RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 total letters
Searching..................................................done
Query= gi|254780132|ref|YP_003064545.1| guanylate kinase [Candidatus
Liberibacter asiaticus str. psy62]
(186 letters)
>gnl|CDD|132307 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.
Length = 180
Score = 113 bits (285), Expect = 3e-26
Identities = 57/173 (32%), Positives = 86/173 (49%), Gaps = 7/173 (4%)
Query: 4 IFVLIGASGVGKTTIAKQVVLNSEYLVMPVGVTTRRPRVDEKQYIDYRFISQSQFKGWKH 63
+ V+ G SGVGK+T+ K ++ L + TTR+PR E +DY F+S+ +F+
Sbjct: 3 LIVISGPSGVGKSTLVKALLEEDPNLKFSISATTRKPRPGEVDGVDYFFVSKEEFEEMIA 62
Query: 64 TGLFIETTKVRDEYYGYLKEDINNPMEHGYDILLILTHQGLAPLKKLYEDQVTSIFIAPP 123
G F+E +V YYG K + + G D+LL + QG +KK + D SIFI PP
Sbjct: 63 AGEFLEWAEVHGNYYGTPKSPVEEALAAGKDVLLEIDVQGARQVKKKFPD-AVSIFILPP 121
Query: 124 SEAELIQRRIKRREDIPFNLDPDL------FGKNHSYSFTIVNNHLPTACRQV 170
S EL +R KR D ++ L + + IVN+ L A ++
Sbjct: 122 SLEELERRLRKRGTDSEEVIERRLAKAKKEIAHADEFDYVIVNDDLEKAVEEL 174
>gnl|CDD|178968 PRK00300, gmk, guanylate kinase; Provisional.
Length = 205
Score = 109 bits (274), Expect = 7e-25
Identities = 60/182 (32%), Positives = 86/182 (47%), Gaps = 25/182 (13%)
Query: 4 IFVLIGASGVGKTTIAKQVVLNSEYLVMPVGVTTRRPRVDEKQYIDYRFISQSQFKGWKH 63
+ VL G SG GK+T+ K ++ L + V TTR PR E +DY F+S+ +F+
Sbjct: 7 LIVLSGPSGAGKSTLVKALLERDPNLQLSVSATTRAPRPGEVDGVDYFFVSKEEFEEMIE 66
Query: 64 TGLFIETTKVRDEYYGYLKEDINNPMEHGYDILLILTHQGLAPLKKLYEDQVTSIFIAPP 123
G F+E +V YYG + + + G D+LL + QG +KK D SIFI PP
Sbjct: 67 NGEFLEWAEVFGNYYGTPRSPVEEALAAGKDVLLEIDWQGARQVKKKMPD-AVSIFILPP 125
Query: 124 SEAEL--------------IQRRIKR-REDIPFNLDPDLFGKNHSYSFTIVNNHLPTACR 168
S EL I RR+ + RE+I Y + IVN+ L TA
Sbjct: 126 SLEELERRLRGRGTDSEEVIARRLAKAREEIAH---------ASEYDYVIVNDDLDTALE 176
Query: 169 QV 170
++
Sbjct: 177 EL 178
>gnl|CDD|128386 smart00072, GuKc, Guanylate kinase homologues. Active enzymes
catalyze ATP-dependent phosphorylation of GMP to GDP.
Structure resembles that of adenylate kinase. So-called
membrane-associated guanylate kinase homologues (MAGUKs)
do not possess guanylate kinase activities; instead at
least some possess protein-binding functions.
Length = 184
Score = 94.7 bits (236), Expect = 1e-20
Identities = 57/174 (32%), Positives = 83/174 (47%), Gaps = 8/174 (4%)
Query: 4 IFVLIGASGVGKTTIAKQVVL-NSEYLVMPVGVTTRRPRVDEKQYIDYRFISQSQFKGWK 62
VL G SGVGK T+ +++ + V TTR PR E +DY F+S+ +F+
Sbjct: 4 PIVLSGPSGVGKGTLLAELIQEIPDAFERVVSHTTRPPRPGEVNGVDYHFVSREEFEDDI 63
Query: 63 HTGLFIETTKVRDEYYGYLKEDINNPMEHGYDILLILTHQGLAPLKKLYEDQVTSIFIAP 122
+GLF+E + YYG KE I E G LL + QG+ L+K + IFIAP
Sbjct: 64 KSGLFLEWGEYSGNYYGTSKETIRQVAEQGKHCLLDIDPQGVKQLRKAQLYPI-VIFIAP 122
Query: 123 PSEAELIQRRIKRREDIPFNLDPDL------FGKNHSYSFTIVNNHLPTACRQV 170
PS EL +R R + + L + H + + IVN+ L A ++
Sbjct: 123 PSSEELERRLRGRGTETAERIQKRLAAAQKEAQEYHLFDYVIVNDDLEDAYEEL 176
>gnl|CDD|184809 PRK14738, gmk, guanylate kinase; Provisional.
Length = 206
Score = 80.5 bits (199), Expect = 3e-16
Identities = 44/139 (31%), Positives = 68/139 (48%), Gaps = 1/139 (0%)
Query: 6 VLIGASGVGKTTIAKQVVLNSEYLVMPVGVTTRRPRVDEKQYIDYRFISQSQFKGWKHTG 65
V+ G SGVGK + ++ V TTR R E +DY F++ +F+
Sbjct: 17 VISGPSGVGKDAVLARMRERKLPFHFVVTATTRPKRPGEIDGVDYHFVTPEEFREMISQN 76
Query: 66 LFIETTKVRDEYYGYLKEDINNPMEHGYDILLILTHQGLAPLKKLYEDQVTSIFIAPPSE 125
+E +V YYG K + + G D+++ + QG A +K+L + V IF+APPS
Sbjct: 77 ELLEWAEVYGNYYGVPKAPVRQALASGRDVIVKVDVQGAASIKRLVPEAVF-IFLAPPSM 135
Query: 126 AELIQRRIKRREDIPFNLD 144
EL +R RR + P L+
Sbjct: 136 DELTRRLELRRTESPEELE 154
>gnl|CDD|173199 PRK14737, gmk, guanylate kinase; Provisional.
Length = 186
Score = 78.9 bits (194), Expect = 8e-16
Identities = 46/176 (26%), Positives = 88/176 (50%), Gaps = 6/176 (3%)
Query: 4 IFVLIGASGVGKTTIAKQVVLNSEYLVMPVGVTTRRPRVDEKQYIDYRFISQSQFKGWKH 63
+F++ +G GK+TI + ++ + + TTR PR +++ Y F++ +FK
Sbjct: 6 LFIISSVAGGGKSTIIQALLEEHPDFLFSISCTTRAPRPGDEEGKTYFFLTIEEFKKGIA 65
Query: 64 TGLFIETTKVRDEYYGYLKEDINNPMEHGYDILLILTHQGLAPLKKLYEDQVTSIFIAPP 123
G F+E +V D YYG K I + + G ++ + QG +K+ + +++ +IFI PP
Sbjct: 66 DGEFLEWAEVHDNYYGTPKAFIEDAFKEGRSAIMDIDVQGAKIIKEKFPERIVTIFIEPP 125
Query: 124 SEAELIQRRIKRREDIPFNLDPDL------FGKNHSYSFTIVNNHLPTACRQVGLI 173
SE E +R I R D +++ + + + + + I+N+ L A + I
Sbjct: 126 SEEEWEERLIHRGTDSEESIEKRIENGIIELDEANEFDYKIINDDLEDAIADLEAI 181
>gnl|CDD|178371 PLN02772, PLN02772, guanylate kinase.
Length = 398
Score = 49.8 bits (119), Expect = 4e-07
Identities = 44/135 (32%), Positives = 63/135 (46%), Gaps = 9/135 (6%)
Query: 6 VLIGASGVGK-TTIAKQVVLNSEYLVM---PVGVTTRRPRVDEKQYIDYRFISQSQFKGW 61
V+ G SGVGK T I+ L E+ M V TTR PR EK + Y F +S +
Sbjct: 139 VISGPSGVGKGTLISM---LMKEFPSMFGFSVSHTTRAPREMEKDGVHYHFTERSVMEKE 195
Query: 62 KHTGLFIETTKVRDEYYGYLKEDINNPMEHGYDILLILTHQGLAPLKKLYEDQVTSIFIA 121
G F+E V YG E + + G +L + QG ++ + + IFI
Sbjct: 196 IKDGKFLEFASVHGNLYGTSIEAVEVVTDSGKRCILDIDVQGARSVRASSLEAIF-IFIC 254
Query: 122 PPSEAELIQRRIKRR 136
PPS EL ++R++ R
Sbjct: 255 PPSMEEL-EKRLRAR 268
>gnl|CDD|180790 PRK07003, PRK07003, DNA polymerase III subunits gamma and tau;
Validated.
Length = 830
Score = 34.1 bits (78), Expect = 0.024
Identities = 21/54 (38%), Positives = 28/54 (51%), Gaps = 8/54 (14%)
Query: 3 HIFVLIGASGVGKTTI----AKQVVLNSEYLV--MPVGVTTRRPRVDEKQYIDY 50
H ++ G GVGKTT+ AK LN E V P GV +DE +++DY
Sbjct: 39 HAYLFTGTRGVGKTTLSRIFAK--ALNCETGVTSQPCGVCRACREIDEGRFVDY 90
>gnl|CDD|169554 PRK08691, PRK08691, DNA polymerase III subunits gamma and tau;
Validated.
Length = 709
Score = 33.9 bits (77), Expect = 0.028
Identities = 20/51 (39%), Positives = 28/51 (54%), Gaps = 4/51 (7%)
Query: 3 HIFVLIGASGVGKTTIAKQVV--LNSEYLVM--PVGVTTRRPRVDEKQYID 49
H ++L G GVGKTTIA+ + LN E P GV ++D +Y+D
Sbjct: 39 HAYLLTGTRGVGKTTIARILAKSLNCENAQHGEPCGVCQSCTQIDAGRYVD 89
>gnl|CDD|184929 PRK14965, PRK14965, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 576
Score = 32.0 bits (73), Expect = 0.099
Identities = 14/29 (48%), Positives = 19/29 (65%), Gaps = 2/29 (6%)
Query: 1 MAHIFVLIGASGVGKTTIAKQV--VLNSE 27
+AH F+ GA GVGKT+ A+ + LN E
Sbjct: 37 VAHAFLFTGARGVGKTSTARILAKALNCE 65
>gnl|CDD|163294 TIGR03499, FlhF, flagellar biosynthetic protein FlhF.
Length = 282
Score = 31.9 bits (73), Expect = 0.11
Identities = 10/18 (55%), Positives = 14/18 (77%), Gaps = 1/18 (5%)
Query: 4 IFVLIGASGVGKTT-IAK 20
+ L+G +GVGKTT +AK
Sbjct: 196 VIALVGPTGVGKTTTLAK 213
>gnl|CDD|178887 PRK00131, aroK, shikimate kinase; Reviewed.
Length = 175
Score = 31.7 bits (73), Expect = 0.11
Identities = 9/17 (52%), Positives = 12/17 (70%)
Query: 6 VLIGASGVGKTTIAKQV 22
VLIG G GK+TI + +
Sbjct: 8 VLIGFMGAGKSTIGRLL 24
>gnl|CDD|181656 PRK09111, PRK09111, DNA polymerase III subunits gamma and tau;
Validated.
Length = 598
Score = 31.0 bits (71), Expect = 0.20
Identities = 11/18 (61%), Positives = 12/18 (66%)
Query: 2 AHIFVLIGASGVGKTTIA 19
A F+L G GVGKTT A
Sbjct: 46 AQAFMLTGVRGVGKTTTA 63
>gnl|CDD|180787 PRK06995, flhF, flagellar biosynthesis regulator FlhF; Validated.
Length = 484
Score = 30.7 bits (70), Expect = 0.22
Identities = 11/18 (61%), Positives = 14/18 (77%), Gaps = 1/18 (5%)
Query: 4 IFVLIGASGVGK-TTIAK 20
+F L+G +GVGK TT AK
Sbjct: 258 VFALMGPTGVGKTTTTAK 275
>gnl|CDD|184924 PRK14960, PRK14960, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 702
Score = 30.8 bits (69), Expect = 0.23
Identities = 20/51 (39%), Positives = 27/51 (52%), Gaps = 4/51 (7%)
Query: 3 HIFVLIGASGVGKTTIAKQVV--LNSEYLV--MPVGVTTRRPRVDEKQYID 49
H ++ G GVGKTTIA+ + LN E V P V V+E ++ID
Sbjct: 38 HAYLFTGTRGVGKTTIARILAKCLNCETGVTSTPCEVCATCKAVNEGRFID 88
>gnl|CDD|162298 TIGR01313, therm_gnt_kin, carbohydrate kinase, thermoresistant
glucokinase family. This model represents a subfamily
of proteins that includes thermoresistant and
thermosensitve isozymes of gluconate kinase
(gluconokinase) in E. coli and other related proteins;
members of this family are often named by similarity to
the thermostable isozyme. These proteins show homology
to shikimate kinases and adenylate kinases but not to
gluconate kinases from the FGGY family of carbohydrate
kinases.
Length = 163
Score = 30.4 bits (69), Expect = 0.26
Identities = 10/18 (55%), Positives = 14/18 (77%)
Query: 5 FVLIGASGVGKTTIAKQV 22
FVL+G +G GK+TIA +
Sbjct: 1 FVLMGVAGSGKSTIASAL 18
>gnl|CDD|162839 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.
Length = 355
Score = 30.6 bits (70), Expect = 0.27
Identities = 9/19 (47%), Positives = 13/19 (68%)
Query: 2 AHIFVLIGASGVGKTTIAK 20
AH ++ G G GKT+IA+
Sbjct: 36 AHAYLFSGPRGTGKTSIAR 54
>gnl|CDD|162028 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.
Length = 775
Score = 30.0 bits (68), Expect = 0.37
Identities = 12/33 (36%), Positives = 20/33 (60%), Gaps = 2/33 (6%)
Query: 4 IFVLIGASGVGKTTIAKQV--VLNSEYLVMPVG 34
I L+G GVGKT++ K + LN +++ +G
Sbjct: 349 ILCLVGPPGVGKTSLGKSIAKALNRKFVRFSLG 381
>gnl|CDD|128665 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 = 30.0 bits (67), Expect = 0.37
Identities = 8/31 (25%), Positives = 15/31 (48%)
Query: 3 HIFVLIGASGVGKTTIAKQVVLNSEYLVMPV 33
+ +++G G GKTT+A+ + V
Sbjct: 3 EVILIVGPPGSGKTTLARALARELGPPGGGV 33
>gnl|CDD|163592 TIGR03880, KaiC_arch_3, KaiC domain protein, AF_0351 family.
This model represents a rather narrowly distributed
archaeal protein family in which members have a single
copy of the KaiC domain. This stands in contrast to the
circadian clock protein KaiC itself, with two copies of
the domain. Members are expected to have weak ATPase
activity, by homology to the
autokinase/autophosphorylase KaiC itself.
Length = 224
Score = 30.1 bits (68), Expect = 0.39
Identities = 10/19 (52%), Positives = 13/19 (68%)
Query: 3 HIFVLIGASGVGKTTIAKQ 21
H+ V+IG G GKTT + Q
Sbjct: 17 HVIVVIGEYGTGKTTFSLQ 35
>gnl|CDD|184933 PRK14969, PRK14969, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 527
Score = 29.7 bits (67), Expect = 0.45
Identities = 18/52 (34%), Positives = 28/52 (53%), Gaps = 4/52 (7%)
Query: 3 HIFVLIGASGVGKTTIAKQVV--LNSEYLVM--PVGVTTRRPRVDEKQYIDY 50
H ++ G GVGKTT+A+ + LN E V P GV + +D +++D
Sbjct: 39 HAYLFTGTRGVGKTTLARILAKSLNCETGVTATPCGVCSACLEIDSGRFVDL 90
>gnl|CDD|184928 PRK14964, PRK14964, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 491
Score = 29.7 bits (67), Expect = 0.48
Identities = 12/18 (66%), Positives = 15/18 (83%)
Query: 7 LIGASGVGKTTIAKQVVL 24
L+GASGVGKTT A+ + L
Sbjct: 40 LVGASGVGKTTCARIISL 57
>gnl|CDD|180683 PRK06762, PRK06762, hypothetical protein; Provisional.
Length = 166
Score = 29.6 bits (67), Expect = 0.51
Identities = 12/22 (54%), Positives = 16/22 (72%)
Query: 1 MAHIFVLIGASGVGKTTIAKQV 22
M + ++ G SG GKTTIAKQ+
Sbjct: 1 MTTLIIIRGNSGSGKTTIAKQL 22
>gnl|CDD|181681 PRK09183, PRK09183, transposase/IS protein; Provisional.
Length = 259
Score = 29.7 bits (67), Expect = 0.53
Identities = 25/104 (24%), Positives = 39/104 (37%), Gaps = 29/104 (27%)
Query: 6 VLIGASGVGKTTIAKQVVLNSEYLVMPVGVTTRRPRVDEKQYIDYRFISQSQFKGWKHTG 65
VL+G SGVGKT +A + L Y + G+ RF + +
Sbjct: 106 VLLGPSGVGKTHLA--IALG--YEAVRAGIKV-------------RFTTAADLL------ 142
Query: 66 LFIETTKVRDEYYGYLKEDINNPMEHGYDILLILTHQGLAPLKK 109
L + T + + Y L+ + P LLI+ G P +
Sbjct: 143 LQLSTAQRQGRYKTTLQRGVMAPR------LLIIDEIGYLPFSQ 180
>gnl|CDD|132313 TIGR03269, met_CoM_red_A2, methyl coenzyme M reductase system,
component A2. The enzyme that catalyzes the final step
in methanogenesis, methyl coenzyme M reductase, contains
alpha, beta, and gamma chains. In older literature, the
complex of alpha, beta, and gamma chains was termed
component C, while this single chain protein was termed
methyl coenzyme M reductase system component A2.
Length = 520
Score = 29.4 bits (66), Expect = 0.55
Identities = 10/19 (52%), Positives = 14/19 (73%)
Query: 2 AHIFVLIGASGVGKTTIAK 20
IF ++G SG GKTT++K
Sbjct: 310 GEIFGIVGTSGAGKTTLSK 328
>gnl|CDD|181925 PRK09518, PRK09518, bifunctional cytidylate kinase/GTPase Der;
Reviewed.
Length = 712
Score = 29.4 bits (66), Expect = 0.60
Identities = 25/84 (29%), Positives = 37/84 (44%), Gaps = 21/84 (25%)
Query: 7 LIGASGVGKTTIAKQVVLNSEYLVMPVGVTTRRPRVDEKQYIDYRFISQSQFKGWKHTGL 66
L+G VGK+++ Q+ +V + TTR P VDE ID + W L
Sbjct: 455 LVGRPNVGKSSLLNQLTHEERAVVNDLAGTTRDP-VDEIVEIDG--------EDW----L 501
Query: 67 FIETTKVRD--------EYYGYLK 82
FI+T ++ EYY L+
Sbjct: 502 FIDTAGIKRRQHKLTGAEYYSSLR 525
>gnl|CDD|184920 PRK14956, PRK14956, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 484
Score = 29.1 bits (65), Expect = 0.64
Identities = 10/20 (50%), Positives = 14/20 (70%)
Query: 1 MAHIFVLIGASGVGKTTIAK 20
+ H ++ G GVGKTTIA+
Sbjct: 39 IGHAYIFFGPRGVGKTTIAR 58
>gnl|CDD|179346 PRK01889, PRK01889, GTPase RsgA; Reviewed.
Length = 356
Score = 29.1 bits (66), Expect = 0.64
Identities = 8/14 (57%), Positives = 12/14 (85%)
Query: 6 VLIGASGVGKTTIA 19
L+G+SGVGK+T+
Sbjct: 199 ALLGSSGVGKSTLV 212
>gnl|CDD|162266 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.
Length = 495
Score = 29.2 bits (66), Expect = 0.66
Identities = 16/45 (35%), Positives = 22/45 (48%), Gaps = 10/45 (22%)
Query: 7 LIGASGVGKTTIAKQV----------VLNSEYLVMPVGVTTRRPR 41
L+G G GKT +AK V + S+++ M VGV R R
Sbjct: 93 LVGPPGTGKTLLAKAVAGEAGVPFFSISGSDFVEMFVGVGASRVR 137
>gnl|CDD|183453 PRK12338, PRK12338, hypothetical protein; Provisional.
Length = 319
Score = 29.0 bits (65), Expect = 0.69
Identities = 14/28 (50%), Positives = 22/28 (78%), Gaps = 3/28 (10%)
Query: 6 VLIG-ASGVGKTTIAKQVV--LNSEYLV 30
+LIG ASG+GK+TIA ++ LN ++L+
Sbjct: 7 ILIGSASGIGKSTIASELARTLNIKHLI 34
>gnl|CDD|163508 TIGR03796, NHPM_micro_ABC1, NHPM bacteriocin system ABC
transporter, peptidase/ATP-binding protein. This
protein describes an multidomain ABC transporter subunit
that is one of three protein families associated with
some regularity with a distinctive family of putative
bacteriocins. It includes a bacteriocin-processing
peptidase domain at the N-terminus. Model TIGR03793
describes a conserved propeptide region for this
bacteriocin family, unusual because it shows obvious
homology a region of the enzyme nitrile hydratase up to
the classic Gly-Gly cleavage motif. This family is
therefore predicted to be a subunit of a bacteriocin
processing and export system characteristic to this
system that we designate NHPM, Nitrile Hydratase
Propeptide Microcin.
Length = 710
Score = 29.1 bits (66), Expect = 0.75
Identities = 11/16 (68%), Positives = 13/16 (81%)
Query: 7 LIGASGVGKTTIAKQV 22
L+G SG GK+TIAK V
Sbjct: 510 LVGGSGSGKSTIAKLV 525
>gnl|CDD|149019 pfam07728, AAA_5, AAA domain (dynein-related subfamily). This
Pfam entry includes some of the AAA proteins not
detected by the pfam00004 model.
Length = 139
Score = 28.8 bits (65), Expect = 0.82
Identities = 7/31 (22%), Positives = 16/31 (51%), Gaps = 3/31 (9%)
Query: 5 FVLIGASGVGKTTIAKQV---VLNSEYLVMP 32
+L+G G GK+ +A+++ + N +
Sbjct: 2 VLLVGPPGTGKSELAERLAAALSNRPVFYVQ 32
>gnl|CDD|182791 PRK10865, PRK10865, protein disaggregation chaperone; Provisional.
Length = 857
Score = 28.7 bits (64), Expect = 0.84
Identities = 17/37 (45%), Positives = 22/37 (59%), Gaps = 6/37 (16%)
Query: 6 VLIGASGVGKTTIAK---QVVLNSEYLVMPVGVTTRR 39
VLIG GVGKT I + Q ++N E +P G+ RR
Sbjct: 203 VLIGEPGVGKTAIVEGLAQRIINGE---VPEGLKGRR 236
>gnl|CDD|184923 PRK14959, PRK14959, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 624
Score = 28.9 bits (64), Expect = 0.88
Identities = 37/135 (27%), Positives = 54/135 (40%), Gaps = 23/135 (17%)
Query: 1 MAHIFVLIGASGVGKTTIAKQV--VLNSEYLVM--PVGVTTRRPRVDEKQYIDYRFISQS 56
+A ++ G GVGKTTIA+ LN E P + +V + ++D I +
Sbjct: 37 VAPAYLFSGTRGVGKTTIARIFAKALNCETAPTGEPCNTCEQCRKVTQGMHVDVVEIDGA 96
Query: 57 QFKGWKHTGLFIETTKVRDEYYGYLKEDINNPMEHGYDILLI-----LTHQGL-APLKKL 110
+G I+ K E GY PME Y + +I LT + A LK L
Sbjct: 97 SNRG-------IDDAKRLKEAIGYA------PMEGRYKVFIIDEAHMLTREAFNALLKTL 143
Query: 111 YEDQVTSIFIAPPSE 125
E F+ +E
Sbjct: 144 EEPPARVTFVLATTE 158
>gnl|CDD|177379 PHA02544, 44, clamp loader, small subunit; Provisional.
Length = 316
Score = 28.8 bits (65), Expect = 0.96
Identities = 9/31 (29%), Positives = 18/31 (58%), Gaps = 2/31 (6%)
Query: 3 HIFVLIGASGVGKTTIAKQVV--LNSEYLVM 31
++ + + G GKTT+AK + + +E L +
Sbjct: 44 NMLLHSPSPGTGKTTVAKALCNEVGAEVLFV 74
>gnl|CDD|179638 PRK03731, aroL, shikimate kinase II; Reviewed.
Length = 171
Score = 28.8 bits (65), Expect = 0.99
Identities = 9/20 (45%), Positives = 11/20 (55%)
Query: 1 MAHIFVLIGASGVGKTTIAK 20
M L+GA G GKTT+
Sbjct: 1 MTQPLFLVGARGCGKTTVGM 20
>gnl|CDD|181235 PRK08118, PRK08118, topology modulation protein; Reviewed.
Length = 167
Score = 28.4 bits (64), Expect = 1.0
Identities = 13/28 (46%), Positives = 20/28 (71%), Gaps = 3/28 (10%)
Query: 6 VLIGASGVGKTTIAKQVVLNSEYLVMPV 33
+LIG+ G GK+T+A+Q+ E L +PV
Sbjct: 5 ILIGSGGSGKSTLARQL---GEKLNIPV 29
>gnl|CDD|180213 PRK05703, flhF, flagellar biosynthesis regulator FlhF; Validated.
Length = 424
Score = 28.3 bits (64), Expect = 1.2
Identities = 10/18 (55%), Positives = 14/18 (77%), Gaps = 1/18 (5%)
Query: 4 IFVLIGASGVGKTT-IAK 20
+ L+G +GVGKTT +AK
Sbjct: 223 VVALVGPTGVGKTTTLAK 240
>gnl|CDD|181191 PRK07994, PRK07994, DNA polymerase III subunits gamma and tau;
Validated.
Length = 647
Score = 28.3 bits (64), Expect = 1.2
Identities = 10/17 (58%), Positives = 12/17 (70%)
Query: 3 HIFVLIGASGVGKTTIA 19
H ++ G GVGKTTIA
Sbjct: 39 HAYLFSGTRGVGKTTIA 55
>gnl|CDD|162958 TIGR02639, ClpA, ATP-dependent Clp protease ATP-binding subunit
clpA.
Length = 731
Score = 28.5 bits (64), Expect = 1.2
Identities = 10/17 (58%), Positives = 13/17 (76%)
Query: 5 FVLIGASGVGKTTIAKQ 21
F+ G +GVGKT +AKQ
Sbjct: 487 FLFTGPTGVGKTELAKQ 503
>gnl|CDD|163223 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.
Length = 852
Score = 28.4 bits (64), Expect = 1.2
Identities = 10/14 (71%), Positives = 10/14 (71%)
Query: 6 VLIGASGVGKTTIA 19
VLIG GVGKT I
Sbjct: 198 VLIGEPGVGKTAIV 211
>gnl|CDD|179793 PRK04220, PRK04220, 2-phosphoglycerate kinase; Provisional.
Length = 301
Score = 28.4 bits (64), Expect = 1.2
Identities = 12/17 (70%), Positives = 14/17 (82%), Gaps = 1/17 (5%)
Query: 4 IFVLIG-ASGVGKTTIA 19
I +LIG ASGVG +TIA
Sbjct: 93 IIILIGGASGVGTSTIA 109
>gnl|CDD|147939 pfam06048, DUF927, Domain of unknown function (DUF927). Family of
bacterial proteins of unknown function.
Length = 284
Score = 28.4 bits (64), Expect = 1.2
Identities = 8/17 (47%), Positives = 9/17 (52%)
Query: 4 IFVLIGASGVGKTTIAK 20
F +G S GKTT K
Sbjct: 193 GFHFVGDSSTGKTTALK 209
>gnl|CDD|163051 TIGR02868, CydC, thiol reductant ABC exporter, CydC subunit. The
gene pair cydCD encodes an ABC-family transporter in
which each gene contains an N-terminal membrane-spanning
domain (pfam00664) and a C-terminal ATP-binding domain
(pfam00005). In E. coli these genes were discovered as
mutants which caused the terminal heme-copper oxidase
complex cytochrome bd to fail to assemble. Recent work
has shown that the transporter is involved in export of
redox-active thiol compounds such as cysteine and
glutathione. The linkage to assembly of the cytochrome
bd complex is further supported by the conserved operon
structure found outside the gammaproteobacteria
(cydABCD) containing both the transporter and oxidase
genes components. The genes used as the seed members for
this model are all either found in the
gammproteobacterial context or the CydABCD context. All
members of this family scoring above trusted at the time
of its creation were from genomes which encode a
cytochrome bd complex.
Length = 529
Score = 28.1 bits (63), Expect = 1.3
Identities = 11/47 (23%), Positives = 18/47 (38%), Gaps = 11/47 (23%)
Query: 7 LIGASGVGKTTIAK-----------QVVLNSEYLVMPVGVTTRRPRV 42
++G SG GK+T+ +V L+ + RR V
Sbjct: 366 ILGPSGSGKSTLLMLLTGLLDPLQGEVTLDGVSVSSLQDELRRRISV 412
>gnl|CDD|163222 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.
Length = 852
Score = 28.0 bits (63), Expect = 1.4
Identities = 10/16 (62%), Positives = 13/16 (81%)
Query: 4 IFVLIGASGVGKTTIA 19
+F+L+G SGVGKT A
Sbjct: 598 VFLLVGPSGVGKTETA 613
>gnl|CDD|179218 PRK01077, PRK01077, cobyrinic acid a,c-diamide synthase;
Validated.
Length = 451
Score = 27.8 bits (63), Expect = 1.5
Identities = 8/16 (50%), Positives = 11/16 (68%), Gaps = 2/16 (12%)
Query: 6 VLIGA--SGVGKTTIA 19
++I A SG GKTT+
Sbjct: 6 LVIAAPASGSGKTTVT 21
>gnl|CDD|183702 PRK12723, PRK12723, flagellar biosynthesis regulator FlhF;
Provisional.
Length = 388
Score = 27.9 bits (62), Expect = 1.6
Identities = 12/24 (50%), Positives = 17/24 (70%), Gaps = 1/24 (4%)
Query: 4 IFVLIGASGVGK-TTIAKQVVLNS 26
+F+L+G +GVGK TTIAK +
Sbjct: 176 VFILVGPTGVGKTTTIAKLAAIYG 199
>gnl|CDD|178657 PLN03110, PLN03110, Rab GTPase; Provisional.
Length = 216
Score = 28.0 bits (62), Expect = 1.7
Identities = 26/81 (32%), Positives = 36/81 (44%), Gaps = 14/81 (17%)
Query: 6 VLIGASGVGKTTIAKQVVLNSEYL----VMPVGVTTRRPRVDEK----QYID------YR 51
VLIG SGVGK+ I + N L + V TR +V+ K Q D YR
Sbjct: 16 VLIGDSGVGKSNILSRFTRNEFCLESKSTIGVEFATRTLQVEGKTVKAQIWDTAGQERYR 75
Query: 52 FISQSQFKGWKHTGLFIETTK 72
I+ + ++G L + TK
Sbjct: 76 AITSAYYRGAVGALLVYDITK 96
>gnl|CDD|162313 TIGR01351, adk, adenylate kinases. 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.
Length = 210
Score = 27.6 bits (62), Expect = 2.0
Identities = 9/19 (47%), Positives = 12/19 (63%)
Query: 5 FVLIGASGVGKTTIAKQVV 23
VL+G G GK T AK++
Sbjct: 2 LVLLGPPGSGKGTQAKRIA 20
>gnl|CDD|173186 PRK14723, flhF, flagellar biosynthesis regulator FlhF; Provisional.
Length = 767
Score = 27.5 bits (61), Expect = 2.0
Identities = 10/18 (55%), Positives = 13/18 (72%), Gaps = 1/18 (5%)
Query: 4 IFVLIGASGVGK-TTIAK 20
+ L+G +GVGK TT AK
Sbjct: 187 VLALVGPTGVGKTTTTAK 204
>gnl|CDD|163225 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.
Length = 1169
Score = 27.7 bits (62), Expect = 2.1
Identities = 7/17 (41%), Positives = 12/17 (70%)
Query: 5 FVLIGASGVGKTTIAKQ 21
+++IG G GKTT+ +
Sbjct: 114 YLVIGPPGSGKTTLLQN 130
>gnl|CDD|184935 PRK14971, PRK14971, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 614
Score = 27.4 bits (61), Expect = 2.2
Identities = 10/20 (50%), Positives = 14/20 (70%)
Query: 1 MAHIFVLIGASGVGKTTIAK 20
+AH ++ G GVGKTT A+
Sbjct: 38 LAHAYLFCGPRGVGKTTCAR 57
>gnl|CDD|178861 PRK00098, PRK00098, GTPase RsgA; Reviewed.
Length = 298
Score = 27.5 bits (62), Expect = 2.2
Identities = 9/16 (56%), Positives = 12/16 (75%)
Query: 3 HIFVLIGASGVGKTTI 18
+ VL G SGVGK+T+
Sbjct: 165 KVTVLAGQSGVGKSTL 180
>gnl|CDD|180615 PRK06547, PRK06547, hypothetical protein; Provisional.
Length = 172
Score = 27.4 bits (61), Expect = 2.4
Identities = 12/21 (57%), Positives = 14/21 (66%), Gaps = 1/21 (4%)
Query: 4 IFVLI-GASGVGKTTIAKQVV 23
I VLI G SG GKTT+A +
Sbjct: 16 ITVLIDGRSGSGKTTLAGALA 36
>gnl|CDD|181939 PRK09544, znuC, high-affinity zinc transporter ATPase; Reviewed.
Length = 251
Score = 27.4 bits (61), Expect = 2.5
Identities = 18/53 (33%), Positives = 26/53 (49%), Gaps = 10/53 (18%)
Query: 3 HIFVLIGASGVGKTTIAKQVVLNSEYLVMPVGVTTRRPR------VDEKQYID 49
I L+G +G GK+T+ + VVL LV P +R V +K Y+D
Sbjct: 31 KILTLLGPNGAGKSTLVR-VVLG---LVAPDEGVIKRNGKLRIGYVPQKLYLD 79
>gnl|CDD|163042 TIGR02857, CydD, thiol reductant ABC exporter, CydD subunit.
Unfortunately, the gene symbol nomenclature adopted
based on this operon in B. subtilis assigns cydC to the
third gene in the operon where this gene is actually
homologous to the E. coli cydD gene. We have chosen to
name all homologs in this family in accordance with the
precedence of publication of the E. coli name, CydD.
Length = 529
Score = 27.3 bits (61), Expect = 2.7
Identities = 7/13 (53%), Positives = 10/13 (76%)
Query: 6 VLIGASGVGKTTI 18
L+G SG GK+T+
Sbjct: 352 ALVGPSGAGKSTL 364
>gnl|CDD|183226 PRK11607, potG, putrescine transporter ATP-binding subunit;
Provisional.
Length = 377
Score = 27.1 bits (60), Expect = 2.8
Identities = 10/15 (66%), Positives = 13/15 (86%)
Query: 4 IFVLIGASGVGKTTI 18
IF L+GASG GK+T+
Sbjct: 47 IFALLGASGCGKSTL 61
>gnl|CDD|182441 PRK10416, PRK10416, signal recognition particle-docking protein
FtsY; Provisional.
Length = 318
Score = 27.0 bits (61), Expect = 2.9
Identities = 9/19 (47%), Positives = 14/19 (73%), Gaps = 1/19 (5%)
Query: 3 HIFVLIGASGVGKTT-IAK 20
+ +++G +GVGKTT I K
Sbjct: 115 FVILVVGVNGVGKTTTIGK 133
>gnl|CDD|179681 PRK03946, pdxA, 4-hydroxythreonine-4-phosphate dehydrogenase;
Provisional.
Length = 307
Score = 26.9 bits (60), Expect = 3.0
Identities = 12/17 (70%), Positives = 13/17 (76%), Gaps = 2/17 (11%)
Query: 102 QGLAPLKKLYEDQVTSI 118
QGLAPLK LY D+ SI
Sbjct: 246 QGLAPLKALYFDE--SI 260
>gnl|CDD|162555 TIGR01842, type_I_sec_PrtD, type I secretion system ABC
transporter, PrtD 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.
Length = 544
Score = 26.9 bits (60), Expect = 3.0
Identities = 9/20 (45%), Positives = 14/20 (70%)
Query: 4 IFVLIGASGVGKTTIAKQVV 23
+IG SG GK+T+A+ +V
Sbjct: 346 ALAIIGPSGSGKSTLARLIV 365
>gnl|CDD|116338 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 = 26.8 bits (60), Expect = 3.1
Identities = 9/18 (50%), Positives = 14/18 (77%)
Query: 5 FVLIGASGVGKTTIAKQV 22
F+ +G +GVGKT +AK +
Sbjct: 6 FLFLGPTGVGKTELAKAL 23
>gnl|CDD|184925 PRK14961, PRK14961, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 363
Score = 27.1 bits (60), Expect = 3.1
Identities = 11/18 (61%), Positives = 14/18 (77%)
Query: 3 HIFVLIGASGVGKTTIAK 20
H ++L G GVGKTTIA+
Sbjct: 39 HAWLLSGTRGVGKTTIAR 56
>gnl|CDD|161928 TIGR00557, pdxA, 4-hydroxythreonine-4-phosphate dehydrogenase.
This model represents PdxA, an NAD+-dependent
4-hydroxythreonine 4-phosphate dehydrogenase (EC
1.1.1.262) active in pyridoxal phosphate biosynthesis.
Length = 320
Score = 27.1 bits (61), Expect = 3.3
Identities = 12/24 (50%), Positives = 15/24 (62%), Gaps = 1/24 (4%)
Query: 92 GYDILLILTH-QGLAPLKKLYEDQ 114
YD +L + H QGL PLK L D+
Sbjct: 252 KYDAVLAMYHDQGLIPLKYLGFDE 275
>gnl|CDD|180682 PRK06761, PRK06761, hypothetical protein; Provisional.
Length = 282
Score = 27.0 bits (60), Expect = 3.3
Identities = 9/29 (31%), Positives = 16/29 (55%), Gaps = 3/29 (10%)
Query: 1 MAHIFVLIGASGVGKTTIAKQVVLNSEYL 29
M + ++ G G GK+T AK + ++ L
Sbjct: 2 MTKLIIIEGLPGFGKSTTAKML---NDIL 27
>gnl|CDD|150614 pfam09960, DUF2194, Uncharacterized protein conserved in bacteria
(DUF2194). This domain, found in various hypothetical
bacterial proteins, has no known function.
Length = 573
Score = 27.0 bits (60), Expect = 3.4
Identities = 21/68 (30%), Positives = 28/68 (41%), Gaps = 22/68 (32%)
Query: 62 KHTGLFIET-------------TKVRDEYYGYLKEDINNPME---HGYDILLILTHQGLA 105
K+TG+ IE K DE+ + KE +N+ E HGY+ HQ L
Sbjct: 290 KYTGVVIENYNNKTTPPFSFFEQKNTDEFIYFGKELLNSGGEIGIHGYN------HQPLL 343
Query: 106 PLKKLYED 113
P Y D
Sbjct: 344 PENVDYGD 351
>gnl|CDD|133910 PHA00540, PHA00540, hypothetical protein.
Length = 715
Score = 26.5 bits (58), Expect = 3.7
Identities = 14/48 (29%), Positives = 23/48 (47%), Gaps = 1/48 (2%)
Query: 24 LNSEYLVMPVGVTTRRPRVDEKQYIDYRFISQSQFKGWKHTGLFIETT 71
LN E + +T + ++E +I+ F+ S F+ W T FI T
Sbjct: 31 LNEEQYTLKQESSTGKG-INETDFINTMFLRSSFFENWSETNYFINPT 77
>gnl|CDD|183986 PRK13342, PRK13342, recombination factor protein RarA; Reviewed.
Length = 413
Score = 26.6 bits (60), Expect = 3.9
Identities = 8/16 (50%), Positives = 11/16 (68%)
Query: 5 FVLIGASGVGKTTIAK 20
+L G G GKTT+A+
Sbjct: 39 MILWGPPGTGKTTLAR 54
>gnl|CDD|183438 PRK12323, PRK12323, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 700
Score = 26.4 bits (58), Expect = 4.3
Identities = 8/18 (44%), Positives = 13/18 (72%)
Query: 3 HIFVLIGASGVGKTTIAK 20
H ++ G GVGKTT+++
Sbjct: 39 HAYLFTGTRGVGKTTLSR 56
>gnl|CDD|149505 pfam08477, Miro, Miro-like protein. Mitochondrial Rho proteins
(Miro-1 and Miro-2), are atypical Rho GTPases. They
have a unique domain organisation, with tandem
GTP-binding domains and two EF hand domains
(pfam00036), that may bind calcium. They are also
larger than classical small GTPases. It has been
proposed that they are involved in mitochondrial
homeostasis and apoptosis.
Length = 118
Score = 26.6 bits (59), Expect = 4.3
Identities = 14/62 (22%), Positives = 25/62 (40%), Gaps = 7/62 (11%)
Query: 5 FVLIGASGVGKTTIAKQVV-------LNSEYLVMPVGVTTRRPRVDEKQYIDYRFISQSQ 57
V+IG G GK+++ Q+V + E + V T D + + F + +
Sbjct: 2 VVVIGDKGSGKSSLLSQLVGGEFPPEIPEEIQGDTLAVDTLEVDGDTELLHIWDFGGREE 61
Query: 58 FK 59
K
Sbjct: 62 LK 63
>gnl|CDD|162366 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.
Length = 720
Score = 26.3 bits (58), Expect = 4.5
Identities = 8/20 (40%), Positives = 13/20 (65%)
Query: 4 IFVLIGASGVGKTTIAKQVV 23
+ +L G G GKTTI + ++
Sbjct: 340 VVILTGGPGTGKTTITRAII 359
>gnl|CDD|128472 smart00175, RAB, Rab subfamily of small GTPases. Rab GTPases are
implicated in vesicle trafficking.
Length = 164
Score = 26.3 bits (59), Expect = 4.9
Identities = 8/14 (57%), Positives = 12/14 (85%)
Query: 5 FVLIGASGVGKTTI 18
+LIG SGVGK+++
Sbjct: 3 IILIGDSGVGKSSL 16
>gnl|CDD|180523 PRK06305, PRK06305, DNA polymerase III subunits gamma and tau;
Validated.
Length = 451
Score = 26.3 bits (58), Expect = 4.9
Identities = 9/20 (45%), Positives = 13/20 (65%)
Query: 1 MAHIFVLIGASGVGKTTIAK 20
AH ++ G G GKTT+A+
Sbjct: 38 AAHAYLFSGIRGTGKTTLAR 57
>gnl|CDD|180730 PRK06851, PRK06851, hypothetical protein; Provisional.
Length = 367
Score = 26.5 bits (59), Expect = 4.9
Identities = 9/20 (45%), Positives = 14/20 (70%)
Query: 3 HIFVLIGASGVGKTTIAKQV 22
IF+L G G GK+T+ K++
Sbjct: 31 RIFILKGGPGTGKSTLMKKI 50
>gnl|CDD|130254 TIGR01186, proV, glycine betaine/L-proline transport ATP binding
subunit. This model describes the glycine
betaine/L-proline ATP binding subunit in bacteria and
its equivalents in archaea. This transport system
belong to the larger ATP-Binding Cassette (ABC)
transporter superfamily. The characteristic feature of
these transporter is the obligatory coupling of ATP
hydrolysis to substrate translocation. The minimal
configuration of bacterial ABC transport system: an
ATPase or ATP binding subunit; An integral membrane
protein; a hydrophilic polypetpide, which likely
functions as substrate binding protein. Functionally,
this transport system is involved in osmoregulation.
Under conditions of stress, the organism recruits these
transport system to accumulate glycine betaine and
other solutes which offer osmo-protection. It has been
demonstrated that glycine betaine uptake is accompanied
by symport with sodium ions. The locus has been named
variously as proU or opuA. A gene library from L.lactis
functionally complements an E.coli proU mutant. The
comlementing locus is similar to a opuA locus in
B.sutlis. This clarifies the differences in
nomenclature.
Length = 363
Score = 26.4 bits (58), Expect = 5.0
Identities = 9/17 (52%), Positives = 13/17 (76%)
Query: 4 IFVLIGASGVGKTTIAK 20
IFV++G SG GK+T +
Sbjct: 21 IFVIMGLSGSGKSTTVR 37
>gnl|CDD|178910 PRK00166, apaH, diadenosine tetraphosphatase; Reviewed.
Length = 275
Score = 26.3 bits (59), Expect = 5.0
Identities = 11/36 (30%), Positives = 18/36 (50%), Gaps = 3/36 (8%)
Query: 94 DILLILTHQGLAPLKKLYEDQVTSIFIAPPSEAELI 129
D+ L+ G+ KK +D + I AP + EL+
Sbjct: 67 DLHLLAVAAGIKRNKK--KDTLDPILEAPDRD-ELL 99
>gnl|CDD|184917 PRK14953, PRK14953, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 486
Score = 26.3 bits (58), Expect = 5.0
Identities = 9/20 (45%), Positives = 14/20 (70%)
Query: 1 MAHIFVLIGASGVGKTTIAK 20
++H ++ G G GKTTIA+
Sbjct: 37 VSHAYIFAGPRGTGKTTIAR 56
>gnl|CDD|179962 PRK05201, hslU, ATP-dependent protease ATP-binding subunit HslU;
Provisional.
Length = 443
Score = 26.2 bits (59), Expect = 5.0
Identities = 9/12 (75%), Positives = 10/12 (83%)
Query: 8 IGASGVGKTTIA 19
IG +GVGKT IA
Sbjct: 56 IGPTGVGKTEIA 67
>gnl|CDD|184172 PRK13600, PRK13600, putative ribosomal protein L7Ae-like;
Provisional.
Length = 84
Score = 26.4 bits (58), Expect = 5.0
Identities = 13/25 (52%), Positives = 16/25 (64%)
Query: 107 LKKLYEDQVTSIFIAPPSEAELIQR 131
LK L +DQVTS+ IA E L+ R
Sbjct: 22 LKALKKDQVTSLIIAEDVEVYLMTR 46
>gnl|CDD|131817 TIGR02770, nickel_nikD, nickel import ATP-binding protein NikD.
This family represents the NikD subunit of a
multisubunit nickel import ABC transporter complex.
Nickel, once imported, may be used in urease and in
certain classes of hydrogenase and superoxide
dismutase. NikD and NikE are homologous.
Length = 230
Score = 26.2 bits (58), Expect = 5.4
Identities = 13/69 (18%), Positives = 28/69 (40%), Gaps = 10/69 (14%)
Query: 1 MAHIFVLIGASGVGKTTIAKQVVLNSEYLVMPVGVTTRRPRVDEKQYIDYRFISQSQFKG 60
+ L+G SG GK+ ++ ++P G+T + +D R + +G
Sbjct: 11 RGEVLALVGESGSGKSLTCLAIL-----GLLPPGLTQTSGEI----LLDGRPLLPLSIRG 61
Query: 61 WKHTGLFIE 69
+H ++
Sbjct: 62 -RHIATIMQ 69
>gnl|CDD|128571 smart00275, G_alpha, G protein alpha subunit. Subunit of G
proteins that contains the guanine nucleotide binding
site.
Length = 342
Score = 26.0 bits (58), Expect = 5.6
Identities = 9/16 (56%), Positives = 12/16 (75%)
Query: 7 LIGASGVGKTTIAKQV 22
L+GA GK+TI KQ+
Sbjct: 26 LLGAGESGKSTILKQM 41
>gnl|CDD|181906 PRK09493, glnQ, glutamine ABC transporter ATP-binding protein;
Reviewed.
Length = 240
Score = 26.2 bits (58), Expect = 5.6
Identities = 17/47 (36%), Positives = 26/47 (55%), Gaps = 5/47 (10%)
Query: 4 IFVLIGASGVGKTT----IAKQVVLNSEYLVMPVGVTTRRPRVDEKQ 46
+ V+IG SG GK+T I K + S L++ G+ P+VDE+
Sbjct: 29 VVVIIGPSGSGKSTLLRCINKLEEITSGDLIVD-GLKVNDPKVDERL 74
>gnl|CDD|183001 PRK11153, metN, DL-methionine transporter ATP-binding subunit;
Provisional.
Length = 343
Score = 25.9 bits (58), Expect = 5.8
Identities = 10/14 (71%), Positives = 12/14 (85%)
Query: 4 IFVLIGASGVGKTT 17
IF +IGASG GK+T
Sbjct: 33 IFGVIGASGAGKST 46
>gnl|CDD|182917 PRK11034, clpA, ATP-dependent Clp protease ATP-binding subunit;
Provisional.
Length = 758
Score = 26.0 bits (57), Expect = 6.1
Identities = 10/15 (66%), Positives = 13/15 (86%)
Query: 6 VLIGASGVGKTTIAK 20
+L+G SGVGKT IA+
Sbjct: 211 LLVGESGVGKTAIAE 225
>gnl|CDD|173184 PRK14721, flhF, flagellar biosynthesis regulator FlhF; Provisional.
Length = 420
Score = 26.1 bits (57), Expect = 6.1
Identities = 9/14 (64%), Positives = 12/14 (85%)
Query: 4 IFVLIGASGVGKTT 17
++ LIG +GVGKTT
Sbjct: 193 VYALIGPTGVGKTT 206
>gnl|CDD|180308 PRK05896, PRK05896, DNA polymerase III subunits gamma and tau;
Validated.
Length = 605
Score = 26.0 bits (57), Expect = 6.2
Identities = 9/20 (45%), Positives = 14/20 (70%)
Query: 1 MAHIFVLIGASGVGKTTIAK 20
+ H ++ G G+GKT+IAK
Sbjct: 37 LTHAYIFSGPRGIGKTSIAK 56
>gnl|CDD|183231 PRK11614, livF, leucine/isoleucine/valine transporter ATP-binding
subunit; Provisional.
Length = 237
Score = 26.0 bits (57), Expect = 6.4
Identities = 10/15 (66%), Positives = 12/15 (80%)
Query: 4 IFVLIGASGVGKTTI 18
I LIGA+G GKTT+
Sbjct: 33 IVTLIGANGAGKTTL 47
>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 = 25.8 bits (57), Expect = 6.6
Identities = 11/25 (44%), Positives = 14/25 (56%), Gaps = 2/25 (8%)
Query: 6 VLIGASGVGKTTIAKQVVLNSEYLV 30
L G SG GK+T+ K + N YL
Sbjct: 38 ALSGPSGAGKSTLLKSLYAN--YLP 60
>gnl|CDD|183080 PRK11300, livG, leucine/isoleucine/valine transporter ATP-binding
subunit; Provisional.
Length = 255
Score = 25.7 bits (57), Expect = 6.7
Identities = 9/15 (60%), Positives = 11/15 (73%)
Query: 4 IFVLIGASGVGKTTI 18
I LIG +G GKTT+
Sbjct: 33 IVSLIGPNGAGKTTV 47
>gnl|CDD|163188 TIGR03223, Phn_opern_protn, putative phosphonate metabolism
protein. This family of proteins is observed in the
vicinity of other caharacterized genes involved in the
catabolism of phosphonates via the3 C-P lyase system
(GenProp0232), its function is unknown. These proteins
are members of the somewhat broader pfam06299 model
"Protein of unknown function (DUF1045)" which contains
proteins found in a different genomic context as well.
Length = 228
Score = 25.8 bits (57), Expect = 6.8
Identities = 13/41 (31%), Positives = 18/41 (43%), Gaps = 3/41 (7%)
Query: 97 LILTHQGLAPLKKLYEDQVTSI--FIAPPSEAELIQRRIKR 135
L L+ L V + F AP +EAEL +RR +
Sbjct: 107 LRPAA-PCPALQALAAACVRELDPFRAPLTEAELARRRPDQ 146
>gnl|CDD|140006 PRK13949, PRK13949, shikimate kinase; Provisional.
Length = 169
Score = 25.8 bits (57), Expect = 6.9
Identities = 12/20 (60%), Positives = 14/20 (70%), Gaps = 1/20 (5%)
Query: 1 MAHIFVLIGASGVGKTTIAK 20
MA IF L+G G GKTT+ K
Sbjct: 1 MARIF-LVGYMGAGKTTLGK 19
>gnl|CDD|180114 PRK05480, PRK05480, uridine/cytidine kinase; Provisional.
Length = 209
Score = 25.9 bits (58), Expect = 6.9
Identities = 8/15 (53%), Positives = 10/15 (66%)
Query: 9 GASGVGKTTIAKQVV 23
G SG GKTT+A +
Sbjct: 13 GGSGSGKTTVASTIY 27
>gnl|CDD|161852 TIGR00390, hslU, ATP-dependent protease HslVU, ATPase subunit.
This model represents the ATPase subunit of HslVU,
while the proteasome-related peptidase subunit is HslV.
Residues 54-61 of the model contain a P-loop
ATP-binding motif. Cys-287 of E. coli (position 308 in
the seed alignment), studied in PubMed:98389714, is Ser
in other members of the seed alignment.
Length = 441
Score = 25.5 bits (56), Expect = 7.4
Identities = 9/17 (52%), Positives = 15/17 (88%)
Query: 6 VLIGASGVGKTTIAKQV 22
++IG +GVGKT IA+++
Sbjct: 51 LMIGPTGVGKTEIARRL 67
>gnl|CDD|184591 PRK14250, PRK14250, phosphate ABC transporter ATP-binding
protein; Provisional.
Length = 241
Score = 25.5 bits (56), Expect = 7.5
Identities = 8/20 (40%), Positives = 13/20 (65%)
Query: 1 MAHIFVLIGASGVGKTTIAK 20
I+ ++G SG GK+T+ K
Sbjct: 28 GGAIYTIVGPSGAGKSTLIK 47
>gnl|CDD|168472 PRK06217, PRK06217, hypothetical protein; Validated.
Length = 183
Score = 25.8 bits (57), Expect = 7.6
Identities = 9/19 (47%), Positives = 11/19 (57%), Gaps = 1/19 (5%)
Query: 1 MAHIFVLIGASGVGKTTIA 19
M I + GASG G TT+
Sbjct: 1 MMRIHIT-GASGSGTTTLG 18
>gnl|CDD|180989 PRK07471, PRK07471, DNA polymerase III subunit delta'; Validated.
Length = 365
Score = 25.8 bits (57), Expect = 7.6
Identities = 7/19 (36%), Positives = 13/19 (68%)
Query: 1 MAHIFVLIGASGVGKTTIA 19
+ H +++ G G+GK T+A
Sbjct: 40 LHHAWLIGGPQGIGKATLA 58
>gnl|CDD|178749 PLN03210, PLN03210, Resistant to P. syringae 6; Provisional.
Length = 1153
Score = 25.6 bits (56), Expect = 7.6
Identities = 15/48 (31%), Positives = 22/48 (45%), Gaps = 12/48 (25%)
Query: 9 GASGVGKTTIAKQVVLNSEYLVMPVGVTTRRPRVDEKQYIDYRFISQS 56
G+SG+GKTTIA+ + + +ID FIS+S
Sbjct: 214 GSSGIGKTTIARALFSRLSR------------QFQSSVFIDRAFISKS 249
>gnl|CDD|161686 TIGR00064, ftsY, signal recognition particle-docking protein
FtsY. There is a weak division between FtsY and SRP54;
both are GTPases. In E.coli, ftsY is an essential gene
located in an operon with cell division genes ftsE and
ftsX, but its apparent function is as the signal
recognition particle docking protein.
Length = 272
Score = 25.7 bits (57), Expect = 8.1
Identities = 10/18 (55%), Positives = 14/18 (77%), Gaps = 1/18 (5%)
Query: 4 IFVLIGASGVGKTT-IAK 20
+ + +G +GVGKTT IAK
Sbjct: 74 VILFVGVNGVGKTTTIAK 91
>gnl|CDD|151168 pfam10662, PduV-EutP, Ethanolamine utilisation - propanediol
utilisation. Members of this family function in
ethanolamine and propanediol degradation pathways,
however the exact roles of these proteins is poorly
understood.
Length = 143
Score = 25.7 bits (57), Expect = 8.3
Identities = 15/29 (51%), Positives = 17/29 (58%), Gaps = 3/29 (10%)
Query: 1 MAHIFVLIGASGVGKTTIAKQVVLNSEYL 29
M I LIG SG GKTT+ + LN E L
Sbjct: 1 MKKIM-LIGRSGCGKTTLTQ--ALNGEEL 26
>gnl|CDD|131367 TIGR02314, ABC_MetN, D-methionine ABC transporter, ATP-binding
protein. Members of this family are the ATP-binding
protein of the D-methionine ABC transporter complex.
Known members belong to the Proteobacteria.
Length = 343
Score = 25.6 bits (56), Expect = 8.6
Identities = 11/21 (52%), Positives = 16/21 (76%)
Query: 4 IFVLIGASGVGKTTIAKQVVL 24
I+ +IGASG GK+T+ + V L
Sbjct: 33 IYGVIGASGAGKSTLIRCVNL 53
>gnl|CDD|130261 TIGR01193, bacteriocin_ABC, ABC-type bacteriocin transporter. This
model describes ABC-type bacteriocin transporter. The
amino terminal domain (pfam03412) processes the
N-terminal leader peptide from the bacteriocin while
C-terminal domains resemble ABC transporter membrane
protein and ATP-binding cassette domain. In general,
bacteriocins are agents which are responsible for
killing or inhibiting the closely related species or
even different strains of the same species. Bacteriocins
are usually encoded by bacterial plasmids. Bacteriocins
are named after the species and hence in literature one
encounters various names e.g., leucocin from Leuconostic
geldium; pedicocin from Pedicoccus acidilactici; sakacin
from Lactobacillus sake etc.
Length = 708
Score = 25.5 bits (56), Expect = 8.9
Identities = 9/17 (52%), Positives = 14/17 (82%)
Query: 7 LIGASGVGKTTIAKQVV 23
++G SG GK+T+AK +V
Sbjct: 505 IVGMSGSGKSTLAKLLV 521
>gnl|CDD|182388 PRK10337, PRK10337, sensor protein QseC; Provisional.
Length = 449
Score = 25.4 bits (56), Expect = 9.0
Identities = 10/16 (62%), Positives = 13/16 (81%)
Query: 95 ILLILTHQGLAPLKKL 110
IL++L + LAPLKKL
Sbjct: 177 ILMVLLGRELAPLKKL 192
>gnl|CDD|131721 TIGR02673, FtsE, cell division ATP-binding protein FtsE. This
model describes FtsE, a member of the ABC transporter
ATP-binding protein family. This protein, and its
permease partner FtsX, localize to the division site.
In a number of species, the ftsEX gene pair is located
next to FtsY, the signal recognition particle-docking
protein.
Length = 214
Score = 25.3 bits (56), Expect = 9.4
Identities = 9/14 (64%), Positives = 10/14 (71%)
Query: 7 LIGASGVGKTTIAK 20
L G SG GKTT+ K
Sbjct: 33 LTGPSGAGKTTLLK 46
>gnl|CDD|184037 PRK13409, PRK13409, putative ATPase RIL; Provisional.
Length = 590
Score = 25.2 bits (56), Expect = 9.8
Identities = 7/14 (50%), Positives = 11/14 (78%)
Query: 7 LIGASGVGKTTIAK 20
++G +G+GKTT K
Sbjct: 104 ILGPNGIGKTTAVK 117
>gnl|CDD|184411 PRK13946, PRK13946, shikimate kinase; Provisional.
Length = 184
Score = 25.3 bits (56), Expect = 9.8
Identities = 7/17 (41%), Positives = 13/17 (76%)
Query: 6 VLIGASGVGKTTIAKQV 22
VL+G G GK+T+ +++
Sbjct: 14 VLVGLMGAGKSTVGRRL 30
>gnl|CDD|184922 PRK14958, PRK14958, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 509
Score = 25.1 bits (54), Expect = 10.0
Identities = 9/20 (45%), Positives = 14/20 (70%)
Query: 1 MAHIFVLIGASGVGKTTIAK 20
+ H ++ G GVGKTTI++
Sbjct: 37 LHHAYLFTGTRGVGKTTISR 56
>gnl|CDD|134001 PHA02150, PHA02150, hypothetical protein.
Length = 77
Score = 25.4 bits (55), Expect = 10.0
Identities = 7/12 (58%), Positives = 9/12 (75%)
Query: 50 YRFISQSQFKGW 61
YRF+S+ QF W
Sbjct: 3 YRFVSEEQFNAW 14
Database: CddB
Posted date: Feb 4, 2011 9:54 PM
Number of letters in database: 5,994,473
Number of sequences in database: 21,608
Lambda K H
0.322 0.140 0.414
Gapped
Lambda K H
0.267 0.0686 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 3,180,612
Number of extensions: 202799
Number of successful extensions: 858
Number of sequences better than 10.0: 1
Number of HSP's gapped: 849
Number of HSP's successfully gapped: 151
Length of query: 186
Length of database: 5,994,473
Length adjustment: 88
Effective length of query: 98
Effective length of database: 4,092,969
Effective search space: 401110962
Effective search space used: 401110962
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 54 (24.7 bits)