Query psy7991
Match_columns 81
No_of_seqs 225 out of 1011
Neff 7.9
Searched_HMMs 46136
Date Sat Aug 17 00:00:47 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy7991.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/7991hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03185 phosphatidylinositol 99.8 4E-20 8.6E-25 139.0 11.0 74 7-81 15-88 (765)
2 PLN03185 phosphatidylinositol 99.8 1.2E-19 2.5E-24 136.5 10.1 71 10-81 110-180 (765)
3 KOG0231|consensus 99.6 8.5E-16 1.8E-20 110.9 6.4 69 11-80 130-198 (455)
4 COG4642 Uncharacterized protei 99.6 7.2E-15 1.6E-19 90.9 5.4 67 13-80 44-110 (139)
5 COG4642 Uncharacterized protei 99.5 5.6E-14 1.2E-18 86.9 7.4 76 5-81 58-134 (139)
6 KOG0231|consensus 99.3 1.5E-12 3.4E-17 94.1 4.7 73 6-79 148-234 (455)
7 smart00698 MORN Possible plasm 98.6 1.1E-07 2.4E-12 43.6 3.9 22 49-70 2-23 (26)
8 PF02493 MORN: MORN repeat; I 98.6 5.4E-08 1.2E-12 43.1 2.8 22 50-71 1-22 (23)
9 smart00698 MORN Possible plasm 98.5 1.8E-07 3.9E-12 42.9 3.6 24 24-48 1-24 (26)
10 PF02493 MORN: MORN repeat; I 98.5 1.4E-07 3E-12 41.7 2.6 23 26-49 1-23 (23)
11 COG2849 Uncharacterized protei 94.2 0.51 1.1E-05 31.6 7.6 51 19-70 116-168 (230)
12 COG2849 Uncharacterized protei 92.7 1.6 3.5E-05 29.2 8.2 60 21-81 94-156 (230)
13 PF14438 SM-ATX: Ataxin 2 SM d 64.7 9.5 0.00021 20.9 2.7 14 65-78 17-30 (77)
14 PF00988 CPSase_sm_chain: Carb 52.3 51 0.0011 20.5 4.6 28 16-44 3-30 (131)
15 PF07617 DUF1579: Protein of u 48.1 68 0.0015 20.4 4.8 35 25-60 52-88 (159)
16 PF10419 TFIIIC_sub6: TFIIIC s 40.8 20 0.00044 17.1 1.2 10 70-79 17-26 (35)
17 PF07661 MORN_2: MORN repeat v 40.3 30 0.00064 13.8 2.9 11 38-48 3-13 (22)
18 PF05580 Peptidase_S55: SpoIVB 36.2 44 0.00096 22.6 2.7 24 23-47 6-29 (218)
19 PF12915 DUF3833: Protein of u 34.3 1.3E+02 0.0028 19.4 7.3 42 33-74 30-78 (164)
20 TIGR02331 rib_alpha Rib/alpha/ 27.2 92 0.002 17.7 2.7 15 57-71 42-56 (80)
21 TIGR02601 autotrns_rpt autotra 24.4 66 0.0014 14.9 1.5 18 59-76 4-21 (32)
22 CHL00197 carA carbamoyl-phosph 21.3 2.2E+02 0.0049 20.7 4.3 32 15-47 6-37 (382)
23 PF12988 DUF3872: Domain of un 20.2 65 0.0014 20.3 1.2 15 59-73 74-88 (137)
24 PRK12564 carbamoyl phosphate s 20.1 2.5E+02 0.0054 20.2 4.3 32 15-47 4-35 (360)
No 1
>PLN03185 phosphatidylinositol phosphate kinase; Provisional
Probab=99.83 E-value=4e-20 Score=139.00 Aligned_cols=74 Identities=27% Similarity=0.491 Sum_probs=67.4
Q ss_pred eEeCCeEEeEEEEcCCCCEEEEEEecCCeEEeeEEEEcCCCCEEEEEEeCCeEEeeEEEEecCCCEEEEEEcCCC
Q psy7991 7 EEYPGVVQHGSFKYDDGTLYIGDWNERGQKHGMGHMKLPDHTRYDGTFHNGLCSGLGVMRFPDGAKAEMSSDEVR 81 (81)
Q Consensus 7 ~~~~~~~g~G~~~~~~g~~Y~G~~~~~~~~~G~G~~~~~~G~~y~G~~~~g~~~G~G~~~~~~G~~y~G~w~~Gr 81 (81)
...+.++|.|++.|+||.+|+|+| +++++||.|+++|++|.+|+|+|.++++||.|+++++++.+|+|.|++|+
T Consensus 15 ~~~g~~hG~G~~~~~DG~~YeGew-~~Gk~hG~G~~~~~nG~~YeGeF~nG~~hG~G~~~~~~G~~YeG~w~~gk 88 (765)
T PLN03185 15 LLGNVPEGPGKYLWSDGCMYEGEW-RRGMRHGNGKISWPSGATYEGEFSGGYMHGSGTYTGTDGTTYKGRWRLNL 88 (765)
T ss_pred EECCccccceEEEECCCCEEEEEE-ECCEeeCcEeEEeCCCCEEEEEEECCEEeceEEEEecCCCEEEEEEeCCc
Confidence 344557899999999999999999 89999999999999999999999999999999999999999999999875
No 2
>PLN03185 phosphatidylinositol phosphate kinase; Provisional
Probab=99.82 E-value=1.2e-19 Score=136.49 Aligned_cols=71 Identities=23% Similarity=0.469 Sum_probs=64.7
Q ss_pred CCeEEeEEEEcCCCCEEEEEEecCCeEEeeEEEEcCCCCEEEEEEeCCeEEeeEEEEecCCCEEEEEEcCCC
Q psy7991 10 PGVVQHGSFKYDDGTLYIGDWNERGQKHGMGHMKLPDHTRYDGTFHNGLCSGLGVMRFPDGAKAEMSSDEVR 81 (81)
Q Consensus 10 ~~~~g~G~~~~~~g~~Y~G~~~~~~~~~G~G~~~~~~G~~y~G~~~~g~~~G~G~~~~~~G~~y~G~w~~Gr 81 (81)
+.++|.|++.|+||.+|+|+| +++++||.|+++|+||++|+|+|.++++||.|+++|+||.+|+|.|++|+
T Consensus 110 G~~~G~G~y~~~nG~~Y~Gef-k~Gk~~G~G~l~~~nG~~YeG~w~nG~~hG~G~y~~~DG~~Y~G~W~~G~ 180 (765)
T PLN03185 110 GLQEGPGKYTWANGNVYLGDM-KGGKMSGKGTLTWVSGDSYEGQWLDGMMHGFGVYTWSDGGCYVGTWTRGL 180 (765)
T ss_pred CceecceeeeccCCCeEEEEe-cCCEEecCEEEEEeCCCeEEEEEeCCcceeeEEEEECCCCEEEEEeeCCc
Confidence 446789999999999999999 89999999999999999999999999999999999999999999998874
No 3
>KOG0231|consensus
Probab=99.62 E-value=8.5e-16 Score=110.87 Aligned_cols=69 Identities=29% Similarity=0.566 Sum_probs=66.5
Q ss_pred CeEEeEEEEcCCCCEEEEEEecCCeEEeeEEEEcCCCCEEEEEEeCCeEEeeEEEEecCCCEEEEEEcCC
Q psy7991 11 GVVQHGSFKYDDGTLYIGDWNERGQKHGMGHMKLPDHTRYDGTFHNGLCSGLGVMRFPDGAKAEMSSDEV 80 (81)
Q Consensus 11 ~~~g~G~~~~~~g~~Y~G~~~~~~~~~G~G~~~~~~G~~y~G~~~~g~~~G~G~~~~~~G~~y~G~w~~G 80 (81)
-+.+.++..++++++|+|+| .+++++|.|++.+++|..|+|+|.++++||+|++++|+|++|+|.|+++
T Consensus 130 ~~~g~g~~~~~~g~~Y~G~~-~~~k~sG~Gv~~~~~G~~Y~Gew~~n~~hG~G~~~~pdGsk~eg~~~~~ 198 (455)
T KOG0231|consen 130 TRSGEGVIELPTGDTYEGEF-KRGKRSGFGVYIRSDGLKYEGEWLDNRRHGYGVLTFPDGSKYEGQYKNN 198 (455)
T ss_pred ccCccceEecCCCCEEEeee-cCCcccccceEEecCCCEeeceecCCCccCCCeEEccCCCEEEEEeecc
Confidence 36789999999999999999 8999999999999999999999999999999999999999999999986
No 4
>COG4642 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=99.56 E-value=7.2e-15 Score=90.85 Aligned_cols=67 Identities=28% Similarity=0.482 Sum_probs=48.1
Q ss_pred EEeEEEEcCCCCEEEEEEecCCeEEeeEEEEcCCCCEEEEEEeCCeEEeeEEEEecCCCEEEEEEcCC
Q psy7991 13 VQHGSFKYDDGTLYIGDWNERGQKHGMGHMKLPDHTRYDGTFHNGLCSGLGVMRFPDGAKAEMSSDEV 80 (81)
Q Consensus 13 ~g~G~~~~~~g~~Y~G~~~~~~~~~G~G~~~~~~G~~y~G~~~~g~~~G~G~~~~~~G~~y~G~w~~G 80 (81)
.|.|++.+.+|..|+|.+ +|++++|.|+++++++++|+|.|++++.+|.|++...+|.+|+|.|.+|
T Consensus 44 ~Gkgs~~~~~G~~Y~Gtl-~ngk~nGqG~~~~~ngd~Y~g~F~s~~F~g~G~~~~~~Gw~~~G~F~~G 110 (139)
T COG4642 44 AGKGSLKYDNGRIYTGTL-KNGKMNGQGTYTFANGDIYEGPFNSGKFRGQGTRGSFNGWLYIGRFTEG 110 (139)
T ss_pred CCCccEEEcCCccccceE-EcCcccCcEEEEecCCCeEeccccCccccceEeeccccCCEEeeeeccc
Confidence 356777777777777777 6777777777777777777777777777777777777777777777665
No 5
>COG4642 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=99.53 E-value=5.6e-14 Score=86.92 Aligned_cols=76 Identities=22% Similarity=0.374 Sum_probs=69.7
Q ss_pred CeeEeCC-eEEeEEEEcCCCCEEEEEEecCCeEEeeEEEEcCCCCEEEEEEeCCeEEeeEEEEecCCCEEEEEEcCCC
Q psy7991 5 DEEEYPG-VVQHGSFKYDDGTLYIGDWNERGQKHGMGHMKLPDHTRYDGTFHNGLCSGLGVMRFPDGAKAEMSSDEVR 81 (81)
Q Consensus 5 ~~~~~~~-~~g~G~~~~~~g~~Y~G~~~~~~~~~G~G~~~~~~G~~y~G~~~~g~~~G~G~~~~~~G~~y~G~w~~Gr 81 (81)
+..+.|+ ..|.|++.++++++|+|+| .+++.+|.|++...+|..|+|.|.+++..|.|.+...++++|+|.++.||
T Consensus 58 ~Gtl~ngk~nGqG~~~~~ngd~Y~g~F-~s~~F~g~G~~~~~~Gw~~~G~F~~Gq~~g~g~l~~~~g~vy~G~fk~g~ 134 (139)
T COG4642 58 TGTLKNGKMNGQGTYTFANGDIYEGPF-NSGKFRGQGTRGSFNGWLYIGRFTEGQANGKGFLLKEDGSVYTGMFKQGR 134 (139)
T ss_pred cceEEcCcccCcEEEEecCCCeEeccc-cCccccceEeeccccCCEEeeeecccccCCceeEEecCCcEEeeeEEeee
Confidence 3444444 4589999999999999999 89999999999999999999999999999999999999999999999986
No 6
>KOG0231|consensus
Probab=99.33 E-value=1.5e-12 Score=94.08 Aligned_cols=73 Identities=29% Similarity=0.537 Sum_probs=66.8
Q ss_pred eeEeCCeEEeEEEEcCCCCEEEEEEecCCeEEeeEEEEcCCCCEEEEEEeCC----eEEeeEEEEecC----------CC
Q psy7991 6 EEEYPGVVQHGSFKYDDGTLYIGDWNERGQKHGMGHMKLPDHTRYDGTFHNG----LCSGLGVMRFPD----------GA 71 (81)
Q Consensus 6 ~~~~~~~~g~G~~~~~~g~~Y~G~~~~~~~~~G~G~~~~~~G~~y~G~~~~g----~~~G~G~~~~~~----------G~ 71 (81)
+.....++|.|++.+++|..|+|+| .++++||+|++++|+|.+|+|+|+++ .+||.+.+.+.+ ..
T Consensus 148 ~~~~~k~sG~Gv~~~~~G~~Y~Gew-~~n~~hG~G~~~~pdGsk~eg~~~~~~l~~l~~gk~~~~~~~~~~~a~ra~~~~ 226 (455)
T KOG0231|consen 148 EFKRGKRSGFGVYIRSDGLKYEGEW-LDNRRHGYGVLTFPDGSKYEGQYKNNILEALRHGKGRYKFDDALEAAQRAATIA 226 (455)
T ss_pred eecCCcccccceEEecCCCEeecee-cCCCccCCCeEEccCCCEEEEEeecccccccccceEEEEEeccchhhhhhhhhh
Confidence 4455678899999999999999999 99999999999999999999999999 899999999985 67
Q ss_pred EEEEEEcC
Q psy7991 72 KAEMSSDE 79 (81)
Q Consensus 72 ~y~G~w~~ 79 (81)
+|.++|.+
T Consensus 227 ~~~~Ew~~ 234 (455)
T KOG0231|consen 227 RYSGEWAA 234 (455)
T ss_pred hhhhhhhh
Confidence 88888865
No 7
>smart00698 MORN Possible plasma membrane-binding motif in junctophilins, PIP-5-kinases and protein kinases.
Probab=98.60 E-value=1.1e-07 Score=43.60 Aligned_cols=22 Identities=36% Similarity=0.797 Sum_probs=15.8
Q ss_pred EEEEEEeCCeEEeeEEEEecCC
Q psy7991 49 RYDGTFHNGLCSGLGVMRFPDG 70 (81)
Q Consensus 49 ~y~G~~~~g~~~G~G~~~~~~G 70 (81)
+|+|+|+++++||.|+++++|.
T Consensus 2 ~Y~G~w~~g~~hG~G~~~~~d~ 23 (26)
T smart00698 2 RYEGEWRNGKRHGRGVYTYANX 23 (26)
T ss_pred eEEEEEECCeEEeeEEEEeccc
Confidence 5777777777777777777653
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=98.60 E-value=5.4e-08 Score=43.08 Aligned_cols=22 Identities=50% Similarity=1.034 Sum_probs=11.4
Q ss_pred EEEEEeCCeEEeeEEEEecCCC
Q psy7991 50 YDGTFHNGLCSGLGVMRFPDGA 71 (81)
Q Consensus 50 y~G~~~~g~~~G~G~~~~~~G~ 71 (81)
|+|+|+++++||.|+++++||+
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 4555555555555555555554
No 9
>smart00698 MORN Possible plasma membrane-binding motif in junctophilins, PIP-5-kinases and protein kinases.
Probab=98.54 E-value=1.8e-07 Score=42.86 Aligned_cols=24 Identities=29% Similarity=0.714 Sum_probs=21.3
Q ss_pred CEEEEEEecCCeEEeeEEEEcCCCC
Q psy7991 24 TLYIGDWNERGQKHGMGHMKLPDHT 48 (81)
Q Consensus 24 ~~Y~G~~~~~~~~~G~G~~~~~~G~ 48 (81)
++|+|+| +++++||.|+++++|..
T Consensus 1 ~~Y~G~w-~~g~~hG~G~~~~~d~~ 24 (26)
T smart00698 1 DRYEGEW-RNGKRHGRGVYTYANXX 24 (26)
T ss_pred CeEEEEE-ECCeEEeeEEEEecccc
Confidence 4699999 99999999999998753
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=98.49 E-value=1.4e-07 Score=41.75 Aligned_cols=23 Identities=48% Similarity=1.099 Sum_probs=19.8
Q ss_pred EEEEEecCCeEEeeEEEEcCCCCE
Q psy7991 26 YIGDWNERGQKHGMGHMKLPDHTR 49 (81)
Q Consensus 26 Y~G~~~~~~~~~G~G~~~~~~G~~ 49 (81)
|+|+| +++++||.|++.++||++
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 89999 899999999999999974
No 11
>COG2849 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=94.21 E-value=0.51 Score=31.64 Aligned_cols=51 Identities=20% Similarity=0.467 Sum_probs=24.3
Q ss_pred EcCCCCEEE-EEEecCCeEEeeEEEEcCCCC-EEEEEEeCCeEEeeEEEEecCC
Q psy7991 19 KYDDGTLYI-GDWNERGQKHGMGHMKLPDHT-RYDGTFHNGLCSGLGVMRFPDG 70 (81)
Q Consensus 19 ~~~~g~~Y~-G~~~~~~~~~G~G~~~~~~G~-~y~G~~~~g~~~G~G~~~~~~G 70 (81)
.+++|...+ -.+ .+++.||.-...+++|. .++..|+++.++|.-...+++|
T Consensus 116 ~y~nGk~~~~~~~-~ng~~~G~~~~yy~nG~~~~e~~~kn~~~~g~~k~yy~nG 168 (230)
T COG2849 116 FYENGKLKSEYNY-KNGKLHGIQKEYYENGKLKSETVYKNGKLEGIAKTYYENG 168 (230)
T ss_pred EEcCCcEeEEEEe-cCCcccceEEEEEcCCCEEEEEEEeCCCccccEEEEcCCC
Confidence 344444333 233 45555555555555543 2355555554444444445544
No 12
>COG2849 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=92.74 E-value=1.6 Score=29.19 Aligned_cols=60 Identities=15% Similarity=0.212 Sum_probs=48.3
Q ss_pred CCCC-EEEEEEecCCeEEeeEEEEcCCCCEE-EEEEeCCeEEeeEEEEecCCC-EEEEEEcCCC
Q psy7991 21 DDGT-LYIGDWNERGQKHGMGHMKLPDHTRY-DGTFHNGLCSGLGVMRFPDGA-KAEMSSDEVR 81 (81)
Q Consensus 21 ~~g~-~Y~G~~~~~~~~~G~G~~~~~~G~~y-~G~~~~g~~~G~G~~~~~~G~-~y~G~w~~Gr 81 (81)
++|. ...-.+ ++++++|.-...+++|... +-.|++++.||.-...+++|. .++..|+++.
T Consensus 94 ~ng~~~~~~~~-kNG~~~g~~~~~y~nGk~~~~~~~~ng~~~G~~~~yy~nG~~~~e~~~kn~~ 156 (230)
T COG2849 94 ENGELEAAIYY-KNGKLDGETKEFYENGKLKSEYNYKNGKLHGIQKEYYENGKLKSETVYKNGK 156 (230)
T ss_pred cCCeEEEEEEe-cCCceeeeEEEEEcCCcEeEEEEecCCcccceEEEEEcCCCEEEEEEEeCCC
Confidence 3443 345567 8999999999999999765 557999999999999999986 6688888763
No 13
>PF14438 SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1.
Probab=64.66 E-value=9.5 Score=20.94 Aligned_cols=14 Identities=14% Similarity=0.014 Sum_probs=7.5
Q ss_pred EEecCCCEEEEEEc
Q psy7991 65 MRFPDGAKAEMSSD 78 (81)
Q Consensus 65 ~~~~~G~~y~G~w~ 78 (81)
.+..||++|+|.|.
T Consensus 17 V~~~~G~~yeGif~ 30 (77)
T PF14438_consen 17 VTTKNGSVYEGIFH 30 (77)
T ss_dssp EEETTS-EEEEEEE
T ss_pred EEECCCCEEEEEEE
Confidence 45556666666553
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=52.34 E-value=51 Score=20.50 Aligned_cols=28 Identities=18% Similarity=0.268 Sum_probs=14.7
Q ss_pred EEEEcCCCCEEEEEEecCCeEEeeEEEEc
Q psy7991 16 GSFKYDDGTLYIGDWNERGQKHGMGHMKL 44 (81)
Q Consensus 16 G~~~~~~g~~Y~G~~~~~~~~~G~G~~~~ 44 (81)
+.+.+.||.+|+|.. ......-.|.+.|
T Consensus 3 a~LvLeDG~~f~G~~-~G~~~~~~GEvVF 30 (131)
T PF00988_consen 3 AYLVLEDGTVFEGKS-FGAPGTVTGEVVF 30 (131)
T ss_dssp EEEEETTS-EEEEEE--SBSEEEEEEEEE
T ss_pred EEEEECCCCEEEEEE-ecCCCcEEEEEEE
Confidence 455666666666666 4444444555444
No 15
>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=48.10 E-value=68 Score=20.40 Aligned_cols=35 Identities=23% Similarity=0.479 Sum_probs=26.0
Q ss_pred EEEEEEec-CCeEEeeEEEEcC-CCCEEEEEEeCCeEE
Q psy7991 25 LYIGDWNE-RGQKHGMGHMKLP-DHTRYDGTFHNGLCS 60 (81)
Q Consensus 25 ~Y~G~~~~-~~~~~G~G~~~~~-~G~~y~G~~~~g~~~ 60 (81)
.|+|.+ . ....++.+++-+. .-.+|++.|.+.+..
T Consensus 52 e~~g~~-~~g~~~~~~~~lGYD~~~~~yvgtWidSM~t 88 (159)
T PF07617_consen 52 EYEGSM-PGGGPFEGIGTLGYDPAKKKYVGTWIDSMGT 88 (159)
T ss_pred EEEeec-CCCCceEEEEEEEECCccCeEEEEEeccCCC
Confidence 477777 6 5567888888764 467899999998544
No 16
>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=40.84 E-value=20 Score=17.08 Aligned_cols=10 Identities=10% Similarity=-0.044 Sum_probs=5.5
Q ss_pred CCEEEEEEcC
Q psy7991 70 GAKAEMSSDE 79 (81)
Q Consensus 70 G~~y~G~w~~ 79 (81)
+.+|+|.|.+
T Consensus 17 ~~vf~G~~~~ 26 (35)
T PF10419_consen 17 NQVFEGEWED 26 (35)
T ss_pred CEEEEEEEhh
Confidence 4556666643
No 17
>PF07661 MORN_2: MORN repeat variant; InterPro: IPR011652 This entry represents an apparent variant of the IPR003409 from INTERPRO repeat.
Probab=40.27 E-value=30 Score=13.76 Aligned_cols=11 Identities=9% Similarity=0.036 Sum_probs=4.4
Q ss_pred eeEEEEcCCCC
Q psy7991 38 GMGHMKLPDHT 48 (81)
Q Consensus 38 G~G~~~~~~G~ 48 (81)
|.-+..+++|.
T Consensus 3 G~~~~yy~nG~ 13 (22)
T PF07661_consen 3 GEWKFYYENGK 13 (22)
T ss_pred ceEEEEeCCCC
Confidence 33334444443
No 18
>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=36.20 E-value=44 Score=22.60 Aligned_cols=24 Identities=33% Similarity=0.671 Sum_probs=12.0
Q ss_pred CCEEEEEEecCCeEEeeEEEEcCCC
Q psy7991 23 GTLYIGDWNERGQKHGMGHMKLPDH 47 (81)
Q Consensus 23 g~~Y~G~~~~~~~~~G~G~~~~~~G 47 (81)
+..-.|-| ..+.-.|-|+++|-+.
T Consensus 6 ~~ykiGlw-VRD~~aGiGTlTf~dp 29 (218)
T PF05580_consen 6 GRYKIGLW-VRDSTAGIGTLTFYDP 29 (218)
T ss_pred CcEEEEEE-EEeCCcCeEEEEEEEC
Confidence 33344555 4555555555555543
No 19
>PF12915 DUF3833: Protein of unknown function (DUF3833); InterPro: IPR024409 This is a family of uncharacterised proteins found in Proteobacteria.
Probab=34.25 E-value=1.3e+02 Score=19.40 Aligned_cols=42 Identities=14% Similarity=0.181 Sum_probs=20.0
Q ss_pred CCeEEeeEEEEcCCCCE-------EEEEEeCCeEEeeEEEEecCCCEEE
Q psy7991 33 RGQKHGMGHMKLPDHTR-------YDGTFHNGLCSGLGVMRFPDGAKAE 74 (81)
Q Consensus 33 ~~~~~G~G~~~~~~G~~-------y~G~~~~g~~~G~G~~~~~~G~~y~ 74 (81)
+|+..-+|++.-+.|.. .+|.|..+...=.-.+.|.||++-.
T Consensus 30 ~G~~~A~G~~~dr~G~v~rrF~v~i~g~w~g~~~tL~E~F~y~DGe~q~ 78 (164)
T PF12915_consen 30 NGKLVAWGMFQDRSGKVTRRFTVDIDGSWDGNTGTLDEDFVYDDGETQT 78 (164)
T ss_pred CCcEEEEEEEECCCCCEEEEEEEEEEEEEECCEEEEEEEEEECCCCEEE
Confidence 44445555555555431 3455555544444445555555433
No 20
>TIGR02331 rib_alpha Rib/alpha/Esp surface antigen repeat. Sequences in this family are tandem repeats of about 79 amino acids, present in up to 14 copies in a protein and highly identical, even at the DNA level, within each protein. Sequences with these repeats are found in the Rib and alpha surface antigens of group B Streptococcus, Esp of Enterococcus faecalis, and related proteins of Lactobacillus. The repeat lacks Cys residues. Most members of this protein family also have the cell wall anchor motif LPXTG shared by many staphyloccal and streptococcal surface antigens.
Probab=27.19 E-value=92 Score=17.67 Aligned_cols=15 Identities=33% Similarity=0.636 Sum_probs=7.8
Q ss_pred CeEEeeEEEEecCCC
Q psy7991 57 GLCSGLGVMRFPDGA 71 (81)
Q Consensus 57 g~~~G~G~~~~~~G~ 71 (81)
+...+.-+.+|+||+
T Consensus 42 G~~~~~V~VtyPDGS 56 (80)
T TIGR02331 42 GDKPAVVVVTYPDGT 56 (80)
T ss_pred CcccceEEEecCCCC
Confidence 334455555556554
No 21
>TIGR02601 autotrns_rpt autotransporter-associated beta strand repeat. This model represent a core 32-residue region of a class of bacterial protein repeat found in one to 30 copies per protein. Most proteins with a copy of this repeat have domains associated with membrane autotransporters (pfam03797, TIGR01414). The repeats occur with a periodicity of 60 to 100 residues. A pattern of sequence conservation is that every second residue is well-conserved across most of the domain. Pfam model pfam05594 is based on a longer, much more poorly conserved multiple sequence alignment and hits some of the same proteins as this model with some overlap between the hit regions of the two models. It describes these repeats as likely to have a beta-helical structure.
Probab=24.35 E-value=66 Score=14.85 Aligned_cols=18 Identities=11% Similarity=0.195 Sum_probs=9.9
Q ss_pred EEeeEEEEecCCCEEEEE
Q psy7991 59 CSGLGVMRFPDGAKAEMS 76 (81)
Q Consensus 59 ~~G~G~~~~~~G~~y~G~ 76 (81)
+.|.|+++++..+.|.|.
T Consensus 4 K~G~Gtl~Lsg~ntytG~ 21 (32)
T TIGR02601 4 KTGAGTLTLTGANTYTGG 21 (32)
T ss_pred EccceEEEEeCcccCCce
Confidence 445566666555555553
No 22
>CHL00197 carA carbamoyl-phosphate synthase arginine-specific small subunit; Provisional
Probab=21.33 E-value=2.2e+02 Score=20.73 Aligned_cols=32 Identities=19% Similarity=0.206 Sum_probs=21.1
Q ss_pred eEEEEcCCCCEEEEEEecCCeEEeeEEEEcCCC
Q psy7991 15 HGSFKYDDGTLYIGDWNERGQKHGMGHMKLPDH 47 (81)
Q Consensus 15 ~G~~~~~~g~~Y~G~~~~~~~~~G~G~~~~~~G 47 (81)
.+.+.+.||.+|+|.. ......-.|.+.|..+
T Consensus 6 ~~~L~LedG~~~~G~~-~G~~~~~~GEvvF~T~ 37 (382)
T CHL00197 6 PAILVLEDGTYYRGWS-FSNPITTIGEVVFNTG 37 (382)
T ss_pred cEEEEECCCCEEEEEe-CCCCccEEEEEEEeCC
Confidence 4677888888888887 4544455566665443
No 23
>PF12988 DUF3872: Domain of unknown function, B. Theta Gene description (DUF3872); InterPro: IPR024355 This entry represents proteins of unknown function found primarily in Bacteroides species. The Bacteroides thetaiotaomicron gene coding for this protein is located in a conjugate transposon and appears to be upregulated in the presence of host or other bacterial species compared to growth in pure culture [, ].; PDB: 2L3B_A 2L7Q_A.
Probab=20.18 E-value=65 Score=20.25 Aligned_cols=15 Identities=33% Similarity=0.576 Sum_probs=8.2
Q ss_pred EEeeEEEEecCCCEE
Q psy7991 59 CSGLGVMRFPDGAKA 73 (81)
Q Consensus 59 ~~G~G~~~~~~G~~y 73 (81)
++|.|++...||.++
T Consensus 74 ~dGkG~L~~~~g~~~ 88 (137)
T PF12988_consen 74 PDGKGTLRMDDGTVL 88 (137)
T ss_dssp SSS-EEEEETTS-EE
T ss_pred ecCCEEEEecCCcEe
Confidence 456777776666654
No 24
>PRK12564 carbamoyl phosphate synthase small subunit; Reviewed
Probab=20.11 E-value=2.5e+02 Score=20.25 Aligned_cols=32 Identities=16% Similarity=0.299 Sum_probs=21.1
Q ss_pred eEEEEcCCCCEEEEEEecCCeEEeeEEEEcCCC
Q psy7991 15 HGSFKYDDGTLYIGDWNERGQKHGMGHMKLPDH 47 (81)
Q Consensus 15 ~G~~~~~~g~~Y~G~~~~~~~~~G~G~~~~~~G 47 (81)
.+.+.+.||.+|+|.. ......-.|.+.|..+
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 4677888888888887 4544445566665443
Done!