RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2281
(287 letters)
>gnl|CDD|234763 PRK00440, rfc, replication factor C small subunit; Reviewed.
Length = 319
Score = 138 bits (349), Expect = 7e-39
Identities = 88/326 (26%), Positives = 140/326 (42%), Gaps = 75/326 (23%)
Query: 3 LWVDKYRPNNLQKLDFHCKQANHLRNLLKEGDFPHLLFYGPSGAGKKTRIMALLKELYG- 61
+WV+KYRP L ++ + L++ +KE + PHLLF GP G GK T +AL +ELYG
Sbjct: 6 IWVEKYRPRTLDEIVGQEEIVERLKSYVKEKNMPHLLFAGPPGTGKTTAALALARELYGE 65
Query: 62 -------------------------------PV-------IILNETDHLTREAQQALRRT 83
PV I L+E D+LT +AQQALRRT
Sbjct: 66 DWRENFLELNASDERGIDVIRNKIKEFARTAPVGGAPFKIIFLDEADNLTSDAQQALRRT 125
Query: 84 MEKYITTCRLILCANSMSQVIPAIRSRCLCIRIPAPTHEEIVSVLTNICKKEGLTIPPEF 143
ME Y R IL N S++I I+SRC R E + L I + EG+ I +
Sbjct: 126 MEMYSQNTRFILSCNYSSKIIDPIQSRCAVFRFSPLKKEAVAERLRYIAENEGIEITDDA 185
Query: 144 --ALRLAQQSDRNLRRAILMCEASKVQQYPFQIDQQIVEPDWKIY----------IRDTA 191
A+ + D +R+AI +A+ +++ E +Y IR+
Sbjct: 186 LEAIYYVSEGD--MRKAINALQAAAA------TGKEVTEE--AVYKITGTARPEEIREMI 235
Query: 192 KLIISEQSPKKLLEVRTRLYELLVH------SIPVNVLFKYLLEGLLANCDSDLKSKSIE 245
+L ++ E R +L +L++ I + + + + + +LK + I+
Sbjct: 236 ELALN----GDFTEAREKLRDLMIDYGLSGEDI-IKQIHREVWSLDI---PEELKVELID 287
Query: 246 MAAMFEHRIHKGSKPIFHIEAYVASF 271
+ RI +G+ +EA +A
Sbjct: 288 AIGEADFRITEGANERIQLEALLAKL 313
>gnl|CDD|237090 PRK12402, PRK12402, replication factor C small subunit 2; Reviewed.
Length = 337
Score = 127 bits (321), Expect = 1e-34
Identities = 64/226 (28%), Positives = 90/226 (39%), Gaps = 70/226 (30%)
Query: 3 LWVDKYRPNNLQKLDFHCKQA---NHLRNLLKEGDFPHLLFYGPSGA------------- 46
LW +KYRP L+ Q L + + PHLL GP G+
Sbjct: 4 LWTEKYRP---ALLEDILGQDEVVERLSRAVDSPNLPHLLVQGPPGSGKTAAVRALAREL 60
Query: 47 ------------------------------------GKKTRIMAL-------LKEL--YG 61
K + LKE Y
Sbjct: 61 YGDPWENNFTEFNVADFFDQGKKYLVEDPRFAHFLGTDKRIRSSKIDNFKHVLKEYASYR 120
Query: 62 PV------IILNETDHLTREAQQALRRTMEKYITTCRLILCANSMSQVIPAIRSRCLCIR 115
P+ I+L+ + L +AQQALRR ME+Y TCR I+ S++IP IRSRCL +
Sbjct: 121 PLSADYKTILLDNAEALREDAQQALRRIMEQYSRTCRFIIATRQPSKLIPPIRSRCLPLF 180
Query: 116 IPAPTHEEIVSVLTNICKKEGLTIPPEFALRLAQQSDRNLRRAILM 161
APT +E+V VL +I + EG+ + +A + +LR+AIL
Sbjct: 181 FRAPTDDELVDVLESIAEAEGVDYDDDGLELIAYYAGGDLRKAILT 226
>gnl|CDD|178596 PLN03025, PLN03025, replication factor C subunit; Provisional.
Length = 319
Score = 109 bits (273), Expect = 7e-28
Identities = 57/179 (31%), Positives = 84/179 (46%), Gaps = 40/179 (22%)
Query: 4 WVDKYRPNNLQKLDFHCKQANHLRNLLKEGDFPHLLFYGPSGAGKKTRIMALLKELYGP- 62
WV+KYRP L + + + L+ + ++G+ P+L+ GP G GK T I+AL EL GP
Sbjct: 3 WVEKYRPTKLDDIVGNEDAVSRLQVIARDGNMPNLILSGPPGTGKTTSILALAHELLGPN 62
Query: 63 ---------------------------------------VIILNETDHLTREAQQALRRT 83
++IL+E D +T AQQALRRT
Sbjct: 63 YKEAVLELNASDDRGIDVVRNKIKMFAQKKVTLPPGRHKIVILDEADSMTSGAQQALRRT 122
Query: 84 MEKYITTCRLILCANSMSQVIPAIRSRCLCIRIPAPTHEEIVSVLTNICKKEGLTIPPE 142
ME Y T R L N+ S++I I+SRC +R + +EI+ L + + E + PE
Sbjct: 123 MEIYSNTTRFALACNTSSKIIEPIQSRCAIVRFSRLSDQEILGRLMKVVEAEKVPYVPE 181
>gnl|CDD|235223 PRK04132, PRK04132, replication factor C small subunit;
Provisional.
Length = 846
Score = 86.0 bits (213), Expect = 7e-19
Identities = 60/217 (27%), Positives = 103/217 (47%), Gaps = 10/217 (4%)
Query: 63 VIILNETDHLTREAQQALRRTMEKYITTCRLILCANSMSQVIPAIRSRCLCIRIPAPTHE 122
+I L+E D LT++AQQALRRTME + + R IL N S++I I+SRC R E
Sbjct: 633 IIFLDEADALTQDAQQALRRTMEMFSSNVRFILSCNYSSKIIEPIQSRCAIFRFRPLRDE 692
Query: 123 EIVSVLTNICKKEGLTIPPEFALRLAQQSDRNLRRAILMCEASKVQQYPFQIDQQIVEPD 182
+I L I + EGL + E + ++ ++RRAI + +A+ +I + V
Sbjct: 693 DIAKRLRYIAENEGLELTEEGLQAILYIAEGDMRRAINILQAAAALDD--KITDENV--- 747
Query: 183 WKIYIR---DTAKLIISEQSPKKLLEVRTRLYELLVHS--IPVNVLFKYLLEGLLANCDS 237
+ + R + + ++ L+ R +L E+L+ +VL + E D
Sbjct: 748 FLVASRARPEDIREMMLLALKGNFLKAREKLREILLKQGLSGEDVLVQMHREVFNLPIDE 807
Query: 238 DLKSKSIEMAAMFEHRIHKGSKPIFHIEAYVASFMAM 274
K + + + R+ +G+ + +EA +A F M
Sbjct: 808 PKKVELADKIGEYNFRLVEGANEMIQLEALLAQFTLM 844
Score = 45.2 bits (107), Expect = 2e-05
Identities = 20/45 (44%), Positives = 25/45 (55%)
Query: 4 WVDKYRPNNLQKLDFHCKQANHLRNLLKEGDFPHLLFYGPSGAGK 48
WV+KYRP L + L++ +K G PHLLF GP G GK
Sbjct: 9 WVEKYRPQRLDDIVGQEHIVKRLKHYVKTGSMPHLLFAGPPGVGK 53
>gnl|CDD|222866 PHA02544, 44, clamp loader, small subunit; Provisional.
Length = 316
Score = 79.6 bits (197), Expect = 3e-17
Identities = 55/203 (27%), Positives = 88/203 (43%), Gaps = 45/203 (22%)
Query: 3 LWVDKYRPNNLQK--LDFHCKQANHLRNLLKEGDFPHLLFYGPS-GAGKKTRIMALLKEL 59
+W KYRP+ + + L K+ ++++K+G P++L + PS G GK T AL E+
Sbjct: 10 MWEQKYRPSTIDECILPAADKET--FKSIVKKGRIPNMLLHSPSPGTGKTTVAKALCNEV 67
Query: 60 --------------------------------YGPVIILNETDHL-TREAQQALRRTMEK 86
G VII++E D L +AQ+ LR ME
Sbjct: 68 GAEVLFVNGSDCRIDFVRNRLTRFASTVSLTGGGKVIIIDEFDRLGLADAQRHLRSFMEA 127
Query: 87 YITTCRLILCANSMSQVIPAIRSRCLCIRIPAPTHEEIVSV-------LTNICKKEGLTI 139
Y C I+ AN+ + +I +RSRC I PT EE + + I + EG+ +
Sbjct: 128 YSKNCSFIITANNKNGIIEPLRSRCRVIDFGVPTKEEQIEMMKQMIVRCKGILEAEGVEV 187
Query: 140 PPEFALRLAQQSDRNLRRAILMC 162
+ L +++ + RR I
Sbjct: 188 DMKVLAALVKKNFPDFRRTINEL 210
>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 = 67.5 bits (166), Expect = 1e-14
Identities = 30/87 (34%), Positives = 41/87 (47%), Gaps = 5/87 (5%)
Query: 186 YIRDTAKLIISEQSPKKLLEVRTRLYELLVHSIPVNVLFKYLLEGLLANCDSD-LKSKSI 244
I++ I+ E R LYELLV I + K L E L+ D LK + I
Sbjct: 7 DIKEILDSILKG----DFDEARETLYELLVEGISAEDILKQLHEVLIRLDIPDSLKLEII 62
Query: 245 EMAAMFEHRIHKGSKPIFHIEAYVASF 271
+ A EHR+ G+K I +EA +A F
Sbjct: 63 KELAEIEHRLSDGAKEIIQLEALIAKF 89
>gnl|CDD|223546 COG0470, HolB, ATPase involved in DNA replication [DNA replication,
recombination, and repair].
Length = 230
Score = 65.4 bits (159), Expect = 2e-12
Identities = 53/263 (20%), Positives = 89/263 (33%), Gaps = 52/263 (19%)
Query: 26 LRNLLKEGDFPH-LLFYGPSGAGKKTRIMALLKELYGPVIILNETDHLTREAQQALRRTM 84
L L+ G PH LLFYGP G GK T
Sbjct: 14 LVQALESGRLPHALLFYGPPGVGKTT---------------------------------- 39
Query: 85 EKYITTCRLILCANSMSQVIPAIRSRCLCIRIPAPTHEEIVSVLTNICKKEGLTIPPEFA 144
R IL N S+++P IRSRC IR P+ E I E +
Sbjct: 40 -APPKNTRFILITNDPSKILPTIRSRCQRIRFKPPSRLEA------IAWLE-----DQGL 87
Query: 145 LRLAQQSDRNLRRAILMCEASKVQQ----YPFQIDQQI-VEPDWKIYIRDTAKLIISEQS 199
+A ++ + R+AI +A + ++ E ++ + KL ++
Sbjct: 88 EEIAAVAEGDARKAINPLQALAALEIGEESIYEALLLALPESLAQLAALELLKLAENKFL 147
Query: 200 PKKLLEVRTRLYELLVHSIPVNVLFKYLLEGLLANCDSDLKSKSIEMAAMFEHRIHKGSK 259
L E L+ ++ L + LL+ A + ++ ++ A R+ G
Sbjct: 148 EALEKLWLLLLLEGLLGEDLLDQLQRELLKLDKALIQEEKAAELLDALAQARRRLLDGLL 207
Query: 260 PIFHIEAYVASFMAMYLQFMEDT 282
+ +E +A + + L
Sbjct: 208 ALIQLENLLAELLLLQLLLEGVK 230
>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 = 59.6 bits (145), Expect = 8e-11
Identities = 33/138 (23%), Positives = 57/138 (41%), Gaps = 14/138 (10%)
Query: 29 LLKEGDFPHLLFYGPSGAG-KKTRIMALLKELYGP-------VIILNETDHLTREAQQAL 80
L++ G+ P L P G K ++ L++ L V+I+ + + + A AL
Sbjct: 57 LIEAGNHPDLHRLEPEGQSIKVDQVRELVEFLSRTPQESGRRVVIIEDAERMNEAAANAL 116
Query: 81 RRTMEKYITTCRLILCANSMSQVIPAIRSRCLCIRIPAPTHEEIVSVLTNICKKEGLTIP 140
+T+E+ IL S +++P IRSRC + P + E ++ L I
Sbjct: 117 LKTLEEPPPNTLFILITPSPEKLLPTIRSRCQVLPFPPLSEEALLQWLIR------QGIS 170
Query: 141 PEFALRLAQQSDRNLRRA 158
E A L + + A
Sbjct: 171 EEAAELLLALAGGSPGAA 188
Score = 32.2 bits (74), Expect = 0.16
Identities = 15/35 (42%), Positives = 20/35 (57%), Gaps = 1/35 (2%)
Query: 26 LRNLLKEGDFPH-LLFYGPSGAGKKTRIMALLKEL 59
L+ L++G H LF GP G GK+ +AL K L
Sbjct: 4 LKRALEKGRLAHAYLFAGPEGVGKELLALALAKAL 38
>gnl|CDD|237355 PRK13342, PRK13342, recombination factor protein RarA; Reviewed.
Length = 413
Score = 61.3 bits (150), Expect = 1e-10
Identities = 43/221 (19%), Positives = 82/221 (37%), Gaps = 57/221 (25%)
Query: 6 DKYRPNNLQKLDFHCKQANH-------LRNLLKEGDFPHLLFYGPSGAGKKT--RIMAL- 55
++ RP L + ++ H LR +++ G ++ +GP G GK T RI+A
Sbjct: 4 ERMRPKTLD--EVVGQE--HLLGPGKPLRRMIEAGRLSSMILWGPPGTGKTTLARIIAGA 59
Query: 56 --------------LKEL--------------YGPVIILNETDHLTREAQQALRRTMEKY 87
+K+L ++ ++E + Q AL +E
Sbjct: 60 TDAPFEALSAVTSGVKDLREVIEEARQRRSAGRRTILFIDEIHRFNKAQQDALLPHVEDG 119
Query: 88 ITTCRLILCA----N-SMSQVIPAIRSRCLCIRIPAPTHEEIVSVLTNICKKEG---LTI 139
+ L N S V PA+ SR + + E+I +L + + + +
Sbjct: 120 T----ITLIGATTENPSFE-VNPALLSRAQVFELKPLSEEDIEQLLKRALEDKERGLVEL 174
Query: 140 PPEFALRLAQQSDRNLRRAILMCEASKVQQYPFQIDQQIVE 180
E LA+ ++ + RRA+ + E I +++E
Sbjct: 175 DDEALDALARLANGDARRALNLLEL--AALGVDSITLELLE 213
>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit;
Provisional.
Length = 482
Score = 61.5 bits (150), Expect = 1e-10
Identities = 59/208 (28%), Positives = 83/208 (39%), Gaps = 45/208 (21%)
Query: 1 MSLWVDKYRPNNLQKLDFHCKQANHLR----NLLKEGDFPHLLFYGPSGAGKKTRIMALL 56
M WV+KYRP L + + K LR + LK LL YGP G GK + AL
Sbjct: 1 MMPWVEKYRPKTLSDVVGNEKAKEQLREWIESWLKGKPKKALLLYGPPGVGKTSLAHALA 60
Query: 57 KELYGPVIILNETDHLTRE-----AQQALR-----------------------------R 82
+ VI LN +D T + A +A R
Sbjct: 61 NDYGWEVIELNASDQRTADVIERVAGEAATSGSLFGARRKLILLDEVDGIHGNEDRGGAR 120
Query: 83 TMEKYITTCR--LILCAN---SMSQVIPAIRSRCLCIRIPAPTHEEIVSVLTNICKKEGL 137
+ + I + +IL AN S + +R+ CL I + IV VL IC+KEG+
Sbjct: 121 AILELIKKAKQPIILTANDPYDPS--LRELRNACLMIEFKRLSTRSIVPVLKRICRKEGI 178
Query: 138 TIPPEFALRLAQQSDRNLRRAILMCEAS 165
E +A++S +LR AI +A
Sbjct: 179 ECDDEALKEIAERSGGDLRSAINDLQAI 206
>gnl|CDD|237867 PRK14953, PRK14953, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 486
Score = 60.2 bits (146), Expect = 3e-10
Identities = 36/97 (37%), Positives = 49/97 (50%), Gaps = 2/97 (2%)
Query: 63 VIILNETDHLTREAQQALRRTMEKYITTCRLILCANSMSQVIPAIRSRCLCIRIPAPTHE 122
V I++E LT+EA AL +T+E+ ILC ++ P I SRC PT E
Sbjct: 122 VYIIDEAHMLTKEAFNALLKTLEEPPPRTIFILCTTEYDKIPPTILSRCQRFIFSKPTKE 181
Query: 123 EIVSVLTNICKKEGLTIPPEFALR-LAQQSDRNLRRA 158
+I L IC +E + E AL LAQ S+ +R A
Sbjct: 182 QIKEYLKRICNEEKIEY-EEKALDLLAQASEGGMRDA 217
>gnl|CDD|236134 PRK07940, PRK07940, DNA polymerase III subunit delta'; Validated.
Length = 394
Score = 58.8 bits (143), Expect = 7e-10
Identities = 31/96 (32%), Positives = 52/96 (54%), Gaps = 5/96 (5%)
Query: 63 VIILNETDHLTREAQQALRRTMEKYITTCRLILCANSMSQVIPAIRSRCLCIRIPAPTHE 122
++++ + D LT A AL + +E+ +LCA S V+P IRSRC + + P+ E
Sbjct: 120 IVVIEDADRLTERAANALLKAVEEPPPRTVWLLCAPSPEDVLPTIRSRCRHVALRTPSVE 179
Query: 123 EIVSVLTNICKKEGLTIPPEFALRLAQQSDRNLRRA 158
+ VL +++G + PE A R A+ S ++ RA
Sbjct: 180 AVAEVLV---RRDG--VDPETARRAARASQGHIGRA 210
>gnl|CDD|237869 PRK14962, PRK14962, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 472
Score = 53.6 bits (129), Expect = 4e-08
Identities = 35/119 (29%), Positives = 61/119 (51%), Gaps = 3/119 (2%)
Query: 63 VIILNETDHLTREAQQALRRTMEKYITTCRLILCANSMSQVIPAIRSRCLCIRIPAPTHE 122
V I++E LT+EA AL +T+E+ + +L ++ +V P I SRC I + E
Sbjct: 120 VYIIDEVHMLTKEAFNALLKTLEEPPSHVVFVLATTNLEKVPPTIISRCQVIEFRNISDE 179
Query: 123 EIVSVLTNICKKEGLTIPPEFALRLAQQSDRNLRRAILMCEASKVQQYPF-QIDQQIVE 180
I+ L + + EG+ I E +A+++ LR A+ M E +V ++ +I + V
Sbjct: 180 LIIKRLQEVAEAEGIEIDREALSFIAKRASGGLRDALTMLE--QVWKFSEGKITLETVH 236
Score = 30.9 bits (70), Expect = 0.78
Identities = 20/53 (37%), Positives = 27/53 (50%), Gaps = 7/53 (13%)
Query: 7 KYRPNNLQKL--DFHCKQANHLRNLLKEGDFPH-LLFYGPSGAGKKT--RIMA 54
KYRP ++ H K+ + N LK+ H +F GP G GK T RI+A
Sbjct: 7 KYRPKTFSEVVGQDHVKKL--IINALKKNSISHAYIFAGPRGTGKTTVARILA 57
>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 = 50.6 bits (121), Expect = 7e-08
Identities = 31/137 (22%), Positives = 44/137 (32%), Gaps = 48/137 (35%)
Query: 26 LRNLLKEGDFPHLLFYGPSGAGKKTRIMALLKELY------------------------- 60
LR L+ +LL YGP G GK T A+ EL+
Sbjct: 10 LREALELPPPKNLLLYGPPGTGKTTLARAIANELFRPGAPFLYLNASDLLEGLVVAELFG 69
Query: 61 ---------------GPVIILNETDHLTREAQQALRRTMEKYITT------CRLILCAN- 98
V+ ++E D L+R AQ AL R +E R+I N
Sbjct: 70 HFLVRLLFELAEKAKPGVLFIDEIDSLSRGAQNALLRVLETLNDLRIDRENVRVIGATNR 129
Query: 99 -SMSQVIPAIRSRCLCI 114
+ + A+ R
Sbjct: 130 PLLGDLDRALYDRLDIR 146
>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 = 49.9 bits (120), Expect = 1e-07
Identities = 26/103 (25%), Positives = 48/103 (46%), Gaps = 14/103 (13%)
Query: 29 LLKEGDFPHLLFYGPSGAG-KKTRIMALLKELY-----GP--VIILNETDHLTREAQQAL 80
++ G+ P ++ P G K +I L++E G V I+ + + +T A AL
Sbjct: 62 RIENGNHPDVIIIEPEGKSIKIDQIRELIEEFSKKPFEGKKKVYIIEDAEKMTESAANAL 121
Query: 81 RRTME---KYITTCRLILCANSMSQVIPAIRSRCLCIRIPAPT 120
+T+E + IL ++ ++++P IRSRC I +
Sbjct: 122 LKTLEEPPENTY---FILLTSNPNKLLPTIRSRCQVINFKPLS 161
Score = 34.9 bits (81), Expect = 0.018
Identities = 13/37 (35%), Positives = 17/37 (45%), Gaps = 1/37 (2%)
Query: 24 NHLRNLLKEGDFPH-LLFYGPSGAGKKTRIMALLKEL 59
L+N +K+ H LF GP G GK + K L
Sbjct: 7 KLLKNSIKKNKLSHAYLFSGPDGVGKLELALEFAKAL 43
>gnl|CDD|180394 PRK06090, PRK06090, DNA polymerase III subunit delta'; Validated.
Length = 319
Score = 49.0 bits (117), Expect = 9e-07
Identities = 37/168 (22%), Positives = 68/168 (40%), Gaps = 15/168 (8%)
Query: 25 HLRNLLKEGDFPHLLFYGPSGAGKK---------TRIMALLKELYG-PVIILNETDHLTR 74
H L++ G+ P L P GK R+ +L G + ++ D +
Sbjct: 63 HSCELMQSGNHPDLHVIKPEKEGKSITVEQIRQCNRLAQESSQLNGYRLFVIEPADAMNE 122
Query: 75 EAQQALRRTMEKYITTCRLILCANSMSQVIPAIRSRCLCIRIPAPTHEEIVSVLTNICKK 134
A AL +T+E+ C +L ++ +++P I SRC + P+ + + L K
Sbjct: 123 SASNALLKTLEEPAPNCLFLLVTHNQKRLLPTIVSRCQQWVVTPPSTAQAMQWL----KG 178
Query: 135 EGLTIPPEFALRLAQQSDRNLRRAILMCEASKVQQYPFQIDQQIVEPD 182
+G+T+ P +AL+L S + K + Q+ + P
Sbjct: 179 QGITV-PAYALKLNMGSPLKTLAMMKEGGLEKYHKLERQLVDALSGPV 225
>gnl|CDD|184927 PRK14963, PRK14963, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 504
Score = 48.7 bits (116), Expect = 2e-06
Identities = 33/106 (31%), Positives = 48/106 (45%), Gaps = 2/106 (1%)
Query: 55 LLKELYGP--VIILNETDHLTREAQQALRRTMEKYITTCRLILCANSMSQVIPAIRSRCL 112
LL L G V IL+E +++ A AL +T+E+ IL ++ P I SR
Sbjct: 109 LLAPLRGGRKVYILDEAHMMSKSAFNALLKTLEEPPEHVIFILATTEPEKMPPTILSRTQ 168
Query: 113 CIRIPAPTHEEIVSVLTNICKKEGLTIPPEFALRLAQQSDRNLRRA 158
R T EEI L + + EG PE +A+ +D +R A
Sbjct: 169 HFRFRRLTEEEIAGKLRRLLEAEGREAEPEALQLVARLADGAMRDA 214
>gnl|CDD|225165 COG2256, MGS1, ATPase related to the helicase subunit of the
Holliday junction resolvase [DNA replication,
recombination, and repair].
Length = 436
Score = 48.4 bits (116), Expect = 2e-06
Identities = 35/176 (19%), Positives = 62/176 (35%), Gaps = 46/176 (26%)
Query: 26 LRNLLKEGDFPHLLFYGPSGAGKKT--RIMA----------------------------- 54
LR ++ G ++ +GP G GK T R++A
Sbjct: 39 LRRAVEAGHLHSMILWGPPGTGKTTLARLIAGTTNAAFEALSAVTSGVKDLREIIEEARK 98
Query: 55 LLKELYGPVIILNETDHLTREAQQALRRTMEKYITTCRLILCA----NSMSQVIPAIRSR 110
++ L+E + Q AL +E +IL N ++ PA+ SR
Sbjct: 99 NRLLGRRTILFLDEIHRFNKAQQDALLPHVENG----TIILIGATTENPSFELNPALLSR 154
Query: 111 CLCIRIPAPTHEEIVSVLTNIC--KKEGL-----TIPPEFALRLAQQSDRNLRRAI 159
+ + E+I +L ++ GL + E L + S+ + RRA+
Sbjct: 155 ARVFELKPLSSEDIKKLLKRALLDEERGLGGQIIVLDEEALDYLVRLSNGDARRAL 210
>gnl|CDD|225369 COG2812, DnaX, DNA polymerase III, gamma/tau subunits [DNA
replication, recombination, and repair].
Length = 515
Score = 47.8 bits (114), Expect = 3e-06
Identities = 28/96 (29%), Positives = 47/96 (48%)
Query: 63 VIILNETDHLTREAQQALRRTMEKYITTCRLILCANSMSQVIPAIRSRCLCIRIPAPTHE 122
V I++E L+++A AL +T+E+ + + IL ++ I SRC E
Sbjct: 122 VYIIDEVHMLSKQAFNALLKTLEEPPSHVKFILATTEPQKIPNTILSRCQRFDFKRLDLE 181
Query: 123 EIVSVLTNICKKEGLTIPPEFALRLAQQSDRNLRRA 158
EI L I KEG+ I + +A+ ++ +LR A
Sbjct: 182 EIAKHLAAILDKEGINIEEDALSLIARAAEGSLRDA 217
>gnl|CDD|184925 PRK14961, PRK14961, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 363
Score = 46.3 bits (110), Expect = 8e-06
Identities = 25/101 (24%), Positives = 49/101 (48%)
Query: 63 VIILNETDHLTREAQQALRRTMEKYITTCRLILCANSMSQVIPAIRSRCLCIRIPAPTHE 122
V +++E L+R + AL +T+E+ + IL + ++ I SRCL ++ + E
Sbjct: 122 VYLIDEVHMLSRHSFNALLKTLEEPPQHIKFILATTDVEKIPKTILSRCLQFKLKIISEE 181
Query: 123 EIVSVLTNICKKEGLTIPPEFALRLAQQSDRNLRRAILMCE 163
+I + L I KE + +A + ++R A+ + E
Sbjct: 182 KIFNFLKYILIKESIDTDEYALKLIAYHAHGSMRDALNLLE 222
>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 = 45.2 bits (108), Expect = 2e-05
Identities = 33/98 (33%), Positives = 48/98 (48%), Gaps = 2/98 (2%)
Query: 63 VIILNETDHLTREAQQALRRTMEKYITTCRLILCANSMSQVIPAIRSRCLCIRIPAPTHE 122
V I++E L++ A AL +T+E+ IL ++ I SRC E
Sbjct: 120 VYIIDEVHMLSKSAFNALLKTLEEPPEHVVFILATTEPHKIPATILSRCQRFDFKRIPLE 179
Query: 123 EIVSVLTNICKKEGLTIPPEFALRL-AQQSDRNLRRAI 159
+IV L I KEG+ I E AL L A+ +D +LR A+
Sbjct: 180 DIVERLKKILDKEGIKIEDE-ALELIARAADGSLRDAL 216
Score = 32.2 bits (74), Expect = 0.26
Identities = 22/56 (39%), Positives = 26/56 (46%), Gaps = 13/56 (23%)
Query: 7 KYRPNNL-----QKLDFHCKQANHLRNLLKEGDFPH-LLFYGPSGAGKKT--RIMA 54
KYRP Q+ H Q L+N +K G H LF GP G GK + RI A
Sbjct: 7 KYRPQTFEDVIGQE---HIVQT--LKNAIKNGRIAHAYLFSGPRGTGKTSIARIFA 57
>gnl|CDD|184934 PRK14970, PRK14970, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 367
Score = 44.9 bits (106), Expect = 3e-05
Identities = 49/200 (24%), Positives = 74/200 (37%), Gaps = 45/200 (22%)
Query: 7 KYRPNNLQKLDFHCKQANHLRNLLKEGDFPH-LLFYGPSGAGKKT--RIMA--------- 54
KYRP + N L N ++ LLF GP G GK T RI+A
Sbjct: 10 KYRPQTFDDVVGQSHITNTLLNAIENNHLAQALLFCGPRGVGKTTCARILARKINQPGYD 69
Query: 55 --------------------------LLKELYGP-------VIILNETDHLTREAQQALR 81
L+ ++ P + I++E L+ A A
Sbjct: 70 DPNEDFSFNIFELDAASNNSVDDIRNLIDQVRIPPQTGKYKIYIIDEVHMLSSAAFNAFL 129
Query: 82 RTMEKYITTCRLILCANSMSQVIPAIRSRCLCIRIPAPTHEEIVSVLTNICKKEGLTIPP 141
+T+E+ IL ++IP I SRC T ++I L I KEG+
Sbjct: 130 KTLEEPPAHAIFILATTEKHKIIPTILSRCQIFDFKRITIKDIKEHLAGIAVKEGIKFED 189
Query: 142 EFALRLAQQSDRNLRRAILM 161
+ +AQ++D LR A+ +
Sbjct: 190 DALHIIAQKADGALRDALSI 209
>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 = 43.4 bits (102), Expect = 8e-05
Identities = 24/62 (38%), Positives = 30/62 (48%), Gaps = 5/62 (8%)
Query: 3 LWVDKYRPNNLQKLDFHCKQANHLRNLLKEGDFPH-----LLFYGPSGAGKKTRIMALLK 57
WV+KY+P +L H K+ + LK + LL GPSG GK T I L K
Sbjct: 73 PWVEKYKPETQHELAVHKKKIEEVETWLKAQVLENAPKRILLITGPSGCGKSTTIKILSK 132
Query: 58 EL 59
EL
Sbjct: 133 EL 134
>gnl|CDD|237874 PRK14971, PRK14971, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 614
Score = 42.8 bits (101), Expect = 1e-04
Identities = 32/103 (31%), Positives = 54/103 (52%), Gaps = 8/103 (7%)
Query: 63 VIILNETDHLTREAQQALRRTMEKYITTCRLILCANSMSQVIPAIRSRCLCI---RIPAP 119
+ I++E L++ A A +T+E+ + IL +++P I SRC RI
Sbjct: 124 IYIIDEVHMLSQAAFNAFLKTLEEPPSYAIFILATTEKHKILPTILSRCQIFDFNRIQV- 182
Query: 120 THEEIVSVLTNICKKEGLTIPPEFALRL-AQQSDRNLRRAILM 161
+IV+ L + KEG+T PE AL + AQ++D +R A+ +
Sbjct: 183 --ADIVNHLQYVASKEGITAEPE-ALNVIAQKADGGMRDALSI 222
>gnl|CDD|223666 COG0593, DnaA, ATPase involved in DNA replication initiation [DNA
replication, recombination, and repair].
Length = 408
Score = 42.3 bits (100), Expect = 2e-04
Identities = 19/72 (26%), Positives = 36/72 (50%), Gaps = 7/72 (9%)
Query: 92 RLILCA----NSMSQVIPAIRSR---CLCIRIPAPTHEEIVSVLTNICKKEGLTIPPEFA 144
+++L + ++ + +RSR L + I P E +++L + G+ IP E
Sbjct: 210 QIVLTSDRPPKELNGLEDRLRSRLEWGLVVEIEPPDDETRLAILRKKAEDRGIEIPDEVL 269
Query: 145 LRLAQQSDRNLR 156
LA++ DRN+R
Sbjct: 270 EFLAKRLDRNVR 281
>gnl|CDD|169667 PRK09112, PRK09112, DNA polymerase III subunit delta'; Validated.
Length = 351
Score = 41.6 bits (98), Expect = 3e-04
Identities = 26/99 (26%), Positives = 52/99 (52%), Gaps = 2/99 (2%)
Query: 63 VIILNETDHLTREAQQALRRTMEKYITTCRLILCANSMSQVIPAIRSRCLCIRIPAPTHE 122
++I++ D + R A A+ +T+E+ IL ++S +++P IRSRC I + +
Sbjct: 144 IVIIDPADDMNRNAANAILKTLEEPPARALFILISHSSGRLLPTIRSRCQPISLKPLDDD 203
Query: 123 EIVSVLTNICKKEGLTIPPEFALRLAQQSDRNLRRAILM 161
E+ L+++ E L Q+S ++R+A+L+
Sbjct: 204 ELKKALSHL--GSSQGSDGEITEALLQRSKGSVRKALLL 240
>gnl|CDD|180132 PRK05564, PRK05564, DNA polymerase III subunit delta'; Validated.
Length = 313
Score = 40.4 bits (95), Expect = 5e-04
Identities = 19/68 (27%), Positives = 38/68 (55%)
Query: 63 VIILNETDHLTREAQQALRRTMEKYITTCRLILCANSMSQVIPAIRSRCLCIRIPAPTHE 122
VII+ ++ +T +AQ A +T+E+ +IL ++ Q++ I+SRC ++ + E
Sbjct: 96 VIIIYNSEKMTEQAQNAFLKTIEEPPKGVFIILLCENLEQILDTIKSRCQIYKLNRLSKE 155
Query: 123 EIVSVLTN 130
EI ++
Sbjct: 156 EIEKFISY 163
>gnl|CDD|180523 PRK06305, PRK06305, DNA polymerase III subunits gamma and tau;
Validated.
Length = 451
Score = 40.9 bits (96), Expect = 6e-04
Identities = 30/99 (30%), Positives = 49/99 (49%), Gaps = 6/99 (6%)
Query: 63 VIILNETDHLTREAQQALRRTMEKYITTCRLILCANSMSQVIPAIRSRC---LCIRIPAP 119
+ I++E LT+EA +L +T+E+ + L + ++ I SRC RIP
Sbjct: 124 IYIIDEVHMLTKEAFNSLLKTLEEPPQHVKFFLATTEIHKIPGTILSRCQKMHLKRIP-- 181
Query: 120 THEEIVSVLTNICKKEGLTIPPEFALRLAQQSDRNLRRA 158
E I+ L I K+EG+ E L +A+ + +LR A
Sbjct: 182 -EETIIDKLALIAKQEGIETSREALLPIARAAQGSLRDA 219
>gnl|CDD|181538 PRK08699, PRK08699, DNA polymerase III subunit delta'; Validated.
Length = 325
Score = 40.2 bits (94), Expect = 7e-04
Identities = 19/67 (28%), Positives = 41/67 (61%)
Query: 63 VIILNETDHLTREAQQALRRTMEKYITTCRLILCANSMSQVIPAIRSRCLCIRIPAPTHE 122
VI+++ + + +A +L + +E+ +L +++ +V+P I+SRC + +PAP+HE
Sbjct: 116 VILIHPAESMNLQAANSLLKVLEEPPPQVVFLLVSHAADKVLPTIKSRCRKMVLPAPSHE 175
Query: 123 EIVSVLT 129
E ++ L
Sbjct: 176 EALAYLR 182
>gnl|CDD|217429 pfam03215, Rad17, Rad17 cell cycle checkpoint protein.
Length = 490
Score = 40.0 bits (93), Expect = 0.001
Identities = 26/69 (37%), Positives = 34/69 (49%), Gaps = 8/69 (11%)
Query: 3 LWVDKYRPNNLQKLDFHCKQANHLRNLLKEGDF----PHLLFY--GPSGAGKKTRIMALL 56
LW +KY+P +L H K+ + + LK F L+ GPSG GK T + L
Sbjct: 8 LWTEKYKPRRRDELAIHKKKIAEVDHWLK-AVFLESNKQLILLLTGPSGCGKSTTVKVLS 66
Query: 57 KELYGPVII 65
KEL G II
Sbjct: 67 KEL-GIEII 74
>gnl|CDD|180643 PRK06645, PRK06645, DNA polymerase III subunits gamma and tau;
Validated.
Length = 507
Score = 39.8 bits (93), Expect = 0.001
Identities = 44/158 (27%), Positives = 77/158 (48%), Gaps = 13/158 (8%)
Query: 63 VIILNETDHLTREAQQALRRTMEKYITTCRLILCANSMSQVIPA-IRSRCLCIRIPAPTH 121
+ I++E L++ A AL +T+E+ I A + Q IPA I SRC + +
Sbjct: 131 IFIIDEVHMLSKGAFNALLKTLEEPPPHIIFIF-ATTEVQKIPATIISRCQRYDLRRLSF 189
Query: 122 EEIVSVLTNICKKEGLTIPPEFALR-LAQQSDRNLRRAILMCE--ASKVQQYPFQIDQQI 178
EEI +L I K+E L E ALR +A +S+ + R A+ + + AS + I Q+
Sbjct: 190 EEIFKLLEYITKQENLKTDIE-ALRIIAYKSEGSARDAVSILDQAASMSAKSDNIISPQV 248
Query: 179 VEPDWKIYIRDTAKLI-----ISEQSPKKLLEVRTRLY 211
+ + + D++ +I I + +K + + +LY
Sbjct: 249 INQ--MLGLVDSSVIIEFVEYIIHRETEKAINLINKLY 284
>gnl|CDD|236011 PRK07399, PRK07399, DNA polymerase III subunit delta'; Validated.
Length = 314
Score = 39.5 bits (93), Expect = 0.001
Identities = 28/89 (31%), Positives = 44/89 (49%), Gaps = 1/89 (1%)
Query: 63 VIILNETDHLTREAQQALRRTMEKYITTCRLILCANSMSQVIPAIRSRCLCIRIPAPTHE 122
V+++ + + + A AL +T+E+ LIL A S ++P I SRC I + E
Sbjct: 127 VVVIEDAETMNEAAANALLKTLEE-PGNGTLILIAPSPESLLPTIVSRCQIIPFYRLSDE 185
Query: 123 EIVSVLTNICKKEGLTIPPEFALRLAQQS 151
++ VL + +E L I L LAQ S
Sbjct: 186 QLEQVLKRLGDEEILNINFPELLALAQGS 214
>gnl|CDD|237870 PRK14964, PRK14964, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 491
Score = 39.0 bits (91), Expect = 0.002
Identities = 37/143 (25%), Positives = 64/143 (44%), Gaps = 24/143 (16%)
Query: 63 VIILNETDHLTREAQQALRRTMEKYITTCRLILCANSMSQVIPAIRSRCLCIRIPAPTHE 122
V I++E L+ A AL +T+E+ + IL + ++ I SRC + +
Sbjct: 119 VYIIDEVHMLSNSAFNALLKTLEEPAPHVKFILATTEVKKIPVTIISRCQRFDLQKIPTD 178
Query: 123 EIVSVLTNICKKEGLTIPPEFALRL-AQQSDRNLRRAILMCEASKVQQYPFQIDQQIVEP 181
++V L +I KKE + E +L+L A+ S ++R A+ + E +
Sbjct: 179 KLVEHLVDIAKKENIEHDEE-SLKLIAENSSGSMRNALFLLEQA---------------- 221
Query: 182 DWKIYIRDTAKLIISEQSPKKLL 204
IY + ISE+S + LL
Sbjct: 222 --AIYSNN----KISEKSVRDLL 238
>gnl|CDD|180215 PRK05707, PRK05707, DNA polymerase III subunit delta'; Validated.
Length = 328
Score = 38.1 bits (89), Expect = 0.003
Identities = 34/124 (27%), Positives = 61/124 (49%), Gaps = 12/124 (9%)
Query: 63 VIILNETDHLTREAQQALRRTMEKYITTCRLILCANSMSQVIPAIRSRCLCIRIPAPTHE 122
V+++ + + R A AL +++E+ L+L ++ S+++P I+SRC P P++E
Sbjct: 109 VVLIEPAEAMNRNAANALLKSLEEPSGDTVLLLISHQPSRLLPTIKSRCQQQACPLPSNE 168
Query: 123 EIVSVL-------TNICKKEGLTIP---PEFALRLAQQSDRNLRRAIL--MCEASKVQQY 170
E + L + E LT+ P AL+L +Q R R +L + + K QQ
Sbjct: 169 ESLQWLQQALPESDERERIELLTLAGGSPLRALQLHEQGVREQRARVLDGVKKLLKQQQS 228
Query: 171 PFQI 174
Q+
Sbjct: 229 ASQL 232
>gnl|CDD|181551 PRK08769, PRK08769, DNA polymerase III subunit delta'; Validated.
Length = 319
Score = 37.6 bits (87), Expect = 0.005
Identities = 34/125 (27%), Positives = 58/125 (46%), Gaps = 19/125 (15%)
Query: 23 ANHLRNLLKEGDFP--HLLFYGPSGAGKKTRIMALLKEL------------YG--PVIIL 66
A R L+ G P L+ + P+ G K R +++++ YG V+I+
Sbjct: 60 AQRTRQLIAAGTHPDLQLVSFIPNRTGDKLRTEIVIEQVREISQKLALTPQYGIAQVVIV 119
Query: 67 NETDHLTREAQQALRRTMEKYITTCRLILCANSMSQVIPAIRSRC--LCIRIPAPTHEEI 124
+ D + R A AL +T+E+ L L + +++ IRSRC L ++P P HE +
Sbjct: 120 DPADAINRAACNALLKTLEEPSPGRYLWLISAQPARLPATIRSRCQRLEFKLP-PAHEAL 178
Query: 125 VSVLT 129
+L
Sbjct: 179 AWLLA 183
>gnl|CDD|213264 cd03297, ABC_ModC_molybdenum_transporter, ATP-binding cassette
domain of the molybdenum transport system. ModC is an
ABC-type transporter and the ATPase component of a
molybdate transport system that also includes the
periplasmic binding protein ModA and the membrane
protein ModB. ABC transporters are a large family of
proteins involved in the transport of a wide variety of
different compounds, like sugars, ions, peptides and
more complex organic molecules. The nucleotide binding
domain shows the highest similarity between all members
of the family. ABC transporters are a subset of
nucleotide hydrolases that contain a signature motif,
Q-loop, and H-loop/switch region, in addition to, the
Walker A motif/P-loop and Walker B motif commonly found
in a number of ATP- and GTP-binding and hydrolyzing
proteins.
Length = 214
Score = 36.5 bits (85), Expect = 0.009
Identities = 16/56 (28%), Positives = 27/56 (48%), Gaps = 2/56 (3%)
Query: 16 LDFHCKQANHLRNLLKEGDFPHLLFYGPSGAGKKT--RIMALLKELYGPVIILNET 69
+D + + + + + +G SGAGK T R +A L++ G I+LN T
Sbjct: 4 VDIEKRLPDFTLKIDFDLNEEVTGIFGASGAGKSTLLRCIAGLEKPDGGTIVLNGT 59
>gnl|CDD|184918 PRK14954, PRK14954, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 620
Score = 36.8 bits (85), Expect = 0.012
Identities = 31/108 (28%), Positives = 50/108 (46%), Gaps = 12/108 (11%)
Query: 60 YGP------VIILNETDHLTREAQQALRRTMEKYITTCRLILCANSMSQVIPAIRSRCLC 113
YGP V I++E L+ A A +T+E+ I + ++ I SRC
Sbjct: 121 YGPQKGRYRVYIIDEVHMLSTAAFNAFLKTLEEPPPHAIFIFATTELHKIPATIASRCQR 180
Query: 114 I---RIPAPTHEEIVSVLTNICKKEGLTIPPEFALRLAQQSDRNLRRA 158
RIP +EI S L IC+ EG+ I + +A+++ ++R A
Sbjct: 181 FNFKRIPL---DEIQSQLQMICRAEGIQIDADALQLIARKAQGSMRDA 225
>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 = 36.7 bits (85), Expect = 0.013
Identities = 23/69 (33%), Positives = 32/69 (46%), Gaps = 2/69 (2%)
Query: 92 RLILCANSMSQVI-PAIRSRCLCIRIPAPTHEEIVSVLTNICKKEGLTIPPEFALRLAQQ 150
RLI + I PA+RSRC+ I EEI + N +K G+ + AL L +
Sbjct: 235 RLIGATTRNPEEIPPALRSRCVEIFFRPLLDEEIKEIAKNAAEKIGINLEKH-ALELIVK 293
Query: 151 SDRNLRRAI 159
N R A+
Sbjct: 294 YASNGREAV 302
>gnl|CDD|235638 PRK05896, PRK05896, DNA polymerase III subunits gamma and tau;
Validated.
Length = 605
Score = 36.4 bits (84), Expect = 0.015
Identities = 29/98 (29%), Positives = 48/98 (48%), Gaps = 8/98 (8%)
Query: 63 VIILNETDHLTREAQQALRRTME---KYITTCRLILCANSMSQVIP-AIRSRCLCIRIPA 118
V I++E L+ A AL +T+E K++ + + A + Q IP I SRC
Sbjct: 122 VYIIDEAHMLSTSAWNALLKTLEEPPKHV----VFIFATTEFQKIPLTIISRCQRYNFKK 177
Query: 119 PTHEEIVSVLTNICKKEGLTIPPEFALRLAQQSDRNLR 156
+ E+ +L +I KKE + I ++A +D +LR
Sbjct: 178 LNNSELQELLKSIAKKEKIKIEDNAIDKIADLADGSLR 215
>gnl|CDD|184919 PRK14955, PRK14955, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 397
Score = 36.0 bits (83), Expect = 0.016
Identities = 34/108 (31%), Positives = 50/108 (46%), Gaps = 17/108 (15%)
Query: 60 YGP------VIILNETDHLTREAQQALRRTMEKYITTCRLILCANSMSQVIPAIRSRCLC 113
YGP V I++E L+ A A +T+E+ I + ++ I SRC
Sbjct: 121 YGPQKGRYRVYIIDEVHMLSIAAFNAFLKTLEEPPPHAIFIFATTELHKIPATIASRCQR 180
Query: 114 I---RIPAPTHEEIVSVLTNICKKEGLTIPPEFALRL----AQQSDRN 154
RIP EEI L IC+ EG+++ + AL+L AQ S R+
Sbjct: 181 FNFKRIPL---EEIQQQLQGICEAEGISVDAD-ALQLIGRKAQGSMRD 224
>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 = 35.0 bits (80), Expect = 0.017
Identities = 18/47 (38%), Positives = 23/47 (48%), Gaps = 3/47 (6%)
Query: 37 HLLFYGPSGAGKKTRIMALLKEL---YGPVIILNETDHLTREAQQAL 80
+L GP G+GK T AL +EL G VI ++ D L Q L
Sbjct: 4 VILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLL 50
>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 = 34.9 bits (81), Expect = 0.026
Identities = 37/173 (21%), Positives = 64/173 (36%), Gaps = 43/173 (24%)
Query: 24 NHLRNLLKEGDFPHLLFYGPSGAGKKTRIMAL---------------LKELYG------- 61
LR L L +G SG+GK + A L EL
Sbjct: 27 AALRQLAAGKGDRFLYLWGESGSGKSHLLQAACAAAEERGKSAIYLPLAELAQADPEVLE 86
Query: 62 -----PVIILNETDHLT--REAQQAL----RRTMEKYITTCRLILCAN----SMSQVIPA 106
++ L++ + + E Q+AL R E RL++ + +P
Sbjct: 87 GLEQADLVCLDDVEAIAGQPEWQEALFHLYNRVRE---AGGRLLIAGRAAPAQLPLRLPD 143
Query: 107 IRSR---CLCIRIPAPTHEEIVSVLTNICKKEGLTIPPEFALRLAQQSDRNLR 156
+R+R L ++P + EE ++ L + + GL +P E A L + R++
Sbjct: 144 LRTRLAWGLVFQLPPLSDEEKIAALQSRAARRGLQLPDEVADYLLRHGSRDMG 196
>gnl|CDD|184923 PRK14959, PRK14959, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 624
Score = 35.4 bits (81), Expect = 0.034
Identities = 25/85 (29%), Positives = 39/85 (45%), Gaps = 1/85 (1%)
Query: 63 VIILNETDHLTREAQQALRRTMEKYITTCRLILCANSMSQVIPAIRSRCLCIRIPAPTHE 122
V I++E LTREA AL +T+E+ +L + I SRC +
Sbjct: 122 VFIIDEAHMLTREAFNALLKTLEEPPARVTFVLATTEPHKFPVTIVSRCQHFTFTRLSEA 181
Query: 123 EIVSVLTNICKKEGLTIPPEFALRL 147
+ + LT + +EG+ P A+RL
Sbjct: 182 GLEAHLTKVLGREGVDYDPA-AVRL 205
>gnl|CDD|235898 PRK06964, PRK06964, DNA polymerase III subunit delta'; Validated.
Length = 342
Score = 35.1 bits (81), Expect = 0.035
Identities = 27/104 (25%), Positives = 44/104 (42%), Gaps = 6/104 (5%)
Query: 63 VIILNETDHLTREAQQALRRTMEKYITTCRLILCANSMSQVIPAIRSRCLCIRIPAPTHE 122
V++L + L A AL +T+E+ +L + + +++P I SRC + P E
Sbjct: 135 VVVLYPAEALNVAAANALLKTLEEPPPGTVFLLVSARIDRLLPTILSRCRQFPMTVPAPE 194
Query: 123 EIVSVLT--NICKKEGLTI----PPEFALRLAQQSDRNLRRAIL 160
+ L + + L P AL LA +R LR L
Sbjct: 195 AAAAWLAAQGVADADALLAEAGGAPLAALALASDENRPLRDWTL 238
>gnl|CDD|237862 PRK14948, PRK14948, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 620
Score = 34.9 bits (81), Expect = 0.039
Identities = 27/60 (45%), Positives = 33/60 (55%), Gaps = 8/60 (13%)
Query: 103 VIPAIRSRCLCI---RIPAPTHEEIVSVLTNICKKEGLTIPPEFALRL-AQQSDRNLRRA 158
V+P I SRC RIP E +V L+ I +KE + I PE AL L AQ+S LR A
Sbjct: 164 VLPTIISRCQRFDFRRIPL---EAMVQHLSEIAEKESIEIEPE-ALTLVAQRSQGGLRDA 219
>gnl|CDD|213228 cd03261, ABC_Org_Solvent_Resistant, ATP-binding cassette
transport system involved in resistant to organic
solvents. ABC transporters are a large family of
proteins involved in the transport of a wide variety of
different compounds, like sugars, ions, peptides, and
more complex organic molecules. The nucleotide binding
domain shows the highest similarity between all members
of the family. ABC transporters are a subset of
nucleotide hydrolases that contain a signature motif,
Q-loop, and H-loop/switch region, in addition to, the
Walker A motif/P-loop and Walker B motif commonly found
in a number of ATP- and GTP-binding and hydrolyzing
proteins.
Length = 235
Score = 34.4 bits (80), Expect = 0.039
Identities = 19/47 (40%), Positives = 25/47 (53%), Gaps = 4/47 (8%)
Query: 42 GPSGAGKKT--RIMA-LLKELYGPVIILNE-TDHLTREAQQALRRTM 84
GPSG+GK T R++ LL+ G V+I E L+ LRR M
Sbjct: 33 GPSGSGKSTLLRLIVGLLRPDSGEVLIDGEDISGLSEAELYRLRRRM 79
>gnl|CDD|232941 TIGR00362, DnaA, chromosomal replication initiator protein DnaA.
DnaA is involved in DNA biosynthesis; initiation of
chromosome replication and can also be transcription
regulator. The C-terminal of the family hits the pfam
bacterial DnaA (bac_dnaA) domain family. For a review,
see Kaguni (2006) [DNA metabolism, DNA replication,
recombination, and repair].
Length = 405
Score = 34.4 bits (80), Expect = 0.063
Identities = 16/53 (30%), Positives = 27/53 (50%), Gaps = 3/53 (5%)
Query: 107 IRSRC---LCIRIPAPTHEEIVSVLTNICKKEGLTIPPEFALRLAQQSDRNLR 156
+RSR L + I P E +++L ++EGL +P E +A+ N+R
Sbjct: 253 LRSRFEWGLVVDIEPPDLETRLAILQKKAEEEGLELPDEVLEFIAKNIRSNVR 305
>gnl|CDD|131688 TIGR02640, gas_vesic_GvpN, gas vesicle protein GvpN. Members of
this family are the GvpN protein associated with the
production of gas vesicles produced in some prokaryotes
to give cells buoyancy. This family belongs to a larger
family of ATPases (pfam07728) [Cellular processes,
Other].
Length = 262
Score = 34.0 bits (78), Expect = 0.067
Identities = 13/40 (32%), Positives = 22/40 (55%), Gaps = 1/40 (2%)
Query: 34 DFPHLLFYGPSGAGKKTRIMALLKELYGPVIILNETDHLT 73
+P + GP+G GK T M + ++ PV+++N LT
Sbjct: 21 GYP-VHLRGPAGTGKTTLAMHVARKRDRPVMLINGDAELT 59
>gnl|CDD|237864 PRK14950, PRK14950, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 585
Score = 34.4 bits (79), Expect = 0.071
Identities = 24/96 (25%), Positives = 43/96 (44%)
Query: 63 VIILNETDHLTREAQQALRRTMEKYITTCRLILCANSMSQVIPAIRSRCLCIRIPAPTHE 122
V I++E L+ A AL +T+E+ IL + +V I SRC +
Sbjct: 123 VYIIDEVHMLSTAAFNALLKTLEEPPPHAIFILATTEVHKVPATILSRCQRFDFHRHSVA 182
Query: 123 EIVSVLTNICKKEGLTIPPEFALRLAQQSDRNLRRA 158
++ + L I EG+ + P +A+ + ++R A
Sbjct: 183 DMAAHLRKIAAAEGINLEPGALEAIARAATGSMRDA 218
Score = 32.1 bits (73), Expect = 0.39
Identities = 19/51 (37%), Positives = 24/51 (47%), Gaps = 3/51 (5%)
Query: 7 KYRPNNLQKLDFHCKQANHLRNLLKEGDFPH-LLFYGPSGAGKKT--RIMA 54
K+R +L LRN + EG H LF GP G GK + RI+A
Sbjct: 9 KWRSQTFAELVGQEHVVQTLRNAIAEGRVAHAYLFTGPRGVGKTSTARILA 59
>gnl|CDD|224025 COG1100, COG1100, GTPase SAR1 and related small G proteins [General
function prediction only].
Length = 219
Score = 33.8 bits (77), Expect = 0.072
Identities = 14/85 (16%), Positives = 27/85 (31%), Gaps = 18/85 (21%)
Query: 38 LLFYGPSGAGKKTRIMALLKELYGPVI---ILNETDHLTREA--------------QQAL 80
++ G G GK T + L+ + + I N T E Q+
Sbjct: 8 IVVLGDGGVGKTTLLNRLVGDEFPEGYPPTIGNLDPAKTIEPYRRNIKLQLWDTAGQEEY 67
Query: 81 RRTMEKYITTCR-LILCANSMSQVI 104
R +Y +++ +S +
Sbjct: 68 RSLRPEYYRGANGILIVYDSTLRES 92
>gnl|CDD|237873 PRK14969, PRK14969, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 527
Score = 34.0 bits (78), Expect = 0.088
Identities = 30/99 (30%), Positives = 52/99 (52%), Gaps = 4/99 (4%)
Query: 63 VIILNETDHLTREAQQALRRTMEKYITTCRLILCANSMSQVIP-AIRSRCLCIRIPAPTH 121
V I++E L++ A A+ +T+E+ + IL A + Q IP + SRCL +
Sbjct: 122 VYIIDEVHMLSKSAFNAMLKTLEEPPEHVKFIL-ATTDPQKIPVTVLSRCLQFNLKQMPP 180
Query: 122 EEIVSVLTNICKKEGLTIPPEFALRL-AQQSDRNLRRAI 159
IVS L +I ++E + AL+L A+ + ++R A+
Sbjct: 181 PLIVSHLQHILEQENIPFDAT-ALQLLARAAAGSMRDAL 218
>gnl|CDD|236022 PRK07471, PRK07471, DNA polymerase III subunit delta'; Validated.
Length = 365
Score = 33.8 bits (78), Expect = 0.091
Identities = 23/97 (23%), Positives = 50/97 (51%), Gaps = 4/97 (4%)
Query: 63 VIILNETDHLTREAQQALRRTMEKYITTCRLILCANSMSQVIPAIRSRCLCIRIPAPTHE 122
V+I++ D + A AL + +E+ +L +++ ++++P IRSRC +R+ E
Sbjct: 144 VVIVDTADEMNANAANALLKVLEEPPARSLFLLVSHAPARLLPTIRSRCRKLRLRPLAPE 203
Query: 123 EIVSVLTNICKKEGLTIPPEFALRLAQQSDRNLRRAI 159
+++ L G +P + LA ++ ++ RA+
Sbjct: 204 DVIDALA----AAGPDLPDDPRAALAALAEGSVGRAL 236
>gnl|CDD|223455 COG0378, HypB, Ni2+-binding GTPase involved in regulation of
expression and maturation of urease and hydrogenase
[Posttranslational modification, protein turnover,
chaperones / Transcription].
Length = 202
Score = 33.0 bits (76), Expect = 0.11
Identities = 15/47 (31%), Positives = 20/47 (42%), Gaps = 5/47 (10%)
Query: 42 GPSGAGKKTRIMALLKEL---YGPVIILNETDHLTREAQQALRRTME 85
GP G+GK I L+ L Y +I D T+E LR+
Sbjct: 20 GPPGSGKTALIEKTLRALKDEYKIAVITG--DIYTKEDADRLRKLPG 64
>gnl|CDD|213196 cd03229, ABC_Class3, ATP-binding cassette domain of the binding
protein-dependent transport systems. This class is
comprised of all BPD (Binding Protein Dependent)
systems that are largely represented in archaea and
eubacteria and are primarily involved in scavenging
solutes from the environment. ABC transporters are a
large family of proteins involved in the transport of a
wide variety of different compounds, like sugars, ions,
peptides, and more complex organic molecules. The
nucleotide binding domain shows the highest similarity
between all members of the family. ABC transporters are
a subset of nucleotide hydrolases that contain a
signature motif, Q-loop, and H-loop/switch region, in
addition to, the Walker A motif/P-loop and Walker B
motif commonly found in a number of ATP- and
GTP-binding and hydrolyzing proteins.
Length = 178
Score = 32.5 bits (75), Expect = 0.11
Identities = 22/77 (28%), Positives = 36/77 (46%), Gaps = 11/77 (14%)
Query: 12 NLQKLDFHCKQANHLRNL---LKEGDFPHLLFYGPSGAGKKT--RIMALLKEL-YGPVII 65
N+ K + K L ++ ++ G+ + GPSG+GK T R +A L+E G ++I
Sbjct: 5 NVSK-RYGQKTV--LNDVSLNIEAGEI--VALLGPSGSGKSTLLRCIAGLEEPDSGSILI 59
Query: 66 LNETDHLTREAQQALRR 82
E + LRR
Sbjct: 60 DGEDLTDLEDELPPLRR 76
>gnl|CDD|188394 TIGR03864, PQQ_ABC_ATP, ABC transporter, ATP-binding subunit,
PQQ-dependent alcohol dehydrogenase system. Members of
this protein family are the ATP-binding subunit of an
ABC transporter system that is associated with PQQ
biosynthesis and PQQ-dependent alcohol dehydrogenases.
While this family shows homology to several efflux ABC
transporter subunits, the presence of a periplasmic
substrate-binding protein and association with systems
for catabolism of alcohols suggests a role in import
rather than detoxification [Transport and binding
proteins, Carbohydrates, organic alcohols, and acids].
Length = 236
Score = 32.7 bits (75), Expect = 0.16
Identities = 21/57 (36%), Positives = 29/57 (50%), Gaps = 9/57 (15%)
Query: 30 LKEGDFPHLLFYGPSGAGKKTRIMALLKELY----GPVIILNETDHLTREAQQALRR 82
++ G F LL GP+GAGK T + +LL LY G + + L R + AL R
Sbjct: 24 VRPGRFVALL--GPNGAGKST-LFSLLTRLYVAQEGQISVAG--HDLRRAPRAALAR 75
>gnl|CDD|224144 COG1223, COG1223, Predicted ATPase (AAA+ superfamily) [General
function prediction only].
Length = 368
Score = 32.9 bits (75), Expect = 0.17
Identities = 21/65 (32%), Positives = 32/65 (49%), Gaps = 2/65 (3%)
Query: 25 HLRNLLKEGDFP--HLLFYGPSGAGKKTRIMALLKELYGPVIILNETDHLTREAQQALRR 82
+L N + GD+ ++LFYGP G GK AL E P++++ T+ + RR
Sbjct: 139 YLENPERFGDWAPKNVLFYGPPGTGKTMMAKALANEAKVPLLLVKATELIGEHVGDGARR 198
Query: 83 TMEKY 87
E Y
Sbjct: 199 IHELY 203
>gnl|CDD|234152 TIGR03265, PhnT2, putative 2-aminoethylphosphonate ABC
transporter, ATP-binding protein. This ABC transporter
ATP-binding protein is found in a number of genomes in
operon-like contexts strongly suggesting a substrate
specificity for 2-aminoethylphosphonate (2-AEP). The
characterized PhnSTUV system is absent in the genomes
in which this system is found. These genomes encode
systems for the catabolism of 2-AEP, making the need
for a 2-AEP-specific transporter likely [Transport and
binding proteins, Amino acids, peptides and amines].
Length = 353
Score = 32.7 bits (75), Expect = 0.18
Identities = 21/68 (30%), Positives = 29/68 (42%), Gaps = 11/68 (16%)
Query: 20 CKQANHLRNL------LKEGDFPHLLFYGPSGAGKKT--RIMALLKELYGPVIILNETDH 71
K+ L +K+G+F + GPSG GK T RI+A L+ I D
Sbjct: 11 RKRFGAFTALKDISLSVKKGEF--VCLLGPSGCGKTTLLRIIAGLERQTAGTIYQGGRD- 67
Query: 72 LTREAQQA 79
+TR Q
Sbjct: 68 ITRLPPQK 75
>gnl|CDD|224052 COG1127, Ttg2A, ABC-type transport system involved in resistance
to organic solvents, ATPase component [Secondary
metabolites biosynthesis, transport, and catabolism].
Length = 263
Score = 32.6 bits (75), Expect = 0.19
Identities = 16/47 (34%), Positives = 25/47 (53%), Gaps = 4/47 (8%)
Query: 42 GPSGAGKKT--RIMA-LLKELYGPVIILNE-TDHLTREAQQALRRTM 84
G SG+GK T R++ LL+ G ++I E L+ E +R+ M
Sbjct: 41 GGSGSGKSTLLRLILGLLRPDKGEILIDGEDIPQLSEEELYEIRKRM 87
>gnl|CDD|184920 PRK14956, PRK14956, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 484
Score = 33.0 bits (75), Expect = 0.19
Identities = 20/51 (39%), Positives = 26/51 (50%), Gaps = 3/51 (5%)
Query: 7 KYRPNNLQKLDFHCKQANHLRNLLKEGDFPH-LLFYGPSGAGKKT--RIMA 54
KYRP + + L+N LK G H +F+GP G GK T RI+A
Sbjct: 11 KYRPQFFRDVIHQDLAIGALQNALKSGKIGHAYIFFGPRGVGKTTIARILA 61
Score = 32.6 bits (74), Expect = 0.21
Identities = 26/101 (25%), Positives = 47/101 (46%), Gaps = 14/101 (13%)
Query: 63 VIILNETDHLTREAQQALRRTMEKYITTCRLILCANSMSQVIPAIRSRC---LCIRIPAP 119
V I++E LT ++ AL +T+E+ IL ++ I SRC + ++P
Sbjct: 124 VYIIDEVHMLTDQSFNALLKTLEEPPAHIVFILATTEFHKIPETILSRCQDFIFKKVP-- 181
Query: 120 THEEIVSVLTN----ICKKEGLTIPPEFALRLAQQSDRNLR 156
+SVL + +CK E + E +A++ D ++R
Sbjct: 182 -----LSVLQDYSEKLCKIENVQYDQEGLFWIAKKGDGSVR 217
>gnl|CDD|226359 COG3839, MalK, ABC-type sugar transport systems, ATPase
components [Carbohydrate transport and metabolism].
Length = 338
Score = 32.6 bits (75), Expect = 0.19
Identities = 22/63 (34%), Positives = 35/63 (55%), Gaps = 6/63 (9%)
Query: 11 NNLQKLDFHCKQANHLRNL-LKEGDFPHLLFYGPSGAGKKT--RIMALLKELYGPVIILN 67
N++K F + NL +++G+F LL GPSG GK T R++A L+E I+++
Sbjct: 7 KNVRK-SFGSFEVLKDVNLDIEDGEFVVLL--GPSGCGKSTLLRMIAGLEEPTSGEILID 63
Query: 68 ETD 70
D
Sbjct: 64 GRD 66
>gnl|CDD|236333 PRK08691, PRK08691, DNA polymerase III subunits gamma and tau;
Validated.
Length = 709
Score = 32.8 bits (74), Expect = 0.20
Identities = 25/95 (26%), Positives = 44/95 (46%), Gaps = 3/95 (3%)
Query: 63 VIILNETDHLTREAQQALRRTMEKYITTCRLILCANSMSQVIPAIRSRCLCIRIPAPTHE 122
V I++E L++ A A+ +T+E+ + IL +V + SRCL + T +
Sbjct: 122 VYIIDEVHMLSKSAFNAMLKTLEEPPEHVKFILATTDPHKVPVTVLSRCLQFVLRNMTAQ 181
Query: 123 EIVSVLTNICKKEGLTI-PPEFAL--RLAQQSDRN 154
++ L ++ E + PP L R A S R+
Sbjct: 182 QVADHLAHVLDSEKIAYEPPALQLLGRAAAGSMRD 216
>gnl|CDD|131721 TIGR02673, FtsE, cell division ATP-binding protein FtsE. This
model describes FtsE, a member of the ABC transporter
ATP-binding protein family. This protein, and its
permease partner FtsX, localize to the division site.
In a number of species, the ftsEX gene pair is located
next to FtsY, the signal recognition particle-docking
protein [Cellular processes, Cell division].
Length = 214
Score = 32.2 bits (74), Expect = 0.23
Identities = 26/80 (32%), Positives = 33/80 (41%), Gaps = 24/80 (30%)
Query: 13 LQKLDFHCKQANHLRNLLKEGDFPHLLFYGPSGAGKKTRIMALLKELY-------GPVII 65
L + H +++G+F L GPSGAGK T LLK LY G V I
Sbjct: 18 LHDVSLH----------IRKGEF--LFLTGPSGAGKTT----LLKLLYGALTPSRGQVRI 61
Query: 66 LNE-TDHLTREAQQALRRTM 84
E + L LRR +
Sbjct: 62 AGEDVNRLRGRQLPLLRRRI 81
>gnl|CDD|227570 COG5245, DYN1, Dynein, heavy chain [Cytoskeleton].
Length = 3164
Score = 32.7 bits (74), Expect = 0.28
Identities = 23/85 (27%), Positives = 32/85 (37%), Gaps = 9/85 (10%)
Query: 18 FHCKQANHLRNLLKEGDFPHLLFYGPSGAGKKTRIM--ALLKELYGPVIILN-ETDHLTR 74
F +N N L+ ++ GP G+GK +M +L EL V N T +T
Sbjct: 1482 FVDSFSNEALNTLRS-----YIYCGPPGSGK-EMLMCPSLRSELITEVKYFNFSTCTMTP 1535
Query: 75 EAQQALRRTMEKYITTCRLILCANS 99
L R E Y T + L
Sbjct: 1536 SKLSVLERETEYYPNTGVVRLYPKP 1560
>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 = 31.0 bits (71), Expect = 0.31
Identities = 15/30 (50%), Positives = 18/30 (60%)
Query: 38 LLFYGPSGAGKKTRIMALLKELYGPVIILN 67
LL YGP G GK T A+ KEL P I ++
Sbjct: 1 LLLYGPPGTGKTTLAKAVAKELGAPFIEIS 30
>gnl|CDD|180855 PRK07132, PRK07132, DNA polymerase III subunit delta'; Validated.
Length = 299
Score = 32.0 bits (73), Expect = 0.31
Identities = 15/68 (22%), Positives = 35/68 (51%)
Query: 63 VIILNETDHLTREAQQALRRTMEKYITTCRLILCANSMSQVIPAIRSRCLCIRIPAPTHE 122
++I+ + + AL +T+E+ +L ++++V+P I SRC + P +
Sbjct: 93 ILIIKNIEKTSNSLLNALLKTIEEPPKDTYFLLTTKNINKVLPTIVSRCQVFNVKEPDQQ 152
Query: 123 EIVSVLTN 130
+I++ L +
Sbjct: 153 KILAKLLS 160
>gnl|CDD|213179 cd00267, ABC_ATPase, ATP-binding cassette transporter
nucleotide-binding domain. ABC transporters are a
large family of proteins involved in the transport of a
wide variety of different compounds, like sugars, ions,
peptides, and more complex organic molecules. The
nucleotide-binding domain shows the highest similarity
between all members of the family. ABC transporters are
a subset of nucleotide hydrolases that contain a
signature motif, Q-loop, and H-loop/switch region, in
addition to, the Walker A motif/P-loop and Walker B
motif commonly found in a number of ATP- and
GTP-binding and hydrolyzing proteins.
Length = 157
Score = 31.1 bits (71), Expect = 0.37
Identities = 21/75 (28%), Positives = 35/75 (46%), Gaps = 7/75 (9%)
Query: 13 LQKLDFHCKQANHLRNL---LKEGDFPHLLFYGPSGAGKKT--RIMALLKELYGPVIILN 67
++ L F L N+ LK G+ L+ GP+G+GK T R +A L + I+++
Sbjct: 2 IENLSFRYGGRTALDNVSLTLKAGEIVALV--GPNGSGKSTLLRAIAGLLKPTSGEILID 59
Query: 68 ETDHLTREAQQALRR 82
D ++ RR
Sbjct: 60 GKDIAKLPLEELRRR 74
>gnl|CDD|238540 cd01120, RecA-like_NTPases, RecA-like NTPases. This family
includes the NTP binding domain of F1 and V1 H+ATPases,
DnaB and related helicases as well as bacterial RecA
and related eukaryotic and archaeal recombinases. This
group also includes bacterial conjugation proteins and
related DNA transfer proteins involved in type II and
type IV secretion.
Length = 165
Score = 30.9 bits (70), Expect = 0.39
Identities = 12/52 (23%), Positives = 22/52 (42%), Gaps = 2/52 (3%)
Query: 37 HLLFYGPSGAGKKTRIMALLKE--LYGPVIILNETDHLTREAQQALRRTMEK 86
+L +GP+G+GK T + L G ++ + + E + L K
Sbjct: 1 LILVFGPTGSGKTTLALQLALNIATKGGKVVYVDIEEEIEELTERLIGESLK 52
>gnl|CDD|237871 PRK14965, PRK14965, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 576
Score = 31.6 bits (72), Expect = 0.46
Identities = 30/101 (29%), Positives = 49/101 (48%), Gaps = 8/101 (7%)
Query: 63 VIILNETDHLTREAQQALRRTMEKYITTCRLILCANSMSQVIPAIRSRCLCI---RIPAP 119
+ I++E L+ A AL +T+E+ + I +V I SRC RIP
Sbjct: 122 IFIIDEVHMLSTNAFNALLKTLEEPPPHVKFIFATTEPHKVPITILSRCQRFDFRRIPLQ 181
Query: 120 THEEIVSVLTNICKKEGLTIPPEFALRL-AQQSDRNLRRAI 159
+IV L I +EG++I AL L A++ D ++R ++
Sbjct: 182 ---KIVDRLRYIADQEGISISDA-ALALVARKGDGSMRDSL 218
Score = 29.7 bits (67), Expect = 2.1
Identities = 18/51 (35%), Positives = 23/51 (45%), Gaps = 3/51 (5%)
Query: 7 KYRPNNLQKLDFHCKQANHLRNLLKEGDFPH-LLFYGPSGAGKKT--RIMA 54
KYRP L + L+N + G H LF G G GK + RI+A
Sbjct: 9 KYRPQTFSDLTGQEHVSRTLQNAIDTGRVAHAFLFTGARGVGKTSTARILA 59
>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 = 31.1 bits (71), Expect = 0.49
Identities = 21/60 (35%), Positives = 31/60 (51%), Gaps = 6/60 (10%)
Query: 6 DKYRPN-NLQKLDFHCKQANHLRNLLKEGDFPH--LLFYGPSGAGKKTRIMALLKELYGP 62
DK +L+KL + R LL++ PH +L GP+G+GK T + + L EL P
Sbjct: 51 DKKNQILDLEKLGLKPENLEIFRKLLEK---PHGIILVTGPTGSGKTTTLYSALSELNTP 107
>gnl|CDD|222104 pfam13401, AAA_22, AAA domain.
Length = 124
Score = 30.3 bits (69), Expect = 0.52
Identities = 14/46 (30%), Positives = 24/46 (52%)
Query: 51 RIMALLKELYGPVIILNETDHLTREAQQALRRTMEKYITTCRLILC 96
I+ LK P++I++E HL+ EA + LR + ++IL
Sbjct: 70 AILDALKRRGRPLLIIDEAQHLSLEALEELRDLYDLSEKGIQVILV 115
Score = 27.2 bits (61), Expect = 5.8
Identities = 8/30 (26%), Positives = 15/30 (50%)
Query: 37 HLLFYGPSGAGKKTRIMALLKELYGPVIIL 66
+ G SG+GK T + L ++L ++
Sbjct: 6 IGVLTGESGSGKTTLLRRLARQLPNRRVVY 35
>gnl|CDD|184922 PRK14958, PRK14958, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 509
Score = 31.6 bits (71), Expect = 0.55
Identities = 38/182 (20%), Positives = 74/182 (40%), Gaps = 20/182 (10%)
Query: 20 CKQANHLRNLLKEGDFPHLLFYGPSGAGKKTRIMALLKEL-YGP------VIILNETDHL 72
C + R + EG FP L + K LL + Y P V +++E L
Sbjct: 73 CNDCENCREI-DEGRFPDLFEVDAASRTKVEDTRELLDNIPYAPTKGRFKVYLIDEVHML 131
Query: 73 TREAQQALRRTMEKYITTCRLILCANSMSQVIPAIRSRCLCIRIPAPTHEEIVSVLTNIC 132
+ + AL +T+E+ + + IL ++ + SRCL + +I + ++
Sbjct: 132 SGHSFNALLKTLEEPPSHVKFILATTDHHKLPVTVLSRCLQFHLAQLPPLQIAAHCQHLL 191
Query: 133 KKEGLTIPPEFALRLAQQSDRNLRRAILMCEASKVQQYPFQIDQQIVEPDWKIYIRDTAK 192
K+E + LA+ ++ ++R A+ + +DQ I + K+ I D
Sbjct: 192 KEENVEFENAALDLLARAANGSVRDALSL------------LDQSIAYGNGKVLIADVKT 239
Query: 193 LI 194
++
Sbjct: 240 ML 241
>gnl|CDD|213216 cd03249, ABC_MTABC3_MDL1_MDL2, ATP-binding cassette domain of a
mitochondrial protein MTABC3 and related proteins.
MTABC3 (also known as ABCB6) is a mitochondrial
ATP-binding cassette protein involved in iron
homeostasis and one of four ABC transporters expressed
in the mitochondrial inner membrane, the other three
being MDL1(ABC7), MDL2, and ATM1. In fact, the yeast
MDL1 (multidrug resistance-like protein 1) and MDL2
(multidrug resistance-like protein 2) transporters are
also included in this CD. MDL1 is an ATP-dependent
permease that acts as a high-copy suppressor of ATM1
and is thought to have a role in resistance to
oxidative stress. Interestingly, subfamily B is more
closely related to the carboxyl-terminal component of
subfamily C than the two halves of ABCC molecules are
with one another.
Length = 238
Score = 31.0 bits (71), Expect = 0.60
Identities = 15/48 (31%), Positives = 24/48 (50%), Gaps = 9/48 (18%)
Query: 26 LRNL---LKEGDFPHLLFYGPSGAGKKTRIMALLKELYGPV---IILN 67
L+ L + G + G SG GK T +++LL+ Y P I+L+
Sbjct: 19 LKGLSLTIPPGKT--VALVGSSGCGKST-VVSLLERFYDPTSGEILLD 63
>gnl|CDD|225164 COG2255, RuvB, Holliday junction resolvasome, helicase subunit
[DNA replication, recombination, and repair].
Length = 332
Score = 31.0 bits (71), Expect = 0.66
Identities = 10/20 (50%), Positives = 13/20 (65%), Gaps = 2/20 (10%)
Query: 37 HLLFYGPSGAGKKT--RIMA 54
H+L +GP G GK T I+A
Sbjct: 54 HVLLFGPPGLGKTTLAHIIA 73
>gnl|CDD|225363 COG2804, PulE, Type II secretory pathway, ATPase PulE/Tfp pilus
assembly pathway, ATPase PilB [Cell motility and
secretion / Intracellular trafficking and secretion].
Length = 500
Score = 31.1 bits (71), Expect = 0.68
Identities = 19/50 (38%), Positives = 25/50 (50%), Gaps = 5/50 (10%)
Query: 12 NLQKLDFHCKQANHLRNLLKEGDFPH--LLFYGPSGAGKKTRIMALLKEL 59
+L+KL Q L LL P +L GP+G+GK T + A L EL
Sbjct: 236 DLEKLGMSPFQLARLLRLLNR---PQGLILVTGPTGSGKTTTLYAALSEL 282
>gnl|CDD|237868 PRK14960, PRK14960, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 702
Score = 31.2 bits (70), Expect = 0.70
Identities = 21/97 (21%), Positives = 45/97 (46%)
Query: 63 VIILNETDHLTREAQQALRRTMEKYITTCRLILCANSMSQVIPAIRSRCLCIRIPAPTHE 122
V +++E L+ + AL +T+E+ + + ++ + SRCL + +
Sbjct: 121 VYLIDEVHMLSTHSFNALLKTLEEPPEHVKFLFATTDPQKLPITVISRCLQFTLRPLAVD 180
Query: 123 EIVSVLTNICKKEGLTIPPEFALRLAQQSDRNLRRAI 159
EI L I +KE + + ++A+ + +LR A+
Sbjct: 181 EITKHLGAILEKEQIAADQDAIWQIAESAQGSLRDAL 217
>gnl|CDD|224048 COG1123, COG1123, ATPase components of various ABC-type transport
systems, contain duplicated ATPase [General function
prediction only].
Length = 539
Score = 31.0 bits (71), Expect = 0.71
Identities = 18/46 (39%), Positives = 24/46 (52%), Gaps = 3/46 (6%)
Query: 42 GPSGAGKKT--RIMA-LLKELYGPVIILNETDHLTREAQQALRRTM 84
G SG+GK T RI+A LL G +I + LT + LRR +
Sbjct: 324 GESGSGKSTLARILAGLLPPSSGSIIFDGQDLDLTGGELRRLRRRI 369
>gnl|CDD|235943 PRK07133, PRK07133, DNA polymerase III subunits gamma and tau;
Validated.
Length = 725
Score = 30.9 bits (70), Expect = 0.75
Identities = 31/105 (29%), Positives = 51/105 (48%), Gaps = 8/105 (7%)
Query: 63 VIILNETDHLTREAQQALRRTME---KYITTCRLILCANSMSQVIP-AIRSRCLCIRIPA 118
+ I++E L++ A AL +T+E K++ IL A + IP I SR
Sbjct: 121 IYIIDEVHMLSKSAFNALLKTLEEPPKHVI---FIL-ATTEVHKIPLTILSRVQRFNFRR 176
Query: 119 PTHEEIVSVLTNICKKEGLTIPPEFALRLAQQSDRNLRRAILMCE 163
+ +EIVS L I +KE ++ +A+ S +LR A+ + E
Sbjct: 177 ISEDEIVSRLEFILEKENISYEKNALKLIAKLSSGSLRDALSIAE 221
Score = 27.5 bits (61), Expect = 9.9
Identities = 18/58 (31%), Positives = 25/58 (43%), Gaps = 11/58 (18%)
Query: 4 WVDKYRPNNLQKLDFHCKQANH----LRNLLKEGDFPH-LLFYGPSGAGKKT--RIMA 54
KYRP + +H L+N++K H LF GP G GK + +I A
Sbjct: 8 LYRKYRPKTFDDI----VGQDHIVQTLKNIIKSNKISHAYLFSGPRGTGKTSVAKIFA 61
>gnl|CDD|213259 cd03292, ABC_FtsE_transporter, ATP-binding cassette domain of the
cell division transporter. FtsE is a hydrophilic
nucleotide-binding protein that binds FtsX to form a
heterodimeric ATP-binding cassette (ABC)-type
transporter that associates with the bacterial inner
membrane. The FtsE/X transporter is thought to be
involved in cell division and is important for assembly
or stability of the septal ring.
Length = 214
Score = 30.5 bits (69), Expect = 0.75
Identities = 24/83 (28%), Positives = 35/83 (42%), Gaps = 6/83 (7%)
Query: 30 LKEGDFPHLLFYGPSGAGKKTRIMALLKELY---GPVIILN-ETDHLTREAQQALRRTME 85
+ G+F L+ GPSGAGK T + + KE G + + + L A LRR +
Sbjct: 24 ISAGEFVFLV--GPSGAGKSTLLKLIYKEELPTSGTIRVNGQDVSDLRGRAIPYLRRKIG 81
Query: 86 KYITTCRLILCANSMSQVIPAIR 108
RL+ N V A+
Sbjct: 82 VVFQDFRLLPDRNVYENVAFALE 104
>gnl|CDD|102059 PRK05917, PRK05917, DNA polymerase III subunit delta'; Validated.
Length = 290
Score = 30.5 bits (69), Expect = 0.76
Identities = 25/92 (27%), Positives = 40/92 (43%), Gaps = 10/92 (10%)
Query: 36 PHLLFYGPSGAGK----------KTRIMALLKELYGPVIILNETDHLTREAQQALRRTME 85
P + + P G G+ K +I E + I++E D +T +A A + +E
Sbjct: 61 PDIHEFSPQGKGRLHSIETPRAIKKQIWIHPYESPYKIYIIHEADRMTLDAISAFLKVLE 120
Query: 86 KYITTCRLILCANSMSQVIPAIRSRCLCIRIP 117
+IL + ++ P IRSR L I IP
Sbjct: 121 DPPQHGVIILTSAKPQRLPPTIRSRSLSIHIP 152
>gnl|CDD|235505 PRK05563, PRK05563, DNA polymerase III subunits gamma and tau;
Validated.
Length = 559
Score = 31.0 bits (71), Expect = 0.83
Identities = 25/63 (39%), Positives = 32/63 (50%), Gaps = 9/63 (14%)
Query: 102 QVIPA-IRSRCLCI---RIPAPTHEEIVSVLTNICKKEGLTIPPEFALRL-AQQSDRNLR 156
IPA I SRC RI E+IV L I KEG+ E ALRL A+ ++ +R
Sbjct: 160 HKIPATILSRCQRFDFKRISV---EDIVERLKYILDKEGIEYEDE-ALRLIARAAEGGMR 215
Query: 157 RAI 159
A+
Sbjct: 216 DAL 218
>gnl|CDD|213192 cd03225, ABC_cobalt_CbiO_domain1, First domain of the ATP-binding
cassette component of cobalt transport system. Domain
I of the ABC component of a cobalt transport family
found in bacteria, archaea, and eukaryota. The
transition metal cobalt is an essential component of
many enzymes and must be transported into cells in
appropriate amounts when needed. This ABC transport
system of the CbiMNQO family is involved in cobalt
transport in association with the cobalamin (vitamin
B12) biosynthetic pathways. Most of cobalt (Cbi)
transport systems possess a separate CbiN component,
the cobalt-binding periplasmic protein, and they are
encoded by the conserved gene cluster cbiMNQO. Both the
CbiM and CbiQ proteins are integral cytoplasmic
membrane proteins, and the CbiO protein has the linker
peptide and the Walker A and B motifs commonly found in
the ATPase components of the ABC-type transport
systems.
Length = 211
Score = 30.1 bits (69), Expect = 0.91
Identities = 16/49 (32%), Positives = 29/49 (59%), Gaps = 8/49 (16%)
Query: 26 LRNL---LKEGDFPHLLFYGPSGAGKKT--RIMA-LLKELYGPVIILNE 68
L ++ +K+G+F +L GP+G+GK T R++ LL G V++ +
Sbjct: 17 LDDISLTIKKGEF--VLIVGPNGSGKSTLLRLLNGLLGPTSGEVLVDGK 63
>gnl|CDD|234619 PRK00080, ruvB, Holliday junction DNA helicase RuvB; Reviewed.
Length = 328
Score = 30.5 bits (70), Expect = 0.93
Identities = 14/37 (37%), Positives = 18/37 (48%), Gaps = 11/37 (29%)
Query: 37 HLLFYGPSGAGKKT--RIMALLKEL-------YGPVI 64
H+L YGP G GK T I+A E+ GP +
Sbjct: 53 HVLLYGPPGLGKTTLANIIA--NEMGVNIRITSGPAL 87
>gnl|CDD|184921 PRK14957, PRK14957, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 546
Score = 30.8 bits (69), Expect = 0.93
Identities = 22/97 (22%), Positives = 46/97 (47%)
Query: 63 VIILNETDHLTREAQQALRRTMEKYITTCRLILCANSMSQVIPAIRSRCLCIRIPAPTHE 122
V +++E L++++ AL +T+E+ + IL ++ I SRC+ + + +
Sbjct: 122 VYLIDEVHMLSKQSFNALLKTLEEPPEYVKFILATTDYHKIPVTILSRCIQLHLKHISQA 181
Query: 123 EIVSVLTNICKKEGLTIPPEFALRLAQQSDRNLRRAI 159
+I L I KE + + +A + +LR A+
Sbjct: 182 DIKDQLKIILAKENINSDEQSLEYIAYHAKGSLRDAL 218
>gnl|CDD|131585 TIGR02533, type_II_gspE, type II secretion system protein E. This
family describes GspE, the E protein of the type II
secretion system, also called the main terminal branch
of the general secretion pathway. This model separates
GspE from the PilB protein of type IV pilin biosynthesis
[Protein fate, Protein and peptide secretion and
trafficking, Cellular processes, Pathogenesis].
Length = 486
Score = 30.8 bits (70), Expect = 0.96
Identities = 15/50 (30%), Positives = 25/50 (50%), Gaps = 5/50 (10%)
Query: 12 NLQKLDFHCKQANHLRNLLKEGDFPH--LLFYGPSGAGKKTRIMALLKEL 59
+L+ L + + L++ PH +L GP+G+GK T + A L L
Sbjct: 220 DLETLGMSPELLSRFERLIRR---PHGIILVTGPTGSGKTTTLYAALSRL 266
>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 = 29.7 bits (68), Expect = 1.2
Identities = 12/35 (34%), Positives = 16/35 (45%), Gaps = 7/35 (20%)
Query: 37 HLLFYGPSGAGKKTRIMALLKEL-------YGPVI 64
H+L YGP G GK T + E+ GP +
Sbjct: 52 HVLLYGPPGLGKTTLANIIANEMGVNIRITSGPAL 86
>gnl|CDD|236274 PRK08485, PRK08485, DNA polymerase III subunit delta'; Validated.
Length = 206
Score = 29.6 bits (67), Expect = 1.3
Identities = 14/40 (35%), Positives = 22/40 (55%)
Query: 75 EAQQALRRTMEKYITTCRLILCANSMSQVIPAIRSRCLCI 114
EAQ AL + +E+ I+ A S + ++P IRSR +
Sbjct: 69 EAQNALLKILEEPPKNICFIIVAKSKNLLLPTIRSRLIIE 108
>gnl|CDD|237039 PRK12288, PRK12288, GTPase RsgA; Reviewed.
Length = 347
Score = 30.2 bits (69), Expect = 1.4
Identities = 8/26 (30%), Positives = 15/26 (57%)
Query: 62 PVIILNETDHLTREAQQALRRTMEKY 87
P+I+LN+ D L E + + ++ Y
Sbjct: 153 PLIVLNKIDLLDDEGRAFVNEQLDIY 178
>gnl|CDD|217088 pfam02534, T4SS-DNA_transf, Type IV secretory system Conjugative
DNA transfer. These proteins contain a P-loop and
walker-B site for nucleotide binding. TraG is essential
for DNA transfer in bacterial conjugation. These
proteins are thought to mediate interactions between
the DNA-processing (Dtr) and the mating pair formation
(Mpf) systems. The C-terminus of this domain interacts
with the relaxosome component TraM via the latter's
tetramerisation domain. TraD is a hexameric ring ATPase
that forms the cytoplasmic face of the conjugative
pore. The family contains a number of different DNA
transfer proteins.
Length = 468
Score = 30.1 bits (68), Expect = 1.5
Identities = 13/43 (30%), Positives = 21/43 (48%), Gaps = 2/43 (4%)
Query: 8 YRPN-NLQKLDFHCKQANHLRNLL-KEGDFPHLLFYGPSGAGK 48
R N + + A + LL +GDF H+L + +G+GK
Sbjct: 15 TRENTIIGDVYTKDPDAWYAGGLLNTDGDFSHVLVFAGTGSGK 57
>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 = 30.0 bits (68), Expect = 1.5
Identities = 18/59 (30%), Positives = 28/59 (47%), Gaps = 1/59 (1%)
Query: 110 RCLCIRIPAPTHEEIVSVLTNICKKEGLTIPPEFALRLAQ-QSDRNLRRAILMCEASKV 167
R L I T EEI +L ++EG+ I E LA+ + +LR AI + + +
Sbjct: 336 RLLIITTEPYTREEIKQILEIRAQEEGVEISEEALDLLAKIGEETSLRYAIQLLTPASI 394
>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 = 29.1 bits (65), Expect = 1.5
Identities = 14/43 (32%), Positives = 22/43 (51%), Gaps = 3/43 (6%)
Query: 21 KQANHLRNLLK---EGDFPHLLFYGPSGAGKKTRIMALLKELY 60
++ L + L+ G P +L GPSG GK + + LL+ L
Sbjct: 7 EELERLLDALRRARSGGPPSVLLTGPSGTGKTSLLRELLEGLL 49
>gnl|CDD|205733 pfam13555, AAA_29, P-loop containing region of AAA domain.
Length = 60
Score = 27.1 bits (61), Expect = 1.8
Identities = 11/24 (45%), Positives = 13/24 (54%)
Query: 39 LFYGPSGAGKKTRIMALLKELYGP 62
L GPSG+GK T I A+ L
Sbjct: 25 LLTGPSGSGKSTLIDAIQTLLVPA 48
>gnl|CDD|226648 COG4185, COG4185, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 187
Score = 29.0 bits (65), Expect = 1.9
Identities = 10/35 (28%), Positives = 18/35 (51%), Gaps = 1/35 (2%)
Query: 38 LLFYGPSGAGKKTRIMALLKELYGPVIILNETDHL 72
+ GP+G+GK T + L L ++ +N D +
Sbjct: 5 DIVAGPNGSGKSTVYASTLAPLLPGIVFVN-ADEI 38
>gnl|CDD|213188 cd03221, ABCF_EF-3, ATP-binding cassette domain of elongation
factor 3, subfamily F. Elongation factor 3 (EF-3) is a
cytosolic protein required by fungal ribosomes for in
vitro protein synthesis and for in vivo growth. EF-3
stimulates the binding of the EF-1: GTP: aa-tRNA ternary
complex to the ribosomal A site by facilitated release
of the deacylated tRNA from the E site. The reaction
requires ATP hydrolysis. EF-3 contains two ATP
nucleotide binding sequence (NBS) motifs. NBSI is
sufficient for the intrinsic ATPase activity. NBSII is
essential for the ribosome-stimulated functions.
Length = 144
Score = 28.6 bits (65), Expect = 1.9
Identities = 19/56 (33%), Positives = 31/56 (55%), Gaps = 10/56 (17%)
Query: 35 FPHLLFYGPSGAGKKTRIMALLKELYGP--VIILNE-TDHLTREAQQALRRTMEKY 87
F L SG G+K R+ L K L +++L+E T+HL E+ +AL +++Y
Sbjct: 68 FEQL-----SG-GEKMRLA-LAKLLLENPNLLLLDEPTNHLDLESIEALEEALKEY 116
>gnl|CDD|213222 cd03255, ABC_MJ0796_LolCDE_FtsE, ATP-binding cassette domain of
the transporters involved in export of lipoprotein and
macrolide, and cell division protein. This family is
comprised of MJ0796 ATP-binding cassette,
macrolide-specific ABC-type efflux carrier (MacAB), and
proteins involved in cell division (FtsE), and release
of lipoproteins from the cytoplasmic membrane (LolCDE).
They are clustered together phylogenetically. MacAB is
an exporter that confers resistance to macrolides,
while the LolCDE system is not a transporter at all. An
FtsE null mutants showed filamentous growth and
appeared viable on high salt medium only, indicating a
role for FtsE in cell division and/or salt transport.
The LolCDE complex catalyzes the release of
lipoproteins from the cytoplasmic membrane prior to
their targeting to the outer membrane.
Length = 218
Score = 29.4 bits (67), Expect = 1.9
Identities = 17/57 (29%), Positives = 28/57 (49%), Gaps = 6/57 (10%)
Query: 30 LKEGDFPHLLFYGPSGAGKKT--RIMALLKELY-GPVIILN-ETDHLTREAQQALRR 82
+++G+F + GPSG+GK T I+ L G V + + L+ + A RR
Sbjct: 27 IEKGEF--VAIVGPSGSGKSTLLNILGGLDRPTSGEVRVDGTDISKLSEKELAAFRR 81
>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 = 29.0 bits (66), Expect = 2.0
Identities = 10/26 (38%), Positives = 14/26 (53%), Gaps = 3/26 (11%)
Query: 37 HLLFYGPSGAGKKT---RIMALLKEL 59
+LL GP G+GK R+ +L L
Sbjct: 24 NLLMIGPPGSGKTMLAKRLPGILPPL 49
>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 = 29.6 bits (67), Expect = 2.0
Identities = 12/20 (60%), Positives = 13/20 (65%), Gaps = 2/20 (10%)
Query: 37 HLLFYGPSGAGKKT--RIMA 54
HLL YGP G GK T I+A
Sbjct: 32 HLLLYGPPGLGKTTLAHIIA 51
>gnl|CDD|110723 pfam01745, IPT, Isopentenyl transferase. Isopentenyl transferase /
dimethylallyl transferase synthesises
isopentenyladensosine 5'-monophosphate, a cytokinin that
induces shoot formation on host plants infected with the
Ti plasmid.
Length = 232
Score = 29.3 bits (66), Expect = 2.0
Identities = 23/102 (22%), Positives = 46/102 (45%), Gaps = 12/102 (11%)
Query: 39 LFYGPSGAGKKTRIMALLKELYGPVIILNETDHLTREAQQALRRTMEKYITTCRLILCAN 98
L +G + GK +AL KE PVI+L+ ++ A + R + T R+ L
Sbjct: 5 LIWGATCTGKTAEAIALAKETGWPVIVLDRVQCCSQLATGSGRPLPAELQGTRRIYLDNR 64
Query: 99 SMSQ-VIPAIRSRCLCIRIPAPTHEEIVSVLTNICKKEGLTI 139
+S+ +I A + H+ +++ +T+ + G+ +
Sbjct: 65 PLSEGIIDAEEA-----------HDRLIAEVTSHKDEGGVIL 95
>gnl|CDD|215414 PLN02772, PLN02772, guanylate kinase.
Length = 398
Score = 29.4 bits (66), Expect = 2.0
Identities = 19/45 (42%), Positives = 21/45 (46%), Gaps = 7/45 (15%)
Query: 42 GPSGAGKKTRIMALLKELYGPVIILNETDHLTREAQQALRRTMEK 86
GPSG GK T I L+KE P + H TR R MEK
Sbjct: 142 GPSGVGKGTLISMLMKEF--PSMFGFSVSHTTRAP-----REMEK 179
>gnl|CDD|223786 COG0714, COG0714, MoxR-like ATPases [General function prediction
only].
Length = 329
Score = 29.3 bits (66), Expect = 2.0
Identities = 13/39 (33%), Positives = 17/39 (43%)
Query: 37 HLLFYGPSGAGKKTRIMALLKELYGPVIILNETDHLTRE 75
H+L GP G GK AL + L P + + T L
Sbjct: 45 HVLLEGPPGVGKTLLARALARALGLPFVRIQCTPDLLPS 83
>gnl|CDD|237354 PRK13341, PRK13341, recombination factor protein RarA/unknown
domain fusion protein; Reviewed.
Length = 725
Score = 29.6 bits (67), Expect = 2.1
Identities = 14/31 (45%), Positives = 17/31 (54%), Gaps = 2/31 (6%)
Query: 26 LRNLLKEGDFPHLLFYGPSGAGKKT--RIMA 54
LR +K L+ YGP G GK T RI+A
Sbjct: 43 LRRAIKADRVGSLILYGPPGVGKTTLARIIA 73
>gnl|CDD|227321 COG4988, CydD, ABC-type transport system involved in cytochrome bd
biosynthesis, ATPase and permease components [Energy
production and conversion / Posttranslational
modification, protein turnover, chaperones].
Length = 559
Score = 29.5 bits (67), Expect = 2.1
Identities = 16/45 (35%), Positives = 22/45 (48%), Gaps = 3/45 (6%)
Query: 42 GPSGAGKKTRIMALLKEL--YGPVIILNETDHLTREAQQALRRTM 84
G SGAGK T + LL L I +N D L + +A R+ +
Sbjct: 354 GASGAGKSTLLNLLLGFLAPTQGEIRVNGID-LRDLSPEAWRKQI 397
>gnl|CDD|188353 TIGR03608, L_ocin_972_ABC, putative bacteriocin export ABC
transporter, lactococcin 972 group. A gene pair with a
fairly wide distribution consists of a polypeptide
related to the lactococcin 972 (see TIGR01653) and
multiple-membrane-spanning putative immunity protein
(see TIGR01654). This model represents a small clade
within the ABC transporters that regularly are found
adjacent to these bacteriocin system gene pairs and are
likely serve as export proteins [Cellular processes,
Toxin production and resistance, Transport and binding
proteins, Unknown substrate].
Length = 206
Score = 29.1 bits (66), Expect = 2.2
Identities = 19/72 (26%), Positives = 33/72 (45%), Gaps = 6/72 (8%)
Query: 12 NLQKLDFHCKQANHLRNL-LKEGDFPHLLFYGPSGAGKKT--RIMALLKELYGPVIILNE 68
N+ K F K NL +++G + G SG+GK T I+ LL++ + LN
Sbjct: 3 NISK-KFGDKVILDDLNLTIEKGKMYAI--IGESGSGKSTLLNIIGLLEKFDSGQVYLNG 59
Query: 69 TDHLTREAQQAL 80
+ +++A
Sbjct: 60 QETPPLNSKKAS 71
>gnl|CDD|224051 COG1126, GlnQ, ABC-type polar amino acid transport system, ATPase
component [Amino acid transport and metabolism].
Length = 240
Score = 29.0 bits (66), Expect = 2.2
Identities = 15/45 (33%), Positives = 23/45 (51%), Gaps = 2/45 (4%)
Query: 42 GPSGAGKKT--RIMALLKELYGPVIILNETDHLTREAQQALRRTM 84
GPSG+GK T R + L+E I ++ D ++ LRR +
Sbjct: 35 GPSGSGKSTLLRCLNGLEEPDSGSITVDGEDVGDKKDILKLRRKV 79
>gnl|CDD|213226 cd03259, ABC_Carb_Solutes_like, ATP-binding cassette domain of
the carbohydrate and solute transporters-like. This
family is comprised of proteins involved in the
transport of apparently unrelated solutes and proteins
specific for di- and oligosaccharides and polyols. ABC
transporters are a large family of proteins involved in
the transport of a wide variety of different compounds,
like sugars, ions, peptides and more complex organic
molecules. The nucleotide-binding domain shows the
highest similarity between all members of the family.
ABC transporters are a subset of nucleotide hydrolases
that contain a signature motif, Q-loop, and
H-loop/switch region, in addition to, the Walker A
motif/P-loop and Walker B motif commonly found in a
number of ATP- and GTP-binding and hydrolyzing
proteins.
Length = 213
Score = 29.0 bits (66), Expect = 2.3
Identities = 18/59 (30%), Positives = 30/59 (50%), Gaps = 7/59 (11%)
Query: 25 HLRNL---LKEGDFPHLLFYGPSGAGKKT--RIMALLKELYGPVIILNETDHLTREAQQ 78
L +L ++ G+F LL GPSG GK T R++A L+ I+++ D ++
Sbjct: 15 ALDDLSLTVEPGEFLALL--GPSGCGKTTLLRLIAGLERPDSGEILIDGRDVTGVPPER 71
>gnl|CDD|181214 PRK08058, PRK08058, DNA polymerase III subunit delta'; Validated.
Length = 329
Score = 29.1 bits (66), Expect = 2.3
Identities = 16/56 (28%), Positives = 23/56 (41%), Gaps = 6/56 (10%)
Query: 94 ILCANSMSQVIPAIRSRCLCIRIPAPTHEEIVSVLTNICKKEGLTIPPEFALRLAQ 149
IL + Q++P I SRC + E ++ L +EG I A LA
Sbjct: 144 ILLTENKHQILPTILSRCQVVEFRPLPPESLIQRLQ----EEG--ISESLATLLAG 193
>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 = 28.9 bits (65), Expect = 2.4
Identities = 13/41 (31%), Positives = 19/41 (46%), Gaps = 2/41 (4%)
Query: 22 QANHLRNLLKEGDFPHLLFYGPSGAGKKTRIMALLKELYGP 62
Q ++ L D L GP G GK T I+ ++K+L
Sbjct: 6 QREAIKKALSSSDI--TLIQGPPGTGKTTTIVEIIKQLLSN 44
>gnl|CDD|144046 pfam00308, Bac_DnaA, Bacterial dnaA protein.
Length = 219
Score = 28.8 bits (65), Expect = 2.4
Identities = 17/54 (31%), Positives = 27/54 (50%), Gaps = 3/54 (5%)
Query: 107 IRSRC---LCIRIPAPTHEEIVSVLTNICKKEGLTIPPEFALRLAQQSDRNLRR 157
+RSR L I I P E +++L ++E + IP E +AQ+ N+R
Sbjct: 151 LRSRFEWGLIIAIEPPDLETRLAILRKKAEEENINIPNEVLNFIAQRITDNVRE 204
>gnl|CDD|240128 cd04824, eu_ALAD_PBGS_cysteine_rich, Porphobilinogen synthase
(PBGS), which is also called delta-aminolevulinic acid
dehydratase (ALAD), catalyzes the condensation of two
5-aminolevulinic acid (ALA) molecules to form the
pyrrole porphobilinogen (PBG), which is the second step
in the biosynthesis of tetrapyrroles, such as heme,
vitamin B12 and chlorophyll. This reaction involves the
formation of a Schiff base link between the substrate
and the enzyme. PBGSs are metalloenzymes, some of which
have a second, allosteric metal binding site, beside the
metal ion binding site in their active site. Although
PBGS is a family of homologous enzymes, its metal ion
utilization at catalytic site varies between zinc and
magnesium and/or potassium. PBGS can be classified into
two groups based on differences in their active site
metal binding site. The eukaryotic PBGSs represented by
this model, which contain a cysteine-rich zinc binding
motif (DXCXCX(Y/F)X3G(H/Q)CG), require zinc for their
activity, they do not contain an additional allosteric
metal binding site and do not bind magnesium.
Length = 320
Score = 29.3 bits (66), Expect = 2.5
Identities = 19/73 (26%), Positives = 30/73 (41%), Gaps = 10/73 (13%)
Query: 25 HLRNLLKEGDFPHLLFYGPSGAGKKTRIMALLKELYGPVIILNETDHLTREAQQALRRTM 84
LR L+ +G +LF P GK R + + GPVI +A + +R
Sbjct: 56 FLRPLVAKGLRSVILFGVPLKPGKDDRSGSAADDEDGPVI----------QAIKLIREEF 105
Query: 85 EKYITTCRLILCA 97
+ + C + LC
Sbjct: 106 PELLIACDVCLCE 118
>gnl|CDD|225438 COG2884, FtsE, Predicted ATPase involved in cell division [Cell
division and chromosome partitioning].
Length = 223
Score = 28.7 bits (65), Expect = 2.6
Identities = 19/49 (38%), Positives = 25/49 (51%), Gaps = 16/49 (32%)
Query: 13 LQKLDFHCKQANHLRNLLKEGDFPHLLFYGPSGAGKKTRIMALLKELYG 61
L+ + FH + +G+F L GPSGAGK T LLK +YG
Sbjct: 18 LRDVSFH----------IPKGEFVFLT--GPSGAGKST----LLKLIYG 50
>gnl|CDD|213195 cd03228, ABCC_MRP_Like, ATP-binding cassette domain of multidrug
resistance protein-like transporters. The MRP
(Multidrug Resistance Protein)-like transporters are
involved in drug, peptide, and lipid export. They
belong to the subfamily C of the ATP-binding cassette
(ABC) superfamily of transport proteins. The ABCC
subfamily contains transporters with a diverse
functional spectrum that includes ion transport, cell
surface receptor, and toxin secretion activities. The
MRP-like family, similar to all ABC proteins, have a
common four-domain core structure constituted by two
membrane-spanning domains, each composed of six
transmembrane (TM) helices, and two nucleotide-binding
domains (NBD). ABC transporters are a subset of
nucleotide hydrolases that contain a signature motif,
Q-loop, and H-loop/switch region, in addition to, the
Walker A motif/P-loop and Walker B motif commonly found
in a number of ATP- and GTP-binding and hydrolyzing
proteins.
Length = 171
Score = 28.5 bits (65), Expect = 2.7
Identities = 17/46 (36%), Positives = 27/46 (58%), Gaps = 5/46 (10%)
Query: 42 GPSGAGKKTRIMALLKELYGP---VIILNETDHLTREAQQALRRTM 84
GPSG+GK T + LL+ LY P I+++ D L ++LR+ +
Sbjct: 35 GPSGSGKSTLLKLLLR-LYDPTSGEILIDGVD-LRDLDLESLRKNI 78
>gnl|CDD|180738 PRK06871, PRK06871, DNA polymerase III subunit delta'; Validated.
Length = 325
Score = 28.9 bits (65), Expect = 2.9
Identities = 23/85 (27%), Positives = 38/85 (44%), Gaps = 2/85 (2%)
Query: 63 VIILNETDHLTREAQQALRRTMEKYITTCRLILCANSMSQVIPAIRSRCLCIRIPAPTHE 122
V+ + + LT A AL +T+E+ +L A+ + ++P I SRC I P +
Sbjct: 110 VVYIQGAERLTEAAANALLKTLEEPRPNTYFLLQADLSAALLPTIYSRCQTWLIHPPEEQ 169
Query: 123 EIVSVLTNICKKEGLTIPPEFALRL 147
+ + L E I ALR+
Sbjct: 170 QALDWLQAQSSAEISEI--LTALRI 192
>gnl|CDD|224043 COG1118, CysA, ABC-type sulfate/molybdate transport systems,
ATPase component [Inorganic ion transport and
metabolism].
Length = 345
Score = 28.9 bits (65), Expect = 3.1
Identities = 14/45 (31%), Positives = 21/45 (46%), Gaps = 4/45 (8%)
Query: 41 YGPSGAGKKT--RIMA-LLKELYGPVIILNETDH-LTREAQQALR 81
GPSGAGK T RI+A L G + + ++ A + +
Sbjct: 34 LGPSGAGKSTLLRIIAGLETPDAGRIRLNGRVLFDVSNLAVRDRK 78
>gnl|CDD|213788 TIGR03263, guanyl_kin, guanylate kinase. Members of this family
are the enzyme guanylate kinase, also called GMP
kinase. This enzyme transfers a phosphate from ATP to
GMP, yielding ADP and GDP [Purines, pyrimidines,
nucleosides, and nucleotides, Nucleotide and nucleoside
interconversions].
Length = 179
Score = 28.2 bits (64), Expect = 3.2
Identities = 12/17 (70%), Positives = 14/17 (82%)
Query: 42 GPSGAGKKTRIMALLKE 58
GPSGAGK T + ALL+E
Sbjct: 7 GPSGAGKSTLVKALLEE 23
>gnl|CDD|213268 cd03301, ABC_MalK_N, The N-terminal ATPase domain of the maltose
transporter, MalK. ATP binding cassette (ABC) proteins
function from bacteria to human, mediating the
translocation of substances into and out of cells or
organelles. ABC transporters contain two
transmembrane-spanning domains (TMDs) or subunits and
two nucleotide binding domains (NBDs) or subunits that
couple transport to the hydrolysis of ATP. In the
maltose transport system, the periplasmic maltose
binding protein (MBP) stimulates the ATPase activity of
the membrane-associated transporter, which consists of
two transmembrane subunits, MalF and MalG, and two
copies of the ATP binding subunit, MalK, and becomes
tightly bound to the transporter in the catalytic
transition state, ensuring that maltose is passed to
the transporter as ATP is hydrolyzed.
Length = 213
Score = 28.4 bits (64), Expect = 3.2
Identities = 17/50 (34%), Positives = 27/50 (54%), Gaps = 7/50 (14%)
Query: 26 LRNL---LKEGDFPHLLFYGPSGAGKKT--RIMALLKELYGPVIILNETD 70
L +L + +G+F ++ GPSG GK T R++A L+E I + D
Sbjct: 16 LDDLNLDIADGEF--VVLLGPSGCGKTTTLRMIAGLEEPTSGRIYIGGRD 63
>gnl|CDD|234719 PRK00300, gmk, guanylate kinase; Provisional.
Length = 205
Score = 28.5 bits (65), Expect = 3.3
Identities = 11/17 (64%), Positives = 13/17 (76%)
Query: 42 GPSGAGKKTRIMALLKE 58
GPSGAGK T + ALL+
Sbjct: 12 GPSGAGKSTLVKALLER 28
>gnl|CDD|234667 PRK00149, dnaA, chromosomal replication initiation protein;
Reviewed.
Length = 401
Score = 28.9 bits (66), Expect = 3.3
Identities = 15/53 (28%), Positives = 27/53 (50%), Gaps = 3/53 (5%)
Query: 107 IRSRC---LCIRIPAPTHEEIVSVLTNICKKEGLTIPPEFALRLAQQSDRNLR 156
+RSR L + I P E +++L ++EG+ +P E +A+ N+R
Sbjct: 216 LRSRFEWGLTVDIEPPDLETRIAILKKKAEEEGIDLPDEVLEFIAKNITSNVR 268
>gnl|CDD|236523 PRK09452, potA, putrescine/spermidine ABC transporter ATPase
protein; Reviewed.
Length = 375
Score = 28.8 bits (65), Expect = 3.4
Identities = 18/51 (35%), Positives = 26/51 (50%), Gaps = 7/51 (13%)
Query: 26 LRNL---LKEGDFPHLLFYGPSGAGKKT--RIMALLKELYGPVIILNETDH 71
+ NL + G+F LL GPSG GK T R++A + I+L+ D
Sbjct: 30 ISNLDLTINNGEFLTLL--GPSGCGKTTVLRLIAGFETPDSGRIMLDGQDI 78
>gnl|CDD|233209 TIGR00958, 3a01208, Conjugate Transporter-2 (CT2) Family protein.
[Transport and binding proteins, Other].
Length = 711
Score = 28.9 bits (65), Expect = 3.5
Identities = 13/21 (61%), Positives = 16/21 (76%), Gaps = 1/21 (4%)
Query: 42 GPSGAGKKTRIMALLKELYGP 62
GPSG+GK T + ALL+ LY P
Sbjct: 514 GPSGSGKST-VAALLQNLYQP 533
>gnl|CDD|233369 TIGR01351, adk, adenylate kinase. Adenylate kinase (EC 2.7.4.3)
converts ATP + AMP to ADP + ADP, that is, uses ATP as a
phosphate donor for AMP. Most members of this family
are known or believed to be adenylate kinase. However,
some members accept other nucleotide triphosphates as
donors, may be unable to use ATP, and may fail to
complement adenylate kinase mutants. An example of a
nucleoside-triphosphate--adenylate kinase (EC 2.7.4.10)
is a GTP:AMP phosphotransferase. This family is
designated subfamily rather than equivalog for this
reason [Purines, pyrimidines, nucleosides, and
nucleotides, Nucleotide and nucleoside
interconversions].
Length = 210
Score = 28.3 bits (64), Expect = 3.5
Identities = 17/54 (31%), Positives = 24/54 (44%), Gaps = 6/54 (11%)
Query: 38 LLFYGPSGAGKKTRIMALLKELYGPVIILNETDHLTRE---AQQALRRTMEKYI 88
L+ GP G+GK T + E YG I T L R A L + ++Y+
Sbjct: 2 LVLLGPPGSGKGT-QAKRIAEKYGLPHI--STGDLLRAEIKAGTPLGKKAKEYM 52
>gnl|CDD|223562 COG0488, Uup, ATPase components of ABC transporters with duplicated
ATPase domains [General function prediction only].
Length = 530
Score = 28.8 bits (65), Expect = 3.5
Identities = 24/96 (25%), Positives = 42/96 (43%), Gaps = 28/96 (29%)
Query: 4 WVDKYRPNNLQKLDFHCKQANHLRNLLKEGDFPHLLFYGP---------SGAGKKTRIMA 54
+ + P+ ++ +R L G F F G SG G+K R++
Sbjct: 406 ELSEGFPDGDEQ---------EVRAYL--GRF---GFTGEDQEKPVGVLSG-GEKARLL- 449
Query: 55 LLKELYGP--VIILNE-TDHLTREAQQALRRTMEKY 87
L K L P +++L+E T+HL E+ +AL + +
Sbjct: 450 LAKLLLQPPNLLLLDEPTNHLDIESLEALEEALLDF 485
>gnl|CDD|237043 PRK12292, hisZ, ATP phosphoribosyltransferase regulatory subunit;
Provisional.
Length = 391
Score = 28.7 bits (65), Expect = 3.8
Identities = 17/72 (23%), Positives = 26/72 (36%), Gaps = 6/72 (8%)
Query: 13 LQKLDFHCKQANHLRNLLKEGDFPHL--LFYGPSGAGKKTRIMALLKELYGPVIILNETD 70
L+ + LR L D+ L L S + ++AL L G +L E
Sbjct: 170 LEAAGLSEELEEVLRRALANKDYVALEELVLDLSEE-LRDALLALP-RLRGGREVLEEAR 227
Query: 71 HLTR--EAQQAL 80
L ++AL
Sbjct: 228 KLLPSLPIKRAL 239
>gnl|CDD|217424 pfam03205, MobB, Molybdopterin guanine dinucleotide synthesis
protein B. This protein contains a P-loop.
Length = 126
Score = 27.7 bits (62), Expect = 3.9
Identities = 14/40 (35%), Positives = 18/40 (45%), Gaps = 5/40 (12%)
Query: 36 PHLLFYGPSGAGKKTRIMALLKEL----YGPVIILNETDH 71
P +L GP +GK T I LL L Y ++ DH
Sbjct: 1 PIVLVVGPKDSGKTTLIRKLLNYLKRRGYRVAVVK-HLDH 39
>gnl|CDD|224054 COG1131, CcmA, ABC-type multidrug transport system, ATPase
component [Defense mechanisms].
Length = 293
Score = 28.4 bits (64), Expect = 4.1
Identities = 18/56 (32%), Positives = 30/56 (53%), Gaps = 7/56 (12%)
Query: 30 LKEGDFPHLLFYGPSGAGKKT--RIMA-LLKELYGPVIILNETDHLTREAQQALRR 82
++ G+ GP+GAGK T +I+A LLK G +++L + +E + RR
Sbjct: 28 VEPGEI--FGLLGPNGAGKTTLLKILAGLLKPTSGEILVLGY--DVVKEPAKVRRR 79
>gnl|CDD|226647 COG4181, COG4181, Predicted ABC-type transport system involved in
lysophospholipase L1 biosynthesis, ATPase component
[Secondary metabolites biosynthesis, transport, and
catabolism].
Length = 228
Score = 28.1 bits (63), Expect = 4.3
Identities = 22/80 (27%), Positives = 34/80 (42%), Gaps = 9/80 (11%)
Query: 12 NLQKLDFHCKQANHLRNLLKEGDF-----PHLLFYGPSGAGKKTRIMAL--LKEL-YGPV 63
+ L Q ++LK + + GPSG+GK T + L L + G V
Sbjct: 8 EVHHLSKTVGQGEGELSILKGVELVVKRGETVAIVGPSGSGKSTLLAVLAGLDDPSSGEV 67
Query: 64 IILNETDH-LTREAQQALRR 82
+L + H L +A+ ALR
Sbjct: 68 RLLGQPLHKLDEDARAALRA 87
>gnl|CDD|226635 COG4161, ArtP, ABC-type arginine transport system, ATPase
component [Amino acid transport and metabolism].
Length = 242
Score = 28.3 bits (63), Expect = 4.3
Identities = 17/52 (32%), Positives = 27/52 (51%), Gaps = 7/52 (13%)
Query: 38 LLFYGPSGAGKKT--RIMALLK-ELYGPVIILNE----TDHLTREAQQALRR 82
L+ GPSGAGK + R++ LL+ G + I + + +A + LRR
Sbjct: 31 LVLLGPSGAGKSSLLRVLNLLEMPRSGTLNIAGNHFDFSKTPSDKAIRDLRR 82
>gnl|CDD|236382 PRK09111, PRK09111, DNA polymerase III subunits gamma and tau;
Validated.
Length = 598
Score = 28.7 bits (65), Expect = 4.3
Identities = 16/45 (35%), Positives = 23/45 (51%), Gaps = 9/45 (20%)
Query: 107 IRSRC----LCIRIPAPTHEEIVSVLTNICKKEGLTIPPEFALRL 147
+ SRC L RI A + + + L+ I KEG+ + E AL L
Sbjct: 179 VLSRCQRFDL-RRIEA---DVLAAHLSRIAAKEGVEVEDE-ALAL 218
>gnl|CDD|223540 COG0464, SpoVK, ATPases of the AAA+ class [Posttranslational
modification, protein turnover, chaperones].
Length = 494
Score = 28.6 bits (64), Expect = 4.6
Identities = 10/30 (33%), Positives = 13/30 (43%)
Query: 37 HLLFYGPSGAGKKTRIMALLKELYGPVIIL 66
+L YGP G GK A+ E I +
Sbjct: 278 GVLLYGPPGTGKTLLAKAVALESRSRFISV 307
>gnl|CDD|182893 PRK11000, PRK11000, maltose/maltodextrin transporter ATP-binding
protein; Provisional.
Length = 369
Score = 28.5 bits (64), Expect = 4.7
Identities = 16/35 (45%), Positives = 25/35 (71%), Gaps = 5/35 (14%)
Query: 28 NL-LKEGDFPHLLFYGPSGAGKKT--RIMALLKEL 59
NL + EG+F ++F GPSG GK T R++A L+++
Sbjct: 23 NLDIHEGEF--VVFVGPSGCGKSTLLRMIAGLEDI 55
>gnl|CDD|225982 COG3451, VirB4, Type IV secretory pathway, VirB4 components
[Intracellular trafficking and secretion].
Length = 796
Score = 28.5 bits (64), Expect = 4.7
Identities = 12/40 (30%), Positives = 16/40 (40%)
Query: 21 KQANHLRNLLKEGDFPHLLFYGPSGAGKKTRIMALLKELY 60
+ N D H L GP+GAGK + LL +
Sbjct: 422 DGSPFYFNFHVGEDVGHTLIIGPTGAGKTVLLSFLLAQAL 461
>gnl|CDD|213267 cd03300, ABC_PotA_N, ATP-binding cassette domain of the polyamine
transporter. PotA is an ABC-type transporter and the
ATPase component of the
spermidine/putrescine-preferential uptake system
consisting of PotA, -B, -C, and -D. PotA has two
domains with the N-terminal domain containing the
ATPase activity and the residues required for
homodimerization with PotA and heterdimerization with
PotB. ABC transporters are a large family of proteins
involved in the transport of a wide variety of
different compounds, like sugars, ions, peptides, and
more complex organic molecules. The nucleotide binding
domain shows the highest similarity between all members
of the family. ABC transporters are a subset of
nucleotide hydrolases that contain a signature motif,
Q-loop, and H-loop/switch region, in addition to, the
Walker A motif/P-loop and Walker B motif commonly found
in a number of ATP- and GTP-binding and hydrolyzing
proteins.
Length = 232
Score = 28.0 bits (63), Expect = 5.0
Identities = 15/26 (57%), Positives = 18/26 (69%), Gaps = 4/26 (15%)
Query: 31 KEGDFPHLLFYGPSGAGKKT--RIMA 54
KEG+F LL GPSG GK T R++A
Sbjct: 24 KEGEFFTLL--GPSGCGKTTLLRLIA 47
>gnl|CDD|221983 pfam13207, AAA_17, AAA domain.
Length = 114
Score = 27.3 bits (60), Expect = 5.1
Identities = 22/103 (21%), Positives = 34/103 (33%), Gaps = 9/103 (8%)
Query: 39 LFYGPSGAGKKTRIMALLKELYGPVIILNETDHLTREAQQALRRTMEKYITTCR------ 92
L GP G+G K+ + L E G +I D L RE A E
Sbjct: 3 LITGPPGSG-KSTLAKKLAEKLGIPVI--SLDDLLREEGLAELDDGELDDIDIDLELLEE 59
Query: 93 LILCANSMSQVIPAIRSRCLCIRIPAPTHEEIVSVLTNICKKE 135
++ VI +R L +R+ + + C+
Sbjct: 60 ILDELAKQEWVIDGVRESTLELRLEEADLVVFLDLPLPACRFR 102
>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 = 28.3 bits (63), Expect = 5.1
Identities = 11/33 (33%), Positives = 15/33 (45%)
Query: 37 HLLFYGPSGAGKKTRIMALLKELYGPVIILNET 69
H+LF GP G GK T + K G ++
Sbjct: 314 HMLFAGPPGTGKTTIARVVAKIYCGLGVLRKPL 346
>gnl|CDD|218381 pfam05011, DBR1, Lariat debranching enzyme, C-terminal domain.
This presumed domain is found at the C-terminus of
lariat debranching enzyme. This domain is always found
in association with pfam00149.
Length = 147
Score = 27.7 bits (62), Expect = 5.1
Identities = 12/23 (52%), Positives = 12/23 (52%)
Query: 122 EEIVSVLTNICKKEGLTIPPEFA 144
EE V NI KK LTIP F
Sbjct: 85 EEREWVEENIVKKGKLTIPENFV 107
>gnl|CDD|221803 pfam12846, AAA_10, AAA-like domain. This family of domains
contain a P-loop motif that is characteristic of the
AAA superfamily. Many of the proteins in this family
are conjugative transfer proteins.
Length = 316
Score = 28.2 bits (63), Expect = 5.2
Identities = 12/34 (35%), Positives = 18/34 (52%), Gaps = 4/34 (11%)
Query: 36 PHLLFYGPSGAGK----KTRIMALLKELYGPVII 65
P++L GPSG+GK K + LL ++I
Sbjct: 2 PNMLIVGPSGSGKSTLLKLLALRLLARGGRVIVI 35
>gnl|CDD|216586 pfam01583, APS_kinase, Adenylylsulphate kinase. Enzyme that
catalyzes the phosphorylation of adenylylsulphate to
3'-phosphoadenylylsulfate. This domain contains an ATP
binding P-loop motif.
Length = 157
Score = 27.6 bits (62), Expect = 5.3
Identities = 10/23 (43%), Positives = 15/23 (65%)
Query: 38 LLFYGPSGAGKKTRIMALLKELY 60
+ F G SG+GK T AL ++L+
Sbjct: 5 IWFTGLSGSGKSTIANALERKLF 27
>gnl|CDD|150276 pfam09547, Spore_IV_A, Stage IV sporulation protein A (spore_IV_A).
SpoIVA is designated stage IV sporulation protein A. It
acts in the mother cell compartment and plays a role in
spore coat morphogenesis. A comparative genome analysis
of all sequenced genomes of Firmicutes shows that the
proteins are strictly conserved among the sub-set of
endospore-forming species.
Length = 492
Score = 28.3 bits (64), Expect = 5.4
Identities = 16/49 (32%), Positives = 23/49 (46%), Gaps = 1/49 (2%)
Query: 51 RIMALLKELYGPVIILNETDHLTREAQQALRRTM-EKYITTCRLILCAN 98
R++ LKE+ P IIL + E + LR + EKY + CA
Sbjct: 171 RVIEELKEIGKPFIILLNSQRPYSEETKELRDELEEKYDVPVLPVNCAQ 219
>gnl|CDD|213266 cd03299, ABC_ModC_like, ATP-binding cassette domain similar to
the molybdate transporter. Archaeal protein closely
related to ModC. ModC is an ABC-type transporter and
the ATPase component of a molybdate transport system
that also includes the periplasmic binding protein ModA
and the membrane protein ModB. ABC transporters are a
large family of proteins involved in the transport of a
wide variety of different compounds, like sugars, ions,
peptides, and more complex organic molecules. The
nucleotide binding domain shows the highest similarity
between all members of the family. ABC transporters are
a subset of nucleotide hydrolases that contain a
signature motif, Q-loop, and H-loop/switch region, in
addition to, the Walker A motif/P-loop and Walker B
motif commonly found in a number of ATP- and
GTP-binding and hydrolyzing proteins.
Length = 235
Score = 28.1 bits (63), Expect = 5.5
Identities = 13/50 (26%), Positives = 25/50 (50%), Gaps = 5/50 (10%)
Query: 25 HLRNL-LKEGDFPHLLFYGPSGAGKKTRIMALLKELYGPV---IILNETD 70
L+N+ L+ + + GP+G+G K+ ++ + P I+LN D
Sbjct: 14 KLKNVSLEVERGDYFVILGPTGSG-KSVLLETIAGFIKPDSGKILLNGKD 62
>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 = 27.9 bits (63), Expect = 5.5
Identities = 10/29 (34%), Positives = 14/29 (48%), Gaps = 5/29 (17%)
Query: 42 GPSGAGKKTRIMALLKELY----GPVIIL 66
GP+G G KT + +E + VI L
Sbjct: 25 GPAGTG-KTTSLKAAREAWEAAGYRVIGL 52
>gnl|CDD|131259 TIGR02204, MsbA_rel, ABC transporter, permease/ATP-binding protein.
This protein is related to a Proteobacterial ATP
transporter that exports lipid A and to eukaryotic
P-glycoproteins.
Length = 576
Score = 28.1 bits (63), Expect = 5.7
Identities = 12/23 (52%), Positives = 13/23 (56%), Gaps = 1/23 (4%)
Query: 40 FYGPSGAGKKTRIMALLKELYGP 62
GPSGAGK T + LL Y P
Sbjct: 371 LVGPSGAGKST-LFQLLLRFYDP 392
>gnl|CDD|236267 PRK08451, PRK08451, DNA polymerase III subunits gamma and tau;
Validated.
Length = 535
Score = 28.1 bits (63), Expect = 5.7
Identities = 40/115 (34%), Positives = 53/115 (46%), Gaps = 27/115 (23%)
Query: 65 ILNETDHLTREAQQALRRTME------KYI--TTCRLILCANSMSQVIPA-IRSRCLCIR 115
I++E LT+EA AL +T+E K+I TT L L PA I SR R
Sbjct: 122 IIDEVHMLTKEAFNALLKTLEEPPSYVKFILATTDPLKL---------PATILSRTQHFR 172
Query: 116 IPAPTHEEIVSVLTNICKKEGLTIPPEFAL----RLAQQSDRN----LRRAILMC 162
I+S L I +KEG++ PE AL R S R+ L +AI+ C
Sbjct: 173 FKQIPQNSIISHLKTILEKEGVSYEPE-ALEILARSGNGSLRDTLTLLDQAIIYC 226
>gnl|CDD|217007 pfam02383, Syja_N, SacI homology domain. This Pfam family
represents a protein domain which shows homology to the
yeast protein SacI. The SacI homology domain is most
notably found at the amino terminal of the inositol
5'-phosphatase synaptojanin.
Length = 298
Score = 27.9 bits (63), Expect = 5.9
Identities = 10/36 (27%), Positives = 18/36 (50%), Gaps = 2/36 (5%)
Query: 56 LKELYGPVIILNETDHLTREAQQALRRTMEKYITTC 91
L + YGP+ I+N D + +++ L E+ I
Sbjct: 241 LIKRYGPIYIVNLLDK--KGSEKKLSEAYEEAINYL 274
>gnl|CDD|213217 cd03250, ABCC_MRP_domain1, ATP-binding cassette domain 1 of
multidrug resistance-associated protein, subfamily C.
This subfamily is also known as MRP (multidrug
resistance-associated protein). Some of the MRP members
have five additional transmembrane segments in their
N-terminus, but the function of these additional
membrane-spanning domains is not clear. The MRP was
found in the multidrug-resisting lung cancer cell in
which p-glycoprotein was not overexpressed. MRP exports
glutathione by drug stimulation, as well as, certain
substrates in conjugated forms with anions, such as
glutathione, glucuronate, and sulfate.
Length = 204
Score = 27.4 bits (62), Expect = 6.1
Identities = 10/19 (52%), Positives = 13/19 (68%)
Query: 42 GPSGAGKKTRIMALLKELY 60
GP G+GK + + ALL EL
Sbjct: 38 GPVGSGKSSLLSALLGELE 56
>gnl|CDD|224401 COG1484, DnaC, DNA replication protein [DNA replication,
recombination, and repair].
Length = 254
Score = 27.8 bits (62), Expect = 6.4
Identities = 18/77 (23%), Positives = 31/77 (40%), Gaps = 13/77 (16%)
Query: 22 QANHLRNLLKEGDFPHLLFYGPSGAGKKTRIMALLKEL--YG-PVIILNETDHLTR---- 74
L + G+ L+ GP G GK +A+ EL G V+ + D L++
Sbjct: 94 DLASLVEFFERGEN--LVLLGPPGVGKTHLAIAIGNELLKAGISVLFITAPDLLSKLKAA 151
Query: 75 ----EAQQALRRTMEKY 87
++ L R ++K
Sbjct: 152 FDEGRLEEKLLRELKKV 168
>gnl|CDD|180916 PRK07276, PRK07276, DNA polymerase III subunit delta'; Validated.
Length = 290
Score = 27.7 bits (62), Expect = 6.5
Identities = 25/97 (25%), Positives = 44/97 (45%), Gaps = 8/97 (8%)
Query: 29 LLKEGDFPHLLFYGPSGAGKKT-RIMALLK-------ELYGPVIILNETDHLTREAQQAL 80
L+++G+F + P G KT I L+K E V I+ + D + A +L
Sbjct: 65 LIEQGEFSDVTVIEPQGQVIKTDTIRELVKNFSQSGYEGKQQVFIIKDADKMHVNAANSL 124
Query: 81 RRTMEKYITTCRLILCANSMSQVIPAIRSRCLCIRIP 117
+ +E+ + + L N ++V+P I+SR P
Sbjct: 125 LKVIEEPQSEIYIFLLTNDENKVLPTIKSRTQIFHFP 161
>gnl|CDD|179433 PRK02496, adk, adenylate kinase; Provisional.
Length = 184
Score = 27.4 bits (61), Expect = 6.6
Identities = 16/39 (41%), Positives = 23/39 (58%), Gaps = 3/39 (7%)
Query: 38 LLFYGPSGAGKKTRIMALLKELYGPVIILNETDHLTREA 76
L+F GP GAGK T+ + L + L+ P I T + R+A
Sbjct: 4 LIFLGPPGAGKGTQAVVLAEHLHIPHI---STGDILRQA 39
>gnl|CDD|182342 PRK10261, PRK10261, glutathione transporter ATP-binding protein;
Provisional.
Length = 623
Score = 27.9 bits (62), Expect = 6.9
Identities = 22/52 (42%), Positives = 27/52 (51%), Gaps = 4/52 (7%)
Query: 38 LLFYGPSGAGKKTRIMALLK--ELYGPVIILN--ETDHLTREAQQALRRTME 85
L G SG+GK T ALL+ E G II N D L+ QALRR ++
Sbjct: 353 LSLVGESGSGKSTTGRALLRLVESQGGEIIFNGQRIDTLSPGKLQALRRDIQ 404
>gnl|CDD|238026 cd00071, GMPK, Guanosine monophosphate kinase (GMPK, EC 2.7.4.8),
also known as guanylate kinase (GKase), catalyzes the
reversible phosphoryl transfer from adenosine
triphosphate (ATP) to guanosine monophosphate (GMP) to
yield adenosine diphosphate (ADP) and guanosine
diphosphate (GDP). It plays an essential role in the
biosynthesis of guanosine triphosphate (GTP). This
enzyme is also important for the activation of some
antiviral and anticancer agents, such as acyclovir,
ganciclovir, carbovir, and thiopurines.
Length = 137
Score = 27.1 bits (61), Expect = 7.1
Identities = 10/17 (58%), Positives = 12/17 (70%)
Query: 42 GPSGAGKKTRIMALLKE 58
GPSG GK T + LL+E
Sbjct: 6 GPSGVGKSTLLKRLLEE 22
>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 = 27.3 bits (61), Expect = 7.2
Identities = 11/24 (45%), Positives = 15/24 (62%)
Query: 36 PHLLFYGPSGAGKKTRIMALLKEL 59
PHLL G +G+GK T + L+ L
Sbjct: 39 PHLLIAGATGSGKSTFLNTLILSL 62
>gnl|CDD|223603 COG0529, CysC, Adenylylsulfate kinase and related kinases
[Inorganic ion transport and metabolism].
Length = 197
Score = 27.2 bits (61), Expect = 7.3
Identities = 10/23 (43%), Positives = 15/23 (65%)
Query: 38 LLFYGPSGAGKKTRIMALLKELY 60
+ F G SG+GK T AL ++L+
Sbjct: 26 IWFTGLSGSGKSTIANALEEKLF 48
>gnl|CDD|226361 COG3842, PotA, ABC-type spermidine/putrescine transport systems,
ATPase components [Amino acid transport and
metabolism].
Length = 352
Score = 27.6 bits (62), Expect = 7.7
Identities = 19/58 (32%), Positives = 31/58 (53%), Gaps = 9/58 (15%)
Query: 18 FHCKQANHLRNL---LKEGDFPHLLFYGPSGAGKKT--RIMALLKELYGPVIILNETD 70
F A + ++ +K+G+F LL GPSG GK T R++A ++ I+L+ D
Sbjct: 15 FGDFTA--VDDISLDIKKGEFVTLL--GPSGCGKTTLLRMIAGFEQPSSGEILLDGED 68
>gnl|CDD|234988 PRK01889, PRK01889, GTPase RsgA; Reviewed.
Length = 356
Score = 27.6 bits (62), Expect = 7.8
Identities = 10/19 (52%), Positives = 11/19 (57%)
Query: 40 FYGPSGAGKKTRIMALLKE 58
G SG GK T + ALL E
Sbjct: 200 LLGSSGVGKSTLVNALLGE 218
>gnl|CDD|182300 PRK10200, PRK10200, putative racemase; Provisional.
Length = 230
Score = 27.2 bits (60), Expect = 8.2
Identities = 10/19 (52%), Positives = 14/19 (73%)
Query: 93 LILCANSMSQVIPAIRSRC 111
++LC N+M +V AI SRC
Sbjct: 79 IVLCTNTMHKVADAIESRC 97
>gnl|CDD|222307 pfam13671, AAA_33, AAA domain. This family of domains contain
only a P-loop motif, that is characteristic of the AAA
superfamily. Many of the proteins in this family are
just short fragments so there is no Walker B motif.
Length = 143
Score = 26.9 bits (60), Expect = 8.3
Identities = 11/27 (40%), Positives = 15/27 (55%)
Query: 38 LLFYGPSGAGKKTRIMALLKELYGPVI 64
+L G G+GK T LL+EL V+
Sbjct: 2 ILMVGLPGSGKSTFARRLLRELGAVVL 28
>gnl|CDD|227118 COG4778, PhnL, ABC-type phosphonate transport system, ATPase
component [Inorganic ion transport and metabolism].
Length = 235
Score = 27.4 bits (61), Expect = 8.6
Identities = 11/20 (55%), Positives = 13/20 (65%), Gaps = 4/20 (20%)
Query: 42 GPSGAGKKTRIMALLKELYG 61
GPSG+GK T LL+ LY
Sbjct: 44 GPSGSGKST----LLRSLYA 59
>gnl|CDD|206648 cd00882, Ras_like_GTPase, Rat sarcoma (Ras)-like superfamily of
small guanosine triphosphatases (GTPases). Ras-like
GTPase superfamily. The Ras-like superfamily of small
GTPases consists of several families with an extremely
high degree of structural and functional similarity.
The Ras superfamily is divided into at least four
families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf
families. This superfamily also includes proteins like
the GTP translation factors, Era-like GTPases, and
G-alpha chain of the heterotrimeric G proteins. Members
of the Ras superfamily regulate a wide variety of
cellular functions: the Ras family regulates gene
expression, the Rho family regulates cytoskeletal
reorganization and gene expression, the Rab and
Sar1/Arf families regulate vesicle trafficking, and the
Ran family regulates nucleocytoplasmic transport and
microtubule organization. The GTP translation factor
family regulates initiation, elongation, termination,
and release in translation, and the Era-like GTPase
family regulates cell division, sporulation, and DNA
replication. Members of the Ras superfamily are
identified by the GTP binding site, which is made up of
five characteristic sequence motifs, and the switch I
and switch II regions.
Length = 161
Score = 27.0 bits (60), Expect = 9.3
Identities = 15/58 (25%), Positives = 22/58 (37%), Gaps = 6/58 (10%)
Query: 39 LFYGPSGAGKKTRIMALLKELYGPVIILNETDHLTREAQQALRRTMEKYITTCRLILC 96
+ G G GK + + ALL G V + T TR+ E +L+L
Sbjct: 1 VVVGRGGVGKSSLLNALLGGEVGEVSDVPGT---TRDPD---VYVKELDKGKVKLVLV 52
>gnl|CDD|224059 COG1136, SalX, ABC-type antimicrobial peptide transport system,
ATPase component [Defense mechanisms].
Length = 226
Score = 27.1 bits (61), Expect = 9.5
Identities = 16/57 (28%), Positives = 30/57 (52%), Gaps = 6/57 (10%)
Query: 30 LKEGDFPHLLFYGPSGAGKKT--RIMALLKELYGPVIILNETD--HLTREAQQALRR 82
++ G+F ++ GPSG+GK T ++ L + +++N D L+ + LRR
Sbjct: 28 IEAGEFVAIV--GPSGSGKSTLLNLLGGLDKPTSGEVLINGKDLTKLSEKELAKLRR 82
>gnl|CDD|237536 PRK13873, PRK13873, conjugal transfer ATPase TrbE; Provisional.
Length = 811
Score = 27.6 bits (62), Expect = 9.5
Identities = 12/24 (50%), Positives = 16/24 (66%), Gaps = 1/24 (4%)
Query: 33 GDFPHLLFYGPSGAGKKTRIMALL 56
GD H L GP+GAGK ++AL+
Sbjct: 439 GDVGHTLVVGPTGAGKSV-LLALM 461
>gnl|CDD|224047 COG1122, CbiO, ABC-type cobalt transport system, ATPase component
[Inorganic ion transport and metabolism].
Length = 235
Score = 27.2 bits (61), Expect = 9.5
Identities = 13/39 (33%), Positives = 23/39 (58%), Gaps = 5/39 (12%)
Query: 30 LKEGDFPHLLFYGPSGAGKKTRIMA---LLKELYGPVII 65
+++G+ +L GP+G+GK T + LLK G V++
Sbjct: 27 IEKGER--VLLIGPNGSGKSTLLKLLNGLLKPTSGEVLV 63
>gnl|CDD|163539 TIGR03827, GNAT_ablB, putative beta-lysine N-acetyltransferase.
Members of this protein family are GNAT family
acetyltransferases, based on a seed alignment in which
every member is associated with a lysine 2,3-aminomutase
family protein, usually as the adjacent gene. This
family includes AblB, the enzyme beta-lysine
acetyltransferase that completes the two-step synthesis
of the osmolyte (compatible solute)
N-epsilon-acetyl-beta-lysine; all members of the family
may have this function. Note that
N-epsilon-acetyl-beta-lysine has been observed only in
methanogenic archaea (e.g. Methanosarcina) but that this
model, paired with TIGR03820, suggests a much broader
distribution.
Length = 266
Score = 27.2 bits (61), Expect = 9.6
Identities = 20/73 (27%), Positives = 30/73 (41%), Gaps = 15/73 (20%)
Query: 122 EEIVSVLTNICKKEG---LTIPPEFALRLAQQSDRNLRRAILMCEASKV-QQYPFQIDQQ 177
E+ VL K + +P F LR+A + D + A+ KV YPF I
Sbjct: 92 EKEDEVLEAALSKPRKPKIALPEGFTLRIATEDDADAMAALY----RKVFPTYPFPIH-- 145
Query: 178 IVEPDWKIYIRDT 190
+P Y+ +T
Sbjct: 146 --DPA---YLLET 153
>gnl|CDD|131377 TIGR02324, CP_lyasePhnL, phosphonate C-P lyase system protein
PhnL. Members of this family are the PhnL protein of
C-P lyase systems for utilization of phosphonates.
These systems resemble phosphonatase-based systems in
having a three component ABC transporter, where
TIGR01097 is the permease, TIGR01098 is the
phosphonates binding protein, and TIGR02315 is the
ATP-binding cassette (ABC) protein. They differ,
however, in having, typically, ten or more additional
genes, many of which are believed to form a
membrane-associated C-P lysase complex. This protein
(PhnL) and the adjacent-encoded PhnK (TIGR02323)
resemble transporter ATP-binding proteins but are
suggested, based on mutatgenesis studies, to be part of
this C-P lyase complex rather than part of a
transporter per se.
Length = 224
Score = 27.0 bits (60), Expect = 9.9
Identities = 14/32 (43%), Positives = 17/32 (53%), Gaps = 6/32 (18%)
Query: 30 LKEGDFPHLLFYGPSGAGKKTRIMALLKELYG 61
+ G+ + GPSGAGK T LLK LY
Sbjct: 31 VNAGEC--VALSGPSGAGKST----LLKSLYA 56
>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 = 27.6 bits (62), Expect = 10.0
Identities = 12/23 (52%), Positives = 14/23 (60%)
Query: 39 LFYGPSGAGKKTRIMALLKELYG 61
L GPSG GK +AL + LYG
Sbjct: 600 LLVGPSGVGKTETALALAELLYG 622
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
0.324 0.138 0.408
Gapped
Lambda K H
0.267 0.0534 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 14,584,944
Number of extensions: 1399545
Number of successful extensions: 2465
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2428
Number of HSP's successfully gapped: 261
Length of query: 287
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 191
Effective length of database: 6,679,618
Effective search space: 1275807038
Effective search space used: 1275807038
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 58 (26.6 bits)