Query 011319
Match_columns 488
No_of_seqs 35 out of 37
Neff 2.6
Searched_HMMs 46136
Date Fri Mar 29 00:01:40 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/011319.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/011319hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF00595 PDZ: PDZ domain (Also 89.9 0.43 9.3E-06 37.4 3.7 40 300-343 2-44 (81)
2 PF13180 PDZ_2: PDZ domain; PD 78.9 9.6 0.00021 30.2 6.7 45 40-104 31-75 (82)
3 KOG3553 Tax interaction protei 77.5 1.9 4.1E-05 39.2 2.6 31 309-343 35-78 (124)
4 cd00136 PDZ PDZ domain, also c 77.3 1.4 3.1E-05 33.1 1.5 46 310-368 2-47 (70)
5 cd00986 PDZ_LON_protease PDZ d 69.4 42 0.00091 26.2 8.1 60 19-103 8-67 (79)
6 cd00992 PDZ_signaling PDZ doma 65.9 6 0.00013 30.3 2.7 33 308-343 11-45 (82)
7 PF13180 PDZ_2: PDZ domain; PD 64.2 5 0.00011 31.8 2.0 68 310-404 2-70 (82)
8 smart00228 PDZ Domain present 60.7 8.5 0.00018 29.2 2.6 45 309-366 12-58 (85)
9 cd00989 PDZ_metalloprotease PD 59.1 40 0.00087 25.7 6.1 44 39-103 28-71 (79)
10 PF10647 Gmad1: Lipoprotein Lp 55.0 84 0.0018 30.4 8.9 153 221-376 27-199 (253)
11 PF14685 Tricorn_PDZ: Tricorn 45.3 81 0.0018 27.1 6.4 60 17-103 12-81 (88)
12 PF04495 GRASP55_65: GRASP55/6 43.4 30 0.00066 31.6 3.7 38 306-346 23-65 (138)
13 cd04454 S1_Rrp4_like S1_Rrp4_l 41.1 66 0.0014 25.6 5.0 56 39-100 2-63 (82)
14 PF02470 MCE: mce related prot 40.0 39 0.00085 26.9 3.5 32 275-308 22-53 (81)
15 PHA00008 J DNA packaging prote 39.7 14 0.00029 26.2 0.7 9 284-292 12-20 (26)
16 cd00991 PDZ_archaeal_metallopr 38.6 1.3E+02 0.0028 23.9 6.2 45 39-103 26-70 (79)
17 cd03034 ArsC_ArsC Arsenate Red 36.9 36 0.00079 29.2 3.1 27 212-241 10-36 (112)
18 PF09255 Antig_Caf1: Caf1 Caps 33.8 16 0.00035 33.8 0.5 63 223-287 8-75 (136)
19 cd00431 cysteine_hydrolases Cy 33.7 77 0.0017 27.4 4.6 32 208-239 20-51 (161)
20 cd00988 PDZ_CTP_protease PDZ d 33.7 38 0.00083 26.3 2.5 46 309-368 2-47 (85)
21 cd00990 PDZ_glycyl_aminopeptid 32.8 31 0.00066 26.6 1.8 43 310-366 2-44 (80)
22 KOG3129 26S proteasome regulat 32.5 22 0.00047 35.8 1.1 38 321-368 139-176 (231)
23 PF00857 Isochorismatase: Isoc 32.4 54 0.0012 28.7 3.5 33 207-239 19-51 (174)
24 PF12910 RelB_N: Antitoxin of 32.0 68 0.0015 24.2 3.5 31 337-367 8-38 (46)
25 KOG3209 WW domain-containing p 31.8 82 0.0018 36.9 5.5 72 313-410 757-841 (984)
26 cd00987 PDZ_serine_protease PD 31.4 1.3E+02 0.0028 23.3 5.1 44 40-103 41-84 (90)
27 PF13501 SoxY: Sulfur oxidatio 30.1 1.5E+02 0.0033 26.3 5.8 45 285-329 59-103 (111)
28 PF11243 DUF3045: Protein of u 29.0 20 0.00044 31.4 0.3 15 314-328 39-53 (89)
29 TIGR01713 typeII_sec_gspC gene 28.9 1.3E+02 0.0029 29.9 5.9 46 38-103 206-251 (259)
30 PF04726 Microvir_J: Microviru 28.7 13 0.00028 25.9 -0.8 10 284-293 11-20 (24)
31 cd05790 S1_Rrp40 S1_Rrp40: Rrp 27.2 1.9E+02 0.0041 24.9 5.7 55 39-103 2-65 (86)
32 PRK10942 serine endoprotease; 26.9 1.5E+02 0.0033 31.8 6.3 57 22-103 410-466 (473)
33 TIGR02860 spore_IV_B stage IV 26.8 1.9E+02 0.0041 31.2 6.9 45 38-103 128-172 (402)
34 TIGR02037 degP_htrA_DO peripla 23.8 2E+02 0.0043 29.9 6.3 44 40-103 379-422 (428)
35 TIGR00054 RIP metalloprotease 23.0 2E+02 0.0044 30.2 6.2 53 39-115 219-271 (420)
36 PRK04163 exosome complex RNA-b 22.8 1.3E+02 0.0029 29.4 4.5 56 39-100 59-124 (235)
37 TIGR02038 protease_degS peripl 22.0 2.2E+02 0.0049 29.1 6.2 44 40-103 295-338 (351)
38 PF13243 Prenyltrans_1: Prenyl 20.9 31 0.00068 28.0 -0.1 57 155-225 3-59 (109)
39 PRK11609 nicotinamidase/pyrazi 20.4 1.1E+02 0.0024 28.4 3.4 27 209-235 24-50 (212)
No 1
>PF00595 PDZ: PDZ domain (Also known as DHR or GLGF) Coordinates are not yet available; InterPro: IPR001478 PDZ domains are found in diverse signalling proteins in bacteria, yeasts, plants, insects and vertebrates [, ]. PDZ domains can occur in one or multiple copies and are nearly always found in cytoplasmic proteins. They bind either the carboxyl-terminal sequences of proteins or internal peptide sequences []. In most cases, interaction between a PDZ domain and its target is constitutive, with a binding affinity of 1 to 10 microns. However, agonist-dependent activation of cell surface receptors is sometimes required to promote interaction with a PDZ protein. PDZ domain proteins are frequently associated with the plasma membrane, a compartment where high concentrations of phosphatidylinositol 4,5-bisphosphate (PIP2) are found. Direct interaction between PIP2 and a subset of class II PDZ domains (syntenin, CASK, Tiam-1) has been demonstrated. PDZ domains consist of 80 to 90 amino acids comprising six beta-strands (beta-A to beta-F) and two alpha-helices, A and B, compactly arranged in a globular structure. Peptide binding of the ligand takes place in an elongated surface groove as an anti-parallel beta-strand interacts with the beta-B strand and the B helix. The structure of PDZ domains allows binding to a free carboxylate group at the end of a peptide through a carboxylate-binding loop between the beta-A and beta-B strands.; GO: 0005515 protein binding; PDB: 3AXA_A 1WF8_A 1QAV_B 1QAU_A 1B8Q_A 1MC7_A 2KAW_A 1I16_A 1VB7_A 1WI4_A ....
Probab=89.85 E-value=0.43 Score=37.44 Aligned_cols=40 Identities=25% Similarity=0.625 Sum_probs=33.1
Q ss_pred eEeeecCCCcceeeeeeecccc---eEEEEEeecCCCCCccchhhHH
Q 011319 300 IEIKLKEGDSKLGFAISRTEEG---FIYISTVIDDDENIPSTRSGLS 343 (488)
Q Consensus 300 lEi~~~~gdtRlGfaIsRTEEG---FiyVsSV~~~~~g~~a~RsGL~ 343 (488)
|+|..+ ++..|||.+..-.+. .+||++|.. +.||.++||+
T Consensus 2 v~l~k~-~~~~lG~~l~~~~~~~~~~~~V~~v~~---~~~a~~~gl~ 44 (81)
T PF00595_consen 2 VTLEKS-GNGPLGFTLRGGSDNDEKGVFVSSVVP---GSPAERAGLK 44 (81)
T ss_dssp EEEEES-TTSBSSEEEEEESTSSSEEEEEEEECT---TSHHHHHTSS
T ss_pred EEEEeC-CCCCcCEEEEecCCCCcCCEEEEEEeC---CChHHhcccc
Confidence 455555 789999999987774 999999996 6999999963
No 2
>PF13180 PDZ_2: PDZ domain; PDB: 2L97_A 1Y8T_A 2Z9I_A 1LCY_A 2PZD_B 2P3W_A 1VCW_C 1TE0_B 1SOZ_C 1SOT_C ....
Probab=78.86 E-value=9.6 Score=30.20 Aligned_cols=45 Identities=31% Similarity=0.425 Sum_probs=31.7
Q ss_pred cccCCceeeeEeecCCCCCCCCCCceeeeecCCCCchhhHHHHHhhhhcCccceEEEEEecCccc
Q 011319 40 MLQTGDIVEEFTIGGGSGLGSGSGSCRTYKAPFKNGRSGVQKILHGSFKNKETSILVRVRRGAEE 104 (488)
Q Consensus 40 m~l~GDIVE~~~~g~~~~~~~~~~~~v~~~apFk~gksgl~k~L~k~~k~~e~si~vrVrRG~~~ 104 (488)
-+++||+|.+|. | ..+ +....|.+.|. .++ ..+.|.++|.|++..
T Consensus 31 Gl~~GD~I~~in-g------------~~v-----~~~~~~~~~l~-~~~-~g~~v~l~v~R~g~~ 75 (82)
T PF13180_consen 31 GLQPGDIILAIN-G------------KPV-----NSSEDLVNILS-KGK-PGDTVTLTVLRDGEE 75 (82)
T ss_dssp TS-TTEEEEEET-T------------EES-----SSHHHHHHHHH-CSS-TTSEEEEEEEETTEE
T ss_pred CCCCCcEEEEEC-C------------EEc-----CCHHHHHHHHH-hCC-CCCEEEEEEEECCEE
Confidence 399999999986 2 223 44478888887 333 344899999998863
No 3
>KOG3553 consensus Tax interaction protein TIP1 [Cell wall/membrane/envelope biogenesis]
Probab=77.46 E-value=1.9 Score=39.22 Aligned_cols=31 Identities=42% Similarity=0.723 Sum_probs=25.0
Q ss_pred cceeeee-------------eecccceEEEEEeecCCCCCccchhhHH
Q 011319 309 SKLGFAI-------------SRTEEGFIYISTVIDDDENIPSTRSGLS 343 (488)
Q Consensus 309 tRlGfaI-------------sRTEEGFiyVsSV~~~~~g~~a~RsGL~ 343 (488)
-++||.| +-|+-| |||--|.+ |+||+++||+
T Consensus 35 l~~GFkIGGGIDQDp~k~Pf~ytD~G-iYvT~V~e---GsPA~~AGLr 78 (124)
T KOG3553|consen 35 LILGFKIGGGIDQDPSKNPFSYTDKG-IYVTRVSE---GSPAEIAGLR 78 (124)
T ss_pred EEEEEEeccccCCCcccCCCCcCCcc-EEEEEecc---CChhhhhcce
Confidence 3677776 467777 79998986 7999999997
No 4
>cd00136 PDZ PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(pos
Probab=77.33 E-value=1.4 Score=33.07 Aligned_cols=46 Identities=28% Similarity=0.439 Sum_probs=33.6
Q ss_pred ceeeeeeecccceEEEEEeecCCCCCccchhhHHHHHHHHHhcCcEEEEEeecCeeecc
Q 011319 310 KLGFAISRTEEGFIYISTVIDDDENIPSTRSGLSILYKEAVSASKLLVVSRVSNQKVLP 368 (488)
Q Consensus 310 RlGfaIsRTEEGFiyVsSV~~~~~g~~a~RsGL~~Ly~~A~~a~kLLVISRv~g~kVlP 368 (488)
.|||.+.-.+++.++|++|.+ ++||.++||+. |-. |-.+.|+++.=
T Consensus 2 ~~G~~~~~~~~~~~~V~~v~~---~s~a~~~gl~~--------GD~--I~~Ing~~v~~ 47 (70)
T cd00136 2 GLGFSIRGGTEGGVVVLSVEP---GSPAERAGLQA--------GDV--ILAVNGTDVKN 47 (70)
T ss_pred CccEEEecCCCCCEEEEEeCC---CCHHHHcCCCC--------CCE--EEEECCEECCC
Confidence 478998888877899999986 68999999853 433 33566665543
No 5
>cd00986 PDZ_LON_protease PDZ domain of ATP-dependent LON serine proteases. Most PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this bacterial subfamily of protease-associated PDZ domains a C-terminal beta-strand is thought to form the peptide-binding groove base, a circular permutation with respect to PDZ domains found in Eumetazoan signaling proteins.
Probab=69.44 E-value=42 Score=26.22 Aligned_cols=60 Identities=15% Similarity=0.343 Sum_probs=36.2
Q ss_pred ccEEEEEEccCCccccccccccccCCceeeeEeecCCCCCCCCCCceeeeecCCCCchhhHHHHHhhhhcCccceEEEEE
Q 011319 19 YTVLSIDCLKGTSKADEWTADMLQTGDIVEEFTIGGGSGLGSGSGSCRTYKAPFKNGRSGVQKILHGSFKNKETSILVRV 98 (488)
Q Consensus 19 ~~V~~i~Cv~gss~aeEW~e~m~l~GDIVE~~~~g~~~~~~~~~~~~v~~~apFk~gksgl~k~L~k~~k~~e~si~vrV 98 (488)
.+|+-.....++ .|+ +. +++||+|..|. + ..+ ..-..+.++|..... ++ .+.+.+
T Consensus 8 ~Gv~V~~V~~~s-~A~---~g-L~~GD~I~~In-g------------~~v-----~~~~~~~~~l~~~~~-~~-~v~l~v 62 (79)
T cd00986 8 HGVYVTSVVEGM-PAA---GK-LKAGDHIIAVD-G------------KPF-----KEAEELIDYIQSKKE-GD-TVKLKV 62 (79)
T ss_pred cCEEEEEECCCC-chh---hC-CCCCCEEEEEC-C------------EEC-----CCHHHHHHHHHhCCC-CC-EEEEEE
Confidence 355544534444 344 33 99999999984 1 122 112457777754322 44 799999
Q ss_pred ecCcc
Q 011319 99 RRGAE 103 (488)
Q Consensus 99 rRG~~ 103 (488)
.|++.
T Consensus 63 ~r~g~ 67 (79)
T cd00986 63 KREEK 67 (79)
T ss_pred EECCE
Confidence 99876
No 6
>cd00992 PDZ_signaling PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of PDZ domains an N-terminal beta-strand forms the peptide-binding groove base, a circular permutation with respect to PDZ domains found in proteases.
Probab=65.86 E-value=6 Score=30.26 Aligned_cols=33 Identities=33% Similarity=0.587 Sum_probs=26.1
Q ss_pred Ccceeeeeeeccc--ceEEEEEeecCCCCCccchhhHH
Q 011319 308 DSKLGFAISRTEE--GFIYISTVIDDDENIPSTRSGLS 343 (488)
Q Consensus 308 dtRlGfaIsRTEE--GFiyVsSV~~~~~g~~a~RsGL~ 343 (488)
...|||.+.-..+ ..++|..|.. ++||.++||+
T Consensus 11 ~~~~G~~~~~~~~~~~~~~V~~v~~---~s~a~~~gl~ 45 (82)
T cd00992 11 GGGLGFSLRGGKDSGGGIFVSRVEP---GGPAERGGLR 45 (82)
T ss_pred CCCcCEEEeCcccCCCCeEEEEECC---CChHHhCCCC
Confidence 6778998875543 5699999986 6899999985
No 7
>PF13180 PDZ_2: PDZ domain; PDB: 2L97_A 1Y8T_A 2Z9I_A 1LCY_A 2PZD_B 2P3W_A 1VCW_C 1TE0_B 1SOZ_C 1SOT_C ....
Probab=64.20 E-value=5 Score=31.82 Aligned_cols=68 Identities=21% Similarity=0.382 Sum_probs=43.6
Q ss_pred ceeeeeeeccc-ceEEEEEeecCCCCCccchhhHHHHHHHHHhcCcEEEEEeecCeeecceeeecCCceeccCccccccc
Q 011319 310 KLGFAISRTEE-GFIYISTVIDDDENIPSTRSGLSILYKEAVSASKLLVVSRVSNQKVLPWIVSSTGAVRCFDTVSLSQK 388 (488)
Q Consensus 310 RlGfaIsRTEE-GFiyVsSV~~~~~g~~a~RsGL~~Ly~~A~~a~kLLVISRv~g~kVlPwmVsSsGaIrC~Dt~slsqk 388 (488)
.||+.+..... +-++|.+|.+ ++||.++||. .|-. |=.+.|++|- +...+.+.
T Consensus 2 ~lGv~~~~~~~~~g~~V~~V~~---~spA~~aGl~--------~GD~--I~~ing~~v~-------------~~~~~~~~ 55 (82)
T PF13180_consen 2 GLGVTVQNLSDTGGVVVVSVIP---GSPAAKAGLQ--------PGDI--ILAINGKPVN-------------SSEDLVNI 55 (82)
T ss_dssp E-SEEEEECSCSSSEEEEEEST---TSHHHHTTS---------TTEE--EEEETTEESS-------------SHHHHHHH
T ss_pred EECeEEEEccCCCeEEEEEeCC---CCcHHHCCCC--------CCcE--EEEECCEEcC-------------CHHHHHHH
Confidence 36777776664 7789999996 7999999984 4443 4467777762 22344455
Q ss_pred ccccccccCceEEEEE
Q 011319 389 LSLHRHAKVPILLHVF 404 (488)
Q Consensus 389 Lslhr~a~~pI~lHvm 404 (488)
|. .......+.|+|+
T Consensus 56 l~-~~~~g~~v~l~v~ 70 (82)
T PF13180_consen 56 LS-KGKPGDTVTLTVL 70 (82)
T ss_dssp HH-CSSTTSEEEEEEE
T ss_pred HH-hCCCCCEEEEEEE
Confidence 54 4455666777665
No 8
>smart00228 PDZ Domain present in PSD-95, Dlg, and ZO-1/2. Also called DHR (Dlg homologous region) or GLGF (relatively well conserved tetrapeptide in these domains). Some PDZs have been shown to bind C-terminal polypeptides; others appear to bind internal (non-C-terminal) polypeptides. Different PDZs possess different binding specificities.
Probab=60.68 E-value=8.5 Score=29.22 Aligned_cols=45 Identities=24% Similarity=0.535 Sum_probs=32.6
Q ss_pred cceeeeeeeccc--ceEEEEEeecCCCCCccchhhHHHHHHHHHhcCcEEEEEeecCeee
Q 011319 309 SKLGFAISRTEE--GFIYISTVIDDDENIPSTRSGLSILYKEAVSASKLLVVSRVSNQKV 366 (488)
Q Consensus 309 tRlGfaIsRTEE--GFiyVsSV~~~~~g~~a~RsGL~~Ly~~A~~a~kLLVISRv~g~kV 366 (488)
..|||.+.-... ..++|..|.. ++|+.++|| +.|..+ =.+.|+.+
T Consensus 12 ~~~G~~~~~~~~~~~~~~i~~v~~---~s~a~~~gl--------~~GD~I--~~In~~~v 58 (85)
T smart00228 12 GGLGFSLVGGKDEGGGVVVSSVVP---GSPAAKAGL--------KVGDVI--LEVNGTSV 58 (85)
T ss_pred CcccEEEECCCCCCCCEEEEEECC---CCHHHHcCC--------CCCCEE--EEECCEEC
Confidence 788888876543 5699999986 689999996 455533 36666555
No 9
>cd00989 PDZ_metalloprotease PDZ domain of bacterial and plant zinc metalloprotases, presumably membrane-associated or integral membrane proteases, which may be involved in signalling and regulatory mechanisms. May be responsible for substrate recognition and/or binding, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of protease-associated PDZ domains a C-terminal beta-strand forms the peptide-binding groove base, a circular permutation with respect to PDZ domains found in Eumetazoan signaling proteins.
Probab=59.05 E-value=40 Score=25.70 Aligned_cols=44 Identities=16% Similarity=0.277 Sum_probs=29.0
Q ss_pred ccccCCceeeeEeecCCCCCCCCCCceeeeecCCCCchhhHHHHHhhhhcCccceEEEEEecCcc
Q 011319 39 DMLQTGDIVEEFTIGGGSGLGSGSGSCRTYKAPFKNGRSGVQKILHGSFKNKETSILVRVRRGAE 103 (488)
Q Consensus 39 ~m~l~GDIVE~~~~g~~~~~~~~~~~~v~~~apFk~gksgl~k~L~k~~k~~e~si~vrVrRG~~ 103 (488)
.-+++||+|.+|. | ..+ ..-..+.+.|.+.. ++ .+.+.++|++.
T Consensus 28 ~gl~~GD~I~~in-g------------~~i-----~~~~~~~~~l~~~~--~~-~~~l~v~r~~~ 71 (79)
T cd00989 28 AGLKAGDRILAIN-G------------QKI-----KSWEDLVDAVQENP--GK-PLTLTVERNGE 71 (79)
T ss_pred cCCCCCCEEEEEC-C------------EEC-----CCHHHHHHHHHHCC--Cc-eEEEEEEECCE
Confidence 3499999999885 1 122 11256777776632 33 78899998875
No 10
>PF10647 Gmad1: Lipoprotein LpqB beta-propeller domain; InterPro: IPR018910 The Gmad1 domain is found associated with IPR019606 from INTERPRO, in bacterial spore formation. It is predicted to have a beta-propeller fold and to have a passive binding role rather than a catalytic function owing to the low number of conserved hydrophilic residues.
Probab=54.98 E-value=84 Score=30.42 Aligned_cols=153 Identities=18% Similarity=0.299 Sum_probs=87.0
Q ss_pred HHhhhc-CCCcEEEEe--echhhhhhhccccccceeecCCCcCccchhcccccccccccccccccee-------eEEEee
Q 011319 221 LNASQA-TGVPIVFMN--IQTESLLTKISGETASSTVNSGSLSDLSNVANASLYGFEDYHGVDLGVV-------RAVRLW 290 (488)
Q Consensus 221 lsAsqa-SGVPIvFvN--IQTE~llTkisge~as~tvn~gsl~dl~n~an~slygfedyhg~digVV-------ravRLW 290 (488)
.++|++ .|--+.|++ =-...|++--.|.........+++.-++--.+..+|.+++-.+.-..+. ..+.+-
T Consensus 27 ~s~AvS~dg~~~A~v~~~~~~~~L~~~~~~~~~~~~~~g~~l~~PS~d~~g~~W~v~~~~~~~~~~~~~~~g~~~~~~v~ 106 (253)
T PF10647_consen 27 TSPAVSPDGSRVAAVSEGDGGRSLYVGPAGGPVRPVLTGGSLTRPSWDPDGWVWTVDDGSGGVRVVRDSASGTGEPVEVD 106 (253)
T ss_pred cceEECCCCCeEEEEEEcCCCCEEEEEcCCCcceeeccCCccccccccCCCCEEEEEcCCCceEEEEecCCCcceeEEec
Confidence 344444 455677777 3333444332222222222334555555555666777776322211111 011111
Q ss_pred eccccceeee-EeeecCCCcceeeeeeecccceEEEEEeecCCCCCccchhhHHHHH----HHH-----HhcCcEEEEEe
Q 011319 291 YAPVGGELAI-EIKLKEGDSKLGFAISRTEEGFIYISTVIDDDENIPSTRSGLSILY----KEA-----VSASKLLVVSR 360 (488)
Q Consensus 291 y~P~~~E~~l-Ei~~~~gdtRlGfaIsRTEEGFiyVsSV~~~~~g~~a~RsGL~~Ly----~~A-----~~a~kLLVISR 360 (488)
.....+ .| ++.+-++-+|+-|-+++-++|.+||..|..++.|+|....+...+- ..+ ...+.|+|..+
T Consensus 107 ~~~~~~--~I~~l~vSpDG~RvA~v~~~~~~~~v~va~V~r~~~g~~~~l~~~~~~~~~~~~~v~~v~W~~~~~L~V~~~ 184 (253)
T PF10647_consen 107 WPGLRG--RITALRVSPDGTRVAVVVEDGGGGRVYVAGVVRDGDGVPRRLTGPRRVAPPLLSDVTDVAWSDDSTLVVLGR 184 (253)
T ss_pred ccccCC--ceEEEEECCCCcEEEEEEecCCCCeEEEEEEEeCCCCCcceeccceEecccccCcceeeeecCCCEEEEEeC
Confidence 111112 34 6888999999999999999999999999987667555555444443 222 23468888888
Q ss_pred ecCeeecceeeecCCc
Q 011319 361 VSNQKVLPWIVSSTGA 376 (488)
Q Consensus 361 v~g~kVlPwmVsSsGa 376 (488)
-.+..+.. .|+..|.
T Consensus 185 ~~~~~~~~-~v~~dG~ 199 (253)
T PF10647_consen 185 SAGGPVVR-LVSVDGG 199 (253)
T ss_pred CCCCceeE-EEEccCC
Confidence 88887766 5555543
No 11
>PF14685 Tricorn_PDZ: Tricorn protease PDZ domain; PDB: 1N6F_D 1N6D_C 1N6E_C 1K32_A.
Probab=45.34 E-value=81 Score=27.11 Aligned_cols=60 Identities=20% Similarity=0.449 Sum_probs=32.4
Q ss_pred ccccEEEEEEccCCccccccccc----------cccCCceeeeEeecCCCCCCCCCCceeeeecCCCCchhhHHHHHhhh
Q 011319 17 KSYTVLSIDCLKGTSKADEWTAD----------MLQTGDIVEEFTIGGGSGLGSGSGSCRTYKAPFKNGRSGVQKILHGS 86 (488)
Q Consensus 17 ~~~~V~~i~Cv~gss~aeEW~e~----------m~l~GDIVE~~~~g~~~~~~~~~~~~v~~~apFk~gksgl~k~L~k~ 86 (488)
..|.|.-|- +.|.|+++ .+.+||+|+.|. | ..+ +....+.+.|..-
T Consensus 12 ~~y~I~~I~------~gd~~~~~~~sPL~~pGv~v~~GD~I~aIn-G------------~~v-----~~~~~~~~lL~~~ 67 (88)
T PF14685_consen 12 GGYRIARIY------PGDPWNPNARSPLAQPGVDVREGDYILAIN-G------------QPV-----TADANPYRLLEGK 67 (88)
T ss_dssp TEEEEEEE-------BS-TTSSS-B-GGGGGS----TT-EEEEET-T------------EE------BTTB-HHHHHHTT
T ss_pred CEEEEEEEe------CCCCCCccccCCccCCCCCCCCCCEEEEEC-C------------EEC-----CCCCCHHHHhccc
Confidence 345555554 45677744 577999999997 2 334 3335566666532
Q ss_pred hcCccceEEEEEecCcc
Q 011319 87 FKNKETSILVRVRRGAE 103 (488)
Q Consensus 87 ~k~~e~si~vrVrRG~~ 103 (488)
....|.+.|++++.
T Consensus 68 ---agk~V~Ltv~~~~~ 81 (88)
T PF14685_consen 68 ---AGKQVLLTVNRKPG 81 (88)
T ss_dssp ---TTSEEEEEEE-STT
T ss_pred ---CCCEEEEEEecCCC
Confidence 33478999999886
No 12
>PF04495 GRASP55_65: GRASP55/65 PDZ-like domain ; InterPro: IPR007583 GRASP55 (Golgi reassembly stacking protein of 55 kDa) and GRASP65 (a 65 kDa) protein are highly homologous. GRASP55 is a component of the Golgi stacking machinery. GRASP65, an N-ethylmaleimide-sensitive membrane protein required for the stacking of Golgi cisternae in a cell-free system [].; PDB: 3RLE_A 4EDJ_A.
Probab=43.41 E-value=30 Score=31.60 Aligned_cols=38 Identities=24% Similarity=0.389 Sum_probs=27.2
Q ss_pred CCCcceeeeeeecc-----cceEEEEEeecCCCCCccchhhHHHHH
Q 011319 306 EGDSKLGFAISRTE-----EGFIYISTVIDDDENIPSTRSGLSILY 346 (488)
Q Consensus 306 ~gdtRlGfaIsRTE-----EGFiyVsSV~~~~~g~~a~RsGL~~Ly 346 (488)
.|...||+.|..++ +.+..|=.|.+ ++||..|||..-+
T Consensus 23 ~~~g~LG~sv~~~~~~~~~~~~~~Vl~V~p---~SPA~~AGL~p~~ 65 (138)
T PF04495_consen 23 GGQGLLGISVRFESFEGAEEEGWHVLRVAP---NSPAAKAGLEPFF 65 (138)
T ss_dssp SSSSSS-EEEEEEE-TTGCCCEEEEEEE-T---TSHHHHTT--TTT
T ss_pred CCCCCCcEEEEEecccccccceEEEeEecC---CCHHHHCCccccc
Confidence 35689999998754 55999999995 7999999997543
No 13
>cd04454 S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein, and Rrp40 and Csl4 proteins, also represented in this group, are subunits of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=41.10 E-value=66 Score=25.60 Aligned_cols=56 Identities=18% Similarity=0.056 Sum_probs=29.9
Q ss_pred ccccCCceeeeEeecCCCCCCCCCCceeeeecC------CCCchhhHHHHHhhhhcCccceEEEEEec
Q 011319 39 DMLQTGDIVEEFTIGGGSGLGSGSGSCRTYKAP------FKNGRSGVQKILHGSFKNKETSILVRVRR 100 (488)
Q Consensus 39 ~m~l~GDIVE~~~~g~~~~~~~~~~~~v~~~ap------Fk~gksgl~k~L~k~~k~~e~si~vrVrR 100 (488)
+.|..||+|.+.-++-.+. +.++.+.++ +..-...-.+.+++.++-+| -|.++|-+
T Consensus 2 y~p~~GdiV~G~V~~v~~~-----~~~V~i~~~~~g~l~~~~~~~~~~~~~~~~~~~GD-~i~~~V~~ 63 (82)
T cd04454 2 YLPDVGDIVIGIVTEVNSR-----FWKVDILSRGTARLEDSSATEKDKKEIRKSLQPGD-LILAKVIS 63 (82)
T ss_pred CCCCCCCEEEEEEEEEcCC-----EEEEEeCCCceEEeechhccCcchHHHHhcCCCCC-EEEEEEEE
Confidence 4688999999877655442 333433221 11100112455666677666 66666654
No 14
>PF02470 MCE: mce related protein; InterPro: IPR003399 This domain is found in all 24 mce genes associated with the four mammalian cell entry (mce) operons of Mycobacterium tuberculosis and their homologs in other Actinomycetales [, ]. The archetype (mce1A, Rv0169), was isolated as being necessary for colonisation of, and survival within, the macrophage []. The domain is also found in: Chloroplast Ycf22 and related cyanobacterial homologs, the majority of which have an N-terminal transmembrane domain and are putative ABC transporters. Proteobacterial homologs, which include YrbD, YebT, VpsC and Ttg2C, the latter being annotated as a toluene tolerance proteins, belong to the periplasmic substrate-binding ABC transporter superfamily.
Probab=40.00 E-value=39 Score=26.92 Aligned_cols=32 Identities=25% Similarity=0.635 Sum_probs=27.5
Q ss_pred cccccccceeeEEEeeeccccceeeeEeeecCCC
Q 011319 275 DYHGVDLGVVRAVRLWYAPVGGELAIEIKLKEGD 308 (488)
Q Consensus 275 dyhg~digVVravRLWy~P~~~E~~lEi~~~~gd 308 (488)
-|.|++||-|..|+| .+....+.+++.++++-
T Consensus 22 ~~~Gv~VG~V~~i~l--~~~~~~v~v~~~i~~~~ 53 (81)
T PF02470_consen 22 RYRGVEVGKVTSIEL--DPDGNRVRVTLRIDPDY 53 (81)
T ss_pred EECCEEEEEEEEEEE--cCCCCEEEEEEEEcCCc
Confidence 377999999999999 88888888888888755
No 15
>PHA00008 J DNA packaging protein
Probab=39.69 E-value=14 Score=26.20 Aligned_cols=9 Identities=44% Similarity=1.187 Sum_probs=7.4
Q ss_pred eeEEEeeec
Q 011319 284 VRAVRLWYA 292 (488)
Q Consensus 284 VravRLWy~ 292 (488)
-+|.||||-
T Consensus 12 ~KGARLWYV 20 (26)
T PHA00008 12 RKGARLWYV 20 (26)
T ss_pred cCceEEEEe
Confidence 368999995
No 16
>cd00991 PDZ_archaeal_metalloprotease PDZ domain of archaeal zinc metalloprotases, presumably membrane-associated or integral membrane proteases, which may be involved in signalling and regulatory mechanisms. May be responsible for substrate recognition and/or binding, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of protease-associated PDZ domains a C-terminal beta-strand forms the peptide-binding groove base, a circular permutation with respect to PDZ domains found in Eumetazoan signaling proteins.
Probab=38.63 E-value=1.3e+02 Score=23.87 Aligned_cols=45 Identities=22% Similarity=0.279 Sum_probs=29.7
Q ss_pred ccccCCceeeeEeecCCCCCCCCCCceeeeecCCCCchhhHHHHHhhhhcCccceEEEEEecCcc
Q 011319 39 DMLQTGDIVEEFTIGGGSGLGSGSGSCRTYKAPFKNGRSGVQKILHGSFKNKETSILVRVRRGAE 103 (488)
Q Consensus 39 ~m~l~GDIVE~~~~g~~~~~~~~~~~~v~~~apFk~gksgl~k~L~k~~k~~e~si~vrVrRG~~ 103 (488)
.-+++||+|.+|. | ..+ ..-..+.++|.+... ++ .+.+.|.|++.
T Consensus 26 aGL~~GDiI~~In-g------------~~v-----~~~~d~~~~l~~~~~-g~-~v~l~v~r~g~ 70 (79)
T cd00991 26 AVLHTGDVIYSIN-G------------TPI-----TTLEDFMEALKPTKP-GE-VITVTVLPSTT 70 (79)
T ss_pred cCCCCCCEEEEEC-C------------EEc-----CCHHHHHHHHhcCCC-CC-EEEEEEEECCE
Confidence 4699999999984 1 122 122567777765322 33 78899998875
No 17
>cd03034 ArsC_ArsC Arsenate Reductase (ArsC) family, ArsC subfamily; arsenic reductases similar to that encoded by arsC on the R733 plasmid of Escherichia coli. E. coli ArsC catalyzes the reduction of arsenate [As(V)] to arsenite [As(III)], the first step in the detoxification of arsenic, using reducing equivalents derived from glutathione (GSH) via glutaredoxin (GRX). ArsC contains a single catalytic cysteine, within a thioredoxin fold, that forms a covalent thiolate-As(V) intermediate, which is reduced by GRX through a mixed GSH-arsenate intermediate. This family of predominantly bacterial enzymes is unrelated to two other families of arsenate reductases which show similarity to low-molecular-weight acid phosphatases and phosphotyrosyl phosphatases.
Probab=36.87 E-value=36 Score=29.24 Aligned_cols=27 Identities=15% Similarity=0.117 Sum_probs=22.8
Q ss_pred HHHHHHHHHHHhhhcCCCcEEEEeechhhh
Q 011319 212 DTLARANAWLNASQATGVPIVFMNIQTESL 241 (488)
Q Consensus 212 dT~ARa~AWlsAsqaSGVPIvFvNIQTE~l 241 (488)
+|..+|.+||-+. |+|..|.||-.+++
T Consensus 10 ~t~rkA~~~L~~~---~i~~~~~di~~~~~ 36 (112)
T cd03034 10 SKSRNALALLEEA---GIEPEIVEYLKTPP 36 (112)
T ss_pred HHHHHHHHHHHHC---CCCeEEEecccCCc
Confidence 5788999999854 99999999986664
No 18
>PF09255 Antig_Caf1: Caf1 Capsule antigen; InterPro: IPR015335 Members of this family represent the F1 capsule antigen Caf1 synthesised by Yersinia bacteria. They adopt a structure consisting of a seven strands arranged in two beta-sheets, in a Greek-key topology, and mediate targeting of the bacterium to sites of infection []. ; PDB: 3DOS_E 1P5U_C 3DPB_C 1Z9S_B 1P5V_B 3DSN_E.
Probab=33.85 E-value=16 Score=33.78 Aligned_cols=63 Identities=24% Similarity=0.312 Sum_probs=33.0
Q ss_pred hhhcCCCcEEEE---eechhhhhh--hccccccceeecCCCcCccchhccccccccccccccccceeeEE
Q 011319 223 ASQATGVPIVFM---NIQTESLLT--KISGETASSTVNSGSLSDLSNVANASLYGFEDYHGVDLGVVRAV 287 (488)
Q Consensus 223 AsqaSGVPIvFv---NIQTE~llT--kisge~as~tvn~gsl~dl~n~an~slygfedyhg~digVVrav 287 (488)
+--.-|.||..| |||||-+.- .++|++.+.++-.=+.+|....+....+.-+ .|-|-+.+.+|
T Consensus 8 ~T~~~GA~iT~mDN~~~~tel~vG~lTL~GYK~~~~~~~~~FtD~~G~~~~Lt~~~~--~GN~~~~~~~v 75 (136)
T PF09255_consen 8 LTYKEGAPITIMDNGNIDTELLVGTLTLGGYKTGTTSTSVNFTDAAGDPMYLTFTSQ--DGNNHQFTTKV 75 (136)
T ss_dssp EEEEE-S-EEB-TTS-B-SS-EEEEEEEES--TT-BGGGEEEEESS--TT-EEEEES--SSS--EEEEEE
T ss_pred EEecCCCceEEecCCcccceEEEEEEEeccccCCceeeeeeeeecCCCceEEEEecc--cCCceEEEeee
Confidence 334568999996 899998854 3578988888776667787777665554444 46666666665
No 19
>cd00431 cysteine_hydrolases Cysteine hydrolases; This family contains amidohydrolases, like CSHase (N-carbamoylsarcosine amidohydrolase), involved in creatine metabolism and nicotinamidase, converting nicotinamide to nicotinic acid and ammonia in the pyridine nucleotide cycle. It also contains isochorismatase, an enzyme that catalyzes the conversion of isochorismate to 2,3-dihydroxybenzoate and pyruvate, via the hydrolysis of the vinyl ether bond, and other related enzymes with unknown function.
Probab=33.71 E-value=77 Score=27.45 Aligned_cols=32 Identities=22% Similarity=0.440 Sum_probs=27.9
Q ss_pred ccHHHHHHHHHHHHHhhhcCCCcEEEEeechh
Q 011319 208 NDVEDTLARANAWLNASQATGVPIVFMNIQTE 239 (488)
Q Consensus 208 nsvEdT~ARa~AWlsAsqaSGVPIvFvNIQTE 239 (488)
...++.+++.+..+.++...|+||||++.-..
T Consensus 20 ~~~~~~~~~i~~l~~~ar~~~~~vi~~~~~~~ 51 (161)
T cd00431 20 PGADELVPNINRLLAAARAAGIPVIFTRDWHP 51 (161)
T ss_pred ccHHHHHHHHHHHHHHHHHcCCeEEEEEeeec
Confidence 46789999999999999999999999985443
No 20
>cd00988 PDZ_CTP_protease PDZ domain of C-terminal processing-, tail-specific-, and tricorn proteases, which function in posttranslational protein processing, maturation, and disassembly or degradation, in Bacteria, Archaea, and plant chloroplasts. May be responsible for substrate recognition and/or binding, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of protease-associated PDZ domains a C-terminal beta-strand forms the peptide-binding groove base, a circular permutation with respect to PDZ domains found in Eumetazoan signaling proteins.
Probab=33.68 E-value=38 Score=26.27 Aligned_cols=46 Identities=17% Similarity=0.478 Sum_probs=30.1
Q ss_pred cceeeeeeecccceEEEEEeecCCCCCccchhhHHHHHHHHHhcCcEEEEEeecCeeecc
Q 011319 309 SKLGFAISRTEEGFIYISTVIDDDENIPSTRSGLSILYKEAVSASKLLVVSRVSNQKVLP 368 (488)
Q Consensus 309 tRlGfaIsRTEEGFiyVsSV~~~~~g~~a~RsGL~~Ly~~A~~a~kLLVISRv~g~kVlP 368 (488)
.+||+.+.--+.| ++|+.|.. ++|+.++||. .|-.+ -.+.|+.+--
T Consensus 2 ~~lG~~~~~~~~~-~~V~~v~~---~s~a~~~gl~--------~GD~I--~~vng~~i~~ 47 (85)
T cd00988 2 GGIGLELKYDDGG-LVITSVLP---GSPAAKAGIK--------AGDII--VAIDGEPVDG 47 (85)
T ss_pred eEEEEEEEEcCCe-EEEEEecC---CCCHHHcCCC--------CCCEE--EEECCEEcCC
Confidence 3688888643334 77889885 6899999984 34333 3566665543
No 21
>cd00990 PDZ_glycyl_aminopeptidase PDZ domain associated with archaeal and bacterial M61 glycyl-aminopeptidases. May be responsible for substrate recognition and/or binding, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of protease-associated PDZ domains a C-terminal beta-strand is presumed to form the peptide-binding groove base, a circular permutation with respect to PDZ domains found in Eumetazoan signaling proteins.
Probab=32.81 E-value=31 Score=26.61 Aligned_cols=43 Identities=28% Similarity=0.482 Sum_probs=28.5
Q ss_pred ceeeeeeecccceEEEEEeecCCCCCccchhhHHHHHHHHHhcCcEEEEEeecCeee
Q 011319 310 KLGFAISRTEEGFIYISTVIDDDENIPSTRSGLSILYKEAVSASKLLVVSRVSNQKV 366 (488)
Q Consensus 310 RlGfaIsRTEEGFiyVsSV~~~~~g~~a~RsGL~~Ly~~A~~a~kLLVISRv~g~kV 366 (488)
.||+.+.-. +|=+.|+.|.. ++||.++||+ .|-. |-.+.|+++
T Consensus 2 ~~G~~~~~~-~~~~~V~~V~~---~s~a~~aGl~--------~GD~--I~~Ing~~v 44 (80)
T cd00990 2 YLGLTLDKE-EGLGKVTFVRD---DSPADKAGLV--------AGDE--LVAVNGWRV 44 (80)
T ss_pred cccEEEEcc-CCcEEEEEECC---CChHHHhCCC--------CCCE--EEEECCEEh
Confidence 367777544 44477999985 7899999973 3433 346677765
No 22
>KOG3129 consensus 26S proteasome regulatory complex, subunit PSMD9 [Posttranslational modification, protein turnover, chaperones]
Probab=32.52 E-value=22 Score=35.82 Aligned_cols=38 Identities=24% Similarity=0.497 Sum_probs=26.3
Q ss_pred ceEEEEEeecCCCCCccchhhHHHHHHHHHhcCcEEEEEeecCeeecc
Q 011319 321 GFIYISTVIDDDENIPSTRSGLSILYKEAVSASKLLVVSRVSNQKVLP 368 (488)
Q Consensus 321 GFiyVsSV~~~~~g~~a~RsGL~~Ly~~A~~a~kLLVISRv~g~kVlP 368 (488)
-|+.|+||.. ++||+++||+ .--.+|=++-|.+..-+|
T Consensus 139 ~Fa~V~sV~~---~SPA~~aGl~-------~gD~il~fGnV~sgn~~~ 176 (231)
T KOG3129|consen 139 PFAVVDSVVP---GSPADEAGLC-------VGDEILKFGNVHSGNFLP 176 (231)
T ss_pred ceEEEeecCC---CChhhhhCcc-------cCceEEEecccccccchh
Confidence 4999999995 7999999995 334445455554444444
No 23
>PF00857 Isochorismatase: Isochorismatase family; InterPro: IPR000868 This is a family of hydrolase enzymes. Isochorismatase, also known as 2,3 dihydro-2,3 dihydroxybenzoate synthase catalyses the conversion of isochorismate, in the presence of water, to 2,3-dihydroxybenzoate and pyruvate (3.3.2.1 from EC).; GO: 0003824 catalytic activity, 0008152 metabolic process; PDB: 1XN4_A 3KL2_F 1YZV_A 3IRV_A 1IM5_A 1ILW_A 3PL1_A 1NF9_A 1NF8_A 1X9G_A ....
Probab=32.42 E-value=54 Score=28.66 Aligned_cols=33 Identities=24% Similarity=0.409 Sum_probs=30.3
Q ss_pred cccHHHHHHHHHHHHHhhhcCCCcEEEEeechh
Q 011319 207 YNDVEDTLARANAWLNASQATGVPIVFMNIQTE 239 (488)
Q Consensus 207 ynsvEdT~ARa~AWlsAsqaSGVPIvFvNIQTE 239 (488)
-...++.+.+.+.++.++.+.|+||+|++...+
T Consensus 19 ~~~~~~~i~~i~~l~~~~r~~~~~Vi~~~~~~~ 51 (174)
T PF00857_consen 19 PPNAEAIIPNINRLLDAARAAGVPVIHTRDIHD 51 (174)
T ss_dssp STTHHHHHHHHHHHHHHHHHTTEEEEEEEESBS
T ss_pred ccCHHHHHHHHHHHHHHHHHhCCCeEEEEeeec
Confidence 457889999999999999999999999998887
No 24
>PF12910 RelB_N: Antitoxin of toxin-antitoxin stability system N-terminal; PDB: 3K6Q_C.
Probab=32.04 E-value=68 Score=24.23 Aligned_cols=31 Identities=23% Similarity=0.449 Sum_probs=23.7
Q ss_pred cchhhHHHHHHHHHhcCcEEEEEeecCeeec
Q 011319 337 STRSGLSILYKEAVSASKLLVVSRVSNQKVL 367 (488)
Q Consensus 337 a~RsGL~~Ly~~A~~a~kLLVISRv~g~kVl 367 (488)
..|..|..|.+.|.+-...++|.|=+++.+.
T Consensus 8 eAR~~ls~l~d~v~~~~~~viI~R~~~~~v~ 38 (46)
T PF12910_consen 8 EARNNLSKLIDRVVNGEEVVIITRRGKPSVV 38 (46)
T ss_dssp HHHHTHHHHHHHHHHT--EE-EEE-TTEEEE
T ss_pred HHHHhHHHHHHHHHcCCCeEEEEecCCCcEE
Confidence 4689999999999999999889999988763
No 25
>KOG3209 consensus WW domain-containing protein [General function prediction only]
Probab=31.76 E-value=82 Score=36.91 Aligned_cols=72 Identities=29% Similarity=0.418 Sum_probs=49.7
Q ss_pred eeeeeccc---ceEEEEEeecC-------CCCCccchhhHHHHHHHHHhcCcEEE---EEeecCeeecceeeecCCceec
Q 011319 313 FAISRTEE---GFIYISTVIDD-------DENIPSTRSGLSILYKEAVSASKLLV---VSRVSNQKVLPWIVSSTGAVRC 379 (488)
Q Consensus 313 faIsRTEE---GFiyVsSV~~~-------~~g~~a~RsGL~~Ly~~A~~a~kLLV---ISRv~g~kVlPwmVsSsGaIrC 379 (488)
+-|-|-|. ||+.+||+.+. .+|+||||-| ||=| |.-|.|+.++-
T Consensus 757 V~lhR~ENeGFGFVi~sS~~kp~sgiGrIieGSPAdRCg------------kLkVGDrilAVNG~sI~~----------- 813 (984)
T KOG3209|consen 757 VVLHRKENEGFGFVIMSSQNKPESGIGRIIEGSPADRCG------------KLKVGDRILAVNGQSILN----------- 813 (984)
T ss_pred eEEecccCCceeEEEEecccCCCCCccccccCChhHhhc------------cccccceEEEecCeeeec-----------
Confidence 44566665 88999999863 5789999876 4444 34455555542
Q ss_pred cCcccccccccccccccCceEEEEEEecCcc
Q 011319 380 FDTVSLSQKLSLHRHAKVPILLHVFLWDQAL 410 (488)
Q Consensus 380 ~Dt~slsqkLslhr~a~~pI~lHvm~W~~~~ 410 (488)
.|-.+..+|-.++.-.++|-+.-=+..-
T Consensus 814 ---lsHadiv~LIKdaGlsVtLtIip~ee~~ 841 (984)
T KOG3209|consen 814 ---LSHADIVSLIKDAGLSVTLTIIPPEEAG 841 (984)
T ss_pred ---cCchhHHHHHHhcCceEEEEEcChhccC
Confidence 2335788899999999999987655433
No 26
>cd00987 PDZ_serine_protease PDZ domain of tryspin-like serine proteases, such as DegP/HtrA, which are oligomeric proteins involved in heat-shock response, chaperone function, and apoptosis. May be responsible for substrate recognition and/or binding, as most PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of protease-associated PDZ domains a C-terminal beta-strand forms the peptide-binding groove base, a circular permutation with respect to PDZ domains found in Eumetazoan signaling proteins.
Probab=31.41 E-value=1.3e+02 Score=23.32 Aligned_cols=44 Identities=18% Similarity=0.339 Sum_probs=28.7
Q ss_pred cccCCceeeeEeecCCCCCCCCCCceeeeecCCCCchhhHHHHHhhhhcCccceEEEEEecCcc
Q 011319 40 MLQTGDIVEEFTIGGGSGLGSGSGSCRTYKAPFKNGRSGVQKILHGSFKNKETSILVRVRRGAE 103 (488)
Q Consensus 40 m~l~GDIVE~~~~g~~~~~~~~~~~~v~~~apFk~gksgl~k~L~k~~k~~e~si~vrVrRG~~ 103 (488)
-+++||+|-+|. | ..+ ..-..+.++|.+.. ....+.+.+.|++.
T Consensus 41 gl~~GD~I~~In-g------------~~i-----~~~~~~~~~l~~~~--~~~~i~l~v~r~g~ 84 (90)
T cd00987 41 GLKPGDVILAVN-G------------KPV-----KSVADLRRALAELK--PGDKVTLTVLRGGK 84 (90)
T ss_pred CCCcCCEEEEEC-C------------EEC-----CCHHHHHHHHHhcC--CCCEEEEEEEECCE
Confidence 499999999885 2 122 22245677776532 24478899888774
No 27
>PF13501 SoxY: Sulfur oxidation protein SoxY; PDB: 2OXG_B 2OX5_B 2OXH_F 2NNF_A 2NNC_B.
Probab=30.09 E-value=1.5e+02 Score=26.33 Aligned_cols=45 Identities=20% Similarity=0.361 Sum_probs=38.2
Q ss_pred eEEEeeeccccceeeeEeeecCCCcceeeeeeecccceEEEEEee
Q 011319 285 RAVRLWYAPVGGELAIEIKLKEGDSKLGFAISRTEEGFIYISTVI 329 (488)
Q Consensus 285 ravRLWy~P~~~E~~lEi~~~~gdtRlGfaIsRTEEGFiyVsSV~ 329 (488)
.+..+.|.|..++..+...++-+++--=.+|-+|..|-.|+.+-.
T Consensus 59 ~~a~f~~~p~~~~~~~stRir~~~~s~V~ava~t~dG~~~~a~~~ 103 (111)
T PF13501_consen 59 LAATFELTPAGGEPYVSTRIRMAQTSPVRAVAETSDGKLYMASKE 103 (111)
T ss_dssp EEEEEEE-TTCCEEEEEEEEE-SSSEEEEEEEEETTTEEEEEEEE
T ss_pred EEEEEEEcCCCCCceeEEEEEecCcccEEEEEEecCCeEEEeeEE
Confidence 467888999999999999999999999999999999999998743
No 28
>PF11243 DUF3045: Protein of unknown function (DUF3045); InterPro: IPR021405 This entry is represented by Bacteriophage T4, Gp30.1; it is a family of uncharacterised viral proteins.
Probab=29.02 E-value=20 Score=31.39 Aligned_cols=15 Identities=40% Similarity=0.636 Sum_probs=11.9
Q ss_pred eeeecccceEEEEEe
Q 011319 314 AISRTEEGFIYISTV 328 (488)
Q Consensus 314 aIsRTEEGFiyVsSV 328 (488)
=+.|-|.||||||--
T Consensus 39 f~eCVeqGFiYVs~~ 53 (89)
T PF11243_consen 39 FKECVEQGFIYVSKY 53 (89)
T ss_pred HHHHHhcceEEEEee
Confidence 367899999999653
No 29
>TIGR01713 typeII_sec_gspC general secretion pathway protein C. This model represents GspC, protein C of the main terminal branch of the general secretion pathway, also called type II secretion. This system transports folded proteins across the bacterial outer membrane and is widely distributed in Gram-negative pathogens.
Probab=28.88 E-value=1.3e+02 Score=29.92 Aligned_cols=46 Identities=24% Similarity=0.285 Sum_probs=30.4
Q ss_pred cccccCCceeeeEeecCCCCCCCCCCceeeeecCCCCchhhHHHHHhhhhcCccceEEEEEecCcc
Q 011319 38 ADMLQTGDIVEEFTIGGGSGLGSGSGSCRTYKAPFKNGRSGVQKILHGSFKNKETSILVRVRRGAE 103 (488)
Q Consensus 38 e~m~l~GDIVE~~~~g~~~~~~~~~~~~v~~~apFk~gksgl~k~L~k~~k~~e~si~vrVrRG~~ 103 (488)
.--+++||||.+|. | ..+ .--..+.+++.+.. ..+.+.+.|.|++.
T Consensus 206 ~aGLr~GDvIv~IN-G------------~~i-----~~~~~~~~~l~~~~--~~~~v~l~V~R~G~ 251 (259)
T TIGR01713 206 KSGLQDGDIAVALN-G------------LDL-----RDPEQAFQALQMLR--EETNLTLTVERDGQ 251 (259)
T ss_pred HcCCCCCCEEEEEC-C------------EEc-----CCHHHHHHHHHhcC--CCCeEEEEEEECCE
Confidence 44589999999887 2 222 12245666666542 33479999999986
No 30
>PF04726 Microvir_J: Microvirus J protein; InterPro: IPR006815 This small protein is involved in DNA packaging, interacting with DNA via its hydrophobic C terminus. In bacteriophage phi-X174, J is present in 60 copies, and forms an S-shaped polypeptide chain without any secondary structure. It is thought to interact with DNA through simple charge interactions [].; GO: 0003677 DNA binding, 0019073 viral DNA genome packaging, 0019028 viral capsid; PDB: 1M06_J 1GFF_3 1RB8_J 2BPA_3.
Probab=28.69 E-value=13 Score=25.89 Aligned_cols=10 Identities=40% Similarity=1.016 Sum_probs=3.6
Q ss_pred eeEEEeeecc
Q 011319 284 VRAVRLWYAP 293 (488)
Q Consensus 284 VravRLWy~P 293 (488)
-+|.||||--
T Consensus 11 ~kgarlwyvg 20 (24)
T PF04726_consen 11 RKGARLWYVG 20 (24)
T ss_dssp SSSS----SS
T ss_pred cCceEEEEec
Confidence 3688999953
No 31
>cd05790 S1_Rrp40 S1_Rrp40: Rrp40 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=27.17 E-value=1.9e+02 Score=24.88 Aligned_cols=55 Identities=13% Similarity=0.097 Sum_probs=36.2
Q ss_pred ccccCCceeeeEeecCCCCCCCCCCceeeeecC---------CCCchhhHHHHHhhhhcCccceEEEEEecCcc
Q 011319 39 DMLQTGDIVEEFTIGGGSGLGSGSGSCRTYKAP---------FKNGRSGVQKILHGSFKNKETSILVRVRRGAE 103 (488)
Q Consensus 39 ~m~l~GDIVE~~~~g~~~~~~~~~~~~v~~~ap---------Fk~gksgl~k~L~k~~k~~e~si~vrVrRG~~ 103 (488)
+.|.+||+|-++-++.... .-.+.+.+| |.|+ .|.++..++.+| -|..||..=+.
T Consensus 2 Y~P~~gD~VIG~V~~~~~~-----~~~VdI~s~~~a~L~~~~f~ga----tk~~rp~L~~GD-lV~ArV~~~~~ 65 (86)
T cd05790 2 YVPAKGDHVIGIVVAKAGD-----FFKVDIGGSEPASLSYLAFEGA----TKRNRPNLNVGD-LVYARVVKANR 65 (86)
T ss_pred CcCCCCCEEEEEEEEEcCC-----eEEEEcCCCcceEechHHcccc----cccccccCCCCC-EEEEEEEecCC
Confidence 5789999999888765431 222333333 5444 455677788777 89999887665
No 32
>PRK10942 serine endoprotease; Provisional
Probab=26.92 E-value=1.5e+02 Score=31.79 Aligned_cols=57 Identities=21% Similarity=0.331 Sum_probs=37.1
Q ss_pred EEEEEccCCccccccccccccCCceeeeEeecCCCCCCCCCCceeeeecCCCCchhhHHHHHhhhhcCccceEEEEEecC
Q 011319 22 LSIDCLKGTSKADEWTADMLQTGDIVEEFTIGGGSGLGSGSGSCRTYKAPFKNGRSGVQKILHGSFKNKETSILVRVRRG 101 (488)
Q Consensus 22 ~~i~Cv~gss~aeEW~e~m~l~GDIVE~~~~g~~~~~~~~~~~~v~~~apFk~gksgl~k~L~k~~k~~e~si~vrVrRG 101 (488)
+.|..|...+.|+ ..-|++||+|.+|. +. .+ ..-..|.+.|++ + . ..+.+.|+|+
T Consensus 410 vvV~~V~~~S~A~---~aGL~~GDvIv~VN-g~------------~V-----~s~~dl~~~l~~--~-~-~~v~l~V~R~ 464 (473)
T PRK10942 410 VVVDNVKPGTPAA---QIGLKKGDVIIGAN-QQ------------PV-----KNIAELRKILDS--K-P-SVLALNIQRG 464 (473)
T ss_pred eEEEEeCCCChHH---HcCCCCCCEEEEEC-CE------------Ec-----CCHHHHHHHHHh--C-C-CeEEEEEEEC
Confidence 3455565555443 23499999999986 21 12 122677788876 2 3 4899999999
Q ss_pred cc
Q 011319 102 AE 103 (488)
Q Consensus 102 ~~ 103 (488)
+.
T Consensus 465 g~ 466 (473)
T PRK10942 465 DS 466 (473)
T ss_pred CE
Confidence 86
No 33
>TIGR02860 spore_IV_B stage IV sporulation protein B. SpoIVB, the stage IV sporulation protein B of endospore-forming bacteria such as Bacillus subtilis, is a serine proteinase, expressed in the spore (rather than mother cell) compartment, that participates in a proteolytic activation cascade for Sigma-K. It appears to be universal among endospore-forming bacteria and occurs nowhere else.
Probab=26.77 E-value=1.9e+02 Score=31.24 Aligned_cols=45 Identities=13% Similarity=0.315 Sum_probs=32.1
Q ss_pred cccccCCceeeeEeecCCCCCCCCCCceeeeecCCCCchhhHHHHHhhhhcCccceEEEEEecCcc
Q 011319 38 ADMLQTGDIVEEFTIGGGSGLGSGSGSCRTYKAPFKNGRSGVQKILHGSFKNKETSILVRVRRGAE 103 (488)
Q Consensus 38 e~m~l~GDIVE~~~~g~~~~~~~~~~~~v~~~apFk~gksgl~k~L~k~~k~~e~si~vrVrRG~~ 103 (488)
+.-+++||+|.+|. + ..+ .....|.++|++.- ...+.+.|+|+..
T Consensus 128 ~AGLq~GDiIvsIN-G------------~~V-----~s~~DL~~iL~~~~---g~~V~LtV~R~Ge 172 (402)
T TIGR02860 128 EAGIQIGDRILKIN-G------------EKI-----KNMDDLANLINKAG---GEKLTLTIERGGK 172 (402)
T ss_pred HcCCCCCCEEEEEC-C------------EEC-----CCHHHHHHHHHhCC---CCeEEEEEEECCE
Confidence 34699999999985 2 223 33467888887663 3479999999885
No 34
>TIGR02037 degP_htrA_DO periplasmic serine protease, Do/DeqQ family. This family consists of a set proteins various designated DegP, heat shock protein HtrA, and protease DO. The ortholog in Pseudomonas aeruginosa is designated MucD and is found in an operon that controls mucoid phenotype. This family also includes the DegQ (HhoA) paralog in E. coli which can rescue a DegP mutant, but not the smaller DegS paralog, which cannot. Members of this family are located in the periplasm and have separable functions as both protease and chaperone. Members have a trypsin domain and two copies of a PDZ domain. This protein protects bacteria from thermal and other stresses and may be important for the survival of bacterial pathogens.// The chaperone function is dominant at low temperatures, whereas the proteolytic activity is turned on at elevated temperatures.
Probab=23.84 E-value=2e+02 Score=29.89 Aligned_cols=44 Identities=20% Similarity=0.366 Sum_probs=30.2
Q ss_pred cccCCceeeeEeecCCCCCCCCCCceeeeecCCCCchhhHHHHHhhhhcCccceEEEEEecCcc
Q 011319 40 MLQTGDIVEEFTIGGGSGLGSGSGSCRTYKAPFKNGRSGVQKILHGSFKNKETSILVRVRRGAE 103 (488)
Q Consensus 40 m~l~GDIVE~~~~g~~~~~~~~~~~~v~~~apFk~gksgl~k~L~k~~k~~e~si~vrVrRG~~ 103 (488)
-+++||+|.+|. + ..+ ..-..+.++|++. +.++ .+.+.|.|++.
T Consensus 379 GL~~GDvI~~In-g------------~~V-----~s~~d~~~~l~~~-~~g~-~v~l~v~R~g~ 422 (428)
T TIGR02037 379 GLQPGDVILSVN-Q------------QPV-----SSVAELRKVLDRA-KKGG-RVALLILRGGA 422 (428)
T ss_pred CCCCCCEEEEEC-C------------EEc-----CCHHHHHHHHHhc-CCCC-EEEEEEEECCE
Confidence 499999999986 2 122 2225677777653 3234 79999999986
No 35
>TIGR00054 RIP metalloprotease RseP. A model that detects fragments as well matches a number of members of the PEPTIDASE FAMILY S2C. The region of match appears not to overlap the active site domain.
Probab=23.04 E-value=2e+02 Score=30.18 Aligned_cols=53 Identities=21% Similarity=0.394 Sum_probs=34.5
Q ss_pred ccccCCceeeeEeecCCCCCCCCCCceeeeecCCCCchhhHHHHHhhhhcCccceEEEEEecCcccceeeeEEeecC
Q 011319 39 DMLQTGDIVEEFTIGGGSGLGSGSGSCRTYKAPFKNGRSGVQKILHGSFKNKETSILVRVRRGAEEFAELQACIVPE 115 (488)
Q Consensus 39 ~m~l~GDIVE~~~~g~~~~~~~~~~~~v~~~apFk~gksgl~k~L~k~~k~~e~si~vrVrRG~~~~~eL~AciVpe 115 (488)
.-+++||+|.++. | ..+ ..-..+.+.|.+. ....+.+.|+|++. .+...+.|+
T Consensus 219 aGL~~GD~Iv~Vn-g------------~~V-----~s~~dl~~~l~~~---~~~~v~l~v~R~g~---~~~~~v~~~ 271 (420)
T TIGR00054 219 AGLKEGDYIQSIN-G------------EKL-----RSWTDFVSAVKEN---PGKSMDIKVERNGE---TLSISLTPE 271 (420)
T ss_pred cCCCCCCEEEEEC-C------------EEC-----CCHHHHHHHHHhC---CCCceEEEEEECCE---EEEEEEEEc
Confidence 4599999999885 2 122 1235788888762 23369999999885 344445554
No 36
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=22.81 E-value=1.3e+02 Score=29.37 Aligned_cols=56 Identities=18% Similarity=0.135 Sum_probs=33.8
Q ss_pred ccccCCceeeeEeecCCCCCCCCCCceeeeecCCCCch--hh--------HHHHHhhhhcCccceEEEEEec
Q 011319 39 DMLQTGDIVEEFTIGGGSGLGSGSGSCRTYKAPFKNGR--SG--------VQKILHGSFKNKETSILVRVRR 100 (488)
Q Consensus 39 ~m~l~GDIVE~~~~g~~~~~~~~~~~~v~~~apFk~gk--sg--------l~k~L~k~~k~~e~si~vrVrR 100 (488)
+.|..||||.+.-++-... +-++.+.++|.+-= +. -.+.+++.|+-+| -|.+||-.
T Consensus 59 y~P~vGDiViG~V~~i~~~-----~~~vdI~~~~~g~L~~s~i~~~~~~~d~~~~~~~~~~GD-lV~akV~~ 124 (235)
T PRK04163 59 YIPKVGDLVIGKVTDVTFS-----GWEVDINSPYKAYLPVSEVLGRPVNVEGTDLRKYLDIGD-YIIAKVKD 124 (235)
T ss_pred ccCCCCCEEEEEEEEEeCc-----eEEEEeCCCceeEEEHHHcCCCccccchhhhHhhCCCCC-EEEEEEEE
Confidence 8899999999988765442 56677766654210 11 1244555566566 66666543
No 37
>TIGR02038 protease_degS periplasmic serine pepetdase DegS. This family consists of the periplasmic serine protease DegS (HhoB), a shorter paralog of protease DO (HtrA, DegP) and DegQ (HhoA). It is found in E. coli and several other Proteobacteria of the gamma subdivision. It contains a trypsin domain and a single copy of PDZ domain (in contrast to DegP with two copies). A critical role of this DegS is to sense stress in the periplasm and partially degrade an inhibitor of sigma(E).
Probab=21.99 E-value=2.2e+02 Score=29.09 Aligned_cols=44 Identities=14% Similarity=0.306 Sum_probs=30.4
Q ss_pred cccCCceeeeEeecCCCCCCCCCCceeeeecCCCCchhhHHHHHhhhhcCccceEEEEEecCcc
Q 011319 40 MLQTGDIVEEFTIGGGSGLGSGSGSCRTYKAPFKNGRSGVQKILHGSFKNKETSILVRVRRGAE 103 (488)
Q Consensus 40 m~l~GDIVE~~~~g~~~~~~~~~~~~v~~~apFk~gksgl~k~L~k~~k~~e~si~vrVrRG~~ 103 (488)
-+++||||.+|. + ..+ .....|..+|.+. +.++ .+.++|.|++.
T Consensus 295 GL~~GDvI~~In-g------------~~V-----~s~~dl~~~l~~~-~~g~-~v~l~v~R~g~ 338 (351)
T TIGR02038 295 GILVRDVILKYD-G------------KDV-----IGAEELMDRIAET-RPGS-KVMVTVLRQGK 338 (351)
T ss_pred CCCCCCEEEEEC-C------------EEc-----CCHHHHHHHHHhc-CCCC-EEEEEEEECCE
Confidence 499999999985 1 223 2335677777754 3344 79999999875
No 38
>PF13243 Prenyltrans_1: Prenyltransferase-like; PDB: 3SDR_A 3SAE_A 3SDV_A 3SDT_A 3SDQ_A 3SDU_A.
Probab=20.89 E-value=31 Score=28.00 Aligned_cols=57 Identities=25% Similarity=0.368 Sum_probs=13.5
Q ss_pred hhhhHHHHhhhccccccchhhhhhhhhccCCCCceeEeeeeccccccccccccccHHHHHHHHHHHHHhhh
Q 011319 155 RIVSALARARLQEGYVSYPWERRKQEVLSVPNSSCFLSMLLLPKASDVVASRYNDVEDTLARANAWLNASQ 225 (488)
Q Consensus 155 rvv~al~~~~l~d~yV~YpWe~KM~~~Lp~p~SS~~~SiL~lP~a~d~~~~~ynsvEdT~ARa~AWlsAsq 225 (488)
+.+..|.+.|..||.-.|+|.. .-....++ ++.+=... ...+++.+.||..||..-|
T Consensus 3 ~~~~~l~~~Q~~dG~W~~~~~~-------~~~~t~~~-~~al~~~~------~~~~~~ai~ka~~~l~~~Q 59 (109)
T PF13243_consen 3 RAAEWLLSQQNPDGSWGYNWGS-------DVFVTAAL-ILALAAAG------DAAVDEAIKKAIDWLLSHQ 59 (109)
T ss_dssp ----------------------------------------------------TS-SSBSSHHHHHHHHH--
T ss_pred cccccccccccccccccccccc-------cccccccc-cccccccC------CCCcHHHHHHHHHHHHHhc
Confidence 4567778889999999999882 11111111 11111111 2367888999999999764
No 39
>PRK11609 nicotinamidase/pyrazinamidase; Provisional
Probab=20.43 E-value=1.1e+02 Score=28.43 Aligned_cols=27 Identities=22% Similarity=0.447 Sum_probs=24.0
Q ss_pred cHHHHHHHHHHHHHhhhcCCCcEEEEe
Q 011319 209 DVEDTLARANAWLNASQATGVPIVFMN 235 (488)
Q Consensus 209 svEdT~ARa~AWlsAsqaSGVPIvFvN 235 (488)
..++.+++.+..+.++.+.|+||+|++
T Consensus 24 ~~~~~v~~i~~l~~~ar~~g~pVi~~~ 50 (212)
T PRK11609 24 EGDSTIDVANRLIDWCQSRGIPVIASQ 50 (212)
T ss_pred CHHHHHHHHHHHHHHHHhcCCeEEEEe
Confidence 356788899999999999999999997
Done!