RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 016417
(390 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 = 209 bits (533), Expect = 5e-65
Identities = 104/321 (32%), Positives = 158/321 (49%), Gaps = 38/321 (11%)
Query: 90 KYYMLGGKGGVGKTSCAASLAVKFANNGHPTLVVSTDPAHSLSDSFAQDLTGGQLVPVEG 149
++ GGKGGVGKT+ + + AV+ + G L+VSTDPAHSLSDSF Q G + ++G
Sbjct: 2 RWIFFGGKGGVGKTTVSCATAVRLSEQGKKVLLVSTDPAHSLSDSFNQKF-GHEPTKIKG 60
Query: 150 PDFPLFALEINPEKAREEFRNVTQKDGGTGVKDFMDGMGLGMLVEQLGELKLGELLDTPP 209
+ L A+EI+P+ EE+R Q M G+L E+L L
Sbjct: 61 VE-NLSAMEIDPQMELEEYRGEVQDPIN---AVLGLDMLEGILAEELSSL---------- 106
Query: 210 PGLDEAIA---ISK-----------------GHTLRLLSLPDFLDASIGKILKLREKIAS 249
PG+DE + K GHTLRLLSLP L + KI+KL+ +I
Sbjct: 107 PGIDEIASFDEFKKYMDEGEYDVVIFDTAPTGHTLRLLSLPTVLSWYLEKIVKLKNQIGP 166
Query: 250 ATSAIKSVFGQEQNRQGASDKLERLRERMVKVRELFRDTDSTEFVIVTIPTVMAVSESSR 309
K + A + LE +E++ K RE+ D + T F +V IP M++ E+ R
Sbjct: 167 LAKPFKGMGMGGSCLPEALESLEETKEQIEKAREILSDPERTSFRLVCIPEKMSLYETER 226
Query: 310 LSESLKKENVPVKRLIVNQIIPPSASDCKFCAMKRKDQMRALEMIKSDSELSSLMLIEAP 369
+ L K + V +IVNQ++P + C FC +++ Q + L+ I+ S L + + P
Sbjct: 227 AIQELAKYGIDVDAVIVNQVLPET-EQCPFCEARKEIQQKYLKEIEEL--FSDLPVAKLP 283
Query: 370 LVDVEIRGVPALRFMGDIIWK 390
L+ E+ G+ AL ++
Sbjct: 284 LLPEEVVGLEALEKFSQTLYG 304
>gnl|CDD|223082 COG0003, ArsA, Predicted ATPase involved in chromosome partitioning
[Cell division and chromosome partitioning].
Length = 322
Score = 191 bits (488), Expect = 4e-58
Identities = 109/320 (34%), Positives = 164/320 (51%), Gaps = 41/320 (12%)
Query: 90 KYYMLGGKGGVGKTSCAASLAVKFANNGHPTLVVSTDPAHSLSDSFAQDLTGGQLVPVEG 149
+ GKGGVGKT+ AA+ AVK A +G L+VSTDPAHSL D F +L P +
Sbjct: 3 RIVFFTGKGGVGKTTIAAATAVKLAESGKKVLLVSTDPAHSLGDVFDLELGHD---PRKV 59
Query: 150 PDFPLFALEINPEKAREEFRNVTQKDGGTGVKDFMDGMGLGMLVEQLGELKLGELLDTPP 209
L ALE++PEKA EE+ + KD + G+ ++L L
Sbjct: 60 GPN-LDALELDPEKALEEYWDEV-KDYLARL--LRTRGLGGIYADELATL---------- 105
Query: 210 PGLDEAIAISK--------------------GHTLRLLSLPDFLDASIGKILKLR-EKIA 248
PG+DEA+A+ K GHTLRLLSLP+ L + K+ K R +++
Sbjct: 106 PGIDEALALLKILEYYVSGEYDVIVVDTAPTGHTLRLLSLPEVLGWYLEKLFKPRRKRMV 165
Query: 249 SATSAIKSVFGQEQNRQGASDKLERLRERMVKVRELFRDTDSTEFVIVTIPTVMAVSESS 308
A ++ + G + LE L+ER+ VRE+ + D T F +V+IP +++ E+
Sbjct: 166 KALKSLSTAAGSPLPDDAVLEALEELKERIADVREVLTNPDGTSFRLVSIPEKLSLYETK 225
Query: 309 RLSESLKKENVPVKRLIVNQIIPPSASDCKFCAMKRKDQMRALEMIKSDSELSSLMLIEA 368
R E L +PV +IVN+I+P A D F +RK Q + L+ + + S L +++
Sbjct: 226 RAVERLSLYGIPVDAVIVNKILPDEA-DQPFLEARRKIQQKYLKEL--EETFSDLAVVKV 282
Query: 369 PLVDVEIRGVPALRFMGDII 388
PL+ E G+ AL +GD++
Sbjct: 283 PLLAEEPVGLEALEKLGDLL 302
>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 = 175 bits (447), Expect = 3e-53
Identities = 76/279 (27%), Positives = 103/279 (36%), Gaps = 85/279 (30%)
Query: 91 YYMLGGKGGVGKTSCAASLAVKFANNGHPTLVVSTDPAHSLSDSFAQDLTGGQLVPVEGP 150
GKGGVGKT+ AA+ AV+ A G L+VSTDPAH+LSD +L+
Sbjct: 1 VIFFTGKGGVGKTTIAAATAVRLAEEGKKVLLVSTDPAHNLSDKGLPNLSDA-------- 52
Query: 151 DFPLFALEINPEKAREEF---RNVTQKDGGTGVKDFMDGMGLGMLVEQLGELKLGEL--- 204
F + EI P REE R V + GG G L + E L +
Sbjct: 53 -FIVEDPEIAPNLYREEVDATRRVERAWGGEGGLMLELAAALPGIEELASLLAVFREFSE 111
Query: 205 -------LDTPPPGLDEAIAISKGHTLRLLSLPDFLDASIGKILKLREKIASATSAIKSV 257
DT P GHTLRLL
Sbjct: 112 GLYDVIVFDTAP----------TGHTLRLL------------------------------ 131
Query: 258 FGQEQNRQGASDKLERLRERMVKVRELFRDTDSTEFVIVTIPTVMAVSESSRLSESLKKE 317
VREL D + T F +VT+P + + E+ R L
Sbjct: 132 -----------------------VRELLTDPERTSFRLVTLPEKLPLYETERAITELALY 168
Query: 318 NVPVKRLIVNQIIPPSASDCKFCAMKRKDQMRALEMIKS 356
+PV ++VN+++P D F A +R+ Q + L I+
Sbjct: 169 GIPVDAVVVNRVLPAEVDDDPFLAARRQIQQKYLAEIEE 207
>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 = 164 bits (418), Expect = 3e-48
Identities = 98/300 (32%), Positives = 146/300 (48%), Gaps = 48/300 (16%)
Query: 106 AASLAVKFANNGHPTLVVSTDPAHSLSDSFAQDL--TGGQLVPVEGPDFPLFALEINPEK 163
+A+ A++ A G L+VSTDPAHSLSD F Q++ T ++ VE L A+EI+P+
Sbjct: 2 SAATAIRLAEQGKKVLLVSTDPAHSLSDVFEQEIGHTPTKVTGVEN----LSAVEIDPQA 57
Query: 164 AREEFRNVTQKDGGTGVKDFMDGMGLGMLVEQLGELKLGELLDTPPPGLDEAIAISK--- 220
A EE+R + G G ML +QL L PG+DE A +
Sbjct: 58 ALEEYRAKL-VEQIKGNL----PDG-DMLGDQLEGAALS-------PGIDEIAAFDEFLK 104
Query: 221 -------------------GHTLRLLSLPDFLDASIGKILKLREKIASATSAIKSVFGQE 261
GHTLRLL LP+ L + + K +K+R K+ +F
Sbjct: 105 HMTDAENEFDVVIFDTAPTGHTLRLLQLPEVLSSFLEKFIKIRSKLGPM----AKLFMGA 160
Query: 262 QNRQGASDKLERLRERMVKVRELFRDTDSTEFVIVTIPTVMAVSESSRLSESLKKENVPV 321
A +KLE L+E++ RE+ D + T FV+V IP M++ ES R + L K + V
Sbjct: 161 GEDDEALEKLEELKEQIEAAREILSDPERTSFVLVVIPEKMSLYESERAHKELAKYGIKV 220
Query: 322 KRLIVNQIIPPSASDCKFCAMKRKDQMRALEMIKSDSELSSLMLIEAPLVDVEIRGVPAL 381
+IVNQ++P +A +FC + + Q + L+ I + L + E PL E+ G+ AL
Sbjct: 221 DAVIVNQVLPENA-QDEFCQARWELQQKYLKQIPEK--FADLPVAEVPLQKEEMVGLEAL 277
>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 = 99.8 bits (249), Expect = 9e-23
Identities = 91/328 (27%), Positives = 137/328 (41%), Gaps = 82/328 (25%)
Query: 90 KYYMLGGKGGVGKTSCAASLAVKFANNGHPTLVVSTDPAHSLSDSFAQDLTGGQLVPVEG 149
Y GKGGVGKTS A + A+ A+ G L+VSTDPA ++ F Q + G ++ + G
Sbjct: 4 PYLFFTGKGGVGKTSIACATAINLADQGKRVLLVSTDPASNVGQVFGQTI-GNKITAIAG 62
Query: 150 PDFPLFALEINPEKAREEFRN-VTQKDGGTGVKDFMDGMGLGMLVEQL------------ 196
LFALEI+P+ A + +R + G D + + EQL
Sbjct: 63 VP-GLFALEIDPQAAAQAYRARIVDPVRGVLPDDVVSSIE-----EQLSGACTTEIAAFD 116
Query: 197 ---GELKLGELL--------DTPPPGLDEAIAISKGHTLRLLSLP----DFLDASIGKIL 241
G L EL DT P GHT+RLL LP DFLD
Sbjct: 117 EFTGLLTDAELTQDFDHIIFDTAP----------TGHTIRLLQLPGAWSDFLDT------ 160
Query: 242 KLREKIASATSAIKSVFGQEQNRQGAS-----DKLERLRERMVKVRELFRDTDSTEFVIV 296
N GAS LE+ R + K E D + T ++V
Sbjct: 161 ---------------------NPNGASCLGPLAGLEKQRAQYAKAVEALSDPERTRLILV 199
Query: 297 TIPTVMAVSESSRLSESLKKENVPVKRLIVNQIIPPSAS--DCKFCAMKRKDQMRALEMI 354
P + E +R + L + + L++N ++PP+ + D A+ +++Q +AL+ +
Sbjct: 200 ARPQKSTLLEVARTHQELAAIGLKNQYLVINGVLPPTEASDDPLAQAIYKREQ-KALQHM 258
Query: 355 KSDSELSSLMLIEAPLVDVEIRGVPALR 382
+ L++L PL + G+ ALR
Sbjct: 259 PAI--LANLPRYTLPLKPYNLVGLEALR 284
Score = 68.2 bits (167), Expect = 2e-12
Identities = 61/273 (22%), Positives = 101/273 (36%), Gaps = 80/273 (29%)
Query: 79 GFDEMV---AGTQRKYYMLGGKGGVGKTSCAASLAVKFANNGHPTLVVSTDPAHSLSDSF 135
++ A +++ M GKGGVGKT+ AA++AV+ AN G + ++DPA LS +
Sbjct: 308 SLSRLIDEIAKSEKGLIMTMGKGGVGKTTVAAAIAVRLANKGLDVHLTTSDPAAHLSVTL 367
Query: 136 AQDLTGGQLVPVEGPDFPLFALEINPEKAREEFR-NVTQKDGGTGVKDFMDGMGLGMLVE 194
L Q+ I+P++ E +R V G +D G L E
Sbjct: 368 TGSLNNLQVS------------RIDPKQETERYRQEVLATKGKE-----LDEDGKAYLEE 410
Query: 195 QLGELKLGEL-------------------LDTPPPGLDEAIAISKGHTLRLLSLPDFLDA 235
L E+ +DT P GHTL L LDA
Sbjct: 411 DLRSPCTEEIAVFQAFSRIIREAGDRFVVMDTAP----------TGHTLLL------LDA 454
Query: 236 SIGKILKLREKIASATSAIKSVFGQEQNRQGASDKLERLRERMVKVRELFRDTDSTEFVI 295
+ ++ K+ + + Q Q+ + T+ ++
Sbjct: 455 TGAYHREVERKMGDTPEHVTTPMMQLQDPE------------------------RTKVLL 490
Query: 296 VTIPTVMAVSESSRLSESLKKENVPVKRLIVNQ 328
VT+P V E++RL E L++ + ++N
Sbjct: 491 VTLPETTPVLEAARLQEDLRRAGIEPWWWVINN 523
>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 = 50.3 bits (121), Expect = 5e-08
Identities = 15/31 (48%), Positives = 19/31 (61%)
Query: 97 KGGVGKTSCAASLAVKFANNGHPTLVVSTDP 127
KGGVGKT+ A +LA A G L++ 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 = 49.6 bits (119), Expect = 1e-07
Identities = 22/56 (39%), Positives = 31/56 (55%), Gaps = 1/56 (1%)
Query: 94 LGGKGGVGKTSCAASLAVKFANNGHPTLVVSTDPAHSLSDSFAQDLTGGQLVPVEG 149
+ GKGGVGKT+ AA LA A G P L + DP L + + ++ +L+ V G
Sbjct: 4 ITGKGGVGKTTIAALLARYLAEKGKPVLAIDADPD-DLPERLSVEVGEIKLLLVMG 58
>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 = 44.3 bits (105), Expect = 5e-06
Identities = 15/33 (45%), Positives = 21/33 (63%)
Query: 91 YYMLGGKGGVGKTSCAASLAVKFANNGHPTLVV 123
++ GKGGVGKT+ AA+LA A G L++
Sbjct: 1 VIVVTGKGGVGKTTLAANLAAALAKRGKRVLLI 33
>gnl|CDD|224113 COG1192, Soj, ATPases involved in chromosome partitioning [Cell
division and chromosome partitioning].
Length = 259
Score = 46.7 bits (111), Expect = 6e-06
Identities = 44/244 (18%), Positives = 79/244 (32%), Gaps = 31/244 (12%)
Query: 97 KGGVGKTSCAASLAVKFANN-GHPTLVVSTDPAHSLSDSFAQDLTGGQL---VPVEGPDF 152
KGGVGKT+ A +LA A G L++ DP SL+ + +
Sbjct: 11 KGGVGKTTTAVNLAAALAKRGGKKVLLIDLDPQGSLTSWLGLRPDLEGDLYNLLSGLKER 70
Query: 153 PLFALEINPEKAREEFRNVTQKDGGTGVKDFMDGMGLGMLVEQLGELKLGE--------L 204
P + + + + + + E L + L +
Sbjct: 71 PDILDYTVVIE------GLDLIPSNIDLAEGAEIELNAVAKELLLKRLLDPVKDDYDYII 124
Query: 205 LDTPP---PGLDEAIAIS-------KGHTLRLLSLPDFLDASIGKILKLREKIASATSAI 254
+DTPP A+A + + L L L L+ + +LKLR +
Sbjct: 125 IDTPPSLGVLTLNALAAADHVLIPVQPEFLDLEGLEQLLNT-LEDLLKLRRNKLIVVGIL 183
Query: 255 KSVF-GQEQNRQGASDKLERLRERMVKVRELFRDTDSTEFVIVTIPTVMAVSESSRLSES 313
+ F + + +L++L V ++ R E P + S+ +E
Sbjct: 184 ITRFDSRTKLADEVLQELKQLLGDPVLKTKIPRRVAYREAAAEGKP-LYEYDPKSKAAEE 242
Query: 314 LKKE 317
+
Sbjct: 243 YYEL 246
>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 = 46.6 bits (111), Expect = 7e-06
Identities = 17/46 (36%), Positives = 23/46 (50%)
Query: 95 GGKGGVGKTSCAASLAVKFANNGHPTLVVSTDPAHSLSDSFAQDLT 140
+GGVGKT+ A+LA G P L + DP + L F D +
Sbjct: 8 SVRGGVGKTTLTANLASALKLLGEPVLAIDLDPQNLLRLHFGMDWS 53
>gnl|CDD|222854 PHA02518, PHA02518, ParA-like protein; Provisional.
Length = 211
Score = 46.0 bits (109), Expect = 8e-06
Identities = 21/51 (41%), Positives = 27/51 (52%)
Query: 97 KGGVGKTSCAASLAVKFANNGHPTLVVSTDPAHSLSDSFAQDLTGGQLVPV 147
KGG GKT+ A +LA +GH L+V DP S +D G L+PV
Sbjct: 9 KGGAGKTTVATNLASWLHADGHKVLLVDLDPQGSSTDWAEAREEGEPLIPV 59
>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 = 44.7 bits (106), Expect = 2e-05
Identities = 18/42 (42%), Positives = 24/42 (57%)
Query: 95 GGKGGVGKTSCAASLAVKFANNGHPTLVVSTDPAHSLSDSFA 136
G KGGVGKT+ AA+LA A G+ L++ DP + S
Sbjct: 5 GTKGGVGKTTLAANLARALAKRGYRVLLIDLDPQANNSSYLG 46
>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 = 42.5 bits (101), Expect = 5e-05
Identities = 15/32 (46%), Positives = 21/32 (65%)
Query: 95 GGKGGVGKTSCAASLAVKFANNGHPTLVVSTD 126
GKGGVGKT+ +A+LA+ A G L++ 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 = 41.8 bits (99), Expect = 2e-04
Identities = 13/36 (36%), Positives = 20/36 (55%)
Query: 93 MLGGKGGVGKTSCAASLAVKFANNGHPTLVVSTDPA 128
+ GKGGVGKT+ A+L A G+ +++ D
Sbjct: 4 VTSGKGGVGKTTTTANLGTALAQLGYKVVLIDADLG 39
Score = 32.9 bits (76), Expect = 0.17
Identities = 10/39 (25%), Positives = 23/39 (58%)
Query: 291 TEFVIVTIPTVMAVSESSRLSESLKKENVPVKRLIVNQI 329
E ++VT P + ++ ++ R+ L+ + V +IVN++
Sbjct: 86 DEALLVTTPEISSLRDADRVKGLLEALGIKVVGVIVNRV 124
>gnl|CDD|224071 COG1149, COG1149, MinD superfamily P-loop ATPase containing an
inserted ferredoxin domain [Energy production and
conversion].
Length = 284
Score = 42.0 bits (99), Expect = 3e-04
Identities = 20/76 (26%), Positives = 29/76 (38%), Gaps = 22/76 (28%)
Query: 94 LGGKGGVGKTSCAASLAVKFANNGHPTLVVSTDPAHSLSDSFAQDLTGGQLVPVEGPDFP 153
GKGG GKT+ AA+LAV + + ++ D VE P+
Sbjct: 7 ASGKGGTGKTTVAANLAVLLGDK-YKLVLADCD--------------------VEAPNLH 45
Query: 154 LFALEINPEKAREEFR 169
L L + + E R
Sbjct: 46 LL-LGVEVLEEEEVIR 60
>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 = 18/41 (43%), Positives = 25/41 (60%), Gaps = 1/41 (2%)
Query: 96 GKGGVGKTSCAASLAVK-FANNGHPTLVVSTDPAHSLSDSF 135
GKGGVGKT+ AA L + + G+ LVV DP +L ++
Sbjct: 7 GKGGVGKTTIAALLLKRLLSKGGYNVLVVDADPDSNLPEAL 47
>gnl|CDD|225447 COG2894, MinD, Septum formation inhibitor-activating ATPase [Cell
division and chromosome partitioning].
Length = 272
Score = 38.0 bits (89), Expect = 0.005
Identities = 12/31 (38%), Positives = 18/31 (58%)
Query: 96 GKGGVGKTSCAASLAVKFANNGHPTLVVSTD 126
GKGGVGKT+ A++ A G +++ D
Sbjct: 10 GKGGVGKTTTTANIGTALAQLGKKVVLIDFD 40
Score = 28.4 bits (64), Expect = 5.7
Identities = 15/47 (31%), Positives = 26/47 (55%), Gaps = 7/47 (14%)
Query: 292 EFVIVTIPTVMAVSESSRL-----SESLKKEN--VPVKRLIVNQIIP 331
E ++VT P V +V +S R+ S+S + E P + L++N+ P
Sbjct: 138 EAIVVTNPEVSSVRDSDRIIGLLESKSRRAEIGEEPKEHLLLNRYRP 184
>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 = 37.1 bits (87), Expect = 0.006
Identities = 12/23 (52%), Positives = 17/23 (73%)
Query: 96 GKGGVGKTSCAASLAVKFANNGH 118
GKGGVGK++ A +LA+ A G+
Sbjct: 7 GKGGVGKSTVAVNLALALAKLGY 29
>gnl|CDD|224267 COG1348, NifH, Nitrogenase subunit NifH (ATPase) [Inorganic ion
transport and metabolism].
Length = 278
Score = 37.7 bits (88), Expect = 0.006
Identities = 20/51 (39%), Positives = 29/51 (56%), Gaps = 4/51 (7%)
Query: 96 GKGGVGKTSCAASLAVKFANNGHPTLVVSTDPAHSLSDSFAQDLTGGQLVP 146
GKGG+GK++ + +LA A G L+V DP DS + L GG+ +P
Sbjct: 8 GKGGIGKSTTSQNLAAALAELGKKVLIVGCDPKA---DS-TRLLLGGKAIP 54
>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 = 37.1 bits (87), Expect = 0.007
Identities = 13/37 (35%), Positives = 17/37 (45%)
Query: 90 KYYMLGGKGGVGKTSCAASLAVKFANNGHPTLVVSTD 126
+L G G GKT+ A LA G L+V+ D
Sbjct: 2 NVILLVGLQGSGKTTTIAKLAAYLKKQGKKVLLVAAD 38
>gnl|CDD|184370 PRK13886, PRK13886, conjugal transfer protein TraL; Provisional.
Length = 241
Score = 37.4 bits (87), Expect = 0.007
Identities = 17/37 (45%), Positives = 24/37 (64%)
Query: 94 LGGKGGVGKTSCAASLAVKFANNGHPTLVVSTDPAHS 130
L GKGGVGK+ AA++A A+ G L + TDP ++
Sbjct: 8 LQGKGGVGKSFIAATIAQYKASKGQKPLCIDTDPVNA 44
>gnl|CDD|223563 COG0489, Mrp, ATPases involved in chromosome partitioning [Cell
division and chromosome partitioning].
Length = 265
Score = 37.4 bits (87), Expect = 0.008
Identities = 24/97 (24%), Positives = 40/97 (41%), Gaps = 2/97 (2%)
Query: 30 NAVSFMGLLSFSPKTSSFSTGLISISLKQRRSKNSFQVRAVAAPSEAVSGFDEMVAGTQR 89
V L F+ S L++ +L K++ A+ A + + G +
Sbjct: 1 ATVEIELALPFASS-SEEIPELLAKALAALLPKSTASE-ALRALRTNLKFAKVLRKGVKN 58
Query: 90 KYYMLGGKGGVGKTSCAASLAVKFANNGHPTLVVSTD 126
+ GKGGVGK++ A +LA A G L++ D
Sbjct: 59 VIAVTSGKGGVGKSTVAVNLAAALAQLGKRVLLLDAD 95
>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 = 37.7 bits (88), Expect = 0.009
Identities = 18/36 (50%), Positives = 21/36 (58%)
Query: 97 KGGVGKTSCAASLAVKFANNGHPTLVVSTDPAHSLS 132
KGG GKT+ AA LA A G+ L + DP SLS
Sbjct: 113 KGGSGKTTTAAHLAQYLALRGYRVLAIDLDPQASLS 148
>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 = 36.6 bits (85), Expect = 0.012
Identities = 14/34 (41%), Positives = 18/34 (52%)
Query: 93 MLGGKGGVGKTSCAASLAVKFANNGHPTLVVSTD 126
+ GKGG GKT+ A+L V A G L + D
Sbjct: 5 IASGKGGTGKTTITANLGVALAKLGKKVLALDAD 38
>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 = 35.7 bits (83), Expect = 0.012
Identities = 12/42 (28%), Positives = 16/42 (38%)
Query: 94 LGGKGGVGKTSCAASLAVKFANNGHPTLVVSTDPAHSLSDSF 135
GG GKT+ A +LA A G L + + F
Sbjct: 6 YSPVGGEGKTTFALNLAQSLAEEGPKVLYLDLEEYSGDLALF 47
>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 = 36.0 bits (84), Expect = 0.014
Identities = 15/34 (44%), Positives = 20/34 (58%)
Query: 93 MLGGKGGVGKTSCAASLAVKFANNGHPTLVVSTD 126
+L G GVGKT+ AA LA+ G L+V+ D
Sbjct: 4 LLVGLQGVGKTTTAAKLALYLKKKGKKVLLVAAD 37
>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 = 35.7 bits (83), Expect = 0.016
Identities = 11/22 (50%), Positives = 14/22 (63%)
Query: 94 LGGKGGVGKTSCAASLAVKFAN 115
+ GKGG GKT+ A+LA N
Sbjct: 5 ISGKGGTGKTTVTAALAALLKN 26
>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 = 36.3 bits (84), Expect = 0.016
Identities = 15/34 (44%), Positives = 23/34 (67%)
Query: 96 GKGGVGKTSCAASLAVKFANNGHPTLVVSTDPAH 129
GKGG+GK++ +++L+V FA G L + DP H
Sbjct: 7 GKGGIGKSTTSSNLSVAFAKLGKRVLQIGCDPKH 40
>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 = 36.0 bits (84), Expect = 0.019
Identities = 18/52 (34%), Positives = 26/52 (50%), Gaps = 4/52 (7%)
Query: 96 GKGGVGKTSCAASLAVKFANNGHPTLVVSTDPAHSLSDSFAQDLTGGQLVPV 147
GKGG+GK++ + +L+ A G L V DP DS + L GG+
Sbjct: 7 GKGGIGKSTTSQNLSAALAEMGKKVLQVGCDPKA---DS-TRLLLGGKAPTT 54
>gnl|CDD|183903 PRK13230, PRK13230, nitrogenase reductase-like protein; Reviewed.
Length = 279
Score = 35.9 bits (83), Expect = 0.025
Identities = 14/34 (41%), Positives = 20/34 (58%)
Query: 96 GKGGVGKTSCAASLAVKFANNGHPTLVVSTDPAH 129
GKGG+GK++ ++A A +G LVV DP
Sbjct: 8 GKGGIGKSTTVCNIAAALAESGKKVLVVGCDPKA 41
>gnl|CDD|237293 PRK13185, chlL, protochlorophyllide reductase iron-sulfur
ATP-binding protein; Provisional.
Length = 270
Score = 35.7 bits (83), Expect = 0.029
Identities = 23/52 (44%), Positives = 32/52 (61%), Gaps = 7/52 (13%)
Query: 96 GKGGVGKTSCAASLAVKFANNGHPTLVVSTDPAHSLSDS-FAQDLTGGQLVP 146
GKGG+GK++ +++L+ FA G L + DP H DS F LT G+LVP
Sbjct: 9 GKGGIGKSTTSSNLSAAFAKLGKKVLQIGCDPKH---DSTFT--LT-GKLVP 54
>gnl|CDD|182756 PRK10818, PRK10818, cell division inhibitor MinD; Provisional.
Length = 270
Score = 35.7 bits (82), Expect = 0.031
Identities = 15/31 (48%), Positives = 21/31 (67%)
Query: 96 GKGGVGKTSCAASLAVKFANNGHPTLVVSTD 126
GKGGVGKT+ +A++A A G T+V+ D
Sbjct: 10 GKGGVGKTTSSAAIATGLAQKGKKTVVIDFD 40
>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 = 0.033
Identities = 22/52 (42%), Positives = 31/52 (59%), Gaps = 7/52 (13%)
Query: 96 GKGGVGKTSCAASLAVKFANNGHPTLVVSTDPAHSLSDS-FAQDLTGGQLVP 146
GKGG+GK++ +++L+V A G L + DP H DS F LT G L+P
Sbjct: 7 GKGGIGKSTTSSNLSVALAKRGKKVLQIGCDPKH---DSTFT--LT-GFLIP 52
>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 = 34.6 bits (80), Expect = 0.059
Identities = 13/31 (41%), Positives = 18/31 (58%)
Query: 96 GKGGVGKTSCAASLAVKFANNGHPTLVVSTD 126
GKGGVGKT+ A+L A G +++ D
Sbjct: 9 GKGGVGKTTTTANLGTALARLGKKVVLIDAD 39
Score = 28.8 bits (65), Expect = 5.0
Identities = 14/40 (35%), Positives = 24/40 (60%)
Query: 292 EFVIVTIPTVMAVSESSRLSESLKKENVPVKRLIVNQIIP 331
E ++VT P V AV ++ R+ L+ + + LIVN++ P
Sbjct: 136 EAIVVTTPEVSAVRDADRVIGLLEAKGIEKIHLIVNRLRP 175
>gnl|CDD|183904 PRK13231, PRK13231, nitrogenase reductase-like protein; Reviewed.
Length = 264
Score = 34.0 bits (78), Expect = 0.099
Identities = 13/32 (40%), Positives = 23/32 (71%), Gaps = 1/32 (3%)
Query: 96 GKGGVGKTSCAASLAVKFANNGHPTLVVSTDP 127
GKGG+GK++ +++A ++N+ H LV+ DP
Sbjct: 9 GKGGIGKSTTVSNMAAAYSND-HRVLVIGCDP 39
>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 = 33.9 bits (78), Expect = 0.12
Identities = 16/34 (47%), Positives = 24/34 (70%)
Query: 94 LGGKGGVGKTSCAASLAVKFANNGHPTLVVSTDP 127
+GG+GG G ++ AA+LA+ A +G TL+V DP
Sbjct: 99 IGGRGGAGASTLAAALALAAARHGLRTLLVDADP 132
>gnl|CDD|233343 TIGR01287, nifH, nitrogenase iron protein. This model describes
nitrogenase (EC 1.18.6.1) iron protein, also called
nitrogenase reductase or nitrogenase component II. This
model includes molybdenum-iron nitrogenase reductase
(nifH), vanadium-iron nitrogenase reductase (vnfH), and
iron-iron nitrogenase reductase (anfH). The model
excludes the homologous protein from the
light-independent protochlorophyllide reductase [Central
intermediary metabolism, Nitrogen fixation].
Length = 275
Score = 33.1 bits (76), Expect = 0.19
Identities = 12/34 (35%), Positives = 19/34 (55%)
Query: 96 GKGGVGKTSCAASLAVKFANNGHPTLVVSTDPAH 129
GKGG+GK++ ++A A G ++V DP
Sbjct: 7 GKGGIGKSTTTQNIAAALAEMGKKVMIVGCDPKA 40
>gnl|CDD|139929 PRK13869, PRK13869, plasmid-partitioning protein RepA; Provisional.
Length = 405
Score = 33.5 bits (76), Expect = 0.20
Identities = 18/36 (50%), Positives = 21/36 (58%)
Query: 97 KGGVGKTSCAASLAVKFANNGHPTLVVSTDPAHSLS 132
KGG GKT+ +A LA A G+ L V DP SLS
Sbjct: 130 KGGSGKTTTSAHLAQYLALQGYRVLAVDLDPQASLS 165
>gnl|CDD|223543 COG0467, RAD55, RecA-superfamily ATPases implicated in signal
transduction [Signal transduction mechanisms].
Length = 260
Score = 32.8 bits (75), Expect = 0.23
Identities = 17/52 (32%), Positives = 25/52 (48%), Gaps = 2/52 (3%)
Query: 77 VSGFDEMVAGT--QRKYYMLGGKGGVGKTSCAASLAVKFANNGHPTLVVSTD 126
+ G DE++ G + ++ G G GKT A + A G P L VST+
Sbjct: 9 IPGLDEILGGGLPRGSVVLITGPPGTGKTIFALQFLYEGAREGEPVLYVSTE 60
>gnl|CDD|224401 COG1484, DnaC, DNA replication protein [DNA replication,
recombination, and repair].
Length = 254
Score = 32.8 bits (75), Expect = 0.26
Identities = 15/78 (19%), Positives = 28/78 (35%), Gaps = 8/78 (10%)
Query: 53 SISLKQRRSKNSFQVRAV-----AAPSEAVSGFDEMVAGTQRKYYMLGGKGGVGKTSCAA 107
S S +++ F A + S + + + +L G GVGKT A
Sbjct: 67 SASFPAKKTFEEFDFEFQPGIDKKALEDLASLVEFF---ERGENLVLLGPPGVGKTHLAI 123
Query: 108 SLAVKFANNGHPTLVVST 125
++ + G L ++
Sbjct: 124 AIGNELLKAGISVLFITA 141
>gnl|CDD|181896 PRK09482, PRK09482, flap endonuclease-like protein; Provisional.
Length = 256
Score = 32.2 bits (74), Expect = 0.34
Identities = 12/21 (57%), Positives = 14/21 (66%)
Query: 106 AASLAVKFANNGHPTLVVSTD 126
A+LAVK A GH +VSTD
Sbjct: 112 IATLAVKVAQAGHQATIVSTD 132
>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 = 32.2 bits (74), Expect = 0.37
Identities = 12/34 (35%), Positives = 19/34 (55%)
Query: 96 GKGGVGKTSCAASLAVKFANNGHPTLVVSTDPAH 129
GKGG+GK++ +L+ A G ++V DP
Sbjct: 8 GKGGIGKSTTTQNLSAALAEMGKKVMIVGCDPKA 41
>gnl|CDD|173102 PRK14639, PRK14639, hypothetical protein; Provisional.
Length = 140
Score = 31.3 bits (71), Expect = 0.37
Identities = 26/100 (26%), Positives = 43/100 (43%), Gaps = 16/100 (16%)
Query: 154 LFALEINPEKAREEFRNVTQKDGGTGVKDFMDGMGLGMLVEQLGELKLGELLD-TPPPGL 212
+ E+ E R+ +R K+GG + D E+L EL L + D PP
Sbjct: 14 FYDDELVSENGRKIYRVYITKEGGVNLDD----------CERLSEL-LSPIFDVEPPVSG 62
Query: 213 DEAIAISKGHTLRLLSLPDFLDASIGKILKL----REKIA 248
+ + +S R LS + SIG+++K+ +EK
Sbjct: 63 EYFLEVSSPGLERKLSKIEHFAKSIGELVKITTNEKEKFE 102
>gnl|CDD|214385 CHL00175, minD, septum-site determining protein; Validated.
Length = 281
Score = 32.0 bits (73), Expect = 0.39
Identities = 16/46 (34%), Positives = 23/46 (50%)
Query: 81 DEMVAGTQRKYYMLGGKGGVGKTSCAASLAVKFANNGHPTLVVSTD 126
E A R + GKGGVGKT+ A+L + A G+ ++ D
Sbjct: 8 KEKSATMSRIIVITSGKGGVGKTTTTANLGMSIARLGYRVALIDAD 53
>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 = 32.1 bits (73), Expect = 0.47
Identities = 17/51 (33%), Positives = 23/51 (45%), Gaps = 4/51 (7%)
Query: 96 GKGGVGKTSCAASLAVKFANNGHPTLVVSTDPAHSLSDSFAQDLTGGQLVP 146
GKGG GK+ +L+ A G L + DP H + L GG +P
Sbjct: 7 GKGGSGKSFTTTNLSHMMAEMGKRVLQLGCDPKHDSTSL----LFGGISLP 53
>gnl|CDD|177011 CHL00072, chlL, photochlorophyllide reductase subunit L.
Length = 290
Score = 32.0 bits (73), Expect = 0.51
Identities = 17/36 (47%), Positives = 21/36 (58%), Gaps = 4/36 (11%)
Query: 96 GKGGVGK--TSCAASLAVKFANNGHPTLVVSTDPAH 129
GKGG+GK TSC S+A+ A G L + DP H
Sbjct: 7 GKGGIGKSTTSCNISIAL--ARRGKKVLQIGCDPKH 40
>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 = 31.2 bits (72), Expect = 0.54
Identities = 12/39 (30%), Positives = 17/39 (43%), Gaps = 12/39 (30%)
Query: 107 ASLAVKFANNGHPTLVVSTDPAHSLSDSFAQDLTGGQLV 145
+LA K G+ ++VS D +DL QLV
Sbjct: 112 GTLAKKAEEEGYEVVIVSGD----------KDLL--QLV 138
>gnl|CDD|182204 PRK10037, PRK10037, cell division protein; Provisional.
Length = 250
Score = 31.4 bits (71), Expect = 0.59
Identities = 19/46 (41%), Positives = 23/46 (50%)
Query: 95 GGKGGVGKTSCAASLAVKFANNGHPTLVVSTDPAHSLSDSFAQDLT 140
G +GGVG TS A+LA G LV+ P + L SF D T
Sbjct: 8 GVRGGVGTTSITAALAWSLQMLGENVLVIDACPDNLLRLSFNVDFT 53
>gnl|CDD|201032 pfam00142, Fer4_NifH, 4Fe-4S iron sulfur cluster binding proteins,
NifH/frxC family.
Length = 272
Score = 31.6 bits (72), Expect = 0.61
Identities = 12/34 (35%), Positives = 18/34 (52%)
Query: 96 GKGGVGKTSCAASLAVKFANNGHPTLVVSTDPAH 129
GKGG+GK++ + + A G L+V DP
Sbjct: 7 GKGGIGKSTTTQNTSAALAEMGKKVLIVGCDPKA 40
>gnl|CDD|223531 COG0455, flhG, Antiactivator of flagellar biosynthesis FleN, an
ATPase [Cell motility].
Length = 262
Score = 31.5 bits (72), Expect = 0.64
Identities = 14/36 (38%), Positives = 19/36 (52%), Gaps = 1/36 (2%)
Query: 94 LGGKGGVGKTSCAASLAVKFANNGHPT-LVVSTDPA 128
+ GKGGVGKT+ A+L A G L++ D
Sbjct: 8 VSGKGGVGKTTITANLGAALAALGGKVVLLIDADLG 43
Score = 27.6 bits (62), Expect = 9.4
Identities = 18/98 (18%), Positives = 42/98 (42%), Gaps = 3/98 (3%)
Query: 290 STEFVIVTIPTVMAVSESSRLSESLKKE--NVPVKRLIVNQIIPPSASDCKFCAMKRK-D 346
S E VIVT P +++++ + + L K ++ +R+++N++ + +
Sbjct: 135 SDELVIVTTPEPTSITDAYKTIKILSKLGLDLLGRRVVLNRVRSTKEGVDVAALLIQVVK 194
Query: 347 QMRALEMIKSDSELSSLMLIEAPLVDVEIRGVPALRFM 384
Q+ L++I D E+ + P+V +
Sbjct: 195 QVPVLQVIPFDPEVRRALAEGKPIVLYSPNSKASQAIK 232
>gnl|CDD|223615 COG0541, Ffh, Signal recognition particle GTPase [Intracellular
trafficking and secretion].
Length = 451
Score = 31.3 bits (72), Expect = 0.81
Identities = 12/34 (35%), Positives = 17/34 (50%)
Query: 93 MLGGKGGVGKTSCAASLAVKFANNGHPTLVVSTD 126
++ G G GKT+ A LA G L+V+ D
Sbjct: 104 LMVGLQGSGKTTTAGKLAKYLKKKGKKVLLVAAD 137
>gnl|CDD|222163 pfam13479, AAA_24, AAA domain. This AAA domain is found in a wide
variety of presumed phage proteins.
Length = 201
Score = 30.7 bits (70), Expect = 0.81
Identities = 20/77 (25%), Positives = 30/77 (38%), Gaps = 16/77 (20%)
Query: 96 GKGGVGKTSCAASLAVKFANNGHPTLVVSTDPAHSLSDSFAQDLTGGQLVPVE-GPDFPL 154
G G+GKTS A +L K TL + D + L+ G V + D
Sbjct: 10 GPPGIGKTSLAKTLPPK-------TLFLDLD------AGTTKVLSRGDNVDIRSWQDLRD 56
Query: 155 FALEINPEKAREEFRNV 171
F E+ + A E+ +
Sbjct: 57 FLDELAEDLA--EYDTL 71
>gnl|CDD|133330 cd04130, Wrch_1, Wnt-1 responsive Cdc42 homolog (Wrch-1) is a Rho
family GTPase similar to Cdc42. Wrch-1 (Wnt-1
responsive Cdc42 homolog) is a Rho family GTPase that
shares significant sequence and functional similarity
with Cdc42. Wrch-1 was first identified in mouse mammary
epithelial cells, where its transcription is upregulated
in Wnt-1 transformation. Wrch-1 contains N- and
C-terminal extensions relative to cdc42, suggesting
potential differences in cellular localization and
function. The Wrch-1 N-terminal extension contains
putative SH3 domain-binding motifs and has been shown to
bind the SH3 domain-containing protein Grb2, which
increases the level of active Wrch-1 in cells. Unlike
Cdc42, which localizes to the cytosol and perinuclear
membranes, Wrch-1 localizes extensively with the plasma
membrane and endosomes. The membrane association,
localization, and biological activity of Wrch-1 indicate
an atypical model of regulation distinct from other Rho
family GTPases. Most Rho proteins contain a lipid
modification site at the C-terminus, with a typical
sequence motif CaaX, where a = an aliphatic amino acid
and X = any amino acid. Lipid binding is essential for
membrane attachment, a key feature of most Rho proteins.
Due to the presence of truncated sequences in this CD,
the lipid modification site is not available for
annotation.
Length = 173
Score = 30.4 bits (69), Expect = 0.88
Identities = 33/99 (33%), Positives = 46/99 (46%), Gaps = 26/99 (26%)
Query: 93 MLGGKGGVGKTSCAASLAVKFANNGHPT-----------LVVSTD--PAH-SLSDSFAQD 138
+L G G VGKT SL V + NG+PT +VV D P L D+ QD
Sbjct: 4 VLVGDGAVGKT----SLIVSYTTNGYPTEYVPTAFDNFSVVVLVDGKPVRLQLCDTAGQD 59
Query: 139 LTGGQLVPVEGPDFPLFAL---EINPEKAREEFRNVTQK 174
+L P+ PD +F L +NP F+N+++K
Sbjct: 60 -EFDKLRPLCYPDTDVFLLCFSVVNP----SSFQNISEK 93
>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 = 30.9 bits (70), Expect = 1.0
Identities = 16/46 (34%), Positives = 20/46 (43%)
Query: 95 GGKGGVGKTSCAASLAVKFANNGHPTLVVSTDPAHSLSDSFAQDLT 140
G +GGVG TS A+L G LV+ P + L F D
Sbjct: 8 GVRGGVGTTSLTAALGWALQQLGESVLVIDASPDNLLRLHFNVDFD 53
>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 = 29.9 bits (68), Expect = 1.3
Identities = 13/40 (32%), Positives = 18/40 (45%)
Query: 87 TQRKYYMLGGKGGVGKTSCAASLAVKFANNGHPTLVVSTD 126
Q + +L G GVGKT A +L + G+ L T
Sbjct: 45 EQAENLLLLGPPGVGKTHLACALGHQACRAGYSVLFTRTP 84
>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 = 1.6
Identities = 14/41 (34%), Positives = 22/41 (53%)
Query: 242 KLREKIASATSAIKSVFGQEQNRQGASDKLERLRERMVKVR 282
K+RE++ +F E+ + A D++E LRER VR
Sbjct: 413 KIREELGDTMDDNVGIFRTEELLKKAVDEIEELRERYKNVR 453
>gnl|CDD|214940 smart00962, SRP54, SRP54-type protein, GTPase domain. This entry
represents the GTPase domain of the 54 kDa SRP54
component, a GTP-binding protein that interacts with the
signal sequence when it emerges from the ribosome. SRP54
of the signal recognition particle has a three-domain
structure: an N-terminal helical bundle domain, a GTPase
domain, and the M-domain that binds the 7s RNA and also
binds the signal sequence. The extreme C-terminal region
is glycine-rich and lower in complexity and poorly
conserved between species. The GTPase domain is
evolutionary related to P-loop NTPase domains found in a
variety of other proteins.
Length = 197
Score = 29.7 bits (68), Expect = 1.8
Identities = 13/45 (28%), Positives = 19/45 (42%), Gaps = 11/45 (24%)
Query: 83 MVAGTQRKYYMLGGKGGVGKTSCAASLAVKFA-NNGHPTLVVSTD 126
++ G GVGKT+ A LA + G L+V+ D
Sbjct: 5 LLVGPN----------GVGKTTTIAKLAARLKLKGGKKVLLVAAD 39
>gnl|CDD|183270 PRK11670, PRK11670, antiporter inner membrane protein; Provisional.
Length = 369
Score = 30.0 bits (68), Expect = 1.9
Identities = 13/22 (59%), Positives = 16/22 (72%)
Query: 96 GKGGVGKTSCAASLAVKFANNG 117
GKGGVGK+S A +LA+ A G
Sbjct: 115 GKGGVGKSSTAVNLALALAAEG 136
>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 = 29.2 bits (66), Expect = 2.0
Identities = 12/29 (41%), Positives = 15/29 (51%), Gaps = 1/29 (3%)
Query: 93 MLGGKGGVGKTSCAASLAVKFANNGHPTL 121
+L G G GK++ A LA A G P L
Sbjct: 37 LLAGAPGTGKSTLALDLAAAVA-TGRPFL 64
>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 = 29.7 bits (67), Expect = 2.0
Identities = 13/30 (43%), Positives = 21/30 (70%)
Query: 97 KGGVGKTSCAASLAVKFANNGHPTLVVSTD 126
K G GK++ +A++AV FA G+ TL++ D
Sbjct: 26 KPGEGKSTTSANIAVAFAQAGYKTLLIDGD 55
>gnl|CDD|213372 cd11745, Yos9_DD, C-terminal dimerization domain (DD) of
Saccharomyces cerevisiae Yos9 and related proteins.
Yos9 participates in the ER-associated protein
degradation pathway that targets misfolded proteins for
proteolysis. Yos9 is a component of the reductase
degradation (HRD) ubiquitin-ligase complex, specifically
part of the luminal submodule of the ligase. Yos9 scans
proteins for specific oligosaccharide modifications,
which are critical determinants of degradation signal.
It has been shown to be involved in the degradation of
glycosylated proteins and various nonglycosylated
proteins. Yos9 functions as a homodimer where this
domain is responsible for the self-association; it has
an alphabeta-roll domain architecture, and is found at
the C-terminus of the protein. The N-terminal portion of
Yos9 which includes an MRH domain is required for
binding to Hrd3p, another component of the HRD complex.
The DD domain does not appear to be directly binding
Hrd3p.
Length = 124
Score = 28.8 bits (65), Expect = 2.5
Identities = 15/44 (34%), Positives = 17/44 (38%), Gaps = 2/44 (4%)
Query: 197 GELKLGELLDTPPPGLDE--AIAISKGHTLRLLSLPDFLDASIG 238
G L E D L + A S+ L LL LPD L G
Sbjct: 30 GNLNSDEEWDEVEEELYKKFGNAFSRMLGLGLLLLPDGLPLQPG 73
>gnl|CDD|217843 pfam04012, PspA_IM30, PspA/IM30 family. This family includes PspA
a protein that suppresses sigma54-dependent
transcription. The PspA protein, a negative regulator of
the Escherichia coli phage shock psp operon, is produced
when virulence factors are exported through secretins in
many Gram-negative pathogenic bacteria and its homologue
in plants, VIPP1, plays a critical role in thylakoid
biogenesis, essential for photosynthesis. Activation of
transcription by the enhancer-dependent bacterial
sigma(54) containing RNA polymerase occurs through ATP
hydrolysis-driven protein conformational changes enabled
by activator proteins that belong to the large AAA(+)
mechanochemical protein family. It has been shown that
PspA directly and specifically acts upon and binds to
the AAA(+) domain of the PspF transcription activator.
Length = 220
Score = 29.3 bits (66), Expect = 2.5
Identities = 16/49 (32%), Positives = 24/49 (48%), Gaps = 2/49 (4%)
Query: 239 KILKLREKIASATSAIKSVFGQEQNRQGASDKLERLRERMVKVRELFRD 287
LK R K A A A+ + G + A+D ER+ E+ ++ RE D
Sbjct: 136 TALKARLKAAKAQEAVNTSLGSAST-ESATDSFERIEEK-IEEREARAD 182
>gnl|CDD|106194 PRK13232, nifH, nitrogenase reductase; Reviewed.
Length = 273
Score = 29.6 bits (66), Expect = 3.0
Identities = 12/32 (37%), Positives = 19/32 (59%)
Query: 96 GKGGVGKTSCAASLAVKFANNGHPTLVVSTDP 127
GKGG+GK++ +L + G+ L+V DP
Sbjct: 8 GKGGIGKSTTTQNLTAALSTMGNKILLVGCDP 39
>gnl|CDD|225707 COG3166, PilN, Tfp pilus assembly protein PilN [Cell motility and
secretion / Intracellular trafficking and secretion].
Length = 206
Score = 29.3 bits (66), Expect = 3.0
Identities = 20/91 (21%), Positives = 35/91 (38%), Gaps = 7/91 (7%)
Query: 187 MGLGMLVEQLGELKLGELLDTPPPGLDEAIAISKGHTLRLLSLPDFLDASIGKILKLREK 246
+G +L+ G L D + A+ L DA I +I +L+E+
Sbjct: 28 LGGAVLLGIAALALGGLLQDRQIAEQQQRNALLTTEIALL-------DAEIAEIQQLKEQ 80
Query: 247 IASATSAIKSVFGQEQNRQGASDKLERLRER 277
+ ++ + +Q R G S LE+L
Sbjct: 81 TQALLQRLQVIEQLQQKRAGWSVLLEQLANL 111
>gnl|CDD|178101 PLN02483, PLN02483, serine palmitoyltransferase.
Length = 489
Score = 29.7 bits (67), Expect = 3.1
Identities = 34/131 (25%), Positives = 55/131 (41%), Gaps = 21/131 (16%)
Query: 251 TSAIKSVFGQEQNRQGASDKLERLRERMVKVR--------ELFRDTDSTEFVIVTI-PTV 301
SAIK + G++ +GA KL ++RE R E+ D DS I+ P
Sbjct: 352 ISAIKVILGEDGTNRGAQ-KLAQIRENSNFFRSELQKMGFEVLGDNDSPVMPIMLYNPAK 410
Query: 302 MAVSESSRLSESLKKENVPVKRLIVN----QIIPPSASDCKFCAMKRKDQMRALEMIKSD 357
+ S K+NV V ++V ++ A C + R+D ++ALE+I
Sbjct: 411 IPA-----FSRECLKQNVAV--VVVGFPATPLLLARARICISASHSREDLIKALEVISEV 463
Query: 358 SELSSLMLIEA 368
+L + A
Sbjct: 464 GDLVGIKYFPA 474
>gnl|CDD|214682 smart00475, 53EXOc, 5'-3' exonuclease.
Length = 259
Score = 29.1 bits (66), Expect = 3.2
Identities = 8/22 (36%), Positives = 11/22 (50%)
Query: 105 CAASLAVKFANNGHPTLVVSTD 126
A+LA K G+ +VS D
Sbjct: 111 VIATLAKKAEAEGYEVRIVSGD 132
>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 = 29.5 bits (66), Expect = 3.2
Identities = 19/51 (37%), Positives = 28/51 (54%), Gaps = 4/51 (7%)
Query: 96 GKGGVGKTSCAASLAVKFANNGHPTLVVSTDPAHSLSDSFAQDLTGGQLVP 146
GKGG+GK+ A+L+ A G L++ DP SD+ + L GG+ P
Sbjct: 38 GKGGIGKSFTLANLSYMMAQQGKRVLLIGCDPK---SDTTSL-LFGGKACP 84
>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 = 26.6 bits (60), Expect = 5.4
Identities = 12/37 (32%), Positives = 20/37 (54%)
Query: 291 TEFVIVTIPTVMAVSESSRLSESLKKENVPVKRLIVN 327
VIVT P +A+ + + + KK NVP+ ++ N
Sbjct: 26 DGAVIVTTPQDVALLDVRKAIDMFKKVNVPILGVVEN 62
>gnl|CDD|183906 PRK13234, nifH, nitrogenase reductase; Reviewed.
Length = 295
Score = 28.6 bits (64), Expect = 5.8
Identities = 11/32 (34%), Positives = 17/32 (53%)
Query: 96 GKGGVGKTSCAASLAVKFANNGHPTLVVSTDP 127
GKGG+GK++ + + G L+V DP
Sbjct: 11 GKGGIGKSTTSQNTLAALVEMGQKILIVGCDP 42
>gnl|CDD|239860 cd04395, RhoGAP_ARHGAP21, RhoGAP_ARHGAP21: RhoGAP (GTPase-activator
protein [GAP] for Rho-like small GTPases) domain of
ArhGAP21-like proteins. ArhGAP21 is a multi-domain
protein, containing RhoGAP, PH and PDZ domains, and is
believed to play a role in the organization of the
cell-cell junction complex. It has been shown to
function as a GAP of Cdc42 and RhoA, and to interact
with alpha-catenin and Arf6. Small GTPases cluster into
distinct families, and all act as molecular switches,
active in their GTP-bound form but inactive when
GDP-bound. The Rho family of GTPases activates effectors
involved in a wide variety of developmental processes,
including regulation of cytoskeleton formation, cell
proliferation and the JNK signaling pathway. GTPases
generally have a low intrinsic GTPase hydrolytic
activity but there are family-specific groups of GAPs
that enhance the rate of GTP hydrolysis by several
orders of magnitude.
Length = 196
Score = 28.1 bits (63), Expect = 5.9
Identities = 10/49 (20%), Positives = 25/49 (51%), Gaps = 5/49 (10%)
Query: 267 ASDKLERLRERMVKVRELFRDT-----DSTEFVIVTIPTVMAVSESSRL 310
++++E ER+ ++R L ++ + +I + TV SE +++
Sbjct: 102 EANRIEDPVERLKELRRLIHSLPDHHYETLKHLIRHLKTVADNSEVNKM 150
>gnl|CDD|234302 TIGR03664, fut_nucase, futalosine nucleosidase. This enzyme
catalyzes the conversion of futalosine to
de-hypoxanthine futalosine in a pathway for the
biosynthesis of menaquinone distinct from the pathway
observed in E. coli.
Length = 222
Score = 28.5 bits (64), Expect = 6.0
Identities = 19/60 (31%), Positives = 25/60 (41%), Gaps = 2/60 (3%)
Query: 67 VRAVAAPSEAV-SGFDEMVAGTQRKYYMLGGKGGVGKTSCAASLAVKFANNGHPTLVVST 125
V AV A +EAV +G AG GVG + AA+ A A LV++
Sbjct: 4 VTAVTAEAEAVLAGLGGRYAGPIGGARFDVLVTGVGPVNAAAATARLLARA-PYELVINA 62
>gnl|CDD|237312 PRK13236, PRK13236, nitrogenase reductase; Reviewed.
Length = 296
Score = 28.5 bits (63), Expect = 6.1
Identities = 12/32 (37%), Positives = 18/32 (56%)
Query: 96 GKGGVGKTSCAASLAVKFANNGHPTLVVSTDP 127
GKGG+GK++ + + A G L+V DP
Sbjct: 13 GKGGIGKSTTSQNTLAAMAEMGQRILIVGCDP 44
>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 = 6.2
Identities = 12/33 (36%), Positives = 18/33 (54%)
Query: 94 LGGKGGVGKTSCAASLAVKFANNGHPTLVVSTD 126
+ G G GKT+ A L+ + NG +V+S D
Sbjct: 4 IAGPSGSGKTTFAKKLSNQLRVNGIGPVVISLD 36
>gnl|CDD|232804 TIGR00064, ftsY, signal recognition particle-docking protein FtsY.
There is a weak division between FtsY and SRP54; both
are GTPases. In E.coli, ftsY is an essential gene
located in an operon with cell division genes ftsE and
ftsX, but its apparent function is as the signal
recognition particle docking protein [Protein fate,
Protein and peptide secretion and trafficking].
Length = 272
Score = 28.4 bits (64), Expect = 6.4
Identities = 13/35 (37%), Positives = 17/35 (48%)
Query: 92 YMLGGKGGVGKTSCAASLAVKFANNGHPTLVVSTD 126
+ G GVGKT+ A LA K G L+ + D
Sbjct: 75 ILFVGVNGVGKTTTIAKLANKLKKQGKSVLLAAGD 109
>gnl|CDD|236153 PRK08116, PRK08116, hypothetical protein; Validated.
Length = 268
Score = 28.4 bits (64), Expect = 6.6
Identities = 23/85 (27%), Positives = 35/85 (41%), Gaps = 11/85 (12%)
Query: 51 LISISLKQRRSKNS----FQVRAVAAPS-----EAVSGFDEMVAGTQRKYYMLGGKGGVG 101
L S SL + +NS F + + + V F+EM + +L G G G
Sbjct: 69 LKSNSLLDEKFRNSTFENFLFDKGSEKAYKIARKYVKKFEEM--KKENVGLLLWGSVGTG 126
Query: 102 KTSCAASLAVKFANNGHPTLVVSTD 126
KT AA +A + G P + V+
Sbjct: 127 KTYLAACIANELIEKGVPVIFVNFP 151
>gnl|CDD|184774 PRK14635, PRK14635, hypothetical protein; Provisional.
Length = 162
Score = 28.0 bits (62), Expect = 6.8
Identities = 29/131 (22%), Positives = 52/131 (39%), Gaps = 16/131 (12%)
Query: 150 PDFPLFALEINPEKARE----EFRNVTQKDGGTGVKDFMDGMGLGMLVEQLGELKLGELL 205
L++L++N N+ G + + EQ+ KL E L
Sbjct: 18 LPVKLYSLKVNQRPNHSLIEVVLDNLEHPYGSVSLLE----------CEQVSR-KLKEEL 66
Query: 206 DTPPPGLDEAIAISKGHTLRLLSLPDFLDASIGKILKLREKIASATSAIKSVFGQEQNRQ 265
+ P LD + +S R L LP+ LD G ++L + + + +F + NR
Sbjct: 67 ERISPDLDFTLKVSSAGAERKLRLPEDLDRFRGIPVRLVFRSEESEKWQEGIF-RLVNRD 125
Query: 266 GASDKLERLRE 276
G +LE+ ++
Sbjct: 126 GDQVELEKFQK 136
>gnl|CDD|224699 COG1785, PhoA, Alkaline phosphatase [Inorganic ion transport and
metabolism].
Length = 482
Score = 28.5 bits (64), Expect = 7.1
Identities = 9/27 (33%), Positives = 11/27 (40%), Gaps = 1/27 (3%)
Query: 106 AASLAVKFANNGHPTLVVST-DPAHSL 131
A A+ FA TLV+ T D
Sbjct: 331 AVQAALDFAEKDGNTLVIVTADHETGG 357
>gnl|CDD|233459 TIGR01541, tape_meas_lam_C, phage tail tape measure protein, lambda
family. This model represents a relatively
well-conserved region near the C-terminus of the tape
measure protein of a lambda and related phage. This
protein, which controls phage tail length, is typically
about 1000 residues in length. Both low-complexity
sequence and insertion/deletion events appear common in
this family. Mutational studies suggest a ruler or
template role in the determination of phage tail length.
Similar behavior is attributed to proteins from
distantly related or unrelated families in other phage
[Mobile and extrachromosomal element functions, Prophage
functions].
Length = 332
Score = 28.3 bits (63), Expect = 7.2
Identities = 18/64 (28%), Positives = 34/64 (53%), Gaps = 1/64 (1%)
Query: 215 AIAISKGHTLRLLSLPDFLDASIGKILKLREKIASATSAIKSVFGQEQNRQGASDKL-ER 273
++ + L+ L L+ + K L+ +K+A AT++I++ ++ +R G DK ER
Sbjct: 25 SLQSRSDEIIALIKLEKLLEEAERKALEALKKLAEATASIRAQNKRQLDRFGLGDKQRER 84
Query: 274 LRER 277
L R
Sbjct: 85 LDAR 88
>gnl|CDD|130386 TIGR01319, glmL_fam, conserved hypothetical protein. This small
family includes, so far, an uncharacterized protein from
E. coli O157:H7 and GlmL from Clostridium tetanomorphum
and Clostridium cochlearium. GlmL is located between the
genes for the two subunits, epsilon (GlmE) and sigma
(GlmS), of the coenzyme-B12-dependent glutamate mutase
(methylaspartate mutase), the first enzyme in a pathway
of glutamate fermentation. Members shows significant
sequence similarity to the hydantoinase branch of the
hydantoinase/oxoprolinase family (pfam01968).
Length = 463
Score = 28.5 bits (63), Expect = 7.5
Identities = 23/79 (29%), Positives = 37/79 (46%), Gaps = 12/79 (15%)
Query: 160 NPEKAREEFRNVTQKDGGTGVKDFMDGMGLGMLVEQLGELKLGELLDTPPPGLDEAIAIS 219
NPE ARE ++ +K ++ GL + +G EL+ TP + A AI+
Sbjct: 191 NPEAAREAICDIF-------LKKIVEAKGLDNAEDFIG----EELMPTPAAVFEAAKAIA 239
Query: 220 KGHTLRLLSLPDFLDASIG 238
+G T + + DF+ IG
Sbjct: 240 EG-TDKDDGIGDFILIDIG 257
>gnl|CDD|176509 cd08566, GDPD_AtGDE_like, Glycerophosphodiester phosphodiesterase
domain of Agrobacterium tumefaciens and similar
proteins. This subfamily corresponds to the
glycerophosphodiester phosphodiesterase domain (GDPD)
present in Agrobacterium tumefaciens
glycerophosphodiester phosphodiesterase (AtGDE, EC
3.1.4.46) and its uncharacterized eukaryotic homolgoues.
Members in this family shows high sequence similarity to
Escherichia coli GP-GDE, which catalyzes the degradation
of glycerophosphodiesters to produce
sn-glycerol-3-phosphate (G3P) and the corresponding
alcohols. AtGDE exists as a hexamer that is a trimer of
dimers, which is unique among current known GDPD family
members. However, it remains unclear if the hexamer
plays a physiological role in AtGDE enzymatic function.
Length = 240
Score = 28.0 bits (63), Expect = 7.8
Identities = 19/57 (33%), Positives = 34/57 (59%), Gaps = 7/57 (12%)
Query: 191 MLVEQLGELKL----GELLDTPPPGLDEAIAISKGHTLRLLSLPDFLDASIGKILKL 243
+ + ++ +L+L GE+ D P L+EA+A +KG LL+L D DA + +++ L
Sbjct: 65 LTLAEIRKLRLKDGDGEVTDEKVPTLEEALAWAKGKI--LLNL-DLKDADLDEVIAL 118
>gnl|CDD|236482 PRK09361, radB, DNA repair and recombination protein RadB;
Provisional.
Length = 225
Score = 27.9 bits (63), Expect = 7.9
Identities = 11/22 (50%), Positives = 13/22 (59%)
Query: 96 GKGGVGKTSCAASLAVKFANNG 117
G G GKT+ LAV+ A NG
Sbjct: 30 GPPGSGKTNICLQLAVEAAKNG 51
>gnl|CDD|183703 PRK12724, PRK12724, flagellar biosynthesis regulator FlhF;
Provisional.
Length = 432
Score = 28.4 bits (63), Expect = 7.9
Identities = 20/49 (40%), Positives = 25/49 (51%), Gaps = 3/49 (6%)
Query: 68 RAVAAPSEAVSGFDEMVAGT---QRKYYMLGGKGGVGKTSCAASLAVKF 113
RAV E VS ++ +GT QRK G G GKT+ A LA K+
Sbjct: 199 RAVTYLEERVSVDSDLFSGTGKNQRKVVFFVGPTGSGKTTSIAKLAAKY 247
>gnl|CDD|227298 COG4963, CpaE, Flp pilus assembly protein, ATPase CpaE
[Intracellular trafficking and secretion].
Length = 366
Score = 28.2 bits (63), Expect = 8.3
Identities = 16/65 (24%), Positives = 28/65 (43%), Gaps = 9/65 (13%)
Query: 290 STEFVIVTIPTVMAVSESSRLSESLKK--ENVPVKRLIVNQIIPPSASDCKFCAMKRKDQ 347
S E VIV P++ ++ + L + LK+ N P L++N++ P + D
Sbjct: 240 SDEIVIVAEPSLASLRNAKELLDELKRLRPNDPKPILVLNRVGVPKRPE-------PSDL 292
Query: 348 MRALE 352
L
Sbjct: 293 EEILG 297
>gnl|CDD|183907 PRK13235, nifH, nitrogenase reductase; Reviewed.
Length = 274
Score = 27.9 bits (62), Expect = 8.3
Identities = 12/32 (37%), Positives = 17/32 (53%)
Query: 96 GKGGVGKTSCAASLAVKFANNGHPTLVVSTDP 127
GKGG+GK++ + A G +VV DP
Sbjct: 8 GKGGIGKSTTTQNTVAGLAEMGKKVMVVGCDP 39
>gnl|CDD|132062 TIGR03017, EpsF, chain length determinant protein EpsF. Sequences
in this family of proteins are members of the chain
length determinant family (pfam02706) which includes the
wzc protein from E.coli. This family of proteins are
homologous to the EpsF protein of the methanolan
biosynthesis operon of Methylobacillus species strain
12S. The distribution of this protein appears to be
restricted to a subset of exopolysaccharide operons
containing a syntenic grouping of genes including a
variant of the EpsH exosortase protein. Exosortase has
been proposed to be involved in the targetting and
processing of proteins containing the PEP-CTERM domain
to the exopolysaccharide layer.
Length = 444
Score = 28.2 bits (63), Expect = 9.0
Identities = 11/49 (22%), Positives = 22/49 (44%), Gaps = 4/49 (8%)
Query: 242 KLREKIASATSAIKSVFG-QEQNRQGASDKLERLRERMVKVRELFRDTD 289
+L +I TS++ + +Q + LE + +++ EL R D
Sbjct: 297 QLNAEIKKVTSSVGTNSRILKQREAELREALENQKAKVL---ELNRQRD 342
>gnl|CDD|234232 TIGR03499, FlhF, flagellar biosynthetic protein FlhF. [Cellular
processes, Chemotaxis and motility].
Length = 283
Score = 28.1 bits (63), Expect = 9.1
Identities = 13/44 (29%), Positives = 20/44 (45%), Gaps = 2/44 (4%)
Query: 85 AGTQRKYYMLGGKGGVGKTSCAASLAVKFA--NNGHPTLVVSTD 126
+ L G GVGKT+ A LA +F + +++TD
Sbjct: 191 ILERGGVIALVGPTGVGKTTTLAKLAARFVLEHGKKKVALITTD 234
>gnl|CDD|223382 COG0305, DnaB, Replicative DNA helicase [DNA replication,
recombination, and repair].
Length = 435
Score = 28.0 bits (63), Expect = 9.2
Identities = 13/50 (26%), Positives = 28/50 (56%), Gaps = 4/50 (8%)
Query: 78 SGF---DEMVAGTQR-KYYMLGGKGGVGKTSCAASLAVKFANNGHPTLVV 123
+GF DE+ +G + ++ + G+GKT+ A ++A+ A +G + +
Sbjct: 181 TGFTDLDEITSGFRPGDLIIVAARPGMGKTALALNIALNAAADGRKPVAI 230
>gnl|CDD|182010 PRK09638, PRK09638, RNA polymerase sigma factor SigY; Reviewed.
Length = 176
Score = 27.3 bits (61), Expect = 9.4
Identities = 13/35 (37%), Positives = 16/35 (45%), Gaps = 6/35 (17%)
Query: 34 FMGLLSFSPKTSSFSTGLISISLK-----QRRSKN 63
L SF S FST LISI+ + R+ K
Sbjct: 57 IENLSSFQG-RSKFSTWLISIASRLYKDHLRKQKR 90
>gnl|CDD|223626 COG0552, FtsY, Signal recognition particle GTPase [Intracellular
trafficking and secretion].
Length = 340
Score = 28.0 bits (63), Expect = 9.5
Identities = 12/35 (34%), Positives = 16/35 (45%)
Query: 92 YMLGGKGGVGKTSCAASLAVKFANNGHPTLVVSTD 126
+ G GVGKT+ A LA G L+ + D
Sbjct: 142 ILFVGVNGVGKTTTIAKLAKYLKQQGKSVLLAAGD 176
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 0.132 0.368
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: 19,618,693
Number of extensions: 1918667
Number of successful extensions: 2244
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2219
Number of HSP's successfully gapped: 137
Length of query: 390
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 291
Effective length of database: 6,546,556
Effective search space: 1905047796
Effective search space used: 1905047796
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 (21.7 bits)
S2: 60 (26.6 bits)