RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14166
(264 letters)
>gnl|CDD|201353 pfam00625, Guanylate_kin, Guanylate kinase.
Length = 183
Score = 146 bits (371), Expect = 5e-44
Identities = 56/122 (45%), Positives = 83/122 (68%)
Query: 110 RRPVVLIGPSGVGRSELKRRLIALDPDKFTQVTPYTTRPKKPGEEDGKEYHFVSHETMTS 169
RRP+VL GPSGVG+S +K+ L+ P+KF +TTRP +PGE DGK+YHFVS E M +
Sbjct: 2 RRPIVLSGPSGVGKSHIKKALLDEYPEKFGYSVSHTTRPPRPGEVDGKDYHFVSKEEMEN 61
Query: 170 LISAGKMIEFGEYKGHLYGTSSDSVLELVNSGRVAVLNPAYQSLKVLRSPAFKPLVLFIA 229
ISA + +E+ E+ G+ YGTS +++ ++ SG++ +L+ Q +K LR P+ +FI
Sbjct: 62 DISANEFLEYAEFNGNYYGTSKEAIEQIAESGKICILDVDIQGVKQLRKAELSPISVFIK 121
Query: 230 PP 231
PP
Sbjct: 122 PP 123
>gnl|CDD|214504 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 = 174
Score = 129 bits (327), Expect = 2e-37
Identities = 50/120 (41%), Positives = 73/120 (60%)
Query: 119 SGVGRSELKRRLIALDPDKFTQVTPYTTRPKKPGEEDGKEYHFVSHETMTSLISAGKMIE 178
SGVG+ L LI PD F +V +TTRP +PGE +G +YHFVS E I +G +E
Sbjct: 1 SGVGKGTLLAELIQEIPDAFERVVSHTTRPPRPGEVNGVDYHFVSKEEFEDDIKSGLFLE 60
Query: 179 FGEYKGHLYGTSSDSVLELVNSGRVAVLNPAYQSLKVLRSPAFKPLVLFIAPPPFAALKE 238
+GEY+G+ YGTS +++ ++ G+ +L+ Q +K LR P+V+FIAPP L+
Sbjct: 61 WGEYEGNYYGTSKETIRQVAEKGKHCLLDIDPQGVKQLRKAQLYPIVIFIAPPSSEELER 120
>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 = 127 bits (321), Expect = 4e-37
Identities = 46/120 (38%), Positives = 68/120 (56%)
Query: 112 PVVLIGPSGVGRSELKRRLIALDPDKFTQVTPYTTRPKKPGEEDGKEYHFVSHETMTSLI 171
+VL GPSGVG+S L +RL+ F +TTR +PGE DG +YHFVS E LI
Sbjct: 1 LIVLSGPSGVGKSTLLKRLLEEFDPNFGFSVSHTTRKPRPGEVDGVDYHFVSKEEFERLI 60
Query: 172 SAGKMIEFGEYKGHLYGTSSDSVLELVNSGRVAVLNPAYQSLKVLRSPAFKPLVLFIAPP 231
G+ +E+ E+ G+ YGTS +V E + G++ +L Q + ++ + +FI PP
Sbjct: 61 ENGEFLEWAEFHGNYYGTSKAAVEEALAEGKIVILEIDVQGARQVKKSYPDAVSIFILPP 120
>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 = 112 bits (283), Expect = 9e-31
Identities = 44/131 (33%), Positives = 70/131 (53%), Gaps = 2/131 (1%)
Query: 111 RPVVLIGPSGVGRSELKRRLIALDPDKFTQVTPYTTRPKKPGEEDGKEYHFVSHETMTSL 170
+V+ GPSG G+S L + L+ DP+ ++ TTR +PGE DG +Y FVS E +
Sbjct: 1 LLIVISGPSGAGKSTLVKALLEEDPNLKFSIS-ATTRKPRPGEVDGVDYFFVSKEEFEEM 59
Query: 171 ISAGKMIEFGEYKGHLYGTSSDSVLELVNSGRVAVLNPAYQSLKVLRSPAFKPLVLFIAP 230
I AG+ +E+ E G+ YGT V E + +G+ +L Q + ++ + +FI P
Sbjct: 60 IKAGEFLEWAEVHGNYYGTPKSPVEEALAAGKDVLLEIDVQGARQVKKKFPDAVSIFILP 119
Query: 231 PPFAALKESRI 241
P L+ R+
Sbjct: 120 PSLEELER-RL 129
>gnl|CDD|223272 COG0194, Gmk, Guanylate kinase [Nucleotide transport and
metabolism].
Length = 191
Score = 106 bits (266), Expect = 3e-28
Identities = 46/129 (35%), Positives = 69/129 (53%), Gaps = 4/129 (3%)
Query: 111 RPVVLIGPSGVGRSELKRRLIALDPDKFTQVTPYTTRPKKPGEEDGKEYHFVSHETMTSL 170
+VL GPSGVG+S L + L+ D +F+ V+ TTR +PGE DG +Y FV+ E L
Sbjct: 5 LLIVLSGPSGVGKSTLVKALLEDDKLRFS-VS-ATTRKPRPGEVDGVDYFFVTEEEFEEL 62
Query: 171 ISAGKMIEFGEYKGHLYGTSSDSVLELVNSGRVAVLNPAYQSLKVLRSPAFKPLVL-FIA 229
I + +E+ EY G+ YGTS + V + + G+ +L+ Q ++ V FI
Sbjct: 63 IERDEFLEWAEYHGNYYGTSREPVEQALAEGKDVILDIDVQGALQVKK-KMPNAVSIFIL 121
Query: 230 PPPFAALKE 238
PP L+
Sbjct: 122 PPSLEELER 130
>gnl|CDD|234719 PRK00300, gmk, guanylate kinase; Provisional.
Length = 205
Score = 100 bits (253), Expect = 5e-26
Identities = 46/131 (35%), Positives = 69/131 (52%), Gaps = 4/131 (3%)
Query: 113 VVLIGPSGVGRSELKRRLIALDPDKFTQVTPYTTRPKKPGEEDGKEYHFVSHETMTSLIS 172
+VL GPSG G+S L + L+ DP+ V+ TTR +PGE DG +Y FVS E +I
Sbjct: 8 IVLSGPSGAGKSTLVKALLERDPNLQLSVS-ATTRAPRPGEVDGVDYFFVSKEEFEEMIE 66
Query: 173 AGKMIEFGEYKGHLYGTSSDSVLELVNSGRVAVLNPAYQSLKVLRSPAFKPLVL-FIAPP 231
G+ +E+ E G+ YGT V E + +G+ +L +Q + ++ V FI PP
Sbjct: 67 NGEFLEWAEVFGNYYGTPRSPVEEALAAGKDVLLEIDWQGARQVKK-KMPDAVSIFILPP 125
Query: 232 PFAALKESRIT 242
L+ R+
Sbjct: 126 SLEELER-RLR 135
>gnl|CDD|215414 PLN02772, PLN02772, guanylate kinase.
Length = 398
Score = 93.7 bits (233), Expect = 5e-22
Identities = 63/216 (29%), Positives = 96/216 (44%), Gaps = 22/216 (10%)
Query: 49 VKIADTV---YSSP----SKAKSPTGLSCSAAVKTKKIIYDLAETDD----FDREEIPTY 97
V+I D + + SP + K G S K + ++ D F + P
Sbjct: 53 VQILDKITNNWVSPIVLGTGPKPCKGYSAVVLNKDRILVIKKGSAPDDSIWFLEVDTPFV 112
Query: 98 EEVAKLYPME----------TLRRPVVLIGPSGVGRSELKRRLIALDPDKFTQVTPYTTR 147
E KL E +P+V+ GPSGVG+ L L+ P F +TTR
Sbjct: 113 REQKKLLGTEVVAWSKGVRGNAEKPIVISGPSGVGKGTLISMLMKEFPSMFGFSVSHTTR 172
Query: 148 PKKPGEEDGKEYHFVSHETMTSLISAGKMIEFGEYKGHLYGTSSDSVLELVNSGRVAVLN 207
+ E+DG YHF M I GK +EF G+LYGTS ++V + +SG+ +L+
Sbjct: 173 APREMEKDGVHYHFTERSVMEKEIKDGKFLEFASVHGNLYGTSIEAVEVVTDSGKRCILD 232
Query: 208 PAYQSLKVLRSPAFKPLVLFIAPPPFAALKESRITA 243
Q + +R+ + + + +FI PP L E R+ A
Sbjct: 233 IDVQGARSVRASSLEAIFIFICPPSMEEL-EKRLRA 267
>gnl|CDD|237809 PRK14738, gmk, guanylate kinase; Provisional.
Length = 206
Score = 79.0 bits (195), Expect = 7e-18
Identities = 46/133 (34%), Positives = 69/133 (51%), Gaps = 4/133 (3%)
Query: 113 VVLIGPSGVGRSELKRRLIALDPDKFTQVTPYTTRPKKPGEEDGKEYHFVSHETMTSLIS 172
VV+ GPSGVG+ + R+ F V TTRPK+PGE DG +YHFV+ E +IS
Sbjct: 16 VVISGPSGVGKDAVLARMRERKLP-FHFVVTATTRPKRPGEIDGVDYHFVTPEEFREMIS 74
Query: 173 AGKMIEFGEYKGHLYGTSSDSVLELVNSGRVAVLNPAYQSLKVLRSPAFKPLVLFIAPPP 232
+++E+ E G+ YG V + + SGR ++ Q ++ + + +F+APP
Sbjct: 75 QNELLEWAEVYGNYYGVPKAPVRQALASGRDVIVKVDVQGAASIKRLVPEAVFIFLAPPS 134
Query: 233 FAALK---ESRIT 242
L E R T
Sbjct: 135 MDELTRRLELRRT 147
>gnl|CDD|173199 PRK14737, gmk, guanylate kinase; Provisional.
Length = 186
Score = 59.2 bits (143), Expect = 9e-11
Identities = 34/119 (28%), Positives = 64/119 (53%), Gaps = 2/119 (1%)
Query: 114 VLIGPSGVGRSELKRRLIALDPDKFTQVTPYTTRPKKPGEEDGKEYHFVSHETMTSLISA 173
++ +G G+S + + L+ PD ++ TTR +PG+E+GK Y F++ E I+
Sbjct: 8 IISSVAGGGKSTIIQALLEEHPDFLFSIS-CTTRAPRPGDEEGKTYFFLTIEEFKKGIAD 66
Query: 174 GKMIEFGEYKGHLYGTSSDSVLELVNSGRVAVLNPAYQSLKVLRSPAFKPLV-LFIAPP 231
G+ +E+ E + YGT + + GR A+++ Q K+++ + +V +FI PP
Sbjct: 67 GEFLEWAEVHDNYYGTPKAFIEDAFKEGRSAIMDIDVQGAKIIKEKFPERIVTIFIEPP 125
>gnl|CDD|226232 COG3709, COG3709, Uncharacterized component of phosphonate
metabolism [Inorganic ion transport and metabolism].
Length = 192
Score = 35.0 bits (81), Expect = 0.017
Identities = 33/142 (23%), Positives = 49/142 (34%), Gaps = 35/142 (24%)
Query: 113 VVLIGPSGVGRSEL---KRRLIALDPDKFTQVTPYTTRPKKPGEEDGKEYHFVSHETMTS 169
+ ++GPSG G+ L R +A P V TRP G ED H+ ++
Sbjct: 8 IAVVGPSGAGKDTLLDAARARLAGRPR-LHFVRRVITRPADAGGED--------HDALS- 57
Query: 170 LISAGKMIEFGEYK------------GHLYGTSSDSVLELVNSGRVAVLNPAYQSLKVLR 217
EF G YG ++ L L G V ++N + L R
Sbjct: 58 ------EAEFNTRAGQGAFALSWQAHGLSYGIPAEIDLWLAA-GDVVLVNGSRAVLPQAR 110
Query: 218 S--PAFKPLVLFIAPPPFAALK 237
P + + A P A +
Sbjct: 111 RRYPQLLVVCI-TASPEVLAQR 131
>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 = 34.3 bits (79), Expect = 0.029
Identities = 29/129 (22%), Positives = 46/129 (35%), Gaps = 17/129 (13%)
Query: 111 RPVVLIGPSGVGRSELKRRLIALDPDKFTQVTP------YTTRPKKPGEEDGKEYHFVSH 164
R + ++GPSG G K L+ + TRP G E+ + +S
Sbjct: 2 RLIYVVGPSGAG----KDTLLDYARARLAGDPRVHFVRRVITRPASAGGEN---HIALST 54
Query: 165 ETMTSLISAGKMIEFGEYKGHLYGTSSDSVLELVNSGRVAVLNPAYQSLKVLRS--PAFK 222
E G + G YG ++ + + + +G V V+N + L R P
Sbjct: 55 EEFDHREDGGAFALSWQAHGLSYGIPAE-IDQWLEAGDVVVVNGSRAVLPEARQRYPNLL 113
Query: 223 PLVLFIAPP 231
V A P
Sbjct: 114 V-VNITASP 121
>gnl|CDD|193251 pfam12775, AAA_7, P-loop containing dynein motor region D3. the
380 kDa motor unit of dynein belongs to the AAA class of
chaperone-like ATPases. The core of the 380 kDa motor
unit contains a concatenated chain of six AAA modules,
of which four correspond to the ATP binding sites with
P-loop signatures described previously, and two are
modules in which the P loop has been lost in evolution.
This particular family is the D3 and is an ATP binding
site.
Length = 272
Score = 34.5 bits (79), Expect = 0.039
Identities = 42/149 (28%), Positives = 64/149 (42%), Gaps = 29/149 (19%)
Query: 96 TYEEVAKLYPMETL---RRPVVLIGPSGVGRSEL-KRRLIALDPDKF-TQVTP---YTTR 147
T E + Y M+ L +RPV+L+G +G G+S L +L +LDPD + + P YTT
Sbjct: 16 TSETIRVRYFMDLLMERQRPVMLVGNAGTGKSVLVGDKLASLDPDAYLVKNVPFNYYTTS 75
Query: 148 P------KKPGEED-GKEYHFVSHETMTSLISAGKMIEFGEY--------------KGHL 186
+KP E+ G+ Y + + I M E Y GH
Sbjct: 76 AMLQAVLEKPLEKKAGRNYGPPGTKKLVYFIDDMNMPEVDAYGTVQPHTLIRQHMDYGHW 135
Query: 187 YGTSSDSVLELVNSGRVAVLNPAYQSLKV 215
Y S ++ E+ N V+ +NP S +
Sbjct: 136 YDRSKLTLKEIHNCQYVSCMNPTAGSFTI 164
>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 = 33.4 bits (77), Expect = 0.040
Identities = 17/39 (43%), Positives = 21/39 (53%), Gaps = 3/39 (7%)
Query: 112 PVVLIGPSGVGRSELKRRLI-ALDPDKFT--QVTPYTTR 147
V+L+GP G G+SEL RL AL Q+T TT
Sbjct: 1 GVLLVGPPGTGKSELAERLAAALSNRPVFYVQLTRDTTE 39
>gnl|CDD|224141 COG1220, HslU, ATP-dependent protease HslVU (ClpYQ), ATPase subunit
[Posttranslational modification, protein turnover,
chaperones].
Length = 444
Score = 33.4 bits (77), Expect = 0.12
Identities = 19/48 (39%), Positives = 27/48 (56%), Gaps = 13/48 (27%)
Query: 107 ETLRRPVV-----LIGPSGVGRSELKRRL--------IALDPDKFTQV 141
E LR V +IGP+GVG++E+ RRL I ++ KFT+V
Sbjct: 42 EELRDEVTPKNILMIGPTGVGKTEIARRLAKLAGAPFIKVEATKFTEV 89
>gnl|CDD|213527 TIGR00390, hslU, ATP-dependent protease HslVU, ATPase subunit.
This model represents the ATPase subunit of HslVU, while
the proteasome-related peptidase subunit is HslV.
Residues 54-61 of the model contain a P-loop ATP-binding
motif. Cys-287 of E. coli (position 308 in the seed
alignment), studied in MEDLINE:98389714, is Ser in other
members of the seed alignment [Protein fate, Protein
folding and stabilization].
Length = 441
Score = 33.2 bits (76), Expect = 0.14
Identities = 16/43 (37%), Positives = 27/43 (62%), Gaps = 8/43 (18%)
Query: 107 ETLRRPVVLIGPSGVGRSELKRRL--------IALDPDKFTQV 141
E + +++IGP+GVG++E+ RRL I ++ KFT+V
Sbjct: 44 EVTPKNILMIGPTGVGKTEIARRLAKLANAPFIKVEATKFTEV 86
>gnl|CDD|234988 PRK01889, PRK01889, GTPase RsgA; Reviewed.
Length = 356
Score = 32.6 bits (75), Expect = 0.18
Identities = 12/36 (33%), Positives = 18/36 (50%)
Query: 96 TYEEVAKLYPMETLRRPVVLIGPSGVGRSELKRRLI 131
E + L + + V L+G SGVG+S L L+
Sbjct: 181 DGEGLDVLAAWLSGGKTVALLGSSGVGKSTLVNALL 216
>gnl|CDD|222104 pfam13401, AAA_22, AAA domain.
Length = 124
Score = 30.7 bits (70), Expect = 0.26
Identities = 11/27 (40%), Positives = 14/27 (51%)
Query: 110 RRPVVLIGPSGVGRSELKRRLIALDPD 136
VL G SG G++ L RRL P+
Sbjct: 4 AGIGVLTGESGSGKTTLLRRLARQLPN 30
>gnl|CDD|225138 COG2229, COG2229, Predicted GTPase [General function prediction
only].
Length = 187
Score = 31.3 bits (71), Expect = 0.30
Identities = 17/77 (22%), Positives = 26/77 (33%), Gaps = 14/77 (18%)
Query: 113 VVLIGPSGVGRSELKRRLIALDPDKFTQVTPYTTRPKKPGEEDGKEYHFVSHETMTSLIS 172
+V+IGP G G++ R L + T GK T +
Sbjct: 13 IVVIGPVGAGKTTFVRALS-------DKPLVITEADASSVSGKGK-------RPTTVAMD 58
Query: 173 AGKMIEFGEYKGHLYGT 189
G + + HL+GT
Sbjct: 59 FGSIELDEDTGVHLFGT 75
>gnl|CDD|238899 cd01918, HprK_C, HprK/P, the bifunctional histidine-containing
protein kinase/phosphatase, controls the phosphorylation
state of the phosphocarrier protein HPr and regulates
the utilization of carbon sources by gram-positive
bacteria. It catalyzes both the ATP-dependent
phosphorylation of Ser-46 of HPr and its
dephosphorylation by phosphorolysis. The latter reaction
uses inorganic phosphate as substrate and produces
pyrophosphate. Phosphoenolpyruvate carboxykinase (PEPCK)
and the C-terminal catalytic domain of HprK/P are
structurally similar with conserved active site residues
suggesting these two phosphotransferases have related
functions. The HprK/P N-terminal domain is structurally
similar to the N-terminal domains of the MurE and MurF
amino acid ligases.
Length = 149
Score = 30.7 bits (70), Expect = 0.40
Identities = 12/26 (46%), Positives = 17/26 (65%)
Query: 106 METLRRPVVLIGPSGVGRSELKRRLI 131
+E V++ GPSG+G+SEL LI
Sbjct: 10 VEVGGIGVLITGPSGIGKSELALELI 35
>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 = 31.0 bits (71), Expect = 0.52
Identities = 12/23 (52%), Positives = 16/23 (69%)
Query: 113 VVLIGPSGVGRSELKRRLIALDP 135
VV+IGPSG G+S L R + L+
Sbjct: 29 VVIIGPSGSGKSTLLRCINLLEE 51
>gnl|CDD|219373 pfam07318, DUF1464, Protein of unknown function (DUF1464). This
family consists of several hypothetical archaeal
proteins of around 350 residues in length. The function
of this family is unknown.
Length = 336
Score = 30.9 bits (70), Expect = 0.56
Identities = 20/50 (40%), Positives = 25/50 (50%), Gaps = 10/50 (20%)
Query: 81 YDLAETDD---FDREEIPTYEEVAKLYPMETLR-----RPVVLIGPSGVG 122
YD+A DD + IPT +EV K P +R RP + GPSG G
Sbjct: 9 YDVAGVDDGNVILDKSIPT-DEVTK-DPRSLVRLIEEARPDAIAGPSGYG 56
>gnl|CDD|237040 PRK12289, PRK12289, GTPase RsgA; Reviewed.
Length = 352
Score = 30.8 bits (70), Expect = 0.70
Identities = 12/18 (66%), Positives = 14/18 (77%)
Query: 114 VLIGPSGVGRSELKRRLI 131
V+ GPSGVG+S L RLI
Sbjct: 176 VVAGPSGVGKSSLINRLI 193
>gnl|CDD|226997 COG4650, RtcR, Sigma54-dependent transcription regulator containing
an AAA-type ATPase domain and a DNA-binding domain
[Transcription / Signal transduction mechanisms].
Length = 531
Score = 30.7 bits (69), Expect = 0.82
Identities = 12/24 (50%), Positives = 17/24 (70%)
Query: 110 RRPVVLIGPSGVGRSELKRRLIAL 133
R P++L GP+G G+S L RR+ L
Sbjct: 208 RAPILLNGPTGAGKSFLARRIYEL 231
>gnl|CDD|223786 COG0714, COG0714, MoxR-like ATPases [General function prediction
only].
Length = 329
Score = 30.5 bits (69), Expect = 0.83
Identities = 18/64 (28%), Positives = 24/64 (37%), Gaps = 7/64 (10%)
Query: 108 TLRRPVVLIGPSGVGRSELKRRLI-ALDPDKFT-QVTPYTTRPKKPGEEDGKEYHFVSHE 165
V+L GP GVG++ L R L AL Q TP P + G Y + +
Sbjct: 41 LAGGHVLLEGPPGVGKTLLARALARALGLPFVRIQCTPDLL----PSDLLG-TYAYAALL 95
Query: 166 TMTS 169
Sbjct: 96 LEPG 99
>gnl|CDD|237053 PRK12315, PRK12315, 1-deoxy-D-xylulose-5-phosphate synthase;
Provisional.
Length = 581
Score = 30.7 bits (70), Expect = 0.90
Identities = 16/43 (37%), Positives = 21/43 (48%), Gaps = 6/43 (13%)
Query: 128 RRLIALDPDKFTQVTPYTTRPKKPGEEDGKEYHFVSHETMTSL 170
R+ LDPD + VT YT EE ++ V H T TS+
Sbjct: 83 RKEAFLDPDHYDDVTGYTNP-----EESEHDFFTVGH-TSTSI 119
>gnl|CDD|233088 TIGR00679, hpr-ser, Hpr(Ser) kinase/phosphatase. Members of this
family are the bifunctional enzyme, HPr
kinase/phosphatase. All members of the seed alignment
(n=57) have a gene tightly clustered with a gene for the
phospocarrier protein HPr, its target [Regulatory
functions, Protein interactions, Signal transduction,
PTS].
Length = 300
Score = 30.1 bits (69), Expect = 0.97
Identities = 14/38 (36%), Positives = 22/38 (57%), Gaps = 7/38 (18%)
Query: 113 VVLIGPSGVGRSEL-----KR--RLIALDPDKFTQVTP 143
V++ G SG+G+SEL KR RL+A D + ++
Sbjct: 146 VLITGESGIGKSELALELIKRGHRLVADDAVEIKRIAG 183
>gnl|CDD|224084 COG1162, COG1162, Predicted GTPases [General function prediction
only].
Length = 301
Score = 30.0 bits (68), Expect = 1.1
Identities = 18/61 (29%), Positives = 30/61 (49%), Gaps = 10/61 (16%)
Query: 76 TKKIIYDLAETDDFDREEIPTYEEVAKLYPMETLRRPVVLIGPSGVGRSELKRRLIALDP 135
+ I Y + + + + EE+A+L + VL+G SGVG+S L + AL P
Sbjct: 137 YEDIGYPVLFVSAKNGDGL---EELAELLAGKI----TVLLGQSGVGKSTL---INALLP 186
Query: 136 D 136
+
Sbjct: 187 E 187
>gnl|CDD|181906 PRK09493, glnQ, glutamine ABC transporter ATP-binding protein;
Reviewed.
Length = 240
Score = 29.7 bits (67), Expect = 1.2
Identities = 12/23 (52%), Positives = 16/23 (69%)
Query: 113 VVLIGPSGVGRSELKRRLIALDP 135
VV+IGPSG G+S L R + L+
Sbjct: 30 VVIIGPSGSGKSTLLRCINKLEE 52
>gnl|CDD|184190 PRK13628, PRK13628, serine/threonine transporter SstT; Provisional.
Length = 402
Score = 30.2 bits (69), Expect = 1.2
Identities = 18/44 (40%), Positives = 23/44 (52%), Gaps = 10/44 (22%)
Query: 205 VLNPAYQSLKVLRSPAFKPLVLFIAPPPFAALKESRITAF-ARS 247
V+NP K+ R+P PLV F L+ES +TAF RS
Sbjct: 230 VVNPLIVFWKIRRNPY--PLV-------FTCLRESGVTAFFTRS 264
>gnl|CDD|182980 PRK11124, artP, arginine transporter ATP-binding subunit;
Provisional.
Length = 242
Score = 29.6 bits (67), Expect = 1.4
Identities = 11/18 (61%), Positives = 14/18 (77%)
Query: 113 VVLIGPSGVGRSELKRRL 130
+VL+GPSG G+S L R L
Sbjct: 31 LVLLGPSGAGKSSLLRVL 48
>gnl|CDD|213223 cd03256, ABC_PhnC_transporter, ATP-binding cassette domain of the
binding protein-dependent phosphonate transport system.
Phosphonates are a class of organophosphorus compounds
characterized by a chemically stable
carbon-to-phosphorus (C-P) bond. Phosphonates are
widespread among naturally occurring compounds in all
kingdoms of wildlife, but only prokaryotic
microorganisms are able to cleave this bond. Certain
bacteria such as E. coli can use alkylphosphonates as a
phosphorus source. 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 = 241
Score = 29.5 bits (67), Expect = 1.6
Identities = 39/142 (27%), Positives = 57/142 (40%), Gaps = 30/142 (21%)
Query: 113 VVLIGPSGVGRSELKR---RLIALDPDKFTQVTPYTTRPKKPGEEDGKEYHFVSHETMTS 169
V LIGPSG G+S L R L+ +P + DG + + + + +
Sbjct: 30 VALIGPSGAGKSTLLRCLNGLV--EPTSGS------------VLIDGTDINKLKGKALRQ 75
Query: 170 LISAGKMIEFGEYKGHLYGTSSDSVLELVNSGRVAVLNPAYQSLKVLRSPAFKPLVLFIA 229
L MI F ++ +L SVLE V SGR+ + ++SL L K L
Sbjct: 76 LRRQIGMI-FQQF--NLIERL--SVLENVLSGRLGRRST-WRSLFGLFPKEEKQRAL--- 126
Query: 230 PPPFAALKESRITAFARSPFDQ 251
AAL+ + A DQ
Sbjct: 127 ----AALERVGLLDKAYQRADQ 144
>gnl|CDD|236648 PRK10078, PRK10078, ribose 1,5-bisphosphokinase; Provisional.
Length = 186
Score = 29.3 bits (66), Expect = 1.6
Identities = 14/41 (34%), Positives = 19/41 (46%)
Query: 115 LIGPSGVGRSELKRRLIALDPDKFTQVTPYTTRPKKPGEED 155
L+GPSG G+ L L + + Y TRP G E+
Sbjct: 7 LMGPSGSGKDSLLAALRQREQTQLLVAHRYITRPASAGSEN 47
>gnl|CDD|235825 PRK06547, PRK06547, hypothetical protein; Provisional.
Length = 172
Score = 28.9 bits (65), Expect = 1.6
Identities = 12/34 (35%), Positives = 15/34 (44%), Gaps = 4/34 (11%)
Query: 100 VAKLYPMETLRRPVVLI-GPSGVGRSELKRRLIA 132
A+L VLI G SG G++ L L A
Sbjct: 7 AARLCGG---GMITVLIDGRSGSGKTTLAGALAA 37
>gnl|CDD|217416 pfam03193, DUF258, Protein of unknown function, DUF258.
Length = 161
Score = 29.1 bits (66), Expect = 1.6
Identities = 10/19 (52%), Positives = 12/19 (63%)
Query: 113 VVLIGPSGVGRSELKRRLI 131
VL G SGVG+S L L+
Sbjct: 38 SVLAGQSGVGKSTLLNALL 56
>gnl|CDD|148849 pfam07475, Hpr_kinase_C, HPr Serine kinase C-terminal domain. This
family represents the C terminal kinase domain of Hpr
Serine/threonine kinase PtsK. This kinase is the sensor
in a multicomponent phosphorelay system in control of
carbon catabolic repression in bacteria. This kinase in
unusual in that it recognises the tertiary structure of
its target and is a member of a novel family unrelated
to any previously described protein phosphorylating
enzymes. X-ray analysis of the full-length crystalline
enzyme from Staphylococcus xylosus at a resolution of
1.95 A shows the enzyme to consist of two clearly
separated domains that are assembled in a hexameric
structure resembling a three-bladed propeller.
Length = 171
Score = 28.9 bits (66), Expect = 1.6
Identities = 13/29 (44%), Positives = 18/29 (62%), Gaps = 7/29 (24%)
Query: 113 VVLIGPSGVGRSEL-----KR--RLIALD 134
V++ G SG+G+SE KR RL+A D
Sbjct: 21 VLITGESGIGKSETALELIKRGHRLVADD 49
>gnl|CDD|235459 PRK05428, PRK05428, HPr kinase/phosphorylase; Provisional.
Length = 308
Score = 29.4 bits (67), Expect = 1.7
Identities = 13/29 (44%), Positives = 18/29 (62%), Gaps = 7/29 (24%)
Query: 113 VVLIGPSGVGRSEL-----KR--RLIALD 134
V++ G SG+G+SE KR RL+A D
Sbjct: 149 VLITGESGIGKSETALELIKRGHRLVADD 177
>gnl|CDD|181681 PRK09183, PRK09183, transposase/IS protein; Provisional.
Length = 259
Score = 29.3 bits (66), Expect = 1.7
Identities = 12/21 (57%), Positives = 16/21 (76%), Gaps = 3/21 (14%)
Query: 113 VVLIGPSGVGRSELKRRLIAL 133
+VL+GPSGVG++ L IAL
Sbjct: 105 IVLLGPSGVGKTHLA---IAL 122
>gnl|CDD|213227 cd03260, ABC_PstB_phosphate_transporter, ATP-binding cassette
domain of the phosphate transport system. Phosphate
uptake is of fundamental importance in the cell
physiology of bacteria because phosphate is required as
a nutrient. The Pst system of E. coli comprises four
distinct subunits encoded by the pstS, pstA, pstB, and
pstC genes. The PstS protein is a phosphate-binding
protein located in the periplasmic space. PstA and PstC
are hydrophobic and they form the transmembrane portion
of the Pst system. PstB is the catalytic subunit, which
couples the energy of ATP hydrolysis to the import of
phosphate across cellular membranes through the Pst
system, often referred as ABC-protein. PstB belongs to
one of the largest superfamilies of proteins
characterized by a highly conserved adenosine
triphosphate (ATP) binding cassette (ABC), which is also
a nucleotide binding domain (NBD).
Length = 227
Score = 29.1 bits (66), Expect = 1.8
Identities = 14/26 (53%), Positives = 15/26 (57%), Gaps = 3/26 (11%)
Query: 113 VVLIGPSGVGRSELKR---RLIALDP 135
LIGPSG G+S L R RL L P
Sbjct: 29 TALIGPSGCGKSTLLRLLNRLNDLIP 54
>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 = 28.8 bits (65), Expect = 1.9
Identities = 12/47 (25%), Positives = 25/47 (53%), Gaps = 4/47 (8%)
Query: 84 AETDDFDREEIPTYEE--VAKLYPMETLRRP--VVLIGPSGVGRSEL 126
+DFD + +A+L ++ + + ++L+GP GVG++ L
Sbjct: 17 KTLEDFDFRAARGLDRRLIAELAGLDWIEQAENLLLLGPPGVGKTHL 63
>gnl|CDD|176202 cd08240, 6_hydroxyhexanoate_dh_like, 6-hydroxyhexanoate
dehydrogenase. 6-hydroxyhexanoate dehydrogenase, an
enzyme of the zinc-dependent alcohol dehydrogenase-like
family of medium chain dehydrogenases/reductases
catalyzes the conversion of 6-hydroxyhexanoate and
NAD(+) to 6-oxohexanoate + NADH and H+.
NAD(P)(H)-dependent oxidoreductases are the major
enzymes in the interconversion of alcohols and
aldehydes, or ketones. Alcohol dehydrogenase in the
liver converts ethanol and NAD+ to acetaldehyde and
NADH, while in yeast and some other microorganisms ADH
catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. ADH is a member of the medium
chain alcohol dehydrogenase family (MDR), which has a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. A GxGxxG motif after the first
mononucleotide contact half allows the close contact of
the coenzyme with the ADH backbone. The N-terminal
catalytic domain has a distant homology to GroES. These
proteins typically form dimers (typically higher plants,
mammals) or tetramers (yeast, bacteria), and have 2
tightly bound zinc atoms per subunit, a catalytic zinc
at the active site and a structural zinc in a lobe of
the catalytic domain. NAD(H)-binding occurs in the
cleft between the catalytic and coenzyme-binding
domains, at the active site, and coenzyme binding
induces a conformational closing of this cleft. Coenzyme
binding typically precedes and contributes to substrate
binding. In human ADH catalysis, the zinc ion helps
coordinate the alcohol, followed by deprotonation of a
histidine, the ribose of NAD, a serine, then the
alcohol, which allows the transfer of a hydride to NAD+,
creating NADH and a zinc-bound aldehyde or ketone. In
yeast and some bacteria, the active site zinc binds an
aldehyde, polarizing it, and leading to the reverse
reaction.
Length = 350
Score = 29.1 bits (66), Expect = 2.1
Identities = 15/50 (30%), Positives = 23/50 (46%), Gaps = 8/50 (16%)
Query: 94 IPTYEEVAKLYPMETLRRPVVLIGPSGVG-------RSELKRRLIALDPD 136
+ Y V KL P+ PVV+IG G+G ++ +I +D D
Sbjct: 161 LTAYSAVKKLMPL-VADEPVVIIGAGGLGLMALALLKALGPANIIVVDID 209
>gnl|CDD|235364 PRK05201, hslU, ATP-dependent protease ATP-binding subunit HslU;
Provisional.
Length = 443
Score = 29.3 bits (67), Expect = 2.1
Identities = 15/34 (44%), Positives = 22/34 (64%), Gaps = 8/34 (23%)
Query: 116 IGPSGVGRSELKRRL--------IALDPDKFTQV 141
IGP+GVG++E+ RRL I ++ KFT+V
Sbjct: 56 IGPTGVGKTEIARRLAKLANAPFIKVEATKFTEV 89
>gnl|CDD|197555 smart00175, RAB, Rab subfamily of small GTPases. Rab GTPases are
implicated in vesicle trafficking.
Length = 164
Score = 28.6 bits (65), Expect = 2.2
Identities = 12/26 (46%), Positives = 15/26 (57%), Gaps = 3/26 (11%)
Query: 113 VVLIGPSGVGRSELKRRLIALDPDKF 138
++LIG SGVG+S L R KF
Sbjct: 3 IILIGDSGVGKSSLLSRFTD---GKF 25
>gnl|CDD|184411 PRK13946, PRK13946, shikimate kinase; Provisional.
Length = 184
Score = 28.7 bits (65), Expect = 2.5
Identities = 11/22 (50%), Positives = 15/22 (68%)
Query: 109 LRRPVVLIGPSGVGRSELKRRL 130
+R VVL+G G G+S + RRL
Sbjct: 9 GKRTVVLVGLMGAGKSTVGRRL 30
>gnl|CDD|206660 cd01868, Rab11_like, Rab GTPase family 11 (Rab11)-like includes
Rab11a, Rab11b, and Rab25. Rab11a, Rab11b, and Rab25
are closely related, evolutionary conserved Rab proteins
that are differentially expressed. Rab11a is
ubiquitously synthesized, Rab11b is enriched in brain
and heart and Rab25 is only found in epithelia. Rab11/25
proteins seem to regulate recycling pathways from
endosomes to the plasma membrane and to the trans-Golgi
network. Furthermore, Rab11a is thought to function in
the histamine-induced fusion of tubulovesicles
containing H+, K+ ATPase with the plasma membrane in
gastric parietal cells and in insulin-stimulated
insertion of GLUT4 in the plasma membrane of
cardiomyocytes. Overexpression of Rab25 has recently
been observed in ovarian cancer and breast cancer, and
has been correlated with worsened outcomes in both
diseases. In addition, Rab25 overexpression has also
been observed in prostate cancer, transitional cell
carcinoma of the bladder, and invasive breast tumor
cells. GTPase activating proteins (GAPs) interact with
GTP-bound Rab and accelerate the hydrolysis of GTP to
GDP. Guanine nucleotide exchange factors (GEFs) interact
with GDP-bound Rabs to promote the formation of the
GTP-bound state. Rabs are further regulated by guanine
nucleotide dissociation inhibitors (GDIs), which
facilitate Rab recycling by masking C-terminal lipid
binding and promoting cytosolic localization. Most Rab
GTPases contain a lipid modification site at the
C-terminus, with sequence motifs CC, CXC, or CCX. Lipid
binding is essential for membrane attachment, a key
feature of most Rab proteins. Due to the presence of
truncated sequences in this CD, the lipid modification
site is not available for annotation.
Length = 165
Score = 28.3 bits (64), Expect = 2.5
Identities = 11/18 (61%), Positives = 13/18 (72%)
Query: 113 VVLIGPSGVGRSELKRRL 130
+VLIG SGVG+S L R
Sbjct: 6 IVLIGDSGVGKSNLLSRF 23
>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 = 29.0 bits (65), Expect = 3.1
Identities = 14/40 (35%), Positives = 22/40 (55%), Gaps = 2/40 (5%)
Query: 110 RRPVVLIGPSGVGRSELKRRLIALDPDKFTQVTPYTTRPK 149
+R V+LIG GVG+S L + + L PD+ ++ P
Sbjct: 37 KRNVLLIGEPGVGKSMLAKAMAELLPDE--ELEDILVYPN 74
>gnl|CDD|206747 cd01854, YjeQ_EngC, Ribosomal interacting GTPase YjeQ/EngC, a
circularly permuted subfamily of the Ras GTPases. YjeQ
(YloQ in Bacillus subtilis) is a ribosomal small
subunit-dependent GTPase; hence also known as RsgA. YjeQ
is a late-stage ribosomal biogenesis factor involved in
the 30S subunit maturation, and it represents a protein
family whose members are broadly conserved in bacteria
and have been shown to be essential to the growth of E.
coli and B. subtilis. Proteins of the YjeQ family
contain all sequence motifs typical of the vast class of
P-loop-containing GTPases, but show a circular
permutation, with a G4-G1-G3 pattern of motifs as
opposed to the regular G1-G3-G4 pattern seen in most
GTPases. All YjeQ family proteins display a unique
domain architecture, which includes an N-terminal
OB-fold RNA-binding domain, the central permuted GTPase
domain, and a zinc knuckle-like C-terminal cysteine
domain.
Length = 211
Score = 28.5 bits (65), Expect = 3.1
Identities = 22/71 (30%), Positives = 35/71 (49%), Gaps = 22/71 (30%)
Query: 82 DLAETDDFDREEIPTYEEVAKLYP-----------METLR-----RPVVLIGPSGVGRSE 125
DL + ++ + E + YE++ YP ++ LR + VL+G SGVG+S
Sbjct: 44 DLVDDEELE-ELLEIYEKLG--YPVLAVSAKTGEGLDELRELLKGKTSVLVGQSGVGKST 100
Query: 126 LKRRLIALDPD 136
L L AL P+
Sbjct: 101 L---LNALLPE 108
>gnl|CDD|226635 COG4161, ArtP, ABC-type arginine transport system, ATPase component
[Amino acid transport and metabolism].
Length = 242
Score = 28.6 bits (64), Expect = 3.1
Identities = 12/22 (54%), Positives = 16/22 (72%)
Query: 113 VVLIGPSGVGRSELKRRLIALD 134
+VL+GPSG G+S L R L L+
Sbjct: 31 LVLLGPSGAGKSSLLRVLNLLE 52
>gnl|CDD|224051 COG1126, GlnQ, ABC-type polar amino acid transport system, ATPase
component [Amino acid transport and metabolism].
Length = 240
Score = 28.2 bits (64), Expect = 3.7
Identities = 13/23 (56%), Positives = 16/23 (69%)
Query: 113 VVLIGPSGVGRSELKRRLIALDP 135
VV+IGPSG G+S L R L L+
Sbjct: 31 VVIIGPSGSGKSTLLRCLNGLEE 53
>gnl|CDD|224025 COG1100, COG1100, GTPase SAR1 and related small G proteins [General
function prediction only].
Length = 219
Score = 28.0 bits (62), Expect = 4.0
Identities = 21/96 (21%), Positives = 37/96 (38%), Gaps = 12/96 (12%)
Query: 106 METLRRPVVLIGPSGVGRSELKRRLIALDPDKFTQVTPYTTRPKKPGEED-GKEYHFVSH 164
M+ + +V++G GVG++ L RL+ D+F + P T G D K
Sbjct: 3 MKEFK--IVVLGDGGVGKTTLLNRLVG---DEFPEGYPPTI-----GNLDPAKTIEPYRR 52
Query: 165 ETMTSLISAGKMIEFGEYKGHLYGTSSDSVLELVNS 200
L E+ Y ++ +L + +S
Sbjct: 53 NIKLQLWDTAGQEEYRSL-RPEYYRGANGILIVYDS 87
>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 = 27.7 bits (61), Expect = 4.2
Identities = 7/24 (29%), Positives = 13/24 (54%)
Query: 110 RRPVVLIGPSGVGRSELKRRLIAL 133
++++GP G G++ L R L
Sbjct: 2 GEVILIVGPPGSGKTTLARALARE 25
>gnl|CDD|182893 PRK11000, PRK11000, maltose/maltodextrin transporter ATP-binding
protein; Provisional.
Length = 369
Score = 28.5 bits (64), Expect = 4.3
Identities = 12/20 (60%), Positives = 15/20 (75%), Gaps = 1/20 (5%)
Query: 113 VVLIGPSGVGRSELKRRLIA 132
VV +GPSG G+S L R+IA
Sbjct: 32 VVFVGPSGCGKSTL-LRMIA 50
>gnl|CDD|224085 COG1163, DRG, Predicted GTPase [General function prediction only].
Length = 365
Score = 28.4 bits (64), Expect = 4.5
Identities = 15/52 (28%), Positives = 22/52 (42%), Gaps = 4/52 (7%)
Query: 113 VVLIGPSGVGRSELKRRLIALDPDKFTQVTPYTTRPKKPG--EEDGKEYHFV 162
V L+G VG+S L +L + P+TT PG E G + +
Sbjct: 66 VALVGFPSVGKSTLLNKLTNTKSE--VADYPFTTLEPVPGMLEYKGAQIQLL 115
>gnl|CDD|132050 TIGR03005, ectoine_ehuA, ectoine/hydroxyectoine ABC transporter,
ATP-binding protein. Members of this family are the
ATP-binding protein of a conserved four gene ABC
transporter operon found next to ectoine unilization
operons and ectoine biosynthesis operons. Ectoine is a
compatible solute that protects enzymes from high
osmolarity. It is released by some species in response
to hypoosmotic shock, and it is taken up by a number of
bacteria as a compatible solute or for consumption. This
family shows strong sequence similiarity to a number of
amino acid ABC transporter ATP-binding proteins.
Length = 252
Score = 27.9 bits (62), Expect = 4.8
Identities = 13/23 (56%), Positives = 17/23 (73%)
Query: 113 VVLIGPSGVGRSELKRRLIALDP 135
V LIGPSG G+S + R L+ L+P
Sbjct: 29 VALIGPSGSGKSTILRILMTLEP 51
>gnl|CDD|226164 COG3638, COG3638, ABC-type phosphate/phosphonate transport system,
ATPase component [Inorganic ion transport and
metabolism].
Length = 258
Score = 28.0 bits (63), Expect = 4.9
Identities = 11/18 (61%), Positives = 13/18 (72%)
Query: 113 VVLIGPSGVGRSELKRRL 130
V +IGPSG G+S L R L
Sbjct: 33 VAIIGPSGAGKSTLLRSL 50
>gnl|CDD|206640 cd00154, Rab, Ras-related in brain (Rab) family of small guanosine
triphosphatases (GTPases). Rab GTPases form the largest
family within the Ras superfamily. There are at least 60
Rab genes in the human genome, and a number of Rab
GTPases are conserved from yeast to humans. Rab GTPases
are small, monomeric proteins that function as molecular
switches to regulate vesicle trafficking pathways. The
different Rab GTPases are localized to the cytosolic
face of specific intracellular membranes, where they
regulate distinct steps in membrane traffic pathways. In
the GTP-bound form, Rab GTPases recruit specific sets of
effector proteins onto membranes. Through their
effectors, Rab GTPases regulate vesicle formation,
actin- and tubulin-dependent vesicle movement, and
membrane fusion. GTPase activating proteins (GAPs)
interact with GTP-bound Rab and accelerate the
hydrolysis of GTP to GDP. Guanine nucleotide exchange
factors (GEFs) interact with GDP-bound Rabs to promote
the formation of the GTP-bound state. Rabs are further
regulated by guanine nucleotide dissociation inhibitors
(GDIs), which mask C-terminal lipid binding and promote
cytosolic localization. While most unicellular organisms
possess 5-20 Rab members, several have been found to
possess 60 or more Rabs; for many of these Rab isoforms,
homologous proteins are not found in other organisms.
Most Rab GTPases contain a lipid modification site at
the C-terminus, with sequence motifs CC, CXC, or CCX.
Lipid binding is essential for membrane attachment, a
key feature of most Rab proteins. Since crystal
structures often lack C-terminal residues, the lipid
modification site is not available for annotation in
many of the CDs in the hierarchy, but is included where
possible.
Length = 159
Score = 27.4 bits (62), Expect = 5.4
Identities = 13/33 (39%), Positives = 20/33 (60%), Gaps = 3/33 (9%)
Query: 113 VVLIGPSGVGRSELKRRLIALDPDKFTQVTPYT 145
+VLIG SGVG++ L R + +KF++ T
Sbjct: 3 IVLIGDSGVGKTSLLLRFVD---NKFSENYKST 32
>gnl|CDD|188099 TIGR00972, 3a0107s01c2, phosphate ABC transporter, ATP-binding
protein. This model represents the ATP-binding protein
of a family of ABC transporters for inorganic phosphate.
In the model species Escherichia coli, a constitutive
transporter for inorganic phosphate, with low affinity,
is also present. The high affinity transporter that
includes this polypeptide is induced when extracellular
phosphate concentrations are low. The proteins most
similar to the members of this family but not included
appear to be amino acid transporters [Transport and
binding proteins, Anions].
Length = 247
Score = 27.6 bits (62), Expect = 5.4
Identities = 12/26 (46%), Positives = 16/26 (61%), Gaps = 1/26 (3%)
Query: 106 METLRRPVV-LIGPSGVGRSELKRRL 130
++ + V LIGPSG G+S L R L
Sbjct: 22 LDIPKNQVTALIGPSGCGKSTLLRSL 47
>gnl|CDD|224410 COG1493, HprK, Serine kinase of the HPr protein, regulates
carbohydrate metabolism [Signal transduction
mechanisms].
Length = 308
Score = 28.0 bits (63), Expect = 5.5
Identities = 17/29 (58%), Positives = 19/29 (65%), Gaps = 8/29 (27%)
Query: 114 VLI-GPSGVGRSEL-----KR--RLIALD 134
VLI GPSG G+SEL KR RL+A D
Sbjct: 148 VLITGPSGAGKSELALELIKRGHRLVADD 176
>gnl|CDD|130041 TIGR00968, 3a0106s01, sulfate ABC transporter, ATP-binding protein.
[Transport and binding proteins, Anions].
Length = 237
Score = 27.8 bits (62), Expect = 5.7
Identities = 13/25 (52%), Positives = 17/25 (68%), Gaps = 1/25 (4%)
Query: 113 VVLIGPSGVGRSELKRRLIALD-PD 136
V L+GPSG G+S L R + L+ PD
Sbjct: 29 VALLGPSGSGKSTLLRIIAGLEQPD 53
>gnl|CDD|236947 PRK11650, ugpC, glycerol-3-phosphate transporter ATP-binding
subunit; Provisional.
Length = 356
Score = 27.9 bits (63), Expect = 5.8
Identities = 11/20 (55%), Positives = 16/20 (80%), Gaps = 1/20 (5%)
Query: 113 VVLIGPSGVGRSELKRRLIA 132
+VL+GPSG G+S L R++A
Sbjct: 33 IVLVGPSGCGKSTL-LRMVA 51
>gnl|CDD|224042 COG1117, PstB, ABC-type phosphate transport system, ATPase
component [Inorganic ion transport and metabolism].
Length = 253
Score = 27.9 bits (63), Expect = 5.8
Identities = 13/24 (54%), Positives = 15/24 (62%), Gaps = 3/24 (12%)
Query: 115 LIGPSGVGRSELKR---RLIALDP 135
LIGPSG G+S L R R+ L P
Sbjct: 38 LIGPSGCGKSTLLRCLNRMNDLIP 61
>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 = 27.6 bits (62), Expect = 6.0
Identities = 14/50 (28%), Positives = 22/50 (44%), Gaps = 5/50 (10%)
Query: 89 FDRE-EIPTYEEVAKLYPMETLRRPVVLIGPSGVGRSELKRRLIALDPDK 137
FDRE E+ EE A+ +V+ GP G++ L R + +
Sbjct: 2 FDREKELKELEEWAE----RGTYPIIVVYGPRRCGKTALLREFLEELREL 47
>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 = 28.0 bits (63), Expect = 6.1
Identities = 9/27 (33%), Positives = 14/27 (51%)
Query: 107 ETLRRPVVLIGPSGVGRSELKRRLIAL 133
E ++ + L+GP G G+S L L
Sbjct: 75 EERKQILYLLGPVGGGKSSLVECLKRG 101
>gnl|CDD|213228 cd03261, ABC_Org_Solvent_Resistant, ATP-binding cassette transport
system involved in resistant to organic solvents. 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 = 235
Score = 27.5 bits (62), Expect = 6.1
Identities = 12/26 (46%), Positives = 17/26 (65%), Gaps = 1/26 (3%)
Query: 113 VVLIGPSGVGRSELKRRLIALD-PDK 137
+ +IGPSG G+S L R ++ L PD
Sbjct: 29 LAIIGPSGSGKSTLLRLIVGLLRPDS 54
>gnl|CDD|172741 PRK14253, PRK14253, phosphate ABC transporter ATP-binding protein;
Provisional.
Length = 249
Score = 27.5 bits (61), Expect = 6.2
Identities = 12/21 (57%), Positives = 14/21 (66%)
Query: 110 RRPVVLIGPSGVGRSELKRRL 130
R+ LIGPSG G+S L R L
Sbjct: 29 RQVTALIGPSGCGKSTLLRCL 49
>gnl|CDD|206656 cd01863, Rab18, Rab GTPase family 18 (Rab18). Rab18 subfamily.
Mammalian Rab18 is implicated in endocytic transport and
is expressed most highly in polarized epithelial cells.
However, trypanosomal Rab, TbRAB18, is upregulated in
the BSF (Blood Stream Form) stage and localized
predominantly to elements of the Golgi complex. In human
and mouse cells, Rab18 has been identified in lipid
droplets, organelles that store neutral lipids. GTPase
activating proteins (GAPs) interact with GTP-bound Rab
and accelerate the hydrolysis of GTP to GDP. Guanine
nucleotide exchange factors (GEFs) interact with
GDP-bound Rabs to promote the formation of the GTP-bound
state. Rabs are further regulated by guanine nucleotide
dissociation inhibitors (GDIs), which facilitate Rab
recycling by masking C-terminal lipid binding and
promoting cytosolic localization. Most Rab GTPases
contain a lipid modification site at the C-terminus,
with sequence motifs CC, CXC, or CCX. Lipid binding is
essential for membrane attachment, a key feature of most
Rab proteins. Due to the presence of truncated sequences
in this CD, the lipid modification site is not available
for annotation.
Length = 161
Score = 27.3 bits (61), Expect = 6.3
Identities = 10/17 (58%), Positives = 13/17 (76%)
Query: 113 VVLIGPSGVGRSELKRR 129
++LIG SGVG+S L R
Sbjct: 3 ILLIGDSGVGKSSLLLR 19
>gnl|CDD|232848 TIGR00157, TIGR00157, ribosome small subunit-dependent GTPase A.
Members of this protein were designated YjeQ and are now
designated RsgA (ribosome small subunit-dependent GTPase
A). The strongest motif in the alignment of these
proteins is GXSGVGKS[ST], a classic P-loop for
nucleotide binding. This protein has been shown to
cleave GTP and remain bound to GDP. A role as a
regulator of translation has been suggested. The Aquifex
aeolicus ortholog is split into consecutive open reading
frames. Consequently, this model was build in fragment
mode (-f option) [Protein synthesis, Translation
factors].
Length = 245
Score = 27.4 bits (61), Expect = 6.6
Identities = 14/40 (35%), Positives = 19/40 (47%), Gaps = 4/40 (10%)
Query: 96 TYEEVAKLYPMETLRRPVVLIGPSGVGRSELKRRLIALDP 135
+ + +L R V G SGVG+S L + ALDP
Sbjct: 107 NQDGLKELIEALQNRI-SVFAGQSGVGKSSL---INALDP 142
>gnl|CDD|183226 PRK11607, potG, putrescine transporter ATP-binding subunit;
Provisional.
Length = 377
Score = 27.9 bits (62), Expect = 6.6
Identities = 17/44 (38%), Positives = 20/44 (45%), Gaps = 11/44 (25%)
Query: 115 LIGPSGVGRSELKRRL----------IALDPDKFTQVTPYTTRP 148
L+G SG G+S L R L I LD + V PY RP
Sbjct: 50 LLGASGCGKSTLLRMLAGFEQPTAGQIMLDGVDLSHVPPY-QRP 92
>gnl|CDD|131368 TIGR02315, ABC_phnC, phosphonate ABC transporter, ATP-binding
protein. Phosphonates are a class of
phosphorus-containing organic compound with a stable
direct C-P bond rather than a C-O-P linkage. A number of
bacterial species have operons, typically about 14 genes
in size, with genes for ATP-dependent transport of
phosphonates, degradation, and regulation of the
expression of the system. Members of this protein family
are the ATP-binding cassette component of tripartite ABC
transporters of phosphonates [Transport and binding
proteins, Anions].
Length = 243
Score = 27.6 bits (62), Expect = 6.9
Identities = 12/22 (54%), Positives = 15/22 (68%), Gaps = 3/22 (13%)
Query: 113 VVLIGPSGVGRSELKR---RLI 131
V +IGPSG G+S L R RL+
Sbjct: 31 VAIIGPSGAGKSTLLRCINRLV 52
>gnl|CDD|234631 PRK00098, PRK00098, GTPase RsgA; Reviewed.
Length = 298
Score = 27.5 bits (62), Expect = 6.9
Identities = 14/23 (60%), Positives = 15/23 (65%), Gaps = 3/23 (13%)
Query: 114 VLIGPSGVGRSELKRRLIALDPD 136
VL G SGVG+S L L AL PD
Sbjct: 168 VLAGQSGVGKSTL---LNALAPD 187
>gnl|CDD|182182 PRK09984, PRK09984, phosphonate/organophosphate ester transporter
subunit; Provisional.
Length = 262
Score = 27.7 bits (61), Expect = 7.0
Identities = 12/21 (57%), Positives = 14/21 (66%)
Query: 113 VVLIGPSGVGRSELKRRLIAL 133
V L+GPSG G+S L R L L
Sbjct: 33 VALLGPSGSGKSTLLRHLSGL 53
>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 = 27.2 bits (61), Expect = 7.1
Identities = 12/35 (34%), Positives = 18/35 (51%), Gaps = 6/35 (17%)
Query: 111 RPVV---LIGPSGVGRSELKRRLIAL---DPDKFT 139
RP+ +GP+GVG++EL + L L D
Sbjct: 1 RPIGSFLFLGPTGVGKTELAKALAELLFGDERALI 35
>gnl|CDD|183088 PRK11331, PRK11331, 5-methylcytosine-specific restriction enzyme
subunit McrB; Provisional.
Length = 459
Score = 27.7 bits (61), Expect = 7.2
Identities = 11/26 (42%), Positives = 19/26 (73%)
Query: 108 TLRRPVVLIGPSGVGRSELKRRLIAL 133
T+++ ++L GP GVG++ + RRL L
Sbjct: 192 TIKKNIILQGPPGVGKTFVARRLAYL 217
>gnl|CDD|227596 COG5271, MDN1, AAA ATPase containing von Willebrand factor type A
(vWA) domain [General function prediction only].
Length = 4600
Score = 28.0 bits (62), Expect = 7.2
Identities = 16/63 (25%), Positives = 31/63 (49%), Gaps = 3/63 (4%)
Query: 71 SAAVKTKKIIYDLAETDDFDREEIPTYEEVAKLYPMETLRRPVVLIGPSGVGRSELKRRL 130
S V+ K+ L ++ ++ E V + M P++L+G +GVG++ L R L
Sbjct: 1814 SVTVRMKERRPRLDDSFVLLHSQLQVLESVMRCINMNW---PLILVGDTGVGKTSLLRFL 1870
Query: 131 IAL 133
++
Sbjct: 1871 ASI 1873
>gnl|CDD|179793 PRK04220, PRK04220, 2-phosphoglycerate kinase; Provisional.
Length = 301
Score = 27.6 bits (62), Expect = 7.2
Identities = 19/44 (43%), Positives = 25/44 (56%), Gaps = 10/44 (22%)
Query: 97 YEEVAKLYPM-ETLRRP----VVLIG-PSGVGRS----ELKRRL 130
YEEVA+ Y + +R+ ++LIG SGVG S EL RL
Sbjct: 73 YEEVAEKYLLWRRIRKSKEPIIILIGGASGVGTSTIAFELASRL 116
>gnl|CDD|234654 PRK00131, aroK, shikimate kinase; Reviewed.
Length = 175
Score = 27.1 bits (61), Expect = 7.2
Identities = 9/21 (42%), Positives = 12/21 (57%)
Query: 110 RRPVVLIGPSGVGRSELKRRL 130
+VLIG G G+S + R L
Sbjct: 4 GPNIVLIGFMGAGKSTIGRLL 24
>gnl|CDD|226970 COG4619, COG4619, ABC-type uncharacterized transport system, ATPase
component [General function prediction only].
Length = 223
Score = 27.1 bits (60), Expect = 7.4
Identities = 8/23 (34%), Positives = 14/23 (60%)
Query: 113 VVLIGPSGVGRSELKRRLIALDP 135
+ + GPSG G+S L + + +L
Sbjct: 32 IAITGPSGCGKSTLLKIVASLIS 54
>gnl|CDD|179732 PRK04056, PRK04056, Maf-like protein; Reviewed.
Length = 180
Score = 27.2 bits (61), Expect = 7.6
Identities = 10/36 (27%), Positives = 16/36 (44%), Gaps = 4/36 (11%)
Query: 68 LSCSAAVKTKKIIYDLAET----DDFDREEIPTYEE 99
L+C +K DL+ T FD +++ Y E
Sbjct: 102 LTCMILKSPEKEWLDLSVTTYRFKKFDEDDLEKYLE 137
>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 = 27.1 bits (61), Expect = 7.7
Identities = 9/24 (37%), Positives = 16/24 (66%)
Query: 113 VVLIGPSGVGRSELKRRLIALDPD 136
+++IGP G G++ L +RL + P
Sbjct: 25 LLMIGPPGSGKTMLAKRLPGILPP 48
>gnl|CDD|236936 PRK11608, pspF, phage shock protein operon transcriptional
activator; Provisional.
Length = 326
Score = 27.3 bits (61), Expect = 7.8
Identities = 14/38 (36%), Positives = 22/38 (57%), Gaps = 3/38 (7%)
Query: 98 EEVAKLYPMETLRRPVVLIGPSGVGRSELKRRLIALDP 135
E+V++L P L +PV++IG G G+ + RL L
Sbjct: 20 EQVSRLAP---LDKPVLIIGERGTGKELIASRLHYLSS 54
>gnl|CDD|227118 COG4778, PhnL, ABC-type phosphonate transport system, ATPase
component [Inorganic ion transport and metabolism].
Length = 235
Score = 27.4 bits (61), Expect = 7.9
Identities = 13/20 (65%), Positives = 14/20 (70%)
Query: 113 VVLIGPSGVGRSELKRRLIA 132
VVL GPSG G+S L R L A
Sbjct: 40 VVLHGPSGSGKSTLLRSLYA 59
>gnl|CDD|224041 COG1116, TauB, ABC-type nitrate/sulfonate/bicarbonate transport
system, ATPase component [Inorganic ion transport and
metabolism].
Length = 248
Score = 27.1 bits (61), Expect = 8.1
Identities = 12/20 (60%), Positives = 15/20 (75%), Gaps = 1/20 (5%)
Query: 113 VVLIGPSGVGRSELKRRLIA 132
V ++GPSG G+S L RLIA
Sbjct: 32 VAILGPSGCGKSTL-LRLIA 50
>gnl|CDD|213260 cd03293, ABC_NrtD_SsuB_transporters, ATP-binding cassette domain of
the nitrate and sulfonate transporters. NrtD and SsuB
are the ATP-binding subunits of the bacterial ABC-type
nitrate and sulfonate transport systems, respectively.
ABC transporters are a large family of proteins involved
in the transport of a wide variety of different
compounds, like sugars, ions, peptides, and more complex
organic molecules. The nucleotide binding domain shows
the highest similarity between all members of the
family. ABC transporters are a subset of nucleotide
hydrolases that contain a signature motif, Q-loop, and
H-loop/switch region, in addition to, the Walker A
motif/P-loop and Walker B motif commonly found in a
number of ATP- and GTP-binding and hydrolyzing proteins.
Length = 220
Score = 27.1 bits (61), Expect = 8.9
Identities = 12/20 (60%), Positives = 15/20 (75%), Gaps = 1/20 (5%)
Query: 113 VVLIGPSGVGRSELKRRLIA 132
V L+GPSG G+S L R+IA
Sbjct: 33 VALVGPSGCGKSTL-LRIIA 51
>gnl|CDD|219856 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 = 116
Score = 26.2 bits (58), Expect = 9.5
Identities = 13/54 (24%), Positives = 19/54 (35%)
Query: 113 VVLIGPSGVGRSELKRRLIALDPDKFTQVTPYTTRPKKPGEEDGKEYHFVSHET 166
VV+IG G G+S L +L+ + T E DG +
Sbjct: 2 VVVIGDKGSGKSSLLSQLVGGEFPPEPLEIQGDTLAVDTLEVDGDTGLLNIWDF 55
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
0.317 0.134 0.392
Gapped
Lambda K H
0.267 0.0740 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 13,670,625
Number of extensions: 1295617
Number of successful extensions: 1543
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1534
Number of HSP's successfully gapped: 108
Length of query: 264
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 169
Effective length of database: 6,723,972
Effective search space: 1136351268
Effective search space used: 1136351268
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 58 (26.1 bits)