RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6772
(80 letters)
>gnl|CDD|240423 PTZ00454, PTZ00454, 26S protease regulatory subunit 6B-like
protein; Provisional.
Length = 398
Score = 157 bits (399), Expect = 1e-48
Identities = 59/69 (85%), Positives = 63/69 (91%)
Query: 10 DEKPDVQYSDIGGMDMQKQEIREAVELPLTHFDLYKQIGIDPPRGVLLYGPPGCGKTMLA 69
EKPDV YSDIGG+D+QKQEIREAVELPLT +LY+QIGIDPPRGVLLYGPPG GKTMLA
Sbjct: 137 SEKPDVTYSDIGGLDIQKQEIREAVELPLTCPELYEQIGIDPPRGVLLYGPPGTGKTMLA 196
Query: 70 KAVAHHTTV 78
KAVAHHTT
Sbjct: 197 KAVAHHTTA 205
>gnl|CDD|179699 PRK03992, PRK03992, proteasome-activating nucleotidase;
Provisional.
Length = 389
Score = 139 bits (354), Expect = 6e-42
Identities = 43/67 (64%), Positives = 56/67 (83%)
Query: 10 DEKPDVQYSDIGGMDMQKQEIREAVELPLTHFDLYKQIGIDPPRGVLLYGPPGCGKTMLA 69
E P+V Y DIGG++ Q +E+REAVELPL +L++++GI+PP+GVLLYGPPG GKT+LA
Sbjct: 123 IESPNVTYEDIGGLEEQIREVREAVELPLKKPELFEEVGIEPPKGVLLYGPPGTGKTLLA 182
Query: 70 KAVAHHT 76
KAVAH T
Sbjct: 183 KAVAHET 189
>gnl|CDD|224143 COG1222, RPT1, ATP-dependent 26S proteasome regulatory subunit
[Posttranslational modification, protein turnover,
chaperones].
Length = 406
Score = 139 bits (352), Expect = 1e-41
Identities = 47/67 (70%), Positives = 58/67 (86%)
Query: 10 DEKPDVQYSDIGGMDMQKQEIREAVELPLTHFDLYKQIGIDPPRGVLLYGPPGCGKTMLA 69
+EKPDV Y DIGG+D Q QEIRE VELPL + +L++++GIDPP+GVLLYGPPG GKT+LA
Sbjct: 143 EEKPDVTYEDIGGLDEQIQEIREVVELPLKNPELFEELGIDPPKGVLLYGPPGTGKTLLA 202
Query: 70 KAVAHHT 76
KAVA+ T
Sbjct: 203 KAVANQT 209
>gnl|CDD|130309 TIGR01242, 26Sp45, 26S proteasome subunit P45 family. Many
proteins may score above the trusted cutoff because an
internal.
Length = 364
Score = 118 bits (297), Expect = 7e-34
Identities = 45/67 (67%), Positives = 59/67 (88%)
Query: 10 DEKPDVQYSDIGGMDMQKQEIREAVELPLTHFDLYKQIGIDPPRGVLLYGPPGCGKTMLA 69
+E+P+V Y DIGG++ Q +EIREAVELPL H +L++++GI+PP+GVLLYGPPG GKT+LA
Sbjct: 114 EERPNVSYEDIGGLEEQIREIREAVELPLKHPELFEEVGIEPPKGVLLYGPPGTGKTLLA 173
Query: 70 KAVAHHT 76
KAVAH T
Sbjct: 174 KAVAHET 180
>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 = 111 bits (279), Expect = 1e-30
Identities = 41/64 (64%), Positives = 54/64 (84%)
Query: 10 DEKPDVQYSDIGGMDMQKQEIREAVELPLTHFDLYKQIGIDPPRGVLLYGPPGCGKTMLA 69
+E PDV Y+DIGG+ Q ++IR+AVELP H +LY++ G+ PP+GVLLYGPPGCGKT++A
Sbjct: 174 EEVPDVTYADIGGLGSQIEQIRDAVELPFLHPELYREYGLKPPKGVLLYGPPGCGKTLIA 233
Query: 70 KAVA 73
KAVA
Sbjct: 234 KAVA 237
>gnl|CDD|185575 PTZ00361, PTZ00361, 26 proteosome regulatory subunit 4-like
protein; Provisional.
Length = 438
Score = 106 bits (267), Expect = 3e-29
Identities = 46/70 (65%), Positives = 57/70 (81%)
Query: 8 KNDEKPDVQYSDIGGMDMQKQEIREAVELPLTHFDLYKQIGIDPPRGVLLYGPPGCGKTM 67
K D+ P Y+DIGG++ Q QEI+EAVELPLTH +LY IGI PP+GV+LYGPPG GKT+
Sbjct: 173 KVDKAPLESYADIGGLEQQIQEIKEAVELPLTHPELYDDIGIKPPKGVILYGPPGTGKTL 232
Query: 68 LAKAVAHHTT 77
LAKAVA+ T+
Sbjct: 233 LAKAVANETS 242
>gnl|CDD|223540 COG0464, SpoVK, ATPases of the AAA+ class [Posttranslational
modification, protein turnover, chaperones].
Length = 494
Score = 106 bits (265), Expect = 1e-28
Identities = 36/66 (54%), Positives = 51/66 (77%)
Query: 11 EKPDVQYSDIGGMDMQKQEIREAVELPLTHFDLYKQIGIDPPRGVLLYGPPGCGKTMLAK 70
E DV DIGG++ K+E++EA+E PL +L++++G+ PP+GVLLYGPPG GKT+LAK
Sbjct: 235 EDEDVTLDDIGGLEEAKEELKEAIETPLKRPELFRKLGLRPPKGVLLYGPPGTGKTLLAK 294
Query: 71 AVAHHT 76
AVA +
Sbjct: 295 AVALES 300
Score = 51.0 bits (122), Expect = 3e-09
Identities = 25/39 (64%), Positives = 35/39 (89%)
Query: 35 ELPLTHFDLYKQIGIDPPRGVLLYGPPGCGKTMLAKAVA 73
ELPL +L+K++GI+PP+GVLL+GPPG GKT+LA+A+A
Sbjct: 1 ELPLKEPELFKKLGIEPPKGVLLHGPPGTGKTLLARALA 39
>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 = 96.9 bits (241), Expect = 2e-25
Identities = 40/63 (63%), Positives = 55/63 (87%)
Query: 11 EKPDVQYSDIGGMDMQKQEIREAVELPLTHFDLYKQIGIDPPRGVLLYGPPGCGKTMLAK 70
E P+V++SDIGG++ KQE+REAVE PL H ++++++GI PP+GVLL+GPPG GKT+LAK
Sbjct: 446 EVPNVRWSDIGGLEEVKQELREAVEWPLKHPEIFEKMGIRPPKGVLLFGPPGTGKTLLAK 505
Query: 71 AVA 73
AVA
Sbjct: 506 AVA 508
Score = 95.7 bits (238), Expect = 6e-25
Identities = 39/62 (62%), Positives = 51/62 (82%)
Query: 13 PDVQYSDIGGMDMQKQEIREAVELPLTHFDLYKQIGIDPPRGVLLYGPPGCGKTMLAKAV 72
P V Y DIGG+ K++IRE VELP+ H +L++ +GI+PP+GVLLYGPPG GKT+LAKAV
Sbjct: 173 PKVTYEDIGGLKEAKEKIREMVELPMKHPELFEHLGIEPPKGVLLYGPPGTGKTLLAKAV 232
Query: 73 AH 74
A+
Sbjct: 233 AN 234
>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 = 76.2 bits (188), Expect = 4e-18
Identities = 32/65 (49%), Positives = 45/65 (69%), Gaps = 1/65 (1%)
Query: 9 NDEKPDVQYSDIGGMDMQKQEIREAVELPLTHFDLYKQIGIDPPRGVLLYGPPGCGKTML 68
N+EKP V + D+ G+D K+E+ E V+ L + + ++G P+GVLL GPPG GKT+L
Sbjct: 46 NEEKPKVTFKDVAGIDEAKEELMEIVDF-LKNPSKFTKLGAKIPKGVLLVGPPGTGKTLL 104
Query: 69 AKAVA 73
AKAVA
Sbjct: 105 AKAVA 109
>gnl|CDD|214386 CHL00176, ftsH, cell division protein; Validated.
Length = 638
Score = 66.6 bits (163), Expect = 1e-14
Identities = 26/62 (41%), Positives = 37/62 (59%), Gaps = 1/62 (1%)
Query: 12 KPDVQYSDIGGMDMQKQEIREAVELPLTHFDLYKQIGIDPPRGVLLYGPPGCGKTMLAKA 71
+ + DI G++ K+E E V L + + +G P+GVLL GPPG GKT+LAKA
Sbjct: 177 DTGITFRDIAGIEEAKEEFEEVVSF-LKKPERFTAVGAKIPKGVLLVGPPGTGKTLLAKA 235
Query: 72 VA 73
+A
Sbjct: 236 IA 237
>gnl|CDD|223541 COG0465, HflB, ATP-dependent Zn proteases [Posttranslational
modification, protein turnover, chaperones].
Length = 596
Score = 60.8 bits (148), Expect = 1e-12
Identities = 29/65 (44%), Positives = 44/65 (67%), Gaps = 1/65 (1%)
Query: 9 NDEKPDVQYSDIGGMDMQKQEIREAVELPLTHFDLYKQIGIDPPRGVLLYGPPGCGKTML 68
+++ V ++D+ G+D K+E+ E V+ L + Y+ +G P+GVLL GPPG GKT+L
Sbjct: 141 LEDQVKVTFADVAGVDEAKEELSELVD-FLKNPKKYQALGAKIPKGVLLVGPPGTGKTLL 199
Query: 69 AKAVA 73
AKAVA
Sbjct: 200 AKAVA 204
>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 = 55.6 bits (134), Expect = 1e-11
Identities = 23/55 (41%), Positives = 32/55 (58%), Gaps = 13/55 (23%)
Query: 21 GGMDMQKQEIREAVELPLTHFDLYKQIGIDPPRGVLLYGPPGCGKTMLAKAVAHH 75
G + + +REA+ELP PP+ +LLYGPPG GKT LA+A+A+
Sbjct: 1 VGQEEAIEALREALELP-------------PPKNLLLYGPPGTGKTTLARAIANE 42
>gnl|CDD|182683 PRK10733, hflB, ATP-dependent metalloprotease; Reviewed.
Length = 644
Score = 54.3 bits (130), Expect = 2e-10
Identities = 27/62 (43%), Positives = 40/62 (64%), Gaps = 1/62 (1%)
Query: 17 YSDIGGMDMQKQEIREAVELPLTHFDLYKQIGIDPPRGVLLYGPPGCGKTMLAKAVAHHT 76
++D+ G D K+E+ E VE L ++++G P+GVL+ GPPG GKT+LAKA+A
Sbjct: 151 FADVAGCDEAKEEVAELVEY-LREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAGEA 209
Query: 77 TV 78
V
Sbjct: 210 KV 211
>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 = 52.2 bits (126), Expect = 3e-10
Identities = 16/22 (72%), Positives = 17/22 (77%)
Query: 55 VLLYGPPGCGKTMLAKAVAHHT 76
+LLYGPPG GKT LAKAVA
Sbjct: 1 LLLYGPPGTGKTTLAKAVAKEL 22
>gnl|CDD|224144 COG1223, COG1223, Predicted ATPase (AAA+ superfamily) [General
function prediction only].
Length = 368
Score = 51.4 bits (123), Expect = 3e-09
Identities = 28/81 (34%), Positives = 43/81 (53%), Gaps = 10/81 (12%)
Query: 1 METCKPTKNDEKPDVQYSDIGGMDMQKQEIR---EAVELPLTHFDLYKQIGIDPPRGVLL 57
+ET + + D+ D+ G + K++ R E +E P ++ G P+ VL
Sbjct: 104 LETPREEDREIISDITLDDVIGQEEAKRKCRLIMEYLENP-------ERFGDWAPKNVLF 156
Query: 58 YGPPGCGKTMLAKAVAHHTTV 78
YGPPG GKTM+AKA+A+ V
Sbjct: 157 YGPPGTGKTMMAKALANEAKV 177
>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit;
Provisional.
Length = 482
Score = 46.1 bits (110), Expect = 1e-07
Identities = 15/24 (62%), Positives = 19/24 (79%)
Query: 51 PPRGVLLYGPPGCGKTMLAKAVAH 74
P + +LLYGPPG GKT LA A+A+
Sbjct: 38 PKKALLLYGPPGVGKTSLAHALAN 61
>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 = 45.3 bits (107), Expect = 2e-07
Identities = 13/38 (34%), Positives = 17/38 (44%)
Query: 42 DLYKQIGIDPPRGVLLYGPPGCGKTMLAKAVAHHTTVL 79
D ++ P VLL GP G GKT L + + V
Sbjct: 14 DALRRARSGGPPSVLLTGPSGTGKTSLLRELLEGLLVA 51
>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 = 43.9 bits (103), Expect = 5e-07
Identities = 13/25 (52%), Positives = 17/25 (68%)
Query: 51 PPRGVLLYGPPGCGKTMLAKAVAHH 75
P +L+ GPPG GKT LA+A+A
Sbjct: 1 PGEVILIVGPPGSGKTTLARALARE 25
>gnl|CDD|237355 PRK13342, PRK13342, recombination factor protein RarA; Reviewed.
Length = 413
Score = 44.7 bits (107), Expect = 6e-07
Identities = 14/34 (41%), Positives = 20/34 (58%)
Query: 43 LYKQIGIDPPRGVLLYGPPGCGKTMLAKAVAHHT 76
L + I ++L+GPPG GKT LA+ +A T
Sbjct: 27 LRRMIEAGRLSSMILWGPPGTGKTTLARIIAGAT 60
>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 = 40.4 bits (95), Expect = 8e-06
Identities = 13/24 (54%), Positives = 17/24 (70%)
Query: 54 GVLLYGPPGCGKTMLAKAVAHHTT 77
GVLL GPPG GK+ LA+ +A +
Sbjct: 1 GVLLVGPPGTGKSELAERLAAALS 24
>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 = 40.6 bits (96), Expect = 1e-05
Identities = 12/17 (70%), Positives = 14/17 (82%)
Query: 55 VLLYGPPGCGKTMLAKA 71
+L+ GPPG GKTMLAK
Sbjct: 25 LLMIGPPGSGKTMLAKR 41
>gnl|CDD|223786 COG0714, COG0714, MoxR-like ATPases [General function prediction
only].
Length = 329
Score = 40.5 bits (95), Expect = 2e-05
Identities = 14/21 (66%), Positives = 17/21 (80%)
Query: 53 RGVLLYGPPGCGKTMLAKAVA 73
VLL GPPG GKT+LA+A+A
Sbjct: 44 GHVLLEGPPGVGKTLLARALA 64
>gnl|CDD|177094 CHL00195, ycf46, Ycf46; Provisional.
Length = 489
Score = 39.6 bits (93), Expect = 3e-05
Identities = 23/65 (35%), Positives = 35/65 (53%), Gaps = 9/65 (13%)
Query: 13 PDVQYSDIGGMDMQKQEIREAVELPLTHFDLYKQ---IGIDPPRGVLLYGPPGCGKTMLA 69
+ + SDIGG+D K +++ KQ G+ PRG+LL G G GK++ A
Sbjct: 223 VNEKISDIGGLDNLKDWLKKRST------SFSKQASNYGLPTPRGLLLVGIQGTGKSLTA 276
Query: 70 KAVAH 74
KA+A+
Sbjct: 277 KAIAN 281
>gnl|CDD|237354 PRK13341, PRK13341, recombination factor protein RarA/unknown
domain fusion protein; Reviewed.
Length = 725
Score = 39.3 bits (92), Expect = 5e-05
Identities = 14/21 (66%), Positives = 18/21 (85%)
Query: 56 LLYGPPGCGKTMLAKAVAHHT 76
+LYGPPG GKT LA+ +A+HT
Sbjct: 56 ILYGPPGVGKTTLARIIANHT 76
>gnl|CDD|225165 COG2256, MGS1, ATPase related to the helicase subunit of the
Holliday junction resolvase [DNA replication,
recombination, and repair].
Length = 436
Score = 38.8 bits (91), Expect = 7e-05
Identities = 12/20 (60%), Positives = 15/20 (75%)
Query: 57 LYGPPGCGKTMLAKAVAHHT 76
L+GPPG GKT LA+ +A T
Sbjct: 53 LWGPPGTGKTTLARLIAGTT 72
>gnl|CDD|234619 PRK00080, ruvB, Holliday junction DNA helicase RuvB; Reviewed.
Length = 328
Score = 38.6 bits (91), Expect = 7e-05
Identities = 14/20 (70%), Positives = 16/20 (80%)
Query: 55 VLLYGPPGCGKTMLAKAVAH 74
VLLYGPPG GKT LA +A+
Sbjct: 54 VLLYGPPGLGKTTLANIIAN 73
>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 = 7e-05
Identities = 14/20 (70%), Positives = 16/20 (80%)
Query: 55 VLLYGPPGCGKTMLAKAVAH 74
VLLYGPPG GKT LA +A+
Sbjct: 53 VLLYGPPGLGKTTLANIIAN 72
>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 = 38.5 bits (90), Expect = 8e-05
Identities = 16/31 (51%), Positives = 18/31 (58%), Gaps = 4/31 (12%)
Query: 45 KQIGIDPPRG-VLLYGPPGCGKTMLAKAVAH 74
KQ G R V YGP GKT LA+A+AH
Sbjct: 108 KQGG---KRNTVWFYGPASTGKTNLAQAIAH 135
>gnl|CDD|226646 COG4178, COG4178, ABC-type uncharacterized transport system,
permease and ATPase components [General function
prediction only].
Length = 604
Score = 38.1 bits (89), Expect = 1e-04
Identities = 15/72 (20%), Positives = 26/72 (36%), Gaps = 8/72 (11%)
Query: 11 EKPDVQYSDIGGMDMQKQEIREAVE---LPLTHFD---LYKQIGIDPPRG--VLLYGPPG 62
+ + + G + L L D L ++ + G +L+ G G
Sbjct: 370 QMDTEKPARTGRRIDFDDNADHGITLENLSLRTPDGQTLLSELNFEVRPGERLLITGESG 429
Query: 63 CGKTMLAKAVAH 74
GKT L +A+A
Sbjct: 430 AGKTSLLRALAG 441
>gnl|CDD|224402 COG1485, COG1485, Predicted ATPase [General function prediction
only].
Length = 367
Score = 37.3 bits (87), Expect = 2e-04
Identities = 16/39 (41%), Positives = 18/39 (46%), Gaps = 2/39 (5%)
Query: 32 EAVELPLTHFDLYKQIGID--PPRGVLLYGPPGCGKTML 68
E V L G D P RG+ L+G G GKTML
Sbjct: 43 ELVAPRSARKALGWLFGRDHGPVRGLYLWGGVGRGKTML 81
>gnl|CDD|218685 pfam05673, DUF815, Protein of unknown function (DUF815). This
family consists of several bacterial proteins of
unknown function.
Length = 248
Score = 37.1 bits (87), Expect = 2e-04
Identities = 21/71 (29%), Positives = 30/71 (42%), Gaps = 20/71 (28%)
Query: 11 EKPD-VQYSDIGGMDMQKQEIREAVE-----LPLTHFDLYKQIGIDPPRGVLLYGPPGCG 64
PD V D+ G+D QK+ + E LP + VLL+G G G
Sbjct: 20 PHPDPVDLDDLVGIDRQKEALLRNTEQFLAGLPANN--------------VLLWGARGTG 65
Query: 65 KTMLAKAVAHH 75
K+ L KA+ +
Sbjct: 66 KSSLVKALLNE 76
>gnl|CDD|237495 PRK13765, PRK13765, ATP-dependent protease Lon; Provisional.
Length = 637
Score = 36.9 bits (86), Expect = 3e-04
Identities = 13/21 (61%), Positives = 17/21 (80%)
Query: 53 RGVLLYGPPGCGKTMLAKAVA 73
R V++ G PG GK+MLAKA+A
Sbjct: 51 RHVMMIGSPGTGKSMLAKAMA 71
>gnl|CDD|225164 COG2255, RuvB, Holliday junction resolvasome, helicase subunit
[DNA replication, recombination, and repair].
Length = 332
Score = 36.8 bits (86), Expect = 3e-04
Identities = 13/20 (65%), Positives = 16/20 (80%)
Query: 55 VLLYGPPGCGKTMLAKAVAH 74
VLL+GPPG GKT LA +A+
Sbjct: 55 VLLFGPPGLGKTTLAHIIAN 74
>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 = 3e-04
Identities = 13/21 (61%), Positives = 16/21 (76%)
Query: 55 VLLYGPPGCGKTMLAKAVAHH 75
+ LYGPPGCGK+ LAK +A
Sbjct: 1 IWLYGPPGCGKSTLAKYLARA 21
>gnl|CDD|223666 COG0593, DnaA, ATPase involved in DNA replication initiation [DNA
replication, recombination, and repair].
Length = 408
Score = 36.9 bits (86), Expect = 3e-04
Identities = 8/21 (38%), Positives = 13/21 (61%)
Query: 55 VLLYGPPGCGKTMLAKAVAHH 75
+ +YG G GKT L +A+ +
Sbjct: 116 LFIYGGVGLGKTHLLQAIGNE 136
>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 = 36.5 bits (85), Expect = 4e-04
Identities = 13/20 (65%), Positives = 16/20 (80%)
Query: 55 VLLYGPPGCGKTMLAKAVAH 74
+LLYGPPG GKT LA +A+
Sbjct: 33 LLLYGPPGLGKTTLAHIIAN 52
>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 = 36.1 bits (84), Expect = 6e-04
Identities = 13/46 (28%), Positives = 21/46 (45%), Gaps = 6/46 (13%)
Query: 31 REAVELPLTHFD-LYKQIGIDPPRGVLLYGPPGCGKTM-LAKAVAH 74
E +EL L + +L G G GK++ LA+A+A+
Sbjct: 5 EETLEL----TKKLKEADASKKVVRFVLTGERGSGKSVLLAQAMAY 46
>gnl|CDD|184311 PRK13764, PRK13764, ATPase; Provisional.
Length = 602
Score = 36.0 bits (84), Expect = 6e-04
Identities = 10/21 (47%), Positives = 15/21 (71%)
Query: 53 RGVLLYGPPGCGKTMLAKAVA 73
G+L+ G PG GK+ A+A+A
Sbjct: 258 EGILIAGAPGAGKSTFAQALA 278
>gnl|CDD|222194 pfam13521, AAA_28, AAA domain.
Length = 162
Score = 35.2 bits (82), Expect = 8e-04
Identities = 8/21 (38%), Positives = 13/21 (61%)
Query: 55 VLLYGPPGCGKTMLAKAVAHH 75
+++ G P GKT L +A+A
Sbjct: 2 IVITGGPSTGKTTLLEALAAR 22
>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 = 35.7 bits (83), Expect = 8e-04
Identities = 10/22 (45%), Positives = 12/22 (54%)
Query: 51 PPRGVLLYGPPGCGKTMLAKAV 72
P V +YG G GKT + K V
Sbjct: 39 RPSNVFIYGKTGTGKTAVTKYV 60
>gnl|CDD|224145 COG1224, TIP49, DNA helicase TIP49, TBP-interacting protein
[Transcription].
Length = 450
Score = 35.4 bits (82), Expect = 0.001
Identities = 13/21 (61%), Positives = 16/21 (76%)
Query: 53 RGVLLYGPPGCGKTMLAKAVA 73
RG+L+ GPPG GKT LA +A
Sbjct: 66 RGILIVGPPGTGKTALAMGIA 86
>gnl|CDD|236153 PRK08116, PRK08116, hypothetical protein; Validated.
Length = 268
Score = 35.4 bits (82), Expect = 0.001
Identities = 11/23 (47%), Positives = 15/23 (65%)
Query: 53 RGVLLYGPPGCGKTMLAKAVAHH 75
G+LL+G G GKT LA +A+
Sbjct: 115 VGLLLWGSVGTGKTYLAACIANE 137
>gnl|CDD|223679 COG0606, COG0606, Predicted ATPase with chaperone activity
[Posttranslational modification, protein turnover,
chaperones].
Length = 490
Score = 35.3 bits (82), Expect = 0.001
Identities = 12/18 (66%), Positives = 13/18 (72%)
Query: 53 RGVLLYGPPGCGKTMLAK 70
+LL GPPG GKTMLA
Sbjct: 199 HNLLLVGPPGTGKTMLAS 216
>gnl|CDD|224401 COG1484, DnaC, DNA replication protein [DNA replication,
recombination, and repair].
Length = 254
Score = 35.1 bits (81), Expect = 0.001
Identities = 14/52 (26%), Positives = 27/52 (51%), Gaps = 5/52 (9%)
Query: 24 DMQKQEIREAVELPLTHFDLYKQIGIDPPRGVLLYGPPGCGKTMLAKAVAHH 75
+ Q ++A+E + + +++ ++L GPPG GKT LA A+ +
Sbjct: 82 EFQPGIDKKALEDLASLVEFFER-----GENLVLLGPPGVGKTHLAIAIGNE 128
>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 = 34.6 bits (80), Expect = 0.002
Identities = 10/22 (45%), Positives = 13/22 (59%)
Query: 53 RGVLLYGPPGCGKTMLAKAVAH 74
R V+L G G GKT L + +A
Sbjct: 1 RTVILQGEAGSGKTTLLQKIAL 22
>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 = 34.8 bits (80), Expect = 0.002
Identities = 15/21 (71%), Positives = 17/21 (80%)
Query: 53 RGVLLYGPPGCGKTMLAKAVA 73
R VLL G PG GK+MLAKA+A
Sbjct: 38 RNVLLIGEPGVGKSMLAKAMA 58
>gnl|CDD|222104 pfam13401, AAA_22, AAA domain.
Length = 124
Score = 33.8 bits (78), Expect = 0.002
Identities = 8/23 (34%), Positives = 11/23 (47%)
Query: 52 PRGVLLYGPPGCGKTMLAKAVAH 74
+L G G GKT L + +A
Sbjct: 4 AGIGVLTGESGSGKTTLLRRLAR 26
>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 = 34.2 bits (79), Expect = 0.003
Identities = 13/21 (61%), Positives = 16/21 (76%)
Query: 53 RGVLLYGPPGCGKTMLAKAVA 73
R VL+ GPPG GKT LA A++
Sbjct: 51 RAVLIAGPPGTGKTALAIAIS 71
>gnl|CDD|223542 COG0466, Lon, ATP-dependent Lon protease, bacterial type
[Posttranslational modification, protein turnover,
chaperones].
Length = 782
Score = 34.1 bits (79), Expect = 0.003
Identities = 11/18 (61%), Positives = 13/18 (72%)
Query: 56 LLYGPPGCGKTMLAKAVA 73
L GPPG GKT L K++A
Sbjct: 354 CLVGPPGVGKTSLGKSIA 371
>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 = 33.8 bits (78), Expect = 0.004
Identities = 12/25 (48%), Positives = 15/25 (60%), Gaps = 2/25 (8%)
Query: 56 LLYGPPGCGKTMLAKAVAHHTTVLC 80
L GP G GK +LA A+A +LC
Sbjct: 18 LFAGPEGVGKELLALALAKA--LLC 40
>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 = 33.7 bits (78), Expect = 0.004
Identities = 12/19 (63%), Positives = 13/19 (68%)
Query: 55 VLLYGPPGCGKTMLAKAVA 73
L GP G GKT LAKA+A
Sbjct: 6 FLFLGPTGVGKTELAKALA 24
>gnl|CDD|214396 CHL00206, ycf2, Ycf2; Provisional.
Length = 2281
Score = 33.7 bits (77), Expect = 0.004
Identities = 10/28 (35%), Positives = 18/28 (64%)
Query: 46 QIGIDPPRGVLLYGPPGCGKTMLAKAVA 73
++ + P RG+L+ G G G++ L K +A
Sbjct: 1624 RLALSPSRGILVIGSIGTGRSYLVKYLA 1651
>gnl|CDD|129465 TIGR00368, TIGR00368, Mg chelatase-related protein. The N-terminal
end matches very strongly a pfam Mg_chelatase domain
[Unknown function, General].
Length = 499
Score = 33.7 bits (77), Expect = 0.004
Identities = 21/69 (30%), Positives = 30/69 (43%), Gaps = 15/69 (21%)
Query: 6 PTKNDEKPDVQYSDIGGMDMQ----KQEIREAVELPLTHFDLYKQIGIDPPRGVLLYGPP 61
T K + S I +D++ +Q + A+E I +LL+GPP
Sbjct: 172 RTNTKPKSIINKSYIIDLDLKDIKGQQHAKRALE-----------IAAAGGHNLLLFGPP 220
Query: 62 GCGKTMLAK 70
G GKTMLA
Sbjct: 221 GSGKTMLAS 229
>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 = 33.4 bits (77), Expect = 0.004
Identities = 13/26 (50%), Positives = 15/26 (57%), Gaps = 2/26 (7%)
Query: 52 PRG--VLLYGPPGCGKTMLAKAVAHH 75
PRG LL G PG GK+ LA +A
Sbjct: 31 PRGGLTLLAGAPGTGKSTLALDLAAA 56
>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 = 33.3 bits (77), Expect = 0.005
Identities = 11/35 (31%), Positives = 14/35 (40%), Gaps = 8/35 (22%)
Query: 48 GIDPPRGVL--LYGPPGCGKTMLAKAVAHHTTVLC 80
GI P G + ++G G GKT L V
Sbjct: 15 GI--PTGRITEIFGEFGSGKTQL----CLQLAVEA 43
>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 = 33.0 bits (76), Expect = 0.006
Identities = 13/21 (61%), Positives = 15/21 (71%)
Query: 52 PRGVLLYGPPGCGKTMLAKAV 72
P VLL G PG GKT LA+A+
Sbjct: 12 PVAVLLGGQPGAGKTELARAL 32
>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 = 33.0 bits (76), Expect = 0.007
Identities = 14/39 (35%), Positives = 19/39 (48%), Gaps = 4/39 (10%)
Query: 38 LTHFDLYKQIGIDPPRGVLLYGPPGCGKTMLAKAVAHHT 76
L F + P VL+ G PG G + L KA+A+ T
Sbjct: 23 LKDFSGV----VKPGEMVLVLGRPGSGCSTLLKALANRT 57
>gnl|CDD|233119 TIGR00763, lon, ATP-dependent protease La. This protein is induced
by heat shock and other stresses in E. coli, B.
subtilis, and other species. The yeast member,
designated PIM1, is located in the mitochondrial matrix,
required for mitochondrial function, and also induced by
heat shock [Protein fate, Degradation of proteins,
peptides, and glycopeptides].
Length = 775
Score = 33.0 bits (76), Expect = 0.007
Identities = 11/17 (64%), Positives = 13/17 (76%)
Query: 57 LYGPPGCGKTMLAKAVA 73
L GPPG GKT L K++A
Sbjct: 352 LVGPPGVGKTSLGKSIA 368
>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 = 33.2 bits (76), Expect = 0.007
Identities = 12/21 (57%), Positives = 16/21 (76%)
Query: 52 PRGVLLYGPPGCGKTMLAKAV 72
P+ V++YGPPG GKT A+ V
Sbjct: 86 PQHVIIYGPPGVGKTAAARLV 106
>gnl|CDD|221983 pfam13207, AAA_17, AAA domain.
Length = 114
Score = 32.3 bits (73), Expect = 0.007
Identities = 11/22 (50%), Positives = 15/22 (68%)
Query: 55 VLLYGPPGCGKTMLAKAVAHHT 76
+L+ GPPG GK+ LAK +A
Sbjct: 2 ILITGPPGSGKSTLAKKLAEKL 23
>gnl|CDD|224768 COG1855, COG1855, ATPase (PilT family) [General function prediction
only].
Length = 604
Score = 32.7 bits (75), Expect = 0.008
Identities = 10/21 (47%), Positives = 15/21 (71%)
Query: 53 RGVLLYGPPGCGKTMLAKAVA 73
G+L+ G PG GK+ A+A+A
Sbjct: 264 EGILIAGAPGAGKSTFAQALA 284
>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 = 32.5 bits (75), Expect = 0.008
Identities = 11/30 (36%), Positives = 14/30 (46%), Gaps = 8/30 (26%)
Query: 46 QIGIDPPRGVLLYGPPGCGKTMLAKAVAHH 75
I ID GP G GK+ +AK +A
Sbjct: 1 IIAID--------GPAGSGKSTVAKLLAKK 22
>gnl|CDD|216202 pfam00931, NB-ARC, NB-ARC domain.
Length = 285
Score = 32.7 bits (75), Expect = 0.009
Identities = 10/24 (41%), Positives = 14/24 (58%)
Query: 55 VLLYGPPGCGKTMLAKAVAHHTTV 78
V + G G GKT LAK + + +V
Sbjct: 22 VGIVGMGGVGKTTLAKQIYNDDSV 45
>gnl|CDD|116340 pfam07726, AAA_3, ATPase family associated with various cellular
activities (AAA). This Pfam entry includes some of the
AAA proteins not detected by the pfam00004 model.
Length = 131
Score = 32.1 bits (74), Expect = 0.009
Identities = 11/19 (57%), Positives = 14/19 (73%)
Query: 55 VLLYGPPGCGKTMLAKAVA 73
VLL G PG KT+LA+ +A
Sbjct: 2 VLLEGVPGLAKTLLARTLA 20
>gnl|CDD|224140 COG1219, ClpX, ATP-dependent protease Clp, ATPase subunit
[Posttranslational modification, protein turnover,
chaperones].
Length = 408
Score = 32.6 bits (75), Expect = 0.009
Identities = 11/19 (57%), Positives = 15/19 (78%)
Query: 55 VLLYGPPGCGKTMLAKAVA 73
+LL GP G GKT+LA+ +A
Sbjct: 100 ILLIGPTGSGKTLLAQTLA 118
>gnl|CDD|223543 COG0467, RAD55, RecA-superfamily ATPases implicated in signal
transduction [Signal transduction mechanisms].
Length = 260
Score = 32.8 bits (75), Expect = 0.009
Identities = 11/27 (40%), Positives = 15/27 (55%)
Query: 48 GIDPPRGVLLYGPPGCGKTMLAKAVAH 74
G+ VL+ GPPG GKT+ A +
Sbjct: 19 GLPRGSVVLITGPPGTGKTIFALQFLY 45
>gnl|CDD|234203 TIGR03420, DnaA_homol_Hda, DnaA regulatory inactivator Hda.
Members of this protein family are Hda (Homologous to
DnaA). These proteins are about half the length of DnaA
and homologous over length of Hda. In the model species
Escherichia coli, the initiation of DNA replication
requires DnaA bound to ATP rather than ADP; Hda helps
facilitate the conversion of DnaA-ATP to DnaA-ADP [DNA
metabolism, DNA replication, recombination, and
repair].
Length = 226
Score = 32.5 bits (75), Expect = 0.009
Identities = 8/24 (33%), Positives = 12/24 (50%)
Query: 52 PRGVLLYGPPGCGKTMLAKAVAHH 75
R + L+G G GK+ L +A
Sbjct: 38 DRFLYLWGESGSGKSHLLQAACAA 61
>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 = 32.9 bits (75), Expect = 0.010
Identities = 15/58 (25%), Positives = 28/58 (48%), Gaps = 10/58 (17%)
Query: 22 GMDMQKQEI---REAVELPLTHFDLYKQIGIDPP---RGVLLYGPPGCGKTMLAKAVA 73
G++ K+++ + + + L + G+ +L GPPG GKT +A+ VA
Sbjct: 280 GLERVKRQVAALKSSTAMALAR----AERGLPVAQTSNHMLFAGPPGTGKTTIARVVA 333
>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 = 32.5 bits (74), Expect = 0.010
Identities = 11/21 (52%), Positives = 15/21 (71%)
Query: 52 PRGVLLYGPPGCGKTMLAKAV 72
P+ ++LYGPPG GKT A+
Sbjct: 175 PQHIILYGPPGVGKTTAARLA 195
>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 = 31.9 bits (73), Expect = 0.014
Identities = 13/36 (36%), Positives = 18/36 (50%), Gaps = 11/36 (30%)
Query: 31 REAVELPLTHFDLYKQIGIDPPRGVLLYGPPGCGKT 66
REA++ L+ D+ L+ GPPG GKT
Sbjct: 7 REAIKKALSSSDIT-----------LIQGPPGTGKT 31
>gnl|CDD|236347 PRK08903, PRK08903, DnaA regulatory inactivator Hda; Validated.
Length = 227
Score = 31.9 bits (73), Expect = 0.016
Identities = 7/26 (26%), Positives = 12/26 (46%)
Query: 51 PPRGVLLYGPPGCGKTMLAKAVAHHT 76
R L+G G G++ L +A+
Sbjct: 41 ADRFFYLWGEAGSGRSHLLQALVADA 66
>gnl|CDD|235422 PRK05342, clpX, ATP-dependent protease ATP-binding subunit ClpX;
Provisional.
Length = 412
Score = 31.7 bits (73), Expect = 0.018
Identities = 11/19 (57%), Positives = 15/19 (78%)
Query: 55 VLLYGPPGCGKTMLAKAVA 73
+LL GP G GKT+LA+ +A
Sbjct: 111 ILLIGPTGSGKTLLAQTLA 129
>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 = 31.5 bits (72), Expect = 0.019
Identities = 13/21 (61%), Positives = 15/21 (71%)
Query: 54 GVLLYGPPGCGKTMLAKAVAH 74
+LL GPPG GKT LA A+ H
Sbjct: 49 NLLLLGPPGVGKTHLACALGH 69
>gnl|CDD|222163 pfam13479, AAA_24, AAA domain. This AAA domain is found in a
wide variety of presumed phage proteins.
Length = 201
Score = 31.5 bits (72), Expect = 0.021
Identities = 13/16 (81%), Positives = 14/16 (87%)
Query: 55 VLLYGPPGCGKTMLAK 70
VL+YGPPG GKT LAK
Sbjct: 6 VLIYGPPGIGKTSLAK 21
>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 = 0.024
Identities = 14/23 (60%), Positives = 16/23 (69%), Gaps = 1/23 (4%)
Query: 52 PRGVLLY-GPPGCGKTMLAKAVA 73
P G L+ GP G GKT LAKA+A
Sbjct: 520 PIGSFLFLGPTGVGKTELAKALA 542
>gnl|CDD|215758 pfam00158, Sigma54_activat, Sigma-54 interaction domain.
Length = 168
Score = 30.8 bits (71), Expect = 0.031
Identities = 8/18 (44%), Positives = 12/18 (66%)
Query: 55 VLLYGPPGCGKTMLAKAV 72
VL+ G G GK + A+A+
Sbjct: 25 VLITGESGTGKELFARAI 42
>gnl|CDD|215599 PLN03140, PLN03140, ABC transporter G family member; Provisional.
Length = 1470
Score = 31.4 bits (71), Expect = 0.032
Identities = 14/25 (56%), Positives = 15/25 (60%)
Query: 49 IDPPRGVLLYGPPGCGKTMLAKAVA 73
I P R LL GPP GKT L A+A
Sbjct: 188 IKPSRMTLLLGPPSSGKTTLLLALA 212
>gnl|CDD|182140 PRK09912, PRK09912, L-glyceraldehyde 3-phosphate reductase;
Provisional.
Length = 346
Score = 31.1 bits (70), Expect = 0.032
Identities = 13/38 (34%), Positives = 22/38 (57%), Gaps = 2/38 (5%)
Query: 17 YSDIGGMDMQKQEIREAVELPLTHFDLYKQIGIDPPRG 54
+ + ++ Q+ +R+A +L +THFDL G PP G
Sbjct: 36 FGHVNALESQRAILRKAFDLGITHFDLANNYG--PPPG 71
>gnl|CDD|234763 PRK00440, rfc, replication factor C small subunit; Reviewed.
Length = 319
Score = 31.0 bits (71), Expect = 0.033
Identities = 11/19 (57%), Positives = 12/19 (63%)
Query: 56 LLYGPPGCGKTMLAKAVAH 74
L GPPG GKT A A+A
Sbjct: 42 LFAGPPGTGKTTAALALAR 60
>gnl|CDD|235244 PRK04182, PRK04182, cytidylate kinase; Provisional.
Length = 180
Score = 30.9 bits (71), Expect = 0.034
Identities = 9/17 (52%), Positives = 12/17 (70%)
Query: 59 GPPGCGKTMLAKAVAHH 75
GPPG GKT +A+ +A
Sbjct: 7 GPPGSGKTTVARLLAEK 23
>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 = 0.037
Identities = 11/28 (39%), Positives = 16/28 (57%)
Query: 47 IGIDPPRGVLLYGPPGCGKTMLAKAVAH 74
I P +L+ GP G GK+ L +A+A
Sbjct: 22 FEIKPGDRLLITGPSGTGKSSLFRALAG 49
>gnl|CDD|215651 pfam00006, ATP-synt_ab, ATP synthase alpha/beta family,
nucleotide-binding domain. This family includes the
ATP synthase alpha and beta subunits, the ATP synthase
associated with flagella and the termination factor
Rho.
Length = 213
Score = 30.9 bits (71), Expect = 0.038
Identities = 7/22 (31%), Positives = 13/22 (59%)
Query: 55 VLLYGPPGCGKTMLAKAVAHHT 76
+ ++G G GKT+L +A +
Sbjct: 18 IGIFGGSGTGKTVLLGMIARNA 39
>gnl|CDD|224027 COG1102, Cmk, Cytidylate kinase [Nucleotide transport and
metabolism].
Length = 179
Score = 30.8 bits (70), Expect = 0.039
Identities = 9/18 (50%), Positives = 12/18 (66%)
Query: 59 GPPGCGKTMLAKAVAHHT 76
G PG GKT +A+ +A H
Sbjct: 7 GLPGSGKTTVARELAEHL 24
>gnl|CDD|234152 TIGR03265, PhnT2, putative 2-aminoethylphosphonate ABC
transporter, ATP-binding protein. This ABC transporter
ATP-binding protein is found in a number of genomes in
operon-like contexts strongly suggesting a substrate
specificity for 2-aminoethylphosphonate (2-AEP). The
characterized PhnSTUV system is absent in the genomes
in which this system is found. These genomes encode
systems for the catabolism of 2-AEP, making the need
for a 2-AEP-specific transporter likely [Transport and
binding proteins, Amino acids, peptides and amines].
Length = 353
Score = 30.8 bits (70), Expect = 0.042
Identities = 15/44 (34%), Positives = 21/44 (47%), Gaps = 2/44 (4%)
Query: 32 EAVELPLTHFDLYKQIGIDPPRG--VLLYGPPGCGKTMLAKAVA 73
+ + F K I + +G V L GP GCGKT L + +A
Sbjct: 8 DNIRKRFGAFTALKDISLSVKKGEFVCLLGPSGCGKTTLLRIIA 51
>gnl|CDD|224391 COG1474, CDC6, Cdc6-related protein, AAA superfamily ATPase [DNA
replication, recombination, and repair /
Posttranslational modification, protein turnover,
chaperones].
Length = 366
Score = 30.8 bits (70), Expect = 0.042
Identities = 10/22 (45%), Positives = 13/22 (59%)
Query: 52 PRGVLLYGPPGCGKTMLAKAVA 73
P +++YGP G GKT K V
Sbjct: 42 PSNIIIYGPTGTGKTATVKFVM 63
>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 = 30.7 bits (70), Expect = 0.044
Identities = 16/41 (39%), Positives = 20/41 (48%), Gaps = 10/41 (24%)
Query: 38 LTHF----DLYKQI------GIDPPRGVLLYGPPGCGKTML 68
L H+ L KQ+ I+P V+L GP G GKT L
Sbjct: 7 LNHYYGHGSLRKQVLFDINLEINPGEIVILTGPSGSGKTTL 47
>gnl|CDD|183133 PRK11432, fbpC, ferric transporter ATP-binding subunit;
Provisional.
Length = 351
Score = 30.8 bits (70), Expect = 0.046
Identities = 12/24 (50%), Positives = 15/24 (62%), Gaps = 2/24 (8%)
Query: 52 PRG--VLLYGPPGCGKTMLAKAVA 73
+G V L GP GCGKT + + VA
Sbjct: 30 KQGTMVTLLGPSGCGKTTVLRLVA 53
>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 = 30.2 bits (69), Expect = 0.048
Identities = 6/21 (28%), Positives = 9/21 (42%)
Query: 55 VLLYGPPGCGKTMLAKAVAHH 75
+++ GP GKT L
Sbjct: 5 IVITGPRQVGKTTLLLQFLKE 25
>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 = 30.7 bits (70), Expect = 0.048
Identities = 11/21 (52%), Positives = 13/21 (61%), Gaps = 2/21 (9%)
Query: 52 PRG--VLLYGPPGCGKTMLAK 70
PRG VL+ G PG GKT+
Sbjct: 17 PRGRVVLITGGPGTGKTIFGL 37
>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 = 0.049
Identities = 12/24 (50%), Positives = 16/24 (66%)
Query: 55 VLLYGPPGCGKTMLAKAVAHHTTV 78
+LL GP G GKT+LA+ +A V
Sbjct: 119 ILLIGPTGSGKTLLAQTLARILNV 142
>gnl|CDD|105560 PRK12339, PRK12339, 2-phosphoglycerate kinase; Provisional.
Length = 197
Score = 30.5 bits (69), Expect = 0.051
Identities = 8/24 (33%), Positives = 13/24 (54%)
Query: 55 VLLYGPPGCGKTMLAKAVAHHTTV 78
+ G PG GKT ++ +A H +
Sbjct: 6 HFIGGIPGVGKTSISGYIARHRAI 29
>gnl|CDD|182120 PRK09862, PRK09862, putative ATP-dependent protease; Provisional.
Length = 506
Score = 30.7 bits (69), Expect = 0.052
Identities = 12/15 (80%), Positives = 13/15 (86%)
Query: 55 VLLYGPPGCGKTMLA 69
+LL GPPG GKTMLA
Sbjct: 213 LLLIGPPGTGKTMLA 227
>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 = 30.3 bits (69), Expect = 0.052
Identities = 8/19 (42%), Positives = 12/19 (63%)
Query: 55 VLLYGPPGCGKTMLAKAVA 73
+++YGP CGKT L +
Sbjct: 23 IVVYGPRRCGKTALLREFL 41
>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 = 30.5 bits (69), Expect = 0.053
Identities = 12/21 (57%), Positives = 12/21 (57%)
Query: 53 RGVLLYGPPGCGKTMLAKAVA 73
V L GP G GKT LA VA
Sbjct: 22 YPVHLRGPAGTGKTTLAMHVA 42
>gnl|CDD|222160 pfam13476, AAA_23, AAA domain.
Length = 204
Score = 30.6 bits (69), Expect = 0.054
Identities = 13/30 (43%), Positives = 20/30 (66%), Gaps = 1/30 (3%)
Query: 44 YKQIGIDPPRGV-LLYGPPGCGKTMLAKAV 72
+K + ID +G+ L+YGP G GKT + A+
Sbjct: 10 FKDLEIDFSKGLTLIYGPNGSGKTTILDAI 39
>gnl|CDD|237090 PRK12402, PRK12402, replication factor C small subunit 2;
Reviewed.
Length = 337
Score = 30.3 bits (69), Expect = 0.057
Identities = 10/19 (52%), Positives = 13/19 (68%)
Query: 56 LLYGPPGCGKTMLAKAVAH 74
L+ GPPG GKT +A+A
Sbjct: 40 LVQGPPGSGKTAAVRALAR 58
>gnl|CDD|234667 PRK00149, dnaA, chromosomal replication initiation protein;
Reviewed.
Length = 401
Score = 30.5 bits (70), Expect = 0.059
Identities = 8/20 (40%), Positives = 12/20 (60%)
Query: 56 LLYGPPGCGKTMLAKAVAHH 75
+YG G GKT L A+ ++
Sbjct: 103 FIYGGVGLGKTHLLHAIGNY 122
>gnl|CDD|235871 PRK06835, PRK06835, DNA replication protein DnaC; Validated.
Length = 329
Score = 30.3 bits (69), Expect = 0.060
Identities = 16/68 (23%), Positives = 29/68 (42%), Gaps = 14/68 (20%)
Query: 6 PTKNDEKPDVQYSDIGGMDMQKQEIREAVELPLTHFDLYKQIGIDPPRGVLLYGPPGCGK 65
K+D++P ++ ++I E + + +FD +L YG G GK
Sbjct: 151 DEKDDDEPLSPRKNM-------EKILEKCKNFIENFD-------KNNENLLFYGNTGTGK 196
Query: 66 TMLAKAVA 73
T L+ +A
Sbjct: 197 TFLSNCIA 204
>gnl|CDD|223989 COG1061, SSL2, DNA or RNA helicases of superfamily II
[Transcription / DNA replication, recombination, and
repair].
Length = 442
Score = 30.5 bits (69), Expect = 0.060
Identities = 13/61 (21%), Positives = 21/61 (34%), Gaps = 16/61 (26%)
Query: 24 DMQKQEIREAVELPLTHFDLYKQIGIDPPRGVLLYGPPGCGKTMLAKAVAHH----TTVL 79
Q++ + V+ T R ++ P G GKT++A T VL
Sbjct: 39 PYQEEALDALVKNRRTE------------RRGVIVLPTGAGKTVVAAEAIAELKRSTLVL 86
Query: 80 C 80
Sbjct: 87 V 87
>gnl|CDD|232941 TIGR00362, DnaA, chromosomal replication initiator protein DnaA.
DnaA is involved in DNA biosynthesis; initiation of
chromosome replication and can also be transcription
regulator. The C-terminal of the family hits the pfam
bacterial DnaA (bac_dnaA) domain family. For a review,
see Kaguni (2006) [DNA metabolism, DNA replication,
recombination, and repair].
Length = 405
Score = 30.2 bits (69), Expect = 0.067
Identities = 8/21 (38%), Positives = 12/21 (57%)
Query: 55 VLLYGPPGCGKTMLAKAVAHH 75
+ +YG G GKT L A+ +
Sbjct: 139 LFIYGGVGLGKTHLLHAIGNE 159
>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 = 0.075
Identities = 13/48 (27%), Positives = 26/48 (54%), Gaps = 5/48 (10%)
Query: 25 MQKQEIRE-AVELPLTHFDLYKQIGIDPPRGVLLYGPPGCGKTMLAKA 71
+ Q++ E + +P+ + + PP V++ GPPG GK+ L ++
Sbjct: 15 QRTQDLEEKKLHVPV----VDRTPEEPPPLVVVVVGPPGVGKSTLIRS 58
>gnl|CDD|233959 TIGR02639, ClpA, ATP-dependent Clp protease ATP-binding subunit
clpA. [Protein fate, Degradation of proteins, peptides,
and glycopeptides].
Length = 730
Score = 30.0 bits (68), Expect = 0.075
Identities = 13/25 (52%), Positives = 15/25 (60%), Gaps = 1/25 (4%)
Query: 50 DPPRGVLL-YGPPGCGKTMLAKAVA 73
+ P G L GP G GKT LAK +A
Sbjct: 480 NKPVGSFLFVGPTGVGKTELAKQLA 504
>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 = 30.1 bits (68), Expect = 0.077
Identities = 9/19 (47%), Positives = 12/19 (63%)
Query: 57 LYGPPGCGKTMLAKAVAHH 75
L G G GK+ +A A+AH
Sbjct: 3 LMGVAGSGKSTIASALAHR 21
>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 = 0.079
Identities = 11/27 (40%), Positives = 16/27 (59%)
Query: 51 PPRGVLLYGPPGCGKTMLAKAVAHHTT 77
PP V + GPPG GK+ L +++ T
Sbjct: 68 PPFIVAVVGPPGTGKSTLIRSLVRRFT 94
>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 = 30.3 bits (68), Expect = 0.080
Identities = 10/23 (43%), Positives = 15/23 (65%)
Query: 51 PPRGVLLYGPPGCGKTMLAKAVA 73
P R +L+ GP GCGK+ K ++
Sbjct: 109 PKRILLITGPSGCGKSTTIKILS 131
>gnl|CDD|180750 PRK06921, PRK06921, hypothetical protein; Provisional.
Length = 266
Score = 29.7 bits (67), Expect = 0.086
Identities = 15/46 (32%), Positives = 23/46 (50%)
Query: 28 QEIREAVELPLTHFDLYKQIGIDPPRGVLLYGPPGCGKTMLAKAVA 73
Q I++A E + + +++I + L G PG GKT L A A
Sbjct: 93 QAIKDAYECAVEYVKDFEKIQESRKNSIALLGQPGSGKTHLLTAAA 138
>gnl|CDD|217821 pfam03969, AFG1_ATPase, AFG1-like ATPase. This family of
proteins contains a P-loop motif and are predicted to
be ATPases.
Length = 361
Score = 29.7 bits (67), Expect = 0.091
Identities = 10/18 (55%), Positives = 12/18 (66%)
Query: 51 PPRGVLLYGPPGCGKTML 68
P RG+ L+G G GKT L
Sbjct: 60 PVRGLYLWGGVGRGKTHL 77
>gnl|CDD|213213 cd03246, ABCC_Protease_Secretion, ATP-binding cassette domain of
PrtD, subfamily C. This family represents the ABC
component of the protease secretion system PrtD, a
60-kDa integral membrane protein sharing 37% identity
with HlyB, the ABC component of the alpha-hemolysin
secretion pathway, in the C-terminal domain. They
export degradative enzymes by using a type I protein
secretion system and lack an N-terminal signal peptide,
but contain a C-terminal secretion signal. The Type I
secretion apparatus is made up of three components, an
ABC transporter, a membrane fusion protein (MFP), and
an outer membrane protein (OMP). For the HlyA
transporter complex, HlyB (ABC transporter) and HlyD
(MFP) reside in the inner membrane of E. coli. The OMP
component is TolC, which is thought to interact with
the MFP to form a continuous channel across the
periplasm from the cytoplasm to the exterior. HlyB
belongs to the family of ABC transporters, which are
ubiquitous, ATP-dependent transmembrane pumps or
channels. The spectrum of transport substrates ranges
from inorganic ions, nutrients such as amino acids,
sugars, or peptides, hydrophobic drugs, to large
polypeptides, such as HlyA.
Length = 173
Score = 29.5 bits (67), Expect = 0.092
Identities = 9/25 (36%), Positives = 15/25 (60%)
Query: 49 IDPPRGVLLYGPPGCGKTMLAKAVA 73
I+P + + GP G GK+ LA+ +
Sbjct: 25 IEPGESLAIIGPSGSGKSTLARLIL 49
>gnl|CDD|234751 PRK00411, cdc6, cell division control protein 6; Reviewed.
Length = 394
Score = 29.8 bits (68), Expect = 0.093
Identities = 14/25 (56%), Positives = 15/25 (60%), Gaps = 1/25 (4%)
Query: 48 GIDPPRGVLLYGPPGCGKTMLAKAV 72
G P VL+YGPPG GKT K V
Sbjct: 52 GSRPLN-VLIYGPPGTGKTTTVKKV 75
>gnl|CDD|180215 PRK05707, PRK05707, DNA polymerase III subunit delta'; Validated.
Length = 328
Score = 29.7 bits (67), Expect = 0.097
Identities = 13/29 (44%), Positives = 17/29 (58%), Gaps = 2/29 (6%)
Query: 52 PRGVLLYGPPGCGKTMLAKAVAHHTTVLC 80
P LL+GP G GK LA+ +A +LC
Sbjct: 22 PHAYLLHGPAGIGKRALAERLA--AALLC 48
>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 = 29.5 bits (67), Expect = 0.098
Identities = 7/21 (33%), Positives = 13/21 (61%)
Query: 55 VLLYGPPGCGKTMLAKAVAHH 75
+++ G G GK+ + KA+A
Sbjct: 2 IVVMGVSGSGKSTVGKALAER 22
>gnl|CDD|224142 COG1221, PspF, Transcriptional regulators containing an AAA-type
ATPase domain and a DNA-binding domain [Transcription /
Signal transduction mechanisms].
Length = 403
Score = 29.7 bits (67), Expect = 0.10
Identities = 12/34 (35%), Positives = 18/34 (52%), Gaps = 2/34 (5%)
Query: 42 DLYKQIGIDPPRG--VLLYGPPGCGKTMLAKAVA 73
+L +QI P G VL+ G G GK + A+ +
Sbjct: 89 ELREQIKAYAPSGLPVLIIGETGTGKELFARLIH 122
>gnl|CDD|136670 PRK08181, PRK08181, transposase; Validated.
Length = 269
Score = 29.9 bits (67), Expect = 0.10
Identities = 11/18 (61%), Positives = 15/18 (83%)
Query: 55 VLLYGPPGCGKTMLAKAV 72
+LL+GPPG GK+ LA A+
Sbjct: 109 LLLFGPPGGGKSHLAAAI 126
>gnl|CDD|235825 PRK06547, PRK06547, hypothetical protein; Provisional.
Length = 172
Score = 29.3 bits (66), Expect = 0.11
Identities = 12/27 (44%), Positives = 14/27 (51%)
Query: 52 PRGVLLYGPPGCGKTMLAKAVAHHTTV 78
VL+ G G GKT LA A+A T
Sbjct: 15 MITVLIDGRSGSGKTTLAGALAARTGF 41
>gnl|CDD|223873 COG0802, COG0802, Predicted ATPase or kinase [General function
prediction only].
Length = 149
Score = 29.1 bits (66), Expect = 0.12
Identities = 12/36 (33%), Positives = 17/36 (47%), Gaps = 2/36 (5%)
Query: 42 DLYKQIGIDPPRG--VLLYGPPGCGKTMLAKAVAHH 75
L +++ G VLL G G GKT L + +A
Sbjct: 13 ALGERLAEALKAGDVVLLSGDLGAGKTTLVRGIAKG 48
>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 = 29.4 bits (66), Expect = 0.12
Identities = 12/25 (48%), Positives = 14/25 (56%)
Query: 55 VLLYGPPGCGKTMLAKAVAHHTTVL 79
L+YG PG GKT K + T VL
Sbjct: 15 YLIYGKPGTGKTSTIKYLPGKTLVL 39
>gnl|CDD|223544 COG0468, RecA, RecA/RadA recombinase [DNA replication,
recombination, and repair].
Length = 279
Score = 29.6 bits (67), Expect = 0.12
Identities = 11/31 (35%), Positives = 13/31 (41%), Gaps = 6/31 (19%)
Query: 52 PRGVL--LYGPPGCGKTMLAKAVAHHTTVLC 80
PRG + +YGP GKT L A
Sbjct: 58 PRGRITEIYGPESSGKTTL----ALQLVANA 84
>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 = 29.3 bits (66), Expect = 0.13
Identities = 10/21 (47%), Positives = 14/21 (66%)
Query: 55 VLLYGPPGCGKTMLAKAVAHH 75
+ + GPPG GKT +AK +A
Sbjct: 3 ITISGPPGSGKTTVAKILAEK 23
>gnl|CDD|224043 COG1118, CysA, ABC-type sulfate/molybdate transport systems,
ATPase component [Inorganic ion transport and
metabolism].
Length = 345
Score = 29.6 bits (67), Expect = 0.13
Identities = 9/19 (47%), Positives = 12/19 (63%)
Query: 55 VLLYGPPGCGKTMLAKAVA 73
V L GP G GK+ L + +A
Sbjct: 31 VALLGPSGAGKSTLLRIIA 49
>gnl|CDD|183088 PRK11331, PRK11331, 5-methylcytosine-specific restriction enzyme
subunit McrB; Provisional.
Length = 459
Score = 29.3 bits (65), Expect = 0.14
Identities = 11/25 (44%), Positives = 18/25 (72%)
Query: 53 RGVLLYGPPGCGKTMLAKAVAHHTT 77
+ ++L GPPG GKT +A+ +A+ T
Sbjct: 195 KNIILQGPPGVGKTFVARRLAYLLT 219
>gnl|CDD|236461 PRK09302, PRK09302, circadian clock protein KaiC; Reviewed.
Length = 509
Score = 29.5 bits (67), Expect = 0.14
Identities = 15/48 (31%), Positives = 21/48 (43%), Gaps = 3/48 (6%)
Query: 25 MQKQEIREAVE-LP--LTHFDLYKQIGIDPPRGVLLYGPPGCGKTMLA 69
M + +E LP + FD G+ R L+ G G GKT+ A
Sbjct: 1 MNQPSASPGIEKLPTGIEGFDDITHGGLPKGRPTLVSGTAGTGKTLFA 48
>gnl|CDD|234172 TIGR03345, VI_ClpV1, type VI secretion ATPase, ClpV1 family.
Members of this protein family are homologs of ClpB, an
ATPase associated with chaperone-related functions.
These ClpB homologs, designated ClpV1, are a key
component of the bacterial pathogenicity-associated type
VI secretion system [Protein fate, Protein and peptide
secretion and trafficking, Cellular processes,
Pathogenesis].
Length = 852
Score = 29.5 bits (67), Expect = 0.14
Identities = 16/27 (59%), Positives = 17/27 (62%), Gaps = 3/27 (11%)
Query: 50 DP--PRGV-LLYGPPGCGKTMLAKAVA 73
DP P GV LL GP G GKT A A+A
Sbjct: 591 DPRKPLGVFLLVGPSGVGKTETALALA 617
>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 = 29.1 bits (66), Expect = 0.14
Identities = 10/21 (47%), Positives = 13/21 (61%)
Query: 55 VLLYGPPGCGKTMLAKAVAHH 75
+LL GPPG GK A+ +A
Sbjct: 2 ILLLGPPGSGKGTQAERLAKK 22
>gnl|CDD|222000 pfam13238, AAA_18, AAA domain.
Length = 128
Score = 28.9 bits (65), Expect = 0.15
Identities = 11/19 (57%), Positives = 14/19 (73%)
Query: 55 VLLYGPPGCGKTMLAKAVA 73
+L+ G PG GKT LAK +A
Sbjct: 1 ILITGTPGSGKTTLAKELA 19
>gnl|CDD|227596 COG5271, MDN1, AAA ATPase containing von Willebrand factor type A
(vWA) domain [General function prediction only].
Length = 4600
Score = 29.6 bits (66), Expect = 0.15
Identities = 12/24 (50%), Positives = 15/24 (62%)
Query: 53 RGVLLYGPPGCGKTMLAKAVAHHT 76
+ +LL G PG GKT L A+A T
Sbjct: 1544 KPILLEGSPGVGKTSLITALARKT 1567
>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 = 29.2 bits (66), Expect = 0.15
Identities = 10/23 (43%), Positives = 14/23 (60%)
Query: 53 RGVLLYGPPGCGKTMLAKAVAHH 75
R ++L PPG GK+ L A+A
Sbjct: 109 RALILPAPPGSGKSTLCAALALR 131
>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 = 29.2 bits (66), Expect = 0.15
Identities = 16/27 (59%), Positives = 18/27 (66%), Gaps = 3/27 (11%)
Query: 50 DP--PRGVLLY-GPPGCGKTMLAKAVA 73
DP P G L+ GP G GKT LAKA+A
Sbjct: 590 DPNRPIGSFLFLGPTGVGKTELAKALA 616
>gnl|CDD|226970 COG4619, COG4619, ABC-type uncharacterized transport system,
ATPase component [General function prediction only].
Length = 223
Score = 29.1 bits (65), Expect = 0.16
Identities = 10/25 (40%), Positives = 14/25 (56%)
Query: 49 IDPPRGVLLYGPPGCGKTMLAKAVA 73
+ + + GP GCGK+ L K VA
Sbjct: 26 VRAGEFIAITGPSGCGKSTLLKIVA 50
>gnl|CDD|221803 pfam12846, AAA_10, AAA-like domain. This family of domains
contain a P-loop motif that is characteristic of the
AAA superfamily. Many of the proteins in this family
are conjugative transfer proteins.
Length = 316
Score = 29.3 bits (66), Expect = 0.16
Identities = 9/21 (42%), Positives = 13/21 (61%)
Query: 55 VLLYGPPGCGKTMLAKAVAHH 75
+L+ GP G GK+ L K +A
Sbjct: 4 MLIVGPSGSGKSTLLKLLALR 24
>gnl|CDD|144046 pfam00308, Bac_DnaA, Bacterial dnaA protein.
Length = 219
Score = 29.2 bits (66), Expect = 0.16
Identities = 8/22 (36%), Positives = 13/22 (59%)
Query: 55 VLLYGPPGCGKTMLAKAVAHHT 76
+ +YG G GKT L A+ ++
Sbjct: 37 LFIYGGVGLGKTHLLHAIGNYA 58
>gnl|CDD|238540 cd01120, RecA-like_NTPases, RecA-like NTPases. This family
includes the NTP binding domain of F1 and V1 H+ATPases,
DnaB and related helicases as well as bacterial RecA
and related eukaryotic and archaeal recombinases. This
group also includes bacterial conjugation proteins and
related DNA transfer proteins involved in type II and
type IV secretion.
Length = 165
Score = 29.0 bits (65), Expect = 0.16
Identities = 10/19 (52%), Positives = 14/19 (73%)
Query: 55 VLLYGPPGCGKTMLAKAVA 73
+L++GP G GKT LA +A
Sbjct: 2 ILVFGPTGSGKTTLALQLA 20
>gnl|CDD|178596 PLN03025, PLN03025, replication factor C subunit; Provisional.
Length = 319
Score = 28.9 bits (65), Expect = 0.17
Identities = 11/20 (55%), Positives = 14/20 (70%)
Query: 55 VLLYGPPGCGKTMLAKAVAH 74
++L GPPG GKT A+AH
Sbjct: 37 LILSGPPGTGKTTSILALAH 56
>gnl|CDD|213217 cd03250, ABCC_MRP_domain1, ATP-binding cassette domain 1 of
multidrug resistance-associated protein, subfamily C.
This subfamily is also known as MRP (multidrug
resistance-associated protein). Some of the MRP members
have five additional transmembrane segments in their
N-terminus, but the function of these additional
membrane-spanning domains is not clear. The MRP was
found in the multidrug-resisting lung cancer cell in
which p-glycoprotein was not overexpressed. MRP exports
glutathione by drug stimulation, as well as, certain
substrates in conjugated forms with anions, such as
glutathione, glucuronate, and sulfate.
Length = 204
Score = 29.0 bits (66), Expect = 0.17
Identities = 12/30 (40%), Positives = 18/30 (60%), Gaps = 2/30 (6%)
Query: 45 KQIGIDPPRG--VLLYGPPGCGKTMLAKAV 72
K I ++ P+G V + GP G GK+ L A+
Sbjct: 22 KDINLEVPKGELVAIVGPVGSGKSSLLSAL 51
>gnl|CDD|234579 PRK00023, cmk, cytidylate kinase; Provisional.
Length = 225
Score = 28.9 bits (66), Expect = 0.17
Identities = 11/30 (36%), Positives = 13/30 (43%), Gaps = 8/30 (26%)
Query: 46 QIGIDPPRGVLLYGPPGCGKTMLAKAVAHH 75
I ID GP G GK +AK +A
Sbjct: 6 VIAID--------GPAGSGKGTVAKILAKK 27
>gnl|CDD|233208 TIGR00956, 3a01205, Pleiotropic Drug Resistance (PDR) Family
protein. [Transport and binding proteins, Other].
Length = 1394
Score = 28.9 bits (65), Expect = 0.21
Identities = 10/28 (35%), Positives = 15/28 (53%)
Query: 49 IDPPRGVLLYGPPGCGKTMLAKAVAHHT 76
I P ++ G PG G + L K +A +T
Sbjct: 84 IKPGELTVVLGRPGSGCSTLLKTIASNT 111
>gnl|CDD|225327 COG2607, COG2607, Predicted ATPase (AAA+ superfamily) [General
function prediction only].
Length = 287
Score = 28.8 bits (65), Expect = 0.21
Identities = 18/65 (27%), Positives = 28/65 (43%), Gaps = 19/65 (29%)
Query: 13 PDVQYSDIGGMDMQKQEIREAVE-----LPLTHFDLYKQIGIDPPRGVLLYGPPGCGKTM 67
+ +D+ G+D QK+ + E LP + VLL+G G GK+
Sbjct: 55 DPIDLADLVGVDRQKEALVRNTEQFAEGLPANN--------------VLLWGARGTGKSS 100
Query: 68 LAKAV 72
L KA+
Sbjct: 101 LVKAL 105
>gnl|CDD|181681 PRK09183, PRK09183, transposase/IS protein; Provisional.
Length = 259
Score = 28.9 bits (65), Expect = 0.21
Identities = 10/23 (43%), Positives = 14/23 (60%)
Query: 55 VLLYGPPGCGKTMLAKAVAHHTT 77
++L GP G GKT LA A+ +
Sbjct: 105 IVLLGPSGVGKTHLAIALGYEAV 127
>gnl|CDD|224047 COG1122, CbiO, ABC-type cobalt transport system, ATPase component
[Inorganic ion transport and metabolism].
Length = 235
Score = 28.8 bits (65), Expect = 0.24
Identities = 11/27 (40%), Positives = 15/27 (55%)
Query: 47 IGIDPPRGVLLYGPPGCGKTMLAKAVA 73
+ I+ VLL GP G GK+ L K +
Sbjct: 25 LEIEKGERVLLIGPNGSGKSTLLKLLN 51
>gnl|CDD|227570 COG5245, DYN1, Dynein, heavy chain [Cytoskeleton].
Length = 3164
Score = 28.8 bits (64), Expect = 0.24
Identities = 9/16 (56%), Positives = 10/16 (62%)
Query: 53 RGVLLYGPPGCGKTML 68
R + GPPG GK ML
Sbjct: 1495 RSYIYCGPPGSGKEML 1510
>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 = 0.25
Identities = 11/31 (35%), Positives = 16/31 (51%), Gaps = 2/31 (6%)
Query: 45 KQIGIDPPRG--VLLYGPPGCGKTMLAKAVA 73
+ + G V L GP G GK+ L +A+A
Sbjct: 16 DNVSLTLKAGEIVALVGPNGSGKSTLLRAIA 46
>gnl|CDD|234042 TIGR02870, spore_II_D, stage II sporulation protein D. Stage II
sporulation protein D (SpoIID) is a protein of the
endospore formation program in a number of lineages in
the Firmicutes (low-GC Gram-positive bacteria). It is
expressed in the mother cell compartment, under control
of Sigma-E. SpoIID, along with SpoIIM and SpoIIP, is one
of three major proteins involved in engulfment of the
forespore by the mother cell [Cellular processes,
Sporulation and germination].
Length = 338
Score = 28.5 bits (64), Expect = 0.26
Identities = 11/29 (37%), Positives = 16/29 (55%)
Query: 20 IGGMDMQKQEIREAVELPLTHFDLYKQIG 48
IGG+ ++ +EIRE + L T F Q
Sbjct: 264 IGGVTLKGREIRERLGLNSTDFTWKVQGD 292
>gnl|CDD|222005 pfam13245, AAA_19, Part of AAA domain.
Length = 73
Score = 27.7 bits (62), Expect = 0.27
Identities = 9/27 (33%), Positives = 12/27 (44%), Gaps = 2/27 (7%)
Query: 51 PPRGVLLY-GPPGCGKT-MLAKAVAHH 75
R + + G PG GKT A +A
Sbjct: 8 SGRSLFVVDGGPGTGKTATAAAIIARL 34
>gnl|CDD|224160 COG1239, ChlI, Mg-chelatase subunit ChlI [Coenzyme metabolism].
Length = 423
Score = 28.5 bits (64), Expect = 0.28
Identities = 9/20 (45%), Positives = 13/20 (65%)
Query: 54 GVLLYGPPGCGKTMLAKAVA 73
G L+ G G K+ LA+A+A
Sbjct: 40 GALIAGEKGTAKSTLARALA 59
>gnl|CDD|214361 CHL00095, clpC, Clp protease ATP binding subunit.
Length = 821
Score = 28.5 bits (64), Expect = 0.28
Identities = 11/18 (61%), Positives = 12/18 (66%)
Query: 56 LLYGPPGCGKTMLAKAVA 73
L GP G GKT L KA+A
Sbjct: 543 LFSGPTGVGKTELTKALA 560
>gnl|CDD|213263 cd03296, ABC_CysA_sulfate_importer, ATP-binding cassette domain
of the sulfate transporter. Part of the ABC
transporter complex cysAWTP involved in sulfate import.
Responsible for energy coupling to the transport
system. The complex is composed of two ATP-binding
proteins (cysA), two transmembrane proteins (cysT and
cysW), and a solute-binding protein (cysP). 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 = 239
Score = 28.5 bits (64), Expect = 0.28
Identities = 13/30 (43%), Positives = 17/30 (56%), Gaps = 2/30 (6%)
Query: 46 QIGIDPPRG--VLLYGPPGCGKTMLAKAVA 73
+ +D P G V L GP G GKT L + +A
Sbjct: 20 DVSLDIPSGELVALLGPSGSGKTTLLRLIA 49
>gnl|CDD|223637 COG0563, Adk, Adenylate kinase and related kinases [Nucleotide
transport and metabolism].
Length = 178
Score = 28.4 bits (64), Expect = 0.29
Identities = 11/19 (57%), Positives = 15/19 (78%)
Query: 55 VLLYGPPGCGKTMLAKAVA 73
+L+ GPPG GK+ LAK +A
Sbjct: 3 ILILGPPGAGKSTLAKKLA 21
>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 = 27.3 bits (61), Expect = 0.30
Identities = 7/20 (35%), Positives = 12/20 (60%)
Query: 55 VLLYGPPGCGKTMLAKAVAH 74
+ + G G GK+ +AK +A
Sbjct: 2 IAITGGSGSGKSTVAKKLAE 21
>gnl|CDD|224292 COG1373, COG1373, Predicted ATPase (AAA+ superfamily) [General
function prediction only].
Length = 398
Score = 28.5 bits (64), Expect = 0.32
Identities = 11/29 (37%), Positives = 16/29 (55%), Gaps = 1/29 (3%)
Query: 42 DLYKQIGIDPPRGVLLYGPPGCGKTMLAK 70
L K++ + P +L+ GP GKT L K
Sbjct: 28 RLIKKLDLRPFI-ILILGPRQVGKTTLLK 55
>gnl|CDD|223718 COG0645, COG0645, Predicted kinase [General function prediction
only].
Length = 170
Score = 28.1 bits (63), Expect = 0.33
Identities = 11/22 (50%), Positives = 15/22 (68%)
Query: 52 PRGVLLYGPPGCGKTMLAKAVA 73
R VL+ G PG GK+ LA+ +A
Sbjct: 1 GRLVLVGGLPGSGKSTLARGLA 22
>gnl|CDD|224586 COG1672, COG1672, Predicted ATPase (AAA+ superfamily) [General
function prediction only].
Length = 359
Score = 28.2 bits (63), Expect = 0.34
Identities = 17/42 (40%), Positives = 20/42 (47%), Gaps = 5/42 (11%)
Query: 31 REAVELPLTHFDLYKQIGIDPPRGVLLYGPPGCGKTMLAKAV 72
RE EL +L K I +PP V +YG GKT L K
Sbjct: 7 RE-KELE----ELLKIIESEPPSIVFIYGRRRVGKTSLLKEF 43
>gnl|CDD|238543 cd01123, Rad51_DMC1_radA, Rad51_DMC1_radA,B. This group of
recombinases includes the eukaryotic proteins RAD51,
RAD55/57 and the meiosis-specific protein DMC1, and the
archaeal proteins radA and radB. They are closely
related to the bacterial RecA group. Rad51 proteins
catalyze a similiar recombination reaction as RecA,
using ATP-dependent DNA binding activity and a
DNA-dependent ATPase. However, this reaction is less
efficient and requires accessory proteins such as
RAD55/57 .
Length = 235
Score = 27.9 bits (63), Expect = 0.37
Identities = 6/13 (46%), Positives = 8/13 (61%)
Query: 57 LYGPPGCGKTMLA 69
++G G GKT L
Sbjct: 24 IFGEFGSGKTQLC 36
>gnl|CDD|223775 COG0703, AroK, Shikimate kinase [Amino acid transport and
metabolism].
Length = 172
Score = 27.9 bits (63), Expect = 0.37
Identities = 7/23 (30%), Positives = 13/23 (56%)
Query: 51 PPRGVLLYGPPGCGKTMLAKAVA 73
++L G G GK+ + +A+A
Sbjct: 1 RNMNIVLIGFMGAGKSTIGRALA 23
>gnl|CDD|224124 COG1203, COG1203, CRISPR-associated helicase Cas3 [Defense
mechanisms].
Length = 733
Score = 28.2 bits (63), Expect = 0.38
Identities = 12/48 (25%), Positives = 18/48 (37%), Gaps = 8/48 (16%)
Query: 28 QEIREAVELPLTHFDLYKQIGIDPPRGVLLYGPPGCGKTMLAKAVAHH 75
+ +A+EL L V+L P G GKT + +A
Sbjct: 198 ELQEKALELILR--------LEKRSLLVVLEAPTGYGKTEASLILALA 237
>gnl|CDD|180607 PRK06526, PRK06526, transposase; Provisional.
Length = 254
Score = 27.9 bits (62), Expect = 0.38
Identities = 10/19 (52%), Positives = 12/19 (63%)
Query: 55 VLLYGPPGCGKTMLAKAVA 73
V+ GPPG GKT LA +
Sbjct: 101 VVFLGPPGTGKTHLAIGLG 119
>gnl|CDD|224616 COG1702, PhoH, Phosphate starvation-inducible protein PhoH,
predicted ATPase [Signal transduction mechanisms].
Length = 348
Score = 28.0 bits (63), Expect = 0.40
Identities = 10/15 (66%), Positives = 10/15 (66%)
Query: 59 GPPGCGKTMLAKAVA 73
GP G GKT LA A A
Sbjct: 150 GPAGTGKTYLAVAKA 164
>gnl|CDD|237150 PRK12608, PRK12608, transcription termination factor Rho;
Provisional.
Length = 380
Score = 28.1 bits (63), Expect = 0.41
Identities = 14/33 (42%), Positives = 18/33 (54%), Gaps = 2/33 (6%)
Query: 42 DLYKQIGIDPPRGVLLYGPPGCGKTMLAKAVAH 74
DL IG RG L+ PP GKT+L + +A
Sbjct: 125 DLVAPIGKGQ-RG-LIVAPPRAGKTVLLQQIAA 155
>gnl|CDD|224025 COG1100, COG1100, GTPase SAR1 and related small G proteins
[General function prediction only].
Length = 219
Score = 28.0 bits (62), Expect = 0.43
Identities = 6/22 (27%), Positives = 10/22 (45%)
Query: 55 VLLYGPPGCGKTMLAKAVAHHT 76
+++ G G GKT L +
Sbjct: 8 IVVLGDGGVGKTTLLNRLVGDE 29
>gnl|CDD|213192 cd03225, ABC_cobalt_CbiO_domain1, First domain of the ATP-binding
cassette component of cobalt transport system. Domain
I of the ABC component of a cobalt transport family
found in bacteria, archaea, and eukaryota. The
transition metal cobalt is an essential component of
many enzymes and must be transported into cells in
appropriate amounts when needed. This ABC transport
system of the CbiMNQO family is involved in cobalt
transport in association with the cobalamin (vitamin
B12) biosynthetic pathways. Most of cobalt (Cbi)
transport systems possess a separate CbiN component,
the cobalt-binding periplasmic protein, and they are
encoded by the conserved gene cluster cbiMNQO. Both the
CbiM and CbiQ proteins are integral cytoplasmic
membrane proteins, and the CbiO protein has the linker
peptide and the Walker A and B motifs commonly found in
the ATPase components of the ABC-type transport
systems.
Length = 211
Score = 27.8 bits (63), Expect = 0.46
Identities = 8/19 (42%), Positives = 12/19 (63%)
Query: 55 VLLYGPPGCGKTMLAKAVA 73
VL+ GP G GK+ L + +
Sbjct: 30 VLIVGPNGSGKSTLLRLLN 48
>gnl|CDD|236482 PRK09361, radB, DNA repair and recombination protein RadB;
Provisional.
Length = 225
Score = 27.9 bits (63), Expect = 0.47
Identities = 10/19 (52%), Positives = 13/19 (68%), Gaps = 2/19 (10%)
Query: 53 RGVL--LYGPPGCGKTMLA 69
RG + +YGPPG GKT +
Sbjct: 22 RGTITQIYGPPGSGKTNIC 40
>gnl|CDD|236442 PRK09270, PRK09270, nucleoside triphosphate hydrolase
domain-containing protein; Reviewed.
Length = 229
Score = 27.6 bits (62), Expect = 0.48
Identities = 9/20 (45%), Positives = 13/20 (65%)
Query: 55 VLLYGPPGCGKTMLAKAVAH 74
V + GPPG GK+ LA+ +
Sbjct: 36 VGIAGPPGAGKSTLAEFLEA 55
>gnl|CDD|183452 PRK12337, PRK12337, 2-phosphoglycerate kinase; Provisional.
Length = 475
Score = 27.8 bits (62), Expect = 0.49
Identities = 13/26 (50%), Positives = 18/26 (69%), Gaps = 2/26 (7%)
Query: 51 PPRG--VLLYGPPGCGKTMLAKAVAH 74
PPR VL+ G G GK++LA A+A+
Sbjct: 252 PPRPLHVLIGGVSGVGKSVLASALAY 277
>gnl|CDD|225804 COG3265, GntK, Gluconate kinase [Carbohydrate transport and
metabolism].
Length = 161
Score = 27.7 bits (62), Expect = 0.50
Identities = 6/17 (35%), Positives = 9/17 (52%)
Query: 59 GPPGCGKTMLAKAVAHH 75
G G GK+ + A+A
Sbjct: 2 GVSGSGKSTVGSALAER 18
>gnl|CDD|226905 COG4525, TauB, ABC-type taurine transport system, ATPase
component [Inorganic ion transport and metabolism].
Length = 259
Score = 27.8 bits (62), Expect = 0.51
Identities = 11/27 (40%), Positives = 15/27 (55%)
Query: 47 IGIDPPRGVLLYGPPGCGKTMLAKAVA 73
+ I V++ GP GCGKT L +A
Sbjct: 26 LTIASGELVVVLGPSGCGKTTLLNLIA 52
>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 = 27.7 bits (62), Expect = 0.51
Identities = 15/36 (41%), Positives = 21/36 (58%), Gaps = 2/36 (5%)
Query: 42 DLYKQIGIDPPRGVLLYGPPGCGKTMLAKAVAHHTT 77
DL+ IG RG L+ PP GKT L +++A+ T
Sbjct: 8 DLFAPIG-KGQRG-LIVAPPKAGKTTLLQSIANAIT 41
>gnl|CDD|182331 PRK10247, PRK10247, putative ABC transporter ATP-binding protein
YbbL; Provisional.
Length = 225
Score = 27.8 bits (62), Expect = 0.52
Identities = 11/18 (61%), Positives = 13/18 (72%)
Query: 56 LLYGPPGCGKTMLAKAVA 73
L+ GP GCGK+ L K VA
Sbjct: 37 LITGPSGCGKSTLLKIVA 54
>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 = 27.5 bits (62), Expect = 0.57
Identities = 7/19 (36%), Positives = 10/19 (52%)
Query: 57 LYGPPGCGKTMLAKAVAHH 75
L G G GKT + + +A
Sbjct: 4 LIGMMGAGKTTVGRLLAKA 22
>gnl|CDD|233847 TIGR02397, dnaX_nterm, DNA polymerase III, subunit gamma and tau.
This model represents the well-conserved first ~ 365
amino acids of the translation of the dnaX gene. The
full-length product of the dnaX gene in the model
bacterium E. coli is the DNA polymerase III tau
subunit. A translational frameshift leads to early
termination and a truncated protein subunit gamma,
about 1/3 shorter than tau and present in roughly equal
amounts. This frameshift mechanism is not necessarily
universal for species with DNA polymerase III but
appears conserved in the exterme thermophile Thermus
thermophilis [DNA metabolism, DNA replication,
recombination, and repair].
Length = 355
Score = 27.5 bits (62), Expect = 0.58
Identities = 9/18 (50%), Positives = 11/18 (61%)
Query: 56 LLYGPPGCGKTMLAKAVA 73
L GP G GKT +A+ A
Sbjct: 40 LFSGPRGTGKTSIARIFA 57
>gnl|CDD|201353 pfam00625, Guanylate_kin, Guanylate kinase.
Length = 183
Score = 27.3 bits (61), Expect = 0.59
Identities = 9/24 (37%), Positives = 14/24 (58%)
Query: 52 PRGVLLYGPPGCGKTMLAKAVAHH 75
R ++L GP G GK+ + KA+
Sbjct: 2 RRPIVLSGPSGVGKSHIKKALLDE 25
>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 = 27.3 bits (61), Expect = 0.59
Identities = 9/15 (60%), Positives = 9/15 (60%)
Query: 55 VLLYGPPGCGKTMLA 69
LL G PG GKT A
Sbjct: 2 TLLSGGPGTGKTTFA 16
>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 = 27.4 bits (62), Expect = 0.63
Identities = 9/32 (28%), Positives = 14/32 (43%), Gaps = 7/32 (21%)
Query: 55 VLLYGPPGCGKTMLAKAVAH-------HTTVL 79
+ L G G GK+ +A+A+ VL
Sbjct: 2 IWLTGLSGSGKSTIARALEEKLFQRGRPVYVL 33
>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 = 27.4 bits (61), Expect = 0.63
Identities = 12/23 (52%), Positives = 16/23 (69%), Gaps = 2/23 (8%)
Query: 53 RGVL--LYGPPGCGKTMLAKAVA 73
RG + +YGPPG GKT +A +A
Sbjct: 18 RGTVTQVYGPPGTGKTNIAIQLA 40
>gnl|CDD|182730 PRK10787, PRK10787, DNA-binding ATP-dependent protease La;
Provisional.
Length = 784
Score = 27.6 bits (61), Expect = 0.66
Identities = 11/20 (55%), Positives = 14/20 (70%)
Query: 57 LYGPPGCGKTMLAKAVAHHT 76
L GPPG GKT L +++A T
Sbjct: 354 LVGPPGVGKTSLGQSIAKAT 373
>gnl|CDD|183521 PRK12422, PRK12422, chromosomal replication initiation protein;
Provisional.
Length = 445
Score = 27.5 bits (61), Expect = 0.68
Identities = 10/20 (50%), Positives = 13/20 (65%)
Query: 55 VLLYGPPGCGKTMLAKAVAH 74
+ L+GP G GKT L +A H
Sbjct: 144 IYLFGPEGSGKTHLMQAAVH 163
>gnl|CDD|132302 TIGR03258, PhnT, 2-aminoethylphosphonate ABC transport system,
ATP-binding component PhnT. This ATP-binding component
of an ABC transport system is found in Salmonella and
Burkholderia lineages in the vicinity of enzymes for
the breakdown of 2-aminoethylphosphonate.
Length = 362
Score = 27.3 bits (60), Expect = 0.69
Identities = 11/25 (44%), Positives = 15/25 (60%)
Query: 49 IDPPRGVLLYGPPGCGKTMLAKAVA 73
I+ + L G GCGKT L +A+A
Sbjct: 28 IEAGELLALIGKSGCGKTTLLRAIA 52
>gnl|CDD|213227 cd03260, ABC_PstB_phosphate_transporter, ATP-binding cassette
domain of the phosphate transport system. Phosphate
uptake is of fundamental importance in the cell
physiology of bacteria because phosphate is required as
a nutrient. The Pst system of E. coli comprises four
distinct subunits encoded by the pstS, pstA, pstB, and
pstC genes. The PstS protein is a phosphate-binding
protein located in the periplasmic space. PstA and PstC
are hydrophobic and they form the transmembrane portion
of the Pst system. PstB is the catalytic subunit, which
couples the energy of ATP hydrolysis to the import of
phosphate across cellular membranes through the Pst
system, often referred as ABC-protein. PstB belongs to
one of the largest superfamilies of proteins
characterized by a highly conserved adenosine
triphosphate (ATP) binding cassette (ABC), which is
also a nucleotide binding domain (NBD).
Length = 227
Score = 27.1 bits (61), Expect = 0.69
Identities = 13/26 (50%), Positives = 16/26 (61%), Gaps = 2/26 (7%)
Query: 45 KQIGIDPPRG--VLLYGPPGCGKTML 68
K I +D P+G L GP GCGK+ L
Sbjct: 17 KDISLDIPKGEITALIGPSGCGKSTL 42
>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 = 27.1 bits (61), Expect = 0.71
Identities = 15/44 (34%), Positives = 17/44 (38%), Gaps = 10/44 (22%)
Query: 31 REAVELPLTHFDLYKQIGIDPPRGVLLYGPPGCGKTMLAKAVAH 74
REAV LT D ++ GP G GKT KA
Sbjct: 7 REAVRHVLTSGDRV----------AVVQGPAGTGKTTSLKAARE 40
>gnl|CDD|225114 COG2204, AtoC, Response regulator containing CheY-like receiver,
AAA-type ATPase, and DNA-binding domains [Signal
transduction mechanisms].
Length = 464
Score = 27.3 bits (61), Expect = 0.73
Identities = 11/35 (31%), Positives = 17/35 (48%), Gaps = 6/35 (17%)
Query: 42 DLYKQIG----IDPPRGVLLYGPPGCGKTMLAKAV 72
L + I D VL+ G G GK ++A+A+
Sbjct: 152 QLRRLIAKVAPSDAS--VLITGESGTGKELVARAI 184
>gnl|CDD|236490 PRK09376, rho, transcription termination factor Rho; Provisional.
Length = 416
Score = 27.4 bits (62), Expect = 0.74
Identities = 10/22 (45%), Positives = 15/22 (68%), Gaps = 1/22 (4%)
Query: 53 RGVLLYGPPGCGKTMLAKAVAH 74
RG L+ PP GKT+L + +A+
Sbjct: 171 RG-LIVAPPKAGKTVLLQNIAN 191
>gnl|CDD|205733 pfam13555, AAA_29, P-loop containing region of AAA domain.
Length = 60
Score = 26.0 bits (58), Expect = 0.74
Identities = 19/50 (38%), Positives = 22/50 (44%), Gaps = 11/50 (22%)
Query: 38 LTHFDLY-------KQIGIDPPRGVLLYGPPGCGKTMLAKAVAHHTTVLC 80
LT L I IDP +G LL GP G GK+ L A T+L
Sbjct: 1 LTRLQLVNWGTFDGHTIPIDP-KGTLLTGPSGSGKSTLIDA---IQTLLV 46
>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 = 27.0 bits (61), Expect = 0.74
Identities = 8/18 (44%), Positives = 10/18 (55%)
Query: 57 LYGPPGCGKTMLAKAVAH 74
L G G GK+ L K +A
Sbjct: 31 LVGRNGAGKSTLLKLIAG 48
>gnl|CDD|166155 PLN02514, PLN02514, cinnamyl-alcohol dehydrogenase.
Length = 357
Score = 27.5 bits (61), Expect = 0.74
Identities = 19/43 (44%), Positives = 25/43 (58%), Gaps = 3/43 (6%)
Query: 37 PLTHFDLYKQIGIDPPRGVLLYGPPGCGKTMLAKAVAHHTTVL 79
PL+HF L KQ G+ G+L G G +AKA+ HH TV+
Sbjct: 171 PLSHFGL-KQSGLRG--GILGLGGVGHMGVKIAKAMGHHVTVI 210
>gnl|CDD|226372 COG3854, SpoIIIAA, ncharacterized protein conserved in bacteria
[Function unknown].
Length = 308
Score = 27.1 bits (60), Expect = 0.75
Identities = 9/19 (47%), Positives = 12/19 (63%)
Query: 55 VLLYGPPGCGKTMLAKAVA 73
L+ GPP GKT L + +A
Sbjct: 140 TLIIGPPQVGKTTLLRDIA 158
>gnl|CDD|213209 cd03242, ABC_RecF, ATP-binding cassette domain of RecF. RecF is
a recombinational DNA repair ATPase that maintains
replication in the presence of DNA damage. When
replication is prematurely disrupted by DNA damage,
several recF pathway gene products play critical roles
processing the arrested replication fork, allowing it
to resume and complete its task. This CD represents the
nucleotide binding domain of RecF. RecF belongs to a
large superfamily of ABC transporters 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 with 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 = 270
Score = 27.3 bits (61), Expect = 0.76
Identities = 12/38 (31%), Positives = 20/38 (52%), Gaps = 1/38 (2%)
Query: 36 LPLTHFDLYKQIGID-PPRGVLLYGPPGCGKTMLAKAV 72
L L +F Y ++ ++ P +L G GKT L +A+
Sbjct: 4 LELRNFRNYAELELEFEPGVTVLVGENAQGKTNLLEAI 41
>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 = 27.3 bits (61), Expect = 0.79
Identities = 9/13 (69%), Positives = 10/13 (76%)
Query: 56 LLYGPPGCGKTML 68
L+ GPPG GKT L
Sbjct: 115 LVIGPPGSGKTTL 127
>gnl|CDD|183044 PRK11231, fecE, iron-dicitrate transporter ATP-binding subunit;
Provisional.
Length = 255
Score = 27.3 bits (61), Expect = 0.84
Identities = 12/27 (44%), Positives = 14/27 (51%), Gaps = 2/27 (7%)
Query: 49 IDPPRG--VLLYGPPGCGKTMLAKAVA 73
+ P G L GP GCGK+ L K A
Sbjct: 23 LSLPTGKITALIGPNGCGKSTLLKCFA 49
>gnl|CDD|184132 PRK13547, hmuV, hemin importer ATP-binding subunit; Provisional.
Length = 272
Score = 27.1 bits (60), Expect = 0.86
Identities = 12/27 (44%), Positives = 16/27 (59%)
Query: 47 IGIDPPRGVLLYGPPGCGKTMLAKAVA 73
+ I+P R L G G GK+ L KA+A
Sbjct: 22 LRIEPGRVTALLGRNGAGKSTLLKALA 48
>gnl|CDD|182778 PRK10851, PRK10851, sulfate/thiosulfate transporter subunit;
Provisional.
Length = 353
Score = 27.0 bits (60), Expect = 0.86
Identities = 16/36 (44%), Positives = 20/36 (55%), Gaps = 5/36 (13%)
Query: 47 IGIDPPRG--VLLYGPPGCGKTMLAKAVA---HHTT 77
I +D P G V L GP G GKT L + +A H T+
Sbjct: 21 ISLDIPSGQMVALLGPSGSGKTTLLRIIAGLEHQTS 56
>gnl|CDD|182791 PRK10865, PRK10865, protein disaggregation chaperone; Provisional.
Length = 857
Score = 27.1 bits (60), Expect = 0.87
Identities = 14/27 (51%), Positives = 16/27 (59%), Gaps = 3/27 (11%)
Query: 50 DPPRGV---LLYGPPGCGKTMLAKAVA 73
DP R + L GP G GKT L KA+A
Sbjct: 593 DPNRPIGSFLFLGPTGVGKTELCKALA 619
>gnl|CDD|224985 COG2074, COG2074, 2-phosphoglycerate kinase [Carbohydrate transport
and metabolism].
Length = 299
Score = 26.9 bits (60), Expect = 0.88
Identities = 8/23 (34%), Positives = 13/23 (56%)
Query: 52 PRGVLLYGPPGCGKTMLAKAVAH 74
P +L+ G G GK+ +A +A
Sbjct: 89 PLIILIGGASGVGKSTIAGELAR 111
>gnl|CDD|226361 COG3842, PotA, ABC-type spermidine/putrescine transport systems,
ATPase components [Amino acid transport and
metabolism].
Length = 352
Score = 27.2 bits (61), Expect = 0.88
Identities = 10/17 (58%), Positives = 12/17 (70%)
Query: 57 LYGPPGCGKTMLAKAVA 73
L GP GCGKT L + +A
Sbjct: 36 LLGPSGCGKTTLLRMIA 52
>gnl|CDD|222866 PHA02544, 44, clamp loader, small subunit; Provisional.
Length = 316
Score = 26.9 bits (60), Expect = 0.89
Identities = 11/20 (55%), Positives = 15/20 (75%), Gaps = 1/20 (5%)
Query: 56 LLYGP-PGCGKTMLAKAVAH 74
LL+ P PG GKT +AKA+ +
Sbjct: 46 LLHSPSPGTGKTTVAKALCN 65
>gnl|CDD|190347 pfam02562, PhoH, PhoH-like protein. PhoH is a cytoplasmic
protein and predicted ATPase that is induced by
phosphate starvation.
Length = 205
Score = 27.0 bits (61), Expect = 0.90
Identities = 11/19 (57%), Positives = 11/19 (57%)
Query: 55 VLLYGPPGCGKTMLAKAVA 73
V GP G GKT LA A A
Sbjct: 22 VFGIGPAGTGKTYLAVAAA 40
>gnl|CDD|237475 PRK13695, PRK13695, putative NTPase; Provisional.
Length = 174
Score = 26.8 bits (60), Expect = 0.93
Identities = 9/19 (47%), Positives = 12/19 (63%)
Query: 55 VLLYGPPGCGKTMLAKAVA 73
+ + GPPG GKT L +A
Sbjct: 3 IGITGPPGVGKTTLVLKIA 21
>gnl|CDD|213226 cd03259, ABC_Carb_Solutes_like, ATP-binding cassette domain of
the carbohydrate and solute transporters-like. This
family is comprised of proteins involved in the
transport of apparently unrelated solutes and proteins
specific for di- and oligosaccharides and polyols. 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 = 213
Score = 26.7 bits (60), Expect = 0.93
Identities = 11/34 (32%), Positives = 16/34 (47%), Gaps = 2/34 (5%)
Query: 42 DLYKQIGIDPPRG--VLLYGPPGCGKTMLAKAVA 73
+ + G + L GP GCGKT L + +A
Sbjct: 14 RALDDLSLTVEPGEFLALLGPSGCGKTTLLRLIA 47
>gnl|CDD|234041 TIGR02868, CydC, thiol reductant ABC exporter, CydC subunit. The
gene pair cydCD encodes an ABC-family transporter in
which each gene contains an N-terminal membrane-spanning
domain (pfam00664) and a C-terminal ATP-binding domain
(pfam00005). In E. coli these genes were discovered as
mutants which caused the terminal heme-copper oxidase
complex cytochrome bd to fail to assemble. Recent work
has shown that the transporter is involved in export of
redox-active thiol compounds such as cysteine and
glutathione. The linkage to assembly of the cytochrome
bd complex is further supported by the conserved operon
structure found outside the gammaproteobacteria
(cydABCD) containing both the transporter and oxidase
genes components. The genes used as the seed members for
this model are all either found in the
gammproteobacterial context or the CydABCD context. All
members of this family scoring above trusted at the time
of its creation were from genomes which encode a
cytochrome bd complex.
Length = 530
Score = 26.9 bits (60), Expect = 1.00
Identities = 9/23 (39%), Positives = 12/23 (52%)
Query: 51 PPRGVLLYGPPGCGKTMLAKAVA 73
P V + GP G GK+ L +A
Sbjct: 360 PGERVAILGPSGSGKSTLLATLA 382
>gnl|CDD|226620 COG4136, COG4136, ABC-type uncharacterized transport system,
ATPase component [General function prediction only].
Length = 213
Score = 26.7 bits (59), Expect = 1.0
Identities = 11/27 (40%), Positives = 14/27 (51%), Gaps = 1/27 (3%)
Query: 49 IDPPRGVLLYGPPGCGK-TMLAKAVAH 74
I V L GP GCGK T+L+ +
Sbjct: 25 IAKGEIVTLMGPSGCGKSTLLSWMIGA 51
>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 = 26.5 bits (59), Expect = 1.0
Identities = 7/19 (36%), Positives = 12/19 (63%)
Query: 55 VLLYGPPGCGKTMLAKAVA 73
+L+ G PG GK+ A+ +
Sbjct: 2 ILMVGLPGSGKSTFARRLL 20
>gnl|CDD|217429 pfam03215, Rad17, Rad17 cell cycle checkpoint protein.
Length = 490
Score = 26.9 bits (59), Expect = 1.1
Identities = 9/23 (39%), Positives = 13/23 (56%)
Query: 51 PPRGVLLYGPPGCGKTMLAKAVA 73
+LL GP GCGK+ K ++
Sbjct: 44 KQLILLLTGPSGCGKSTTVKVLS 66
>gnl|CDD|225183 COG2274, SunT, ABC-type bacteriocin/lantibiotic exporters, contain
an N-terminal double-glycine peptidase domain [Defense
mechanisms].
Length = 709
Score = 26.8 bits (60), Expect = 1.1
Identities = 9/22 (40%), Positives = 11/22 (50%)
Query: 49 IDPPRGVLLYGPPGCGKTMLAK 70
I P V + G G GK+ L K
Sbjct: 496 IPPGEKVAIVGRSGSGKSTLLK 517
>gnl|CDD|130041 TIGR00968, 3a0106s01, sulfate ABC transporter, ATP-binding
protein. [Transport and binding proteins, Anions].
Length = 237
Score = 26.7 bits (59), Expect = 1.1
Identities = 12/35 (34%), Positives = 18/35 (51%), Gaps = 2/35 (5%)
Query: 41 FDLYKQIGIDPPRG--VLLYGPPGCGKTMLAKAVA 73
F + ++ P G V L GP G GK+ L + +A
Sbjct: 13 FQALDDVNLEVPTGSLVALLGPSGSGKSTLLRIIA 47
>gnl|CDD|163508 TIGR03796, NHLM_micro_ABC1, NHLM bacteriocin system ABC
transporter, peptidase/ATP-binding protein. This
protein describes a multidomain ABC transporter subunit
that is one of three protein families associated with
some regularity with a distinctive family of putative
bacteriocins. It includes a bacteriocin-processing
peptidase domain at the N-terminus. Model TIGR03793
describes a conserved propeptide region for this
bacteriocin family, unusual because it shows obvious
homology a region of the enzyme nitrile hydratase up to
the classic Gly-Gly cleavage motif. This family is
therefore predicted to be a subunit of a bacteriocin
processing and export system characteristic to this
system that we designate NHLM, Nitrile Hydratase Leader
Microcin [Transport and binding proteins, Amino acids,
peptides and amines, Cellular processes, Biosynthesis of
natural products].
Length = 710
Score = 26.8 bits (60), Expect = 1.1
Identities = 16/42 (38%), Positives = 22/42 (52%), Gaps = 5/42 (11%)
Query: 33 AVELPL-THFDLYKQIGIDPPRGVLLYGPPGCGKTMLAKAVA 73
+E PL +F L + P + V L G G GK+ +AK VA
Sbjct: 489 PLEPPLIENFSL----TLQPGQRVALVGGSGSGKSTIAKLVA 526
>gnl|CDD|238418 cd00820, PEPCK_HprK, Phosphoenolpyruvate carboxykinase (PEPCK), a
critical gluconeogenic enzyme, catalyzes the first
committed step in the diversion of tricarboxylic acid
cycle intermediates toward gluconeogenesis. It
catalyzes the reversible decarboxylation and
phosphorylation of oxaloacetate to yield
phosphoenolpyruvate and carbon dioxide, using a
nucleotide molecule (ATP or GTP) for the phosphoryl
transfer, and has a strict requirement for divalent
metal ions for activity. PEPCK's separate into two
phylogenetic groups based on their nucleotide substrate
specificity (the ATP-, and GTP-dependent
groups).HprK/P, the bifunctional histidine-containing
protein kinase/phosphatase, controls the
phosphorylation state of the phosphocarrier protein HPr
and regulates the utilization of carbon sources by
gram-positive bacteria. It catalyzes both the
ATP-dependent phosphorylation of HPr and its
dephosphorylation by phosphorolysis. PEPCK and the
C-terminal catalytic domain of HprK/P are structurally
similar with conserved active site residues suggesting
that these two phosphotransferases have related
functions.
Length = 107
Score = 26.5 bits (58), Expect = 1.1
Identities = 10/23 (43%), Positives = 13/23 (56%)
Query: 47 IGIDPPRGVLLYGPPGCGKTMLA 69
+ + GVL+ G G GKT LA
Sbjct: 10 VDVYGKVGVLITGDSGIGKTELA 32
>gnl|CDD|234654 PRK00131, aroK, shikimate kinase; Reviewed.
Length = 175
Score = 26.7 bits (60), Expect = 1.1
Identities = 6/25 (24%), Positives = 12/25 (48%)
Query: 51 PPRGVLLYGPPGCGKTMLAKAVAHH 75
++L G G GK+ + + +A
Sbjct: 3 KGPNIVLIGFMGAGKSTIGRLLAKR 27
>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 = 26.7 bits (59), Expect = 1.2
Identities = 22/62 (35%), Positives = 29/62 (46%), Gaps = 15/62 (24%)
Query: 5 KPTKNDEKPDVQYSDIGGMDMQKQEIREAVELPLTHFDLYKQIGIDPPRGVLLYGPPGCG 64
P+K E D Q+ D + QK EAV L+ DL+ L++GPPG G
Sbjct: 141 APSKASEIHDFQFFDPNLNESQK----EAVLFALSSKDLF-----------LIHGPPGTG 185
Query: 65 KT 66
KT
Sbjct: 186 KT 187
>gnl|CDD|226359 COG3839, MalK, ABC-type sugar transport systems, ATPase
components [Carbohydrate transport and metabolism].
Length = 338
Score = 26.8 bits (60), Expect = 1.2
Identities = 11/19 (57%), Positives = 14/19 (73%), Gaps = 1/19 (5%)
Query: 55 VLLYGPPGCGKTMLAKAVA 73
VLL GP GCGK+ L + +A
Sbjct: 33 VLL-GPSGCGKSTLLRMIA 50
>gnl|CDD|236861 PRK11147, PRK11147, ABC transporter ATPase component; Reviewed.
Length = 635
Score = 26.8 bits (60), Expect = 1.2
Identities = 12/20 (60%), Positives = 13/20 (65%), Gaps = 2/20 (10%)
Query: 53 RG--VLLYGPPGCGKTMLAK 70
RG + L GP GCGKT L K
Sbjct: 344 RGDKIALIGPNGCGKTTLLK 363
>gnl|CDD|223401 COG0324, MiaA, tRNA delta(2)-isopentenylpyrophosphate transferase
[Translation, ribosomal structure and biogenesis].
Length = 308
Score = 26.8 bits (60), Expect = 1.2
Identities = 10/22 (45%), Positives = 15/22 (68%)
Query: 52 PRGVLLYGPPGCGKTMLAKAVA 73
P+ +++ GP GKT LA A+A
Sbjct: 3 PKLIVIAGPTASGKTALAIALA 24
>gnl|CDD|226573 COG4088, COG4088, Predicted nucleotide kinase [Nucleotide
transport and metabolism].
Length = 261
Score = 26.7 bits (59), Expect = 1.2
Identities = 10/19 (52%), Positives = 13/19 (68%)
Query: 55 VLLYGPPGCGKTMLAKAVA 73
++L G PG GKT AK +A
Sbjct: 4 IILTGYPGSGKTTFAKELA 22
>gnl|CDD|172747 PRK14259, PRK14259, phosphate ABC transporter ATP-binding
protein; Provisional.
Length = 269
Score = 26.7 bits (59), Expect = 1.2
Identities = 13/34 (38%), Positives = 21/34 (61%), Gaps = 2/34 (5%)
Query: 41 FDLYKQIGIDPPRGVL--LYGPPGCGKTMLAKAV 72
F+ K + D PRG + L GP GCGK+ + +++
Sbjct: 26 FEAVKNVFCDIPRGKVTALIGPSGCGKSTVLRSL 59
>gnl|CDD|213267 cd03300, ABC_PotA_N, ATP-binding cassette domain of the polyamine
transporter. PotA is an ABC-type transporter and the
ATPase component of the
spermidine/putrescine-preferential uptake system
consisting of PotA, -B, -C, and -D. PotA has two
domains with the N-terminal domain containing the
ATPase activity and the residues required for
homodimerization with PotA and heterdimerization with
PotB. 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 = 232
Score = 26.4 bits (59), Expect = 1.2
Identities = 10/17 (58%), Positives = 12/17 (70%)
Query: 57 LYGPPGCGKTMLAKAVA 73
L GP GCGKT L + +A
Sbjct: 31 LLGPSGCGKTTLLRLIA 47
>gnl|CDD|233793 TIGR02237, recomb_radB, DNA repair and recombination protein
RadB. This family consists exclusively of archaeal
RadB protein, a homolog of bacterial RecA (TIGR02012),
eukaryotic RAD51 (TIGR02239) and DMC1 (TIGR02238), and
archaeal RadA (TIGR02236).
Length = 209
Score = 26.6 bits (59), Expect = 1.2
Identities = 11/23 (47%), Positives = 15/23 (65%), Gaps = 2/23 (8%)
Query: 53 RGVL--LYGPPGCGKTMLAKAVA 73
RG + +YGPPG GKT + +A
Sbjct: 11 RGTITQIYGPPGSGKTNICMILA 33
>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 = 26.4 bits (59), Expect = 1.2
Identities = 10/19 (52%), Positives = 12/19 (63%)
Query: 55 VLLYGPPGCGKTMLAKAVA 73
+ + GPPG GKT L K V
Sbjct: 2 IFITGPPGVGKTTLVKKVI 20
>gnl|CDD|213193 cd03226, ABC_cobalt_CbiO_domain2, Second domain of the
ATP-binding cassette component of cobalt transport
system. Domain II of the ABC component of a cobalt
transport family found in bacteria, archaea, and
eukaryota. The transition metal cobalt is an essential
component of many enzymes and must be transported into
cells in appropriate amounts when needed. The CbiMNQO
family ABC transport system is involved in cobalt
transport in association with the cobalamin (vitamin
B12) biosynthetic pathways. Most cobalt (Cbi) transport
systems possess a separate CbiN component, the
cobalt-binding periplasmic protein, and they are
encoded by the conserved gene cluster cbiMNQO. Both the
CbiM and CbiQ proteins are integral cytoplasmic
membrane proteins, and the CbiO protein has the linker
peptide and the Walker A and B motifs commonly found in
the ATPase components of the ABC-type transport
systems.
Length = 205
Score = 26.5 bits (59), Expect = 1.3
Identities = 12/31 (38%), Positives = 16/31 (51%), Gaps = 2/31 (6%)
Query: 45 KQIGIDPPRG--VLLYGPPGCGKTMLAKAVA 73
+ +D G + L G G GKT LAK +A
Sbjct: 17 DDLSLDLYAGEIIALTGKNGAGKTTLAKILA 47
>gnl|CDD|213195 cd03228, ABCC_MRP_Like, ATP-binding cassette domain of multidrug
resistance protein-like transporters. The MRP
(Multidrug Resistance Protein)-like transporters are
involved in drug, peptide, and lipid export. They
belong to the subfamily C of the ATP-binding cassette
(ABC) superfamily of transport proteins. The ABCC
subfamily contains transporters with a diverse
functional spectrum that includes ion transport, cell
surface receptor, and toxin secretion activities. The
MRP-like family, similar to all ABC proteins, have a
common four-domain core structure constituted by two
membrane-spanning domains, each composed of six
transmembrane (TM) helices, and two nucleotide-binding
domains (NBD). ABC transporters are a subset of
nucleotide hydrolases that contain a signature motif,
Q-loop, and H-loop/switch region, in addition to, the
Walker A motif/P-loop and Walker B motif commonly found
in a number of ATP- and GTP-binding and hydrolyzing
proteins.
Length = 171
Score = 26.6 bits (60), Expect = 1.3
Identities = 9/24 (37%), Positives = 12/24 (50%), Gaps = 2/24 (8%)
Query: 52 PRG--VLLYGPPGCGKTMLAKAVA 73
G V + GP G GK+ L K +
Sbjct: 26 KPGEKVAIVGPSGSGKSTLLKLLL 49
>gnl|CDD|213264 cd03297, ABC_ModC_molybdenum_transporter, ATP-binding cassette
domain of the molybdenum transport system. ModC is an
ABC-type transporter and the ATPase component of a
molybdate transport system that also includes the
periplasmic binding protein ModA and the membrane
protein ModB. ABC transporters are a large family of
proteins involved in the transport of a wide variety of
different compounds, like sugars, ions, peptides and
more complex organic molecules. The nucleotide binding
domain shows the highest similarity between all members
of the family. ABC transporters are a subset of
nucleotide hydrolases that contain a signature motif,
Q-loop, and H-loop/switch region, in addition to, the
Walker A motif/P-loop and Walker B motif commonly found
in a number of ATP- and GTP-binding and hydrolyzing
proteins.
Length = 214
Score = 26.5 bits (59), Expect = 1.3
Identities = 11/34 (32%), Positives = 17/34 (50%), Gaps = 3/34 (8%)
Query: 41 FDLYKQIGIDPPRGVL-LYGPPGCGKTMLAKAVA 73
F L +I D V ++G G GK+ L + +A
Sbjct: 13 FTL--KIDFDLNEEVTGIFGASGAGKSTLLRCIA 44
>gnl|CDD|235898 PRK06964, PRK06964, DNA polymerase III subunit delta'; Validated.
Length = 342
Score = 26.6 bits (59), Expect = 1.3
Identities = 11/29 (37%), Positives = 16/29 (55%), Gaps = 2/29 (6%)
Query: 52 PRGVLLYGPPGCGKTMLAKAVAHHTTVLC 80
P +LL+G G GK A+ +A +LC
Sbjct: 21 PHALLLHGQAGIGKLDFAQHLAQ--GLLC 47
>gnl|CDD|188099 TIGR00972, 3a0107s01c2, phosphate ABC transporter, ATP-binding
protein. This model represents the ATP-binding protein
of a family of ABC transporters for inorganic
phosphate. In the model species Escherichia coli, a
constitutive transporter for inorganic phosphate, with
low affinity, is also present. The high affinity
transporter that includes this polypeptide is induced
when extracellular phosphate concentrations are low.
The proteins most similar to the members of this family
but not included appear to be amino acid transporters
[Transport and binding proteins, Anions].
Length = 247
Score = 26.5 bits (59), Expect = 1.3
Identities = 13/41 (31%), Positives = 21/41 (51%), Gaps = 9/41 (21%)
Query: 40 HFDLY-------KQIGIDPPRG--VLLYGPPGCGKTMLAKA 71
+ +L+ K I +D P+ L GP GCGK+ L ++
Sbjct: 6 NLNLFYGEKEALKNINLDIPKNQVTALIGPSGCGKSTLLRS 46
>gnl|CDD|224049 COG1124, DppF, ABC-type dipeptide/oligopeptide/nickel transport
system, ATPase component [Amino acid transport and
metabolism / Inorganic ion transport and metabolism].
Length = 252
Score = 26.5 bits (59), Expect = 1.3
Identities = 7/17 (41%), Positives = 11/17 (64%)
Query: 57 LYGPPGCGKTMLAKAVA 73
+ G G GK+ LA+ +A
Sbjct: 38 IVGESGSGKSTLARLLA 54
>gnl|CDD|224116 COG1195, RecF, Recombinational DNA repair ATPase (RecF pathway)
[DNA replication, recombination, and repair].
Length = 363
Score = 26.4 bits (59), Expect = 1.4
Identities = 14/39 (35%), Positives = 21/39 (53%), Gaps = 1/39 (2%)
Query: 35 ELPLTHFDLYKQIGIDP-PRGVLLYGPPGCGKTMLAKAV 72
L L +F Y ++ +D P +L G G GKT L +A+
Sbjct: 5 SLLLRNFRNYAELDLDLSPGVNVLVGENGQGKTNLLEAI 43
>gnl|CDD|236353 PRK08939, PRK08939, primosomal protein DnaI; Reviewed.
Length = 306
Score = 26.4 bits (59), Expect = 1.4
Identities = 10/22 (45%), Positives = 15/22 (68%)
Query: 53 RGVLLYGPPGCGKTMLAKAVAH 74
+G+ LYG G GK+ L A+A+
Sbjct: 157 KGLYLYGDFGVGKSYLLAAIAN 178
>gnl|CDD|163671 cd08164, MPP_Ted1, Saccharomyces cerevisiae Ted1 and related
proteins, metallophosphatase domain. Saccharomyces
cerevisiae Ted1 (trafficking of Emp24p/Erv25p-dependent
cargo disrupted 1) is a metallophosphatase
domain-containing protein which acts together with
Emp24p and Erv25p in cargo exit from the ER. Ted1
belongs to the metallophosphatase (MPP) superfamily.
MPPs are functionally diverse, but all share a conserved
domain with an active site consisting of two metal ions
(usually manganese, iron, or zinc) coordinated with
octahedral geometry by a cage of histidine, aspartate,
and asparagine residues. The MPP superfamily includes:
Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat
debranching enzymes, YfcE-like phosphodiesterases,
purple acid phosphatases (PAPs), YbbF-like
UDP-2,3-diacylglucosamine hydrolases, and acid
sphingomyelinases (ASMases). The conserved domain is a
double beta-sheet sandwich with a di-metal active site
made up of residues located at the C-terminal side of
the sheets. This domain is thought to allow for
productive metal coordination.
Length = 193
Score = 26.2 bits (58), Expect = 1.4
Identities = 17/51 (33%), Positives = 26/51 (50%), Gaps = 3/51 (5%)
Query: 14 DVQYSDIGGMDMQKQEIREAVELPLTHFDLYKQIGIDPPRGVLLYGPPGCG 64
DV Y G + + E E++ + LTH LYK I ++ G++L G G
Sbjct: 109 DVGYG--GEVTEARIERFESLFILLTHVPLYK-IFLEGKPGLILTGHDHEG 156
>gnl|CDD|216999 pfam02367, UPF0079, Uncharacterized P-loop hydrolase UPF0079.
This uncharacterized family contains a P-loop.
Length = 123
Score = 26.1 bits (58), Expect = 1.4
Identities = 9/21 (42%), Positives = 11/21 (52%)
Query: 55 VLLYGPPGCGKTMLAKAVAHH 75
VLL G G GKT + +A
Sbjct: 18 VLLSGDLGAGKTTFVRGLAQG 38
>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 = 26.6 bits (59), Expect = 1.4
Identities = 11/26 (42%), Positives = 15/26 (57%), Gaps = 1/26 (3%)
Query: 53 RGVLLYGPPGCGKTMLAKAVAHHTTV 78
RG L+ PP GKT+L + +A T
Sbjct: 170 RG-LIVAPPKAGKTVLLQKIAQAITR 194
>gnl|CDD|172760 PRK14272, PRK14272, phosphate ABC transporter ATP-binding
protein; Provisional.
Length = 252
Score = 26.5 bits (58), Expect = 1.5
Identities = 13/30 (43%), Positives = 18/30 (60%), Gaps = 2/30 (6%)
Query: 45 KQIGIDPPRGVL--LYGPPGCGKTMLAKAV 72
K + +D RG + L GP GCGKT +A+
Sbjct: 21 KNVNLDVQRGTVNALIGPSGCGKTTFLRAI 50
>gnl|CDD|233822 TIGR02329, propionate_PrpR, propionate catabolism operon regulatory
protein PrpR. At least five distinct pathways exists
for the catabolism of propionate by way of
propionyl-CoA. Members of this family represent the
transcriptional regulatory protein PrpR, whose gene is
found in most cases divergently transcribed from an
operon for the methylcitric acid cycle of propionate
catabolism. 2-methylcitric acid, a catabolite by this
pathway, is a coactivator of PrpR.
Length = 526
Score = 26.4 bits (58), Expect = 1.5
Identities = 15/67 (22%), Positives = 27/67 (40%), Gaps = 11/67 (16%)
Query: 6 PTKNDEKPDVQYSDIGGMDMQKQEIREAVELPLTHFDLYKQIGIDPPRGVLLYGPPGCGK 65
T+N + + D+ G +++R V L VL+ G G GK
Sbjct: 200 ATRNQLRTRYRLDDLLGASAPMEQVRALVRLYARS-----------DATVLILGESGTGK 248
Query: 66 TMLAKAV 72
++A+A+
Sbjct: 249 ELVAQAI 255
>gnl|CDD|238899 cd01918, HprK_C, HprK/P, the bifunctional histidine-containing
protein kinase/phosphatase, controls the
phosphorylation state of the phosphocarrier protein HPr
and regulates the utilization of carbon sources by
gram-positive bacteria. It catalyzes both the
ATP-dependent phosphorylation of Ser-46 of HPr and its
dephosphorylation by phosphorolysis. The latter
reaction uses inorganic phosphate as substrate and
produces pyrophosphate. Phosphoenolpyruvate
carboxykinase (PEPCK) and the C-terminal catalytic
domain of HprK/P are structurally similar with
conserved active site residues suggesting these two
phosphotransferases have related functions. The HprK/P
N-terminal domain is structurally similar to the
N-terminal domains of the MurE and MurF amino acid
ligases.
Length = 149
Score = 26.4 bits (59), Expect = 1.5
Identities = 10/17 (58%), Positives = 12/17 (70%)
Query: 53 RGVLLYGPPGCGKTMLA 69
GVL+ GP G GK+ LA
Sbjct: 15 IGVLITGPSGIGKSELA 31
>gnl|CDD|206733 cd04170, EF-G_bact, Elongation factor G (EF-G) family.
Translocation is mediated by EF-G (also called
translocase). The structure of EF-G closely resembles
that of the complex between EF-Tu and tRNA. This is an
example of molecular mimicry; a protein domain evolved
so that it mimics the shape of a tRNA molecule. EF-G in
the GTP form binds to the ribosome, primarily through
the interaction of its EF-Tu-like domain with the 50S
subunit. The binding of EF-G to the ribosome in this
manner stimulates the GTPase activity of EF-G. On GTP
hydrolysis, EF-G undergoes a conformational change that
forces its arm deeper into the A site on the 30S
subunit. To accommodate this domain, the peptidyl-tRNA
in the A site moves to the P site, carrying the mRNA
and the deacylated tRNA with it. The ribosome may be
prepared for these rearrangements by the initial
binding of EF-G as well. The dissociation of EF-G
leaves the ribosome ready to accept the next
aminoacyl-tRNA into the A site. This group contains
only bacterial members.
Length = 268
Score = 26.4 bits (59), Expect = 1.6
Identities = 10/20 (50%), Positives = 13/20 (65%)
Query: 57 LYGPPGCGKTMLAKAVAHHT 76
L G G GKT LA+A+ + T
Sbjct: 4 LVGHSGSGKTTLAEALLYAT 23
>gnl|CDD|233665 TIGR01978, sufC, FeS assembly ATPase SufC. SufC is part of the
SUF system, shown in E. coli to consist of six proteins
and believed to act in Fe-S cluster formation during
oxidative stress. SufC forms a complex with SufB and
SufD. SufC belongs to the ATP-binding cassette
transporter family (pfam00005) but is no longer thought
to be part of a transporter. The complex is reported as
cytosolic (PMID:12554644) or associated with the
membrane (PMID:11943156). The SUF system also includes
a cysteine desulfurase (SufS, enhanced by SufE) and a
probable iron-sulfur cluster assembly scaffold protein,
SufA [Biosynthesis of cofactors, prosthetic groups, and
carriers, Other].
Length = 243
Score = 26.5 bits (59), Expect = 1.6
Identities = 9/21 (42%), Positives = 13/21 (61%)
Query: 55 VLLYGPPGCGKTMLAKAVAHH 75
+ GP G GK+ L+K +A H
Sbjct: 29 HAIMGPNGSGKSTLSKTIAGH 49
>gnl|CDD|213527 TIGR00390, hslU, ATP-dependent protease HslVU, ATPase subunit.
This model represents the ATPase subunit of HslVU,
while the proteasome-related peptidase subunit is HslV.
Residues 54-61 of the model contain a P-loop
ATP-binding motif. Cys-287 of E. coli (position 308 in
the seed alignment), studied in MEDLINE:98389714, is
Ser in other members of the seed alignment [Protein
fate, Protein folding and stabilization].
Length = 441
Score = 26.3 bits (58), Expect = 1.6
Identities = 10/22 (45%), Positives = 16/22 (72%)
Query: 52 PRGVLLYGPPGCGKTMLAKAVA 73
P+ +L+ GP G GKT +A+ +A
Sbjct: 47 PKNILMIGPTGVGKTEIARRLA 68
>gnl|CDD|206691 cd04105, SR_beta, Signal recognition particle receptor, beta
subunit (SR-beta), together with SR-alpha, forms the
heterodimeric signal recognition particle (SRP).
Signal recognition particle receptor, beta subunit
(SR-beta). SR-beta and SR-alpha form the heterodimeric
signal recognition particle (SRP or SR) receptor that
binds SRP to regulate protein translocation across the
ER membrane. Nascent polypeptide chains are synthesized
with an N-terminal hydrophobic signal sequence that
binds SRP54, a component of the SRP. SRP directs
targeting of the ribosome-nascent chain complex (RNC)
to the ER membrane via interaction with the SR, which
is localized to the ER membrane. The RNC is then
transferred to the protein-conducting channel, or
translocon, which facilitates polypeptide translation
across the ER membrane or integration into the ER
membrane. SR-beta is found only in eukaryotes; it is
believed to control the release of the signal sequence
from SRP54 upon binding of the ribosome to the
translocon. High expression of SR-beta has been
observed in human colon cancer, suggesting it may play
a role in the development of this type of cancer.
Length = 202
Score = 26.1 bits (58), Expect = 1.6
Identities = 9/14 (64%), Positives = 9/14 (64%)
Query: 55 VLLYGPPGCGKTML 68
VLL GP GKT L
Sbjct: 3 VLLLGPSDSGKTAL 16
>gnl|CDD|226997 COG4650, RtcR, Sigma54-dependent transcription regulator containing
an AAA-type ATPase domain and a DNA-binding domain
[Transcription / Signal transduction mechanisms].
Length = 531
Score = 26.4 bits (58), Expect = 1.6
Identities = 9/18 (50%), Positives = 13/18 (72%)
Query: 55 VLLYGPPGCGKTMLAKAV 72
+LL GP G GK+ LA+ +
Sbjct: 211 ILLNGPTGAGKSFLARRI 228
>gnl|CDD|179433 PRK02496, adk, adenylate kinase; Provisional.
Length = 184
Score = 26.3 bits (58), Expect = 1.7
Identities = 9/25 (36%), Positives = 13/25 (52%)
Query: 54 GVLLYGPPGCGKTMLAKAVAHHTTV 78
++ GPPG GK A +A H +
Sbjct: 3 RLIFLGPPGAGKGTQAVVLAEHLHI 27
>gnl|CDD|238483 cd00983, recA, 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.
Length = 325
Score = 26.4 bits (59), Expect = 1.7
Identities = 10/20 (50%), Positives = 13/20 (65%), Gaps = 2/20 (10%)
Query: 52 PRG--VLLYGPPGCGKTMLA 69
P+G + +YGP GKT LA
Sbjct: 53 PKGRIIEIYGPESSGKTTLA 72
>gnl|CDD|224048 COG1123, COG1123, ATPase components of various ABC-type transport
systems, contain duplicated ATPase [General function
prediction only].
Length = 539
Score = 26.4 bits (59), Expect = 1.7
Identities = 7/15 (46%), Positives = 10/15 (66%)
Query: 59 GPPGCGKTMLAKAVA 73
G G GK+ LA+ +A
Sbjct: 324 GESGSGKSTLARILA 338
>gnl|CDD|168630 PRK06620, PRK06620, hypothetical protein; Validated.
Length = 214
Score = 26.3 bits (58), Expect = 1.7
Identities = 11/24 (45%), Positives = 14/24 (58%), Gaps = 1/24 (4%)
Query: 48 GIDPPRGVLLY-GPPGCGKTMLAK 70
G++P + LL GP GKT L K
Sbjct: 39 GVNPYKFTLLIKGPSSSGKTYLTK 62
>gnl|CDD|234608 PRK00064, recF, recombination protein F; Reviewed.
Length = 361
Score = 26.3 bits (59), Expect = 1.8
Identities = 12/32 (37%), Positives = 18/32 (56%), Gaps = 1/32 (3%)
Query: 36 LPLTHFDLYKQIGIDP-PRGVLLYGPPGCGKT 66
L LT F Y+++ ++ P +L G G GKT
Sbjct: 6 LSLTDFRNYEELDLELSPGVNVLVGENGQGKT 37
>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 = 26.1 bits (58), Expect = 1.8
Identities = 7/17 (41%), Positives = 9/17 (52%)
Query: 59 GPPGCGKTMLAKAVAHH 75
G G GKT L + +A
Sbjct: 7 GIDGAGKTTLIELLAER 23
>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 = 26.2 bits (58), Expect = 1.9
Identities = 13/31 (41%), Positives = 16/31 (51%), Gaps = 8/31 (25%)
Query: 43 LYKQIGIDPPRGVLLYGPPGCGKTMLAKAVA 73
+ I ID GP G GK+ +AKAVA
Sbjct: 1 MAMIIAID--------GPSGAGKSTVAKAVA 23
>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 = 26.0 bits (58), Expect = 1.9
Identities = 10/19 (52%), Positives = 12/19 (63%)
Query: 57 LYGPPGCGKTMLAKAVAHH 75
L GP G GK+ LAK + H
Sbjct: 31 LMGPNGSGKSTLAKTIMGH 49
>gnl|CDD|222927 PHA02774, PHA02774, E1; Provisional.
Length = 613
Score = 26.0 bits (58), Expect = 1.9
Identities = 7/14 (50%), Positives = 10/14 (71%)
Query: 56 LLYGPPGCGKTMLA 69
++YGPP GK+M
Sbjct: 438 VIYGPPDTGKSMFC 451
>gnl|CDD|224041 COG1116, TauB, ABC-type nitrate/sulfonate/bicarbonate transport
system, ATPase component [Inorganic ion transport and
metabolism].
Length = 248
Score = 26.0 bits (58), Expect = 1.9
Identities = 9/19 (47%), Positives = 13/19 (68%)
Query: 55 VLLYGPPGCGKTMLAKAVA 73
V + GP GCGK+ L + +A
Sbjct: 32 VAILGPSGCGKSTLLRLIA 50
>gnl|CDD|236476 PRK09354, recA, recombinase A; Provisional.
Length = 349
Score = 25.9 bits (58), Expect = 2.0
Identities = 14/25 (56%), Positives = 16/25 (64%), Gaps = 3/25 (12%)
Query: 52 PRG--VLLYGPPGCGKTMLA-KAVA 73
PRG V +YGP GKT LA A+A
Sbjct: 58 PRGRIVEIYGPESSGKTTLALHAIA 82
>gnl|CDD|234232 TIGR03499, FlhF, flagellar biosynthetic protein FlhF. [Cellular
processes, Chemotaxis and motility].
Length = 283
Score = 26.1 bits (58), Expect = 2.0
Identities = 13/57 (22%), Positives = 21/57 (36%), Gaps = 4/57 (7%)
Query: 23 MDMQKQEIREAVELPLTH---FDLYKQIGIDPPRGVLLYGPPGCGKTM-LAKAVAHH 75
D+ ++ + L + ++ + L GP G GKT LAK A
Sbjct: 163 EDLDAEDAWRWLREALEGMLPVKPEEDPILERGGVIALVGPTGVGKTTTLAKLAARF 219
>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 = 25.9 bits (57), Expect = 2.0
Identities = 8/19 (42%), Positives = 13/19 (68%)
Query: 55 VLLYGPPGCGKTMLAKAVA 73
++L G PG GK+ +K +A
Sbjct: 2 IILTGLPGVGKSTFSKELA 20
>gnl|CDD|213268 cd03301, ABC_MalK_N, The N-terminal ATPase domain of the maltose
transporter, MalK. ATP binding cassette (ABC) proteins
function from bacteria to human, mediating the
translocation of substances into and out of cells or
organelles. ABC transporters contain two
transmembrane-spanning domains (TMDs) or subunits and
two nucleotide binding domains (NBDs) or subunits that
couple transport to the hydrolysis of ATP. In the
maltose transport system, the periplasmic maltose
binding protein (MBP) stimulates the ATPase activity of
the membrane-associated transporter, which consists of
two transmembrane subunits, MalF and MalG, and two
copies of the ATP binding subunit, MalK, and becomes
tightly bound to the transporter in the catalytic
transition state, ensuring that maltose is passed to
the transporter as ATP is hydrolyzed.
Length = 213
Score = 26.1 bits (58), Expect = 2.0
Identities = 10/19 (52%), Positives = 13/19 (68%)
Query: 55 VLLYGPPGCGKTMLAKAVA 73
V+L GP GCGKT + +A
Sbjct: 29 VVLLGPSGCGKTTTLRMIA 47
>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 = 26.2 bits (58), Expect = 2.0
Identities = 10/23 (43%), Positives = 15/23 (65%)
Query: 55 VLLYGPPGCGKTMLAKAVAHHTT 77
VLL G G GK ++AKA+ + +
Sbjct: 222 VLLRGESGTGKELIAKAIHYLSP 244
>gnl|CDD|213181 cd03214, ABC_Iron-Siderophores_B12_Hemin, ATP-binding component
of iron-siderophores, vitamin B12 and hemin
transporters and related proteins. ABC transporters,
involved in the uptake of siderophores, heme, and
vitamin B12, are widely conserved in bacteria and
archaea. Only very few species lack representatives of
the siderophore family transporters. The E. coli BtuCD
protein is an ABC transporter mediating vitamin B12
uptake. The two ATP-binding cassettes (BtuD) are in
close contact with each other, as are the two
membrane-spanning subunits (BtuC); this arrangement is
distinct from that observed for the E. coli lipid
flippase MsbA. The BtuC subunits provide 20
transmembrane helices grouped around a translocation
pathway that is closed to the cytoplasm by a gate
region, whereas the dimer arrangement of the BtuD
subunits resembles the ATP-bound form of the Rad50 DNA
repair enzyme. A prominent cytoplasmic loop of BtuC
forms the contact region with the ATP-binding cassette
and represent a conserved motif among the ABC
transporters.
Length = 180
Score = 25.9 bits (58), Expect = 2.0
Identities = 9/31 (29%), Positives = 15/31 (48%), Gaps = 2/31 (6%)
Query: 45 KQIGIDPPRGVLLY--GPPGCGKTMLAKAVA 73
+ + G ++ GP G GK+ L K +A
Sbjct: 16 DDLSLSIEAGEIVGILGPNGAGKSTLLKTLA 46
>gnl|CDD|169667 PRK09112, PRK09112, DNA polymerase III subunit delta'; Validated.
Length = 351
Score = 26.2 bits (58), Expect = 2.0
Identities = 10/21 (47%), Positives = 13/21 (61%)
Query: 55 VLLYGPPGCGKTMLAKAVAHH 75
+L GP G GK LA +A+H
Sbjct: 48 LLFEGPEGIGKATLAFHLANH 68
>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 = 25.7 bits (57), Expect = 2.1
Identities = 9/17 (52%), Positives = 12/17 (70%)
Query: 55 VLLYGPPGCGKTMLAKA 71
++L G GCGKT L +A
Sbjct: 4 IMLIGRSGCGKTTLTQA 20
>gnl|CDD|224847 COG1936, COG1936, Predicted nucleotide kinase (related to CMP and
AMP kinases) [Nucleotide transport and metabolism].
Length = 180
Score = 25.7 bits (57), Expect = 2.1
Identities = 7/19 (36%), Positives = 11/19 (57%)
Query: 55 VLLYGPPGCGKTMLAKAVA 73
+ + G PG GKT + K +
Sbjct: 3 IAITGTPGVGKTTVCKLLR 21
>gnl|CDD|215947 pfam00493, MCM, MCM2/3/5 family.
Length = 327
Score = 26.0 bits (58), Expect = 2.2
Identities = 13/25 (52%), Positives = 14/25 (56%), Gaps = 3/25 (12%)
Query: 53 RG---VLLYGPPGCGKTMLAKAVAH 74
RG VLL G PG K+ L K VA
Sbjct: 55 RGDINVLLVGDPGTAKSQLLKYVAK 79
>gnl|CDD|234033 TIGR02857, CydD, thiol reductant ABC exporter, CydD subunit. The
gene pair cydCD encodes an ABC-family transporter in
which each gene contains an N-terminal membrane-spanning
domain (pfam00664) and a C-terminal ATP-binding domain
(pfam00005). In E. coli these genes were discovered as
mutants which caused the terminal heme-copper oxidase
complex cytochrome bd to fail to assemble. Recent work
has shown that the transporter is involved in export of
redox-active thiol compounds such as cysteine and
glutathione. The linkage to assembly of the cytochrome
bd complex is further supported by the conserved operon
structure found outside the gammaproteobacteria
(cydABCD) containing both the transporter and oxidase
genes components. The genes used as the seed members for
this model are all either found in the
gammproteobacterial context or the CydABCD context. All
members of this family scoring above trusted at the time
of its creation were from genomes which encode a
cytochrome bd complex. Unfortunately, the gene symbol
nomenclature adopted based on this operon in B. subtilis
assigns cydC to the third gene in the operon where this
gene is actually homologous to the E. coli cydD gene. We
have chosen to name all homologs in this family in
accordance with the precedence of publication of the E.
coli name, CydD.
Length = 529
Score = 26.1 bits (58), Expect = 2.2
Identities = 9/25 (36%), Positives = 12/25 (48%)
Query: 49 IDPPRGVLLYGPPGCGKTMLAKAVA 73
+ P V L GP G GK+ L +
Sbjct: 345 VPPGERVALVGPSGAGKSTLLNLLL 369
>gnl|CDD|235845 PRK06647, PRK06647, DNA polymerase III subunits gamma and tau;
Validated.
Length = 563
Score = 25.9 bits (57), Expect = 2.2
Identities = 9/18 (50%), Positives = 11/18 (61%)
Query: 56 LLYGPPGCGKTMLAKAVA 73
+ GP G GKT A+A A
Sbjct: 42 IFSGPRGVGKTSSARAFA 59
>gnl|CDD|224410 COG1493, HprK, Serine kinase of the HPr protein, regulates
carbohydrate metabolism [Signal transduction
mechanisms].
Length = 308
Score = 25.7 bits (57), Expect = 2.3
Identities = 10/17 (58%), Positives = 12/17 (70%)
Query: 53 RGVLLYGPPGCGKTMLA 69
GVL+ GP G GK+ LA
Sbjct: 146 VGVLITGPSGAGKSELA 162
>gnl|CDD|168719 PRK06893, PRK06893, DNA replication initiation factor; Validated.
Length = 229
Score = 25.9 bits (57), Expect = 2.3
Identities = 8/19 (42%), Positives = 13/19 (68%)
Query: 57 LYGPPGCGKTMLAKAVAHH 75
++G GK+ L KAV++H
Sbjct: 44 IWGGKSSGKSHLLKAVSNH 62
>gnl|CDD|213218 cd03251, ABCC_MsbA, ATP-binding cassette domain of the bacterial
lipid flippase and related proteins, subfamily C. MsbA
is an essential ABC transporter, closely related to
eukaryotic MDR proteins. ABC transporters are a large
family of proteins involved in the transport of a wide
variety of different compounds, like sugars, ions,
peptides, and more complex organic molecules. The
nucleotide binding domain shows the highest similarity
between all members of the family. ABC transporters are
a subset of nucleotide hydrolases that contain a
signature motif, Q-loop, and H-loop/switch region, in
addition to, the Walker A motif/P-loop and Walker B
motif commonly found in a number of ATP- and
GTP-binding and hydrolyzing proteins.
Length = 234
Score = 25.7 bits (57), Expect = 2.4
Identities = 12/28 (42%), Positives = 15/28 (53%), Gaps = 2/28 (7%)
Query: 45 KQIGIDPPRG--VLLYGPPGCGKTMLAK 70
+ I +D P G V L GP G GK+ L
Sbjct: 19 RDISLDIPAGETVALVGPSGSGKSTLVN 46
>gnl|CDD|233658 TIGR01962, NuoD, NADH dehydrogenase I, D subunit. This model
recognizes specificially the D subunit of NADH
dehydrogenase I complex. It excludes the related chain
of NAD(P)H-quinone oxidoreductases from chloroplast and
Synechocystis, where the quinone may be plastoquinone
rather than ubiquinone. This subunit often appears as a
C/D fusion [Energy metabolism, Electron transport].
Length = 386
Score = 25.8 bits (57), Expect = 2.4
Identities = 8/28 (28%), Positives = 14/28 (50%), Gaps = 1/28 (3%)
Query: 27 KQEIREAVELPLTHFDLYKQIGIDPPRG 54
K+ + ++E + HF L + G P G
Sbjct: 291 KERMLTSMEALIHHFKLVTE-GFRVPAG 317
>gnl|CDD|181551 PRK08769, PRK08769, DNA polymerase III subunit delta'; Validated.
Length = 319
Score = 26.1 bits (57), Expect = 2.4
Identities = 11/22 (50%), Positives = 15/22 (68%)
Query: 54 GVLLYGPPGCGKTMLAKAVAHH 75
G+L+ GP G GK +A A+A H
Sbjct: 28 GLLICGPEGLGKRAVALALAEH 49
>gnl|CDD|224337 COG1419, FlhF, Flagellar GTP-binding protein [Cell motility and
secretion].
Length = 407
Score = 25.8 bits (57), Expect = 2.4
Identities = 12/31 (38%), Positives = 17/31 (54%), Gaps = 1/31 (3%)
Query: 45 KQIGIDPPRGVLLYGPPGCGKTM-LAKAVAH 74
+ + ++ R + L GP G GKT LAK A
Sbjct: 196 ENLIVEQKRVIALVGPTGVGKTTTLAKLAAR 226
>gnl|CDD|204242 pfam09439, SRPRB, Signal recognition particle receptor beta
subunit. The beta subunit of the signal recognition
particle receptor (SRP) is a transmembrane GTPase which
anchors the alpha subunit to the endoplasmic reticulum
membrane.
Length = 181
Score = 25.8 bits (57), Expect = 2.4
Identities = 6/16 (37%), Positives = 8/16 (50%)
Query: 53 RGVLLYGPPGCGKTML 68
V++ G GKT L
Sbjct: 4 PAVIIAGLCDSGKTSL 19
>gnl|CDD|180518 PRK06294, PRK06294, coproporphyrinogen III oxidase; Provisional.
Length = 370
Score = 25.9 bits (57), Expect = 2.5
Identities = 10/25 (40%), Positives = 16/25 (64%), Gaps = 1/25 (4%)
Query: 27 KQEIREAVELPLTHFDLYKQIGIDP 51
++ +A+ LP+TH LY + IDP
Sbjct: 173 IVDLHQAITLPITHISLY-NLTIDP 196
>gnl|CDD|183056 PRK11248, tauB, taurine transporter ATP-binding subunit;
Provisional.
Length = 255
Score = 25.8 bits (57), Expect = 2.5
Identities = 9/25 (36%), Positives = 15/25 (60%)
Query: 49 IDPPRGVLLYGPPGCGKTMLAKAVA 73
++ +++ GP GCGKT L +A
Sbjct: 24 LESGELLVVLGPSGCGKTTLLNLIA 48
>gnl|CDD|183175 PRK11522, PRK11522, putrescine--2-oxoglutarate aminotransferase;
Provisional.
Length = 459
Score = 25.9 bits (57), Expect = 2.6
Identities = 14/49 (28%), Positives = 19/49 (38%), Gaps = 12/49 (24%)
Query: 28 QEIREAVELPLTHFDLYKQIGIDPPRGVLLYGPPGCGKTMLAKAVAHHT 76
+ AV+ L L+ Q +DP R MLAK +A T
Sbjct: 101 PVVVSAVQNQLAKQPLHSQELLDPLRA------------MLAKTLAALT 137
>gnl|CDD|224045 COG1120, FepC, ABC-type cobalamin/Fe3+-siderophores transport
systems, ATPase components [Inorganic ion transport and
metabolism / Coenzyme metabolism].
Length = 258
Score = 25.6 bits (57), Expect = 2.6
Identities = 8/16 (50%), Positives = 10/16 (62%)
Query: 59 GPPGCGKTMLAKAVAH 74
GP G GK+ L K +A
Sbjct: 35 GPNGSGKSTLLKCLAG 50
>gnl|CDD|182529 PRK10536, PRK10536, hypothetical protein; Provisional.
Length = 262
Score = 25.9 bits (57), Expect = 2.6
Identities = 13/59 (22%), Positives = 23/59 (38%)
Query: 15 VQYSDIGGMDMQKQEIREAVELPLTHFDLYKQIGIDPPRGVLLYGPPGCGKTMLAKAVA 73
VQ + + M + + L + I+ + + G GCGKT ++ A A
Sbjct: 37 VQMGGVEAIGMARDSRDTSPILARNEAQAHYLKAIESKQLIFATGEAGCGKTWISAAKA 95
>gnl|CDD|238666 cd01370, KISc_KIP3_like, Kinesin motor domain, KIP3-like subgroup.
The yeast kinesin KIP3 plays a role in positioning the
mitotic spindle. This catalytic (head) domain has ATPase
activity and belongs to the larger group of P-loop
NTPases. Kinesins are microtubule-dependent molecular
motors that play important roles in intracellular
transport and in cell division. In most kinesins, the
motor domain is found at the N-terminus (N-type). N-type
kinesins are (+) end-directed motors, i.e. they
transport cargo towards the (+) end of the microtubule.
Kinesin motor domains hydrolyze ATP at a rate of about
80 per second, and move along the microtubule at a speed
of about 6400 Angstroms per second. To achieve that,
kinesin head groups work in pairs. Upon replacing ADP
with ATP, a kinesin motor domain increases its affinity
for microtubule binding and locks in place. Also, the
neck linker binds to the motor domain, which repositions
the other head domain through the coiled-coil domain
close to a second tubulin dimer, about 80 Angstroms
along the microtubule. Meanwhile, ATP hydrolysis takes
place, and when the second head domain binds to the
microtubule, the first domain again replaces ADP with
ATP, triggering a conformational change that pulls the
first domain forward.
Length = 338
Score = 25.7 bits (57), Expect = 2.7
Identities = 9/16 (56%), Positives = 9/16 (56%), Gaps = 2/16 (12%)
Query: 55 VLLYGPPGCGK--TML 68
V YG G GK TML
Sbjct: 91 VFAYGATGAGKTHTML 106
>gnl|CDD|215967 pfam00519, PPV_E1_C, Papillomavirus helicase. This protein is a
DNA helicase that is required for initiation of viral
DNA replication. This protein forms a complex with the
E2 protein pfam00508.
Length = 432
Score = 25.6 bits (57), Expect = 2.7
Identities = 7/14 (50%), Positives = 10/14 (71%)
Query: 56 LLYGPPGCGKTMLA 69
++YGPP GK+M
Sbjct: 266 VIYGPPDTGKSMFC 279
>gnl|CDD|184729 PRK14532, PRK14532, adenylate kinase; Provisional.
Length = 188
Score = 25.6 bits (56), Expect = 2.8
Identities = 8/16 (50%), Positives = 11/16 (68%)
Query: 55 VLLYGPPGCGKTMLAK 70
++L+GPP GK AK
Sbjct: 3 LILFGPPAAGKGTQAK 18
>gnl|CDD|183702 PRK12723, PRK12723, flagellar biosynthesis regulator FlhF;
Provisional.
Length = 388
Score = 25.6 bits (56), Expect = 2.9
Identities = 12/30 (40%), Positives = 15/30 (50%), Gaps = 1/30 (3%)
Query: 47 IGIDPPRGVLLYGPPGCGK-TMLAKAVAHH 75
I R +L GP G GK T +AK A +
Sbjct: 169 IDNLKKRVFILVGPTGVGKTTTIAKLAAIY 198
>gnl|CDD|224080 COG1158, Rho, Transcription termination factor [Transcription].
Length = 422
Score = 25.7 bits (57), Expect = 2.9
Identities = 10/22 (45%), Positives = 14/22 (63%), Gaps = 1/22 (4%)
Query: 53 RGVLLYGPPGCGKTMLAKAVAH 74
RG L+ PP GKT L + +A+
Sbjct: 175 RG-LIVAPPKAGKTTLLQNIAN 195
>gnl|CDD|184586 PRK14240, PRK14240, phosphate transporter ATP-binding protein;
Provisional.
Length = 250
Score = 25.4 bits (56), Expect = 3.1
Identities = 13/40 (32%), Positives = 18/40 (45%), Gaps = 9/40 (22%)
Query: 40 HFDLY-------KQIGID-PPRGVL-LYGPPGCGKTMLAK 70
DL+ K+I +D V L GP GCGK+ +
Sbjct: 8 DLDLFYGDFQALKKINLDIEENQVTALIGPSGCGKSTFLR 47
>gnl|CDD|237963 PRK15424, PRK15424, propionate catabolism operon regulatory protein
PrpR; Provisional.
Length = 538
Score = 25.5 bits (56), Expect = 3.3
Identities = 16/74 (21%), Positives = 28/74 (37%), Gaps = 12/74 (16%)
Query: 6 PTKNDEKPDVQYSDIGGMDMQKQEIREAVELPLTHFDLYKQIGIDPPRGVLLYGPPGCGK 65
T+N + D+ G Q +++R+ + L VL+ G G GK
Sbjct: 207 ATRNALRTRYVLGDLLGQSPQMEQVRQTILLYARS-----------SAAVLIQGETGTGK 255
Query: 66 TMLAKAVAHHTTVL 79
+ A+A+ H
Sbjct: 256 ELAAQAI-HREYFA 268
>gnl|CDD|237651 PRK14266, PRK14266, phosphate ABC transporter ATP-binding
protein; Provisional.
Length = 250
Score = 25.3 bits (55), Expect = 3.5
Identities = 13/39 (33%), Positives = 22/39 (56%), Gaps = 5/39 (12%)
Query: 39 THFD---LYKQIGIDPPRGVL--LYGPPGCGKTMLAKAV 72
T+FD + K + +D P+ + L GP GCGK+ + +
Sbjct: 11 TYFDDAHILKNVNLDIPKNSVTALIGPSGCGKSTFIRTL 49
>gnl|CDD|235281 PRK04328, PRK04328, hypothetical protein; Provisional.
Length = 249
Score = 25.4 bits (56), Expect = 3.6
Identities = 12/24 (50%), Positives = 16/24 (66%), Gaps = 2/24 (8%)
Query: 48 GIDPPRG-VLLYGPPGCGKTMLAK 70
GI P R VLL G PG GK++ ++
Sbjct: 19 GI-PERNVVLLSGGPGTGKSIFSQ 41
>gnl|CDD|237745 PRK14527, PRK14527, adenylate kinase; Provisional.
Length = 191
Score = 25.1 bits (55), Expect = 3.6
Identities = 9/25 (36%), Positives = 13/25 (52%)
Query: 49 IDPPRGVLLYGPPGCGKTMLAKAVA 73
+ V+ GPPG GK A+ +A
Sbjct: 3 QTKNKVVIFLGPPGAGKGTQAERLA 27
>gnl|CDD|131197 TIGR02142, modC_ABC, molybdenum ABC transporter, ATP-binding
protein. This model represents the ATP-binding
cassette (ABC) protein of the three subunit molybdate
ABC transporter. The three proteins of this complex are
homologous to proteins of the sulfate ABC transporter.
Molybdenum may be used in nitrogenases of
nitrogen-fixing bacteria and in molybdopterin
cofactors. In some cases, molybdate may be transported
by a sulfate transporter rather than by a specific
molybdate transporter [Transport and binding proteins,
Anions].
Length = 354
Score = 25.5 bits (56), Expect = 3.6
Identities = 10/24 (41%), Positives = 15/24 (62%), Gaps = 1/24 (4%)
Query: 51 PPRGVL-LYGPPGCGKTMLAKAVA 73
P +GV ++G G GKT L + +A
Sbjct: 21 PGQGVTAIFGRSGSGKTTLIRLIA 44
>gnl|CDD|233603 TIGR01862, N2-ase-Ialpha, nitrogenase component I, alpha chain.
This model represents the alpha chain of all three
varieties (Mo-Fe, V-Fe, and Fe-Fe) of component I of
nitrogenase [Central intermediary metabolism, Nitrogen
fixation].
Length = 443
Score = 25.5 bits (56), Expect = 3.7
Identities = 15/38 (39%), Positives = 18/38 (47%), Gaps = 6/38 (15%)
Query: 14 DVQYSDI--GGMDMQKQEIREAVELPLTHFDLYKQIGI 49
D+Q SDI GG K+ I EA F L K I +
Sbjct: 91 DMQESDIVFGGEKKLKKLIHEAFTE----FPLIKAISV 124
>gnl|CDD|184596 PRK14267, PRK14267, phosphate ABC transporter ATP-binding
protein; Provisional.
Length = 253
Score = 25.2 bits (55), Expect = 3.7
Identities = 13/28 (46%), Positives = 16/28 (57%), Gaps = 4/28 (14%)
Query: 48 GID---PPRGVL-LYGPPGCGKTMLAKA 71
G+D P GV L GP GCGK+ L +
Sbjct: 22 GVDLKIPQNGVFALMGPSGCGKSTLLRT 49
>gnl|CDD|223562 COG0488, Uup, ATPase components of ABC transporters with duplicated
ATPase domains [General function prediction only].
Length = 530
Score = 25.3 bits (56), Expect = 3.8
Identities = 10/28 (35%), Positives = 14/28 (50%)
Query: 46 QIGIDPPRGVLLYGPPGCGKTMLAKAVA 73
ID + + GP G GK+ L K +A
Sbjct: 342 SFRIDRGDRIAIVGPNGAGKSTLLKLLA 369
>gnl|CDD|213222 cd03255, ABC_MJ0796_LolCDE_FtsE, ATP-binding cassette domain of
the transporters involved in export of lipoprotein and
macrolide, and cell division protein. This family is
comprised of MJ0796 ATP-binding cassette,
macrolide-specific ABC-type efflux carrier (MacAB), and
proteins involved in cell division (FtsE), and release
of lipoproteins from the cytoplasmic membrane (LolCDE).
They are clustered together phylogenetically. MacAB is
an exporter that confers resistance to macrolides,
while the LolCDE system is not a transporter at all. An
FtsE null mutants showed filamentous growth and
appeared viable on high salt medium only, indicating a
role for FtsE in cell division and/or salt transport.
The LolCDE complex catalyzes the release of
lipoproteins from the cytoplasmic membrane prior to
their targeting to the outer membrane.
Length = 218
Score = 25.1 bits (56), Expect = 3.8
Identities = 7/14 (50%), Positives = 9/14 (64%)
Query: 55 VLLYGPPGCGKTML 68
V + GP G GK+ L
Sbjct: 33 VAIVGPSGSGKSTL 46
>gnl|CDD|213180 cd03213, ABCG_EPDR, Eye pigment and drug resistance transporter
subfamily G of the ATP-binding cassette superfamily.
ABCG transporters are involved in eye pigment (EP)
precursor transport, regulation of lipid-trafficking
mechanisms, and pleiotropic drug resistance (DR). DR is
a well-described phenomenon occurring in fungi and
shares several similarities with processes in bacteria
and higher eukaryotes. Compared to other members of the
ABC transporter subfamilies, the ABCG transporter
family is composed of proteins that have an ATP-binding
cassette domain at the N-terminus and a TM
(transmembrane) domain at the C-terminus.
Length = 194
Score = 25.2 bits (56), Expect = 3.9
Identities = 8/19 (42%), Positives = 11/19 (57%)
Query: 55 VLLYGPPGCGKTMLAKAVA 73
+ GP G GK+ L A+A
Sbjct: 38 TAIMGPSGAGKSTLLNALA 56
>gnl|CDD|131703 TIGR02655, circ_KaiC, circadian clock protein KaiC. Members of
this family are the circadian clock protein KaiC, part
of the kaiABC operon that controls circadian rhythm. It
may be universal in Cyanobacteria. Each member has two
copies of the KaiC domain (pfam06745), which is also
found in other proteins. KaiC performs
autophosphorylation and acts as its own transcriptional
repressor [Cellular processes, Other].
Length = 484
Score = 25.3 bits (55), Expect = 3.9
Identities = 13/48 (27%), Positives = 21/48 (43%), Gaps = 4/48 (8%)
Query: 28 QEIREAVELPLTHFDLYKQIGIDPPRGVLLYGPPGCGKTMLAKAVAHH 75
+IR +E FD G+ R L+ G G GKT+ + ++
Sbjct: 1 AKIRTMIE----GFDDISHGGLPIGRSTLVSGTSGTGKTLFSIQFLYN 44
>gnl|CDD|233206 TIGR00954, 3a01203, Peroxysomal Fatty Acyl CoA Transporter (FAT)
Family protei. [Transport and binding proteins,
Carbohydrates, organic alcohols, and acids].
Length = 659
Score = 25.5 bits (56), Expect = 4.0
Identities = 11/28 (39%), Positives = 17/28 (60%), Gaps = 2/28 (7%)
Query: 43 LYKQIGIDPPRG--VLLYGPPGCGKTML 68
L + + + P G +L+ GP GCGK+ L
Sbjct: 467 LIESLSFEVPSGNNLLICGPNGCGKSSL 494
>gnl|CDD|214372 CHL00131, ycf16, sulfate ABC transporter protein; Validated.
Length = 252
Score = 25.0 bits (55), Expect = 4.0
Identities = 9/17 (52%), Positives = 12/17 (70%)
Query: 59 GPPGCGKTMLAKAVAHH 75
GP G GK+ L+K +A H
Sbjct: 40 GPNGSGKSTLSKVIAGH 56
>gnl|CDD|223360 COG0283, Cmk, Cytidylate kinase [Nucleotide transport and
metabolism].
Length = 222
Score = 25.2 bits (56), Expect = 4.2
Identities = 11/32 (34%), Positives = 14/32 (43%), Gaps = 8/32 (25%)
Query: 44 YKQIGIDPPRGVLLYGPPGCGKTMLAKAVAHH 75
I ID GP G GK+ +AK +A
Sbjct: 4 AIIIAID--------GPAGSGKSTVAKILAEK 27
>gnl|CDD|224533 COG1618, COG1618, Predicted nucleotide kinase [Nucleotide
transport and metabolism].
Length = 179
Score = 25.0 bits (55), Expect = 4.3
Identities = 8/19 (42%), Positives = 11/19 (57%)
Query: 55 VLLYGPPGCGKTMLAKAVA 73
+ + G PG GKT L +A
Sbjct: 8 IFITGRPGVGKTTLVLKIA 26
>gnl|CDD|227470 COG5141, COG5141, PHD zinc finger-containing protein [General
function prediction only].
Length = 669
Score = 25.3 bits (55), Expect = 4.4
Identities = 15/47 (31%), Positives = 23/47 (48%), Gaps = 1/47 (2%)
Query: 10 DEKP-DVQYSDIGGMDMQKQEIREAVELPLTHFDLYKQIGIDPPRGV 55
+EK QY ++ M K + A +H + K I I+PPRG+
Sbjct: 81 NEKSYKAQYRNLELPRMHKFVSKHAPMSEESHDEGKKFIDIEPPRGL 127
>gnl|CDD|184590 PRK14249, PRK14249, phosphate ABC transporter ATP-binding
protein; Provisional.
Length = 251
Score = 25.0 bits (54), Expect = 4.4
Identities = 13/30 (43%), Positives = 19/30 (63%), Gaps = 2/30 (6%)
Query: 45 KQIGID-PPRGVL-LYGPPGCGKTMLAKAV 72
K I +D P R + + GP GCGK+ L +A+
Sbjct: 21 KNINMDFPERQITAIIGPSGCGKSTLLRAL 50
>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 = 25.0 bits (55), Expect = 4.4
Identities = 9/18 (50%), Positives = 12/18 (66%)
Query: 56 LLYGPPGCGKTMLAKAVA 73
L+ PP CGKT L + +A
Sbjct: 115 LIISPPQCGKTTLLRDLA 132
>gnl|CDD|236947 PRK11650, ugpC, glycerol-3-phosphate transporter ATP-binding
subunit; Provisional.
Length = 356
Score = 25.2 bits (56), Expect = 4.5
Identities = 10/19 (52%), Positives = 14/19 (73%)
Query: 55 VLLYGPPGCGKTMLAKAVA 73
++L GP GCGK+ L + VA
Sbjct: 33 IVLVGPSGCGKSTLLRMVA 51
>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 = 25.0 bits (55), Expect = 4.6
Identities = 10/25 (40%), Positives = 14/25 (56%)
Query: 55 VLLYGPPGCGKTMLAKAVAHHTTVL 79
V + GP G GKT AK +++ V
Sbjct: 2 VGIAGPSGSGKTTFAKKLSNQLRVN 26
>gnl|CDD|235570 PRK05703, flhF, flagellar biosynthesis regulator FlhF; Validated.
Length = 424
Score = 24.9 bits (55), Expect = 4.8
Identities = 15/60 (25%), Positives = 25/60 (41%), Gaps = 12/60 (20%)
Query: 23 MDMQKQEIREAVE--LPLTHFDLYKQIGIDPPRGVLLYGPPGCGKT-----MLAKAVAHH 75
+ + E + +P+ D+ KQ G+ V L GP G GKT + A+ +
Sbjct: 195 ERTAWRYLLELLANMIPVRVEDILKQGGV-----VALVGPTGVGKTTTLAKLAARYALLY 249
>gnl|CDD|213260 cd03293, ABC_NrtD_SsuB_transporters, ATP-binding cassette domain
of the nitrate and sulfonate transporters. NrtD and
SsuB are the ATP-binding subunits of the bacterial
ABC-type nitrate and sulfonate transport systems,
respectively. 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 = 220
Score = 24.7 bits (55), Expect = 4.8
Identities = 10/19 (52%), Positives = 13/19 (68%)
Query: 55 VLLYGPPGCGKTMLAKAVA 73
V L GP GCGK+ L + +A
Sbjct: 33 VALVGPSGCGKSTLLRIIA 51
>gnl|CDD|214692 smart00487, DEXDc, DEAD-like helicases superfamily.
Length = 201
Score = 24.8 bits (54), Expect = 5.0
Identities = 9/17 (52%), Positives = 11/17 (64%)
Query: 53 RGVLLYGPPGCGKTMLA 69
R V+L P G GKT+ A
Sbjct: 25 RDVILAAPTGSGKTLAA 41
>gnl|CDD|223487 COG0410, LivF, ABC-type branched-chain amino acid transport
systems, ATPase component [Amino acid transport and
metabolism].
Length = 237
Score = 24.7 bits (55), Expect = 5.0
Identities = 11/29 (37%), Positives = 12/29 (41%), Gaps = 2/29 (6%)
Query: 52 PRG--VLLYGPPGCGKTMLAKAVAHHTTV 78
RG V L G G GKT L K +
Sbjct: 27 ERGEIVALLGRNGAGKTTLLKTIMGLVRP 55
>gnl|CDD|236523 PRK09452, potA, putrescine/spermidine ABC transporter ATPase
protein; Reviewed.
Length = 375
Score = 24.9 bits (55), Expect = 5.0
Identities = 9/17 (52%), Positives = 12/17 (70%)
Query: 57 LYGPPGCGKTMLAKAVA 73
L GP GCGKT + + +A
Sbjct: 45 LLGPSGCGKTTVLRLIA 61
>gnl|CDD|184458 PRK14021, PRK14021, bifunctional shikimate
kinase/3-dehydroquinate synthase; Provisional.
Length = 542
Score = 25.2 bits (55), Expect = 5.0
Identities = 10/23 (43%), Positives = 14/23 (60%), Gaps = 1/23 (4%)
Query: 52 PRGVLLYGPPGCGKTMLAKAVAH 74
P+ V++ G G GKT + K VA
Sbjct: 7 PQAVII-GMMGAGKTRVGKEVAQ 28
>gnl|CDD|213196 cd03229, ABC_Class3, ATP-binding cassette domain of the binding
protein-dependent transport systems. This class is
comprised of all BPD (Binding Protein Dependent)
systems that are largely represented in archaea and
eubacteria and are primarily involved in scavenging
solutes from the environment. 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 = 178
Score = 24.8 bits (55), Expect = 5.0
Identities = 9/19 (47%), Positives = 12/19 (63%)
Query: 55 VLLYGPPGCGKTMLAKAVA 73
V L GP G GK+ L + +A
Sbjct: 29 VALLGPSGSGKSTLLRCIA 47
>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 = 24.9 bits (55), Expect = 5.0
Identities = 10/19 (52%), Positives = 13/19 (68%)
Query: 55 VLLYGPPGCGKTMLAKAVA 73
++L GPPG GK AK +A
Sbjct: 2 LVLLGPPGSGKGTQAKRIA 20
>gnl|CDD|223521 COG0444, DppD, ABC-type dipeptide/oligopeptide/nickel transport
system, ATPase component [Amino acid transport and
metabolism / Inorganic ion transport and metabolism].
Length = 316
Score = 24.8 bits (55), Expect = 5.1
Identities = 7/11 (63%), Positives = 10/11 (90%)
Query: 62 GCGKTMLAKAV 72
G GK++LAKA+
Sbjct: 41 GSGKSVLAKAI 51
>gnl|CDD|236982 PRK11784, PRK11784, tRNA 2-selenouridine synthase; Provisional.
Length = 345
Score = 24.8 bits (55), Expect = 5.1
Identities = 10/19 (52%), Positives = 13/19 (68%)
Query: 55 VLLYGPPGCGKTMLAKAVA 73
V+L G G GKT L +A+A
Sbjct: 144 VVLGGNTGSGKTELLQALA 162
>gnl|CDD|235153 PRK03731, aroL, shikimate kinase II; Reviewed.
Length = 171
Score = 24.9 bits (55), Expect = 5.1
Identities = 9/19 (47%), Positives = 12/19 (63%)
Query: 55 VLLYGPPGCGKTMLAKAVA 73
+ L G GCGKT + A+A
Sbjct: 5 LFLVGARGCGKTTVGMALA 23
>gnl|CDD|222264 pfam13614, AAA_31, AAA domain. This family includes a wide
variety of AAA domains including some that have lost
essential nucleotide binding residues in the P-loop.
Length = 145
Score = 24.9 bits (55), Expect = 5.2
Identities = 8/18 (44%), Positives = 9/18 (50%), Gaps = 1/18 (5%)
Query: 58 YGP-PGCGKTMLAKAVAH 74
Y P G GKT A +A
Sbjct: 6 YSPVGGEGKTTFALNLAQ 23
>gnl|CDD|236134 PRK07940, PRK07940, DNA polymerase III subunit delta'; Validated.
Length = 394
Score = 24.9 bits (55), Expect = 5.2
Identities = 9/18 (50%), Positives = 13/18 (72%)
Query: 56 LLYGPPGCGKTMLAKAVA 73
L GPPG G+++ A+A A
Sbjct: 40 LFTGPPGSGRSVAARAFA 57
>gnl|CDD|224141 COG1220, HslU, ATP-dependent protease HslVU (ClpYQ), ATPase
subunit [Posttranslational modification, protein
turnover, chaperones].
Length = 444
Score = 24.9 bits (55), Expect = 5.3
Identities = 10/22 (45%), Positives = 16/22 (72%)
Query: 52 PRGVLLYGPPGCGKTMLAKAVA 73
P+ +L+ GP G GKT +A+ +A
Sbjct: 50 PKNILMIGPTGVGKTEIARRLA 71
>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 = 24.9 bits (55), Expect = 5.4
Identities = 8/21 (38%), Positives = 13/21 (61%)
Query: 55 VLLYGPPGCGKTMLAKAVAHH 75
++L G P GK+ AK +A +
Sbjct: 2 IILTGLPSSGKSTRAKELAKY 22
>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 = 24.7 bits (54), Expect = 5.5
Identities = 9/21 (42%), Positives = 13/21 (61%)
Query: 55 VLLYGPPGCGKTMLAKAVAHH 75
V+L G PG GKT + +A+
Sbjct: 341 VILTGGPGTGKTTITRAIIEL 361
>gnl|CDD|226628 COG4148, ModC, ABC-type molybdate transport system, ATPase
component [Inorganic ion transport and metabolism].
Length = 352
Score = 25.0 bits (55), Expect = 5.5
Identities = 12/25 (48%), Positives = 15/25 (60%), Gaps = 1/25 (4%)
Query: 50 DPPRGVL-LYGPPGCGKTMLAKAVA 73
P RG+ L+GP G GKT L +A
Sbjct: 21 LPARGITALFGPSGSGKTSLINMIA 45
>gnl|CDD|238836 cd01673, dNK, Deoxyribonucleoside kinase (dNK) catalyzes the
phosphorylation of deoxyribonucleosides to yield
corresponding monophosphates (dNMPs). This family
consists of various deoxynucleoside kinases including
deoxyribo- cytidine (EC 2.7.1.74), guanosine (EC
2.7.1.113), adenosine (EC 2.7.1.76), and thymidine (EC
2.7.1.21) kinases. They are key enzymes in the salvage
of deoxyribonucleosides originating from extra- or
intracellular breakdown of DNA.
Length = 193
Score = 24.9 bits (55), Expect = 5.6
Identities = 9/17 (52%), Positives = 11/17 (64%)
Query: 59 GPPGCGKTMLAKAVAHH 75
G G GK+ LAK +A H
Sbjct: 6 GNIGAGKSTLAKELAEH 22
>gnl|CDD|223645 COG0572, Udk, Uridine kinase [Nucleotide transport and
metabolism].
Length = 218
Score = 24.5 bits (54), Expect = 5.6
Identities = 11/39 (28%), Positives = 15/39 (38%), Gaps = 13/39 (33%)
Query: 47 IGIDPPRGVLLYGPPGCGKTMLAKAVA-----HHTTVLC 80
IGI G G GKT +AK ++ V+
Sbjct: 11 IGIA--------GGSGSGKTTVAKELSEQLGVEKVVVIS 41
>gnl|CDD|224787 COG1875, COG1875, NYN ribonuclease and ATPase of PhoH family
domains [General function prediction only].
Length = 436
Score = 25.0 bits (55), Expect = 5.7
Identities = 10/24 (41%), Positives = 12/24 (50%)
Query: 55 VLLYGPPGCGKTMLAKAVAHHTTV 78
V L G G GKT+LA A +
Sbjct: 248 VSLGGKAGTGKTLLALAAGLEQVL 271
>gnl|CDD|172741 PRK14253, PRK14253, phosphate ABC transporter ATP-binding
protein; Provisional.
Length = 249
Score = 24.8 bits (54), Expect = 5.7
Identities = 15/43 (34%), Positives = 21/43 (48%), Gaps = 9/43 (20%)
Query: 35 ELPLTHFDLY-------KQIGID-PPRGVL-LYGPPGCGKTML 68
+ + + DL+ K I + P R V L GP GCGK+ L
Sbjct: 3 KFNIENLDLFYGENQALKSINLPIPARQVTALIGPSGCGKSTL 45
>gnl|CDD|213224 cd03257, ABC_NikE_OppD_transporters, ATP-binding cassette domain
of nickel/oligopeptides specific transporters. The ABC
transporter subfamily specific for the transport of
dipeptides, oligopeptides (OppD), and nickel (NikDE).
The NikABCDE system of E. coli belongs to this family
and is composed of the periplasmic binding protein
NikA, two integral membrane components (NikB and NikC),
and two ATPase (NikD and NikE). The NikABCDE
transporter is synthesized under anaerobic conditions
to meet the increased demand for nickel resulting from
hydrogenase synthesis. The molecular mechanism of
nickel uptake in many bacteria and most archaea is not
known. Many other members of this ABC family are also
involved in the uptake of dipeptides and oligopeptides.
The oligopeptide transport system (Opp) is a
five-component ABC transport composed of a
membrane-anchored substrate binding proteins (SRP),
OppA, two transmembrane proteins, OppB and OppC, and
two ATP-binding domains, OppD and OppF.
Length = 228
Score = 24.8 bits (55), Expect = 6.0
Identities = 7/17 (41%), Positives = 10/17 (58%)
Query: 59 GPPGCGKTMLAKAVAHH 75
G G GK+ LA+A+
Sbjct: 38 GESGSGKSTLARAILGL 54
>gnl|CDD|225369 COG2812, DnaX, DNA polymerase III, gamma/tau subunits [DNA
replication, recombination, and repair].
Length = 515
Score = 24.7 bits (54), Expect = 6.1
Identities = 10/25 (40%), Positives = 14/25 (56%), Gaps = 2/25 (8%)
Query: 56 LLYGPPGCGKTMLAKAVAHHTTVLC 80
L GP G GKT +A+ +A + C
Sbjct: 42 LFSGPRGVGKTTIARILA--KALNC 64
>gnl|CDD|237866 PRK14952, PRK14952, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 584
Score = 24.8 bits (54), Expect = 6.3
Identities = 10/18 (55%), Positives = 12/18 (66%)
Query: 56 LLYGPPGCGKTMLAKAVA 73
L GP GCGKT A+ +A
Sbjct: 39 LFSGPRGCGKTSSARILA 56
>gnl|CDD|177083 CHL00181, cbbX, CbbX; Provisional.
Length = 287
Score = 24.7 bits (54), Expect = 6.4
Identities = 18/50 (36%), Positives = 24/50 (48%), Gaps = 4/50 (8%)
Query: 27 KQEIREAVELPLTHFDLYKQIGI---DPPRGVLLYGPPGCGKTMLAKAVA 73
K IRE L L L K +G+ +P + G PG GKT +A +A
Sbjct: 32 KTRIREIAALLLID-RLRKNLGLTSSNPGLHMSFTGSPGTGKTTVALKMA 80
>gnl|CDD|226412 COG3896, COG3896, Chloramphenicol 3-O-phosphotransferase [Defense
mechanisms].
Length = 205
Score = 24.5 bits (53), Expect = 6.4
Identities = 10/25 (40%), Positives = 13/25 (52%)
Query: 48 GIDPPRGVLLYGPPGCGKTMLAKAV 72
G+ R VLL G GK+ +A A
Sbjct: 19 GMPEGRIVLLNGGSSAGKSSIALAF 43
>gnl|CDD|235858 PRK06762, PRK06762, hypothetical protein; Provisional.
Length = 166
Score = 24.5 bits (54), Expect = 6.5
Identities = 7/21 (33%), Positives = 12/21 (57%)
Query: 55 VLLYGPPGCGKTMLAKAVAHH 75
+++ G G GKT +AK +
Sbjct: 5 IIIRGNSGSGKTTIAKQLQER 25
>gnl|CDD|236346 PRK08898, PRK08898, coproporphyrinogen III oxidase; Provisional.
Length = 394
Score = 24.6 bits (54), Expect = 6.5
Identities = 12/34 (35%), Positives = 16/34 (47%), Gaps = 8/34 (23%)
Query: 29 EIREAVELPLTHFDLYKQIGIDPPRGVLLYGPPG 62
E R A+E+ HFD +D L+Y PG
Sbjct: 159 EARAAIEIAAKHFD---NFNLD-----LMYALPG 184
>gnl|CDD|182893 PRK11000, PRK11000, maltose/maltodextrin transporter ATP-binding
protein; Provisional.
Length = 369
Score = 24.6 bits (54), Expect = 6.5
Identities = 9/19 (47%), Positives = 13/19 (68%)
Query: 55 VLLYGPPGCGKTMLAKAVA 73
V+ GP GCGK+ L + +A
Sbjct: 32 VVFVGPSGCGKSTLLRMIA 50
>gnl|CDD|172749 PRK14261, PRK14261, phosphate ABC transporter ATP-binding
protein; Provisional.
Length = 253
Score = 24.8 bits (54), Expect = 6.5
Identities = 11/22 (50%), Positives = 12/22 (54%)
Query: 47 IGIDPPRGVLLYGPPGCGKTML 68
I I R L GP GCGK+ L
Sbjct: 27 ISIPKNRVTALIGPSGCGKSTL 48
>gnl|CDD|226350 COG3829, RocR, Transcriptional regulator containing PAS, AAA-type
ATPase, and DNA-binding domains [Transcription / Signal
transduction mechanisms].
Length = 560
Score = 24.6 bits (54), Expect = 6.6
Identities = 8/18 (44%), Positives = 12/18 (66%)
Query: 55 VLLYGPPGCGKTMLAKAV 72
VL+ G G GK + A+A+
Sbjct: 271 VLILGESGTGKELFARAI 288
>gnl|CDD|224054 COG1131, CcmA, ABC-type multidrug transport system, ATPase
component [Defense mechanisms].
Length = 293
Score = 24.6 bits (54), Expect = 6.8
Identities = 10/19 (52%), Positives = 11/19 (57%)
Query: 55 VLLYGPPGCGKTMLAKAVA 73
L GP G GKT L K +A
Sbjct: 34 FGLLGPNGAGKTTLLKILA 52
>gnl|CDD|129630 TIGR00539, hemN_rel, putative oxygen-independent coproporphyrinogen
III oxidase. Experimentally determined examples of
oxygen-independent coproporphyrinogen III oxidase, an
enzyme that replaces HemF function under anaerobic
conditions, belong to a family of proteins described by
the model hemN. This model, hemN_rel, models a closely
related protein, shorter at the amino end and lacking
the region containing the motif PYRT[SC]YP found in
members of the hemN family. Several species, including
E. coli, Helicobacter pylori, Aquifex aeolicus, and
Chlamydia trachomatis, have members of both this family
and the E. coli hemN family. The member of this family
from Bacillus subtilis was shown to complement an
hemF/hemN double mutant of Salmonella typimurium and to
prevent accumulation of coproporphyrinogen III under
anaerobic conditions, but the exact role of this protein
is still uncertain. It is found in a number of species
that do not synthesize heme de novo [Biosynthesis of
cofactors, prosthetic groups, and carriers, Heme,
porphyrin, and cobalamin].
Length = 360
Score = 24.5 bits (53), Expect = 7.0
Identities = 9/35 (25%), Positives = 16/35 (45%), Gaps = 2/35 (5%)
Query: 27 KQEIREAVELPLTHFDLYKQIGIDPPRGVLLYGPP 61
K+E++ A ELP+ H Y + ++ P
Sbjct: 170 KEELKLAKELPINHLSAY-ALSVE-PNTNFEKNAK 202
>gnl|CDD|215427 PLN02796, PLN02796, D-glycerate 3-kinase.
Length = 347
Score = 24.7 bits (54), Expect = 7.1
Identities = 10/24 (41%), Positives = 14/24 (58%)
Query: 51 PPRGVLLYGPPGCGKTMLAKAVAH 74
PP + + P GCGKT L A+ +
Sbjct: 99 PPLVIGISAPQGCGKTTLVFALVY 122
>gnl|CDD|180120 PRK05506, PRK05506, bifunctional sulfate adenylyltransferase
subunit 1/adenylylsulfate kinase protein; Provisional.
Length = 632
Score = 24.5 bits (54), Expect = 7.3
Identities = 11/35 (31%), Positives = 14/35 (40%), Gaps = 7/35 (20%)
Query: 52 PRGVLLYGPPGCGKTMLAKAV-------AHHTTVL 79
P V G G GK+ +A V HT +L
Sbjct: 460 PATVWFTGLSGSGKSTIANLVERRLHALGRHTYLL 494
>gnl|CDD|215755 pfam00154, RecA, recA bacterial DNA recombination protein. RecA
is a DNA-dependent ATPase and functions in DNA repair
systems. RecA protein catalyzes an ATP-dependent DNA
strand-exchange reaction that is the central step in
the repair of dsDNA breaks by homologous recombination.
Length = 322
Score = 24.5 bits (54), Expect = 7.4
Identities = 12/25 (48%), Positives = 16/25 (64%), Gaps = 3/25 (12%)
Query: 52 PRG--VLLYGPPGCGKTMLA-KAVA 73
P+G + +YGP GKT LA A+A
Sbjct: 50 PKGRIIEIYGPESSGKTTLALHAIA 74
>gnl|CDD|216065 pfam00693, Herpes_TK, Thymidine kinase from herpesvirus.
Length = 279
Score = 24.6 bits (54), Expect = 7.5
Identities = 8/19 (42%), Positives = 12/19 (63%)
Query: 59 GPPGCGKTMLAKAVAHHTT 77
G G GKT A+A+A ++
Sbjct: 1 GAHGIGKTTTARALAAASS 19
>gnl|CDD|224557 COG1643, HrpA, HrpA-like helicases [DNA replication,
recombination, and repair].
Length = 845
Score = 24.6 bits (54), Expect = 7.6
Identities = 6/12 (50%), Positives = 8/12 (66%)
Query: 55 VLLYGPPGCGKT 66
V++ G G GKT
Sbjct: 68 VIIVGETGSGKT 79
>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 = 24.3 bits (53), Expect = 7.6
Identities = 10/23 (43%), Positives = 14/23 (60%)
Query: 48 GIDPPRGVLLYGPPGCGKTMLAK 70
GI VLL G PG GK++ ++
Sbjct: 17 GIPERNVVLLSGGPGTGKSIFSQ 39
>gnl|CDD|177538 PHA03136, PHA03136, thymidine kinase; Provisional.
Length = 378
Score = 24.7 bits (53), Expect = 7.9
Identities = 19/50 (38%), Positives = 23/50 (46%), Gaps = 3/50 (6%)
Query: 24 DMQKQEIREAVELPLTHF-DLYKQIGIDPPRGVLLY--GPPGCGKTMLAK 70
D ++ IR A F ++ D R VLLY GP G GKT AK
Sbjct: 5 DACERLIRRAFSSGGMPFCSEFENDDSDFRRLVLLYLDGPFGTGKTTTAK 54
>gnl|CDD|118716 pfam10188, Oscp1, Organic solute transport protein 1. Oscp1 is a
family of proteins conserved from plants to humans. It
is called organic solute transport protein or oxido-red-
nitro domain-containing protein 1, however no reference
could be find to confirm the function of the protein.
Length = 173
Score = 24.2 bits (53), Expect = 8.1
Identities = 15/44 (34%), Positives = 18/44 (40%), Gaps = 10/44 (22%)
Query: 31 REAVELPLTHFDLYKQIGIDPPRGVL----------LYGPPGCG 64
E +EL L H D K+I +P L LY P G G
Sbjct: 93 LELLELTLNHLDAIKRIIPNPEIQALVDPVKKTLIDLYSPLGPG 136
>gnl|CDD|223708 COG0635, HemN, Coproporphyrinogen III oxidase and related Fe-S
oxidoreductases [Coenzyme metabolism].
Length = 416
Score = 24.5 bits (54), Expect = 8.1
Identities = 7/19 (36%), Positives = 12/19 (63%)
Query: 27 KQEIREAVELPLTHFDLYK 45
K+++ +A+EL H LY
Sbjct: 207 KEDLEQALELGPDHLSLYS 225
>gnl|CDD|225364 COG2805, PilT, Tfp pilus assembly protein, pilus retraction ATPase
PilT [Cell motility and secretion / Intracellular
trafficking and secretion].
Length = 353
Score = 24.1 bits (53), Expect = 8.3
Identities = 12/28 (42%), Positives = 17/28 (60%), Gaps = 2/28 (7%)
Query: 49 IDPPRG-VLLYGPPGCGK-TMLAKAVAH 74
+ PRG +L+ GP G GK T LA + +
Sbjct: 121 AESPRGLILVTGPTGSGKSTTLAAMIDY 148
>gnl|CDD|184582 PRK14236, PRK14236, phosphate transporter ATP-binding protein;
Provisional.
Length = 272
Score = 24.2 bits (53), Expect = 8.5
Identities = 12/46 (26%), Positives = 19/46 (41%), Gaps = 9/46 (19%)
Query: 32 EAVELPLTHFDLY-------KQIGIDPPRG--VLLYGPPGCGKTML 68
E L + + +L+ I + P+ GP GCGK+ L
Sbjct: 22 EQTALEVRNLNLFYGDKQALFDISMRIPKNRVTAFIGPSGCGKSTL 67
>gnl|CDD|162659 TIGR02012, tigrfam_recA, protein RecA. This model describes
orthologs of the recA protein. RecA promotes
hybridization of homolgous regions of DNA. A segment of
ssDNA can be hybridized to another ssDNA region, or to
a dsDNA region. ATP is hydrolyzed in the process. Part
of the SOS respones, it is regulated by LexA via
autocatalytic cleavage [DNA metabolism, DNA
replication, recombination, and repair].
Length = 321
Score = 24.3 bits (53), Expect = 8.5
Identities = 11/20 (55%), Positives = 13/20 (65%), Gaps = 2/20 (10%)
Query: 52 PRG--VLLYGPPGCGKTMLA 69
PRG + +YGP GKT LA
Sbjct: 53 PRGRIIEIYGPESSGKTTLA 72
>gnl|CDD|162242 TIGR01187, potA, spermidine/putrescine ABC transporter
ATP-binding subunit. This model describes
spermidine/putrescine ABC transporter, ATP binding
subunit in bacteria and its equivalents in archaea.
This transport system belong to the larger ATP-Binding
Cassette (ABC) transporter superfamily. The
characteristic feature of these transporter is the
obligatory coupling of ATP hydrolysis to substrate
translocation. The minimal configuration of bacterial
ABC transport system: an ATPase or ATP binding subunit;
An integral membrane protein; a hydrophilic
polypetpide, which likely functions as substrate
binding protein. Polyamines like spermidine and
putrescine play vital role in cell proliferation,
differentiation, and ion homeostasis. The concentration
of polyamines within the cell are regulated by
biosynthesis, degradation and transport (uptake and
efflux included) [Transport and binding proteins, Amino
acids, peptides and amines].
Length = 325
Score = 24.4 bits (53), Expect = 8.6
Identities = 10/17 (58%), Positives = 12/17 (70%)
Query: 57 LYGPPGCGKTMLAKAVA 73
L GP GCGKT L + +A
Sbjct: 1 LLGPSGCGKTTLLRLLA 17
>gnl|CDD|184129 PRK13543, PRK13543, cytochrome c biogenesis protein CcmA;
Provisional.
Length = 214
Score = 24.0 bits (52), Expect = 8.8
Identities = 9/25 (36%), Positives = 14/25 (56%)
Query: 49 IDPPRGVLLYGPPGCGKTMLAKAVA 73
+D +L+ G G GKT L + +A
Sbjct: 34 VDAGEALLVQGDNGAGKTTLLRVLA 58
>gnl|CDD|172744 PRK14256, PRK14256, phosphate ABC transporter ATP-binding
protein; Provisional.
Length = 252
Score = 24.2 bits (52), Expect = 8.9
Identities = 9/30 (30%), Positives = 18/30 (60%), Gaps = 2/30 (6%)
Query: 45 KQIGIDPPRGVL--LYGPPGCGKTMLAKAV 72
K + +D P + + GP GCGK+ + +++
Sbjct: 21 KDVSMDFPENSVTAIIGPSGCGKSTVLRSI 50
>gnl|CDD|145542 pfam02456, Adeno_IVa2, Adenovirus IVa2 protein. IVa2 protein can
interact with the adenoviral packaging signal and that
this interaction involves DNA sequences that have
previously been demonstrated to be required for
packaging. During the course of lytic infection, the
adenovirus major late promoter (MLP) is induced to high
levels after replication of viral DNA has started. IVa2
is a transcriptional activator of the major late
promoter.
Length = 370
Score = 24.3 bits (53), Expect = 9.8
Identities = 9/17 (52%), Positives = 12/17 (70%)
Query: 52 PRGVLLYGPPGCGKTML 68
P ++YGP GCGK+ L
Sbjct: 87 PVIGVVYGPTGCGKSQL 103
>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 = 23.9 bits (52), Expect = 9.9
Identities = 9/21 (42%), Positives = 11/21 (52%)
Query: 55 VLLYGPPGCGKTMLAKAVAHH 75
VLL G G GKT L + +
Sbjct: 25 VLLKGDLGAGKTTLVQGLLQG 45
>gnl|CDD|184377 PRK13894, PRK13894, conjugal transfer ATPase TrbB; Provisional.
Length = 319
Score = 23.9 bits (52), Expect = 10.0
Identities = 18/60 (30%), Positives = 25/60 (41%), Gaps = 16/60 (26%)
Query: 16 QYSDIGGM-DMQKQEIREAVELPLTHFDLYKQIGIDPPRGVLLYGPPGCGKTMLAKAVAH 74
QY + G M Q++ I AV H R +L+ G G GKT L A+ +
Sbjct: 126 QYVERGIMTAAQREAIIAAVR---AH------------RNILVIGGTGSGKTTLVNAIIN 170
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 0.138 0.428
Gapped
Lambda K H
0.267 0.0643 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,074,359
Number of extensions: 322035
Number of successful extensions: 1056
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1051
Number of HSP's successfully gapped: 347
Length of query: 80
Length of database: 10,937,602
Length adjustment: 49
Effective length of query: 31
Effective length of database: 8,764,256
Effective search space: 271691936
Effective search space used: 271691936
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: 53 (24.4 bits)