RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13262
(229 letters)
>gnl|CDD|220646 pfam10240, DUF2464, Protein of unknown function (DUF2464). This is
a family of proteins conserved from worms to humans.
Members have been annotated as FAM125A proteins, but
their function is unknown.
Length = 251
Score = 101 bits (254), Expect = 3e-26
Identities = 40/101 (39%), Positives = 62/101 (61%), Gaps = 8/101 (7%)
Query: 15 PITAIAVIEDIQKCPSGYTVISKTVDQDTDADMWRESAFFLRKTRYLCVSKTESLFQI-D 73
PITA+ + D +KCP G++ ISKTVD DAD+WR+ F R TRYLC S +ES +
Sbjct: 2 PITALGWVADFEKCPKGFSPISKTVD-GADADLWRDG-FGSRSTRYLCYSTSESKNGLPG 59
Query: 74 YIVENICIINEKETPPDGFCLIARTLDSDQG-----QICER 109
+V ++ +I++K+T P G+ I T D+ + ++C +
Sbjct: 60 NVVVDLQVIDDKDTLPVGYSAIPETADTREKVWRKKRLCVK 100
>gnl|CDD|235444 PRK05399, PRK05399, DNA mismatch repair protein MutS; Provisional.
Length = 854
Score = 77.1 bits (191), Expect = 3e-16
Identities = 24/60 (40%), Positives = 33/60 (55%), Gaps = 13/60 (21%)
Query: 164 ATGDQTYIPNSTVIGRCKEDVESGGEGNRKPTVLLLTGPNMGGKSTVMRQLGLITILAQM 223
G + ++PN + E R +LL+TGPNM GKST MRQ+ LI +LAQ+
Sbjct: 590 VLGGEPFVPNDCDLD----------EERR---LLLITGPNMAGKSTYMRQVALIVLLAQI 636
>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 = 70.7 bits (174), Expect = 8e-15
Identities = 25/87 (28%), Positives = 38/87 (43%), Gaps = 19/87 (21%)
Query: 140 CVPTFLGLEEPHPYISALESLYPC---ATGDQTYIPNSTVIGRCKEDVESGGEGNRKPTV 196
P F + +P ++PN +G+ + +
Sbjct: 2 VRPEFT----ESAALHIEGGRHPVVEAVLDAGNFVPNDVSLGK------------ERSRI 45
Query: 197 LLLTGPNMGGKSTVMRQLGLITILAQM 223
LL+TGPNMGGKST +RQ+ LI I+AQ+
Sbjct: 46 LLITGPNMGGKSTYLRQVALIVIMAQI 72
>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 = 66.7 bits (163), Expect = 2e-13
Identities = 24/65 (36%), Positives = 35/65 (53%), Gaps = 14/65 (21%)
Query: 161 YPCATGDQ--TYIPNSTVIGRCKEDVESGGEGNRKPTVLLLTGPNMGGKSTVMRQLGLIT 218
+PC +++PN +G P +L+LTGPNMGGKST++R + L
Sbjct: 7 HPCLNASTASSFVPNDVDLGA------------TSPRILVLTGPNMGGKSTLLRTVCLAV 54
Query: 219 ILAQM 223
I+AQM
Sbjct: 55 IMAQM 59
>gnl|CDD|223327 COG0249, MutS, Mismatch repair ATPase (MutS family) [DNA
replication, recombination, and repair].
Length = 843
Score = 68.1 bits (167), Expect = 3e-13
Identities = 22/57 (38%), Positives = 32/57 (56%), Gaps = 13/57 (22%)
Query: 167 DQTYIPNSTVIGRCKEDVESGGEGNRKPTVLLLTGPNMGGKSTVMRQLGLITILAQM 223
D ++PN + + ++L+TGPNMGGKST +RQ+ LI ILAQ+
Sbjct: 593 DNGFVPNDIDL-------------SGNRRIILITGPNMGGKSTYLRQVALIVILAQI 636
>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 = 64.2 bits (157), Expect = 1e-12
Identities = 27/78 (34%), Positives = 38/78 (48%), Gaps = 23/78 (29%)
Query: 146 GLEEPHPYISALESLYPCATGDQTYIPNSTVIGRCKEDVESGGEGNRKPTVLLLTGPNMG 205
G P L +L T +T++PN +G +LL+TGPNMG
Sbjct: 4 GGRHPV-----LLAL----TKGETFVPNDINLGS--------------GRLLLITGPNMG 40
Query: 206 GKSTVMRQLGLITILAQM 223
GKST +R +GL +LAQ+
Sbjct: 41 GKSTYLRSIGLAVLLAQI 58
>gnl|CDD|197777 smart00534, MUTSac, ATPase domain of DNA mismatch repair MUTS
family.
Length = 185
Score = 63.0 bits (154), Expect = 2e-12
Identities = 18/28 (64%), Positives = 25/28 (89%)
Query: 196 VLLLTGPNMGGKSTVMRQLGLITILAQM 223
V+++TGPNMGGKST +RQ+ LI I+AQ+
Sbjct: 1 VVIITGPNMGGKSTYLRQVALIVIMAQI 28
>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 = 63.1 bits (154), Expect = 3e-12
Identities = 21/60 (35%), Positives = 34/60 (56%), Gaps = 13/60 (21%)
Query: 164 ATGDQTYIPNSTVIGRCKEDVESGGEGNRKPTVLLLTGPNMGGKSTVMRQLGLITILAQM 223
++ ++PN T + + + +LL+TGPNM GKST +RQ+ LI +LAQ+
Sbjct: 13 VLDNEPFVPNDTEL-------------DPERQILLITGPNMAGKSTYLRQVALIALLAQI 59
>gnl|CDD|233259 TIGR01070, mutS1, DNA mismatch repair protein MutS. [DNA
metabolism, DNA replication, recombination, and repair].
Length = 840
Score = 56.7 bits (137), Expect = 2e-09
Identities = 26/57 (45%), Positives = 34/57 (59%), Gaps = 13/57 (22%)
Query: 167 DQTYIPNSTVIGRCKEDVESGGEGNRKPTVLLLTGPNMGGKSTVMRQLGLITILAQM 223
++PN D+E NR+ +LL+TGPNMGGKST MRQ LI +LAQ+
Sbjct: 578 RTPFVPN---------DLEMAH--NRR--MLLITGPNMGGKSTYMRQTALIALLAQI 621
>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 = 55.1 bits (133), Expect = 3e-09
Identities = 28/67 (41%), Positives = 39/67 (58%), Gaps = 14/67 (20%)
Query: 158 ESLYPC--ATGDQTYIPNSTVIGRCKEDVESGGEGNRKPTVLLLTGPNMGGKSTVMRQLG 215
E+ +PC A D +IPN DV +R L++TGPNMGGKST +RQ+G
Sbjct: 4 EARHPCVEAQDDVAFIPN---------DVTLTRGKSR---FLIITGPNMGGKSTYIRQIG 51
Query: 216 LITILAQ 222
+I ++AQ
Sbjct: 52 VIVLMAQ 58
>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 = 50.6 bits (121), Expect = 1e-07
Identities = 27/72 (37%), Positives = 39/72 (54%), Gaps = 20/72 (27%)
Query: 151 HPYISALESLYPCATGDQTYIPNSTVIGRCKEDVESGGEGNRKPTVLLLTGPNMGGKSTV 210
HP I +L D++++PN D+ EG ++TGPNMGGKS+
Sbjct: 8 HPMIESLL--------DKSFVPN---------DIHLSAEGGY---CQIITGPNMGGKSSY 47
Query: 211 MRQLGLITILAQ 222
+RQ+ LITI+AQ
Sbjct: 48 IRQVALITIMAQ 59
>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 = 50.4 bits (121), Expect = 1e-07
Identities = 18/55 (32%), Positives = 29/55 (52%), Gaps = 12/55 (21%)
Query: 168 QTYIPNSTVIGRCKEDVESGGEGNRKPTVLLLTGPNMGGKSTVMRQLGLITILAQ 222
+++PN T IG P+++++TGPN GKS ++Q+ LI LA
Sbjct: 15 DSFVPNDTEIGG------------GGPSIMVITGPNSSGKSVYLKQVALIVFLAH 57
>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 = 46.6 bits (111), Expect = 2e-06
Identities = 14/26 (53%), Positives = 22/26 (84%)
Query: 198 LLTGPNMGGKSTVMRQLGLITILAQM 223
++TGPNM GKST ++Q+ L+ I+AQ+
Sbjct: 33 IITGPNMSGKSTYLKQIALLAIMAQI 58
>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 = 45.8 bits (109), Expect = 3e-06
Identities = 17/34 (50%), Positives = 22/34 (64%)
Query: 193 KPTVLLLTGPNMGGKSTVMRQLGLITILAQMENP 226
K +L+TG NM GKST +R +G+ ILAQ P
Sbjct: 24 KKNGILITGSNMSGKSTFLRTIGVNVILAQAGAP 57
>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 = 45.4 bits (108), Expect = 3e-06
Identities = 12/30 (40%), Positives = 20/30 (66%)
Query: 193 KPTVLLLTGPNMGGKSTVMRQLGLITILAQ 222
+ ++ ++TGPN GKST++ +GL AQ
Sbjct: 20 EGSLTIITGPNGSGKSTILDAIGLALGGAQ 49
>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 = 44.2 bits (105), Expect = 1e-05
Identities = 18/35 (51%), Positives = 26/35 (74%), Gaps = 3/35 (8%)
Query: 188 GEGNRKPTVLLLTGPNMGGKSTVMRQLGLITILAQ 222
GE R VL++TGPN GGK+ ++ LGL+T++AQ
Sbjct: 25 GENKR---VLVITGPNAGGKTVTLKTLGLLTLMAQ 56
>gnl|CDD|224114 COG1193, COG1193, Mismatch repair ATPase (MutS family) [DNA
replication, recombination, and repair].
Length = 753
Score = 43.9 bits (104), Expect = 3e-05
Identities = 19/49 (38%), Positives = 29/49 (59%)
Query: 181 KEDVESGGEGNRKPTVLLLTGPNMGGKSTVMRQLGLITILAQMENPQLI 229
KEDV + E + L++TGPN GGK+ ++ LGL+ ++AQ P
Sbjct: 304 KEDVPNDLELGEELDRLIITGPNTGGKTVTLKTLGLLRLMAQSGLPIPA 352
Score = 31.2 bits (71), Expect = 0.46
Identities = 23/87 (26%), Positives = 37/87 (42%), Gaps = 6/87 (6%)
Query: 145 LGLEEPHPYISALESLYPCATGD--QTYIPNSTVIGRCKEDVESGGEGNRKPTVLLLTGP 202
LGL P P I ++ + + V +E++E + + V LLTG
Sbjct: 485 LGL--PEPIIEEAKTEFGEEKELLEELIEKLEEVRKELEEELEEVEKLLDE--VELLTGA 540
Query: 203 NMGGKSTVMRQLGLITILAQMENPQLI 229
N GGK++++ I +LA M P
Sbjct: 541 NSGGKTSLLELKAQIVVLAHMGLPVPA 567
>gnl|CDD|234750 PRK00409, PRK00409, recombination and DNA strand exchange inhibitor
protein; Reviewed.
Length = 782
Score = 39.4 bits (93), Expect = 0.001
Identities = 14/28 (50%), Positives = 22/28 (78%)
Query: 195 TVLLLTGPNMGGKSTVMRQLGLITILAQ 222
TVL++TGPN GGK+ ++ LGL ++A+
Sbjct: 328 TVLVITGPNTGGKTVTLKTLGLAALMAK 355
>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 = 37.6 bits (88), Expect = 0.002
Identities = 9/31 (29%), Positives = 16/31 (51%)
Query: 192 RKPTVLLLTGPNMGGKSTVMRQLGLITILAQ 222
+ ++ L GPN GKST++R + +
Sbjct: 23 KAGEIVALVGPNGSGKSTLLRAIAGLLKPTS 53
>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 = 37.9 bits (88), Expect = 0.003
Identities = 13/32 (40%), Positives = 21/32 (65%)
Query: 191 NRKPTVLLLTGPNMGGKSTVMRQLGLITILAQ 222
+ VL +TGPN GGK+ ++ LGL+ ++ Q
Sbjct: 319 KFEKRVLAITGPNTGGKTVTLKTLGLLALMFQ 350
>gnl|CDD|237421 PRK13539, PRK13539, cytochrome c biogenesis protein CcmA;
Provisional.
Length = 207
Score = 32.2 bits (74), Expect = 0.14
Identities = 13/26 (50%), Positives = 19/26 (73%), Gaps = 1/26 (3%)
Query: 197 LLLTGPNMGGKSTVMRQL-GLITILA 221
L+LTGPN GK+T++R + GL+ A
Sbjct: 31 LVLTGPNGSGKTTLLRLIAGLLPPAA 56
>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 = 31.7 bits (73), Expect = 0.23
Identities = 11/27 (40%), Positives = 16/27 (59%), Gaps = 1/27 (3%)
Query: 193 KPTVLLLTGPNMGGKSTVMRQ-LGLIT 218
L + GPN GKST+++ LGL+
Sbjct: 24 PGEFLAIVGPNGAGKSTLLKAILGLLK 50
>gnl|CDD|217429 pfam03215, Rad17, Rad17 cell cycle checkpoint protein.
Length = 490
Score = 31.5 bits (71), Expect = 0.33
Identities = 13/39 (33%), Positives = 22/39 (56%), Gaps = 6/39 (15%)
Query: 191 NRKPTVLLLTGPNMGGKSTVMRQLGLITILAQMENPQLI 229
+ K +LLLTGP+ GKST + +L++ ++I
Sbjct: 42 SNKQLILLLTGPSGCGKSTT------VKVLSKELGIEII 74
>gnl|CDD|224046 COG1121, ZnuC, ABC-type Mn/Zn transport systems, ATPase component
[Inorganic ion transport and metabolism].
Length = 254
Score = 31.0 bits (71), Expect = 0.39
Identities = 12/28 (42%), Positives = 17/28 (60%), Gaps = 1/28 (3%)
Query: 192 RKPTVLLLTGPNMGGKSTVMRQ-LGLIT 218
K + L GPN GKST+++ LGL+
Sbjct: 28 EKGEITALIGPNGAGKSTLLKAILGLLK 55
>gnl|CDD|205733 pfam13555, AAA_29, P-loop containing region of AAA domain.
Length = 60
Score = 27.1 bits (61), Expect = 1.4
Identities = 10/18 (55%), Positives = 13/18 (72%)
Query: 194 PTVLLLTGPNMGGKSTVM 211
P LLTGP+ GKST++
Sbjct: 21 PKGTLLTGPSGSGKSTLI 38
>gnl|CDD|233206 TIGR00954, 3a01203, Peroxysomal Fatty Acyl CoA Transporter (FAT)
Family protei. [Transport and binding proteins,
Carbohydrates, organic alcohols, and acids].
Length = 659
Score = 29.3 bits (66), Expect = 1.7
Identities = 18/46 (39%), Positives = 22/46 (47%), Gaps = 8/46 (17%)
Query: 171 IPNSTV-IGRCKEDVESGGEGNRKPTVLLLTGPNMGGKSTVMRQLG 215
PN V I +V SG LL+ GPN GKS++ R LG
Sbjct: 461 TPNGDVLIESLSFEVPSG-------NNLLICGPNGCGKSSLFRILG 499
>gnl|CDD|173617 PTZ00427, PTZ00427, isoleucine-tRNA ligase, putative; Provisional.
Length = 1205
Score = 29.5 bits (66), Expect = 1.7
Identities = 14/33 (42%), Positives = 23/33 (69%), Gaps = 1/33 (3%)
Query: 53 FFLRK-TRYLCVSKTESLFQIDYIVENICIINE 84
FF ++ TRY C++K + LF DYI +N I+++
Sbjct: 782 FFSQEVTRYECLNKKQFLFNTDYIYKNDNIMDQ 814
>gnl|CDD|214810 smart00763, AAA_PrkA, PrkA AAA domain. This is a family of PrkA
bacterial and archaeal serine kinases approximately 630
residues long. This is the N-terminal AAA domain.
Length = 361
Score = 29.2 bits (66), Expect = 1.9
Identities = 17/63 (26%), Positives = 25/63 (39%), Gaps = 3/63 (4%)
Query: 167 DQTYIPNSTVIGRCKEDVESGGEG-NRKPTVLLLTGPNMGGKSTVMRQL--GLITILAQM 223
D + I R +S +G + +L L GP GGKS+++ L GL
Sbjct: 50 DHDFFGMEEAIERFVNYFKSAAQGLEERKQILYLLGPVGGGKSSLVECLKRGLEEYSKTD 109
Query: 224 ENP 226
E
Sbjct: 110 EGR 112
>gnl|CDD|181939 PRK09544, znuC, high-affinity zinc transporter ATPase; Reviewed.
Length = 251
Score = 28.9 bits (65), Expect = 2.0
Identities = 13/23 (56%), Positives = 17/23 (73%), Gaps = 1/23 (4%)
Query: 196 VLLLTGPNMGGKSTVMR-QLGLI 217
+L L GPN GKST++R LGL+
Sbjct: 32 ILTLLGPNGAGKSTLVRVVLGLV 54
>gnl|CDD|226929 COG4559, COG4559, ABC-type hemin transport system, ATPase component
[Inorganic ion transport and metabolism].
Length = 259
Score = 28.9 bits (65), Expect = 2.3
Identities = 10/19 (52%), Positives = 14/19 (73%)
Query: 196 VLLLTGPNMGGKSTVMRQL 214
VL + GPN GKST+++ L
Sbjct: 29 VLAILGPNGAGKSTLLKAL 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 = 28.3 bits (64), Expect = 2.4
Identities = 10/19 (52%), Positives = 14/19 (73%)
Query: 197 LLLTGPNMGGKSTVMRQLG 215
LL+TGP+ GKS++ R L
Sbjct: 30 LLITGPSGTGKSSLFRALA 48
>gnl|CDD|198225 cd10362, SH2_Src_Lck, Src homology 2 (SH2) domain in lymphocyte
cell kinase (Lck). Lck is a member of the Src
non-receptor type tyrosine kinase family of proteins. It
is expressed in the brain, T-cells, and NK cells. The
unique domain of Lck mediates its interaction with two
T-cell surface molecules, CD4 and CD8. It associates
with their cytoplasmic tails on CD4 T helper cells and
CD8 cytotoxic T cells to assist signaling from the T
cell receptor (TCR) complex. When the T cell receptor is
engaged by the specific antigen presented by MHC, Lck
phosphorylase the intracellular chains of the CD3 and
zeta-chains of the TCR complex, allowing ZAP-70 to bind
them. Lck then phosphorylates and activates ZAP-70,
which in turn phosphorylates Linker of Activated T cells
(LAT), a transmembrane protein that serves as a docking
site for proteins including: Shc-Grb2-SOS, PI3K, and
phospholipase C (PLC). The tyrosine phosphorylation
cascade culminates in the intracellular mobilization of
a calcium ions and activation of important signaling
cascades within the lymphocyte, including the
Ras-MEK-ERK pathway, which goes on to activate certain
transcription factors such as NFAT, NF-kappaB, and AP-1.
These transcription factors regulate the production
cytokines such as Interleukin-2 that promote long-term
proliferation and differentiation of the activated
lymphocytes. The N-terminal tail of Lck is
myristoylated and palmitoylated and it tethers the
protein to the plasma membrane of the cell. Lck also
contains a SH3 domain, a SH2 domain, and a C-terminal
tyrosine kinase domain. Lck has 2 phosphorylation sites,
the first an autophosphorylation site that is linked to
activation of the protein and the second which is
phosphorylated by Csk, which inhibits it. Lck is also
inhibited by SHP-1 dephosphorylation and by Cbl
ubiquitin ligase, which is part of the
ubiquitin-mediated pathway. In general SH2 domains are
involved in signal transduction. They typically bind
pTyr-containing ligands via two surface pockets, a pTyr
and hydrophobic binding pocket, allowing proteins with
SH2 domains to localize to tyrosine phosphorylated
sites.
Length = 101
Score = 27.5 bits (61), Expect = 2.5
Identities = 10/26 (38%), Positives = 14/26 (53%)
Query: 81 IINEKETPPDGFCLIARTLDSDQGQI 106
+I E ET F L R D +QG++
Sbjct: 30 LIRESETTAGSFSLSVRDFDQNQGEV 55
>gnl|CDD|163483 TIGR03771, anch_rpt_ABC, anchored repeat-type ABC transporter,
ATP-binding subunit. This protein family is the
ATP-binding cassette subunit of binding
protein-dependent ABC transporter complex that strictly
co-occurs with TIGR03769. TIGRFAMs model TIGR03769
describes a protein domain that occurs singly or as one
of up to three repeats in proteins of a number of
Actinobacteria, including Propionibacterium acnes
KPA171202. The TIGR03769 domain occurs both in an
adjacent gene for the substrate-binding protein and in
additional (often nearby) proteins, often with
LPXTG-like sortase recognition signals. Homologous
ATP-binding subunits outside the scope of this family
include manganese transporter MntA in Synechocystis sp.
PCC 6803 and chelated iron transporter subunits. The
function of this transporter complex is unknown
[Transport and binding proteins, Unknown substrate].
Length = 223
Score = 28.3 bits (63), Expect = 2.9
Identities = 12/20 (60%), Positives = 15/20 (75%), Gaps = 1/20 (5%)
Query: 199 LTGPNMGGKSTVMRQ-LGLI 217
L GPN GK+T++R LGLI
Sbjct: 11 LLGPNGAGKTTLLRAILGLI 30
>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 = 3.1
Identities = 13/27 (48%), Positives = 19/27 (70%), Gaps = 1/27 (3%)
Query: 192 RKPTVLLLTGPNMGGKSTVMRQL-GLI 217
+K +L+ GPN GKST++R L GL+
Sbjct: 25 KKGEFVLIVGPNGSGKSTLLRLLNGLL 51
>gnl|CDD|237422 PRK13548, hmuV, hemin importer ATP-binding subunit; Provisional.
Length = 258
Score = 28.2 bits (64), Expect = 3.8
Identities = 10/19 (52%), Positives = 14/19 (73%)
Query: 196 VLLLTGPNMGGKSTVMRQL 214
V+ + GPN GKST++R L
Sbjct: 30 VVAILGPNGAGKSTLLRAL 48
>gnl|CDD|224043 COG1118, CysA, ABC-type sulfate/molybdate transport systems, ATPase
component [Inorganic ion transport and metabolism].
Length = 345
Score = 28.1 bits (63), Expect = 4.0
Identities = 15/44 (34%), Positives = 24/44 (54%), Gaps = 13/44 (29%)
Query: 183 DVESGGEGNRKPTVLLLTGPNMGGKSTVMRQLGLITILAQMENP 226
D++SG ++ L GP+ GKST++R I+A +E P
Sbjct: 24 DIKSG-------ELVALLGPSGAGKSTLLR------IIAGLETP 54
>gnl|CDD|227590 COG5265, ATM1, ABC-type transport system involved in Fe-S cluster
assembly, permease and ATPase components
[Posttranslational modification, protein turnover,
chaperones].
Length = 497
Score = 28.1 bits (63), Expect = 4.5
Identities = 14/61 (22%), Positives = 22/61 (36%), Gaps = 15/61 (24%)
Query: 170 YIPNSTVIGRCKEDVESGGEGNRKPTVLLLTGPNMGGKSTVMR--------QLGLITILA 221
Y P ++ + G + + G + GKST++R G ITI
Sbjct: 272 YDPRRPILNGISFTIPLG-------KTVAIVGESGAGKSTILRLLFRFYDVNSGSITIDG 324
Query: 222 Q 222
Q
Sbjct: 325 Q 325
>gnl|CDD|224047 COG1122, CbiO, ABC-type cobalt transport system, ATPase component
[Inorganic ion transport and metabolism].
Length = 235
Score = 27.6 bits (62), Expect = 5.2
Identities = 12/23 (52%), Positives = 17/23 (73%), Gaps = 1/23 (4%)
Query: 197 LLLTGPNMGGKSTVMRQL-GLIT 218
+LL GPN GKST+++ L GL+
Sbjct: 33 VLLIGPNGSGKSTLLKLLNGLLK 55
>gnl|CDD|129690 TIGR00602, rad24, checkpoint protein rad24. All proteins in this
family for which functions are known are involved in DNA
damage tolerance (likely cell cycle checkpoints).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 = 637
Score = 28.0 bits (62), Expect = 5.4
Identities = 14/39 (35%), Positives = 20/39 (51%), Gaps = 6/39 (15%)
Query: 191 NRKPTVLLLTGPNMGGKSTVMRQLGLITILAQMENPQLI 229
N +LL+TGP+ GKST I IL++ Q+
Sbjct: 107 NAPKRILLITGPSGCGKSTT------IKILSKELGIQVQ 139
>gnl|CDD|213226 cd03259, ABC_Carb_Solutes_like, ATP-binding cassette domain of the
carbohydrate and solute transporters-like. This family
is comprised of proteins involved in the transport of
apparently unrelated solutes and proteins specific for
di- and oligosaccharides and polyols. 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 = 213
Score = 27.5 bits (62), Expect = 5.6
Identities = 10/25 (40%), Positives = 15/25 (60%), Gaps = 3/25 (12%)
Query: 195 TVLLLTGPNMGGKSTVMRQL-GLIT 218
LL GP+ GK+T++R + GL
Sbjct: 29 LALL--GPSGCGKTTLLRLIAGLER 51
>gnl|CDD|147087 pfam04753, Corona_NS2, Coronavirus non-structural protein NS2.
Length = 109
Score = 26.4 bits (58), Expect = 6.9
Identities = 11/30 (36%), Positives = 18/30 (60%), Gaps = 1/30 (3%)
Query: 46 DMWRESAFFLRKTRYLCVSKTESL-FQIDY 74
++WR S +LR TR V++ E F+ +Y
Sbjct: 2 EIWRPSIKYLRYTRGFGVTELEDACFKFNY 31
>gnl|CDD|182182 PRK09984, PRK09984, phosphonate/organophosphate ester transporter
subunit; Provisional.
Length = 262
Score = 27.3 bits (60), Expect = 7.2
Identities = 13/21 (61%), Positives = 16/21 (76%), Gaps = 1/21 (4%)
Query: 199 LTGPNMGGKSTVMRQL-GLIT 218
L GP+ GKST++R L GLIT
Sbjct: 35 LLGPSGSGKSTLLRHLSGLIT 55
>gnl|CDD|237894 PRK15064, PRK15064, ABC transporter ATP-binding protein;
Provisional.
Length = 530
Score = 27.5 bits (62), Expect = 7.4
Identities = 14/28 (50%), Positives = 15/28 (53%), Gaps = 4/28 (14%)
Query: 188 GEGNRKPTVLLLTGPNMGGKSTVMRQLG 215
G GNR L G N GKST M+ LG
Sbjct: 25 GGGNRYG----LIGANGCGKSTFMKILG 48
>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 = 8.6
Identities = 16/41 (39%), Positives = 21/41 (51%), Gaps = 10/41 (24%)
Query: 199 LTGPNMGGKSTVMRQL--------GLITILAQ--MENPQLI 229
L GPN GK+T+MR L G I I Q ++ PQ +
Sbjct: 30 LLGPNGAGKTTLMRILATLTPPSSGTIRIDGQDVLKQPQKL 70
>gnl|CDD|213235 cd03268, ABC_BcrA_bacitracin_resist, ATP-binding cassette domain of
the bacitracin-resistance transporter. The BcrA
subfamily represents ABC transporters involved in
peptide antibiotic resistance. Bacitracin is a
dodecapeptide antibiotic produced by B. licheniformis
and B. subtilis. The synthesis of bacitracin is
non-ribosomally catalyzed by a multi-enzyme complex
BcrABC. Bacitracin has potent antibiotic activity
against gram-positive bacteria. The inhibition of
peptidoglycan biosynthesis is the best characterized
bacterial effect of bacitracin. The bacitracin
resistance of B. licheniformis is mediated by the ABC
transporter Bcr which is composed of two identical BcrA
ATP-binding subunits and one each of the integral
membrane proteins, BcrB and BcrC. B. subtilis cells
carrying bcr genes on high-copy number plasmids develop
collateral detergent sensitivity, a similar phenomenon
in human cells with overexpressed multi-drug resistance
P-glycoprotein.
Length = 208
Score = 26.8 bits (60), Expect = 8.9
Identities = 10/22 (45%), Positives = 13/22 (59%), Gaps = 1/22 (4%)
Query: 199 LTGPNMGGKSTVMRQL-GLITI 219
GPN GK+T M+ + GLI
Sbjct: 31 FLGPNGAGKTTTMKIILGLIKP 52
>gnl|CDD|237875 PRK14974, PRK14974, cell division protein FtsY; Provisional.
Length = 336
Score = 26.9 bits (60), Expect = 9.1
Identities = 8/19 (42%), Positives = 11/19 (57%)
Query: 191 NRKPTVLLLTGPNMGGKST 209
KP V++ G N GK+T
Sbjct: 137 KGKPVVIVFVGVNGTGKTT 155
>gnl|CDD|130234 TIGR01166, cbiO, cobalt transport protein ATP-binding subunit.
This model describes the ATP binding subunit of the
multisubunit cobalt transporter in bacteria and its
equivalents in archaea. The model is restricted to ATP
subunit that is a part of the cobalt transporter, which
belongs to the ABC transporter superfamily (ATP Binding
Cassette). The model excludes ATP binding subunit that
are associated with other transporters belonging to ABC
transporter superfamily. This superfamily includes two
groups, one which catalyze the uptake of small
molecules, including ions from the external milieu and
the other group which is engaged in the efflux of small
molecular weight compounds and ions from within the
cell. Energy derived from the hydrolysis of ATP drive
the both the process of uptake and efflux [Transport and
binding proteins, Cations and iron carrying compounds].
Length = 190
Score = 26.6 bits (59), Expect = 9.3
Identities = 10/20 (50%), Positives = 12/20 (60%)
Query: 195 TVLLLTGPNMGGKSTVMRQL 214
VL L G N GKST++ L
Sbjct: 19 EVLALLGANGAGKSTLLLHL 38
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
0.319 0.137 0.408
Gapped
Lambda K H
0.267 0.0740 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,476,400
Number of extensions: 1041269
Number of successful extensions: 1032
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1025
Number of HSP's successfully gapped: 62
Length of query: 229
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 135
Effective length of database: 6,768,326
Effective search space: 913724010
Effective search space used: 913724010
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 57 (25.7 bits)