Query 016357
Match_columns 391
No_of_seqs 168 out of 316
Neff 3.4
Searched_HMMs 46136
Date Fri Mar 29 06:07:42 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/016357.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/016357hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF05922 Inhibitor_I9: Peptida 99.2 1.4E-11 2.9E-16 95.0 4.6 77 107-187 1-81 (82)
2 KOG1924 RhoA GTPase effector D 98.4 6.9E-07 1.5E-11 97.1 9.3 14 47-60 286-299 (1102)
3 KOG1924 RhoA GTPase effector D 97.8 0.00014 3E-09 79.9 10.4 8 366-373 631-638 (1102)
4 KOG4849 mRNA cleavage factor I 91.0 2.7 5.9E-05 43.9 11.4 87 106-213 79-167 (498)
5 KOG4849 mRNA cleavage factor I 88.1 5.2 0.00011 41.9 10.9 12 158-169 163-174 (498)
6 KOG3671 Actin regulatory prote 87.8 4.9 0.00011 43.4 10.8 9 264-272 332-340 (569)
7 TIGR01628 PABP-1234 polyadenyl 79.6 74 0.0016 33.4 15.2 14 156-169 328-341 (562)
8 KOG1984 Vesicle coat complex C 61.9 28 0.00061 40.2 7.8 8 267-274 16-23 (1007)
9 KOG1984 Vesicle coat complex C 61.6 74 0.0016 37.0 10.9 6 265-270 8-13 (1007)
10 KOG2236 Uncharacterized conser 57.1 79 0.0017 34.2 9.7 11 104-114 219-229 (483)
11 KOG0132 RNA polymerase II C-te 54.8 68 0.0015 36.8 9.2 40 131-174 437-478 (894)
12 KOG0132 RNA polymerase II C-te 52.9 1.5E+02 0.0033 34.2 11.5 25 166-190 500-524 (894)
13 KOG4594 Sequence-specific sing 48.1 1.7E+02 0.0037 30.4 10.0 15 138-152 11-26 (354)
14 KOG4368 Predicted RNA binding 45.7 1.3E+02 0.0029 33.7 9.5 10 148-157 191-200 (757)
15 cd04901 ACT_3PGDH C-terminal A 41.8 37 0.0008 24.9 3.4 19 162-180 49-67 (69)
16 KOG3168 U1 snRNP component [Tr 33.8 1E+02 0.0023 29.4 5.7 8 124-131 33-40 (177)
17 cd04888 ACT_PheB-BS C-terminal 25.4 1.9E+02 0.0042 21.5 5.0 14 167-180 60-73 (76)
18 PHA03378 EBNA-3B; Provisional 21.6 8.3E+02 0.018 28.5 10.7 8 267-274 686-693 (991)
No 1
>PF05922 Inhibitor_I9: Peptidase inhibitor I9; InterPro: IPR010259 Peptide proteinase inhibitors can be found as single domain proteins or as single or multiple domains within proteins; these are referred to as either simple or compound inhibitors, respectively. In many cases they are synthesised as part of a larger precursor protein, either as a prepropeptide or as an N-terminal domain associated with an inactive peptidase or zymogen. This domain prevents access of the substrate to the active site. Removal of the N-terminal inhibitor domain either by interaction with a second peptidase or by autocatalytic cleavage activates the zymogen. Other inhibitors interact direct with proteinases using a simple noncovalent lock and key mechanism; while yet others use a conformational change-based trapping mechanism that depends on their structural and thermodynamic properties. Limited proteolysis of most large protein precursors is carried out in vivo by the subtilisin-like pro-protein convertases. Many important biological processes such as peptide hormone synthesis, viral protein processing and receptor maturation involve proteolytic processing by these enzymes []. The subtilisin-serine protease (SRSP) family hormone and pro-protein convertases (furin, PC1/3, PC2, PC4, PACE4, PC5/6, and PC7/7/LPC) act within the secretory pathway to cleave polypeptide precursors at specific basic sites, generating their biologically active forms. Serum proteins, pro-hormones, receptors, zymogens, viral surface glycoproteins, bacterial toxins, amongst others, are activated by this route []. The SRSPs share the same domain structure, including a signal peptide, the pro-peptide, the catalytic domain, the P/middle or homo B domain, and the C terminus. Proteinase propeptide inhibitors (sometimes refered to as activation peptides) are responsible for the modulation of folding and activity of the pro-enzyme or zymogen. The pro-segment docks into the enzyme moiety shielding the substrate binding site, thereby promoting inhibition of the enzyme. Several such propeptides share a similar topology [], despite often low sequence identities []. The propeptide region has an open-sandwich antiparallel-alpha/antiparallel-beta fold, with two alpha-helices and four beta-strands with a (beta/alpha/beta)x2 topology. This group of sequences contain the propeptide domain at the N terminus of peptidases belonging to MEROPS family S8A, subtilisins. A number of the members of this group of sequences belong to MEROPS inhibitor family I9, clan I-. The propeptide is removed by proteolytic cleavage; removal activating the enzyme.; GO: 0004252 serine-type endopeptidase activity, 0042802 identical protein binding, 0043086 negative regulation of catalytic activity; PDB: 3CNQ_P 1SPB_P 3CO0_P 1ITP_A 1V5I_B 1SCJ_B 3P5B_P 2XTJ_P 2W2M_P 2P4E_P ....
Probab=99.21 E-value=1.4e-11 Score=94.96 Aligned_cols=77 Identities=21% Similarity=0.315 Sum_probs=56.8
Q ss_pred EEEEEecCCCCCCChHHHHHHHHHHHHHHcCCCc----hhhhhhheeeecCcceeeeeecCHHHHHHhcCCCCeEEEcCC
Q 016357 107 HWLVVMEKPEGDPTRDEIIDRYIKTLATVFDGRE----DEARMKIYSVSTKHYYAFGALVDEETSYKLKELPGVRWVLPD 182 (391)
Q Consensus 107 hYIVyMgkP~g~~t~~~~idsH~q~LASVL~GSe----EeAk~sIyYSYthsfnGFAAkLTeEEA~kLs~lPGVVSVfPD 182 (391)
.|||.|..... .+...+.|.+++++++ .+. ......++|+|+..|+||+|+||++++++|+++|+|.+|.||
T Consensus 1 ~YIV~~k~~~~---~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~y~~~~~Gfs~~l~~~~i~~L~~~p~V~~Ve~D 76 (82)
T PF05922_consen 1 RYIVVFKDDAS---AASSFSSHKSWQASIL-KSALKSASSINAKVLYSYDNAFNGFSAKLSEEEIEKLRKDPGVKSVEPD 76 (82)
T ss_dssp EEEEEE-TTST---HHCHHHHHHHHHH-----HHHHTH-TTT-EEEEEESSTSSEEEEEE-HHHHHHHHTSTTEEEEEEE
T ss_pred CEEEEECCCCC---cchhHHHHHHHHHHHH-hhhhhhhcccCCceEEEEeeeEEEEEEEeCHHHHHHHHcCCCeEEEEeC
Confidence 59999998643 2224667777777665 321 345778999999999999999999999999999999999999
Q ss_pred CcccC
Q 016357 183 SYLDV 187 (391)
Q Consensus 183 s~l~L 187 (391)
..+++
T Consensus 77 ~~v~l 81 (82)
T PF05922_consen 77 QVVSL 81 (82)
T ss_dssp CEEEE
T ss_pred ceEec
Confidence 98764
No 2
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=98.43 E-value=6.9e-07 Score=97.14 Aligned_cols=14 Identities=36% Similarity=0.786 Sum_probs=9.0
Q ss_pred hhccCccchhhccC
Q 016357 47 LNRFRPLSTAVRFG 60 (391)
Q Consensus 47 ~~~~~p~~~~~~~~ 60 (391)
..||+|++.+..|.
T Consensus 286 veRF~piv~gl~~~ 299 (1102)
T KOG1924|consen 286 VERFRPIVEGLDFL 299 (1102)
T ss_pred hhhhhhHHHHHhcc
Confidence 56777777666543
No 3
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=97.76 E-value=0.00014 Score=79.90 Aligned_cols=8 Identities=13% Similarity=0.696 Sum_probs=3.5
Q ss_pred Hhhhchhh
Q 016357 366 WRNAATTE 373 (391)
Q Consensus 366 w~n~~~~~ 373 (391)
|.--.+++
T Consensus 631 W~kI~p~d 638 (1102)
T KOG1924|consen 631 WSKIVPRD 638 (1102)
T ss_pred ccccCccc
Confidence 44444444
No 4
>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]
Probab=91.04 E-value=2.7 Score=43.91 Aligned_cols=87 Identities=14% Similarity=0.135 Sum_probs=41.8
Q ss_pred eEEEEEecCCCCC-CChHHHHHHHHHHHHHHcCCCchhhhhhheeeecCc-ceeeeeecCHHHHHHhcCCCCeEEEcCCC
Q 016357 106 EHWLVVMEKPEGD-PTRDEIIDRYIKTLATVFDGREDEARMKIYSVSTKH-YYAFGALVDEETSYKLKELPGVRWVLPDS 183 (391)
Q Consensus 106 ehYIVyMgkP~g~-~t~~~~idsH~q~LASVL~GSeEeAk~sIyYSYths-fnGFAAkLTeEEA~kLs~lPGVVSVfPDs 183 (391)
+.|-.|+|.--=. .+.+.+.+-|.-=|+.+ |..+.+..-+.+ --|||-..--.+|..-+-| .+
T Consensus 79 rk~~~YvGNL~W~TTD~DL~~A~~S~G~~~~-------~dmKFFENR~NGQSKG~AL~~~~SdAa~Kq~M----ei---- 143 (498)
T KOG4849|consen 79 RKYCCYVGNLLWYTTDADLLKALQSTGLAQF-------ADMKFFENRTNGQSKGYALLVLNSDAAVKQTM----EI---- 143 (498)
T ss_pred ceEEEEecceeEEeccHHHHHHHHhhhHHHH-------hhhhhhhcccCCcccceEEEEecchHHHHHHH----Hh----
Confidence 4567777765421 23332222232223333 445555555554 3588866544444322111 12
Q ss_pred cccCCCCCCCCCcccccccccCCchhhHHH
Q 016357 184 YLDVKNKDYGGEPFINGQAVPYDPKYHEEW 213 (391)
Q Consensus 184 ~l~L~nKdYgge~f~ng~~v~~~p~~~~~~ 213 (391)
|..|.-.|.. =.+.+|.-.++.++
T Consensus 144 ---LP~k~iHGQ~---P~V~~~NK~~~ak~ 167 (498)
T KOG4849|consen 144 ---LPTKTIHGQS---PTVLSYNKTNQAKL 167 (498)
T ss_pred ---cccceecCCC---CeeeccchhhHHHH
Confidence 3344444533 46777777776653
No 5
>KOG4849 consensus mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification]
Probab=88.10 E-value=5.2 Score=41.91 Aligned_cols=12 Identities=8% Similarity=0.091 Sum_probs=6.3
Q ss_pred eeeecCHHHHHH
Q 016357 158 FGALVDEETSYK 169 (391)
Q Consensus 158 FAAkLTeEEA~k 169 (391)
|.|+|...+++.
T Consensus 163 ~~ak~E~~~~K~ 174 (498)
T KOG4849|consen 163 NQAKLEDAQAKN 174 (498)
T ss_pred hHHHHHHHHhhh
Confidence 445555555544
No 6
>KOG3671 consensus Actin regulatory protein (Wiskott-Aldrich syndrome protein) [Signal transduction mechanisms; Cytoskeleton]
Probab=87.77 E-value=4.9 Score=43.43 Aligned_cols=9 Identities=33% Similarity=0.501 Sum_probs=4.1
Q ss_pred CCCCCCCCC
Q 016357 264 SGMPPNNVP 272 (391)
Q Consensus 264 ~~~p~~~~~ 272 (391)
+|+++++..
T Consensus 332 ~gnq~p~r~ 340 (569)
T KOG3671|consen 332 GGNQPPNRS 340 (569)
T ss_pred CCCCCCccc
Confidence 455544433
No 7
>TIGR01628 PABP-1234 polyadenylate binding protein, human types 1, 2, 3, 4 family. There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed, or of unknown tissue range.
Probab=79.56 E-value=74 Score=33.37 Aligned_cols=14 Identities=14% Similarity=0.439 Sum_probs=6.9
Q ss_pred eeeeeecCHHHHHH
Q 016357 156 YAFGALVDEETSYK 169 (391)
Q Consensus 156 nGFAAkLTeEEA~k 169 (391)
+||.+--|.++|.+
T Consensus 328 ~gfV~f~~~~~A~~ 341 (562)
T TIGR01628 328 FGFVCFSNPEEANR 341 (562)
T ss_pred eEEEEeCCHHHHHH
Confidence 44555555554444
No 8
>KOG1984 consensus Vesicle coat complex COPII, subunit SFB3 [Intracellular trafficking, secretion, and vesicular transport]
Probab=61.86 E-value=28 Score=40.20 Aligned_cols=8 Identities=50% Similarity=0.659 Sum_probs=5.1
Q ss_pred CCCCCCCC
Q 016357 267 PPNNVPSS 274 (391)
Q Consensus 267 p~~~~~g~ 274 (391)
+|...+|+
T Consensus 16 ~~~~~~g~ 23 (1007)
T KOG1984|consen 16 PPNFYGGS 23 (1007)
T ss_pred CCCcCCCC
Confidence 56666665
No 9
>KOG1984 consensus Vesicle coat complex COPII, subunit SFB3 [Intracellular trafficking, secretion, and vesicular transport]
Probab=61.63 E-value=74 Score=37.02 Aligned_cols=6 Identities=50% Similarity=0.883 Sum_probs=3.6
Q ss_pred CCCCCC
Q 016357 265 GMPPNN 270 (391)
Q Consensus 265 ~~p~~~ 270 (391)
|.|+++
T Consensus 8 g~p~p~ 13 (1007)
T KOG1984|consen 8 GQPQPN 13 (1007)
T ss_pred CCCCCC
Confidence 556666
No 10
>KOG2236 consensus Uncharacterized conserved protein [Function unknown]
Probab=57.12 E-value=79 Score=34.23 Aligned_cols=11 Identities=9% Similarity=-0.085 Sum_probs=4.8
Q ss_pred CceEEEEEecC
Q 016357 104 DFEHWLVVMEK 114 (391)
Q Consensus 104 d~ehYIVyMgk 114 (391)
|.++-|..|-.
T Consensus 219 ~~~VII~s~~~ 229 (483)
T KOG2236|consen 219 DQQVIIESTCN 229 (483)
T ss_pred hhceEEEeccC
Confidence 34444444444
No 11
>KOG0132 consensus RNA polymerase II C-terminal domain-binding protein RA4, contains RPR and RRM domains [RNA processing and modification; Transcription]
Probab=54.82 E-value=68 Score=36.83 Aligned_cols=40 Identities=25% Similarity=0.286 Sum_probs=23.9
Q ss_pred HHHHHcCCCchhhhhh-heeeecCcceeeeeecCHHHHHH-hcCCC
Q 016357 131 TLATVFDGREDEARMK-IYSVSTKHYYAFGALVDEETSYK-LKELP 174 (391)
Q Consensus 131 ~LASVL~GSeEeAk~s-IyYSYthsfnGFAAkLTeEEA~k-Ls~lP 174 (391)
-|+++| +.-.+++.- |+..|.+ +|.++..-.+|++ |.+|-
T Consensus 437 dL~~~f-eefGeiqSi~li~~R~c---AfI~M~~RqdA~kalqkl~ 478 (894)
T KOG0132|consen 437 DLANLF-EEFGEIQSIILIPPRGC---AFIKMVRRQDAEKALQKLS 478 (894)
T ss_pred HHHHHH-HhcccceeEeeccCCce---eEEEEeehhHHHHHHHHHh
Confidence 367776 443334332 3455655 6788888888876 45554
No 12
>KOG0132 consensus RNA polymerase II C-terminal domain-binding protein RA4, contains RPR and RRM domains [RNA processing and modification; Transcription]
Probab=52.88 E-value=1.5e+02 Score=34.16 Aligned_cols=25 Identities=8% Similarity=-0.187 Sum_probs=15.0
Q ss_pred HHHHhcCCCCeEEEcCCCcccCCCC
Q 016357 166 TSYKLKELPGVRWVLPDSYLDVKNK 190 (391)
Q Consensus 166 EA~kLs~lPGVVSVfPDs~l~L~nK 190 (391)
|-+.+-.+.==|+++|=..|++..+
T Consensus 500 e~k~~wD~~lGVt~IP~~kLt~dl~ 524 (894)
T KOG0132|consen 500 EYKDYWDVELGVTYIPWEKLTDDLE 524 (894)
T ss_pred hhhhhhhcccCeeEeehHhcCHHHH
Confidence 4444555555577888777665533
No 13
>KOG4594 consensus Sequence-specific single-stranded-DNA-binding protein [Replication, recombination and repair; Transcription; General function prediction only]
Probab=48.06 E-value=1.7e+02 Score=30.36 Aligned_cols=15 Identities=27% Similarity=0.306 Sum_probs=8.3
Q ss_pred CCchhhhhhh-eeeec
Q 016357 138 GREDEARMKI-YSVST 152 (391)
Q Consensus 138 GSeEeAk~sI-yYSYt 152 (391)
-|+..|+++| +|+|.
T Consensus 11 pSd~qArekLa~YvYE 26 (354)
T KOG4594|consen 11 PSDSQAREKLALYVYE 26 (354)
T ss_pred CcchhHHHHHHHHHHH
Confidence 4555566665 45543
No 14
>KOG4368 consensus Predicted RNA binding protein, contains SWAP, RPR and G-patch domains [General function prediction only]
Probab=45.75 E-value=1.3e+02 Score=33.72 Aligned_cols=10 Identities=10% Similarity=0.248 Sum_probs=7.2
Q ss_pred eeeecCccee
Q 016357 148 YSVSTKHYYA 157 (391)
Q Consensus 148 yYSYthsfnG 157 (391)
+|.||..|..
T Consensus 191 ~~~yc~~~~~ 200 (757)
T KOG4368|consen 191 VPIYCTSFLA 200 (757)
T ss_pred HHHHHhhhhh
Confidence 7788877654
No 15
>cd04901 ACT_3PGDH C-terminal ACT (regulatory) domain of D-3-Phosphoglycerate Dehydrogenase (3PGDH) found in fungi and bacteria. The C-terminal ACT (regulatory) domain of D-3-Phosphoglycerate Dehydrogenase (3PGDH) found in fungi and bacteria. 3PGDH is an enzyme that belongs to the D-isomer specific, 2-hydroxyacid dehydrogenase family and catalyzes the oxidation of D-3-phosphoglycerate to 3- phosphohydroxypyruvate, which is the first step in the biosynthesis of L-serine, using NAD+ as the oxidizing agent. In Escherichia coli, the SerA 3PGDH is feedback-controlled by the end product L-serine in an allosteric manner. In the homotetrameric enzyme, the interface at adjacent ACT (regulatory) domains couples to create an extended beta-sheet. Each regulatory interface forms two serine-binding sites. The mechanism by which serine transmits inhibition to the active site is postulated to involve the tethering of the regulatory domains together to create a rigid quaternary structure with a solvent-
Probab=41.76 E-value=37 Score=24.90 Aligned_cols=19 Identities=37% Similarity=0.448 Sum_probs=15.8
Q ss_pred cCHHHHHHhcCCCCeEEEc
Q 016357 162 VDEETSYKLKELPGVRWVL 180 (391)
Q Consensus 162 LTeEEA~kLs~lPGVVSVf 180 (391)
..++..++|++++||..|.
T Consensus 49 ~l~~li~~l~~~~~V~~v~ 67 (69)
T cd04901 49 VSEELLEALRAIPGTIRVR 67 (69)
T ss_pred CCHHHHHHHHcCCCeEEEE
Confidence 4567779999999999984
No 16
>KOG3168 consensus U1 snRNP component [Transcription]
Probab=33.84 E-value=1e+02 Score=29.35 Aligned_cols=8 Identities=13% Similarity=0.310 Sum_probs=4.0
Q ss_pred HHHHHHHH
Q 016357 124 IIDRYIKT 131 (391)
Q Consensus 124 ~idsH~q~ 131 (391)
.-|.|.++
T Consensus 33 afDkhmNl 40 (177)
T KOG3168|consen 33 AFDKHMNL 40 (177)
T ss_pred hhHHHHHH
Confidence 45555443
No 17
>cd04888 ACT_PheB-BS C-terminal ACT domain of a small (~147 a.a.) putative phenylalanine biosynthetic pathway protein described in Bacillus subtilis (BS) PheB (PheB-BS) and related domains. This CD includes the C-terminal ACT domain of a small (~147 a.a.) putative phenylalanine biosynthetic pathway protein described in Bacillus subtilis (BS) PheB (PheB-BS) and other related ACT domains. In B. subtilis, the upstream gene of pheB, pheA encodes prephenate dehydratase (PDT). The presumed product of the pheB gene is chorismate mutase (CM). The deduced product of the B. subtilis pheB gene, however, has no significant homology to the CM portion of the bifunctional CM-PDT of Escherichia coli. The presence of an ACT domain lends support to the prediction that these proteins function as a phenylalanine-binding regulatory protein. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=25.42 E-value=1.9e+02 Score=21.47 Aligned_cols=14 Identities=36% Similarity=0.390 Sum_probs=12.0
Q ss_pred HHHhcCCCCeEEEc
Q 016357 167 SYKLKELPGVRWVL 180 (391)
Q Consensus 167 A~kLs~lPGVVSVf 180 (391)
.++|++++||.+|-
T Consensus 60 ~~~L~~i~~V~~v~ 73 (76)
T cd04888 60 LEELREIDGVEKVE 73 (76)
T ss_pred HHHHhcCCCeEEEE
Confidence 56799999999983
No 18
>PHA03378 EBNA-3B; Provisional
Probab=21.60 E-value=8.3e+02 Score=28.51 Aligned_cols=8 Identities=25% Similarity=0.489 Sum_probs=4.3
Q ss_pred CCCCCCCC
Q 016357 267 PPNNVPSS 274 (391)
Q Consensus 267 p~~~~~g~ 274 (391)
+..|..+.
T Consensus 686 ~~~~ap~~ 693 (991)
T PHA03378 686 PIQWAPGT 693 (991)
T ss_pred ccccCccc
Confidence 44566663
Done!