Query 035404
Match_columns 53
No_of_seqs 32 out of 34
Neff 3.0
Searched_HMMs 46136
Date Fri Mar 29 02:46:15 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/035404.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/035404hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF05680 ATP-synt_E: ATP synth 99.7 7.8E-17 1.7E-21 98.7 3.7 39 11-49 6-44 (86)
2 KOG4326 Mitochondrial F1F0-ATP 98.4 3.2E-07 7E-12 57.2 4.3 32 11-42 8-39 (81)
3 COG5454 Predicted secreted pro 80.5 1.1 2.4E-05 28.5 1.4 18 20-37 59-76 (89)
4 KOG3300 NADH:ubiquinone oxidor 72.4 10 0.00022 26.0 4.5 31 9-39 34-65 (146)
5 PF06783 UPF0239: Uncharacteri 69.3 8.2 0.00018 24.2 3.2 29 3-36 7-35 (85)
6 PF03648 Glyco_hydro_67N: Glyc 67.6 2.8 6.1E-05 25.7 0.9 10 25-34 113-122 (122)
7 TIGR03725 bact_YeaZ universal 63.5 5.3 0.00011 26.2 1.7 37 4-40 63-100 (202)
8 PF12617 LdpA_C: Iron-Sulfur b 59.7 8.1 0.00018 26.9 2.1 36 3-39 100-150 (183)
9 COG1214 Inactive homolog of me 48.6 15 0.00033 24.9 2.0 34 3-36 66-100 (220)
10 PF10766 DUF2592: Protein of u 47.9 21 0.00045 20.0 2.1 22 13-34 8-29 (41)
11 PHA02047 phage lambda Rz1-like 43.1 74 0.0016 20.7 4.4 25 13-37 4-29 (101)
12 COG3777 Uncharacterized conser 42.8 7.2 0.00016 28.9 -0.3 24 2-25 156-181 (273)
13 COG3855 Fbp Uncharacterized pr 40.1 20 0.00043 29.3 1.8 18 6-23 233-251 (648)
14 PF08636 Pkr1: ER protein Pkr1 36.8 42 0.00091 20.4 2.5 19 3-24 13-31 (75)
15 COG3105 Uncharacterized protei 35.3 89 0.0019 21.3 4.1 32 15-46 7-38 (138)
16 PRK01617 hypothetical protein; 33.3 21 0.00046 23.6 0.9 14 15-28 33-46 (154)
17 PRK04233 hypothetical protein; 33.2 21 0.00045 23.2 0.8 13 16-28 38-50 (129)
18 PRK01752 hypothetical protein; 32.7 22 0.00048 23.7 0.8 14 15-28 36-49 (156)
19 PRK01842 hypothetical protein; 32.6 22 0.00048 23.8 0.8 13 16-28 53-65 (149)
20 PRK00183 hypothetical protein; 31.1 24 0.00053 23.6 0.9 14 15-28 33-46 (157)
21 PF00814 Peptidase_M22: Glycop 30.9 25 0.00054 24.3 0.9 39 4-42 59-98 (268)
22 PF01214 CK_II_beta: Casein ki 29.7 40 0.00087 22.9 1.7 15 25-39 69-83 (184)
23 smart00735 ZM ZASP-like motif. 29.1 28 0.0006 16.8 0.7 11 3-13 9-19 (26)
24 PF10947 DUF2628: Protein of u 28.1 66 0.0014 19.0 2.3 20 20-39 40-59 (108)
25 COG3776 Predicted membrane pro 28.1 39 0.00085 21.6 1.4 22 18-43 67-88 (91)
26 TIGR01947 rnfG electron transp 27.7 1.5E+02 0.0032 19.6 4.1 34 13-46 3-36 (186)
27 PF06305 DUF1049: Protein of u 27.3 1.1E+02 0.0024 16.4 3.3 20 21-40 26-49 (68)
28 KOG2467 Glycine/serine hydroxy 26.2 36 0.00078 27.1 1.1 17 6-24 111-127 (477)
29 TIGR03368 cellulose_yhjU cellu 25.3 41 0.00089 27.0 1.3 15 6-21 234-248 (518)
30 PRK12705 hypothetical protein; 25.0 2E+02 0.0044 22.6 5.0 30 11-40 4-33 (508)
31 KOG4085 Uncharacterized conser 24.9 41 0.00089 23.6 1.1 15 20-34 127-141 (175)
32 PF11658 DUF3260: Protein of u 24.3 44 0.00096 26.7 1.3 15 6-21 236-250 (518)
33 PRK11677 hypothetical protein; 23.9 93 0.002 20.4 2.6 19 21-39 8-26 (134)
34 PRK06770 hypothetical protein; 23.3 64 0.0014 22.6 1.8 15 20-34 14-28 (180)
35 PF03824 NicO: High-affinity n 23.3 50 0.0011 22.5 1.3 14 20-33 2-15 (282)
36 TIGR00329 gcp_kae1 metallohydr 22.6 72 0.0016 22.3 2.0 35 3-37 77-112 (305)
37 PF01386 Ribosomal_L25p: Ribos 22.5 25 0.00054 20.7 -0.3 22 10-32 10-31 (88)
38 PRK12821 aspartyl/glutamyl-tRN 22.3 1.1E+02 0.0024 24.4 3.1 27 2-34 127-153 (477)
39 PRK01908 electron transport co 22.0 2.6E+02 0.0057 18.9 4.7 34 13-46 7-40 (205)
40 PF07330 DUF1467: Protein of u 21.9 79 0.0017 19.3 1.9 36 4-39 36-78 (85)
41 PF02838 Glyco_hydro_20b: Glyc 21.1 68 0.0015 18.7 1.4 17 24-40 94-110 (124)
42 PF10335 DUF294_C: Putative nu 20.9 1.2E+02 0.0025 19.1 2.5 31 9-39 41-71 (145)
43 PF07047 OPA3: Optic atrophy 3 20.7 1.5E+02 0.0033 18.7 3.1 26 23-48 87-112 (134)
44 PRK06531 yajC preprotein trans 20.7 95 0.0021 19.8 2.1 9 21-29 9-17 (113)
45 KOG4236 Serine/threonine prote 20.7 19 0.00041 30.3 -1.4 14 25-38 577-590 (888)
46 PTZ00396 Casein kinase II subu 20.4 78 0.0017 22.8 1.8 15 26-40 91-105 (251)
47 COG1102 Cmk Cytidylate kinase 20.0 78 0.0017 22.3 1.7 11 3-15 7-17 (179)
48 PF07857 DUF1632: CEO family ( 20.0 58 0.0013 23.2 1.1 27 17-43 183-209 (254)
No 1
>PF05680 ATP-synt_E: ATP synthase E chain; InterPro: IPR008386 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. F-ATPases (also known as F1F0-ATPase, or H(+)-transporting two-sector ATPase) (3.6.3.14 from EC) are composed of two linked complexes: the F1 ATPase complex is the catalytic core and is composed of 5 subunits (alpha, beta, gamma, delta, epsilon), while the F0 ATPase complex is the membrane-embedded proton channel that is composed of at least 3 subunits (A-C), nine in mitochondria (A-G, F6, F8). Both the F1 and F0 complexes are rotary motors that are coupled back-to-back. In the F1 complex, the central gamma subunit forms the rotor inside the cylinder made of the alpha(3)beta(3) subunits, while in the F0 complex, the ring-shaped C subunits forms the rotor. The two rotors rotate in opposite directions, but the F0 rotor is usually stronger, using the force from the proton gradient to push the F1 rotor in reverse in order to drive ATP synthesis []. These ATPases can also work in reverse to hydrolyse ATP to create a proton gradient. This entry represents subunit E found in the F0 complex of F-ATPases. Mitochondrial F-ATPases can associate together to form dimeric or oligomeric complexes, such interactions involving the physical association of membrane-embedded F0 complexes. In yeast, the F0 complex E subunit appears to play an important role in supporting F-ATPase dimerisation. This subunit is anchored to the inner mitochondrial membrane via its N-terminal region, which is involved in stabilising subunits G and K of the F0 complex. The C-terminal region of subunit E is hydrophilic, protruding into the intermembrane space where it can also help stabilise the F-ATPase dimer complex []. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0015078 hydrogen ion transmembrane transporter activity, 0015986 ATP synthesis coupled proton transport, 0000276 mitochondrial proton-transporting ATP synthase complex, coupling factor F(o)
Probab=99.66 E-value=7.8e-17 Score=98.69 Aligned_cols=39 Identities=41% Similarity=0.513 Sum_probs=33.2
Q ss_pred hhHHHHHHHHhhhhhhhhhhhHHHHHHHHhhhhhHHHHH
Q 035404 11 TSTLALVARASAFTFGVVYGNMKLKILKMKAKTHSKAEA 49 (53)
Q Consensus 11 tSt~anV~R~SAl~~GvvYG~~h~~~Lka~~~~~k~~~e 49 (53)
.|+++||+|||||++||+||++|+++|++++++++.+++
T Consensus 6 VSp~inv~RySaL~~Gv~YG~~~~~~L~~~~~~~~~~~e 44 (86)
T PF05680_consen 6 VSPLINVLRYSALGLGVVYGAYHQRYLKAKAKKEAAERE 44 (86)
T ss_pred cCcchHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHH
Confidence 477899999999999999999999999976666555544
No 2
>KOG4326 consensus Mitochondrial F1F0-ATP synthase, subunit e [Energy production and conversion]
Probab=98.45 E-value=3.2e-07 Score=57.22 Aligned_cols=32 Identities=34% Similarity=0.552 Sum_probs=28.5
Q ss_pred hhHHHHHHHHhhhhhhhhhhhHHHHHHHHhhh
Q 035404 11 TSTLALVARASAFTFGVVYGNMKLKILKMKAK 42 (53)
Q Consensus 11 tSt~anV~R~SAl~~GvvYG~~h~~~Lka~~~ 42 (53)
.|-|....|||||.+||.||+.|++.|+..+.
T Consensus 8 vSPLIkfGRysaL~lGvaYGa~r~~~l~~~~e 39 (81)
T KOG4326|consen 8 VSPLIKFGRYSALSLGVAYGAFRLRQLREYHE 39 (81)
T ss_pred ecHHHHhhHHHHHHHHHHHhHHHHHHHhHHHH
Confidence 56789999999999999999999999986543
No 3
>COG5454 Predicted secreted protein [Function unknown]
Probab=80.45 E-value=1.1 Score=28.55 Aligned_cols=18 Identities=39% Similarity=0.534 Sum_probs=15.5
Q ss_pred HhhhhhhhhhhhHHHHHH
Q 035404 20 ASAFTFGVVYGNMKLKIL 37 (53)
Q Consensus 20 ~SAl~~GvvYG~~h~~~L 37 (53)
.||+.+|++||.+|-.-+
T Consensus 59 ~savi~gl~y~lt~~~g~ 76 (89)
T COG5454 59 ASAVIFGLFYGLTHFLGY 76 (89)
T ss_pred HHHHHHHHHHHHHHHHcC
Confidence 699999999999997644
No 4
>KOG3300 consensus NADH:ubiquinone oxidoreductase, B16.6 subunit/cell death-regulatory protein [Energy production and conversion; Cell cycle control, cell division, chromosome partitioning]
Probab=72.38 E-value=10 Score=25.97 Aligned_cols=31 Identities=39% Similarity=0.448 Sum_probs=21.4
Q ss_pred CChhHHHHHHHHhhhhhhhhh-hhHHHHHHHH
Q 035404 9 SGTSTLALVARASAFTFGVVY-GNMKLKILKM 39 (53)
Q Consensus 9 sgtSt~anV~R~SAl~~GvvY-G~~h~~~Lka 39 (53)
||-++++-|.=+.|.|.+.+| |+-+++.||.
T Consensus 34 Sg~t~~aa~~gatayG~~~~~~~~kk~rr~ki 65 (146)
T KOG3300|consen 34 SGMTMFAAVSGATAYGMYQVGQGNKKRRRLKI 65 (146)
T ss_pred CcchhhhHHHHHHHHHHHHHHhchhHHHHHHH
Confidence 677777777777777777665 5666666664
No 5
>PF06783 UPF0239: Uncharacterised protein family (UPF0239); InterPro: IPR009621 This is a group of transmembrane proteins of unknown function.; GO: 0016021 integral to membrane
Probab=69.27 E-value=8.2 Score=24.23 Aligned_cols=29 Identities=17% Similarity=0.180 Sum_probs=21.1
Q ss_pred CCCCCCCChhHHHHHHHHhhhhhhhhhhhHHHHH
Q 035404 3 PPPGPYSGTSTLALVARASAFTFGVVYGNMKLKI 36 (53)
Q Consensus 3 ~~~~~ysgtSt~anV~R~SAl~~GvvYG~~h~~~ 36 (53)
+.|--|--.+-+-||+|| |||.|.+-|-+
T Consensus 7 ~sp~ei~Eet~~e~llRY-----GLf~GAIFQli 35 (85)
T PF06783_consen 7 FSPPEIPEETFFENLLRY-----GLFVGAIFQLI 35 (85)
T ss_pred CCCccCCcchHHHHHHHH-----HHHHHHHHHHH
Confidence 445556566777899997 88888887754
No 6
>PF03648 Glyco_hydro_67N: Glycosyl hydrolase family 67 N-terminus; InterPro: IPR005154 O-Glycosyl hydrolases 3.2.1. from EC are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families [, ]. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. This represents a family of alpha-glucuronidases (GH67 from CAZY). Deletion mutants have indicated that the central region is responsible for the catalytic activity. Within this central domain, the invariant Glu and Asp (residues 391 and 364 respectively from Bacillus stearothermophilus (Geobacillus stearothermophilus)) are thought to from the the catalytic centre [].; GO: 0046559 alpha-glucuronidase activity, 0045493 xylan catabolic process; PDB: 1GQL_A 1GQI_B 1GQJ_B 1GQK_A 1H41_A 1MQR_A 1K9F_A 1K9E_A 1L8N_A 1K9D_A ....
Probab=67.55 E-value=2.8 Score=25.65 Aligned_cols=10 Identities=50% Similarity=0.899 Sum_probs=8.3
Q ss_pred hhhhhhhHHH
Q 035404 25 FGVVYGNMKL 34 (53)
Q Consensus 25 ~GvvYG~~h~ 34 (53)
-|++||.+|+
T Consensus 113 ~G~LYGvF~l 122 (122)
T PF03648_consen 113 RGVLYGVFHL 122 (122)
T ss_dssp HHHHHHHHHH
T ss_pred cEEEEEEeeC
Confidence 4899999985
No 7
>TIGR03725 bact_YeaZ universal bacterial protein YeaZ. This family describes a protein family, YeaZ, that appears to be universal in bacteria, but whose function is unknown. This family is related to the gcp (glycoprotease) protein family, also universal in bacteria and unknown in function. In Gram-positive lineages, members of these two related families often belong to the same operon, along with the ribosomal-protein-alanine acetyltransferase gene. Members of this family may occur as fusions with gcp or the ribosomal protein N-acetyltransferase rimI, and is frequently encoded next to rimI.
Probab=63.53 E-value=5.3 Score=26.21 Aligned_cols=37 Identities=24% Similarity=0.452 Sum_probs=32.0
Q ss_pred CCCCCCChhHHHHHHHHhhhhhhh-hhhhHHHHHHHHh
Q 035404 4 PPGPYSGTSTLALVARASAFTFGV-VYGNMKLKILKMK 40 (53)
Q Consensus 4 ~~~~ysgtSt~anV~R~SAl~~Gv-vYG~~h~~~Lka~ 40 (53)
.||.|.|.=.++-++|--|++.++ ++|.-++..|-.+
T Consensus 63 GPGSfTGlRig~~~akgla~~~~~p~~~vssL~~lA~~ 100 (202)
T TIGR03725 63 GPGSFTGLRIGLATAKGLALALGIPLVGVSSLEALAAQ 100 (202)
T ss_pred CCChHHhHHHHHHHHHHHHHHhCCCEEecCHHHHHHhh
Confidence 599999999999999999999997 8888888877544
No 8
>PF12617 LdpA_C: Iron-Sulfur binding protein C terminal; InterPro: IPR021039 This entry represents the C-terminal region of the iron-sulphur protein LdpA (Light dependent period), which is found in phototropic organisms. LdpA was originally identified in cyanobacteria where it is involved in light-dependent modulation of the circadian clock. The presence of iron-sulphur clusters on LdpA suggests that it may modulate the circadian clock as an indirect function of light intensity by sensing changes in cellular physiology [].
Probab=59.74 E-value=8.1 Score=26.93 Aligned_cols=36 Identities=44% Similarity=0.711 Sum_probs=26.6
Q ss_pred CCCCCC---CCh--hHHHHHHHH----------hhhhhhhhhhhHHHHHHHH
Q 035404 3 PPPGPY---SGT--STLALVARA----------SAFTFGVVYGNMKLKILKM 39 (53)
Q Consensus 3 ~~~~~y---sgt--St~anV~R~----------SAl~~GvvYG~~h~~~Lka 39 (53)
-|||++ .|| .| +.-+|- +.+..||-||.|=|+.|+-
T Consensus 100 ~~PG~vQLAGGTN~~T-v~~Lk~~gl~~~~~~~~~~iaGVAyGsyARkll~p 150 (183)
T PF12617_consen 100 KPPGPVQLAGGTNAHT-VEKLKQMGLLQPPPSSSAFIAGVAYGSYARKLLQP 150 (183)
T ss_pred CCCCceEecCccchhH-HHHHHHccCcCCCccccCCCceeeehHHHHHHHHH
Confidence 377866 344 34 455666 7799999999999999875
No 9
>COG1214 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]
Probab=48.64 E-value=15 Score=24.91 Aligned_cols=34 Identities=21% Similarity=0.396 Sum_probs=26.6
Q ss_pred CCCCCCCChhHHHHHHHHhhhhhhh-hhhhHHHHH
Q 035404 3 PPPGPYSGTSTLALVARASAFTFGV-VYGNMKLKI 36 (53)
Q Consensus 3 ~~~~~ysgtSt~anV~R~SAl~~Gv-vYG~~h~~~ 36 (53)
-.||.|.|.=.++=+++--|+++|+ ++|.--+..
T Consensus 66 ~GPGSFTGlRIG~~~AkgLA~~l~iplvgvssL~~ 100 (220)
T COG1214 66 KGPGSFTGLRIGVAFAKGLALALNIPLVGVSSLEA 100 (220)
T ss_pred cCCCcccchhhHHHHHHHHHHHcCCCEEEeCHHHH
Confidence 4699999999999999998888887 566543333
No 10
>PF10766 DUF2592: Protein of unknown function (DUF2592); InterPro: IPR019702 This entry represents proteins with unknown function, and appear to be restricted to Enterobacteriaceae. Some members are annotated as ybhY.
Probab=47.92 E-value=21 Score=19.97 Aligned_cols=22 Identities=23% Similarity=0.501 Sum_probs=16.8
Q ss_pred HHHHHHHHhhhhhhhhhhhHHH
Q 035404 13 TLALVARASAFTFGVVYGNMKL 34 (53)
Q Consensus 13 t~anV~R~SAl~~GvvYG~~h~ 34 (53)
+++.|-=.-|+.+|++||.=..
T Consensus 8 a~iMVPVvma~ilglIyGlGev 29 (41)
T PF10766_consen 8 AVIMVPVVMALILGLIYGLGEV 29 (41)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 3566777889999999996443
No 11
>PHA02047 phage lambda Rz1-like protein
Probab=43.06 E-value=74 Score=20.66 Aligned_cols=25 Identities=20% Similarity=0.410 Sum_probs=18.0
Q ss_pred HHHHHHHHhhhhhhhhhhhHH-HHHH
Q 035404 13 TLALVARASAFTFGVVYGNMK-LKIL 37 (53)
Q Consensus 13 t~anV~R~SAl~~GvvYG~~h-~~~L 37 (53)
|++.++=.-++++|-.||+.. .+.|
T Consensus 4 t~~~~~~~v~~~~g~~y~~~~~~r~~ 29 (101)
T PHA02047 4 TIVAILVLVVVALGASYGFVQSYRAL 29 (101)
T ss_pred hHHHHHHHHHHHhhhhHHHHHHHHHH
Confidence 445566667788899999988 5554
No 12
>COG3777 Uncharacterized conserved protein [Function unknown]
Probab=42.81 E-value=7.2 Score=28.95 Aligned_cols=24 Identities=46% Similarity=0.552 Sum_probs=18.1
Q ss_pred CCCCCCC--CChhHHHHHHHHhhhhh
Q 035404 2 APPPGPY--SGTSTLALVARASAFTF 25 (53)
Q Consensus 2 ~~~~~~y--sgtSt~anV~R~SAl~~ 25 (53)
+.|+|+. -=|+|=+++.||||+.|
T Consensus 156 ~~p~~~w~~~~tptpvllfrYsaltf 181 (273)
T COG3777 156 AEPNGKWLKNFTPTPVLLFRYSALTF 181 (273)
T ss_pred CCCCCchhhcCCCCchheeehhhhcc
Confidence 3456666 44677789999999987
No 13
>COG3855 Fbp Uncharacterized protein conserved in bacteria [Carbohydrate transport and metabolism]
Probab=40.08 E-value=20 Score=29.31 Aligned_cols=18 Identities=39% Similarity=0.429 Sum_probs=15.3
Q ss_pred CCCCChhH-HHHHHHHhhh
Q 035404 6 GPYSGTST-LALVARASAF 23 (53)
Q Consensus 6 ~~ysgtSt-~anV~R~SAl 23 (53)
|.|||++. +|||.|.+|=
T Consensus 233 gA~sGs~vc~aNvIRIcaR 251 (648)
T COG3855 233 GAASGSKVCMANVIRICAR 251 (648)
T ss_pred ecccCChHHHHHHHHHHHh
Confidence 78999874 7899999984
No 14
>PF08636 Pkr1: ER protein Pkr1; InterPro: IPR013945 Pkr1 has been identified as an ER protein of unknown function.
Probab=36.76 E-value=42 Score=20.35 Aligned_cols=19 Identities=32% Similarity=0.375 Sum_probs=14.9
Q ss_pred CCCCCCCChhHHHHHHHHhhhh
Q 035404 3 PPPGPYSGTSTLALVARASAFT 24 (53)
Q Consensus 3 ~~~~~ysgtSt~anV~R~SAl~ 24 (53)
++||+ |+++....+.|...
T Consensus 13 ftPG~---tp~li~a~n~sF~~ 31 (75)
T PF08636_consen 13 FTPGT---TPTLIIATNVSFAA 31 (75)
T ss_pred cCCCC---ChHHHHHHHHHHHH
Confidence 78998 68888888887644
No 15
>COG3105 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=35.34 E-value=89 Score=21.26 Aligned_cols=32 Identities=16% Similarity=0.270 Sum_probs=23.4
Q ss_pred HHHHHHhhhhhhhhhhhHHHHHHHHhhhhhHH
Q 035404 15 ALVARASAFTFGVVYGNMKLKILKMKAKTHSK 46 (53)
Q Consensus 15 anV~R~SAl~~GvvYG~~h~~~Lka~~~~~k~ 46 (53)
.-++=..+|++||+-|++-.|-.+-+.+.+++
T Consensus 7 ~W~~a~igLvvGi~IG~li~Rlt~~~~k~q~~ 38 (138)
T COG3105 7 TWEYALIGLVVGIIIGALIARLTNRKLKQQQK 38 (138)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHcchhhhhHHH
Confidence 44556678999999999988877766555443
No 16
>PRK01617 hypothetical protein; Provisional
Probab=33.34 E-value=21 Score=23.61 Aligned_cols=14 Identities=21% Similarity=0.249 Sum_probs=11.3
Q ss_pred HHHHHHhhhhhhhh
Q 035404 15 ALVARASAFTFGVV 28 (53)
Q Consensus 15 anV~R~SAl~~Gvv 28 (53)
..=.|||||..|-+
T Consensus 33 LMRSRYsAy~~~~~ 46 (154)
T PRK01617 33 LMRSRYCAFVMKDA 46 (154)
T ss_pred HHHHHHHHHHhccc
Confidence 45589999999875
No 17
>PRK04233 hypothetical protein; Provisional
Probab=33.20 E-value=21 Score=23.18 Aligned_cols=13 Identities=31% Similarity=0.217 Sum_probs=10.9
Q ss_pred HHHHHhhhhhhhh
Q 035404 16 LVARASAFTFGVV 28 (53)
Q Consensus 16 nV~R~SAl~~Gvv 28 (53)
.=.|||||.+|-+
T Consensus 38 MRSRYsAfv~~~~ 50 (129)
T PRK04233 38 MRARYSAYVRRDA 50 (129)
T ss_pred HHHHHHHHHhCcc
Confidence 4579999999986
No 18
>PRK01752 hypothetical protein; Provisional
Probab=32.69 E-value=22 Score=23.75 Aligned_cols=14 Identities=14% Similarity=0.325 Sum_probs=11.6
Q ss_pred HHHHHHhhhhhhhh
Q 035404 15 ALVARASAFTFGVV 28 (53)
Q Consensus 15 anV~R~SAl~~Gvv 28 (53)
..=.|||||..|-+
T Consensus 36 LMRSRYSAy~~~~~ 49 (156)
T PRK01752 36 LMRSRYAAYVLKNI 49 (156)
T ss_pred HHHHHHHHHHhccc
Confidence 35689999999976
No 19
>PRK01842 hypothetical protein; Provisional
Probab=32.62 E-value=22 Score=23.77 Aligned_cols=13 Identities=31% Similarity=0.585 Sum_probs=11.0
Q ss_pred HHHHHhhhhhhhh
Q 035404 16 LVARASAFTFGVV 28 (53)
Q Consensus 16 nV~R~SAl~~Gvv 28 (53)
.=.|||||.+|-+
T Consensus 53 MRSRYSAy~l~~~ 65 (149)
T PRK01842 53 MRSRYSAYVLGAT 65 (149)
T ss_pred HHHHHHHHHhccc
Confidence 4579999999975
No 20
>PRK00183 hypothetical protein; Provisional
Probab=31.09 E-value=24 Score=23.60 Aligned_cols=14 Identities=36% Similarity=0.636 Sum_probs=11.2
Q ss_pred HHHHHHhhhhhhhh
Q 035404 15 ALVARASAFTFGVV 28 (53)
Q Consensus 15 anV~R~SAl~~Gvv 28 (53)
..=.|||||.+|.+
T Consensus 33 LMRSRYsAf~~~~~ 46 (157)
T PRK00183 33 LMRSRYSAYVLGLV 46 (157)
T ss_pred HHHHHHHHHHhccc
Confidence 34579999999975
No 21
>PF00814 Peptidase_M22: Glycoprotease family; InterPro: IPR000905 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. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to MEROPS peptidase family M22 (clan MK). The type example being O-sialoglycoprotein endopeptidase (3.4.24.57 from EC) from Pasteurella haemolytica (Mannheimia haemolytica). O-Sialoglycoprotein endopeptidase is secreted by the bacterium P. haemolytica, and digests only proteins that are heavily sialylated, in particular those with sialylated serine and threonine residues []. Substrate proteins include glycophorin A and leukocyte surface antigens CD34, CD43, CD44 and CD45 [, ]. Removal of glycosylation, by treatment with neuraminidase, completely negates susceptibility to O-sialoglycoprotein endopeptidase digestion [, ]. Sequence similarity searches have revealed other members of the M22 family, from yeast, Mycobacterium, Haemophilus influenzae and the cyanobacterium Synechocystis []. The zinc-binding and catalytic residues of this family have not been determined, although the motif HMEGH may be a zinc-binding region [].; GO: 0004222 metalloendopeptidase activity, 0006508 proteolysis; PDB: 2A6A_A 2GEL_G 2GEM_B 1OKJ_B 3ENO_A 3EN9_B 2VWB_B 3ENH_B 2IVO_D 2IVP_A ....
Probab=30.90 E-value=25 Score=24.27 Aligned_cols=39 Identities=21% Similarity=0.393 Sum_probs=30.5
Q ss_pred CCCCCCChhHHHHHHHHhhhhhhh-hhhhHHHHHHHHhhh
Q 035404 4 PPGPYSGTSTLALVARASAFTFGV-VYGNMKLKILKMKAK 42 (53)
Q Consensus 4 ~~~~ysgtSt~anV~R~SAl~~Gv-vYG~~h~~~Lka~~~ 42 (53)
.||.|.|--.++.+++--|+.+++ +||.-|+..+-....
T Consensus 59 GPGsftgLrvG~~~Ak~La~~~~~Pli~v~~l~a~a~~~~ 98 (268)
T PF00814_consen 59 GPGSFTGLRVGLSFAKGLALALNIPLIGVSHLEAHALSAR 98 (268)
T ss_dssp ESS-HHHHHHHHHHHHHHHHHTT--EEEEEHHHHHHHHHH
T ss_pred CCCcccccHHHHHHHHHHHHHhCCCeEeeccHHHHHHhHh
Confidence 489999999999999999999988 788888877665443
No 22
>PF01214 CK_II_beta: Casein kinase II regulatory subunit; InterPro: IPR000704 Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases. Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. Phosphoprotein phosphatases catalyse the reverse process. Protein kinases fall into three broad classes, characterised with respect to substrate specificity []: Serine/threonine-protein kinases Tyrosine-protein kinases Dual specific protein kinases (e.g. MEK - phosphorylates both Thr and Tyr on target proteins) Protein kinase function has been evolutionarily conserved from Escherichia coli to human []. Protein kinases play a role in a multitude of cellular processes, including division, proliferation, apoptosis, and differentiation []. Phosphorylation usually results in a functional change of the target protein by changing enzyme activity, cellular location, or association with other proteins. The catalytic subunits of protein kinases are highly conserved, and several structures have been solved [], leading to large screens to develop kinase-specific inhibitors for the treatments of a number of diseases []. Casein kinase, a ubiquitous, well-conserved protein kinase involved in cell metabolism and differentiation, is characterised by its preference for Ser or Thr in acidic stretches of amino acids. The enzyme is a tetramer of 2 alpha- and 2 beta-subunits [, ]. However, some species (e.g., mammals) possess 2 related forms of the alpha-subunit (alpha and alpha'), while others (e.g., fungi) possess 2 related beta-subunits (beta and beta') []. The alpha-subunit is the catalytic unit and contains regions characteristic of serine/threonine protein kinases. The beta-subunit is believed to be regulatory, possessing an N-terminal auto-phosphorylation site, an internal acidic domain, and a potential metal-binding motif []. The beta subunit is a highly conserved protein of about 25kDa that contains, in its central section, a cysteine-rich motif, CX(n)C, that could be involved in binding a metal such as zinc []. The mammalian beta-subunit gene promoter shares common features with those of other mammalian protein kinases and is closely related to the promoter of the regulatory subunit of cAMP-dependent protein kinase [].; GO: 0019887 protein kinase regulator activity, 0005956 protein kinase CK2 complex; PDB: 2R6M_B 1RQF_K 1DS5_G 1QF8_B 3EED_A 4DGL_A 1JWH_D.
Probab=29.72 E-value=40 Score=22.87 Aligned_cols=15 Identities=13% Similarity=0.350 Sum_probs=12.4
Q ss_pred hhhhhhhHHHHHHHH
Q 035404 25 FGVVYGNMKLKILKM 39 (53)
Q Consensus 25 ~GvvYG~~h~~~Lka 39 (53)
+-.+||.+|.|.|-.
T Consensus 69 a~~LYGLIHaRyI~T 83 (184)
T PF01214_consen 69 AEMLYGLIHARYILT 83 (184)
T ss_dssp HHHHHHHHHHHHTTS
T ss_pred HHHHHhhhHHHHhhc
Confidence 457899999999765
No 23
>smart00735 ZM ZASP-like motif. Short motif (26 amino acids) present in an alpha-actinin-binding protein, ZASP, and similar molecules.
Probab=29.09 E-value=28 Score=16.78 Aligned_cols=11 Identities=36% Similarity=0.616 Sum_probs=7.8
Q ss_pred CCCCCCCChhH
Q 035404 3 PPPGPYSGTST 13 (53)
Q Consensus 3 ~~~~~ysgtSt 13 (53)
-|+|+||-.+.
T Consensus 9 ~P~glys~~n~ 19 (26)
T smart00735 9 SPIGLYSSENI 19 (26)
T ss_pred CCCCCCCcccH
Confidence 48999976554
No 24
>PF10947 DUF2628: Protein of unknown function (DUF2628) ; InterPro: IPR024399 Some members in this family of proteins have been annotated as YigF. Their function is currently unknown.
Probab=28.09 E-value=66 Score=19.01 Aligned_cols=20 Identities=25% Similarity=0.152 Sum_probs=16.6
Q ss_pred HhhhhhhhhhhhHHHHHHHH
Q 035404 20 ASAFTFGVVYGNMKLKILKM 39 (53)
Q Consensus 20 ~SAl~~GvvYG~~h~~~Lka 39 (53)
|.||.+|.+|-.+++-.+.+
T Consensus 40 w~Af~f~~~w~l~r~mw~~~ 59 (108)
T PF10947_consen 40 WWAFFFGPLWLLYRKMWLYA 59 (108)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 66999999999998876554
No 25
>COG3776 Predicted membrane protein [Function unknown]
Probab=28.07 E-value=39 Score=21.57 Aligned_cols=22 Identities=27% Similarity=0.386 Sum_probs=16.2
Q ss_pred HHHhhhhhhhhhhhHHHHHHHHhhhh
Q 035404 18 ARASAFTFGVVYGNMKLKILKMKAKT 43 (53)
Q Consensus 18 ~R~SAl~~GvvYG~~h~~~Lka~~~~ 43 (53)
=|++-|.||| .|+..++++.+.
T Consensus 67 ek~~IllFGV----f~Ll~~~~k~~~ 88 (91)
T COG3776 67 EKLQILLFGV----FELLAWQKKFKM 88 (91)
T ss_pred HHHHHHHHHH----HHHHHHHHhccc
Confidence 4777777766 589999987654
No 26
>TIGR01947 rnfG electron transport complex, RnfABCDGE type, G subunit. The six subunit complex RnfABCDGE in Rhodobacter capsulatus encodes an apparent NADH oxidoreductase responsible for electron transport to nitrogenase, necessary for nitrogen fixation. A closely related complex in E. coli, RsxABCDGE (Reducer of SoxR), reduces the 2Fe-2S-containing superoxide sensor SoxR, active as a transcription factor when oxidized. This family of putative NADH oxidoreductase complexes exists in many of the same species as the related NQR, a Na(+)-translocating NADH-quinone reductase, but is distinct. This model describes the A subunit.
Probab=27.71 E-value=1.5e+02 Score=19.58 Aligned_cols=34 Identities=29% Similarity=0.185 Sum_probs=25.2
Q ss_pred HHHHHHHHhhhhhhhhhhhHHHHHHHHhhhhhHH
Q 035404 13 TLALVARASAFTFGVVYGNMKLKILKMKAKTHSK 46 (53)
Q Consensus 13 t~anV~R~SAl~~GvvYG~~h~~~Lka~~~~~k~ 46 (53)
.|+.+.=.|++.++++|...+-++-+.+.+..++
T Consensus 3 ~L~~i~~v~~~~La~v~~~T~~~I~~~~~~~~~~ 36 (186)
T TIGR01947 3 ILGLFAAVSAGLLALVNQFTKEVIAEAEAKQQLE 36 (186)
T ss_pred hHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHH
Confidence 3556667889999999999998887765554443
No 27
>PF06305 DUF1049: Protein of unknown function (DUF1049); InterPro: IPR010445 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=27.26 E-value=1.1e+02 Score=16.38 Aligned_cols=20 Identities=20% Similarity=0.217 Sum_probs=8.7
Q ss_pred hhhhhhhh----hhhHHHHHHHHh
Q 035404 21 SAFTFGVV----YGNMKLKILKMK 40 (53)
Q Consensus 21 SAl~~Gvv----YG~~h~~~Lka~ 40 (53)
.+|++|++ ++......++.+
T Consensus 26 ~~f~~G~llg~l~~~~~~~~~r~~ 49 (68)
T PF06305_consen 26 IAFLLGALLGWLLSLPSRLRLRRR 49 (68)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34445544 444444444433
No 28
>KOG2467 consensus Glycine/serine hydroxymethyltransferase [Amino acid transport and metabolism]
Probab=26.16 E-value=36 Score=27.08 Aligned_cols=17 Identities=35% Similarity=0.503 Sum_probs=14.0
Q ss_pred CCCCChhHHHHHHHHhhhh
Q 035404 6 GPYSGTSTLALVARASAFT 24 (53)
Q Consensus 6 ~~ysgtSt~anV~R~SAl~ 24 (53)
-||||+++ |.+=|.|+.
T Consensus 111 Qp~SGSPA--NfavYtall 127 (477)
T KOG2467|consen 111 QPYSGSPA--NFAVYTALL 127 (477)
T ss_pred ccCCCCch--hhHHHhhhc
Confidence 38999997 888888874
No 29
>TIGR03368 cellulose_yhjU cellulose synthase operon protein YhjU. This protein was identified by the partial phylogenetic profiling algorithm (PubMed:16930487) as part of the system for cellulose biosynthesis in bacteria, and in fact is found in cellulose biosynthesis gene regions. The protein was designated YhjU in Salmonella enteritidis, where disruption of its gene disrupts cellulose biosynthesis and biofilm formation (PubMed:11929533).
Probab=25.29 E-value=41 Score=26.96 Aligned_cols=15 Identities=40% Similarity=0.547 Sum_probs=13.1
Q ss_pred CCCCChhHHHHHHHHh
Q 035404 6 GPYSGTSTLALVARAS 21 (53)
Q Consensus 6 ~~ysgtSt~anV~R~S 21 (53)
-.|||..+ .+++|+|
T Consensus 234 tSYSGPAa-IRlLRAS 248 (518)
T TIGR03368 234 TSYSGPAA-IRLLRAS 248 (518)
T ss_pred cccchHHH-HHHHHhc
Confidence 37999988 6999998
No 30
>PRK12705 hypothetical protein; Provisional
Probab=24.97 E-value=2e+02 Score=22.59 Aligned_cols=30 Identities=17% Similarity=0.127 Sum_probs=24.3
Q ss_pred hhHHHHHHHHhhhhhhhhhhhHHHHHHHHh
Q 035404 11 TSTLALVARASAFTFGVVYGNMKLKILKMK 40 (53)
Q Consensus 11 tSt~anV~R~SAl~~GvvYG~~h~~~Lka~ 40 (53)
|.-++.++=.+.|.+|++|-+++.+.+..+
T Consensus 4 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 33 (508)
T PRK12705 4 SILLVILLLLIGLLLGVLVVLLKKRQRLAK 33 (508)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 455778888999999999999888876655
No 31
>KOG4085 consensus Uncharacterized conserved protein [Function unknown]
Probab=24.90 E-value=41 Score=23.61 Aligned_cols=15 Identities=47% Similarity=0.764 Sum_probs=11.7
Q ss_pred HhhhhhhhhhhhHHH
Q 035404 20 ASAFTFGVVYGNMKL 34 (53)
Q Consensus 20 ~SAl~~GvvYG~~h~ 34 (53)
-.+|+-||+||.+-+
T Consensus 127 g~iFatGV~YG~mAL 141 (175)
T KOG4085|consen 127 GIIFATGVLYGLMAL 141 (175)
T ss_pred chhhhhHHHHHHHHh
Confidence 456888999998754
No 32
>PF11658 DUF3260: Protein of unknown function (DUF3260); InterPro: IPR017744 This protein was identified by the partial phylogenetic profiling algorithm [] as part of the system for cellulose biosynthesis in bacteria, and in fact is found in cellulose biosynthesis gene regions. The protein was designated YhjU in Salmonella enteritidis, where disruption of its gene disrupts cellulose biosynthesis and biofilm formation [].
Probab=24.30 E-value=44 Score=26.72 Aligned_cols=15 Identities=40% Similarity=0.547 Sum_probs=13.1
Q ss_pred CCCCChhHHHHHHHHh
Q 035404 6 GPYSGTSTLALVARAS 21 (53)
Q Consensus 6 ~~ysgtSt~anV~R~S 21 (53)
-.|||..+ ++++|+|
T Consensus 236 tSYSGPAa-IRLLRAS 250 (518)
T PF11658_consen 236 TSYSGPAA-IRLLRAS 250 (518)
T ss_pred cccchHHH-HHHHHhc
Confidence 36999998 7999998
No 33
>PRK11677 hypothetical protein; Provisional
Probab=23.89 E-value=93 Score=20.41 Aligned_cols=19 Identities=11% Similarity=0.380 Sum_probs=13.3
Q ss_pred hhhhhhhhhhhHHHHHHHH
Q 035404 21 SAFTFGVVYGNMKLKILKM 39 (53)
Q Consensus 21 SAl~~GvvYG~~h~~~Lka 39 (53)
.+|++|++=|++=.|.+..
T Consensus 8 i~livG~iiG~~~~R~~~~ 26 (134)
T PRK11677 8 IGLVVGIIIGAVAMRFGNR 26 (134)
T ss_pred HHHHHHHHHHHHHHhhccc
Confidence 5778888888776665543
No 34
>PRK06770 hypothetical protein; Provisional
Probab=23.32 E-value=64 Score=22.58 Aligned_cols=15 Identities=27% Similarity=0.563 Sum_probs=11.2
Q ss_pred HhhhhhhhhhhhHHH
Q 035404 20 ASAFTFGVVYGNMKL 34 (53)
Q Consensus 20 ~SAl~~GvvYG~~h~ 34 (53)
.-.|++|++||.+..
T Consensus 14 m~vl~~g~t~G~l~y 28 (180)
T PRK06770 14 MAVLGIGVTYGMLYY 28 (180)
T ss_pred HHHHHHHHHHHHHHh
Confidence 346779999997765
No 35
>PF03824 NicO: High-affinity nickel-transport protein; InterPro: IPR011541 High affinity nickel transporters are involved in the incorporation of nickel into H2-uptake hydrogenase [, ] and urease [] enzymes and are essential for the expression of catalytically active hydrogenase and urease. Ion uptake is dependent on proton motive force. HoxN in Ralstonia eutropha (Alcaligenes eutrophus) is thought to be an integral membrane protein with seven transmembrane helices []. The family also includes a cobalt transporter. ; GO: 0046872 metal ion binding, 0030001 metal ion transport, 0055085 transmembrane transport, 0016021 integral to membrane
Probab=23.31 E-value=50 Score=22.49 Aligned_cols=14 Identities=21% Similarity=0.470 Sum_probs=9.8
Q ss_pred HhhhhhhhhhhhHH
Q 035404 20 ASAFTFGVVYGNMK 33 (53)
Q Consensus 20 ~SAl~~GvvYG~~h 33 (53)
++.+.++++||..|
T Consensus 2 l~ll~laf~~G~~H 15 (282)
T PF03824_consen 2 LSLLLLAFLYGLLH 15 (282)
T ss_pred HHHHHHHHHHHHHH
Confidence 45667777777775
No 36
>TIGR00329 gcp_kae1 metallohydrolase, glycoprotease/Kae1 family. This subfamily includes the well-studied secreted O-sialoglycoprotein endopeptidase (glycoprotease, EC 3.4.24.57) of Pasteurella haemolytica, a pathogen. A member from Riemerella anatipestifer, associated with cohemolysin activity, likewise is exported without benefit of a classical signal peptide and shows glycoprotease activity on the test substrate glycophorin. However, archaeal members of this subfamily show unrelated activities as demonstrated in Pyrococcus abyssi: DNA binding, iron binding, apurinic endonuclease activity, genomic association with a kinase domain, and no glycoprotease activity. This family thus pulls together a set of proteins as a homology group that appears to be near-universal in life, yet heterogeneous in assayed function between bacteria and archaea.
Probab=22.63 E-value=72 Score=22.29 Aligned_cols=35 Identities=23% Similarity=0.135 Sum_probs=27.0
Q ss_pred CCCCCCCChhHHHHHHHHhhhhhhh-hhhhHHHHHH
Q 035404 3 PPPGPYSGTSTLALVARASAFTFGV-VYGNMKLKIL 37 (53)
Q Consensus 3 ~~~~~ysgtSt~anV~R~SAl~~Gv-vYG~~h~~~L 37 (53)
--||.|.|-..++.++|--|+.+++ ++|+-|+..+
T Consensus 77 ~GPG~~tglrvg~~~Ak~la~~~~~p~~~v~hl~~h 112 (305)
T TIGR00329 77 QGPGLGGSLRVGATFARSLALSLDKPLIGVNHLLGH 112 (305)
T ss_pred cCCCchhhHHHHHHHHHHHHHHhCCCEeecccHHHH
Confidence 3699999999999999999998886 4555555443
No 37
>PF01386 Ribosomal_L25p: Ribosomal L25p family; InterPro: IPR020055 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This entry models the short-form of the ribosomal L25 protein. The long-form has homology to the general stress protein Ctc of Bacillus subtilis, a mesophile, and ribosomal protein TL5 of Thermus thermophilus, a thermophile. Ribosomal protein L25 of Escherichia coli and Haemophilus influenzae appear to be orthologous but consist only of the N-terminal half of Ctc and TL5. Both short (L25-like) and full-length (CTC-like) members of this family bind the E-loop of bacterial 5S rRNA.; GO: 0003735 structural constituent of ribosome, 0008097 5S rRNA binding, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2HGQ_Y 2HGJ_Y 2Y19_Z 2WRL_Z 3KIT_Z 2WH2_Z 2WDN_Z 3V25_Z 3HUZ_Z 3KIY_Z ....
Probab=22.54 E-value=25 Score=20.68 Aligned_cols=22 Identities=32% Similarity=0.339 Sum_probs=18.2
Q ss_pred ChhHHHHHHHHhhhhhhhhhhhH
Q 035404 10 GTSTLALVARASAFTFGVVYGNM 32 (53)
Q Consensus 10 gtSt~anV~R~SAl~~GvvYG~~ 32 (53)
|++. ++-+|.+-+.=||+||-=
T Consensus 10 gk~~-~r~LR~~G~iPaviYG~~ 31 (88)
T PF01386_consen 10 GKSA-ARRLRREGKIPAVIYGKG 31 (88)
T ss_dssp SSSH-HHHHHHTTEEEEEEEESS
T ss_pred CCHH-HHHHHHcCCceEEEECCC
Confidence 4555 799999999999999953
No 38
>PRK12821 aspartyl/glutamyl-tRNA amidotransferase subunit C-like protein; Provisional
Probab=22.26 E-value=1.1e+02 Score=24.40 Aligned_cols=27 Identities=19% Similarity=0.223 Sum_probs=21.1
Q ss_pred CCCCCCCCChhHHHHHHHHhhhhhhhhhhhHHH
Q 035404 2 APPPGPYSGTSTLALVARASAFTFGVVYGNMKL 34 (53)
Q Consensus 2 ~~~~~~ysgtSt~anV~R~SAl~~GvvYG~~h~ 34 (53)
-+|||+|-=-=|+ ||+..|++||...-
T Consensus 127 if~~G~fFpGFTL------sA~L~GlIyGl~r~ 153 (477)
T PRK12821 127 IFSGGVFNYGYVL------GAILTGMIAGILRE 153 (477)
T ss_pred hcCCCCccHHHHH------HHHHHHHHHHHHHH
Confidence 4578888766664 79999999998753
No 39
>PRK01908 electron transport complex protein RnfG; Validated
Probab=22.05 E-value=2.6e+02 Score=18.94 Aligned_cols=34 Identities=29% Similarity=0.100 Sum_probs=25.6
Q ss_pred HHHHHHHHhhhhhhhhhhhHHHHHHHHhhhhhHH
Q 035404 13 TLALVARASAFTFGVVYGNMKLKILKMKAKTHSK 46 (53)
Q Consensus 13 t~anV~R~SAl~~GvvYG~~h~~~Lka~~~~~k~ 46 (53)
.|..+.=.|++.++++|...+-++-+++++..++
T Consensus 7 ~L~~i~~i~~~lLa~v~~~T~~~I~~~~~~~~~~ 40 (205)
T PRK01908 7 TLALFAALCTGLTAVVNQLTKDTIAEQAALQQKA 40 (205)
T ss_pred HHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHH
Confidence 4566777889999999999998887765554443
No 40
>PF07330 DUF1467: Protein of unknown function (DUF1467); InterPro: IPR009935 This family consists of several bacterial proteins of around 90 residues in length. The function of this family is unknown.
Probab=21.89 E-value=79 Score=19.32 Aligned_cols=36 Identities=17% Similarity=0.291 Sum_probs=25.4
Q ss_pred CCCCCCChhHHHHHHH-------HhhhhhhhhhhhHHHHHHHH
Q 035404 4 PPGPYSGTSTLALVAR-------ASAFTFGVVYGNMKLKILKM 39 (53)
Q Consensus 4 ~~~~ysgtSt~anV~R-------~SAl~~GvvYG~~h~~~Lka 39 (53)
.||.=+|.+.-.+..| .|++.++++|.++.-..+.-
T Consensus 36 v~Gt~~sAP~~~~l~rk~~~TTiiaavi~~~~~~~~~~g~i~~ 78 (85)
T PF07330_consen 36 VPGTDPSAPANPRLKRKALITTIIAAVIFAIIYLIIVSGWISL 78 (85)
T ss_pred CCCCCCCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHhccccH
Confidence 4676677666556555 58899999999887655443
No 41
>PF02838 Glyco_hydro_20b: Glycosyl hydrolase family 20, domain 2; InterPro: IPR015882 Glycoside hydrolase family 20 GH20 from CAZY comprises enzymes with several known activities; beta-hexosaminidase (3.2.1.52 from EC); lacto-N-biosidase (3.2.1.140 from EC). Carbonyl oxygen of the C-2 acetamido group of the substrate acts as the catalytic nucleophile/base in this family of enzymes. In the brain and other tissues, beta-hexosaminidase A degrades GM2 gangliosides; specifically, the enzyme hydrolyses terminal non-reducing N-acetyl-D-hexosamine residues in N-acetyl-beta-D-hexosaminides. There are 3 forms of beta-hexosaminidase: hexosaminidase A is a trimer, with one alpha, one beta-A and one beta-B chain; hexosaminidase B is a tetramer of two beta-A and two beta-B chains; and hexosaminidase S is a homodimer of alpha chains. The two beta chains are derived from the cleavage of a precursor. Mutations in the beta-chain lead to Sandhoff disease, a lysosomal storage disorder characterised by accumulation of GM2 ganglioside []. This entry represents the alpha and beta subunit of beta-N-acetylhexosaminidase. It contains a similar fold but lacks the catalytic centre.; GO: 0004563 beta-N-acetylhexosaminidase activity, 0005975 carbohydrate metabolic process; PDB: 3SUT_A 3SUS_A 3GH7_A 3SUR_A 3SUW_A 3SUV_A 3SUU_A 3GH5_A 3GH4_A 2J4G_B ....
Probab=21.12 E-value=68 Score=18.72 Aligned_cols=17 Identities=29% Similarity=0.458 Sum_probs=12.3
Q ss_pred hhhhhhhhHHHHHHHHh
Q 035404 24 TFGVVYGNMKLKILKMK 40 (53)
Q Consensus 24 ~~GvvYG~~h~~~Lka~ 40 (53)
..|+|||..-++-|-..
T Consensus 94 ~~G~~yg~qTL~Qll~~ 110 (124)
T PF02838_consen 94 PAGLFYGLQTLRQLLRQ 110 (124)
T ss_dssp HHHHHHHHHHHHHHSBT
T ss_pred chHHHHHHHHHHHHhhc
Confidence 36999999877666443
No 42
>PF10335 DUF294_C: Putative nucleotidyltransferase substrate binding domain; InterPro: IPR018821 This entry is found associated with presumed nucleotidyltransferase domains and seems to be distantly related to other helical substrate binding domains.
Probab=20.87 E-value=1.2e+02 Score=19.06 Aligned_cols=31 Identities=16% Similarity=0.177 Sum_probs=24.4
Q ss_pred CChhHHHHHHHHhhhhhhhhhhhHHHHHHHH
Q 035404 9 SGTSTLALVARASAFTFGVVYGNMKLKILKM 39 (53)
Q Consensus 9 sgtSt~anV~R~SAl~~GvvYG~~h~~~Lka 39 (53)
.|..-+|+.+|+-||-.|+.=.+...|.-..
T Consensus 41 ~gl~piv~~~R~lAL~~gi~~~~T~eRl~~L 71 (145)
T PF10335_consen 41 GGLFPIVNAARLLALRHGISETSTLERLEAL 71 (145)
T ss_pred hhHHHHHHHHHHHHHHcCCCCCCHHHHHHHH
Confidence 3667789999999999998777776665554
No 43
>PF07047 OPA3: Optic atrophy 3 protein (OPA3); InterPro: IPR010754 OPA3 deficiency causes type III 3-methylglutaconic aciduria (MGA) in humans. This disease manifests with early bilateral optic atrophy, spasticity, extrapyramidal dysfunction, ataxia, and cognitive deficits, but normal longevity []. This family consists of several optic atrophy 3 (OPA3) proteins and related proteins from other eukaryotic species, the function is unknown.
Probab=20.75 E-value=1.5e+02 Score=18.74 Aligned_cols=26 Identities=15% Similarity=0.037 Sum_probs=17.2
Q ss_pred hhhhhhhhhHHHHHHHHhhhhhHHHH
Q 035404 23 FTFGVVYGNMKLKILKMKAKTHSKAE 48 (53)
Q Consensus 23 l~~GvvYG~~h~~~Lka~~~~~k~~~ 48 (53)
.+.|+++.-+.++.-+.+.+++..++
T Consensus 87 Va~~li~~E~~Rs~~ke~~Ke~~~~~ 112 (134)
T PF07047_consen 87 VAAGLIIYEYWRSARKEAKKEEELQE 112 (134)
T ss_pred HHHHHHHHHHHHHHhhHHHHHHHHHH
Confidence 45677777788877776655555443
No 44
>PRK06531 yajC preprotein translocase subunit YajC; Validated
Probab=20.69 E-value=95 Score=19.85 Aligned_cols=9 Identities=11% Similarity=0.571 Sum_probs=6.0
Q ss_pred hhhhhhhhh
Q 035404 21 SAFTFGVVY 29 (53)
Q Consensus 21 SAl~~GvvY 29 (53)
-++.++++|
T Consensus 9 ~vv~~~i~y 17 (113)
T PRK06531 9 FVVMLGLIF 17 (113)
T ss_pred HHHHHHHHH
Confidence 456677777
No 45
>KOG4236 consensus Serine/threonine protein kinase PKC mu/PKD and related proteins [Signal transduction mechanisms]
Probab=20.69 E-value=19 Score=30.30 Aligned_cols=14 Identities=43% Similarity=0.707 Sum_probs=11.7
Q ss_pred hhhhhhhHHHHHHH
Q 035404 25 FGVVYGNMKLKILK 38 (53)
Q Consensus 25 ~GvvYG~~h~~~Lk 38 (53)
||+|||-+|+++=+
T Consensus 577 FG~VYgg~hRktGr 590 (888)
T KOG4236|consen 577 FGTVYGGKHRKTGR 590 (888)
T ss_pred ceeeecceecccCc
Confidence 79999999998643
No 46
>PTZ00396 Casein kinase II subunit beta; Provisional
Probab=20.39 E-value=78 Score=22.81 Aligned_cols=15 Identities=13% Similarity=0.401 Sum_probs=12.2
Q ss_pred hhhhhhHHHHHHHHh
Q 035404 26 GVVYGNMKLKILKMK 40 (53)
Q Consensus 26 GvvYG~~h~~~Lka~ 40 (53)
-.+||.+|.|+|...
T Consensus 91 ~~LYGLIHARyI~T~ 105 (251)
T PTZ00396 91 SDLYGLIHARFITTP 105 (251)
T ss_pred HHHHHHHhHhHhcCH
Confidence 378999999998643
No 47
>COG1102 Cmk Cytidylate kinase [Nucleotide transport and metabolism]
Probab=20.05 E-value=78 Score=22.25 Aligned_cols=11 Identities=55% Similarity=0.830 Sum_probs=7.9
Q ss_pred CCCCCCCChhHHH
Q 035404 3 PPPGPYSGTSTLA 15 (53)
Q Consensus 3 ~~~~~ysgtSt~a 15 (53)
.+|| ||+||++
T Consensus 7 G~pG--sG~TTva 17 (179)
T COG1102 7 GLPG--SGKTTVA 17 (179)
T ss_pred cCCC--CChhHHH
Confidence 4566 8999954
No 48
>PF07857 DUF1632: CEO family (DUF1632); InterPro: IPR012435 These sequences are found in hypothetical eukaryotic proteins of unknown function. The region concerned is approximately 280 residues long.
Probab=20.04 E-value=58 Score=23.18 Aligned_cols=27 Identities=22% Similarity=0.342 Sum_probs=20.0
Q ss_pred HHHHhhhhhhhhhhhHHHHHHHHhhhh
Q 035404 17 VARASAFTFGVVYGNMKLKILKMKAKT 43 (53)
Q Consensus 17 V~R~SAl~~GvvYG~~h~~~Lka~~~~ 43 (53)
|.-..|+..|++||+.=-=....|++.
T Consensus 183 vG~~LAv~aGvlyGs~fvPv~Yi~~~~ 209 (254)
T PF07857_consen 183 VGIILAVFAGVLYGSNFVPVIYIQDHP 209 (254)
T ss_pred HhHHHHHHHHHHHhcccchHHHHHhCc
Confidence 445678999999999876666665554
Done!