RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11347
(294 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 = 258 bits (663), Expect = 8e-88
Identities = 107/218 (49%), Positives = 127/218 (58%), Gaps = 49/218 (22%)
Query: 49 KVLVLSGKGGVGKSTFTNLLARVLAKSNESVDVGVLDLDICGPSMPRMMGLLNEQVHQSA 108
+ V+SGKGGVGKST LA LAK V G+LD DI GPS+P+M
Sbjct: 1 VIAVMSGKGGVGKSTVAVNLALALAKLGYKV--GLLDADIYGPSIPKM------------ 46
Query: 109 SGWSPVFLEENLSVMSIGFLLNSPDDAVIWRGPKKNTMIRQFLSEVDWGNGLEYLLIDTP 168
WRGP K I+QFL++VDWG L+YL+ID P
Sbjct: 47 -----------------------------WRGPMKMGAIKQFLTDVDWGE-LDYLVIDMP 76
Query: 169 PGTSDEHLSLVQYLKGLPDIGAIVVTTPQEVSLLDVRKEIDFCRKVNIPIIGVVENMATF 228
PGT DEHL+L Q LP GA++VTTPQEV+L DVRK ID +KVNIPI+GVVENM+ F
Sbjct: 77 PGTGDEHLTLAQ---SLPIDGAVIVTTPQEVALDDVRKAIDMFKKVNIPILGVVENMSYF 133
Query: 229 VCPKCTKPSEIFPKDSGGAEKMCAELSVPFLGSVPIDP 266
VCP C K IF K GG EK+ EL VP LG +P+DP
Sbjct: 134 VCPHCGKKIYIFGK--GGGEKLAEELGVPLLGKIPLDP 169
>gnl|CDD|223563 COG0489, Mrp, ATPases involved in chromosome partitioning [Cell
division and chromosome partitioning].
Length = 265
Score = 216 bits (553), Expect = 7e-70
Identities = 93/242 (38%), Positives = 133/242 (54%), Gaps = 23/242 (9%)
Query: 28 AAKSVDPGIELVKSHLSNVKHKVLVLSGKGGVGKSTFTNLLARVLAKSNESVDVGVLDLD 87
A +++ ++ K VK+ + V SGKGGVGKST LA LA+ + V +LD D
Sbjct: 38 ALRALRTNLKFAKVLRKGVKNVIAVTSGKGGVGKSTVAVNLAAALAQLGKRV--LLLDAD 95
Query: 88 ICGPSMPRMMGLLNEQVHQSAS---GWSPVFLEENLSVMSIGFLLNSPDDAVIWRGPKKN 144
+ GPS+PRM+GL N PV + + V+SI L P VI RG +
Sbjct: 96 LRGPSIPRMLGLENLPGLTELLAGEALEPVIQHDGIKVLSILPLGPVP---VIPRGLLGS 152
Query: 145 TMIRQFLSEVDWGNGLEYLLIDTPPGTSDEHLSLVQYLKGLPDIGAIVVTTPQEVSLLDV 204
+ Q L +V WG +Y++IDTPPGT D +++Q + G ++VTTP + +L DV
Sbjct: 153 KAMLQLLEDVLWGE-YDYVIIDTPPGTGDADATVLQRIPD----GVVIVTTPGKTALEDV 207
Query: 205 RKEIDFCRKVNIPIIGVVENMATFVCPKCTKPSEIFPKDSGGAEKMCAELSVPFLGSVPI 264
+K ID K IP++GVVENM+ F+CP+C + GG EK P+LGS+P+
Sbjct: 208 KKAIDMLEKAGIPVLGVVENMSYFICPRCGE---------GGGEKYAERYG-PYLGSIPL 257
Query: 265 DP 266
DP
Sbjct: 258 DP 259
>gnl|CDD|183270 PRK11670, PRK11670, antiporter inner membrane protein; Provisional.
Length = 369
Score = 173 bits (441), Expect = 9e-52
Identities = 92/221 (41%), Positives = 135/221 (61%), Gaps = 13/221 (5%)
Query: 46 VKHKVLVLSGKGGVGKSTFTNLLARVLAKSNESVDVGVLDLDICGPSMPRMMGLLNEQVH 105
VK+ + V SGKGGVGKS+ LA LA E VG+LD DI GPS+P M+G +++
Sbjct: 106 VKNIIAVSSGKGGVGKSSTAVNLALALAA--EGAKVGILDADIYGPSIPTMLGAEDQR-P 162
Query: 106 QSASG--WSPVFLEENLSVMSIGFLLNSPDDAVIWRGPKKNTMIRQFLSEVDWGNGLEYL 163
S G +P+ + L+ SIG+L+ D+A++WRGP + + Q L E W + L+YL
Sbjct: 163 TSPDGTHMAPI-MAHGLATNSIGYLVT-DDNAMVWRGPMASKALMQMLQETLWPD-LDYL 219
Query: 164 LIDTPPGTSDEHLSLVQYLKGLPDIGAIVVTTPQEVSLLDVRKEIDFCRKVNIPIIGVVE 223
++D PPGT D L+L Q +P GA+VVTTPQ+++L+D +K I KV +P++G+VE
Sbjct: 220 VLDMPPGTGDIQLTLAQ---NIPVTGAVVVTTPQDIALIDAKKGIVMFEKVEVPVLGIVE 276
Query: 224 NMATFVCPKCTKPSEIFPKDSGGAEKMCAELSVPFLGSVPI 264
NM+ +C C IF +GGAEK+ + LG +P+
Sbjct: 277 NMSMHICSNCGHHEPIF--GTGGAEKLAEKYHTQLLGQMPL 315
>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 = 147 bits (374), Expect = 2e-45
Identities = 53/84 (63%), Positives = 64/84 (76%), Gaps = 3/84 (3%)
Query: 160 LEYLLIDTPPGTSDEHLSLVQYLKGLPDIGAIVVTTPQEVSLLDVRKEIDFCRKVNIPII 219
L+YLLID PPGT DEHL+L Q L P GA++VTTPQ+V+LLDVRK ID +KVN+PI+
Sbjct: 1 LDYLLIDLPPGTGDEHLTLAQSL---PVDGAVIVTTPQDVALLDVRKAIDMFKKVNVPIL 57
Query: 220 GVVENMATFVCPKCTKPSEIFPKD 243
GVVENM+ FVCP C + IF K
Sbjct: 58 GVVENMSYFVCPDCGEKIYIFGKG 81
>gnl|CDD|223531 COG0455, flhG, Antiactivator of flagellar biosynthesis FleN, an
ATPase [Cell motility].
Length = 262
Score = 70.4 bits (173), Expect = 4e-14
Identities = 65/266 (24%), Positives = 109/266 (40%), Gaps = 51/266 (19%)
Query: 48 HKVLVLSGKGGVGKSTFT-NLLARVLAKSNESVDVGVLDLDICGPSMPRMMGL------L 100
+ V+SGKGGVGK+T T NL A + A + V ++D D+ ++ ++G+ L
Sbjct: 3 KVIAVVSGKGGVGKTTITANLGAALAALGGK--VVLLIDADLGLGNLSLLLGVESKPTTL 60
Query: 101 NEQVHQSASGWSPVFLE---ENLSVMSIG-----FLLNSPDDAVIWRGPKKNTMIRQFLS 152
++ + AS + E + L V+ G P+D +I++
Sbjct: 61 HDVLAGEAS-IEDIIYETPQDGLYVLPGGSGLEDLAKLDPED--------LEDVIKELEE 111
Query: 153 EVDWGNGLEYLLIDTPPGTSDEHLSLVQYLKGLPDIGAIVVTTPQEVSLLDVRKEIDFCR 212
D Y+LIDT G S + LS + L ++VTTP+ S+ D K I
Sbjct: 112 LYD------YILIDTGAGLSRDTLSFI-----LSSDELVIVTTPEPTSITDAYKTIKILS 160
Query: 213 KVNIPIIG--VVENMATFVCPKCTKPSEIFPKDSGGAEKMCAELSVPFLGSVPIDPLVTR 270
K+ + ++G VV N + ++ ++ VP L +P DP V R
Sbjct: 161 KLGLDLLGRRVVLNRVR----STKEGVDVAALLIQVVKQ------VPVLQVIPFDPEVRR 210
Query: 271 HCDEGTSAIDTPSAC--VDAIQQIVQ 294
EG + AI+++
Sbjct: 211 ALAEGKPIVLYSPNSKASQAIKELAA 236
>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 = 66.7 bits (163), Expect = 5e-13
Identities = 41/186 (22%), Positives = 76/186 (40%), Gaps = 17/186 (9%)
Query: 50 VLVLSGKGGVGKSTFTNLLARVLAKSNESV-----DVGVLDLDICGPSMPRMMGLLNEQV 104
+ + KGGVGK+T LAR LAK V D + G + L
Sbjct: 1 IAIAGTKGGVGKTTLAANLARALAKRGYRVLLIDLDPQANNSSYLGKVEEVLPEGLEIVD 60
Query: 105 HQS----ASGWSPVFLEENLSVMSIGFLLNSPDDAVIWRGPKKNTMIRQFLSEVDWGNGL 160
Q+ A+ P + L ++ L + + +I G +++ + S +
Sbjct: 61 AQALQAIAAAIVPSRNLDPLLLIPSNLSLENFESELIVEGKRESRLRAALESLIK--LAY 118
Query: 161 EYLLIDTPPGTSDEHLSLVQYLKGLPDIGAIVVTTPQEVSLLDVRKEIDFCRKVNIP-II 219
+Y++ID PPG + + + DI +V P+ V++ ++ ++ + + I+
Sbjct: 119 DYVIIDGPPGLGELTANALV----AADI-LVVPIEPEGVAVEGAQRLLELIEDLGVLDIL 173
Query: 220 GVVENM 225
GVV N
Sbjct: 174 GVVLNK 179
>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 = 62.2 bits (152), Expect = 7e-12
Identities = 54/233 (23%), Positives = 82/233 (35%), Gaps = 70/233 (30%)
Query: 50 VLVLSGKGGVGKSTFTNLLARVLAKSNESVDVGVLDLDICGPSMPRMMGLLNEQVHQSAS 109
++V SGKGGVGK+T T L LA+ V ++D D+ +
Sbjct: 2 IVVTSGKGGVGKTTTTANLGTALAQLGYKV--VLIDADL---GLR--------------- 41
Query: 110 GWSPVFLEENLSVMSIGFLLNSPDDAVIWRGPKKNTMIRQFLSEVDWGNGLEYLLIDTPP 169
NL + I L N + D G +Y+LID+P
Sbjct: 42 ---------NLDL--ILGLENRVV-----------------YTLHDVLAG-DYILIDSPA 72
Query: 170 GTSDE---HLSLVQYLKGLPDIGAIVVTTPQEVSLLDVRKEIDFCRKVNIPIIGVVENMA 226
G ++ A++VTTP+ SL D + + I ++GV+ N
Sbjct: 73 GIERGFITAIAPADE--------ALLVTTPEISSLRDADRVKGLLEALGIKVVGVIVNRV 124
Query: 227 TFVCPKCTKPSEIFPKDSGGAEKMCAELSVPFLGSVPIDPLVTRHCDEGTSAI 279
+ E + L VP LG +P DP V R + G +
Sbjct: 125 R----------PDMVEGGDMVEDIEEILGVPLLGVIPEDPAVIRATNRGEPVV 167
>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 = 60.3 bits (147), Expect = 4e-11
Identities = 56/218 (25%), Positives = 87/218 (39%), Gaps = 42/218 (19%)
Query: 49 KVLVLSGKGGVGKSTFTNLLARVLAKSNESVDVGVLDLDICGPSMPRMMGLLNEQVHQ-S 107
++ V+SGKGG GK+T T LA +L + D D+ P++ + E+
Sbjct: 1 QIAVISGKGGTGKTTVTAALAALLKNVV------LADCDVDAPNLHLFLKPEIEEEEDFI 54
Query: 108 ASGWSPVFLEENLSVMSIGFLLNSPDDAVIWRG--PKKNTMIRQFLSEVDWGNGLEYLLI 165
G V E I G K T +R+ E+ G E ++I
Sbjct: 55 VGGKKAVIDPE----------------LCISCGLCGKLVTEVRKHAKEIAKAEGAELIII 98
Query: 166 DTPPGTSDEHLSLVQYLKGLPDIGAIVVTTPQEVSLLDVRKEIDFCRKVNIPIIGVVENM 225
D PPG ++ L G D A++VT P L D+ + ++ R IP +GVV N
Sbjct: 99 DGPPGIG---CPVIASLTGA-DA-ALLVTEPTPSGLHDLERAVELVRHFGIP-VGVVIN- 151
Query: 226 ATFVCPKCTKPSEIFPKDSGGAEKMCAELSVPFLGSVP 263
++ + + E C E +P LG +P
Sbjct: 152 ----------KYDLNDEIAEEIEDYCEEEGIPILGKIP 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 = 58.6 bits (142), Expect = 4e-10
Identities = 60/234 (25%), Positives = 100/234 (42%), Gaps = 29/234 (12%)
Query: 50 VLVLSGKGGVGKSTFTNLLARVLAKSNESVDVGVLDLDICGPSMPRMMGLLNEQV--HQS 107
+ + SGKGG GK+T T L LAK + V LD DI ++ ++G+ ++ V H
Sbjct: 3 ITIASGKGGTGKTTITANLGVALAKLGK--KVLALDADITMANLELILGMEDKPVTLHDV 60
Query: 108 ASGWSPVFLEENLSVMSIGFLLNSPDDAVIWRGPKKNT--MIRQFLSEVDWGNGLEYLLI 165
+G + +++ + G + V G +K + L E+ + ++LLI
Sbjct: 61 LAGEAD--IKDAIYEGPFGVKVIPA--GVSLEGLRKADPDKLEDVLKEI--IDDTDFLLI 114
Query: 166 DTPPGTSDEHLSLVQYLKGLPDIGAIVVTTPQEVSLLDVRKEIDFCRKVNIPIIGVVENM 225
D P G + ++ + L ++V P+ S+ D K K+ I+GVV N
Sbjct: 115 DAPAGLERDAVTALAAADEL-----LLVVNPEISSITDALKTKIVAEKLGTAILGVVLN- 168
Query: 226 ATFVCPKCTKPSEIFPKDSGGAEKMCAELSVPFLGSVPIDPLVTRHCDEGTSAI 279
+ T+ ++ E + L VP LG VP DP V R G +
Sbjct: 169 ------RVTRDKTELGREE--IETI---LEVPVLGVVPEDPEVRRAAAFGEPVV 211
>gnl|CDD|226166 COG3640, CooC, CO dehydrogenase maturation factor [Cell division
and chromosome partitioning].
Length = 255
Score = 52.6 bits (127), Expect = 4e-08
Identities = 57/253 (22%), Positives = 95/253 (37%), Gaps = 60/253 (23%)
Query: 49 KVLVLSGKGGVGKSTFTNLLARVLAKSNESVDVGVLDLDICGPSMPRMMG---------- 98
K+ + +GKGGVGK+T LL + L +V V+D D ++P +G
Sbjct: 2 KIAI-TGKGGVGKTTIAALLLKRLLSKGGY-NVLVVDAD-PDSNLPEALGVEEPMKYLGG 58
Query: 99 ---LLNEQVHQSASGWSPVFLEENLSVMSIGFLLNSPDDAVIWRGPKK------------ 143
LL ++ G +EN V + PD+ ++ G
Sbjct: 59 KRELLKKRTGAEPGGPPGEMFKENPLVSDL------PDEYLVENGDIDLLVMGKIEEGGE 112
Query: 144 ------NTMIRQFLSEVDWGNGLEYLLIDTPPGTSDEHLSLVQYLKGLPDIGAIVVTTPQ 197
N ++R+ L + N E +++DT G EH ++G+ + IVV P
Sbjct: 113 GCACPMNALLRRLLRHLIL-NRYEVVIVDTEAGI--EHFGR-GTIEGVDLV--IVVVDPS 166
Query: 198 EVSLLDVRKEIDFCRKVNIPIIGVVENMATFVCPKCTKPSEIFPKDSGGAEKMCAELSVP 257
SL + + ++ I I VV N ++ ++ EL +
Sbjct: 167 YKSLRTAERIKELAEELGIKRIFVVLNKVD--------------EEEELLRELAEELGLE 212
Query: 258 FLGSVPIDPLVTR 270
LG +P DP V
Sbjct: 213 VLGVIPYDPEVVE 225
>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 = 45.3 bits (108), Expect = 3e-06
Identities = 15/30 (50%), Positives = 21/30 (70%)
Query: 50 VLVLSGKGGVGKSTFTNLLARVLAKSNESV 79
+ ++GKGGVGK+T LLAR LA+ + V
Sbjct: 1 KIAITGKGGVGKTTIAALLARYLAEKGKPV 30
>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 = 47.3 bits (113), Expect = 3e-06
Identities = 59/236 (25%), Positives = 95/236 (40%), Gaps = 55/236 (23%)
Query: 50 VLVLSGKGGVGKSTFTNLLARVLAKSNESV-----DVGVLDLDICGPSMPRMMGLLNEQV 104
+++ SGKGGVGK+T T L LA+ + V D+G+ +LD+ ++GL N V
Sbjct: 4 IVITSGKGGVGKTTTTANLGTALARLGKKVVLIDADIGLRNLDL-------LLGLENRIV 56
Query: 105 HQSASGWSPVFLE---------------ENLSVMSIGFLLNSPDDAVIWRGPKKNTMIRQ 149
+ +E +NL ++ DAV KK ++ +
Sbjct: 57 YTLVD-----VVEGECRLQQALIKDKRLKNLYLLPAS--QTRDKDAVTPEQMKK--LVNE 107
Query: 150 FLSEVDWGNGLEYLLIDTPPGTSDEHLSLVQYLKGLPDIGAIVVTTPQEVSLLDVRKEID 209
E D Y++ID P G + V P AIVVTTP+ ++ D + I
Sbjct: 108 LKEEFD------YVIIDCPAGIESGFRNAV-----APADEAIVVTTPEVSAVRDADRVIG 156
Query: 210 FCRKVNIPIIGVVENMATFVCPKCTKPSEIFPKDSGGAEKMCAELSVPFLGSVPID 265
I I ++ N +P + D + + LS+P +G +P D
Sbjct: 157 LLEAKGIEKIHLIVNR--------LRPEMVKKGDMLSVDDVLEILSIPLIGVIPED 204
>gnl|CDD|224113 COG1192, Soj, ATPases involved in chromosome partitioning [Cell
division and chromosome partitioning].
Length = 259
Score = 45.6 bits (108), Expect = 1e-05
Identities = 32/132 (24%), Positives = 53/132 (40%), Gaps = 15/132 (11%)
Query: 52 VLSGKGGVGKSTFTNLLARVLAKSNESVDVGVLDLDICGPS----------MPRMMGLLN 101
V + KGGVGK+T LA LAK V ++DLD G + LL+
Sbjct: 7 VANQKGGVGKTTTAVNLAAALAK-RGGKKVLLIDLDPQGSLTSWLGLRPDLEGDLYNLLS 65
Query: 102 EQVHQSASGWSPVFLEENLSVMSIGFLLNSPDDAVIWRGPKKNTMIRQFLSEVDWGNGLE 161
+ + E L ++ L + + K+ ++++ L V + +
Sbjct: 66 GLK-ERPDILDYTVVIEGLDLIPSNIDLAEGAEIELNAVAKEL-LLKRLLDPVK--DDYD 121
Query: 162 YLLIDTPPGTSD 173
Y++IDTPP
Sbjct: 122 YIIIDTPPSLGV 133
>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 = 42.8 bits (101), Expect = 1e-05
Identities = 17/36 (47%), Positives = 24/36 (66%), Gaps = 2/36 (5%)
Query: 50 VLVLSGKGGVGKSTFTNLLARVLAKSNESVDVGVLD 85
V+V++GKGGVGK+T LA LAK + V ++D
Sbjct: 1 VIVVTGKGGVGKTTLAANLAAALAKRGKR--VLLID 34
Score = 38.9 bits (91), Expect = 3e-04
Identities = 20/62 (32%), Positives = 33/62 (53%), Gaps = 2/62 (3%)
Query: 161 EYLLIDTPPGTSDEHLSLVQYLKGLPDIGAIVVTTPQEVSLLDVRKEIDFCRKVNIPIIG 220
+Y+LIDTPPG L + L L I+VTTP+ +++L R+ + ++ I +
Sbjct: 35 DYVLIDTPPGLGLLVLLCLLAL--LAADLVIIVTTPEALAVLGARRLTEVVLELAIEGLR 92
Query: 221 VV 222
V
Sbjct: 93 PV 94
>gnl|CDD|225447 COG2894, MinD, Septum formation inhibitor-activating ATPase [Cell
division and chromosome partitioning].
Length = 272
Score = 44.5 bits (106), Expect = 2e-05
Identities = 75/284 (26%), Positives = 114/284 (40%), Gaps = 84/284 (29%)
Query: 50 VLVLSGKGGVGKSTFTNLLARVLAKSNESV-----DVGVLDLDICGPSMPRMMGLLNEQV 104
++V SGKGGVGK+T T + LA+ + V D+G+ +LD+ +MGL N V
Sbjct: 5 IVVTSGKGGVGKTTTTANIGTALAQLGKKVVLIDFDIGLRNLDL-------IMGLENRIV 57
Query: 105 HQSASGWSPVFLE------------------ENLSVMSIGFLL----NSPDDAVIWRGPK 142
+ ++ ENL FLL DA+ G K
Sbjct: 58 YD--------LVDVIEGEATLNQALIKDKRLENL------FLLPASQTRDKDALTPEGVK 103
Query: 143 KNTMIRQFLSEVDWGNGLEYLLIDTPPGTSDEHLSLVQYLKGLPDIGAIVVTTPQEVSLL 202
K ++ + + +Y++ID+P G + V AIVVT P EVS
Sbjct: 104 K--VVNELKAM-----DFDYIIIDSPAGIEQGFKNAV-----YFADEAIVVTNP-EVS-- 148
Query: 203 DVRKEIDFCRKVNIPIIGVVENMATFVCPKCTKPSE------IFPK-----DSGGAEKMC 251
VR D R IIG++E+ + +P E P+ + E +
Sbjct: 149 SVR---DSDR-----IIGLLESK-SRRAEIGEEPKEHLLLNRYRPEMVKRGEMLSVEDVL 199
Query: 252 AELSVPFLGSVPIDPLVTRHCDEGTSAI-DTPSACVDAIQQIVQ 294
LS+P +G +P D V R ++G I D S A + I +
Sbjct: 200 EILSIPLIGVIPEDQDVLRASNKGEPVILDDNSDAGKAYRDIAR 243
>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 = 42.9 bits (102), Expect = 3e-05
Identities = 18/37 (48%), Positives = 23/37 (62%), Gaps = 2/37 (5%)
Query: 52 VLSGKGGVGKSTFTNLLARVLAKSNESVDVGVLDLDI 88
V SGKGGVGK+ + LA LAK + V +LD D+
Sbjct: 4 VTSGKGGVGKTNISANLALALAKLGKR--VLLLDADL 38
Score = 37.9 bits (89), Expect = 0.002
Identities = 31/108 (28%), Positives = 43/108 (39%), Gaps = 17/108 (15%)
Query: 160 LEYLLIDTPPGTSDEHLSLVQYLKGLPDIGAIVVTTPQEVSLLDVRKEIDFCRKVNI-PI 218
+Y++IDT G SD L D IVVTTP+ S+ D I K
Sbjct: 45 YDYIIIDTGAGISDNVLDFFL----AADEV-IVVTTPEPTSITDAYALIKKLAKQLRVLN 99
Query: 219 IGVVENMATFVCPKCTKPSE---IFPKDSGGAEKMCAELSVPFLGSVP 263
VV N P E +F + S + + LS+ +LG +P
Sbjct: 100 FRVVVNR-------AESPKEGKKVFKRLSNVSNRF-LGLSLDYLGFIP 139
>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 = 42.6 bits (101), Expect = 4e-05
Identities = 30/128 (23%), Positives = 49/128 (38%), Gaps = 22/128 (17%)
Query: 52 VLSGKGGVGKSTFTNLLARVLAKSNESVDVGVLDLDICGPSMPRMMGLLNEQVHQSASGW 111
V S GG GK+TF LA+ LA+ V LDL+ + +GL G
Sbjct: 5 VYSPVGGEGKTTFALNLAQSLAEEGPK--VLYLDLEEYSGDLALFLGL-------EPKGL 55
Query: 112 SPV-FLEENLSVMSIGFLLNSPDDAVIWRGPKKNTMIRQFLSEVDWGNGLE-------YL 163
S + + + L L+ + P+ +R+ +S +W LE +
Sbjct: 56 SDLLYYLKRLD----SMLIQAMGGLDYLAPPRNPEDLRE-VSPEEWEQLLERLRERYDVI 110
Query: 164 LIDTPPGT 171
++D P
Sbjct: 111 VLDLGPLV 118
>gnl|CDD|224071 COG1149, COG1149, MinD superfamily P-loop ATPase containing an
inserted ferredoxin domain [Energy production and
conversion].
Length = 284
Score = 43.9 bits (104), Expect = 4e-05
Identities = 18/50 (36%), Positives = 28/50 (56%), Gaps = 3/50 (6%)
Query: 49 KVLVLSGKGGVGKSTFTNLLARVLAKSNESVDVGVLDLDICGPSMPRMMG 98
+V V SGKGG GK+T LA +L + V + D D+ P++ ++G
Sbjct: 3 QVAVASGKGGTGKTTVAANLAVLLGDKYKLV---LADCDVEAPNLHLLLG 49
Score = 39.6 bits (93), Expect = 0.001
Identities = 35/136 (25%), Positives = 57/136 (41%), Gaps = 20/136 (14%)
Query: 159 GLEYLLIDTPPGTSDEHLSLVQYLKGLPDIGAIVVTTPQEVSLLDVRKEIDFCRKVNIPI 218
+ L+ID+ GT ++ LKG D+ AI+VT P L D+++ ++ IP
Sbjct: 163 LADLLIIDSAAGT---GCPVIASLKGA-DL-AILVTEPTPFGLHDLKRALELVEHFGIP- 216
Query: 219 IGVVENMATFVCPKCTKPSEIFPKDSGGAEKMCAELSVPFLGSVPIDPLVTRHCDEGTSA 278
G+V N DS E+ C E +P LG +P D + G
Sbjct: 217 TGIVINRYN-------------LGDS-EIEEYCEEEGIPILGEIPYDKDIPEAYVNGEPF 262
Query: 279 IDTPSACVDAIQQIVQ 294
++ S +AI + +
Sbjct: 263 VEPDSKEAEAILEEAE 278
>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 = 40.3 bits (95), Expect = 1e-04
Identities = 16/38 (42%), Positives = 23/38 (60%), Gaps = 2/38 (5%)
Query: 50 VLVLSGKGGVGKSTFTNLLARVLAKSNESVDVGVLDLD 87
+ V + KGGVGK+T LA LA+ + V ++DLD
Sbjct: 2 IAVANQKGGVGKTTTAVNLAAALARRGK--RVLLIDLD 37
>gnl|CDD|214385 CHL00175, minD, septum-site determining protein; Validated.
Length = 281
Score = 41.3 bits (97), Expect = 3e-04
Identities = 60/248 (24%), Positives = 101/248 (40%), Gaps = 52/248 (20%)
Query: 40 KSHLSNVKHKVLVLSGKGGVGKSTFTNLLARVLAKSNESV-----DVGVLDLDICGPSMP 94
K + + +++ SGKGGVGK+T T L +A+ V D+G+ +LD+
Sbjct: 8 KEKSATMSRIIVITSGKGGVGKTTTTANLGMSIARLGYRVALIDADIGLRNLDL------ 61
Query: 95 RMMGLLNEQVHQSASGWSPVF-----LEE---------NLSVMSIGFLLNSPDDAVIWRG 140
++GL N ++ + V L++ NLS+++I N V
Sbjct: 62 -LLGLENRVLYTAMD----VLEGECRLDQALIRDKRWKNLSLLAIS--KNRQRYNVT--- 111
Query: 141 PKKNTMIRQFLSEVDWGNGLEYLLIDTPPGTSDEHLSLVQYLKGLPDIGAIVVTTPQEVS 200
+KN L + G +Y+LID P G ++ + P AIVVTTP+ +
Sbjct: 112 -RKNM---NMLVDSLKNRGYDYILIDCPAGIDVGFINAIA-----PAQEAIVVTTPEITA 162
Query: 201 LLDVRKEIDFCRKVNIPIIGVVENMATFVCPKCTKPSEIFPKDSGGAEKMCAELSVPFLG 260
+ D + I + ++ N +P I D + L +P LG
Sbjct: 163 IRDADRVAGLLEANGIYNVKLLVNR--------VRPDMIQANDMMSVRDVQEMLGIPLLG 214
Query: 261 SVPIDPLV 268
++P D V
Sbjct: 215 AIPEDENV 222
>gnl|CDD|224084 COG1162, COG1162, Predicted GTPases [General function prediction
only].
Length = 301
Score = 40.0 bits (94), Expect = 8e-04
Identities = 15/37 (40%), Positives = 20/37 (54%), Gaps = 3/37 (8%)
Query: 33 DPGIELVKSHLSNVKHKVLVLSGKGGVGKSTFTNLLA 69
G+E + L+ K+ VL G+ GVGKST N L
Sbjct: 152 GDGLEELAELLAG---KITVLLGQSGVGKSTLINALL 185
>gnl|CDD|206747 cd01854, YjeQ_EngC, Ribosomal interacting GTPase YjeQ/EngC, a
circularly permuted subfamily of the Ras GTPases. YjeQ
(YloQ in Bacillus subtilis) is a ribosomal small
subunit-dependent GTPase; hence also known as RsgA. YjeQ
is a late-stage ribosomal biogenesis factor involved in
the 30S subunit maturation, and it represents a protein
family whose members are broadly conserved in bacteria
and have been shown to be essential to the growth of E.
coli and B. subtilis. Proteins of the YjeQ family
contain all sequence motifs typical of the vast class of
P-loop-containing GTPases, but show a circular
permutation, with a G4-G1-G3 pattern of motifs as
opposed to the regular G1-G3-G4 pattern seen in most
GTPases. All YjeQ family proteins display a unique
domain architecture, which includes an N-terminal
OB-fold RNA-binding domain, the central permuted GTPase
domain, and a zinc knuckle-like C-terminal cysteine
domain.
Length = 211
Score = 39.3 bits (93), Expect = 0.001
Identities = 14/37 (37%), Positives = 19/37 (51%), Gaps = 3/37 (8%)
Query: 33 DPGIELVKSHLSNVKHKVLVLSGKGGVGKSTFTNLLA 69
G++ ++ L K VL G+ GVGKST N L
Sbjct: 73 GEGLDELRELLKG---KTSVLVGQSGVGKSTLLNALL 106
>gnl|CDD|234631 PRK00098, PRK00098, GTPase RsgA; Reviewed.
Length = 298
Score = 39.4 bits (93), Expect = 0.001
Identities = 17/35 (48%), Positives = 22/35 (62%), Gaps = 3/35 (8%)
Query: 35 GIELVKSHLSNVKHKVLVLSGKGGVGKSTFTNLLA 69
G++ +K L KV VL+G+ GVGKST N LA
Sbjct: 154 GLDELKPLL---AGKVTVLAGQSGVGKSTLLNALA 185
>gnl|CDD|217416 pfam03193, DUF258, Protein of unknown function, DUF258.
Length = 161
Score = 38.3 bits (90), Expect = 0.001
Identities = 17/35 (48%), Positives = 20/35 (57%), Gaps = 3/35 (8%)
Query: 35 GIELVKSHLSNVKHKVLVLSGKGGVGKSTFTNLLA 69
GIE +K L K VL+G+ GVGKST N L
Sbjct: 25 GIEELKPLLKG---KTSVLAGQSGVGKSTLLNALL 56
>gnl|CDD|177007 CHL00067, rps2, ribosomal protein S2.
Length = 230
Score = 38.3 bits (90), Expect = 0.002
Identities = 16/48 (33%), Positives = 28/48 (58%), Gaps = 7/48 (14%)
Query: 175 HLSLVQYLKGLPDIGAIVVTTPQEVSLLDVRKEIDFCRKVNIPIIGVV 222
+L ++Y+ LPDI I++ +E + L +E CRK+ IP I ++
Sbjct: 151 YLGGIKYMTKLPDI-VIIIDQQEEYTAL---RE---CRKLGIPTISIL 191
>gnl|CDD|223082 COG0003, ArsA, Predicted ATPase involved in chromosome partitioning
[Cell division and chromosome partitioning].
Length = 322
Score = 38.5 bits (90), Expect = 0.003
Identities = 30/145 (20%), Positives = 50/145 (34%), Gaps = 32/145 (22%)
Query: 47 KHKVLVLSGKGGVGKSTFTNLLARVLAKSNESVDVGVLD--------LDICGPSMPR--- 95
+++ +GKGGVGK+T A LA+S + V + D D+ PR
Sbjct: 1 MTRIVFFTGKGGVGKTTIAAATAVKLAESGKKVLLVSTDPAHSLGDVFDLELGHDPRKVG 60
Query: 96 ---------MMGLLNEQVHQSASGWSPV--FLEENLSVMSIGFLLNSPDDAVIWRGPKKN 144
L E W V +L L +G + D+ G +
Sbjct: 61 PNLDALELDPEKALEE-------YWDEVKDYLARLLRTRGLGGIY--ADELATLPGIDEA 111
Query: 145 TMIRQFLSEVDWGNGLEYLLIDTPP 169
+ + L + +++DT P
Sbjct: 112 LALLKILEYYV-SGEYDVIVVDTAP 135
>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 = 37.8 bits (88), Expect = 0.003
Identities = 47/192 (24%), Positives = 79/192 (41%), Gaps = 25/192 (13%)
Query: 43 LSNVKHKVL-VLSGKGGVGKSTFTNLLARVLAKSNESVDVGVLDLDICGPSMP------- 94
S + KVL + S K G GKST + +A A++ ++D D+ M
Sbjct: 12 FSGAEIKVLLITSVKPGEGKSTTSANIAVAFAQA--GYKTLLIDGDMRNSVMSGTFKSQN 69
Query: 95 RMMGLLNEQVHQSASGWSPVFLE-ENLSVMSIGFLLNSPDDAVIWRGPKKNTMIRQFLSE 153
++ GL N + + ENL V++ G + P+ + + T+I
Sbjct: 70 KITGLTNFLSGTTDLSDAICDTNIENLFVITSGPV--PPNPTELLQSSNFKTLIETLRKY 127
Query: 154 VDWGNGLEYLLIDTPP-GTSDEHLSLVQYLKGLPDIGAIVVTTPQEVSLLDVRKEIDFCR 212
D Y++IDTPP GT + + + +I+VT E+ DV+K +
Sbjct: 128 FD------YIIIDTPPIGTVTDAAIIARACDA-----SILVTDAGEIKKRDVQKAKEQLE 176
Query: 213 KVNIPIIGVVEN 224
+ +GVV N
Sbjct: 177 QTGSNFLGVVLN 188
>gnl|CDD|215856 pfam00318, Ribosomal_S2, Ribosomal protein S2.
Length = 205
Score = 36.8 bits (86), Expect = 0.007
Identities = 15/50 (30%), Positives = 23/50 (46%), Gaps = 13/50 (26%)
Query: 176 LSLVQYLKGLPDIGAIVVTTPQEVSLLDVRKE---IDFCRKVNIPIIGVV 222
L ++ +K LPD ++V D KE I K+ IP+I +V
Sbjct: 128 LGGIKNMKKLPD--LVIVV--------DPNKEHIAIKEASKLGIPVIAIV 167
>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 = 36.5 bits (85), Expect = 0.009
Identities = 42/201 (20%), Positives = 74/201 (36%), Gaps = 47/201 (23%)
Query: 50 VLVLSGKGGVGKSTFTNLLARVLAKSNESVDV---------------------GVLDLDI 88
V+ +GKGGVGK+T A LA+ + V + V D +I
Sbjct: 1 VIFFTGKGGVGKTTIAAATAVRLAEEGKKVLLVSTDPAHNLSDKGLPNLSDAFIVEDPEI 60
Query: 89 CGPSMPRMMGLLNEQVHQSASGWSPVFLEENLSVMSIGFLLNSPDDAVIWRGPKKNTMIR 148
P++ R +V ++ G + LE ++ I ++ + R
Sbjct: 61 A-PNLYREEVDATRRVERAWGGEGGLMLELAAALPGI-------EELAS-----LLAVFR 107
Query: 149 QFLSEVDWGNGLEYLLIDTPP-GTSDEH---LSLVQYLKGLPDIGAIVVTTPQEVSLLDV 204
+F + + ++ DT P G H L + + L +VT P+++ L +
Sbjct: 108 EFSEGLY-----DVIVFDTAPTG----HTLRLLVRELLTDPERTSFRLVTLPEKLPLYET 158
Query: 205 RKEIDFCRKVNIPIIGVVENM 225
+ I IP+ VV N
Sbjct: 159 ERAITELALYGIPVDAVVVNR 179
>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 = 36.3 bits (84), Expect = 0.011
Identities = 19/45 (42%), Positives = 30/45 (66%), Gaps = 2/45 (4%)
Query: 50 VLVLSGKGGVGKSTFTNLLARVLAKSNESVDVGVLDLDICGPSMP 94
+++L+G GVGKSTF+ LA+ L++ N +DV +L D+ S P
Sbjct: 1 LIILTGLPGVGKSTFSKELAKKLSEKN--IDVIILGTDLIRESFP 43
>gnl|CDD|130674 TIGR01613, primase_Cterm, phage/plasmid primase, P4 family,
C-terminal domain. This model represents a clade within
a larger family of proteins from viruses of bacteria and
animals. Members of this family are found in phage and
plasmids of bacteria and archaea only. The model
describes a domain of about 300 residues, found
generally toward the protein C-terminus [DNA metabolism,
DNA replication, recombination, and repair, Mobile and
extrachromosomal element functions, Prophage functions].
Length = 304
Score = 36.5 bits (85), Expect = 0.012
Identities = 14/37 (37%), Positives = 20/37 (54%)
Query: 44 SNVKHKVLVLSGKGGVGKSTFTNLLARVLAKSNESVD 80
+ + K+ L G GG GKSTF NLL+ +L +
Sbjct: 72 NYTEQKLFFLYGNGGNGKSTFQNLLSNLLGDYATTAV 108
>gnl|CDD|100106 cd01425, RPS2, Ribosomal protein S2 (RPS2), involved in formation
of the translation initiation complex, where it might
contact the messenger RNA and several components of the
ribosome. It has been shown that in Escherichia coli
RPS2 is essential for the binding of ribosomal protein
S1 to the 30s ribosomal subunit. In humans, most likely
in all vertebrates, and perhaps in all metazoans, the
protein also functions as the 67 kDa laminin receptor
(LAMR1 or 67LR), which is formed from a 37 kDa
precursor, and is overexpressed in many tumors. 67LR is
a cell surface receptor which interacts with a variety
of ligands, laminin-1 and others. It is assumed that the
ligand interactions are mediated via the conserved
C-terminus, which becomes extracellular as the protein
undergoes conformational changes which are not well
understood. Specifically, a conserved palindromic motif,
LMWWML, may participate in the interactions. 67LR plays
essential roles in the adhesion of cells to the basement
membrane and subsequent signalling events, and has been
linked to several diseases. Some evidence also suggests
that the precursor of 67LR, 37LRP is also present in the
nucleus in animals, where it appears associated with
histones.
Length = 193
Score = 35.3 bits (82), Expect = 0.018
Identities = 13/49 (26%), Positives = 25/49 (51%), Gaps = 9/49 (18%)
Query: 175 HLSLVQYLKGLPDIGAIVVTTPQ-EVSLLDVRKEIDFCRKVNIPIIGVV 222
+L ++ + LPD ++V P+ E + +E K+ IP+I +V
Sbjct: 117 NLGGIKDMFRLPD--LVIVLDPRKEHQAI---RE---ASKLGIPVIAIV 157
>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 = 35.8 bits (83), Expect = 0.026
Identities = 11/32 (34%), Positives = 19/32 (59%)
Query: 43 LSNVKHKVLVLSGKGGVGKSTFTNLLARVLAK 74
++ + +++ GKGGVGK+T +A LA
Sbjct: 316 IAKSEKGLIMTMGKGGVGKTTVAAAIAVRLAN 347
>gnl|CDD|235396 PRK05299, rpsB, 30S ribosomal protein S2; Provisional.
Length = 258
Score = 35.1 bits (82), Expect = 0.029
Identities = 14/44 (31%), Positives = 21/44 (47%), Gaps = 13/44 (29%)
Query: 182 LKGLPDIGAIVVTTPQEVSLLDVRKE---IDFCRKVNIPIIGVV 222
+ GLPD A+ V D KE + RK+ IP++ +V
Sbjct: 154 MGGLPD--ALFVV--------DPNKEHIAVKEARKLGIPVVAIV 187
>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 = 33.8 bits (78), Expect = 0.038
Identities = 17/51 (33%), Positives = 24/51 (47%), Gaps = 5/51 (9%)
Query: 50 VLVLSGKGGVGKSTFTNLLARVLAKSNESVDVGVLDLDICGPSMPRMMGLL 100
V+ ++G G GKST + L L + V VL +D PS P G +
Sbjct: 1 VIGITGVPGAGKSTLIDALITALRARGKR--VAVLAID---PSSPFSGGAI 46
>gnl|CDD|182756 PRK10818, PRK10818, cell division inhibitor MinD; Provisional.
Length = 270
Score = 34.5 bits (79), Expect = 0.039
Identities = 53/241 (21%), Positives = 97/241 (40%), Gaps = 28/241 (11%)
Query: 50 VLVLSGKGGVGKSTFTNLLARVLA-KSNESVDVGVLDLDICGPSMPRMMGLLNEQVH--- 105
++V SGKGGVGK+T + +A LA K ++V V+D DI ++ +MG V+
Sbjct: 5 IVVTSGKGGVGKTTSSAAIATGLAQKGKKTV---VIDFDIGLRNLDLIMGCERRVVYDFV 61
Query: 106 ---QSASGWSPVFLE----ENLSVMSIGFLLNSPDDAVIWRGPKKNTMIRQFLSEVDWGN 158
Q + + ++ ENL ++ DA+ G + + L ++
Sbjct: 62 NVIQGDATLNQALIKDKRTENLYILPAS--QTRDKDALTREG------VAKVLDDLK-AM 112
Query: 159 GLEYLLIDTPPGTSDEHLSLVQYLKGLPDIGAIVVTTPQEVSLLDVRKEIDFCRKVNIPI 218
E+++ D+P G L + + AI+ T P+ S+ D + + +
Sbjct: 113 DFEFIVCDSPAGIETGALMALYFAD-----EAIITTNPEVSSVRDSDRILGILASKSRRA 167
Query: 219 IGVVENMATFVCPKCTKPSEIFPKDSGGAEKMCAELSVPFLGSVPIDPLVTRHCDEGTSA 278
E + + P + D E + L + +G +P D V R ++G
Sbjct: 168 ENGEEPIKEHLLLTRYNPGRVSRGDMLSMEDVLEILRIKLVGVIPEDQSVLRASNQGEPV 227
Query: 279 I 279
I
Sbjct: 228 I 228
>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 = 0.043
Identities = 17/41 (41%), Positives = 22/41 (53%), Gaps = 3/41 (7%)
Query: 49 KVLVLSG-KGGVGKSTFTNLLARVLAKSNESVDVGVLDLDI 88
KV+ + +GGVGK+T T LA L E V +DLD
Sbjct: 2 KVIAIVSVRGGVGKTTLTANLASALKLLGEPVL--AIDLDP 40
>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 = 32.6 bits (75), Expect = 0.051
Identities = 12/27 (44%), Positives = 13/27 (48%)
Query: 51 LVLSGKGGVGKSTFTNLLARVLAKSNE 77
+ L G G GKST LAR L K
Sbjct: 1 IWLYGPPGCGKSTLAKYLARALLKHLG 27
>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 = 33.5 bits (76), Expect = 0.052
Identities = 11/33 (33%), Positives = 16/33 (48%)
Query: 47 KHKVLVLSGKGGVGKSTFTNLLARVLAKSNESV 79
+V+++ G G GK+T LAR L V
Sbjct: 1 PGEVILIVGPPGSGKTTLARALARELGPPGGGV 33
>gnl|CDD|223130 COG0052, RpsB, Ribosomal protein S2 [Translation, ribosomal
structure and biogenesis].
Length = 252
Score = 34.2 bits (79), Expect = 0.057
Identities = 15/50 (30%), Positives = 24/50 (48%), Gaps = 13/50 (26%)
Query: 176 LSLVQYLKGLPDIGAIVVTTPQEVSLLDVRKE---IDFCRKVNIPIIGVV 222
L ++ +KGLPD + V D RKE + K+ IP++ +V
Sbjct: 147 LGGIKDMKGLPD--VLFVI--------DPRKEKIAVKEANKLGIPVVALV 186
>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 = 34.3 bits (79), Expect = 0.059
Identities = 11/32 (34%), Positives = 18/32 (56%)
Query: 48 HKVLVLSGKGGVGKSTFTNLLARVLAKSNESV 79
+ + GKGGVGK+T + A L++ + V
Sbjct: 1 MRWIFFGGKGGVGKTTVSCATAVRLSEQGKKV 32
>gnl|CDD|213218 cd03251, ABCC_MsbA, ATP-binding cassette domain of the bacterial
lipid flippase and related proteins, subfamily C. MsbA
is an essential ABC transporter, closely related to
eukaryotic MDR proteins. 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 = 234
Score = 33.7 bits (78), Expect = 0.065
Identities = 17/58 (29%), Positives = 29/58 (50%), Gaps = 1/58 (1%)
Query: 49 KVLVLSGKGGVGKSTFTNLLARVLAKSNESVDVGVLDL-DICGPSMPRMMGLLNEQVH 105
+ + L G G GKST NL+ R + + + D+ D S+ R +GL+++ V
Sbjct: 29 ETVALVGPSGSGKSTLVNLIPRFYDVDSGRILIDGHDVRDYTLASLRRQIGLVSQDVF 86
>gnl|CDD|224617 COG1703, ArgK, Putative periplasmic protein kinase ArgK and
related GTPases of G3E family [Amino acid transport and
metabolism].
Length = 323
Score = 33.5 bits (77), Expect = 0.095
Identities = 18/49 (36%), Positives = 23/49 (46%), Gaps = 5/49 (10%)
Query: 50 VLVLSGKGGVGKSTFTNLLARVLAKSNESVDVGVLDLDICGPSMPRMMG 98
V+ ++G G GKST L R L + V VL +D PS P G
Sbjct: 53 VIGITGVPGAGKSTLIEALGRELRE--RGHRVAVLAVD---PSSPFTGG 96
>gnl|CDD|225913 COG3378, COG3378, Phage associated DNA primase [General function
prediction only].
Length = 517
Score = 33.9 bits (78), Expect = 0.095
Identities = 12/25 (48%), Positives = 17/25 (68%)
Query: 48 HKVLVLSGKGGVGKSTFTNLLARVL 72
K+ L G GG GKSTF +L++ +L
Sbjct: 230 QKLFWLYGPGGNGKSTFVDLISNLL 254
>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 = 31.5 bits (72), Expect = 0.12
Identities = 15/39 (38%), Positives = 21/39 (53%), Gaps = 1/39 (2%)
Query: 50 VLVLSGKGGVGKSTFTNLLARVLAKSNESVDVGVLDLDI 88
+ + KGGVG +T LA LAK V ++DLD+
Sbjct: 2 IAFIGAKGGVGATTLAANLAVALAKEAGR-RVLLVDLDL 39
>gnl|CDD|219519 pfam07693, KAP_NTPase, KAP family P-loop domain. The KAP (after
Kidins220/ARMS and PifA) family of predicted NTPases
are sporadically distributed across a wide phylogenetic
range in bacteria and in animals. Many of the
prokaryotic KAP NTPases are encoded in plasmids and
tend to undergo disruption to form pseudogenes. A
unique feature of all eukaryotic and certain bacterial
KAP NTPases is the presence of two or four
transmembrane helices inserted into the P-loop NTPase
domain. These transmembrane helices anchor KAP NTPases
in the membrane such that the P-loop domain is located
on the intracellular side.
Length = 301
Score = 33.1 bits (76), Expect = 0.12
Identities = 12/29 (41%), Positives = 16/29 (55%)
Query: 50 VLVLSGKGGVGKSTFTNLLARVLAKSNES 78
V+ L G G GK++F NLL L + E
Sbjct: 22 VIGLYGAWGSGKTSFLNLLEDELKEFPEE 50
>gnl|CDD|237040 PRK12289, PRK12289, GTPase RsgA; Reviewed.
Length = 352
Score = 33.5 bits (77), Expect = 0.13
Identities = 14/34 (41%), Positives = 20/34 (58%), Gaps = 3/34 (8%)
Query: 35 GIELVKSHLSNVKHKVLVLSGKGGVGKSTFTNLL 68
G+E + L N K+ V++G GVGKS+ N L
Sbjct: 162 GLEALLEQLRN---KITVVAGPSGVGKSSLINRL 192
>gnl|CDD|238977 cd02019, NK, Nucleoside/nucleotide kinase (NK) is a protein
superfamily consisting of multiple families of enzymes
that share structural similarity and are functionally
related to the catalysis of the reversible phosphate
group transfer from nucleoside triphosphates to
nucleosides/nucleotides, nucleoside monophosphates, or
sugars. Members of this family play a wide variety of
essential roles in nucleotide metabolism, the
biosynthesis of coenzymes and aromatic compounds, as
well as the metabolism of sugar and sulfate.
Length = 69
Score = 30.0 bits (68), Expect = 0.20
Identities = 12/56 (21%), Positives = 22/56 (39%)
Query: 50 VLVLSGKGGVGKSTFTNLLARVLAKSNESVDVGVLDLDICGPSMPRMMGLLNEQVH 105
++ ++G G GKST LA L + V ++ L+ S + +
Sbjct: 1 IIAITGGSGSGKSTVAKKLAEQLGGRSVVVLDEIVILEGLYASYKSRDARIRDLAD 56
>gnl|CDD|221983 pfam13207, AAA_17, AAA domain.
Length = 114
Score = 31.1 bits (70), Expect = 0.22
Identities = 9/23 (39%), Positives = 14/23 (60%)
Query: 50 VLVLSGKGGVGKSTFTNLLARVL 72
+++++G G GKST LA L
Sbjct: 1 IILITGPPGSGKSTLAKKLAEKL 23
>gnl|CDD|130084 TIGR01011, rpsB_bact, ribosomal protein S2, bacterial type. This
model describes the bacterial, ribosomal, and
chloroplast forms of ribosomal protein S2. TIGR01012
describes the archaeal and cytosolic forms [Protein
synthesis, Ribosomal proteins: synthesis and
modification].
Length = 225
Score = 32.3 bits (74), Expect = 0.23
Identities = 13/47 (27%), Positives = 23/47 (48%), Gaps = 13/47 (27%)
Query: 179 VQYLKGLPDIGAIVVTTPQEVSLLDVRKE---IDFCRKVNIPIIGVV 222
++ +K LPD + V +D KE + RK+ IP++ +V
Sbjct: 149 IKDMKKLPD--LLFV--------IDPVKEKIAVAEARKLGIPVVAIV 185
>gnl|CDD|235210 PRK04040, PRK04040, adenylate kinase; Provisional.
Length = 188
Score = 31.8 bits (73), Expect = 0.24
Identities = 14/42 (33%), Positives = 24/42 (57%)
Query: 47 KHKVLVLSGKGGVGKSTFTNLLARVLAKSNESVDVGVLDLDI 88
KV+V++G GVGK+T N L + + V+ G + L++
Sbjct: 1 MMKVVVVTGVPGVGKTTVLNKALEKLKEDYKIVNFGDVMLEV 42
>gnl|CDD|173172 PRK14709, PRK14709, hypothetical protein; Provisional.
Length = 469
Score = 32.4 bits (74), Expect = 0.26
Identities = 12/26 (46%), Positives = 17/26 (65%)
Query: 48 HKVLVLSGKGGVGKSTFTNLLARVLA 73
H ++ + G GG GKS F N+LA +L
Sbjct: 205 HALVFVFGGGGNGKSVFLNVLAGILG 230
>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 = 31.9 bits (73), Expect = 0.29
Identities = 16/51 (31%), Positives = 24/51 (47%), Gaps = 2/51 (3%)
Query: 48 HKVLVLSGKGGVGKSTFTNLLARVLAKSNESVDVGVLDLDICGPSMPRMMG 98
H ++V + KGG GKST +A L V +DLD+ ++ R
Sbjct: 1 HVIVVGNEKGGSGKSTTAVHVAVALLYLGAR--VATIDLDLRQRTLTRYFE 49
>gnl|CDD|224260 COG1341, COG1341, Predicted GTPase or GTP-binding protein [General
function prediction only].
Length = 398
Score = 32.4 bits (74), Expect = 0.30
Identities = 13/43 (30%), Positives = 21/43 (48%), Gaps = 10/43 (23%)
Query: 50 VLVLSGKGGVGKSTFTNLLARVLAKSNESV----DVGVLDLDI 88
V+++ G GKST T LA N+ + V ++D D+
Sbjct: 75 VVMVVGPVDSGKSTLTTYLA------NKLLARGRKVAIIDADV 111
>gnl|CDD|213204 cd03237, ABC_RNaseL_inhibitor_domain2, The ATP-binding cassette
domain 2 of RNase L inhibitor. The ABC ATPase, RNase L
inhibitor (RLI), is a key enzyme in ribosomal
biogenesis, formation of translation preinitiation
complexes, and assembly of HIV capsids. RLI's are not
transport proteins and thus cluster with a group of
soluble proteins that lack the transmembrane components
commonly found in other members of the family.
Structurally, RLI's have an N-terminal Fe-S domain and
two nucleotide-binding domains which are arranged to
form two composite active sites in their interface
cleft. RLI is one of the most conserved enzymes between
archaea and eukaryotes with a sequence identity of more
than 48%. The high degree of evolutionary conservation
suggests that RLI performs a central role in archaeal
and eukaryotic physiology.
Length = 246
Score = 32.0 bits (73), Expect = 0.31
Identities = 11/40 (27%), Positives = 23/40 (57%)
Query: 47 KHKVLVLSGKGGVGKSTFTNLLARVLAKSNESVDVGVLDL 86
+ +V+ + G G+GK+TF +LA VL +++ + +
Sbjct: 24 ESEVIGILGPNGIGKTTFIKMLAGVLKPDEGDIEIELDTV 63
>gnl|CDD|226929 COG4559, COG4559, ABC-type hemin transport system, ATPase component
[Inorganic ion transport and metabolism].
Length = 259
Score = 31.9 bits (73), Expect = 0.34
Identities = 15/60 (25%), Positives = 27/60 (45%), Gaps = 1/60 (1%)
Query: 49 KVLVLSGKGGVGKSTFTNLLARVLAKSNESVDVGVLDLDICGPS-MPRMMGLLNEQVHQS 107
+VL + G G GKST L+ L+ + V + + L+ P + R +L + +
Sbjct: 28 EVLAILGPNGAGKSTLLKALSGELSPDSGEVTLNGVPLNSWPPEELARHRAVLPQNSSLA 87
>gnl|CDD|225183 COG2274, SunT, ABC-type bacteriocin/lantibiotic exporters, contain
an N-terminal double-glycine peptidase domain [Defense
mechanisms].
Length = 709
Score = 32.2 bits (74), Expect = 0.34
Identities = 10/43 (23%), Positives = 19/43 (44%)
Query: 49 KVLVLSGKGGVGKSTFTNLLARVLAKSNESVDVGVLDLDICGP 91
+ + + G+ G GKST LL + + + +DL+
Sbjct: 500 EKVAIVGRSGSGKSTLLKLLLGLYKPQQGRILLDGVDLNDIDL 542
>gnl|CDD|227320 COG4987, CydC, ABC-type transport system involved in cytochrome bd
biosynthesis, fused ATPase and permease components
[Energy production and conversion / Posttranslational
modification, protein turnover, chaperones].
Length = 573
Score = 31.9 bits (73), Expect = 0.36
Identities = 30/124 (24%), Positives = 48/124 (38%), Gaps = 35/124 (28%)
Query: 53 LSGKGGVGKSTFTNLLARVLAKSNESVDVGVLDLDICGPS-MPRMMGLLNEQVHQSASGW 111
+ G+ G GKST LLA S+ + +++ + + +L ++VH
Sbjct: 369 ILGRSGSGKSTLLQLLAGAWDPQQGSITLNGVEIASLDEQALRETISVLTQRVH------ 422
Query: 112 SPVF---LEENLSVMSIGFLLNSPD--DAVIWRGPKKNTMIRQFLSEVDWGNGLEYLLID 166
+F L +NL L +PD D +W ++Q GLE LL
Sbjct: 423 --LFSGTLRDNL-------RLANPDASDEELWA------ALQQV--------GLEKLLES 459
Query: 167 TPPG 170
P G
Sbjct: 460 APDG 463
>gnl|CDD|237502 PRK13779, PRK13779, bifunctional PTS system fructose-specific
transporter subunit IIA/HPr protein; Provisional.
Length = 503
Score = 31.8 bits (72), Expect = 0.42
Identities = 20/50 (40%), Positives = 28/50 (56%), Gaps = 4/50 (8%)
Query: 139 RGPKKNT--MIRQFLSEVDWGNG-LEYLLIDTPPGTSDEHLSLVQYLKGL 185
R KNT I QF ++WG G + Y++I SDEHLSL++ L +
Sbjct: 68 RHMVKNTGVQIFQFPQGIEWGEGNIAYVVIGIA-ARSDEHLSLLRQLTHV 116
>gnl|CDD|223562 COG0488, Uup, ATPase components of ABC transporters with duplicated
ATPase domains [General function prediction only].
Length = 530
Score = 31.8 bits (73), Expect = 0.45
Identities = 18/62 (29%), Positives = 28/62 (45%), Gaps = 9/62 (14%)
Query: 27 GAAKSVDPGIELVKSHLSNVKHKV-----LVLSGKGGVGKSTFTNLLARVLAKSNESVDV 81
+K D G L+K ++ ++ + + G G GKST LLA L + +V V
Sbjct: 326 NVSKGYDGGRLLLK----DLSFRIDRGDRIAIVGPNGAGKSTLLKLLAGELGPLSGTVKV 381
Query: 82 GV 83
G
Sbjct: 382 GE 383
>gnl|CDD|213214 cd03247, ABCC_cytochrome_bd, ATP-binding cassette domain of CydCD,
subfamily C. The CYD subfamily implicated in cytochrome
bd biogenesis. The CydC and CydD proteins are important
for the formation of cytochrome bd terminal oxidase of
E. coli and it has been proposed that they were
necessary for biosynthesis of the cytochrome bd quinol
oxidase and for periplasmic c-type cytochromes. CydCD
were proposed to determine a heterooligomeric complex
important for heme export into the periplasm or to be
involved in the maintenance of the proper redox state of
the periplasmic space. In Bacillus subtilis, the absence
of CydCD does not affect the presence of halo-cytochrome
c in the membrane and this observation suggests that
CydCD proteins are not involved in the export of heme in
this organism.
Length = 178
Score = 30.7 bits (70), Expect = 0.55
Identities = 12/53 (22%), Positives = 25/53 (47%)
Query: 53 LSGKGGVGKSTFTNLLARVLAKSNESVDVGVLDLDICGPSMPRMMGLLNEQVH 105
L G+ G GKST LL L + + + + ++ ++ +LN++ +
Sbjct: 33 LLGRSGSGKSTLLQLLTGDLKPQQGEITLDGVPVSDLEKALSSLISVLNQRPY 85
>gnl|CDD|226573 COG4088, COG4088, Predicted nucleotide kinase [Nucleotide
transport and metabolism].
Length = 261
Score = 31.0 bits (70), Expect = 0.55
Identities = 11/30 (36%), Positives = 18/30 (60%)
Query: 50 VLVLSGKGGVGKSTFTNLLARVLAKSNESV 79
+++L+G G GK+TF LA+ L + V
Sbjct: 3 LIILTGYPGSGKTTFAKELAKELRQEIWRV 32
>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 = 31.1 bits (71), Expect = 0.57
Identities = 13/38 (34%), Positives = 21/38 (55%), Gaps = 3/38 (7%)
Query: 36 IELVKSHLSNVKHKVLVLSGKGGVGKSTFTNLLARVLA 73
+ +K ++ K VL+G+ G GKS LLA+ +A
Sbjct: 11 TKKLKEADASKKVVRFVLTGERGSGKSV---LLAQAMA 45
>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 = 30.9 bits (70), Expect = 0.61
Identities = 13/31 (41%), Positives = 20/31 (64%)
Query: 49 KVLVLSGKGGVGKSTFTNLLARVLAKSNESV 79
+L + GKGG+GKST ++ L+ AK + V
Sbjct: 1 MILAVYGKGGIGKSTTSSNLSVAFAKLGKRV 31
>gnl|CDD|223272 COG0194, Gmk, Guanylate kinase [Nucleotide transport and
metabolism].
Length = 191
Score = 30.6 bits (70), Expect = 0.61
Identities = 13/32 (40%), Positives = 17/32 (53%), Gaps = 3/32 (9%)
Query: 45 NVKHKVLVLSGKGGVGKSTFTNLLARVLAKSN 76
K ++VLSG GVGKST L+ +L
Sbjct: 1 MSKGLLIVLSGPSGVGKST---LVKALLEDDK 29
>gnl|CDD|217323 pfam03023, MVIN, MviN-like protein. Deletion of the mviN virulence
gene in Salmonella enterica serovar. Typhimurium greatly
reduces virulence in a mouse model of typhoid-like
disease. Open reading frames encoding homologues of MviN
have since been identified in a variety of bacteria,
including pathogens and non-pathogens and
plant-symbionts. In the nitrogen-fixing symbiont
Rhizobium tropici, mviN is required for motility. The
MviM protein is predicted to be membrane-associated.
Length = 452
Score = 31.1 bits (71), Expect = 0.63
Identities = 12/34 (35%), Positives = 16/34 (47%), Gaps = 4/34 (11%)
Query: 96 MMGLLNEQVHQSASGWSPVFLEENLSVMSIGFLL 129
+LN + A +SPV L N+ V I LL
Sbjct: 117 FGAVLNARKKFFAPAFSPVLL--NIGV--ILTLL 146
>gnl|CDD|237293 PRK13185, chlL, protochlorophyllide reductase iron-sulfur
ATP-binding protein; Provisional.
Length = 270
Score = 31.1 bits (71), Expect = 0.64
Identities = 14/31 (45%), Positives = 20/31 (64%)
Query: 49 KVLVLSGKGGVGKSTFTNLLARVLAKSNESV 79
VL + GKGG+GKST ++ L+ AK + V
Sbjct: 3 LVLAVYGKGGIGKSTTSSNLSAAFAKLGKKV 33
>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 = 30.7 bits (70), Expect = 0.65
Identities = 13/40 (32%), Positives = 20/40 (50%), Gaps = 2/40 (5%)
Query: 51 LVLSGKGGVGKSTFTNLLARVLAKSNESVDVGVLDLDICG 90
++L+G GKST LA+ L + DV V+ + G
Sbjct: 2 IILTGLPSSGKSTRAKELAKYLEEKG--YDVIVISDESLG 39
>gnl|CDD|214854 smart00849, Lactamase_B, Metallo-beta-lactamase superfamily. Apart
from the beta-lactamases a number of other proteins
contain this domain. These proteins include
thiolesterases, members of the glyoxalase II family,
that catalyse the hydrolysis of S-D-lactoyl-glutathione
to form glutathione and D-lactic acid and a competence
protein that is essential for natural transformation in
Neisseria gonorrhoeae and could be a transporter
involved in DNA uptake. Except for the competence
protein these proteins bind two zinc ions per molecule
as cofactor.
Length = 177
Score = 30.2 bits (68), Expect = 0.70
Identities = 13/34 (38%), Positives = 22/34 (64%), Gaps = 1/34 (2%)
Query: 161 EYLLIDTPPGTSDEHLSLVQYLKGLPDIGAIVVT 194
+LIDT PG +++ L+ ++ L G I AI++T
Sbjct: 10 GAILIDTGPGEAEDLLAELKKL-GPKKIDAIILT 42
>gnl|CDD|233596 TIGR01846, type_I_sec_HlyB, type I secretion system ABC
transporter, HlyB family. Type I protein secretion is a
system in some Gram-negative bacteria to export proteins
(often proteases) across both inner and outer membranes
to the extracellular medium. This is one of three
proteins of the type I secretion apparatus. Targeted
proteins are not cleaved at the N-terminus, but rather
carry signals located toward the extreme C-terminus to
direct type I secretion [Protein fate, Protein and
peptide secretion and trafficking].
Length = 694
Score = 31.3 bits (71), Expect = 0.78
Identities = 24/62 (38%), Positives = 31/62 (50%), Gaps = 2/62 (3%)
Query: 50 VLVLSGKGGVGKSTFTNLLARVLAKSNESVDVGVLDLDICGP-SMPRMMG-LLNEQVHQS 107
+ + G G GKST T LL R+ + V V +DL I P + R MG +L E V S
Sbjct: 485 FIGIVGPSGSGKSTLTKLLQRLYTPQHGQVLVDGVDLAIADPAWLRRQMGVVLQENVLFS 544
Query: 108 AS 109
S
Sbjct: 545 RS 546
>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 = 31.1 bits (70), Expect = 0.82
Identities = 11/30 (36%), Positives = 19/30 (63%)
Query: 43 LSNVKHKVLVLSGKGGVGKSTFTNLLARVL 72
L N ++L+++G G GKST +L++ L
Sbjct: 105 LENAPKRILLITGPSGCGKSTTIKILSKEL 134
>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 = 30.1 bits (68), Expect = 0.83
Identities = 17/43 (39%), Positives = 21/43 (48%), Gaps = 4/43 (9%)
Query: 47 KHK--VLVLSGKGGVGKSTFTNLLARVLAKSNESVDVGVLDLD 87
H+ V+ L+G G GKST N L + L V VLD D
Sbjct: 15 GHRGVVIWLTGLSGSGKSTIANALEKKLESKGYRVY--VLDGD 55
>gnl|CDD|234401 TIGR03925, T7SS_EccC_b, type VII secretion protein EccCb. This
model represents the C-terminal domain or EccCb subunit
of the type VII secretion protein EccC as found in the
Actinobacteria. Type VII secretion is defined more
broadly as including secretion systems for ESAT-6-like
proteins in the Firmicutes as well as in the
Actinobacteria, but this family does not show close
homologs in the Firmicutes [Protein fate, Protein and
peptide secretion and trafficking].
Length = 566
Score = 30.7 bits (70), Expect = 0.85
Identities = 33/154 (21%), Positives = 61/154 (39%), Gaps = 28/154 (18%)
Query: 51 LVLSGKGGVGKSTFTNLLARVLAKSN--ESVDVGVLDLDICGPSMPR--MMGLLNEQVHQ 106
L++ G GK+T +AR + + + + ++D R ++G + + H
Sbjct: 366 LLVFGDSESGKTTLLRAIARGITRRYSPQQARLVLVD--------YRRSLLGAV-PEEHL 416
Query: 107 SASGWSPVFLEENLSVMSIGFLLNSPDDAVIWRGPKKNTMIRQFLSEVDWGNGLE-YLLI 165
+ S L E ++ ++ LL R P + +Q L W +G E Y+L+
Sbjct: 417 AGYAASSAALTELIAALAA--LLER-------RLPGPDVTPQQ-LRARSWWSGPEIYVLV 466
Query: 166 D----TPPGTSDEHLSLVQYLKGLPDIGAIVVTT 195
D + + L++ L DIG VV
Sbjct: 467 DDYDLVATASGNPLAPLLELLPHARDIGLHVVVA 500
>gnl|CDD|213788 TIGR03263, guanyl_kin, guanylate kinase. Members of this family
are the enzyme guanylate kinase, also called GMP
kinase. This enzyme transfers a phosphate from ATP to
GMP, yielding ADP and GDP [Purines, pyrimidines,
nucleosides, and nucleotides, Nucleotide and nucleoside
interconversions].
Length = 179
Score = 30.2 bits (69), Expect = 0.94
Identities = 9/20 (45%), Positives = 12/20 (60%)
Query: 49 KVLVLSGKGGVGKSTFTNLL 68
++V+SG G GKST L
Sbjct: 1 LLIVISGPSGAGKSTLVKAL 20
>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 = 30.5 bits (69), Expect = 0.96
Identities = 13/35 (37%), Positives = 17/35 (48%), Gaps = 2/35 (5%)
Query: 51 LVLSGKGGVGKSTFTNLLARVLAKSNESVDVGVLD 85
+++ G G GKST LLA L V V+D
Sbjct: 4 MLIVGPSGSGKSTLLKLLALRLLARG--GRVIVID 36
>gnl|CDD|184370 PRK13886, PRK13886, conjugal transfer protein TraL; Provisional.
Length = 241
Score = 30.5 bits (69), Expect = 0.97
Identities = 12/28 (42%), Positives = 16/28 (57%)
Query: 51 LVLSGKGGVGKSTFTNLLARVLAKSNES 78
+VL GKGGVGKS +A+ A +
Sbjct: 6 MVLQGKGGVGKSFIAATIAQYKASKGQK 33
>gnl|CDD|227321 COG4988, CydD, ABC-type transport system involved in cytochrome bd
biosynthesis, ATPase and permease components [Energy
production and conversion / Posttranslational
modification, protein turnover, chaperones].
Length = 559
Score = 30.7 bits (70), Expect = 1.0
Identities = 15/39 (38%), Positives = 20/39 (51%)
Query: 49 KVLVLSGKGGVGKSTFTNLLARVLAKSNESVDVGVLDLD 87
++ L G G GKST NLL LA + + V +DL
Sbjct: 348 QLTALVGASGAGKSTLLNLLLGFLAPTQGEIRVNGIDLR 386
>gnl|CDD|222854 PHA02518, PHA02518, ParA-like protein; Provisional.
Length = 211
Score = 30.2 bits (68), Expect = 1.0
Identities = 24/83 (28%), Positives = 36/83 (43%), Gaps = 17/83 (20%)
Query: 50 VLVLSGKGGVGKSTFTNLLARVLAKSNESVDVGVLDLDICG-------------PSMP-- 94
+ VL+ KGG GK+T LA L V ++DLD G P +P
Sbjct: 3 IAVLNQKGGAGKTTVATNLASWLHADGHK--VLLVDLDPQGSSTDWAEAREEGEPLIPVV 60
Query: 95 RMMGLLNEQVHQSASGWSPVFLE 117
RM + + + ASG+ V ++
Sbjct: 61 RMGKSIRADLPKVASGYDYVVVD 83
>gnl|CDD|99707 cd00009, AAA, The AAA+ (ATPases Associated with a wide variety of
cellular Activities) superfamily represents an ancient
group of ATPases belonging to the ASCE (for additional
strand, catalytic E) division of the P-loop NTPase
fold. The ASCE division also includes ABC, RecA-like,
VirD4-like, PilT-like, and SF1/2 helicases. Members of
the AAA+ ATPases function as molecular chaperons,
ATPase subunits of proteases, helicases, or
nucleic-acid stimulated ATPases. The AAA+ proteins
contain several distinct features in addition to the
conserved alpha-beta-alpha core domain structure and
the Walker A and B motifs of the P-loop NTPases.
Length = 151
Score = 29.4 bits (66), Expect = 1.2
Identities = 13/44 (29%), Positives = 19/44 (43%)
Query: 36 IELVKSHLSNVKHKVLVLSGKGGVGKSTFTNLLARVLAKSNESV 79
IE ++ L K L+L G G GK+T +A L +
Sbjct: 7 IEALREALELPPPKNLLLYGPPGTGKTTLARAIANELFRPGAPF 50
>gnl|CDD|224166 COG1245, COG1245, Predicted ATPase, RNase L inhibitor (RLI) homolog
[General function prediction only].
Length = 591
Score = 30.3 bits (69), Expect = 1.2
Identities = 13/39 (33%), Positives = 21/39 (53%), Gaps = 4/39 (10%)
Query: 50 VLVLSGKGGVGKSTFTNLLARVLAKSNESVDVGVLDLDI 88
V+ + G G+GK+TF LLA V+ + + DL +
Sbjct: 369 VIGILGPNGIGKTTFVKLLAGVI----KPDEGSEEDLKV 403
>gnl|CDD|169051 PRK07667, PRK07667, uridine kinase; Provisional.
Length = 193
Score = 29.7 bits (67), Expect = 1.3
Identities = 14/57 (24%), Positives = 24/57 (42%), Gaps = 4/57 (7%)
Query: 31 SVDPGIELVKSHLSNVKHKVLVLSGKGGVGKSTFTNLLARVLAKSNESVDVGVLDLD 87
S + I ++K H N +L + G GK+TF L + E + + +D
Sbjct: 2 STNELINIMKKHKEN--RFILGIDGLSRSGKTTFVANLKENM--KQEGIPFHIFHID 54
>gnl|CDD|224345 COG1428, COG1428, Deoxynucleoside kinases [Nucleotide transport
and metabolism].
Length = 216
Score = 30.0 bits (68), Expect = 1.3
Identities = 13/34 (38%), Positives = 16/34 (47%), Gaps = 2/34 (5%)
Query: 49 KVLVLSGKGGVGKSTFTNLLARVL--AKSNESVD 80
V+V+ G G GKST LA L E V+
Sbjct: 5 MVIVIEGMIGAGKSTLAQALAEHLGFKVFYELVE 38
>gnl|CDD|206643 cd00877, Ran, Ras-related nuclear proteins (Ran)/TC4 family of
small GTPases. Ran GTPase is involved in diverse
biological functions, such as nuclear transport,
spindle formation during mitosis, DNA replication, and
cell division. Among the Ras superfamily, Ran is a
unique small G protein. It does not have a lipid
modification motif at the C-terminus to bind to the
membrane, which is often observed within the Ras
superfamily. Ran may therefore interact with a wide
range of proteins in various intracellular locations.
Like other GTPases, Ran exists in GTP- and GDP-bound
conformations that interact differently with effectors.
Conversion between these forms and the assembly or
disassembly of effector complexes requires the
interaction of regulator proteins. The intrinsic GTPase
activity of Ran is very low, but it is greatly
stimulated by a GTPase-activating protein (RanGAP1)
located in the cytoplasm. By contrast, RCC1, a guanine
nucleotide exchange factor that generates RanGTP, is
bound to chromatin and confined to the nucleus. Ran
itself is mobile and is actively imported into the
nucleus by a mechanism involving NTF-2. Together with
the compartmentalization of its regulators, this is
thought to produce a relatively high concentration of
RanGTP in the nucleus.
Length = 166
Score = 29.6 bits (67), Expect = 1.3
Identities = 10/16 (62%), Positives = 11/16 (68%)
Query: 51 LVLSGKGGVGKSTFTN 66
LVL G GG GK+TF
Sbjct: 3 LVLVGDGGTGKTTFVK 18
>gnl|CDD|180682 PRK06761, PRK06761, hypothetical protein; Provisional.
Length = 282
Score = 30.1 bits (68), Expect = 1.3
Identities = 17/64 (26%), Positives = 31/64 (48%), Gaps = 8/64 (12%)
Query: 46 VKHKVLVLSGKGGVGKSTFTNLLARVLAKSNESVDV---GVLD--LDICGP---SMPRMM 97
+ K++++ G G GKST +L +L+++ V++ G LD D G +
Sbjct: 1 MMTKLIIIEGLPGFGKSTTAKMLNDILSQNGIEVELYLEGNLDHPADYDGVACFTKEEFD 60
Query: 98 GLLN 101
LL+
Sbjct: 61 RLLS 64
>gnl|CDD|234654 PRK00131, aroK, shikimate kinase; Reviewed.
Length = 175
Score = 29.4 bits (67), Expect = 1.3
Identities = 15/42 (35%), Positives = 20/42 (47%), Gaps = 7/42 (16%)
Query: 47 KHKVLVLSGKGGVGKSTFTNLLARVLAKSNESVDVGVLDLDI 88
K +VL G G GKST + R+LAK + +D D
Sbjct: 3 KGPNIVLIGFMGAGKST----IGRLLAK---RLGYDFIDTDH 37
>gnl|CDD|234033 TIGR02857, CydD, thiol reductant ABC exporter, CydD subunit. The
gene pair cydCD encodes an ABC-family transporter in
which each gene contains an N-terminal membrane-spanning
domain (pfam00664) and a C-terminal ATP-binding domain
(pfam00005). In E. coli these genes were discovered as
mutants which caused the terminal heme-copper oxidase
complex cytochrome bd to fail to assemble. Recent work
has shown that the transporter is involved in export of
redox-active thiol compounds such as cysteine and
glutathione. The linkage to assembly of the cytochrome
bd complex is further supported by the conserved operon
structure found outside the gammaproteobacteria
(cydABCD) containing both the transporter and oxidase
genes components. The genes used as the seed members for
this model are all either found in the
gammproteobacterial context or the CydABCD context. All
members of this family scoring above trusted at the time
of its creation were from genomes which encode a
cytochrome bd complex. Unfortunately, the gene symbol
nomenclature adopted based on this operon in B. subtilis
assigns cydC to the third gene in the operon where this
gene is actually homologous to the E. coli cydD gene. We
have chosen to name all homologs in this family in
accordance with the precedence of publication of the E.
coli name, CydD.
Length = 529
Score = 30.3 bits (69), Expect = 1.3
Identities = 12/34 (35%), Positives = 17/34 (50%)
Query: 49 KVLVLSGKGGVGKSTFTNLLARVLAKSNESVDVG 82
+ + L G G GKST NLL + + S+ V
Sbjct: 349 ERVALVGPSGAGKSTLLNLLLGFVDPTEGSIAVN 382
>gnl|CDD|224045 COG1120, FepC, ABC-type cobalamin/Fe3+-siderophores transport
systems, ATPase components [Inorganic ion transport and
metabolism / Coenzyme metabolism].
Length = 258
Score = 29.8 bits (68), Expect = 1.3
Identities = 12/38 (31%), Positives = 17/38 (44%)
Query: 42 HLSNVKHKVLVLSGKGGVGKSTFTNLLARVLAKSNESV 79
S K ++ + G G GKST LA +L + V
Sbjct: 22 SFSIPKGEITGILGPNGSGKSTLLKCLAGLLKPKSGEV 59
>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 = 1.3
Identities = 8/31 (25%), Positives = 14/31 (45%)
Query: 50 VLVLSGKGGVGKSTFTNLLARVLAKSNESVD 80
+ ++G GVGK+T + +L V
Sbjct: 1 RIFITGPPGVGKTTLVKKVIELLKSEGVKVG 31
>gnl|CDD|224930 COG2019, AdkA, Archaeal adenylate kinase [Nucleotide transport
and metabolism].
Length = 189
Score = 29.7 bits (67), Expect = 1.3
Identities = 11/26 (42%), Positives = 17/26 (65%)
Query: 49 KVLVLSGKGGVGKSTFTNLLARVLAK 74
KV+V++G GVGK+T + + L K
Sbjct: 5 KVVVITGVPGVGKTTVLKIALKELVK 30
>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 = 29.9 bits (68), Expect = 1.4
Identities = 13/25 (52%), Positives = 17/25 (68%)
Query: 55 GKGGVGKSTFTNLLARVLAKSNESV 79
GKGG+GKST T L+ LA+ + V
Sbjct: 8 GKGGIGKSTTTQNLSAALAEMGKKV 32
>gnl|CDD|184693 PRK14467, PRK14467, ribosomal RNA large subunit methyltransferase
N; Provisional.
Length = 348
Score = 30.1 bits (68), Expect = 1.4
Identities = 26/109 (23%), Positives = 40/109 (36%), Gaps = 23/109 (21%)
Query: 94 PRMMGLLNEQVHQSASGW---------SPVFLEENLSVMSIGFLLNSPDD---AVIWRGP 141
P + L ++ S SG PV E NL+V LN+ I
Sbjct: 176 PWGLDLSKRRITISTSGIIHQIKRMAEDPVMPEVNLAVS-----LNASSQKLRERIMPIS 230
Query: 142 KKNTM------IRQFLSEVDWGNGLEYLLIDTPPGTSDEHLSLVQYLKG 184
K NT+ ++Q+ LEY+LI + ++ L L Q +
Sbjct: 231 KTNTLEELMEVLKQYPLPPGRRIMLEYVLIKGVNDSPEDALRLAQLIGK 279
>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 = 29.1 bits (66), Expect = 1.5
Identities = 10/38 (26%), Positives = 20/38 (52%)
Query: 49 KVLVLSGKGGVGKSTFTNLLARVLAKSNESVDVGVLDL 86
+++ L G G GKST +A +L ++ + + D+
Sbjct: 26 EIVALVGPNGSGKSTLLRAIAGLLKPTSGEILIDGKDI 63
>gnl|CDD|183903 PRK13230, PRK13230, nitrogenase reductase-like protein; Reviewed.
Length = 279
Score = 29.7 bits (67), Expect = 1.5
Identities = 14/27 (51%), Positives = 18/27 (66%)
Query: 55 GKGGVGKSTFTNLLARVLAKSNESVDV 81
GKGG+GKST +A LA+S + V V
Sbjct: 8 GKGGIGKSTTVCNIAAALAESGKKVLV 34
>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 = 29.7 bits (67), Expect = 1.5
Identities = 15/31 (48%), Positives = 21/31 (67%)
Query: 49 KVLVLSGKGGVGKSTFTNLLARVLAKSNESV 79
VL + GKGG+GKST ++ L+ LAK + V
Sbjct: 1 MVLAVYGKGGIGKSTTSSNLSVALAKRGKKV 31
>gnl|CDD|224267 COG1348, NifH, Nitrogenase subunit NifH (ATPase) [Inorganic ion
transport and metabolism].
Length = 278
Score = 29.6 bits (67), Expect = 1.6
Identities = 13/25 (52%), Positives = 17/25 (68%)
Query: 55 GKGGVGKSTFTNLLARVLAKSNESV 79
GKGG+GKST + LA LA+ + V
Sbjct: 8 GKGGIGKSTTSQNLAAALAELGKKV 32
>gnl|CDD|236353 PRK08939, PRK08939, primosomal protein DnaI; Reviewed.
Length = 306
Score = 29.8 bits (68), Expect = 1.6
Identities = 15/43 (34%), Positives = 21/43 (48%)
Query: 37 ELVKSHLSNVKHKVLVLSGKGGVGKSTFTNLLARVLAKSNESV 79
+ ++++ K K L L G GVGKS +A LAK S
Sbjct: 145 DFLEAYPPGEKVKGLYLYGDFGVGKSYLLAAIANELAKKGVSS 187
>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 = 29.0 bits (66), Expect = 1.6
Identities = 11/19 (57%), Positives = 13/19 (68%)
Query: 50 VLVLSGKGGVGKSTFTNLL 68
++VLSG GVGKST L
Sbjct: 1 LIVLSGPSGVGKSTLLKRL 19
>gnl|CDD|213195 cd03228, ABCC_MRP_Like, ATP-binding cassette domain of multidrug
resistance protein-like transporters. The MRP
(Multidrug Resistance Protein)-like transporters are
involved in drug, peptide, and lipid export. They
belong to the subfamily C of the ATP-binding cassette
(ABC) superfamily of transport proteins. The ABCC
subfamily contains transporters with a diverse
functional spectrum that includes ion transport, cell
surface receptor, and toxin secretion activities. The
MRP-like family, similar to all ABC proteins, have a
common four-domain core structure constituted by two
membrane-spanning domains, each composed of six
transmembrane (TM) helices, and two nucleotide-binding
domains (NBD). ABC transporters are a subset of
nucleotide hydrolases that contain a signature motif,
Q-loop, and H-loop/switch region, in addition to, the
Walker A motif/P-loop and Walker B motif commonly found
in a number of ATP- and GTP-binding and hydrolyzing
proteins.
Length = 171
Score = 29.3 bits (67), Expect = 1.6
Identities = 11/33 (33%), Positives = 15/33 (45%), Gaps = 5/33 (15%)
Query: 43 LSNV-----KHKVLVLSGKGGVGKSTFTNLLAR 70
L +V + + + G G GKST LL R
Sbjct: 18 LKDVSLTIKPGEKVAIVGPSGSGKSTLLKLLLR 50
>gnl|CDD|233031 TIGR00577, fpg, formamidopyrimidine-DNA glycosylase (fpg). All
proteins in the FPG family with known functions are
FAPY-DNA glycosylases that function in base excision
repair. Homologous to endonuclease VIII (nei). 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 = 272
Score = 29.6 bits (67), Expect = 1.7
Identities = 9/29 (31%), Positives = 14/29 (48%), Gaps = 1/29 (3%)
Query: 206 KEIDFCRKVNIPIIG-VVENMATFVCPKC 233
++ + CR+ PI V T CP+C
Sbjct: 243 RKGEPCRRCGTPIEKIKVGGRGTHFCPQC 271
>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 = 29.7 bits (67), Expect = 1.7
Identities = 21/65 (32%), Positives = 30/65 (46%), Gaps = 8/65 (12%)
Query: 49 KVLVLSG-KGGVGKSTFTNLLARVLAKSNESVDVGVLDLDICGPSMPRMMGLLNEQVHQS 107
VL L G +GGVG ++ T L L + ES VL +D ++ R+ N S
Sbjct: 2 AVLALQGVRGGVGTTSLTAALGWALQQLGES----VLVIDASPDNLLRLH--FNVDFDHS 55
Query: 108 ASGWS 112
GW+
Sbjct: 56 -DGWA 59
>gnl|CDD|226426 COG3911, COG3911, Predicted ATPase [General function prediction
only].
Length = 183
Score = 29.5 bits (66), Expect = 1.7
Identities = 11/24 (45%), Positives = 15/24 (62%)
Query: 47 KHKVLVLSGKGGVGKSTFTNLLAR 70
+HK +L+G G GK+T LAR
Sbjct: 8 RHKRFILTGGPGAGKTTLLAALAR 31
>gnl|CDD|161785 TIGR00239, 2oxo_dh_E1, 2-oxoglutarate dehydrogenase, E1 component.
The 2-oxoglutarate dehydrogenase complex consists of
this thiamine pyrophosphate-binding subunit (E1),
dihydrolipoamide succinyltransferase (E2), and lipoamide
dehydrogenase (E3). The E1 ortholog from Corynebacterium
glutamicum is unusual in having an N-terminal extension
that resembles the dihydrolipoamide succinyltransferase
(E2) component of 2-oxoglutarate dehydrogenase [Energy
metabolism, TCA cycle].
Length = 929
Score = 30.2 bits (68), Expect = 1.7
Identities = 29/85 (34%), Positives = 38/85 (44%), Gaps = 12/85 (14%)
Query: 111 WSPVFLEENLSVMSIGFLLNSPDDAVIWR---GPKKNT---MIRQFLS--EVDWGN--GL 160
W+ V EE++ G+ SP VIW G N +I QF+S E WG GL
Sbjct: 650 WNSVLSEESVLGFEYGYATTSPRTLVIWEAQFGDFANGAQVVIDQFISSGEQKWGQMSGL 709
Query: 161 EYLLIDTPPGTSDEHLS--LVQYLK 183
LL G EH S L ++L+
Sbjct: 710 VMLLPHGYEGQGPEHSSGRLERFLQ 734
>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit;
Provisional.
Length = 482
Score = 29.9 bits (68), Expect = 1.7
Identities = 13/35 (37%), Positives = 19/35 (54%)
Query: 36 IELVKSHLSNVKHKVLVLSGKGGVGKSTFTNLLAR 70
E ++S L K L+L G GVGK++ + LA
Sbjct: 27 REWIESWLKGKPKKALLLYGPPGVGKTSLAHALAN 61
>gnl|CDD|213192 cd03225, ABC_cobalt_CbiO_domain1, First domain of the ATP-binding
cassette component of cobalt transport system. Domain
I of the ABC component of a cobalt transport family
found in bacteria, archaea, and eukaryota. The
transition metal cobalt is an essential component of
many enzymes and must be transported into cells in
appropriate amounts when needed. This ABC transport
system of the CbiMNQO family is involved in cobalt
transport in association with the cobalamin (vitamin
B12) biosynthetic pathways. Most of cobalt (Cbi)
transport systems possess a separate CbiN component,
the cobalt-binding periplasmic protein, and they are
encoded by the conserved gene cluster cbiMNQO. Both the
CbiM and CbiQ proteins are integral cytoplasmic
membrane proteins, and the CbiO protein has the linker
peptide and the Walker A and B motifs commonly found in
the ATPase components of the ABC-type transport
systems.
Length = 211
Score = 29.4 bits (67), Expect = 2.0
Identities = 12/35 (34%), Positives = 19/35 (54%)
Query: 47 KHKVLVLSGKGGVGKSTFTNLLARVLAKSNESVDV 81
K + +++ G G GKST LL +L ++ V V
Sbjct: 26 KGEFVLIVGPNGSGKSTLLRLLNGLLGPTSGEVLV 60
>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 = 28.8 bits (65), Expect = 2.0
Identities = 14/36 (38%), Positives = 19/36 (52%), Gaps = 3/36 (8%)
Query: 38 LVKSHLSNVKHKVLVLSGKGGVGKSTFT-NLLARVL 72
LVK L + + +L+G G GKST +L A V
Sbjct: 25 LVKGLL--PRGGLTLLAGAPGTGKSTLALDLAAAVA 58
>gnl|CDD|234988 PRK01889, PRK01889, GTPase RsgA; Reviewed.
Length = 356
Score = 29.5 bits (67), Expect = 2.0
Identities = 14/34 (41%), Positives = 20/34 (58%), Gaps = 2/34 (5%)
Query: 35 GIELVKSHLSNVKHKVLVLSGKGGVGKSTFTNLL 68
G++++ + LS K + L G GVGKST N L
Sbjct: 184 GLDVLAAWLS--GGKTVALLGSSGVGKSTLVNAL 215
>gnl|CDD|224041 COG1116, TauB, ABC-type nitrate/sulfonate/bicarbonate transport
system, ATPase component [Inorganic ion transport and
metabolism].
Length = 248
Score = 29.4 bits (67), Expect = 2.1
Identities = 13/55 (23%), Positives = 20/55 (36%), Gaps = 8/55 (14%)
Query: 55 GKGGVGKSTFTNLLARVLAKSNESVDVGVLDLDICGPSMPRMMGLLNEQVHQSAS 109
G G GKST L+A + ++ V + + GP V Q +
Sbjct: 36 GPSGCGKSTLLRLIAGLEKPTSGEVLLD--GRPVTGPGPDIGY------VFQEDA 82
>gnl|CDD|233418 TIGR01448, recD_rel, helicase, putative, RecD/TraA family. This
model describes a family similar to RecD, the
exodeoxyribonuclease V alpha chain of TIGR01447. Members
of this family, however, are not found in a context of
RecB and RecC and are longer by about 200 amino acids at
the amino end. Chlamydia muridarum has both a member of
this family and a RecD [Unknown function, Enzymes of
unknown specificity].
Length = 720
Score = 29.8 bits (67), Expect = 2.1
Identities = 10/27 (37%), Positives = 17/27 (62%)
Query: 48 HKVLVLSGKGGVGKSTFTNLLARVLAK 74
HKV++L+G G GK+T T + + +
Sbjct: 338 HKVVILTGGPGTGKTTITRAIIELAEE 364
>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 = 28.8 bits (65), Expect = 2.1
Identities = 14/39 (35%), Positives = 20/39 (51%), Gaps = 7/39 (17%)
Query: 50 VLVLSGKGGVGKSTFTNLLARVLAKSNESVDVGVLDLDI 88
++++ G G GKSTF AR L + +V VL D
Sbjct: 1 LILMVGLPGSGKSTF----ARRLLRELGAV---VLSSDT 32
>gnl|CDD|224054 COG1131, CcmA, ABC-type multidrug transport system, ATPase
component [Defense mechanisms].
Length = 293
Score = 29.2 bits (66), Expect = 2.3
Identities = 15/66 (22%), Positives = 29/66 (43%), Gaps = 5/66 (7%)
Query: 43 LSNV-----KHKVLVLSGKGGVGKSTFTNLLARVLAKSNESVDVGVLDLDICGPSMPRMM 97
L V ++ L G G GK+T +LA +L ++ + V D+ + R +
Sbjct: 21 LDGVSFEVEPGEIFGLLGPNGAGKTTLLKILAGLLKPTSGEILVLGYDVVKEPAKVRRRI 80
Query: 98 GLLNEQ 103
G + ++
Sbjct: 81 GYVPQE 86
>gnl|CDD|232848 TIGR00157, TIGR00157, ribosome small subunit-dependent GTPase A.
Members of this protein were designated YjeQ and are now
designated RsgA (ribosome small subunit-dependent GTPase
A). The strongest motif in the alignment of these
proteins is GXSGVGKS[ST], a classic P-loop for
nucleotide binding. This protein has been shown to
cleave GTP and remain bound to GDP. A role as a
regulator of translation has been suggested. The Aquifex
aeolicus ortholog is split into consecutive open reading
frames. Consequently, this model was build in fragment
mode (-f option) [Protein synthesis, Translation
factors].
Length = 245
Score = 29.3 bits (66), Expect = 2.3
Identities = 12/35 (34%), Positives = 20/35 (57%), Gaps = 3/35 (8%)
Query: 34 PGIELVKSHLSNVKHKVLVLSGKGGVGKSTFTNLL 68
G++ + L N ++ V +G+ GVGKS+ N L
Sbjct: 109 DGLKELIEALQN---RISVFAGQSGVGKSSLINAL 140
>gnl|CDD|232806 TIGR00067, glut_race, glutamate racemase. This family consists of
glutamate racemase, a protein required for making the
UDP-N-acetylmuramoyl-pentapeptide used as a precursor in
bacterial peptidoglycan biosynthesis. The most closely
related proteins differing in function are aspartate
racemases [Cell envelope, Biosynthesis and degradation
of murein sacculus and peptidoglycan].
Length = 251
Score = 28.9 bits (65), Expect = 2.4
Identities = 16/50 (32%), Positives = 28/50 (56%), Gaps = 8/50 (16%)
Query: 176 LSLVQYLKGLPDIGAIVVT--TPQEVSLLDVRKEIDFCRKVNIPIIGVVE 223
L L+ +LK +I +VV T ++L D+++ DF P++GV+E
Sbjct: 50 LELLTFLKERHNIKLLVVACNTASALALEDLQRNFDF------PVVGVIE 93
>gnl|CDD|184037 PRK13409, PRK13409, putative ATPase RIL; Provisional.
Length = 590
Score = 29.4 bits (67), Expect = 2.6
Identities = 14/34 (41%), Positives = 19/34 (55%)
Query: 50 VLVLSGKGGVGKSTFTNLLARVLAKSNESVDVGV 83
V+ + G G+GK+TF LLA VL VD +
Sbjct: 367 VIGIVGPNGIGKTTFAKLLAGVLKPDEGEVDPEL 400
>gnl|CDD|217429 pfam03215, Rad17, Rad17 cell cycle checkpoint protein.
Length = 490
Score = 29.2 bits (65), Expect = 2.6
Identities = 12/30 (40%), Positives = 19/30 (63%)
Query: 43 LSNVKHKVLVLSGKGGVGKSTFTNLLARVL 72
L + K +L+L+G G GKST +L++ L
Sbjct: 40 LESNKQLILLLTGPSGCGKSTTVKVLSKEL 69
>gnl|CDD|184925 PRK14961, PRK14961, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 363
Score = 29.0 bits (65), Expect = 2.6
Identities = 15/28 (53%), Positives = 19/28 (67%), Gaps = 4/28 (14%)
Query: 48 HKVLVLSGKGGVGKSTFTNLLARVLAKS 75
H +LSG GVGK+T +AR+LAKS
Sbjct: 38 HHAWLLSGTRGVGKTT----IARLLAKS 61
>gnl|CDD|236442 PRK09270, PRK09270, nucleoside triphosphate hydrolase
domain-containing protein; Reviewed.
Length = 229
Score = 28.7 bits (65), Expect = 2.7
Identities = 10/34 (29%), Positives = 17/34 (50%)
Query: 50 VLVLSGKGGVGKSTFTNLLARVLAKSNESVDVGV 83
++ ++G G GKST L +L + E + V
Sbjct: 35 IVGIAGPPGAGKSTLAEFLEALLQQDGELPAIQV 68
>gnl|CDD|224337 COG1419, FlhF, Flagellar GTP-binding protein [Cell motility and
secretion].
Length = 407
Score = 29.2 bits (66), Expect = 2.7
Identities = 12/42 (28%), Positives = 19/42 (45%)
Query: 46 VKHKVLVLSGKGGVGKSTFTNLLARVLAKSNESVDVGVLDLD 87
+ +V+ L G GVGK+T LA + V ++ D
Sbjct: 201 EQKRVIALVGPTGVGKTTTLAKLAARYVMLKKKKKVAIITTD 242
>gnl|CDD|213259 cd03292, ABC_FtsE_transporter, ATP-binding cassette domain of the
cell division transporter. FtsE is a hydrophilic
nucleotide-binding protein that binds FtsX to form a
heterodimeric ATP-binding cassette (ABC)-type
transporter that associates with the bacterial inner
membrane. The FtsE/X transporter is thought to be
involved in cell division and is important for assembly
or stability of the septal ring.
Length = 214
Score = 28.9 bits (65), Expect = 2.7
Identities = 8/20 (40%), Positives = 11/20 (55%)
Query: 51 LVLSGKGGVGKSTFTNLLAR 70
+ L G G GKST L+ +
Sbjct: 30 VFLVGPSGAGKSTLLKLIYK 49
>gnl|CDD|237873 PRK14969, PRK14969, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 527
Score = 29.3 bits (66), Expect = 2.8
Identities = 14/28 (50%), Positives = 18/28 (64%), Gaps = 4/28 (14%)
Query: 48 HKVLVLSGKGGVGKSTFTNLLARVLAKS 75
H + +G GVGK+T LAR+LAKS
Sbjct: 38 HHAYLFTGTRGVGKTT----LARILAKS 61
>gnl|CDD|238557 cd01137, PsaA, Metal binding protein PsaA. These proteins have
been shown to function as initial receptors in ABC
transport of Mn2+ and as surface adhesins in some
eubacterial species. They belong to the TroA
superfamily of periplasmic metal binding proteins that
share a distinct fold and ligand binding mechanism. A
typical TroA protein is comprised of two globular
subdomains connected by a single helix and can bind the
metal ion in the cleft between these domains. In
addition, these proteins sometimes have a low complexity
region containing a metal-binding histidine-rich motif
(repetitive HDH sequence).
Length = 287
Score = 28.8 bits (65), Expect = 2.9
Identities = 12/62 (19%), Positives = 25/62 (40%), Gaps = 7/62 (11%)
Query: 184 GLPDIGAIVVTTPQEVSLLDVRKEIDFCRKVNIPIIGVVENMATFVCPKCTKPSEIFPKD 243
GL + + T +E + V I+ +K +P + VE+ + + K+
Sbjct: 195 GLKEAYLWPINTEEEGTPKQVATLIEQVKKEKVPAV-FVESTVN------DRLMKQVAKE 247
Query: 244 SG 245
+G
Sbjct: 248 TG 249
>gnl|CDD|183704 PRK12726, PRK12726, flagellar biosynthesis regulator FlhF;
Provisional.
Length = 407
Score = 28.9 bits (64), Expect = 2.9
Identities = 29/106 (27%), Positives = 49/106 (46%), Gaps = 10/106 (9%)
Query: 48 HKVLVLSGKGGVGKSTFTNLLARVLAKSNESVDVGVLDLDICGPSMPRMMGLLNEQVHQS 107
H+++ L G+ GVGK+T L L K N +V D G ++ + G ++ +
Sbjct: 206 HRIISLIGQTGVGKTTTLVKLGWQLLKQNRTVGFITTDTFRSG-AVEQFQGYADKLDVEL 264
Query: 108 ASGWSPVFLEENLSVMSIGFLLNSPDDAVIWRGPKKNTMIRQFLSE 153
SP LEE + M+ +N D +I +T+ R +L+E
Sbjct: 265 IVATSPAELEEAVQYMT---YVNCVDHILI------DTVGRNYLAE 301
>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 = 28.7 bits (65), Expect = 3.0
Identities = 12/31 (38%), Positives = 20/31 (64%)
Query: 49 KVLVLSGKGGVGKSTFTNLLARVLAKSNESV 79
+ + + GKGG+GKST + L+ LA+ + V
Sbjct: 1 RQIAIYGKGGIGKSTTSQNLSAALAEMGKKV 31
>gnl|CDD|237611 PRK14105, PRK14105, selenophosphate synthetase; Provisional.
Length = 345
Score = 29.0 bits (65), Expect = 3.0
Identities = 13/46 (28%), Positives = 24/46 (52%), Gaps = 6/46 (13%)
Query: 181 YLKGLPDI--GAIVVTTPQEVSLLDVRKEI----DFCRKVNIPIIG 220
Y GL +I +++ P E+ + ++ + DFCR+ + IIG
Sbjct: 90 YAMGLSEIIGVLVILGIPPELPIEVAKEMLQGFQDFCRENDTTIIG 135
>gnl|CDD|224026 COG1101, PhnK, ABC-type uncharacterized transport system, ATPase
component [General function prediction only].
Length = 263
Score = 28.8 bits (65), Expect = 3.0
Identities = 15/49 (30%), Positives = 22/49 (44%), Gaps = 5/49 (10%)
Query: 26 SGAAKSVDPGIELVKSHLSNV-----KHKVLVLSGKGGVGKSTFTNLLA 69
S A K+ G L K L+ + + + + G G GKST N +A
Sbjct: 5 SNATKTFFKGTPLEKRALNGLSLEIAEGDFVTVIGSNGAGKSTLLNAIA 53
>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 = 28.3 bits (64), Expect = 3.0
Identities = 13/30 (43%), Positives = 17/30 (56%)
Query: 50 VLVLSGKGGVGKSTFTNLLARVLAKSNESV 79
V++L G GVGK+T LA L K + V
Sbjct: 2 VILLVGLQGVGKTTTAAKLALYLKKKGKKV 31
>gnl|CDD|206746 cd01849, YlqF_related_GTPase, Circularly permuted YlqF-related
GTPases. These proteins are found in bacteria,
eukaryotes, and archaea. They all exhibit a circular
permutation of the GTPase signature motifs so that the
order of the conserved G box motifs is G4-G5-G1-G2-G3,
with G4 and G5 being permuted from the C-terminal region
of proteins in the Ras superfamily to the N-terminus of
YlqF-related GTPases.
Length = 146
Score = 28.1 bits (63), Expect = 3.0
Identities = 12/42 (28%), Positives = 16/42 (38%)
Query: 40 KSHLSNVKHKVLVLSGKGGVGKSTFTNLLARVLAKSNESVDV 81
K L K + + G VGKS+F N L S+
Sbjct: 83 KLKLKYKKGIRVGVVGLPNVGKSSFINALLNKFKLKVGSIPG 124
>gnl|CDD|238836 cd01673, dNK, Deoxyribonucleoside kinase (dNK) catalyzes the
phosphorylation of deoxyribonucleosides to yield
corresponding monophosphates (dNMPs). This family
consists of various deoxynucleoside kinases including
deoxyribo- cytidine (EC 2.7.1.74), guanosine (EC
2.7.1.113), adenosine (EC 2.7.1.76), and thymidine (EC
2.7.1.21) kinases. They are key enzymes in the salvage
of deoxyribonucleosides originating from extra- or
intracellular breakdown of DNA.
Length = 193
Score = 28.3 bits (64), Expect = 3.1
Identities = 10/20 (50%), Positives = 12/20 (60%)
Query: 50 VLVLSGKGGVGKSTFTNLLA 69
V+V+ G G GKST LA
Sbjct: 1 VIVVEGNIGAGKSTLAKELA 20
>gnl|CDD|223603 COG0529, CysC, Adenylylsulfate kinase and related kinases
[Inorganic ion transport and metabolism].
Length = 197
Score = 28.4 bits (64), Expect = 3.2
Identities = 15/41 (36%), Positives = 18/41 (43%), Gaps = 2/41 (4%)
Query: 47 KHKVLVLSGKGGVGKSTFTNLLARVLAKSNESVDVGVLDLD 87
K V+ +G G GKST N L L V +LD D
Sbjct: 22 KGAVIWFTGLSGSGKSTIANALEEKLFAKGYHVY--LLDGD 60
>gnl|CDD|213264 cd03297, ABC_ModC_molybdenum_transporter, ATP-binding cassette
domain of the molybdenum transport system. ModC is an
ABC-type transporter and the ATPase component of a
molybdate transport system that also includes the
periplasmic binding protein ModA and the membrane
protein ModB. ABC transporters are a large family of
proteins involved in the transport of a wide variety of
different compounds, like sugars, ions, peptides and
more complex organic molecules. The nucleotide binding
domain shows the highest similarity between all members
of the family. ABC transporters are a subset of
nucleotide hydrolases that contain a signature motif,
Q-loop, and H-loop/switch region, in addition to, the
Walker A motif/P-loop and Walker B motif commonly found
in a number of ATP- and GTP-binding and hydrolyzing
proteins.
Length = 214
Score = 28.4 bits (64), Expect = 3.2
Identities = 18/64 (28%), Positives = 26/64 (40%), Gaps = 15/64 (23%)
Query: 50 VLVLSGKGGVGKSTFTNLLARVLAKSNESVDVGVLDLD----------ICGPSMPRMMGL 99
V + G G GKST +A + E D G + L+ I P R +GL
Sbjct: 25 VTGIFGASGAGKSTLLRCIAGL-----EKPDGGTIVLNGTVLFDSRKKINLPPQQRKIGL 79
Query: 100 LNEQ 103
+ +Q
Sbjct: 80 VFQQ 83
>gnl|CDD|223998 COG1072, CoaA, Panthothenate kinase [Coenzyme metabolism].
Length = 283
Score = 28.8 bits (65), Expect = 3.2
Identities = 13/48 (27%), Positives = 25/48 (52%), Gaps = 3/48 (6%)
Query: 43 LSNVKHK---VLVLSGKGGVGKSTFTNLLARVLAKSNESVDVGVLDLD 87
L + ++ ++G VGKST +L +L++ ES V ++ +D
Sbjct: 74 LGTNNQQRPFIIGIAGSVAVGKSTTARILQALLSRWPESPKVDLVTMD 121
>gnl|CDD|223800 COG0728, MviN, Uncharacterized membrane protein, putative virulence
factor [General function prediction only].
Length = 518
Score = 29.2 bits (66), Expect = 3.3
Identities = 9/34 (26%), Positives = 14/34 (41%), Gaps = 4/34 (11%)
Query: 96 MMGLLNEQVHQSASGWSPVFLEENLSVMSIGFLL 129
+LN + ++PV L+V IG L
Sbjct: 152 FGAILNSRNRFFIPAFAPVL----LNVSVIGLAL 181
>gnl|CDD|234041 TIGR02868, CydC, thiol reductant ABC exporter, CydC subunit. The
gene pair cydCD encodes an ABC-family transporter in
which each gene contains an N-terminal membrane-spanning
domain (pfam00664) and a C-terminal ATP-binding domain
(pfam00005). In E. coli these genes were discovered as
mutants which caused the terminal heme-copper oxidase
complex cytochrome bd to fail to assemble. Recent work
has shown that the transporter is involved in export of
redox-active thiol compounds such as cysteine and
glutathione. The linkage to assembly of the cytochrome
bd complex is further supported by the conserved operon
structure found outside the gammaproteobacteria
(cydABCD) containing both the transporter and oxidase
genes components. The genes used as the seed members for
this model are all either found in the
gammproteobacterial context or the CydABCD context. All
members of this family scoring above trusted at the time
of its creation were from genomes which encode a
cytochrome bd complex.
Length = 530
Score = 28.9 bits (65), Expect = 3.4
Identities = 16/59 (27%), Positives = 25/59 (42%), Gaps = 2/59 (3%)
Query: 48 HKVLVLSGKGGVGKSTFTNLLARVLAKSNESVDV-GVLDLDICGPSMPRMMGLLNEQVH 105
+V +L G G GKST LA +L V + GV + + R + + + H
Sbjct: 362 ERVAIL-GPSGSGKSTLLATLAGLLDPLQGEVTLDGVPVSSLDQDEVRRRVSVCAQDAH 419
>gnl|CDD|213221 cd03254, ABCC_Glucan_exporter_like, ATP-binding cassette domain
of glucan transporter and related proteins, subfamily
C. Glucan exporter ATP-binding protein. In A.
tumefaciens cyclic beta-1, 2-glucan must be transported
into the periplasmic space to exert its action as a
virulence factor. This subfamily belongs to the
MRP-like family and is involved in drug, peptide, and
lipid export. The MRP-like family, similar to all ABC
proteins, have a common four-domain core structure
constituted by two membrane-spanning domains each
composed of six transmembrane (TM) helices and two
nucleotide-binding domains (NBD). ABC transporters are
a subset of nucleotide hydrolases that contain a
signature motif, Q-loop, and H-loop/switch region, in
addition to, the Walker A motif/P-loop and Walker B
motif commonly found in a number of ATP- and
GTP-binding and hydrolyzing proteins.
Length = 229
Score = 28.7 bits (65), Expect = 3.4
Identities = 13/41 (31%), Positives = 20/41 (48%), Gaps = 1/41 (2%)
Query: 31 SVDPGIELVKS-HLSNVKHKVLVLSGKGGVGKSTFTNLLAR 70
S D ++K + S + + + G G GK+T NLL R
Sbjct: 11 SYDEKKPVLKDINFSIKPGETVAIVGPTGAGKTTLINLLMR 51
>gnl|CDD|225982 COG3451, VirB4, Type IV secretory pathway, VirB4 components
[Intracellular trafficking and secretion].
Length = 796
Score = 28.9 bits (65), Expect = 3.5
Identities = 10/46 (21%), Positives = 16/46 (34%), Gaps = 2/46 (4%)
Query: 42 HLSNVKHKVLVLSGKGGVGKSTFTNLLARVLAKSNESVDVGVLDLD 87
H+ L++ G G GK+ + L K + D D
Sbjct: 431 HVGEDVGHTLII-GPTGAGKTVLLSFLLAQALKYGNP-QIVAFDKD 474
>gnl|CDD|215451 PLN02840, PLN02840, tRNA dimethylallyltransferase.
Length = 421
Score = 28.6 bits (64), Expect = 3.7
Identities = 17/38 (44%), Positives = 21/38 (55%), Gaps = 3/38 (7%)
Query: 47 KHKVLVLSGKGGVGKSTFTNLLARVLAK---SNESVDV 81
K KV+V+SG G GKS LA+ L S +SV V
Sbjct: 20 KEKVIVISGPTGAGKSRLALELAKRLNGEIISADSVQV 57
>gnl|CDD|236333 PRK08691, PRK08691, DNA polymerase III subunits gamma and tau;
Validated.
Length = 709
Score = 28.9 bits (64), Expect = 3.8
Identities = 14/28 (50%), Positives = 19/28 (67%), Gaps = 4/28 (14%)
Query: 48 HKVLVLSGKGGVGKSTFTNLLARVLAKS 75
H +L+G GVGK+T +AR+LAKS
Sbjct: 38 HHAYLLTGTRGVGKTT----IARILAKS 61
>gnl|CDD|217424 pfam03205, MobB, Molybdopterin guanine dinucleotide synthesis
protein B. This protein contains a P-loop.
Length = 126
Score = 27.7 bits (62), Expect = 3.9
Identities = 11/48 (22%), Positives = 19/48 (39%), Gaps = 6/48 (12%)
Query: 49 KVLVLSGKGGVGKSTFTNLLARVLAKSNESV------DVGVLDLDICG 90
++++ G GK+T L L + V D G ++D G
Sbjct: 1 PIVLVVGPKDSGKTTLIRKLLNYLKRRGYRVAVVKHLDHGQGEIDKPG 48
>gnl|CDD|233536 TIGR01695, mviN, integral membrane protein MviN. This model
represents MviN, a family of integral membrane proteins
predicted to have ten or more transmembrane regions.
Although frequently listed as a virulence protein, it is
not restricted to pathogens and it is an essential
protein in Sinorhizobium meliloti. In a number of
species its gene is adjacent to that of the
uridylyltransferase GlnD , the signal-transducing enzyme
that performs the key modification to the nitrogen
regulatory protein PII [Unknown function, General].
Length = 502
Score = 28.8 bits (65), Expect = 4.0
Identities = 9/37 (24%), Positives = 17/37 (45%), Gaps = 3/37 (8%)
Query: 96 MMGLLNEQVHQSASGWSPVFLEENLSVM-SIGFLLNS 131
G+LN + +SP+ N+ V+ S+ F +
Sbjct: 143 FGGILNARKRFFIPSFSPILF--NIGVILSLLFFDWN 177
>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 = 28.4 bits (64), Expect = 4.0
Identities = 11/17 (64%), Positives = 13/17 (76%), Gaps = 1/17 (5%)
Query: 50 VLVLSGKGGVGKSTFTN 66
+LVL GK GVGKS+ N
Sbjct: 34 ILVL-GKTGVGKSSTIN 49
>gnl|CDD|235466 PRK05439, PRK05439, pantothenate kinase; Provisional.
Length = 311
Score = 28.6 bits (65), Expect = 4.1
Identities = 10/23 (43%), Positives = 13/23 (56%)
Query: 59 VGKSTFTNLLARVLAKSNESVDV 81
VGKST LL +L++ E V
Sbjct: 97 VGKSTTARLLQALLSRWPEHPKV 119
>gnl|CDD|225369 COG2812, DnaX, DNA polymerase III, gamma/tau subunits [DNA
replication, recombination, and repair].
Length = 515
Score = 28.5 bits (64), Expect = 4.1
Identities = 18/46 (39%), Positives = 26/46 (56%), Gaps = 9/46 (19%)
Query: 35 GIELVKSHLSN-VKHKVLV----LSGKGGVGKSTFTNLLARVLAKS 75
G E V LSN +++ + SG GVGK+T +AR+LAK+
Sbjct: 20 GQEHVVKTLSNALENGRIAHAYLFSGPRGVGKTT----IARILAKA 61
>gnl|CDD|183016 PRK11176, PRK11176, lipid transporter ATP-binding/permease protein;
Provisional.
Length = 582
Score = 28.8 bits (65), Expect = 4.2
Identities = 12/22 (54%), Positives = 14/22 (63%)
Query: 49 KVLVLSGKGGVGKSTFTNLLAR 70
K + L G+ G GKST NLL R
Sbjct: 370 KTVALVGRSGSGKSTIANLLTR 391
>gnl|CDD|236982 PRK11784, PRK11784, tRNA 2-selenouridine synthase; Provisional.
Length = 345
Score = 28.6 bits (65), Expect = 4.2
Identities = 13/40 (32%), Positives = 18/40 (45%), Gaps = 8/40 (20%)
Query: 47 KHKVLVLSGKGGVGKSTFTNLLARVLAKSNESVDVGVLDL 86
+ ++VL G G GK+ LA A+ VLDL
Sbjct: 140 QFPLVVLGGNTGSGKTELLQALANAGAQ--------VLDL 171
>gnl|CDD|218401 pfam05049, IIGP, Interferon-inducible GTPase (IIGP).
Interferon-inducible GTPase (IIGP) is thought to play a
role in in intracellular defence. IIGP is predominantly
associated with the Golgi apparatus and also localises
to the endoplasmic reticulum and exerts a distinct role
in IFN-induced intracellular membrane trafficking or
processing.
Length = 375
Score = 28.6 bits (64), Expect = 4.3
Identities = 15/50 (30%), Positives = 25/50 (50%), Gaps = 1/50 (2%)
Query: 35 GIELVKSHLSNVKHKVLVLSGKGGVGKSTFTNLLARVLAKSNESVDVGVL 84
I+ +S+ K+ V +G G GKS+F N L + + + S GV+
Sbjct: 23 IIKKAIQEISSAPLKIAV-TGDSGNGKSSFINALRGIGHEEDGSAPTGVV 71
>gnl|CDD|234132 TIGR03167, tRNA_sel_U_synt, tRNA 2-selenouridine synthase. The
Escherichia coli YbbB protein was shown to encode a
selenophosphate-dependent tRNA 2-selenouridine synthase,
essential for modification of some tRNAs to replace a
sulfur atom with selenium. This enzyme works with SelD,
the selenium donor protein, which also acts in
selenocysteine incorporation. Although the members of
this protein family show a fairly deep split, sequences
from both sides of the split are supported by
co-occurence with, and often proximity to, the selD gene
[Protein synthesis, tRNA and rRNA base modification].
Length = 311
Score = 28.3 bits (64), Expect = 4.3
Identities = 15/40 (37%), Positives = 18/40 (45%), Gaps = 8/40 (20%)
Query: 47 KHKVLVLSGKGGVGKSTFTNLLARVLAKSNESVDVGVLDL 86
++VL G G GK T LL LA + VLDL
Sbjct: 126 PFPLIVLGGMTGSGK---TELLHA-LANAGAQ----VLDL 157
>gnl|CDD|216584 pfam01580, FtsK_SpoIIIE, FtsK/SpoIIIE family. FtsK has extensive
sequence similarity to wide variety of proteins from
prokaryotes and plasmids, termed the FtsK/SpoIIIE
family. This domain contains a putative ATP binding
P-loop motif. It is found in the FtsK cell division
protein from E. coli and the stage III sporulation
protein E SpoIIIE, which has roles in regulation of
prespore specific gene expression in B. subtilis. A
mutation in FtsK causes a temperature sensitive block in
cell division and it is involved in peptidoglycan
synthesis or modification. The SpoIIIE protein is
implicated in intercellular chromosomal DNA transfer.
Length = 201
Score = 28.1 bits (63), Expect = 4.4
Identities = 18/62 (29%), Positives = 27/62 (43%), Gaps = 8/62 (12%)
Query: 39 VKSHLSNVKHKVLVLSGKGGVGKSTFTNLLARVLAKSNESVDVGVLDLDICGPSMPRMMG 98
V + L + H +L+ G GKSTF N L LA + +V + +D P+
Sbjct: 31 VVADLVKMPH-LLIAGATGS-GKSTFLNTLILSLAARHSPEEVRLYLID------PKGGE 82
Query: 99 LL 100
L
Sbjct: 83 LA 84
>gnl|CDD|184130 PRK13545, tagH, teichoic acids export protein ATP-binding subunit;
Provisional.
Length = 549
Score = 28.7 bits (64), Expect = 4.5
Identities = 21/87 (24%), Positives = 41/87 (47%), Gaps = 27/87 (31%)
Query: 43 LSNV-----KHKVLVLSGKGGVGKSTFTNLLARVLAKSNESVDV---------------- 81
L+N+ + +++ + G G GKST +NL+A V + +VD+
Sbjct: 40 LNNISFEVPEGEIVGIIGLNGSGKSTLSNLIAGVTMPNKGTVDIKGSAALIAISSGLNGQ 99
Query: 82 --GVLDLDICGPSMPRMMGLLNEQVHQ 106
G+ ++++ G MMGL E++ +
Sbjct: 100 LTGIENIELKG----LMMGLTKEKIKE 122
>gnl|CDD|223873 COG0802, COG0802, Predicted ATPase or kinase [General function
prediction only].
Length = 149
Score = 27.6 bits (62), Expect = 4.6
Identities = 10/25 (40%), Positives = 15/25 (60%)
Query: 49 KVLVLSGKGGVGKSTFTNLLARVLA 73
V++LSG G GK+T +A+ L
Sbjct: 26 DVVLLSGDLGAGKTTLVRGIAKGLG 50
>gnl|CDD|132313 TIGR03269, met_CoM_red_A2, methyl coenzyme M reductase system,
component A2. The enzyme that catalyzes the final step
in methanogenesis, methyl coenzyme M reductase, contains
alpha, beta, and gamma chains. In older literature, the
complex of alpha, beta, and gamma chains was termed
component C, while this single chain protein was termed
methyl coenzyme M reductase system component A2 [Energy
metabolism, Methanogenesis].
Length = 520
Score = 28.6 bits (64), Expect = 4.6
Identities = 24/83 (28%), Positives = 43/83 (51%), Gaps = 10/83 (12%)
Query: 31 SVDPG-IELVKSHLSNVKHK-VLVLSGKGGVGKSTFTNLLARVLAKSNESVDVGVLD--L 86
SVD G ++ V + VK + + G G GK+T + ++A VL ++ V+V V D +
Sbjct: 291 SVDRGVVKAVDNVSLEVKEGEIFGIVGTSGAGKTTLSKIIAGVLEPTSGEVNVRVGDEWV 350
Query: 87 DICGPSM------PRMMGLLNEQ 103
D+ P R +G+L+++
Sbjct: 351 DMTKPGPDGRGRAKRYIGILHQE 373
>gnl|CDD|223565 COG0491, GloB, Zn-dependent hydrolases, including glyoxylases
[General function prediction only].
Length = 252
Score = 28.2 bits (62), Expect = 4.6
Identities = 11/38 (28%), Positives = 16/38 (42%)
Query: 157 GNGLEYLLIDTPPGTSDEHLSLVQYLKGLPDIGAIVVT 194
+LIDT G +D L D+ AI++T
Sbjct: 32 DGEGGAVLIDTGLGDADAEALLEALAALGLDVDAILLT 69
>gnl|CDD|238984 cd02026, PRK, Phosphoribulokinase (PRK) is an enzyme involved in
the Benson-Calvin cycle in chloroplasts or
photosynthetic prokaryotes. This enzyme catalyzes the
phosphorylation of D-ribulose 5-phosphate to form
D-ribulose 1, 5-biphosphate, using ATP and NADPH
produced by the primary reactions of photosynthesis.
Length = 273
Score = 28.1 bits (63), Expect = 4.7
Identities = 9/30 (30%), Positives = 15/30 (50%)
Query: 50 VLVLSGKGGVGKSTFTNLLARVLAKSNESV 79
++ ++G G GKSTF L + +V
Sbjct: 1 IIGVAGDSGCGKSTFLRRLTSLFGSDLVTV 30
>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 = 28.1 bits (63), Expect = 4.9
Identities = 13/25 (52%), Positives = 17/25 (68%)
Query: 55 GKGGVGKSTFTNLLARVLAKSNESV 79
GKGG+GKST T +A LA+ + V
Sbjct: 7 GKGGIGKSTTTQNIAAALAEMGKKV 31
>gnl|CDD|235927 PRK07078, PRK07078, hypothetical protein; Validated.
Length = 759
Score = 28.6 bits (64), Expect = 5.0
Identities = 12/25 (48%), Positives = 14/25 (56%)
Query: 48 HKVLVLSGKGGVGKSTFTNLLARVL 72
H + L G G GKS F N LA +L
Sbjct: 491 HALFFLYGTGANGKSVFVNTLATIL 515
>gnl|CDD|240284 PTZ00132, PTZ00132, GTP-binding nuclear protein Ran; Provisional.
Length = 215
Score = 28.1 bits (63), Expect = 5.3
Identities = 10/14 (71%), Positives = 12/14 (85%)
Query: 51 LVLSGKGGVGKSTF 64
L+L G GGVGK+TF
Sbjct: 12 LILVGDGGVGKTTF 25
>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 = 28.1 bits (63), Expect = 5.5
Identities = 16/49 (32%), Positives = 21/49 (42%), Gaps = 5/49 (10%)
Query: 50 VLVLSGKGGVGKSTFTNLLARVLAKSNESVDVGVLDLDICGPSMPRMMG 98
+ ++G G GKST L L + V VL +D PS P G
Sbjct: 31 RVGITGVPGAGKSTLIEALGMELRR--RGHRVAVLAVD---PSSPFTGG 74
>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 = 27.6 bits (62), Expect = 5.5
Identities = 11/31 (35%), Positives = 13/31 (41%)
Query: 49 KVLVLSGKGGVGKSTFTNLLARVLAKSNESV 79
+V G G GK+T LLA L V
Sbjct: 1 MFIVFEGIDGAGKTTLIELLAERLEARGYEV 31
>gnl|CDD|223775 COG0703, AroK, Shikimate kinase [Amino acid transport and
metabolism].
Length = 172
Score = 27.6 bits (62), Expect = 5.6
Identities = 13/37 (35%), Positives = 18/37 (48%), Gaps = 7/37 (18%)
Query: 51 LVLSGKGGVGKSTFTNLLARVLAKSNESVDVGVLDLD 87
+VL G G GKST LA+ L ++ +D D
Sbjct: 5 IVLIGFMGAGKSTIGRALAKAL-------NLPFIDTD 34
>gnl|CDD|233686 TIGR02016, BchX, chlorophyllide reductase iron protein subunit X.
This model represents the X subunit of the
three-subunit enzyme, (bacterio)chlorophyllide
reductase. This enzyme is responsible for the reduction
of the chlorin B-ring and is closely related to the
protochlorophyllide reductase complex which reduces the
D-ring. Both of these complexes in turn are homologous
to nitrogenase. This subunit is homologous to the
nitrogenase component II, or "iron" protein [Energy
metabolism, Photosynthesis].
Length = 296
Score = 27.9 bits (62), Expect = 5.7
Identities = 11/31 (35%), Positives = 20/31 (64%)
Query: 49 KVLVLSGKGGVGKSTFTNLLARVLAKSNESV 79
+++ + GKGG GKS T L+ ++A+ + V
Sbjct: 1 RIIAIYGKGGSGKSFTTTNLSHMMAEMGKRV 31
>gnl|CDD|237875 PRK14974, PRK14974, cell division protein FtsY; Provisional.
Length = 336
Score = 28.0 bits (63), Expect = 5.8
Identities = 18/49 (36%), Positives = 24/49 (48%)
Query: 31 SVDPGIELVKSHLSNVKHKVLVLSGKGGVGKSTFTNLLARVLAKSNESV 79
SV +L++ S K V+V G G GK+T LA L K+ SV
Sbjct: 123 SVGDLFDLIEEIKSKGKPVVIVFVGVNGTGKTTTIAKLAYYLKKNGFSV 171
>gnl|CDD|218528 pfam05272, VirE, Virulence-associated protein E. This family
contains several bacterial virulence-associated protein
E like proteins. These proteins contain a P-loop motif.
Length = 198
Score = 27.7 bits (62), Expect = 6.0
Identities = 11/20 (55%), Positives = 12/20 (60%)
Query: 50 VLVLSGKGGVGKSTFTNLLA 69
VL+L G G GKSTF L
Sbjct: 54 VLILQGAQGSGKSTFLKKLG 73
>gnl|CDD|216999 pfam02367, UPF0079, Uncharacterized P-loop hydrolase UPF0079.
This uncharacterized family contains a P-loop.
Length = 123
Score = 27.2 bits (61), Expect = 6.0
Identities = 12/29 (41%), Positives = 17/29 (58%)
Query: 49 KVLVLSGKGGVGKSTFTNLLARVLAKSNE 77
V++LSG G GK+TF LA+ L +
Sbjct: 16 DVVLLSGDLGAGKTTFVRGLAQGLGITGN 44
>gnl|CDD|236570 PRK09563, rbgA, GTPase YlqF; Reviewed.
Length = 287
Score = 27.8 bits (63), Expect = 6.2
Identities = 10/18 (55%), Positives = 13/18 (72%), Gaps = 1/18 (5%)
Query: 59 VGKSTFTNLLA-RVLAKS 75
VGKST N LA + +AK+
Sbjct: 132 VGKSTLINRLAGKKIAKT 149
>gnl|CDD|218236 pfam04735, Baculo_helicase, Baculovirus DNA helicase.
Length = 1173
Score = 28.4 bits (64), Expect = 6.4
Identities = 10/18 (55%), Positives = 12/18 (66%)
Query: 51 LVLSGKGGVGKSTFTNLL 68
L L+GK GKS+F LL
Sbjct: 882 LYLNGKPNCGKSSFFELL 899
>gnl|CDD|236216 PRK08277, PRK08277, D-mannonate oxidoreductase; Provisional.
Length = 278
Score = 27.9 bits (63), Expect = 6.5
Identities = 16/42 (38%), Positives = 21/42 (50%), Gaps = 6/42 (14%)
Query: 45 NVKHKVLVLSGKGGVGKSTFTNLLARVLAKSNESVDVGVLDL 86
++K KV V++G GGV LAR AK V +LD
Sbjct: 7 SLKGKVAVITGGGGVLGGAMAKELARAGAK------VAILDR 42
>gnl|CDD|223203 COG0125, Tmk, Thymidylate kinase [Nucleotide transport and
metabolism].
Length = 208
Score = 27.6 bits (62), Expect = 6.5
Identities = 11/33 (33%), Positives = 15/33 (45%)
Query: 47 KHKVLVLSGKGGVGKSTFTNLLARVLAKSNESV 79
K +V+ G G GK+T LL L + V
Sbjct: 2 KGMFIVIEGIDGAGKTTQAELLKERLEERGIKV 34
>gnl|CDD|182204 PRK10037, PRK10037, cell division protein; Provisional.
Length = 250
Score = 27.9 bits (62), Expect = 6.5
Identities = 21/69 (30%), Positives = 32/69 (46%), Gaps = 8/69 (11%)
Query: 50 VLVLSG-KGGVGKSTFTNLLARVLAKSNESVDVGVLDLDICGPSMPRMMGLLNEQVHQSA 108
+L L G +GGVG ++ T LA L E+ VL +D C ++ R+ N
Sbjct: 3 ILGLQGVRGGVGTTSITAALAWSLQMLGEN----VLVIDACPDNLLRLS--FNVDFTHR- 55
Query: 109 SGWSPVFLE 117
GW+ L+
Sbjct: 56 QGWARALLD 64
>gnl|CDD|216099 pfam00753, Lactamase_B, Metallo-beta-lactamase superfamily.
Length = 148
Score = 27.3 bits (60), Expect = 6.6
Identities = 13/34 (38%), Positives = 16/34 (47%)
Query: 161 EYLLIDTPPGTSDEHLSLVQYLKGLPDIGAIVVT 194
+LIDT G D L L DI AI++T
Sbjct: 16 GAVLIDTGLGADDALLLLALLGLDPKDIDAIILT 49
>gnl|CDD|188353 TIGR03608, L_ocin_972_ABC, putative bacteriocin export ABC
transporter, lactococcin 972 group. A gene pair with a
fairly wide distribution consists of a polypeptide
related to the lactococcin 972 (see TIGR01653) and
multiple-membrane-spanning putative immunity protein
(see TIGR01654). This model represents a small clade
within the ABC transporters that regularly are found
adjacent to these bacteriocin system gene pairs and are
likely serve as export proteins [Cellular processes,
Toxin production and resistance, Transport and binding
proteins, Unknown substrate].
Length = 206
Score = 27.6 bits (62), Expect = 6.7
Identities = 15/50 (30%), Positives = 24/50 (48%), Gaps = 5/50 (10%)
Query: 38 LVKSHLSNVKHKVLVLSGKGGVGKSTFTNLLARVLAKSNESVDVGVLDLD 87
L +L+ K K+ + G+ G GKST N++ E D G + L+
Sbjct: 14 LDDLNLTIEKGKMYAIIGESGSGKSTLLNIIGL-----LEKFDSGQVYLN 58
>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 = 27.2 bits (60), Expect = 6.7
Identities = 10/42 (23%), Positives = 19/42 (45%), Gaps = 6/42 (14%)
Query: 36 IELVKSHLSNVKH---KVLVLSGKGGVGKSTFTNLLARVLAK 74
+E + L + ++L+G G GK++ LL +L
Sbjct: 9 LERLLDALRRARSGGPPSVLLTGPSGTGKTS---LLRELLEG 47
>gnl|CDD|237039 PRK12288, PRK12288, GTPase RsgA; Reviewed.
Length = 347
Score = 27.9 bits (63), Expect = 6.9
Identities = 11/34 (32%), Positives = 20/34 (58%), Gaps = 3/34 (8%)
Query: 35 GIELVKSHLSNVKHKVLVLSGKGGVGKSTFTNLL 68
G+E +++ L ++ + G+ GVGKS+ N L
Sbjct: 195 GLEELEAAL---TGRISIFVGQSGVGKSSLINAL 225
>gnl|CDD|234719 PRK00300, gmk, guanylate kinase; Provisional.
Length = 205
Score = 27.4 bits (62), Expect = 6.9
Identities = 10/20 (50%), Positives = 12/20 (60%)
Query: 49 KVLVLSGKGGVGKSTFTNLL 68
++VLSG G GKST L
Sbjct: 6 LLIVLSGPSGAGKSTLVKAL 25
>gnl|CDD|213193 cd03226, ABC_cobalt_CbiO_domain2, Second domain of the
ATP-binding cassette component of cobalt transport
system. Domain II of the ABC component of a cobalt
transport family found in bacteria, archaea, and
eukaryota. The transition metal cobalt is an essential
component of many enzymes and must be transported into
cells in appropriate amounts when needed. The CbiMNQO
family ABC transport system is involved in cobalt
transport in association with the cobalamin (vitamin
B12) biosynthetic pathways. Most cobalt (Cbi) transport
systems possess a separate CbiN component, the
cobalt-binding periplasmic protein, and they are
encoded by the conserved gene cluster cbiMNQO. Both the
CbiM and CbiQ proteins are integral cytoplasmic
membrane proteins, and the CbiO protein has the linker
peptide and the Walker A and B motifs commonly found in
the ATPase components of the ABC-type transport
systems.
Length = 205
Score = 27.6 bits (62), Expect = 6.9
Identities = 11/24 (45%), Positives = 17/24 (70%), Gaps = 4/24 (16%)
Query: 50 VLVLSGKGGVGKSTFTNLLARVLA 73
++ L+GK G GK+T LA++LA
Sbjct: 28 IIALTGKNGAGKTT----LAKILA 47
>gnl|CDD|232886 TIGR00231, small_GTP, small GTP-binding protein domain. Proteins
with a small GTP-binding domain recognized by this
model include Ras, RhoA, Rab11, translation elongation
factor G, translation initiation factor IF-2,
tetratcycline resistance protein TetM, CDC42, Era,
ADP-ribosylation factors, tdhF, and many others. In
some proteins the domain occurs more than once.This
model recognizes a large number of small GTP-binding
proteins and related domains in larger proteins. Note
that the alpha chains of heterotrimeric G proteins are
larger proteins in which the NKXD motif is separated
from the GxxxxGK[ST] motif (P-loop) by a long insert
and are not easily detected by this model [Unknown
function, General].
Length = 162
Score = 27.0 bits (60), Expect = 7.8
Identities = 9/23 (39%), Positives = 11/23 (47%)
Query: 49 KVLVLSGKGGVGKSTFTNLLARV 71
+V+ G VGKST N L
Sbjct: 2 IKIVIVGDPNVGKSTLLNRLLGN 24
>gnl|CDD|237646 PRK14237, PRK14237, phosphate transporter ATP-binding protein;
Provisional.
Length = 267
Score = 27.4 bits (61), Expect = 7.8
Identities = 13/35 (37%), Positives = 21/35 (60%), Gaps = 4/35 (11%)
Query: 47 KHKVLVLSGKGGVGKSTFTNLLARVLAKSNESVDV 81
K+K+ L G G GKST+ R L + N+++D+
Sbjct: 45 KNKITALIGPSGSGKSTYL----RSLNRMNDTIDI 75
>gnl|CDD|236849 PRK11109, PRK11109, bifunctional PTS system fructose-specific
transporter subunit IIA/HPr protein; Provisional.
Length = 375
Score = 27.6 bits (62), Expect = 8.6
Identities = 16/43 (37%), Positives = 21/43 (48%), Gaps = 4/43 (9%)
Query: 143 KNT--MIRQFLSEVDWGNG-LEYLLIDTPPGTSDEHLSLVQYL 182
T + QF V WG+G Y+ I SDEHL L++ L
Sbjct: 72 LKTGVQVFQFPQGVTWGDGQTAYVAIGIA-AKSDEHLGLLRQL 113
>gnl|CDD|106194 PRK13232, nifH, nitrogenase reductase; Reviewed.
Length = 273
Score = 27.3 bits (60), Expect = 8.7
Identities = 21/57 (36%), Positives = 31/57 (54%), Gaps = 10/57 (17%)
Query: 51 LVLSGKGGVGKSTFT-NLLARVLAKSNESVDVGVLDLDICGP---SMPRMMGLLNEQ 103
+ + GKGG+GKST T NL A + N+ + VG C P S ++G LN++
Sbjct: 4 IAIYGKGGIGKSTTTQNLTAALSTMGNKILLVG------CDPKADSTRMLLGGLNQK 54
>gnl|CDD|238683 cd01387, MYSc_type_XV, Myosin motor domain, type XV myosins. In
vertebrates, myosin XV appears to be expressed in
sensory tissue and play a role in hearing. This
catalytic (head) domain has ATPase activity and belongs
to the larger group of P-loop NTPases. Myosins are
actin-dependent molecular motors that play important
roles in muscle contraction, cell motility, and
organelle transport. The head domain is a molecular
motor, which utilizes ATP hydrolysis to generate
directed movement toward the plus end along actin
filaments. A cyclical interaction between myosin and
actin provides the driving force. Rates of ATP
hydrolysis and consequently the speed of movement along
actin filaments vary widely, from about 0.04 micrometer
per second for myosin I to 4.5 micrometer per second for
myosin II in skeletal muscle. Myosin II moves in
discrete steps about 5-10 nm long and generates 1-5
piconewtons of force. Upon ATP binding, the myosin head
dissociates from an actin filament. ATP hydrolysis
causes the head to pivot and associate with a new actin
subunit. The release of Pi causes the head to pivot and
move the filament (power stroke). Release of ADP
completes the cycle.
Length = 677
Score = 27.6 bits (61), Expect = 8.8
Identities = 12/35 (34%), Positives = 22/35 (62%)
Query: 43 LSNVKHKVLVLSGKGGVGKSTFTNLLARVLAKSNE 77
L +++ +++SG+ G GK+ T L+ R LA N+
Sbjct: 82 LDAKQNQCVIISGESGSGKTEATKLILRYLAAMNQ 116
>gnl|CDD|183702 PRK12723, PRK12723, flagellar biosynthesis regulator FlhF;
Provisional.
Length = 388
Score = 27.6 bits (61), Expect = 8.8
Identities = 16/54 (29%), Positives = 32/54 (59%), Gaps = 2/54 (3%)
Query: 36 IELVKSHLSNVKHKVLVLSGKGGVGKSTFTNLLARV--LAKSNESVDVGVLDLD 87
I+ S + N+K +V +L G GVGK+T LA + + ++S+++ ++ +D
Sbjct: 162 IKCSGSIIDNLKKRVFILVGPTGVGKTTTIAKLAAIYGINSDDKSLNIKIITID 215
>gnl|CDD|226905 COG4525, TauB, ABC-type taurine transport system, ATPase
component [Inorganic ion transport and metabolism].
Length = 259
Score = 27.4 bits (61), Expect = 8.8
Identities = 15/45 (33%), Positives = 22/45 (48%), Gaps = 2/45 (4%)
Query: 51 LVLSGKGGVGKSTFTNLLARVLAKSNESVDVGVLDLDICGPSMPR 95
+V+ G G GK+T NL+A + S S+ + I GP R
Sbjct: 34 VVVLGPSGCGKTTLLNLIAGFVTPSRGSIQLN--GRRIEGPGAER 76
>gnl|CDD|180975 PRK07429, PRK07429, phosphoribulokinase; Provisional.
Length = 327
Score = 27.3 bits (61), Expect = 9.2
Identities = 10/25 (40%), Positives = 14/25 (56%)
Query: 55 GKGGVGKSTFTNLLARVLAKSNESV 79
G G GK+TF LA +L + +V
Sbjct: 15 GDSGCGKTTFLRGLADLLGEELVTV 39
>gnl|CDD|184411 PRK13946, PRK13946, shikimate kinase; Provisional.
Length = 184
Score = 27.2 bits (61), Expect = 9.3
Identities = 11/25 (44%), Positives = 14/25 (56%)
Query: 48 HKVLVLSGKGGVGKSTFTNLLARVL 72
+ +VL G G GKST LA +L
Sbjct: 10 KRTVVLVGLMGAGKSTVGRRLATML 34
>gnl|CDD|197466 smart00010, small_GTPase, Small GTPase of the Ras superfamily;
ill-defined subfamily. SMART predicts Ras-like small
GTPases of the ARF, RAB, RAN, RAS, and SAR subfamilies.
Others that could not be classified in this way are
predicted to be members of the small GTPase superfamily
without predictions of the subfamily.
Length = 166
Score = 26.8 bits (60), Expect = 9.8
Identities = 11/18 (61%), Positives = 14/18 (77%), Gaps = 1/18 (5%)
Query: 48 HKVLVLSGKGGVGKSTFT 65
+K++VL G GGVGKS T
Sbjct: 3 YKLVVL-GGGGVGKSALT 19
>gnl|CDD|223874 COG0803, LraI, ABC-type metal ion transport system, periplasmic
component/surface adhesin [Inorganic ion transport and
metabolism].
Length = 303
Score = 27.3 bits (61), Expect = 9.9
Identities = 22/86 (25%), Positives = 31/86 (36%), Gaps = 17/86 (19%)
Query: 184 GLPDIGAIVVTTPQEVSLLDVRKEIDFCRKVNIPIIGVVENMATFVCPKCTKPSEIFPKD 243
GL + ++ E S D+ K +D +K NI I V N
Sbjct: 210 GLKQVAIAGISPEAEPSPKDLAKLVDLIKKKNIKAIFVESN---------------VSSK 254
Query: 244 SGGAEKMCAELSVPFLGSVPIDPLVT 269
S AE + E V LG + +D L
Sbjct: 255 S--AETLAKETGVKILGLLYLDSLGD 278
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
0.317 0.135 0.404
Gapped
Lambda K H
0.267 0.0616 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 14,556,751
Number of extensions: 1385432
Number of successful extensions: 2062
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2023
Number of HSP's successfully gapped: 231
Length of query: 294
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 198
Effective length of database: 6,679,618
Effective search space: 1322564364
Effective search space used: 1322564364
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 59 (26.7 bits)