RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3997
(256 letters)
>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 = 100 bits (252), Expect = 6e-27
Identities = 44/116 (37%), Positives = 64/116 (55%), Gaps = 18/116 (15%)
Query: 19 VLLHGPPGTGKTSLCKAVAQKLSIRLQSKYKITEFIEINSHSLFSKYFSESGKLVQKMFN 78
+LL+GPPGTGKT+L KAVA++L FIEI+ L SKY ES K ++++F
Sbjct: 1 LLLYGPPGTGKTTLAKAVAKELGAP---------FIEISGSELVSKYVGESEKRLRELFE 51
Query: 79 KIKEAVEYEESLVCLLIDEIESLTRARESVMSGTEPSDGVRVVNAVLTQIDQLKKK 134
K + + + IDEI++L +R S S+ RVVN +LT++D
Sbjct: 52 AAK-----KLAPCVIFIDEIDALAGSRGSGGD----SESRRVVNQLLTELDGFTSS 98
>gnl|CDD|223540 COG0464, SpoVK, ATPases of the AAA+ class [Posttranslational
modification, protein turnover, chaperones].
Length = 494
Score = 90.3 bits (224), Expect = 1e-20
Identities = 43/119 (36%), Positives = 63/119 (52%), Gaps = 18/119 (15%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQKLSIRLQSKYKITEFIEINSHSLFSKYFSESGKLVQKM 76
+ VLL+GPPGTGKT L KAVA + R FI + L SK+ ES K ++++
Sbjct: 277 KGVLLYGPPGTGKTLLAKAVALESRSR---------FISVKGSELLSKWVGESEKNIREL 327
Query: 77 FNKIKEAVEYEESLVCLLIDEIESLTRARESVMSGTEPSDGVRVVNAVLTQIDQLKKKS 135
F K + + + + IDEI+SL R +E G RVV +LT++D ++K
Sbjct: 328 FEKAR-----KLAPSIIFIDEIDSLASGR----GPSEDGSGRRVVGQLLTELDGIEKAE 377
Score = 59.1 bits (143), Expect = 4e-10
Identities = 51/159 (32%), Positives = 70/159 (44%), Gaps = 26/159 (16%)
Query: 19 VLLHGPPGTGKTSLCKAVAQKLSIRLQSKYKITEFIEINSHSLFSKYFSESGKLVQKMFN 78
VLLHGPPGTGKT L +A+A + EF+ IN + SKY ES ++
Sbjct: 21 VLLHGPPGTGKTLLARALANEG----------AEFLSINGPEILSKYVGES---ELRLRE 67
Query: 79 KIKEAVEYEESLVCLLIDEIESLTRARESVMSGTEPSDGVRVVNAVLTQIDQLKKKSTGL 138
+EA + S+ + IDEI++L R S E RVV +L +D LK+ +
Sbjct: 68 LFEEAEKLAPSI--IFIDEIDALAPKRSSDQGEVER----RVVAQLLALMDGLKRGQVIV 121
Query: 139 SGRTLR-------KIPFLTFVKYISNNSVSMENFLIALE 170
G T R K F + I N L L+
Sbjct: 122 IGATNRPDGLDPAKRRPGRFDREIEVNLPDEAGRLEILQ 160
>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 = 70.3 bits (172), Expect = 4e-15
Identities = 36/138 (26%), Positives = 56/138 (40%), Gaps = 18/138 (13%)
Query: 19 VLLHGPPGTGKTSLCKAVAQKLSIRLQSKYKITEFIEINSHSLFSKYFSESGKLVQKMFN 78
+LL+GPPGTGKT+L +A+A +L F+ +N+ L + +
Sbjct: 22 LLLYGPPGTGKTTLARAIANEL------FRPGAPFLYLNASDLLEGL-VVAELFGHFLVR 74
Query: 79 KIKEAVEYEESLVCLLIDEIESLT--------RARESVMSGTEPSDGVRVVNAVLTQIDQ 130
+ E E + L IDEI+SL+ R E++ + VRV+ T
Sbjct: 75 LLFELAEKAK-PGVLFIDEIDSLSRGAQNALLRVLETLNDLRIDRENVRVI--GATNRPL 131
Query: 131 LKKKSTGLSGRTLRKIPF 148
L L R +I
Sbjct: 132 LGDLDRALYDRLDIRIVI 149
>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 = 73.0 bits (179), Expect = 1e-14
Identities = 47/116 (40%), Positives = 64/116 (55%), Gaps = 18/116 (15%)
Query: 19 VLLHGPPGTGKTSLCKAVAQKLSIRLQSKYKITEFIEINSHSLFSKYFSESGKLVQKMFN 78
VLL+GPPGTGKT L KAVA + FI IN + SKY+ ES + ++++F
Sbjct: 215 VLLYGPPGTGKTLLAKAVANEAG---------AYFISINGPEIMSKYYGESEERLREIF- 264
Query: 79 KIKEAVEYEESLVCLLIDEIESLTRARESVMSGTEPSDGVRVVNAVLTQIDQLKKK 134
KEA E S++ IDEI+++ RE V E RVV +LT +D LK +
Sbjct: 265 --KEAEENAPSII--FIDEIDAIAPKREEVTGEVEK----RVVAQLLTLMDGLKGR 312
Score = 67.6 bits (165), Expect = 6e-13
Identities = 40/121 (33%), Positives = 62/121 (51%), Gaps = 21/121 (17%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQKLSIRLQSKYKITEFIEINSHSLFSKYFSESGKLVQKM 76
+ VLL GPPGTGKT L KAVA + FI + + SK+ ES K ++++
Sbjct: 488 KGVLLFGPPGTGKTLLAKAVATESG---------ANFIAVRGPEILSKWVGESEKAIREI 538
Query: 77 FNKIKEAVEYEESLVCLLIDEIESLTRARESVMSGTEPSDGV--RVVNAVLTQIDQLKKK 134
F K ++A + DEI+++ AR G V R+VN +LT++D +++
Sbjct: 539 FRKARQAAP-----AIIFFDEIDAIAPAR-----GARFDTSVTDRIVNQLLTEMDGIQEL 588
Query: 135 S 135
S
Sbjct: 589 S 589
>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 = 65.9 bits (161), Expect = 2e-12
Identities = 41/113 (36%), Positives = 62/113 (54%), Gaps = 7/113 (6%)
Query: 19 VLLHGPPGTGKTSLCKAVAQKLSIRLQSKYKITE-FIEINSHSLFSKYFSESGKLVQKMF 77
VLL+GPPG GKT + KAVA L+ R+ ++ F+ I L +KY E+ + ++ +F
Sbjct: 219 VLLYGPPGCGKTLIAKAVANSLAARIGAEGGGKSYFLNIKGPELLNKYVGETERQIRLIF 278
Query: 78 NKIKEAVEYEESLVCLLIDEIESLTRARES-VMSGTEPSDGVRVVNAVLTQID 129
+ +E E V + DE++SL R R S V S E + VV +L +ID
Sbjct: 279 QRAREKAS-EGRPVIVFFDEMDSLFRTRGSGVSSDVETT----VVPQLLAEID 326
>gnl|CDD|224143 COG1222, RPT1, ATP-dependent 26S proteasome regulatory subunit
[Posttranslational modification, protein turnover,
chaperones].
Length = 406
Score = 61.1 bits (149), Expect = 8e-11
Identities = 38/123 (30%), Positives = 55/123 (44%), Gaps = 32/123 (26%)
Query: 19 VLLHGPPGTGKTSLCKAVAQKLSIRLQSKYKITEFIEINSHSLFSKYFSESGKLVQKMFN 78
VLL+GPPGTGKT L KAVA + FI + L KY E +LV+++F
Sbjct: 188 VLLYGPPGTGKTLLAKAVANQTD---------ATFIRVVGSELVQKYIGEGARLVRELF- 237
Query: 79 KIKEAVEYEESLVCLLIDEIESL--TRARESV----------------MSGTEPSDGVRV 120
+ A E S++ IDEI+++ R + G +P V+V
Sbjct: 238 --ELAREKAPSII--FIDEIDAIGAKRFDSGTSGDREVQRTMLELLNQLDGFDPRGNVKV 293
Query: 121 VNA 123
+ A
Sbjct: 294 IMA 296
>gnl|CDD|185575 PTZ00361, PTZ00361, 26 proteosome regulatory subunit 4-like
protein; Provisional.
Length = 438
Score = 60.6 bits (147), Expect = 1e-10
Identities = 40/111 (36%), Positives = 58/111 (52%), Gaps = 15/111 (13%)
Query: 19 VLLHGPPGTGKTSLCKAVAQKLSIRLQSKYKITEFIEINSHSLFSKYFSESGKLVQKMFN 78
V+L+GPPGTGKT L KAVA + S F+ + L KY + KLV+++F
Sbjct: 220 VILYGPPGTGKTLLAKAVANETS---------ATFLRVVGSELIQKYLGDGPKLVRELF- 269
Query: 79 KIKEAVEYEESLVCLLIDEIESLTRARESVMSGTEPSDGVRVVNAVLTQID 129
+ A E S+V IDEI+++ R SG E + R + +L Q+D
Sbjct: 270 --RVAEENAPSIV--FIDEIDAIGTKRYDATSGGE-KEIQRTMLELLNQLD 315
>gnl|CDD|130309 TIGR01242, 26Sp45, 26S proteasome subunit P45 family. Many
proteins may score above the trusted cutoff because an
internal.
Length = 364
Score = 59.0 bits (143), Expect = 3e-10
Identities = 37/110 (33%), Positives = 53/110 (48%), Gaps = 19/110 (17%)
Query: 19 VLLHGPPGTGKTSLCKAVAQKLSIRLQSKYKITEFIEINSHSLFSKYFSESGKLVQKMFN 78
VLL+GPPGTGKT L KAVA + + FI + L KY E +LV+++F
Sbjct: 159 VLLYGPPGTGKTLLAKAVAHETN---------ATFIRVVGSELVRKYIGEGARLVREIFE 209
Query: 79 KIKEAVEYEESLVCLLIDEIESLTRARESVMSGTEPSDGVRVVNAVLTQI 128
K E++ + IDEI+++ R + G R V L Q+
Sbjct: 210 LAK-----EKAPSIIFIDEIDAIAAKRTDSGTS-----GDREVQRTLMQL 249
>gnl|CDD|224144 COG1223, COG1223, Predicted ATPase (AAA+ superfamily) [General
function prediction only].
Length = 368
Score = 59.1 bits (143), Expect = 3e-10
Identities = 28/117 (23%), Positives = 59/117 (50%), Gaps = 19/117 (16%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQKLSIRLQSKYKITEFIEINSHSLFSKYFSESGKLVQKM 76
+ VL +GPPGTGKT + KA+A + + + + L ++ + + + ++
Sbjct: 152 KNVLFYGPPGTGKTMMAKALANEAK---------VPLLLVKATELIGEHVGDGARRIHEL 202
Query: 77 FNKIKEAVEYEESLVCLLIDEIESLTRARE-SVMSGTEPSDGVRVVNAVLTQIDQLK 132
+ + ++A + + IDE++++ R + G D +VNA+LT++D +K
Sbjct: 203 YERARKA-----APCIVFIDELDAIALDRRYQELRG----DVSEIVNALLTELDGIK 250
>gnl|CDD|179699 PRK03992, PRK03992, proteasome-activating nucleotidase;
Provisional.
Length = 389
Score = 58.3 bits (142), Expect = 6e-10
Identities = 41/123 (33%), Positives = 58/123 (47%), Gaps = 32/123 (26%)
Query: 19 VLLHGPPGTGKTSLCKAVAQKLSIRLQSKYKITEFIEINSHSLFSKYFSESGKLVQKMFN 78
VLL+GPPGTGKT L KAVA + T FI + L K+ E +LV+++F
Sbjct: 168 VLLYGPPGTGKTLLAKAVA--------HETNAT-FIRVVGSELVQKFIGEGARLVRELF- 217
Query: 79 KIKEAVEYEESLVCLLIDEI--------ESLTRA-RE---------SVMSGTEPSDGVRV 120
+ A E S++ IDEI +S T RE + M G +P V++
Sbjct: 218 --ELAREKAPSII--FIDEIDAIAAKRTDSGTSGDREVQRTLMQLLAEMDGFDPRGNVKI 273
Query: 121 VNA 123
+ A
Sbjct: 274 IAA 276
>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 = 53.9 bits (129), Expect = 3e-09
Identities = 22/102 (21%), Positives = 41/102 (40%), Gaps = 13/102 (12%)
Query: 16 NRVVLLHGPPGTGKTSLCKAVAQKL--------SIRLQSKYKITEFIEINSHSLFSKYFS 67
V+L+ GPPG+GKT+L +A+A++L I + + + K
Sbjct: 2 GEVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKASG 61
Query: 68 ESGKLVQKMFNKIKEAVEYEESLVCLLIDEIESLTRARESVM 109
++ + + L++DEI SL A + +
Sbjct: 62 SGELRLRLALALAR-----KLKPDVLILDEITSLLDAEQEAL 98
>gnl|CDD|240423 PTZ00454, PTZ00454, 26S protease regulatory subunit 6B-like
protein; Provisional.
Length = 398
Score = 53.6 bits (129), Expect = 2e-08
Identities = 35/113 (30%), Positives = 55/113 (48%), Gaps = 15/113 (13%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQKLSIRLQSKYKITEFIEINSHSLFSKYFSESGKLVQKM 76
R VLL+GPPGTGKT L KAVA + FI + KY E ++V+ +
Sbjct: 180 RGVLLYGPPGTGKTMLAKAVAHHTT---------ATFIRVVGSEFVQKYLGEGPRMVRDV 230
Query: 77 FNKIKEAVEYEESLVCLLIDEIESLTRARESVMSGTEPSDGVRVVNAVLTQID 129
F + E + + IDE++S+ R +G + + R++ +L Q+D
Sbjct: 231 FRLAR-----ENAPSIIFIDEVDSIATKRFDAQTGAD-REVQRILLELLNQMD 277
>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 = 50.4 bits (121), Expect = 3e-07
Identities = 34/95 (35%), Positives = 48/95 (50%), Gaps = 18/95 (18%)
Query: 19 VLLHGPPGTGKTSLCKAVAQKLSIRLQSKYKITEFIEINSHSLFSKYFSESG-KLVQKMF 77
VLL GPPGTGKT L KAVA + + F I S S F + F G V+ +F
Sbjct: 91 VLLVGPPGTGKTLLAKAVAGEAGV---------PFFSI-SGSDFVEMFVGVGASRVRDLF 140
Query: 78 NKIKEAVEYEESLVCLL-IDEIESLTRARESVMSG 111
+ K+ C++ IDEI+++ R R + + G
Sbjct: 141 EQAKKNAP------CIIFIDEIDAVGRQRGAGLGG 169
>gnl|CDD|214386 CHL00176, ftsH, cell division protein; Validated.
Length = 638
Score = 50.4 bits (121), Expect = 4e-07
Identities = 40/119 (33%), Positives = 58/119 (48%), Gaps = 19/119 (15%)
Query: 19 VLLHGPPGTGKTSLCKAVAQKLSIRLQSKYKITEFIEINSHSLFSKYFSESGKL-VQKMF 77
VLL GPPGTGKT L KA+A + F I S S F + F G V+ +F
Sbjct: 219 VLLVGPPGTGKTLLAKAIAGEAE---------VPFFSI-SGSEFVEMFVGVGAARVRDLF 268
Query: 78 NKIKEAVEYEESLVCLLIDEIESLTRARES-VMSGTEPSDGVRVVNAVLTQIDQLKKKS 135
K K E S + IDEI+++ R R + + G + + + +N +LT++D K
Sbjct: 269 KKAK-----ENSPCIVFIDEIDAVGRQRGAGIGGGNDERE--QTLNQLLTEMDGFKGNK 320
>gnl|CDD|237355 PRK13342, PRK13342, recombination factor protein RarA; Reviewed.
Length = 413
Score = 48.9 bits (118), Expect = 9e-07
Identities = 21/87 (24%), Positives = 38/87 (43%), Gaps = 19/87 (21%)
Query: 19 VLLHGPPGTGKTSLCKAVAQKLSIRLQSKYKITEFIEINSHSLFSKYFSESG-KLVQKMF 77
++L GPPGTGKT+L + +A F +++ SG K ++++
Sbjct: 39 MILWGPPGTGKTTLARIIAGATD---------APFEALSA--------VTSGVKDLREVI 81
Query: 78 NKIKEAVEYEESLVCLLIDEIESLTRA 104
+ ++ + L IDEI +A
Sbjct: 82 EEARQRRSAGRRTI-LFIDEIHRFNKA 107
>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 = 45.6 bits (108), Expect = 1e-05
Identities = 32/151 (21%), Positives = 58/151 (38%), Gaps = 34/151 (22%)
Query: 20 LLHGPPGTGKTSLCKAVAQKLS-IRLQSKYKITEFIEINSHSLFSKYFSESGKLVQKMFN 78
L GPPGTGKT++ + VA+ + + K + E++ L +Y ES ++ +
Sbjct: 316 LFAGPPGTGKTTIARVVAKIYCGLGVLRKPLV---REVSRADLIGQYIGESEAKTNEIID 372
Query: 79 KIKEAVEYEESLVCLLIDEIESLTRARESVMSGTEPSDGVRVVNAVLT------------ 126
V L +DE +L G + G+ ++ +L
Sbjct: 373 SALGGV--------LFLDEAYTLVETGY----GQKDPFGLEAIDTLLARMENDRDRLVVI 420
Query: 127 ------QIDQLKKKSTGLSGRTLRKIPFLTF 151
+D+ + + GL R R I F ++
Sbjct: 421 GAGYRKDLDKFLEVNEGLRSRFTRVIEFPSY 451
>gnl|CDD|182683 PRK10733, hflB, ATP-dependent metalloprotease; Reviewed.
Length = 644
Score = 45.4 bits (107), Expect = 2e-05
Identities = 32/112 (28%), Positives = 54/112 (48%), Gaps = 17/112 (15%)
Query: 19 VLLHGPPGTGKTSLCKAVAQKLSIRLQSKYKITEFIEINSHSLFSKYFSESGKLVQKMFN 78
VL+ GPPGTGKT L KA+A + + F I+ + V+ MF
Sbjct: 188 VLMVGPPGTGKTLLAKAIAGEAKV---------PFFTISGSDFVEMFVGVGASRVRDMFE 238
Query: 79 KIKEAVEYEESLVCLL-IDEIESLTRARESVMSGTEPSDGVRVVNAVLTQID 129
+ K+A C++ IDEI+++ R R + + G + + +N +L ++D
Sbjct: 239 QAKKAAP------CIIFIDEIDAVGRQRGAGLGGGH-DEREQTLNQMLVEMD 283
>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit;
Provisional.
Length = 482
Score = 44.9 bits (107), Expect = 2e-05
Identities = 16/42 (38%), Positives = 22/42 (52%), Gaps = 9/42 (21%)
Query: 5 HSKVKSNIISW---------NRVVLLHGPPGTGKTSLCKAVA 37
+ K K + W + +LL+GPPG GKTSL A+A
Sbjct: 19 NEKAKEQLREWIESWLKGKPKKALLLYGPPGVGKTSLAHALA 60
>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 = 44.2 bits (105), Expect = 3e-05
Identities = 33/97 (34%), Positives = 50/97 (51%), Gaps = 13/97 (13%)
Query: 8 VKSNIISWNRVVLLHGPPGTGKTSLCKAVAQKLSIRLQSKYKITEFIEINSHSLFSKYFS 67
+K I+ R VL+ GPPGTGKT+L A++++L + T F I+ ++S
Sbjct: 43 IKEGKIA-GRAVLIAGPPGTGKTALAIAISKELG-------EDTPFCPISGSEVYSLEMK 94
Query: 68 ESGKLVQKMFN----KIKEAVE-YEESLVCLLIDEIE 99
++ L Q +IKE E YE +V L I+E E
Sbjct: 95 KTEALTQAFRKAIGVRIKEEKEVYEGEVVELEIEEAE 131
>gnl|CDD|222104 pfam13401, AAA_22, AAA domain.
Length = 124
Score = 41.9 bits (99), Expect = 3e-05
Identities = 17/95 (17%), Positives = 37/95 (38%), Gaps = 12/95 (12%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQKL------SIRLQSKYKITEFIEINSHSLFSKYFSESG 70
+ +L G G+GKT+L + +A++L + S + + +
Sbjct: 5 GIGVLTGESGSGKTTLLRRLARQLPNRRVVYVEAPSLGTPKDLL----RKILRALGLPLS 60
Query: 71 KL-VQKMFNKIKEAVEYEESLVCLLIDEIESLTRA 104
++ I +A++ L+IDE + L+
Sbjct: 61 GGTTAELLEAILDALK-RRGRPLLIIDEAQHLSLE 94
>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 = 43.8 bits (104), Expect = 4e-05
Identities = 19/107 (17%), Positives = 45/107 (42%), Gaps = 16/107 (14%)
Query: 19 VLLHGPPGTGKTSLCKAVAQKLSIRLQSKYKITEFIEINSHSLFSKY------------- 65
V ++G GTGKT++ K V ++L + + + +N L + Y
Sbjct: 43 VFIYGKTGTGKTAVTKYVMKELEEAAEDRDVRVVTVYVNCQILDTLYQVLVELANQLRGS 102
Query: 66 ---FSESGKLVQKMFNKIKEAVEYEESLVCLLIDEIESLTRARESVM 109
+G ++F ++ + + + +++DEI+ L + ++
Sbjct: 103 GEEVPTTGLSTSEVFRRLYKELNERGDSLIIVLDEIDYLVGDDDDLL 149
>gnl|CDD|221983 pfam13207, AAA_17, AAA domain.
Length = 114
Score = 41.5 bits (97), Expect = 5e-05
Identities = 13/27 (48%), Positives = 22/27 (81%)
Query: 18 VVLLHGPPGTGKTSLCKAVAQKLSIRL 44
++L+ GPPG+GK++L K +A+KL I +
Sbjct: 1 IILITGPPGSGKSTLAKKLAEKLGIPV 27
>gnl|CDD|224145 COG1224, TIP49, DNA helicase TIP49, TBP-interacting protein
[Transcription].
Length = 450
Score = 43.5 bits (103), Expect = 6e-05
Identities = 28/98 (28%), Positives = 48/98 (48%), Gaps = 13/98 (13%)
Query: 8 VKSNIISWNRVVLLHGPPGTGKTSLCKAVAQKLSIRLQSKYKITEFIEINSHSLFSKYFS 67
+K ++ R +L+ GPPGTGKT+L +A++L + F+ I+ ++S
Sbjct: 58 IKQGKMA-GRGILIVGPPGTGKTALAMGIARELG-------EDVPFVAISGSEIYSLEVK 109
Query: 68 ESGKLVQKMFN----KIKEAVE-YEESLVCLLIDEIES 100
++ L Q + +IKE E YE +V L I +
Sbjct: 110 KTEALTQALRRAIGVRIKETREVYEGEVVELEIRRARN 147
>gnl|CDD|223786 COG0714, COG0714, MoxR-like ATPases [General function prediction
only].
Length = 329
Score = 43.2 bits (102), Expect = 6e-05
Identities = 29/101 (28%), Positives = 41/101 (40%), Gaps = 25/101 (24%)
Query: 19 VLLHGPPGTGKTSLCKAVAQKLS---IRLQ--SKYKITEFI---EINSHSLFSKYFS-ES 69
VLL GPPG GKT L +A+A+ L +R+Q ++ + + L F
Sbjct: 46 VLLEGPPGVGKTLLARALARALGLPFVRIQCTPDLLPSDLLGTYAYAALLLEPGEFRFVP 105
Query: 70 GKLVQKMFNKIKEAVEYEESLVCLLIDEIESLTRARESVMS 110
G L + V LL+DEI RA V +
Sbjct: 106 GPLFAAVR-------------VILLLDEI---NRAPPEVQN 130
>gnl|CDD|223541 COG0465, HflB, ATP-dependent Zn proteases [Posttranslational
modification, protein turnover, chaperones].
Length = 596
Score = 43.5 bits (103), Expect = 6e-05
Identities = 32/95 (33%), Positives = 46/95 (48%), Gaps = 18/95 (18%)
Query: 19 VLLHGPPGTGKTSLCKAVAQKLSIRLQSKYKITEFIEINSHSLFSKYFSESG-KLVQKMF 77
VLL GPPGTGKT L KAVA + + S S F + F G V+ +F
Sbjct: 186 VLLVGPPGTGKTLLAKAVAGEAGV--PFFSI--------SGSDFVEMFVGVGASRVRDLF 235
Query: 78 NKIKEAVEYEESLVCLL-IDEIESLTRARESVMSG 111
+ K+ C++ IDEI+++ R R + + G
Sbjct: 236 EQAKKNAP------CIIFIDEIDAVGRQRGAGLGG 264
>gnl|CDD|225164 COG2255, RuvB, Holliday junction resolvasome, helicase subunit [DNA
replication, recombination, and repair].
Length = 332
Score = 42.5 bits (101), Expect = 1e-04
Identities = 31/98 (31%), Positives = 42/98 (42%), Gaps = 36/98 (36%)
Query: 19 VLLHGPPGTGKTSLCKAVAQKLSIRLQSKYKITEFIEINSHSLFSKYFSESGKLVQK--- 75
VLL GPPG GKT+L +A +L + L KIT SG ++K
Sbjct: 55 VLLFGPPGLGKTTLAHIIANELGVNL----KIT-----------------SGPALEKPGD 93
Query: 76 ---MFNKIKEA-VEYEESLVCLLIDEIESLTRARESVM 109
+ ++E V L IDEI L+ A E V+
Sbjct: 94 LAAILTNLEEGDV--------LFIDEIHRLSPAVEEVL 123
>gnl|CDD|225165 COG2256, MGS1, ATPase related to the helicase subunit of the
Holliday junction resolvase [DNA replication,
recombination, and repair].
Length = 436
Score = 42.6 bits (101), Expect = 1e-04
Identities = 36/175 (20%), Positives = 72/175 (41%), Gaps = 43/175 (24%)
Query: 21 LHGPPGTGKTSLCKAVAQKLSIRLQSKYKITEFIEINSHSLFSKYFSESGKLVQKMFNKI 80
L GPPGTGKT+L + +A + F +++ K ++++ +
Sbjct: 53 LWGPPGTGKTTLARLIAGTTNA---------AFEALSA-VTSGV------KDLREIIEEA 96
Query: 81 KEAVEYEESLVCLLIDEIESLTRARE----SVM-SG--------TE-PSDGVRVVNAVL- 125
++ + L +DEI +A++ + +G TE PS + A+L
Sbjct: 97 RKNRLLGRRTI-LFLDEIHRFNKAQQDALLPHVENGTIILIGATTENPS--FELNPALLS 153
Query: 126 -TQIDQLKKKSTGLSGRTLRKIPFLTFVKYISNNSVSMENFLIALEKTVLDLLVE 179
++ +LK LS ++K+ + + + + +I L++ LD LV
Sbjct: 154 RARVFELKP----LSSEDIKKL----LKRALLDEERGLGGQIIVLDEEALDYLVR 200
>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 = 40.9 bits (96), Expect = 1e-04
Identities = 25/83 (30%), Positives = 45/83 (54%), Gaps = 15/83 (18%)
Query: 18 VVLLHGPPGTGKTSLCKAVAQKLSIRLQSKYKI---------TEFIEINSHSLFSKYFSE 68
++ + GPPG+GKT++ K +A+KLS++L S I + IE F Y E
Sbjct: 2 IITISGPPGSGKTTVAKILAEKLSLKLISAGDIFRELAAKMGLDLIE------FLNYAEE 55
Query: 69 SGKLVQKMFNKIKEAVEYEESLV 91
+ ++ +K+ +I E E+++V
Sbjct: 56 NPEIDKKIDRRIHEIALKEKNVV 78
>gnl|CDD|222000 pfam13238, AAA_18, AAA domain.
Length = 128
Score = 40.1 bits (94), Expect = 2e-04
Identities = 18/80 (22%), Positives = 38/80 (47%)
Query: 19 VLLHGPPGTGKTSLCKAVAQKLSIRLQSKYKITEFIEINSHSLFSKYFSESGKLVQKMFN 78
+L+ G PG+GKT+L K +A++L L+ K + + + + K+ +
Sbjct: 1 ILITGTPGSGKTTLAKELAERLGDVLRDLAKENGLVLELDEEITDESKRLDEDKLAKLLD 60
Query: 79 KIKEAVEYEESLVCLLIDEI 98
K+++ +E ++ID
Sbjct: 61 KLEKIIEELAEGENVIIDGH 80
>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 = 39.9 bits (93), Expect = 3e-04
Identities = 13/24 (54%), Positives = 16/24 (66%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQKL 40
VLL GP GTGKTSL + + + L
Sbjct: 25 PSVLLTGPSGTGKTSLLRELLEGL 48
>gnl|CDD|234619 PRK00080, ruvB, Holliday junction DNA helicase RuvB; Reviewed.
Length = 328
Score = 40.9 bits (97), Expect = 3e-04
Identities = 26/98 (26%), Positives = 39/98 (39%), Gaps = 36/98 (36%)
Query: 19 VLLHGPPGTGKTSLCKAVAQKLSIRLQSKYKITEFIEINSHSLFSKYFSESGKLVQK--- 75
VLL+GPPG GKT+L +A + +IT SG ++K
Sbjct: 54 VLLYGPPGLGKTTLANIIAN----EMGVNIRIT-----------------SGPALEKPGD 92
Query: 76 ---MFNKIKEA-VEYEESLVCLLIDEIESLTRARESVM 109
+ ++E V L IDEI L+ E ++
Sbjct: 93 LAAILTNLEEGDV--------LFIDEIHRLSPVVEEIL 122
>gnl|CDD|224391 COG1474, CDC6, Cdc6-related protein, AAA superfamily ATPase [DNA
replication, recombination, and repair /
Posttranslational modification, protein turnover,
chaperones].
Length = 366
Score = 40.8 bits (96), Expect = 4e-04
Identities = 22/103 (21%), Positives = 49/103 (47%), Gaps = 16/103 (15%)
Query: 19 VLLHGPPGTGKTSLCKAVAQKLSIRLQSKYKITEFIEIN------SHSLFSKYFSESGKL 72
++++GP GTGKT+ K V + L+ E + IN + + SK ++ GK+
Sbjct: 45 IIIYGPTGTGKTATVKFVME----ELEESSANVEVVYINCLELRTPYQVLSKILNKLGKV 100
Query: 73 V------QKMFNKIKEAVEYEESLVCLLIDEIESLTRARESVM 109
++ ++ + + + V +++DE+++L V+
Sbjct: 101 PLTGDSSLEILKRLYDNLSKKGKTVIVILDEVDALVDKDGEVL 143
>gnl|CDD|215599 PLN03140, PLN03140, ABC transporter G family member; Provisional.
Length = 1470
Score = 41.4 bits (97), Expect = 4e-04
Identities = 28/84 (33%), Positives = 44/84 (52%), Gaps = 13/84 (15%)
Query: 10 SNIISWNRVVLLHGPPGTGKTSLCKAVAQKLSIRLQSK-------YKITEFIEINSHSLF 62
S II +R+ LL GPP +GKT+L A+A KL L+ Y++ EF+ +
Sbjct: 185 SGIIKPSRMTLLLGPPSSGKTTLLLALAGKLDPSLKVSGEITYNGYRLNEFVPRKT---- 240
Query: 63 SKYFSESGKLVQKMFNKIKEAVEY 86
S Y S++ V M +KE +++
Sbjct: 241 SAYISQNDVHVGVM--TVKETLDF 262
>gnl|CDD|234751 PRK00411, cdc6, cell division control protein 6; Reviewed.
Length = 394
Score = 39.4 bits (93), Expect = 0.001
Identities = 24/94 (25%), Positives = 43/94 (45%), Gaps = 18/94 (19%)
Query: 19 VLLHGPPGTGKTSLCKAVAQKLSIRLQSKYKITEFIEINSH--------------SLFSK 64
VL++GPPGTGKT+ +K+ L+ ++ IN LF
Sbjct: 58 VLIYGPPGTGKTT----TVKKVFEELEEIAVKVVYVYINCQIDRTRYAIFSEIARQLFGH 113
Query: 65 YFSESGKLVQKMFNKIKEAVEYEESLVCLLIDEI 98
SG ++F+KI E ++ + ++ + +D+I
Sbjct: 114 PPPSSGLSFDELFDKIAEYLDERDRVLIVALDDI 147
>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 = 38.6 bits (91), Expect = 0.001
Identities = 15/30 (50%), Positives = 22/30 (73%), Gaps = 2/30 (6%)
Query: 19 VLLHGPPGTGKTSLCKAVAQKL--SIRLQS 46
VLL+GPPG GKT+L +A ++ +IR+ S
Sbjct: 53 VLLYGPPGLGKTTLANIIANEMGVNIRITS 82
>gnl|CDD|223873 COG0802, COG0802, Predicted ATPase or kinase [General function
prediction only].
Length = 149
Score = 37.2 bits (87), Expect = 0.002
Identities = 12/28 (42%), Positives = 17/28 (60%)
Query: 18 VVLLHGPPGTGKTSLCKAVAQKLSIRLQ 45
VVLL G G GKT+L + +A+ L +
Sbjct: 27 VVLLSGDLGAGKTTLVRGIAKGLGVDGN 54
>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 = 36.9 bits (86), Expect = 0.003
Identities = 15/66 (22%), Positives = 35/66 (53%)
Query: 18 VVLLHGPPGTGKTSLCKAVAQKLSIRLQSKYKITEFIEINSHSLFSKYFSESGKLVQKMF 77
++L+ G PG+GK++ + + ++L + S + + + + S Y SG++ Q++
Sbjct: 1 LILMVGLPGSGKSTFARRLLRELGAVVLSSDTLRKRLRGDGPPDISYYARASGRVYQRLL 60
Query: 78 NKIKEA 83
+EA
Sbjct: 61 ELAREA 66
>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 = 36.7 bits (86), Expect = 0.003
Identities = 9/22 (40%), Positives = 16/22 (72%)
Query: 23 GPPGTGKTSLCKAVAQKLSIRL 44
GP G+GK+++ K +A+KL +
Sbjct: 6 GPAGSGKSTVAKLLAKKLGLPY 27
>gnl|CDD|222194 pfam13521, AAA_28, AAA domain.
Length = 162
Score = 37.2 bits (87), Expect = 0.003
Identities = 11/22 (50%), Positives = 16/22 (72%), Gaps = 1/22 (4%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQ 38
R+V+ G P TGKT+L +A+A
Sbjct: 1 RIVIT-GGPSTGKTTLLEALAA 21
>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 = 36.8 bits (86), Expect = 0.003
Identities = 8/26 (30%), Positives = 19/26 (73%)
Query: 18 VVLLHGPPGTGKTSLCKAVAQKLSIR 43
++++ G G+GK+++ KA+A++L
Sbjct: 1 IIVVMGVSGSGKSTVGKALAERLGAP 26
>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 = 37.7 bits (88), Expect = 0.003
Identities = 29/91 (31%), Positives = 42/91 (46%), Gaps = 22/91 (24%)
Query: 19 VLLHGPPGTGKTSLCKAVAQKLSIRLQSKYKITEFIEINSHSLFSKYFSESGKLVQKMFN 78
+LL+GPPG GKT+L +A ++ + L KIT SG ++K +
Sbjct: 33 LLLYGPPGLGKTTLAHIIANEMGVNL----KIT-----------------SGPALEKPGD 71
Query: 79 KIKEAVEYEESLVCLLIDEIESLTRARESVM 109
EE V L IDEI L+ A E ++
Sbjct: 72 LAAILTNLEEGDV-LFIDEIHRLSPAVEELL 101
>gnl|CDD|222258 pfam13604, AAA_30, 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. There is a Walker A and
Walker B.
Length = 195
Score = 37.2 bits (87), Expect = 0.004
Identities = 11/23 (47%), Positives = 16/23 (69%)
Query: 16 NRVVLLHGPPGTGKTSLCKAVAQ 38
+RV ++ GP GTGKT+ KA +
Sbjct: 18 DRVAVVQGPAGTGKTTSLKAARE 40
>gnl|CDD|216186 pfam00910, RNA_helicase, RNA helicase. This family includes RNA
helicases thought to be involved in duplex unwinding
during viral RNA replication. Members of this family
are found in a variety of single stranded RNA viruses.
Length = 105
Score = 35.7 bits (83), Expect = 0.004
Identities = 14/49 (28%), Positives = 25/49 (51%), Gaps = 4/49 (8%)
Query: 19 VLLHGPPGTGKTSLCKAVAQKLSIRLQSKYKITEFIEINSHSLFSKYFS 67
+ L+GPPG GK++L K +A+ L L K + + S + ++
Sbjct: 1 IWLYGPPGCGKSTLAKYLARALLKHLGLPKKDS----VYSRNPDDDFWD 45
>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 = 37.7 bits (88), Expect = 0.005
Identities = 26/90 (28%), Positives = 46/90 (51%), Gaps = 14/90 (15%)
Query: 18 VVLLHGPPGTGKTSLCKAVAQKLS---IRLQSKYKITEFIEINSHSLFSKYF-SESGKLV 73
++ L GPPG GKTSL K++A+ L+ +R S + + EI H Y + G+++
Sbjct: 349 ILCLVGPPGVGKTSLGKSIAKALNRKFVRF-SLGGVRDEAEIRGHR--RTYVGAMPGRII 405
Query: 74 QKMFNKIKEAVEYEESLVCLLIDEIESLTR 103
Q + + + + L L+DEI+ +
Sbjct: 406 QGL-----KKAKTKNPLF--LLDEIDKIGS 428
>gnl|CDD|235878 PRK06851, PRK06851, hypothetical protein; Provisional.
Length = 367
Score = 37.3 bits (87), Expect = 0.005
Identities = 14/37 (37%), Positives = 22/37 (59%)
Query: 5 HSKVKSNIISWNRVVLLHGPPGTGKTSLCKAVAQKLS 41
+S S I NR+ +L G PGTGK++L K + ++
Sbjct: 19 YSLYDSIIDGANRIFILKGGPGTGKSTLMKKIGEEFL 55
Score = 27.6 bits (62), Expect = 7.7
Identities = 10/28 (35%), Positives = 15/28 (53%)
Query: 16 NRVVLLHGPPGTGKTSLCKAVAQKLSIR 43
L G PGTGK+++ K +A+ R
Sbjct: 214 KNRYFLKGRPGTGKSTMLKKIAKAAEER 241
>gnl|CDD|223637 COG0563, Adk, Adenylate kinase and related kinases [Nucleotide
transport and metabolism].
Length = 178
Score = 36.1 bits (84), Expect = 0.007
Identities = 13/27 (48%), Positives = 21/27 (77%), Gaps = 1/27 (3%)
Query: 16 NRVVLLHGPPGTGKTSLCKAVAQKLSI 42
R+++L GPPG GK++L K +A+KL +
Sbjct: 1 MRILIL-GPPGAGKSTLAKKLAKKLGL 26
>gnl|CDD|222005 pfam13245, AAA_19, Part of AAA domain.
Length = 73
Score = 34.3 bits (79), Expect = 0.007
Identities = 9/25 (36%), Positives = 15/25 (60%)
Query: 16 NRVVLLHGPPGTGKTSLCKAVAQKL 40
+ ++ G PGTGKT+ A+ +L
Sbjct: 10 RSLFVVDGGPGTGKTATAAAIIARL 34
>gnl|CDD|216999 pfam02367, UPF0079, Uncharacterized P-loop hydrolase UPF0079.
This uncharacterized family contains a P-loop.
Length = 123
Score = 34.9 bits (81), Expect = 0.009
Identities = 13/26 (50%), Positives = 16/26 (61%)
Query: 18 VVLLHGPPGTGKTSLCKAVAQKLSIR 43
VVLL G G GKT+ + +AQ L I
Sbjct: 17 VVLLSGDLGAGKTTFVRGLAQGLGIT 42
>gnl|CDD|235244 PRK04182, PRK04182, cytidylate kinase; Provisional.
Length = 180
Score = 35.6 bits (83), Expect = 0.009
Identities = 11/24 (45%), Positives = 19/24 (79%)
Query: 23 GPPGTGKTSLCKAVAQKLSIRLQS 46
GPPG+GKT++ + +A+KL ++ S
Sbjct: 7 GPPGSGKTTVARLLAEKLGLKHVS 30
>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 = 35.7 bits (83), Expect = 0.011
Identities = 25/132 (18%), Positives = 46/132 (34%), Gaps = 34/132 (25%)
Query: 16 NRVVLLHGPPGTGKTSLCKAVAQKLSIRLQ-------SKYKITEFIEINSHSLFSKYFSE 68
R++L+ GP GK++ +++ + Q I I +
Sbjct: 29 GRLLLITGPNMGGKSTYLRSIGL-AVLLAQIGCFVPAESASIPLVDRIFTR------IGA 81
Query: 69 SGKLVQKM--F----NKIKEAVEY--EESLVCLLIDEIESLTRARESVMSGTEPSDGVRV 120
+ F ++KE + SLV LIDE+ GT ++G+ +
Sbjct: 82 EDSISDGRSTFMAELLELKEILSLATPRSLV--LIDEL----------GRGTSTAEGLAI 129
Query: 121 VNAVLTQIDQLK 132
AVL + +
Sbjct: 130 AYAVLEHLLEKG 141
>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 = 35.2 bits (82), Expect = 0.012
Identities = 31/93 (33%), Positives = 46/93 (49%), Gaps = 23/93 (24%)
Query: 18 VVLLHGPPGTGKTSLCKAVAQKLSIRLQSKYKI--TEFIEINSHSLFSK-------Y--F 66
L GP G GKT L KA+A+ L ++ +I +E++E HS+ S+ Y +
Sbjct: 5 SFLFLGPTGVGKTELAKALAELLFGDERALIRIDMSEYME--EHSV-SRLIGAPPGYVGY 61
Query: 67 SESGKLVQKMFNKIKEAVEYEESLVCLLIDEIE 99
E G+L EAV + + +LIDEIE
Sbjct: 62 EEGGQLT--------EAVRRKPYSI-VLIDEIE 85
>gnl|CDD|236153 PRK08116, PRK08116, hypothetical protein; Validated.
Length = 268
Score = 35.8 bits (83), Expect = 0.014
Identities = 15/55 (27%), Positives = 22/55 (40%), Gaps = 3/55 (5%)
Query: 16 NRVVLLHGPPGTGKTSLCKAVAQKLSIRLQSKYKITEFIEI--NSHSLFSKYFSE 68
N +LL G GTGKT L +A +L + F ++ S + E
Sbjct: 114 NVGLLLWGSVGTGKTYLAACIANELIEK-GVPVIFVNFPQLLNRIKSTYKSSGKE 167
>gnl|CDD|237090 PRK12402, PRK12402, replication factor C small subunit 2; Reviewed.
Length = 337
Score = 35.7 bits (83), Expect = 0.015
Identities = 26/104 (25%), Positives = 36/104 (34%), Gaps = 24/104 (23%)
Query: 20 LLHGPPGTGKTSLCKAVAQKLSIRLQSKYKITEFIEINSHSLFS---KYFSE-------- 68
L+ GPPG+GKT+ +A+A+ L F E N F KY E
Sbjct: 40 LVQGPPGSGKTAAVRALAR----ELYGDPWENNFTEFNVADFFDQGKKYLVEDPRFAHFL 95
Query: 69 -----SGKLVQKMFNKI-KEAVEY---EESLVCLLIDEIESLTR 103
F + KE Y +L+D E+L
Sbjct: 96 GTDKRIRSSKIDNFKHVLKEYASYRPLSADYKTILLDNAEALRE 139
>gnl|CDD|237354 PRK13341, PRK13341, recombination factor protein RarA/unknown
domain fusion protein; Reviewed.
Length = 725
Score = 36.2 bits (84), Expect = 0.016
Identities = 10/18 (55%), Positives = 15/18 (83%)
Query: 20 LLHGPPGTGKTSLCKAVA 37
+L+GPPG GKT+L + +A
Sbjct: 56 ILYGPPGVGKTTLARIIA 73
>gnl|CDD|151168 pfam10662, PduV-EutP, Ethanolamine utilisation - propanediol
utilisation. Members of this family function in
ethanolamine and propanediol degradation pathways,
however the exact roles of these proteins is poorly
understood.
Length = 143
Score = 34.1 bits (79), Expect = 0.020
Identities = 14/40 (35%), Positives = 22/40 (55%), Gaps = 5/40 (12%)
Query: 19 VLLHGPPGTGKTSLCKAVAQKLSIRLQSKYKITEFIEINS 58
++L G G GKT+L +A+ + KYK T+ IE +
Sbjct: 4 IMLIGRSGCGKTTLTQALNG-----EELKYKKTQAIEFSD 38
>gnl|CDD|223542 COG0466, Lon, ATP-dependent Lon protease, bacterial type
[Posttranslational modification, protein turnover,
chaperones].
Length = 782
Score = 35.6 bits (83), Expect = 0.020
Identities = 16/35 (45%), Positives = 21/35 (60%), Gaps = 6/35 (17%)
Query: 6 SKVKSNIISWNRVVLLHGPPGTGKTSLCKAVAQKL 40
K+K I+ L GPPG GKTSL K++A+ L
Sbjct: 346 KKLKGPIL------CLVGPPGVGKTSLGKSIAKAL 374
>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 = 34.1 bits (79), Expect = 0.020
Identities = 13/30 (43%), Positives = 18/30 (60%), Gaps = 3/30 (10%)
Query: 19 VLLHGPPGTGKTSLCKAVAQKLSI---RLQ 45
VLL G PG KT L + +A+ L + R+Q
Sbjct: 2 VLLEGVPGLAKTLLARTLARSLGLDFRRIQ 31
>gnl|CDD|218685 pfam05673, DUF815, Protein of unknown function (DUF815). This
family consists of several bacterial proteins of
unknown function.
Length = 248
Score = 35.2 bits (82), Expect = 0.022
Identities = 17/48 (35%), Positives = 24/48 (50%), Gaps = 12/48 (25%)
Query: 19 VLLHGPPGTGKTSLCKAVAQKLS---IRLQSKYKITEFIEINSHSLFS 63
VLL G GTGK+SL KA+ + + +RL IE++ L
Sbjct: 56 VLLWGARGTGKSSLVKALLNEYADQGLRL---------IEVDKDDLGD 94
>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 = 34.4 bits (79), Expect = 0.022
Identities = 19/114 (16%), Positives = 39/114 (34%), Gaps = 21/114 (18%)
Query: 18 VVLLHGPPGTGKTSLCKAVAQKLSIRLQSKYKITEFIEIN--------SHSLFSKYFSES 69
++L+ GP G+GKT+L +A + +K +++I S +
Sbjct: 1 LILVFGPTGSGKTTLALQLALN----IATKGGKVVYVDIEEEIEELTERLIGESLKGALD 56
Query: 70 GKLVQKMFNK------IKEAVEY---EESLVCLLIDEIESLTRARESVMSGTEP 114
++ + E +++DE+ L RA + G
Sbjct: 57 NLIIVFATADDPAAARLLSKAERLRERGGDDLIILDELTRLVRALREIREGYPG 110
>gnl|CDD|220440 pfam09848, DUF2075, Uncharacterized conserved protein (DUF2075).
This domain, found in various prokaryotic proteins
(including putative ATP/GTP binding proteins), has no
known function.
Length = 348
Score = 35.3 bits (82), Expect = 0.023
Identities = 22/94 (23%), Positives = 33/94 (35%), Gaps = 21/94 (22%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQKLSIRLQSK--YKITEFIEINSHSLFSKYFSESGKLVQ 74
V L+ G PGTGKT VA L L + F+ N H L + L
Sbjct: 2 AVFLVTGGPGTGKT----VVALNLFAELSDSDLGRTAVFLSGN-HPLVLVLYE---ALAG 53
Query: 75 KMFNKIKEAVEYEESLV-----------CLLIDE 97
+ + K+ S + +++DE
Sbjct: 54 DLKVRKKKLFRKPTSFINNLHKAPPHEDVVIVDE 87
>gnl|CDD|217465 pfam03266, NTPase_1, NTPase. This domain is found across all
species from bacteria to human, and the function was
determined first in a hyperthermophilic bacterium to be
an NTPase. The structure of one member-sequence
represents a variation of the RecA fold, and implies
that the function might be that of a DNA/RNA modifying
enzyme. The sequence carries both a Walker A and Walker
B motif which together are characteristic of ATPases or
GTPases. The protein exhibits an increased expression
profile in human liver cholangiocarcinoma when compared
to normal tissue.
Length = 168
Score = 34.5 bits (80), Expect = 0.024
Identities = 13/37 (35%), Positives = 18/37 (48%), Gaps = 3/37 (8%)
Query: 18 VVLLHGPPGTGKTSLCKAVAQKLSIRLQSKYKITEFI 54
+ + GPPG GKT+L K V + L K+ F
Sbjct: 1 RIFITGPPGVGKTTLVKKVIELLK---SEGVKVGGFY 34
>gnl|CDD|235825 PRK06547, PRK06547, hypothetical protein; Provisional.
Length = 172
Score = 34.3 bits (79), Expect = 0.027
Identities = 11/28 (39%), Positives = 17/28 (60%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQKLSIRL 44
VL+ G G+GKT+L A+A + +L
Sbjct: 16 ITVLIDGRSGSGKTTLAGALAARTGFQL 43
>gnl|CDD|223718 COG0645, COG0645, Predicted kinase [General function prediction
only].
Length = 170
Score = 34.3 bits (79), Expect = 0.027
Identities = 15/31 (48%), Positives = 25/31 (80%), Gaps = 1/31 (3%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQKL-SIRLQS 46
R+VL+ G PG+GK++L + +A+ L +IRL+S
Sbjct: 2 RLVLVGGLPGSGKSTLARGLAELLGAIRLRS 32
>gnl|CDD|223360 COG0283, Cmk, Cytidylate kinase [Nucleotide transport and
metabolism].
Length = 222
Score = 34.5 bits (80), Expect = 0.031
Identities = 9/22 (40%), Positives = 15/22 (68%)
Query: 23 GPPGTGKTSLCKAVAQKLSIRL 44
GP G+GK+++ K +A+KL
Sbjct: 11 GPAGSGKSTVAKILAEKLGFHY 32
>gnl|CDD|216619 pfam01637, Arch_ATPase, Archaeal ATPase. This family contain a
conserved P-loop motif that is involved in binding ATP.
This family is almost exclusively found in
archaebacteria and particularly in Methanococcus
jannaschii that encodes sixteen members of this family.
Length = 223
Score = 34.6 bits (80), Expect = 0.032
Identities = 14/84 (16%), Positives = 35/84 (41%), Gaps = 4/84 (4%)
Query: 16 NRVVLLHGPPGTGKTSLCKAVAQKLSIRLQSKYKI-TEFIEINSHSLFSKYFSESGKLVQ 74
+++++GP GKT+L + ++L R I + + F E+ +L +
Sbjct: 20 YPIIVVYGPRRCGKTALLREFLEEL--RELGYRVIYYDPLRREFEEKL-DRFEEAKRLAE 76
Query: 75 KMFNKIKEAVEYEESLVCLLIDEI 98
+ + + + + L L + +
Sbjct: 77 ALGDALPKIGIAKSKLAFLSLTLL 100
>gnl|CDD|234579 PRK00023, cmk, cytidylate kinase; Provisional.
Length = 225
Score = 34.3 bits (80), Expect = 0.033
Identities = 9/22 (40%), Positives = 14/22 (63%)
Query: 23 GPPGTGKTSLCKAVAQKLSIRL 44
GP G+GK ++ K +A+KL
Sbjct: 11 GPAGSGKGTVAKILAKKLGFHY 32
>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 = 34.1 bits (79), Expect = 0.033
Identities = 11/26 (42%), Positives = 19/26 (73%), Gaps = 1/26 (3%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQKLSI 42
R++LL GPPG+GK + + +A+K +
Sbjct: 1 RILLL-GPPGSGKGTQAERLAKKYGL 25
>gnl|CDD|237475 PRK13695, PRK13695, putative NTPase; Provisional.
Length = 174
Score = 33.7 bits (78), Expect = 0.037
Identities = 13/36 (36%), Positives = 20/36 (55%), Gaps = 3/36 (8%)
Query: 19 VLLHGPPGTGKTSLCKAVAQKLSIRLQSKYKITEFI 54
+ + GPPG GKT+L +A+ L + YK+ F
Sbjct: 3 IGITGPPGVGKTTLVLKIAELLK---EEGYKVGGFY 35
>gnl|CDD|222163 pfam13479, AAA_24, AAA domain. This AAA domain is found in a
wide variety of presumed phage proteins.
Length = 201
Score = 34.2 bits (79), Expect = 0.039
Identities = 12/16 (75%), Positives = 14/16 (87%)
Query: 19 VLLHGPPGTGKTSLCK 34
VL++GPPG GKTSL K
Sbjct: 6 VLIYGPPGIGKTSLAK 21
>gnl|CDD|224345 COG1428, COG1428, Deoxynucleoside kinases [Nucleotide transport
and metabolism].
Length = 216
Score = 33.8 bits (78), Expect = 0.048
Identities = 23/77 (29%), Positives = 34/77 (44%), Gaps = 11/77 (14%)
Query: 16 NRVVLLHGPPGTGKTSLCKAVAQKLSIRLQSKYKITEFIEINSH-SLFSKYFSESGKLVQ 74
V+++ G G GK++L AQ L+ L K E +E N LF + L+Q
Sbjct: 4 AMVIVIEGMIGAGKSTL----AQALAEHLGFKV-FYELVEDNPFLDLFYEDPERYAFLLQ 58
Query: 75 -----KMFNKIKEAVEY 86
F KIK+A+
Sbjct: 59 IYFLLNRFKKIKKALSD 75
>gnl|CDD|237495 PRK13765, PRK13765, ATP-dependent protease Lon; Provisional.
Length = 637
Score = 34.2 bits (79), Expect = 0.060
Identities = 13/24 (54%), Positives = 18/24 (75%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQKL 40
R V++ G PGTGK+ L KA+A+ L
Sbjct: 51 RHVMMIGSPGTGKSMLAKAMAELL 74
>gnl|CDD|214361 CHL00095, clpC, Clp protease ATP binding subunit.
Length = 821
Score = 34.3 bits (79), Expect = 0.066
Identities = 27/103 (26%), Positives = 53/103 (51%), Gaps = 25/103 (24%)
Query: 7 KVKSNIISWNRVVLLHGPPGTGKTSLCKAVAQKLSIRLQSKYKITEF------IEINSHS 60
+ K+N I L G PG GKT A+A+ L+ R+ ++ + + I ++
Sbjct: 198 RTKNNPI-------LIGEPGVGKT----AIAEGLAQRIVNR-DVPDILEDKLVITLDIGL 245
Query: 61 LF--SKYFSESGKLVQKMFNKIKEAVEYEESLVCLLIDEIESL 101
L +KY E + ++++F++I+E + + L+IDE+ +L
Sbjct: 246 LLAGTKYRGEFEERLKRIFDEIQEN-----NNIILVIDEVHTL 283
Score = 33.5 bits (77), Expect = 0.10
Identities = 34/103 (33%), Positives = 48/103 (46%), Gaps = 35/103 (33%)
Query: 12 IISWNRVVLLHGPPGTGKTSLCKAVA------QKLSIRLQSKYKITEFIEINSHSLFSK- 64
I S+ L GP G GKT L KA+A + IRL ++E++E H++ SK
Sbjct: 539 IASF----LFSGPTGVGKTELTKALASYFFGSEDAMIRLD----MSEYME--KHTV-SKL 587
Query: 65 ------Y--FSESGKLVQKMFNKIKEAVEYEESLVCLLIDEIE 99
Y ++E G+L EAV + V +L DEIE
Sbjct: 588 IGSPPGYVGYNEGGQLT--------EAVRKKPYTV-VLFDEIE 621
>gnl|CDD|224027 COG1102, Cmk, Cytidylate kinase [Nucleotide transport and
metabolism].
Length = 179
Score = 33.1 bits (76), Expect = 0.075
Identities = 12/34 (35%), Positives = 22/34 (64%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQKLSIRLQSKYKI 50
V+ + G PG+GKT++ + +A+ L ++L S I
Sbjct: 1 MVITISGLPGSGKTTVARELAEHLGLKLVSAGTI 34
>gnl|CDD|235210 PRK04040, PRK04040, adenylate kinase; Provisional.
Length = 188
Score = 32.9 bits (76), Expect = 0.078
Identities = 14/38 (36%), Positives = 20/38 (52%), Gaps = 4/38 (10%)
Query: 16 NRVVLLHGPPGTGKTSLCKAVAQKLSIRLQSKYKITEF 53
+VV++ G PG GKT++ +KL YKI F
Sbjct: 2 MKVVVVTGVPGVGKTTVLNKALEKLKE----DYKIVNF 35
>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 = 32.7 bits (75), Expect = 0.086
Identities = 10/24 (41%), Positives = 15/24 (62%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQKL 40
R V+L G G+GKT+L + +A
Sbjct: 1 RTVILQGEAGSGKTTLLQKIALLW 24
>gnl|CDD|236442 PRK09270, PRK09270, nucleoside triphosphate hydrolase
domain-containing protein; Reviewed.
Length = 229
Score = 33.0 bits (76), Expect = 0.094
Identities = 9/25 (36%), Positives = 15/25 (60%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQKLS 41
+V + GPPG GK++L + + L
Sbjct: 34 TIVGIAGPPGAGKSTLAEFLEALLQ 58
>gnl|CDD|235898 PRK06964, PRK06964, DNA polymerase III subunit delta'; Validated.
Length = 342
Score = 33.2 bits (76), Expect = 0.097
Identities = 13/37 (35%), Positives = 17/37 (45%), Gaps = 10/37 (27%)
Query: 14 SWNRV----------VLLHGPPGTGKTSLCKAVAQKL 40
WNR+ +LLHG G GK + +AQ L
Sbjct: 9 DWNRLQALRARLPHALLLHGQAGIGKLDFAQHLAQGL 45
>gnl|CDD|105560 PRK12339, PRK12339, 2-phosphoglycerate kinase; Provisional.
Length = 197
Score = 32.8 bits (75), Expect = 0.11
Identities = 13/40 (32%), Positives = 21/40 (52%), Gaps = 3/40 (7%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQKLSIR--LQSKYKITEFI 54
+ + G PG GKTS+ +A+ +I L Y + EF+
Sbjct: 4 TIHFIGGIPGVGKTSISGYIARHRAIDIVLSGDY-LREFL 42
>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 = 32.3 bits (74), Expect = 0.11
Identities = 14/23 (60%), Positives = 17/23 (73%)
Query: 19 VLLHGPPGTGKTSLCKAVAQKLS 41
VLL GPPGTGK+ L + +A LS
Sbjct: 2 VLLVGPPGTGKSELAERLAAALS 24
>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 = 32.6 bits (75), Expect = 0.11
Identities = 13/26 (50%), Positives = 19/26 (73%), Gaps = 1/26 (3%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQKLSI 42
R+VLL GPPG+GK + K +A+K +
Sbjct: 1 RLVLL-GPPGSGKGTQAKRIAEKYGL 25
>gnl|CDD|180215 PRK05707, PRK05707, DNA polymerase III subunit delta'; Validated.
Length = 328
Score = 33.1 bits (76), Expect = 0.11
Identities = 11/22 (50%), Positives = 14/22 (63%)
Query: 20 LLHGPPGTGKTSLCKAVAQKLS 41
LLHGP G GK +L + +A L
Sbjct: 26 LLHGPAGIGKRALAERLAAALL 47
>gnl|CDD|233418 TIGR01448, recD_rel, helicase, putative, RecD/TraA family. This
model describes a family similar to RecD, the
exodeoxyribonuclease V alpha chain of TIGR01447. Members
of this family, however, are not found in a context of
RecB and RecC and are longer by about 200 amino acids at
the amino end. Chlamydia muridarum has both a member of
this family and a RecD [Unknown function, Enzymes of
unknown specificity].
Length = 720
Score = 33.2 bits (76), Expect = 0.11
Identities = 13/38 (34%), Positives = 23/38 (60%), Gaps = 1/38 (2%)
Query: 13 ISWNRVVLLHGPPGTGKTSLCKAVAQKLSIRLQSKYKI 50
++VV+L G PGTGKT++ +A+ + L+ L +
Sbjct: 335 AIQHKVVILTGGPGTGKTTITRAIIE-LAEELGGLLPV 371
>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 = 32.4 bits (75), Expect = 0.13
Identities = 15/39 (38%), Positives = 19/39 (48%), Gaps = 4/39 (10%)
Query: 16 NRVVLLHGPPGTGKTSLCKAVAQKLSIRLQSKYKITEFI 54
N +V GP GTGKT L AVA ++ K+ I
Sbjct: 19 NDIVFGIGPAGTGKTYL--AVA--AAVDALKDGKVKRII 53
>gnl|CDD|224985 COG2074, COG2074, 2-phosphoglycerate kinase [Carbohydrate transport
and metabolism].
Length = 299
Score = 32.7 bits (75), Expect = 0.13
Identities = 9/27 (33%), Positives = 18/27 (66%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQKLSIR 43
++L+ G G GK+++ +A++L IR
Sbjct: 90 LIILIGGASGVGKSTIAGELARRLGIR 116
>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 = 32.7 bits (75), Expect = 0.13
Identities = 14/39 (35%), Positives = 22/39 (56%), Gaps = 1/39 (2%)
Query: 10 SNIISWNRVVLLHGPPGTGKTS-LCKAVAQKLSIRLQSK 47
+S + + L+ GPPGTGKT+ + + + Q LS K
Sbjct: 11 KKALSSSDITLIQGPPGTGKTTTIVEIIKQLLSNAPGKK 49
>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 = 32.7 bits (75), Expect = 0.14
Identities = 11/22 (50%), Positives = 17/22 (77%)
Query: 16 NRVVLLHGPPGTGKTSLCKAVA 37
R ++L PPG+GK++LC A+A
Sbjct: 108 GRALILPAPPGSGKSTLCAALA 129
>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 = 31.4 bits (72), Expect = 0.15
Identities = 18/84 (21%), Positives = 30/84 (35%), Gaps = 17/84 (20%)
Query: 16 NRVVLLHGPPGTGKTSLCKAVAQKLSIRLQSKYKITEFIEINSHSLFSKYFSESGKL-VQ 74
N+++++ GP GKT+L + + + IN L F L +
Sbjct: 2 NKIIVITGPRQVGKTTLLLQFLK--------ELLSENILYIN---LDDPRFLRLALLDLL 50
Query: 75 KMFNKIKEAVEYEESLVCLLIDEI 98
+ F K L +DEI
Sbjct: 51 EEFLK-----LLLPGKKYLFLDEI 69
>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 = 32.6 bits (75), Expect = 0.16
Identities = 11/36 (30%), Positives = 19/36 (52%), Gaps = 5/36 (13%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQKLSIRLQSKYKITE 52
+++ L GP G GK+SL + + R +Y T+
Sbjct: 79 QILYLLGPVGGGKSSLVECL-----KRGLEEYSKTD 109
>gnl|CDD|224401 COG1484, DnaC, DNA replication protein [DNA replication,
recombination, and repair].
Length = 254
Score = 32.4 bits (74), Expect = 0.16
Identities = 21/81 (25%), Positives = 36/81 (44%), Gaps = 13/81 (16%)
Query: 19 VLLHGPPGTGKTSLCKAVAQKLSIRLQSKYKITEFIEINSHSLFSKY-FSESGKLVQKMF 77
++L GPPG GKT L A+ +L S + I + L SK + +++
Sbjct: 108 LVLLGPPGVGKTHLAIAIGNELLKAGIS------VLFITAPDLLSKLKAAFDEGRLEEKL 161
Query: 78 NKIKEAVEYEESLVCLLIDEI 98
+ + V+ L+ID+I
Sbjct: 162 LRELKKVDL------LIIDDI 176
>gnl|CDD|107157 PHA02244, PHA02244, ATPase-like protein.
Length = 383
Score = 32.8 bits (74), Expect = 0.16
Identities = 19/83 (22%), Positives = 40/83 (48%), Gaps = 10/83 (12%)
Query: 12 IISWNRVVLLHGPPGTGKTSLCKAVAQKLSI------RLQSKYKITEFIEINSH---SLF 62
I++ N V L G G+GK + + +A+ L + + ++++ FI+ N + F
Sbjct: 115 IVNANIPVFLKGGAGSGKNHIAEQIAEALDLDFYFMNAIMDEFELKGFIDANGKFHETPF 174
Query: 63 SKYFSESGKL-VQKMFNKIKEAV 84
+ F + G + ++ I EA+
Sbjct: 175 YEAFKKGGLFFIDEIDASIPEAL 197
>gnl|CDD|236546 PRK09518, PRK09518, bifunctional cytidylate kinase/GTPase Der;
Reviewed.
Length = 712
Score = 32.8 bits (75), Expect = 0.17
Identities = 11/23 (47%), Positives = 17/23 (73%)
Query: 18 VVLLHGPPGTGKTSLCKAVAQKL 40
+V + GP G GK+S+ +A+AQ L
Sbjct: 3 IVAIDGPAGVGKSSVSRALAQYL 25
>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 = 31.8 bits (73), Expect = 0.19
Identities = 9/25 (36%), Positives = 16/25 (64%), Gaps = 1/25 (4%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQKLS 41
+VL+ G G GKT++ + +A+ L
Sbjct: 1 NIVLI-GMMGAGKTTVGRLLAKALG 24
>gnl|CDD|223775 COG0703, AroK, Shikimate kinase [Amino acid transport and
metabolism].
Length = 172
Score = 31.8 bits (73), Expect = 0.20
Identities = 9/29 (31%), Positives = 19/29 (65%)
Query: 16 NRVVLLHGPPGTGKTSLCKAVAQKLSIRL 44
N ++L G G GK+++ +A+A+ L++
Sbjct: 2 NMNIVLIGFMGAGKSTIGRALAKALNLPF 30
>gnl|CDD|235422 PRK05342, clpX, ATP-dependent protease ATP-binding subunit ClpX;
Provisional.
Length = 412
Score = 32.4 bits (75), Expect = 0.22
Identities = 15/32 (46%), Positives = 19/32 (59%), Gaps = 7/32 (21%)
Query: 9 KSNIISWNRVVLLHGPPGTGKTSLCKAVAQKL 40
KSNI LL GP G+GKT L + +A+ L
Sbjct: 108 KSNI-------LLIGPTGSGKTLLAQTLARIL 132
>gnl|CDD|129690 TIGR00602, rad24, checkpoint protein rad24. All proteins in this
family for which functions are known are involved in DNA
damage tolerance (likely cell cycle checkpoints).This
family is based on the phylogenomic analysis of JA Eisen
(1999, Ph.D. Thesis, Stanford University) [DNA
metabolism, DNA replication, recombination, and repair].
Length = 637
Score = 32.6 bits (74), Expect = 0.22
Identities = 30/175 (17%), Positives = 76/175 (43%), Gaps = 27/175 (15%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQKLSIRLQ------------SKYKITEFIEINSHSLFSK 64
R++L+ GP G GK++ K ++++L I++Q + +K+T +E + S+
Sbjct: 111 RILLITGPSGCGKSTTIKILSKELGIQVQEWSNPTLPDFQKNDHKVTLSLESCFSNFQSQ 170
Query: 65 --YFSESGKLVQKMFNKIKEAVEYEESLVCLLIDEIESL----TRARESVMSGTEPSDGV 118
FSE + + + ++ ++ L++++ + TRA ++ S G
Sbjct: 171 IEVFSEFLLRATNKLQMLGDDLMTDKKII--LVEDLPNQFYRDTRALHEILRWKYVSIGR 228
Query: 119 RVVNAVLTQI-------DQLKKKSTGLSGRTLRKIPFLTFVKYISNNSVSMENFL 166
+ ++T+ +L + + + + + P ++ + + M+ FL
Sbjct: 229 CPLVFIITESLEGDNNQRRLLFPAETIMNKEILEEPRVSNISFNPIAPTIMKKFL 283
>gnl|CDD|237745 PRK14527, PRK14527, adenylate kinase; Provisional.
Length = 191
Score = 31.7 bits (72), Expect = 0.22
Identities = 12/31 (38%), Positives = 21/31 (67%)
Query: 13 ISWNRVVLLHGPPGTGKTSLCKAVAQKLSIR 43
+ N+VV+ GPPG GK + + +AQ+L ++
Sbjct: 3 QTKNKVVIFLGPPGAGKGTQAERLAQELGLK 33
>gnl|CDD|223543 COG0467, RAD55, RecA-superfamily ATPases implicated in signal
transduction [Signal transduction mechanisms].
Length = 260
Score = 32.1 bits (73), Expect = 0.23
Identities = 25/116 (21%), Positives = 40/116 (34%), Gaps = 30/116 (25%)
Query: 16 NRVVLLHGPPGTGKTSLCKAVA--------------------QKLSIRLQSKYKITEFIE 55
VVL+ GPPGTGKT + L + + +IE
Sbjct: 23 GSVVLITGPPGTGKTIFALQFLYEGAREGEPVLYVSTEESPEELLENARSFGWDLEVYIE 82
Query: 56 I---------NSHSLFSKYFSESGKLVQKMFNKIKEAVEYEESLVCLLIDEIESLT 102
S ++++ ++I+E VE +E ++ID I LT
Sbjct: 83 KGKLAILDAFLSEKGLVSIVVGDPLDLEELLDRIREIVE-KEGADRVVIDSITELT 137
>gnl|CDD|182791 PRK10865, PRK10865, protein disaggregation chaperone; Provisional.
Length = 857
Score = 32.5 bits (74), Expect = 0.24
Identities = 28/82 (34%), Positives = 40/82 (48%), Gaps = 5/82 (6%)
Query: 20 LLHGPPGTGKTSLCKAVAQKL--SIRLQSKYKITEFIEINSHSLFSKYFSESGKLVQKMF 77
L GP G GKT LCKA+A + S + ++EF+E HS+ + G + +
Sbjct: 602 LFLGPTGVGKTELCKALANFMFDSDDAMVRIDMSEFME--KHSVSRLVGAPPGYVGYEEG 659
Query: 78 NKIKEAVEYEESLVCLLIDEIE 99
+ EAV V LL DE+E
Sbjct: 660 GYLTEAVRRRPYSVILL-DEVE 680
>gnl|CDD|182730 PRK10787, PRK10787, DNA-binding ATP-dependent protease La;
Provisional.
Length = 784
Score = 32.2 bits (73), Expect = 0.25
Identities = 32/101 (31%), Positives = 51/101 (50%), Gaps = 20/101 (19%)
Query: 6 SKVKSNIISWNRVVLLHGPPGTGKTSLCKAVAQ---KLSIRLQSKYKITEFIEINSHSLF 62
+K+K I+ L GPPG GKTSL +++A+ + +R+ + + + EI H
Sbjct: 345 NKIKGPILC------LVGPPGVGKTSLGQSIAKATGRKYVRM-ALGGVRDEAEIRGHR-- 395
Query: 63 SKYF-SESGKLVQKMFNKIKEAVEYEESLVCLLIDEIESLT 102
Y S GKL+QKM V + L L+DEI+ ++
Sbjct: 396 RTYIGSMPGKLIQKM-----AKVGVKNPL--FLLDEIDKMS 429
>gnl|CDD|233959 TIGR02639, ClpA, ATP-dependent Clp protease ATP-binding subunit
clpA. [Protein fate, Degradation of proteins, peptides,
and glycopeptides].
Length = 730
Score = 32.3 bits (74), Expect = 0.25
Identities = 27/87 (31%), Positives = 41/87 (47%), Gaps = 18/87 (20%)
Query: 20 LLHGPPGTGKTSLCKAVAQKLSIRLQSKYKITEFIE-------INSHSLFSKYFSESGKL 72
L GP G GKT L K +A++L + L ++ ++E++E I S + + E G L
Sbjct: 487 LFVGPTGVGKTELAKQLAEELGVHLL-RFDMSEYMEKHTVSRLIGSPPGYVGF--EQGGL 543
Query: 73 VQKMFNKIKEAVEYEESLVCLLIDEIE 99
+ K V LL+DEIE
Sbjct: 544 LTDAVRKHPHCV--------LLLDEIE 562
>gnl|CDD|129128 TIGR00017, cmk, cytidylate kinase. This family consists of
cytidylate kinase, which catalyzes the phosphorylation
of cytidine 5-monophosphate (dCMP) to cytidine 5
-diphosphate (dCDP) in the presence of ATP or GTP. UMP
and dCMP can also act as acceptors [Purines,
pyrimidines, nucleosides, and nucleotides, Nucleotide
and nucleoside interconversions].
Length = 217
Score = 31.6 bits (72), Expect = 0.25
Identities = 11/28 (39%), Positives = 16/28 (57%)
Query: 23 GPPGTGKTSLCKAVAQKLSIRLQSKYKI 50
GP G GK+++ KAVA+KL +
Sbjct: 9 GPSGAGKSTVAKAVAEKLGYAYLDSGAM 36
>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 = 32.1 bits (73), Expect = 0.25
Identities = 14/25 (56%), Positives = 17/25 (68%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQKLS 41
R VLL G PG GK+ L KA+A+ L
Sbjct: 38 RNVLLIGEPGVGKSMLAKAMAELLP 62
>gnl|CDD|183088 PRK11331, PRK11331, 5-methylcytosine-specific restriction enzyme
subunit McrB; Provisional.
Length = 459
Score = 32.0 bits (72), Expect = 0.26
Identities = 22/85 (25%), Positives = 43/85 (50%), Gaps = 5/85 (5%)
Query: 19 VLLHGPPGTGKTSLCKAVAQKLS-IRLQSKYKITEFIEINSHSLFSKYFSESGKLVQK-- 75
++L GPPG GKT + + +A L+ + + + +F + S+ F + + +G ++
Sbjct: 197 IILQGPPGVGKTFVARRLAYLLTGEKAPQRVNMVQFHQSYSYEDFIQGYRPNGVGFRRKD 256
Query: 76 --MFNKIKEAVEYEESLVCLLIDEI 98
+N ++A E E +IDEI
Sbjct: 257 GIFYNFCQQAKEQPEKKYVFIIDEI 281
>gnl|CDD|238548 cd01128, rho_factor, Transcription termination factor rho is a
bacterial ATP-dependent RNA/DNA helicase. It is a
homohexamer. Each monomer consists of an N-terminal
domain of the OB fold, which is responsible for binding
to cysteine rich nucleotides. This alignment is of the
C-terminal ATP binding domain.
Length = 249
Score = 31.9 bits (73), Expect = 0.27
Identities = 31/116 (26%), Positives = 50/116 (43%), Gaps = 18/116 (15%)
Query: 20 LLHGPPGTGKTSLCKAVAQKLSIRLQSKYKI-----------TEFIEINSHSLFSKYFSE 68
L+ PP GKT+L +++A ++ Y I T+ + + F E
Sbjct: 20 LIVAPPKAGKTTLLQSIANAITKNHPEVYLIVLLIDERPEEVTDMQRSVKGEVIASTFDE 79
Query: 69 SG----KLVQKMFNKIKEAVEYEESLVCLLIDEIESLTRARESVM--SGTEPSDGV 118
++ + + K K VE+ + +V LL D I L RA +V+ SG S GV
Sbjct: 80 PPERHVQVAEMVLEKAKRLVEHGKDVVILL-DSITRLARAYNTVVPPSGKILSGGV 134
>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 = 31.6 bits (72), Expect = 0.29
Identities = 29/107 (27%), Positives = 46/107 (42%), Gaps = 14/107 (13%)
Query: 1 MKFSHSKVKSNIISWNRVVLLHGPPGTGKTSLCKAVAQKL-SIRLQSKYKITEFIEINSH 59
K +K++ + ++ G PGTGKT++ + + + + + SK IE+
Sbjct: 29 EKRKEEGLKTSKQVLH--MIFKGNPGTGKTTVARILGKLFKEMNVLSK---GHLIEVERA 83
Query: 60 SLFSKYFSESGKLVQKMFNKIKEAVEYEESLVCLLIDEIESLTRARE 106
L +Y G QK IK+A+ L IDE SL R E
Sbjct: 84 DLVGEYI---GHTAQKTREVIKKALGG-----VLFIDEAYSLARGGE 122
>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 = 31.1 bits (71), Expect = 0.32
Identities = 10/24 (41%), Positives = 16/24 (66%)
Query: 18 VVLLHGPPGTGKTSLCKAVAQKLS 41
+ LL G PGTGK++L +A ++
Sbjct: 35 LTLLAGAPGTGKSTLALDLAAAVA 58
>gnl|CDD|179660 PRK03839, PRK03839, putative kinase; Provisional.
Length = 180
Score = 31.2 bits (71), Expect = 0.32
Identities = 17/67 (25%), Positives = 31/67 (46%), Gaps = 9/67 (13%)
Query: 23 GPPGTGKTSLCKAVAQKLSIRLQSKYKITEFIEINSHSLFSKYFSESGKLVQKMFNKIKE 82
G PG GKT++ K +A+KL E++++ +L E ++ F+K+
Sbjct: 7 GTPGVGKTTVSKLLAEKLGY---------EYVDLTEFALKKGIGEEKDDEMEIDFDKLAY 57
Query: 83 AVEYEES 89
+E E
Sbjct: 58 FIEEEFK 64
>gnl|CDD|178596 PLN03025, PLN03025, replication factor C subunit; Provisional.
Length = 319
Score = 31.6 bits (72), Expect = 0.33
Identities = 15/31 (48%), Positives = 20/31 (64%), Gaps = 3/31 (9%)
Query: 19 VLLHGPPGTGKTSLCKAVAQKLSIRLQSKYK 49
++L GPPGTGKT+ A+A +L L YK
Sbjct: 37 LILSGPPGTGKTTSILALAHEL---LGPNYK 64
>gnl|CDD|234173 TIGR03346, chaperone_ClpB, ATP-dependent chaperone ClpB. Members
of this protein family are the bacterial ATP-dependent
chaperone ClpB. This protein belongs to the AAA family,
ATPases associated with various cellular activities
(pfam00004). This molecular chaperone does not act as a
protease, but rather serves to disaggregate misfolded
and aggregated proteins [Protein fate, Protein folding
and stabilization].
Length = 852
Score = 31.9 bits (73), Expect = 0.34
Identities = 11/18 (61%), Positives = 13/18 (72%)
Query: 23 GPPGTGKTSLCKAVAQKL 40
GP G GKT L KA+A+ L
Sbjct: 602 GPTGVGKTELAKALAEFL 619
>gnl|CDD|140006 PRK13949, PRK13949, shikimate kinase; Provisional.
Length = 169
Score = 30.9 bits (70), Expect = 0.38
Identities = 23/78 (29%), Positives = 38/78 (48%), Gaps = 11/78 (14%)
Query: 19 VLLHGPPGTGKTSLCKAVAQKLSIRLQSKYKITEFIEINSHSLFSKYFSESG-----KLV 73
+ L G G GKT+L KA+A++L + + FIE H F+E G +L
Sbjct: 4 IFLVGYMGAGKTTLGKALARELGLSF---IDLDFFIENRFHKTVGDIFAERGEAVFRELE 60
Query: 74 QKMFNKIKEAVEYEESLV 91
+ M + E E+E+ ++
Sbjct: 61 RNM---LHEVAEFEDVVI 75
>gnl|CDD|213190 cd03223, ABCD_peroxisomal_ALDP, ATP-binding cassette domain of
peroxisomal transporter, subfamily D. Peroxisomal
ATP-binding cassette transporter (Pat) is involved in
the import of very long-chain fatty acids (VLCFA) into
the peroxisome. The peroxisomal membrane forms a
permeability barrier for a wide variety of metabolites
required for and formed during fatty acid
beta-oxidation. To communicate with the cytoplasm and
mitochondria, peroxisomes need dedicated proteins to
transport such hydrophilic molecules across their
membranes. X-linked adrenoleukodystrophy (X-ALD) is
caused by mutations in the ALD gene, which encodes ALDP
(adrenoleukodystrophy protein ), a peroxisomal integral
membrane protein that is a member of the ATP-binding
cassette (ABC) transporter protein family. The disease
is characterized by a striking and unpredictable
variation in phenotypic expression. Phenotypes include
the rapidly progressive childhood cerebral form
(CCALD), the milder adult form, adrenomyeloneuropathy
(AMN), and variants without neurologic involvement
(i.e. asymptomatic).
Length = 166
Score = 30.6 bits (70), Expect = 0.44
Identities = 11/19 (57%), Positives = 16/19 (84%)
Query: 19 VLLHGPPGTGKTSLCKAVA 37
+L+ GP GTGK+SL +A+A
Sbjct: 30 LLITGPSGTGKSSLFRALA 48
>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 = 31.3 bits (71), Expect = 0.44
Identities = 15/37 (40%), Positives = 20/37 (54%), Gaps = 3/37 (8%)
Query: 7 KVKSNIISW---NRVVLLHGPPGTGKTSLCKAVAQKL 40
+V S + + V L GP GTGKT+L VA+K
Sbjct: 9 RVTSRALRYLKSGYPVHLRGPAGTGKTTLAMHVARKR 45
>gnl|CDD|213200 cd03233, ABCG_PDR_domain1, First domain of the pleiotropic drug
resistance-like subfamily G of ATP-binding cassette
transporters. The pleiotropic drug resistance (PDR) is
a well-described phenomenon occurring in fungi and
shares several similarities with processes in bacteria
and higher eukaryotes. This PDR subfamily represents
domain I of its (ABC-IM)2 organization. ABC
transporters are a large family of proteins involved in
the transport of a wide variety of different compounds
including 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 = 202
Score = 30.7 bits (70), Expect = 0.44
Identities = 15/53 (28%), Positives = 25/53 (47%), Gaps = 1/53 (1%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQKLSIRLQSKYKITEFIEINSHSLFSKYFSES 69
+VL+ G PG+G ++L KA+A + + + I + I KY E
Sbjct: 34 EMVLVLGRPGSGCSTLLKALANRTEGNVSVEGDIH-YNGIPYKEFAEKYPGEI 85
>gnl|CDD|240274 PTZ00112, PTZ00112, origin recognition complex 1 protein;
Provisional.
Length = 1164
Score = 31.5 bits (71), Expect = 0.46
Identities = 30/113 (26%), Positives = 56/113 (49%), Gaps = 23/113 (20%)
Query: 16 NRVVLLHGPPGTGKTSLCKAVAQKLSIRLQSKYKITEF--IEINSHS----------LFS 63
N+++ + G PGTGKT+ +V Q L + + K + F EIN + L+
Sbjct: 781 NQILYISGMPGTGKTATVYSVIQLLQHKTKQKL-LPSFNVFEINGMNVVHPNAAYQVLYK 839
Query: 64 KYFSE-------SGKLVQKMFNKIKEAVEYEESLVCLLIDEIESLTRARESVM 109
+ F++ S K++ ++FN+ K+ ++ L+IDEI+ L + V+
Sbjct: 840 QLFNKKPPNALNSFKILDRLFNQNKKD---NRNVSILIIDEIDYLITKTQKVL 889
>gnl|CDD|182937 PRK11061, PRK11061, fused phosphoenolpyruvate-protein
phosphotransferase PtsP/GAF domain; Provisional.
Length = 748
Score = 31.5 bits (72), Expect = 0.48
Identities = 15/34 (44%), Positives = 20/34 (58%), Gaps = 2/34 (5%)
Query: 174 LDLLVEEKSLPLKRNTEVPNTYLHSNQRIHIYLM 207
LD+LV E L + +TEV + YL + R YLM
Sbjct: 22 LDILVTETCLAM--DTEVCSVYLADHDRRCYYLM 53
>gnl|CDD|224768 COG1855, COG1855, ATPase (PilT family) [General function prediction
only].
Length = 604
Score = 31.2 bits (71), Expect = 0.49
Identities = 10/32 (31%), Positives = 19/32 (59%)
Query: 7 KVKSNIISWNRVVLLHGPPGTGKTSLCKAVAQ 38
K+K + +L+ G PG GK++ +A+A+
Sbjct: 254 KLKERLEERAEGILIAGAPGAGKSTFAQALAE 285
>gnl|CDD|179157 PRK00889, PRK00889, adenylylsulfate kinase; Provisional.
Length = 175
Score = 30.4 bits (69), Expect = 0.50
Identities = 10/27 (37%), Positives = 15/27 (55%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQKLSIR 43
V G G GKT++ +A+A+KL
Sbjct: 5 VTVWFTGLSGAGKTTIARALAEKLREA 31
>gnl|CDD|129254 TIGR00150, T6A_YjeE, tRNA threonylcarbamoyl adenosine
modification protein YjeE. This protein family belongs
to a four-gene system responsible for the
threonylcarbamoyl adenosine (t6A) tRNA modification.
Members of this family have a conserved
nucleotide-binding motif GXXGXGKT and a
nucleotide-binding fold. Member protein YjeE of
Haemophilus influenzae (HI0065) was shown to have
(weak) ATPase activity [Protein synthesis, tRNA and
rRNA base modification].
Length = 133
Score = 30.1 bits (68), Expect = 0.51
Identities = 13/30 (43%), Positives = 17/30 (56%)
Query: 18 VVLLHGPPGTGKTSLCKAVAQKLSIRLQSK 47
VVLL G G GKT+L + + Q L I+
Sbjct: 24 VVLLKGDLGAGKTTLVQGLLQGLGIQGNVT 53
>gnl|CDD|223616 COG0542, clpA, ATP-binding subunits of Clp protease and DnaK/DnaJ
chaperones [Posttranslational modification, protein
turnover, chaperones].
Length = 786
Score = 31.5 bits (72), Expect = 0.53
Identities = 32/93 (34%), Positives = 44/93 (47%), Gaps = 23/93 (24%)
Query: 18 VVLLHGPPGTGKTSLCKAVAQKLSIRLQSKYKI--TEFIEINSHSLFSK-------Y--F 66
L GP G GKT L KA+A+ L Q+ +I +E++E +S S+ Y +
Sbjct: 523 SFLFLGPTGVGKTELAKALAEALFGDEQALIRIDMSEYMEKHS---VSRLIGAPPGYVGY 579
Query: 67 SESGKLVQKMFNKIKEAVEYEESLVCLLIDEIE 99
E G+L EAV + V LL DEIE
Sbjct: 580 EEGGQL--------TEAVRRKPYSVILL-DEIE 603
>gnl|CDD|183452 PRK12337, PRK12337, 2-phosphoglycerate kinase; Provisional.
Length = 475
Score = 31.3 bits (71), Expect = 0.54
Identities = 11/25 (44%), Positives = 15/25 (60%)
Query: 18 VVLLHGPPGTGKTSLCKAVAQKLSI 42
VL+ G G GK+ L A+A +L I
Sbjct: 257 HVLIGGVSGVGKSVLASALAYRLGI 281
>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 = 30.5 bits (69), Expect = 0.55
Identities = 23/109 (21%), Positives = 41/109 (37%), Gaps = 24/109 (22%)
Query: 17 RVVL-LHGPPGTGKTSLCKAVAQKLSIRLQ----------SKYKITEFIEINSHSLFSKY 65
V ++GPPGTGKT++ +A + + + + S + + S
Sbjct: 19 GTVTQVYGPPGTGKTNIAIQLAVETAGQGKKVAYIDTEGLSSERFRQIAGDRPERAASSI 78
Query: 66 -------FSESGKLVQKMFNKIKEAVEYEESLVCLLIDEIESLTRARES 107
F+E G+ +Q+ E V LV ++D +L R
Sbjct: 79 IVFEPMDFNEQGRAIQETETFADEKV----DLV--VVDSATALYRLELG 121
>gnl|CDD|216202 pfam00931, NB-ARC, NB-ARC domain.
Length = 285
Score = 30.8 bits (70), Expect = 0.55
Identities = 10/26 (38%), Positives = 14/26 (53%)
Query: 18 VVLLHGPPGTGKTSLCKAVAQKLSIR 43
VV + G G GKT+L K + S+
Sbjct: 21 VVGIVGMGGVGKTTLAKQIYNDDSVG 46
>gnl|CDD|224025 COG1100, COG1100, GTPase SAR1 and related small G proteins
[General function prediction only].
Length = 219
Score = 30.7 bits (69), Expect = 0.56
Identities = 6/47 (12%), Positives = 11/47 (23%)
Query: 19 VLLHGPPGTGKTSLCKAVAQKLSIRLQSKYKITEFIEINSHSLFSKY 65
+++ G G GKT+L +
Sbjct: 8 IVVLGDGGVGKTTLLNRLVGDEFPEGYPPTIGNLDPAKTIEPYRRNI 54
>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 = 30.3 bits (69), Expect = 0.58
Identities = 10/21 (47%), Positives = 12/21 (57%)
Query: 20 LLHGPPGTGKTSLCKAVAQKL 40
L GP G GK L A+A+ L
Sbjct: 18 LFAGPEGVGKELLALALAKAL 38
>gnl|CDD|226646 COG4178, COG4178, ABC-type uncharacterized transport system,
permease and ATPase components [General function
prediction only].
Length = 604
Score = 31.1 bits (71), Expect = 0.59
Identities = 10/19 (52%), Positives = 14/19 (73%)
Query: 19 VLLHGPPGTGKTSLCKAVA 37
+L+ G G GKTSL +A+A
Sbjct: 422 LLITGESGAGKTSLLRALA 440
>gnl|CDD|224533 COG1618, COG1618, Predicted nucleotide kinase [Nucleotide
transport and metabolism].
Length = 179
Score = 30.4 bits (69), Expect = 0.60
Identities = 10/23 (43%), Positives = 15/23 (65%)
Query: 19 VLLHGPPGTGKTSLCKAVAQKLS 41
+ + G PG GKT+L +A+KL
Sbjct: 8 IFITGRPGVGKTTLVLKIAEKLR 30
>gnl|CDD|224140 COG1219, ClpX, ATP-dependent protease Clp, ATPase subunit
[Posttranslational modification, protein turnover,
chaperones].
Length = 408
Score = 31.0 bits (71), Expect = 0.62
Identities = 15/32 (46%), Positives = 19/32 (59%), Gaps = 7/32 (21%)
Query: 9 KSNIISWNRVVLLHGPPGTGKTSLCKAVAQKL 40
KSNI LL GP G+GKT L + +A+ L
Sbjct: 97 KSNI-------LLIGPTGSGKTLLAQTLAKIL 121
>gnl|CDD|182778 PRK10851, PRK10851, sulfate/thiosulfate transporter subunit;
Provisional.
Length = 353
Score = 30.8 bits (70), Expect = 0.66
Identities = 14/38 (36%), Positives = 24/38 (63%), Gaps = 3/38 (7%)
Query: 3 FSHSKVKSNI---ISWNRVVLLHGPPGTGKTSLCKAVA 37
F ++V ++I I ++V L GP G+GKT+L + +A
Sbjct: 12 FGRTQVLNDISLDIPSGQMVALLGPSGSGKTTLLRIIA 49
>gnl|CDD|178991 PRK00373, PRK00373, V-type ATP synthase subunit D; Reviewed.
Length = 204
Score = 30.2 bits (69), Expect = 0.67
Identities = 15/43 (34%), Positives = 24/43 (55%), Gaps = 2/43 (4%)
Query: 63 SKYFSESGKLVQKMFNKIKEAVEYEESLVCLLIDEIESLTRAR 105
S E+ + +++ KI E E E+++ LL DEIE T+ R
Sbjct: 125 SAELDEAAEKFEELLEKILELAEVEKTIQ-LLADEIEK-TKRR 165
>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 = 28.5 bits (64), Expect = 0.68
Identities = 11/58 (18%), Positives = 28/58 (48%), Gaps = 3/58 (5%)
Query: 18 VVLLHGPPGTGKTSLCKAVAQKLSIRLQSKYKITEFIEIN-SHSLFSKYFSESGKLVQ 74
++ + G G+GK+++ K +A++L R S + E + + ++ + + L
Sbjct: 1 IIAITGGSGSGKSTVAKKLAEQLGGR--SVVVLDEIVILEGLYASYKSRDARIRDLAD 56
>gnl|CDD|224847 COG1936, COG1936, Predicted nucleotide kinase (related to CMP and
AMP kinases) [Nucleotide transport and metabolism].
Length = 180
Score = 30.0 bits (68), Expect = 0.70
Identities = 8/19 (42%), Positives = 13/19 (68%)
Query: 19 VLLHGPPGTGKTSLCKAVA 37
+ + G PG GKT++CK +
Sbjct: 3 IAITGTPGVGKTTVCKLLR 21
>gnl|CDD|235281 PRK04328, PRK04328, hypothetical protein; Provisional.
Length = 249
Score = 30.4 bits (69), Expect = 0.77
Identities = 10/17 (58%), Positives = 12/17 (70%)
Query: 18 VVLLHGPPGTGKTSLCK 34
VVLL G PGTGK+ +
Sbjct: 25 VVLLSGGPGTGKSIFSQ 41
>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 = 29.9 bits (68), Expect = 0.81
Identities = 17/71 (23%), Positives = 34/71 (47%), Gaps = 10/71 (14%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQKLS----IRL---QSKYKITEFIEINSH--SLFSKYFS 67
VLL G PG GKT L +A+ ++L +R+ + + ++ E+ S+
Sbjct: 13 VAVLLGGQPGAGKTELARALLEELGGGNVVRIDPDELRTYHPDYDELQKADPKDASELTQ 72
Query: 68 -ESGKLVQKMF 77
++ + V+K+
Sbjct: 73 PDASRWVEKLI 83
>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 = 30.5 bits (69), Expect = 0.88
Identities = 36/127 (28%), Positives = 61/127 (48%), Gaps = 28/127 (22%)
Query: 9 KSNIISWNRVVLLHGPPGTGKTSLCKAVAQKLSIRLQSKYKITEFIEINSHSLFSKYFSE 68
KSNI LL GP G+GKT L + +A+ L++ F ++ +L +E
Sbjct: 116 KSNI-------LLIGPTGSGKTLLAQTLARILNV---------PFAIADATTL-----TE 154
Query: 69 SGKL---VQKMFNKIKEAVEYEESLV---CLLIDEIESLTRARESVMSGTEPSDGVRVVN 122
+G + V+ + K+ +A +Y+ + IDEI+ ++R E+ S T G V
Sbjct: 155 AGYVGEDVENILLKLLQAADYDVEKAQKGIIYIDEIDKISRKSENP-SITRDVSGEGVQQ 213
Query: 123 AVLTQID 129
A+L I+
Sbjct: 214 ALLKIIE 220
>gnl|CDD|206669 cd01882, BMS1, Bms1, an essential GTPase, promotes assembly of
preribosomal RNA processing complexes. Bms1 is an
essential, evolutionarily conserved, nucleolar protein.
Its depletion interferes with processing of the 35S
pre-rRNA at sites A0, A1, and A2, and the formation of
40S subunits. Bms1, the putative endonuclease Rc11, and
the essential U3 small nucleolar RNA form a stable
subcomplex that is believed to control an early step in
the formation of the 40S subumit. The C-terminal domain
of Bms1 contains a GTPase-activating protein (GAP) that
functions intramolecularly. It is believed that Rc11
activates Bms1 by acting as a guanine-nucleotide
exchange factor (GEF) to promote GDP/GTP exchange, and
that activated (GTP-bound) Bms1 delivers Rc11 to the
preribosomes.
Length = 231
Score = 30.0 bits (68), Expect = 0.96
Identities = 38/136 (27%), Positives = 59/136 (43%), Gaps = 30/136 (22%)
Query: 18 VVLLHGPPGTGKTSLCKAVAQKLSIRLQSKYKITEF---IEINSHSLFSKYFSESGKLVQ 74
VV++ GPPG GK++L +++ I+ +K +++ I I + F E +
Sbjct: 41 VVVVVGPPGVGKSTLIRSL-----IKRYTKQNLSDIKGPITIVTGKKRRLTFIECPNDIN 95
Query: 75 KMFNKIKEAVEYEESLVCLLID-----EIESLTRARESVMSGTEPSDGVRVVNAVLTQID 129
M + K A LV LLID E+E+ E + G V VLT +D
Sbjct: 96 SMIDVAKIA-----DLVLLLIDGSYGFEMETF----EFL--NILQVHGFPKVMGVLTHLD 144
Query: 130 QLKKKSTGLSGRTLRK 145
+ K +TLRK
Sbjct: 145 KFKN------NKTLRK 154
>gnl|CDD|223455 COG0378, HypB, Ni2+-binding GTPase involved in regulation of
expression and maturation of urease and hydrogenase
[Posttranslational modification, protein turnover,
chaperones / Transcription].
Length = 202
Score = 29.9 bits (68), Expect = 0.97
Identities = 10/30 (33%), Positives = 17/30 (56%), Gaps = 4/30 (13%)
Query: 17 RVVLLHGPPGTGKTSL----CKAVAQKLSI 42
+ + GPPG+GKT+L +A+ + I
Sbjct: 14 LRIGVGGPPGSGKTALIEKTLRALKDEYKI 43
>gnl|CDD|225327 COG2607, COG2607, Predicted ATPase (AAA+ superfamily) [General
function prediction only].
Length = 287
Score = 30.0 bits (68), Expect = 1.0
Identities = 12/18 (66%), Positives = 14/18 (77%)
Query: 19 VLLHGPPGTGKTSLCKAV 36
VLL G GTGK+SL KA+
Sbjct: 88 VLLWGARGTGKSSLVKAL 105
>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 = 30.6 bits (69), Expect = 1.0
Identities = 12/24 (50%), Positives = 16/24 (66%)
Query: 20 LLHGPPGTGKTSLCKAVAQKLSIR 43
L+HGPPGTGKT + ++L R
Sbjct: 177 LIHGPPGTGKTRTLVELIRQLVKR 200
>gnl|CDD|110677 pfam01695, IstB_IS21, IstB-like ATP binding protein. This
protein contains an ATP/GTP binding P-loop motif. It is
found associated with IS21 family insertion sequences.
The function of this protein is unknown, but it may
perform a transposase function.
Length = 178
Score = 29.5 bits (67), Expect = 1.0
Identities = 11/21 (52%), Positives = 14/21 (66%)
Query: 19 VLLHGPPGTGKTSLCKAVAQK 39
+LL GPPG GKT L A+ +
Sbjct: 50 LLLLGPPGVGKTHLACALGHQ 70
>gnl|CDD|223645 COG0572, Udk, Uridine kinase [Nucleotide transport and
metabolism].
Length = 218
Score = 29.9 bits (68), Expect = 1.1
Identities = 12/53 (22%), Positives = 24/53 (45%), Gaps = 12/53 (22%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQKLS------------IRLQSKYKITEFIEIN 57
++ + G G+GKT++ K ++++L + QS E +IN
Sbjct: 9 IIIGIAGGSGSGKTTVAKELSEQLGVEKVVVISLDDYYKDQSHLPFEERNKIN 61
>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 = 29.8 bits (68), Expect = 1.1
Identities = 10/17 (58%), Positives = 13/17 (76%)
Query: 19 VLLHGPPGTGKTSLCKA 35
+L+ GPPG+GKT L K
Sbjct: 25 LLMIGPPGSGKTMLAKR 41
>gnl|CDD|105491 PRK12269, PRK12269, bifunctional cytidylate kinase/ribosomal
protein S1; Provisional.
Length = 863
Score = 30.5 bits (68), Expect = 1.1
Identities = 10/23 (43%), Positives = 18/23 (78%)
Query: 18 VVLLHGPPGTGKTSLCKAVAQKL 40
++ L GP G+GK+S+C+ +A +L
Sbjct: 36 IIALDGPAGSGKSSVCRLLASRL 58
>gnl|CDD|236982 PRK11784, PRK11784, tRNA 2-selenouridine synthase; Provisional.
Length = 345
Score = 30.2 bits (69), Expect = 1.1
Identities = 10/23 (43%), Positives = 15/23 (65%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQK 39
+V+L G G+GKT L +A+A
Sbjct: 142 PLVVLGGNTGSGKTELLQALANA 164
>gnl|CDD|238985 cd02027, APSK, Adenosine 5'-phosphosulfate kinase (APSK)
catalyzes the phosphorylation of adenosine
5'-phosphosulfate to form 3'-phosphoadenosine
5'-phosphosulfate (PAPS). The end-product PAPS is a
biologically "activated" sulfate form important for the
assimilation of inorganic sulfate.
Length = 149
Score = 29.4 bits (67), Expect = 1.2
Identities = 9/23 (39%), Positives = 17/23 (73%)
Query: 18 VVLLHGPPGTGKTSLCKAVAQKL 40
V+ L G G+GK+++ +A+ +KL
Sbjct: 1 VIWLTGLSGSGKSTIARALEEKL 23
>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 = 29.8 bits (67), Expect = 1.2
Identities = 11/24 (45%), Positives = 18/24 (75%)
Query: 18 VVLLHGPPGTGKTSLCKAVAQKLS 41
+++L G PG GK++ K +A+KLS
Sbjct: 1 LIILTGLPGVGKSTFSKELAKKLS 24
>gnl|CDD|144046 pfam00308, Bac_DnaA, Bacterial dnaA protein.
Length = 219
Score = 29.6 bits (67), Expect = 1.2
Identities = 20/90 (22%), Positives = 34/90 (37%), Gaps = 20/90 (22%)
Query: 19 VLLHGPPGTGKTSLCKAVAQKLSIRLQSKYKITEFIEINSHSLFSKYFSESGKLVQKMF- 77
+ ++G G GKT L A+ N +L Y + S + +
Sbjct: 37 LFIYGGVGLGKTHLLHAIGNY--------------ALRNFPNLRVVYLT-SEEFLNDFVD 81
Query: 78 ----NKIKEAVEYEESLVCLLIDEIESLTR 103
NKI+ + ++ LLID+I+ L
Sbjct: 82 ALRDNKIEAFKKSYRNVDLLLIDDIQFLAG 111
>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 = 30.0 bits (68), Expect = 1.2
Identities = 10/20 (50%), Positives = 14/20 (70%)
Query: 19 VLLHGPPGTGKTSLCKAVAQ 38
V +GP TGKT+L +A+A
Sbjct: 116 VWFYGPASTGKTNLAQAIAH 135
>gnl|CDD|227519 COG5192, BMS1, GTP-binding protein required for 40S ribosome
biogenesis [Translation, ribosomal structure and
biogenesis].
Length = 1077
Score = 30.1 bits (67), Expect = 1.3
Identities = 41/141 (29%), Positives = 61/141 (43%), Gaps = 24/141 (17%)
Query: 18 VVLLHGPPGTGKTSLCKAVAQKLSIRLQSKYKITEF---IEINSHSLFSKYFSESGKLVQ 74
+V + GPPGTGK++L +++ +R +K I E I + S F E +
Sbjct: 71 IVAVVGPPGTGKSTLIRSL-----VRRFTKQTIDEIRGPITVVSGKTRRITFLECPSDLH 125
Query: 75 KMFNKIKEAVEYEESLVCLLID-----EIESLTRARESVMSGTEPSDGVRVVNAVLTQID 129
+M + K A LV LLID E+E++ S G+ V V+T +D
Sbjct: 126 QMIDVAKIA-----DLVLLLIDGNFGFEMETME------FLNILISHGMPRVLGVVTHLD 174
Query: 130 QLKKKSTGLSGRTLRKIPFLT 150
K ST S + K F T
Sbjct: 175 LFKNPSTLRSIKKRLKHRFWT 195
>gnl|CDD|226573 COG4088, COG4088, Predicted nucleotide kinase [Nucleotide
transport and metabolism].
Length = 261
Score = 29.8 bits (67), Expect = 1.3
Identities = 13/41 (31%), Positives = 22/41 (53%), Gaps = 6/41 (14%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQKLS------IRLQSKYKIT 51
+++L G PG+GKT+ K +A++L I L+ Y
Sbjct: 2 PLIILTGYPGSGKTTFAKELAKELRQEIWRVIHLEKDYLRG 42
>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 = 29.5 bits (67), Expect = 1.3
Identities = 11/19 (57%), Positives = 12/19 (63%)
Query: 16 NRVVLLHGPPGTGKTSLCK 34
RVVL+ G PGTGKT
Sbjct: 19 GRVVLITGGPGTGKTIFGL 37
>gnl|CDD|234340 TIGR03744, traC_PFL_4706, conjugative transfer ATPase, PFL_4706
family. Members of this protein family are predicted
ATP-binding proteins apparently associated with DNA
conjugal transfer. Members are found both in plasmids
and in bacterial chromosomal regions that appear to
derive from integrative elements such as conjugative
transposons. More distant homologs, outside the scope of
this family, include type IV secretion/conjugal transfer
proteins such as TraC, VirB4 and TrsE. The granularity
of this protein family definition is chosen so as to
represent one distinctive clade and act as a marker
through which to define and recognize the class of
mobile element it serves [Mobile and extrachromosomal
element functions, Plasmid functions].
Length = 893
Score = 30.0 bits (68), Expect = 1.3
Identities = 22/77 (28%), Positives = 33/77 (42%), Gaps = 18/77 (23%)
Query: 20 LLHGPPGTGKT-SLCKAVAQKLSI---RLQSKYKITEFI-EI-NSHSLFSKYFSESGKLV 73
L+ GP G GK+ +L + Q +++ RL FI E NS L + Y + G V
Sbjct: 479 LILGPTGAGKSATLTNLLMQVMAVHRPRL--------FIVEAGNSFGLLADYAARLGLSV 530
Query: 74 QKMFNKIKEAVEYEESL 90
N++ SL
Sbjct: 531 ----NRVSLKPGSGVSL 543
>gnl|CDD|224930 COG2019, AdkA, Archaeal adenylate kinase [Nucleotide transport
and metabolism].
Length = 189
Score = 29.3 bits (66), Expect = 1.3
Identities = 10/24 (41%), Positives = 17/24 (70%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQKL 40
+VV++ G PG GKT++ K ++L
Sbjct: 5 KVVVITGVPGVGKTTVLKIALKEL 28
>gnl|CDD|234711 PRK00279, adk, adenylate kinase; Reviewed.
Length = 215
Score = 29.3 bits (67), Expect = 1.4
Identities = 13/26 (50%), Positives = 18/26 (69%), Gaps = 1/26 (3%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQKLSI 42
R++LL GPPG GK + K +A+K I
Sbjct: 2 RLILL-GPPGAGKGTQAKFIAEKYGI 26
>gnl|CDD|181235 PRK08118, PRK08118, topology modulation protein; Reviewed.
Length = 167
Score = 29.2 bits (66), Expect = 1.4
Identities = 9/29 (31%), Positives = 21/29 (72%), Gaps = 1/29 (3%)
Query: 16 NRVVLLHGPPGTGKTSLCKAVAQKLSIRL 44
+++L+ G G+GK++L + + +KL+I +
Sbjct: 2 KKIILI-GSGGSGKSTLARQLGEKLNIPV 29
>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 = 29.8 bits (67), Expect = 1.4
Identities = 11/44 (25%), Positives = 24/44 (54%), Gaps = 1/44 (2%)
Query: 19 VLLHGPPGTGKTSLCKAVAQKLSIRLQSKYKI-TEFIEINSHSL 61
++L+GPPG GKT+ + ++ + + F+E++ +L
Sbjct: 178 IILYGPPGVGKTTAARLALEEAKKLKHTPFAEDAPFVEVDGTTL 221
>gnl|CDD|184311 PRK13764, PRK13764, ATPase; Provisional.
Length = 602
Score = 29.8 bits (68), Expect = 1.4
Identities = 14/51 (27%), Positives = 23/51 (45%), Gaps = 4/51 (7%)
Query: 5 HSKVKSNIISWNRVVLLHGPPGTGKTSLCKAVAQKLSIRLQSKYKITEFIE 55
K+K + +L+ G PG GK++ AQ L+ KI + +E
Sbjct: 246 SEKLKERLEERAEGILIAGAPGAGKSTF----AQALAEFYADMGKIVKTME 292
>gnl|CDD|227596 COG5271, MDN1, AAA ATPase containing von Willebrand factor type A
(vWA) domain [General function prediction only].
Length = 4600
Score = 30.0 bits (67), Expect = 1.5
Identities = 12/41 (29%), Positives = 22/41 (53%), Gaps = 9/41 (21%)
Query: 19 VLLHGPPGTGKTSLCKAVAQKLSIRLQSKYKITEFIEINSH 59
+L+ GP +GKTS+ +A++ + F+ IN+H
Sbjct: 891 LLIQGPTSSGKTSMILYLARETGHK---------FVRINNH 922
Score = 29.6 bits (66), Expect = 2.2
Identities = 14/28 (50%), Positives = 19/28 (67%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQKLSIRL 44
+ +LL G PG GKTSL A+A+K +L
Sbjct: 1544 KPILLEGSPGVGKTSLITALARKTGKKL 1571
>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 = 29.3 bits (66), Expect = 1.5
Identities = 10/17 (58%), Positives = 12/17 (70%)
Query: 18 VVLLHGPPGTGKTSLCK 34
VVLL G PGTGK+ +
Sbjct: 23 VVLLSGGPGTGKSIFSQ 39
>gnl|CDD|226415 COG3899, COG3899, Predicted ATPase [General function prediction
only].
Length = 849
Score = 30.1 bits (68), Expect = 1.5
Identities = 30/136 (22%), Positives = 47/136 (34%), Gaps = 18/136 (13%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQKLSIRLQSKYKITEFIE---INS---------HSLFSK 64
VVL+ G G GK++L V + I Q Y I + N L +
Sbjct: 25 EVVLVAGESGIGKSALVNEVHKP--ITQQRGYFIKGKFDQFERNIPLSPLVQAFRDLMGQ 82
Query: 65 YFSESGKLVQKMFNKIKEAVEYEESLVCLLIDEIESLTRARESV--MSGTEPSDGVRVVN 122
SES + ++ A+ ++ +I E+E + R +S T R
Sbjct: 83 LLSESDTRILSWRARLLAALGENGQVIIDVIPELELIIGKRPPALELSPTAAQ--NRFNL 140
Query: 123 AVLTQIDQLKKKSTGL 138
A L I + L
Sbjct: 141 AFLRFIQVFTAEEHPL 156
>gnl|CDD|223603 COG0529, CysC, Adenylylsulfate kinase and related kinases
[Inorganic ion transport and metabolism].
Length = 197
Score = 29.2 bits (66), Expect = 1.5
Identities = 8/24 (33%), Positives = 15/24 (62%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQKL 40
V+ G G+GK+++ A+ +KL
Sbjct: 24 AVIWFTGLSGSGKSTIANALEEKL 47
>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 = 29.2 bits (66), Expect = 1.5
Identities = 9/16 (56%), Positives = 10/16 (62%)
Query: 18 VVLLHGPPGTGKTSLC 33
LL G PGTGKT+
Sbjct: 1 STLLSGGPGTGKTTFA 16
>gnl|CDD|215451 PLN02840, PLN02840, tRNA dimethylallyltransferase.
Length = 421
Score = 29.8 bits (67), Expect = 1.6
Identities = 9/26 (34%), Positives = 18/26 (69%)
Query: 16 NRVVLLHGPPGTGKTSLCKAVAQKLS 41
+V+++ GP G GK+ L +A++L+
Sbjct: 21 EKVIVISGPTGAGKSRLALELAKRLN 46
>gnl|CDD|116541 pfam07931, CPT, Chloramphenicol phosphotransferase-like protein.
The members of this family are all similar to
chloramphenicol 3-O phosphotransferase (CPT) expressed
by Streptomyces venezuelae. Chloramphenicol (Cm) is a
metabolite produced by this bacterium that can inhibit
ribosomal peptidyl transferase activity and therefore
protein production. By transferring a phosphate group
to the C-3 hydroxyl group of Cm, CPT inactivates this
potentially lethal metabolite.
Length = 174
Score = 28.9 bits (65), Expect = 1.6
Identities = 9/25 (36%), Positives = 18/25 (72%), Gaps = 1/25 (4%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQKLS 41
R++LL+G +GK+S+ +A+ Q +
Sbjct: 2 RIILLNGGSSSGKSSIARAL-QDIL 25
>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 = 29.5 bits (67), Expect = 1.6
Identities = 9/23 (39%), Positives = 14/23 (60%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQK 39
+++L G G+GKT L A+A
Sbjct: 128 PLIVLGGMTGSGKTELLHALANA 150
>gnl|CDD|237864 PRK14950, PRK14950, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 585
Score = 29.8 bits (67), Expect = 1.7
Identities = 16/33 (48%), Positives = 17/33 (51%), Gaps = 7/33 (21%)
Query: 11 NIISWNRVV---LLHGPPGTGKTS----LCKAV 36
N I+ RV L GP G GKTS L KAV
Sbjct: 30 NAIAEGRVAHAYLFTGPRGVGKTSTARILAKAV 62
>gnl|CDD|213188 cd03221, ABCF_EF-3, ATP-binding cassette domain of elongation
factor 3, subfamily F. Elongation factor 3 (EF-3) is a
cytosolic protein required by fungal ribosomes for in
vitro protein synthesis and for in vivo growth. EF-3
stimulates the binding of the EF-1: GTP: aa-tRNA
ternary complex to the ribosomal A site by facilitated
release of the deacylated tRNA from the E site. The
reaction requires ATP hydrolysis. EF-3 contains two ATP
nucleotide binding sequence (NBS) motifs. NBSI is
sufficient for the intrinsic ATPase activity. NBSII is
essential for the ribosome-stimulated functions.
Length = 144
Score = 28.6 bits (65), Expect = 1.7
Identities = 13/39 (33%), Positives = 20/39 (51%), Gaps = 6/39 (15%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQKL-----SIRLQSKYKI 50
R+ L+ G G GK++L K +A +L + S KI
Sbjct: 28 RIGLV-GRNGAGKSTLLKLIAGELEPDEGIVTWGSTVKI 65
>gnl|CDD|224160 COG1239, ChlI, Mg-chelatase subunit ChlI [Coenzyme metabolism].
Length = 423
Score = 29.7 bits (67), Expect = 1.7
Identities = 8/19 (42%), Positives = 13/19 (68%)
Query: 19 VLLHGPPGTGKTSLCKAVA 37
L+ G GT K++L +A+A
Sbjct: 41 ALIAGEKGTAKSTLARALA 59
>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 = 29.7 bits (67), Expect = 1.7
Identities = 17/53 (32%), Positives = 29/53 (54%), Gaps = 4/53 (7%)
Query: 19 VLLHGPPGTGKTSLCKAVAQKLSIRLQSKYK-ITEFIEINSHSLFSKYFSESG 70
V+++GPPG GKT+ + V ++ S +K F+EI++ + F E G
Sbjct: 89 VIIYGPPGVGKTAAARLVLEEAKKNPASPFKEGAAFVEIDATTA---RFDERG 138
>gnl|CDD|237150 PRK12608, PRK12608, transcription termination factor Rho;
Provisional.
Length = 380
Score = 29.3 bits (66), Expect = 1.8
Identities = 25/116 (21%), Positives = 49/116 (42%), Gaps = 18/116 (15%)
Query: 20 LLHGPPGTGKTSLCKAVAQKLS-----IRL------QSKYKITEFIEINSHSLFSKYFSE 68
L+ PP GKT L + +A ++ + L + ++T+ +++ F
Sbjct: 137 LIVAPPRAGKTVLLQQIAAAVAANHPEVHLMVLLIDERPEEVTDMRRSVKGEVYASTFDR 196
Query: 69 SGK----LVQKMFNKIKEAVEYEESLVCLLIDEIESLTRARESVM--SGTEPSDGV 118
+ + + + K VE + +V +L+D + L RA + + SG S GV
Sbjct: 197 PPDEHIRVAELVLERAKRLVEQGKDVV-ILLDSLTRLARAYNNEVESSGRTLSGGV 251
>gnl|CDD|233208 TIGR00956, 3a01205, Pleiotropic Drug Resistance (PDR) Family
protein. [Transport and binding proteins, Other].
Length = 1394
Score = 29.7 bits (67), Expect = 1.8
Identities = 8/31 (25%), Positives = 16/31 (51%)
Query: 10 SNIISWNRVVLLHGPPGTGKTSLCKAVAQKL 40
+I + ++ G PG+G ++L K +A
Sbjct: 81 DGLIKPGELTVVLGRPGSGCSTLLKTIASNT 111
>gnl|CDD|217424 pfam03205, MobB, Molybdopterin guanine dinucleotide synthesis
protein B. This protein contains a P-loop.
Length = 126
Score = 28.5 bits (64), Expect = 1.9
Identities = 10/27 (37%), Positives = 16/27 (59%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQKLSIR 43
+VL+ GP +GKT+L + + L R
Sbjct: 1 PIVLVVGPKDSGKTTLIRKLLNYLKRR 27
>gnl|CDD|215082 PLN00161, PLN00161, histone H3; Provisional.
Length = 135
Score = 28.4 bits (63), Expect = 1.9
Identities = 20/52 (38%), Positives = 28/52 (53%), Gaps = 10/52 (19%)
Query: 133 KKSTGLSGRTLRKIPFLTFVKYISNNSVSMENF------LIALEKTVLDLLV 178
+KST L +RK+PF V+ IS N + E F L+AL++ D LV
Sbjct: 49 QKSTEL---LIRKLPFARLVREIS-NEMLREPFRWTAEALLALQEATEDFLV 96
>gnl|CDD|213788 TIGR03263, guanyl_kin, guanylate kinase. Members of this family
are the enzyme guanylate kinase, also called GMP
kinase. This enzyme transfers a phosphate from ATP to
GMP, yielding ADP and GDP [Purines, pyrimidines,
nucleosides, and nucleotides, Nucleotide and nucleoside
interconversions].
Length = 179
Score = 29.0 bits (66), Expect = 1.9
Identities = 8/20 (40%), Positives = 15/20 (75%)
Query: 17 RVVLLHGPPGTGKTSLCKAV 36
++++ GP G GK++L KA+
Sbjct: 1 LLIVISGPSGAGKSTLVKAL 20
>gnl|CDD|237854 PRK14898, PRK14898, DNA-directed RNA polymerase subunit A'';
Provisional.
Length = 858
Score = 29.5 bits (66), Expect = 1.9
Identities = 27/97 (27%), Positives = 45/97 (46%), Gaps = 9/97 (9%)
Query: 68 ESGKLVQKMFNKIKEAVEYEESLVCLLIDEIESLTRARESVMSGTEPSDGVRVVNAVLTQ 127
E GKLV ++ +K + VC L EI +L+ + E R+++ + +
Sbjct: 95 EIGKLVDELIDK-FGFEKIGGHEVCDLPIEIYALS------LDQDEKVHWKRIISVIRHK 147
Query: 128 I-DQLKKKSTGLSGRTLRKIPFLTFVKYISNNSVSME 163
+L K T SGRT+R P+ +FV N + +E
Sbjct: 148 ANGKLIKIKTE-SGRTIRATPYHSFVTRKDNEVIPVE 183
>gnl|CDD|162030 TIGR00767, rho, transcription termination factor Rho. This RNA
helicase, the transcription termination factor Rho,
occurs in nearly all bacteria but is missing from the
Cyanobacteria, the Mollicutes (Mycoplasmas), and various
Lactobacillales including Streptococcus. It is also
missing, of course, from the Archaea, which also lack
Nus factors. Members of this family from Micrococcus
luteus, Mycobacterium tuberculosis, and related species
have a related but highly variable long, highly charged
insert near the amino end. Members of this family differ
in the specificity of RNA binding [Transcription,
Transcription factors].
Length = 415
Score = 29.3 bits (66), Expect = 2.0
Identities = 31/116 (26%), Positives = 48/116 (41%), Gaps = 18/116 (15%)
Query: 20 LLHGPPGTGKTSLCKAVAQKLSIRLQSKYKI-----------TEFIEINSHSLFSKYFSE 68
L+ PP GKT L + +AQ ++ I T+ + + F E
Sbjct: 172 LIVAPPKAGKTVLLQKIAQAITRNHPEVELIVLLIDERPEEVTDMQRSVKGEVVASTFDE 231
Query: 69 SG----KLVQKMFNKIKEAVEYEESLVCLLIDEIESLTRARESVM--SGTEPSDGV 118
++ + + K K VE+++ +V LL D I L RA +V SG S GV
Sbjct: 232 PASRHVQVAEMVIEKAKRLVEHKKDVVILL-DSITRLARAYNTVTPASGKVLSGGV 286
>gnl|CDD|223272 COG0194, Gmk, Guanylate kinase [Nucleotide transport and
metabolism].
Length = 191
Score = 28.7 bits (65), Expect = 2.0
Identities = 10/28 (35%), Positives = 18/28 (64%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQKLSIRL 44
+++L GP G GK++L KA+ + +R
Sbjct: 5 LLIVLSGPSGVGKSTLVKALLEDDKLRF 32
>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 = 28.9 bits (65), Expect = 2.0
Identities = 7/16 (43%), Positives = 12/16 (75%)
Query: 23 GPPGTGKTSLCKAVAQ 38
GP G+GKT+ A+++
Sbjct: 3 GPAGSGKTTFVGALSE 18
>gnl|CDD|234654 PRK00131, aroK, shikimate kinase; Reviewed.
Length = 175
Score = 28.6 bits (65), Expect = 2.1
Identities = 8/24 (33%), Positives = 17/24 (70%), Gaps = 1/24 (4%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQKL 40
+VL+ G G GK+++ + +A++L
Sbjct: 6 NIVLI-GFMGAGKSTIGRLLAKRL 28
>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 = 28.4 bits (64), Expect = 2.1
Identities = 10/25 (40%), Positives = 17/25 (68%)
Query: 13 ISWNRVVLLHGPPGTGKTSLCKAVA 37
+ +V L GP G+GK++L +A+A
Sbjct: 22 LKAGEIVALVGPNGSGKSTLLRAIA 46
>gnl|CDD|226459 COG3950, COG3950, Predicted ATP-binding protein involved in
virulence [General function prediction only].
Length = 440
Score = 29.1 bits (65), Expect = 2.2
Identities = 18/101 (17%), Positives = 37/101 (36%), Gaps = 17/101 (16%)
Query: 2 KFSHSKVKSNIISWNRVVLLHGPPGTGKTSLCKAVAQKLS--------IRLQSKYKITEF 53
F + + + ++ GP G+GKT++ A+ L+ +R +S +
Sbjct: 13 CFLNLDITF---GESETTIIVGPNGSGKTTVLDAIRNALNKFIDFFIYLRFKSLKIELDD 69
Query: 54 IEINSHSLFSKYFS------ESGKLVQKMFNKIKEAVEYEE 88
IE+ S + + E+ K + K K +
Sbjct: 70 IELCIMSQSNPTVAVAVVEYENDKKRTWVLTKNKNKELDVD 110
>gnl|CDD|215633 PLN03210, PLN03210, Resistant to P. syringae 6; Provisional.
Length = 1153
Score = 29.5 bits (66), Expect = 2.4
Identities = 12/30 (40%), Positives = 20/30 (66%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQKLSIRLQS 46
R+V + G G GKT++ +A+ +LS + QS
Sbjct: 208 RMVGIWGSSGIGKTTIARALFSRLSRQFQS 237
>gnl|CDD|234175 TIGR03348, VI_IcmF, type VI secretion protein IcmF. Members of
this protein family are IcmF homologs and tend to be
associated with type VI secretion systems [Cellular
processes, Pathogenesis].
Length = 1169
Score = 29.2 bits (66), Expect = 2.4
Identities = 9/13 (69%), Positives = 12/13 (92%)
Query: 20 LLHGPPGTGKTSL 32
L+ GPPG+GKT+L
Sbjct: 115 LVIGPPGSGKTTL 127
>gnl|CDD|214940 smart00962, SRP54, SRP54-type protein, GTPase domain. This entry
represents the GTPase domain of the 54 kDa SRP54
component, a GTP-binding protein that interacts with
the signal sequence when it emerges from the ribosome.
SRP54 of the signal recognition particle has a
three-domain structure: an N-terminal helical bundle
domain, a GTPase domain, and the M-domain that binds
the 7s RNA and also binds the signal sequence. The
extreme C-terminal region is glycine-rich and lower in
complexity and poorly conserved between species. The
GTPase domain is evolutionary related to P-loop NTPase
domains found in a variety of other proteins.
Length = 197
Score = 28.5 bits (65), Expect = 2.5
Identities = 15/33 (45%), Positives = 20/33 (60%), Gaps = 4/33 (12%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQKLSIRLQSKYK 49
V+LL GP G GKT+ +A KL+ RL+ K
Sbjct: 2 GVILLVGPNGVGKTT---TIA-KLAARLKLKGG 30
>gnl|CDD|234232 TIGR03499, FlhF, flagellar biosynthetic protein FlhF. [Cellular
processes, Chemotaxis and motility].
Length = 283
Score = 28.8 bits (65), Expect = 2.6
Identities = 12/32 (37%), Positives = 17/32 (53%), Gaps = 2/32 (6%)
Query: 17 RVVLLHGPPGTGK-TSLCKAVAQKLSIRLQSK 47
V+ L GP G GK T+L K +A + + K
Sbjct: 196 GVIALVGPTGVGKTTTLAK-LAARFVLEHGKK 226
>gnl|CDD|131580 TIGR02528, EutP, ethanolamine utilization protein, EutP. This
protein is found within operons which code for
polyhedral organelles containing the enzyme
ethanolamine ammonia lyase. The function of this gene
is unknown, although the presence of an N-terminal
GxxGxGK motif implies a GTP-binding site [Energy
metabolism, Amino acids and amines].
Length = 142
Score = 28.2 bits (63), Expect = 2.7
Identities = 13/40 (32%), Positives = 19/40 (47%), Gaps = 5/40 (12%)
Query: 19 VLLHGPPGTGKTSLCKAVAQKLSIRLQSKYKITEFIEINS 58
++ G G GKT+L Q L + YK T+ +E N
Sbjct: 3 IMFIGSVGCGKTTLT----QALQ-GEEILYKKTQAVEYND 37
>gnl|CDD|238986 cd02028, UMPK_like, Uridine monophosphate kinase_like (UMPK_like)
is a family of proteins highly similar to the uridine
monophosphate kinase (UMPK, EC 2.7.1.48), also known as
uridine kinase or uridine-cytidine kinase (UCK).
Length = 179
Score = 28.4 bits (64), Expect = 2.7
Identities = 13/28 (46%), Positives = 19/28 (67%), Gaps = 4/28 (14%)
Query: 18 VVLLHGPPGTGKTSLCKAVAQKLSIRLQ 45
VV + GP G+GKT+ A+KLS +L+
Sbjct: 1 VVGIAGPSGSGKTTF----AKKLSNQLR 24
>gnl|CDD|236482 PRK09361, radB, DNA repair and recombination protein RadB;
Provisional.
Length = 225
Score = 28.7 bits (65), Expect = 2.7
Identities = 8/11 (72%), Positives = 11/11 (100%)
Query: 23 GPPGTGKTSLC 33
GPPG+GKT++C
Sbjct: 30 GPPGSGKTNIC 40
>gnl|CDD|225804 COG3265, GntK, Gluconate kinase [Carbohydrate transport and
metabolism].
Length = 161
Score = 28.0 bits (63), Expect = 2.8
Identities = 9/33 (27%), Positives = 18/33 (54%), Gaps = 9/33 (27%)
Query: 23 GPPGTGKTSLCKAVAQKLSIRLQSKYKITEFIE 55
G G+GK+++ A+A++L +FI+
Sbjct: 2 GVSGSGKSTVGSALAERLGA---------KFID 25
>gnl|CDD|226056 COG3525, Chb, N-acetyl-beta-hexosaminidase [Carbohydrate transport
and metabolism].
Length = 732
Score = 29.0 bits (65), Expect = 3.2
Identities = 15/75 (20%), Positives = 27/75 (36%), Gaps = 15/75 (20%)
Query: 57 NSHSLFSKYFSESGKLVQKMFNKIKEAVEYEESLVCLLIDEIESLTRARESVMS------ 110
++++ + I+E V Y + +I EI+ AR +V++
Sbjct: 334 YGPERMGGFYTQ---------DDIRELVAYASARQITVIPEIDMPGHARAAVVAYPDLNL 384
Query: 111 GTEPSDGVRVVNAVL 125
G D V A L
Sbjct: 385 GRADPDSYDSVQAYL 399
>gnl|CDD|234763 PRK00440, rfc, replication factor C small subunit; Reviewed.
Length = 319
Score = 28.7 bits (65), Expect = 3.2
Identities = 12/21 (57%), Positives = 16/21 (76%)
Query: 20 LLHGPPGTGKTSLCKAVAQKL 40
L GPPGTGKT+ A+A++L
Sbjct: 42 LFAGPPGTGKTTAALALAREL 62
>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 = 28.5 bits (64), Expect = 3.2
Identities = 14/37 (37%), Positives = 23/37 (62%), Gaps = 2/37 (5%)
Query: 7 KVKSNIISWNRVV--LLHGPPGTGKTSLCKAVAQKLS 41
K+ ++ NRV+ L+ PP GKT+L + +A+ LS
Sbjct: 100 KLLPYLVRNNRVLNTLIISPPQCGKTTLLRDLARILS 136
>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 = 27.7 bits (62), Expect = 3.2
Identities = 23/112 (20%), Positives = 37/112 (33%), Gaps = 30/112 (26%)
Query: 17 RVVLLHGPPGTGKT--------------------------SLCKAVAQKLSIRLQSKYKI 50
R VLL P G+GKT L VA++L K+
Sbjct: 1 RDVLLAAPTGSGKTLAALLPILELLDSLKGGQVLVLAPTRELANQVAERLKELFGEGIKV 60
Query: 51 TEFIEINSHSLFSKYFSESGKLV----QKMFNKIKEAVEYEESLVCLLIDEI 98
I S K S +V ++ ++++ + L L++DE
Sbjct: 61 GYLIGGTSIKQQEKLLSGKTDIVVGTPGRLLDELERLKLSLKKLDLLILDEA 112
>gnl|CDD|226372 COG3854, SpoIIIAA, ncharacterized protein conserved in bacteria
[Function unknown].
Length = 308
Score = 28.6 bits (64), Expect = 3.3
Identities = 11/23 (47%), Positives = 16/23 (69%)
Query: 19 VLLHGPPGTGKTSLCKAVAQKLS 41
L+ GPP GKT+L + +A+ LS
Sbjct: 140 TLIIGPPQVGKTTLLRDIARLLS 162
>gnl|CDD|226412 COG3896, COG3896, Chloramphenicol 3-O-phosphotransferase [Defense
mechanisms].
Length = 205
Score = 28.3 bits (63), Expect = 3.4
Identities = 9/20 (45%), Positives = 13/20 (65%)
Query: 17 RVVLLHGPPGTGKTSLCKAV 36
R+VLL+G GK+S+ A
Sbjct: 24 RIVLLNGGSSAGKSSIALAF 43
>gnl|CDD|223401 COG0324, MiaA, tRNA delta(2)-isopentenylpyrophosphate transferase
[Translation, ribosomal structure and biogenesis].
Length = 308
Score = 28.4 bits (64), Expect = 3.5
Identities = 9/24 (37%), Positives = 19/24 (79%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQKL 40
+++++ GP +GKT+L A+A++L
Sbjct: 4 KLIVIAGPTASGKTALAIALAKRL 27
>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 = 28.6 bits (64), Expect = 3.6
Identities = 18/46 (39%), Positives = 23/46 (50%), Gaps = 6/46 (13%)
Query: 12 IISWNRVVLLHGPPGTGKTSLCKAVAQKLSIRLQSKYKITEFIEIN 57
I + VLL G GTGK L +A+ +LS R K F+ IN
Sbjct: 158 IAPSDITVLLLGESGTGKEVLARAL-HQLSDR-----KDKRFVAIN 197
>gnl|CDD|235943 PRK07133, PRK07133, DNA polymerase III subunits gamma and tau;
Validated.
Length = 725
Score = 28.6 bits (64), Expect = 3.6
Identities = 16/33 (48%), Positives = 19/33 (57%), Gaps = 3/33 (9%)
Query: 11 NIISWNRVV---LLHGPPGTGKTSLCKAVAQKL 40
NII N++ L GP GTGKTS+ K A L
Sbjct: 32 NIIKSNKISHAYLFSGPRGTGKTSVAKIFANAL 64
>gnl|CDD|224616 COG1702, PhoH, Phosphate starvation-inducible protein PhoH,
predicted ATPase [Signal transduction mechanisms].
Length = 348
Score = 28.4 bits (64), Expect = 3.7
Identities = 11/20 (55%), Positives = 12/20 (60%)
Query: 18 VVLLHGPPGTGKTSLCKAVA 37
+V GP GTGKT L A A
Sbjct: 145 IVFGIGPAGTGKTYLAVAKA 164
>gnl|CDD|238835 cd01672, TMPK, Thymidine monophosphate kinase (TMPK), also known
as thymidylate kinase, catalyzes the phosphorylation of
thymidine monophosphate (TMP) to thymidine diphosphate
(TDP) utilizing ATP as its preferred phophoryl donor.
TMPK represents the rate-limiting step in either de
novo or salvage biosynthesis of thymidine triphosphate
(TTP).
Length = 200
Score = 28.0 bits (63), Expect = 3.8
Identities = 8/18 (44%), Positives = 13/18 (72%)
Query: 23 GPPGTGKTSLCKAVAQKL 40
G G GKT+L + +A++L
Sbjct: 7 GIDGAGKTTLIELLAERL 24
>gnl|CDD|217429 pfam03215, Rad17, Rad17 cell cycle checkpoint protein.
Length = 490
Score = 28.5 bits (63), Expect = 3.9
Identities = 10/29 (34%), Positives = 19/29 (65%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQKLSIRLQ 45
++LL GP G GK++ K ++++L I +
Sbjct: 46 LILLLTGPSGCGKSTTVKVLSKELGIEII 74
>gnl|CDD|234626 PRK00091, miaA, tRNA delta(2)-isopentenylpyrophosphate
transferase; Reviewed.
Length = 307
Score = 28.2 bits (64), Expect = 4.0
Identities = 9/24 (37%), Positives = 18/24 (75%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQKL 40
+V+++ GP +GKT+L +A++L
Sbjct: 5 KVIVIVGPTASGKTALAIELAKRL 28
>gnl|CDD|218253 pfam04765, DUF616, Protein of unknown function (DUF616). Family of
uncharacterized proteins.
Length = 306
Score = 28.1 bits (63), Expect = 4.1
Identities = 23/85 (27%), Positives = 42/85 (49%), Gaps = 5/85 (5%)
Query: 117 GVRVVNAVLTQIDQLKKKSTGLSGRTLRKIPFLTFVKYISNNSVSMENFLIALEKTV-LD 175
V V +A+ D++++ G+S R+ + + F+ FV + +++ E + V L
Sbjct: 65 RVVVASAIFGDYDKIRQ-PKGISKRSKKNVCFVMFVDEETLSTLKSEGHVPDDNGRVGLW 123
Query: 176 LLVEEKSLPLK---RNTEVPNTYLH 197
+V K+LP RN +VP LH
Sbjct: 124 RIVVVKNLPYTDPRRNGKVPKYLLH 148
>gnl|CDD|215758 pfam00158, Sigma54_activat, Sigma-54 interaction domain.
Length = 168
Score = 27.7 bits (63), Expect = 4.1
Identities = 14/39 (35%), Positives = 19/39 (48%), Gaps = 6/39 (15%)
Query: 19 VLLHGPPGTGKTSLCKAVAQKLSIRLQSKYKITEFIEIN 57
VL+ G GTGK +A+ Q LS R F+ +N
Sbjct: 25 VLITGESGTGKELFARAIHQ-LSPRADGP-----FVAVN 57
>gnl|CDD|233793 TIGR02237, recomb_radB, DNA repair and recombination protein RadB.
This family consists exclusively of archaeal RadB
protein, a homolog of bacterial RecA (TIGR02012),
eukaryotic RAD51 (TIGR02239) and DMC1 (TIGR02238), and
archaeal RadA (TIGR02236).
Length = 209
Score = 28.1 bits (63), Expect = 4.2
Identities = 25/109 (22%), Positives = 42/109 (38%), Gaps = 32/109 (29%)
Query: 21 LHGPPGTGKTSLCKAVA---------------QKLSI-RLQS------KYKITEFIEINS 58
++GPPG+GKT++C +A + LS R + + ++ FI
Sbjct: 17 IYGPPGSGKTNICMILAVNAARQGKKVVYIDTEGLSPERFKQIAEDRPERALSNFIVFEV 76
Query: 59 HSLFSKYFSESGKLVQKMFNKIKEAVEYEESLVCLLIDEIESLTRARES 107
F E G +QK I +S +++D +L R S
Sbjct: 77 FD-----FDEQGVAIQKTSKFID-----RDSASLVVVDSFTALYRLELS 115
>gnl|CDD|180607 PRK06526, PRK06526, transposase; Provisional.
Length = 254
Score = 28.3 bits (63), Expect = 4.2
Identities = 10/21 (47%), Positives = 13/21 (61%)
Query: 19 VLLHGPPGTGKTSLCKAVAQK 39
V+ GPPGTGKT L + +
Sbjct: 101 VVFLGPPGTGKTHLAIGLGIR 121
>gnl|CDD|179433 PRK02496, adk, adenylate kinase; Provisional.
Length = 184
Score = 27.8 bits (62), Expect = 4.3
Identities = 11/26 (42%), Positives = 16/26 (61%), Gaps = 1/26 (3%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQKLSI 42
R++ L GPPG GK + +A+ L I
Sbjct: 3 RLIFL-GPPGAGKGTQAVVLAEHLHI 27
>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 = 28.3 bits (63), Expect = 4.4
Identities = 20/60 (33%), Positives = 29/60 (48%), Gaps = 7/60 (11%)
Query: 19 VLLHGPPGTGKTSLCKAVAQKLSIRLQSKYKITEFIEINS-HSLFSKYFSESGKLVQKMF 77
+LL GPPG+GKT L Q + L ++ E IE SL K + ++ Q+ F
Sbjct: 214 LLLFGPPGSGKTMLASR-LQGILPPLTNE----EAIETARIWSLVGK-LIDRKQIKQRPF 267
>gnl|CDD|233584 TIGR01817, nifA, Nif-specific regulatory protein. This model
represents NifA, a DNA-binding regulatory protein for
nitrogen fixation. The model produces scores between the
trusted and noise cutoffs for a well-described NifA
homolog in Aquifex aeolicus (which lacks nitrogenase),
for transcriptional activators of alternative
nitrogenases (VFe or FeFe instead of MoFe), and
truncated forms [Central intermediary metabolism,
Nitrogen fixation, Regulatory functions, DNA
interactions].
Length = 534
Score = 28.1 bits (63), Expect = 4.5
Identities = 17/47 (36%), Positives = 24/47 (51%), Gaps = 6/47 (12%)
Query: 15 WNRVVLLHGPPGTGKTSLCKAVAQKLSIRLQSKYKITEFIEINSHSL 61
N VLL G GTGK + KA+ LS R + F+++N +L
Sbjct: 218 SNSTVLLRGESGTGKELIAKAIHY-LSPR-AKR----PFVKVNCAAL 258
>gnl|CDD|222866 PHA02544, 44, clamp loader, small subunit; Provisional.
Length = 316
Score = 28.0 bits (63), Expect = 4.5
Identities = 14/35 (40%), Positives = 22/35 (62%), Gaps = 3/35 (8%)
Query: 12 IISWNRV--VLLHGP-PGTGKTSLCKAVAQKLSIR 43
I+ R+ +LLH P PGTGKT++ KA+ ++
Sbjct: 36 IVKKGRIPNMLLHSPSPGTGKTTVAKALCNEVGAE 70
>gnl|CDD|206745 cd11385, RagC_like, Rag GTPase, subfamily of Ras-related GTPases,
includes Ras-related GTP-binding proteins C and D.
RagC and RagD are closely related Rag GTPases
(ras-related GTP-binding protein C and D) that
constitute a unique subgroup of the Ras superfamily,
and are functional homologs of Saccharomyces cerevisiae
Gtr2. These domains form heterodimers with RagA or
RagB, and similarly, Gtr2 dimerizes with Gtr1 in order
to function. They play an essential role in regulating
amino acid-induced target of rapamycin complex 1
(TORC1) kinase signaling, exocytic cargo sorting at
endosomes, and epigenetic control of gene expression.
In response to amino acids, the Rag GTPases guide the
TORC1 complex to activate the platform containing Rheb
proto-oncogene by driving the relocalization of mTORC1
from discrete locations in the cytoplasm to a late
endosomal and/or lysosomal compartment that is
Rheb-enriched and contains Rab-7.
Length = 175
Score = 27.6 bits (62), Expect = 4.6
Identities = 10/23 (43%), Positives = 15/23 (65%)
Query: 19 VLLHGPPGTGKTSLCKAVAQKLS 41
+LL G +GK+S+ K V K+S
Sbjct: 2 ILLMGLRRSGKSSIQKVVFHKMS 24
>gnl|CDD|234011 TIGR02782, TrbB_P, P-type conjugative transfer ATPase TrbB. The
TrbB protein is found in the trb locus of Agrobacterium
Ti plasmids where it is involved in the type IV
secretion system for plasmid conjugative transfer. TrbB
is a homolog of the vir system VirB11 ATPase , and the
Flp pilus sytem ATPase TadA [Cellular processes,
Conjugation].
Length = 299
Score = 28.2 bits (63), Expect = 4.7
Identities = 8/27 (29%), Positives = 17/27 (62%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQKLSIR 43
+ +L+ G G+GKT+L A+ +++
Sbjct: 133 KNILVVGGTGSGKTTLANALLAEIAKN 159
>gnl|CDD|221968 pfam13189, Cytidylate_kin2, Cytidylate kinase-like family. This
family includes enzymes related to cytidylate kinase.
Length = 176
Score = 27.5 bits (62), Expect = 4.8
Identities = 8/28 (28%), Positives = 14/28 (50%)
Query: 25 PGTGKTSLCKAVAQKLSIRLQSKYKITE 52
G+G + K +A+KL I + + E
Sbjct: 8 FGSGGREIGKKLAEKLGIPYYDREILDE 35
>gnl|CDD|218203 pfam04670, Gtr1_RagA, Gtr1/RagA G protein conserved region. GTR1
was first identified in S. cerevisiae as a suppressor
of a mutation in RCC1. Biochemical analysis revealed
that Gtr1 is in fact a G protein of the Ras family. The
RagA/B proteins are the human homologues of Gtr1.
Included in this family is the human Rag C, a novel
protein that has been shown to interact with RagA/B.
Length = 230
Score = 27.9 bits (63), Expect = 5.0
Identities = 10/25 (40%), Positives = 14/25 (56%)
Query: 19 VLLHGPPGTGKTSLCKAVAQKLSIR 43
VLL G G+GK+S+ + S R
Sbjct: 2 VLLMGLRGSGKSSMRSIIFSNYSPR 26
>gnl|CDD|227608 COG5283, COG5283, Phage-related tail protein [Function unknown].
Length = 1213
Score = 28.4 bits (63), Expect = 5.1
Identities = 16/84 (19%), Positives = 30/84 (35%), Gaps = 11/84 (13%)
Query: 35 AVAQKLSIRLQSKYKITEFIEINSHSLFSKYFSES----------GKLVQKMFNKIKEAV 84
++Q LS RL+ + + S K G + F I AV
Sbjct: 202 KLSQALSARLER-LQESRTQMSQSSGQLGKRLETDKAGAGALGLLGAALAGSFAAIGAAV 260
Query: 85 EYEESLVCLLIDEIESLTRARESV 108
+ L+D+ + + AR+++
Sbjct: 261 RRTAQMNGELMDKTKQVKGARDNL 284
>gnl|CDD|237393 PRK13477, PRK13477, bifunctional pantoate ligase/cytidylate kinase;
Provisional.
Length = 512
Score = 28.3 bits (64), Expect = 5.1
Identities = 10/18 (55%), Positives = 15/18 (83%)
Query: 23 GPPGTGKTSLCKAVAQKL 40
GP G GK+++ +AVA+KL
Sbjct: 291 GPAGAGKSTVTRAVAKKL 308
>gnl|CDD|224292 COG1373, COG1373, Predicted ATPase (AAA+ superfamily) [General
function prediction only].
Length = 398
Score = 28.1 bits (63), Expect = 5.1
Identities = 20/85 (23%), Positives = 36/85 (42%), Gaps = 16/85 (18%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQKLSIRLQSKYKITEFIEINSHSLFSKYFSESGKLVQKM 76
++L+ GP GKT+L K + + L + E I IN L +L+ +
Sbjct: 38 FIILILGPRQVGKTTLLKLLIKGL---------LEEIIYINFDDLRLDRI----ELLDLL 84
Query: 77 FNKIKEAVEYEESLVCLLIDEIESL 101
I+ E + +DEI+++
Sbjct: 85 RAYIE---LKEREKSYIFLDEIQNV 106
>gnl|CDD|219519 pfam07693, KAP_NTPase, KAP family P-loop domain. The KAP (after
Kidins220/ARMS and PifA) family of predicted NTPases
are sporadically distributed across a wide phylogenetic
range in bacteria and in animals. Many of the
prokaryotic KAP NTPases are encoded in plasmids and
tend to undergo disruption to form pseudogenes. A
unique feature of all eukaryotic and certain bacterial
KAP NTPases is the presence of two or four
transmembrane helices inserted into the P-loop NTPase
domain. These transmembrane helices anchor KAP NTPases
in the membrane such that the P-loop domain is located
on the intracellular side.
Length = 301
Score = 27.7 bits (62), Expect = 5.3
Identities = 18/74 (24%), Positives = 31/74 (41%), Gaps = 13/74 (17%)
Query: 18 VVLLHGPPGTGKTSLCKAVAQKLSIRLQSKYKITEFIEINSHSLFSKYFSESGK--LVQK 75
V+ L+G G+GKTS + +L ++ I F + SG+ V
Sbjct: 22 VIGLYGAWGSGKTSFLNLLEDELKEF-PEEFHIVYF----------DPWLFSGQDDAVAS 70
Query: 76 MFNKIKEAVEYEES 89
+ + +A+E E S
Sbjct: 71 LLAALADALEEEYS 84
>gnl|CDD|213184 cd03217, ABC_FeS_Assembly, ABC-type transport system involved in
Fe-S cluster assembly, ATPase component. Biosynthesis
of iron-sulfur clusters (Fe-S) depends on multi-protein
systems. The SUF system of E. coli and Erwinia
chrysanthemi is important for Fe-S biogenesis under
stressful conditions. The SUF system is made of six
proteins: SufC is an atypical cytoplasmic ABC-ATPase,
which forms a complex with SufB and SufD; SufA plays
the role of a scaffold protein for assembly of
iron-sulfur clusters and delivery to target proteins;
SufS is a cysteine desulfurase which mobilizes the
sulfur atom from cysteine and provides it to the
cluster; SufE has no associated function yet.
Length = 200
Score = 27.5 bits (62), Expect = 5.3
Identities = 13/37 (35%), Positives = 19/37 (51%), Gaps = 6/37 (16%)
Query: 16 NRVVLLHGPPGTGKTSLCKAVAQKLSIRLQSKYKITE 52
V L GP G+GK++L K + KY++TE
Sbjct: 26 GEVHALMGPNGSGKSTLAKTIMGH------PKYEVTE 56
>gnl|CDD|183702 PRK12723, PRK12723, flagellar biosynthesis regulator FlhF;
Provisional.
Length = 388
Score = 27.9 bits (62), Expect = 5.6
Identities = 15/48 (31%), Positives = 24/48 (50%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQKLSIRLQSKYKITEFIEINSHSLFSK 64
RV +L GP G GKT+ +A I K + I I+++ + +K
Sbjct: 175 RVFILVGPTGVGKTTTIAKLAAIYGINSDDKSLNIKIITIDNYRIGAK 222
>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 = 27.5 bits (61), Expect = 5.6
Identities = 28/94 (29%), Positives = 42/94 (44%), Gaps = 20/94 (21%)
Query: 19 VLLHGPPGTGKTSLCKAVAQK---LSIRLQSKYKI-TEFIEINSHSLFSKYFSESGKLVQ 74
L++G PGTGKTS K + K LS + SK I E ++I H + +Q
Sbjct: 15 YLIYGKPGTGKTSTIKYLPGKTLVLSFDMSSKVLIGDENVDIADH--------DDMPPIQ 66
Query: 75 KMFNKIK----EAVEYEESLVCLLIDEIESLTRA 104
M +AV+Y+ ++ID I +L
Sbjct: 67 AMVEFYVMQNIQAVKYDN----IVIDNISALQNL 96
>gnl|CDD|233355 TIGR01313, therm_gnt_kin, carbohydrate kinase, thermoresistant
glucokinase family. This model represents a subfamily
of proteins that includes thermoresistant and
thermosensitve isozymes of gluconate kinase
(gluconokinase) in E. coli and other related proteins;
members of this family are often named by similarity to
the thermostable isozyme. These proteins show homology
to shikimate kinases and adenylate kinases but not to
gluconate kinases from the FGGY family of carbohydrate
kinases.
Length = 163
Score = 27.4 bits (61), Expect = 5.7
Identities = 8/21 (38%), Positives = 14/21 (66%)
Query: 21 LHGPPGTGKTSLCKAVAQKLS 41
L G G+GK+++ A+A +L
Sbjct: 3 LMGVAGSGKSTIASALAHRLG 23
>gnl|CDD|131364 TIGR02311, HpaI, 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase.
This model represents the aldolase which performs the
final step unique to the 4-hydroxyphenylacetic acid
catabolism pathway in which
2,4-dihydroxyhept-2-ene-1,7-dioic acid is split into
pyruvate and succinate-semialdehyde. The gene for enzyme
is generally found adjacent to other genes for this
pathway organized into an operon.
Length = 249
Score = 27.8 bits (62), Expect = 5.8
Identities = 11/35 (31%), Positives = 19/35 (54%)
Query: 93 LLIDEIESLTRARESVMSGTEPSDGVRVVNAVLTQ 127
LL+ IE+ +A +V + P G+R V + L +
Sbjct: 88 LLVPMIETAEQAEAAVAATRYPPMGIRGVGSALAR 122
>gnl|CDD|197777 smart00534, MUTSac, ATPase domain of DNA mismatch repair MUTS
family.
Length = 185
Score = 27.5 bits (62), Expect = 5.8
Identities = 27/126 (21%), Positives = 45/126 (35%), Gaps = 40/126 (31%)
Query: 18 VVLLHGPPGTGKTSLCKAVAQKLSIRLQ-------SKYKITEFIEI-----------NSH 59
VV++ GP GK++ + VA + I Q ++ F I
Sbjct: 1 VVIITGPNMGGKSTYLRQVAL-IVIMAQIGSFVPAESAELPVFDRIFTRIGASDSLAQGL 59
Query: 60 SLFSKYFSESGKLVQKMFNKIKEAVEYEESLVCLLIDEIESLTRARESVMSGTEPSDGVR 119
S F E+ +++ + SLV L+DE+ GT DG+
Sbjct: 60 STFMVEMKETANILKN---------ATKNSLV--LLDELGR----------GTSTYDGLA 98
Query: 120 VVNAVL 125
+ A+L
Sbjct: 99 IAAAIL 104
>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 = 27.6 bits (62), Expect = 5.9
Identities = 8/25 (32%), Positives = 16/25 (64%)
Query: 19 VLLHGPPGTGKTSLCKAVAQKLSIR 43
++L G P +GK++ K +A+ L +
Sbjct: 2 IILTGLPSSGKSTRAKELAKYLEEK 26
>gnl|CDD|216360 pfam01202, SKI, Shikimate kinase.
Length = 158
Score = 27.2 bits (61), Expect = 6.2
Identities = 5/20 (25%), Positives = 12/20 (60%)
Query: 25 PGTGKTSLCKAVAQKLSIRL 44
G GK+++ + +A+ L +
Sbjct: 1 MGAGKSTIGRLLAKALGLPF 20
>gnl|CDD|218292 pfam04851, ResIII, Type III restriction enzyme, res subunit.
Length = 100
Score = 26.4 bits (59), Expect = 6.4
Identities = 12/44 (27%), Positives = 17/44 (38%), Gaps = 5/44 (11%)
Query: 11 NIISWNRVVLLHGPPGTGKTSLCKAVAQKLSIRLQSKYKITEFI 54
++ R L+ G+GKT A L RL K F+
Sbjct: 14 RLLEKKRG-LIVMATGSGKT----LTAAALIARLAKGKKKVLFV 52
>gnl|CDD|227922 COG5635, COG5635, Predicted NTPase (NACHT family) [Signal
transduction mechanisms].
Length = 824
Score = 27.8 bits (62), Expect = 6.8
Identities = 23/99 (23%), Positives = 50/99 (50%), Gaps = 14/99 (14%)
Query: 15 WNRVVLLHGPPGTGKTSLCKAVAQKLSIRLQSKYKITEFIEINSHSLFSKYFSESG---K 71
+ ++++L G PG+GKT+ + +A L+ R + F+ +N+ +L K+ +
Sbjct: 222 YAKLLIL-GAPGSGKTTFLQRLALWLAQRTLEPEDVPIFLLLNAFALARKFEKQLSLIDY 280
Query: 72 LVQKMFNK------IKEAVEYEESLVCLL----IDEIES 100
L +++F++ I+ E ++ LL +DE+E
Sbjct: 281 LAEELFSQGIAKQLIEAHQELLKTGKLLLLLDGLDELEP 319
>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 = 26.9 bits (60), Expect = 6.9
Identities = 7/23 (30%), Positives = 14/23 (60%)
Query: 18 VVLLHGPPGTGKTSLCKAVAQKL 40
+ G G+GK+++ A+ +KL
Sbjct: 4 TIWFTGLSGSGKSTIANALERKL 26
>gnl|CDD|164934 PHA02538, N, capsid protein; Provisional.
Length = 348
Score = 27.8 bits (62), Expect = 7.0
Identities = 12/40 (30%), Positives = 23/40 (57%)
Query: 60 SLFSKYFSESGKLVQKMFNKIKEAVEYEESLVCLLIDEIE 99
S SK F+ + QK+ I+E+ E+ + + + +DEI+
Sbjct: 25 SDVSKKFAVEPSVQQKLEEAIQESSEFLKRINVVPVDEIK 64
>gnl|CDD|134335 PRK00625, PRK00625, shikimate kinase; Provisional.
Length = 173
Score = 27.0 bits (60), Expect = 7.1
Identities = 12/24 (50%), Positives = 16/24 (66%)
Query: 19 VLLHGPPGTGKTSLCKAVAQKLSI 42
+ L G P GKTS KA+A+ LS+
Sbjct: 3 IFLCGLPTVGKTSFGKALAKFLSL 26
>gnl|CDD|181547 PRK08760, PRK08760, replicative DNA helicase; Provisional.
Length = 476
Score = 27.6 bits (61), Expect = 7.3
Identities = 14/56 (25%), Positives = 31/56 (55%), Gaps = 3/56 (5%)
Query: 18 VVLLHGPPGTGKTSLCKAVAQKLSIRLQSKYKITEF-IEINSHSLFSKYFSESGKL 72
+++L P GKT+ +A+ +I+ SK + F +E+++ L + S +G++
Sbjct: 231 LIILAARPAMGKTTFALNIAEYAAIK--SKKGVAVFSMEMSASQLAMRLISSNGRI 284
>gnl|CDD|180666 PRK06710, PRK06710, long-chain-fatty-acid--CoA ligase; Validated.
Length = 563
Score = 27.7 bits (61), Expect = 7.3
Identities = 10/32 (31%), Positives = 18/32 (56%)
Query: 190 EVPNTYLHSNQRIHIYLMFCGTSYPLQHSKHF 221
E+P+T + Q +H Y+ + YP + + HF
Sbjct: 14 EIPSTISYDIQPLHKYVEQMASRYPEKKALHF 45
>gnl|CDD|218676 pfam05649, Peptidase_M13_N, Peptidase family M13. M13 peptidases
are well-studied proteases found in a wide range of
organisms including mammals and bacteria. In mammals
they participate in processes such as cardiovascular
development, blood-pressure regulation, nervous control
of respiration, and regulation of the function of
neuropeptides in the central nervous system. In bacteria
they may be used for digestion of milk.
Length = 380
Score = 27.3 bits (61), Expect = 7.7
Identities = 11/28 (39%), Positives = 16/28 (57%), Gaps = 3/28 (10%)
Query: 64 KYFS-ESGKLVQKMFNKIKEAVEYEESL 90
KYF E+ V++M IK+A + E L
Sbjct: 327 KYFPPEAKADVEEMVKNIKKA--FRERL 352
>gnl|CDD|234719 PRK00300, gmk, guanylate kinase; Provisional.
Length = 205
Score = 27.0 bits (61), Expect = 7.9
Identities = 10/25 (40%), Positives = 16/25 (64%), Gaps = 5/25 (20%)
Query: 23 GPPGTGKTSLCKAVAQ-----KLSI 42
GP G GK++L KA+ + +LS+
Sbjct: 12 GPSGAGKSTLVKALLERDPNLQLSV 36
>gnl|CDD|163593 TIGR03881, KaiC_arch_4, KaiC domain protein, PAE1156 family.
Members of this protein family are archaeal
single-domain KaiC_related proteins, homologous to the
Cyanobacterial circadian clock cycle protein KaiC, an
autokinase/autophosphorylase that has two copies of the
domain.
Length = 229
Score = 27.0 bits (60), Expect = 7.9
Identities = 30/92 (32%), Positives = 40/92 (43%), Gaps = 13/92 (14%)
Query: 18 VVLLHGPPGTGKTSLCKAVAQKLSIRLQSK--YKITE--FIEINSHSL-----FSKYFSE 68
V + G PGTGKT C A K +R Y TE I + F K E
Sbjct: 22 FVAVTGEPGTGKTIFCLHFAYK-GLRDGDPVIYVTTEESRESIIRQAAQFGMDFEKA-IE 79
Query: 69 SGKLVQKMFNKIKEAVEYEESLVCLLIDEIES 100
GKLV + + + + E E SL L I+E+ +
Sbjct: 80 EGKLV--IIDALMKEKEDEWSLRELSIEELLN 109
>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 = 27.4 bits (61), Expect = 8.0
Identities = 11/30 (36%), Positives = 20/30 (66%), Gaps = 2/30 (6%)
Query: 14 SWNRVVLLHGPPGTGKTSLCKAVAQKLSIR 43
+ N +++ GP G+GK++L K +A +L R
Sbjct: 1 NPNMLIV--GPSGSGKSTLLKLLALRLLAR 28
>gnl|CDD|223666 COG0593, DnaA, ATPase involved in DNA replication initiation [DNA
replication, recombination, and repair].
Length = 408
Score = 27.2 bits (61), Expect = 8.2
Identities = 21/89 (23%), Positives = 35/89 (39%), Gaps = 11/89 (12%)
Query: 18 VVLLHGPPGTGKTSLCKAVAQKLSIRLQSKYKITEFIEINSHSLFSKYFSESGKLVQKMF 77
+ ++G G GKT L +A+ + L + + + S + + L
Sbjct: 115 PLFIYGGVGLGKTHLLQAIGNEA---LANGPN-ARVVYLTSEDFTNDFVKA---LRDNEM 167
Query: 78 NKIKEAVEYEESLVCLLIDEIESLTRARE 106
K KE +Y L LLID+I+ L
Sbjct: 168 EKFKE--KYSLDL--LLIDDIQFLAGKER 192
>gnl|CDD|235570 PRK05703, flhF, flagellar biosynthesis regulator FlhF; Validated.
Length = 424
Score = 27.6 bits (62), Expect = 8.3
Identities = 16/43 (37%), Positives = 24/43 (55%), Gaps = 3/43 (6%)
Query: 9 KSNIISWNRVVLLHGPPGTGK-TSLCKAVAQKLSIRLQSKYKI 50
+I+ VV L GP G GK T+L K +A + ++ L K K+
Sbjct: 214 VEDILKQGGVVALVGPTGVGKTTTLAK-LAARYAL-LYGKKKV 254
>gnl|CDD|180750 PRK06921, PRK06921, hypothetical protein; Provisional.
Length = 266
Score = 27.1 bits (60), Expect = 8.6
Identities = 13/30 (43%), Positives = 17/30 (56%), Gaps = 1/30 (3%)
Query: 16 NRVVLLHGPPGTGKTSLCKAVAQKLSIRLQ 45
N + LL G PG+GKT L A A +L +
Sbjct: 118 NSIALL-GQPGSGKTHLLTAAANELMRKKG 146
>gnl|CDD|233070 TIGR00644, recJ, single-stranded-DNA-specific exonuclease RecJ.
All proteins in this family are 5'-3' single-strand DNA
exonucleases. These proteins are used in some aspects of
mismatch repair, recombination, and recombinational
repair [DNA metabolism, DNA replication, recombination,
and repair].
Length = 539
Score = 27.2 bits (61), Expect = 8.8
Identities = 14/83 (16%), Positives = 30/83 (36%), Gaps = 12/83 (14%)
Query: 39 KLSIRLQSKYKITEFIEINSHSLFSKY--------FS---ESGKLVQKMFN-KIKEAVEY 86
K S R S + + + +LF K+ + E+ + ++ K K+ +
Sbjct: 366 KGSARSISGIDLYDLLSELREALFLKFGGHAMAAGLTLKRENLEEFREKLEEKFKKILFA 425
Query: 87 EESLVCLLIDEIESLTRARESVM 109
+ES L +D ++
Sbjct: 426 DESEEILPVDAELKAEEITRELI 448
>gnl|CDD|239255 cd02957, Phd_like, Phosducin (Phd)-like family; composed of Phd
and Phd-like proteins (PhLP), characterized as
cytosolic regulators of G protein functions. Phd and
PhLPs specifically bind G protein betagamma
(Gbg)-subunits with high affinity, resulting in the
solubilization of Gbg from the plasma membrane and
impeding G protein-mediated signal transduction by
inhibiting the formation of a functional G protein
trimer (G protein alphabetagamma). Phd also inhibits
the GTPase activity of G protein alpha. Phd can be
phosphorylated by protein kinase A and G
protein-coupled receptor kinase 2, leading to its
inactivation. Phd was originally isolated from the
retina, where it is highly expressed and has been
implicated to play an important role in light
adaptation. It is also found in the pineal gland,
liver, spleen, striated muscle and the brain. The
C-terminal domain of Phd adopts a thioredoxin fold, but
it does not contain a CXXC motif. Phd interacts with G
protein beta mostly through the N-terminal helical
domain. Also included in this family is a PhLP
characterized as a viral inhibitor of apoptosis
(IAP)-associated factor, named VIAF, that functions in
caspase activation during apoptosis.
Length = 113
Score = 26.4 bits (59), Expect = 8.8
Identities = 12/36 (33%), Positives = 18/36 (50%), Gaps = 2/36 (5%)
Query: 33 CKAVAQKLSIRLQSKYKITEFIEINSHSLF-SKYFS 67
CK + L L +KY T+F++IN+ F Y
Sbjct: 39 CKILDSHLEE-LAAKYPETKFVKINAEKAFLVNYLD 73
>gnl|CDD|213189 cd03222, ABC_RNaseL_inhibitor, ATP-binding cassette domain of
RNase L inhibitor. The ABC ATPase RNase L inhibitor
(RLI) is a key enzyme in ribosomal biogenesis,
formation of translation preinitiation complexes, and
assembly of HIV capsids. RLI's are not transport
proteins, and thus cluster with a group of soluble
proteins that lack the transmembrane components
commonly found in other members of the family.
Structurally, RLI's have an N-terminal Fe-S domain and
two nucleotide-binding domains, which are arranged to
form two composite active sites in their interface
cleft. RLI is one of the most conserved enzymes between
archaea and eukaryotes with a sequence identity more
than 48%. The high degree of evolutionary conservation
suggests that RLI performs a central role in archaeal
and eukaryotic physiology.
Length = 177
Score = 26.8 bits (59), Expect = 8.8
Identities = 12/36 (33%), Positives = 20/36 (55%)
Query: 5 HSKVKSNIISWNRVVLLHGPPGTGKTSLCKAVAQKL 40
V+ ++ V+ + GP GTGKT+ K +A +L
Sbjct: 14 FLLVELGVVKEGEVIGIVGPNGTGKTTAVKILAGQL 49
>gnl|CDD|222859 PHA02535, P, terminase ATPase subunit; Provisional.
Length = 581
Score = 27.3 bits (61), Expect = 8.9
Identities = 14/42 (33%), Positives = 19/42 (45%), Gaps = 2/42 (4%)
Query: 81 KEAVEYEESLVCLLIDEIESLTRARESVMSGTEPSDGVRVVN 122
K +Y+E + LLI + E L R R +G E V N
Sbjct: 70 KTGGDYKE--IDLLIRQHERLARVRRYSGTGNEADLNPNVAN 109
>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 = 27.2 bits (61), Expect = 8.9
Identities = 10/23 (43%), Positives = 14/23 (60%), Gaps = 2/23 (8%)
Query: 16 NRVVLLHGPPGTGKT-SLCKAVA 37
R VL G G+GK+ L +A+A
Sbjct: 24 VRFVL-TGERGSGKSVLLAQAMA 45
>gnl|CDD|182120 PRK09862, PRK09862, putative ATP-dependent protease; Provisional.
Length = 506
Score = 27.3 bits (60), Expect = 9.0
Identities = 11/14 (78%), Positives = 12/14 (85%)
Query: 19 VLLHGPPGTGKTSL 32
+LL GPPGTGKT L
Sbjct: 213 LLLIGPPGTGKTML 226
>gnl|CDD|224677 COG1763, MobB, Molybdopterin-guanine dinucleotide biosynthesis
protein [Coenzyme metabolism].
Length = 161
Score = 26.5 bits (59), Expect = 9.1
Identities = 8/21 (38%), Positives = 13/21 (61%)
Query: 23 GPPGTGKTSLCKAVAQKLSIR 43
G +GKT+L + + +KL R
Sbjct: 9 GYKNSGKTTLIEKLVRKLKAR 29
>gnl|CDD|132027 TIGR02982, heterocyst_DevA, ABC exporter ATP-binding subunit,
DevA family. Members of this protein family are found
mostly in the Cyanobacteria, but also in the
Planctomycetes. Cyanobacterial examples are involved in
heterocyst formation, by which some fraction of members
of the colony undergo a developmental change and become
capable of nitrogen fixation. The DevBCA proteins are
thought export of either heterocyst-specific
glycolipids or an enzyme essential for formation of the
laminated layer found in heterocysts.
Length = 220
Score = 26.9 bits (60), Expect = 9.2
Identities = 9/15 (60%), Positives = 13/15 (86%)
Query: 18 VVLLHGPPGTGKTSL 32
+V+L GP G+GKT+L
Sbjct: 33 IVILTGPSGSGKTTL 47
>gnl|CDD|215137 PLN02246, PLN02246, 4-coumarate--CoA ligase.
Length = 537
Score = 27.3 bits (61), Expect = 9.2
Identities = 12/32 (37%), Positives = 15/32 (46%), Gaps = 11/32 (34%)
Query: 190 EVPNTYLHSNQRI-------HIY----LMFCG 210
E PN Y HS+ I HIY ++ CG
Sbjct: 215 ENPNLYFHSDDVILCVLPMFHIYSLNSVLLCG 246
>gnl|CDD|217004 pfam02374, ArsA_ATPase, Anion-transporting ATPase. This Pfam
family represents a conserved domain, which is sometimes
repeated, in an anion-transporting ATPase. The ATPase is
involved in the removal of arsenate, antimonite, and
arsenate from the cell.
Length = 304
Score = 26.9 bits (60), Expect = 9.3
Identities = 33/143 (23%), Positives = 53/143 (37%), Gaps = 20/143 (13%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQKLSIRLQSKYKITEFIEINSHSLFSKYFS-ESGKLVQK 75
R + G G GKT++ A A +LS + K+ +HSL S F+ + G K
Sbjct: 2 RWIFFGGKGGVGKTTVSCATAVRLS---EQGKKVLLVSTDPAHSL-SDSFNQKFGHEPTK 57
Query: 76 MFNKIKEAVEYEESLVCLLIDEIESLTRARESVMSGTEPSDGVRVVNAVLTQIDQLKKKS 135
++ E+L + ID L R V G+ ++ L ++
Sbjct: 58 --------IKGVENLSAMEIDPQMELEEYRGEVQDPINAVLGLDML------EGILAEEL 103
Query: 136 TGLSGRTLRKIPFLTFVKYISNN 158
+ L G F F KY+
Sbjct: 104 SSLPG-IDEIASFDEFKKYMDEG 125
>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 = 26.8 bits (60), Expect = 9.4
Identities = 8/17 (47%), Positives = 11/17 (64%)
Query: 17 RVVLLHGPPGTGKTSLC 33
R+ + G G+GKT LC
Sbjct: 20 RITEIFGEFGSGKTQLC 36
>gnl|CDD|214692 smart00487, DEXDc, DEAD-like helicases superfamily.
Length = 201
Score = 26.7 bits (59), Expect = 9.5
Identities = 8/15 (53%), Positives = 10/15 (66%)
Query: 16 NRVVLLHGPPGTGKT 30
R V+L P G+GKT
Sbjct: 24 LRDVILAAPTGSGKT 38
>gnl|CDD|225369 COG2812, DnaX, DNA polymerase III, gamma/tau subunits [DNA
replication, recombination, and repair].
Length = 515
Score = 27.4 bits (61), Expect = 9.8
Identities = 13/38 (34%), Positives = 20/38 (52%), Gaps = 3/38 (7%)
Query: 6 SKVKSNIISWNRVV---LLHGPPGTGKTSLCKAVAQKL 40
K SN + R+ L GP G GKT++ + +A+ L
Sbjct: 25 VKTLSNALENGRIAHAYLFSGPRGVGKTTIARILAKAL 62
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
0.318 0.132 0.371
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: 12,348,277
Number of extensions: 1127901
Number of successful extensions: 1945
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1915
Number of HSP's successfully gapped: 325
Length of query: 256
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 161
Effective length of database: 6,723,972
Effective search space: 1082559492
Effective search space used: 1082559492
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 58 (25.8 bits)