGGVDDTRELRDRAF-YAPAQ----SRYRIFIVDEAHMVTTAGFNALLKIVE 143
Query: 397 KFTTNVRFCIICNYLSKIPPAIQSRCTRFRF 427
+ ++ F K+ P I+SR + F
Sbjct: 144 EPPEHLIFIFATTEPEKVLPTIRSRTHHYPF 174
Score = 28.7 bits (64), Expect = 9.9
Identities = 19/62 (30%), Positives = 34/62 (54%), Gaps = 8/62 (12%)
Query: 164 SARDKLEVLELNASDDRGIG---IVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQN 220
+ ++V+EL+A+ G+ +RD+ F +A + S Y++ I+DEA +T N
Sbjct: 82 NGPGSIDVVELDAASHGGVDDTRELRDRAF-YAPAQ----SRYRIFIVDEAHMVTTAGFN 136
Query: 221 AL 222
AL
Sbjct: 137 AL 138
>gnl|CDD|236333 PRK08691, PRK08691, DNA polymerase III subunits gamma and tau;
Validated.
Length = 709
Score = 47.0 bits (111), Expect = 2e-05
Identities = 40/144 (27%), Positives = 66/144 (45%), Gaps = 21/144 (14%)
Query: 301 IDENELPH-LLFYGPPGTGKTTTILACARKLYTK--------------AQFNAM----VL 341
+DE L H L G G GKTT A+ L + Q +A +L
Sbjct: 32 LDEGRLHHAYLLTGTRGVGKTTIARILAKSLNCENAQHGEPCGVCQSCTQIDAGRYVDLL 91
Query: 342 ELNASDDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTN 401
E++A+ + GI +R+ + T K YK+ I+DE ++ A NA+ + +E+ +
Sbjct: 92 EIDAASNTGIDNIREVLENAQYAPTAGK--YKVYIIDEVHMLSKSAFNAMLKTLEEPPEH 149
Query: 402 VRFCIICNYLSKIPPAIQSRCTRF 425
V+F + K+P + SRC +F
Sbjct: 150 VKFILATTDPHKVPVTVLSRCLQF 173
Score = 34.7 bits (79), Expect = 0.12
Identities = 23/116 (19%), Positives = 55/116 (47%)
Query: 1 IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDG 60
+E+ +V+F + K+ + SRC +F + + + L +V++ EK+ P
Sbjct: 143 LEEPPEHVKFILATTDPHKVPVTVLSRCLQFVLRNMTAQQVADHLAHVLDSEKIAYEPPA 202
Query: 61 KKAIIDLSDGDMRKVLNILQSAATAHADEVNEDTIFTLLVSRVEKYRPSTLDELVS 116
+ + + G MR L++L A + +V E+ + ++ + ++Y L +++
Sbjct: 203 LQLLGRAAAGSMRDALSLLDQAIALGSGKVAENDVRQMIGAVDKQYLYELLTGIIN 258
Score = 34.3 bits (78), Expect = 0.18
Identities = 21/73 (28%), Positives = 40/73 (54%), Gaps = 2/73 (2%)
Query: 169 LEVLELNASDDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRKLPV 228
+++LE++A+ + GI +R+ + T K YK+ I+DE ++ A NA+ + L
Sbjct: 88 VDLLEIDAASNTGIDNIREVLENAQYAPTAGK--YKVYIIDEVHMLSKSAFNAMLKTLEE 145
Query: 229 TPDGKKAIIDLSD 241
P+ K I+ +D
Sbjct: 146 PPEHVKFILATTD 158
>gnl|CDD|237354 PRK13341, PRK13341, recombination factor protein RarA/unknown
domain fusion protein; Reviewed.
Length = 725
Score = 47.0 bits (112), Expect = 2e-05
Identities = 38/148 (25%), Positives = 60/148 (40%), Gaps = 36/148 (24%)
Query: 299 RFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAM------VLELNASDDRGIG 352
R I + + L+ YGPPG GKTT LA +T+A F+++ V +L A DR
Sbjct: 45 RAIKADRVGSLILYGPPGVGKTT--LARIIANHTRAHFSSLNAVLAGVKDLRAEVDRA-- 100
Query: 353 IVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEK--------FTTNVRF 404
++++ + +T ++ +DE Q+AL +E T N F
Sbjct: 101 --KERLERHGK-RT-------ILFIDEVHRFNKAQQDALLPWVENGTITLIGATTENPYF 150
Query: 405 CIICNYLSKIPPAIQSRCTRFRFGPLDS 432
+ A+ SR FR L
Sbjct: 151 EVN--------KALVSRSRLFRLKSLSD 170
Score = 42.3 bits (100), Expect = 5e-04
Identities = 19/70 (27%), Positives = 36/70 (51%), Gaps = 7/70 (10%)
Query: 20 ITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQE-------KVNVTPDGKKAIIDLSDGDM 72
+ A+ SR FR L + L ++ + KV++ P+ +K ++D+++GD
Sbjct: 152 VNKALVSRSRLFRLKSLSDEDLHQLLKRALQDKERGYGDRKVDLEPEAEKHLVDVANGDA 211
Query: 73 RKVLNILQSA 82
R +LN L+ A
Sbjct: 212 RSLLNALELA 221
Score = 31.9 bits (73), Expect = 1.0
Identities = 12/31 (38%), Positives = 23/31 (74%)
Query: 224 RKLPVTPDGKKAIIDLSDGDMRKVLNILQSA 254
RK+ + P+ +K ++D+++GD R +LN L+ A
Sbjct: 191 RKVDLEPEAEKHLVDVANGDARSLLNALELA 221
>gnl|CDD|237057 PRK12323, PRK12323, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 700
Score = 46.0 bits (109), Expect = 4e-05
Identities = 44/166 (26%), Positives = 76/166 (45%), Gaps = 30/166 (18%)
Query: 301 IDENELPH-LLFYGPPGTGKTTT--ILA------------------CAR-KLYTKAQFNA 338
+++ L H LF G G GKTT ILA C + + T+
Sbjct: 32 LEQQRLHHAYLFTGTRGVGKTTLSRILAKSLNCTGADGEGGITAQPCGQCRACTEIDAGR 91
Query: 339 MV--LELNASDDRGIGIVRDQIFQFASTKTMHKSS--YKLIILDEADAMTNDAQNALRRI 394
V +E++A+ +RG+ D++ Q ++ +K+ ++DE +TN A NA+ +
Sbjct: 92 FVDYIEMDAASNRGV----DEMAQLLDKAVYAPTAGRFKVYMIDEVHMLTNHAFNAMLKT 147
Query: 395 IEKFTTNVRFCIICNYLSKIPPAIQSRCTRFRFGPLDSSLIMSRLD 440
+E+ +V+F + KIP + SRC +F + I+S LD
Sbjct: 148 LEEPPEHVKFILATTDPQKIPVTVLSRCLQFNLKQMPPGHIVSHLD 193
Score = 42.6 bits (100), Expect = 4e-04
Identities = 27/112 (24%), Positives = 52/112 (46%), Gaps = 1/112 (0%)
Query: 19 KITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNI 78
KI + SRC +F + I+S LD ++ +E + + + + + G MR L++
Sbjct: 166 KIPVTVLSRCLQFNLKQMPPGHIVSHLDAILGEEGIAHEVNALRLLAQAAQGSMRDALSL 225
Query: 79 LQSAATAHADEVNEDTIFTLLVSRVEKYRPSTLDELVSHQDIISTIEIPESM 130
A A V+E+ + +L + + Y LD L + +D + + I + M
Sbjct: 226 TDQAIAYSAGNVSEEAVRGMLGAIDQSYLVRLLDALAA-EDGAALLAIADEM 276
Score = 29.5 bits (66), Expect = 6.2
Identities = 19/72 (26%), Positives = 39/72 (54%), Gaps = 6/72 (8%)
Query: 172 LELNASDDRGIGIVRDQIFQFASTKTMHKSS--YKLIILDEADAMTNDAQNALRRKLPVT 229
+E++A+ +RG+ D++ Q ++ +K+ ++DE +TN A NA+ + L
Sbjct: 96 IEMDAASNRGV----DEMAQLLDKAVYAPTAGRFKVYMIDEVHMLTNHAFNAMLKTLEEP 151
Query: 230 PDGKKAIIDLSD 241
P+ K I+ +D
Sbjct: 152 PEHVKFILATTD 163
>gnl|CDD|235898 PRK06964, PRK06964, DNA polymerase III subunit delta'; Validated.
Length = 342
Score = 44.4 bits (105), Expect = 9e-05
Identities = 39/170 (22%), Positives = 63/170 (37%), Gaps = 53/170 (31%)
Query: 306 LPH-LLFYGPPGTGKTTTILACARKLYTK------------------AQFN--------- 337
LPH LL +G G GK A+ L + AQ N
Sbjct: 20 LPHALLLHGQAGIGKLDFAQHLAQGLLCETPQPDGEPCGTCAACNWFAQGNHPDYRIVRP 79
Query: 338 -AMVLELNAS---------DDRG---------IGIVRDQI---FQFASTKTMHKSSYKLI 375
A+ E + D+ G I I +Q+ F T H+ +++
Sbjct: 80 EALAAEAPGAADEAKEADADEGGKKTKAPSKEIKI--EQVRALLDFCGVGT-HRGGARVV 136
Query: 376 ILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTRF 425
+L A+A+ A NAL + +E+ F ++ + ++ P I SRC +F
Sbjct: 137 VLYPAEALNVAAANALLKTLEEPPPGTVFLLVSARIDRLLPTILSRCRQF 186
>gnl|CDD|184919 PRK14955, PRK14955, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 397
Score = 44.1 bits (104), Expect = 1e-04
Identities = 24/79 (30%), Positives = 34/79 (43%)
Query: 17 LSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVL 76
L KI I SRC RF F + I +L + E E ++V D + I + G MR
Sbjct: 167 LHKIPATIASRCQRFNFKRIPLEEIQQQLQGICEAEGISVDADALQLIGRKAQGSMRDAQ 226
Query: 77 NILQSAATAHADEVNEDTI 95
+IL + E +I
Sbjct: 227 SILDQVIAFSVESEGEGSI 245
Score = 42.6 bits (100), Expect = 4e-04
Identities = 21/60 (35%), Positives = 30/60 (50%)
Query: 368 HKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTRFRF 427
K Y++ I+DE ++ A NA + +E+ + F L KIP I SRC RF F
Sbjct: 124 QKGRYRVYIIDEVHMLSIAAFNAFLKTLEEPPPHAIFIFATTELHKIPATIASRCQRFNF 183
>gnl|CDD|180643 PRK06645, PRK06645, DNA polymerase III subunits gamma and tau;
Validated.
Length = 507
Score = 44.1 bits (104), Expect = 2e-04
Identities = 28/102 (27%), Positives = 52/102 (50%), Gaps = 2/102 (1%)
Query: 340 VLELNASDDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFT 399
++E++A+ + +R +I + A K + + +K+ I+DE ++ A NAL + +E+
Sbjct: 99 IIEIDAASKTSVDDIR-RIIESAEYKPL-QGKHKIFIIDEVHMLSKGAFNALLKTLEEPP 156
Query: 400 TNVRFCIICNYLSKIPPAIQSRCTRFRFGPLDSSLIMSRLDY 441
++ F + KIP I SRC R+ L I L+Y
Sbjct: 157 PHIIFIFATTEVQKIPATIISRCQRYDLRRLSFEEIFKLLEY 198
Score = 39.1 bits (91), Expect = 0.005
Identities = 23/75 (30%), Positives = 35/75 (46%)
Query: 17 LSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVL 76
+ KI I SRC R+ L I L+Y+ +QE + + + I S+G R +
Sbjct: 168 VQKIPATIISRCQRYDLRRLSFEEIFKLLEYITKQENLKTDIEALRIIAYKSEGSARDAV 227
Query: 77 NILQSAATAHADEVN 91
+IL AA+ A N
Sbjct: 228 SILDQAASMSAKSDN 242
>gnl|CDD|181538 PRK08699, PRK08699, DNA polymerase III subunit delta'; Validated.
Length = 325
Score = 42.9 bits (101), Expect = 2e-04
Identities = 20/83 (24%), Positives = 39/83 (46%), Gaps = 2/83 (2%)
Query: 351 IGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNY 410
I VR+ I T + ++I++ A++M A N+L +++E+ V F ++ +
Sbjct: 95 IDAVRE-IIDNVYL-TSVRGGLRVILIHPAESMNLQAANSLLKVLEEPPPQVVFLLVSHA 152
Query: 411 LSKIPPAIQSRCTRFRFGPLDSS 433
K+ P I+SRC +
Sbjct: 153 ADKVLPTIKSRCRKMVLPAPSHE 175
>gnl|CDD|184918 PRK14954, PRK14954, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 620
Score = 43.0 bits (101), Expect = 3e-04
Identities = 24/66 (36%), Positives = 33/66 (50%), Gaps = 2/66 (3%)
Query: 368 HKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTRFRF 427
K Y++ I+DE ++ A NA + +E+ + F L KIP I SRC RF F
Sbjct: 124 QKGRYRVYIIDEVHMLSTAAFNAFLKTLEEPPPHAIFIFATTELHKIPATIASRCQRFNF 183
Query: 428 G--PLD 431
PLD
Sbjct: 184 KRIPLD 189
Score = 38.0 bits (88), Expect = 0.011
Identities = 24/65 (36%), Positives = 31/65 (47%), Gaps = 4/65 (6%)
Query: 17 LSKITPAIQSRCTRFRFG--PLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRK 74
L KI I SRC RF F PLD I S+L + E + + D + I + G MR
Sbjct: 167 LHKIPATIASRCQRFNFKRIPLDE--IQSQLQMICRAEGIQIDADALQLIARKAQGSMRD 224
Query: 75 VLNIL 79
+IL
Sbjct: 225 AQSIL 229
>gnl|CDD|102059 PRK05917, PRK05917, DNA polymerase III subunit delta'; Validated.
Length = 290
Score = 42.5 bits (100), Expect = 3e-04
Identities = 28/104 (26%), Positives = 50/104 (48%), Gaps = 6/104 (5%)
Query: 368 HKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTRFRF 427
++S YK+ I+ EAD MT DA +A +++E + + ++PP I+SR
Sbjct: 92 YESPYKIYIIHEADRMTLDAISAFLKVLEDPPQHGVIILTSAKPQRLPPTIRSRSLSIHI 151
Query: 428 GPLDSSLIMSRLDYDDISF-FNIIIWYIKIQEI-KIEKGLALTD 469
+ +L+ +DI++ + E+ +I KG A TD
Sbjct: 152 PMEEKTLV----SKEDIAYLIGYAQGKESVTEVGQIVKGSADTD 191
>gnl|CDD|237874 PRK14971, PRK14971, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 614
Score = 42.5 bits (100), Expect = 5e-04
Identities = 22/60 (36%), Positives = 31/60 (51%)
Query: 19 KITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNI 78
KI P I SRC F F + + I++ L YV +E + P+ I +DG MR L+I
Sbjct: 163 KILPTILSRCQIFDFNRIQVADIVNHLQYVASKEGITAEPEALNVIAQKADGGMRDALSI 222
Score = 42.5 bits (100), Expect = 5e-04
Identities = 46/167 (27%), Positives = 70/167 (41%), Gaps = 34/167 (20%)
Query: 301 IDENELPH-LLFYGPPGTGKTTTILACARKLY-------------------------TKA 334
I N+L H LF GP G GKTT CAR +
Sbjct: 33 IATNKLAHAYLFCGPRGVGKTT----CARIFAKTINCQNLTADGEACNECESCVAFNEQR 88
Query: 335 QFNAMVLELNASDDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRI 394
+N + EL+A+ + + +R+ I Q + K YK+ I+DE ++ A NA +
Sbjct: 89 SYN--IHELDAASNNSVDDIRNLIEQVRIPPQIGK--YKIYIIDEVHMLSQAAFNAFLKT 144
Query: 395 IEKFTTNVRFCIICNYLSKIPPAIQSRCTRFRFGPLDSSLIMSRLDY 441
+E+ + F + KI P I SRC F F + + I++ L Y
Sbjct: 145 LEEPPSYAIFILATTEKHKILPTILSRCQIFDFNRIQVADIVNHLQY 191
>gnl|CDD|234619 PRK00080, ruvB, Holliday junction DNA helicase RuvB; Reviewed.
Length = 328
Score = 41.3 bits (98), Expect = 8e-04
Identities = 14/22 (63%), Positives = 16/22 (72%), Gaps = 2/22 (9%)
Query: 306 LPHLLFYGPPGTGKTT--TILA 325
L H+L YGPPG GKTT I+A
Sbjct: 51 LDHVLLYGPPGLGKTTLANIIA 72
>gnl|CDD|181551 PRK08769, PRK08769, DNA polymerase III subunit delta'; Validated.
Length = 319
Score = 41.1 bits (96), Expect = 0.001
Identities = 42/159 (26%), Positives = 67/159 (42%), Gaps = 25/159 (15%)
Query: 301 IDENELPH-LLFYGPPGTGKTTTILACARKLYTKAQFNAMV--------------LEL-- 343
+D L H LL GP G GK LA A + A L+L
Sbjct: 20 LDAGRLGHGLLICGPEGLGKRAVALALAEHVLASGPDPAAAQRTRQLIAAGTHPDLQLVS 79
Query: 344 ---NASDDR-GIGIVRDQIFQFAS--TKTMHKSSYKLIILDEADAMTNDAQNALRRIIEK 397
N + D+ IV +Q+ + + T +++I+D ADA+ A NAL + +E+
Sbjct: 80 FIPNRTGDKLRTEIVIEQVREISQKLALTPQYGIAQVVIVDPADAINRAACNALLKTLEE 139
Query: 398 FTTNVRFCIICNYLSKIPPAIQSRCTR--FRFGPLDSSL 434
+ +I +++P I+SRC R F+ P +L
Sbjct: 140 PSPGRYLWLISAQPARLPATIRSRCQRLEFKLPPAHEAL 178
Score = 29.9 bits (67), Expect = 3.6
Identities = 25/84 (29%), Positives = 38/84 (45%), Gaps = 15/84 (17%)
Query: 145 LAAGTSEKIQLSALIAAFNSARDKLEVLELNASDDRGIGIVRDQIFQFAS--TKTMHKSS 202
+AAGT +QL + I N DKL IV +Q+ + + T
Sbjct: 67 IAAGTHPDLQLVSFIP--NRTGDKLRT-----------EIVIEQVREISQKLALTPQYGI 113
Query: 203 YKLIILDEADAMTNDAQNALRRKL 226
+++I+D ADA+ A NAL + L
Sbjct: 114 AQVVIVDPADAINRAACNALLKTL 137
>gnl|CDD|235906 PRK07003, PRK07003, DNA polymerase III subunits gamma and tau;
Validated.
Length = 830
Score = 41.4 bits (97), Expect = 0.001
Identities = 27/109 (24%), Positives = 51/109 (46%)
Query: 8 VRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDL 67
V+F + KI + SRC +F + + I+S L+ ++ +E++ P + +
Sbjct: 150 VKFILATTDPQKIPVTVLSRCLQFNLKQMPAGHIVSHLERILGEERIAFEPQALRLLARA 209
Query: 68 SDGDMRKVLNILQSAATAHADEVNEDTIFTLLVSRVEKYRPSTLDELVS 116
+ G MR L++ A A+EV E + +L + + Y LD L +
Sbjct: 210 AQGSMRDALSLTDQAIAYSANEVTETAVSGMLGALDQTYMVRLLDALAA 258
Score = 39.1 bits (91), Expect = 0.006
Identities = 21/69 (30%), Positives = 39/69 (56%)
Query: 372 YKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTRFRFGPLD 431
+K+ ++DE +TN A NA+ + +E+ +V+F + KIP + SRC +F +
Sbjct: 120 FKVYMIDEVHMLTNHAFNAMLKTLEEPPPHVKFILATTDPQKIPVTVLSRCLQFNLKQMP 179
Query: 432 SSLIMSRLD 440
+ I+S L+
Sbjct: 180 AGHIVSHLE 188
>gnl|CDD|240423 PTZ00454, PTZ00454, 26S protease regulatory subunit 6B-like
protein; Provisional.
Length = 398
Score = 40.9 bits (96), Expect = 0.001
Identities = 42/141 (29%), Positives = 62/141 (43%), Gaps = 32/141 (22%)
Query: 309 LLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIG--IVRDQIFQFASTKT 366
+L YGPPGTGKT A A +T A F +V G G +VRD +F+ A
Sbjct: 182 VLLYGPPGTGKTMLAKAVAH--HTTATFIRVVGSEFVQKYLGEGPRMVRD-VFRLA---- 234
Query: 367 MHKSSYKLIILDEADAMTN---DAQNALRRIIEKF-------------TTNVRFCIICNY 410
+++ +I +DE D++ DAQ R +++ TTNV+ + N
Sbjct: 235 -RENAPSIIFIDEVDSIATKRFDAQTGADREVQRILLELLNQMDGFDQTTNVKVIMATNR 293
Query: 411 LSKIPPAIQSRCTRFRFGPLD 431
+ PA+ R G LD
Sbjct: 294 ADTLDPAL------LRPGRLD 308
>gnl|CDD|180855 PRK07132, PRK07132, DNA polymerase III subunit delta'; Validated.
Length = 299
Score = 40.1 bits (94), Expect = 0.002
Identities = 20/94 (21%), Positives = 35/94 (37%), Gaps = 9/94 (9%)
Query: 365 KTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTR 424
+ +S K++I+ + +N NAL + IE+ + F + ++K+ P I SRC
Sbjct: 84 SSFVQSQKKILIIKNIEKTSNSLLNALLKTIEEPPKDTYFLLTTKNINKVLPTIVSRCQV 143
Query: 425 FRFGPLDSSLIMSRLDYDDISFFNIIIWYIKIQE 458
F D I + K
Sbjct: 144 FNV---------KEPDQQKILAKLLSKNKEKEYN 168
>gnl|CDD|224391 COG1474, CDC6, Cdc6-related protein, AAA superfamily ATPase [DNA
replication, recombination, and repair /
Posttranslational modification, protein turnover,
chaperones].
Length = 366
Score = 40.4 bits (95), Expect = 0.002
Identities = 28/126 (22%), Positives = 47/126 (37%), Gaps = 19/126 (15%)
Query: 300 FIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRG--------- 350
+ +++ YGP GTGKT T+ +L + N V+ +N + R
Sbjct: 36 ALRGERPSNIIIYGPTGTGKTATVKFVMEELEESSA-NVEVVYINCLELRTPYQVLSKIL 94
Query: 351 --------IGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTN- 401
G +I + K ++ILDE DA+ + L ++ N
Sbjct: 95 NKLGKVPLTGDSSLEILKRLYDNLSKKGKTVIVILDEVDALVDKDGEVLYSLLRAPGENK 154
Query: 402 VRFCII 407
V+ II
Sbjct: 155 VKVSII 160
>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 = 37.9 bits (89), Expect = 0.002
Identities = 22/98 (22%), Positives = 45/98 (45%), Gaps = 9/98 (9%)
Query: 309 LLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFASTKTMH 368
++ GP GKTT +L ++L ++ +L +N D R + + + + +
Sbjct: 5 IVITGPRQVGKTTLLLQFLKELLSEN-----ILYINLDDPRFLRLALLDLLEEF--LKLL 57
Query: 369 KSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCI 406
K + LDE + D ++AL+R+ + N+R +
Sbjct: 58 LPGKKYLFLDEIQKV-PDWEDALKRLYDDG-RNLRIIL 93
>gnl|CDD|224143 COG1222, RPT1, ATP-dependent 26S proteasome regulatory subunit
[Posttranslational modification, protein turnover,
chaperones].
Length = 406
Score = 39.9 bits (94), Expect = 0.003
Identities = 27/79 (34%), Positives = 38/79 (48%), Gaps = 18/79 (22%)
Query: 310 LFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASD--DRGIG----IVRDQIFQFAS 363
L YGPPGTGKT A A Q +A + + S+ + IG +VR+ +F+ A
Sbjct: 189 LLYGPPGTGKTLLAKAVA------NQTDATFIRVVGSELVQKYIGEGARLVRE-LFELAR 241
Query: 364 TKTMHKSSYKLIILDEADA 382
S +I +DE DA
Sbjct: 242 ---EKAPS--IIFIDEIDA 255
>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 = 39.8 bits (93), Expect = 0.003
Identities = 27/72 (37%), Positives = 36/72 (50%), Gaps = 21/72 (29%)
Query: 308 HLLFYGPPGTGKTTTILACAR------KLYTKAQFN--AMVLELNAS----DDRGI---- 351
H++ YGPPG GKT A AR K + F A +E++A+ D+RGI
Sbjct: 88 HVIIYGPPGVGKT----AAARLVLEEAKKNPASPFKEGAAFVEIDATTARFDERGIADPL 143
Query: 352 -GIVRDQIFQFA 362
G V D I+Q A
Sbjct: 144 IGSVHDPIYQGA 155
Score = 35.1 bits (81), Expect = 0.088
Identities = 19/65 (29%), Positives = 31/65 (47%), Gaps = 1/65 (1%)
Query: 19 KITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNI 78
+I PA++SRC F PL I E+ +N+ + I+ + R+ +NI
Sbjct: 246 EIPPALRSRCVEIFFRPLLDEEIKEIAKNAAEKIGINLEKHALELIVKYASNG-REAVNI 304
Query: 79 LQSAA 83
+Q AA
Sbjct: 305 VQLAA 309
Score = 29.0 bits (65), Expect = 6.9
Identities = 11/23 (47%), Positives = 14/23 (60%)
Query: 413 KIPPAIQSRCTRFRFGPLDSSLI 435
+IPPA++SRC F PL I
Sbjct: 246 EIPPALRSRCVEIFFRPLLDEEI 268
>gnl|CDD|235833 PRK06581, PRK06581, DNA polymerase III subunit delta'; Validated.
Length = 263
Score = 38.7 bits (90), Expect = 0.004
Identities = 23/77 (29%), Positives = 39/77 (50%)
Query: 346 SDDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFC 405
S+ + I I + + Q +KT S YK+ I+ A+ M +A N+ +I+E N
Sbjct: 64 SNAKNISIEQIRKLQDFLSKTSAISGYKVAIIYSAELMNLNAANSCLKILEDAPKNSYIF 123
Query: 406 IICNYLSKIPPAIQSRC 422
+I + + I I+SRC
Sbjct: 124 LITSRAASIISTIRSRC 140
Score = 28.7 bits (64), Expect = 7.6
Identities = 16/54 (29%), Positives = 27/54 (50%)
Query: 177 SDDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRKLPVTP 230
S+ + I I + + Q +KT S YK+ I+ A+ M +A N+ + L P
Sbjct: 64 SNAKNISIEQIRKLQDFLSKTSAISGYKVAIIYSAELMNLNAANSCLKILEDAP 117
>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 = 38.1 bits (89), Expect = 0.006
Identities = 14/25 (56%), Positives = 18/25 (72%)
Query: 310 LFYGPPGTGKTTTILACARKLYTKA 334
L GPPGTGKTTTI+ ++L + A
Sbjct: 21 LIQGPPGTGKTTTIVEIIKQLLSNA 45
>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 = 38.2 bits (90), Expect = 0.006
Identities = 14/23 (60%), Positives = 16/23 (69%), Gaps = 2/23 (8%)
Query: 306 LPHLLFYGPPGTGKTT--TILAC 326
L H+L YGPPG GKTT I+A
Sbjct: 50 LDHVLLYGPPGLGKTTLANIIAN 72
>gnl|CDD|236090 PRK07764, PRK07764, DNA polymerase III subunits gamma and tau;
Validated.
Length = 824
Score = 39.2 bits (92), Expect = 0.006
Identities = 42/136 (30%), Positives = 59/136 (43%), Gaps = 44/136 (32%)
Query: 301 IDENELPH-LLFYGPPGTGKTTT--ILA----CA--------------RKLYTKAQFNAM 339
+D + H LF GP G GKT++ ILA C L +
Sbjct: 31 LDSGRINHAYLFSGPRGCGKTSSARILARSLNCVEGPTSTPCGECDSCVALAPGGPGSLD 90
Query: 340 VLELNAS-----DD-RGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRR 393
V E++A+ DD R + R++ F FA +S YK+ I+DEA +T NAL +
Sbjct: 91 VTEIDAASHGGVDDAREL---RERAF-FAPA----ESRYKIFIIDEAHMVTPQGFNALLK 142
Query: 394 IIE------KF---TT 400
I+E KF TT
Sbjct: 143 IVEEPPEHLKFIFATT 158
>gnl|CDD|224144 COG1223, COG1223, Predicted ATPase (AAA+ superfamily) [General
function prediction only].
Length = 368
Score = 38.6 bits (90), Expect = 0.007
Identities = 37/132 (28%), Positives = 59/132 (44%), Gaps = 30/132 (22%)
Query: 309 LLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRG--IGIVRDQI---FQFAS 363
+LFYGPPGTGKT A+ L +A +L + A++ G +G +I ++ A
Sbjct: 154 VLFYGPPGTGKTMM----AKALANEA--KVPLLLVKATELIGEHVGDGARRIHELYERAR 207
Query: 364 TKTMHKSSYKLIILDEADAMTNDAQ------------NALRRIIEKFTTNVRFCIIC--N 409
K++ ++ +DE DA+ D + NAL ++ N I N
Sbjct: 208 -----KAAPCIVFIDELDAIALDRRYQELRGDVSEIVNALLTELDGIKENEGVVTIAATN 262
Query: 410 YLSKIPPAIQSR 421
+ PAI+SR
Sbjct: 263 RPELLDPAIRSR 274
>gnl|CDD|236274 PRK08485, PRK08485, DNA polymerase III subunit delta'; Validated.
Length = 206
Score = 37.7 bits (88), Expect = 0.008
Identities = 27/84 (32%), Positives = 42/84 (50%), Gaps = 9/84 (10%)
Query: 370 SSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLSKIPPAIQSRCTRFRF-- 427
S K+I++ A + +AQNAL +I+E+ N+ F I+ + + P I+SR +
Sbjct: 54 SEEKIIVI-AAPSYGIEAQNALLKILEEPPKNICFIIVAKSKNLLLPTIRSRLIIEKRKQ 112
Query: 428 ----GPLDSSLIMSRLDYDDISFF 447
PLD L +LD DI F
Sbjct: 113 KKPVKPLDLDL--KKLDLKDIYEF 134
>gnl|CDD|184922 PRK14958, PRK14958, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 509
Score = 38.6 bits (89), Expect = 0.009
Identities = 35/149 (23%), Positives = 64/149 (42%), Gaps = 21/149 (14%)
Query: 301 IDENELPH-LLFYGPPGTGKTTTILACARKLYTKAQFNAM------------------VL 341
+D+ L H LF G G GKTT A+ L + +A +
Sbjct: 32 LDQQYLHHAYLFTGTRGVGKTTISRILAKCLNCEKGVSANPCNDCENCREIDEGRFPDLF 91
Query: 342 ELNASDDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTN 401
E++A+ + R+ + T K +K+ ++DE ++ + NAL + +E+ ++
Sbjct: 92 EVDAASRTKVEDTRELLDNIPYAPT--KGRFKVYLIDEVHMLSGHSFNALLKTLEEPPSH 149
Query: 402 VRFCIICNYLSKIPPAIQSRCTRFRFGPL 430
V+F + K+P + SRC +F L
Sbjct: 150 VKFILATTDHHKLPVTVLSRCLQFHLAQL 178
>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 = 36.8 bits (85), Expect = 0.009
Identities = 19/111 (17%), Positives = 35/111 (31%), Gaps = 4/111 (3%)
Query: 299 RFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGI-VRDQ 357
R P +L GP GTGKT+ + L A + + +R+
Sbjct: 17 RRARSGGPPSVLLTGPSGTGKTSLLRELLEGLLVAA---GKCDQAERNPPYAFSQALREL 73
Query: 358 IFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIIC 408
+ Q + +L A + L ++E+ R ++
Sbjct: 74 LRQLLRELAAELLLLREALLAALGAELIEGLQDLVELLERLLARARPLVLV 124
>gnl|CDD|225164 COG2255, RuvB, Holliday junction resolvasome, helicase subunit [DNA
replication, recombination, and repair].
Length = 332
Score = 37.9 bits (89), Expect = 0.010
Identities = 11/16 (68%), Positives = 13/16 (81%)
Query: 306 LPHLLFYGPPGTGKTT 321
L H+L +GPPG GKTT
Sbjct: 52 LDHVLLFGPPGLGKTT 67
>gnl|CDD|237862 PRK14948, PRK14948, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 620
Score = 38.0 bits (89), Expect = 0.013
Identities = 46/158 (29%), Positives = 70/158 (44%), Gaps = 56/158 (35%)
Query: 307 PHLLFYGPPGTGKTTT--ILACARKL-------------------YTKAQFNAM-VLELN 344
P LF GP GTGKT++ ILA + L A NA+ V+E++
Sbjct: 39 PAYLFTGPRGTGKTSSARILA--KSLNCLNSDKPTPEPCGKCELCRAIAAGNALDVIEID 96
Query: 345 ASDDRGIGIVRDQI--FQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEK----- 397
A+ + G+ +R+ I QFA + + +K+ ++DE ++ A NAL + +E+
Sbjct: 97 AASNTGVDNIRELIERAQFAPVQ----ARWKVYVIDECHMLSTAAFNALLKTLEEPPPRV 152
Query: 398 -F---TTNVRFCIICNYLSKIP----PAIQSRCTRFRF 427
F TT+ P P I SRC RF F
Sbjct: 153 VFVLATTD-------------PQRVLPTIISRCQRFDF 177
Score = 34.9 bits (81), Expect = 0.12
Identities = 17/54 (31%), Positives = 28/54 (51%), Gaps = 4/54 (7%)
Query: 22 PAIQSRCTRFRFG--PLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMR 73
P I SRC RF F PL++ ++ L + E+E + + P+ + S G +R
Sbjct: 166 PTIISRCQRFDFRRIPLEA--MVQHLSEIAEKESIEIEPEALTLVAQRSQGGLR 217
Score = 30.7 bits (70), Expect = 2.5
Identities = 11/19 (57%), Positives = 13/19 (68%), Gaps = 1/19 (5%)
Query: 105 KYRPSTLDELVSHQDIIST 123
KYRP DELV Q+ I+T
Sbjct: 9 KYRPQRFDELVG-QEAIAT 26
>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 = 37.9 bits (88), Expect = 0.013
Identities = 19/63 (30%), Positives = 31/63 (49%), Gaps = 3/63 (4%)
Query: 18 SKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLS-DGDMRKVL 76
+I PA++SRC F PL I + E+ V++ ++ I + +G RK +
Sbjct: 335 EEINPALRSRCAEVFFEPLTPEDIALIVLNAAEKINVHLAAGVEELIARYTIEG--RKAV 392
Query: 77 NIL 79
NIL
Sbjct: 393 NIL 395
Score = 35.9 bits (83), Expect = 0.048
Identities = 46/183 (25%), Positives = 73/183 (39%), Gaps = 54/183 (29%)
Query: 308 HLLFYGPPGTGKTTTILAC---ARKL-YTKAQFNAMVLELNAS----DDRGI-----GIV 354
H++ YGPPG GKTT A+KL +T +A +E++ + D R + G V
Sbjct: 177 HIILYGPPGVGKTTAARLALEEAKKLKHTPFAEDAPFVEVDGTTLRWDPREVTNPLLGSV 236
Query: 355 RDQIFQFA------------STKTMHKSSYKLIILDEADAMTNDAQNALRRIIE----KF 398
D I+Q A T + + ++ +DE + QN L +++E +F
Sbjct: 237 HDPIYQGARRDLAETGVPEPKTGLVTDAHGGVLFIDEIGELDPLLQNKLLKVLEDKRVEF 296
Query: 399 TT--------NV--------------RFCII---CNYLSKIPPAIQSRCTRFRFGPLDSS 433
++ NV F +I +I PA++SRC F PL
Sbjct: 297 SSSYYDPDDPNVPKYIKKLFEEGAPADFVLIGATTRDPEEINPALRSRCAEVFFEPLTPE 356
Query: 434 LIM 436
I
Sbjct: 357 DIA 359
>gnl|CDD|179699 PRK03992, PRK03992, proteasome-activating nucleotidase;
Provisional.
Length = 389
Score = 37.1 bits (87), Expect = 0.021
Identities = 30/79 (37%), Positives = 41/79 (51%), Gaps = 18/79 (22%)
Query: 310 LFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASD--DRGIG----IVRDQIFQFAS 363
L YGPPGTGK T+LA A T A F +V S+ + IG +VR+ +F+ A
Sbjct: 169 LLYGPPGTGK--TLLAKAVAHETNATFIRVV----GSELVQKFIGEGARLVRE-LFELAR 221
Query: 364 TKTMHKSSYKLIILDEADA 382
K + +I +DE DA
Sbjct: 222 EK-----APSIIFIDEIDA 235
>gnl|CDD|222005 pfam13245, AAA_19, Part of AAA domain.
Length = 73
Score = 33.9 bits (78), Expect = 0.022
Identities = 10/19 (52%), Positives = 11/19 (57%)
Query: 313 GPPGTGKTTTILACARKLY 331
G PGTGKT T A +L
Sbjct: 17 GGPGTGKTATAAAIIARLL 35
>gnl|CDD|184921 PRK14957, PRK14957, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 546
Score = 37.0 bits (85), Expect = 0.027
Identities = 34/148 (22%), Positives = 61/148 (41%), Gaps = 20/148 (13%)
Query: 310 LFYGPPGTGKTTTILACARKLYTKAQFNAM------------------VLELNASDDRGI 351
LF G G GKTT A+ L K A ++E++A+ G+
Sbjct: 42 LFTGTRGVGKTTLGRLLAKCLNCKTGVTAEPCNKCENCVAINNNSFIDLIEIDAASRTGV 101
Query: 352 GIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYL 411
++ + + + YK+ ++DE ++ + NAL + +E+ V+F +
Sbjct: 102 EETKEILDNIQYMPS--QGRYKVYLIDEVHMLSKQSFNALLKTLEEPPEYVKFILATTDY 159
Query: 412 SKIPPAIQSRCTRFRFGPLDSSLIMSRL 439
KIP I SRC + + + I +L
Sbjct: 160 HKIPVTILSRCIQLHLKHISQADIKDQL 187
Score = 30.4 bits (68), Expect = 2.8
Identities = 21/92 (22%), Positives = 40/92 (43%)
Query: 8 VRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDL 67
V+F + KI I SRC + + + I +L ++ +E +N + I
Sbjct: 150 VKFILATTDYHKIPVTILSRCIQLHLKHISQADIKDQLKIILAKENINSDEQSLEYIAYH 209
Query: 68 SDGDMRKVLNILQSAATAHADEVNEDTIFTLL 99
+ G +R L++L A + E+ + I +L
Sbjct: 210 AKGSLRDALSLLDQAISFCGGELKQAQIKQML 241
>gnl|CDD|236382 PRK09111, PRK09111, DNA polymerase III subunits gamma and tau;
Validated.
Length = 598
Score = 36.8 bits (86), Expect = 0.030
Identities = 43/148 (29%), Positives = 62/148 (41%), Gaps = 55/148 (37%)
Query: 316 GTGKTTT--ILACARKL-YTKAQFNA----------------M------VLELNASDDRG 350
G GKTTT ILA R L Y + M VLE++A+ G
Sbjct: 56 GVGKTTTARILA--RALNYEGPDGDGGPTIDLCGVGEHCQAIMEGRHVDVLEMDAASHTG 113
Query: 351 IGIVRDQI----FQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIE------KF-- 398
+ +R+ I ++ S + YK+ I+DE ++ A NAL + +E KF
Sbjct: 114 VDDIREIIESVRYRPVSAR------YKVYIIDEVHMLSTAAFNALLKTLEEPPPHVKFIF 167
Query: 399 -TTNVRFCIICNYLSKIPPAIQSRCTRF 425
TT +R K+P + SRC RF
Sbjct: 168 ATTEIR---------KVPVTVLSRCQRF 186
Score = 35.6 bits (83), Expect = 0.070
Identities = 27/102 (26%), Positives = 47/102 (46%), Gaps = 16/102 (15%)
Query: 3 KF---TTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPD 59
KF TT +R K+ + SRC RF +++ ++ + L + +E V V +
Sbjct: 164 KFIFATTEIR---------KVPVTVLSRCQRFDLRRIEADVLAAHLSRIAAKEGVEVEDE 214
Query: 60 GKKAIIDLSDGDMRKVLNIL-QSAATAHAD-EVNEDTIFTLL 99
I ++G +R L++L Q A AH EV + + +L
Sbjct: 215 ALALIARAAEGSVRDGLSLLDQ--AIAHGAGEVTAEAVRDML 254
>gnl|CDD|237868 PRK14960, PRK14960, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 702
Score = 36.6 bits (84), Expect = 0.033
Identities = 46/187 (24%), Positives = 76/187 (40%), Gaps = 33/187 (17%)
Query: 1 IEKFTTNVRFCIICNYLSKITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDG 60
+E+ +V+F K+ + SRC +F PL I L ++E+E++ D
Sbjct: 142 LEEPPEHVKFLFATTDPQKLPITVISRCLQFTLRPLAVDEITKHLGAILEKEQIAADQDA 201
Query: 61 KKAIIDLSDGDMRKVLNILQSA-----ATAHADEVNE-----------DTIFTLLVSRVE 104
I + + G +R L++ A H +V E D I + ++ E
Sbjct: 202 IWQIAESAQGSLRDALSLTDQAIAYGQGAVHHQDVKEMLGLIDRTIIYDLILAVHQNQRE 261
Query: 105 K-------YRPSTLDELVSHQDIISTIEIPESM--LVDLVLKMSDIEYRLAAGTSEKI-Q 154
K +R LD + +IST+ + L +L LK S+ + KI Q
Sbjct: 262 KVSQLLLQFRYQALDVSLVLDQLISTLHELALLQYLPELGLKYSE-------EINAKILQ 314
Query: 155 LSALIAA 161
LS LI+A
Sbjct: 315 LSKLISA 321
Score = 35.8 bits (82), Expect = 0.069
Identities = 46/184 (25%), Positives = 79/184 (42%), Gaps = 27/184 (14%)
Query: 310 LFYGPPGTGKTTT--ILA----------------CAR-KLYTKAQFNAMVLELNASDDRG 350
LF G G GKTT ILA CA K + +F ++ E++A+
Sbjct: 41 LFTGTRGVGKTTIARILAKCLNCETGVTSTPCEVCATCKAVNEGRFIDLI-EIDAASRTK 99
Query: 351 IGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNY 410
+ R+ + T + +K+ ++DE ++ + NAL + +E+ +V+F
Sbjct: 100 VEDTRELLDNVPYAPT--QGRFKVYLIDEVHMLSTHSFNALLKTLEEPPEHVKFLFATTD 157
Query: 411 LSKIPPAIQSRCTRFRFGPLDSSLIMSR----LDYDDISFFNIIIWYI-KIQEIKIEKGL 465
K+P + SRC +F PL I L+ + I+ IW I + + + L
Sbjct: 158 PQKLPITVISRCLQFTLRPLAVDEITKHLGAILEKEQIAADQDAIWQIAESAQGSLRDAL 217
Query: 466 ALTD 469
+LTD
Sbjct: 218 SLTD 221
>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 = 36.4 bits (84), Expect = 0.041
Identities = 13/23 (56%), Positives = 15/23 (65%)
Query: 308 HLLFYGPPGTGKTTTILACARKL 330
H+LF GPPGTGKTT A+
Sbjct: 314 HMLFAGPPGTGKTTIARVVAKIY 336
>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 = 35.7 bits (83), Expect = 0.051
Identities = 15/23 (65%), Positives = 16/23 (69%), Gaps = 2/23 (8%)
Query: 306 LPHLLFYGPPGTGKTT--TILAC 326
L HLL YGPPG GKTT I+A
Sbjct: 30 LDHLLLYGPPGLGKTTLAHIIAN 52
>gnl|CDD|130309 TIGR01242, 26Sp45, 26S proteasome subunit P45 family. Many
proteins may score above the trusted cutoff because an
internal.
Length = 364
Score = 35.5 bits (82), Expect = 0.051
Identities = 29/77 (37%), Positives = 40/77 (51%), Gaps = 10/77 (12%)
Query: 309 LLFYGPPGTGKTTTILACARKLYTKAQFNAMVLE--LNASDDRGIGIVRDQIFQFASTKT 366
+L YGPPGTGK T+LA A T A F +V + G +VR+ IF+ A K
Sbjct: 159 VLLYGPPGTGK--TLLAKAVAHETNATFIRVVGSELVRKYIGEGARLVRE-IFELAKEK- 214
Query: 367 MHKSSYKLIILDEADAM 383
+ +I +DE DA+
Sbjct: 215 ----APSIIFIDEIDAI 227
>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 = 34.2 bits (79), Expect = 0.056
Identities = 25/127 (19%), Positives = 46/127 (36%), Gaps = 22/127 (17%)
Query: 297 INRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAM-------VLELNASDDR 349
+ + L L G PGTGK+T L A + T F VL L+ +D
Sbjct: 26 VKGLLPRGGL--TLLAGAPGTGKSTLALDLAAAVATGRPFLGPFPVEPGRVLYLDG-EDS 82
Query: 350 GIGIVR--DQIFQFASTKTMHKSSYKLIILDEADAMT------NDAQNALRRIIEKFTTN 401
G+ R + + + + L+++D ++ N A AL +++
Sbjct: 83 EAGLRRRLRALGEAL--EEIEG--PDLVVIDPLASLLGGDENDNAAVGALLAALDRLARR 138
Query: 402 VRFCIIC 408
++
Sbjct: 139 TGAAVLL 145
>gnl|CDD|180738 PRK06871, PRK06871, DNA polymerase III subunit delta'; Validated.
Length = 325
Score = 35.5 bits (82), Expect = 0.059
Identities = 22/81 (27%), Positives = 41/81 (50%), Gaps = 10/81 (12%)
Query: 347 DDRGIGI--VRD---QIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTN 401
D++ IG+ VR+ ++ Q A + K++ + A+ +T A NAL + +E+ N
Sbjct: 83 DNKDIGVDQVREINEKVSQHA-----QQGGNKVVYIQGAERLTEAAANALLKTLEEPRPN 137
Query: 402 VRFCIICNYLSKIPPAIQSRC 422
F + + + + P I SRC
Sbjct: 138 TYFLLQADLSAALLPTIYSRC 158
>gnl|CDD|217429 pfam03215, Rad17, Rad17 cell cycle checkpoint protein.
Length = 490
Score = 35.8 bits (82), Expect = 0.064
Identities = 14/73 (19%), Positives = 31/73 (42%), Gaps = 5/73 (6%)
Query: 24 IQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDL----SDGDMRKVLNIL 79
I R F P+ + + L + QE +P + +++ + GD+R +N L
Sbjct: 197 IMPRIDTITFNPIAPTFMKKALVRISVQEGKLKSPK-SDSKLEVICQEAGGDLRSAINSL 255
Query: 80 QSAATAHADEVNE 92
Q +++ ++
Sbjct: 256 QFSSSGPNNDRKS 268
Score = 32.7 bits (74), Expect = 0.56
Identities = 40/204 (19%), Positives = 63/204 (30%), Gaps = 50/204 (24%)
Query: 276 KTEITNILRWLLNESMDLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQ 335
K +I + WL F++ N+ LL GP G GK+TT+ +++L +
Sbjct: 25 KKKIAEVDHWLKAV----------FLESNKQLILLLTGPSGCGKSTTVKVLSKELGIEII 74
Query: 336 --FNAMVL-----ELNASDDRGIGIVRDQI-------FQFASTK----TMHKSSYKLIIL 377
N L E D RG IV F + KLI++
Sbjct: 75 EWSNPEYLHNPDNECQKPDFRGDCIVNSLSQMEQFREFLLRGARYGSLQGGGLKKKLILV 134
Query: 378 DEADAMTNDAQNALRRIIEKFTTNVR-----FCI-ICNYLSKI--------------PPA 417
+E R +I + ++ FC+ CN L
Sbjct: 135 EELPNQFYSDAEKFREVIREVLQSIWHLPLIFCLTECNSLEGDNNQDRFGIDAETIMTKD 194
Query: 418 IQSRC--TRFRFGPLDSSLIMSRL 439
I F P+ + + L
Sbjct: 195 ILIMPRIDTITFNPIAPTFMKKAL 218
>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 = 34.4 bits (80), Expect = 0.076
Identities = 9/14 (64%), Positives = 11/14 (78%)
Query: 308 HLLFYGPPGTGKTT 321
+LL GPPG+GKT
Sbjct: 24 NLLMIGPPGSGKTM 37
>gnl|CDD|224145 COG1224, TIP49, DNA helicase TIP49, TBP-interacting protein
[Transcription].
Length = 450
Score = 35.0 bits (81), Expect = 0.096
Identities = 14/32 (43%), Positives = 18/32 (56%)
Query: 309 LLFYGPPGTGKTTTILACARKLYTKAQFNAMV 340
+L GPPGTGKT + AR+L F A+
Sbjct: 68 ILIVGPPGTGKTALAMGIARELGEDVPFVAIS 99
>gnl|CDD|223540 COG0464, SpoVK, ATPases of the AAA+ class [Posttranslational
modification, protein turnover, chaperones].
Length = 494
Score = 34.8 bits (80), Expect = 0.10
Identities = 14/54 (25%), Positives = 20/54 (37%), Gaps = 1/54 (1%)
Query: 277 TEITNILRWLLNESMDLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKL 330
E L+ + + + +L YGPPGTGKT A A +
Sbjct: 248 EEAKEELKEAIETPLKRPELFRKLGLRPPK-GVLLYGPPGTGKTLLAKAVALES 300
>gnl|CDD|237865 PRK14951, PRK14951, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 618
Score = 34.7 bits (80), Expect = 0.14
Identities = 26/102 (25%), Positives = 53/102 (51%), Gaps = 8/102 (7%)
Query: 342 ELNASDDRGIGIVRDQIFQFASTKTMHKSS---YKLIILDEADAMTNDAQNALRRIIEKF 398
EL+A+ +RG+ D++ Q + ++K +K+ ++DE +TN A NA+ + +E+
Sbjct: 97 ELDAASNRGV----DEVQQLLE-QAVYKPVQGRFKVFMIDEVHMLTNTAFNAMLKTLEEP 151
Query: 399 TTNVRFCIICNYLSKIPPAIQSRCTRFRFGPLDSSLIMSRLD 440
++F + K+P + SRC +F P+ ++ L
Sbjct: 152 PEYLKFVLATTDPQKVPVTVLSRCLQFNLRPMAPETVLEHLT 193
Score = 29.7 bits (67), Expect = 4.1
Identities = 18/81 (22%), Positives = 35/81 (43%)
Query: 19 KITPAIQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLSDGDMRKVLNI 78
K+ + SRC +F P+ ++ L V+ E V P + + + G MR L++
Sbjct: 166 KVPVTVLSRCLQFNLRPMAPETVLEHLTQVLAAENVPAEPQALRLLARAARGSMRDALSL 225
Query: 79 LQSAATAHADEVNEDTIFTLL 99
A + ++ E + +L
Sbjct: 226 TDQAIAFGSGQLQEAAVRQML 246
>gnl|CDD|223626 COG0552, FtsY, Signal recognition particle GTPase [Intracellular
trafficking and secretion].
Length = 340
Score = 34.2 bits (79), Expect = 0.17
Identities = 18/73 (24%), Positives = 30/73 (41%), Gaps = 7/73 (9%)
Query: 265 DTVYNSVGYPTKTEITNILRWLLNESMDLCYKINRFID-------ENELPHLLFYGPPGT 317
+ + G K + ++ L E++ + +D E + +LF G G
Sbjct: 91 EELRKREGKKKKIKDEETVKEALREALIEILRPVDKVDLPLEIPKEKKPFVILFVGVNGV 150
Query: 318 GKTTTILACARKL 330
GKTTTI A+ L
Sbjct: 151 GKTTTIAKLAKYL 163
>gnl|CDD|234232 TIGR03499, FlhF, flagellar biosynthetic protein FlhF. [Cellular
processes, Chemotaxis and motility].
Length = 283
Score = 33.8 bits (78), Expect = 0.18
Identities = 21/88 (23%), Positives = 34/88 (38%), Gaps = 14/88 (15%)
Query: 241 DGDMRKVLNILQSAATAHADEVNEDTVYNSVGY-PTKTEITNILRWLLNESMDLCYKINR 299
D + K+L L A V+E+ + P + + RWL L +
Sbjct: 134 DPEGAKLLERLLEA------GVSEELARELLEKLPEDLDAEDAWRWLREA---LEGMLPV 184
Query: 300 FIDENELPH----LLFYGPPGTGKTTTI 323
+E+ + + GP G GKTTT+
Sbjct: 185 KPEEDPILERGGVIALVGPTGVGKTTTL 212
>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 = 32.1 bits (74), Expect = 0.25
Identities = 17/57 (29%), Positives = 24/57 (42%), Gaps = 6/57 (10%)
Query: 308 HLLFYGPPGTGKTTTILACARKL---YTKAQFNAMVLELNASDDRGIGIVRDQIFQF 361
H+L G PG KT AR L + + QF +L SD G + + +F
Sbjct: 1 HVLLEGVPGLAKTLLARTLARSLGLDFRRIQFTP---DLLPSDITGTEVYDQKTREF 54
>gnl|CDD|147949 pfam06068, TIP49, TIP49 C-terminus. This family consists of the
C-terminal region of several eukaryotic and archaeal
RuvB-like 1 (Pontin or TIP49a) and RuvB-like 2 (Reptin
or TIP49b) proteins. The N-terminal domain contains the
pfam00004 domain. In zebrafish, the liebeskummer (lik)
mutation, causes development of hyperplastic embryonic
hearts. lik encodes Reptin, a component of a
DNA-stimulated ATPase complex. Beta-catenin and Pontin,
a DNA-stimulated ATPase that is often part of complexes
with Reptin, are in the same genetic pathways. The
Reptin/Pontin ratio serves to regulate heart growth
during development, at least in part via the
beta-catenin pathway. TBP-interacting protein 49 (TIP49)
was originally identified as a TBP-binding protein, and
two related proteins are encoded by individual genes,
tip49a and b. Although the function of this gene family
has not been elucidated, they are supposed to play a
critical role in nuclear events because they interact
with various kinds of nuclear factors and have DNA
helicase activities.TIP49a has been suggested to act as
an autoantigen in some patients with autoimmune
diseases.
Length = 395
Score = 33.4 bits (77), Expect = 0.30
Identities = 12/32 (37%), Positives = 18/32 (56%)
Query: 309 LLFYGPPGTGKTTTILACARKLYTKAQFNAMV 340
+L GPPGTGKT +A +++L F +
Sbjct: 53 VLIAGPPGTGKTALAIAISKELGEDTPFCPIS 84
>gnl|CDD|238005 cd00046, DEXDc, DEAD-like helicases superfamily. A diverse family
of proteins involved in ATP-dependent RNA or DNA
unwinding. This domain contains the ATP-binding region.
Length = 144
Score = 31.9 bits (73), Expect = 0.30
Identities = 20/133 (15%), Positives = 32/133 (24%), Gaps = 38/133 (28%)
Query: 313 GPPGTGKTTT-ILACARKLYTKAQFNAMVL-----------------------------E 342
P G+GKT +L L + +VL
Sbjct: 7 APTGSGKTLAALLPILELLDSLKGGQVLVLAPTRELANQVAERLKELFGEGIKVGYLIGG 66
Query: 343 LNASDDRGIGIVRDQI--------FQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRI 394
+ + + I + L+ILDEA + N L
Sbjct: 67 TSIKQQEKLLSGKTDIVVGTPGRLLDELERLKLSLKKLDLLILDEAHRLLNQGFGLLGLK 126
Query: 395 IEKFTTNVRFCII 407
I R ++
Sbjct: 127 ILLKLPKDRQVLL 139
>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 = 31.9 bits (73), Expect = 0.30
Identities = 19/94 (20%), Positives = 37/94 (39%), Gaps = 8/94 (8%)
Query: 308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVL--ELNASDDRGIGIVRDQIFQFAS-- 363
+L GPPGTGK+ A L + + L + D +G + +
Sbjct: 1 GVLLVGPPGTGKSELAERLAAAL-SNRPVFYVQLTRDTTEEDLKGRRNIDPGGASWVDGP 59
Query: 364 -TKTMHKSSYKLIILDEADAMTNDAQNALRRIIE 396
+ + ++ +LDE + D N+L +++
Sbjct: 60 LVRAAREG--EIAVLDEINRANPDVLNSLLSLLD 91
>gnl|CDD|237875 PRK14974, PRK14974, cell division protein FtsY; Provisional.
Length = 336
Score = 33.0 bits (76), Expect = 0.31
Identities = 20/68 (29%), Positives = 30/68 (44%), Gaps = 11/68 (16%)
Query: 264 EDTVYNSVGYPTKTEITNILRWLLNESMDLCYKINRFIDENELPH-LLFYGPPGTGKTTT 322
E+ V N++ K + +L S+ + + I P ++F G GTGKTTT
Sbjct: 107 EEIVKNAL----KEALLEVL------SVGDLFDLIEEIKSKGKPVVIVFVGVNGTGKTTT 156
Query: 323 ILACARKL 330
I A L
Sbjct: 157 IAKLAYYL 164
>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 = 31.8 bits (73), Expect = 0.43
Identities = 32/126 (25%), Positives = 52/126 (41%), Gaps = 36/126 (28%)
Query: 299 RFIDENELPHLLFYGPPGTGKTTTILACA----------RKLYTKAQFNAMVLELNASDD 348
+I++ E +LL GPPG GKT LACA L+T+ +V +L +
Sbjct: 42 DWIEQAE--NLLLLGPPGVGKTH--LACALGHQACRAGYSVLFTRTP--DLVEQLKRARG 95
Query: 349 RGIGIVRDQIFQFASTKTMHKSSYKLIILDEAD--AMTNDAQNALRRIIEKF-------- 398
G + A T + L+ILD+ ++ +A + L +I
Sbjct: 96 DG---------RLARTLQ-RLAKADLLILDDIGYLPLSQEAAHLLFELISDRYERRSTIL 145
Query: 399 TTNVRF 404
T+N+ F
Sbjct: 146 TSNLPF 151
>gnl|CDD|227596 COG5271, MDN1, AAA ATPase containing von Willebrand factor type A
(vWA) domain [General function prediction only].
Length = 4600
Score = 33.4 bits (76), Expect = 0.44
Identities = 22/63 (34%), Positives = 28/63 (44%), Gaps = 2/63 (3%)
Query: 288 NESMDLCYKINRFIDENELPHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASD 347
+ S+ L ++ I NE L G GTGKTT I A KL+ K + SD
Sbjct: 448 SCSLWLLEQLLWNIQNNE--PTLLVGETGTGKTTMIQYLALKLHFKLTVINKSQQTEMSD 505
Query: 348 DRG 350
D G
Sbjct: 506 DLG 508
>gnl|CDD|236153 PRK08116, PRK08116, hypothetical protein; Validated.
Length = 268
Score = 32.3 bits (74), Expect = 0.58
Identities = 10/19 (52%), Positives = 11/19 (57%), Gaps = 2/19 (10%)
Query: 309 LLFYGPPGTGKTTTILACA 327
LL +G GTGK T LA
Sbjct: 117 LLLWGSVGTGK--TYLAAC 133
>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 = 31.3 bits (71), Expect = 0.59
Identities = 17/85 (20%), Positives = 35/85 (41%), Gaps = 9/85 (10%)
Query: 308 HLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFASTKTM 367
+L +GP G+GKTT L A + TK + ++ I +++ + +++
Sbjct: 1 LILVFGPTGSGKTTLALQLALNIATKG-GKVVYVD--------IEEEIEELTERLIGESL 51
Query: 368 HKSSYKLIILDEADAMTNDAQNALR 392
+ LII+ A+ +
Sbjct: 52 KGALDNLIIVFATADDPAAARLLSK 76
>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 = 32.2 bits (73), Expect = 0.80
Identities = 37/206 (17%), Positives = 67/206 (32%), Gaps = 54/206 (26%)
Query: 276 KTEITNILRWLLNESMDLCYKINRFIDENELPH--LLFYGPPGTGKTTTILACARKLYTK 333
K +I + WL + + EN P LL GP G GK+TTI +++L +
Sbjct: 90 KKKIEEVETWLKAQVL-----------ENA-PKRILLITGPSGCGKSTTIKILSKELGIQ 137
Query: 334 AQ--FNAMVLELNASD-----DRGIGIVRDQI-------FQFASTKTMHK------SSYK 373
Q N + + +D Q F +T + + K
Sbjct: 138 VQEWSNPTLPDFQKNDHKVTLSLESCFSNFQSQIEVFSEFLLRATNKLQMLGDDLMTDKK 197
Query: 374 LIILDEADAMTNDAQNALRRIIEKFTTNVRFC--IIC---------NYLSKIPPAIQS-- 420
+I++++ AL I+ ++ C + N + PA
Sbjct: 198 IILVEDLPNQFYRDTRALHEILRWKYVSIGRCPLVFIITESLEGDNNQRRLLFPAETIMN 257
Query: 421 -------RCTRFRFGPLDSSLIMSRL 439
R + F P+ +++ L
Sbjct: 258 KEILEEPRVSNISFNPIAPTIMKKFL 283
>gnl|CDD|224401 COG1484, DnaC, DNA replication protein [DNA replication,
recombination, and repair].
Length = 254
Score = 31.6 bits (72), Expect = 0.81
Identities = 18/88 (20%), Positives = 30/88 (34%), Gaps = 15/88 (17%)
Query: 309 LLFYGPPGTGKTTTILACARKLYTK------AQFNAMVLELNASDDRGIGIVRDQIFQFA 362
L+ GPPG GKT +A +L ++ +L A+ D G +
Sbjct: 108 LVLLGPPGVGKTHLAIAIGNELLKAGISVLFITAPDLLSKLKAAFDEG---------RLE 158
Query: 363 STKTMHKSSYKLIILDEADAMTNDAQNA 390
L+I+D+ + A
Sbjct: 159 EKLLRELKKVDLLIIDDIGYEPFSQEEA 186
>gnl|CDD|234402 TIGR03928, T7_EssCb_Firm, type VII secretion protein EssC,
C-terminal domain. This model describes the C-terminal
domain, or longer subunit, of the Firmicutes type VII
secretion protein EssC. This protein (homologous to EccC
in Actinobacteria) and the WXG100 target proteins are
the only homologous parts of type VII secretion between
Firmicutes and Actinobacteria [Protein fate, Protein and
peptide secretion and trafficking].
Length = 1296
Score = 32.3 bits (74), Expect = 0.83
Identities = 13/48 (27%), Positives = 26/48 (54%), Gaps = 5/48 (10%)
Query: 300 FIDENELPHLLFYGPPGTGKTTT----ILACARKLYTKAQFNAMVLEL 343
+D ++ HL +G PG GK+T I++ AR+ ++ Q + + +
Sbjct: 804 TLDLSKDGHLAIFGSPGYGKSTFLQTLIMSLARQ-HSPEQLHFYLFDF 850
>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 = 31.4 bits (72), Expect = 0.85
Identities = 24/95 (25%), Positives = 38/95 (40%), Gaps = 11/95 (11%)
Query: 313 GPPGTGKTTTILACARKLYTKAQFNAMVLEL--NASDD--RGIGIVRDQIFQFASTKTMH 368
GP GTGKTT+ L AR+ + A + + L A+ +GI +
Sbjct: 25 GPAGTGKTTS-LKAAREAWEAAGYRVIGLAPTGKAAKVLGEELGIEARTLASLLHRWDKG 83
Query: 369 KSSY------KLIILDEADAMTNDAQNALRRIIEK 397
+ L+++DEA + L R+ EK
Sbjct: 84 EDPGRVLDAGTLLVVDEAGMVGTRQMARLLRLAEK 118
>gnl|CDD|234751 PRK00411, cdc6, cell division control protein 6; Reviewed.
Length = 394
Score = 31.7 bits (73), Expect = 0.92
Identities = 12/14 (85%), Positives = 13/14 (92%)
Query: 310 LFYGPPGTGKTTTI 323
L YGPPGTGKTTT+
Sbjct: 59 LIYGPPGTGKTTTV 72
>gnl|CDD|177083 CHL00181, cbbX, CbbX; Provisional.
Length = 287
Score = 31.2 bits (71), Expect = 1.0
Identities = 14/24 (58%), Positives = 15/24 (62%)
Query: 308 HLLFYGPPGTGKTTTILACARKLY 331
H+ F G PGTGKTT L A LY
Sbjct: 61 HMSFTGSPGTGKTTVALKMADILY 84
>gnl|CDD|222163 pfam13479, AAA_24, AAA domain. This AAA domain is found in a wide
variety of presumed phage proteins.
Length = 201
Score = 31.1 bits (71), Expect = 1.1
Identities = 9/14 (64%), Positives = 10/14 (71%)
Query: 310 LFYGPPGTGKTTTI 323
L YGPPG GKT+
Sbjct: 7 LIYGPPGIGKTSLA 20
>gnl|CDD|225398 COG2842, COG2842, Uncharacterized ATPase, putative transposase
[General function prediction only].
Length = 297
Score = 31.2 bits (71), Expect = 1.4
Identities = 28/95 (29%), Positives = 38/95 (40%), Gaps = 12/95 (12%)
Query: 312 YGPPGTGKTTTILACA----RKLYTKAQ--FNAMVLELNASDDRGI---GIVRDQIFQFA 362
YG G GKT A L +A + A+VL L G + D
Sbjct: 100 YGYAGLGKTQAAKNYAPSNPNALLIEADPSYTALVLILIICAAAFGATDGTINDL---TE 156
Query: 363 STKTMHKSSYKLIILDEADAMTNDAQNALRRIIEK 397
+ + +LII+DEAD + A LRRI +K
Sbjct: 157 RLMIRLRDTVRLIIVDEADRLPYRALEELRRIHDK 191
>gnl|CDD|235871 PRK06835, PRK06835, DNA replication protein DnaC; Validated.
Length = 329
Score = 31.0 bits (71), Expect = 1.4
Identities = 14/24 (58%), Positives = 15/24 (62%), Gaps = 2/24 (8%)
Query: 297 INRFIDENELPHLLFYGPPGTGKT 320
I F NE +LLFYG GTGKT
Sbjct: 176 IENFDKNNE--NLLFYGNTGTGKT 197
>gnl|CDD|216584 pfam01580, FtsK_SpoIIIE, FtsK/SpoIIIE family. FtsK has extensive
sequence similarity to wide variety of proteins from
prokaryotes and plasmids, termed the FtsK/SpoIIIE
family. This domain contains a putative ATP binding
P-loop motif. It is found in the FtsK cell division
protein from E. coli and the stage III sporulation
protein E SpoIIIE, which has roles in regulation of
prespore specific gene expression in B. subtilis. A
mutation in FtsK causes a temperature sensitive block in
cell division and it is involved in peptidoglycan
synthesis or modification. The SpoIIIE protein is
implicated in intercellular chromosomal DNA transfer.
Length = 201
Score = 30.4 bits (69), Expect = 1.4
Identities = 13/33 (39%), Positives = 19/33 (57%), Gaps = 4/33 (12%)
Query: 301 IDENELPHLLFYGPPGTGKTTT----ILACARK 329
D ++PHLL G G+GK+T IL+ A +
Sbjct: 33 ADLVKMPHLLIAGATGSGKSTFLNTLILSLAAR 65
>gnl|CDD|200217 TIGR02880, cbbX_cfxQ, probable Rubsico expression protein CbbX.
Proteins in this family are now designated CbbX. Some
previously were CfxQ (carbon fixation Q). Its gene is
often found immmediately downstream of the Rubisco large
and small chain genes, and it is suggested to be
necessary for Rubisco expression. CbbX has been shown to
be necessary for photoautotrophic growth. This protein
belongs to the larger family of pfam00004, ATPase family
Associated with various cellular Activities. Within that
larger family, members of this family are most closely
related to the stage V sporulation protein K, or SpoVK,
in endospore-forming bacteria such as Bacillus subtilis.
Length = 284
Score = 31.0 bits (70), Expect = 1.5
Identities = 23/84 (27%), Positives = 34/84 (40%), Gaps = 4/84 (4%)
Query: 249 NILQSAATAHADEVNEDTVYNSVGY-PTKTEITNILRWLLNESMDLCYKINRFIDENELP 307
++ + EV + +G P KT I I LL ++ +
Sbjct: 3 DLRAEYEGSGITEVLDQLDRELIGLKPVKTRIREIAALLL---VERARQKLGLASAAPTL 59
Query: 308 HLLFYGPPGTGKTTTILACARKLY 331
H+ F G PGTGKTT L A+ L+
Sbjct: 60 HMSFTGNPGTGKTTVALRMAQILH 83
>gnl|CDD|236138 PRK07994, PRK07994, DNA polymerase III subunits gamma and tau;
Validated.
Length = 647
Score = 31.4 bits (72), Expect = 1.5
Identities = 17/53 (32%), Positives = 28/53 (52%), Gaps = 6/53 (11%)
Query: 24 IQSRCTRFRFGPLDSSLIMSRLDYVIEQEKVNVTPDGKKAIIDLS---DGDMR 73
I SRC +F LD I +L+++++ E++ P A+ L+ DG MR
Sbjct: 166 ILSRCLQFHLKALDVEQIRQQLEHILQAEQIPFEPR---ALQLLARAADGSMR 215
>gnl|CDD|215599 PLN03140, PLN03140, ABC transporter G family member; Provisional.
Length = 1470
Score = 31.4 bits (71), Expect = 1.6
Identities = 13/21 (61%), Positives = 15/21 (71%)
Query: 310 LFYGPPGTGKTTTILACARKL 330
L GPP +GKTT +LA A KL
Sbjct: 195 LLLGPPSSGKTTLLLALAGKL 215
>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 = 30.4 bits (69), Expect = 1.6
Identities = 18/101 (17%), Positives = 32/101 (31%), Gaps = 25/101 (24%)
Query: 309 LLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIV----RDQIFQFAST 364
L G PGTGKTT + LY + G+ + +++ + A +
Sbjct: 2 TLLSGGPGTGKTT---FALQFLYAGLARG----------EPGLYVTLEESPEELIENAES 48
Query: 365 KTMHKSSY----KLIILDEADAMTNDA----QNALRRIIEK 397
L I+D A + L + ++
Sbjct: 49 LGWDLERLEDEGLLAIVDADPDEIGPAESSLRLELIQRLKD 89
>gnl|CDD|180916 PRK07276, PRK07276, DNA polymerase III subunit delta'; Validated.
Length = 290
Score = 30.8 bits (70), Expect = 1.8
Identities = 19/75 (25%), Positives = 42/75 (56%), Gaps = 2/75 (2%)
Query: 353 IVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKFTTNVRFCIICNYLS 412
+R+ + F+ + ++ ++ I+ +AD M +A N+L ++IE+ + + ++ N +
Sbjct: 88 TIRELVKNFSQSG--YEGKQQVFIIKDADKMHVNAANSLLKVIEEPQSEIYIFLLTNDEN 145
Query: 413 KIPPAIQSRCTRFRF 427
K+ P I+SR F F
Sbjct: 146 KVLPTIKSRTQIFHF 160
>gnl|CDD|240669 cd12223, RRM_SR140, RNA recognition motif (RRM) in U2-associated
protein SR140 and similar proteins. This subgroup
corresponds to the RRM of SR140 (also termed U2
snRNP-associated SURP motif-containing protein orU2SURP,
or 140 kDa Ser/Arg-rich domain protein) which is a
putative splicing factor mainly found in higher
eukaryotes. Although it is initially identified as one
of the 17S U2 snRNP-associated proteins, the molecular
and physiological function of SR140 remains unclear.
SR140 contains an N-terminal RNA recognition motif
(RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), a SWAP/SURP domain that is
found in a number of pre-mRNA splicing factors in the
middle region, and a C-terminal arginine/serine-rich
domain (RS domain).
Length = 84
Score = 28.8 bits (65), Expect = 1.8
Identities = 15/41 (36%), Positives = 20/41 (48%), Gaps = 10/41 (24%)
Query: 399 TTNVRFCIICNYLSKIPPAI--QSRCTRF-RFGPLDSSLIM 436
TTN+ Y+ + P + + C F RFGPL S IM
Sbjct: 1 TTNL-------YVGNLNPKVTEEVLCQEFGRFGPLASVKIM 34
>gnl|CDD|226054 COG3523, IcmF, Type VI protein secretion system component VasK
[Intracellular trafficking, secretion, and vesicular
transport].
Length = 1188
Score = 31.2 bits (71), Expect = 1.9
Identities = 23/81 (28%), Positives = 34/81 (41%), Gaps = 10/81 (12%)
Query: 244 MRKVLNILQSAATAHADEVNEDTVYNSVGYPTKTEITNILRWLLNESMDLCYKINRFIDE 303
+ K L Q A ADE++ + ++ LR L R++ E
Sbjct: 73 LSKRLEDEQGRRKAVADEIDAELEE------LNAQLGEALRTLKRRKRGR--PGRRYLYE 124
Query: 304 NELPHLLFYGPPGTGKTTTIL 324
LP + GPPG+GKTT +L
Sbjct: 125 --LPWYMVIGPPGSGKTTALL 143
>gnl|CDD|223786 COG0714, COG0714, MoxR-like ATPases [General function prediction
only].
Length = 329
Score = 30.5 bits (69), Expect = 2.0
Identities = 13/23 (56%), Positives = 14/23 (60%)
Query: 308 HLLFYGPPGTGKTTTILACARKL 330
H+L GPPG GKT A AR L
Sbjct: 45 HVLLEGPPGVGKTLLARALARAL 67
>gnl|CDD|163057 TIGR02881, spore_V_K, stage V sporulation protein K. Members of
this protein family are the stage V sporulation protein
K (SpoVK), a close homolog of the Rubisco expression
protein CbbX (TIGR02880) and a members of the ATPase
family associated with various cellular activities
(pfam00004). Members are strictly limited to bacterial
endospore-forming species, but are not universal in this
group and are missing from the Clostridium group
[Cellular processes, Sporulation and germination].
Length = 261
Score = 30.5 bits (69), Expect = 2.0
Identities = 13/29 (44%), Positives = 17/29 (58%), Gaps = 4/29 (13%)
Query: 302 DENELPHLLFYGPPGTGKTTTILACARKL 330
++ H++F G PGTGKTT AR L
Sbjct: 38 TSKQVLHMIFKGNPGTGKTTV----ARIL 62
>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 = 2.1
Identities = 14/27 (51%), Positives = 14/27 (51%)
Query: 310 LFYGPPGTGKTTTILACARKLYTKAQF 336
L GP G GKT T LA A LY Q
Sbjct: 600 LLVGPSGVGKTETALALAELLYGGEQN 626
>gnl|CDD|233119 TIGR00763, lon, ATP-dependent protease La. This protein is induced
by heat shock and other stresses in E. coli, B.
subtilis, and other species. The yeast member,
designated PIM1, is located in the mitochondrial matrix,
required for mitochondrial function, and also induced by
heat shock [Protein fate, Degradation of proteins,
peptides, and glycopeptides].
Length = 775
Score = 30.7 bits (70), Expect = 2.2
Identities = 35/142 (24%), Positives = 57/142 (40%), Gaps = 33/142 (23%)
Query: 307 PHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLE--LNASDDRG-----IGIVRDQIF 359
P L GPPG GKT+ + A+ L K F L + ++ RG +G + +I
Sbjct: 348 PILCLVGPPGVGKTSLGKSIAKALNRK--FVRFSLGGVRDEAEIRGHRRTYVGAMPGRII 405
Query: 360 Q-FASTKTMHKSSYKLIILDEADAMTNDAQ----NALRRIIE-----KFT---------- 399
Q KT + L +LDE D + + + +AL +++ F+
Sbjct: 406 QGLKKAKTKN----PLFLLDEIDKIGSSFRGDPASALLEVLDPEQNNAFSDHYLDVPFDL 461
Query: 400 TNVRFCIICNYLSKIPPAIQSR 421
+ V F N + IP + R
Sbjct: 462 SKVIFIATANSIDTIPRPLLDR 483
>gnl|CDD|214692 smart00487, DEXDc, DEAD-like helicases superfamily.
Length = 201
Score = 30.2 bits (68), Expect = 2.2
Identities = 25/138 (18%), Positives = 47/138 (34%), Gaps = 41/138 (29%)
Query: 308 HLLFYGPPGTGKTTT-ILACARKLYTKAQFNAMVL----------------ELNASDDRG 350
++ P G+GKT +L L +VL + +
Sbjct: 26 DVILAAPTGSGKTLAALLPALEALKRGKGGRVLVLVPTRELAEQWAEELKKLGPSLGLKV 85
Query: 351 IGIV-----RDQIFQFASTKT------------------MHKSSYKLIILDEADAMTNDA 387
+G+ R+Q+ + S KT + S+ L+ILDEA + +
Sbjct: 86 VGLYGGDSKREQLRKLESGKTDILVTTPGRLLDLLENDKLSLSNVDLVILDEAHRLLDGG 145
Query: 388 QN-ALRRIIEKFTTNVRF 404
L ++++ NV+
Sbjct: 146 FGDQLEKLLKLLPKNVQL 163
Score = 28.2 bits (63), Expect = 9.2
Identities = 10/52 (19%), Positives = 22/52 (42%), Gaps = 1/52 (1%)
Query: 187 DQIFQFASTKTMHKSSYKLIILDEADAMTNDAQN-ALRRKLPVTPDGKKAII 237
++ + S+ L+ILDEA + + L + L + P + ++
Sbjct: 114 GRLLDLLENDKLSLSNVDLVILDEAHRLLDGGFGDQLEKLLKLLPKNVQLLL 165
>gnl|CDD|153199 cd04927, ACT_ACR-like_2, Second ACT domain, of a novel type of
ACT domain-containing protein which is composed almost
entirely of four ACT domain repeats (the "ACR"
protein). This CD includes the second ACT domain, of
a novel type of ACT domain-containing protein which is
composed almost entirely of four ACT domain repeats
(the "ACR" protein). ACR proteins, found only in
Arabidopsis and Oryza, as yet, are proposed to function
as novel regulatory or sensor proteins in plants. Nine
ACR gene products (ACR1-8 in Arabidopsis and OsARC1-9
in Oryza) have been described, however, the ACR-like
sequences in this CD are distinct from those
characterized. This CD includes the Oryza sativa
ACR-like protein (Os05g0113000) encoded on chromosome 5
and the Arabidopsis thaliana predicted gene product,
At2g39570. Members of this CD belong to the superfamily
of ACT regulatory domains.
Length = 76
Score = 28.2 bits (63), Expect = 2.5
Identities = 12/31 (38%), Positives = 21/31 (67%), Gaps = 2/31 (6%)
Query: 37 DSSLIMSRLDYVIEQEKVNVTPDGKKAIIDL 67
D + ++ L+ IE+ KV+ TPDG+ ++DL
Sbjct: 16 DVTEVLYELELTIERVKVSTTPDGR--VLDL 44
>gnl|CDD|223679 COG0606, COG0606, Predicted ATPase with chaperone activity
[Posttranslational modification, protein turnover,
chaperones].
Length = 490
Score = 30.3 bits (69), Expect = 2.7
Identities = 10/13 (76%), Positives = 11/13 (84%)
Query: 308 HLLFYGPPGTGKT 320
+LL GPPGTGKT
Sbjct: 200 NLLLVGPPGTGKT 212
>gnl|CDD|224588 COG1674, FtsK, DNA segregation ATPase FtsK/SpoIIIE and related
proteins [Cell division and chromosome partitioning].
Length = 858
Score = 30.6 bits (69), Expect = 2.8
Identities = 13/57 (22%), Positives = 25/57 (43%), Gaps = 6/57 (10%)
Query: 291 MDLCYKINRF---IDENELPHLLFYGPPGTGKTT---TILACARKLYTKAQFNAMVL 341
+DL I + ID + HLL G G+GK+ T++ ++ + ++
Sbjct: 512 IDLPKDIRQEPIVIDLAKAGHLLIAGATGSGKSVALNTMILSLLYTHSPEEVRFYII 568
>gnl|CDD|238549 cd01129, PulE-GspE, PulE/GspE The type II secretory pathway is the
main terminal branch of the general secretory pathway
(GSP). It is responsible for the export the majority of
Gram-negative bacterial exoenzymes and toxins. PulE is a
cytoplasmic protein of the GSP, which contains an ATP
binding site and a tetracysteine motif. This subgroup
also includes PillB and HofB.
Length = 264
Score = 29.9 bits (68), Expect = 2.9
Identities = 15/40 (37%), Positives = 21/40 (52%), Gaps = 2/40 (5%)
Query: 295 YKINRFIDENELPH--LLFYGPPGTGKTTTILACARKLYT 332
+ F E PH +L GP G+GKTTT+ + +L T
Sbjct: 67 ENLEIFRKLLEKPHGIILVTGPTGSGKTTTLYSALSELNT 106
>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 = 29.9 bits (68), Expect = 2.9
Identities = 16/35 (45%), Positives = 18/35 (51%), Gaps = 1/35 (2%)
Query: 297 INRFIDENELPH-LLFYGPPGTGKTTTILACARKL 330
I E P+ +LF G G GKTTTI A KL
Sbjct: 62 DLELIVEENKPNVILFVGVNGVGKTTTIAKLANKL 96
>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 = 28.4 bits (64), Expect = 3.0
Identities = 8/13 (61%), Positives = 10/13 (76%)
Query: 309 LLFYGPPGTGKTT 321
+ YGPPG GK+T
Sbjct: 1 IWLYGPPGCGKST 13
>gnl|CDD|234401 TIGR03925, T7SS_EccC_b, type VII secretion protein EccCb. This
model represents the C-terminal domain or EccCb subunit
of the type VII secretion protein EccC as found in the
Actinobacteria. Type VII secretion is defined more
broadly as including secretion systems for ESAT-6-like
proteins in the Firmicutes as well as in the
Actinobacteria, but this family does not show close
homologs in the Firmicutes [Protein fate, Protein and
peptide secretion and trafficking].
Length = 566
Score = 30.3 bits (69), Expect = 3.0
Identities = 16/39 (41%), Positives = 23/39 (58%), Gaps = 3/39 (7%)
Query: 300 FIDENELPHLLFYGPPGTGKTTTILACARKL---YTKAQ 335
++D E PHLL +G +GKTT + A AR + Y+ Q
Sbjct: 357 YLDFAESPHLLVFGDSESGKTTLLRAIARGITRRYSPQQ 395
>gnl|CDD|173403 PTZ00111, PTZ00111, DNA replication licensing factor MCM4;
Provisional.
Length = 915
Score = 30.3 bits (68), Expect = 3.1
Identities = 30/124 (24%), Positives = 56/124 (45%), Gaps = 21/124 (16%)
Query: 288 NESMDLCYKINRFIDENELPHLLFYGPPGTGKTT----TILACARKLYTKAQFNAMV--- 340
N+S D CYK++ F ++L G PGT K+ T L R +YT + ++ V
Sbjct: 477 NKSPDACYKVDNFRGI---INVLLCGDPGTAKSQLLHYTHLLSPRSIYTSGKSSSSVGLT 533
Query: 341 --LELNASDDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRIIEKF 398
++ N SD+ + Q + + + +DE D N+++ +L ++E+
Sbjct: 534 ASIKFNESDNG------RAMIQPGAVVLANGG---VCCIDELDKCHNESRLSLYEVMEQQ 584
Query: 399 TTNV 402
T +
Sbjct: 585 TVTI 588
>gnl|CDD|224017 COG1092, COG1092, Predicted SAM-dependent methyltransferases
[General function prediction only].
Length = 393
Score = 30.0 bits (68), Expect = 3.2
Identities = 19/87 (21%), Positives = 32/87 (36%), Gaps = 9/87 (10%)
Query: 316 GTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFASTKTMHKSSYKLI 375
G + T++ R L A+ NA ELN D + +F++ + LI
Sbjct: 239 GASEVTSVDLSKRAL-EWARENA---ELNGLDGDRHRFIVGDVFKWLRKAERRGEKFDLI 294
Query: 376 ILD-----EADAMTNDAQNALRRIIEK 397
ILD + AQ + + +
Sbjct: 295 ILDPPSFARSKKQEFSAQRDYKDLNDL 321
>gnl|CDD|222194 pfam13521, AAA_28, AAA domain.
Length = 162
Score = 29.1 bits (66), Expect = 3.2
Identities = 9/18 (50%), Positives = 10/18 (55%)
Query: 311 FYGPPGTGKTTTILACAR 328
G P TGKTT + A A
Sbjct: 4 ITGGPSTGKTTLLEALAA 21
>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 = 29.9 bits (68), Expect = 3.6
Identities = 11/18 (61%), Positives = 11/18 (61%)
Query: 310 LFYGPPGTGKTTTILACA 327
L GPPGTGKT A A
Sbjct: 92 LLVGPPGTGKTLLAKAVA 109
>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 = 30.2 bits (68), Expect = 3.7
Identities = 12/21 (57%), Positives = 16/21 (76%)
Query: 310 LFYGPPGTGKTTTILACARKL 330
L +GPPGTGKT T++ R+L
Sbjct: 177 LIHGPPGTGKTRTLVELIRQL 197
>gnl|CDD|214940 smart00962, SRP54, SRP54-type protein, GTPase domain. This entry
represents the GTPase domain of the 54 kDa SRP54
component, a GTP-binding protein that interacts with the
signal sequence when it emerges from the ribosome. SRP54
of the signal recognition particle has a three-domain
structure: an N-terminal helical bundle domain, a GTPase
domain, and the M-domain that binds the 7s RNA and also
binds the signal sequence. The extreme C-terminal region
is glycine-rich and lower in complexity and poorly
conserved between species. The GTPase domain is
evolutionary related to P-loop NTPase domains found in a
variety of other proteins.
Length = 197
Score = 29.3 bits (67), Expect = 3.8
Identities = 10/14 (71%), Positives = 10/14 (71%)
Query: 310 LFYGPPGTGKTTTI 323
L GP G GKTTTI
Sbjct: 5 LLVGPNGVGKTTTI 18
>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 = 29.5 bits (67), Expect = 4.2
Identities = 22/109 (20%), Positives = 39/109 (35%), Gaps = 24/109 (22%)
Query: 307 PHLLFYGPPGTGKTTTILACARKLYTKAQ---FNAMVLELNASDDRGIGIVRDQIFQFA- 362
++ YG GTGKT ++L A+ + + +N + V ++
Sbjct: 41 SNVFIYGKTGTGKTAVTKYVMKELEEAAEDRDVRVVTVYVNCQILDTLYQVLVELANQLR 100
Query: 363 -----------STKTMHKSSYK---------LIILDEADAMTNDAQNAL 391
ST + + YK +I+LDE D + D + L
Sbjct: 101 GSGEEVPTTGLSTSEVFRRLYKELNERGDSLIIVLDEIDYLVGDDDDLL 149
>gnl|CDD|221983 pfam13207, AAA_17, AAA domain.
Length = 114
Score = 28.4 bits (63), Expect = 4.4
Identities = 13/36 (36%), Positives = 19/36 (52%), Gaps = 6/36 (16%)
Query: 310 LFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNA 345
L GPPG+GK+T A+KL + V+ L+
Sbjct: 3 LITGPPGSGKSTL----AKKL--AEKLGIPVISLDD 32
>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 = 28.7 bits (65), Expect = 4.9
Identities = 9/23 (39%), Positives = 11/23 (47%)
Query: 308 HLLFYGPPGTGKTTTILACARKL 330
+ GPPG GKTT + L
Sbjct: 1 RIFITGPPGVGKTTLVKKVIELL 23
>gnl|CDD|234175 TIGR03348, VI_IcmF, type VI secretion protein IcmF. Members of
this protein family are IcmF homologs and tend to be
associated with type VI secretion systems [Cellular
processes, Pathogenesis].
Length = 1169
Score = 29.6 bits (67), Expect = 5.0
Identities = 11/19 (57%), Positives = 14/19 (73%)
Query: 305 ELPHLLFYGPPGTGKTTTI 323
+LP L GPPG+GKTT +
Sbjct: 110 DLPWYLVIGPPGSGKTTLL 128
>gnl|CDD|238688 cd01394, radB, RadB. The archaeal protein radB shares similarity
radA, the archaeal functional homologue to the bacterial
RecA. The precise function of radB is unclear.
Length = 218
Score = 29.0 bits (65), Expect = 5.2
Identities = 10/17 (58%), Positives = 11/17 (64%)
Query: 311 FYGPPGTGKTTTILACA 327
YGPPGTGKT + A
Sbjct: 24 VYGPPGTGKTNIAIQLA 40
>gnl|CDD|227519 COG5192, BMS1, GTP-binding protein required for 40S ribosome
biogenesis [Translation, ribosomal structure and
biogenesis].
Length = 1077
Score = 29.3 bits (65), Expect = 6.6
Identities = 14/42 (33%), Positives = 24/42 (57%), Gaps = 2/42 (4%)
Query: 297 INRFIDENELPHLL-FYGPPGTGKTTTILACARKLYTKAQFN 337
++R + P ++ GPPGTGK+T I + R+ +TK +
Sbjct: 59 VDRTPKDLPPPFIVAVVGPPGTGKSTLIRSLVRR-FTKQTID 99
>gnl|CDD|130679 TIGR01618, phage_P_loop, phage nucleotide-binding protein. This
model represents an uncharacterized family of proteins
from a number of phage of Gram-positive bacteria. This
protein contains a P-loop motif, G/A-X-X-G-X-G-K-T near
its amino end. The function of this protein is unknown
[Mobile and extrachromosomal element functions, Prophage
functions].
Length = 220
Score = 28.6 bits (64), Expect = 6.7
Identities = 13/29 (44%), Positives = 17/29 (58%), Gaps = 4/29 (13%)
Query: 299 RFIDENELPH----LLFYGPPGTGKTTTI 323
+FI+ + L YG PGTGKT+TI
Sbjct: 1 KFIEAGNIKRIPNMYLIYGKPGTGKTSTI 29
>gnl|CDD|218843 pfam05988, DUF899, Bacterial protein of unknown function (DUF899).
This family consists of several uncharacterized
bacterial proteins of unknown function.
Length = 211
Score = 28.7 bits (65), Expect = 6.7
Identities = 13/36 (36%), Positives = 14/36 (38%), Gaps = 10/36 (27%)
Query: 217 DAQNALRRKLP----------VTPDGKKAIIDLSDG 242
DA A RR LP PDG + DL G
Sbjct: 31 DALAAERRALPWVEVDKDYRFDGPDGPVTLADLFGG 66
>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 = 28.8 bits (65), Expect = 6.9
Identities = 12/41 (29%), Positives = 19/41 (46%), Gaps = 13/41 (31%)
Query: 309 LLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDR 349
+L G G+GKTT + A++ E+N D+R
Sbjct: 132 ILVSGGTGSGKTTLL-------------YALLNEINTDDER 159
>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 = 28.3 bits (64), Expect = 7.2
Identities = 11/27 (40%), Positives = 15/27 (55%)
Query: 309 LLFYGPPGTGKTTTILACARKLYTKAQ 335
+L G G+GKTTTI A L + +
Sbjct: 4 ILLVGLQGSGKTTTIAKLAAYLKKQGK 30
>gnl|CDD|233793 TIGR02237, recomb_radB, DNA repair and recombination protein RadB.
This family consists exclusively of archaeal RadB
protein, a homolog of bacterial RecA (TIGR02012),
eukaryotic RAD51 (TIGR02239) and DMC1 (TIGR02238), and
archaeal RadA (TIGR02236).
Length = 209
Score = 28.5 bits (64), Expect = 7.2
Identities = 26/114 (22%), Positives = 42/114 (36%), Gaps = 39/114 (34%)
Query: 311 FYGPPGTGKTTT--ILAC-------------------------ARKLYTKAQFNAMVLEL 343
YGPPG+GKT ILA A +A N +V E+
Sbjct: 17 IYGPPGSGKTNICMILAVNAARQGKKVVYIDTEGLSPERFKQIAEDRPERALSNFIVFEV 76
Query: 344 NASDDRGIGIVRDQIFQFASTKTMHKSSYKLIILDEADAM-----TNDAQNALR 392
D++G+ I + +F S L+++D A+ ++D + R
Sbjct: 77 FDFDEQGVAIQK--TSKFIDRD-----SASLVVVDSFTALYRLELSDDRISRNR 123
>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 = 29.0 bits (65), Expect = 7.3
Identities = 9/15 (60%), Positives = 11/15 (73%)
Query: 309 LLFYGPPGTGKTTTI 323
LL +GPPG+GKT
Sbjct: 214 LLLFGPPGSGKTMLA 228
>gnl|CDD|185575 PTZ00361, PTZ00361, 26 proteosome regulatory subunit 4-like
protein; Provisional.
Length = 438
Score = 29.0 bits (65), Expect = 7.4
Identities = 15/28 (53%), Positives = 18/28 (64%), Gaps = 2/28 (7%)
Query: 309 LLFYGPPGTGKTTTILACARKLYTKAQF 336
++ YGPPGTGK T+LA A T A F
Sbjct: 220 VILYGPPGTGK--TLLAKAVANETSATF 245
>gnl|CDD|223542 COG0466, Lon, ATP-dependent Lon protease, bacterial type
[Posttranslational modification, protein turnover,
chaperones].
Length = 782
Score = 29.1 bits (66), Expect = 7.7
Identities = 9/14 (64%), Positives = 9/14 (64%)
Query: 307 PHLLFYGPPGTGKT 320
P L GPPG GKT
Sbjct: 351 PILCLVGPPGVGKT 364
>gnl|CDD|234208 TIGR03436, acidobact_VWFA, VWFA-related Acidobacterial domain.
Members of this family are bacterial domains that
include a region related to the von Willebrand factor
type A (VWFA) domain (pfam00092). These domains are
restricted to, and have undergone a large paralogous
family expansion in, the Acidobacteria, including
Solibacter usitatus and Acidobacterium capsulatum ATCC
51196.
Length = 296
Score = 28.4 bits (64), Expect = 8.7
Identities = 14/31 (45%), Positives = 18/31 (58%), Gaps = 1/31 (3%)
Query: 212 DAMTNDAQNALRRKLPVTPDGKKAIIDLSDG 242
DA+T A L L P G+KA+I +SDG
Sbjct: 145 DAITLAALEQLANALAGIP-GRKALIVISDG 174
>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 = 28.3 bits (64), Expect = 8.7
Identities = 13/82 (15%), Positives = 28/82 (34%), Gaps = 13/82 (15%)
Query: 307 PHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVLELNASDDRGIGIVRDQIFQFASTKT 366
L +G G+GK+ + A + +A+ L L ++ +
Sbjct: 39 RFLYLWGESGSGKSHLLQAACAA-AEERGKSAIYLPLAELAQADP-----EVLEGL---- 88
Query: 367 MHKSSYKLIILDEADAMTNDAQ 388
L+ LD+ +A+ +
Sbjct: 89 ---EQADLVCLDDVEAIAGQPE 107
>gnl|CDD|233328 TIGR01243, CDC48, AAA family ATPase, CDC48 subfamily. This
subfamily of the AAA family ATPases includes two members
each from three archaeal species. It also includes yeast
CDC48 (cell division control protein 48) and the human
ortholog, transitional endoplasmic reticulum ATPase
(valosin-containing protein). These proteins in
eukaryotes are involved in the budding and transfer of
membrane from the transitional endoplasmic reticulum to
the Golgi apparatus.
Length = 733
Score = 28.7 bits (64), Expect = 9.1
Identities = 15/31 (48%), Positives = 20/31 (64%), Gaps = 2/31 (6%)
Query: 309 LLFYGPPGTGKTTTILACARKLYTKAQFNAM 339
+L +GPPGTGK T+LA A + A F A+
Sbjct: 490 VLLFGPPGTGK--TLLAKAVATESGANFIAV 518
>gnl|CDD|219567 pfam07775, PaRep2b, PaRep2b protein. This is a family of proteins,
expressed in the crenarchaeon Pyrobaculum aerophilum,
whose members are variable in length and level of
conservation. The presence of numerous frameshifts and
internal stop codons in multiple alignments are thought
to indicate that most family members are no longer
functional.
Length = 510
Score = 28.7 bits (64), Expect = 9.3
Identities = 26/125 (20%), Positives = 51/125 (40%), Gaps = 22/125 (17%)
Query: 135 VLKMSDIEYRLAAGTSEKIQL---SALIAAFNSARDKLEVLELNASDDRGI--GIVRDQI 189
V+K + +E+ + S++I + A+ N+A +NA G+ G+
Sbjct: 194 VVKFAGVEFSVYYKRSKRIMIKYQPRSEASKNAA--------VNALKAAGLKEGV----- 240
Query: 190 FQFASTKTMHKSSYKLIILDEADAMTNDAQNALRRKLPVTPDGKKAIIDLSDGDMRKVLN 249
F + Y++ + EA A +A + L+ GK+ I + V+N
Sbjct: 241 -HFTVKR---PGGYEIRVTKEAYAKAVEALSGLKEGEHYAVYGKRREIRVKAPHKDAVVN 296
Query: 250 ILQSA 254
L++A
Sbjct: 297 ALKAA 301
>gnl|CDD|237475 PRK13695, PRK13695, putative NTPase; Provisional.
Length = 174
Score = 28.0 bits (63), Expect = 9.4
Identities = 11/18 (61%), Positives = 12/18 (66%)
Query: 313 GPPGTGKTTTILACARKL 330
GPPG GKTT +L A L
Sbjct: 7 GPPGVGKTTLVLKIAELL 24
>gnl|CDD|200312 TIGR03689, pup_AAA, proteasome ATPase. In the Actinobacteria, as
shown for Mycobacterium tuberculosis, some proteins are
modified by ligation between an epsilon-amino group of a
lysine side chain and the C-terminal carboxylate of the
ubiquitin-like protein Pup. This modification leads to
protein degradation by the archaeal-like proteasome
found in the Actinobacteria. Members of this protein
family belong to the AAA family of ATPases and tend to
be clustered with the genes for Pup, the Pup ligase
PafA, and structural components of the proteasome. This
protein forms hexameric rings with ATPase activity
[Protein fate, Degradation of proteins, peptides, and
glycopeptides].
Length = 512
Score = 28.5 bits (64), Expect = 9.7
Identities = 12/22 (54%), Positives = 13/22 (59%)
Query: 309 LLFYGPPGTGKTTTILACARKL 330
+L YGPPG GKT A A L
Sbjct: 219 VLLYGPPGCGKTLIAKAVANSL 240
>gnl|CDD|182730 PRK10787, PRK10787, DNA-binding ATP-dependent protease La;
Provisional.
Length = 784
Score = 28.8 bits (64), Expect = 9.7
Identities = 27/89 (30%), Positives = 39/89 (43%), Gaps = 16/89 (17%)
Query: 307 PHLLFYGPPGTGKTTTILACARKLYTKAQFNAMVL-------ELNASDDRGIGIVRDQIF 359
P L GPPG GKT+ + A+ T ++ M L E+ IG + ++
Sbjct: 350 PILCLVGPPGVGKTSLGQSIAKA--TGRKYVRMALGGVRDEAEIRGHRRTYIGSMPGKLI 407
Query: 360 QFASTKTMHKSSYK--LIILDEADAMTND 386
Q M K K L +LDE D M++D
Sbjct: 408 Q-----KMAKVGVKNPLFLLDEIDKMSSD 431
>gnl|CDD|236482 PRK09361, radB, DNA repair and recombination protein RadB;
Provisional.
Length = 225
Score = 28.3 bits (64), Expect = 9.7
Identities = 8/11 (72%), Positives = 9/11 (81%)
Query: 311 FYGPPGTGKTT 321
YGPPG+GKT
Sbjct: 28 IYGPPGSGKTN 38
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
0.320 0.135 0.379
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: 27,095,212
Number of extensions: 2695574
Number of successful extensions: 3678
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3594
Number of HSP's successfully gapped: 350
Length of query: 533
Length of database: 10,937,602
Length adjustment: 101
Effective length of query: 432
Effective length of database: 6,457,848
Effective search space: 2789790336
Effective search space used: 2789790336
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 61 (27.0 bits)