RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12735
(233 letters)
>gnl|CDD|227570 COG5245, DYN1, Dynein, heavy chain [Cytoskeleton].
Length = 3164
Score = 51.9 bits (124), Expect = 9e-08
Identities = 37/141 (26%), Positives = 71/141 (50%), Gaps = 12/141 (8%)
Query: 63 GGKSVVINALVKTSTVLGYPARTYT---LNPKAVSVIELYGVLNPETRDWYDGLLSNIFR 119
G V + ++K + G LNP+ ++ E++G + T D+ D L R
Sbjct: 1831 GLLVVGGHGVLKGVLIRGACDAREFVCWLNPR--NMREIFGHRDELTGDFRDSLKVQDLR 1888
Query: 120 AVNKPLDPGSKERKYILFDGD-VDALWIENMNSVMDDNKILTLANG-ERIRLLAHCQLLF 177
G +E +F+ V++ ++E+ N ++D+N+ L L +G ERIR+ + + +F
Sbjct: 1889 RNIH----GGRE-CLFIFESIPVESSFLEDFNPLLDNNRFLCLFSGNERIRIPENLRFVF 1943
Query: 178 EVGDLQYASPATVSRAGMVYV 198
E L+ + AT++R +VY+
Sbjct: 1944 ESTSLEKDTEATLTRVFLVYM 1964
Score = 40.0 bits (93), Expect = 8e-04
Identities = 8/57 (14%), Positives = 18/57 (31%), Gaps = 10/57 (17%)
Query: 145 WIENMNSVMDDNKILTLANGERIRLLAHCQLLFEVGDLQYASPATVSRAGMVYVDPI 201
++E + + K+ + GE Q++ + V R + Y
Sbjct: 1253 YVEKTKAEVSSLKLELSSVGEG-------QVVVSNLG---SIGDKVGRCLVEYDSIS 1299
>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 = 38.4 bits (90), Expect = 6e-04
Identities = 31/150 (20%), Positives = 53/150 (35%), Gaps = 31/150 (20%)
Query: 56 MIVGPTGGGKSVV---INALVKTSTVLGYPARTYTLNPKAVSVIELYGVLNPETRD--WY 110
++VGP G GKS + + A + V Y + + +L G N + W
Sbjct: 3 LLVGPPGTGKSELAERLAAALSNRPVF------YVQLTRDTTEEDLKGRRNIDPGGASWV 56
Query: 111 DGLLSNIFRAVNKPLDPGSKERKYILFDGDVDAL---WIENMNSVMDDNKILTLANGERI 167
DG L R I +++ + ++ S++D+ ++L GE +
Sbjct: 57 DGPLVRAAR------------EGEIAVLDEINRANPDVLNSLLSLLDERRLLLPEGGELV 104
Query: 168 RLLAHCQLLFEVG-----DLQYASPATVSR 192
+ L L SPA SR
Sbjct: 105 KAAPDGFRLIATMNPLDRGLNELSPALRSR 134
>gnl|CDD|205733 pfam13555, AAA_29, P-loop containing region of AAA domain.
Length = 60
Score = 31.8 bits (73), Expect = 0.039
Identities = 15/44 (34%), Positives = 24/44 (54%), Gaps = 4/44 (9%)
Query: 49 MLTRHSTMIVGPTGGGKSVVINALVKTSTVLGYPARTYTLNPKA 92
+ T++ GP+G GKS +I+A+ T+L PA+ N A
Sbjct: 18 PIDPKGTLLTGPSGSGKSTLIDAI---QTLL-VPAKRVAFNKAA 57
>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 = 33.5 bits (76), Expect = 0.040
Identities = 20/109 (18%), Positives = 34/109 (31%), Gaps = 20/109 (18%)
Query: 51 TRHSTMIVGPTGGGKSVVINALVKTSTVLGYPARTYTLNPKAVSVIELYGVLNPETRDWY 110
+IVGP G GK+ + AL + L P VI ++ E
Sbjct: 1 PGEVILIVGPPGSGKTTLARALAR------------ELGPPGGGVI----YIDGEDILEE 44
Query: 111 DGLLSNIFRAVNKPLDPGSKERKYILFD----GDVDALWIENMNSVMDD 155
+ K + R + D L ++ + S++D
Sbjct: 45 VLDQLLLIIVGGKKASGSGELRLRLALALARKLKPDVLILDEITSLLDA 93
>gnl|CDD|237536 PRK13873, PRK13873, conjugal transfer ATPase TrbE; Provisional.
Length = 811
Score = 34.5 bits (80), Expect = 0.041
Identities = 10/18 (55%), Positives = 15/18 (83%)
Query: 55 TMIVGPTGGGKSVVINAL 72
T++VGPTG GKSV++ +
Sbjct: 444 TLVVGPTGAGKSVLLALM 461
>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 = 33.1 bits (76), Expect = 0.052
Identities = 9/20 (45%), Positives = 14/20 (70%)
Query: 53 HSTMIVGPTGGGKSVVINAL 72
T+I GP G GKS +++A+
Sbjct: 22 SLTIITGPNGSGKSTILDAI 41
>gnl|CDD|172418 PRK13898, PRK13898, type IV secretion system ATPase VirB4;
Provisional.
Length = 800
Score = 34.0 bits (78), Expect = 0.059
Identities = 11/18 (61%), Positives = 16/18 (88%)
Query: 55 TMIVGPTGGGKSVVINAL 72
T+I+GPTG GK+V++N L
Sbjct: 449 TLIIGPTGAGKTVLMNFL 466
>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 = 33.3 bits (77), Expect = 0.082
Identities = 10/25 (40%), Positives = 15/25 (60%), Gaps = 1/25 (4%)
Query: 51 TRHSTMIVGPTGGGKSVVINALVKT 75
T+H +IVG TG GK+ + L+
Sbjct: 15 TQH-ILIVGTTGTGKTQALRELLDQ 38
>gnl|CDD|234631 PRK00098, PRK00098, GTPase RsgA; Reviewed.
Length = 298
Score = 32.9 bits (76), Expect = 0.11
Identities = 14/36 (38%), Positives = 19/36 (52%), Gaps = 8/36 (22%)
Query: 53 HSTMIVGPTGGGKSVVINALV-----KT---STVLG 80
T++ G +G GKS ++NAL KT S LG
Sbjct: 165 KVTVLAGQSGVGKSTLLNALAPDLELKTGEISEALG 200
>gnl|CDD|225982 COG3451, VirB4, Type IV secretory pathway, VirB4 components
[Intracellular trafficking and secretion].
Length = 796
Score = 33.1 bits (76), Expect = 0.13
Identities = 11/25 (44%), Positives = 17/25 (68%), Gaps = 1/25 (4%)
Query: 48 TMLTRHSTMIVGPTGGGKSVVINAL 72
H T+I+GPTG GK+V+++ L
Sbjct: 433 GEDVGH-TLIIGPTGAGKTVLLSFL 456
>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 = 32.8 bits (75), Expect = 0.14
Identities = 9/21 (42%), Positives = 14/21 (66%)
Query: 53 HSTMIVGPTGGGKSVVINALV 73
+ +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 = 32.2 bits (74), Expect = 0.16
Identities = 11/18 (61%), Positives = 15/18 (83%)
Query: 57 IVGPTGGGKSVVINALVK 74
IVGPTG GK+ +IN L++
Sbjct: 34 IVGPTGAGKTTLINLLMR 51
>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 = 32.4 bits (74), Expect = 0.21
Identities = 9/21 (42%), Positives = 13/21 (61%)
Query: 47 ETMLTRHSTMIVGPTGGGKSV 67
+L ++V PTGGGKS+
Sbjct: 23 SHVLDGRDVLVVMPTGGGKSL 43
>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 = 31.5 bits (72), Expect = 0.28
Identities = 13/30 (43%), Positives = 19/30 (63%), Gaps = 3/30 (10%)
Query: 55 TMIVGPTGGGKSVVINALVKTSTVLGYPAR 84
+ 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 = 31.1 bits (71), Expect = 0.30
Identities = 14/48 (29%), Positives = 21/48 (43%), Gaps = 6/48 (12%)
Query: 53 HSTMIVGPTGGGKSVVINALVKTSTVLGYPARTYTLNPKAVSVIELYG 100
IVGP G GKS +++A+ VLG + L + + G
Sbjct: 23 SFNAIVGPNGSGKSNIVDAI---CFVLGG--KAAKLRRGS-LLFLAGG 64
>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 = 31.3 bits (72), Expect = 0.30
Identities = 10/18 (55%), Positives = 13/18 (72%)
Query: 55 TMIVGPTGGGKSVVINAL 72
IVGP G GKS +++AL
Sbjct: 34 VAIVGPVGSGKSSLLSAL 51
>gnl|CDD|218632 pfam05549, Allexi_40kDa, Allexivirus 40kDa protein.
Length = 271
Score = 31.3 bits (71), Expect = 0.35
Identities = 16/34 (47%), Positives = 20/34 (58%), Gaps = 3/34 (8%)
Query: 71 ALVKTSTVLGY--PARTYTLNPKAVSVIELYGVL 102
AL T +LG+ PAR Y L P + + ELYG L
Sbjct: 11 ALDATRNLLGHVPPAR-YNLPPTTLPLDELYGQL 43
>gnl|CDD|217051 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain. This domain
is found at the N terminus of SMC proteins. The SMC
(structural maintenance of chromosomes) superfamily
proteins have ATP-binding domains at the N- and
C-termini, and two extended coiled-coil domains
separated by a hinge in the middle. The eukaryotic SMC
proteins form two kind of heterodimers: the SMC1/SMC3
and the SMC2/SMC4 types. These heterodimers constitute
an essential part of higher order complexes, which are
involved in chromatin and DNA dynamics. This family
also includes the RecF and RecN proteins that are
involved in DNA metabolism and recombination.
Length = 1162
Score = 31.1 bits (70), Expect = 0.51
Identities = 13/29 (44%), Positives = 18/29 (62%), Gaps = 3/29 (10%)
Query: 55 TMIVGPTGGGKSVVINALVKTSTVLGYPA 83
T IVGP G GKS +++A+ VLG +
Sbjct: 26 TAIVGPNGSGKSNILDAI---LFVLGERS 51
>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication,
recombination, and repair].
Length = 908
Score = 30.9 bits (70), Expect = 0.60
Identities = 9/18 (50%), Positives = 14/18 (77%)
Query: 55 TMIVGPTGGGKSVVINAL 72
+IVGP G GKS +++A+
Sbjct: 28 FLIVGPNGAGKSSILDAI 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 = 30.7 bits (70), Expect = 0.60
Identities = 10/20 (50%), Positives = 14/20 (70%)
Query: 53 HSTMIVGPTGGGKSVVINAL 72
T+I GPTG GK+ ++N L
Sbjct: 435 GHTLIFGPTGSGKTTLLNFL 454
>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 = 29.9 bits (68), Expect = 0.62
Identities = 8/18 (44%), Positives = 12/18 (66%)
Query: 55 TMIVGPTGGGKSVVINAL 72
+VGP G GKS ++ A+
Sbjct: 28 VALVGPNGSGKSTLLRAI 45
>gnl|CDD|222160 pfam13476, AAA_23, AAA domain.
Length = 204
Score = 30.2 bits (68), Expect = 0.63
Identities = 8/23 (34%), Positives = 16/23 (69%)
Query: 50 LTRHSTMIVGPTGGGKSVVINAL 72
++ T+I GP G GK+ +++A+
Sbjct: 17 FSKGLTLIYGPNGSGKTTILDAI 39
>gnl|CDD|223786 COG0714, COG0714, MoxR-like ATPases [General function prediction
only].
Length = 329
Score = 30.5 bits (69), Expect = 0.66
Identities = 26/105 (24%), Positives = 40/105 (38%), Gaps = 11/105 (10%)
Query: 35 VPVQVDKVVQ-MYETMLTRHSTMIVGPTGGGKSVVINALVKTSTVLGYPARTYTLNPKAV 93
V V ++V++ +L ++ GP G GK+++ AL + LG P P +
Sbjct: 25 VVVGDEEVIELALLALLAGGHVLLEGPPGVGKTLLARAL---ARALGLPFVRIQCTPD-L 80
Query: 94 SVIELYGVLNPETRDWYDGLLSNIFRAVNKPLDPGSKERKYILFD 138
+L G L FR V PL R +L D
Sbjct: 81 LPSDLLGTYAYAALL----LEPGEFRFVPGPLFAA--VRVILLLD 119
>gnl|CDD|236781 PRK10869, PRK10869, recombination and repair protein;
Provisional.
Length = 553
Score = 30.7 bits (70), Expect = 0.68
Identities = 11/18 (61%), Positives = 14/18 (77%)
Query: 55 TMIVGPTGGGKSVVINAL 72
T+I G TG GKS+ I+AL
Sbjct: 25 TVITGETGAGKSIAIDAL 42
>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 = 30.4 bits (69), Expect = 0.73
Identities = 12/30 (40%), Positives = 16/30 (53%), Gaps = 1/30 (3%)
Query: 51 TRHSTMIVGPTGGGKSVVINALVKTSTVLG 80
H TMI+G TG GK+ I L+ + G
Sbjct: 42 EAH-TMIIGTTGTGKTTQIRELLASIRARG 70
>gnl|CDD|217416 pfam03193, DUF258, Protein of unknown function, DUF258.
Length = 161
Score = 29.4 bits (67), Expect = 0.86
Identities = 9/25 (36%), Positives = 18/25 (72%)
Query: 49 MLTRHSTMIVGPTGGGKSVVINALV 73
+L ++++ G +G GKS ++NAL+
Sbjct: 32 LLKGKTSVLAGQSGVGKSTLLNALL 56
>gnl|CDD|213834 TIGR03597, GTPase_YqeH, ribosome biogenesis GTPase YqeH. This
family describes YqeH, a member of a larger family of
GTPases involved in ribosome biogenesis. Like YqlF, it
shows a cyclical permutation relative to GTPases EngA
(in which the GTPase domain is duplicated), Era, and
others. Members of this protein family are found in a
relatively small number of bacterial species, including
Bacillus subtilis but not Escherichia coli [Protein
synthesis, Other].
Length = 360
Score = 30.3 bits (69), Expect = 0.86
Identities = 11/39 (28%), Positives = 21/39 (53%)
Query: 39 VDKVVQMYETMLTRHSTMIVGPTGGGKSVVINALVKTST 77
+D+++ + + +VG T GKS +IN L+K +
Sbjct: 141 IDELLDKIKKARNKKDVYVVGVTNVGKSSLINKLLKQNN 179
>gnl|CDD|184214 PRK13657, PRK13657, cyclic beta-1,2-glucan ABC transporter;
Provisional.
Length = 588
Score = 30.3 bits (69), Expect = 0.89
Identities = 12/16 (75%), Positives = 13/16 (81%)
Query: 57 IVGPTGGGKSVVINAL 72
IVGPTG GKS +IN L
Sbjct: 366 IVGPTGAGKSTLINLL 381
>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 = 29.5 bits (67), Expect = 1.1
Identities = 10/18 (55%), Positives = 13/18 (72%)
Query: 55 TMIVGPTGGGKSVVINAL 72
T+IVG G GK+ +I AL
Sbjct: 25 TLIVGQNGAGKTTIIEAL 42
>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 = 29.6 bits (67), Expect = 1.1
Identities = 10/21 (47%), Positives = 15/21 (71%)
Query: 52 RHSTMIVGPTGGGKSVVINAL 72
R + +I G TG GK+ ++NAL
Sbjct: 25 RKNILISGGTGSGKTTLLNAL 45
>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 = 1.2
Identities = 8/22 (36%), Positives = 13/22 (59%)
Query: 44 QMYETMLTRHSTMIVGPTGGGK 65
+M+ L S +++ PTG GK
Sbjct: 20 EMWAAALEGRSGLLIAPTGSGK 41
>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 = 29.4 bits (67), Expect = 1.3
Identities = 11/21 (52%), Positives = 13/21 (61%)
Query: 56 MIVGPTGGGKSVVINALVKTS 76
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 = 29.8 bits (68), Expect = 1.3
Identities = 9/20 (45%), Positives = 14/20 (70%)
Query: 53 HSTMIVGPTGGGKSVVINAL 72
+VGP+G GK+ ++NAL
Sbjct: 377 QRIALVGPSGAGKTSLLNAL 396
>gnl|CDD|222804 PHA00520, PHA00520, packaging NTPase P4.
Length = 330
Score = 29.5 bits (66), Expect = 1.3
Identities = 15/57 (26%), Positives = 27/57 (47%), Gaps = 8/57 (14%)
Query: 55 TMIVGPTGGGKSVVINAL-------VKTSTV-LGYPARTYTLNPKAVSVIELYGVLN 103
++VG TG GK+ ++NAL K + + G P Y + + + L +L+
Sbjct: 127 EVVVGGTGSGKTPLLNALAPDVGGGDKYAVIRWGEPLEGYDTDLHVFAALILAAMLD 183
>gnl|CDD|226124 COG3596, COG3596, Predicted GTPase [General function prediction
only].
Length = 296
Score = 29.4 bits (66), Expect = 1.4
Identities = 18/68 (26%), Positives = 35/68 (51%), Gaps = 7/68 (10%)
Query: 20 TAALETVLK--QDNYEMVPVQVDKVVQMYETMLTRH-STMIVGPTGGGKSVVINAL---- 72
+ +L VLK ++ ++ + ++M + + +++G TG GKS +INAL
Sbjct: 4 SDSLNNVLKGLLGLPSLLSERILEQLRMLQLTEKEPVNVLLMGATGAGKSSLINALFQGE 63
Query: 73 VKTSTVLG 80
VK + +G
Sbjct: 64 VKEVSKVG 71
>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and
chromosome partitioning].
Length = 1163
Score = 29.7 bits (67), Expect = 1.4
Identities = 10/18 (55%), Positives = 14/18 (77%)
Query: 55 TMIVGPTGGGKSVVINAL 72
T IVGP G GKS +++A+
Sbjct: 27 TAIVGPNGSGKSNIVDAI 44
>gnl|CDD|223588 COG0514, RecQ, Superfamily II DNA helicase [DNA replication,
recombination, and repair].
Length = 590
Score = 29.6 bits (67), Expect = 1.5
Identities = 14/36 (38%), Positives = 21/36 (58%), Gaps = 2/36 (5%)
Query: 46 YETMLTRHSTMIVGPTGGGKSVV--INALVKTSTVL 79
+ +L+ T++V PTGGGKS+ I AL+ L
Sbjct: 26 IDALLSGKDTLVVMPTGGGKSLCYQIPALLLEGLTL 61
>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 = 29.6 bits (67), Expect = 1.5
Identities = 8/24 (33%), Positives = 14/24 (58%)
Query: 50 LTRHSTMIVGPTGGGKSVVINALV 73
T ++ +VG +G GKS + L+
Sbjct: 428 STNYNIAVVGGSGAGKSFFMQELI 451
>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 = 1.5
Identities = 11/39 (28%), Positives = 15/39 (38%), Gaps = 3/39 (7%)
Query: 56 MIVGPTGGGKSVVINALVK---TSTVLGYPARTYTLNPK 91
+ GP G GKS + L + L Y+ NP
Sbjct: 2 WLYGPPGCGKSTLAKYLARALLKHLGLPKKDSVYSRNPD 40
>gnl|CDD|215920 pfam00437, T2SE, Type II/IV secretion system protein. This family
contains both type II and type IV pathway secretion
proteins from bacteria. VirB11 ATPase is a subunit of
the Agrobacterium tumefaciens transfer DNA (T-DNA)
transfer system, a type IV secretion pathway required
for delivery of T-DNA and effector proteins to plant
cells during infection.
Length = 273
Score = 29.1 bits (66), Expect = 1.7
Identities = 10/45 (22%), Positives = 20/45 (44%), Gaps = 1/45 (2%)
Query: 30 DNYEMVPVQVDKVVQMYETMLTRHSTMIV-GPTGGGKSVVINALV 73
D+ M + + + ++V G TG GK+ ++ AL+
Sbjct: 106 DDLGMTGAFDADIAEFLRQAVQARGNILVSGGTGSGKTTLLYALL 150
>gnl|CDD|222104 pfam13401, AAA_22, AAA domain.
Length = 124
Score = 28.4 bits (64), Expect = 1.7
Identities = 21/126 (16%), Positives = 38/126 (30%), Gaps = 25/126 (19%)
Query: 51 TRHSTMIVGPTGGGKSVVINALVKTSTVLGYPARTYTLNPKAVSVIELYGVLNPETRDWY 110
++ G +G GK+ ++ L + N + V V P
Sbjct: 3 GAGIGVLTGESGSGKTTLLRRLARQ-----------LPNRRVVYVE------APSLGTP- 44
Query: 111 DGLLSNIFRAVNKPLDPGSKER-----KYILFDGDVDALWIENMNSVMDD--NKILTLAN 163
LL I RA+ PL G+ L L I+ + + ++ L +
Sbjct: 45 KDLLRKILRALGLPLSGGTTAELLEAILDALKRRGRPLLIIDEAQHLSLEALEELRDLYD 104
Query: 164 GERIRL 169
+
Sbjct: 105 LSEKGI 110
>gnl|CDD|234005 TIGR02774, rexB_recomb, ATP-dependent nuclease subunit B. DNA
repair is accomplished by several different systems in
prokaryotes. Recombinational repair of double-stranded
DNA breaks involves the RecBCD pathway in some lineages,
and AddAB (also called RecAB) in other. The AddA protein
is conserved between the firmicutes and the
alphaproteobacteria, while the partner protein is not.
The partner may be designated AddB, as in Bacillus and
in alphaproteobacteria, or RexB as in Streptococcus and
Lactococcus. Note, however, that RexB proteins lack an
N-terminal GxxGxGK[ST] ATP-binding motif found in
Bacillus subtilis and related species, and this
difference may be important; this model represents
specifically RexB proteins as found in Streptococcus and
Lactococcus [DNA metabolism, DNA replication,
recombination, and repair].
Length = 1076
Score = 29.4 bits (66), Expect = 1.7
Identities = 12/37 (32%), Positives = 19/37 (51%), Gaps = 1/37 (2%)
Query: 12 SRVSYPEFTAALETVLKQDNYEMVPVQVDKV-VQMYE 47
++S +F A L + + Y VP VD V V+ Y+
Sbjct: 515 EKLSLDDFLALLHSGMSLSQYRTVPATVDVVTVKSYD 551
>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 = 28.7 bits (64), Expect = 1.7
Identities = 24/125 (19%), Positives = 43/125 (34%), Gaps = 21/125 (16%)
Query: 57 IVGPTGGGKSVVINALVKTSTVLGYPARTYTLNPKAVSVIELYGVLNPETRDWYDGLLSN 116
+ GP+G GK+ ++ L++ V NP L LL
Sbjct: 29 LTGPSGTGKTSLLRELLEGLLVAAGKCDQAERNPPYAFSQAL------------RELLRQ 76
Query: 117 IFRAVNKPLDPGSKERKYILFDGDVDAL--WIENMNSVMDDNKILTL-------ANGERI 167
+ R + L + L ++ L +E + ++ + L L A+ E +
Sbjct: 77 LLRELAAELLLLREALLAALGAELIEGLQDLVELLERLLARARPLVLVLDDLQWADEESL 136
Query: 168 RLLAH 172
LLA
Sbjct: 137 DLLAA 141
>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 = 1.8
Identities = 12/26 (46%), Positives = 14/26 (53%)
Query: 57 IVGPTGGGKSVVINALVKTSTVLGYP 82
IVGP GK+ +I LVK GY
Sbjct: 4 IVGPKNSGKTTLIERLVKALKARGYR 29
>gnl|CDD|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common
bacterial type. SMC (structural maintenance of
chromosomes) proteins bind DNA and act in organizing
and segregating chromosomes for partition. SMC proteins
are found in bacteria, archaea, and eukaryotes. This
family represents the SMC protein of most bacteria. The
smc gene is often associated with scpB (TIGR00281) and
scpA genes, where scp stands for segregation and
condensation protein. SMC was shown (in Caulobacter
crescentus) to be induced early in S phase but present
and bound to DNA throughout the cell cycle [Cellular
processes, Cell division, DNA metabolism,
Chromosome-associated proteins].
Length = 1179
Score = 29.6 bits (67), Expect = 1.8
Identities = 10/18 (55%), Positives = 14/18 (77%)
Query: 55 TMIVGPTGGGKSVVINAL 72
T IVGP G GKS +++A+
Sbjct: 26 TGIVGPNGCGKSNIVDAI 43
>gnl|CDD|237040 PRK12289, PRK12289, GTPase RsgA; Reviewed.
Length = 352
Score = 29.2 bits (66), Expect = 1.8
Identities = 11/24 (45%), Positives = 16/24 (66%)
Query: 50 LTRHSTMIVGPTGGGKSVVINALV 73
L T++ GP+G GKS +IN L+
Sbjct: 170 LRNKITVVAGPSGVGKSSLINRLI 193
>gnl|CDD|234719 PRK00300, gmk, guanylate kinase; Provisional.
Length = 205
Score = 28.9 bits (66), Expect = 1.9
Identities = 8/20 (40%), Positives = 15/20 (75%)
Query: 56 MIVGPTGGGKSVVINALVKT 75
++ GP+G GKS ++ AL++
Sbjct: 9 VLSGPSGAGKSTLVKALLER 28
>gnl|CDD|213245 cd03278, ABC_SMC_barmotin, ATP-binding cassette domain of
barmotin, a member of the SMC protein family. Barmotin
is a tight junction-associated protein expressed in rat
epithelial cells which is thought to have an important
regulatory role in tight junction barrier function.
Barmotin belongs to the SMC protein family. 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 = 197
Score = 28.6 bits (65), Expect = 2.0
Identities = 11/18 (61%), Positives = 14/18 (77%)
Query: 55 TMIVGPTGGGKSVVINAL 72
T IVGP G GKS +I+A+
Sbjct: 25 TAIVGPNGSGKSNIIDAI 42
>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 = 29.0 bits (65), Expect = 2.1
Identities = 18/56 (32%), Positives = 27/56 (48%), Gaps = 2/56 (3%)
Query: 17 PEFTAALETVLKQDNYEMVPVQVDKVVQMYETMLTRHSTMIVGPTGGGKSVVINAL 72
PE +ET L++ N + V + K +Q + + G +G GKS INAL
Sbjct: 2 PEVITLIETALREGNLQKVVSIIKKAIQEISS--APLKIAVTGDSGNGKSSFINAL 55
>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 = 28.5 bits (65), Expect = 2.1
Identities = 9/20 (45%), Positives = 14/20 (70%)
Query: 55 TMIVGPTGGGKSVVINALVK 74
IVGP+G GKS ++ L++
Sbjct: 31 VAIVGPSGSGKSTLLKLLLR 50
>gnl|CDD|224084 COG1162, COG1162, Predicted GTPases [General function prediction
only].
Length = 301
Score = 28.8 bits (65), Expect = 2.2
Identities = 11/24 (45%), Positives = 17/24 (70%)
Query: 50 LTRHSTMIVGPTGGGKSVVINALV 73
L T+++G +G GKS +INAL+
Sbjct: 162 LAGKITVLLGQSGVGKSTLINALL 185
>gnl|CDD|213215 cd03248, ABCC_TAP, ATP-binding cassette domain of the Transporter
Associated with Antigen Processing, subfamily C. TAP
(Transporter Associated with Antigen Processing) is
essential for peptide delivery from the cytosol into
the lumen of the endoplasmic reticulum (ER), where
these peptides are loaded on major histocompatibility
complex (MHC) I molecules. Loaded MHC I leave the ER
and display their antigenic cargo on the cell surface
to cytotoxic T cells. Subsequently, virus-infected or
malignantly transformed cells can be eliminated. TAP
belongs to the large family of ATP-binding cassette
(ABC) transporters, which translocate a vast variety of
solutes across membranes.
Length = 226
Score = 28.6 bits (64), Expect = 2.2
Identities = 17/58 (29%), Positives = 26/58 (44%), Gaps = 17/58 (29%)
Query: 15 SYPEFTAALETVLKQDNYEMVPVQVDKVVQMYETMLTRHSTMIVGPTGGGKSVVINAL 72
+YP L VL+ ++ + P +V T +VGP+G GKS V+ L
Sbjct: 20 AYPTRPDTL--VLQDVSFTLHPGEV---------------TALVGPSGSGKSTVVALL 60
>gnl|CDD|130260 TIGR01192, chvA, glucan exporter ATP-binding protein. This model
describes glucan exporter ATP binding protein in
bacteria. It belongs to the larger ABC transporter
superfamily with the characteristic ATP binding motif.
The In general, this protein is in some ways implicated
in osmoregulation and suggested to participate in the
export of glucan from the cytoplasm to periplasm. The
cyclic beta-1,2-glucan in the bactrerial periplasmic
space is suggested to confer the property of high
osmolority. It has also been demonstrated that mutants
in this loci have lost functions of virulence and
motility. It is unclear as to how virulence and
osmoadaptaion are related [Transport and binding
proteins, Carbohydrates, organic alcohols, and acids].
Length = 585
Score = 29.1 bits (65), Expect = 2.2
Identities = 11/16 (68%), Positives = 13/16 (81%)
Query: 57 IVGPTGGGKSVVINAL 72
IVGPTG GK+ +IN L
Sbjct: 366 IVGPTGAGKTTLINLL 381
>gnl|CDD|213242 cd03275, ABC_SMC1_euk, ATP-binding cassette domain of eukaryotic
SMC1 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 = 247
Score = 28.7 bits (65), Expect = 2.2
Identities = 13/26 (50%), Positives = 18/26 (69%), Gaps = 3/26 (11%)
Query: 55 TMIVGPTGGGKSVVINALVKTSTVLG 80
T I+GP G GKS +++A+ S VLG
Sbjct: 25 TCIIGPNGSGKSNLMDAI---SFVLG 47
>gnl|CDD|216584 pfam01580, FtsK_SpoIIIE, FtsK/SpoIIIE family. FtsK has extensive
sequence similarity to wide variety of proteins from
prokaryotes and plasmids, termed the FtsK/SpoIIIE
family. This domain contains a putative ATP binding
P-loop motif. It is found in the FtsK cell division
protein from E. coli and the stage III sporulation
protein E SpoIIIE, which has roles in regulation of
prespore specific gene expression in B. subtilis. A
mutation in FtsK causes a temperature sensitive block
in cell division and it is involved in peptidoglycan
synthesis or modification. The SpoIIIE protein is
implicated in intercellular chromosomal DNA transfer.
Length = 201
Score = 28.5 bits (64), Expect = 2.3
Identities = 9/20 (45%), Positives = 12/20 (60%)
Query: 55 TMIVGPTGGGKSVVINALVK 74
+I G TG GKS +N L+
Sbjct: 41 LLIAGATGSGKSTFLNTLIL 60
>gnl|CDD|221983 pfam13207, AAA_17, AAA domain.
Length = 114
Score = 27.6 bits (61), Expect = 2.3
Identities = 11/27 (40%), Positives = 14/27 (51%), Gaps = 3/27 (11%)
Query: 56 MIVGPTGGGKSVVINALVKTSTVLGYP 82
+I GP G GKS + L + LG P
Sbjct: 3 LITGPPGSGKSTLAKKLAEK---LGIP 26
>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 = 28.1 bits (63), Expect = 2.4
Identities = 10/21 (47%), Positives = 13/21 (61%)
Query: 57 IVGPTGGGKSVVINALVKTST 77
++G TG GKS + NAL T
Sbjct: 2 LMGKTGAGKSSLCNALFGTEV 22
>gnl|CDD|201420 pfam00735, Septin, Septin. Members of this family include CDC3,
CDC10, CDC11 and CDC12/Septin. Members of this family
bind GTP. As regards the septins, these are
polypeptides of 30-65kDa with three characteristic
GTPase motifs (G-1, G-3 and G-4) that are similar to
those of the Ras family. The G-4 motif is strictly
conserved with a unique septin consensus of AKAD. Most
septins are thought to have at least one coiled-coil
region, which in some cases is necessary for
intermolecular interactions that allow septins to
polymerise to form rod-shaped complexes. In turn, these
are arranged into tandem arrays to form filaments. They
are multifunctional proteins, with roles in
cytokinesis, sporulation, germ cell development,
exocytosis and apoptosis.
Length = 280
Score = 28.4 bits (64), Expect = 2.6
Identities = 12/31 (38%), Positives = 16/31 (51%), Gaps = 3/31 (9%)
Query: 56 MIVGPTGGGKSVVINALVKTSTVLGYPARTY 86
M+VG +G GK+ +IN L T P R
Sbjct: 8 MVVGESGLGKTTLINTLFLTDL---IPERGI 35
>gnl|CDD|213218 cd03251, ABCC_MsbA, ATP-binding cassette domain of the bacterial
lipid flippase and related proteins, subfamily C. MsbA
is an essential ABC transporter, closely related to
eukaryotic MDR 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 = 234
Score = 28.4 bits (64), Expect = 2.6
Identities = 20/67 (29%), Positives = 34/67 (50%), Gaps = 11/67 (16%)
Query: 58 VGPTGGGKSVVINAL-----VKTSTVL--GYPARTYTLNPKAVSVIELYGVLNPETRDWY 110
VGP+G GKS ++N + V + +L G+ R YTL S+ G+++ + +
Sbjct: 34 VGPSGSGKSTLVNLIPRFYDVDSGRILIDGHDVRDYTLA----SLRRQIGLVSQDVFLFN 89
Query: 111 DGLLSNI 117
D + NI
Sbjct: 90 DTVAENI 96
>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 = 28.8 bits (64), Expect = 2.7
Identities = 14/45 (31%), Positives = 19/45 (42%), Gaps = 1/45 (2%)
Query: 55 TMIVGPTGGGKSVVINALVKTSTV-LGYPARTYTLNPKAVSVIEL 98
++ G TG GKS +N T+ G P Y V V +L
Sbjct: 114 VIVTGKTGSGKSEALNGKDPDVTIRWGEPLEGYDTLDFNVFVDDL 158
>gnl|CDD|183656 PRK12656, PRK12656, fructose-6-phosphate aldolase; Reviewed.
Length = 222
Score = 28.6 bits (64), Expect = 2.7
Identities = 8/24 (33%), Positives = 14/24 (58%)
Query: 207 PYWTRWVNLNVKADEELRELLNGI 230
PY+ R NLN+ ++ + +L I
Sbjct: 132 PYYNRMENLNIDSNAVIGQLAEAI 155
>gnl|CDD|99707 cd00009, AAA, The AAA+ (ATPases Associated with a wide variety of
cellular Activities) superfamily represents an ancient
group of ATPases belonging to the ASCE (for additional
strand, catalytic E) division of the P-loop NTPase
fold. The ASCE division also includes ABC, RecA-like,
VirD4-like, PilT-like, and SF1/2 helicases. Members of
the AAA+ ATPases function as molecular chaperons,
ATPase subunits of proteases, helicases, or
nucleic-acid stimulated ATPases. The AAA+ proteins
contain several distinct features in addition to the
conserved alpha-beta-alpha core domain structure and
the Walker A and B motifs of the P-loop NTPases.
Length = 151
Score = 27.9 bits (62), Expect = 2.7
Identities = 8/27 (29%), Positives = 13/27 (48%)
Query: 56 MIVGPTGGGKSVVINALVKTSTVLGYP 82
++ GP G GK+ + A+ G P
Sbjct: 23 LLYGPPGTGKTTLARAIANELFRPGAP 49
>gnl|CDD|206669 cd01882, BMS1, Bms1, an essential GTPase, promotes assembly of
preribosomal RNA processing complexes. Bms1 is an
essential, evolutionarily conserved, nucleolar protein.
Its depletion interferes with processing of the 35S
pre-rRNA at sites A0, A1, and A2, and the formation of
40S subunits. Bms1, the putative endonuclease Rc11, and
the essential U3 small nucleolar RNA form a stable
subcomplex that is believed to control an early step in
the formation of the 40S subumit. The C-terminal domain
of Bms1 contains a GTPase-activating protein (GAP) that
functions intramolecularly. It is believed that Rc11
activates Bms1 by acting as a guanine-nucleotide
exchange factor (GEF) to promote GDP/GTP exchange, and
that activated (GTP-bound) Bms1 delivers Rc11 to the
preribosomes.
Length = 231
Score = 28.5 bits (64), Expect = 2.9
Identities = 11/21 (52%), Positives = 15/21 (71%)
Query: 57 IVGPTGGGKSVVINALVKTST 77
+VGP G GKS +I +L+K T
Sbjct: 44 VVGPPGVGKSTLIRSLIKRYT 64
>gnl|CDD|213788 TIGR03263, guanyl_kin, guanylate kinase. Members of this family
are the enzyme guanylate kinase, also called GMP
kinase. This enzyme transfers a phosphate from ATP to
GMP, yielding ADP and GDP [Purines, pyrimidines,
nucleosides, and nucleotides, Nucleotide and nucleoside
interconversions].
Length = 179
Score = 28.2 bits (64), Expect = 3.0
Identities = 10/26 (38%), Positives = 17/26 (65%)
Query: 56 MIVGPTGGGKSVVINALVKTSTVLGY 81
+I GP+G GKS ++ AL++ L +
Sbjct: 4 VISGPSGAGKSTLVKALLEEDPNLKF 29
>gnl|CDD|213244 cd03277, ABC_SMC5_euk, ATP-binding cassette domain of eukaryotic
SMC5 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 = 213
Score = 28.3 bits (64), Expect = 3.0
Identities = 9/18 (50%), Positives = 13/18 (72%)
Query: 56 MIVGPTGGGKSVVINALV 73
MI+GP G GKS ++ A+
Sbjct: 27 MIIGPNGSGKSSIVCAIC 44
>gnl|CDD|163495 TIGR03783, Bac_Flav_CT_G, Bacteroides conjugation system ATPase,
TraG family. Members of this family include the
predicted ATPase, TraG, encoded by transfer region genes
of conjugative transposons of Bacteroides, such as
CTnDOT, found on the main chromosome. Members also
include TraG homologs borne on plasmids in Bacteroides.
The protein family is related to the conjugative
transfer system ATPase VirB4 [Cellular processes, DNA
transformation].
Length = 829
Score = 28.6 bits (64), Expect = 3.1
Identities = 14/40 (35%), Positives = 23/40 (57%), Gaps = 1/40 (2%)
Query: 36 PVQVD-KVVQMYETMLTRHSTMIVGPTGGGKSVVINALVK 74
P+ +D + M ++T + I+GP+G GKS N LV+
Sbjct: 421 PLHLDISDLPMKRGIITNRNKFILGPSGSGKSFFTNHLVR 460
>gnl|CDD|222878 PHA02562, 46, endonuclease subunit; Provisional.
Length = 562
Score = 28.4 bits (64), Expect = 3.4
Identities = 13/31 (41%), Positives = 17/31 (54%), Gaps = 2/31 (6%)
Query: 54 STMIVGPTGGGKSVVINALVKTSTVLGYPAR 84
T+I G G GKS ++ AL T + G P R
Sbjct: 29 KTLITGKNGAGKSTMLEAL--TFALFGKPFR 57
>gnl|CDD|213180 cd03213, ABCG_EPDR, Eye pigment and drug resistance transporter
subfamily G of the ATP-binding cassette superfamily.
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 = 27.9 bits (63), Expect = 3.5
Identities = 11/18 (61%), Positives = 15/18 (83%)
Query: 55 TMIVGPTGGGKSVVINAL 72
T I+GP+G GKS ++NAL
Sbjct: 38 TAIMGPSGAGKSTLLNAL 55
>gnl|CDD|217424 pfam03205, MobB, Molybdopterin guanine dinucleotide synthesis
protein B. This protein contains a P-loop.
Length = 126
Score = 27.4 bits (61), Expect = 3.5
Identities = 9/27 (33%), Positives = 14/27 (51%)
Query: 56 MIVGPTGGGKSVVINALVKTSTVLGYP 82
++VGP GK+ +I L+ GY
Sbjct: 4 LVVGPKDSGKTTLIRKLLNYLKRRGYR 30
>gnl|CDD|223989 COG1061, SSL2, DNA or RNA helicases of superfamily II
[Transcription / DNA replication, recombination, and
repair].
Length = 442
Score = 28.2 bits (63), Expect = 3.9
Identities = 9/20 (45%), Positives = 12/20 (60%)
Query: 56 MIVGPTGGGKSVVINALVKT 75
+IV PTG GK+VV +
Sbjct: 59 VIVLPTGAGKTVVAAEAIAE 78
>gnl|CDD|206747 cd01854, YjeQ_EngC, Ribosomal interacting GTPase YjeQ/EngC, a
circularly permuted subfamily of the Ras GTPases. YjeQ
(YloQ in Bacillus subtilis) is a ribosomal small
subunit-dependent GTPase; hence also known as RsgA. YjeQ
is a late-stage ribosomal biogenesis factor involved in
the 30S subunit maturation, and it represents a protein
family whose members are broadly conserved in bacteria
and have been shown to be essential to the growth of E.
coli and B. subtilis. Proteins of the YjeQ family
contain all sequence motifs typical of the vast class of
P-loop-containing GTPases, but show a circular
permutation, with a G4-G1-G3 pattern of motifs as
opposed to the regular G1-G3-G4 pattern seen in most
GTPases. All YjeQ family proteins display a unique
domain architecture, which includes an N-terminal
OB-fold RNA-binding domain, the central permuted GTPase
domain, and a zinc knuckle-like C-terminal cysteine
domain.
Length = 211
Score = 27.7 bits (63), Expect = 4.1
Identities = 10/24 (41%), Positives = 18/24 (75%)
Query: 50 LTRHSTMIVGPTGGGKSVVINALV 73
L ++++VG +G GKS ++NAL+
Sbjct: 83 LKGKTSVLVGQSGVGKSTLLNALL 106
>gnl|CDD|233209 TIGR00958, 3a01208, Conjugate Transporter-2 (CT2) Family protein.
[Transport and binding proteins, Other].
Length = 711
Score = 28.2 bits (63), Expect = 4.3
Identities = 9/19 (47%), Positives = 11/19 (57%)
Query: 54 STMIVGPTGGGKSVVINAL 72
+VGP+G GKS V L
Sbjct: 509 VVALVGPSGSGKSTVAALL 527
>gnl|CDD|222258 pfam13604, AAA_30, AAA 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. There is a Walker A and
Walker B.
Length = 195
Score = 27.5 bits (62), Expect = 4.5
Identities = 11/41 (26%), Positives = 16/41 (39%)
Query: 57 IVGPTGGGKSVVINALVKTSTVLGYPARTYTLNPKAVSVIE 97
+ GP G GK+ + A + GY KA V+
Sbjct: 23 VQGPAGTGKTTSLKAAREAWEAAGYRVIGLAPTGKAAKVLG 63
>gnl|CDD|240339 PTZ00265, PTZ00265, multidrug resistance protein (mdr1); Provisional.
Length = 1466
Score = 28.1 bits (62), Expect = 4.6
Identities = 11/24 (45%), Positives = 18/24 (75%)
Query: 51 TRHSTMIVGPTGGGKSVVINALVK 74
++ +T IVG TG GKS V++ L++
Sbjct: 1193 SKKTTAIVGETGSGKSTVMSLLMR 1216
>gnl|CDD|129547 TIGR00455, apsK, adenylylsulfate kinase (apsK). This protein,
adenylylsulfate kinase, is often found as a fusion
protein with sulfate adenylyltransferase. Important
residue (active site in E.coli) is residue 100 of the
seed alignment [Central intermediary metabolism, Sulfur
metabolism].
Length = 184
Score = 27.4 bits (61), Expect = 4.7
Identities = 14/33 (42%), Positives = 18/33 (54%), Gaps = 2/33 (6%)
Query: 57 IVGPTGGGKSVVINALVKTSTVLGYPARTYTLN 89
+ G +G GKS + NAL K GY R Y L+
Sbjct: 23 LTGLSGSGKSTIANALEKKLESKGY--RVYVLD 53
>gnl|CDD|215832 pfam00270, DEAD, DEAD/DEAH box helicase. Members of this family
include the DEAD and DEAH box helicases. Helicases are
involved in unwinding nucleic acids. The DEAD box
helicases are involved in various aspects of RNA
metabolism, including nuclear transcription, pre mRNA
splicing, ribosome biogenesis, nucleocytoplasmic
transport, translation, RNA decay and organellar gene
expression.
Length = 169
Score = 27.2 bits (61), Expect = 5.0
Identities = 7/25 (28%), Positives = 13/25 (52%)
Query: 44 QMYETMLTRHSTMIVGPTGGGKSVV 68
Q +L+ ++ PTG GK++
Sbjct: 6 QAIPAILSGKDVLVQAPTGSGKTLA 30
>gnl|CDD|234011 TIGR02782, TrbB_P, P-type conjugative transfer ATPase TrbB. The
TrbB protein is found in the trb locus of Agrobacterium
Ti plasmids where it is involved in the type IV
secretion system for plasmid conjugative transfer. TrbB
is a homolog of the vir system VirB11 ATPase , and the
Flp pilus sytem ATPase TadA [Cellular processes,
Conjugation].
Length = 299
Score = 27.8 bits (62), Expect = 5.1
Identities = 15/40 (37%), Positives = 23/40 (57%), Gaps = 3/40 (7%)
Query: 34 MVPVQVDKVVQMYETMLTRHSTMIVGPTGGGKSVVINALV 73
M Q D + E +L R + ++VG TG GK+ + NAL+
Sbjct: 117 MTAAQRDVLR---EAVLARKNILVVGGTGSGKTTLANALL 153
>gnl|CDD|234033 TIGR02857, CydD, thiol reductant ABC exporter, CydD 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. Unfortunately, the gene symbol
nomenclature adopted based on this operon in B. subtilis
assigns cydC to the third gene in the operon where this
gene is actually homologous to the E. coli cydD gene. We
have chosen to name all homologs in this family in
accordance with the precedence of publication of the E.
coli name, CydD.
Length = 529
Score = 28.0 bits (63), Expect = 5.1
Identities = 9/18 (50%), Positives = 13/18 (72%)
Query: 55 TMIVGPTGGGKSVVINAL 72
+VGP+G GKS ++N L
Sbjct: 351 VALVGPSGAGKSTLLNLL 368
>gnl|CDD|184205 PRK13646, cbiO, cobalt transporter ATP-binding subunit;
Provisional.
Length = 286
Score = 27.4 bits (61), Expect = 5.5
Identities = 14/24 (58%), Positives = 17/24 (70%), Gaps = 3/24 (12%)
Query: 57 IVGPTGGGKSVVI---NALVKTST 77
IVG TG GKS +I NAL+K +T
Sbjct: 38 IVGQTGSGKSTLIQNINALLKPTT 61
>gnl|CDD|233758 TIGR02169, SMC_prok_A, chromosome segregation protein SMC,
primarily archaeal type. SMC (structural maintenance
of chromosomes) proteins bind DNA and act in organizing
and segregating chromosomes for partition. SMC proteins
are found in bacteria, archaea, and eukaryotes. It is
found in a single copy and is homodimeric in
prokaryotes, but six paralogs (excluded from this
family) are found in eukarotes, where SMC proteins are
heterodimeric. This family represents the SMC protein
of archaea and a few bacteria (Aquifex, Synechocystis,
etc); the SMC of other bacteria is described by
TIGR02168. The N- and C-terminal domains of this
protein are well conserved, but the central hinge
region is skewed in composition and highly divergent
[Cellular processes, Cell division, DNA metabolism,
Chromosome-associated proteins].
Length = 1164
Score = 28.1 bits (63), Expect = 5.5
Identities = 9/18 (50%), Positives = 13/18 (72%)
Query: 55 TMIVGPTGGGKSVVINAL 72
T+I GP G GKS + +A+
Sbjct: 26 TVISGPNGSGKSNIGDAI 43
>gnl|CDD|213216 cd03249, ABC_MTABC3_MDL1_MDL2, ATP-binding cassette domain of a
mitochondrial protein MTABC3 and related proteins.
MTABC3 (also known as ABCB6) is a mitochondrial
ATP-binding cassette protein involved in iron
homeostasis and one of four ABC transporters expressed
in the mitochondrial inner membrane, the other three
being MDL1(ABC7), MDL2, and ATM1. In fact, the yeast
MDL1 (multidrug resistance-like protein 1) and MDL2
(multidrug resistance-like protein 2) transporters are
also included in this CD. MDL1 is an ATP-dependent
permease that acts as a high-copy suppressor of ATM1
and is thought to have a role in resistance to
oxidative stress. Interestingly, subfamily B is more
closely related to the carboxyl-terminal component of
subfamily C than the two halves of ABCC molecules are
with one another.
Length = 238
Score = 27.5 bits (62), Expect = 5.6
Identities = 8/19 (42%), Positives = 13/19 (68%)
Query: 54 STMIVGPTGGGKSVVINAL 72
+ +VG +G GKS V++ L
Sbjct: 31 TVALVGSSGCGKSTVVSLL 49
>gnl|CDD|206646 cd00880, Era_like, E. coli Ras-like protein (Era)-like GTPase.
The Era (E. coli Ras-like protein)-like family includes
several distinct subfamilies (TrmE/ThdF, FeoB, YihA
(EngB), Era, and EngA/YfgK) that 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. TrmE is ubiquitous in bacteria and is
a widespread mitochondrial protein in eukaryotes, but
is absent from archaea. The yeast member of TrmE
family, MSS1, is involved in mitochondrial translation;
bacterial members are often present in
translation-related operons. FeoB represents an unusual
adaptation of GTPases for high-affinity iron (II)
transport. YihA (EngB) family of GTPases is typified by
the E. coli YihA, which is an essential protein
involved in cell division control. Era is characterized
by a distinct derivative of the KH domain (the
pseudo-KH domain) which is located C-terminal to the
GTPase domain. EngA and its orthologs are composed of
two GTPase domains and, since the sequences of the two
domains are more similar to each other than to other
GTPases, it is likely that an ancient gene duplication,
rather than a fusion of evolutionarily distinct
GTPases, gave rise to this family.
Length = 161
Score = 27.2 bits (61), Expect = 5.9
Identities = 8/18 (44%), Positives = 11/18 (61%)
Query: 57 IVGPTGGGKSVVINALVK 74
I G GKS ++NAL+
Sbjct: 2 IFGRPNVGKSSLLNALLG 19
>gnl|CDD|193561 cd08013, M20_ArgE_DapE_like3, M20 Peptidases with similarity to
acetylornithine deacetylases and
succinyl-diaminopimelate desuccinylases. Peptidase M20
family, Uncharacterized protein subfamily with
similarity to acetylornithine
deacetylase/succinyl-diaminopimelate desuccinylase
(ArgE/DapE) subfamily. This group includes the
hypothetical protein ygeY from Escherichia coli, a
putative deacetylase, but many in this subfamily are
classified as unassigned peptidases. ArgE/DapE enzymes
catalyze analogous reactions and share a common
activator, the metal ion (usually Co2+ or Zn2+). ArgE
catalyzes a broad range of substrates, including
N-acetylornithine, alpha-N-acetylmethionine and
alpha-N-formylmethionine, while DapE catalyzes the
hydrolysis of N-succinyl-L,L-diaminopimelate (L,L-SDAP)
to L,L-diaminopimelate and succinate. Proteins in this
subfamily are mostly fungal and bacterial, and have
been inferred by homology as being related to both ArgE
and DapE.
Length = 377
Score = 27.7 bits (62), Expect = 6.1
Identities = 9/22 (40%), Positives = 16/22 (72%)
Query: 61 TGGGKSVVINALVKTSTVLGYP 82
TGGG+S+++N + T ++ GY
Sbjct: 64 TGGGRSLMLNGHIDTVSLGGYE 85
>gnl|CDD|238026 cd00071, GMPK, Guanosine monophosphate kinase (GMPK, EC 2.7.4.8),
also known as guanylate kinase (GKase), catalyzes the
reversible phosphoryl transfer from adenosine
triphosphate (ATP) to guanosine monophosphate (GMP) to
yield adenosine diphosphate (ADP) and guanosine
diphosphate (GDP). It plays an essential role in the
biosynthesis of guanosine triphosphate (GTP). This
enzyme is also important for the activation of some
antiviral and anticancer agents, such as acyclovir,
ganciclovir, carbovir, and thiopurines.
Length = 137
Score = 26.7 bits (60), Expect = 6.1
Identities = 7/19 (36%), Positives = 14/19 (73%)
Query: 56 MIVGPTGGGKSVVINALVK 74
++ GP+G GKS ++ L++
Sbjct: 3 VLSGPSGVGKSTLLKRLLE 21
>gnl|CDD|234063 TIGR02928, TIGR02928, orc1/cdc6 family replication initiation
protein. Members of this protein family are found
exclusively in the archaea. This set of DNA binding
proteins shows homology to the origin recognition
complex subunit 1/cell division control protein 6
family in eukaryotes. Several members may be found in
genome and interact with each other [DNA metabolism,
DNA replication, recombination, and repair].
Length = 365
Score = 27.6 bits (62), Expect = 6.3
Identities = 8/19 (42%), Positives = 11/19 (57%)
Query: 56 MIVGPTGGGKSVVINALVK 74
I G TG GK+ V ++K
Sbjct: 44 FIYGKTGTGKTAVTKYVMK 62
>gnl|CDD|182838 PRK10919, PRK10919, ATP-dependent DNA helicase Rep; Provisional.
Length = 672
Score = 27.5 bits (61), Expect = 6.4
Identities = 10/29 (34%), Positives = 15/29 (51%)
Query: 150 NSVMDDNKILTLANGERIRLLAHCQLLFE 178
N + + A GER R+ AHC L++
Sbjct: 144 NDLKTPAQAAAGAKGERDRIFAHCYGLYD 172
>gnl|CDD|227321 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 = 27.6 bits (62), Expect = 6.4
Identities = 9/18 (50%), Positives = 13/18 (72%)
Query: 55 TMIVGPTGGGKSVVINAL 72
T +VG +G GKS ++N L
Sbjct: 350 TALVGASGAGKSTLLNLL 367
>gnl|CDD|223571 COG0497, RecN, ATPase involved in DNA repair [DNA replication,
recombination, and repair].
Length = 557
Score = 27.6 bits (62), Expect = 6.8
Identities = 10/18 (55%), Positives = 15/18 (83%)
Query: 55 TMIVGPTGGGKSVVINAL 72
T++ G TG GKS++I+AL
Sbjct: 25 TVLTGETGAGKSIIIDAL 42
>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 = 27.2 bits (61), Expect = 6.8
Identities = 12/24 (50%), Positives = 16/24 (66%)
Query: 52 RHSTMIVGPTGGGKSVVINALVKT 75
R +VG T GKS +INAL+K+
Sbjct: 125 RGDVYVVGATNVGKSTLINALLKS 148
>gnl|CDD|237511 PRK13796, PRK13796, GTPase YqeH; Provisional.
Length = 365
Score = 27.5 bits (62), Expect = 7.1
Identities = 10/21 (47%), Positives = 14/21 (66%)
Query: 57 IVGPTGGGKSVVINALVKTST 77
+VG T GKS +IN ++K T
Sbjct: 165 VVGVTNVGKSTLINRIIKEIT 185
>gnl|CDD|129694 TIGR00606, rad50, rad50. All proteins in this family for which
functions are known are involvedin recombination,
recombinational repair, and/or non-homologous end
joining.They are components of an exonuclease complex
with MRE11 homologs. This family is distantly related
to the SbcC family of bacterial proteins.This family is
based on the phylogenomic analysis of JA Eisen (1999,
Ph.D. Thesis, Stanford University).
Length = 1311
Score = 27.7 bits (61), Expect = 7.3
Identities = 9/18 (50%), Positives = 13/18 (72%)
Query: 55 TMIVGPTGGGKSVVINAL 72
T++VGP G GK+ +I L
Sbjct: 31 TILVGPNGAGKTTIIECL 48
>gnl|CDD|184590 PRK14249, PRK14249, phosphate ABC transporter ATP-binding
protein; Provisional.
Length = 251
Score = 27.3 bits (60), Expect = 7.3
Identities = 11/28 (39%), Positives = 19/28 (67%)
Query: 52 RHSTMIVGPTGGGKSVVINALVKTSTVL 79
R T I+GP+G GKS ++ AL + + ++
Sbjct: 30 RQITAIIGPSGCGKSTLLRALNRMNDIV 57
>gnl|CDD|227519 COG5192, BMS1, GTP-binding protein required for 40S ribosome
biogenesis [Translation, ribosomal structure and
biogenesis].
Length = 1077
Score = 27.4 bits (60), Expect = 7.5
Identities = 11/21 (52%), Positives = 15/21 (71%)
Query: 57 IVGPTGGGKSVVINALVKTST 77
+VGP G GKS +I +LV+ T
Sbjct: 74 VVGPPGTGKSTLIRSLVRRFT 94
>gnl|CDD|224047 COG1122, CbiO, ABC-type cobalt transport system, ATPase component
[Inorganic ion transport and metabolism].
Length = 235
Score = 27.2 bits (61), Expect = 7.5
Identities = 7/18 (38%), Positives = 12/18 (66%)
Query: 55 TMIVGPTGGGKSVVINAL 72
+++GP G GKS ++ L
Sbjct: 33 VLLIGPNGSGKSTLLKLL 50
>gnl|CDD|227352 COG5019, CDC3, Septin family protein [Cell division and
chromosome partitioning / Cytoskeleton].
Length = 373
Score = 27.3 bits (61), Expect = 7.5
Identities = 11/21 (52%), Positives = 14/21 (66%)
Query: 56 MIVGPTGGGKSVVINALVKTS 76
M+VG +G GK+ IN L TS
Sbjct: 27 MVVGESGLGKTTFINTLFGTS 47
>gnl|CDD|131806 TIGR02759, TraD_Ftype, type IV conjugative transfer system coupling
protein TraD. The TraD protein performs an essential
coupling function in conjugative type IV secretion
systems. This protein sits at the inner membrane in
contact with the assembled pilus and its scaffold as
well as the relaxosome-plasmid DNA complex (through
TraM).
Length = 566
Score = 27.4 bits (61), Expect = 7.7
Identities = 13/31 (41%), Positives = 16/31 (51%)
Query: 56 MIVGPTGGGKSVVINALVKTSTVLGYPARTY 86
+I G TG GKSV I L++ G A Y
Sbjct: 180 LIHGTTGSGKSVAIRKLLRWIRQRGDRAIIY 210
>gnl|CDD|226592 COG4107, PhnK, ABC-type phosphonate transport system, ATPase
component [Inorganic ion transport and metabolism].
Length = 258
Score = 27.0 bits (60), Expect = 7.7
Identities = 16/58 (27%), Positives = 25/58 (43%), Gaps = 8/58 (13%)
Query: 57 IVGPTGGGKSVVINALVKTSTVLGYPARTYTLNPKAVSVIELYGVLNPETR-----DW 109
IVG +G GK+ ++ + S L A T T + +LY + E R +W
Sbjct: 37 IVGESGSGKTTLLKCI---SGRLTPDAGTVTYRMRDGQPRDLYTMSEAERRRLLRTEW 91
>gnl|CDD|213224 cd03257, ABC_NikE_OppD_transporters, ATP-binding cassette domain
of nickel/oligopeptides specific transporters. The ABC
transporter subfamily specific for the transport of
dipeptides, oligopeptides (OppD), and nickel (NikDE).
The NikABCDE system of E. coli belongs to this family
and is composed of the periplasmic binding protein
NikA, two integral membrane components (NikB and NikC),
and two ATPase (NikD and NikE). The NikABCDE
transporter is synthesized under anaerobic conditions
to meet the increased demand for nickel resulting from
hydrogenase synthesis. The molecular mechanism of
nickel uptake in many bacteria and most archaea is not
known. Many other members of this ABC family are also
involved in the uptake of dipeptides and oligopeptides.
The oligopeptide transport system (Opp) is a
five-component ABC transport composed of a
membrane-anchored substrate binding proteins (SRP),
OppA, two transmembrane proteins, OppB and OppC, and
two ATP-binding domains, OppD and OppF.
Length = 228
Score = 27.1 bits (61), Expect = 7.9
Identities = 7/18 (38%), Positives = 12/18 (66%)
Query: 57 IVGPTGGGKSVVINALVK 74
+VG +G GKS + A++
Sbjct: 36 LVGESGSGKSTLARAILG 53
>gnl|CDD|237652 PRK14275, PRK14275, phosphate ABC transporter ATP-binding
protein; Provisional.
Length = 286
Score = 27.2 bits (60), Expect = 8.0
Identities = 10/24 (41%), Positives = 18/24 (75%)
Query: 49 MLTRHSTMIVGPTGGGKSVVINAL 72
+L+++ T I+GP+G GKS + A+
Sbjct: 62 ILSKYVTAIIGPSGCGKSTFLRAI 85
>gnl|CDD|233065 TIGR00634, recN, DNA repair protein RecN. All proteins in this
family for which functions are known are ATP binding
proteins involved in the initiation of recombination
and recombinational repair [DNA metabolism, DNA
replication, recombination, and repair].
Length = 563
Score = 27.4 bits (61), Expect = 8.1
Identities = 10/18 (55%), Positives = 15/18 (83%)
Query: 55 TMIVGPTGGGKSVVINAL 72
T++ G TG GKS++I+AL
Sbjct: 25 TVLTGETGAGKSMIIDAL 42
>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 = 27.1 bits (61), Expect = 8.1
Identities = 10/16 (62%), Positives = 12/16 (75%)
Query: 57 IVGPTGGGKSVVINAL 72
IVG TG GKS ++ AL
Sbjct: 35 IVGRTGSGKSSLLLAL 50
>gnl|CDD|222036 pfam13304, AAA_21, AAA domain.
Length = 256
Score = 27.0 bits (59), Expect = 8.2
Identities = 9/19 (47%), Positives = 13/19 (68%)
Query: 54 STMIVGPTGGGKSVVINAL 72
+I+GP G GKS ++ AL
Sbjct: 1 LNVIIGPNGSGKSNLLKAL 19
>gnl|CDD|222000 pfam13238, AAA_18, AAA domain.
Length = 128
Score = 26.2 bits (58), Expect = 8.4
Identities = 19/84 (22%), Positives = 36/84 (42%), Gaps = 6/84 (7%)
Query: 56 MIVGPTGGGKSVVINALVKTSTVLGYPARTYTLNPKAVSVIELYGVLNPETRDWYDGLLS 115
+I G G GK+ + L + LG R L + V+EL + E++ + L+
Sbjct: 2 LITGTPGSGKTTLAKELAER---LGDVLR--DLAKENGLVLELDEEITDESKRLDEDKLA 56
Query: 116 NIFRAVNKPLDPGSKERKYILFDG 139
+ + K + E + ++ DG
Sbjct: 57 KLLDKLEK-IIEELAEGENVIIDG 79
>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 = 26.5 bits (59), Expect = 8.7
Identities = 7/20 (35%), Positives = 11/20 (55%)
Query: 55 TMIVGPTGGGKSVVINALVK 74
++VG G GKS L++
Sbjct: 2 ILMVGLPGSGKSTFARRLLR 21
>gnl|CDD|215595 PLN03130, PLN03130, ABC transporter C family member; Provisional.
Length = 1622
Score = 27.4 bits (61), Expect = 8.8
Identities = 11/16 (68%), Positives = 13/16 (81%)
Query: 57 IVGPTGGGKSVVINAL 72
IVG TG GKS ++NAL
Sbjct: 1270 IVGRTGAGKSSMLNAL 1285
>gnl|CDD|213243 cd03276, ABC_SMC6_euk, ATP-binding cassette domain of eukaryotic
SM6 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 = 198
Score = 26.8 bits (60), Expect = 8.8
Identities = 9/16 (56%), Positives = 11/16 (68%)
Query: 57 IVGPTGGGKSVVINAL 72
IVG G GKS ++ AL
Sbjct: 26 IVGNNGSGKSAILTAL 41
>gnl|CDD|223543 COG0467, RAD55, RecA-superfamily ATPases implicated in signal
transduction [Signal transduction mechanisms].
Length = 260
Score = 27.0 bits (60), Expect = 9.1
Identities = 13/85 (15%), Positives = 23/85 (27%)
Query: 52 RHSTMIVGPTGGGKSVVINALVKTSTVLGYPARTYTLNPKAVSVIELYGVLNPETRDWYD 111
+I GP G GK++ + G P + ++E + + +
Sbjct: 23 GSVVLITGPPGTGKTIFALQFLYEGAREGEPVLYVSTEESPEELLENARSFGWDLEVYIE 82
Query: 112 GLLSNIFRAVNKPLDPGSKERKYIL 136
I A S L
Sbjct: 83 KGKLAILDAFLSEKGLVSIVVGDPL 107
>gnl|CDD|182933 PRK11057, PRK11057, ATP-dependent DNA helicase RecQ; Provisional.
Length = 607
Score = 27.4 bits (61), Expect = 9.1
Identities = 14/38 (36%), Positives = 22/38 (57%), Gaps = 2/38 (5%)
Query: 44 QMYETMLTRHSTMIVGPTGGGKSVV--INALVKTSTVL 79
++ + +L+ ++V PTGGGKS+ I ALV L
Sbjct: 32 EIIDAVLSGRDCLVVMPTGGGKSLCYQIPALVLDGLTL 69
>gnl|CDD|213196 cd03229, ABC_Class3, ATP-binding cassette domain of the binding
protein-dependent transport systems. This class is
comprised of all BPD (Binding Protein Dependent)
systems that are largely represented in archaea and
eubacteria and are primarily involved in scavenging
solutes from the environment. 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 = 178
Score = 26.8 bits (60), Expect = 9.2
Identities = 6/18 (33%), Positives = 12/18 (66%)
Query: 57 IVGPTGGGKSVVINALVK 74
++GP+G GKS ++ +
Sbjct: 31 LLGPSGSGKSTLLRCIAG 48
>gnl|CDD|213208 cd03241, ABC_RecN, ATP-binding cassette domain of RecN. RecN
ATPase involved in DNA repair; similar to 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 including 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 = 276
Score = 26.8 bits (60), Expect = 9.4
Identities = 9/18 (50%), Positives = 15/18 (83%)
Query: 55 TMIVGPTGGGKSVVINAL 72
T++ G TG GKS++++AL
Sbjct: 24 TVLTGETGAGKSILLDAL 41
>gnl|CDD|218292 pfam04851, ResIII, Type III restriction enzyme, res subunit.
Length = 100
Score = 25.6 bits (57), Expect = 9.6
Identities = 13/44 (29%), Positives = 21/44 (47%), Gaps = 4/44 (9%)
Query: 31 NYEMVPVQVDKVVQMYETMLTRHSTMIVGPTGGGKSVVINALVK 74
E+ P Q + E +L + +IV TG GK++ AL+
Sbjct: 1 KLELRPYQE----EAIERLLEKKRGLIVMATGSGKTLTAAALIA 40
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
0.319 0.137 0.408
Gapped
Lambda K H
0.267 0.0740 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,025,679
Number of extensions: 1131487
Number of successful extensions: 1607
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1606
Number of HSP's successfully gapped: 156
Length of query: 233
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 139
Effective length of database: 6,768,326
Effective search space: 940797314
Effective search space used: 940797314
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 (21.7 bits)
S2: 57 (25.7 bits)