Query 047859
Match_columns 214
No_of_seqs 160 out of 373
Neff 4.1
Searched_HMMs 46136
Date Fri Mar 29 03:54:10 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/047859.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/047859hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF03745 DUF309: Domain of unk 99.9 7.4E-26 1.6E-30 162.4 7.3 62 39-100 1-62 (62)
2 COG1547 Predicted metal-depend 99.4 3.2E-13 6.9E-18 112.5 8.3 90 43-137 17-109 (156)
3 COG1547 Predicted metal-depend 96.9 0.0011 2.5E-08 55.5 4.3 71 40-110 64-138 (156)
4 PF09670 Cas_Cas02710: CRISPR- 92.5 0.57 1.2E-05 43.9 7.9 68 38-107 132-199 (379)
5 PF13432 TPR_16: Tetratricopep 91.6 1.6 3.5E-05 29.3 7.4 60 41-106 1-60 (65)
6 cd00189 TPR Tetratricopeptide 88.7 2.3 5E-05 27.1 6.0 60 41-106 4-63 (100)
7 PF12862 Apc5: Anaphase-promot 87.2 6.1 0.00013 29.5 8.3 68 41-110 2-74 (94)
8 TIGR03302 OM_YfiO outer membra 85.6 5.5 0.00012 33.0 8.0 73 32-107 28-100 (235)
9 TIGR02710 CRISPR-associated pr 85.3 3 6.5E-05 39.9 7.1 64 38-101 131-195 (380)
10 PRK02603 photosystem I assembl 84.2 5.6 0.00012 32.0 7.3 66 38-106 36-101 (172)
11 PF13525 YfiO: Outer membrane 82.6 5.6 0.00012 33.4 6.9 67 36-105 4-70 (203)
12 PF13424 TPR_12: Tetratricopep 81.2 7.9 0.00017 26.7 6.3 67 42-108 10-77 (78)
13 TIGR02795 tol_pal_ybgF tol-pal 80.1 12 0.00026 26.7 7.1 67 37-106 2-68 (119)
14 PRK15359 type III secretion sy 78.8 8.4 0.00018 30.6 6.5 60 40-105 27-86 (144)
15 PF13414 TPR_11: TPR repeat; P 78.8 9.5 0.00021 25.6 5.9 60 40-105 6-66 (69)
16 PF07719 TPR_2: Tetratricopept 76.0 7.9 0.00017 22.5 4.3 28 79-106 3-30 (34)
17 PF13374 TPR_10: Tetratricopep 71.5 14 0.00031 22.0 4.8 32 79-110 4-35 (42)
18 PF13428 TPR_14: Tetratricopep 71.2 10 0.00023 24.2 4.3 27 80-106 4-30 (44)
19 PRK10866 outer membrane biogen 68.5 37 0.00079 29.7 8.4 70 34-106 29-98 (243)
20 PLN03088 SGT1, suppressor of 68.1 24 0.00051 32.5 7.5 27 41-67 6-32 (356)
21 PF13371 TPR_9: Tetratricopept 66.3 8 0.00017 26.2 3.1 29 40-68 32-60 (73)
22 PF13371 TPR_9: Tetratricopept 65.5 30 0.00065 23.3 5.9 55 45-105 3-57 (73)
23 PF03704 BTAD: Bacterial trans 64.6 53 0.0011 25.3 7.8 57 47-109 72-128 (146)
24 PRK10803 tol-pal system protei 62.5 41 0.00089 30.1 7.7 71 34-107 139-210 (263)
25 cd00189 TPR Tetratricopeptide 61.9 35 0.00075 21.4 5.4 62 38-105 35-96 (100)
26 COG3898 Uncharacterized membra 61.4 27 0.0006 34.6 6.8 135 37-188 263-413 (531)
27 PRK15331 chaperone protein Sic 58.9 21 0.00045 30.6 4.9 67 34-106 34-100 (165)
28 PF14559 TPR_19: Tetratricopep 58.7 18 0.00038 24.1 3.7 53 47-105 1-53 (68)
29 TIGR03302 OM_YfiO outer membra 58.2 48 0.0011 27.3 7.0 67 40-107 110-196 (235)
30 PF13512 TPR_18: Tetratricopep 56.6 73 0.0016 26.6 7.7 68 34-104 7-74 (142)
31 PF09976 TPR_21: Tetratricopep 56.3 43 0.00092 26.2 6.1 62 38-102 49-110 (145)
32 CHL00033 ycf3 photosystem I as 53.8 83 0.0018 25.0 7.4 67 37-106 35-101 (168)
33 PRK15359 type III secretion sy 53.7 61 0.0013 25.7 6.6 65 36-106 57-121 (144)
34 TIGR02917 PEP_TPR_lipo putativ 52.3 57 0.0012 30.9 7.1 64 36-105 21-84 (899)
35 PRK15363 pathogenicity island 51.4 42 0.00091 28.5 5.6 64 36-105 34-97 (157)
36 PF03704 BTAD: Bacterial trans 50.1 28 0.00061 26.8 4.1 64 37-105 25-90 (146)
37 KOG3581 Creatine kinases [Ener 49.6 10 0.00022 36.0 1.7 30 179-208 271-300 (363)
38 PF12895 Apc3: Anaphase-promot 48.9 55 0.0012 23.0 5.1 58 39-103 27-84 (84)
39 PF13176 TPR_7: Tetratricopept 47.6 45 0.00097 20.4 4.0 24 82-105 4-27 (36)
40 TIGR02521 type_IV_pilW type IV 46.3 1.3E+02 0.0028 23.1 7.2 63 38-106 32-94 (234)
41 TIGR02552 LcrH_SycD type III s 46.1 1.1E+02 0.0023 22.8 6.6 60 40-105 54-113 (135)
42 TIGR02521 type_IV_pilW type IV 45.6 1.2E+02 0.0026 23.3 7.0 62 38-105 66-127 (234)
43 PF07721 TPR_4: Tetratricopept 45.1 34 0.00073 19.8 2.9 23 80-102 4-26 (26)
44 KOG1840 Kinesin light chain [C 44.4 1.1E+02 0.0023 30.5 8.0 84 43-135 205-290 (508)
45 PRK04841 transcriptional regul 43.7 75 0.0016 31.8 6.9 68 43-110 497-564 (903)
46 PLN03088 SGT1, suppressor of 43.4 1.1E+02 0.0023 28.3 7.4 64 37-106 36-99 (356)
47 PRK11788 tetratricopeptide rep 43.0 1.1E+02 0.0024 26.9 7.2 53 46-104 189-241 (389)
48 TIGR02917 PEP_TPR_lipo putativ 42.1 70 0.0015 30.3 6.0 56 43-104 843-898 (899)
49 TIGR00540 hemY_coli hemY prote 42.0 87 0.0019 28.9 6.6 64 41-111 339-404 (409)
50 cd05804 StaR_like StaR_like; a 41.7 81 0.0018 27.4 6.1 58 42-105 119-176 (355)
51 PF00515 TPR_1: Tetratricopept 41.6 51 0.0011 19.2 3.5 25 82-106 6-30 (34)
52 PF13174 TPR_6: Tetratricopept 41.5 64 0.0014 18.2 3.8 27 78-106 3-29 (33)
53 PF06212 GRIM-19: GRIM-19 prot 40.4 95 0.0021 25.6 5.9 78 72-171 33-112 (130)
54 PRK11788 tetratricopeptide rep 39.2 1.2E+02 0.0026 26.7 6.8 63 39-106 216-278 (389)
55 COG5010 TadD Flp pilus assembl 38.5 1.3E+02 0.0029 27.6 7.1 67 37-109 98-166 (257)
56 TIGR00208 fliS flagellar biosy 37.6 1.7E+02 0.0036 23.4 6.8 38 74-111 27-65 (124)
57 PF09613 HrpB1_HrpK: Bacterial 36.6 47 0.001 28.3 3.7 25 79-103 46-70 (160)
58 PHA02103 hypothetical protein 35.4 11 0.00024 31.0 -0.3 36 16-59 74-110 (135)
59 PF11672 DUF3268: Protein of u 35.2 38 0.00083 26.9 2.7 34 37-78 55-88 (102)
60 TIGR02552 LcrH_SycD type III s 33.9 1.9E+02 0.004 21.4 6.3 64 37-106 17-80 (135)
61 PF13424 TPR_12: Tetratricopep 33.9 1.5E+02 0.0033 20.1 5.6 34 77-110 5-38 (78)
62 PF13181 TPR_8: Tetratricopept 33.6 98 0.0021 17.8 4.4 25 82-106 6-30 (34)
63 PF13414 TPR_11: TPR repeat; P 33.5 90 0.002 20.7 4.1 28 79-106 5-32 (69)
64 PRK11189 lipoprotein NlpI; Pro 32.9 1.3E+02 0.0029 26.5 6.1 62 38-107 133-195 (296)
65 PRK10747 putative protoheme IX 32.8 1.7E+02 0.0037 27.0 7.0 65 36-107 327-391 (398)
66 cd00716 creatine_kinase_like P 32.1 29 0.00063 33.0 1.9 30 179-208 262-291 (357)
67 cd05804 StaR_like StaR_like; a 31.3 2.7E+02 0.0058 24.2 7.6 69 42-110 269-340 (355)
68 PRK15179 Vi polysaccharide bio 31.1 1.2E+02 0.0025 31.2 6.1 66 36-107 153-218 (694)
69 smart00028 TPR Tetratricopepti 30.2 71 0.0015 16.1 2.6 22 84-105 8-29 (34)
70 CHL00033 ycf3 photosystem I as 29.5 2.8E+02 0.0062 21.9 8.9 67 40-110 75-146 (168)
71 PRK04841 transcriptional regul 29.3 2.2E+02 0.0048 28.5 7.6 67 40-106 412-481 (903)
72 TIGR02561 HrpB1_HrpK type III 29.3 54 0.0012 28.0 2.8 48 50-104 23-71 (153)
73 smart00745 MIT Microtubule Int 28.5 1.9E+02 0.0041 20.4 5.2 34 77-110 8-41 (77)
74 PF04212 MIT: MIT (microtubule 28.2 1.8E+02 0.004 20.2 5.1 34 77-110 5-38 (69)
75 PF14938 SNAP: Soluble NSF att 27.3 2.8E+02 0.0061 24.3 7.2 62 43-105 161-224 (282)
76 PLN03098 LPA1 LOW PSII ACCUMUL 27.0 3E+02 0.0066 27.3 7.8 68 36-106 74-141 (453)
77 PF13429 TPR_15: Tetratricopep 26.3 77 0.0017 27.1 3.4 54 46-105 189-242 (280)
78 KOG4431 Uncharacterized protei 25.3 72 0.0016 25.5 2.7 21 81-101 43-64 (100)
79 cd02679 MIT_spastin MIT: domai 24.8 3.1E+02 0.0067 20.7 7.1 36 74-109 5-40 (79)
80 TIGR02795 tol_pal_ybgF tol-pal 24.7 2.5E+02 0.0055 19.7 6.5 66 38-106 40-105 (119)
81 PRK11189 lipoprotein NlpI; Pro 23.4 4.1E+02 0.009 23.4 7.5 62 38-105 65-126 (296)
82 TIGR00990 3a0801s09 mitochondr 23.1 3E+02 0.0064 26.8 7.0 22 84-105 406-427 (615)
83 PRK11447 cellulose synthase su 23.0 3.3E+02 0.0072 29.0 7.9 68 38-105 304-379 (1157)
84 PF03947 Ribosomal_L2_C: Ribos 22.8 27 0.00059 28.6 -0.1 45 158-202 8-55 (130)
85 PF02561 FliS: Flagellar prote 22.7 2.8E+02 0.006 21.6 5.6 38 74-111 25-63 (122)
86 PRK10803 tol-pal system protei 21.6 3.1E+02 0.0066 24.6 6.3 66 37-105 180-245 (263)
87 PF09976 TPR_21: Tetratricopep 21.6 3.9E+02 0.0084 20.7 7.1 67 37-106 11-77 (145)
88 PRK02603 photosystem I assembl 21.3 4.2E+02 0.0092 21.0 6.6 68 39-110 74-146 (172)
89 cd07931 eukaryotic_phosphagen_ 21.0 48 0.001 31.3 1.2 28 179-206 249-276 (338)
90 PF15256 SPATIAL: SPATIAL 21.0 51 0.0011 29.1 1.2 22 63-84 174-196 (196)
91 cd02678 MIT_VPS4 MIT: domain c 20.8 3.1E+02 0.0067 19.6 5.2 30 81-110 10-39 (75)
92 KOG1125 TPR repeat-containing 20.6 3.5E+02 0.0075 27.8 7.0 74 22-104 272-346 (579)
93 PF00617 RasGEF: RasGEF domain 20.2 1.4E+02 0.003 24.0 3.5 59 37-100 42-100 (188)
No 1
>PF03745 DUF309: Domain of unknown function (DUF309); InterPro: IPR005500 This family consists of eubacterial and archaebacterial proteins of unknown function. The proteins contain a motif HXXXEXX(W/Y) where X can be any amino acid. This motif is likely to be functionally important and may be involved in metal binding.; PDB: 2CXD_B 2CWY_A 2IJQ_B.
Probab=99.93 E-value=7.4e-26 Score=162.36 Aligned_cols=62 Identities=37% Similarity=0.724 Sum_probs=57.3
Q ss_pred hhHHHHHHHhccCCchhhhhhhHHhhccCCcchhhHHHHHHHHHHHHHHHhcCCHHHHHHHH
Q 047859 39 CSFDEAVALFNERAYYKCHDCLESLWYTAEEPTRTLIHGVLQCAVGFYHLFNQNHKGAMMEL 100 (214)
Q Consensus 39 ~~l~~gi~LFN~G~YfEAHEVLEe~Wk~~~g~er~~lqGLIQlAvAl~H~~rGN~~GA~~Ll 100 (214)
+.|..|+.+||+|+|||||||||++|+..+++++.+||||||+|||+||+++||++||++|+
T Consensus 1 ~~~~~~~~l~n~g~f~EaHEvlE~~W~~~~~~~~~~lqglIq~A~a~~h~~~gn~~gA~~l~ 62 (62)
T PF03745_consen 1 EALEEGIELFNAGDFFEAHEVLEELWKAAPGPERDFLQGLIQLAVALYHLRRGNPRGARRLL 62 (62)
T ss_dssp -HHHHHHHHHHTT-HHHHHHHHHHHCCCT-CCHHHHHHHHHHHHHHHHHHHCTSHHHHHHHH
T ss_pred CHHHHHHHHHcCCCHHHhHHHHHHHHHHCCcchHHHHHHHHHHHHHHHHHHhCCHHHHHHhC
Confidence 47899999999999999999999999999888999999999999999999999999999986
No 2
>COG1547 Predicted metal-dependent hydrolase [General function prediction only]
Probab=99.44 E-value=3.2e-13 Score=112.48 Aligned_cols=90 Identities=24% Similarity=0.344 Sum_probs=76.8
Q ss_pred HHHHHhccCCchhhhhhhHHhhccCC-cchh-hHHHHHHHHHHHHH-HHhcCCHHHHHHHHHHHHHHHhhccCCCCCCcc
Q 047859 43 EAVALFNERAYYKCHDCLESLWYTAE-EPTR-TLIHGVLQCAVGFY-HLFNQNHKGAMMELGEGLGKLRKMNLRSGPFHE 119 (214)
Q Consensus 43 ~gi~LFN~G~YfEAHEVLEe~Wk~~~-g~er-~~lqGLIQlAvAl~-H~~rGN~~GA~~Ll~rAl~~L~~~~~~~~p~~~ 119 (214)
-++..||+++||+||+++|+.|+... +.++ .+|+|+||+|+++| |.++.|+.||.++|.+|.+.|...+ -.+
T Consensus 17 ~~~~~~~~~~~~~~h~~~E~~w~~~~~~~~~~~~~v~liq~a~~~y~h~r~~~~l~a~~~f~ea~e~L~d~~-----r~~ 91 (156)
T COG1547 17 PLVEVFNRGHYIECHDDLEDSWKEVSEGLRKERYVVGLIQIAVALYRHVRRRNLLGAEERFWEAHEYLEDAW-----REY 91 (156)
T ss_pred hhHHHHhccchhhhhhHHHHHHhhccccccccchhhhhHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHhhh-----HHh
Confidence 59999999999999999999999998 4545 89999999999999 9999999999999999999999873 446
Q ss_pred cccCHHHHHHHHHHhhHH
Q 047859 120 FENEISAALEFIYRTQIE 137 (214)
Q Consensus 120 ~GvDV~aLl~~i~~l~~E 137 (214)
.|+|+..+..++++...-
T Consensus 92 ~~~~~~~~~~L~q~~i~~ 109 (156)
T COG1547 92 RGVDLDSLLLLLQAIILL 109 (156)
T ss_pred cCcchhHHHHHHHHHHHH
Confidence 888888544444444433
No 3
>COG1547 Predicted metal-dependent hydrolase [General function prediction only]
Probab=96.93 E-value=0.0011 Score=55.46 Aligned_cols=71 Identities=14% Similarity=0.147 Sum_probs=56.2
Q ss_pred hHHHHHHHhccCCchhhhhhhHHhhccCCcchhh----HHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHhhc
Q 047859 40 SFDEAVALFNERAYYKCHDCLESLWYTAEEPTRT----LIHGVLQCAVGFYHLFNQNHKGAMMELGEGLGKLRKM 110 (214)
Q Consensus 40 ~l~~gi~LFN~G~YfEAHEVLEe~Wk~~~g~er~----~lqGLIQlAvAl~H~~rGN~~GA~~Ll~rAl~~L~~~ 110 (214)
..+..-.++...+||||||++|+.|....+..-. +.|.+|....+.-|+..++..-+..+.++++...+..
T Consensus 64 h~r~~~~l~a~~~f~ea~e~L~d~~r~~~~~~~~~~~~L~q~~i~~~~~~~~~~~~~l~~~~~~~q~~~~~is~~ 138 (156)
T COG1547 64 HVRRRNLLGAEERFWEAHEYLEDAWREYRGVDLDSLLLLLQAIILLLETLSHWSEGILPIADELEQKALRDISEV 138 (156)
T ss_pred hhhhhhHHHHHHHHHHHHHHHHhhhHHhcCcchhHHHHHHHHHHHHHhchhhhhccccchhHHHHHHHHHHHHHH
Confidence 3445555677889999999999999999965444 7777777888888999999999999988866655543
No 4
>PF09670 Cas_Cas02710: CRISPR-associated protein (Cas_Cas02710)
Probab=92.52 E-value=0.57 Score=43.88 Aligned_cols=68 Identities=21% Similarity=0.164 Sum_probs=58.6
Q ss_pred chhHHHHHHHhccCCchhhhhhhHHhhccCCcchhhHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHH
Q 047859 38 NCSFDEAVALFNERAYYKCHDCLESLWYTAEEPTRTLIHGVLQCAVGFYHLFNQNHKGAMMELGEGLGKL 107 (214)
Q Consensus 38 ~~~l~~gi~LFN~G~YfEAHEVLEe~Wk~~~g~er~~lqGLIQlAvAl~H~~rGN~~GA~~Ll~rAl~~L 107 (214)
...+..+..+||.++|=+|=+++++++...++..+ ++-+..++-|+.+|.+-.++.|...+++.....
T Consensus 132 ~~~~~~a~~l~n~~~y~aA~~~l~~l~~rl~~~~~--~~~~~~l~~~y~~WD~fd~~~A~~~l~~~~~~~ 199 (379)
T PF09670_consen 132 DREWRRAKELFNRYDYGAAARILEELLRRLPGREE--YQRYKDLCEGYDAWDRFDHKEALEYLEKLLKRD 199 (379)
T ss_pred HHHHHHHHHHHhcCCHHHHHHHHHHHHHhCCchhh--HHHHHHHHHHHHHHHccCHHHHHHHHHHHHHHh
Confidence 34578899999999999999999999987554444 888999999999999999999999999877653
No 5
>PF13432 TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL_A 3CVQ_A 3CV0_A 2GW1_B 3CVN_A 3QKY_A 2PL2_B.
Probab=91.57 E-value=1.6 Score=29.30 Aligned_cols=60 Identities=13% Similarity=0.075 Sum_probs=45.5
Q ss_pred HHHHHHHhccCCchhhhhhhHHhhccCCcchhhHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHH
Q 047859 41 FDEAVALFNERAYYKCHDCLESLWYTAEEPTRTLIHGVLQCAVGFYHLFNQNHKGAMMELGEGLGK 106 (214)
Q Consensus 41 l~~gi~LFN~G~YfEAHEVLEe~Wk~~~g~er~~lqGLIQlAvAl~H~~rGN~~GA~~Ll~rAl~~ 106 (214)
|..|..++..|+|=+|=++++.+=+..|+ ... +....|..+.+.|++..|...+++++..
T Consensus 1 ~~~a~~~~~~g~~~~A~~~~~~~l~~~P~----~~~--a~~~lg~~~~~~g~~~~A~~~~~~a~~~ 60 (65)
T PF13432_consen 1 YALARALYQQGDYDEAIAAFEQALKQDPD----NPE--AWYLLGRILYQQGRYDEALAYYERALEL 60 (65)
T ss_dssp HHHHHHHHHCTHHHHHHHHHHHHHCCSTT----HHH--HHHHHHHHHHHTT-HHHHHHHHHHHHHH
T ss_pred ChHHHHHHHcCCHHHHHHHHHHHHHHCCC----CHH--HHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence 46789999999999999999998887653 122 2233355566899999999999998853
No 6
>cd00189 TPR Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and C
Probab=88.71 E-value=2.3 Score=27.06 Aligned_cols=60 Identities=7% Similarity=-0.024 Sum_probs=45.7
Q ss_pred HHHHHHHhccCCchhhhhhhHHhhccCCcchhhHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHH
Q 047859 41 FDEAVALFNERAYYKCHDCLESLWYTAEEPTRTLIHGVLQCAVGFYHLFNQNHKGAMMELGEGLGK 106 (214)
Q Consensus 41 l~~gi~LFN~G~YfEAHEVLEe~Wk~~~g~er~~lqGLIQlAvAl~H~~rGN~~GA~~Ll~rAl~~ 106 (214)
+..|..++..|+|-+|-+.++...+..+... .+....|..+...|++..|...+.+++..
T Consensus 4 ~~~a~~~~~~~~~~~A~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~a~~~~~~~~~~ 63 (100)
T cd00189 4 LNLGNLYYKLGDYDEALEYYEKALELDPDNA------DAYYNLAAAYYKLGKYEEALEDYEKALEL 63 (100)
T ss_pred HHHHHHHHHHhcHHHHHHHHHHHHhcCCccH------HHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence 5677888899999999999999887765332 33344555666779999999999988764
No 7
>PF12862 Apc5: Anaphase-promoting complex subunit 5
Probab=87.19 E-value=6.1 Score=29.45 Aligned_cols=68 Identities=15% Similarity=0.123 Sum_probs=50.0
Q ss_pred HHHHHHHhccCCchhhhhhhHHhhccCC--cchh---hHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHhhc
Q 047859 41 FDEAVALFNERAYYKCHDCLESLWYTAE--EPTR---TLIHGVLQCAVGFYHLFNQNHKGAMMELGEGLGKLRKM 110 (214)
Q Consensus 41 l~~gi~LFN~G~YfEAHEVLEe~Wk~~~--g~er---~~lqGLIQlAvAl~H~~rGN~~GA~~Ll~rAl~~L~~~ 110 (214)
|.....-...|+|.+|=|.|...+=-.. .... .+-.+ .+..|..|...|++..|...+++|+..-+..
T Consensus 2 ~l~~~~~~~~~dy~~A~d~L~~~fD~~~~~~~~~~~~~~~~a--ll~lA~~~~~~G~~~~A~~~l~eAi~~Are~ 74 (94)
T PF12862_consen 2 YLRYLNALRSGDYSEALDALHRYFDYAKQSNNSSSNSGLAYA--LLNLAELHRRFGHYEEALQALEEAIRLAREN 74 (94)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHHHHHHhhcccchhhHHHHHH--HHHHHHHHHHhCCHHHHHHHHHHHHHHHHHH
Confidence 4455666779999999999988885544 1211 23334 4445668999999999999999999887765
No 8
>TIGR03302 OM_YfiO outer membrane assembly lipoprotein YfiO. Members of this protein family include YfiO, a near-essential protein of the outer membrane, part of a complex involved in protein insertion into the bacterial outer membrane. Many proteins in this family are annotated as ComL, based on the involvement of this protein in natural transformation with exogenous DNA in Neisseria gonorrhoeae. This protein family shows sequence similarity to, but is distinct from, the tol-pal system protein YbgF (TIGR02795).
Probab=85.61 E-value=5.5 Score=32.95 Aligned_cols=73 Identities=10% Similarity=-0.008 Sum_probs=56.0
Q ss_pred CCCCCcchhHHHHHHHhccCCchhhhhhhHHhhccCCcchhhHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHH
Q 047859 32 DDNDGENCSFDEAVALFNERAYYKCHDCLESLWYTAEEPTRTLIHGVLQCAVGFYHLFNQNHKGAMMELGEGLGKL 107 (214)
Q Consensus 32 ~~~~e~~~~l~~gi~LFN~G~YfEAHEVLEe~Wk~~~g~er~~lqGLIQlAvAl~H~~rGN~~GA~~Ll~rAl~~L 107 (214)
+++...+.-+..|..+++.|+|=+|-+.++.+....|... +..-+.+..|..+...|++..|...+.++++.-
T Consensus 28 ~~~~~~~~~~~~g~~~~~~~~~~~A~~~~~~~~~~~p~~~---~~~~a~~~la~~~~~~~~~~~A~~~~~~~l~~~ 100 (235)
T TIGR03302 28 VEEWPAEELYEEAKEALDSGDYTEAIKYFEALESRYPFSP---YAEQAQLDLAYAYYKSGDYAEAIAAADRFIRLH 100 (235)
T ss_pred cccCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCch---hHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHC
Confidence 4466678889999999999999999999999988766321 222223444667788899999999999988643
No 9
>TIGR02710 CRISPR-associated protein, TIGR02710 family. Members of this family are found, exclusively in the vicinity of CRISPR repeats and other CRISPR-associated (cas) genes, in Methanothermobacter thermautotrophicus (Archaea), Thermus thermophilus (Deinococcus-Thermus), Chloroflexus aurantiacus (Chloroflexi), and Thermomicrobium roseum (Thermomicrobia).
Probab=85.34 E-value=3 Score=39.85 Aligned_cols=64 Identities=20% Similarity=0.186 Sum_probs=56.1
Q ss_pred chhHHHHHHHhccCCchhhhhhhHHhhccCC-cchhhHHHHHHHHHHHHHHHhcCCHHHHHHHHH
Q 047859 38 NCSFDEAVALFNERAYYKCHDCLESLWYTAE-EPTRTLIHGVLQCAVGFYHLFNQNHKGAMMELG 101 (214)
Q Consensus 38 ~~~l~~gi~LFN~G~YfEAHEVLEe~Wk~~~-g~er~~lqGLIQlAvAl~H~~rGN~~GA~~Ll~ 101 (214)
...+..+..+||.++|=.|+++++++=.... +..+..++-+..++-|+.+|.+-+++.|...++
T Consensus 131 ~~e~~~~r~l~n~~dy~aA~~~~~~L~~r~l~~~~~~~~~~~~~l~~~y~~WD~fd~~~A~~~L~ 195 (380)
T TIGR02710 131 NTEQGYARRAINAFDYLFAHARLETLLRRLLSAVNHTFYEAMIKLTRAYLHWDRFEHEEALDYLN 195 (380)
T ss_pred HHHHHHHHHHHHhcChHHHHHHHHHHHhcccChhhhhHHHHHHHHHHHHHHHHccCHHHHHHHHh
Confidence 3446678899999999999999999776644 567889999999999999999999999999998
No 10
>PRK02603 photosystem I assembly protein Ycf3; Provisional
Probab=84.20 E-value=5.6 Score=32.04 Aligned_cols=66 Identities=14% Similarity=0.168 Sum_probs=51.2
Q ss_pred chhHHHHHHHhccCCchhhhhhhHHhhccCCcchhhHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHH
Q 047859 38 NCSFDEAVALFNERAYYKCHDCLESLWYTAEEPTRTLIHGVLQCAVGFYHLFNQNHKGAMMELGEGLGK 106 (214)
Q Consensus 38 ~~~l~~gi~LFN~G~YfEAHEVLEe~Wk~~~g~er~~lqGLIQlAvAl~H~~rGN~~GA~~Ll~rAl~~ 106 (214)
..-+..|..++..|+|-+|.+.++......+.+. ..+.+....|..+...|++..|...+.+|+..
T Consensus 36 ~~~~~lg~~~~~~g~~~~A~~~~~~al~~~~~~~---~~~~~~~~la~~~~~~g~~~~A~~~~~~al~~ 101 (172)
T PRK02603 36 FVYYRDGMSAQADGEYAEALENYEEALKLEEDPN---DRSYILYNMGIIYASNGEHDKALEYYHQALEL 101 (172)
T ss_pred HHHHHHHHHHHHcCCHHHHHHHHHHHHHHhhccc---hHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence 3457888889999999999999999876554322 12345556677778889999999999999875
No 11
>PF13525 YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M_A 2YHC_A.
Probab=82.56 E-value=5.6 Score=33.36 Aligned_cols=67 Identities=9% Similarity=0.069 Sum_probs=48.9
Q ss_pred CcchhHHHHHHHhccCCchhhhhhhHHhhccCCcchhhHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 047859 36 GENCSFDEAVALFNERAYYKCHDCLESLWYTAEEPTRTLIHGVLQCAVGFYHLFNQNHKGAMMELGEGLG 105 (214)
Q Consensus 36 e~~~~l~~gi~LFN~G~YfEAHEVLEe~Wk~~~g~er~~lqGLIQlAvAl~H~~rGN~~GA~~Ll~rAl~ 105 (214)
+...-|..|..+|+.|+|-+|=+.|+.+...-|+.. +..-.++..|.-+...|++..|...+.+-+.
T Consensus 4 ~~~~lY~~a~~~~~~g~y~~Ai~~f~~l~~~~P~s~---~a~~A~l~la~a~y~~~~y~~A~~~~~~fi~ 70 (203)
T PF13525_consen 4 TAEALYQKALEALQQGDYEEAIKLFEKLIDRYPNSP---YAPQAQLMLAYAYYKQGDYEEAIAAYERFIK 70 (203)
T ss_dssp -HHHHHHHHHHHHHCT-HHHHHHHHHHHHHH-TTST---THHHHHHHHHHHHHHTT-HHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCCCCh---HHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence 456789999999999999999999999999877422 2223344455567788999999999886654
No 12
>PF13424 TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15_A 3ASG_A 3ASD_A 3AS5_A 3AS4_A 3ASH_B 4A1S_B 3CEQ_B 3EDT_H ....
Probab=81.20 E-value=7.9 Score=26.70 Aligned_cols=67 Identities=12% Similarity=-0.063 Sum_probs=48.4
Q ss_pred HHHHHHhccCCchhhhhhhHHhhccCC-cchhhHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHh
Q 047859 42 DEAVALFNERAYYKCHDCLESLWYTAE-EPTRTLIHGVLQCAVGFYHLFNQNHKGAMMELGEGLGKLR 108 (214)
Q Consensus 42 ~~gi~LFN~G~YfEAHEVLEe~Wk~~~-g~er~~lqGLIQlAvAl~H~~rGN~~GA~~Ll~rAl~~L~ 108 (214)
.-|..++..|+|=+|=+.++..=.-.. -+......+.+..-.|..+...|+...|...+.+|+...+
T Consensus 10 ~la~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~al~i~~ 77 (78)
T PF13424_consen 10 NLARVYRELGRYDEALDYYEKALDIEEQLGDDHPDTANTLNNLGECYYRLGDYEEALEYYQKALDIFE 77 (78)
T ss_dssp HHHHHHHHTT-HHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHcCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhhc
Confidence 456677889999999888887554422 1223444466667777788899999999999999997654
No 13
>TIGR02795 tol_pal_ybgF tol-pal system protein YbgF. Members of this protein family are the product of one of seven genes regularly clustered in operons to encode the proteins of the tol-pal system, which is critical for maintaining the integrity of the bacterial outer membrane. The gene for this periplasmic protein has been designated orf2 and ybgF. All members of the seed alignment were from unique tol-pal gene regions from completed bacterial genomes. The architecture of this protein is a signal sequence, a low-complexity region usually rich in Asn and Gln, a well-conserved region with tandem repeats that resemble the tetratricopeptide (TPR) repeat, involved in protein-protein interaction.
Probab=80.10 E-value=12 Score=26.68 Aligned_cols=67 Identities=12% Similarity=0.092 Sum_probs=49.4
Q ss_pred cchhHHHHHHHhccCCchhhhhhhHHhhccCCcchhhHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHH
Q 047859 37 ENCSFDEAVALFNERAYYKCHDCLESLWYTAEEPTRTLIHGVLQCAVGFYHLFNQNHKGAMMELGEGLGK 106 (214)
Q Consensus 37 ~~~~l~~gi~LFN~G~YfEAHEVLEe~Wk~~~g~er~~lqGLIQlAvAl~H~~rGN~~GA~~Ll~rAl~~ 106 (214)
.+.-+..|..++..|+|=+|-+.++.+....++... .-.. .+-.|......|++..|..++++++..
T Consensus 2 ~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~-~~~~--~~~l~~~~~~~~~~~~A~~~~~~~~~~ 68 (119)
T TIGR02795 2 EEAYYDAALLVLKAGDYADAIQAFQAFLKKYPKSTY-APNA--HYWLGEAYYAQGKYADAAKAFLAVVKK 68 (119)
T ss_pred cHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCccc-cHHH--HHHHHHHHHhhccHHHHHHHHHHHHHH
Confidence 345688999999999999999999998876553221 1222 233455567789999999999998854
No 14
>PRK15359 type III secretion system chaperone protein SscB; Provisional
Probab=78.79 E-value=8.4 Score=30.60 Aligned_cols=60 Identities=12% Similarity=0.024 Sum_probs=46.0
Q ss_pred hHHHHHHHhccCCchhhhhhhHHhhccCCcchhhHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 047859 40 SFDEAVALFNERAYYKCHDCLESLWYTAEEPTRTLIHGVLQCAVGFYHLFNQNHKGAMMELGEGLG 105 (214)
Q Consensus 40 ~l~~gi~LFN~G~YfEAHEVLEe~Wk~~~g~er~~lqGLIQlAvAl~H~~rGN~~GA~~Ll~rAl~ 105 (214)
.+..|..++..|+|=+|.+.+..++...|... ..+ .. -|..+.+.|++..|...+++|+.
T Consensus 27 ~~~~g~~~~~~g~~~~A~~~~~~al~~~P~~~-~a~---~~--lg~~~~~~g~~~~A~~~y~~Al~ 86 (144)
T PRK15359 27 VYASGYASWQEGDYSRAVIDFSWLVMAQPWSW-RAH---IA--LAGTWMMLKEYTTAINFYGHALM 86 (144)
T ss_pred HHHHHHHHHHcCCHHHHHHHHHHHHHcCCCcH-HHH---HH--HHHHHHHHhhHHHHHHHHHHHHh
Confidence 55679999999999999999999998876432 222 22 34445567889999999999985
No 15
>PF13414 TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2PL2_B 3IEG_B 2FBN_A ....
Probab=78.77 E-value=9.5 Score=25.58 Aligned_cols=60 Identities=10% Similarity=0.121 Sum_probs=45.9
Q ss_pred hHHHHHHHhccCCchhhhhhhHHhhccCCcchhhHHHHHHHHHHHHHHHhcC-CHHHHHHHHHHHHH
Q 047859 40 SFDEAVALFNERAYYKCHDCLESLWYTAEEPTRTLIHGVLQCAVGFYHLFNQ-NHKGAMMELGEGLG 105 (214)
Q Consensus 40 ~l~~gi~LFN~G~YfEAHEVLEe~Wk~~~g~er~~lqGLIQlAvAl~H~~rG-N~~GA~~Ll~rAl~ 105 (214)
-+..|..+|+.|+|=+|=+.++..=...+.. .. +....|+.+...| ++..|...+.+|+.
T Consensus 6 ~~~~g~~~~~~~~~~~A~~~~~~ai~~~p~~----~~--~~~~~g~~~~~~~~~~~~A~~~~~~al~ 66 (69)
T PF13414_consen 6 WYNLGQIYFQQGDYEEAIEYFEKAIELDPNN----AE--AYYNLGLAYMKLGKDYEEAIEDFEKALK 66 (69)
T ss_dssp HHHHHHHHHHTTHHHHHHHHHHHHHHHSTTH----HH--HHHHHHHHHHHTTTHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHcCCHHHHHHHHHHHHHcCCCC----HH--HHHHHHHHHHHhCccHHHHHHHHHHHHH
Confidence 4678999999999999999988866654422 22 4455566688888 79999999999985
No 16
>PF07719 TPR_2: Tetratricopeptide repeat; InterPro: IPR013105 The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [, , ]. It mediates protein-protein interactions and the assembly of multiprotein complexes []. The TPR motif consists of 3-16 tandem-repeats of 34 amino acids residues, although individual TPR motifs can be dispersed in the protein sequence. Sequence alignment of the TPR domains reveals a consensus sequence defined by a pattern of small and large amino acids. TPR motifs have been identified in various different organisms, ranging from bacteria to humans. Proteins containing TPRs are involved in a variety of biological processes, such as cell cycle regulation, transcriptional control, mitochondrial and peroxisomal protein transport, neurogenesis and protein folding. This repeat includes outlying Tetratricopeptide-like repeats (TPR) that are not matched by IPR001440 from INTERPRO.; PDB: 1XNF_B 3Q15_A 4ABN_A 1OUV_A 3U4T_A 3MA5_C 2KCV_A 2KCL_A 2XEV_A 3NF1_A ....
Probab=76.04 E-value=7.9 Score=22.46 Aligned_cols=28 Identities=14% Similarity=-0.064 Sum_probs=22.5
Q ss_pred HHHHHHHHHHhcCCHHHHHHHHHHHHHH
Q 047859 79 LQCAVGFYHLFNQNHKGAMMELGEGLGK 106 (214)
Q Consensus 79 IQlAvAl~H~~rGN~~GA~~Ll~rAl~~ 106 (214)
+....|..+...|++..|+..+++|+..
T Consensus 3 ~~~~lg~~~~~~~~~~~A~~~~~~al~l 30 (34)
T PF07719_consen 3 AWYYLGQAYYQLGNYEEAIEYFEKALEL 30 (34)
T ss_dssp HHHHHHHHHHHTT-HHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHhCCHHHHHHHHHHHHHH
Confidence 3456688899999999999999999854
No 17
>PF13374 TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT_H 3NF1_A.
Probab=71.47 E-value=14 Score=21.99 Aligned_cols=32 Identities=13% Similarity=-0.038 Sum_probs=23.8
Q ss_pred HHHHHHHHHHhcCCHHHHHHHHHHHHHHHhhc
Q 047859 79 LQCAVGFYHLFNQNHKGAMMELGEGLGKLRKM 110 (214)
Q Consensus 79 IQlAvAl~H~~rGN~~GA~~Ll~rAl~~L~~~ 110 (214)
++--.|..+..+|++..|..++++++..-++.
T Consensus 4 ~~~~la~~~~~~g~~~~A~~~~~~al~~~~~~ 35 (42)
T PF13374_consen 4 ALNNLANAYRAQGRYEEALELLEEALEIRERL 35 (42)
T ss_dssp HHHHHHHHHHHCT-HHHHHHHHHHHHHHH---
T ss_pred HHHHHHHHHHhhhhcchhhHHHHHHHHHHHHH
Confidence 34556778888999999999999999887765
No 18
>PF13428 TPR_14: Tetratricopeptide repeat
Probab=71.18 E-value=10 Score=24.15 Aligned_cols=27 Identities=15% Similarity=-0.182 Sum_probs=22.5
Q ss_pred HHHHHHHHHhcCCHHHHHHHHHHHHHH
Q 047859 80 QCAVGFYHLFNQNHKGAMMELGEGLGK 106 (214)
Q Consensus 80 QlAvAl~H~~rGN~~GA~~Ll~rAl~~ 106 (214)
+..-|-.+.+.|++..|.+++++++..
T Consensus 4 ~~~la~~~~~~G~~~~A~~~~~~~l~~ 30 (44)
T PF13428_consen 4 WLALARAYRRLGQPDEAERLLRRALAL 30 (44)
T ss_pred HHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence 345577889999999999999999864
No 19
>PRK10866 outer membrane biogenesis protein BamD; Provisional
Probab=68.46 E-value=37 Score=29.74 Aligned_cols=70 Identities=10% Similarity=-0.059 Sum_probs=54.7
Q ss_pred CCCcchhHHHHHHHhccCCchhhhhhhHHhhccCCcchhhHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHH
Q 047859 34 NDGENCSFDEAVALFNERAYYKCHDCLESLWYTAEEPTRTLIHGVLQCAVGFYHLFNQNHKGAMMELGEGLGK 106 (214)
Q Consensus 34 ~~e~~~~l~~gi~LFN~G~YfEAHEVLEe~Wk~~~g~er~~lqGLIQlAvAl~H~~rGN~~GA~~Ll~rAl~~ 106 (214)
+......|..|..+++.|+|=+|=+.+|.+=...|+. ...-++ ++-.|..|.+.++...|...+++.+..
T Consensus 29 ~~~~~~~Y~~A~~~~~~g~y~~Ai~~f~~l~~~yP~s-~~a~~a--~l~la~ayy~~~~y~~A~~~~e~fi~~ 98 (243)
T PRK10866 29 DNPPSEIYATAQQKLQDGNWKQAITQLEALDNRYPFG-PYSQQV--QLDLIYAYYKNADLPLAQAAIDRFIRL 98 (243)
T ss_pred CCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCC-hHHHHH--HHHHHHHHHhcCCHHHHHHHHHHHHHh
Confidence 3456778899999999999999999999987766644 333444 555666777889999999999988653
No 20
>PLN03088 SGT1, suppressor of G2 allele of SKP1; Provisional
Probab=68.15 E-value=24 Score=32.50 Aligned_cols=27 Identities=15% Similarity=0.047 Sum_probs=13.2
Q ss_pred HHHHHHHhccCCchhhhhhhHHhhccC
Q 047859 41 FDEAVALFNERAYYKCHDCLESLWYTA 67 (214)
Q Consensus 41 l~~gi~LFN~G~YfEAHEVLEe~Wk~~ 67 (214)
+..|..+|..|+|-+|-+.++.+-...
T Consensus 6 ~~~a~~a~~~~~~~~Ai~~~~~Al~~~ 32 (356)
T PLN03088 6 EDKAKEAFVDDDFALAVDLYTQAIDLD 32 (356)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHHHHhC
Confidence 344555555555555555555444433
No 21
>PF13371 TPR_9: Tetratricopeptide repeat
Probab=66.25 E-value=8 Score=26.16 Aligned_cols=29 Identities=21% Similarity=0.171 Sum_probs=13.5
Q ss_pred hHHHHHHHhccCCchhhhhhhHHhhccCC
Q 047859 40 SFDEAVALFNERAYYKCHDCLESLWYTAE 68 (214)
Q Consensus 40 ~l~~gi~LFN~G~YfEAHEVLEe~Wk~~~ 68 (214)
-+..|..++..|+|=+|.+.|+.++...|
T Consensus 32 ~~~~a~~~~~~g~~~~A~~~l~~~l~~~p 60 (73)
T PF13371_consen 32 WLQRARCLFQLGRYEEALEDLERALELSP 60 (73)
T ss_pred hHHHHHHHHHhccHHHHHHHHHHHHHHCC
Confidence 33344444444444444444444444444
No 22
>PF13371 TPR_9: Tetratricopeptide repeat
Probab=65.47 E-value=30 Score=23.26 Aligned_cols=55 Identities=13% Similarity=0.079 Sum_probs=41.7
Q ss_pred HHHhccCCchhhhhhhHHhhccCCcchhhHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 047859 45 VALFNERAYYKCHDCLESLWYTAEEPTRTLIHGVLQCAVGFYHLFNQNHKGAMMELGEGLG 105 (214)
Q Consensus 45 i~LFN~G~YfEAHEVLEe~Wk~~~g~er~~lqGLIQlAvAl~H~~rGN~~GA~~Ll~rAl~ 105 (214)
..+++.++|=+|-+++|.+=...|.+-. .....|..+...|++..|+..+.+++.
T Consensus 3 ~~~~~~~~~~~A~~~~~~~l~~~p~~~~------~~~~~a~~~~~~g~~~~A~~~l~~~l~ 57 (73)
T PF13371_consen 3 QIYLQQEDYEEALEVLERALELDPDDPE------LWLQRARCLFQLGRYEEALEDLERALE 57 (73)
T ss_pred HHHHhCCCHHHHHHHHHHHHHhCcccch------hhHHHHHHHHHhccHHHHHHHHHHHHH
Confidence 3568899999999999988776664222 223356677888999999999999984
No 23
>PF03704 BTAD: Bacterial transcriptional activator domain; InterPro: IPR005158 Found in the DNRI/REDD/AFSR family of regulators, this region of AFSR (P25941 from SWISSPROT) along with the C-terminal region is capable of independently directing actinorhodin production. It is important for the formation of secondary metabolites.; PDB: 2FF4_B 2FEZ_A.
Probab=64.60 E-value=53 Score=25.32 Aligned_cols=57 Identities=11% Similarity=0.042 Sum_probs=28.6
Q ss_pred HhccCCchhhhhhhHHhhccCCcchhhHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHhh
Q 047859 47 LFNERAYYKCHDCLESLWYTAEEPTRTLIHGVLQCAVGFYHLFNQNHKGAMMELGEGLGKLRK 109 (214)
Q Consensus 47 LFN~G~YfEAHEVLEe~Wk~~~g~er~~lqGLIQlAvAl~H~~rGN~~GA~~Ll~rAl~~L~~ 109 (214)
+...|+|-+|-+.++.+=...| -...+++.||++ +...||...|.+.+++....|..
T Consensus 72 ~~~~~~~~~a~~~~~~~l~~dP-~~E~~~~~lm~~-----~~~~g~~~~A~~~Y~~~~~~l~~ 128 (146)
T PF03704_consen 72 LLEAGDYEEALRLLQRALALDP-YDEEAYRLLMRA-----LAAQGRRAEALRVYERYRRRLRE 128 (146)
T ss_dssp HHHTT-HHHHHHHHHHHHHHST-T-HHHHHHHHHH-----HHHTT-HHHHHHHHHHHHHHHHH
T ss_pred HHhccCHHHHHHHHHHHHhcCC-CCHHHHHHHHHH-----HHHCcCHHHHHHHHHHHHHHHHH
Confidence 3345555555555544332222 233455555553 33556667777777766666653
No 24
>PRK10803 tol-pal system protein YbgF; Provisional
Probab=62.50 E-value=41 Score=30.10 Aligned_cols=71 Identities=10% Similarity=0.089 Sum_probs=52.2
Q ss_pred CCCcchhHHHHHHH-hccCCchhhhhhhHHhhccCCcchhhHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHH
Q 047859 34 NDGENCSFDEAVAL-FNERAYYKCHDCLESLWYTAEEPTRTLIHGVLQCAVGFYHLFNQNHKGAMMELGEGLGKL 107 (214)
Q Consensus 34 ~~e~~~~l~~gi~L-FN~G~YfEAHEVLEe~Wk~~~g~er~~lqGLIQlAvAl~H~~rGN~~GA~~Ll~rAl~~L 107 (214)
+.++...|..|+.+ ++.|+|-+|-+.|+.+=+..|... +..-.+.-.|..++..|++..|...|++.+.+.
T Consensus 139 ~~~e~~~Y~~A~~l~~~~~~y~~Ai~af~~fl~~yP~s~---~a~~A~y~LG~~y~~~g~~~~A~~~f~~vv~~y 210 (263)
T PRK10803 139 SGDANTDYNAAIALVQDKSRQDDAIVAFQNFVKKYPDST---YQPNANYWLGQLNYNKGKKDDAAYYFASVVKNY 210 (263)
T ss_pred CCCHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHCcCCc---chHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHC
Confidence 44567889999998 678999999999999888877431 222223344455567899999999998877543
No 25
>cd00189 TPR Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and C
Probab=61.93 E-value=35 Score=21.40 Aligned_cols=62 Identities=11% Similarity=0.084 Sum_probs=42.6
Q ss_pred chhHHHHHHHhccCCchhhhhhhHHhhccCCcchhhHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 047859 38 NCSFDEAVALFNERAYYKCHDCLESLWYTAEEPTRTLIHGVLQCAVGFYHLFNQNHKGAMMELGEGLG 105 (214)
Q Consensus 38 ~~~l~~gi~LFN~G~YfEAHEVLEe~Wk~~~g~er~~lqGLIQlAvAl~H~~rGN~~GA~~Ll~rAl~ 105 (214)
..-+..|..++..++|-+|.+.++..=...+... -+....|..+...|+...|...+.+++.
T Consensus 35 ~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~a~~~~~~~~~ 96 (100)
T cd00189 35 DAYYNLAAAYYKLGKYEEALEDYEKALELDPDNA------KAYYNLGLAYYKLGKYEEALEAYEKALE 96 (100)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcch------hHHHHHHHHHHHHHhHHHHHHHHHHHHc
Confidence 3455677778888999999998887544443222 2234445567778889999988887764
No 26
>COG3898 Uncharacterized membrane-bound protein [Function unknown]
Probab=61.40 E-value=27 Score=34.57 Aligned_cols=135 Identities=19% Similarity=0.257 Sum_probs=78.5
Q ss_pred cchhHHHHHHHhccCCchhhhhhhHHhhccCCcchhhHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHhhccCCCCC
Q 047859 37 ENCSFDEAVALFNERAYYKCHDCLESLWYTAEEPTRTLIHGVLQCAVGFYHLFNQNHKGAMMELGEGLGKLRKMNLRSGP 116 (214)
Q Consensus 37 ~~~~l~~gi~LFN~G~YfEAHEVLEe~Wk~~~g~er~~lqGLIQlAvAl~H~~rGN~~GA~~Ll~rAl~~L~~~~~~~~p 116 (214)
....+..+-.||.+|.-..+--+||-.||..|.| ++|-.+.|.+.|. .+.--++|+ ++|..+. |
T Consensus 263 vPaav~AAralf~d~~~rKg~~ilE~aWK~ePHP---------~ia~lY~~ar~gd--ta~dRlkRa-~~L~slk----~ 326 (531)
T COG3898 263 VPAAVVAARALFRDGNLRKGSKILETAWKAEPHP---------DIALLYVRARSGD--TALDRLKRA-KKLESLK----P 326 (531)
T ss_pred chHHHHHHHHHHhccchhhhhhHHHHHHhcCCCh---------HHHHHHHHhcCCC--cHHHHHHHH-HHHHhcC----c
Confidence 3556788999999999999999999999998865 2555666777776 344444554 3555542 1
Q ss_pred CcccccCHHHHHHHHHHhhHHHHhcccCceeeecCcchhHHhhhcccccC---c---------eeeeccCC----CCceE
Q 047859 117 FHEFENEISAALEFIYRTQIELAACADDICLAMDQSERSYQLLGDYAAGQ---Q---------LYHLESDH----NQIMY 180 (214)
Q Consensus 117 ~~~~GvDV~aLl~~i~~l~~Elaa~~~d~~l~~dgs~~~~~~Lg~~~~g~---~---------~~~~~~~~----~~~~~ 180 (214)
.. ..-...-...-++......+...-.....++.+++-|-+|.+...-+ + -.+---|| |++.+
T Consensus 327 nn-aes~~~va~aAlda~e~~~ARa~Aeaa~r~~pres~~lLlAdIeeAetGDqg~vR~wlAqav~APrdPaW~adg~vs 405 (531)
T COG3898 327 NN-AESSLAVAEAALDAGEFSAARAKAEAAAREAPRESAYLLLADIEEAETGDQGKVRQWLAQAVKAPRDPAWTADGVVS 405 (531)
T ss_pred cc-hHHHHHHHHHHHhccchHHHHHHHHHHhhhCchhhHHHHHHHHHhhccCchHHHHHHHHHHhcCCCCCcccccCccc
Confidence 10 00001111222222222222223333445667777787777554321 1 11111244 78999
Q ss_pred EEEcCCCC
Q 047859 181 IVFDPQRS 188 (214)
Q Consensus 181 i~~~~~~~ 188 (214)
-.|.|.+.
T Consensus 406 e~wapvsp 413 (531)
T COG3898 406 EAWAPVSP 413 (531)
T ss_pred ccccccCC
Confidence 99999886
No 27
>PRK15331 chaperone protein SicA; Provisional
Probab=58.86 E-value=21 Score=30.62 Aligned_cols=67 Identities=9% Similarity=0.027 Sum_probs=53.6
Q ss_pred CCCcchhHHHHHHHhccCCchhhhhhhHHhhccCCcchhhHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHH
Q 047859 34 NDGENCSFDEAVALFNERAYYKCHDCLESLWYTAEEPTRTLIHGVLQCAVGFYHLFNQNHKGAMMELGEGLGK 106 (214)
Q Consensus 34 ~~e~~~~l~~gi~LFN~G~YfEAHEVLEe~Wk~~~g~er~~lqGLIQlAvAl~H~~rGN~~GA~~Ll~rAl~~ 106 (214)
+.+.+..+..|..+|+.|+|=+|+-++--+=.-.+.. .++|.|| |..+...+++..|..++..|.-.
T Consensus 34 ~~~le~iY~~Ay~~y~~Gk~~eA~~~F~~L~~~d~~n-~~Y~~GL-----aa~~Q~~k~y~~Ai~~Y~~A~~l 100 (165)
T PRK15331 34 QDMMDGLYAHAYEFYNQGRLDEAETFFRFLCIYDFYN-PDYTMGL-----AAVCQLKKQFQKACDLYAVAFTL 100 (165)
T ss_pred HHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCcCc-HHHHHHH-----HHHHHHHHHHHHHHHHHHHHHHc
Confidence 3357788999999999999999999998877654433 4577666 55677789999999999999753
No 28
>PF14559 TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN_B 3QOU_A 3ASG_A 3ASD_A 3AS5_A 3AS4_A 3ASH_B 3FP3_A 3LCA_A ....
Probab=58.69 E-value=18 Score=24.09 Aligned_cols=53 Identities=15% Similarity=0.013 Sum_probs=37.3
Q ss_pred HhccCCchhhhhhhHHhhccCCcchhhHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 047859 47 LFNERAYYKCHDCLESLWYTAEEPTRTLIHGVLQCAVGFYHLFNQNHKGAMMELGEGLG 105 (214)
Q Consensus 47 LFN~G~YfEAHEVLEe~Wk~~~g~er~~lqGLIQlAvAl~H~~rGN~~GA~~Ll~rAl~ 105 (214)
|+..|+|=+|=+.++.++...|+... .+.. .|....+.|++..|..++.+.+.
T Consensus 1 ll~~~~~~~A~~~~~~~l~~~p~~~~-~~~~-----la~~~~~~g~~~~A~~~l~~~~~ 53 (68)
T PF14559_consen 1 LLKQGDYDEAIELLEKALQRNPDNPE-ARLL-----LAQCYLKQGQYDEAEELLERLLK 53 (68)
T ss_dssp HHHTTHHHHHHHHHHHHHHHTTTSHH-HHHH-----HHHHHHHTT-HHHHHHHHHCCHG
T ss_pred ChhccCHHHHHHHHHHHHHHCCCCHH-HHHH-----HHHHHHHcCCHHHHHHHHHHHHH
Confidence 45678888999999999998775433 2223 34455678999999988887654
No 29
>TIGR03302 OM_YfiO outer membrane assembly lipoprotein YfiO. Members of this protein family include YfiO, a near-essential protein of the outer membrane, part of a complex involved in protein insertion into the bacterial outer membrane. Many proteins in this family are annotated as ComL, based on the involvement of this protein in natural transformation with exogenous DNA in Neisseria gonorrhoeae. This protein family shows sequence similarity to, but is distinct from, the tol-pal system protein YbgF (TIGR02795).
Probab=58.23 E-value=48 Score=27.30 Aligned_cols=67 Identities=9% Similarity=0.044 Sum_probs=48.9
Q ss_pred hHHHHHHHhcc--------CCchhhhhhhHHhhccCCcchhhHHHHHH------------HHHHHHHHHhcCCHHHHHHH
Q 047859 40 SFDEAVALFNE--------RAYYKCHDCLESLWYTAEEPTRTLIHGVL------------QCAVGFYHLFNQNHKGAMME 99 (214)
Q Consensus 40 ~l~~gi~LFN~--------G~YfEAHEVLEe~Wk~~~g~er~~lqGLI------------QlAvAl~H~~rGN~~GA~~L 99 (214)
.+..|..+|+. |++=+|-+.++.+....|.... .++.+. +.+.|.++..+|++..|...
T Consensus 110 ~~~~g~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~p~~~~-~~~a~~~~~~~~~~~~~~~~~~a~~~~~~g~~~~A~~~ 188 (235)
T TIGR03302 110 YYLRGLSNYNQIDRVDRDQTAAREAFEAFQELIRRYPNSEY-APDAKKRMDYLRNRLAGKELYVARFYLKRGAYVAAINR 188 (235)
T ss_pred HHHHHHHHHHhcccccCCHHHHHHHHHHHHHHHHHCCCChh-HHHHHHHHHHHHHHHHHHHHHHHHHHHHcCChHHHHHH
Confidence 46667777765 7888899999999888774321 122222 24678889999999999999
Q ss_pred HHHHHHHH
Q 047859 100 LGEGLGKL 107 (214)
Q Consensus 100 l~rAl~~L 107 (214)
+++++...
T Consensus 189 ~~~al~~~ 196 (235)
T TIGR03302 189 FETVVENY 196 (235)
T ss_pred HHHHHHHC
Confidence 99988653
No 30
>PF13512 TPR_18: Tetratricopeptide repeat
Probab=56.55 E-value=73 Score=26.61 Aligned_cols=68 Identities=12% Similarity=0.041 Sum_probs=54.4
Q ss_pred CCCcchhHHHHHHHhccCCchhhhhhhHHhhccCCcchhhHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 047859 34 NDGENCSFDEAVALFNERAYYKCHDCLESLWYTAEEPTRTLIHGVLQCAVGFYHLFNQNHKGAMMELGEGL 104 (214)
Q Consensus 34 ~~e~~~~l~~gi~LFN~G~YfEAHEVLEe~Wk~~~g~er~~lqGLIQlAvAl~H~~rGN~~GA~~Ll~rAl 104 (214)
+.....-+.+|...+..|.|-+|-+.||.+=..-|..+ +---.|+-.+..+..++++..|+..+.+=+
T Consensus 7 ~~~~~~ly~~a~~~l~~~~Y~~A~~~le~L~~ryP~g~---ya~qAqL~l~yayy~~~~y~~A~a~~~rFi 74 (142)
T PF13512_consen 7 DKSPQELYQEAQEALQKGNYEEAIKQLEALDTRYPFGE---YAEQAQLDLAYAYYKQGDYEEAIAAYDRFI 74 (142)
T ss_pred CCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHhcCCCCc---ccHHHHHHHHHHHHHccCHHHHHHHHHHHH
Confidence 44567889999999999999999999999888777321 223566777788899999999998887654
No 31
>PF09976 TPR_21: Tetratricopeptide repeat; InterPro: IPR018704 This domain, found in various hypothetical prokaryotic proteins, has no known function.
Probab=56.31 E-value=43 Score=26.17 Aligned_cols=62 Identities=15% Similarity=0.132 Sum_probs=38.6
Q ss_pred chhHHHHHHHhccCCchhhhhhhHHhhccCCcchhhHHHHHHHHHHHHHHHhcCCHHHHHHHHHH
Q 047859 38 NCSFDEAVALFNERAYYKCHDCLESLWYTAEEPTRTLIHGVLQCAVGFYHLFNQNHKGAMMELGE 102 (214)
Q Consensus 38 ~~~l~~gi~LFN~G~YfEAHEVLEe~Wk~~~g~er~~lqGLIQlAvAl~H~~rGN~~GA~~Ll~r 102 (214)
...|..|-.+|..|+|=+|-+.|+.+=...+ ..-++.++.+-.|......|++..|...+..
T Consensus 49 ~A~l~lA~~~~~~g~~~~A~~~l~~~~~~~~---d~~l~~~a~l~LA~~~~~~~~~d~Al~~L~~ 110 (145)
T PF09976_consen 49 LAALQLAKAAYEQGDYDEAKAALEKALANAP---DPELKPLARLRLARILLQQGQYDEALATLQQ 110 (145)
T ss_pred HHHHHHHHHHHHCCCHHHHHHHHHHHHhhCC---CHHHHHHHHHHHHHHHHHcCCHHHHHHHHHh
Confidence 4456667777777777777777776554332 2244555555555666677777777777654
No 32
>CHL00033 ycf3 photosystem I assembly protein Ycf3
Probab=53.84 E-value=83 Score=24.96 Aligned_cols=67 Identities=13% Similarity=0.155 Sum_probs=49.7
Q ss_pred cchhHHHHHHHhccCCchhhhhhhHHhhccCCcchhhHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHH
Q 047859 37 ENCSFDEAVALFNERAYYKCHDCLESLWYTAEEPTRTLIHGVLQCAVGFYHLFNQNHKGAMMELGEGLGK 106 (214)
Q Consensus 37 ~~~~l~~gi~LFN~G~YfEAHEVLEe~Wk~~~g~er~~lqGLIQlAvAl~H~~rGN~~GA~~Ll~rAl~~ 106 (214)
...-+..|..++..|+|=+|.+.++..=...+++ ...+.+....|+.+...|+...|...+++|+..
T Consensus 35 a~~~~~~g~~~~~~g~~~~A~~~~~~al~l~~~~---~~~~~~~~~lg~~~~~~g~~~eA~~~~~~Al~~ 101 (168)
T CHL00033 35 AFTYYRDGMSAQSEGEYAEALQNYYEAMRLEIDP---YDRSYILYNIGLIHTSNGEHTKALEYYFQALER 101 (168)
T ss_pred HHHHHHHHHHHHHcCCHHHHHHHHHHHHhccccc---hhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence 3445677888888999999999988754332222 223446677788888899999999999999864
No 33
>PRK15359 type III secretion system chaperone protein SscB; Provisional
Probab=53.69 E-value=61 Score=25.67 Aligned_cols=65 Identities=8% Similarity=-0.040 Sum_probs=48.4
Q ss_pred CcchhHHHHHHHhccCCchhhhhhhHHhhccCCcchhhHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHH
Q 047859 36 GENCSFDEAVALFNERAYYKCHDCLESLWYTAEEPTRTLIHGVLQCAVGFYHLFNQNHKGAMMELGEGLGK 106 (214)
Q Consensus 36 e~~~~l~~gi~LFN~G~YfEAHEVLEe~Wk~~~g~er~~lqGLIQlAvAl~H~~rGN~~GA~~Ll~rAl~~ 106 (214)
+...-+.-|..+...|+|-+|-+.++......++.... + ...|..+.+.|+...|...+.+|+..
T Consensus 57 ~~~a~~~lg~~~~~~g~~~~A~~~y~~Al~l~p~~~~a----~--~~lg~~l~~~g~~~eAi~~~~~Al~~ 121 (144)
T PRK15359 57 SWRAHIALAGTWMMLKEYTTAINFYGHALMLDASHPEP----V--YQTGVCLKMMGEPGLAREAFQTAIKM 121 (144)
T ss_pred cHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCCCcHH----H--HHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence 34455667788888999999999999999877743222 2 22244566789999999999999753
No 34
>TIGR02917 PEP_TPR_lipo putative PEP-CTERM system TPR-repeat lipoprotein. This protein family occurs in strictly within a subset of Gram-negative bacterial species with the proposed PEP-CTERM/exosortase system, analogous to the LPXTG/sortase system common in Gram-positive bacteria. This protein occurs in a species if and only if a transmembrane histidine kinase (TIGR02916) and a DNA-binding response regulator (TIGR02915) also occur. The present of tetratricopeptide repeats (TPR) suggests protein-protein interaction, possibly for the regulation of PEP-CTERM protein expression, since many PEP-CTERM proteins in these genomes are preceded by a proposed DNA binding site for the response regulator.
Probab=52.28 E-value=57 Score=30.85 Aligned_cols=64 Identities=14% Similarity=0.099 Sum_probs=49.7
Q ss_pred CcchhHHHHHHHhccCCchhhhhhhHHhhccCCcchhhHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 047859 36 GENCSFDEAVALFNERAYYKCHDCLESLWYTAEEPTRTLIHGVLQCAVGFYHLFNQNHKGAMMELGEGLG 105 (214)
Q Consensus 36 e~~~~l~~gi~LFN~G~YfEAHEVLEe~Wk~~~g~er~~lqGLIQlAvAl~H~~rGN~~GA~~Ll~rAl~ 105 (214)
..+..+..|..+++.|+|-+|-..++...+..|.... .....|......|++..|...+++++.
T Consensus 21 ~~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~p~~~~------~~~~l~~~~~~~g~~~~A~~~~~~~~~ 84 (899)
T TIGR02917 21 SPESLIEAAKSYLQKNKYKAAIIQLKNALQKDPNDAE------ARFLLGKIYLALGDYAAAEKELRKALS 84 (899)
T ss_pred CHHHHHHHHHHHHHcCChHhHHHHHHHHHHhCCCCHH------HHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence 4567899999999999999999999999988774221 122234555667999999999998865
No 35
>PRK15363 pathogenicity island 2 chaperone protein SscA; Provisional
Probab=51.43 E-value=42 Score=28.47 Aligned_cols=64 Identities=11% Similarity=0.048 Sum_probs=51.7
Q ss_pred CcchhHHHHHHHhccCCchhhhhhhHHhhccCCcchhhHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 047859 36 GENCSFDEAVALFNERAYYKCHDCLESLWYTAEEPTRTLIHGVLQCAVGFYHLFNQNHKGAMMELGEGLG 105 (214)
Q Consensus 36 e~~~~l~~gi~LFN~G~YfEAHEVLEe~Wk~~~g~er~~lqGLIQlAvAl~H~~rGN~~GA~~Ll~rAl~ 105 (214)
+.+.-+..|..+++.|+|=+|+.+++-+=+-.+ ....+|-|| |+.+.+.|++..|...+.+|..
T Consensus 34 ~l~~lY~~A~~ly~~G~l~~A~~~f~~L~~~Dp-~~~~y~~gL-----G~~~Q~~g~~~~AI~aY~~A~~ 97 (157)
T PRK15363 34 PLNTLYRYAMQLMEVKEFAGAARLFQLLTIYDA-WSFDYWFRL-----GECCQAQKHWGEAIYAYGRAAQ 97 (157)
T ss_pred HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCc-ccHHHHHHH-----HHHHHHHhhHHHHHHHHHHHHh
Confidence 456788899999999999999999998766543 233455555 7788899999999999999974
No 36
>PF03704 BTAD: Bacterial transcriptional activator domain; InterPro: IPR005158 Found in the DNRI/REDD/AFSR family of regulators, this region of AFSR (P25941 from SWISSPROT) along with the C-terminal region is capable of independently directing actinorhodin production. It is important for the formation of secondary metabolites.; PDB: 2FF4_B 2FEZ_A.
Probab=50.13 E-value=28 Score=26.85 Aligned_cols=64 Identities=19% Similarity=0.183 Sum_probs=38.8
Q ss_pred cchhHHHHHHHhccCCchhhhhhhHHhhccCC--cchhhHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 047859 37 ENCSFDEAVALFNERAYYKCHDCLESLWYTAE--EPTRTLIHGVLQCAVGFYHLFNQNHKGAMMELGEGLG 105 (214)
Q Consensus 37 ~~~~l~~gi~LFN~G~YfEAHEVLEe~Wk~~~--g~er~~lqGLIQlAvAl~H~~rGN~~GA~~Ll~rAl~ 105 (214)
....+.+++.+|. |+|+.-.+. .-|.... .-++.++..+.+++. .+...|++..|..++.+++.
T Consensus 25 ~~~~~~~al~ly~-G~~l~~~~~--~~W~~~~r~~l~~~~~~~~~~l~~--~~~~~~~~~~a~~~~~~~l~ 90 (146)
T PF03704_consen 25 AIELLEEALALYR-GDFLPDLDD--EEWVEPERERLRELYLDALERLAE--ALLEAGDYEEALRLLQRALA 90 (146)
T ss_dssp HHHHHHHHHTT---SSTTGGGTT--STTHHHHHHHHHHHHHHHHHHHHH--HHHHTT-HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHhC-CCCCCCCCc--cHHHHHHHHHHHHHHHHHHHHHHH--HHHhccCHHHHHHHHHHHHh
Confidence 3456777777776 778876555 4455432 123334444444444 56788999999999998874
No 37
>KOG3581 consensus Creatine kinases [Energy production and conversion]
Probab=49.59 E-value=10 Score=35.97 Aligned_cols=30 Identities=27% Similarity=0.436 Sum_probs=26.2
Q ss_pred eEEEEcCCCCCCCCCCCceeeccccccchh
Q 047859 179 MYIVFDPQRSYGSDDKSIKVKLPTLNATEE 208 (214)
Q Consensus 179 ~~i~~~~~~~~~~~~~~~~~klp~~~~~~~ 208 (214)
-+|+|||++-..+-..++.+|||.|++-+.
T Consensus 271 G~ltfCPsNLGT~~RasVHIklPkls~~~~ 300 (363)
T KOG3581|consen 271 GYLTFCPSNLGTTLRASVHIKLPKLSKDPD 300 (363)
T ss_pred cceeecccccccceeeeEEEecccccccch
Confidence 489999999888888889999999998754
No 38
>PF12895 Apc3: Anaphase-promoting complex, cyclosome, subunit 3; PDB: 3KAE_D 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2XPI_A 3ULQ_A.
Probab=48.86 E-value=55 Score=23.02 Aligned_cols=58 Identities=14% Similarity=0.095 Sum_probs=38.4
Q ss_pred hhHHHHHHHhccCCchhhhhhhHHhhccCCcchhhHHHHHHHHHHHHHHHhcCCHHHHHHHHHHH
Q 047859 39 CSFDEAVALFNERAYYKCHDCLESLWYTAEEPTRTLIHGVLQCAVGFYHLFNQNHKGAMMELGEG 103 (214)
Q Consensus 39 ~~l~~gi~LFN~G~YfEAHEVLEe~Wk~~~g~er~~lqGLIQlAvAl~H~~rGN~~GA~~Ll~rA 103 (214)
-.+.-|..+|+.|+|-+|=+++.. ... ++ + .......+ |.-+...|++..|+..+.+|
T Consensus 27 ~~~~la~~~~~~~~y~~A~~~~~~--~~~-~~-~-~~~~~~l~--a~~~~~l~~y~eAi~~l~~~ 84 (84)
T PF12895_consen 27 YLYNLAQCYFQQGKYEEAIELLQK--LKL-DP-S-NPDIHYLL--ARCLLKLGKYEEAIKALEKA 84 (84)
T ss_dssp HHHHHHHHHHHTTHHHHHHHHHHC--HTH-HH-C-HHHHHHHH--HHHHHHTT-HHHHHHHHHHH
T ss_pred HHHHHHHHHHHCCCHHHHHHHHHH--hCC-CC-C-CHHHHHHH--HHHHHHhCCHHHHHHHHhcC
Confidence 344459999999999999888877 211 11 1 12222222 56677889999999998875
No 39
>PF13176 TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_A 3RO2_A.
Probab=47.59 E-value=45 Score=20.45 Aligned_cols=24 Identities=13% Similarity=0.045 Sum_probs=19.6
Q ss_pred HHHHHHHhcCCHHHHHHHHHHHHH
Q 047859 82 AVGFYHLFNQNHKGAMMELGEGLG 105 (214)
Q Consensus 82 AvAl~H~~rGN~~GA~~Ll~rAl~ 105 (214)
..|-.|.+.|++..|+..+++++.
T Consensus 4 ~Lg~~~~~~g~~~~Ai~~y~~aL~ 27 (36)
T PF13176_consen 4 NLGRIYRQQGDYEKAIEYYEQALA 27 (36)
T ss_dssp HHHHHHHHCT-HHHHHHHHHHHHH
T ss_pred HHHHHHHHcCCHHHHHHHHHHHHH
Confidence 346678999999999999999883
No 40
>TIGR02521 type_IV_pilW type IV pilus biogenesis/stability protein PilW. Members of this family are designated PilF in ref (PubMed:8973346) and PilW in ref (PubMed:15612916). This outer membrane protein is required both for pilus stability and for pilus function such as adherence to human cells. Members of this family contain copies of the TPR (tetratricopeptide repeat) domain.
Probab=46.30 E-value=1.3e+02 Score=23.12 Aligned_cols=63 Identities=10% Similarity=0.020 Sum_probs=41.5
Q ss_pred chhHHHHHHHhccCCchhhhhhhHHhhccCCcchhhHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHH
Q 047859 38 NCSFDEAVALFNERAYYKCHDCLESLWYTAEEPTRTLIHGVLQCAVGFYHLFNQNHKGAMMELGEGLGK 106 (214)
Q Consensus 38 ~~~l~~gi~LFN~G~YfEAHEVLEe~Wk~~~g~er~~lqGLIQlAvAl~H~~rGN~~GA~~Ll~rAl~~ 106 (214)
...+..|..++..|+|=+|-+.++..=...+.. .......|..+...|++..|...+++++..
T Consensus 32 ~~~~~la~~~~~~~~~~~A~~~~~~~l~~~p~~------~~~~~~la~~~~~~~~~~~A~~~~~~al~~ 94 (234)
T TIGR02521 32 KIRVQLALGYLEQGDLEVAKENLDKALEHDPDD------YLAYLALALYYQQLGELEKAEDSFRRALTL 94 (234)
T ss_pred HHHHHHHHHHHHCCCHHHHHHHHHHHHHhCccc------HHHHHHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence 445666788888888888888888753332221 122333456667778888888888887754
No 41
>TIGR02552 LcrH_SycD type III secretion low calcium response chaperone LcrH/SycD. ScyD/LcrH contains three central tetratricopeptide-like repeats that are predicted to fold into an all-alpha-helical array.
Probab=46.14 E-value=1.1e+02 Score=22.77 Aligned_cols=60 Identities=10% Similarity=-0.064 Sum_probs=27.9
Q ss_pred hHHHHHHHhccCCchhhhhhhHHhhccCCcchhhHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 047859 40 SFDEAVALFNERAYYKCHDCLESLWYTAEEPTRTLIHGVLQCAVGFYHLFNQNHKGAMMELGEGLG 105 (214)
Q Consensus 40 ~l~~gi~LFN~G~YfEAHEVLEe~Wk~~~g~er~~lqGLIQlAvAl~H~~rGN~~GA~~Ll~rAl~ 105 (214)
.+..|..++..|+|=+|.++++.+=...+.. .... .--|..+...|++..|...+++++.
T Consensus 54 ~~~la~~~~~~~~~~~A~~~~~~~~~~~p~~----~~~~--~~la~~~~~~g~~~~A~~~~~~al~ 113 (135)
T TIGR02552 54 WLGLAACCQMLKEYEEAIDAYALAAALDPDD----PRPY--FHAAECLLALGEPESALKALDLAIE 113 (135)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhcCCCC----hHHH--HHHHHHHHHcCCHHHHHHHHHHHHH
Confidence 3344445555555555555555433322211 1111 1122344455666666666666654
No 42
>TIGR02521 type_IV_pilW type IV pilus biogenesis/stability protein PilW. Members of this family are designated PilF in ref (PubMed:8973346) and PilW in ref (PubMed:15612916). This outer membrane protein is required both for pilus stability and for pilus function such as adherence to human cells. Members of this family contain copies of the TPR (tetratricopeptide repeat) domain.
Probab=45.56 E-value=1.2e+02 Score=23.28 Aligned_cols=62 Identities=10% Similarity=0.022 Sum_probs=44.0
Q ss_pred chhHHHHHHHhccCCchhhhhhhHHhhccCCcchhhHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 047859 38 NCSFDEAVALFNERAYYKCHDCLESLWYTAEEPTRTLIHGVLQCAVGFYHLFNQNHKGAMMELGEGLG 105 (214)
Q Consensus 38 ~~~l~~gi~LFN~G~YfEAHEVLEe~Wk~~~g~er~~lqGLIQlAvAl~H~~rGN~~GA~~Ll~rAl~ 105 (214)
......|..++..|+|=+|-+.++..-...+.... +....|......|++..|...+.+++.
T Consensus 66 ~~~~~la~~~~~~~~~~~A~~~~~~al~~~~~~~~------~~~~~~~~~~~~g~~~~A~~~~~~~~~ 127 (234)
T TIGR02521 66 LAYLALALYYQQLGELEKAEDSFRRALTLNPNNGD------VLNNYGTFLCQQGKYEQAMQQFEQAIE 127 (234)
T ss_pred HHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCCHH------HHHHHHHHHHHcccHHHHHHHHHHHHh
Confidence 34456778888899999999999988776553221 222234455678888888888888875
No 43
>PF07721 TPR_4: Tetratricopeptide repeat; InterPro: IPR011717 This entry includes tetratricopeptide-like repeats not detected by the IPR001440 from INTERPRO, IPR013105 from INTERPRO and IPR011716 from INTERPRO models. The tetratricopeptide repeat (TPR) motif is a protein-protein interaction module found in multiple copies in a number of functionally different proteins that facilitates specific interactions with a partner protein(s) [].; GO: 0042802 identical protein binding
Probab=45.11 E-value=34 Score=19.81 Aligned_cols=23 Identities=17% Similarity=-0.013 Sum_probs=17.8
Q ss_pred HHHHHHHHHhcCCHHHHHHHHHH
Q 047859 80 QCAVGFYHLFNQNHKGAMMELGE 102 (214)
Q Consensus 80 QlAvAl~H~~rGN~~GA~~Ll~r 102 (214)
++.-|..|+..|++..|.+++++
T Consensus 4 ~~~la~~~~~~G~~~eA~~~l~~ 26 (26)
T PF07721_consen 4 RLALARALLAQGDPDEAERLLRR 26 (26)
T ss_pred HHHHHHHHHHcCCHHHHHHHHhC
Confidence 34557788899999999988763
No 44
>KOG1840 consensus Kinesin light chain [Cytoskeleton]
Probab=44.41 E-value=1.1e+02 Score=30.51 Aligned_cols=84 Identities=11% Similarity=-0.020 Sum_probs=61.0
Q ss_pred HHHHHhccCCchhhhhhhHHhhccCC--cchhhHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHhhccCCCCCCccc
Q 047859 43 EAVALFNERAYYKCHDCLESLWYTAE--EPTRTLIHGVLQCAVGFYHLFNQNHKGAMMELGEGLGKLRKMNLRSGPFHEF 120 (214)
Q Consensus 43 ~gi~LFN~G~YfEAHEVLEe~Wk~~~--g~er~~lqGLIQlAvAl~H~~rGN~~GA~~Ll~rAl~~L~~~~~~~~p~~~~ 120 (214)
-+..++.+|+|=.|++.++..=.... ...+....+-.+-..|+++...++++-|..++.+|+..+... +
T Consensus 205 La~~y~~~g~~e~A~~l~k~Al~~l~k~~G~~hl~va~~l~~~a~~y~~~~k~~eAv~ly~~AL~i~e~~---------~ 275 (508)
T KOG1840|consen 205 LAEMYAVQGRLEKAEPLCKQALRILEKTSGLKHLVVASMLNILALVYRSLGKYDEAVNLYEEALTIREEV---------F 275 (508)
T ss_pred HHHHHHHhccHHHHHHHHHHHHHHHHHccCccCHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHh---------c
Confidence 45667779999999988776544422 113445555555578999999999999999999999999876 5
Q ss_pred ccCHHHHHHHHHHhh
Q 047859 121 ENEISAALEFIYRTQ 135 (214)
Q Consensus 121 GvDV~aLl~~i~~l~ 135 (214)
|-+-.++...+.++.
T Consensus 276 G~~h~~va~~l~nLa 290 (508)
T KOG1840|consen 276 GEDHPAVAATLNNLA 290 (508)
T ss_pred CCCCHHHHHHHHHHH
Confidence 666666666665544
No 45
>PRK04841 transcriptional regulator MalT; Provisional
Probab=43.72 E-value=75 Score=31.80 Aligned_cols=68 Identities=3% Similarity=-0.187 Sum_probs=44.1
Q ss_pred HHHHHhccCCchhhhhhhHHhhccCCcchhhHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHhhc
Q 047859 43 EAVALFNERAYYKCHDCLESLWYTAEEPTRTLIHGVLQCAVGFYHLFNQNHKGAMMELGEGLGKLRKM 110 (214)
Q Consensus 43 ~gi~LFN~G~YfEAHEVLEe~Wk~~~g~er~~lqGLIQlAvAl~H~~rGN~~GA~~Ll~rAl~~L~~~ 110 (214)
.|..++..|+|-+|-+.++...............+......|..+...|++..|...+++++......
T Consensus 497 lg~~~~~~G~~~~A~~~~~~al~~~~~~g~~~~~~~~~~~la~~~~~~G~~~~A~~~~~~al~~~~~~ 564 (903)
T PRK04841 497 LGEVHHCKGELARALAMMQQTEQMARQHDVYHYALWSLLQQSEILFAQGFLQAAYETQEKAFQLIEEQ 564 (903)
T ss_pred HHHHHHHcCCHHHHHHHHHHHHHHHhhhcchHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHh
Confidence 34556668888888777777665444211122222333444666788999999999999998876654
No 46
>PLN03088 SGT1, suppressor of G2 allele of SKP1; Provisional
Probab=43.36 E-value=1.1e+02 Score=28.26 Aligned_cols=64 Identities=13% Similarity=-0.018 Sum_probs=48.5
Q ss_pred cchhHHHHHHHhccCCchhhhhhhHHhhccCCcchhhHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHH
Q 047859 37 ENCSFDEAVALFNERAYYKCHDCLESLWYTAEEPTRTLIHGVLQCAVGFYHLFNQNHKGAMMELGEGLGK 106 (214)
Q Consensus 37 ~~~~l~~gi~LFN~G~YfEAHEVLEe~Wk~~~g~er~~lqGLIQlAvAl~H~~rGN~~GA~~Ll~rAl~~ 106 (214)
...-+..|..++..|+|=+|-..++.+....+.. ..+..++ |..+...|++..|...+++|+..
T Consensus 36 ~~a~~~~a~~~~~~g~~~eAl~~~~~Al~l~P~~----~~a~~~l--g~~~~~lg~~~eA~~~~~~al~l 99 (356)
T PLN03088 36 AELYADRAQANIKLGNFTEAVADANKAIELDPSL----AKAYLRK--GTACMKLEEYQTAKAALEKGASL 99 (356)
T ss_pred HHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcCC----HHHHHHH--HHHHHHhCCHHHHHHHHHHHHHh
Confidence 4455677888889999999999999998876643 2233344 44556679999999999999853
No 47
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=43.01 E-value=1.1e+02 Score=26.89 Aligned_cols=53 Identities=9% Similarity=0.016 Sum_probs=24.5
Q ss_pred HHhccCCchhhhhhhHHhhccCCcchhhHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 047859 46 ALFNERAYYKCHDCLESLWYTAEEPTRTLIHGVLQCAVGFYHLFNQNHKGAMMELGEGL 104 (214)
Q Consensus 46 ~LFN~G~YfEAHEVLEe~Wk~~~g~er~~lqGLIQlAvAl~H~~rGN~~GA~~Ll~rAl 104 (214)
.++..|++=+|-+.++.+....+.. .+. ....|..+.+.|++..|..+++++.
T Consensus 189 ~~~~~~~~~~A~~~~~~al~~~p~~----~~~--~~~la~~~~~~g~~~~A~~~~~~~~ 241 (389)
T PRK11788 189 QALARGDLDAARALLKKALAADPQC----VRA--SILLGDLALAQGDYAAAIEALERVE 241 (389)
T ss_pred HHHhCCCHHHHHHHHHHHHhHCcCC----HHH--HHHHHHHHHHCCCHHHHHHHHHHHH
Confidence 3444555555555555555443321 111 1222333444555555555555554
No 48
>TIGR02917 PEP_TPR_lipo putative PEP-CTERM system TPR-repeat lipoprotein. This protein family occurs in strictly within a subset of Gram-negative bacterial species with the proposed PEP-CTERM/exosortase system, analogous to the LPXTG/sortase system common in Gram-positive bacteria. This protein occurs in a species if and only if a transmembrane histidine kinase (TIGR02916) and a DNA-binding response regulator (TIGR02915) also occur. The present of tetratricopeptide repeats (TPR) suggests protein-protein interaction, possibly for the regulation of PEP-CTERM protein expression, since many PEP-CTERM proteins in these genomes are preceded by a proposed DNA binding site for the response regulator.
Probab=42.14 E-value=70 Score=30.28 Aligned_cols=56 Identities=16% Similarity=0.064 Sum_probs=30.4
Q ss_pred HHHHHhccCCchhhhhhhHHhhccCCcchhhHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 047859 43 EAVALFNERAYYKCHDCLESLWYTAEEPTRTLIHGVLQCAVGFYHLFNQNHKGAMMELGEGL 104 (214)
Q Consensus 43 ~gi~LFN~G~YfEAHEVLEe~Wk~~~g~er~~lqGLIQlAvAl~H~~rGN~~GA~~Ll~rAl 104 (214)
-|..++..|+|=+|.+.++.++...+.+. -+....+......|+...|..++++.+
T Consensus 843 ~~~~~~~~g~~~~A~~~~~~a~~~~~~~~------~~~~~l~~~~~~~g~~~~A~~~~~~~~ 898 (899)
T TIGR02917 843 LGWLLVEKGEADRALPLLRKAVNIAPEAA------AIRYHLALALLATGRKAEARKELDKLL 898 (899)
T ss_pred HHHHHHHcCCHHHHHHHHHHHHhhCCCCh------HHHHHHHHHHHHcCCHHHHHHHHHHHh
Confidence 34455566666666666666666554311 122223444455666666666666554
No 49
>TIGR00540 hemY_coli hemY protein. This is an uncharacterized protein encoded next to a heme-biosynthetic enzyme in two gamma division proteobacteria (E. coli and H. influenzae). It is known in no other species. The gene symbol hemY is unfortunate in that an unrelated protein, protoporphyrinogen oxidase, is designated as HemG in E. coli but as HemY in Bacillus subtilis.
Probab=41.96 E-value=87 Score=28.92 Aligned_cols=64 Identities=8% Similarity=0.048 Sum_probs=49.3
Q ss_pred HHHHHHHhccCCchhhhhhhH--HhhccCCcchhhHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHhhcc
Q 047859 41 FDEAVALFNERAYYKCHDCLE--SLWYTAEEPTRTLIHGVLQCAVGFYHLFNQNHKGAMMELGEGLGKLRKMN 111 (214)
Q Consensus 41 l~~gi~LFN~G~YfEAHEVLE--e~Wk~~~g~er~~lqGLIQlAvAl~H~~rGN~~GA~~Ll~rAl~~L~~~~ 111 (214)
..-|..+|..|+|=+|.+.|| ......|+++. + ..-|...++.|+...|..++++|+..+-..+
T Consensus 339 ~sLg~l~~~~~~~~~A~~~le~a~a~~~~p~~~~--~-----~~La~ll~~~g~~~~A~~~~~~~l~~~~~~~ 404 (409)
T TIGR00540 339 RALGQLLMKHGEFIEAADAFKNVAACKEQLDAND--L-----AMAADAFDQAGDKAEAAAMRQDSLGLMLAIQ 404 (409)
T ss_pred HHHHHHHHHcccHHHHHHHHHHhHHhhcCCCHHH--H-----HHHHHHHHHcCCHHHHHHHHHHHHHHHhccc
Confidence 367888999999999999999 57776654432 1 1336677888999999999999988876653
No 50
>cd05804 StaR_like StaR_like; a well-conserved protein found in bacteria, plants, and animals. A family member from Streptomyces toyocaensis, StaR is part of a gene cluster involved in the biosynthesis of glycopeptide antibiotics (GPAs), specifically A47934. It has been speculated that StaR could be a flavoprotein hydroxylating a tyrosine sidechain. Some family members have been annotated as proteins containing tetratricopeptide (TPR) repeats, which may at least indicate mostly alpha-helical secondary structure.
Probab=41.73 E-value=81 Score=27.42 Aligned_cols=58 Identities=10% Similarity=-0.021 Sum_probs=36.8
Q ss_pred HHHHHHhccCCchhhhhhhHHhhccCCcchhhHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 047859 42 DEAVALFNERAYYKCHDCLESLWYTAEEPTRTLIHGVLQCAVGFYHLFNQNHKGAMMELGEGLG 105 (214)
Q Consensus 42 ~~gi~LFN~G~YfEAHEVLEe~Wk~~~g~er~~lqGLIQlAvAl~H~~rGN~~GA~~Ll~rAl~ 105 (214)
..|..+...|+|=+|.+.++..-...+.. ..+....|..+.+.|+++.|...+.+++.
T Consensus 119 ~~a~~~~~~G~~~~A~~~~~~al~~~p~~------~~~~~~la~i~~~~g~~~eA~~~l~~~l~ 176 (355)
T cd05804 119 MLAFGLEEAGQYDRAEEAARRALELNPDD------AWAVHAVAHVLEMQGRFKEGIAFMESWRD 176 (355)
T ss_pred HHHHHHHHcCCHHHHHHHHHHHHhhCCCC------cHHHHHHHHHHHHcCCHHHHHHHHHhhhh
Confidence 44556777888888888888877765533 22233344455566777777777666654
No 51
>PF00515 TPR_1: Tetratricopeptide repeat; InterPro: IPR001440 The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [, , ]. It mediates protein-protein interactions and the assembly of multiprotein complexes []. The TPR motif consists of 3-16 tandem-repeats of 34 amino acids residues, although individual TPR motifs can be dispersed in the protein sequence. Sequence alignment of the TPR domains reveals a consensus sequence defined by a pattern of small and large amino acids. TPR motifs have been identified in various different organisms, ranging from bacteria to humans. Proteins containing TPRs are involved in a variety of biological processes, such as cell cycle regulation, transcriptional control, mitochondrial and peroxisomal protein transport, neurogenesis and protein folding. The X-ray structure of a domain containing three TPRs from protein phosphatase 5 revealed that TPR adopts a helix-turn-helix arrangement, with adjacent TPR motifs packing in a parallel fashion, resulting in a spiral of repeating anti-parallel alpha-helices []. The two helices are denoted helix A and helix B. The packing angle between helix A and helix B is ~24 degrees; within a single TPR and generates a right-handed superhelical shape. Helix A interacts with helix B and with helix A' of the next TPR. Two protein surfaces are generated: the inner concave surface is contributed to mainly by residue on helices A, and the other surface presents residues from both helices A and B. ; GO: 0005515 protein binding; PDB: 3SF4_C 2LNI_A 1ELW_A 2C0M_A 1FCH_B 3R9A_B 2J9Q_A 2C0L_A 1KT1_A 3FWV_A ....
Probab=41.64 E-value=51 Score=19.21 Aligned_cols=25 Identities=12% Similarity=-0.025 Sum_probs=20.0
Q ss_pred HHHHHHHhcCCHHHHHHHHHHHHHH
Q 047859 82 AVGFYHLFNQNHKGAMMELGEGLGK 106 (214)
Q Consensus 82 AvAl~H~~rGN~~GA~~Ll~rAl~~ 106 (214)
-.|..+...|++..|..-+++|++.
T Consensus 6 ~~g~~~~~~~~~~~A~~~~~~al~~ 30 (34)
T PF00515_consen 6 NLGNAYFQLGDYEEALEYYQRALEL 30 (34)
T ss_dssp HHHHHHHHTT-HHHHHHHHHHHHHH
T ss_pred HHHHHHHHhCCchHHHHHHHHHHHH
Confidence 3467788899999999999999864
No 52
>PF13174 TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_A 3URZ_B 2Q7F_A.
Probab=41.51 E-value=64 Score=18.23 Aligned_cols=27 Identities=7% Similarity=-0.006 Sum_probs=18.5
Q ss_pred HHHHHHHHHHHhcCCHHHHHHHHHHHHHH
Q 047859 78 VLQCAVGFYHLFNQNHKGAMMELGEGLGK 106 (214)
Q Consensus 78 LIQlAvAl~H~~rGN~~GA~~Ll~rAl~~ 106 (214)
+.++|.+. ...|++..|...+++.+..
T Consensus 3 ~~~~a~~~--~~~g~~~~A~~~~~~~~~~ 29 (33)
T PF13174_consen 3 LYRLARCY--YKLGDYDEAIEYFQRLIKR 29 (33)
T ss_dssp HHHHHHHH--HHHCHHHHHHHHHHHHHHH
T ss_pred HHHHHHHH--HHccCHHHHHHHHHHHHHH
Confidence 44444444 4579999999999877653
No 53
>PF06212 GRIM-19: GRIM-19 protein; InterPro: IPR009346 This family consists of several eukaryotic gene associated with retinoic-interferon-induced mortality 19 (GRIM-19) proteins. GRIM-19, was reported to encode a small protein primarily distributed in the nucleus and was able to promote cell death induced by IFN-beta and RA. A bovine homologue of GRIM-19 was co-purified with mitochondrial NADH:ubiquinone oxidoreductase (complex I) in bovine heart. Therefore, its exact cellular localisation and function are unclear. It has now been discovered that GRIM-19 is a specific interacting protein which negatively regulates Stat3 activity [].
Probab=40.37 E-value=95 Score=25.57 Aligned_cols=78 Identities=15% Similarity=0.241 Sum_probs=51.8
Q ss_pred hhHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHhhccCCCCCCcccccCHHHHHHHHHHhh--HHHHhcccCceeee
Q 047859 72 RTLIHGVLQCAVGFYHLFNQNHKGAMMELGEGLGKLRKMNLRSGPFHEFENEISAALEFIYRTQ--IELAACADDICLAM 149 (214)
Q Consensus 72 r~~lqGLIQlAvAl~H~~rGN~~GA~~Ll~rAl~~L~~~~~~~~p~~~~GvDV~aLl~~i~~l~--~Elaa~~~d~~l~~ 149 (214)
.-|.-++.-++.|+|..-.||..--....++--.++.-. |+-....|-.-|...-..+. +++....+
T Consensus 33 ~~~~~~~~~~~~G~y~~~~~~r~~r~~~~E~~~ar~al~-----PlLqAE~DR~~lr~~~~~~~~E~~lMkdVp------ 101 (130)
T PF06212_consen 33 TMFAGGAGIMAYGFYKVGQGNRERRELKREKRWARIALL-----PLLQAEEDRRYLRRLKANREEEAELMKDVP------ 101 (130)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHh-----HHHHHHHHHHHHHHHHHHHHHHHHHhCCCC------
Confidence 335556666899999999998777666666666666655 45445566666666555555 45555544
Q ss_pred cCcchhHHhhhcccccCceeee
Q 047859 150 DQSERSYQLLGDYAAGQQLYHL 171 (214)
Q Consensus 150 dgs~~~~~~Lg~~~~g~~~~~~ 171 (214)
++.+|+.+|+-
T Consensus 102 -----------gW~vGe~vY~t 112 (130)
T PF06212_consen 102 -----------GWKVGEPVYNT 112 (130)
T ss_pred -----------CCcCCCCcccC
Confidence 67779888876
No 54
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=39.15 E-value=1.2e+02 Score=26.66 Aligned_cols=63 Identities=11% Similarity=-0.033 Sum_probs=44.6
Q ss_pred hhHHHHHHHhccCCchhhhhhhHHhhccCCcchhhHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHH
Q 047859 39 CSFDEAVALFNERAYYKCHDCLESLWYTAEEPTRTLIHGVLQCAVGFYHLFNQNHKGAMMELGEGLGK 106 (214)
Q Consensus 39 ~~l~~gi~LFN~G~YfEAHEVLEe~Wk~~~g~er~~lqGLIQlAvAl~H~~rGN~~GA~~Ll~rAl~~ 106 (214)
..+.-|..++..|+|=+|.+.++.++...+......+ ...+..+...|++..|...+++++..
T Consensus 216 ~~~~la~~~~~~g~~~~A~~~~~~~~~~~p~~~~~~~-----~~l~~~~~~~g~~~~A~~~l~~~~~~ 278 (389)
T PRK11788 216 ASILLGDLALAQGDYAAAIEALERVEEQDPEYLSEVL-----PKLMECYQALGDEAEGLEFLRRALEE 278 (389)
T ss_pred HHHHHHHHHHHCCCHHHHHHHHHHHHHHChhhHHHHH-----HHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence 4455667778899999999999999986543222222 22333456789999999999988754
No 55
>COG5010 TadD Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking and secretion]
Probab=38.53 E-value=1.3e+02 Score=27.58 Aligned_cols=67 Identities=7% Similarity=-0.086 Sum_probs=48.9
Q ss_pred cchhHH--HHHHHhccCCchhhhhhhHHhhccCCcchhhHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHhh
Q 047859 37 ENCSFD--EAVALFNERAYYKCHDCLESLWYTAEEPTRTLIHGVLQCAVGFYHLFNQNHKGAMMELGEGLGKLRK 109 (214)
Q Consensus 37 ~~~~l~--~gi~LFN~G~YfEAHEVLEe~Wk~~~g~er~~lqGLIQlAvAl~H~~rGN~~GA~~Ll~rAl~~L~~ 109 (214)
++..+. .|..+|++|+|.+|=.++-.+=.-.| ++-.+|.++ |.--.++|+..+|++-+.+|++..-.
T Consensus 98 ~d~~ll~~~gk~~~~~g~~~~A~~~~rkA~~l~p-~d~~~~~~l-----gaaldq~Gr~~~Ar~ay~qAl~L~~~ 166 (257)
T COG5010 98 KDRELLAAQGKNQIRNGNFGEAVSVLRKAARLAP-TDWEAWNLL-----GAALDQLGRFDEARRAYRQALELAPN 166 (257)
T ss_pred ccHHHHHHHHHHHHHhcchHHHHHHHHHHhccCC-CChhhhhHH-----HHHHHHccChhHHHHHHHHHHHhccC
Confidence 555666 99999999999999999887655544 233344443 33336889999999999999866543
No 56
>TIGR00208 fliS flagellar biosynthetic protein FliS. The function of this protein in flagellar biosynthesis is unknown, but appears to be regulatory. The member of this family in Vibrio parahaemolyticus is designated FlaJ (creating a synonym for FliS) and was shown essential for flagellin biosynthesis.
Probab=37.58 E-value=1.7e+02 Score=23.37 Aligned_cols=38 Identities=16% Similarity=0.199 Sum_probs=33.6
Q ss_pred HHHHHHH-HHHHHHHHhcCCHHHHHHHHHHHHHHHhhcc
Q 047859 74 LIHGVLQ-CAVGFYHLFNQNHKGAMMELGEGLGKLRKMN 111 (214)
Q Consensus 74 ~lqGLIQ-lAvAl~H~~rGN~~GA~~Ll~rAl~~L~~~~ 111 (214)
++.|+|+ +..|..+.++|+...+...+.||...|..+.
T Consensus 27 Lydg~i~~l~~a~~ai~~~d~~~~~~~i~ka~~Ii~eL~ 65 (124)
T TIGR00208 27 LYNGCLKFIRLAAQAIENDDIERKNENLIKAQNIIQELN 65 (124)
T ss_pred HHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHH
Confidence 7888888 7777888999999999999999999998763
No 57
>PF09613 HrpB1_HrpK: Bacterial type III secretion protein (HrpB1_HrpK); InterPro: IPR013394 This family of proteins is encoded by genes found within type III secretion operons in a limited range of species including Xanthomonas, Ralstonia and Burkholderia.
Probab=36.56 E-value=47 Score=28.31 Aligned_cols=25 Identities=24% Similarity=0.288 Sum_probs=20.8
Q ss_pred HHHHHHHHHHhcCCHHHHHHHHHHH
Q 047859 79 LQCAVGFYHLFNQNHKGAMMELGEG 103 (214)
Q Consensus 79 IQlAvAl~H~~rGN~~GA~~Ll~rA 103 (214)
+.+.-|..|.+||||.+|+++++..
T Consensus 46 ~~~~~~~l~i~r~~w~dA~rlLr~l 70 (160)
T PF09613_consen 46 LDLFDGWLHIVRGDWDDALRLLREL 70 (160)
T ss_pred HHHHHHHHHHHhCCHHHHHHHHHHH
Confidence 3455677899999999999999975
No 58
>PHA02103 hypothetical protein
Probab=35.38 E-value=11 Score=31.01 Aligned_cols=36 Identities=25% Similarity=0.669 Sum_probs=22.5
Q ss_pred cccceeeeeeecccCCCCCCCcchhHHHHHHHhc-cCCchhhhhh
Q 047859 16 NFKSFRVLYRYSAKEEDDNDGENCSFDEAVALFN-ERAYYKCHDC 59 (214)
Q Consensus 16 ~~~~~~~~~~~~~~~~~~~~e~~~~l~~gi~LFN-~G~YfEAHEV 59 (214)
.|.-|+=-||||-.+++ .+| -|. -|. .|.+|.|||.
T Consensus 74 df~~ipdyyryf~ee~e-~ie---~we----~ygve~l~~p~he~ 110 (135)
T PHA02103 74 DFNHIPDYYRYFGEEAE-GVE---LWE----EYGVEGLCWPCHEC 110 (135)
T ss_pred ccccChHHHHHhcccch-hhh---HHH----HhCcceeeeccccc
Confidence 35556667999986655 322 121 122 7889999984
No 59
>PF11672 DUF3268: Protein of unknown function (DUF3268); InterPro: IPR021686 This entry is represented by Listeria phage P100, Gp150. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=35.24 E-value=38 Score=26.90 Aligned_cols=34 Identities=12% Similarity=0.277 Sum_probs=22.9
Q ss_pred cchhHHHHHHHhccCCchhhhhhhHHhhccCCcchhhHHHHH
Q 047859 37 ENCSFDEAVALFNERAYYKCHDCLESLWYTAEEPTRTLIHGV 78 (214)
Q Consensus 37 ~~~~l~~gi~LFN~G~YfEAHEVLEe~Wk~~~g~er~~lqGL 78 (214)
-++.++.+- -+||.+|+.+|+...-.+.+.++=|
T Consensus 55 Ad~~lR~~R--------~~ah~~fd~lw~~~~~~R~~aY~wL 88 (102)
T PF11672_consen 55 ADAELRRAR--------KAAHRAFDPLWQSGHMSRSDAYRWL 88 (102)
T ss_pred CCHHHHHHH--------HHHHHHHHHHHHhCcccHHHHHHHH
Confidence 356676664 4799999999997654454444433
No 60
>TIGR02552 LcrH_SycD type III secretion low calcium response chaperone LcrH/SycD. ScyD/LcrH contains three central tetratricopeptide-like repeats that are predicted to fold into an all-alpha-helical array.
Probab=33.92 E-value=1.9e+02 Score=21.42 Aligned_cols=64 Identities=9% Similarity=0.006 Sum_probs=44.0
Q ss_pred cchhHHHHHHHhccCCchhhhhhhHHhhccCCcchhhHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHH
Q 047859 37 ENCSFDEAVALFNERAYYKCHDCLESLWYTAEEPTRTLIHGVLQCAVGFYHLFNQNHKGAMMELGEGLGK 106 (214)
Q Consensus 37 ~~~~l~~gi~LFN~G~YfEAHEVLEe~Wk~~~g~er~~lqGLIQlAvAl~H~~rGN~~GA~~Ll~rAl~~ 106 (214)
....+..|..++..|+|=+|.+.++.+=...+ ....++..+ |......|++..|...+.+++..
T Consensus 17 ~~~~~~~a~~~~~~~~~~~A~~~~~~~~~~~p-~~~~~~~~l-----a~~~~~~~~~~~A~~~~~~~~~~ 80 (135)
T TIGR02552 17 LEQIYALAYNLYQQGRYDEALKLFQLLAAYDP-YNSRYWLGL-----AACCQMLKEYEEAIDAYALAAAL 80 (135)
T ss_pred HHHHHHHHHHHHHcccHHHHHHHHHHHHHhCC-CcHHHHHHH-----HHHHHHHHHHHHHHHHHHHHHhc
Confidence 45578889999999999999999988633333 223333333 33334458888999999887753
No 61
>PF13424 TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15_A 3ASG_A 3ASD_A 3AS5_A 3AS4_A 3ASH_B 4A1S_B 3CEQ_B 3EDT_H ....
Probab=33.85 E-value=1.5e+02 Score=20.10 Aligned_cols=34 Identities=6% Similarity=-0.182 Sum_probs=26.6
Q ss_pred HHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHhhc
Q 047859 77 GVLQCAVGFYHLFNQNHKGAMMELGEGLGKLRKM 110 (214)
Q Consensus 77 GLIQlAvAl~H~~rGN~~GA~~Ll~rAl~~L~~~ 110 (214)
+-+..-.|..+...|++.-|...+.+|+...+..
T Consensus 5 a~~~~~la~~~~~~~~~~~A~~~~~~al~~~~~~ 38 (78)
T PF13424_consen 5 ANAYNNLARVYRELGRYDEALDYYEKALDIEEQL 38 (78)
T ss_dssp HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHT
T ss_pred HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHH
Confidence 3445566778889999999999999999996555
No 62
>PF13181 TPR_8: Tetratricopeptide repeat; PDB: 3GW4_B 3MA5_C 2KCV_A 2KCL_A 3FP3_A 3LCA_A 3FP4_A 3FP2_A 1W3B_B 1ELW_A ....
Probab=33.58 E-value=98 Score=17.80 Aligned_cols=25 Identities=12% Similarity=-0.032 Sum_probs=20.8
Q ss_pred HHHHHHHhcCCHHHHHHHHHHHHHH
Q 047859 82 AVGFYHLFNQNHKGAMMELGEGLGK 106 (214)
Q Consensus 82 AvAl~H~~rGN~~GA~~Ll~rAl~~ 106 (214)
..|..+...|+...|...++++++.
T Consensus 6 ~lg~~y~~~~~~~~A~~~~~~a~~~ 30 (34)
T PF13181_consen 6 NLGKIYEQLGDYEEALEYFEKALEL 30 (34)
T ss_dssp HHHHHHHHTTSHHHHHHHHHHHHHH
T ss_pred HHHHHHHHcCCHHHHHHHHHHHHhh
Confidence 3466778899999999999999853
No 63
>PF13414 TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2PL2_B 3IEG_B 2FBN_A ....
Probab=33.51 E-value=90 Score=20.67 Aligned_cols=28 Identities=7% Similarity=0.011 Sum_probs=23.3
Q ss_pred HHHHHHHHHHhcCCHHHHHHHHHHHHHH
Q 047859 79 LQCAVGFYHLFNQNHKGAMMELGEGLGK 106 (214)
Q Consensus 79 IQlAvAl~H~~rGN~~GA~~Ll~rAl~~ 106 (214)
+..-.|..+...|++..|...+.+|+..
T Consensus 5 ~~~~~g~~~~~~~~~~~A~~~~~~ai~~ 32 (69)
T PF13414_consen 5 AWYNLGQIYFQQGDYEEAIEYFEKAIEL 32 (69)
T ss_dssp HHHHHHHHHHHTTHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHcCCHHHHHHHHHHHHHc
Confidence 3445677888899999999999999975
No 64
>PRK11189 lipoprotein NlpI; Provisional
Probab=32.93 E-value=1.3e+02 Score=26.52 Aligned_cols=62 Identities=19% Similarity=0.169 Sum_probs=40.6
Q ss_pred chhHHHHHHHhccCCchhhhhhhHHhhccCCcc-hhhHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHH
Q 047859 38 NCSFDEAVALFNERAYYKCHDCLESLWYTAEEP-TRTLIHGVLQCAVGFYHLFNQNHKGAMMELGEGLGKL 107 (214)
Q Consensus 38 ~~~l~~gi~LFN~G~YfEAHEVLEe~Wk~~~g~-er~~lqGLIQlAvAl~H~~rGN~~GA~~Ll~rAl~~L 107 (214)
..-+..|+.++..|+|=+|.+.++......|.+ .+.+|.. .+...++...|...+.++...+
T Consensus 133 ~a~~~lg~~l~~~g~~~eA~~~~~~al~~~P~~~~~~~~~~--------l~~~~~~~~~A~~~l~~~~~~~ 195 (296)
T PRK11189 133 YAYLNRGIALYYGGRYELAQDDLLAFYQDDPNDPYRALWLY--------LAESKLDPKQAKENLKQRYEKL 195 (296)
T ss_pred HHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHHHHHHHH--------HHHccCCHHHHHHHHHHHHhhC
Confidence 344667777888888888888888888877643 2222221 1234677888888887765443
No 65
>PRK10747 putative protoheme IX biogenesis protein; Provisional
Probab=32.84 E-value=1.7e+02 Score=27.00 Aligned_cols=65 Identities=6% Similarity=-0.158 Sum_probs=50.3
Q ss_pred CcchhHHHHHHHhccCCchhhhhhhHHhhccCCcchhhHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHH
Q 047859 36 GENCSFDEAVALFNERAYYKCHDCLESLWYTAEEPTRTLIHGVLQCAVGFYHLFNQNHKGAMMELGEGLGKL 107 (214)
Q Consensus 36 e~~~~l~~gi~LFN~G~YfEAHEVLEe~Wk~~~g~er~~lqGLIQlAvAl~H~~rGN~~GA~~Ll~rAl~~L 107 (214)
+..-.+..|..+...++|=+|.+.||..+...|++..-. .-+..+.+.|+...|...+++|+...
T Consensus 327 ~~~l~l~lgrl~~~~~~~~~A~~~le~al~~~P~~~~~~-------~La~~~~~~g~~~~A~~~~~~~l~~~ 391 (398)
T PRK10747 327 TPLLWSTLGQLLMKHGEWQEASLAFRAALKQRPDAYDYA-------WLADALDRLHKPEEAAAMRRDGLMLT 391 (398)
T ss_pred CHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCHHHHH-------HHHHHHHHcCCHHHHHHHHHHHHhhh
Confidence 445567889999999999999999999999876543312 22444567899999999999998744
No 66
>cd00716 creatine_kinase_like Phosphagen (guanidino) kinases such as creatine kinase and similar enzymes. Eukaryotic creatine kinase-like phosphagen (guanidino) kinases are enzymes that transphosphorylate a high energy phosphoguanidino compound, like phosphocreatine (PCr) in the case of creatine kinase (CK), which is used as an energy-storage and -transport metabolite, to ADP, thereby creating ATP. The substrate binding site is located in the cleft between the N and C-terminal domains, but most of the catalytic residues are found in the larger C-terminal domain. In higher eukaryotes, CKs are found as tissue-specific (muscle, brain), as well as compartment-specific (mitochondrial, cytosolic, and flagellar) isoforms. Mitochondrial and cytoplasmic CKs are dimeric or octameric, while the flagellar isoforms are trimers with three CD domains fused as a single protein chain. CKs are either coupled to glycolysis (cytosolic form) or oxidative phosphorylation (mitochondrial form). Besides CK, one
Probab=32.08 E-value=29 Score=33.04 Aligned_cols=30 Identities=27% Similarity=0.328 Sum_probs=26.1
Q ss_pred eEEEEcCCCCCCCCCCCceeeccccccchh
Q 047859 179 MYIVFDPQRSYGSDDKSIKVKLPTLNATEE 208 (214)
Q Consensus 179 ~~i~~~~~~~~~~~~~~~~~klp~~~~~~~ 208 (214)
-++++||++-..+-..+.-||||.|..+.+
T Consensus 262 GYLTsCPTNlGTGlRASV~i~LP~L~~~~~ 291 (357)
T cd00716 262 GYVLTCPSNLGTGLRASVHVKLPNLSKDPR 291 (357)
T ss_pred eEeeeCCCCCCcccEEEEEEEccccccchh
Confidence 489999999988888888999999998754
No 67
>cd05804 StaR_like StaR_like; a well-conserved protein found in bacteria, plants, and animals. A family member from Streptomyces toyocaensis, StaR is part of a gene cluster involved in the biosynthesis of glycopeptide antibiotics (GPAs), specifically A47934. It has been speculated that StaR could be a flavoprotein hydroxylating a tyrosine sidechain. Some family members have been annotated as proteins containing tetratricopeptide (TPR) repeats, which may at least indicate mostly alpha-helical secondary structure.
Probab=31.28 E-value=2.7e+02 Score=24.20 Aligned_cols=69 Identities=20% Similarity=0.108 Sum_probs=47.8
Q ss_pred HHHHHHhccCCchhhhhhhHHhhccCCc---chhhHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHhhc
Q 047859 42 DEAVALFNERAYYKCHDCLESLWYTAEE---PTRTLIHGVLQCAVGFYHLFNQNHKGAMMELGEGLGKLRKM 110 (214)
Q Consensus 42 ~~gi~LFN~G~YfEAHEVLEe~Wk~~~g---~er~~lqGLIQlAvAl~H~~rGN~~GA~~Ll~rAl~~L~~~ 110 (214)
..+..+-..|++-+|...|+.+=..... .......--+.+.-|+..+..||+..|.+++..|+..-..+
T Consensus 269 ~~a~~~~~~~~~~~a~~~L~~l~~~~~~~~~~~~~~~~~~~~~l~A~~~~~~g~~~~A~~~L~~al~~a~~~ 340 (355)
T cd05804 269 HAALALAGAGDKDALDKLLAALKGRASSADDNKQPARDVGLPLAEALYAFAEGNYATALELLGPVRDDLARI 340 (355)
T ss_pred HHHHHHhcCCCHHHHHHHHHHHHHHHhccCchhhhHHhhhHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHh
Confidence 3444455577787888888776332222 22223344556788889999999999999999999887665
No 68
>PRK15179 Vi polysaccharide biosynthesis protein TviE; Provisional
Probab=31.10 E-value=1.2e+02 Score=31.23 Aligned_cols=66 Identities=15% Similarity=-0.053 Sum_probs=48.2
Q ss_pred CcchhHHHHHHHhccCCchhhhhhhHHhhccCCcchhhHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHH
Q 047859 36 GENCSFDEAVALFNERAYYKCHDCLESLWYTAEEPTRTLIHGVLQCAVGFYHLFNQNHKGAMMELGEGLGKL 107 (214)
Q Consensus 36 e~~~~l~~gi~LFN~G~YfEAHEVLEe~Wk~~~g~er~~lqGLIQlAvAl~H~~rGN~~GA~~Ll~rAl~~L 107 (214)
+....+..|..|=..|+|=||.++++.+=...+++.. +++.-|.-+..+|....|...|++|+...
T Consensus 153 ~~~~~~~~a~~l~~~g~~~~A~~~y~~~~~~~p~~~~------~~~~~a~~l~~~G~~~~A~~~~~~a~~~~ 218 (694)
T PRK15179 153 SAREILLEAKSWDEIGQSEQADACFERLSRQHPEFEN------GYVGWAQSLTRRGALWRARDVLQAGLDAI 218 (694)
T ss_pred CHHHHHHHHHHHHHhcchHHHHHHHHHHHhcCCCcHH------HHHHHHHHHHHcCCHHHHHHHHHHHHHhh
Confidence 5567788888888899999999999998774443322 22334555667788888888888886554
No 69
>smart00028 TPR Tetratricopeptide repeats. Repeats present in 4 or more copies in proteins. Contain a minimum of 34 amino acids each and self-associate via a "knobs and holes" mechanism.
Probab=30.19 E-value=71 Score=16.09 Aligned_cols=22 Identities=18% Similarity=0.004 Sum_probs=17.3
Q ss_pred HHHHHhcCCHHHHHHHHHHHHH
Q 047859 84 GFYHLFNQNHKGAMMELGEGLG 105 (214)
Q Consensus 84 Al~H~~rGN~~GA~~Ll~rAl~ 105 (214)
|..+...||...|...+.+++.
T Consensus 8 a~~~~~~~~~~~a~~~~~~~~~ 29 (34)
T smart00028 8 GNAYLKLGDYDEALEYYEKALE 29 (34)
T ss_pred HHHHHHHhhHHHHHHHHHHHHc
Confidence 5566677889999998888874
No 70
>CHL00033 ycf3 photosystem I assembly protein Ycf3
Probab=29.55 E-value=2.8e+02 Score=21.86 Aligned_cols=67 Identities=6% Similarity=-0.116 Sum_probs=46.0
Q ss_pred hHHHHHHHhccCCchhhhhhhHHhhccCCcchhhHHHHHHHHHHHHH-----HHhcCCHHHHHHHHHHHHHHHhhc
Q 047859 40 SFDEAVALFNERAYYKCHDCLESLWYTAEEPTRTLIHGVLQCAVGFY-----HLFNQNHKGAMMELGEGLGKLRKM 110 (214)
Q Consensus 40 ~l~~gi~LFN~G~YfEAHEVLEe~Wk~~~g~er~~lqGLIQlAvAl~-----H~~rGN~~GA~~Ll~rAl~~L~~~ 110 (214)
-+.-|+.+...|++=+|.+.++.+=...+.. ..++..++..++ ....|+...|...+.+|+....+.
T Consensus 75 ~~~lg~~~~~~g~~~eA~~~~~~Al~~~~~~----~~~~~~la~i~~~~~~~~~~~g~~~~A~~~~~~a~~~~~~a 146 (168)
T CHL00033 75 LYNIGLIHTSNGEHTKALEYYFQALERNPFL----PQALNNMAVICHYRGEQAIEQGDSEIAEAWFDQAAEYWKQA 146 (168)
T ss_pred HHHHHHHHHHcCCHHHHHHHHHHHHHhCcCc----HHHHHHHHHHHHHhhHHHHHcccHHHHHHHHHHHHHHHHHH
Confidence 4566778888999999999888765543321 223334433333 347899999999999998887664
No 71
>PRK04841 transcriptional regulator MalT; Provisional
Probab=29.27 E-value=2.2e+02 Score=28.52 Aligned_cols=67 Identities=7% Similarity=-0.018 Sum_probs=47.1
Q ss_pred hHHHHHHHhccCCchhhhhhhHHhhccCCc---chhhHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHH
Q 047859 40 SFDEAVALFNERAYYKCHDCLESLWYTAEE---PTRTLIHGVLQCAVGFYHLFNQNHKGAMMELGEGLGK 106 (214)
Q Consensus 40 ~l~~gi~LFN~G~YfEAHEVLEe~Wk~~~g---~er~~lqGLIQlAvAl~H~~rGN~~GA~~Ll~rAl~~ 106 (214)
.+..+..++..|++=+|-+.++.+...... .....+++.+....|..+...|++..|...+++|+..
T Consensus 412 ~~~~a~~~~~~g~~~~a~~~l~~a~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~g~~~~A~~~~~~al~~ 481 (903)
T PRK04841 412 VLLQAWLAQSQHRYSEVNTLLARAEQELKDRNIELDGTLQAEFNALRAQVAINDGDPEEAERLAELALAE 481 (903)
T ss_pred HHHHHHHHHHCCCHHHHHHHHHHHHHhccccCcccchhHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHhc
Confidence 355677778888988888888877554331 1123456777777777788888888888888887764
No 72
>TIGR02561 HrpB1_HrpK type III secretion protein HrpB1/HrpK. This gene is found within type III secretion operons in a limited range of species including Xanthomonas, Ralstonia and Burkholderia.
Probab=29.26 E-value=54 Score=27.96 Aligned_cols=48 Identities=21% Similarity=0.166 Sum_probs=32.7
Q ss_pred cCCchhhhhhhHHhhccCCc-chhhHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHH
Q 047859 50 ERAYYKCHDCLESLWYTAEE-PTRTLIHGVLQCAVGFYHLFNQNHKGAMMELGEGL 104 (214)
Q Consensus 50 ~G~YfEAHEVLEe~Wk~~~g-~er~~lqGLIQlAvAl~H~~rGN~~GA~~Ll~rAl 104 (214)
..+..++-++|+.+=--.|. ++ +.+--|..|.+||||..|.+++++-.
T Consensus 23 ~~d~~D~e~lLdALrvLrP~~~e-------~d~~dg~l~i~rg~w~eA~rvlr~l~ 71 (153)
T TIGR02561 23 SADPYDAQAMLDALRVLRPNLKE-------LDMFDGWLLIARGNYDEAARILRELL 71 (153)
T ss_pred cCCHHHHHHHHHHHHHhCCCccc-------cchhHHHHHHHcCCHHHHHHHHHhhh
Confidence 66777777777765544442 33 23445667889999999999987543
No 73
>smart00745 MIT Microtubule Interacting and Trafficking molecule domain.
Probab=28.54 E-value=1.9e+02 Score=20.42 Aligned_cols=34 Identities=6% Similarity=-0.155 Sum_probs=26.7
Q ss_pred HHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHhhc
Q 047859 77 GVLQCAVGFYHLFNQNHKGAMMELGEGLGKLRKM 110 (214)
Q Consensus 77 GLIQlAvAl~H~~rGN~~GA~~Ll~rAl~~L~~~ 110 (214)
++-.+.-|+-.-..|+...|..++.+|+..|...
T Consensus 8 A~~li~~Av~~d~~g~~~eAl~~Y~~a~e~l~~~ 41 (77)
T smart00745 8 AKELISKALKADEAGDYEEALELYKKAIEYLLEG 41 (77)
T ss_pred HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHH
Confidence 3333445566777999999999999999999874
No 74
>PF04212 MIT: MIT (microtubule interacting and transport) domain; InterPro: IPR007330 The MIT domain is found in vacuolar sorting proteins, spastin (probable ATPase involved in the assembly or function of nuclear protein complexes), and a sorting nexin, which may play a role in intracellular trafficking.; PDB: 2DL1_A 2JQK_A 1WR0_A 2CPT_A 2JQH_A 2V6Y_A 2JQ9_A 2K3W_A 1YXR_A 3EAB_E ....
Probab=28.18 E-value=1.8e+02 Score=20.17 Aligned_cols=34 Identities=12% Similarity=-0.073 Sum_probs=27.2
Q ss_pred HHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHhhc
Q 047859 77 GVLQCAVGFYHLFNQNHKGAMMELGEGLGKLRKM 110 (214)
Q Consensus 77 GLIQlAvAl~H~~rGN~~GA~~Ll~rAl~~L~~~ 110 (214)
|+..+--|+-.-..||...|..++.+|+..|...
T Consensus 5 A~~~~~~Av~~D~~g~~~~A~~~Y~~ai~~l~~~ 38 (69)
T PF04212_consen 5 AIELIKKAVEADEAGNYEEALELYKEAIEYLMQA 38 (69)
T ss_dssp HHHHHHHHHHHHHTTSHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 4444555666677999999999999999999764
No 75
>PF14938 SNAP: Soluble NSF attachment protein, SNAP; PDB: 1QQE_A 2IFU_A.
Probab=27.35 E-value=2.8e+02 Score=24.28 Aligned_cols=62 Identities=13% Similarity=-0.064 Sum_probs=39.4
Q ss_pred HHHHHhccCCchhhhhhhHHhhccCCc-ch-hhHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 047859 43 EAVALFNERAYYKCHDCLESLWYTAEE-PT-RTLIHGVLQCAVGFYHLFNQNHKGAMMELGEGLG 105 (214)
Q Consensus 43 ~gi~LFN~G~YfEAHEVLEe~Wk~~~g-~e-r~~lqGLIQlAvAl~H~~rGN~~GA~~Ll~rAl~ 105 (214)
.|..+...|+|-+|.+.+|.+....-. +. +.-.+.. -+.+++.|+..|...+|.+.+.+...
T Consensus 161 ~A~l~~~l~~y~~A~~~~e~~~~~~l~~~l~~~~~~~~-~l~a~l~~L~~~D~v~A~~~~~~~~~ 224 (282)
T PF14938_consen 161 AADLYARLGRYEEAIEIYEEVAKKCLENNLLKYSAKEY-FLKAILCHLAMGDYVAARKALERYCS 224 (282)
T ss_dssp HHHHHHHTT-HHHHHHHHHHHHHTCCCHCTTGHHHHHH-HHHHHHHHHHTT-HHHHHHHHHHHGT
T ss_pred HHHHHHHhCCHHHHHHHHHHHHHHhhcccccchhHHHH-HHHHHHHHHHcCCHHHHHHHHHHHHh
Confidence 334444589999999999999986542 21 2112221 24456788889999999888776643
No 76
>PLN03098 LPA1 LOW PSII ACCUMULATION1; Provisional
Probab=26.96 E-value=3e+02 Score=27.27 Aligned_cols=68 Identities=15% Similarity=0.126 Sum_probs=50.2
Q ss_pred CcchhHHHHHHHhccCCchhhhhhhHHhhccCCcchhhHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHH
Q 047859 36 GENCSFDEAVALFNERAYYKCHDCLESLWYTAEEPTRTLIHGVLQCAVGFYHLFNQNHKGAMMELGEGLGK 106 (214)
Q Consensus 36 e~~~~l~~gi~LFN~G~YfEAHEVLEe~Wk~~~g~er~~lqGLIQlAvAl~H~~rGN~~GA~~Ll~rAl~~ 106 (214)
.....+..|..||..|+|=||-+.++..=.-.|++.. .-..+.++| ..+...||...|...+++|++.
T Consensus 74 ~a~a~~NLG~AL~~lGryeEAIa~f~rALeL~Pd~ae-A~~A~yNLA--caya~LGr~dEAla~LrrALel 141 (453)
T PLN03098 74 TAEDAVNLGLSLFSKGRVKDALAQFETALELNPNPDE-AQAAYYNKA--CCHAYREEGKKAADCLRTALRD 141 (453)
T ss_pred CHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCchH-HHHHHHHHH--HHHHHcCCHHHHHHHHHHHHHh
Confidence 4566788899999999999999999887666554321 112234444 4556679999999999999985
No 77
>PF13429 TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2_B.
Probab=26.33 E-value=77 Score=27.14 Aligned_cols=54 Identities=17% Similarity=0.131 Sum_probs=25.7
Q ss_pred HHhccCCchhhhhhhHHhhccCCcchhhHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 047859 46 ALFNERAYYKCHDCLESLWYTAEEPTRTLIHGVLQCAVGFYHLFNQNHKGAMMELGEGLG 105 (214)
Q Consensus 46 ~LFN~G~YfEAHEVLEe~Wk~~~g~er~~lqGLIQlAvAl~H~~rGN~~GA~~Ll~rAl~ 105 (214)
.+...|++=++.++++. |+....+...+|..+ |.....-|+...|...+++++.
T Consensus 189 ~li~~~~~~~~~~~l~~-~~~~~~~~~~~~~~l-----a~~~~~lg~~~~Al~~~~~~~~ 242 (280)
T PF13429_consen 189 LLIDMGDYDEAREALKR-LLKAAPDDPDLWDAL-----AAAYLQLGRYEEALEYLEKALK 242 (280)
T ss_dssp HHCTTCHHHHHHHHHHH-HHHH-HTSCCHCHHH-----HHHHHHHT-HHHHHHHHHHHHH
T ss_pred HHHHCCChHHHHHHHHH-HHHHCcCHHHHHHHH-----HHHhcccccccccccccccccc
Confidence 34446666666666665 333321122233222 3333344666666666666654
No 78
>KOG4431 consensus Uncharacterized protein, induced by hypoxia [General function prediction only]
Probab=25.35 E-value=72 Score=25.52 Aligned_cols=21 Identities=19% Similarity=0.246 Sum_probs=17.6
Q ss_pred HHHHHHHHh-cCCHHHHHHHHH
Q 047859 81 CAVGFYHLF-NQNHKGAMMELG 101 (214)
Q Consensus 81 lAvAl~H~~-rGN~~GA~~Ll~ 101 (214)
++.|+|..+ |||..++..+++
T Consensus 43 l~~g~y~~r~rGn~~~sq~lmr 64 (100)
T KOG4431|consen 43 LTAGLYKFRSRGNSKMSQHLMR 64 (100)
T ss_pred HHHHhhhhhhccchHHHHHHHH
Confidence 445779999 999999988886
No 79
>cd02679 MIT_spastin MIT: domain contained within Microtubule Interacting and Trafficking molecules. This MIT domain sub-family is found in the AAA protein spastin, a probable ATPase involved in the assembly or function of nuclear protein complexes; spastins might also be involved in microtubule dynamics. The molecular function of the MIT domain is unclear.
Probab=24.78 E-value=3.1e+02 Score=20.67 Aligned_cols=36 Identities=11% Similarity=0.084 Sum_probs=32.1
Q ss_pred HHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHhh
Q 047859 74 LIHGVLQCAVGFYHLFNQNHKGAMMELGEGLGKLRK 109 (214)
Q Consensus 74 ~lqGLIQlAvAl~H~~rGN~~GA~~Ll~rAl~~L~~ 109 (214)
+=++..++.-|+-+-..|.+..|..++++|+..|..
T Consensus 5 ~~~A~~~I~kaL~~dE~g~~e~Al~~Y~~gi~~l~e 40 (79)
T cd02679 5 YKQAFEEISKALRADEWGDKEQALAHYRKGLRELEE 40 (79)
T ss_pred HHHHHHHHHHHhhhhhcCCHHHHHHHHHHHHHHHHH
Confidence 446788899999998899999999999999999976
No 80
>TIGR02795 tol_pal_ybgF tol-pal system protein YbgF. Members of this protein family are the product of one of seven genes regularly clustered in operons to encode the proteins of the tol-pal system, which is critical for maintaining the integrity of the bacterial outer membrane. The gene for this periplasmic protein has been designated orf2 and ybgF. All members of the seed alignment were from unique tol-pal gene regions from completed bacterial genomes. The architecture of this protein is a signal sequence, a low-complexity region usually rich in Asn and Gln, a well-conserved region with tandem repeats that resemble the tetratricopeptide (TPR) repeat, involved in protein-protein interaction.
Probab=24.67 E-value=2.5e+02 Score=19.68 Aligned_cols=66 Identities=9% Similarity=0.071 Sum_probs=46.8
Q ss_pred chhHHHHHHHhccCCchhhhhhhHHhhccCCcchhhHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHH
Q 047859 38 NCSFDEAVALFNERAYYKCHDCLESLWYTAEEPTRTLIHGVLQCAVGFYHLFNQNHKGAMMELGEGLGK 106 (214)
Q Consensus 38 ~~~l~~gi~LFN~G~YfEAHEVLEe~Wk~~~g~er~~lqGLIQlAvAl~H~~rGN~~GA~~Ll~rAl~~ 106 (214)
...+..|..++..|+|=+|-+.++.+=...++.. ..-..+.+++.. ....|+...|...+.+++..
T Consensus 40 ~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p~~~-~~~~~~~~~~~~--~~~~~~~~~A~~~~~~~~~~ 105 (119)
T TIGR02795 40 NAHYWLGEAYYAQGKYADAAKAFLAVVKKYPKSP-KAPDALLKLGMS--LQELGDKEKAKATLQQVIKR 105 (119)
T ss_pred HHHHHHHHHHHhhccHHHHHHHHHHHHHHCCCCC-cccHHHHHHHHH--HHHhCChHHHHHHHHHHHHH
Confidence 4568889999999999999999998766554321 112233344433 35689999999999988765
No 81
>PRK11189 lipoprotein NlpI; Provisional
Probab=23.38 E-value=4.1e+02 Score=23.42 Aligned_cols=62 Identities=10% Similarity=-0.000 Sum_probs=38.5
Q ss_pred chhHHHHHHHhccCCchhhhhhhHHhhccCCcchhhHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 047859 38 NCSFDEAVALFNERAYYKCHDCLESLWYTAEEPTRTLIHGVLQCAVGFYHLFNQNHKGAMMELGEGLG 105 (214)
Q Consensus 38 ~~~l~~gi~LFN~G~YfEAHEVLEe~Wk~~~g~er~~lqGLIQlAvAl~H~~rGN~~GA~~Ll~rAl~ 105 (214)
..-+..|+.+...|++-+|.+.++..=...|... -.....|.+....|++..|...+.+|++
T Consensus 65 ~~~~~~g~~~~~~g~~~~A~~~~~~Al~l~P~~~------~a~~~lg~~~~~~g~~~~A~~~~~~Al~ 126 (296)
T PRK11189 65 QLHYERGVLYDSLGLRALARNDFSQALALRPDMA------DAYNYLGIYLTQAGNFDAAYEAFDSVLE 126 (296)
T ss_pred HHHHHHHHHHHHCCCHHHHHHHHHHHHHcCCCCH------HHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4466777877888888888877776544443221 1223345556666777777777776664
No 82
>TIGR00990 3a0801s09 mitochondrial precursor proteins import receptor (72 kDa mitochondrial outermembrane protein) (mitochondrial import receptor for the ADP/ATP carrier) (translocase of outermembrane tom70).
Probab=23.15 E-value=3e+02 Score=26.80 Aligned_cols=22 Identities=9% Similarity=0.150 Sum_probs=14.4
Q ss_pred HHHHHhcCCHHHHHHHHHHHHH
Q 047859 84 GFYHLFNQNHKGAMMELGEGLG 105 (214)
Q Consensus 84 Al~H~~rGN~~GA~~Ll~rAl~ 105 (214)
|..+...|++..|...+++++.
T Consensus 406 g~~~~~~g~~~~A~~~~~kal~ 427 (615)
T TIGR00990 406 AQLHFIKGEFAQAGKDYQKSID 427 (615)
T ss_pred HHHHHHcCCHHHHHHHHHHHHH
Confidence 3445566777777777777764
No 83
>PRK11447 cellulose synthase subunit BcsC; Provisional
Probab=23.04 E-value=3.3e+02 Score=29.02 Aligned_cols=68 Identities=12% Similarity=-0.062 Sum_probs=41.0
Q ss_pred chhHHHHHHHhccCCchhhhhhhHHhhccCCcc-hhhHHHHHHH-------HHHHHHHHhcCCHHHHHHHHHHHHH
Q 047859 38 NCSFDEAVALFNERAYYKCHDCLESLWYTAEEP-TRTLIHGVLQ-------CAVGFYHLFNQNHKGAMMELGEGLG 105 (214)
Q Consensus 38 ~~~l~~gi~LFN~G~YfEAHEVLEe~Wk~~~g~-er~~lqGLIQ-------lAvAl~H~~rGN~~GA~~Ll~rAl~ 105 (214)
+..+.-|..++..|+|=+|-+.++.+=...+.. ....|+.++. +.-|..+...|++..|...+++++.
T Consensus 304 ~a~~~Lg~~~~~~g~~~eA~~~l~~Al~~~p~~~~~~~~~~ll~~~~~~~~~~~g~~~~~~g~~~eA~~~~~~Al~ 379 (1157)
T PRK11447 304 EALGALGQAYSQQGDRARAVAQFEKALALDPHSSNRDKWESLLKVNRYWLLIQQGDAALKANNLAQAERLYQQARQ 379 (1157)
T ss_pred HHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCccchhHHHHHHHhhhHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 344556677778888888888888877665532 2233433332 2224445566666666666666654
No 84
>PF03947 Ribosomal_L2_C: Ribosomal Proteins L2, C-terminal domain; InterPro: IPR022669 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 [, ]. Ribosomal protein L2 is one of the proteins from the large ribosomal subunit. This entry represents the best conserved region located in the C-terminal section of these proteins.In Escherichia coli, L2 is known to bind to the 23S rRNA and to have peptidyltransferase activity. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities [, ], groups: Eubacterial L2. Algal and plant chloroplast L2. Cyanelle L2. Archaebacterial L2. Plant L2. Slime mold L2. Marchantia polymorpha mitochondrial L2. Paramecium tetraurelia mitochondrial L2. Fission yeast K5, K37 and KD4. Yeast YL6. Vertebrate L8. ; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3MRZ_C 3F1H_D 3PYO_C 3F1F_D 3PYV_C 3PYR_C 1VSA_B 3D5B_D 3PYT_C 3MS1_C ....
Probab=22.82 E-value=27 Score=28.56 Aligned_cols=45 Identities=16% Similarity=0.200 Sum_probs=29.9
Q ss_pred hhhcccccCceeeeccCCCCceEEEEcCCCCCC---CCCCCceeeccc
Q 047859 158 LLGDYAAGQQLYHLESDHNQIMYIVFDPQRSYG---SDDKSIKVKLPT 202 (214)
Q Consensus 158 ~Lg~~~~g~~~~~~~~~~~~~~~i~~~~~~~~~---~~~~~~~~klp~ 202 (214)
-|++++.|-.++.+|..++..-.++=|+..... ....-..||||.
T Consensus 8 pL~~ip~Gt~I~nIE~~pg~g~~~~RaAGt~a~ii~k~~~~~~ikLPS 55 (130)
T PF03947_consen 8 PLGNIPIGTIIHNIELKPGDGGKLARAAGTYAQIISKEGNYVVIKLPS 55 (130)
T ss_dssp EGGGSSTTEEEESBESSTTSSEEBSSSTTBBEEEEEEESSEEEEEETT
T ss_pred hHhhCCCCCEEEEEecCCCCCceEEeeCCCEEEEEEeccceeEEEecC
Confidence 488999999999999988766555444433310 111335888885
No 85
>PF02561 FliS: Flagellar protein FliS; InterPro: IPR003713 The fliD operon of several bacteria consists of three flagellar genes, fliD, fliS, and fliT, and is transcribed in this order []. In Bacillus subtilis the operon encoding the flagellar proteins FliD, FliS, and FliT is sigma D-dependent [].; GO: 0009296 flagellum assembly, 0009288 bacterial-type flagellum; PDB: 1VH6_A 3IQC_B 3K1I_B 1ORJ_B 1ORY_A.
Probab=22.68 E-value=2.8e+02 Score=21.59 Aligned_cols=38 Identities=8% Similarity=0.073 Sum_probs=31.8
Q ss_pred HHHHHHH-HHHHHHHHhcCCHHHHHHHHHHHHHHHhhcc
Q 047859 74 LIHGVLQ-CAVGFYHLFNQNHKGAMMELGEGLGKLRKMN 111 (214)
Q Consensus 74 ~lqGLIQ-lAvAl~H~~rGN~~GA~~Ll~rAl~~L~~~~ 111 (214)
++.|+|. +..|......|++..+...+.||...+..+.
T Consensus 25 Lyd~ai~~l~~a~~a~~~~~~~~~~~~l~ka~~Ii~~L~ 63 (122)
T PF02561_consen 25 LYDGAIEFLKQAKEAIEQGDIEEKNEALQKAQDIITELQ 63 (122)
T ss_dssp HHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHH
Confidence 5667666 6667778899999999999999999998764
No 86
>PRK10803 tol-pal system protein YbgF; Provisional
Probab=21.64 E-value=3.1e+02 Score=24.57 Aligned_cols=66 Identities=8% Similarity=-0.019 Sum_probs=46.2
Q ss_pred cchhHHHHHHHhccCCchhhhhhhHHhhccCCcchhhHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHH
Q 047859 37 ENCSFDEAVALFNERAYYKCHDCLESLWYTAEEPTRTLIHGVLQCAVGFYHLFNQNHKGAMMELGEGLG 105 (214)
Q Consensus 37 ~~~~l~~gi~LFN~G~YfEAHEVLEe~Wk~~~g~er~~lqGLIQlAvAl~H~~rGN~~GA~~Ll~rAl~ 105 (214)
....|.-|..+|+.|+|=+|-+.++.+=...|+.. ....++..++. .....|+...|...+++.+.
T Consensus 180 ~~A~y~LG~~y~~~g~~~~A~~~f~~vv~~yP~s~-~~~dAl~klg~--~~~~~g~~~~A~~~~~~vi~ 245 (263)
T PRK10803 180 PNANYWLGQLNYNKGKKDDAAYYFASVVKNYPKSP-KAADAMFKVGV--IMQDKGDTAKAKAVYQQVIK 245 (263)
T ss_pred HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCCc-chhHHHHHHHH--HHHHcCCHHHHHHHHHHHHH
Confidence 45678899999999999999999988876655311 12222333322 23367999999999997754
No 87
>PF09976 TPR_21: Tetratricopeptide repeat; InterPro: IPR018704 This domain, found in various hypothetical prokaryotic proteins, has no known function.
Probab=21.56 E-value=3.9e+02 Score=20.69 Aligned_cols=67 Identities=10% Similarity=0.043 Sum_probs=50.6
Q ss_pred cchhHHHHHHHhccCCchhhhhhhHHhhccCCcchhhHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHH
Q 047859 37 ENCSFDEAVALFNERAYYKCHDCLESLWYTAEEPTRTLIHGVLQCAVGFYHLFNQNHKGAMMELGEGLGK 106 (214)
Q Consensus 37 ~~~~l~~gi~LFN~G~YfEAHEVLEe~Wk~~~g~er~~lqGLIQlAvAl~H~~rGN~~GA~~Ll~rAl~~ 106 (214)
....|...+..++.+++=.+.+.++.+=...++. -+-.+.++..|-.....|+...|...|.+++..
T Consensus 11 a~~~y~~~~~~~~~~~~~~~~~~~~~l~~~~~~s---~ya~~A~l~lA~~~~~~g~~~~A~~~l~~~~~~ 77 (145)
T PF09976_consen 11 ASALYEQALQALQAGDPAKAEAAAEQLAKDYPSS---PYAALAALQLAKAAYEQGDYDEAKAALEKALAN 77 (145)
T ss_pred HHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCCCC---hHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHhh
Confidence 3556788888888888888888888877765432 356666777777777889999998888877754
No 88
>PRK02603 photosystem I assembly protein Ycf3; Provisional
Probab=21.29 E-value=4.2e+02 Score=21.05 Aligned_cols=68 Identities=6% Similarity=-0.040 Sum_probs=42.3
Q ss_pred hhHHHHHHHhccCCchhhhhhhHHhhccCCcchhhHHHHHHHHHHHHH-----HHhcCCHHHHHHHHHHHHHHHhhc
Q 047859 39 CSFDEAVALFNERAYYKCHDCLESLWYTAEEPTRTLIHGVLQCAVGFY-----HLFNQNHKGAMMELGEGLGKLRKM 110 (214)
Q Consensus 39 ~~l~~gi~LFN~G~YfEAHEVLEe~Wk~~~g~er~~lqGLIQlAvAl~-----H~~rGN~~GA~~Ll~rAl~~L~~~ 110 (214)
.-+..|..++..|+|=+|=+.++..=...+.. ...+..++..+. ....++..-|+..+.+|+..+...
T Consensus 74 ~~~~la~~~~~~g~~~~A~~~~~~al~~~p~~----~~~~~~lg~~~~~~g~~~~a~~~~~~A~~~~~~A~~~~~~a 146 (172)
T PRK02603 74 ILYNMGIIYASNGEHDKALEYYHQALELNPKQ----PSALNNIAVIYHKRGEKAEEAGDQDEAEALFDKAAEYWKQA 146 (172)
T ss_pred HHHHHHHHHHHcCCHHHHHHHHHHHHHhCccc----HHHHHHHHHHHHHcCChHhHhhCHHHHHHHHHHHHHHHHHH
Confidence 45667788888999988877777655443322 222223333322 233567788888888888877664
No 89
>cd07931 eukaryotic_phosphagen_kinases Phosphagen (guanidino) kinases mostly found in eukaryotes. Phosphagen (guanidino) kinases are enzymes that transphosphorylate a high energy phosphoguanidino compound, like phosphocreatine (PCr) in the case of creatine kinase (CK) or phosphoarginine in the case of arginine kinase, which is used as an energy-storage and -transport metabolite, to ADP, thereby creating ATP. The substrate binding site is located in the cleft between the N and C-terminal domains, but most of the catalytic residues are found in the larger C-terminal domain. In higher eukaryotes, CK exists in tissue-specific (muscle, brain), as well as compartment-specific (mitochondrial and cytosolic) isoforms. They are either coupled to glycolysis (cytosolic form) or oxidative phosphorylation (mitochondrial form). Besides CK and AK, the most studied members of this family are also other phosphagen kinases with different substrate specificities, like glycocyamine kinase (GK), lombricine k
Probab=20.98 E-value=48 Score=31.31 Aligned_cols=28 Identities=32% Similarity=0.300 Sum_probs=25.2
Q ss_pred eEEEEcCCCCCCCCCCCceeeccccccc
Q 047859 179 MYIVFDPQRSYGSDDKSIKVKLPTLNAT 206 (214)
Q Consensus 179 ~~i~~~~~~~~~~~~~~~~~klp~~~~~ 206 (214)
-++++||++-..+-..+..||||.|..+
T Consensus 249 GYLTsCPtNlGTGlRASV~v~LP~L~~~ 276 (338)
T cd07931 249 GYITSCPTNLGTGMRASVHVKLPNLIKD 276 (338)
T ss_pred eeEeeCCCCCccceEEEEEEEcchhhhc
Confidence 4899999999888888899999999987
No 90
>PF15256 SPATIAL: SPATIAL
Probab=20.95 E-value=51 Score=29.06 Aligned_cols=22 Identities=23% Similarity=0.637 Sum_probs=18.1
Q ss_pred hhccCC-cchhhHHHHHHHHHHH
Q 047859 63 LWYTAE-EPTRTLIHGVLQCAVG 84 (214)
Q Consensus 63 ~Wk~~~-g~er~~lqGLIQlAvA 84 (214)
.|+-.. ..||+++.||||.|+|
T Consensus 174 ~WLl~A~~kEK~lv~~Li~ta~a 196 (196)
T PF15256_consen 174 QWLLSASDKEKELVSGLIQTALA 196 (196)
T ss_pred HHHHhCChhhHHHHHHHHHHhhC
Confidence 377555 6899999999999985
No 91
>cd02678 MIT_VPS4 MIT: domain contained within Microtubule Interacting and Trafficking molecules. This sub-family of MIT domains is found in intracellular protein transport proteins of the AAA-ATPase family. The molecular function of the MIT domain is unclear.
Probab=20.76 E-value=3.1e+02 Score=19.65 Aligned_cols=30 Identities=10% Similarity=-0.079 Sum_probs=24.8
Q ss_pred HHHHHHHHhcCCHHHHHHHHHHHHHHHhhc
Q 047859 81 CAVGFYHLFNQNHKGAMMELGEGLGKLRKM 110 (214)
Q Consensus 81 lAvAl~H~~rGN~~GA~~Ll~rAl~~L~~~ 110 (214)
+--|+-.-..||...|..++.+|+..|-..
T Consensus 10 ~~~Av~~D~~g~y~eA~~~Y~~aie~l~~~ 39 (75)
T cd02678 10 VKKAIEEDNAGNYEEALRLYQHALEYFMHA 39 (75)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHHHHHHHHH
Confidence 334466778999999999999999999764
No 92
>KOG1125 consensus TPR repeat-containing protein [General function prediction only]
Probab=20.63 E-value=3.5e+02 Score=27.77 Aligned_cols=74 Identities=16% Similarity=0.129 Sum_probs=51.5
Q ss_pred eeeeecccCCCCCCCcchhHHHHHHHhccCCchhhhhhhHHhhccCCcc-hhhHHHHHHHHHHHHHHHhcCCHHHHHHHH
Q 047859 22 VLYRYSAKEEDDNDGENCSFDEAVALFNERAYYKCHDCLESLWYTAEEP-TRTLIHGVLQCAVGFYHLFNQNHKGAMMEL 100 (214)
Q Consensus 22 ~~~~~~~~~~~~~~e~~~~l~~gi~LFN~G~YfEAHEVLEe~Wk~~~g~-er~~lqGLIQlAvAl~H~~rGN~~GA~~Ll 100 (214)
.-|-|+..-+. .+...+|.+|..|+..|+-=+|==++|..=++.|+. +--.+- |+.|..++|-.-|+.-+
T Consensus 272 ~~Y~F~e~Np~--~~~pdPf~eG~~lm~nG~L~~A~LafEAAVkqdP~haeAW~~L-------G~~qaENE~E~~ai~AL 342 (579)
T KOG1125|consen 272 KGYQFSEENPY--IDHPDPFKEGCNLMKNGDLSEAALAFEAAVKQDPQHAEAWQKL-------GITQAENENEQNAISAL 342 (579)
T ss_pred ccceecccCcc--cCCCChHHHHHHHHhcCCchHHHHHHHHHHhhChHHHHHHHHh-------hhHhhhccchHHHHHHH
Confidence 45666665554 456678999999999999999999999887776642 222333 44556666666666666
Q ss_pred HHHH
Q 047859 101 GEGL 104 (214)
Q Consensus 101 ~rAl 104 (214)
+|++
T Consensus 343 ~rcl 346 (579)
T KOG1125|consen 343 RRCL 346 (579)
T ss_pred HHHH
Confidence 6665
No 93
>PF00617 RasGEF: RasGEF domain; InterPro: IPR001895 Ras proteins are membrane-associated molecular switches that bind GTP and GDP and slowly hydrolyze GTP to GDP []. The balance between the GTP bound (active) and GDP bound (inactive) states is regulated by the opposite action of proteins activating the GTPase activity and that of proteins which promote the loss of bound GDP and the uptake of fresh GTP [, ]. The latter proteins are known as guanine-nucleotide dissociation stimulators (GDSs) (or also as guanine-nucleotide releasing (or exchange) factors (GRFs)). Proteins that act as GDS can be classified into at least two families, on the basis of sequence similarities, the CDC24 family (see IPR001331 from INTERPRO) and the CDC25 family. The size of the proteins of the CDC25 family range from 309 residues (LTE1) to 1596 residues (sos). The sequence similarity shared by all these proteins is limited to a region of about 250 amino acids generally located in their C-terminal section (currently the only exceptions are sos and ralGDS where this domain makes up the central part of the protein). This domain has been shown, in CDC25 an SCD25, to be essential for the activity of these proteins.; GO: 0005085 guanyl-nucleotide exchange factor activity, 0007264 small GTPase mediated signal transduction, 0005622 intracellular; PDB: 2IJE_S 3T6G_A 1NVW_S 1BKD_S 1XDV_A 2II0_A 1NVU_S 1NVX_S 1NVV_S 1XD4_B ....
Probab=20.17 E-value=1.4e+02 Score=23.96 Aligned_cols=59 Identities=19% Similarity=0.238 Sum_probs=48.0
Q ss_pred cchhHHHHHHHhccCCchhhhhhhHHhhccCCcchhhHHHHHHHHHHHHHHHhcCCHHHHHHHH
Q 047859 37 ENCSFDEAVALFNERAYYKCHDCLESLWYTAEEPTRTLIHGVLQCAVGFYHLFNQNHKGAMMEL 100 (214)
Q Consensus 37 ~~~~l~~gi~LFN~G~YfEAHEVLEe~Wk~~~g~er~~lqGLIQlAvAl~H~~rGN~~GA~~Ll 100 (214)
..+.+...+..||.=-.|-+++++-.- ....+..++.-+|++|-.++ .-||..++...+
T Consensus 42 ~~~~i~~~~~~~n~ls~wv~~~Il~~~---~~~~R~~~i~~~I~va~~l~--~l~Nf~s~~aI~ 100 (188)
T PF00617_consen 42 QSPNINKLIDRFNKLSNWVISEILSQP---DPEERAKIIEKFIQVAKKLY--ELGNFNSLMAIL 100 (188)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHTSS---SHHHHHHHHHHHHHHHHHHH--HTTBHHHHHHHH
T ss_pred cChhHHHHHHHhhhHHHHHHHHhhccc---cHHHHHHHHHHHHhHHHHHH--HhcCchHHHHHH
Confidence 468899999999999999999998761 22456679999999998765 778999987764
Done!