RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3632
(121 letters)
>gnl|CDD|223540 COG0464, SpoVK, ATPases of the AAA+ class [Posttranslational
modification, protein turnover, chaperones].
Length = 494
Score = 82.9 bits (205), Expect = 9e-20
Identities = 40/97 (41%), Positives = 58/97 (59%), Gaps = 2/97 (2%)
Query: 21 IGGLDKEFTAIFRRAFASRVFPPEVVEQLGCQHVKGILLYGPPGTGKTLMARQIGQMLNA 80
IGGL+ E + A + + PE+ +LG + KG+LLYGPPGTGKTL+A+ + +
Sbjct: 244 IGGLE-EAKEELKEAIETPLKRPELFRKLGLRPPKGVLLYGPPGTGKTLLAKAVALESRS 302
Query: 81 REPKIVNGPQVLDKYVGESEANVRRLFADAEEEEKRV 117
R V G ++L K+VGESE N+R LF A + +
Sbjct: 303 RFIS-VKGSELLSKWVGESEKNIRELFEKARKLAPSI 338
Score = 61.4 bits (149), Expect = 3e-12
Identities = 36/75 (48%), Positives = 51/75 (68%), Gaps = 2/75 (2%)
Query: 43 PEVVEQLGCQHVKGILLYGPPGTGKTLMARQIGQMLNAREPKIVNGPQVLDKYVGESEAN 102
PE+ ++LG + KG+LL+GPPGTGKTL+AR + E +NGP++L KYVGESE
Sbjct: 7 PELFKKLGIEPPKGVLLHGPPGTGKTLLARALAN--EGAEFLSINGPEILSKYVGESELR 64
Query: 103 VRRLFADAEEEEKRV 117
+R LF +AE+ +
Sbjct: 65 LRELFEEAEKLAPSI 79
>gnl|CDD|233328 TIGR01243, CDC48, AAA family ATPase, CDC48 subfamily. This
subfamily of the AAA family ATPases includes two members
each from three archaeal species. It also includes yeast
CDC48 (cell division control protein 48) and the human
ortholog, transitional endoplasmic reticulum ATPase
(valosin-containing protein). These proteins in
eukaryotes are involved in the budding and transfer of
membrane from the transitional endoplasmic reticulum to
the Golgi apparatus.
Length = 733
Score = 80.7 bits (199), Expect = 6e-19
Identities = 42/92 (45%), Positives = 56/92 (60%), Gaps = 2/92 (2%)
Query: 21 IGGLDKEFTAIFRRAFASRVFPPEVVEQLGCQHVKGILLYGPPGTGKTLMARQIGQMLNA 80
IGGL + I R + PE+ E LG + KG+LLYGPPGTGKTL+A+ + A
Sbjct: 180 IGGLKEAKEKI-REMVELPMKHPELFEHLGIEPPKGVLLYGPPGTGKTLLAKAVANEAGA 238
Query: 81 REPKIVNGPQVLDKYVGESEANVRRLFADAEE 112
I NGP+++ KY GESE +R +F +AEE
Sbjct: 239 YFISI-NGPEIMSKYYGESEERLREIFKEAEE 269
Score = 68.8 bits (168), Expect = 8e-15
Identities = 39/92 (42%), Positives = 56/92 (60%), Gaps = 2/92 (2%)
Query: 21 IGGLDKEFTAIFRRAFASRVFPPEVVEQLGCQHVKGILLYGPPGTGKTLMARQIGQMLNA 80
IGGL+ E R A + PE+ E++G + KG+LL+GPPGTGKTL+A+ + A
Sbjct: 455 IGGLE-EVKQELREAVEWPLKHPEIFEKMGIRPPKGVLLFGPPGTGKTLLAKAVATESGA 513
Query: 81 REPKIVNGPQVLDKYVGESEANVRRLFADAEE 112
V GP++L K+VGESE +R +F A +
Sbjct: 514 NFIA-VRGPEILSKWVGESEKAIREIFRKARQ 544
>gnl|CDD|215649 pfam00004, AAA, ATPase family associated with various cellular
activities (AAA). AAA family proteins often perform
chaperone-like functions that assist in the assembly,
operation, or disassembly of protein complexes.
Length = 131
Score = 73.8 bits (182), Expect = 4e-18
Identities = 26/57 (45%), Positives = 39/57 (68%), Gaps = 1/57 (1%)
Query: 57 ILLYGPPGTGKTLMARQIGQMLNAREPKIVNGPQVLDKYVGESEANVRRLFADAEEE 113
+LLYGPPGTGKT +A+ + + L A ++G +++ KYVGESE +R LF A++
Sbjct: 1 LLLYGPPGTGKTTLAKAVAKELGAP-FIEISGSELVSKYVGESEKRLRELFEAAKKL 56
>gnl|CDD|224143 COG1222, RPT1, ATP-dependent 26S proteasome regulatory subunit
[Posttranslational modification, protein turnover,
chaperones].
Length = 406
Score = 75.8 bits (187), Expect = 2e-17
Identities = 41/104 (39%), Positives = 59/104 (56%), Gaps = 4/104 (3%)
Query: 11 SPSFDFNKMGIGGLDKEFTAIFRRAFASRVFPPEVVEQLGCQHVKGILLYGPPGTGKTLM 70
P + IGGLD++ I R + PE+ E+LG KG+LLYGPPGTGKTL+
Sbjct: 145 KPDVTYE--DIGGLDEQIQEI-REVVELPLKNPELFEELGIDPPKGVLLYGPPGTGKTLL 201
Query: 71 ARQIGQMLNAREPKIVNGPQVLDKYVGESEANVRRLFADAEEEE 114
A+ + +A ++V G +++ KY+GE VR LF A E+
Sbjct: 202 AKAVANQTDATFIRVV-GSELVQKYIGEGARLVRELFELAREKA 244
>gnl|CDD|200312 TIGR03689, pup_AAA, proteasome ATPase. In the Actinobacteria, as
shown for Mycobacterium tuberculosis, some proteins are
modified by ligation between an epsilon-amino group of a
lysine side chain and the C-terminal carboxylate of the
ubiquitin-like protein Pup. This modification leads to
protein degradation by the archaeal-like proteasome
found in the Actinobacteria. Members of this protein
family belong to the AAA family of ATPases and tend to
be clustered with the genes for Pup, the Pup ligase
PafA, and structural components of the proteasome. This
protein forms hexameric rings with ATPase activity
[Protein fate, Degradation of proteins, peptides, and
glycopeptides].
Length = 512
Score = 72.8 bits (179), Expect = 3e-16
Identities = 41/101 (40%), Positives = 57/101 (56%), Gaps = 10/101 (9%)
Query: 21 IGGLDKEFTAIFRRAFASRVFPPEVVEQLGCQHVKGILLYGPPGTGKTLMARQIGQMLNA 80
IGGL + I R A PE+ + G + KG+LLYGPPG GKTL+A+ + L A
Sbjct: 184 IGGLGSQIEQI-RDAVELPFLHPELYREYGLKPPKGVLLYGPPGCGKTLIAKAVANSLAA 242
Query: 81 R-------EPKIVN--GPQVLDKYVGESEANVRRLFADAEE 112
R + +N GP++L+KYVGE+E +R +F A E
Sbjct: 243 RIGAEGGGKSYFLNIKGPELLNKYVGETERQIRLIFQRARE 283
>gnl|CDD|130309 TIGR01242, 26Sp45, 26S proteasome subunit P45 family. Many
proteins may score above the trusted cutoff because an
internal.
Length = 364
Score = 72.1 bits (177), Expect = 5e-16
Identities = 44/113 (38%), Positives = 68/113 (60%), Gaps = 9/113 (7%)
Query: 1 MEVQPRQSIISPSFDFNKMGIGGLDKEFTAIFRRAFASRVFPPEVVEQLGCQHVKGILLY 60
MEV+ R P+ + IGGL+++ I R A + PE+ E++G + KG+LLY
Sbjct: 111 MEVEER-----PNVSYED--IGGLEEQIREI-REAVELPLKHPELFEEVGIEPPKGVLLY 162
Query: 61 GPPGTGKTLMARQIGQMLNAREPKIVNGPQVLDKYVGESEANVRRLFADAEEE 113
GPPGTGKTL+A+ + NA ++V G +++ KY+GE VR +F A+E+
Sbjct: 163 GPPGTGKTLLAKAVAHETNATFIRVV-GSELVRKYIGEGARLVREIFELAKEK 214
>gnl|CDD|179699 PRK03992, PRK03992, proteasome-activating nucleotidase;
Provisional.
Length = 389
Score = 69.1 bits (170), Expect = 6e-15
Identities = 44/114 (38%), Positives = 67/114 (58%), Gaps = 9/114 (7%)
Query: 1 MEVQPRQSIISPSFDFNKMGIGGLDKEFTAIFRRAFASRVFPPEVVEQLGCQHVKGILLY 60
MEV I SP+ + IGGL+++ + R A + PE+ E++G + KG+LLY
Sbjct: 120 MEV-----IESPNVTYED--IGGLEEQIREV-REAVELPLKKPELFEEVGIEPPKGVLLY 171
Query: 61 GPPGTGKTLMARQIGQMLNAREPKIVNGPQVLDKYVGESEANVRRLFADAEEEE 114
GPPGTGKTL+A+ + NA ++V G +++ K++GE VR LF A E+
Sbjct: 172 GPPGTGKTLLAKAVAHETNATFIRVV-GSELVQKFIGEGARLVRELFELAREKA 224
>gnl|CDD|185575 PTZ00361, PTZ00361, 26 proteosome regulatory subunit 4-like
protein; Provisional.
Length = 438
Score = 65.2 bits (159), Expect = 2e-13
Identities = 36/92 (39%), Positives = 58/92 (63%), Gaps = 2/92 (2%)
Query: 21 IGGLDKEFTAIFRRAFASRVFPPEVVEQLGCQHVKGILLYGPPGTGKTLMARQIGQMLNA 80
IGGL+++ I + A + PE+ + +G + KG++LYGPPGTGKTL+A+ + +A
Sbjct: 185 IGGLEQQIQEI-KEAVELPLTHPELYDDIGIKPPKGVILYGPPGTGKTLLAKAVANETSA 243
Query: 81 REPKIVNGPQVLDKYVGESEANVRRLFADAEE 112
++V G +++ KY+G+ VR LF AEE
Sbjct: 244 TFLRVV-GSELIQKYLGDGPKLVRELFRVAEE 274
>gnl|CDD|240423 PTZ00454, PTZ00454, 26S protease regulatory subunit 6B-like
protein; Provisional.
Length = 398
Score = 61.3 bits (149), Expect = 3e-12
Identities = 38/92 (41%), Positives = 54/92 (58%), Gaps = 2/92 (2%)
Query: 21 IGGLDKEFTAIFRRAFASRVFPPEVVEQLGCQHVKGILLYGPPGTGKTLMARQIGQMLNA 80
IGGLD + I R A + PE+ EQ+G +G+LLYGPPGTGKT++A+ + A
Sbjct: 147 IGGLDIQKQEI-REAVELPLTCPELYEQIGIDPPRGVLLYGPPGTGKTMLAKAVAHHTTA 205
Query: 81 REPKIVNGPQVLDKYVGESEANVRRLFADAEE 112
++V G + + KY+GE VR +F A E
Sbjct: 206 TFIRVV-GSEFVQKYLGEGPRMVRDVFRLARE 236
>gnl|CDD|99707 cd00009, AAA, The AAA+ (ATPases Associated with a wide variety of
cellular Activities) superfamily represents an ancient
group of ATPases belonging to the ASCE (for additional
strand, catalytic E) division of the P-loop NTPase fold.
The ASCE division also includes ABC, RecA-like,
VirD4-like, PilT-like, and SF1/2 helicases. Members of
the AAA+ ATPases function as molecular chaperons, ATPase
subunits of proteases, helicases, or nucleic-acid
stimulated ATPases. The AAA+ proteins contain several
distinct features in addition to the conserved
alpha-beta-alpha core domain structure and the Walker A
and B motifs of the P-loop NTPases.
Length = 151
Score = 54.5 bits (131), Expect = 2e-10
Identities = 22/64 (34%), Positives = 28/64 (43%), Gaps = 2/64 (3%)
Query: 55 KGILLYGPPGTGKTLMARQIGQMLNAREPKI--VNGPQVLDKYVGESEANVRRLFADAEE 112
K +LLYGPPGTGKT +AR I L +N +L+ V + E
Sbjct: 20 KNLLLYGPPGTGKTTLARAIANELFRPGAPFLYLNASDLLEGLVVAELFGHFLVRLLFEL 79
Query: 113 EEKR 116
EK
Sbjct: 80 AEKA 83
>gnl|CDD|214386 CHL00176, ftsH, cell division protein; Validated.
Length = 638
Score = 54.7 bits (132), Expect = 7e-10
Identities = 35/96 (36%), Positives = 52/96 (54%), Gaps = 11/96 (11%)
Query: 21 IGGLD---KEFTAIFRRAFASRVFPPEVVEQLGCQHVKGILLYGPPGTGKTLMARQIGQM 77
I G++ +EF + S + PE +G + KG+LL GPPGTGKTL+A+ I
Sbjct: 185 IAGIEEAKEEFEEV-----VSFLKKPERFTAVGAKIPKGVLLVGPPGTGKTLLAKAIAG- 238
Query: 78 LNAREPKI-VNGPQVLDKYVGESEANVRRLFADAEE 112
A P ++G + ++ +VG A VR LF A+E
Sbjct: 239 -EAEVPFFSISGSEFVEMFVGVGAARVRDLFKKAKE 273
>gnl|CDD|224144 COG1223, COG1223, Predicted ATPase (AAA+ superfamily) [General
function prediction only].
Length = 368
Score = 52.5 bits (126), Expect = 3e-09
Identities = 19/59 (32%), Positives = 33/59 (55%), Gaps = 3/59 (5%)
Query: 55 KGILLYGPPGTGKTLMARQIGQMLNAREPKI-VNGPQVLDKYVGESEANVRRLFADAEE 112
K +L YGPPGTGKT+MA+ + P + V +++ ++VG+ + L+ A +
Sbjct: 152 KNVLFYGPPGTGKTMMAKALANEAKV--PLLLVKATELIGEHVGDGARRIHELYERARK 208
>gnl|CDD|233327 TIGR01241, FtsH_fam, ATP-dependent metalloprotease FtsH.
HflB(FtsH) is a pleiotropic protein required for correct
cell division in bacteria. It has ATP-dependent zinc
metalloprotease activity. It was formerly designated
cell division protein FtsH [Cellular processes, Cell
division, Protein fate, Degradation of proteins,
peptides, and glycopeptides].
Length = 495
Score = 50.7 bits (122), Expect = 1e-08
Identities = 27/74 (36%), Positives = 42/74 (56%), Gaps = 9/74 (12%)
Query: 43 PEVVEQLGCQHVKGILLYGPPGTGKTLMARQIGQMLNAREPKI----VNGPQVLDKYVGE 98
P +LG + KG+LL GPPGTGKTL+A+ + A E + ++G ++ +VG
Sbjct: 77 PSKFTKLGAKIPKGVLLVGPPGTGKTLLAKAV-----AGEAGVPFFSISGSDFVEMFVGV 131
Query: 99 SEANVRRLFADAEE 112
+ VR LF A++
Sbjct: 132 GASRVRDLFEQAKK 145
>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 = 46.6 bits (110), Expect = 2e-07
Identities = 19/79 (24%), Positives = 30/79 (37%), Gaps = 16/79 (20%)
Query: 55 KGILLYGPPGTGKTLMARQIGQMLNAREPKIV----------------NGPQVLDKYVGE 98
+ IL+ GPPG+GKT +AR + + L ++ K G
Sbjct: 3 EVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKASGS 62
Query: 99 SEANVRRLFADAEEEEKRV 117
E +R A A + + V
Sbjct: 63 GELRLRLALALARKLKPDV 81
>gnl|CDD|182683 PRK10733, hflB, ATP-dependent metalloprotease; Reviewed.
Length = 644
Score = 47.0 bits (111), Expect = 3e-07
Identities = 27/74 (36%), Positives = 44/74 (59%), Gaps = 9/74 (12%)
Query: 43 PEVVEQLGCQHVKGILLYGPPGTGKTLMARQIGQMLNAREPKI----VNGPQVLDKYVGE 98
P ++LG + KG+L+ GPPGTGKTL+A+ I A E K+ ++G ++ +VG
Sbjct: 174 PSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAI-----AGEAKVPFFTISGSDFVEMFVGV 228
Query: 99 SEANVRRLFADAEE 112
+ VR +F A++
Sbjct: 229 GASRVRDMFEQAKK 242
>gnl|CDD|223541 COG0465, HflB, ATP-dependent Zn proteases [Posttranslational
modification, protein turnover, chaperones].
Length = 596
Score = 43.8 bits (104), Expect = 4e-06
Identities = 27/72 (37%), Positives = 41/72 (56%), Gaps = 9/72 (12%)
Query: 43 PEVVEQLGCQHVKGILLYGPPGTGKTLMARQIGQMLNAREPKI----VNGPQVLDKYVGE 98
P+ + LG + KG+LL GPPGTGKTL+A+ + A E + ++G ++ +VG
Sbjct: 172 PKKYQALGAKIPKGVLLVGPPGTGKTLLAKAV-----AGEAGVPFFSISGSDFVEMFVGV 226
Query: 99 SEANVRRLFADA 110
+ VR LF A
Sbjct: 227 GASRVRDLFEQA 238
>gnl|CDD|225164 COG2255, RuvB, Holliday junction resolvasome, helicase subunit
[DNA replication, recombination, and repair].
Length = 332
Score = 41.4 bits (98), Expect = 3e-05
Identities = 18/38 (47%), Positives = 23/38 (60%), Gaps = 2/38 (5%)
Query: 57 ILLYGPPGTGKTLMARQIGQMLNAREPKIVNGPQVLDK 94
+LL+GPPG GKT +A I L KI +GP L+K
Sbjct: 55 VLLFGPPGLGKTTLAHIIANELGVN-LKITSGP-ALEK 90
>gnl|CDD|237355 PRK13342, PRK13342, recombination factor protein RarA; Reviewed.
Length = 413
Score = 41.2 bits (98), Expect = 3e-05
Identities = 15/52 (28%), Positives = 21/52 (40%), Gaps = 13/52 (25%)
Query: 30 AIFRRAFASRVFPPEVVEQLGCQHVKGILLYGPPGTGKTLMARQIGQMLNAR 81
RR + ++L+GPPGTGKT +AR I +A
Sbjct: 25 KPLRRMIEAGRLSS-------------MILWGPPGTGKTTLARIIAGATDAP 63
>gnl|CDD|234619 PRK00080, ruvB, Holliday junction DNA helicase RuvB; Reviewed.
Length = 328
Score = 40.9 bits (97), Expect = 4e-05
Identities = 17/38 (44%), Positives = 23/38 (60%), Gaps = 2/38 (5%)
Query: 57 ILLYGPPGTGKTLMARQIGQMLNAREPKIVNGPQVLDK 94
+LLYGPPG GKT +A I + +I +GP L+K
Sbjct: 54 VLLYGPPGLGKTTLANIIANEMGVN-IRITSGP-ALEK 89
>gnl|CDD|188437 TIGR03922, T7SS_EccA, type VII secretion AAA-ATPase EccA. This
model represents the AAA family ATPase, EccA, of the
actinobacterial flavor of type VII secretion systems.
Species such as Mycobacterium tuberculosis have several
instances of this system per genome, designated EccA1,
EccA2, etc [Protein fate, Protein and peptide secretion
and trafficking].
Length = 557
Score = 41.0 bits (96), Expect = 4e-05
Identities = 21/57 (36%), Positives = 33/57 (57%), Gaps = 6/57 (10%)
Query: 52 QHVKGILLYGPPGTGKTLMARQIGQMLNA----REPKI--VNGPQVLDKYVGESEAN 102
Q +L GPPGTGKT +AR + ++ R+P + V+ ++ +Y+GESEA
Sbjct: 310 QTSNHMLFAGPPGTGKTTIARVVAKIYCGLGVLRKPLVREVSRADLIGQYIGESEAK 366
>gnl|CDD|225165 COG2256, MGS1, ATPase related to the helicase subunit of the
Holliday junction resolvase [DNA replication,
recombination, and repair].
Length = 436
Score = 39.9 bits (94), Expect = 9e-05
Identities = 23/70 (32%), Positives = 30/70 (42%), Gaps = 16/70 (22%)
Query: 28 FTAIFRRAFASRVFPPEVVEQLGCQHV---KGIL-------------LYGPPGTGKTLMA 71
FR A R+ P + E +G +H+ L L+GPPGTGKT +A
Sbjct: 6 SDNEFRMPLAERLRPKSLDEVVGQEHLLGEGKPLRRAVEAGHLHSMILWGPPGTGKTTLA 65
Query: 72 RQIGQMLNAR 81
R I NA
Sbjct: 66 RLIAGTTNAA 75
>gnl|CDD|219538 pfam07728, AAA_5, AAA domain (dynein-related subfamily). This
Pfam entry includes some of the AAA proteins not
detected by the pfam00004 model.
Length = 135
Score = 38.8 bits (91), Expect = 1e-04
Identities = 14/35 (40%), Positives = 21/35 (60%)
Query: 56 GILLYGPPGTGKTLMARQIGQMLNAREPKIVNGPQ 90
G+LL GPPGTGK+ +A ++ L+ R V +
Sbjct: 1 GVLLVGPPGTGKSELAERLAAALSNRPVFYVQLTR 35
>gnl|CDD|147949 pfam06068, TIP49, TIP49 C-terminus. This family consists of the
C-terminal region of several eukaryotic and archaeal
RuvB-like 1 (Pontin or TIP49a) and RuvB-like 2 (Reptin
or TIP49b) proteins. The N-terminal domain contains the
pfam00004 domain. In zebrafish, the liebeskummer (lik)
mutation, causes development of hyperplastic embryonic
hearts. lik encodes Reptin, a component of a
DNA-stimulated ATPase complex. Beta-catenin and Pontin,
a DNA-stimulated ATPase that is often part of complexes
with Reptin, are in the same genetic pathways. The
Reptin/Pontin ratio serves to regulate heart growth
during development, at least in part via the
beta-catenin pathway. TBP-interacting protein 49 (TIP49)
was originally identified as a TBP-binding protein, and
two related proteins are encoded by individual genes,
tip49a and b. Although the function of this gene family
has not been elucidated, they are supposed to play a
critical role in nuclear events because they interact
with various kinds of nuclear factors and have DNA
helicase activities.TIP49a has been suggested to act as
an autoantigen in some patients with autoimmune
diseases.
Length = 395
Score = 38.1 bits (89), Expect = 4e-04
Identities = 22/67 (32%), Positives = 35/67 (52%), Gaps = 4/67 (5%)
Query: 55 KGILLYGPPGTGKTLMARQIGQMLNAREP-KIVNGPQVLDKYVGESEA---NVRRLFADA 110
+ +L+ GPPGTGKT +A I + L P ++G +V + ++EA R+
Sbjct: 51 RAVLIAGPPGTGKTALAIAISKELGEDTPFCPISGSEVYSLEMKKTEALTQAFRKAIGVR 110
Query: 111 EEEEKRV 117
+EEK V
Sbjct: 111 IKEEKEV 117
>gnl|CDD|129721 TIGR00635, ruvB, Holliday junction DNA helicase, RuvB subunit.
All proteins in this family for which functions are
known are 5'-3' DNA helicases that, as part of a
complex with RuvA homologs serve as a 5'-3' Holliday
junction helicase. RuvA specifically binds Holliday
junctions as a sandwich of two tetramers and maintains
the configuration of the junction. It forms a complex
with two hexameric rings of RuvB, the subunit that
contains helicase activity. The complex drives
ATP-dependent branch migration of the Holliday junction
recombination intermediate. The endonuclease RuvC
resolves junctions [DNA metabolism, DNA replication,
recombination, and repair].
Length = 305
Score = 38.0 bits (89), Expect = 4e-04
Identities = 18/38 (47%), Positives = 23/38 (60%), Gaps = 2/38 (5%)
Query: 57 ILLYGPPGTGKTLMARQIGQMLNAREPKIVNGPQVLDK 94
+LLYGPPG GKT +A I + KI +GP L+K
Sbjct: 33 LLLYGPPGLGKTTLAHIIANEMGV-NLKITSGP-ALEK 68
>gnl|CDD|216186 pfam00910, RNA_helicase, RNA helicase. This family includes RNA
helicases thought to be involved in duplex unwinding
during viral RNA replication. Members of this family
are found in a variety of single stranded RNA viruses.
Length = 105
Score = 36.4 bits (85), Expect = 5e-04
Identities = 11/22 (50%), Positives = 16/22 (72%)
Query: 57 ILLYGPPGTGKTLMARQIGQML 78
I LYGPPG GK+ +A+ + + L
Sbjct: 1 IWLYGPPGCGKSTLAKYLARAL 22
>gnl|CDD|235422 PRK05342, clpX, ATP-dependent protease ATP-binding subunit ClpX;
Provisional.
Length = 412
Score = 37.8 bits (89), Expect = 5e-04
Identities = 12/23 (52%), Positives = 19/23 (82%)
Query: 57 ILLYGPPGTGKTLMARQIGQMLN 79
ILL GP G+GKTL+A+ + ++L+
Sbjct: 111 ILLIGPTGSGKTLLAQTLARILD 133
>gnl|CDD|234063 TIGR02928, TIGR02928, orc1/cdc6 family replication initiation
protein. Members of this protein family are found
exclusively in the archaea. This set of DNA binding
proteins shows homology to the origin recognition
complex subunit 1/cell division control protein 6
family in eukaryotes. Several members may be found in
genome and interact with each other [DNA metabolism,
DNA replication, recombination, and repair].
Length = 365
Score = 37.6 bits (88), Expect = 6e-04
Identities = 8/24 (33%), Positives = 14/24 (58%)
Query: 57 ILLYGPPGTGKTLMARQIGQMLNA 80
+ +YG GTGKT + + + + L
Sbjct: 43 VFIYGKTGTGKTAVTKYVMKELEE 66
>gnl|CDD|203260 pfam05496, RuvB_N, Holliday junction DNA helicase ruvB
N-terminus. The RuvB protein makes up part of the
RuvABC revolvasome which catalyzes the resolution of
Holliday junctions that arise during genetic
recombination and DNA repair. Branch migration is
catalyzed by the RuvB protein that is targeted to the
Holliday junction by the structure specific RuvA
protein. This family contains the N-terminal region of
the protein.
Length = 231
Score = 37.0 bits (87), Expect = 7e-04
Identities = 19/42 (45%), Positives = 24/42 (57%), Gaps = 5/42 (11%)
Query: 53 HVKGILLYGPPGTGKTLMARQIGQMLNAREPKIVNGPQVLDK 94
HV LLYGPPG GKT +A I + +I +GP L+K
Sbjct: 52 HV---LLYGPPGLGKTTLANIIANEMGV-NIRITSGP-ALEK 88
>gnl|CDD|144608 pfam01078, Mg_chelatase, Magnesium chelatase, subunit ChlI.
Magnesium-chelatase is a three-component enzyme that
catalyzes the insertion of Mg2+ into protoporphyrin IX.
This is the first unique step in the synthesis of
(bacterio)chlorophyll. Due to this, it is thought that
Mg-chelatase has an important role in channelling
inter- mediates into the (bacterio)chlorophyll branch
in response to conditions suitable for photosynthetic
growth. ChlI and BchD have molecular weight between
38-42 kDa.
Length = 207
Score = 36.3 bits (85), Expect = 0.001
Identities = 9/18 (50%), Positives = 17/18 (94%)
Query: 57 ILLYGPPGTGKTLMARQI 74
+L+ GPPG+GKT++A+++
Sbjct: 25 LLMIGPPGSGKTMLAKRL 42
>gnl|CDD|223786 COG0714, COG0714, MoxR-like ATPases [General function prediction
only].
Length = 329
Score = 36.6 bits (85), Expect = 0.001
Identities = 14/29 (48%), Positives = 19/29 (65%)
Query: 57 ILLYGPPGTGKTLMARQIGQMLNAREPKI 85
+LL GPPG GKTL+AR + + L +I
Sbjct: 46 VLLEGPPGVGKTLLARALARALGLPFVRI 74
>gnl|CDD|236153 PRK08116, PRK08116, hypothetical protein; Validated.
Length = 268
Score = 36.2 bits (84), Expect = 0.002
Identities = 18/62 (29%), Positives = 32/62 (51%), Gaps = 10/62 (16%)
Query: 56 GILLYGPPGTGKTLMARQIGQMLNARE--PKIVNGPQVLDKYVGESEANVRRLFADAEEE 113
G+LL+G GTGKT +A I L + VN PQ+L++ ++ + + +E
Sbjct: 116 GLLLWGSVGTGKTYLAACIANELIEKGVPVIFVNFPQLLNR--------IKSTYKSSGKE 167
Query: 114 EK 115
++
Sbjct: 168 DE 169
>gnl|CDD|221983 pfam13207, AAA_17, AAA domain.
Length = 114
Score = 35.0 bits (80), Expect = 0.002
Identities = 10/25 (40%), Positives = 18/25 (72%)
Query: 57 ILLYGPPGTGKTLMARQIGQMLNAR 81
IL+ GPPG+GK+ +A+++ + L
Sbjct: 2 ILITGPPGSGKSTLAKKLAEKLGIP 26
>gnl|CDD|224145 COG1224, TIP49, DNA helicase TIP49, TBP-interacting protein
[Transcription].
Length = 450
Score = 36.2 bits (84), Expect = 0.002
Identities = 21/55 (38%), Positives = 33/55 (60%), Gaps = 4/55 (7%)
Query: 55 KGILLYGPPGTGKTLMARQIGQMLNAREPKI-VNGPQVLDKYVGESEA---NVRR 105
+GIL+ GPPGTGKT +A I + L P + ++G ++ V ++EA +RR
Sbjct: 66 RGILIVGPPGTGKTALAMGIARELGEDVPFVAISGSEIYSLEVKKTEALTQALRR 120
>gnl|CDD|183088 PRK11331, PRK11331, 5-methylcytosine-specific restriction enzyme
subunit McrB; Provisional.
Length = 459
Score = 36.2 bits (83), Expect = 0.002
Identities = 19/45 (42%), Positives = 26/45 (57%), Gaps = 1/45 (2%)
Query: 55 KGILLYGPPGTGKTLMARQIGQMLNA-REPKIVNGPQVLDKYVGE 98
K I+L GPPG GKT +AR++ +L + P+ VN Q Y E
Sbjct: 195 KNIILQGPPGVGKTFVARRLAYLLTGEKAPQRVNMVQFHQSYSYE 239
>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 = 35.6 bits (82), Expect = 0.002
Identities = 17/65 (26%), Positives = 25/65 (38%), Gaps = 8/65 (12%)
Query: 57 ILLYGPPGTGKTLMARQIGQMLNAREPKIVNGPQVLDKYVGESEANVRRLFADAEEEEKR 116
IL++GP G+GKT +A Q+ + + K+V YV E E K
Sbjct: 2 ILVFGPTGSGKTTLALQLALNIATKGGKVV--------YVDIEEEIEELTERLIGESLKG 53
Query: 117 VSHKW 121
Sbjct: 54 ALDNL 58
>gnl|CDD|224140 COG1219, ClpX, ATP-dependent protease Clp, ATPase subunit
[Posttranslational modification, protein turnover,
chaperones].
Length = 408
Score = 35.7 bits (83), Expect = 0.003
Identities = 13/23 (56%), Positives = 19/23 (82%)
Query: 57 ILLYGPPGTGKTLMARQIGQMLN 79
ILL GP G+GKTL+A+ + ++LN
Sbjct: 100 ILLIGPTGSGKTLLAQTLAKILN 122
>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit;
Provisional.
Length = 482
Score = 35.7 bits (83), Expect = 0.003
Identities = 12/17 (70%), Positives = 14/17 (82%)
Query: 55 KGILLYGPPGTGKTLMA 71
K +LLYGPPG GKT +A
Sbjct: 40 KALLLYGPPGVGKTSLA 56
>gnl|CDD|237354 PRK13341, PRK13341, recombination factor protein RarA/unknown
domain fusion protein; Reviewed.
Length = 725
Score = 35.4 bits (82), Expect = 0.004
Identities = 13/24 (54%), Positives = 15/24 (62%)
Query: 58 LLYGPPGTGKTLMARQIGQMLNAR 81
+LYGPPG GKT +AR I A
Sbjct: 56 ILYGPPGVGKTTLARIIANHTRAH 79
>gnl|CDD|234751 PRK00411, cdc6, cell division control protein 6; Reviewed.
Length = 394
Score = 35.2 bits (82), Expect = 0.004
Identities = 13/30 (43%), Positives = 20/30 (66%)
Query: 57 ILLYGPPGTGKTLMARQIGQMLNAREPKIV 86
+L+YGPPGTGKT +++ + L K+V
Sbjct: 58 VLIYGPPGTGKTTTVKKVFEELEEIAVKVV 87
>gnl|CDD|216270 pfam01057, Parvo_NS1, Parvovirus non-structural protein NS1. This
family also contains the NS2 protein. Parvoviruses
encode two non-structural proteins, NS1 and NS2. The
mRNA for NS2 contains the coding sequence for the first
87 amino acids of NS1, then by an alternative splicing
mechanism mRNA from a different reading frame, encoding
the last 78 amino acids, makes up the full length of the
NS2 mRNA. NS1, is the major non-structural protein. It
is essential for DNA replication. It is an 83-kDa
nuclear phosphoprotein. It has DNA helicase and ATPase
activity.
Length = 271
Score = 34.6 bits (80), Expect = 0.005
Identities = 10/28 (35%), Positives = 13/28 (46%), Gaps = 4/28 (14%)
Query: 51 CQHVKG----ILLYGPPGTGKTLMARQI 74
G + YGP TGKT +A+ I
Sbjct: 106 LSKQGGKRNTVWFYGPASTGKTNLAQAI 133
>gnl|CDD|224391 COG1474, CDC6, Cdc6-related protein, AAA superfamily ATPase [DNA
replication, recombination, and repair /
Posttranslational modification, protein turnover,
chaperones].
Length = 366
Score = 34.6 bits (80), Expect = 0.006
Identities = 10/23 (43%), Positives = 15/23 (65%)
Query: 57 ILLYGPPGTGKTLMARQIGQMLN 79
I++YGP GTGKT + + + L
Sbjct: 45 IIIYGPTGTGKTATVKFVMEELE 67
>gnl|CDD|221970 pfam13191, AAA_16, AAA ATPase domain. This family of domains
contain a P-loop motif that is characteristic of the
AAA superfamily.
Length = 154
Score = 34.1 bits (78), Expect = 0.006
Identities = 12/30 (40%), Positives = 17/30 (56%)
Query: 57 ILLYGPPGTGKTLMARQIGQMLNAREPKIV 86
+LL GP GTGKT + R++ + L K
Sbjct: 27 VLLTGPSGTGKTSLLRELLEGLLVAAGKCD 56
>gnl|CDD|232949 TIGR00382, clpX, endopeptidase Clp ATP-binding regulatory subunit
(clpX). A member of the ATP-dependent proteases, ClpX
has ATP-dependent chaperone activity and is required for
specific ATP-dependent proteolytic activities expressed
by ClpPX. The gene is also found to be involved in
stress tolerance in Bacillus subtilis and is essential
for the efficient acquisition of genes specifying type
IA and IB restriction [Protein fate, Protein folding and
stabilization, Protein fate, Degradation of proteins,
peptides, and glycopeptides].
Length = 413
Score = 34.7 bits (80), Expect = 0.006
Identities = 20/49 (40%), Positives = 29/49 (59%), Gaps = 4/49 (8%)
Query: 57 ILLYGPPGTGKTLMARQIGQMLNAREPKIVNGPQVLDK--YVGESEANV 103
ILL GP G+GKTL+A+ + ++LN P + L + YVGE N+
Sbjct: 119 ILLIGPTGSGKTLLAQTLARILNV--PFAIADATTLTEAGYVGEDVENI 165
>gnl|CDD|222104 pfam13401, AAA_22, AAA domain.
Length = 124
Score = 33.8 bits (78), Expect = 0.006
Identities = 9/26 (34%), Positives = 15/26 (57%)
Query: 57 ILLYGPPGTGKTLMARQIGQMLNARE 82
+L G G+GKT + R++ + L R
Sbjct: 7 GVLTGESGSGKTTLLRRLARQLPNRR 32
>gnl|CDD|219536 pfam07724, AAA_2, AAA domain (Cdc48 subfamily). This Pfam entry
includes some of the AAA proteins not detected by the
pfam00004 model.
Length = 168
Score = 34.1 bits (79), Expect = 0.008
Identities = 10/30 (33%), Positives = 17/30 (56%)
Query: 57 ILLYGPPGTGKTLMARQIGQMLNAREPKIV 86
L GP G GKT +A+ + ++L E ++
Sbjct: 6 FLFLGPTGVGKTELAKALAELLFGDERALI 35
>gnl|CDD|181235 PRK08118, PRK08118, topology modulation protein; Reviewed.
Length = 167
Score = 33.4 bits (77), Expect = 0.011
Identities = 13/25 (52%), Positives = 19/25 (76%)
Query: 55 KGILLYGPPGTGKTLMARQIGQMLN 79
K I+L G G+GK+ +ARQ+G+ LN
Sbjct: 2 KKIILIGSGGSGKSTLARQLGEKLN 26
>gnl|CDD|223542 COG0466, Lon, ATP-dependent Lon protease, bacterial type
[Posttranslational modification, protein turnover,
chaperones].
Length = 782
Score = 34.1 bits (79), Expect = 0.012
Identities = 12/28 (42%), Positives = 17/28 (60%), Gaps = 2/28 (7%)
Query: 54 VKG--ILLYGPPGTGKTLMARQIGQMLN 79
+KG + L GPPG GKT + + I + L
Sbjct: 348 LKGPILCLVGPPGVGKTSLGKSIAKALG 375
>gnl|CDD|224401 COG1484, DnaC, DNA replication protein [DNA replication,
recombination, and repair].
Length = 254
Score = 33.5 bits (77), Expect = 0.012
Identities = 19/61 (31%), Positives = 28/61 (45%), Gaps = 6/61 (9%)
Query: 55 KGILLYGPPGTGKTLMARQIGQMLNAREPKIVNGPQVLDKYVGESEANVRRLFADAEEEE 114
+ ++L GPPG GKT +A IG L G VL + + ++ F + EE
Sbjct: 106 ENLVLLGPPGVGKTHLAIAIGNELLKA------GISVLFITAPDLLSKLKAAFDEGRLEE 159
Query: 115 K 115
K
Sbjct: 160 K 160
>gnl|CDD|116340 pfam07726, AAA_3, ATPase family associated with various cellular
activities (AAA). This Pfam entry includes some of the
AAA proteins not detected by the pfam00004 model.
Length = 131
Score = 32.9 bits (76), Expect = 0.013
Identities = 11/25 (44%), Positives = 15/25 (60%)
Query: 57 ILLYGPPGTGKTLMARQIGQMLNAR 81
+LL G PG KTL+AR + + L
Sbjct: 2 VLLEGVPGLAKTLLARTLARSLGLD 26
>gnl|CDD|129465 TIGR00368, TIGR00368, Mg chelatase-related protein. The N-terminal
end matches very strongly a pfam Mg_chelatase domain
[Unknown function, General].
Length = 499
Score = 33.7 bits (77), Expect = 0.014
Identities = 11/22 (50%), Positives = 19/22 (86%)
Query: 57 ILLYGPPGTGKTLMARQIGQML 78
+LL+GPPG+GKT++A ++ +L
Sbjct: 214 LLLFGPPGSGKTMLASRLQGIL 235
>gnl|CDD|233119 TIGR00763, lon, ATP-dependent protease La. This protein is induced
by heat shock and other stresses in E. coli, B.
subtilis, and other species. The yeast member,
designated PIM1, is located in the mitochondrial matrix,
required for mitochondrial function, and also induced by
heat shock [Protein fate, Degradation of proteins,
peptides, and glycopeptides].
Length = 775
Score = 33.0 bits (76), Expect = 0.021
Identities = 11/23 (47%), Positives = 15/23 (65%)
Query: 57 ILLYGPPGTGKTLMARQIGQMLN 79
+ L GPPG GKT + + I + LN
Sbjct: 350 LCLVGPPGVGKTSLGKSIAKALN 372
>gnl|CDD|234053 TIGR02903, spore_lon_C, ATP-dependent protease, Lon family.
Members of this protein family resemble the widely
distributed ATP-dependent protease La, also called Lon
and LonA. It resembles even more closely LonB, which is
a LonA paralog found in genomes if and only if the
species is capable of endospore formation (as in
Bacillus subtilis, Clostridium tetani, and select other
members of the Firmicutes) and expressed specifically in
the forespore compartment. Members of this family are
restricted to a subset of spore-forming species, and are
very likely to participate in the program of endospore
formation. We propose the designation LonC [Protein
fate, Degradation of proteins, peptides, and
glycopeptides, Cellular processes, Sporulation and
germination].
Length = 615
Score = 33.2 bits (76), Expect = 0.022
Identities = 14/21 (66%), Positives = 15/21 (71%), Gaps = 3/21 (14%)
Query: 52 QHVKGILLYGPPGTGKTLMAR 72
QH I+LYGPPG GKT AR
Sbjct: 176 QH---IILYGPPGVGKTTAAR 193
>gnl|CDD|218528 pfam05272, VirE, Virulence-associated protein E. This family
contains several bacterial virulence-associated protein
E like proteins. These proteins contain a P-loop motif.
Length = 198
Score = 32.7 bits (75), Expect = 0.024
Identities = 13/50 (26%), Positives = 25/50 (50%), Gaps = 6/50 (12%)
Query: 27 EFTAIFRRAFASRVFPPEVVEQLGCQHVKGILLYGPPGTGKTLMARQIGQ 76
E + +F +RV+ P GC+ ++L G G+GK+ +++G
Sbjct: 31 EVSKLFLIGAVARVYEP------GCKFDHVLILQGAQGSGKSTFLKKLGG 74
>gnl|CDD|226997 COG4650, RtcR, Sigma54-dependent transcription regulator containing
an AAA-type ATPase domain and a DNA-binding domain
[Transcription / Signal transduction mechanisms].
Length = 531
Score = 33.0 bits (75), Expect = 0.025
Identities = 15/38 (39%), Positives = 24/38 (63%)
Query: 44 EVVEQLGCQHVKGILLYGPPGTGKTLMARQIGQMLNAR 81
E +E++ + ILL GP G GK+ +AR+I ++ AR
Sbjct: 198 EQIERVAIRSRAPILLNGPTGAGKSFLARRIYELKQAR 235
>gnl|CDD|238544 cd01124, KaiC, KaiC is a circadian clock protein primarily found
in cyanobacteria KaiC is a RecA-like ATPase, having
both Walker A and Walker B motifs. A related protein is
found in archaea.
Length = 187
Score = 32.3 bits (74), Expect = 0.033
Identities = 11/17 (64%), Positives = 11/17 (64%)
Query: 57 ILLYGPPGTGKTLMARQ 73
LL G PGTGKT A Q
Sbjct: 2 TLLSGGPGTGKTTFALQ 18
>gnl|CDD|234763 PRK00440, rfc, replication factor C small subunit; Reviewed.
Length = 319
Score = 32.5 bits (75), Expect = 0.033
Identities = 16/33 (48%), Positives = 20/33 (60%), Gaps = 6/33 (18%)
Query: 44 EVVEQLGCQHVKG-----ILLYGPPGTGKTLMA 71
E+VE+L +VK +L GPPGTGKT A
Sbjct: 24 EIVERLK-SYVKEKNMPHLLFAGPPGTGKTTAA 55
>gnl|CDD|177094 CHL00195, ycf46, Ycf46; Provisional.
Length = 489
Score = 32.3 bits (74), Expect = 0.036
Identities = 20/57 (35%), Positives = 32/57 (56%), Gaps = 1/57 (1%)
Query: 55 KGILLYGPPGTGKTLMARQIGQMLNAREPKIVNGPQVLDKYVGESEANVRRLFADAE 111
+G+LL G GTGK+L A+ I ++ G ++ VGESE+ +R++ AE
Sbjct: 260 RGLLLVGIQGTGKSLTAKAIANDWQLPLLRLDVG-KLFGGIVGESESRMRQMIRIAE 315
>gnl|CDD|215651 pfam00006, ATP-synt_ab, ATP synthase alpha/beta family,
nucleotide-binding domain. This family includes the ATP
synthase alpha and beta subunits, the ATP synthase
associated with flagella and the termination factor Rho.
Length = 213
Score = 32.0 bits (74), Expect = 0.041
Identities = 17/63 (26%), Positives = 26/63 (41%), Gaps = 9/63 (14%)
Query: 54 VKG--ILLYGPPGTGKTLMARQIGQMLNAREPKIVNGPQVLDKYVGESEANVRRLFADAE 111
KG I ++G GTGKT++ I + A ++ VL +GE V +
Sbjct: 13 GKGQRIGIFGGSGTGKTVLLGMIARNAKADVVEVY----VL---IGERGREVAEFIEELL 65
Query: 112 EEE 114
E
Sbjct: 66 GEG 68
>gnl|CDD|219158 pfam06745, KaiC, KaiC. This family represents a conserved region
within bacterial and archaeal proteins, most of which
are hypothetical. More than one copy is sometimes found
in each protein. This family includes KaiC, which is
one of the Kai proteins among which direct
protein-protein association may be a critical process
in the generation of circadian rhythms in
cyanobacteria.
Length = 231
Score = 32.2 bits (74), Expect = 0.043
Identities = 9/17 (52%), Positives = 12/17 (70%)
Query: 57 ILLYGPPGTGKTLMARQ 73
+L+ G PGTGKT+ Q
Sbjct: 22 VLITGGPGTGKTIFGLQ 38
>gnl|CDD|224142 COG1221, PspF, Transcriptional regulators containing an AAA-type
ATPase domain and a DNA-binding domain [Transcription /
Signal transduction mechanisms].
Length = 403
Score = 32.4 bits (74), Expect = 0.043
Identities = 14/34 (41%), Positives = 16/34 (47%), Gaps = 3/34 (8%)
Query: 57 ILLYGPPGTGKTLMARQI--GQMLNAREPKI-VN 87
+L+ G GTGK L AR I A P I N
Sbjct: 104 VLIIGETGTGKELFARLIHALSARRAEAPFIAFN 137
>gnl|CDD|233087 TIGR00678, holB, DNA polymerase III, delta' subunit. This model
describes the N-terminal half of the delta' subunit of
DNA polymerase III. Delta' is homologous to the gamma
and tau subunits, which form an outgroup for
phylogenetic comparison. The gamma/tau branch of the
tree is much more tighly conserved than the delta'
branch, and some members of that branch score more
highly against this model than some proteins
classisified as delta'. The noise cutoff is set to
detect weakly scoring delta' subunits rather than to
exclude gamma/tau subunits. At position 126-127 of the
seed alignment, this family lacks the HM motif of
gamma/tau; at 132 it has a near-invariant A vs. an
invariant F in gamma/tau [DNA metabolism, DNA
replication, recombination, and repair].
Length = 188
Score = 31.8 bits (73), Expect = 0.044
Identities = 10/31 (32%), Positives = 14/31 (45%)
Query: 58 LLYGPPGTGKTLMARQIGQMLNAREPKIVNG 88
L GP G GK L+A + + L +P
Sbjct: 18 LFAGPEGVGKELLALALAKALLCEQPGGGEP 48
>gnl|CDD|182120 PRK09862, PRK09862, putative ATP-dependent protease; Provisional.
Length = 506
Score = 32.3 bits (73), Expect = 0.046
Identities = 13/22 (59%), Positives = 18/22 (81%)
Query: 57 ILLYGPPGTGKTLMARQIGQML 78
+LL GPPGTGKT++A +I +L
Sbjct: 213 LLLIGPPGTGKTMLASRINGLL 234
>gnl|CDD|235871 PRK06835, PRK06835, DNA replication protein DnaC; Validated.
Length = 329
Score = 31.8 bits (73), Expect = 0.052
Identities = 8/17 (47%), Positives = 12/17 (70%)
Query: 55 KGILLYGPPGTGKTLMA 71
+ +L YG GTGKT ++
Sbjct: 184 ENLLFYGNTGTGKTFLS 200
>gnl|CDD|222163 pfam13479, AAA_24, AAA domain. This AAA domain is found in a
wide variety of presumed phage proteins.
Length = 201
Score = 31.5 bits (72), Expect = 0.056
Identities = 10/16 (62%), Positives = 14/16 (87%)
Query: 57 ILLYGPPGTGKTLMAR 72
+L+YGPPG GKT +A+
Sbjct: 6 VLIYGPPGIGKTSLAK 21
>gnl|CDD|223679 COG0606, COG0606, Predicted ATPase with chaperone activity
[Posttranslational modification, protein turnover,
chaperones].
Length = 490
Score = 31.8 bits (73), Expect = 0.057
Identities = 11/20 (55%), Positives = 16/20 (80%)
Query: 55 KGILLYGPPGTGKTLMARQI 74
+LL GPPGTGKT++A ++
Sbjct: 199 HNLLLVGPPGTGKTMLASRL 218
>gnl|CDD|222866 PHA02544, 44, clamp loader, small subunit; Provisional.
Length = 316
Score = 31.5 bits (72), Expect = 0.064
Identities = 15/33 (45%), Positives = 21/33 (63%), Gaps = 2/33 (6%)
Query: 57 ILLYGP-PGTGKTLMARQIGQMLNAREPKIVNG 88
+LL+ P PGTGKT +A+ + + A E VNG
Sbjct: 45 MLLHSPSPGTGKTTVAKALCNEVGA-EVLFVNG 76
>gnl|CDD|224141 COG1220, HslU, ATP-dependent protease HslVU (ClpYQ), ATPase
subunit [Posttranslational modification, protein
turnover, chaperones].
Length = 444
Score = 31.9 bits (73), Expect = 0.066
Identities = 12/26 (46%), Positives = 18/26 (69%)
Query: 55 KGILLYGPPGTGKTLMARQIGQMLNA 80
K IL+ GP G GKT +AR++ ++ A
Sbjct: 51 KNILMIGPTGVGKTEIARRLAKLAGA 76
>gnl|CDD|213527 TIGR00390, hslU, ATP-dependent protease HslVU, ATPase subunit.
This model represents the ATPase subunit of HslVU, while
the proteasome-related peptidase subunit is HslV.
Residues 54-61 of the model contain a P-loop ATP-binding
motif. Cys-287 of E. coli (position 308 in the seed
alignment), studied in MEDLINE:98389714, is Ser in other
members of the seed alignment [Protein fate, Protein
folding and stabilization].
Length = 441
Score = 31.7 bits (72), Expect = 0.066
Identities = 24/66 (36%), Positives = 34/66 (51%), Gaps = 5/66 (7%)
Query: 55 KGILLYGPPGTGKTLMARQIGQMLNAREPKIVNGPQVLDKYVG-ESEANVRRLFADA--- 110
K IL+ GP G GKT +AR++ ++ NA K+ YVG + E+ VR L A
Sbjct: 48 KNILMIGPTGVGKTEIARRLAKLANAPFIKVEATKFTEVGYVGRDVESMVRDLVDIAVKL 107
Query: 111 -EEEEK 115
+EE
Sbjct: 108 VKEEMI 113
>gnl|CDD|215758 pfam00158, Sigma54_activat, Sigma-54 interaction domain.
Length = 168
Score = 31.2 bits (72), Expect = 0.066
Identities = 10/18 (55%), Positives = 12/18 (66%)
Query: 57 ILLYGPPGTGKTLMARQI 74
+L+ G GTGK L AR I
Sbjct: 25 VLITGESGTGKELFARAI 42
>gnl|CDD|222000 pfam13238, AAA_18, AAA domain.
Length = 128
Score = 30.9 bits (70), Expect = 0.067
Identities = 14/57 (24%), Positives = 27/57 (47%)
Query: 57 ILLYGPPGTGKTLMARQIGQMLNAREPKIVNGPQVLDKYVGESEANVRRLFADAEEE 113
IL+ G PG+GKT +A+++ + L + ++ + E +RL D +
Sbjct: 1 ILITGTPGSGKTTLAKELAERLGDVLRDLAKENGLVLELDEEITDESKRLDEDKLAK 57
>gnl|CDD|131948 TIGR02902, spore_lonB, ATP-dependent protease LonB. Members of
this protein are LonB, a paralog of the ATP-dependent
protease La (LonA, TIGR00763). LonB proteins are found
strictly, and almost universally, in endospore-forming
bacteria. This protease was shown, in Bacillus subtilis,
to be expressed specifically in the forespore, during
sporulation, under control of sigma(F). The lonB gene,
despite location immediately upstream of lonA, was shown
to be monocistronic. LonB appears able to act on
sigma(H) for post-translation control, but lonB mutation
did not produce an obvious sporulation defect under the
conditions tested. Note that additional paralogs of LonA
and LonB occur in the Clostridium lineage and this model
selects only one per species as the protein that
corresponds to LonB in B. subtilis [Protein fate,
Degradation of proteins, peptides, and glycopeptides,
Cellular processes, Sporulation and germination].
Length = 531
Score = 31.7 bits (72), Expect = 0.068
Identities = 13/21 (61%), Positives = 15/21 (71%), Gaps = 3/21 (14%)
Query: 52 QHVKGILLYGPPGTGKTLMAR 72
QHV ++YGPPG GKT AR
Sbjct: 87 QHV---IIYGPPGVGKTAAAR 104
>gnl|CDD|214361 CHL00095, clpC, Clp protease ATP binding subunit.
Length = 821
Score = 31.6 bits (72), Expect = 0.076
Identities = 30/127 (23%), Positives = 52/127 (40%), Gaps = 19/127 (14%)
Query: 5 PRQSIISPSFDFNKMGIGGLDKEFTAIFRRAFASRVFP--------PEVVEQLGCQHVKG 56
+ ++ L++ T + + A + P V++ LG +
Sbjct: 143 GEIIEAILGAEQSRSKTPTLEEFGTNLTKEAIDGNLDPVIGREKEIERVIQILGRRTKNN 202
Query: 57 ILLYGPPGTGKTLMARQIGQMLNARE-PKIVNGPQV--LD--------KYVGESEANVRR 105
+L G PG GKT +A + Q + R+ P I+ V LD KY GE E ++R
Sbjct: 203 PILIGEPGVGKTAIAEGLAQRIVNRDVPDILEDKLVITLDIGLLLAGTKYRGEFEERLKR 262
Query: 106 LFADAEE 112
+F + +E
Sbjct: 263 IFDEIQE 269
>gnl|CDD|224160 COG1239, ChlI, Mg-chelatase subunit ChlI [Coenzyme metabolism].
Length = 423
Score = 31.6 bits (72), Expect = 0.080
Identities = 11/32 (34%), Positives = 17/32 (53%)
Query: 54 VKGILLYGPPGTGKTLMARQIGQMLNAREPKI 85
+ G L+ G GT K+ +AR + +L E I
Sbjct: 38 IGGALIAGEKGTAKSTLARALADLLPEIEVVI 69
>gnl|CDD|221912 pfam13086, AAA_11, AAA domain. This family of domains contain a
P-loop motif that is characteristic of the AAA
superfamily. Many of the proteins in this family are
conjugative transfer proteins.
Length = 220
Score = 30.8 bits (70), Expect = 0.11
Identities = 21/65 (32%), Positives = 33/65 (50%), Gaps = 10/65 (15%)
Query: 58 LLYGPPGTGKTLMARQ-IGQML-NAREPKI-VNGP------QVLDKYVGES-EANVRRLF 107
L+ GPPGTGKT + I Q+L NA K+ V P +L++ + + + R+
Sbjct: 21 LIQGPPGTGKTTTIVEIIKQLLSNAPGKKVLVCAPSNSAVDNILERLLEQKFGLKIVRIG 80
Query: 108 ADAEE 112
+ A E
Sbjct: 81 SPARE 85
>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 = 30.3 bits (69), Expect = 0.15
Identities = 11/21 (52%), Positives = 14/21 (66%)
Query: 56 GILLYGPPGTGKTLMARQIGQ 76
+LL GPPG GKT +A +G
Sbjct: 49 NLLLLGPPGVGKTHLACALGH 69
>gnl|CDD|238688 cd01394, radB, RadB. The archaeal protein radB shares similarity
radA, the archaeal functional homologue to the bacterial
RecA. The precise function of radB is unclear.
Length = 218
Score = 30.1 bits (68), Expect = 0.18
Identities = 18/58 (31%), Positives = 26/58 (44%), Gaps = 11/58 (18%)
Query: 59 LYGPPGTGKTLMARQIGQMLNAREPKIVNGPQVLDKYV---GESEANVRRLFADAEEE 113
+YGPPGTGKT +A Q+ + K+ Y+ G S R++ D E
Sbjct: 24 VYGPPGTGKTNIAIQLAVETAGQGKKVA--------YIDTEGLSSERFRQIAGDRPER 73
>gnl|CDD|136670 PRK08181, PRK08181, transposase; Validated.
Length = 269
Score = 30.3 bits (68), Expect = 0.21
Identities = 17/36 (47%), Positives = 22/36 (61%), Gaps = 6/36 (16%)
Query: 57 ILLYGPPGTGKTLMARQIGQMLNAREPKIVNGPQVL 92
+LL+GPPG GK+ +A IG L I NG +VL
Sbjct: 109 LLLFGPPGGGKSHLAAAIGLAL------IENGWRVL 138
>gnl|CDD|236353 PRK08939, PRK08939, primosomal protein DnaI; Reviewed.
Length = 306
Score = 29.8 bits (68), Expect = 0.23
Identities = 9/18 (50%), Positives = 12/18 (66%)
Query: 53 HVKGILLYGPPGTGKTLM 70
VKG+ LYG G GK+ +
Sbjct: 155 KVKGLYLYGDFGVGKSYL 172
>gnl|CDD|216065 pfam00693, Herpes_TK, Thymidine kinase from herpesvirus.
Length = 279
Score = 30.0 bits (68), Expect = 0.25
Identities = 17/48 (35%), Positives = 20/48 (41%), Gaps = 9/48 (18%)
Query: 61 GPPGTGKTLMARQIGQMLNAREPKIVNGPQVLDKYVGESEANVRRLFA 108
G G GKT AR + +A P +L YV E A R LF
Sbjct: 1 GAHGIGKTTTARALAAASSAGGP-------IL--YVPEPMAYWRTLFG 39
>gnl|CDD|223616 COG0542, clpA, ATP-binding subunits of Clp protease and DnaK/DnaJ
chaperones [Posttranslational modification, protein
turnover, chaperones].
Length = 786
Score = 29.9 bits (68), Expect = 0.26
Identities = 20/76 (26%), Positives = 31/76 (40%), Gaps = 25/76 (32%)
Query: 58 LLYGPPGTGKTLMARQIGQMLNAREPKIVNG--PQVLD----------------KYVGES 99
+L G PG GKT + + Q +IVNG P+ L KY GE
Sbjct: 195 VLVGEPGVGKTAIVEGLAQ-------RIVNGDVPESLKDKRIYSLDLGSLVAGAKYRGEF 247
Query: 100 EANVRRLFADAEEEEK 115
E ++ + + E+ +
Sbjct: 248 EERLKAVLKEVEKSKN 263
>gnl|CDD|180215 PRK05707, PRK05707, DNA polymerase III subunit delta'; Validated.
Length = 328
Score = 30.1 bits (68), Expect = 0.26
Identities = 11/32 (34%), Positives = 16/32 (50%)
Query: 52 QHVKGILLYGPPGTGKTLMARQIGQMLNAREP 83
+H LL+GP G GK +A ++ L P
Sbjct: 20 RHPHAYLLHGPAGIGKRALAERLAAALLCEAP 51
>gnl|CDD|184920 PRK14956, PRK14956, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 484
Score = 29.9 bits (67), Expect = 0.27
Identities = 11/26 (42%), Positives = 16/26 (61%)
Query: 58 LLYGPPGTGKTLMARQIGQMLNAREP 83
+ +GP G GKT +AR + + LN P
Sbjct: 44 IFFGPRGVGKTTIARILAKRLNCENP 69
>gnl|CDD|223543 COG0467, RAD55, RecA-superfamily ATPases implicated in signal
transduction [Signal transduction mechanisms].
Length = 260
Score = 29.7 bits (67), Expect = 0.28
Identities = 11/18 (61%), Positives = 14/18 (77%)
Query: 57 ILLYGPPGTGKTLMARQI 74
+L+ GPPGTGKT+ A Q
Sbjct: 26 VLITGPPGTGKTIFALQF 43
>gnl|CDD|236982 PRK11784, PRK11784, tRNA 2-selenouridine synthase; Provisional.
Length = 345
Score = 29.8 bits (68), Expect = 0.29
Identities = 15/51 (29%), Positives = 22/51 (43%), Gaps = 12/51 (23%)
Query: 45 VVEQL--GCQHVKGILLYGPPGTGKTLMARQIGQMLNAREPKIVNGPQVLD 93
V++ L ++L G G+GKT ++L A G QVLD
Sbjct: 130 VIDTLEEAPAQFPLVVLGGNTGSGKT-------ELLQALAN---AGAQVLD 170
>gnl|CDD|184311 PRK13764, PRK13764, ATPase; Provisional.
Length = 602
Score = 29.8 bits (68), Expect = 0.33
Identities = 14/46 (30%), Positives = 24/46 (52%), Gaps = 2/46 (4%)
Query: 41 FPPEVVEQLGCQHVKGILLYGPPGTGKTLMARQIGQMLNAREPKIV 86
++ E+L + +GIL+ G PG GK+ A+ + + KIV
Sbjct: 245 LSEKLKERLE-ERAEGILIAGAPGAGKSTFAQALAEFYADMG-KIV 288
>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 = 0.33
Identities = 9/19 (47%), Positives = 12/19 (63%)
Query: 57 ILLYGPPGTGKTLMARQIG 75
LL G PGTGK+ +A +
Sbjct: 36 TLLAGAPGTGKSTLALDLA 54
>gnl|CDD|235335 PRK05057, aroK, shikimate kinase I; Reviewed.
Length = 172
Score = 29.3 bits (66), Expect = 0.33
Identities = 21/61 (34%), Positives = 32/61 (52%), Gaps = 7/61 (11%)
Query: 54 VKGILLYGPPGTGKTLMARQIGQMLNAREPKIVNGPQVLDKYVGESEANVRRLFADAEEE 113
+ I L GP G GK+ + RQ+ Q LN + + Q ++K G A++ +F D E E
Sbjct: 4 KRNIFLVGPMGAGKSTIGRQLAQQLNM---EFYDSDQEIEKRTG---ADIGWVF-DVEGE 56
Query: 114 E 114
E
Sbjct: 57 E 57
>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 = 29.6 bits (67), Expect = 0.33
Identities = 8/30 (26%), Positives = 18/30 (60%)
Query: 57 ILLYGPPGTGKTLMARQIGQMLNAREPKIV 86
I+L G P +GK+ A+++ + L + ++
Sbjct: 2 IILTGLPSSGKSTRAKELAKYLEEKGYDVI 31
>gnl|CDD|221955 pfam13173, AAA_14, AAA domain. This family of domains contain a
P-loop motif that is characteristic of the AAA
superfamily.
Length = 127
Score = 29.1 bits (66), Expect = 0.36
Identities = 9/31 (29%), Positives = 15/31 (48%)
Query: 57 ILLYGPPGTGKTLMARQIGQMLNAREPKIVN 87
I++ GP GKT + Q + L + +N
Sbjct: 5 IVITGPRQVGKTTLLLQFLKELLSENILYIN 35
>gnl|CDD|226573 COG4088, COG4088, Predicted nucleotide kinase [Nucleotide
transport and metabolism].
Length = 261
Score = 29.4 bits (66), Expect = 0.39
Identities = 10/25 (40%), Positives = 16/25 (64%)
Query: 57 ILLYGPPGTGKTLMARQIGQMLNAR 81
I+L G PG+GKT A+++ + L
Sbjct: 4 IILTGYPGSGKTTFAKELAKELRQE 28
>gnl|CDD|227922 COG5635, COG5635, Predicted NTPase (NACHT family) [Signal
transduction mechanisms].
Length = 824
Score = 29.4 bits (66), Expect = 0.40
Identities = 17/71 (23%), Positives = 23/71 (32%), Gaps = 11/71 (15%)
Query: 2 EVQPRQSIISPSFDFNKMGIGGLDKEFTAIFRRAFASRVFPPEVVEQLGCQHVKG----I 57
EV FD N G D+EF + + L +
Sbjct: 173 EVPLASQRSKRIFDLNTKGEKRFDEEF-------LLELTQSADDQDALPGLEALEKYAKL 225
Query: 58 LLYGPPGTGKT 68
L+ G PG+GKT
Sbjct: 226 LILGAPGSGKT 236
>gnl|CDD|222005 pfam13245, AAA_19, Part of AAA domain.
Length = 73
Score = 28.1 bits (63), Expect = 0.40
Identities = 20/64 (31%), Positives = 24/64 (37%), Gaps = 11/64 (17%)
Query: 44 EVVEQLGCQHVKGILLY-GPPGTGKTLMARQIGQMLNAREPKIVNGPQVLDKYVGESEAN 102
E VE + + G PGTGKT A I L + G VL V +
Sbjct: 1 EAVEAAASGR--SLFVVDGGPGTGKTATAAAIIARL------LAAGRSVL--VVAPTGRA 50
Query: 103 VRRL 106
RRL
Sbjct: 51 ARRL 54
>gnl|CDD|184927 PRK14963, PRK14963, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 504
Score = 29.4 bits (66), Expect = 0.43
Identities = 22/69 (31%), Positives = 29/69 (42%), Gaps = 19/69 (27%)
Query: 29 TAIFRRAFASRVFPPEVVEQLGCQHVKGILL--------------YGPPGTGKTLMARQI 74
+A+++RA EVV Q +HVK +LL GP G GKT AR I
Sbjct: 2 SALYQRARPITF--DEVVGQ---EHVKEVLLAALRQGRLGHAYLFSGPRGVGKTTTARLI 56
Query: 75 GQMLNAREP 83
+N
Sbjct: 57 AMAVNCSGE 65
>gnl|CDD|223718 COG0645, COG0645, Predicted kinase [General function prediction
only].
Length = 170
Score = 28.9 bits (65), Expect = 0.43
Identities = 10/27 (37%), Positives = 19/27 (70%)
Query: 55 KGILLYGPPGTGKTLMARQIGQMLNAR 81
+ +L+ G PG+GK+ +AR + ++L A
Sbjct: 2 RLVLVGGLPGSGKSTLARGLAELLGAI 28
>gnl|CDD|237870 PRK14964, PRK14964, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 491
Score = 29.4 bits (66), Expect = 0.45
Identities = 16/33 (48%), Positives = 16/33 (48%), Gaps = 5/33 (15%)
Query: 57 ILLYGPPGTGKTLMARQIGQMLNAREPKIVNGP 89
ILL G G GKT AR I LN NGP
Sbjct: 38 ILLVGASGVGKTTCARIISLCLNC-----SNGP 65
>gnl|CDD|223666 COG0593, DnaA, ATPase involved in DNA replication initiation [DNA
replication, recombination, and repair].
Length = 408
Score = 29.2 bits (66), Expect = 0.47
Identities = 14/64 (21%), Positives = 23/64 (35%), Gaps = 8/64 (12%)
Query: 57 ILLYGPPGTGKTLMARQIGQMLNAREPKIVNGPQVLDKYVGESEANVRRLFADAEEEEKR 116
+ +YG G GKT + + IG A P + V + + F A + +
Sbjct: 116 LFIYGGVGLGKTHLLQAIGNEALANGPN--------ARVVYLTSEDFTNDFVKALRDNEM 167
Query: 117 VSHK 120
K
Sbjct: 168 EKFK 171
>gnl|CDD|177538 PHA03136, PHA03136, thymidine kinase; Provisional.
Length = 378
Score = 29.3 bits (65), Expect = 0.51
Identities = 25/84 (29%), Positives = 37/84 (44%), Gaps = 12/84 (14%)
Query: 31 IFRRAFASRVFP-PEVVEQLGCQHVKGILLY--GPPGTGKTLMARQIGQMLNAREPKIVN 87
+ RRAF+S P E + +LLY GP GTGKT A+ + +M + ++
Sbjct: 10 LIRRAFSSGGMPFCSEFENDDSDFRRLVLLYLDGPFGTGKTTTAKLLMEMPDTLAARL-- 67
Query: 88 GPQVLDKYVGESEANVRRLFADAE 111
Y+ E A R F A+
Sbjct: 68 -------YLAEPMAAWRNHFGGAD 84
>gnl|CDD|223401 COG0324, MiaA, tRNA delta(2)-isopentenylpyrophosphate transferase
[Translation, ribosomal structure and biogenesis].
Length = 308
Score = 28.8 bits (65), Expect = 0.54
Identities = 9/28 (32%), Positives = 15/28 (53%)
Query: 53 HVKGILLYGPPGTGKTLMARQIGQMLNA 80
K I++ GP +GKT +A + + L
Sbjct: 2 KPKLIVIAGPTASGKTALAIALAKRLGG 29
>gnl|CDD|238260 cd00464, SK, Shikimate kinase (SK) is the fifth enzyme in the
shikimate pathway, a seven-step biosynthetic pathway
which converts erythrose-4-phosphate to chorismic acid,
found in bacteria, fungi and plants. Chorismic acid is
a important intermediate in the synthesis of aromatic
compounds, such as aromatic amino acids, p-aminobenzoic
acid, folate and ubiquinone. Shikimate kinase catalyses
the phosphorylation of the 3-hydroxyl group of shikimic
acid using ATP.
Length = 154
Score = 28.7 bits (65), Expect = 0.55
Identities = 9/23 (39%), Positives = 13/23 (56%)
Query: 57 ILLYGPPGTGKTLMARQIGQMLN 79
I+L G G GKT + R + + L
Sbjct: 2 IVLIGMMGAGKTTVGRLLAKALG 24
>gnl|CDD|237150 PRK12608, PRK12608, transcription termination factor Rho;
Provisional.
Length = 380
Score = 28.9 bits (65), Expect = 0.56
Identities = 10/28 (35%), Positives = 17/28 (60%)
Query: 58 LLYGPPGTGKTLMARQIGQMLNAREPKI 85
L+ PP GKT++ +QI + A P++
Sbjct: 137 LIVAPPRAGKTVLLQQIAAAVAANHPEV 164
>gnl|CDD|237867 PRK14953, PRK14953, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 486
Score = 29.0 bits (65), Expect = 0.57
Identities = 20/63 (31%), Positives = 27/63 (42%), Gaps = 14/63 (22%)
Query: 35 AFASRVFPPEVVEQLGCQHVKGILL--------------YGPPGTGKTLMARQIGQMLNA 80
FA + P E +G + V IL GP GTGKT +AR + ++LN
Sbjct: 5 PFARKYRPKFFKEVIGQEIVVRILKNAVKLQRVSHAYIFAGPRGTGKTTIARILAKVLNC 64
Query: 81 REP 83
P
Sbjct: 65 LNP 67
>gnl|CDD|236482 PRK09361, radB, DNA repair and recombination protein RadB;
Provisional.
Length = 225
Score = 28.7 bits (65), Expect = 0.58
Identities = 10/23 (43%), Positives = 16/23 (69%), Gaps = 2/23 (8%)
Query: 55 KGIL--LYGPPGTGKTLMARQIG 75
+G + +YGPPG+GKT + Q+
Sbjct: 22 RGTITQIYGPPGSGKTNICLQLA 44
>gnl|CDD|233847 TIGR02397, dnaX_nterm, DNA polymerase III, subunit gamma and tau.
This model represents the well-conserved first ~ 365
amino acids of the translation of the dnaX gene. The
full-length product of the dnaX gene in the model
bacterium E. coli is the DNA polymerase III tau
subunit. A translational frameshift leads to early
termination and a truncated protein subunit gamma,
about 1/3 shorter than tau and present in roughly equal
amounts. This frameshift mechanism is not necessarily
universal for species with DNA polymerase III but
appears conserved in the exterme thermophile Thermus
thermophilis [DNA metabolism, DNA replication,
recombination, and repair].
Length = 355
Score = 29.1 bits (66), Expect = 0.59
Identities = 12/27 (44%), Positives = 15/27 (55%)
Query: 58 LLYGPPGTGKTLMARQIGQMLNAREPK 84
L GP GTGKT +AR + LN +
Sbjct: 40 LFSGPRGTGKTSIARIFAKALNCQNGP 66
>gnl|CDD|237869 PRK14962, PRK14962, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 472
Score = 29.0 bits (65), Expect = 0.61
Identities = 20/57 (35%), Positives = 26/57 (45%), Gaps = 17/57 (29%)
Query: 44 EVVEQLGCQHVKGILL--------------YGPPGTGKTLMARQIGQMLNAREPKIV 86
EVV Q HVK +++ GP GTGKT +AR + + LN K V
Sbjct: 15 EVVGQD---HVKKLIINALKKNSISHAYIFAGPRGTGKTTVARILAKSLNCENRKGV 68
>gnl|CDD|233761 TIGR02173, cyt_kin_arch, cytidylate kinase, putative. Proteins
in this family are believed to be cytidylate kinase.
Members of this family are found in the archaea and in
spirochaetes, and differ considerably from the common
bacterial form of cytidylate kinase described by
TIGR00017.
Length = 171
Score = 28.5 bits (64), Expect = 0.61
Identities = 10/25 (40%), Positives = 18/25 (72%)
Query: 57 ILLYGPPGTGKTLMARQIGQMLNAR 81
I + GPPG+GKT +A+ + + L+ +
Sbjct: 3 ITISGPPGSGKTTVAKILAEKLSLK 27
>gnl|CDD|224768 COG1855, COG1855, ATPase (PilT family) [General function prediction
only].
Length = 604
Score = 28.9 bits (65), Expect = 0.62
Identities = 12/32 (37%), Positives = 20/32 (62%), Gaps = 1/32 (3%)
Query: 55 KGILLYGPPGTGKTLMARQIGQMLNAREPKIV 86
+GIL+ G PG GK+ A+ + + ++ KIV
Sbjct: 264 EGILIAGAPGAGKSTFAQALAEFYASQG-KIV 294
>gnl|CDD|223775 COG0703, AroK, Shikimate kinase [Amino acid transport and
metabolism].
Length = 172
Score = 28.3 bits (64), Expect = 0.63
Identities = 9/23 (39%), Positives = 14/23 (60%)
Query: 57 ILLYGPPGTGKTLMARQIGQMLN 79
I+L G G GK+ + R + + LN
Sbjct: 5 IVLIGFMGAGKSTIGRALAKALN 27
>gnl|CDD|237963 PRK15424, PRK15424, propionate catabolism operon regulatory protein
PrpR; Provisional.
Length = 538
Score = 28.9 bits (65), Expect = 0.67
Identities = 12/43 (27%), Positives = 17/43 (39%)
Query: 48 QLGCQHVKGILLYGPPGTGKTLMARQIGQMLNAREPKIVNGPQ 90
L + +L+ G GTGK L A+ I + AR
Sbjct: 236 LLYARSSAAVLIQGETGTGKELAAQAIHREYFARHDARQGKKS 278
>gnl|CDD|224985 COG2074, COG2074, 2-phosphoglycerate kinase [Carbohydrate transport
and metabolism].
Length = 299
Score = 28.5 bits (64), Expect = 0.69
Identities = 13/58 (22%), Positives = 23/58 (39%), Gaps = 7/58 (12%)
Query: 24 LDKEFTAIFRRAFASRVFPPEVVEQLGCQHVKGILLYGPPGTGKTLMARQIGQMLNAR 81
L+K + +R R + IL+ G G GK+ +A ++ + L R
Sbjct: 66 LEKGDPEVAKRYLLWRRI-------RKMKRPLIILIGGASGVGKSTIAGELARRLGIR 116
>gnl|CDD|220642 pfam10236, DAP3, Mitochondrial ribosomal death-associated protein
3. This is a family of conserved proteins which were
originally described as death-associated-protein-3
(DAP-3). The proteins carry a P-loop DNA-binding motif,
and induce apoptosis. DAP3 has been shown to be a
pro-apoptotic factor in the mitochondrial matrix and to
be crucial for mitochondrial biogenesis and so has also
been designated as MRP-S29 (mitochondrial ribosomal
protein subunit 29).
Length = 274
Score = 28.8 bits (65), Expect = 0.70
Identities = 13/62 (20%), Positives = 24/62 (38%), Gaps = 10/62 (16%)
Query: 57 ILLYGPPGTGKTLMARQIGQMLNAREPK--IVNGPQVLDKYVGESEANVRRLFADAEEEE 114
+L G G+GK+++ Q M A +++ P+ D +V N +A
Sbjct: 26 FVLTGERGSGKSVLLAQA--MAYAFTQGWIVLHVPEAED-WV-----NGTTDYAPDPGNP 77
Query: 115 KR 116
Sbjct: 78 GL 79
>gnl|CDD|238713 cd01428, ADK, Adenylate kinase (ADK) catalyzes the reversible
phosphoryl transfer from adenosine triphosphates (ATP)
to adenosine monophosphates (AMP) and to yield
adenosine diphosphates (ADP). This enzyme is required
for the biosynthesis of ADP and is essential for
homeostasis of adenosine phosphates.
Length = 194
Score = 28.4 bits (64), Expect = 0.71
Identities = 10/18 (55%), Positives = 13/18 (72%)
Query: 57 ILLYGPPGTGKTLMARQI 74
ILL GPPG+GK A ++
Sbjct: 2 ILLLGPPGSGKGTQAERL 19
>gnl|CDD|235281 PRK04328, PRK04328, hypothetical protein; Provisional.
Length = 249
Score = 28.1 bits (63), Expect = 0.87
Identities = 9/17 (52%), Positives = 14/17 (82%)
Query: 57 ILLYGPPGTGKTLMARQ 73
+LL G PGTGK++ ++Q
Sbjct: 26 VLLSGGPGTGKSIFSQQ 42
>gnl|CDD|163057 TIGR02881, spore_V_K, stage V sporulation protein K. Members of
this protein family are the stage V sporulation protein
K (SpoVK), a close homolog of the Rubisco expression
protein CbbX (TIGR02880) and a members of the ATPase
family associated with various cellular activities
(pfam00004). Members are strictly limited to bacterial
endospore-forming species, but are not universal in
this group and are missing from the Clostridium group
[Cellular processes, Sporulation and germination].
Length = 261
Score = 28.1 bits (63), Expect = 0.87
Identities = 10/18 (55%), Positives = 14/18 (77%)
Query: 61 GPPGTGKTLMARQIGQML 78
G PGTGKT +AR +G++
Sbjct: 49 GNPGTGKTTVARILGKLF 66
>gnl|CDD|237495 PRK13765, PRK13765, ATP-dependent protease Lon; Provisional.
Length = 637
Score = 28.4 bits (64), Expect = 0.89
Identities = 8/22 (36%), Positives = 18/22 (81%)
Query: 57 ILLYGPPGTGKTLMARQIGQML 78
+++ G PGTGK+++A+ + ++L
Sbjct: 53 VMMIGSPGTGKSMLAKAMAELL 74
>gnl|CDD|181180 PRK07952, PRK07952, DNA replication protein DnaC; Validated.
Length = 244
Score = 28.2 bits (63), Expect = 0.94
Identities = 16/59 (27%), Positives = 30/59 (50%), Gaps = 6/59 (10%)
Query: 61 GPPGTGKTLMARQIGQMLNAREPKIVNGPQVLDKYVGESEANVRRLFADAEEEEKRVSH 119
G PGTGK +A I L ++ G VL V + + ++ F+++E E+++ +
Sbjct: 106 GKPGTGKNHLAAAICNEL------LLRGKSVLIITVADIMSAMKDTFSNSETSEEQLLN 158
>gnl|CDD|238549 cd01129, PulE-GspE, PulE/GspE The type II secretory pathway is
the main terminal branch of the general secretory
pathway (GSP). It is responsible for the export the
majority of Gram-negative bacterial exoenzymes and
toxins. PulE is a cytoplasmic protein of the GSP, which
contains an ATP binding site and a tetracysteine motif.
This subgroup also includes PillB and HofB.
Length = 264
Score = 28.4 bits (64), Expect = 0.94
Identities = 17/59 (28%), Positives = 23/59 (38%), Gaps = 19/59 (32%)
Query: 11 SPSFDFNKMGIGGLDKEFTAIFRRAFASRVFPPEVVEQLGCQHVKGILLY-GPPGTGKT 68
+ D K+G L E IFR+ + GI+L GP G+GKT
Sbjct: 54 NQILDLEKLG---LKPENLEIFRKL---------------LEKPHGIILVTGPTGSGKT 94
>gnl|CDD|237965 PRK15429, PRK15429, formate hydrogenlyase transcriptional activator
FhlA; Provisional.
Length = 686
Score = 28.3 bits (63), Expect = 0.99
Identities = 21/68 (30%), Positives = 31/68 (45%), Gaps = 6/68 (8%)
Query: 21 IGGLDKEFTAIFRRAFA-SRVFPP-EVVEQLGCQHVKGILLYGPPGTGKTLMARQIGQML 78
+ +D EF I R+ A V E+V Q +L+ G GTGK L+AR I +
Sbjct: 368 LNNVDSEFGEIIGRSEAMYSVLKQVEMVAQSDST----VLILGETGTGKELIARAIHNLS 423
Query: 79 NAREPKIV 86
++V
Sbjct: 424 GRNNRRMV 431
>gnl|CDD|226372 COG3854, SpoIIIAA, ncharacterized protein conserved in bacteria
[Function unknown].
Length = 308
Score = 28.3 bits (63), Expect = 1.0
Identities = 10/22 (45%), Positives = 14/22 (63%)
Query: 57 ILLYGPPGTGKTLMARQIGQML 78
L+ GPP GKT + R I ++L
Sbjct: 140 TLIIGPPQVGKTTLLRDIARLL 161
>gnl|CDD|233120 TIGR00764, lon_rel, lon-related putative ATP-dependent protease.
This model represents a set of proteins with extensive
C-terminal homology to the ATP-dependent protease La,
product of the lon gene of E. coli. The model is based
on a seed alignment containing only archaeal members,
but several bacterial proteins match the model well.
Because several species, including Thermotoga maritima
and Treponema pallidum, contain both a close homolog of
the lon protease and nearly full-length homolog of the
members of this family, we suggest there may also be a
functional division between the two families. Members
of this family from Pyrococcus horikoshii and
Pyrococcus abyssi each contain a predicted intein
[Protein fate, Degradation of proteins, peptides, and
glycopeptides].
Length = 608
Score = 28.3 bits (63), Expect = 1.1
Identities = 10/28 (35%), Positives = 19/28 (67%)
Query: 55 KGILLYGPPGTGKTLMARQIGQMLNARE 82
+ +LL G PG GK+++A+ + ++L E
Sbjct: 38 RNVLLIGEPGVGKSMLAKAMAELLPDEE 65
>gnl|CDD|232945 TIGR00376, TIGR00376, DNA helicase, putative. The gene product may
represent a DNA helicase. Eukaryotic members of this
family have been characterized as binding certain
single-stranded G-rich DNA sequences (GGGGT and GGGCT).
A number of related proteins are characterized as
helicases [DNA metabolism, DNA replication,
recombination, and repair].
Length = 637
Score = 28.2 bits (63), Expect = 1.1
Identities = 11/28 (39%), Positives = 18/28 (64%)
Query: 58 LLYGPPGTGKTLMARQIGQMLNAREPKI 85
L++GPPGTGKT ++ + L R ++
Sbjct: 177 LIHGPPGTGKTRTLVELIRQLVKRGLRV 204
>gnl|CDD|223637 COG0563, Adk, Adenylate kinase and related kinases [Nucleotide
transport and metabolism].
Length = 178
Score = 27.6 bits (62), Expect = 1.2
Identities = 9/22 (40%), Positives = 16/22 (72%)
Query: 55 KGILLYGPPGTGKTLMARQIGQ 76
IL+ GPPG GK+ +A+++ +
Sbjct: 1 MRILILGPPGAGKSTLAKKLAK 22
>gnl|CDD|222307 pfam13671, AAA_33, AAA domain. This family of domains contain only
a P-loop motif, that is characteristic of the AAA
superfamily. Many of the proteins in this family are
just short fragments so there is no Walker B motif.
Length = 143
Score = 27.7 bits (62), Expect = 1.2
Identities = 20/64 (31%), Positives = 30/64 (46%), Gaps = 8/64 (12%)
Query: 57 ILLYGPPGTGKTLMARQIGQMLNA--------REPKIVNGPQVLDKYVGESEANVRRLFA 108
IL+ G PG+GK+ AR++ + L A R+ +GP + Y S +RL
Sbjct: 2 ILMVGLPGSGKSTFARRLLRELGAVVLSSDTLRKRLRGDGPPDISYYARASGRVYQRLLE 61
Query: 109 DAEE 112
A E
Sbjct: 62 LARE 65
>gnl|CDD|182791 PRK10865, PRK10865, protein disaggregation chaperone; Provisional.
Length = 857
Score = 27.9 bits (62), Expect = 1.3
Identities = 21/71 (29%), Positives = 34/71 (47%), Gaps = 11/71 (15%)
Query: 58 LLYGPPGTGKTLMARQIGQ-MLNAREPKIVNGPQVLD----------KYVGESEANVRRL 106
+L G PG GKT + + Q ++N P+ + G +VL KY GE E ++ +
Sbjct: 203 VLIGEPGVGKTAIVEGLAQRIINGEVPEGLKGRRVLALDMGALVAGAKYRGEFEERLKGV 262
Query: 107 FADAEEEEKRV 117
D ++E V
Sbjct: 263 LNDLAKQEGNV 273
>gnl|CDD|215967 pfam00519, PPV_E1_C, Papillomavirus helicase. This protein is a
DNA helicase that is required for initiation of viral
DNA replication. This protein forms a complex with the
E2 protein pfam00508.
Length = 432
Score = 27.9 bits (63), Expect = 1.3
Identities = 7/13 (53%), Positives = 12/13 (92%)
Query: 57 ILLYGPPGTGKTL 69
+++YGPP TGK++
Sbjct: 265 LVIYGPPDTGKSM 277
>gnl|CDD|222856 PHA02530, pseT, polynucleotide kinase; Provisional.
Length = 300
Score = 27.7 bits (62), Expect = 1.3
Identities = 14/31 (45%), Positives = 18/31 (58%), Gaps = 4/31 (12%)
Query: 57 ILLYGPPGTGKTLMARQIGQMLNAREPKIVN 87
IL G PG+GK+ AR+ A+ PK VN
Sbjct: 5 ILTVGVPGSGKSTWAREFA----AKNPKAVN 31
>gnl|CDD|238569 cd01149, HutB, Hemin binding protein HutB. These proteins have
been shown to function as initial receptors in ABC
transport of hemin and hemoproteins in many eubacterial
species. They belong to the TroA superfamily of
periplasmic metal binding proteins that share a distinct
fold and ligand binding mechanism. A typical TroA
protein is comprised of two globular subdomains
connected by a single helix and can bind the metal ion
in the cleft between these domains.
Length = 235
Score = 27.6 bits (62), Expect = 1.3
Identities = 16/79 (20%), Positives = 27/79 (34%), Gaps = 11/79 (13%)
Query: 41 FPPEVVEQLGCQHVKGILLYGPPGTGKTLMAR--QIGQMLNAREPKIVNGPQVLDKYVGE 98
PPE ++QL V + + P T L+ + Q+ Q L P+ + E
Sbjct: 69 GPPEALDQLRAAGVPVVTVPSTP-TLDGLLTKIRQVAQALGV--------PEKGEALAQE 119
Query: 99 SEANVRRLFADAEEEEKRV 117
+ L +K
Sbjct: 120 VRQRLAALRKTVAAHKKPP 138
>gnl|CDD|234034 TIGR02858, spore_III_AA, stage III sporulation protein AA. Members
of this protein are the stage III sporulation protein
AA, encoded by one of several genes in the spoIIIA
locus. It seems that this protein is found in a species
if and only if that species is capable of endospore
formation [Cellular processes, Sporulation and
germination].
Length = 270
Score = 27.7 bits (62), Expect = 1.3
Identities = 8/32 (25%), Positives = 16/32 (50%)
Query: 58 LLYGPPGTGKTLMARQIGQMLNAREPKIVNGP 89
L+ PP GKT + R + ++L+ ++
Sbjct: 115 LIISPPQCGKTTLLRDLARILSTGISQLGLRG 146
>gnl|CDD|238977 cd02019, NK, Nucleoside/nucleotide kinase (NK) is a protein
superfamily consisting of multiple families of enzymes
that share structural similarity and are functionally
related to the catalysis of the reversible phosphate
group transfer from nucleoside triphosphates to
nucleosides/nucleotides, nucleoside monophosphates, or
sugars. Members of this family play a wide variety of
essential roles in nucleotide metabolism, the
biosynthesis of coenzymes and aromatic compounds, as
well as the metabolism of sugar and sulfate.
Length = 69
Score = 26.5 bits (59), Expect = 1.4
Identities = 9/41 (21%), Positives = 22/41 (53%)
Query: 57 ILLYGPPGTGKTLMARQIGQMLNAREPKIVNGPQVLDKYVG 97
I + G G+GK+ +A+++ + L R +++ +L+
Sbjct: 2 IAITGGSGSGKSTVAKKLAEQLGGRSVVVLDEIVILEGLYA 42
>gnl|CDD|217326 pfam03029, ATP_bind_1, Conserved hypothetical ATP binding protein.
Members of this family are found in a range of archaea
and eukaryotes and have hypothesised ATP binding
activity.
Length = 235
Score = 27.7 bits (62), Expect = 1.4
Identities = 15/56 (26%), Positives = 25/56 (44%), Gaps = 2/56 (3%)
Query: 61 GPPGTGKTLMARQIGQ--MLNAREPKIVNGPQVLDKYVGESEANVRRLFADAEEEE 114
GP G+GKT + + L R +VN + E++ ++R L A+ E
Sbjct: 3 GPAGSGKTTFVGALSEILPLLGRSVYVVNLDPAAENLPYEADIDIRELITVADVME 58
>gnl|CDD|236461 PRK09302, PRK09302, circadian clock protein KaiC; Reviewed.
Length = 509
Score = 27.9 bits (63), Expect = 1.4
Identities = 10/16 (62%), Positives = 11/16 (68%)
Query: 58 LLYGPPGTGKTLMARQ 73
L+ G GTGKTL A Q
Sbjct: 35 LVSGTAGTGKTLFALQ 50
Score = 27.2 bits (61), Expect = 2.2
Identities = 10/15 (66%), Positives = 12/15 (80%)
Query: 57 ILLYGPPGTGKTLMA 71
IL+ G GTGKTL+A
Sbjct: 276 ILVSGATGTGKTLLA 290
>gnl|CDD|235364 PRK05201, hslU, ATP-dependent protease ATP-binding subunit HslU;
Provisional.
Length = 443
Score = 27.7 bits (63), Expect = 1.4
Identities = 13/26 (50%), Positives = 19/26 (73%)
Query: 55 KGILLYGPPGTGKTLMARQIGQMLNA 80
K IL+ GP G GKT +AR++ ++ NA
Sbjct: 51 KNILMIGPTGVGKTEIARRLAKLANA 76
>gnl|CDD|215920 pfam00437, T2SE, Type II/IV secretion system protein. This family
contains both type II and type IV pathway secretion
proteins from bacteria. VirB11 ATPase is a subunit of
the Agrobacterium tumefaciens transfer DNA (T-DNA)
transfer system, a type IV secretion pathway required
for delivery of T-DNA and effector proteins to plant
cells during infection.
Length = 273
Score = 27.6 bits (62), Expect = 1.5
Identities = 17/75 (22%), Positives = 30/75 (40%), Gaps = 16/75 (21%)
Query: 13 SFDFNKMGIGG-LDKEFTAIFRRAFASRVFPPEVVEQLGCQHVKGILLYGPPGTGKTLMA 71
S + +G+ G D + R+A +R IL+ G G+GKT +
Sbjct: 102 SLTLDDLGMTGAFDADIAEFLRQAVQAR---------------GNILVSGGTGSGKTTLL 146
Query: 72 RQIGQMLNAREPKIV 86
+ +N + +IV
Sbjct: 147 YALLNEINTDDERIV 161
>gnl|CDD|237090 PRK12402, PRK12402, replication factor C small subunit 2;
Reviewed.
Length = 337
Score = 27.6 bits (62), Expect = 1.5
Identities = 14/36 (38%), Positives = 19/36 (52%), Gaps = 8/36 (22%)
Query: 43 PEVVEQLGCQH------VKGILLYGPPGTGKTLMAR 72
EVVE+L + +L+ GPPG+GKT R
Sbjct: 21 DEVVERL--SRAVDSPNLPHLLVQGPPGSGKTAAVR 54
>gnl|CDD|163589 TIGR03877, thermo_KaiC_1, KaiC domain protein, Ph0284 family.
Members of this family contain a single copy of the
KaiC domain (pfam06745) that occurs in two copies of
the circadian clock protein kinase KaiC itself. Members
occur primarily in thermophilic archaea and in
Thermotoga.
Length = 237
Score = 27.8 bits (62), Expect = 1.5
Identities = 9/17 (52%), Positives = 14/17 (82%)
Query: 57 ILLYGPPGTGKTLMARQ 73
+LL G PGTGK++ ++Q
Sbjct: 24 VLLSGGPGTGKSIFSQQ 40
>gnl|CDD|214692 smart00487, DEXDc, DEAD-like helicases superfamily.
Length = 201
Score = 27.5 bits (61), Expect = 1.6
Identities = 8/20 (40%), Positives = 13/20 (65%)
Query: 52 QHVKGILLYGPPGTGKTLMA 71
++ ++L P G+GKTL A
Sbjct: 22 SGLRDVILAAPTGSGKTLAA 41
>gnl|CDD|225114 COG2204, AtoC, Response regulator containing CheY-like receiver,
AAA-type ATPase, and DNA-binding domains [Signal
transduction mechanisms].
Length = 464
Score = 27.7 bits (62), Expect = 1.6
Identities = 10/18 (55%), Positives = 13/18 (72%)
Query: 57 ILLYGPPGTGKTLMARQI 74
+L+ G GTGK L+AR I
Sbjct: 167 VLITGESGTGKELVARAI 184
>gnl|CDD|224402 COG1485, COG1485, Predicted ATPase [General function prediction
only].
Length = 367
Score = 27.6 bits (62), Expect = 1.7
Identities = 10/19 (52%), Positives = 13/19 (68%), Gaps = 1/19 (5%)
Query: 54 VKGILLYGPPGTGKT-LMA 71
V+G+ L+G G GKT LM
Sbjct: 65 VRGLYLWGGVGRGKTMLMD 83
>gnl|CDD|219014 pfam06414, Zeta_toxin, Zeta toxin. This family consists of
several bacterial zeta toxin proteins. Zeta toxin is
thought to be part of a postregulational killing system
in bacteria. It relies on antitoxin/toxin systems that
secure stable inheritance of low and medium copy number
plasmids during cell division and kill cells that have
lost the plasmid.
Length = 191
Score = 27.2 bits (61), Expect = 1.8
Identities = 11/37 (29%), Positives = 18/37 (48%)
Query: 52 QHVKGILLYGPPGTGKTLMARQIGQMLNAREPKIVNG 88
+ +LL G PG GKT +AR + + L ++
Sbjct: 10 ERPVAVLLGGQPGAGKTELARALLEELGGGNVVRIDP 46
>gnl|CDD|238978 cd02020, CMPK, Cytidine monophosphate kinase (CMPK) catalyzes the
reversible phosphorylation of cytidine monophosphate
(CMP) to produce cytidine diphosphate (CDP), using ATP
as the preferred phosphoryl donor.
Length = 147
Score = 27.1 bits (61), Expect = 1.8
Identities = 7/19 (36%), Positives = 13/19 (68%)
Query: 61 GPPGTGKTLMARQIGQMLN 79
GP G+GK+ +A+ + + L
Sbjct: 6 GPAGSGKSTVAKLLAKKLG 24
>gnl|CDD|132613 TIGR03574, selen_PSTK, L-seryl-tRNA(Sec) kinase, archaeal.
Members of this protein are L-seryl-tRNA(Sec) kinase.
This enzyme is part of a two-step pathway in Eukaryota
and Archaea for performing selenocysteine biosynthesis
by changing serine misacylated on selenocysteine-tRNA
to selenocysteine. This enzyme performs the first step,
phosphorylation of the OH group of the serine side
chain. This family represents archaeal proteins with
this activity [Protein synthesis, tRNA aminoacylation].
Length = 249
Score = 27.5 bits (61), Expect = 1.8
Identities = 8/22 (36%), Positives = 15/22 (68%)
Query: 57 ILLYGPPGTGKTLMARQIGQML 78
I+L G PG GK+ ++++ + L
Sbjct: 2 IILTGLPGVGKSTFSKELAKKL 23
>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 = 27.3 bits (61), Expect = 1.8
Identities = 9/30 (30%), Positives = 15/30 (50%)
Query: 57 ILLYGPPGTGKTLMARQIGQMLNAREPKIV 86
+ + GP G+GKT A+++ L V
Sbjct: 2 VGIAGPSGSGKTTFAKKLSNQLRVNGIGPV 31
>gnl|CDD|218292 pfam04851, ResIII, Type III restriction enzyme, res subunit.
Length = 100
Score = 26.8 bits (60), Expect = 1.8
Identities = 12/43 (27%), Positives = 20/43 (46%), Gaps = 3/43 (6%)
Query: 55 KGILLYGPPGTGKTLMARQIGQMLNAREPK---IVNGPQVLDK 94
K L+ G+GKTL A + L + K +V +L++
Sbjct: 19 KRGLIVMATGSGKTLTAAALIARLAKGKKKVLFVVPRKDLLEQ 61
>gnl|CDD|233692 TIGR02031, BchD-ChlD, magnesium chelatase ATPase subunit D. This
model represents one of two ATPase subunits of the
trimeric magnesium chelatase responsible for insertion
of magnesium ion into protoporphyrin IX. This is an
essential step in the biosynthesis of both chlorophyll
and bacteriochlorophyll. This subunit is found in green
plants, photosynthetic algae, cyanobacteria and other
photosynthetic bacteria. Unlike subunit I (TIGR02030),
this subunit is not found in archaea [Biosynthesis of
cofactors, prosthetic groups, and carriers, Chlorophyll
and bacteriochlorphyll].
Length = 589
Score = 27.5 bits (61), Expect = 1.9
Identities = 10/33 (30%), Positives = 18/33 (54%)
Query: 53 HVKGILLYGPPGTGKTLMARQIGQMLNAREPKI 85
+ G+ + GTGKT +AR + ++L P +
Sbjct: 15 SLGGVAIRARAGTGKTALARALAEILPPIMPFV 47
>gnl|CDD|216999 pfam02367, UPF0079, Uncharacterized P-loop hydrolase UPF0079.
This uncharacterized family contains a P-loop.
Length = 123
Score = 26.9 bits (60), Expect = 1.9
Identities = 10/27 (37%), Positives = 12/27 (44%)
Query: 57 ILLYGPPGTGKTLMARQIGQMLNAREP 83
+LL G G GKT R + Q L
Sbjct: 18 VLLSGDLGAGKTTFVRGLAQGLGITGN 44
>gnl|CDD|190347 pfam02562, PhoH, PhoH-like protein. PhoH is a cytoplasmic
protein and predicted ATPase that is induced by
phosphate starvation.
Length = 205
Score = 27.0 bits (61), Expect = 1.9
Identities = 8/11 (72%), Positives = 9/11 (81%)
Query: 61 GPPGTGKTLMA 71
GP GTGKT +A
Sbjct: 26 GPAGTGKTYLA 36
>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 = 26.6 bits (59), Expect = 1.9
Identities = 12/40 (30%), Positives = 21/40 (52%), Gaps = 4/40 (10%)
Query: 57 ILLYGPPGTGKTLMARQIGQMLNAREPKIVNGPQVLDKYV 96
I++ G G GKT +A + L R +++ ++D YV
Sbjct: 2 IVVTGKGGVGKTTLAANLAAALAKRGKRVL----LIDDYV 37
>gnl|CDD|130679 TIGR01618, phage_P_loop, phage nucleotide-binding protein. This
model represents an uncharacterized family of proteins
from a number of phage of Gram-positive bacteria. This
protein contains a P-loop motif, G/A-X-X-G-X-G-K-T near
its amino end. The function of this protein is unknown
[Mobile and extrachromosomal element functions,
Prophage functions].
Length = 220
Score = 27.1 bits (60), Expect = 2.0
Identities = 9/18 (50%), Positives = 12/18 (66%)
Query: 57 ILLYGPPGTGKTLMARQI 74
L+YG PGTGKT + +
Sbjct: 15 YLIYGKPGTGKTSTIKYL 32
>gnl|CDD|238054 cd00106, KISc, Kinesin motor domain. This catalytic (head) domain
has ATPase activity and belongs to the larger group of
P-loop NTPases. Kinesins are microtubule-dependent
molecular motors that play important roles in
intracellular transport and in cell division. In most
kinesins, the motor domain is found at the N-terminus
(N-type), in some its is found in the middle (M-type),
or C-terminal (C-type). N-type and M-type kinesins are
(+) end-directed motors, while C-type kinesins are (-)
end-directed motors, i.e. they transport cargo towards
the (-) end of the microtubule. Kinesin motor domains
hydrolyze ATP at a rate of about 80 per second, and
move along the microtubule at a speed of about 6400
Angstroms per second. To achieve that, kinesin head
groups work in pairs. Upon replacing ADP with ATP, a
kinesin motor domain increases its affinity for
microtubule binding and locks in place. Also, the neck
linker binds to the motor domain, which repositions the
other head domain through the coiled-coil domain close
to a second tubulin dimer, about 80 Angstroms along the
microtubule. Meanwhile, ATP hydrolysis takes place, and
when the second head domain binds to the microtubule,
the first domain again replaces ADP with ATP,
triggering a conformational change that pulls the first
domain forward.
Length = 328
Score = 27.2 bits (61), Expect = 2.0
Identities = 19/83 (22%), Positives = 26/83 (31%), Gaps = 27/83 (32%)
Query: 1 MEVQPRQS--IISPSFDFNKMGIGGLDKEFTAIFRRAFASRVFPP-----EVVEQLGCQH 53
+ V ++ + P K FT F VF P +V E
Sbjct: 23 ITVDDNKTVTLTPPKDGRKAG-----PKSFT------F-DHVFDPNSTQEDVYETTAKPL 70
Query: 54 VKG--------ILLYGPPGTGKT 68
V+ I YG G+GKT
Sbjct: 71 VESVLEGYNGTIFAYGQTGSGKT 93
>gnl|CDD|224260 COG1341, COG1341, Predicted GTPase or GTP-binding protein [General
function prediction only].
Length = 398
Score = 27.4 bits (61), Expect = 2.0
Identities = 13/44 (29%), Positives = 24/44 (54%), Gaps = 4/44 (9%)
Query: 57 ILLYGPPGTGKTLMARQIGQMLNAREPKIVNGPQVLDKYVGESE 100
+++ GP +GK+ + + L AR K+ ++D VG+SE
Sbjct: 76 VMVVGPVDSGKSTLTTYLANKLLARGRKVA----IIDADVGQSE 115
>gnl|CDD|222927 PHA02774, PHA02774, E1; Provisional.
Length = 613
Score = 27.2 bits (61), Expect = 2.1
Identities = 7/13 (53%), Positives = 12/13 (92%)
Query: 57 ILLYGPPGTGKTL 69
+++YGPP TGK++
Sbjct: 437 LVIYGPPDTGKSM 449
>gnl|CDD|221074 pfam11312, DUF3115, Protein of unknown function (DUF3115). This
eukaryotic family of proteins has no known function.
Length = 284
Score = 27.2 bits (61), Expect = 2.2
Identities = 11/30 (36%), Positives = 18/30 (60%), Gaps = 3/30 (10%)
Query: 31 IFRRAFASRVFPPEVVEQLGCQHVKGILLY 60
+F+ AF S ++ ++ E + Q VKG LY
Sbjct: 1 LFKDAFLSELYSDDLQELI--QAVKG-DLY 27
>gnl|CDD|235878 PRK06851, PRK06851, hypothetical protein; Provisional.
Length = 367
Score = 27.2 bits (61), Expect = 2.5
Identities = 12/26 (46%), Positives = 17/26 (65%), Gaps = 2/26 (7%)
Query: 57 ILLYGPPGTGK-TLMARQIGQMLNAR 81
+L G PGTGK TLM ++IG+ +
Sbjct: 33 FILKGGPGTGKSTLM-KKIGEEFLEK 57
>gnl|CDD|227596 COG5271, MDN1, AAA ATPase containing von Willebrand factor type A
(vWA) domain [General function prediction only].
Length = 4600
Score = 27.3 bits (60), Expect = 2.8
Identities = 14/28 (50%), Positives = 17/28 (60%), Gaps = 4/28 (14%)
Query: 55 KGILLYGPPGTGKT----LMARQIGQML 78
K ILL G PG GKT +AR+ G+ L
Sbjct: 1544 KPILLEGSPGVGKTSLITALARKTGKKL 1571
Score = 26.1 bits (57), Expect = 5.9
Identities = 14/35 (40%), Positives = 19/35 (54%), Gaps = 2/35 (5%)
Query: 46 VEQL--GCQHVKGILLYGPPGTGKTLMARQIGQML 78
+EQL Q+ + LL G GTGKT M + + L
Sbjct: 454 LEQLLWNIQNNEPTLLVGETGTGKTTMIQYLALKL 488
>gnl|CDD|180523 PRK06305, PRK06305, DNA polymerase III subunits gamma and tau;
Validated.
Length = 451
Score = 27.0 bits (60), Expect = 2.8
Identities = 12/26 (46%), Positives = 15/26 (57%)
Query: 58 LLYGPPGTGKTLMARQIGQMLNAREP 83
L G GTGKT +AR + LN + P
Sbjct: 43 LFSGIRGTGKTTLARIFAKALNCQNP 68
>gnl|CDD|180607 PRK06526, PRK06526, transposase; Provisional.
Length = 254
Score = 26.8 bits (59), Expect = 2.9
Identities = 10/19 (52%), Positives = 14/19 (73%)
Query: 57 ILLYGPPGTGKTLMARQIG 75
++ GPPGTGKT +A +G
Sbjct: 101 VVFLGPPGTGKTHLAIGLG 119
>gnl|CDD|183108 PRK11377, PRK11377, dihydroxyacetone kinase subunit M; Provisional.
Length = 473
Score = 27.0 bits (60), Expect = 2.9
Identities = 15/40 (37%), Positives = 23/40 (57%), Gaps = 2/40 (5%)
Query: 37 ASRVFPPEVVEQLGCQHVKGILLY-GPPGTGKTLMARQIG 75
A ++P V+ QL VKGI L G P + ++AR++G
Sbjct: 402 AENIYPSTVL-QLDPAVVKGICLSAGSPLSHSAIIARELG 440
>gnl|CDD|234232 TIGR03499, FlhF, flagellar biosynthetic protein FlhF. [Cellular
processes, Chemotaxis and motility].
Length = 283
Score = 26.9 bits (60), Expect = 2.9
Identities = 10/43 (23%), Positives = 15/43 (34%), Gaps = 5/43 (11%)
Query: 26 KEFTAIFRRAFASRVFPPEVVEQLGCQHVKGILLYGPPGTGKT 68
+ + ++E+ G I L GP G GKT
Sbjct: 172 RWLREALEGMLPVKPEEDPILERGGV-----IALVGPTGVGKT 209
>gnl|CDD|184925 PRK14961, PRK14961, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 363
Score = 27.1 bits (60), Expect = 2.9
Identities = 11/22 (50%), Positives = 14/22 (63%)
Query: 58 LLYGPPGTGKTLMARQIGQMLN 79
LL G G GKT +AR + + LN
Sbjct: 42 LLSGTRGVGKTTIARLLAKSLN 63
>gnl|CDD|237475 PRK13695, PRK13695, putative NTPase; Provisional.
Length = 174
Score = 26.4 bits (59), Expect = 3.3
Identities = 13/32 (40%), Positives = 18/32 (56%), Gaps = 1/32 (3%)
Query: 57 ILLYGPPGTGKTLMARQIGQMLNAREPKIVNG 88
I + GPPG GKT + +I ++L E V G
Sbjct: 3 IGITGPPGVGKTTLVLKIAELL-KEEGYKVGG 33
>gnl|CDD|237864 PRK14950, PRK14950, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 585
Score = 26.7 bits (59), Expect = 3.5
Identities = 10/26 (38%), Positives = 13/26 (50%)
Query: 58 LLYGPPGTGKTLMARQIGQMLNAREP 83
L GP G GKT AR + + +N
Sbjct: 42 LFTGPRGVGKTSTARILAKAVNCTTN 67
>gnl|CDD|235244 PRK04182, PRK04182, cytidylate kinase; Provisional.
Length = 180
Score = 26.3 bits (59), Expect = 3.6
Identities = 10/19 (52%), Positives = 14/19 (73%)
Query: 61 GPPGTGKTLMARQIGQMLN 79
GPPG+GKT +AR + + L
Sbjct: 7 GPPGSGKTTVARLLAEKLG 25
>gnl|CDD|233417 TIGR01447, recD, exodeoxyribonuclease V, alpha subunit. This
family describes the exodeoxyribonuclease V alpha
subunit, RecD. RecD is part of a RecBCD complex. A
related family in the Gram-positive bacteria separates
in a phylogenetic tree, has an additional N-terminal
extension of about 200 residues, and is not supported as
a member of a RecBCD complex by neighboring genes. The
related family is consequently described by a different
model [DNA metabolism, DNA replication, recombination,
and repair].
Length = 586
Score = 26.7 bits (59), Expect = 3.6
Identities = 11/34 (32%), Positives = 16/34 (47%), Gaps = 5/34 (14%)
Query: 58 LLYGPPGTGKT-----LMARQIGQMLNAREPKIV 86
L+ G PGTGKT L+ + Q + +I
Sbjct: 164 LITGGPGTGKTTTVARLLLALVKQSPKQGKLRIA 197
>gnl|CDD|234522 TIGR04249, SCM_chp_ScmC, SynChlorMet cassette protein ScmC. A
biosynthesis cassette found in Syntrophobacter
fumaroxidans MPOB, Chlorobium limicola DSM 245,
Methanocella paludicola SANAE, and delta proteobacterium
NaphS2 contains two PqqE-like radical SAM/SPASM domain
proteins, a PqqD homolog, and a conserved hypothetical
protein. These components suggest modification of a
ribosomally produced peptide precursor, but the
precursor has not been identified. Members of this
family are designated ScmC.
Length = 292
Score = 26.4 bits (58), Expect = 3.6
Identities = 10/21 (47%), Positives = 13/21 (61%)
Query: 55 KGILLYGPPGTGKTLMARQIG 75
+G LL GTGK+ R+IG
Sbjct: 138 EGYLLAASGGTGKSTCCRRIG 158
>gnl|CDD|222194 pfam13521, AAA_28, AAA domain.
Length = 162
Score = 26.4 bits (59), Expect = 3.6
Identities = 7/12 (58%), Positives = 9/12 (75%)
Query: 57 ILLYGPPGTGKT 68
I++ G P TGKT
Sbjct: 2 IVITGGPSTGKT 13
>gnl|CDD|216202 pfam00931, NB-ARC, NB-ARC domain.
Length = 285
Score = 26.5 bits (59), Expect = 3.8
Identities = 8/16 (50%), Positives = 11/16 (68%)
Query: 59 LYGPPGTGKTLMARQI 74
+ G G GKT +A+QI
Sbjct: 24 IVGMGGVGKTTLAKQI 39
>gnl|CDD|233959 TIGR02639, ClpA, ATP-dependent Clp protease ATP-binding subunit
clpA. [Protein fate, Degradation of proteins, peptides,
and glycopeptides].
Length = 730
Score = 26.5 bits (59), Expect = 3.8
Identities = 10/22 (45%), Positives = 14/22 (63%)
Query: 58 LLYGPPGTGKTLMARQIGQMLN 79
L GP G GKT +A+Q+ + L
Sbjct: 487 LFVGPTGVGKTELAKQLAEELG 508
>gnl|CDD|234132 TIGR03167, tRNA_sel_U_synt, tRNA 2-selenouridine synthase. The
Escherichia coli YbbB protein was shown to encode a
selenophosphate-dependent tRNA 2-selenouridine synthase,
essential for modification of some tRNAs to replace a
sulfur atom with selenium. This enzyme works with SelD,
the selenium donor protein, which also acts in
selenocysteine incorporation. Although the members of
this protein family show a fairly deep split, sequences
from both sides of the split are supported by
co-occurence with, and often proximity to, the selD gene
[Protein synthesis, tRNA and rRNA base modification].
Length = 311
Score = 26.4 bits (59), Expect = 3.8
Identities = 18/51 (35%), Positives = 25/51 (49%), Gaps = 12/51 (23%)
Query: 45 VVEQLG--CQHVKGILLYGPPGTGKTLMARQIGQMLNAREPKIVNGPQVLD 93
V++QL Q I+L G G+GKT + + + NA G QVLD
Sbjct: 116 VIDQLEELPQPFPLIVLGGMTGSGKTEL---LHALANA-------GAQVLD 156
>gnl|CDD|226350 COG3829, RocR, Transcriptional regulator containing PAS, AAA-type
ATPase, and DNA-binding domains [Transcription / Signal
transduction mechanisms].
Length = 560
Score = 26.5 bits (59), Expect = 3.9
Identities = 10/18 (55%), Positives = 12/18 (66%)
Query: 57 ILLYGPPGTGKTLMARQI 74
+L+ G GTGK L AR I
Sbjct: 271 VLILGESGTGKELFARAI 288
>gnl|CDD|225822 COG3284, AcoR, Transcriptional activator of acetoin/glycerol
metabolism [Secondary metabolites biosynthesis,
transport, and catabolism / Transcription].
Length = 606
Score = 26.6 bits (59), Expect = 4.0
Identities = 17/57 (29%), Positives = 23/57 (40%), Gaps = 16/57 (28%)
Query: 22 GGLDKEFTAIFRRA--FASRVFPPEVVEQLGCQHVKGILLYGPPGTGKTLMARQIGQ 76
LD + R+A A+ P +LL G GTGK ++AR I Q
Sbjct: 316 PLLDPSRATLLRKAERVAATDLP--------------VLLQGETGTGKEVLARAIHQ 358
>gnl|CDD|213512 TIGR00174, miaA, tRNA dimethylallyltransferase. Alternate names
include delta(2)-isopentenylpyrophosphate transferase,
IPP transferase, 2-methylthio-N6-isopentyladenosine
tRNA modification enzyme. Catalyzes the first step in
the modification of an adenosine near the anticodon to
2-methylthio-N6-isopentyladenosine. Understanding of
substrate specificity has changed [Protein synthesis,
tRNA and rRNA base modification].
Length = 287
Score = 26.6 bits (59), Expect = 4.0
Identities = 11/24 (45%), Positives = 16/24 (66%)
Query: 57 ILLYGPPGTGKTLMARQIGQMLNA 80
I L GP +GK+ ++ Q+ Q LNA
Sbjct: 2 IFLMGPTASGKSQLSIQLAQKLNA 25
>gnl|CDD|236011 PRK07399, PRK07399, DNA polymerase III subunit delta'; Validated.
Length = 314
Score = 26.4 bits (59), Expect = 4.1
Identities = 8/21 (38%), Positives = 10/21 (47%)
Query: 58 LLYGPPGTGKTLMARQIGQML 78
L GP G G+ L A + L
Sbjct: 30 LFAGPEGVGRKLAALCFIEGL 50
>gnl|CDD|224027 COG1102, Cmk, Cytidylate kinase [Nucleotide transport and
metabolism].
Length = 179
Score = 26.1 bits (58), Expect = 4.1
Identities = 10/23 (43%), Positives = 16/23 (69%)
Query: 57 ILLYGPPGTGKTLMARQIGQMLN 79
I + G PG+GKT +AR++ + L
Sbjct: 3 ITISGLPGSGKTTVARELAEHLG 25
>gnl|CDD|213179 cd00267, ABC_ATPase, ATP-binding cassette transporter
nucleotide-binding domain. ABC transporters are a
large family of proteins involved in the transport of a
wide variety of different compounds, like sugars, ions,
peptides, and more complex organic molecules. The
nucleotide-binding domain shows the highest similarity
between all members of the family. ABC transporters are
a subset of nucleotide hydrolases that contain a
signature motif, Q-loop, and H-loop/switch region, in
addition to, the Walker A motif/P-loop and Walker B
motif commonly found in a number of ATP- and
GTP-binding and hydrolyzing proteins.
Length = 157
Score = 26.1 bits (58), Expect = 4.1
Identities = 10/35 (28%), Positives = 18/35 (51%), Gaps = 1/35 (2%)
Query: 61 GPPGTGKTLMARQIGQMLNAREPKI-VNGPQVLDK 94
GP G+GK+ + R I +L +I ++G +
Sbjct: 32 GPNGSGKSTLLRAIAGLLKPTSGEILIDGKDIAKL 66
>gnl|CDD|237672 PRK14318, glmM, phosphoglucosamine mutase; Provisional.
Length = 448
Score = 26.4 bits (59), Expect = 4.4
Identities = 21/57 (36%), Positives = 25/57 (43%), Gaps = 8/57 (14%)
Query: 65 TGKTLMAR--QIGQMLNAREPKIVNGPQVL------DKYVGESEANVRRLFADAEEE 113
TG LMAR Q G+ L + PQVL DK + +VR A AE E
Sbjct: 346 TGLRLMARMAQTGKSLAELASAMTVLPQVLINVPVVDKTTAATAPSVRAAVARAEAE 402
>gnl|CDD|225895 COG3359, COG3359, Predicted exonuclease [DNA replication,
recombination, and repair].
Length = 278
Score = 26.3 bits (58), Expect = 4.5
Identities = 8/25 (32%), Positives = 11/25 (44%)
Query: 95 YVGESEANVRRLFADAEEEEKRVSH 119
+ +VR+ F A EEE V
Sbjct: 124 RGVDDTMHVRQHFLPAPEEEVAVLE 148
>gnl|CDD|132348 TIGR03305, alt_F1F0_F1_bet, alternate F1F0 ATPase, F1 subunit
beta. A small number of taxonomically diverse
prokaryotic species have what appears to be a second
ATP synthase, in addition to the normal F1F0 ATPase in
bacteria and A1A0 ATPase in archaea. These enzymes use
ion gradients to synthesize ATP, and in principle may
run in either direction. This model represents the F1
beta subunit of this apparent second ATP synthase.
Length = 449
Score = 26.3 bits (58), Expect = 4.5
Identities = 14/37 (37%), Positives = 18/37 (48%)
Query: 44 EVVEQLGCQHVKGILLYGPPGTGKTLMARQIGQMLNA 80
EV+ QL HV+GI L G + + R G L A
Sbjct: 37 EVLSQLDAHHVRGIALTPTQGLARGMPVRDSGGPLKA 73
>gnl|CDD|178596 PLN03025, PLN03025, replication factor C subunit; Provisional.
Length = 319
Score = 26.2 bits (58), Expect = 4.5
Identities = 10/22 (45%), Positives = 15/22 (68%), Gaps = 4/22 (18%)
Query: 57 ILLYGPPGTGKT----LMARQI 74
++L GPPGTGKT +A ++
Sbjct: 37 LILSGPPGTGKTTSILALAHEL 58
>gnl|CDD|233793 TIGR02237, recomb_radB, DNA repair and recombination protein
RadB. This family consists exclusively of archaeal
RadB protein, a homolog of bacterial RecA (TIGR02012),
eukaryotic RAD51 (TIGR02239) and DMC1 (TIGR02238), and
archaeal RadA (TIGR02236).
Length = 209
Score = 26.2 bits (58), Expect = 4.6
Identities = 13/34 (38%), Positives = 21/34 (61%), Gaps = 3/34 (8%)
Query: 55 KGIL--LYGPPGTGKTLMARQIGQMLNAREPKIV 86
+G + +YGPPG+GKT + + + AR+ K V
Sbjct: 11 RGTITQIYGPPGSGKTNICMILA-VNAARQGKKV 43
>gnl|CDD|224847 COG1936, COG1936, Predicted nucleotide kinase (related to CMP and
AMP kinases) [Nucleotide transport and metabolism].
Length = 180
Score = 26.1 bits (58), Expect = 4.7
Identities = 7/18 (38%), Positives = 11/18 (61%)
Query: 57 ILLYGPPGTGKTLMARQI 74
I + G PG GKT + + +
Sbjct: 3 IAITGTPGVGKTTVCKLL 20
>gnl|CDD|131806 TIGR02759, TraD_Ftype, type IV conjugative transfer system coupling
protein TraD. The TraD protein performs an essential
coupling function in conjugative type IV secretion
systems. This protein sits at the inner membrane in
contact with the assembled pilus and its scaffold as
well as the relaxosome-plasmid DNA complex (through
TraM).
Length = 566
Score = 26.2 bits (58), Expect = 4.7
Identities = 11/37 (29%), Positives = 22/37 (59%), Gaps = 4/37 (10%)
Query: 51 CQHVKGILLYGPPGTGKTLMARQIGQMLNAR-EPKIV 86
QH IL++G G+GK++ R++ + + R + I+
Sbjct: 176 TQH---ILIHGTTGSGKSVAIRKLLRWIRQRGDRAII 209
>gnl|CDD|226132 COG3604, FhlA, Transcriptional regulator containing GAF, AAA-type
ATPase, and DNA binding domains [Transcription / Signal
transduction mechanisms].
Length = 550
Score = 26.5 bits (59), Expect = 4.7
Identities = 12/26 (46%), Positives = 17/26 (65%)
Query: 57 ILLYGPPGTGKTLMARQIGQMLNARE 82
+L+ G GTGK L+AR I Q+ R+
Sbjct: 249 VLIRGETGTGKELVARAIHQLSPRRD 274
>gnl|CDD|220739 pfam10412, TrwB_AAD_bind, Type IV secretion-system coupling
protein DNA-binding domain. The plasmid conjugative
coupling protein TrwB forms hexamers from six
structurally very similar protomers. This hexamer
contains a central channel running from the cytosolic
pole (made up by the AADs) to the membrane pole ending
at the transmembrane pore shaped by 12 transmembrane
helices, rendering an overall mushroom-like structure.
The TrwB_AAD (all-alpha domain) domain appears to be
the DNA-binding domain of the structure. TrwB, a basic
integral inner-membrane nucleoside-triphosphate-binding
protein, is the structural prototype for the type IV
secretion system coupling proteins, a family of
proteins essential for macromolecular transport between
cells and export.
Length = 386
Score = 26.4 bits (59), Expect = 4.7
Identities = 12/41 (29%), Positives = 20/41 (48%), Gaps = 4/41 (9%)
Query: 54 VKGILLYGPPGTGKTLMARQIGQMLNAREPKIVNGPQVLDK 94
+ IL+ G GTGKT R++ + AR + + + D
Sbjct: 15 TQHILIVGTTGTGKTQALRELLDQIRARGDRAI----IYDP 51
>gnl|CDD|214810 smart00763, AAA_PrkA, PrkA AAA domain. This is a family of PrkA
bacterial and archaeal serine kinases approximately 630
residues long. This is the N-terminal AAA domain.
Length = 361
Score = 26.1 bits (58), Expect = 4.7
Identities = 6/18 (33%), Positives = 10/18 (55%)
Query: 57 ILLYGPPGTGKTLMARQI 74
+ L GP G GK+ + +
Sbjct: 81 LYLLGPVGGGKSSLVECL 98
>gnl|CDD|236442 PRK09270, PRK09270, nucleoside triphosphate hydrolase
domain-containing protein; Reviewed.
Length = 229
Score = 26.0 bits (58), Expect = 4.7
Identities = 10/47 (21%), Positives = 19/47 (40%), Gaps = 5/47 (10%)
Query: 42 PPEVVEQLG-CQHVKG----ILLYGPPGTGKTLMARQIGQMLNAREP 83
++ +L Q + + GPPG GK+ +A + +L
Sbjct: 16 HKPLLRRLAALQAEPQRRTIVGIAGPPGAGKSTLAEFLEALLQQDGE 62
>gnl|CDD|233406 TIGR01420, pilT_fam, pilus retraction protein PilT. This model
represents the PilT subfamily of proteins related to
GspE, a protein involved in type II secretion (also
called the General Secretion Pathway). PilT is an
apparent cytosolic ATPase associated with type IV pilus
systems. It is not required for pilin biogenesis, but is
required for twitching motility and social gliding
behaviors, shown in some species, powered by pilus
retraction. Members of this family may be found in some
species that type IV pili but have related structures
for DNA uptake and natural transformation [Cell
envelope, Surface structures, Cellular processes,
Chemotaxis and motility].
Length = 343
Score = 26.1 bits (58), Expect = 5.0
Identities = 10/26 (38%), Positives = 16/26 (61%)
Query: 43 PEVVEQLGCQHVKGILLYGPPGTGKT 68
P V+ +L + IL+ GP G+GK+
Sbjct: 111 PPVLRELAERPRGLILVTGPTGSGKS 136
>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 = 26.2 bits (58), Expect = 5.0
Identities = 9/38 (23%), Positives = 17/38 (44%)
Query: 44 EVVEQLGCQHVKGILLYGPPGTGKTLMARQIGQMLNAR 81
+++++ I+ G G GKT +A I L +
Sbjct: 311 RLIDEIAKSEKGLIMTMGKGGVGKTTVAAAIAVRLANK 348
>gnl|CDD|238979 cd02021, GntK, Gluconate kinase (GntK) catalyzes the phosphoryl
transfer from ATP to gluconate. The resulting product
gluconate-6-phoshate is an important precursor of
gluconate metabolism. GntK acts as a dimmer composed of
two identical subunits.
Length = 150
Score = 25.7 bits (57), Expect = 5.0
Identities = 7/25 (28%), Positives = 15/25 (60%)
Query: 57 ILLYGPPGTGKTLMARQIGQMLNAR 81
I++ G G+GK+ + + + + L A
Sbjct: 2 IVVMGVSGSGKSTVGKALAERLGAP 26
>gnl|CDD|224337 COG1419, FlhF, Flagellar GTP-binding protein [Cell motility and
secretion].
Length = 407
Score = 26.2 bits (58), Expect = 5.1
Identities = 15/64 (23%), Positives = 23/64 (35%), Gaps = 12/64 (18%)
Query: 15 DFNKMGIGGLDKEFTA----------IFRRAFASRVFPPEVVEQLGCQHVKGILLYGPPG 64
N++ GL+ E F + ++E L + + I L GP G
Sbjct: 156 LINELLRAGLELEILDMKDESYEDLRYFSEKLRKLL--LSLIENLIVEQKRVIALVGPTG 213
Query: 65 TGKT 68
GKT
Sbjct: 214 VGKT 217
>gnl|CDD|224025 COG1100, COG1100, GTPase SAR1 and related small G proteins
[General function prediction only].
Length = 219
Score = 26.1 bits (57), Expect = 5.1
Identities = 9/33 (27%), Positives = 15/33 (45%), Gaps = 2/33 (6%)
Query: 57 ILLYGPPGTGKTLMARQI--GQMLNAREPKIVN 87
I++ G G GKT + ++ + P I N
Sbjct: 8 IVVLGDGGVGKTTLLNRLVGDEFPEGYPPTIGN 40
>gnl|CDD|233870 TIGR02442, Cob-chelat-sub, cobaltochelatase subunit.
Cobaltochelatase is responsible for the insertion of
cobalt into the corrin ring of coenzyme B12 during its
biosynthesis. Two versions have been well described.
CbiK/CbiX is a monomeric, anaerobic version which acts
early in the biosynthesis (pfam06180). CobNST is a
trimeric, ATP-dependent, aerobic version which acts
late in the biosynthesis
(TIGR02257/TIGR01650/TIGR01651). A number of genomes
(actinobacteria, cyanobacteria, betaproteobacteria and
pseudomonads) which apparently biosynthesize B12,
encode a cobN gene but are demonstrably lacking cobS
and cobT. These genomes do, however contain a homolog
(modelled here) of the magnesium chelatase subunits
BchI/BchD family. Aside from the cyanobacteria (which
have a separate magnesium chelatase trimer), these
species do not make chlorins, so do not have any use
for a magnesium chelatase. Furthermore, in nearly all
cases the members of this family are proximal to either
CobN itself or other genes involved in cobalt transport
or B12 biosynthesis.
Length = 633
Score = 26.2 bits (58), Expect = 5.8
Identities = 9/27 (33%), Positives = 15/27 (55%)
Query: 56 GILLYGPPGTGKTLMARQIGQMLNARE 82
G+L+ G GT K+ AR + +L +
Sbjct: 27 GVLIRGEKGTAKSTAARGLAALLPPID 53
>gnl|CDD|181538 PRK08699, PRK08699, DNA polymerase III subunit delta'; Validated.
Length = 325
Score = 26.0 bits (57), Expect = 5.8
Identities = 15/62 (24%), Positives = 21/62 (33%), Gaps = 4/62 (6%)
Query: 58 LLYGPPGTGKTLMARQIGQMLNAREPKIVNGP----QVLDKYVGESEANVRRLFADAEEE 113
L G G GKT AR Q L P + P + S + + ++E
Sbjct: 25 LFAGKKGIGKTAFARFAAQALLCETPAPGHKPCGECMSCHLFGQGSHPDFYEITPLSDEP 84
Query: 114 EK 115
E
Sbjct: 85 EN 86
>gnl|CDD|172994 PRK14528, PRK14528, adenylate kinase; Provisional.
Length = 186
Score = 25.7 bits (56), Expect = 5.9
Identities = 13/35 (37%), Positives = 20/35 (57%), Gaps = 2/35 (5%)
Query: 54 VKGILLYGPPGTGKTLMARQIGQMLNAREPKIVNG 88
+K I+ GPPG GK A+ + + L+ P+I G
Sbjct: 1 MKNIIFMGPPGAGKGTQAKILCERLSI--PQISTG 33
>gnl|CDD|107157 PHA02244, PHA02244, ATPase-like protein.
Length = 383
Score = 25.8 bits (56), Expect = 6.0
Identities = 9/23 (39%), Positives = 14/23 (60%)
Query: 57 ILLYGPPGTGKTLMARQIGQMLN 79
+ L G G+GK +A QI + L+
Sbjct: 122 VFLKGGAGSGKNHIAEQIAEALD 144
>gnl|CDD|233822 TIGR02329, propionate_PrpR, propionate catabolism operon regulatory
protein PrpR. At least five distinct pathways exists
for the catabolism of propionate by way of
propionyl-CoA. Members of this family represent the
transcriptional regulatory protein PrpR, whose gene is
found in most cases divergently transcribed from an
operon for the methylcitric acid cycle of propionate
catabolism. 2-methylcitric acid, a catabolite by this
pathway, is a coactivator of PrpR.
Length = 526
Score = 26.0 bits (57), Expect = 6.2
Identities = 13/39 (33%), Positives = 21/39 (53%)
Query: 48 QLGCQHVKGILLYGPPGTGKTLMARQIGQMLNAREPKIV 86
+L + +L+ G GTGK L+A+ I Q+ R+ V
Sbjct: 229 RLYARSDATVLILGESGTGKELVAQAIHQLSGRRDFPFV 267
>gnl|CDD|235898 PRK06964, PRK06964, DNA polymerase III subunit delta'; Validated.
Length = 342
Score = 25.9 bits (57), Expect = 6.2
Identities = 9/22 (40%), Positives = 13/22 (59%)
Query: 57 ILLYGPPGTGKTLMARQIGQML 78
+LL+G G GK A+ + Q L
Sbjct: 24 LLLHGQAGIGKLDFAQHLAQGL 45
>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 = 25.8 bits (57), Expect = 6.5
Identities = 12/38 (31%), Positives = 23/38 (60%), Gaps = 6/38 (15%)
Query: 57 ILLYGPPGTGKT-LMARQIGQMLNAREPKIVNGPQVLD 93
+L+ GP G+GK+ L+ ++L AR +++ V+D
Sbjct: 4 MLIVGPSGSGKSTLLKLLALRLL-ARGGRVI----VID 36
>gnl|CDD|221959 pfam13177, DNA_pol3_delta2, DNA polymerase III, delta subunit.
DNA polymerase III, delta subunit (EC 2.7.7.7) is
required for, along with delta' subunit, the assembly
of the processivity factor beta(2) onto primed DNA in
the DNA polymerase III holoenzyme-catalyzed reaction.
The delta subunit is also known as HolA.
Length = 161
Score = 25.6 bits (57), Expect = 6.5
Identities = 9/29 (31%), Positives = 13/29 (44%)
Query: 56 GILLYGPPGTGKTLMARQIGQMLNAREPK 84
L GP G GK +A + + L P+
Sbjct: 21 AYLFSGPDGVGKLELALEFAKALFCENPQ 49
>gnl|CDD|238005 cd00046, DEXDc, DEAD-like helicases superfamily. A diverse family
of proteins involved in ATP-dependent RNA or DNA
unwinding. This domain contains the ATP-binding region.
Length = 144
Score = 25.4 bits (56), Expect = 6.5
Identities = 12/38 (31%), Positives = 17/38 (44%), Gaps = 4/38 (10%)
Query: 55 KGILLYGPPGTGKTLMARQIGQMLNAREPKIVNGPQVL 92
+ +LL P G+GKTL + + G QVL
Sbjct: 1 RDVLLAAPTGSGKTL---AALLPI-LELLDSLKGGQVL 34
>gnl|CDD|214396 CHL00206, ycf2, Ycf2; Provisional.
Length = 2281
Score = 26.0 bits (57), Expect = 6.6
Identities = 8/25 (32%), Positives = 15/25 (60%)
Query: 48 QLGCQHVKGILLYGPPGTGKTLMAR 72
+L +GIL+ G GTG++ + +
Sbjct: 1624 RLALSPSRGILVIGSIGTGRSYLVK 1648
>gnl|CDD|226646 COG4178, COG4178, ABC-type uncharacterized transport system,
permease and ATPase components [General function
prediction only].
Length = 604
Score = 25.7 bits (57), Expect = 6.6
Identities = 7/19 (36%), Positives = 11/19 (57%)
Query: 57 ILLYGPPGTGKTLMARQIG 75
+L+ G G GKT + R +
Sbjct: 422 LLITGESGAGKTSLLRALA 440
>gnl|CDD|140343 PTZ00322, PTZ00322,
6-phosphofructo-2-kinase/fructose-2,6-biphosphatase;
Provisional.
Length = 664
Score = 26.0 bits (57), Expect = 6.8
Identities = 10/18 (55%), Positives = 14/18 (77%)
Query: 57 ILLYGPPGTGKTLMARQI 74
+++ G PG GKT +ARQI
Sbjct: 218 VIMVGLPGRGKTYVARQI 235
>gnl|CDD|238687 cd01393, recA_like, RecA is a bacterial enzyme which has roles
in homologous recombination, DNA repair, and the
induction of the SOS response. RecA couples ATP
hydrolysis to DNA strand exchange. While prokaryotes
have a single RecA protein, eukaryotes have multiple
RecA homologs such as Rad51, DMC1 and Rad55/57.
Archaea have the RecA-like homologs radA and radB.
Length = 226
Score = 25.6 bits (57), Expect = 6.8
Identities = 6/16 (37%), Positives = 11/16 (68%)
Query: 59 LYGPPGTGKTLMARQI 74
++G G+GKT + Q+
Sbjct: 24 IFGEFGSGKTQLCLQL 39
>gnl|CDD|236539 PRK09490, metH, B12-dependent methionine synthase; Provisional.
Length = 1229
Score = 25.9 bits (58), Expect = 6.9
Identities = 16/35 (45%), Positives = 23/35 (65%), Gaps = 5/35 (14%)
Query: 89 PQVL-DKYVGESEANVRRLFADAEEEEKR-VSHKW 121
P +L D+ VGE EA R+LFADA+ + ++ KW
Sbjct: 967 PAILEDEVVGE-EA--RKLFADAQAMLDKIIAEKW 998
>gnl|CDD|234711 PRK00279, adk, adenylate kinase; Reviewed.
Length = 215
Score = 25.5 bits (57), Expect = 7.0
Identities = 9/18 (50%), Positives = 12/18 (66%)
Query: 57 ILLYGPPGTGKTLMARQI 74
++L GPPG GK A+ I
Sbjct: 3 LILLGPPGAGKGTQAKFI 20
>gnl|CDD|224533 COG1618, COG1618, Predicted nucleotide kinase [Nucleotide
transport and metabolism].
Length = 179
Score = 25.4 bits (56), Expect = 7.0
Identities = 9/22 (40%), Positives = 13/22 (59%)
Query: 57 ILLYGPPGTGKTLMARQIGQML 78
I + G PG GKT + +I + L
Sbjct: 8 IFITGRPGVGKTTLVLKIAEKL 29
>gnl|CDD|222160 pfam13476, AAA_23, AAA domain.
Length = 204
Score = 25.6 bits (56), Expect = 7.1
Identities = 20/75 (26%), Positives = 32/75 (42%), Gaps = 12/75 (16%)
Query: 57 ILLYGPPGTGKT--LMARQIGQML--------NAREPKIVNGPQVLDKYVGESEANVRRL 106
L+YGP G+GKT L A I L ++ IV G ++K G+ + V
Sbjct: 22 TLIYGPNGSGKTTILDA--IRWALYGKTSRLKKSKGRGIVKGDIEIEKDEGKKKTYVEIT 79
Query: 107 FADAEEEEKRVSHKW 121
F + + + K +
Sbjct: 80 FENNKGKLKLRLIEE 94
>gnl|CDD|232941 TIGR00362, DnaA, chromosomal replication initiator protein DnaA.
DnaA is involved in DNA biosynthesis; initiation of
chromosome replication and can also be transcription
regulator. The C-terminal of the family hits the pfam
bacterial DnaA (bac_dnaA) domain family. For a review,
see Kaguni (2006) [DNA metabolism, DNA replication,
recombination, and repair].
Length = 405
Score = 25.6 bits (57), Expect = 7.2
Identities = 7/15 (46%), Positives = 10/15 (66%), Gaps = 1/15 (6%)
Query: 57 ILLYGPPGTGKT-LM 70
+ +YG G GKT L+
Sbjct: 139 LFIYGGVGLGKTHLL 153
>gnl|CDD|184118 PRK13531, PRK13531, regulatory ATPase RavA; Provisional.
Length = 498
Score = 25.7 bits (57), Expect = 7.3
Identities = 9/18 (50%), Positives = 14/18 (77%)
Query: 57 ILLYGPPGTGKTLMARQI 74
+ L GPPG K+L+AR++
Sbjct: 42 VFLLGPPGIAKSLIARRL 59
>gnl|CDD|218719 pfam05729, NACHT, NACHT domain. This NTPase domain is found in
apoptosis proteins as well as those involved in MHC
transcription activation. This family is closely
related to pfam00931.
Length = 165
Score = 25.4 bits (56), Expect = 7.4
Identities = 7/18 (38%), Positives = 13/18 (72%)
Query: 57 ILLYGPPGTGKTLMARQI 74
++L G G+GKT + ++I
Sbjct: 3 VILQGEAGSGKTTLLQKI 20
>gnl|CDD|234057 TIGR02915, PEP_resp_reg, PEP-CTERM-box response regulator
transcription factor. Members of this protein family
share full-length homology with (but do not include) the
acetoacetate metabolism regulatory protein AtoC (see
SP|Q06065). These proteins have a Fis family DNA binding
sequence (pfam02954), a response regulator receiver
domain (pfam00072), and sigma-54 interaction domain
(pfam00158) [Regulatory functions, DNA interactions].
Length = 445
Score = 25.9 bits (57), Expect = 7.6
Identities = 11/30 (36%), Positives = 20/30 (66%)
Query: 57 ILLYGPPGTGKTLMARQIGQMLNAREPKIV 86
+LL G GTGK ++AR + Q+ + ++ + V
Sbjct: 165 VLLLGESGTGKEVLARALHQLSDRKDKRFV 194
>gnl|CDD|235638 PRK05896, PRK05896, DNA polymerase III subunits gamma and tau;
Validated.
Length = 605
Score = 25.6 bits (56), Expect = 7.7
Identities = 10/24 (41%), Positives = 14/24 (58%)
Query: 61 GPPGTGKTLMARQIGQMLNAREPK 84
GP G GKT +A+ + +N PK
Sbjct: 45 GPRGIGKTSIAKIFAKAINCLNPK 68
>gnl|CDD|233369 TIGR01351, adk, adenylate kinase. Adenylate kinase (EC 2.7.4.3)
converts ATP + AMP to ADP + ADP, that is, uses ATP as a
phosphate donor for AMP. Most members of this family
are known or believed to be adenylate kinase. However,
some members accept other nucleotide triphosphates as
donors, may be unable to use ATP, and may fail to
complement adenylate kinase mutants. An example of a
nucleoside-triphosphate--adenylate kinase (EC 2.7.4.10)
is a GTP:AMP phosphotransferase. This family is
designated subfamily rather than equivalog for this
reason [Purines, pyrimidines, nucleosides, and
nucleotides, Nucleotide and nucleoside
interconversions].
Length = 210
Score = 25.3 bits (56), Expect = 7.9
Identities = 9/18 (50%), Positives = 14/18 (77%)
Query: 57 ILLYGPPGTGKTLMARQI 74
++L GPPG+GK A++I
Sbjct: 2 LVLLGPPGSGKGTQAKRI 19
>gnl|CDD|235825 PRK06547, PRK06547, hypothetical protein; Provisional.
Length = 172
Score = 25.5 bits (56), Expect = 8.0
Identities = 7/25 (28%), Positives = 13/25 (52%)
Query: 57 ILLYGPPGTGKTLMARQIGQMLNAR 81
+L+ G G+GKT +A + +
Sbjct: 18 VLIDGRSGSGKTTLAGALAARTGFQ 42
>gnl|CDD|223873 COG0802, COG0802, Predicted ATPase or kinase [General function
prediction only].
Length = 149
Score = 25.3 bits (56), Expect = 8.0
Identities = 13/38 (34%), Positives = 18/38 (47%), Gaps = 2/38 (5%)
Query: 44 EVVEQLGCQHVKG--ILLYGPPGTGKTLMARQIGQMLN 79
+ E+L G +LL G G GKT + R I + L
Sbjct: 13 ALGERLAEALKAGDVVLLSGDLGAGKTTLVRGIAKGLG 50
>gnl|CDD|110723 pfam01745, IPT, Isopentenyl transferase. Isopentenyl transferase
/ dimethylallyl transferase synthesises
isopentenyladensosine 5'-monophosphate, a cytokinin
that induces shoot formation on host plants infected
with the Ti plasmid.
Length = 232
Score = 25.4 bits (56), Expect = 8.0
Identities = 7/19 (36%), Positives = 11/19 (57%)
Query: 58 LLYGPPGTGKTLMARQIGQ 76
L++G TGKT A + +
Sbjct: 5 LIWGATCTGKTAEAIALAK 23
>gnl|CDD|183521 PRK12422, PRK12422, chromosomal replication initiation protein;
Provisional.
Length = 445
Score = 25.6 bits (56), Expect = 8.1
Identities = 11/30 (36%), Positives = 16/30 (53%)
Query: 57 ILLYGPPGTGKTLMARQIGQMLNAREPKIV 86
I L+GP G+GKT + + L KI+
Sbjct: 144 IYLFGPEGSGKTHLMQAAVHALRESGGKIL 173
>gnl|CDD|215832 pfam00270, DEAD, DEAD/DEAH box helicase. Members of this family
include the DEAD and DEAH box helicases. Helicases are
involved in unwinding nucleic acids. The DEAD box
helicases are involved in various aspects of RNA
metabolism, including nuclear transcription, pre mRNA
splicing, ribosome biogenesis, nucleocytoplasmic
transport, translation, RNA decay and organellar gene
expression.
Length = 169
Score = 25.3 bits (56), Expect = 8.4
Identities = 8/17 (47%), Positives = 11/17 (64%)
Query: 55 KGILLYGPPGTGKTLMA 71
K +L+ P G+GKTL
Sbjct: 15 KDVLVQAPTGSGKTLAF 31
>gnl|CDD|213210 cd03243, ABC_MutS_homologs, ATP-binding cassette domain of MutS
homologs. The MutS protein initiates DNA mismatch
repair by recognizing mispaired and unpaired bases
embedded in duplex DNA and activating endo- and
exonucleases to remove the mismatch. Members of the
MutS family also possess a conserved ATPase activity
that belongs to the ATP binding cassette (ABC)
superfamily. MutS homologs (MSH) have been identified
in most prokaryotic and all eukaryotic organisms
examined. Prokaryotes have two homologs (MutS1 and
MutS2), whereas seven MSH proteins (MSH1 to MSH7) have
been identified in eukaryotes. The homodimer MutS1 and
heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily
involved in mitotic mismatch repair, whereas MSH4-MSH5
is involved in resolution of Holliday junctions during
meiosis. All members of the MutS family contain the
highly conserved Walker A/B ATPase domain, and many
share a common mechanism of action. MutS1, MSH2-MSH3,
MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding
clamps, and recognition of specific DNA structures or
lesions results in ADP/ATP exchange.
Length = 202
Score = 25.3 bits (56), Expect = 8.5
Identities = 8/20 (40%), Positives = 11/20 (55%)
Query: 57 ILLYGPPGTGKTLMARQIGQ 76
+L+ GP GK+ R IG
Sbjct: 32 LLITGPNMGGKSTYLRSIGL 51
>gnl|CDD|222290 pfam13654, AAA_32, 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 = 509
Score = 25.5 bits (57), Expect = 8.7
Identities = 7/14 (50%), Positives = 10/14 (71%)
Query: 61 GPPGTGKTLMARQI 74
G PGTG+T + R+
Sbjct: 37 GEPGTGRTTLVRRY 50
>gnl|CDD|216586 pfam01583, APS_kinase, Adenylylsulphate kinase. Enzyme that
catalyzes the phosphorylation of adenylylsulphate to
3'-phosphoadenylylsulfate. This domain contains an ATP
binding P-loop motif.
Length = 157
Score = 25.3 bits (56), Expect = 8.7
Identities = 23/69 (33%), Positives = 35/69 (50%), Gaps = 15/69 (21%)
Query: 57 ILLYGPPGTGKTLMARQIGQMLNAREPKI--VNGPQV---LDKYVGESEA----NVRR-- 105
I G G+GK+ +A + + L A+ + ++G V L+K +G SE N+RR
Sbjct: 5 IWFTGLSGSGKSTIANALERKLFAQGISVYVLDGDNVRHGLNKDLGFSEEDRTENIRRIA 64
Query: 106 ----LFADA 110
LFADA
Sbjct: 65 EVAKLFADA 73
>gnl|CDD|218685 pfam05673, DUF815, Protein of unknown function (DUF815). This
family consists of several bacterial proteins of
unknown function.
Length = 248
Score = 25.2 bits (56), Expect = 9.0
Identities = 9/22 (40%), Positives = 12/22 (54%), Gaps = 5/22 (22%)
Query: 51 CQHVKG-----ILLYGPPGTGK 67
Q + G +LL+G GTGK
Sbjct: 45 EQFLAGLPANNVLLWGARGTGK 66
>gnl|CDD|225713 COG3172, NadR, Predicted ATPase/kinase involved in NAD metabolism
[Coenzyme metabolism].
Length = 187
Score = 25.1 bits (55), Expect = 9.0
Identities = 6/28 (21%), Positives = 14/28 (50%)
Query: 54 VKGILLYGPPGTGKTLMARQIGQMLNAR 81
VK + + G +GK+ + ++ + N
Sbjct: 8 VKTVAILGGESSGKSTLVNKLANIFNTT 35
>gnl|CDD|213965 TIGR04352, HprK_rel_A, HprK-related kinase A. A number of protein
families resemble HPr kinase (see TIGR00679) but do not
belong to that system. They include this family, which
appears instead to be the marker for a different type of
gene neighborhood, in which one of the conserved
neighboring proteins resembles (but is distinct from)
PqqD.
Length = 280
Score = 25.3 bits (56), Expect = 9.0
Identities = 12/28 (42%), Positives = 18/28 (64%), Gaps = 5/28 (17%)
Query: 45 VVEQLGCQHVKGILLYGPPGTGK-TLMA 71
V+E+ G + ++L PPG+GK TL A
Sbjct: 103 VLERDG----RALILPAPPGSGKSTLCA 126
>gnl|CDD|218709 pfam05707, Zot, Zonular occludens toxin (Zot). This family
consists of bacterial and viral proteins which are very
similar to the Zonular occludens toxin (Zot). Zot is
elaborated by bacteriophages present in toxigenic
strains of Vibrio cholerae. Zot is a single polypeptide
chain of 44.8 kDa, with the ability to reversibly alter
intestinal epithelial tight junctions, allowing the
passage of macromolecules through mucosal barriers.
Length = 183
Score = 25.4 bits (56), Expect = 9.3
Identities = 9/14 (64%), Positives = 11/14 (78%)
Query: 58 LLYGPPGTGKTLMA 71
L+ G PG+GKTL A
Sbjct: 4 LITGKPGSGKTLEA 17
>gnl|CDD|223645 COG0572, Udk, Uridine kinase [Nucleotide transport and
metabolism].
Length = 218
Score = 25.3 bits (56), Expect = 9.6
Identities = 11/39 (28%), Positives = 22/39 (56%), Gaps = 4/39 (10%)
Query: 57 ILLYGPPGTGKTLMARQIGQMLNAREPKIVNGPQVLDKY 95
I + G G+GKT +A+++ + L + +++ LD Y
Sbjct: 11 IGIAGGSGSGKTTVAKELSEQLGVEKVVVIS----LDDY 45
>gnl|CDD|225369 COG2812, DnaX, DNA polymerase III, gamma/tau subunits [DNA
replication, recombination, and repair].
Length = 515
Score = 25.4 bits (56), Expect = 9.7
Identities = 11/24 (45%), Positives = 14/24 (58%)
Query: 56 GILLYGPPGTGKTLMARQIGQMLN 79
L GP G GKT +AR + + LN
Sbjct: 40 AYLFSGPRGVGKTTIARILAKALN 63
>gnl|CDD|214007 cd12808, Esterase_713_like-1, Uncharacterized enzymes similar to
novel bacterial esterase that cleaves esters on
halogenated cyclic compounds. This family contains
uncharacterized proteins similar to a novel bacterial
esterase (Alcaligenes esterase 713) with the alpha/beta
hydrolase fold but does not contain the GXSXXG
pentapeptide around the active site serine residue as
commonly seen in other enzymes of this class. Esterase
713 shows negligible sequence homology to other esterase
and lipase enzymes. It is active as a dimer and cleaves
esters on halogenated cyclic compounds though its
natural substrate is unknown.
Length = 309
Score = 25.3 bits (56), Expect = 9.7
Identities = 8/22 (36%), Positives = 10/22 (45%)
Query: 33 RRAFASRVFPPEVVEQLGCQHV 54
RRAF + FP + Q V
Sbjct: 145 RRAFPGQQFPLAAFDAFAKQFV 166
>gnl|CDD|131688 TIGR02640, gas_vesic_GvpN, gas vesicle protein GvpN. Members of
this family are the GvpN protein associated with the
production of gas vesicles produced in some prokaryotes
to give cells buoyancy. This family belongs to a larger
family of ATPases (pfam07728) [Cellular processes,
Other].
Length = 262
Score = 25.1 bits (55), Expect = 9.8
Identities = 12/30 (40%), Positives = 18/30 (60%), Gaps = 1/30 (3%)
Query: 59 LYGPPGTGKTLMARQIGQMLNAREPKIVNG 88
L GP GTGKT +A + + + R ++NG
Sbjct: 26 LRGPAGTGKTTLAMHVARKRD-RPVMLING 54
>gnl|CDD|237017 PRK11904, PRK11904, bifunctional proline
dehydrogenase/pyrroline-5-carboxylate dehydrogenase;
Reviewed.
Length = 1038
Score = 25.5 bits (57), Expect = 10.0
Identities = 11/22 (50%), Positives = 13/22 (59%)
Query: 65 TGKTLMARQIGQMLNAREPKIV 86
TG T AR I + L AR+ IV
Sbjct: 770 TGSTETARIINRTLAARDGPIV 791
>gnl|CDD|200217 TIGR02880, cbbX_cfxQ, probable Rubsico expression protein CbbX.
Proteins in this family are now designated CbbX. Some
previously were CfxQ (carbon fixation Q). Its gene is
often found immmediately downstream of the Rubisco
large and small chain genes, and it is suggested to be
necessary for Rubisco expression. CbbX has been shown
to be necessary for photoautotrophic growth. This
protein belongs to the larger family of pfam00004,
ATPase family Associated with various cellular
Activities. Within that larger family, members of this
family are most closely related to the stage V
sporulation protein K, or SpoVK, in endospore-forming
bacteria such as Bacillus subtilis.
Length = 284
Score = 25.2 bits (55), Expect = 10.0
Identities = 10/18 (55%), Positives = 14/18 (77%)
Query: 61 GPPGTGKTLMARQIGQML 78
G PGTGKT +A ++ Q+L
Sbjct: 65 GNPGTGKTTVALRMAQIL 82
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 0.138 0.405
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: 6,390,039
Number of extensions: 574736
Number of successful extensions: 1204
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1189
Number of HSP's successfully gapped: 302
Length of query: 121
Length of database: 10,937,602
Length adjustment: 84
Effective length of query: 37
Effective length of database: 7,211,866
Effective search space: 266839042
Effective search space used: 266839042
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: 53 (23.9 bits)