RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5297
(185 letters)
>gnl|CDD|213252 cd03285, ABC_MSH2_euk, ATP-binding cassette domain of eukaryotic
MutS2 homolog. The MutS protein initiates DNA mismatch
repair by recognizing mispaired and unpaired bases
embedded in duplex DNA and activating endo- and
exonucleases to remove the mismatch. Members of the MutS
family possess C-terminal domain with a conserved ATPase
activity that belongs to the ATP binding cassette (ABC)
superfamily. MutS homologs (MSH) have been identified in
most prokaryotic and all eukaryotic organisms examined.
Prokaryotes have two homologs (MutS1 and MutS2), whereas
seven MSH proteins (MSH1 to MSH7) have been identified
in eukaryotes. The homodimer MutS1 and heterodimers
MSH2-MSH3 and MSH2-MSH6 are primarily involved in
mitotic mismatch repair, whereas MSH4-MSH5 is involved
in resolution of Holliday junctions during meiosis. All
members of the MutS family contain the highly conserved
Walker A/B ATPase domain, and many share a common
mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and
MSH4-MSH5 dimerize to form sliding clamps, and
recognition of specific DNA structures or lesions
results in ADP/ATP exchange.
Length = 222
Score = 268 bits (688), Expect = 1e-92
Identities = 104/169 (61%), Positives = 129/169 (76%)
Query: 7 VLNQCRHPIVELQGGVSYIPNDVYFKSGEVSFNLVTGPNMGGKSTYIRSIGVSVFLAQIG 66
VL + RHP VE Q V++IPNDV G+ F ++TGPNMGGKSTYIR IGV V +AQIG
Sbjct: 1 VLKEARHPCVEAQDDVAFIPNDVTLTRGKSRFLIITGPNMGGKSTYIRQIGVIVLMAQIG 60
Query: 67 CFVPCDSATISVVDQIFTRVGAADSQYRGISTFMMEMKETATVIKKCTENSLVIIDELGR 126
CFVPCDSA I +VD I RVGA+DSQ +G+STFM EM ETA ++K TENSL+IIDELGR
Sbjct: 61 CFVPCDSADIPIVDCILARVGASDSQLKGVSTFMAEMLETAAILKSATENSLIIIDELGR 120
Query: 127 GTSTFDGFGMACSIARELASNRQPFTLFATHFHEIALLSRVIPTFRNVH 175
GTST+DGFG+A +IA +A+ + F LFATHFHE+ L+ +P +N+H
Sbjct: 121 GTSTYDGFGLAWAIAEYIATQIKCFCLFATHFHELTALADEVPNVKNLH 169
>gnl|CDD|215944 pfam00488, MutS_V, MutS domain V. This domain is found in proteins
of the MutS family (DNA mismatch repair proteins) and is
found associated with pfam01624, pfam05188, pfam05192
and pfam05190. The mutS family of proteins is named
after the Salmonella typhimurium MutS protein involved
in mismatch repair; other members of the family included
the eukaryotic MSH 1,2,3, 4,5 and 6 proteins. These have
various roles in DNA repair and recombination. Human MSH
has been implicated in non-polyposis colorectal
carcinoma (HNPCC) and is a mismatch binding protein. The
aligned region corresponds with domain V of Thermus
aquaticus MutS as characterized in, which contains a
Walker A motif, and is structurally similar to the
ATPase domain of ABC transporters.
Length = 235
Score = 262 bits (673), Expect = 4e-90
Identities = 86/173 (49%), Positives = 116/173 (67%), Gaps = 1/173 (0%)
Query: 4 GTLVLNQCRHPIVELQ-GGVSYIPNDVYFKSGEVSFNLVTGPNMGGKSTYIRSIGVSVFL 62
L + RHP+VE +++PNDV L+TGPNMGGKSTY+R + + V +
Sbjct: 10 AALHIEGGRHPVVEAVLDAGNFVPNDVSLGKERSRILLITGPNMGGKSTYLRQVALIVIM 69
Query: 63 AQIGCFVPCDSATISVVDQIFTRVGAADSQYRGISTFMMEMKETATVIKKCTENSLVIID 122
AQIG FVP +SA I +VD+IFTR+GA+D G STFM+EM ETA ++ T+ SLVI+D
Sbjct: 70 AQIGSFVPAESARIGIVDRIFTRIGASDDLASGRSTFMVEMLETANILHNATDKSLVILD 129
Query: 123 ELGRGTSTFDGFGMACSIARELASNRQPFTLFATHFHEIALLSRVIPTFRNVH 175
ELGRGTST+DG +A ++A LA + TLFATH+HE+ L+ +P +NVH
Sbjct: 130 ELGRGTSTYDGLAIAWAVAEHLAEKIRARTLFATHYHELTKLAEKLPAVKNVH 182
>gnl|CDD|223327 COG0249, MutS, Mismatch repair ATPase (MutS family) [DNA
replication, recombination, and repair].
Length = 843
Score = 260 bits (667), Expect = 1e-82
Identities = 85/166 (51%), Positives = 110/166 (66%), Gaps = 1/166 (0%)
Query: 12 RHPIVELQGGVSYIPNDVYFKSGEVSFNLVTGPNMGGKSTYIRSIGVSVFLAQIGCFVPC 71
RHP+VE ++PND+ SG L+TGPNMGGKSTY+R + + V LAQIG FVP
Sbjct: 584 RHPVVEAVLDNGFVPNDIDL-SGNRRIILITGPNMGGKSTYLRQVALIVILAQIGSFVPA 642
Query: 72 DSATISVVDQIFTRVGAADSQYRGISTFMMEMKETATVIKKCTENSLVIIDELGRGTSTF 131
+ A I +VD+IFTR+GAAD G STFM+EM ETA ++ TE SLVI+DE+GRGTST+
Sbjct: 643 EKARIGIVDRIFTRIGAADDLASGRSTFMVEMLETANILDNATERSLVILDEIGRGTSTY 702
Query: 132 DGFGMACSIARELASNRQPFTLFATHFHEIALLSRVIPTFRNVHES 177
DG +A ++ L TLFATH+HE+ L +P +N H S
Sbjct: 703 DGLAIAWAVLEYLHEKIGCRTLFATHYHELTELEEKLPQVKNYHMS 748
>gnl|CDD|235444 PRK05399, PRK05399, DNA mismatch repair protein MutS; Provisional.
Length = 854
Score = 256 bits (656), Expect = 7e-81
Identities = 85/173 (49%), Positives = 115/173 (66%), Gaps = 2/173 (1%)
Query: 4 GTLVLNQCRHPIVE-LQGGVSYIPNDVYFKSGEVSFNLVTGPNMGGKSTYIRSIGVSVFL 62
+ + + RHP+VE + GG ++PND E L+TGPNM GKSTY+R + + V L
Sbjct: 575 PGIDIEEGRHPVVEQVLGGEPFVPNDCDL-DEERRLLLITGPNMAGKSTYMRQVALIVLL 633
Query: 63 AQIGCFVPCDSATISVVDQIFTRVGAADSQYRGISTFMMEMKETATVIKKCTENSLVIID 122
AQIG FVP +SA I +VD+IFTR+GA+D G STFM+EM ETA ++ TE SLV++D
Sbjct: 634 AQIGSFVPAESARIGIVDRIFTRIGASDDLASGRSTFMVEMTETANILNNATERSLVLLD 693
Query: 123 ELGRGTSTFDGFGMACSIARELASNRQPFTLFATHFHEIALLSRVIPTFRNVH 175
E+GRGTST+DG +A ++A L TLFATH+HE+ L +P +NVH
Sbjct: 694 EIGRGTSTYDGLSIAWAVAEYLHDKIGAKTLFATHYHELTELEEKLPGVKNVH 746
>gnl|CDD|197777 smart00534, MUTSac, ATPase domain of DNA mismatch repair MUTS
family.
Length = 185
Score = 218 bits (559), Expect = 1e-73
Identities = 76/138 (55%), Positives = 102/138 (73%)
Query: 38 FNLVTGPNMGGKSTYIRSIGVSVFLAQIGCFVPCDSATISVVDQIFTRVGAADSQYRGIS 97
++TGPNMGGKSTY+R + + V +AQIG FVP +SA + V D+IFTR+GA+DS +G+S
Sbjct: 1 VVIITGPNMGGKSTYLRQVALIVIMAQIGSFVPAESAELPVFDRIFTRIGASDSLAQGLS 60
Query: 98 TFMMEMKETATVIKKCTENSLVIIDELGRGTSTFDGFGMACSIARELASNRQPFTLFATH 157
TFM+EMKETA ++K T+NSLV++DELGRGTST+DG +A +I L TLFATH
Sbjct: 61 TFMVEMKETANILKNATKNSLVLLDELGRGTSTYDGLAIAAAILEYLLEKIGARTLFATH 120
Query: 158 FHEIALLSRVIPTFRNVH 175
+HE+ L+ P RN+H
Sbjct: 121 YHELTKLADNHPGVRNLH 138
>gnl|CDD|213251 cd03284, ABC_MutS1, ATP-binding cassette domain of MutS1 homolog.
The MutS protein initiates DNA mismatch repair by
recognizing mispaired and unpaired bases embedded in
duplex DNA and activating endo- and exonucleases to
remove the mismatch. Members of the MutS family possess
C-terminal domain with a conserved ATPase activity that
belongs to the ATP binding cassette (ABC) superfamily.
MutS homologs (MSH) have been identified in most
prokaryotic and all eukaryotic organisms examined.
Prokaryotes have two homologs (MutS1 and MutS2), whereas
seven MSH proteins (MSH1 to MSH7) have been identified
in eukaryotes. The homodimer MutS1 and heterodimers
MSH2-MSH3 and MSH2-MSH6 are primarily involved in
mitotic mismatch repair, whereas MSH4-MSH5 is involved
in resolution of Holliday junctions during meiosis. All
members of the MutS family contain the highly conserved
Walker A/B ATPase domain, and many share a common
mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and
MSH4-MSH5 dimerize to form sliding clamps, and
recognition of specific DNA structures or lesions
results in ADP/ATP exchange.
Length = 216
Score = 218 bits (557), Expect = 8e-73
Identities = 81/165 (49%), Positives = 105/165 (63%), Gaps = 2/165 (1%)
Query: 12 RHPIVE-LQGGVSYIPNDVYFKSGEVSFNLVTGPNMGGKSTYIRSIGVSVFLAQIGCFVP 70
RHP+VE + ++PND E L+TGPNM GKSTY+R + + LAQIG FVP
Sbjct: 6 RHPVVEQVLDNEPFVPNDTEL-DPERQILLITGPNMAGKSTYLRQVALIALLAQIGSFVP 64
Query: 71 CDSATISVVDQIFTRVGAADSQYRGISTFMMEMKETATVIKKCTENSLVIIDELGRGTST 130
A I VVD+IFTR+GA+D G STFM+EM ETA ++ TE SLV++DE+GRGTST
Sbjct: 65 ASKAEIGVVDRIFTRIGASDDLAGGRSTFMVEMVETANILNNATERSLVLLDEIGRGTST 124
Query: 131 FDGFGMACSIARELASNRQPFTLFATHFHEIALLSRVIPTFRNVH 175
+DG +A +I L TLFATH+HE+ L +P +N H
Sbjct: 125 YDGLSIAWAIVEYLHEKIGAKTLFATHYHELTELEGKLPRVKNFH 169
>gnl|CDD|213210 cd03243, ABC_MutS_homologs, ATP-binding cassette domain of MutS
homologs. The MutS protein initiates DNA mismatch
repair by recognizing mispaired and unpaired bases
embedded in duplex DNA and activating endo- and
exonucleases to remove the mismatch. Members of the MutS
family also possess a conserved ATPase activity that
belongs to the ATP binding cassette (ABC) superfamily.
MutS homologs (MSH) have been identified in most
prokaryotic and all eukaryotic organisms examined.
Prokaryotes have two homologs (MutS1 and MutS2), whereas
seven MSH proteins (MSH1 to MSH7) have been identified
in eukaryotes. The homodimer MutS1 and heterodimers
MSH2-MSH3 and MSH2-MSH6 are primarily involved in
mitotic mismatch repair, whereas MSH4-MSH5 is involved
in resolution of Holliday junctions during meiosis. All
members of the MutS family contain the highly conserved
Walker A/B ATPase domain, and many share a common
mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and
MSH4-MSH5 dimerize to form sliding clamps, and
recognition of specific DNA structures or lesions
results in ADP/ATP exchange.
Length = 202
Score = 207 bits (528), Expect = 1e-68
Identities = 87/170 (51%), Positives = 116/170 (68%), Gaps = 4/170 (2%)
Query: 7 VLNQCRHPIVE-LQGGVSYIPNDVYFKSGEVSFNLVTGPNMGGKSTYIRSIGVSVFLAQI 65
+ RHP++ L G +++PND+ SG L+TGPNMGGKSTY+RSIG++V LAQI
Sbjct: 1 EIKGGRHPVLLALTKGETFVPNDINLGSG--RLLLITGPNMGGKSTYLRSIGLAVLLAQI 58
Query: 66 GCFVPCDSATISVVDQIFTRVGAADSQYRGISTFMMEMKETATVIKKCTENSLVIIDELG 125
GCFVP +SA+I +VD+IFTR+GA DS G STFM E+ E ++ T SLV+IDELG
Sbjct: 59 GCFVPAESASIPLVDRIFTRIGAEDSISDGRSTFMAELLELKEILSLATPRSLVLIDELG 118
Query: 126 RGTSTFDGFGMACSIARELASNRQPFTLFATHFHEIALLSRVIPTFRNVH 175
RGTST +G +A ++ L + TLFATHFHE+A L +P +N+H
Sbjct: 119 RGTSTAEGLAIAYAVLEHL-LEKGCRTLFATHFHELADLPEQVPGVKNLH 167
>gnl|CDD|233259 TIGR01070, mutS1, DNA mismatch repair protein MutS. [DNA
metabolism, DNA replication, recombination, and repair].
Length = 840
Score = 210 bits (535), Expect = 8e-64
Identities = 80/164 (48%), Positives = 108/164 (65%), Gaps = 1/164 (0%)
Query: 12 RHPIVELQGGVSYIPNDVYFKSGEVSFNLVTGPNMGGKSTYIRSIGVSVFLAQIGCFVPC 71
RHP+VE ++PND+ + L+TGPNMGGKSTY+R + LAQIG FVP
Sbjct: 569 RHPVVEQVLRTPFVPNDLEM-AHNRRMLLITGPNMGGKSTYMRQTALIALLAQIGSFVPA 627
Query: 72 DSATISVVDQIFTRVGAADSQYRGISTFMMEMKETATVIKKCTENSLVIIDELGRGTSTF 131
+SA + + D+IFTR+GA+D G STFM+EM E A ++ TENSLV+ DE+GRGTST+
Sbjct: 628 ESAELPLFDRIFTRIGASDDLASGRSTFMVEMTEAANILHNATENSLVLFDEIGRGTSTY 687
Query: 132 DGFGMACSIARELASNRQPFTLFATHFHEIALLSRVIPTFRNVH 175
DG +A +IA L + + TLFATH+ E+ L +P +NVH
Sbjct: 688 DGLALAWAIAEYLHEHIRAKTLFATHYFELTALEESLPGLKNVH 731
>gnl|CDD|213254 cd03287, ABC_MSH3_euk, ATP-binding cassette domain of eukaryotic
MutS3 homolog. The MutS protein initiates DNA mismatch
repair by recognizing mispaired and unpaired bases
embedded in duplex DNA and activating endo- and
exonucleases to remove the mismatch. Members of the MutS
family possess C-terminal domain with a conserved ATPase
activity that belongs to the ATP binding cassette (ABC)
superfamily. MutS homologs (MSH) have been identified in
most prokaryotic and all eukaryotic organisms examined.
Prokaryotes have two homologs (MutS1 and MutS2), whereas
seven MSH proteins (MSH1 to MSH7) have been identified
in eukaryotes. The homodimer MutS1 and heterodimers
MSH2-MSH3 and MSH2-MSH6 are primarily involved in
mitotic mismatch repair, whereas MSH4-MSH5 is involved
in resolution of Holliday junctions during meiosis. All
members of the MutS family contain the highly conserved
Walker A/B ATPase domain, and many share a common
mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and
MSH4-MSH5 dimerize to form sliding clamps, and
recognition of specific DNA structures or lesions
results in ADP/ATP exchange.
Length = 222
Score = 190 bits (484), Expect = 9e-62
Identities = 74/167 (44%), Positives = 107/167 (64%), Gaps = 1/167 (0%)
Query: 12 RHPIVELQGGVSYIPNDVYFKSGEVSFNLVTGPNMGGKSTYIRSIGVSVFLAQIGCFVPC 71
RHP++E S++PND++ + ++TGPNMGGKS+YIR + + +AQIG FVP
Sbjct: 7 RHPMIESLLDKSFVPNDIHLSAEGGYCQIITGPNMGGKSSYIRQVALITIMAQIGSFVPA 66
Query: 72 DSATISVVDQIFTRVGAADSQYRGISTFMMEMKETATVIKKCTENSLVIIDELGRGTSTF 131
SAT+S+ D + TR+GA+DS G+STFM+E+ ET+ ++ CT SLVI+DELGRGTST
Sbjct: 67 SSATLSIFDSVLTRMGASDSIQHGMSTFMVELSETSHILSNCTSRSLVILDELGRGTSTH 126
Query: 132 DGFGMACSIARELASNRQPFTLFATHFHEIALLSRVIP-TFRNVHES 177
DG +A + L ++ LF TH+ + + R + RN H S
Sbjct: 127 DGIAIAYATLHYLLEEKKCLVLFVTHYPSLGEILRRFEGSIRNYHMS 173
>gnl|CDD|213253 cd03286, ABC_MSH6_euk, ATP-binding cassette domain of eukaryotic
MutS6 homolog. The MutS protein initiates DNA mismatch
repair by recognizing mispaired and unpaired bases
embedded in duplex DNA and activating endo- and
exonucleases to remove the mismatch. Members of the MutS
family possess C-terminal domain with a conserved ATPase
activity that belongs to the ATP binding cassette (ABC)
superfamily. MutS homologs (MSH) have been identified in
most prokaryotic and all eukaryotic organisms examined.
Prokaryotes have two homologs (MutS1 and MutS2), whereas
seven MSH proteins (MSH1 to MSH7) have been identified
in eukaryotes. The homodimer MutS1 and heterodimers
MSH2-MSH3 and MSH2-MSH6 are primarily involved in
mitotic mismatch repair, whereas MSH4-MSH5 is involved
in resolution of Holliday junctions during meiosis. All
members of the MutS family contain the highly conserved
Walker A/B ATPase domain, and many share a common
mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and
MSH4-MSH5 dimerize to form sliding clamps, and
recognition of specific DNA structures or lesions
results in ADP/ATP exchange.
Length = 218
Score = 184 bits (468), Expect = 3e-59
Identities = 69/155 (44%), Positives = 103/155 (66%)
Query: 8 LNQCRHPIVELQGGVSYIPNDVYFKSGEVSFNLVTGPNMGGKSTYIRSIGVSVFLAQIGC 67
+ RHP + S++PNDV + ++TGPNMGGKST +R++ ++V +AQ+G
Sbjct: 2 FEELRHPCLNASTASSFVPNDVDLGATSPRILVLTGPNMGGKSTLLRTVCLAVIMAQMGM 61
Query: 68 FVPCDSATISVVDQIFTRVGAADSQYRGISTFMMEMKETATVIKKCTENSLVIIDELGRG 127
VP S +S+VD+IFTR+GA D +G STFM+E+ ETA +++ T +SLVI+DELGRG
Sbjct: 62 DVPAKSMRLSLVDRIFTRIGARDDIMKGESTFMVELSETANILRHATPDSLVILDELGRG 121
Query: 128 TSTFDGFGMACSIARELASNRQPFTLFATHFHEIA 162
TST DG+ +A ++ L + TLF+TH+H +
Sbjct: 122 TSTHDGYAIAHAVLEYLVKKVKCLTLFSTHYHSLC 156
>gnl|CDD|213248 cd03281, ABC_MSH5_euk, ATP-binding cassette domain of eukaryotic
MutS5 homolog. The MutS protein initiates DNA mismatch
repair by recognizing mispaired and unpaired bases
embedded in duplex DNA and activating endo- and
exonucleases to remove the mismatch. Members of the MutS
family possess C-terminal domain with a conserved ATPase
activity that belongs to the ATP binding cassette (ABC)
superfamily. MutS homologs (MSH) have been identified in
most prokaryotic and all eukaryotic organisms examined.
Prokaryotes have two homologs (MutS1 and MutS2), whereas
seven MSH proteins (MSH1 to MSH7) have been identified
in eukaryotes. The homodimer MutS1 and heterodimers
MSH2-MSH3 and MSH2-MSH6 are primarily involved in
mitotic mismatch repair, whereas MSH4-MSH5 is involved
in resolution of Holliday junctions during meiosis. All
members of the MutS family contain the highly conserved
Walker A/B ATPase domain, and many share a common
mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and
MSH4-MSH5 dimerize to form sliding clamps, and
recognition of specific DNA structures or lesions
results in ADP/ATP exchange.
Length = 213
Score = 164 bits (417), Expect = 1e-51
Identities = 65/152 (42%), Positives = 94/152 (61%), Gaps = 3/152 (1%)
Query: 12 RHPIVELQGGVSYIPNDVYFKSGEVSFNLVTGPNMGGKSTYIRSIGVSVFLAQIGCFVPC 71
RHP++EL S++PND G S ++TGPN GKS Y++ + + VFLA IG FVP
Sbjct: 6 RHPLLELFVD-SFVPNDTEIGGGGPSIMVITGPNSSGKSVYLKQVALIVFLAHIGSFVPA 64
Query: 72 DSATISVVDQIFTRVGAADSQYRGISTFMMEMKETATVIKKCTENSLVIIDELGRGTSTF 131
DSATI +VD+IFTR+ + +S G S FM+++ + + ++ T SLV+IDE G+GT T
Sbjct: 65 DSATIGLVDKIFTRMSSRESVSSGQSAFMIDLYQVSKALRLATRRSLVLIDEFGKGTDTE 124
Query: 132 DGFGMACSIARELAS--NRQPFTLFATHFHEI 161
DG G+ + L P + +THFHE+
Sbjct: 125 DGAGLLIATIEHLLKRGPECPRVIVSTHFHEL 156
>gnl|CDD|213249 cd03282, ABC_MSH4_euk, ATP-binding cassette domain of eukaryotic
MutS4 homolog. The MutS protein initiates DNA mismatch
repair by recognizing mispaired and unpaired bases
embedded in duplex DNA and activating endo- and
exonucleases to remove the mismatch. Members of the MutS
family possess C-terminal domain with a conserved ATPase
activity that belongs to the ATP binding cassette (ABC)
superfamily. MutS homologs (MSH) have been identified in
most prokaryotic and all eukaryotic organisms examined.
Prokaryotes have two homologs (MutS1 and MutS2), whereas
seven MSH proteins (MSH1 to MSH7) have been identified
in eukaryotes. The homodimer MutS1 and heterodimers
MSH2-MSH3 and MSH2-MSH6 are primarily involved in
mitotic mismatch repair, whereas MSH4-MSH5 is involved
in resolution of Holliday junctions during meiosis. All
members of the MutS family contain the highly conserved
Walker A/B ATPase domain, and many share a common
mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and
MSH4-MSH5 dimerize to form sliding clamps, and
recognition of specific DNA structures or lesions
results in ADP/ATP exchange.
Length = 204
Score = 157 bits (399), Expect = 4e-49
Identities = 69/166 (41%), Positives = 103/166 (62%), Gaps = 2/166 (1%)
Query: 10 QCRHPIVELQGGVSYIPNDVYFKSGEVSFNLVTGPNMGGKSTYIRSIGVSVFLAQIGCFV 69
RHPI++ +IPND+Y G F+++TGPNM GKSTY++ I + +AQIGCFV
Sbjct: 4 DSRHPILDRDKKN-FIPNDIYLTRGSSRFHIITGPNMSGKSTYLKQIALLAIMAQIGCFV 62
Query: 70 PCDSATISVVDQIFTRVGAADSQYRGISTFMMEMKETATVIKKCTENSLVIIDELGRGTS 129
P + AT+ + +++ +R+ DS R +STF EM ETA ++ +SLV+IDELGRGTS
Sbjct: 63 PAEYATLPIFNRLLSRLSNDDSMERNLSTFASEMSETAYILDYADGDSLVLIDELGRGTS 122
Query: 130 TFDGFGMACSIARELASNRQPFTLFATHFHEIALLSRVIPTFRNVH 175
+ DGF ++ +I L ++ FATHF +IA + ++H
Sbjct: 123 SADGFAISLAILECL-IKKESTVFFATHFRDIAAILGNKSCVVHLH 167
>gnl|CDD|213250 cd03283, ABC_MutS-like, ATP-binding cassette domain of MutS-like
homolog. The MutS protein initiates DNA mismatch repair
by recognizing mispaired and unpaired bases embedded in
duplex DNA and activating endo- and exonucleases to
remove the mismatch. Members of the MutS family possess
C-terminal domain with a conserved ATPase activity that
belongs to the ATP binding cassette (ABC) superfamily.
MutS homologs (MSH) have been identified in most
prokaryotic and all eukaryotic organisms examined.
Prokaryotes have two homologs (MutS1 and MutS2), whereas
seven MSH proteins (MSH1 to MSH7) have been identified
in eukaryotes. The homodimer MutS1 and heterodimers
MSH2-MSH3 and MSH2-MSH6 are primarily involved in
mitotic mismatch repair, whereas MSH4-MSH5 is involved
in resolution of Holliday junctions during meiosis. All
members of the MutS family contain the highly conserved
Walker A/B ATPase domain, and many share a common
mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and
MSH4-MSH5 dimerize to form sliding clamps, and
recognition of specific DNA structures or lesions
results in ADP/ATP exchange.
Length = 199
Score = 116 bits (292), Expect = 6e-33
Identities = 52/166 (31%), Positives = 88/166 (53%), Gaps = 9/166 (5%)
Query: 12 RHPIVELQGGVSYIPNDVYFKSGEVSFNLVTGPNMGGKSTYIRSIGVSVFLAQIGCFVPC 71
HP++ + V+ ND+ + + L+TG NM GKST++R+IGV+V LAQ G V
Sbjct: 6 GHPLIGREKRVA---NDIDM--EKKNGILITGSNMSGKSTFLRTIGVNVILAQAGAPVCA 60
Query: 72 DSATISVVDQIFTRVGAADSQYRGISTFMMEMKETATVIK--KCTENSLVIIDELGRGTS 129
S + V IFT + +D GIS F E++ +++ K E L ++DE+ +GT+
Sbjct: 61 SSFELPPVK-IFTSIRVSDDLRDGISYFYAELRRLKEIVEKAKKGEPVLFLLDEIFKGTN 119
Query: 130 TFDGFGMACSIARELASNRQPFTLFATHFHEIALLSRVIPTFRNVH 175
+ + + ++ + L N+ + +TH E+A L + RN H
Sbjct: 120 SRERQAASAAVLKFLK-NKNTIGIISTHDLELADLLDLDSAVRNYH 164
>gnl|CDD|213247 cd03280, ABC_MutS2, ATP-binding cassette domain of MutS2. MutS2
homologs in bacteria and eukaryotes. The MutS protein
initiates DNA mismatch repair by recognizing mispaired
and unpaired bases embedded in duplex DNA and activating
endo- and exonucleases to remove the mismatch. Members
of the MutS family also possess a conserved ATPase
activity that belongs to the ATP binding cassette (ABC)
superfamily. MutS homologs (MSH) have been identified in
most prokaryotic and all eukaryotic organisms examined.
Prokaryotes have two homologs (MutS1 and MutS2), whereas
seven MSH proteins (MSH1 to MSH7) have been identified
in eukaryotes. The homodimer MutS1 and heterodimers
MSH2-MSH3 and MSH2-MSH6 are primarily involved in
mitotic mismatch repair, whereas MSH4-MSH5 is involved
in resolution of Holliday junctions during meiosis. All
members of the MutS family contain the highly conserved
Walker A/B ATPase domain, and many share a common
mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and
MSH4-MSH5 dimerize to form sliding clamps, and
recognition of specific DNA structures or lesions
results in ADP/ATP exchange.
Length = 200
Score = 112 bits (282), Expect = 2e-31
Identities = 51/167 (30%), Positives = 87/167 (52%), Gaps = 4/167 (2%)
Query: 8 LNQCRHPIVELQGGVSYIPNDVYFKSGEVSFNLVTGPNMGGKSTYIRSIGVSVFLAQIGC 67
L + RHP++ LQG +P D+ + ++TGPN GGK+ ++++G+ +AQ G
Sbjct: 2 LREARHPLLPLQGEKV-VPLDIQLGENKRVL-VITGPNAGGKTVTLKTLGLLTLMAQSGL 59
Query: 68 FVPCD-SATISVVDQIFTRVGAADSQYRGISTFMMEMKETATVIKKCTENSLVIIDELGR 126
+P +++ V + IF +G S + +STF MK A +++ +SLV++DELG
Sbjct: 60 PIPAAEGSSLPVFENIFADIGDEQSIEQSLSTFSSHMKNIARILQHADPDSLVLLDELGS 119
Query: 127 GTSTFDGFGMACSIARELASNRQPFTLFATHFHEIALLSRVIPTFRN 173
GT +G +A +I EL R + TH+ E+ + N
Sbjct: 120 GTDPVEGAALAIAILEELL-ERGALVIATTHYGELKAYAYKREGVEN 165
>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 = 102 bits (256), Expect = 5e-28
Identities = 51/178 (28%), Positives = 79/178 (44%), Gaps = 33/178 (18%)
Query: 15 IVELQGGVSYIPNDVYFKSGEVSFNLVTGPNMGGKSTYIRSIGVSVFLA----------Q 64
IV + ++PNDV F GE S ++TGPN GKST + +IG+++ A +
Sbjct: 2 IVLGRFPSYFVPNDVTF--GEGSLTIITGPNGSGKSTILDAIGLALGGAQSATRRRSGVK 59
Query: 65 IGCFVPCDSATISVVDQIFTRVGAADSQYRGISTFMMEMKETATVIKKCTEN--SLVIID 122
GC V SA + IFTR+ +S E+ A ++ + L I+D
Sbjct: 60 AGCIVAAVSAEL-----IFTRL--------QLSGGEKELSALALILALASLKPRPLYILD 106
Query: 123 ELGRGTSTFDGFGMACSIARELASNRQPFTLFATHFHEIALLS----RVIPTFRNVHE 176
E+ RG DG +A +I L Q + TH E+A L+ + V++
Sbjct: 107 EIDRGLDPRDGQALAEAILEHLVKGAQ--VIVITHLPELAELADKLIHIKKVITGVYK 162
>gnl|CDD|130141 TIGR01069, mutS2, MutS2 family protein. Function of MutS2 is
unknown. It should not be considered a DNA mismatch
repair protein. It is likely a DNA mismatch binding
protein of unknown cellular function [DNA metabolism,
Other].
Length = 771
Score = 108 bits (271), Expect = 1e-27
Identities = 53/164 (32%), Positives = 85/164 (51%), Gaps = 6/164 (3%)
Query: 3 TGTLVLNQCRHPIVELQGGVSYIPNDVYFKSGEVSFNLVTGPNMGGKSTYIRSIGVSVFL 62
TG ++L RHP+++ +P + K E +TGPN GGK+ ++++G+ +
Sbjct: 293 TGKIILENARHPLLKEP---KVVPFTLNLKF-EKRVLAITGPNTGGKTVTLKTLGLLALM 348
Query: 63 AQIGCFVPCD-SATISVVDQIFTRVGAADSQYRGISTFMMEMKETATVIKKCTENSLVII 121
Q G +P + + I ++IF +G S + +STF MK + ++ K TENSLV+
Sbjct: 349 FQSGIPIPANEHSEIPYFEEIFADIGDEQSIEQNLSTFSGHMKNISAILSKTTENSLVLF 408
Query: 122 DELGRGTSTFDGFGMACSIARELASNRQPFTLFATHFHEIALLS 165
DELG GT +G +A SI L + L TH+ E+ L
Sbjct: 409 DELGAGTDPDEGSALAISILEYLL-KQNAQVLITTHYKELKALM 451
>gnl|CDD|224114 COG1193, COG1193, Mismatch repair ATPase (MutS family) [DNA
replication, recombination, and repair].
Length = 753
Score = 97.8 bits (244), Expect = 6e-24
Identities = 51/166 (30%), Positives = 87/166 (52%), Gaps = 12/166 (7%)
Query: 3 TGTLVLNQCRHPIVELQGGVSYIPNDVYFKSGEVSFNLVTGPNMGGKSTYIRSIGVSVFL 62
G L L RHP+++ +PND+ E+ ++TGPN GGK+ ++++G+ +
Sbjct: 290 DGVLELLDARHPLLKED-----VPNDLELGE-ELDRLIITGPNTGGKTVTLKTLGLLRLM 343
Query: 63 AQIGCFVPCDSAT-ISVVDQIFTRVGAADSQYRGISTFMMEMKETATVIKKCTENSLVII 121
AQ G +P + + V +IF +G S + +STF M +++K +SLV+
Sbjct: 344 AQSGLPIPALEGSELPVFVKIFADIGDEQSIEQSLSTFSSHMTNIVEILEK--ADSLVLF 401
Query: 122 DELGRGTSTFDGFGMACSIARELASNRQPFTLFA-THFHEIALLSR 166
DELG GT +G +A +I +L +P + A TH+ E+ L+
Sbjct: 402 DELGSGTDPDEGAALAIAILEDL--LEKPAKIVATTHYRELKALAA 445
>gnl|CDD|234750 PRK00409, PRK00409, recombination and DNA strand exchange inhibitor
protein; Reviewed.
Length = 782
Score = 94.1 bits (235), Expect = 9e-23
Identities = 51/166 (30%), Positives = 89/166 (53%), Gaps = 8/166 (4%)
Query: 2 GTGTLVLNQCRHPIVELQGGVSYIPNDVYFKSGEVSFNLVTGPNMGGKSTYIRSIGVSVF 61
G + L Q RHP+++ + V P D+ + + ++TGPN GGK+ ++++G++
Sbjct: 297 DEGKIDLRQARHPLLDGEKVV---PKDISL-GFDKTVLVITGPNTGGKTVTLKTLGLAAL 352
Query: 62 LAQIGCFVPCDS-ATISVVDQIFTRVGAADSQYRGISTFMMEMKETATVIKKCTENSLVI 120
+A+ G +P + + I V +IF +G S + +STF M +++K +NSLV+
Sbjct: 353 MAKSGLPIPANEPSEIPVFKEIFADIGDEQSIEQSLSTFSGHMTNIVRILEKADKNSLVL 412
Query: 121 IDELGRGTSTFDGFGMACSIARELASNRQPFTLFA-THFHEIALLS 165
DELG GT +G +A SI L ++ + A TH+ E+ L
Sbjct: 413 FDELGAGTDPDEGAALAISILEYLR--KRGAKIIATTHYKELKALM 456
>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 = 51.5 bits (124), Expect = 1e-08
Identities = 31/157 (19%), Positives = 54/157 (34%), Gaps = 22/157 (14%)
Query: 19 QGGVSYIPNDVYFKSGEVSFNLVTGPNMGGKSTYIRSIGVSVFLAQIGCFVPCDSATISV 78
G + + K+GE + GPN GKST +R I + S I +
Sbjct: 10 GGRTALDNVSLTLKAGE--IVALVGPNGSGKSTLLR---------AIAGLLKPTSGEILI 58
Query: 79 VDQIFTRVGAADSQYR-----GISTFMMEMKETATVIKKCTENSLVIIDELGRGTSTFDG 133
+ ++ + + R +S + A + L+++DE G
Sbjct: 59 DGKDIAKLPLEELRRRIGYVPQLSGGQRQRVALARAL--LLNPDLLLLDEPTSGLDPASR 116
Query: 134 FGMACSIARELASNRQPFTLFATHFHEIALLS--RVI 168
+ + R + TH E+A L+ RVI
Sbjct: 117 ERLLELLRELAEEGRT--VIIVTHDPELAELAADRVI 151
>gnl|CDD|222160 pfam13476, AAA_23, AAA domain.
Length = 204
Score = 31.0 bits (70), Expect = 0.26
Identities = 12/30 (40%), Positives = 17/30 (56%), Gaps = 4/30 (13%)
Query: 31 FKSGEVSF----NLVTGPNMGGKSTYIRSI 56
FK E+ F L+ GPN GK+T + +I
Sbjct: 10 FKDLEIDFSKGLTLIYGPNGSGKTTILDAI 39
>gnl|CDD|235175 PRK03918, PRK03918, chromosome segregation protein; Provisional.
Length = 880
Score = 31.2 bits (71), Expect = 0.33
Identities = 17/62 (27%), Positives = 26/62 (41%), Gaps = 10/62 (16%)
Query: 29 VYFKSGEVSFNLVTGPNMGGKSTYIRSIGVSVFLAQIGCFVPCDSATISVVDQIFTRVGA 88
V F G NL+ G N GKS+ + +I V ++ + D FTR+G
Sbjct: 19 VEFDDG---INLIIGQNGSGKSSILEAILVGLYWGH-----GSKPKGLKKDD--FTRIGG 68
Query: 89 AD 90
+
Sbjct: 69 SG 70
>gnl|CDD|213206 cd03239, ABC_SMC_head, The SMC head domain belongs to the
ATP-binding cassette superfamily. The structural
maintenance of chromosomes (SMC) proteins are essential
for successful chromosome transmission during
replication and segregation of the genome in all
organisms. SMCs are generally present as single
proteins in bacteria, and as at least six distinct
proteins in eukaryotes. The proteins range in size from
approximately 110 to 170 kDa, and each has five
distinct domains: amino- and carboxy-terminal globular
domains, which contain sequences characteristic of
ATPases, two coiled-coil regions separating the
terminal domains , and a central flexible hinge. SMC
proteins function together with other proteins in a
range of chromosomal transactions, including chromosome
condensation, sister-chromatid cohesion, recombination,
DNA repair, and epigenetic silencing of gene
expression.
Length = 178
Score = 30.4 bits (69), Expect = 0.34
Identities = 22/77 (28%), Positives = 32/77 (41%), Gaps = 15/77 (19%)
Query: 16 VELQGGVSYIPNDVYFKSGEVSFNLVTGPNMGGKSTYIRSI-------------GVSVFL 62
+ L+ SY D G SFN + GPN GKS + +I G +FL
Sbjct: 4 ITLKNFKSY--RDETVVGGSNSFNAIVGPNGSGKSNIVDAICFVLGGKAAKLRRGSLLFL 61
Query: 63 AQIGCFVPCDSATISVV 79
A G +SA++ +
Sbjct: 62 AGGGVKAGINSASVEIT 78
>gnl|CDD|100796 PRK01156, PRK01156, chromosome segregation protein; Provisional.
Length = 895
Score = 31.0 bits (70), Expect = 0.35
Identities = 13/46 (28%), Positives = 28/46 (60%), Gaps = 3/46 (6%)
Query: 16 VELQGGVSYIPNDVYFKSGEVSFNLVTGPNMGGKSTYIRSIGVSVF 61
+ L+ +S+ +++ F +G N++TG N GKS+ + +I ++F
Sbjct: 6 IRLKNFLSHDDSEIEFDTG---INIITGKNGAGKSSIVDAIRFALF 48
>gnl|CDD|224046 COG1121, ZnuC, ABC-type Mn/Zn transport systems, ATPase component
[Inorganic ion transport and metabolism].
Length = 254
Score = 29.9 bits (68), Expect = 0.57
Identities = 14/48 (29%), Positives = 25/48 (52%), Gaps = 5/48 (10%)
Query: 14 PIVELQG-GVSY----IPNDVYFKSGEVSFNLVTGPNMGGKSTYIRSI 56
P++E++ VSY + D+ + + GPN GKST +++I
Sbjct: 3 PMIEVENLTVSYGNRPVLEDISLSVEKGEITALIGPNGAGKSTLLKAI 50
>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 = 29.9 bits (68), Expect = 0.62
Identities = 21/74 (28%), Positives = 34/74 (45%), Gaps = 13/74 (17%)
Query: 16 VELQGGVSYIPNDVYFKSGEVSFNLVTGPNMGGKSTYIRSI-----GVSVFL---AQIGC 67
++L+ V+Y + S N++ GPN GKS+ + +I G L ++G
Sbjct: 6 IKLENFVTYDETEFRPGP---SLNMIIGPNGSGKSSIVCAICLGLGGKPKLLGRAKKVGE 62
Query: 68 FVP--CDSATISVV 79
FV CD TI +
Sbjct: 63 FVKRGCDEGTIEIE 76
>gnl|CDD|182331 PRK10247, PRK10247, putative ABC transporter ATP-binding protein
YbbL; Provisional.
Length = 225
Score = 29.7 bits (67), Expect = 0.63
Identities = 16/43 (37%), Positives = 26/43 (60%), Gaps = 4/43 (9%)
Query: 16 VELQGGVSYIPNDVYF--KSGEVSFNLVTGPNMGGKSTYIRSI 56
V G + I N++ F ++GE F L+TGP+ GKST ++ +
Sbjct: 13 VGYLAGDAKILNNISFSLRAGE--FKLITGPSGCGKSTLLKIV 53
>gnl|CDD|237421 PRK13539, PRK13539, cytochrome c biogenesis protein CcmA;
Provisional.
Length = 207
Score = 29.5 bits (67), Expect = 0.81
Identities = 14/37 (37%), Positives = 18/37 (48%), Gaps = 9/37 (24%)
Query: 27 NDVYFKSGEVSFNL-------VTGPNMGGKSTYIRSI 56
V F +SF L +TGPN GK+T +R I
Sbjct: 14 GRVLFSG--LSFTLAAGEALVLTGPNGSGKTTLLRLI 48
>gnl|CDD|213202 cd03235, ABC_Metallic_Cations, ATP-binding cassette domain of the
metal-type transporters. This family includes
transporters involved in the uptake of various metallic
cations such as iron, manganese, and zinc. The ATPases
of this group of transporters are very similar to
members of iron-siderophore uptake family suggesting
that they share a common ancestor. The best
characterized metal-type ABC transporters are the
YfeABCD system of Y. pestis, the SitABCD system of
Salmonella enterica serovar Typhimurium, and the
SitABCD transporter of Shigella flexneri. Moreover
other uncharacterized homologs of these metal-type
transporters are mainly found in pathogens like
Haemophilus or enteroinvasive E. coli isolates.
Length = 213
Score = 28.7 bits (65), Expect = 1.3
Identities = 17/45 (37%), Positives = 23/45 (51%), Gaps = 10/45 (22%)
Query: 12 RHPIVELQGGVSYIPNDVYFKSGEVSFNLVTGPNMGGKSTYIRSI 56
HP++E VS K GE F + GPN GKST +++I
Sbjct: 11 GHPVLE---DVS-----FEVKPGE--FLAIVGPNGAGKSTLLKAI 45
>gnl|CDD|225438 COG2884, FtsE, Predicted ATPase involved in cell division [Cell
division and chromosome partitioning].
Length = 223
Score = 28.7 bits (65), Expect = 1.4
Identities = 12/30 (40%), Positives = 17/30 (56%)
Query: 27 NDVYFKSGEVSFNLVTGPNMGGKSTYIRSI 56
DV F + F +TGP+ GKST ++ I
Sbjct: 19 RDVSFHIPKGEFVFLTGPSGAGKSTLLKLI 48
>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 = 1.7
Identities = 18/73 (24%), Positives = 28/73 (38%), Gaps = 9/73 (12%)
Query: 27 NDVYFKSGEVSFNLVTGPNMGGKSTYIRSIGVSVFLAQIGCFVPCDSATISVVD---QIF 83
DV + + L+ GPN GKST ++ + + G V D S ++
Sbjct: 21 KDVSLEIEKGERVLLIGPNGSGKSTLLKLLNG-LLKPTSGE-VLVDGLDTSSEKSLLELR 78
Query: 84 TRVG----AADSQ 92
+VG D Q
Sbjct: 79 QKVGLVFQNPDDQ 91
>gnl|CDD|227061 COG4717, COG4717, Uncharacterized conserved protein [Function
unknown].
Length = 984
Score = 28.7 bits (64), Expect = 2.1
Identities = 12/32 (37%), Positives = 18/32 (56%), Gaps = 3/32 (9%)
Query: 28 DVYFKSGEVSFNLVTGPNMGGKST---YIRSI 56
+ +F GE F ++ G N GKST +I S+
Sbjct: 16 ERHFDFGESKFQVIYGENEAGKSTLFSFIHSM 47
>gnl|CDD|222878 PHA02562, 46, endonuclease subunit; Provisional.
Length = 562
Score = 28.4 bits (64), Expect = 2.2
Identities = 9/23 (39%), Positives = 15/23 (65%)
Query: 39 NLVTGPNMGGKSTYIRSIGVSVF 61
L+TG N GKST + ++ ++F
Sbjct: 30 TLITGKNGAGKSTMLEALTFALF 52
>gnl|CDD|132251 TIGR03207, cyc_hxne_CoA_dh, cyclohexanecarboxyl-CoA dehydrogenase.
Cyclohex-1-ene-1carboxyl-CoA is an intermediate in the
anaerobic degradation of benzoyl-CoA derived from
varioius aromatic compounds, in Rhodopseudomonas
palustris but not Thauera aromatica. The aliphatic
compound cyclohexanecarboxylate, can be converted to the
same intermediate in two steps. The first step is its
ligation to coenzyme A. The second is the action of this
enzyme, cyclohexanecarboxyl-CoA dehydrogenase.
Length = 372
Score = 28.3 bits (63), Expect = 2.2
Identities = 19/68 (27%), Positives = 30/68 (44%), Gaps = 12/68 (17%)
Query: 72 DSATISVVDQ-----IFTRVGAADSQYRGISTFMMEMKETATVIKKCTENSLVIIDE--L 124
+ +IS DQ +F R G+ RGIS F++ M + T N + +
Sbjct: 148 EKTSISAADQADAAVVFARTGSEAEGARGISAFLVPMD-----LPGITRNRFDCHGQRAI 202
Query: 125 GRGTSTFD 132
GRG+ F+
Sbjct: 203 GRGSIFFE 210
>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 = 4.3
Identities = 10/29 (34%), Positives = 17/29 (58%), Gaps = 2/29 (6%)
Query: 28 DVYFKSGEVSFNLVTGPNMGGKSTYIRSI 56
+ + GEV + GPN GKST ++++
Sbjct: 21 SLDLRPGEV--LAILGPNGAGKSTLLKAL 47
>gnl|CDD|234572 PRK00012, gatA, aspartyl/glutamyl-tRNA amidotransferase subunit A;
Reviewed.
Length = 459
Score = 27.4 bits (62), Expect = 4.6
Identities = 11/29 (37%), Positives = 15/29 (51%), Gaps = 5/29 (17%)
Query: 107 ATVIKKCTENSLVII-----DELGRGTST 130
ATV++K VI+ DE G+ST
Sbjct: 90 ATVVEKLKAAGAVILGKTNMDEFAMGSST 118
>gnl|CDD|236554 PRK09536, btuD, corrinoid ABC transporter ATPase; Reviewed.
Length = 402
Score = 27.5 bits (61), Expect = 4.7
Identities = 12/37 (32%), Positives = 19/37 (51%), Gaps = 1/37 (2%)
Query: 20 GGVSYIPNDVYFKSGEVSFNLVTGPNMGGKSTYIRSI 56
G + + + V E S + GPN GK+T +R+I
Sbjct: 14 GDTT-VLDGVDLSVREGSLVGLVGPNGAGKTTLLRAI 49
>gnl|CDD|232842 TIGR00132, gatA, aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase,
A subunit. In many species, Gln--tRNA ligase is
missing. tRNA(Gln) is misacylated with Glu after which a
heterotrimeric amidotransferase converts Glu to Gln.
This model represents the amidase chain of that
heterotrimer, encoded by the gatA gene. In the Archaea,
Asn--tRNA ligase is also missing. This amidase subunit
may also function in the conversion of Asp-tRNA(Asn) to
Asn-tRNA(Asn), presumably with a different recognition
unit to replace gatB. Both Methanococcus jannaschii and
Methanobacterium thermoautotrophicum have both authentic
gatB and a gatB-related gene, but only one gene like
gatA. It has been shown that gatA can be expressed only
when gatC is also expressed. In most species expressing
the amidotransferase, the gatC ortholog is about 90
residues in length, but in Mycoplasma genitalium and
Mycoplasma pneumoniae the gatC equivalent is as the
C-terminal domain of a much longer protein. Not
surprisingly, the Mycoplasmas also represent the most
atypical lineage of gatA orthology. This orthology group
is more narrowly defined here than in Proc Natl Acad Aci
USA 94, 11819-11826 (1997). In particular, a Rhodococcus
homolog found in association with nitrile hydratase
genes and described as an enantiomer-selective amidase
active on several 2-aryl propionamides, is excluded
here. It is likely, however, that the amidase subunit
GatA is not exclusively a part of the Glu-tRNA(Gln)
amidotransferase heterotrimer and restricted to that
function in all species [Protein synthesis, tRNA
aminoacylation].
Length = 460
Score = 26.9 bits (60), Expect = 6.4
Identities = 13/35 (37%), Positives = 18/35 (51%), Gaps = 6/35 (17%)
Query: 107 ATVIKKCTENSLVII-----DELGRGTST-FDGFG 135
ATVI++ + +II DE G+ST FG
Sbjct: 90 ATVIERLKQAGALIIGKTNMDEFAMGSSTETSAFG 124
>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 = 26.7 bits (60), Expect = 6.5
Identities = 13/26 (50%), Positives = 16/26 (61%), Gaps = 2/26 (7%)
Query: 31 FKSGEVSFNLVTGPNMGGKSTYIRSI 56
K GE F L+ GPN GKST +R +
Sbjct: 24 IKKGE--FVLIVGPNGSGKSTLLRLL 47
>gnl|CDD|213190 cd03223, ABCD_peroxisomal_ALDP, ATP-binding cassette domain of
peroxisomal transporter, subfamily D. Peroxisomal
ATP-binding cassette transporter (Pat) is involved in
the import of very long-chain fatty acids (VLCFA) into
the peroxisome. The peroxisomal membrane forms a
permeability barrier for a wide variety of metabolites
required for and formed during fatty acid
beta-oxidation. To communicate with the cytoplasm and
mitochondria, peroxisomes need dedicated proteins to
transport such hydrophilic molecules across their
membranes. X-linked adrenoleukodystrophy (X-ALD) is
caused by mutations in the ALD gene, which encodes ALDP
(adrenoleukodystrophy protein ), a peroxisomal integral
membrane protein that is a member of the ATP-binding
cassette (ABC) transporter protein family. The disease
is characterized by a striking and unpredictable
variation in phenotypic expression. Phenotypes include
the rapidly progressive childhood cerebral form
(CCALD), the milder adult form, adrenomyeloneuropathy
(AMN), and variants without neurologic involvement
(i.e. asymptomatic).
Length = 166
Score = 26.3 bits (59), Expect = 7.3
Identities = 12/39 (30%), Positives = 18/39 (46%), Gaps = 2/39 (5%)
Query: 19 QGGVSYIPNDVYFKSGEVSFNLVTGPNMGGKSTYIRSIG 57
G V K G+ L+TGP+ GKS+ R++
Sbjct: 12 DGRVLLKDLSFEIKPGDRL--LITGPSGTGKSSLFRALA 48
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
0.323 0.137 0.404
Gapped
Lambda K H
0.267 0.0803 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,182,715
Number of extensions: 825226
Number of successful extensions: 895
Number of sequences better than 10.0: 1
Number of HSP's gapped: 870
Number of HSP's successfully gapped: 50
Length of query: 185
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 94
Effective length of database: 6,901,388
Effective search space: 648730472
Effective search space used: 648730472
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 56 (25.2 bits)