Query psy10040
Match_columns 93
No_of_seqs 129 out of 1635
Neff 6.7
Searched_HMMs 46136
Date Fri Aug 16 16:19:58 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy10040.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/10040hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03185 phosphatidylinositol 99.6 3.9E-15 8.4E-20 122.4 8.5 61 3-67 33-93 (765)
2 PLN03185 phosphatidylinositol 99.6 6.6E-15 1.4E-19 121.0 9.1 64 2-69 9-72 (765)
3 KOG0231|consensus 99.5 3.2E-14 6.9E-19 111.6 3.4 80 2-85 143-228 (455)
4 COG4642 Uncharacterized protei 99.1 2.6E-10 5.7E-15 77.1 5.0 61 3-67 56-116 (139)
5 COG4642 Uncharacterized protei 99.0 2.5E-10 5.5E-15 77.1 4.4 65 2-70 32-96 (139)
6 KOG0231|consensus 98.7 5.2E-09 1.1E-13 82.4 2.6 65 2-66 166-241 (455)
7 smart00698 MORN Possible plasm 98.5 2E-07 4.3E-12 46.5 3.5 21 26-46 2-22 (26)
8 PF02493 MORN: MORN repeat; I 98.5 1.7E-07 3.7E-12 44.9 2.7 22 4-25 1-22 (23)
9 smart00698 MORN Possible plasm 98.4 4.6E-07 9.9E-12 45.1 4.0 22 2-23 1-22 (26)
10 PF02493 MORN: MORN repeat; I 98.3 5.1E-07 1.1E-11 43.2 2.3 22 27-48 1-22 (23)
11 COG2849 Uncharacterized protei 95.2 0.065 1.4E-06 38.8 5.7 52 8-62 104-156 (230)
12 COG2849 Uncharacterized protei 93.8 0.54 1.2E-05 34.0 7.7 57 7-66 127-184 (230)
13 PF07661 MORN_2: MORN repeat v 78.8 4 8.7E-05 18.1 2.8 21 37-60 2-22 (22)
14 PF07617 DUF1579: Protein of u 68.4 14 0.0003 25.5 4.6 37 2-38 51-89 (159)
15 PF12915 DUF3833: Protein of u 58.2 61 0.0013 22.6 6.9 50 7-60 27-83 (164)
16 PF07617 DUF1579: Protein of u 52.9 40 0.00087 23.2 4.7 46 15-63 37-87 (159)
17 PF14438 SM-ATX: Ataxin 2 SM d 40.9 39 0.00084 19.9 2.8 17 18-34 16-32 (77)
18 PF00988 CPSase_sm_chain: Carb 37.2 1.3E+02 0.0028 20.2 5.2 33 17-49 3-35 (131)
19 PF05580 Peptidase_S55: SpoIVB 33.3 53 0.0011 24.1 2.9 19 28-46 10-28 (218)
20 PF10419 TFIIIC_sub6: TFIIIC s 24.4 47 0.001 17.2 1.1 12 23-34 16-27 (35)
21 PF11258 DUF3048: Protein of u 22.2 77 0.0017 23.7 2.2 30 19-48 243-272 (283)
No 1
>PLN03185 phosphatidylinositol phosphate kinase; Provisional
Probab=99.59 E-value=3.9e-15 Score=122.36 Aligned_cols=61 Identities=36% Similarity=0.543 Sum_probs=32.3
Q ss_pred eEEEEeeCCEEeceeEEEecCCCEEEEEEeCCeEEeeEEEEeeCCCccCCeEEEEEeCCeecccc
Q psy10040 3 RYEGELLQGWFHGHGVFWRADGMKFEGEFRGGRIWGHGLVTYADGTHGFPKNEGYFQDCKMMKRK 67 (93)
Q Consensus 3 ~Y~G~f~~g~~hG~G~~~~~~G~~y~G~f~~g~~~G~G~~~~~dG~~~~~~y~G~w~~~~~~~~~ 67 (93)
.|+|+|.+|++||.|++.|++|.+|+|+|.+|++||.|++++++|.. |+|.|+++++++.+
T Consensus 33 ~YeGew~~Gk~hG~G~~~~~nG~~YeGeF~nG~~hG~G~~~~~~G~~----YeG~w~~gkkhG~G 93 (765)
T PLN03185 33 MYEGEWRRGMRHGNGKISWPSGATYEGEFSGGYMHGSGTYTGTDGTT----YKGRWRLNLKHGLG 93 (765)
T ss_pred EEEEEEECCEeeCcEeEEeCCCCEEEEEEECCEEeceEEEEecCCCE----EEEEEeCCccccee
Confidence 45555555555555555555555555555555555555555555553 55555555555443
No 2
>PLN03185 phosphatidylinositol phosphate kinase; Provisional
Probab=99.58 E-value=6.6e-15 Score=121.00 Aligned_cols=64 Identities=31% Similarity=0.534 Sum_probs=58.2
Q ss_pred ceEEEEeeCCEEeceeEEEecCCCEEEEEEeCCeEEeeEEEEeeCCCccCCeEEEEEeCCeecccccc
Q psy10040 2 TRYEGELLQGWFHGHGVFWRADGMKFEGEFRGGRIWGHGLVTYADGTHGFPKNEGYFQDCKMMKRKKC 69 (93)
Q Consensus 2 ~~Y~G~f~~g~~hG~G~~~~~~G~~y~G~f~~g~~~G~G~~~~~dG~~~~~~y~G~w~~~~~~~~~~~ 69 (93)
+.|+|+|.++++||.|++.|+||..|+|+|.+|++||.|+++|++|.+ |+|+|.++.+++.+..
T Consensus 9 d~Y~Ge~~~g~~hG~G~~~~~DG~~YeGew~~Gk~hG~G~~~~~nG~~----YeGeF~nG~~hG~G~~ 72 (765)
T PLN03185 9 DFYSGSLLGNVPEGPGKYLWSDGCMYEGEWRRGMRHGNGKISWPSGAT----YEGEFSGGYMHGSGTY 72 (765)
T ss_pred CEEEEEEECCccccceEEEECCCCEEEEEEECCEeeCcEeEEeCCCCE----EEEEEECCEEeceEEE
Confidence 579999999999999999999999999999999999999999999996 9999999999887653
No 3
>KOG0231|consensus
Probab=99.46 E-value=3.2e-14 Score=111.61 Aligned_cols=80 Identities=38% Similarity=0.673 Sum_probs=65.8
Q ss_pred ceEEEEeeCCEEeceeEEEecCCCEEEEEEeCCeEEeeEEEEeeCCCccCCeEEEEEeCCee----cc--ccccHHHHHH
Q psy10040 2 TRYEGELLQGWFHGHGVFWRADGMKFEGEFRGGRIWGHGLVTYADGTHGFPKNEGYFQDCKM----MK--RKKCLDVVKK 75 (93)
Q Consensus 2 ~~Y~G~f~~g~~hG~G~~~~~~G~~y~G~f~~g~~~G~G~~~~~dG~~~~~~y~G~w~~~~~----~~--~~~~~~~v~~ 75 (93)
++|+|+|.++++||+|++.+++|.+|+|.|.++++||+|+++++||+. |+|.|+++.+ .+ ......++..
T Consensus 143 ~~Y~G~~~~~k~sG~Gv~~~~~G~~Y~Gew~~n~~hG~G~~~~pdGsk----~eg~~~~~~l~~l~~gk~~~~~~~~~~~ 218 (455)
T KOG0231|consen 143 DTYEGEFKRGKRSGFGVYIRSDGLKYEGEWLDNRRHGYGVLTFPDGSK----YEGQYKNNILEALRHGKGRYKFDDALEA 218 (455)
T ss_pred CEEEeeecCCcccccceEEecCCCEeeceecCCCccCCCeEEccCCCE----EEEEeecccccccccceEEEEEeccchh
Confidence 689999999999999999999999999999999999999999999996 9999999954 22 2234444555
Q ss_pred HHHHHHHHHh
Q psy10040 76 AQKVSLMARM 85 (93)
Q Consensus 76 a~~~~~~a~~ 85 (93)
|+.++..++.
T Consensus 219 a~ra~~~~~~ 228 (455)
T KOG0231|consen 219 AQRAATIARY 228 (455)
T ss_pred hhhhhhhhhh
Confidence 5555544443
No 4
>COG4642 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=99.06 E-value=2.6e-10 Score=77.06 Aligned_cols=61 Identities=28% Similarity=0.477 Sum_probs=36.4
Q ss_pred eEEEEeeCCEEeceeEEEecCCCEEEEEEeCCeEEeeEEEEeeCCCccCCeEEEEEeCCeecccc
Q psy10040 3 RYEGELLQGWFHGHGVFWRADGMKFEGEFRGGRIWGHGLVTYADGTHGFPKNEGYFQDCKMMKRK 67 (93)
Q Consensus 3 ~Y~G~f~~g~~hG~G~~~~~~G~~y~G~f~~g~~~G~G~~~~~dG~~~~~~y~G~w~~~~~~~~~ 67 (93)
.|+|.+++++++|.|+++++||+.|+|.|.+++.+|.|++...+|.. |.|.|.+++.++.+
T Consensus 56 ~Y~Gtl~ngk~nGqG~~~~~ngd~Y~g~F~s~~F~g~G~~~~~~Gw~----~~G~F~~Gq~~g~g 116 (139)
T COG4642 56 IYTGTLKNGKMNGQGTYTFANGDIYEGPFNSGKFRGQGTRGSFNGWL----YIGRFTEGQANGKG 116 (139)
T ss_pred cccceEEcCcccCcEEEEecCCCeEeccccCccccceEeeccccCCE----EeeeecccccCCce
Confidence 35666666666666666666666666666666666666666666654 66666665555443
No 5
>COG4642 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=99.04 E-value=2.5e-10 Score=77.13 Aligned_cols=65 Identities=29% Similarity=0.486 Sum_probs=57.5
Q ss_pred ceEEEEeeCCEEeceeEEEecCCCEEEEEEeCCeEEeeEEEEeeCCCccCCeEEEEEeCCeeccccccH
Q psy10040 2 TRYEGELLQGWFHGHGVFWRADGMKFEGEFRGGRIWGHGLVTYADGTHGFPKNEGYFQDCKMMKRKKCL 70 (93)
Q Consensus 2 ~~Y~G~f~~g~~hG~G~~~~~~G~~y~G~f~~g~~~G~G~~~~~dG~~~~~~y~G~w~~~~~~~~~~~~ 70 (93)
+++.|.++.++..|.|++++.+|..|+|+++|++++|.|+++++++.+ |+|.|+++++.+.+..+
T Consensus 32 ar~~g~~kqg~~~Gkgs~~~~~G~~Y~Gtl~ngk~nGqG~~~~~ngd~----Y~g~F~s~~F~g~G~~~ 96 (139)
T COG4642 32 ARVGGSLKQGKLAGKGSLKYDNGRIYTGTLKNGKMNGQGTYTFANGDI----YEGPFNSGKFRGQGTRG 96 (139)
T ss_pred cEEeeeEeeeecCCCccEEEcCCccccceEEcCcccCcEEEEecCCCe----EeccccCccccceEeec
Confidence 355677788999999999999999999999999999999999999997 99999999887665543
No 6
>KOG0231|consensus
Probab=98.73 E-value=5.2e-09 Score=82.40 Aligned_cols=65 Identities=29% Similarity=0.518 Sum_probs=53.9
Q ss_pred ceEEEEeeCCEEeceeEEEecCCCEEEEEEeCC----eEEeeEEEEeeCCCc------cCCeEEEEEeC-Ceeccc
Q psy10040 2 TRYEGELLQGWFHGHGVFWRADGMKFEGEFRGG----RIWGHGLVTYADGTH------GFPKNEGYFQD-CKMMKR 66 (93)
Q Consensus 2 ~~Y~G~f~~g~~hG~G~~~~~~G~~y~G~f~~g----~~~G~G~~~~~dG~~------~~~~y~G~w~~-~~~~~~ 66 (93)
.+|+|+|.++++||+|+.++++|++|+|.|+++ .++|.+.+.+.+... ...+|.++|.+ ..-...
T Consensus 166 ~~Y~Gew~~n~~hG~G~~~~pdGsk~eg~~~~~~l~~l~~gk~~~~~~~~~~~a~ra~~~~~~~~Ew~~~~~~~~~ 241 (455)
T KOG0231|consen 166 LKYEGEWLDNRRHGYGVLTFPDGSKYEGQYKNNILEALRHGKGRYKFDDALEAAQRAATIARYSGEWAARGQSHGR 241 (455)
T ss_pred CEeeceecCCCccCCCeEEccCCCEEEEEeecccccccccceEEEEEeccchhhhhhhhhhhhhhhhhhhcCCCcc
Confidence 479999999999999999999999999999999 899999999997311 11259999998 443333
No 7
>smart00698 MORN Possible plasma membrane-binding motif in junctophilins, PIP-5-kinases and protein kinases.
Probab=98.50 E-value=2e-07 Score=46.47 Aligned_cols=21 Identities=48% Similarity=1.044 Sum_probs=10.3
Q ss_pred EEEEEEeCCeEEeeEEEEeeC
Q psy10040 26 KFEGEFRGGRIWGHGLVTYAD 46 (93)
Q Consensus 26 ~y~G~f~~g~~~G~G~~~~~d 46 (93)
+|+|+|.++++||.|+++++|
T Consensus 2 ~Y~G~w~~g~~hG~G~~~~~d 22 (26)
T smart00698 2 RYEGEWRNGKRHGRGVYTYAN 22 (26)
T ss_pred eEEEEEECCeEEeeEEEEecc
Confidence 345555555555555554443
No 8
>PF02493 MORN: MORN repeat; InterPro: IPR003409 The MORN (Membrane Occupation and Recognition Nexus) motif is found in multiple copies in several proteins including junctophilins (). The function of this motif is unknown.; PDB: 1H3I_B 1MT6_A 1N6C_A 3OS5_A 3M53_A 3M55_A 3CBP_A 4E47_B 3M58_A 3CBO_A ....
Probab=98.47 E-value=1.7e-07 Score=44.90 Aligned_cols=22 Identities=50% Similarity=0.708 Sum_probs=12.6
Q ss_pred EEEEeeCCEEeceeEEEecCCC
Q psy10040 4 YEGELLQGWFHGHGVFWRADGM 25 (93)
Q Consensus 4 Y~G~f~~g~~hG~G~~~~~~G~ 25 (93)
|+|+|.++++||.|++.++||+
T Consensus 1 Y~G~~~~g~~~G~G~~~~~~G~ 22 (23)
T PF02493_consen 1 YEGEWKNGKKHGYGVYTFPDGD 22 (23)
T ss_dssp ECCEEETTEEECEEEEE-TTS-
T ss_pred CEEEEEECcccccEEEEeCCCC
Confidence 5566666666666666666654
No 9
>smart00698 MORN Possible plasma membrane-binding motif in junctophilins, PIP-5-kinases and protein kinases.
Probab=98.44 E-value=4.6e-07 Score=45.13 Aligned_cols=22 Identities=50% Similarity=0.782 Sum_probs=20.4
Q ss_pred ceEEEEeeCCEEeceeEEEecC
Q psy10040 2 TRYEGELLQGWFHGHGVFWRAD 23 (93)
Q Consensus 2 ~~Y~G~f~~g~~hG~G~~~~~~ 23 (93)
++|+|+|.++++||.|+++|+|
T Consensus 1 ~~Y~G~w~~g~~hG~G~~~~~d 22 (26)
T smart00698 1 DRYEGEWRNGKRHGRGVYTYAN 22 (26)
T ss_pred CeEEEEEECCeEEeeEEEEecc
Confidence 5799999999999999999975
No 10
>PF02493 MORN: MORN repeat; InterPro: IPR003409 The MORN (Membrane Occupation and Recognition Nexus) motif is found in multiple copies in several proteins including junctophilins (). The function of this motif is unknown.; PDB: 1H3I_B 1MT6_A 1N6C_A 3OS5_A 3M53_A 3M55_A 3CBP_A 4E47_B 3M58_A 3CBO_A ....
Probab=98.31 E-value=5.1e-07 Score=43.22 Aligned_cols=22 Identities=41% Similarity=0.952 Sum_probs=19.5
Q ss_pred EEEEEeCCeEEeeEEEEeeCCC
Q psy10040 27 FEGEFRGGRIWGHGLVTYADGT 48 (93)
Q Consensus 27 y~G~f~~g~~~G~G~~~~~dG~ 48 (93)
|+|+|.+++++|.|+++++||+
T Consensus 1 Y~G~~~~g~~~G~G~~~~~~G~ 22 (23)
T PF02493_consen 1 YEGEWKNGKKHGYGVYTFPDGD 22 (23)
T ss_dssp ECCEEETTEEECEEEEE-TTS-
T ss_pred CEEEEEECcccccEEEEeCCCC
Confidence 7899999999999999999987
No 11
>COG2849 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=95.19 E-value=0.065 Score=38.80 Aligned_cols=52 Identities=19% Similarity=0.339 Sum_probs=25.6
Q ss_pred eeCCEEeceeEEEecCCCEEE-EEEeCCeEEeeEEEEeeCCCccCCeEEEEEeCCe
Q psy10040 8 LLQGWFHGHGVFWRADGMKFE-GEFRGGRIWGHGLVTYADGTHGFPKNEGYFQDCK 62 (93)
Q Consensus 8 f~~g~~hG~G~~~~~~G~~y~-G~f~~g~~~G~G~~~~~dG~~~~~~y~G~w~~~~ 62 (93)
+.+++.+|.-...+++|...+ -.|.+|+.||.-+..+++|.+ ..+..|+++.
T Consensus 104 ~kNG~~~g~~~~~y~nGk~~~~~~~~ng~~~G~~~~yy~nG~~---~~e~~~kn~~ 156 (230)
T COG2849 104 YKNGKLDGETKEFYENGKLKSEYNYKNGKLHGIQKEYYENGKL---KSETVYKNGK 156 (230)
T ss_pred ecCCceeeeEEEEEcCCcEeEEEEecCCcccceEEEEEcCCCE---EEEEEEeCCC
Confidence 445555555555555554332 345555555555555555554 4455555544
No 12
>COG2849 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=93.78 E-value=0.54 Score=34.03 Aligned_cols=57 Identities=21% Similarity=0.295 Sum_probs=50.1
Q ss_pred EeeCCEEeceeEEEecCCC-EEEEEEeCCeEEeeEEEEeeCCCccCCeEEEEEeCCeeccc
Q psy10040 7 ELLQGWFHGHGVFWRADGM-KFEGEFRGGRIWGHGLVTYADGTHGFPKNEGYFQDCKMMKR 66 (93)
Q Consensus 7 ~f~~g~~hG~G~~~~~~G~-~y~G~f~~g~~~G~G~~~~~dG~~~~~~y~G~w~~~~~~~~ 66 (93)
.|.+++.||.-+..++||. .++..|++++++|.-.+.+++|.+ ..+-.++++.+.+.
T Consensus 127 ~~~ng~~~G~~~~yy~nG~~~~e~~~kn~~~~g~~k~yy~nGkl---~~e~~~knG~~~G~ 184 (230)
T COG2849 127 NYKNGKLHGIQKEYYENGKLKSETVYKNGKLEGIAKTYYENGKL---LSEVPYKNGKKNGV 184 (230)
T ss_pred EecCCcccceEEEEEcCCCEEEEEEEeCCCccccEEEEcCCCcE---EEeecccCCcccce
Confidence 5789999999999999999 579999999998999999999998 77888888777543
No 13
>PF07661 MORN_2: MORN repeat variant; InterPro: IPR011652 This entry represents an apparent variant of the IPR003409 from INTERPRO repeat.
Probab=78.75 E-value=4 Score=18.10 Aligned_cols=21 Identities=29% Similarity=0.471 Sum_probs=12.0
Q ss_pred EeeEEEEeeCCCccCCeEEEEEeC
Q psy10040 37 WGHGLVTYADGTHGFPKNEGYFQD 60 (93)
Q Consensus 37 ~G~G~~~~~dG~~~~~~y~G~w~~ 60 (93)
+|.-+..+++|.+ ..++.++|
T Consensus 2 ~G~~~~yy~nG~l---~~~~~y~n 22 (22)
T PF07661_consen 2 DGEWKFYYENGKL---KSEGHYKN 22 (22)
T ss_pred cceEEEEeCCCCE---EEEEEEEC
Confidence 4555566666666 55555543
No 14
>PF07617 DUF1579: Protein of unknown function (DUF1579); InterPro: IPR011473 This is a family of paralogous hypothetical proteins identified in Rhodopirellula baltica that also has members in Gloeobacter violaceus, Rhizobium meliloti and Agrobacterium tumefaciens, amongst others.
Probab=68.38 E-value=14 Score=25.46 Aligned_cols=37 Identities=27% Similarity=0.382 Sum_probs=27.7
Q ss_pred ceEEEEee-CCEEeceeEEEecC-CCEEEEEEeCCeEEe
Q psy10040 2 TRYEGELL-QGWFHGHGVFWRAD-GMKFEGEFRGGRIWG 38 (93)
Q Consensus 2 ~~Y~G~f~-~g~~hG~G~~~~~~-G~~y~G~f~~g~~~G 38 (93)
..|+|.+. ...++|.+++-|.+ -.+|+|.|.+++..+
T Consensus 51 ~e~~g~~~~g~~~~~~~~lGYD~~~~~yvgtWidSM~t~ 89 (159)
T PF07617_consen 51 QEYEGSMPGGGPFEGIGTLGYDPAKKKYVGTWIDSMGTG 89 (159)
T ss_pred EEEEeecCCCCceEEEEEEEECCccCeEEEEEeccCCCc
Confidence 35778887 77788888888864 447999999885543
No 15
>PF12915 DUF3833: Protein of unknown function (DUF3833); InterPro: IPR024409 This is a family of uncharacterised proteins found in Proteobacteria.
Probab=58.23 E-value=61 Score=22.62 Aligned_cols=50 Identities=20% Similarity=0.316 Sum_probs=39.8
Q ss_pred EeeCCEEeceeEEEecCCCE-------EEEEEeCCeEEeeEEEEeeCCCccCCeEEEEEeC
Q psy10040 7 ELLQGWFHGHGVFWRADGMK-------FEGEFRGGRIWGHGLVTYADGTHGFPKNEGYFQD 60 (93)
Q Consensus 7 ~f~~g~~hG~G~~~~~~G~~-------y~G~f~~g~~~G~G~~~~~dG~~~~~~y~G~w~~ 60 (93)
+|.+|.-..+|+..-..|.. .+|.|..+...=.-.++|.||.. ..-.|.=
T Consensus 27 ~fF~G~~~A~G~~~dr~G~v~rrF~v~i~g~w~g~~~tL~E~F~y~DGe~----q~R~W~l 83 (164)
T PF12915_consen 27 EFFNGKLVAWGMFQDRSGKVTRRFTVDIDGSWDGNTGTLDEDFVYDDGET----QTRVWTL 83 (164)
T ss_pred HHCCCcEEEEEEEECCCCCEEEEEEEEEEEEEECCEEEEEEEEEECCCCE----EEEEEEE
Confidence 35678888899999888874 67999988877778899999995 6666753
No 16
>PF07617 DUF1579: Protein of unknown function (DUF1579); InterPro: IPR011473 This is a family of paralogous hypothetical proteins identified in Rhodopirellula baltica that also has members in Gloeobacter violaceus, Rhizobium meliloti and Agrobacterium tumefaciens, amongst others.
Probab=52.90 E-value=40 Score=23.17 Aligned_cols=46 Identities=26% Similarity=0.415 Sum_probs=32.6
Q ss_pred ceeEEEecCCC----EEEEEEe-CCeEEeeEEEEeeCCCccCCeEEEEEeCCee
Q psy10040 15 GHGVFWRADGM----KFEGEFR-GGRIWGHGLVTYADGTHGFPKNEGYFQDCKM 63 (93)
Q Consensus 15 G~G~~~~~~G~----~y~G~f~-~g~~~G~G~~~~~dG~~~~~~y~G~w~~~~~ 63 (93)
+..+...-.|. .|+|..- ....+|.+++-|..-+. +|++.|.+...
T Consensus 37 ~~~~~r~LgG~~l~~e~~g~~~~g~~~~~~~~lGYD~~~~---~yvgtWidSM~ 87 (159)
T PF07617_consen 37 GTETVRMLGGRWLIQEYEGSMPGGGPFEGIGTLGYDPAKK---KYVGTWIDSMG 87 (159)
T ss_pred EEEEEEEeCCEEEEEEEEeecCCCCceEEEEEEEECCccC---eEEEEEeccCC
Confidence 44444443333 4677777 66778999998877666 79999999853
No 17
>PF14438 SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1.
Probab=40.88 E-value=39 Score=19.91 Aligned_cols=17 Identities=24% Similarity=0.411 Sum_probs=11.0
Q ss_pred EEEecCCCEEEEEEeCC
Q psy10040 18 VFWRADGMKFEGEFRGG 34 (93)
Q Consensus 18 ~~~~~~G~~y~G~f~~g 34 (93)
..+..||.+|+|-|.--
T Consensus 16 ~V~~~~G~~yeGif~s~ 32 (77)
T PF14438_consen 16 EVTTKNGSVYEGIFHSA 32 (77)
T ss_dssp EEEETTS-EEEEEEEEE
T ss_pred EEEECCCCEEEEEEEeC
Confidence 34567888888877643
No 18
>PF00988 CPSase_sm_chain: Carbamoyl-phosphate synthase small chain, CPSase domain; InterPro: IPR002474 Carbamoyl phosphate synthase (CPSase) is a heterodimeric enzyme composed of a small and a large subunit (with the exception of CPSase III, see below). CPSase catalyses the synthesis of carbamoyl phosphate from biocarbonate, ATP and glutamine (6.3.5.5 from EC) or ammonia (6.3.4.16 from EC), and represents the first committed step in pyrimidine and arginine biosynthesis in prokaryotes and eukaryotes, and in the urea cycle in most terrestrial vertebrates [, ]. CPSase has three active sites, one in the small subunit and two in the large subunit. The small subunit contains the glutamine binding site and catalyses the hydrolysis of glutamine to glutamate and ammonia. The large subunit has two homologous carboxy phosphate domains, both of which have ATP-binding sites; however, the N-terminal carboxy phosphate domain catalyses the phosphorylation of biocarbonate, while the C-terminal domain catalyses the phosphorylation of the carbamate intermediate []. The carboxy phosphate domain found duplicated in the large subunit of CPSase is also present as a single copy in the biotin-dependent enzymes acetyl-CoA carboxylase (6.4.1.2 from EC) (ACC), propionyl-CoA carboxylase (6.4.1.3 from EC) (PCCase), pyruvate carboxylase (6.4.1.1 from EC) (PC) and urea carboxylase (6.3.4.6 from EC). Most prokaryotes carry one form of CPSase that participates in both arginine and pyrimidine biosynthesis, however certain bacteria can have separate forms. The large subunit in bacterial CPSase has four structural domains: the carboxy phosphate domain 1, the oligomerisation domain, the carbamoyl phosphate domain 2 and the allosteric domain []. CPSase heterodimers from Escherichia coli contain two molecular tunnels: an ammonia tunnel and a carbamate tunnel. These inter-domain tunnels connect the three distinct active sites, and function as conduits for the transport of unstable reaction intermediates (ammonia and carbamate) between successive active sites []. The catalytic mechanism of CPSase involves the diffusion of carbamate through the interior of the enzyme from the site of synthesis within the N-terminal domain of the large subunit to the site of phosphorylation within the C-terminal domain. Eukaryotes have two distinct forms of CPSase: a mitochondrial enzyme (CPSase I) that participates in both arginine biosynthesis and the urea cycle; and a cytosolic enzyme (CPSase II) involved in pyrimidine biosynthesis. CPSase II occurs as part of a multi-enzyme complex along with aspartate transcarbamoylase and dihydroorotase; this complex is referred to as the CAD protein []. The hepatic expression of CPSase is transcriptionally regulated by glucocorticoids and/or cAMP []. There is a third form of the enzyme, CPSase III, found in fish, which uses glutamine as a nitrogen source instead of ammonia []. CPSase III is closely related to CPSase I, and is composed of a single polypeptide that may have arisen from gene fusion of the glutaminase and synthetase domains []. This entry represents the N-terminal domain of the small subunit of carbamoyl phosphate synthase. The small subunit has a 3-layer beta/beta/alpha structure, and is thought to be mobile in most proteins that carry it. The C-terminal domain of the small subunit of CPSase has glutamine amidotransferase activity.; GO: 0006807 nitrogen compound metabolic process; PDB: 1CE8_B 1KEE_B 1CS0_D 1T36_D 1M6V_H 1A9X_F 1JDB_I 1BXR_F 1C3O_B 1C30_F ....
Probab=37.22 E-value=1.3e+02 Score=20.24 Aligned_cols=33 Identities=27% Similarity=0.308 Sum_probs=23.9
Q ss_pred eEEEecCCCEEEEEEeCCeEEeeEEEEeeCCCc
Q psy10040 17 GVFWRADGMKFEGEFRGGRIWGHGLVTYADGTH 49 (93)
Q Consensus 17 G~~~~~~G~~y~G~f~~g~~~G~G~~~~~dG~~ 49 (93)
+.+...||..|+|.+......-.|.+.|..+-.
T Consensus 3 a~LvLeDG~~f~G~~~G~~~~~~GEvVFnT~Mt 35 (131)
T PF00988_consen 3 AYLVLEDGTVFEGKSFGAPGTVTGEVVFNTGMT 35 (131)
T ss_dssp EEEEETTS-EEEEEE-SBSEEEEEEEEEE--SS
T ss_pred EEEEECCCCEEEEEEecCCCcEEEEEEEEcccc
Confidence 567889999999999888878888888865543
No 19
>PF05580 Peptidase_S55: SpoIVB peptidase S55; InterPro: IPR008763 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This group of serine peptidases belong to the MEROPS peptidase family S55 (SpoIVB peptidase family, clan PA(S)). The protein SpoIVB plays a key role in signalling in the final sigma-K checkpoint of Bacillus subtilis [, ].
Probab=33.25 E-value=53 Score=24.07 Aligned_cols=19 Identities=26% Similarity=0.335 Sum_probs=9.2
Q ss_pred EEEEeCCeEEeeEEEEeeC
Q psy10040 28 EGEFRGGRIWGHGLVTYAD 46 (93)
Q Consensus 28 ~G~f~~g~~~G~G~~~~~d 46 (93)
.|-|..+.-.|.|++||-|
T Consensus 10 iGlwVRD~~aGiGTlTf~d 28 (218)
T PF05580_consen 10 IGLWVRDSTAGIGTLTFYD 28 (218)
T ss_pred EEEEEEeCCcCeEEEEEEE
Confidence 3455555555555554433
No 20
>PF10419 TFIIIC_sub6: TFIIIC subunit; InterPro: IPR019481 This conserved domain is found in a family of proteins that function as subunits of transcription factor IIIC (TFIIIC) []. TFIIIC in yeast and humans is required for transcription of tRNA and 5 S RNA genes by RNA polymerase III. The yeast proteins in this entry are fused to phosphoglycerate mutase domain.
Probab=24.42 E-value=47 Score=17.21 Aligned_cols=12 Identities=33% Similarity=0.601 Sum_probs=8.5
Q ss_pred CCCEEEEEEeCC
Q psy10040 23 DGMKFEGEFRGG 34 (93)
Q Consensus 23 ~G~~y~G~f~~g 34 (93)
++..|+|+|.+-
T Consensus 16 ~~~vf~G~~~~~ 27 (35)
T PF10419_consen 16 GNQVFEGEWEDT 27 (35)
T ss_pred CCEEEEEEEhhh
Confidence 456788888764
No 21
>PF11258 DUF3048: Protein of unknown function (DUF3048); InterPro: IPR021416 This entry represents a family of proteins with unknown function. It includes the YerB protein from Bacillus subtilis. ; PDB: 2PSB_A.
Probab=22.16 E-value=77 Score=23.65 Aligned_cols=30 Identities=23% Similarity=0.310 Sum_probs=16.7
Q ss_pred EEecCCCEEEEEEeCCeEEeeEEEEeeCCC
Q psy10040 19 FWRADGMKFEGEFRGGRIWGHGLVTYADGT 48 (93)
Q Consensus 19 ~~~~~G~~y~G~f~~g~~~G~G~~~~~dG~ 48 (93)
+.+.+|..++++|.+....+.=+|+..+|.
T Consensus 243 ~~~~~Gk~~~~tW~k~~~~~~~~~~d~~G~ 272 (283)
T PF11258_consen 243 YYFTNGKAIEGTWSKDSGDGPTRYYDADGN 272 (283)
T ss_dssp EEEETTEEEEEEEEEETTEEEEE---ETTE
T ss_pred EEEECCEEEEeEEeeCCCCCCCEEecCCCC
Confidence 344577777777777555555555556664
Done!