Query psy5667
Match_columns 79
No_of_seqs 114 out of 1601
Neff 7.9
Searched_HMMs 46136
Date Fri Aug 16 23:31:10 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy5667.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/5667hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03185 phosphatidylinositol 99.8 1.4E-19 3E-24 134.9 10.9 76 2-78 4-85 (765)
2 PLN03185 phosphatidylinositol 99.8 8.1E-19 1.8E-23 130.9 9.4 67 12-79 112-178 (765)
3 COG4642 Uncharacterized protei 99.5 2.2E-14 4.7E-19 88.0 5.4 64 14-78 45-108 (139)
4 KOG0231|consensus 99.5 3.1E-14 6.8E-19 101.9 6.5 66 12-78 131-196 (455)
5 COG4642 Uncharacterized protei 99.5 3.1E-13 6.7E-18 83.0 7.4 66 12-78 66-131 (139)
6 KOG0231|consensus 99.3 1.9E-12 4.2E-17 92.8 4.7 73 5-78 147-233 (455)
7 PF02493 MORN: MORN repeat; I 98.6 7.4E-08 1.6E-12 42.3 2.9 23 50-72 1-23 (23)
8 smart00698 MORN Possible plasm 98.6 2E-07 4.2E-12 42.4 4.0 22 49-70 2-23 (26)
9 smart00698 MORN Possible plasm 98.4 5.2E-07 1.1E-11 41.0 3.7 23 24-47 1-23 (26)
10 PF02493 MORN: MORN repeat; I 98.4 3.4E-07 7.5E-12 40.1 2.6 23 26-49 1-23 (23)
11 COG2849 Uncharacterized protei 90.5 3.5 7.6E-05 27.4 7.9 52 19-71 116-169 (230)
12 COG2849 Uncharacterized protei 84.0 8.1 0.00018 25.6 6.7 58 14-72 135-194 (230)
13 PF14438 SM-ATX: Ataxin 2 SM d 64.0 11 0.00023 20.6 2.7 13 65-77 17-29 (77)
14 PF00988 CPSase_sm_chain: Carb 57.8 29 0.00064 21.4 4.1 31 16-47 3-33 (131)
15 PF14977 FAM194: FAM194 protei 53.9 40 0.00086 22.4 4.5 54 14-72 24-79 (208)
16 PF07617 DUF1579: Protein of u 39.8 97 0.0021 19.5 5.5 32 26-58 53-86 (159)
17 CHL00197 carA carbamoyl-phosph 28.5 1.3E+02 0.0028 21.8 4.2 33 14-47 5-37 (382)
18 TIGR01368 CPSaseIIsmall carbam 28.1 1.2E+02 0.0026 21.7 3.9 30 17-47 2-31 (358)
19 PRK12564 carbamoyl phosphate s 27.9 1.3E+02 0.0029 21.5 4.1 32 15-47 4-35 (360)
20 PF10419 TFIIIC_sub6: TFIIIC s 24.1 53 0.0012 15.5 1.1 7 48-54 18-24 (35)
21 PF07661 MORN_2: MORN repeat v 24.0 64 0.0014 12.6 3.1 7 41-47 6-12 (22)
22 PRK12838 carbamoyl phosphate s 23.1 1.9E+02 0.0041 20.7 4.2 32 15-47 2-33 (354)
23 PLN02771 carbamoyl-phosphate s 22.6 2E+02 0.0043 21.2 4.2 32 15-47 56-87 (415)
24 PF05580 Peptidase_S55: SpoIVB 21.7 1.1E+02 0.0024 20.6 2.6 26 22-48 5-30 (218)
No 1
>PLN03185 phosphatidylinositol phosphate kinase; Provisional
Probab=99.82 E-value=1.4e-19 Score=134.91 Aligned_cols=76 Identities=29% Similarity=0.622 Sum_probs=67.2
Q ss_pred eecCceEeCCee------eeeEEEcCCCCEEEEEEecCCeEeeeEEEEcCCCCEEEEEEeCCeEEeeEEEEecCCCEEEE
Q psy5667 2 SQKDEEEYPGVV------QHGSFKYDDGTLYIGDWNERGQKHGMGHMKLPDHTRYDGTFHNGLCSGLGVMRFPDGANSTY 75 (79)
Q Consensus 2 ~~~~~~~~~~~~------g~G~~~~~~g~~Y~G~~~~~~~~~G~G~~~~~~G~~y~G~f~~~~~~G~G~~~~~~G~~Y~G 75 (79)
.++++.+|.|.+ |.|++.|+||++|+|+| +++++||.|++.+++|.+|+|+|.++++||.|++++++|.+|+|
T Consensus 4 ~~~nGd~Y~Ge~~~g~~hG~G~~~~~DG~~YeGew-~~Gk~hG~G~~~~~nG~~YeGeF~nG~~hG~G~~~~~~G~~YeG 82 (765)
T PLN03185 4 VLSNGDFYSGSLLGNVPEGPGKYLWSDGCMYEGEW-RRGMRHGNGKISWPSGATYEGEFSGGYMHGSGTYTGTDGTTYKG 82 (765)
T ss_pred EecCCCEEEEEEECCccccceEEEECCCCEEEEEE-ECCEeeCcEeEEeCCCCEEEEEEECCEEeceEEEEecCCCEEEE
Confidence 455666666544 78999999999999999 89999999999999999999999999999999999999999999
Q ss_pred EEe
Q psy5667 76 SDI 78 (79)
Q Consensus 76 ~~~ 78 (79)
+|.
T Consensus 83 ~w~ 85 (765)
T PLN03185 83 RWR 85 (765)
T ss_pred EEe
Confidence 996
No 2
>PLN03185 phosphatidylinositol phosphate kinase; Provisional
Probab=99.78 E-value=8.1e-19 Score=130.88 Aligned_cols=67 Identities=25% Similarity=0.576 Sum_probs=60.4
Q ss_pred eeeeeEEEcCCCCEEEEEEecCCeEeeeEEEEcCCCCEEEEEEeCCeEEeeEEEEecCCCEEEEEEeC
Q psy5667 12 VVQHGSFKYDDGTLYIGDWNERGQKHGMGHMKLPDHTRYDGTFHNGLCSGLGVMRFPDGANSTYSDIR 79 (79)
Q Consensus 12 ~~g~G~~~~~~g~~Y~G~~~~~~~~~G~G~~~~~~G~~y~G~f~~~~~~G~G~~~~~~G~~Y~G~~~~ 79 (79)
..|.|++.+++|..|+|+| +++++||.|++++++|++|+|+|.++++||.|+++++||.+|+|.|.+
T Consensus 112 ~~G~G~y~~~nG~~Y~Gef-k~Gk~~G~G~l~~~nG~~YeG~w~nG~~hG~G~y~~~DG~~Y~G~W~~ 178 (765)
T PLN03185 112 QEGPGKYTWANGNVYLGDM-KGGKMSGKGTLTWVSGDSYEGQWLDGMMHGFGVYTWSDGGCYVGTWTR 178 (765)
T ss_pred eecceeeeccCCCeEEEEe-cCCEEecCEEEEEeCCCeEEEEEeCCcceeeEEEEECCCCEEEEEeeC
Confidence 3478899999999999999 899999999999999999999999999999999999999999999964
No 3
>COG4642 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=99.52 E-value=2.2e-14 Score=88.03 Aligned_cols=64 Identities=28% Similarity=0.496 Sum_probs=44.4
Q ss_pred eeeEEEcCCCCEEEEEEecCCeEeeeEEEEcCCCCEEEEEEeCCeEEeeEEEEecCCCEEEEEEe
Q psy5667 14 QHGSFKYDDGTLYIGDWNERGQKHGMGHMKLPDHTRYDGTFHNGLCSGLGVMRFPDGANSTYSDI 78 (79)
Q Consensus 14 g~G~~~~~~g~~Y~G~~~~~~~~~G~G~~~~~~G~~y~G~f~~~~~~G~G~~~~~~G~~Y~G~~~ 78 (79)
|.|++.+.+|.+|+|.+ +|++++|+|++.++++++|+|.|.+++.+|.|++...+|++|+|.|.
T Consensus 45 Gkgs~~~~~G~~Y~Gtl-~ngk~nGqG~~~~~ngd~Y~g~F~s~~F~g~G~~~~~~Gw~~~G~F~ 108 (139)
T COG4642 45 GKGSLKYDNGRIYTGTL-KNGKMNGQGTYTFANGDIYEGPFNSGKFRGQGTRGSFNGWLYIGRFT 108 (139)
T ss_pred CCccEEEcCCccccceE-EcCcccCcEEEEecCCCeEeccccCccccceEeeccccCCEEeeeec
Confidence 45666666777777777 67777777777777777777777777777777777777777777664
No 4
>KOG0231|consensus
Probab=99.51 E-value=3.1e-14 Score=101.92 Aligned_cols=66 Identities=27% Similarity=0.555 Sum_probs=62.9
Q ss_pred eeeeeEEEcCCCCEEEEEEecCCeEeeeEEEEcCCCCEEEEEEeCCeEEeeEEEEecCCCEEEEEEe
Q psy5667 12 VVQHGSFKYDDGTLYIGDWNERGQKHGMGHMKLPDHTRYDGTFHNGLCSGLGVMRFPDGANSTYSDI 78 (79)
Q Consensus 12 ~~g~G~~~~~~g~~Y~G~~~~~~~~~G~G~~~~~~G~~y~G~f~~~~~~G~G~~~~~~G~~Y~G~~~ 78 (79)
..+.++..++++++|+|+| .+++++|.|++.+++|..|+|+|.++++||+|++++|+|++|+|.|.
T Consensus 131 ~~g~g~~~~~~g~~Y~G~~-~~~k~sG~Gv~~~~~G~~Y~Gew~~n~~hG~G~~~~pdGsk~eg~~~ 196 (455)
T KOG0231|consen 131 RSGEGVIELPTGDTYEGEF-KRGKRSGFGVYIRSDGLKYEGEWLDNRRHGYGVLTFPDGSKYEGQYK 196 (455)
T ss_pred cCccceEecCCCCEEEeee-cCCcccccceEEecCCCEeeceecCCCccCCCeEEccCCCEEEEEee
Confidence 3468999999999999999 99999999999999999999999999999999999999999999985
No 5
>COG4642 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=99.47 E-value=3.1e-13 Score=82.97 Aligned_cols=66 Identities=24% Similarity=0.403 Sum_probs=63.3
Q ss_pred eeeeeEEEcCCCCEEEEEEecCCeEeeeEEEEcCCCCEEEEEEeCCeEEeeEEEEecCCCEEEEEEe
Q psy5667 12 VVQHGSFKYDDGTLYIGDWNERGQKHGMGHMKLPDHTRYDGTFHNGLCSGLGVMRFPDGANSTYSDI 78 (79)
Q Consensus 12 ~~g~G~~~~~~g~~Y~G~~~~~~~~~G~G~~~~~~G~~y~G~f~~~~~~G~G~~~~~~G~~Y~G~~~ 78 (79)
+.|.|+++++++++|+|+| .+++++|+|+....+|.+|+|.|..++..|.|.+..+++.+|+|.|.
T Consensus 66 ~nGqG~~~~~ngd~Y~g~F-~s~~F~g~G~~~~~~Gw~~~G~F~~Gq~~g~g~l~~~~g~vy~G~fk 131 (139)
T COG4642 66 MNGQGTYTFANGDIYEGPF-NSGKFRGQGTRGSFNGWLYIGRFTEGQANGKGFLLKEDGSVYTGMFK 131 (139)
T ss_pred ccCcEEEEecCCCeEeccc-cCccccceEeeccccCCEEeeeecccccCCceeEEecCCcEEeeeEE
Confidence 4489999999999999999 89999999999999999999999999999999999999999999874
No 6
>KOG0231|consensus
Probab=99.32 E-value=1.9e-12 Score=92.78 Aligned_cols=73 Identities=29% Similarity=0.521 Sum_probs=63.8
Q ss_pred CceEeCCeeeeeEEEcCCCCEEEEEEecCCeEeeeEEEEcCCCCEEEEEEeCC----eEEeeEEEEecC----------C
Q psy5667 5 DEEEYPGVVQHGSFKYDDGTLYIGDWNERGQKHGMGHMKLPDHTRYDGTFHNG----LCSGLGVMRFPD----------G 70 (79)
Q Consensus 5 ~~~~~~~~~g~G~~~~~~g~~Y~G~~~~~~~~~G~G~~~~~~G~~y~G~f~~~----~~~G~G~~~~~~----------G 70 (79)
+.+-..+..|.|++.+++|..|+|+| +++++||+|++++|+|++|+|+|+++ ++||++.+.+.+ .
T Consensus 147 G~~~~~k~sG~Gv~~~~~G~~Y~Gew-~~n~~hG~G~~~~pdGsk~eg~~~~~~l~~l~~gk~~~~~~~~~~~a~ra~~~ 225 (455)
T KOG0231|consen 147 GEFKRGKRSGFGVYIRSDGLKYEGEW-LDNRRHGYGVLTFPDGSKYEGQYKNNILEALRHGKGRYKFDDALEAAQRAATI 225 (455)
T ss_pred eeecCCcccccceEEecCCCEeecee-cCCCccCCCeEEccCCCEEEEEeecccccccccceEEEEEeccchhhhhhhhh
Confidence 33334444478999999999999999 99999999999999999999999999 899999999996 7
Q ss_pred CEEEEEEe
Q psy5667 71 ANSTYSDI 78 (79)
Q Consensus 71 ~~Y~G~~~ 78 (79)
.+|.++|.
T Consensus 226 ~~~~~Ew~ 233 (455)
T KOG0231|consen 226 ARYSGEWA 233 (455)
T ss_pred hhhhhhhh
Confidence 78877764
No 7
>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=98.58 E-value=7.4e-08 Score=42.34 Aligned_cols=23 Identities=48% Similarity=0.993 Sum_probs=13.7
Q ss_pred EEEEEeCCeEEeeEEEEecCCCE
Q psy5667 50 YDGTFHNGLCSGLGVMRFPDGAN 72 (79)
Q Consensus 50 y~G~f~~~~~~G~G~~~~~~G~~ 72 (79)
|+|+|.+++++|.|+++++||++
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 56666666666666666666653
No 8
>smart00698 MORN Possible plasma membrane-binding motif in junctophilins, PIP-5-kinases and protein kinases.
Probab=98.55 E-value=2e-07 Score=42.44 Aligned_cols=22 Identities=36% Similarity=0.797 Sum_probs=16.3
Q ss_pred EEEEEEeCCeEEeeEEEEecCC
Q psy5667 49 RYDGTFHNGLCSGLGVMRFPDG 70 (79)
Q Consensus 49 ~y~G~f~~~~~~G~G~~~~~~G 70 (79)
+|+|+|.++++||.|+++++|.
T Consensus 2 ~Y~G~w~~g~~hG~G~~~~~d~ 23 (26)
T smart00698 2 RYEGEWRNGKRHGRGVYTYANX 23 (26)
T ss_pred eEEEEEECCeEEeeEEEEeccc
Confidence 5777777777777777777753
No 9
>smart00698 MORN Possible plasma membrane-binding motif in junctophilins, PIP-5-kinases and protein kinases.
Probab=98.43 E-value=5.2e-07 Score=41.02 Aligned_cols=23 Identities=30% Similarity=0.797 Sum_probs=20.9
Q ss_pred CEEEEEEecCCeEeeeEEEEcCCC
Q psy5667 24 TLYIGDWNERGQKHGMGHMKLPDH 47 (79)
Q Consensus 24 ~~Y~G~~~~~~~~~G~G~~~~~~G 47 (79)
++|+|+| +++++||.|+++++|.
T Consensus 1 ~~Y~G~w-~~g~~hG~G~~~~~d~ 23 (26)
T smart00698 1 DRYEGEW-RNGKRHGRGVYTYANX 23 (26)
T ss_pred CeEEEEE-ECCeEEeeEEEEeccc
Confidence 4699999 9999999999999874
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=98.39 E-value=3.4e-07 Score=40.13 Aligned_cols=23 Identities=48% Similarity=1.099 Sum_probs=19.8
Q ss_pred EEEEEecCCeEeeeEEEEcCCCCE
Q psy5667 26 YIGDWNERGQKHGMGHMKLPDHTR 49 (79)
Q Consensus 26 Y~G~~~~~~~~~G~G~~~~~~G~~ 49 (79)
|+|+| +++++||.|++.++||++
T Consensus 1 Y~G~~-~~g~~~G~G~~~~~~G~~ 23 (23)
T PF02493_consen 1 YEGEW-KNGKKHGYGVYTFPDGDR 23 (23)
T ss_dssp ECCEE-ETTEEECEEEEE-TTS-E
T ss_pred CEEEE-EECcccccEEEEeCCCCC
Confidence 78999 899999999999999874
No 11
>COG2849 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=90.50 E-value=3.5 Score=27.38 Aligned_cols=52 Identities=19% Similarity=0.455 Sum_probs=29.2
Q ss_pred EcCCCCEEE-EEEecCCeEeeeEEEEcCCCC-EEEEEEeCCeEEeeEEEEecCCC
Q psy5667 19 KYDDGTLYI-GDWNERGQKHGMGHMKLPDHT-RYDGTFHNGLCSGLGVMRFPDGA 71 (79)
Q Consensus 19 ~~~~g~~Y~-G~~~~~~~~~G~G~~~~~~G~-~y~G~f~~~~~~G~G~~~~~~G~ 71 (79)
.+++|.+.. -.+ ++++.||.-...+++|. ..+..|+++.+.|.-...+++|.
T Consensus 116 ~y~nGk~~~~~~~-~ng~~~G~~~~yy~nG~~~~e~~~kn~~~~g~~k~yy~nGk 169 (230)
T COG2849 116 FYENGKLKSEYNY-KNGKLHGIQKEYYENGKLKSETVYKNGKLEGIAKTYYENGK 169 (230)
T ss_pred EEcCCcEeEEEEe-cCCcccceEEEEEcCCCEEEEEEEeCCCccccEEEEcCCCc
Confidence 355554432 234 56666666666666654 34666666665566666666654
No 12
>COG2849 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=84.04 E-value=8.1 Score=25.64 Aligned_cols=58 Identities=16% Similarity=0.267 Sum_probs=37.3
Q ss_pred eeeEEEcCCCCE-EEEEEecCCeEeeeEEEEcCCCCE-EEEEEeCCeEEeeEEEEecCCCE
Q psy5667 14 QHGSFKYDDGTL-YIGDWNERGQKHGMGHMKLPDHTR-YDGTFHNGLCSGLGVMRFPDGAN 72 (79)
Q Consensus 14 g~G~~~~~~g~~-Y~G~~~~~~~~~G~G~~~~~~G~~-y~G~f~~~~~~G~G~~~~~~G~~ 72 (79)
|--+..+++|.. .+..+ +++.++|.-...+++|.. .+-.++++.+.|.-...+++|..
T Consensus 135 G~~~~yy~nG~~~~e~~~-kn~~~~g~~k~yy~nGkl~~e~~~knG~~~G~~k~Y~enGkl 194 (230)
T COG2849 135 GIQKEYYENGKLKSETVY-KNGKLEGIAKTYYENGKLLSEVPYKNGKKNGVVKIYYENGKL 194 (230)
T ss_pred ceEEEEEcCCCEEEEEEE-eCCCccccEEEEcCCCcEEEeecccCCcccceEEEEccCCCE
Confidence 344556777765 56777 677777777777777753 44556666666666666665543
No 13
>PF14438 SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1.
Probab=63.96 E-value=11 Score=20.58 Aligned_cols=13 Identities=8% Similarity=-0.151 Sum_probs=6.8
Q ss_pred EEecCCCEEEEEE
Q psy5667 65 MRFPDGANSTYSD 77 (79)
Q Consensus 65 ~~~~~G~~Y~G~~ 77 (79)
.+..||.+|+|-|
T Consensus 17 V~~~~G~~yeGif 29 (77)
T PF14438_consen 17 VTTKNGSVYEGIF 29 (77)
T ss_dssp EEETTS-EEEEEE
T ss_pred EEECCCCEEEEEE
Confidence 4555666666655
No 14
>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=57.80 E-value=29 Score=21.38 Aligned_cols=31 Identities=16% Similarity=0.218 Sum_probs=21.0
Q ss_pred eEEEcCCCCEEEEEEecCCeEeeeEEEEcCCC
Q psy5667 16 GSFKYDDGTLYIGDWNERGQKHGMGHMKLPDH 47 (79)
Q Consensus 16 G~~~~~~g~~Y~G~~~~~~~~~G~G~~~~~~G 47 (79)
+.+.+.||.++.|.+ ......-.|.+++..+
T Consensus 3 a~LvLeDG~~f~G~~-~G~~~~~~GEvVFnT~ 33 (131)
T PF00988_consen 3 AYLVLEDGTVFEGKS-FGAPGTVTGEVVFNTG 33 (131)
T ss_dssp EEEEETTS-EEEEEE--SBSEEEEEEEEEE--
T ss_pred EEEEECCCCEEEEEE-ecCCCcEEEEEEEEcc
Confidence 567888888888888 6766677777777643
No 15
>PF14977 FAM194: FAM194 protein
Probab=53.94 E-value=40 Score=22.38 Aligned_cols=54 Identities=24% Similarity=0.306 Sum_probs=33.0
Q ss_pred eeeEEEcCCCCEEEEEEecCCeEeeeEEEEcCCCC--EEEEEEeCCeEEeeEEEEecCCCE
Q psy5667 14 QHGSFKYDDGTLYIGDWNERGQKHGMGHMKLPDHT--RYDGTFHNGLCSGLGVMRFPDGAN 72 (79)
Q Consensus 14 g~G~~~~~~g~~Y~G~~~~~~~~~G~G~~~~~~G~--~y~G~f~~~~~~G~G~~~~~~G~~ 72 (79)
|-|...||+|.+=.-.. .. .+.+.-.+++.|.. ...+.|.. +|+|++++++|+.
T Consensus 24 Gsg~i~YPSGnlAi~~~-~~-~~~~~~~~v~eD~~~~~ilA~Fd~---~G~g~~y~~~g~~ 79 (208)
T PF14977_consen 24 GSGQIFYPSGNLAICIS-PT-CRGGFTYIVYEDSPENTILALFDS---SGHGTCYHPNGNI 79 (208)
T ss_pred CCEEEEeCCCCEEEEEe-cc-CCCceEEEEEecCCCCceEEEEcC---CCCEEEEcCCCCE
Confidence 56777888887755544 33 44445555555543 24455443 4788888888863
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=39.80 E-value=97 Score=19.54 Aligned_cols=32 Identities=25% Similarity=0.554 Sum_probs=20.7
Q ss_pred EEEEEec-CCeEeeeEEEEcCC-CCEEEEEEeCCe
Q psy5667 26 YIGDWNE-RGQKHGMGHMKLPD-HTRYDGTFHNGL 58 (79)
Q Consensus 26 Y~G~~~~-~~~~~G~G~~~~~~-G~~y~G~f~~~~ 58 (79)
|+|.. - ....++.+++-|.+ -.+|++.|.++.
T Consensus 53 ~~g~~-~~g~~~~~~~~lGYD~~~~~yvgtWidSM 86 (159)
T PF07617_consen 53 YEGSM-PGGGPFEGIGTLGYDPAKKKYVGTWIDSM 86 (159)
T ss_pred EEeec-CCCCceEEEEEEEECCccCeEEEEEeccC
Confidence 55555 4 44567777776665 457888887773
No 17
>CHL00197 carA carbamoyl-phosphate synthase arginine-specific small subunit; Provisional
Probab=28.54 E-value=1.3e+02 Score=21.78 Aligned_cols=33 Identities=18% Similarity=0.181 Sum_probs=25.7
Q ss_pred eeeEEEcCCCCEEEEEEecCCeEeeeEEEEcCCC
Q psy5667 14 QHGSFKYDDGTLYIGDWNERGQKHGMGHMKLPDH 47 (79)
Q Consensus 14 g~G~~~~~~g~~Y~G~~~~~~~~~G~G~~~~~~G 47 (79)
-.+.+.+.||.+|+|.. ......-.|.+++..+
T Consensus 5 ~~~~L~LedG~~~~G~~-~G~~~~~~GEvvF~T~ 37 (382)
T CHL00197 5 IPAILVLEDGTYYRGWS-FSNPITTIGEVVFNTG 37 (382)
T ss_pred CcEEEEECCCCEEEEEe-CCCCccEEEEEEEeCC
Confidence 35788999999999988 6655667788887754
No 18
>TIGR01368 CPSaseIIsmall carbamoyl-phosphate synthase, small subunit. This model represents the whole of the small chain of the glutamine-dependent form (EC 6.3.5.5) of carbamoyl phosphate synthase, CPSase II. The C-terminal domain has glutamine amidotransferase activity. Note that the sequence from the mammalian urea cycle form has lost the active site Cys, resulting in an ammonia-dependent form, CPSase I (EC 6.3.4.16). CPSases of pyrimidine biosynthesis, arginine biosynthesis, and the urea cycle may be encoded by one or by several genes, depending on the species.
Probab=28.09 E-value=1.2e+02 Score=21.67 Aligned_cols=30 Identities=17% Similarity=0.206 Sum_probs=22.8
Q ss_pred EEEcCCCCEEEEEEecCCeEeeeEEEEcCCC
Q psy5667 17 SFKYDDGTLYIGDWNERGQKHGMGHMKLPDH 47 (79)
Q Consensus 17 ~~~~~~g~~Y~G~~~~~~~~~G~G~~~~~~G 47 (79)
.+.+.||++|.|.. ......-.|.+++..+
T Consensus 2 ~L~LedG~~~~G~~-~g~~~~~~GEvvF~T~ 31 (358)
T TIGR01368 2 YLVLEDGTVFRGYS-FGAEGTVAGEVVFNTG 31 (358)
T ss_pred EEEECCCCEEEEEe-cCCCccEEEEEEEeCC
Confidence 57889999999988 6655566778877754
No 19
>PRK12564 carbamoyl phosphate synthase small subunit; Reviewed
Probab=27.88 E-value=1.3e+02 Score=21.47 Aligned_cols=32 Identities=16% Similarity=0.299 Sum_probs=24.3
Q ss_pred eeEEEcCCCCEEEEEEecCCeEeeeEEEEcCCC
Q psy5667 15 HGSFKYDDGTLYIGDWNERGQKHGMGHMKLPDH 47 (79)
Q Consensus 15 ~G~~~~~~g~~Y~G~~~~~~~~~G~G~~~~~~G 47 (79)
.+.+.+.||.+|.|.. ......-.|.+++..+
T Consensus 4 ~~~L~LedG~~~~G~~-~g~~~~~~GE~vF~T~ 35 (360)
T PRK12564 4 KAYLVLEDGTVFEGKA-FGAEGETVGEVVFNTS 35 (360)
T ss_pred cEEEEECCCCEEEEEe-cCCCccEEEEEEEECC
Confidence 4678899999999988 6655566778877754
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=24.12 E-value=53 Score=15.46 Aligned_cols=7 Identities=14% Similarity=0.757 Sum_probs=3.1
Q ss_pred CEEEEEE
Q psy5667 48 TRYDGTF 54 (79)
Q Consensus 48 ~~y~G~f 54 (79)
..|+|+|
T Consensus 18 ~vf~G~~ 24 (35)
T PF10419_consen 18 QVFEGEW 24 (35)
T ss_pred EEEEEEE
Confidence 3444444
No 21
>PF07661 MORN_2: MORN repeat variant; InterPro: IPR011652 This entry represents an apparent variant of the IPR003409 from INTERPRO repeat.
Probab=24.03 E-value=64 Score=12.56 Aligned_cols=7 Identities=0% Similarity=0.021 Sum_probs=2.8
Q ss_pred EEEcCCC
Q psy5667 41 HMKLPDH 47 (79)
Q Consensus 41 ~~~~~~G 47 (79)
+..+++|
T Consensus 6 ~~yy~nG 12 (22)
T PF07661_consen 6 KFYYENG 12 (22)
T ss_pred EEEeCCC
Confidence 3334444
No 22
>PRK12838 carbamoyl phosphate synthase small subunit; Reviewed
Probab=23.07 E-value=1.9e+02 Score=20.67 Aligned_cols=32 Identities=16% Similarity=0.282 Sum_probs=23.5
Q ss_pred eeEEEcCCCCEEEEEEecCCeEeeeEEEEcCCC
Q psy5667 15 HGSFKYDDGTLYIGDWNERGQKHGMGHMKLPDH 47 (79)
Q Consensus 15 ~G~~~~~~g~~Y~G~~~~~~~~~G~G~~~~~~G 47 (79)
.+.+.+.||.+|.|.. ......-.|.+++..+
T Consensus 2 ~~~l~LedG~~~~g~~-~g~~~~~~GE~vf~T~ 33 (354)
T PRK12838 2 KAYLILEDGTVFEGEL-IGAPIDVTGEIVFNTG 33 (354)
T ss_pred CeEEEeCCCCEEEEEE-CCCCCcEEEEEEEeCC
Confidence 3578899999999987 5655556677777653
No 23
>PLN02771 carbamoyl-phosphate synthase (glutamine-hydrolyzing)
Probab=22.61 E-value=2e+02 Score=21.20 Aligned_cols=32 Identities=9% Similarity=0.232 Sum_probs=21.7
Q ss_pred eeEEEcCCCCEEEEEEecCCeEeeeEEEEcCCC
Q psy5667 15 HGSFKYDDGTLYIGDWNERGQKHGMGHMKLPDH 47 (79)
Q Consensus 15 ~G~~~~~~g~~Y~G~~~~~~~~~G~G~~~~~~G 47 (79)
.+.+.+.||.+|.|.. ......-.|.+++..+
T Consensus 56 ~a~LvLedGt~f~G~~-fG~~~~~~GEvVFnT~ 87 (415)
T PLN02771 56 DARLVLEDGSVWKAKS-FGARGTQVGEVVFNTS 87 (415)
T ss_pred CEEEEECCCCEEEEEE-cCCCCcEEEEEEEeCC
Confidence 4677888888888877 5544555566766643
No 24
>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=21.72 E-value=1.1e+02 Score=20.57 Aligned_cols=26 Identities=35% Similarity=0.678 Sum_probs=19.8
Q ss_pred CCCEEEEEEecCCeEeeeEEEEcCCCC
Q psy5667 22 DGTLYIGDWNERGQKHGMGHMKLPDHT 48 (79)
Q Consensus 22 ~g~~Y~G~~~~~~~~~G~G~~~~~~G~ 48 (79)
++..-.|-| +++...|-|+++|-+..
T Consensus 5 ~~~ykiGlw-VRD~~aGiGTlTf~dp~ 30 (218)
T PF05580_consen 5 DGRYKIGLW-VRDSTAGIGTLTFYDPE 30 (218)
T ss_pred CCcEEEEEE-EEeCCcCeEEEEEEECC
Confidence 455556888 78888888888888753
Done!