Query 037549
Match_columns 102
No_of_seqs 182 out of 1492
Neff 6.7
Searched_HMMs 46136
Date Fri Mar 29 13:23:58 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/037549.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/037549hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03185 phosphatidylinositol 99.6 4.4E-16 9.5E-21 130.6 8.6 72 1-76 20-91 (765)
2 PLN03185 phosphatidylinositol 99.6 9E-16 1.9E-20 128.7 7.0 75 1-79 112-186 (765)
3 KOG0231 Junctional membrane co 99.3 4.8E-12 1E-16 101.5 6.4 69 2-74 132-200 (455)
4 COG4642 Uncharacterized protei 99.2 1.3E-11 2.7E-16 84.9 5.2 71 2-76 44-114 (139)
5 KOG0231 Junctional membrane co 99.2 1.1E-11 2.3E-16 99.5 4.1 75 1-75 154-238 (455)
6 COG4642 Uncharacterized protei 99.1 5.4E-10 1.2E-14 76.9 6.3 70 1-74 66-135 (139)
7 smart00698 MORN Possible plasm 98.6 6.5E-08 1.4E-12 49.0 3.2 24 13-36 1-24 (26)
8 PF02493 MORN: MORN repeat; I 98.5 8.7E-08 1.9E-12 46.7 2.3 23 15-37 1-23 (23)
9 smart00698 MORN Possible plasm 97.1 0.00047 1E-08 34.7 2.3 19 36-54 1-19 (26)
10 PF02493 MORN: MORN repeat; I 95.9 0.0043 9.3E-08 29.7 1.2 17 38-54 1-17 (23)
11 COG2849 Uncharacterized protei 75.6 10 0.00022 27.9 5.6 40 8-47 116-157 (230)
12 COG2849 Uncharacterized protei 55.8 37 0.00081 24.9 5.3 52 1-52 133-186 (230)
13 PF07617 DUF1579: Protein of u 55.2 29 0.00062 24.4 4.4 36 14-49 52-89 (159)
14 PF07661 MORN_2: MORN repeat v 35.7 46 0.001 14.6 3.2 12 2-13 2-13 (22)
15 PF10419 TFIIIC_sub6: TFIIIC s 32.8 27 0.00058 18.5 1.0 12 11-22 16-27 (35)
16 PF14438 SM-ATX: Ataxin 2 SM d 29.3 74 0.0016 19.0 2.8 15 30-44 17-31 (77)
17 PF00988 CPSase_sm_chain: Carb 28.5 1.3E+02 0.0028 20.6 4.1 31 5-35 3-33 (131)
18 PF08300 HCV_NS5a_1a: Hepatiti 27.6 1.2E+02 0.0026 18.2 3.3 34 15-53 10-45 (62)
19 PF05580 Peptidase_S55: SpoIVB 22.5 1.3E+02 0.0028 22.4 3.5 29 10-38 4-34 (218)
No 1
>PLN03185 phosphatidylinositol phosphate kinase; Provisional
Probab=99.65 E-value=4.4e-16 Score=130.55 Aligned_cols=72 Identities=21% Similarity=0.310 Sum_probs=64.3
Q ss_pred CcceeEEEeccCCEEEEeeecCeeccceEEEecCCCEEEEEeeCCeeccccccccccccccceeEeeeeeeheehh
Q 037549 1 MHGFGVCRFANRHWYEGAWRERIRQGLGMYTFRNGETQSGHRQNGLLDIPSAQNTTHLISSIAIYHYKVLNVVQMF 76 (102)
Q Consensus 1 ~hG~G~~~~~~G~~YeG~w~~g~~~G~G~~~~~~G~~y~G~w~~g~~~G~g~~~~~~~~~~~~~~~g~~~~~v~~~ 76 (102)
+||.|++.|+||.+|+|+|++|++||.|+++|++|.+|+|+|.+|.+||.|+ ....++..|+|.|.++..++
T Consensus 20 ~hG~G~~~~~DG~~YeGew~~Gk~hG~G~~~~~nG~~YeGeF~nG~~hG~G~----~~~~~G~~YeG~w~~gkkhG 91 (765)
T PLN03185 20 PEGPGKYLWSDGCMYEGEWRRGMRHGNGKISWPSGATYEGEFSGGYMHGSGT----YTGTDGTTYKGRWRLNLKHG 91 (765)
T ss_pred cccceEEEECCCCEEEEEEECCEeeCcEeEEeCCCCEEEEEEECCEEeceEE----EEecCCCEEEEEEeCCcccc
Confidence 6899999999999999999999999999999999999999999999999995 45567788899988888775
No 2
>PLN03185 phosphatidylinositol phosphate kinase; Provisional
Probab=99.61 E-value=9e-16 Score=128.69 Aligned_cols=75 Identities=19% Similarity=0.174 Sum_probs=67.3
Q ss_pred CcceeEEEeccCCEEEEeeecCeeccceEEEecCCCEEEEEeeCCeeccccccccccccccceeEeeeeeeheehhhhc
Q 037549 1 MHGFGVCRFANRHWYEGAWRERIRQGLGMYTFRNGETQSGHRQNGLLDIPSAQNTTHLISSIAIYHYKVLNVVQMFQCS 79 (102)
Q Consensus 1 ~hG~G~~~~~~G~~YeG~w~~g~~~G~G~~~~~~G~~y~G~w~~g~~~G~g~~~~~~~~~~~~~~~g~~~~~v~~~~~~ 79 (102)
+||.|++.|+||++|+|+|++|++||.|+++|+||+.|+|+|.+|++||.|+ ..++++..|+|.|.++++++...
T Consensus 112 ~~G~G~y~~~nG~~Y~Gefk~Gk~~G~G~l~~~nG~~YeG~w~nG~~hG~G~----y~~~DG~~Y~G~W~~G~~~G~G~ 186 (765)
T PLN03185 112 QEGPGKYTWANGNVYLGDMKGGKMSGKGTLTWVSGDSYEGQWLDGMMHGFGV----YTWSDGGCYVGTWTRGLKDGKGV 186 (765)
T ss_pred eecceeeeccCCCeEEEEecCCEEecCEEEEEeCCCeEEEEEeCCcceeeEE----EEECCCCEEEEEeeCCceEeEEE
Confidence 5899999999999999999999999999999999999999999999999995 56778889999999998876543
No 3
>KOG0231 consensus Junctional membrane complex protein Junctophilin and related MORN repeat proteins [General function prediction only]
Probab=99.30 E-value=4.8e-12 Score=101.51 Aligned_cols=69 Identities=20% Similarity=0.274 Sum_probs=63.5
Q ss_pred cceeEEEeccCCEEEEeeecCeeccceEEEecCCCEEEEEeeCCeeccccccccccccccceeEeeeeeehee
Q 037549 2 HGFGVCRFANRHWYEGAWRERIRQGLGMYTFRNGETQSGHRQNGLLDIPSAQNTTHLISSIAIYHYKVLNVVQ 74 (102)
Q Consensus 2 hG~G~~~~~~G~~YeG~w~~g~~~G~G~~~~~~G~~y~G~w~~g~~~G~g~~~~~~~~~~~~~~~g~~~~~v~ 74 (102)
+|.|+..++++++|+|+|.+++++|.|++.+++|..|+|+|.++++||.|. ...+++.+|+|+|.+.+.
T Consensus 132 ~g~g~~~~~~g~~Y~G~~~~~k~sG~Gv~~~~~G~~Y~Gew~~n~~hG~G~----~~~pdGsk~eg~~~~~~l 200 (455)
T KOG0231|consen 132 SGEGVIELPTGDTYEGEFKRGKRSGFGVYIRSDGLKYEGEWLDNRRHGYGV----LTFPDGSKYEGQYKNNIL 200 (455)
T ss_pred CccceEecCCCCEEEeeecCCcccccceEEecCCCEeeceecCCCccCCCe----EEccCCCEEEEEeecccc
Confidence 577899999999999999999999999999999999999999999999995 577899999999999843
No 4
>COG4642 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=99.24 E-value=1.3e-11 Score=84.91 Aligned_cols=71 Identities=21% Similarity=0.252 Sum_probs=64.1
Q ss_pred cceeEEEeccCCEEEEeeecCeeccceEEEecCCCEEEEEeeCCeeccccccccccccccceeEeeeeeeheehh
Q 037549 2 HGFGVCRFANRHWYEGAWRERIRQGLGMYTFRNGETQSGHRQNGLLDIPSAQNTTHLISSIAIYHYKVLNVVQMF 76 (102)
Q Consensus 2 hG~G~~~~~~G~~YeG~w~~g~~~G~G~~~~~~G~~y~G~w~~g~~~G~g~~~~~~~~~~~~~~~g~~~~~v~~~ 76 (102)
.|.|++.+.+|..|+|.++|++++|.|++++++++.|+|.|.+++++|.|+ .+..++-+|+|.|.+++...
T Consensus 44 ~Gkgs~~~~~G~~Y~Gtl~ngk~nGqG~~~~~ngd~Y~g~F~s~~F~g~G~----~~~~~Gw~~~G~F~~Gq~~g 114 (139)
T COG4642 44 AGKGSLKYDNGRIYTGTLKNGKMNGQGTYTFANGDIYEGPFNSGKFRGQGT----RGSFNGWLYIGRFTEGQANG 114 (139)
T ss_pred CCCccEEEcCCccccceEEcCcccCcEEEEecCCCeEeccccCccccceEe----eccccCCEEeeeecccccCC
Confidence 578999999999999999999999999999999999999999999999995 45567779999998887764
No 5
>KOG0231 consensus Junctional membrane complex protein Junctophilin and related MORN repeat proteins [General function prediction only]
Probab=99.21 E-value=1.1e-11 Score=99.49 Aligned_cols=75 Identities=28% Similarity=0.389 Sum_probs=62.7
Q ss_pred CcceeEEEeccCCEEEEeeecCeeccceEEEecCCCEEEEEeeCC----eeccccccccccc------cccceeEeeeee
Q 037549 1 MHGFGVCRFANRHWYEGAWRERIRQGLGMYTFRNGETQSGHRQNG----LLDIPSAQNTTHL------ISSIAIYHYKVL 70 (102)
Q Consensus 1 ~hG~G~~~~~~G~~YeG~w~~g~~~G~G~~~~~~G~~y~G~w~~g----~~~G~g~~~~~~~------~~~~~~~~g~~~ 70 (102)
+||+|+++++||..|+|+|.++++||+|++++|||.+|+|.|+++ +.+|.+....... ...+.+|.++|.
T Consensus 154 ~sG~Gv~~~~~G~~Y~Gew~~n~~hG~G~~~~pdGsk~eg~~~~~~l~~l~~gk~~~~~~~~~~~a~ra~~~~~~~~Ew~ 233 (455)
T KOG0231|consen 154 RSGFGVYIRSDGLKYEGEWLDNRRHGYGVLTFPDGSKYEGQYKNNILEALRHGKGRYKFDDALEAAQRAATIARYSGEWA 233 (455)
T ss_pred ccccceEEecCCCEeeceecCCCccCCCeEEccCCCEEEEEeecccccccccceEEEEEeccchhhhhhhhhhhhhhhhh
Confidence 689999999999999999999999999999999999999999999 7888886543221 225777888887
Q ss_pred eheeh
Q 037549 71 NVVQM 75 (102)
Q Consensus 71 ~~v~~ 75 (102)
+.-+.
T Consensus 234 ~~~~~ 238 (455)
T KOG0231|consen 234 ARGQS 238 (455)
T ss_pred hhcCC
Confidence 75444
No 6
>COG4642 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=99.05 E-value=5.4e-10 Score=76.91 Aligned_cols=70 Identities=24% Similarity=0.213 Sum_probs=63.4
Q ss_pred CcceeEEEeccCCEEEEeeecCeeccceEEEecCCCEEEEEeeCCeeccccccccccccccceeEeeeeeehee
Q 037549 1 MHGFGVCRFANRHWYEGAWRERIRQGLGMYTFRNGETQSGHRQNGLLDIPSAQNTTHLISSIAIYHYKVLNVVQ 74 (102)
Q Consensus 1 ~hG~G~~~~~~G~~YeG~w~~g~~~G~G~~~~~~G~~y~G~w~~g~~~G~g~~~~~~~~~~~~~~~g~~~~~v~ 74 (102)
|+|.|++.++||+.|+|.|++++.+|.|++...+|.+|.|.|.+++.+|.+. ....+..+|+|.+....-
T Consensus 66 ~nGqG~~~~~ngd~Y~g~F~s~~F~g~G~~~~~~Gw~~~G~F~~Gq~~g~g~----l~~~~g~vy~G~fk~g~f 135 (139)
T COG4642 66 MNGQGTYTFANGDIYEGPFNSGKFRGQGTRGSFNGWLYIGRFTEGQANGKGF----LLKEDGSVYTGMFKQGRF 135 (139)
T ss_pred ccCcEEEEecCCCeEeccccCccccceEeeccccCCEEeeeecccccCCcee----EEecCCcEEeeeEEeeec
Confidence 5799999999999999999999999999999999999999999999999995 455778889998876653
No 7
>smart00698 MORN Possible plasma membrane-binding motif in junctophilins, PIP-5-kinases and protein kinases.
Probab=98.58 E-value=6.5e-08 Score=49.03 Aligned_cols=24 Identities=46% Similarity=0.976 Sum_probs=21.4
Q ss_pred CEEEEeeecCeeccceEEEecCCC
Q 037549 13 HWYEGAWRERIRQGLGMYTFRNGE 36 (102)
Q Consensus 13 ~~YeG~w~~g~~~G~G~~~~~~G~ 36 (102)
++|+|+|.++++||.|+|+|+|..
T Consensus 1 ~~Y~G~w~~g~~hG~G~~~~~d~~ 24 (26)
T smart00698 1 DRYEGEWRNGKRHGRGVYTYANXX 24 (26)
T ss_pred CeEEEEEECCeEEeeEEEEecccc
Confidence 479999999999999999998753
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=98.50 E-value=8.7e-08 Score=46.73 Aligned_cols=23 Identities=43% Similarity=1.145 Sum_probs=20.0
Q ss_pred EEEeeecCeeccceEEEecCCCE
Q 037549 15 YEGAWRERIRQGLGMYTFRNGET 37 (102)
Q Consensus 15 YeG~w~~g~~~G~G~~~~~~G~~ 37 (102)
|+|+|.+++++|.|+++++||++
T Consensus 1 Y~G~~~~g~~~G~G~~~~~~G~~ 23 (23)
T PF02493_consen 1 YEGEWKNGKKHGYGVYTFPDGDR 23 (23)
T ss_dssp ECCEEETTEEECEEEEE-TTS-E
T ss_pred CEEEEEECcccccEEEEeCCCCC
Confidence 89999999999999999999975
No 9
>smart00698 MORN Possible plasma membrane-binding motif in junctophilins, PIP-5-kinases and protein kinases.
Probab=97.12 E-value=0.00047 Score=34.67 Aligned_cols=19 Identities=16% Similarity=0.148 Sum_probs=16.7
Q ss_pred CEEEEEeeCCeeccccccc
Q 037549 36 ETQSGHRQNGLLDIPSAQN 54 (102)
Q Consensus 36 ~~y~G~w~~g~~~G~g~~~ 54 (102)
++|+|+|++|++||.|++.
T Consensus 1 ~~Y~G~w~~g~~hG~G~~~ 19 (26)
T smart00698 1 DRYEGEWRNGKRHGRGVYT 19 (26)
T ss_pred CeEEEEEECCeEEeeEEEE
Confidence 4799999999999999754
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=95.93 E-value=0.0043 Score=29.68 Aligned_cols=17 Identities=18% Similarity=0.075 Sum_probs=15.1
Q ss_pred EEEEeeCCeeccccccc
Q 037549 38 QSGHRQNGLLDIPSAQN 54 (102)
Q Consensus 38 y~G~w~~g~~~G~g~~~ 54 (102)
|+|+|++++++|.|++.
T Consensus 1 Y~G~~~~g~~~G~G~~~ 17 (23)
T PF02493_consen 1 YEGEWKNGKKHGYGVYT 17 (23)
T ss_dssp ECCEEETTEEECEEEEE
T ss_pred CEEEEEECcccccEEEE
Confidence 78999999999999643
No 11
>COG2849 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=75.56 E-value=10 Score=27.93 Aligned_cols=40 Identities=20% Similarity=0.276 Sum_probs=19.1
Q ss_pred EeccCCEE-EEeeecCeeccceEEEecCCCE-EEEEeeCCee
Q 037549 8 RFANRHWY-EGAWRERIRQGLGMYTFRNGET-QSGHRQNGLL 47 (102)
Q Consensus 8 ~~~~G~~Y-eG~w~~g~~~G~G~~~~~~G~~-y~G~w~~g~~ 47 (102)
.+++|... +-.+.+++.+|.-...+++|.. ++..|+++.+
T Consensus 116 ~y~nGk~~~~~~~~ng~~~G~~~~yy~nG~~~~e~~~kn~~~ 157 (230)
T COG2849 116 FYENGKLKSEYNYKNGKLHGIQKEYYENGKLKSETVYKNGKL 157 (230)
T ss_pred EEcCCcEeEEEEecCCcccceEEEEEcCCCEEEEEEEeCCCc
Confidence 34444332 2334555555555555555542 3555555554
No 12
>COG2849 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=55.80 E-value=37 Score=24.94 Aligned_cols=52 Identities=17% Similarity=0.236 Sum_probs=41.0
Q ss_pred CcceeEEEeccCCE-EEEeeecCeeccceEEEecCCCEE-EEEeeCCeeccccc
Q 037549 1 MHGFGVCRFANRHW-YEGAWRERIRQGLGMYTFRNGETQ-SGHRQNGLLDIPSA 52 (102)
Q Consensus 1 ~hG~G~~~~~~G~~-YeG~w~~g~~~G~G~~~~~~G~~y-~G~w~~g~~~G~g~ 52 (102)
.||.-..+|+||.. ++..|++++++|.-...+++|..- +=.+++|.++|.-.
T Consensus 133 ~~G~~~~yy~nG~~~~e~~~kn~~~~g~~k~yy~nGkl~~e~~~knG~~~G~~k 186 (230)
T COG2849 133 LHGIQKEYYENGKLKSETVYKNGKLEGIAKTYYENGKLLSEVPYKNGKKNGVVK 186 (230)
T ss_pred ccceEEEEEcCCCEEEEEEEeCCCccccEEEEcCCCcEEEeecccCCcccceEE
Confidence 36777888999876 799999999888888888999753 67777777776654
No 13
>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=55.23 E-value=29 Score=24.36 Aligned_cols=36 Identities=17% Similarity=0.206 Sum_probs=25.8
Q ss_pred EEEEeee-cCeeccceEEEe-cCCCEEEEEeeCCeecc
Q 037549 14 WYEGAWR-ERIRQGLGMYTF-RNGETQSGHRQNGLLDI 49 (102)
Q Consensus 14 ~YeG~w~-~g~~~G~G~~~~-~~G~~y~G~w~~g~~~G 49 (102)
.|+|..- ....+|.+++-| +....|+|.|.+.+..+
T Consensus 52 e~~g~~~~g~~~~~~~~lGYD~~~~~yvgtWidSM~t~ 89 (159)
T PF07617_consen 52 EYEGSMPGGGPFEGIGTLGYDPAKKKYVGTWIDSMGTG 89 (159)
T ss_pred EEEeecCCCCceEEEEEEEECCccCeEEEEEeccCCCc
Confidence 3666666 566677777777 56788999998885443
No 14
>PF07661 MORN_2: MORN repeat variant; InterPro: IPR011652 This entry represents an apparent variant of the IPR003409 from INTERPRO repeat.
Probab=35.67 E-value=46 Score=14.62 Aligned_cols=12 Identities=17% Similarity=0.094 Sum_probs=5.4
Q ss_pred cceeEEEeccCC
Q 037549 2 HGFGVCRFANRH 13 (102)
Q Consensus 2 hG~G~~~~~~G~ 13 (102)
||.=...++||.
T Consensus 2 ~G~~~~yy~nG~ 13 (22)
T PF07661_consen 2 DGEWKFYYENGK 13 (22)
T ss_pred cceEEEEeCCCC
Confidence 344444444444
No 15
>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=32.76 E-value=27 Score=18.46 Aligned_cols=12 Identities=25% Similarity=0.880 Sum_probs=9.0
Q ss_pred cCCEEEEeeecC
Q 037549 11 NRHWYEGAWRER 22 (102)
Q Consensus 11 ~G~~YeG~w~~g 22 (102)
++.+|+|+|.+-
T Consensus 16 ~~~vf~G~~~~~ 27 (35)
T PF10419_consen 16 GNQVFEGEWEDT 27 (35)
T ss_pred CCEEEEEEEhhh
Confidence 456788888775
No 16
>PF14438 SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1.
Probab=29.25 E-value=74 Score=19.03 Aligned_cols=15 Identities=27% Similarity=0.319 Sum_probs=10.7
Q ss_pred EEecCCCEEEEEeeC
Q 037549 30 YTFRNGETQSGHRQN 44 (102)
Q Consensus 30 ~~~~~G~~y~G~w~~ 44 (102)
-+..||.+|+|.|.-
T Consensus 17 V~~~~G~~yeGif~s 31 (77)
T PF14438_consen 17 VTTKNGSVYEGIFHS 31 (77)
T ss_dssp EEETTS-EEEEEEEE
T ss_pred EEECCCCEEEEEEEe
Confidence 456889999998864
No 17
>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=28.51 E-value=1.3e+02 Score=20.62 Aligned_cols=31 Identities=16% Similarity=0.141 Sum_probs=17.1
Q ss_pred eEEEeccCCEEEEeeecCeeccceEEEecCC
Q 037549 5 GVCRFANRHWYEGAWRERIRQGLGMYTFRNG 35 (102)
Q Consensus 5 G~~~~~~G~~YeG~w~~g~~~G~G~~~~~~G 35 (102)
+.+...||.+|+|.+......-.|...|..+
T Consensus 3 a~LvLeDG~~f~G~~~G~~~~~~GEvVFnT~ 33 (131)
T PF00988_consen 3 AYLVLEDGTVFEGKSFGAPGTVTGEVVFNTG 33 (131)
T ss_dssp EEEEETTS-EEEEEE-SBSEEEEEEEEEE--
T ss_pred EEEEECCCCEEEEEEecCCCcEEEEEEEEcc
Confidence 3456677777777776665555666555444
No 18
>PF08300 HCV_NS5a_1a: Hepatitis C virus non-structural 5a zinc finger domain; InterPro: IPR013192 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in the non-structural 5a protein (NS5a) in Hepatitis C virus. The molecular function of NS5a is uncertain, but it is phosphorylated when expressed in mammalian cells. It is thought to interact with the dsRNA dependent (interferon inducible) kinase PKR, P19525 from SWISSPROT [, ]. This region corresponds to the N-terminal zinc binding domain (1a) []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003968 RNA-directed RNA polymerase activity, 0004252 serine-type endopeptidase activity, 0008270 zinc ion binding, 0017111 nucleoside-triphosphatase activity, 0006355 regulation of transcription, DNA-dependent, 0006915 apoptosis, 0030683 evasion by virus of host immune response, 0005789 endoplasmic reticulum membrane, 0016021 integral to membrane; PDB: 1ZH1_B 3FQM_A 3FQQ_B.
Probab=27.64 E-value=1.2e+02 Score=18.25 Aligned_cols=34 Identities=32% Similarity=0.672 Sum_probs=22.3
Q ss_pred EEEeeecCeeccceEEEe--cCCCEEEEEeeCCeecccccc
Q 037549 15 YEGAWRERIRQGLGMYTF--RNGETQSGHRQNGLLDIPSAQ 53 (102)
Q Consensus 15 YeG~w~~g~~~G~G~~~~--~~G~~y~G~w~~g~~~G~g~~ 53 (102)
|.|.|+-+ |++.- +-|....|.-+||.+.-.|..
T Consensus 10 y~G~W~Gd-----G~~~TrC~CGa~ItGhVknG~mri~gpk 45 (62)
T PF08300_consen 10 YKGVWRGD-----GVMHTRCPCGAVITGHVKNGSMRIYGPK 45 (62)
T ss_dssp B-SEEES------EEEEEE-TTS-EEEEEEETTEEEEE--T
T ss_pred CCcEEcCC-----CEEEecCCCCCEEeEEEeCCeEEEecCh
Confidence 77888755 66544 788999999999988766643
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=22.55 E-value=1.3e+02 Score=22.44 Aligned_cols=29 Identities=24% Similarity=0.460 Sum_probs=22.7
Q ss_pred ccCCEEEEeeecCeeccceEEEecC--CCEE
Q 037549 10 ANRHWYEGAWRERIRQGLGMYTFRN--GETQ 38 (102)
Q Consensus 10 ~~G~~YeG~w~~g~~~G~G~~~~~~--G~~y 38 (102)
.++..--|-|.++.-.|.|++||-| ...|
T Consensus 4 ~~~~ykiGlwVRD~~aGiGTlTf~dp~~~~f 34 (218)
T PF05580_consen 4 EDGRYKIGLWVRDSTAGIGTLTFYDPETGTF 34 (218)
T ss_pred cCCcEEEEEEEEeCCcCeEEEEEEECCCCcE
Confidence 3566778999999999999999844 4455
Done!