RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8556
(298 letters)
>gnl|CDD|234626 PRK00091, miaA, tRNA delta(2)-isopentenylpyrophosphate transferase;
Reviewed.
Length = 307
Score = 305 bits (783), Expect = e-104
Identities = 112/298 (37%), Positives = 168/298 (56%), Gaps = 44/298 (14%)
Query: 40 VAILGPTASGKSSVALKISEYIPCEIISIDSALVYCDMDIGTNKPSIIEREITPHHLIDI 99
+ I+GPTASGK+++A+++++ + EIIS DS VY MDIGT KP+ ER PHHLIDI
Sbjct: 7 IVIVGPTASGKTALAIELAKRLNGEIISADSMQVYRGMDIGTAKPTAEERAGVPHHLIDI 66
Query: 100 IEPTKSYSVIQFCEDALFSIKNILKKKKLPLLVGGTMLYFKALRDGINKLPPANLKLRTK 159
++PT+SYSV F DAL +I +IL + KLP+LVGGT LY KAL +G++ LPPA+ +LR +
Sbjct: 67 LDPTESYSVADFQRDALAAIADILARGKLPILVGGTGLYIKALLEGLSPLPPADPELRAE 126
Query: 160 FNIDINKYGISFLYDKLKLLDPVTANQ--PSN---------------------------- 189
+ G L+ +L +DP A + P++
Sbjct: 127 LEALAAEEGWEALHAELAEIDPEAAARIHPNDPQRIIRALEVYELTGKPLSELQKRGKPP 186
Query: 190 ------------RHILHKRISDRFKKMLDQDLLINEVKKIRKKWNLNLNLPSMKCIGYRQ 237
R L++RI+ R +ML+Q L+ EV+ + + L +LP+M+ IGY++
Sbjct: 187 PYRVLIIGLDPDREELYERINQRVDQMLEQG-LLEEVRALLARGYLP-DLPAMRAIGYKE 244
Query: 238 TWEYIDGLIDRNTLKEKSIIATRQLAKQQLTWLRNMNEKITIDCLEKNCVQKILNLIK 295
Y+DG I EK ATRQ AK+QLTW R + +D + +++IL L++
Sbjct: 245 LLAYLDGEISLEEAIEKIKQATRQYAKRQLTWFRRQPDIHWLDLSPEEALEEILRLLE 302
>gnl|CDD|223401 COG0324, MiaA, tRNA delta(2)-isopentenylpyrophosphate transferase
[Translation, ribosomal structure and biogenesis].
Length = 308
Score = 260 bits (667), Expect = 2e-86
Identities = 108/278 (38%), Positives = 159/278 (57%), Gaps = 46/278 (16%)
Query: 40 VAILGPTASGKSSVALKISEYIPCEIISIDSALVYCDMDIGTNKPSIIEREITPHHLIDI 99
+ I GPTASGK+++A+ +++ + EIIS+DS VY +DIGT KPS+ E PHHLIDI
Sbjct: 6 IVIAGPTASGKTALAIALAKRLGGEIISLDSMQVYRGLDIGTAKPSLEELAGVPHHLIDI 65
Query: 100 IEPTKSYSVIQFCEDALFSIKNILKKKKLPLLVGGTMLYFKALRDGINKLPPANLKLRTK 159
+PT+SYS +F DAL +I +IL + KLP+LVGGT LY KAL +G++ LP A+ ++R +
Sbjct: 66 RDPTESYSAAEFQRDALAAIDDILARGKLPILVGGTGLYLKALLEGLSLLPEADPEVRRR 125
Query: 160 FNIDINKYGISFLYDKLKLLDPVTANQ--PSN---------------------------- 189
++ + G L+ +LK +DP A + P++
Sbjct: 126 LEAELAELGNDALHAELKKIDPEAAAKIHPNDPQRIIRALEVYYLTGKPISELQKRSRPI 185
Query: 190 --------------RHILHKRISDRFKKMLDQDLLINEVKKIRKKWNLNLNLPSMKCIGY 235
R +L++RI+ R ML+Q LI EVK + + L+L+LP+M+ IGY
Sbjct: 186 LEPYDILIIALAADREVLYERINRRVDAMLEQ-GLIEEVKALYAR-GLHLDLPAMQAIGY 243
Query: 236 RQTWEYIDGLIDRNTLKEKSIIATRQLAKQQLTWLRNM 273
++ Y+DG I E+ ATRQ AK+QLTW RN
Sbjct: 244 KEILAYLDGGISLEEAIERIKTATRQYAKRQLTWFRNQ 281
>gnl|CDD|213512 TIGR00174, miaA, tRNA dimethylallyltransferase. Alternate names
include delta(2)-isopentenylpyrophosphate transferase,
IPP transferase, 2-methylthio-N6-isopentyladenosine tRNA
modification enzyme. Catalyzes the first step in the
modification of an adenosine near the anticodon to
2-methylthio-N6-isopentyladenosine. Understanding of
substrate specificity has changed [Protein synthesis,
tRNA and rRNA base modification].
Length = 287
Score = 209 bits (533), Expect = 2e-66
Identities = 103/277 (37%), Positives = 152/277 (54%), Gaps = 45/277 (16%)
Query: 40 VAILGPTASGKSSVALKISEYIPCEIISIDSALVYCDMDIGTNKPSIIEREITPHHLIDI 99
+ ++GPTASGKS +++++++ + EIIS+DS +Y MDIGT KPS+ ERE PHHLIDI
Sbjct: 2 IFLMGPTASGKSQLSIQLAQKLNAEIISVDSMQIYKGMDIGTAKPSLQEREGIPHHLIDI 61
Query: 100 IEPTKSYSVIQFCEDALFSIKNILKKKKLPLLVGGTMLYFKALRDGINKLPPANLKLRTK 159
++P++SYS F AL +I +I + K+PLLVGGT LY KAL +G++ P A+ +R +
Sbjct: 62 LDPSESYSAADFQTQALNAIADITARGKIPLLVGGTGLYLKALLEGLSPTPSADKLIREQ 121
Query: 160 FNIDINKYGISFLYDKLKLLDPVTANQ--PSN---------------------------- 189
I + G FLY++LK +DPV A + P++
Sbjct: 122 LEILAEEQGWDFLYNELKKVDPVAAAKIHPNDTRRVQRALEVFYATGKPPSELFKEQKIE 181
Query: 190 -------------RHILHKRISDRFKKMLDQDLLINEVKKIRKKWNLNLNLPSMKCIGYR 236
R LH+RI R ML+ LL EVK + + +LPS++ IGY+
Sbjct: 182 LFYDIVQIGLASSREPLHQRIEQRVHDMLESGLL-AEVKALYAQ-YDLCDLPSIQAIGYK 239
Query: 237 QTWEYIDGLIDRNTLKEKSIIATRQLAKQQLTWLRNM 273
+ Y++G + E+ TRQ AK+QLTW R
Sbjct: 240 EFLLYLEGTVSLEDAIERIKCNTRQYAKRQLTWFRKW 276
>gnl|CDD|216659 pfam01715, IPPT, IPP transferase. This is a family of IPP
transferases EC:2.5.1.8 also known as tRNA
delta(2)-isopentenylpyrophosphate transferase. These
enzymes modify both cytoplasmic and mitochondrial tRNAs
at A(37) to give isopentenyl A(37).
Length = 253
Score = 196 bits (500), Expect = 5e-62
Identities = 93/253 (36%), Positives = 133/253 (52%), Gaps = 45/253 (17%)
Query: 71 ALVYCDMDIGTNKPSIIEREITPHHLIDIIEPTKSYSVIQFCEDALFSIKNILKKKKLPL 130
VY MDIGT KPS+ ER+ PHHLIDI++PT+SYS +F DAL +I I + K+PL
Sbjct: 1 MQVYKGMDIGTAKPSLEERKGVPHHLIDILDPTESYSAAEFQRDALEAIAEIRARGKIPL 60
Query: 131 LVGGTMLYFKALRDGINKLPPANLKLRTKFNIDINKYGISFLYDKLKLLDPVTAN--QPS 188
LVGGT LYFKAL DG++ P A+ K+R K + + G +L+ +L +DP A P+
Sbjct: 61 LVGGTGLYFKALLDGLSDTPSADPKVRAKLEEQLEELGNDYLHAELASVDPEAAAKIHPN 120
Query: 189 N-----------------------------------------RHILHKRISDRFKKMLDQ 207
+ R +LH+RI+ R ML+
Sbjct: 121 DGRRIVRALEVFYATGKPISEFQKEQKNALPYDIVQIGLARDREVLHERIARRVDDMLES 180
Query: 208 DLLINEVKKIRKKWNLNLNLPSMKCIGYRQTWEYIDGLIDRNTLKEKSIIATRQLAKQQL 267
L+ EVK + LN +LP+++ IGY++ Y+DG E+ I ATRQ AK+Q+
Sbjct: 181 GLV-EEVKALY-AQGLNEDLPAIRAIGYKEFLLYLDGECTLEEAIERIIKATRQYAKRQM 238
Query: 268 TWLRNMNEKITID 280
TW R ++ +D
Sbjct: 239 TWFRKDSQVHWLD 251
>gnl|CDD|173191 PRK14729, miaA, tRNA delta(2)-isopentenylpyrophosphate transferase;
Provisional.
Length = 300
Score = 116 bits (293), Expect = 7e-31
Identities = 76/239 (31%), Positives = 113/239 (47%), Gaps = 44/239 (18%)
Query: 40 VAILGPTASGKSSVALKISEYIPCEIISIDSALVYCDMDIGTNKPSIIEREITPHHLIDI 99
V I GPTA GKS++ + EII++DS VY + DI + KPS R+ HHL+D
Sbjct: 7 VFIFGPTAVGKSNILFHFPKGK-AEIINVDSIQVYKEFDIASCKPSKELRKHIKHHLVDF 65
Query: 100 IEPTKSYSVIQFCEDALFSIKNILKKKKLPLLVGGTMLYFKALRDGINKLPPANLKLRTK 159
+EP K Y++ F ++AL IK + ++KK+P+ VGG+ YFK L+ G+ PP + K+R
Sbjct: 66 LEPIKEYNLGIFYKEALKIIKELRQQKKIPIFVGGSAFYFKHLKYGLPSTPPVSSKIRIY 125
Query: 160 FNIDINKYGISFLYDKLKLLDPVTANQPSNRHI--------------------------- 192
N G S+L ++LK +D + + I
Sbjct: 126 VNNLFTLKGKSYLLEELKRVDFIRYESINKNDIYRIKRSLEVYYQTGIPISQFLKKQNMF 185
Query: 193 --------------LHKRISDRFKKMLDQDLLINEVKKIRKKWNLNLNLPSMKCIGYRQ 237
+ RI R M+D LL +E+K + K N N P+ K IGYR+
Sbjct: 186 KNILAIGLKRPMEEMKSRIISRVNNMIDCGLL-SEIKSLLGK-GYNENTPAFKGIGYRE 242
>gnl|CDD|215451 PLN02840, PLN02840, tRNA dimethylallyltransferase.
Length = 421
Score = 110 bits (276), Expect = 1e-27
Identities = 49/106 (46%), Positives = 74/106 (69%), Gaps = 1/106 (0%)
Query: 36 RKTKV-AILGPTASGKSSVALKISEYIPCEIISIDSALVYCDMDIGTNKPSIIEREITPH 94
+K KV I GPT +GKS +AL++++ + EIIS DS VY +D+G+ KPS+ ER+ PH
Sbjct: 19 KKEKVIVISGPTGAGKSRLALELAKRLNGEIISADSVQVYRGLDVGSAKPSLSERKEVPH 78
Query: 95 HLIDIIEPTKSYSVIQFCEDALFSIKNILKKKKLPLLVGGTMLYFK 140
HLIDI+ P+ YSV F +DA + ++IL + ++P++ GGT LY +
Sbjct: 79 HLIDILHPSDDYSVGAFFDDARRATQDILNRGRVPIVAGGTGLYLR 124
Score = 41.3 bits (97), Expect = 4e-04
Identities = 39/128 (30%), Positives = 62/128 (48%), Gaps = 30/128 (23%)
Query: 188 SNRHILHKRISDRFKKML-DQDLLINEVKKIRKKWNLNLNL-----PSMKCIGYRQTWEY 241
S R L++ I R ++ML + +++E W L+L L + + IGYRQ EY
Sbjct: 241 SPRLDLYRSIDLRCEEMLAGTNGILSEAS-----WLLDLGLLPNSNSATRAIGYRQAMEY 295
Query: 242 I-----DGLIDRNTLKE------KSIIATRQLAKQQLTWLRNMNEKIT--IDCLEKNCVQ 288
+ +G ++ +E K A+R AK+Q+TW R NE I +D + ++
Sbjct: 296 LLQCRQNG--GESSPQEFLAFLSKFQTASRNFAKRQMTWFR--NEPIYHWLDASQP--LE 349
Query: 289 KILNLIKD 296
KIL I D
Sbjct: 350 KILQFIYD 357
>gnl|CDD|215399 PLN02748, PLN02748, tRNA dimethylallyltransferase.
Length = 468
Score = 97.6 bits (243), Expect = 6e-23
Identities = 55/174 (31%), Positives = 90/174 (51%), Gaps = 22/174 (12%)
Query: 40 VAILGPTASGKSSVALKISEYIPCEIISIDSALVYCDMDIGTNKPSIIEREITPHHLIDI 99
V ++GPT SGKS +A+ ++ + P EII+ DS VY +D+ TNK + E++ PHHL+ +
Sbjct: 25 VVVMGPTGSGKSKLAVDLASHFPVEIINADSMQVYSGLDVLTNKVPLHEQKGVPHHLLGV 84
Query: 100 IEPTKSYSVIQFCEDALFSIKNILKKKKLPLLVGGTMLYFKAL--------------RDG 145
I P+ ++ F + A+ I+ IL + LP++VGGT Y +AL
Sbjct: 85 ISPSVEFTAKDFRDHAVPLIEEILSRNGLPVIVGGTNYYIQALVSPFLLDDMAEETEDCT 144
Query: 146 INKLPPANLKLRTKFNIDINKYGISFLYDKLKLLDPVTANQ--PSNRHILHKRI 197
+ + + + + Y+ LK LDPV AN+ P+N H++I
Sbjct: 145 FVVASVLDEHMDVESGLGND--DEDHGYELLKELDPVAANRIHPNN----HRKI 192
>gnl|CDD|177823 PLN02165, PLN02165, adenylate isopentenyltransferase.
Length = 334
Score = 72.9 bits (179), Expect = 9e-15
Identities = 39/109 (35%), Positives = 60/109 (55%), Gaps = 2/109 (1%)
Query: 36 RKTK-VAILGPTASGKSSVALKISEYIPCEIISIDSALVYCDMDIGTNKPSIIEREITPH 94
K K V I+G T SGKS +++ ++ P EII+ D VY + I TN+ +I +R PH
Sbjct: 41 CKDKVVVIMGATGSGKSRLSVDLATRFPSEIINSDKMQVYDGLKITTNQITIQDRRGVPH 100
Query: 95 HLIDIIEPTKS-YSVIQFCEDALFSIKNILKKKKLPLLVGGTMLYFKAL 142
HL+ + P + +F A SI I ++KLP++ GG+ + AL
Sbjct: 101 HLLGELNPDDGELTASEFRSLASLSISEITSRQKLPIVAGGSNSFIHAL 149
>gnl|CDD|221983 pfam13207, AAA_17, AAA domain.
Length = 114
Score = 37.7 bits (87), Expect = 0.001
Identities = 17/71 (23%), Positives = 34/71 (47%), Gaps = 1/71 (1%)
Query: 39 KVAILGPTASGKSSVALKISEYIPCEIISIDSALVYCDMDIGTNKPSIIEREITPHHLID 98
+ I GP SGKS++A K++E + +IS+D L + + + + +I L +
Sbjct: 1 IILITGPPGSGKSTLAKKLAEKLGIPVISLDDLLREEGL-AELDDGELDDIDIDLELLEE 59
Query: 99 IIEPTKSYSVI 109
I++ +
Sbjct: 60 ILDELAKQEWV 70
>gnl|CDD|180911 PRK07261, PRK07261, topology modulation protein; Provisional.
Length = 171
Score = 35.5 bits (82), Expect = 0.015
Identities = 13/32 (40%), Positives = 25/32 (78%)
Query: 39 KVAILGPTASGKSSVALKISEYIPCEIISIDS 70
K+AI+G + SGKS++A K+S++ C ++ +D+
Sbjct: 2 KIAIIGYSGSGKSTLARKLSQHYNCPVLHLDT 33
>gnl|CDD|238981 cd02023, UMPK, Uridine monophosphate kinase (UMPK, EC 2.7.1.48),
also known as uridine kinase or uridine-cytidine kinase
(UCK), catalyzes the reversible phosphoryl transfer
from ATP to uridine or cytidine to yield UMP or CMP. In
the primidine nucleotide-salvage pathway, this enzyme
combined with nucleoside diphosphate kinases further
phosphorylates UMP and CMP to form UTP and CTP. This
kinase also catalyzes the phosphorylation of several
cytotoxic ribonucleoside analogs such as
5-flurrouridine and cyclopentenyl-cytidine.
Length = 198
Score = 34.5 bits (80), Expect = 0.041
Identities = 14/34 (41%), Positives = 20/34 (58%), Gaps = 3/34 (8%)
Query: 40 VAILGPTASGKSSVALKISEYIPCE---IISIDS 70
+ I G + SGK++VA +I E + IIS DS
Sbjct: 2 IGIAGGSGSGKTTVAEEIIEQLGNPKVVIISQDS 35
>gnl|CDD|235492 PRK05480, PRK05480, uridine/cytidine kinase; Provisional.
Length = 209
Score = 33.2 bits (77), Expect = 0.10
Identities = 13/34 (38%), Positives = 19/34 (55%), Gaps = 3/34 (8%)
Query: 40 VAILGPTASGKSSVALKISEYIPCE---IISIDS 70
+ I G + SGK++VA I E + E +I DS
Sbjct: 9 IGIAGGSGSGKTTVASTIYEELGDESIAVIPQDS 42
>gnl|CDD|238978 cd02020, CMPK, Cytidine monophosphate kinase (CMPK) catalyzes the
reversible phosphorylation of cytidine monophosphate
(CMP) to produce cytidine diphosphate (CDP), using ATP
as the preferred phosphoryl donor.
Length = 147
Score = 32.5 bits (75), Expect = 0.10
Identities = 10/23 (43%), Positives = 16/23 (69%)
Query: 39 KVAILGPTASGKSSVALKISEYI 61
+AI GP SGKS+VA +++ +
Sbjct: 1 IIAIDGPAGSGKSTVAKLLAKKL 23
>gnl|CDD|110723 pfam01745, IPT, Isopentenyl transferase. Isopentenyl transferase
/ dimethylallyl transferase synthesises
isopentenyladensosine 5'-monophosphate, a cytokinin
that induces shoot formation on host plants infected
with the Ti plasmid.
Length = 232
Score = 33.1 bits (76), Expect = 0.12
Identities = 12/52 (23%), Positives = 25/52 (48%)
Query: 41 AILGPTASGKSSVALKISEYIPCEIISIDSALVYCDMDIGTNKPSIIEREIT 92
I G T +GK++ A+ +++ +I +D + G+ +P E + T
Sbjct: 5 LIWGATCTGKTAEAIALAKETGWPVIVLDRVQCCSQLATGSGRPLPAELQGT 56
>gnl|CDD|238977 cd02019, NK, Nucleoside/nucleotide kinase (NK) is a protein
superfamily consisting of multiple families of enzymes
that share structural similarity and are functionally
related to the catalysis of the reversible phosphate
group transfer from nucleoside triphosphates to
nucleosides/nucleotides, nucleoside monophosphates, or
sugars. Members of this family play a wide variety of
essential roles in nucleotide metabolism, the
biosynthesis of coenzymes and aromatic compounds, as
well as the metabolism of sugar and sulfate.
Length = 69
Score = 30.4 bits (69), Expect = 0.18
Identities = 13/53 (24%), Positives = 26/53 (49%), Gaps = 1/53 (1%)
Query: 40 VAILGPTASGKSSVALKISEYIPCEIIS-IDSALVYCDMDIGTNKPSIIEREI 91
+AI G + SGKS+VA K++E + + +D ++ + R++
Sbjct: 2 IAITGGSGSGKSTVAKKLAEQLGGRSVVVLDEIVILEGLYASYKSRDARIRDL 54
>gnl|CDD|232890 TIGR00235, udk, uridine kinase. Model contains a number of
longer eukaryotic proteins and starts bringing in
phosphoribulokinase hits at scores of 160 and below
[Purines, pyrimidines, nucleosides, and nucleotides,
Salvage of nucleosides and nucleotides].
Length = 207
Score = 32.0 bits (73), Expect = 0.22
Identities = 14/34 (41%), Positives = 20/34 (58%), Gaps = 3/34 (8%)
Query: 40 VAILGPTASGKSSVALKISEYIPCE---IISIDS 70
+ I G + SGK++VA KI E + IIS D+
Sbjct: 9 IGIGGGSGSGKTTVARKIYEQLGKLEIVIISQDN 42
>gnl|CDD|223360 COG0283, Cmk, Cytidylate kinase [Nucleotide transport and
metabolism].
Length = 222
Score = 32.2 bits (74), Expect = 0.25
Identities = 11/21 (52%), Positives = 15/21 (71%)
Query: 39 KVAILGPTASGKSSVALKISE 59
+AI GP SGKS+VA ++E
Sbjct: 6 IIAIDGPAGSGKSTVAKILAE 26
>gnl|CDD|236865 PRK11160, PRK11160, cysteine/glutathione ABC transporter
membrane/ATP-binding component; Reviewed.
Length = 574
Score = 32.1 bits (74), Expect = 0.38
Identities = 9/14 (64%), Positives = 11/14 (78%)
Query: 39 KVAILGPTASGKSS 52
KVA+LG T GKS+
Sbjct: 368 KVALLGRTGCGKST 381
>gnl|CDD|234457 TIGR04075, bacter_Pnkp, polynucleotide kinase-phosphatase.
Members of this protein family are the bacterial
polynucleotide kinase-phosphatase (Pnkp) whose genes
occur paired with genes for the 3' terminal RNA ribose
2'-O-methyltransferase Hen1. All members of the seed
alignment belong to a cassette with the Hen1. The pair
acts in bacterial RNA repair. This enzyme performs
end-healing reactions on broken RNA, preparing from the
RNA ligase to close the break. The working hypothesis
is that the combination of Pnkp (RNA repair) and Hen1
(RNA modification) serves to first repair RNA damage
from ribotoxins and then perform a modification that
prevents the damage from recurring [Transcription, RNA
processing].
Length = 851
Score = 31.9 bits (73), Expect = 0.48
Identities = 12/30 (40%), Positives = 19/30 (63%), Gaps = 2/30 (6%)
Query: 40 VAILGPTASGKSSVALKISEYIPCEIISID 69
V ++G + SGKS+ A K + P E++S D
Sbjct: 11 VVLVGASGSGKSTFARK--HFKPTEVLSSD 38
>gnl|CDD|213217 cd03250, ABCC_MRP_domain1, ATP-binding cassette domain 1 of
multidrug resistance-associated protein, subfamily C.
This subfamily is also known as MRP (multidrug
resistance-associated protein). Some of the MRP members
have five additional transmembrane segments in their
N-terminus, but the function of these additional
membrane-spanning domains is not clear. The MRP was
found in the multidrug-resisting lung cancer cell in
which p-glycoprotein was not overexpressed. MRP exports
glutathione by drug stimulation, as well as, certain
substrates in conjugated forms with anions, such as
glutathione, glucuronate, and sulfate.
Length = 204
Score = 30.9 bits (71), Expect = 0.49
Identities = 12/26 (46%), Positives = 15/26 (57%), Gaps = 6/26 (23%)
Query: 27 RIRTGKLLFRKTKVAILGPTASGKSS 52
+ G+L VAI+GP SGKSS
Sbjct: 27 EVPKGEL------VAIVGPVGSGKSS 46
>gnl|CDD|200134 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 [Protein fate, Protein and
peptide secretion and trafficking].
Length = 544
Score = 31.5 bits (72), Expect = 0.51
Identities = 13/34 (38%), Positives = 20/34 (58%), Gaps = 2/34 (5%)
Query: 40 VAILGPTASGKSSVALKISEYIPCE--IISIDSA 71
+AI+GP+ SGKS++A I P + +D A
Sbjct: 347 LAIIGPSGSGKSTLARLIVGIWPPTSGSVRLDGA 380
>gnl|CDD|234579 PRK00023, cmk, cytidylate kinase; Provisional.
Length = 225
Score = 31.2 bits (72), Expect = 0.51
Identities = 9/20 (45%), Positives = 14/20 (70%)
Query: 40 VAILGPTASGKSSVALKISE 59
+AI GP SGK +VA +++
Sbjct: 7 IAIDGPAGSGKGTVAKILAK 26
>gnl|CDD|223645 COG0572, Udk, Uridine kinase [Nucleotide transport and
metabolism].
Length = 218
Score = 31.1 bits (71), Expect = 0.56
Identities = 13/34 (38%), Positives = 22/34 (64%), Gaps = 3/34 (8%)
Query: 40 VAILGPTASGKSSVALKISEYIPCE---IISIDS 70
+ I G + SGK++VA ++SE + E +IS+D
Sbjct: 11 IGIAGGSGSGKTTVAKELSEQLGVEKVVVISLDD 44
>gnl|CDD|131424 TIGR02371, ala_DH_arch, alanine dehydrogenase, Archaeoglobus
fulgidus type. This enzyme, a homolog of bacterial
ornithine cyclodeaminases and marsupial mu-crystallins,
is a homodimeric, NAD-dependent alanine dehydrogenase
found in Archaeoglobus fulgidus and several other
Archaea. For a number of close homologs, scoring between
trusted and noise cutoffs, it is not clear at present
what is the enzymatic activity.
Length = 325
Score = 31.0 bits (70), Expect = 0.61
Identities = 14/53 (26%), Positives = 22/53 (41%), Gaps = 1/53 (1%)
Query: 34 LFRKTKVAILGPTASGKSSVALKISEYIPCEIISIDSALVYCDMDI-GTNKPS 85
+F +V++ T S + AL+ S+Y + D DI T PS
Sbjct: 150 VFDLEEVSVYCRTPSTREKFALRASDYEVPVRAATDPREAVEGCDILVTTTPS 202
>gnl|CDD|238986 cd02028, UMPK_like, Uridine monophosphate kinase_like (UMPK_like)
is a family of proteins highly similar to the uridine
monophosphate kinase (UMPK, EC 2.7.1.48), also known as
uridine kinase or uridine-cytidine kinase (UCK).
Length = 179
Score = 30.4 bits (69), Expect = 0.78
Identities = 20/71 (28%), Positives = 34/71 (47%), Gaps = 9/71 (12%)
Query: 40 VAILGPTASGKSSVALKIS-----EYIPCEIISIDS----ALVYCDMDIGTNKPSIIERE 90
V I GP+ SGK++ A K+S I +IS+D D D + SI++ +
Sbjct: 2 VGIAGPSGSGKTTFAKKLSNQLRVNGIGPVVISLDDYYVPRKTPRDEDGNYDFESILDLD 61
Query: 91 ITPHHLIDIIE 101
+ +L D++
Sbjct: 62 LLNKNLHDLLN 72
>gnl|CDD|223637 COG0563, Adk, Adenylate kinase and related kinases [Nucleotide
transport and metabolism].
Length = 178
Score = 29.9 bits (68), Expect = 0.94
Identities = 9/31 (29%), Positives = 19/31 (61%)
Query: 39 KVAILGPTASGKSSVALKISEYIPCEIISID 69
++ ILGP +GKS++A K+++ + +
Sbjct: 2 RILILGPPGAGKSTLAKKLAKKLGLPHLDTG 32
>gnl|CDD|180660 PRK06696, PRK06696, uridine kinase; Validated.
Length = 223
Score = 29.9 bits (68), Expect = 1.2
Identities = 17/39 (43%), Positives = 23/39 (58%), Gaps = 5/39 (12%)
Query: 36 RKTKVAILGPTASGKSSVALKISEYI-----PCEIISID 69
R +VAI G TASGK++ A +++E I P SID
Sbjct: 21 RPLRVAIDGITASGKTTFADELAEEIKKRGRPVIRASID 59
>gnl|CDD|238550 cd01130, VirB11-like_ATPase, Type IV secretory pathway component
VirB11, and related ATPases. The homohexamer, VirB11 is
one of eleven Vir proteins, which are required for
T-pilus biogenesis and virulence in the transfer of
T-DNA from the Ti (tumor-inducing) plasmid of bacterial
to plant cells. The pilus is a fibrous cell surface
organelle, which mediates adhesion between bacteria
during conjugative transfer or between bacteria and
host eukaryotic cells during infection. VirB11- related
ATPases include the archaeal flagella biosynthesis
protein and the pilus assembly proteins CpaF/TadA and
TrbB. This alignment contains the C-terminal domain,
which is the ATPase.
Length = 186
Score = 29.9 bits (68), Expect = 1.2
Identities = 13/33 (39%), Positives = 21/33 (63%), Gaps = 3/33 (9%)
Query: 42 ILGPTASGKSSVALKISEYIPCE--IISI-DSA 71
I G T SGK+++ + +IP + II+I D+A
Sbjct: 30 ISGGTGSGKTTLLNALLAFIPPDERIITIEDTA 62
>gnl|CDD|226969 COG4618, ArpD, ABC-type protease/lipase transport system, ATPase
and permease components [General function prediction
only].
Length = 580
Score = 30.3 bits (69), Expect = 1.3
Identities = 8/15 (53%), Positives = 13/15 (86%)
Query: 40 VAILGPTASGKSSVA 54
+ I+GP+ SGKS++A
Sbjct: 365 LGIIGPSGSGKSTLA 379
>gnl|CDD|233761 TIGR02173, cyt_kin_arch, cytidylate kinase, putative. Proteins
in this family are believed to be cytidylate kinase.
Members of this family are found in the archaea and in
spirochaetes, and differ considerably from the common
bacterial form of cytidylate kinase described by
TIGR00017.
Length = 171
Score = 29.3 bits (66), Expect = 1.5
Identities = 11/29 (37%), Positives = 19/29 (65%)
Query: 39 KVAILGPTASGKSSVALKISEYIPCEIIS 67
+ I GP SGK++VA ++E + ++IS
Sbjct: 2 IITISGPPGSGKTTVAKILAEKLSLKLIS 30
>gnl|CDD|221970 pfam13191, AAA_16, AAA ATPase domain. This family of domains
contain a P-loop motif that is characteristic of the
AAA superfamily.
Length = 154
Score = 29.1 bits (65), Expect = 1.5
Identities = 14/62 (22%), Positives = 26/62 (41%), Gaps = 4/62 (6%)
Query: 15 DPQQRQLTADFRRIRTGKLLFRKTKVAILGPTASGKSSVALKISEYIPCEIISIDSALVY 74
+ + +L RR R+G V + GP+ +GK+S+ ++ E + D A
Sbjct: 6 EEELERLLDALRRARSGGPPS----VLLTGPSGTGKTSLLRELLEGLLVAAGKCDQAERN 61
Query: 75 CD 76
Sbjct: 62 PP 63
>gnl|CDD|237434 PRK13578, PRK13578, ornithine decarboxylase; Provisional.
Length = 720
Score = 30.3 bits (69), Expect = 1.5
Identities = 11/19 (57%), Positives = 13/19 (68%), Gaps = 1/19 (5%)
Query: 133 GGTML-YFKALRDGINKLP 150
GG + YF AL +GIN LP
Sbjct: 674 GGAVQRYFLALEEGINLLP 692
>gnl|CDD|224048 COG1123, COG1123, ATPase components of various ABC-type transport
systems, contain duplicated ATPase [General function
prediction only].
Length = 539
Score = 30.2 bits (69), Expect = 1.6
Identities = 10/40 (25%), Positives = 20/40 (50%)
Query: 40 VAILGPTASGKSSVALKISEYIPCEIISIDSALVYCDMDI 79
+ I+G + SGKS++AL + +P ++ D+
Sbjct: 38 LGIVGESGSGKSTLALALMGLLPEGGRITSGEVILDGRDL 77
>gnl|CDD|235244 PRK04182, PRK04182, cytidylate kinase; Provisional.
Length = 180
Score = 29.0 bits (66), Expect = 1.9
Identities = 10/29 (34%), Positives = 18/29 (62%)
Query: 39 KVAILGPTASGKSSVALKISEYIPCEIIS 67
+ I GP SGK++VA ++E + + +S
Sbjct: 2 IITISGPPGSGKTTVARLLAEKLGLKHVS 30
>gnl|CDD|221955 pfam13173, AAA_14, AAA domain. This family of domains contain a
P-loop motif that is characteristic of the AAA
superfamily.
Length = 127
Score = 28.7 bits (65), Expect = 2.0
Identities = 15/90 (16%), Positives = 32/90 (35%), Gaps = 9/90 (10%)
Query: 40 VAILGPTASGKSSVALK-ISEYIPCEIISIDSALVYCDMDIGTNKPSIIEREITPHHLID 98
+ I GP GK+++ L+ + E + I+ I+ + + + P
Sbjct: 5 IVITGPRQVGKTTLLLQFLKELLSENILYINLDDPRFLRLALLDLLEEFLKLLLPGKKYL 64
Query: 99 II-EPTKSYSVIQFCEDALFSIKNILKKKK 127
+ E IQ D ++K + +
Sbjct: 65 FLDE-------IQKVPDWEDALKRLYDDGR 87
>gnl|CDD|227320 COG4987, CydC, ABC-type transport system involved in cytochrome bd
biosynthesis, fused ATPase and permease components
[Energy production and conversion / Posttranslational
modification, protein turnover, chaperones].
Length = 573
Score = 29.6 bits (67), Expect = 2.1
Identities = 10/16 (62%), Positives = 13/16 (81%)
Query: 39 KVAILGPTASGKSSVA 54
KVAILG + SGKS++
Sbjct: 366 KVAILGRSGSGKSTLL 381
>gnl|CDD|237003 PRK11860, PRK11860, bifunctional 3-phosphoshikimate
1-carboxyvinyltransferase/cytidine monophosphate kinase;
Provisional.
Length = 661
Score = 29.6 bits (67), Expect = 2.1
Identities = 11/20 (55%), Positives = 16/20 (80%)
Query: 40 VAILGPTASGKSSVALKISE 59
+ I GPTASGK +VA +++E
Sbjct: 445 ICIDGPTASGKGTVAARVAE 464
>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 = 28.9 bits (64), Expect = 2.2
Identities = 20/97 (20%), Positives = 38/97 (39%), Gaps = 14/97 (14%)
Query: 36 RKTKVAILGPTASGKSSVALKISEYIPCEIISIDSALVYCDMDIGTNKPSIIEREITPHH 95
+ I+GP SGK+++A ++ + + +Y D + I+E +
Sbjct: 1 PGEVILIVGPPGSGKTTLARALARELGPPGGGV----IYIDGED------ILEEVLDQLL 50
Query: 96 LIDIIEPTKSYSVIQFCEDALFSIKNILKKKKLPLLV 132
LI + S S AL + +K K +L+
Sbjct: 51 LIIVGGKKASGSGELRLRLAL----ALARKLKPDVLI 83
>gnl|CDD|238551 cd01131, PilT, Pilus retraction ATPase PilT. PilT is a nucleotide
binding protein responsible for the retraction of type
IV pili, likely by pili disassembly. This retraction
provides the force required for travel of bacteria in
low water environments by a mechanism known as
twitching motility.
Length = 198
Score = 28.8 bits (65), Expect = 2.2
Identities = 17/57 (29%), Positives = 31/57 (54%), Gaps = 9/57 (15%)
Query: 40 VAILGPTASGKSSVALKISEYI----PCEIISIDSALVYCDMDIGTNKPSII-EREI 91
V + GPT SGKS+ + +YI I++I+ + + + +K S+I +RE+
Sbjct: 4 VLVTGPTGSGKSTTLAAMIDYINKNKTHHILTIEDPIEF----VHESKRSLINQREV 56
>gnl|CDD|185067 PRK15112, PRK15112, antimicrobial peptide ABC system ATP-binding
protein SapF; Provisional.
Length = 267
Score = 29.4 bits (66), Expect = 2.3
Identities = 25/83 (30%), Positives = 36/83 (43%), Gaps = 22/83 (26%)
Query: 13 ETDPQQRQLTADFRRIRTGKLLFRKTKV----------------AILGPTASGKSSVALK 56
ET + R L+ FR RTG FR+ V AI+G SGKS++A
Sbjct: 2 ETLLEVRNLSKTFR-YRTG--WFRRQTVEAVKPLSFTLREGQTLAIIGENGSGKSTLAKM 58
Query: 57 ISEYIP---CEIISIDSALVYCD 76
++ I E++ D L + D
Sbjct: 59 LAGMIEPTSGELLIDDHPLHFGD 81
>gnl|CDD|213195 cd03228, ABCC_MRP_Like, ATP-binding cassette domain of multidrug
resistance protein-like transporters. The MRP
(Multidrug Resistance Protein)-like transporters are
involved in drug, peptide, and lipid export. They
belong to the subfamily C of the ATP-binding cassette
(ABC) superfamily of transport proteins. The ABCC
subfamily contains transporters with a diverse
functional spectrum that includes ion transport, cell
surface receptor, and toxin secretion activities. The
MRP-like family, similar to all ABC proteins, have a
common four-domain core structure constituted by two
membrane-spanning domains, each composed of six
transmembrane (TM) helices, and two nucleotide-binding
domains (NBD). ABC transporters are a subset of
nucleotide hydrolases that contain a signature motif,
Q-loop, and H-loop/switch region, in addition to, the
Walker A motif/P-loop and Walker B motif commonly found
in a number of ATP- and GTP-binding and hydrolyzing
proteins.
Length = 171
Score = 28.9 bits (66), Expect = 2.3
Identities = 10/17 (58%), Positives = 14/17 (82%)
Query: 38 TKVAILGPTASGKSSVA 54
KVAI+GP+ SGKS++
Sbjct: 29 EKVAIVGPSGSGKSTLL 45
>gnl|CDD|233209 TIGR00958, 3a01208, Conjugate Transporter-2 (CT2) Family protein.
[Transport and binding proteins, Other].
Length = 711
Score = 29.3 bits (66), Expect = 2.9
Identities = 10/16 (62%), Positives = 14/16 (87%)
Query: 40 VAILGPTASGKSSVAL 55
VA++GP+ SGKS+VA
Sbjct: 510 VALVGPSGSGKSTVAA 525
>gnl|CDD|213213 cd03246, ABCC_Protease_Secretion, ATP-binding cassette domain of
PrtD, subfamily C. This family represents the ABC
component of the protease secretion system PrtD, a
60-kDa integral membrane protein sharing 37% identity
with HlyB, the ABC component of the alpha-hemolysin
secretion pathway, in the C-terminal domain. They
export degradative enzymes by using a type I protein
secretion system and lack an N-terminal signal peptide,
but contain a C-terminal secretion signal. The Type I
secretion apparatus is made up of three components, an
ABC transporter, a membrane fusion protein (MFP), and
an outer membrane protein (OMP). For the HlyA
transporter complex, HlyB (ABC transporter) and HlyD
(MFP) reside in the inner membrane of E. coli. The OMP
component is TolC, which is thought to interact with
the MFP to form a continuous channel across the
periplasm from the cytoplasm to the exterior. HlyB
belongs to the family of ABC transporters, which are
ubiquitous, ATP-dependent transmembrane pumps or
channels. The spectrum of transport substrates ranges
from inorganic ions, nutrients such as amino acids,
sugars, or peptides, hydrophobic drugs, to large
polypeptides, such as HlyA.
Length = 173
Score = 28.3 bits (64), Expect = 2.9
Identities = 9/15 (60%), Positives = 14/15 (93%)
Query: 40 VAILGPTASGKSSVA 54
+AI+GP+ SGKS++A
Sbjct: 31 LAIIGPSGSGKSTLA 45
>gnl|CDD|223561 COG0486, ThdF, Predicted GTPase [General function prediction only].
Length = 454
Score = 29.1 bits (66), Expect = 3.4
Identities = 15/52 (28%), Positives = 24/52 (46%), Gaps = 5/52 (9%)
Query: 6 DVLDRDTETDPQQ-RQLTADFRRIRT----GKLLFRKTKVAILGPTASGKSS 52
D+ + E ++ +L A+ + GK+L KV I+G GKSS
Sbjct: 181 DIEELVLEKIREKLEELIAELDELLATAKQGKILREGLKVVIIGRPNVGKSS 232
>gnl|CDD|224260 COG1341, COG1341, Predicted GTPase or GTP-binding protein [General
function prediction only].
Length = 398
Score = 28.9 bits (65), Expect = 3.5
Identities = 11/47 (23%), Positives = 25/47 (53%), Gaps = 4/47 (8%)
Query: 36 RKTKVAILGPTASGKSSVALKISEYIPCEIISIDSALVYCDMDIGTN 82
+ V ++GP SGKS+ ++ Y+ ++++ + D D+G +
Sbjct: 72 KVGVVMVVGPVDSGKST----LTTYLANKLLARGRKVAIIDADVGQS 114
>gnl|CDD|234751 PRK00411, cdc6, cell division control protein 6; Reviewed.
Length = 394
Score = 28.7 bits (65), Expect = 3.6
Identities = 17/65 (26%), Positives = 24/65 (36%), Gaps = 15/65 (23%)
Query: 15 DPQQRQLTADFRRIRTGKLLFRKTKVAILGPTASGKSSVALKISE------------YIP 62
+ Q +L R G R V I GP +GK++ K+ E YI
Sbjct: 36 EEQIEELAFALRPALRGS---RPLNVLIYGPPGTGKTTTVKKVFEELEEIAVKVVYVYIN 92
Query: 63 CEIIS 67
C+I
Sbjct: 93 CQIDR 97
>gnl|CDD|181235 PRK08118, PRK08118, topology modulation protein; Reviewed.
Length = 167
Score = 28.0 bits (63), Expect = 3.6
Identities = 9/32 (28%), Positives = 20/32 (62%)
Query: 39 KVAILGPTASGKSSVALKISEYIPCEIISIDS 70
K+ ++G SGKS++A ++ E + + +D+
Sbjct: 3 KIILIGSGGSGKSTLARQLGEKLNIPVHHLDA 34
>gnl|CDD|225138 COG2229, COG2229, Predicted GTPase [General function prediction
only].
Length = 187
Score = 28.2 bits (63), Expect = 3.6
Identities = 11/60 (18%), Positives = 25/60 (41%), Gaps = 7/60 (11%)
Query: 31 GKLLFRKTKVAILGPTASGKSSVALKISEYIPCEIISIDSALVY-------CDMDIGTNK 83
+TK+ ++GP +GK++ +S+ + S++ MD G+ +
Sbjct: 4 AANKMIETKIVVIGPVGAGKTTFVRALSDKPLVITEADASSVSGKGKRPTTVAMDFGSIE 63
>gnl|CDD|129128 TIGR00017, cmk, cytidylate kinase. This family consists of
cytidylate kinase, which catalyzes the phosphorylation
of cytidine 5-monophosphate (dCMP) to cytidine 5
-diphosphate (dCDP) in the presence of ATP or GTP. UMP
and dCMP can also act as acceptors [Purines,
pyrimidines, nucleosides, and nucleotides, Nucleotide
and nucleoside interconversions].
Length = 217
Score = 28.5 bits (64), Expect = 3.8
Identities = 10/24 (41%), Positives = 16/24 (66%)
Query: 36 RKTKVAILGPTASGKSSVALKISE 59
+AI GP+ +GKS+VA ++E
Sbjct: 1 MAMIIAIDGPSGAGKSTVAKAVAE 24
>gnl|CDD|234041 TIGR02868, CydC, thiol reductant ABC exporter, CydC subunit. The
gene pair cydCD encodes an ABC-family transporter in
which each gene contains an N-terminal membrane-spanning
domain (pfam00664) and a C-terminal ATP-binding domain
(pfam00005). In E. coli these genes were discovered as
mutants which caused the terminal heme-copper oxidase
complex cytochrome bd to fail to assemble. Recent work
has shown that the transporter is involved in export of
redox-active thiol compounds such as cysteine and
glutathione. The linkage to assembly of the cytochrome
bd complex is further supported by the conserved operon
structure found outside the gammaproteobacteria
(cydABCD) containing both the transporter and oxidase
genes components. The genes used as the seed members for
this model are all either found in the
gammproteobacterial context or the CydABCD context. All
members of this family scoring above trusted at the time
of its creation were from genomes which encode a
cytochrome bd complex.
Length = 530
Score = 28.9 bits (65), Expect = 3.9
Identities = 10/24 (41%), Positives = 17/24 (70%)
Query: 39 KVAILGPTASGKSSVALKISEYIP 62
+VAILGP+ SGKS++ ++ +
Sbjct: 363 RVAILGPSGSGKSTLLATLAGLLD 386
>gnl|CDD|225713 COG3172, NadR, Predicted ATPase/kinase involved in NAD metabolism
[Coenzyme metabolism].
Length = 187
Score = 28.2 bits (63), Expect = 4.1
Identities = 25/93 (26%), Positives = 41/93 (44%), Gaps = 17/93 (18%)
Query: 35 FRKTKVAILGPTASGKSSVALKIS-------------EYIPCEIISIDSALVYCDMD-IG 80
F KT VAILG +SGKS++ K++ EY+ + D AL Y D I
Sbjct: 7 FVKT-VAILGGESSGKSTLVNKLANIFNTTSAWEYGREYVFEHLGG-DEALQYSDYAKIA 64
Query: 81 TNKPSIIEREITPHHLIDIIEPTKSYSVIQFCE 113
+ + + + + + I+ T + FC+
Sbjct: 65 LGQAAYEDAAVRYANKVAFID-TDFLTTQAFCK 96
>gnl|CDD|233448 TIGR01526, nadR_NMN_Atrans, nicotinamide-nucleotide
adenylyltransferase, NadR type. The NadR protein of E.
coli and closely related bacteria is both enzyme and
regulatory protein. The first 60 or so amino acids,
N-terminal to the region covered by this model, is a
DNA-binding helix-turn-helix domain (pfam01381)
responsible for repressing the nadAB genes of NAD de
novo biosynthesis. The NadR homologs in Mycobacterium
tuberculosis, Haemophilus influenzae, and others appear
to lack the repressor domain. NadR has recently been
shown to act as an enzyme of the salvage pathway of NAD
biosynthesis, nicotinamide-nucleotide
adenylyltransferase; members of this family are presumed
to share this activity. E. coli NadR has also been found
to regulate the import of its substrate, nicotinamide
ribonucleotide, but it is not known if the other members
of this model share that activity.
Length = 325
Score = 28.7 bits (64), Expect = 4.4
Identities = 17/62 (27%), Positives = 27/62 (43%), Gaps = 9/62 (14%)
Query: 2 RDVKDVLDRDTETDPQQ--RQLTADFRRIRTGKLLFRKTKVAILGPTASGKSSVALKISE 59
R V +P Q + + + R F KT VAILG ++GKS++ K++
Sbjct: 132 RTFFSVSATQIRENPFQHWKHIPREVRP------FFVKT-VAILGGESTGKSTLVNKLAA 184
Query: 60 YI 61
Sbjct: 185 VF 186
>gnl|CDD|213263 cd03296, ABC_CysA_sulfate_importer, ATP-binding cassette domain
of the sulfate transporter. Part of the ABC
transporter complex cysAWTP involved in sulfate import.
Responsible for energy coupling to the transport
system. The complex is composed of two ATP-binding
proteins (cysA), two transmembrane proteins (cysT and
cysW), and a solute-binding protein (cysP). ABC
transporters are a large family of proteins involved in
the transport of a wide variety of different compounds,
like sugars, ions, peptides, and more complex organic
molecules. The nucleotide binding domain shows the
highest similarity between all members of the family.
ABC transporters are a subset of nucleotide hydrolases
that contain a signature motif, Q-loop, and
H-loop/switch region, in addition to, the Walker A
motif/P-loop and Walker B motif commonly found in a
number of ATP- and GTP-binding and hydrolyzing
proteins.
Length = 239
Score = 28.1 bits (63), Expect = 4.8
Identities = 11/26 (42%), Positives = 18/26 (69%), Gaps = 6/26 (23%)
Query: 28 IRTGKLLFRKTKVAILGPTASGKSSV 53
I +G+L VA+LGP+ SGK+++
Sbjct: 25 IPSGEL------VALLGPSGSGKTTL 44
>gnl|CDD|213214 cd03247, ABCC_cytochrome_bd, ATP-binding cassette domain of
CydCD, subfamily C. The CYD subfamily implicated in
cytochrome bd biogenesis. The CydC and CydD proteins
are important for the formation of cytochrome bd
terminal oxidase of E. coli and it has been proposed
that they were necessary for biosynthesis of the
cytochrome bd quinol oxidase and for periplasmic c-type
cytochromes. CydCD were proposed to determine a
heterooligomeric complex important for heme export into
the periplasm or to be involved in the maintenance of
the proper redox state of the periplasmic space. In
Bacillus subtilis, the absence of CydCD does not affect
the presence of halo-cytochrome c in the membrane and
this observation suggests that CydCD proteins are not
involved in the export of heme in this organism.
Length = 178
Score = 27.7 bits (62), Expect = 5.0
Identities = 8/19 (42%), Positives = 14/19 (73%)
Query: 36 RKTKVAILGPTASGKSSVA 54
+ K+A+LG + SGKS++
Sbjct: 27 QGEKIALLGRSGSGKSTLL 45
>gnl|CDD|234189 TIGR03375, type_I_sec_LssB, type I secretion system ATPase, LssB
family. Type I protein secretion is a system in some
Gram-negative bacteria to export proteins (often
proteases) across both inner and outer membranes to the
extracellular medium. This is one of three proteins of
the type I secretion apparatus. Targeted proteins are
not cleaved at the N-terminus, but rather carry signals
located toward the extreme C-terminus to direct type I
secretion. This model is related to models TIGR01842 and
TIGR01846, and to bacteriocin ABC transporters that
cleave their substrates during export [Protein fate,
Protein and peptide secretion and trafficking, Cellular
processes, Pathogenesis].
Length = 694
Score = 28.7 bits (65), Expect = 5.1
Identities = 19/55 (34%), Positives = 28/55 (50%), Gaps = 8/55 (14%)
Query: 39 KVAILGPTASGKSSVA-LKISEYIPCE-IISIDSALVYCDMDIGTNKPSIIEREI 91
KVAI+G SGKS++ L + Y P E + +D +DI P+ + R I
Sbjct: 493 KVAIIGRIGSGKSTLLKLLLGLYQPTEGSVLLD------GVDIRQIDPADLRRNI 541
>gnl|CDD|213211 cd03244, ABCC_MRP_domain2, ATP-binding cassette domain 2 of
multidrug resistance-associated protein. The ABC
subfamily C is also known as MRP (multidrug
resistance-associated protein). Some of the MRP members
have five additional transmembrane segments in their
N-terminus, but the function of these additional
membrane-spanning domains is not clear. The MRP was
found in the multidrug-resistance lung cancer cell in
which p-glycoprotein was not overexpressed. MRP exports
glutathione by drug stimulation, as well as, certain
substrates in conjugated forms with anions, such as
glutathione, glucuronate, and sulfate.
Length = 221
Score = 27.8 bits (63), Expect = 5.1
Identities = 11/17 (64%), Positives = 13/17 (76%)
Query: 39 KVAILGPTASGKSSVAL 55
KV I+G T SGKSS+ L
Sbjct: 32 KVGIVGRTGSGKSSLLL 48
>gnl|CDD|236546 PRK09518, PRK09518, bifunctional cytidylate kinase/GTPase Der;
Reviewed.
Length = 712
Score = 28.6 bits (64), Expect = 5.1
Identities = 11/21 (52%), Positives = 15/21 (71%)
Query: 40 VAILGPTASGKSSVALKISEY 60
VAI GP GKSSV+ +++Y
Sbjct: 4 VAIDGPAGVGKSSVSRALAQY 24
>gnl|CDD|222036 pfam13304, AAA_21, AAA domain.
Length = 256
Score = 28.2 bits (62), Expect = 5.5
Identities = 29/188 (15%), Positives = 56/188 (29%), Gaps = 8/188 (4%)
Query: 41 AILGPTASGKSSV-------ALKISEYIPCEIISIDSALVYCDMDIGTNKPSIIEREITP 93
I+GP SGKS++ L +S + + + + +E EI
Sbjct: 3 VIIGPNGSGKSNLLKALALLLLLLSLGLTLDRGLNVGIKLLPFLLDENEIEIPLEFEIEE 62
Query: 94 HHLIDII-EPTKSYSVIQFCEDALFSIKNILKKKKLPLLVGGTMLYFKALRDGINKLPPA 152
+ I E+ L+ + + + + + L
Sbjct: 63 FLIDGIRYRYGFELDKEDILEELLYEYRKGEELLFERERSKESFEKSPEKKRELRGLREV 122
Query: 153 NLKLRTKFNIDINKYGISFLYDKLKLLDPVTANQPSNRHILHKRISDRFKKMLDQDLLIN 212
L L + + + L L + N + R+I K + + L+ DLL
Sbjct: 123 LLLLNLSLSSFLLLASLEILLSILLPFSFILGNLRNLRNIELKLLDLVKRLFLESDLLRL 182
Query: 213 EVKKIRKK 220
I+
Sbjct: 183 LKLLIKGI 190
>gnl|CDD|224027 COG1102, Cmk, Cytidylate kinase [Nucleotide transport and
metabolism].
Length = 179
Score = 27.7 bits (62), Expect = 5.7
Identities = 9/29 (31%), Positives = 20/29 (68%)
Query: 39 KVAILGPTASGKSSVALKISEYIPCEIIS 67
+ I G SGK++VA +++E++ +++S
Sbjct: 2 VITISGLPGSGKTTVARELAEHLGLKLVS 30
>gnl|CDD|163542 TIGR03830, CxxCG_CxxCG_HTH, putative zinc finger/helix-turn-helix
protein, YgiT family. This model describes a family of
predicted regulatory proteins with a conserved zinc
finger/HTH architecture. The amino-terminal region
contains a novel domain, featuring two CXXC motifs and
occuring in a number of small bacterial proteins as well
as in the present family. The carboxyl-terminal region
consists of a helix-turn-helix domain, modeled by
pfam01381. The predicted function is DNA binding and
transcriptional regulation.
Length = 127
Score = 27.2 bits (61), Expect = 5.8
Identities = 10/32 (31%), Positives = 18/32 (56%), Gaps = 1/32 (3%)
Query: 193 LHKRISDRFKKMLDQDLLINEVKKIRKKWNLN 224
++D F + +D L E+++IRKK L+
Sbjct: 50 NSAALAD-FYRKVDGLLTPPEIRRIRKKLGLS 80
>gnl|CDD|213269 cd03369, ABCC_NFT1, ATP-binding cassette domain 2 of NFT1,
subfamily C. Domain 2 of NFT1 (New full-length
MRP-type transporter 1). NFT1 belongs to the MRP
(multidrug resistance-associated protein) family of ABC
transporters. Some of the MRP members have five
additional transmembrane segments in their N-terminus,
but the function of these additional membrane-spanning
domains is not clear. The MRP was found in the
multidrug-resisting lung cancer cell in which
p-glycoprotein was not overexpressed. MRP exports
glutathione by drug stimulation, as well as, certain
substrates in conjugated forms with anions such as
glutathione, glucuronate, and sulfate.
Length = 207
Score = 27.8 bits (62), Expect = 6.3
Identities = 15/48 (31%), Positives = 24/48 (50%), Gaps = 8/48 (16%)
Query: 36 RKTKVAILGPTASGKSSVALKISEYIPCE--IISIDSALVYCDMDIGT 81
K+ I+G T +GKS++ L + ++ E I ID +DI T
Sbjct: 33 AGEKIGIVGRTGAGKSTLILALFRFLEAEEGKIEID------GIDIST 74
>gnl|CDD|224116 COG1195, RecF, Recombinational DNA repair ATPase (RecF pathway)
[DNA replication, recombination, and repair].
Length = 363
Score = 28.0 bits (63), Expect = 6.6
Identities = 6/30 (20%), Positives = 12/30 (40%)
Query: 24 DFRRIRTGKLLFRKTKVAILGPTASGKSSV 53
+FR L ++G GK+++
Sbjct: 10 NFRNYAELDLDLSPGVNVLVGENGQGKTNL 39
>gnl|CDD|184214 PRK13657, PRK13657, cyclic beta-1,2-glucan ABC transporter;
Provisional.
Length = 588
Score = 28.0 bits (63), Expect = 6.9
Identities = 17/44 (38%), Positives = 22/44 (50%), Gaps = 8/44 (18%)
Query: 40 VAILGPTASGKSS-VALKISEYIPCE-IISIDSALVYCDMDIGT 81
VAI+GPT +GKS+ + L + P I ID DI T
Sbjct: 364 VAIVGPTGAGKSTLINLLQRVFDPQSGRILIDG------TDIRT 401
>gnl|CDD|213221 cd03254, ABCC_Glucan_exporter_like, ATP-binding cassette domain
of glucan transporter and related proteins, subfamily
C. Glucan exporter ATP-binding protein. In A.
tumefaciens cyclic beta-1, 2-glucan must be transported
into the periplasmic space to exert its action as a
virulence factor. This subfamily belongs to the
MRP-like family and is involved in drug, peptide, and
lipid export. The MRP-like family, similar to all ABC
proteins, have a common four-domain core structure
constituted by two membrane-spanning domains each
composed of six transmembrane (TM) helices and two
nucleotide-binding domains (NBD). ABC transporters are
a subset of nucleotide hydrolases that contain a
signature motif, Q-loop, and H-loop/switch region, in
addition to, the Walker A motif/P-loop and Walker B
motif commonly found in a number of ATP- and
GTP-binding and hydrolyzing proteins.
Length = 229
Score = 27.6 bits (62), Expect = 6.9
Identities = 8/16 (50%), Positives = 13/16 (81%)
Query: 39 KVAILGPTASGKSSVA 54
VAI+GPT +GK+++
Sbjct: 31 TVAIVGPTGAGKTTLI 46
>gnl|CDD|172200 PRK13652, cbiO, cobalt transporter ATP-binding subunit;
Provisional.
Length = 277
Score = 27.8 bits (62), Expect = 7.0
Identities = 7/18 (38%), Positives = 15/18 (83%)
Query: 36 RKTKVAILGPTASGKSSV 53
R +++A++GP +GKS++
Sbjct: 29 RNSRIAVIGPNGAGKSTL 46
>gnl|CDD|222307 pfam13671, AAA_33, AAA domain. This family of domains contain
only a P-loop motif, that is characteristic of the AAA
superfamily. Many of the proteins in this family are
just short fragments so there is no Walker B motif.
Length = 143
Score = 26.9 bits (60), Expect = 7.5
Identities = 8/26 (30%), Positives = 14/26 (53%)
Query: 44 GPTASGKSSVALKISEYIPCEIISID 69
G SGKS+ A ++ + ++S D
Sbjct: 6 GLPGSGKSTFARRLLRELGAVVLSSD 31
>gnl|CDD|225364 COG2805, PilT, Tfp pilus assembly protein, pilus retraction ATPase
PilT [Cell motility and secretion / Intracellular
trafficking and secretion].
Length = 353
Score = 27.6 bits (62), Expect = 7.7
Identities = 17/60 (28%), Positives = 31/60 (51%), Gaps = 9/60 (15%)
Query: 40 VAILGPTASGKSSVALKISEYI----PCEIISIDSALVYCDMDIGTNKPSII-EREITPH 94
+ + GPT SGKS+ + +YI I++I+ + Y + +K S+I +RE+
Sbjct: 128 ILVTGPTGSGKSTTLAAMIDYINKHKAKHILTIEDPIEY----VHESKKSLINQREVGRD 183
>gnl|CDD|224533 COG1618, COG1618, Predicted nucleotide kinase [Nucleotide
transport and metabolism].
Length = 179
Score = 27.3 bits (61), Expect = 7.9
Identities = 9/23 (39%), Positives = 15/23 (65%)
Query: 39 KVAILGPTASGKSSVALKISEYI 61
K+ I G GK+++ LKI+E +
Sbjct: 7 KIFITGRPGVGKTTLVLKIAEKL 29
>gnl|CDD|213220 cd03253, ABCC_ATM1_transporter, ATP-binding cassette domain of
iron-sulfur clusters transporter, subfamily C. ATM1 is
an ABC transporter that is expressed in the
mitochondria. Although the specific function of ATM1 is
unknown, its disruption results in the accumulation of
excess mitochondrial iron, loss of mitochondrial
cytochromes, oxidative damage to mitochondrial DNA, and
decreased levels of cytosolic heme proteins. ABC
transporters are a large family of proteins involved in
the transport of a wide variety of different compounds,
like sugars, ions, peptides, and more complex organic
molecules. The nucleotide binding domain shows the
highest similarity between all members of the family.
ABC transporters are a subset of nucleotide hydrolases
that contain a signature motif, Q-loop, and
H-loop/switch region, in addition to, the Walker A
motif/P-loop and Walker B motif commonly found in a
number of ATP- and GTP-binding and hydrolyzing
proteins.
Length = 236
Score = 27.6 bits (62), Expect = 8.0
Identities = 10/16 (62%), Positives = 14/16 (87%)
Query: 39 KVAILGPTASGKSSVA 54
KVAI+GP+ SGKS++
Sbjct: 29 KVAIVGPSGSGKSTIL 44
>gnl|CDD|163508 TIGR03796, NHLM_micro_ABC1, NHLM bacteriocin system ABC
transporter, peptidase/ATP-binding protein. This
protein describes a multidomain ABC transporter subunit
that is one of three protein families associated with
some regularity with a distinctive family of putative
bacteriocins. It includes a bacteriocin-processing
peptidase domain at the N-terminus. Model TIGR03793
describes a conserved propeptide region for this
bacteriocin family, unusual because it shows obvious
homology a region of the enzyme nitrile hydratase up to
the classic Gly-Gly cleavage motif. This family is
therefore predicted to be a subunit of a bacteriocin
processing and export system characteristic to this
system that we designate NHLM, Nitrile Hydratase Leader
Microcin [Transport and binding proteins, Amino acids,
peptides and amines, Cellular processes, Biosynthesis of
natural products].
Length = 710
Score = 28.0 bits (63), Expect = 8.1
Identities = 21/82 (25%), Positives = 38/82 (46%), Gaps = 26/82 (31%)
Query: 16 PQQRQLTADFR-RIRTGKLLFRKTKVAILGPTASGKSSVALKIS---------------- 58
P + L +F ++ G+ +VA++G + SGKS++A ++
Sbjct: 489 PLEPPLIENFSLTLQPGQ------RVALVGGSGSGKSTIAKLVAGLYQPWSGEILFDGIP 542
Query: 59 -EYIPCEIISIDSALVYCDMDI 79
E IP E+++ A+V D DI
Sbjct: 543 REEIPREVLANSVAMV--DQDI 562
>gnl|CDD|213212 cd03245, ABCC_bacteriocin_exporters, ATP-binding cassette domain
of bacteriocin exporters, subfamily C. Many
non-lantibiotic bacteriocins of lactic acid bacteria
are produced as precursors which have N-terminal leader
peptides that share similarities in amino acid sequence
and contain a conserved processing site of two glycine
residues in positions -1 and -2. A dedicated
ATP-binding cassette (ABC) transporter is responsible
for the proteolytic cleavage of the leader peptides and
subsequent translocation of the bacteriocins across the
cytoplasmic membrane.
Length = 220
Score = 27.2 bits (61), Expect = 8.6
Identities = 18/55 (32%), Positives = 25/55 (45%), Gaps = 8/55 (14%)
Query: 39 KVAILGPTASGKSSVA-LKISEYIPCE-IISIDSALVYCDMDIGTNKPSIIEREI 91
KVAI+G SGKS++ L Y P + +D DI P+ + R I
Sbjct: 32 KVAIIGRVGSGKSTLLKLLAGLYKPTSGSVLLD------GTDIRQLDPADLRRNI 80
>gnl|CDD|238979 cd02021, GntK, Gluconate kinase (GntK) catalyzes the phosphoryl
transfer from ATP to gluconate. The resulting product
gluconate-6-phoshate is an important precursor of
gluconate metabolism. GntK acts as a dimmer composed of
two identical subunits.
Length = 150
Score = 26.8 bits (60), Expect = 8.8
Identities = 8/27 (29%), Positives = 16/27 (59%)
Query: 40 VAILGPTASGKSSVALKISEYIPCEII 66
+ ++G + SGKS+V ++E + I
Sbjct: 2 IVVMGVSGSGKSTVGKALAERLGAPFI 28
>gnl|CDD|233406 TIGR01420, pilT_fam, pilus retraction protein PilT. This model
represents the PilT subfamily of proteins related to
GspE, a protein involved in type II secretion (also
called the General Secretion Pathway). PilT is an
apparent cytosolic ATPase associated with type IV pilus
systems. It is not required for pilin biogenesis, but is
required for twitching motility and social gliding
behaviors, shown in some species, powered by pilus
retraction. Members of this family may be found in some
species that type IV pili but have related structures
for DNA uptake and natural transformation [Cell
envelope, Surface structures, Cellular processes,
Chemotaxis and motility].
Length = 343
Score = 27.3 bits (61), Expect = 9.7
Identities = 19/57 (33%), Positives = 31/57 (54%), Gaps = 9/57 (15%)
Query: 40 VAILGPTASGKSSVALKISEYI----PCEIISIDSALVYCDMDIGTNKPSII-EREI 91
+ + GPT SGKS+ + +YI II+I+ + Y + NK S+I +RE+
Sbjct: 125 ILVTGPTGSGKSTTLASMIDYINKNKAYHIITIEDPIEY----VHKNKRSLINQREV 177
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
0.322 0.139 0.404
Gapped
Lambda K H
0.267 0.0534 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 15,453,092
Number of extensions: 1519374
Number of successful extensions: 1962
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1951
Number of HSP's successfully gapped: 125
Length of query: 298
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 202
Effective length of database: 6,679,618
Effective search space: 1349282836
Effective search space used: 1349282836
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: 59 (27.0 bits)