RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17514
(159 letters)
>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 = 258 bits (661), Expect = 2e-88
Identities = 103/156 (66%), Positives = 121/156 (77%), Gaps = 1/156 (0%)
Query: 1 MYIKSMVLDGFKSYGTRVEINDFDREFNAITGLNGTGKSNILDGICFVLGIQ-VKQVRAN 59
M+IK ++LDGFKSY TR I+ FD +FNAITGLNG+GKSNILD ICFVLGI + VRA+
Sbjct: 1 MHIKEIILDGFKSYATRTVISGFDPQFNAITGLNGSGKSNILDAICFVLGITNLSTVRAS 60
Query: 60 TLQELIYKNGQAGVTKASVTLTFDNSDKKNCPIGYENDNTIVICRQISIPSNTRYMINGS 119
LQ+LIYK GQAG+TKASVT+ FDNSDK PIG+EN I + RQI + +Y+ING
Sbjct: 61 NLQDLIYKRGQAGITKASVTIVFDNSDKSQSPIGFENYPEITVTRQIVLGGTNKYLINGH 120
Query: 120 SVNPKRVSDLFSSVNLNVNNPHFLIMQGRVTKVLNM 155
+RV DLF SV LNVNNPHFLIMQGR+TKVLNM
Sbjct: 121 RAQQQRVQDLFQSVQLNVNNPHFLIMQGRITKVLNM 156
>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and
chromosome partitioning].
Length = 1163
Score = 185 bits (471), Expect = 6e-55
Identities = 65/162 (40%), Positives = 90/162 (55%), Gaps = 9/162 (5%)
Query: 1 MYIKSMVLDGFKSYGTRVEINDFDREFNAITGLNGTGKSNILDGICFVLGIQ-VKQVRAN 59
MY+K + L GFKS+ EIN F F AI G NG+GKSNI+D I FVLG Q K +RA+
Sbjct: 1 MYLKRIELKGFKSFADPTEIN-FSPGFTAIVGPNGSGKSNIVDAIRFVLGEQSAKNLRAS 59
Query: 60 TLQELIYK--NGQAGVTKASVTLTFDNSDKKNCPIGYENDNTIVICRQISIPSNTRYMIN 117
+ +LI+ + A V LTFDNSD P+ YE I + R+I + Y IN
Sbjct: 60 KMSDLIFAGSGNRKPANYAEVELTFDNSDNTL-PLEYE---EISVTRRIYRDGESEYYIN 115
Query: 118 GSSVNPKRVSDLFSSVNLNVNNPHFLIMQGRVTKVLNMKPHE 159
G V K + DL + + + ++ QG+V +++N KP E
Sbjct: 116 GEKVRLKDIQDLLADSGIGKESY-SIVSQGKVEEIINAKPEE 156
>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 = 172 bits (437), Expect = 2e-50
Identities = 62/158 (39%), Positives = 89/158 (56%), Gaps = 7/158 (4%)
Query: 2 YIKSMVLDGFKSYGTRVEINDFDREFNAITGLNGTGKSNILDGICFVLGIQ-VKQVRANT 60
Y+K + ++GFKSY V + F F AI G NG+GKSNILD I FVLG + K +R+
Sbjct: 1 YLKRIEIEGFKSYAKTVIL-PFSPGFTAIVGPNGSGKSNILDAILFVLGERSAKSLRSER 59
Query: 61 LQELIYK-NGQAGVTKASVTLTFDNSDKKNCPIGYENDNTIVICRQISIPSNTRYMINGS 119
L +LI+ A V A VT+TFDN DK+ +D + I R++ ++ Y ING
Sbjct: 60 LSDLIHYSKSGAFVNSAEVTITFDNEDKE----LPIDDPEVSIRRRVYRGGDSEYYINGK 115
Query: 120 SVNPKRVSDLFSSVNLNVNNPHFLIMQGRVTKVLNMKP 157
V K V++L S ++ +FL+ G+V + MKP
Sbjct: 116 DVTKKDVAELLESAGISPEAYNFLVQGGKVEIIAMMKP 153
>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 = 125 bits (315), Expect = 7e-34
Identities = 51/163 (31%), Positives = 81/163 (49%), Gaps = 14/163 (8%)
Query: 2 YIKSMVLDGFKSYGTRVEINDFDREFNAITGLNGTGKSNILDGICFVLGIQ-VKQVRANT 60
YI+ + L+ FKS+G + I F + F I+G NG+GKSNI D I F LG+ K +RA
Sbjct: 1 YIERIELENFKSFGKKKVIP-FSKGFTVISGPNGSGKSNIGDAILFALGLSSSKAMRAER 59
Query: 61 LQELIYK-NGQAGVTKASVTLTFDNSDKKNCPIGYENDNTIVICRQISI---PSNTRYMI 116
L +LI +A VT+TF N D K + + + R++ + + Y +
Sbjct: 60 LSDLISNGKNGQSGNEAYVTVTFKNDDGK-------FPDELEVVRRLKVTDDGKYSYYYL 112
Query: 117 NGSSVNPKRVSDLFSSVNLNVNNPHFLIMQGRVTKVLNMKPHE 159
NG V + D ++ + + ++QG VT ++M P E
Sbjct: 113 NGQRVRLSEIHDFLAAAGIYPEGYNV-VLQGDVTDFISMSPVE 154
>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 = 108 bits (272), Expect = 3e-28
Identities = 57/162 (35%), Positives = 85/162 (52%), Gaps = 10/162 (6%)
Query: 2 YIKSMVLDGFKSYGTRVEINDFDREFNAITGLNGTGKSNILDGICFVLGIQ-VKQVRANT 60
+K + L GFKS+ IN FD+ I G NG GKSNI+D I +VLG Q K +R
Sbjct: 1 RLKKLELAGFKSFADPTTIN-FDKGITGIVGPNGCGKSNIVDAIRWVLGEQSAKALRGGK 59
Query: 61 LQELIYKNG---QAGVTKASVTLTFDNSDKKNCPIGYENDNTIVICRQISIPSNTRYMIN 117
++++I+ NG + ++ A V L FDNSD Y I I R++ + Y IN
Sbjct: 60 MEDVIF-NGSETRKPLSLAEVELVFDNSDGLLPGADYS---EISITRRLYRDGESEYFIN 115
Query: 118 GSSVNPKRVSDLFSSVNLNVNNPHFLIMQGRVTKVLNMKPHE 159
G K + DLF L + + +I QG++++++ KP E
Sbjct: 116 GQPCRLKDIQDLFLDTGLGKRS-YSIIEQGKISEIIEAKPEE 156
>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 = 98.3 bits (246), Expect = 2e-26
Identities = 37/89 (41%), Positives = 51/89 (57%), Gaps = 4/89 (4%)
Query: 3 IKSMVLDGFKSYGTRVEINDFDREFNAITGLNGTGKSNILDGICFVLGIQ-VKQVRANTL 61
+K + L GFKS+ + I F AI G NG+GKSNI+D I +VLG Q K +R +
Sbjct: 1 LKKLELKGFKSFADKTTIP-FPPGLTAIVGPNGSGKSNIIDAIRWVLGEQSAKSLRGEKM 59
Query: 62 QELIYK--NGQAGVTKASVTLTFDNSDKK 88
++I+ + A VTLTFDNSD +
Sbjct: 60 SDVIFAGSETRKPANFAEVTLTFDNSDGR 88
>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 = 98.1 bits (245), Expect = 6e-26
Identities = 48/154 (31%), Positives = 79/154 (51%), Gaps = 5/154 (3%)
Query: 3 IKSMVLDGFKSYGTRVEINDFDREFNAITGLNGTGKSNILDGICFVLGIQVKQVRANTLQ 62
IK +++ GFKSY + I F + N + G NG+GKSN I FVL + +R Q
Sbjct: 1 IKQVIIQGFKSYKDQTVIEPFSPKHNVVVGRNGSGKSNFFAAIRFVLSDEYTHLREEQRQ 60
Query: 63 ELIYKNGQAGVTKASVTLTFDNSDKKNCPIGYENDNTIVICRQISIPSNTRYMINGSSVN 122
L+++ V A V + FDNSD + PI + + R I + + Y ++ +V
Sbjct: 61 ALLHEGSGPSVMSAYVEIIFDNSDNR-FPID---KEEVRLRRTIGLKKD-EYFLDKKNVT 115
Query: 123 PKRVSDLFSSVNLNVNNPHFLIMQGRVTKVLNMK 156
V +L S + +NP++++ QG++ + NMK
Sbjct: 116 KNDVMNLLESAGFSRSNPYYIVPQGKINSLTNMK 149
>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 = 93.0 bits (232), Expect = 7e-24
Identities = 51/157 (32%), Positives = 79/157 (50%), Gaps = 14/157 (8%)
Query: 3 IKSMVLDGFKSYGTRVEINDFDREFNAITGLNGTGKSNILDGICFVLGIQVKQVRANTLQ 62
+K + L+ FKSY R I FDR F I G NG+GKSN++D I FVLG + +R+ L+
Sbjct: 1 LKRLELENFKSYKGRHVIGPFDR-FTCIIGPNGSGKSNLMDAISFVLGEKSSHLRSKNLK 59
Query: 63 ELIY--KNGQAGVTKASVTLTFDNSDKKNCPIGYENDNTIVICRQISIPSNTRYMINGSS 120
+LIY + G+ A VT ++ ++ R I ++ Y ING
Sbjct: 60 DLIYRARVGKPDSNSAYVTAVYE----------DDDGEEKTFRRII-TGGSSSYRINGKV 108
Query: 121 VNPKRVSDLFSSVNLNVNNPHFLIMQGRVTKVLNMKP 157
V+ K ++ +N+ V +FL+ QG V + + P
Sbjct: 109 VSLKEYNEELEKINILVKARNFLVFQGDVESIASKNP 145
>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 = 88.5 bits (220), Expect = 9e-23
Identities = 38/83 (45%), Positives = 50/83 (60%), Gaps = 1/83 (1%)
Query: 3 IKSMVLDGFKSYGTRVEINDFDREFNAITGLNGTGKSNILDGICFVLGIQVKQVRANTLQ 62
IK + L FKSY + + FNAI G NG+GKSNI+D ICFVLG + ++R +L
Sbjct: 1 IKQITLKNFKSYRDETVVGGSNS-FNAIVGPNGSGKSNIVDAICFVLGGKAAKLRRGSLL 59
Query: 63 ELIYKNGQAGVTKASVTLTFDNS 85
L +AG+ ASV +TFD S
Sbjct: 60 FLAGGGVKAGINSASVEITFDKS 82
>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 = 77.7 bits (192), Expect = 3e-18
Identities = 31/83 (37%), Positives = 47/83 (56%), Gaps = 1/83 (1%)
Query: 1 MYIKSMVLDGFKSYGTRVEINDFDREFNAITGLNGTGKSNILDGICFVLGIQVKQVRANT 60
+ I +VL+ FKSY I F + F+AI G NG+GKSN++D + FV G + ++R
Sbjct: 1 LIITKLVLENFKSYAGEQVIGPFHKSFSAIVGPNGSGKSNVIDSMLFVFGFRASKMRQKK 60
Query: 61 LQELIYK-NGQAGVTKASVTLTF 82
L +LI+ G + SV + F
Sbjct: 61 LSDLIHNSAGHPNLDSCSVEVHF 83
>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication,
recombination, and repair].
Length = 908
Score = 69.4 bits (170), Expect = 2e-14
Identities = 32/88 (36%), Positives = 43/88 (48%), Gaps = 4/88 (4%)
Query: 1 MYIKSMVLDGFKSYGTRVEINDFDREFNAITGLNGTGKSNILDGICFVLGIQVKQVRANT 60
M I + L F+S+ FD I G NG GKS+ILD I F L + ++ A +
Sbjct: 1 MKILRLRLKNFRSFKDIDIEKLFDSGIFLIVGPNGAGKSSILDAITFALYGKTPRLGAFS 60
Query: 61 LQELIYKNGQAGVTKASVTLTFDNSDKK 88
L +LI G ASV L F+ + KK
Sbjct: 61 LDDLIRA----GEKSASVELEFEVNGKK 84
>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 = 64.5 bits (158), Expect = 4e-13
Identities = 40/113 (35%), Positives = 60/113 (53%), Gaps = 16/113 (14%)
Query: 22 DFDREFNAITGLNGTGKSNILDGICFVLGIQVKQVRANTLQELIYKNGQAGVTKASVTLT 81
DF+ +TG G GKS +LD + +LG RA+ +LI ++G KA V
Sbjct: 18 DFEEGLTVLTGETGAGKSILLDALSLLLGG-----RASA--DLI----RSGAEKAVVEGV 66
Query: 82 FDNSDKKN-----CPIGYENDNTIVICRQISIPSNTRYMINGSSVNPKRVSDL 129
FD SD++ +G E+D+ ++I R+IS +RY ING SV K + +L
Sbjct: 67 FDISDEEEAKALLLELGIEDDDDLIIRREISRKGRSRYFINGQSVTLKLLREL 119
>gnl|CDD|222160 pfam13476, AAA_23, AAA domain.
Length = 204
Score = 60.3 bits (146), Expect = 8e-12
Identities = 26/102 (25%), Positives = 45/102 (44%), Gaps = 6/102 (5%)
Query: 5 SMVLDGFKSYGTRVEINDFDREFNAITGLNGTGKSNILDGICFVLGIQVKQVRANTLQEL 64
+ + F S+ +EI DF + I G NG+GK+ ILD I + L + +++ + + +
Sbjct: 1 KLTIKNFGSFK-DLEI-DFSKGLTLIYGPNGSGKTTILDAIRWALYGKTSRLKKSKGRGI 58
Query: 65 ----IYKNGQAGVTKASVTLTFDNSDKKNCPIGYENDNTIVI 102
I G K V +TF+N+ K E +
Sbjct: 59 VKGDIEIEKDEGKKKTYVEITFENNKGKLKLRLIEESRELTK 100
>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 = 59.3 bits (144), Expect = 9e-12
Identities = 23/78 (29%), Positives = 31/78 (39%), Gaps = 7/78 (8%)
Query: 5 SMVLDGFKSYGTRVEINDFDREFNAITGLNGTGKSNILDGICFVLGIQVKQVRANTLQEL 64
+VL F SY ++ + ITG NG+GKS ILD I LG
Sbjct: 1 KIVLGRFPSYFVPNDVTFGEGSLTIITGPNGSGKSTILDAIGLALGGA-------QSATR 53
Query: 65 IYKNGQAGVTKASVTLTF 82
+AG A+V+
Sbjct: 54 RRSGVKAGCIVAAVSAEL 71
>gnl|CDD|223571 COG0497, RecN, ATPase involved in DNA repair [DNA replication,
recombination, and repair].
Length = 557
Score = 56.1 bits (136), Expect = 7e-10
Identities = 31/112 (27%), Positives = 50/112 (44%), Gaps = 18/112 (16%)
Query: 22 DFDREFNAITGLNGTGKSNILDGICFVLGIQVKQVRANTLQELIYKNGQAGVTKASVTLT 81
+F++ +TG G GKS I+D + +LG RA+ L+ G +A V
Sbjct: 19 EFEKGLTVLTGETGAGKSIIIDALGLLLG-----GRADA--SLVRH----GAKRAEVEAI 67
Query: 82 FDNSDKKNCPI----GYENDNTIVICRQISIPSNTRYMINGSSVNPKRVSDL 129
FD + G E+D +++ R IS +R ING V+ ++ L
Sbjct: 68 FDLDNPPARAWLEENGIEDDEEVILRRVISADGRSRAFINGQPVS---LAQL 116
>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 = 51.8 bits (125), Expect = 9e-09
Identities = 29/110 (26%), Positives = 48/110 (43%), Gaps = 15/110 (13%)
Query: 3 IKSMVLDGFKSYGTRVEINDFDREFNAITGLNGTGKSNILDGICFVL-GIQVKQVRANT- 60
I + + +S+ R EI +F I G NG GK+ I++ + + L G +
Sbjct: 1 IDKLSIRNIRSFHERSEI-EFFSPLTLIVGQNGAGKTTIIEALKYALTGELPPNSKGGAH 59
Query: 61 LQELIYKNGQAGVTKASVTLTFDNSDKKNCPIG-----YENDNTIVICRQ 105
+LI + G +A V L F+N++ K I EN ++ C Q
Sbjct: 60 DPKLIRE----GEVRAQVKLAFENANGKKYTITRSLAILEN---VIFCHQ 102
>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 = 52.0 bits (125), Expect = 1e-08
Identities = 28/138 (20%), Positives = 54/138 (39%), Gaps = 22/138 (15%)
Query: 18 VEINDFDREFNAITGLNGTGKSNILDGICFVLGIQVKQVRANTLQELIYKNGQAGVTKAS 77
+ + F+R +TG G GKS I+D + + G ++ A+ ++ G +A
Sbjct: 16 LTVE-FERGLTVLTGETGAGKSMIIDALSLLGG---QRAGASRVRS--------GENRAV 63
Query: 78 VTLTFDNSDKKNC------PIGYENDNTIVIC---RQISIPSNTRYMINGSSVNPKRVSD 128
V F + I E ++ R IS +R +NG V+ + +
Sbjct: 64 VEGRFTTESLDDADYPALQAIELEEEDEDGEVILRRSISRDGRSRAYLNGKPVSASSLLE 123
Query: 129 LFSS-VNLNVNNPHFLIM 145
S ++L+ + L+
Sbjct: 124 FTSELLDLHGQHDQQLLF 141
>gnl|CDD|234608 PRK00064, recF, recombination protein F; Reviewed.
Length = 361
Score = 49.8 bits (120), Expect = 1e-07
Identities = 28/130 (21%), Positives = 56/130 (43%), Gaps = 23/130 (17%)
Query: 1 MYIKSMVLDGFKSYGTRVEINDFDREFNAITGLNGTGKSNILDGICFV-LGIQVKQVRAN 59
MY+ + L F++Y +++ + N + G NG GK+N+L+ I + G + R
Sbjct: 1 MYLTRLSLTDFRNY-EELDL-ELSPGVNVLVGENGQGKTNLLEAIYLLAPG---RSHRTA 55
Query: 60 TLQELIYKNGQAGVTKASVTLTFDNSDKKNCPIGYENDNTIVICRQISIPSNTRYMINGS 119
+ELI + G A + + ++ P+G +I + ING
Sbjct: 56 RDKELI-RFGAEA---AVIHGRVEKGGRE-LPLG----------LEIDKKGGRKVRINGE 100
Query: 120 SVNPKRVSDL 129
+++++L
Sbjct: 101 PQ--RKLAEL 108
>gnl|CDD|224116 COG1195, RecF, Recombinational DNA repair ATPase (RecF pathway)
[DNA replication, recombination, and repair].
Length = 363
Score = 48.8 bits (117), Expect = 2e-07
Identities = 33/136 (24%), Positives = 63/136 (46%), Gaps = 23/136 (16%)
Query: 1 MYIKSMVLDGFKSYGTRVEINDFDREFNAITGLNGTGKSNILDGICFV-LGIQVKQVRAN 59
MY+ S++L F++Y +++ D N + G NG GK+N+L+ I + LG + R +
Sbjct: 1 MYLLSLLLRNFRNY-AELDL-DLSPGVNVLVGENGQGKTNLLEAIYLLALG---RSHRTS 55
Query: 60 TLQELIYKNGQAGVTKASVTLTFDNSDKKNCPIGYENDNTIVICRQISIPSNTRYMINGS 119
+ELI + G +A ++ G E + I ++ R ING+
Sbjct: 56 RDKELI----RTGADEAEISARVQR-------KGREGTLGLQISKK----GRRRVRINGT 100
Query: 120 SVNPKRVSDLFSSVNL 135
++++L +N+
Sbjct: 101 KAR--KLAELAGHLNV 114
>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 = 47.3 bits (113), Expect = 4e-07
Identities = 27/93 (29%), Positives = 34/93 (36%), Gaps = 10/93 (10%)
Query: 1 MYIKSMVLDGFKSYGTRVEINDF----DREFNAITGLNGTGKSNILDGICFVL-GIQVKQ 55
M + L F + I DF + I G G GKS ILD I + L G +
Sbjct: 1 MKPLKLELKNFGPFREEQVI-DFTGLDNNGLFLICGPTGAGKSTILDAITYALYG----K 55
Query: 56 VRANTLQELIYKNGQAGVTKASVTLTFDNSDKK 88
QE + G A V+ TF KK
Sbjct: 56 TPRYGRQENLRSVFAPGEDTAEVSFTFQLGGKK 88
>gnl|CDD|233051 TIGR00611, recf, recF protein. All proteins in this family for
which functions are known are DNA binding proteins that
assist the filamentation of RecA onto DNA for the
initiation of recombination or recombinational 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 = 365
Score = 47.4 bits (113), Expect = 5e-07
Identities = 20/65 (30%), Positives = 34/65 (52%), Gaps = 4/65 (6%)
Query: 1 MYIKSMVLDGFKSYGTRVEINDFDREFNAITGLNGTGKSNILDGICFVLGIQVKQVRANT 60
MY+ + L F++Y V++ + N I G NG GK+N+L+ I + L + R +
Sbjct: 1 MYLSRLELTDFRNY-DAVDL-ELSPGVNVIVGPNGQGKTNLLEAIYY-LA-LGRSHRTSR 56
Query: 61 LQELI 65
+ LI
Sbjct: 57 DKPLI 61
>gnl|CDD|235175 PRK03918, PRK03918, chromosome segregation protein; Provisional.
Length = 880
Score = 43.5 bits (103), Expect = 1e-05
Identities = 25/91 (27%), Positives = 43/91 (47%), Gaps = 11/91 (12%)
Query: 1 MYIKSMVLDGFKSY-GTRVEINDFDREFNAITGLNGTGKSNILDGICFVLGIQVKQVRAN 59
M I+ + + F+S+ + VE FD N I G NG+GKS+IL+ I V +
Sbjct: 1 MKIEELKIKNFRSHKSSVVE---FDDGINLIIGQNGSGKSSILEAI-LVGLYWGHGSKPK 56
Query: 60 TLQ--ELIYKNGQAGVTKASVTLTFDNSDKK 88
L+ + + G + + L F+ + +K
Sbjct: 57 GLKKDDFT----RIGGSGTEIELKFEKNGRK 83
>gnl|CDD|213209 cd03242, ABC_RecF, ATP-binding cassette domain of RecF. RecF is a
recombinational DNA repair ATPase that maintains
replication in the presence of DNA damage. When
replication is prematurely disrupted by DNA damage,
several recF pathway gene products play critical roles
processing the arrested replication fork, allowing it to
resume and complete its task. This CD represents the
nucleotide binding domain of RecF. RecF belongs to a
large superfamily of ABC transporters 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 with 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 = 270
Score = 43.1 bits (102), Expect = 2e-05
Identities = 32/132 (24%), Positives = 58/132 (43%), Gaps = 21/132 (15%)
Query: 3 IKSMVLDGFKSYGTRVEINDFDREFNAITGLNGTGKSNILDGICFVLGIQVKQVRANTLQ 62
+KS+ L F++Y +E+ +F+ + G N GK+N+L+ I + K R + +
Sbjct: 1 LKSLELRNFRNY-AELEL-EFEPGVTVLVGENAQGKTNLLEAISLLA--TGKSHRTSRDK 56
Query: 63 ELIYKNGQAGVTKASVTLTFDNSDKKNCPIGYENDNTIVICRQISIPSNTRYMINGSSVN 122
ELI + G +A ++ + G E + I + +NG V
Sbjct: 57 ELI----RWGAEEAKISAVLERQ-------GGELALELTIRS----GGGRKARLNGIKV- 100
Query: 123 PKRVSDLFSSVN 134
+R+SDL +N
Sbjct: 101 -RRLSDLLGVLN 111
>gnl|CDD|129705 TIGR00618, sbcc, exonuclease SbcC. All proteins in this family
for which functions are known are part of an
exonuclease complex with sbcD homologs. This complex is
involved in the initiation of recombination to regulate
the levels of palindromic sequences in DNA. 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 = 1042
Score = 43.0 bits (101), Expect = 2e-05
Identities = 16/51 (31%), Positives = 20/51 (39%), Gaps = 3/51 (5%)
Query: 1 MYIKSMVLDGFKSYGTRVEINDFDRE--FNAITGLNGTGKSNILDGICFVL 49
M + L F SY DF I G G GK+ +LD I + L
Sbjct: 1 MKPLRLTLKNFGSY-KGTHTIDFTALGPIFLICGKTGAGKTTLLDAITYAL 50
>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 = 41.8 bits (99), Expect = 3e-05
Identities = 23/65 (35%), Positives = 36/65 (55%), Gaps = 5/65 (7%)
Query: 22 DFDREFNAITGLNGTGKSNILDGICFVLGIQVKQV-RANTLQELIYKNGQAGVTKASVTL 80
+F N I G NG+GKS IL + LG + R ++L++LI K+G+ + A +T+
Sbjct: 18 EFGPRVNFIVGNNGSGKSAILTALTIGLGGKASDTNRGSSLKDLI-KDGE---SSAKITV 73
Query: 81 TFDNS 85
T N
Sbjct: 74 TLKNQ 78
>gnl|CDD|179385 PRK02224, PRK02224, chromosome segregation protein; Provisional.
Length = 880
Score = 42.3 bits (100), Expect = 4e-05
Identities = 38/168 (22%), Positives = 73/168 (43%), Gaps = 27/168 (16%)
Query: 1 MYIKSMVLDGFKSYGTRVEINDFDREFNAITGLNGTGKSNILDGICFVLGIQVKQVRANT 60
M + L+ FK Y ++ + I G+NG+GKS++L+ CF + + +T
Sbjct: 1 MRFDRVRLENFKCYA-DADL-RLEDGVTVIHGVNGSGKSSLLEA-CF-FALYGSKALDDT 56
Query: 61 LQELIYKNGQAGVTKASVTLTF--DNSD---KKNCPIGYENDNTIVICRQISIPSNTRYM 115
L ++I G +A + L F + ++ + + T C + P T
Sbjct: 57 LDDVITI----GAEEAEIELWFEHAGGEYHIERRVRLSGDRATT-AKC-VLETPEGT--- 107
Query: 116 INGSSVNPKRVSDLFSSVNLNVNNPHFL----IMQGRVTKVLNMKPHE 159
I+G+ + V++L L ++ F+ + QG V K++N P +
Sbjct: 108 IDGARDVREEVTEL-----LRMDAEAFVNCAYVRQGEVNKLINATPSD 150
>gnl|CDD|226984 COG4637, COG4637, Predicted ATPase [General function prediction
only].
Length = 373
Score = 42.1 bits (99), Expect = 4e-05
Identities = 23/70 (32%), Positives = 33/70 (47%), Gaps = 9/70 (12%)
Query: 1 MYIKSMVLDGFKSYGT-RVEINDFDREFNAITGLNGTGKSNILDGICFVLGIQVKQVRAN 59
M + S+ + ++S+ + +EI R N I G NG GKSN D L + VR N
Sbjct: 1 MMLVSIKVKNYRSFRSLDLEI----RRVNVIIGANGAGKSNFYD----ALRLLADAVRGN 52
Query: 60 TLQELIYKNG 69
Q L + G
Sbjct: 53 LQQALQREGG 62
>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 = 38.0 bits (89), Expect = 6e-04
Identities = 14/43 (32%), Positives = 21/43 (48%), Gaps = 5/43 (11%)
Query: 12 KSYGTRVEINDFD-----REFNAITGLNGTGKSNILDGICFVL 49
YG R +++ E A+ G NG+GKS +L I +L
Sbjct: 7 FRYGGRTALDNVSLTLKAGEIVALVGPNGSGKSTLLRAIAGLL 49
>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 = 38.0 bits (89), Expect = 7e-04
Identities = 24/87 (27%), Positives = 39/87 (44%), Gaps = 7/87 (8%)
Query: 3 IKSMVLDGFKSYGTRVEINDFDREFNAITGLNGTGKSNILDGICFVLGIQVKQV-RANTL 61
I + L+ F +Y E N I G NG+GKS+I+ IC LG + K + RA +
Sbjct: 3 IVRIKLENFVTY-DETEFR-PGPSLNMIIGPNGSGKSSIVCAICLGLGGKPKLLGRAKKV 60
Query: 62 QELIYKNGQAGVTKASVTLTFDNSDKK 88
E + K G + ++ + +
Sbjct: 61 GEFV-KRGC---DEGTIEIELYGNPGN 83
>gnl|CDD|226121 COG3593, COG3593, Predicted ATP-dependent endonuclease of the OLD
family [DNA replication, recombination, and repair].
Length = 581
Score = 38.2 bits (89), Expect = 9e-04
Identities = 31/153 (20%), Positives = 58/153 (37%), Gaps = 25/153 (16%)
Query: 1 MYIKSMVLDGFKSYGTRVEINDFDREF----NAITGLNGTGKSNILDGICFVLGIQVKQV 56
M+++ + + F+ IN EF N + G N +GKS++LD + +L +
Sbjct: 1 MHLERVKIKNFRG------INRLSLEFEEGLNVLIGENNSGKSSLLDALRLLLDP-ESDL 53
Query: 57 RANTLQELIYKNGQAGVTKAS-------VTLTFDNSDKKNCPIGYENDNTI--VICRQIS 107
+ TL + + +++ + LTF SD + + +
Sbjct: 54 YSFTLDDFHF-----PISEFDEKSQHLHIELTFAESDPNERAVVRYRLLEPGALWIPNLD 108
Query: 108 IPSNTRYMINGSSVNPKRVSDLFSSVNLNVNNP 140
RY + G ++ V L S +NL N
Sbjct: 109 GIEKIRYRLEGEALEDGIVMTLRSFLNLGRNKD 141
>gnl|CDD|205733 pfam13555, AAA_29, P-loop containing region of AAA domain.
Length = 60
Score = 35.6 bits (83), Expect = 9e-04
Identities = 10/28 (35%), Positives = 17/28 (60%)
Query: 22 DFDREFNAITGLNGTGKSNILDGICFVL 49
D + +TG +G+GKS ++D I +L
Sbjct: 18 PIDPKGTLLTGPSGSGKSTLIDAIQTLL 45
>gnl|CDD|100796 PRK01156, PRK01156, chromosome segregation protein; Provisional.
Length = 895
Score = 38.0 bits (88), Expect = 0.001
Identities = 38/142 (26%), Positives = 53/142 (37%), Gaps = 26/142 (18%)
Query: 1 MYIKSMVLDGFKSYGTRVEINDFDREFNAITGLNGTGKSNILDGICFVLGIQVKQVRANT 60
M IK + L F S+ EI +FD N ITG NG GKS+I+D I F L R
Sbjct: 1 MIIKRIRLKNFLSH-DDSEI-EFDTGINIITGKNGAGKSSIVDAIRFAL---FTDKRTEK 55
Query: 61 LQELIYKNGQAGVTKASVTLTFDNSDKKNCPIGYENDNTIVICRQI-----SIPSNTRYM 115
++++I K G V L F + I R I
Sbjct: 56 IEDMIKK----GKNNLEVELEF-----------RIGGHVYQIRRSIERRGKGSRREAYIK 100
Query: 116 INGSSVNPKRVSDLFSSVNLNV 137
+GS + + D + N+
Sbjct: 101 KDGSIIA-EGFDDTTKYIEKNI 121
>gnl|CDD|234141 TIGR03185, DNA_S_dndD, DNA sulfur modification protein DndD.
This model describes the DndB protein encoded by an
operon associated with a sulfur-containing modification
to DNA. The operon is sporadically distributed in
bacteria, much like some restriction enzyme operons.
DndD is described as a putative ATPase. The small
number of examples known so far include species from
among the Firmicutes, Actinomycetes, Proteobacteria,
and Cyanobacteria [DNA metabolism,
Restriction/modification].
Length = 650
Score = 37.4 bits (87), Expect = 0.002
Identities = 31/94 (32%), Positives = 43/94 (45%), Gaps = 15/94 (15%)
Query: 1 MYIKSMVLDGFKSYGTRVEINDFDREFNA------ITGLNGTGKSNILDGICFVL-GIQV 53
M I + L+ F Y R FD ++ I GLNG GK+ +LD I L G +
Sbjct: 1 MIILQLTLENFGPYRGR---QTFDLSPSSPKPIILIGGLNGAGKTTLLDAIQLALYGKRA 57
Query: 54 K--QVRANTLQELI--YKNGQAGVT-KASVTLTF 82
+ ++ + N QAG T AS+TLTF
Sbjct: 58 LCSGRGNKSYEQYLRGLINRQAGKTNPASITLTF 91
>gnl|CDD|221957 pfam13175, AAA_15, AAA ATPase domain. This family of domains
contain a P-loop motif that is characteristic of the
AAA superfamily.
Length = 320
Score = 36.6 bits (85), Expect = 0.003
Identities = 15/48 (31%), Positives = 25/48 (52%), Gaps = 1/48 (2%)
Query: 3 IKSMVLDGFKSYGTRVEINDFDREFNAITGLNGTGKSNILDGICFVLG 50
+K + + FKS EI+ + N I G NG+GK+ IL+ + +
Sbjct: 1 LKKIKIKNFKSIKNLEEIS-LNEGINVIIGENGSGKTTILEALDNLKE 47
>gnl|CDD|222878 PHA02562, 46, endonuclease subunit; Provisional.
Length = 562
Score = 36.1 bits (84), Expect = 0.005
Identities = 11/22 (50%), Positives = 14/22 (63%)
Query: 28 NAITGLNGTGKSNILDGICFVL 49
ITG NG GKS +L+ + F L
Sbjct: 30 TLITGKNGAGKSTMLEALTFAL 51
>gnl|CDD|224031 COG1106, COG1106, Predicted ATPases [General function prediction
only].
Length = 371
Score = 36.0 bits (83), Expect = 0.005
Identities = 21/49 (42%), Positives = 31/49 (63%), Gaps = 2/49 (4%)
Query: 3 IKSMVLDGFKSYGTRVEINDFDREFNAITGLNGTGKSNILDGICFVLGI 51
IKS + FKS+ +E+ DF + N I G NG GKSN+L+ + F+ G+
Sbjct: 2 IKSFKIKNFKSFR-ELELEDF-GKINIIYGANGAGKSNLLEALYFLKGL 48
>gnl|CDD|222036 pfam13304, AAA_21, AAA domain.
Length = 256
Score = 34.7 bits (79), Expect = 0.010
Identities = 11/25 (44%), Positives = 16/25 (64%)
Query: 27 FNAITGLNGTGKSNILDGICFVLGI 51
N I G NG+GKSN+L + +L +
Sbjct: 1 LNVIIGPNGSGKSNLLKALALLLLL 25
>gnl|CDD|182330 PRK10246, PRK10246, exonuclease subunit SbcC; Provisional.
Length = 1047
Score = 34.8 bits (80), Expect = 0.013
Identities = 22/56 (39%), Positives = 26/56 (46%), Gaps = 9/56 (16%)
Query: 1 MYIKSMVLDGFKSYGTRVEINDFDRE-------FNAITGLNGTGKSNILDGICFVL 49
M I S+ L S +I DF E F AITG G GK+ +LD IC L
Sbjct: 1 MKILSLRLKNLNSLKGEWKI-DFTAEPFASNGLF-AITGPTGAGKTTLLDAICLAL 54
>gnl|CDD|184491 PRK14079, recF, recombination protein F; Provisional.
Length = 349
Score = 33.6 bits (77), Expect = 0.026
Identities = 14/50 (28%), Positives = 24/50 (48%), Gaps = 7/50 (14%)
Query: 29 AITGLNGTGKSNILDGICFVLGIQVKQVRANTLQELIYKNGQAGVTKASV 78
A+ G N GK+N+L+ I L ++ L +L+ + G +A V
Sbjct: 27 AVVGENAAGKTNLLEAIYLALT---GELPNGRLADLV----RFGEGEAWV 69
>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 = 32.0 bits (74), Expect = 0.064
Identities = 12/36 (33%), Positives = 18/36 (50%), Gaps = 5/36 (13%)
Query: 12 KSYGTRVEINDFDREFN-----AITGLNGTGKSNIL 42
K+YG ++ + D N + G NG GKS +L
Sbjct: 8 KTYGGKLLLKDISLTINPGDRIGLVGRNGAGKSTLL 43
>gnl|CDD|234200 TIGR03411, urea_trans_UrtD, urea ABC transporter, ATP-binding
protein UrtD. Members of this protein family are ABC
transporter ATP-binding subunits associated with urea
transport and metabolism. This protein is found in a
conserved five-gene transport operon typically found
adjacent to urease genes. It was shown in Cyanobacteria
that disruption leads to the loss of high-affinity urea
transport activity [Transport and binding proteins,
Amino acids, peptides and amines].
Length = 242
Score = 31.4 bits (72), Expect = 0.13
Identities = 15/43 (34%), Positives = 20/43 (46%), Gaps = 11/43 (25%)
Query: 9 DGFKSYGTRVEINDFD-----REFNAITGLNGTGKSNILDGIC 46
DGFK+ +ND E I G NG GK+ ++D I
Sbjct: 13 DGFKA------LNDLSLYVDPGELRVIIGPNGAGKTTMMDVIT 49
>gnl|CDD|226359 COG3839, MalK, ABC-type sugar transport systems, ATPase
components [Carbohydrate transport and metabolism].
Length = 338
Score = 31.1 bits (71), Expect = 0.19
Identities = 13/42 (30%), Positives = 21/42 (50%), Gaps = 8/42 (19%)
Query: 12 KSYGTRVEINDF-----DREFNAITGLNGTGKS---NILDGI 45
KS+G+ + D D EF + G +G GKS ++ G+
Sbjct: 11 KSFGSFEVLKDVNLDIEDGEFVVLLGPSGCGKSTLLRMIAGL 52
>gnl|CDD|227061 COG4717, COG4717, Uncharacterized conserved protein [Function
unknown].
Length = 984
Score = 31.4 bits (71), Expect = 0.19
Identities = 12/45 (26%), Positives = 22/45 (48%), Gaps = 1/45 (2%)
Query: 1 MYIKSMVLDGFKSYGTRVEINDFDREFNAITGLNGTGKSNILDGI 45
M I+S+ + G+ + + + + +F I G N GKS + I
Sbjct: 1 MRIQSLEIVGYGKF-SERHFDFGESKFQVIYGENEAGKSTLFSFI 44
>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 = 30.5 bits (70), Expect = 0.25
Identities = 13/39 (33%), Positives = 17/39 (43%), Gaps = 5/39 (12%)
Query: 13 SYGTRVEINDFD-----REFNAITGLNGTGKSNILDGIC 46
YG R ++D E I G NG GKS +L +
Sbjct: 8 GYGGRTVLDDLSLSIEAGEIVGILGPNGAGKSTLLKTLA 46
>gnl|CDD|221952 pfam13166, AAA_13, AAA domain. This family of domains contain a
P-loop motif that is characteristic of the AAA
superfamily. Many of the proteins in this family are
conjugative transfer proteins. This family includes the
PrrC protein that is thought to be the active component
of the anticodon nuclease.
Length = 713
Score = 30.4 bits (69), Expect = 0.36
Identities = 10/32 (31%), Positives = 15/32 (46%)
Query: 10 GFKSYGTRVEINDFDREFNAITGLNGTGKSNI 41
SY D ++ N I G NG+GK+ +
Sbjct: 1 NVASYDDWGNELDDLKKVNLIYGRNGSGKTTL 32
>gnl|CDD|226425 COG3910, COG3910, Predicted ATPase [General function prediction
only].
Length = 233
Score = 29.7 bits (67), Expect = 0.48
Identities = 13/24 (54%), Positives = 16/24 (66%), Gaps = 4/24 (16%)
Query: 26 EFNA----ITGLNGTGKSNILDGI 45
EF A ITG NG+GKS +L+ I
Sbjct: 34 EFRAPITFITGENGSGKSTLLEAI 57
>gnl|CDD|183055 PRK11247, ssuB, aliphatic sulfonates transport ATP-binding
subunit; Provisional.
Length = 257
Score = 29.6 bits (67), Expect = 0.53
Identities = 14/36 (38%), Positives = 19/36 (52%), Gaps = 5/36 (13%)
Query: 12 KSYGTRVEINDFDR-----EFNAITGLNGTGKSNIL 42
K YG R +N D +F A+ G +G GKS +L
Sbjct: 20 KRYGERTVLNQLDLHIPAGQFVAVVGRSGCGKSTLL 55
>gnl|CDD|222170 pfam13486, Dehalogenase, Reductive dehalogenase subunit. This
family is most frequently associated with a Fer4
iron-sulfur cluster towards the C-terminal region.
Length = 300
Score = 29.1 bits (66), Expect = 0.86
Identities = 12/53 (22%), Positives = 19/53 (35%), Gaps = 13/53 (24%)
Query: 64 LIYKNGQAGVTKASVTLTFDNSDKKNCPIGYENDNTIVICRQISIPSNTRYMI 116
L Y + F++ DK YE D V IP+ +++I
Sbjct: 164 LFYTYDKGDAPG--KPYVFEDVDK-----PYETDTKRV------IPNKCKWVI 203
>gnl|CDD|188394 TIGR03864, PQQ_ABC_ATP, ABC transporter, ATP-binding subunit,
PQQ-dependent alcohol dehydrogenase system. Members of
this protein family are the ATP-binding subunit of an
ABC transporter system that is associated with PQQ
biosynthesis and PQQ-dependent alcohol dehydrogenases.
While this family shows homology to several efflux ABC
transporter subunits, the presence of a periplasmic
substrate-binding protein and association with systems
for catabolism of alcohols suggests a role in import
rather than detoxification [Transport and binding
proteins, Carbohydrates, organic alcohols, and acids].
Length = 236
Score = 28.8 bits (65), Expect = 0.92
Identities = 12/33 (36%), Positives = 15/33 (45%), Gaps = 5/33 (15%)
Query: 12 KSYGTRVEINDFD-----REFNAITGLNGTGKS 39
YG R ++D F A+ G NG GKS
Sbjct: 9 FRYGARRALDDVSFTVRPGRFVALLGPNGAGKS 41
>gnl|CDD|213268 cd03301, ABC_MalK_N, The N-terminal ATPase domain of the maltose
transporter, MalK. ATP binding cassette (ABC) proteins
function from bacteria to human, mediating the
translocation of substances into and out of cells or
organelles. ABC transporters contain two
transmembrane-spanning domains (TMDs) or subunits and
two nucleotide binding domains (NBDs) or subunits that
couple transport to the hydrolysis of ATP. In the
maltose transport system, the periplasmic maltose
binding protein (MBP) stimulates the ATPase activity of
the membrane-associated transporter, which consists of
two transmembrane subunits, MalF and MalG, and two
copies of the ATP binding subunit, MalK, and becomes
tightly bound to the transporter in the catalytic
transition state, ensuring that maltose is passed to
the transporter as ATP is hydrolyzed.
Length = 213
Score = 28.8 bits (65), Expect = 1.0
Identities = 11/36 (30%), Positives = 17/36 (47%), Gaps = 5/36 (13%)
Query: 12 KSYGTRVEINDF-----DREFNAITGLNGTGKSNIL 42
K +G ++D D EF + G +G GK+ L
Sbjct: 8 KRFGNVTALDDLNLDIADGEFVVLLGPSGCGKTTTL 43
>gnl|CDD|236781 PRK10869, PRK10869, recombination and repair protein; Provisional.
Length = 553
Score = 29.1 bits (66), Expect = 1.1
Identities = 33/113 (29%), Positives = 46/113 (40%), Gaps = 27/113 (23%)
Query: 19 EINDFDREFNAITGLNGTGKSNILD--GICFVLGIQVKQVRANTLQELIYKNGQAGVTKA 76
EI DF ITG G GKS +D G+C LG + A+ + + G T+A
Sbjct: 17 EI-DFQSGMTVITGETGAGKSIAIDALGLC--LG---GRAEASMV--------RPGATRA 62
Query: 77 SVTLTFDNSDKKNCPIG--------YENDNTIVICRQISIPSNTRYMINGSSV 121
+ F D P E+ N ++ R IS +R ING+ V
Sbjct: 63 DLCARFSLKDT---PAALRWLEDNQLEDGNECLLRRVISSDGRSRGFINGTPV 112
>gnl|CDD|213192 cd03225, ABC_cobalt_CbiO_domain1, First domain of the ATP-binding
cassette component of cobalt transport system. Domain
I of the ABC component of a cobalt transport family
found in bacteria, archaea, and eukaryota. The
transition metal cobalt is an essential component of
many enzymes and must be transported into cells in
appropriate amounts when needed. This ABC transport
system of the CbiMNQO family is involved in cobalt
transport in association with the cobalamin (vitamin
B12) biosynthetic pathways. Most of cobalt (Cbi)
transport systems possess a separate CbiN component,
the cobalt-binding periplasmic protein, and they are
encoded by the conserved gene cluster cbiMNQO. Both the
CbiM and CbiQ proteins are integral cytoplasmic
membrane proteins, and the CbiO protein has the linker
peptide and the Walker A and B motifs commonly found in
the ATPase components of the ABC-type transport
systems.
Length = 211
Score = 28.2 bits (64), Expect = 1.4
Identities = 17/49 (34%), Positives = 24/49 (48%), Gaps = 13/49 (26%)
Query: 26 EFNAITGLNGTGKS---NILDGI-------CFVLGIQVKQVRANTLQEL 64
EF I G NG+GKS +L+G+ V G K + +L+EL
Sbjct: 28 EFVLIVGPNGSGKSTLLRLLNGLLGPTSGEVLVDG---KDLTKLSLKEL 73
>gnl|CDD|129694 TIGR00606, rad50, rad50. All proteins in this family for which
functions are known are involvedin recombination,
recombinational repair, and/or non-homologous end
joining.They are components of an exonuclease complex
with MRE11 homologs. This family is distantly related
to the SbcC family of bacterial proteins.This family is
based on the phylogenomic analysis of JA Eisen (1999,
Ph.D. Thesis, Stanford University).
Length = 1311
Score = 28.9 bits (64), Expect = 1.4
Identities = 22/92 (23%), Positives = 39/92 (42%), Gaps = 5/92 (5%)
Query: 3 IKSMVLDGFKSYGTR---VEINDFDREFNAITGLNGTGKSNILDGICFV-LGIQVKQVRA 58
M + G +S+G +I DF + G NG GK+ I++ + ++ G +
Sbjct: 3 FLKMSILGVRSFGIEDKDKQIIDFFSPLTILVGPNGAGKTTIIECLKYICTGDFPPGTKG 62
Query: 59 NTLQELIYKNGQAGVTKASVTLTFDNSDKKNC 90
NT K Q +A + L F + + + C
Sbjct: 63 NTFVHDP-KVAQETDVRAQIRLQFRDVNGEEC 93
>gnl|CDD|224045 COG1120, FepC, ABC-type cobalamin/Fe3+-siderophores transport
systems, ATPase components [Inorganic ion transport and
metabolism / Coenzyme metabolism].
Length = 258
Score = 27.9 bits (63), Expect = 1.9
Identities = 12/39 (30%), Positives = 18/39 (46%), Gaps = 5/39 (12%)
Query: 13 SYGTRVEINDFD-----REFNAITGLNGTGKSNILDGIC 46
YG + ++D E I G NG+GKS +L +
Sbjct: 11 GYGGKPILDDLSFSIPKGEITGILGPNGSGKSTLLKCLA 49
>gnl|CDD|227019 COG4674, COG4674, Uncharacterized ABC-type transport system,
ATPase component [General function prediction only].
Length = 249
Score = 28.1 bits (63), Expect = 1.9
Identities = 13/43 (30%), Positives = 19/43 (44%), Gaps = 11/43 (25%)
Query: 9 DGFKSYGTRVEINDF-----DREFNAITGLNGTGKSNILDGIC 46
GFK+ +ND E + G NG GK+ ++D I
Sbjct: 16 GGFKA------LNDLSFSVDPGELRVLIGPNGAGKTTLMDVIT 52
>gnl|CDD|182852 PRK10938, PRK10938, putative molybdenum transport ATP-binding
protein ModF; Provisional.
Length = 490
Score = 28.1 bits (63), Expect = 2.1
Identities = 13/39 (33%), Positives = 19/39 (48%), Gaps = 5/39 (12%)
Query: 9 DGFKSYGTRVEINDFDREFNA-----ITGLNGTGKSNIL 42
+G SY R +++ + N I G NG GKS +L
Sbjct: 265 NGVVSYNDRPILHNLSWQVNPGEHWQIVGPNGAGKSTLL 303
>gnl|CDD|193607 cd09633, Deltex_C, Domain found at the C-terminus of deltex-like.
The deltex family of proteins is involved in the
regulation of Notch signaling, and therefore may play
roles in cell-to-cell communications that regulate
mechanisms determining cell fate. They have a central
RING-type zinc finger domain and contain a C-terminal
domain, described here, that is also found in other
domain architectures. Deltex-1 (DTX1) contains a RING
finger and two WWE domains, indicating that it may be an
E3 ubiquitin ligase. Human deltex 3-like, which contains
an additional N-terminal domain (presumably with
ubiquitin ligase activity) is also described as E3
ubiquitin-protein ligase DTX3L, B-lymphoma- and
BAL-associated protein (BBAP), or rhysin-2. DTX3L
mediates monoubiquitination of K91 of histone H4 in
response to DNA damage.
Length = 131
Score = 27.2 bits (61), Expect = 2.6
Identities = 11/25 (44%), Positives = 13/25 (52%), Gaps = 3/25 (12%)
Query: 86 DKKNCPIGYENDNTIVICRQISIPS 110
+ P GYE TIVI +IPS
Sbjct: 13 IDTSLP-GYEGCGTIVI--VYNIPS 34
>gnl|CDD|226164 COG3638, COG3638, ABC-type phosphate/phosphonate transport
system, ATPase component [Inorganic ion transport and
metabolism].
Length = 258
Score = 27.6 bits (62), Expect = 2.7
Identities = 12/26 (46%), Positives = 15/26 (57%), Gaps = 2/26 (7%)
Query: 17 RVEINDFDREFNAITGLNGTGKSNIL 42
+EIN E AI G +G GKS +L
Sbjct: 24 NLEINQG--EMVAIIGPSGAGKSTLL 47
>gnl|CDD|188353 TIGR03608, L_ocin_972_ABC, putative bacteriocin export ABC
transporter, lactococcin 972 group. A gene pair with a
fairly wide distribution consists of a polypeptide
related to the lactococcin 972 (see TIGR01653) and
multiple-membrane-spanning putative immunity protein
(see TIGR01654). This model represents a small clade
within the ABC transporters that regularly are found
adjacent to these bacteriocin system gene pairs and are
likely serve as export proteins [Cellular processes,
Toxin production and resistance, Transport and binding
proteins, Unknown substrate].
Length = 206
Score = 27.6 bits (62), Expect = 2.8
Identities = 13/40 (32%), Positives = 22/40 (55%), Gaps = 5/40 (12%)
Query: 11 FKSYGTRVEINDF-----DREFNAITGLNGTGKSNILDGI 45
K +G +V ++D + AI G +G+GKS +L+ I
Sbjct: 5 SKKFGDKVILDDLNLTIEKGKMYAIIGESGSGKSTLLNII 44
>gnl|CDD|226970 COG4619, COG4619, ABC-type uncharacterized transport system,
ATPase component [General function prediction only].
Length = 223
Score = 27.5 bits (61), Expect = 2.8
Identities = 11/21 (52%), Positives = 14/21 (66%)
Query: 26 EFNAITGLNGTGKSNILDGIC 46
EF AITG +G GKS +L +
Sbjct: 30 EFIAITGPSGCGKSTLLKIVA 50
>gnl|CDD|224060 COG1137, YhbG, ABC-type (unclassified) transport system, ATPase
component [General function prediction only].
Length = 243
Score = 27.6 bits (62), Expect = 3.1
Identities = 15/33 (45%), Positives = 18/33 (54%), Gaps = 5/33 (15%)
Query: 12 KSYGTRVEINDFDREFNA--ITGL---NGTGKS 39
KSY R +ND E N+ I GL NG GK+
Sbjct: 12 KSYKKRKVVNDVSLEVNSGEIVGLLGPNGAGKT 44
>gnl|CDD|213228 cd03261, ABC_Org_Solvent_Resistant, ATP-binding cassette
transport system involved in resistant to organic
solvents. 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 = 235
Score = 27.5 bits (62), Expect = 3.1
Identities = 13/36 (36%), Positives = 19/36 (52%), Gaps = 5/36 (13%)
Query: 12 KSYGTRVEINDFDREFN-----AITGLNGTGKSNIL 42
KS+G R + D + AI G +G+GKS +L
Sbjct: 8 KSFGGRTVLKGVDLDVRRGEILAIIGPSGSGKSTLL 43
>gnl|CDD|182336 PRK10253, PRK10253, iron-enterobactin transporter ATP-binding
protein; Provisional.
Length = 265
Score = 27.6 bits (61), Expect = 3.2
Identities = 18/81 (22%), Positives = 30/81 (37%), Gaps = 10/81 (12%)
Query: 10 GFKSYGTRVEINDFDREFNAITGLNGTGKSNIL----------DGICFVLGIQVKQVRAN 59
G + + + D F AI G NG GKS +L G ++ G ++ +
Sbjct: 18 GKYTVAENLTVEIPDGHFTAIIGPNGCGKSTLLRTLSRLMTPAHGHVWLDGEHIQHYASK 77
Query: 60 TLQELIYKNGQAGVTKASVTL 80
+ I Q T +T+
Sbjct: 78 EVARRIGLLAQNATTPGDITV 98
>gnl|CDD|226963 COG4604, CeuD, ABC-type enterochelin transport system, ATPase
component [Inorganic ion transport and metabolism].
Length = 252
Score = 27.3 bits (61), Expect = 3.2
Identities = 15/40 (37%), Positives = 22/40 (55%), Gaps = 5/40 (12%)
Query: 12 KSYGTRVEINDFDREF-----NAITGLNGTGKSNILDGIC 46
KSYGT+V ++D + +I G NG GKS +L +
Sbjct: 9 KSYGTKVVLDDVSLDIPKGGITSIIGPNGAGKSTLLSMMS 48
>gnl|CDD|226929 COG4559, COG4559, ABC-type hemin transport system, ATPase
component [Inorganic ion transport and metabolism].
Length = 259
Score = 27.3 bits (61), Expect = 3.4
Identities = 10/21 (47%), Positives = 12/21 (57%)
Query: 26 EFNAITGLNGTGKSNILDGIC 46
E AI G NG GKS +L +
Sbjct: 28 EVLAILGPNGAGKSTLLKALS 48
>gnl|CDD|213197 cd03230, ABC_DR_subfamily_A, ATP-binding cassette domain of the
drug resistance transporter and related proteins,
subfamily A. This family of ATP-binding proteins
belongs to a multi-subunit transporter involved in drug
resistance (BcrA and DrrA), nodulation, lipid
transport, and lantibiotic immunity. In bacteria and
archaea, these transporters usually include an
ATP-binding protein and one or two integral membrane
proteins. Eukaryotic systems of the ABCA subfamily
display ABC domains that are quite similar to this
family. The ATP-binding domain shows the highest
similarity between all members of the ABC transporter
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 = 173
Score = 27.0 bits (61), Expect = 3.7
Identities = 18/70 (25%), Positives = 27/70 (38%), Gaps = 15/70 (21%)
Query: 12 KSYGTRVEINDFDREFNA--ITGL---NGTGKS---NIL-------DGICFVLGIQVKQV 56
K YG + ++D I GL NG GK+ I+ G VLG +K+
Sbjct: 8 KRYGKKTALDDISLTVEKGEIYGLLGPNGAGKTTLIKIILGLLKPDSGEIKVLGKDIKKE 67
Query: 57 RANTLQELIY 66
+ + Y
Sbjct: 68 PEEVKRRIGY 77
>gnl|CDD|224044 COG1119, ModF, ABC-type molybdenum transport system, ATPase
component/photorepair protein PhrA [Inorganic ion
transport and metabolism].
Length = 257
Score = 27.3 bits (61), Expect = 3.8
Identities = 8/14 (57%), Positives = 10/14 (71%)
Query: 29 AITGLNGTGKSNIL 42
AI G NG GK+ +L
Sbjct: 61 AIVGPNGAGKTTLL 74
>gnl|CDD|213231 cd03264, ABC_drug_resistance_like, ABC-type multidrug transport
system, ATPase component. The biological function of
this family is not well characterized, but display ABC
domains similar to members of ABCA subfamily. 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 = 211
Score = 26.8 bits (60), Expect = 4.4
Identities = 11/41 (26%), Positives = 17/41 (41%), Gaps = 7/41 (17%)
Query: 12 KSYGTRVEINDFDREF-NAITGL---NGTGKS---NILDGI 45
K YG + ++ + GL NG GK+ IL +
Sbjct: 8 KRYGKKRALDGVSLTLGPGMYGLLGPNGAGKTTLMRILATL 48
>gnl|CDD|224059 COG1136, SalX, ABC-type antimicrobial peptide transport system,
ATPase component [Defense mechanisms].
Length = 226
Score = 26.7 bits (60), Expect = 5.1
Identities = 16/53 (30%), Positives = 24/53 (45%), Gaps = 10/53 (18%)
Query: 26 EFNAITGLNGTGKS---NIL-------DGICFVLGIQVKQVRANTLQELIYKN 68
EF AI G +G+GKS N+L G + G + ++ L +L K
Sbjct: 32 EFVAIVGPSGSGKSTLLNLLGGLDKPTSGEVLINGKDLTKLSEKELAKLRRKK 84
>gnl|CDD|226617 COG4133, CcmA, ABC-type transport system involved in cytochrome c
biogenesis, ATPase component [Posttranslational
modification, protein turnover, chaperones].
Length = 209
Score = 26.5 bits (59), Expect = 5.7
Identities = 13/33 (39%), Positives = 16/33 (48%), Gaps = 5/33 (15%)
Query: 15 GTRVEINDFDREFNA-----ITGLNGTGKSNIL 42
G R +D NA ITG NG GK+ +L
Sbjct: 13 GERTLFSDLSFTLNAGEALQITGPNGAGKTTLL 45
>gnl|CDD|224046 COG1121, ZnuC, ABC-type Mn/Zn transport systems, ATPase component
[Inorganic ion transport and metabolism].
Length = 254
Score = 26.4 bits (59), Expect = 6.4
Identities = 10/21 (47%), Positives = 12/21 (57%)
Query: 26 EFNAITGLNGTGKSNILDGIC 46
E A+ G NG GKS +L I
Sbjct: 31 EITALIGPNGAGKSTLLKAIL 51
>gnl|CDD|181226 PRK08087, PRK08087, L-fuculose phosphate aldolase; Provisional.
Length = 215
Score = 26.2 bits (58), Expect = 7.5
Identities = 8/13 (61%), Positives = 11/13 (84%)
Query: 7 VLDGFKSYGTRVE 19
VL+ FK+YG R+E
Sbjct: 202 VLEKFKTYGLRIE 214
>gnl|CDD|235717 PRK06153, PRK06153, hypothetical protein; Provisional.
Length = 393
Score = 26.5 bits (59), Expect = 7.5
Identities = 13/33 (39%), Positives = 15/33 (45%), Gaps = 5/33 (15%)
Query: 17 RVEINDFDREFN----AITGLNGTGKSNILDGI 45
R I + AI GL GTG S ILD +
Sbjct: 164 RAGIGALSAKLEGQRIAIIGLGGTG-SYILDLV 195
>gnl|CDD|224047 COG1122, CbiO, ABC-type cobalt transport system, ATPase component
[Inorganic ion transport and metabolism].
Length = 235
Score = 26.1 bits (58), Expect = 8.1
Identities = 9/23 (39%), Positives = 14/23 (60%), Gaps = 3/23 (13%)
Query: 26 EFNAITGLNGTGKS---NILDGI 45
E + G NG+GKS +L+G+
Sbjct: 31 ERVLLIGPNGSGKSTLLKLLNGL 53
>gnl|CDD|223488 COG0411, LivG, ABC-type branched-chain amino acid transport
systems, ATPase component [Amino acid transport and
metabolism].
Length = 250
Score = 26.0 bits (58), Expect = 8.2
Identities = 14/42 (33%), Positives = 19/42 (45%), Gaps = 8/42 (19%)
Query: 12 KSYGTRVEINDFDREFNA--ITGL---NGTGKS---NILDGI 45
K +G +ND E I GL NG GK+ N++ G
Sbjct: 12 KRFGGLTAVNDVSLEVRPGEIVGLIGPNGAGKTTLFNLITGF 53
>gnl|CDD|234319 TIGR03705, poly_P_kin, polyphosphate kinase 1. Members of this
protein family are the enzyme polyphosphate kinase 1
(PPK1). This family is found in many prokaryotes and
also in Dictyostelium. Sequences in the seed alignment
were taken from prokaryotic consecutive two-gene pairs
in which the other gene encodes an exopolyphosphatase.
It synthesizes polyphosphate from the terminal phosphate
of ATP but not GTP, in contrast to PPK2 [Central
intermediary metabolism, Phosphorus compounds].
Length = 672
Score = 26.3 bits (59), Expect = 8.3
Identities = 9/43 (20%), Positives = 21/43 (48%), Gaps = 2/43 (4%)
Query: 101 VICRQISIPSNTRYMINGSSVNPKRVSDLFSSVNL-NVNNPHF 142
+ ++ + + Y++ G VN K +S L V+ ++ P +
Sbjct: 268 FLLEELGLSEDDVYVVGG-PVNLKDLSQLPDLVDRPDLKFPPY 309
>gnl|CDD|236311 PRK08609, PRK08609, hypothetical protein; Provisional.
Length = 570
Score = 26.5 bits (59), Expect = 8.5
Identities = 12/31 (38%), Positives = 16/31 (51%), Gaps = 1/31 (3%)
Query: 54 KQVRANTLQ-ELIYKNGQAGVTKASVTLTFD 83
+ VR LQ I + AG TK SV L ++
Sbjct: 204 EAVREQLLQLPNIVEVIAAGDTKVSVELEYE 234
>gnl|CDD|236523 PRK09452, potA, putrescine/spermidine ABC transporter ATPase
protein; Reviewed.
Length = 375
Score = 26.4 bits (59), Expect = 8.5
Identities = 11/36 (30%), Positives = 19/36 (52%), Gaps = 5/36 (13%)
Query: 12 KSYGTRVEINDFDR-----EFNAITGLNGTGKSNIL 42
KS+ + I++ D EF + G +G GK+ +L
Sbjct: 22 KSFDGKEVISNLDLTINNGEFLTLLGPSGCGKTTVL 57
>gnl|CDD|223562 COG0488, Uup, ATPase components of ABC transporters with
duplicated ATPase domains [General function prediction
only].
Length = 530
Score = 26.1 bits (58), Expect = 9.1
Identities = 10/33 (30%), Positives = 14/33 (42%), Gaps = 5/33 (15%)
Query: 12 KSYGTRVEINDFDREFNA-----ITGLNGTGKS 39
+YG R + + N + G NG GKS
Sbjct: 11 LAYGDRPLLENVSLTLNPGERIGLVGRNGAGKS 43
>gnl|CDD|206715 cd04148, RGK, Rem, Rem2, Rad, Gem/Kir (RGK) subfamily of Ras
GTPases. RGK subfamily. The RGK (Rem, Rem2, Rad,
Gem/Kir) subfamily of Ras GTPases are expressed in a
tissue-specific manner and are dynamically regulated by
transcriptional and posttranscriptional mechanisms in
response to environmental cues. RGK proteins bind to
the beta subunit of L-type calcium channels, causing
functional down-regulation of these voltage-dependent
calcium channels, and either termination of
calcium-dependent secretion or modulation of electrical
conduction and contractile function. Inhibition of
L-type calcium channels by Rem2 may provide a mechanism
for modulating calcium-triggered exocytosis in
hormone-secreting cells, and has been proposed to
influence the secretion of insulin in pancreatic beta
cells. RGK proteins also interact with and inhibit the
Rho/Rho kinase pathway to modulate remodeling of the
cytoskeleton. Two characteristics of RGK proteins cited
in the literature are N-terminal and C-terminal
extensions beyond the GTPase domain typical of Ras
superfamily members. The N-terminal extension is not
conserved among family members; the C-terminal
extension is reported to be conserved among the family
and lack the CaaX prenylation motif typical of
membrane-associated Ras proteins. However, a putative
CaaX motif has been identified in the alignment of the
C-terminal residues of this CD.
Length = 219
Score = 25.8 bits (57), Expect = 9.2
Identities = 8/31 (25%), Positives = 14/31 (45%)
Query: 69 GQAGVTKASVTLTFDNSDKKNCPIGYENDNT 99
G +GV K+S+ F ++ D+T
Sbjct: 7 GDSGVGKSSLANIFTAGVYEDSAYEASGDDT 37
>gnl|CDD|224057 COG1134, TagH, ABC-type polysaccharide/polyol phosphate transport
system, ATPase component [Carbohydrate transport and
metabolism / Cell envelope biogenesis, outer membrane].
Length = 249
Score = 26.0 bits (58), Expect = 9.3
Identities = 14/55 (25%), Positives = 18/55 (32%), Gaps = 11/55 (20%)
Query: 2 YIKSMVLDGFKSYGTRVEI---NDFDREFN-----AITGLNGTGKS---NILDGI 45
+K + K E D E I G NG GKS ++ GI
Sbjct: 22 SLKKRLKGLAKGGRKVAEFWALKDISFEIYKGERVGIIGHNGAGKSTLLKLIAGI 76
>gnl|CDD|234357 TIGR03797, NHLM_micro_ABC2, NHLM bacteriocin system ABC
transporter, ATP-binding protein. Members of this
protein family are ABC transporter ATP-binding subunits,
part of a three-gene putative bacteriocin transport
operon. The other subunits include another ATP-binding
subunit (TIGR03796), which has an N-terminal leader
sequence cleavage domain, and an HlyD homolog
(TIGR03794). In a number of genomes, members of protein
families related to nitrile hydratase alpha subunit or
to nif11 have undergone paralogous family expansions,
with members possessing a putative bacteriocin cleavage
region ending with a classic Gly-Gly motif. Those sets
of putative bacteriocins, members of this protein family
and its partners TIGR03794 and TIGR03796, and
cyclodehydratase/docking scaffold fusion proteins of
thiazole/oxazole biosynthesis frequently show correlated
species distribution and co-clustering within many of
those genomes [Transport and binding proteins, Amino
acids, peptides and amines, Cellular processes,
Biosynthesis of natural products].
Length = 686
Score = 26.1 bits (58), Expect = 9.5
Identities = 10/17 (58%), Positives = 13/17 (76%)
Query: 26 EFNAITGLNGTGKSNIL 42
EF AI G +G+GKS +L
Sbjct: 480 EFVAIVGPSGSGKSTLL 496
>gnl|CDD|188107 TIGR01086, fucA, L-fuculose phosphate aldolase. Members of this
family are L-fuculose phosphate aldolase from various
Proteobacteria, encoded in fucose utilization operons.
Homologs in other bacteria given similar annotation but
scoring below the trusted cutoff may share extensive
sequence similarity but are not experimenally
characterized and are not found in apparent fucose
utilization operons; we consider their annotation as
L-fuculose phosphate aldolase to be tenuous. This model
has been narrowed in scope from the previous version
[Energy metabolism, Sugars].
Length = 214
Score = 26.1 bits (57), Expect = 9.5
Identities = 8/15 (53%), Positives = 12/15 (80%)
Query: 5 SMVLDGFKSYGTRVE 19
++VL FK+YG R+E
Sbjct: 199 AVVLGKFKTYGLRIE 213
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
0.318 0.136 0.389
Gapped
Lambda K H
0.267 0.0705 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,674,539
Number of extensions: 664940
Number of successful extensions: 899
Number of sequences better than 10.0: 1
Number of HSP's gapped: 869
Number of HSP's successfully gapped: 103
Length of query: 159
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 70
Effective length of database: 6,990,096
Effective search space: 489306720
Effective search space used: 489306720
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 (25.0 bits)