RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9977
(192 letters)
>gnl|CDD|238994 cd02037, MRP-like, MRP (Multiple Resistance and pH adaptation) is a
homologue of the Fer4_NifH superfamily. Like the other
members of the superfamily, MRP contains a ATP-binding
domain at the N-termini. It is found in bacteria as a
membrane-spanning protein and functions as a Na+/H+
antiporter.
Length = 169
Score = 232 bits (595), Expect = 5e-79
Identities = 83/185 (44%), Positives = 105/185 (56%), Gaps = 46/185 (24%)
Query: 8 VILVLSGKGGVGKSTVSTQLALGLKDKGFKVGILDIDLCGPSVPHLLNIENSDVHQCPEG 67
VI V+SGKGGVGKSTV+ LAL L G+KVG+LD D+ GPS+P +
Sbjct: 1 VIAVMSGKGGVGKSTVAVNLALALAKLGYKVGLLDADIYGPSIPKM-------------- 46
Query: 68 WVPVYTDASQTLAVMSIGFLLKNRDDAIIWRGPKKTAMIRQIINDVCWKDVDYLIIDTPP 127
WRGP K I+Q + DV W ++DYL+ID PP
Sbjct: 47 -----------------------------WRGPMKMGAIKQFLTDVDWGELDYLVIDMPP 77
Query: 128 GTSDEHITVMECLREVQCDGAVLVTTPQAVSIEDVRKEITFCKKTNIKILGLIENMSGYT 187
GT DEH+T+ + L DGAV+VTTPQ V+++DVRK I KK NI ILG++ENMS +
Sbjct: 78 GTGDEHLTLAQSLP---IDGAVIVTTPQEVALDDVRKAIDMFKKVNIPILGVVENMSYFV 134
Query: 188 CPHCK 192
CPHC
Sbjct: 135 CPHCG 139
>gnl|CDD|223563 COG0489, Mrp, ATPases involved in chromosome partitioning [Cell
division and chromosome partitioning].
Length = 265
Score = 205 bits (524), Expect = 5e-67
Identities = 83/192 (43%), Positives = 113/192 (58%), Gaps = 12/192 (6%)
Query: 3 DGVKHVILVLSGKGGVGKSTVSTQLALGLKDKGFKVGILDIDLCGPSVPHLLNIENSD-V 61
GVK+VI V SGKGGVGKSTV+ LA L G +V +LD DL GPS+P +L +EN +
Sbjct: 54 KGVKNVIAVTSGKGGVGKSTVAVNLAAALAQLGKRVLLLDADLRGPSIPRMLGLENLPGL 113
Query: 62 HQCPEG--WVPVYTDASQTLAVMSIGFLLKNRDDAIIWRGPKKTAMIRQIINDVCWKDVD 119
+ G PV + V+SI L +I RG + + Q++ DV W + D
Sbjct: 114 TELLAGEALEPVIQHD--GIKVLSILPLG---PVPVIPRGLLGSKAMLQLLEDVLWGEYD 168
Query: 120 YLIIDTPPGTSDEHITVMECLREVQCDGAVLVTTPQAVSIEDVRKEITFCKKTNIKILGL 179
Y+IIDTPPGT D TV++ + DG V+VTTP ++EDV+K I +K I +LG+
Sbjct: 169 YVIIDTPPGTGDADATVLQRI----PDGVVIVTTPGKTALEDVKKAIDMLEKAGIPVLGV 224
Query: 180 IENMSGYTCPHC 191
+ENMS + CP C
Sbjct: 225 VENMSYFICPRC 236
>gnl|CDD|183270 PRK11670, PRK11670, antiporter inner membrane protein; Provisional.
Length = 369
Score = 174 bits (442), Expect = 2e-53
Identities = 80/190 (42%), Positives = 121/190 (63%), Gaps = 10/190 (5%)
Query: 4 GVKHVILVLSGKGGVGKSTVSTQLALGLKDKGFKVGILDIDLCGPSVPHLLNIENSDVHQ 63
GVK++I V SGKGGVGKS+ + LAL L +G KVGILD D+ GPS+P +L E+
Sbjct: 105 GVKNIIAVSSGKGGVGKSSTAVNLALALAAEGAKVGILDADIYGPSIPTMLGAEDQR-PT 163
Query: 64 CPEG--WVPVYTDASQTLAVMSIGFLLKNRDDAIIWRGPKKTAMIRQIINDVCWKDVDYL 121
P+G P+ + LA SIG+L+ D+A++WRGP + + Q++ + W D+DYL
Sbjct: 164 SPDGTHMAPI---MAHGLATNSIGYLV-TDDNAMVWRGPMASKALMQMLQETLWPDLDYL 219
Query: 122 IIDTPPGTSDEHITVMECLREVQCDGAVLVTTPQAVSIEDVRKEITFCKKTNIKILGLIE 181
++D PPGT D +T+ + + GAV+VTTPQ +++ D +K I +K + +LG++E
Sbjct: 220 VLDMPPGTGDIQLTLAQ---NIPVTGAVVVTTPQDIALIDAKKGIVMFEKVEVPVLGIVE 276
Query: 182 NMSGYTCPHC 191
NMS + C +C
Sbjct: 277 NMSMHICSNC 286
>gnl|CDD|204531 pfam10609, ParA, ParA/MinD ATPase like. This family contains
ATPases involved in plasmid partitioning. It also
contains the cytosolic Fe-S cluster assembling factor
NBP35 which is required for biogenesis and export of
both ribosomal subunits.
Length = 81
Score = 130 bits (331), Expect = 3e-40
Identities = 41/74 (55%), Positives = 53/74 (71%), Gaps = 3/74 (4%)
Query: 119 DYLIIDTPPGTSDEHITVMECLREVQCDGAVLVTTPQAVSIEDVRKEITFCKKTNIKILG 178
DYL+ID PPGT DEH+T+ + + DGAV+VTTPQ V++ DVRK I KK N+ ILG
Sbjct: 2 DYLLIDLPPGTGDEHLTLAQ---SLPVDGAVIVTTPQDVALLDVRKAIDMFKKVNVPILG 58
Query: 179 LIENMSGYTCPHCK 192
++ENMS + CP C
Sbjct: 59 VVENMSYFVCPDCG 72
>gnl|CDD|238993 cd02036, MinD, Bacterial cell division requires the formation of a
septum at mid-cell. The site is determined by the min
operon products MinC, MinD and MinE. MinC is a
nonspecific inhibitor of the septum protein FtsZ. MinE
is the supressor of MinC. MinD plays a pivotal role,
selecting the mid-cell over other sites through the
activation and regulation of MinC and MinE. MinD is a
membrane-associated ATPase, related to nitrogenase iron
protein. More distantly related proteins include
flagellar biosynthesis proteins and ParA chromosome
partitioning proteins. MinD is a monomer.
Length = 179
Score = 71.8 bits (177), Expect = 5e-16
Identities = 50/179 (27%), Positives = 74/179 (41%), Gaps = 53/179 (29%)
Query: 8 VILVLSGKGGVGKSTVSTQLALGLKDKGFKVGILDIDLCGPSVPHLLNIENSDVHQCPEG 67
VI+V SGKGGVGK+T + L L G+KV ++D DL ++ +L +EN
Sbjct: 1 VIVVTSGKGGVGKTTTTANLGTALAQLGYKVVLIDADLGLRNLDLILGLENR-------- 52
Query: 68 WVPVYTDASQTLAVMSIGFLLKNRDDAIIWRGPKKTAMIRQIINDVCWKDVDYLIIDTPP 127
VYT ++DV DY++ID+P
Sbjct: 53 --VVYT------------------------------------LHDVL--AGDYILIDSPA 72
Query: 128 GTSDEHITVMECLREVQCDGAVLVTTPQAVSIEDVRKEITFCKKTNIKILGLIENMSGY 186
G IT + D A+LVTTP+ S+ D + + IK++G+I N
Sbjct: 73 GIERGFITAIA-----PADEALLVTTPEISSLRDADRVKGLLEALGIKVVGVIVNRVRP 126
>gnl|CDD|216631 pfam01656, CbiA, CobQ/CobB/MinD/ParA nucleotide binding domain.
This family consists of various cobyrinic acid
a,c-diamide synthases. These include CbiA and CbiP from
S.typhimurium, and CobQ from R. capsulatus. These
amidases catalyze amidations to various side chains of
hydrogenobyrinic acid or cobyrinic acid a,c-diamide in
the biosynthesis of cobalamin (vitamin B12) from
uroporphyrinogen III. Vitamin B12 is an important
cofactor and an essential nutrient for many plants and
animals and is primarily produced by bacteria. The
family also contains dethiobiotin synthetases as well as
the plasmid partitioning proteins of the MinD/ParA
family.
Length = 217
Score = 70.9 bits (174), Expect = 2e-15
Identities = 44/187 (23%), Positives = 79/187 (42%), Gaps = 20/187 (10%)
Query: 9 ILVLSGKGGVGKSTVSTQLALGLKDKGFKVGILDID--------LCGPSVPHLLNIENSD 60
I + KGGVGK+T++ LA L +G++V ++D+D L +E D
Sbjct: 1 IAIAGTKGGVGKTTLAANLARALAKRGYRVLLIDLDPQANNSSYLGKVEEVLPEGLEIVD 60
Query: 61 VHQCPE---GWVPVYTDASQTLAVMSIGFLLKNRDDAIIWRGPKKTAMIRQIINDVCWKD 117
VP L ++ L+N + +I G K+ + +R + +
Sbjct: 61 AQALQAIAAAIVPSRNLDP--LLLIPSNLSLENFESELIVEG-KRESRLRAALESLIKLA 117
Query: 118 VDYLIIDTPPGTSDEHITVMECLREVQCDGAVLVTTPQAVSIEDVRKEITFCKKTNI-KI 176
DY+IID PPG + + D V+ P+ V++E ++ + + + I
Sbjct: 118 YDYVIIDGPPGLGELTANALVA-----ADILVVPIEPEGVAVEGAQRLLELIEDLGVLDI 172
Query: 177 LGLIENM 183
LG++ N
Sbjct: 173 LGVVLNK 179
>gnl|CDD|131024 TIGR01969, minD_arch, cell division ATPase MinD, archaeal. This
model represents the archaeal branch of the MinD family.
MinD, a weak ATPase, works in bacteria with MinC as a
generalized cell division inhibitor and, through
interaction with MinE, prevents septum placement
inappropriate sites. Often several members of this
family are found in archaeal genomes, and the function
is uncharacterized. More distantly related proteins
include flagellar biosynthesis proteins and ParA
chromosome partitioning proteins. The exact roles of the
various archaeal MinD homologs are unknown.
Length = 251
Score = 70.9 bits (174), Expect = 3e-15
Identities = 49/184 (26%), Positives = 81/184 (44%), Gaps = 16/184 (8%)
Query: 8 VILVLSGKGGVGKSTVSTQLALGLKDKGFKVGILDIDLCGPSVPHLLNIENSDV--HQCP 65
+I + SGKGG GK+T++ L + L G KV LD D+ ++ +L +E+ V H
Sbjct: 2 IITIASGKGGTGKTTITANLGVALAKLGKKVLALDADITMANLELILGMEDKPVTLHDVL 61
Query: 66 EGWVPVYTDASQTLAVMSIGFLLKNRDDAIIWRGPKKT--AMIRQIINDVCWKDVDYLII 123
G +A A+ F +K + G +K + ++ ++ D D+L+I
Sbjct: 62 AG------EADIKDAIYEGPFGVKVIPAGVSLEGLRKADPDKLEDVLKEII-DDTDFLLI 114
Query: 124 DTPPGTSDEHITVMECLREVQCDGAVLVTTPQAVSIEDVRKEITFCKKTNIKILGLIENM 183
D P G + +T + D +LV P+ SI D K +K ILG++ N
Sbjct: 115 DAPAGLERDAVTAL-----AAADELLLVVNPEISSITDALKTKIVAEKLGTAILGVVLNR 169
Query: 184 SGYT 187
Sbjct: 170 VTRD 173
>gnl|CDD|223531 COG0455, flhG, Antiactivator of flagellar biosynthesis FleN, an
ATPase [Cell motility].
Length = 262
Score = 69.2 bits (170), Expect = 1e-14
Identities = 50/187 (26%), Positives = 82/187 (43%), Gaps = 24/187 (12%)
Query: 7 HVILVLSGKGGVGKSTVSTQL-ALGLKDKGFKVGILDIDLCGPSVPHLLNIENSDVH--- 62
VI V+SGKGGVGK+T++ L A G V ++D DL ++ LL +E+
Sbjct: 3 KVIAVVSGKGGVGKTTITANLGAALAALGGKVVLLIDADLGLGNLSLLLGVESKPTTLHD 62
Query: 63 ----QCPEGWVPVYTDASQTLAVMSIGFLLKNRDDAIIWRGPKKTAMIRQIINDVCWKDV 118
+ + T L V+ G L++ P+ + + + ++
Sbjct: 63 VLAGEASIEDIIYET-PQDGLYVLPGGSGLEDLAKL----DPEDLEDVIKELEELY---- 113
Query: 119 DYLIIDTPPGTSDEHITVMECLREVQCDGAVLVTTPQAVSIEDVRKEITFCKKTNIKILG 178
DY++IDT G S + + + D V+VTTP+ SI D K I K + +LG
Sbjct: 114 DYILIDTGAGLSRD---TLSFIL--SSDELVIVTTPEPTSITDAYKTIKILSKLGLDLLG 168
Query: 179 --LIENM 183
++ N
Sbjct: 169 RRVVLNR 175
>gnl|CDD|238992 cd02035, ArsA, ArsA ATPase functionas as an efflux pump located on
the inner membrane of the cell. This ATP-driven oxyanion
pump catalyzes the extrusion of arsenite, antimonite and
arsenate. Maintenance of a low intracellular
concentration of oxyanion produces resistance to the
toxic agents. The pump is composed of two subunits, the
catalytic ArsA subunit and the membrane subunit ArsB,
which are encoded by arsA and arsB genes respectively.
Arsenic efflux in bacteria is catalyzed by either ArsB
alone or by ArsAB complex. The ATP-coupled pump,
however, is more efficient. ArsA is composed of two
homologous halves, A1 and A2, connected by a short
linker sequence.
Length = 217
Score = 60.3 bits (147), Expect = 1e-11
Identities = 45/202 (22%), Positives = 80/202 (39%), Gaps = 28/202 (13%)
Query: 9 ILVLSGKGGVGKSTVSTQLALGLKDKGFKVGILDID----LCGPSVPHL--LNIENSDVH 62
++ +GKGGVGK+T++ A+ L ++G KV ++ D L +P+L I D
Sbjct: 1 VIFFTGKGGVGKTTIAAATAVRLAEEGKKVLLVSTDPAHNLSDKGLPNLSDAFIV-EDPE 59
Query: 63 QCPEGWVP-VYTDASQTLAVMSIGFLLKNRDDAIIWRGPKKTAM---IRQIINDVCWKDV 118
P + V A G L+ A+ G ++ A + + ++ +
Sbjct: 60 IAPNLYREEVDATRRVERAWGGEGGLMLELAAALP--GIEELASLLAVFREFSEGLY--- 114
Query: 119 DYLIIDTPP-GTSDEHIT---VMECLREVQCDGAVLVTTPQAVSIEDVRKEITFCKKTNI 174
D ++ DT P G H V E L + + LVT P+ + + + + IT I
Sbjct: 115 DVIVFDTAPTG----HTLRLLVRELLTDPERTSFRLVTLPEKLPLYETERAITELALYGI 170
Query: 175 KILGLIEN----MSGYTCPHCK 192
+ ++ N P
Sbjct: 171 PVDAVVVNRVLPAEVDDDPFLA 192
>gnl|CDD|222264 pfam13614, AAA_31, AAA domain. This family includes a wide variety
of AAA domains including some that have lost essential
nucleotide binding residues in the P-loop.
Length = 145
Score = 58.4 bits (142), Expect = 3e-11
Identities = 33/161 (20%), Positives = 57/161 (35%), Gaps = 26/161 (16%)
Query: 8 VILVLSGKGGVGKSTVSTQLALGLKDKGFKVGILDIDLCGPSVPHLLNIENSDVHQCPEG 67
VI V S GG GK+T + LA L ++G KV LD++ + L +E
Sbjct: 2 VIGVYSPVGGEGKTTFALNLAQSLAEEGPKVLYLDLEEYSGDLALFLGLEPKG------- 54
Query: 68 WVPVYTDASQTLAVMSIGFLLKNRDDAIIWRGPKKTAMIRQI--------INDVCWKDVD 119
+D L + L++ P+ +R++ + + + D
Sbjct: 55 ----LSDLLYYLKRLD-SMLIQAMGGLDYLAPPRNPEDLREVSPEEWEQLLERLR-ERYD 108
Query: 120 YLIIDTPPGTSDEHITVMECLREVQCDGAVLVTTPQAVSIE 160
+++D P + V+ CD LV S
Sbjct: 109 VIVLDLGPLVPSDFALVLSL-----CDRVYLVVRADVASKR 144
>gnl|CDD|238995 cd02038, FleN-like, FleN is a member of the Fer4_NifH
superfamily. It shares the common function as an
ATPase, with the ATP-binding domain at the N-terminus.
In Pseudomonas aeruginosa, FleN gene is involved in
regulating the number of flagella and chemotactic
motility by influencing FleQ activity.
Length = 139
Score = 57.9 bits (141), Expect = 4e-11
Identities = 21/38 (55%), Positives = 26/38 (68%)
Query: 8 VILVLSGKGGVGKSTVSTQLALGLKDKGFKVGILDIDL 45
+I V SGKGGVGK+ +S LAL L G +V +LD DL
Sbjct: 1 IIAVTSGKGGVGKTNISANLALALAKLGKRVLLLDADL 38
Score = 42.5 bits (101), Expect = 1e-05
Identities = 19/45 (42%), Positives = 24/45 (53%), Gaps = 5/45 (11%)
Query: 117 DVDYLIIDTPPGTSDEHITVMECLREVQCDGAVLVTTPQAVSIED 161
D DY+IIDT G SD + EV ++VTTP+ SI D
Sbjct: 44 DYDYIIIDTGAGISDNVLDFFLAADEV-----IVVTTPEPTSITD 83
>gnl|CDD|214385 CHL00175, minD, septum-site determining protein; Validated.
Length = 281
Score = 59.4 bits (144), Expect = 7e-11
Identities = 44/189 (23%), Positives = 87/189 (46%), Gaps = 21/189 (11%)
Query: 2 LDGVKHVILVLSGKGGVGKSTVSTQLALGLKDKGFKVGILDIDLCGPSVPHLLNIENSDV 61
+ +I++ SGKGGVGK+T + L + + G++V ++D D+ ++ LL +EN +
Sbjct: 11 SATMSRIIVITSGKGGVGKTTTTANLGMSIARLGYRVALIDADIGLRNLDLLLGLENRVL 70
Query: 62 H--------QCPEGWVPVYTDASQTLAVMSIGFLLKNRDDAIIWRGPKKTAMIRQIINDV 113
+ +C + + L++++I KNR R + +++ +
Sbjct: 71 YTAMDVLEGECRLDQALIRDKRWKNLSLLAIS---KNRQ-----RYNVTRKNMNMLVDSL 122
Query: 114 CWKDVDYLIIDTPPGTSDEHITVMECLREVQCDGAVLVTTPQAVSIEDVRKEITFCKKTN 173
+ DY++ID P G I + +E A++VTTP+ +I D + +
Sbjct: 123 KNRGYDYILIDCPAGIDVGFINAIAPAQE-----AIVVTTPEITAIRDADRVAGLLEANG 177
Query: 174 IKILGLIEN 182
I + L+ N
Sbjct: 178 IYNVKLLVN 186
>gnl|CDD|131023 TIGR01968, minD_bact, septum site-determining protein MinD. This
model describes the bacterial and chloroplast form of
MinD, a multifunctional cell division protein that
guides correct placement of the septum. The homologous
archaeal MinD proteins, with many archaeal genomes
having two or more forms, are described by a separate
model [Cellular processes, Cell division].
Length = 261
Score = 57.0 bits (138), Expect = 4e-10
Identities = 46/183 (25%), Positives = 86/183 (46%), Gaps = 33/183 (18%)
Query: 8 VILVLSGKGGVGKSTVSTQLALGLKDKGFKVGILDIDLCGPSVPHLLNIENSDVH----- 62
VI++ SGKGGVGK+T + L L G KV ++D D+ ++ LL +EN V+
Sbjct: 3 VIVITSGKGGVGKTTTTANLGTALARLGKKVVLIDADIGLRNLDLLLGLENRIVYTLVDV 62
Query: 63 ---QCPEGWVPVYTDASQTLAVMSIGFLLKNRDDAIIWRGPKKTAMIRQIINDVCWKDVD 119
+C + + L ++ + RD + P++ +++++N++ ++ D
Sbjct: 63 VEGECRLQQALIKDKRLKNLYLLPAS---QTRDKDAV--TPEQ---MKKLVNELK-EEFD 113
Query: 120 YLIIDTPPGTSDEHITVMECLREVQCDGAVLVTTPQAVSIEDVRKEITFCKKTNIKILGL 179
Y+IID P G + D A++VTTP+ ++ D +++GL
Sbjct: 114 YVIIDCPAGIESGFRNAV-----APADEAIVVTTPEVSAVRDAD-----------RVIGL 157
Query: 180 IEN 182
+E
Sbjct: 158 LEA 160
>gnl|CDD|225447 COG2894, MinD, Septum formation inhibitor-activating ATPase [Cell
division and chromosome partitioning].
Length = 272
Score = 56.9 bits (138), Expect = 4e-10
Identities = 55/193 (28%), Positives = 86/193 (44%), Gaps = 48/193 (24%)
Query: 8 VILVLSGKGGVGKSTVSTQLALGLKDKGFKVGILDIDLCGPSVPHLLNIENSDVHQCPEG 67
+I+V SGKGGVGK+T + + L G KV ++D D + + N D+ E
Sbjct: 4 IIVVTSGKGGVGKTTTTANIGTALAQLGKKVVLIDFD---------IGLRNLDLIMGLEN 54
Query: 68 WVPVYT--DASQTLAVMSIG----------FLL---KNRD-DAIIWRGPKKTAMIRQIIN 111
+ VY D + A ++ FLL + RD DA+ G KK ++N
Sbjct: 55 RI-VYDLVDVIEGEATLNQALIKDKRLENLFLLPASQTRDKDALTPEGVKK------VVN 107
Query: 112 DVCWKDVDYLIIDTPPGTSDEHITVMECLREVQCDGAVLVTTPQAVSIEDVRKEITFCKK 171
++ D DY+IID+P G + D A++VT P+ S+ D
Sbjct: 108 ELKAMDFDYIIIDSPAGIEQGFKNAV-----YFADEAIVVTNPEVSSVRDSD-------- 154
Query: 172 TNIKILGLIENMS 184
+I+GL+E+ S
Sbjct: 155 ---RIIGLLESKS 164
>gnl|CDD|224113 COG1192, Soj, ATPases involved in chromosome partitioning [Cell
division and chromosome partitioning].
Length = 259
Score = 56.4 bits (136), Expect = 6e-10
Identities = 40/164 (24%), Positives = 70/164 (42%), Gaps = 19/164 (11%)
Query: 7 HVILVLSGKGGVGKSTVSTQLALGL-KDKGFKVGILDIDLCGPS-----VPHLLNIENSD 60
+I V + KGGVGK+T + LA L K G KV ++D+D G + L + +
Sbjct: 3 KIIAVANQKGGVGKTTTAVNLAAALAKRGGKKVLLIDLDPQGSLTSWLGLRPDLEGDLYN 62
Query: 61 VHQCPEGWVPVYTDASQTLAVMSIGFLLKNRDDA----IIWRGPKKTAMIRQIINDVCWK 116
+ G T+ + + + N D A I K +++++++ V
Sbjct: 63 LL---SGLKERPDILDYTVVIEGLDLIPSNIDLAEGAEIELNAVAKELLLKRLLDPV-KD 118
Query: 117 DVDYLIIDTPPGTSDEHITVMECLREVQCDGAVLVTTPQAVSIE 160
D DY+IIDTPP + + D ++ P+ + +E
Sbjct: 119 DYDYIIIDTPPSLGVLTLNALAA-----ADHVLIPVQPEFLDLE 157
>gnl|CDD|130080 TIGR01007, eps_fam, capsular exopolysaccharide family. This model
describes the capsular exopolysaccharide proteins in
bacteria. The exopolysaccharide gene cluster consists of
several genes which encode a number of proteins which
regulate the exoploysaccharide biosynthesis(EPS).
Atleast 13 genes espA to espM in streptococcus species
seem to direct the EPS proteins and all of which share
high homology. Functional roles were characterized by
gene disruption experiments which resulted in
exopolysaccharide-deficient phenotypes [Transport and
binding proteins, Carbohydrates, organic alcohols, and
acids].
Length = 204
Score = 55.9 bits (135), Expect = 6e-10
Identities = 52/197 (26%), Positives = 81/197 (41%), Gaps = 40/197 (20%)
Query: 3 DGVKHVILVLSGKGGVGKSTVSTQLALGLKDKGFKVGILDIDLCGPSVPHLLNIENSDV- 61
+K V+L+ S K G GKST S +A+ G+K ++D D+ + +N
Sbjct: 15 AEIK-VLLITSVKPGEGKSTTSANIAVAFAQAGYKTLLIDGDMRNSVMSGTFKSQNKITG 73
Query: 62 ------HQCPEGWVPVYTDASQTLAVMSIGFLLKNRDDAIIWRG---PKKTAMI-----R 107
TD S + +I L +I G P T ++ +
Sbjct: 74 LTNFLSGT---------TDLSDAICDTNIENLF------VITSGPVPPNPTELLQSSNFK 118
Query: 108 QIINDVCWKDVDYLIIDTPP-GT-SDEHITVMECLREVQCDGAVLVTTPQAVSIEDVRKE 165
+I + K DY+IIDTPP GT +D I CD ++LVT + DV+K
Sbjct: 119 TLIETLR-KYFDYIIIDTPPIGTVTDAAIIAR------ACDASILVTDAGEIKKRDVQKA 171
Query: 166 ITFCKKTNIKILGLIEN 182
++T LG++ N
Sbjct: 172 KEQLEQTGSNFLGVVLN 188
>gnl|CDD|239384 cd03110, Fer4_NifH_child, This protein family's function is unkown.
It contains nucleotide binding site. It uses NTP as
energy source to transfer electron or ion.
Length = 179
Score = 54.9 bits (133), Expect = 1e-09
Identities = 45/183 (24%), Positives = 72/183 (39%), Gaps = 36/183 (19%)
Query: 9 ILVLSGKGGVGKSTVSTQLALGLKDKGFKVGILDIDLCGPSVPHLLN---IENSDVHQCP 65
I V+SGKGG GK+TV+ LA LK+ V + D D+ P++ L E D
Sbjct: 2 IAVISGKGGTGKTTVTAALAALLKN----VVLADCDVDAPNLHLFLKPEIEEEEDFIVGG 57
Query: 66 EGWVPVYTDASQTLAVMSIGFLLKNRDDAIIWRG--PKKTAMIRQIINDVCWKDV-DYLI 122
+ V + I G K +R+ ++ + + +I
Sbjct: 58 KKAVI--------------------DPELCISCGLCGKLVTEVRKHAKEIAKAEGAELII 97
Query: 123 IDTPPGTSDEHITVMECLREVQCDGAVLVTTPQAVSIEDVRKEITFCKKTNIKILGLIEN 182
ID PPG V+ L D A+LVT P + D+ + + + I + G++ N
Sbjct: 98 IDGPPGIG---CPVIASLTG--ADAALLVTEPTPSGLHDLERAVELVRHFGIPV-GVVIN 151
Query: 183 MSG 185
Sbjct: 152 KYD 154
>gnl|CDD|238997 cd02042, ParA, ParA and ParB of Caulobacter crescentus belong to
a conserved family of bacterial proteins implicated in
chromosome segregation. ParB binds to DNA sequences
adjacent to the origin of replication and localizes to
opposite cell poles shortly following the initiation of
DNA replication. ParB regulates the ParA ATPase
activity by promoting nucleotide exchange in a fashion
reminiscent of the exchange factors of eukaryotic G
proteins. ADP-bound ParA binds single-stranded DNA,
whereas the ATP-bound form dissociates ParB from its
DNA binding sites. Increasing the fraction of ParA-ADP
in the cell inhibits cell division, suggesting that
this simple nucleotide switch may regulate cytokinesis.
ParA shares sequence similarity to a conserved and
widespread family of ATPases which includes the repA
protein of the repABC operon in R. etli Sym plasmid.
This operon is involved in the plasmid replication and
partition.
Length = 104
Score = 52.6 bits (127), Expect = 2e-09
Identities = 17/37 (45%), Positives = 25/37 (67%)
Query: 8 VILVLSGKGGVGKSTVSTQLALGLKDKGFKVGILDID 44
VI V + KGGVGK+T + LA L +G +V ++D+D
Sbjct: 1 VIAVANQKGGVGKTTTAVNLAAALARRGKRVLLIDLD 37
Score = 31.8 bits (73), Expect = 0.052
Identities = 10/42 (23%), Positives = 17/42 (40%), Gaps = 5/42 (11%)
Query: 119 DYLIIDTPPGTSDEHITVMECLREVQCDGAVLVTTPQAVSIE 160
DY+IIDTPP + D ++ P + ++
Sbjct: 41 DYIIIDTPPSLGLLTRNALAA-----ADLVLIPVQPSPLDLD 77
>gnl|CDD|182756 PRK10818, PRK10818, cell division inhibitor MinD; Provisional.
Length = 270
Score = 53.0 bits (127), Expect = 1e-08
Identities = 41/163 (25%), Positives = 75/163 (46%), Gaps = 23/163 (14%)
Query: 8 VILVLSGKGGVGKSTVSTQLALGLKDKGFKVGILDIDLCGPSVPHLLNIENSD-VHQCPE 66
+I+V SGKGGVGK+T S +A GL KG K ++D D + + N D + C
Sbjct: 4 IIVVTSGKGGVGKTTSSAAIATGLAQKGKKTVVIDFD---------IGLRNLDLIMGCER 54
Query: 67 GWVPVYTDASQTLAVMSIGFLLKNRDDAIIWRGPKKT----AMIR----QIINDVCWKDV 118
V + + Q A ++ + R + + +T A+ R ++++D+ D
Sbjct: 55 RVVYDFVNVIQGDATLNQALIKDKRTENLYILPASQTRDKDALTREGVAKVLDDLKAMDF 114
Query: 119 DYLIIDTPPGTSDEHITVMECLREVQCDGAVLVTTPQAVSIED 161
++++ D+P G + + D A++ T P+ S+ D
Sbjct: 115 EFIVCDSPAGIETGALMAL-----YFADEAIITTNPEVSSVRD 152
>gnl|CDD|238941 cd01983, Fer4_NifH, The Fer4_NifH superfamily contains a variety
of proteins which share a common ATP-binding domain.
Functionally, proteins in this superfamily use the
energy from hydrolysis of NTP to transfer electron or
ion.
Length = 99
Score = 50.1 bits (120), Expect = 1e-08
Identities = 18/46 (39%), Positives = 30/46 (65%), Gaps = 5/46 (10%)
Query: 9 ILVLSGKGGVGKSTVSTQLALGLKDKGFKVGILD----IDLCGPSV 50
++V++GKGGVGK+T++ LA L +G +V ++D ID P +
Sbjct: 1 VIVVTGKGGVGKTTLAANLAAALAKRGKRVLLIDDYVLID-TPPGL 45
Score = 39.7 bits (93), Expect = 7e-05
Identities = 18/62 (29%), Positives = 34/62 (54%), Gaps = 2/62 (3%)
Query: 119 DYLIIDTPPGTSDEHITVMECLREVQCDGAVLVTTPQAVSIEDVRKEITFCKKTNIKILG 178
DY++IDTPPG + ++ L + D ++VTTP+A+++ R+ + I+ L
Sbjct: 35 DYVLIDTPPGLGL--LVLLCLLALLAADLVIIVTTPEALAVLGARRLTEVVLELAIEGLR 92
Query: 179 LI 180
+
Sbjct: 93 PV 94
>gnl|CDD|220125 pfam09140, MipZ, ATPase MipZ. MipZ is an ATPase that forms a
complex with the chromosome partitioning protein ParB
near the chromosomal origin of replication. It is
responsible for the temporal and spatial regulation of
FtsZ ring formation.
Length = 262
Score = 48.5 bits (116), Expect = 4e-07
Identities = 18/39 (46%), Positives = 26/39 (66%)
Query: 7 HVILVLSGKGGVGKSTVSTQLALGLKDKGFKVGILDIDL 45
HVI+V + KGG GKST + +A+ L G +V +D+DL
Sbjct: 1 HVIVVGNEKGGSGKSTTAVHVAVALLYLGARVATIDLDL 39
>gnl|CDD|224071 COG1149, COG1149, MinD superfamily P-loop ATPase containing an
inserted ferredoxin domain [Energy production and
conversion].
Length = 284
Score = 48.1 bits (115), Expect = 5e-07
Identities = 24/63 (38%), Positives = 38/63 (60%), Gaps = 1/63 (1%)
Query: 9 ILVLSGKGGVGKSTVSTQLALGLKDKGFKVGILDIDLCGPSVPHLLNIENSDVHQCPEGW 68
+ V SGKGG GK+TV+ LA+ L DK +K+ + D D+ P++ LL +E + + G
Sbjct: 4 VAVASGKGGTGKTTVAANLAVLLGDK-YKLVLADCDVEAPNLHLLLGVEVLEEEEVIRGE 62
Query: 69 VPV 71
+P
Sbjct: 63 IPE 65
Score = 38.9 bits (91), Expect = 7e-04
Identities = 19/67 (28%), Positives = 31/67 (46%), Gaps = 6/67 (8%)
Query: 119 DYLIIDTPPGTSDEHITVMECLREVQCDGAVLVTTPQAVSIEDVRKEITFCKKTNIKILG 178
D LIID+ GT V+ L+ D A+LVT P + D+++ + + I G
Sbjct: 165 DLLIIDSAAGT---GCPVIASLKG--ADLAILVTEPTPFGLHDLKRALELVEHFGIPT-G 218
Query: 179 LIENMSG 185
++ N
Sbjct: 219 IVINRYN 225
>gnl|CDD|213904 TIGR04291, arsen_driv_ArsA, arsenical pump-driving ATPase. The
broader family (TIGR00345) to which the current family
belongs consists of transport-energizing ATPases,
including to TRC40/GET3 family involved in
post-translational insertion of protein C-terminal
transmembrane anchors into membranes from the cyotosolic
face. This family, however, is restricted to ATPases
that energize pumps that export arsenite (or
antimonite).
Length = 566
Score = 48.2 bits (115), Expect = 8e-07
Identities = 14/33 (42%), Positives = 23/33 (69%)
Query: 6 KHVILVLSGKGGVGKSTVSTQLALGLKDKGFKV 38
+ +++ GKGGVGK+TV+ +A+ L +KG V
Sbjct: 320 EKGLIMTMGKGGVGKTTVAAAIAVRLANKGLDV 352
Score = 37.0 bits (86), Expect = 0.004
Identities = 14/35 (40%), Positives = 24/35 (68%)
Query: 10 LVLSGKGGVGKSTVSTQLALGLKDKGFKVGILDID 44
L +GKGGVGK++++ A+ L D+G +V ++ D
Sbjct: 6 LFFTGKGGVGKTSIACATAINLADQGKRVLLVSTD 40
>gnl|CDD|238991 cd02034, CooC, The accessory protein CooC, which contains a
nucleotide-binding domain (P-loop) near the N-terminus,
participates in the maturation of the nickel center of
carbon monoxide dehydrogenase (CODH). CODH from
Rhodospirillum rubrum catalyzes the reversible
oxidation of CO to CO2. CODH contains a
nickel-iron-sulfur cluster (C-center) and an
iron-sulfur cluster (B-center). CO oxidation occurs at
the C-center. Three accessory proteins encoded by
cooCTJ genes are involved in nickel incorporation into
a nickel site. CooC functions as a nickel insertase
that mobilizes nickel to apoCODH using energy released
from ATP hydrolysis. CooC is a homodimer and has NTPase
activities. Mutation at the P-loop abolishs its
function.
Length = 116
Score = 43.4 bits (103), Expect = 5e-06
Identities = 17/36 (47%), Positives = 24/36 (66%), Gaps = 2/36 (5%)
Query: 9 ILVLSGKGGVGKSTVSTQLALGLKDKGFKVGILDID 44
+ ++GKGGVGK+T++ LA L +KG V L ID
Sbjct: 1 KIAITGKGGVGKTTIAALLARYLAEKGKPV--LAID 34
>gnl|CDD|222854 PHA02518, PHA02518, ParA-like protein; Provisional.
Length = 211
Score = 44.8 bits (106), Expect = 6e-06
Identities = 19/37 (51%), Positives = 26/37 (70%)
Query: 8 VILVLSGKGGVGKSTVSTQLALGLKDKGFKVGILDID 44
+I VL+ KGG GK+TV+T LA L G KV ++D+D
Sbjct: 2 IIAVLNQKGGAGKTTVATNLASWLHADGHKVLLVDLD 38
>gnl|CDD|223082 COG0003, ArsA, Predicted ATPase involved in chromosome partitioning
[Cell division and chromosome partitioning].
Length = 322
Score = 41.6 bits (98), Expect = 1e-04
Identities = 31/137 (22%), Positives = 58/137 (42%), Gaps = 23/137 (16%)
Query: 9 ILVLSGKGGVGKSTVSTQLALGLKDKGFKVGILDIDLCGP--SVPHLLNIE-NSDVHQCP 65
I+ +GKGGVGK+T++ A+ L + G KV ++ D P S+ + ++E D +
Sbjct: 4 IVFFTGKGGVGKTTIAAATAVKLAESGKKVLLVSTD---PAHSLGDVFDLELGHDPRKVG 60
Query: 66 ---------------EGWVPVYTDASQTLAVMSIGFLLKNRDDAIIWRGPKKTAMIRQII 110
E W V ++ L +G + D+ G + + +I+
Sbjct: 61 PNLDALELDPEKALEEYWDEVKDYLARLLRTRGLGGI--YADELATLPGIDEALALLKIL 118
Query: 111 NDVCWKDVDYLIIDTPP 127
+ D +++DT P
Sbjct: 119 EYYVSGEYDVIVVDTAP 135
>gnl|CDD|239388 cd03114, ArgK-like, The function of this protein family is
unkown. The protein sequences are similar to the ArgK
protein in E. coli. ArgK protein is a membrane ATPase
which is required for transporting arginine, ornithine
and lysine into the cells by the arginine and ornithine
(AO system) and lysine, arginine and ornithine (LAO)
transport systems.
Length = 148
Score = 40.4 bits (95), Expect = 1e-04
Identities = 16/43 (37%), Positives = 25/43 (58%), Gaps = 3/43 (6%)
Query: 9 ILVLSGKGGVGKSTVSTQLALGLKDKGFKVGILDIDLCGPSVP 51
++ ++G G GKST+ L L+ +G +V +L ID PS P
Sbjct: 1 VIGITGVPGAGKSTLIDALITALRARGKRVAVLAID---PSSP 40
>gnl|CDD|239385 cd03111, CpaE_like, This protein family consists of proteins
similar to the cpaE protein of the Caulobacter pilus
assembly and the orf4 protein of Actinobacillus pilus
formation gene cluster. The function of these proteins
are unkown. The Caulobacter pilus assembly contains 7
genes: pilA, cpaA, cpaB, cpaC, cpaD, cpaE and cpaF.
These genes are clustered together on chromosome.
Length = 106
Score = 38.9 bits (91), Expect = 2e-04
Identities = 17/39 (43%), Positives = 27/39 (69%), Gaps = 1/39 (2%)
Query: 8 VILVLSGKGGVGKSTVSTQLALGL-KDKGFKVGILDIDL 45
VI + KGGVG +T++ LA+ L K+ G +V ++D+DL
Sbjct: 1 VIAFIGAKGGVGATTLAANLAVALAKEAGRRVLLVDLDL 39
Score = 28.5 bits (64), Expect = 1.0
Identities = 10/45 (22%), Positives = 19/45 (42%), Gaps = 5/45 (11%)
Query: 119 DYLIIDTPPGTSDEHITVMECLREVQCDGAVLVTTPQAVSIEDVR 163
DY+++D + + ++ Q D LVT SI + +
Sbjct: 44 DYVVVDLGRSLDEVSLAALD-----QADRVFLVTQQDLPSIRNAK 83
>gnl|CDD|217004 pfam02374, ArsA_ATPase, Anion-transporting ATPase. This Pfam
family represents a conserved domain, which is
sometimes repeated, in an anion-transporting ATPase.
The ATPase is involved in the removal of arsenate,
antimonite, and arsenate from the cell.
Length = 304
Score = 40.4 bits (95), Expect = 2e-04
Identities = 16/36 (44%), Positives = 23/36 (63%)
Query: 9 ILVLSGKGGVGKSTVSTQLALGLKDKGFKVGILDID 44
+ GKGGVGK+TVS A+ L ++G KV ++ D
Sbjct: 3 WIFFGGKGGVGKTTVSCATAVRLSEQGKKVLLVSTD 38
>gnl|CDD|225267 COG2403, COG2403, Predicted GTPase [General function prediction
only].
Length = 449
Score = 40.1 bits (94), Expect = 4e-04
Identities = 50/205 (24%), Positives = 78/205 (38%), Gaps = 54/205 (26%)
Query: 1 MLDGVKHVILVLSGKGGVGKSTVSTQLALGLKDKGFKVGI---------LDIDLCGPSVP 51
ML K VI V + + GVGKS VS +A L+++G++V + I++ +V
Sbjct: 121 MLKLEKPVIAVTATRTGVGKSAVSRYVARLLRERGYRVCVVRHPMIYRGDRIEI---TVE 177
Query: 52 HLLNIENSDVHQCPEGWVPVYTDASQTLAVMSIGF----LLKNRD---DAIIWRGPKKTA 104
L +E+ D H + Y T + G +LK + D I+W G
Sbjct: 178 RLAKLEDLDRHAATDEEREEYESYIPTGGGVLAGVDYGTVLKEGEKEADFILWDGGN--- 234
Query: 105 MIRQIINDVCWKDVDYLIIDTPPGTSDEHITVMECLREVQ-------------CDGAVLV 151
ND P D HI V++ LR + D V++
Sbjct: 235 ------NDF------------PFVKPDLHIVVVDALRPGEEIGSFPGELRIRLAD-LVII 275
Query: 152 TTPQAVSIEDVRKEITFCKKTNIKI 176
T + E VRK + ++ N K
Sbjct: 276 TKVEEAMAEKVRKIVRNIEEINPKA 300
>gnl|CDD|224617 COG1703, ArgK, Putative periplasmic protein kinase ArgK and
related GTPases of G3E family [Amino acid transport and
metabolism].
Length = 323
Score = 37.7 bits (88), Expect = 0.002
Identities = 15/43 (34%), Positives = 26/43 (60%), Gaps = 3/43 (6%)
Query: 9 ILVLSGKGGVGKSTVSTQLALGLKDKGFKVGILDIDLCGPSVP 51
++ ++G G GKST+ L L+++G +V +L +D PS P
Sbjct: 53 VIGITGVPGAGKSTLIEALGRELRERGHRVAVLAVD---PSSP 92
>gnl|CDD|226166 COG3640, CooC, CO dehydrogenase maturation factor [Cell division
and chromosome partitioning].
Length = 255
Score = 37.2 bits (87), Expect = 0.002
Identities = 18/54 (33%), Positives = 31/54 (57%), Gaps = 2/54 (3%)
Query: 8 VILVLSGKGGVGKSTVSTQLALGLKDK-GFKVGILDIDLCGPSVPHLLNIENSD 60
+ + ++GKGGVGK+T++ L L K G+ V ++D D ++P L +E
Sbjct: 1 MKIAITGKGGVGKTTIAALLLKRLLSKGGYNVLVVDAD-PDSNLPEALGVEEPM 53
>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 = 36.3 bits (84), Expect = 0.003
Identities = 28/93 (30%), Positives = 43/93 (46%), Gaps = 7/93 (7%)
Query: 8 VILVLSGKGGVGKSTVSTQLALGLKDKGFKVGILDIDLCGPSVPHLLNIENSDVHQCPEG 67
+ILV G GK+T++ QLAL + KG KV +DI+ + L E+ +
Sbjct: 1 LILVFGP-TGSGKTTLALQLALNIATKGGKVVYVDIEEEIEELTERLIGESLKGA--LDN 57
Query: 68 WVPVY--TDASQTLAVMSIGFLLKNR--DDAII 96
+ V+ D ++S L+ R DD II
Sbjct: 58 LIIVFATADDPAAARLLSKAERLRERGGDDLII 90
>gnl|CDD|132613 TIGR03574, selen_PSTK, L-seryl-tRNA(Sec) kinase, archaeal. Members
of this protein are L-seryl-tRNA(Sec) kinase. This
enzyme is part of a two-step pathway in Eukaryota and
Archaea for performing selenocysteine biosynthesis by
changing serine misacylated on selenocysteine-tRNA to
selenocysteine. This enzyme performs the first step,
phosphorylation of the OH group of the serine side
chain. This family represents archaeal proteins with
this activity [Protein synthesis, tRNA aminoacylation].
Length = 249
Score = 36.7 bits (85), Expect = 0.004
Identities = 34/115 (29%), Positives = 50/115 (43%), Gaps = 15/115 (13%)
Query: 9 ILVLSGKGGVGKSTVSTQLALGLKDKGFKVGILDIDLCGPSVPHLLNIENSDVHQCPEGW 68
+++L+G GVGKST S +LA L +K V IL DL S P W
Sbjct: 1 LIILTGLPGVGKSTFSKELAKKLSEKNIDVIILGTDLIRESFPV---------------W 45
Query: 69 VPVYTDASQTLAVMSIGFLLKNRDDAIIWRGPKKTAMIRQIINDVCWKDVDYLII 123
Y + + + I LKN+ I+ +M R +IN + +Y+II
Sbjct: 46 KEKYEEFIRDSTLYLIKTALKNKYSVIVDDTNYYNSMRRDLINIAKEYNKNYIII 100
>gnl|CDD|239389 cd03115, SRP, The signal recognition particle (SRP) mediates the
transport to or across the plasma membrane in bacteria
and the endoplasmic reticulum in eukaryotes. SRP
recognizes N-terminal sighnal sequences of newly
synthesized polypeptides at the ribosome. The
SRP-polypeptide complex is then targeted to the
membrane by an interaction between SRP and its cognated
receptor (SR). In mammals, SRP consists of six protein
subunits and a 7SL RNA. One of these subunits is a 54
kd protein (SRP54), which is a GTP-binding protein that
interacts with the signal sequence when it emerges from
the ribosome. SRP54 is a multidomain protein that
consists of an N-terminal domain, followed by a central
G (GTPase) domain and a C-terminal M domain.
Length = 173
Score = 35.6 bits (83), Expect = 0.006
Identities = 17/37 (45%), Positives = 25/37 (67%)
Query: 9 ILVLSGKGGVGKSTVSTQLALGLKDKGFKVGILDIDL 45
+++L G GVGK+T + +LAL LK KG KV ++ D
Sbjct: 2 VILLVGLQGVGKTTTAAKLALYLKKKGKKVLLVAADT 38
>gnl|CDD|112137 pfam03308, ArgK, ArgK protein. The ArgK protein acts as an
ATPase enzyme and as a kinase, and phosphorylates
periplasmic binding proteins involved in the LAO
(lysine, arginine, ornithine)/AO transport systems.
Length = 267
Score = 35.8 bits (83), Expect = 0.007
Identities = 15/43 (34%), Positives = 25/43 (58%), Gaps = 3/43 (6%)
Query: 9 ILVLSGKGGVGKSTVSTQLALGLKDKGFKVGILDIDLCGPSVP 51
+ ++G G GKST+ L + L+ +G +V +L +D PS P
Sbjct: 31 RVGITGVPGAGKSTLIEALGMELRRRGHRVAVLAVD---PSSP 70
>gnl|CDD|234363 TIGR03815, CpaE_hom_Actino, helicase/secretion neighborhood
CpaE-like protein. Members of this protein family
belong to the MinD/ParA family of P-loop NTPases, and in
particular show homology to the CpaE family of pilus
assembly proteins (see PMID:12370432). Nearly all
members are found, not only in a gene context consistent
with pilus biogenesis or a pilus-like secretion
apparatus, but also near a DEAD/DEAH-box helicase,
suggesting an involvement in DNA transfer activity. The
model describes a clade restricted to the
Actinobacteria.
Length = 322
Score = 36.2 bits (84), Expect = 0.007
Identities = 18/54 (33%), Positives = 28/54 (51%)
Query: 7 HVILVLSGKGGVGKSTVSTQLALGLKDKGFKVGILDIDLCGPSVPHLLNIENSD 60
V+ V+ G+GG G ST++ LAL G + ++D D G + LL E+
Sbjct: 94 VVVAVIGGRGGAGASTLAAALALAAARHGLRTLLVDADPWGGGLDLLLGAEDVP 147
>gnl|CDD|130348 TIGR01281, DPOR_bchL, light-independent protochlorophyllide
reductase, iron-sulfur ATP-binding protein. The BchL
peptide (ChlL in chloroplast and cyanobacteria) is an
ATP-binding iron-sulfur protein of the dark form
protochlorophyllide reductase, an enzyme similar to
nitrogenase. This subunit resembles the nitrogenase
NifH subunit [Biosynthesis of cofactors, prosthetic
groups, and carriers, Chlorophyll and
bacteriochlorphyll].
Length = 268
Score = 35.2 bits (81), Expect = 0.012
Identities = 14/30 (46%), Positives = 20/30 (66%)
Query: 9 ILVLSGKGGVGKSTVSTQLALGLKDKGFKV 38
IL + GKGG+GKST S+ L++ G +V
Sbjct: 2 ILAVYGKGGIGKSTTSSNLSVAFAKLGKRV 31
>gnl|CDD|179157 PRK00889, PRK00889, adenylylsulfate kinase; Provisional.
Length = 175
Score = 34.6 bits (80), Expect = 0.012
Identities = 14/38 (36%), Positives = 23/38 (60%)
Query: 8 VILVLSGKGGVGKSTVSTQLALGLKDKGFKVGILDIDL 45
V + +G G GK+T++ LA L++ G+ V +LD D
Sbjct: 5 VTVWFTGLSGAGKTTIARALAEKLREAGYPVEVLDGDA 42
>gnl|CDD|132063 TIGR03018, pepcterm_TyrKin, exopolysaccharide/PEP-CTERM locus
tyrosine autokinase. Members of this protein family are
related to a known protein-tyrosine autokinase and to
numerous homologs from exopolysaccharide biosynthesis
region proteins, many of which are designated as chain
length determinants. Most members of this family contain
a short region, immediately C-terminal to the region
modeled here, with an abundance of Tyr residues. These
C-terminal tyrosine residues are likely to be
autophosphorylation sites. Some members of this family
are fusion proteins.
Length = 207
Score = 35.0 bits (81), Expect = 0.013
Identities = 42/197 (21%), Positives = 74/197 (37%), Gaps = 48/197 (24%)
Query: 8 VILVLSGKGGVGKSTVSTQLALGL-KDKGFKVGILDIDLCGPSVPHLLNIENSDVHQCPE 66
+I+V S G GKS + LA+ L ++ V ++D DL PS+ L +E
Sbjct: 37 LIMVTSSLPGEGKSFTAINLAISLAQEYDKTVLLIDADLRRPSLHRTLGLEAE------P 90
Query: 67 GWVPVYTDASQTLAVMSIGFLLKNRDDAIIWRGPKK------------------TAMIRQ 108
G D LA D ++ + + +R
Sbjct: 91 GLSDCLLDPVLDLA------------DVLVPTNIGRLSLLPAGRRHPNPTELLASQRMRS 138
Query: 109 IINDVCWKDVD-YLIIDTPP--GTSDEHITVMECLREVQCDGAVLVTTPQAVSIEDVRKE 165
+++++ + D +IIDTPP S+ L VLV + E V++
Sbjct: 139 LLHELARRYPDRIIIIDTPPLLVFSEARA-----LAR-LVGQIVLVVEEGRTTQEAVKEA 192
Query: 166 ITFCKKTNIKILGLIEN 182
++ + K+LG++ N
Sbjct: 193 LSALESC--KVLGVVLN 207
>gnl|CDD|129833 TIGR00750, lao, LAO/AO transport system ATPase. In E. coli,
mutation of this kinase blocks phosphorylation of two
transporter system periplasmic binding proteins and
consequently inhibits those transporters. This kinase
is also found in Gram-positive bacteria, archaea, and
the roundworm C. elegans. It may have a more general,
but still unknown function. Mutations have also been
found that do not phosphorylate the periplasmic binding
proteins, yet still allow transport. The ATPase
activity of this protein seems to be necessary, however
[Transport and binding proteins, Amino acids, peptides
and amines, Regulatory functions, Protein
interactions].
Length = 300
Score = 35.1 bits (81), Expect = 0.015
Identities = 14/43 (32%), Positives = 25/43 (58%), Gaps = 3/43 (6%)
Query: 9 ILVLSGKGGVGKSTVSTQLALGLKDKGFKVGILDIDLCGPSVP 51
+ ++G G GKST+ L + L+ +G +V ++ +D PS P
Sbjct: 36 RVGITGTPGAGKSTLLEALGMELRRRGLRVAVIAVD---PSSP 75
>gnl|CDD|238996 cd02040, NifH, NifH gene encodes component II (iron protein) of
nitrogenase. Nitrogenase is responsible for the
biological nitrogen fixation, i.e. reduction of
molecular nitrogen to ammonia. NifH consists of two
oxygen-sensitive metallosulfur proteins: the
mollybdenum-iron (alternatively, vanadium-iron or
iron-iron) protein (commonly referred to as component
1), and the iron protein (commonly referred to as
component 2). The iron protein is a homodimer, with an
Fe4S4 cluster bound between the subunits and two
ATP-binding domains. It supplies energy by ATP
hydrolysis, and transfers electrons from reduced
ferredoxin or flavodoxin to component 1 for the
reduction of molecular nitrogen to ammonia.
Length = 270
Score = 34.9 bits (81), Expect = 0.015
Identities = 13/25 (52%), Positives = 17/25 (68%)
Query: 14 GKGGVGKSTVSTQLALGLKDKGFKV 38
GKGG+GKST + L+ L + G KV
Sbjct: 8 GKGGIGKSTTTQNLSAALAEMGKKV 32
>gnl|CDD|219839 pfam08433, KTI12, Chromatin associated protein KTI12. This is a
family of chromatin associated proteins which interact
with the Elongator complex, a component of the
elongating form of RNA polymerase II. The Elongator
complex has histone acetyltransferase activity.
Length = 266
Score = 34.6 bits (80), Expect = 0.018
Identities = 13/38 (34%), Positives = 24/38 (63%)
Query: 10 LVLSGKGGVGKSTVSTQLALGLKDKGFKVGILDIDLCG 47
++L+G GKST + +LA L++KG+ V ++ + G
Sbjct: 2 IILTGLPSSGKSTRAKELAKYLEEKGYDVIVISDESLG 39
>gnl|CDD|234188 TIGR03371, cellulose_yhjQ, cellulose synthase operon protein
YhjQ. Members of this family are the YhjQ protein,
found immediately upsteam of bacterial cellulose
synthase (bcs) genes in a broad range of bacteria,
including both copies of the bcs locus in Klebsiella
pneumoniae. In several species it is seen clearly as
part of the bcs operon. It is identified as a probable
component of the bacterial cellulose metabolic process
not only by gene location, but also by partial
phylogenetic profiling, or Haft-Selengut algorithm
(PMID:16930487), based on a bacterial cellulose
biosynthesis genome property profile. Cellulose plays
an important role in biofilm formation and structural
integrity in some bacteria. Mutants in yhjQ in
Escherichia coli, show altered morphology an growth,
but the function of YhjQ has not yet been determined
[Cell envelope, Biosynthesis and degradation of surface
polysaccharides and lipopolysaccharides].
Length = 246
Score = 34.6 bits (80), Expect = 0.018
Identities = 17/38 (44%), Positives = 25/38 (65%)
Query: 7 HVILVLSGKGGVGKSTVSTQLALGLKDKGFKVGILDID 44
VI ++S +GGVGK+T++ LA LK G V +D+D
Sbjct: 2 KVIAIVSVRGGVGKTTLTANLASALKLLGEPVLAIDLD 39
>gnl|CDD|224267 COG1348, NifH, Nitrogenase subunit NifH (ATPase) [Inorganic ion
transport and metabolism].
Length = 278
Score = 34.6 bits (80), Expect = 0.019
Identities = 17/31 (54%), Positives = 20/31 (64%)
Query: 14 GKGGVGKSTVSTQLALGLKDKGFKVGILDID 44
GKGG+GKST S LA L + G KV I+ D
Sbjct: 8 GKGGIGKSTTSQNLAAALAELGKKVLIVGCD 38
>gnl|CDD|238989 cd02032, Bchl_like, This family of proteins contains bchL and
chlL. Protochlorophyllide reductase catalyzes the
reductive formation of chlorophyllide from
protochlorophyllide during biosynthesis of chlorophylls
and bacteriochlorophylls. Three genes, bchL, bchN and
bchB, are involved in light-independent
protochlorophyllide reduction in bacteriochlorophyll
biosynthesis. In cyanobacteria, algae, and gymnosperms,
three similar genes, chlL, chlN and chlB are involved
in protochlorophyllide reduction during chlorophylls
biosynthesis. BchL/chlL, bchN/chlN and bchB/chlB
exhibit significant sequence similarity to the nifH,
nifD and nifK subunits of nitrogenase, respectively.
Nitrogenase catalyzes the reductive formation of
ammonia from dinitrogen.
Length = 267
Score = 34.7 bits (80), Expect = 0.019
Identities = 15/30 (50%), Positives = 22/30 (73%)
Query: 9 ILVLSGKGGVGKSTVSTQLALGLKDKGFKV 38
+L + GKGG+GKST S+ L++ L +G KV
Sbjct: 2 VLAVYGKGGIGKSTTSSNLSVALAKRGKKV 31
>gnl|CDD|239034 cd02117, NifH_like, This family contains the NifH (iron protein)
of nitrogenase, L subunit (BchL/ChlL) of the
protochlorophyllide reductase and the BchX subunit of
the Chlorophyllide reductase. Members of this family
use energey from ATP hydrolysis and transfer electrons
through a Fe4-S4 cluster to other subunit for reduction
of substrate.
Length = 212
Score = 34.5 bits (80), Expect = 0.019
Identities = 14/25 (56%), Positives = 17/25 (68%)
Query: 14 GKGGVGKSTVSTQLALGLKDKGFKV 38
GKGG+GKST S L+ L + G KV
Sbjct: 7 GKGGIGKSTTSQNLSAALAEMGKKV 31
>gnl|CDD|237293 PRK13185, chlL, protochlorophyllide reductase iron-sulfur
ATP-binding protein; Provisional.
Length = 270
Score = 34.2 bits (79), Expect = 0.027
Identities = 16/31 (51%), Positives = 20/31 (64%), Gaps = 2/31 (6%)
Query: 10 LVLS--GKGGVGKSTVSTQLALGLKDKGFKV 38
LVL+ GKGG+GKST S+ L+ G KV
Sbjct: 3 LVLAVYGKGGIGKSTTSSNLSAAFAKLGKKV 33
>gnl|CDD|224260 COG1341, COG1341, Predicted GTPase or GTP-binding protein [General
function prediction only].
Length = 398
Score = 34.3 bits (79), Expect = 0.027
Identities = 17/42 (40%), Positives = 24/42 (57%), Gaps = 1/42 (2%)
Query: 3 DGVKHVILVLSGKGGVGKSTVSTQLALGLKDKGFKVGILDID 44
G V++V+ GKST++T LA L +G KV I+D D
Sbjct: 70 AGKVGVVMVVGPVD-SGKSTLTTYLANKLLARGRKVAIIDAD 110
>gnl|CDD|184370 PRK13886, PRK13886, conjugal transfer protein TraL; Provisional.
Length = 241
Score = 33.9 bits (78), Expect = 0.028
Identities = 16/35 (45%), Positives = 21/35 (60%)
Query: 10 LVLSGKGGVGKSTVSTQLALGLKDKGFKVGILDID 44
+VL GKGGVGKS ++ +A KG K +D D
Sbjct: 6 MVLQGKGGVGKSFIAATIAQYKASKGQKPLCIDTD 40
>gnl|CDD|129547 TIGR00455, apsK, adenylylsulfate kinase (apsK). This protein,
adenylylsulfate kinase, is often found as a fusion
protein with sulfate adenylyltransferase. Important
residue (active site in E.coli) is residue 100 of the
seed alignment [Central intermediary metabolism, Sulfur
metabolism].
Length = 184
Score = 33.6 bits (77), Expect = 0.030
Identities = 22/54 (40%), Positives = 34/54 (62%), Gaps = 4/54 (7%)
Query: 2 LDGVKHVILVLSGKGGVGKSTVSTQLALGLKDKGFKVGILDIDLCGPSVPHLLN 55
L+G + V++ L+G G GKST++ L L+ KG++V +LD G +V H LN
Sbjct: 13 LNGHRGVVIWLTGLSGSGKSTIANALEKKLESKGYRVYVLD----GDNVRHGLN 62
>gnl|CDD|233343 TIGR01287, nifH, nitrogenase iron protein. This model describes
nitrogenase (EC 1.18.6.1) iron protein, also called
nitrogenase reductase or nitrogenase component II. This
model includes molybdenum-iron nitrogenase reductase
(nifH), vanadium-iron nitrogenase reductase (vnfH), and
iron-iron nitrogenase reductase (anfH). The model
excludes the homologous protein from the
light-independent protochlorophyllide reductase
[Central intermediary metabolism, Nitrogen fixation].
Length = 275
Score = 33.5 bits (77), Expect = 0.046
Identities = 15/31 (48%), Positives = 20/31 (64%)
Query: 14 GKGGVGKSTVSTQLALGLKDKGFKVGILDID 44
GKGG+GKST + +A L + G KV I+ D
Sbjct: 7 GKGGIGKSTTTQNIAAALAEMGKKVMIVGCD 37
>gnl|CDD|139929 PRK13869, PRK13869, plasmid-partitioning protein RepA; Provisional.
Length = 405
Score = 33.5 bits (76), Expect = 0.050
Identities = 17/38 (44%), Positives = 24/38 (63%)
Query: 7 HVILVLSGKGGVGKSTVSTQLALGLKDKGFKVGILDID 44
VI V + KGG GK+T S LA L +G++V +D+D
Sbjct: 122 QVIAVTNFKGGSGKTTTSAHLAQYLALQGYRVLAVDLD 159
>gnl|CDD|234215 TIGR03453, partition_RepA, plasmid partitioning protein RepA.
Members of this family are the RepA (or ParA) protein
involved in replicon partitioning. All known examples
occur in bacterial species with two or more replicons,
on a plasmid or the smaller chromosome. Note that an
apparent exception may be seen as a pseudomolecule from
assembly of an incompletely sequenced genome. Members of
this family belong to a larger family that also includes
the enzyme cobyrinic acid a,c-diamide synthase, but
assignment of that name to members of this family would
be in error [Mobile and extrachromosomal element
functions, Plasmid functions].
Length = 387
Score = 33.4 bits (77), Expect = 0.052
Identities = 18/38 (47%), Positives = 24/38 (63%), Gaps = 2/38 (5%)
Query: 8 VILVLSGKGGVGKSTVSTQLALGLKDKGFKVGILDIDL 45
VI V + KGG GK+T + LA L +G++V L IDL
Sbjct: 106 VIAVTNFKGGSGKTTTAAHLAQYLALRGYRV--LAIDL 141
>gnl|CDD|177011 CHL00072, chlL, photochlorophyllide reductase subunit L.
Length = 290
Score = 33.2 bits (76), Expect = 0.052
Identities = 14/29 (48%), Positives = 20/29 (68%)
Query: 10 LVLSGKGGVGKSTVSTQLALGLKDKGFKV 38
L + GKGG+GKST S +++ L +G KV
Sbjct: 3 LAVYGKGGIGKSTTSCNISIALARRGKKV 31
>gnl|CDD|224401 COG1484, DnaC, DNA replication protein [DNA replication,
recombination, and repair].
Length = 254
Score = 33.1 bits (76), Expect = 0.061
Identities = 11/34 (32%), Positives = 16/34 (47%)
Query: 10 LVLSGKGGVGKSTVSTQLALGLKDKGFKVGILDI 43
LVL G GVGK+ ++ + L G V +
Sbjct: 108 LVLLGPPGVGKTHLAIAIGNELLKAGISVLFITA 141
>gnl|CDD|223603 COG0529, CysC, Adenylylsulfate kinase and related kinases
[Inorganic ion transport and metabolism].
Length = 197
Score = 32.6 bits (75), Expect = 0.063
Identities = 19/50 (38%), Positives = 27/50 (54%), Gaps = 4/50 (8%)
Query: 6 KHVILVLSGKGGVGKSTVSTQLALGLKDKGFKVGILDIDLCGPSVPHLLN 55
K ++ +G G GKST++ L L KG+ V +LD G +V H LN
Sbjct: 22 KGAVIWFTGLSGSGKSTIANALEEKLFAKGYHVYLLD----GDNVRHGLN 67
>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 = 33.2 bits (76), Expect = 0.065
Identities = 22/134 (16%), Positives = 46/134 (34%), Gaps = 18/134 (13%)
Query: 10 LVLSGKGGVGKSTVSTQLALGLKDKGFKVGILDIDLCGPSVPHLLNIENSDVHQCPEGWV 69
+++ G G GKST+ LAL L +G +V ++D L +
Sbjct: 4 MLIVGPSGSGKSTLLKLLALRLLARGGRVIVIDP---KGEYSGL-------ARALGGEVI 53
Query: 70 PVYTDASQTLAVMSIGFLLKNRDDAIIWRGPKKTAMIRQIINDVCWKDVDYLIIDTPPGT 129
+ + +L + I ++ ++ +K ++ ++ D T
Sbjct: 54 DLGPGSGISLNPLDIFPTGEDAEELEADAHARKLDLLLALLELAALLGRDL--------T 105
Query: 130 SDEHITVMECLREV 143
E + LR +
Sbjct: 106 PREETALDRALRAL 119
>gnl|CDD|227298 COG4963, CpaE, Flp pilus assembly protein, ATPase CpaE
[Intracellular trafficking and secretion].
Length = 366
Score = 33.2 bits (76), Expect = 0.068
Identities = 41/179 (22%), Positives = 73/179 (40%), Gaps = 25/179 (13%)
Query: 8 VILVLSGKGGVGKSTVSTQLALGLKDK-GFKVGILDIDLCGPSVPHLLNIEN----SDVH 62
+ L KGGVG ST++ LA GL G V ++D+DL G + L+ + ++
Sbjct: 106 ELAFLGAKGGVGTSTLAHNLAKGLAILSGAAVLLVDLDLQGGTAALYLDQDPAFGIAEAV 165
Query: 63 QCPEGWVPVYTDASQT-----LAVMS-IGFLLKNRDDAIIWRGPKKTAMIRQIINDVCWK 116
+ PE V D+ T L +++ L KN D + + D+
Sbjct: 166 KQPERLDQVLLDSLLTRLASGLKLLAAPTELAKNYD---------LKTGAVERLLDLLRG 216
Query: 117 DVDYLIIDTPPGTSDEHITVMECLREVQCDGAVLVTTPQAVSIEDVRKEITFCKKTNIK 175
D++++D P +D V+ D V+V P S+ + ++ + K+
Sbjct: 217 SFDFVVVDLPNIWTDWTRQVL-----SGSDEIVIVAEPSLASLRNAKELLDELKRLRPN 270
>gnl|CDD|215925 pfam00448, SRP54, SRP54-type protein, GTPase domain. This family
includes relatives of the G-domain of the SRP54 family
of proteins.
Length = 196
Score = 32.5 bits (75), Expect = 0.074
Identities = 15/33 (45%), Positives = 21/33 (63%), Gaps = 1/33 (3%)
Query: 8 VILVLSGKGGVGKSTVSTQLALGLKDKGFKVGI 40
VIL++ G G GK+T +LA LK +G KV +
Sbjct: 3 VILLV-GLQGSGKTTTIAKLAAYLKKQGKKVLL 34
>gnl|CDD|234896 PRK01077, PRK01077, cobyrinic acid a,c-diamide synthase;
Validated.
Length = 451
Score = 32.8 bits (76), Expect = 0.083
Identities = 14/36 (38%), Positives = 20/36 (55%), Gaps = 6/36 (16%)
Query: 10 LVLSGKG-GVGKSTVSTQLALGLKDKG-----FKVG 39
LV++ G GK+TV+ L L+ +G FKVG
Sbjct: 6 LVIAAPASGSGKTTVTLGLMRALRRRGLRVQPFKVG 41
>gnl|CDD|130492 TIGR01425, SRP54_euk, signal recognition particle protein SRP54.
This model represents examples from the eukaryotic
cytosol of the signal recognition particle protein
component, SRP54. This GTP-binding protein is a
component of the eukaryotic signal recognition particle,
along with several other protein subunits and a 7S RNA.
Some species, including Arabidopsis, have several
closely related forms. The extreme C-terminal region is
glycine-rich and lower in complexity, poorly conserved
between species, and excluded from this model.
Length = 429
Score = 32.9 bits (75), Expect = 0.094
Identities = 16/41 (39%), Positives = 25/41 (60%), Gaps = 1/41 (2%)
Query: 4 GVKHVILVLSGKGGVGKSTVSTQLALGLKDKGFKVGILDID 44
G ++VI+ + G G GK+T T+LA + KGFK ++ D
Sbjct: 98 GKQNVIMFV-GLQGSGKTTTCTKLAYYYQRKGFKPCLVCAD 137
>gnl|CDD|224533 COG1618, COG1618, Predicted nucleotide kinase [Nucleotide
transport and metabolism].
Length = 179
Score = 32.3 bits (74), Expect = 0.098
Identities = 13/30 (43%), Positives = 24/30 (80%)
Query: 10 LVLSGKGGVGKSTVSTQLALGLKDKGFKVG 39
+ ++G+ GVGK+T+ ++A L++KG+KVG
Sbjct: 8 IFITGRPGVGKTTLVLKIAEKLREKGYKVG 37
>gnl|CDD|224337 COG1419, FlhF, Flagellar GTP-binding protein [Cell motility and
secretion].
Length = 407
Score = 32.3 bits (74), Expect = 0.13
Identities = 15/45 (33%), Positives = 22/45 (48%), Gaps = 2/45 (4%)
Query: 2 LDGVKHVILVLSGKGGVGKSTVSTQLA--LGLKDKGFKVGILDID 44
L + ++ L G GVGK+T +LA + K KV I+ D
Sbjct: 198 LIVEQKRVIALVGPTGVGKTTTLAKLAARYVMLKKKKKVAIITTD 242
>gnl|CDD|183903 PRK13230, PRK13230, nitrogenase reductase-like protein; Reviewed.
Length = 279
Score = 32.1 bits (73), Expect = 0.15
Identities = 18/51 (35%), Positives = 27/51 (52%), Gaps = 8/51 (15%)
Query: 14 GKGGVGKSTVSTQLALGLKDKGFKVGILDID--------LCGPSVPHLLNI 56
GKGG+GKST +A L + G KV ++ D L G +P +L++
Sbjct: 8 GKGGIGKSTTVCNIAAALAESGKKVLVVGCDPKADCTRNLVGEKIPTVLDV 58
>gnl|CDD|238978 cd02020, CMPK, Cytidine monophosphate kinase (CMPK) catalyzes the
reversible phosphorylation of cytidine monophosphate
(CMP) to produce cytidine diphosphate (CDP), using ATP
as the preferred phosphoryl donor.
Length = 147
Score = 31.3 bits (72), Expect = 0.16
Identities = 13/26 (50%), Positives = 16/26 (61%), Gaps = 2/26 (7%)
Query: 9 ILVLSGKGGVGKSTVSTQLA--LGLK 32
I+ + G G GKSTV+ LA LGL
Sbjct: 1 IIAIDGPAGSGKSTVAKLLAKKLGLP 26
>gnl|CDD|224710 COG1797, CobB, Cobyrinic acid a,c-diamide synthase [Coenzyme
metabolism].
Length = 451
Score = 32.2 bits (74), Expect = 0.16
Identities = 14/36 (38%), Positives = 21/36 (58%), Gaps = 6/36 (16%)
Query: 10 LVLSGKG-GVGKSTVSTQLALGLKDKG-----FKVG 39
+V++G G GK+TV+ L L+ +G FKVG
Sbjct: 3 VVIAGTSSGSGKTTVTLGLMRALRRRGLKVQPFKVG 38
>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 = 31.4 bits (71), Expect = 0.17
Identities = 9/36 (25%), Positives = 18/36 (50%)
Query: 9 ILVLSGKGGVGKSTVSTQLALGLKDKGFKVGILDID 44
++L+G G GK+++ +L GL K + +
Sbjct: 26 SVLLTGPSGTGKTSLLRELLEGLLVAAGKCDQAERN 61
>gnl|CDD|179118 PRK00771, PRK00771, signal recognition particle protein Srp54;
Provisional.
Length = 437
Score = 31.7 bits (73), Expect = 0.19
Identities = 31/119 (26%), Positives = 44/119 (36%), Gaps = 34/119 (28%)
Query: 9 ILVLSGKGGVGKSTVSTQLALGLKDKGFKVGILDIDLCGPSVPHLLNIENSDVHQCPEGW 68
++L G G GK+T + +LA K KG KVG++ D P+ L +
Sbjct: 97 TIMLVGLQGSGKTTTAAKLARYFKKKGLKVGLVAADTYRPAAYDQL------KQLAEKIG 150
Query: 69 VPVYTDASQTLAVMSIGFLLKNRDDA--IIWRGPKKTAMIRQIINDVCWKDVDYLIIDT 125
VP Y D + DA I G +K K D +I+DT
Sbjct: 151 VPFYGD--------------PDNKDAVEIAKEGLEKF------------KKADVIIVDT 183
>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 = 31.0 bits (71), Expect = 0.20
Identities = 11/19 (57%), Positives = 15/19 (78%)
Query: 9 ILVLSGKGGVGKSTVSTQL 27
++VLSG GVGKST+ +L
Sbjct: 1 LIVLSGPSGVGKSTLLKRL 19
>gnl|CDD|221983 pfam13207, AAA_17, AAA domain.
Length = 114
Score = 30.7 bits (69), Expect = 0.20
Identities = 11/26 (42%), Positives = 19/26 (73%), Gaps = 2/26 (7%)
Query: 9 ILVLSGKGGVGKSTVSTQLA--LGLK 32
I++++G G GKST++ +LA LG+
Sbjct: 1 IILITGPPGSGKSTLAKKLAEKLGIP 26
>gnl|CDD|237186 PRK12740, PRK12740, elongation factor G; Reviewed.
Length = 668
Score = 31.6 bits (73), Expect = 0.20
Identities = 16/39 (41%), Positives = 19/39 (48%), Gaps = 3/39 (7%)
Query: 113 VCWKDVDYLIIDTPPGTSDEHITVMECLREVQCDGAVLV 151
WK +IDT PG D V LR + DGAV+V
Sbjct: 55 CEWKGHKINLIDT-PGHVDFTGEVERALRVL--DGAVVV 90
>gnl|CDD|184261 PRK13705, PRK13705, plasmid-partitioning protein SopA; Provisional.
Length = 388
Score = 31.5 bits (71), Expect = 0.21
Identities = 34/113 (30%), Positives = 46/113 (40%), Gaps = 29/113 (25%)
Query: 8 VILVLSGKGGVGKSTVSTQLALGLKDKGFKVGILDIDLCGPSVPHLLNIENSDVHQCPEG 67
VI V + KGGV K++VS LA L KG +V L ++ P + G
Sbjct: 108 VIGVAAHKGGVYKTSVSVHLAQDLALKGLRV--LLVEGNDPQGTASMY----------HG 155
Query: 68 WVP-VYTDASQTLAVMSIGFLLKNRDDAIIWRGPKKTAMIRQIINDVCWKDVD 119
WVP ++ A TL + F L +DDA I CW +D
Sbjct: 156 WVPDLHIHAEDTL----LPFYLGEKDDA------------TYAIKPTCWPGLD 192
>gnl|CDD|223272 COG0194, Gmk, Guanylate kinase [Nucleotide transport and
metabolism].
Length = 191
Score = 31.0 bits (71), Expect = 0.22
Identities = 13/32 (40%), Positives = 19/32 (59%), Gaps = 3/32 (9%)
Query: 9 ILVLSGKGGVGKSTVSTQLALGLKDKGFKVGI 40
++VLSG GVGKST+ L L+D + +
Sbjct: 6 LIVLSGPSGVGKSTLVKAL---LEDDKLRFSV 34
>gnl|CDD|223626 COG0552, FtsY, Signal recognition particle GTPase [Intracellular
trafficking and secretion].
Length = 340
Score = 31.5 bits (72), Expect = 0.23
Identities = 15/32 (46%), Positives = 19/32 (59%), Gaps = 1/32 (3%)
Query: 7 HVILVLSGKGGVGKSTVSTQLALGLKDKGFKV 38
VIL + G GVGK+T +LA LK +G V
Sbjct: 140 FVILFV-GVNGVGKTTTIAKLAKYLKQQGKSV 170
>gnl|CDD|148269 pfam06564, YhjQ, YhjQ protein. This family consists of several
bacterial YhjQ proteins. The function of this family is
unknown. However, the family does contain a P-loop
sequence motif suggesting a nucleotide binding
function.
Length = 244
Score = 31.2 bits (71), Expect = 0.26
Identities = 21/62 (33%), Positives = 31/62 (50%), Gaps = 8/62 (12%)
Query: 9 ILVLSG-KGGVGKSTVSTQLALGLKDKGFKVGILDIDLCGPSVPHLLNIE-NSDVHQCPE 66
+L L G +GGVG ++++ L L+ G V L ID P +LL + N D +
Sbjct: 3 VLALQGVRGGVGTTSLTAALGWALQQLGESV--LVIDAS-PD--NLLRLHFNVDFDH-SD 56
Query: 67 GW 68
GW
Sbjct: 57 GW 58
>gnl|CDD|236515 PRK09435, PRK09435, membrane ATPase/protein kinase; Provisional.
Length = 332
Score = 30.9 bits (71), Expect = 0.32
Identities = 16/38 (42%), Positives = 23/38 (60%), Gaps = 3/38 (7%)
Query: 12 LSGKGGVGKSTVSTQLALGLKDKGFKVGILDIDLCGPS 49
++G GVGKST L + L ++G KV +L +D PS
Sbjct: 61 ITGVPGVGKSTFIEALGMHLIEQGHKVAVLAVD---PS 95
>gnl|CDD|239387 cd03113, CTGs, CTP synthetase (CTPs) is a two-domain protein,
which consists of an N-terminal synthetase domain and
C-terminal glutaminase domain. The enzymes hydrolyze
the amide bond of glutamine to ammonia and glutamate at
the glutaminase domains and transfer nascent ammonia to
the acceptor substrate at the synthetase domain to form
an aminated product. Glutaminase domains have evolved
from the same ancestor, whereas the synthetase domains
are evolutionarily unrelated and have different
functions. This protein family is classified based on
the N-terminal synthetase domain.
Length = 255
Score = 30.6 bits (70), Expect = 0.34
Identities = 9/28 (32%), Positives = 13/28 (46%)
Query: 17 GVGKSTVSTQLALGLKDKGFKVGILDID 44
+GK + L LK +G KV +D
Sbjct: 12 SLGKGITAASLGRLLKARGLKVTAQKLD 39
>gnl|CDD|223364 COG0287, TyrA, Prephenate dehydrogenase [Amino acid transport and
metabolism].
Length = 279
Score = 30.8 bits (70), Expect = 0.35
Identities = 13/42 (30%), Positives = 19/42 (45%), Gaps = 6/42 (14%)
Query: 4 GVKHVILVLSGKGGVGKSTVSTQLALGLKDKGFKVGILDIDL 45
G + ++ G G +G S LA LK+ G V I+ D
Sbjct: 1 GASMKVGIV-GLGLMGGS-----LARALKEAGLVVRIIGRDR 36
>gnl|CDD|237475 PRK13695, PRK13695, putative NTPase; Provisional.
Length = 174
Score = 30.3 bits (69), Expect = 0.37
Identities = 13/30 (43%), Positives = 23/30 (76%)
Query: 10 LVLSGKGGVGKSTVSTQLALGLKDKGFKVG 39
+ ++G GVGK+T+ ++A LK++G+KVG
Sbjct: 3 IGITGPPGVGKTTLVLKIAELLKEEGYKVG 32
>gnl|CDD|183907 PRK13235, nifH, nitrogenase reductase; Reviewed.
Length = 274
Score = 30.5 bits (69), Expect = 0.39
Identities = 14/31 (45%), Positives = 19/31 (61%)
Query: 14 GKGGVGKSTVSTQLALGLKDKGFKVGILDID 44
GKGG+GKST + GL + G KV ++ D
Sbjct: 8 GKGGIGKSTTTQNTVAGLAEMGKKVMVVGCD 38
>gnl|CDD|222165 pfam13481, AAA_25, AAA domain. This AAA domain is found in a
wide variety of presumed DNA repair proteins.
Length = 154
Score = 29.9 bits (68), Expect = 0.40
Identities = 9/27 (33%), Positives = 16/27 (59%)
Query: 5 VKHVILVLSGKGGVGKSTVSTQLALGL 31
+ + +L+G G GKST++ LA +
Sbjct: 31 PRGGLTLLAGAPGTGKSTLALDLAAAV 57
>gnl|CDD|201032 pfam00142, Fer4_NifH, 4Fe-4S iron sulfur cluster binding
proteins, NifH/frxC family.
Length = 272
Score = 30.4 bits (69), Expect = 0.45
Identities = 14/31 (45%), Positives = 19/31 (61%)
Query: 14 GKGGVGKSTVSTQLALGLKDKGFKVGILDID 44
GKGG+GKST + + L + G KV I+ D
Sbjct: 7 GKGGIGKSTTTQNTSAALAEMGKKVLIVGCD 37
>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 = 30.0 bits (67), Expect = 0.46
Identities = 11/39 (28%), Positives = 20/39 (51%)
Query: 6 KHVILVLSGKGGVGKSTVSTQLALGLKDKGFKVGILDID 44
++++ G G GK+T++ LA L G V +D +
Sbjct: 1 PGEVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGE 39
>gnl|CDD|224027 COG1102, Cmk, Cytidylate kinase [Nucleotide transport and
metabolism].
Length = 179
Score = 30.0 bits (68), Expect = 0.52
Identities = 13/27 (48%), Positives = 20/27 (74%), Gaps = 2/27 (7%)
Query: 8 VILVLSGKGGVGKSTVSTQLA--LGLK 32
+++ +SG G GK+TV+ +LA LGLK
Sbjct: 1 MVITISGLPGSGKTTVARELAEHLGLK 27
>gnl|CDD|183906 PRK13234, nifH, nitrogenase reductase; Reviewed.
Length = 295
Score = 30.2 bits (68), Expect = 0.55
Identities = 18/47 (38%), Positives = 24/47 (51%)
Query: 14 GKGGVGKSTVSTQLALGLKDKGFKVGILDIDLCGPSVPHLLNIENSD 60
GKGG+GKST S L + G K+ I+ D S +LN + D
Sbjct: 11 GKGGIGKSTTSQNTLAALVEMGQKILIVGCDPKADSTRLILNAKAQD 57
>gnl|CDD|183702 PRK12723, PRK12723, flagellar biosynthesis regulator FlhF;
Provisional.
Length = 388
Score = 30.3 bits (68), Expect = 0.55
Identities = 16/48 (33%), Positives = 26/48 (54%), Gaps = 4/48 (8%)
Query: 1 MLDGVKHVILVLSGKGGVGKSTVSTQLA----LGLKDKGFKVGILDID 44
++D +K + +L G GVGK+T +LA + DK + I+ ID
Sbjct: 168 IIDNLKKRVFILVGPTGVGKTTTIAKLAAIYGINSDDKSLNIKIITID 215
>gnl|CDD|223926 COG0857, Pta, BioD-like N-terminal domain of
phosphotransacetylase [General function prediction
only].
Length = 354
Score = 30.4 bits (69), Expect = 0.56
Identities = 12/32 (37%), Positives = 20/32 (62%)
Query: 9 ILVLSGKGGVGKSTVSTQLALGLKDKGFKVGI 40
+L++ + GVGK+++S L L+ KG KV
Sbjct: 5 LLLIPTETGVGKTSISLGLLRALEQKGLKVAY 36
>gnl|CDD|223578 COG0504, PyrG, CTP synthase (UTP-ammonia lyase) [Nucleotide
transport and metabolism].
Length = 533
Score = 30.2 bits (69), Expect = 0.59
Identities = 13/42 (30%), Positives = 21/42 (50%), Gaps = 6/42 (14%)
Query: 6 KHVIL---VLSGKGGVGKSTVSTQLALGLKDKGFKVGILDID 44
K++ + V+S +GK + L LK +G KV I +D
Sbjct: 2 KYIFVTGGVVSS---LGKGITAASLGRLLKARGLKVTIQKLD 40
>gnl|CDD|237875 PRK14974, PRK14974, cell division protein FtsY; Provisional.
Length = 336
Score = 30.3 bits (69), Expect = 0.62
Identities = 15/33 (45%), Positives = 19/33 (57%)
Query: 6 KHVILVLSGKGGVGKSTVSTQLALGLKDKGFKV 38
K V++V G G GK+T +LA LK GF V
Sbjct: 139 KPVVIVFVGVNGTGKTTTIAKLAYYLKKNGFSV 171
>gnl|CDD|206731 cd04168, TetM_like, Tet(M)-like family includes Tet(M), Tet(O),
Tet(W), and OtrA, containing tetracycline resistant
proteins. Tet(M), Tet(O), Tet(W), and OtrA are
tetracycline resistance genes found in Gram-positive and
Gram-negative bacteria. Tetracyclines inhibit protein
synthesis by preventing aminoacyl-tRNA from binding to
the ribosomal acceptor site. This subfamily contains
tetracycline resistance proteins that function through
ribosomal protection and are typically found on mobile
genetic elements, such as transposons or plasmids, and
are often conjugative. Ribosomal protection proteins are
homologous to the elongation factors EF-Tu and EF-G.
EF-G and Tet(M) compete for binding on the ribosomes.
Tet(M) has a higher affinity than EF-G, suggesting these
two proteins may have overlapping binding sites and that
Tet(M) must be released before EF-G can bind. Tet(M) and
Tet(O) have been shown to have ribosome-dependent GTPase
activity. These proteins are part of the GTP translation
factor family, which includes EF-G, EF-Tu, EF2, LepA,
and SelB.
Length = 237
Score = 29.9 bits (68), Expect = 0.65
Identities = 17/37 (45%), Positives = 20/37 (54%), Gaps = 3/37 (8%)
Query: 115 WKDVDYLIIDTPPGTSDEHITVMECLREVQCDGAVLV 151
W+D IIDT PG D I +E V DGA+LV
Sbjct: 61 WEDTKVNIIDT-PGHMD-FIAEVERSLSV-LDGAILV 94
>gnl|CDD|179661 PRK03846, PRK03846, adenylylsulfate kinase; Provisional.
Length = 198
Score = 29.9 bits (68), Expect = 0.65
Identities = 21/54 (38%), Positives = 27/54 (50%), Gaps = 4/54 (7%)
Query: 2 LDGVKHVILVLSGKGGVGKSTVSTQLALGLKDKGFKVGILDIDLCGPSVPHLLN 55
L G K V+L +G G GKSTV+ L L + G +LD G +V H L
Sbjct: 19 LHGHKGVVLWFTGLSGSGKSTVAGALEEALHELGVSTYLLD----GDNVRHGLC 68
>gnl|CDD|217465 pfam03266, NTPase_1, NTPase. This domain is found across all
species from bacteria to human, and the function was
determined first in a hyperthermophilic bacterium to be
an NTPase. The structure of one member-sequence
represents a variation of the RecA fold, and implies
that the function might be that of a DNA/RNA modifying
enzyme. The sequence carries both a Walker A and Walker
B motif which together are characteristic of ATPases or
GTPases. The protein exhibits an increased expression
profile in human liver cholangiocarcinoma when compared
to normal tissue.
Length = 168
Score = 29.5 bits (67), Expect = 0.71
Identities = 12/30 (40%), Positives = 20/30 (66%)
Query: 10 LVLSGKGGVGKSTVSTQLALGLKDKGFKVG 39
+ ++G GVGK+T+ ++ LK +G KVG
Sbjct: 2 IFITGPPGVGKTTLVKKVIELLKSEGVKVG 31
>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 = 29.6 bits (67), Expect = 0.72
Identities = 17/48 (35%), Positives = 24/48 (50%), Gaps = 4/48 (8%)
Query: 8 VILVLSGKGGVGKSTVSTQLALGLKDKGFKVGILDIDLCGPSVPHLLN 55
+ +G G GKST++ L L +G V +LD G +V H LN
Sbjct: 3 CTIWFTGLSGSGKSTIANALERKLFAQGISVYVLD----GDNVRHGLN 46
>gnl|CDD|236442 PRK09270, PRK09270, nucleoside triphosphate hydrolase
domain-containing protein; Reviewed.
Length = 229
Score = 29.9 bits (68), Expect = 0.73
Identities = 10/27 (37%), Positives = 16/27 (59%)
Query: 9 ILVLSGKGGVGKSTVSTQLALGLKDKG 35
I+ ++G G GKST++ L L+ G
Sbjct: 35 IVGIAGPPGAGKSTLAEFLEALLQQDG 61
>gnl|CDD|235244 PRK04182, PRK04182, cytidylate kinase; Provisional.
Length = 180
Score = 29.4 bits (67), Expect = 0.74
Identities = 14/27 (51%), Positives = 19/27 (70%), Gaps = 2/27 (7%)
Query: 8 VILVLSGKGGVGKSTVSTQLA--LGLK 32
+I+ +SG G GK+TV+ LA LGLK
Sbjct: 1 MIITISGPPGSGKTTVARLLAEKLGLK 27
>gnl|CDD|235878 PRK06851, PRK06851, hypothetical protein; Provisional.
Length = 367
Score = 29.9 bits (68), Expect = 0.84
Identities = 12/38 (31%), Positives = 21/38 (55%), Gaps = 1/38 (2%)
Query: 1 MLDGVKHVILVLSGKGGVGKSTVSTQLALGLKDKGFKV 38
++DG + +L G G GKST+ ++ +KG+ V
Sbjct: 25 IIDGANRIF-ILKGGPGTGKSTLMKKIGEEFLEKGYDV 61
>gnl|CDD|219017 pfam06418, CTP_synth_N, CTP synthase N-terminus. This family
consists of the N-terminal region of the CTP synthase
protein (EC:6.3.4.2). This family is found in
conjunction with pfam00117 located in the C-terminal
region of the protein. CTP synthase catalyzes the
synthesis of CTP from UTP by amination of the
pyrimidine ring at the 4-position.
Length = 276
Score = 29.7 bits (68), Expect = 0.88
Identities = 14/43 (32%), Positives = 21/43 (48%), Gaps = 6/43 (13%)
Query: 5 VKHVIL---VLSGKGGVGKSTVSTQLALGLKDKGFKVGILDID 44
K++ + V+S +GK + L LK +G KV I ID
Sbjct: 1 TKYIFVTGGVVSS---LGKGITAASLGRLLKSRGLKVTIQKID 40
>gnl|CDD|236994 PRK11823, PRK11823, DNA repair protein RadA; Provisional.
Length = 446
Score = 29.7 bits (68), Expect = 0.94
Identities = 14/31 (45%), Positives = 19/31 (61%), Gaps = 1/31 (3%)
Query: 8 VILVLSGKGGVGKSTVSTQLALGLKDKGFKV 38
V+L + G G+GKST+ Q+A L G KV
Sbjct: 82 VVL-IGGDPGIGKSTLLLQVAARLAAAGGKV 111
>gnl|CDD|206673 cd01886, EF-G, Elongation factor G (EF-G) family involved in both
the elongation and ribosome recycling phases of protein
synthesis. Translocation is mediated by EF-G (also
called translocase). The structure of EF-G closely
resembles that of the complex between EF-Tu and tRNA.
This is an example of molecular mimicry; a protein
domain evolved so that it mimics the shape of a tRNA
molecule. EF-G in the GTP form binds to the ribosome,
primarily through the interaction of its EF-Tu-like
domain with the 50S subunit. The binding of EF-G to the
ribosome in this manner stimulates the GTPase activity
of EF-G. On GTP hydrolysis, EF-G undergoes a
conformational change that forces its arm deeper into
the A site on the 30S subunit. To accommodate this
domain, the peptidyl-tRNA in the A site moves to the P
site, carrying the mRNA and the deacylated tRNA with it.
The ribosome may be prepared for these rearrangements by
the initial binding of EF-G as well. The dissociation of
EF-G leaves the ribosome ready to accept the next
aminoacyl-tRNA into the A site. This group contains both
eukaryotic and bacterial members.
Length = 270
Score = 29.4 bits (67), Expect = 0.97
Identities = 19/37 (51%), Positives = 20/37 (54%), Gaps = 3/37 (8%)
Query: 115 WKDVDYLIIDTPPGTSDEHITVMECLREVQCDGAVLV 151
WKD IIDT PG D I V LR + DGAV V
Sbjct: 61 WKDHRINIIDT-PGHVDFTIEVERSLRVL--DGAVAV 94
>gnl|CDD|179793 PRK04220, PRK04220, 2-phosphoglycerate kinase; Provisional.
Length = 301
Score = 29.5 bits (67), Expect = 0.98
Identities = 13/30 (43%), Positives = 20/30 (66%), Gaps = 3/30 (10%)
Query: 6 KHVILVL-SGKGGVGKSTVSTQLA--LGLK 32
K I++L G GVG ST++ +LA LG++
Sbjct: 90 KEPIIILIGGASGVGTSTIAFELASRLGIR 119
>gnl|CDD|223615 COG0541, Ffh, Signal recognition particle GTPase [Intracellular
trafficking and secretion].
Length = 451
Score = 29.4 bits (67), Expect = 1.1
Identities = 17/38 (44%), Positives = 23/38 (60%), Gaps = 1/38 (2%)
Query: 8 VILVLSGKGGVGKSTVSTQLALGLKDKGFKVGILDIDL 45
VIL + G G GK+T + +LA LK KG KV ++ D
Sbjct: 102 VIL-MVGLQGSGKTTTAGKLAKYLKKKGKKVLLVAADT 138
>gnl|CDD|239383 cd03109, DTBS, Dethiobiotin synthetase (DTBS) is the penultimate
enzyme in the biotin biosynthesis pathway in
Escherichia coli and other microorganisms. The enzyme
catalyzes formation of the ureido ring of dethiobiotin
from (7R,8S)-7,8-diaminononanoic acid (DAPA) and carbon
dioxide. The enzyme utilizes carbon dioxide instead of
hydrogen carbonate as substrate and is dependent on ATP
and divalent metal ions as cofactors.
Length = 134
Score = 28.5 bits (64), Expect = 1.2
Identities = 10/25 (40%), Positives = 16/25 (64%)
Query: 17 GVGKSTVSTQLALGLKDKGFKVGIL 41
+GK+ + LA LK+KG++V L
Sbjct: 9 DIGKTVATAILARALKEKGYRVAPL 33
>gnl|CDD|163543 TIGR03831, YgiT_finger, YgiT-type zinc finger domain. This domain
model describes a small domain with two copies of a
putative zinc-binding motif CXXC (usually CXXCG). Most
member proteins consist largely of this domain or else
carry an additional C-terminal helix-turn-helix domain,
resembling that of the phage protein Cro and modeled by
pfam01381.
Length = 46
Score = 26.9 bits (60), Expect = 1.2
Identities = 8/33 (24%), Positives = 13/33 (39%), Gaps = 3/33 (9%)
Query: 159 IEDVRKEITFCKKTNIKILGLIENMSGYTCPHC 191
+E T+ + + IEN+ CP C
Sbjct: 9 LEGKTTTETYEYGGELIV---IENVPALVCPQC 38
>gnl|CDD|237498 PRK13768, PRK13768, GTPase; Provisional.
Length = 253
Score = 29.1 bits (66), Expect = 1.3
Identities = 15/46 (32%), Positives = 29/46 (63%), Gaps = 3/46 (6%)
Query: 8 VILVLSGKGGVGKSTVSTQLALGLKDKGFKVGILDIDLCGPSVPHL 53
I+ G G GK+T++ L+ L+++G+ V I+++D P+V +L
Sbjct: 3 YIVFFLGTAGSGKTTLTKALSDWLEEQGYDVAIVNLD---PAVEYL 45
>gnl|CDD|106587 PRK13644, cbiO, cobalt transporter ATP-binding subunit;
Provisional.
Length = 274
Score = 29.2 bits (65), Expect = 1.4
Identities = 14/38 (36%), Positives = 20/38 (52%)
Query: 12 LSGKGGVGKSTVSTQLALGLKDKGFKVGILDIDLCGPS 49
+ GK G GKST++ L L+ + KV + ID S
Sbjct: 33 IIGKNGSGKSTLALHLNGLLRPQKGKVLVSGIDTGDFS 70
>gnl|CDD|238985 cd02027, APSK, Adenosine 5'-phosphosulfate kinase (APSK)
catalyzes the phosphorylation of adenosine
5'-phosphosulfate to form 3'-phosphoadenosine
5'-phosphosulfate (PAPS). The end-product PAPS is a
biologically "activated" sulfate form important for the
assimilation of inorganic sulfate.
Length = 149
Score = 28.6 bits (65), Expect = 1.4
Identities = 14/33 (42%), Positives = 19/33 (57%)
Query: 12 LSGKGGVGKSTVSTQLALGLKDKGFKVGILDID 44
L+G G GKST++ L L +G V +LD D
Sbjct: 4 LTGLSGSGKSTIARALEEKLFQRGRPVYVLDGD 36
>gnl|CDD|206652 cd01853, Toc34_like, Translocon at the Outer-envelope membrane of
Chloroplasts 34-like (Toc34-like). The Toc34-like
(Translocon at the Outer-envelope membrane of
Chloroplasts) family contains several Toc proteins,
including Toc34, Toc33, Toc120, Toc159, Toc86, Toc125,
and Toc90. The Toc complex at the outer envelope
membrane of chloroplasts is a molecular machine of ~500
kDa that contains a single Toc159 protein, four Toc75
molecules, and four or five copies of Toc34. Toc64 and
Toc12 are associated with the translocon, but do not
appear to be part of the core complex. The Toc
translocon initiates the import of nuclear-encoded
preproteins from the cytosol into the organelle. Toc34
and Toc159 are both GTPases, while Toc75 is a
beta-barrel integral membrane protein. Toc159 is
equally distributed between a soluble cytoplasmic form
and a membrane-inserted form, suggesting that assembly
of the Toc complex is dynamic. Toc34 and Toc75 act
sequentially to mediate docking and insertion of Toc159
resulting in assembly of the functional translocon.
Length = 248
Score = 28.8 bits (65), Expect = 1.4
Identities = 11/15 (73%), Positives = 12/15 (80%), Gaps = 1/15 (6%)
Query: 9 ILVLSGKGGVGKSTV 23
ILVL GK GVGKS+
Sbjct: 34 ILVL-GKTGVGKSST 47
>gnl|CDD|234654 PRK00131, aroK, shikimate kinase; Reviewed.
Length = 175
Score = 28.6 bits (65), Expect = 1.5
Identities = 16/41 (39%), Positives = 19/41 (46%), Gaps = 9/41 (21%)
Query: 6 KHVILVLSGKGGVGKSTVSTQLA--LGLKDKGFKVGILDID 44
K +VL G G GKST+ LA LG F +D D
Sbjct: 3 KGPNIVLIGFMGAGKSTIGRLLAKRLGY---DF----IDTD 36
>gnl|CDD|217138 pfam02606, LpxK, Tetraacyldisaccharide-1-P 4'-kinase. This
family consists of tetraacyldisaccharide-1-P 4'-kinase
also known as Lipid-A 4'-kinase or Lipid A biosynthesis
protein LpxK, EC:2.7.1.130. This enzyme catalyzes the
reaction: ATP + 2,3-bis(3-hydroxytetradecanoyl)-D
-glucosaminyl-(beta-D-1,6)-2,
3-bis(3-hydroxytetradecanoyl)-D-glu cosam inyl
beta-phosphate <=> ADP +
2,3,2',3'-tetrakis(3-hydroxytetradecanoyl)-D-
glucosaminyl-1,6-beta-D-glucosamine 1,4'-bisphosphate.
This enzyme is involved in the synthesis of lipid A
portion of the bacterial lipopolysaccharide layer
(LPS). The family contains a P-loop motif at the N
terminus.
Length = 318
Score = 29.1 bits (66), Expect = 1.6
Identities = 10/26 (38%), Positives = 16/26 (61%)
Query: 16 GGVGKSTVSTQLALGLKDKGFKVGIL 41
GG GK+ + LA L+ +G + G+L
Sbjct: 46 GGTGKTPLVIALAELLRARGLRPGVL 71
>gnl|CDD|206733 cd04170, EF-G_bact, Elongation factor G (EF-G) family.
Translocation is mediated by EF-G (also called
translocase). The structure of EF-G closely resembles
that of the complex between EF-Tu and tRNA. This is an
example of molecular mimicry; a protein domain evolved
so that it mimics the shape of a tRNA molecule. EF-G in
the GTP form binds to the ribosome, primarily through
the interaction of its EF-Tu-like domain with the 50S
subunit. The binding of EF-G to the ribosome in this
manner stimulates the GTPase activity of EF-G. On GTP
hydrolysis, EF-G undergoes a conformational change that
forces its arm deeper into the A site on the 30S
subunit. To accommodate this domain, the peptidyl-tRNA
in the A site moves to the P site, carrying the mRNA and
the deacylated tRNA with it. The ribosome may be
prepared for these rearrangements by the initial binding
of EF-G as well. The dissociation of EF-G leaves the
ribosome ready to accept the next aminoacyl-tRNA into
the A site. This group contains only bacterial members.
Length = 268
Score = 28.7 bits (65), Expect = 1.6
Identities = 14/44 (31%), Positives = 21/44 (47%), Gaps = 3/44 (6%)
Query: 113 VCWKDVDYLIIDTPPGTSDEHITVMECLREVQCDGAVLVTTPQA 156
+ W +IDT PG +D + LR V D A++V Q+
Sbjct: 59 LEWNGHKINLIDT-PGYADFVGETLSALRAV--DAALIVVEAQS 99
>gnl|CDD|234719 PRK00300, gmk, guanylate kinase; Provisional.
Length = 205
Score = 28.5 bits (65), Expect = 1.7
Identities = 10/19 (52%), Positives = 13/19 (68%)
Query: 9 ILVLSGKGGVGKSTVSTQL 27
++VLSG G GKST+ L
Sbjct: 7 LIVLSGPSGAGKSTLVKAL 25
>gnl|CDD|238688 cd01394, radB, RadB. The archaeal protein radB shares similarity
radA, the archaeal functional homologue to the
bacterial RecA. The precise function of radB is
unclear.
Length = 218
Score = 28.6 bits (64), Expect = 1.7
Identities = 11/35 (31%), Positives = 19/35 (54%)
Query: 8 VILVLSGKGGVGKSTVSTQLALGLKDKGFKVGILD 42
+ + G G GK+ ++ QLA+ +G KV +D
Sbjct: 20 TVTQVYGPPGTGKTNIAIQLAVETAGQGKKVAYID 54
>gnl|CDD|238979 cd02021, GntK, Gluconate kinase (GntK) catalyzes the phosphoryl
transfer from ATP to gluconate. The resulting product
gluconate-6-phoshate is an important precursor of
gluconate metabolism. GntK acts as a dimmer composed of
two identical subunits.
Length = 150
Score = 28.4 bits (64), Expect = 1.7
Identities = 11/20 (55%), Positives = 13/20 (65%)
Query: 9 ILVLSGKGGVGKSTVSTQLA 28
I+V+ G G GKSTV LA
Sbjct: 1 IIVVMGVSGSGKSTVGKALA 20
>gnl|CDD|220642 pfam10236, DAP3, Mitochondrial ribosomal death-associated protein
3. This is a family of conserved proteins which were
originally described as death-associated-protein-3
(DAP-3). The proteins carry a P-loop DNA-binding motif,
and induce apoptosis. DAP3 has been shown to be a
pro-apoptotic factor in the mitochondrial matrix and to
be crucial for mitochondrial biogenesis and so has also
been designated as MRP-S29 (mitochondrial ribosomal
protein subunit 29).
Length = 274
Score = 28.8 bits (65), Expect = 1.8
Identities = 12/33 (36%), Positives = 17/33 (51%)
Query: 6 KHVILVLSGKGGVGKSTVSTQLALGLKDKGFKV 38
K V VL+G+ G GKS + Q +G+ V
Sbjct: 22 KVVRFVLTGERGSGKSVLLAQAMAYAFTQGWIV 54
>gnl|CDD|222000 pfam13238, AAA_18, AAA domain.
Length = 128
Score = 27.8 bits (62), Expect = 1.9
Identities = 10/42 (23%), Positives = 19/42 (45%), Gaps = 1/42 (2%)
Query: 11 VLSGKGGVGKSTVSTQLALGLKDKGFKVGILDIDLCGPSVPH 52
+++G G GK+T++ +LA L D + + L
Sbjct: 2 LITGTPGSGKTTLAKELAERLGDVLRDL-AKENGLVLELDEE 42
>gnl|CDD|238541 cd01121, Sms, Sms (bacterial radA) DNA repair protein. This protein
is not related to archael radA any more than is to other
RecA-like NTPases. Sms has a role in recombination and
recombinational repair and is responsible for the
stabilization or processing of branched DNA molecules.
Length = 372
Score = 28.7 bits (65), Expect = 2.0
Identities = 15/31 (48%), Positives = 20/31 (64%), Gaps = 1/31 (3%)
Query: 8 VILVLSGKGGVGKSTVSTQLALGLKDKGFKV 38
VIL+ G G+GKST+ Q+A L +G KV
Sbjct: 84 VILI-GGDPGIGKSTLLLQVAARLAKRGGKV 113
>gnl|CDD|224577 COG1663, LpxK, Tetraacyldisaccharide-1-P 4'-kinase [Cell envelope
biogenesis, outer membrane].
Length = 336
Score = 28.4 bits (64), Expect = 2.1
Identities = 16/44 (36%), Positives = 23/44 (52%), Gaps = 2/44 (4%)
Query: 16 GGVGKSTVSTQLALGLKDKGFKVGILDIDLCG--PSVPHLLNIE 57
GG GK+ V LA L+ +G +VG++ G VP + NI
Sbjct: 58 GGTGKTPVVIWLAEALQARGVRVGVVSRGYGGKLKVVPLVDNIH 101
>gnl|CDD|226573 COG4088, COG4088, Predicted nucleotide kinase [Nucleotide
transport and metabolism].
Length = 261
Score = 28.3 bits (63), Expect = 2.3
Identities = 12/36 (33%), Positives = 24/36 (66%)
Query: 9 ILVLSGKGGVGKSTVSTQLALGLKDKGFKVGILDID 44
+++L+G G GK+T + +LA L+ + ++V L+ D
Sbjct: 3 LIILTGYPGSGKTTFAKELAKELRQEIWRVIHLEKD 38
>gnl|CDD|233793 TIGR02237, recomb_radB, DNA repair and recombination protein
RadB. This family consists exclusively of archaeal
RadB protein, a homolog of bacterial RecA (TIGR02012),
eukaryotic RAD51 (TIGR02239) and DMC1 (TIGR02238), and
archaeal RadA (TIGR02236).
Length = 209
Score = 28.1 bits (63), Expect = 2.4
Identities = 14/53 (26%), Positives = 21/53 (39%), Gaps = 2/53 (3%)
Query: 8 VILVLSGKGGVGKSTVSTQLALGLKDKGFKVGILDIDLCGPSVPHLLNIENSD 60
I + G G GK+ + LA+ +G KV +D + G S I
Sbjct: 13 TITQIYGPPGSGKTNICMILAVNAARQGKKVVYIDTE--GLSPERFKQIAEDR 63
>gnl|CDD|233090 TIGR00682, lpxK, tetraacyldisaccharide 4'-kinase. Also called
lipid-A 4'-kinase. This essential gene encodes an
enzyme in the pathway of lipid A biosynthesis in
Gram-negative organisms. A single copy of this protein
is found in Gram-negative bacteria. PSI-BLAST converges
on this set of apparent orthologs without identifying
any other homologs [Cell envelope, Biosynthesis and
degradation of surface polysaccharides and
lipopolysaccharides].
Length = 311
Score = 28.2 bits (63), Expect = 2.4
Identities = 14/26 (53%), Positives = 18/26 (69%)
Query: 16 GGVGKSTVSTQLALGLKDKGFKVGIL 41
GG GK+ V LA LKD+G +VG+L
Sbjct: 39 GGTGKTPVVVWLAELLKDRGLRVGVL 64
>gnl|CDD|106194 PRK13232, nifH, nitrogenase reductase; Reviewed.
Length = 273
Score = 28.4 bits (63), Expect = 2.4
Identities = 16/45 (35%), Positives = 23/45 (51%)
Query: 10 LVLSGKGGVGKSTVSTQLALGLKDKGFKVGILDIDLCGPSVPHLL 54
+ + GKGG+GKST + L L G K+ ++ D S LL
Sbjct: 4 IAIYGKGGIGKSTTTQNLTAALSTMGNKILLVGCDPKADSTRMLL 48
>gnl|CDD|129575 TIGR00484, EF-G, translation elongation factor EF-G. After peptide
bond formation, this elongation factor of bacteria and
organelles catalyzes the translocation of the tRNA-mRNA
complex, with its attached nascent polypeptide chain,
from the A-site to the P-site of the ribosome. Every
completed bacterial genome has at least one copy, but
some species have additional EF-G-like proteins. The
closest homolog to canonical (e.g. E. coli) EF-G in the
spirochetes clusters as if it is derived from
mitochondrial forms, while a more distant second copy is
also present. Synechocystis PCC6803 has a few proteins
more closely related to EF-G than to any other
characterized protein. Two of these resemble E. coli
EF-G more closely than does the best match from the
spirochetes; it may be that both function as authentic
EF-G [Protein synthesis, Translation factors].
Length = 689
Score = 28.6 bits (64), Expect = 2.6
Identities = 18/44 (40%), Positives = 20/44 (45%), Gaps = 3/44 (6%)
Query: 113 VCWKDVDYLIIDTPPGTSDEHITVMECLREVQCDGAVLVTTPQA 156
V WK IIDT PG D + V LR + DGAV V
Sbjct: 70 VFWKGHRINIIDT-PGHVDFTVEVERSLRVL--DGAVAVLDAVG 110
>gnl|CDD|187598 cd05339, 17beta-HSDXI-like_SDR_c, human 17-beta-hydroxysteroid
dehydrogenase XI-like, classical (c) SDRs.
17-beta-hydroxysteroid dehydrogenases (17betaHSD) are a
group of isozymes that catalyze activation and
inactivation of estrogen and androgens. 17betaHSD type
XI, a classical SDR, preferentially converts
3alpha-adiol to androsterone but not numerous other
tested steroids. This subgroup of classical SDRs also
includes members identified as retinol dehydrogenases,
which convert retinol to retinal, a property that
overlaps with 17betaHSD activity. SDRs are a
functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold (alpha/beta folding pattern with a
central beta-sheet), an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Classical SDRs
are typically about 250 residues long, while extended
SDRS are approximately 350 residues. Sequence identity
between different SDR enzymes are typically in the
15-30% range, but the enzymes share the Rossmann fold
NAD-binding motif and characteristic NAD-binding and
catalytic sequence patterns. These enzymes have a
3-glycine N-terminal NAD(P)(H)-binding pattern
(typically, TGxxxGxG in classical SDRs and TGxxGxxG in
extended SDRs), while substrate binding is in the
C-terminal region. A critical catalytic Tyr residue
(Tyr-151, human 15-hydroxyprostaglandin dehydrogenase
(15-PGDH) numbering), is often found in a conserved
YXXXK pattern. In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) or
additional Ser, contributing to the active site.
Substrates for these enzymes include sugars, steroids,
alcohols, and aromatic compounds. The standard reaction
mechanism is a proton relay involving the conserved Tyr
and Lys, as well as Asn (or Ser). Some SDR family
members, including 17 beta-hydroxysteroid dehydrogenase
contain an additional helix-turn-helix motif that is
not generally found among SDRs.
Length = 243
Score = 28.0 bits (63), Expect = 2.7
Identities = 17/56 (30%), Positives = 26/56 (46%), Gaps = 6/56 (10%)
Query: 8 VILVLSGKGGVGKSTVSTQLALGLKDKGFKVGILDIDLCG-PSVPHLLNIENSDVH 62
++L+ G G+G+ LAL +G KV ILDI+ G + + VH
Sbjct: 1 IVLITGGGSGIGR-----LLALEFAKRGAKVVILDINEKGAEETANNVRKAGGKVH 51
>gnl|CDD|219014 pfam06414, Zeta_toxin, Zeta toxin. This family consists of several
bacterial zeta toxin proteins. Zeta toxin is thought to
be part of a postregulational killing system in
bacteria. It relies on antitoxin/toxin systems that
secure stable inheritance of low and medium copy number
plasmids during cell division and kill cells that have
lost the plasmid.
Length = 191
Score = 28.0 bits (63), Expect = 2.7
Identities = 21/127 (16%), Positives = 45/127 (35%), Gaps = 12/127 (9%)
Query: 8 VILVLSGKGGVGKSTVSTQLALGLKDKGFKVGILDIDLCGPSVPHLLNIENSDVHQCPEG 67
V ++L G+ G GK+ ++ L L V +D D P ++ +D
Sbjct: 13 VAVLLGGQPGAGKTELARALLEELGGGN--VVRIDPDELRTYHPDYDELQKADPKD---- 66
Query: 68 WVPVYTDASQTLAVMSIGFLLKNRDDAIIWRGPKKTAMIRQIINDVCWKDVDY----LII 123
+ + I + ++ + I+ + + R++ + K Y ++
Sbjct: 67 ASELTQPDASRWVEKLIDYAIERGYNIILEGTLRSPDVARKLARKL--KAAGYEVEVYVV 124
Query: 124 DTPPGTS 130
PP S
Sbjct: 125 AVPPELS 131
>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 = 27.8 bits (63), Expect = 2.8
Identities = 9/19 (47%), Positives = 13/19 (68%)
Query: 9 ILVLSGKGGVGKSTVSTQL 27
++V+SG G GKST+ L
Sbjct: 2 LIVISGPSGAGKSTLVKAL 20
>gnl|CDD|182106 PRK09841, PRK09841, cryptic autophosphorylating protein tyrosine
kinase Etk; Provisional.
Length = 726
Score = 28.3 bits (63), Expect = 2.8
Identities = 29/138 (21%), Positives = 55/138 (39%), Gaps = 24/138 (17%)
Query: 1 MLDGVKHVILVLSGKGGVGKSTVSTQLALGLKDKGFKVGILDIDLCGPSVPHLLNIEN-- 58
M++ +++++ GK+ VS+ LA + KV +D DL +L + N
Sbjct: 526 MMETENNILMITGATPDSGKTFVSSTLAAVIAQSDQKVLFIDADLRRGYSHNLFTVSNEH 585
Query: 59 --SDVHQCPEGWVPVYTDASQTLA-----VMSIGFLLKNRDDAIIWRGPKKTAMIRQIIN 111
S+ G Q V++ G + N + ++ +RQ++
Sbjct: 586 GLSEYL---AGKDE-LNKVIQHFGKGGFDVITRGQVPPNPSELLMRDR------MRQLLE 635
Query: 112 DVCWKDVDY--LIIDTPP 127
W + Y +I+DTPP
Sbjct: 636 ---WANDHYDLVIVDTPP 650
>gnl|CDD|223745 COG0673, MviM, Predicted dehydrogenases and related proteins
[General function prediction only].
Length = 342
Score = 28.3 bits (63), Expect = 2.8
Identities = 16/73 (21%), Positives = 32/73 (43%), Gaps = 12/73 (16%)
Query: 106 IRQIINDVCWKDVDYLIIDTPPGTSDEHI-TVMECLREVQCDG-AVLVTTPQAVSIEDVR 163
+ +++ D D+D + I TP H + L G VL P A+++E+
Sbjct: 59 LEELLAD---PDIDAVYIATPNAL---HAELALAALEA----GKHVLCEKPLALTLEEAE 108
Query: 164 KEITFCKKTNIKI 176
+ + +K +K+
Sbjct: 109 ELVELARKAGVKL 121
>gnl|CDD|133338 cd04138, H_N_K_Ras_like, Ras GTPase family containing H-Ras,N-Ras
and K-Ras4A/4B. H-Ras/N-Ras/K-Ras subfamily. H-Ras,
N-Ras, and K-Ras4A/4B are the prototypical members of
the Ras family. These isoforms generate distinct signal
outputs despite interacting with a common set of
activators and effectors, and are strongly associated
with oncogenic progression in tumor initiation. Mutated
versions of Ras that are insensitive to GAP stimulation
(and are therefore constitutively active) are found in
a significant fraction of human cancers. Many Ras
guanine nucleotide exchange factors (GEFs) have been
identified. They are sequestered in the cytosol until
activation by growth factors triggers recruitment to
the plasma membrane or Golgi, where the GEF colocalizes
with Ras. Active (GTP-bound) Ras interacts with several
effector proteins that stimulate a variety of diverse
cytoplasmic signaling activities. Some are known to
positively mediate the oncogenic properties of Ras,
including Raf, phosphatidylinositol 3-kinase (PI3K),
RalGEFs, and Tiam1. Others are proposed to play
negative regulatory roles in oncogenesis, including
RASSF and NORE/MST1. Most Ras proteins contain a lipid
modification site at the C-terminus, with a typical
sequence motif CaaX, where a = an aliphatic amino acid
and X = any amino acid. Lipid binding is essential for
membrane attachment, a key feature of most Ras
proteins. Due to the presence of truncated sequences in
this CD, the lipid modification site is not available
for annotation.
Length = 162
Score = 27.8 bits (62), Expect = 2.9
Identities = 11/18 (61%), Positives = 14/18 (77%)
Query: 10 LVLSGKGGVGKSTVSTQL 27
LV+ G GGVGKS ++ QL
Sbjct: 4 LVVVGAGGVGKSALTIQL 21
>gnl|CDD|206642 cd00876, Ras, Rat sarcoma (Ras) family of small guanosine
triphosphatases (GTPases). The Ras family of the Ras
superfamily includes classical N-Ras, H-Ras, and K-Ras,
as well as R-Ras, Rap, Ral, Rheb, Rhes, ARHI, RERG,
Rin/Rit, RSR1, RRP22, Ras2, Ras-dva, and RGK proteins.
Ras proteins regulate cell growth, proliferation and
differentiation. Ras is activated by guanine nucleotide
exchange factors (GEFs) that release GDP and allow GTP
binding. Many RasGEFs have been identified. These are
sequestered in the cytosol until activation by growth
factors triggers recruitment to the plasma membrane or
Golgi, where the GEF colocalizes with Ras. Active
GTP-bound Ras interacts with several effector proteins:
among the best characterized are the Raf kinases,
phosphatidylinositol 3-kinase (PI3K), RalGEFs and
NORE/MST1. Most Ras proteins contain a lipid
modification site at the C-terminus, with a typical
sequence motif CaaX, where a = an aliphatic amino acid
and X = any amino acid. Lipid binding is essential for
membrane attachment, a key feature of most Ras
proteins. Due to the presence of truncated sequences in
this CD, the lipid modification site is not available
for annotation.
Length = 160
Score = 27.5 bits (62), Expect = 3.3
Identities = 10/21 (47%), Positives = 14/21 (66%)
Query: 10 LVLSGKGGVGKSTVSTQLALG 30
LV+ G GGVGKS ++ + G
Sbjct: 2 LVVLGAGGVGKSALTIRFVSG 22
>gnl|CDD|184411 PRK13946, PRK13946, shikimate kinase; Provisional.
Length = 184
Score = 27.6 bits (62), Expect = 3.5
Identities = 12/22 (54%), Positives = 14/22 (63%)
Query: 10 LVLSGKGGVGKSTVSTQLALGL 31
+VL G G GKSTV +LA L
Sbjct: 13 VVLVGLMGAGKSTVGRRLATML 34
>gnl|CDD|223203 COG0125, Tmk, Thymidylate kinase [Nucleotide transport and
metabolism].
Length = 208
Score = 27.6 bits (62), Expect = 3.6
Identities = 12/33 (36%), Positives = 20/33 (60%)
Query: 6 KHVILVLSGKGGVGKSTVSTQLALGLKDKGFKV 38
K + +V+ G G GK+T + L L+++G KV
Sbjct: 2 KGMFIVIEGIDGAGKTTQAELLKERLEERGIKV 34
>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 = 27.3 bits (61), Expect = 3.6
Identities = 7/20 (35%), Positives = 13/20 (65%)
Query: 9 ILVLSGKGGVGKSTVSTQLA 28
++++ G G GKST + +L
Sbjct: 1 LILMVGLPGSGKSTFARRLL 20
>gnl|CDD|226691 COG4240, COG4240, Predicted kinase [General function prediction
only].
Length = 300
Score = 27.9 bits (62), Expect = 3.7
Identities = 14/37 (37%), Positives = 20/37 (54%), Gaps = 1/37 (2%)
Query: 9 ILVLSGKGGVGKSTVSTQLALGLKDKG-FKVGILDID 44
I+ +SG G GKST+S + L KG + L +D
Sbjct: 52 IVGISGPQGSGKSTLSALIVRLLAAKGLERTATLSLD 88
>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 = 28.0 bits (62), Expect = 3.7
Identities = 13/37 (35%), Positives = 20/37 (54%), Gaps = 3/37 (8%)
Query: 2 LDGVKHVILVLSGKGGVGKSTVSTQLALGLKDKGFKV 38
L+ IL+++G G GKST L+ K+ G +V
Sbjct: 105 LENAPKRILLITGPSGCGKSTTIKILS---KELGIQV 138
>gnl|CDD|233761 TIGR02173, cyt_kin_arch, cytidylate kinase, putative. Proteins
in this family are believed to be cytidylate kinase.
Members of this family are found in the archaea and in
spirochaetes, and differ considerably from the common
bacterial form of cytidylate kinase described by
TIGR00017.
Length = 171
Score = 27.4 bits (61), Expect = 3.8
Identities = 13/27 (48%), Positives = 18/27 (66%), Gaps = 2/27 (7%)
Query: 8 VILVLSGKGGVGKSTVSTQLA--LGLK 32
+I+ +SG G GK+TV+ LA L LK
Sbjct: 1 MIITISGPPGSGKTTVAKILAEKLSLK 27
>gnl|CDD|129447 TIGR00347, bioD, dethiobiotin synthase. Dethiobiotin synthase is
involved in biotin biosynthesis and catalyses the
reaction (CO2 + 7,8-diaminononanoate + ATP =
dethiobiotin + phosphate + ADP). The enzyme binds ATP
(see motif in first 12 residues of the SEED alignment)
and requires magnesium as a co-factor [Biosynthesis of
cofactors, prosthetic groups, and carriers, Biotin].
Length = 166
Score = 27.3 bits (61), Expect = 3.9
Identities = 12/25 (48%), Positives = 15/25 (60%)
Query: 17 GVGKSTVSTQLALGLKDKGFKVGIL 41
GVGK+ S+ LA LK G+ VG
Sbjct: 8 GVGKTVASSALAAKLKKAGYSVGYY 32
>gnl|CDD|169051 PRK07667, PRK07667, uridine kinase; Provisional.
Length = 193
Score = 27.4 bits (61), Expect = 3.9
Identities = 12/36 (33%), Positives = 16/36 (44%)
Query: 9 ILVLSGKGGVGKSTVSTQLALGLKDKGFKVGILDID 44
IL + G GK+T L +K +G I ID
Sbjct: 19 ILGIDGLSRSGKTTFVANLKENMKQEGIPFHIFHID 54
>gnl|CDD|129256 TIGR00152, TIGR00152, dephospho-CoA kinase. This model produces
scores in the range of 0-25 bits against adenylate,
guanylate, uridine, and thymidylate kinases
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Pantothenate and coenzyme A].
Length = 188
Score = 27.3 bits (61), Expect = 4.1
Identities = 16/44 (36%), Positives = 21/44 (47%), Gaps = 5/44 (11%)
Query: 9 ILVLSGKGGVGKSTVSTQLALGLKDKGFKVGILDIDLCGPSVPH 52
I+ L+G G GKSTV+ LA DK ++D D V
Sbjct: 1 IIGLTGGIGSGKSTVANYLA----DKY-HFPVIDADKIAHQVVE 39
>gnl|CDD|237727 PRK14489, PRK14489, putative bifunctional molybdopterin-guanine
dinucleotide biosynthesis protein MobA/MobB;
Provisional.
Length = 366
Score = 27.8 bits (62), Expect = 4.2
Identities = 19/65 (29%), Positives = 31/65 (47%), Gaps = 10/65 (15%)
Query: 14 GKGGVGKSTVSTQLALGLKDKGFKVGI-------LDIDLCGPSVPHLLNIENSD--VHQC 64
G G GK+T+ +L L +G+++G+ +DID G H L ++ + C
Sbjct: 212 GYSGTGKTTLLEKLIPELIARGYRIGLIKHSHHRVDIDKPGKD-SHRLRAAGANPTMIVC 270
Query: 65 PEGWV 69
PE W
Sbjct: 271 PERWA 275
>gnl|CDD|224985 COG2074, COG2074, 2-phosphoglycerate kinase [Carbohydrate transport
and metabolism].
Length = 299
Score = 27.7 bits (62), Expect = 4.3
Identities = 12/26 (46%), Positives = 20/26 (76%), Gaps = 2/26 (7%)
Query: 9 ILVLSGKGGVGKSTVSTQLA--LGLK 32
I+++ G GVGKST++ +LA LG++
Sbjct: 91 IILIGGASGVGKSTIAGELARRLGIR 116
>gnl|CDD|236241 PRK08324, PRK08324, short chain dehydrogenase; Validated.
Length = 681
Score = 27.9 bits (63), Expect = 4.4
Identities = 14/38 (36%), Positives = 19/38 (50%), Gaps = 5/38 (13%)
Query: 7 HVILVLSGKGGVGKSTVSTQLALGLKDKGFKVGILDID 44
V LV GG+GK+T A L +G V + D+D
Sbjct: 423 KVALVTGAAGGIGKAT-----AKRLAAEGACVVLADLD 455
>gnl|CDD|214692 smart00487, DEXDc, DEAD-like helicases superfamily.
Length = 201
Score = 27.1 bits (60), Expect = 4.6
Identities = 14/43 (32%), Positives = 22/43 (51%), Gaps = 4/43 (9%)
Query: 1 MLDGVKHVILVLSGKGGVGKSTVSTQLAL--GLKDKGFKVGIL 41
+L G++ VIL G GK+ + AL + KG +V +L
Sbjct: 20 LLSGLRDVILA--APTGSGKTLAALLPALEALKRGKGGRVLVL 60
>gnl|CDD|217429 pfam03215, Rad17, Rad17 cell cycle checkpoint protein.
Length = 490
Score = 27.7 bits (61), Expect = 4.7
Identities = 14/37 (37%), Positives = 22/37 (59%), Gaps = 3/37 (8%)
Query: 2 LDGVKHVILVLSGKGGVGKSTVSTQLALGLKDKGFKV 38
L+ K +IL+L+G G GKST L+ K+ G ++
Sbjct: 40 LESNKQLILLLTGPSGCGKSTTVKVLS---KELGIEI 73
>gnl|CDD|232857 TIGR00176, mobB, molybdopterin-guanine dinucleotide biosynthesis
protein MobB. This molybdenum cofactor biosynthesis
enzyme is similar to the urease accessory protein UreG
and to the hydrogenase accessory protein HypB, both GTP
hydrolases involved in loading nickel into the
metallocenters of their respective target enzymes
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Molybdopterin].
Length = 155
Score = 27.0 bits (60), Expect = 4.9
Identities = 12/42 (28%), Positives = 22/42 (52%), Gaps = 5/42 (11%)
Query: 9 ILVLSGKGGVGKSTVSTQLALGLKDKGFKVGIL-----DIDL 45
+L + G GK+T+ +L LK +G++V + D D+
Sbjct: 1 VLQIVGPKNSGKTTLIERLVKALKARGYRVATIKHDHHDFDI 42
>gnl|CDD|180120 PRK05506, PRK05506, bifunctional sulfate adenylyltransferase
subunit 1/adenylylsulfate kinase protein; Provisional.
Length = 632
Score = 27.6 bits (62), Expect = 4.9
Identities = 17/54 (31%), Positives = 24/54 (44%), Gaps = 4/54 (7%)
Query: 2 LDGVKHVILVLSGKGGVGKSTVSTQLALGLKDKGFKVGILDIDLCGPSVPHLLN 55
G K + +G G GKST++ + L G +LD G +V H LN
Sbjct: 455 RKGQKPATVWFTGLSGSGKSTIANLVERRLHALGRHTYLLD----GDNVRHGLN 504
>gnl|CDD|226126 COG3598, RepA, RecA-family ATPase [DNA replication, recombination,
and repair].
Length = 402
Score = 27.6 bits (61), Expect = 5.0
Identities = 14/38 (36%), Positives = 18/38 (47%), Gaps = 4/38 (10%)
Query: 5 VKHVILVLSGKGGVGKSTVSTQL----ALGLKDKGFKV 38
K + +L G GVGK+T+ L A G G KV
Sbjct: 87 RKGYVSILYGDSGVGKTTLLLYLCIALAAGKNLFGNKV 124
>gnl|CDD|237312 PRK13236, PRK13236, nitrogenase reductase; Reviewed.
Length = 296
Score = 27.3 bits (60), Expect = 5.5
Identities = 12/31 (38%), Positives = 18/31 (58%)
Query: 14 GKGGVGKSTVSTQLALGLKDKGFKVGILDID 44
GKGG+GKST S + + G ++ I+ D
Sbjct: 13 GKGGIGKSTTSQNTLAAMAEMGQRILIVGCD 43
>gnl|CDD|178439 PLN02847, PLN02847, triacylglycerol lipase.
Length = 633
Score = 27.5 bits (61), Expect = 5.7
Identities = 10/22 (45%), Positives = 16/22 (72%)
Query: 146 DGAVLVTTPQAVSIEDVRKEIT 167
+G+ LV T A S++D+R E+T
Sbjct: 309 NGSDLVPTFSAASVDDLRSEVT 330
>gnl|CDD|201778 pfam01408, GFO_IDH_MocA, Oxidoreductase family, NAD-binding
Rossmann fold. This family of enzymes utilise NADP or
NAD. This family is called the GFO/IDH/MOCA family in
swiss-prot.
Length = 120
Score = 26.4 bits (59), Expect = 5.7
Identities = 16/69 (23%), Positives = 31/69 (44%), Gaps = 10/69 (14%)
Query: 106 IRQIINDVCWKDVDYLIIDTPPGTSDEHITVMECLREVQCDG-AVLVTTPQAVSIEDVRK 164
+ +++ D D+D + + TPPG E + L G VL P A ++E+ ++
Sbjct: 54 LEELLADP---DIDAVSVATPPGLHFEL--ALAALEA----GKHVLCEKPLATTVEEAKE 104
Query: 165 EITFCKKTN 173
+ +K
Sbjct: 105 LVELAEKAG 113
>gnl|CDD|232945 TIGR00376, TIGR00376, DNA helicase, putative. The gene product may
represent a DNA helicase. Eukaryotic members of this
family have been characterized as binding certain
single-stranded G-rich DNA sequences (GGGGT and GGGCT).
A number of related proteins are characterized as
helicases [DNA metabolism, DNA replication,
recombination, and repair].
Length = 637
Score = 27.5 bits (61), Expect = 5.8
Identities = 19/62 (30%), Positives = 34/62 (54%), Gaps = 5/62 (8%)
Query: 119 DYLIIDTPPGTSDEHITVMECLR-EVQCDGAVLVTTPQAVSIEDVRKEITFCKKTNIKIL 177
D +I PPGT T++E +R V+ VLVT P ++++++ + + C + KI+
Sbjct: 174 DLFLIHGPPGTGKTR-TLVELIRQLVKRGLRVLVTAPSNIAVDNLLERLALC---DQKIV 229
Query: 178 GL 179
L
Sbjct: 230 RL 231
>gnl|CDD|232926 TIGR00337, PyrG, CTP synthase. CTP synthase is involved in
pyrimidine ribonucleotide/ribonucleoside metabolism.
The enzyme catalyzes the reaction L-glutamine + H2O +
UTP + ATP = CTP + phosphate + ADP + L-glutamate. The
enzyme exists as a dimer of identical chains that
aggregates as a tetramer. This gene has been found
circa 500 bp 5' upstream of enolase in both beta
(Nitrosomonas europaea) and gamma (E.coli) subdivisions
of proteobacterium (FEMS Microbiol Lett 1998 Aug
1;165(1):153-7) [Purines, pyrimidines, nucleosides, and
nucleotides, Pyrimidine ribonucleotide biosynthesis].
Length = 525
Score = 27.3 bits (61), Expect = 5.9
Identities = 10/28 (35%), Positives = 15/28 (53%)
Query: 17 GVGKSTVSTQLALGLKDKGFKVGILDID 44
+GK + + LK +G KV I+ ID
Sbjct: 13 SLGKGITAASIGRLLKARGLKVTIIKID 40
>gnl|CDD|227596 COG5271, MDN1, AAA ATPase containing von Willebrand factor type A
(vWA) domain [General function prediction only].
Length = 4600
Score = 27.7 bits (61), Expect = 5.9
Identities = 13/37 (35%), Positives = 21/37 (56%), Gaps = 5/37 (13%)
Query: 7 HVILVLSGKGGVGKSTVSTQLALGLKDKGFKVGILDI 43
+LV G+ G GK+T+ LAL L FK+ +++
Sbjct: 466 PTLLV--GETGTGKTTMIQYLALKL---HFKLTVINK 497
>gnl|CDD|238980 cd02022, DPCK, Dephospho-coenzyme A kinase (DPCK, EC 2.7.1.24)
catalyzes the phosphorylation of dephosphocoenzyme A
(dCoA) to yield CoA, which is the final step in CoA
biosynthesis.
Length = 179
Score = 26.7 bits (60), Expect = 5.9
Identities = 14/30 (46%), Positives = 19/30 (63%), Gaps = 4/30 (13%)
Query: 9 ILVLSGKGGVGKSTVSTQLALGLKDKGFKV 38
I+ L+G G GKSTV+ +L LK+ G V
Sbjct: 1 IIGLTGGIGSGKSTVA-KL---LKELGIPV 26
>gnl|CDD|225827 COG3290, CitA, Signal transduction histidine kinase regulating
citrate/malate metabolism [Signal transduction
mechanisms].
Length = 537
Score = 27.3 bits (61), Expect = 6.0
Identities = 9/40 (22%), Positives = 18/40 (45%), Gaps = 3/40 (7%)
Query: 67 GWVPVYTDASQTLAVMSIGFLLKNRDDAIIWRGPKKTAMI 106
VP++ + + + V+S+G+LL DD +
Sbjct: 141 AKVPIFDEDGKQIGVVSVGYLLSEIDD---VILEFLRPLA 177
>gnl|CDD|217424 pfam03205, MobB, Molybdopterin guanine dinucleotide synthesis
protein B. This protein contains a P-loop.
Length = 126
Score = 26.6 bits (59), Expect = 6.0
Identities = 13/47 (27%), Positives = 25/47 (53%), Gaps = 8/47 (17%)
Query: 9 ILVLSGKGGVGKSTVSTQLALGLKDKGFKVGIL--------DIDLCG 47
I+++ G GK+T+ +L LK +G++V ++ +ID G
Sbjct: 2 IVLVVGPKDSGKTTLIRKLLNYLKRRGYRVAVVKHLDHGQGEIDKPG 48
>gnl|CDD|198062 smart00994, zf-C4_ClpX, ClpX C4-type zinc finger. The ClpX heat
shock protein of Escherichia coli is a member of the
universally conserved Hsp100 family of proteins, and
possesses a putative zinc finger motif of the C4 type.
This presumed zinc binding domain is found at the
N-terminus of the ClpX protein. ClpX is an ATPase which
functions both as a substrate specificity component of
the ClpXP protease and as a molecular chaperone. The
molecular function of this domain is now known.
Length = 39
Score = 24.8 bits (55), Expect = 6.0
Identities = 8/24 (33%), Positives = 11/24 (45%)
Query: 168 FCKKTNIKILGLIENMSGYTCPHC 191
FC K+ ++ LI Y C C
Sbjct: 5 FCGKSESEVRKLIAGPGVYICDEC 28
>gnl|CDD|234232 TIGR03499, FlhF, flagellar biosynthetic protein FlhF. [Cellular
processes, Chemotaxis and motility].
Length = 283
Score = 26.9 bits (60), Expect = 6.0
Identities = 13/41 (31%), Positives = 21/41 (51%), Gaps = 2/41 (4%)
Query: 6 KHVILVLSGKGGVGKSTVSTQLA--LGLKDKGFKVGILDID 44
+ ++ L G GVGK+T +LA L+ KV ++ D
Sbjct: 194 RGGVIALVGPTGVGKTTTLAKLAARFVLEHGKKKVALITTD 234
>gnl|CDD|224557 COG1643, HrpA, HrpA-like helicases [DNA replication, recombination,
and repair].
Length = 845
Score = 27.3 bits (61), Expect = 6.2
Identities = 12/39 (30%), Positives = 21/39 (53%), Gaps = 3/39 (7%)
Query: 6 KHVILVLSGKGGVGKSTVSTQ--LALGLKDKGFKVGILD 42
++ ++++ G+ G GK+T Q L GL G K+G
Sbjct: 64 QNQVVIIVGETGSGKTTQLPQFLLEEGLGIAG-KIGCTQ 101
>gnl|CDD|223543 COG0467, RAD55, RecA-superfamily ATPases implicated in signal
transduction [Signal transduction mechanisms].
Length = 260
Score = 27.0 bits (60), Expect = 6.3
Identities = 7/30 (23%), Positives = 15/30 (50%)
Query: 9 ILVLSGKGGVGKSTVSTQLALGLKDKGFKV 38
+++++G G GK+ + Q +G V
Sbjct: 25 VVLITGPPGTGKTIFALQFLYEGAREGEPV 54
>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 = 26.4 bits (59), Expect = 6.5
Identities = 13/37 (35%), Positives = 19/37 (51%)
Query: 9 ILVLSGKGGVGKSTVSTQLALGLKDKGFKVGILDIDL 45
I+ L G G GKST+ +A LK ++ I D+
Sbjct: 27 IVALVGPNGSGKSTLLRAIAGLLKPTSGEILIDGKDI 63
>gnl|CDD|216999 pfam02367, UPF0079, Uncharacterized P-loop hydrolase UPF0079.
This uncharacterized family contains a P-loop.
Length = 123
Score = 26.1 bits (58), Expect = 6.5
Identities = 12/27 (44%), Positives = 16/27 (59%)
Query: 9 ILVLSGKGGVGKSTVSTQLALGLKDKG 35
+++LSG G GK+T LA GL G
Sbjct: 17 VVLLSGDLGAGKTTFVRGLAQGLGITG 43
>gnl|CDD|236353 PRK08939, PRK08939, primosomal protein DnaI; Reviewed.
Length = 306
Score = 27.1 bits (61), Expect = 6.6
Identities = 13/32 (40%), Positives = 16/32 (50%)
Query: 10 LVLSGKGGVGKSTVSTQLALGLKDKGFKVGIL 41
L L G GVGKS + +A L KG +L
Sbjct: 159 LYLYGDFGVGKSYLLAAIANELAKKGVSSTLL 190
>gnl|CDD|223775 COG0703, AroK, Shikimate kinase [Amino acid transport and
metabolism].
Length = 172
Score = 26.8 bits (60), Expect = 6.6
Identities = 15/37 (40%), Positives = 18/37 (48%), Gaps = 9/37 (24%)
Query: 10 LVLSGKGGVGKSTVSTQLA--LGLKDKGFKVGILDID 44
+VL G G GKST+ LA L L F +D D
Sbjct: 5 IVLIGFMGAGKSTIGRALAKALNLP---F----IDTD 34
>gnl|CDD|183173 PRK11519, PRK11519, tyrosine kinase; Provisional.
Length = 719
Score = 27.0 bits (60), Expect = 6.7
Identities = 33/136 (24%), Positives = 55/136 (40%), Gaps = 29/136 (21%)
Query: 6 KHVILVLSGKG-GVGKSTVSTQLALGLKDKGFKVGILDIDLCGPSVPHLLNIENSD---- 60
++ +L+++G +GK+ V LA + +V ++D D+ LL N +
Sbjct: 525 QNNVLMMTGVSPSIGKTFVCANLAAVISQTNKRVLLIDCDMRKGYTHELLGTNNVNGLSD 584
Query: 61 --VHQCPEGWVPVYTDASQTLAVMSIGFLLKNRDDAIIWRG-----PKKTAMIRQIINDV 113
+ Q D + SI N D +I RG P + M + V
Sbjct: 585 ILIGQG---------DITTAAKPTSI----ANFD--LIPRGQVPPNPSELLMSERFAELV 629
Query: 114 CW--KDVDYLIIDTPP 127
W K+ D ++IDTPP
Sbjct: 630 NWASKNYDLVLIDTPP 645
>gnl|CDD|206712 cd04141, Rit_Rin_Ric, Ras-like protein in all tissues (Rit),
Ras-like protein in neurons (Rin) and Ras-related
protein which interacts with calmodulin (Ric). Rit
(Ras-like protein in all tissues), Rin (Ras-like
protein in neurons) and Ric (Ras-related protein which
interacts with calmodulin) form a subfamily with
several unique structural and functional
characteristics. These proteins all lack a the
C-terminal CaaX lipid-binding motif typical of Ras
family proteins, and Rin and Ric contain
calmodulin-binding domains. Rin, which is expressed
only in neurons, induces neurite outgrowth in rat
pheochromocytoma cells through its association with
calmodulin and its activation of endogenous Rac/cdc42.
Rit, which is ubiquitously expressed in mammals,
inhibits growth-factor withdrawl-mediated apoptosis and
induces neurite extension in pheochromocytoma cells.
Rit and Rin are both able to form a ternary complex
with PAR6, a cell polarity-regulating protein, and
Rac/cdc42. This ternary complex is proposed to have
physiological function in processes such as
tumorigenesis. Activated Ric is likely to signal in
parallel with the Ras pathway or stimulate the Ras
pathway at some upstream point, and binding of
calmodulin to Ric may negatively regulate Ric activity.
Length = 172
Score = 26.7 bits (59), Expect = 6.9
Identities = 10/17 (58%), Positives = 13/17 (76%)
Query: 10 LVLSGKGGVGKSTVSTQ 26
+V+ G GGVGKS V+ Q
Sbjct: 5 IVMLGAGGVGKSAVTMQ 21
>gnl|CDD|213248 cd03281, ABC_MSH5_euk, ATP-binding cassette domain of eukaryotic
MutS5 homolog. The MutS protein initiates DNA mismatch
repair by recognizing mispaired and unpaired bases
embedded in duplex DNA and activating endo- and
exonucleases to remove the mismatch. Members of the
MutS family possess C-terminal domain with a conserved
ATPase activity that belongs to the ATP binding
cassette (ABC) superfamily. MutS homologs (MSH) have
been identified in most prokaryotic and all eukaryotic
organisms examined. Prokaryotes have two homologs
(MutS1 and MutS2), whereas seven MSH proteins (MSH1 to
MSH7) have been identified in eukaryotes. The homodimer
MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are
primarily involved in mitotic mismatch repair, whereas
MSH4-MSH5 is involved in resolution of Holliday
junctions during meiosis. All members of the MutS
family contain the highly conserved Walker A/B ATPase
domain, and many share a common mechanism of action.
MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to
form sliding clamps, and recognition of specific DNA
structures or lesions results in ADP/ATP exchange.
Length = 213
Score = 26.5 bits (59), Expect = 7.3
Identities = 10/29 (34%), Positives = 15/29 (51%)
Query: 1 MLDGVKHVILVLSGKGGVGKSTVSTQLAL 29
+ G I+V++G GKS Q+AL
Sbjct: 23 EIGGGGPSIMVITGPNSSGKSVYLKQVAL 51
>gnl|CDD|187565 cd05255, SQD1_like_SDR_e, UDP_sulfoquinovose_synthase
(Arabidopsis thaliana SQD1 and related proteins),
extended (e) SDRs. Arabidopsis thaliana
UDP-sulfoquinovose-synthase ( SQD1), an extended SDR,
catalyzes the transfer of SO(3)(-) to UDP-glucose in
the biosynthesis of plant sulfolipids. Members of this
subgroup share the conserved SDR catalytic residues,
and a partial match to the characteristic extended-SDR
NAD-binding motif. Extended SDRs are distinct from
classical SDRs. In addition to the Rossmann fold
(alpha/beta folding pattern with a central beta-sheet)
core region typical of all SDRs, extended SDRs have a
less conserved C-terminal extension of approximately
100 amino acids. Extended SDRs are a diverse collection
of proteins, and include isomerases, epimerases,
oxidoreductases, and lyases; they typically have a
TGXXGXXG cofactor binding motif. SDRs are a
functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold, an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Sequence
identity between different SDR enzymes is typically in
the 15-30% range; they catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase numbering). In addition to the Tyr and
Lys, there is often an upstream Ser and/or an Asn,
contributing to the active site; while substrate
binding is in the C-terminal region, which determines
specificity. The standard reaction mechanism is a
4-pro-S hydride transfer and proton relay involving the
conserved Tyr and Lys, a water molecule stabilized by
Asn, and nicotinamide. Atypical SDRs generally lack the
catalytic residues characteristic of the SDRs, and
their glycine-rich NAD(P)-binding motif is often
different from the forms normally seen in classical or
extended SDRs. Complex (multidomain) SDRs such as
ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 382
Score = 27.0 bits (60), Expect = 7.4
Identities = 13/34 (38%), Positives = 18/34 (52%), Gaps = 5/34 (14%)
Query: 9 ILVLSGKGGVGKSTVSTQLALGLKDKGFKVGILD 42
+L+L G G G T AL L +G +V I+D
Sbjct: 3 VLILGGDGYCGWPT-----ALHLSKRGHEVCIVD 31
>gnl|CDD|223315 COG0237, CoaE, Dephospho-CoA kinase [Coenzyme metabolism].
Length = 201
Score = 26.5 bits (59), Expect = 7.5
Identities = 13/30 (43%), Positives = 17/30 (56%), Gaps = 4/30 (13%)
Query: 9 ILVLSGKGGVGKSTVSTQLALGLKDKGFKV 38
I+ L+G G GKSTV+ L + GF V
Sbjct: 4 IIGLTGGIGSGKSTVAK----ILAELGFPV 29
>gnl|CDD|216186 pfam00910, RNA_helicase, RNA helicase. This family includes RNA
helicases thought to be involved in duplex unwinding
during viral RNA replication. Members of this family
are found in a variety of single stranded RNA viruses.
Length = 105
Score = 25.7 bits (57), Expect = 7.7
Identities = 10/25 (40%), Positives = 13/25 (52%)
Query: 10 LVLSGKGGVGKSTVSTQLALGLKDK 34
+ L G G GKST++ LA L
Sbjct: 1 IWLYGPPGCGKSTLAKYLARALLKH 25
>gnl|CDD|225063 COG2152, COG2152, Predicted glycosylase [Carbohydrate transport and
metabolism].
Length = 314
Score = 26.9 bits (60), Expect = 7.9
Identities = 12/39 (30%), Positives = 21/39 (53%), Gaps = 2/39 (5%)
Query: 65 PEGWVPVYTDASQTLAVMSIGFLLKNRDDA--IIWRGPK 101
EGW+ +Y +TL V +G L + +D ++ R P+
Sbjct: 215 EEGWLVLYHGVDETLTVYRLGAALLDLEDPTKVLARSPE 253
>gnl|CDD|235437 PRK05380, pyrG, CTP synthetase; Validated.
Length = 533
Score = 26.9 bits (61), Expect = 8.1
Identities = 13/33 (39%), Positives = 16/33 (48%), Gaps = 4/33 (12%)
Query: 16 GGV----GKSTVSTQLALGLKDKGFKVGILDID 44
GGV GK + L LK +G KV I +D
Sbjct: 9 GGVVSSLGKGITAASLGRLLKARGLKVTIQKLD 41
>gnl|CDD|213816 TIGR03470, HpnH, hopanoid biosynthesis associated radical SAM
protein HpnH. The sequences represented by this model
are members of the radical SAM superfamily of enzymes
(pfam04055). These enzymes utilize an iron-sulfur redox
cluster and S-adenosylmethionine to carry out diverse
radical mediated reactions. The members of this clade
are frequently found in the same locus as
squalene-hopene cyclase (SHC, TIGR01507) and other genes
associated with the biosynthesis of hopanoid natural
products. The linkage between SHC and this radical SAM
enzyme is strong; one is nearly always observed in the
same genome where the other is found. A hopanoid
biosynthesis locus was described in Zymomonas mobilis
consisting of the genes HpnA-E and SHC (HpnF).
Continuing past SHC are found a phosphorylase enzyme
(ZMO0873, i.e. HpnG, TIGR03468) and this radical SAM
enzyme (ZMO0874) which we name here HpnH. Granted, in Z.
mobilis, HpnH is in a convergent orientation with
respect to HpnA-G, but one gene beyond HpnH and running
in the same convergent direction is IspH (ZM0875,
4-hydroxy-3-methylbut-2-enyl diphosphate reductase), an
essential enzyme of IPP biosynthesis and therefore
essential for the biosynthesis of hopanoids. One of the
well-described hopanoid intermediates is
bacteriohopanetetrol. In the conversion from hopene
several reactions must occur in the side chain for which
a radical mechanism might be reasonable. These include
the four (presumably anaerobic) hydroxylations and a
methyl shift.
Length = 318
Score = 26.6 bits (59), Expect = 8.2
Identities = 12/32 (37%), Positives = 17/32 (53%)
Query: 123 IDTPPGTSDEHITVMECLREVQCDGAVLVTTP 154
I P + ++V ECLR V GA +V+ P
Sbjct: 48 IQYPAEILKQRLSVEECLRAVDECGAPVVSIP 79
>gnl|CDD|238899 cd01918, HprK_C, HprK/P, the bifunctional histidine-containing
protein kinase/phosphatase, controls the
phosphorylation state of the phosphocarrier protein HPr
and regulates the utilization of carbon sources by
gram-positive bacteria. It catalyzes both the
ATP-dependent phosphorylation of Ser-46 of HPr and its
dephosphorylation by phosphorolysis. The latter
reaction uses inorganic phosphate as substrate and
produces pyrophosphate. Phosphoenolpyruvate
carboxykinase (PEPCK) and the C-terminal catalytic
domain of HprK/P are structurally similar with
conserved active site residues suggesting these two
phosphotransferases have related functions. The HprK/P
N-terminal domain is structurally similar to the
N-terminal domains of the MurE and MurF amino acid
ligases.
Length = 149
Score = 26.0 bits (58), Expect = 8.2
Identities = 10/27 (37%), Positives = 16/27 (59%), Gaps = 4/27 (14%)
Query: 10 LVLSGKGGVGKSTVSTQLALGLKDKGF 36
++++G G+GKS LAL L +G
Sbjct: 17 VLITGPSGIGKSE----LALELIKRGH 39
>gnl|CDD|236982 PRK11784, PRK11784, tRNA 2-selenouridine synthase; Provisional.
Length = 345
Score = 26.7 bits (60), Expect = 8.2
Identities = 13/37 (35%), Positives = 19/37 (51%), Gaps = 8/37 (21%)
Query: 9 ILVLSGKGGVGKSTVSTQLALGLKDKGFKVGILDIDL 45
++VL G G GK T+L L + G +V +DL
Sbjct: 143 LVVLGGNTGSGK----TELLQALANAGAQV----LDL 171
>gnl|CDD|238835 cd01672, TMPK, Thymidine monophosphate kinase (TMPK), also known
as thymidylate kinase, catalyzes the phosphorylation of
thymidine monophosphate (TMP) to thymidine diphosphate
(TDP) utilizing ATP as its preferred phophoryl donor.
TMPK represents the rate-limiting step in either de
novo or salvage biosynthesis of thymidine triphosphate
(TTP).
Length = 200
Score = 26.5 bits (59), Expect = 8.8
Identities = 11/28 (39%), Positives = 17/28 (60%)
Query: 11 VLSGKGGVGKSTVSTQLALGLKDKGFKV 38
V G G GK+T+ LA L+ +G++V
Sbjct: 4 VFEGIDGAGKTTLIELLAERLEARGYEV 31
>gnl|CDD|239390 cd03116, MobB, Molybdenum is an essential trace element in the
form of molybdenum cofactor (Moco) which is associated
with the metabolism of nitrogen, carbon and sulfur by
redox active enzymes. In E. coli, the synthesis of Moco
involves genes from several loci: moa, mob, mod, moe
and mog. The mob locus contains mobA and mobB genes.
MobB catalyzes the attachment of the guanine
dinucleotide to molybdopterin.
Length = 159
Score = 26.1 bits (58), Expect = 8.9
Identities = 9/33 (27%), Positives = 18/33 (54%)
Query: 9 ILVLSGKGGVGKSTVSTQLALGLKDKGFKVGIL 41
++ G G GK+T+ +L L +G +V ++
Sbjct: 3 VIGFVGYSGSGKTTLLEKLIPALSARGLRVAVI 35
>gnl|CDD|232932 TIGR00345, GET3_arsA_TRC40, transport-energizing ATPase,
TRC40/GET3/ArsA family. Members of this family are
ATPases that energize transport, although with different
partner proteins for different functions. Recent
findings show that TRC40 (GET3 in yeast) in involved in
the insertion of tail-anchored membrane proteins in
eukaryotes. A similar function is expected for members
of this family in archaea. However, the earliest
discovery of a function for this protein family is ArsA,
an arsenic resistance protein that partners with ArsB
(see pfam02040) for As(III) efflux [Hypothetical
proteins, Conserved].
Length = 284
Score = 26.7 bits (59), Expect = 8.9
Identities = 10/34 (29%), Positives = 17/34 (50%)
Query: 149 VLVTTPQAVSIEDVRKEITFCKKTNIKILGLIEN 182
VLV P+ +S+ + + K IK+ +I N
Sbjct: 193 VLVVIPEKMSLYESERAHKELAKYGIKVDAVIVN 226
>gnl|CDD|237393 PRK13477, PRK13477, bifunctional pantoate ligase/cytidylate kinase;
Provisional.
Length = 512
Score = 26.8 bits (60), Expect = 8.9
Identities = 12/25 (48%), Positives = 16/25 (64%), Gaps = 2/25 (8%)
Query: 9 ILVLSGKGGVGKSTVSTQLA--LGL 31
I+ + G G GKSTV+ +A LGL
Sbjct: 286 IIAIDGPAGAGKSTVTRAVAKKLGL 310
>gnl|CDD|237066 PRK12338, PRK12338, hypothetical protein; Provisional.
Length = 319
Score = 26.6 bits (59), Expect = 9.4
Identities = 12/28 (42%), Positives = 20/28 (71%), Gaps = 3/28 (10%)
Query: 7 HVILVLSGKGGVGKSTVSTQLA--LGLK 32
+VIL+ G+GKST++++LA L +K
Sbjct: 5 YVILI-GSASGIGKSTIASELARTLNIK 31
>gnl|CDD|206708 cd04136, Rap_like, Rap-like family consists of Rap1, Rap2 and
RSR1. The Rap subfamily consists of the Rap1, Rap2,
and RSR1. Rap subfamily proteins perform different
cellular functions, depending on the isoform and its
subcellular localization. For example, in rat salivary
gland, neutrophils, and platelets, Rap1 localizes to
secretory granules and is believed to regulate
exocytosis or the formation of secretory granules. Rap1
has also been shown to localize in the Golgi of rat
fibroblasts, zymogen granules, plasma membrane, and
microsomal membrane of the pancreatic acini, as well as
in the endocytic compartment of skeletal muscle cells
and fibroblasts. Rap1 localizes in the nucleus of human
oropharyngeal squamous cell carcinomas (SCCs) and cell
lines. Rap1 plays a role in phagocytosis by controlling
the binding of adhesion receptors (typically integrins)
to their ligands. In yeast, Rap1 has been implicated in
multiple functions, including activation and silencing
of transcription and maintenance of telomeres. Rap2 is
involved in multiple functions, including activation of
c-Jun N-terminal kinase (JNK) to regulate the actin
cytoskeleton and activation of the Wnt/beta-catenin
signaling pathway in embryonic Xenopus. A number of
effector proteins for Rap2 have been identified,
including isoform 3 of the human mitogen-activated
protein kinase kinase kinase kinase 4 (MAP4K4) and
Traf2- and Nck-interacting kinase (TNIK), and the
RalGEFs RalGDS, RGL, and Rlf, which also interact with
Rap1 and Ras. RSR1 is the fungal homolog of Rap1 and
Rap2. In budding yeasts, it is involved in selecting a
site for bud growth, which directs the establishment of
cell polarization. The Rho family GTPase Cdc42 and its
GEF, Cdc24, then establish an axis of polarized growth.
It is believed that Cdc42 interacts directly with RSR1
in vivo. In filamentous fungi such as Ashbya gossypii,
RSR1 is a key regulator of polar growth in the hypha.
Most Ras proteins contain a lipid modification site at
the C-terminus, with a typical sequence motif CaaX,
where a = an aliphatic amino acid and X = any amino
acid. Lipid binding is essential for membrane
attachment, a key feature of most Ras proteins. Due to
the presence of truncated sequences in this CD, the
lipid modification site is not available for
annotation.
Length = 164
Score = 26.0 bits (57), Expect = 9.5
Identities = 11/22 (50%), Positives = 15/22 (68%)
Query: 10 LVLSGKGGVGKSTVSTQLALGL 31
LV+ G GGVGKS ++ Q G+
Sbjct: 4 LVVLGSGGVGKSALTVQFVQGI 25
>gnl|CDD|183704 PRK12726, PRK12726, flagellar biosynthesis regulator FlhF;
Provisional.
Length = 407
Score = 26.6 bits (58), Expect = 9.5
Identities = 14/38 (36%), Positives = 20/38 (52%)
Query: 7 HVILVLSGKGGVGKSTVSTQLALGLKDKGFKVGILDID 44
H I+ L G+ GVGK+T +L L + VG + D
Sbjct: 206 HRIISLIGQTGVGKTTTLVKLGWQLLKQNRTVGFITTD 243
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
0.321 0.139 0.431
Gapped
Lambda K H
0.267 0.0797 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,641,758
Number of extensions: 889542
Number of successful extensions: 1653
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1619
Number of HSP's successfully gapped: 242
Length of query: 192
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 100
Effective length of database: 6,857,034
Effective search space: 685703400
Effective search space used: 685703400
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 56 (25.2 bits)