RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4924
(105 letters)
>gnl|CDD|215649 pfam00004, AAA, ATPase family associated with various cellular
activities (AAA). AAA family proteins often perform
chaperone-like functions that assist in the assembly,
operation, or disassembly of protein complexes.
Length = 131
Score = 50.3 bits (121), Expect = 3e-09
Identities = 16/26 (61%), Positives = 21/26 (80%)
Query: 19 VLLHGPPGTGKTSLCKAVAQKLSIRL 44
+LL+GPPGTGKT+L KAVA++L
Sbjct: 1 LLLYGPPGTGKTTLAKAVAKELGAPF 26
>gnl|CDD|223540 COG0464, SpoVK, ATPases of the AAA+ class [Posttranslational
modification, protein turnover, chaperones].
Length = 494
Score = 52.1 bits (125), Expect = 4e-09
Identities = 34/151 (22%), Positives = 44/151 (29%), Gaps = 63/151 (41%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQKLSIRL-----------------------------QTP 47
+ VLL+GPPGTGKT L KAVA + R P
Sbjct: 277 KGVLLYGPPGTGKTLLAKAVALESRSRFISVKGSELLSKWVGESEKNIRELFEKARKLAP 336
Query: 48 QAIFF--------------------------------KKYPNVLIFTTSNLTGAIDLAFL 75
IF +K VL+ +N +D A L
Sbjct: 337 SIIFIDEIDSLASGRGPSEDGSGRRVVGQLLTELDGIEKAEGVLVIAATNRPDDLDPALL 396
Query: 76 --DRADIKQYIGFPSAAAIFNIFSSCVEELK 104
R D Y+ P IF + + K
Sbjct: 397 RPGRFDRLIYVPLPDLEERLEIFKIHLRDKK 427
Score = 30.9 bits (70), Expect = 0.073
Identities = 16/32 (50%), Positives = 21/32 (65%), Gaps = 2/32 (6%)
Query: 19 VLLHGPPGTGKTSLCKAVAQ--KLSIRLQTPQ 48
VLLHGPPGTGKT L +A+A + + P+
Sbjct: 21 VLLHGPPGTGKTLLARALANEGAEFLSINGPE 52
>gnl|CDD|179699 PRK03992, PRK03992, proteasome-activating nucleotidase;
Provisional.
Length = 389
Score = 48.3 bits (116), Expect = 7e-08
Identities = 16/19 (84%), Positives = 17/19 (89%)
Query: 19 VLLHGPPGTGKTSLCKAVA 37
VLL+GPPGTGKT L KAVA
Sbjct: 168 VLLYGPPGTGKTLLAKAVA 186
>gnl|CDD|224143 COG1222, RPT1, ATP-dependent 26S proteasome regulatory subunit
[Posttranslational modification, protein turnover,
chaperones].
Length = 406
Score = 46.5 bits (111), Expect = 3e-07
Identities = 20/40 (50%), Positives = 25/40 (62%), Gaps = 5/40 (12%)
Query: 19 VLLHGPPGTGKTSLCKAVAQKLS---IRLQTPQAIFFKKY 55
VLL+GPPGTGKT L KAVA + IR+ + +KY
Sbjct: 188 VLLYGPPGTGKTLLAKAVANQTDATFIRVVGSE--LVQKY 225
>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 = 45.2 bits (107), Expect = 3e-07
Identities = 20/64 (31%), Positives = 32/64 (50%), Gaps = 11/64 (17%)
Query: 19 VLLHGPPGTGKTSLCKAVAQKLSIRLQTPQAIFFKKYPNVLIFTTSNLTGAIDLAFLDRA 78
+LL+GPPGTGKT+L +A+A +L F+ L S+L + +A L
Sbjct: 22 LLLYGPPGTGKTTLARAIANEL-----------FRPGAPFLYLNASDLLEGLVVAELFGH 70
Query: 79 DIKQ 82
+ +
Sbjct: 71 FLVR 74
>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit;
Provisional.
Length = 482
Score = 44.9 bits (107), Expect = 1e-06
Identities = 16/42 (38%), Positives = 22/42 (52%), Gaps = 9/42 (21%)
Query: 5 HSKVKSNIISW---------NRVVLLHGPPGTGKTSLCKAVA 37
+ K K + W + +LL+GPPG GKTSL A+A
Sbjct: 19 NEKAKEQLREWIESWLKGKPKKALLLYGPPGVGKTSLAHALA 60
>gnl|CDD|221983 pfam13207, AAA_17, AAA domain.
Length = 114
Score = 41.1 bits (96), Expect = 8e-06
Identities = 13/27 (48%), Positives = 22/27 (81%)
Query: 18 VVLLHGPPGTGKTSLCKAVAQKLSIRL 44
++L+ GPPG+GK++L K +A+KL I +
Sbjct: 1 IILITGPPGSGKSTLAKKLAEKLGIPV 27
>gnl|CDD|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 = 41.2 bits (96), Expect = 1e-05
Identities = 15/82 (18%), Positives = 30/82 (36%), Gaps = 11/82 (13%)
Query: 16 NRVVLLHGPPGTGKTSLCKAVAQKLSIRLQTPQAIFFKKYPNVLIFTTSNLTGAIDLAFL 75
V+L+ GPPG+GKT+L +A+A++L V+ ++ + L
Sbjct: 2 GEVILIVGPPGSGKTTLARALAREL-----------GPPGGGVIYIDGEDILEEVLDQLL 50
Query: 76 DRADIKQYIGFPSAAAIFNIFS 97
+ + +
Sbjct: 51 LIIVGGKKASGSGELRLRLALA 72
>gnl|CDD|240423 PTZ00454, PTZ00454, 26S protease regulatory subunit 6B-like
protein; Provisional.
Length = 398
Score = 42.1 bits (99), Expect = 1e-05
Identities = 17/21 (80%), Positives = 18/21 (85%)
Query: 17 RVVLLHGPPGTGKTSLCKAVA 37
R VLL+GPPGTGKT L KAVA
Sbjct: 180 RGVLLYGPPGTGKTMLAKAVA 200
>gnl|CDD|223786 COG0714, COG0714, MoxR-like ATPases [General function prediction
only].
Length = 329
Score = 41.7 bits (98), Expect = 1e-05
Identities = 25/82 (30%), Positives = 34/82 (41%), Gaps = 19/82 (23%)
Query: 19 VLLHGPPGTGKTSLCKAVAQKLS---IRLQ-----TPQAIFF-------KKYPNVLIFTT 63
VLL GPPG GKT L +A+A+ L +R+Q P + P F
Sbjct: 46 VLLEGPPGVGKTLLARALARALGLPFVRIQCTPDLLPSDLLGTYAYAALLLEPGEFRFVP 105
Query: 64 SNLTGAID-LAFLD---RADIK 81
L A+ + LD RA +
Sbjct: 106 GPLFAAVRVILLLDEINRAPPE 127
>gnl|CDD|130309 TIGR01242, 26Sp45, 26S proteasome subunit P45 family. Many
proteins may score above the trusted cutoff because an
internal.
Length = 364
Score = 41.7 bits (98), Expect = 2e-05
Identities = 16/19 (84%), Positives = 17/19 (89%)
Query: 19 VLLHGPPGTGKTSLCKAVA 37
VLL+GPPGTGKT L KAVA
Sbjct: 159 VLLYGPPGTGKTLLAKAVA 177
>gnl|CDD|225164 COG2255, RuvB, Holliday junction resolvasome, helicase subunit
[DNA replication, recombination, and repair].
Length = 332
Score = 41.0 bits (97), Expect = 2e-05
Identities = 14/31 (45%), Positives = 19/31 (61%)
Query: 19 VLLHGPPGTGKTSLCKAVAQKLSIRLQTPQA 49
VLL GPPG GKT+L +A +L + L+
Sbjct: 55 VLLFGPPGLGKTTLAHIIANELGVNLKITSG 85
>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 = 40.7 bits (96), Expect = 3e-05
Identities = 16/19 (84%), Positives = 16/19 (84%)
Query: 19 VLLHGPPGTGKTSLCKAVA 37
VLL GPPGTGKT L KAVA
Sbjct: 91 VLLVGPPGTGKTLLAKAVA 109
>gnl|CDD|221970 pfam13191, AAA_16, AAA ATPase domain. This family of domains
contain a P-loop motif that is characteristic of the
AAA superfamily.
Length = 154
Score = 39.9 bits (93), Expect = 3e-05
Identities = 15/63 (23%), Positives = 20/63 (31%), Gaps = 1/63 (1%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQKLSIRLQTPQAIFFKKYPNVLIFTTSNLTGAIDLAFLD 76
VLL GP GTGKTSL + + + L + P L +
Sbjct: 25 PSVLLTGPSGTGKTSLLRELLEGLL-VAAGKCDQAERNPPYAFSQALRELLRQLLRELAA 83
Query: 77 RAD 79
Sbjct: 84 ELL 86
>gnl|CDD|185575 PTZ00361, PTZ00361, 26 proteosome regulatory subunit 4-like
protein; Provisional.
Length = 438
Score = 40.1 bits (94), Expect = 4e-05
Identities = 16/23 (69%), Positives = 19/23 (82%)
Query: 19 VLLHGPPGTGKTSLCKAVAQKLS 41
V+L+GPPGTGKT L KAVA + S
Sbjct: 220 VILYGPPGTGKTLLAKAVANETS 242
>gnl|CDD|224145 COG1224, TIP49, DNA helicase TIP49, TBP-interacting protein
[Transcription].
Length = 450
Score = 40.0 bits (94), Expect = 5e-05
Identities = 14/33 (42%), Positives = 23/33 (69%), Gaps = 1/33 (3%)
Query: 8 VKSNIISWNRVVLLHGPPGTGKTSLCKAVAQKL 40
+K ++ R +L+ GPPGTGKT+L +A++L
Sbjct: 58 IKQGKMA-GRGILIVGPPGTGKTALAMGIAREL 89
>gnl|CDD|225165 COG2256, MGS1, ATPase related to the helicase subunit of the
Holliday junction resolvase [DNA replication,
recombination, and repair].
Length = 436
Score = 39.9 bits (94), Expect = 6e-05
Identities = 12/34 (35%), Positives = 18/34 (52%)
Query: 21 LHGPPGTGKTSLCKAVAQKLSIRLQTPQAIFFKK 54
L GPPGTGKT+L + +A + + A+
Sbjct: 53 LWGPPGTGKTTLARLIAGTTNAAFEALSAVTSGV 86
>gnl|CDD|237355 PRK13342, PRK13342, recombination factor protein RarA; Reviewed.
Length = 413
Score = 39.7 bits (94), Expect = 6e-05
Identities = 12/36 (33%), Positives = 19/36 (52%)
Query: 19 VLLHGPPGTGKTSLCKAVAQKLSIRLQTPQAIFFKK 54
++L GPPGTGKT+L + +A + A+
Sbjct: 39 MILWGPPGTGKTTLARIIAGATDAPFEALSAVTSGV 74
>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 = 39.7 bits (93), Expect = 8e-05
Identities = 15/22 (68%), Positives = 17/22 (77%)
Query: 19 VLLHGPPGTGKTSLCKAVAQKL 40
VLL+GPPG GKT + KAVA L
Sbjct: 219 VLLYGPPGCGKTLIAKAVANSL 240
Score = 29.3 bits (66), Expect = 0.35
Identities = 17/43 (39%), Positives = 22/43 (51%), Gaps = 2/43 (4%)
Query: 57 NVLIFTTSNLTGAIDLAFL--DRADIKQYIGFPSAAAIFNIFS 97
NV++ SN ID A L R D+K I P A A +IF+
Sbjct: 333 NVIVIGASNREDMIDPAILRPGRLDVKIRIERPDAEAAADIFA 375
>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 = 39.6 bits (93), Expect = 8e-05
Identities = 16/34 (47%), Positives = 24/34 (70%), Gaps = 1/34 (2%)
Query: 8 VKSNIISWNRVVLLHGPPGTGKTSLCKAVAQKLS 41
+K I+ R VL+ GPPGTGKT+L A++++L
Sbjct: 43 IKEGKIA-GRAVLIAGPPGTGKTALAIAISKELG 75
>gnl|CDD|224144 COG1223, COG1223, Predicted ATPase (AAA+ superfamily) [General
function prediction only].
Length = 368
Score = 39.0 bits (91), Expect = 1e-04
Identities = 14/28 (50%), Positives = 20/28 (71%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQKLSIRL 44
+ VL +GPPGTGKT + KA+A + + L
Sbjct: 152 KNVLFYGPPGTGKTMMAKALANEAKVPL 179
>gnl|CDD|222000 pfam13238, AAA_18, AAA domain.
Length = 128
Score = 38.2 bits (89), Expect = 1e-04
Identities = 12/26 (46%), Positives = 19/26 (73%)
Query: 19 VLLHGPPGTGKTSLCKAVAQKLSIRL 44
+L+ G PG+GKT+L K +A++L L
Sbjct: 1 ILITGTPGSGKTTLAKELAERLGDVL 26
>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 = 39.1 bits (91), Expect = 1e-04
Identities = 16/21 (76%), Positives = 17/21 (80%)
Query: 17 RVVLLHGPPGTGKTSLCKAVA 37
+ VLL GPPGTGKT L KAVA
Sbjct: 488 KGVLLFGPPGTGKTLLAKAVA 508
Score = 38.3 bits (89), Expect = 2e-04
Identities = 16/21 (76%), Positives = 18/21 (85%)
Query: 19 VLLHGPPGTGKTSLCKAVAQK 39
VLL+GPPGTGKT L KAVA +
Sbjct: 215 VLLYGPPGTGKTLLAKAVANE 235
>gnl|CDD|129721 TIGR00635, ruvB, Holliday junction DNA helicase, RuvB subunit.
All proteins in this family for which functions are
known are 5'-3' DNA helicases that, as part of a
complex with RuvA homologs serve as a 5'-3' Holliday
junction helicase. RuvA specifically binds Holliday
junctions as a sandwich of two tetramers and maintains
the configuration of the junction. It forms a complex
with two hexameric rings of RuvB, the subunit that
contains helicase activity. The complex drives
ATP-dependent branch migration of the Holliday junction
recombination intermediate. The endonuclease RuvC
resolves junctions [DNA metabolism, DNA replication,
recombination, and repair].
Length = 305
Score = 38.8 bits (91), Expect = 1e-04
Identities = 20/58 (34%), Positives = 32/58 (55%), Gaps = 2/58 (3%)
Query: 19 VLLHGPPGTGKTSLCKAVAQKLSIRLQTPQAIFFKKYPNVLIFTTSNLTGAIDLAFLD 76
+LL+GPPG GKT+L +A ++ + L+ +K P L +NL D+ F+D
Sbjct: 33 LLLYGPPGLGKTTLAHIIANEMGVNLKITSGPALEK-PGDLAAILTNLE-EGDVLFID 88
>gnl|CDD|234619 PRK00080, ruvB, Holliday junction DNA helicase RuvB; Reviewed.
Length = 328
Score = 38.6 bits (91), Expect = 1e-04
Identities = 12/31 (38%), Positives = 20/31 (64%)
Query: 19 VLLHGPPGTGKTSLCKAVAQKLSIRLQTPQA 49
VLL+GPPG GKT+L +A ++ + ++
Sbjct: 54 VLLYGPPGLGKTTLANIIANEMGVNIRITSG 84
>gnl|CDD|223873 COG0802, COG0802, Predicted ATPase or kinase [General function
prediction only].
Length = 149
Score = 37.6 bits (88), Expect = 2e-04
Identities = 12/28 (42%), Positives = 17/28 (60%)
Query: 18 VVLLHGPPGTGKTSLCKAVAQKLSIRLQ 45
VVLL G G GKT+L + +A+ L +
Sbjct: 27 VVLLSGDLGAGKTTLVRGIAKGLGVDGN 54
>gnl|CDD|203260 pfam05496, RuvB_N, Holliday junction DNA helicase ruvB
N-terminus. The RuvB protein makes up part of the
RuvABC revolvasome which catalyzes the resolution of
Holliday junctions that arise during genetic
recombination and DNA repair. Branch migration is
catalyzed by the RuvB protein that is targeted to the
Holliday junction by the structure specific RuvA
protein. This family contains the N-terminal region of
the protein.
Length = 231
Score = 37.8 bits (89), Expect = 3e-04
Identities = 12/28 (42%), Positives = 20/28 (71%)
Query: 19 VLLHGPPGTGKTSLCKAVAQKLSIRLQT 46
VLL+GPPG GKT+L +A ++ + ++
Sbjct: 53 VLLYGPPGLGKTTLANIIANEMGVNIRI 80
>gnl|CDD|222194 pfam13521, AAA_28, AAA domain.
Length = 162
Score = 36.8 bits (86), Expect = 5e-04
Identities = 11/22 (50%), Positives = 16/22 (72%), Gaps = 1/22 (4%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQ 38
R+V+ G P TGKT+L +A+A
Sbjct: 1 RIVIT-GGPSTGKTTLLEALAA 21
>gnl|CDD|235878 PRK06851, PRK06851, hypothetical protein; Provisional.
Length = 367
Score = 37.3 bits (87), Expect = 5e-04
Identities = 14/37 (37%), Positives = 22/37 (59%)
Query: 5 HSKVKSNIISWNRVVLLHGPPGTGKTSLCKAVAQKLS 41
+S S I NR+ +L G PGTGK++L K + ++
Sbjct: 19 YSLYDSIIDGANRIFILKGGPGTGKSTLMKKIGEEFL 55
Score = 27.6 bits (62), Expect = 1.3
Identities = 10/28 (35%), Positives = 15/28 (53%)
Query: 16 NRVVLLHGPPGTGKTSLCKAVAQKLSIR 43
L G PGTGK+++ K +A+ R
Sbjct: 214 KNRYFLKGRPGTGKSTMLKKIAKAAEER 241
>gnl|CDD|238979 cd02021, GntK, Gluconate kinase (GntK) catalyzes the phosphoryl
transfer from ATP to gluconate. The resulting product
gluconate-6-phoshate is an important precursor of
gluconate metabolism. GntK acts as a dimmer composed of
two identical subunits.
Length = 150
Score = 36.5 bits (85), Expect = 5e-04
Identities = 8/26 (30%), Positives = 19/26 (73%)
Query: 18 VVLLHGPPGTGKTSLCKAVAQKLSIR 43
++++ G G+GK+++ KA+A++L
Sbjct: 1 IIVVMGVSGSGKSTVGKALAERLGAP 26
>gnl|CDD|216186 pfam00910, RNA_helicase, RNA helicase. This family includes RNA
helicases thought to be involved in duplex unwinding
during viral RNA replication. Members of this family
are found in a variety of single stranded RNA viruses.
Length = 105
Score = 36.1 bits (84), Expect = 6e-04
Identities = 13/30 (43%), Positives = 20/30 (66%)
Query: 19 VLLHGPPGTGKTSLCKAVAQKLSIRLQTPQ 48
+ L+GPPG GK++L K +A+ L L P+
Sbjct: 1 IWLYGPPGCGKSTLAKYLARALLKHLGLPK 30
>gnl|CDD|214386 CHL00176, ftsH, cell division protein; Validated.
Length = 638
Score = 37.0 bits (86), Expect = 7e-04
Identities = 15/19 (78%), Positives = 16/19 (84%)
Query: 19 VLLHGPPGTGKTSLCKAVA 37
VLL GPPGTGKT L KA+A
Sbjct: 219 VLLVGPPGTGKTLLAKAIA 237
>gnl|CDD|222104 pfam13401, AAA_22, AAA domain.
Length = 124
Score = 35.7 bits (83), Expect = 7e-04
Identities = 9/24 (37%), Positives = 17/24 (70%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQKL 40
+ +L G G+GKT+L + +A++L
Sbjct: 5 GIGVLTGESGSGKTTLLRRLARQL 28
>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 = 36.2 bits (84), Expect = 8e-04
Identities = 15/34 (44%), Positives = 26/34 (76%)
Query: 18 VVLLHGPPGTGKTSLCKAVAQKLSIRLQTPQAIF 51
++ + GPPG+GKT++ K +A+KLS++L + IF
Sbjct: 2 IITISGPPGSGKTTVAKILAEKLSLKLISAGDIF 35
>gnl|CDD|216999 pfam02367, UPF0079, Uncharacterized P-loop hydrolase UPF0079.
This uncharacterized family contains a P-loop.
Length = 123
Score = 35.7 bits (83), Expect = 9e-04
Identities = 13/26 (50%), Positives = 16/26 (61%)
Query: 18 VVLLHGPPGTGKTSLCKAVAQKLSIR 43
VVLL G G GKT+ + +AQ L I
Sbjct: 17 VVLLSGDLGAGKTTFVRGLAQGLGIT 42
>gnl|CDD|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 = 35.9 bits (84), Expect = 9e-04
Identities = 9/22 (40%), Positives = 16/22 (72%)
Query: 23 GPPGTGKTSLCKAVAQKLSIRL 44
GP G+GK+++ K +A+KL +
Sbjct: 6 GPAGSGKSTVAKLLAKKLGLPY 27
>gnl|CDD|215599 PLN03140, PLN03140, ABC transporter G family member; Provisional.
Length = 1470
Score = 36.7 bits (85), Expect = 0.001
Identities = 20/46 (43%), Positives = 27/46 (58%)
Query: 10 SNIISWNRVVLLHGPPGTGKTSLCKAVAQKLSIRLQTPQAIFFKKY 55
S II +R+ LL GPP +GKT+L A+A KL L+ I + Y
Sbjct: 185 SGIIKPSRMTLLLGPPSSGKTTLLLALAGKLDPSLKVSGEITYNGY 230
>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 = 36.0 bits (84), Expect = 0.001
Identities = 11/23 (47%), Positives = 16/23 (69%)
Query: 16 NRVVLLHGPPGTGKTSLCKAVAQ 38
+RV ++ GP GTGKT+ KA +
Sbjct: 18 DRVAVVQGPAGTGKTTSLKAARE 40
>gnl|CDD|223542 COG0466, Lon, ATP-dependent Lon protease, bacterial type
[Posttranslational modification, protein turnover,
chaperones].
Length = 782
Score = 36.4 bits (85), Expect = 0.001
Identities = 16/35 (45%), Positives = 21/35 (60%), Gaps = 6/35 (17%)
Query: 6 SKVKSNIISWNRVVLLHGPPGTGKTSLCKAVAQKL 40
K+K I+ L GPPG GKTSL K++A+ L
Sbjct: 346 KKLKGPIL------CLVGPPGVGKTSLGKSIAKAL 374
>gnl|CDD|223541 COG0465, HflB, ATP-dependent Zn proteases [Posttranslational
modification, protein turnover, chaperones].
Length = 596
Score = 36.1 bits (84), Expect = 0.001
Identities = 16/19 (84%), Positives = 16/19 (84%)
Query: 19 VLLHGPPGTGKTSLCKAVA 37
VLL GPPGTGKT L KAVA
Sbjct: 186 VLLVGPPGTGKTLLAKAVA 204
>gnl|CDD|223637 COG0563, Adk, Adenylate kinase and related kinases [Nucleotide
transport and metabolism].
Length = 178
Score = 35.7 bits (83), Expect = 0.001
Identities = 13/27 (48%), Positives = 21/27 (77%), Gaps = 1/27 (3%)
Query: 16 NRVVLLHGPPGTGKTSLCKAVAQKLSI 42
R+++L GPPG GK++L K +A+KL +
Sbjct: 1 MRILIL-GPPGAGKSTLAKKLAKKLGL 26
>gnl|CDD|237354 PRK13341, PRK13341, recombination factor protein RarA/unknown
domain fusion protein; Reviewed.
Length = 725
Score = 36.2 bits (84), Expect = 0.001
Identities = 10/18 (55%), Positives = 15/18 (83%)
Query: 20 LLHGPPGTGKTSLCKAVA 37
+L+GPPG GKT+L + +A
Sbjct: 56 ILYGPPGVGKTTLARIIA 73
>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 = 36.1 bits (84), Expect = 0.001
Identities = 13/23 (56%), Positives = 18/23 (78%)
Query: 18 VVLLHGPPGTGKTSLCKAVAQKL 40
++ L GPPG GKTSL K++A+ L
Sbjct: 349 ILCLVGPPGVGKTSLGKSIAKAL 371
>gnl|CDD|235244 PRK04182, PRK04182, cytidylate kinase; Provisional.
Length = 180
Score = 35.6 bits (83), Expect = 0.002
Identities = 10/22 (45%), Positives = 18/22 (81%)
Query: 23 GPPGTGKTSLCKAVAQKLSIRL 44
GPPG+GKT++ + +A+KL ++
Sbjct: 7 GPPGSGKTTVARLLAEKLGLKH 28
>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 = 35.2 bits (82), Expect = 0.002
Identities = 15/33 (45%), Positives = 20/33 (60%), Gaps = 4/33 (12%)
Query: 19 VLLHGPPGTGKTSLCKAVAQKLSI---RLQ-TP 47
VLL G PG KT L + +A+ L + R+Q TP
Sbjct: 2 VLLEGVPGLAKTLLARTLARSLGLDFRRIQFTP 34
>gnl|CDD|222163 pfam13479, AAA_24, AAA domain. This AAA domain is found in a
wide variety of presumed phage proteins.
Length = 201
Score = 35.0 bits (81), Expect = 0.003
Identities = 21/66 (31%), Positives = 31/66 (46%), Gaps = 4/66 (6%)
Query: 19 VLLHGPPGTGKTSLCK-AVAQKLSIRLQTPQAIFFKKYPNVLIFTTSNLTGAIDLAFLDR 77
VL++GPPG GKTSL K + L + L + NV I + +L +D
Sbjct: 6 VLIYGPPGIGKTSLAKTLPPKTLFLDLDAGTTKVLSRGDNVDIRSWQDLRDFLDEL---A 62
Query: 78 ADIKQY 83
D+ +Y
Sbjct: 63 EDLAEY 68
>gnl|CDD|238713 cd01428, ADK, Adenylate kinase (ADK) catalyzes the reversible
phosphoryl transfer from adenosine triphosphates (ATP)
to adenosine monophosphates (AMP) and to yield
adenosine diphosphates (ADP). This enzyme is required
for the biosynthesis of ADP and is essential for
homeostasis of adenosine phosphates.
Length = 194
Score = 34.5 bits (80), Expect = 0.003
Identities = 11/26 (42%), Positives = 19/26 (73%), Gaps = 1/26 (3%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQKLSI 42
R++LL GPPG+GK + + +A+K +
Sbjct: 1 RILLL-GPPGSGKGTQAERLAKKYGL 25
>gnl|CDD|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 = 34.2 bits (79), Expect = 0.004
Identities = 7/23 (30%), Positives = 17/23 (73%)
Query: 18 VVLLHGPPGTGKTSLCKAVAQKL 40
++L+ G PG+GK++ + + ++L
Sbjct: 1 LILMVGLPGSGKSTFARRLLREL 23
>gnl|CDD|180215 PRK05707, PRK05707, DNA polymerase III subunit delta'; Validated.
Length = 328
Score = 34.7 bits (80), Expect = 0.004
Identities = 13/30 (43%), Positives = 17/30 (56%), Gaps = 2/30 (6%)
Query: 20 LLHGPPGTGKTSLCKAVAQKLSIRLQTPQA 49
LLHGP G GK +L + +A L + PQ
Sbjct: 26 LLHGPAGIGKRALAERLAAALLC--EAPQG 53
>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 = 34.3 bits (79), Expect = 0.005
Identities = 19/63 (30%), Positives = 29/63 (46%), Gaps = 13/63 (20%)
Query: 10 SNIISWNRVVLLHGPPGTGKTS-LCKAVAQKLSIRLQTPQAIFFKKYPNVLIFTTSNLTG 68
+S + + L+ GPPGTGKT+ + + + Q LS VL+ SN
Sbjct: 11 KKALSSSDITLIQGPPGTGKTTTIVEIIKQLLSNAPG----------KKVLVCAPSNS-- 58
Query: 69 AID 71
A+D
Sbjct: 59 AVD 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 = 34.4 bits (79), Expect = 0.005
Identities = 11/21 (52%), Positives = 15/21 (71%)
Query: 20 LLHGPPGTGKTSLCKAVAQKL 40
L GPPGTGKT++ + VA+
Sbjct: 316 LFAGPPGTGKTTIARVVAKIY 336
>gnl|CDD|237495 PRK13765, PRK13765, ATP-dependent protease Lon; Provisional.
Length = 637
Score = 34.2 bits (79), Expect = 0.006
Identities = 13/24 (54%), Positives = 18/24 (75%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQKL 40
R V++ G PGTGK+ L KA+A+ L
Sbjct: 51 RHVMMIGSPGTGKSMLAKAMAELL 74
>gnl|CDD|224391 COG1474, CDC6, Cdc6-related protein, AAA superfamily ATPase [DNA
replication, recombination, and repair /
Posttranslational modification, protein turnover,
chaperones].
Length = 366
Score = 34.2 bits (79), Expect = 0.006
Identities = 14/46 (30%), Positives = 23/46 (50%), Gaps = 4/46 (8%)
Query: 19 VLLHGPPGTGKTSLCKAVAQKLSIRLQTPQAIFFKKYPNVLIFTTS 64
++++GP GTGKT+ K V ++L + + Y N L T
Sbjct: 45 IIIYGPTGTGKTATVKFVMEELEESSANVEVV----YINCLELRTP 86
>gnl|CDD|218685 pfam05673, DUF815, Protein of unknown function (DUF815). This
family consists of several bacterial proteins of
unknown function.
Length = 248
Score = 34.0 bits (79), Expect = 0.007
Identities = 12/23 (52%), Positives = 16/23 (69%)
Query: 19 VLLHGPPGTGKTSLCKAVAQKLS 41
VLL G GTGK+SL KA+ + +
Sbjct: 56 VLLWGARGTGKSSLVKALLNEYA 78
>gnl|CDD|236153 PRK08116, PRK08116, hypothetical protein; Validated.
Length = 268
Score = 33.8 bits (78), Expect = 0.007
Identities = 12/26 (46%), Positives = 15/26 (57%)
Query: 16 NRVVLLHGPPGTGKTSLCKAVAQKLS 41
N +LL G GTGKT L +A +L
Sbjct: 114 NVGLLLWGSVGTGKTYLAACIANELI 139
>gnl|CDD|224985 COG2074, COG2074, 2-phosphoglycerate kinase [Carbohydrate transport
and metabolism].
Length = 299
Score = 33.9 bits (78), Expect = 0.007
Identities = 9/27 (33%), Positives = 18/27 (66%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQKLSIR 43
++L+ G G GK+++ +A++L IR
Sbjct: 90 LIILIGGASGVGKSTIAGELARRLGIR 116
>gnl|CDD|223360 COG0283, Cmk, Cytidylate kinase [Nucleotide transport and
metabolism].
Length = 222
Score = 33.7 bits (78), Expect = 0.007
Identities = 9/22 (40%), Positives = 15/22 (68%)
Query: 23 GPPGTGKTSLCKAVAQKLSIRL 44
GP G+GK+++ K +A+KL
Sbjct: 11 GPAGSGKSTVAKILAEKLGFHY 32
>gnl|CDD|224401 COG1484, DnaC, DNA replication protein [DNA replication,
recombination, and repair].
Length = 254
Score = 33.9 bits (78), Expect = 0.008
Identities = 18/58 (31%), Positives = 26/58 (44%), Gaps = 11/58 (18%)
Query: 19 VLLHGPPGTGKTSLCKAVAQKLSIRLQTPQAIFFKKYPNVLIFTTSNLTGAIDLAFLD 76
++L GPPG GKT L A+ +L K +VL T +L + AF +
Sbjct: 108 LVLLGPPGVGKTHLAIAIGNELL-----------KAGISVLFITAPDLLSKLKAAFDE 154
>gnl|CDD|235825 PRK06547, PRK06547, hypothetical protein; Provisional.
Length = 172
Score = 33.6 bits (77), Expect = 0.008
Identities = 11/28 (39%), Positives = 17/28 (60%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQKLSIRL 44
VL+ G G+GKT+L A+A + +L
Sbjct: 16 ITVLIDGRSGSGKTTLAGALAARTGFQL 43
>gnl|CDD|234579 PRK00023, cmk, cytidylate kinase; Provisional.
Length = 225
Score = 33.6 bits (78), Expect = 0.008
Identities = 9/22 (40%), Positives = 14/22 (63%)
Query: 23 GPPGTGKTSLCKAVAQKLSIRL 44
GP G+GK ++ K +A+KL
Sbjct: 11 GPAGSGKGTVAKILAKKLGFHY 32
>gnl|CDD|223718 COG0645, COG0645, Predicted kinase [General function prediction
only].
Length = 170
Score = 33.5 bits (77), Expect = 0.009
Identities = 12/34 (35%), Positives = 20/34 (58%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQKLSIRLQTPQAI 50
R+VL+ G PG+GK++L + +A+ L I
Sbjct: 2 RLVLVGGLPGSGKSTLARGLAELLGAIRLRSDVI 35
>gnl|CDD|222005 pfam13245, AAA_19, Part of AAA domain.
Length = 73
Score = 32.3 bits (74), Expect = 0.009
Identities = 9/25 (36%), Positives = 15/25 (60%)
Query: 16 NRVVLLHGPPGTGKTSLCKAVAQKL 40
+ ++ G PGTGKT+ A+ +L
Sbjct: 10 RSLFVVDGGPGTGKTATAAAIIARL 34
>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 = 33.3 bits (77), Expect = 0.009
Identities = 11/23 (47%), Positives = 15/23 (65%)
Query: 18 VVLLHGPPGTGKTSLCKAVAQKL 40
+ + GPPG GKT+L K V + L
Sbjct: 1 RIFITGPPGVGKTTLVKKVIELL 23
>gnl|CDD|235210 PRK04040, PRK04040, adenylate kinase; Provisional.
Length = 188
Score = 33.3 bits (77), Expect = 0.009
Identities = 10/30 (33%), Positives = 17/30 (56%)
Query: 16 NRVVLLHGPPGTGKTSLCKAVAQKLSIRLQ 45
+VV++ G PG GKT++ +KL +
Sbjct: 2 MKVVVVTGVPGVGKTTVLNKALEKLKEDYK 31
>gnl|CDD|233418 TIGR01448, recD_rel, helicase, putative, RecD/TraA family. This
model describes a family similar to RecD, the
exodeoxyribonuclease V alpha chain of TIGR01447. Members
of this family, however, are not found in a context of
RecB and RecC and are longer by about 200 amino acids at
the amino end. Chlamydia muridarum has both a member of
this family and a RecD [Unknown function, Enzymes of
unknown specificity].
Length = 720
Score = 33.6 bits (77), Expect = 0.011
Identities = 13/38 (34%), Positives = 23/38 (60%), Gaps = 1/38 (2%)
Query: 13 ISWNRVVLLHGPPGTGKTSLCKAVAQKLSIRLQTPQAI 50
++VV+L G PGTGKT++ +A+ + L+ L +
Sbjct: 335 AIQHKVVILTGGPGTGKTTITRAIIE-LAEELGGLLPV 371
>gnl|CDD|182683 PRK10733, hflB, ATP-dependent metalloprotease; Reviewed.
Length = 644
Score = 33.5 bits (76), Expect = 0.012
Identities = 14/19 (73%), Positives = 16/19 (84%)
Query: 19 VLLHGPPGTGKTSLCKAVA 37
VL+ GPPGTGKT L KA+A
Sbjct: 188 VLMVGPPGTGKTLLAKAIA 206
>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 = 33.2 bits (76), Expect = 0.012
Identities = 23/70 (32%), Positives = 30/70 (42%), Gaps = 21/70 (30%)
Query: 7 KVKSNIISW---NRVVLLHGPPGTGKTSLCKAVAQKLSIRLQTPQAIFFKKYPNVLI--- 60
+V S + + V L GP GTGKT+L VA+K P +LI
Sbjct: 9 RVTSRALRYLKSGYPVHLRGPAGTGKTTLAMHVARKR-------------DRPVMLINGD 55
Query: 61 --FTTSNLTG 68
TTS+L G
Sbjct: 56 AELTTSDLVG 65
>gnl|CDD|224027 COG1102, Cmk, Cytidylate kinase [Nucleotide transport and
metabolism].
Length = 179
Score = 32.7 bits (75), Expect = 0.014
Identities = 12/35 (34%), Positives = 23/35 (65%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQKLSIRLQTPQAIF 51
V+ + G PG+GKT++ + +A+ L ++L + IF
Sbjct: 1 MVITISGLPGSGKTTVARELAEHLGLKLVSAGTIF 35
>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 = 33.0 bits (76), Expect = 0.015
Identities = 13/26 (50%), Positives = 19/26 (73%), Gaps = 1/26 (3%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQKLSI 42
R+VLL GPPG+GK + K +A+K +
Sbjct: 1 RLVLL-GPPGSGKGTQAKRIAEKYGL 25
>gnl|CDD|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 = 32.6 bits (75), Expect = 0.015
Identities = 13/41 (31%), Positives = 23/41 (56%), Gaps = 3/41 (7%)
Query: 19 VLLHGPPGTGKTSLCKAVAQKLSIRLQTPQAIFFKKYPNVL 59
++L G G GKT+L +A+ ++ + QAI F N++
Sbjct: 4 IMLIGRSGCGKTTLTQAL-NGEELKYKKTQAIEF--SDNMI 41
>gnl|CDD|236093 PRK07773, PRK07773, replicative DNA helicase; Validated.
Length = 886
Score = 33.2 bits (76), Expect = 0.016
Identities = 10/33 (30%), Positives = 17/33 (51%)
Query: 19 VLLHGPPGTGKTSLCKAVAQKLSIRLQTPQAIF 51
+++ P GKT+ A+ +IR + AIF
Sbjct: 220 IIVAARPSMGKTTFGLDFARNCAIRHRLAVAIF 252
>gnl|CDD|223775 COG0703, AroK, Shikimate kinase [Amino acid transport and
metabolism].
Length = 172
Score = 32.6 bits (75), Expect = 0.016
Identities = 11/51 (21%), Positives = 24/51 (47%), Gaps = 12/51 (23%)
Query: 16 NRVVLLHGPPGTGKTSLCKAVAQKLSIRL------------QTPQAIFFKK 54
N ++L G G GK+++ +A+A+ L++ + IF ++
Sbjct: 2 NMNIVLIGFMGAGKSTIGRALAKALNLPFIDTDQEIEKRTGMSIAEIFEEE 52
>gnl|CDD|218719 pfam05729, NACHT, NACHT domain. This NTPase domain is found in
apoptosis proteins as well as those involved in MHC
transcription activation. This family is closely
related to pfam00931.
Length = 165
Score = 32.7 bits (75), Expect = 0.016
Identities = 10/24 (41%), Positives = 15/24 (62%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQKL 40
R V+L G G+GKT+L + +A
Sbjct: 1 RTVILQGEAGSGKTTLLQKIALLW 24
>gnl|CDD|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 = 32.6 bits (75), Expect = 0.018
Identities = 10/23 (43%), Positives = 16/23 (69%)
Query: 19 VLLHGPPGTGKTSLCKAVAQKLS 41
V ++G GTGKT++ K V ++L
Sbjct: 43 VFIYGKTGTGKTAVTKYVMKELE 65
>gnl|CDD|214810 smart00763, AAA_PrkA, PrkA AAA domain. This is a family of PrkA
bacterial and archaeal serine kinases approximately 630
residues long. This is the N-terminal AAA domain.
Length = 361
Score = 32.6 bits (75), Expect = 0.018
Identities = 8/20 (40%), Positives = 14/20 (70%)
Query: 17 RVVLLHGPPGTGKTSLCKAV 36
+++ L GP G GK+SL + +
Sbjct: 79 QILYLLGPVGGGKSSLVECL 98
>gnl|CDD|219538 pfam07728, AAA_5, AAA domain (dynein-related subfamily). This
Pfam entry includes some of the AAA proteins not
detected by the pfam00004 model.
Length = 135
Score = 32.3 bits (74), Expect = 0.018
Identities = 14/23 (60%), Positives = 17/23 (73%)
Query: 19 VLLHGPPGTGKTSLCKAVAQKLS 41
VLL GPPGTGK+ L + +A LS
Sbjct: 2 VLLVGPPGTGKSELAERLAAALS 24
>gnl|CDD|235422 PRK05342, clpX, ATP-dependent protease ATP-binding subunit ClpX;
Provisional.
Length = 412
Score = 32.8 bits (76), Expect = 0.019
Identities = 20/42 (47%), Positives = 22/42 (52%), Gaps = 11/42 (26%)
Query: 9 KSNIISWNRVVLLHGPPGTGKTSLCKAVAQKLSIRLQTPQAI 50
KSNI LL GP G+GKT L AQ L+ L P AI
Sbjct: 108 KSNI-------LLIGPTGSGKTLL----AQTLARILDVPFAI 138
>gnl|CDD|235898 PRK06964, PRK06964, DNA polymerase III subunit delta'; Validated.
Length = 342
Score = 32.8 bits (75), Expect = 0.020
Identities = 15/46 (32%), Positives = 21/46 (45%), Gaps = 12/46 (26%)
Query: 14 SWNRV----------VLLHGPPGTGKTSLCKAVAQKLSIRLQTPQA 49
WNR+ +LLHG G GK + +AQ + +TPQ
Sbjct: 9 DWNRLQALRARLPHALLLHGQAGIGKLDFAQHLAQ--GLLCETPQP 52
>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 = 32.2 bits (74), Expect = 0.022
Identities = 16/55 (29%), Positives = 27/55 (49%), Gaps = 9/55 (16%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQKLSIRLQT---------PQAIFFKKYPNVLIFT 62
+VL+ G PG+G ++L KA+A + + P F +KYP +I+
Sbjct: 34 EMVLVLGRPGSGCSTLLKALANRTEGNVSVEGDIHYNGIPYKEFAEKYPGEIIYV 88
>gnl|CDD|236442 PRK09270, PRK09270, nucleoside triphosphate hydrolase
domain-containing protein; Reviewed.
Length = 229
Score = 32.2 bits (74), Expect = 0.022
Identities = 9/25 (36%), Positives = 15/25 (60%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQKLS 41
+V + GPPG GK++L + + L
Sbjct: 34 TIVGIAGPPGAGKSTLAEFLEALLQ 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 = 32.1 bits (73), Expect = 0.022
Identities = 10/35 (28%), Positives = 20/35 (57%), Gaps = 2/35 (5%)
Query: 18 VVLLHGPPGTGKTSLCKAVAQKLSIRLQTPQAIFF 52
++L+ GP G+GKT+L +A I + + ++
Sbjct: 1 LILVFGPTGSGKTTLALQLALN--IATKGGKVVYV 33
>gnl|CDD|236546 PRK09518, PRK09518, bifunctional cytidylate kinase/GTPase Der;
Reviewed.
Length = 712
Score = 32.5 bits (74), Expect = 0.023
Identities = 11/23 (47%), Positives = 17/23 (73%)
Query: 18 VVLLHGPPGTGKTSLCKAVAQKL 40
+V + GP G GK+S+ +A+AQ L
Sbjct: 3 IVAIDGPAGVGKSSVSRALAQYL 25
>gnl|CDD|237745 PRK14527, PRK14527, adenylate kinase; Provisional.
Length = 191
Score = 32.1 bits (73), Expect = 0.025
Identities = 12/31 (38%), Positives = 21/31 (67%)
Query: 13 ISWNRVVLLHGPPGTGKTSLCKAVAQKLSIR 43
+ N+VV+ GPPG GK + + +AQ+L ++
Sbjct: 3 QTKNKVVIFLGPPGAGKGTQAERLAQELGLK 33
>gnl|CDD|233120 TIGR00764, lon_rel, lon-related putative ATP-dependent protease.
This model represents a set of proteins with extensive
C-terminal homology to the ATP-dependent protease La,
product of the lon gene of E. coli. The model is based
on a seed alignment containing only archaeal members,
but several bacterial proteins match the model well.
Because several species, including Thermotoga maritima
and Treponema pallidum, contain both a close homolog of
the lon protease and nearly full-length homolog of the
members of this family, we suggest there may also be a
functional division between the two families. Members
of this family from Pyrococcus horikoshii and
Pyrococcus abyssi each contain a predicted intein
[Protein fate, Degradation of proteins, peptides, and
glycopeptides].
Length = 608
Score = 32.5 bits (74), Expect = 0.026
Identities = 14/25 (56%), Positives = 17/25 (68%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQKLS 41
R VLL G PG GK+ L KA+A+ L
Sbjct: 38 RNVLLIGEPGVGKSMLAKAMAELLP 62
>gnl|CDD|238260 cd00464, SK, Shikimate kinase (SK) is the fifth enzyme in the
shikimate pathway, a seven-step biosynthetic pathway
which converts erythrose-4-phosphate to chorismic acid,
found in bacteria, fungi and plants. Chorismic acid is
a important intermediate in the synthesis of aromatic
compounds, such as aromatic amino acids, p-aminobenzoic
acid, folate and ubiquinone. Shikimate kinase catalyses
the phosphorylation of the 3-hydroxyl group of shikimic
acid using ATP.
Length = 154
Score = 31.8 bits (73), Expect = 0.026
Identities = 9/25 (36%), Positives = 16/25 (64%), Gaps = 1/25 (4%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQKLS 41
+VL+ G G GKT++ + +A+ L
Sbjct: 1 NIVLI-GMMGAGKTTVGRLLAKALG 24
>gnl|CDD|224847 COG1936, COG1936, Predicted nucleotide kinase (related to CMP and
AMP kinases) [Nucleotide transport and metabolism].
Length = 180
Score = 31.9 bits (73), Expect = 0.029
Identities = 8/19 (42%), Positives = 13/19 (68%)
Query: 19 VLLHGPPGTGKTSLCKAVA 37
+ + G PG GKT++CK +
Sbjct: 3 IAITGTPGVGKTTVCKLLR 21
>gnl|CDD|224140 COG1219, ClpX, ATP-dependent protease Clp, ATPase subunit
[Posttranslational modification, protein turnover,
chaperones].
Length = 408
Score = 32.2 bits (74), Expect = 0.029
Identities = 20/42 (47%), Positives = 22/42 (52%), Gaps = 11/42 (26%)
Query: 9 KSNIISWNRVVLLHGPPGTGKTSLCKAVAQKLSIRLQTPQAI 50
KSNI LL GP G+GKT L AQ L+ L P AI
Sbjct: 97 KSNI-------LLIGPTGSGKTLL----AQTLAKILNVPFAI 127
>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 = 32.2 bits (74), Expect = 0.029
Identities = 11/18 (61%), Positives = 13/18 (72%)
Query: 23 GPPGTGKTSLCKAVAQKL 40
GP G GKT L KA+A+ L
Sbjct: 602 GPTGVGKTELAKALAEFL 619
>gnl|CDD|129690 TIGR00602, rad24, checkpoint protein rad24. All proteins in this
family for which functions are known are involved in DNA
damage tolerance (likely cell cycle checkpoints).This
family is based on the phylogenomic analysis of JA Eisen
(1999, Ph.D. Thesis, Stanford University) [DNA
metabolism, DNA replication, recombination, and repair].
Length = 637
Score = 32.2 bits (73), Expect = 0.029
Identities = 14/54 (25%), Positives = 26/54 (48%), Gaps = 4/54 (7%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQKLSIRLQT-PQAIFFKKYPN---VLIFTTSNL 66
R++L+ GP G GK++ K ++++L I++Q N V + S
Sbjct: 111 RILLITGPSGCGKSTTIKILSKELGIQVQEWSNPTLPDFQKNDHKVTLSLESCF 164
>gnl|CDD|234011 TIGR02782, TrbB_P, P-type conjugative transfer ATPase TrbB. The
TrbB protein is found in the trb locus of Agrobacterium
Ti plasmids where it is involved in the type IV
secretion system for plasmid conjugative transfer. TrbB
is a homolog of the vir system VirB11 ATPase , and the
Flp pilus sytem ATPase TadA [Cellular processes,
Conjugation].
Length = 299
Score = 32.0 bits (73), Expect = 0.030
Identities = 18/72 (25%), Positives = 36/72 (50%), Gaps = 9/72 (12%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQKLSIRLQTPQAIFFK-------KYPNVLIFTTSNLTGA 69
+ +L+ G G+GKT+L A+ +++ T + + + PNV+ TS+ A
Sbjct: 133 KNILVVGGTGSGKTTLANALLAEIAKNDPTDRVVIIEDTRELQCAAPNVVQLRTSD--DA 190
Query: 70 IDLAFLDRADIK 81
I + L +A ++
Sbjct: 191 ISMTRLLKATLR 202
>gnl|CDD|216202 pfam00931, NB-ARC, NB-ARC domain.
Length = 285
Score = 31.9 bits (73), Expect = 0.031
Identities = 10/26 (38%), Positives = 14/26 (53%)
Query: 18 VVLLHGPPGTGKTSLCKAVAQKLSIR 43
VV + G G GKT+L K + S+
Sbjct: 21 VVGIVGMGGVGKTTLAKQIYNDDSVG 46
>gnl|CDD|221955 pfam13173, AAA_14, AAA domain. This family of domains contain a
P-loop motif that is characteristic of the AAA
superfamily.
Length = 127
Score = 31.4 bits (72), Expect = 0.031
Identities = 8/25 (32%), Positives = 16/25 (64%)
Query: 16 NRVVLLHGPPGTGKTSLCKAVAQKL 40
N+++++ GP GKT+L ++L
Sbjct: 2 NKIIVITGPRQVGKTTLLLQFLKEL 26
>gnl|CDD|224768 COG1855, COG1855, ATPase (PilT family) [General function prediction
only].
Length = 604
Score = 32.0 bits (73), Expect = 0.033
Identities = 10/32 (31%), Positives = 19/32 (59%)
Query: 7 KVKSNIISWNRVVLLHGPPGTGKTSLCKAVAQ 38
K+K + +L+ G PG GK++ +A+A+
Sbjct: 254 KLKERLEERAEGILIAGAPGAGKSTFAQALAE 285
>gnl|CDD|223543 COG0467, RAD55, RecA-superfamily ATPases implicated in signal
transduction [Signal transduction mechanisms].
Length = 260
Score = 32.1 bits (73), Expect = 0.035
Identities = 11/22 (50%), Positives = 12/22 (54%)
Query: 16 NRVVLLHGPPGTGKTSLCKAVA 37
VVL+ GPPGTGKT
Sbjct: 23 GSVVLITGPPGTGKTIFALQFL 44
>gnl|CDD|183452 PRK12337, PRK12337, 2-phosphoglycerate kinase; Provisional.
Length = 475
Score = 32.1 bits (73), Expect = 0.036
Identities = 11/25 (44%), Positives = 15/25 (60%)
Query: 18 VVLLHGPPGTGKTSLCKAVAQKLSI 42
VL+ G G GK+ L A+A +L I
Sbjct: 257 HVLIGGVSGVGKSVLASALAYRLGI 281
>gnl|CDD|237475 PRK13695, PRK13695, putative NTPase; Provisional.
Length = 174
Score = 31.4 bits (72), Expect = 0.043
Identities = 10/22 (45%), Positives = 15/22 (68%)
Query: 19 VLLHGPPGTGKTSLCKAVAQKL 40
+ + GPPG GKT+L +A+ L
Sbjct: 3 IGITGPPGVGKTTLVLKIAELL 24
>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 = 31.5 bits (72), Expect = 0.048
Identities = 11/22 (50%), Positives = 17/22 (77%)
Query: 16 NRVVLLHGPPGTGKTSLCKAVA 37
R ++L PPG+GK++LC A+A
Sbjct: 108 GRALILPAPPGSGKSTLCAALA 129
>gnl|CDD|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 = 31.7 bits (72), Expect = 0.049
Identities = 18/52 (34%), Positives = 26/52 (50%), Gaps = 13/52 (25%)
Query: 20 LLHGPPGTGKTSLCKAVAQKLSIRLQTPQAIFFKKYPNVLIFTTSNLTGAID 71
L+HGPPGTGKT + ++L K+ VL+ SN+ A+D
Sbjct: 177 LIHGPPGTGKTRTLVELIRQL-----------VKRGLRVLVTAPSNI--AVD 215
>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 = 31.0 bits (71), Expect = 0.051
Identities = 12/25 (48%), Positives = 14/25 (56%)
Query: 18 VVLLHGPPGTGKTSLCKAVAQKLSI 42
L GP G GKT L KA+A+ L
Sbjct: 5 SFLFLGPTGVGKTELAKALAELLFG 29
>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 = 31.7 bits (72), Expect = 0.052
Identities = 20/42 (47%), Positives = 22/42 (52%), Gaps = 11/42 (26%)
Query: 9 KSNIISWNRVVLLHGPPGTGKTSLCKAVAQKLSIRLQTPQAI 50
KSNI LL GP G+GKT L AQ L+ L P AI
Sbjct: 116 KSNI-------LLIGPTGSGKTLL----AQTLARILNVPFAI 146
>gnl|CDD|105560 PRK12339, PRK12339, 2-phosphoglycerate kinase; Provisional.
Length = 197
Score = 31.3 bits (71), Expect = 0.058
Identities = 9/28 (32%), Positives = 16/28 (57%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQKLSIRL 44
+ + G PG GKTS+ +A+ +I +
Sbjct: 4 TIHFIGGIPGVGKTSISGYIARHRAIDI 31
>gnl|CDD|182778 PRK10851, PRK10851, sulfate/thiosulfate transporter subunit;
Provisional.
Length = 353
Score = 31.2 bits (71), Expect = 0.060
Identities = 14/38 (36%), Positives = 24/38 (63%), Gaps = 3/38 (7%)
Query: 3 FSHSKVKSNI---ISWNRVVLLHGPPGTGKTSLCKAVA 37
F ++V ++I I ++V L GP G+GKT+L + +A
Sbjct: 12 FGRTQVLNDISLDIPSGQMVALLGPSGSGKTTLLRIIA 49
>gnl|CDD|179157 PRK00889, PRK00889, adenylylsulfate kinase; Provisional.
Length = 175
Score = 31.1 bits (71), Expect = 0.061
Identities = 10/27 (37%), Positives = 15/27 (55%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQKLSIR 43
V G G GKT++ +A+A+KL
Sbjct: 5 VTVWFTGLSGAGKTTIARALAEKLREA 31
>gnl|CDD|129128 TIGR00017, cmk, cytidylate kinase. This family consists of
cytidylate kinase, which catalyzes the phosphorylation
of cytidine 5-monophosphate (dCMP) to cytidine 5
-diphosphate (dCDP) in the presence of ATP or GTP. UMP
and dCMP can also act as acceptors [Purines,
pyrimidines, nucleosides, and nucleotides, Nucleotide
and nucleoside interconversions].
Length = 217
Score = 31.2 bits (71), Expect = 0.063
Identities = 11/19 (57%), Positives = 15/19 (78%)
Query: 23 GPPGTGKTSLCKAVAQKLS 41
GP G GK+++ KAVA+KL
Sbjct: 9 GPSGAGKSTVAKAVAEKLG 27
>gnl|CDD|224533 COG1618, COG1618, Predicted nucleotide kinase [Nucleotide
transport and metabolism].
Length = 179
Score = 30.7 bits (70), Expect = 0.066
Identities = 10/23 (43%), Positives = 15/23 (65%)
Query: 19 VLLHGPPGTGKTSLCKAVAQKLS 41
+ + G PG GKT+L +A+KL
Sbjct: 8 IFITGRPGVGKTTLVLKIAEKLR 30
>gnl|CDD|180750 PRK06921, PRK06921, hypothetical protein; Provisional.
Length = 266
Score = 30.9 bits (70), Expect = 0.073
Identities = 15/36 (41%), Positives = 19/36 (52%), Gaps = 1/36 (2%)
Query: 16 NRVVLLHGPPGTGKTSLCKAVAQKLSIRLQTPQAIF 51
N + LL G PG+GKT L A A +L + P F
Sbjct: 118 NSIALL-GQPGSGKTHLLTAAANELMRKKGVPVLYF 152
>gnl|CDD|237090 PRK12402, PRK12402, replication factor C small subunit 2;
Reviewed.
Length = 337
Score = 31.1 bits (71), Expect = 0.074
Identities = 11/21 (52%), Positives = 18/21 (85%)
Query: 20 LLHGPPGTGKTSLCKAVAQKL 40
L+ GPPG+GKT+ +A+A++L
Sbjct: 40 LVQGPPGSGKTAAVRALAREL 60
>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 = 0.076
Identities = 11/19 (57%), Positives = 16/19 (84%)
Query: 19 VLLHGPPGTGKTSLCKAVA 37
+L+ GP GTGK+SL +A+A
Sbjct: 30 LLITGPSGTGKSSLFRALA 48
>gnl|CDD|226573 COG4088, COG4088, Predicted nucleotide kinase [Nucleotide
transport and metabolism].
Length = 261
Score = 31.0 bits (70), Expect = 0.083
Identities = 10/25 (40%), Positives = 18/25 (72%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQKLS 41
+++L G PG+GKT+ K +A++L
Sbjct: 2 PLIILTGYPGSGKTTFAKELAKELR 26
>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 = 30.9 bits (70), Expect = 0.085
Identities = 11/24 (45%), Positives = 18/24 (75%)
Query: 18 VVLLHGPPGTGKTSLCKAVAQKLS 41
+++L G PG GK++ K +A+KLS
Sbjct: 1 LIILTGLPGVGKSTFSKELAKKLS 24
>gnl|CDD|234751 PRK00411, cdc6, cell division control protein 6; Reviewed.
Length = 394
Score = 31.0 bits (71), Expect = 0.086
Identities = 13/23 (56%), Positives = 18/23 (78%)
Query: 19 VLLHGPPGTGKTSLCKAVAQKLS 41
VL++GPPGTGKT+ K V ++L
Sbjct: 58 VLIYGPPGTGKTTTVKKVFEELE 80
>gnl|CDD|182791 PRK10865, PRK10865, protein disaggregation chaperone; Provisional.
Length = 857
Score = 31.0 bits (70), Expect = 0.088
Identities = 12/18 (66%), Positives = 13/18 (72%)
Query: 20 LLHGPPGTGKTSLCKAVA 37
L GP G GKT LCKA+A
Sbjct: 602 LFLGPTGVGKTELCKALA 619
Score = 26.0 bits (57), Expect = 4.3
Identities = 11/25 (44%), Positives = 18/25 (72%), Gaps = 1/25 (4%)
Query: 16 NRVVLLHGPPGTGKTSLCKAVAQKL 40
N VL+ G PG GKT++ + +AQ++
Sbjct: 200 NNPVLI-GEPGVGKTAIVEGLAQRI 223
>gnl|CDD|233959 TIGR02639, ClpA, ATP-dependent Clp protease ATP-binding subunit
clpA. [Protein fate, Degradation of proteins, peptides,
and glycopeptides].
Length = 730
Score = 30.8 bits (70), Expect = 0.097
Identities = 12/25 (48%), Positives = 16/25 (64%)
Query: 20 LLHGPPGTGKTSLCKAVAQKLSIRL 44
L GP G GKT L K +A++L + L
Sbjct: 487 LFVGPTGVGKTELAKQLAEELGVHL 511
>gnl|CDD|227596 COG5271, MDN1, AAA ATPase containing von Willebrand factor type A
(vWA) domain [General function prediction only].
Length = 4600
Score = 30.7 bits (69), Expect = 0.10
Identities = 14/28 (50%), Positives = 19/28 (67%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQKLSIRL 44
+ +LL G PG GKTSL A+A+K +L
Sbjct: 1544 KPILLEGSPGVGKTSLITALARKTGKKL 1571
Score = 27.3 bits (60), Expect = 1.6
Identities = 8/21 (38%), Positives = 15/21 (71%)
Query: 19 VLLHGPPGTGKTSLCKAVAQK 39
+L+ GP +GKTS+ +A++
Sbjct: 891 LLIQGPTSSGKTSMILYLARE 911
Score = 26.9 bits (59), Expect = 2.4
Identities = 14/34 (41%), Positives = 19/34 (55%)
Query: 13 ISWNRVVLLHGPPGTGKTSLCKAVAQKLSIRLQT 46
I N LL G GTGKT++ + +A KL +L
Sbjct: 461 IQNNEPTLLVGETGTGKTTMIQYLALKLHFKLTV 494
>gnl|CDD|235281 PRK04328, PRK04328, hypothetical protein; Provisional.
Length = 249
Score = 30.4 bits (69), Expect = 0.10
Identities = 10/17 (58%), Positives = 12/17 (70%)
Query: 18 VVLLHGPPGTGKTSLCK 34
VVLL G PGTGK+ +
Sbjct: 25 VVLLSGGPGTGKSIFSQ 41
>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 = 30.3 bits (69), Expect = 0.11
Identities = 10/24 (41%), Positives = 16/24 (66%)
Query: 18 VVLLHGPPGTGKTSLCKAVAQKLS 41
+ LL G PGTGK++L +A ++
Sbjct: 35 LTLLAGAPGTGKSTLALDLAAAVA 58
>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 = 30.5 bits (69), Expect = 0.11
Identities = 10/29 (34%), Positives = 17/29 (58%)
Query: 19 VLLHGPPGTGKTSLCKAVAQKLSIRLQTP 47
++L+GPPG GKT+ + ++ TP
Sbjct: 178 IILYGPPGVGKTTAARLALEEAKKLKHTP 206
>gnl|CDD|182730 PRK10787, PRK10787, DNA-binding ATP-dependent protease La;
Provisional.
Length = 784
Score = 30.7 bits (69), Expect = 0.11
Identities = 14/33 (42%), Positives = 21/33 (63%), Gaps = 6/33 (18%)
Query: 6 SKVKSNIISWNRVVLLHGPPGTGKTSLCKAVAQ 38
+K+K I+ L GPPG GKTSL +++A+
Sbjct: 345 NKIKGPILC------LVGPPGVGKTSLGQSIAK 371
>gnl|CDD|129254 TIGR00150, T6A_YjeE, tRNA threonylcarbamoyl adenosine
modification protein YjeE. This protein family belongs
to a four-gene system responsible for the
threonylcarbamoyl adenosine (t6A) tRNA modification.
Members of this family have a conserved
nucleotide-binding motif GXXGXGKT and a
nucleotide-binding fold. Member protein YjeE of
Haemophilus influenzae (HI0065) was shown to have
(weak) ATPase activity [Protein synthesis, tRNA and
rRNA base modification].
Length = 133
Score = 30.1 bits (68), Expect = 0.11
Identities = 13/28 (46%), Positives = 17/28 (60%)
Query: 18 VVLLHGPPGTGKTSLCKAVAQKLSIRLQ 45
VVLL G G GKT+L + + Q L I+
Sbjct: 24 VVLLKGDLGAGKTTLVQGLLQGLGIQGN 51
>gnl|CDD|107157 PHA02244, PHA02244, ATPase-like protein.
Length = 383
Score = 30.5 bits (68), Expect = 0.12
Identities = 16/60 (26%), Positives = 24/60 (40%), Gaps = 10/60 (16%)
Query: 12 IISWNRVVLLHGPPGTGKTSLCKAVAQKLSIRLQTPQAIFFKKYPNVLIFTTSNLTGAID 71
I++ N V L G G+GK + + +A+ L + Y I L G ID
Sbjct: 115 IVNANIPVFLKGGAGSGKNHIAEQIAEALDLDF----------YFMNAIMDEFELKGFID 164
>gnl|CDD|105491 PRK12269, PRK12269, bifunctional cytidylate kinase/ribosomal
protein S1; Provisional.
Length = 863
Score = 30.5 bits (68), Expect = 0.12
Identities = 10/23 (43%), Positives = 18/23 (78%)
Query: 18 VVLLHGPPGTGKTSLCKAVAQKL 40
++ L GP G+GK+S+C+ +A +L
Sbjct: 36 IIALDGPAGSGKSSVCRLLASRL 58
>gnl|CDD|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 = 30.0 bits (68), Expect = 0.13
Identities = 9/16 (56%), Positives = 10/16 (62%)
Query: 18 VVLLHGPPGTGKTSLC 33
LL G PGTGKT+
Sbjct: 1 STLLSGGPGTGKTTFA 16
>gnl|CDD|217326 pfam03029, ATP_bind_1, Conserved hypothetical ATP binding
protein. Members of this family are found in a range
of archaea and eukaryotes and have hypothesised ATP
binding activity.
Length = 235
Score = 30.4 bits (69), Expect = 0.13
Identities = 8/28 (28%), Positives = 17/28 (60%)
Query: 23 GPPGTGKTSLCKAVAQKLSIRLQTPQAI 50
GP G+GKT+ A+++ L + ++ +
Sbjct: 3 GPAGSGKTTFVGALSEILPLLGRSVYVV 30
>gnl|CDD|226646 COG4178, COG4178, ABC-type uncharacterized transport system,
permease and ATPase components [General function
prediction only].
Length = 604
Score = 30.4 bits (69), Expect = 0.13
Identities = 10/19 (52%), Positives = 14/19 (73%)
Query: 19 VLLHGPPGTGKTSLCKAVA 37
+L+ G G GKTSL +A+A
Sbjct: 422 LLITGESGAGKTSLLRALA 440
>gnl|CDD|224025 COG1100, COG1100, GTPase SAR1 and related small G proteins
[General function prediction only].
Length = 219
Score = 30.3 bits (68), Expect = 0.13
Identities = 13/65 (20%), Positives = 20/65 (30%), Gaps = 5/65 (7%)
Query: 19 VLLHGPPGTGKTSLCKAVAQKLSIRLQTPQAIFFKKYPNVLIFTTSNLTGAIDLAFLDRA 78
+++ G G GKT+L + P T I L D A
Sbjct: 8 IVVLGDGGVGKTTLLNRLVGDEFPEGYPPTIG-----NLDPAKTIEPYRRNIKLQLWDTA 62
Query: 79 DIKQY 83
++Y
Sbjct: 63 GQEEY 67
>gnl|CDD|225327 COG2607, COG2607, Predicted ATPase (AAA+ superfamily) [General
function prediction only].
Length = 287
Score = 30.0 bits (68), Expect = 0.14
Identities = 12/18 (66%), Positives = 14/18 (77%)
Query: 19 VLLHGPPGTGKTSLCKAV 36
VLL G GTGK+SL KA+
Sbjct: 88 VLLWGARGTGKSSLVKAL 105
>gnl|CDD|236982 PRK11784, PRK11784, tRNA 2-selenouridine synthase; Provisional.
Length = 345
Score = 30.2 bits (69), Expect = 0.15
Identities = 10/23 (43%), Positives = 15/23 (65%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQK 39
+V+L G G+GKT L +A+A
Sbjct: 142 PLVVLGGNTGSGKTELLQALANA 164
>gnl|CDD|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 = 29.9 bits (68), Expect = 0.15
Identities = 10/21 (47%), Positives = 12/21 (57%)
Query: 20 LLHGPPGTGKTSLCKAVAQKL 40
L GP G GK L A+A+ L
Sbjct: 18 LFAGPEGVGKELLALALAKAL 38
>gnl|CDD|181235 PRK08118, PRK08118, topology modulation protein; Reviewed.
Length = 167
Score = 30.0 bits (68), Expect = 0.15
Identities = 14/42 (33%), Positives = 28/42 (66%), Gaps = 3/42 (7%)
Query: 16 NRVVLLHGPPGTGKTSLCKAVAQKLSIRLQTPQAIFFKKYPN 57
+++L+ G G+GK++L + + +KL+I + A+F+K PN
Sbjct: 2 KKIILI-GSGGSGKSTLARQLGEKLNIPVHHLDALFWK--PN 40
>gnl|CDD|214361 CHL00095, clpC, Clp protease ATP binding subunit.
Length = 821
Score = 30.0 bits (68), Expect = 0.16
Identities = 13/26 (50%), Positives = 15/26 (57%), Gaps = 4/26 (15%)
Query: 12 IISWNRVVLLHGPPGTGKTSLCKAVA 37
I S+ L GP G GKT L KA+A
Sbjct: 539 IASF----LFSGPTGVGKTELTKALA 560
Score = 25.8 bits (57), Expect = 5.4
Identities = 16/60 (26%), Positives = 24/60 (40%), Gaps = 11/60 (18%)
Query: 7 KVKSNIISWNRVVLLHGPPGTGKTSLCKAVAQKLSIRLQTPQAIFFKKYPNVLIFTTSNL 66
+ K+N I L G PG GKT A+A+ L+ R+ + V+ L
Sbjct: 198 RTKNNPI-------LIGEPGVGKT----AIAEGLAQRIVNRDVPDILEDKLVITLDIGLL 246
>gnl|CDD|222290 pfam13654, AAA_32, AAA domain. This family includes a wide
variety of AAA domains including some that have lost
essential nucleotide binding residues in the P-loop.
Length = 509
Score = 30.1 bits (69), Expect = 0.16
Identities = 9/25 (36%), Positives = 16/25 (64%)
Query: 23 GPPGTGKTSLCKAVAQKLSIRLQTP 47
G PGTG+T+L + ++ + + TP
Sbjct: 37 GEPGTGRTTLVRRYLEERAKKEPTP 61
>gnl|CDD|224930 COG2019, AdkA, Archaeal adenylate kinase [Nucleotide transport
and metabolism].
Length = 189
Score = 30.1 bits (68), Expect = 0.16
Identities = 10/24 (41%), Positives = 17/24 (70%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQKL 40
+VV++ G PG GKT++ K ++L
Sbjct: 5 KVVVITGVPGVGKTTVLKIALKEL 28
>gnl|CDD|178596 PLN03025, PLN03025, replication factor C subunit; Provisional.
Length = 319
Score = 30.1 bits (68), Expect = 0.16
Identities = 12/22 (54%), Positives = 17/22 (77%)
Query: 19 VLLHGPPGTGKTSLCKAVAQKL 40
++L GPPGTGKT+ A+A +L
Sbjct: 37 LILSGPPGTGKTTSILALAHEL 58
>gnl|CDD|224345 COG1428, COG1428, Deoxynucleoside kinases [Nucleotide transport
and metabolism].
Length = 216
Score = 30.0 bits (68), Expect = 0.17
Identities = 9/25 (36%), Positives = 17/25 (68%)
Query: 16 NRVVLLHGPPGTGKTSLCKAVAQKL 40
V+++ G G GK++L +A+A+ L
Sbjct: 4 AMVIVIEGMIGAGKSTLAQALAEHL 28
>gnl|CDD|219014 pfam06414, Zeta_toxin, Zeta toxin. This family consists of
several bacterial zeta toxin proteins. Zeta toxin is
thought to be part of a postregulational killing system
in bacteria. It relies on antitoxin/toxin systems that
secure stable inheritance of low and medium copy number
plasmids during cell division and kill cells that have
lost the plasmid.
Length = 191
Score = 29.9 bits (68), Expect = 0.17
Identities = 12/24 (50%), Positives = 16/24 (66%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQKL 40
VLL G PG GKT L +A+ ++L
Sbjct: 13 VAVLLGGQPGAGKTELARALLEEL 36
>gnl|CDD|213212 cd03245, ABCC_bacteriocin_exporters, ATP-binding cassette domain
of bacteriocin exporters, subfamily C. Many
non-lantibiotic bacteriocins of lactic acid bacteria
are produced as precursors which have N-terminal leader
peptides that share similarities in amino acid sequence
and contain a conserved processing site of two glycine
residues in positions -1 and -2. A dedicated
ATP-binding cassette (ABC) transporter is responsible
for the proteolytic cleavage of the leader peptides and
subsequent translocation of the bacteriocins across the
cytoplasmic membrane.
Length = 220
Score = 29.9 bits (68), Expect = 0.17
Identities = 19/70 (27%), Positives = 33/70 (47%), Gaps = 19/70 (27%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQKLSIRLQTPQAIFFKKYPNVLIFTTSNLTGAIDLAFLD 76
+V ++ G G+GK++L KL L P + +VL+ D+ LD
Sbjct: 32 KVAII-GRVGSGKSTL-----LKLLAGLYKPTS------GSVLL-------DGTDIRQLD 72
Query: 77 RADIKQYIGF 86
AD+++ IG+
Sbjct: 73 PADLRRNIGY 82
>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 = 29.7 bits (68), Expect = 0.18
Identities = 11/25 (44%), Positives = 14/25 (56%), Gaps = 2/25 (8%)
Query: 16 NRVVLLHGPPGTGKT--SLCKAVAQ 38
N +V GP GTGKT ++ AV
Sbjct: 19 NDIVFGIGPAGTGKTYLAVAAAVDA 43
>gnl|CDD|223455 COG0378, HypB, Ni2+-binding GTPase involved in regulation of
expression and maturation of urease and hydrogenase
[Posttranslational modification, protein turnover,
chaperones / Transcription].
Length = 202
Score = 29.9 bits (68), Expect = 0.19
Identities = 10/30 (33%), Positives = 17/30 (56%), Gaps = 4/30 (13%)
Query: 17 RVVLLHGPPGTGKTSL----CKAVAQKLSI 42
+ + GPPG+GKT+L +A+ + I
Sbjct: 14 LRIGVGGPPGSGKTALIEKTLRALKDEYKI 43
>gnl|CDD|215451 PLN02840, PLN02840, tRNA dimethylallyltransferase.
Length = 421
Score = 29.8 bits (67), Expect = 0.19
Identities = 9/26 (34%), Positives = 18/26 (69%)
Query: 16 NRVVLLHGPPGTGKTSLCKAVAQKLS 41
+V+++ GP G GK+ L +A++L+
Sbjct: 21 EKVIVISGPTGAGKSRLALELAKRLN 46
>gnl|CDD|219158 pfam06745, KaiC, KaiC. This family represents a conserved region
within bacterial and archaeal proteins, most of which
are hypothetical. More than one copy is sometimes found
in each protein. This family includes KaiC, which is
one of the Kai proteins among which direct
protein-protein association may be a critical process
in the generation of circadian rhythms in
cyanobacteria.
Length = 231
Score = 29.5 bits (67), Expect = 0.20
Identities = 11/19 (57%), Positives = 12/19 (63%)
Query: 16 NRVVLLHGPPGTGKTSLCK 34
RVVL+ G PGTGKT
Sbjct: 19 GRVVLITGGPGTGKTIFGL 37
>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 = 29.6 bits (67), Expect = 0.20
Identities = 10/20 (50%), Positives = 14/20 (70%)
Query: 19 VLLHGPPGTGKTSLCKAVAQ 38
V +GP TGKT+L +A+A
Sbjct: 116 VWFYGPASTGKTNLAQAIAH 135
>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 = 29.7 bits (67), Expect = 0.22
Identities = 10/22 (45%), Positives = 15/22 (68%), Gaps = 1/22 (4%)
Query: 17 RVVL-LHGPPGTGKTSLCKAVA 37
V ++GPPGTGKT++ +A
Sbjct: 19 GTVTQVYGPPGTGKTNIAIQLA 40
>gnl|CDD|183044 PRK11231, fecE, iron-dicitrate transporter ATP-binding subunit;
Provisional.
Length = 255
Score = 29.6 bits (67), Expect = 0.22
Identities = 14/34 (41%), Positives = 19/34 (55%), Gaps = 5/34 (14%)
Query: 16 NRVVLLHGPPGTGKTSLCKAVAQKLSIRLQTPQA 49
++ L GP G GK++L K A RL TPQ+
Sbjct: 28 GKITALIGPNGCGKSTLLKCFA-----RLLTPQS 56
>gnl|CDD|144608 pfam01078, Mg_chelatase, Magnesium chelatase, subunit ChlI.
Magnesium-chelatase is a three-component enzyme that
catalyzes the insertion of Mg2+ into protoporphyrin IX.
This is the first unique step in the synthesis of
(bacterio)chlorophyll. Due to this, it is thought that
Mg-chelatase has an important role in channelling
inter- mediates into the (bacterio)chlorophyll branch
in response to conditions suitable for photosynthetic
growth. ChlI and BchD have molecular weight between
38-42 kDa.
Length = 207
Score = 29.4 bits (67), Expect = 0.22
Identities = 10/17 (58%), Positives = 13/17 (76%)
Query: 19 VLLHGPPGTGKTSLCKA 35
+L+ GPPG+GKT L K
Sbjct: 25 LLMIGPPGSGKTMLAKR 41
>gnl|CDD|223603 COG0529, CysC, Adenylylsulfate kinase and related kinases
[Inorganic ion transport and metabolism].
Length = 197
Score = 29.6 bits (67), Expect = 0.23
Identities = 8/24 (33%), Positives = 15/24 (62%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQKL 40
V+ G G+GK+++ A+ +KL
Sbjct: 24 AVIWFTGLSGSGKSTIANALEEKL 47
>gnl|CDD|223616 COG0542, clpA, ATP-binding subunits of Clp protease and DnaK/DnaJ
chaperones [Posttranslational modification, protein
turnover, chaperones].
Length = 786
Score = 29.6 bits (67), Expect = 0.23
Identities = 12/23 (52%), Positives = 14/23 (60%)
Query: 18 VVLLHGPPGTGKTSLCKAVAQKL 40
L GP G GKT L KA+A+ L
Sbjct: 523 SFLFLGPTGVGKTELAKALAEAL 545
>gnl|CDD|214890 smart00893, ETF, Electron transfer flavoprotein domain. Electron
transfer flavoproteins (ETFs) serve as specific electron
acceptors for primary dehydrogenases, transferring the
electrons to terminal respiratory systems. They can be
functionally classified into constitutive,
"housekeeping" ETFs, mainly involved in the oxidation of
fatty acids (Group I), and ETFs produced by some
prokaryotes under specific growth conditions, receiving
electrons only from the oxidation of specific substrates
(Group II). ETFs are heterodimeric proteins composed of
an alpha and beta subunit, and contain an FAD cofactor
and AMP. ETF consists of three domains: domains I and II
are formed by the N- and C-terminal portions of the
alpha subunit, respectively, while domain III is formed
by the beta subunit. Domains I and III share an almost
identical alpha-beta-alpha sandwich fold, while domain
II forms an alpha-beta-alpha sandwich similar to that of
bacterial flavodoxins. FAD is bound in a cleft between
domains II and III, while domain III binds the AMP
molecule. Interactions between domains I and III
stabilise the protein, forming a shallow bowl where
domain II resides. This entry represents the N-terminal
domain of both the alpha and beta subunits from Group I
and Group II ETFs.
Length = 185
Score = 29.5 bits (67), Expect = 0.23
Identities = 9/23 (39%), Positives = 12/23 (52%)
Query: 27 TGKTSLCKAVAQKLSIRLQTPQA 49
G TS K +A +L+ L PQ
Sbjct: 89 AGATSDGKQLAPRLAALLGVPQI 111
>gnl|CDD|234132 TIGR03167, tRNA_sel_U_synt, tRNA 2-selenouridine synthase. The
Escherichia coli YbbB protein was shown to encode a
selenophosphate-dependent tRNA 2-selenouridine synthase,
essential for modification of some tRNAs to replace a
sulfur atom with selenium. This enzyme works with SelD,
the selenium donor protein, which also acts in
selenocysteine incorporation. Although the members of
this protein family show a fairly deep split, sequences
from both sides of the split are supported by
co-occurence with, and often proximity to, the selD gene
[Protein synthesis, tRNA and rRNA base modification].
Length = 311
Score = 29.5 bits (67), Expect = 0.24
Identities = 9/23 (39%), Positives = 14/23 (60%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQK 39
+++L G G+GKT L A+A
Sbjct: 128 PLIVLGGMTGSGKTELLHALANA 150
>gnl|CDD|163589 TIGR03877, thermo_KaiC_1, KaiC domain protein, Ph0284 family.
Members of this family contain a single copy of the
KaiC domain (pfam06745) that occurs in two copies of
the circadian clock protein kinase KaiC itself. Members
occur primarily in thermophilic archaea and in
Thermotoga.
Length = 237
Score = 29.3 bits (66), Expect = 0.24
Identities = 10/17 (58%), Positives = 12/17 (70%)
Query: 18 VVLLHGPPGTGKTSLCK 34
VVLL G PGTGK+ +
Sbjct: 23 VVLLSGGPGTGKSIFSQ 39
>gnl|CDD|224160 COG1239, ChlI, Mg-chelatase subunit ChlI [Coenzyme metabolism].
Length = 423
Score = 29.7 bits (67), Expect = 0.24
Identities = 8/19 (42%), Positives = 13/19 (68%)
Query: 19 VLLHGPPGTGKTSLCKAVA 37
L+ G GT K++L +A+A
Sbjct: 41 ALIAGEKGTAKSTLARALA 59
>gnl|CDD|110677 pfam01695, IstB_IS21, IstB-like ATP binding protein. This
protein contains an ATP/GTP binding P-loop motif. It is
found associated with IS21 family insertion sequences.
The function of this protein is unknown, but it may
perform a transposase function.
Length = 178
Score = 29.2 bits (66), Expect = 0.24
Identities = 11/21 (52%), Positives = 14/21 (66%)
Query: 19 VLLHGPPGTGKTSLCKAVAQK 39
+LL GPPG GKT L A+ +
Sbjct: 50 LLLLGPPGVGKTHLACALGHQ 70
>gnl|CDD|223272 COG0194, Gmk, Guanylate kinase [Nucleotide transport and
metabolism].
Length = 191
Score = 29.4 bits (67), Expect = 0.25
Identities = 10/28 (35%), Positives = 18/28 (64%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQKLSIRL 44
+++L GP G GK++L KA+ + +R
Sbjct: 5 LLIVLSGPSGVGKSTLVKALLEDDKLRF 32
>gnl|CDD|234711 PRK00279, adk, adenylate kinase; Reviewed.
Length = 215
Score = 29.3 bits (67), Expect = 0.26
Identities = 13/26 (50%), Positives = 18/26 (69%), Gaps = 1/26 (3%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQKLSI 42
R++LL GPPG GK + K +A+K I
Sbjct: 2 RLILL-GPPGAGKGTQAKFIAEKYGI 26
>gnl|CDD|184311 PRK13764, PRK13764, ATPase; Provisional.
Length = 602
Score = 29.4 bits (67), Expect = 0.27
Identities = 10/33 (30%), Positives = 18/33 (54%)
Query: 5 HSKVKSNIISWNRVVLLHGPPGTGKTSLCKAVA 37
K+K + +L+ G PG GK++ +A+A
Sbjct: 246 SEKLKERLEERAEGILIAGAPGAGKSTFAQALA 278
>gnl|CDD|215633 PLN03210, PLN03210, Resistant to P. syringae 6; Provisional.
Length = 1153
Score = 29.5 bits (66), Expect = 0.28
Identities = 24/79 (30%), Positives = 38/79 (48%), Gaps = 14/79 (17%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQKLSIRLQTPQAI---FFKKYPNVLIFTTSN-------- 65
R+V + G G GKT++ +A+ +LS + Q+ I F K I++++N
Sbjct: 208 RMVGIWGSSGIGKTTIARALFSRLSRQFQSSVFIDRAFISKSME--IYSSANPDDYNMKL 265
Query: 66 -LTGAIDLAFLDRADIKQY 83
L A LD+ DIK Y
Sbjct: 266 HLQRAFLSEILDKKDIKIY 284
>gnl|CDD|213788 TIGR03263, guanyl_kin, guanylate kinase. Members of this family
are the enzyme guanylate kinase, also called GMP
kinase. This enzyme transfers a phosphate from ATP to
GMP, yielding ADP and GDP [Purines, pyrimidines,
nucleosides, and nucleotides, Nucleotide and nucleoside
interconversions].
Length = 179
Score = 29.0 bits (66), Expect = 0.29
Identities = 8/20 (40%), Positives = 15/20 (75%)
Query: 17 RVVLLHGPPGTGKTSLCKAV 36
++++ GP G GK++L KA+
Sbjct: 1 LLIVISGPSGAGKSTLVKAL 20
>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 = 29.2 bits (66), Expect = 0.29
Identities = 13/29 (44%), Positives = 19/29 (65%), Gaps = 4/29 (13%)
Query: 18 VVLLHGPPGTGKTSLCKAVAQKLSIRLQT 46
VV + GP G+GKT+ A+KLS +L+
Sbjct: 1 VVGIAGPSGSGKTTF----AKKLSNQLRV 25
>gnl|CDD|234654 PRK00131, aroK, shikimate kinase; Reviewed.
Length = 175
Score = 29.0 bits (66), Expect = 0.31
Identities = 8/24 (33%), Positives = 17/24 (70%), Gaps = 1/24 (4%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQKL 40
+VL+ G G GK+++ + +A++L
Sbjct: 6 NIVLI-GFMGAGKSTIGRLLAKRL 28
>gnl|CDD|238985 cd02027, APSK, Adenosine 5'-phosphosulfate kinase (APSK)
catalyzes the phosphorylation of adenosine
5'-phosphosulfate to form 3'-phosphoadenosine
5'-phosphosulfate (PAPS). The end-product PAPS is a
biologically "activated" sulfate form important for the
assimilation of inorganic sulfate.
Length = 149
Score = 29.0 bits (66), Expect = 0.31
Identities = 9/23 (39%), Positives = 17/23 (73%)
Query: 18 VVLLHGPPGTGKTSLCKAVAQKL 40
V+ L G G+GK+++ +A+ +KL
Sbjct: 1 VIWLTGLSGSGKSTIARALEEKL 23
>gnl|CDD|217429 pfam03215, Rad17, Rad17 cell cycle checkpoint protein.
Length = 490
Score = 29.2 bits (65), Expect = 0.31
Identities = 10/29 (34%), Positives = 19/29 (65%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQKLSIRLQ 45
++LL GP G GK++ K ++++L I +
Sbjct: 46 LILLLTGPSGCGKSTTVKVLSKELGIEII 74
>gnl|CDD|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 = 29.0 bits (66), Expect = 0.31
Identities = 10/24 (41%), Positives = 16/24 (66%), Gaps = 1/24 (4%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQKL 40
R+ L+ G G GK++L K +A +L
Sbjct: 28 RIGLV-GRNGAGKSTLLKLIAGEL 50
>gnl|CDD|116541 pfam07931, CPT, Chloramphenicol phosphotransferase-like protein.
The members of this family are all similar to
chloramphenicol 3-O phosphotransferase (CPT) expressed
by Streptomyces venezuelae. Chloramphenicol (Cm) is a
metabolite produced by this bacterium that can inhibit
ribosomal peptidyl transferase activity and therefore
protein production. By transferring a phosphate group
to the C-3 hydroxyl group of Cm, CPT inactivates this
potentially lethal metabolite.
Length = 174
Score = 28.9 bits (65), Expect = 0.32
Identities = 9/25 (36%), Positives = 18/25 (72%), Gaps = 1/25 (4%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQKLS 41
R++LL+G +GK+S+ +A+ Q +
Sbjct: 2 RIILLNGGSSSGKSSIARAL-QDIL 25
>gnl|CDD|233208 TIGR00956, 3a01205, Pleiotropic Drug Resistance (PDR) Family
protein. [Transport and binding proteins, Other].
Length = 1394
Score = 29.3 bits (66), Expect = 0.32
Identities = 8/31 (25%), Positives = 16/31 (51%)
Query: 10 SNIISWNRVVLLHGPPGTGKTSLCKAVAQKL 40
+I + ++ G PG+G ++L K +A
Sbjct: 81 DGLIKPGELTVVLGRPGSGCSTLLKTIASNT 111
>gnl|CDD|226372 COG3854, SpoIIIAA, ncharacterized protein conserved in bacteria
[Function unknown].
Length = 308
Score = 29.0 bits (65), Expect = 0.34
Identities = 11/23 (47%), Positives = 16/23 (69%)
Query: 19 VLLHGPPGTGKTSLCKAVAQKLS 41
L+ GPP GKT+L + +A+ LS
Sbjct: 140 TLIIGPPQVGKTTLLRDIARLLS 162
>gnl|CDD|235943 PRK07133, PRK07133, DNA polymerase III subunits gamma and tau;
Validated.
Length = 725
Score = 29.4 bits (66), Expect = 0.35
Identities = 16/33 (48%), Positives = 19/33 (57%), Gaps = 3/33 (9%)
Query: 11 NIISWNRVV---LLHGPPGTGKTSLCKAVAQKL 40
NII N++ L GP GTGKTS+ K A L
Sbjct: 32 NIIKSNKISHAYLFSGPRGTGKTSVAKIFANAL 64
>gnl|CDD|217424 pfam03205, MobB, Molybdopterin guanine dinucleotide synthesis
protein B. This protein contains a P-loop.
Length = 126
Score = 28.5 bits (64), Expect = 0.36
Identities = 10/27 (37%), Positives = 16/27 (59%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQKLSIR 43
+VL+ GP +GKT+L + + L R
Sbjct: 1 PIVLVVGPKDSGKTTLIRKLLNYLKRR 27
>gnl|CDD|237864 PRK14950, PRK14950, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 585
Score = 29.0 bits (65), Expect = 0.37
Identities = 16/33 (48%), Positives = 17/33 (51%), Gaps = 7/33 (21%)
Query: 11 NIISWNRVV---LLHGPPGTGKTS----LCKAV 36
N I+ RV L GP G GKTS L KAV
Sbjct: 30 NAIAEGRVAHAYLFTGPRGVGKTSTARILAKAV 62
>gnl|CDD|236482 PRK09361, radB, DNA repair and recombination protein RadB;
Provisional.
Length = 225
Score = 28.7 bits (65), Expect = 0.41
Identities = 8/11 (72%), Positives = 11/11 (100%)
Query: 23 GPPGTGKTSLC 33
GPPG+GKT++C
Sbjct: 30 GPPGSGKTNIC 40
>gnl|CDD|227519 COG5192, BMS1, GTP-binding protein required for 40S ribosome
biogenesis [Translation, ribosomal structure and
biogenesis].
Length = 1077
Score = 28.9 bits (64), Expect = 0.42
Identities = 9/24 (37%), Positives = 19/24 (79%)
Query: 18 VVLLHGPPGTGKTSLCKAVAQKLS 41
+V + GPPGTGK++L +++ ++ +
Sbjct: 71 IVAVVGPPGTGKSTLIRSLVRRFT 94
>gnl|CDD|234034 TIGR02858, spore_III_AA, stage III sporulation protein AA. Members
of this protein are the stage III sporulation protein
AA, encoded by one of several genes in the spoIIIA
locus. It seems that this protein is found in a species
if and only if that species is capable of endospore
formation [Cellular processes, Sporulation and
germination].
Length = 270
Score = 28.8 bits (65), Expect = 0.42
Identities = 14/37 (37%), Positives = 23/37 (62%), Gaps = 2/37 (5%)
Query: 7 KVKSNIISWNRVV--LLHGPPGTGKTSLCKAVAQKLS 41
K+ ++ NRV+ L+ PP GKT+L + +A+ LS
Sbjct: 100 KLLPYLVRNNRVLNTLIISPPQCGKTTLLRDLARILS 136
>gnl|CDD|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 = 0.44
Identities = 10/25 (40%), Positives = 17/25 (68%)
Query: 13 ISWNRVVLLHGPPGTGKTSLCKAVA 37
+ +V L GP G+GK++L +A+A
Sbjct: 22 LKAGEIVALVGPNGSGKSTLLRAIA 46
>gnl|CDD|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 = 0.47
Identities = 8/26 (30%), Positives = 18/26 (69%)
Query: 18 VVLLHGPPGTGKTSLCKAVAQKLSIR 43
++ + G G+GK+++ K +A++L R
Sbjct: 1 IIAITGGSGSGKSTVAKKLAEQLGGR 26
>gnl|CDD|233584 TIGR01817, nifA, Nif-specific regulatory protein. This model
represents NifA, a DNA-binding regulatory protein for
nitrogen fixation. The model produces scores between the
trusted and noise cutoffs for a well-described NifA
homolog in Aquifex aeolicus (which lacks nitrogenase),
for transcriptional activators of alternative
nitrogenases (VFe or FeFe instead of MoFe), and
truncated forms [Central intermediary metabolism,
Nitrogen fixation, Regulatory functions, DNA
interactions].
Length = 534
Score = 28.9 bits (65), Expect = 0.48
Identities = 15/33 (45%), Positives = 18/33 (54%), Gaps = 1/33 (3%)
Query: 15 WNRVVLLHGPPGTGKTSLCKAVAQKLSIRLQTP 47
N VLL G GTGK + KA+ LS R + P
Sbjct: 218 SNSTVLLRGESGTGKELIAKAIHY-LSPRAKRP 249
>gnl|CDD|224616 COG1702, PhoH, Phosphate starvation-inducible protein PhoH,
predicted ATPase [Signal transduction mechanisms].
Length = 348
Score = 28.8 bits (65), Expect = 0.51
Identities = 11/20 (55%), Positives = 12/20 (60%)
Query: 18 VVLLHGPPGTGKTSLCKAVA 37
+V GP GTGKT L A A
Sbjct: 145 IVFGIGPAGTGKTYLAVAKA 164
Score = 26.8 bits (60), Expect = 2.1
Identities = 8/21 (38%), Positives = 11/21 (52%)
Query: 16 NRVVLLHGPPGTGKTSLCKAV 36
N +V L GP T + L A+
Sbjct: 24 NELVALFGPTDTNLSLLEIAL 44
>gnl|CDD|172994 PRK14528, PRK14528, adenylate kinase; Provisional.
Length = 186
Score = 28.4 bits (63), Expect = 0.55
Identities = 15/50 (30%), Positives = 23/50 (46%), Gaps = 13/50 (26%)
Query: 19 VLLHGPPGTGKTSLCKAVAQKLSI-------------RLQTPQAIFFKKY 55
++ GPPG GK + K + ++LSI + QT I K+Y
Sbjct: 4 IIFMGPPGAGKGTQAKILCERLSIPQISTGDILREAVKNQTAMGIEAKRY 53
>gnl|CDD|238988 cd02030, NDUO42, NADH:Ubiquinone oxioreductase, 42 kDa (NDUO42)
is a family of proteins that are highly similar to
deoxyribonucleoside kinases (dNK). Members of this
family have been identified as one of the subunits of
NADH:Ubiquinone oxioreductase (complex I), a
multi-protein complex located in the inner
mitochondrial membrane. The main function of the
complex is to transport electrons from NADH to
ubiquinone, which is accompanied by the translocation
of protons from the mitochondrial matrix to the inter
membrane space.
Length = 219
Score = 28.5 bits (64), Expect = 0.57
Identities = 14/51 (27%), Positives = 21/51 (41%), Gaps = 10/51 (19%)
Query: 18 VVLLHGPPGTGKTSLCKAVAQKLSIRLQTPQAIFFKKYPNVLIFTTSNLTG 68
V+ + G +GK L K +A+KL K +P I + TG
Sbjct: 1 VITVDGNIASGKGKLAKELAEKLG----------MKYFPEAGIHYLDSTTG 41
>gnl|CDD|223382 COG0305, DnaB, Replicative DNA helicase [DNA replication,
recombination, and repair].
Length = 435
Score = 28.4 bits (64), Expect = 0.58
Identities = 11/34 (32%), Positives = 19/34 (55%)
Query: 18 VVLLHGPPGTGKTSLCKAVAQKLSIRLQTPQAIF 51
++++ PG GKT+L +A + + P AIF
Sbjct: 198 LIIVAARPGMGKTALALNIALNAAADGRKPVAIF 231
>gnl|CDD|218203 pfam04670, Gtr1_RagA, Gtr1/RagA G protein conserved region. GTR1
was first identified in S. cerevisiae as a suppressor
of a mutation in RCC1. Biochemical analysis revealed
that Gtr1 is in fact a G protein of the Ras family. The
RagA/B proteins are the human homologues of Gtr1.
Included in this family is the human Rag C, a novel
protein that has been shown to interact with RagA/B.
Length = 230
Score = 28.3 bits (64), Expect = 0.61
Identities = 10/25 (40%), Positives = 14/25 (56%)
Query: 19 VLLHGPPGTGKTSLCKAVAQKLSIR 43
VLL G G+GK+S+ + S R
Sbjct: 2 VLLMGLRGSGKSSMRSIIFSNYSPR 26
>gnl|CDD|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 = 28.4 bits (64), Expect = 0.64
Identities = 8/25 (32%), Positives = 16/25 (64%)
Query: 19 VLLHGPPGTGKTSLCKAVAQKLSIR 43
++L G P +GK++ K +A+ L +
Sbjct: 2 IILTGLPSSGKSTRAKELAKYLEEK 26
>gnl|CDD|226412 COG3896, COG3896, Chloramphenicol 3-O-phosphotransferase [Defense
mechanisms].
Length = 205
Score = 28.3 bits (63), Expect = 0.64
Identities = 9/20 (45%), Positives = 13/20 (65%)
Query: 17 RVVLLHGPPGTGKTSLCKAV 36
R+VLL+G GK+S+ A
Sbjct: 24 RIVLLNGGSSAGKSSIALAF 43
>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 = 28.5 bits (64), Expect = 0.65
Identities = 9/13 (69%), Positives = 12/13 (92%)
Query: 20 LLHGPPGTGKTSL 32
L+ GPPG+GKT+L
Sbjct: 115 LVIGPPGSGKTTL 127
>gnl|CDD|234763 PRK00440, rfc, replication factor C small subunit; Reviewed.
Length = 319
Score = 28.3 bits (64), Expect = 0.65
Identities = 12/21 (57%), Positives = 16/21 (76%)
Query: 20 LLHGPPGTGKTSLCKAVAQKL 40
L GPPGTGKT+ A+A++L
Sbjct: 42 LFAGPPGTGKTTAALALAREL 62
>gnl|CDD|206745 cd11385, RagC_like, Rag GTPase, subfamily of Ras-related GTPases,
includes Ras-related GTP-binding proteins C and D.
RagC and RagD are closely related Rag GTPases
(ras-related GTP-binding protein C and D) that
constitute a unique subgroup of the Ras superfamily,
and are functional homologs of Saccharomyces cerevisiae
Gtr2. These domains form heterodimers with RagA or
RagB, and similarly, Gtr2 dimerizes with Gtr1 in order
to function. They play an essential role in regulating
amino acid-induced target of rapamycin complex 1
(TORC1) kinase signaling, exocytic cargo sorting at
endosomes, and epigenetic control of gene expression.
In response to amino acids, the Rag GTPases guide the
TORC1 complex to activate the platform containing Rheb
proto-oncogene by driving the relocalization of mTORC1
from discrete locations in the cytoplasm to a late
endosomal and/or lysosomal compartment that is
Rheb-enriched and contains Rab-7.
Length = 175
Score = 28.0 bits (63), Expect = 0.73
Identities = 10/23 (43%), Positives = 15/23 (65%)
Query: 19 VLLHGPPGTGKTSLCKAVAQKLS 41
+LL G +GK+S+ K V K+S
Sbjct: 2 ILLMGLRRSGKSSIQKVVFHKMS 24
>gnl|CDD|223401 COG0324, MiaA, tRNA delta(2)-isopentenylpyrophosphate transferase
[Translation, ribosomal structure and biogenesis].
Length = 308
Score = 28.0 bits (63), Expect = 0.74
Identities = 9/24 (37%), Positives = 19/24 (79%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQKL 40
+++++ GP +GKT+L A+A++L
Sbjct: 4 KLIVIAGPTASGKTALAIALAKRL 27
>gnl|CDD|223645 COG0572, Udk, Uridine kinase [Nucleotide transport and
metabolism].
Length = 218
Score = 28.0 bits (63), Expect = 0.77
Identities = 7/24 (29%), Positives = 17/24 (70%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQKL 40
++ + G G+GKT++ K ++++L
Sbjct: 9 IIIGIAGGSGSGKTTVAKELSEQL 32
>gnl|CDD|179660 PRK03839, PRK03839, putative kinase; Provisional.
Length = 180
Score = 27.8 bits (62), Expect = 0.77
Identities = 10/21 (47%), Positives = 14/21 (66%)
Query: 23 GPPGTGKTSLCKAVAQKLSIR 43
G PG GKT++ K +A+KL
Sbjct: 7 GTPGVGKTTVSKLLAEKLGYE 27
>gnl|CDD|223666 COG0593, DnaA, ATPase involved in DNA replication initiation [DNA
replication, recombination, and repair].
Length = 408
Score = 28.0 bits (63), Expect = 0.77
Identities = 13/61 (21%), Positives = 21/61 (34%), Gaps = 13/61 (21%)
Query: 18 VVLLHGPPGTGKTSLCKAVAQKLSIRLQTPQAIFFKKYPNVLIF--TTSNLTGAIDLAFL 75
+ ++G G GKT L +A+ PN + T+ + T A
Sbjct: 115 PLFIYGGVGLGKTHLLQAIG-----------NEALANGPNARVVYLTSEDFTNDFVKALR 163
Query: 76 D 76
D
Sbjct: 164 D 164
>gnl|CDD|179433 PRK02496, adk, adenylate kinase; Provisional.
Length = 184
Score = 27.8 bits (62), Expect = 0.78
Identities = 11/26 (42%), Positives = 16/26 (61%), Gaps = 1/26 (3%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQKLSI 42
R++ L GPPG GK + +A+ L I
Sbjct: 3 RLIFL-GPPGAGKGTQAVVLAEHLHI 27
>gnl|CDD|238484 cd00984, DnaB_C, DnaB helicase C terminal domain. The hexameric
helicase DnaB unwinds the DNA duplex at the chromosome
replication fork. Although the mechanism by which DnaB
both couples ATP hydrolysis to translocation along DNA
and denatures the duplex is unknown, a change in the
quaternary structure of the protein involving
dimerization of the N-terminal domain has been observed
and may occur during the enzymatic cycle. This
C-terminal domain contains an ATP-binding site and is
therefore probably the site of ATP hydrolysis.
Length = 242
Score = 27.9 bits (63), Expect = 0.83
Identities = 7/33 (21%), Positives = 16/33 (48%)
Query: 19 VLLHGPPGTGKTSLCKAVAQKLSIRLQTPQAIF 51
+++ P GKT+ +A+ ++ + P F
Sbjct: 16 IIIAARPSMGKTAFALNIAENIAKKQGKPVLFF 48
>gnl|CDD|220642 pfam10236, DAP3, Mitochondrial ribosomal death-associated protein
3. This is a family of conserved proteins which were
originally described as death-associated-protein-3
(DAP-3). The proteins carry a P-loop DNA-binding motif,
and induce apoptosis. DAP3 has been shown to be a
pro-apoptotic factor in the mitochondrial matrix and to
be crucial for mitochondrial biogenesis and so has also
been designated as MRP-S29 (mitochondrial ribosomal
protein subunit 29).
Length = 274
Score = 28.0 bits (63), Expect = 0.86
Identities = 10/23 (43%), Positives = 14/23 (60%), Gaps = 2/23 (8%)
Query: 16 NRVVLLHGPPGTGKT-SLCKAVA 37
R VL G G+GK+ L +A+A
Sbjct: 24 VRFVL-TGERGSGKSVLLAQAMA 45
>gnl|CDD|216360 pfam01202, SKI, Shikimate kinase.
Length = 158
Score = 27.6 bits (62), Expect = 0.89
Identities = 5/20 (25%), Positives = 12/20 (60%)
Query: 25 PGTGKTSLCKAVAQKLSIRL 44
G GK+++ + +A+ L +
Sbjct: 1 MGAGKSTIGRLLAKALGLPF 20
>gnl|CDD|222866 PHA02544, 44, clamp loader, small subunit; Provisional.
Length = 316
Score = 28.0 bits (63), Expect = 0.90
Identities = 14/35 (40%), Positives = 22/35 (62%), Gaps = 3/35 (8%)
Query: 12 IISWNRV--VLLHGP-PGTGKTSLCKAVAQKLSIR 43
I+ R+ +LLH P PGTGKT++ KA+ ++
Sbjct: 36 IVKKGRIPNMLLHSPSPGTGKTTVAKALCNEVGAE 70
>gnl|CDD|234626 PRK00091, miaA, tRNA delta(2)-isopentenylpyrophosphate
transferase; Reviewed.
Length = 307
Score = 27.8 bits (63), Expect = 0.90
Identities = 9/24 (37%), Positives = 18/24 (75%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQKL 40
+V+++ GP +GKT+L +A++L
Sbjct: 5 KVIVIVGPTASGKTALAIELAKRL 28
>gnl|CDD|180607 PRK06526, PRK06526, transposase; Provisional.
Length = 254
Score = 27.9 bits (62), Expect = 0.96
Identities = 10/21 (47%), Positives = 13/21 (61%)
Query: 19 VLLHGPPGTGKTSLCKAVAQK 39
V+ GPPGTGKT L + +
Sbjct: 101 VVFLGPPGTGKTHLAIGLGIR 121
>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 = 27.6 bits (62), Expect = 0.97
Identities = 8/18 (44%), Positives = 13/18 (72%)
Query: 23 GPPGTGKTSLCKAVAQKL 40
G G GKT+L + +A++L
Sbjct: 7 GIDGAGKTTLIELLAERL 24
>gnl|CDD|237393 PRK13477, PRK13477, bifunctional pantoate ligase/cytidylate kinase;
Provisional.
Length = 512
Score = 27.9 bits (63), Expect = 0.97
Identities = 10/18 (55%), Positives = 15/18 (83%)
Query: 23 GPPGTGKTSLCKAVAQKL 40
GP G GK+++ +AVA+KL
Sbjct: 291 GPAGAGKSTVTRAVAKKL 308
>gnl|CDD|134335 PRK00625, PRK00625, shikimate kinase; Provisional.
Length = 173
Score = 27.4 bits (61), Expect = 0.99
Identities = 12/24 (50%), Positives = 16/24 (66%)
Query: 19 VLLHGPPGTGKTSLCKAVAQKLSI 42
+ L G P GKTS KA+A+ LS+
Sbjct: 3 IFLCGLPTVGKTSFGKALAKFLSL 26
>gnl|CDD|161676 TIGR00041, DTMP_kinase, thymidylate kinase. Function:
phosphorylation of DTMP to form DTDP in both de novo
and salvage pathways of DTTP synthesis. Catalytic
activity: ATP + thymidine 5'-phosphate = ADP +
thymidine 5'-diphosphate [Purines, pyrimidines,
nucleosides, and nucleotides, Nucleotide and nucleoside
interconversions].
Length = 195
Score = 27.7 bits (62), Expect = 1.00
Identities = 8/38 (21%), Positives = 17/38 (44%), Gaps = 3/38 (7%)
Query: 19 VLLHGPPGTGKTSLCKAVAQKLSIRLQTPQAIFFKKYP 56
+++ G G GKT+ + + L + + F + P
Sbjct: 6 IVIEGIDGAGKTTQANLLKKLLQ---ENGYDVLFTREP 40
>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 = 27.8 bits (62), Expect = 1.0
Identities = 9/17 (52%), Positives = 15/17 (88%)
Query: 21 LHGPPGTGKTSLCKAVA 37
++GPPG+GKT++C +A
Sbjct: 17 IYGPPGSGKTNICMILA 33
>gnl|CDD|227922 COG5635, COG5635, Predicted NTPase (NACHT family) [Signal
transduction mechanisms].
Length = 824
Score = 27.8 bits (62), Expect = 1.1
Identities = 11/36 (30%), Positives = 23/36 (63%), Gaps = 1/36 (2%)
Query: 15 WNRVVLLHGPPGTGKTSLCKAVAQKLSIRLQTPQAI 50
+ ++++L G PG+GKT+ + +A L+ R P+ +
Sbjct: 222 YAKLLIL-GAPGSGKTTFLQRLALWLAQRTLEPEDV 256
>gnl|CDD|236783 PRK10875, recD, exonuclease V subunit alpha; Provisional.
Length = 615
Score = 27.6 bits (62), Expect = 1.1
Identities = 14/40 (35%), Positives = 22/40 (55%), Gaps = 9/40 (22%)
Query: 17 RVVLLHGPPGTGKTS-LCKAVA--------QKLSIRLQTP 47
R+ ++ G PGTGKT+ + K +A ++ IRL P
Sbjct: 168 RISVISGGPGTGKTTTVAKLLAALIQLADGERCRIRLAAP 207
>gnl|CDD|234719 PRK00300, gmk, guanylate kinase; Provisional.
Length = 205
Score = 27.4 bits (62), Expect = 1.1
Identities = 10/25 (40%), Positives = 16/25 (64%), Gaps = 5/25 (20%)
Query: 23 GPPGTGKTSLCKAVAQ-----KLSI 42
GP G GK++L KA+ + +LS+
Sbjct: 12 GPSGAGKSTLVKALLERDPNLQLSV 36
>gnl|CDD|238005 cd00046, DEXDc, DEAD-like helicases superfamily. A diverse family
of proteins involved in ATP-dependent RNA or DNA
unwinding. This domain contains the ATP-binding region.
Length = 144
Score = 27.3 bits (61), Expect = 1.1
Identities = 9/14 (64%), Positives = 10/14 (71%)
Query: 17 RVVLLHGPPGTGKT 30
R VLL P G+GKT
Sbjct: 1 RDVLLAAPTGSGKT 14
>gnl|CDD|237150 PRK12608, PRK12608, transcription termination factor Rho;
Provisional.
Length = 380
Score = 27.7 bits (62), Expect = 1.1
Identities = 8/19 (42%), Positives = 11/19 (57%)
Query: 20 LLHGPPGTGKTSLCKAVAQ 38
L+ PP GKT L + +A
Sbjct: 137 LIVAPPRAGKTVLLQQIAA 155
>gnl|CDD|234189 TIGR03375, type_I_sec_LssB, type I secretion system ATPase, LssB
family. Type I protein secretion is a system in some
Gram-negative bacteria to export proteins (often
proteases) across both inner and outer membranes to the
extracellular medium. This is one of three proteins of
the type I secretion apparatus. Targeted proteins are
not cleaved at the N-terminus, but rather carry signals
located toward the extreme C-terminus to direct type I
secretion. This model is related to models TIGR01842 and
TIGR01846, and to bacteriocin ABC transporters that
cleave their substrates during export [Protein fate,
Protein and peptide secretion and trafficking, Cellular
processes, Pathogenesis].
Length = 694
Score = 27.5 bits (62), Expect = 1.1
Identities = 18/70 (25%), Positives = 34/70 (48%), Gaps = 19/70 (27%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQKLSIRLQTPQAIFFKKYPNVLIFTTSNLTGAIDLAFLD 76
+V ++ G G+GK++L KL + L P +VL+ +D+ +D
Sbjct: 493 KVAII-GRIGSGKSTL-----LKLLLGLYQPTE------GSVLL-------DGVDIRQID 533
Query: 77 RADIKQYIGF 86
AD+++ IG+
Sbjct: 534 PADLRRNIGY 543
>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 = 27.7 bits (62), Expect = 1.1
Identities = 9/15 (60%), Positives = 13/15 (86%)
Query: 18 VVLLHGPPGTGKTSL 32
+V+L GP G+GKT+L
Sbjct: 33 IVILTGPSGSGKTTL 47
>gnl|CDD|235871 PRK06835, PRK06835, DNA replication protein DnaC; Validated.
Length = 329
Score = 27.6 bits (62), Expect = 1.2
Identities = 10/21 (47%), Positives = 14/21 (66%)
Query: 20 LLHGPPGTGKTSLCKAVAQKL 40
L +G GTGKT L +A++L
Sbjct: 187 LFYGNTGTGKTFLSNCIAKEL 207
>gnl|CDD|217419 pfam03198, Glyco_hydro_72, Glucanosyltransferase. This is a family
of glycosylphosphatidylinositol-anchored
beta(1-3)glucanosyltransferases. The active site
residues in the Aspergillus fumigatus example are the
two glutamate residues at 160 and 261.
Length = 313
Score = 27.7 bits (62), Expect = 1.2
Identities = 15/40 (37%), Positives = 21/40 (52%), Gaps = 7/40 (17%)
Query: 52 FKKYPNVLIF-----TTSNLTGAIDLAFLDRA--DIKQYI 84
FK YPNVL F ++ + A++ A D+KQYI
Sbjct: 129 FKNYPNVLGFFAGNEVINDASNTDASAYVKAAVRDMKQYI 168
>gnl|CDD|234057 TIGR02915, PEP_resp_reg, PEP-CTERM-box response regulator
transcription factor. Members of this protein family
share full-length homology with (but do not include) the
acetoacetate metabolism regulatory protein AtoC (see
SP|Q06065). These proteins have a Fis family DNA binding
sequence (pfam02954), a response regulator receiver
domain (pfam00072), and sigma-54 interaction domain
(pfam00158) [Regulatory functions, DNA interactions].
Length = 445
Score = 27.4 bits (61), Expect = 1.2
Identities = 14/32 (43%), Positives = 18/32 (56%), Gaps = 1/32 (3%)
Query: 12 IISWNRVVLLHGPPGTGKTSLCKAVAQKLSIR 43
I + VLL G GTGK L +A+ +LS R
Sbjct: 158 IAPSDITVLLLGESGTGKEVLARAL-HQLSDR 188
>gnl|CDD|182120 PRK09862, PRK09862, putative ATP-dependent protease; Provisional.
Length = 506
Score = 27.6 bits (61), Expect = 1.2
Identities = 11/14 (78%), Positives = 12/14 (85%)
Query: 19 VLLHGPPGTGKTSL 32
+LL GPPGTGKT L
Sbjct: 213 LLLIGPPGTGKTML 226
>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 = 27.2 bits (61), Expect = 1.3
Identities = 7/25 (28%), Positives = 16/25 (64%)
Query: 16 NRVVLLHGPPGTGKTSLCKAVAQKL 40
+++++GP GKT+L + ++L
Sbjct: 20 YPIIVVYGPRRCGKTALLREFLEEL 44
>gnl|CDD|233355 TIGR01313, therm_gnt_kin, carbohydrate kinase, thermoresistant
glucokinase family. This model represents a subfamily
of proteins that includes thermoresistant and
thermosensitve isozymes of gluconate kinase
(gluconokinase) in E. coli and other related proteins;
members of this family are often named by similarity to
the thermostable isozyme. These proteins show homology
to shikimate kinases and adenylate kinases but not to
gluconate kinases from the FGGY family of carbohydrate
kinases.
Length = 163
Score = 27.4 bits (61), Expect = 1.3
Identities = 8/21 (38%), Positives = 14/21 (66%)
Query: 21 LHGPPGTGKTSLCKAVAQKLS 41
L G G+GK+++ A+A +L
Sbjct: 3 LMGVAGSGKSTIASALAHRLG 23
>gnl|CDD|222927 PHA02774, PHA02774, E1; Provisional.
Length = 613
Score = 27.5 bits (62), Expect = 1.5
Identities = 10/32 (31%), Positives = 15/32 (46%), Gaps = 6/32 (18%)
Query: 2 KFSHSKVKSNIISWNRVVLLHGPPGTGKTSLC 33
F K N + +++GPP TGK+ C
Sbjct: 426 DFLKGIPKKNCL------VIYGPPDTGKSMFC 451
>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 = 27.0 bits (61), Expect = 1.5
Identities = 23/89 (25%), Positives = 36/89 (40%), Gaps = 25/89 (28%)
Query: 16 NRVVLLHGPPGTGKTSLCKAVAQKLSIRLQTPQAIFFKKYPNVLIFTTSNLTGAIDLAFL 75
V + GP G+GK++L K + RL P + +LI +DL L
Sbjct: 28 GEKVAIVGPSGSGKSTLLKLLL-----RLYDPTS------GEILI-------DGVDLRDL 69
Query: 76 DRADIKQYIGF-PSAAAIF------NIFS 97
D +++ I + P +F NI S
Sbjct: 70 DLESLRKNIAYVPQDPFLFSGTIRENILS 98
>gnl|CDD|238943 cd01985, ETF, The electron transfer flavoprotein (ETF) serves as a
specific electron acceptor for various mitochondrial
dehydrogenases. ETF transfers electrons to the main
respiratory chain via ETF-ubiquinone oxidoreductase. ETF
is an heterodimer that consists of an alpha and a beta
subunit which binds one molecule of FAD per dimer . A
similar system also exists in some bacteria. The
homologous pair of proteins (FixA/FixB) are essential
for nitrogen fixation. The alpha subunit of ETF is
structurally related to the bacterial nitrogen fixation
protein fixB which could play a role in a redox process
and feed electrons to ferredoxin. The beta subunit
protein is distantly related to and forms a heterodimer
with the alpha subunit.
Length = 181
Score = 27.2 bits (61), Expect = 1.5
Identities = 8/23 (34%), Positives = 13/23 (56%)
Query: 27 TGKTSLCKAVAQKLSIRLQTPQA 49
G TS+ K +A +++ L PQ
Sbjct: 97 AGATSIGKQLAPRVAALLGVPQI 119
>gnl|CDD|180518 PRK06294, PRK06294, coproporphyrinogen III oxidase; Provisional.
Length = 370
Score = 27.4 bits (61), Expect = 1.5
Identities = 14/59 (23%), Positives = 23/59 (38%), Gaps = 2/59 (3%)
Query: 4 SHSKVKSNIISWNRVVLLHGPPGTGKTSLCKAVAQK--LSIRLQTPQAIFFKKYPNVLI 60
SK S I + R + + P L K L++RL+ + I +P+ L
Sbjct: 274 IRSKNLSRISHYLRALRKNLPTQESSEELPPNERIKEALALRLRLCEGIPLADFPSELT 332
>gnl|CDD|206680 cd01893, Miro1, Mitochondrial Rho family 1 (Miro1), N-terminal.
Miro1 subfamily. Miro (mitochondrial Rho) proteins have
tandem GTP-binding domains separated by a linker region
containing putative calcium-binding EF hand motifs.
Genes encoding Miro-like proteins were found in several
eukaryotic organisms. This CD represents the N-terminal
GTPase domain of Miro proteins. These atypical Rho
GTPases have roles in mitochondrial homeostasis and
apoptosis. Most Rho proteins contain a lipid
modification site at the C-terminus; however, Miro is
one of few Rho subfamilies that lack this feature.
Length = 168
Score = 26.9 bits (60), Expect = 1.5
Identities = 9/22 (40%), Positives = 14/22 (63%), Gaps = 1/22 (4%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQ 38
R+VL+ G G GK+SL ++
Sbjct: 4 RIVLI-GDEGVGKSSLIMSLVS 24
>gnl|CDD|224166 COG1245, COG1245, Predicted ATPase, RNase L inhibitor (RLI) homolog
[General function prediction only].
Length = 591
Score = 27.3 bits (61), Expect = 1.6
Identities = 15/55 (27%), Positives = 24/55 (43%), Gaps = 11/55 (20%)
Query: 7 KVKSNIISWNRVVLLHGPPGTGKTSLCKAVA----------QKLSIRLQTPQAIF 51
+V+ I V+ + GP G GKT+ K +A + L + + PQ I
Sbjct: 358 EVEEGEIYDGEVIGILGPNGIGKTTFVKLLAGVIKPDEGSEEDLKVSYK-PQYIS 411
>gnl|CDD|213189 cd03222, ABC_RNaseL_inhibitor, ATP-binding cassette domain of
RNase L inhibitor. The ABC ATPase RNase L inhibitor
(RLI) is a key enzyme in ribosomal biogenesis,
formation of translation preinitiation complexes, and
assembly of HIV capsids. RLI's are not transport
proteins, and thus cluster with a group of soluble
proteins that lack the transmembrane components
commonly found in other members of the family.
Structurally, RLI's have an N-terminal Fe-S domain and
two nucleotide-binding domains, which are arranged to
form two composite active sites in their interface
cleft. RLI is one of the most conserved enzymes between
archaea and eukaryotes with a sequence identity more
than 48%. The high degree of evolutionary conservation
suggests that RLI performs a central role in archaeal
and eukaryotic physiology.
Length = 177
Score = 27.2 bits (60), Expect = 1.6
Identities = 12/36 (33%), Positives = 20/36 (55%)
Query: 5 HSKVKSNIISWNRVVLLHGPPGTGKTSLCKAVAQKL 40
V+ ++ V+ + GP GTGKT+ K +A +L
Sbjct: 14 FLLVELGVVKEGEVIGIVGPNGTGKTTAVKILAGQL 49
>gnl|CDD|216586 pfam01583, APS_kinase, Adenylylsulphate kinase. Enzyme that
catalyzes the phosphorylation of adenylylsulphate to
3'-phosphoadenylylsulfate. This domain contains an ATP
binding P-loop motif.
Length = 157
Score = 26.9 bits (60), Expect = 1.6
Identities = 7/23 (30%), Positives = 14/23 (60%)
Query: 18 VVLLHGPPGTGKTSLCKAVAQKL 40
+ G G+GK+++ A+ +KL
Sbjct: 4 TIWFTGLSGSGKSTIANALERKL 26
>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 = 27.2 bits (61), Expect = 1.6
Identities = 6/18 (33%), Positives = 12/18 (66%)
Query: 21 LHGPPGTGKTSLCKAVAQ 38
+ G G+GK++L + +A
Sbjct: 38 IVGESGSGKSTLARLLAG 55
>gnl|CDD|223546 COG0470, HolB, ATPase involved in DNA replication [DNA
replication, recombination, and repair].
Length = 230
Score = 27.3 bits (60), Expect = 1.6
Identities = 9/31 (29%), Positives = 16/31 (51%), Gaps = 3/31 (9%)
Query: 5 HSKVKSNIISWNRV---VLLHGPPGTGKTSL 32
++ + R+ +L +GPPG GKT+
Sbjct: 10 VKRLLVQALESGRLPHALLFYGPPGVGKTTA 40
>gnl|CDD|237730 PRK14493, PRK14493, putative bifunctional molybdopterin-guanine
dinucleotide biosynthesis protein MobB/MoaE;
Provisional.
Length = 274
Score = 27.3 bits (61), Expect = 1.6
Identities = 9/21 (42%), Positives = 13/21 (61%)
Query: 23 GPPGTGKTSLCKAVAQKLSIR 43
G TGKT+L + + +LS R
Sbjct: 8 GYKATGKTTLVERLVDRLSGR 28
>gnl|CDD|240359 PTZ00324, PTZ00324, glutamate dehydrogenase 2; Provisional.
Length = 1002
Score = 27.5 bits (61), Expect = 1.6
Identities = 12/59 (20%), Positives = 20/59 (33%), Gaps = 19/59 (32%)
Query: 5 HSKVKSNIISWNRVVLLHGPPGTGKTSLCKAVAQKLSIRL-----------QTPQAIFF 52
+ S +S+N +L KT+ K L+ RL + P +F
Sbjct: 430 DRTIFSAFLSFNEHIL--------KTNFYKTEKTALAFRLDPSFLSELEYPRVPYGVFL 480
>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 = 26.9 bits (60), Expect = 1.8
Identities = 9/18 (50%), Positives = 15/18 (83%)
Query: 18 VVLLHGPPGTGKTSLCKA 35
VV++ GPPG GK++L ++
Sbjct: 41 VVVVVGPPGVGKSTLIRS 58
>gnl|CDD|225804 COG3265, GntK, Gluconate kinase [Carbohydrate transport and
metabolism].
Length = 161
Score = 26.9 bits (60), Expect = 1.8
Identities = 7/20 (35%), Positives = 14/20 (70%)
Query: 23 GPPGTGKTSLCKAVAQKLSI 42
G G+GK+++ A+A++L
Sbjct: 2 GVSGSGKSTVGSALAERLGA 21
>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 = 27.1 bits (60), Expect = 1.9
Identities = 10/16 (62%), Positives = 12/16 (75%)
Query: 19 VLLHGPPGTGKTSLCK 34
+LL GPPG+GKT L
Sbjct: 214 LLLFGPPGSGKTMLAS 229
>gnl|CDD|240274 PTZ00112, PTZ00112, origin recognition complex 1 protein;
Provisional.
Length = 1164
Score = 27.3 bits (60), Expect = 1.9
Identities = 11/28 (39%), Positives = 18/28 (64%)
Query: 16 NRVVLLHGPPGTGKTSLCKAVAQKLSIR 43
N+++ + G PGTGKT+ +V Q L +
Sbjct: 781 NQILYISGMPGTGKTATVYSVIQLLQHK 808
>gnl|CDD|238139 cd00227, CPT, Chloramphenicol (Cm) phosphotransferase (CPT).
Cm-inactivating enzyme; modifies the primary (C-3)
hydroxyl of the antibiotic. Related structurally to
shikimate kinase II.
Length = 175
Score = 26.7 bits (59), Expect = 2.0
Identities = 7/20 (35%), Positives = 15/20 (75%)
Query: 17 RVVLLHGPPGTGKTSLCKAV 36
R+++L+G GK+S+ +A+
Sbjct: 3 RIIILNGGSSAGKSSIARAL 22
>gnl|CDD|225369 COG2812, DnaX, DNA polymerase III, gamma/tau subunits [DNA
replication, recombination, and repair].
Length = 515
Score = 27.0 bits (60), Expect = 2.0
Identities = 13/38 (34%), Positives = 20/38 (52%), Gaps = 3/38 (7%)
Query: 6 SKVKSNIISWNRVV---LLHGPPGTGKTSLCKAVAQKL 40
K SN + R+ L GP G GKT++ + +A+ L
Sbjct: 25 VKTLSNALENGRIAHAYLFSGPRGVGKTTIARILAKAL 62
>gnl|CDD|235315 PRK04841, PRK04841, transcriptional regulator MalT; Provisional.
Length = 903
Score = 27.2 bits (61), Expect = 2.0
Identities = 10/25 (40%), Positives = 16/25 (64%), Gaps = 3/25 (12%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQKLS 41
R+VL+ P G GKT+L ++Q +
Sbjct: 33 RLVLVTSPAGYGKTTL---ISQWAA 54
>gnl|CDD|217733 pfam03796, DnaB_C, DnaB-like helicase C terminal domain. The
hexameric helicase DnaB unwinds the DNA duplex at the
Escherichia coli chromosome replication fork. Although
the mechanism by which DnaB both couples ATP hydrolysis
to translocation along DNA and denatures the duplex is
unknown, a change in the quaternary structure of the
protein involving dimerisation of the N-terminal domain
has been observed and may occur during the enzymatic
cycle. This C-terminal domain contains an ATP-binding
site and is therefore probably the site of ATP
hydrolysis.
Length = 260
Score = 26.8 bits (60), Expect = 2.0
Identities = 8/33 (24%), Positives = 17/33 (51%)
Query: 19 VLLHGPPGTGKTSLCKAVAQKLSIRLQTPQAIF 51
+++ P GKT+ +A+ +++R P F
Sbjct: 22 IIIAARPSMGKTAFALNIARNIALRQGKPVLFF 54
>gnl|CDD|225806 COG3267, ExeA, Type II secretory pathway, component ExeA
(predicted ATPase) [Intracellular trafficking and
secretion].
Length = 269
Score = 27.0 bits (60), Expect = 2.0
Identities = 8/24 (33%), Positives = 14/24 (58%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQKL 40
++ + G G+GKT L +A+ L
Sbjct: 52 GILAVTGEVGSGKTVLRRALLASL 75
>gnl|CDD|214692 smart00487, DEXDc, DEAD-like helicases superfamily.
Length = 201
Score = 26.7 bits (59), Expect = 2.0
Identities = 8/15 (53%), Positives = 10/15 (66%)
Query: 16 NRVVLLHGPPGTGKT 30
R V+L P G+GKT
Sbjct: 24 LRDVILAAPTGSGKT 38
>gnl|CDD|213904 TIGR04291, arsen_driv_ArsA, arsenical pump-driving ATPase. The
broader family (TIGR00345) to which the current family
belongs consists of transport-energizing ATPases,
including to TRC40/GET3 family involved in
post-translational insertion of protein C-terminal
transmembrane anchors into membranes from the cyotosolic
face. This family, however, is restricted to ATPases
that energize pumps that export arsenite (or
antimonite).
Length = 566
Score = 27.0 bits (60), Expect = 2.0
Identities = 8/24 (33%), Positives = 16/24 (66%)
Query: 18 VVLLHGPPGTGKTSLCKAVAQKLS 41
+++ G G GKT++ A+A +L+
Sbjct: 323 LIMTMGKGGVGKTTVAAAIAVRLA 346
>gnl|CDD|238687 cd01393, recA_like, RecA is a bacterial enzyme which has roles
in homologous recombination, DNA repair, and the
induction of the SOS response. RecA couples ATP
hydrolysis to DNA strand exchange. While prokaryotes
have a single RecA protein, eukaryotes have multiple
RecA homologs such as Rad51, DMC1 and Rad55/57.
Archaea have the RecA-like homologs radA and radB.
Length = 226
Score = 26.8 bits (60), Expect = 2.0
Identities = 8/17 (47%), Positives = 11/17 (64%)
Query: 17 RVVLLHGPPGTGKTSLC 33
R+ + G G+GKT LC
Sbjct: 20 RITEIFGEFGSGKTQLC 36
>gnl|CDD|206679 cd01892, Miro2, Mitochondrial Rho family 2 (Miro2), C-terminal.
Miro2 subfamily. Miro (mitochondrial Rho) proteins have
tandem GTP-binding domains separated by a linker region
containing putative calcium-binding EF hand motifs.
Genes encoding Miro-like proteins were found in several
eukaryotic organisms. This CD represents the putative
GTPase domain in the C terminus of Miro proteins. These
atypical Rho GTPases have roles in mitochondrial
homeostasis and apoptosis. Most Rho proteins contain a
lipid modification site at the C-terminus; however,
Miro is one of few Rho subfamilies that lack this
feature.
Length = 180
Score = 26.8 bits (60), Expect = 2.0
Identities = 8/26 (30%), Positives = 15/26 (57%), Gaps = 1/26 (3%)
Query: 23 GPPGTGKTSLCKA-VAQKLSIRLQTP 47
G G+GK++L +A + + S +P
Sbjct: 11 GAKGSGKSALLQAFLGRSFSQNAYSP 36
>gnl|CDD|181541 PRK08727, PRK08727, hypothetical protein; Validated.
Length = 233
Score = 26.7 bits (59), Expect = 2.1
Identities = 12/24 (50%), Positives = 14/24 (58%), Gaps = 4/24 (16%)
Query: 19 VLLHGPPGTGKT----SLCKAVAQ 38
+ L GP GTGKT +LC A Q
Sbjct: 44 LYLSGPAGTGKTHLALALCAAAEQ 67
>gnl|CDD|129547 TIGR00455, apsK, adenylylsulfate kinase (apsK). This protein,
adenylylsulfate kinase, is often found as a fusion
protein with sulfate adenylyltransferase. Important
residue (active site in E.coli) is residue 100 of the
seed alignment [Central intermediary metabolism, Sulfur
metabolism].
Length = 184
Score = 26.7 bits (59), Expect = 2.1
Identities = 10/37 (27%), Positives = 20/37 (54%), Gaps = 6/37 (16%)
Query: 4 SHSKVKSNIISWNRVVLLHGPPGTGKTSLCKAVAQKL 40
+ + + +I W L G G+GK+++ A+ +KL
Sbjct: 12 ALNGHRGVVI-W-----LTGLSGSGKSTIANALEKKL 42
>gnl|CDD|184125 PRK13538, PRK13538, cytochrome c biogenesis protein CcmA;
Provisional.
Length = 204
Score = 26.7 bits (60), Expect = 2.1
Identities = 9/15 (60%), Positives = 11/15 (73%)
Query: 18 VVLLHGPPGTGKTSL 32
+V + GP G GKTSL
Sbjct: 29 LVQIEGPNGAGKTSL 43
>gnl|CDD|224677 COG1763, MobB, Molybdopterin-guanine dinucleotide biosynthesis
protein [Coenzyme metabolism].
Length = 161
Score = 26.5 bits (59), Expect = 2.1
Identities = 8/21 (38%), Positives = 13/21 (61%)
Query: 23 GPPGTGKTSLCKAVAQKLSIR 43
G +GKT+L + + +KL R
Sbjct: 9 GYKNSGKTTLIEKLVRKLKAR 29
>gnl|CDD|234814 PRK00698, tmk, thymidylate kinase; Validated.
Length = 205
Score = 26.7 bits (60), Expect = 2.2
Identities = 7/33 (21%), Positives = 15/33 (45%), Gaps = 2/33 (6%)
Query: 19 VLLHGPPGTGKTSLCKAVAQKLSIRLQTPQAIF 51
+ + G G GK++ + + + L Q +F
Sbjct: 6 ITIEGIDGAGKSTQIELLKELL--EQQGRDVVF 36
>gnl|CDD|201213 pfam00406, ADK, Adenylate kinase.
Length = 186
Score = 26.5 bits (59), Expect = 2.2
Identities = 9/20 (45%), Positives = 12/20 (60%)
Query: 23 GPPGTGKTSLCKAVAQKLSI 42
GPPG GK + + + QK I
Sbjct: 3 GPPGAGKGTQAERIVQKYGI 22
>gnl|CDD|224557 COG1643, HrpA, HrpA-like helicases [DNA replication,
recombination, and repair].
Length = 845
Score = 26.9 bits (60), Expect = 2.2
Identities = 8/15 (53%), Positives = 12/15 (80%)
Query: 16 NRVVLLHGPPGTGKT 30
N+VV++ G G+GKT
Sbjct: 65 NQVVIIVGETGSGKT 79
>gnl|CDD|206642 cd00876, Ras, Rat sarcoma (Ras) family of small guanosine
triphosphatases (GTPases). The Ras family of the Ras
superfamily includes classical N-Ras, H-Ras, and K-Ras,
as well as R-Ras, Rap, Ral, Rheb, Rhes, ARHI, RERG,
Rin/Rit, RSR1, RRP22, Ras2, Ras-dva, and RGK proteins.
Ras proteins regulate cell growth, proliferation and
differentiation. Ras is activated by guanine nucleotide
exchange factors (GEFs) that release GDP and allow GTP
binding. Many RasGEFs have been identified. These are
sequestered in the cytosol until activation by growth
factors triggers recruitment to the plasma membrane or
Golgi, where the GEF colocalizes with Ras. Active
GTP-bound Ras interacts with several effector proteins:
among the best characterized are the Raf kinases,
phosphatidylinositol 3-kinase (PI3K), RalGEFs and
NORE/MST1. Most Ras proteins contain a lipid
modification site at the C-terminus, with a typical
sequence motif CaaX, where a = an aliphatic amino acid
and X = any amino acid. Lipid binding is essential for
membrane attachment, a key feature of most Ras
proteins. Due to the presence of truncated sequences in
this CD, the lipid modification site is not available
for annotation.
Length = 160
Score = 26.3 bits (59), Expect = 2.3
Identities = 7/18 (38%), Positives = 12/18 (66%), Gaps = 1/18 (5%)
Query: 17 RVVLLHGPPGTGKTSLCK 34
++V+L G G GK++L
Sbjct: 1 KLVVL-GAGGVGKSALTI 17
>gnl|CDD|213229 cd03262, ABC_HisP_GlnQ, ATP-binding cassette domain of the
histidine and glutamine transporters. HisP and GlnQ
are the ATP-binding components of the bacterial
periplasmic histidine and glutamine permeases,
respectively. Histidine permease is a multi-subunit
complex containing the HisQ and HisM integral membrane
subunits and two copies of HisP. HisP has properties
intermediate between those of integral and peripheral
membrane proteins and is accessible from both sides of
the membrane, presumably by its interaction with HisQ
and HisM. The two HisP subunits form a homodimer within
the complex. The domain structure of the amino acid
uptake systems is typical for prokaryotic extracellular
solute binding protein-dependent uptake systems. All of
the amino acid uptake systems also have at least one,
and in a few cases, two extracellular solute binding
proteins located in the periplasm of Gram-negative
bacteria, or attached to the cell membrane of
Gram-positive bacteria. The best-studied member of the
PAAT (polar amino acid transport) family is the HisJQMP
system of S. typhimurium, where HisJ is the
extracellular solute binding proteins and HisP is the
ABC protein.
Length = 213
Score = 26.7 bits (60), Expect = 2.3
Identities = 10/32 (31%), Positives = 19/32 (59%), Gaps = 5/32 (15%)
Query: 18 VVLLHGPPGTGKTSLCKAVAQKLSIRLQTPQA 49
VV++ GP G+GK++L + + L+ P +
Sbjct: 28 VVVIIGPSGSGKSTLLRCIN-----LLEEPDS 54
>gnl|CDD|215758 pfam00158, Sigma54_activat, Sigma-54 interaction domain.
Length = 168
Score = 26.6 bits (60), Expect = 2.3
Identities = 12/25 (48%), Positives = 15/25 (60%), Gaps = 1/25 (4%)
Query: 19 VLLHGPPGTGKTSLCKAVAQKLSIR 43
VL+ G GTGK +A+ Q LS R
Sbjct: 25 VLITGESGTGKELFARAIHQ-LSPR 48
>gnl|CDD|224047 COG1122, CbiO, ABC-type cobalt transport system, ATPase component
[Inorganic ion transport and metabolism].
Length = 235
Score = 26.8 bits (60), Expect = 2.3
Identities = 11/25 (44%), Positives = 15/25 (60%)
Query: 13 ISWNRVVLLHGPPGTGKTSLCKAVA 37
I VLL GP G+GK++L K +
Sbjct: 27 IEKGERVLLIGPNGSGKSTLLKLLN 51
>gnl|CDD|213207 cd03240, ABC_Rad50, ATP-binding cassette domain of Rad50. The
catalytic domains of Rad50 are similar to the
ATP-binding cassette of ABC transporters, but are not
associated with membrane-spanning domains. The
conserved ATP-binding motifs common to Rad50 and the
ABC transporter family include the Walker A and Walker
B motifs, the Q loop, a histidine residue in the switch
region, a D-loop, and a conserved LSGG sequence. This
conserved sequence, LSGG, is the most specific and
characteristic motif of this family and is thus known
as the ABC signature sequence.
Length = 204
Score = 26.4 bits (59), Expect = 2.3
Identities = 17/77 (22%), Positives = 32/77 (41%), Gaps = 4/77 (5%)
Query: 6 SKVKSNIISWNR-VVLLHGPPGTGKTSLCKAVAQKLSIRLQTPQAIFFKKYPNVLIFTTS 64
S + + I + + L+ G G GKT++ +A+ K ++ + P + LI
Sbjct: 11 SFHERSEIEFFSPLTLIVGQNGAGKTTIIEAL--KYALTGELPPNSKGGAHDPKLIREGE 68
Query: 65 NLTGAIDLAFLDRADIK 81
+ LAF + K
Sbjct: 69 VR-AQVKLAFENANGKK 84
>gnl|CDD|131580 TIGR02528, EutP, ethanolamine utilization protein, EutP. This
protein is found within operons which code for
polyhedral organelles containing the enzyme
ethanolamine ammonia lyase. The function of this gene
is unknown, although the presence of an N-terminal
GxxGxGK motif implies a GTP-binding site [Energy
metabolism, Amino acids and amines].
Length = 142
Score = 26.3 bits (58), Expect = 2.3
Identities = 11/35 (31%), Positives = 19/35 (54%), Gaps = 1/35 (2%)
Query: 19 VLLHGPPGTGKTSLCKAVAQKLSIRLQTPQAIFFK 53
++ G G GKT+L +A+ Q I + QA+ +
Sbjct: 3 IMFIGSVGCGKTTLTQAL-QGEEILYKKTQAVEYN 36
>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 = 26.7 bits (60), Expect = 2.4
Identities = 10/32 (31%), Positives = 15/32 (46%), Gaps = 6/32 (18%)
Query: 2 KFSHSKVKSNIISWNRVVLLHGPPGTGKTSLC 33
F K N + +++GPP TGK+ C
Sbjct: 254 DFLKGIPKKNCL------VIYGPPDTGKSMFC 279
>gnl|CDD|236353 PRK08939, PRK08939, primosomal protein DnaI; Reviewed.
Length = 306
Score = 26.8 bits (60), Expect = 2.4
Identities = 9/21 (42%), Positives = 14/21 (66%)
Query: 21 LHGPPGTGKTSLCKAVAQKLS 41
L+G G GK+ L A+A +L+
Sbjct: 161 LYGDFGVGKSYLLAAIANELA 181
>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 = 26.8 bits (60), Expect = 2.4
Identities = 13/31 (41%), Positives = 16/31 (51%), Gaps = 3/31 (9%)
Query: 10 SNIISWNRV---VLLHGPPGTGKTSLCKAVA 37
N I R+ L GP GTGKTS+ + A
Sbjct: 27 KNAIKNGRIAHAYLFSGPRGTGKTSIARIFA 57
>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 = 26.6 bits (59), Expect = 2.4
Identities = 11/30 (36%), Positives = 20/30 (66%), Gaps = 2/30 (6%)
Query: 14 SWNRVVLLHGPPGTGKTSLCKAVAQKLSIR 43
+ N +++ GP G+GK++L K +A +L R
Sbjct: 1 NPNMLIV--GPSGSGKSTLLKLLALRLLAR 28
>gnl|CDD|234232 TIGR03499, FlhF, flagellar biosynthetic protein FlhF. [Cellular
processes, Chemotaxis and motility].
Length = 283
Score = 26.5 bits (59), Expect = 2.5
Identities = 11/28 (39%), Positives = 16/28 (57%), Gaps = 2/28 (7%)
Query: 17 RVVLLHGPPGTGK-TSLCKAVAQKLSIR 43
V+ L GP G GK T+L K +A + +
Sbjct: 196 GVIALVGPTGVGKTTTLAK-LAARFVLE 222
>gnl|CDD|224119 COG1198, PriA, Primosomal protein N' (replication factor Y) -
superfamily II helicase [DNA replication, recombination,
and repair].
Length = 730
Score = 26.9 bits (60), Expect = 2.5
Identities = 17/52 (32%), Positives = 22/52 (42%), Gaps = 14/52 (26%)
Query: 17 RVVLLHGPPGTGKTS-LCKAVAQKL-----------SIRLQTPQAI-FFKKY 55
LL G G+GKT +A+A+ L I L TPQ + FK
Sbjct: 218 APFLLDGVTGSGKTEVYLEAIAKVLAQGKQVLVLVPEIAL-TPQLLARFKAR 268
>gnl|CDD|213210 cd03243, ABC_MutS_homologs, ATP-binding cassette domain of MutS
homologs. The MutS protein initiates DNA mismatch
repair by recognizing mispaired and unpaired bases
embedded in duplex DNA and activating endo- and
exonucleases to remove the mismatch. Members of the
MutS family also possess a conserved ATPase activity
that belongs to the ATP binding cassette (ABC)
superfamily. MutS homologs (MSH) have been identified
in most prokaryotic and all eukaryotic organisms
examined. Prokaryotes have two homologs (MutS1 and
MutS2), whereas seven MSH proteins (MSH1 to MSH7) have
been identified in eukaryotes. The homodimer MutS1 and
heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily
involved in mitotic mismatch repair, whereas MSH4-MSH5
is involved in resolution of Holliday junctions during
meiosis. All members of the MutS family contain the
highly conserved Walker A/B ATPase domain, and many
share a common mechanism of action. MutS1, MSH2-MSH3,
MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding
clamps, and recognition of specific DNA structures or
lesions results in ADP/ATP exchange.
Length = 202
Score = 26.4 bits (59), Expect = 2.5
Identities = 6/23 (26%), Positives = 14/23 (60%)
Query: 16 NRVVLLHGPPGTGKTSLCKAVAQ 38
R++L+ GP GK++ +++
Sbjct: 29 GRLLLITGPNMGGKSTYLRSIGL 51
>gnl|CDD|227118 COG4778, PhnL, ABC-type phosphonate transport system, ATPase
component [Inorganic ion transport and metabolism].
Length = 235
Score = 26.6 bits (59), Expect = 2.5
Identities = 9/16 (56%), Positives = 14/16 (87%)
Query: 19 VLLHGPPGTGKTSLCK 34
V+LHGP G+GK++L +
Sbjct: 40 VVLHGPSGSGKSTLLR 55
>gnl|CDD|203706 pfam07647, SAM_2, SAM domain (Sterile alpha motif).
Length = 66
Score = 25.3 bits (56), Expect = 2.6
Identities = 12/45 (26%), Positives = 17/45 (37%), Gaps = 2/45 (4%)
Query: 60 IFTTSNLTGAIDLAFLDRADIKQYIGFPSAAAIFNIFSSCVEELK 104
F +TG L L D+K +G S I ++ LK
Sbjct: 24 NFRDQGITGGELLLRLTEEDLKA-LGITSVGHRKKILKK-IQRLK 66
>gnl|CDD|224337 COG1419, FlhF, Flagellar GTP-binding protein [Cell motility and
secretion].
Length = 407
Score = 26.5 bits (59), Expect = 2.7
Identities = 20/61 (32%), Positives = 29/61 (47%), Gaps = 11/61 (18%)
Query: 6 SKVKSNIISWNRVVLLHGPPGTGK-TSLCKAVAQKLSIRLQTPQAIFFKKYPNVLIFTTS 64
S +++ I+ RV+ L GP G GK T+L K A+ + + KK V I TT
Sbjct: 193 SLIENLIVEQKRVIALVGPTGVGKTTTLAKLAARYVML----------KKKKKVAIITTD 242
Query: 65 N 65
Sbjct: 243 T 243
>gnl|CDD|136670 PRK08181, PRK08181, transposase; Validated.
Length = 269
Score = 26.4 bits (58), Expect = 2.9
Identities = 11/22 (50%), Positives = 14/22 (63%)
Query: 19 VLLHGPPGTGKTSLCKAVAQKL 40
+LL GPPG GK+ L A+ L
Sbjct: 109 LLLFGPPGGGKSHLAAAIGLAL 130
>gnl|CDD|163057 TIGR02881, spore_V_K, stage V sporulation protein K. Members of
this protein family are the stage V sporulation protein
K (SpoVK), a close homolog of the Rubisco expression
protein CbbX (TIGR02880) and a members of the ATPase
family associated with various cellular activities
(pfam00004). Members are strictly limited to bacterial
endospore-forming species, but are not universal in
this group and are missing from the Clostridium group
[Cellular processes, Sporulation and germination].
Length = 261
Score = 26.2 bits (58), Expect = 3.0
Identities = 9/38 (23%), Positives = 20/38 (52%), Gaps = 2/38 (5%)
Query: 1 MKFSHSKVKSNIISWNRVVLLHGPPGTGKTSLCKAVAQ 38
K +K++ + ++ G PGTGKT++ + + +
Sbjct: 29 EKRKEEGLKTSKQVLH--MIFKGNPGTGKTTVARILGK 64
>gnl|CDD|226054 COG3523, IcmF, Type VI protein secretion system component VasK
[Intracellular trafficking, secretion, and vesicular
transport].
Length = 1188
Score = 26.6 bits (59), Expect = 3.0
Identities = 9/18 (50%), Positives = 12/18 (66%), Gaps = 3/18 (16%)
Query: 15 WNRVVLLHGPPGTGKTSL 32
W V+ GPPG+GKT+
Sbjct: 127 WYMVI---GPPGSGKTTA 141
>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication,
recombination, and repair].
Length = 908
Score = 26.6 bits (59), Expect = 3.0
Identities = 8/29 (27%), Positives = 15/29 (51%)
Query: 4 SHSKVKSNIISWNRVVLLHGPPGTGKTSL 32
S + + + + L+ GP G GK+S+
Sbjct: 13 SFKDIDIEKLFDSGIFLIVGPNGAGKSSI 41
>gnl|CDD|183088 PRK11331, PRK11331, 5-methylcytosine-specific restriction enzyme
subunit McrB; Provisional.
Length = 459
Score = 26.6 bits (58), Expect = 3.1
Identities = 12/32 (37%), Positives = 20/32 (62%), Gaps = 1/32 (3%)
Query: 19 VLLHGPPGTGKTSLCKAVAQKLSIRLQTPQAI 50
++L GPPG GKT + + +A L+ + PQ +
Sbjct: 197 IILQGPPGVGKTFVARRLAYLLTGE-KAPQRV 227
>gnl|CDD|232966 TIGR00416, sms, DNA repair protein RadA. The gene protuct codes
for a probable ATP-dependent protease involved in both
DNA repair and degradation of proteins, peptides,
glycopeptides. Also known as sms. Residues 11-28 of the
SEED alignment contain a putative Zn binding domain.
Residues 110-117 of the seed contain a putative ATP
binding site both documented in Haemophilus and in
Listeria monocytogenes. for E.coli see ( J. BACTERIOL.
178:5045-5048(1996)) [DNA metabolism, DNA replication,
recombination, and repair].
Length = 454
Score = 26.3 bits (58), Expect = 3.1
Identities = 10/28 (35%), Positives = 16/28 (57%)
Query: 19 VLLHGPPGTGKTSLCKAVAQKLSIRLQT 46
+L+ G PG GK++L VA +L+
Sbjct: 97 ILIGGDPGIGKSTLLLQVACQLAKNQMK 124
>gnl|CDD|225461 COG2909, MalT, ATP-dependent transcriptional regulator
[Transcription].
Length = 894
Score = 26.6 bits (59), Expect = 3.1
Identities = 8/24 (33%), Positives = 13/24 (54%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQKL 40
R++L+ P G GKT+L +
Sbjct: 38 RLILISAPAGFGKTTLLAQWRELA 61
>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 = 26.2 bits (58), Expect = 3.1
Identities = 10/33 (30%), Positives = 15/33 (45%)
Query: 19 VLLHGPPGTGKTSLCKAVAQKLSIRLQTPQAIF 51
VL+ G GTGK + + + R + P F
Sbjct: 104 VLIIGETGTGKELFARLIHALSARRAEAPFIAF 136
>gnl|CDD|235570 PRK05703, flhF, flagellar biosynthesis regulator FlhF; Validated.
Length = 424
Score = 26.4 bits (59), Expect = 3.2
Identities = 10/22 (45%), Positives = 12/22 (54%)
Query: 9 KSNIISWNRVVLLHGPPGTGKT 30
+I+ VV L GP G GKT
Sbjct: 214 VEDILKQGGVVALVGPTGVGKT 235
>gnl|CDD|226952 COG4586, COG4586, ABC-type uncharacterized transport system,
ATPase component [General function prediction only].
Length = 325
Score = 26.2 bits (58), Expect = 3.2
Identities = 7/22 (31%), Positives = 10/22 (45%)
Query: 13 ISWNRVVLLHGPPGTGKTSLCK 34
I +V G G GK++ K
Sbjct: 47 IPKGEIVGFLGANGAGKSTTLK 68
>gnl|CDD|140006 PRK13949, PRK13949, shikimate kinase; Provisional.
Length = 169
Score = 26.2 bits (58), Expect = 3.2
Identities = 11/25 (44%), Positives = 17/25 (68%)
Query: 19 VLLHGPPGTGKTSLCKAVAQKLSIR 43
+ L G G GKT+L KA+A++L +
Sbjct: 4 IFLVGYMGAGKTTLGKALARELGLS 28
>gnl|CDD|233821 TIGR02322, phosphon_PhnN, phosphonate metabolism
protein/1,5-bisphosphokinase (PRPP-forming) PhnN.
Members of this family resemble PhnN of phosphonate
utilization operons, where different such operons
confer the ability to use somewhat different profiles
of C-P bond-containing compounds (see PMID:15231805),
including phosphites as well as phosphonates. PhnN in
E. coli shows considerable homology to guanylate
kinases (EC 2.7.4.8), and has actually been shown to
act as a ribose 1,5-bisphosphokinase (PRPP forming).
This suggests an analogous kinase reaction for
phosphonate metabolism, converting
5-phosphoalpha-1-(methylphosphono)ribose to
methylphosphono-PRPP [Central intermediary metabolism,
Phosphorus compounds].
Length = 179
Score = 26.2 bits (58), Expect = 3.2
Identities = 8/25 (32%), Positives = 14/25 (56%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQKLS 41
R++ + GP G GK +L +L+
Sbjct: 2 RLIYVVGPSGAGKDTLLDYARARLA 26
>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 = 26.3 bits (58), Expect = 3.2
Identities = 9/18 (50%), Positives = 14/18 (77%)
Query: 19 VLLHGPPGTGKTSLCKAV 36
V+++GPPG GKT+ + V
Sbjct: 89 VIIYGPPGVGKTAAARLV 106
>gnl|CDD|225363 COG2804, PulE, Type II secretory pathway, ATPase PulE/Tfp pilus
assembly pathway, ATPase PilB [Cell motility and
secretion / Intracellular trafficking and secretion].
Length = 500
Score = 26.5 bits (59), Expect = 3.2
Identities = 9/22 (40%), Positives = 14/22 (63%)
Query: 19 VLLHGPPGTGKTSLCKAVAQKL 40
+L+ GP G+GKT+ A +L
Sbjct: 261 ILVTGPTGSGKTTTLYAALSEL 282
>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 = 26.2 bits (58), Expect = 3.3
Identities = 9/33 (27%), Positives = 14/33 (42%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQKLSIRLQTPQA 49
V++ G +GKTSL + + T Q
Sbjct: 4 PAVIIAGLCDSGKTSLFTLLTTGTVKKTVTSQE 36
>gnl|CDD|235153 PRK03731, aroL, shikimate kinase II; Reviewed.
Length = 171
Score = 26.1 bits (58), Expect = 3.3
Identities = 10/21 (47%), Positives = 13/21 (61%)
Query: 23 GPPGTGKTSLCKAVAQKLSIR 43
G G GKT++ A+AQ L R
Sbjct: 9 GARGCGKTTVGMALAQALGYR 29
>gnl|CDD|226426 COG3911, COG3911, Predicted ATPase [General function prediction
only].
Length = 183
Score = 26.0 bits (57), Expect = 3.3
Identities = 10/23 (43%), Positives = 15/23 (65%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQK 39
+ +L G PG GKT+L A+A+
Sbjct: 10 KRFILTGGPGAGKTTLLAALARA 32
>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 = 26.0 bits (58), Expect = 3.3
Identities = 7/11 (63%), Positives = 8/11 (72%)
Query: 23 GPPGTGKTSLC 33
G G+GKT LC
Sbjct: 26 GEFGSGKTQLC 36
>gnl|CDD|110723 pfam01745, IPT, Isopentenyl transferase. Isopentenyl transferase
/ dimethylallyl transferase synthesises
isopentenyladensosine 5'-monophosphate, a cytokinin
that induces shoot formation on host plants infected
with the Ti plasmid.
Length = 232
Score = 26.2 bits (58), Expect = 3.4
Identities = 8/22 (36%), Positives = 13/22 (59%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQ 38
+ L+ G TGKT+ A+A+
Sbjct: 2 GLYLIWGATCTGKTAEAIALAK 23
>gnl|CDD|225713 COG3172, NadR, Predicted ATPase/kinase involved in NAD metabolism
[Coenzyme metabolism].
Length = 187
Score = 26.3 bits (58), Expect = 3.4
Identities = 9/33 (27%), Positives = 15/33 (45%), Gaps = 4/33 (12%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQKLSIRLQTPQA 49
+ V + G +GK++L KL+ T A
Sbjct: 9 KTVAILGGESSGKSTL----VNKLANIFNTTSA 37
>gnl|CDD|206743 cd11383, YfjP, YfjP GTPase. The Era (E. coli Ras-like
protein)-like YfjP subfamily includes several
uncharacterized bacterial GTPases that are similar to
Era. They generally show sequence conservation in the
region between the Walker A and B motifs (G1 and G3 box
motifs), to the exclusion of other GTPases. Era is
characterized by a distinct derivative of the KH domain
(the pseudo-KH domain) which is located C-terminal to
the GTPase domain.
Length = 140
Score = 25.8 bits (57), Expect = 3.5
Identities = 9/19 (47%), Positives = 11/19 (57%)
Query: 20 LLHGPPGTGKTSLCKAVAQ 38
L G G GK+SLC A+
Sbjct: 1 GLMGKTGAGKSSLCNALFG 19
>gnl|CDD|180424 PRK06144, PRK06144, enoyl-CoA hydratase; Provisional.
Length = 262
Score = 26.1 bits (58), Expect = 3.5
Identities = 16/59 (27%), Positives = 24/59 (40%), Gaps = 19/59 (32%)
Query: 31 SLCKAVAQKLSIRLQTPQAIFFKKYPNVLIFTTSNLTGAIDLAFLDRADIKQYIGFPSA 89
+C+A+A SIR ++ GA D AF+ DI Q+ F +A
Sbjct: 42 EICEAIAADPSIR--------------AVVLR-----GAGDKAFVAGTDIAQFRAFSTA 81
>gnl|CDD|206648 cd00882, Ras_like_GTPase, Rat sarcoma (Ras)-like superfamily of
small guanosine triphosphatases (GTPases). Ras-like
GTPase superfamily. The Ras-like superfamily of small
GTPases consists of several families with an extremely
high degree of structural and functional similarity.
The Ras superfamily is divided into at least four
families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf
families. This superfamily also includes proteins like
the GTP translation factors, Era-like GTPases, and
G-alpha chain of the heterotrimeric G proteins. Members
of the Ras superfamily regulate a wide variety of
cellular functions: the Ras family regulates gene
expression, the Rho family regulates cytoskeletal
reorganization and gene expression, the Rab and
Sar1/Arf families regulate vesicle trafficking, and the
Ran family regulates nucleocytoplasmic transport and
microtubule organization. The GTP translation factor
family regulates initiation, elongation, termination,
and release in translation, and the Era-like GTPase
family regulates cell division, sporulation, and DNA
replication. Members of the Ras superfamily are
identified by the GTP binding site, which is made up of
five characteristic sequence motifs, and the switch I
and switch II regions.
Length = 161
Score = 25.9 bits (57), Expect = 3.5
Identities = 7/17 (41%), Positives = 9/17 (52%)
Query: 23 GPPGTGKTSLCKAVAQK 39
G G GK+SL A+
Sbjct: 4 GRGGVGKSSLLNALLGG 20
>gnl|CDD|225822 COG3284, AcoR, Transcriptional activator of acetoin/glycerol
metabolism [Secondary metabolites biosynthesis,
transport, and catabolism / Transcription].
Length = 606
Score = 26.2 bits (58), Expect = 3.5
Identities = 11/20 (55%), Positives = 13/20 (65%)
Query: 19 VLLHGPPGTGKTSLCKAVAQ 38
VLL G GTGK L +A+ Q
Sbjct: 339 VLLQGETGTGKEVLARAIHQ 358
>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 = 26.0 bits (58), Expect = 3.5
Identities = 9/32 (28%), Positives = 16/32 (50%)
Query: 10 SNIISWNRVVLLHGPPGTGKTSLCKAVAQKLS 41
S + + GP G GK++L A+A + +
Sbjct: 29 SGKAKPGELTAIMGPSGAGKSTLLNALAGRRT 60
>gnl|CDD|181214 PRK08058, PRK08058, DNA polymerase III subunit delta'; Validated.
Length = 329
Score = 26.0 bits (58), Expect = 3.6
Identities = 15/38 (39%), Positives = 18/38 (47%), Gaps = 7/38 (18%)
Query: 10 SNIISWNRVV---LLHGPPGTGKTSLCKAVAQKLSIRL 44
N I+ NR+ L G GTGK KA A L+ L
Sbjct: 19 QNSIAKNRLSHAYLFEGAKGTGK----KATALWLAKSL 52
>gnl|CDD|188534 TIGR04019, B_thiol_YtxJ, bacillithiol system protein YtxJ.
Members of this protein family, including YtxJ from
Bacillus subtilis, occur in species that encode
proteins for synthesizing bacillithiol. The protein is
described as thioredoxin-like, while another
bacillithiol-associated protein, YpdA (TIGR04018), is
described as thioredoxin reductase-like [Unknown
function, Enzymes of unknown specificity].
Length = 105
Score = 25.6 bits (57), Expect = 3.6
Identities = 5/19 (26%), Positives = 11/19 (57%)
Query: 35 AVAQKLSIRLQTPQAIFFK 53
+A+ ++ ++PQ I K
Sbjct: 67 EIAETFGVKHESPQVIVIK 85
>gnl|CDD|131377 TIGR02324, CP_lyasePhnL, phosphonate C-P lyase system protein
PhnL. Members of this family are the PhnL protein of
C-P lyase systems for utilization of phosphonates.
These systems resemble phosphonatase-based systems in
having a three component ABC transporter, where
TIGR01097 is the permease, TIGR01098 is the
phosphonates binding protein, and TIGR02315 is the
ATP-binding cassette (ABC) protein. They differ,
however, in having, typically, ten or more additional
genes, many of which are believed to form a
membrane-associated C-P lysase complex. This protein
(PhnL) and the adjacent-encoded PhnK (TIGR02323)
resemble transporter ATP-binding proteins but are
suggested, based on mutatgenesis studies, to be part of
this C-P lyase complex rather than part of a
transporter per se.
Length = 224
Score = 26.2 bits (58), Expect = 3.7
Identities = 9/18 (50%), Positives = 13/18 (72%)
Query: 19 VLLHGPPGTGKTSLCKAV 36
V L GP G GK++L K++
Sbjct: 37 VALSGPSGAGKSTLLKSL 54
>gnl|CDD|220938 pfam11009, DUF2847, Protein of unknown function (DUF2847). Some
members in this bacterial family of proteins with
unknown function are annotated as YtxJ, a putative
general stress protein. This cannot be confirmed.
Length = 104
Score = 25.6 bits (57), Expect = 3.7
Identities = 6/19 (31%), Positives = 12/19 (63%)
Query: 35 AVAQKLSIRLQTPQAIFFK 53
+A+K ++ ++PQ I K
Sbjct: 67 EIAEKFGVKHESPQVIVIK 85
>gnl|CDD|223203 COG0125, Tmk, Thymidylate kinase [Nucleotide transport and
metabolism].
Length = 208
Score = 26.1 bits (58), Expect = 3.8
Identities = 6/18 (33%), Positives = 11/18 (61%)
Query: 23 GPPGTGKTSLCKAVAQKL 40
G G GKT+ + + ++L
Sbjct: 10 GIDGAGKTTQAELLKERL 27
>gnl|CDD|217066 pfam02492, cobW, CobW/HypB/UreG, nucleotide-binding domain. This
domain is found in HypB, a hydrogenase expression /
formation protein, and UreG a urease accessory protein.
Both these proteins contain a P-loop nucleotide binding
motif. HypB has GTPase activity and is a guanine
nucleotide binding protein. It is not known whether
UreG binds GTP or some other nucleotide. Both enzymes
are involved in nickel binding. HypB can store nickel
and is required for nickel dependent hydrogenase
expression. UreG is required for functional
incorporation of the urease nickel metallocenter. GTP
hydrolysis may required by these proteins for nickel
incorporation into other nickel proteins. This family
of domains also contains P47K, a Pseudomonas
chlororaphis protein needed for nitrile hydratase
expression, and the cobW gene product, which may be
involved in cobalamin biosynthesis in Pseudomonas
denitrificans.
Length = 178
Score = 26.0 bits (58), Expect = 3.8
Identities = 8/15 (53%), Positives = 11/15 (73%)
Query: 18 VVLLHGPPGTGKTSL 32
V +L G G+GKT+L
Sbjct: 2 VTVLTGFLGSGKTTL 16
>gnl|CDD|224054 COG1131, CcmA, ABC-type multidrug transport system, ATPase
component [Defense mechanisms].
Length = 293
Score = 26.1 bits (58), Expect = 3.9
Identities = 11/26 (42%), Positives = 14/26 (53%)
Query: 16 NRVVLLHGPPGTGKTSLCKAVAQKLS 41
+ L GP G GKT+L K +A L
Sbjct: 31 GEIFGLLGPNGAGKTTLLKILAGLLK 56
>gnl|CDD|181906 PRK09493, glnQ, glutamine ABC transporter ATP-binding protein;
Reviewed.
Length = 240
Score = 25.8 bits (57), Expect = 4.0
Identities = 13/34 (38%), Positives = 20/34 (58%), Gaps = 3/34 (8%)
Query: 2 KFSHSKVKSNI---ISWNRVVLLHGPPGTGKTSL 32
F ++V NI I VV++ GP G+GK++L
Sbjct: 10 HFGPTQVLHNIDLNIDQGEVVVIIGPSGSGKSTL 43
>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 = 25.7 bits (57), Expect = 4.0
Identities = 9/16 (56%), Positives = 11/16 (68%)
Query: 17 RVVLLHGPPGTGKTSL 32
VLL GP +GKT+L
Sbjct: 1 PTVLLLGPSDSGKTAL 16
>gnl|CDD|215947 pfam00493, MCM, MCM2/3/5 family.
Length = 327
Score = 26.0 bits (58), Expect = 4.1
Identities = 12/20 (60%), Positives = 14/20 (70%)
Query: 19 VLLHGPPGTGKTSLCKAVAQ 38
VLL G PGT K+ L K VA+
Sbjct: 60 VLLVGDPGTAKSQLLKYVAK 79
>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 = 25.9 bits (58), Expect = 4.2
Identities = 8/19 (42%), Positives = 11/19 (57%)
Query: 19 VLLHGPPGTGKTSLCKAVA 37
+ + G GTGKT L +A
Sbjct: 18 IGIFGGSGTGKTVLLGMIA 36
>gnl|CDD|235505 PRK05563, PRK05563, DNA polymerase III subunits gamma and tau;
Validated.
Length = 559
Score = 26.0 bits (58), Expect = 4.2
Identities = 11/18 (61%), Positives = 11/18 (61%), Gaps = 4/18 (22%)
Query: 23 GPPGTGKTS----LCKAV 36
GP GTGKTS KAV
Sbjct: 45 GPRGTGKTSAAKIFAKAV 62
>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 = 26.0 bits (58), Expect = 4.2
Identities = 8/22 (36%), Positives = 12/22 (54%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQ 38
R + L G G+GK+ L +A
Sbjct: 39 RFLYLWGESGSGKSHLLQAACA 60
>gnl|CDD|221968 pfam13189, Cytidylate_kin2, Cytidylate kinase-like family. This
family includes enzymes related to cytidylate kinase.
Length = 176
Score = 25.6 bits (57), Expect = 4.2
Identities = 7/20 (35%), Positives = 11/20 (55%)
Query: 25 PGTGKTSLCKAVAQKLSIRL 44
G+G + K +A+KL I
Sbjct: 8 FGSGGREIGKKLAEKLGIPY 27
>gnl|CDD|238026 cd00071, GMPK, Guanosine monophosphate kinase (GMPK, EC 2.7.4.8),
also known as guanylate kinase (GKase), catalyzes the
reversible phosphoryl transfer from adenosine
triphosphate (ATP) to guanosine monophosphate (GMP) to
yield adenosine diphosphate (ADP) and guanosine
diphosphate (GDP). It plays an essential role in the
biosynthesis of guanosine triphosphate (GTP). This
enzyme is also important for the activation of some
antiviral and anticancer agents, such as acyclovir,
ganciclovir, carbovir, and thiopurines.
Length = 137
Score = 25.6 bits (57), Expect = 4.3
Identities = 8/19 (42%), Positives = 14/19 (73%)
Query: 18 VVLLHGPPGTGKTSLCKAV 36
+++L GP G GK++L K +
Sbjct: 1 LIVLSGPSGVGKSTLLKRL 19
>gnl|CDD|129208 TIGR00101, ureG, urease accessory protein UreG. This model
represents UreG, a GTP hydrolase that acts in the
assembly of the nickel metallocenter of urease. It is
found only in urease-positive species, although some
urease-positive species (e.g. Bacillus subtilis) lack
this protein. A similar protein, hypB, is an accessory
protein for expression of hydrogenase, which also uses
nickel [Central intermediary metabolism, Nitrogen
metabolism].
Length = 199
Score = 26.0 bits (57), Expect = 4.3
Identities = 11/28 (39%), Positives = 17/28 (60%), Gaps = 4/28 (14%)
Query: 23 GPPGTGKTS----LCKAVAQKLSIRLQT 46
GP G+GKT+ L +A+ QK + + T
Sbjct: 8 GPVGSGKTALIEALTRALRQKYQLAVIT 35
>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 = 25.7 bits (57), Expect = 4.6
Identities = 8/20 (40%), Positives = 14/20 (70%)
Query: 18 VVLLHGPPGTGKTSLCKAVA 37
+ + GP G+GK++L K +A
Sbjct: 28 IHAIMGPNGSGKSTLSKTIA 47
>gnl|CDD|182331 PRK10247, PRK10247, putative ABC transporter ATP-binding protein
YbbL; Provisional.
Length = 225
Score = 25.8 bits (57), Expect = 4.7
Identities = 11/22 (50%), Positives = 15/22 (68%)
Query: 20 LLHGPPGTGKTSLCKAVAQKLS 41
L+ GP G GK++L K VA +S
Sbjct: 37 LITGPSGCGKSTLLKIVASLIS 58
>gnl|CDD|178346 PLN02745, PLN02745, Putative pectinesterase/pectinesterase
inhibitor.
Length = 596
Score = 26.0 bits (57), Expect = 4.9
Identities = 19/56 (33%), Positives = 28/56 (50%), Gaps = 11/56 (19%)
Query: 38 QKLSIRLQTPQAIF----FKKYPNVLIFTTSN-------LTGAIDLAFLDRADIKQ 82
Q ++IR+Q+ ++IF F+ Y + L T +TG ID F D A I Q
Sbjct: 391 QAVAIRVQSDRSIFLNCRFEGYQDTLYAQTHRQFYRSCVITGTIDFIFGDAAAIFQ 446
>gnl|CDD|216584 pfam01580, FtsK_SpoIIIE, FtsK/SpoIIIE family. FtsK has extensive
sequence similarity to wide variety of proteins from
prokaryotes and plasmids, termed the FtsK/SpoIIIE
family. This domain contains a putative ATP binding
P-loop motif. It is found in the FtsK cell division
protein from E. coli and the stage III sporulation
protein E SpoIIIE, which has roles in regulation of
prespore specific gene expression in B. subtilis. A
mutation in FtsK causes a temperature sensitive block in
cell division and it is involved in peptidoglycan
synthesis or modification. The SpoIIIE protein is
implicated in intercellular chromosomal DNA transfer.
Length = 201
Score = 25.8 bits (57), Expect = 4.9
Identities = 14/88 (15%), Positives = 29/88 (32%), Gaps = 11/88 (12%)
Query: 18 VVLLHGPPGTGKTSLCKAVAQKLSIRLQTPQAIFFKKYPNVLIFTTSNLTGAIDLAFLDR 77
+L+ G G+GK++ + L+ R + + ++ L DL L
Sbjct: 40 HLLIAGATGSGKSTFLNTLILSLAARHSPEEVRLY-----LIDPKGGELAALEDLPHLLS 94
Query: 78 ADIKQYIGFPSAAAIFNIFSSCVEELKR 105
+ + V E++R
Sbjct: 95 PVATD------PEDALSALRALVAEMER 116
>gnl|CDD|234608 PRK00064, recF, recombination protein F; Reviewed.
Length = 361
Score = 25.9 bits (58), Expect = 5.0
Identities = 9/21 (42%), Positives = 13/21 (61%)
Query: 16 NRVVLLHGPPGTGKTSLCKAV 36
V +L G G GKT+L +A+
Sbjct: 23 PGVNVLVGENGQGKTNLLEAI 43
>gnl|CDD|237869 PRK14962, PRK14962, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 472
Score = 25.9 bits (57), Expect = 5.1
Identities = 9/18 (50%), Positives = 14/18 (77%)
Query: 23 GPPGTGKTSLCKAVAQKL 40
GP GTGKT++ + +A+ L
Sbjct: 43 GPRGTGKTTVARILAKSL 60
>gnl|CDD|232941 TIGR00362, DnaA, chromosomal replication initiator protein DnaA.
DnaA is involved in DNA biosynthesis; initiation of
chromosome replication and can also be transcription
regulator. The C-terminal of the family hits the pfam
bacterial DnaA (bac_dnaA) domain family. For a review,
see Kaguni (2006) [DNA metabolism, DNA replication,
recombination, and repair].
Length = 405
Score = 25.6 bits (57), Expect = 5.1
Identities = 7/19 (36%), Positives = 11/19 (57%)
Query: 19 VLLHGPPGTGKTSLCKAVA 37
+ ++G G GKT L A+
Sbjct: 139 LFIYGGVGLGKTHLLHAIG 157
>gnl|CDD|218709 pfam05707, Zot, Zonular occludens toxin (Zot). This family
consists of bacterial and viral proteins which are very
similar to the Zonular occludens toxin (Zot). Zot is
elaborated by bacteriophages present in toxigenic
strains of Vibrio cholerae. Zot is a single polypeptide
chain of 44.8 kDa, with the ability to reversibly alter
intestinal epithelial tight junctions, allowing the
passage of macromolecules through mucosal barriers.
Length = 183
Score = 25.4 bits (56), Expect = 5.1
Identities = 7/14 (50%), Positives = 10/14 (71%)
Query: 18 VVLLHGPPGTGKTS 31
+ L+ G PG+GKT
Sbjct: 2 IYLITGKPGSGKTL 15
>gnl|CDD|226415 COG3899, COG3899, Predicted ATPase [General function prediction
only].
Length = 849
Score = 25.8 bits (57), Expect = 5.5
Identities = 9/22 (40%), Positives = 13/22 (59%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQ 38
VVL+ G G GK++L V +
Sbjct: 25 EVVLVAGESGIGKSALVNEVHK 46
>gnl|CDD|215832 pfam00270, DEAD, DEAD/DEAH box helicase. Members of this family
include the DEAD and DEAH box helicases. Helicases are
involved in unwinding nucleic acids. The DEAD box
helicases are involved in various aspects of RNA
metabolism, including nuclear transcription, pre mRNA
splicing, ribosome biogenesis, nucleocytoplasmic
transport, translation, RNA decay and organellar gene
expression.
Length = 169
Score = 25.3 bits (56), Expect = 5.5
Identities = 12/34 (35%), Positives = 18/34 (52%), Gaps = 1/34 (2%)
Query: 19 VLLHGPPGTGKT-SLCKAVAQKLSIRLQTPQAIF 51
VL+ P G+GKT + + Q L + PQA+
Sbjct: 17 VLVQAPTGSGKTLAFLLPILQALLPKKGGPQALV 50
>gnl|CDD|220758 pfam10443, RNA12, RNA12 protein. This family includes RNA12 from
S. cerevisiae. That protein contains an RRM domain.
This region is C-terminal to that and includes a P-loop
motif suggesting this region binds to NTP. The RNA12
proteins is involved in pre-rRNA maturation.
Length = 428
Score = 25.7 bits (57), Expect = 5.5
Identities = 7/17 (41%), Positives = 11/17 (64%)
Query: 16 NRVVLLHGPPGTGKTSL 32
N +++ GP G+GK L
Sbjct: 17 NTFIVVQGPRGSGKREL 33
>gnl|CDD|238550 cd01130, VirB11-like_ATPase, Type IV secretory pathway component
VirB11, and related ATPases. The homohexamer, VirB11 is
one of eleven Vir proteins, which are required for
T-pilus biogenesis and virulence in the transfer of
T-DNA from the Ti (tumor-inducing) plasmid of bacterial
to plant cells. The pilus is a fibrous cell surface
organelle, which mediates adhesion between bacteria
during conjugative transfer or between bacteria and
host eukaryotic cells during infection. VirB11- related
ATPases include the archaeal flagella biosynthesis
protein and the pilus assembly proteins CpaF/TadA and
TrbB. This alignment contains the C-terminal domain,
which is the ATPase.
Length = 186
Score = 25.3 bits (56), Expect = 5.6
Identities = 8/22 (36%), Positives = 14/22 (63%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQ 38
+ +L+ G G+GKT+L A+
Sbjct: 26 KNILISGGTGSGKTTLLNALLA 47
>gnl|CDD|169652 PRK09087, PRK09087, hypothetical protein; Validated.
Length = 226
Score = 25.4 bits (56), Expect = 5.6
Identities = 11/22 (50%), Positives = 14/22 (63%)
Query: 18 VVLLHGPPGTGKTSLCKAVAQK 39
VV+L GP G+GKT L +K
Sbjct: 46 VVVLAGPVGSGKTHLASIWREK 67
>gnl|CDD|216243 pfam01012, ETF, Electron transfer flavoprotein domain. This family
includes the homologous domain shared between the alpha
and beta subunits of the electron transfer flavoprotein.
Length = 160
Score = 25.2 bits (56), Expect = 5.7
Identities = 8/23 (34%), Positives = 12/23 (52%)
Query: 27 TGKTSLCKAVAQKLSIRLQTPQA 49
G TS+ K +A +L+ L P
Sbjct: 93 AGATSIGKDLAPRLAALLGAPLI 115
>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 = 25.5 bits (57), Expect = 5.8
Identities = 8/19 (42%), Positives = 14/19 (73%)
Query: 19 VLLHGPPGTGKTSLCKAVA 37
VL+ GP G+GK++L + +
Sbjct: 30 VLIVGPNGSGKSTLLRLLN 48
>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 = 25.4 bits (56), Expect = 5.9
Identities = 10/25 (40%), Positives = 14/25 (56%)
Query: 13 ISWNRVVLLHGPPGTGKTSLCKAVA 37
+ V L GP G GKT+L + +A
Sbjct: 27 VKKGEFVCLLGPSGCGKTTLLRIIA 51
>gnl|CDD|218788 pfam05872, DUF853, Bacterial protein of unknown function
(DUF853). This family consists of several bacterial
proteins of unknown function. BMEI1370 is thought to be
an ATPase.
Length = 504
Score = 25.4 bits (56), Expect = 5.9
Identities = 11/26 (42%), Positives = 15/26 (57%)
Query: 16 NRVVLLHGPPGTGKTSLCKAVAQKLS 41
NR L+ G GTGKT + +A+ S
Sbjct: 21 NRHGLIAGATGTGKTVTLQVLAESFS 46
>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 = 5.9
Identities = 8/25 (32%), Positives = 14/25 (56%)
Query: 13 ISWNRVVLLHGPPGTGKTSLCKAVA 37
+ V + G G+GKT+L + +A
Sbjct: 20 LPGQGVTAIFGRSGSGKTTLIRLIA 44
>gnl|CDD|183482 PRK12377, PRK12377, putative replication protein; Provisional.
Length = 248
Score = 25.6 bits (56), Expect = 5.9
Identities = 12/48 (25%), Positives = 20/48 (41%), Gaps = 11/48 (22%)
Query: 23 GPPGTGKTSLCKAVAQKLSIRLQTPQAIFFKKYPNVLIFTTSNLTGAI 70
G PGTGK L A+ +L K +V++ T ++ +
Sbjct: 108 GKPGTGKNHLAAAIGNRL-----------LAKGRSVIVVTVPDVMSRL 144
>gnl|CDD|223487 COG0410, LivF, ABC-type branched-chain amino acid transport
systems, ATPase component [Amino acid transport and
metabolism].
Length = 237
Score = 25.5 bits (57), Expect = 5.9
Identities = 9/20 (45%), Positives = 12/20 (60%)
Query: 18 VVLLHGPPGTGKTSLCKAVA 37
+V L G G GKT+L K +
Sbjct: 31 IVALLGRNGAGKTTLLKTIM 50
>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 = 25.5 bits (56), Expect = 5.9
Identities = 10/16 (62%), Positives = 12/16 (75%)
Query: 19 VLLHGPPGTGKTSLCK 34
L++G PGTGKTS K
Sbjct: 15 YLIYGKPGTGKTSTIK 30
>gnl|CDD|233080 TIGR00665, DnaB, replicative DNA helicase. This model describes
the helicase DnaB, a homohexameric protein required for
DNA replication. The homohexamer can form a ring around
a single strand of DNA near a replication fork. An
intein of > 400 residues is found at a conserved
location in DnaB of Synechocystis PCC6803, Rhodothermus
marinus (both experimentally confirmed), and
Mycobacterium tuberculosis. The intein removes itself by
a self-splicing reaction. The seed alignment contains
inteins so that the model built from the seed alignment
will model a low cost at common intein insertion sites
[DNA metabolism, DNA replication, recombination, and
repair].
Length = 434
Score = 25.5 bits (57), Expect = 6.0
Identities = 9/27 (33%), Positives = 14/27 (51%)
Query: 25 PGTGKTSLCKAVAQKLSIRLQTPQAIF 51
P GKT+ +A+ +I+ P A F
Sbjct: 204 PSMGKTAFALNIAENAAIKEGKPVAFF 230
>gnl|CDD|226628 COG4148, ModC, ABC-type molybdate transport system, ATPase
component [Inorganic ion transport and metabolism].
Length = 352
Score = 25.4 bits (56), Expect = 6.0
Identities = 10/22 (45%), Positives = 13/22 (59%)
Query: 16 NRVVLLHGPPGTGKTSLCKAVA 37
+ L GP G+GKTSL +A
Sbjct: 24 RGITALFGPSGSGKTSLINMIA 45
>gnl|CDD|223544 COG0468, RecA, RecA/RadA recombinase [DNA replication,
recombination, and repair].
Length = 279
Score = 25.3 bits (56), Expect = 6.0
Identities = 7/17 (41%), Positives = 12/17 (70%)
Query: 17 RVVLLHGPPGTGKTSLC 33
R+ ++GP +GKT+L
Sbjct: 61 RITEIYGPESSGKTTLA 77
>gnl|CDD|236648 PRK10078, PRK10078, ribose 1,5-bisphosphokinase; Provisional.
Length = 186
Score = 25.5 bits (56), Expect = 6.1
Identities = 11/28 (39%), Positives = 18/28 (64%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQKLSIRL 44
+++ L GP G+GK SL A+ Q+ +L
Sbjct: 3 KLIWLMGPSGSGKDSLLAALRQREQTQL 30
>gnl|CDD|238541 cd01121, Sms, Sms (bacterial radA) DNA repair protein. This protein
is not related to archael radA any more than is to other
RecA-like NTPases. Sms has a role in recombination and
recombinational repair and is responsible for the
stabilization or processing of branched DNA molecules.
Length = 372
Score = 25.7 bits (57), Expect = 6.2
Identities = 13/48 (27%), Positives = 23/48 (47%), Gaps = 10/48 (20%)
Query: 4 SHSKVKSNIISWNRV----------VLLHGPPGTGKTSLCKAVAQKLS 41
++ + I +RV +L+ G PG GK++L VA +L+
Sbjct: 60 EEERIPTGIEELDRVLGGGLVPGSVILIGGDPGIGKSTLLLQVAARLA 107
>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 = 25.2 bits (56), Expect = 6.2
Identities = 9/22 (40%), Positives = 13/22 (59%)
Query: 16 NRVVLLHGPPGTGKTSLCKAVA 37
V L GP G+GK++L K +
Sbjct: 26 GEVHALMGPNGSGKSTLAKTIM 47
>gnl|CDD|216936 pfam02223, Thymidylate_kin, Thymidylate kinase.
Length = 186
Score = 25.3 bits (56), Expect = 6.3
Identities = 6/19 (31%), Positives = 11/19 (57%)
Query: 23 GPPGTGKTSLCKAVAQKLS 41
G G GKT+ + + ++L
Sbjct: 3 GLDGAGKTTQAELLKERLK 21
>gnl|CDD|222178 pfam13500, AAA_26, AAA domain. This domain is found in a number
of proteins involved in cofactor biosynthesis such as
dethiobiotin synthase and cobyric acid synthase. This
domain contains a P-loop motif.
Length = 197
Score = 25.3 bits (56), Expect = 6.4
Identities = 6/29 (20%), Positives = 13/29 (44%), Gaps = 3/29 (10%)
Query: 25 PGTGKTSLCKAVAQKLSIRLQTPQAIFFK 53
G GKT + + + L + + ++K
Sbjct: 10 TGVGKTVVSLGLVRALK---RGVKVGYWK 35
>gnl|CDD|213191 cd03224, ABC_TM1139_LivF_branched, ATP-binding cassette domain of
branched-chain amino acid transporter. LivF (TM1139)
is part of the LIV-I bacterial ABC-type two-component
transport system that imports neutral, branched-chain
amino acids. The E. coli branched-chain amino acid
transporter comprises a heterodimer of ABC transporters
(LivF and LivG), a heterodimer of six-helix TM domains
(LivM and LivH), and one of two alternative soluble
periplasmic substrate binding proteins (LivK or LivJ).
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.
Length = 222
Score = 25.5 bits (57), Expect = 6.4
Identities = 9/25 (36%), Positives = 13/25 (52%)
Query: 13 ISWNRVVLLHGPPGTGKTSLCKAVA 37
+ +V L G G GKT+L K +
Sbjct: 23 VPEGEIVALLGRNGAGKTTLLKTIM 47
>gnl|CDD|220440 pfam09848, DUF2075, Uncharacterized conserved protein (DUF2075).
This domain, found in various prokaryotic proteins
(including putative ATP/GTP binding proteins), has no
known function.
Length = 348
Score = 25.3 bits (56), Expect = 6.4
Identities = 9/14 (64%), Positives = 10/14 (71%)
Query: 17 RVVLLHGPPGTGKT 30
V L+ G PGTGKT
Sbjct: 2 AVFLVTGGPGTGKT 15
>gnl|CDD|222160 pfam13476, AAA_23, AAA domain.
Length = 204
Score = 25.2 bits (55), Expect = 6.4
Identities = 8/21 (38%), Positives = 15/21 (71%)
Query: 16 NRVVLLHGPPGTGKTSLCKAV 36
+ L++GP G+GKT++ A+
Sbjct: 19 KGLTLIYGPNGSGKTTILDAI 39
>gnl|CDD|233448 TIGR01526, nadR_NMN_Atrans, nicotinamide-nucleotide
adenylyltransferase, NadR type. The NadR protein of E.
coli and closely related bacteria is both enzyme and
regulatory protein. The first 60 or so amino acids,
N-terminal to the region covered by this model, is a
DNA-binding helix-turn-helix domain (pfam01381)
responsible for repressing the nadAB genes of NAD de
novo biosynthesis. The NadR homologs in Mycobacterium
tuberculosis, Haemophilus influenzae, and others appear
to lack the repressor domain. NadR has recently been
shown to act as an enzyme of the salvage pathway of NAD
biosynthesis, nicotinamide-nucleotide
adenylyltransferase; members of this family are presumed
to share this activity. E. coli NadR has also been found
to regulate the import of its substrate, nicotinamide
ribonucleotide, but it is not known if the other members
of this model share that activity.
Length = 325
Score = 25.6 bits (56), Expect = 6.5
Identities = 14/64 (21%), Positives = 22/64 (34%), Gaps = 9/64 (14%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQKLSIRLQTPQAIFFKKYPNVLIFTTSNLTGAIDLAFLD 76
+ V + G TGK++L +A +Y + L G L + D
Sbjct: 163 KTVAILGGESTGKSTLVNKLAAVF-------NTTSAWEYAREYVE--EKLGGDEALQYSD 213
Query: 77 RADI 80
A I
Sbjct: 214 YAQI 217
>gnl|CDD|215277 PLN02501, PLN02501, digalactosyldiacylglycerol synthase.
Length = 794
Score = 25.7 bits (56), Expect = 6.6
Identities = 13/38 (34%), Positives = 19/38 (50%), Gaps = 5/38 (13%)
Query: 32 LCKAVAQKLS-----IRLQTPQAIFFKKYPNVLIFTTS 64
LC A A+ L+ + P FF+ +PN L + TS
Sbjct: 631 LCTATAEALAMGKFVVCADHPSNEFFRSFPNCLTYKTS 668
>gnl|CDD|181547 PRK08760, PRK08760, replicative DNA helicase; Provisional.
Length = 476
Score = 25.6 bits (56), Expect = 6.7
Identities = 9/34 (26%), Positives = 19/34 (55%)
Query: 18 VVLLHGPPGTGKTSLCKAVAQKLSIRLQTPQAIF 51
+++L P GKT+ +A+ +I+ + A+F
Sbjct: 231 LIILAARPAMGKTTFALNIAEYAAIKSKKGVAVF 264
>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 = 25.4 bits (56), Expect = 6.7
Identities = 8/19 (42%), Positives = 13/19 (68%)
Query: 20 LLHGPPGTGKTSLCKAVAQ 38
L+ PP GKT+L +++A
Sbjct: 20 LIVAPPKAGKTTLLQSIAN 38
>gnl|CDD|235335 PRK05057, aroK, shikimate kinase I; Reviewed.
Length = 172
Score = 25.1 bits (55), Expect = 6.9
Identities = 10/26 (38%), Positives = 19/26 (73%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQKLSI 42
R + L GP G GK+++ + +AQ+L++
Sbjct: 5 RNIFLVGPMGAGKSTIGRQLAQQLNM 30
>gnl|CDD|237422 PRK13548, hmuV, hemin importer ATP-binding subunit; Provisional.
Length = 258
Score = 25.1 bits (56), Expect = 7.0
Identities = 12/33 (36%), Positives = 20/33 (60%), Gaps = 5/33 (15%)
Query: 18 VVLLHGPPGTGKTSLCKAVAQKL-----SIRLQ 45
VV + GP G GK++L +A++ +L +RL
Sbjct: 30 VVAILGPNGAGKSTLLRALSGELSPDSGEVRLN 62
>gnl|CDD|226232 COG3709, COG3709, Uncharacterized component of phosphonate
metabolism [Inorganic ion transport and metabolism].
Length = 192
Score = 25.0 bits (55), Expect = 7.1
Identities = 10/27 (37%), Positives = 16/27 (59%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQKLSIR 43
R++ + GP G GK +L A +L+ R
Sbjct: 6 RLIAVVGPSGAGKDTLLDAARARLAGR 32
>gnl|CDD|218528 pfam05272, VirE, Virulence-associated protein E. This family
contains several bacterial virulence-associated protein
E like proteins. These proteins contain a P-loop motif.
Length = 198
Score = 25.0 bits (55), Expect = 7.3
Identities = 7/21 (33%), Positives = 13/21 (61%)
Query: 18 VVLLHGPPGTGKTSLCKAVAQ 38
V++L G G+GK++ K +
Sbjct: 54 VLILQGAQGSGKSTFLKKLGG 74
>gnl|CDD|236815 PRK10997, yieM, hypothetical protein; Provisional.
Length = 487
Score = 25.3 bits (56), Expect = 7.3
Identities = 8/16 (50%), Positives = 13/16 (81%), Gaps = 1/16 (6%)
Query: 44 LQTPQ-AIFFKKYPNV 58
L +PQ A+FF+K+P +
Sbjct: 27 LASPQLAVFFEKFPRL 42
>gnl|CDD|236347 PRK08903, PRK08903, DnaA regulatory inactivator Hda; Validated.
Length = 227
Score = 25.3 bits (56), Expect = 7.3
Identities = 7/21 (33%), Positives = 12/21 (57%)
Query: 17 RVVLLHGPPGTGKTSLCKAVA 37
R L G G+G++ L +A+
Sbjct: 43 RFFYLWGEAGSGRSHLLQALV 63
>gnl|CDD|224043 COG1118, CysA, ABC-type sulfate/molybdate transport systems,
ATPase component [Inorganic ion transport and
metabolism].
Length = 345
Score = 25.4 bits (56), Expect = 7.4
Identities = 14/38 (36%), Positives = 20/38 (52%), Gaps = 7/38 (18%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQKLSIRLQTPQA--IFF 52
+V L GP G GK++L + +A L+TP A I
Sbjct: 29 ELVALLGPSGAGKSTLLRIIAG-----LETPDAGRIRL 61
>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 = 7.4
Identities = 10/24 (41%), Positives = 17/24 (70%), Gaps = 1/24 (4%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQKL 40
R+ ++ GP G GK++L K +A +L
Sbjct: 350 RIAIV-GPNGAGKSTLLKLLAGEL 372
>gnl|CDD|237862 PRK14948, PRK14948, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 620
Score = 25.3 bits (56), Expect = 7.5
Identities = 12/25 (48%), Positives = 14/25 (56%), Gaps = 3/25 (12%)
Query: 10 SNIISWNRVV---LLHGPPGTGKTS 31
N + NR+ L GP GTGKTS
Sbjct: 29 KNALISNRIAPAYLFTGPRGTGKTS 53
>gnl|CDD|183703 PRK12724, PRK12724, flagellar biosynthesis regulator FlhF;
Provisional.
Length = 432
Score = 25.3 bits (55), Expect = 7.5
Identities = 10/28 (35%), Positives = 16/28 (57%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQKLSIRL 44
+VV GP G+GKT+ +A K + +
Sbjct: 224 KVVFFVGPTGSGKTTSIAKLAAKYFLHM 251
>gnl|CDD|240312 PTZ00202, PTZ00202, tuzin; Provisional.
Length = 550
Score = 25.5 bits (56), Expect = 7.6
Identities = 10/23 (43%), Positives = 16/23 (69%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQK 39
R+V+ G G GK+SLC++ +K
Sbjct: 287 RIVVFTGFRGCGKSSLCRSAVRK 309
>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 = 25.3 bits (56), Expect = 7.7
Identities = 12/23 (52%), Positives = 14/23 (60%)
Query: 18 VVLLHGPPGTGKTSLCKAVAQKL 40
V LL GP G GKT A+A+ L
Sbjct: 598 VFLLVGPSGVGKTETALALAELL 620
>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 = 25.3 bits (55), Expect = 7.7
Identities = 9/20 (45%), Positives = 14/20 (70%)
Query: 18 VVLLHGPPGTGKTSLCKAVA 37
++ L G G GKT+L +A+A
Sbjct: 33 LLALIGKSGCGKTTLLRAIA 52
>gnl|CDD|226970 COG4619, COG4619, ABC-type uncharacterized transport system,
ATPase component [General function prediction only].
Length = 223
Score = 25.2 bits (55), Expect = 7.7
Identities = 9/19 (47%), Positives = 13/19 (68%)
Query: 19 VLLHGPPGTGKTSLCKAVA 37
+ + GP G GK++L K VA
Sbjct: 32 IAITGPSGCGKSTLLKIVA 50
>gnl|CDD|217138 pfam02606, LpxK, Tetraacyldisaccharide-1-P 4'-kinase. This
family consists of tetraacyldisaccharide-1-P 4'-kinase
also known as Lipid-A 4'-kinase or Lipid A biosynthesis
protein LpxK, EC:2.7.1.130. This enzyme catalyzes the
reaction: ATP + 2,3-bis(3-hydroxytetradecanoyl)-D
-glucosaminyl-(beta-D-1,6)-2,
3-bis(3-hydroxytetradecanoyl)-D-glu cosam inyl
beta-phosphate <=> ADP +
2,3,2',3'-tetrakis(3-hydroxytetradecanoyl)-D-
glucosaminyl-1,6-beta-D-glucosamine 1,4'-bisphosphate.
This enzyme is involved in the synthesis of lipid A
portion of the bacterial lipopolysaccharide layer
(LPS). The family contains a P-loop motif at the N
terminus.
Length = 318
Score = 25.2 bits (56), Expect = 7.8
Identities = 9/15 (60%), Positives = 11/15 (73%)
Query: 26 GTGKTSLCKAVAQKL 40
GTGKT L A+A+ L
Sbjct: 47 GTGKTPLVIALAELL 61
>gnl|CDD|163593 TIGR03881, KaiC_arch_4, KaiC domain protein, PAE1156 family.
Members of this protein family are archaeal
single-domain KaiC_related proteins, homologous to the
Cyanobacterial circadian clock cycle protein KaiC, an
autokinase/autophosphorylase that has two copies of the
domain.
Length = 229
Score = 25.1 bits (55), Expect = 7.8
Identities = 9/16 (56%), Positives = 10/16 (62%)
Query: 18 VVLLHGPPGTGKTSLC 33
V + G PGTGKT C
Sbjct: 22 FVAVTGEPGTGKTIFC 37
>gnl|CDD|181939 PRK09544, znuC, high-affinity zinc transporter ATPase; Reviewed.
Length = 251
Score = 25.1 bits (55), Expect = 7.9
Identities = 11/37 (29%), Positives = 21/37 (56%), Gaps = 3/37 (8%)
Query: 3 FSHSKVKSNI---ISWNRVVLLHGPPGTGKTSLCKAV 36
F +V S++ + +++ L GP G GK++L + V
Sbjct: 14 FGQRRVLSDVSLELKPGKILTLLGPNGAGKSTLVRVV 50
>gnl|CDD|226126 COG3598, RepA, RecA-family ATPase [DNA replication, recombination,
and repair].
Length = 402
Score = 25.3 bits (55), Expect = 8.0
Identities = 16/55 (29%), Positives = 22/55 (40%), Gaps = 7/55 (12%)
Query: 6 SKVKSNIISWNR---VVLLHGPPGTGKTSLCKAVAQKLSIRLQTPQAIFFKKYPN 57
S I + R V +L+G G GKT+L L I L + +F K
Sbjct: 76 SNSPQLIDEFFRKGYVSILYGDSGVGKTTL----LLYLCIALAAGKNLFGNKVKE 126
>gnl|CDD|237040 PRK12289, PRK12289, GTPase RsgA; Reviewed.
Length = 352
Score = 25.4 bits (56), Expect = 8.0
Identities = 8/17 (47%), Positives = 13/17 (76%)
Query: 16 NRVVLLHGPPGTGKTSL 32
N++ ++ GP G GK+SL
Sbjct: 172 NKITVVAGPSGVGKSSL 188
>gnl|CDD|236490 PRK09376, rho, transcription termination factor Rho; Provisional.
Length = 416
Score = 25.1 bits (56), Expect = 8.1
Identities = 8/19 (42%), Positives = 11/19 (57%)
Query: 20 LLHGPPGTGKTSLCKAVAQ 38
L+ PP GKT L + +A
Sbjct: 173 LIVAPPKAGKTVLLQNIAN 191
>gnl|CDD|225488 COG2937, PlsB, Glycerol-3-phosphate O-acyltransferase [Lipid
metabolism].
Length = 810
Score = 25.1 bits (55), Expect = 8.2
Identities = 19/67 (28%), Positives = 29/67 (43%), Gaps = 12/67 (17%)
Query: 19 VLLHGPPGTGK---TSLCKAVAQKLSI--RLQTPQAIFFKKYPNVLIFTTSNLTGAIDLA 73
+L PP G+ VAQ+LS+ + P+ FF K +F+T+ T D
Sbjct: 716 LLRAAPPDIGRAELEKESLGVAQRLSVLHGINAPE--FFDK----ALFSTAIQT-LRDQG 768
Query: 74 FLDRADI 80
+D A
Sbjct: 769 LIDDAGA 775
>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 = 24.9 bits (55), Expect = 8.3
Identities = 11/21 (52%), Positives = 14/21 (66%), Gaps = 1/21 (4%)
Query: 17 RVVLLHGPPGTGKTSLCKAVA 37
VVLL GP G GKT+ + +A
Sbjct: 28 FVVLL-GPSGCGKTTTLRMIA 47
>gnl|CDD|223679 COG0606, COG0606, Predicted ATPase with chaperone activity
[Posttranslational modification, protein turnover,
chaperones].
Length = 490
Score = 25.3 bits (56), Expect = 8.6
Identities = 11/15 (73%), Positives = 11/15 (73%)
Query: 20 LLHGPPGTGKTSLCK 34
LL GPPGTGKT L
Sbjct: 202 LLVGPPGTGKTMLAS 216
>gnl|CDD|130041 TIGR00968, 3a0106s01, sulfate ABC transporter, ATP-binding
protein. [Transport and binding proteins, Anions].
Length = 237
Score = 25.1 bits (55), Expect = 8.7
Identities = 9/20 (45%), Positives = 15/20 (75%)
Query: 18 VVLLHGPPGTGKTSLCKAVA 37
+V L GP G+GK++L + +A
Sbjct: 28 LVALLGPSGSGKSTLLRIIA 47
>gnl|CDD|177538 PHA03136, PHA03136, thymidine kinase; Provisional.
Length = 378
Score = 25.1 bits (54), Expect = 8.7
Identities = 13/40 (32%), Positives = 23/40 (57%), Gaps = 2/40 (5%)
Query: 6 SKVKSNIISWNRVVLLH--GPPGTGKTSLCKAVAQKLSIR 43
S+ +++ + R+VLL+ GP GTGKT+ K + +
Sbjct: 24 SEFENDDSDFRRLVLLYLDGPFGTGKTTTAKLLMEMPDTL 63
>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 = 25.0 bits (55), Expect = 8.7
Identities = 10/19 (52%), Positives = 14/19 (73%)
Query: 19 VLLHGPPGTGKTSLCKAVA 37
V L GP G+GKT+L + +A
Sbjct: 31 VALLGPSGSGKTTLLRLIA 49
>gnl|CDD|214940 smart00962, SRP54, SRP54-type protein, GTPase domain. This entry
represents the GTPase domain of the 54 kDa SRP54
component, a GTP-binding protein that interacts with
the signal sequence when it emerges from the ribosome.
SRP54 of the signal recognition particle has a
three-domain structure: an N-terminal helical bundle
domain, a GTPase domain, and the M-domain that binds
the 7s RNA and also binds the signal sequence. The
extreme C-terminal region is glycine-rich and lower in
complexity and poorly conserved between species. The
GTPase domain is evolutionary related to P-loop NTPase
domains found in a variety of other proteins.
Length = 197
Score = 24.7 bits (55), Expect = 8.9
Identities = 9/14 (64%), Positives = 10/14 (71%)
Query: 17 RVVLLHGPPGTGKT 30
V+LL GP G GKT
Sbjct: 2 GVILLVGPNGVGKT 15
>gnl|CDD|219519 pfam07693, KAP_NTPase, KAP family P-loop domain. The KAP (after
Kidins220/ARMS and PifA) family of predicted NTPases
are sporadically distributed across a wide phylogenetic
range in bacteria and in animals. Many of the
prokaryotic KAP NTPases are encoded in plasmids and
tend to undergo disruption to form pseudogenes. A
unique feature of all eukaryotic and certain bacterial
KAP NTPases is the presence of two or four
transmembrane helices inserted into the P-loop NTPase
domain. These transmembrane helices anchor KAP NTPases
in the membrane such that the P-loop domain is located
on the intracellular side.
Length = 301
Score = 25.0 bits (55), Expect = 9.0
Identities = 9/24 (37%), Positives = 14/24 (58%)
Query: 18 VVLLHGPPGTGKTSLCKAVAQKLS 41
V+ L+G G+GKTS + +L
Sbjct: 22 VIGLYGAWGSGKTSFLNLLEDELK 45
>gnl|CDD|238549 cd01129, PulE-GspE, PulE/GspE The type II secretory pathway is the
main terminal branch of the general secretory pathway
(GSP). It is responsible for the export the majority of
Gram-negative bacterial exoenzymes and toxins. PulE is a
cytoplasmic protein of the GSP, which contains an ATP
binding site and a tetracysteine motif. This subgroup
also includes PillB and HofB.
Length = 264
Score = 24.9 bits (55), Expect = 9.1
Identities = 8/24 (33%), Positives = 16/24 (66%)
Query: 18 VVLLHGPPGTGKTSLCKAVAQKLS 41
++L+ GP G+GKT+ + +L+
Sbjct: 82 IILVTGPTGSGKTTTLYSALSELN 105
>gnl|CDD|130711 TIGR01650, PD_CobS, cobaltochelatase, CobS subunit. This model
describes Pseudomonas denitrificans CobS gene product,
which is a cobalt chelatase subunit that functions in
cobalamin biosynthesis. Cobalamin (vitamin B12) can be
synthesized via several pathways, including an aerobic
pathway (found in Pseudomonas denitrificans) and an
anaerobic pathway (found in P. shermanii and Salmonella
typhimurium). These pathways differ in the point of
cobalt insertion during corrin ring formation. There
are apparently a number of variations on these two
pathways, where the major differences seem to be
concerned with the process of ring contraction.
Confusion regarding the functions of enzymes found in
the aerobic vs. anaerobic pathways has arisen because
nonhomologous genes in these different pathways were
given the same gene symbols. Thus, cobS in the aerobic
pathway (P. denitrificans) is not a homolog of cobS in
the anaerobic pathway (S. typhimurium). It should be
noted that E. coli synthesizes cobalamin only when it
is supplied with the precursor cobinamide, which is a
complex intermediate. Additionally, all E. coli
cobalamin synthesis genes (cobU, cobS and cobT) were
named after their Salmonella typhimurium homologs which
function in the anaerobic cobalamin synthesis pathway.
This model describes the aerobic cobalamin pathway
Pseudomonas denitrificans CobS gene product, which is a
cobalt chelatase subunit, with a MW ~37 kDa. The
aerobic pathway cobalt chelatase is a heterotrimeric,
ATP-dependent enzyme that catalyzes cobalt insertion
during cobalamin biosynthesis. The other two subunits
are the P. denitrificans CobT (TIGR01651) and CobN
(pfam02514 CobN/Magnesium Chelatase) proteins. To avoid
potential confusion with the nonhomologous Salmonella
typhimurium/E.coli cobS gene product, the P.
denitrificans gene symbol is not used in the name of
this model [Biosynthesis of cofactors, prosthetic
groups, and carriers, Heme, porphyrin, and cobalamin].
Length = 327
Score = 25.0 bits (54), Expect = 9.1
Identities = 9/28 (32%), Positives = 20/28 (71%)
Query: 14 SWNRVVLLHGPPGTGKTSLCKAVAQKLS 41
+++R V++ G GTGK++ + +A +L+
Sbjct: 62 AYDRRVMVQGYHGTGKSTHIEQIAARLN 89
>gnl|CDD|223989 COG1061, SSL2, DNA or RNA helicases of superfamily II
[Transcription / DNA replication, recombination, and
repair].
Length = 442
Score = 25.1 bits (55), Expect = 9.2
Identities = 6/24 (25%), Positives = 10/24 (41%)
Query: 20 LLHGPPGTGKTSLCKAVAQKLSIR 43
++ P G GKT + +L
Sbjct: 59 VIVLPTGAGKTVVAAEAIAELKRS 82
>gnl|CDD|226132 COG3604, FhlA, Transcriptional regulator containing GAF, AAA-type
ATPase, and DNA binding domains [Transcription / Signal
transduction mechanisms].
Length = 550
Score = 25.0 bits (55), Expect = 9.2
Identities = 12/25 (48%), Positives = 16/25 (64%), Gaps = 1/25 (4%)
Query: 19 VLLHGPPGTGKTSLCKAVAQKLSIR 43
VL+ G GTGK + +A+ Q LS R
Sbjct: 249 VLIRGETGTGKELVARAIHQ-LSPR 272
>gnl|CDD|184412 PRK13947, PRK13947, shikimate kinase; Provisional.
Length = 171
Score = 24.7 bits (54), Expect = 9.5
Identities = 12/23 (52%), Positives = 16/23 (69%)
Query: 19 VLLHGPPGTGKTSLCKAVAQKLS 41
++L G GTGKT++ K VA LS
Sbjct: 4 IVLIGFMGTGKTTVGKRVATTLS 26
>gnl|CDD|227570 COG5245, DYN1, Dynein, heavy chain [Cytoskeleton].
Length = 3164
Score = 25.3 bits (55), Expect = 9.6
Identities = 8/28 (28%), Positives = 13/28 (46%)
Query: 5 HSKVKSNIISWNRVVLLHGPPGTGKTSL 32
+ ++ R + GPPG+GK L
Sbjct: 1483 VDSFSNEALNTLRSYIYCGPPGSGKEML 1510
>gnl|CDD|201353 pfam00625, Guanylate_kin, Guanylate kinase.
Length = 183
Score = 24.6 bits (54), Expect = 9.7
Identities = 9/28 (32%), Positives = 16/28 (57%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQKLSIRL 44
R ++L GP G GK+ + KA+ + +
Sbjct: 3 RPIVLSGPSGVGKSHIKKALLDEYPEKF 30
>gnl|CDD|180120 PRK05506, PRK05506, bifunctional sulfate adenylyltransferase
subunit 1/adenylylsulfate kinase protein; Provisional.
Length = 632
Score = 24.9 bits (55), Expect = 9.7
Identities = 7/24 (29%), Positives = 13/24 (54%)
Query: 17 RVVLLHGPPGTGKTSLCKAVAQKL 40
V G G+GK+++ V ++L
Sbjct: 461 ATVWFTGLSGSGKSTIANLVERRL 484
>gnl|CDD|224577 COG1663, LpxK, Tetraacyldisaccharide-1-P 4'-kinase [Cell envelope
biogenesis, outer membrane].
Length = 336
Score = 25.0 bits (55), Expect = 9.9
Identities = 7/15 (46%), Positives = 10/15 (66%)
Query: 26 GTGKTSLCKAVAQKL 40
GTGKT + +A+ L
Sbjct: 59 GTGKTPVVIWLAEAL 73
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
0.324 0.136 0.401
Gapped
Lambda K H
0.267 0.0889 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,387,031
Number of extensions: 452720
Number of successful extensions: 1466
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1465
Number of HSP's successfully gapped: 449
Length of query: 105
Length of database: 10,937,602
Length adjustment: 70
Effective length of query: 35
Effective length of database: 7,832,822
Effective search space: 274148770
Effective search space used: 274148770
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 53 (23.9 bits)