Query psy11173
Match_columns 280
No_of_seqs 207 out of 523
Neff 3.7
Searched_HMMs 46136
Date Fri Aug 16 19:53:42 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy11173.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/11173hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN02701 alpha-mannosidase 100.0 1.7E-49 3.7E-54 417.0 12.2 154 31-187 2-169 (1050)
2 KOG1958|consensus 100.0 5.7E-47 1.2E-51 388.7 10.8 156 29-186 122-291 (1129)
3 KOG1959|consensus 100.0 2.1E-40 4.7E-45 339.0 9.1 129 60-189 26-178 (996)
4 PF01074 Glyco_hydro_38: Glyco 100.0 1.5E-29 3.3E-34 226.3 8.5 112 73-186 1-126 (275)
5 PRK09819 alpha-mannosidase; Pr 99.9 6.1E-25 1.3E-29 227.2 9.4 114 71-187 3-131 (875)
6 KOG4342|consensus 99.4 9.8E-13 2.1E-17 134.4 7.1 110 70-185 279-388 (1078)
7 COG0383 AMS1 Alpha-mannosidase 98.6 1.2E-08 2.7E-13 108.3 1.4 95 71-169 197-291 (943)
8 COG0383 AMS1 Alpha-mannosidase 98.2 1.1E-07 2.4E-12 101.2 -2.0 97 71-169 3-100 (943)
9 PF03065 Glyco_hydro_57: Glyco 93.8 0.11 2.5E-06 49.2 5.6 22 137-158 113-134 (360)
10 PF12395 DUF3658: Protein of u 81.6 0.95 2.1E-05 36.9 1.9 68 74-160 41-108 (111)
11 TIGR03826 YvyF flagellar opero 72.8 3.5 7.6E-05 35.6 2.9 50 99-155 29-78 (137)
12 PRK00035 hemH ferrochelatase; 64.2 6.2 0.00013 37.2 2.9 68 94-166 210-281 (333)
13 PF08672 APC2: Anaphase promot 63.9 6.9 0.00015 29.3 2.6 23 134-156 36-58 (60)
14 PF10074 DUF2285: Uncharacteri 58.9 2.6 5.7E-05 34.6 -0.5 28 127-157 75-102 (106)
15 cd00419 Ferrochelatase_C Ferro 58.1 5.9 0.00013 33.3 1.5 79 74-166 25-110 (135)
16 PF02082 Rrf2: Transcriptional 57.2 35 0.00075 25.9 5.5 53 106-160 14-69 (83)
17 COG1448 TyrB Aspartate/tyrosin 55.1 9.3 0.0002 38.4 2.5 77 74-153 291-379 (396)
18 PF01479 S4: S4 domain; Inter 51.7 16 0.00035 24.7 2.6 26 132-158 10-36 (48)
19 PRK12864 YciI-like protein; Re 50.5 10 0.00022 29.7 1.6 55 130-185 19-73 (89)
20 TIGR02147 Fsuc_second hypothet 50.3 25 0.00054 33.3 4.5 36 134-169 154-190 (271)
21 COG0276 HemH Protoheme ferro-l 48.4 11 0.00024 36.7 1.9 79 74-162 191-272 (320)
22 TIGR00109 hemH ferrochelatase. 46.8 14 0.0003 35.2 2.3 67 96-167 211-280 (322)
23 COG4213 XylF ABC-type xylose t 46.7 42 0.00092 33.3 5.5 73 76-158 115-196 (341)
24 COG3977 Alanine-alpha-ketoisov 44.1 28 0.00061 34.8 3.9 53 105-158 317-373 (417)
25 PRK13378 protocatechuate 4,5-d 43.3 32 0.00069 29.4 3.6 51 88-143 16-67 (117)
26 cd00092 HTH_CRP helix_turn_hel 42.8 87 0.0019 21.8 5.3 38 122-159 28-66 (67)
27 PRK12866 YciI-like protein; Re 42.7 15 0.00032 29.4 1.5 55 130-185 18-73 (97)
28 TIGR02792 PCA_ligA protocatech 42.0 35 0.00076 29.2 3.7 50 88-142 10-60 (117)
29 PRK13377 protocatechuate 4,5-d 40.8 36 0.00079 29.5 3.6 50 88-142 16-66 (129)
30 PF01522 Polysacc_deac_1: Poly 39.9 1.1E+02 0.0024 23.5 6.0 51 101-161 19-70 (123)
31 TIGR02988 YaaA_near_RecF S4 do 37.1 36 0.00077 24.3 2.6 21 136-157 23-43 (59)
32 PF03344 Daxx: Daxx Family; I 35.1 13 0.00027 39.9 0.0 67 98-164 325-399 (713)
33 PF09551 Spore_II_R: Stage II 35.1 2.8E+02 0.0061 24.0 8.2 65 69-146 2-67 (130)
34 PF08220 HTH_DeoR: DeoR-like h 35.0 1.7E+02 0.0037 20.9 6.0 38 124-161 19-56 (57)
35 cd07924 PCA_45_Doxase_A The A 34.8 40 0.00087 29.0 2.9 50 88-142 13-63 (121)
36 smart00419 HTH_CRP helix_turn_ 33.9 75 0.0016 20.6 3.6 36 123-158 12-47 (48)
37 PRK04517 hypothetical protein; 33.4 41 0.0009 30.6 3.0 23 124-146 193-215 (216)
38 smart00420 HTH_DEOR helix_turn 33.0 1.4E+02 0.003 19.4 5.4 36 122-157 17-52 (53)
39 PRK12865 YciI-like protein; Re 32.6 25 0.00054 27.8 1.3 55 131-186 19-77 (97)
40 PF10549 ORF11CD3: ORF11CD3 do 32.6 41 0.00088 25.3 2.3 29 122-151 26-54 (57)
41 PF11625 DUF3253: Protein of u 31.7 67 0.0015 25.9 3.6 57 101-157 8-67 (83)
42 PRK01904 hypothetical protein; 31.6 50 0.0011 30.1 3.2 24 123-146 194-217 (219)
43 PF12995 DUF3879: Domain of un 30.7 1.2E+02 0.0027 27.7 5.5 38 54-112 66-103 (186)
44 PRK09897 hypothetical protein; 30.0 48 0.001 34.1 3.1 26 131-156 389-414 (534)
45 PRK13379 protocatechuate 4,5-d 30.0 65 0.0014 27.7 3.4 57 76-142 10-67 (119)
46 PF06044 DRP: Dam-replacing fa 29.8 86 0.0019 30.1 4.5 53 104-156 191-250 (254)
47 PRK03641 hypothetical protein; 29.8 51 0.0011 30.0 3.0 24 124-147 194-217 (220)
48 cd00165 S4 S4/Hsp/ tRNA synthe 29.2 65 0.0014 21.6 2.8 22 135-157 14-35 (70)
49 PF00538 Linker_histone: linke 28.5 2.2E+02 0.0047 21.5 5.8 19 135-153 47-65 (77)
50 COG1347 NqrD Na+-transporting 28.3 34 0.00074 31.4 1.5 27 137-163 148-181 (208)
51 cd03562 CID CID (CTD-Interacti 26.9 52 0.0011 26.1 2.3 47 98-145 57-104 (114)
52 PF08721 Tn7_Tnp_TnsA_C: TnsA 26.9 72 0.0016 23.2 2.9 47 104-151 31-77 (79)
53 PF08679 DsrD: Dissimilatory s 25.8 99 0.0022 24.2 3.5 47 104-152 5-53 (67)
54 PF00762 Ferrochelatase: Ferro 25.8 55 0.0012 31.3 2.5 85 72-169 188-277 (316)
55 PF08359 TetR_C_4: YsiA-like p 25.6 33 0.00072 27.2 0.9 54 96-149 24-82 (133)
56 KOG0634|consensus 24.7 1.2E+02 0.0025 31.5 4.7 75 85-160 349-431 (472)
57 smart00526 H15 Domain in histo 24.5 66 0.0014 23.5 2.3 20 135-154 47-66 (66)
58 smart00363 S4 S4 RNA-binding d 24.3 96 0.0021 20.1 2.9 22 135-157 14-35 (60)
59 PLN03014 carbonic anhydrase 23.9 1.6E+02 0.0034 29.5 5.3 30 137-166 295-324 (347)
60 COG1861 SpsF Spore coat polysa 23.5 34 0.00074 32.5 0.7 65 44-115 164-229 (241)
61 COG1543 Uncharacterized conser 23.5 1.2E+02 0.0025 31.8 4.5 31 126-156 115-145 (504)
62 PRK11179 DNA-binding transcrip 22.5 1.1E+02 0.0024 25.7 3.6 43 104-151 13-55 (153)
63 PF10835 DUF2573: Protein of u 22.3 34 0.00075 27.6 0.4 32 115-146 37-68 (82)
64 PF02608 Bmp: Basic membrane p 22.2 2.6E+02 0.0056 26.0 6.2 73 72-162 3-76 (306)
65 cd02983 P5_C P5 family, C-term 22.0 1.4E+02 0.0029 24.9 3.9 42 73-122 24-65 (130)
66 PRK11753 DNA-binding transcrip 22.0 2.1E+02 0.0045 24.1 5.2 32 129-160 177-209 (211)
67 COG2350 Uncharacterized protei 21.7 1E+02 0.0022 25.0 3.0 33 130-163 18-50 (92)
68 PF14595 Thioredoxin_9: Thiore 21.6 57 0.0012 27.2 1.6 26 132-157 28-53 (129)
69 cd01779 Myosin_IXb_RA ubitquit 21.5 75 0.0016 26.7 2.2 27 98-124 37-63 (105)
70 PF03795 YCII: YCII-related do 21.2 35 0.00076 25.8 0.2 31 132-163 20-50 (95)
71 COG3811 Uncharacterized protei 21.1 55 0.0012 26.5 1.3 35 135-169 6-54 (85)
72 PF14394 DUF4423: Domain of un 21.0 3E+02 0.0065 24.1 6.0 64 101-166 24-89 (171)
73 KOG1189|consensus 21.0 31 0.00066 37.9 -0.2 45 69-113 812-859 (960)
74 PF09106 SelB-wing_2: Elongati 20.5 87 0.0019 22.5 2.2 46 110-157 10-57 (59)
No 1
>PLN02701 alpha-mannosidase
Probab=100.00 E-value=1.7e-49 Score=416.98 Aligned_cols=154 Identities=46% Similarity=0.817 Sum_probs=146.5
Q ss_pred ccchhhhhHHHHHHHhcCCCcccccceeeecCCCCCCCCCceEEEEecCccCCcchhccHHHHHHHHHHHHHHHHHHHHH
Q psy11173 31 KESMGKVYEDEIEFANINGGKWTQGWNIGLDLAHETDPENLLRVFVVPHSHNDPGWKQTFESYFVHSTKSILDTMVTKLL 110 (280)
Q Consensus 31 ~~~ml~~y~~~l~f~~~dgg~wkqG~~i~y~~~~~w~~~~~l~VHVVPHSH~D~GWLkT~eEYy~~~v~~ILdsVl~~L~ 110 (280)
+|||+++| +.|+|+|+|||||||||+|+|+. ++|+ ..+++||||||||||+|||||+++||...+++||++||..|.
T Consensus 2 ~~~~~~~y-~~~~f~~~~gg~w~qg~~~~y~~-~~~~-~~~l~VhlVpHSH~D~gWl~T~~eyy~~~~~~ild~vv~~L~ 78 (1050)
T PLN02701 2 DITTKDLY-DRIEFLDKDGGAWKQGWRVKYRG-DEWD-REKLKVFVVPHSHNDPGWILTVEEYYQEQSRHILDTIVESLS 78 (1050)
T ss_pred ccchhhhh-hcCcccCCCCCeeccccceeecc-cccC-CcceEEEEeCCCCCCHHHcCcHHHHHHHHHHHHHHHHHHHHH
Confidence 79999999 99999999999999999999999 9999 889999999999999999999999999999999999999999
Q ss_pred hCCCCcEEeechHHHHHHHhccChHHHHHHHHHHHcCCceeeccccccccccccccccCC--------------CCCchh
Q psy11173 111 ENEKRKFIWAEMSYLSLWWKTISEDTKDKVRLLVKSGQLEIVTGGWVMTDEANSCNVSDN--------------SGSTDV 176 (280)
Q Consensus 111 ~dp~rkFi~aEisff~~Ww~eq~pe~ke~VKkLVknGRLEfVgGGWVM~DEA~thYeS~~--------------~~Sid~ 176 (280)
+||+|||+|++++||.+||++++|++|++||+||++|||+||||||||||+|++||.|++ +.-+++
T Consensus 79 ~dp~rkFi~~E~~fl~~Ww~~~~pe~~~~vk~LV~~GrLE~vgGgwvm~DEa~~~~esiI~Ql~~G~~~l~~~fG~~P~~ 158 (1050)
T PLN02701 79 KDPRRKFIWEEMSYLERWWRDASPSKKEAFTKLVKNGQLEIVGGGWVMNDEANSHYFAIIEQITEGNMWLNDTIGVAPKN 158 (1050)
T ss_pred hCcCcceeeccHHHHHHHHHhcCHHHHHHHHHHHHcCCEEEECCceecccccccCHHHHHHHHHhhhHHHHhhcCCCCCc
Confidence 999999999999999999999999999999999999999999999999999999999972 222667
Q ss_pred hhcccccCcch
Q psy11173 177 LTHMMPFYKEE 187 (280)
Q Consensus 177 ~~~~~~f~kee 187 (280)
+|+++||||..
T Consensus 159 ~W~iDpFGhs~ 169 (1050)
T PLN02701 159 SWAIDPFGYSS 169 (1050)
T ss_pred CccCCCCCCCH
Confidence 88889999875
No 2
>KOG1958|consensus
Probab=100.00 E-value=5.7e-47 Score=388.70 Aligned_cols=156 Identities=48% Similarity=0.814 Sum_probs=145.3
Q ss_pred ccccchhhhhHHHHHHHhcCCCcccccceeeecCCCCCCCCCceEEEEecCccCCcchhccHHHHHHHHHHHHHHHHHHH
Q psy11173 29 IGKESMGKVYEDEIEFANINGGKWTQGWNIGLDLAHETDPENLLRVFVVPHSHNDPGWKQTFESYFVHSTKSILDTMVTK 108 (280)
Q Consensus 29 ~~~~~ml~~y~~~l~f~~~dgg~wkqG~~i~y~~~~~w~~~~~l~VHVVPHSH~D~GWLkT~eEYy~~~v~~ILdsVl~~ 108 (280)
..++||+++| +.++|+|+|||||||||+|+|++ +.|+...+|+|+||||||+||||++||.+||+.++++||++++..
T Consensus 122 ~~d~qml~ly-d~~~f~~~dggvWkqG~~i~yd~-~~~~~~~~LkvfVvPHSHnDPGW~~Tf~~Yy~~~tr~Il~~~v~~ 199 (1129)
T KOG1958|consen 122 NTDLQMLDLY-DRMPFLNPDGGVWKQGFKITYDP-KKWDKEPFLKVFVVPHSHNDPGWIKTFEEYYQRQTRHILNNMVNK 199 (1129)
T ss_pred cchHHHHHHH-HhhhhhCCCcchhhcCceeecCh-hhcccccceEEEEeeccCCCcchhhhHHHHHHHHHHHHHHHHHHH
Confidence 3589999999 99999999999999999999999 999966669999999999999999999999999999999999999
Q ss_pred HHhCCCCcEEeechHHHHHHHhccChHHHHHHHHHHHcCCceeeccccccccccccccccCC--------------CCCc
Q psy11173 109 LLENEKRKFIWAEMSYLSLWWKTISEDTKDKVRLLVKSGQLEIVTGGWVMTDEANSCNVSDN--------------SGST 174 (280)
Q Consensus 109 L~~dp~rkFi~aEisff~~Ww~eq~pe~ke~VKkLVknGRLEfVgGGWVM~DEA~thYeS~~--------------~~Si 174 (280)
|.++|++||||+||+||.+||+.++|++|.+||+||++||||||+|||||||+|++||.+++ +.-+
T Consensus 200 L~e~~~~~FIwaEiS~~~~ww~~~~~~kk~a~k~lv~~GqlEIvtGGWVMpDEAn~Hy~~~i~qliEGh~Wl~~~igv~P 279 (1129)
T KOG1958|consen 200 LSEDPRMKFIWAEISFLERWWDDASPTKKNAVKRLVKNGQLEIVTGGWVMPDEANSHYFAMIDQLIEGHQWLKNNIGVTP 279 (1129)
T ss_pred hhhCcccchhhhhHHHHHHhhhhcChHHHHHHHHHHhcCcEEEEeCccccCcccchhHHHHHHHHhhhhhHHhccCCCCC
Confidence 99999999999999999999999999999999999999999999999999999999999972 2335
Q ss_pred hhhhcccccCcc
Q psy11173 175 DVLTHMMPFYKE 186 (280)
Q Consensus 175 d~~~~~~~f~ke 186 (280)
+.-|.++||+++
T Consensus 280 ~s~WaiDPFG~S 291 (1129)
T KOG1958|consen 280 QSGWAIDPFGYS 291 (1129)
T ss_pred CcccccCCCCCC
Confidence 556667777765
No 3
>KOG1959|consensus
Probab=100.00 E-value=2.1e-40 Score=338.99 Aligned_cols=129 Identities=36% Similarity=0.717 Sum_probs=122.3
Q ss_pred ecCCCCCCCCCceEEEEecCccCCcchhccHHHHHH--------HHHHHHHHHHHHHHHhCCCCcEEeechHHHHHHHhc
Q psy11173 60 LDLAHETDPENLLRVFVVPHSHNDPGWKQTFESYFV--------HSTKSILDTMVTKLLENEKRKFIWAEMSYLSLWWKT 131 (280)
Q Consensus 60 y~~~~~w~~~~~l~VHVVPHSH~D~GWLkT~eEYy~--------~~v~~ILdsVl~~L~~dp~rkFi~aEisff~~Ww~e 131 (280)
|.+|+... ++|+|||||||||+|+|||||+++||+ .-|++|||+||..|.+||+||||++|++||.+||..
T Consensus 26 y~t~~~~~-~~~invHlVPHSHDDVGWLKTVDQyy~G~~n~Iq~AgVqyIldSVV~eLl~dp~RRFI~VE~aFF~rWW~~ 104 (996)
T KOG1959|consen 26 YNTCHKVV-PNMINVHLVPHSHDDVGWLKTVDQYYYGSKNKIQHAGVQYILDSVVEELLKDPNRRFIYVETAFFARWWNE 104 (996)
T ss_pred cCCCcccc-CceeEEEecCCccCccceeeeehhheecCCcccchhhHHHHHHHHHHHHhcCCccceehhhHHHHHHHHHh
Confidence 58999999 889999999999999999999999998 459999999999999999999999999999999999
Q ss_pred cChHHHHHHHHHHHcCCceeeccccccccccccccccCC--------------C--CCchhhhcccccCcchhh
Q psy11173 132 ISEDTKDKVRLLVKSGQLEIVTGGWVMTDEANSCNVSDN--------------S--GSTDVLTHMMPFYKEEEE 189 (280)
Q Consensus 132 q~pe~ke~VKkLVknGRLEfVgGGWVM~DEA~thYeS~~--------------~--~Sid~~~~~~~f~keeee 189 (280)
|++.+|.+||+||++||||||||||||||+|++||.+++ + +-+++.||++||+|+++-
T Consensus 105 qS~~~k~~Vk~LV~~GrLEFi~Ggw~MnDEA~~hY~dvIDQ~TlGlrfL~~tFG~cgrPrvgWqIDPFGHSreq 178 (996)
T KOG1959|consen 105 QSETQKEQVKKLVNEGRLEFIGGGWSMNDEATTHYQDVIDQFTLGLRFLKDTFGECGRPRVGWQIDPFGHSREQ 178 (996)
T ss_pred cCHHHHHHHHHHHhcCCEEEecCeeeecchhhhhHHHHHHHHHHHHHHHHHHhcccCCcceeeeeCCCCcchHH
Confidence 999999999999999999999999999999999999974 2 558899999999999873
No 4
>PF01074 Glyco_hydro_38: Glycosyl hydrolases family 38 N-terminal domain; InterPro: IPR000602 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. Glycoside hydrolase family 38 GH38 from CAZY comprises enzymes with only one known activity; alpha-mannosidase (3.2.1.24 from EC) (3.2.1.114 from EC). Lysosomal alpha-mannosidase is necessary for the catabolism of N-linked carbohydrates released during glycoprotein turnover. The enzyme catalyses the hydrolysis of terminal, non-reducing alpha-D-mannose residues in alpha-D-mannosides, and can cleave all known types of alpha-mannosidic linkages. Defects in the gene cause lysosomal alpha-mannosidosis (AM), a lysosomal storage disease characterised by the accumulation of unbranched oligo-saccharide chains.; GO: 0004559 alpha-mannosidase activity, 0005975 carbohydrate metabolic process; PDB: 2WYI_A 2WYH_A 1O7D_A 3CZN_A 2FYV_A 3D50_A 3EJU_A 3EJS_A 3DX3_A 3BVX_A ....
Probab=99.96 E-value=1.5e-29 Score=226.26 Aligned_cols=112 Identities=32% Similarity=0.443 Sum_probs=89.8
Q ss_pred EEEEecCccCCcchhccHHHHHHHHHHHHHHHHHHHHHhCCCCcEEeechHHHHHHHhccChHHHHHHHHHHHcCCceee
Q psy11173 73 RVFVVPHSHNDPGWKQTFESYFVHSTKSILDTMVTKLLENEKRKFIWAEMSYLSLWWKTISEDTKDKVRLLVKSGQLEIV 152 (280)
Q Consensus 73 ~VHVVPHSH~D~GWLkT~eEYy~~~v~~ILdsVl~~L~~dp~rkFi~aEisff~~Ww~eq~pe~ke~VKkLVknGRLEfV 152 (280)
+||||||||||+||++|+++|. .++.++|++|+..|.++|++||++.++++|.+||.. .|..+.++|+||++|||+||
T Consensus 1 ~v~~i~HsH~D~~W~~t~~~~~-~~~~~~~~~~l~~l~~~~~~~f~~~~~~~~~~~~~~-~p~~~~~~~~lv~~Gri~~v 78 (275)
T PF01074_consen 1 TVHVIPHSHWDRGWLWTFEEYR-RYLVNILDSVLDLLEEDPDFRFIDGQTAYLEDYLED-APEEFKRIKKLVKEGRIEIV 78 (275)
T ss_dssp EEEEEEEEB--SSSSS-HHHHH-HHHHHHHHHHHHHHHH-TT--EECTBCHHHHHHHHC-SGHHHHHHHHHHHTTSEEES
T ss_pred CEEEccccccchhhcccHHHHH-HHHHHHHHHHHHHHHhCCcceEeechhHHHHHHHHh-CCHHHHHHHHHHHhceeEEe
Confidence 6999999999999999999995 678899999999999999999999999999877765 88999999999999999999
Q ss_pred ccccccccccccccccCC--------------CCCchhhhcccccCcc
Q psy11173 153 TGGWVMTDEANSCNVSDN--------------SGSTDVLTHMMPFYKE 186 (280)
Q Consensus 153 gGGWVM~DEA~thYeS~~--------------~~Sid~~~~~~~f~ke 186 (280)
||||||+|+++++++|++ +..+++++++++|++.
T Consensus 79 gg~~~~~D~~l~~~Eslirql~~G~~~~~~~fg~~~~~~~~~D~FG~~ 126 (275)
T PF01074_consen 79 GGWYVQPDENLPSGESLIRQLLYGHKYLRKEFGVRPKVAWQPDSFGHS 126 (275)
T ss_dssp SSBSS-B-SSSS-HHHHHHHHHHHHHHHHHHHTG--SEEEESSSSSB-
T ss_pred CceeeeccccCCCHHHHHHHHhhhHHHHHHhcCCCCCeEEeCCCCCCc
Confidence 999999999999999972 3446677777788764
No 5
>PRK09819 alpha-mannosidase; Provisional
Probab=99.91 E-value=6.1e-25 Score=227.24 Aligned_cols=114 Identities=21% Similarity=0.280 Sum_probs=97.1
Q ss_pred ceEEEEecCccCCcchhccHHHHHHHHHHHHHHHHHHHHHhCCCCcEEee--chHHHHHHHhccChHHHHHHHHHHHcCC
Q psy11173 71 LLRVFVVPHSHNDPGWKQTFESYFVHSTKSILDTMVTKLLENEKRKFIWA--EMSYLSLWWKTISEDTKDKVRLLVKSGQ 148 (280)
Q Consensus 71 ~l~VHVVPHSH~D~GWLkT~eEYy~~~v~~ILdsVl~~L~~dp~rkFi~a--Eisff~~Ww~eq~pe~ke~VKkLVknGR 148 (280)
+++||||||||||++||||++++.. ++.++|++||..|.++|+++|++. .+++|..|| .+.|++|.+||+||++||
T Consensus 3 ~~~v~~v~HtH~D~~Wl~~~~~~~~-~~~~~~~~vl~lle~~p~~~f~~~d~q~~~l~~~~-~~~Pe~~~~ik~lV~~Gr 80 (875)
T PRK09819 3 KSKVHIVPHMHWDREWYFTTERSRI-LLVNNMEEILDRLEQDNDYKYYVLDGQTSLLEDYL-AVKPEDKERVKKLVQAGK 80 (875)
T ss_pred ceEEEEeCCCCCChhhcCChHHhHH-HHHHHHHHHHHHHHhCCCcceEEEchhHHHHHHHH-HhChHHHHHHHHHHHcCC
Confidence 3679999999999999999999975 577899999999999999998753 456666555 789999999999999999
Q ss_pred ceeeccccccccccccccccCC-------------CCCchhhhcccccCcch
Q psy11173 149 LEIVTGGWVMTDEANSCNVSDN-------------SGSTDVLTHMMPFYKEE 187 (280)
Q Consensus 149 LEfVgGGWVM~DEA~thYeS~~-------------~~Sid~~~~~~~f~kee 187 (280)
| ++||||||||+++++++|++ +....++|.+++|++.-
T Consensus 81 l-~~G~W~v~~D~~l~sgEsliRqll~G~~~~~~fG~~~~vgwlpD~FG~s~ 131 (875)
T PRK09819 81 L-IIGPWYTQTDQLVVSGESIVRNLLYGIRDCREFGEPMKIGYLPDSFGQSG 131 (875)
T ss_pred E-eECcEEeecccccCCHHHHHHHHHHHHHHHHHcCCCCceeeecCCCCCcH
Confidence 9 66666699999999999984 45566777888888753
No 6
>KOG4342|consensus
Probab=99.36 E-value=9.8e-13 Score=134.38 Aligned_cols=110 Identities=19% Similarity=0.206 Sum_probs=96.9
Q ss_pred CceEEEEecCccCCcchhccHHHHHHHHHHHHHHHHHHHHHhCCCCcEEeechHHHHHHHhccChHHHHHHHHHHHcCCc
Q psy11173 70 NLLRVFVVPHSHNDPGWKQTFESYFVHSTKSILDTMVTKLLENEKRKFIWAEMSYLSLWWKTISEDTKDKVRLLVKSGQL 149 (280)
Q Consensus 70 ~~l~VHVVPHSH~D~GWLkT~eEYy~~~v~~ILdsVl~~L~~dp~rkFi~aEisff~~Ww~eq~pe~ke~VKkLVknGRL 149 (280)
..-+||.|+|-|+|.+|||+|-+... ++.+-..+.+..|..+|.++|+-+.. .-..|.+...|..+.+++.+|..||+
T Consensus 279 s~~nv~aiGhCHIDTAWLWPFaETrR-KivRSW~tq~~lMdR~PEy~FvcSQA-qQ~~WlkedhP~~f~kl~e~~~q~qF 356 (1078)
T KOG4342|consen 279 SQHNVHAIGHCHIDTAWLWPFAETRR-KIVRSWVTQLQLMDRNPEYIFVCSQA-QQLEWLKEDHPGLFSKLQEFACQGQF 356 (1078)
T ss_pred cccceeeeccccccchhhcChHHHHH-HHHHHHHHHHhHHhhCcceeEehhhH-HHHHHHhhhChhHHHHHHHHHhcCce
Confidence 35679999999999999999999975 44456778899999999999997654 44459999999999999999999999
Q ss_pred eeeccccccccccccccccCCCCCchhhhcccccCc
Q psy11173 150 EIVTGGWVMTDEANSCNVSDNSGSTDVLTHMMPFYK 185 (280)
Q Consensus 150 EfVgGGWVM~DEA~thYeS~~~~Sid~~~~~~~f~k 185 (280)
-.|||.||.+|.++|+++|+ ++||-.++.||-
T Consensus 357 ~pvGGtWVE~DtNiPsGEsl----vRQFl~GQ~FFl 388 (1078)
T KOG4342|consen 357 VPVGGTWVEMDTNIPSGESL----VRQFLQGQNFFL 388 (1078)
T ss_pred eeccceEEecCCCCCChHHH----HHHHHhhhhHHH
Confidence 99999999999999999999 789988888763
No 7
>COG0383 AMS1 Alpha-mannosidase [Carbohydrate transport and metabolism]
Probab=98.60 E-value=1.2e-08 Score=108.29 Aligned_cols=95 Identities=20% Similarity=0.208 Sum_probs=85.5
Q ss_pred ceEEEEecCccCCcchhccHHHHHHHHHHHHHHHHHHHHHhCCCCcEEeechHHHHHHHhccChHHHHHHHHHHHcCCce
Q psy11173 71 LLRVFVVPHSHNDPGWKQTFESYFVHSTKSILDTMVTKLLENEKRKFIWAEMSYLSLWWKTISEDTKDKVRLLVKSGQLE 150 (280)
Q Consensus 71 ~l~VHVVPHSH~D~GWLkT~eEYy~~~v~~ILdsVl~~L~~dp~rkFi~aEisff~~Ww~eq~pe~ke~VKkLVknGRLE 150 (280)
..+|+.+.|+|.|..|+|++.+... .+...+.+++..|...|.++|+.+-+.++ .|.....|....+ ++|..|+++
T Consensus 197 g~~I~~~ghahid~aWlw~l~et~r-~a~ts~~~~~~l~D~~p~~~~~~s~~~~y-~~l~~d~p~l~~~--~~v~~~~~~ 272 (943)
T COG0383 197 GNEIPAVGHAHIDTAWLWPLDETER-KASTSFSLVMNLMDHYPVQKFVQSAAALY-NWLKPDVPFLFSR--PAVEFEQWE 272 (943)
T ss_pred cccccccchhhHHHHHhccHHHHHH-HHhhhhhheecccccChhhhhhhhHHHHH-HHhcCccHHHhhc--ccccccceE
Confidence 3449999999999999999999874 56678889999999999999999755544 4999999999998 999999999
Q ss_pred eeccccccccccccccccC
Q psy11173 151 IVTGGWVMTDEANSCNVSD 169 (280)
Q Consensus 151 fVgGGWVM~DEA~thYeS~ 169 (280)
+++|+||-+|+++++++|.
T Consensus 273 ~~~g~~ve~d~n~~sGEsl 291 (943)
T COG0383 273 IVGGMWVEEDLNTPSGESL 291 (943)
T ss_pred EeecccccccCCccccchh
Confidence 9999999999999999997
No 8
>COG0383 AMS1 Alpha-mannosidase [Carbohydrate transport and metabolism]
Probab=98.24 E-value=1.1e-07 Score=101.18 Aligned_cols=97 Identities=23% Similarity=0.281 Sum_probs=81.4
Q ss_pred ceEEEEecCccCCcchhccHHHHHHHHHHHHHHHHHHHHHhCCCC-cEEeechHHHHHHHhccChHHHHHHHHHHHcCCc
Q psy11173 71 LLRVFVVPHSHNDPGWKQTFESYFVHSTKSILDTMVTKLLENEKR-KFIWAEMSYLSLWWKTISEDTKDKVRLLVKSGQL 149 (280)
Q Consensus 71 ~l~VHVVPHSH~D~GWLkT~eEYy~~~v~~ILdsVl~~L~~dp~r-kFi~aEisff~~Ww~eq~pe~ke~VKkLVknGRL 149 (280)
++.+|+|+|||||++|+++.+.++...+ ..|++++..+.++|.. .|....+......+....|..+++|+.++..|+|
T Consensus 3 ~~~~~ii~~~~wdrew~~~~e~~~~~~~-~~~~~i~~~~~~~~~~~~~~~d~qt~~l~d~l~v~~~~~~~~~~~~~~~~l 81 (943)
T COG0383 3 KKKVHIISHSHWDREWYFTSESHRILLD-ELFEEIIELLQKDPEFAGFHLDGQTIWLDDYLAVPPELKDRVKLLIASGKL 81 (943)
T ss_pred ccccccchhhhhhhhceeeccceEeech-hhhhhhhhccccCcccceecCccceeeeeeeEEecccchhhHHHHHhhcCc
Confidence 4567999999999999999999886544 4699999999999944 4555555555556777889999999999999999
Q ss_pred eeeccccccccccccccccC
Q psy11173 150 EIVTGGWVMTDEANSCNVSD 169 (280)
Q Consensus 150 EfVgGGWVM~DEA~thYeS~ 169 (280)
++|.++.+.|.+.++..|.
T Consensus 82 -~ig~~~~~~~~~~~~~e~~ 100 (943)
T COG0383 82 -GIGPWYTQTDTFILSGESN 100 (943)
T ss_pred -cccCCCCeeEEEEeccccc
Confidence 7788999999999998884
No 9
>PF03065 Glyco_hydro_57: Glycosyl hydrolase family 57; InterPro: IPR004300 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. Glycoside hydrolase family 57 GH57 from CAZY comprises enzymes with two known activities; alpha-amylase (3.2.1.1 from EC) and 4-alpha-glucanotransferase (2.4.1 from EC).; GO: 0003824 catalytic activity, 0005975 carbohydrate metabolic process; PDB: 1K1X_B 1K1W_A 1K1Y_A 3N98_A 3N8T_A 3N92_A 1UFA_A 3P0B_A.
Probab=93.84 E-value=0.11 Score=49.22 Aligned_cols=22 Identities=27% Similarity=0.465 Sum_probs=18.9
Q ss_pred HHHHHHHHHcCCceeecccccc
Q psy11173 137 KDKVRLLVKSGQLEIVTGGWVM 158 (280)
Q Consensus 137 ke~VKkLVknGRLEfVgGGWVM 158 (280)
-..+|+|++.|+++|++++|.-
T Consensus 113 i~~~~~l~~~G~iEll~~~~~h 134 (360)
T PF03065_consen 113 IEAFRELAERGQIELLTSPYYH 134 (360)
T ss_dssp HHHHHHHHHTTSEEEEEE-TT-
T ss_pred HHHHHHHHHCCCEEEEeCchHH
Confidence 8899999999999999999954
No 10
>PF12395 DUF3658: Protein of unknown function ; InterPro: IPR022123 This domain family is found in bacteria, and is approximately 110 amino acids in length. The family is found in association with PF08874 from PFAM. There are two completely conserved residues (D and R) that may be functionally important.
Probab=81.62 E-value=0.95 Score=36.94 Aligned_cols=68 Identities=18% Similarity=0.223 Sum_probs=44.9
Q ss_pred EEEecCccCCcchhccHHHHHHHHHHHHHHHHHHHHHhCCCCcEEeechHHHHHHHhccChHHHHHHHHHHHcCCceeec
Q psy11173 74 VFVVPHSHNDPGWKQTFESYFVHSTKSILDTMVTKLLENEKRKFIWAEMSYLSLWWKTISEDTKDKVRLLVKSGQLEIVT 153 (280)
Q Consensus 74 VHVVPHSH~D~GWLkT~eEYy~~~v~~ILdsVl~~L~~dp~rkFi~aEisff~~Ww~eq~pe~ke~VKkLVknGRLEfVg 153 (280)
|+=||=.|.|.--+.....-|. .+.+++-.|+..+..... .|| ..-+|+.||+.|+|++.|
T Consensus 41 i~sv~ed~yD~~Il~~~~~~~~-~~arvIg~vl~~~~~~i~------------D~f------~~~Ri~~Li~~G~le~~g 101 (111)
T PF12395_consen 41 IVSVPEDYYDDFILEQAPDEFQ-KAARVIGEVLGHSDQGIG------------DWF------LEYRIRELISQGVLEIKG 101 (111)
T ss_pred EEecChHHhhHHHHhcCCcccc-HHHHHHHHHHHhcCcCCC------------hHH------HHHHHHHHHHCCCEEEec
Confidence 5556777888887776655553 356677777777532211 122 234899999999999988
Q ss_pred ccccccc
Q psy11173 154 GGWVMTD 160 (280)
Q Consensus 154 GGWVM~D 160 (280)
..-.|.+
T Consensus 102 ~~~~mr~ 108 (111)
T PF12395_consen 102 DPKDMRH 108 (111)
T ss_pred CCCcccc
Confidence 6655543
No 11
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=72.83 E-value=3.5 Score=35.62 Aligned_cols=50 Identities=12% Similarity=0.179 Sum_probs=35.8
Q ss_pred HHHHHHHHHHHHhCCCCcEEeechHHHHHHHhccChHHHHHHHHHHHcCCceeeccc
Q psy11173 99 KSILDTMVTKLLENEKRKFIWAEMSYLSLWWKTISEDTKDKVRLLVKSGQLEIVTGG 155 (280)
Q Consensus 99 ~~ILdsVl~~L~~dp~rkFi~aEisff~~Ww~eq~pe~ke~VKkLVknGRLEfVgGG 155 (280)
...|..|-.-|..+|.+.....+++ ..+.-.-..|.++|+.|||+|+...
T Consensus 29 e~~f~kV~~yLr~~p~~~ati~eV~-------e~tgVs~~~I~~~IreGRL~~~~~~ 78 (137)
T TIGR03826 29 EREFEKVYKFLRKHENRQATVSEIV-------EETGVSEKLILKFIREGRLQLKHFP 78 (137)
T ss_pred HHHHHHHHHHHHHCCCCCCCHHHHH-------HHHCcCHHHHHHHHHcCCeeccCCC
Confidence 3456677777889999887766543 2233356789999999999886643
No 12
>PRK00035 hemH ferrochelatase; Reviewed
Probab=64.20 E-value=6.2 Score=37.21 Aligned_cols=68 Identities=16% Similarity=0.311 Sum_probs=44.6
Q ss_pred HHHHHHHHHHHHHHHHHh-CCCCcEEeech-HHHHHHHhccChHHHHHHHHHHHcC--Cceeecccccccccccccc
Q psy11173 94 FVHSTKSILDTMVTKLLE-NEKRKFIWAEM-SYLSLWWKTISEDTKDKVRLLVKSG--QLEIVTGGWVMTDEANSCN 166 (280)
Q Consensus 94 y~~~v~~ILdsVl~~L~~-dp~rkFi~aEi-sff~~Ww~eq~pe~ke~VKkLVknG--RLEfVgGGWVM~DEA~thY 166 (280)
|..++..+.+.|...|.. .....+.|-.. .- ..| ..|...+.|++|.+.| ++-++.-|+|. |+.-|-|
T Consensus 210 Y~~~~~~t~~~l~~~l~~~~~~~~~~fqs~~g~-~~W---l~P~~~~~l~~l~~~g~k~V~v~P~~Fv~-D~lEtl~ 281 (333)
T PRK00035 210 YQQQCEETARLLAEALGLPDEDYDLTYQSRFGP-EPW---LEPYTDDTLEELAEKGVKKVVVVPPGFVS-DHLETLE 281 (333)
T ss_pred hHHHHHHHHHHHHHHhCCCCCCeEEEeeCCCCC-Ccc---CCCCHHHHHHHHHHcCCCeEEEECCeeec-cchhHHH
Confidence 445677788888888763 23333322110 00 135 4699999999999998 78888888877 8866644
No 13
>PF08672 APC2: Anaphase promoting complex (APC) subunit 2; InterPro: IPR014786 The anaphase-promoting complex (APC) or cyclosome is a multi-subunit E3 protein ubiquitin ligase that regulates important events in mitosis such as the initiation of anaphase and exit from telophase. The APC, in conjunction with other enzymes, assembles multi-ubiquitin chains on a variety of regulatory proteins, thereby targeting them for proteolysis by the 26S proteasome. Anaphase is initiated when the APC triggers the destruction of securin, thereby allowing the protease, separase, to disrupt sister-chromatid cohesion. Securin ubiquitination by the APC is inhibited by cyclin-dependent kinase 1 (Cdk1)-dependent phosphorylation []. Forkhead Box M1 (FoxM1), which is a transcription factor that is over-expressed in many cancers, is degraded in late mitosis and early G1 phase by the APC/cyclosome (APC/C) E3 ubiquitin ligase []. The APC/C targets mitotic cyclins for destruction in mitosis and G1 phase and is then inactivated at S phase. It thereby generates alternating states of high and low cyclin-Cdk activity, which is required for the alternation of mitosis and DNA replication []. The APC/C is composed of at least 13 subunits that stay tightly associated throughout the cell cycle: APC1, APC2, APC4, APC5, APC9, APC11, CDC16, CDC23, CDC26, CDC27, DOC1, MND2 and SWM1[], []. In fission yeast the 13 subunits are known as: Apc1, Apc2, Nuc2, Apc4, Apc5, Cut9, Apc8, Apc10, Apc11, Hcn1, Apc13, Apc14 and Apc15 []. This entry represents a C-terminal domain found in APC subunit 2. ; PDB: 1LDD_A.
Probab=63.89 E-value=6.9 Score=29.27 Aligned_cols=23 Identities=30% Similarity=0.546 Sum_probs=17.4
Q ss_pred hHHHHHHHHHHHcCCceeecccc
Q psy11173 134 EDTKDKVRLLVKSGQLEIVTGGW 156 (280)
Q Consensus 134 pe~ke~VKkLVknGRLEfVgGGW 156 (280)
.+.+.-+.++|++|+|+++||-|
T Consensus 36 ~eL~~fL~~lv~e~~L~~~~G~Y 58 (60)
T PF08672_consen 36 EELQEFLDRLVEEGKLECSGGSY 58 (60)
T ss_dssp HHHHHHHHHHHHTTSEE--TTEE
T ss_pred HHHHHHHHHHHHCCcEEecCCEE
Confidence 45677788999999999998766
No 14
>PF10074 DUF2285: Uncharacterized conserved protein (DUF2285); InterPro: IPR018754 This entry contains uncharacterised proteins of unknown function.
Probab=58.92 E-value=2.6 Score=34.63 Aligned_cols=28 Identities=25% Similarity=0.575 Sum_probs=23.9
Q ss_pred HHHhccChHHHHHHHHHHHcCCceeeccccc
Q psy11173 127 LWWKTISEDTKDKVRLLVKSGQLEIVTGGWV 157 (280)
Q Consensus 127 ~Ww~eq~pe~ke~VKkLVknGRLEfVgGGWV 157 (280)
.||+. ...|.++++||+.|+. +++|||-
T Consensus 75 ~~W~~--~~~R~~~~rll~~a~~-l~~gGYr 102 (106)
T PF10074_consen 75 DEWKD--SSLRRRVRRLLRRARA-LMEGGYR 102 (106)
T ss_pred ccccC--hHHHHHHHHHHHHHHH-HHHhhHH
Confidence 46665 7789999999999999 9999983
No 15
>cd00419 Ferrochelatase_C Ferrochelatase, C-terminal domain: Ferrochelatase (protoheme ferrolyase or HemH) is the terminal enzyme of the heme biosynthetic pathway. It catalyzes the insertion of ferrous iron into the protoporphyrin IX ring yielding protoheme. This enzyme is ubiquitous in nature and widely distributed in bacteria and eukaryotes. Recently, some archaeal members have been identified. The oligomeric state of these enzymes varies depending on the presence of a dimerization motif at the C-terminus.
Probab=58.12 E-value=5.9 Score=33.35 Aligned_cols=79 Identities=19% Similarity=0.332 Sum_probs=47.1
Q ss_pred EEEecCccCCcchhccHHHHHHHHHHHHHHHHHHHHHhCCCCcEEeechHHHH-----HHHhccChHHHHHHHHHHHcC-
Q psy11173 74 VFVVPHSHNDPGWKQTFESYFVHSTKSILDTMVTKLLENEKRKFIWAEMSYLS-----LWWKTISEDTKDKVRLLVKSG- 147 (280)
Q Consensus 74 VHVVPHSH~D~GWLkT~eEYy~~~v~~ILdsVl~~L~~dp~rkFi~aEisff~-----~Ww~eq~pe~ke~VKkLVknG- 147 (280)
.|=+|.++.+.| +- |..++..+.+.|...|.. +...+.. +|.+ .| ..|.+.+.|++|.+.|
T Consensus 25 aHgiP~~~~~~g-----d~-Y~~~~~~~~~~v~~~l~~-~~~~~~~---~fqS~~g~~~W---l~P~~~~~l~~l~~~G~ 91 (135)
T cd00419 25 AHGLPVRDIKKG-----DP-YPDQCEETARLVAERLGL-PFDEYEL---AYQSRFGPGEW---LEPSTDDALEELAKEGV 91 (135)
T ss_pred cCCCHHHHhhCC-----CC-HHHHHHHHHHHHHHHhCC-CCCCEEE---EecCCCCCCCC---CCCCHHHHHHHHHHcCC
Confidence 444555555433 22 345677677777777752 2222222 3333 45 4699999999999998
Q ss_pred -Cceeecccccccccccccc
Q psy11173 148 -QLEIVTGGWVMTDEANSCN 166 (280)
Q Consensus 148 -RLEfVgGGWVM~DEA~thY 166 (280)
++-++..|++ +|+.-|-|
T Consensus 92 ~~i~v~p~gF~-~D~~Etl~ 110 (135)
T cd00419 92 KNVVVVPIGFV-SDHLETLY 110 (135)
T ss_pred CeEEEECCccc-cccHHHHH
Confidence 6777777764 35554444
No 16
>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulfovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis sp. (strain PCC 6803) hypothetical protein slr0846. These are small proteins of 12 to 18kDa which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.; PDB: 3T8T_A 3T8R_A 3K69_A 3LWF_C 1XD7_A 2Y75_E 1YLF_C.
Probab=57.25 E-value=35 Score=25.88 Aligned_cols=53 Identities=15% Similarity=0.173 Sum_probs=34.9
Q ss_pred HHHHHhCCCCcEEeechHHHHHHHhccChHHHHHHHHHHHcCCceee---cccccccc
Q psy11173 106 VTKLLENEKRKFIWAEMSYLSLWWKTISEDTKDKVRLLVKSGQLEIV---TGGWVMTD 160 (280)
Q Consensus 106 l~~L~~dp~rkFi~aEisff~~Ww~eq~pe~ke~VKkLVknGRLEfV---gGGWVM~D 160 (280)
+-.|...+..+.+ -+..+..-..-..+..+..+++|++.|=+... +|||..+.
T Consensus 14 l~~la~~~~~~~~--s~~eiA~~~~i~~~~l~kil~~L~~~Gli~s~~G~~GGy~L~~ 69 (83)
T PF02082_consen 14 LLYLARHPDGKPV--SSKEIAERLGISPSYLRKILQKLKKAGLIESSRGRGGGYRLAR 69 (83)
T ss_dssp HHHHHCTTTSC-B--EHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETSTTSEEEESS
T ss_pred HHHHHhCCCCCCC--CHHHHHHHHCcCHHHHHHHHHHHhhCCeeEecCCCCCceeecC
Confidence 3345566665542 23455555555556779999999999998877 78887654
No 17
>COG1448 TyrB Aspartate/tyrosine/aromatic aminotransferase [Amino acid transport and metabolism]
Probab=55.12 E-value=9.3 Score=38.43 Aligned_cols=77 Identities=25% Similarity=0.410 Sum_probs=54.1
Q ss_pred EEEecCccCCc----chhccHHHHHHHHHHHHHHHHHHHHH---hCCCCcEEeechHHHHHHHhccChHHHHHHHH----
Q psy11173 74 VFVVPHSHNDP----GWKQTFESYFVHSTKSILDTMVTKLL---ENEKRKFIWAEMSYLSLWWKTISEDTKDKVRL---- 142 (280)
Q Consensus 74 VHVVPHSH~D~----GWLkT~eEYy~~~v~~ILdsVl~~L~---~dp~rkFi~aEisff~~Ww~eq~pe~ke~VKk---- 142 (280)
..||.+.-.|| .|.+-+..++. ++..+=..+++.|. ...++.||..-..+|+ |.+.+|++=.++|.
T Consensus 291 a~vva~IL~~p~Lra~W~~El~~Mr~-Ri~~mR~~lv~~L~~~~~~~~f~~i~~Q~GMFs--y~Gls~~QV~rLree~~I 367 (396)
T COG1448 291 AAVVATILNNPELRAEWEQELEEMRQ-RILEMRQALVDALKALGAPRNFDFIISQRGMFS--YTGLSPEQVDRLREEFGI 367 (396)
T ss_pred HHHHHHHhCCHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHhhCCCcccchHhhcCceee--cCCCCHHHHHHHHHhccE
Confidence 34555555666 69998888774 34434344444454 4557889988888998 67888988888887
Q ss_pred -HHHcCCceeec
Q psy11173 143 -LVKSGQLEIVT 153 (280)
Q Consensus 143 -LVknGRLEfVg 153 (280)
+|++||+-+.|
T Consensus 368 Y~v~sGRi~vaG 379 (396)
T COG1448 368 YLVASGRINVAG 379 (396)
T ss_pred EEecCCeeeecc
Confidence 88999986543
No 18
>PF01479 S4: S4 domain; InterPro: IPR002942 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 [, ]. The S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4, eukaryotic ribosomal S9, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast protein containing a pseudouridine synthetase and a deaminase domain, bacterial tyrosyl-tRNA synthetases, and a number of uncharacterised, small proteins that may be involved in translation regulation []. The S4 domain probably mediates binding to RNA.; GO: 0003723 RNA binding; PDB: 3BBU_A 1DM9_B 2K6P_A 3U5G_E 3U5C_E 3IZB_D 2XZM_D 2XZN_D 3O30_E 3O2Z_E ....
Probab=51.70 E-value=16 Score=24.73 Aligned_cols=26 Identities=27% Similarity=0.459 Sum_probs=19.8
Q ss_pred cChH-HHHHHHHHHHcCCceeecccccc
Q psy11173 132 ISED-TKDKVRLLVKSGQLEIVTGGWVM 158 (280)
Q Consensus 132 q~pe-~ke~VKkLVknGRLEfVgGGWVM 158 (280)
.... .|..+++||++|++ .|+|-=|-
T Consensus 10 ~~~~~sr~~a~~~I~~g~V-~VNg~~v~ 36 (48)
T PF01479_consen 10 LGLASSRSEARRLIKQGRV-KVNGKVVK 36 (48)
T ss_dssp TTSSSSHHHHHHHHHTTTE-EETTEEES
T ss_pred cCCcCCHHHHHHhcCCCEE-EECCEEEc
Confidence 4444 48999999999999 67776544
No 19
>PRK12864 YciI-like protein; Reviewed
Probab=50.47 E-value=10 Score=29.74 Aligned_cols=55 Identities=16% Similarity=0.187 Sum_probs=32.6
Q ss_pred hccChHHHHHHHHHHHcCCceeeccccccccccccccccCCCCCchhhhcccccCc
Q psy11173 130 KTISEDTKDKVRLLVKSGQLEIVTGGWVMTDEANSCNVSDNSGSTDVLTHMMPFYK 185 (280)
Q Consensus 130 ~eq~pe~ke~VKkLVknGRLEfVgGGWVM~DEA~thYeS~~~~Sid~~~~~~~f~k 185 (280)
....|.=+.-+++|++.|+| +++|..+-++.+.--+.+..-..+..+..-+||.+
T Consensus 19 ~~~r~~H~~~l~~~~~~G~~-~~~Gp~~~~~g~~~i~~a~s~eea~~~~~~DPy~~ 73 (89)
T PRK12864 19 APFREAHLDRLAKLKEQGIL-ITLGPTKDLTYVFGIFEAEDEETVRQLIEADPYWQ 73 (89)
T ss_pred HHhHHHHHHHHHHHHhCCeE-EEecCCCCCCCEEEEEEeCCHHHHHHHHHcCCchh
Confidence 34567778889999999999 66677754332221111111122455566777765
No 20
>TIGR02147 Fsuc_second hypothetical protein, TIGR02147. This family consists of the 40 members of a paralogous protein family in the rumen anaerobe Fibrobacter succinogenes S85. Member proteins are about 270 residues long and appear to lack signal sequences and transmembrane helices. The only perfectly conserved residue is a glycine in an otherwise poorly conserved region, suggesting members are not enzymes. The family is not characterized.
Probab=50.26 E-value=25 Score=33.29 Aligned_cols=36 Identities=28% Similarity=0.339 Sum_probs=28.6
Q ss_pred hHHHHHHHHHHHcCCceeeccc-cccccccccccccC
Q psy11173 134 EDTKDKVRLLVKSGQLEIVTGG-WVMTDEANSCNVSD 169 (280)
Q Consensus 134 pe~ke~VKkLVknGRLEfVgGG-WVM~DEA~thYeS~ 169 (280)
.+.+..|.-|++-|=|.-.+-| |+++|-.++.....
T Consensus 154 ~ev~~sL~~L~~~glikk~~~g~y~~t~~~l~~~~~~ 190 (271)
T TIGR02147 154 EQVKESLDLLERLGLIKKNEDGFYKQTDKAVSTGDEV 190 (271)
T ss_pred HHHHHHHHHHHHCCCeeECCCCcEEeecceeecCCcc
Confidence 4468899999999999876555 99999988855444
No 21
>COG0276 HemH Protoheme ferro-lyase (ferrochelatase) [Coenzyme metabolism]
Probab=48.39 E-value=11 Score=36.70 Aligned_cols=79 Identities=18% Similarity=0.233 Sum_probs=48.3
Q ss_pred EEEecCccCCcchhccHHHHHHHHHHHHHHHHHHHHHh-CCCCcEEeechHHHHHHHhccChHHHHHHHHHHHcC--Cce
Q psy11173 74 VFVVPHSHNDPGWKQTFESYFVHSTKSILDTMVTKLLE-NEKRKFIWAEMSYLSLWWKTISEDTKDKVRLLVKSG--QLE 150 (280)
Q Consensus 74 VHVVPHSH~D~GWLkT~eEYy~~~v~~ILdsVl~~L~~-dp~rkFi~aEisff~~Ww~eq~pe~ke~VKkLVknG--RLE 150 (280)
.|-+|+++.+.| +.|..+++.+.+-|..+|.- .+.+.+.|-...=-..| ..|.+-+.+++|.+.| ++-
T Consensus 191 aHglP~~~~~~G------DpY~~q~~~t~~li~e~lg~~~~~~~~~~QS~~G~~~W---L~P~t~~~l~~L~~~g~k~ii 261 (320)
T COG0276 191 AHGLPKRYIDEG------DPYPQQCQETTRLIAEALGLPEEEYDLTFQSRFGPEPW---LQPYTDDLLEELGEKGVKKII 261 (320)
T ss_pred cCCCchhhhhcC------CchHHHHHHHHHHHHHHcCCCchheeEEeecCCCCCCC---CCCCHHHHHHHHHhcCCCeEE
Confidence 445555555432 12445577777777777763 44555555321112334 3488999999999987 788
Q ss_pred eecccccccccc
Q psy11173 151 IVTGGWVMTDEA 162 (280)
Q Consensus 151 fVgGGWVM~DEA 162 (280)
++..|+|- |+.
T Consensus 262 v~pigFvs-Dhl 272 (320)
T COG0276 262 VVPIGFVS-DHL 272 (320)
T ss_pred EECCchhh-hhH
Confidence 88888864 443
No 22
>TIGR00109 hemH ferrochelatase. Human ferrochelatase, found at the mitochondrial inner membrane inner surface, was shown in an active recombinant form to be a homodimer. This contrasts to an earlier finding by gel filtration that overexpressed E. coli ferrochelatase runs as a monomer.
Probab=46.77 E-value=14 Score=35.22 Aligned_cols=67 Identities=15% Similarity=0.280 Sum_probs=40.4
Q ss_pred HHHHHHHHHHHHHHHhCCCCcEEeec-hHHHHHHHhccChHHHHHHHHHHHcC--Cceeeccccccccccccccc
Q psy11173 96 HSTKSILDTMVTKLLENEKRKFIWAE-MSYLSLWWKTISEDTKDKVRLLVKSG--QLEIVTGGWVMTDEANSCNV 167 (280)
Q Consensus 96 ~~v~~ILdsVl~~L~~dp~rkFi~aE-isff~~Ww~eq~pe~ke~VKkLVknG--RLEfVgGGWVM~DEA~thYe 167 (280)
.++..+...|...|...+...+.|-. ..- ..| ..|.+.+.+++|.+.| ++-+|..|+|+ |+.=|-|.
T Consensus 211 ~~~~~ta~~l~~~l~~~~~~~~~fQS~~g~-~~W---l~P~~~~~l~~l~~~G~k~V~vvP~gFv~-D~lETl~e 280 (322)
T TIGR00109 211 AECEATTRLIAEKLGFPNEYRLTWQSRVGP-EPW---LGPYTEELLEKLGEQGVQHIVVVPIGFTA-DHLETLYE 280 (322)
T ss_pred HHHHHHHHHHHHHcCCCCCeEEEEeCCCCC-CCc---CCCCHHHHHHHHHHcCCceEEEECCcccc-cchhHHHh
Confidence 34555555556666522333333211 000 124 4599999999999998 68888888876 66655554
No 23
>COG4213 XylF ABC-type xylose transport system, periplasmic component [Carbohydrate transport and metabolism]
Probab=46.67 E-value=42 Score=33.29 Aligned_cols=73 Identities=15% Similarity=0.290 Sum_probs=51.3
Q ss_pred EecCccCCcchhccHHHHHHHHHHHHHHHHHHHHHhCC---CCcEEeech------HHHHHHHhccChHHHHHHHHHHHc
Q psy11173 76 VVPHSHNDPGWKQTFESYFVHSTKSILDTMVTKLLENE---KRKFIWAEM------SYLSLWWKTISEDTKDKVRLLVKS 146 (280)
Q Consensus 76 VVPHSH~D~GWLkT~eEYy~~~v~~ILdsVl~~L~~dp---~rkFi~aEi------sff~~Ww~eq~pe~ke~VKkLVkn 146 (280)
+|+. .|+-||-||+.|-.++++ -.+++..|...| ...|+..-. ++|. +.+ .-..+|-+|..
T Consensus 115 lI~n--~dvd~YvsFDN~~VG~lQ--a~~l~~~lk~k~~~~~gn~~l~~GSp~DnNA~lf--~~G----~m~VLkp~ids 184 (341)
T COG4213 115 LINN--ADVDFYVSFDNEKVGELQ--AKALVKGLKLKPLTSEGNYVLLGGSPDDNNAKLF--FAG----AMKVLKPLIDS 184 (341)
T ss_pred cccc--CCccEEEEecchhHHHHH--HHHHHHHhccCCCCCCCCEEEecCCCCCcchHHH--Hhc----HHHHHHHHhhC
Confidence 5566 566699999999887664 457778888777 555555322 3333 122 45678889999
Q ss_pred CCceeecccccc
Q psy11173 147 GQLEIVTGGWVM 158 (280)
Q Consensus 147 GRLEfVgGGWVM 158 (280)
|++-++|-+|+-
T Consensus 185 Gkik~~Ge~~~d 196 (341)
T COG4213 185 GKIKVVGEQWTD 196 (341)
T ss_pred CceEEeeecccc
Confidence 999998888864
No 24
>COG3977 Alanine-alpha-ketoisovalerate (or valine-pyruvate) aminotransferase [Amino acid transport and metabolism]
Probab=44.07 E-value=28 Score=34.81 Aligned_cols=53 Identities=25% Similarity=0.437 Sum_probs=36.4
Q ss_pred HHHHHHh-CCCCc-EEee-c-hHHHHHHHhccChHHHHHHHHHHHcCCceeecccccc
Q psy11173 105 MVTKLLE-NEKRK-FIWA-E-MSYLSLWWKTISEDTKDKVRLLVKSGQLEIVTGGWVM 158 (280)
Q Consensus 105 Vl~~L~~-dp~rk-Fi~a-E-isff~~Ww~eq~pe~ke~VKkLVknGRLEfVgGGWVM 158 (280)
++..|.. -|..+ |||. | ..|+..|+++..-.+....++|-+.|-| +|.|-+..
T Consensus 317 ~~~~l~~~lp~~~~~iHkpEGAIFlWLWf~dLPItt~~LYq~LKa~Gvl-~VPG~~FF 373 (417)
T COG3977 317 TIAILRRYLPEYRCLIHKPEGAIFLWLWFKDLPITTEELYQRLKARGVL-MVPGHYFF 373 (417)
T ss_pred HHHHHHHhcCccceeeecCCcceeehhhhccCCCCHHHHHHHHHhCeEE-EecccccC
Confidence 3344433 23444 5553 3 4677889999888888888889999999 88887644
No 25
>PRK13378 protocatechuate 4,5-dioxygenase subunit alpha; Provisional
Probab=43.31 E-value=32 Score=29.44 Aligned_cols=51 Identities=18% Similarity=0.209 Sum_probs=38.3
Q ss_pred ccHHHHHHHHHHHHHHHHHHHHHhCC-CCcEEeechHHHHHHHhccChHHHHHHHHH
Q psy11173 88 QTFESYFVHSTKSILDTMVTKLLENE-KRKFIWAEMSYLSLWWKTISEDTKDKVRLL 143 (280)
Q Consensus 88 kT~eEYy~~~v~~ILdsVl~~L~~dp-~rkFi~aEisff~~Ww~eq~pe~ke~VKkL 143 (280)
++.+...+ -+-||.++-.|.+-. +-+|.-.+.+|+.+| ..++++|..|+.+
T Consensus 16 Fd~~~srk---gY~LN~fc~sl~~~~nRe~F~ade~Ay~~~~--~Lteeqk~aV~~R 67 (117)
T PRK13378 16 FDGEQARK---GYALNKMCFSFNDAANRAAFLADEAAYCRKY--GLNEEQKEAIRNR 67 (117)
T ss_pred cCHHHHHH---HHHHHHHHHHhCCHHHHHHHHhCHHHHHHHc--CCCHHHHHHHHhh
Confidence 66666543 356888888887633 445999999999997 6889999988863
No 26
>cd00092 HTH_CRP helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family.
Probab=42.77 E-value=87 Score=21.75 Aligned_cols=38 Identities=11% Similarity=0.149 Sum_probs=29.1
Q ss_pred hHHHHHHHhccChHHHHHHHHHHHcCCceeec-cccccc
Q psy11173 122 MSYLSLWWKTISEDTKDKVRLLVKSGQLEIVT-GGWVMT 159 (280)
Q Consensus 122 isff~~Ww~eq~pe~ke~VKkLVknGRLEfVg-GGWVM~ 159 (280)
+.-+.....-..+.....+++|++.|-|...+ |.|+.+
T Consensus 28 ~~ela~~~g~s~~tv~r~l~~L~~~g~i~~~~~~~~~l~ 66 (67)
T cd00092 28 RQEIADYLGLTRETVSRTLKELEEEGLISRRGRGKYRVN 66 (67)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHCCCEEecCCCeEEeC
Confidence 45566655555677889999999999998887 777654
No 27
>PRK12866 YciI-like protein; Reviewed
Probab=42.67 E-value=15 Score=29.45 Aligned_cols=55 Identities=11% Similarity=0.228 Sum_probs=33.7
Q ss_pred hccChHHHHHHHHHHHcCCceeecccccccc-ccccccccCCCCCchhhhcccccCc
Q psy11173 130 KTISEDTKDKVRLLVKSGQLEIVTGGWVMTD-EANSCNVSDNSGSTDVLTHMMPFYK 185 (280)
Q Consensus 130 ~eq~pe~ke~VKkLVknGRLEfVgGGWVM~D-EA~thYeS~~~~Sid~~~~~~~f~k 185 (280)
....|.-+.-++++++.|+| +.+|.++-+. -.+.-+.+.....+..+.+-+||.+
T Consensus 18 ~~~r~~H~~~L~~~~~~G~l-l~aGp~~~~~~G~~ii~~a~s~~e~~~~l~~DPf~~ 73 (97)
T PRK12866 18 EAYRAEHLALAQAATERGEL-LLAGALADPADGAVLVFEGDSPAAAEAFARADPYVR 73 (97)
T ss_pred HHHHHHHHHHHHHHHhCCEE-EEeCCCCCCCCcEEEEEEeCCHHHHHHHHHcCChhh
Confidence 45678889999999999998 6667664332 1211222222223555666777765
No 28
>TIGR02792 PCA_ligA protocatechuate 4,5-dioxygenase, alpha subunit. Protocatechuate (PCA) 4,5-dioxygenase is the first enzyme in the PCA 4,5-cleavage pathway that is an alternative to PCA 3,4-cleavage and PCA 2,3 cleavage pathways. PCA is an intermediate in the breakdown of lignin (hence the gene symbol ligA) and other compounds. Members of this family are the alpha chain of PCA 4,5-dioxygenase, or the equivalent domain of a fusion protein.
Probab=41.98 E-value=35 Score=29.19 Aligned_cols=50 Identities=20% Similarity=0.296 Sum_probs=37.2
Q ss_pred ccHHHHHHHHHHHHHHHHHHHHHhCC-CCcEEeechHHHHHHHhccChHHHHHHHH
Q psy11173 88 QTFESYFVHSTKSILDTMVTKLLENE-KRKFIWAEMSYLSLWWKTISEDTKDKVRL 142 (280)
Q Consensus 88 kT~eEYy~~~v~~ILdsVl~~L~~dp-~rkFi~aEisff~~Ww~eq~pe~ke~VKk 142 (280)
++.+...+ -+-||.++-.|.+-. +-+|...+.+|+.+| ..++++|..|+.
T Consensus 10 Fd~~~srk---gy~LN~fc~sl~~~~nRerF~ade~Ay~d~~--~Lt~eqk~av~~ 60 (117)
T TIGR02792 10 FDAQQARK---GYNLNQFCMSLMKAENRERFKADESAYLDEW--NLTPAQKQAVLA 60 (117)
T ss_pred cCHHHHHH---HHHHHHHHHHhcCHHHHHHHHhCHHHHHHHc--CCCHHHHHHHHh
Confidence 56555543 356888888886644 445999999999997 688999988876
No 29
>PRK13377 protocatechuate 4,5-dioxygenase subunit alpha; Provisional
Probab=40.78 E-value=36 Score=29.54 Aligned_cols=50 Identities=22% Similarity=0.326 Sum_probs=37.8
Q ss_pred ccHHHHHHHHHHHHHHHHHHHHHhCCC-CcEEeechHHHHHHHhccChHHHHHHHH
Q psy11173 88 QTFESYFVHSTKSILDTMVTKLLENEK-RKFIWAEMSYLSLWWKTISEDTKDKVRL 142 (280)
Q Consensus 88 kT~eEYy~~~v~~ILdsVl~~L~~dp~-rkFi~aEisff~~Ww~eq~pe~ke~VKk 142 (280)
++.+.... -+-||.++-.|.+-.. -+|...+.+|+.+| ..++++|..|+.
T Consensus 16 Fd~~~srk---gY~LN~fc~sL~~~~nRerF~ade~Ay~de~--~Lteeqr~aV~~ 66 (129)
T PRK13377 16 FDADMSRK---GYHLNQFCMSLMKAENRERFKADERAYLDEW--PMTEEQKQAVLA 66 (129)
T ss_pred cCHHHHHH---HHHHHHHHHHhCCHHHHHHHHhCHHHHHHHc--CCCHHHHHHHHh
Confidence 66666543 3568888888876444 45999999999997 688999988876
No 30
>PF01522 Polysacc_deac_1: Polysaccharide deacetylase; InterPro: IPR002509 This domain is found in polysaccharide deacetylase. This family of polysaccharide deacetylases includes NodB (nodulation protein B from Rhizobium) which is a chitooligosaccharide deacetylase []. It also includes chitin deacetylase from yeast [], and endoxylanases which hydrolyses glucosidic bonds in xylan [].; GO: 0016810 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, 0005975 carbohydrate metabolic process; PDB: 2IW0_A 2CC0_B 2VYO_A 2J13_A 2C71_A 2C79_A 1W1A_1 1W1B_1 1W17_A 1NY1_B ....
Probab=39.91 E-value=1.1e+02 Score=23.48 Aligned_cols=51 Identities=24% Similarity=0.356 Sum_probs=31.3
Q ss_pred HHHHHHHHHHhCC-CCcEEeechHHHHHHHhccChHHHHHHHHHHHcCCceeeccccccccc
Q psy11173 101 ILDTMVTKLLENE-KRKFIWAEMSYLSLWWKTISEDTKDKVRLLVKSGQLEIVTGGWVMTDE 161 (280)
Q Consensus 101 ILdsVl~~L~~dp-~rkFi~aEisff~~Ww~eq~pe~ke~VKkLVknGRLEfVgGGWVM~DE 161 (280)
.+..++..|.++. ..+|+..- .++. .....|++++++| .+|.+-||.-++-
T Consensus 19 ~~~~~~~~l~~~~i~at~fv~~-~~~~--------~~~~~l~~l~~~G-~ei~~H~~~H~~~ 70 (123)
T PF01522_consen 19 NYDRLLPLLKKYGIPATFFVIG-SWVE--------RYPDQLRELAAAG-HEIGNHGWSHPNL 70 (123)
T ss_dssp HHHHHHHHHHHTT--EEEEE-H-HHHH--------HHHHHHHHHHHTT--EEEEE-SSSSCG
T ss_pred hHHHHHHHHHhcccceeeeecc-cccc--------cccccchhHHHHH-HHHHhcCCccccc
Confidence 4566777777754 34444432 2232 2378899999999 9999989876544
No 31
>TIGR02988 YaaA_near_RecF S4 domain protein YaaA. This small protein has a single S4 domain (pfam01479), as do bacterial ribosomal protein S4, some pseudouridine synthases, tyrosyl-tRNA synthetases. The S4 domain may bind RNA. Members of this protein family are found almost exclusively in the Firmicutes, and almost invariably just a few nucleotides upstream of the gene for the DNA replication and repair protein RecF. The few members of this family that are not near recF are found instead near dnaA and/or dnaN, the usual neighbors of recF, near the origin of replication. The conserved location suggests a possible role in replication in the Firmicutes lineage.
Probab=37.14 E-value=36 Score=24.35 Aligned_cols=21 Identities=10% Similarity=0.373 Sum_probs=18.1
Q ss_pred HHHHHHHHHHcCCceeeccccc
Q psy11173 136 TKDKVRLLVKSGQLEIVTGGWV 157 (280)
Q Consensus 136 ~ke~VKkLVknGRLEfVgGGWV 157 (280)
.|.++|++++.|++ +|+|.-|
T Consensus 23 SR~~~k~li~~G~V-~VNg~~~ 43 (59)
T TIGR02988 23 SGGQAKWFLQENEV-LVNGELE 43 (59)
T ss_pred CHHHHHHHHHcCCE-EECCEEc
Confidence 58899999999999 7788765
No 32
>PF03344 Daxx: Daxx Family; InterPro: IPR005012 Daxx is a ubiquitously expressed protein that functions, in part, as a transcriptional co-repressor through its interaction with a growing number of nuclear, DNA-associated proteins. Human Daxx contains four structural domains commonly found in transcriptional regulatory proteins: two predicted paired amphipathic helices, an acid-rich domain and a Ser/Pro/Thr (SPT)-rich domain. The post-translational modification status of the SPT-domain of hDaxx regulates its association with transcription factors such as Pax3 and ETS-1, effectively bringing hDaxx to sites of active transcription. Through its presence at the site of active transcription, hDaxx could then be able to associate with acetylated histones present in the nucleosomes and Dek that is associated with chromatin. Through its association with the SPT-domain of hDaxx, histone deacetylases may also be brought to the site of active transcription. As a consequence, nucleosomes in the vicinity of the site of active transcription will have the histone tails deacetylated, allowing the deactylated tail to bind to DNA, thereby leading to an inactive chromatin structure and transcriptional repression []. The Daxx protein (also known as the Fas-binding protein) is thought to play a role in apoptosis as a component of nuclear promyelocytic leukemia protein (PML) oncogenic domains (PODS). Daxx associates with PODs through a direct interaction with PML, a critical component of PODs. The interaction is a dynamic, cell cycle regulated event and is dependent on the post-translational modification of PML by the small ubiquitin-related modifier SUMO-1. ; PDB: 2KZS_A 2KZU_A.
Probab=35.12 E-value=13 Score=39.92 Aligned_cols=67 Identities=12% Similarity=0.089 Sum_probs=0.0
Q ss_pred HHHHHHHHHHHHHhCCCCcEEeechHHHHHHHh-ccChHH--HHHHHHHHHcC-----Cceeecccccccccccc
Q psy11173 98 TKSILDTMVTKLLENEKRKFIWAEMSYLSLWWK-TISEDT--KDKVRLLVKSG-----QLEIVTGGWVMTDEANS 164 (280)
Q Consensus 98 v~~ILdsVl~~L~~dp~rkFi~aEisff~~Ww~-eq~pe~--ke~VKkLVknG-----RLEfVgGGWVM~DEA~t 164 (280)
.+.+|..|-..|++-....+++.=.+||..-|+ ..+|.. ....++|-.|. ||.=|--=|+|-...+.
T Consensus 325 a~~aF~~vG~~lq~rR~~dl~~~~~~~lt~~~~~~~DPA~~d~~L~~kL~eN~~~~~~~l~~v~~ky~~~q~~~~ 399 (713)
T PF03344_consen 325 AQDAFREVGRLLQKRRKNDLWYNFGCHLTDDYKPGKDPALSDPELARKLEENRKLAQSRLSEVIEKYARKQDDTE 399 (713)
T ss_dssp ---------------------------------------------------------------------------
T ss_pred ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Confidence 456777888888766555555544567765443 334333 22334444444 44333344555444443
No 33
>PF09551 Spore_II_R: Stage II sporulation protein R (spore_II_R); InterPro: IPR014202 This entry is designated stage II sporulation protein R. A comparative genome analysis of all sequenced genomes of Firmicutes shows that the proteins are strictly conserved among the sub-set of endospore-forming species. SpoIIR is a signalling protein that links the activation of sigma E to the transcriptional activity of sigma F during sporulation [, ].
Probab=35.10 E-value=2.8e+02 Score=23.97 Aligned_cols=65 Identities=9% Similarity=0.112 Sum_probs=40.4
Q ss_pred CCceEEEEecCccCCcchhccHHHHHHHHHHH-HHHHHHHHHHhCCCCcEEeechHHHHHHHhccChHHHHHHHHHHHc
Q psy11173 69 ENLLRVFVVPHSHNDPGWKQTFESYFVHSTKS-ILDTMVTKLLENEKRKFIWAEMSYLSLWWKTISEDTKDKVRLLVKS 146 (280)
Q Consensus 69 ~~~l~VHVVPHSH~D~GWLkT~eEYy~~~v~~-ILdsVl~~L~~dp~rkFi~aEisff~~Ww~eq~pe~ke~VKkLVkn 146 (280)
.+.++.||+++|-- ..++..+.+||. |+..+-..|..-. ...-...|.....+..+...++.|+.
T Consensus 2 ~~~iRfHVlANSDS------~~DQ~lKl~VRD~Vl~~l~~~~~~~~-------~~~ea~~~i~~~~~~Ie~~A~~~l~~ 67 (130)
T PF09551_consen 2 EEVIRFHVLANSDS------PEDQALKLKVRDAVLEYLSPWLSQAK-------SKEEAREVIRENLPEIEQIAEEVLAE 67 (130)
T ss_pred CceEEEEEEcCCCC------HHHHHHHHHHHHHHHHHHHHHhccCC-------CHHHHHHHHHHhHHHHHHHHHHHHHH
Confidence 56799999999976 667777666654 3333333333222 23445666677778877777765443
No 34
>PF08220 HTH_DeoR: DeoR-like helix-turn-helix domain; InterPro: IPR001034 The deoR-type HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 50-60 amino acids present in transcription regulators of the deoR family, involved in sugar catabolism. This family of prokaryotic regulators is named after the Escherichia coli protein DeoR, a repressor of the deo operon, which encodes nucleotide and deoxyribonucleotide catabolic enzymes. DeoR also negatively regulates the expression of nupG and tsx, a nucleoside-specific transport protein and a channel-forming protein, respectively. DeoR-like transcription repressors occur in diverse bacteria as regulators of sugar and nucleoside metabolic systems. The effector molecules for deoR-like regulators are generally phosphorylated intermediates of the relevant metabolic pathway. The DNA-binding deoR-type HTH domain occurs usually in the N-terminal part. The C-terminal part can contain an effector-binding domain and/or an oligomerisation domain. DeoR occurs as an octamer, whilst glpR and agaR are tetramers. Several operators may be bound simultaneously, which could facilitate DNA looping [, ].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular
Probab=34.95 E-value=1.7e+02 Score=20.93 Aligned_cols=38 Identities=21% Similarity=0.261 Sum_probs=29.0
Q ss_pred HHHHHHhccChHHHHHHHHHHHcCCceeeccccccccc
Q psy11173 124 YLSLWWKTISEDTKDKVRLLVKSGQLEIVTGGWVMTDE 161 (280)
Q Consensus 124 ff~~Ww~eq~pe~ke~VKkLVknGRLEfVgGGWVM~DE 161 (280)
-+..-+.--....|.-+..|.+.|.|.-+.||++..+.
T Consensus 19 ela~~~~VS~~TiRRDl~~L~~~g~i~r~~GG~~~~~~ 56 (57)
T PF08220_consen 19 ELAEEFGVSEMTIRRDLNKLEKQGLIKRTHGGAVLNDS 56 (57)
T ss_pred HHHHHHCcCHHHHHHHHHHHHHCCCEEEEcCEEEeCCC
Confidence 34444444446679999999999999999999987653
No 35
>cd07924 PCA_45_Doxase_A The A subunit of Protocatechuate 4,5-dioxygenase (LigAB) is the smaller, non-catalytic subunit. The A subunit is the non-catalytic subunit of Protocatechuate (PCA) 4,5-dioxygenase (LigAB), which is composed of A and B subunits that form a tetramer. PCA 4,5-dioxygenase catalyzes the oxidization and subsequent ring-opening of PCA (or 3,4-dihydroxybenzoic acid), which is an intermediate in the breakdown of lignin and other compounds. PCA 4,5-dioxygenase is one of the aromatic ring opening dioxygenases which play key roles in the degradation of aromatic compounds. As a member of the Class III extradiol dioxygenase family, LigAB uses a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon.
Probab=34.76 E-value=40 Score=28.99 Aligned_cols=50 Identities=24% Similarity=0.343 Sum_probs=37.7
Q ss_pred ccHHHHHHHHHHHHHHHHHHHHHhCCC-CcEEeechHHHHHHHhccChHHHHHHHH
Q psy11173 88 QTFESYFVHSTKSILDTMVTKLLENEK-RKFIWAEMSYLSLWWKTISEDTKDKVRL 142 (280)
Q Consensus 88 kT~eEYy~~~v~~ILdsVl~~L~~dp~-rkFi~aEisff~~Ww~eq~pe~ke~VKk 142 (280)
++.+...+ -+-||.++-.|.+-.. -+|.-.+.+|+.+| ..++++|..|+.
T Consensus 13 Fd~~~srk---gy~LN~fc~sl~~~~nRerF~ade~Ay~~~~--~Lteeqr~aV~~ 63 (121)
T cd07924 13 FDAERARK---GYHLNQFCMSLMKAENRERFKADERAYLDKW--PMTEEQKQAVLA 63 (121)
T ss_pred cCHHHHHH---HHHHHHHHHHhCCHHHHHHHHhCHHHHHHHc--CCCHHHHHHHHH
Confidence 66666543 3568888888876444 45999999999997 688999988876
No 36
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=33.94 E-value=75 Score=20.63 Aligned_cols=36 Identities=17% Similarity=0.165 Sum_probs=26.5
Q ss_pred HHHHHHHhccChHHHHHHHHHHHcCCceeecccccc
Q psy11173 123 SYLSLWWKTISEDTKDKVRLLVKSGQLEIVTGGWVM 158 (280)
Q Consensus 123 sff~~Ww~eq~pe~ke~VKkLVknGRLEfVgGGWVM 158 (280)
.-+.....-..+.....|++|.+.|-|...+|.|+.
T Consensus 12 ~~la~~l~~s~~tv~~~l~~L~~~g~l~~~~~~~~i 47 (48)
T smart00419 12 QEIAELLGLTRETVSRTLKRLEKEGLISREGGRIVI 47 (48)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHCCCEEEeCCEEEE
Confidence 344555444557789999999999999887776653
No 37
>PRK04517 hypothetical protein; Provisional
Probab=33.38 E-value=41 Score=30.58 Aligned_cols=23 Identities=22% Similarity=0.599 Sum_probs=21.0
Q ss_pred HHHHHHhccChHHHHHHHHHHHc
Q psy11173 124 YLSLWWKTISEDTKDKVRLLVKS 146 (280)
Q Consensus 124 ff~~Ww~eq~pe~ke~VKkLVkn 146 (280)
.|..||.+.++++|.++|+.++.
T Consensus 193 mL~~Wy~qAd~etrk~F~~w~~~ 215 (216)
T PRK04517 193 MLHFWYNKADAETKARFKAYVNQ 215 (216)
T ss_pred HHHHHHHHcCHHHHHHHHHHHhc
Confidence 68999999999999999998854
No 38
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=33.01 E-value=1.4e+02 Score=19.37 Aligned_cols=36 Identities=22% Similarity=0.221 Sum_probs=26.6
Q ss_pred hHHHHHHHhccChHHHHHHHHHHHcCCceeeccccc
Q psy11173 122 MSYLSLWWKTISEDTKDKVRLLVKSGQLEIVTGGWV 157 (280)
Q Consensus 122 isff~~Ww~eq~pe~ke~VKkLVknGRLEfVgGGWV 157 (280)
+.-+...+.-..+..+..|+.|++.|.+....||.|
T Consensus 17 ~~~l~~~l~~s~~tv~~~l~~L~~~g~i~~~~~~~~ 52 (53)
T smart00420 17 VEELAELLGVSEMTIRRDLNKLEEQGLLTRVHGGAV 52 (53)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeecCcc
Confidence 344554444455667999999999999988888765
No 39
>PRK12865 YciI-like protein; Reviewed
Probab=32.57 E-value=25 Score=27.76 Aligned_cols=55 Identities=15% Similarity=0.219 Sum_probs=33.3
Q ss_pred ccChHHHHHHHHHHHcCCceeeccccccccccccc----cccCCCCCchhhhcccccCcc
Q psy11173 131 TISEDTKDKVRLLVKSGQLEIVTGGWVMTDEANSC----NVSDNSGSTDVLTHMMPFYKE 186 (280)
Q Consensus 131 eq~pe~ke~VKkLVknGRLEfVgGGWVM~DEA~th----YeS~~~~Sid~~~~~~~f~ke 186 (280)
...|.-+.-++++.+.|+| +++|.++-++...+. +....-.....+..-+||.+.
T Consensus 19 ~~r~~H~~~l~~~~~~G~l-~~~Gp~~~~~g~~~G~~~i~~a~s~e~a~~~~~~DP~~~~ 77 (97)
T PRK12865 19 DTRPTHLEYLNKLNAEGTL-KIAGPFLDDDGKPCGSLVIVKAETKEAAKALADADPYAKA 77 (97)
T ss_pred HHHHHHHHHHHHHHhCCeE-EEecCCcCCCCCceeEEEEEEcCCHHHHHHHHHcCCchhc
Confidence 4557778889999999998 777777765532111 111111224555667777653
No 40
>PF10549 ORF11CD3: ORF11CD3 domain; InterPro: IPR018877 This entry represents the carboxy-terminal domain from ORF11 (Q9XJS9 from SWISSPROT), one of the proteins of Pseudomonas phage D3 (Bacteriophage D3). The function of these proteins are unknown [].
Probab=32.55 E-value=41 Score=25.28 Aligned_cols=29 Identities=21% Similarity=0.224 Sum_probs=24.8
Q ss_pred hHHHHHHHhccChHHHHHHHHHHHcCCcee
Q psy11173 122 MSYLSLWWKTISEDTKDKVRLLVKSGQLEI 151 (280)
Q Consensus 122 isff~~Ww~eq~pe~ke~VKkLVknGRLEf 151 (280)
..-|.+| +...|....+|++|...+|+.|
T Consensus 26 GrgL~~W-k~~Kp~l~~ki~~l~~~~Q~~L 54 (57)
T PF10549_consen 26 GRGLNRW-KWKKPQLEQKIEELEEQLQITL 54 (57)
T ss_pred hHHHHHH-HHhhHHHHHHHHHHHHHhhhcc
Confidence 3457777 8899999999999999999965
No 41
>PF11625 DUF3253: Protein of unknown function (DUF3253); InterPro: IPR021660 This bacterial family of proteins has no known function. ; PDB: 2NS0_A.
Probab=31.68 E-value=67 Score=25.85 Aligned_cols=57 Identities=16% Similarity=0.264 Sum_probs=37.8
Q ss_pred HHHHHHHHHHh-CCCCcEEeech--HHHHHHHhccChHHHHHHHHHHHcCCceeeccccc
Q psy11173 101 ILDTMVTKLLE-NEKRKFIWAEM--SYLSLWWKTISEDTKDKVRLLVKSGQLEIVTGGWV 157 (280)
Q Consensus 101 ILdsVl~~L~~-dp~rkFi~aEi--sff~~Ww~eq~pe~ke~VKkLVknGRLEfVgGGWV 157 (280)
|-..++.+|.. .|..+|.=+|+ ++.-.-|...-+..|.....|++.|+++|.-+|=+
T Consensus 8 l~~~Il~ll~~R~~~ktiCPSevARal~~~~WR~lm~~vR~~A~~L~~~G~i~I~qkG~~ 67 (83)
T PF11625_consen 8 LEAAILALLAARGPGKTICPSEVARALGPDDWRDLMPPVRAAARRLARAGRIEITQKGKP 67 (83)
T ss_dssp HHHHHHHHHHHS-TT--B-HHHHHHHH-TTS-GGGHHHHHHHHHHHHHTTSEEEEETTEE
T ss_pred HHHHHHHHHHhcCCCCccCHHHHHHHHCchhhHHHHHHHHHHHHHHHHCCcEEEEECCEe
Confidence 44455666664 56777777776 33322377888999999999999999999888863
No 42
>PRK01904 hypothetical protein; Provisional
Probab=31.62 E-value=50 Score=30.09 Aligned_cols=24 Identities=17% Similarity=0.416 Sum_probs=21.5
Q ss_pred HHHHHHHhccChHHHHHHHHHHHc
Q psy11173 123 SYLSLWWKTISEDTKDKVRLLVKS 146 (280)
Q Consensus 123 sff~~Ww~eq~pe~ke~VKkLVkn 146 (280)
..|..||.+.++++|.++|+.++.
T Consensus 194 ~mL~~Wy~qAd~etrk~F~~w~~~ 217 (219)
T PRK01904 194 QQLQYWFQQADKETQTRFLNWAKK 217 (219)
T ss_pred HHHHHHHHHcCHHHHHHHHHHHhh
Confidence 369999999999999999998864
No 43
>PF12995 DUF3879: Domain of unknown function, E. rectale Gene description (DUF3879); InterPro: IPR024540 This entry represents proteins of unknown function found primarily in Firmicutes. The Eubacterium rectale gene appears to be upregulated in the presence of Bacteroides thetaiotaomicron compared to growth in pure culture [].
Probab=30.69 E-value=1.2e+02 Score=27.70 Aligned_cols=38 Identities=13% Similarity=0.230 Sum_probs=26.0
Q ss_pred ccceeeecCCCCCCCCCceEEEEecCccCCcchhccHHHHHHHHHHHHHHHHHHHHHhC
Q psy11173 54 QGWNIGLDLAHETDPENLLRVFVVPHSHNDPGWKQTFESYFVHSTKSILDTMVTKLLEN 112 (280)
Q Consensus 54 qG~~i~y~~~~~w~~~~~l~VHVVPHSH~D~GWLkT~eEYy~~~v~~ILdsVl~~L~~d 112 (280)
.|.+|+-..|+.|. ||||=| +.+ .+.|+++|...+.+.
T Consensus 66 aGldVTg~~~~s~~-------rIi~Vs----------E~~----~q~mfdlvkkef~~e 103 (186)
T PF12995_consen 66 AGLDVTGKNCASWQ-------RIIPVS----------EEV----RQKMFDLVKKEFKNE 103 (186)
T ss_pred ccccccCCCccchh-------heecCC----------HHH----HHHHHHHHHHHHHHh
Confidence 58888888888888 566654 333 345788887776653
No 44
>PRK09897 hypothetical protein; Provisional
Probab=30.00 E-value=48 Score=34.15 Aligned_cols=26 Identities=19% Similarity=0.317 Sum_probs=22.3
Q ss_pred ccChHHHHHHHHHHHcCCceeecccc
Q psy11173 131 TISEDTKDKVRLLVKSGQLEIVTGGW 156 (280)
Q Consensus 131 eq~pe~ke~VKkLVknGRLEfVgGGW 156 (280)
...|..-.+|.+|+++|+|.|+.||=
T Consensus 389 ~mP~~sa~~l~~l~~aG~L~v~~~~~ 414 (534)
T PRK09897 389 AIPSESIRRLLALREAGIIHILALGE 414 (534)
T ss_pred CCChHHHHHHHHHHHcCCEEEEecCc
Confidence 35588889999999999999998775
No 45
>PRK13379 protocatechuate 4,5-dioxygenase subunit alpha; Provisional
Probab=29.98 E-value=65 Score=27.67 Aligned_cols=57 Identities=9% Similarity=0.091 Sum_probs=40.5
Q ss_pred EecCccCCcchhccHHHHHHHHHHHHHHHHHHHHHhC-CCCcEEeechHHHHHHHhccChHHHHHHHH
Q psy11173 76 VVPHSHNDPGWKQTFESYFVHSTKSILDTMVTKLLEN-EKRKFIWAEMSYLSLWWKTISEDTKDKVRL 142 (280)
Q Consensus 76 VVPHSH~D~GWLkT~eEYy~~~v~~ILdsVl~~L~~d-p~rkFi~aEisff~~Ww~eq~pe~ke~VKk 142 (280)
-||-|+. ++.+....+ +-||.++-.|.+- .+-+|.-.+.+|+.+| ..++++|..|+.
T Consensus 10 ~ipGTy~-----Fd~~~srkg---y~LN~fc~sl~~~~~RerF~aDe~ay~~~~--~Lt~eqk~aV~~ 67 (119)
T PRK13379 10 QLGGTYV-----FDLRTSNRA---LRLNRFFWHMIRAPWRDRFLQDAEALMQEA--GLTEQEKELIRA 67 (119)
T ss_pred CCCCCcc-----cCHHHHHHH---HHHHHHHHHHccHHHHHHHHhCHHHHHHHc--CCCHHHHHHHHh
Confidence 3555643 666665433 5677887777543 3445999999999997 688999998886
No 46
>PF06044 DRP: Dam-replacing family; InterPro: IPR010324 Dam-replacing protein (DRP) is a restriction endonuclease that is flanked by pseudo-transposable small repeat elements. The replacement of Dam-methylase by DRP allows phase variation through slippage-like mechanisms in several pathogenic isolates of Neisseria meningitidis [].; PDB: 4ESJ_A.
Probab=29.81 E-value=86 Score=30.07 Aligned_cols=53 Identities=11% Similarity=0.187 Sum_probs=37.7
Q ss_pred HHHHHHHhCCCCcEEeechHHHHHHHhccCh-------HHHHHHHHHHHcCCceeecccc
Q psy11173 104 TMVTKLLENEKRKFIWAEMSYLSLWWKTISE-------DTKDKVRLLVKSGQLEIVTGGW 156 (280)
Q Consensus 104 sVl~~L~~dp~rkFi~aEisff~~Ww~eq~p-------e~ke~VKkLVknGRLEfVgGGW 156 (280)
.|+.-+.+=|...|...++.-|..-.....| ..|.+++.|-..|-|+|+|-|-
T Consensus 191 di~~cid~i~~~~FtL~diY~Fe~~L~~~~P~N~~Ik~KIRQqLQ~LRD~g~IeFl~rG~ 250 (254)
T PF06044_consen 191 DIMKCIDKIPKNEFTLDDIYAFEDELQIKYPNNNHIKAKIRQQLQILRDKGIIEFLGRGR 250 (254)
T ss_dssp HHHHHHHHS-SSEEEHHHHHTTHHHHHHHSTT-S-HHHHHHHHHHHHHHTTSEEE-STTE
T ss_pred HHHHHHHhcCccceeHHHHHHHHHHHHHhCCCCCChhHHHHHHHHHHhhCCceEEecCCc
Confidence 4555566778889999998666655555554 4567777789999999999885
No 47
>PRK03641 hypothetical protein; Provisional
Probab=29.77 E-value=51 Score=30.03 Aligned_cols=24 Identities=17% Similarity=0.411 Sum_probs=21.5
Q ss_pred HHHHHHhccChHHHHHHHHHHHcC
Q psy11173 124 YLSLWWKTISEDTKDKVRLLVKSG 147 (280)
Q Consensus 124 ff~~Ww~eq~pe~ke~VKkLVknG 147 (280)
.|..||.+.++++|.++|+.++.-
T Consensus 194 mL~~Wy~qAd~etrk~F~~w~~~q 217 (220)
T PRK03641 194 RLKYWFKQADPQTRNRFLQWAEKQ 217 (220)
T ss_pred HHHHHHHhcCHHHHHHHHHHHHhC
Confidence 689999999999999999988653
No 48
>cd00165 S4 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized functional similarity between these three protein classes.
Probab=29.25 E-value=65 Score=21.57 Aligned_cols=22 Identities=32% Similarity=0.623 Sum_probs=18.0
Q ss_pred HHHHHHHHHHHcCCceeeccccc
Q psy11173 135 DTKDKVRLLVKSGQLEIVTGGWV 157 (280)
Q Consensus 135 e~ke~VKkLVknGRLEfVgGGWV 157 (280)
..+..++++++.|++ .++|--+
T Consensus 14 ~sr~~~~~~i~~g~V-~vn~~~~ 35 (70)
T cd00165 14 PSRSEARQLIKHGHV-LVNGKVV 35 (70)
T ss_pred cCHHHHHHHHHcCCE-EECCEEc
Confidence 368899999999999 6787665
No 49
>PF00538 Linker_histone: linker histone H1 and H5 family; InterPro: IPR005818 Histone proteins have central roles in both chromatin organisation (as structural units of the nucleosome) and gene regulation (as dynamic components that have a direct impact on DNA transcription and replication). Eukaryotic DNA wraps around a histone octamer to form a nucleosome, the first order of compaction of eukaryotic chromatin. The core histone octamer is composed of a central H3-H4 tetramer and two flanking H2A-H2B dimers. Each of the core histone contains a common structural motif, called the histone fold, which facilitates the interactions between the individual core histones. In addition to the core histones, there is a "linker histone" called H1 (or H5 in avian species). The linker histones present in all multicellular eukaryotes are the most divergent group of histones, with numerous cell type- and stage-specific variant. Linker histone H1 is an essential component of chromatin structure. H1 links nucleosomes into higher order structures. Histone H5 performs the same function as histone H1, and replaces H1 in certain cells. The structure of GH5, the globular domain of the linker histone H5 is known [, ]. The fold is similar to the DNA-binding domain of the catabolite gene activator protein, CAP, thus providing a possible model for the binding of GH5 to DNA. The linker histones, which do not contain the histone fold motif, are critical to the higher-order compaction of chromatin, because they bind to internucleosomal DNA and facilitate interactions between individual nucleosomes. In addition, H1 variants have been shown to be involved in the regulation of developmental genes. A common feature of this protein family is a tripartite structure in which a globular (H15) domain of about 80 amino acids is flanked by two less structured N- and C-terminal tails. The H15 domain is also characterised by high sequence homology among the family of linker histones. The highly conserved H15 domain is essential for the binding of H1 or H5 to the nucleosome. It consists of a three helix bundle (I-III), with a beta-hairpin at the C terminus. There is also a short three-residue stretch between helices I and II that is in the beta-strand conformation. Together with the C-terminal beta-hairpin, this strand forms the third strand of an antiparallel beta-sheet [, , , ]. Proteins known to contain a H15 domain are: - Eukaryotic histone H1. The histones H1 constitute a family with many variants, differing in their affinity for chromatin. Several variants are simultaneously present in a single cell. For example, the nucleated erythrocytes of birds contain both H1 and H5, the latter being an extreme variant of H1. - Eukaryotic MHYST family of histone acetyltransferase. Histone acetyltransferases transfer an acetyl group from acetyl-CoA to the epsylon- amino group of lysine within the basic NH2-termini of histones, which bind the acidic phosphates of DNA []. This entry represents the H15 domain.; GO: 0003677 DNA binding, 0006334 nucleosome assembly, 0000786 nucleosome, 0005634 nucleus; PDB: 2LSO_A 2RQP_A 1UHM_A 1UST_A 1GHC_A 1HST_A 1YQA_A 1USS_A.
Probab=28.46 E-value=2.2e+02 Score=21.45 Aligned_cols=19 Identities=26% Similarity=0.270 Sum_probs=16.9
Q ss_pred HHHHHHHHHHHcCCceeec
Q psy11173 135 DTKDKVRLLVKSGQLEIVT 153 (280)
Q Consensus 135 e~ke~VKkLVknGRLEfVg 153 (280)
..+..|+++|.+|+|..+.
T Consensus 47 ~l~~aLk~~v~~G~l~~~k 65 (77)
T PF00538_consen 47 RLKRALKRGVEKGKLVQVK 65 (77)
T ss_dssp HHHHHHHHHHHCTSEEECS
T ss_pred HHHHHHHHHHHCCcEEeec
Confidence 4688899999999998887
No 50
>COG1347 NqrD Na+-transporting NADH:ubiquinone oxidoreductase, subunit NqrD [Energy production and conversion]
Probab=28.28 E-value=34 Score=31.44 Aligned_cols=27 Identities=37% Similarity=0.527 Sum_probs=23.0
Q ss_pred HHHHHHHHHcCCc-------eeeccccccccccc
Q psy11173 137 KDKVRLLVKSGQL-------EIVTGGWVMTDEAN 163 (280)
Q Consensus 137 ke~VKkLVknGRL-------EfVgGGWVM~DEA~ 163 (280)
-.-||.|+..|+| .|..|||.+||-..
T Consensus 148 v~~iREL~G~Gkl~G~~v~~~i~~ggwy~pnGL~ 181 (208)
T COG1347 148 VGFVRELFGSGKLFGFTVFPTIQDGGWYQPNGLF 181 (208)
T ss_pred HHHHHHHhccCceeeEEeeeeeccCcccCCCceE
Confidence 5678999999999 68899999999744
No 51
>cd03562 CID CID (CTD-Interacting Domain) domain family; CID is present in several RNA-processing factors such as Pcf11 and Nrd1. Pcf11 is a conserved and essential subunit of the yeast cleavage factor IA, which is required for polyadenylation-dependent 3'-RNA processing and transcription termination. Nrd1 is implicated in polyadenylation-independent 3'-RNA processing. CID binds tightly to the carboxy-terminal domain (CTD) of RNA polymerase (Pol) II. During transcription, Pol II synthesizes eukaryotic messenger RNA. Transcription is coupled to RNA processing through the CTD, which consists of up to 52 repeats of the sequence Tyr 1-Ser 2-Pro 3-Thr 4-Ser 5-Pro 6-Ser 7. CID contains eight alpha-helices in a right-handed superhelical arrangement, which closely resembles that of the VHS domains and ARM (Armadillo) repeat proteins, except for its two amino-terminal helices.
Probab=26.92 E-value=52 Score=26.05 Aligned_cols=47 Identities=17% Similarity=0.277 Sum_probs=29.3
Q ss_pred HHHHHHHHHHHHHhCCCCcEEeec-hHHHHHHHhccChHHHHHHHHHHH
Q psy11173 98 TKSILDTMVTKLLENEKRKFIWAE-MSYLSLWWKTISEDTKDKVRLLVK 145 (280)
Q Consensus 98 v~~ILdsVl~~L~~dp~rkFi~aE-isff~~Ww~eq~pe~ke~VKkLVk 145 (280)
+-|++|+|+.... .+...++..- ...|..=+...++..|.+|++|++
T Consensus 57 ~LYL~dsIvkn~~-~~~~~~~~~~~~~~f~~~~~~~~~~~r~kl~rl~~ 104 (114)
T cd03562 57 LLYLLDSIVKNVG-RKYKEFFSEFLVPLFLDAYEKVDEKTRKKLERLLN 104 (114)
T ss_pred HHHHHHHHHHHcc-cchHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHH
Confidence 3456777776642 3333322222 445555567789999999999985
No 52
>PF08721 Tn7_Tnp_TnsA_C: TnsA endonuclease C terminal; InterPro: IPR014832 The Tn7 transposase is composed of proteins TnsA and TnsB. DNA breakage at the 5'-end of the transposon is carried out by TnsA, and breakage and joining at the 3'-end is carried out by TnsB. The C-terminal domain of TnsA binds DNA. ; PDB: 1F1Z_B 1T0F_B.
Probab=26.90 E-value=72 Score=23.16 Aligned_cols=47 Identities=9% Similarity=0.067 Sum_probs=29.6
Q ss_pred HHHHHHHhCCCCcEEeechHHHHHHHhccChHHHHHHHHHHHcCCcee
Q psy11173 104 TMVTKLLENEKRKFIWAEMSYLSLWWKTISEDTKDKVRLLVKSGQLEI 151 (280)
Q Consensus 104 sVl~~L~~dp~rkFi~aEisff~~Ww~eq~pe~ke~VKkLVknGRLEf 151 (280)
.++..|.++|..++...=..++.. +.-.....-..++.||.++++.+
T Consensus 31 ~i~~~l~~~~~~tl~~l~~~~d~~-~~l~~g~~L~~l~~LiA~k~i~~ 77 (79)
T PF08721_consen 31 LILARLRKNPTMTLRDLCKELDKD-YELEPGTALPLLRHLIATKRIKV 77 (79)
T ss_dssp HHHHHHHHTTTSBHHHHHHHHHHH-CT--TTHHHHHHHHHHHTTSEE-
T ss_pred HHHHHHHHcCCCCHHHHHHHHHHh-cCCCcCChHHHHHHHHhCChhcc
Confidence 467888888886555432233331 22344567889999999999853
No 53
>PF08679 DsrD: Dissimilatory sulfite reductase D (DsrD); InterPro: IPR014793 The structure of the dissimilatory sulphite reductase D (DsrD) protein has shown it to contain a winged-helix motif similar to those found in DNA binding proteins []. The structure suggests a possible role for DsrD in transcription or translation of genes, which catalyse dissimilatory sulphite reduction. ; PDB: 1WQ2_B 1UCR_B.
Probab=25.77 E-value=99 Score=24.18 Aligned_cols=47 Identities=23% Similarity=0.347 Sum_probs=25.7
Q ss_pred HHHHHHH--hCCCCcEEeechHHHHHHHhccChHHHHHHHHHHHcCCceee
Q psy11173 104 TMVTKLL--ENEKRKFIWAEMSYLSLWWKTISEDTKDKVRLLVKSGQLEIV 152 (280)
Q Consensus 104 sVl~~L~--~dp~rkFi~aEisff~~Ww~eq~pe~ke~VKkLVknGRLEfV 152 (280)
.||..|. .-+.-+|.+.+. ....-+.-..+.|..+..||++|+|++-
T Consensus 5 ~Ile~L~~k~~~KskfYfkD~--~k~~pd~k~R~vKKi~~~LV~Eg~l~yW 53 (67)
T PF08679_consen 5 KILEFLEAKKKKKSKFYFKDF--YKAFPDAKPREVKKIVNELVNEGKLEYW 53 (67)
T ss_dssp HHHHHHSSCCCHSS-EEHHHH--HHH-TTS-HHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHHHHhccCCCCceeHHHH--HHHCCCcCHHHHHHHHHHHHhhCeEEEE
Confidence 3566665 234556665431 1211112224457778889999999873
No 54
>PF00762 Ferrochelatase: Ferrochelatase; InterPro: IPR001015 Synonym(s): Protohaem ferro-lyase, Iron chelatase, etc. Ferrochelatase catalyses the last step in haem biosynthesis: the chelation of a ferrous ion to proto-porphyrin IX, to form protohaem [, ]. In eukaryotic cells, it binds to the mitochondrial inner membrane with its active site on the matrix side of the membrane. The X-ray structure of Bacillus subtilis and human ferrochelatase have been solved [, ]. The human enzyme exists as a homodimer. Each subunit contains one [2Fe-2S] cluster. The monomer is folded into two similar domains, each with a four-stranded parallel beta-sheet flanked by an alpha-helix in a beta-alpha-beta motif that is reminiscent of the fold found in the periplasmic binding proteins. The topological similarity between the domains suggests that they have arisen from a gene duplication event. However, significant differences exist between the two domains, including an N-terminal section (residues 80-130) that forms part of the active site pocket, and a C-terminal extension (residues 390-423) that is involved in coordination of the [2Fe-2S] cluster and in stabilisation of the homodimer. Ferrochelatase seems to have a structurally conserved core region that is common to the enzyme from bacteria, plants and mammals. Porphyrin binds in the identified cleft; this cleft also includes the metal-binding site of the enzyme. It is likely that the structure of the cleft region will have different conformations upon substrate binding and release [].; GO: 0004325 ferrochelatase activity, 0006783 heme biosynthetic process; PDB: 2QD3_B 2HRE_C 3HCN_B 2PNJ_A 2QD1_C 1HRK_A 2QD4_B 3AQI_B 2HRC_B 3HCO_B ....
Probab=25.76 E-value=55 Score=31.35 Aligned_cols=85 Identities=19% Similarity=0.306 Sum_probs=51.3
Q ss_pred eEEEEecCccC-CcchhccHHHHHHHHHHHHHHHHHHHHHhCCCCcEEeechHHH--HHHHhccChHHHHHHHHHHHcC-
Q psy11173 72 LRVFVVPHSHN-DPGWKQTFESYFVHSTKSILDTMVTKLLENEKRKFIWAEMSYL--SLWWKTISEDTKDKVRLLVKSG- 147 (280)
Q Consensus 72 l~VHVVPHSH~-D~GWLkT~eEYy~~~v~~ILdsVl~~L~~dp~rkFi~aEisff--~~Ww~eq~pe~ke~VKkLVknG- 147 (280)
+..|=+|.+|. +-|- -|+ .++..+.+.+...|. .+..+..|-. -| ..| ..|.+.+.|++|.+.|
T Consensus 188 fSaHglP~~~~~~~Gd-----pY~-~~~~~t~~~i~~~l~-~~~~~~~fQS--~~g~~~W---L~P~~~~~l~~l~~~G~ 255 (316)
T PF00762_consen 188 FSAHGLPQRYVEDKGD-----PYP-AQCEETARLIAERLG-LPEWRLAFQS--RFGPGEW---LGPSTEDVLEELAKEGV 255 (316)
T ss_dssp EEEE--BHHHHTCCT------SHH-HHHHHHHHHHHHHTT-TSSEEEEEES---SSSS-B---SSSBHHHHHHHHHHCT-
T ss_pred EccCCCCccccccCCC-----ChH-HHHHHHHHHHHHHcC-CCceEEEEEC--CCCCCCC---ccccHHHHHHHHHhcCC
Confidence 34566677777 3342 243 557777777777773 3333333321 12 244 5699999999999998
Q ss_pred -CceeeccccccccccccccccC
Q psy11173 148 -QLEIVTGGWVMTDEANSCNVSD 169 (280)
Q Consensus 148 -RLEfVgGGWVM~DEA~thYeS~ 169 (280)
++-++..|+| +|+.=|-|.-.
T Consensus 256 ~~V~v~p~gFv-~D~lETl~eid 277 (316)
T PF00762_consen 256 KRVVVVPPGFV-SDCLETLYEID 277 (316)
T ss_dssp SEEEEEETT-S-SSSHHHHCCCC
T ss_pred CeEEEECCccc-cccHhHHHHHH
Confidence 7888888885 47777766653
No 55
>PF08359 TetR_C_4: YsiA-like protein, C-terminal region; InterPro: IPR013570 The members of this family are thought to be TetR-type (tetracycline resistance) transcriptional regulators that bear particular similarity to YsiA (P94548 from SWISSPROT). This entry represents the C-terminal domain.; PDB: 1VI0_B.
Probab=25.56 E-value=33 Score=27.25 Aligned_cols=54 Identities=15% Similarity=0.207 Sum_probs=30.3
Q ss_pred HHHHHHHHHHHHHHHhCCCCcEEe-ech----HHHHHHHhccChHHHHHHHHHHHcCCc
Q psy11173 96 HSTKSILDTMVTKLLENEKRKFIW-AEM----SYLSLWWKTISEDTKDKVRLLVKSGQL 149 (280)
Q Consensus 96 ~~v~~ILdsVl~~L~~dp~rkFi~-aEi----sff~~Ww~eq~pe~ke~VKkLVknGRL 149 (280)
.+++.++...+..+.++|....+. .++ ..+..............|.++|..|+=
T Consensus 24 ekL~~~i~~~~~~~~~~~~~~~v~~~e~~~~~~~~~~~~~~~~~~~~~~i~~iI~eG~~ 82 (133)
T PF08359_consen 24 EKLRALIEAHLDFLEENPDLAIVLSLELRQSNEELRKKINEIRREYLRIIEEIIEEGQE 82 (133)
T ss_dssp HHHHHHHHHHHHHHHT-HHHHHHHHCTTS-SSHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHhCCChhhhhHHHHhhCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 346778888888888888755433 232 234444444444455555566665554
No 56
>KOG0634|consensus
Probab=24.66 E-value=1.2e+02 Score=31.50 Aligned_cols=75 Identities=25% Similarity=0.498 Sum_probs=41.6
Q ss_pred chhccHHHHHHHHHHHHHHHHHHHHHhC------C-CCcEEeechHHHHHHHhccChHHHHHHH-HHHHcCCceeecccc
Q psy11173 85 GWKQTFESYFVHSTKSILDTMVTKLLEN------E-KRKFIWAEMSYLSLWWKTISEDTKDKVR-LLVKSGQLEIVTGGW 156 (280)
Q Consensus 85 GWLkT~eEYy~~~v~~ILdsVl~~L~~d------p-~rkFi~aEisff~~Ww~eq~pe~ke~VK-kLVknGRLEfVgGGW 156 (280)
.||.-+...|..+...+++-+-..|.+- | .--|+|.++.|..-.-+...++.+..+. .+|++|-+ +|-|-|
T Consensus 349 ~wi~~l~~~Yt~Rrn~~l~Al~kylp~~~~~~~~P~aGmFiwv~i~~~~~~~~~~i~q~~e~i~~~~vk~gV~-~v~G~~ 427 (472)
T KOG0634|consen 349 RWIQHLRSSYTERRNALLSALDKYLPKSVCEYHPPKAGMFIWVEIPYINFDTKKSINQIEEIIFIKAVKNGVK-LVCGSW 427 (472)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhCCCCeeEEecCCcceEEEEEecccccccccchHHHHHHHHHHHHHCCeE-EecCce
Confidence 4555655555544443443333333322 1 2348888875222111233355555554 58888888 889999
Q ss_pred cccc
Q psy11173 157 VMTD 160 (280)
Q Consensus 157 VM~D 160 (280)
-|.|
T Consensus 428 F~v~ 431 (472)
T KOG0634|consen 428 FMVD 431 (472)
T ss_pred eEEc
Confidence 8887
No 57
>smart00526 H15 Domain in histone families 1 and 5.
Probab=24.54 E-value=66 Score=23.46 Aligned_cols=20 Identities=40% Similarity=0.393 Sum_probs=16.0
Q ss_pred HHHHHHHHHHHcCCceeecc
Q psy11173 135 DTKDKVRLLVKSGQLEIVTG 154 (280)
Q Consensus 135 e~ke~VKkLVknGRLEfVgG 154 (280)
-.+..++++|.+|+|..+.|
T Consensus 47 ~l~~~Lk~~v~~G~l~q~kg 66 (66)
T smart00526 47 LLKLALKKLVASGKLVQVKG 66 (66)
T ss_pred HHHHHHHHHHhcCceeecCC
Confidence 35677999999999977655
No 58
>smart00363 S4 S4 RNA-binding domain.
Probab=24.32 E-value=96 Score=20.11 Aligned_cols=22 Identities=27% Similarity=0.513 Sum_probs=17.7
Q ss_pred HHHHHHHHHHHcCCceeeccccc
Q psy11173 135 DTKDKVRLLVKSGQLEIVTGGWV 157 (280)
Q Consensus 135 e~ke~VKkLVknGRLEfVgGGWV 157 (280)
..+..++++++.|++ .|+|--+
T Consensus 14 ~s~~~~~~~i~~g~i-~vng~~~ 35 (60)
T smart00363 14 PSRSQARKLIEQGRV-KVNGKKV 35 (60)
T ss_pred cCHHHHHHHHHcCCE-EECCEEe
Confidence 358889999999999 6777655
No 59
>PLN03014 carbonic anhydrase
Probab=23.91 E-value=1.6e+02 Score=29.47 Aligned_cols=30 Identities=20% Similarity=0.059 Sum_probs=20.6
Q ss_pred HHHHHHHHHcCCceeecccccccccccccc
Q psy11173 137 KDKVRLLVKSGQLEIVTGGWVMTDEANSCN 166 (280)
Q Consensus 137 ke~VKkLVknGRLEfVgGGWVM~DEA~thY 166 (280)
...|+.+|++|+|.|+|+-|-..+-.+.-|
T Consensus 295 ~P~V~eav~~G~L~I~G~~YDi~TG~V~~l 324 (347)
T PLN03014 295 YPFVREGLVKGTLALKGGYYDFVKGAFELW 324 (347)
T ss_pred CHHHHHHHHcCCcEEEEEEEECCCceEEEe
Confidence 356778899999988876665555444443
No 60
>COG1861 SpsF Spore coat polysaccharide biosynthesis protein F, CMP-KDO synthetase homolog [Cell envelope biogenesis, outer membrane]
Probab=23.51 E-value=34 Score=32.48 Aligned_cols=65 Identities=14% Similarity=0.209 Sum_probs=38.1
Q ss_pred HHhcCCCcccccceeeecCCCCCCCCCceEEEEecCccCCcchhccHHHHHH-HHHHHHHHHHHHHHHhCCCC
Q psy11173 44 FANINGGKWTQGWNIGLDLAHETDPENLLRVFVVPHSHNDPGWKQTFESYFV-HSTKSILDTMVTKLLENEKR 115 (280)
Q Consensus 44 f~~~dgg~wkqG~~i~y~~~~~w~~~~~l~VHVVPHSH~D~GWLkT~eEYy~-~~v~~ILdsVl~~L~~dp~r 115 (280)
|-|-+ +.|||+| ......|+.+. +.+.--+--|..-.+.+.+||. .++...++++++.|.++|+-
T Consensus 164 i~n~P-~~fk~~~---l~~p~~~~~~~---~RltvDt~eD~~~~~~vye~~~~~~~~~~~d~iid~ld~npdi 229 (241)
T COG1861 164 IRNNP-ERFKVAY---LEAPEAWKRPD---YRLTVDTQEDFALAKAVYEYFCPENPDFTLDNIIDFLDKNPDI 229 (241)
T ss_pred HHhCC-ceEEEEe---ecChhhccCCc---eEEEeccHHHHHHHHHHHHHhCccCCCCcHHHHHHHHhcCchh
Confidence 33444 3888888 23334566221 4444455666666666666664 33444567888888887763
No 61
>COG1543 Uncharacterized conserved protein [Function unknown]
Probab=23.50 E-value=1.2e+02 Score=31.75 Aligned_cols=31 Identities=23% Similarity=0.431 Sum_probs=26.5
Q ss_pred HHHHhccChHHHHHHHHHHHcCCceeecccc
Q psy11173 126 SLWWKTISEDTKDKVRLLVKSGQLEIVTGGW 156 (280)
Q Consensus 126 ~~Ww~eq~pe~ke~VKkLVknGRLEfVgGGW 156 (280)
...|...+++.-.++|+|..+|.++|++.+.
T Consensus 115 ~~~~e~~d~~ll~~f~~~~~~g~ieilts~a 145 (504)
T COG1543 115 RGYWEQYDGNLLEAFKELQRSGGIEILTSAA 145 (504)
T ss_pred HHHHHHhhHHHHHHHHHHHHcCCceeeeehh
Confidence 3467778888999999999999999998654
No 62
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=22.51 E-value=1.1e+02 Score=25.66 Aligned_cols=43 Identities=14% Similarity=0.215 Sum_probs=31.2
Q ss_pred HHHHHHHhCCCCcEEeechHHHHHHHhccChHHHHHHHHHHHcCCcee
Q psy11173 104 TMVTKLLENEKRKFIWAEMSYLSLWWKTISEDTKDKVRLLVKSGQLEI 151 (280)
Q Consensus 104 sVl~~L~~dp~rkFi~aEisff~~Ww~eq~pe~ke~VKkLVknGRLEf 151 (280)
.+|..|.+|++..|.- +.+-..-..+..+.+|++|..+|-|..
T Consensus 13 ~Il~~Lq~d~R~s~~e-----iA~~lglS~~tV~~Ri~rL~~~GvI~~ 55 (153)
T PRK11179 13 GILEALMENARTPYAE-----LAKQFGVSPGTIHVRVEKMKQAGIITG 55 (153)
T ss_pred HHHHHHHHcCCCCHHH-----HHHHHCcCHHHHHHHHHHHHHCCCeee
Confidence 4578899998766553 444333344778999999999999963
No 63
>PF10835 DUF2573: Protein of unknown function (DUF2573); InterPro: IPR020393 This entry contains proteins with no known function.
Probab=22.30 E-value=34 Score=27.60 Aligned_cols=32 Identities=19% Similarity=0.366 Sum_probs=24.8
Q ss_pred CcEEeechHHHHHHHhccChHHHHHHHHHHHc
Q psy11173 115 RKFIWAEMSYLSLWWKTISEDTKDKVRLLVKS 146 (280)
Q Consensus 115 rkFi~aEisff~~Ww~eq~pe~ke~VKkLVkn 146 (280)
|.+|.-.|.-|.+-|....|+-|..||.+|..
T Consensus 37 YshiaKsMPpL~kHWN~~~PeaK~~ik~li~~ 68 (82)
T PF10835_consen 37 YSHIAKSMPPLAKHWNGTYPEAKEEIKELIEE 68 (82)
T ss_pred HHHHHHhCcHHHHhhcccCchHHHHHHHHHHH
Confidence 34444456668888999999999999999864
No 64
>PF02608 Bmp: Basic membrane protein; InterPro: IPR003760 This is a family of basic membrane lipoproteins from Borrelia and various putative lipoproteins from other bacteria. All of these proteins are outer membrane proteins and are thus antigenic in nature when possessed by the pathogenic members of the family []. The Bacillus subtilis degR, a positive regulator of the production of degradative enzymes, is also a member of this group [].; GO: 0005886 plasma membrane; PDB: 2HQB_A 3S99_A 2FQW_A 2FQY_A 2FQX_A.
Probab=22.18 E-value=2.6e+02 Score=26.01 Aligned_cols=73 Identities=22% Similarity=0.286 Sum_probs=47.3
Q ss_pred eEEEEecCccCCcchhccHHHHHHHHHHHHHHHHHHHHHhCCCCcEEeechHHHHHHHhccChHHHHHHHHHHHcC-Cce
Q psy11173 72 LRVFVVPHSHNDPGWKQTFESYFVHSTKSILDTMVTKLLENEKRKFIWAEMSYLSLWWKTISEDTKDKVRLLVKSG-QLE 150 (280)
Q Consensus 72 l~VHVVPHSH~D~GWLkT~eEYy~~~v~~ILdsVl~~L~~dp~rkFi~aEisff~~Ww~eq~pe~ke~VKkLVknG-RLE 150 (280)
+-+.+.|....|.||.....+-... .-.+.+..+++..+.... ........++++++.| .|
T Consensus 3 ~v~~~~~g~~~D~g~n~~~~~G~~~-----------~~~~~~~i~~~~~e~~~~------~~~~~~~~~~~~~~~g~dl- 64 (306)
T PF02608_consen 3 KVALLDPGGINDKGFNQSAYEGLKR-----------AEKELDGIEIIYVENVPE------TDADYEEAIRQLADQGYDL- 64 (306)
T ss_dssp EEEEESSS-CCCSSHHHHHHHHHHH-----------HHHHCTTEEEEEEES-S-------TCHHHHHHHHHHHHTT-SE-
T ss_pred EEEEEECCCCCCccHHHHHHHHHHH-----------HHHHcCCceEEEEecCCc------cHHHHHHHHHHHHHcCCCE-
Confidence 3467889999999998775544321 122335677777664321 3466788889999999 77
Q ss_pred eecccccccccc
Q psy11173 151 IVTGGWVMTDEA 162 (280)
Q Consensus 151 fVgGGWVM~DEA 162 (280)
||+.|+-+.|-+
T Consensus 65 Ii~~g~~~~~~~ 76 (306)
T PF02608_consen 65 IIGHGFEYSDAL 76 (306)
T ss_dssp EEEESGGGHHHH
T ss_pred EEEccHHHHHHH
Confidence 777777666643
No 65
>cd02983 P5_C P5 family, C-terminal redox inactive TRX-like domain; P5 is a protein disulfide isomerase (PDI)-related protein with a domain structure of aa'b (where a and a' are redox active TRX domains and b is a redox inactive TRX-like domain). Like PDI, P5 is located in the endoplasmic reticulum (ER) and displays both isomerase and chaperone activities, which are independent of each other. Compared to PDI, the isomerase and chaperone activities of P5 are lower. The first cysteine in the CXXC motif of both redox active domains in P5 is necessary for isomerase activity. The P5 gene was first isolated as an amplified gene from a hydroxyurea-resistant hamster cell line. The zebrafish P5 homolog has been implicated to play a critical role in establishing left/right asymmetries in the embryonic midline. The C-terminal domain is likely involved in substrate binding, similar to the b and b' domains of PDI.
Probab=22.04 E-value=1.4e+02 Score=24.89 Aligned_cols=42 Identities=17% Similarity=0.307 Sum_probs=27.6
Q ss_pred EEEEecCccCCcchhccHHHHHHHHHHHHHHHHHHHHHhCCCCcEEeech
Q psy11173 73 RVFVVPHSHNDPGWKQTFESYFVHSTKSILDTMVTKLLENEKRKFIWAEM 122 (280)
Q Consensus 73 ~VHVVPHSH~D~GWLkT~eEYy~~~v~~ILdsVl~~L~~dp~rkFi~aEi 122 (280)
-|.++||++.+ +-+ .+ .....+|..|...+...| ..|+|+..
T Consensus 24 ~i~~l~~~~d~-----~~e-~~-~~~~~~l~~vAk~~kgk~-i~Fv~vd~ 65 (130)
T cd02983 24 IIAFLPHILDC-----QAS-CR-NKYLEILKSVAEKFKKKP-WGWLWTEA 65 (130)
T ss_pred EEEEcCccccC-----CHH-HH-HHHHHHHHHHHHHhcCCc-EEEEEEeC
Confidence 47788999874 222 23 234557778877776544 78999775
No 66
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=22.04 E-value=2.1e+02 Score=24.12 Aligned_cols=32 Identities=13% Similarity=0.143 Sum_probs=23.8
Q ss_pred HhccChHHHHH-HHHHHHcCCceeecccccccc
Q psy11173 129 WKTISEDTKDK-VRLLVKSGQLEIVTGGWVMTD 160 (280)
Q Consensus 129 w~eq~pe~ke~-VKkLVknGRLEfVgGGWVM~D 160 (280)
+.+.++..-.+ +++|-+.|-|.+-++..+.+|
T Consensus 177 ~lG~tr~tvsR~l~~l~~~gii~~~~~~i~i~~ 209 (211)
T PRK11753 177 IVGCSREMVGRVLKMLEDQGLISAHGKTIVVYG 209 (211)
T ss_pred HhCCCHHHHHHHHHHHHHCCCEEecCCEEEEec
Confidence 34677776555 778999999988777777766
No 67
>COG2350 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.75 E-value=1e+02 Score=24.96 Aligned_cols=33 Identities=15% Similarity=0.302 Sum_probs=27.3
Q ss_pred hccChHHHHHHHHHHHcCCceeeccccccccccc
Q psy11173 130 KTISEDTKDKVRLLVKSGQLEIVTGGWVMTDEAN 163 (280)
Q Consensus 130 ~eq~pe~ke~VKkLVknGRLEfVgGGWVM~DEA~ 163 (280)
....|.-++.+++|-..||| ++.|..+-.|-..
T Consensus 18 ~~~r~~H~~~L~~~~a~G~l-l~sGP~~~~dg~~ 50 (92)
T COG2350 18 LAVRPAHLARLKQLYAEGRL-LTSGPFPDRDGGP 50 (92)
T ss_pred hhhhHHHHHHHHHhhhcCeE-EEeCCCCCCCCCC
Confidence 34668889999999999999 7788887777766
No 68
>PF14595 Thioredoxin_9: Thioredoxin; PDB: 1Z6N_A.
Probab=21.61 E-value=57 Score=27.24 Aligned_cols=26 Identities=23% Similarity=0.515 Sum_probs=12.5
Q ss_pred cChHHHHHHHHHHHcCCceeeccccc
Q psy11173 132 ISEDTKDKVRLLVKSGQLEIVTGGWV 157 (280)
Q Consensus 132 q~pe~ke~VKkLVknGRLEfVgGGWV 157 (280)
.++....+++.+-+..+|-+++|.||
T Consensus 28 l~~~~~~~l~~~~~~~~ilvi~e~WC 53 (129)
T PF14595_consen 28 LSEEQIEKLKSIQKPYNILVITETWC 53 (129)
T ss_dssp --HHHHHHHHT--S-EEEEEE--TT-
T ss_pred CCHHHHHHHHhcCCCcEEEEEECCCc
Confidence 34556666777766677777777776
No 69
>cd01779 Myosin_IXb_RA ubitquitin-like domain of Myosin_IXb_RA. Myosin_IXb_RA RasGTP binding domain from guanine nucleotide exchange factors. In some proteins the domain acts as a RasGTP effector (AF6, canoe and RalGDS, for example), but in other cases it may not bind to RasGTP at all.
Probab=21.47 E-value=75 Score=26.70 Aligned_cols=27 Identities=15% Similarity=0.374 Sum_probs=23.8
Q ss_pred HHHHHHHHHHHHHhCCCCcEEeechHH
Q psy11173 98 TKSILDTMVTKLLENEKRKFIWAEMSY 124 (280)
Q Consensus 98 v~~ILdsVl~~L~~dp~rkFi~aEisf 124 (280)
+..++++||..|.-|+.+.|+.+|+.=
T Consensus 37 Aa~VI~~~i~~L~Ld~tk~YvLaEVkE 63 (105)
T cd01779 37 AADVIDDVIASLQLDGTKCYVLAEVKE 63 (105)
T ss_pred HHHHHHHHHHHhCcCccccEEEEEeec
Confidence 566899999999999999999999743
No 70
>PF03795 YCII: YCII-related domain; InterPro: IPR005545 The majority of proteins in this group contain a single copy of this domain, though it is also found as a repeat (e.g. in Q9AJZ7 from SWISSPROT). A strongly conserved histidine and a aspartate suggest that the domain has an enzymatic function. This entry also covers what was previously known as the DGPF domain (COG3795). Although its function is unknown it is found fused to a sigma-70 factor family domain in Q9A8M4 from SWISSPROT, suggesting that this domain may plays a role in transcription initiation. This domain is named after the most conserved motif in the alignment.; PDB: 1S7I_A 1MWQ_A.
Probab=21.20 E-value=35 Score=25.80 Aligned_cols=31 Identities=19% Similarity=0.304 Sum_probs=21.9
Q ss_pred cChHHHHHHHHHHHcCCceeeccccccccccc
Q psy11173 132 ISEDTKDKVRLLVKSGQLEIVTGGWVMTDEAN 163 (280)
Q Consensus 132 q~pe~ke~VKkLVknGRLEfVgGGWVM~DEA~ 163 (280)
..+.-+.-+++|.+.|+| +++|..+-+|-..
T Consensus 20 ~~~~H~~~~~~l~~~G~~-~~~G~~~~~~g~~ 50 (95)
T PF03795_consen 20 LRPAHLAYLKELKEAGVL-VASGPFLDTDGPF 50 (95)
T ss_dssp CHHHHHHHHHHHHHTT-E-EEECEEECCCSSS
T ss_pred HHHHHHHHHHHHHHCCCE-EeccCccCCCCCC
Confidence 445667788999999999 6677777666433
No 71
>COG3811 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.11 E-value=55 Score=26.51 Aligned_cols=35 Identities=20% Similarity=0.393 Sum_probs=27.5
Q ss_pred HHHHHHHHHHHcCCceeec--------------cccccccccccccccC
Q psy11173 135 DTKDKVRLLVKSGQLEIVT--------------GGWVMTDEANSCNVSD 169 (280)
Q Consensus 135 e~ke~VKkLVknGRLEfVg--------------GGWVM~DEA~thYeS~ 169 (280)
..+..+..|-+-||++|.- -||+.||+-+.-|.+.
T Consensus 6 ~eQRtLH~LAqGGrIe~~rd~~grI~~v~C~tRdGw~l~dctlavF~kL 54 (85)
T COG3811 6 PEQRTLHALAQGGRIEIERDASGRITSVECYTRDGWLLPDCTLAVFRKL 54 (85)
T ss_pred HHHHHHHHHhcCCeEEEEecCCCcEEEEEEecccccccCCccHHHHHHH
Confidence 3456788899999998865 5899999988777654
No 72
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=21.02 E-value=3e+02 Score=24.14 Aligned_cols=64 Identities=19% Similarity=0.128 Sum_probs=40.4
Q ss_pred HHHHHHHHHHhCCCCcEEeechHHHHHHHhccC-hHHHHHHHHHHHcCCceeecc-cccccccccccc
Q psy11173 101 ILDTMVTKLLENEKRKFIWAEMSYLSLWWKTIS-EDTKDKVRLLVKSGQLEIVTG-GWVMTDEANSCN 166 (280)
Q Consensus 101 ILdsVl~~L~~dp~rkFi~aEisff~~Ww~eq~-pe~ke~VKkLVknGRLEfVgG-GWVM~DEA~thY 166 (280)
-...||..|..-+.++.....+ ..+=+..++ .+.+..|..|++.|-|+-.++ .|++++..++.-
T Consensus 24 W~~~~ir~l~~l~~~~~d~~~i--ak~l~p~is~~ev~~sL~~L~~~gli~k~~~g~y~~t~~~l~~~ 89 (171)
T PF14394_consen 24 WYHPAIRELLPLMPFAPDPEWI--AKRLRPKISAEEVRDSLEFLEKLGLIKKDGDGKYVQTDKSLTTS 89 (171)
T ss_pred hHHHHHHHHhhcCCCCCCHHHH--HHHhcCCCCHHHHHHHHHHHHHCCCeEECCCCcEEEecceeeCC
Confidence 3445555555544444332221 122122333 667999999999999988877 899999888743
No 73
>KOG1189|consensus
Probab=20.99 E-value=31 Score=37.94 Aligned_cols=45 Identities=11% Similarity=0.330 Sum_probs=25.9
Q ss_pred CCceEEEEecCccCCc--chhccHHHHHHHHHHHH-HHHHHHHHHhCC
Q psy11173 69 ENLLRVFVVPHSHNDP--GWKQTFESYFVHSTKSI-LDTMVTKLLENE 113 (280)
Q Consensus 69 ~~~l~VHVVPHSH~D~--GWLkT~eEYy~~~v~~I-LdsVl~~L~~dp 113 (280)
...+.|--||-+-.|. .||-|.+=-|...++.+ ..+++..+..||
T Consensus 812 k~v~~i~svp~~sLd~iKEWLdscDI~y~Eg~~sLNW~~ImKTI~dDP 859 (960)
T KOG1189|consen 812 KKVTMINSVPMESLDKLKEWLDSCDIKYTEGVQSLNWTKIMKTITDDP 859 (960)
T ss_pred ccceeeeccchhhhhHHHHhhhcccceeecccccccHHHHhhhhccCH
Confidence 4556677778777775 67777665554433221 334555555555
No 74
>PF09106 SelB-wing_2: Elongation factor SelB, winged helix ; InterPro: IPR015190 This entry represents a domain with a winged helix-type fold, which consists of a closed 3-helical bundle with a right-handed twist, and a small beta-sheet wing []. Different winged helix domains share a common structure, but can differ in sequence. This entry is designated "type 2". The winged helix motif is involved in both DNA and RNA binding. In the elongation factor SelB, the winged helix domains recognise RNA, allowing the complex to wrap around the small ribosomal subunit. In bacteria, the incorporation of the amino acid selenocysteine into proteins requires elongation factor SelB, which binds both transfer RNA (tRNA) and mRNA. SelB binds to an mRNA hairpin formed by the selenocysteine insertion sequence (SECIS) with extremely high specificity []. ; GO: 0003723 RNA binding, 0003746 translation elongation factor activity, 0005525 GTP binding, 0001514 selenocysteine incorporation, 0005737 cytoplasm; PDB: 2V9V_A 1LVA_A 2PLY_A 2UWM_A.
Probab=20.48 E-value=87 Score=22.50 Aligned_cols=46 Identities=30% Similarity=0.373 Sum_probs=26.5
Q ss_pred HhCCCCcEEeechHHHHHHHh-ccChH-HHHHHHHHHHcCCceeeccccc
Q psy11173 110 LENEKRKFIWAEMSYLSLWWK-TISED-TKDKVRLLVKSGQLEIVTGGWV 157 (280)
Q Consensus 110 ~~dp~rkFi~aEisff~~Ww~-eq~pe-~ke~VKkLVknGRLEfVgGGWV 157 (280)
.++|.+.=+-.+ .+.++++. ..++. ....|..||+.|.| .+.|+||
T Consensus 10 ~~~Plr~G~~ke-eLrsrl~~~~l~~k~~~~ll~~l~~~g~l-~~~g~~v 57 (59)
T PF09106_consen 10 RENPLRPGMPKE-ELRSRLFKPRLPPKLFNALLEALVAEGRL-KVEGDWV 57 (59)
T ss_dssp HH-TTSS-EEHH-HHHHHCST-TS-HCCHHHHHHHHHHTTSE-EEESSEE
T ss_pred HHCcCccCcCHH-HHHHHHhhccCCHHHHHHHHHHHHHCCCe-eeECCEe
Confidence 456766543322 23445555 44433 35567789999999 5677776
Done!