Query 030517
Match_columns 176
No_of_seqs 95 out of 97
Neff 3.2
Searched_HMMs 46136
Date Fri Mar 29 14:55:34 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030517.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030517hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF13431 TPR_17: Tetratricopep 97.4 0.00011 2.4E-09 45.1 2.1 32 141-173 1-32 (34)
2 COG3063 PilF Tfp pilus assembl 94.5 0.033 7.1E-07 49.2 3.0 31 135-165 85-115 (250)
3 PF13428 TPR_14: Tetratricopep 93.4 0.065 1.4E-06 33.5 2.1 28 134-161 16-43 (44)
4 smart00386 HAT HAT (Half-A-TPR 93.0 0.15 3.2E-06 28.2 3.0 30 135-164 3-32 (33)
5 PF14559 TPR_19: Tetratricopep 91.0 0.24 5.2E-06 32.0 2.7 35 135-170 7-41 (68)
6 PF13371 TPR_9: Tetratricopept 90.4 0.31 6.8E-06 31.9 2.8 34 134-167 10-43 (73)
7 PF13414 TPR_11: TPR repeat; P 88.7 0.22 4.8E-06 32.4 1.1 33 135-167 19-51 (69)
8 PF13429 TPR_15: Tetratricopep 88.6 0.37 8E-06 39.5 2.6 34 135-168 230-263 (280)
9 PRK14720 transcript cleavage f 87.3 0.25 5.3E-06 50.1 1.0 39 133-173 130-168 (906)
10 PLN03138 Protein TOC75; Provis 86.6 1.4 3E-05 44.4 5.7 18 138-155 166-183 (796)
11 PF00244 14-3-3: 14-3-3 protei 85.8 0.48 1E-05 40.1 1.8 38 136-173 143-188 (236)
12 PF13432 TPR_16: Tetratricopep 85.3 0.4 8.7E-06 31.0 0.9 36 135-171 13-48 (65)
13 smart00101 14_3_3 14-3-3 homol 77.4 1.8 3.9E-05 37.6 2.3 39 135-173 144-190 (244)
14 COG3063 PilF Tfp pilus assembl 77.2 2 4.2E-05 38.2 2.5 36 135-171 155-190 (250)
15 PF13432 TPR_16: Tetratricopep 75.1 1.6 3.4E-05 28.2 1.1 19 135-153 47-65 (65)
16 PF00515 TPR_1: Tetratricopept 74.6 2.2 4.7E-05 24.5 1.5 18 135-152 17-34 (34)
17 PRK10370 formate-dependent nit 74.0 3.7 8E-05 33.3 3.2 36 134-169 88-123 (198)
18 PF13429 TPR_15: Tetratricopep 73.2 3.1 6.7E-05 34.1 2.6 31 135-165 162-192 (280)
19 cd00189 TPR Tetratricopeptide 72.4 6.3 0.00014 23.6 3.3 31 135-165 16-46 (100)
20 COG4907 Predicted membrane pro 72.3 2.6 5.6E-05 41.1 2.2 16 33-48 520-535 (595)
21 TIGR02521 type_IV_pilW type IV 70.8 3.4 7.3E-05 30.3 2.1 31 135-165 81-111 (234)
22 PF07719 TPR_2: Tetratricopept 70.4 4.5 9.8E-05 22.7 2.2 18 135-152 17-34 (34)
23 TIGR02521 type_IV_pilW type IV 65.9 5 0.00011 29.4 2.1 37 135-172 151-187 (234)
24 KOG1126 DNA-binding cell divis 64.9 3.6 7.7E-05 40.8 1.5 34 135-168 505-538 (638)
25 PRK12370 invasion protein regu 64.8 4.9 0.00011 37.2 2.3 30 136-165 355-384 (553)
26 PRK15326 type III secretion sy 64.7 6.9 0.00015 29.4 2.7 22 144-165 32-53 (80)
27 TIGR02552 LcrH_SycD type III s 62.8 10 0.00022 27.0 3.3 30 136-165 34-63 (135)
28 PLN03088 SGT1, suppressor of 62.3 7 0.00015 34.5 2.7 32 135-166 18-49 (356)
29 TIGR02917 PEP_TPR_lipo putativ 60.2 8 0.00017 34.5 2.7 32 135-166 853-884 (899)
30 TIGR02552 LcrH_SycD type III s 59.4 8 0.00017 27.6 2.2 37 135-172 67-103 (135)
31 KOG0553 TPR repeat-containing 58.4 11 0.00024 34.4 3.3 33 135-167 97-129 (304)
32 COG4907 Predicted membrane pro 57.8 5.7 0.00012 38.8 1.5 6 104-109 577-582 (595)
33 cd00189 TPR Tetratricopeptide 55.4 23 0.0005 21.1 3.5 32 135-166 50-81 (100)
34 KOG3973 Uncharacterized conser 54.8 11 0.00025 35.7 2.9 14 94-107 351-364 (465)
35 COG4783 Putative Zn-dependent 54.1 12 0.00027 36.1 3.0 35 133-167 354-388 (484)
36 KOG3262 H/ACA small nucleolar 53.9 12 0.00026 32.6 2.7 12 150-161 79-90 (215)
37 PRK15359 type III secretion sy 53.1 18 0.0004 27.5 3.4 32 135-166 74-105 (144)
38 PF13181 TPR_8: Tetratricopept 53.0 6.1 0.00013 22.4 0.6 18 135-152 17-34 (34)
39 PRK10370 formate-dependent nit 51.7 11 0.00025 30.5 2.2 38 135-173 126-163 (198)
40 COG1017 Hmp Hemoglobin-like fl 50.4 9 0.0002 31.9 1.4 37 133-173 20-56 (150)
41 PRK11788 tetratricopeptide rep 44.1 17 0.00038 30.4 2.1 31 135-165 51-81 (389)
42 PRK02603 photosystem I assembl 43.8 27 0.00058 26.9 3.0 32 135-166 88-119 (172)
43 cd05804 StaR_like StaR_like; a 43.4 25 0.00054 29.2 2.9 35 135-170 130-164 (355)
44 PRK15179 Vi polysaccharide bio 43.2 18 0.00038 35.7 2.3 36 135-171 170-205 (694)
45 TIGR00990 3a0801s09 mitochondr 42.8 18 0.00038 33.6 2.2 35 135-170 381-415 (615)
46 PRK15359 type III secretion sy 42.5 14 0.00031 28.2 1.3 32 135-166 40-71 (144)
47 PRK09782 bacteriophage N4 rece 41.4 18 0.00038 37.1 2.1 31 135-165 625-655 (987)
48 PF06552 TOM20_plant: Plant sp 41.1 19 0.00041 30.8 1.9 21 135-155 96-116 (186)
49 TIGR02996 rpt_mate_G_obs repea 39.2 31 0.00068 23.2 2.4 32 141-173 4-35 (42)
50 PF12895 Apc3: Anaphase-promot 38.4 11 0.00024 25.6 0.1 31 135-165 5-37 (84)
51 COG4278 Uncharacterized conser 38.2 26 0.00056 31.6 2.4 9 108-116 252-260 (269)
52 smart00394 RIIa RIIalpha, Regu 38.0 58 0.0013 20.2 3.4 27 139-165 8-35 (38)
53 PF02197 RIIa: Regulatory subu 37.9 65 0.0014 20.5 3.6 29 137-165 6-35 (38)
54 smart00028 TPR Tetratricopepti 37.6 31 0.00068 16.8 1.8 18 135-152 17-34 (34)
55 PRK11189 lipoprotein NlpI; Pro 37.3 31 0.00067 29.3 2.7 35 136-171 81-115 (296)
56 PRK15174 Vi polysaccharide exp 36.8 30 0.00065 33.1 2.8 28 138-165 269-296 (656)
57 KOG3074 Transcriptional regula 34.8 25 0.00054 31.6 1.8 13 162-174 104-116 (263)
58 PRK12370 invasion protein regu 34.4 29 0.00063 32.2 2.2 37 135-172 320-356 (553)
59 PF02184 HAT: HAT (Half-A-TPR) 34.0 49 0.0011 21.0 2.5 27 135-162 3-29 (32)
60 PRK11189 lipoprotein NlpI; Pro 33.3 40 0.00086 28.7 2.7 32 135-166 114-145 (296)
61 TIGR02795 tol_pal_ybgF tol-pal 32.5 64 0.0014 21.8 3.2 31 135-165 55-88 (119)
62 TIGR02917 PEP_TPR_lipo putativ 30.9 62 0.0013 29.0 3.5 30 136-165 820-849 (899)
63 PF12588 PSDC: Phophatidylseri 30.7 61 0.0013 26.3 3.3 33 135-167 15-53 (141)
64 KOG0553 TPR repeat-containing 30.6 34 0.00073 31.3 1.9 25 134-158 164-188 (304)
65 PF13174 TPR_6: Tetratricopept 29.3 43 0.00093 18.3 1.6 18 135-152 16-33 (33)
66 PF05843 Suf: Suppressor of fo 29.3 33 0.00071 29.3 1.6 32 136-167 53-84 (280)
67 PF09295 ChAPs: ChAPs (Chs5p-A 26.8 59 0.0013 30.1 2.9 24 142-165 223-246 (395)
68 PLN03088 SGT1, suppressor of 26.6 64 0.0014 28.5 3.0 32 135-166 52-83 (356)
69 TIGR00990 3a0801s09 mitochondr 26.4 47 0.001 30.8 2.2 28 136-163 416-443 (615)
70 cd01145 TroA_c Periplasmic bin 26.0 1E+02 0.0022 24.9 3.8 33 135-167 118-151 (203)
71 PRK15174 Vi polysaccharide exp 25.9 61 0.0013 31.1 2.8 31 135-165 300-330 (656)
72 COG4683 Uncharacterized protei 25.3 46 0.00099 26.9 1.6 23 124-148 91-113 (120)
73 PRK11447 cellulose synthase su 24.4 53 0.0011 33.4 2.2 37 134-171 618-654 (1157)
74 PF08424 NRDE-2: NRDE-2, neces 24.2 83 0.0018 27.5 3.2 32 136-167 48-79 (321)
75 PF13413 HTH_25: Helix-turn-he 23.8 35 0.00077 23.5 0.7 11 155-165 47-57 (62)
76 KOG0921 Dosage compensation co 23.7 66 0.0014 34.3 2.8 12 36-47 1127-1138(1282)
77 cd01020 TroA_b Metal binding p 23.2 1.2E+02 0.0025 25.7 3.8 34 134-167 104-138 (264)
78 PF11225 DUF3024: Protein of u 23.0 66 0.0014 21.9 1.9 19 157-175 39-57 (57)
79 KOG0547 Translocase of outer m 22.9 60 0.0013 32.2 2.2 28 134-161 130-157 (606)
80 KOG0548 Molecular co-chaperone 22.5 62 0.0013 31.8 2.2 26 135-160 374-399 (539)
81 KOG0376 Serine-threonine phosp 22.4 35 0.00075 33.0 0.5 31 135-166 20-50 (476)
82 PRK11447 cellulose synthase su 22.3 60 0.0013 33.0 2.2 36 135-171 477-512 (1157)
83 KOG3060 Uncharacterized conser 22.2 80 0.0017 28.9 2.7 31 137-167 172-202 (289)
84 PRK10049 pgaA outer membrane p 21.9 1E+02 0.0023 29.9 3.6 31 135-165 132-162 (765)
85 PF12569 NARP1: NMDA receptor- 21.3 98 0.0021 29.6 3.3 31 135-165 54-84 (517)
86 PF08439 Peptidase_M3_N: Oligo 21.1 1.3E+02 0.0028 20.4 3.0 28 139-170 7-34 (70)
87 TIGR00540 hemY_coli hemY prote 20.6 1.1E+02 0.0024 27.0 3.3 31 135-165 315-347 (409)
88 PF05268 GP38: Phage tail fibr 20.5 86 0.0019 28.2 2.5 21 96-116 150-179 (260)
89 PHA00370 III attachment protei 20.2 1.3E+02 0.0028 27.6 3.5 8 142-149 148-155 (297)
90 cd01017 AdcA Metal binding pro 20.1 1.5E+02 0.0032 25.1 3.8 32 136-167 124-156 (282)
No 1
>PF13431 TPR_17: Tetratricopeptide repeat
Probab=97.38 E-value=0.00011 Score=45.09 Aligned_cols=32 Identities=22% Similarity=0.248 Sum_probs=27.7
Q ss_pred HHHHHHHhCCCCchhhhhHHHHHHHHhhcCccc
Q 030517 141 YYQKMIQADPRNPLLLSNYARFLKEVNFCSKSF 173 (176)
Q Consensus 141 yY~~mi~~~P~N~LlL~NYAqFL~~V~~D~~r~ 173 (176)
.|+|+|+.||+|+..+-|+|.+|+. .+|.+.+
T Consensus 1 ~y~kAie~~P~n~~a~~nla~~~~~-~g~~~~A 32 (34)
T PF13431_consen 1 CYKKAIELNPNNAEAYNNLANLYLN-QGDYEEA 32 (34)
T ss_pred ChHHHHHHCCCCHHHHHHHHHHHHH-CcCHHhh
Confidence 4899999999999999999999887 6666543
No 2
>COG3063 PilF Tfp pilus assembly protein PilF [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=94.45 E-value=0.033 Score=49.17 Aligned_cols=31 Identities=35% Similarity=0.541 Sum_probs=29.7
Q ss_pred CCcHHHHHHHHHHhCCCCchhhhhHHHHHHH
Q 030517 135 NNSTDLYYQKMIQADPRNPLLLSNYARFLKE 165 (176)
Q Consensus 135 ~~~te~yY~~mi~~~P~N~LlL~NYAqFL~~ 165 (176)
.+.++++|+++|+.+|+|.=+|-||.-||+.
T Consensus 85 ~~~A~e~YrkAlsl~p~~GdVLNNYG~FLC~ 115 (250)
T COG3063 85 NDLADESYRKALSLAPNNGDVLNNYGAFLCA 115 (250)
T ss_pred hhhHHHHHHHHHhcCCCccchhhhhhHHHHh
Confidence 5889999999999999999999999999987
No 3
>PF13428 TPR_14: Tetratricopeptide repeat
Probab=93.35 E-value=0.065 Score=33.52 Aligned_cols=28 Identities=14% Similarity=0.323 Sum_probs=25.6
Q ss_pred CCCcHHHHHHHHHHhCCCCchhhhhHHH
Q 030517 134 GNNSTDLYYQKMIQADPRNPLLLSNYAR 161 (176)
Q Consensus 134 ~~~~te~yY~~mi~~~P~N~LlL~NYAq 161 (176)
..+.+...|+++|+.+|+|+-.+.++|+
T Consensus 16 ~~~~A~~~~~~~l~~~P~~~~a~~~La~ 43 (44)
T PF13428_consen 16 QPDEAERLLRRALALDPDDPEAWRALAQ 43 (44)
T ss_pred CHHHHHHHHHHHHHHCcCCHHHHHHhhh
Confidence 4588999999999999999999999886
No 4
>smart00386 HAT HAT (Half-A-TPR) repeats. Present in several RNA-binding proteins. Structurally and sequentially thought to be similar to TPRs.
Probab=92.96 E-value=0.15 Score=28.23 Aligned_cols=30 Identities=20% Similarity=0.347 Sum_probs=27.0
Q ss_pred CCcHHHHHHHHHHhCCCCchhhhhHHHHHH
Q 030517 135 NNSTDLYYQKMIQADPRNPLLLSNYARFLK 164 (176)
Q Consensus 135 ~~~te~yY~~mi~~~P~N~LlL~NYAqFL~ 164 (176)
.+.+...|+++|...|.++-+...|++|+.
T Consensus 3 ~~~~r~i~e~~l~~~~~~~~~W~~y~~~e~ 32 (33)
T smart00386 3 IERARKIYERALEKFPKSVELWLKYAEFEE 32 (33)
T ss_pred HHHHHHHHHHHHHHCCCChHHHHHHHHHHh
Confidence 356788999999999999999999999974
No 5
>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=91.01 E-value=0.24 Score=31.99 Aligned_cols=35 Identities=17% Similarity=0.070 Sum_probs=29.8
Q ss_pred CCcHHHHHHHHHHhCCCCchhhhhHHHHHHHHhhcC
Q 030517 135 NNSTDLYYQKMIQADPRNPLLLSNYARFLKEVNFCS 170 (176)
Q Consensus 135 ~~~te~yY~~mi~~~P~N~LlL~NYAqFL~~V~~D~ 170 (176)
.+.+..+|+++++.+|+|+-+.-++|+.+.. .++.
T Consensus 7 ~~~A~~~~~~~l~~~p~~~~~~~~la~~~~~-~g~~ 41 (68)
T PF14559_consen 7 YDEAIELLEKALQRNPDNPEARLLLAQCYLK-QGQY 41 (68)
T ss_dssp HHHHHHHHHHHHHHTTTSHHHHHHHHHHHHH-TT-H
T ss_pred HHHHHHHHHHHHHHCCCCHHHHHHHHHHHHH-cCCH
Confidence 4678899999999999999999999999887 3443
No 6
>PF13371 TPR_9: Tetratricopeptide repeat
Probab=90.37 E-value=0.31 Score=31.88 Aligned_cols=34 Identities=21% Similarity=0.291 Sum_probs=30.5
Q ss_pred CCCcHHHHHHHHHHhCCCCchhhhhHHHHHHHHh
Q 030517 134 GNNSTDLYYQKMIQADPRNPLLLSNYARFLKEVN 167 (176)
Q Consensus 134 ~~~~te~yY~~mi~~~P~N~LlL~NYAqFL~~V~ 167 (176)
....+..+++++|..+|.++.++.++|.++....
T Consensus 10 ~~~~A~~~~~~~l~~~p~~~~~~~~~a~~~~~~g 43 (73)
T PF13371_consen 10 DYEEALEVLERALELDPDDPELWLQRARCLFQLG 43 (73)
T ss_pred CHHHHHHHHHHHHHhCcccchhhHHHHHHHHHhc
Confidence 4578889999999999999999999999998854
No 7
>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=88.66 E-value=0.22 Score=32.36 Aligned_cols=33 Identities=21% Similarity=0.283 Sum_probs=29.4
Q ss_pred CCcHHHHHHHHHHhCCCCchhhhhHHHHHHHHh
Q 030517 135 NNSTDLYYQKMIQADPRNPLLLSNYARFLKEVN 167 (176)
Q Consensus 135 ~~~te~yY~~mi~~~P~N~LlL~NYAqFL~~V~ 167 (176)
...+..+|+++|+.||+|+.++-|.|.-.+...
T Consensus 19 ~~~A~~~~~~ai~~~p~~~~~~~~~g~~~~~~~ 51 (69)
T PF13414_consen 19 YEEAIEYFEKAIELDPNNAEAYYNLGLAYMKLG 51 (69)
T ss_dssp HHHHHHHHHHHHHHSTTHHHHHHHHHHHHHHTT
T ss_pred HHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhC
Confidence 477889999999999999999999999877754
No 8
>PF13429 TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2_B.
Probab=88.58 E-value=0.37 Score=39.50 Aligned_cols=34 Identities=26% Similarity=0.438 Sum_probs=27.0
Q ss_pred CCcHHHHHHHHHHhCCCCchhhhhHHHHHHHHhh
Q 030517 135 NNSTDLYYQKMIQADPRNPLLLSNYARFLKEVNF 168 (176)
Q Consensus 135 ~~~te~yY~~mi~~~P~N~LlL~NYAqFL~~V~~ 168 (176)
...+-.+|++++..+|+||.++.+||..|.+.-+
T Consensus 230 ~~~Al~~~~~~~~~~p~d~~~~~~~a~~l~~~g~ 263 (280)
T PF13429_consen 230 YEEALEYLEKALKLNPDDPLWLLAYADALEQAGR 263 (280)
T ss_dssp HHHHHHHHHHHHHHSTT-HHHHHHHHHHHT----
T ss_pred cccccccccccccccccccccccccccccccccc
Confidence 4777889999999999999999999999988433
No 9
>PRK14720 transcript cleavage factor/unknown domain fusion protein; Provisional
Probab=87.28 E-value=0.25 Score=50.12 Aligned_cols=39 Identities=18% Similarity=0.283 Sum_probs=34.0
Q ss_pred CCCCcHHHHHHHHHHhCCCCchhhhhHHHHHHHHhhcCccc
Q 030517 133 HGNNSTDLYYQKMIQADPRNPLLLSNYARFLKEVNFCSKSF 173 (176)
Q Consensus 133 ~~~~~te~yY~~mi~~~P~N~LlL~NYAqFL~~V~~D~~r~ 173 (176)
....++.+.|+++|+.||.|++.|.|||-||-+. |.+++
T Consensus 130 g~~~ka~~~yer~L~~D~~n~~aLNn~AY~~ae~--dL~KA 168 (906)
T PRK14720 130 NENKKLKGVWERLVKADRDNPEIVKKLATSYEEE--DKEKA 168 (906)
T ss_pred CChHHHHHHHHHHHhcCcccHHHHHHHHHHHHHh--hHHHH
Confidence 3468889999999999999999999999999886 66654
No 10
>PLN03138 Protein TOC75; Provisional
Probab=86.61 E-value=1.4 Score=44.41 Aligned_cols=18 Identities=17% Similarity=0.239 Sum_probs=9.7
Q ss_pred HHHHHHHHHHhCCCCchh
Q 030517 138 TDLYYQKMIQADPRNPLL 155 (176)
Q Consensus 138 te~yY~~mi~~~P~N~Ll 155 (176)
+|+-..+||...|+..+-
T Consensus 166 ~e~~l~~~i~~kpG~v~t 183 (796)
T PLN03138 166 TEDSFFEMVTLRPGGVYT 183 (796)
T ss_pred hHHHHHHHHhcCCCCccC
Confidence 444555566666664443
No 11
>PF00244 14-3-3: 14-3-3 protein; InterPro: IPR023410 The 14-3-3 proteins are a large family of approximately 30kDa acidic proteins which exist primarily as homo- and heterodimeric within all eukaryotic cells [, ]. There is a high degree of sequence identity and conservation between all the 14-3-3 isotypes, particularly in the regions which form the dimer interface or line the central ligand binding channel of the dimeric molecule. Each 14-3-3 protein sequence can be roughly divided into three sections: a divergent amino terminus, the conserved core region and a divergent carboxyl terminus. The conserved middle core region of the 14-3-3s encodes an amphipathic groove that forms the main functional domain, a cradle for interacting with client proteins. The monomer consists of nine helices organised in an antiparallel manner, forming an L-shaped structure. The interior of the L-structure is composed of four helices: H3 and H5, which contain many charged and polar amino acids, and H7 and H9, which contain hydrophobic amino acids. These four helices form the concave amphipathic groove that interacts with target peptides. 14-3-3 proteins mainly bind proteins containing phosphothreonine or phosphoserine motifs however exceptions to this rule do exist. Extensive investigation of the 14-3-3 binding site of the mammalian serine/threonine kinase Raf-1 has produced a consensus sequence for 14-3-3-binding, RSxpSxP (in the single-letter amino-acid code, where x denotes any amino acid and p indicates that the next residue is phosphorylated). 14-3-3 proteins appear to effect intracellular signalling in one of three ways - by direct regulation of the catalytic activity of the bound protein, by regulating interactions between the bound protein and other molecules in the cell by sequestration or modification or by controlling the subcellular localisation of the bound ligand. Proteins appear to initially bind to a single dominant site and then subsequently to many, much weaker secondary interaction sites. The 14-3-3 dimer is capable of changing the conformation of its bound ligand whilst itself undergoing minimal structural alteration. This entry represents the structural domain found in 14-3-3 proteins.; PDB: 2O8P_A 3AXY_D 2C74_A 2C63_A 4DX0_A 1YWT_A 3P1O_A 3P1N_A 4DAU_A 3U9X_A ....
Probab=85.82 E-value=0.48 Score=40.13 Aligned_cols=38 Identities=24% Similarity=0.352 Sum_probs=31.2
Q ss_pred CcHHHHHHHHHH-----hCCCCchhhh---hHHHHHHHHhhcCccc
Q 030517 136 NSTDLYYQKMIQ-----ADPRNPLLLS---NYARFLKEVNFCSKSF 173 (176)
Q Consensus 136 ~~te~yY~~mi~-----~~P~N~LlL~---NYAqFL~~V~~D~~r~ 173 (176)
.++...|+++++ ..|.||+-|+ ||+=|+|++.+|.+.+
T Consensus 143 ~~a~~aY~~A~~~a~~~L~~~~p~rLgl~LN~svF~yei~~~~~~A 188 (236)
T PF00244_consen 143 EKALEAYEEALEIAKKELPPTHPLRLGLALNYSVFYYEILNDPEKA 188 (236)
T ss_dssp HHHHHHHHHHHHHHHHHSCTTSHHHHHHHHHHHHHHHHTSS-HHHH
T ss_pred HHHHHhhhhHHHHHhcccCCCCcHHHHHHHHHHHHHHHHcCChHHH
Confidence 567788998775 5899999887 9999999999987754
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=85.30 E-value=0.4 Score=30.99 Aligned_cols=36 Identities=17% Similarity=0.202 Sum_probs=30.3
Q ss_pred CCcHHHHHHHHHHhCCCCchhhhhHHHHHHHHhhcCc
Q 030517 135 NNSTDLYYQKMIQADPRNPLLLSNYARFLKEVNFCSK 171 (176)
Q Consensus 135 ~~~te~yY~~mi~~~P~N~LlL~NYAqFL~~V~~D~~ 171 (176)
.+.+...|+++|+.+|+|+-.+-++|+.+++ +++.+
T Consensus 13 ~~~A~~~~~~~l~~~P~~~~a~~~lg~~~~~-~g~~~ 48 (65)
T PF13432_consen 13 YDEAIAAFEQALKQDPDNPEAWYLLGRILYQ-QGRYD 48 (65)
T ss_dssp HHHHHHHHHHHHCCSTTHHHHHHHHHHHHHH-TT-HH
T ss_pred HHHHHHHHHHHHHHCCCCHHHHHHHHHHHHH-cCCHH
Confidence 4678899999999999999999999999986 45443
No 13
>smart00101 14_3_3 14-3-3 homologues. 14-3-3 homologues mediates signal transduction by binding to phosphoserine-containing proteins. They are involved in growth factor signalling and also interact with MEK kinases.
Probab=77.38 E-value=1.8 Score=37.58 Aligned_cols=39 Identities=21% Similarity=0.331 Sum_probs=32.1
Q ss_pred CCcHHHHHHHHHH-----hCCCCchhhh---hHHHHHHHHhhcCccc
Q 030517 135 NNSTDLYYQKMIQ-----ADPRNPLLLS---NYARFLKEVNFCSKSF 173 (176)
Q Consensus 135 ~~~te~yY~~mi~-----~~P~N~LlL~---NYAqFL~~V~~D~~r~ 173 (176)
...+...|+++++ ..|.||+-|+ ||+=|+|++.+|.+.+
T Consensus 144 ~~~a~~aY~~A~e~a~~~L~pt~PirLgLaLN~SVF~yEI~~~~~~A 190 (244)
T smart00101 144 AENTLVAYKSAQDIALAELPPTHPIRLGLALNFSVFYYEILNSPDRA 190 (244)
T ss_pred HHHHHHHHHHHHHHHHccCCCCCHHHHHHHHHHHHHHHHHcCCHHHH
Confidence 3577889998876 4599999774 9999999999987765
No 14
>COG3063 PilF Tfp pilus assembly protein PilF [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=77.22 E-value=2 Score=38.25 Aligned_cols=36 Identities=19% Similarity=0.254 Sum_probs=31.6
Q ss_pred CCcHHHHHHHHHHhCCCCchhhhhHHHHHHHHhhcCc
Q 030517 135 NNSTDLYYQKMIQADPRNPLLLSNYARFLKEVNFCSK 171 (176)
Q Consensus 135 ~~~te~yY~~mi~~~P~N~LlL~NYAqFL~~V~~D~~ 171 (176)
.+.+++||+++|+.||++|+-+.--|+-+++ +||.-
T Consensus 155 ~~~A~~~l~raL~~dp~~~~~~l~~a~~~~~-~~~y~ 190 (250)
T COG3063 155 FDQAEEYLKRALELDPQFPPALLELARLHYK-AGDYA 190 (250)
T ss_pred chhHHHHHHHHHHhCcCCChHHHHHHHHHHh-cccch
Confidence 5888999999999999999999999998887 66653
No 15
>PF13432 TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL_A 3CVQ_A 3CV0_A 2GW1_B 3CVN_A 3QKY_A 2PL2_B.
Probab=75.14 E-value=1.6 Score=28.16 Aligned_cols=19 Identities=32% Similarity=0.744 Sum_probs=16.0
Q ss_pred CCcHHHHHHHHHHhCCCCc
Q 030517 135 NNSTDLYYQKMIQADPRNP 153 (176)
Q Consensus 135 ~~~te~yY~~mi~~~P~N~ 153 (176)
.+.+..+|+++|+.+|+||
T Consensus 47 ~~~A~~~~~~a~~~~P~~p 65 (65)
T PF13432_consen 47 YDEALAYYERALELDPDNP 65 (65)
T ss_dssp HHHHHHHHHHHHHHSTT-H
T ss_pred HHHHHHHHHHHHHHCcCCC
Confidence 4677899999999999997
No 16
>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=74.59 E-value=2.2 Score=24.52 Aligned_cols=18 Identities=33% Similarity=0.610 Sum_probs=15.8
Q ss_pred CCcHHHHHHHHHHhCCCC
Q 030517 135 NNSTDLYYQKMIQADPRN 152 (176)
Q Consensus 135 ~~~te~yY~~mi~~~P~N 152 (176)
.+.+..+|+++|+.||+|
T Consensus 17 ~~~A~~~~~~al~~~p~~ 34 (34)
T PF00515_consen 17 YEEALEYYQRALELDPDN 34 (34)
T ss_dssp HHHHHHHHHHHHHHSTTH
T ss_pred chHHHHHHHHHHHHCcCC
Confidence 467889999999999975
No 17
>PRK10370 formate-dependent nitrite reductase complex subunit NrfG; Provisional
Probab=74.04 E-value=3.7 Score=33.35 Aligned_cols=36 Identities=19% Similarity=0.107 Sum_probs=30.3
Q ss_pred CCCcHHHHHHHHHHhCCCCchhhhhHHHHHHHHhhc
Q 030517 134 GNNSTDLYYQKMIQADPRNPLLLSNYARFLKEVNFC 169 (176)
Q Consensus 134 ~~~~te~yY~~mi~~~P~N~LlL~NYAqFL~~V~~D 169 (176)
..+.+...|+++++.+|+|+-++.|||+-|+.-.++
T Consensus 88 ~~~~A~~a~~~Al~l~P~~~~~~~~lA~aL~~~~g~ 123 (198)
T PRK10370 88 DYDNALLAYRQALQLRGENAELYAALATVLYYQAGQ 123 (198)
T ss_pred CHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhcCC
Confidence 357889999999999999999999999977654443
No 18
>PF13429 TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2_B.
Probab=73.17 E-value=3.1 Score=34.12 Aligned_cols=31 Identities=23% Similarity=0.329 Sum_probs=25.7
Q ss_pred CCcHHHHHHHHHHhCCCCchhhhhHHHHHHH
Q 030517 135 NNSTDLYYQKMIQADPRNPLLLSNYARFLKE 165 (176)
Q Consensus 135 ~~~te~yY~~mi~~~P~N~LlL~NYAqFL~~ 165 (176)
.+.+...|+++|+.+|+|+-++.+|+.+|-+
T Consensus 162 ~~~A~~~~~~al~~~P~~~~~~~~l~~~li~ 192 (280)
T PF13429_consen 162 PDKALRDYRKALELDPDDPDARNALAWLLID 192 (280)
T ss_dssp HHHHHHHHHHHHHH-TT-HHHHHHHHHHHCT
T ss_pred HHHHHHHHHHHHHcCCCCHHHHHHHHHHHHH
Confidence 4788999999999999999999999888754
No 19
>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=72.40 E-value=6.3 Score=23.59 Aligned_cols=31 Identities=26% Similarity=0.316 Sum_probs=21.3
Q ss_pred CCcHHHHHHHHHHhCCCCchhhhhHHHHHHH
Q 030517 135 NNSTDLYYQKMIQADPRNPLLLSNYARFLKE 165 (176)
Q Consensus 135 ~~~te~yY~~mi~~~P~N~LlL~NYAqFL~~ 165 (176)
...+..+++++++.+|.++.++.++|..+..
T Consensus 16 ~~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~ 46 (100)
T cd00189 16 YDEALEYYEKALELDPDNADAYYNLAAAYYK 46 (100)
T ss_pred HHHHHHHHHHHHhcCCccHHHHHHHHHHHHH
Confidence 3556667777777777777777677766655
No 20
>COG4907 Predicted membrane protein [Function unknown]
Probab=72.31 E-value=2.6 Score=41.06 Aligned_cols=16 Identities=0% Similarity=0.152 Sum_probs=7.4
Q ss_pred CCCCchhhhhhhcccc
Q 030517 33 SPCDSLKSMTRTLSET 48 (176)
Q Consensus 33 ~~~~~~~~m~ra~Se~ 48 (176)
++..-..+...|+...
T Consensus 520 tALGV~dkVvkam~~~ 535 (595)
T COG4907 520 TALGVSDKVVKAMRKA 535 (595)
T ss_pred hhhccHHHHHHHHHHh
Confidence 3444445544444443
No 21
>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=70.82 E-value=3.4 Score=30.28 Aligned_cols=31 Identities=23% Similarity=0.457 Sum_probs=27.3
Q ss_pred CCcHHHHHHHHHHhCCCCchhhhhHHHHHHH
Q 030517 135 NNSTDLYYQKMIQADPRNPLLLSNYARFLKE 165 (176)
Q Consensus 135 ~~~te~yY~~mi~~~P~N~LlL~NYAqFL~~ 165 (176)
.+.+..+|+++++.+|.++..+.|++.++..
T Consensus 81 ~~~A~~~~~~al~~~~~~~~~~~~~~~~~~~ 111 (234)
T TIGR02521 81 LEKAEDSFRRALTLNPNNGDVLNNYGTFLCQ 111 (234)
T ss_pred HHHHHHHHHHHHhhCCCCHHHHHHHHHHHHH
Confidence 4778899999999999999999999988765
No 22
>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=70.36 E-value=4.5 Score=22.71 Aligned_cols=18 Identities=28% Similarity=0.566 Sum_probs=16.0
Q ss_pred CCcHHHHHHHHHHhCCCC
Q 030517 135 NNSTDLYYQKMIQADPRN 152 (176)
Q Consensus 135 ~~~te~yY~~mi~~~P~N 152 (176)
...+-.+|+++|+.+|+|
T Consensus 17 ~~~A~~~~~~al~l~p~~ 34 (34)
T PF07719_consen 17 YEEAIEYFEKALELDPNN 34 (34)
T ss_dssp HHHHHHHHHHHHHHSTTS
T ss_pred HHHHHHHHHHHHHHCcCC
Confidence 467889999999999987
No 23
>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=65.93 E-value=5 Score=29.40 Aligned_cols=37 Identities=22% Similarity=0.262 Sum_probs=30.8
Q ss_pred CCcHHHHHHHHHHhCCCCchhhhhHHHHHHHHhhcCcc
Q 030517 135 NNSTDLYYQKMIQADPRNPLLLSNYARFLKEVNFCSKS 172 (176)
Q Consensus 135 ~~~te~yY~~mi~~~P~N~LlL~NYAqFL~~V~~D~~r 172 (176)
.+.+..+|+++++.+|+++..+.++|+.++. .+|.++
T Consensus 151 ~~~A~~~~~~~~~~~~~~~~~~~~la~~~~~-~~~~~~ 187 (234)
T TIGR02521 151 FDKAEKYLTRALQIDPQRPESLLELAELYYL-RGQYKD 187 (234)
T ss_pred HHHHHHHHHHHHHhCcCChHHHHHHHHHHHH-cCCHHH
Confidence 5778999999999999999999999988876 555554
No 24
>KOG1126 consensus DNA-binding cell division cycle control protein [Cell cycle control, cell division, chromosome partitioning]
Probab=64.94 E-value=3.6 Score=40.78 Aligned_cols=34 Identities=18% Similarity=0.411 Sum_probs=31.0
Q ss_pred CCcHHHHHHHHHHhCCCCchhhhhHHHHHHHHhh
Q 030517 135 NNSTDLYYQKMIQADPRNPLLLSNYARFLKEVNF 168 (176)
Q Consensus 135 ~~~te~yY~~mi~~~P~N~LlL~NYAqFL~~V~~ 168 (176)
..-++-|||+|++.||.|..++.=+.+++++.++
T Consensus 505 ~e~Ae~~fqkA~~INP~nsvi~~~~g~~~~~~k~ 538 (638)
T KOG1126|consen 505 LEFAEFHFQKAVEINPSNSVILCHIGRIQHQLKR 538 (638)
T ss_pred hhHHHHHHHhhhcCCccchhHHhhhhHHHHHhhh
Confidence 5778999999999999999999999999999655
No 25
>PRK12370 invasion protein regulator; Provisional
Probab=64.76 E-value=4.9 Score=37.22 Aligned_cols=30 Identities=13% Similarity=0.047 Sum_probs=17.4
Q ss_pred CcHHHHHHHHHHhCCCCchhhhhHHHHHHH
Q 030517 136 NSTDLYYQKMIQADPRNPLLLSNYARFLKE 165 (176)
Q Consensus 136 ~~te~yY~~mi~~~P~N~LlL~NYAqFL~~ 165 (176)
+.+..+|+++|+.||+|+..+.++|..+..
T Consensus 355 ~~A~~~~~~Al~l~P~~~~a~~~lg~~l~~ 384 (553)
T PRK12370 355 IVGSLLFKQANLLSPISADIKYYYGWNLFM 384 (553)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHHHHHHH
Confidence 445556666666666666666555555444
No 26
>PRK15326 type III secretion system needle complex protein PrgI; Provisional
Probab=64.74 E-value=6.9 Score=29.43 Aligned_cols=22 Identities=36% Similarity=0.625 Sum_probs=18.0
Q ss_pred HHHHhCCCCchhhhhHHHHHHH
Q 030517 144 KMIQADPRNPLLLSNYARFLKE 165 (176)
Q Consensus 144 ~mi~~~P~N~LlL~NYAqFL~~ 165 (176)
+.++.+|.||.+|++|-.-|-+
T Consensus 32 ~~l~~~pdnP~~LA~~Qa~l~e 53 (80)
T PRK15326 32 DKLAAKPSDPALLAAYQSKLSE 53 (80)
T ss_pred HHhhcCCCCHHHHHHHHHHHHH
Confidence 4568999999999999776644
No 27
>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=62.78 E-value=10 Score=27.04 Aligned_cols=30 Identities=17% Similarity=0.128 Sum_probs=19.4
Q ss_pred CcHHHHHHHHHHhCCCCchhhhhHHHHHHH
Q 030517 136 NSTDLYYQKMIQADPRNPLLLSNYARFLKE 165 (176)
Q Consensus 136 ~~te~yY~~mi~~~P~N~LlL~NYAqFL~~ 165 (176)
..+..+|++++..+|.|+-++.|.|+++..
T Consensus 34 ~~A~~~~~~~~~~~p~~~~~~~~la~~~~~ 63 (135)
T TIGR02552 34 DEALKLFQLLAAYDPYNSRYWLGLAACCQM 63 (135)
T ss_pred HHHHHHHHHHHHhCCCcHHHHHHHHHHHHH
Confidence 445566666666666666666666666655
No 28
>PLN03088 SGT1, suppressor of G2 allele of SKP1; Provisional
Probab=62.34 E-value=7 Score=34.53 Aligned_cols=32 Identities=22% Similarity=0.204 Sum_probs=26.3
Q ss_pred CCcHHHHHHHHHHhCCCCchhhhhHHHHHHHH
Q 030517 135 NNSTDLYYQKMIQADPRNPLLLSNYARFLKEV 166 (176)
Q Consensus 135 ~~~te~yY~~mi~~~P~N~LlL~NYAqFL~~V 166 (176)
+..+..+|+++|+.+|+|+.++.|.|+.+...
T Consensus 18 ~~~Ai~~~~~Al~~~P~~~~a~~~~a~~~~~~ 49 (356)
T PLN03088 18 FALAVDLYTQAIDLDPNNAELYADRAQANIKL 49 (356)
T ss_pred HHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHc
Confidence 56778889999999999998888888877654
No 29
>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=60.15 E-value=8 Score=34.48 Aligned_cols=32 Identities=13% Similarity=0.098 Sum_probs=22.9
Q ss_pred CCcHHHHHHHHHHhCCCCchhhhhHHHHHHHH
Q 030517 135 NNSTDLYYQKMIQADPRNPLLLSNYARFLKEV 166 (176)
Q Consensus 135 ~~~te~yY~~mi~~~P~N~LlL~NYAqFL~~V 166 (176)
.+.+..+|++||+.+|.|+.+.-|||+.|...
T Consensus 853 ~~~A~~~~~~a~~~~~~~~~~~~~l~~~~~~~ 884 (899)
T TIGR02917 853 ADRALPLLRKAVNIAPEAAAIRYHLALALLAT 884 (899)
T ss_pred HHHHHHHHHHHHhhCCCChHHHHHHHHHHHHc
Confidence 45666777777777777777777777776653
No 30
>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=59.35 E-value=8 Score=27.61 Aligned_cols=37 Identities=19% Similarity=0.029 Sum_probs=30.1
Q ss_pred CCcHHHHHHHHHHhCCCCchhhhhHHHHHHHHhhcCcc
Q 030517 135 NNSTDLYYQKMIQADPRNPLLLSNYARFLKEVNFCSKS 172 (176)
Q Consensus 135 ~~~te~yY~~mi~~~P~N~LlL~NYAqFL~~V~~D~~r 172 (176)
.+.+..+|++++..+|.|+-++-|+|..+.. .+|.++
T Consensus 67 ~~~A~~~~~~~~~~~p~~~~~~~~la~~~~~-~g~~~~ 103 (135)
T TIGR02552 67 YEEAIDAYALAAALDPDDPRPYFHAAECLLA-LGEPES 103 (135)
T ss_pred HHHHHHHHHHHHhcCCCChHHHHHHHHHHHH-cCCHHH
Confidence 4677889999999999999999999986665 556554
No 31
>KOG0553 consensus TPR repeat-containing protein [General function prediction only]
Probab=58.40 E-value=11 Score=34.41 Aligned_cols=33 Identities=21% Similarity=0.274 Sum_probs=27.8
Q ss_pred CCcHHHHHHHHHHhCCCCchhhhhHHHHHHHHh
Q 030517 135 NNSTDLYYQKMIQADPRNPLLLSNYARFLKEVN 167 (176)
Q Consensus 135 ~~~te~yY~~mi~~~P~N~LlL~NYAqFL~~V~ 167 (176)
+..+-..|.++|+.+|.||++++|=|+=+-++.
T Consensus 97 Y~eAv~kY~~AI~l~P~nAVyycNRAAAy~~Lg 129 (304)
T KOG0553|consen 97 YQEAVDKYTEAIELDPTNAVYYCNRAAAYSKLG 129 (304)
T ss_pred HHHHHHHHHHHHhcCCCcchHHHHHHHHHHHhc
Confidence 566677899999999999999999998766543
No 32
>COG4907 Predicted membrane protein [Function unknown]
Probab=57.80 E-value=5.7 Score=38.80 Aligned_cols=6 Identities=67% Similarity=1.575 Sum_probs=2.3
Q ss_pred CCCCCc
Q 030517 104 GGGGNM 109 (176)
Q Consensus 104 gGGG~~ 109 (176)
|||+++
T Consensus 577 GGG~G~ 582 (595)
T COG4907 577 GGGGGF 582 (595)
T ss_pred CCCCCc
Confidence 333333
No 33
>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=55.40 E-value=23 Score=21.06 Aligned_cols=32 Identities=19% Similarity=0.185 Sum_probs=27.4
Q ss_pred CCcHHHHHHHHHHhCCCCchhhhhHHHHHHHH
Q 030517 135 NNSTDLYYQKMIQADPRNPLLLSNYARFLKEV 166 (176)
Q Consensus 135 ~~~te~yY~~mi~~~P~N~LlL~NYAqFL~~V 166 (176)
.+.+..+|++++..+|.++-.+.+.|+.+...
T Consensus 50 ~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 81 (100)
T cd00189 50 YEEALEDYEKALELDPDNAKAYYNLGLAYYKL 81 (100)
T ss_pred HHHHHHHHHHHHhCCCcchhHHHHHHHHHHHH
Confidence 46778899999999999998888999887764
No 34
>KOG3973 consensus Uncharacterized conserved glycine-rich protein [Function unknown]
Probab=54.77 E-value=11 Score=35.71 Aligned_cols=14 Identities=36% Similarity=0.470 Sum_probs=6.4
Q ss_pred ceEEeeccccCCCC
Q 030517 94 IGVLVGGGIYGGGG 107 (176)
Q Consensus 94 ~~lv~GGG~~gGGG 107 (176)
+.+-.||+-+|+||
T Consensus 351 ~~~eqgg~Rgg~Gg 364 (465)
T KOG3973|consen 351 QVLEQGGSRGGSGG 364 (465)
T ss_pred chhhccCCCCCCCC
Confidence 33335554444444
No 35
>COG4783 Putative Zn-dependent protease, contains TPR repeats [General function prediction only]
Probab=54.12 E-value=12 Score=36.06 Aligned_cols=35 Identities=26% Similarity=0.282 Sum_probs=31.0
Q ss_pred CCCCcHHHHHHHHHHhCCCCchhhhhHHHHHHHHh
Q 030517 133 HGNNSTDLYYQKMIQADPRNPLLLSNYARFLKEVN 167 (176)
Q Consensus 133 ~~~~~te~yY~~mi~~~P~N~LlL~NYAqFL~~V~ 167 (176)
+....+.+++++|+..+|++++|-=||||-|-++.
T Consensus 354 nk~~~A~e~~~kal~l~P~~~~l~~~~a~all~~g 388 (484)
T COG4783 354 NKAKEAIERLKKALALDPNSPLLQLNLAQALLKGG 388 (484)
T ss_pred CChHHHHHHHHHHHhcCCCccHHHHHHHHHHHhcC
Confidence 34688999999999999999999999999987654
No 36
>KOG3262 consensus H/ACA small nucleolar RNP component GAR1 [Translation, ribosomal structure and biogenesis]
Probab=53.95 E-value=12 Score=32.63 Aligned_cols=12 Identities=25% Similarity=0.390 Sum_probs=6.1
Q ss_pred CCCchhhhhHHH
Q 030517 150 PRNPLLLSNYAR 161 (176)
Q Consensus 150 P~N~LlL~NYAq 161 (176)
+|-|++|.|=-|
T Consensus 79 fNAPIylenk~q 90 (215)
T KOG3262|consen 79 FNAPIYLENKEQ 90 (215)
T ss_pred CCCceeecchhh
Confidence 455555555444
No 37
>PRK15359 type III secretion system chaperone protein SscB; Provisional
Probab=53.06 E-value=18 Score=27.54 Aligned_cols=32 Identities=16% Similarity=0.195 Sum_probs=25.6
Q ss_pred CCcHHHHHHHHHHhCCCCchhhhhHHHHHHHH
Q 030517 135 NNSTDLYYQKMIQADPRNPLLLSNYARFLKEV 166 (176)
Q Consensus 135 ~~~te~yY~~mi~~~P~N~LlL~NYAqFL~~V 166 (176)
...+...|+++++.+|+|+-.+-|-+.-|...
T Consensus 74 ~~~A~~~y~~Al~l~p~~~~a~~~lg~~l~~~ 105 (144)
T PRK15359 74 YTTAINFYGHALMLDASHPEPVYQTGVCLKMM 105 (144)
T ss_pred HHHHHHHHHHHHhcCCCCcHHHHHHHHHHHHc
Confidence 46678888888888888888888888877764
No 38
>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=53.03 E-value=6.1 Score=22.41 Aligned_cols=18 Identities=22% Similarity=0.505 Sum_probs=15.1
Q ss_pred CCcHHHHHHHHHHhCCCC
Q 030517 135 NNSTDLYYQKMIQADPRN 152 (176)
Q Consensus 135 ~~~te~yY~~mi~~~P~N 152 (176)
.+.+..+|+++++.+|+|
T Consensus 17 ~~~A~~~~~~a~~~~~~n 34 (34)
T PF13181_consen 17 YEEALEYFEKALELNPDN 34 (34)
T ss_dssp HHHHHHHHHHHHHHHTT-
T ss_pred HHHHHHHHHHHHhhCCCC
Confidence 577889999999999965
No 39
>PRK10370 formate-dependent nitrite reductase complex subunit NrfG; Provisional
Probab=51.69 E-value=11 Score=30.48 Aligned_cols=38 Identities=13% Similarity=-0.115 Sum_probs=31.8
Q ss_pred CCcHHHHHHHHHHhCCCCchhhhhHHHHHHHHhhcCccc
Q 030517 135 NNSTDLYYQKMIQADPRNPLLLSNYARFLKEVNFCSKSF 173 (176)
Q Consensus 135 ~~~te~yY~~mi~~~P~N~LlL~NYAqFL~~V~~D~~r~ 173 (176)
...+.+.|+++++.+|+|+-.+.|.|.-+++ .+|.+.+
T Consensus 126 ~~~A~~~l~~al~~dP~~~~al~~LA~~~~~-~g~~~~A 163 (198)
T PRK10370 126 TPQTREMIDKALALDANEVTALMLLASDAFM-QADYAQA 163 (198)
T ss_pred cHHHHHHHHHHHHhCCCChhHHHHHHHHHHH-cCCHHHH
Confidence 4788999999999999999999999987776 5665543
No 40
>COG1017 Hmp Hemoglobin-like flavoprotein [Energy production and conversion]
Probab=50.43 E-value=9 Score=31.91 Aligned_cols=37 Identities=24% Similarity=0.327 Sum_probs=27.3
Q ss_pred CCCCcHHHHHHHHHHhCCCCchhhhhHHHHHHHHhhcCccc
Q 030517 133 HGNNSTDLYYQKMIQADPRNPLLLSNYARFLKEVNFCSKSF 173 (176)
Q Consensus 133 ~~~~~te~yY~~mi~~~P~N~LlL~NYAqFL~~V~~D~~r~ 173 (176)
+|..-|..||++|+...| -|+ |+-.--+|-.+|..++
T Consensus 20 ~G~~iT~~FY~~MF~~hP---El~-niFN~~nQ~~G~Q~~a 56 (150)
T COG1017 20 HGETITAHFYKRMFAHHP---ELK-NIFNMANQKNGDQPKA 56 (150)
T ss_pred cchHHHHHHHHHHHhhCH---HHH-HHHhHhhhcccccHHH
Confidence 467899999999999988 233 7766666666666554
No 41
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=44.09 E-value=17 Score=30.42 Aligned_cols=31 Identities=13% Similarity=0.254 Sum_probs=26.1
Q ss_pred CCcHHHHHHHHHHhCCCCchhhhhHHHHHHH
Q 030517 135 NNSTDLYYQKMIQADPRNPLLLSNYARFLKE 165 (176)
Q Consensus 135 ~~~te~yY~~mi~~~P~N~LlL~NYAqFL~~ 165 (176)
.+.+..+|++|++.+|+|+-.+.+.|.++..
T Consensus 51 ~~~A~~~~~~al~~~p~~~~~~~~la~~~~~ 81 (389)
T PRK11788 51 PDKAIDLFIEMLKVDPETVELHLALGNLFRR 81 (389)
T ss_pred hHHHHHHHHHHHhcCcccHHHHHHHHHHHHH
Confidence 5678999999999999999888777776654
No 42
>PRK02603 photosystem I assembly protein Ycf3; Provisional
Probab=43.83 E-value=27 Score=26.91 Aligned_cols=32 Identities=22% Similarity=0.469 Sum_probs=28.1
Q ss_pred CCcHHHHHHHHHHhCCCCchhhhhHHHHHHHH
Q 030517 135 NNSTDLYYQKMIQADPRNPLLLSNYARFLKEV 166 (176)
Q Consensus 135 ~~~te~yY~~mi~~~P~N~LlL~NYAqFL~~V 166 (176)
.+.+..+|+++|+.+|+++-.+.+++..+...
T Consensus 88 ~~~A~~~~~~al~~~p~~~~~~~~lg~~~~~~ 119 (172)
T PRK02603 88 HDKALEYYHQALELNPKQPSALNNIAVIYHKR 119 (172)
T ss_pred HHHHHHHHHHHHHhCcccHHHHHHHHHHHHHc
Confidence 57889999999999999999999998887653
No 43
>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=43.41 E-value=25 Score=29.18 Aligned_cols=35 Identities=9% Similarity=0.103 Sum_probs=30.5
Q ss_pred CCcHHHHHHHHHHhCCCCchhhhhHHHHHHHHhhcC
Q 030517 135 NNSTDLYYQKMIQADPRNPLLLSNYARFLKEVNFCS 170 (176)
Q Consensus 135 ~~~te~yY~~mi~~~P~N~LlL~NYAqFL~~V~~D~ 170 (176)
.+.+..+|+++++.+|+|+..+.++|..+++ .++.
T Consensus 130 ~~~A~~~~~~al~~~p~~~~~~~~la~i~~~-~g~~ 164 (355)
T cd05804 130 YDRAEEAARRALELNPDDAWAVHAVAHVLEM-QGRF 164 (355)
T ss_pred HHHHHHHHHHHHhhCCCCcHHHHHHHHHHHH-cCCH
Confidence 5788999999999999999999999999988 4443
No 44
>PRK15179 Vi polysaccharide biosynthesis protein TviE; Provisional
Probab=43.25 E-value=18 Score=35.75 Aligned_cols=36 Identities=11% Similarity=0.131 Sum_probs=29.2
Q ss_pred CCcHHHHHHHHHHhCCCCchhhhhHHHHHHHHhhcCc
Q 030517 135 NNSTDLYYQKMIQADPRNPLLLSNYARFLKEVNFCSK 171 (176)
Q Consensus 135 ~~~te~yY~~mi~~~P~N~LlL~NYAqFL~~V~~D~~ 171 (176)
++.+++.|++++..+|+++-.|-+||+-|++ .++.+
T Consensus 170 ~~~A~~~y~~~~~~~p~~~~~~~~~a~~l~~-~G~~~ 205 (694)
T PRK15179 170 SEQADACFERLSRQHPEFENGYVGWAQSLTR-RGALW 205 (694)
T ss_pred hHHHHHHHHHHHhcCCCcHHHHHHHHHHHHH-cCCHH
Confidence 6788889999999899888888899988887 45443
No 45
>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=42.81 E-value=18 Score=33.60 Aligned_cols=35 Identities=9% Similarity=0.075 Sum_probs=22.7
Q ss_pred CCcHHHHHHHHHHhCCCCchhhhhHHHHHHHHhhcC
Q 030517 135 NNSTDLYYQKMIQADPRNPLLLSNYARFLKEVNFCS 170 (176)
Q Consensus 135 ~~~te~yY~~mi~~~P~N~LlL~NYAqFL~~V~~D~ 170 (176)
.+.+..+|+++|+.+|+|+.++.+.++.++. .+|.
T Consensus 381 ~~eA~~~~~~al~~~p~~~~~~~~lg~~~~~-~g~~ 415 (615)
T TIGR00990 381 PDKAEEDFDKALKLNSEDPDIYYHRAQLHFI-KGEF 415 (615)
T ss_pred HHHHHHHHHHHHHhCCCCHHHHHHHHHHHHH-cCCH
Confidence 3556667777777777777777777766554 3443
No 46
>PRK15359 type III secretion system chaperone protein SscB; Provisional
Probab=42.46 E-value=14 Score=28.17 Aligned_cols=32 Identities=9% Similarity=-0.014 Sum_probs=25.5
Q ss_pred CCcHHHHHHHHHHhCCCCchhhhhHHHHHHHH
Q 030517 135 NNSTDLYYQKMIQADPRNPLLLSNYARFLKEV 166 (176)
Q Consensus 135 ~~~te~yY~~mi~~~P~N~LlL~NYAqFL~~V 166 (176)
.+.+..+|++++..+|.|+-.+.|.|.-+...
T Consensus 40 ~~~A~~~~~~al~~~P~~~~a~~~lg~~~~~~ 71 (144)
T PRK15359 40 YSRAVIDFSWLVMAQPWSWRAHIALAGTWMML 71 (144)
T ss_pred HHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHH
Confidence 46677888888888888888888888777663
No 47
>PRK09782 bacteriophage N4 receptor, outer membrane subunit; Provisional
Probab=41.35 E-value=18 Score=37.13 Aligned_cols=31 Identities=10% Similarity=0.057 Sum_probs=27.2
Q ss_pred CCcHHHHHHHHHHhCCCCchhhhhHHHHHHH
Q 030517 135 NNSTDLYYQKMIQADPRNPLLLSNYARFLKE 165 (176)
Q Consensus 135 ~~~te~yY~~mi~~~P~N~LlL~NYAqFL~~ 165 (176)
.+.+..+|+++|+.+|+|+.++.|++.+|.+
T Consensus 625 ~deA~~~l~~AL~l~Pd~~~a~~nLG~aL~~ 655 (987)
T PRK09782 625 VPAAVSDLRAALELEPNNSNYQAALGYALWD 655 (987)
T ss_pred HHHHHHHHHHHHHhCCCCHHHHHHHHHHHHH
Confidence 5778888999999999999999999988877
No 48
>PF06552 TOM20_plant: Plant specific mitochondrial import receptor subunit TOM20; InterPro: IPR010547 This family consists of several plant specific mitochondrial import receptor subunit TOM20 (translocase of outer membrane 20 kDa subunit) proteins. Most mitochondrial proteins are encoded by the nuclear genome, and are synthesised in the cytosol. TOM20 is a general import receptor that binds to mitochondrial pre-sequences in the early step of protein import into the mitochondria [].; GO: 0045040 protein import into mitochondrial outer membrane, 0005742 mitochondrial outer membrane translocase complex; PDB: 1ZU2_A.
Probab=41.05 E-value=19 Score=30.79 Aligned_cols=21 Identities=33% Similarity=0.599 Sum_probs=15.9
Q ss_pred CCcHHHHHHHHHHhCCCCchh
Q 030517 135 NNSTDLYYQKMIQADPRNPLL 155 (176)
Q Consensus 135 ~~~te~yY~~mi~~~P~N~Ll 155 (176)
...+..||++++++||+|.+.
T Consensus 96 F~kA~~~FqkAv~~~P~ne~Y 116 (186)
T PF06552_consen 96 FEKATEYFQKAVDEDPNNELY 116 (186)
T ss_dssp HHHHHHHHHHHHHH-TT-HHH
T ss_pred HHHHHHHHHHHHhcCCCcHHH
Confidence 356778999999999999874
No 49
>TIGR02996 rpt_mate_G_obs repeat-companion domain TIGR02996. This model describes an abundant paralogous domain of Gemmata obscuriglobus UQM 2246, a member of the Planctomycetes. The domain also occurs, although rarely, in Myxococcus xanthus DK 1622 and related species. Most member proteins have extensive repeats similar to the leucine-rich repeat, or another repeat class or region of low-complexity sequence. This domain is not repeated, and in Gemmata is usually found at the protein N-terminus.
Probab=39.19 E-value=31 Score=23.19 Aligned_cols=32 Identities=22% Similarity=0.148 Sum_probs=26.8
Q ss_pred HHHHHHHhCCCCchhhhhHHHHHHHHhhcCccc
Q 030517 141 YYQKMIQADPRNPLLLSNYARFLKEVNFCSKSF 173 (176)
Q Consensus 141 yY~~mi~~~P~N~LlL~NYAqFL~~V~~D~~r~ 173 (176)
-+-++|.++|++--.--=||.+|.+ ++|..|.
T Consensus 4 all~AI~~~P~ddt~RLvYADWL~e-~gdp~ra 35 (42)
T TIGR02996 4 ALLRAILAHPDDDTPRLVYADWLDE-HGDPARA 35 (42)
T ss_pred HHHHHHHhCCCCcchHHHHHHHHHH-cCCHHHH
Confidence 3567999999999888899999998 7777654
No 50
>PF12895 Apc3: Anaphase-promoting complex, cyclosome, subunit 3; PDB: 3KAE_D 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2XPI_A 3ULQ_A.
Probab=38.37 E-value=11 Score=25.62 Aligned_cols=31 Identities=29% Similarity=0.476 Sum_probs=24.4
Q ss_pred CCcHHHHHHHHHHhCCC--CchhhhhHHHHHHH
Q 030517 135 NNSTDLYYQKMIQADPR--NPLLLSNYARFLKE 165 (176)
Q Consensus 135 ~~~te~yY~~mi~~~P~--N~LlL~NYAqFL~~ 165 (176)
...+..+|+++++.+|. |+.++-+.|+=+++
T Consensus 5 y~~Ai~~~~k~~~~~~~~~~~~~~~~la~~~~~ 37 (84)
T PF12895_consen 5 YENAIKYYEKLLELDPTNPNSAYLYNLAQCYFQ 37 (84)
T ss_dssp HHHHHHHHHHHHHHHCGTHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHCCCChhHHHHHHHHHHHHH
Confidence 46788999999999995 56666667777776
No 51
>COG4278 Uncharacterized conserved protein [Function unknown]
Probab=38.22 E-value=26 Score=31.57 Aligned_cols=9 Identities=56% Similarity=1.435 Sum_probs=4.0
Q ss_pred CccCCCCCC
Q 030517 108 NMCGGGGGS 116 (176)
Q Consensus 108 ~~CGgg~G~ 116 (176)
.+||||-|+
T Consensus 252 s~CgggcGg 260 (269)
T COG4278 252 SFCGGGCGG 260 (269)
T ss_pred cccCCCCCC
Confidence 455544333
No 52
>smart00394 RIIa RIIalpha, Regulatory subunit portion of type II PKA R-subunit. RIIalpha, Regulatory subunit portion of type II PKA R-subunit. Contains dimerisation interface and binding site for A-kinase-anchoring proteins (AKAPs).
Probab=37.96 E-value=58 Score=20.21 Aligned_cols=27 Identities=19% Similarity=0.375 Sum_probs=21.1
Q ss_pred HHHHHHHHHhCCCCch-hhhhHHHHHHH
Q 030517 139 DLYYQKMIQADPRNPL-LLSNYARFLKE 165 (176)
Q Consensus 139 e~yY~~mi~~~P~N~L-lL~NYAqFL~~ 165 (176)
.++=...+...|.|++ |.+||.+=|.+
T Consensus 8 ~~~~~~vl~~qP~d~~~f~~~yF~kL~~ 35 (38)
T smart00394 8 EDLTVEVLRAQPSDLVQFAADYFEKLEE 35 (38)
T ss_pred HHHHHHHHHHCCCcHHHHHHHHHHHHHH
Confidence 4555678899999999 89999865544
No 53
>PF02197 RIIa: Regulatory subunit of type II PKA R-subunit; InterPro: IPR003117 Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases. Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. Phosphoprotein phosphatases catalyse the reverse process. Protein kinases fall into three broad classes, characterised with respect to substrate specificity []: Serine/threonine-protein kinases Tyrosine-protein kinases Dual specific protein kinases (e.g. MEK - phosphorylates both Thr and Tyr on target proteins) Protein kinase function has been evolutionarily conserved from Escherichia coli to human []. Protein kinases play a role in a multitude of cellular processes, including division, proliferation, apoptosis, and differentiation []. Phosphorylation usually results in a functional change of the target protein by changing enzyme activity, cellular location, or association with other proteins. The catalytic subunits of protein kinases are highly conserved, and several structures have been solved [], leading to large screens to develop kinase-specific inhibitors for the treatments of a number of diseases []. In the absence of cAMP, Protein Kinase A (PKA) exists as an equimolar tetramer of regulatory (R) and catalytic (C) subunits []. In addition to its role as an inhibitor of the C subunit, the R subunit anchors the holoenzyme to specific intracellular locations and prevents the C subunit from entering the nucleus. All R subunits have a conserved domain structure consisting of the N-terminal dimerization domain, inhibitory region, cAMP-binding domain A and cAMP-binding domain B. R subunits interact with C subunits primarily through the inhibitory site. The cAMP-binding domains show extensive sequence similarity and bind cAMP cooperatively. Two types of regulatory (R) subunits exist - types I and I - which differ in molecular weight, sequence, autophosphorylation cabaility, cellular location and tissue distribution. Types I and II were further sub-divided into alpha and beta subtypes, based mainly on sequence similarity. This entry represents types I-alpha, I-beta, II-alpha and II-beta regulatory subunits of PKA proteins. These subunits contain the dimerisation interface and binding site for A-kinase-anchoring proteins (AKAPs).; GO: 0008603 cAMP-dependent protein kinase regulator activity, 0007165 signal transduction; PDB: 2IZY_E 1R2A_A 1L6E_A 2IZX_B 2KYG_A 2EZW_B 3IM4_B 3IM3_A 4F9K_C 2HWN_B ....
Probab=37.90 E-value=65 Score=20.47 Aligned_cols=29 Identities=14% Similarity=0.358 Sum_probs=19.0
Q ss_pred cHHHHHHHHHHhCCCCch-hhhhHHHHHHH
Q 030517 137 STDLYYQKMIQADPRNPL-LLSNYARFLKE 165 (176)
Q Consensus 137 ~te~yY~~mi~~~P~N~L-lL~NYAqFL~~ 165 (176)
-.+++=+..+.++|.|++ |.+||-+=|.+
T Consensus 6 lL~~~~~~vl~~qP~Di~~F~a~yF~~L~~ 35 (38)
T PF02197_consen 6 LLKEFTREVLREQPDDILQFAADYFEKLEK 35 (38)
T ss_dssp HHHHHHHHHHHH--S-HHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHCCCcHHHHHHHHHHHHHH
Confidence 356778899999999998 56777655544
No 54
>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=37.63 E-value=31 Score=16.78 Aligned_cols=18 Identities=33% Similarity=0.636 Sum_probs=14.5
Q ss_pred CCcHHHHHHHHHHhCCCC
Q 030517 135 NNSTDLYYQKMIQADPRN 152 (176)
Q Consensus 135 ~~~te~yY~~mi~~~P~N 152 (176)
...+..+|+++|+.+|.+
T Consensus 17 ~~~a~~~~~~~~~~~~~~ 34 (34)
T smart00028 17 YDEALEYYEKALELDPNN 34 (34)
T ss_pred HHHHHHHHHHHHccCCCC
Confidence 467788999999998864
No 55
>PRK11189 lipoprotein NlpI; Provisional
Probab=37.26 E-value=31 Score=29.29 Aligned_cols=35 Identities=6% Similarity=-0.013 Sum_probs=22.9
Q ss_pred CcHHHHHHHHHHhCCCCchhhhhHHHHHHHHhhcCc
Q 030517 136 NSTDLYYQKMIQADPRNPLLLSNYARFLKEVNFCSK 171 (176)
Q Consensus 136 ~~te~yY~~mi~~~P~N~LlL~NYAqFL~~V~~D~~ 171 (176)
......|+++|+.+|+++..+-|.+..+.. .+|.+
T Consensus 81 ~~A~~~~~~Al~l~P~~~~a~~~lg~~~~~-~g~~~ 115 (296)
T PRK11189 81 ALARNDFSQALALRPDMADAYNYLGIYLTQ-AGNFD 115 (296)
T ss_pred HHHHHHHHHHHHcCCCCHHHHHHHHHHHHH-CCCHH
Confidence 445566788888888888777777765544 34433
No 56
>PRK15174 Vi polysaccharide export protein VexE; Provisional
Probab=36.82 E-value=30 Score=33.10 Aligned_cols=28 Identities=18% Similarity=0.229 Sum_probs=22.1
Q ss_pred HHHHHHHHHHhCCCCchhhhhHHHHHHH
Q 030517 138 TDLYYQKMIQADPRNPLLLSNYARFLKE 165 (176)
Q Consensus 138 te~yY~~mi~~~P~N~LlL~NYAqFL~~ 165 (176)
+..+|+++++.+|+++-.+.|||..|..
T Consensus 269 A~~~~~~Al~l~P~~~~a~~~lg~~l~~ 296 (656)
T PRK15174 269 AAEHWRHALQFNSDNVRIVTLYADALIR 296 (656)
T ss_pred HHHHHHHHHhhCCCCHHHHHHHHHHHHH
Confidence 6778888888888888888888877766
No 57
>KOG3074 consensus Transcriptional regulator of the PUR family, single-stranded-DNA-binding [Transcription]
Probab=34.75 E-value=25 Score=31.61 Aligned_cols=13 Identities=15% Similarity=0.112 Sum_probs=6.3
Q ss_pred HHHHHhhcCcccc
Q 030517 162 FLKEVNFCSKSFS 174 (176)
Q Consensus 162 FL~~V~~D~~r~~ 174 (176)
+=..+.+|++.|+
T Consensus 104 kSe~L~~d~RkfY 116 (263)
T KOG3074|consen 104 KSEELQRDNRKFY 116 (263)
T ss_pred HHHHHhhcCceEE
Confidence 3344455555554
No 58
>PRK12370 invasion protein regulator; Provisional
Probab=34.44 E-value=29 Score=32.20 Aligned_cols=37 Identities=14% Similarity=-0.110 Sum_probs=29.6
Q ss_pred CCcHHHHHHHHHHhCCCCchhhhhHHHHHHHHhhcCcc
Q 030517 135 NNSTDLYYQKMIQADPRNPLLLSNYARFLKEVNFCSKS 172 (176)
Q Consensus 135 ~~~te~yY~~mi~~~P~N~LlL~NYAqFL~~V~~D~~r 172 (176)
.+.+..+|+++|+.||+|+-.+.+.|..+.. .++.+.
T Consensus 320 ~~~A~~~~~~Al~ldP~~~~a~~~lg~~~~~-~g~~~~ 356 (553)
T PRK12370 320 MIKAKEHAIKATELDHNNPQALGLLGLINTI-HSEYIV 356 (553)
T ss_pred HHHHHHHHHHHHhcCCCCHHHHHHHHHHHHH-ccCHHH
Confidence 4778899999999999999999998876554 455443
No 59
>PF02184 HAT: HAT (Half-A-TPR) repeat; InterPro: IPR003107 The HAT (Half A TPR) repeat has a repetitive pattern characterised by three aromatic residues with a conserved spacing. They are structurally and sequentially similar to TPRs (tetratricopeptide repeats), though they lack the highly conserved alanine and glycine residues found in TPRs. The number of HAT repeats found in different proteins varies between 9 and 12. HAT-repeat-containing proteins appear to be components of macromolecular complexes that are required for RNA processing []. The repeats may be involved in protein-protein interactions. The HAT motif has striking structural similarities to HEAT repeats (IPR000357 from INTERPRO), being of a similar length and consisting of two short helices connected by a loop domain, as in HEAT repeats.; GO: 0006396 RNA processing, 0005622 intracellular
Probab=33.95 E-value=49 Score=20.99 Aligned_cols=27 Identities=19% Similarity=0.404 Sum_probs=21.5
Q ss_pred CCcHHHHHHHHHHhCCCCchhhhhHHHH
Q 030517 135 NNSTDLYYQKMIQADPRNPLLLSNYARF 162 (176)
Q Consensus 135 ~~~te~yY~~mi~~~P~N~LlL~NYAqF 162 (176)
.+++-..|++.|...|+-.. .=.||+|
T Consensus 3 ~dRAR~IyeR~v~~hp~~k~-WikyAkF 29 (32)
T PF02184_consen 3 FDRARSIYERFVLVHPEVKN-WIKYAKF 29 (32)
T ss_pred HHHHHHHHHHHHHhCCCchH-HHHHHHh
Confidence 57889999999999987444 4468888
No 60
>PRK11189 lipoprotein NlpI; Provisional
Probab=33.32 E-value=40 Score=28.65 Aligned_cols=32 Identities=13% Similarity=0.046 Sum_probs=27.1
Q ss_pred CCcHHHHHHHHHHhCCCCchhhhhHHHHHHHH
Q 030517 135 NNSTDLYYQKMIQADPRNPLLLSNYARFLKEV 166 (176)
Q Consensus 135 ~~~te~yY~~mi~~~P~N~LlL~NYAqFL~~V 166 (176)
.+.+.+.|+++|+.+|+++-.+.|.+..++..
T Consensus 114 ~~~A~~~~~~Al~l~P~~~~a~~~lg~~l~~~ 145 (296)
T PRK11189 114 FDAAYEAFDSVLELDPTYNYAYLNRGIALYYG 145 (296)
T ss_pred HHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHC
Confidence 57788899999999999999988888877653
No 61
>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=32.53 E-value=64 Score=21.78 Aligned_cols=31 Identities=16% Similarity=0.241 Sum_probs=22.5
Q ss_pred CCcHHHHHHHHHHhCCCCc---hhhhhHHHHHHH
Q 030517 135 NNSTDLYYQKMIQADPRNP---LLLSNYARFLKE 165 (176)
Q Consensus 135 ~~~te~yY~~mi~~~P~N~---LlL~NYAqFL~~ 165 (176)
.+.+..+|++++..+|+++ ..+-+.|..+..
T Consensus 55 ~~~A~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~ 88 (119)
T TIGR02795 55 YADAAKAFLAVVKKYPKSPKAPDALLKLGMSLQE 88 (119)
T ss_pred HHHHHHHHHHHHHHCCCCCcccHHHHHHHHHHHH
Confidence 4667888888888888874 456666666655
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=30.86 E-value=62 Score=29.01 Aligned_cols=30 Identities=23% Similarity=0.350 Sum_probs=20.3
Q ss_pred CcHHHHHHHHHHhCCCCchhhhhHHHHHHH
Q 030517 136 NSTDLYYQKMIQADPRNPLLLSNYARFLKE 165 (176)
Q Consensus 136 ~~te~yY~~mi~~~P~N~LlL~NYAqFL~~ 165 (176)
..+-.+|+++++.+|+|+-++.+++..++.
T Consensus 820 ~~A~~~~~~~~~~~~~~~~~~~~~~~~~~~ 849 (899)
T TIGR02917 820 PRALEYAEKALKLAPNIPAILDTLGWLLVE 849 (899)
T ss_pred HHHHHHHHHHHhhCCCCcHHHHHHHHHHHH
Confidence 345667777777777777777777766554
No 63
>PF12588 PSDC: Phophatidylserine decarboxylase ; InterPro: IPR022237 This domain family is found in bacteria and eukaryotes, and is approximately 140 amino acids in length. The family is found in association with PF02666 from PFAM. Phosphatidylserine decarboxylase (PSD) is an important enzyme in the synthesis of phosphatidylethanolamine in both prokaryotes and eukaryotes.
Probab=30.73 E-value=61 Score=26.29 Aligned_cols=33 Identities=18% Similarity=0.414 Sum_probs=26.5
Q ss_pred CCcHHHHHHHHHHh------CCCCchhhhhHHHHHHHHh
Q 030517 135 NNSTDLYYQKMIQA------DPRNPLLLSNYARFLKEVN 167 (176)
Q Consensus 135 ~~~te~yY~~mi~~------~P~N~LlL~NYAqFL~~V~ 167 (176)
+...-.|.++|+++ ..++++-.+||-+||+.+.
T Consensus 15 dp~l~ml~~~Mf~q~~~~~~p~g~~~~i~~~~~mL~~ln 53 (141)
T PF12588_consen 15 DPRLYMLFTQMFDQPPYNADPTGNPPQIRDYDEMLQLLN 53 (141)
T ss_pred CHHHHHHHHHHHhCcccccCCCCCccccccHHHHHHHHH
Confidence 35566788999999 5566779999999999864
No 64
>KOG0553 consensus TPR repeat-containing protein [General function prediction only]
Probab=30.60 E-value=34 Score=31.33 Aligned_cols=25 Identities=28% Similarity=0.303 Sum_probs=20.3
Q ss_pred CCCcHHHHHHHHHHhCCCCchhhhh
Q 030517 134 GNNSTDLYYQKMIQADPRNPLLLSN 158 (176)
Q Consensus 134 ~~~~te~yY~~mi~~~P~N~LlL~N 158 (176)
....+.++|||+|+.||+|...-.|
T Consensus 164 k~~~A~~aykKaLeldP~Ne~~K~n 188 (304)
T KOG0553|consen 164 KYEEAIEAYKKALELDPDNESYKSN 188 (304)
T ss_pred cHHHHHHHHHhhhccCCCcHHHHHH
Confidence 3577888899999999999955444
No 65
>PF13174 TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_A 3URZ_B 2Q7F_A.
Probab=29.31 E-value=43 Score=18.33 Aligned_cols=18 Identities=22% Similarity=0.490 Sum_probs=15.1
Q ss_pred CCcHHHHHHHHHHhCCCC
Q 030517 135 NNSTDLYYQKMIQADPRN 152 (176)
Q Consensus 135 ~~~te~yY~~mi~~~P~N 152 (176)
.+.+..+|++.|+..|++
T Consensus 16 ~~~A~~~~~~~~~~~P~s 33 (33)
T PF13174_consen 16 YDEAIEYFQRLIKRYPDS 33 (33)
T ss_dssp HHHHHHHHHHHHHHSTTS
T ss_pred HHHHHHHHHHHHHHCcCC
Confidence 467788999999999974
No 66
>PF05843 Suf: Suppressor of forked protein (Suf); InterPro: IPR008847 This domain consists of several eukaryotic suppressor of forked (Suf) like proteins. The Drosophila melanogaster suppressor of forked [Su(f)] protein shares homology with the Saccharomyces cerevisiae RNA14 protein and the 77 kDa subunit of Homo sapiens cleavage stimulation factor, which are proteins involved in mRNA 3' end formation. This suggests a role for Su(f) in mRNA 3' end formation in Drosophila. The su(f) gene produces three transcripts; two of them are polyadenylated at the end of the transcription unit, and one is a truncated transcript, polyadenylated in intron 4. It is thought that su(f) plays a role in the regulation of poly(A) site utilisation and the GU-rich sequence is important for this regulation to occur [].; GO: 0006397 mRNA processing, 0005634 nucleus; PDB: 2L9B_B 2OND_B 2OOE_A 4E85_B 4EBA_C 4E6H_A 2UY1_B.
Probab=29.26 E-value=33 Score=29.25 Aligned_cols=32 Identities=19% Similarity=0.405 Sum_probs=27.6
Q ss_pred CcHHHHHHHHHHhCCCCchhhhhHHHHHHHHh
Q 030517 136 NSTDLYYQKMIQADPRNPLLLSNYARFLKEVN 167 (176)
Q Consensus 136 ~~te~yY~~mi~~~P~N~LlL~NYAqFL~~V~ 167 (176)
..+...|++++..-|.|+.++-.|+.||..+.
T Consensus 53 ~~A~~Ife~glk~f~~~~~~~~~Y~~~l~~~~ 84 (280)
T PF05843_consen 53 KRARKIFERGLKKFPSDPDFWLEYLDFLIKLN 84 (280)
T ss_dssp HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHTT
T ss_pred HHHHHHHHHHHHHCCCCHHHHHHHHHHHHHhC
Confidence 44788999999999999999999999998753
No 67
>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=26.76 E-value=59 Score=30.11 Aligned_cols=24 Identities=25% Similarity=0.455 Sum_probs=17.6
Q ss_pred HHHHHHhCCCCchhhhhHHHHHHH
Q 030517 142 YQKMIQADPRNPLLLSNYARFLKE 165 (176)
Q Consensus 142 Y~~mi~~~P~N~LlL~NYAqFL~~ 165 (176)
.+++|.++|.++.||.-.|+||-.
T Consensus 223 l~~aL~~~p~d~~LL~~Qa~fLl~ 246 (395)
T PF09295_consen 223 LNEALKENPQDSELLNLQAEFLLS 246 (395)
T ss_pred HHHHHHhCCCCHHHHHHHHHHHHh
Confidence 356677777777777778888766
No 68
>PLN03088 SGT1, suppressor of G2 allele of SKP1; Provisional
Probab=26.61 E-value=64 Score=28.53 Aligned_cols=32 Identities=13% Similarity=-0.028 Sum_probs=26.0
Q ss_pred CCcHHHHHHHHHHhCCCCchhhhhHHHHHHHH
Q 030517 135 NNSTDLYYQKMIQADPRNPLLLSNYARFLKEV 166 (176)
Q Consensus 135 ~~~te~yY~~mi~~~P~N~LlL~NYAqFL~~V 166 (176)
...+..+|+++|+.+|+++..+-+.|..++..
T Consensus 52 ~~eAl~~~~~Al~l~P~~~~a~~~lg~~~~~l 83 (356)
T PLN03088 52 FTEAVADANKAIELDPSLAKAYLRKGTACMKL 83 (356)
T ss_pred HHHHHHHHHHHHHhCcCCHHHHHHHHHHHHHh
Confidence 46677888999999999998888888777663
No 69
>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=26.42 E-value=47 Score=30.84 Aligned_cols=28 Identities=21% Similarity=0.116 Sum_probs=14.3
Q ss_pred CcHHHHHHHHHHhCCCCchhhhhHHHHH
Q 030517 136 NSTDLYYQKMIQADPRNPLLLSNYARFL 163 (176)
Q Consensus 136 ~~te~yY~~mi~~~P~N~LlL~NYAqFL 163 (176)
..+..+|+++|+.+|+|...+.|.|..+
T Consensus 416 ~~A~~~~~kal~l~P~~~~~~~~la~~~ 443 (615)
T TIGR00990 416 AQAGKDYQKSIDLDPDFIFSHIQLGVTQ 443 (615)
T ss_pred HHHHHHHHHHHHcCccCHHHHHHHHHHH
Confidence 4445555555555555555544444443
No 70
>cd01145 TroA_c Periplasmic binding protein TroA_c. These proteins are predicted to function as initial receptors in the ABC metal ion uptake in eubacteria and archaea. They belong to the TroA superfamily of helical backbone metal receptor proteins that share a distinct fold and ligand binding mechanism. A typical TroA protein is comprised of two globular subdomains connected by a single helix and can bind their ligands in the cleft between these domains.
Probab=26.04 E-value=1e+02 Score=24.92 Aligned_cols=33 Identities=21% Similarity=0.293 Sum_probs=26.9
Q ss_pred CCcHHHHHHHHHHhCCCCc-hhhhhHHHHHHHHh
Q 030517 135 NNSTDLYYQKMIQADPRNP-LLLSNYARFLKEVN 167 (176)
Q Consensus 135 ~~~te~yY~~mi~~~P~N~-LlL~NYAqFL~~V~ 167 (176)
..-+...+++.++.+|.|. .+-+||.+|+.+++
T Consensus 118 ~~~a~~I~~~L~~~dP~~~~~y~~N~~~~~~~l~ 151 (203)
T cd01145 118 PALAKALADALIELDPSEQEEYKENLRVFLAKLN 151 (203)
T ss_pred HHHHHHHHHHHHHhCcccHHHHHHHHHHHHHHHH
Confidence 4556778889999999986 47789999998875
No 71
>PRK15174 Vi polysaccharide export protein VexE; Provisional
Probab=25.88 E-value=61 Score=31.08 Aligned_cols=31 Identities=26% Similarity=0.400 Sum_probs=27.7
Q ss_pred CCcHHHHHHHHHHhCCCCchhhhhHHHHHHH
Q 030517 135 NNSTDLYYQKMIQADPRNPLLLSNYARFLKE 165 (176)
Q Consensus 135 ~~~te~yY~~mi~~~P~N~LlL~NYAqFL~~ 165 (176)
.+.+..+|+++++.+|+|+.++.|+|+.+..
T Consensus 300 ~~eA~~~l~~al~l~P~~~~a~~~La~~l~~ 330 (656)
T PRK15174 300 NEKAIPLLQQSLATHPDLPYVRAMYARALRQ 330 (656)
T ss_pred HHHHHHHHHHHHHhCCCCHHHHHHHHHHHHH
Confidence 5778899999999999999999999987765
No 72
>COG4683 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=25.34 E-value=46 Score=26.89 Aligned_cols=23 Identities=17% Similarity=0.514 Sum_probs=17.9
Q ss_pred CCCCCCCCCCCCCcHHHHHHHHHHh
Q 030517 124 RWGSWDPNNHGNNSTDLYYQKMIQA 148 (176)
Q Consensus 124 ~~~~~~~~~~~~~~te~yY~~mi~~ 148 (176)
.|.|||+.+ ...+|+.|...|.+
T Consensus 91 ~~krwYden--i~~Ad~~f~ehL~~ 113 (120)
T COG4683 91 NWKRWYDEN--IPIADQRFEEHLAS 113 (120)
T ss_pred chhhHHHhc--CchhHHHHHHHHHH
Confidence 468999888 57788888877754
No 73
>PRK11447 cellulose synthase subunit BcsC; Provisional
Probab=24.44 E-value=53 Score=33.43 Aligned_cols=37 Identities=11% Similarity=0.012 Sum_probs=30.5
Q ss_pred CCCcHHHHHHHHHHhCCCCchhhhhHHHHHHHHhhcCc
Q 030517 134 GNNSTDLYYQKMIQADPRNPLLLSNYARFLKEVNFCSK 171 (176)
Q Consensus 134 ~~~~te~yY~~mi~~~P~N~LlL~NYAqFL~~V~~D~~ 171 (176)
..+.+..+|+++|+.+|+|+-.+-|.|+.+.. .+|.+
T Consensus 618 ~~~~A~~~y~~al~~~P~~~~a~~~la~~~~~-~g~~~ 654 (1157)
T PRK11447 618 DYAAARAAYQRVLTREPGNADARLGLIEVDIA-QGDLA 654 (1157)
T ss_pred CHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHH-CCCHH
Confidence 46788899999999999999999999988765 34443
No 74
>PF08424 NRDE-2: NRDE-2, necessary for RNA interference; InterPro: IPR013633 This is domain is found in eukaryotic proteins of unknown function.
Probab=24.23 E-value=83 Score=27.51 Aligned_cols=32 Identities=16% Similarity=0.170 Sum_probs=26.2
Q ss_pred CcHHHHHHHHHHhCCCCchhhhhHHHHHHHHh
Q 030517 136 NSTDLYYQKMIQADPRNPLLLSNYARFLKEVN 167 (176)
Q Consensus 136 ~~te~yY~~mi~~~P~N~LlL~NYAqFL~~V~ 167 (176)
.+.-.+|++||+.||++.-|+--|.+.-.++.
T Consensus 48 E~klsilerAL~~np~~~~L~l~~l~~~~~~~ 79 (321)
T PF08424_consen 48 ERKLSILERALKHNPDSERLLLGYLEEGEKVW 79 (321)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHHHHHHHhC
Confidence 34456899999999999999999988776654
No 75
>PF13413 HTH_25: Helix-turn-helix domain; PDB: 2WUS_R 3FYM_A.
Probab=23.81 E-value=35 Score=23.50 Aligned_cols=11 Identities=55% Similarity=0.806 Sum_probs=7.7
Q ss_pred hhhhHHHHHHH
Q 030517 155 LLSNYARFLKE 165 (176)
Q Consensus 155 lL~NYAqFL~~ 165 (176)
++++||+||..
T Consensus 47 ~lr~Ya~~Lgl 57 (62)
T PF13413_consen 47 YLRKYARFLGL 57 (62)
T ss_dssp HHHHHHHHTT-
T ss_pred HHHHHHHHhCc
Confidence 57888888753
No 76
>KOG0921 consensus Dosage compensation complex, subunit MLE [Transcription]
Probab=23.73 E-value=66 Score=34.29 Aligned_cols=12 Identities=33% Similarity=0.448 Sum_probs=6.0
Q ss_pred Cchhhhhhhccc
Q 030517 36 DSLKSMTRTLSE 47 (176)
Q Consensus 36 ~~~~~m~ra~Se 47 (176)
.+.-+|.|-+|.
T Consensus 1127 arllnmiRdIs~ 1138 (1282)
T KOG0921|consen 1127 ARLLNMIRDISR 1138 (1282)
T ss_pred HHHHHHHHHhcc
Confidence 344455555554
No 77
>cd01020 TroA_b Metal binding protein TroA_b. These proteins are predicted to function as initial receptors in ABC transport of metal ions. They belong to the TroA superfamily of helical backbone metal receptor proteins that share a distinct fold and ligand binding mechanism. A typical TroA protein is comprised of two globular subdomains connected by a single helix and can bind the metal ion in the cleft between these domains. In addition, these proteins sometimes have a low complexity region containing a metal-binding histidine-rich motif (repetitive HDH sequence).
Probab=23.16 E-value=1.2e+02 Score=25.65 Aligned_cols=34 Identities=18% Similarity=0.361 Sum_probs=27.6
Q ss_pred CCCcHHHHHHHHHHhCCCCc-hhhhhHHHHHHHHh
Q 030517 134 GNNSTDLYYQKMIQADPRNP-LLLSNYARFLKEVN 167 (176)
Q Consensus 134 ~~~~te~yY~~mi~~~P~N~-LlL~NYAqFL~~V~ 167 (176)
...-++...+.+.+.||.|. .+-+||.+|+.++.
T Consensus 104 ~~~~a~~I~~~L~~~dP~~~~~y~~N~~~~~~~l~ 138 (264)
T cd01020 104 MSKVANALADALVKADPDNKKYYQANAKKFVASLK 138 (264)
T ss_pred HHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHHHH
Confidence 34556778889999999998 57799999988865
No 78
>PF11225 DUF3024: Protein of unknown function (DUF3024); InterPro: IPR021388 This entry is represented by Bacteriophage 933W, L0084. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=22.99 E-value=66 Score=21.91 Aligned_cols=19 Identities=11% Similarity=0.228 Sum_probs=16.1
Q ss_pred hhHHHHHHHHhhcCccccc
Q 030517 157 SNYARFLKEVNFCSKSFSF 175 (176)
Q Consensus 157 ~NYAqFL~~V~~D~~r~~~ 175 (176)
.+-.+||.+|..|.++.||
T Consensus 39 ~~L~~~l~~i~~Dp~~~FW 57 (57)
T PF11225_consen 39 KDLEALLREIEKDPERCFW 57 (57)
T ss_pred CCHHHHHHHHhhCCccCcC
Confidence 4567899999999999986
No 79
>KOG0547 consensus Translocase of outer mitochondrial membrane complex, subunit TOM70/TOM72 [Intracellular trafficking, secretion, and vesicular transport]
Probab=22.94 E-value=60 Score=32.23 Aligned_cols=28 Identities=29% Similarity=0.464 Sum_probs=25.1
Q ss_pred CCCcHHHHHHHHHHhCCCCchhhhhHHH
Q 030517 134 GNNSTDLYYQKMIQADPRNPLLLSNYAR 161 (176)
Q Consensus 134 ~~~~te~yY~~mi~~~P~N~LlL~NYAq 161 (176)
.++.+-.||+++|+..|+-|+|..|-|-
T Consensus 130 kY~eAIkyY~~AI~l~p~epiFYsNraA 157 (606)
T KOG0547|consen 130 KYDEAIKYYTQAIELCPDEPIFYSNRAA 157 (606)
T ss_pred cHHHHHHHHHHHHhcCCCCchhhhhHHH
Confidence 4788899999999999999999999653
No 80
>KOG0548 consensus Molecular co-chaperone STI1 [Posttranslational modification, protein turnover, chaperones]
Probab=22.54 E-value=62 Score=31.82 Aligned_cols=26 Identities=31% Similarity=0.361 Sum_probs=23.1
Q ss_pred CCcHHHHHHHHHHhCCCCchhhhhHH
Q 030517 135 NNSTDLYYQKMIQADPRNPLLLSNYA 160 (176)
Q Consensus 135 ~~~te~yY~~mi~~~P~N~LlL~NYA 160 (176)
+..+-.+|.+||..||+|+-+.+|=|
T Consensus 374 y~~Av~~YteAIkr~P~Da~lYsNRA 399 (539)
T KOG0548|consen 374 YPEAVKHYTEAIKRDPEDARLYSNRA 399 (539)
T ss_pred HHHHHHHHHHHHhcCCchhHHHHHHH
Confidence 57778899999999999999999965
No 81
>KOG0376 consensus Serine-threonine phosphatase 2A, catalytic subunit [General function prediction only]
Probab=22.42 E-value=35 Score=33.00 Aligned_cols=31 Identities=23% Similarity=0.271 Sum_probs=26.1
Q ss_pred CCcHHHHHHHHHHhCCCCchhhhhHHHHHHHH
Q 030517 135 NNSTDLYYQKMIQADPRNPLLLSNYARFLKEV 166 (176)
Q Consensus 135 ~~~te~yY~~mi~~~P~N~LlL~NYAqFL~~V 166 (176)
.+.+-+.|.|+|+.|||++.+.+|=| +.+.+
T Consensus 20 fd~avdlysKaI~ldpnca~~~anRa-~a~lK 50 (476)
T KOG0376|consen 20 FDVAVDLYSKAIELDPNCAIYFANRA-LAHLK 50 (476)
T ss_pred HHHHHHHHHHHHhcCCcceeeechhh-hhhee
Confidence 57778899999999999999999987 44443
No 82
>PRK11447 cellulose synthase subunit BcsC; Provisional
Probab=22.28 E-value=60 Score=33.04 Aligned_cols=36 Identities=14% Similarity=0.052 Sum_probs=28.3
Q ss_pred CCcHHHHHHHHHHhCCCCchhhhhHHHHHHHHhhcCc
Q 030517 135 NNSTDLYYQKMIQADPRNPLLLSNYARFLKEVNFCSK 171 (176)
Q Consensus 135 ~~~te~yY~~mi~~~P~N~LlL~NYAqFL~~V~~D~~ 171 (176)
.+.+..+|+++|+.+|+|+-++-+.|+.+.. .+|.+
T Consensus 477 ~~eA~~~~~~Al~~~P~~~~~~~~LA~~~~~-~G~~~ 512 (1157)
T PRK11447 477 WAQAAELQRQRLALDPGSVWLTYRLAQDLRQ-AGQRS 512 (1157)
T ss_pred HHHHHHHHHHHHHhCCCCHHHHHHHHHHHHH-cCCHH
Confidence 4777889999999999999988888886655 44443
No 83
>KOG3060 consensus Uncharacterized conserved protein [Function unknown]
Probab=22.15 E-value=80 Score=28.90 Aligned_cols=31 Identities=19% Similarity=0.375 Sum_probs=25.6
Q ss_pred cHHHHHHHHHHhCCCCchhhhhHHHHHHHHh
Q 030517 137 STDLYYQKMIQADPRNPLLLSNYARFLKEVN 167 (176)
Q Consensus 137 ~te~yY~~mi~~~P~N~LlL~NYAqFL~~V~ 167 (176)
.+---|+++|-.+|-||++..-||..+|-.-
T Consensus 172 kA~fClEE~ll~~P~n~l~f~rlae~~Yt~g 202 (289)
T KOG3060|consen 172 KAAFCLEELLLIQPFNPLYFQRLAEVLYTQG 202 (289)
T ss_pred HHHHHHHHHHHcCCCcHHHHHHHHHHHHHHh
Confidence 3334478999999999999999999998653
No 84
>PRK10049 pgaA outer membrane protein PgaA; Provisional
Probab=21.93 E-value=1e+02 Score=29.93 Aligned_cols=31 Identities=10% Similarity=0.158 Sum_probs=27.9
Q ss_pred CCcHHHHHHHHHHhCCCCchhhhhHHHHHHH
Q 030517 135 NNSTDLYYQKMIQADPRNPLLLSNYARFLKE 165 (176)
Q Consensus 135 ~~~te~yY~~mi~~~P~N~LlL~NYAqFL~~ 165 (176)
...+...|+++++.+|+|+.++.+||+.|..
T Consensus 132 ~~~Al~~l~~al~~~P~~~~~~~~la~~l~~ 162 (765)
T PRK10049 132 HWDELRAMTQALPRAPQTQQYPTEYVQALRN 162 (765)
T ss_pred HHHHHHHHHHHHHhCCCCHHHHHHHHHHHHH
Confidence 4778899999999999999999999998764
No 85
>PF12569 NARP1: NMDA receptor-regulated protein 1 ; InterPro: IPR021183 This group represents N-terminal acetyltransferase A (NatA) auxiliary subunit and represents a non-catalytic component of the NatA N-terminal acetyltransferase, which catalyzes acetylation of proteins beginning with Met-Ser, Met-Gly and Met-Ala. N-terminal acetylation plays a role in normal eukaryotic translation and processing, protect against proteolytic degradation and protein turnover. NAT1 anchors ARD1 and NAT5 to the ribosome and may present the N- terminal of nascent polypeptides for acetylation [], [].
Probab=21.33 E-value=98 Score=29.63 Aligned_cols=31 Identities=16% Similarity=0.266 Sum_probs=27.5
Q ss_pred CCcHHHHHHHHHHhCCCCchhhhhHHHHHHH
Q 030517 135 NNSTDLYYQKMIQADPRNPLLLSNYARFLKE 165 (176)
Q Consensus 135 ~~~te~yY~~mi~~~P~N~LlL~NYAqFL~~ 165 (176)
.+.++..|+..|+.||.|-..+..|.+.+-.
T Consensus 54 ~~eA~~~y~~Li~rNPdn~~Yy~~L~~~~g~ 84 (517)
T PF12569_consen 54 KEEAEKIYRELIDRNPDNYDYYRGLEEALGL 84 (517)
T ss_pred HHHHHHHHHHHHHHCCCcHHHHHHHHHHHhh
Confidence 4678999999999999999999999998844
No 86
>PF08439 Peptidase_M3_N: Oligopeptidase F; InterPro: IPR013647 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This domain is found towards the N terminus of metallopeptidases belonging to MEROPS peptidase subfamily M3B (oligopeptidase F, clan MA). An example protein is Lactococcus lactisPepF []. The function of this N-terminal domain is unknown.; GO: 0008237 metallopeptidase activity, 0008270 zinc ion binding; PDB: 2QR4_B 3CE2_A.
Probab=21.08 E-value=1.3e+02 Score=20.37 Aligned_cols=28 Identities=25% Similarity=0.478 Sum_probs=21.9
Q ss_pred HHHHHHHHHhCCCCchhhhhHHHHHHHHhhcC
Q 030517 139 DLYYQKMIQADPRNPLLLSNYARFLKEVNFCS 170 (176)
Q Consensus 139 e~yY~~mi~~~P~N~LlL~NYAqFL~~V~~D~ 170 (176)
++-.+..|.++| -|+.|+.||.++.+..
T Consensus 7 e~~l~~~~~~~~----~l~~y~~~l~~i~r~k 34 (70)
T PF08439_consen 7 EEKLESLIKEDP----ELKEYRFYLEEIRRYK 34 (70)
T ss_dssp HHHHHHHHHH-C----CCGGGHHHHHHHHGGG
T ss_pred HHHHHHHHhcCc----cHHHHHHHHHHHHHhC
Confidence 566778888888 5899999999998754
No 87
>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=20.58 E-value=1.1e+02 Score=27.03 Aligned_cols=31 Identities=13% Similarity=0.193 Sum_probs=27.2
Q ss_pred CCcHHHHHHHHHHhCCCCc--hhhhhHHHHHHH
Q 030517 135 NNSTDLYYQKMIQADPRNP--LLLSNYARFLKE 165 (176)
Q Consensus 135 ~~~te~yY~~mi~~~P~N~--LlL~NYAqFL~~ 165 (176)
........++.++.+|+|| -++-.|++.++.
T Consensus 315 ~~~~~~~~e~~lk~~p~~~~~~ll~sLg~l~~~ 347 (409)
T TIGR00540 315 NEKLEKLIEKQAKNVDDKPKCCINRALGQLLMK 347 (409)
T ss_pred hHHHHHHHHHHHHhCCCChhHHHHHHHHHHHHH
Confidence 3567888899999999999 999999999876
No 88
>PF05268 GP38: Phage tail fibre adhesin Gp38; InterPro: IPR007932 This entry is represented by Bacteriophage T2, Gp38. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family contains several Gp38 proteins from T-even-like phages. Gp38, together with a second phage protein, Gp57, catalyses the organisation of Gp37 but is absent from the phage particle. Gp37 is responsible for receptor recognition [].
Probab=20.46 E-value=86 Score=28.19 Aligned_cols=21 Identities=52% Similarity=0.999 Sum_probs=11.4
Q ss_pred EEeeccccCCCC---------CccCCCCCC
Q 030517 96 VLVGGGIYGGGG---------NMCGGGGGS 116 (176)
Q Consensus 96 lv~GGG~~gGGG---------~~CGgg~G~ 116 (176)
++.|||++|++. .+|||++|+
T Consensus 150 aIAgGGGGGgg~~~~~~~~~~~~~GGGGGR 179 (260)
T PF05268_consen 150 AIAGGGGGGGGASYQNSWQGNLTFGGGGGR 179 (260)
T ss_pred EEecCCCCccccccCCCcccceeecCCCCC
Confidence 445565555552 277765554
No 89
>PHA00370 III attachment protein
Probab=20.16 E-value=1.3e+02 Score=27.64 Aligned_cols=8 Identities=50% Similarity=0.816 Sum_probs=4.5
Q ss_pred HHHHHHhC
Q 030517 142 YQKMIQAD 149 (176)
Q Consensus 142 Y~~mi~~~ 149 (176)
|.+|-.++
T Consensus 148 ~~kma~a~ 155 (297)
T PHA00370 148 YPKMANAN 155 (297)
T ss_pred cHHHhhhh
Confidence 66665444
No 90
>cd01017 AdcA Metal binding protein AcdA. These proteins have been shown to function in the ABC uptake of Zn2+ and Mn2+ and in competence for genetic transformation and adhesion. The AcdA proteins belong to the TroA superfamily of helical backbone metal receptor proteins that share a distinct fold and ligand binding mechanism. They are comprised of two globular subdomains connected by a long alpha helix and they bind their ligand in the cleft between these domains. In addition, many of these proteins have a low complexity region containing metal binding histidine-rich motif (repetitive HDH sequence).
Probab=20.11 E-value=1.5e+02 Score=25.12 Aligned_cols=32 Identities=22% Similarity=0.338 Sum_probs=25.8
Q ss_pred CcHHHHHHHHHHhCCCCc-hhhhhHHHHHHHHh
Q 030517 136 NSTDLYYQKMIQADPRNP-LLLSNYARFLKEVN 167 (176)
Q Consensus 136 ~~te~yY~~mi~~~P~N~-LlL~NYAqFL~~V~ 167 (176)
.-++...+...+.+|.|. .+-+|+++|+.++.
T Consensus 124 ~~a~~Ia~~L~~~dP~~~~~y~~N~~~~~~~L~ 156 (282)
T cd01017 124 QQVENIKDALIKLDPDNKEYYEKNAAAYAKKLE 156 (282)
T ss_pred HHHHHHHHHHHHhCcccHHHHHHHHHHHHHHHH
Confidence 346677788889999985 68899999998764
Done!