RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13255
(156 letters)
>gnl|CDD|235444 PRK05399, PRK05399, DNA mismatch repair protein MutS; Provisional.
Length = 854
Score = 88.6 bits (221), Expect = 3e-21
Identities = 33/88 (37%), Positives = 51/88 (57%)
Query: 1 ILDSTALANLHVLTNSDNTTEGTLIEQLDHCVTSFGKRMLRAQLVKPLTNLDAIKQRQDA 60
ILD+ NL + N + +L+ LD VT+ G R+LR L +PL + +AI+ R DA
Sbjct: 264 ILDAATRRNLELTENLRGGRKNSLLSVLDRTVTAMGGRLLRRWLHRPLRDREAIEARLDA 323
Query: 61 ISVLLDQKHITEQMRAKMKDLRDLERML 88
+ LL+ + E +R +K + DLER+L
Sbjct: 324 VEELLEDPLLREDLRELLKGVYDLERLL 351
Score = 77.4 bits (192), Expect = 2e-17
Identities = 28/58 (48%), Positives = 43/58 (74%)
Query: 98 GCRVPADSLTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHASKYSLALVDE 155
G VPA+S + VDRIFTR+GA D+L+ +ST++ E+TE+ I+ +A++ SL L+DE
Sbjct: 637 GSFVPAESARIGIVDRIFTRIGASDDLASGRSTFMVEMTETANILNNATERSLVLLDE 694
>gnl|CDD|223327 COG0249, MutS, Mismatch repair ATPase (MutS family) [DNA
replication, recombination, and repair].
Length = 843
Score = 88.1 bits (219), Expect = 5e-21
Identities = 32/89 (35%), Positives = 53/89 (59%), Gaps = 1/89 (1%)
Query: 1 ILDSTALANLHVLTN-SDNTTEGTLIEQLDHCVTSFGKRMLRAQLVKPLTNLDAIKQRQD 59
+LD+ NL + +N N +G+L LD VT G R+L+ L++PL + + I++R D
Sbjct: 261 VLDAATRRNLELFSNLRGNGKKGSLFWLLDRTVTPMGSRLLKRWLLQPLLDKEEIEERLD 320
Query: 60 AISVLLDQKHITEQMRAKMKDLRDLERML 88
A+ L D + E++R +K + DLER+L
Sbjct: 321 AVEELKDNPELREKLREMLKKVPDLERLL 349
Score = 78.9 bits (195), Expect = 9e-18
Identities = 25/59 (42%), Positives = 42/59 (71%)
Query: 98 GCRVPADSLTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHASKYSLALVDEL 156
G VPA+ + VDRIFTR+GA D+L+ +ST++ E+ E+ I+ +A++ SL ++DE+
Sbjct: 637 GSFVPAEKARIGIVDRIFTRIGAADDLASGRSTFMVEMLETANILDNATERSLVILDEI 695
>gnl|CDD|218489 pfam05192, MutS_III, MutS domain III. This domain is found in
proteins of the MutS family (DNA mismatch repair
proteins) and is found associated with pfam00488,
pfam05188, pfam01624 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 III, which is central to the
structure of Thermus aquaticus MutS as characterized
in.
Length = 290
Score = 85.9 bits (213), Expect = 6e-21
Identities = 35/85 (41%), Positives = 52/85 (61%), Gaps = 2/85 (2%)
Query: 4 STALANLHVLTNSDNTTEGTLIEQLDHCVTSFGKRMLRAQLVKPLTNLDAIKQRQDAISV 63
+ L NL + N +G+L+ LD VT GKR+LR L++PLT+LD I R DA+
Sbjct: 1 AATLRNLELFRNLRGGKKGSLLGLLDRTVTPMGKRLLRRWLLRPLTDLDEINARLDAVEE 60
Query: 64 LLDQKHITEQMRAKMKDLRDLERML 88
LL+ + E++R +K + DLER+L
Sbjct: 61 LLE--DLREELREALKGIPDLERLL 83
>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 = 81.7 bits (202), Expect = 8e-20
Identities = 30/59 (50%), Positives = 45/59 (76%)
Query: 98 GCRVPADSLTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHASKYSLALVDEL 156
G VPA S+ L+ VDRIFTR+GA+D++ +ST++ EL+E+ I+RHA+ SL ++DEL
Sbjct: 60 GMDVPAKSMRLSLVDRIFTRIGARDDIMKGESTFMVELSETANILRHATPDSLVILDEL 118
>gnl|CDD|197777 smart00534, MUTSac, ATPase domain of DNA mismatch repair MUTS
family.
Length = 185
Score = 80.3 bits (199), Expect = 1e-19
Identities = 30/71 (42%), Positives = 46/71 (64%)
Query: 86 RMLPSSTFLSFQGCRVPADSLTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHA 145
R + ++ G VPA+S L DRIFTR+GA D+L+ ST++ E+ E+ I+++A
Sbjct: 17 RQVALIVIMAQIGSFVPAESAELPVFDRIFTRIGASDSLAQGLSTFMVEMKETANILKNA 76
Query: 146 SKYSLALVDEL 156
+K SL L+DEL
Sbjct: 77 TKNSLVLLDEL 87
>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 = 76.5 bits (189), Expect = 1e-17
Identities = 27/59 (45%), Positives = 42/59 (71%)
Query: 98 GCRVPADSLTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHASKYSLALVDEL 156
G VPA+S + VDRIFTR+GA D+L+ +ST++ E+ E+ I+ +A+ SL ++DEL
Sbjct: 73 GSFVPAESARIGIVDRIFTRIGASDDLASGRSTFMVEMLETANILHNATDKSLVILDEL 131
>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 = 75.0 bits (185), Expect = 2e-17
Identities = 27/59 (45%), Positives = 42/59 (71%)
Query: 98 GCRVPADSLTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHASKYSLALVDEL 156
G VPA + VDRIFTR+GA D+L+G +ST++ E+ E+ I+ +A++ SL L+DE+
Sbjct: 60 GSFVPASKAEIGVVDRIFTRIGASDDLAGGRSTFMVEMVETANILNNATERSLVLLDEI 118
>gnl|CDD|214710 smart00533, MUTSd, DNA-binding domain of DNA mismatch repair MUTS
family.
Length = 308
Score = 74.3 bits (183), Expect = 2e-16
Identities = 27/68 (39%), Positives = 45/68 (66%)
Query: 21 EGTLIEQLDHCVTSFGKRMLRAQLVKPLTNLDAIKQRQDAISVLLDQKHITEQMRAKMKD 80
+G+L E L+H T GKR+LR L++PL +L I +R DA+ L++ + +++R +K
Sbjct: 1 KGSLFELLNHTKTPMGKRLLRRWLLQPLLDLKEINERLDAVEELVENPELRQKLRQLLKR 60
Query: 81 LRDLERML 88
+ DLER+L
Sbjct: 61 IPDLERLL 68
>gnl|CDD|233259 TIGR01070, mutS1, DNA mismatch repair protein MutS. [DNA
metabolism, DNA replication, recombination, and repair].
Length = 840
Score = 75.2 bits (185), Expect = 2e-16
Identities = 29/65 (44%), Positives = 44/65 (67%)
Query: 92 TFLSFQGCRVPADSLTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHASKYSLA 151
L+ G VPA+S L DRIFTR+GA D+L+ +ST++ E+TE+ I+ +A++ SL
Sbjct: 616 ALLAQIGSFVPAESAELPLFDRIFTRIGASDDLASGRSTFMVEMTEAANILHNATENSLV 675
Query: 152 LVDEL 156
L DE+
Sbjct: 676 LFDEI 680
Score = 64.8 bits (158), Expect = 7e-13
Identities = 29/88 (32%), Positives = 47/88 (53%)
Query: 1 ILDSTALANLHVLTNSDNTTEGTLIEQLDHCVTSFGKRMLRAQLVKPLTNLDAIKQRQDA 60
LD+ NL + N + TL LD T+ G R+L+ L +PL + + ++ RQD
Sbjct: 250 QLDAATRRNLELTENLRGGKQNTLFSVLDETKTAMGSRLLKRWLHRPLRDREVLEARQDT 309
Query: 61 ISVLLDQKHITEQMRAKMKDLRDLERML 88
+ VLL + E +R +K++ DLER+
Sbjct: 310 VEVLLRHFFLREGLRPLLKEVGDLERLA 337
>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 = 67.7 bits (166), Expect = 1e-14
Identities = 32/65 (49%), Positives = 47/65 (72%)
Query: 92 TFLSFQGCRVPADSLTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHASKYSLA 151
L+ GC VPA+S ++ VDRIFTR+GA+D++S +ST++AEL E + I+ A+ SL
Sbjct: 53 VLLAQIGCFVPAESASIPLVDRIFTRIGAEDSISDGRSTFMAELLELKEILSLATPRSLV 112
Query: 152 LVDEL 156
L+DEL
Sbjct: 113 LIDEL 117
>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 = 66.0 bits (161), Expect = 6e-14
Identities = 27/71 (38%), Positives = 43/71 (60%)
Query: 86 RMLPSSTFLSFQGCRVPADSLTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHA 145
R + T ++ G VPA S TL+ D + TRMGA D++ ST++ EL+E+ I+ +
Sbjct: 49 RQVALITIMAQIGSFVPASSATLSIFDSVLTRMGASDSIQHGMSTFMVELSETSHILSNC 108
Query: 146 SKYSLALVDEL 156
+ SL ++DEL
Sbjct: 109 TSRSLVILDEL 119
>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 = 64.2 bits (157), Expect = 3e-13
Identities = 27/64 (42%), Positives = 43/64 (67%)
Query: 92 TFLSFQGCRVPADSLTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHASKYSLA 151
FL+ G VPADS T+ VD+IFTRM +++++S QS ++ +L + +R A++ SL
Sbjct: 53 VFLAHIGSFVPADSATIGLVDKIFTRMSSRESVSSGQSAFMIDLYQVSKALRLATRRSLV 112
Query: 152 LVDE 155
L+DE
Sbjct: 113 LIDE 116
>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 = 61.2 bits (149), Expect = 3e-12
Identities = 25/59 (42%), Positives = 38/59 (64%)
Query: 98 GCRVPADSLTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHASKYSLALVDEL 156
GC VP DS + VD I R+GA D+ ST++AE+ E+ I++ A++ SL ++DEL
Sbjct: 60 GCFVPCDSADIPIVDCILARVGASDSQLKGVSTFMAEMLETAAILKSATENSLIIIDEL 118
>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 = 49.7 bits (119), Expect = 5e-08
Identities = 22/59 (37%), Positives = 37/59 (62%)
Query: 98 GCRVPADSLTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHASKYSLALVDEL 156
GC VPA+ TL +R+ +R+ D++ ST+ +E++E+ I+ +A SL L+DEL
Sbjct: 59 GCFVPAEYATLPIFNRLLSRLSNDDSMERNLSTFASEMSETAYILDYADGDSLVLIDEL 117
>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 = 45.4 bits (108), Expect = 2e-06
Identities = 24/73 (32%), Positives = 35/73 (47%), Gaps = 3/73 (4%)
Query: 86 RMLPSSTFLSFQGCRVPADSLTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHA 145
R + + L+ G V A S L P +IFT + D+L S + AEL + I+ A
Sbjct: 43 RTIGVNVILAQAGAPVCASSFEL-PPVKIFTSIRVSDDLRDGISYFYAELRRLKEIVEKA 101
Query: 146 SK--YSLALVDEL 156
K L L+DE+
Sbjct: 102 KKGEPVLFLLDEI 114
>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 = 33.0 bits (76), Expect = 0.030
Identities = 18/57 (31%), Positives = 32/57 (56%), Gaps = 1/57 (1%)
Query: 101 VPADSLTLTPV-DRIFTRMGAKDNLSGAQSTYLAELTESETIMRHASKYSLALVDEL 156
+PA + PV + IF +G + ++ + ST+ + + I++HA SL L+DEL
Sbjct: 61 IPAAEGSSLPVFENIFADIGDEQSIEQSLSTFSSHMKNIARILQHADPDSLVLLDEL 117
>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 = 32.5 bits (74), Expect = 0.076
Identities = 17/70 (24%), Positives = 31/70 (44%), Gaps = 1/70 (1%)
Query: 88 LPSSTFLSFQGCRVPADSLTLTPV-DRIFTRMGAKDNLSGAQSTYLAELTESETIMRHAS 146
L + G +PA+ + P + IF +G + ++ ST+ + I+ +
Sbjct: 342 LGLLALMFQSGIPIPANEHSEIPYFEEIFADIGDEQSIEQNLSTFSGHMKNISAILSKTT 401
Query: 147 KYSLALVDEL 156
+ SL L DEL
Sbjct: 402 ENSLVLFDEL 411
>gnl|CDD|238130 cd00212, PTS_IIB_glc, PTS_IIB, PTS system, glucose/sucrose
specific IIB subunit. The bacterial
phosphoenolpyruvate: sugar phosphotransferase system
(PTS) is a multi-protein system involved in the
regulation of a variety of metabolic and
transcriptional processes. This family is one of four
structurally and functionally distinct group IIB PTS
system cytoplasmic enzymes, necessary for the uptake of
carbohydrates across the cytoplasmic membrane and their
phosphorylation.
Length = 78
Score = 27.9 bits (63), Expect = 0.76
Identities = 12/47 (25%), Positives = 18/47 (38%), Gaps = 6/47 (12%)
Query: 25 IEQLDHCVTSFGKRMLRAQLVKP-LTNLDAIKQRQDAISVLLDQKHI 70
I LDHC T R LR + + A+K+ V+ +
Sbjct: 17 IVSLDHCAT----R-LRLTVKDESKVDEAALKKLGGVKGVVKNGGQY 58
>gnl|CDD|152000 pfam11564, BpuJI_N, Restriction endonuclease BpuJI - N terminal.
BpuJI is a restriction endonuclease which recognises the
asymmetric sequence 5'-CCCGT and cuts at multiple sites
in the surrounding area of the target sequence. This
family of proteins is the N terminal domain of BpuJI
which has DNA recognition functions. The recognition
domain has two subdomains D1 and D2. The recognition of
the target sequence occurs through major groove contacts
of amino acids on the helix-turn-helix region and the
N-terminal arm.
Length = 294
Score = 28.5 bits (63), Expect = 1.6
Identities = 21/120 (17%), Positives = 51/120 (42%), Gaps = 6/120 (5%)
Query: 10 LHVLTNSDNTTEGTLI---EQLDHCVTSFGKRMLRAQLVKPLTNLDAIKQRQDAISVLLD 66
L + + E + + + HC+ + + L+ + KP+ ++ I + + A + D
Sbjct: 144 LELFLEASQADEKNIQLSDDDIAHCIFN-DLQCLQDK-EKPIEIIEKIIEDR-ANDIAKD 200
Query: 67 QKHITEQMRAKMKDLRDLERMLPSSTFLSFQGCRVPADSLTLTPVDRIFTRMGAKDNLSG 126
KH +++R M+ ++D+ L + + G V +S+ ++ I +G
Sbjct: 201 TKHPGDEIRYAMQHIKDILDYLEIANLIRIDGGLVKINSMEAEAINYIADFLGNDAEFDA 260
>gnl|CDD|235549 PRK05658, PRK05658, RNA polymerase sigma factor RpoD; Validated.
Length = 619
Score = 27.5 bits (62), Expect = 3.1
Identities = 17/80 (21%), Positives = 28/80 (35%), Gaps = 18/80 (22%)
Query: 37 KRMLRAQLVKPLTNLDAIKQRQDAISVLLDQKHIT--------EQMRAKMKDLRDLERML 88
++ ++ L + ++ + L +T EQ+R K +R ER L
Sbjct: 235 RKAQEKKVEGRLAQHKKYAKLREKLKEELKSLRLTSKQIDELVEQLRDINKRVRGQEREL 294
Query: 89 ---------PSSTFL-SFQG 98
P FL FQG
Sbjct: 295 LRLVERLKMPRKDFLKLFQG 314
>gnl|CDD|218890 pfam06089, Asparaginase_II, L-asparaginase II. This family
consists of several bacterial L-asparaginase II
proteins. L-asparaginase (EC:3.5.1.1) catalyzes the
hydrolysis of L-asparagine to L-aspartate and ammonium.
Rhizobium etli possesses two asparaginases: asparaginase
I, which is thermostable and constitutive, and
asparaginase II, which is thermolabile, induced by
asparagine and repressed by the carbon source.
Length = 325
Score = 26.8 bits (60), Expect = 5.4
Identities = 10/47 (21%), Positives = 19/47 (40%), Gaps = 2/47 (4%)
Query: 98 GCRVPADSLTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRH 144
GC P +L L + R + R+ + L ++ L + + H
Sbjct: 182 GCGAPTFALPLRGLARAYARLASAAGLPDERAAAAERLARA--MRAH 226
>gnl|CDD|218912 pfam06148, COG2, COG (conserved oligomeric Golgi) complex
component, COG2. The COG complex comprises eight
proteins COG1-8. The COG complex plays critical roles in
Golgi structure and function. The proposed function of
the complex is to mediate the initial physical contact
between transport vesicles and their membrane targets. A
comparable role in tethering vesicles has been suggested
for at least six additional large multisubunit
complexes, including the exocyst, a complex that
mediates trafficking to the plasma membrane. COG2
structure reveals a six-helix bundle with few conserved
surface features but a general resemblance to recently
determined crystal structures of four different exocyst
subunits. These bundles inCOG2 may act as platforms for
interaction with other trafficing proteins including
SNAREs (soluble N-ethylmaleimide factor attachment
protein receptors) and Rabs.
Length = 133
Score = 26.1 bits (58), Expect = 6.1
Identities = 7/37 (18%), Positives = 19/37 (51%)
Query: 52 DAIKQRQDAISVLLDQKHITEQMRAKMKDLRDLERML 88
++ R + + L++K + + +K L DL+ ++
Sbjct: 90 SELEARLEEVEAKLEEKKDLREKKESLKLLLDLDHVV 126
>gnl|CDD|234709 PRK00275, glnD, PII uridylyl-transferase; Provisional.
Length = 895
Score = 26.6 bits (59), Expect = 6.5
Identities = 26/91 (28%), Positives = 40/91 (43%), Gaps = 14/91 (15%)
Query: 3 DSTALANLHVLTNSD---------NTTEGTLIEQLDHCVTSFGKRMLRAQLVKPLTNLDA 53
D T L L+VLT +D N+ +L+ QL + T KR LR L P+ +
Sbjct: 576 DQTHLDYLYVLTVADINATNPTLWNSWRASLLRQL-YTET---KRALRRGLENPVDREEQ 631
Query: 54 IKQRQD-AISVLLDQKHITEQMRAKMKDLRD 83
I+Q Q A+ +L+ + + L D
Sbjct: 632 IRQTQSAALDILVRKGTDPDDAEQLWSQLGD 662
>gnl|CDD|226856 COG4448, AnsA, L-asparaginase II [Amino acid transport and
metabolism].
Length = 339
Score = 26.3 bits (58), Expect = 7.6
Identities = 16/75 (21%), Positives = 29/75 (38%), Gaps = 4/75 (5%)
Query: 65 LDQKH-ITEQMRAKMKDLRDLERMLPSSTFLSFQGCRVPADSLTLTPVDRIFTRMGAKDN 123
+ H I + +RAKM +L + + GC +P +L L + F M +
Sbjct: 163 VGYGHPIQQLVRAKMAELT---GAPHAEDICAHDGCSIPTYALPLGQLAHGFALMATGNG 219
Query: 124 LSGAQSTYLAELTES 138
L ++ L +
Sbjct: 220 LGAERAKAAERLIRA 234
>gnl|CDD|235108 PRK03180, ligB, ATP-dependent DNA ligase; Reviewed.
Length = 508
Score = 26.1 bits (58), Expect = 9.4
Identities = 10/30 (33%), Positives = 16/30 (53%), Gaps = 5/30 (16%)
Query: 102 PAD--SLTLTPVDRIFTRMGAKDNLSGAQS 129
PA +LT+ VD + + A ++GA S
Sbjct: 67 PAAEPTLTVADVDAALSEIAA---VAGAGS 93
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 0.130 0.353
Gapped
Lambda K H
0.267 0.0677 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,565,092
Number of extensions: 665990
Number of successful extensions: 651
Number of sequences better than 10.0: 1
Number of HSP's gapped: 650
Number of HSP's successfully gapped: 48
Length of query: 156
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 67
Effective length of database: 6,990,096
Effective search space: 468336432
Effective search space used: 468336432
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 (21.8 bits)
S2: 55 (25.1 bits)