Query 033305
Match_columns 122
No_of_seqs 170 out of 1443
Neff 8.1
Searched_HMMs 46136
Date Fri Mar 29 12:17:38 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033305.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033305hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03077 Protein ECB2; Provisi 100.0 5E-38 1.1E-42 262.8 12.5 121 1-122 685-816 (857)
2 PLN03081 pentatricopeptide (PP 100.0 2.1E-35 4.6E-40 242.7 12.4 122 1-122 522-654 (697)
3 PF14432 DYW_deaminase: DYW fa 99.6 7.6E-16 1.7E-20 102.0 4.0 66 43-122 2-82 (116)
4 PF13431 TPR_17: Tetratricopep 96.9 0.00053 1.2E-08 35.4 1.6 27 1-27 7-33 (34)
5 PF13812 PPR_3: Pentatricopept 96.5 0.0047 1E-07 30.9 3.4 31 9-39 3-33 (34)
6 PF01535 PPR: PPR repeat; Int 96.5 0.0029 6.2E-08 31.0 2.5 30 9-38 2-31 (31)
7 PF13041 PPR_2: PPR repeat fam 95.6 0.023 4.9E-07 31.3 3.5 33 7-39 3-35 (50)
8 TIGR00756 PPR pentatricopeptid 95.5 0.026 5.7E-07 27.8 3.3 31 9-39 2-32 (35)
9 PF12854 PPR_1: PPR repeat 95.1 0.033 7.3E-07 28.5 2.9 29 6-34 6-34 (34)
10 PF14559 TPR_19: Tetratricopep 91.2 0.66 1.4E-05 26.4 4.5 31 2-32 20-50 (68)
11 PF13371 TPR_9: Tetratricopept 87.1 0.56 1.2E-05 27.1 2.1 31 1-31 23-53 (73)
12 PF13432 TPR_16: Tetratricopep 85.5 1.2 2.5E-05 25.2 2.9 31 2-32 26-56 (65)
13 PF13176 TPR_7: Tetratricopept 85.2 1 2.2E-05 22.9 2.3 23 9-31 1-23 (36)
14 PF07721 TPR_4: Tetratricopept 81.8 2.2 4.7E-05 20.1 2.5 23 8-30 2-24 (26)
15 PF13428 TPR_14: Tetratricopep 79.5 3.5 7.6E-05 21.7 3.1 25 7-31 1-25 (44)
16 PLN03218 maturation of RBCL 1; 75.3 2.7 5.9E-05 37.5 2.8 33 7-39 684-716 (1060)
17 PF13414 TPR_11: TPR repeat; P 75.2 0.95 2.1E-05 25.9 0.1 28 2-29 32-60 (69)
18 PLN03081 pentatricopeptide (PP 75.0 4.6 9.9E-05 33.9 4.1 37 3-39 286-322 (697)
19 PF13374 TPR_10: Tetratricopep 72.8 5.5 0.00012 19.9 2.7 24 8-31 3-26 (42)
20 PRK10747 putative protoheme IX 72.5 4 8.6E-05 32.0 3.0 38 1-38 181-218 (398)
21 PLN03077 Protein ECB2; Provisi 69.0 8 0.00017 33.3 4.2 35 5-39 552-586 (857)
22 TIGR02552 LcrH_SycD type III s 67.3 9.1 0.0002 24.5 3.4 33 2-34 46-79 (135)
23 PRK10370 formate-dependent nit 67.0 7.7 0.00017 27.5 3.2 31 2-32 139-169 (198)
24 PRK10370 formate-dependent nit 60.5 7.8 0.00017 27.5 2.3 29 2-30 68-96 (198)
25 PF13181 TPR_8: Tetratricopept 59.3 17 0.00037 17.3 2.9 22 9-30 3-24 (34)
26 PF13971 Mei4: Meiosis-specifi 59.0 5.1 0.00011 31.7 1.2 28 90-117 12-40 (375)
27 PF07719 TPR_2: Tetratricopept 58.7 15 0.00032 17.4 2.6 23 8-30 2-24 (34)
28 PF09045 L27_2: L27_2; InterP 56.7 27 0.00059 20.2 3.6 35 57-111 4-38 (58)
29 PLN03218 maturation of RBCL 1; 54.5 18 0.00039 32.5 3.9 29 9-37 616-644 (1060)
30 PF13174 TPR_6: Tetratricopept 54.2 13 0.00028 17.5 1.9 25 9-33 2-26 (33)
31 PRK15359 type III secretion sy 53.7 17 0.00036 24.3 2.9 28 2-29 87-114 (144)
32 PRK15359 type III secretion sy 53.1 12 0.00025 25.0 2.0 31 2-32 53-83 (144)
33 PLN03088 SGT1, suppressor of 52.0 43 0.00092 26.0 5.3 28 2-29 31-58 (356)
34 TIGR00540 hemY_coli hemY prote 51.0 17 0.00036 28.5 2.9 37 2-38 182-218 (409)
35 TIGR02552 LcrH_SycD type III s 50.0 10 0.00022 24.2 1.4 27 3-29 81-107 (135)
36 PRK12370 invasion protein regu 48.2 23 0.0005 29.0 3.4 28 2-29 333-360 (553)
37 PF09613 HrpB1_HrpK: Bacterial 47.0 34 0.00075 23.9 3.6 36 2-37 39-74 (160)
38 COG5010 TadD Flp pilus assembl 46.7 23 0.00049 26.7 2.9 38 1-38 128-166 (257)
39 smart00028 TPR Tetratricopepti 44.8 28 0.00061 14.8 2.6 23 8-30 2-24 (34)
40 PF03704 BTAD: Bacterial trans 44.8 30 0.00065 22.6 3.1 29 2-30 91-119 (146)
41 cd00189 TPR Tetratricopeptide 44.6 28 0.0006 19.1 2.6 25 4-28 31-55 (100)
42 cd05804 StaR_like StaR_like; a 44.4 24 0.00052 26.4 2.8 28 2-29 143-170 (355)
43 PRK11189 lipoprotein NlpI; Pro 43.4 30 0.00066 25.9 3.2 27 2-28 93-119 (296)
44 COG4235 Cytochrome c biogenesi 42.9 28 0.0006 26.6 2.9 36 2-37 151-187 (287)
45 PRK11189 lipoprotein NlpI; Pro 41.4 32 0.0007 25.7 3.1 31 1-31 126-156 (296)
46 PF12895 Apc3: Anaphase-promot 40.7 9.7 0.00021 22.6 0.1 21 9-29 60-80 (84)
47 PRK12370 invasion protein regu 40.1 32 0.00069 28.2 3.1 30 1-30 366-395 (553)
48 PLN03088 SGT1, suppressor of 39.2 35 0.00077 26.4 3.1 31 1-31 64-94 (356)
49 PF09295 ChAPs: ChAPs (Chs5p-A 37.6 29 0.00062 27.7 2.3 31 2-32 263-293 (395)
50 KOG1155 Anaphase-promoting com 37.4 41 0.00089 27.8 3.2 31 1-31 426-456 (559)
51 PLN03098 LPA1 LOW PSII ACCUMUL 37.3 44 0.00096 27.2 3.4 34 1-34 103-140 (453)
52 TIGR02521 type_IV_pilW type IV 37.2 48 0.001 22.2 3.2 22 8-29 136-157 (234)
53 COG4890 Predicted outer membra 37.1 21 0.00045 18.4 1.0 13 98-110 9-21 (37)
54 TIGR02561 HrpB1_HrpK type III 37.0 47 0.001 23.0 3.0 37 2-38 39-75 (153)
55 PRK11788 tetratricopeptide rep 36.9 47 0.001 25.2 3.4 33 2-34 64-96 (389)
56 PRK11788 tetratricopeptide rep 36.5 40 0.00088 25.5 3.0 32 3-34 210-241 (389)
57 TIGR02917 PEP_TPR_lipo putativ 36.1 46 0.001 27.5 3.4 35 2-36 51-85 (899)
58 PF00515 TPR_1: Tetratricopept 35.3 39 0.00085 16.0 1.9 22 9-30 3-24 (34)
59 KOG2499 Beta-N-acetylhexosamin 34.7 54 0.0012 27.2 3.4 38 2-39 303-358 (542)
60 PRK15363 pathogenicity island 34.5 67 0.0014 22.3 3.5 31 2-32 98-128 (157)
61 PRK08057 cobalt-precorrin-6x r 34.0 1.1E+02 0.0024 22.7 4.9 44 19-69 47-91 (248)
62 TIGR02917 PEP_TPR_lipo putativ 33.8 56 0.0012 27.1 3.6 34 3-36 665-698 (899)
63 TIGR02521 type_IV_pilW type IV 33.4 49 0.0011 22.2 2.8 27 3-29 61-87 (234)
64 PRK15174 Vi polysaccharide exp 30.3 60 0.0013 27.4 3.2 28 2-29 105-132 (656)
65 COG4783 Putative Zn-dependent 29.7 82 0.0018 25.9 3.7 31 3-33 404-434 (484)
66 COG3063 PilF Tfp pilus assembl 29.6 71 0.0015 24.0 3.1 35 1-35 63-98 (250)
67 PF08967 DUF1884: Domain of un 28.7 74 0.0016 19.8 2.6 24 57-80 9-32 (85)
68 PF11398 DUF2813: Protein of u 28.0 1.1E+02 0.0024 24.3 4.1 52 62-117 265-318 (373)
69 PF02662 FlpD: Methyl-viologen 27.6 1.8E+02 0.004 19.0 4.9 46 25-73 78-124 (124)
70 PF13424 TPR_12: Tetratricopep 27.6 35 0.00075 19.6 1.0 26 7-32 5-30 (78)
71 PF10925 DUF2680: Protein of u 27.4 1E+02 0.0022 17.7 3.0 25 52-76 35-59 (59)
72 PF06135 DUF965: Bacterial pro 27.3 85 0.0018 19.3 2.7 23 56-78 15-37 (79)
73 PRK10747 putative protoheme IX 25.0 97 0.0021 24.2 3.4 31 3-33 324-354 (398)
74 PF02571 CbiJ: Precorrin-6x re 24.9 1.7E+02 0.0038 21.6 4.6 43 20-69 49-92 (249)
75 KOG1127 TPR repeat-containing 24.5 80 0.0017 28.7 3.0 50 1-50 520-569 (1238)
76 PF14561 TPR_20: Tetratricopep 24.5 83 0.0018 19.4 2.4 27 3-29 18-44 (90)
77 PF13429 TPR_15: Tetratricopep 24.4 50 0.0011 24.1 1.6 30 4-33 143-173 (280)
78 cd06570 GH20_chitobiase-like_1 24.4 1.3E+02 0.0029 23.0 3.9 38 2-39 124-179 (311)
79 TIGR00990 3a0801s09 mitochondr 23.9 94 0.002 25.7 3.3 27 3-29 395-421 (615)
80 PRK05473 hypothetical protein; 23.5 1.1E+02 0.0024 19.1 2.7 22 56-77 18-39 (86)
81 PF08482 HrpB_C: ATP-dependent 23.3 43 0.00093 22.7 1.0 13 110-122 93-105 (133)
82 COG1111 MPH1 ERCC4-like helica 23.2 2.8E+02 0.006 23.3 5.6 99 9-107 148-291 (542)
83 PRK15174 Vi polysaccharide exp 23.0 89 0.0019 26.4 3.0 28 2-29 313-340 (656)
84 KOG1076 Translation initiation 22.5 2.6E+02 0.0057 24.5 5.5 99 4-105 650-784 (843)
85 PF00356 LacI: Bacterial regul 21.6 1.1E+02 0.0023 16.6 2.2 17 61-77 30-46 (46)
86 PTZ00131 glycophorin-binding p 21.5 27 0.00059 26.5 -0.3 22 88-109 38-59 (413)
87 TIGR02795 tol_pal_ybgF tol-pal 20.4 1.5E+02 0.0033 17.7 3.1 26 8-33 40-65 (119)
88 PF13959 DUF4217: Domain of un 20.3 55 0.0012 18.9 0.9 17 96-112 46-62 (65)
No 1
>PLN03077 Protein ECB2; Provisional
Probab=100.00 E-value=5e-38 Score=262.81 Aligned_cols=121 Identities=36% Similarity=0.678 Sum_probs=116.4
Q ss_pred CCCCCCchhHHHHHHHHHHcCCChhHHHHHHHHhccCCCCCCceeEEEec-----------ccchhhhhHHHHHHHHHHH
Q 033305 1 MINLNNMRVYVILSNAYAAARRWKDTARLRVSVRNKGMKKTPACSWTEIK-----------SHPYRLRINEALKDLFERM 69 (122)
Q Consensus 1 el~p~~~~~yvlLsniYa~~G~w~~~~~~r~~m~~~~l~k~~g~S~iev~-----------~h~~~~~i~~~l~~l~~~~ 69 (122)
+++|++++.|++|+|+|+..|+|+++.++|+.|+++|++|.|||||||++ +||+.++||.+|++|..+|
T Consensus 685 ~l~p~~~~~y~ll~n~ya~~g~~~~a~~vr~~M~~~g~~k~~g~s~ie~~~~~~~f~~~d~~h~~~~~i~~~l~~l~~~~ 764 (857)
T PLN03077 685 ELDPNSVGYYILLCNLYADAGKWDEVARVRKTMRENGLTVDPGCSWVEVKGKVHAFLTDDESHPQIKEINTVLEGFYEKM 764 (857)
T ss_pred hhCCCCcchHHHHHHHHHHCCChHHHHHHHHHHHHcCCCCCCCccEEEECCEEEEEecCCCCCcchHHHHHHHHHHHHHH
Confidence 57999999999999999999999999999999999999999999999987 8999999999999999999
Q ss_pred HhcCcccCCCccccccchHhhhhhhhhhHHHHHHHHHhhcCCCCCeEEEecCC
Q 033305 70 EQEGYVPTTKEALHDVEDEQKKNLLHYHSGRFAIVFGAISTPDGRTIRLINNL 122 (122)
Q Consensus 70 ~~~gy~~~~~~~~~~~~ee~~~~~~~~Hseklaia~gl~~~~~~~~irv~kn~ 122 (122)
++.||+|++..++ +.+|++|+..+++||||||||||||++++|+||||+|||
T Consensus 765 ~~~g~~~~~~~~~-~~~~~~k~~~~~~hse~la~a~~l~~~~~~~~i~i~knl 816 (857)
T PLN03077 765 KASGLAGSESSSM-DEIEVSKDDIFCGHSERLAIAFGLINTVPGMPIWVTKNL 816 (857)
T ss_pred HhCCcCCCcchhc-cccHHHHHHHHHhccHHHHHHHhhhcCCCCCeEEEeCCC
Confidence 9999999998877 557888999999999999999999999999999999997
No 2
>PLN03081 pentatricopeptide (PPR) repeat-containing protein; Provisional
Probab=100.00 E-value=2.1e-35 Score=242.67 Aligned_cols=122 Identities=30% Similarity=0.592 Sum_probs=118.7
Q ss_pred CCCCCCchhHHHHHHHHHHcCCChhHHHHHHHHhccCCCCCCceeEEEec-----------ccchhhhhHHHHHHHHHHH
Q 033305 1 MINLNNMRVYVILSNAYAAARRWKDTARLRVSVRNKGMKKTPACSWTEIK-----------SHPYRLRINEALKDLFERM 69 (122)
Q Consensus 1 el~p~~~~~yvlLsniYa~~G~w~~~~~~r~~m~~~~l~k~~g~S~iev~-----------~h~~~~~i~~~l~~l~~~~ 69 (122)
+++|.+.+.|++|+|+|+..|+|++|.++++.|+++|++|.||||||+++ +||+.++||..|++|..+|
T Consensus 522 ~~~p~~~~~y~~L~~~y~~~G~~~~A~~v~~~m~~~g~~k~~g~s~i~~~~~~~~f~~~d~~h~~~~~i~~~l~~l~~~~ 601 (697)
T PLN03081 522 GMGPEKLNNYVVLLNLYNSSGRQAEAAKVVETLKRKGLSMHPACTWIEVKKQDHSFFSGDRLHPQSREIYQKLDELMKEI 601 (697)
T ss_pred CCCCCCCcchHHHHHHHHhCCCHHHHHHHHHHHHHcCCccCCCeeEEEECCeEEEEccCCCCCccHHHHHHHHHHHHHHH
Confidence 46899999999999999999999999999999999999999999999986 7999999999999999999
Q ss_pred HhcCcccCCCccccccchHhhhhhhhhhHHHHHHHHHhhcCCCCCeEEEecCC
Q 033305 70 EQEGYVPTTKEALHDVEDEQKKNLLHYHSGRFAIVFGAISTPDGRTIRLINNL 122 (122)
Q Consensus 70 ~~~gy~~~~~~~~~~~~ee~~~~~~~~Hseklaia~gl~~~~~~~~irv~kn~ 122 (122)
++.||+|++..+++++++++++..+++||||||||||||++++|.||||+|||
T Consensus 602 ~~~gy~~~~~~~~~~~~~~~~~~~~~~hsekla~a~~l~~~~~~~~i~i~knl 654 (697)
T PLN03081 602 SEYGYVAEENELLPDVDEDEEKVSGRYHSEKLAIAFGLINTSEWTPLQITQSH 654 (697)
T ss_pred HHcCCCCCcchhhccccHHHHHHHHHhccHHHHHHhhCccCCCCCeEEEecCC
Confidence 99999999999999999999999999999999999999999999999999997
No 3
>PF14432 DYW_deaminase: DYW family of nucleic acid deaminases
Probab=99.60 E-value=7.6e-16 Score=102.00 Aligned_cols=66 Identities=53% Similarity=0.992 Sum_probs=55.3
Q ss_pred ceeEEEec-------ccchhhhhHHHHHHHHHHHHhcCcccCCCccccccchHhh--------hhhhhhhHHHHHHHHHh
Q 033305 43 ACSWTEIK-------SHPYRLRINEALKDLFERMEQEGYVPTTKEALHDVEDEQK--------KNLLHYHSGRFAIVFGA 107 (122)
Q Consensus 43 g~S~iev~-------~h~~~~~i~~~l~~l~~~~~~~gy~~~~~~~~~~~~ee~~--------~~~~~~Hseklaia~gl 107 (122)
||||+++. +||+. .+..++...||.|+...+.++++++++ +..+++||||||+||||
T Consensus 2 ~~~w~~~h~F~sgd~shp~~--------~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~d~~~~~~~~~~HSEKlAiafgl 73 (116)
T PF14432_consen 2 GCSWIEVHSFVSGDRSHPQS--------ELINKMKEEGYVPDTKEVGHDVDEEEKHDYDEEEKEESLCYHSEKLAIAFGL 73 (116)
T ss_pred CCCccceEEEEeCCCcCccH--------HHHHHHHHcCCcchhhhhCCCchhhhhhhcccccchhhhhccHHHHHHHhcc
Confidence 89999965 89987 555677778999988888887777654 67899999999999999
Q ss_pred hcCCCCCeEEEecCC
Q 033305 108 ISTPDGRTIRLINNL 122 (122)
Q Consensus 108 ~~~~~~~~irv~kn~ 122 (122)
+++ ||+||+
T Consensus 74 i~~------~vvkn~ 82 (116)
T PF14432_consen 74 INT------RVVKNL 82 (116)
T ss_pred cce------eEEecC
Confidence 998 888885
No 4
>PF13431 TPR_17: Tetratricopeptide repeat
Probab=96.94 E-value=0.00053 Score=35.44 Aligned_cols=27 Identities=26% Similarity=0.406 Sum_probs=25.1
Q ss_pred CCCCCCchhHHHHHHHHHHcCCChhHH
Q 033305 1 MINLNNMRVYVILSNAYAAARRWKDTA 27 (122)
Q Consensus 1 el~p~~~~~yvlLsniYa~~G~w~~~~ 27 (122)
+++|+++.+|.-|+++|...|++++|.
T Consensus 7 e~~P~n~~a~~nla~~~~~~g~~~~A~ 33 (34)
T PF13431_consen 7 ELNPNNAEAYNNLANLYLNQGDYEEAI 33 (34)
T ss_pred HHCCCCHHHHHHHHHHHHHCcCHHhhc
Confidence 579999999999999999999999875
No 5
>PF13812 PPR_3: Pentatricopeptide repeat domain
Probab=96.54 E-value=0.0047 Score=30.88 Aligned_cols=31 Identities=26% Similarity=0.263 Sum_probs=28.7
Q ss_pred hHHHHHHHHHHcCCChhHHHHHHHHhccCCC
Q 033305 9 VYVILSNAYAAARRWKDTARLRVSVRNKGMK 39 (122)
Q Consensus 9 ~yvlLsniYa~~G~w~~~~~~r~~m~~~~l~ 39 (122)
.|..+.+.|+..|+++.+.++...|++.|++
T Consensus 3 ty~~ll~a~~~~g~~~~a~~~~~~M~~~gv~ 33 (34)
T PF13812_consen 3 TYNALLRACAKAGDPDAALQLFDEMKEQGVK 33 (34)
T ss_pred HHHHHHHHHHHCCCHHHHHHHHHHHHHhCCC
Confidence 5889999999999999999999999999874
No 6
>PF01535 PPR: PPR repeat; InterPro: IPR002885 This entry represents the PPR repeat. Pentatricopeptide repeat (PPR) proteins are characterised by tandem repeats of a degenerate 35 amino acid motif []. Most of PPR proteins have roles in mitochondria or plastid []. PPR repeats were discovered while screening Arabidopsis proteins for those predicted to be targeted to mitochondria or chloroplast [, ]. Some of these proteins have been shown to play a role in post-transcriptional processes within organelles and they are thought to be sequence-specific RNA-binding proteins [, , ]. Plant genomes have between one hundred to five hundred PPR genes per genome whereas non-plant genomes encode two to six PPR proteins. Although no PPR structures are yet known, the motif is predicted to fold into a helix-turn-helix structure similar to those found in the tetratricopeptide repeat (TPR) family (see PDOC50005 from PROSITEDOC) []. The plant PPR protein family has been divided in two subfamilies on the basis of their motif content and organisation [, ]. Examples of PPR repeat-containing proteins include PET309 P32522 from SWISSPROT, which may be involved in RNA stabilisation [], and crp1, which is involved in RNA processing []. The repeat is associated with a predicted plant protein O49549 from SWISSPROT that has a domain organisation similar to the human BRCA1 protein.
Probab=96.53 E-value=0.0029 Score=30.97 Aligned_cols=30 Identities=17% Similarity=0.416 Sum_probs=27.3
Q ss_pred hHHHHHHHHHHcCCChhHHHHHHHHhccCC
Q 033305 9 VYVILSNAYAAARRWKDTARLRVSVRNKGM 38 (122)
Q Consensus 9 ~yvlLsniYa~~G~w~~~~~~r~~m~~~~l 38 (122)
.|..|-+.|+..|++++|.++...|++.|+
T Consensus 2 ~y~~li~~~~~~~~~~~a~~~~~~M~~~g~ 31 (31)
T PF01535_consen 2 TYNSLISGYCKMGQFEEALEVFDEMRERGI 31 (31)
T ss_pred cHHHHHHHHHccchHHHHHHHHHHHhHCcC
Confidence 478899999999999999999999998874
No 7
>PF13041 PPR_2: PPR repeat family
Probab=95.57 E-value=0.023 Score=31.31 Aligned_cols=33 Identities=21% Similarity=0.498 Sum_probs=30.1
Q ss_pred chhHHHHHHHHHHcCCChhHHHHHHHHhccCCC
Q 033305 7 MRVYVILSNAYAAARRWKDTARLRVSVRNKGMK 39 (122)
Q Consensus 7 ~~~yvlLsniYa~~G~w~~~~~~r~~m~~~~l~ 39 (122)
.-.|-.|-+.|+..|++++|.++.+.|+++|+.
T Consensus 3 ~~~yn~li~~~~~~~~~~~a~~l~~~M~~~g~~ 35 (50)
T PF13041_consen 3 VVTYNTLISGYCKAGKFEEALKLFKEMKKRGIK 35 (50)
T ss_pred hHHHHHHHHHHHHCcCHHHHHHHHHHHHHcCCC
Confidence 456888999999999999999999999999986
No 8
>TIGR00756 PPR pentatricopeptide repeat domain (PPR motif). This family has a similar consensus to the TPR domain (tetratricopeptide), pfam pfam00515, a 33-residue repeat. It is predicted to form a pair of antiparallel helices similar to that of TPR.
Probab=95.48 E-value=0.026 Score=27.83 Aligned_cols=31 Identities=19% Similarity=0.322 Sum_probs=27.8
Q ss_pred hHHHHHHHHHHcCCChhHHHHHHHHhccCCC
Q 033305 9 VYVILSNAYAAARRWKDTARLRVSVRNKGMK 39 (122)
Q Consensus 9 ~yvlLsniYa~~G~w~~~~~~r~~m~~~~l~ 39 (122)
.|..+-+.|+..|++++|.++...|+..|+.
T Consensus 2 ~~n~li~~~~~~~~~~~a~~~~~~M~~~g~~ 32 (35)
T TIGR00756 2 TYNTLIDGLCKAGRVEEALELFKEMLERGIE 32 (35)
T ss_pred cHHHHHHHHHHCCCHHHHHHHHHHHHHcCCC
Confidence 4777888999999999999999999998875
No 9
>PF12854 PPR_1: PPR repeat
Probab=95.09 E-value=0.033 Score=28.49 Aligned_cols=29 Identities=21% Similarity=0.316 Sum_probs=25.6
Q ss_pred CchhHHHHHHHHHHcCCChhHHHHHHHHh
Q 033305 6 NMRVYVILSNAYAAARRWKDTARLRVSVR 34 (122)
Q Consensus 6 ~~~~yvlLsniYa~~G~w~~~~~~r~~m~ 34 (122)
|...|-.|.+.|+..|+.++|.++...|+
T Consensus 6 d~~ty~~lI~~~Ck~G~~~~A~~l~~~M~ 34 (34)
T PF12854_consen 6 DVVTYNTLIDGYCKAGRVDEAFELFDEMK 34 (34)
T ss_pred cHhHHHHHHHHHHHCCCHHHHHHHHHhCc
Confidence 35669999999999999999999988874
No 10
>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=91.23 E-value=0.66 Score=26.41 Aligned_cols=31 Identities=16% Similarity=0.290 Sum_probs=26.5
Q ss_pred CCCCCchhHHHHHHHHHHcCCChhHHHHHHH
Q 033305 2 INLNNMRVYVILSNAYAAARRWKDTARLRVS 32 (122)
Q Consensus 2 l~p~~~~~yvlLsniYa~~G~w~~~~~~r~~ 32 (122)
.+|+++..++.|+.+|...|++++|..+-..
T Consensus 20 ~~p~~~~~~~~la~~~~~~g~~~~A~~~l~~ 50 (68)
T PF14559_consen 20 RNPDNPEARLLLAQCYLKQGQYDEAEELLER 50 (68)
T ss_dssp HTTTSHHHHHHHHHHHHHTT-HHHHHHHHHC
T ss_pred HCCCCHHHHHHHHHHHHHcCCHHHHHHHHHH
Confidence 3799999999999999999999999987553
No 11
>PF13371 TPR_9: Tetratricopeptide repeat
Probab=87.07 E-value=0.56 Score=27.14 Aligned_cols=31 Identities=3% Similarity=0.091 Sum_probs=27.4
Q ss_pred CCCCCCchhHHHHHHHHHHcCCChhHHHHHH
Q 033305 1 MINLNNMRVYVILSNAYAAARRWKDTARLRV 31 (122)
Q Consensus 1 el~p~~~~~yvlLsniYa~~G~w~~~~~~r~ 31 (122)
+++|+++..|...+.+|...|++.+|...-.
T Consensus 23 ~~~p~~~~~~~~~a~~~~~~g~~~~A~~~l~ 53 (73)
T PF13371_consen 23 ELDPDDPELWLQRARCLFQLGRYEEALEDLE 53 (73)
T ss_pred HhCcccchhhHHHHHHHHHhccHHHHHHHHH
Confidence 3689999999999999999999999987644
No 12
>PF13432 TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL_A 3CVQ_A 3CV0_A 2GW1_B 3CVN_A 3QKY_A 2PL2_B.
Probab=85.46 E-value=1.2 Score=25.25 Aligned_cols=31 Identities=10% Similarity=0.164 Sum_probs=26.0
Q ss_pred CCCCCchhHHHHHHHHHHcCCChhHHHHHHH
Q 033305 2 INLNNMRVYVILSNAYAAARRWKDTARLRVS 32 (122)
Q Consensus 2 l~p~~~~~yvlLsniYa~~G~w~~~~~~r~~ 32 (122)
.+|+++..+..++.+|...|++++|...-..
T Consensus 26 ~~P~~~~a~~~lg~~~~~~g~~~~A~~~~~~ 56 (65)
T PF13432_consen 26 QDPDNPEAWYLLGRILYQQGRYDEALAYYER 56 (65)
T ss_dssp CSTTHHHHHHHHHHHHHHTT-HHHHHHHHHH
T ss_pred HCCCCHHHHHHHHHHHHHcCCHHHHHHHHHH
Confidence 5789999999999999999999999876443
No 13
>PF13176 TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_A 3RO2_A.
Probab=85.16 E-value=1 Score=22.88 Aligned_cols=23 Identities=9% Similarity=0.101 Sum_probs=18.7
Q ss_pred hHHHHHHHHHHcCCChhHHHHHH
Q 033305 9 VYVILSNAYAAARRWKDTARLRV 31 (122)
Q Consensus 9 ~yvlLsniYa~~G~w~~~~~~r~ 31 (122)
+|..|.++|...|+|++|...-+
T Consensus 1 al~~Lg~~~~~~g~~~~Ai~~y~ 23 (36)
T PF13176_consen 1 ALNNLGRIYRQQGDYEKAIEYYE 23 (36)
T ss_dssp HHHHHHHHHHHCT-HHHHHHHHH
T ss_pred CHHHHHHHHHHcCCHHHHHHHHH
Confidence 47789999999999999998643
No 14
>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=81.78 E-value=2.2 Score=20.10 Aligned_cols=23 Identities=26% Similarity=0.245 Sum_probs=19.6
Q ss_pred hhHHHHHHHHHHcCCChhHHHHH
Q 033305 8 RVYVILSNAYAAARRWKDTARLR 30 (122)
Q Consensus 8 ~~yvlLsniYa~~G~w~~~~~~r 30 (122)
.....|+..|...|++++|.++-
T Consensus 2 ~a~~~la~~~~~~G~~~eA~~~l 24 (26)
T PF07721_consen 2 RARLALARALLAQGDPDEAERLL 24 (26)
T ss_pred HHHHHHHHHHHHcCCHHHHHHHH
Confidence 45778999999999999998753
No 15
>PF13428 TPR_14: Tetratricopeptide repeat
Probab=79.49 E-value=3.5 Score=21.70 Aligned_cols=25 Identities=20% Similarity=0.258 Sum_probs=21.4
Q ss_pred chhHHHHHHHHHHcCCChhHHHHHH
Q 033305 7 MRVYVILSNAYAAARRWKDTARLRV 31 (122)
Q Consensus 7 ~~~yvlLsniYa~~G~w~~~~~~r~ 31 (122)
|..+..|+..|...|++++|.++-+
T Consensus 1 p~~~~~la~~~~~~G~~~~A~~~~~ 25 (44)
T PF13428_consen 1 PAAWLALARAYRRLGQPDEAERLLR 25 (44)
T ss_pred CHHHHHHHHHHHHcCCHHHHHHHHH
Confidence 4568899999999999999998643
No 16
>PLN03218 maturation of RBCL 1; Provisional
Probab=75.27 E-value=2.7 Score=37.51 Aligned_cols=33 Identities=21% Similarity=0.405 Sum_probs=24.1
Q ss_pred chhHHHHHHHHHHcCCChhHHHHHHHHhccCCC
Q 033305 7 MRVYVILSNAYAAARRWKDTARLRVSVRNKGMK 39 (122)
Q Consensus 7 ~~~yvlLsniYa~~G~w~~~~~~r~~m~~~~l~ 39 (122)
...|..|.++|+..|++++|.++...|+..|+.
T Consensus 684 ~~tynsLI~ay~k~G~~eeA~~lf~eM~~~g~~ 716 (1060)
T PLN03218 684 TVSYSSLMGACSNAKNWKKALELYEDIKSIKLR 716 (1060)
T ss_pred HHHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCC
Confidence 455777777777778777777777777776654
No 17
>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=75.24 E-value=0.95 Score=25.87 Aligned_cols=28 Identities=21% Similarity=0.313 Sum_probs=24.1
Q ss_pred CCCCCchhHHHHHHHHHHcC-CChhHHHH
Q 033305 2 INLNNMRVYVILSNAYAAAR-RWKDTARL 29 (122)
Q Consensus 2 l~p~~~~~yvlLsniYa~~G-~w~~~~~~ 29 (122)
++|.++..|..++.+|...| ++++|.+.
T Consensus 32 ~~p~~~~~~~~~g~~~~~~~~~~~~A~~~ 60 (69)
T PF13414_consen 32 LDPNNAEAYYNLGLAYMKLGKDYEEAIED 60 (69)
T ss_dssp HSTTHHHHHHHHHHHHHHTTTHHHHHHHH
T ss_pred cCCCCHHHHHHHHHHHHHhCccHHHHHHH
Confidence 57999999999999999999 68887764
No 18
>PLN03081 pentatricopeptide (PPR) repeat-containing protein; Provisional
Probab=75.00 E-value=4.6 Score=33.90 Aligned_cols=37 Identities=14% Similarity=0.160 Sum_probs=26.2
Q ss_pred CCCCchhHHHHHHHHHHcCCChhHHHHHHHHhccCCC
Q 033305 3 NLNNMRVYVILSNAYAAARRWKDTARLRVSVRNKGMK 39 (122)
Q Consensus 3 ~p~~~~~yvlLsniYa~~G~w~~~~~~r~~m~~~~l~ 39 (122)
.+.+...|..|.+.|+..|++++|.++...|++.|+.
T Consensus 286 ~~~~~vt~n~li~~y~~~g~~~eA~~lf~~M~~~g~~ 322 (697)
T PLN03081 286 PEKTTVAWNSMLAGYALHGYSEEALCLYYEMRDSGVS 322 (697)
T ss_pred CCCChhHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCC
Confidence 3445666777777777777777777777777776664
No 19
>PF13374 TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT_H 3NF1_A.
Probab=72.76 E-value=5.5 Score=19.92 Aligned_cols=24 Identities=29% Similarity=0.376 Sum_probs=19.1
Q ss_pred hhHHHHHHHHHHcCCChhHHHHHH
Q 033305 8 RVYVILSNAYAAARRWKDTARLRV 31 (122)
Q Consensus 8 ~~yvlLsniYa~~G~w~~~~~~r~ 31 (122)
..+.-|+++|...|++++|..+-.
T Consensus 3 ~~~~~la~~~~~~g~~~~A~~~~~ 26 (42)
T PF13374_consen 3 SALNNLANAYRAQGRYEEALELLE 26 (42)
T ss_dssp HHHHHHHHHHHHCT-HHHHHHHHH
T ss_pred HHHHHHHHHHHhhhhcchhhHHHH
Confidence 356789999999999999998744
No 20
>PRK10747 putative protoheme IX biogenesis protein; Provisional
Probab=72.49 E-value=4 Score=32.00 Aligned_cols=38 Identities=13% Similarity=0.215 Sum_probs=31.9
Q ss_pred CCCCCCchhHHHHHHHHHHcCCChhHHHHHHHHhccCC
Q 033305 1 MINLNNMRVYVILSNAYAAARRWKDTARLRVSVRNKGM 38 (122)
Q Consensus 1 el~p~~~~~yvlLsniYa~~G~w~~~~~~r~~m~~~~l 38 (122)
+.+|+++..+-++..+|...|+|+++.++-..++..+.
T Consensus 181 ~~~P~~~~al~ll~~~~~~~gdw~~a~~~l~~l~k~~~ 218 (398)
T PRK10747 181 EVAPRHPEVLRLAEQAYIRTGAWSSLLDILPSMAKAHV 218 (398)
T ss_pred hcCCCCHHHHHHHHHHHHHHHhHHHHHHHHHHHHHcCC
Confidence 36899999999999999999999999987666665544
No 21
>PLN03077 Protein ECB2; Provisional
Probab=68.95 E-value=8 Score=33.27 Aligned_cols=35 Identities=17% Similarity=0.228 Sum_probs=29.5
Q ss_pred CCchhHHHHHHHHHHcCCChhHHHHHHHHhccCCC
Q 033305 5 NNMRVYVILSNAYAAARRWKDTARLRVSVRNKGMK 39 (122)
Q Consensus 5 ~~~~~yvlLsniYa~~G~w~~~~~~r~~m~~~~l~ 39 (122)
.|...|..|.+.|+..|+.++|.++.+.|.+.|+.
T Consensus 552 ~d~~s~n~lI~~~~~~G~~~~A~~lf~~M~~~g~~ 586 (857)
T PLN03077 552 KDVVSWNILLTGYVAHGKGSMAVELFNRMVESGVN 586 (857)
T ss_pred CChhhHHHHHHHHHHcCCHHHHHHHHHHHHHcCCC
Confidence 45667888888999999999999999999988875
No 22
>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=67.28 E-value=9.1 Score=24.48 Aligned_cols=33 Identities=9% Similarity=0.207 Sum_probs=20.3
Q ss_pred CCCCCchhHHHHHHHHHHcCCChhHHH-HHHHHh
Q 033305 2 INLNNMRVYVILSNAYAAARRWKDTAR-LRVSVR 34 (122)
Q Consensus 2 l~p~~~~~yvlLsniYa~~G~w~~~~~-~r~~m~ 34 (122)
++|.++..|..++.+|...|++++|.. ++..++
T Consensus 46 ~~p~~~~~~~~la~~~~~~~~~~~A~~~~~~~~~ 79 (135)
T TIGR02552 46 YDPYNSRYWLGLAACCQMLKEYEEAIDAYALAAA 79 (135)
T ss_pred hCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 356666666677777777777766664 244444
No 23
>PRK10370 formate-dependent nitrite reductase complex subunit NrfG; Provisional
Probab=67.02 E-value=7.7 Score=27.52 Aligned_cols=31 Identities=10% Similarity=0.213 Sum_probs=17.2
Q ss_pred CCCCCchhHHHHHHHHHHcCCChhHHHHHHH
Q 033305 2 INLNNMRVYVILSNAYAAARRWKDTARLRVS 32 (122)
Q Consensus 2 l~p~~~~~yvlLsniYa~~G~w~~~~~~r~~ 32 (122)
++|.++.++.+|+..|...|++++|......
T Consensus 139 ~dP~~~~al~~LA~~~~~~g~~~~Ai~~~~~ 169 (198)
T PRK10370 139 LDANEVTALMLLASDAFMQADYAQAIELWQK 169 (198)
T ss_pred hCCCChhHHHHHHHHHHHcCCHHHHHHHHHH
Confidence 3555555555555555555555555554443
No 24
>PRK10370 formate-dependent nitrite reductase complex subunit NrfG; Provisional
Probab=60.52 E-value=7.8 Score=27.47 Aligned_cols=29 Identities=14% Similarity=0.188 Sum_probs=25.6
Q ss_pred CCCCCchhHHHHHHHHHHcCCChhHHHHH
Q 033305 2 INLNNMRVYVILSNAYAAARRWKDTARLR 30 (122)
Q Consensus 2 l~p~~~~~yvlLsniYa~~G~w~~~~~~r 30 (122)
.+|+++..|..|+.+|...|+.++|...-
T Consensus 68 ~~P~~~~~w~~Lg~~~~~~g~~~~A~~a~ 96 (198)
T PRK10370 68 ANPQNSEQWALLGEYYLWRNDYDNALLAY 96 (198)
T ss_pred HCCCCHHHHHHHHHHHHHCCCHHHHHHHH
Confidence 57999999999999999999999988754
No 25
>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=59.28 E-value=17 Score=17.34 Aligned_cols=22 Identities=14% Similarity=0.276 Sum_probs=19.3
Q ss_pred hHHHHHHHHHHcCCChhHHHHH
Q 033305 9 VYVILSNAYAAARRWKDTARLR 30 (122)
Q Consensus 9 ~yvlLsniYa~~G~w~~~~~~r 30 (122)
.|..++.+|...|++++|...-
T Consensus 3 ~~~~lg~~y~~~~~~~~A~~~~ 24 (34)
T PF13181_consen 3 AYYNLGKIYEQLGDYEEALEYF 24 (34)
T ss_dssp HHHHHHHHHHHTTSHHHHHHHH
T ss_pred HHHHHHHHHHHcCCHHHHHHHH
Confidence 5889999999999999988753
No 26
>PF13971 Mei4: Meiosis-specific protein Mei4
Probab=58.98 E-value=5.1 Score=31.69 Aligned_cols=28 Identities=14% Similarity=0.322 Sum_probs=20.7
Q ss_pred hhhhhhhhHHHHHHHHHhhcCC-CCCeEE
Q 033305 90 KKNLLHYHSGRFAIVFGAISTP-DGRTIR 117 (122)
Q Consensus 90 ~~~~~~~Hseklaia~gl~~~~-~~~~ir 117 (122)
+......+.-|+|+|+++|.+. +|+..|
T Consensus 12 ~~~~wyl~tsKlAlAlAIIrsKPpg~s~R 40 (375)
T PF13971_consen 12 QQLSWYLKTSKLALALAIIRSKPPGKSSR 40 (375)
T ss_pred cchhHHHHHHHHHHHHHHHHcCCCCCCHH
Confidence 3445556788999999999976 565554
No 27
>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=58.72 E-value=15 Score=17.44 Aligned_cols=23 Identities=13% Similarity=0.274 Sum_probs=18.4
Q ss_pred hhHHHHHHHHHHcCCChhHHHHH
Q 033305 8 RVYVILSNAYAAARRWKDTARLR 30 (122)
Q Consensus 8 ~~yvlLsniYa~~G~w~~~~~~r 30 (122)
..|..++.+|...|++++|.+.-
T Consensus 2 ~~~~~lg~~~~~~~~~~~A~~~~ 24 (34)
T PF07719_consen 2 EAWYYLGQAYYQLGNYEEAIEYF 24 (34)
T ss_dssp HHHHHHHHHHHHTT-HHHHHHHH
T ss_pred HHHHHHHHHHHHhCCHHHHHHHH
Confidence 35778999999999999998753
No 28
>PF09045 L27_2: L27_2; InterPro: IPR015132 The L27_2 domain is a protein-protein interaction domain capable of organising scaffold proteins into supramolecular assemblies by formation of heteromeric L27_2 domain complexes. L27_2 domain-mediated protein assemblies have been shown to play essential roles in cellular processes including asymmetric cell division, establishment and maintenance of cell polarity, and clustering of receptors and ion channels. Members of this family form specific heterotetrameric complexes, in which each domain contains three alpha-helices. The two N-terminal helices of each L27_2 domain pack together to form a tight, four-helix bundle in the heterodimer, whilst the third helix of each L27_2 domain forms another four-helix bundle that assembles the two units of the heterodimer into a tetramer []. ; PDB: 3UIT_A 1VF6_B.
Probab=56.66 E-value=27 Score=20.20 Aligned_cols=35 Identities=23% Similarity=0.470 Sum_probs=23.7
Q ss_pred hhHHHHHHHHHHHHhcCcccCCCccccccchHhhhhhhhhhHHHHHHHHHhhcCC
Q 033305 57 RINEALKDLFERMEQEGYVPTTKEALHDVEDEQKKNLLHYHSGRFAIVFGAISTP 111 (122)
Q Consensus 57 ~i~~~l~~l~~~~~~~gy~~~~~~~~~~~~ee~~~~~~~~Hseklaia~gl~~~~ 111 (122)
.+...+++|..++++.|-. .|+|+|+.-...+.+|
T Consensus 4 ~al~~lerlq~KL~~rGd~--------------------s~~e~L~~l~~~LqSP 38 (58)
T PF09045_consen 4 RALQALERLQAKLKERGDT--------------------SHSEKLSLLKDTLQSP 38 (58)
T ss_dssp HHHHHHHHHHHHHHHCT----------------------TTHHHHHHHHHHHH-H
T ss_pred HHHHHHHHHHHHHHHccCc--------------------ccHHHHHHHHHHHhCh
Confidence 3567789999999988842 2677777766666554
No 29
>PLN03218 maturation of RBCL 1; Provisional
Probab=54.51 E-value=18 Score=32.53 Aligned_cols=29 Identities=24% Similarity=0.455 Sum_probs=12.5
Q ss_pred hHHHHHHHHHHcCCChhHHHHHHHHhccC
Q 033305 9 VYVILSNAYAAARRWKDTARLRVSVRNKG 37 (122)
Q Consensus 9 ~yvlLsniYa~~G~w~~~~~~r~~m~~~~ 37 (122)
.|..|.+.|+..|++++|.++...|+..|
T Consensus 616 tynsLI~ay~k~G~~deAl~lf~eM~~~G 644 (1060)
T PLN03218 616 VYTIAVNSCSQKGDWDFALSIYDDMKKKG 644 (1060)
T ss_pred HHHHHHHHHHhcCCHHHHHHHHHHHHHcC
Confidence 34444444444444444444444444443
No 30
>PF13174 TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_A 3URZ_B 2Q7F_A.
Probab=54.22 E-value=13 Score=17.48 Aligned_cols=25 Identities=8% Similarity=0.130 Sum_probs=19.5
Q ss_pred hHHHHHHHHHHcCCChhHHHHHHHH
Q 033305 9 VYVILSNAYAAARRWKDTARLRVSV 33 (122)
Q Consensus 9 ~yvlLsniYa~~G~w~~~~~~r~~m 33 (122)
++..++.+|...|++++|.+....+
T Consensus 2 a~~~~a~~~~~~g~~~~A~~~~~~~ 26 (33)
T PF13174_consen 2 ALYRLARCYYKLGDYDEAIEYFQRL 26 (33)
T ss_dssp HHHHHHHHHHHHCHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHccCHHHHHHHHHHH
Confidence 3567888999999999998875543
No 31
>PRK15359 type III secretion system chaperone protein SscB; Provisional
Probab=53.74 E-value=17 Score=24.25 Aligned_cols=28 Identities=0% Similarity=-0.210 Sum_probs=19.4
Q ss_pred CCCCCchhHHHHHHHHHHcCCChhHHHH
Q 033305 2 INLNNMRVYVILSNAYAAARRWKDTARL 29 (122)
Q Consensus 2 l~p~~~~~yvlLsniYa~~G~w~~~~~~ 29 (122)
++|.++.++.-++.+|...|+.++|...
T Consensus 87 l~p~~~~a~~~lg~~l~~~g~~~eAi~~ 114 (144)
T PRK15359 87 LDASHPEPVYQTGVCLKMMGEPGLAREA 114 (144)
T ss_pred cCCCCcHHHHHHHHHHHHcCCHHHHHHH
Confidence 5677777777777777777777776654
No 32
>PRK15359 type III secretion system chaperone protein SscB; Provisional
Probab=53.12 E-value=12 Score=25.04 Aligned_cols=31 Identities=6% Similarity=0.115 Sum_probs=27.4
Q ss_pred CCCCCchhHHHHHHHHHHcCCChhHHHHHHH
Q 033305 2 INLNNMRVYVILSNAYAAARRWKDTARLRVS 32 (122)
Q Consensus 2 l~p~~~~~yvlLsniYa~~G~w~~~~~~r~~ 32 (122)
++|.++..|..++.++...|++++|...-..
T Consensus 53 ~~P~~~~a~~~lg~~~~~~g~~~~A~~~y~~ 83 (144)
T PRK15359 53 AQPWSWRAHIALAGTWMMLKEYTTAINFYGH 83 (144)
T ss_pred cCCCcHHHHHHHHHHHHHHhhHHHHHHHHHH
Confidence 6899999999999999999999999986443
No 33
>PLN03088 SGT1, suppressor of G2 allele of SKP1; Provisional
Probab=51.99 E-value=43 Score=25.98 Aligned_cols=28 Identities=14% Similarity=0.191 Sum_probs=19.6
Q ss_pred CCCCCchhHHHHHHHHHHcCCChhHHHH
Q 033305 2 INLNNMRVYVILSNAYAAARRWKDTARL 29 (122)
Q Consensus 2 l~p~~~~~yvlLsniYa~~G~w~~~~~~ 29 (122)
++|.++..|..++.+|...|++++|...
T Consensus 31 ~~P~~~~a~~~~a~~~~~~g~~~eAl~~ 58 (356)
T PLN03088 31 LDPNNAELYADRAQANIKLGNFTEAVAD 58 (356)
T ss_pred hCCCCHHHHHHHHHHHHHcCCHHHHHHH
Confidence 4677777777777777777777776654
No 34
>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=51.01 E-value=17 Score=28.54 Aligned_cols=37 Identities=14% Similarity=0.324 Sum_probs=31.0
Q ss_pred CCCCCchhHHHHHHHHHHcCCChhHHHHHHHHhccCC
Q 033305 2 INLNNMRVYVILSNAYAAARRWKDTARLRVSVRNKGM 38 (122)
Q Consensus 2 l~p~~~~~yvlLsniYa~~G~w~~~~~~r~~m~~~~l 38 (122)
..|+++..+.++..+|...|+|+++.+.-......++
T Consensus 182 ~~P~~~~~l~ll~~~~~~~~d~~~a~~~l~~l~k~~~ 218 (409)
T TIGR00540 182 MAPRHKEVLKLAEEAYIRSGAWQALDDIIDNMAKAGL 218 (409)
T ss_pred hCCCCHHHHHHHHHHHHHHhhHHHHHHHHHHHHHcCC
Confidence 4699999999999999999999999987666665543
No 35
>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=50.03 E-value=10 Score=24.20 Aligned_cols=27 Identities=11% Similarity=0.111 Sum_probs=14.8
Q ss_pred CCCCchhHHHHHHHHHHcCCChhHHHH
Q 033305 3 NLNNMRVYVILSNAYAAARRWKDTARL 29 (122)
Q Consensus 3 ~p~~~~~yvlLsniYa~~G~w~~~~~~ 29 (122)
+|.++..|..++.+|...|++++|.+.
T Consensus 81 ~p~~~~~~~~la~~~~~~g~~~~A~~~ 107 (135)
T TIGR02552 81 DPDDPRPYFHAAECLLALGEPESALKA 107 (135)
T ss_pred CCCChHHHHHHHHHHHHcCCHHHHHHH
Confidence 455555555555555555555555543
No 36
>PRK12370 invasion protein regulator; Provisional
Probab=48.21 E-value=23 Score=29.05 Aligned_cols=28 Identities=14% Similarity=0.106 Sum_probs=18.0
Q ss_pred CCCCCchhHHHHHHHHHHcCCChhHHHH
Q 033305 2 INLNNMRVYVILSNAYAAARRWKDTARL 29 (122)
Q Consensus 2 l~p~~~~~yvlLsniYa~~G~w~~~~~~ 29 (122)
++|+++.+|..++.+|...|++++|...
T Consensus 333 ldP~~~~a~~~lg~~~~~~g~~~~A~~~ 360 (553)
T PRK12370 333 LDHNNPQALGLLGLINTIHSEYIVGSLL 360 (553)
T ss_pred cCCCCHHHHHHHHHHHHHccCHHHHHHH
Confidence 5666666666666666666666666554
No 37
>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=47.04 E-value=34 Score=23.85 Aligned_cols=36 Identities=11% Similarity=0.141 Sum_probs=30.0
Q ss_pred CCCCCchhHHHHHHHHHHcCCChhHHHHHHHHhccC
Q 033305 2 INLNNMRVYVILSNAYAAARRWKDTARLRVSVRNKG 37 (122)
Q Consensus 2 l~p~~~~~yvlLsniYa~~G~w~~~~~~r~~m~~~~ 37 (122)
|.|+.+..-++-..++-..|+|.+|.++-+.+-++.
T Consensus 39 LRP~~~e~~~~~~~l~i~r~~w~dA~rlLr~l~~~~ 74 (160)
T PF09613_consen 39 LRPEFPELDLFDGWLHIVRGDWDDALRLLRELEERA 74 (160)
T ss_pred hCCCchHHHHHHHHHHHHhCCHHHHHHHHHHHhccC
Confidence 568888888888999999999999999877665544
No 38
>COG5010 TadD Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking and secretion]
Probab=46.71 E-value=23 Score=26.69 Aligned_cols=38 Identities=13% Similarity=0.219 Sum_probs=30.8
Q ss_pred CCCCCCchhHHHHHHHHHHcCCChhHHH-HHHHHhccCC
Q 033305 1 MINLNNMRVYVILSNAYAAARRWKDTAR-LRVSVRNKGM 38 (122)
Q Consensus 1 el~p~~~~~yvlLsniYa~~G~w~~~~~-~r~~m~~~~l 38 (122)
.++|.|...|.++.-+|...|+.++|+. .++..+-.+-
T Consensus 128 ~l~p~d~~~~~~lgaaldq~Gr~~~Ar~ay~qAl~L~~~ 166 (257)
T COG5010 128 RLAPTDWEAWNLLGAALDQLGRFDEARRAYRQALELAPN 166 (257)
T ss_pred ccCCCChhhhhHHHHHHHHccChhHHHHHHHHHHHhccC
Confidence 3689999999999999999999999986 4555554433
No 39
>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=44.81 E-value=28 Score=14.83 Aligned_cols=23 Identities=17% Similarity=0.236 Sum_probs=18.9
Q ss_pred hhHHHHHHHHHHcCCChhHHHHH
Q 033305 8 RVYVILSNAYAAARRWKDTARLR 30 (122)
Q Consensus 8 ~~yvlLsniYa~~G~w~~~~~~r 30 (122)
..|..++.+|...|+++++....
T Consensus 2 ~~~~~~a~~~~~~~~~~~a~~~~ 24 (34)
T smart00028 2 EALYNLGNAYLKLGDYDEALEYY 24 (34)
T ss_pred hHHHHHHHHHHHHhhHHHHHHHH
Confidence 35778899999999999888753
No 40
>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=44.78 E-value=30 Score=22.61 Aligned_cols=29 Identities=24% Similarity=0.335 Sum_probs=23.2
Q ss_pred CCCCCchhHHHHHHHHHHcCCChhHHHHH
Q 033305 2 INLNNMRVYVILSNAYAAARRWKDTARLR 30 (122)
Q Consensus 2 l~p~~~~~yvlLsniYa~~G~w~~~~~~r 30 (122)
++|.+-..|..|...|+..|+..+|.++-
T Consensus 91 ~dP~~E~~~~~lm~~~~~~g~~~~A~~~Y 119 (146)
T PF03704_consen 91 LDPYDEEAYRLLMRALAAQGRRAEALRVY 119 (146)
T ss_dssp HSTT-HHHHHHHHHHHHHTT-HHHHHHHH
T ss_pred cCCCCHHHHHHHHHHHHHCcCHHHHHHHH
Confidence 47888889999999999999999888653
No 41
>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=44.58 E-value=28 Score=19.09 Aligned_cols=25 Identities=20% Similarity=0.367 Sum_probs=12.2
Q ss_pred CCCchhHHHHHHHHHHcCCChhHHH
Q 033305 4 LNNMRVYVILSNAYAAARRWKDTAR 28 (122)
Q Consensus 4 p~~~~~yvlLsniYa~~G~w~~~~~ 28 (122)
|.++..+..++.+|...|+++++.+
T Consensus 31 ~~~~~~~~~~~~~~~~~~~~~~a~~ 55 (100)
T cd00189 31 PDNADAYYNLAAAYYKLGKYEEALE 55 (100)
T ss_pred CccHHHHHHHHHHHHHHHHHHHHHH
Confidence 3333344455555555555555544
No 42
>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=44.39 E-value=24 Score=26.44 Aligned_cols=28 Identities=11% Similarity=0.223 Sum_probs=22.1
Q ss_pred CCCCCchhHHHHHHHHHHcCCChhHHHH
Q 033305 2 INLNNMRVYVILSNAYAAARRWKDTARL 29 (122)
Q Consensus 2 l~p~~~~~yvlLsniYa~~G~w~~~~~~ 29 (122)
+.|+++..+..++.+|...|+++++...
T Consensus 143 ~~p~~~~~~~~la~i~~~~g~~~eA~~~ 170 (355)
T cd05804 143 LNPDDAWAVHAVAHVLEMQGRFKEGIAF 170 (355)
T ss_pred hCCCCcHHHHHHHHHHHHcCCHHHHHHH
Confidence 5677777788888888888888887764
No 43
>PRK11189 lipoprotein NlpI; Provisional
Probab=43.43 E-value=30 Score=25.87 Aligned_cols=27 Identities=11% Similarity=0.112 Sum_probs=15.9
Q ss_pred CCCCCchhHHHHHHHHHHcCCChhHHH
Q 033305 2 INLNNMRVYVILSNAYAAARRWKDTAR 28 (122)
Q Consensus 2 l~p~~~~~yvlLsniYa~~G~w~~~~~ 28 (122)
++|+++..|..+..+|...|++++|..
T Consensus 93 l~P~~~~a~~~lg~~~~~~g~~~~A~~ 119 (296)
T PRK11189 93 LRPDMADAYNYLGIYLTQAGNFDAAYE 119 (296)
T ss_pred cCCCCHHHHHHHHHHHHHCCCHHHHHH
Confidence 455555566666666666666665554
No 44
>COG4235 Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]
Probab=42.91 E-value=28 Score=26.65 Aligned_cols=36 Identities=28% Similarity=0.311 Sum_probs=29.5
Q ss_pred CCCCCchhHHHHHHHHHHcCCChhHHH-HHHHHhccC
Q 033305 2 INLNNMRVYVILSNAYAAARRWKDTAR-LRVSVRNKG 37 (122)
Q Consensus 2 l~p~~~~~yvlLsniYa~~G~w~~~~~-~r~~m~~~~ 37 (122)
-+|+|+..|.+|..+|...|+.++|.. .++..+-.|
T Consensus 151 ~nP~d~egW~~Lg~~ym~~~~~~~A~~AY~~A~rL~g 187 (287)
T COG4235 151 QNPGDAEGWDLLGRAYMALGRASDALLAYRNALRLAG 187 (287)
T ss_pred hCCCCchhHHHHHHHHHHhcchhHHHHHHHHHHHhCC
Confidence 379999999999999999999999886 466655433
No 45
>PRK11189 lipoprotein NlpI; Provisional
Probab=41.44 E-value=32 Score=25.74 Aligned_cols=31 Identities=10% Similarity=-0.026 Sum_probs=26.9
Q ss_pred CCCCCCchhHHHHHHHHHHcCCChhHHHHHH
Q 033305 1 MINLNNMRVYVILSNAYAAARRWKDTARLRV 31 (122)
Q Consensus 1 el~p~~~~~yvlLsniYa~~G~w~~~~~~r~ 31 (122)
+++|+++.+|..+..+|...|++++|.+.-+
T Consensus 126 ~l~P~~~~a~~~lg~~l~~~g~~~eA~~~~~ 156 (296)
T PRK11189 126 ELDPTYNYAYLNRGIALYYGGRYELAQDDLL 156 (296)
T ss_pred HhCCCCHHHHHHHHHHHHHCCCHHHHHHHHH
Confidence 4789999999999999999999999987543
No 46
>PF12895 Apc3: Anaphase-promoting complex, cyclosome, subunit 3; PDB: 3KAE_D 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2XPI_A 3ULQ_A.
Probab=40.74 E-value=9.7 Score=22.62 Aligned_cols=21 Identities=5% Similarity=0.267 Sum_probs=10.8
Q ss_pred hHHHHHHHHHHcCCChhHHHH
Q 033305 9 VYVILSNAYAAARRWKDTARL 29 (122)
Q Consensus 9 ~yvlLsniYa~~G~w~~~~~~ 29 (122)
...+++.+|-..|++++|.++
T Consensus 60 ~~~l~a~~~~~l~~y~eAi~~ 80 (84)
T PF12895_consen 60 IHYLLARCLLKLGKYEEAIKA 80 (84)
T ss_dssp HHHHHHHHHHHTT-HHHHHHH
T ss_pred HHHHHHHHHHHhCCHHHHHHH
Confidence 334445666666666655543
No 47
>PRK12370 invasion protein regulator; Provisional
Probab=40.06 E-value=32 Score=28.23 Aligned_cols=30 Identities=3% Similarity=-0.027 Sum_probs=25.2
Q ss_pred CCCCCCchhHHHHHHHHHHcCCChhHHHHH
Q 033305 1 MINLNNMRVYVILSNAYAAARRWKDTARLR 30 (122)
Q Consensus 1 el~p~~~~~yvlLsniYa~~G~w~~~~~~r 30 (122)
+++|.++..|..++.+|...|++++|...-
T Consensus 366 ~l~P~~~~a~~~lg~~l~~~G~~~eAi~~~ 395 (553)
T PRK12370 366 LLSPISADIKYYYGWNLFMAGQLEEALQTI 395 (553)
T ss_pred HhCCCCHHHHHHHHHHHHHCCCHHHHHHHH
Confidence 368999888999999999999999887753
No 48
>PLN03088 SGT1, suppressor of G2 allele of SKP1; Provisional
Probab=39.21 E-value=35 Score=26.42 Aligned_cols=31 Identities=6% Similarity=0.078 Sum_probs=27.1
Q ss_pred CCCCCCchhHHHHHHHHHHcCCChhHHHHHH
Q 033305 1 MINLNNMRVYVILSNAYAAARRWKDTARLRV 31 (122)
Q Consensus 1 el~p~~~~~yvlLsniYa~~G~w~~~~~~r~ 31 (122)
+++|.++.+|..++.+|...|++++|...-.
T Consensus 64 ~l~P~~~~a~~~lg~~~~~lg~~~eA~~~~~ 94 (356)
T PLN03088 64 ELDPSLAKAYLRKGTACMKLEEYQTAKAALE 94 (356)
T ss_pred HhCcCCHHHHHHHHHHHHHhCCHHHHHHHHH
Confidence 3689999999999999999999999988543
No 49
>PF09295 ChAPs: ChAPs (Chs5p-Arf1p-binding proteins); InterPro: IPR015374 ChAPs (Chs5p-Arf1p-binding proteins) are required for the export of specialised cargo from the Golgi. They physically interact with Chs3, Chs5 and the small GTPase Arf1, and they also form interactions with each other [].
Probab=37.57 E-value=29 Score=27.71 Aligned_cols=31 Identities=10% Similarity=0.194 Sum_probs=26.6
Q ss_pred CCCCCchhHHHHHHHHHHcCCChhHHHHHHH
Q 033305 2 INLNNMRVYVILSNAYAAARRWKDTARLRVS 32 (122)
Q Consensus 2 l~p~~~~~yvlLsniYa~~G~w~~~~~~r~~ 32 (122)
+.|.+..+|..|+.+|...|+|++|.-.-..
T Consensus 263 lsP~~f~~W~~La~~Yi~~~d~e~ALlaLNs 293 (395)
T PF09295_consen 263 LSPSEFETWYQLAECYIQLGDFENALLALNS 293 (395)
T ss_pred hCchhHHHHHHHHHHHHhcCCHHHHHHHHhc
Confidence 5688899999999999999999999865443
No 50
>KOG1155 consensus Anaphase-promoting complex (APC), Cdc23 subunit [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=37.37 E-value=41 Score=27.80 Aligned_cols=31 Identities=19% Similarity=0.375 Sum_probs=27.9
Q ss_pred CCCCCCchhHHHHHHHHHHcCCChhHHHHHH
Q 033305 1 MINLNNMRVYVILSNAYAAARRWKDTARLRV 31 (122)
Q Consensus 1 el~p~~~~~yvlLsniYa~~G~w~~~~~~r~ 31 (122)
++.|.|+--++.|.++|...++.+||.+.-+
T Consensus 426 ~~kPnDsRlw~aLG~CY~kl~~~~eAiKCyk 456 (559)
T KOG1155|consen 426 ELKPNDSRLWVALGECYEKLNRLEEAIKCYK 456 (559)
T ss_pred hcCCCchHHHHHHHHHHHHhccHHHHHHHHH
Confidence 3679999999999999999999999998754
No 51
>PLN03098 LPA1 LOW PSII ACCUMULATION1; Provisional
Probab=37.27 E-value=44 Score=27.24 Aligned_cols=34 Identities=26% Similarity=0.210 Sum_probs=23.8
Q ss_pred CCCCCCch---hHHHHHHHHHHcCCChhHHH-HHHHHh
Q 033305 1 MINLNNMR---VYVILSNAYAAARRWKDTAR-LRVSVR 34 (122)
Q Consensus 1 el~p~~~~---~yvlLsniYa~~G~w~~~~~-~r~~m~ 34 (122)
+++|+++. +|.-++..|+..|+.++|.. +++.+.
T Consensus 103 eL~Pd~aeA~~A~yNLAcaya~LGr~dEAla~LrrALe 140 (453)
T PLN03098 103 ELNPNPDEAQAAYYNKACCHAYREEGKKAADCLRTALR 140 (453)
T ss_pred hhCCCchHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence 36777764 37778888888888887776 455554
No 52
>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=37.20 E-value=48 Score=22.24 Aligned_cols=22 Identities=9% Similarity=0.016 Sum_probs=12.2
Q ss_pred hhHHHHHHHHHHcCCChhHHHH
Q 033305 8 RVYVILSNAYAAARRWKDTARL 29 (122)
Q Consensus 8 ~~yvlLsniYa~~G~w~~~~~~ 29 (122)
..+..++.+|...|+++++...
T Consensus 136 ~~~~~l~~~~~~~g~~~~A~~~ 157 (234)
T TIGR02521 136 RSLENAGLCALKAGDFDKAEKY 157 (234)
T ss_pred HHHHHHHHHHHHcCCHHHHHHH
Confidence 3444555566666666655543
No 53
>COG4890 Predicted outer membrane lipoprotein [Function unknown]
Probab=37.05 E-value=21 Score=18.44 Aligned_cols=13 Identities=31% Similarity=0.399 Sum_probs=9.7
Q ss_pred HHHHHHHHHhhcC
Q 033305 98 SGRFAIVFGAIST 110 (122)
Q Consensus 98 seklaia~gl~~~ 110 (122)
.--||-|||+|+.
T Consensus 9 G~lLAcAFgiinA 21 (37)
T COG4890 9 GLLLACAFGIINA 21 (37)
T ss_pred HHHHHHHHHHHHH
Confidence 3568889998863
No 54
>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=36.97 E-value=47 Score=23.05 Aligned_cols=37 Identities=11% Similarity=0.052 Sum_probs=28.7
Q ss_pred CCCCCchhHHHHHHHHHHcCCChhHHHHHHHHhccCC
Q 033305 2 INLNNMRVYVILSNAYAAARRWKDTARLRVSVRNKGM 38 (122)
Q Consensus 2 l~p~~~~~yvlLsniYa~~G~w~~~~~~r~~m~~~~l 38 (122)
|-|+.+..-++-.-+|-..|+|+|+.++.+...+.+.
T Consensus 39 LrP~~~e~d~~dg~l~i~rg~w~eA~rvlr~l~~~~~ 75 (153)
T TIGR02561 39 LRPNLKELDMFDGWLLIARGNYDEAARILRELLSSAG 75 (153)
T ss_pred hCCCccccchhHHHHHHHcCCHHHHHHHHHhhhccCC
Confidence 4577777777778889999999999998766655443
No 55
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=36.93 E-value=47 Score=25.18 Aligned_cols=33 Identities=9% Similarity=0.216 Sum_probs=23.5
Q ss_pred CCCCCchhHHHHHHHHHHcCCChhHHHHHHHHh
Q 033305 2 INLNNMRVYVILSNAYAAARRWKDTARLRVSVR 34 (122)
Q Consensus 2 l~p~~~~~yvlLsniYa~~G~w~~~~~~r~~m~ 34 (122)
++|.+...|..++++|...|+.++|..+...+.
T Consensus 64 ~~p~~~~~~~~la~~~~~~g~~~~A~~~~~~~l 96 (389)
T PRK11788 64 VDPETVELHLALGNLFRRRGEVDRAIRIHQNLL 96 (389)
T ss_pred cCcccHHHHHHHHHHHHHcCcHHHHHHHHHHHh
Confidence 467777777777888888888877777655443
No 56
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=36.54 E-value=40 Score=25.52 Aligned_cols=32 Identities=13% Similarity=0.148 Sum_probs=22.2
Q ss_pred CCCCchhHHHHHHHHHHcCCChhHHHHHHHHh
Q 033305 3 NLNNMRVYVILSNAYAAARRWKDTARLRVSVR 34 (122)
Q Consensus 3 ~p~~~~~yvlLsniYa~~G~w~~~~~~r~~m~ 34 (122)
+|.+...+..++.+|...|++++|.+.-+.+.
T Consensus 210 ~p~~~~~~~~la~~~~~~g~~~~A~~~~~~~~ 241 (389)
T PRK11788 210 DPQCVRASILLGDLALAQGDYAAAIEALERVE 241 (389)
T ss_pred CcCCHHHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence 56666677777788888888877777654443
No 57
>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=36.14 E-value=46 Score=27.55 Aligned_cols=35 Identities=11% Similarity=0.117 Sum_probs=29.2
Q ss_pred CCCCCchhHHHHHHHHHHcCCChhHHHHHHHHhcc
Q 033305 2 INLNNMRVYVILSNAYAAARRWKDTARLRVSVRNK 36 (122)
Q Consensus 2 l~p~~~~~yvlLsniYa~~G~w~~~~~~r~~m~~~ 36 (122)
..|.++..+..++.+|...|+|++|...-..+.+.
T Consensus 51 ~~p~~~~~~~~l~~~~~~~g~~~~A~~~~~~~~~~ 85 (899)
T TIGR02917 51 KDPNDAEARFLLGKIYLALGDYAAAEKELRKALSL 85 (899)
T ss_pred hCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHc
Confidence 47899999999999999999999999876555443
No 58
>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=35.29 E-value=39 Score=16.02 Aligned_cols=22 Identities=23% Similarity=0.356 Sum_probs=17.7
Q ss_pred hHHHHHHHHHHcCCChhHHHHH
Q 033305 9 VYVILSNAYAAARRWKDTARLR 30 (122)
Q Consensus 9 ~yvlLsniYa~~G~w~~~~~~r 30 (122)
.|..+..+|...|++++|..--
T Consensus 3 ~~~~~g~~~~~~~~~~~A~~~~ 24 (34)
T PF00515_consen 3 AYYNLGNAYFQLGDYEEALEYY 24 (34)
T ss_dssp HHHHHHHHHHHTT-HHHHHHHH
T ss_pred HHHHHHHHHHHhCCchHHHHHH
Confidence 5788999999999999988753
No 59
>KOG2499 consensus Beta-N-acetylhexosaminidase [Carbohydrate transport and metabolism]
Probab=34.74 E-value=54 Score=27.17 Aligned_cols=38 Identities=26% Similarity=0.516 Sum_probs=33.2
Q ss_pred CCCCCchhHHHHHHHHHH------------------cCCChhHHHHHHHHhccCCC
Q 033305 2 INLNNMRVYVILSNAYAA------------------ARRWKDTARLRVSVRNKGMK 39 (122)
Q Consensus 2 l~p~~~~~yvlLsniYa~------------------~G~w~~~~~~r~~m~~~~l~ 39 (122)
++|-+...|-+|+++|.+ .+.|+.-.+++.-|+.+|..
T Consensus 303 lnP~~n~tydvls~i~~dv~evFp~~~~HlGGDEV~~~CW~s~~~Iq~fM~~kGfg 358 (542)
T KOG2499|consen 303 LNPTNNHTYDVLSEIFEDVSEVFPDEFFHLGGDEVSTPCWKSNPEIQDFMRKKGFG 358 (542)
T ss_pred CCCCchhHHHHHHHHHHHHHHhCcHHHeecCCceeecccccCChHHHHHHHhCCCC
Confidence 578888889999999986 47899999999999998875
No 60
>PRK15363 pathogenicity island 2 chaperone protein SscA; Provisional
Probab=34.51 E-value=67 Score=22.33 Aligned_cols=31 Identities=10% Similarity=0.038 Sum_probs=26.9
Q ss_pred CCCCCchhHHHHHHHHHHcCCChhHHHHHHH
Q 033305 2 INLNNMRVYVILSNAYAAARRWKDTARLRVS 32 (122)
Q Consensus 2 l~p~~~~~yvlLsniYa~~G~w~~~~~~r~~ 32 (122)
++|++|.+|.-+...|-..|+.+.|.+-.+.
T Consensus 98 L~~ddp~~~~~ag~c~L~lG~~~~A~~aF~~ 128 (157)
T PRK15363 98 IKIDAPQAPWAAAECYLACDNVCYAIKALKA 128 (157)
T ss_pred cCCCCchHHHHHHHHHHHcCCHHHHHHHHHH
Confidence 7899999999999999999999998886543
No 61
>PRK08057 cobalt-precorrin-6x reductase; Reviewed
Probab=34.00 E-value=1.1e+02 Score=22.68 Aligned_cols=44 Identities=18% Similarity=0.355 Sum_probs=33.8
Q ss_pred HcCCChhHHHHHHHHhccCCCCCCceeEEEec-ccchhhhhHHHHHHHHHHH
Q 033305 19 AARRWKDTARLRVSVRNKGMKKTPACSWTEIK-SHPYRLRINEALKDLFERM 69 (122)
Q Consensus 19 ~~G~w~~~~~~r~~m~~~~l~k~~g~S~iev~-~h~~~~~i~~~l~~l~~~~ 69 (122)
-.|+..+...++..++++++. .-|| +||...+|.....+.-.++
T Consensus 47 ~~G~l~~~~~l~~~l~~~~i~-------~VIDATHPfA~~is~~a~~ac~~~ 91 (248)
T PRK08057 47 RVGGFGGAEGLAAYLREEGID-------LVIDATHPYAAQISANAAAACRAL 91 (248)
T ss_pred EECCCCCHHHHHHHHHHCCCC-------EEEECCCccHHHHHHHHHHHHHHh
Confidence 357787888899999888876 2355 8999999988777766655
No 62
>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=33.81 E-value=56 Score=27.05 Aligned_cols=34 Identities=18% Similarity=0.260 Sum_probs=19.6
Q ss_pred CCCCchhHHHHHHHHHHcCCChhHHHHHHHHhcc
Q 033305 3 NLNNMRVYVILSNAYAAARRWKDTARLRVSVRNK 36 (122)
Q Consensus 3 ~p~~~~~yvlLsniYa~~G~w~~~~~~r~~m~~~ 36 (122)
+|.+...+..+.++|...|+++++.++...+.+.
T Consensus 665 ~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~ 698 (899)
T TIGR02917 665 KPDNTEAQIGLAQLLLAAKRTESAKKIAKSLQKQ 698 (899)
T ss_pred CCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHhh
Confidence 4555555566666666666666666555555443
No 63
>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=33.42 E-value=49 Score=22.18 Aligned_cols=27 Identities=11% Similarity=0.193 Sum_probs=15.8
Q ss_pred CCCCchhHHHHHHHHHHcCCChhHHHH
Q 033305 3 NLNNMRVYVILSNAYAAARRWKDTARL 29 (122)
Q Consensus 3 ~p~~~~~yvlLsniYa~~G~w~~~~~~ 29 (122)
+|.++..+..++.+|...|+++++.+.
T Consensus 61 ~p~~~~~~~~la~~~~~~~~~~~A~~~ 87 (234)
T TIGR02521 61 DPDDYLAYLALALYYQQLGELEKAEDS 87 (234)
T ss_pred CcccHHHHHHHHHHHHHcCCHHHHHHH
Confidence 455555556666666666666655554
No 64
>PRK15174 Vi polysaccharide export protein VexE; Provisional
Probab=30.31 E-value=60 Score=27.36 Aligned_cols=28 Identities=11% Similarity=0.282 Sum_probs=19.9
Q ss_pred CCCCCchhHHHHHHHHHHcCCChhHHHH
Q 033305 2 INLNNMRVYVILSNAYAAARRWKDTARL 29 (122)
Q Consensus 2 l~p~~~~~yvlLsniYa~~G~w~~~~~~ 29 (122)
++|+++.+|..++++|...|++++|...
T Consensus 105 ~~P~~~~a~~~la~~l~~~g~~~~Ai~~ 132 (656)
T PRK15174 105 VNVCQPEDVLLVASVLLKSKQYATVADL 132 (656)
T ss_pred hCCCChHHHHHHHHHHHHcCCHHHHHHH
Confidence 4677777777777777777777776653
No 65
>COG4783 Putative Zn-dependent protease, contains TPR repeats [General function prediction only]
Probab=29.73 E-value=82 Score=25.92 Aligned_cols=31 Identities=16% Similarity=0.179 Sum_probs=25.5
Q ss_pred CCCCchhHHHHHHHHHHcCCChhHHHHHHHH
Q 033305 3 NLNNMRVYVILSNAYAAARRWKDTARLRVSV 33 (122)
Q Consensus 3 ~p~~~~~yvlLsniYa~~G~w~~~~~~r~~m 33 (122)
+|+++..|-+|+.-|+..|+..++..-+..+
T Consensus 404 ~p~dp~~w~~LAqay~~~g~~~~a~~A~AE~ 434 (484)
T COG4783 404 DPEDPNGWDLLAQAYAELGNRAEALLARAEG 434 (484)
T ss_pred CCCCchHHHHHHHHHHHhCchHHHHHHHHHH
Confidence 6899999999999999988888777666543
No 66
>COG3063 PilF Tfp pilus assembly protein PilF [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=29.61 E-value=71 Score=23.95 Aligned_cols=35 Identities=6% Similarity=-0.063 Sum_probs=29.3
Q ss_pred CCCCCCchhHHHHHHHHHHcCCChhHHHH-HHHHhc
Q 033305 1 MINLNNMRVYVILSNAYAAARRWKDTARL-RVSVRN 35 (122)
Q Consensus 1 el~p~~~~~yvlLsniYa~~G~w~~~~~~-r~~m~~ 35 (122)
+.||.+..+|.+++-+|...|.-+.|.+. |+.++.
T Consensus 63 ~~DPs~~~a~~~~A~~Yq~~Ge~~~A~e~YrkAlsl 98 (250)
T COG3063 63 EHDPSYYLAHLVRAHYYQKLGENDLADESYRKALSL 98 (250)
T ss_pred HhCcccHHHHHHHHHHHHHcCChhhHHHHHHHHHhc
Confidence 35899999999999999999999988874 766653
No 67
>PF08967 DUF1884: Domain of unknown function (DUF1884); InterPro: IPR014418 This group represents an uncharacterised conserved protein.; PDB: 2PK8_A.
Probab=28.73 E-value=74 Score=19.81 Aligned_cols=24 Identities=21% Similarity=0.497 Sum_probs=14.7
Q ss_pred hhHHHHHHHHHHHHhcCcccCCCc
Q 033305 57 RINEALKDLFERMEQEGYVPTTKE 80 (122)
Q Consensus 57 ~i~~~l~~l~~~~~~~gy~~~~~~ 80 (122)
.|.+.+++-..+++..||.||.-.
T Consensus 9 ~il~~ie~~inELk~dG~ePDivL 32 (85)
T PF08967_consen 9 RILELIEEKINELKEDGFEPDIVL 32 (85)
T ss_dssp HHHHHHHHHHHHHHHTT----EEE
T ss_pred HHHHHHHHHHHHHHhcCCCCCEEE
Confidence 456677777788999999998543
No 68
>PF11398 DUF2813: Protein of unknown function (DUF2813); InterPro: IPR022602 This entry contains YbjD from Escherichia coli (strain K12), which is a conserved protein with a nucleotide triphosphate binding domain.
Probab=28.01 E-value=1.1e+02 Score=24.31 Aligned_cols=52 Identities=21% Similarity=0.257 Sum_probs=31.9
Q ss_pred HHHHHHHHHhcCcccCC--CccccccchHhhhhhhhhhHHHHHHHHHhhcCCCCCeEE
Q 033305 62 LKDLFERMEQEGYVPTT--KEALHDVEDEQKKNLLHYHSGRFAIVFGAISTPDGRTIR 117 (122)
Q Consensus 62 l~~l~~~~~~~gy~~~~--~~~~~~~~ee~~~~~~~~Hseklaia~gl~~~~~~~~ir 117 (122)
+.-+...+...|.++-. ...+.-+||-| ...|.-.+|+||+|++.-|+..|-
T Consensus 265 l~l~~a~l~a~g~~~l~~~arPIlliEDPE----arLHP~ml~~aW~ll~~lP~QkI~ 318 (373)
T PF11398_consen 265 LGLFSALLQAKGPVELDRDARPILLIEDPE----ARLHPIMLAIAWSLLSLLPGQKIT 318 (373)
T ss_pred HHHHHHHHHhCCccccCCCCcceEEEeCcc----cccCHHHHHHHHHHHhhCCccEEe
Confidence 44444455556654421 12333343321 245999999999999999888763
No 69
>PF02662 FlpD: Methyl-viologen-reducing hydrogenase, delta subunit; InterPro: IPR003813 Methyl-viologen-reducing hydrogenase (MVH) is one of the enzymes involved in methanogenesis and coded in the mth-flp-mvh-mrt cluster of methane genes in Methanothermobacter thermautotrophicus (Methanobacterium thermoformicicum) []. No specific functions have been assigned to the delta subunit.; GO: 0015948 methanogenesis, 0055114 oxidation-reduction process
Probab=27.61 E-value=1.8e+02 Score=19.03 Aligned_cols=46 Identities=24% Similarity=0.446 Sum_probs=28.7
Q ss_pred hHHHHHHHHhccCCC-CCCceeEEEecccchhhhhHHHHHHHHHHHHhcC
Q 033305 25 DTARLRVSVRNKGMK-KTPACSWTEIKSHPYRLRINEALKDLFERMEQEG 73 (122)
Q Consensus 25 ~~~~~r~~m~~~~l~-k~~g~S~iev~~h~~~~~i~~~l~~l~~~~~~~g 73 (122)
.+..+++.+.+.|+. ..-...|+ +.+..+..-..+.++..++++.|
T Consensus 78 Rv~~~k~~L~~~Gi~~eRv~~~~~---~~~~~~~fa~~~~~f~~~i~~lG 124 (124)
T PF02662_consen 78 RVERLKKLLEELGIEPERVRLYWI---SAPEGKRFAEIVNEFTERIKELG 124 (124)
T ss_pred HHHHHHHHHHHcCCChhHeEEEEe---CcccHHHHHHHHHHHHHHHHHcC
Confidence 456678888888887 33356666 34455555556666666665544
No 70
>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=27.59 E-value=35 Score=19.61 Aligned_cols=26 Identities=15% Similarity=0.264 Sum_probs=20.5
Q ss_pred chhHHHHHHHHHHcCCChhHHHHHHH
Q 033305 7 MRVYVILSNAYAAARRWKDTARLRVS 32 (122)
Q Consensus 7 ~~~yvlLsniYa~~G~w~~~~~~r~~ 32 (122)
+..|..++.+|-..|+|++|...-..
T Consensus 5 a~~~~~la~~~~~~~~~~~A~~~~~~ 30 (78)
T PF13424_consen 5 ANAYNNLARVYRELGRYDEALDYYEK 30 (78)
T ss_dssp HHHHHHHHHHHHHTT-HHHHHHHHHH
T ss_pred HHHHHHHHHHHHHcCCHHHHHHHHHH
Confidence 45688899999999999999986443
No 71
>PF10925 DUF2680: Protein of unknown function (DUF2680); InterPro: IPR024485 Members in this family of proteins are annotated as YckD however currently no function is known.
Probab=27.35 E-value=1e+02 Score=17.69 Aligned_cols=25 Identities=28% Similarity=0.434 Sum_probs=19.4
Q ss_pred cchhhhhHHHHHHHHHHHHhcCccc
Q 033305 52 HPYRLRINEALKDLFERMEQEGYVP 76 (122)
Q Consensus 52 h~~~~~i~~~l~~l~~~~~~~gy~~ 76 (122)
-.+.+.|...++.-...+...||+|
T Consensus 35 qeqAd~ik~~id~~~~~~~qnGf~p 59 (59)
T PF10925_consen 35 QEQADAIKKHIDQRQEYMQQNGFVP 59 (59)
T ss_pred HHHHHHHHHHHHHHHHHHHHcCCCC
Confidence 4566777878888888888888887
No 72
>PF06135 DUF965: Bacterial protein of unknown function (DUF965); InterPro: IPR009309 This family consists of several hypothetical bacterial proteins. The function of the family is unknown.
Probab=27.35 E-value=85 Score=19.33 Aligned_cols=23 Identities=35% Similarity=0.707 Sum_probs=18.9
Q ss_pred hhhHHHHHHHHHHHHhcCcccCC
Q 033305 56 LRINEALKDLFERMEQEGYVPTT 78 (122)
Q Consensus 56 ~~i~~~l~~l~~~~~~~gy~~~~ 78 (122)
..+...|..+...+.+.||-|-.
T Consensus 15 ~~~~~iL~~Vy~AL~EKGYnPin 37 (79)
T PF06135_consen 15 KEIREILKQVYAALEEKGYNPIN 37 (79)
T ss_pred hhHHHHHHHHHHHHHHcCCChHH
Confidence 45677888999999999998853
No 73
>PRK10747 putative protoheme IX biogenesis protein; Provisional
Probab=25.04 E-value=97 Score=24.22 Aligned_cols=31 Identities=6% Similarity=0.145 Sum_probs=27.0
Q ss_pred CCCCchhHHHHHHHHHHcCCChhHHHHHHHH
Q 033305 3 NLNNMRVYVILSNAYAAARRWKDTARLRVSV 33 (122)
Q Consensus 3 ~p~~~~~yvlLsniYa~~G~w~~~~~~r~~m 33 (122)
.|+|+..+..+..++...|+|++|.+..+..
T Consensus 324 ~P~~~~l~l~lgrl~~~~~~~~~A~~~le~a 354 (398)
T PRK10747 324 HGDTPLLWSTLGQLLMKHGEWQEASLAFRAA 354 (398)
T ss_pred CCCCHHHHHHHHHHHHHCCCHHHHHHHHHHH
Confidence 6899999999999999999999999865443
No 74
>PF02571 CbiJ: Precorrin-6x reductase CbiJ/CobK; InterPro: IPR003723 Cobalamin (vitamin B12) is a structurally complex cofactor, consisting of a modified tetrapyrrole with a centrally chelated cobalt. Cobalamin is usually found in one of two biologically active forms: methylcobalamin and adocobalamin. Most prokaryotes, as well as animals, have cobalamin-dependent enzymes, whereas plants and fungi do not appear to use it. In bacteria and archaea, these include methionine synthase, ribonucleotide reductase, glutamate and methylmalonyl-CoA mutases, ethanolamine ammonia lyase, and diol dehydratase []. In mammals, cobalamin is obtained through the diet, and is required for methionine synthase and methylmalonyl-CoA mutase []. There are at least two distinct cobalamin biosynthetic pathways in bacteria []: Aerobic pathway that requires oxygen and in which cobalt is inserted late in the pathway []; found in Pseudomonas denitrificans and Rhodobacter capsulatus. Anaerobic pathway in which cobalt insertion is the first committed step towards cobalamin synthesis []; found in Salmonella typhimurium, Bacillus megaterium, and Propionibacterium freudenreichii subsp. shermanii. Either pathway can be divided into two parts: (1) corrin ring synthesis (differs in aerobic and anaerobic pathways) and (2) adenosylation of corrin ring, attachment of aminopropanol arm, and assembly of the nucleotide loop (common to both pathways) []. There are about 30 enzymes involved in either pathway, where those involved in the aerobic pathway are prefixed Cob and those of the anaerobic pathway Cbi. Several of these enzymes are pathway-specific: CbiD, CbiG, and CbiK are specific to the anaerobic route of S. typhimurium, whereas CobE, CobF, CobG, CobN, CobS, CobT, and CobW are unique to the aerobic pathway of P. denitrificans. This entry represents CobK and CbiJ precorrin-6x reductase (1.3.1.54 from EC). In the aerobic pathway, CobK catalyses the reduction of the macrocycle of precorrin-6X to produce precorrin-6Y; while in the anaerobic pathway CbiJ catalyses the reduction of the macrocycle of cobalt-precorrin-6X into cobalt-precorrin-6Y [, ].; GO: 0016994 precorrin-6A reductase activity, 0009236 cobalamin biosynthetic process, 0055114 oxidation-reduction process
Probab=24.95 E-value=1.7e+02 Score=21.64 Aligned_cols=43 Identities=21% Similarity=0.382 Sum_probs=31.8
Q ss_pred cCCChhHHHHHHHHhccCCCCCCceeEEEec-ccchhhhhHHHHHHHHHHH
Q 033305 20 ARRWKDTARLRVSVRNKGMKKTPACSWTEIK-SHPYRLRINEALKDLFERM 69 (122)
Q Consensus 20 ~G~w~~~~~~r~~m~~~~l~k~~g~S~iev~-~h~~~~~i~~~l~~l~~~~ 69 (122)
.|+..+...+...++++++. +| || +||...+|..-......++
T Consensus 49 ~G~lg~~~~l~~~l~~~~i~------~v-IDATHPfA~~is~na~~a~~~~ 92 (249)
T PF02571_consen 49 VGRLGDEEGLAEFLRENGID------AV-IDATHPFAAEISQNAIEACREL 92 (249)
T ss_pred ECCCCCHHHHHHHHHhCCCc------EE-EECCCchHHHHHHHHHHHHhhc
Confidence 56776778888888888775 33 55 8999999887776665554
No 75
>KOG1127 consensus TPR repeat-containing protein [RNA processing and modification]
Probab=24.52 E-value=80 Score=28.67 Aligned_cols=50 Identities=10% Similarity=0.250 Sum_probs=35.8
Q ss_pred CCCCCCchhHHHHHHHHHHcCCChhHHHHHHHHhccCCCCCCceeEEEec
Q 033305 1 MINLNNMRVYVILSNAYAAARRWKDTARLRVSVRNKGMKKTPACSWTEIK 50 (122)
Q Consensus 1 el~p~~~~~yvlLsniYa~~G~w~~~~~~r~~m~~~~l~k~~g~S~iev~ 50 (122)
||||.+.-+.--+...||....|+.|..++..-.++......-.-|+..+
T Consensus 520 eLDatdaeaaaa~adtyae~~~we~a~~I~l~~~qka~a~~~k~nW~~rG 569 (1238)
T KOG1127|consen 520 ELDATDAEAAAASADTYAEESTWEEAFEICLRAAQKAPAFACKENWVQRG 569 (1238)
T ss_pred cCCchhhhhHHHHHHHhhccccHHHHHHHHHHHhhhchHHHHHhhhhhcc
Confidence 58888888888899999999999999988554444333333334566554
No 76
>PF14561 TPR_20: Tetratricopeptide repeat; PDB: 3QOU_A 2R5S_A 3QDN_B.
Probab=24.50 E-value=83 Score=19.40 Aligned_cols=27 Identities=19% Similarity=0.277 Sum_probs=21.9
Q ss_pred CCCCchhHHHHHHHHHHcCCChhHHHH
Q 033305 3 NLNNMRVYVILSNAYAAARRWKDTARL 29 (122)
Q Consensus 3 ~p~~~~~yvlLsniYa~~G~w~~~~~~ 29 (122)
+|.|...-..|+..|...|++++|...
T Consensus 18 ~P~D~~ar~~lA~~~~~~g~~e~Al~~ 44 (90)
T PF14561_consen 18 NPDDLDARYALADALLAAGDYEEALDQ 44 (90)
T ss_dssp STT-HHHHHHHHHHHHHTT-HHHHHHH
T ss_pred CCCCHHHHHHHHHHHHHCCCHHHHHHH
Confidence 688888888999999999999998864
No 77
>PF13429 TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2_B.
Probab=24.39 E-value=50 Score=24.09 Aligned_cols=30 Identities=17% Similarity=0.249 Sum_probs=23.1
Q ss_pred CCCchhHHHHHHHHHHcCCChhHHHH-HHHH
Q 033305 4 LNNMRVYVILSNAYAAARRWKDTARL-RVSV 33 (122)
Q Consensus 4 p~~~~~yvlLsniYa~~G~w~~~~~~-r~~m 33 (122)
|.++..|+.++++|...|++++|.+. ++.+
T Consensus 143 ~~~~~~~~~~a~~~~~~G~~~~A~~~~~~al 173 (280)
T PF13429_consen 143 PDSARFWLALAEIYEQLGDPDKALRDYRKAL 173 (280)
T ss_dssp -T-HHHHHHHHHHHHHCCHHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence 45677889999999999999999875 4433
No 78
>cd06570 GH20_chitobiase-like_1 A functionally uncharacterized subgroup of the Glycosyl hydrolase family 20 (GH20) catalytic domain found in proteins similar to the chitobiase of Serratia marcescens, a beta-N-1,4-acetylhexosaminidase that hydrolyzes the beta-1,4-glycosidic linkages in oligomers derived from chitin. Chitin is degraded by a two step process: i) a chitinase hydrolyzes the chitin to oligosaccharides and disaccharides such as di-N-acetyl-D-glucosamine and chitobiose, ii) chitobiase then further degrades these oligomers into monomers. This subgroup lacks the C-terminal PKD (polycystic kidney disease I)-like domain found in the chitobiases. The GH20 hexosaminidases are thought to act via a catalytic mechanism in which the catalytic nucleophile is not provided by solvent or the enzyme, but by the substrate itself.
Probab=24.36 E-value=1.3e+02 Score=23.02 Aligned_cols=38 Identities=21% Similarity=0.655 Sum_probs=28.0
Q ss_pred CCCCCchhHHHHHHHHHH------------------cCCChhHHHHHHHHhccCCC
Q 033305 2 INLNNMRVYVILSNAYAA------------------ARRWKDTARLRVSVRNKGMK 39 (122)
Q Consensus 2 l~p~~~~~yvlLsniYa~------------------~G~w~~~~~~r~~m~~~~l~ 39 (122)
|+|.++.+|-++-+++.+ .+.|+....+++.|++.|+.
T Consensus 124 l~~~~p~t~~f~~~l~~E~~~lF~~~~iHiGgDE~~~~~W~~~p~~~~~~~~~g~~ 179 (311)
T cd06570 124 LDPTNEETYTFLDNLFGEMAELFPDEYFHIGGDEVDPKQWNENPRIQAFMKEHGLK 179 (311)
T ss_pred cCCCChhHHHHHHHHHHHHHHhCCCCceEeeccCCCCCcccCCHHHHHHHHHcCCC
Confidence 678889999999888875 24566666777777777664
No 79
>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=23.89 E-value=94 Score=25.71 Aligned_cols=27 Identities=7% Similarity=0.073 Sum_probs=14.1
Q ss_pred CCCCchhHHHHHHHHHHcCCChhHHHH
Q 033305 3 NLNNMRVYVILSNAYAAARRWKDTARL 29 (122)
Q Consensus 3 ~p~~~~~yvlLsniYa~~G~w~~~~~~ 29 (122)
+|.++..|..++.+|...|++++|...
T Consensus 395 ~p~~~~~~~~lg~~~~~~g~~~~A~~~ 421 (615)
T TIGR00990 395 NSEDPDIYYHRAQLHFIKGEFAQAGKD 421 (615)
T ss_pred CCCCHHHHHHHHHHHHHcCCHHHHHHH
Confidence 455555555555555555555555443
No 80
>PRK05473 hypothetical protein; Provisional
Probab=23.53 E-value=1.1e+02 Score=19.15 Aligned_cols=22 Identities=27% Similarity=0.688 Sum_probs=18.6
Q ss_pred hhhHHHHHHHHHHHHhcCcccC
Q 033305 56 LRINEALKDLFERMEQEGYVPT 77 (122)
Q Consensus 56 ~~i~~~l~~l~~~~~~~gy~~~ 77 (122)
.++...|......+.+.||-|-
T Consensus 18 ~~v~eiL~~Vy~AL~EKGYNPi 39 (86)
T PRK05473 18 KDVREILTTVYDALEEKGYNPI 39 (86)
T ss_pred HHHHHHHHHHHHHHHHcCCChH
Confidence 4578888999999999999885
No 81
>PF08482 HrpB_C: ATP-dependent helicase C-terminal; InterPro: IPR013689 This domain is found near the C terminus of bacterial ATP-dependent helicases such as HrpB.
Probab=23.25 E-value=43 Score=22.66 Aligned_cols=13 Identities=38% Similarity=0.866 Sum_probs=10.0
Q ss_pred CCCCCeEEEecCC
Q 033305 110 TPDGRTIRLINNL 122 (122)
Q Consensus 110 ~~~~~~irv~kn~ 122 (122)
+|.|+||.|+++|
T Consensus 93 SPa~RPiqvT~DL 105 (133)
T PF08482_consen 93 SPAGRPIQVTQDL 105 (133)
T ss_pred CCCCCceeeeCCH
Confidence 3678899988875
No 82
>COG1111 MPH1 ERCC4-like helicases [DNA replication, recombination, and repair]
Probab=23.17 E-value=2.8e+02 Score=23.29 Aligned_cols=99 Identities=19% Similarity=0.334 Sum_probs=56.4
Q ss_pred hHHHHHHHHHHcCCC-----------hhHHHHHHHHhccCCCCCC----------------ceeEEEecccchhhhhHHH
Q 033305 9 VYVILSNAYAAARRW-----------KDTARLRVSVRNKGMKKTP----------------ACSWTEIKSHPYRLRINEA 61 (122)
Q Consensus 9 ~yvlLsniYa~~G~w-----------~~~~~~r~~m~~~~l~k~~----------------g~S~iev~~h~~~~~i~~~ 61 (122)
+||.++.-|-...+- .+..++++.++.-|+.+.. -.-||.|+..+...+|-+.
T Consensus 148 AYv~Va~~y~~~~k~~~ilgLTASPGs~~ekI~eV~~nLgIe~vevrTE~d~DV~~Yv~~~kve~ikV~lp~e~~~ir~~ 227 (542)
T COG1111 148 AYVFVAKEYLRSAKNPLILGLTASPGSDLEKIQEVVENLGIEKVEVRTEEDPDVRPYVKKIKVEWIKVDLPEEIKEIRDL 227 (542)
T ss_pred hHHHHHHHHHHhccCceEEEEecCCCCCHHHHHHHHHhCCcceEEEecCCCccHHHhhccceeEEEeccCcHHHHHHHHH
Confidence 477777766554332 3456677777766665421 2346666655566666554
Q ss_pred ----HHHHHHHHHhcCcccCCCcc----cc----------ccchHhhhhhhhhhHHHHHHHHHh
Q 033305 62 ----LKDLFERMEQEGYVPTTKEA----LH----------DVEDEQKKNLLHYHSGRFAIVFGA 107 (122)
Q Consensus 62 ----l~~l~~~~~~~gy~~~~~~~----~~----------~~~ee~~~~~~~~Hseklaia~gl 107 (122)
|+.....+++.|+....+.+ +. --++..+...+.+|.+.+-+++++
T Consensus 228 l~~~l~~~Lk~L~~~g~~~~~~~~~~kdl~~~~~~~~~~a~~~~~~~~~~l~~~a~~~kl~~a~ 291 (542)
T COG1111 228 LRDALKPRLKPLKELGVIESSSPVSKKDLLELRQIRLIMAKNEDSDKFRLLSVLAEAIKLAHAL 291 (542)
T ss_pred HHHHHHHHHHHHHHcCceeccCcccHhHHHHHHHHHHHhccCccHHHHHHHHHHHHHHHHHHHH
Confidence 44455567888987654410 00 011344556777888877776654
No 83
>PRK15174 Vi polysaccharide export protein VexE; Provisional
Probab=23.02 E-value=89 Score=26.38 Aligned_cols=28 Identities=7% Similarity=0.045 Sum_probs=17.0
Q ss_pred CCCCCchhHHHHHHHHHHcCCChhHHHH
Q 033305 2 INLNNMRVYVILSNAYAAARRWKDTARL 29 (122)
Q Consensus 2 l~p~~~~~yvlLsniYa~~G~w~~~~~~ 29 (122)
++|+++..+..++.+|...|++++|...
T Consensus 313 l~P~~~~a~~~La~~l~~~G~~~eA~~~ 340 (656)
T PRK15174 313 THPDLPYVRAMYARALRQVGQYTAASDE 340 (656)
T ss_pred hCCCCHHHHHHHHHHHHHCCCHHHHHHH
Confidence 3566666666666666666666666553
No 84
>KOG1076 consensus Translation initiation factor 3, subunit c (eIF-3c) [Translation, ribosomal structure and biogenesis]
Probab=22.46 E-value=2.6e+02 Score=24.50 Aligned_cols=99 Identities=15% Similarity=0.218 Sum_probs=54.2
Q ss_pred CCCchhHHHHHHHHHHcCCChhHHH-HHHHHhccCCCCCCc-------------------------eeEEEec-------
Q 033305 4 LNNMRVYVILSNAYAAARRWKDTAR-LRVSVRNKGMKKTPA-------------------------CSWTEIK------- 50 (122)
Q Consensus 4 p~~~~~yvlLsniYa~~G~w~~~~~-~r~~m~~~~l~k~~g-------------------------~S~iev~------- 50 (122)
|++.--||+.+.=-...|.|.++.. ++...+-..+-+..- ++.+.+.
T Consensus 650 PEn~RehVvaAsKAm~~Gnw~~c~~fi~nn~KvW~Lfpn~d~V~~Ml~~rIqEEsLRTYLftYss~Y~SvSl~~LA~mFd 729 (843)
T KOG1076|consen 650 PENTREHVVAASKAMQKGNWQKCFEFIVNNIKVWDLFPNADTVLDMLTERIQEESLRTYLFTYSSVYDSVSLAKLADMFD 729 (843)
T ss_pred chhHHHHHHHHHHHHhcCCHHHHHHHHHhhhhHHHhcccHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhccHHHHHHHhC
Confidence 6677779888777778899998876 444333333322110 1112111
Q ss_pred -ccchhhhhHHHHHHHHHHHHhcC--cccCCCccccccchHhhhhhhhhhHHHHHHHH
Q 033305 51 -SHPYRLRINEALKDLFERMEQEG--YVPTTKEALHDVEDEQKKNLLHYHSGRFAIVF 105 (122)
Q Consensus 51 -~h~~~~~i~~~l~~l~~~~~~~g--y~~~~~~~~~~~~ee~~~~~~~~Hseklaia~ 105 (122)
+-| .+++.+..+........ --|....++|-++....+.....-+||+++.-
T Consensus 730 Lp~~---~VhsIiSkmiineEl~AslDqpt~~iv~hrvE~srlq~La~qL~eKl~~L~ 784 (843)
T KOG1076|consen 730 LPEP---KVHSIISKMIINEELHASLDQPTQCIVMHRVEPSRLQSLAVQLSEKLAILA 784 (843)
T ss_pred CCch---hHHHHHHHHHHHHHhhhccCCCcceEEEeeccchHHHHHHHHHHHHHHHHH
Confidence 122 23333333332222221 13556677777776666777777899999854
No 85
>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....
Probab=21.65 E-value=1.1e+02 Score=16.57 Aligned_cols=17 Identities=29% Similarity=0.577 Sum_probs=10.8
Q ss_pred HHHHHHHHHHhcCcccC
Q 033305 61 ALKDLFERMEQEGYVPT 77 (122)
Q Consensus 61 ~l~~l~~~~~~~gy~~~ 77 (122)
.-+++...+.+.||.|+
T Consensus 30 tr~rI~~~a~~lgY~pN 46 (46)
T PF00356_consen 30 TRERILEAAEELGYRPN 46 (46)
T ss_dssp HHHHHHHHHHHHTB-SS
T ss_pred HHHHHHHHHHHHCCCCC
Confidence 34556667778888875
No 86
>PTZ00131 glycophorin-binding protein; Provisional
Probab=21.51 E-value=27 Score=26.54 Aligned_cols=22 Identities=36% Similarity=0.677 Sum_probs=18.5
Q ss_pred HhhhhhhhhhHHHHHHHHHhhc
Q 033305 88 EQKKNLLHYHSGRFAIVFGAIS 109 (122)
Q Consensus 88 e~~~~~~~~Hseklaia~gl~~ 109 (122)
|.+.++..+||.++-+.||+|.
T Consensus 38 ekk~sl~~fhsk~i~lifgiiy 59 (413)
T PTZ00131 38 EKKNSLGAFHSKKIILIFGIIY 59 (413)
T ss_pred hhhcchhhhhhcceeehHHHHH
Confidence 4567777899999999999885
No 87
>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=20.37 E-value=1.5e+02 Score=17.69 Aligned_cols=26 Identities=27% Similarity=0.367 Sum_probs=20.9
Q ss_pred hhHHHHHHHHHHcCCChhHHHHHHHH
Q 033305 8 RVYVILSNAYAAARRWKDTARLRVSV 33 (122)
Q Consensus 8 ~~yvlLsniYa~~G~w~~~~~~r~~m 33 (122)
..+..++.+|...|+++.|...-...
T Consensus 40 ~~~~~l~~~~~~~~~~~~A~~~~~~~ 65 (119)
T TIGR02795 40 NAHYWLGEAYYAQGKYADAAKAFLAV 65 (119)
T ss_pred HHHHHHHHHHHhhccHHHHHHHHHHH
Confidence 46778999999999999988875544
No 88
>PF13959 DUF4217: Domain of unknown function (DUF4217)
Probab=20.30 E-value=55 Score=18.94 Aligned_cols=17 Identities=29% Similarity=0.606 Sum_probs=14.7
Q ss_pred hhHHHHHHHHHhhcCCC
Q 033305 96 YHSGRFAIVFGAISTPD 112 (122)
Q Consensus 96 ~Hseklaia~gl~~~~~ 112 (122)
.|-+.+|-+|||..+|.
T Consensus 46 L~l~~~A~sfGL~~~P~ 62 (65)
T PF13959_consen 46 LDLGHLAKSFGLLEAPK 62 (65)
T ss_pred CCHHHHHHHcCCCCCCC
Confidence 47799999999999875
Done!