RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy832
(80 letters)
>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 = 79.2 bits (196), Expect = 9e-20
Identities = 27/60 (45%), Positives = 39/60 (65%), Gaps = 2/60 (3%)
Query: 1 MYRYKPSPFLLLDEIDAALDNINIWKTIQYIR--TVPKMNVIAVSLKPQFYFHSDILFGI 58
++ Y+P+PF +LDE+DAALDN N+ K YIR P I +SLK +F+ +D L G+
Sbjct: 172 IHSYQPAPFFVLDEVDAALDNTNVGKVASYIREQAGPNFQFIVISLKEEFFSKADALVGV 231
>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 = 60.8 bits (147), Expect = 1e-12
Identities = 23/60 (38%), Positives = 38/60 (63%), Gaps = 1/60 (1%)
Query: 1 MYRYKPSPFLLLDEIDAALDNINIWKTIQYIRTVPK-MNVIAVSLKPQFYFHSDILFGIT 59
+ +Y+P+PF LLDEIDAALD+ N+ + Y++ + K I +SL+ + +D L G+
Sbjct: 1095 IQKYRPAPFYLLDEIDAALDDQNVSRVANYLKELSKNAQFIVISLREEMLEKADRLVGVY 1154
>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 = 53.9 bits (130), Expect = 3e-10
Identities = 19/68 (27%), Positives = 34/68 (50%), Gaps = 17/68 (25%)
Query: 1 MYRYKPSPFLLLDEIDAALDNINIWKTIQYIRTVPKMNVIAVSLKPQFYF---------H 51
+++ KP+PF +LDE+DA LD+ N+ + ++ + S QF
Sbjct: 1106 IFKVKPAPFCILDEVDAPLDDANVERFANLLK---EF-----SKNTQFIVITHNKGTMEV 1157
Query: 52 SDILFGIT 59
+D L+G+T
Sbjct: 1158 ADQLYGVT 1165
>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and
chromosome partitioning].
Length = 1163
Score = 53.2 bits (128), Expect = 6e-10
Identities = 20/65 (30%), Positives = 39/65 (60%), Gaps = 1/65 (1%)
Query: 1 MYRYKPSPFLLLDEIDAALDNINIWKTIQYIRT-VPKMNVIAVSLKPQFYFHSDILFGIT 59
+ +Y+P+PF +LDE+DAALD+ N+ + + I+ + I ++ + +D L G+T
Sbjct: 1083 IQKYRPAPFYVLDEVDAALDDANVERVARLIKEMSKETQFIVITHRKGTMEAADRLVGVT 1142
Query: 60 LKMLG 64
++ G
Sbjct: 1143 MQEKG 1147
>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 = 48.2 bits (116), Expect = 2e-08
Identities = 19/61 (31%), Positives = 38/61 (62%), Gaps = 1/61 (1%)
Query: 1 MYRYKPSPFLLLDEIDAALDNINIWKTIQYIRT-VPKMNVIAVSLKPQFYFHSDILFGIT 59
++R +PSPF +LDE+DAALD+ N+ + + ++ + I ++ + +D L+G+T
Sbjct: 130 IFRVRPSPFCVLDEVDAALDDANVERFARLLKEFSKETQFIVITHRKGTMEAADRLYGVT 189
Query: 60 L 60
+
Sbjct: 190 M 190
>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 = 46.6 bits (111), Expect = 1e-07
Identities = 22/60 (36%), Positives = 32/60 (53%), Gaps = 3/60 (5%)
Query: 3 RYKPSPFLLLDEIDAALDNINIWKTIQYIRTVPK-MNVIAVSLK-PQFYFHSDILFGITL 60
RYKPSPF DE+D LD +N+ + + IR I VSL+ P + + G+T+
Sbjct: 1093 RYKPSPFYAFDEVDMFLDGVNVERVAKLIREKAGEAQFIVVSLRSPMIEYADRAI-GVTM 1151
>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 = 45.0 bits (107), Expect = 3e-07
Identities = 25/78 (32%), Positives = 36/78 (46%), Gaps = 13/78 (16%)
Query: 1 MYRYKPSPFLLLDEIDAALDNINIWKTIQYIR--TVPKMNVIAVSLKPQFYFHSDILFGI 58
+ KPSPF +LDEIDAALD N + I+ I ++LK + + ++D L G+
Sbjct: 111 LQEIKPSPFYVLDEIDAALDPTNRRRVSDMIKEMAKHTSQFIVITLKKEMFENADKLIGV 170
Query: 59 TLKMLGSLTIKGRVHKAS 76
VH S
Sbjct: 171 L-----------FVHGVS 177
>gnl|CDD|213240 cd03273, ABC_SMC2_euk, ATP-binding cassette domain of eukaryotic
SMC2 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 = 251
Score = 45.0 bits (107), Expect = 4e-07
Identities = 22/62 (35%), Positives = 34/62 (54%), Gaps = 11/62 (17%)
Query: 1 MYRYKPSPFLLLDEIDAALD-----NINIWKTIQYIRT-VPKMNVIAVSLKPQFYFHSDI 54
+ +KP+P +LDE+DAALD NI + I+T I VSLK + ++++
Sbjct: 183 LLLFKPAPMYILDEVDAALDLSHTQNIG-----RMIKTHFKGSQFIVVSLKEGMFNNANV 237
Query: 55 LF 56
LF
Sbjct: 238 LF 239
>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 = 44.2 bits (105), Expect = 7e-07
Identities = 23/59 (38%), Positives = 34/59 (57%), Gaps = 1/59 (1%)
Query: 1 MYRYKPSPFLLLDEIDAALDNINIWKTIQYIRTVPK-MNVIAVSLKPQFYFHSDILFGI 58
++ YKP+P ++DEIDAALD N+ YI+ K I +SL+ + +D L GI
Sbjct: 144 LHHYKPTPLYVMDEIDAALDFRNVSIVANYIKERTKNAQFIVISLRNNMFELADRLVGI 202
>gnl|CDD|213239 cd03272, ABC_SMC3_euk, ATP-binding cassette domain of eukaryotic
SMC3 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 = 243
Score = 34.5 bits (80), Expect = 0.002
Identities = 12/15 (80%), Positives = 13/15 (86%)
Query: 6 PSPFLLLDEIDAALD 20
P+PF L DEIDAALD
Sbjct: 180 PAPFYLFDEIDAALD 194
>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 = 0.011
Identities = 18/58 (31%), Positives = 25/58 (43%), Gaps = 2/58 (3%)
Query: 4 YKPSPFLLLDEIDAALDNINIWKTIQYIR--TVPKMNVIAVSLKPQFYFHSDILFGIT 59
KP P +LDEID LD + + I V VI ++ P+ +D L I
Sbjct: 97 LKPRPLYILDEIDRGLDPRDGQALAEAILEHLVKGAQVIVITHLPELAELADKLIHIK 154
>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 = 0.22
Identities = 9/29 (31%), Positives = 15/29 (51%), Gaps = 3/29 (10%)
Query: 4 YKPSPFLLLDEIDAALDNIN---IWKTIQ 29
+ P L+LDE +ALD I + ++
Sbjct: 112 LRDPPILILDEATSALDPETEALILEALR 140
>gnl|CDD|131258 TIGR02203, MsbA_lipidA, lipid A export permease/ATP-binding protein
MsbA. This family consists of a single polypeptide
chain transporter in the ATP-binding cassette (ABC)
transporter family, MsbA, which exports lipid A. It may
also act in multidrug resistance. Lipid A, a part of
lipopolysaccharide, is found in the outer leaflet of the
outer membrane of most Gram-negative bacteria. Members
of this family are restricted to the Proteobacteria
(although lipid A is more broadly distributed) and often
are clustered with lipid A biosynthesis genes [Cell
envelope, Biosynthesis and degradation of surface
polysaccharides and lipopolysaccharides, Transport and
binding proteins, Other].
Length = 571
Score = 28.5 bits (64), Expect = 0.32
Identities = 10/18 (55%), Positives = 13/18 (72%)
Query: 4 YKPSPFLLLDEIDAALDN 21
K +P L+LDE +ALDN
Sbjct: 485 LKDAPILILDEATSALDN 502
>gnl|CDD|131377 TIGR02324, CP_lyasePhnL, phosphonate C-P lyase system protein PhnL.
Members of this family are the PhnL protein of C-P
lyase systems for utilization of phosphonates. These
systems resemble phosphonatase-based systems in having a
three component ABC transporter, where TIGR01097 is the
permease, TIGR01098 is the phosphonates binding protein,
and TIGR02315 is the ATP-binding cassette (ABC) protein.
They differ, however, in having, typically, ten or more
additional genes, many of which are believed to form a
membrane-associated C-P lysase complex. This protein
(PhnL) and the adjacent-encoded PhnK (TIGR02323)
resemble transporter ATP-binding proteins but are
suggested, based on mutatgenesis studies, to be part of
this C-P lyase complex rather than part of a transporter
per se.
Length = 224
Score = 28.1 bits (63), Expect = 0.39
Identities = 11/28 (39%), Positives = 14/28 (50%)
Query: 5 KPSPFLLLDEIDAALDNINIWKTIQYIR 32
P LLLDE A+LD N ++ I
Sbjct: 166 ADYPILLLDEPTASLDAANRQVVVELIA 193
>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 = 26.8 bits (60), Expect = 0.81
Identities = 12/44 (27%), Positives = 22/44 (50%), Gaps = 2/44 (4%)
Query: 7 SPFLLLDEIDAALDNINIWKTIQYIRTVPKMN--VIAVSLKPQF 48
LLLDE + LD + + ++ +R + + VI V+ P+
Sbjct: 99 PDLLLLDEPTSGLDPASRERLLELLRELAEEGRTVIIVTHDPEL 142
>gnl|CDD|234806 PRK00635, PRK00635, excinuclease ABC subunit A; Provisional.
Length = 1809
Score = 27.1 bits (60), Expect = 1.0
Identities = 17/52 (32%), Positives = 26/52 (50%), Gaps = 3/52 (5%)
Query: 6 PSPFLLLDEIDAALDNINIWKTIQYIRTVPKM--NVIAVSLKPQFYFHSDIL 55
P+ FLL DEI +LDN + +RT+ + +VI + P +D L
Sbjct: 1721 PTLFLL-DEIATSLDNQQKSALLVQLRTLVSLGHSVIYIDHDPALLKQADYL 1771
>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 = 26.0 bits (58), Expect = 1.9
Identities = 7/18 (38%), Positives = 11/18 (61%)
Query: 6 PSPFLLLDEIDAALDNIN 23
PF ++DEI+ +D N
Sbjct: 148 RCPFRVVDEINQGMDPTN 165
>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 = 26.1 bits (58), Expect = 2.0
Identities = 9/17 (52%), Positives = 11/17 (64%)
Query: 4 YKPSPFLLLDEIDAALD 20
+ +P LLLDE A LD
Sbjct: 474 LRDAPLLLLDEPTAHLD 490
>gnl|CDD|203009 pfam04428, Choline_kin_N, Choline kinase N terminus. Found N
terminal to choline/ethanolamine kinase regions
(pfam01633) in some plant and fungal choline kinase
enzymes (EC:2.7.1.32). This region is only found in
some members of the choline kinase family, and is
therefore unlikely to contribute to catalysis.
Length = 52
Score = 24.8 bits (54), Expect = 2.3
Identities = 10/38 (26%), Positives = 16/38 (42%), Gaps = 5/38 (13%)
Query: 33 TVPKMNVIAVSLKPQFYFHSDILFGITLKMLGSLTIKG 70
VP + + P YF +I L++L +L I
Sbjct: 10 EVPSVKATLDNSLPSDYFKEEI-----LRLLHTLAISK 42
>gnl|CDD|237184 PRK12736, PRK12736, elongation factor Tu; Reviewed.
Length = 394
Score = 25.7 bits (57), Expect = 2.6
Identities = 8/17 (47%), Positives = 11/17 (64%), Gaps = 1/17 (5%)
Query: 45 KPQFYFH-SDILFGITL 60
+PQFYF +D+ I L
Sbjct: 328 RPQFYFRTTDVTGSIEL 344
>gnl|CDD|183077 PRK11288, araG, L-arabinose transporter ATP-binding protein;
Provisional.
Length = 501
Score = 25.6 bits (57), Expect = 3.0
Identities = 9/26 (34%), Positives = 15/26 (57%)
Query: 12 LDEIDAALDNINIWKTIQYIRTVPKM 37
++EI A D I ++K +Y+ T M
Sbjct: 200 MEEIFALCDAITVFKDGRYVATFDDM 225
>gnl|CDD|132329 TIGR03286, methan_mark_15, putative methanogenesis marker protein
15. Members of this protein family, to date, are found
in a completed prokaryotic genome if and only if the
species is one of the archaeal methanogens. The exact
function is unknown, but likely is linked to
methanogenesis or a process closely connected to it.
Related proteins include the BadF/BadG/BcrA/BcrD ATPase
family (pfam01869), which includes an activator for
(R)-2-hydroxyglutaryl-CoA dehydratase [Energy
metabolism, Methanogenesis].
Length = 404
Score = 25.6 bits (56), Expect = 3.4
Identities = 9/23 (39%), Positives = 13/23 (56%)
Query: 57 GITLKMLGSLTIKGRVHKASLNS 79
G+ + LG L +KG K +NS
Sbjct: 288 GVDITELGKLALKGMPEKVRMNS 310
>gnl|CDD|227118 COG4778, PhnL, ABC-type phosphonate transport system, ATPase
component [Inorganic ion transport and metabolism].
Length = 235
Score = 25.1 bits (55), Expect = 4.0
Identities = 12/25 (48%), Positives = 15/25 (60%)
Query: 8 PFLLLDEIDAALDNINIWKTIQYIR 32
P LLLDE A+LD N ++ IR
Sbjct: 172 PILLLDEPTASLDATNRAVVVELIR 196
>gnl|CDD|213230 cd03263, ABC_subfamily_A, ATP-binding cassette domain of the lipid
transporters, subfamily A. The ABCA subfamily mediates
the transport of a variety of lipid compounds. Mutations
of members of ABCA subfamily are associated with human
genetic diseases, such as, familial high-density
lipoprotein (HDL) deficiency, neonatal surfactant
deficiency, degenerative retinopathies, and congenital
keratinization disorders. The ABCA1 protein is involved
in disorders of cholesterol transport and high-density
lipoprotein (HDL) biosynthesis. The ABCA4 (ABCR) protein
transports vitamin A derivatives in the outer segments
of photoreceptor cells, and therefore, performs a
crucial step in the visual cycle. The ABCA genes are not
present in yeast. However, evolutionary studies of ABCA
genes indicate that they arose as transporters that
subsequently duplicated and that certain sets of ABCA
genes were lost in different eukaryotic lineages.
Length = 220
Score = 25.2 bits (56), Expect = 4.3
Identities = 11/29 (37%), Positives = 13/29 (44%), Gaps = 3/29 (10%)
Query: 7 SPFLLLDEIDAALDNI---NIWKTIQYIR 32
LLLDE + LD IW I +R
Sbjct: 152 PSVLLLDEPTSGLDPASRRAIWDLILEVR 180
>gnl|CDD|235974 PRK07229, PRK07229, aconitate hydratase; Validated.
Length = 646
Score = 25.1 bits (56), Expect = 4.9
Identities = 8/17 (47%), Positives = 12/17 (70%)
Query: 58 ITLKMLGSLTIKGRVHK 74
+ L++L LT+KG V K
Sbjct: 174 VILELLRRLTVKGGVGK 190
>gnl|CDD|213227 cd03260, ABC_PstB_phosphate_transporter, ATP-binding cassette
domain of the phosphate transport system. Phosphate
uptake is of fundamental importance in the cell
physiology of bacteria because phosphate is required as
a nutrient. The Pst system of E. coli comprises four
distinct subunits encoded by the pstS, pstA, pstB, and
pstC genes. The PstS protein is a phosphate-binding
protein located in the periplasmic space. PstA and PstC
are hydrophobic and they form the transmembrane portion
of the Pst system. PstB is the catalytic subunit, which
couples the energy of ATP hydrolysis to the import of
phosphate across cellular membranes through the Pst
system, often referred as ABC-protein. PstB belongs to
one of the largest superfamilies of proteins
characterized by a highly conserved adenosine
triphosphate (ATP) binding cassette (ABC), which is also
a nucleotide binding domain (NBD).
Length = 227
Score = 24.8 bits (55), Expect = 5.1
Identities = 9/15 (60%), Positives = 11/15 (73%)
Query: 9 FLLLDEIDAALDNIN 23
LLLDE +ALD I+
Sbjct: 162 VLLLDEPTSALDPIS 176
>gnl|CDD|213185 cd03218, ABC_YhbG, ATP-binding cassette component of YhbG transport
system. The ABC transporters belonging to the YhbG
family are similar to members of the Mj1267_LivG family,
which is involved in the transport of branched-chain
amino acids. The genes yhbG and yhbN are located in a
single operon and may function together in cell envelope
during biogenesis. YhbG is the putative ATP-binding
cassette component and YhbN is the putative
periplasmic-binding protein. Depletion of each gene
product leads to growth arrest, irreversible cell damage
and loss of viability in E. coli. The YhbG homolog
(NtrA) is essential in Rhizobium meliloti, a symbiotic
nitrogen-fixing bacterium.
Length = 232
Score = 24.8 bits (55), Expect = 5.2
Identities = 12/23 (52%), Positives = 15/23 (65%), Gaps = 1/23 (4%)
Query: 9 FLLLDEIDAALDNINIWKTIQYI 31
FLLLDE A +D I + + IQ I
Sbjct: 154 FLLLDEPFAGVDPIAV-QDIQKI 175
>gnl|CDD|182331 PRK10247, PRK10247, putative ABC transporter ATP-binding protein
YbbL; Provisional.
Length = 225
Score = 24.7 bits (54), Expect = 5.2
Identities = 10/14 (71%), Positives = 11/14 (78%)
Query: 10 LLLDEIDAALDNIN 23
LLLDEI +ALD N
Sbjct: 159 LLLDEITSALDESN 172
>gnl|CDD|224026 COG1101, PhnK, ABC-type uncharacterized transport system, ATPase
component [General function prediction only].
Length = 263
Score = 24.6 bits (54), Expect = 6.1
Identities = 11/20 (55%), Positives = 11/20 (55%)
Query: 1 MYRYKPSPFLLLDEIDAALD 20
M P LLLDE AALD
Sbjct: 161 MATLHPPKILLLDEHTAALD 180
>gnl|CDD|220532 pfam10033, ATG13, Autophagy-related protein 13. Members of this
family of phosphoproteins are involved in cytoplasm to
vacuole transport (Cvt), and more specifically in Cvt
vesicle formation. They are probably involved in the
switching machinery regulating the conversion between
the Cvt pathway and autophagy. Finally, ATG13 is also
required for glycogen storage.
Length = 228
Score = 24.7 bits (54), Expect = 6.3
Identities = 11/37 (29%), Positives = 19/37 (51%), Gaps = 2/37 (5%)
Query: 10 LLLDEIDAALDNINIWKTIQYIRT-VPKMNVIAVSLK 45
L +DE D + + +W+ I R+ +P + VI L
Sbjct: 38 LEIDESDELREELKLWRAIDDGRSRLPPL-VIETYLD 73
>gnl|CDD|220197 pfam09351, DUF1993, Domain of unknown function (DUF1993). This
family of proteins are functionally uncharacterized.
Length = 162
Score = 24.1 bits (53), Expect = 7.9
Identities = 8/19 (42%), Positives = 10/19 (52%), Gaps = 1/19 (5%)
Query: 46 PQFYFHSDILFGITLKMLG 64
P FYFH + I L+ G
Sbjct: 135 PNFYFHVTTAYAI-LRHNG 152
>gnl|CDD|236870 PRK11174, PRK11174, cysteine/glutathione ABC transporter
membrane/ATP-binding component; Reviewed.
Length = 588
Score = 24.4 bits (54), Expect = 8.5
Identities = 9/17 (52%), Positives = 11/17 (64%)
Query: 4 YKPSPFLLLDEIDAALD 20
+P LLLDE A+LD
Sbjct: 501 LQPCQLLLLDEPTASLD 517
>gnl|CDD|214631 smart00350, MCM, minichromosome maintenance proteins.
Length = 509
Score = 24.1 bits (53), Expect = 8.5
Identities = 11/27 (40%), Positives = 13/27 (48%)
Query: 38 NVIAVSLKPQFYFHSDILFGITLKMLG 64
+A SL P Y H DI I L + G
Sbjct: 195 ERLARSLAPSIYGHEDIKKAILLLLFG 221
>gnl|CDD|224045 COG1120, FepC, ABC-type cobalamin/Fe3+-siderophores transport
systems, ATPase components [Inorganic ion transport and
metabolism / Coenzyme metabolism].
Length = 258
Score = 24.1 bits (53), Expect = 8.5
Identities = 11/40 (27%), Positives = 20/40 (50%), Gaps = 3/40 (7%)
Query: 7 SPFLLLDEIDAALD---NINIWKTIQYIRTVPKMNVIAVS 43
+P LLLDE + LD I + + ++ + + V+ V
Sbjct: 157 TPILLLDEPTSHLDIAHQIEVLELLRDLNREKGLTVVMVL 196
>gnl|CDD|224054 COG1131, CcmA, ABC-type multidrug transport system, ATPase
component [Defense mechanisms].
Length = 293
Score = 24.2 bits (53), Expect = 8.8
Identities = 7/26 (26%), Positives = 13/26 (50%)
Query: 8 PFLLLDEIDAALDNINIWKTIQYIRT 33
L+LDE + LD + + + +R
Sbjct: 156 ELLILDEPTSGLDPESRREIWELLRE 181
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
0.326 0.141 0.414
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: 4,087,534
Number of extensions: 316778
Number of successful extensions: 509
Number of sequences better than 10.0: 1
Number of HSP's gapped: 506
Number of HSP's successfully gapped: 45
Length of query: 80
Length of database: 10,937,602
Length adjustment: 49
Effective length of query: 31
Effective length of database: 8,764,256
Effective search space: 271691936
Effective search space used: 271691936
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 53 (24.6 bits)