RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254781225|ref|YP_003065638.1| P4 family phage/plasmid
primase [Candidatus Liberibacter asiaticus str. psy62]
(789 letters)
>gnl|CDD|33185 COG3378, COG3378, Predicted ATPase [General function prediction
only].
Length = 517
Score = 128 bits (322), Expect = 7e-30
Identities = 111/472 (23%), Positives = 179/472 (37%), Gaps = 44/472 (9%)
Query: 302 LLASRFSDAYNKAMFSIYKKGHFLYTADTKAWYKKDKNNVYIWSLTLDKITASIMNFLVS 361
+ A R +D Y + ++ +G + D + W K D L + +I
Sbjct: 42 INAVRLADRYTDKLRAVSAQGTWHV-WDGRRWAKDDA-------LLFLPLDVAIRGLKRQ 93
Query: 362 MKEDVFDLSEEPEDNNKNSKSPRFWFNTDYRRQNVEENSKAKSTAQSLEAGSIFSITSDL 421
D +K Y E + A + T
Sbjct: 94 AAIKADHDRGLKADPDKLEAPLSTAGVRSYFPNPTEV--------KEALALVKKAATPKQ 145
Query: 422 LDSSSRFLGEQDGILDLETGQKVKPTKELYITKSTGTPFVEGEP-------SQEFLDLVS 474
D + +G+LDL TGQ E T+ + + +E+LD V+
Sbjct: 146 QDPDPHLINFANGVLDLRTGQLEPHDPEDRFTRIIPVDYTDPAADPSHCPKWREWLDRVA 205
Query: 475 GYFESEEVMDYFTRCVGMALLGGNKAQRFIHIRGVGGSGKSTLMNLIKYAFGNQYVINAE 534
G E+ + R +G +L G Q+ + G GG+GKST ++LI G V +A
Sbjct: 206 G--GDPELRNLLQRIIGASLTGRVSEQKLFWLYGPGGNGKSTFVDLISNLLGRYNVTSAP 263
Query: 535 ASDIMQNRPPEAGKANPS-LIRLMGSRIVIISETNENDEINAAKIKQMTGGDCMTARLNY 593
+D+ EA +P L L+G R+V +SET + + K+K +TGGD ++A
Sbjct: 264 LTDL------EADDRHPFGLAALVGKRLVTVSETEKGRLDDEGKLKALTGGDVISAERKR 317
Query: 594 GNTYSESPASFTPFIVPNKHLFVRNPDDAWWRRYIVIPFDKPIANRDASFAQKLETKYTL 653
+ +S +P + N +R D+A WRR +++PF+K + KL+ K
Sbjct: 318 KDFFSFTP-NAKLIQATNHPPRIRGDDEAIWRRLLIVPFEKQFPPAERDD--KLDEKLAA 374
Query: 654 EAK---KWFLKGVKAYISKGLDVDIPEVCLKAKEEERQGTDTYQAWIDDCCDIGENLWEE 710
E W + G +GL D P+ L A EE ++ D + DD C +GE
Sbjct: 375 ERPGILNWLVAGFLDLQREGL--DQPQAVLDALEEYKRENDPVFQFCDDECVLGETDGTP 432
Query: 711 SHSLAKS---YSEYREQELNYDRKRISTRTVTLNLK-QKGFIGGIKREKIEK 758
+ Y Y+E ++T KG G KR + E
Sbjct: 433 TAFDNIVLELYEAYQEWCEANGYVVELSKTRFGKELPTKGVPKGRKRHQGET 484
>gnl|CDD|80309 cd04859, Prim_Pol, Prim_Pol: Primase-polymerase (primpol) domain of
the type found in bifunctional replicases from archaeal
plasmids, including ORF904 protein of the crenarchaeal
plasmid pRN1 from Sulfolobus islandicus (pRN1 primpol).
These primpol domains belong to the archaeal/eukaryal
primase (AEP) superfamily. This group includes archaeal
plasmids and bacteriophage AEPs. The ORF904 protein is a
multifunctional protein having ATPase, primase and DNA
polymerase activity, and may play a role in the
replication of the archaeal plasmid. The pRN1 primpol
domain exhibits DNA polymerase and primase activities; a
cluster of active site residues (three acidic residues,
and a histidine) is required for both these activities.
For pRN1 primpol, the primase activity prefers dNTPs to
rNTPs; incorporation of dNTPs requires rNTP as cofactor.
The pRN1 primpol contains an unusual zinc-binding stem,
which is not conserved in other members of this group..
Length = 152
Score = 58.9 bits (142), Expect = 5e-09
Identities = 36/144 (25%), Positives = 51/144 (35%), Gaps = 11/144 (7%)
Query: 18 FKLIPLRLGDKRP-QRLGKWEEQLLSSEKIDKL----PACGFGFVCGVGEQPLYAFDIDS 72
F +IPL G KRP + + E+I+ P G G L DID
Sbjct: 1 FAVIPLDPGSKRPLIKGWPKDAATTDPEQIEAWWRDGPDANIGLRTGPSG--LVVIDIDV 58
Query: 73 KDEKTANTFK--DTFEILHGTPIVRIGQKPKILIPFRMNKEGIKKKKTTESTQGHLDILG 130
K + A + ++ T VR G + FR+ +G+ K +DI G
Sbjct: 59 KHDGAAALAALAELGKLPPLTLTVRTG-SGGRHLYFRVP-DGVPVKSVKGKGGPGIDIRG 116
Query: 131 CGQYFVAYNIHPKTKKEYTWTTPP 154
G Y VA Y W +
Sbjct: 117 GGGYVVAPPSVHPGGGYYVWKSTV 140
>gnl|CDD|29996 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 = 34.1 bits (78), Expect = 0.14
Identities = 16/51 (31%), Positives = 24/51 (47%), Gaps = 8/51 (15%)
Query: 471 DLVSGYFESEEVMDYFTRCVGMALLGGNKAQRFIHIRGVGGSGKSTLMNLI 521
DL++ S Y V +A++ I I G GSGK+TL+N +
Sbjct: 3 DLIAQGTFSPLQAAYLWLAV--------EARKNILISGGTGSGKTTLLNAL 45
>gnl|CDD|31331 COG1136, SalX, ABC-type antimicrobial peptide transport system,
ATPase component [Defense mechanisms].
Length = 226
Score = 33.6 bits (77), Expect = 0.24
Identities = 12/19 (63%), Positives = 15/19 (78%)
Query: 503 FIHIRGVGGSGKSTLMNLI 521
F+ I G GSGKSTL+NL+
Sbjct: 33 FVAIVGPSGSGKSTLLNLL 51
>gnl|CDD|73014 cd03255, ABC_MJ0796_Lo1CDE_FtsE, This family is comprised of MJ0796
ATP-binding cassette, macrolide-specific ABC-type efflux
carrier (MacAB), and proteins involved in cell division
(FtsE), and release of liporoteins from the cytoplasmic
membrane (LolCDE). They are clustered together
phylogenetically. MacAB is an exporter that confers
resistance to macrolides, while the LolCDE system is not
a transporter at all. An FtsE null mutants showed
filamentous growth and appeared viable on high salt
medium only, indicating a role for FtsE in cell division
and/or salt transport. The LolCDE complex catalyses the
release of lipoproteins from the cytoplasmic membrane
prior to their targeting to the outer membrane..
Length = 218
Score = 33.2 bits (76), Expect = 0.28
Identities = 11/19 (57%), Positives = 15/19 (78%)
Query: 503 FIHIRGVGGSGKSTLMNLI 521
F+ I G GSGKSTL+N++
Sbjct: 32 FVAIVGPSGSGKSTLLNIL 50
>gnl|CDD|30527 COG0178, UvrA, Excinuclease ATPase subunit [DNA replication,
recombination, and repair].
Length = 935
Score = 32.8 bits (75), Expect = 0.40
Identities = 11/24 (45%), Positives = 13/24 (54%)
Query: 501 QRFIHIRGVGGSGKSTLMNLIKYA 524
F + GV GSGKSTL+N
Sbjct: 627 GVFTCVTGVSGSGKSTLINDTLVP 650
>gnl|CDD|30768 COG0419, SbcC, ATPase involved in DNA repair [DNA replication,
recombination, and repair].
Length = 908
Score = 31.9 bits (72), Expect = 0.65
Identities = 44/282 (15%), Positives = 93/282 (32%), Gaps = 40/282 (14%)
Query: 506 IRGVGGSGKSTLMNLIKYA-FGNQYVINAEASDIMQNRPPEAGKANPSLIRLMGSRIVII 564
I G G+GKS++++ I +A +G + A + D + ++ + G + I
Sbjct: 30 IVGPNGAGKSSILDAITFALYGKTPRLGAFSLDDLIRAGEKSASVE-LEFEVNGKKYRIE 88
Query: 565 SETNENDEINAAKIKQMTGGDCMTARLNYGNTYSESPASFTPFIVPNKHLFVRNPDDAWW 624
E + ++ + G ++ I L D +
Sbjct: 89 REFRRGRGQSTGSLQIIEVD---------GERIADGKKDVNEKIEELLGL-----DKDTF 134
Query: 625 RRYIVIP---FDKPI----ANRDASFAQKLETKYTLEAKKWFLKGVKAYISKGLDV---- 673
R + +P FD + R + + E LK V ++
Sbjct: 135 TRSVYLPQGEFDAFLKSKPKERKEILDELFGLEK-YEKLSELLKEVIKEAKAKIEELEGQ 193
Query: 674 -----DIPEVCLKAKEEERQGTDTYQAWIDDCCDIGENLWEESHSLAKSYSEYREQELNY 728
+ E L+A EEE + + ++ E L +E +L + +E E++
Sbjct: 194 LSELLEDIEDLLEALEEELKELKKLEEIQEE--QEEEELEQEIEALEERLAELEEEKERL 251
Query: 729 DRKRISTRTVTLNLKQKGF-----IGGIKREKIEKEWKSKRI 765
+ + + + + ++R E E K +R+
Sbjct: 252 EELKARLLEIESLELEALKIREEELRELERLLEELEEKIERL 293
>gnl|CDD|73297 cd02034, CooC, The accessory protein CooC, which contains a
nucleotide-binding domain (P-loop) near the N-terminus,
participates in the maturation of the nickel center of
carbon monoxide dehydrogenase (CODH). CODH from
Rhodospirillum rubrum catalyzes the reversible oxidation
of CO to CO2. CODH contains a nickel-iron-sulfur cluster
(C-center) and an iron-sulfur cluster (B-center). CO
oxidation occurs at the C-center. Three accessory
proteins encoded by cooCTJ genes are involved in nickel
incorporation into a nickel site. CooC functions as a
nickel insertase that mobilizes nickel to apoCODH using
energy released from ATP hydrolysis. CooC is a homodimer
and has NTPase activities. Mutation at the P-loop
abolishs its function..
Length = 116
Score = 31.3 bits (71), Expect = 1.1
Identities = 14/58 (24%), Positives = 23/58 (39%), Gaps = 8/58 (13%)
Query: 504 IHIRGVGGSGKSTLMNLIKYAFGNQ----YVINAEASDIMQNRPPEAGKANPSLIRLM 557
I I G GG GK+T+ L+ + I+A+ D+ P + L+
Sbjct: 2 IAITGKGGVGKTTIAALLARYLAEKGKPVLAIDADPDDL----PERLSVEVGEIKLLL 55
>gnl|CDD|73030 cd03271, ABC_UvrA_II, The excision repair protein UvrA domain II;
Nucleotide excision repair in eubacteria is a process
that repairs DNA damage by the removal of a 12-13-mer
oligonucleotide containing the lesion. Recognition and
cleavage of the damaged DNA is a multistep ATP-dependent
reaction that requires the UvrA, UvrB, and UvrC
proteins. Both UvrA and UvrB are ATPases, with UvrA
having two ATP binding sites, which have the
characteristic signature of the family of ABC proteins
and UvrB having one ATP binding site that is
structurally related to that of helicases..
Length = 261
Score = 31.3 bits (71), Expect = 1.2
Identities = 10/23 (43%), Positives = 13/23 (56%)
Query: 502 RFIHIRGVGGSGKSTLMNLIKYA 524
+ GV GSGKS+L+N Y
Sbjct: 22 VLTCVTGVSGSGKSSLINDTLYP 44
>gnl|CDD|72973 cd03214, ABC_Iron-Siderophores_B12_Hemin, ABC transporters,
involved in the uptake of siderophores, heme, and
vitamin B12, are widely conserved in bacteria and
archaea. Only very few species lack representatives of
the siderophore family transporters. The E. coli BtuCD
protein is an ABC transporter mediating vitamin B12
uptake. The two ATP-binding cassettes (BtuD) are in
close contact with each other, as are the two
membrane-spanning subunits (BtuC); this arrangement is
distinct from that observed for the E. coli lipid
flippase MsbA. The BtuC subunits provide 20
transmembrane helices grouped around a translocation
pathway that is closed to the cytoplasm by a gate
region, whereas the dimer arrangement of the BtuD
subunits resembles the ATP-bound form of the Rad50 DNA
repair enzyme. A prominent cytoplasmic loop of BtuC
forms the contact region with the ATP-binding cassette
and represent a conserved motif among the ABC
transporters..
Length = 180
Score = 31.2 bits (71), Expect = 1.2
Identities = 9/23 (39%), Positives = 14/23 (60%)
Query: 499 KAQRFIHIRGVGGSGKSTLMNLI 521
+A + I G G+GKSTL+ +
Sbjct: 23 EAGEIVGILGPNGAGKSTLLKTL 45
>gnl|CDD|31297 COG1100, COG1100, GTPase SAR1 and related small G proteins [General
function prediction only].
Length = 219
Score = 30.7 bits (68), Expect = 1.7
Identities = 15/52 (28%), Positives = 19/52 (36%), Gaps = 1/52 (1%)
Query: 508 GVGGSGKSTLMN-LIKYAFGNQYVINAEASDIMQNRPPEAGKANPSLIRLMG 558
G GG GK+TL+N L+ F Y D + P L G
Sbjct: 12 GDGGVGKTTLLNRLVGDEFPEGYPPTIGNLDPAKTIEPYRRNIKLQLWDTAG 63
>gnl|CDD|33632 COG3840, ThiQ, ABC-type thiamine transport system, ATPase component
[Coenzyme metabolism].
Length = 231
Score = 30.7 bits (69), Expect = 1.7
Identities = 12/22 (54%), Positives = 15/22 (68%)
Query: 500 AQRFIHIRGVGGSGKSTLMNLI 521
A + I G G+GKSTL+NLI
Sbjct: 24 AGEIVAILGPSGAGKSTLLNLI 45
>gnl|CDD|30190 cd01672, TMPK, Thymidine monophosphate kinase (TMPK), also known as
thymidylate kinase, catalyzes the phosphorylation of
thymidine monophosphate (TMP) to thymidine diphosphate
(TDP) utilizing ATP as its preferred phophoryl donor.
TMPK represents the rate-limiting step in either de novo
or salvage biosynthesis of thymidine triphosphate
(TTP)..
Length = 200
Score = 30.6 bits (69), Expect = 1.9
Identities = 9/21 (42%), Positives = 14/21 (66%)
Query: 502 RFIHIRGVGGSGKSTLMNLIK 522
FI G+ G+GK+TL+ L+
Sbjct: 1 MFIVFEGIDGAGKTTLIELLA 21
>gnl|CDD|110446 pfam01443, Viral_helicase1, Viral (Superfamily 1) RNA helicase.
Helicase activity for this family has been demonstrated
and NTPase activity. This helicase has multiple roles at
different stages of viral RNA replication, as dissected
by mutational analysis.
Length = 226
Score = 30.0 bits (68), Expect = 2.3
Identities = 9/14 (64%), Positives = 10/14 (71%)
Query: 504 IHIRGVGGSGKSTL 517
I + GV G GKSTL
Sbjct: 1 IVVHGVPGCGKSTL 14
>gnl|CDD|35284 KOG0061, KOG0061, KOG0061, Transporter, ABC superfamily (Breast
cancer resistance protein) [Secondary metabolites
biosynthesis, transport and catabolism].
Length = 613
Score = 30.3 bits (68), Expect = 2.3
Identities = 14/57 (24%), Positives = 25/57 (43%), Gaps = 21/57 (36%)
Query: 465 PSQEFLDLVSGYFESEEVMDYFTRCVGMALLGGNKAQRFIHIRGVGGSGKSTLMNLI 521
++ L VSG + E++ A++G + GSGK+TL+N +
Sbjct: 41 KTKTILKGVSGTAKPGELL---------AIMGPS------------GSGKTTLLNAL 76
>gnl|CDD|30474 COG0125, Tmk, Thymidylate kinase [Nucleotide transport and
metabolism].
Length = 208
Score = 30.2 bits (68), Expect = 2.4
Identities = 10/21 (47%), Positives = 14/21 (66%)
Query: 502 RFIHIRGVGGSGKSTLMNLIK 522
FI I G+ G+GK+T L+K
Sbjct: 4 MFIVIEGIDGAGKTTQAELLK 24
>gnl|CDD|72971 cd00267, ABC_ATPase, ABC (ATP-binding cassette) transporter
nucleotide-binding domain; ABC transporters are a large
family of proteins involved in the transport of a wide
variety of different compounds, like sugars, ions,
peptides, and more complex organic molecules. The
nucleotide-binding domain shows the highest similarity
between all members of the family. ABC transporters are
a subset of nucleotide hydrolases that contain a
signature motif, Q-loop, and H-loop/switch region, in
addition to, the Walker A motif/P-loop and Walker B
motif commonly found in a number of ATP- and GTP-binding
and hydrolyzing proteins..
Length = 157
Score = 29.9 bits (67), Expect = 2.7
Identities = 11/23 (47%), Positives = 14/23 (60%)
Query: 499 KAQRFIHIRGVGGSGKSTLMNLI 521
KA + + G GSGKSTL+ I
Sbjct: 23 KAGEIVALVGPNGSGKSTLLRAI 45
>gnl|CDD|32455 COG2274, SunT, ABC-type bacteriocin/lantibiotic exporters, contain
an N-terminal double-glycine peptidase domain [Defense
mechanisms].
Length = 709
Score = 29.8 bits (67), Expect = 3.1
Identities = 10/23 (43%), Positives = 13/23 (56%)
Query: 499 KAQRFIHIRGVGGSGKSTLMNLI 521
+ I G GSGKSTL+ L+
Sbjct: 497 PPGEKVAIVGRSGSGKSTLLKLL 519
>gnl|CDD|72987 cd03228, ABCC_MRP_Like, The MRP (Mutidrug 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, simlar 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 = 29.6 bits (67), Expect = 3.5
Identities = 11/23 (47%), Positives = 14/23 (60%)
Query: 499 KAQRFIHIRGVGGSGKSTLMNLI 521
K + I G GSGKSTL+ L+
Sbjct: 26 KPGEKVAIVGPSGSGKSTLLKLL 48
>gnl|CDD|72972 cd03213, ABCG_EPDR, ABCG transporters are involved in eye pigment
(EP) precursor transport, regulation of
lipid-trafficking mechanisms, and pleiotropic drug
resistance (DR). DR is a well-described phenomenon
occurring in fungi and shares several similarities with
processes in bacteria and higher eukaryotes. Compared
to other members of the ABC transporter subfamilies, the
ABCG transporter family is composed of proteins that
have an ATP-binding cassette domain at the N-terminus
and a TM (transmembrane) domain at the C-terminus..
Length = 194
Score = 29.4 bits (66), Expect = 3.6
Identities = 9/20 (45%), Positives = 12/20 (60%)
Query: 502 RFIHIRGVGGSGKSTLMNLI 521
I G G+GKSTL+N +
Sbjct: 36 ELTAIMGPSGAGKSTLLNAL 55
>gnl|CDD|31313 COG1116, TauB, ABC-type nitrate/sulfonate/bicarbonate transport
system, ATPase component [Inorganic ion transport and
metabolism].
Length = 248
Score = 29.4 bits (66), Expect = 3.7
Identities = 11/19 (57%), Positives = 13/19 (68%)
Query: 503 FIHIRGVGGSGKSTLMNLI 521
F+ I G G GKSTL+ LI
Sbjct: 31 FVAILGPSGCGKSTLLRLI 49
>gnl|CDD|34593 COG4988, CydD, ABC-type transport system involved in cytochrome bd
biosynthesis, ATPase and permease components [Energy
production and conversion / Posttranslational
modification, protein turnover, chaperones].
Length = 559
Score = 29.4 bits (66), Expect = 3.8
Identities = 11/23 (47%), Positives = 16/23 (69%)
Query: 499 KAQRFIHIRGVGGSGKSTLMNLI 521
KA + + G G+GKSTL+NL+
Sbjct: 345 KAGQLTALVGASGAGKSTLLNLL 367
>gnl|CDD|30197 cd02024, NRK1, Nicotinamide riboside kinase (NRK) is an enzyme
involved in the metabolism of nicotinamide adenine
dinucleotide (NAD+). This enzyme catalyzes the
phosphorylation of nicotinamide riboside (NR) to form
nicotinamide mononucleotide (NMN). It defines the NR
salvage pathway of NAD+ biosynthesis in addition to the
pathways through nicotinic acid mononucleotide (NaMN).
This enzyme can also phosphorylate the anticancer drug
tiazofurin, which is an analog of nicotinamide
riboside..
Length = 187
Score = 29.5 bits (66), Expect = 4.2
Identities = 12/29 (41%), Positives = 17/29 (58%)
Query: 504 IHIRGVGGSGKSTLMNLIKYAFGNQYVIN 532
+ I GV SGK+TL L++ N VI+
Sbjct: 2 VGISGVTNSGKTTLAKLLQRILPNCCVIH 30
>gnl|CDD|73052 cd03293, ABC_NrtD_SsuB_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 = 29.3 bits (66), Expect = 4.2
Identities = 9/19 (47%), Positives = 13/19 (68%)
Query: 503 FIHIRGVGGSGKSTLMNLI 521
F+ + G G GKSTL+ +I
Sbjct: 32 FVALVGPSGCGKSTLLRII 50
>gnl|CDD|72986 cd03227, ABC_Class2, ABC-type Class 2 contains systems involved in
cellular processes other than transport. These families
are characterised by the fact that the ABC subunit is
made up of duplicated, fused ABC modules (ABC2). No
known transmembrane proteins or domains are associated
with these proteins..
Length = 162
Score = 29.2 bits (65), Expect = 4.3
Identities = 11/31 (35%), Positives = 14/31 (45%)
Query: 500 AQRFIHIRGVGGSGKSTLMNLIKYAFGNQYV 530
I G GSGKST+++ I A G
Sbjct: 20 EGSLTIITGPNGSGKSTILDAIGLALGGAQS 50
>gnl|CDD|30727 COG0378, HypB, Ni2+-binding GTPase involved in regulation of
expression and maturation of urease and hydrogenase
[Posttranslational modification, protein turnover,
chaperones / Transcription].
Length = 202
Score = 29.0 bits (65), Expect = 5.0
Identities = 19/87 (21%), Positives = 35/87 (40%), Gaps = 9/87 (10%)
Query: 498 NKAQRFIHIRGVGGSGKSTLMNLIKYAFGNQYVINAEASDIMQNRPPEAGKANPSLIRLM 557
N+ I + G GSGK+ L+ A ++Y I DI + L +L
Sbjct: 10 NRPMLRIGVGGPPGSGKTALIEKTLRALKDEYKIAVITGDIYTKEDADR------LRKLP 63
Query: 558 GSRIVII---SETNENDEINAAKIKQM 581
G I+ + + + +N I+++
Sbjct: 64 GEPIIGVETGKGCHLDASMNLEAIEEL 90
>gnl|CDD|72993 cd03234, ABCG_White, The White subfamily represents ABC
transporters homologous to the Drosophila white gene,
which acts as a dimeric importer for eye pigment
precursors. The eye pigmentation of Drosophila is
developed from the synthesis and deposition in the cells
of red pigments, which are synthesized from guanine, and
brown pigments, which are synthesized from tryptophan.
The pigment precursors are encoded by the white, brown,
and scarlet genes, respectively. Evidence from genetic
and biochemical studies suggest that the White and Brown
proteins function as heterodimers to import guanine,
while the White and Scarlet proteins function to import
tryptophan. However, a recent study also suggests that
White may be involved in the transport of a metabolite,
such as 3-hydroxykynurenine, across intracellular
membranes. Mammalian ABC transporters belonging to the
White subfamily (ABCG1, ABCG5, and ABCG8) have been
shown to be involved in the regulation of
lipid-trafficking mechanisms in macrophages,
hepatocytes, and intestinal mucosa cells. ABCG1 (ABC8),
the human homolog of the Drosophila white gene is
induced in monocyte-derived macrophages during
cholesterol influx mediated by acetylated low-density
lipoprotein. It is possible that human ABCG1 forms
heterodimers with several heterologous partners..
Length = 226
Score = 29.0 bits (65), Expect = 5.2
Identities = 19/74 (25%), Positives = 28/74 (37%), Gaps = 27/74 (36%)
Query: 473 VSGYFESEEVMDYFTRCVGMALLGGNKAQRFIHIRGVGGSGKSTLMNLI------KYAFG 526
VS + ES +VM A+LG + GSGK+TL++ I
Sbjct: 26 VSLHVESGQVM---------AILGSS------------GSGKTTLLDAISGRVEGGGTTS 64
Query: 527 NQYVINAEASDIMQ 540
Q + N + Q
Sbjct: 65 GQILFNGQPRKPDQ 78
>gnl|CDD|73034 cd03275, ABC_SMC1_euk, Eukaryotic SMC1 proteins; SMC proteins are
large (approximately 110 to 170 kDa), and each is
arranged into five recognizable domains. Amino-acid
sequence homology of SMC proteins between species is
largely confined to the amino- and carboxy-terminal
globular domains. The amino-terminal domain contains a
'Walker A' nucleotide-binding domain (GxxGxGKS/T, in the
single-letter amino-acid code), which by mutational
studies has been shown to be essential in several
proteins. The carboxy-terminal domain contains a
sequence (the DA-box) that resembles a 'Walker B' motif,
and a motif with homology to the signature sequence of
the ATP-binding cassette (ABC) family of ATPases. The
sequence homology within the carboxy-terminal domain is
relatively high within the SMC1-SMC4 group, whereas SMC5
and SMC6 show some divergence in both of these
sequences. In eukaryotic cells, the proteins are found
as heterodimers of SMC1 paired with SMC3, SMC2 with
SMC4, and SMC5 with SMC6 (formerly known as Rad18)..
Length = 247
Score = 29.0 bits (65), Expect = 5.4
Identities = 13/25 (52%), Positives = 15/25 (60%)
Query: 502 RFIHIRGVGGSGKSTLMNLIKYAFG 526
RF I G GSGKS LM+ I + G
Sbjct: 23 RFTCIIGPNGSGKSNLMDAISFVLG 47
>gnl|CDD|33194 COG3387, SGA1, Glucoamylase and related glycosyl hydrolases
[Carbohydrate transport and metabolism].
Length = 612
Score = 28.8 bits (64), Expect = 5.4
Identities = 17/82 (20%), Positives = 28/82 (34%), Gaps = 14/82 (17%)
Query: 320 KKGHFLYTADTK----------AWYKKDKNNVYIWSLTLDKITASIMNFLVSMKEDVFDL 369
+ GHF YT T A DK + W T D++ +++ + F
Sbjct: 411 RGGHFTYTKATVYAGLDAAADLAEEFGDKGSAEHWRKTADELKEAVLRRGYAEDGGYFVR 470
Query: 370 SEEPEDNNKNSKS----PRFWF 387
S + ++ S F F
Sbjct: 471 SLGRKPDDTVDASLLGLVLFGF 492
>gnl|CDD|32710 COG2884, FtsE, Predicted ATPase involved in cell division [Cell
division and chromosome partitioning].
Length = 223
Score = 29.0 bits (65), Expect = 5.5
Identities = 16/42 (38%), Positives = 21/42 (50%), Gaps = 10/42 (23%)
Query: 490 VGMALLGGNKAQR----------FIHIRGVGGSGKSTLMNLI 521
V A GG +A R F+ + G G+GKSTL+ LI
Sbjct: 7 VSKAYPGGREALRDVSFHIPKGEFVFLTGPSGAGKSTLLKLI 48
>gnl|CDD|30586 COG0237, CoaE, Dephospho-CoA kinase [Coenzyme metabolism].
Length = 201
Score = 28.7 bits (64), Expect = 6.2
Identities = 19/82 (23%), Positives = 35/82 (42%), Gaps = 9/82 (10%)
Query: 504 IHIRGVGGSGKSTLMNLIKYAFGNQYVINAEASDIMQNRPPEAGKANPSLIRLMGSRIVI 563
I + G GSGKST+ ++ VI+ A D+ + G+A + G I
Sbjct: 5 IGLTGGIGSGKSTVAKILAE--LGFPVID--ADDVAREVVEPGGEALQEIAERFGLEI-- 58
Query: 564 ISETNENDEINAAKIKQMTGGD 585
+E+ ++ K+++ D
Sbjct: 59 ---LDEDGGLDRRKLREKVFND 77
>gnl|CDD|73013 cd03254, ABCC_Glucan_exporter_like, 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 virluence 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 = 28.6 bits (64), Expect = 6.6
Identities = 10/23 (43%), Positives = 15/23 (65%)
Query: 499 KAQRFIHIRGVGGSGKSTLMNLI 521
K + I G G+GK+TL+NL+
Sbjct: 27 KPGETVAIVGPTGAGKTTLINLL 49
>gnl|CDD|34687 COG5083, SMP2, Uncharacterized protein involved in plasmid
maintenance [General function prediction only].
Length = 580
Score = 28.5 bits (63), Expect = 6.7
Identities = 41/207 (19%), Positives = 63/207 (30%), Gaps = 34/207 (16%)
Query: 255 KQGSTYDEENFNYKWDTFDFEEIGDTAKKRS--TFTSLFYHHG------------KLIPK 300
GS + NF+ +IG R+ T + +G L K
Sbjct: 125 GSGSDLSKLNFDIVLKEPKNLDIGFRKYSRNKRTENTGKRMYGQSSRQRGHKDSYHLFEK 184
Query: 301 GLLASRFSDAYNKA---MFSIYKKGHFLYTADTKAWYKKDKNNVYIWSLTLDKITASIMN 357
+ +F NK M I+K + YK N + S+ D+ T+
Sbjct: 185 RFV--KFGSLLNKTLHFMSLIFKTKTNGDLLTDISLYKPGGNKILDLSVN-DRDTSKDEF 241
Query: 358 FLVSMKEDVFDLSEEPEDNNKNSKSPRFWFNTDYRRQNVEENSKAKSTAQSLEAGSIFS- 416
F E +PED NS R + N + K+ QS+ ++S
Sbjct: 242 FDFKDIE-----FVKPEDTEFNSWINREHVTKLHPHHNGSDEVYGKNPPQSISGDFLYSD 296
Query: 417 --------ITSDLLDSSSRFLGEQDGI 435
S L S S + I
Sbjct: 297 VRVSLANDEVSILEYSHSSSEPSWNKI 323
>gnl|CDD|33631 COG3839, MalK, ABC-type sugar transport systems, ATPase components
[Carbohydrate transport and metabolism].
Length = 338
Score = 28.7 bits (64), Expect = 7.1
Identities = 9/19 (47%), Positives = 13/19 (68%)
Query: 503 FIHIRGVGGSGKSTLMNLI 521
F+ + G G GKSTL+ +I
Sbjct: 31 FVVLLGPSGCGKSTLLRMI 49
>gnl|CDD|31316 COG1119, ModF, ABC-type molybdenum transport system, ATPase
component/photorepair protein PhrA [Inorganic ion
transport and metabolism].
Length = 257
Score = 28.7 bits (64), Expect = 7.4
Identities = 8/17 (47%), Positives = 13/17 (76%)
Query: 505 HIRGVGGSGKSTLMNLI 521
I G G+GK+TL++L+
Sbjct: 61 AIVGPNGAGKTTLLSLL 77
>gnl|CDD|111487 pfam02594, DUF167, Uncharacterized ACR, YggU family COG1872.
Length = 78
Score = 28.3 bits (64), Expect = 7.4
Identities = 11/30 (36%), Positives = 15/30 (50%), Gaps = 7/30 (23%)
Query: 543 PPEAGKANPSLIRLMG-------SRIVIIS 565
PP GKAN LI+ + S + I+S
Sbjct: 36 PPVDGKANAELIKFLAKTLGVPKSDVEIVS 65
>gnl|CDD|35241 KOG0018, KOG0018, KOG0018, Structural maintenance of chromosome
protein 1 (sister chromatid cohesion complex Cohesin,
subunit SMC1) [Cell cycle control, cell division,
chromosome partitioning].
Length = 1141
Score = 28.3 bits (63), Expect = 8.2
Identities = 13/26 (50%), Positives = 15/26 (57%)
Query: 501 QRFIHIRGVGGSGKSTLMNLIKYAFG 526
RF I G GSGKS LM+ I + G
Sbjct: 25 DRFTAIIGPNGSGKSNLMDAISFVLG 50
>gnl|CDD|33900 COG4148, ModC, ABC-type molybdate transport system, ATPase
component [Inorganic ion transport and metabolism].
Length = 352
Score = 28.3 bits (63), Expect = 8.4
Identities = 9/22 (40%), Positives = 15/22 (68%)
Query: 500 AQRFIHIRGVGGSGKSTLMNLI 521
A+ + G GSGK++L+N+I
Sbjct: 23 ARGITALFGPSGSGKTSLINMI 44
>gnl|CDD|31325 COG1129, MglA, ABC-type sugar transport system, ATPase component
[Carbohydrate transport and metabolism].
Length = 500
Score = 28.2 bits (63), Expect = 8.4
Identities = 12/30 (40%), Positives = 15/30 (50%), Gaps = 12/30 (40%)
Query: 492 MALLGGNKAQRFIHIRGVGGSGKSTLMNLI 521
ALLG N G+GKSTLM ++
Sbjct: 37 HALLGEN------------GAGKSTLMKIL 54
>gnl|CDD|72984 cd03225, ABC_cobalt_CbiO_domain1, Domain I of the ABC component of
a cobalt transport family found in bacteria, archaea,
and eukaryota. The transition metal cobalt is an
essential component of many enzymes and must be
transported into cells in appropriate amounts when
needed. This ABC transport system of the CbiMNQO family
is involved in cobalt transport in association with the
cobalamin (vitamin B12) biosynthetic pathways. Most of
cobalt (Cbi) transport systems possess a separate CbiN
component, the cobalt-binding periplasmic protein, and
they are encoded by the conserved gene cluster cbiMNQO.
Both the CbiM and CbiQ proteins are integral cytoplasmic
membrane proteins, and the CbiO protein has the linker
peptide and the Walker A and B motifs commonly found in
the ATPase components of the ABC-type transport
systems..
Length = 211
Score = 28.2 bits (63), Expect = 9.1
Identities = 11/19 (57%), Positives = 14/19 (73%)
Query: 503 FIHIRGVGGSGKSTLMNLI 521
F+ I G GSGKSTL+ L+
Sbjct: 29 FVLIVGPNGSGKSTLLRLL 47
>gnl|CDD|147768 pfam05794, Tcp11, T-complex protein 11. This family consists of
several eukaryotic T-complex protein 11 (Tcp11) related
sequences. Tcp11 is only expressed in fertile adult
mammalian testes and is thought to be important in sperm
function and fertility. The family also contains the
yeast Sok1 protein which is known to suppress cyclic
AMP-dependent protein kinase mutants.
Length = 423
Score = 28.0 bits (63), Expect = 9.2
Identities = 15/35 (42%), Positives = 19/35 (54%), Gaps = 3/35 (8%)
Query: 163 PLLSEEDVEYLFKFFQEITVPLVKDKKSIIPSKTW 197
PLL E VEY K FQE+ L + S+ +K W
Sbjct: 160 PLLIENSVEYERKKFQEL---LEEAPNSLPLTKKW 191
Database: CddA
Posted date: Feb 4, 2011 9:38 PM
Number of letters in database: 6,263,737
Number of sequences in database: 21,609
Lambda K H
0.316 0.134 0.401
Gapped
Lambda K H
0.267 0.0745 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 9,783,549
Number of extensions: 528045
Number of successful extensions: 1495
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1490
Number of HSP's successfully gapped: 62
Length of query: 789
Length of database: 6,263,737
Length adjustment: 102
Effective length of query: 687
Effective length of database: 4,059,619
Effective search space: 2788958253
Effective search space used: 2788958253
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: 61 (27.2 bits)