RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 043873
(413 letters)
>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 = 250 bits (641), Expect = 7e-81
Identities = 113/325 (34%), Positives = 181/325 (55%), Gaps = 26/325 (8%)
Query: 90 MLGGKGGVGKTSCAASLAVKFANHGHPTIVISTDPAHSLSDSFAQDLSGGTLVPVEGVDS 149
GGKGGVGKT+ + + AV+ + G +++STDPAHSLSDSF Q G ++GV++
Sbjct: 5 FFGGKGGVGKTTVSCATAVRLSEQGKKVLLVSTDPAHSLSDSFNQKF-GHEPTKIKGVEN 63
Query: 150 PLFALEINPEKAREEFRTASQGSGGSGDGMKD-LMDSMGLGMLADQLGELKLGELLDTPP 208
L A+EI+P+ EE+R Q D + L M G+LA++L L
Sbjct: 64 -LSAMEIDPQMELEEYRGEVQ------DPINAVLGLDMLEGILAEELSSL---------- 106
Query: 209 PGLDEAIAISKVMQFVESQQYNMFTRIVFDTAPTGHTLRLLSLPDFLDASIGKMMKLKKK 268
PG+DE + + ++++ +Y++ ++FDTAPTGHTLRLLSLP L + K++KLK +
Sbjct: 107 PGIDEIASFDEFKKYMDEGEYDV---VIFDTAPTGHTLRLLSLPTVLSWYLEKIVKLKNQ 163
Query: 269 LASTTSAFKSVFGKEKKQQDVASDKVEQLRERMAKVRDLFRDPDATEFVIVTIPTVMAIS 328
+ FK + G A + +E+ +E++ K R++ DP+ T F +V IP M++
Sbjct: 164 IGPLAKPFKGM-GMGGSCLPEALESLEETKEQIEKAREILSDPERTSFRLVCIPEKMSLY 222
Query: 329 ESSRLHASLRKECIPVQRLIVNQVLPPSASDCKFCAMKRKDQMRVLETIMSDPQLANLRL 388
E+ R L K I V +IVNQVLP + C FC +++ Q + L+ I ++L +
Sbjct: 223 ETERAIQELAKYGIDVDAVIVNQVLPET-EQCPFCEARKEIQQKYLKEIEEL--FSDLPV 279
Query: 389 VQAPLVDVEIRGVPALKFMGDMIWK 413
+ PL+ E+ G+ AL+ ++
Sbjct: 280 AKLPLLPEEVVGLEALEKFSQTLYG 304
>gnl|CDD|223082 COG0003, ArsA, Predicted ATPase involved in chromosome partitioning
[Cell division and chromosome partitioning].
Length = 322
Score = 213 bits (544), Expect = 4e-66
Identities = 120/329 (36%), Positives = 180/329 (54%), Gaps = 37/329 (11%)
Query: 89 YMLGGKGGVGKTSCAASLAVKFANHGHPTIVISTDPAHSLSDSFAQDLSGGTLVPVEGVD 148
GKGGVGKT+ AA+ AVK A G +++STDPAHSL D F +L V
Sbjct: 5 VFFTGKGGVGKTTIAAATAVKLAESGKKVLLVSTDPAHSLGDVFDLELGHD----PRKVG 60
Query: 149 SPLFALEINPEKAREEFRTASQGSGGSGDGMKD-----LMDSMGLGMLADQLGELKLGEL 203
L ALE++PEKA EE+ D +KD L G+ AD+L L
Sbjct: 61 PNLDALELDPEKALEEY----------WDEVKDYLARLLRTRGLGGIYADELATL----- 105
Query: 204 LDTPPPGLDEAIAISKVMQFVESQQYNMFTRIVFDTAPTGHTLRLLSLPDFLDASIGKMM 263
PG+DEA+A+ K++++ S +Y+ IV DTAPTGHTLRLLSLP+ L + K+
Sbjct: 106 -----PGIDEALALLKILEYYVSGEYD---VIVVDTAPTGHTLRLLSLPEVLGWYLEKLF 157
Query: 264 KLK-KKLASTTSAFKSVFGKEKKQQDVASDKVEQLRERMAKVRDLFRDPDATEFVIVTIP 322
K + K++ + + G D + +E+L+ER+A VR++ +PD T F +V+IP
Sbjct: 158 KPRRKRMVKALKSLSTAAGSPLP-DDAVLEALEELKERIADVREVLTNPDGTSFRLVSIP 216
Query: 323 TVMAISESSRLHASLRKECIPVQRLIVNQVLPPSASDCKFCAMKRKDQMRVLETIMSDPQ 382
+++ E+ R L IPV +IVN++LP A D F +RK Q + L+ +
Sbjct: 217 EKLSLYETKRAVERLSLYGIPVDAVIVNKILPDEA-DQPFLEARRKIQQKYLKELEET-- 273
Query: 383 LANLRLVQAPLVDVEIRGVPALKFMGDMI 411
++L +V+ PL+ E G+ AL+ +GD++
Sbjct: 274 FSDLAVVKVPLLAEEPVGLEALEKLGDLL 302
>gnl|CDD|232932 TIGR00345, GET3_arsA_TRC40, transport-energizing ATPase,
TRC40/GET3/ArsA family. Members of this family are
ATPases that energize transport, although with different
partner proteins for different functions. Recent
findings show that TRC40 (GET3 in yeast) in involved in
the insertion of tail-anchored membrane proteins in
eukaryotes. A similar function is expected for members
of this family in archaea. However, the earliest
discovery of a function for this protein family is ArsA,
an arsenic resistance protein that partners with ArsB
(see pfam02040) for As(III) efflux [Hypothetical
proteins, Conserved].
Length = 284
Score = 201 bits (514), Expect = 3e-62
Identities = 114/305 (37%), Positives = 168/305 (55%), Gaps = 30/305 (9%)
Query: 103 AASLAVKFANHGHPTIVISTDPAHSLSDSFAQDLSGGTLVPVEGVDSPLFALEINPEKAR 162
+A+ A++ A G +++STDPAHSLSD F Q++ G T V GV++ L A+EI+P+ A
Sbjct: 2 SAATAIRLAEQGKKVLLVSTDPAHSLSDVFEQEI-GHTPTKVTGVEN-LSAVEIDPQAAL 59
Query: 163 EEFRT--ASQGSGGSGDGMKDLMDSMGLGMLADQLGELKLGELLDTPPPGLDEAIAISKV 220
EE+R Q G DG ML DQL L PG+DE A +
Sbjct: 60 EEYRAKLVEQIKGNLPDG----------DMLGDQLEGAALS-------PGIDEIAAFDEF 102
Query: 221 MQFVESQQYNMFTRIVFDTAPTGHTLRLLSLPDFLDASIGKMMKLKKKLASTTSAFKSVF 280
++ + + N F ++FDTAPTGHTLRLL LP+ L + + K +K++ KL F
Sbjct: 103 LKHMTDAE-NEFDVVIFDTAPTGHTLRLLQLPEVLSSFLEKFIKIRSKLGPMAKLFMG-- 159
Query: 281 GKEKKQQDVASDKVEQLRERMAKVRDLFRDPDATEFVIVTIPTVMAISESSRLHASLRKE 340
+ D A +K+E+L+E++ R++ DP+ T FV+V IP M++ ES R H L K
Sbjct: 160 ---AGEDDEALEKLEELKEQIEAAREILSDPERTSFVLVVIPEKMSLYESERAHKELAKY 216
Query: 341 CIPVQRLIVNQVLPPSASDCKFCAMKRKDQMRVLETIMSDPQLANLRLVQAPLVDVEIRG 400
I V +IVNQVLP +A +FC + + Q + L+ I A+L + + PL E+ G
Sbjct: 217 GIKVDAVIVNQVLPENA-QDEFCQARWELQQKYLKQIPEK--FADLPVAEVPLQKEEMVG 273
Query: 401 VPALK 405
+ ALK
Sbjct: 274 LEALK 278
>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 = 198 bits (506), Expect = 8e-62
Identities = 84/288 (29%), Positives = 114/288 (39%), Gaps = 85/288 (29%)
Query: 90 MLGGKGGVGKTSCAASLAVKFANHGHPTIVISTDPAHSLSDSFAQDLSGGTLVPVEGVDS 149
GKGGVGKT+ AA+ AV+ A G +++STDPAH+LSD +LS V+
Sbjct: 3 FFTGKGGVGKTTIAAATAVRLAEEGKKVLLVSTDPAHNLSDKGLPNLSD-----AFIVED 57
Query: 150 PLFALEINPEKAREEFRTASQGSGGSGDGMKDLMDSMGLGMLADQLGELKLGELLDTPPP 209
P EI P REE + + GE L L P
Sbjct: 58 P----EIAPNLYREEVDATRR-------------------VERAWGGEGGLMLELAAALP 94
Query: 210 GLDEAIAISKVMQFVESQQYNMFTRIVFDTAPTGHTLRLLSLPDFLDASIGKMMKLKKKL 269
G++E ++ V + Y+ IVFDTAPTGHTLRLL
Sbjct: 95 GIEELASLLAVFREFSEGLYD---VIVFDTAPTGHTLRLL-------------------- 131
Query: 270 ASTTSAFKSVFGKEKKQQDVASDKVEQLRERMAKVRDLFRDPDATEFVIVTIPTVMAISE 329
+RE DP+ T F +VT+P + + E
Sbjct: 132 ---------------------------VREL-------LTDPERTSFRLVTLPEKLPLYE 157
Query: 330 SSRLHASLRKECIPVQRLIVNQVLPPSASDCKFCAMKRKDQMRVLETI 377
+ R L IPV ++VN+VLP D F A +R+ Q + L I
Sbjct: 158 TERAITELALYGIPVDAVVVNRVLPAEVDDDPFLAARRQIQQKYLAEI 205
>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 = 123 bits (311), Expect = 9e-31
Identities = 93/326 (28%), Positives = 148/326 (45%), Gaps = 64/326 (19%)
Query: 93 GKGGVGKTSCAASLAVKFANHGHPTIVISTDPAHSLSDSFAQDLSGGTLVPVEGVDSPLF 152
GKGGVGKTS A + A+ A+ G +++STDPA ++ F Q + G + + GV LF
Sbjct: 10 GKGGVGKTSIACATAINLADQGKRVLLVSTDPASNVGQVFGQTI-GNKITAIAGVPG-LF 67
Query: 153 ALEINPEKAREEFRTASQGSGGSGDGMKDLMDSMGLGMLADQLGELKLGELLDTPPPGLD 212
ALEI+P+ A + +R D ++ ++ + + +QL E+ D
Sbjct: 68 ALEIDPQAAAQAYRARIV------DPVRGVLPDDVVSSIEEQLSGACTTEI-----AAFD 116
Query: 213 EAIAISKVMQFVESQQYNMFTRIVFDTAPTGHTLRLLSLP----DFLDAS------IGKM 262
E + +++ F I+FDTAPTGHT+RLL LP DFLD + +G +
Sbjct: 117 EFTGL-----LTDAELTQDFDHIIFDTAPTGHTIRLLQLPGAWSDFLDTNPNGASCLGPL 171
Query: 263 MKLKKKLASTTSAFKSVFGKEKKQQDVASDKVEQLRERMAKVRDLFRDPDATEFVIVTIP 322
L+K+ R + AK + DP+ T ++V P
Sbjct: 172 AGLEKQ-----------------------------RAQYAKAVEALSDPERTRLILVARP 202
Query: 323 TVMAISESSRLHASLRKECIPVQRLIVNQVLPPSAS--DCKFCAMKRKDQMRVLETIMSD 380
+ E +R H L + Q L++N VLPP+ + D A+ +++Q + +
Sbjct: 203 QKSTLLEVARTHQELAAIGLKNQYLVINGVLPPTEASDDPLAQAIYKREQ----KALQHM 258
Query: 381 PQ-LANLRLVQAPLVDVEIRGVPALK 405
P LANL PL + G+ AL+
Sbjct: 259 PAILANLPRYTLPLKPYNLVGLEALR 284
Score = 93.6 bits (233), Expect = 1e-20
Identities = 70/284 (24%), Positives = 118/284 (41%), Gaps = 72/284 (25%)
Query: 76 GFDEMV---AGTQRKHYMLGGKGGVGKTSCAASLAVKFANHGHPTIVISTDPAHSLSDSF 132
++ A +++ M GKGGVGKT+ AA++AV+ AN G + ++DPA LS +
Sbjct: 308 SLSRLIDEIAKSEKGLIMTMGKGGVGKTTVAAAIAVRLANKGLDVHLTTSDPAAHLSVTL 367
Query: 133 AQDLSGGTLVPVEGVDSPLFALEINPEKAREEFRT---ASQGSGGSGDGMKDLMDSMGLG 189
L+ L I+P++ E +R A++G +D G
Sbjct: 368 TGSLNN------------LQVSRIDPKQETERYRQEVLATKGKE---------LDEDGKA 406
Query: 190 MLADQLGELKLGELLDTPPPGLDEAIAISKVMQFVESQQYNMFTRIVFDTAPTGHTLRLL 249
L E L +P E IA+ + + + + F +V DTAPTGHTL L
Sbjct: 407 YLE---------EDLRSP---CTEEIAVFQAFSRIIREAGDRF--VVMDTAPTGHTLLL- 451
Query: 250 SLPDFLDASIGKMMKLKKKLASTTSAFKSVFGKEKKQQDVASDKVEQLRERMAKVRDLFR 309
LDA+ ++++K+ T + + +
Sbjct: 452 -----LDATGAYHREVERKMGDTPEHVTTPMMQ-------------------------LQ 481
Query: 310 DPDATEFVIVTIPTVMAISESSRLHASLRKECIPVQRLIVNQVL 353
DP+ T+ ++VT+P + E++RL LR+ I ++N L
Sbjct: 482 DPERTKVLLVTLPETTPVLEAARLQEDLRRAGIEPWWWVINNSL 525
>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 = 49.1 bits (118), Expect = 1e-07
Identities = 15/31 (48%), Positives = 19/31 (61%)
Query: 94 KGGVGKTSCAASLAVKFANHGHPTIVISTDP 124
KGGVGKT+ A +LA A G ++I DP
Sbjct: 8 KGGVGKTTTAVNLAAALARRGKRVLLIDLDP 38
>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 = 48.0 bits (115), Expect = 5e-07
Identities = 22/56 (39%), Positives = 30/56 (53%), Gaps = 1/56 (1%)
Query: 91 LGGKGGVGKTSCAASLAVKFANHGHPTIVISTDPAHSLSDSFAQDLSGGTLVPVEG 146
+ GKGGVGKT+ AA LA A G P + I DP L + + ++ L+ V G
Sbjct: 4 ITGKGGVGKTTIAALLARYLAEKGKPVLAIDADPD-DLPERLSVEVGEIKLLLVMG 58
>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 = 47.0 bits (112), Expect = 5e-06
Identities = 18/46 (39%), Positives = 23/46 (50%)
Query: 92 GGKGGVGKTSCAASLAVKFANHGHPTIVISTDPAHSLSDSFAQDLS 137
+GGVGKT+ A+LA G P + I DP + L F D S
Sbjct: 8 SVRGGVGKTTLTANLASALKLLGEPVLAIDLDPQNLLRLHFGMDWS 53
>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 = 43.5 bits (103), Expect = 1e-05
Identities = 15/31 (48%), Positives = 21/31 (67%)
Query: 90 MLGGKGGVGKTSCAASLAVKFANHGHPTIVI 120
++ GKGGVGKT+ AA+LA A G ++I
Sbjct: 3 VVTGKGGVGKTTLAANLAAALAKRGKRVLLI 33
>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 = 45.9 bits (109), Expect = 1e-05
Identities = 36/166 (21%), Positives = 56/166 (33%), Gaps = 29/166 (17%)
Query: 92 GGKGGVGKTSCAASLAVKFANHGHPTIVISTDPAHSLSDSFAQDLSGGTLVPVEGVDSPL 151
G KGGVGKT+ AA+LA A G+ ++I DP + S + +
Sbjct: 5 GTKGGVGKTTLAANLARALAKRGYRVLLIDLDPQANNSSYLG-----------KVEEVLP 53
Query: 152 FALEINPEKAREEFRTASQGSGGSGDGMKDLMDSMGLGMLADQLGELKLGELLDTPPPGL 211
LEI +A + A S +D L ++ L L
Sbjct: 54 EGLEIVDAQALQAIAAAIVPS--------RNLD--PLLLIP---SNLSLENFESELIVEG 100
Query: 212 DEAIAISKVMQFVESQQYNMFTRIVFDTAPT-GH-TLRLLSLPDFL 255
+ ++ + Y+ ++ D P G T L D L
Sbjct: 101 KRESRLRAALESLIKLAYDY---VIIDGPPGLGELTANALVAADIL 143
>gnl|CDD|224113 COG1192, Soj, ATPases involved in chromosome partitioning [Cell
division and chromosome partitioning].
Length = 259
Score = 46.0 bits (109), Expect = 1e-05
Identities = 17/50 (34%), Positives = 23/50 (46%), Gaps = 1/50 (2%)
Query: 94 KGGVGKTSCAASLAVKFA-NHGHPTIVISTDPAHSLSDSFAQDLSGGTLV 142
KGGVGKT+ A +LA A G ++I DP SL+ +
Sbjct: 11 KGGVGKTTTAVNLAAALAKRGGKKVLLIDLDPQGSLTSWLGLRPDLEGDL 60
>gnl|CDD|222854 PHA02518, PHA02518, ParA-like protein; Provisional.
Length = 211
Score = 43.7 bits (103), Expect = 5e-05
Identities = 19/51 (37%), Positives = 26/51 (50%)
Query: 94 KGGVGKTSCAASLAVKFANHGHPTIVISTDPAHSLSDSFAQDLSGGTLVPV 144
KGG GKT+ A +LA GH +++ DP S +D G L+PV
Sbjct: 9 KGGAGKTTVATNLASWLHADGHKVLLVDLDPQGSSTDWAEAREEGEPLIPV 59
>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 = 40.6 bits (96), Expect = 2e-04
Identities = 14/32 (43%), Positives = 21/32 (65%)
Query: 92 GGKGGVGKTSCAASLAVKFANHGHPTIVISTD 123
GKGGVGKT+ +A+LA+ A G +++ D
Sbjct: 6 SGKGGVGKTNISANLALALAKLGKRVLLLDAD 37
>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 = 40.3 bits (95), Expect = 6e-04
Identities = 14/36 (38%), Positives = 20/36 (55%)
Query: 90 MLGGKGGVGKTSCAASLAVKFANHGHPTIVISTDPA 125
+ GKGGVGKT+ A+L A G+ ++I D
Sbjct: 4 VTSGKGGVGKTTTTANLGTALAQLGYKVVLIDADLG 39
Score = 34.9 bits (81), Expect = 0.034
Identities = 19/72 (26%), Positives = 34/72 (47%), Gaps = 8/72 (11%)
Query: 313 ATEFVIVTIPTVMAISESSRLHASLRKECIPVQRLIVNQVLPPSASDCKFCAMKRKDQMR 372
A E ++VT P + ++ ++ R+ L I V +IVN+V P ++ D +
Sbjct: 85 ADEALLVTTPEISSLRDADRVKGLLEALGIKVVGVIVNRVRPD--------MVEGGDMVE 136
Query: 373 VLETIMSDPQLA 384
+E I+ P L
Sbjct: 137 DIEEILGVPLLG 148
>gnl|CDD|226166 COG3640, CooC, CO dehydrogenase maturation factor [Cell division
and chromosome partitioning].
Length = 255
Score = 39.9 bits (94), Expect = 0.001
Identities = 17/50 (34%), Positives = 27/50 (54%), Gaps = 1/50 (2%)
Query: 93 GKGGVGKTSCAASLAVK-FANHGHPTIVISTDPAHSLSDSFAQDLSGGTL 141
GKGGVGKT+ AA L + + G+ +V+ DP +L ++ + L
Sbjct: 7 GKGGVGKTTIAALLLKRLLSKGGYNVLVVDADPDSNLPEALGVEEPMKYL 56
>gnl|CDD|184370 PRK13886, PRK13886, conjugal transfer protein TraL; Provisional.
Length = 241
Score = 38.9 bits (91), Expect = 0.002
Identities = 18/40 (45%), Positives = 26/40 (65%)
Query: 88 HYMLGGKGGVGKTSCAASLAVKFANHGHPTIVISTDPAHS 127
H +L GKGGVGK+ AA++A A+ G + I TDP ++
Sbjct: 5 HMVLQGKGGVGKSFIAATIAQYKASKGQKPLCIDTDPVNA 44
>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 = 37.8 bits (89), Expect = 0.003
Identities = 12/23 (52%), Positives = 17/23 (73%)
Query: 93 GKGGVGKTSCAASLAVKFANHGH 115
GKGGVGK++ A +LA+ A G+
Sbjct: 7 GKGGVGKSTVAVNLALALAKLGY 29
>gnl|CDD|224071 COG1149, COG1149, MinD superfamily P-loop ATPase containing an
inserted ferredoxin domain [Energy production and
conversion].
Length = 284
Score = 38.1 bits (89), Expect = 0.006
Identities = 12/22 (54%), Positives = 15/22 (68%)
Query: 91 LGGKGGVGKTSCAASLAVKFAN 112
GKGG GKT+ AA+LAV +
Sbjct: 7 ASGKGGTGKTTVAANLAVLLGD 28
>gnl|CDD|225447 COG2894, MinD, Septum formation inhibitor-activating ATPase [Cell
division and chromosome partitioning].
Length = 272
Score = 38.0 bits (89), Expect = 0.006
Identities = 13/31 (41%), Positives = 18/31 (58%)
Query: 93 GKGGVGKTSCAASLAVKFANHGHPTIVISTD 123
GKGGVGKT+ A++ A G ++I D
Sbjct: 10 GKGGVGKTTTTANIGTALAQLGKKVVLIDFD 40
>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 = 37.8 bits (88), Expect = 0.007
Identities = 13/34 (38%), Positives = 18/34 (52%)
Query: 90 MLGGKGGVGKTSCAASLAVKFANHGHPTIVISTD 123
+ GKGG GKT+ A+L V A G + + D
Sbjct: 5 IASGKGGTGKTTITANLGVALAKLGKKVLALDAD 38
Score = 27.8 bits (62), Expect = 9.1
Identities = 8/40 (20%), Positives = 21/40 (52%)
Query: 313 ATEFVIVTIPTVMAISESSRLHASLRKECIPVQRLIVNQV 352
A E ++V P + +I+++ + K + +++N+V
Sbjct: 131 ADELLLVVNPEISSITDALKTKIVAEKLGTAILGVVLNRV 170
>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 = 37.5 bits (87), Expect = 0.008
Identities = 21/70 (30%), Positives = 38/70 (54%), Gaps = 8/70 (11%)
Query: 93 GKGGVGKTSCAASLAVKFANHGHPTIVISTDPAHSLSDSFAQDLSGGTLVP--VEGVDSP 150
GKGG+GK++ +++L+V FA G + I DP H + + G L+P ++ + +
Sbjct: 7 GKGGIGKSTTSSNLSVAFAKLGKRVLQIGCDPKHDSTFTLT-----GRLIPTVIDVLQAV 61
Query: 151 LFALE-INPE 159
+ E + PE
Sbjct: 62 NYHYEDVRPE 71
>gnl|CDD|182756 PRK10818, PRK10818, cell division inhibitor MinD; Provisional.
Length = 270
Score = 37.2 bits (86), Expect = 0.009
Identities = 16/31 (51%), Positives = 21/31 (67%)
Query: 93 GKGGVGKTSCAASLAVKFANHGHPTIVISTD 123
GKGGVGKT+ +A++A A G T+VI D
Sbjct: 10 GKGGVGKTTSSAAIATGLAQKGKKTVVIDFD 40
>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 = 36.5 bits (85), Expect = 0.010
Identities = 11/23 (47%), Positives = 14/23 (60%)
Query: 91 LGGKGGVGKTSCAASLAVKFANH 113
+ GKGG GKT+ A+LA N
Sbjct: 5 ISGKGGTGKTTVTAALAALLKNV 27
>gnl|CDD|234215 TIGR03453, partition_RepA, plasmid partitioning protein RepA.
Members of this family are the RepA (or ParA) protein
involved in replicon partitioning. All known examples
occur in bacterial species with two or more replicons,
on a plasmid or the smaller chromosome. Note that an
apparent exception may be seen as a pseudomolecule from
assembly of an incompletely sequenced genome. Members of
this family belong to a larger family that also includes
the enzyme cobyrinic acid a,c-diamide synthase, but
assignment of that name to members of this family would
be in error [Mobile and extrachromosomal element
functions, Plasmid functions].
Length = 387
Score = 36.5 bits (85), Expect = 0.019
Identities = 18/36 (50%), Positives = 21/36 (58%)
Query: 94 KGGVGKTSCAASLAVKFANHGHPTIVISTDPAHSLS 129
KGG GKT+ AA LA A G+ + I DP SLS
Sbjct: 113 KGGSGKTTTAAHLAQYLALRGYRVLAIDLDPQASLS 148
>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 = 35.8 bits (83), Expect = 0.026
Identities = 14/31 (45%), Positives = 18/31 (58%)
Query: 93 GKGGVGKTSCAASLAVKFANHGHPTIVISTD 123
GKGGVGKT+ A+L A G ++I D
Sbjct: 9 GKGGVGKTTTTANLGTALARLGKKVVLIDAD 39
Score = 29.6 bits (67), Expect = 3.0
Identities = 15/42 (35%), Positives = 24/42 (57%)
Query: 313 ATEFVIVTIPTVMAISESSRLHASLRKECIPVQRLIVNQVLP 354
A E ++VT P V A+ ++ R+ L + I LIVN++ P
Sbjct: 134 ADEAIVVTTPEVSAVRDADRVIGLLEAKGIEKIHLIVNRLRP 175
>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 = 35.4 bits (82), Expect = 0.038
Identities = 14/34 (41%), Positives = 22/34 (64%)
Query: 93 GKGGVGKTSCAASLAVKFANHGHPTIVISTDPAH 126
GKGG+GK++ +++L+V A G + I DP H
Sbjct: 7 GKGGIGKSTTSSNLSVALAKRGKKVLQIGCDPKH 40
>gnl|CDD|183904 PRK13231, PRK13231, nitrogenase reductase-like protein; Reviewed.
Length = 264
Score = 35.2 bits (81), Expect = 0.041
Identities = 13/32 (40%), Positives = 22/32 (68%), Gaps = 1/32 (3%)
Query: 93 GKGGVGKTSCAASLAVKFANHGHPTIVISTDP 124
GKGG+GK++ +++A ++N H +VI DP
Sbjct: 9 GKGGIGKSTTVSNMAAAYSND-HRVLVIGCDP 39
>gnl|CDD|183903 PRK13230, PRK13230, nitrogenase reductase-like protein; Reviewed.
Length = 279
Score = 35.1 bits (81), Expect = 0.042
Identities = 12/34 (35%), Positives = 19/34 (55%)
Query: 93 GKGGVGKTSCAASLAVKFANHGHPTIVISTDPAH 126
GKGG+GK++ ++A A G +V+ DP
Sbjct: 8 GKGGIGKSTTVCNIAAALAESGKKVLVVGCDPKA 41
>gnl|CDD|237293 PRK13185, chlL, protochlorophyllide reductase iron-sulfur
ATP-binding protein; Provisional.
Length = 270
Score = 34.6 bits (80), Expect = 0.068
Identities = 14/34 (41%), Positives = 22/34 (64%)
Query: 93 GKGGVGKTSCAASLAVKFANHGHPTIVISTDPAH 126
GKGG+GK++ +++L+ FA G + I DP H
Sbjct: 9 GKGGIGKSTTSSNLSAAFAKLGKKVLQIGCDPKH 42
>gnl|CDD|234363 TIGR03815, CpaE_hom_Actino, helicase/secretion neighborhood
CpaE-like protein. Members of this protein family
belong to the MinD/ParA family of P-loop NTPases, and in
particular show homology to the CpaE family of pilus
assembly proteins (see PMID:12370432). Nearly all
members are found, not only in a gene context consistent
with pilus biogenesis or a pilus-like secretion
apparatus, but also near a DEAD/DEAH-box helicase,
suggesting an involvement in DNA transfer activity. The
model describes a clade restricted to the
Actinobacteria.
Length = 322
Score = 34.6 bits (80), Expect = 0.076
Identities = 15/34 (44%), Positives = 24/34 (70%)
Query: 91 LGGKGGVGKTSCAASLAVKFANHGHPTIVISTDP 124
+GG+GG G ++ AA+LA+ A HG T+++ DP
Sbjct: 99 IGGRGGAGASTLAAALALAAARHGLRTLLVDADP 132
>gnl|CDD|224267 COG1348, NifH, Nitrogenase subunit NifH (ATPase) [Inorganic ion
transport and metabolism].
Length = 278
Score = 34.2 bits (79), Expect = 0.092
Identities = 18/51 (35%), Positives = 28/51 (54%), Gaps = 4/51 (7%)
Query: 93 GKGGVGKTSCAASLAVKFANHGHPTIVISTDPAHSLSDSFAQDLSGGTLVP 143
GKGG+GK++ + +LA A G +++ DP DS + L GG +P
Sbjct: 8 GKGGIGKSTTSQNLAAALAELGKKVLIVGCDPKA---DS-TRLLLGGKAIP 54
>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 = 33.7 bits (78), Expect = 0.10
Identities = 13/39 (33%), Positives = 21/39 (53%), Gaps = 3/39 (7%)
Query: 93 GKGGVGKTSCAASLAVKFANHGHPTIVISTDPAHSLSDS 131
GKGG+GK++ + +L+ A G + + DP DS
Sbjct: 7 GKGGIGKSTTSQNLSAALAEMGKKVLQVGCDPKA---DS 42
>gnl|CDD|223543 COG0467, RAD55, RecA-superfamily ATPases implicated in signal
transduction [Signal transduction mechanisms].
Length = 260
Score = 34.0 bits (78), Expect = 0.10
Identities = 15/52 (28%), Positives = 25/52 (48%), Gaps = 2/52 (3%)
Query: 74 VAGFDEMVAGT--QRKHYMLGGKGGVGKTSCAASLAVKFANHGHPTIVISTD 123
+ G DE++ G + ++ G G GKT A + A G P + +ST+
Sbjct: 9 IPGLDEILGGGLPRGSVVLITGPPGTGKTIFALQFLYEGAREGEPVLYVSTE 60
>gnl|CDD|181896 PRK09482, PRK09482, flap endonuclease-like protein; Provisional.
Length = 256
Score = 33.7 bits (78), Expect = 0.12
Identities = 11/21 (52%), Positives = 14/21 (66%)
Query: 103 AASLAVKFANHGHPTIVISTD 123
A+LAVK A GH ++STD
Sbjct: 112 IATLAVKVAQAGHQATIVSTD 132
>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 = 32.6 bits (75), Expect = 0.13
Identities = 13/51 (25%), Positives = 18/51 (35%), Gaps = 1/51 (1%)
Query: 91 LGGKGGVGKTSCAASLAVKFANHGHPTIVISTDPAHSLSDSFAQDLSGGTL 141
GG GKT+ A +LA A G + + + F L L
Sbjct: 6 YSPVGGEGKTTFALNLAQSLAEEGPKVLYLDLEEYSGDLALF-LGLEPKGL 55
>gnl|CDD|223563 COG0489, Mrp, ATPases involved in chromosome partitioning [Cell
division and chromosome partitioning].
Length = 265
Score = 32.4 bits (74), Expect = 0.37
Identities = 13/31 (41%), Positives = 19/31 (61%)
Query: 93 GKGGVGKTSCAASLAVKFANHGHPTIVISTD 123
GKGGVGK++ A +LA A G +++ D
Sbjct: 65 GKGGVGKSTVAVNLAAALAQLGKRVLLLDAD 95
>gnl|CDD|215925 pfam00448, SRP54, SRP54-type protein, GTPase domain. This family
includes relatives of the G-domain of the SRP54 family
of proteins.
Length = 196
Score = 31.7 bits (73), Expect = 0.38
Identities = 11/35 (31%), Positives = 17/35 (48%)
Query: 89 YMLGGKGGVGKTSCAASLAVKFANHGHPTIVISTD 123
+L G G GKT+ A LA G ++++ D
Sbjct: 4 ILLVGLQGSGKTTTIAKLAAYLKKQGKKVLLVAAD 38
>gnl|CDD|214385 CHL00175, minD, septum-site determining protein; Validated.
Length = 281
Score = 32.4 bits (74), Expect = 0.38
Identities = 17/46 (36%), Positives = 23/46 (50%)
Query: 78 DEMVAGTQRKHYMLGGKGGVGKTSCAASLAVKFANHGHPTIVISTD 123
E A R + GKGGVGKT+ A+L + A G+ +I D
Sbjct: 8 KEKSATMSRIIVITSGKGGVGKTTTTANLGMSIARLGYRVALIDAD 53
Score = 30.1 bits (68), Expect = 2.2
Identities = 18/61 (29%), Positives = 29/61 (47%), Gaps = 8/61 (13%)
Query: 313 ATEFVIVTIPTVMAISESSRLHASLRKECIPVQRLIVNQVLPPSASDCKFCAMKRKDQMR 372
A E ++VT P + AI ++ R+ L I +L+VN+V P ++ D M
Sbjct: 149 AQEAIVVTTPEITAIRDADRVAGLLEANGIYNVKLLVNRVRPD--------MIQANDMMS 200
Query: 373 V 373
V
Sbjct: 201 V 201
>gnl|CDD|223531 COG0455, flhG, Antiactivator of flagellar biosynthesis FleN, an
ATPase [Cell motility].
Length = 262
Score = 32.2 bits (74), Expect = 0.39
Identities = 19/98 (19%), Positives = 39/98 (39%), Gaps = 3/98 (3%)
Query: 313 ATEFVIVTIPTVMAISESSRL--HASLRKECIPVQRLIVNQVLPPSASDCKFCAMKRK-D 369
+ E VIVT P +I+++ + S + +R+++N+V + +
Sbjct: 135 SDELVIVTTPEPTSITDAYKTIKILSKLGLDLLGRRVVLNRVRSTKEGVDVAALLIQVVK 194
Query: 370 QMRVLETIMSDPQLANLRLVQAPLVDVEIRGVPALKFM 407
Q+ VL+ I DP++ P+V +
Sbjct: 195 QVPVLQVIPFDPEVRRALAEGKPIVLYSPNSKASQAIK 232
Score = 30.7 bits (70), Expect = 1.3
Identities = 11/21 (52%), Positives = 14/21 (66%)
Query: 91 LGGKGGVGKTSCAASLAVKFA 111
+ GKGGVGKT+ A+L A
Sbjct: 8 VSGKGGVGKTTITANLGAALA 28
>gnl|CDD|177011 CHL00072, chlL, photochlorophyllide reductase subunit L.
Length = 290
Score = 32.0 bits (73), Expect = 0.47
Identities = 17/36 (47%), Positives = 21/36 (58%), Gaps = 4/36 (11%)
Query: 93 GKGGVGK--TSCAASLAVKFANHGHPTIVISTDPAH 126
GKGG+GK TSC S+A+ A G + I DP H
Sbjct: 7 GKGGIGKSTTSCNISIAL--ARRGKKVLQIGCDPKH 40
>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 = 31.8 bits (72), Expect = 0.58
Identities = 16/51 (31%), Positives = 23/51 (45%), Gaps = 4/51 (7%)
Query: 93 GKGGVGKTSCAASLAVKFANHGHPTIVISTDPAHSLSDSFAQDLSGGTLVP 143
GKGG GK+ +L+ A G + + DP H + L GG +P
Sbjct: 7 GKGGSGKSFTTTNLSHMMAEMGKRVLQLGCDPKHDSTSL----LFGGISLP 53
>gnl|CDD|139929 PRK13869, PRK13869, plasmid-partitioning protein RepA; Provisional.
Length = 405
Score = 31.6 bits (71), Expect = 0.77
Identities = 16/36 (44%), Positives = 21/36 (58%)
Query: 94 KGGVGKTSCAASLAVKFANHGHPTIVISTDPAHSLS 129
KGG GKT+ +A LA A G+ + + DP SLS
Sbjct: 130 KGGSGKTTTSAHLAQYLALQGYRVLAVDLDPQASLS 165
>gnl|CDD|224466 COG1549, COG1549, Queuine tRNA-ribosyltransferases, contain PUA
domain [Translation, ribosomal structure and
biogenesis].
Length = 519
Score = 31.6 bits (72), Expect = 0.83
Identities = 19/70 (27%), Positives = 32/70 (45%), Gaps = 3/70 (4%)
Query: 280 FGKEKKQQDVASDKVEQLRERMAKVRDLFRDPDATEFVIVTIPTVM---AISESSRLHAS 336
FG ++D+ D VE LRE + +VR R+ E V + T A+ + R +
Sbjct: 138 FGISFDREDLPRDNVEFLREMLERVRRAIRNGTLRELVEKALVTPWLAAALRIADREYGY 197
Query: 337 LRKECIPVQR 346
++ P +R
Sbjct: 198 YEEKIPPFRR 207
>gnl|CDD|227596 COG5271, MDN1, AAA ATPase containing von Willebrand factor type A
(vWA) domain [General function prediction only].
Length = 4600
Score = 31.9 bits (72), Expect = 0.85
Identities = 62/255 (24%), Positives = 86/255 (33%), Gaps = 63/255 (24%)
Query: 87 KHYMLGGKGGVGKTSCAASLAVKFANHGHPTIVISTDPAHSLSDSFAQDLSGGTLVPVEG 146
K +L G GVGKTS +LA K G I I+ L D F DL
Sbjct: 1544 KPILLEGSPGVGKTSLITALARKT---GKKLIRINLSEQTDLCDLFGSDLPVEEGGEFRW 1600
Query: 147 VDSPLFAL----------EIN----------------------PE-----KAREEFRT-A 168
+D+P EIN PE FR A
Sbjct: 1601 MDAPFLHAMRDGGWVLLDEINLASQSVLEGLNACLDHRREAYIPELDKTFDVHPNFRVFA 1660
Query: 169 SQGSGGSGDGMKDLMDSM---GLGMLADQLGELKLGELLDTPPPGLDEAIAISKVMQFVE 225
+Q G G K L S + D L + + + P ++E K+++F+
Sbjct: 1661 AQNPQDQGGGRKGLPKSFLNRFSVVKMDGLTTDDITHIANKMYPQVNEDW-RLKIIKFMS 1719
Query: 226 SQQYNMFTRIVFDTAPT------GHTLRLLSL------------PDFLDASIGKMMKLKK 267
Q N+ I F + + TLR L L DF+D S+ + M+ +
Sbjct: 1720 RLQDNIEKDISFGSFGSPWEFNLRDTLRWLILLNQVGTLEDVDTSDFIDESVVRRMRTVE 1779
Query: 268 KLASTTSAFKSVFGK 282
T FK VFG
Sbjct: 1780 DRVRTCELFKEVFGD 1794
>gnl|CDD|185734 cd08993, GH43_DUF377, Glycosyl hydrolase family 43 containing a
domain of unknown function. This subfamily has
sequences similar to the glycosyl hydrolase family 43
(GH43) and contains uncharacterized proteins. GH43
proteins are inverting enzymes (i.e. they invert the
stereochemistry of the anomeric carbon atom of the
substrate) that have an aspartate as the catalytic
general base, a glutamate as the catalytic general acid
and another aspartate that is responsible for pKa
modulation and orienting the catalytic acid. Many of the
GH43 enzymes display both alpha-L-arabinofuranosidase
and beta-D-xylosidase activity using aryl-glycosides as
substrates. A common structural feature of GH43 enzymes
is a 5-bladed beta-propeller domain that contains the
catalytic acid and catalytic base. A long V-shaped
groove, partially enclosed at one end, forms a single
extended substrate-binding surface across the face of
the propeller.
Length = 268
Score = 31.2 bits (71), Expect = 0.88
Identities = 14/72 (19%), Positives = 23/72 (31%), Gaps = 5/72 (6%)
Query: 35 NYTSLCRIARS-----FEFVSAPLYRIPLKSPFQVRSISTPRETVAGFDEMVAGTQRKHY 89
+ +ARS FE P P + F+ + PR + R +
Sbjct: 22 DGVIRLGLARSRDGLHFEIDPDPPVWPPPEDGFEEGGVEDPRIVKIDDTYYITYAARPNA 81
Query: 90 MLGGKGGVGKTS 101
G + G+ T
Sbjct: 82 PNGTRIGLATTK 93
>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 = 31.2 bits (71), Expect = 0.92
Identities = 11/34 (32%), Positives = 19/34 (55%)
Query: 93 GKGGVGKTSCAASLAVKFANHGHPTIVISTDPAH 126
GKGG+GK++ ++A A G +++ DP
Sbjct: 7 GKGGIGKSTTTQNIAAALAEMGKKVMIVGCDPKA 40
>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 = 31.1 bits (71), Expect = 0.98
Identities = 11/34 (32%), Positives = 19/34 (55%)
Query: 93 GKGGVGKTSCAASLAVKFANHGHPTIVISTDPAH 126
GKGG+GK++ +L+ A G +++ DP
Sbjct: 8 GKGGIGKSTTTQNLSAALAEMGKKVMIVGCDPKA 41
>gnl|CDD|222163 pfam13479, AAA_24, AAA domain. This AAA domain is found in a wide
variety of presumed phage proteins.
Length = 201
Score = 30.3 bits (69), Expect = 1.1
Identities = 15/57 (26%), Positives = 21/57 (36%), Gaps = 13/57 (22%)
Query: 93 GKGGVGKTSCAASLAVKFANHGHPTIVISTDPAHSLSDSFAQDLSGGTLVPVEGVDS 149
G G+GKTS A +L K T+ + D + LS G V +
Sbjct: 10 GPPGIGKTSLAKTLPPK-------TLFLDLD------AGTTKVLSRGDNVDIRSWQD 53
>gnl|CDD|214640 smart00382, AAA, ATPases associated with a variety of cellular
activities. AAA - ATPases associated with a variety of
cellular activities. This profile/alignment only detects
a fraction of this vast family. The poorly conserved
N-terminal helix is missing from the alignment.
Length = 148
Score = 30.0 bits (67), Expect = 1.2
Identities = 17/73 (23%), Positives = 27/73 (36%), Gaps = 1/73 (1%)
Query: 85 QRKHYMLGGKGGVGKTSCAASLAVKFANHGHPTIVISTDPAHS-LSDSFAQDLSGGTLVP 143
+ ++ G G GKT+ A +LA + G I I + + D + GG
Sbjct: 1 PGEVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKAS 60
Query: 144 VEGVDSPLFALEI 156
G AL +
Sbjct: 61 GSGELRLRLALAL 73
>gnl|CDD|223746 COG0674, PorA, Pyruvate:ferredoxin oxidoreductase and related
2-oxoacid:ferredoxin oxidoreductases, alpha subunit
[Energy production and conversion].
Length = 365
Score = 30.7 bits (70), Expect = 1.2
Identities = 26/98 (26%), Positives = 41/98 (41%), Gaps = 9/98 (9%)
Query: 290 ASDKVEQLRERMAKVRDLFRDPDATEFVIVTIPTVMAISESSRLHA---SLRKECIPVQR 346
A K+ +L R + + DA E VIV M S+ S A LR + V
Sbjct: 234 ALRKINELTGREYEPFLYYGYEDA-EIVIVA----MGSSKGSTAEAVVDLLRDKGEKVGL 288
Query: 347 LIVNQVLPPSASDCKFCAMKRKDQMRVLETIMSDPQLA 384
L V + P A + + + + + + VL+ +S LA
Sbjct: 289 LKVRTLRPFPAEEIR-EVLPKTNAVVVLDVEISLGGLA 325
>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 = 30.1 bits (68), Expect = 1.6
Identities = 13/30 (43%), Positives = 21/30 (70%)
Query: 94 KGGVGKTSCAASLAVKFANHGHPTIVISTD 123
K G GK++ +A++AV FA G+ T++I D
Sbjct: 26 KPGEGKSTTSANIAVAFAQAGYKTLLIDGD 55
>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 = 29.6 bits (67), Expect = 1.6
Identities = 14/51 (27%), Positives = 21/51 (41%), Gaps = 8/51 (15%)
Query: 91 LGGKGGVGKTSCAASLAVKFANHGHPTIVISTDPAHSLSDSFAQDLSGGTL 141
+ G G GK++ +L G V++ DP S F SGG +
Sbjct: 4 ITGVPGAGKSTLIDALITALRARGKRVAVLAIDP----SSPF----SGGAI 46
>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 = 30.3 bits (69), Expect = 1.6
Identities = 12/37 (32%), Positives = 17/37 (45%)
Query: 96 GVGKTSCAASLAVKFANHGHPTIVISTDPAHSLSDSF 132
GK++ A LA G+ IVIS + SD +
Sbjct: 9 SSGKSTRAKELAKYLEEKGYDVIVISDESLGIESDDY 45
>gnl|CDD|189029 cd09859, PIN_53EXO, PIN domain of the 5'-3' exonuclease of Taq DNA
polymerase I and homologs. The 5'-3' exonuclease
(53EXO) PIN (PilT N terminus) domain of multi-domain DNA
polymerase I and single domain protein homologs are
included in this family. Taq contains a polymerase
domain for synthesizing a new DNA strand and a 53EXO PIN
domain for cleaving RNA primers or damaged DNA strands.
Taq's 53EXO PIN domain recognizes and
endonucleolytically cleaves a structure-specific DNA
substrate that has a bifurcated downstream duplex and an
upstream template-primer duplex that overlaps the
downstream duplex by 1 bp. The 53EXO PIN domain cleaves
the unpaired 5'-arm of the overlap flap DNA substrate.
5'-3' exonucleases are members of the
structure-specific, 5' nuclease family that catalyzes
hydrolysis of DNA duplex-containing nucleic acid
structures during DNA replication, repair, and
recombination. These nucleases contain a PIN domain with
a helical arch/clamp region (I domain) of variable
length (approximately 16 residues in 53EXO PIN domains)
and a H3TH (helix-3-turn-helix) domain, an atypical
helix-hairpin-helix-2-like region. Both the H3TH domain
(not included here) and the helical arch/clamp region
are involved in DNA/RNA binding. The active site
includes a set of conserved acidic residues that are
essential for binding divalent metal ions required for
nuclease activity.
Length = 174
Score = 29.7 bits (68), Expect = 1.7
Identities = 6/20 (30%), Positives = 11/20 (55%)
Query: 104 ASLAVKFANHGHPTIVISTD 123
+LA K G+ +++S D
Sbjct: 112 GTLAKKAEEEGYEVVIVSGD 131
>gnl|CDD|222165 pfam13481, AAA_25, AAA domain. This AAA domain is found in a wide
variety of presumed DNA repair proteins.
Length = 154
Score = 29.6 bits (67), Expect = 1.8
Identities = 11/27 (40%), Positives = 14/27 (51%), Gaps = 1/27 (3%)
Query: 90 MLGGKGGVGKTSCAASLAVKFANHGHP 116
+L G G GK++ A LA A G P
Sbjct: 37 LLAGAPGTGKSTLALDLAAAVA-TGRP 62
>gnl|CDD|201032 pfam00142, Fer4_NifH, 4Fe-4S iron sulfur cluster binding proteins,
NifH/frxC family.
Length = 272
Score = 30.0 bits (68), Expect = 1.8
Identities = 10/34 (29%), Positives = 18/34 (52%)
Query: 93 GKGGVGKTSCAASLAVKFANHGHPTIVISTDPAH 126
GKGG+GK++ + + A G +++ DP
Sbjct: 7 GKGGIGKSTTTQNTSAALAEMGKKVLIVGCDPKA 40
>gnl|CDD|233582 TIGR01812, sdhA_frdA_Gneg, succinate dehydrogenase or fumarate
reductase, flavoprotein
subunitGram-negative/mitochondrial subgroup. This model
represents the succinate dehydrogenase flavoprotein
subunit as found in Gram-negative bacteria,
mitochondria, and some Archaea. Mitochondrial forms
interact with ubiquinone and are designated EC 1.3.5.1,
but can be degraded to 1.3.99.1. Some isozymes in E.
coli and other species run primarily in the opposite
direction and are designated fumarate reductase [Energy
metabolism, Aerobic, Energy metabolism, Anaerobic,
Energy metabolism, TCA cycle].
Length = 541
Score = 30.4 bits (69), Expect = 1.9
Identities = 14/42 (33%), Positives = 24/42 (57%), Gaps = 1/42 (2%)
Query: 264 KLKKKLASTTSAFKSVFGKEKKQQDVASDKVEQLRERMAKVR 305
K++++L T +F E+ + A D++E+LRER VR
Sbjct: 413 KIREELGDTMDDNVGIFRTEELLKK-AVDEIEELRERYKNVR 453
>gnl|CDD|132780 cd06870, PX_CISK, The phosphoinositide binding Phox Homology Domain
of Cytokine-Independent Survival Kinase. The PX domain
is a phosphoinositide (PI) binding module present in
many proteins with diverse functions.
Cytokine-independent survival kinase (CISK), also called
Serum- and Glucocorticoid-induced Kinase 3 (SGK3), plays
a role in cell growth and survival. It is expressed in
most tissues and is most abundant in the embryo and
adult heart and spleen. It was originally discovered in
a screen for antiapoptotic genes. It phosphorylates and
inhibits the proapoptotic proteins, Bad and FKHRL1.
CISK/SGK3 also regulates many transporters, ion
channels, and receptors. It plays a critical role in
hair follicle morphogenesis and hair cycling. N-terminal
to a catalytic kinase domain, CISK contains a PX domain
which binds highly phosphorylated PIs, directs membrane
localization, and regulates the enzyme's activity.
Length = 109
Score = 28.9 bits (65), Expect = 1.9
Identities = 20/70 (28%), Positives = 33/70 (47%), Gaps = 12/70 (17%)
Query: 328 SESSRLHASLRKEC------IPVQRLIVNQVLPPSASDCKFCAMKRKDQMRVLETIMSDP 381
+E +L+ SL+K+ IP +RL N P F +R ++ ++SDP
Sbjct: 41 AEFDKLYESLKKQFPASNLKIPGKRLFGNNFDP------DFIKQRRAGLDEFIQRLVSDP 94
Query: 382 QLANLRLVQA 391
+L N V+A
Sbjct: 95 KLLNHPDVRA 104
>gnl|CDD|227200 COG4863, COG4863, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 439
Score = 30.2 bits (68), Expect = 1.9
Identities = 18/86 (20%), Positives = 29/86 (33%), Gaps = 9/86 (10%)
Query: 225 ESQQYNMFTRIVFDTAPT-GHTLRLLSLPD--------FLDASIGKMMKLKKKLASTTSA 275
ES +Y+ F RIV D G+ L D + + K S +A
Sbjct: 140 ESLEYSSFNRIVIDFNEDKGNKKIYLVSYDKQLILEVTVESKNYDNIEADLKDRQSYMAA 199
Query: 276 FKSVFGKEKKQQDVASDKVEQLRERM 301
F V +K+ + S + +
Sbjct: 200 FSLVSIGSRKEFFLPSKPTKLDTKEY 225
>gnl|CDD|234339 TIGR03743, SXT_TraD, conjugative coupling factor TraD, SXT/TOL
subfamily. Members of this protein family are the
putative conjugative coupling factor, TraD (or TraG),
rather distantly related to the well-characterized TraD
of the F plasmid. Members are associated with
conjugative-transposon-like mobile genetic elements of
the class that includes SXT, an antibiotic resistance
transfer element in some Vibrio cholerae strains [Mobile
and extrachromosomal element functions, Other].
Length = 634
Score = 30.3 bits (69), Expect = 2.0
Identities = 15/37 (40%), Positives = 18/37 (48%), Gaps = 2/37 (5%)
Query: 88 HYMLGGKGGVGKTSCAASLAVKFANHGHPTIVISTDP 124
H ++ G GVGKT A L + G IVI DP
Sbjct: 178 HTLVLGTTGVGKTRLAELLITQDIRRGDVVIVI--DP 212
>gnl|CDD|224401 COG1484, DnaC, DNA replication protein [DNA replication,
recombination, and repair].
Length = 254
Score = 30.1 bits (68), Expect = 2.1
Identities = 9/30 (30%), Positives = 14/30 (46%)
Query: 93 GKGGVGKTSCAASLAVKFANHGHPTIVIST 122
G GVGKT A ++ + G + I+
Sbjct: 112 GPPGVGKTHLAIAIGNELLKAGISVLFITA 141
>gnl|CDD|234625 PRK00090, bioD, dithiobiotin synthetase; Reviewed.
Length = 222
Score = 29.8 bits (68), Expect = 2.1
Identities = 26/105 (24%), Positives = 35/105 (33%), Gaps = 26/105 (24%)
Query: 96 GVGKTSCAASLAVKFANHGHPTIVI-----STDPAHSLSDSFA-QDLSGGTLVPVEGVD- 148
VGKT A+LA G+ + D+ A Q LSG L +
Sbjct: 10 DVGKTVVTAALAQALREAGYSVAGYKPVQSGCEETDRNGDALALQRLSGLPLDYEDVNPY 69
Query: 149 ------SPLFA-----LEINPEKAREEFRTASQ--------GSGG 174
SP A + I+ EK R +Q G+GG
Sbjct: 70 RFEEPLSPHLAAALEGVAIDLEKISAALRRLAQQYDLVLVEGAGG 114
>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 = 2.2
Identities = 16/45 (35%), Positives = 20/45 (44%)
Query: 92 GGKGGVGKTSCAASLAVKFANHGHPTIVISTDPAHSLSDSFAQDL 136
G +GGVG TS A+L G +VI P + L F D
Sbjct: 8 GVRGGVGTTSLTAALGWALQQLGESVLVIDASPDNLLRLHFNVDF 52
>gnl|CDD|149804 pfam08859, DGC, DGC domain. This domain appears to be a zinc
binding domain from the conservation of four potential
chelating cysteines. The domain is named after a
conserved central motif. The function of this domain is
unknown.
Length = 110
Score = 28.8 bits (65), Expect = 2.2
Identities = 12/33 (36%), Positives = 15/33 (45%), Gaps = 6/33 (18%)
Query: 94 KGGVGKTSCAASLA------VKFANHGHPTIVI 120
+ G G+ SC A + VK A G P I I
Sbjct: 25 REGGGEMSCLAGVGGGVEGLVKLARSGRPIIAI 57
>gnl|CDD|183270 PRK11670, PRK11670, antiporter inner membrane protein; Provisional.
Length = 369
Score = 30.0 bits (68), Expect = 2.2
Identities = 13/22 (59%), Positives = 16/22 (72%)
Query: 93 GKGGVGKTSCAASLAVKFANHG 114
GKGGVGK+S A +LA+ A G
Sbjct: 115 GKGGVGKSSTAVNLALALAAEG 136
>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 = 29.4 bits (67), Expect = 2.4
Identities = 13/34 (38%), Positives = 20/34 (58%)
Query: 90 MLGGKGGVGKTSCAASLAVKFANHGHPTIVISTD 123
+L G GVGKT+ AA LA+ G ++++ D
Sbjct: 4 LLVGLQGVGKTTTAAKLALYLKKKGKKVLLVAAD 37
>gnl|CDD|182204 PRK10037, PRK10037, cell division protein; Provisional.
Length = 250
Score = 29.8 bits (67), Expect = 2.4
Identities = 18/44 (40%), Positives = 22/44 (50%)
Query: 92 GGKGGVGKTSCAASLAVKFANHGHPTIVISTDPAHSLSDSFAQD 135
G +GGVG TS A+LA G +VI P + L SF D
Sbjct: 8 GVRGGVGTTSITAALAWSLQMLGENVLVIDACPDNLLRLSFNVD 51
>gnl|CDD|236482 PRK09361, radB, DNA repair and recombination protein RadB;
Provisional.
Length = 225
Score = 29.4 bits (67), Expect = 2.5
Identities = 17/43 (39%), Positives = 22/43 (51%), Gaps = 4/43 (9%)
Query: 93 GKGGVGKTSCAASLAVKFANHGHPTIVISTDPAHSLS-DSFAQ 134
G G GKT+ LAV+ A +G I I T+ LS + F Q
Sbjct: 30 GPPGSGKTNICLQLAVEAAKNGKKVIYIDTE---GLSPERFKQ 69
>gnl|CDD|205018 pfam12683, DUF3798, Protein of unknown function (DUF3798). This
family of proteins is functionally uncharacterized. This
family of proteins is found in bacteria. Proteins in
this family are typically between 247 and 417 amino
acids in length. Most of the proteins in this family
have an N-terminal lipoprotein attachment site. These
proteins have distant similarity to periplasmic ligand
binding families such as pfam02608, which suggests that
this family have a similar role.
Length = 275
Score = 29.6 bits (67), Expect = 2.5
Identities = 22/92 (23%), Positives = 33/92 (35%), Gaps = 29/92 (31%)
Query: 272 TTSAFKSVFGKEKKQQ------DVASDKVEQLRERMAKVRDLFRDPD------------- 312
T AF+ + KEK+ D E M+KV DL +PD
Sbjct: 75 TLPAFQKI--KEKRPDILLIAAPPHEDPEE-----MSKVADLVLNPDEESRGKAIVEAAH 127
Query: 313 ---ATEFVIVTIPTVMAISESSRLHASLRKEC 341
A FV + P ++ SR +++ C
Sbjct: 128 EMGAKTFVHYSFPRHLSYETLSRRRDDMKEAC 159
>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 = 29.7 bits (67), Expect = 2.5
Identities = 19/71 (26%), Positives = 32/71 (45%), Gaps = 8/71 (11%)
Query: 88 HYMLGGKGGVGKTSCAASLAVKFANHGHPTIVISTDPAHSLSDSFAQDLSGGTLVPVEGV 147
+ ++ G G GK++ LA++ G IVI DP S A+ L GG ++ +
Sbjct: 3 NMLIVGPSGSGKSTLLKLLALRLLARGGRVIVI--DPKGEYSG-LARAL-GGEVIDLGPG 58
Query: 148 DSPLFALEINP 158
+ +NP
Sbjct: 59 SG----ISLNP 65
>gnl|CDD|234232 TIGR03499, FlhF, flagellar biosynthetic protein FlhF. [Cellular
processes, Chemotaxis and motility].
Length = 283
Score = 29.6 bits (67), Expect = 2.6
Identities = 16/44 (36%), Positives = 22/44 (50%), Gaps = 2/44 (4%)
Query: 82 AGTQRKHYMLGGKGGVGKTSCAASLAVKFA-NHGHPTI-VISTD 123
+ L G GVGKT+ A LA +F HG + +I+TD
Sbjct: 191 ILERGGVIALVGPTGVGKTTTLAKLAARFVLEHGKKKVALITTD 234
>gnl|CDD|238540 cd01120, RecA-like_NTPases, RecA-like NTPases. This family includes
the NTP binding domain of F1 and V1 H+ATPases, DnaB and
related helicases as well as bacterial RecA and related
eukaryotic and archaeal recombinases. This group also
includes bacterial conjugation proteins and related DNA
transfer proteins involved in type II and type IV
secretion.
Length = 165
Score = 29.0 bits (65), Expect = 3.0
Identities = 10/31 (32%), Positives = 15/31 (48%)
Query: 93 GKGGVGKTSCAASLAVKFANHGHPTIVISTD 123
G G GKT+ A LA+ A G + + +
Sbjct: 6 GPTGSGKTTLALQLALNIATKGGKVVYVDIE 36
>gnl|CDD|214682 smart00475, 53EXOc, 5'-3' exonuclease.
Length = 259
Score = 29.5 bits (67), Expect = 3.1
Identities = 7/22 (31%), Positives = 11/22 (50%)
Query: 102 CAASLAVKFANHGHPTIVISTD 123
A+LA K G+ ++S D
Sbjct: 111 VIATLAKKAEAEGYEVRIVSGD 132
>gnl|CDD|110677 pfam01695, IstB_IS21, IstB-like ATP binding protein. This protein
contains an ATP/GTP binding P-loop motif. It is found
associated with IS21 family insertion sequences. The
function of this protein is unknown, but it may perform
a transposase function.
Length = 178
Score = 29.2 bits (66), Expect = 3.1
Identities = 12/40 (30%), Positives = 19/40 (47%)
Query: 84 TQRKHYMLGGKGGVGKTSCAASLAVKFANHGHPTIVISTD 123
Q ++ +L G GVGKT A +L + G+ + T
Sbjct: 45 EQAENLLLLGPPGVGKTHLACALGHQACRAGYSVLFTRTP 84
>gnl|CDD|223615 COG0541, Ffh, Signal recognition particle GTPase [Intracellular
trafficking and secretion].
Length = 451
Score = 29.8 bits (68), Expect = 3.2
Identities = 10/34 (29%), Positives = 17/34 (50%)
Query: 90 MLGGKGGVGKTSCAASLAVKFANHGHPTIVISTD 123
++ G G GKT+ A LA G ++++ D
Sbjct: 104 LMVGLQGSGKTTTAGKLAKYLKKKGKKVLLVAAD 137
>gnl|CDD|176651 cd06139, DNA_polA_I_Ecoli_like_exo, DEDDy 3'-5' exonuclease domain
of Escherichia coli DNA polymerase I and similar
bacterial family-A DNA polymerases. Escherichia
coli-like Polymerase I (Pol I), a subgroup of family-A
DNA polymerases, contains a DEDDy-type DnaQ-like 3'-5'
exonuclease domain in the same polypeptide chain as the
polymerase domain. The exonuclease domain contains three
conserved sequence motifs termed ExoI, ExoII and ExoIII,
with a specific YX(3)D pattern at ExoIII. These motifs
are clustered around the active site and contain four
conserved acidic residues that serve as ligands for the
two metal ions required for catalysis. The 3'-5'
exonuclease domain of DNA polymerases has a fundamental
role in reducing polymerase errors and is involved in
proofreading activity. E. coli DNA Pol I is involved in
genome replication but is not the main replicating
enzyme. It is also implicated in DNA repair.
Length = 193
Score = 28.6 bits (65), Expect = 3.8
Identities = 17/68 (25%), Positives = 27/68 (39%), Gaps = 12/68 (17%)
Query: 235 IVFDTAPTGHTLRLLSLPDFLDASIGK--MMKL-KKKLASTTSAFKSVFGKEKKQQDVAS 291
FDT L S L+ + + L ++ L T +F+ + GK KKQ
Sbjct: 92 PAFDTM-------LASY--LLNPGRRRHGLDDLAERYLGHKTISFEDLVGKGKKQITFDQ 142
Query: 292 DKVEQLRE 299
+E+ E
Sbjct: 143 VPLEKAAE 150
>gnl|CDD|223820 COG0749, PolA, DNA polymerase I - 3'-5' exonuclease and polymerase
domains [DNA replication, recombination, and repair].
Length = 593
Score = 29.2 bits (66), Expect = 4.4
Identities = 15/44 (34%), Positives = 21/44 (47%)
Query: 265 LKKKLASTTSAFKSVFGKEKKQQDVASDKVEQLRERMAKVRDLF 308
K+ L T F+ + GK KKQ A K+E+ E A+ D
Sbjct: 126 AKRYLGLETITFEDIAGKGKKQLTFADVKLEKATEYAAEDADAT 169
>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 = 28.9 bits (65), Expect = 4.5
Identities = 11/31 (35%), Positives = 14/31 (45%)
Query: 94 KGGVGKTSCAASLAVKFANHGHPTIVISTDP 124
KGG GK++ A +AV G I D
Sbjct: 9 KGGSGKSTTAVHVAVALLYLGARVATIDLDL 39
>gnl|CDD|224337 COG1419, FlhF, Flagellar GTP-binding protein [Cell motility and
secretion].
Length = 407
Score = 29.2 bits (66), Expect = 4.5
Identities = 14/41 (34%), Positives = 22/41 (53%), Gaps = 2/41 (4%)
Query: 85 QRKHYMLGGKGGVGKTSCAASLAVKFAN-HGHPTI-VISTD 123
Q++ L G GVGKT+ A LA ++ + +I+TD
Sbjct: 202 QKRVIALVGPTGVGKTTTLAKLAARYVMLKKKKKVAIITTD 242
>gnl|CDD|214940 smart00962, SRP54, SRP54-type protein, GTPase domain. This entry
represents the GTPase domain of the 54 kDa SRP54
component, a GTP-binding protein that interacts with the
signal sequence when it emerges from the ribosome. SRP54
of the signal recognition particle has a three-domain
structure: an N-terminal helical bundle domain, a GTPase
domain, and the M-domain that binds the 7s RNA and also
binds the signal sequence. The extreme C-terminal region
is glycine-rich and lower in complexity and poorly
conserved between species. The GTPase domain is
evolutionary related to P-loop NTPase domains found in a
variety of other proteins.
Length = 197
Score = 28.5 bits (65), Expect = 4.6
Identities = 11/45 (24%), Positives = 19/45 (42%), Gaps = 11/45 (24%)
Query: 80 MVAGTQRKHYMLGGKGGVGKTSCAASLAVKFA-NHGHPTIVISTD 123
++ G GVGKT+ A LA + G ++++ D
Sbjct: 5 LLVGPN----------GVGKTTTIAKLAARLKLKGGKKVLLVAAD 39
>gnl|CDD|238990 cd02033, BchX, Chlorophyllide reductase converts chlorophylls into
bacteriochlorophylls by reducing the chlorin B-ring.
This family contains the X subunit of this three-subunit
enzyme. Sequence and structure similarity between bchX,
protochlorophyllide reductase L subunit (bchL and chlL)
and nitrogenase Fe protein (nifH gene) suggest their
functional similarity. Members of the BchX family serve
as the unique electron donors to their respective
catalytic subunits (bchN-bchB, bchY-bchZ and nitrogenase
component 1). Mechanistically, they hydrolyze ATP and
transfer electrons through a Fe4-S4 cluster.
Length = 329
Score = 28.8 bits (64), Expect = 5.0
Identities = 13/32 (40%), Positives = 19/32 (59%)
Query: 93 GKGGVGKTSCAASLAVKFANHGHPTIVISTDP 124
GKGG+GK+ A+L+ A G ++I DP
Sbjct: 38 GKGGIGKSFTLANLSYMMAQQGKRVLLIGCDP 69
>gnl|CDD|106194 PRK13232, nifH, nitrogenase reductase; Reviewed.
Length = 273
Score = 28.4 bits (63), Expect = 6.2
Identities = 10/32 (31%), Positives = 19/32 (59%)
Query: 93 GKGGVGKTSCAASLAVKFANHGHPTIVISTDP 124
GKGG+GK++ +L + G+ +++ DP
Sbjct: 8 GKGGIGKSTTTQNLTAALSTMGNKILLVGCDP 39
>gnl|CDD|105560 PRK12339, PRK12339, 2-phosphoglycerate kinase; Provisional.
Length = 197
Score = 28.2 bits (63), Expect = 6.5
Identities = 14/34 (41%), Positives = 18/34 (52%), Gaps = 4/34 (11%)
Query: 90 MLGGKGGVGKTSCAASLAVKFANHGHPTIVISTD 123
+GG GVGKT S++ A H IV+S D
Sbjct: 7 FIGGIPGVGKT----SISGYIARHRAIDIVLSGD 36
>gnl|CDD|183452 PRK12337, PRK12337, 2-phosphoglycerate kinase; Provisional.
Length = 475
Score = 28.6 bits (64), Expect = 6.7
Identities = 14/36 (38%), Positives = 22/36 (61%), Gaps = 4/36 (11%)
Query: 88 HYMLGGKGGVGKTSCAASLAVKFANHGHPTIVISTD 123
H ++GG GVGK+ A++LA + T ++STD
Sbjct: 257 HVLIGGVSGVGKSVLASALAYRLG----ITRIVSTD 288
>gnl|CDD|183428 PRK12311, rpsB, 30S ribosomal protein S2/unknown domain fusion
protein; Provisional.
Length = 326
Score = 28.6 bits (64), Expect = 6.7
Identities = 25/88 (28%), Positives = 41/88 (46%), Gaps = 13/88 (14%)
Query: 257 ASIGKMMKLKKKLASTTSAFKSVFGKEKKQQDVASDKVEQLRERMAKVRDLFRDPDATEF 316
SI ++ KL + L+S + G KK++ + ++L + ++D+ PD F
Sbjct: 104 GSIQRLRKLDEVLSSGEAN-----GYTKKERLTLQRERDKLDRALGGIKDMGGLPDLL-F 157
Query: 317 VIVTIPTVMAISESSRLHASLRKECIPV 344
VI T +AI E+ RL IPV
Sbjct: 158 VIDTNKEDIAIQEAQRLG-------IPV 178
>gnl|CDD|238986 cd02028, UMPK_like, Uridine monophosphate kinase_like (UMPK_like)
is a family of proteins highly similar to the uridine
monophosphate kinase (UMPK, EC 2.7.1.48), also known as
uridine kinase or uridine-cytidine kinase (UCK).
Length = 179
Score = 28.0 bits (63), Expect = 7.1
Identities = 12/33 (36%), Positives = 18/33 (54%)
Query: 91 LGGKGGVGKTSCAASLAVKFANHGHPTIVISTD 123
+ G G GKT+ A L+ + +G +VIS D
Sbjct: 4 IAGPSGSGKTTFAKKLSNQLRVNGIGPVVISLD 36
>gnl|CDD|224985 COG2074, COG2074, 2-phosphoglycerate kinase [Carbohydrate transport
and metabolism].
Length = 299
Score = 28.1 bits (63), Expect = 8.0
Identities = 14/34 (41%), Positives = 19/34 (55%), Gaps = 4/34 (11%)
Query: 90 MLGGKGGVGKTSCAASLAVKFANHGHPTIVISTD 123
++GG GVGK++ A LA + VISTD
Sbjct: 93 LIGGASGVGKSTIAGELARRLG----IRSVISTD 122
>gnl|CDD|218784 pfam05861, PhnI, Bacterial phosphonate metabolism protein (PhnI).
This family consists of several Proteobacterial
phosphonate metabolism protein (PhnI) sequences.
Bacteria that use phosphonates as a phosphorus source
must be able to break the stable carbon-phosphorus bond.
In Escherichia coli phosphonates are broken down by a
C-P lyase that has a broad substrate specificity. The
genes for phosphonate uptake and degradation in E. coli
are organised in an operon of 14 genes, named phnC to
phnP. Three gene products (PhnC, PhnD and PhnE) comprise
a binding protein-dependent phosphonate transporter,
which also transports phosphate, phosphite, and certain
phosphate esters such as phosphoserine; two gene
products (PhnF and PhnO) may have a role in gene
regulation; and nine gene products (PhnG, PhnH, PhnI,
PhnJ, PhnK, PhnL, PhnM, PhnN, and PhnP) probably
comprise a membrane-associated C-P lyase enzyme complex.
Length = 356
Score = 28.3 bits (64), Expect = 8.8
Identities = 21/72 (29%), Positives = 31/72 (43%), Gaps = 21/72 (29%)
Query: 326 AISESSRLHASLRKECIPVQRLIVNQVLPPSASDCKFCAMKRKDQMRVL-ETIMS----- 379
AI + L A LR+ V L V Q+ +Q+R+ + +MS
Sbjct: 11 AIDNAHALLAELRRGDPAVPELSVAQIE---------------EQLRLAVDRVMSEGSLY 55
Query: 380 DPQLANLRLVQA 391
DP+LA L + QA
Sbjct: 56 DPELAALAIKQA 67
>gnl|CDD|234763 PRK00440, rfc, replication factor C small subunit; Reviewed.
Length = 319
Score = 27.9 bits (63), Expect = 8.8
Identities = 9/20 (45%), Positives = 12/20 (60%)
Query: 88 HYMLGGKGGVGKTSCAASLA 107
H + G G GKT+ A +LA
Sbjct: 40 HLLFAGPPGTGKTTAALALA 59
>gnl|CDD|223382 COG0305, DnaB, Replicative DNA helicase [DNA replication,
recombination, and repair].
Length = 435
Score = 28.0 bits (63), Expect = 9.6
Identities = 12/44 (27%), Positives = 24/44 (54%), Gaps = 1/44 (2%)
Query: 78 DEMVAGTQRKH-YMLGGKGGVGKTSCAASLAVKFANHGHPTIVI 120
DE+ +G + ++ + G+GKT+ A ++A+ A G + I
Sbjct: 187 DEITSGFRPGDLIIVAARPGMGKTALALNIALNAAADGRKPVAI 230
>gnl|CDD|133219 cd05088, PTKc_Tie2, Catalytic domain of the Protein Tyrosine
Kinase, Tie2. Protein Tyrosine Kinase (PTK) family;
Tie2; catalytic (c) domain. The PTKc family is part of a
larger superfamily that includes the catalytic domains
of other kinases such as protein serine/threonine
kinases, RIO kinases, and phosphoinositide 3-kinase
(PI3K). PTKs catalyze the transfer of the
gamma-phosphoryl group from ATP to tyrosine (tyr)
residues in protein substrates. Tie2 is a receptor tyr
kinase (RTK) containing an extracellular region, a
transmembrane segment, and an intracellular catalytic
domain. The extracellular region contains an
immunoglobulin (Ig)-like domain, three epidermal growth
factor (EGF)-like domains, a second Ig-like domain, and
three fibronectin type III repeats. Tie2 is expressed
mainly in endothelial cells and hematopoietic stem
cells. It is also found in a subset of tumor-associated
monocytes and eosinophils. The angiopoietins (Ang-1 to
Ang-4) serve as ligands for Tie2. The binding of Ang-1
to Tie2 leads to receptor autophosphorylation and
activation, promoting cell migration and survival. In
contrast, Ang-2 binding to Tie2 does not result in the
same response, suggesting that Ang-2 may function as an
antagonist. Tie2 signaling plays key regulatory roles in
vascular integrity and quiescence, and in inflammation.
Length = 303
Score = 28.0 bits (62), Expect = 9.7
Identities = 15/43 (34%), Positives = 26/43 (60%), Gaps = 6/43 (13%)
Query: 106 LAVKFANHGH------PTIVISTDPAHSLSDSFAQDLSGGTLV 142
LA+++A HG+ + V+ TDPA ++++S A LS L+
Sbjct: 85 LAIEYAPHGNLLDFLRKSRVLETDPAFAIANSTASTLSSQQLL 127
>gnl|CDD|183703 PRK12724, PRK12724, flagellar biosynthesis regulator FlhF;
Provisional.
Length = 432
Score = 28.0 bits (62), Expect = 9.8
Identities = 21/63 (33%), Positives = 32/63 (50%), Gaps = 4/63 (6%)
Query: 65 RSISTPRETVAGFDEMVAGT---QRKHYMLGGKGGVGKTSCAASLAVKFANH-GHPTIVI 120
R+++ E V+ ++ +GT QRK G G GKT+ A LA K+ H G +
Sbjct: 199 RAVTYLEERVSVDSDLFSGTGKNQRKVVFFVGPTGSGKTTSIAKLAAKYFLHMGKSVSLY 258
Query: 121 STD 123
+TD
Sbjct: 259 TTD 261
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
0.319 0.133 0.375
Gapped
Lambda K H
0.267 0.0889 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 20,837,961
Number of extensions: 2013716
Number of successful extensions: 2357
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2325
Number of HSP's successfully gapped: 131
Length of query: 413
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 314
Effective length of database: 6,546,556
Effective search space: 2055618584
Effective search space used: 2055618584
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 60 (26.6 bits)