RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17517
(163 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 = 143 bits (364), Expect = 1e-43
Identities = 50/58 (86%), Positives = 54/58 (93%)
Query: 106 APGKRFQPMTNLSGGEKTVAALALLFAIHSYHPAPFFVLDEIDAALDNTNIGKVASYI 163
PGKRF+ M NLSGGEKT+AALALLFAIHSY PAPFFVLDE+DAALDNTN+GKVASYI
Sbjct: 145 PPGKRFRDMDNLSGGEKTMAALALLFAIHSYQPAPFFVLDEVDAALDNTNVGKVASYI 202
Score = 71.8 bits (177), Expect = 8e-16
Identities = 24/29 (82%), Positives = 26/29 (89%)
Query: 31 APGKRFQPMTNLSGGEKTVAALALLFAIH 59
PGKRF+ M NLSGGEKT+AALALLFAIH
Sbjct: 145 PPGKRFRDMDNLSGGEKTMAALALLFAIH 173
>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 = 145 bits (368), Expect = 4e-41
Identities = 46/118 (38%), Positives = 68/118 (57%), Gaps = 10/118 (8%)
Query: 46 EKTVAALALLFAIHRIATIRSLGLEDLRSMALAQNQSAQAFLGPENPEEPYLQGVNYNCV 105
++ L L +I+R L + A L E+ ++P+ G+ +
Sbjct: 1018 QRFKEFLELFVSINR----------GLNKVFFYLELGGSAELRLEDSDDPFSGGIEISAR 1067
Query: 106 APGKRFQPMTNLSGGEKTVAALALLFAIHSYHPAPFFVLDEIDAALDNTNIGKVASYI 163
PGK + + NLSGGEKT+ ALAL+FAI Y PAPF++LDEIDAALD+ N+ +VA+Y+
Sbjct: 1068 PPGKGVKNLDNLSGGEKTLVALALIFAIQKYRPAPFYLLDEIDAALDDQNVSRVANYL 1125
Score = 89.3 bits (221), Expect = 3e-21
Identities = 23/54 (42%), Positives = 34/54 (62%)
Query: 7 SAQAFLGPENPEEPYLQGVNYNCVAPGKRFQPMTNLSGGEKTVAALALLFAIHR 60
A L E+ ++P+ G+ + PGK + + NLSGGEKT+ ALAL+FAI +
Sbjct: 1044 GGSAELRLEDSDDPFSGGIEISARPPGKGVKNLDNLSGGEKTLVALALIFAIQK 1097
>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and
chromosome partitioning].
Length = 1163
Score = 111 bits (279), Expect = 4e-29
Identities = 41/79 (51%), Positives = 55/79 (69%)
Query: 85 AFLGPENPEEPYLQGVNYNCVAPGKRFQPMTNLSGGEKTVAALALLFAIHSYHPAPFFVL 144
A L P++P G+ + PGK+ Q ++ LSGGEK++ ALALLFAI Y PAPF+VL
Sbjct: 1035 AELELTEPDDPLTAGIEISARPPGKKLQSLSLLSGGEKSLTALALLFAIQKYRPAPFYVL 1094
Query: 145 DEIDAALDNTNIGKVASYI 163
DE+DAALD+ N+ +VA I
Sbjct: 1095 DEVDAALDDANVERVARLI 1113
Score = 66.3 bits (162), Expect = 2e-13
Identities = 23/51 (45%), Positives = 33/51 (64%)
Query: 10 AFLGPENPEEPYLQGVNYNCVAPGKRFQPMTNLSGGEKTVAALALLFAIHR 60
A L P++P G+ + PGK+ Q ++ LSGGEK++ ALALLFAI +
Sbjct: 1035 AELELTEPDDPLTAGIEISARPPGKKLQSLSLLSGGEKSLTALALLFAIQK 1085
>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 = 93.3 bits (233), Expect = 2e-24
Identities = 33/58 (56%), Positives = 43/58 (74%)
Query: 106 APGKRFQPMTNLSGGEKTVAALALLFAIHSYHPAPFFVLDEIDAALDNTNIGKVASYI 163
APGK+ Q ++ LSGGEK + ALALLFAI P+PF VLDE+DAALD+ N+ + A +
Sbjct: 103 APGKKVQRLSLLSGGEKALTALALLFAIFRVRPSPFCVLDEVDAALDDANVERFARLL 160
Score = 52.9 bits (128), Expect = 4e-09
Identities = 20/31 (64%), Positives = 25/31 (80%)
Query: 31 APGKRFQPMTNLSGGEKTVAALALLFAIHRI 61
APGK+ Q ++ LSGGEK + ALALLFAI R+
Sbjct: 103 APGKKVQRLSLLSGGEKALTALALLFAIFRV 133
>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 = 87.4 bits (217), Expect = 6e-22
Identities = 33/57 (57%), Positives = 46/57 (80%)
Query: 107 PGKRFQPMTNLSGGEKTVAALALLFAIHSYHPAPFFVLDEIDAALDNTNIGKVASYI 163
P K ++ ++NLSGGEKT+++LAL+FA+H Y P P +V+DEIDAALD N+ VA+YI
Sbjct: 118 PKKSWKNISNLSGGEKTLSSLALVFALHHYKPTPLYVMDEIDAALDFRNVSIVANYI 174
Score = 44.6 bits (106), Expect = 4e-06
Identities = 16/28 (57%), Positives = 25/28 (89%)
Query: 32 PGKRFQPMTNLSGGEKTVAALALLFAIH 59
P K ++ ++NLSGGEKT+++LAL+FA+H
Sbjct: 118 PKKSWKNISNLSGGEKTLSSLALVFALH 145
>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 = 83.2 bits (206), Expect = 3e-19
Identities = 31/57 (54%), Positives = 42/57 (73%)
Query: 107 PGKRFQPMTNLSGGEKTVAALALLFAIHSYHPAPFFVLDEIDAALDNTNIGKVASYI 163
PGK+ Q ++ LSGGEK + ALALLFAI PAPF +LDE+DA LD+ N+ + A+ +
Sbjct: 1080 PGKKNQNLSLLSGGEKALTALALLFAIFKVKPAPFCILDEVDAPLDDANVERFANLL 1136
Score = 48.1 bits (115), Expect = 5e-07
Identities = 18/30 (60%), Positives = 24/30 (80%)
Query: 32 PGKRFQPMTNLSGGEKTVAALALLFAIHRI 61
PGK+ Q ++ LSGGEK + ALALLFAI ++
Sbjct: 1080 PGKKNQNLSLLSGGEKALTALALLFAIFKV 1109
>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 = 78.5 bits (194), Expect = 8e-19
Identities = 29/47 (61%), Positives = 38/47 (80%)
Query: 117 LSGGEKTVAALALLFAIHSYHPAPFFVLDEIDAALDNTNIGKVASYI 163
LSGGEK+++ALAL+FA+ P+PF+VLDEIDAALD TN +V+ I
Sbjct: 95 LSGGEKSLSALALIFALQEIKPSPFYVLDEIDAALDPTNRRRVSDMI 141
Score = 39.6 bits (93), Expect = 2e-04
Identities = 13/21 (61%), Positives = 18/21 (85%)
Query: 42 LSGGEKTVAALALLFAIHRIA 62
LSGGEK+++ALAL+FA+ I
Sbjct: 95 LSGGEKSLSALALIFALQEIK 115
>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 = 80.5 bits (199), Expect = 3e-18
Identities = 32/82 (39%), Positives = 50/82 (60%), Gaps = 2/82 (2%)
Query: 82 SAQAFLGPENPEEPYLQGVNYNCVAPGKRFQPMTNLSGGEKTVAALALLFAIHSYHPAPF 141
+ + L ENP++P+ G+ + GK Q + +SGGEK++ AL+ +FAI Y P+PF
Sbjct: 1042 TGELIL--ENPDDPFAGGLELSAKPKGKPVQRLEAMSGGEKSLTALSFIFAIQRYKPSPF 1099
Query: 142 FVLDEIDAALDNTNIGKVASYI 163
+ DE+D LD N+ +VA I
Sbjct: 1100 YAFDEVDMFLDGVNVERVAKLI 1121
Score = 47.0 bits (112), Expect = 1e-06
Identities = 20/54 (37%), Positives = 33/54 (61%), Gaps = 2/54 (3%)
Query: 7 SAQAFLGPENPEEPYLQGVNYNCVAPGKRFQPMTNLSGGEKTVAALALLFAIHR 60
+ + L ENP++P+ G+ + GK Q + +SGGEK++ AL+ +FAI R
Sbjct: 1042 TGELIL--ENPDDPFAGGLELSAKPKGKPVQRLEAMSGGEKSLTALSFIFAIQR 1093
>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 = 70.8 bits (174), Expect = 2e-15
Identities = 26/41 (63%), Positives = 32/41 (78%)
Query: 112 QPMTNLSGGEKTVAALALLFAIHSYHPAPFFVLDEIDAALD 152
Q M LSGG+K++ ALAL+FAI PAPF++ DEIDAALD
Sbjct: 154 QEMQQLSGGQKSLVALALIFAIQKCDPAPFYLFDEIDAALD 194
Score = 42.2 bits (100), Expect = 3e-05
Identities = 14/25 (56%), Positives = 19/25 (76%)
Query: 37 QPMTNLSGGEKTVAALALLFAIHRI 61
Q M LSGG+K++ ALAL+FAI +
Sbjct: 154 QEMQQLSGGQKSLVALALIFAIQKC 178
>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 = 60.5 bits (147), Expect = 3e-12
Identities = 23/47 (48%), Positives = 31/47 (65%)
Query: 117 LSGGEKTVAALALLFAIHSYHPAPFFVLDEIDAALDNTNIGKVASYI 163
LSGGEK ++ALAL+ A+ S P P ++LDEID LD + +A I
Sbjct: 78 LSGGEKELSALALILALASLKPRPLYILDEIDRGLDPRDGQALAEAI 124
Score = 29.6 bits (67), Expect = 0.44
Identities = 11/21 (52%), Positives = 16/21 (76%)
Query: 42 LSGGEKTVAALALLFAIHRIA 62
LSGGEK ++ALAL+ A+ +
Sbjct: 78 LSGGEKELSALALILALASLK 98
>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 = 60.8 bits (148), Expect = 9e-12
Identities = 24/50 (48%), Positives = 39/50 (78%), Gaps = 3/50 (6%)
Query: 112 QPMTNLSGGEKTVAALALLFAIHSYHPAPFFVLDEIDAALD--NT-NIGK 158
+ +T LSGG++++ AL+L+ A+ + PAP ++LDE+DAALD +T NIG+
Sbjct: 162 ESLTELSGGQRSLVALSLILALLLFKPAPMYILDEVDAALDLSHTQNIGR 211
Score = 26.9 bits (60), Expect = 4.3
Identities = 9/22 (40%), Positives = 18/22 (81%)
Query: 37 QPMTNLSGGEKTVAALALLFAI 58
+ +T LSGG++++ AL+L+ A+
Sbjct: 162 ESLTELSGGQRSLVALSLILAL 183
>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 = 46.8 bits (112), Expect = 6e-07
Identities = 15/39 (38%), Positives = 23/39 (58%)
Query: 117 LSGGEKTVAALALLFAIHSYHPAPFFVLDEIDAALDNTN 155
LSGGE++ + + LL ++ +PF LDE D +D N
Sbjct: 110 LSGGERSFSTVCLLLSLWEVMESPFRCLDEFDVFMDMVN 148
Score = 27.6 bits (62), Expect = 2.8
Identities = 9/28 (32%), Positives = 17/28 (60%), Gaps = 2/28 (7%)
Query: 42 LSGGEKTVAALALLFAIHRI--ATIRSL 67
LSGGE++ + + LL ++ + + R L
Sbjct: 110 LSGGERSFSTVCLLLSLWEVMESPFRCL 137
>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 = 42.6 bits (101), Expect = 2e-05
Identities = 15/38 (39%), Positives = 24/38 (63%)
Query: 118 SGGEKTVAALALLFAIHSYHPAPFFVLDEIDAALDNTN 155
SGGE++V+ + L ++ PF V+DEI+ +D TN
Sbjct: 128 SGGERSVSTMLYLLSLQELTRCPFRVVDEINQGMDPTN 165
>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 = 41.8 bits (99), Expect = 2e-05
Identities = 12/47 (25%), Positives = 20/47 (42%), Gaps = 4/47 (8%)
Query: 117 LSGGEKTVAALALLFAIHSYHPAPFFVLDEIDAALDNTNIGKVASYI 163
LSGG++ ALA +LDE + LD + ++ +
Sbjct: 81 LSGGQRQRVALARALL----LNPDLLLLDEPTSGLDPASRERLLELL 123
>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication,
recombination, and repair].
Length = 908
Score = 39.4 bits (92), Expect = 5e-04
Identities = 18/55 (32%), Positives = 26/55 (47%), Gaps = 4/55 (7%)
Query: 113 PMTNLSGGEKTVAALALLFAIH----SYHPAPFFVLDEIDAALDNTNIGKVASYI 163
P+ LSGGE+ +A+LAL A+ LDE LD + K+A +
Sbjct: 812 PIKTLSGGERFLASLALRLALSDLLQGRARLELLFLDEPFGTLDEERLEKLAEIL 866
Score = 28.6 bits (64), Expect = 1.6
Identities = 11/21 (52%), Positives = 16/21 (76%)
Query: 38 PMTNLSGGEKTVAALALLFAI 58
P+ LSGGE+ +A+LAL A+
Sbjct: 812 PIKTLSGGERFLASLALRLAL 832
>gnl|CDD|222219 pfam13558, SbcCD_C, Putative exonuclease SbcCD, C subunit.
Possible exonuclease SbcCD, C subunit, on AAA proteins.
Length = 79
Score = 36.0 bits (84), Expect = 0.001
Identities = 22/55 (40%), Positives = 26/55 (47%), Gaps = 8/55 (14%)
Query: 117 LSGGEKTV-------AALALLFAIHSYHPAP-FFVLDEIDAALDNTNIGKVASYI 163
LSGGEK V AALA + + PAP LDE A LD NI + +
Sbjct: 23 LSGGEKQVLAYLALAAALAAQYGSNRGGPAPRLIFLDEAFAKLDEENIRSLLELL 77
>gnl|CDD|100796 PRK01156, PRK01156, chromosome segregation protein; Provisional.
Length = 895
Score = 35.3 bits (81), Expect = 0.009
Identities = 19/56 (33%), Positives = 28/56 (50%), Gaps = 5/56 (8%)
Query: 112 QPMTNLSGGEKTVAALALLFAIHSYHPA--PFFVLDEIDAALDN---TNIGKVASY 162
+ + +LSGGEKT A AL A+ + ++DE A LD TN+ + Y
Sbjct: 797 EGIDSLSGGEKTAVAFALRVAVAQFLNNDKSLLIMDEPTAFLDEDRRTNLKDIIEY 852
Score = 28.3 bits (63), Expect = 2.1
Identities = 11/22 (50%), Positives = 15/22 (68%)
Query: 37 QPMTNLSGGEKTVAALALLFAI 58
+ + +LSGGEKT A AL A+
Sbjct: 797 EGIDSLSGGEKTAVAFALRVAV 818
>gnl|CDD|226970 COG4619, COG4619, ABC-type uncharacterized transport system, ATPase
component [General function prediction only].
Length = 223
Score = 34.8 bits (80), Expect = 0.010
Identities = 19/52 (36%), Positives = 26/52 (50%), Gaps = 4/52 (7%)
Query: 112 QPMTNLSGGEKTVAALALLFAIHSYHPAPFFVLDEIDAALDNTNIGKVASYI 163
+ +T LSGGEK AL + P +LDEI +ALD +N + I
Sbjct: 129 KNITELSGGEKQRIALIRNL---QFMPK-ILLLDEITSALDESNKRNIEEMI 176
>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 = 34.5 bits (80), Expect = 0.016
Identities = 20/56 (35%), Positives = 27/56 (48%), Gaps = 7/56 (12%)
Query: 107 PGKRFQPMT-NLSGGEKTVAALALLFAIHSYHPAPFFVLDEIDAALDNTNI-GKVA 160
PG+ +P+ SGGE + LAL + P + DEID T I G+VA
Sbjct: 160 PGEPLKPLAKIASGGELSRLMLALKAILARKDAVPTLIFDEID-----TGISGEVA 210
>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 = 33.7 bits (78), Expect = 0.019
Identities = 15/48 (31%), Positives = 20/48 (41%), Gaps = 2/48 (4%)
Query: 111 FQPMTNLSGGEKTVAALALLFAIHSYHPA--PFFVLDEIDAALDNTNI 156
SGGEK +A+L + A+ + LDE LD NI
Sbjct: 110 LDMRGRCSGGEKVLASLIIRLALAETFGSNCGILALDEPTTNLDEENI 157
Score = 28.7 bits (65), Expect = 1.2
Identities = 10/33 (30%), Positives = 15/33 (45%), Gaps = 5/33 (15%)
Query: 36 FQPMTNLSGGEKTVAALALLFAIHRIATIRSLG 68
SGGEK +A+L + R+A + G
Sbjct: 110 LDMRGRCSGGEKVLASLII-----RLALAETFG 137
>gnl|CDD|223562 COG0488, Uup, ATPase components of ABC transporters with duplicated
ATPase domains [General function prediction only].
Length = 530
Score = 34.1 bits (79), Expect = 0.023
Identities = 16/53 (30%), Positives = 25/53 (47%), Gaps = 6/53 (11%)
Query: 112 QPMTNLSGGEKTVAALA-LLFAIHSYHPAPFFVLDEIDAALDNTNIGKVASYI 163
+P+++LSGG + ALA L +LDE LD +I + Y+
Sbjct: 149 RPVSSLSGGWRRRVALARALLE-----EPDLLLLDEPTNHLDLESIEWLEDYL 196
Score = 33.4 bits (77), Expect = 0.045
Identities = 9/22 (40%), Positives = 14/22 (63%), Gaps = 1/22 (4%)
Query: 37 QPMTNLSGGEKTVAALA-LLFA 57
+P+++LSGG + ALA L
Sbjct: 149 RPVSSLSGGWRRRVALARALLE 170
Score = 31.8 bits (73), Expect = 0.13
Identities = 14/36 (38%), Positives = 17/36 (47%), Gaps = 4/36 (11%)
Query: 111 FQPMTNLSGGEKTVAALALLFAIHSYHPAPFFVLDE 146
+P+ LSGGEK LA L P +LDE
Sbjct: 434 EKPVGVLSGGEKARLLLAKLLL----QPPNLLLLDE 465
Score = 26.8 bits (60), Expect = 6.3
Identities = 10/22 (45%), Positives = 12/22 (54%)
Query: 36 FQPMTNLSGGEKTVAALALLFA 57
+P+ LSGGEK LA L
Sbjct: 434 EKPVGVLSGGEKARLLLAKLLL 455
>gnl|CDD|225183 COG2274, SunT, ABC-type bacteriocin/lantibiotic exporters, contain
an N-terminal double-glycine peptidase domain [Defense
mechanisms].
Length = 709
Score = 33.7 bits (78), Expect = 0.035
Identities = 14/49 (28%), Positives = 20/49 (40%), Gaps = 4/49 (8%)
Query: 115 TNLSGGEKTVAALALLFAIHSYHPAPFFVLDEIDAALDNTNIGKVASYI 163
NLSGG++ ALA +LDE +ALD + +
Sbjct: 608 ANLSGGQRQRLALARAL----LSKPKILLLDEATSALDPETEAIILQNL 652
>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 = 32.7 bits (76), Expect = 0.045
Identities = 13/39 (33%), Positives = 18/39 (46%), Gaps = 4/39 (10%)
Query: 117 LSGGEKTVAALALLFAIHSYHPAPFFVLDEIDAALDNTN 155
LSGG++ A+A P +LDE +ALD
Sbjct: 97 LSGGQRQRIAIARAL----LRDPPILILDEATSALDPET 131
>gnl|CDD|223571 COG0497, RecN, ATPase involved in DNA repair [DNA replication,
recombination, and repair].
Length = 557
Score = 33.0 bits (76), Expect = 0.049
Identities = 19/59 (32%), Positives = 28/59 (47%), Gaps = 7/59 (11%)
Query: 107 PGKRFQPMT-NLSGGEKTVAALALLFAIHSYHPAPFFVLDEIDAALDNTNI-GKVASYI 163
PG+ +P+ SGGE + LAL + P + DE+D T I G+VA +
Sbjct: 421 PGEPLKPLAKVASGGELSRIMLALKVILSRKDDTPTLIFDEVD-----TGISGRVAQAV 474
>gnl|CDD|213205 cd03238, ABC_UvrA, ATP-binding cassette domain of the excision
repair protein UvrA. Nucleotide excision repair in
eubacteria is a process that repairs DNA damage by the
removal of a 12-13-mer oligonucleotide containing the
lesion. Recognition and cleavage of the damaged DNA is a
multistep ATP-dependent reaction that requires the UvrA,
UvrB, and UvrC proteins. Both UvrA and UvrB are ATPases,
with UvrA having two ATP binding sites, which have the
characteristic signature of the family of ABC proteins,
and UvrB having one ATP binding site that is
structurally related to that of helicases.
Length = 176
Score = 32.7 bits (75), Expect = 0.050
Identities = 14/45 (31%), Positives = 18/45 (40%), Gaps = 2/45 (4%)
Query: 112 QPMTNLSGGEKTVAALALLFAIHSYHPAPFFVLDEIDAALDNTNI 156
Q ++ LSGGE LA F+LDE L +I
Sbjct: 83 QKLSTLSGGELQRVKLASELFSEPPG--TLFILDEPSTGLHQQDI 125
>gnl|CDD|224026 COG1101, PhnK, ABC-type uncharacterized transport system, ATPase
component [General function prediction only].
Length = 263
Score = 32.7 bits (75), Expect = 0.053
Identities = 18/41 (43%), Positives = 23/41 (56%), Gaps = 4/41 (9%)
Query: 112 QPMTNLSGGEKTVAALALLFAIHSYHPAPFFVLDEIDAALD 152
+ LSGG++ AL+LL A HP +LDE AALD
Sbjct: 144 DRIGLLSGGQRQ--ALSLLMAT--LHPPKILLLDEHTAALD 180
>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 = 32.4 bits (75), Expect = 0.053
Identities = 16/49 (32%), Positives = 26/49 (53%), Gaps = 8/49 (16%)
Query: 115 TNLSGGEKTVAALALLFAIHSYHPAPFFVLDEIDAALDNTNIGKVASYI 163
NLSGG+K ++L A+ Y A ++LD+ +A+D V +I
Sbjct: 126 INLSGGQK--QRISLARAV--YSDADIYLLDDPLSAVDA----HVGRHI 166
>gnl|CDD|222036 pfam13304, AAA_21, AAA domain.
Length = 256
Score = 31.6 bits (71), Expect = 0.12
Identities = 10/47 (21%), Positives = 20/47 (42%), Gaps = 1/47 (2%)
Query: 117 LSGGEKTVAALALLFAIHSYHPAPFFVLDEIDAALDNTNIGKVASYI 163
+S G K + AL L + + ++DE + L + K+ +
Sbjct: 190 ISDGTKRLLALLLAL-LSALPKGSLLLIDEPENGLHPKLLRKLVELL 235
>gnl|CDD|233206 TIGR00954, 3a01203, Peroxysomal Fatty Acyl CoA Transporter (FAT)
Family protei. [Transport and binding proteins,
Carbohydrates, organic alcohols, and acids].
Length = 659
Score = 31.6 bits (72), Expect = 0.16
Identities = 18/38 (47%), Positives = 22/38 (57%), Gaps = 4/38 (10%)
Query: 114 MTNLSGGEKTVAALALLFAIHSYHPAPFFVLDEIDAAL 151
M LSGGEK A+A LF YH F +LDE +A+
Sbjct: 580 MDVLSGGEKQRIAMARLF----YHKPQFAILDECTSAV 613
>gnl|CDD|213188 cd03221, ABCF_EF-3, ATP-binding cassette domain of elongation
factor 3, subfamily F. Elongation factor 3 (EF-3) is a
cytosolic protein required by fungal ribosomes for in
vitro protein synthesis and for in vivo growth. EF-3
stimulates the binding of the EF-1: GTP: aa-tRNA ternary
complex to the ribosomal A site by facilitated release
of the deacylated tRNA from the E site. The reaction
requires ATP hydrolysis. EF-3 contains two ATP
nucleotide binding sequence (NBS) motifs. NBSI is
sufficient for the intrinsic ATPase activity. NBSII is
essential for the ribosome-stimulated functions.
Length = 144
Score = 30.9 bits (71), Expect = 0.16
Identities = 16/40 (40%), Positives = 18/40 (45%), Gaps = 4/40 (10%)
Query: 117 LSGGEKTVAALALLFAIHSYHPAPFFVLDEIDAALDNTNI 156
LSGGEK ALA L +LDE LD +I
Sbjct: 71 LSGGEKMRLALAKLL----LENPNLLLLDEPTNHLDLESI 106
Score = 26.3 bits (59), Expect = 5.1
Identities = 10/15 (66%), Positives = 10/15 (66%)
Query: 42 LSGGEKTVAALALLF 56
LSGGEK ALA L
Sbjct: 71 LSGGEKMRLALAKLL 85
>gnl|CDD|213212 cd03245, ABCC_bacteriocin_exporters, ATP-binding cassette domain of
bacteriocin exporters, subfamily C. Many
non-lantibiotic bacteriocins of lactic acid bacteria are
produced as precursors which have N-terminal leader
peptides that share similarities in amino acid sequence
and contain a conserved processing site of two glycine
residues in positions -1 and -2. A dedicated ATP-binding
cassette (ABC) transporter is responsible for the
proteolytic cleavage of the leader peptides and
subsequent translocation of the bacteriocins across the
cytoplasmic membrane.
Length = 220
Score = 31.0 bits (71), Expect = 0.19
Identities = 13/40 (32%), Positives = 19/40 (47%), Gaps = 4/40 (10%)
Query: 116 NLSGGEKTVAALALLFAIHSYHPAPFFVLDEIDAALDNTN 155
LSGG++ ALA P +LDE +A+D +
Sbjct: 140 GLSGGQRQAVALARALLNDP----PILLLDEPTSAMDMNS 175
>gnl|CDD|213184 cd03217, ABC_FeS_Assembly, ABC-type transport system involved in
Fe-S cluster assembly, ATPase component. Biosynthesis
of iron-sulfur clusters (Fe-S) depends on multi-protein
systems. The SUF system of E. coli and Erwinia
chrysanthemi is important for Fe-S biogenesis under
stressful conditions. The SUF system is made of six
proteins: SufC is an atypical cytoplasmic ABC-ATPase,
which forms a complex with SufB and SufD; SufA plays the
role of a scaffold protein for assembly of iron-sulfur
clusters and delivery to target proteins; SufS is a
cysteine desulfurase which mobilizes the sulfur atom
from cysteine and provides it to the cluster; SufE has
no associated function yet.
Length = 200
Score = 30.6 bits (70), Expect = 0.25
Identities = 20/75 (26%), Positives = 27/75 (36%), Gaps = 26/75 (34%)
Query: 86 FLGPENPEE-------PYLQGVNYNCVAPGKRFQPMTNLSGGEKTVAALALLFAIHSYHP 138
FL + P E +L+ VN SGGEK + L +
Sbjct: 80 FLAFQYPPEIPGVKNADFLRYVNEG-------------FSGGEKKRNEILQLLLLE---- 122
Query: 139 AP-FFVLDEIDAALD 152
P +LDE D+ LD
Sbjct: 123 -PDLAILDEPDSGLD 136
>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 = 31.1 bits (71), Expect = 0.25
Identities = 15/37 (40%), Positives = 17/37 (45%), Gaps = 4/37 (10%)
Query: 116 NLSGGEKTVAALALLFAIHSYHPAPFFVLDEIDAALD 152
LSGG+ ALA PA +LDE A LD
Sbjct: 456 GLSGGQAQRLALARAL----LSPASLLLLDEPTAHLD 488
>gnl|CDD|215650 pfam00005, ABC_tran, ABC transporter. ABC transporters for a large
family of proteins responsible for translocation of a
variety of compounds across biological membranes. ABC
transporters are the largest family of proteins in many
completely sequenced bacteria. ABC transporters are
composed of two copies of this domain and two copies of
a transmembrane domain pfam00664. These four domains may
belong to a single polypeptide as in human CFTR, or
belong in different polypeptide chains.
Length = 119
Score = 29.6 bits (67), Expect = 0.37
Identities = 11/35 (31%), Positives = 16/35 (45%), Gaps = 4/35 (11%)
Query: 112 QPMTNLSGGEKTVAALALLFAIHSYHPAPFFVLDE 146
+P+ LSGG+K A+A +LDE
Sbjct: 86 EPVGTLSGGQKQRVAIARALLKK----PKLLLLDE 116
>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 = 30.3 bits (69), Expect = 0.42
Identities = 16/36 (44%), Positives = 18/36 (50%), Gaps = 4/36 (11%)
Query: 117 LSGGEKTVAALALLFAIHSYHPAPFFVLDEIDAALD 152
LSGG+ ALA F AP +LDE A LD
Sbjct: 459 LSGGQAQRLALARAF----LRDAPLLLLDEPTAHLD 490
>gnl|CDD|224055 COG1132, MdlB, ABC-type multidrug transport system, ATPase and
permease components [Defense mechanisms].
Length = 567
Score = 30.5 bits (69), Expect = 0.42
Identities = 14/48 (29%), Positives = 21/48 (43%), Gaps = 4/48 (8%)
Query: 116 NLSGGEKTVAALALLFAIHSYHPAPFFVLDEIDAALDNTNIGKVASYI 163
NLSGG++ A+A P +LDE +ALD + +
Sbjct: 465 NLSGGQRQRLAIARAL----LRNPPILILDEATSALDTETEALIQDAL 508
>gnl|CDD|233973 TIGR02680, TIGR02680, TIGR02680 family protein. Members of this
protein family belong to a conserved gene four-gene
neighborhood found sporadically in a phylogenetically
broad range of bacteria: Nocardia farcinica,
Symbiobacterium thermophilum, and Streptomyces
avermitilis (Actinobacteria), Geobacillus kaustophilus
(Firmicutes), Azoarcus sp. EbN1 and Ralstonia
solanacearum (Betaproteobacteria). Proteins in this
family average over 1400 amino acids in length
[Hypothetical proteins, Conserved].
Length = 1353
Score = 30.5 bits (69), Expect = 0.43
Identities = 17/51 (33%), Positives = 23/51 (45%), Gaps = 8/51 (15%)
Query: 117 LSGGEKTVAALALLFAIHSYH-------PAPFFV-LDEIDAALDNTNIGKV 159
SGGE+ +A LFA S H AP + LDE A +D+ +
Sbjct: 1248 ASGGERALALYVPLFAAASSHYTQEAYPHAPRLILLDEAFAGVDDNARAHL 1298
>gnl|CDD|224166 COG1245, COG1245, Predicted ATPase, RNase L inhibitor (RLI) homolog
[General function prediction only].
Length = 591
Score = 30.3 bits (69), Expect = 0.43
Identities = 16/43 (37%), Positives = 21/43 (48%), Gaps = 8/43 (18%)
Query: 112 QPMTNLSGGE--KTVAALALLFAIHSYHPAPFFVLDEIDAALD 152
+P+ LSGGE + A AL A ++LDE A LD
Sbjct: 451 RPVDELSGGELQRVAIAAALS------READLYLLDEPSAYLD 487
>gnl|CDD|213198 cd03231, ABC_CcmA_heme_exporter, Cytochrome c biogenesis
ATP-binding export protein. CcmA, the ATP-binding
component of the bacterial CcmAB transporter. The CCM
family is involved in bacterial cytochrome c biogenesis.
Cytochrome c maturation in E. coli requires the ccm
operon, which encodes eight membrane proteins
(CcmABCDEFGH). CcmE is a periplasmic heme chaperon that
binds heme covalently and transfers it onto
apocytochrome c in the presence of CcmF, CcmG, and CcmH.
The CcmAB proteins represent an ABC transporter and the
CcmCD proteins participate in heme transfer to CcmE.
Length = 201
Score = 29.8 bits (67), Expect = 0.43
Identities = 16/49 (32%), Positives = 23/49 (46%), Gaps = 4/49 (8%)
Query: 113 PMTNLSGGEKTVAALALLFAIHSYHPAPFFVLDEIDAALDNTNIGKVAS 161
P+ LS G++ ALA L P ++LDE ALD + + A
Sbjct: 122 PVAQLSAGQQRRVALARLLLSG----RPLWILDEPTTALDKAGVARFAE 166
>gnl|CDD|184210 PRK13651, PRK13651, cobalt transporter ATP-binding subunit;
Provisional.
Length = 305
Score = 30.1 bits (68), Expect = 0.47
Identities = 16/37 (43%), Positives = 19/37 (51%), Gaps = 4/37 (10%)
Query: 116 NLSGGEKTVAALALLFAIHSYHPAPFFVLDEIDAALD 152
LSGG+K ALA + A+ F V DE A LD
Sbjct: 165 ELSGGQKRRVALAGILAME----PDFLVFDEPTAGLD 197
>gnl|CDD|234806 PRK00635, PRK00635, excinuclease ABC subunit A; Provisional.
Length = 1809
Score = 30.2 bits (68), Expect = 0.48
Identities = 16/42 (38%), Positives = 23/42 (54%), Gaps = 1/42 (2%)
Query: 112 QPMTNLSGGEKTVAALALLFAIHSYHPAPFFVLDEIDAALDN 153
Q +++LS EK +A + HP F+LDEI +LDN
Sbjct: 1695 QNLSSLSLSEKIAIKIAKFLYLPPKHPT-LFLLDEIATSLDN 1735
>gnl|CDD|226617 COG4133, CcmA, ABC-type transport system involved in cytochrome c
biogenesis, ATPase component [Posttranslational
modification, protein turnover, chaperones].
Length = 209
Score = 29.6 bits (67), Expect = 0.63
Identities = 17/40 (42%), Positives = 23/40 (57%), Gaps = 4/40 (10%)
Query: 113 PMTNLSGGEKTVAALALLFAIHSYHPAPFFVLDEIDAALD 152
P+ LS G++ ALA L+ PAP ++LDE ALD
Sbjct: 127 PVGQLSAGQQRRVALARLWL----SPAPLWILDEPFTALD 162
>gnl|CDD|236554 PRK09536, btuD, corrinoid ABC transporter ATPase; Reviewed.
Length = 402
Score = 29.8 bits (67), Expect = 0.68
Identities = 17/41 (41%), Positives = 23/41 (56%), Gaps = 4/41 (9%)
Query: 112 QPMTNLSGGEKTVAALALLFAIHSYHPAPFFVLDEIDAALD 152
+P+T+LSGGE+ LA A P +LDE A+LD
Sbjct: 135 RPVTSLSGGERQRVLLARALA----QATPVLLLDEPTASLD 171
>gnl|CDD|182331 PRK10247, PRK10247, putative ABC transporter ATP-binding protein
YbbL; Provisional.
Length = 225
Score = 29.3 bits (66), Expect = 0.75
Identities = 19/53 (35%), Positives = 26/53 (49%), Gaps = 6/53 (11%)
Query: 112 QPMTNLSGGEKTVAALALLFAIHSYHPAP-FFVLDEIDAALDNTNIGKVASYI 163
+ + LSGGEK +L I + P +LDEI +ALD +N V I
Sbjct: 133 KNIAELSGGEKQRISL-----IRNLQFMPKVLLLDEITSALDESNKHNVNEII 180
>gnl|CDD|184037 PRK13409, PRK13409, putative ATPase RIL; Provisional.
Length = 590
Score = 29.4 bits (67), Expect = 0.76
Identities = 14/43 (32%), Positives = 20/43 (46%), Gaps = 8/43 (18%)
Query: 112 QPMTNLSGGE--KTVAALALLFAIHSYHPAPFFVLDEIDAALD 152
+ + +LSGGE + A L A ++LDE A LD
Sbjct: 449 KNVKDLSGGELQRVAIAACLS------RDADLYLLDEPSAHLD 485
>gnl|CDD|224047 COG1122, CbiO, ABC-type cobalt transport system, ATPase component
[Inorganic ion transport and metabolism].
Length = 235
Score = 28.8 bits (65), Expect = 1.00
Identities = 16/56 (28%), Positives = 25/56 (44%), Gaps = 4/56 (7%)
Query: 108 GKRFQPMTNLSGGEKTVAALALLFAIHSYHPAPFFVLDEIDAALDNTNIGKVASYI 163
+P NLSGG+K A+A + A+ +LDE A LD ++ +
Sbjct: 130 ELLDRPPFNLSGGQKQRVAIAGVLAMGPE----ILLLDEPTAGLDPKGRRELLELL 181
>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 = 29.3 bits (66), Expect = 1.0
Identities = 16/38 (42%), Positives = 22/38 (57%), Gaps = 4/38 (10%)
Query: 116 NLSGGEKTVAALALLFAIHSYHPAPFFVLDEIDAALDN 153
LSGG++ A+A A+ AP +LDE +ALDN
Sbjct: 469 LLSGGQRQRLAIAR--AL--LKDAPILILDEATSALDN 502
>gnl|CDD|224046 COG1121, ZnuC, ABC-type Mn/Zn transport systems, ATPase component
[Inorganic ion transport and metabolism].
Length = 254
Score = 28.7 bits (65), Expect = 1.1
Identities = 13/48 (27%), Positives = 18/48 (37%), Gaps = 4/48 (8%)
Query: 108 GKRFQPMTNLSGGEKTVAALALLFAIHSYHPAPFFVLDEIDAALDNTN 155
R + + LSGG+K LA A +LDE +D
Sbjct: 131 DLRDRQIGELSGGQKQRVLLARALAQ----NPDLLLLDEPFTGVDVAG 174
>gnl|CDD|213204 cd03237, ABC_RNaseL_inhibitor_domain2, The ATP-binding cassette
domain 2 of RNase L inhibitor. The ABC ATPase, RNase L
inhibitor (RLI), is a key enzyme in ribosomal
biogenesis, formation of translation preinitiation
complexes, and assembly of HIV capsids. RLI's are not
transport proteins and thus cluster with a group of
soluble proteins that lack the transmembrane components
commonly found in other members of the family.
Structurally, RLI's have an N-terminal Fe-S domain and
two nucleotide-binding domains which are arranged to
form two composite active sites in their interface
cleft. RLI is one of the most conserved enzymes between
archaea and eukaryotes with a sequence identity of more
than 48%. The high degree of evolutionary conservation
suggests that RLI performs a central role in archaeal
and eukaryotic physiology.
Length = 246
Score = 28.9 bits (65), Expect = 1.1
Identities = 14/41 (34%), Positives = 20/41 (48%), Gaps = 4/41 (9%)
Query: 112 QPMTNLSGGEKTVAALALLFAIHSYHPAPFFVLDEIDAALD 152
+ + LSGGE A+A + A ++LDE A LD
Sbjct: 111 REVPELSGGELQRVAIAACLS----KDADIYLLDEPSAYLD 147
>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 = 28.9 bits (65), Expect = 1.2
Identities = 16/57 (28%), Positives = 26/57 (45%), Gaps = 5/57 (8%)
Query: 108 GKRFQPMTNL-SGGEKTVAALALLFAIHSYHPAPFFVLDEIDAALDNTNIGKVASYI 163
G+ +P+ + SGGE + LAL + S + DE+D + G+ A I
Sbjct: 431 GEPVKPLAKVASGGELSRVMLALKVVLSSSAAVTTLIFDEVDVGVS----GETAQAI 483
>gnl|CDD|213246 cd03279, ABC_sbcCD, ATP-binding cassette domain of sbcCD. SbcCD
and other Mre11/Rad50 (MR) complexes are implicated in
the metabolism of DNA ends. They cleave ends sealed by
hairpin structures and are thought to play a role in
removing protein bound to DNA termini.
Length = 213
Score = 28.4 bits (64), Expect = 1.3
Identities = 32/135 (23%), Positives = 52/135 (38%), Gaps = 40/135 (29%)
Query: 40 TNLSGGEKTVAALALLFAI----HRIATIRSLGLED---LRSMALAQNQSAQAFLGPENP 92
+ + GE T A ++ F + +R+ RS GL+ R + L Q + + FL
Sbjct: 67 SVFAPGEDT-AEVSFTFQLGGKKYRV--ERSRGLDYDQFTRIVLLPQGEFDR-FL----- 117
Query: 93 EEPYLQGVNYNCVAPGKRFQPMTNLSGGEKTVAALALLFAIHSY------HPAPFFVLDE 146
R P++ LSGGE +A+L+L A+ +DE
Sbjct: 118 ----------------AR--PVSTLSGGETFLASLSLALALSEVLQNRGGARLEALFIDE 159
Query: 147 IDAALDNTNIGKVAS 161
LD + VA+
Sbjct: 160 GFGTLDPEALEAVAT 174
>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 = 28.5 bits (64), Expect = 1.4
Identities = 16/47 (34%), Positives = 20/47 (42%), Gaps = 4/47 (8%)
Query: 113 PMTNLSGGEKTVAALALLFAIHSYHPAPFFVLDEIDAALDNTNIGKV 159
P SGGE+ +A F P +LDE A+LD N V
Sbjct: 146 PPATFSGGEQQRVNIARGFIA----DYPILLLDEPTASLDAANRQVV 188
>gnl|CDD|213181 cd03214, ABC_Iron-Siderophores_B12_Hemin, ATP-binding component of
iron-siderophores, vitamin B12 and hemin transporters
and related proteins. ABC transporters, involved in the
uptake of siderophores, heme, and vitamin B12, are
widely conserved in bacteria and archaea. Only very few
species lack representatives of the siderophore family
transporters. The E. coli BtuCD protein is an ABC
transporter mediating vitamin B12 uptake. The two
ATP-binding cassettes (BtuD) are in close contact with
each other, as are the two membrane-spanning subunits
(BtuC); this arrangement is distinct from that observed
for the E. coli lipid flippase MsbA. The BtuC subunits
provide 20 transmembrane helices grouped around a
translocation pathway that is closed to the cytoplasm by
a gate region, whereas the dimer arrangement of the BtuD
subunits resembles the ATP-bound form of the Rad50 DNA
repair enzyme. A prominent cytoplasmic loop of BtuC
forms the contact region with the ATP-binding cassette
and represent a conserved motif among the ABC
transporters.
Length = 180
Score = 28.2 bits (64), Expect = 1.8
Identities = 15/41 (36%), Positives = 19/41 (46%), Gaps = 4/41 (9%)
Query: 112 QPMTNLSGGEKTVAALALLFAIHSYHPAPFFVLDEIDAALD 152
+P LSGGE+ LA A P +LDE + LD
Sbjct: 93 RPFNELSGGERQRVLLARALAQE----PPILLLDEPTSHLD 129
>gnl|CDD|130261 TIGR01193, bacteriocin_ABC, ABC-type bacteriocin transporter. This
model describes ABC-type bacteriocin transporter. The
amino terminal domain (pfam03412) processes the
N-terminal leader peptide from the bacteriocin while
C-terminal domains resemble ABC transporter membrane
protein and ATP-binding cassette domain. In general,
bacteriocins are agents which are responsible for
killing or inhibiting the closely related species or
even different strains of the same species. Bacteriocins
are usually encoded by bacterial plasmids. Bacteriocins
are named after the species and hence in literature one
encounters various names e.g., leucocin from Leuconostic
geldium; pedicocin from Pedicoccus acidilactici; sakacin
from Lactobacillus sake etc [Protein fate, Protein and
peptide secretion and trafficking, Protein fate, Protein
modification and repair, Transport and binding proteins,
Other].
Length = 708
Score = 28.6 bits (64), Expect = 1.8
Identities = 14/40 (35%), Positives = 21/40 (52%), Gaps = 8/40 (20%)
Query: 115 TNLSGGEKTVAALA--LLFAIHSYHPAPFFVLDEIDAALD 152
+++SGG+K ALA LL + +LDE + LD
Sbjct: 610 SSISGGQKQRIALARALL------TDSKVLILDESTSNLD 643
>gnl|CDD|237453 PRK13633, PRK13633, cobalt transporter ATP-binding subunit;
Provisional.
Length = 280
Score = 28.1 bits (63), Expect = 2.2
Identities = 26/76 (34%), Positives = 35/76 (46%), Gaps = 15/76 (19%)
Query: 85 AFLGPEN----PEEPYLQGVNYNCVAPG----KRFQPMTNLSGGEKTVAALALLFAIHSY 136
AF GPEN PEE + V+ + G +R P LSGG+K A+A + A+
Sbjct: 108 AF-GPENLGIPPEEIRER-VDESLKKVGMYEYRRHAPHL-LSGGQKQRVAIAGILAMRP- 163
Query: 137 HPAPFFVLDEIDAALD 152
+ DE A LD
Sbjct: 164 ---ECIIFDEPTAMLD 176
>gnl|CDD|226360 COG3840, ThiQ, ABC-type thiamine transport system, ATPase component
[Coenzyme metabolism].
Length = 231
Score = 27.7 bits (62), Expect = 2.5
Identities = 14/36 (38%), Positives = 18/36 (50%), Gaps = 4/36 (11%)
Query: 117 LSGGEKTVAALALLFAIHSYHPAPFFVLDEIDAALD 152
LSGG++ ALA P +LDE +ALD
Sbjct: 130 LSGGQRQRVALARCLV----REQPILLLDEPFSALD 161
>gnl|CDD|239449 cd03333, chaperonin_like, chaperonin_like superfamily. Chaperonins
are involved in productive folding of proteins. They
share a common general morphology, a double toroid of 2
stacked rings, each composed of 7-9 subunits. There are
2 main chaperonin groups. The symmetry of type I is
seven-fold and they are found in eubacteria (GroEL) and
in organelles of eubacterial descent (hsp60 and RBP).
The symmetry of type II is eight- or nine-fold and they
are found in archea (thermosome), thermophilic bacteria
(TF55) and in the eukaryotic cytosol (CTT). Their
common function is to sequester nonnative proteins
inside their central cavity and promote folding by using
energy derived from ATP hydrolysis. This superfamily
also contains related domains from Fab1-like
phosphatidylinositol 3-phosphate (PtdIns3P) 5-kinases
that only contain the intermediate and apical domains.
Length = 209
Score = 27.4 bits (62), Expect = 2.8
Identities = 16/53 (30%), Positives = 21/53 (39%), Gaps = 3/53 (5%)
Query: 46 EKTVAALAL-LFAIHRIATIRSLGLEDLRSMALAQNQSAQAFLGPENPEEPYL 97
EK + LAL A I +R + EDL +A A A E+ L
Sbjct: 99 EKGIDDLALHYLAKAGIMAVRRVKKEDLERIARATG--ATIVSSLEDLTPEDL 149
>gnl|CDD|190986 pfam04431, Pec_lyase_N, Pectate lyase, N terminus. This region is
found N terminal to the pectate lyase domain (pfam00544)
in some plant pectate lyase enzymes.
Length = 54
Score = 25.8 bits (57), Expect = 2.9
Identities = 7/26 (26%), Positives = 11/26 (42%)
Query: 125 AALALLFAIHSYHPAPFFVLDEIDAA 150
A A A+ +Y P P V + +
Sbjct: 13 AEEARKAALEAYVPDPENVTNHFNKH 38
>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 = 27.5 bits (61), Expect = 3.3
Identities = 18/36 (50%), Positives = 21/36 (58%), Gaps = 4/36 (11%)
Query: 117 LSGGEKTVAALALLFAIHSYHPAPFFVLDEIDAALD 152
LSGGE+ A+A AI AP VLDE +ALD
Sbjct: 472 LSGGERQRLAIAR--AI--LKNAPILVLDEATSALD 503
>gnl|CDD|223473 COG0396, sufC, Cysteine desulfurase activator ATPase
[Posttranslational modification, protein turnover,
chaperones].
Length = 251
Score = 27.2 bits (61), Expect = 3.9
Identities = 16/42 (38%), Positives = 18/42 (42%), Gaps = 16/42 (38%)
Query: 117 LSGGEKT---VAALALL---FAIHSYHPAPFFVLDEIDAALD 152
SGGEK + L LL AI LDE D+ LD
Sbjct: 145 FSGGEKKRNEILQLLLLEPKLAI----------LDEPDSGLD 176
>gnl|CDD|227245 COG4908, COG4908, Uncharacterized protein containing a NRPS
condensation (elongation) domain [General function
prediction only].
Length = 439
Score = 27.1 bits (60), Expect = 4.5
Identities = 13/62 (20%), Positives = 19/62 (30%), Gaps = 3/62 (4%)
Query: 103 NCVAPGKRFQPMTNLSGGEKTVA--ALALLFAIHSYHPAPFFVLDEIDAALDNTNIGKVA 160
V + + L+G L L+F Y V D +TNIG +
Sbjct: 310 EKVKGIMNPKKI-GLAGLYSFYLLGILPLMFKRKLYLKLKKLVEDRFVEGKSSTNIGIID 368
Query: 161 SY 162
Sbjct: 369 EE 370
>gnl|CDD|237421 PRK13539, PRK13539, cytochrome c biogenesis protein CcmA;
Provisional.
Length = 207
Score = 26.8 bits (60), Expect = 5.0
Identities = 19/51 (37%), Positives = 24/51 (47%), Gaps = 4/51 (7%)
Query: 113 PMTNLSGGEKTVAALALLFAIHSYHPAPFFVLDEIDAALDNTNIGKVASYI 163
P LS G+K ALA L + P ++LDE AALD + A I
Sbjct: 124 PFGYLSAGQKRRVALARLLVSN----RPIWILDEPTAALDAAAVALFAELI 170
>gnl|CDD|213220 cd03253, ABCC_ATM1_transporter, ATP-binding cassette domain of
iron-sulfur clusters transporter, subfamily C. ATM1 is
an ABC transporter that is expressed in the
mitochondria. Although the specific function of ATM1 is
unknown, its disruption results in the accumulation of
excess mitochondrial iron, loss of mitochondrial
cytochromes, oxidative damage to mitochondrial DNA, and
decreased levels of cytosolic heme proteins. ABC
transporters are a large family of proteins involved in
the transport of a wide variety of different compounds,
like sugars, ions, peptides, and more complex organic
molecules. The nucleotide binding domain shows the
highest similarity between all members of the family.
ABC transporters are a subset of nucleotide hydrolases
that contain a signature motif, Q-loop, and
H-loop/switch region, in addition to, the Walker A
motif/P-loop and Walker B motif commonly found in a
number of ATP- and GTP-binding and hydrolyzing proteins.
Length = 236
Score = 26.8 bits (60), Expect = 5.2
Identities = 16/38 (42%), Positives = 20/38 (52%), Gaps = 8/38 (21%)
Query: 117 LSGGEKTVAALA--LLFAIHSYHPAPFFVLDEIDAALD 152
LSGGEK A+A +L P +LDE +ALD
Sbjct: 138 LSGGEKQRVAIARAILKN------PPILLLDEATSALD 169
>gnl|CDD|200554 cd10928, CE4_u4, Putative catalytic domain of uncharacterized
bacterial proteins from the carbohydrate esterase 4
superfamily. This family corresponds to a group of
uncharacterized bacterial proteins with high sequence
similarity to the catalytic domain of the six-stranded
barrel rhizobial NodB-like proteins, which remove
N-linked or O-linked acetyl groups from cell wall
polysaccharides and belong to the larger carbohydrate
esterase 4 (CE4) superfamily.
Length = 222
Score = 26.5 bits (59), Expect = 5.5
Identities = 35/148 (23%), Positives = 52/148 (35%), Gaps = 30/148 (20%)
Query: 30 VAPGKRFQPMTNLSGGEKTVAALALLFAIHRIATIRSLGLEDLRSMALAQN--------- 80
AP + +L G ALA++ A A +++L + L A+ Q+
Sbjct: 10 GAPTPALDRLLDLFGRHSVPLALAVIPAWRTDALLKALAGDPL--AAVHQHGWAHVNHAP 67
Query: 81 --QSAQAFLGPENPEEPYL----QGVNYNCVAPGKRFQPM-----TNLSGGEKTVAALAL 129
+ Q F GP P E L G+ G RF P L + AL
Sbjct: 68 PGKKKQEF-GPSRPLEDVLAELGAGLARLEALFGDRFVPAFVPPWNRLD--PGLLPALGG 124
Query: 130 L-FAIHSY----HPAPFFVLDEIDAALD 152
L ++ S P P L +D +D
Sbjct: 125 LGYSALSRFGPRKPPPPPGLPRLDVHVD 152
>gnl|CDD|215558 PLN03073, PLN03073, ABC transporter F family; Provisional.
Length = 718
Score = 26.7 bits (59), Expect = 6.1
Identities = 16/41 (39%), Positives = 21/41 (51%), Gaps = 4/41 (9%)
Query: 112 QPMTNLSGGEKTVAALALLFAIHSYHPAPFFVLDEIDAALD 152
QPM LSGG+K+ A FA ++ +LDE LD
Sbjct: 623 QPMYTLSGGQKSRVA----FAKITFKKPHILLLDEPSNHLD 659
>gnl|CDD|184128 PRK13541, PRK13541, cytochrome c biogenesis protein CcmA;
Provisional.
Length = 195
Score = 26.4 bits (58), Expect = 6.1
Identities = 13/40 (32%), Positives = 21/40 (52%), Gaps = 4/40 (10%)
Query: 116 NLSGGEKTVAALALLFAIHSYHPAPFFVLDEIDAALDNTN 155
+LS G + + A+A L A S ++LDE++ L N
Sbjct: 123 SLSSGMQKIVAIARLIACQS----DLWLLDEVETNLSKEN 158
>gnl|CDD|233062 TIGR00630, uvra, excinuclease ABC, A subunit. This family is a
member of the ABC transporter superfamily of proteins of
which all members for which functions are known except
the UvrA proteins are involved in the transport of
material through membranes. UvrA orthologs are involved
in the recognition of DNA damage as a step in nucleotide
excision repair. This family is based on the
phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis,
Stanford University) [DNA metabolism, DNA replication,
recombination, and repair].
Length = 925
Score = 26.9 bits (60), Expect = 6.2
Identities = 14/35 (40%), Positives = 17/35 (48%), Gaps = 1/35 (2%)
Query: 112 QPMTNLSGGEKTVAALALLFAIHSYHPAPFFVLDE 146
QP T LSGGE LA + S ++LDE
Sbjct: 825 QPATTLSGGEAQRIKLAKELSKRSTGRT-LYILDE 858
>gnl|CDD|227320 COG4987, CydC, ABC-type transport system involved in cytochrome bd
biosynthesis, fused ATPase and permease components
[Energy production and conversion / Posttranslational
modification, protein turnover, chaperones].
Length = 573
Score = 26.9 bits (60), Expect = 6.5
Identities = 16/40 (40%), Positives = 19/40 (47%), Gaps = 4/40 (10%)
Query: 116 NLSGGEKTVAALALLFAIHSYHPAPFFVLDEIDAALDNTN 155
LSGGE+ ALA H AP ++LDE LD
Sbjct: 474 RLSGGERRRLALARAL----LHDAPLWLLDEPTEGLDPIT 509
>gnl|CDD|227118 COG4778, PhnL, ABC-type phosphonate transport system, ATPase
component [Inorganic ion transport and metabolism].
Length = 235
Score = 26.6 bits (59), Expect = 6.9
Identities = 17/51 (33%), Positives = 22/51 (43%), Gaps = 4/51 (7%)
Query: 113 PMTNLSGGEKTVAALALLFAIHSYHPAPFFVLDEIDAALDNTNIGKVASYI 163
SGGE+ +A F + P +LDE A+LD TN V I
Sbjct: 149 APATFSGGEQQRVNIARGFIVDY----PILLLDEPTASLDATNRAVVVELI 195
>gnl|CDD|234189 TIGR03375, type_I_sec_LssB, type I secretion system ATPase, LssB
family. Type I protein secretion is a system in some
Gram-negative bacteria to export proteins (often
proteases) across both inner and outer membranes to the
extracellular medium. This is one of three proteins of
the type I secretion apparatus. Targeted proteins are
not cleaved at the N-terminus, but rather carry signals
located toward the extreme C-terminus to direct type I
secretion. This model is related to models TIGR01842 and
TIGR01846, and to bacteriocin ABC transporters that
cleave their substrates during export [Protein fate,
Protein and peptide secretion and trafficking, Cellular
processes, Pathogenesis].
Length = 694
Score = 26.8 bits (60), Expect = 7.2
Identities = 14/40 (35%), Positives = 21/40 (52%), Gaps = 4/40 (10%)
Query: 116 NLSGGEKTVAALALLFAIHSYHPAPFFVLDEIDAALDNTN 155
+LSGG++ ALA P +LDE +A+DN +
Sbjct: 601 SLSGGQRQAVALARAL----LRDPPILLLDEPTSAMDNRS 636
>gnl|CDD|200134 TIGR01842, type_I_sec_PrtD, type I secretion system ABC
transporter, PrtD family. Type I protein secretion is a
system in some Gram-negative bacteria to export proteins
(often proteases) across both inner and outer membranes
to the extracellular medium. This is one of three
proteins of the type I secretion apparatus. Targeted
proteins are not cleaved at the N-terminus, but rather
carry signals located toward the extreme C-terminus to
direct type I secretion [Protein fate, Protein and
peptide secretion and trafficking].
Length = 544
Score = 26.5 bits (59), Expect = 7.7
Identities = 14/38 (36%), Positives = 19/38 (50%), Gaps = 6/38 (15%)
Query: 116 NLSGGEKTVAALALLFAIHSYHPAPFFV-LDEIDAALD 152
LSGG++ ALA + P V LDE ++ LD
Sbjct: 454 TLSGGQRQRIALARAL-----YGDPKLVVLDEPNSNLD 486
>gnl|CDD|183044 PRK11231, fecE, iron-dicitrate transporter ATP-binding subunit;
Provisional.
Length = 255
Score = 26.1 bits (58), Expect = 7.8
Identities = 15/41 (36%), Positives = 23/41 (56%), Gaps = 4/41 (9%)
Query: 112 QPMTNLSGGEKTVAALALLFAIHSYHPAPFFVLDEIDAALD 152
+ +T+LSGG++ A LA++ A P +LDE LD
Sbjct: 134 RRLTDLSGGQRQRAFLAMVLA----QDTPVVLLDEPTTYLD 170
>gnl|CDD|233305 TIGR01189, ccmA, heme ABC exporter, ATP-binding protein CcmA. This
model describes the cyt c biogenesis protein encoded by
ccmA in bacteria. An exception is, an arabidopsis
protein. Quite likely this is encoded by an organelle.
Bacterial c-type cytocromes are located on the
periplasmic side of the cytoplasmic membrane. Several
gene products encoded in a locus designated as 'ccm' are
implicated in the transport and assembly of the
functional cytochrome C. This cluster includes genes:
ccmA;B;C;D;E;F;G and H. The posttranslational pathway
includes the transport of heme moiety, the secretion of
the apoprotein and the covalent attachment of the heme
with the apoprotein. The proteins ccmA and B represent
an ABC transporter; ccmC and D participate in heme
transfer to ccmE, which function as a periplasmic heme
chaperone. The presence of ccmF, G and H is suggested to
be obligatory for the final functional assembly of
cytochrome c [Protein fate, Protein and peptide
secretion and trafficking, Transport and binding
proteins, Other].
Length = 198
Score = 26.2 bits (58), Expect = 8.0
Identities = 16/40 (40%), Positives = 21/40 (52%), Gaps = 4/40 (10%)
Query: 113 PMTNLSGGEKTVAALALLFAIHSYHPAPFFVLDEIDAALD 152
P LS G++ ALA L+ AP ++LDE ALD
Sbjct: 124 PAAQLSAGQQRRLALARLWLSR----APLWILDEPTTALD 159
>gnl|CDD|224048 COG1123, COG1123, ATPase components of various ABC-type transport
systems, contain duplicated ATPase [General function
prediction only].
Length = 539
Score = 26.4 bits (59), Expect = 8.4
Identities = 13/36 (36%), Positives = 19/36 (52%), Gaps = 4/36 (11%)
Query: 117 LSGGEKTVAALALLFAIHSYHPAPFFVLDEIDAALD 152
LSGG++ A+A A+ +LDE +ALD
Sbjct: 430 LSGGQRQRVAIARALALEPK----LLILDEPVSALD 461
>gnl|CDD|184198 PRK13638, cbiO, cobalt transporter ATP-binding subunit;
Provisional.
Length = 271
Score = 26.1 bits (57), Expect = 8.5
Identities = 17/47 (36%), Positives = 23/47 (48%), Gaps = 4/47 (8%)
Query: 106 APGKRFQPMTNLSGGEKTVAALALLFAIHSYHPAPFFVLDEIDAALD 152
A R QP+ LS G+K A+A + A + +LDE A LD
Sbjct: 126 AQHFRHQPIQCLSHGQKKRVAIAGALVLQ----ARYLLLDEPTAGLD 168
>gnl|CDD|182993 PRK11144, modC, molybdate transporter ATP-binding protein;
Provisional.
Length = 352
Score = 26.4 bits (59), Expect = 8.9
Identities = 19/47 (40%), Positives = 25/47 (53%), Gaps = 12/47 (25%)
Query: 109 KRFQPMTNLSGGEKTVAAL--ALLFAIHSYHPAP-FFVLDEIDAALD 152
R+ P + LSGGEK A+ ALL AP ++DE A+LD
Sbjct: 123 DRY-PGS-LSGGEKQRVAIGRALL-------TAPELLLMDEPLASLD 160
>gnl|CDD|172759 PRK14271, PRK14271, phosphate ABC transporter ATP-binding protein;
Provisional.
Length = 276
Score = 26.2 bits (57), Expect = 8.9
Identities = 16/47 (34%), Positives = 25/47 (53%), Gaps = 4/47 (8%)
Query: 117 LSGGEKTVAALALLFAIHSYHPAPFFVLDEIDAALDNTNIGKVASYI 163
LSGG++ + LA A++ +LDE +ALD T K+ +I
Sbjct: 164 LSGGQQQLLCLARTLAVNP----EVLLLDEPTSALDPTTTEKIEEFI 206
>gnl|CDD|184132 PRK13547, hmuV, hemin importer ATP-binding subunit; Provisional.
Length = 272
Score = 26.3 bits (58), Expect = 9.1
Identities = 18/44 (40%), Positives = 23/44 (52%), Gaps = 5/44 (11%)
Query: 114 MTNLSGGE----KTVAALALLFAIHSYHPAP-FFVLDEIDAALD 152
+T LSGGE + LA L+ H P + +LDE AALD
Sbjct: 143 VTTLSGGELARVQFARVLAQLWPPHDAAQPPRYLLLDEPTAALD 186
>gnl|CDD|184214 PRK13657, PRK13657, cyclic beta-1,2-glucan ABC transporter;
Provisional.
Length = 588
Score = 26.5 bits (59), Expect = 9.4
Identities = 16/38 (42%), Positives = 20/38 (52%), Gaps = 8/38 (21%)
Query: 117 LSGGEKTVAALA--LLFAIHSYHPAPFFVLDEIDAALD 152
LSGGE+ A+A LL P +LDE +ALD
Sbjct: 472 LSGGERQRLAIARALL------KDPPILILDEATSALD 503
>gnl|CDD|184199 PRK13639, cbiO, cobalt transporter ATP-binding subunit;
Provisional.
Length = 275
Score = 26.2 bits (58), Expect = 9.4
Identities = 15/41 (36%), Positives = 22/41 (53%), Gaps = 4/41 (9%)
Query: 112 QPMTNLSGGEKTVAALALLFAIHSYHPAPFFVLDEIDAALD 152
+P +LSGG+K A+A + A+ VLDE + LD
Sbjct: 133 KPPHHLSGGQKKRVAIAGILAMKP----EIIVLDEPTSGLD 169
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
0.317 0.134 0.388
Gapped
Lambda K H
0.267 0.0793 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,486,710
Number of extensions: 769182
Number of successful extensions: 967
Number of sequences better than 10.0: 1
Number of HSP's gapped: 955
Number of HSP's successfully gapped: 138
Length of query: 163
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 74
Effective length of database: 6,990,096
Effective search space: 517267104
Effective search space used: 517267104
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 55 (24.8 bits)