RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17620
(741 letters)
>gnl|CDD|193250 pfam12774, AAA_6, Hydrolytic ATP binding site of dynein motor
region D1. 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 D1 unit of the
motor and contains the hydrolytic ATP binding site.
Length = 231
Score = 263 bits (673), Expect = 3e-83
Identities = 124/229 (54%), Positives = 153/229 (66%), Gaps = 29/229 (12%)
Query: 367 YGYEYMGLNGRLVITPLTDRIYLTITQALSMRLGAAPAG--------------------- 405
Y YEY+G RLVITPLTDR Y+T+TQ+L + + APAG
Sbjct: 1 YSYEYLGNTPRLVITPLTDRCYITLTQSLHLTMSGAPAGPAGTGKTETTKDLGRALGIMV 60
Query: 406 --------MDFLAFGKILSGLSQCGAWGCFDEFNRIDVSVLSVISTQLLTIRTALLINAT 457
MD+ + G I GL+Q GAWGCFDEFNRI V VLSV++ Q+ ++ A+
Sbjct: 61 YVFNCSEQMDYKSCGNIYKGLAQTGAWGCFDEFNRISVEVLSVVAVQVKCVQDAIRDKKQ 120
Query: 458 RFQFEGHDIIMNNKVGIFITMNPGYAGRTELPESVKALFRPVVCIVPDFELICQIMLFSE 517
F F G +I + VGIFITMNPGYAGRTELPE++KALFRP +VPDFELIC+IML +E
Sbjct: 121 WFNFLGEEISLIPSVGIFITMNPGYAGRTELPENLKALFRPCAMVVPDFELICEIMLVAE 180
Query: 518 GFLEAKVLAKKMAVLYKLSKEQLSKQCHYDFGMRALKSVLVMAGELKRA 566
GFLEA++LA+K LY L KE LSKQ HYD+G+RA+KSVLV+AG LKR
Sbjct: 181 GFLEARLLARKFITLYTLCKELLSKQDHYDWGLRAIKSVLVVAGSLKRG 229
>gnl|CDD|219818 pfam08393, DHC_N2, Dynein heavy chain, N-terminal region 2.
Dyneins are described as motor proteins of eukaryotic
cells, as they can convert energy derived from the
hydrolysis of ATP to force and movement along
cytoskeletal polymers, such as microtubules. This region
is found C-terminal to the dynein heavy chain N-terminal
region 1 (pfam08385) in many members of this family. No
functions seem to have been attributed specifically to
this region.
Length = 408
Score = 111 bits (280), Expect = 3e-26
Identities = 40/80 (50%), Positives = 57/80 (71%), Gaps = 1/80 (1%)
Query: 232 IMWETHKNPRVIEQCLVPNRLEHLEQLKDGLEACEKSLQDYLTDKRNAFPRFFFISDDEL 291
+M + +K+P V+E C +P LE LE+L + LE +KSL +YL KR+AFPRF+F+S+D+L
Sbjct: 263 LMKKANKDPNVLEVCNIPGLLEKLEKLNEQLEKIQKSLNEYLESKRSAFPRFYFLSNDDL 322
Query: 292 LSILGSSS-PTAIQEHIVKF 310
L IL S PTA+Q H+ K
Sbjct: 323 LEILSQSKDPTAVQPHLKKL 342
>gnl|CDD|227570 COG5245, DYN1, Dynein, heavy chain [Cytoskeleton].
Length = 3164
Score = 52.7 bits (126), Expect = 7e-07
Identities = 82/339 (24%), Positives = 144/339 (42%), Gaps = 69/339 (20%)
Query: 422 GAWGCFDEFNRIDVSVLSVISTQLLTIRTALLINATRFQFEGHDIIMNNKVGIFITMNPG 481
G++ CFDEFNR+ +S S +L L + + +F F+ MN G
Sbjct: 1660 GSYLCFDEFNRLSEETMSA-SVELY------LSSKDKTKF-------------FLQMNYG 1699
Query: 482 YAGRTELPESVKALFRPVVCIV--PDFELICQIMLFSEGFLEAKVLAKKMAVLYKLSKEQ 539
Y R EL S++A+F + PD LI I + E E + + + + Q
Sbjct: 1700 YKPR-ELTRSLRAIFGYAETRIDTPDVSLI--IDWYCEAIRE--KIDRLVQQKESSTSRQ 1754
Query: 540 LSKQCHYDFGMRALKSVLVMAG-----------ELKRAALQLEESVVLMRALRDMNLPKF 588
YDFG+RA++ ++ A L ++ V + +R F
Sbjct: 1755 D----LYDFGLRAIREMIAGHIGEAEITFSMILFFGMACLLKKDLAVFVEEVRK----IF 1806
Query: 589 VSEDV-VQM--YETMLT-----RHSTMIVGPTGGGKSVVINALVKTSTVLGYPARTYTLN 640
S + V+ Y+ L R ++VG G K V+I + + LN
Sbjct: 1807 GSSHLDVEAVAYKDALLHILRSRRGLLVVGGHGVLKGVLIRGACDAREFVCW------LN 1860
Query: 641 PKAVSVIELYGVLNPETRDWYDGLLSNIFRAVNKPLDPGSKERKYILFDGD-VDALWIEN 699
P+ ++ E++G + T D+ D L R G +E +F+ V++ ++E+
Sbjct: 1861 PR--NMREIFGHRDELTGDFRDSLKVQDLRRNIH----GGRE-CLFIFESIPVESSFLED 1913
Query: 700 MNSVMDDNKILTLANG-ERIRLLAHCQLLFEIHPIQSDS 737
N ++D+N+ L L +G ERIR+ + + +FE ++ D+
Sbjct: 1914 FNPLLDNNRFLCLFSGNERIRIPENLRFVFESTSLEKDT 1952
Score = 48.1 bits (114), Expect = 2e-05
Identities = 44/398 (11%), Positives = 104/398 (26%), Gaps = 84/398 (21%)
Query: 366 EYGYEYMGLNGRLVITPLTDRIYLTITQAL------------SMRLGAAPAGMDFLAFG- 412
+ + + + + + +A+ S G AG + G
Sbjct: 915 AEMFAKNTIPFFVFEHSMDTSQHQKLFEAVCDEVCRFVDTENSRVYGMLVAGKGRIYDGT 974
Query: 413 ----KILSGLSQCGAWGCFDEFNRIDVSVLSVISTQLLTIRTALLINATRFQFEGHDIIM 468
+I +G G +E +D +++ + L + +
Sbjct: 975 EPRSRIEAGPICEEERG-TEESALLDEISRTILVDEYL-NSDEFRMLEELNSAVVEHGLK 1032
Query: 469 NNKVGIFITMNPGYAGRTELPESVKALFRPVVCIVPDFELICQIMLFSEGFLEAKVLAKK 528
+ + + +N R + E + + +P F I + L ++
Sbjct: 1033 SPSTPVEMIINE----RNIVLEIGRRALDMFLSNIP-FGAIKSRR---------ESLDRE 1078
Query: 529 MAVLYKLSKEQLSKQCHYDF-----GMRALKSVLVMAGELKRAALQLEESVVLMRALRDM 583
+ ++ F ++A +L E L + ++ LR+
Sbjct: 1079 IGAFNNEVDGIAREEDELMFYPMFKSLKAKHRMLEEKTEYLNKILSITGLPLISDTLRER 1138
Query: 584 ----------------NLPKFVSEDV--------VQMYETMLTRHSTMIVGPTGGGKSVV 619
+L K+ S+ V V ++ T K
Sbjct: 1139 IDTLDAEWDSFCRISESLKKYESQQVSGLDVAQFVSFLRSVDTGAFHAEYFRVFLCK--- 1195
Query: 620 INALVKTSTVLGYPARTYTLNPKAVSVIELYGVLNPETRDWYDGLLSNIFRAVNKPLDPG 679
I L + Y + +EL R+ + L++
Sbjct: 1196 IKHYTDACDYLWHVKSPYVKKKYFDADMELRQFFLMFNREDMEARLAD------------ 1243
Query: 680 SKERKYILFDGDVDALWIENMNSVMDDNKILTLANGER 717
+ + ++E + + K+ + GE
Sbjct: 1244 --SKMEYEVER-----YVEKTKAEVSSLKLELSSVGEG 1274
>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 = 34.2 bits (79), Expect = 0.066
Identities = 24/121 (19%), Positives = 46/121 (38%), Gaps = 26/121 (21%)
Query: 607 MIVGPTGGGKSVV---INALVKTSTVLGYPARTYTLNPKAVSVIELYGVLNPETRD--WY 661
++VGP G GKS + + A + V Y + + +L G N + W
Sbjct: 3 LLVGPPGTGKSELAERLAAALSNRPVF------YVQLTRDTTEEDLKGRRNIDPGGASWV 56
Query: 662 DGLLSNIFRAVNKPLDPGSKERKYILFDGDVDAL---WIENMNSVMDDNKILTLANGERI 718
DG L R I +++ + ++ S++D+ ++L GE +
Sbjct: 57 DGPLVRAAR------------EGEIAVLDEINRANPDVLNSLLSLLDERRLLLPEGGELV 104
Query: 719 R 719
+
Sbjct: 105 K 105
Score = 29.2 bits (66), Expect = 3.4
Identities = 18/75 (24%), Positives = 29/75 (38%), Gaps = 6/75 (8%)
Query: 422 GAWGCFDEFNRIDVSVLSVISTQLLTIRTALLINATRFQFEGHDIIMNNKVGIFITMNPG 481
G DE NR + VL+ + + L R L + + + TMNP
Sbjct: 67 GEIAVLDEINRANPDVLNSLLSLLDERRLLLPEGGELVKAA------PDGFRLIATMNPL 120
Query: 482 YAGRTELPESVKALF 496
G EL ++++ F
Sbjct: 121 DRGLNELSPALRSRF 135
>gnl|CDD|205733 pfam13555, AAA_29, P-loop containing region of AAA domain.
Length = 60
Score = 31.8 bits (73), Expect = 0.12
Identities = 15/44 (34%), Positives = 24/44 (54%), Gaps = 4/44 (9%)
Query: 600 MLTRHSTMIVGPTGGGKSVVINALVKTSTVLGYPARTYTLNPKA 643
+ T++ GP+G GKS +I+A+ T+L PA+ N A
Sbjct: 18 PIDPKGTLLTGPSGSGKSTLIDAI---QTLL-VPAKRVAFNKAA 57
>gnl|CDD|237536 PRK13873, PRK13873, conjugal transfer ATPase TrbE; Provisional.
Length = 811
Score = 34.5 bits (80), Expect = 0.22
Identities = 10/18 (55%), Positives = 15/18 (83%)
Query: 606 TMIVGPTGGGKSVVINAL 623
T++VGPTG GKSV++ +
Sbjct: 444 TLVVGPTGAGKSVLLALM 461
>gnl|CDD|227680 COG5391, COG5391, Phox homology (PX) domain protein [Intracellular
trafficking and secretion / General function prediction
only].
Length = 524
Score = 34.0 bits (78), Expect = 0.32
Identities = 16/72 (22%), Positives = 35/72 (48%), Gaps = 9/72 (12%)
Query: 253 EHLEQLKDGLEACEKSLQDYLTDKRNAFPRFFFISDDELLSILGSSSPTAIQEHIVKFAA 312
+ E+L++ L EK Q+ + +N FF + + +L IL S + + +++A
Sbjct: 454 QDKEKLEEQLAIAEKDAQEINEELKNELKFFFSVRNSDLEKILKSVA-----DSHIEWAE 508
Query: 313 KIMDAEEFQWES 324
+ ++ W+S
Sbjct: 509 ENLE----IWKS 516
>gnl|CDD|172418 PRK13898, PRK13898, type IV secretion system ATPase VirB4;
Provisional.
Length = 800
Score = 33.6 bits (77), Expect = 0.39
Identities = 11/18 (61%), Positives = 16/18 (88%)
Query: 606 TMIVGPTGGGKSVVINAL 623
T+I+GPTG GK+V++N L
Sbjct: 449 TLIIGPTGAGKTVLMNFL 466
>gnl|CDD|213194 cd03227, ABC_Class2, ATP-binding cassette domain of non-transporter
proteins. ABC-type Class 2 contains systems involved in
cellular processes other than transport. These families
are characterized 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 = 32.3 bits (74), Expect = 0.43
Identities = 9/20 (45%), Positives = 14/20 (70%)
Query: 604 HSTMIVGPTGGGKSVVINAL 623
T+I GP G GKS +++A+
Sbjct: 22 SLTIITGPNGSGKSTILDAI 41
>gnl|CDD|223786 COG0714, COG0714, MoxR-like ATPases [General function prediction
only].
Length = 329
Score = 33.2 bits (76), Expect = 0.45
Identities = 27/110 (24%), Positives = 37/110 (33%), Gaps = 13/110 (11%)
Query: 427 FDEFNRIDVSVLSVISTQLLTIRTALLINATRFQFEGHD-IIMNNKVGIFITMNPG-YAG 484
DE NR V + LL + + G I + + T NPG Y G
Sbjct: 118 LDEINRAPPEVQNA----LLE-----ALEERQVTVPGLTTIRLPPPFIVIATQNPGEYEG 168
Query: 485 RTELPESVK--ALFRPVVCIVPDFELICQIMLFSEGFLEAKVLAKKMAVL 532
LPE++ L R V E I+ G E + + VL
Sbjct: 169 TYPLPEALLDRFLLRIYVDYPDSEEEERIILARVGGVDELDLESLVKPVL 218
Score = 31.6 bits (72), Expect = 1.3
Identities = 25/101 (24%), Positives = 38/101 (37%), Gaps = 11/101 (10%)
Query: 590 SEDVVQ-MYETMLTRHSTMIVGPTGGGKSVVINALVKTSTVLGYPARTYTLNPKAVSVIE 648
E+V++ +L ++ GP G GK+++ AL + LG P P + +
Sbjct: 29 DEEVIELALLALLAGGHVLLEGPPGVGKTLLARAL---ARALGLPFVRIQCTPD-LLPSD 84
Query: 649 LYGVLNPETRDWYDGLLSNIFRAVNKPLDPGSKERKYILFD 689
L G L FR V PL R +L D
Sbjct: 85 LLGTYAYAALL----LEPGEFRFVPGPLFAA--VRVILLLD 119
>gnl|CDD|220739 pfam10412, TrwB_AAD_bind, Type IV secretion-system coupling protein
DNA-binding domain. The plasmid conjugative coupling
protein TrwB forms hexamers from six structurally very
similar protomers. This hexamer contains a central
channel running from the cytosolic pole (made up by the
AADs) to the membrane pole ending at the transmembrane
pore shaped by 12 transmembrane helices, rendering an
overall mushroom-like structure. The TrwB_AAD (all-alpha
domain) domain appears to be the DNA-binding domain of
the structure. TrwB, a basic integral inner-membrane
nucleoside-triphosphate-binding protein, is the
structural prototype for the type IV secretion system
coupling proteins, a family of proteins essential for
macromolecular transport between cells and export.
Length = 386
Score = 32.9 bits (76), Expect = 0.58
Identities = 10/25 (40%), Positives = 15/25 (60%), Gaps = 1/25 (4%)
Query: 602 TRHSTMIVGPTGGGKSVVINALVKT 626
T+H +IVG TG GK+ + L+
Sbjct: 15 TQH-ILIVGTTGTGKTQALRELLDQ 38
>gnl|CDD|222804 PHA00520, PHA00520, packaging NTPase P4.
Length = 330
Score = 32.5 bits (74), Expect = 0.66
Identities = 37/180 (20%), Positives = 61/180 (33%), Gaps = 52/180 (28%)
Query: 606 TMIVGPTGGGKSVVINAL-------VKTSTV-LGYPARTYTLNPKAVSVIELYGVLNPET 657
++VG TG GK+ ++NAL K + + G P Y + + + L +L+ +
Sbjct: 127 EVVVGGTGSGKTPLLNALAPDVGGGDKYAVIRWGEPLEGYDTDLHVFAALILAAMLDVDV 186
Query: 658 ------RDWYDGL-------------------LSNIFRAVN----KPLDPGSKERKYILF 688
R+ L L NI + L+P S + K
Sbjct: 187 VVVDSLRNVLFELGGNATSGGISRGAYGLLTDLGNIAASRGCRVVATLNPMSDDEK---- 242
Query: 689 DGDVDALWIENMNS------VMDDN--KILTLANGERIRLLAHCQLLFEIHPIQSDSHPR 740
++A+ E S V DN + L IR+ A F + + PR
Sbjct: 243 ---IEAVVREVSKSNSGSMVVARDNVWRTLFRTGEGLIRIFAVLATSFTDETVLTLHAPR 299
>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 = 31.6 bits (71), Expect = 0.77
Identities = 20/109 (18%), Positives = 34/109 (31%), Gaps = 20/109 (18%)
Query: 602 TRHSTMIVGPTGGGKSVVINALVKTSTVLGYPARTYTLNPKAVSVIELYGVLNPETRDWY 661
+IVGP G GK+ + AL + L P VI ++ E
Sbjct: 1 PGEVILIVGPPGSGKTTLARALAR------------ELGPPGGGVI----YIDGEDILEE 44
Query: 662 DGLLSNIFRAVNKPLDPGSKERKYILFD----GDVDALWIENMNSVMDD 706
+ K + R + D L ++ + S++D
Sbjct: 45 VLDQLLLIIVGGKKASGSGELRLRLALALARKLKPDVLILDEITSLLDA 93
>gnl|CDD|234631 PRK00098, PRK00098, GTPase RsgA; Reviewed.
Length = 298
Score = 32.5 bits (75), Expect = 0.77
Identities = 14/36 (38%), Positives = 19/36 (52%), Gaps = 8/36 (22%)
Query: 604 HSTMIVGPTGGGKSVVINALV-----KT---STVLG 631
T++ G +G GKS ++NAL KT S LG
Sbjct: 165 KVTVLAGQSGVGKSTLLNALAPDLELKTGEISEALG 200
>gnl|CDD|201784 pfam01418, HTH_6, Helix-turn-helix domain, rpiR family. This
domain contains a helix-turn-helix motif. The best
characterized member of this family is Escherichia coli
rpiR, a regulator of the expression of rpiB gene.
Length = 77
Score = 29.6 bits (67), Expect = 0.90
Identities = 16/65 (24%), Positives = 25/65 (38%), Gaps = 8/65 (12%)
Query: 250 NRLEHLEQLKDGLEACEKSLQDYLTDKRNAFPRFFFISDDELLSILGSSSPTAIQEHIVK 309
LE ++ L L EK + DY+ + S EL G S + +V+
Sbjct: 2 GLLEKIQSLYSKLTKSEKKIADYILASPDNAIHL---SIAELAKAAGVSEAS-----VVR 53
Query: 310 FAAKI 314
F K+
Sbjct: 54 FCRKL 58
>gnl|CDD|190460 pfam02877, PARP_reg, Poly(ADP-ribose) polymerase, regulatory
domain. Poly(ADP-ribose) polymerase catalyzes the
covalent attachment of ADP-ribose units from NAD+ to
itself and to a limited number of other DNA binding
proteins, which decreases their affinity for DNA.
Poly(ADP-ribose) polymerase is a regulatory component
induced by DNA damage. The carboxyl-terminal region is
the most highly conserved region of the protein.
Experiments have shown that a carboxyl 40 kDa fragment
is still catalytically active.
Length = 130
Score = 31.0 bits (71), Expect = 0.92
Identities = 25/85 (29%), Positives = 34/85 (40%), Gaps = 19/85 (22%)
Query: 488 LPESVKALFRPVVCIVPDFELICQIMLFSEGFLEAKVLAKKMAVLYKLSKEQLSKQCHYD 547
LP V+ L + LI + + + E AKKM L KLSK Q+ K
Sbjct: 1 LPPPVQDLMK----------LIFDVKMMKKTMKEMGYDAKKMP-LGKLSKRQIQK----- 44
Query: 548 FGMRALKSV--LVMAGELKRAALQL 570
G LK + L+ G+ A L
Sbjct: 45 -GYEVLKEIQELLKKGKSGSALEDL 68
>gnl|CDD|221803 pfam12846, AAA_10, AAA-like domain. This family of domains contain
a P-loop motif that is characteristic of the AAA
superfamily. Many of the proteins in this family are
conjugative transfer proteins.
Length = 316
Score = 32.0 bits (73), Expect = 1.1
Identities = 9/21 (42%), Positives = 14/21 (66%)
Query: 604 HSTMIVGPTGGGKSVVINALV 624
+ +IVGP+G GKS ++ L
Sbjct: 2 PNMLIVGPSGSGKSTLLKLLA 22
>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 = 31.4 bits (72), Expect = 1.1
Identities = 11/18 (61%), Positives = 15/18 (83%)
Query: 608 IVGPTGGGKSVVINALVK 625
IVGPTG GK+ +IN L++
Sbjct: 34 IVGPTGAGKTTLINLLMR 51
>gnl|CDD|218632 pfam05549, Allexi_40kDa, Allexivirus 40kDa protein.
Length = 271
Score = 31.7 bits (72), Expect = 1.1
Identities = 16/34 (47%), Positives = 20/34 (58%), Gaps = 3/34 (8%)
Query: 622 ALVKTSTVLGY--PARTYTLNPKAVSVIELYGVL 653
AL T +LG+ PAR Y L P + + ELYG L
Sbjct: 11 ALDATRNLLGHVPPAR-YNLPPTTLPLDELYGQL 43
>gnl|CDD|225982 COG3451, VirB4, Type IV secretory pathway, VirB4 components
[Intracellular trafficking and secretion].
Length = 796
Score = 32.0 bits (73), Expect = 1.3
Identities = 11/25 (44%), Positives = 17/25 (68%), Gaps = 1/25 (4%)
Query: 599 TMLTRHSTMIVGPTGGGKSVVINAL 623
H T+I+GPTG GK+V+++ L
Sbjct: 433 GEDVGH-TLIIGPTGAGKTVLLSFL 456
>gnl|CDD|130456 TIGR01389, recQ, ATP-dependent DNA helicase RecQ. The
ATP-dependent DNA helicase RecQ of E. coli is about 600
residues long. This model represents bacterial proteins
with a high degree of similarity in domain architecture
and in primary sequence to E. coli RecQ. The model
excludes eukaryotic and archaeal proteins with RecQ-like
regions, as well as more distantly related bacterial
helicases related to RecQ [DNA metabolism, DNA
replication, recombination, and repair].
Length = 591
Score = 32.0 bits (73), Expect = 1.3
Identities = 9/21 (42%), Positives = 13/21 (61%)
Query: 598 ETMLTRHSTMIVGPTGGGKSV 618
+L ++V PTGGGKS+
Sbjct: 23 SHVLDGRDVLVVMPTGGGKSL 43
>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 = 1.6
Identities = 10/18 (55%), Positives = 13/18 (72%)
Query: 606 TMIVGPTGGGKSVVINAL 623
IVGP G GKS +++AL
Sbjct: 34 VAIVGPVGSGKSSLLSAL 51
>gnl|CDD|213241 cd03274, ABC_SMC4_euk, ATP-binding cassette domain of eukaryotic
SMC4 proteins. The structural maintenance of
chromosomes (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 = 212
Score = 30.7 bits (70), Expect = 2.1
Identities = 13/30 (43%), Positives = 19/30 (63%), Gaps = 3/30 (10%)
Query: 606 TMIVGPTGGGKSVVINALVKTSTVLGYPAR 635
+ IVGP G GKS VI++++ V G+ A
Sbjct: 28 SAIVGPNGSGKSNVIDSML---FVFGFRAS 54
>gnl|CDD|213206 cd03239, ABC_SMC_head, The SMC head domain belongs to the
ATP-binding cassette superfamily. The structural
maintenance of chromosomes (SMC) proteins are essential
for successful chromosome transmission during
replication and segregation of the genome in all
organisms. SMCs are generally present as single proteins
in bacteria, and as at least six distinct proteins in
eukaryotes. The proteins range in size from
approximately 110 to 170 kDa, and each has five distinct
domains: amino- and carboxy-terminal globular domains,
which contain sequences characteristic of ATPases, two
coiled-coil regions separating the terminal domains ,
and a central flexible hinge. SMC proteins function
together with other proteins in a range of chromosomal
transactions, including chromosome condensation,
sister-chromatid cohesion, recombination, DNA repair,
and epigenetic silencing of gene expression.
Length = 178
Score = 30.0 bits (68), Expect = 3.2
Identities = 14/48 (29%), Positives = 21/48 (43%), Gaps = 6/48 (12%)
Query: 604 HSTMIVGPTGGGKSVVINALVKTSTVLGYPARTYTLNPKAVSVIELYG 651
IVGP G GKS +++A+ VLG + L + + G
Sbjct: 23 SFNAIVGPNGSGKSNIVDAI---CFVLGG--KAAKLRRGS-LLFLAGG 64
>gnl|CDD|206748 cd01855, YqeH, Circularly permuted YqeH GTPase. YqeH is an
essential GTP-binding protein. Depletion of YqeH induces
an excess initiation of DNA replication, suggesting that
it negatively controls initiation of chromosome
replication. The YqeH subfamily is common in eukaryotes
and sporadically present in bacteria with probable
acquisition by plants from chloroplasts. Proteins of the
YqeH 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.
Length = 191
Score = 29.9 bits (68), Expect = 3.3
Identities = 16/53 (30%), Positives = 28/53 (52%), Gaps = 4/53 (7%)
Query: 574 VVLMRALRDMNLPKFVSEDVVQMYETMLTRHSTMIVGPTGGGKSVVINALVKT 626
V+L+ A + + + + E + + R +VG T GKS +INAL+K+
Sbjct: 100 VILVSAKKGWGVEELIEE----IKKLAKYRGDVYVVGATNVGKSTLINALLKS 148
>gnl|CDD|213179 cd00267, ABC_ATPase, ATP-binding cassette transporter
nucleotide-binding domain. ABC transporters are a large
family of proteins involved in the transport of a wide
variety of different compounds, like sugars, ions,
peptides, and more complex organic molecules. The
nucleotide-binding domain shows the highest similarity
between all members of the family. ABC transporters are
a subset of nucleotide hydrolases that contain a
signature motif, Q-loop, and H-loop/switch region, in
addition to, the Walker A motif/P-loop and Walker B
motif commonly found in a number of ATP- and GTP-binding
and hydrolyzing proteins.
Length = 157
Score = 29.5 bits (67), Expect = 4.0
Identities = 8/18 (44%), Positives = 12/18 (66%)
Query: 606 TMIVGPTGGGKSVVINAL 623
+VGP G GKS ++ A+
Sbjct: 28 VALVGPNGSGKSTLLRAI 45
>gnl|CDD|233193 TIGR00929, VirB4_CagE, type IV secretion/conjugal transfer ATPase,
VirB4 family. Type IV secretion systems are found in
Gram-negative pathogens. They export proteins, DNA, or
complexes in different systems and are related to
plasmid conjugation systems. This model represents
related ATPases that include VirB4 in Agrobacterium
tumefaciens (DNA export) CagE in Helicobacter pylori
(protein export) and plasmid TraB (conjugation).
Length = 785
Score = 30.4 bits (69), Expect = 4.2
Identities = 10/20 (50%), Positives = 14/20 (70%)
Query: 604 HSTMIVGPTGGGKSVVINAL 623
T+I GPTG GK+ ++N L
Sbjct: 435 GHTLIFGPTGSGKTTLLNFL 454
>gnl|CDD|216186 pfam00910, RNA_helicase, RNA helicase. This family includes RNA
helicases thought to be involved in duplex unwinding
during viral RNA replication. Members of this family are
found in a variety of single stranded RNA viruses.
Length = 105
Score = 28.4 bits (64), Expect = 4.2
Identities = 11/39 (28%), Positives = 15/39 (38%), Gaps = 3/39 (7%)
Query: 607 MIVGPTGGGKSVVINALVK---TSTVLGYPARTYTLNPK 642
+ GP G GKS + L + L Y+ NP
Sbjct: 2 WLYGPPGCGKSTLAKYLARALLKHLGLPKKDSVYSRNPD 40
>gnl|CDD|217416 pfam03193, DUF258, Protein of unknown function, DUF258.
Length = 161
Score = 29.1 bits (66), Expect = 4.5
Identities = 9/25 (36%), Positives = 18/25 (72%)
Query: 600 MLTRHSTMIVGPTGGGKSVVINALV 624
+L ++++ G +G GKS ++NAL+
Sbjct: 32 LLKGKTSVLAGQSGVGKSTLLNALL 56
>gnl|CDD|238547 cd01127, TrwB, Bacterial conjugation protein TrwB, ATP binding
domain. TrwB is a homohexamer encoded by conjugative
plasmids in Gram-negative bacteria. TrwB also has an all
alpha domain which has been hypothesized to be
responsible for DNA binding. TrwB is a component of Type
IV secretion and is responsible for the horizontal
transfer of DNA between bacteria.
Length = 410
Score = 30.0 bits (68), Expect = 4.5
Identities = 12/30 (40%), Positives = 16/30 (53%), Gaps = 1/30 (3%)
Query: 602 TRHSTMIVGPTGGGKSVVINALVKTSTVLG 631
H TMI+G TG GK+ I L+ + G
Sbjct: 42 EAH-TMIIGTTGTGKTTQIRELLASIRARG 70
>gnl|CDD|218401 pfam05049, IIGP, Interferon-inducible GTPase (IIGP).
Interferon-inducible GTPase (IIGP) is thought to play a
role in in intracellular defence. IIGP is predominantly
associated with the Golgi apparatus and also localises
to the endoplasmic reticulum and exerts a distinct role
in IFN-induced intracellular membrane trafficking or
processing.
Length = 375
Score = 30.1 bits (68), Expect = 4.7
Identities = 18/50 (36%), Positives = 25/50 (50%), Gaps = 4/50 (8%)
Query: 576 LMRALRDMNLPKFVS--EDVVQMYETMLTRHSTMIVGPTGGGKSVVINAL 623
+ ALR+ NL K VS + +Q + + G +G GKS INAL
Sbjct: 8 IETALREGNLQKVVSIIKKAIQEISS--APLKIAVTGDSGNGKSSFINAL 55
>gnl|CDD|236781 PRK10869, PRK10869, recombination and repair protein; Provisional.
Length = 553
Score = 29.9 bits (68), Expect = 5.2
Identities = 11/18 (61%), Positives = 14/18 (77%)
Query: 606 TMIVGPTGGGKSVVINAL 623
T+I G TG GKS+ I+AL
Sbjct: 25 TVITGETGAGKSIAIDAL 42
>gnl|CDD|241308 cd10572, PH_RhoGEF3_XPLN, Rho guanine nucleotide exchange factor 3
Pleckstrin homology (PH) domain. RhoGEF3/XPLN, a Rho
family GEF, preferentially stimulates guanine nucleotide
exchange on RhoA and RhoB, but not RhoC, RhoG, Rac1, or
Cdc42 in vitro. It also possesses transforming activity.
RhoGEF3/XPLN contains a tandem Dbl homology and PH
domain, but lacks homology with other known functional
domains or motifs. It is expressed in the brain,
skeletal muscle, heart, kidney, platelets, and
macrophage and neuronal cell lines. PH domains have
diverse functions, but in general are involved in
targeting proteins to the appropriate cellular location
or in the interaction with a binding partner. They share
little sequence conservation, but all have a common
fold, which is electrostatically polarized. Less than
10% of PH domains bind phosphoinositide phosphates
(PIPs) with high affinity and specificity. PH domains
are distinguished from other PIP-binding domains by
their specific high-affinity binding to PIPs with two
vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2
or PtdIns(3,4,5)P3 which results in targeting some PH
domain proteins to the plasma membrane. A few display
strong specificity in lipid binding. Any specificity is
usually determined by loop regions or insertions in the
N-terminus of the domain, which are not conserved across
all PH domains. PH domains are found in cellular
signaling proteins such as serine/threonine kinase,
tyrosine kinases, regulators of G-proteins, endocytotic
GTPases, adaptors, as well as cytoskeletal associated
molecules and in lipid associated enzymes.
Length = 143
Score = 28.8 bits (65), Expect = 5.3
Identities = 13/47 (27%), Positives = 24/47 (51%), Gaps = 4/47 (8%)
Query: 158 TKNDRKKFNT----VLIVDVHARDIIDNFVRDGSAVRGELTKNDRKK 200
T+N++ + + + D+ D+ D VR G + RG + ND+ K
Sbjct: 60 TRNEQLCYQVYRQPIPVQDLVLEDLPDGEVRLGGSFRGAFSNNDKAK 106
>gnl|CDD|182838 PRK10919, PRK10919, ATP-dependent DNA helicase Rep; Provisional.
Length = 672
Score = 30.2 bits (68), Expect = 5.3
Identities = 11/31 (35%), Positives = 16/31 (51%)
Query: 701 NSVMDDNKILTLANGERIRLLAHCQLLFEIH 731
N + + A GER R+ AHC L++ H
Sbjct: 144 NDLKTPAQAAAGAKGERDRIFAHCYGLYDAH 174
>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 = 29.2 bits (66), Expect = 6.1
Identities = 10/21 (47%), Positives = 15/21 (71%)
Query: 603 RHSTMIVGPTGGGKSVVINAL 623
R + +I G TG GK+ ++NAL
Sbjct: 25 RKNILISGGTGSGKTTLLNAL 45
>gnl|CDD|184214 PRK13657, PRK13657, cyclic beta-1,2-glucan ABC transporter;
Provisional.
Length = 588
Score = 29.9 bits (68), Expect = 6.2
Identities = 12/16 (75%), Positives = 13/16 (81%)
Query: 608 IVGPTGGGKSVVINAL 623
IVGPTG GKS +IN L
Sbjct: 366 IVGPTGAGKSTLINLL 381
>gnl|CDD|234478 TIGR04121, DEXH_lig_assoc, DEXH box helicase, DNA
ligase-associated. Members of this protein family are
DEAD/DEAH box helicases found associated with a
bacterial ATP-dependent DNA ligase, part of a four-gene
system that occurs in about 12 % of prokaryotic
reference genomes. The actual motif in this family is
DE[VILW]H.
Length = 803
Score = 29.8 bits (68), Expect = 6.8
Identities = 8/22 (36%), Positives = 13/22 (59%)
Query: 595 QMYETMLTRHSTMIVGPTGGGK 616
+M+ L S +++ PTG GK
Sbjct: 20 EMWAAALEGRSGLLIAPTGSGK 41
>gnl|CDD|206743 cd11383, YfjP, YfjP GTPase. The Era (E. coli Ras-like
protein)-like YfjP subfamily includes several
uncharacterized bacterial GTPases that are similar to
Era. They generally show sequence conservation in the
region between the Walker A and B motifs (G1 and G3 box
motifs), to the exclusion of other GTPases. Era is
characterized by a distinct derivative of the KH domain
(the pseudo-KH domain) which is located C-terminal to
the GTPase domain.
Length = 140
Score = 28.5 bits (64), Expect = 7.0
Identities = 10/21 (47%), Positives = 13/21 (61%)
Query: 608 IVGPTGGGKSVVINALVKTST 628
++G TG GKS + NAL T
Sbjct: 2 LMGKTGAGKSSLCNALFGTEV 22
>gnl|CDD|240339 PTZ00265, PTZ00265, multidrug resistance protein (mdr1); Provisional.
Length = 1466
Score = 29.6 bits (66), Expect = 7.2
Identities = 16/50 (32%), Positives = 31/50 (62%), Gaps = 5/50 (10%)
Query: 580 LRDMNLPKFVSEDVVQMYETML----TRHSTMIVGPTGGGKSVVINALVK 625
+ D+N +++S V +Y+ + ++ +T IVG TG GKS V++ L++
Sbjct: 1168 IMDVNF-RYISRPNVPIYKDLTFSCDSKKTTAIVGETGSGKSTVMSLLMR 1216
>gnl|CDD|152038 pfam11602, NTPase_P4, ATPase P4 of dsRNA bacteriophage phi-12. P4
is a packaging motor which is involved in the packaging
of phi-12 genome into preformed capsids using ATP. P4 is
located at the vertices of the icosahedral capsid. ATP
drives RNA translocation through cooperative
conformational changes.
Length = 320
Score = 29.2 bits (65), Expect = 7.4
Identities = 14/45 (31%), Positives = 19/45 (42%), Gaps = 1/45 (2%)
Query: 606 TMIVGPTGGGKSVVINALVKTSTV-LGYPARTYTLNPKAVSVIEL 649
++ G TG GKS +N T+ G P Y V V +L
Sbjct: 114 VIVTGKTGSGKSEALNGKDPDVTIRWGEPLEGYDTLDFNVFVDDL 158
>gnl|CDD|206649 cd01850, CDC_Septin, CDC/Septin GTPase family. Septins are a
conserved family of GTP-binding proteins associated with
diverse processes in dividing and non-dividing cells.
They were first discovered in the budding yeast S.
cerevisiae as a set of genes (CDC3, CDC10, CDC11 and
CDC12) required for normal bud morphology. Septins are
also present in metazoan cells, where they are required
for cytokinesis in some systems, and implicated in a
variety of other processes involving organization of the
cell cortex and exocytosis. In humans, 12 septin genes
generate dozens of polypeptides, many of which comprise
heterooligomeric complexes. Since septin mutants are
commonly defective in cytokinesis and formation of the
neck formation of the neck filaments/septin rings,
septins have been considered to be the primary
constituents of the neck filaments. Septins belong to
the GTPase superfamily for their conserved GTPase motifs
and enzymatic activities.
Length = 275
Score = 29.1 bits (66), Expect = 7.5
Identities = 11/21 (52%), Positives = 13/21 (61%)
Query: 607 MIVGPTGGGKSVVINALVKTS 627
M+VG +G GKS IN L T
Sbjct: 8 MVVGESGLGKSTFINTLFGTK 28
>gnl|CDD|236870 PRK11174, PRK11174, cysteine/glutathione ABC transporter
membrane/ATP-binding component; Reviewed.
Length = 588
Score = 29.4 bits (67), Expect = 8.2
Identities = 9/20 (45%), Positives = 14/20 (70%)
Query: 604 HSTMIVGPTGGGKSVVINAL 623
+VGP+G GK+ ++NAL
Sbjct: 377 QRIALVGPSGAGKTSLLNAL 396
>gnl|CDD|237040 PRK12289, PRK12289, GTPase RsgA; Reviewed.
Length = 352
Score = 29.2 bits (66), Expect = 8.3
Identities = 11/24 (45%), Positives = 16/24 (66%)
Query: 601 LTRHSTMIVGPTGGGKSVVINALV 624
L T++ GP+G GKS +IN L+
Sbjct: 170 LRNKITVVAGPSGVGKSSLINRLI 193
>gnl|CDD|232857 TIGR00176, mobB, molybdopterin-guanine dinucleotide biosynthesis
protein MobB. This molybdenum cofactor biosynthesis
enzyme is similar to the urease accessory protein UreG
and to the hydrogenase accessory protein HypB, both GTP
hydrolases involved in loading nickel into the
metallocenters of their respective target enzymes
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Molybdopterin].
Length = 155
Score = 28.5 bits (64), Expect = 8.6
Identities = 12/26 (46%), Positives = 14/26 (53%)
Query: 608 IVGPTGGGKSVVINALVKTSTVLGYP 633
IVGP GK+ +I LVK GY
Sbjct: 4 IVGPKNSGKTTLIERLVKALKARGYR 29
>gnl|CDD|213207 cd03240, ABC_Rad50, ATP-binding cassette domain of Rad50. The
catalytic domains of Rad50 are similar to the
ATP-binding cassette of ABC transporters, but are not
associated with membrane-spanning domains. The conserved
ATP-binding motifs common to Rad50 and the ABC
transporter family include the Walker A and Walker B
motifs, the Q loop, a histidine residue in the switch
region, a D-loop, and a conserved LSGG sequence. This
conserved sequence, LSGG, is the most specific and
characteristic motif of this family and is thus known as
the ABC signature sequence.
Length = 204
Score = 28.7 bits (65), Expect = 9.4
Identities = 10/18 (55%), Positives = 13/18 (72%)
Query: 606 TMIVGPTGGGKSVVINAL 623
T+IVG G GK+ +I AL
Sbjct: 25 TLIVGQNGAGKTTIIEAL 42
>gnl|CDD|222160 pfam13476, AAA_23, AAA domain.
Length = 204
Score = 28.7 bits (64), Expect = 9.5
Identities = 8/23 (34%), Positives = 16/23 (69%)
Query: 601 LTRHSTMIVGPTGGGKSVVINAL 623
++ T+I GP G GK+ +++A+
Sbjct: 17 FSKGLTLIYGPNGSGKTTILDAI 39
>gnl|CDD|233994 TIGR02746, TraC-F-type, type-IV secretion system protein TraC. The
protein family described here is common among the F, P
and I-like type IV secretion systems. Gene symbols
include TraC (F-type), TrbE/VirB4 (P-type) and TraU
(I-type). The protein conyains the Walker A and B motifs
and so is a putative nucleotide triphosphatase.
Length = 797
Score = 29.2 bits (66), Expect = 9.7
Identities = 8/24 (33%), Positives = 14/24 (58%)
Query: 601 LTRHSTMIVGPTGGGKSVVINALV 624
T ++ +VG +G GKS + L+
Sbjct: 428 STNYNIAVVGGSGAGKSFFMQELI 451
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 0.137 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: 38,196,455
Number of extensions: 3856465
Number of successful extensions: 3817
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3812
Number of HSP's successfully gapped: 94
Length of query: 741
Length of database: 10,937,602
Length adjustment: 104
Effective length of query: 637
Effective length of database: 6,324,786
Effective search space: 4028888682
Effective search space used: 4028888682
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: 63 (28.5 bits)