Query psy16704
Match_columns 146
No_of_seqs 110 out of 219
Neff 4.3
Searched_HMMs 46136
Date Fri Aug 16 19:53:49 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy16704.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/16704hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1586|consensus 100.0 1.2E-48 2.6E-53 327.7 12.1 117 30-146 170-288 (288)
2 PF14938 SNAP: Soluble NSF att 100.0 1.9E-38 4E-43 260.2 9.4 111 30-140 171-282 (282)
3 KOG1585|consensus 95.5 0.031 6.6E-07 48.6 5.7 58 58-116 193-251 (308)
4 PF04190 DUF410: Protein of un 95.3 0.13 2.9E-06 42.8 8.6 85 55-139 141-238 (260)
5 PRK15363 pathogenicity island 91.2 0.75 1.6E-05 36.6 6.1 47 31-84 86-133 (157)
6 KOG3024|consensus 85.7 6.5 0.00014 34.7 8.7 86 54-139 176-280 (312)
7 PRK10866 outer membrane biogen 85.0 7.2 0.00016 32.0 8.3 65 32-100 50-115 (243)
8 PF14559 TPR_19: Tetratricopep 82.9 6.4 0.00014 24.6 5.8 49 31-86 8-57 (68)
9 PF13525 YfiO: Outer membrane 82.7 20 0.00043 28.1 9.7 104 31-139 22-140 (203)
10 PRK15331 chaperone protein Sic 81.9 4.5 9.8E-05 32.5 5.8 50 31-88 88-138 (165)
11 TIGR02795 tol_pal_ybgF tol-pal 80.2 13 0.00028 24.9 6.9 64 31-98 19-83 (119)
12 PF13414 TPR_11: TPR repeat; P 79.0 4.6 9.9E-05 25.5 4.1 64 57-126 5-69 (69)
13 TIGR03302 OM_YfiO outer membra 78.7 20 0.00043 27.7 8.4 88 31-122 50-142 (235)
14 PRK13184 pknD serine/threonine 78.0 3.3 7.1E-05 41.1 4.5 49 74-122 492-546 (932)
15 PF13432 TPR_16: Tetratricopep 77.7 7.1 0.00015 24.4 4.7 49 31-86 14-63 (65)
16 PF01029 NusB: NusB family; I 75.1 3.2 6.9E-05 30.4 2.8 47 57-103 85-132 (134)
17 PRK15359 type III secretion sy 73.6 13 0.00027 27.7 5.8 54 31-91 75-129 (144)
18 PF00515 TPR_1: Tetratricopept 73.6 7.3 0.00016 21.6 3.5 30 58-87 4-34 (34)
19 PF13174 TPR_6: Tetratricopept 72.9 6.8 0.00015 21.1 3.3 29 58-86 3-32 (33)
20 PF13371 TPR_9: Tetratricopept 72.6 21 0.00046 22.5 6.2 57 32-98 13-70 (73)
21 cd00189 TPR Tetratricopeptide 72.3 16 0.00035 21.5 5.1 53 30-89 16-69 (100)
22 TIGR02552 LcrH_SycD type III s 70.9 16 0.00035 25.5 5.6 82 31-126 34-116 (135)
23 TIGR02552 LcrH_SycD type III s 69.3 28 0.0006 24.3 6.5 64 31-101 68-133 (135)
24 cd00620 Methyltransferase_Sun 65.6 24 0.00051 25.8 5.7 70 37-107 55-126 (126)
25 PRK14574 hmsH outer membrane p 65.5 20 0.00044 35.0 6.7 93 32-138 120-212 (822)
26 PF07719 TPR_2: Tetratricopept 64.7 17 0.00037 19.6 3.8 31 56-86 2-33 (34)
27 KOG1684|consensus 62.7 30 0.00066 31.6 6.8 103 26-137 200-307 (401)
28 COG3063 PilF Tfp pilus assembl 61.5 14 0.00031 31.7 4.4 86 44-136 129-215 (250)
29 COG4817 DNA-binding ferritin-l 61.2 44 0.00095 25.6 6.5 69 69-139 28-110 (111)
30 PF08858 IDEAL: IDEAL domain; 60.8 21 0.00046 21.7 3.9 30 89-118 8-37 (37)
31 PRK10803 tol-pal system protei 59.2 35 0.00077 28.6 6.3 83 31-118 160-247 (263)
32 KOG0547|consensus 59.1 30 0.00065 33.0 6.3 81 45-126 318-425 (606)
33 PF14938 SNAP: Soluble NSF att 56.3 1.1E+02 0.0024 25.1 10.7 90 31-122 132-226 (282)
34 TIGR02795 tol_pal_ybgF tol-pal 56.2 57 0.0012 21.6 6.0 63 57-123 4-67 (119)
35 PRK09635 sigI RNA polymerase s 55.4 31 0.00068 29.1 5.4 44 74-117 156-201 (290)
36 PF06304 DUF1048: Protein of u 55.2 34 0.00074 25.5 5.0 68 69-136 23-103 (103)
37 PLN03088 SGT1, suppressor of 54.1 1.2E+02 0.0025 26.2 8.8 93 31-137 19-119 (356)
38 PF13414 TPR_11: TPR repeat; P 48.5 64 0.0014 20.0 5.1 48 31-85 20-69 (69)
39 PF03608 EII-GUT: PTS system e 47.9 44 0.00095 27.2 4.9 29 29-57 42-70 (168)
40 cd00189 TPR Tetratricopeptide 47.8 56 0.0012 19.1 7.8 28 58-85 71-99 (100)
41 PF03399 SAC3_GANP: SAC3/GANP/ 46.6 66 0.0014 24.7 5.6 80 33-115 55-157 (204)
42 PF01817 CM_2: Chorismate muta 45.8 60 0.0013 21.8 4.7 41 76-116 24-67 (81)
43 KOG4703|consensus 45.7 9.8 0.00021 34.2 1.0 18 122-139 392-409 (431)
44 cd00619 Terminator_NusB Transc 45.4 40 0.00087 24.5 4.1 69 37-105 57-128 (130)
45 PRK03636 hypothetical protein; 44.8 31 0.00067 28.0 3.6 35 88-122 143-177 (179)
46 TIGR00990 3a0801s09 mitochondr 44.1 94 0.002 28.3 7.0 83 31-128 144-227 (615)
47 PF14287 DUF4368: Domain of un 43.9 15 0.00033 25.4 1.5 33 104-139 9-41 (71)
48 PF14261 DUF4351: Domain of un 43.6 9.9 0.00022 25.4 0.5 30 98-127 29-58 (59)
49 PF13181 TPR_8: Tetratricopept 42.4 46 0.001 18.0 3.2 29 58-86 4-33 (34)
50 PF15575 Imm29: Immunity prote 42.0 1.6E+02 0.0034 22.8 7.2 92 26-117 64-162 (215)
51 PF13525 YfiO: Outer membrane 41.8 90 0.0019 24.4 5.8 66 31-100 59-133 (203)
52 PF14561 TPR_20: Tetratricopep 40.7 1.3E+02 0.0028 21.2 6.1 50 59-108 26-76 (90)
53 PF01399 PCI: PCI domain; Int 40.6 32 0.00068 23.1 2.7 23 96-118 3-25 (105)
54 TIGR02957 SigX4 RNA polymerase 40.4 83 0.0018 26.0 5.6 45 74-118 146-192 (281)
55 TIGR00821 EII-GUT PTS system, 39.8 69 0.0015 26.4 4.9 27 30-56 46-72 (181)
56 PF11159 DUF2939: Protein of u 39.5 30 0.00066 24.3 2.5 42 95-139 16-57 (95)
57 PRK10370 formate-dependent nit 38.4 2E+02 0.0042 22.7 7.4 18 71-88 127-144 (198)
58 KOG0567|consensus 37.4 48 0.001 29.2 3.8 81 29-111 85-174 (289)
59 PRK10866 outer membrane biogen 36.8 1.6E+02 0.0035 24.1 6.8 71 31-105 86-172 (243)
60 PF07729 FCD: FCD domain; Int 36.7 1.3E+02 0.0028 20.0 6.4 83 35-117 31-121 (125)
61 TIGR00984 3a0801s03tim44 mitoc 35.6 79 0.0017 28.6 5.1 47 70-116 224-275 (378)
62 PF08463 EcoEI_R_C: EcoEI R pr 34.1 1.4E+02 0.0031 22.5 5.7 50 59-110 68-124 (164)
63 KOG2003|consensus 34.0 1E+02 0.0022 29.8 5.6 91 24-124 636-728 (840)
64 KOG0545|consensus 33.9 2.2E+02 0.0047 25.4 7.3 82 28-110 238-322 (329)
65 PF14164 YqzH: YqzH-like prote 33.8 1.2E+02 0.0026 21.1 4.7 46 73-118 10-61 (64)
66 PF04733 Coatomer_E: Coatomer 32.3 2.4E+02 0.0051 23.9 7.2 89 31-131 184-275 (290)
67 PRK07630 CobD/CbiB family prot 31.8 3.3E+02 0.0072 23.4 10.2 54 60-115 99-153 (312)
68 PRK09636 RNA polymerase sigma 30.5 1.5E+02 0.0033 24.5 5.7 43 75-117 154-198 (293)
69 smart00028 TPR Tetratricopepti 30.5 69 0.0015 15.0 3.7 29 58-86 4-33 (34)
70 COG1270 CbiB Cobalamin biosynt 30.1 3.9E+02 0.0085 23.7 11.4 95 29-139 86-181 (320)
71 COG0781 NusB Transcription ter 29.9 30 0.00065 27.1 1.3 62 45-106 76-144 (151)
72 PF02607 B12-binding_2: B12 bi 29.6 1.2E+02 0.0025 19.9 4.0 46 94-139 3-49 (79)
73 TIGR01951 nusB transcription a 29.0 1E+02 0.0022 22.2 4.0 48 57-104 79-127 (129)
74 TIGR02785 addA_Gpos recombinat 29.0 1.9E+02 0.004 29.6 6.9 113 24-138 48-176 (1232)
75 PF13877 RPAP3_C: Potential Mo 27.6 87 0.0019 21.7 3.3 39 87-125 40-82 (94)
76 KOG2580|consensus 27.6 1.6E+02 0.0034 27.6 5.6 44 72-115 300-348 (459)
77 KOG1962|consensus 27.5 2.8E+02 0.0061 23.3 6.7 57 3-61 13-96 (216)
78 PLN03088 SGT1, suppressor of 26.5 2.8E+02 0.0061 23.9 6.8 65 31-104 53-118 (356)
79 PRK11189 lipoprotein NlpI; Pro 26.1 1.8E+02 0.0038 24.1 5.3 29 62-90 105-134 (296)
80 PRK10987 regulatory protein Am 25.9 4.1E+02 0.0088 22.5 12.3 50 60-112 92-145 (284)
81 PRK11447 cellulose synthase su 25.6 2.3E+02 0.0049 28.3 6.7 98 26-124 32-141 (1157)
82 PRK07248 hypothetical protein; 25.5 2.1E+02 0.0045 19.7 4.9 35 81-115 37-71 (87)
83 PRK11447 cellulose synthase su 24.9 3.4E+02 0.0073 27.2 7.8 89 31-129 286-385 (1157)
84 PF08544 GHMP_kinases_C: GHMP 24.7 88 0.0019 20.4 2.7 22 99-120 1-22 (85)
85 TIGR01807 CM_P2 chorismate mut 24.7 2.2E+02 0.0048 19.2 4.8 40 77-116 29-72 (76)
86 smart00830 CM_2 Chorismate mut 24.5 2.1E+02 0.0046 18.7 5.0 37 79-115 29-66 (79)
87 PF13010 pRN1_helical: Primase 24.3 41 0.00088 26.5 1.1 36 104-139 9-46 (135)
88 PF02609 Exonuc_VII_S: Exonucl 23.6 88 0.0019 20.0 2.5 44 95-139 7-50 (53)
89 PF10163 EnY2: Transcription f 23.5 1.7E+02 0.0037 20.5 4.2 44 96-139 40-85 (86)
90 PF13474 SnoaL_3: SnoaL-like d 23.4 98 0.0021 20.8 2.8 23 94-116 3-25 (121)
91 COG4105 ComL DNA uptake lipopr 22.7 5E+02 0.011 22.4 7.7 65 32-100 52-117 (254)
92 PF12895 Apc3: Anaphase-promot 22.7 2.3E+02 0.005 18.5 7.4 49 31-85 6-55 (84)
93 KOG2908|consensus 22.7 1.8E+02 0.0039 26.6 5.0 48 88-136 230-277 (380)
94 PF14649 Spatacsin_C: Spatacsi 22.1 3.1E+02 0.0067 23.9 6.2 84 55-142 23-120 (296)
95 TIGR00990 3a0801s09 mitochondr 21.9 6.1E+02 0.013 23.1 8.7 87 31-124 484-571 (615)
96 cd00781 ketosteroid_isomerase 21.8 99 0.0021 21.3 2.6 25 93-117 6-30 (122)
97 KOG0548|consensus 21.5 5.5E+02 0.012 24.6 8.1 93 32-140 376-471 (539)
98 PRK10049 pgaA outer membrane p 21.2 2.5E+02 0.0055 26.7 5.9 52 31-89 66-118 (765)
99 PF04048 Sec8_exocyst: Sec8 ex 20.5 1.4E+02 0.0031 22.6 3.5 46 93-139 49-95 (142)
100 PF01875 Memo: Memo-like prote 20.4 1.3E+02 0.0028 25.2 3.5 36 97-132 205-241 (276)
101 cd00447 NusB_Sun RNA binding d 20.4 2.9E+02 0.0062 19.7 4.9 71 36-106 54-128 (129)
102 PRK00202 nusB transcription an 20.0 1.3E+02 0.0028 22.1 3.1 70 37-106 59-131 (137)
103 PF05529 Bap31: B-cell recepto 20.0 2.5E+02 0.0054 22.0 4.9 16 3-18 16-31 (192)
No 1
>KOG1586|consensus
Probab=100.00 E-value=1.2e-48 Score=327.69 Aligned_cols=117 Identities=52% Similarity=0.910 Sum_probs=113.2
Q ss_pred HHHHHHHHHHHHHHhhcccchhhchhHHhHHhHHHHHhc-chhHHHHHHhHHHhcCCCCccchHHHHHHHHHHHHhhcCH
Q psy16704 30 RIVYSLLFYSTGKAATENSLMKYNSKEYFFKAGLCHLCI-DLLNCQQALSRYIDLSPAFQDTREYKFLLKLIESLEEEDS 108 (146)
Q Consensus 30 ~~~A~eiyE~VA~~sl~n~LlKysaKeyffkA~LC~L~~-D~v~a~~ale~Y~~~DPsF~~SRE~klL~~LieAve~~D~ 108 (146)
-+.|+++||+||+.+++|||||||||||||||||||||. |++++++|+|+|+++||+|.+|||||||++|++|+|++|.
T Consensus 170 Y~~Ai~iyeqva~~s~~n~LLKys~KdyflkAgLChl~~~D~v~a~~ALeky~~~dP~F~dsREckflk~L~~aieE~d~ 249 (288)
T KOG1586|consen 170 YSKAIDIYEQVARSSLDNNLLKYSAKDYFLKAGLCHLCKADEVNAQRALEKYQELDPAFTDSRECKFLKDLLDAIEEQDI 249 (288)
T ss_pred HHHHHHHHHHHHHHhccchHHHhHHHHHHHHHHHHhHhcccHHHHHHHHHHHHhcCCcccccHHHHHHHHHHHHHhhhhH
Confidence 368999999999999999999999999999999999996 9999999999999999999999999999999999999999
Q ss_pred HHHHHHHHhhhccCCchHHHHHHHHHHHhhcCCC-CCCC
Q psy16704 109 DAFSETVKEFDSISRLDQWYTTMLLKIKRQISTN-EDLR 146 (146)
Q Consensus 109 e~Ft~aV~eYD~isrLD~WKT~mLLkIKk~I~~~-~dl~ 146 (146)
++||++|++||+|||||+|+||||+|||++|+++ |||+
T Consensus 250 e~fte~vkefDsisrLD~W~ttiLlkiK~siq~~edDL~ 288 (288)
T KOG1586|consen 250 EKFTEVVKEFDSISRLDQWKTTILLKIKKSIQGDEDDLR 288 (288)
T ss_pred HHHHHHHHhhhccchHHHHHHHHHHHHHHHHhccccccC
Confidence 9999999999999999999999999999999885 6675
No 2
>PF14938 SNAP: Soluble NSF attachment protein, SNAP; PDB: 1QQE_A 2IFU_A.
Probab=100.00 E-value=1.9e-38 Score=260.25 Aligned_cols=111 Identities=50% Similarity=0.819 Sum_probs=103.8
Q ss_pred HHHHHHHHHHHHHHhhcccchhhchhHHhHHhHHHHHhc-chhHHHHHHhHHHhcCCCCccchHHHHHHHHHHHHhhcCH
Q psy16704 30 RIVYSLLFYSTGKAATENSLMKYNSKEYFFKAGLCHLCI-DLLNCQQALSRYIDLSPAFQDTREYKFLLKLIESLEEEDS 108 (146)
Q Consensus 30 ~~~A~eiyE~VA~~sl~n~LlKysaKeyffkA~LC~L~~-D~v~a~~ale~Y~~~DPsF~~SRE~klL~~LieAve~~D~ 108 (146)
-.+|+++||++++.+++++|+|||+|+|||+|+|||||. |+|+|++++++|.+.||+|.+||||+|+.+|++|+++||+
T Consensus 171 y~~A~~~~e~~~~~~l~~~l~~~~~~~~~l~a~l~~L~~~D~v~A~~~~~~~~~~~~~F~~s~E~~~~~~l~~A~~~~D~ 250 (282)
T PF14938_consen 171 YEEAIEIYEEVAKKCLENNLLKYSAKEYFLKAILCHLAMGDYVAARKALERYCSQDPSFASSREYKFLEDLLEAYEEGDV 250 (282)
T ss_dssp HHHHHHHHHHHHHTCCCHCTTGHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHGTTSTTSTTSHHHHHHHHHHHHHHTT-C
T ss_pred HHHHHHHHHHHHHHhhcccccchhHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCCCCcHHHHHHHHHHHHHHhCCH
Confidence 368999999999999999999999999999999999999 9999999999999999999999999999999999999999
Q ss_pred HHHHHHHHhhhccCCchHHHHHHHHHHHhhcC
Q psy16704 109 DAFSETVKEFDSISRLDQWYTTMLLKIKRQIS 140 (146)
Q Consensus 109 e~Ft~aV~eYD~isrLD~WKT~mLLkIKk~I~ 140 (146)
|+|+++|++||+|+|||+|||+||++||++|+
T Consensus 251 e~f~~av~~~d~~~~ld~w~~~~l~~~k~~~~ 282 (282)
T PF14938_consen 251 EAFTEAVAEYDSISRLDNWKTKMLLKIKKKIE 282 (282)
T ss_dssp CCHHHHCHHHTTSS---HHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHcccCccHHHHHHHHHHHHhhcC
Confidence 99999999999999999999999999999984
No 3
>KOG1585|consensus
Probab=95.52 E-value=0.031 Score=48.60 Aligned_cols=58 Identities=19% Similarity=0.338 Sum_probs=50.5
Q ss_pred hHHhHHHHHhc-chhHHHHHHhHHHhcCCCCccchHHHHHHHHHHHHhhcCHHHHHHHHH
Q psy16704 58 FFKAGLCHLCI-DLLNCQQALSRYIDLSPAFQDTREYKFLLKLIESLEEEDSDAFSETVK 116 (146)
Q Consensus 58 ffkA~LC~L~~-D~v~a~~ale~Y~~~DPsF~~SRE~klL~~LieAve~~D~e~Ft~aV~ 116 (146)
++-+.|-||-. |.+.|++....-.+ -|.|.+|-++.-++.|+.+.++||.|.+++.+.
T Consensus 193 ~va~ilv~L~~~Dyv~aekc~r~~~q-ip~f~~sed~r~lenLL~ayd~gD~E~~~kvl~ 251 (308)
T KOG1585|consen 193 YVAAILVYLYAHDYVQAEKCYRDCSQ-IPAFLKSEDSRSLENLLTAYDEGDIEEIKKVLS 251 (308)
T ss_pred HHHHHHHHhhHHHHHHHHHHhcchhc-CccccChHHHHHHHHHHHHhccCCHHHHHHHHc
Confidence 66778888877 99999998876444 589999999999999999999999999988664
No 4
>PF04190 DUF410: Protein of unknown function (DUF410) ; InterPro: IPR007317 This is a family of conserved eukaryotic proteins with undetermined function.; PDB: 3LKU_E 2WPV_G.
Probab=95.26 E-value=0.13 Score=42.79 Aligned_cols=85 Identities=18% Similarity=0.285 Sum_probs=65.5
Q ss_pred hHHhHHhHHHHHhc-chhHHHHHHhHHHhc----CCC--------CccchHHHHHHHHHHHHhhcCHHHHHHHHHhhhcc
Q psy16704 55 KEYFFKAGLCHLCI-DLLNCQQALSRYIDL----SPA--------FQDTREYKFLLKLIESLEEEDSDAFSETVKEFDSI 121 (146)
Q Consensus 55 KeyffkA~LC~L~~-D~v~a~~ale~Y~~~----DPs--------F~~SRE~klL~~LieAve~~D~e~Ft~aV~eYD~i 121 (146)
--|..||.|.+||. +...|+.+++.|.+. .|. |.++.--.|++=|+.+|+.++.+.|..-...|-..
T Consensus 141 dlfi~RaVL~yL~l~n~~~A~~~~~~f~~~~~~~~p~~~~~~~~~~~~~PllnF~~lLl~t~e~~~~~~F~~L~~~Y~~~ 220 (260)
T PF04190_consen 141 DLFIARAVLQYLCLGNLRDANELFDTFTSKLIESHPKLENSDIEYPPSYPLLNFLQLLLLTCERDNLPLFKKLCEKYKPS 220 (260)
T ss_dssp HHHHHHHHHHHHHTTBHHHHHHHHHHHHHHHHHH---EEEEEEEEESS-HHHHHHHHHHHHHHHT-HHHHHHHHHHTHH-
T ss_pred hHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHhccCcchhccccCCCCCCchHHHHHHHHHHHhcCcHHHHHHHHHHhCcc
Confidence 45788999999999 999999999999988 564 44567789999999999999999999999999884
Q ss_pred CCchHHHHHHHHHHHhhc
Q psy16704 122 SRLDQWYTTMLLKIKRQI 139 (146)
Q Consensus 122 srLD~WKT~mLLkIKk~I 139 (146)
=+=|+=-...|.+|-+..
T Consensus 221 L~rd~~~~~~L~~IG~~y 238 (260)
T PF04190_consen 221 LKRDPSFKEYLDKIGQLY 238 (260)
T ss_dssp --HHHHTHHHHHHHHHHH
T ss_pred ccccHHHHHHHHHHHHHH
Confidence 333644445788887654
No 5
>PRK15363 pathogenicity island 2 chaperone protein SscA; Provisional
Probab=91.19 E-value=0.75 Score=36.63 Aligned_cols=47 Identities=11% Similarity=0.118 Sum_probs=41.2
Q ss_pred HHHHHHHHHHHHHhhcccchhhchhHHhHHhHHHHHhc-chhHHHHHHhHHHhcC
Q psy16704 31 IVYSLLFYSTGKAATENSLMKYNSKEYFFKAGLCHLCI-DLLNCQQALSRYIDLS 84 (146)
Q Consensus 31 ~~A~eiyE~VA~~sl~n~LlKysaKeyffkA~LC~L~~-D~v~a~~ale~Y~~~D 84 (146)
.+|++.|++-+.-..++| .-.+.+|.|+|.. |...|+++++.=.++.
T Consensus 86 ~~AI~aY~~A~~L~~ddp-------~~~~~ag~c~L~lG~~~~A~~aF~~Ai~~~ 133 (157)
T PRK15363 86 GEAIYAYGRAAQIKIDAP-------QAPWAAAECYLACDNVCYAIKALKAVVRIC 133 (157)
T ss_pred HHHHHHHHHHHhcCCCCc-------hHHHHHHHHHHHcCCHHHHHHHHHHHHHHh
Confidence 589999999999988888 5678999999999 9999999999666655
No 6
>KOG3024|consensus
Probab=85.73 E-value=6.5 Score=34.72 Aligned_cols=86 Identities=20% Similarity=0.297 Sum_probs=73.2
Q ss_pred hhHHhHHhHHHHHhc-chhHHHHHHhHHHh------------c------CCCCccchHHHHHHHHHHHHhhcCHHHHHHH
Q psy16704 54 SKEYFFKAGLCHLCI-DLLNCQQALSRYID------------L------SPAFQDTREYKFLLKLIESLEEEDSDAFSET 114 (146)
Q Consensus 54 aKeyffkA~LC~L~~-D~v~a~~ale~Y~~------------~------DPsF~~SRE~klL~~LieAve~~D~e~Ft~a 114 (146)
.-.++.+|.|-+||. |...|-++++.|.+ . +|-|..+.--.||.=|++.++.+|...|..-
T Consensus 176 ~d~f~~~aVlq~L~len~~~A~~s~t~yt~~f~~k~~p~~e~~~~~~~k~~~~~~~pllNFl~~Ll~t~~~k~~~~f~~L 255 (312)
T KOG3024|consen 176 PDVFYVQAVLQYLCLENDSSAARSFTTYTSMFNMKDFPMDEIKHKAGTKNPFPFEYPLLNFLHFLLETIQRKDLPLFLML 255 (312)
T ss_pred chHHHHHHHHHHHhhcchHHHHHHHHHHHHhhccccccchhhcccccccCCCccccchHHHHHHHHHHHhccccHHHHHH
Confidence 347899999999999 99999999999988 3 4577888889999999999999999999999
Q ss_pred HHhhhccCCchHHHHHHHHHHHhhc
Q psy16704 115 VKEFDSISRLDQWYTTMLLKIKRQI 139 (146)
Q Consensus 115 V~eYD~isrLD~WKT~mLLkIKk~I 139 (146)
+..|+.=-|=|.--..-|.||-+..
T Consensus 256 ~~~Y~~slkrd~~~~~~L~~Igely 280 (312)
T KOG3024|consen 256 RVKYQPSLKRDQAYNEYLDRIGELY 280 (312)
T ss_pred HHHccchhhhhHHHHHHHHHHHHHH
Confidence 9999985566766667777776543
No 7
>PRK10866 outer membrane biogenesis protein BamD; Provisional
Probab=84.98 E-value=7.2 Score=32.01 Aligned_cols=65 Identities=14% Similarity=0.068 Sum_probs=54.1
Q ss_pred HHHHHHHHHHHHhhcccchhhchhHHhHHhHHHHHhc-chhHHHHHHhHHHhcCCCCccchHHHHHHHHH
Q psy16704 32 VYSLLFYSTGKAATENSLMKYNSKEYFFKAGLCHLCI-DLLNCQQALSRYIDLSPAFQDTREYKFLLKLI 100 (146)
Q Consensus 32 ~A~eiyE~VA~~sl~n~LlKysaKeyffkA~LC~L~~-D~v~a~~ale~Y~~~DPsF~~SRE~klL~~Li 100 (146)
.|++.||++....-+++.. .+. .+.-+-+|+-. |...|...++++.+.+|+-+..-+..++.+++
T Consensus 50 ~Ai~~f~~l~~~yP~s~~a---~~a-~l~la~ayy~~~~y~~A~~~~e~fi~~~P~~~~~~~a~Y~~g~~ 115 (243)
T PRK10866 50 QAITQLEALDNRYPFGPYS---QQV-QLDLIYAYYKNADLPLAQAAIDRFIRLNPTHPNIDYVLYMRGLT 115 (243)
T ss_pred HHHHHHHHHHHhCCCChHH---HHH-HHHHHHHHHhcCCHHHHHHHHHHHHHhCcCCCchHHHHHHHHHh
Confidence 6888899988876666533 333 45677888888 99999999999999999999999999999987
No 8
>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=82.89 E-value=6.4 Score=24.62 Aligned_cols=49 Identities=16% Similarity=0.125 Sum_probs=40.1
Q ss_pred HHHHHHHHHHHHHhhcccchhhchhHHhHHhHHHHHhc-chhHHHHHHhHHHhcCCC
Q psy16704 31 IVYSLLFYSTGKAATENSLMKYNSKEYFFKAGLCHLCI-DLLNCQQALSRYIDLSPA 86 (146)
Q Consensus 31 ~~A~eiyE~VA~~sl~n~LlKysaKeyffkA~LC~L~~-D~v~a~~ale~Y~~~DPs 86 (146)
.+|.+.|+++....=+|+ +..+.-+-|++.. +...|+..+++....+|+
T Consensus 8 ~~A~~~~~~~l~~~p~~~-------~~~~~la~~~~~~g~~~~A~~~l~~~~~~~~~ 57 (68)
T PF14559_consen 8 DEAIELLEKALQRNPDNP-------EARLLLAQCYLKQGQYDEAEELLERLLKQDPD 57 (68)
T ss_dssp HHHHHHHHHHHHHTTTSH-------HHHHHHHHHHHHTT-HHHHHHHHHCCHGGGTT
T ss_pred HHHHHHHHHHHHHCCCCH-------HHHHHHHHHHHHcCCHHHHHHHHHHHHHHCcC
Confidence 479999999988766655 5555677888888 999999999999999998
No 9
>PF13525 YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M_A 2YHC_A.
Probab=82.74 E-value=20 Score=28.12 Aligned_cols=104 Identities=14% Similarity=0.144 Sum_probs=65.9
Q ss_pred HHHHHHHHHHHHHhhcccchhhchhHHhHHhHHHHHhc-chhHHHHHHhHHHhcCCCCccchHHHHHHHHHHHHh-----
Q psy16704 31 IVYSLLFYSTGKAATENSLMKYNSKEYFFKAGLCHLCI-DLLNCQQALSRYIDLSPAFQDTREYKFLLKLIESLE----- 104 (146)
Q Consensus 31 ~~A~eiyE~VA~~sl~n~LlKysaKeyffkA~LC~L~~-D~v~a~~ale~Y~~~DPsF~~SRE~klL~~LieAve----- 104 (146)
.+|++.|+++....=++++ +.+- .|..+-++... |...|...+++|....|+-+..-+..++.++..--.
T Consensus 22 ~~Ai~~f~~l~~~~P~s~~---a~~A-~l~la~a~y~~~~y~~A~~~~~~fi~~yP~~~~~~~A~Y~~g~~~~~~~~~~~ 97 (203)
T PF13525_consen 22 EEAIKLFEKLIDRYPNSPY---APQA-QLMLAYAYYKQGDYEEAIAAYERFIKLYPNSPKADYALYMLGLSYYKQIPGIL 97 (203)
T ss_dssp HHHHHHHHHHHHH-TTSTT---HHHH-HHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-TTHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHCCCChH---HHHH-HHHHHHHHHHcCCHHHHHHHHHHHHHHCCCCcchhhHHHHHHHHHHHhCccch
Confidence 4799999999998777664 3333 46667778877 999999999999999999998889988888754222
Q ss_pred --hcCHH-------HHHHHHHhhhccCCchHHHHHHHHHHHhhc
Q psy16704 105 --EEDSD-------AFSETVKEFDSISRLDQWYTTMLLKIKRQI 139 (146)
Q Consensus 105 --~~D~e-------~Ft~aV~eYD~isrLD~WKT~mLLkIKk~I 139 (146)
+.|.. .|.+-+..|-.=.. =+.=...+..+++.+
T Consensus 98 ~~~~D~~~~~~A~~~~~~li~~yP~S~y-~~~A~~~l~~l~~~l 140 (203)
T PF13525_consen 98 RSDRDQTSTRKAIEEFEELIKRYPNSEY-AEEAKKRLAELRNRL 140 (203)
T ss_dssp -TT---HHHHHHHHHHHHHHHH-TTSTT-HHHHHHHHHHHHHHH
T ss_pred hcccChHHHHHHHHHHHHHHHHCcCchH-HHHHHHHHHHHHHHH
Confidence 33443 45555555555333 333334444555554
No 10
>PRK15331 chaperone protein SicA; Provisional
Probab=81.86 E-value=4.5 Score=32.53 Aligned_cols=50 Identities=12% Similarity=0.089 Sum_probs=40.4
Q ss_pred HHHHHHHHHHHHHhhcccchhhchhHHhHHhHHHHHhc-chhHHHHHHhHHHhcCCCCc
Q psy16704 31 IVYSLLFYSTGKAATENSLMKYNSKEYFFKAGLCHLCI-DLLNCQQALSRYIDLSPAFQ 88 (146)
Q Consensus 31 ~~A~eiyE~VA~~sl~n~LlKysaKeyffkA~LC~L~~-D~v~a~~ale~Y~~~DPsF~ 88 (146)
..|++.|.--+.-..++|-- .|.||.|+|+. |...|+.+++.=.+ -|+..
T Consensus 88 ~~Ai~~Y~~A~~l~~~dp~p-------~f~agqC~l~l~~~~~A~~~f~~a~~-~~~~~ 138 (165)
T PRK15331 88 QKACDLYAVAFTLLKNDYRP-------VFFTGQCQLLMRKAAKARQCFELVNE-RTEDE 138 (165)
T ss_pred HHHHHHHHHHHHcccCCCCc-------cchHHHHHHHhCCHHHHHHHHHHHHh-CcchH
Confidence 47888888888888888743 89999999999 99999999987766 34433
No 11
>TIGR02795 tol_pal_ybgF tol-pal system protein YbgF. Members of this protein family are the product of one of seven genes regularly clustered in operons to encode the proteins of the tol-pal system, which is critical for maintaining the integrity of the bacterial outer membrane. The gene for this periplasmic protein has been designated orf2 and ybgF. All members of the seed alignment were from unique tol-pal gene regions from completed bacterial genomes. The architecture of this protein is a signal sequence, a low-complexity region usually rich in Asn and Gln, a well-conserved region with tandem repeats that resemble the tetratricopeptide (TPR) repeat, involved in protein-protein interaction.
Probab=80.21 E-value=13 Score=24.86 Aligned_cols=64 Identities=11% Similarity=0.056 Sum_probs=45.2
Q ss_pred HHHHHHHHHHHHHhhcccchhhchhHHhHHhHHHHHhc-chhHHHHHHhHHHhcCCCCccchHHHHHHH
Q psy16704 31 IVYSLLFYSTGKAATENSLMKYNSKEYFFKAGLCHLCI-DLLNCQQALSRYIDLSPAFQDTREYKFLLK 98 (146)
Q Consensus 31 ~~A~eiyE~VA~~sl~n~LlKysaKeyffkA~LC~L~~-D~v~a~~ale~Y~~~DPsF~~SRE~klL~~ 98 (146)
.+|.+.|+++....=+++ +.. +-.+..|.|.+.. +...|...+++....+|......+..+...
T Consensus 19 ~~A~~~~~~~~~~~~~~~---~~~-~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~~~~~~~ 83 (119)
T TIGR02795 19 ADAIQAFQAFLKKYPKST---YAP-NAHYWLGEAYYAQGKYADAAKAFLAVVKKYPKSPKAPDALLKLG 83 (119)
T ss_pred HHHHHHHHHHHHHCCCcc---ccH-HHHHHHHHHHHhhccHHHHHHHHHHHHHHCCCCCcccHHHHHHH
Confidence 468999999987654443 222 3345566667766 999999999999999998876666544433
No 12
>PF13414 TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2PL2_B 3IEG_B 2FBN_A ....
Probab=78.95 E-value=4.6 Score=25.47 Aligned_cols=64 Identities=16% Similarity=0.286 Sum_probs=41.4
Q ss_pred HhHHhHHHHHhc-chhHHHHHHhHHHhcCCCCccchHHHHHHHHHHHHhhcCHHHHHHHHHhhhccCCchH
Q psy16704 57 YFFKAGLCHLCI-DLLNCQQALSRYIDLSPAFQDTREYKFLLKLIESLEEEDSDAFSETVKEFDSISRLDQ 126 (146)
Q Consensus 57 yffkA~LC~L~~-D~v~a~~ale~Y~~~DPsF~~SRE~klL~~LieAve~~D~e~Ft~aV~eYD~isrLD~ 126 (146)
.+..-|.|++-. |...|...+++-.+.||+... ....+-.+..... +.+.+++..|++.-+|||
T Consensus 5 ~~~~~g~~~~~~~~~~~A~~~~~~ai~~~p~~~~-----~~~~~g~~~~~~~-~~~~~A~~~~~~al~l~P 69 (69)
T PF13414_consen 5 AWYNLGQIYFQQGDYEEAIEYFEKAIELDPNNAE-----AYYNLGLAYMKLG-KDYEEAIEDFEKALKLDP 69 (69)
T ss_dssp HHHHHHHHHHHTTHHHHHHHHHHHHHHHSTTHHH-----HHHHHHHHHHHTT-THHHHHHHHHHHHHHHST
T ss_pred HHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCHH-----HHHHHHHHHHHhC-ccHHHHHHHHHHHHHcCc
Confidence 345556666666 888888888888888887643 4444444444432 267777777777655553
No 13
>TIGR03302 OM_YfiO outer membrane assembly lipoprotein YfiO. Members of this protein family include YfiO, a near-essential protein of the outer membrane, part of a complex involved in protein insertion into the bacterial outer membrane. Many proteins in this family are annotated as ComL, based on the involvement of this protein in natural transformation with exogenous DNA in Neisseria gonorrhoeae. This protein family shows sequence similarity to, but is distinct from, the tol-pal system protein YbgF (TIGR02795).
Probab=78.74 E-value=20 Score=27.71 Aligned_cols=88 Identities=16% Similarity=0.150 Sum_probs=60.4
Q ss_pred HHHHHHHHHHHHHhhcccchhhchhHHhHHhHHHHHhc-chhHHHHHHhHHHhcCCCCccchHHHHHHHHHHHHh----h
Q psy16704 31 IVYSLLFYSTGKAATENSLMKYNSKEYFFKAGLCHLCI-DLLNCQQALSRYIDLSPAFQDTREYKFLLKLIESLE----E 105 (146)
Q Consensus 31 ~~A~eiyE~VA~~sl~n~LlKysaKeyffkA~LC~L~~-D~v~a~~ale~Y~~~DPsF~~SRE~klL~~LieAve----~ 105 (146)
..|.+.|+++....-+++. ..+-.+.-|.|+... +...|...+++..+.+|.-....+.-+..+.+-.-. .
T Consensus 50 ~~A~~~~~~~~~~~p~~~~----~~~a~~~la~~~~~~~~~~~A~~~~~~~l~~~p~~~~~~~a~~~~g~~~~~~~~~~~ 125 (235)
T TIGR03302 50 TEAIKYFEALESRYPFSPY----AEQAQLDLAYAYYKSGDYAEAIAAADRFIRLHPNHPDADYAYYLRGLSNYNQIDRVD 125 (235)
T ss_pred HHHHHHHHHHHHhCCCchh----HHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHCcCCCchHHHHHHHHHHHHHhccccc
Confidence 4788888888776555542 223445667888888 999999999999999998777766666655554322 1
Q ss_pred cCHHHHHHHHHhhhccC
Q psy16704 106 EDSDAFSETVKEFDSIS 122 (146)
Q Consensus 106 ~D~e~Ft~aV~eYD~is 122 (146)
.+.+.+.+++..|+++-
T Consensus 126 ~~~~~~~~A~~~~~~~~ 142 (235)
T TIGR03302 126 RDQTAAREAFEAFQELI 142 (235)
T ss_pred CCHHHHHHHHHHHHHHH
Confidence 23355666666666653
No 14
>PRK13184 pknD serine/threonine-protein kinase; Reviewed
Probab=78.00 E-value=3.3 Score=41.13 Aligned_cols=49 Identities=27% Similarity=0.450 Sum_probs=42.2
Q ss_pred HHHHhHHHhcCCCC---ccchHHHHHHHH---HHHHhhcCHHHHHHHHHhhhccC
Q psy16704 74 QQALSRYIDLSPAF---QDTREYKFLLKL---IESLEEEDSDAFSETVKEFDSIS 122 (146)
Q Consensus 74 ~~ale~Y~~~DPsF---~~SRE~klL~~L---ieAve~~D~e~Ft~aV~eYD~is 122 (146)
.+|+..|..+..+| ...||+.|=.++ -+|=|+||.+.|++|+.+|+.+.
T Consensus 492 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 546 (932)
T PRK13184 492 DQALIFYRRIRESFPGRKEGYEAQFRLGITLLEKASEQGDPRDFTQALSEFSYLH 546 (932)
T ss_pred HHHHHHHHHHhhcCCCcccchHHHHHhhHHHHHHHHhcCChHHHHHHHHHHHHhc
Confidence 46899999999999 678999986654 57889999999999999998763
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=77.66 E-value=7.1 Score=24.41 Aligned_cols=49 Identities=14% Similarity=0.055 Sum_probs=36.4
Q ss_pred HHHHHHHHHHHHHhhcccchhhchhHHhHHhHHHHHhc-chhHHHHHHhHHHhcCCC
Q psy16704 31 IVYSLLFYSTGKAATENSLMKYNSKEYFFKAGLCHLCI-DLLNCQQALSRYIDLSPA 86 (146)
Q Consensus 31 ~~A~eiyE~VA~~sl~n~LlKysaKeyffkA~LC~L~~-D~v~a~~ale~Y~~~DPs 86 (146)
.+|.+.|+++.+.. -+..+.++.-|.|+.-. +...|...+++..+.+|.
T Consensus 14 ~~A~~~~~~~l~~~-------P~~~~a~~~lg~~~~~~g~~~~A~~~~~~a~~~~P~ 63 (65)
T PF13432_consen 14 DEAIAAFEQALKQD-------PDNPEAWYLLGRILYQQGRYDEALAYYERALELDPD 63 (65)
T ss_dssp HHHHHHHHHHHCCS-------TTHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT
T ss_pred HHHHHHHHHHHHHC-------CCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCcC
Confidence 46788888877655 23456667777777777 999999999999988885
No 16
>PF01029 NusB: NusB family; InterPro: IPR006027 This domain is found in a number of functionally different proteins: NusB a prokaryotic transcription factor involved in antitermination TIM44, the mitochondrial inner membrane translocase subunit RsmB, the 16S rRNA m5C967 methyltransferase NusB is a prokaryotic transcription factor involved in antitermination processes, during which it interacts with the boxA portion of the mRNA nut site. Previous studies have shown that NusB exhibits an all-helical fold, and that the protein from Escherichia coli forms monomers, while Mycobacterium tuberculosis NusB is a dimer. The functional significance of NusB dimerization is unknown. An N-terminal arginine-rich sequence is the probable RNA binding site, exhibiting aromatic residues as potential stacking partners for the RNA bases. The RNA binding region is hidden in the subunit interface of dimeric NusB proteins, such as NusB from M. tuberculosis, suggesting that such dimers have to undergo a considerable conformational change or dissociate for engagement with RNA. In certain organisms, dimerization may be employed to package NusB in an inactive form until recruitment into antitermination complexes [, ]. The antitermination proteins of E. coli are recruited in the replication cycle of Bacteriophage lambda, where they play an important role in switching from the lysogenic to the lytic cycle.; GO: 0003723 RNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1SQG_A 1SQF_A 3IMQ_A 3D3C_C 3D3B_A 1EY1_A 1EYV_A 1TZV_A 1TZT_B 1TZX_B ....
Probab=75.13 E-value=3.2 Score=30.40 Aligned_cols=47 Identities=13% Similarity=0.311 Sum_probs=41.4
Q ss_pred HhHHhHHHHHhc-chhHHHHHHhHHHhcCCCCccchHHHHHHHHHHHH
Q psy16704 57 YFFKAGLCHLCI-DLLNCQQALSRYIDLSPAFQDTREYKFLLKLIESL 103 (146)
Q Consensus 57 yffkA~LC~L~~-D~v~a~~ale~Y~~~DPsF~~SRE~klL~~LieAv 103 (146)
-.|+-|+|++.. |.+...-++++|.++--.|.+.++++|+.+++..+
T Consensus 85 ~iLrla~~El~~~~~~p~~v~InEaVelak~~~~~~~~~fVNaVL~~~ 132 (134)
T PF01029_consen 85 AILRLAIYELLFLDDIPPHVAINEAVELAKKYGDEKSAGFVNAVLRRI 132 (134)
T ss_dssp HHHHHHHHHHHHSTTSHHHHHHHHHHHHHHHHS-TTHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHhcCCCCccchHHHHHHHHHHhCCCCcchhHHHHHHHh
Confidence 467778888888 89999999999999999999999999999999876
No 17
>PRK15359 type III secretion system chaperone protein SscB; Provisional
Probab=73.62 E-value=13 Score=27.72 Aligned_cols=54 Identities=13% Similarity=0.095 Sum_probs=32.9
Q ss_pred HHHHHHHHHHHHHhhcccchhhchhHHhHHhHHHHHhc-chhHHHHHHhHHHhcCCCCccch
Q psy16704 31 IVYSLLFYSTGKAATENSLMKYNSKEYFFKAGLCHLCI-DLLNCQQALSRYIDLSPAFQDTR 91 (146)
Q Consensus 31 ~~A~eiyE~VA~~sl~n~LlKysaKeyffkA~LC~L~~-D~v~a~~ale~Y~~~DPsF~~SR 91 (146)
.+|++.|++...-.-++ -+.++.-|.|+... +..+|..++++-...+|......
T Consensus 75 ~~A~~~y~~Al~l~p~~-------~~a~~~lg~~l~~~g~~~eAi~~~~~Al~~~p~~~~~~ 129 (144)
T PRK15359 75 TTAINFYGHALMLDASH-------PEPVYQTGVCLKMMGEPGLAREAFQTAIKMSYADASWS 129 (144)
T ss_pred HHHHHHHHHHHhcCCCC-------cHHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCChHHH
Confidence 45666666666533332 35566666666666 77777777777777777665444
No 18
>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=73.61 E-value=7.3 Score=21.56 Aligned_cols=30 Identities=17% Similarity=0.359 Sum_probs=23.2
Q ss_pred hHHhHHHHHhc-chhHHHHHHhHHHhcCCCC
Q psy16704 58 FFKAGLCHLCI-DLLNCQQALSRYIDLSPAF 87 (146)
Q Consensus 58 ffkA~LC~L~~-D~v~a~~ale~Y~~~DPsF 87 (146)
+++=|.|++.. +...|-..+++-.++||++
T Consensus 4 ~~~~g~~~~~~~~~~~A~~~~~~al~~~p~~ 34 (34)
T PF00515_consen 4 YYNLGNAYFQLGDYEEALEYYQRALELDPDN 34 (34)
T ss_dssp HHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH
T ss_pred HHHHHHHHHHhCCchHHHHHHHHHHHHCcCC
Confidence 34456666666 9999999999999999974
No 19
>PF13174 TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_A 3URZ_B 2Q7F_A.
Probab=72.95 E-value=6.8 Score=21.09 Aligned_cols=29 Identities=17% Similarity=0.352 Sum_probs=25.3
Q ss_pred hHHhHHHHHhc-chhHHHHHHhHHHhcCCC
Q psy16704 58 FFKAGLCHLCI-DLLNCQQALSRYIDLSPA 86 (146)
Q Consensus 58 ffkA~LC~L~~-D~v~a~~ale~Y~~~DPs 86 (146)
+++.|.|+.-. |...|...+++..+..|.
T Consensus 3 ~~~~a~~~~~~g~~~~A~~~~~~~~~~~P~ 32 (33)
T PF13174_consen 3 LYRLARCYYKLGDYDEAIEYFQRLIKRYPD 32 (33)
T ss_dssp HHHHHHHHHHHCHHHHHHHHHHHHHHHSTT
T ss_pred HHHHHHHHHHccCHHHHHHHHHHHHHHCcC
Confidence 57888898888 999999999999988885
No 20
>PF13371 TPR_9: Tetratricopeptide repeat
Probab=72.60 E-value=21 Score=22.49 Aligned_cols=57 Identities=14% Similarity=0.244 Sum_probs=37.9
Q ss_pred HHHHHHHHHHHHhhcccchhhchhHHhHHhHHHHHhc-chhHHHHHHhHHHhcCCCCccchHHHHHHH
Q psy16704 32 VYSLLFYSTGKAATENSLMKYNSKEYFFKAGLCHLCI-DLLNCQQALSRYIDLSPAFQDTREYKFLLK 98 (146)
Q Consensus 32 ~A~eiyE~VA~~sl~n~LlKysaKeyffkA~LC~L~~-D~v~a~~ale~Y~~~DPsF~~SRE~klL~~ 98 (146)
.|.+.+|++..-.=+ ++. .++.-|.|+.-. +...|...++++.+.+| +..+...+..
T Consensus 13 ~A~~~~~~~l~~~p~------~~~-~~~~~a~~~~~~g~~~~A~~~l~~~l~~~p---~~~~~~~~~a 70 (73)
T PF13371_consen 13 EALEVLERALELDPD------DPE-LWLQRARCLFQLGRYEEALEDLERALELSP---DDPDARALRA 70 (73)
T ss_pred HHHHHHHHHHHhCcc------cch-hhHHHHHHHHHhccHHHHHHHHHHHHHHCC---CcHHHHHHHH
Confidence 566777776665333 233 344456677766 99999999999999999 4444444443
No 21
>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=72.29 E-value=16 Score=21.52 Aligned_cols=53 Identities=6% Similarity=0.087 Sum_probs=39.5
Q ss_pred HHHHHHHHHHHHHHhhcccchhhchhHHhHHhHHHHHhc-chhHHHHHHhHHHhcCCCCcc
Q psy16704 30 RIVYSLLFYSTGKAATENSLMKYNSKEYFFKAGLCHLCI-DLLNCQQALSRYIDLSPAFQD 89 (146)
Q Consensus 30 ~~~A~eiyE~VA~~sl~n~LlKysaKeyffkA~LC~L~~-D~v~a~~ale~Y~~~DPsF~~ 89 (146)
-..|.+.|+++.+..-+++ ..+..-+.|+... +...|...+++.....|....
T Consensus 16 ~~~A~~~~~~~~~~~~~~~-------~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~ 69 (100)
T cd00189 16 YDEALEYYEKALELDPDNA-------DAYYNLAAAYYKLGKYEEALEDYEKALELDPDNAK 69 (100)
T ss_pred HHHHHHHHHHHHhcCCccH-------HHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcchh
Confidence 4578888888876544443 4566677777776 888899999998888888873
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=70.94 E-value=16 Score=25.52 Aligned_cols=82 Identities=13% Similarity=0.054 Sum_probs=55.9
Q ss_pred HHHHHHHHHHHHHhhcccchhhchhHHhHHhHHHHHhc-chhHHHHHHhHHHhcCCCCccchHHHHHHHHHHHHhhcCHH
Q psy16704 31 IVYSLLFYSTGKAATENSLMKYNSKEYFFKAGLCHLCI-DLLNCQQALSRYIDLSPAFQDTREYKFLLKLIESLEEEDSD 109 (146)
Q Consensus 31 ~~A~eiyE~VA~~sl~n~LlKysaKeyffkA~LC~L~~-D~v~a~~ale~Y~~~DPsF~~SRE~klL~~LieAve~~D~e 109 (146)
.+|.+.|+++....-++ .+.+...+.|+... +...|...+++-.+.+|.-.+.+ .....+-. .. .
T Consensus 34 ~~A~~~~~~~~~~~p~~-------~~~~~~la~~~~~~~~~~~A~~~~~~~~~~~p~~~~~~---~~la~~~~-~~---g 99 (135)
T TIGR02552 34 DEALKLFQLLAAYDPYN-------SRYWLGLAACCQMLKEYEEAIDAYALAAALDPDDPRPY---FHAAECLL-AL---G 99 (135)
T ss_pred HHHHHHHHHHHHhCCCc-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCChHHH---HHHHHHHH-Hc---C
Confidence 56888888877654332 46667778888877 99999999999989998865444 22222222 22 3
Q ss_pred HHHHHHHhhhccCCchH
Q psy16704 110 AFSETVKEFDSISRLDQ 126 (146)
Q Consensus 110 ~Ft~aV~eYD~isrLD~ 126 (146)
.+.+++..|.+..++|+
T Consensus 100 ~~~~A~~~~~~al~~~p 116 (135)
T TIGR02552 100 EPESALKALDLAIEICG 116 (135)
T ss_pred CHHHHHHHHHHHHHhcc
Confidence 47777777777777775
No 23
>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=69.28 E-value=28 Score=24.30 Aligned_cols=64 Identities=16% Similarity=0.169 Sum_probs=43.7
Q ss_pred HHHHHHHHHHHHHhhcccchhhchhHHhHHhHHHHHhc-chhHHHHHHhHHHhcCCCCccchHHHH-HHHHHH
Q psy16704 31 IVYSLLFYSTGKAATENSLMKYNSKEYFFKAGLCHLCI-DLLNCQQALSRYIDLSPAFQDTREYKF-LLKLIE 101 (146)
Q Consensus 31 ~~A~eiyE~VA~~sl~n~LlKysaKeyffkA~LC~L~~-D~v~a~~ale~Y~~~DPsF~~SRE~kl-L~~Lie 101 (146)
..|.+.|++..+..-+ + .+.+...+.|+.-. |...|...+++..+.+|.....++.+. +..++|
T Consensus 68 ~~A~~~~~~~~~~~p~------~-~~~~~~la~~~~~~g~~~~A~~~~~~al~~~p~~~~~~~~~~~~~~~~~ 133 (135)
T TIGR02552 68 EEAIDAYALAAALDPD------D-PRPYFHAAECLLALGEPESALKALDLAIEICGENPEYSELKERAEAMLE 133 (135)
T ss_pred HHHHHHHHHHHhcCCC------C-hHHHHHHHHHHHHcCCHHHHHHHHHHHHHhccccchHHHHHHHHHHHHh
Confidence 4777888876654322 2 34445556677777 999999999999999998876554432 444444
No 24
>cd00620 Methyltransferase_Sun N-terminal RNA binding domain of the methyltransferase Sun. The rRNA-specific 5-methylcytidine transferase Sun, also known as RrmB or Fmu shares the RNA-binding non-catalytic domain with the transcription termination factor NusB. The precise biological role of this domain in Sun is unknown, although it is likely to be involved in sequence-specific RNA binding. The C-terminal methyltransferase domain of Sun has been shown to catalyze formation of m5C at position 967 of 16S rRNA in Escherichia coli.
Probab=65.60 E-value=24 Score=25.77 Aligned_cols=70 Identities=13% Similarity=0.178 Sum_probs=50.4
Q ss_pred HHHHHHHhhcccchhhchhH-HhHHhHHHHHhc-chhHHHHHHhHHHhcCCCCccchHHHHHHHHHHHHhhcC
Q psy16704 37 FYSTGKAATENSLMKYNSKE-YFFKAGLCHLCI-DLLNCQQALSRYIDLSPAFQDTREYKFLLKLIESLEEED 107 (146)
Q Consensus 37 yE~VA~~sl~n~LlKysaKe-yffkA~LC~L~~-D~v~a~~ale~Y~~~DPsF~~SRE~klL~~LieAve~~D 107 (146)
.+.+....+++++.+-+..+ ..|+-|++++.. | +...-+++++.++-..+.+.+..+|+.+++..+...|
T Consensus 55 ld~~i~~~l~~~~~~~~~~~~~iLr~a~~el~~~~-~p~~avvneaVelak~~~~~~~~~fVNaVLr~i~r~~ 126 (126)
T cd00620 55 LDWIINPLLKKPDVGKDPDVRNLLRLGLYQLLYLD-VPPHAAVDETVEIAKIRKDLGRAGLVNAVLRRFERED 126 (126)
T ss_pred HHHHHHHHhCCCccccCHHHHHHHHHHHHHHHhcC-CCchHHHHHHHHHHHHhCCCchhhHHHHHHHHHhccC
Confidence 45555666666553333222 356677777776 7 6777888999999999988899999999998877654
No 25
>PRK14574 hmsH outer membrane protein; Provisional
Probab=65.48 E-value=20 Score=35.03 Aligned_cols=93 Identities=16% Similarity=0.076 Sum_probs=64.5
Q ss_pred HHHHHHHHHHHHhhcccchhhchhHHhHHhHHHHHhcchhHHHHHHhHHHhcCCCCccchHHHHHHHHHHHHhhcCHHHH
Q psy16704 32 VYSLLFYSTGKAATENSLMKYNSKEYFFKAGLCHLCIDLLNCQQALSRYIDLSPAFQDTREYKFLLKLIESLEEEDSDAF 111 (146)
Q Consensus 32 ~A~eiyE~VA~~sl~n~LlKysaKeyffkA~LC~L~~D~v~a~~ale~Y~~~DPsF~~SRE~klL~~LieAve~~D~e~F 111 (146)
.|+++|+++-+..=+|+ +.++ +|..+..|.....+|++.+....|.+++.++++.+..+-. + .++.
T Consensus 120 ~Aiely~kaL~~dP~n~-------~~l~--gLa~~y~~~~q~~eAl~~l~~l~~~dp~~~~~l~layL~~----~-~~~~ 185 (822)
T PRK14574 120 QALALWQSSLKKDPTNP-------DLIS--GMIMTQADAGRGGVVLKQATELAERDPTVQNYMTLSYLNR----A-TDRN 185 (822)
T ss_pred HHHHHHHHHHhhCCCCH-------HHHH--HHHHHHhhcCCHHHHHHHHHHhcccCcchHHHHHHHHHHH----h-cchH
Confidence 89999999988877774 2222 6644444667777777777777777777888855533332 2 4444
Q ss_pred HHHHHhhhccCCchHHHHHHHHHHHhh
Q psy16704 112 SETVKEFDSISRLDQWYTTMLLKIKRQ 138 (146)
Q Consensus 112 t~aV~eYD~isrLD~WKT~mLLkIKk~ 138 (146)
.+++..|.++..+++.....+..--..
T Consensus 186 ~~AL~~~ekll~~~P~n~e~~~~~~~~ 212 (822)
T PRK14574 186 YDALQASSEAVRLAPTSEEVLKNHLEI 212 (822)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHHHH
Confidence 459999999999999988887654433
No 26
>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=64.69 E-value=17 Score=19.62 Aligned_cols=31 Identities=13% Similarity=0.312 Sum_probs=25.4
Q ss_pred HHhHHhHHHHHhc-chhHHHHHHhHHHhcCCC
Q psy16704 56 EYFFKAGLCHLCI-DLLNCQQALSRYIDLSPA 86 (146)
Q Consensus 56 eyffkA~LC~L~~-D~v~a~~ale~Y~~~DPs 86 (146)
+.++.-|.|+.-. +...|.+.+++-.+++|+
T Consensus 2 ~~~~~lg~~~~~~~~~~~A~~~~~~al~l~p~ 33 (34)
T PF07719_consen 2 EAWYYLGQAYYQLGNYEEAIEYFEKALELDPN 33 (34)
T ss_dssp HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT
T ss_pred HHHHHHHHHHHHhCCHHHHHHHHHHHHHHCcC
Confidence 4567778888887 999999999999999985
No 27
>KOG1684|consensus
Probab=62.74 E-value=30 Score=31.58 Aligned_cols=103 Identities=12% Similarity=0.104 Sum_probs=69.4
Q ss_pred HHHHHHHHHHH-HHHHHHHhhcccchhhchhHHhHHhHHHHHhc-ch-hHHHHHHhHHHhc--CCCCccchHHHHHHHHH
Q psy16704 26 MMTFRIVYSLL-FYSTGKAATENSLMKYNSKEYFFKAGLCHLCI-DL-LNCQQALSRYIDL--SPAFQDTREYKFLLKLI 100 (146)
Q Consensus 26 ~~~~~~~A~ei-yE~VA~~sl~n~LlKysaKeyffkA~LC~L~~-D~-v~a~~ale~Y~~~--DPsF~~SRE~klL~~Li 100 (146)
+-.+|+..++. +=-+|...+.|.=+- .+=++.+ ..++ |+ ...+..+++|.+. +|+|.-++ .++.+-
T Consensus 200 LTG~rl~GaD~~~~GlATHyv~S~~l~-----~Lee~L~-~~l~~dp~~~I~~~l~~y~~~~~~~~~~~~~---~~~~i~ 270 (401)
T KOG1684|consen 200 LTGQRLSGADALRCGLATHYVPSEKLP-----SLEERLL-KNLNDDPQSVINETLEKYASPAKDESFSLSL---KLDVIN 270 (401)
T ss_pred hccceecchHHHHhcchhhccchhhhh-----HHHHHHh-hhcCCCcHHHHHHHHHHhcccCCCccccchh---hHHHHH
Confidence 34455544443 334555555443221 1122223 3555 66 5688899999886 77777666 455555
Q ss_pred HHHhhcCHHHHHHHHHhhhccCCchHHHHHHHHHHHh
Q psy16704 101 ESLEEEDSDAFSETVKEFDSISRLDQWYTTMLLKIKR 137 (146)
Q Consensus 101 eAve~~D~e~Ft~aV~eYD~isrLD~WKT~mLLkIKk 137 (146)
.+...+++|.--+++.+|.+=+..+.|-.+-|-++++
T Consensus 271 ~~Fs~~tVeeIie~lk~~q~~~~~~ewak~tlk~L~k 307 (401)
T KOG1684|consen 271 KCFSANTVEEIIEALKNYQQSADGSEWAKETLKTLKK 307 (401)
T ss_pred HhhccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhh
Confidence 5667788999999999999989999999999988886
No 28
>COG3063 PilF Tfp pilus assembly protein PilF [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=61.52 E-value=14 Score=31.71 Aligned_cols=86 Identities=17% Similarity=0.189 Sum_probs=58.1
Q ss_pred hhcccchhhchhHHhHHhHHHHHhc-chhHHHHHHhHHHhcCCCCccchHHHHHHHHHHHHhhcCHHHHHHHHHhhhccC
Q psy16704 44 ATENSLMKYNSKEYFFKAGLCHLCI-DLLNCQQALSRYIDLSPAFQDTREYKFLLKLIESLEEEDSDAFSETVKEFDSIS 122 (146)
Q Consensus 44 sl~n~LlKysaKeyffkA~LC~L~~-D~v~a~~ale~Y~~~DPsF~~SRE~klL~~LieAve~~D~e~Ft~aV~eYD~is 122 (146)
+++.| .=|..-+-|-++|+|.+=. +...|+.-+++-.+.||+|..+++-+. +-.+++-+-.+...|.+.+. +
T Consensus 129 Al~~P-~Y~~~s~t~eN~G~Cal~~gq~~~A~~~l~raL~~dp~~~~~~l~~a-~~~~~~~~y~~Ar~~~~~~~-----~ 201 (250)
T COG3063 129 ALADP-AYGEPSDTLENLGLCALKAGQFDQAEEYLKRALELDPQFPPALLELA-RLHYKAGDYAPARLYLERYQ-----Q 201 (250)
T ss_pred HHhCC-CCCCcchhhhhhHHHHhhcCCchhHHHHHHHHHHhCcCCChHHHHHH-HHHHhcccchHHHHHHHHHH-----h
Confidence 45555 4456677889999999976 999999999999999999999987654 33344444444555544332 2
Q ss_pred CchHHHHHHHHHHH
Q psy16704 123 RLDQWYTTMLLKIK 136 (146)
Q Consensus 123 rLD~WKT~mLLkIK 136 (146)
+.-.=..+++|-|+
T Consensus 202 ~~~~~A~sL~L~ir 215 (250)
T COG3063 202 RGGAQAESLLLGIR 215 (250)
T ss_pred cccccHHHHHHHHH
Confidence 33344555555554
No 29
>COG4817 DNA-binding ferritin-like protein (Dps family) [General function prediction only]
Probab=61.18 E-value=44 Score=25.58 Aligned_cols=69 Identities=20% Similarity=0.356 Sum_probs=54.0
Q ss_pred chhHHHHHHhHHHhcCCCCccchHHHHHHHHHHHHhhc-------------CHHHHHHHHH-hhhccCCchHHHHHHHHH
Q psy16704 69 DLLNCQQALSRYIDLSPAFQDTREYKFLLKLIESLEEE-------------DSDAFSETVK-EFDSISRLDQWYTTMLLK 134 (146)
Q Consensus 69 D~v~a~~ale~Y~~~DPsF~~SRE~klL~~LieAve~~-------------D~e~Ft~aV~-eYD~isrLD~WKT~mLLk 134 (146)
|.-.|=+++++|.=... +.+--|.+++.+++|-+|++ |+..|.+++- +| .=+=-|+|++++=..
T Consensus 28 dY~~aykeIqkYlw~~g-~t~~~~~~Il~~iLelfE~aaadgk~v~dv~GdDvA~F~D~Ll~D~-~ktw~dK~r~kLn~~ 105 (111)
T COG4817 28 DYYTAYKEIQKYLWKSG-PTGWNEMKILGNILELFEEAAADGKEVTDVLGDDVATFCDALLGDY-EKTWRDKYRSKLNKS 105 (111)
T ss_pred HHHHHHHHHHHHHHHcC-cchhHHHHHHHHHHHHHHHHHhccccHHHHhcchHHHHHHHHHcch-HHHHHHHHHHHHHHH
Confidence 77788899999987666 78888889999999988875 6888988764 44 344458888888777
Q ss_pred HHhhc
Q psy16704 135 IKRQI 139 (146)
Q Consensus 135 IKk~I 139 (146)
|++.+
T Consensus 106 v~~~~ 110 (111)
T COG4817 106 VKRKL 110 (111)
T ss_pred HHhhc
Confidence 77754
No 30
>PF08858 IDEAL: IDEAL domain; InterPro: IPR014957 This entry represents the C-terminal domain of Bacteriophage SPP1, p90. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. his domain may also be referred to as the IDEAL domain, after the sequence of the most conserved region of the domain.; PDB: 3DO9_A.
Probab=60.77 E-value=21 Score=21.75 Aligned_cols=30 Identities=27% Similarity=0.391 Sum_probs=24.1
Q ss_pred cchHHHHHHHHHHHHhhcCHHHHHHHHHhh
Q psy16704 89 DTREYKFLLKLIESLEEEDSDAFSETVKEF 118 (146)
Q Consensus 89 ~SRE~klL~~LieAve~~D~e~Ft~aV~eY 118 (146)
..|.-++...|=+|.+++|.+.|-+-..+|
T Consensus 8 ~~~~~~L~~~ID~ALd~~D~e~F~~Ls~eL 37 (37)
T PF08858_consen 8 EFRKEQLLELIDEALDNRDKEWFYELSEEL 37 (37)
T ss_dssp HHHHHHHHHHHHHHHHTT-HHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHcCCHHHHHHHHhhC
Confidence 357788999999999999999998866554
No 31
>PRK10803 tol-pal system protein YbgF; Provisional
Probab=59.23 E-value=35 Score=28.60 Aligned_cols=83 Identities=10% Similarity=0.102 Sum_probs=52.6
Q ss_pred HHHHHHHHHHHHHhhcccchhhchhHHhHHhHHHHHhc-chhHHHHHHhHHHhcCCCCccchHHHHHHHHHHHHhhcCHH
Q psy16704 31 IVYSLLFYSTGKAATENSLMKYNSKEYFFKAGLCHLCI-DLLNCQQALSRYIDLSPAFQDTREYKFLLKLIESLEEEDSD 109 (146)
Q Consensus 31 ~~A~eiyE~VA~~sl~n~LlKysaKeyffkA~LC~L~~-D~v~a~~ale~Y~~~DPsF~~SRE~klL~~LieAve~~D~e 109 (146)
.+|++.|+++.+..=+++... +-.+.-|-+++.. |..+|...++++.+.+|.-....+..+-...+. .+.||.+
T Consensus 160 ~~Ai~af~~fl~~yP~s~~a~----~A~y~LG~~y~~~g~~~~A~~~f~~vv~~yP~s~~~~dAl~klg~~~-~~~g~~~ 234 (263)
T PRK10803 160 DDAIVAFQNFVKKYPDSTYQP----NANYWLGQLNYNKGKKDDAAYYFASVVKNYPKSPKAADAMFKVGVIM-QDKGDTA 234 (263)
T ss_pred HHHHHHHHHHHHHCcCCcchH----HHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCCcchhHHHHHHHHHH-HHcCCHH
Confidence 588888888888887775322 1224556677777 888888888888888887665666544333322 2455544
Q ss_pred H----HHHHHHhh
Q psy16704 110 A----FSETVKEF 118 (146)
Q Consensus 110 ~----Ft~aV~eY 118 (146)
+ |...+.+|
T Consensus 235 ~A~~~~~~vi~~y 247 (263)
T PRK10803 235 KAKAVYQQVIKKY 247 (263)
T ss_pred HHHHHHHHHHHHC
Confidence 3 44444444
No 32
>KOG0547|consensus
Probab=59.06 E-value=30 Score=33.01 Aligned_cols=81 Identities=22% Similarity=0.388 Sum_probs=57.0
Q ss_pred hcccchhhchhHHhHHhHHHHHhcchhHHHHHHhHHHhcCCCCccc---hH---------HHHHHHHHHHHh--hcC---
Q psy16704 45 TENSLMKYNSKEYFFKAGLCHLCIDLLNCQQALSRYIDLSPAFQDT---RE---------YKFLLKLIESLE--EED--- 107 (146)
Q Consensus 45 l~n~LlKysaKeyffkA~LC~L~~D~v~a~~ale~Y~~~DPsF~~S---RE---------~klL~~LieAve--~~D--- 107 (146)
++.+| +|-|.-+.+++.---||.|.++++.-+++-..+||.|.+- |- -+..++.-+|.+ -+|
T Consensus 318 ~d~~l-e~~A~al~~~gtF~fL~g~~~~a~~d~~~~I~l~~~~~~lyI~~a~~y~d~~~~~~~~~~F~~A~~ldp~n~dv 396 (606)
T KOG0547|consen 318 IDAEL-EYMAEALLLRGTFHFLKGDSLGAQEDFDAAIKLDPAFNSLYIKRAAAYADENQSEKMWKDFNKAEDLDPENPDV 396 (606)
T ss_pred cchhH-HHHHHHHHHhhhhhhhcCCchhhhhhHHHHHhcCcccchHHHHHHHHHhhhhccHHHHHHHHHHHhcCCCCCch
Confidence 34454 6778777777766666779999999999999999999871 10 122333333332 222
Q ss_pred ----------HHHHHHHHHhhhccCCchH
Q psy16704 108 ----------SDAFSETVKEFDSISRLDQ 126 (146)
Q Consensus 108 ----------~e~Ft~aV~eYD~isrLD~ 126 (146)
.+.|.+++.+||+-.+||+
T Consensus 397 YyHRgQm~flL~q~e~A~aDF~Kai~L~p 425 (606)
T KOG0547|consen 397 YYHRGQMRFLLQQYEEAIADFQKAISLDP 425 (606)
T ss_pred hHhHHHHHHHHHHHHHHHHHHHHHhhcCh
Confidence 4678899999999888887
No 33
>PF14938 SNAP: Soluble NSF attachment protein, SNAP; PDB: 1QQE_A 2IFU_A.
Probab=56.26 E-value=1.1e+02 Score=25.07 Aligned_cols=90 Identities=12% Similarity=0.081 Sum_probs=64.7
Q ss_pred HHHHHHHHHHHHHhhcccchhhchhHHhHHhHHHHHhc-chhHHHHHHhHHHhcCCCCc----cchHHHHHHHHHHHHhh
Q psy16704 31 IVYSLLFYSTGKAATENSLMKYNSKEYFFKAGLCHLCI-DLLNCQQALSRYIDLSPAFQ----DTREYKFLLKLIESLEE 105 (146)
Q Consensus 31 ~~A~eiyE~VA~~sl~n~LlKysaKeyffkA~LC~L~~-D~v~a~~ale~Y~~~DPsF~----~SRE~klL~~LieAve~ 105 (146)
..|++.|++.+.-.-.++ -..++.+.+.+++-++.-. +...|-..+++-....-.=. +.+++ ++..++=.+-.
T Consensus 132 e~Ai~~Y~~A~~~y~~e~-~~~~a~~~~~~~A~l~~~l~~y~~A~~~~e~~~~~~l~~~l~~~~~~~~-~l~a~l~~L~~ 209 (282)
T PF14938_consen 132 EKAIEYYQKAAELYEQEG-SPHSAAECLLKAADLYARLGRYEEAIEIYEEVAKKCLENNLLKYSAKEY-FLKAILCHLAM 209 (282)
T ss_dssp HHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHTCCCHCTTGHHHHHH-HHHHHHHHHHT
T ss_pred HHHHHHHHHHHHHHHHCC-ChhhHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHhhcccccchhHHHH-HHHHHHHHHHc
Confidence 468888888888877777 7788889999999887777 88888777777655432221 33443 56777777888
Q ss_pred cCHHHHHHHHHhhhccC
Q psy16704 106 EDSDAFSETVKEFDSIS 122 (146)
Q Consensus 106 ~D~e~Ft~aV~eYD~is 122 (146)
||.-.-..++.+|.+..
T Consensus 210 ~D~v~A~~~~~~~~~~~ 226 (282)
T PF14938_consen 210 GDYVAARKALERYCSQD 226 (282)
T ss_dssp T-HHHHHHHHHHHGTTS
T ss_pred CCHHHHHHHHHHHHhhC
Confidence 99988889998888764
No 34
>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=56.24 E-value=57 Score=21.62 Aligned_cols=63 Identities=16% Similarity=0.283 Sum_probs=42.2
Q ss_pred HhHHhHHHHHhc-chhHHHHHHhHHHhcCCCCccchHHHHHHHHHHHHhhcCHHHHHHHHHhhhccCC
Q psy16704 57 YFFKAGLCHLCI-DLLNCQQALSRYIDLSPAFQDTREYKFLLKLIESLEEEDSDAFSETVKEFDSISR 123 (146)
Q Consensus 57 yffkA~LC~L~~-D~v~a~~ale~Y~~~DPsF~~SRE~klL~~LieAve~~D~e~Ft~aV~eYD~isr 123 (146)
.++..|...+.. +...|...+++..+.+|....+.+..+....+ ..+.|+ +..++.-|.++.+
T Consensus 4 ~~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~l~~~-~~~~~~---~~~A~~~~~~~~~ 67 (119)
T TIGR02795 4 AYYDAALLVLKAGDYADAIQAFQAFLKKYPKSTYAPNAHYWLGEA-YYAQGK---YADAAKAFLAVVK 67 (119)
T ss_pred HHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCccccHHHHHHHHHH-HHhhcc---HHHHHHHHHHHHH
Confidence 457778888888 99999999999999999776556665554433 344444 4445555554443
No 35
>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional
Probab=55.36 E-value=31 Score=29.07 Aligned_cols=44 Identities=16% Similarity=0.132 Sum_probs=33.9
Q ss_pred HHHHhHHHhcCCCCc--cchHHHHHHHHHHHHhhcCHHHHHHHHHh
Q psy16704 74 QQALSRYIDLSPAFQ--DTREYKFLLKLIESLEEEDSDAFSETVKE 117 (146)
Q Consensus 74 ~~ale~Y~~~DPsF~--~SRE~klL~~LieAve~~D~e~Ft~aV~e 117 (146)
++|..+-.+..|.|. ..++.+++...++|+++||.+...+-+.+
T Consensus 156 ~RAr~~Lr~~~~~~~~~~~~~~~~~~~f~~a~~~gd~~~l~~ll~~ 201 (290)
T PRK09635 156 HRARRKINESRIAASVEPAQHRVVTRAFIEACSNGDLDTLLEVLDP 201 (290)
T ss_pred HHHHHHHHhhCCCCCCChHHHHHHHHHHHHHHHhCCHHHHHHHhhh
Confidence 355556666677764 34567899999999999999999888755
No 36
>PF06304 DUF1048: Protein of unknown function (DUF1048); InterPro: IPR008316 There are currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.; PDB: 2O3L_B 2HH6_A 2O4T_A.
Probab=55.25 E-value=34 Score=25.46 Aligned_cols=68 Identities=19% Similarity=0.262 Sum_probs=47.3
Q ss_pred chhHHHHHHhHHHhcCCCCccchHHHHHHHHHHHHhhc-------------CHHHHHHHHHhhhccCCchHHHHHHHHHH
Q psy16704 69 DLLNCQQALSRYIDLSPAFQDTREYKFLLKLIESLEEE-------------DSDAFSETVKEFDSISRLDQWYTTMLLKI 135 (146)
Q Consensus 69 D~v~a~~ale~Y~~~DPsF~~SRE~klL~~LieAve~~-------------D~e~Ft~aV~eYD~isrLD~WKT~mLLkI 135 (146)
|.-.|=.++++|.-....+.++-=-..|.+|++-+|++ |+.+|.+.+..=-+-.-.|+|+.++=..|
T Consensus 23 dY~~ay~~i~~Yl~~~~~~~g~~~~~il~dildlfEe~aadG~~V~eviGeD~~~Fcdeli~~~~~~~~dk~r~~Ln~~i 102 (103)
T PF06304_consen 23 DYRIAYKAIQKYLWYFGPTDGRDMMEILSDILDLFEEAAADGKSVREVIGEDVAAFCDELIKNYKTKWRDKWREKLNDAI 102 (103)
T ss_dssp HHHHHHHHHHHHHHHHTBSSHHHHHHHHHHHHHHHHHHHHTT--HHHHH-S-HHHHHHHHHCCSCC-HHHHHHHHHHHHC
T ss_pred HHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHHHHHHHHcCCChhHhhCCCHHHHHHHHHHhcchhhHHHHHHHHHhhc
Confidence 77888888999987655555443447889998877764 89999988764333226789998876555
Q ss_pred H
Q psy16704 136 K 136 (146)
Q Consensus 136 K 136 (146)
|
T Consensus 103 ~ 103 (103)
T PF06304_consen 103 K 103 (103)
T ss_dssp -
T ss_pred C
Confidence 4
No 37
>PLN03088 SGT1, suppressor of G2 allele of SKP1; Provisional
Probab=54.09 E-value=1.2e+02 Score=26.23 Aligned_cols=93 Identities=10% Similarity=0.145 Sum_probs=55.0
Q ss_pred HHHHHHHHHHHHHhhcccchhhchhHHhHHhHHHHHhc-chhHHHHHHhHHHhcCCCCccchHHHHHHHHHHHHhhcCHH
Q psy16704 31 IVYSLLFYSTGKAATENSLMKYNSKEYFFKAGLCHLCI-DLLNCQQALSRYIDLSPAFQDTREYKFLLKLIESLEEEDSD 109 (146)
Q Consensus 31 ~~A~eiyE~VA~~sl~n~LlKysaKeyffkA~LC~L~~-D~v~a~~ale~Y~~~DPsF~~SRE~klL~~LieAve~~D~e 109 (146)
..|++.|++..+..=++. ++++.-+.|++-. +...|...+++=.+++|.... ..+..+.+- .. ..
T Consensus 19 ~~Ai~~~~~Al~~~P~~~-------~a~~~~a~~~~~~g~~~eAl~~~~~Al~l~P~~~~---a~~~lg~~~-~~---lg 84 (356)
T PLN03088 19 ALAVDLYTQAIDLDPNNA-------ELYADRAQANIKLGNFTEAVADANKAIELDPSLAK---AYLRKGTAC-MK---LE 84 (356)
T ss_pred HHHHHHHHHHHHhCCCCH-------HHHHHHHHHHHHcCCHHHHHHHHHHHHHhCcCCHH---HHHHHHHHH-HH---hC
Confidence 367788887776544432 4556666677766 888888888888888887543 333322221 12 23
Q ss_pred HHHHHHHhhhccC-------CchHHHHHHHHHHHh
Q psy16704 110 AFSETVKEFDSIS-------RLDQWYTTMLLKIKR 137 (146)
Q Consensus 110 ~Ft~aV~eYD~is-------rLD~WKT~mLLkIKk 137 (146)
.|.+|+..|++.- .+..|....-.++++
T Consensus 85 ~~~eA~~~~~~al~l~P~~~~~~~~l~~~~~kl~~ 119 (356)
T PLN03088 85 EYQTAKAALEKGASLAPGDSRFTKLIKECDEKIAE 119 (356)
T ss_pred CHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHh
Confidence 4445555554443 344566666666654
No 38
>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=48.54 E-value=64 Score=20.01 Aligned_cols=48 Identities=17% Similarity=0.269 Sum_probs=36.4
Q ss_pred HHHHHHHHHHHHHhhcccchhhchhHHhHHhHHHHHhc--chhHHHHHHhHHHhcCC
Q psy16704 31 IVYSLLFYSTGKAATENSLMKYNSKEYFFKAGLCHLCI--DLLNCQQALSRYIDLSP 85 (146)
Q Consensus 31 ~~A~eiyE~VA~~sl~n~LlKysaKeyffkA~LC~L~~--D~v~a~~ale~Y~~~DP 85 (146)
..|++.|++..+..=+++ +.++.=|+|+.-. +...|...+++..++||
T Consensus 20 ~~A~~~~~~ai~~~p~~~-------~~~~~~g~~~~~~~~~~~~A~~~~~~al~l~P 69 (69)
T PF13414_consen 20 EEAIEYFEKAIELDPNNA-------EAYYNLGLAYMKLGKDYEEAIEDFEKALKLDP 69 (69)
T ss_dssp HHHHHHHHHHHHHSTTHH-------HHHHHHHHHHHHTTTHHHHHHHHHHHHHHHST
T ss_pred HHHHHHHHHHHHcCCCCH-------HHHHHHHHHHHHhCccHHHHHHHHHHHHHcCc
Confidence 478888888887643332 3666677777775 58999999999999998
No 39
>PF03608 EII-GUT: PTS system enzyme II sorbitol-specific factor; InterPro: IPR004699 Bacterial PTS transporters transport and concomitantly phosphorylate their sugar substrates, and typically consist of multiple subunits or protein domains.The Man family is unique in several respects among PTS permease families. It is the only PTS family in which members possess a IID protein. It is the only PTS family in which the IIB constituent is phosphorylated on a histidyl rather than a cysteyl residue. Its permease members exhibit broad specificity for a range of sugars, rather than being specific for just one or a few sugars. The Gut family consists only of glucitol-specific transporters, but these occur both in Gram-negative and Gram-positive bacteria. Escherichia coli consists of IIA protein, a IIC protein and a IIBC protein. This family is specific for the IIC component.; GO: 0009401 phosphoenolpyruvate-dependent sugar phosphotransferase system, 0016021 integral to membrane
Probab=47.87 E-value=44 Score=27.25 Aligned_cols=29 Identities=7% Similarity=0.148 Sum_probs=24.1
Q ss_pred HHHHHHHHHHHHHHHhhcccchhhchhHH
Q psy16704 29 FRIVYSLLFYSTGKAATENSLMKYNSKEY 57 (146)
Q Consensus 29 ~~~~A~eiyE~VA~~sl~n~LlKysaKey 57 (146)
.+..--|..|++|+.|-.|+++||.+=-+
T Consensus 42 i~liGeeRv~k~a~~~~kn~i~RY~vLP~ 70 (168)
T PF03608_consen 42 IKLIGEERVEKFAQKCAKNPITRYTVLPV 70 (168)
T ss_pred HHHHhHHHHHHHHHHHcCCchHHHHHHHH
Confidence 45567789999999999999999986543
No 40
>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=47.79 E-value=56 Score=19.06 Aligned_cols=28 Identities=18% Similarity=0.460 Sum_probs=11.4
Q ss_pred hHHhHHHHHhc-chhHHHHHHhHHHhcCC
Q psy16704 58 FFKAGLCHLCI-DLLNCQQALSRYIDLSP 85 (146)
Q Consensus 58 ffkA~LC~L~~-D~v~a~~ale~Y~~~DP 85 (146)
++..+.|++.. |...|...+++-.+.+|
T Consensus 71 ~~~~~~~~~~~~~~~~a~~~~~~~~~~~~ 99 (100)
T cd00189 71 YYNLGLAYYKLGKYEEALEAYEKALELDP 99 (100)
T ss_pred HHHHHHHHHHHHhHHHHHHHHHHHHccCC
Confidence 33333444433 44444444444433333
No 41
>PF03399 SAC3_GANP: SAC3/GANP/Nin1/mts3/eIF-3 p25 family; InterPro: IPR005062 This large family includes diverse proteins involved in large complexes [, , ]. The alignment contains one highly conserved negatively charged residue and one highly conserved positively charged residue that are probably important for the function of these proteins. The family includes the yeast nuclear export factor Sac3 [], and mammalian GANP/MCM3-associated proteins, which facilitate the nuclear localisation of MCM3, a protein that associates with chromatin in the G1 phase of the cell-cycle. The 26S protease (or 26S proteasome) is responsible for degrading ubiquitin conjugates. It consists of 19S regulatory complexes associated with the ends of 20S proteasomes. The 19S regulatory complex is composed of about 20 different polypeptides and confers ATP-dependence and substrate specificity to the 26S enzyme. The conserved region occurs at the C-terminal of the Nin1-like regulatory subunit [, , ]. This family includes several eukaryotic translation initiation factor 3 subunit 11 (eIF-3 p25) proteins. Eukaryotic initiation factor 3 (eIF3) is a multisubunit complex that is required for binding of mRNA to 40 S ribosomal subunits, stabilisation of ternary complex binding to 40 S subunits, and dissociation of 40 and 60 S subunits [].; PDB: 3T5V_D.
Probab=46.62 E-value=66 Score=24.68 Aligned_cols=80 Identities=19% Similarity=0.235 Sum_probs=47.7
Q ss_pred HHHHHHHHHHHhhcc-cchhhc---------------------hhHHhHHhHHHHHhc-chhHHHHHHhHHHhcCCCCcc
Q psy16704 33 YSLLFYSTGKAATEN-SLMKYN---------------------SKEYFFKAGLCHLCI-DLLNCQQALSRYIDLSPAFQD 89 (146)
Q Consensus 33 A~eiyE~VA~~sl~n-~LlKys---------------------aKeyffkA~LC~L~~-D~v~a~~ale~Y~~~DPsF~~ 89 (146)
+.++||..|+-++.+ ++-+++ -.|+.---.|.+++. ...+....++.. .+...+
T Consensus 55 ~i~v~E~~ar~~i~~~d~~qf~~c~~~L~~lY~~~~~~~~~~~~~ef~~y~lL~~l~~~~~~~~~~~l~~l---~~~~~~ 131 (204)
T PF03399_consen 55 AIKVYERIARFAIESGDLEQFNQCLSQLKELYDDLRDLPPSPNEAEFIAYYLLYLLCQNNIPDFHMELELL---PSEILS 131 (204)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT---TTHHHHHHHHHHHTT-T---THHHHHHTTS----HHHHT
T ss_pred HHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHhhccCCCCCCHHHHHHHHHHHHHHcccchHHHHHHHHC---chhhhc
Confidence 788889888888755 222222 122222233444444 344444444433 334678
Q ss_pred chHHHHHHHHHHHHhhcCHHHHHHHH
Q psy16704 90 TREYKFLLKLIESLEEEDSDAFSETV 115 (146)
Q Consensus 90 SRE~klL~~LieAve~~D~e~Ft~aV 115 (146)
+...++.-++..|+.+||.-.|-..+
T Consensus 132 ~~~i~~al~l~~a~~~gny~~ff~l~ 157 (204)
T PF03399_consen 132 SPYIQFALELCRALMEGNYVRFFRLY 157 (204)
T ss_dssp SHHHHHHHHHHHHH--TTHHHHHHHH
T ss_pred CHHHHHHHHHHHHHHcCCHHHHHHHH
Confidence 88899999999999999999888877
No 42
>PF01817 CM_2: Chorismate mutase type II; InterPro: IPR020822 Chorismate mutase, 5.4.99.5 from EC, catalyses the conversion of chorismate to prephenate in the pathway of tyrosine and phenylalanine biosynthesis. This enzyme is negatively regulated by tyrosine, tryptophan and phenylalanine [, ]. Prephenate dehydratase (IPR001086 from INTERPRO, 4.2.1.51 from EC, PDT) catalyses the decarboxylation of prephenate into phenylpyruvate. In microorganisms PDT is involved in the terminal pathway of the biosynthesis of phenylalanine. In some bacteria, such as Escherichia coli, PDT is part of a bifunctional enzyme (P-protein) that also catalyzes the transformation of chorismate into prephenate (chorismate mutase) while in other bacteria it is a monofunctional enzyme. The sequence of monofunctional chorismate mutase aligns well with the N-terminal part of P-proteins [].; GO: 0046417 chorismate metabolic process; PDB: 1YBZ_A 2GTV_X 2FP1_B 2F6L_B 2FP2_B 2AO2_A 3HGW_C 3HGX_B 2H9C_A 3RET_B ....
Probab=45.80 E-value=60 Score=21.80 Aligned_cols=41 Identities=32% Similarity=0.403 Sum_probs=31.0
Q ss_pred HHhHHHhc--CCCCccchHHHHHHHHHHHHhhcCHH-HHHHHHH
Q psy16704 76 ALSRYIDL--SPAFQDTREYKFLLKLIESLEEEDSD-AFSETVK 116 (146)
Q Consensus 76 ale~Y~~~--DPsF~~SRE~klL~~LieAve~~D~e-~Ft~aV~ 116 (146)
.+.+|+.. -|-+...||.+.++.+.+..++++.+ .+...++
T Consensus 24 ~i~~~K~~~~~~i~d~~RE~~v~~~~~~~~~~~~l~~~~i~~if 67 (81)
T PF01817_consen 24 KIAEYKKENGLPIFDPDREEEVLERLRELAEEGGLDPEFIERIF 67 (81)
T ss_dssp HHHHHHHHTTCCSSTHHHHHHHHHHHHHHHHHTTSEHHHHHHHH
T ss_pred HHHHHHHhCCCCCCCcHHHHHHHHHHHHHhHhCCCCHHHHHHHH
Confidence 34445444 48999999999999999999977765 6666554
No 43
>KOG4703|consensus
Probab=45.65 E-value=9.8 Score=34.15 Aligned_cols=18 Identities=44% Similarity=0.484 Sum_probs=15.8
Q ss_pred CCchHHHHHHHHHHHhhc
Q psy16704 122 SRLDQWYTTMLLKIKRQI 139 (146)
Q Consensus 122 srLD~WKT~mLLkIKk~I 139 (146)
.+=|+|+|++|+||.++|
T Consensus 392 g~kd~~cTTkllkiqqnI 409 (431)
T KOG4703|consen 392 GPKDPICTTKLLKIQQNI 409 (431)
T ss_pred CCCCchhhhhHHhhhhhh
Confidence 455899999999999987
No 44
>cd00619 Terminator_NusB Transcription termination factor NusB (N protein-Utilization Substance B). NusB plays a key role in the regulation of ribosomal RNA biosynthesis in eubacteria by modulating the efficiency of transcriptional antitermination. NusB along with other Nus factors (NusA, NusE/S10 and NusG) forms the core complex with the boxA element of the nut site of the rRNA operons. These interactions help RNA polymerase to counteract polarity during transcription of rRNA operons and allow stable antitermination. The transcription antitermination system can be appropriated by some bacteriophages such as lambda, which use the system to switch between the lysogenic and lytic modes of phage propagation.
Probab=45.37 E-value=40 Score=24.49 Aligned_cols=69 Identities=13% Similarity=0.159 Sum_probs=49.1
Q ss_pred HHHHHHHhhccc-chhhchhH-HhHHhHHHHHhc-chhHHHHHHhHHHhcCCCCccchHHHHHHHHHHHHhh
Q psy16704 37 FYSTGKAATENS-LMKYNSKE-YFFKAGLCHLCI-DLLNCQQALSRYIDLSPAFQDTREYKFLLKLIESLEE 105 (146)
Q Consensus 37 yE~VA~~sl~n~-LlKysaKe-yffkA~LC~L~~-D~v~a~~ale~Y~~~DPsF~~SRE~klL~~LieAve~ 105 (146)
.+.+..+.++++ +-+-+..+ ..|+.|++++.. |.+...-+++++.++-..|.+.+..+|+.+++..+..
T Consensus 57 ld~ii~~~l~~~~~~~l~~~~~~iLria~~el~~~~~~p~~~vinEaV~lak~~~~~~~~~fVNaVLr~i~r 128 (130)
T cd00619 57 IDELIEKHLRNWSLDRLAIVERAILRLAVYELLFLPDVPHPVVINEAIELAKRFGGDDSHKFVNGVLDKIAK 128 (130)
T ss_pred HHHHHHHHccCCCHHHhhHHHHHHHHHHHHHHHhCCCCCCcchHHHHHHHHHHHCCCcchhHHHHHHHHHhh
Confidence 455555555544 33333332 468888888886 6567778888888888888888999999999887653
No 45
>PRK03636 hypothetical protein; Provisional
Probab=44.78 E-value=31 Score=28.02 Aligned_cols=35 Identities=26% Similarity=0.422 Sum_probs=30.6
Q ss_pred ccchHHHHHHHHHHHHhhcCHHHHHHHHHhhhccC
Q psy16704 88 QDTREYKFLLKLIESLEEEDSDAFSETVKEFDSIS 122 (146)
Q Consensus 88 ~~SRE~klL~~LieAve~~D~e~Ft~aV~eYD~is 122 (146)
...|.-+|+..|=+|.++||.|.|..-..+|.++.
T Consensus 143 ~~~r~~~L~~~ID~ALd~~D~e~F~~Ls~~l~~L~ 177 (179)
T PRK03636 143 FQFRREKLLKQIDEALDRRDKEAFHRLSDELNQLR 177 (179)
T ss_pred HHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHh
Confidence 34677899999999999999999999999888764
No 46
>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=44.13 E-value=94 Score=28.27 Aligned_cols=83 Identities=11% Similarity=0.269 Sum_probs=57.2
Q ss_pred HHHHHHHHHHHHHhhcccchhhchhHHhHHhHHHHHhc-chhHHHHHHhHHHhcCCCCccchHHHHHHHHHHHHhhcCHH
Q psy16704 31 IVYSLLFYSTGKAATENSLMKYNSKEYFFKAGLCHLCI-DLLNCQQALSRYIDLSPAFQDTREYKFLLKLIESLEEEDSD 109 (146)
Q Consensus 31 ~~A~eiyE~VA~~sl~n~LlKysaKeyffkA~LC~L~~-D~v~a~~ale~Y~~~DPsF~~SRE~klL~~LieAve~~D~e 109 (146)
..|++.|++..+..= + -.++.+-+.|++.. +...|-..+++-.++||.+... +..+-.+.. ...
T Consensus 144 ~~Ai~~y~~al~~~p-~-------~~~~~n~a~~~~~l~~~~~Ai~~~~~al~l~p~~~~a-----~~~~a~a~~--~lg 208 (615)
T TIGR00990 144 NKAIKLYSKAIECKP-D-------PVYYSNRAACHNALGDWEKVVEDTTAALELDPDYSKA-----LNRRANAYD--GLG 208 (615)
T ss_pred HHHHHHHHHHHhcCC-c-------hHHHHHHHHHHHHhCCHHHHHHHHHHHHHcCCCCHHH-----HHHHHHHHH--HcC
Confidence 579999988654321 1 24788889999998 9999999999999999988522 222223322 234
Q ss_pred HHHHHHHhhhccCCchHHH
Q psy16704 110 AFSETVKEFDSISRLDQWY 128 (146)
Q Consensus 110 ~Ft~aV~eYD~isrLD~WK 128 (146)
.|.+++.+|.+.+.+|++.
T Consensus 209 ~~~eA~~~~~~~~~~~~~~ 227 (615)
T TIGR00990 209 KYADALLDLTASCIIDGFR 227 (615)
T ss_pred CHHHHHHHHHHHHHhCCCc
Confidence 5667777777776666543
No 47
>PF14287 DUF4368: Domain of unknown function (DUF4368)
Probab=43.86 E-value=15 Score=25.35 Aligned_cols=33 Identities=27% Similarity=0.539 Sum_probs=26.1
Q ss_pred hhcCHHHHHHHHHhhhccCCchHHHHHHHHHHHhhc
Q psy16704 104 EEEDSDAFSETVKEFDSISRLDQWYTTMLLKIKRQI 139 (146)
Q Consensus 104 e~~D~e~Ft~aV~eYD~isrLD~WKT~mLLkIKk~I 139 (146)
...|++.|.+.+..|-.+..|++ .||...=+.|
T Consensus 9 ~~~d~~~Fi~~i~kYt~i~ELt~---~il~elIdkI 41 (71)
T PF14287_consen 9 KSEDVDKFIELIRKYTDITELTP---EILNELIDKI 41 (71)
T ss_pred HHhhHHHHHHHHHHhCChhhCCH---HHHHHHHHeE
Confidence 45789999999999999999996 5555554444
No 48
>PF14261 DUF4351: Domain of unknown function (DUF4351)
Probab=43.59 E-value=9.9 Score=25.39 Aligned_cols=30 Identities=30% Similarity=0.673 Sum_probs=26.0
Q ss_pred HHHHHHhhcCHHHHHHHHHhhhccCCchHH
Q psy16704 98 KLIESLEEEDSDAFSETVKEFDSISRLDQW 127 (146)
Q Consensus 98 ~LieAve~~D~e~Ft~aV~eYD~isrLD~W 127 (146)
.-|++......|..++++.+|+++.-|.+|
T Consensus 29 ~~I~~l~~eqLE~l~e~ildf~~l~dL~~w 58 (59)
T PF14261_consen 29 ERIQQLSLEQLEALAEAILDFNSLEDLENW 58 (59)
T ss_pred HHHHcCCHHHHHHHHHHHhCCCCHHHHHhh
Confidence 456667777889999999999999999999
No 49
>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=42.43 E-value=46 Score=18.00 Aligned_cols=29 Identities=14% Similarity=0.348 Sum_probs=21.5
Q ss_pred hHHhHHHHHhc-chhHHHHHHhHHHhcCCC
Q psy16704 58 FFKAGLCHLCI-DLLNCQQALSRYIDLSPA 86 (146)
Q Consensus 58 ffkA~LC~L~~-D~v~a~~ale~Y~~~DPs 86 (146)
++.-|.|+.-. |...|...+++-.+++|.
T Consensus 4 ~~~lg~~y~~~~~~~~A~~~~~~a~~~~~~ 33 (34)
T PF13181_consen 4 YYNLGKIYEQLGDYEEALEYFEKALELNPD 33 (34)
T ss_dssp HHHHHHHHHHTTSHHHHHHHHHHHHHHHTT
T ss_pred HHHHHHHHHHcCCHHHHHHHHHHHHhhCCC
Confidence 33445555555 999999999999988884
No 50
>PF15575 Imm29: Immunity protein 29
Probab=41.98 E-value=1.6e+02 Score=22.84 Aligned_cols=92 Identities=13% Similarity=0.061 Sum_probs=53.4
Q ss_pred HHHHHHHHHHHHHHHHHHhhcccchhhchhHHhHHhHHHH-HhcchhHHHHHHhHHHhcCCCCc-----cchHHH-HHHH
Q psy16704 26 MMTFRIVYSLLFYSTGKAATENSLMKYNSKEYFFKAGLCH-LCIDLLNCQQALSRYIDLSPAFQ-----DTREYK-FLLK 98 (146)
Q Consensus 26 ~~~~~~~A~eiyE~VA~~sl~n~LlKysaKeyffkA~LC~-L~~D~v~a~~ale~Y~~~DPsF~-----~SRE~k-lL~~ 98 (146)
+++=....++.+-++....+.+.-..+.--+|.+-..|+. +..+....++..+++...+|.-. ..+.-. -.-+
T Consensus 64 li~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~p~~~ 143 (215)
T PF15575_consen 64 LISRDPELIDRLCRLPDSILRESGEYPDEYDYAWVDALQAFLLGDDGDPEALIEAMELADPDAEPAPPEYLQKLYYPPFD 143 (215)
T ss_pred HHcCCHHHHHHHHhCChHhhhccccccchhHHHHHHHHHHHHcCCcchHHHHHHHHHHhcccccccchHhhhhhcccHHH
Confidence 3333444555555555555555544444334554445544 44466677777888887777211 111111 2456
Q ss_pred HHHHHhhcCHHHHHHHHHh
Q psy16704 99 LIESLEEEDSDAFSETVKE 117 (146)
Q Consensus 99 LieAve~~D~e~Ft~aV~e 117 (146)
++.|+-++|.++|.+++.+
T Consensus 144 ~~~al~~~D~~~f~~aL~~ 162 (215)
T PF15575_consen 144 FFRALARGDEEAFEEALEE 162 (215)
T ss_pred HHHHHHhCCHHHHHHHHHH
Confidence 7778888999999999875
No 51
>PF13525 YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M_A 2YHC_A.
Probab=41.83 E-value=90 Score=24.42 Aligned_cols=66 Identities=11% Similarity=0.027 Sum_probs=41.4
Q ss_pred HHHHHHHHHHHHHhhcccchhhchhHHhHHhHHHHHh--------c-chhHHHHHHhHHHhcCCCCccchHHHHHHHHH
Q psy16704 31 IVYSLLFYSTGKAATENSLMKYNSKEYFFKAGLCHLC--------I-DLLNCQQALSRYIDLSPAFQDTREYKFLLKLI 100 (146)
Q Consensus 31 ~~A~eiyE~VA~~sl~n~LlKysaKeyffkA~LC~L~--------~-D~v~a~~ale~Y~~~DPsF~~SRE~klL~~Li 100 (146)
..|+..|++..+..=+++.. .+=++.-|+|+.- . |...+++|++.+++.=-.|++|+-..-.+.-+
T Consensus 59 ~~A~~~~~~fi~~yP~~~~~----~~A~Y~~g~~~~~~~~~~~~~~~D~~~~~~A~~~~~~li~~yP~S~y~~~A~~~l 133 (203)
T PF13525_consen 59 EEAIAAYERFIKLYPNSPKA----DYALYMLGLSYYKQIPGILRSDRDQTSTRKAIEEFEELIKRYPNSEYAEEAKKRL 133 (203)
T ss_dssp HHHHHHHHHHHHH-TT-TTH----HHHHHHHHHHHHHHHHHHH-TT---HHHHHHHHHHHHHHHH-TTSTTHHHHHHHH
T ss_pred HHHHHHHHHHHHHCCCCcch----hhHHHHHHHHHHHhCccchhcccChHHHHHHHHHHHHHHHHCcCchHHHHHHHHH
Confidence 68999999999988888854 4446777788764 3 66677777776666666666665554443333
No 52
>PF14561 TPR_20: Tetratricopeptide repeat; PDB: 3QOU_A 2R5S_A 3QDN_B.
Probab=40.69 E-value=1.3e+02 Score=21.21 Aligned_cols=50 Identities=20% Similarity=0.247 Sum_probs=38.9
Q ss_pred HHhHHHHHhc-chhHHHHHHhHHHhcCCCCccchHHHHHHHHHHHHhhcCH
Q psy16704 59 FKAGLCHLCI-DLLNCQQALSRYIDLSPAFQDTREYKFLLKLIESLEEEDS 108 (146)
Q Consensus 59 fkA~LC~L~~-D~v~a~~ale~Y~~~DPsF~~SRE~klL~~LieAve~~D~ 108 (146)
+.-+.++++. |..+|-..+-+-...||.|.+..=.+.+-++++.+..+|+
T Consensus 26 ~~lA~~~~~~g~~e~Al~~Ll~~v~~dr~~~~~~ar~~ll~~f~~lg~~~p 76 (90)
T PF14561_consen 26 YALADALLAAGDYEEALDQLLELVRRDRDYEDDAARKRLLDIFELLGPGDP 76 (90)
T ss_dssp HHHHHHHHHTT-HHHHHHHHHHHHCC-TTCCCCHHHHHHHHHHHHH-TT-H
T ss_pred HHHHHHHHHCCCHHHHHHHHHHHHHhCccccccHHHHHHHHHHHHcCCCCh
Confidence 4445555555 9999999999999999999999999999999999999875
No 53
>PF01399 PCI: PCI domain; InterPro: IPR000717 A homology domain of unclear function, occurs in the C-terminal region of several regulatory components of the 26S proteasome as well as in other proteins. This domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15) []. Apparently, all of the characterised proteins containing PCI domains are parts of larger multi-protein complexes. Proteins with PCI domains include budding yeast proteasome regulatory components Rpn3(Sun2), Rpn5, Rpn6, Rpn7and Rpn9 []; mammalian proteasome regulatory components p55, p58 and p44.5, and translation initiation factor 3 complex subunits p110 and INT6 [, ]; Arabidopsis COP9 and FUS6/COP11 []; mammalian G-protein pathway suppressor GPS1, and several uncharacterised ORFs from plant, nematodes and mammals. The complete homology domain comprises approx. 200 residues, the highest conservation is found in the C-terminal half. Several of the proteins mentioned above have no detectable homology to the N-terminal half of the domain.; GO: 0005515 protein binding; PDB: 3TXM_A 3TXN_A 1UFM_A 3CHM_A 3T5X_A 3T5V_B.
Probab=40.57 E-value=32 Score=23.13 Aligned_cols=23 Identities=17% Similarity=0.369 Sum_probs=20.2
Q ss_pred HHHHHHHHhhcCHHHHHHHHHhh
Q psy16704 96 LLKLIESLEEEDSDAFSETVKEF 118 (146)
Q Consensus 96 L~~LieAve~~D~e~Ft~aV~eY 118 (146)
..++++|+..||...|.+.+.++
T Consensus 3 ~~~l~~~~~~~~~~~~~~~l~~~ 25 (105)
T PF01399_consen 3 YSELLRAFRSGDLQEFEEFLEKH 25 (105)
T ss_dssp HHHHHHHHHCT-HHHHHHHHHHT
T ss_pred HHHHHHHHHhCCHHHHHHHHHHH
Confidence 46899999999999999999999
No 54
>TIGR02957 SigX4 RNA polymerase sigma-70 factor, TIGR02957 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building and bidirectional best hits, to represent a conserved family. This family is found in a limited number of bacterial lineages. This family includes apparent paralogous expansion in Streptomyces coelicolor A3(2), and multiple copies in Mycobacterium smegmatis MC2, Streptomyces avermitilis MA-4680 and Nocardia farcinica IFM10152.
Probab=40.41 E-value=83 Score=26.03 Aligned_cols=45 Identities=20% Similarity=0.266 Sum_probs=33.3
Q ss_pred HHHHhHHHhcCCCC--ccchHHHHHHHHHHHHhhcCHHHHHHHHHhh
Q psy16704 74 QQALSRYIDLSPAF--QDTREYKFLLKLIESLEEEDSDAFSETVKEF 118 (146)
Q Consensus 74 ~~ale~Y~~~DPsF--~~SRE~klL~~LieAve~~D~e~Ft~aV~eY 118 (146)
.+|..+-.+.-|.+ ....+.+++...++|++.||.++...-+.+=
T Consensus 146 ~RAr~~Lr~~~~~~~~~~~~~~~~~~~f~~a~~~gD~~~l~~lL~~d 192 (281)
T TIGR02957 146 SRARRHLDARRPRFEVSREESRQLLERFVEAAQTGDLDGLLELLAED 192 (281)
T ss_pred HHHHHHHHhhCCCCCCChHHHHHHHHHHHHHHHhCCHHHHHHHHhhc
Confidence 34444555555655 4456778999999999999999998877763
No 55
>TIGR00821 EII-GUT PTS system, glucitol/sorbitol-specific, IIC component. Bacterial PTS transporters transport and concomitantly phosphorylate their sugar substrates, and typically consist of multiple subunits or protein domains. The Gut family consists only of glucitol-specific transporters, but these occur both in Gram-negative and Gram-positive bacteria.E. coli consists of IIA protein, a IIC protein and a IIBC protein. This family is specific for the IIC component.
Probab=39.83 E-value=69 Score=26.42 Aligned_cols=27 Identities=7% Similarity=0.028 Sum_probs=22.6
Q ss_pred HHHHHHHHHHHHHHhhcccchhhchhH
Q psy16704 30 RIVYSLLFYSTGKAATENSLMKYNSKE 56 (146)
Q Consensus 30 ~~~A~eiyE~VA~~sl~n~LlKysaKe 56 (146)
+..--|..|++|+.|-.|++++|.+=-
T Consensus 46 ~liGeeRv~~~A~~~~~n~i~RY~vLP 72 (181)
T TIGR00821 46 AFIGQDRIERFAQFCAGNPVLRYLVLP 72 (181)
T ss_pred HHhhHHHHHHHHHHHcCCchhHHHHHH
Confidence 445678899999999999999998644
No 56
>PF11159 DUF2939: Protein of unknown function (DUF2939); InterPro: IPR021330 This bacterial family of proteins has no known function.
Probab=39.50 E-value=30 Score=24.31 Aligned_cols=42 Identities=14% Similarity=0.323 Sum_probs=32.3
Q ss_pred HHHHHHHHHhhcCHHHHHHHHHhhhccCCchHHHHHHHHHHHhhc
Q psy16704 95 FLLKLIESLEEEDSDAFSETVKEFDSISRLDQWYTTMLLKIKRQI 139 (146)
Q Consensus 95 lL~~LieAve~~D~e~Ft~aV~eYD~isrLD~WKT~mLLkIKk~I 139 (146)
-+.+|-+|++++|.++|.+.| +|+++. ++-|.++.....+.+
T Consensus 16 al~~i~~Ai~~~D~~~l~~~V-D~~avr--~slk~ql~~~~~~~~ 57 (95)
T PF11159_consen 16 ALYQIRQAIQAHDAAALARYV-DFPAVR--ASLKDQLNAELVSRI 57 (95)
T ss_pred HHHHHHHHHHHcCHHHHHHHc-CHHHHH--HHHHHHHHHHHHhhc
Confidence 478899999999999998876 566654 566677777776666
No 57
>PRK10370 formate-dependent nitrite reductase complex subunit NrfG; Provisional
Probab=38.40 E-value=2e+02 Score=22.67 Aligned_cols=18 Identities=6% Similarity=0.110 Sum_probs=11.2
Q ss_pred hHHHHHHhHHHhcCCCCc
Q psy16704 71 LNCQQALSRYIDLSPAFQ 88 (146)
Q Consensus 71 v~a~~ale~Y~~~DPsF~ 88 (146)
..|...+++....||+..
T Consensus 127 ~~A~~~l~~al~~dP~~~ 144 (198)
T PRK10370 127 PQTREMIDKALALDANEV 144 (198)
T ss_pred HHHHHHHHHHHHhCCCCh
Confidence 566666666666666654
No 58
>KOG0567|consensus
Probab=37.40 E-value=48 Score=29.15 Aligned_cols=81 Identities=19% Similarity=0.245 Sum_probs=58.2
Q ss_pred HHHHHHHHHHHHHHHhhcccchhhchhHHh--HHhHHHHHhcchhHHHHHHhH------HHhcCCCCc-cchHHHHHHHH
Q psy16704 29 FRIVYSLLFYSTGKAATENSLMKYNSKEYF--FKAGLCHLCIDLLNCQQALSR------YIDLSPAFQ-DTREYKFLLKL 99 (146)
Q Consensus 29 ~~~~A~eiyE~VA~~sl~n~LlKysaKeyf--fkA~LC~L~~D~v~a~~ale~------Y~~~DPsF~-~SRE~klL~~L 99 (146)
-|-+|++.++.++.....+-|.||+ +|-- .+-. |.+|..-+..+...++ |.+.||.=. +.|.-.=|...
T Consensus 85 vRhEAaealga~~~~~~~~~l~k~~-~dp~~~v~ET-c~lAi~rle~~~~~~~~~~~~p~~SvdPa~p~~~ssv~~lr~~ 162 (289)
T KOG0567|consen 85 VRHEAAEALGAIGDPESLEILTKYI-KDPCKEVRET-CELAIKRLEWKDIIDKIANSSPYISVDPAPPANLSSVHELRAE 162 (289)
T ss_pred HHHHHHHHHHhhcchhhHHHHHHHh-cCCccccchH-HHHHHHHHHHhhccccccccCccccCCCCCccccccHHHHHHH
Confidence 5889999999999999999999998 4332 2223 9999877777777666 999999987 66665444444
Q ss_pred HHHHhhcCHHHH
Q psy16704 100 IESLEEEDSDAF 111 (146)
Q Consensus 100 ieAve~~D~e~F 111 (146)
+--..+++.+.+
T Consensus 163 lld~t~~l~~Ry 174 (289)
T KOG0567|consen 163 LLDETKPLFERY 174 (289)
T ss_pred HHhcchhHHHHH
Confidence 444445555555
No 59
>PRK10866 outer membrane biogenesis protein BamD; Provisional
Probab=36.78 E-value=1.6e+02 Score=24.07 Aligned_cols=71 Identities=11% Similarity=0.111 Sum_probs=45.9
Q ss_pred HHHHHHHHHHHHHhhcccchhhchhHHhHHhHHHHHh---------------c-chhHHHHHHhHHHhcCCCCccchHHH
Q psy16704 31 IVYSLLFYSTGKAATENSLMKYNSKEYFFKAGLCHLC---------------I-DLLNCQQALSRYIDLSPAFQDTREYK 94 (146)
Q Consensus 31 ~~A~eiyE~VA~~sl~n~LlKysaKeyffkA~LC~L~---------------~-D~v~a~~ale~Y~~~DPsF~~SRE~k 94 (146)
..|+..||+..+..=+|+ .+..=+++-|+|+.. . |...+++|++.+++.=-.|++|.-..
T Consensus 86 ~~A~~~~e~fi~~~P~~~----~~~~a~Y~~g~~~~~~~~~~~~~~~~~~~~~rD~~~~~~A~~~~~~li~~yP~S~ya~ 161 (243)
T PRK10866 86 PLAQAAIDRFIRLNPTHP----NIDYVLYMRGLTNMALDDSALQGFFGVDRSDRDPQHARAAFRDFSKLVRGYPNSQYTT 161 (243)
T ss_pred HHHHHHHHHHHHhCcCCC----chHHHHHHHHHhhhhcchhhhhhccCCCccccCHHHHHHHHHHHHHHHHHCcCChhHH
Confidence 589999999999998888 455557777888622 2 66777766665555544454555444
Q ss_pred HHHHHHHHHhh
Q psy16704 95 FLLKLIESLEE 105 (146)
Q Consensus 95 lL~~LieAve~ 105 (146)
-.+.-+..+.+
T Consensus 162 ~A~~rl~~l~~ 172 (243)
T PRK10866 162 DATKRLVFLKD 172 (243)
T ss_pred HHHHHHHHHHH
Confidence 44444444433
No 60
>PF07729 FCD: FCD domain; InterPro: IPR011711 Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities. The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon []. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector binding or oligomerisation domain at the C terminus. The winged-helix DNA-binding domain is well conserved in structure for the whole of the GntR family (IPR000524 from INTERPRO), and is similar in structure to other transcriptional regulator families. The C-terminal effector-binding and oligomerisation domains are more variable and are consequently used to define the subfamilies. Based on the sequence and structure of the C-terminal domains, the GtnR family can be divided into four major groups, as represented by FadR (IPR008920 from INTERPRO), HutC, MocR and YtrA, as well as some minor groups such as those represented by AraR and PlmA []. This entry represents the C-terminal ligand binding domain of many members of the GntR family. This domain probably binds to a range of effector molecules that regulate the transcription of genes through the action of the N-terminal DNA-binding domain. This domain is found in P45427 from SWISSPROT and P31460 from SWISSPROT that are regulators of sugar biosynthesis operons.; PDB: 3SXK_A 3SXY_A 3SXM_B 3SXZ_A 3FMS_A 2DI3_B 2HS5_A 3IHU_B 3C7J_A.
Probab=36.65 E-value=1.3e+02 Score=19.99 Aligned_cols=83 Identities=17% Similarity=0.253 Sum_probs=50.5
Q ss_pred HHHHHHHHHhhcccchhhchhHHhHHhHHHHHhc-chh-----HHHHHHhHHHhcCCCCcc--chHHHHHHHHHHHHhhc
Q psy16704 35 LLFYSTGKAATENSLMKYNSKEYFFKAGLCHLCI-DLL-----NCQQALSRYIDLSPAFQD--TREYKFLLKLIESLEEE 106 (146)
Q Consensus 35 eiyE~VA~~sl~n~LlKysaKeyffkA~LC~L~~-D~v-----~a~~ale~Y~~~DPsF~~--SRE~klL~~LieAve~~ 106 (146)
++.++.....-+++..++..=++-|-..+...|. ... .....+..|......... .+-++.-..|++|+++|
T Consensus 31 ~~~~~~~~~~~~~d~~~~~~~~~~fh~~l~~~~~N~~l~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~h~~i~~ai~~~ 110 (125)
T PF07729_consen 31 ELLEQMEEAIEDEDIEEFIEADIEFHRALAEASGNPYLIQILERLRDRLQRFRYLSIRSKEDLERSLEEHREIIDAIRAG 110 (125)
T ss_dssp HHHHHHHHHHHCTHHHHHHHHHHHHHHHHHHTCSSHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHTT
T ss_pred HHHHHHHhhhhhhhhHHHHHHHHHHHHHHHHHcCCchHHHHHHHHHHHHHHHHHHhhhhhhhhhhhHHHHHHHHHHHHcC
Confidence 3445555555566667777777778777777774 211 223333334333333322 33345678999999999
Q ss_pred CHHHHHHHHHh
Q psy16704 107 DSDAFSETVKE 117 (146)
Q Consensus 107 D~e~Ft~aV~e 117 (146)
|.+.-..++.+
T Consensus 111 d~~~a~~~~~~ 121 (125)
T PF07729_consen 111 DPEAAREALRQ 121 (125)
T ss_dssp -HHHHHHHHHH
T ss_pred CHHHHHHHHHH
Confidence 99998887764
No 61
>TIGR00984 3a0801s03tim44 mitochondrial import inner membrane, translocase subunit. translocase (Tom) import receptor, five proteins of the Tom channel complex, five proteins of the inner membrane translocase (Tim) and three "motor" proteins. This family is specific for the Tim proteins.
Probab=35.62 E-value=79 Score=28.62 Aligned_cols=47 Identities=11% Similarity=0.267 Sum_probs=34.8
Q ss_pred hhHHHHHHhHHHhcCCCCccch---HH--HHHHHHHHHHhhcCHHHHHHHHH
Q psy16704 70 LLNCQQALSRYIDLSPAFQDTR---EY--KFLLKLIESLEEEDSDAFSETVK 116 (146)
Q Consensus 70 ~v~a~~ale~Y~~~DPsF~~SR---E~--klL~~LieAve~~D~e~Ft~aV~ 116 (146)
.-.+..++..-...||+|.-+. ++ -.+..|++|.-.||.+....-+.
T Consensus 224 ete~a~~l~eIk~~DPsFd~~~Fl~gar~aI~p~ILeAf~kGD~e~LK~~ls 275 (378)
T TIGR00984 224 ETEVSEVLTEFKKIDPTFDKEHFLRFLREYIVPEILEAYVKGDLEVLKSWCS 275 (378)
T ss_pred CCHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHhhC
Confidence 4567889999999999996443 22 23477899999999887655443
No 62
>PF08463 EcoEI_R_C: EcoEI R protein C-terminal; InterPro: IPR013670 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type I restriction endonucleases are components of prokaryotic DNA restriction-modification mechanisms that protects the organism against invading foreign DNA. Type I enzymes have three different subunits subunits - M (modification), S (specificity) and R (restriction) - that form multifunctional enzymes with restriction (3.1.21.3 from EC), methylase (2.1.1.72 from EC) and ATPase activities [, ]. The S subunit is required for both restriction and modification and is responsible for recognition of the DNA sequence specific for the system. The M subunit is necessary for modification, and the R subunit is required for restriction. These enzymes use S-Adenosyl-L-methionine (AdoMet) as the methyl group donor in the methylation reaction, and have a requirement for ATP. They recognise asymmetric DNA sequences split into two domains of specific sequence, one 3-4 bp long and another 4-5 bp long, separated by a nonspecific spacer 6-8 bp in length. Cleavage occurs a considerable distance from the recognition sites, rarely less than 400 bp away and up to 7000 bp away. Adenosyl residues are methylated, one on each strand of the recognition sequence. These enzymes are widespread in eubacteria and archaea. In enteric bacteria they have been subdivide into four families: types IA, IB, IC and ID. Type III restriction endonucleases (3.1.21.5 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. Type III enzymes are hetero-oligomeric, multifunctional proteins composed of two subunits, Res and Mod. The Mod subunit recognises the DNA sequence specific for the system and is a modification methyltransferase; as such it is functionally equivalent to the M and S subunits of type I restriction endonuclease. Res is required for restriction, although it has no enzymatic activity on its own. Type III enzymes recognise short 5-6 bp long asymmetric DNA sequences and cleave 25-27 bp downstream to leave short, single-stranded 5' protrusions. They require the presence of two inversely oriented unmethylated recognition sites for restriction to occur. These enzymes methylate only one strand of the DNA, at the N-6 position of adenosyl residues, so newly replicated DNA will have only one strand methylated, which is sufficient to protect against restriction. Type III enzymes belong to the beta-subfamily of N6 adenine methyltransferases, containing the nine motifs that characterise this family, including motif I, the AdoMet binding pocket (FXGXG), and motif IV, the catalytic region (S/D/N (PP) Y/F) [, ]. This entry represents the C-terminal domain found in both the R subunit of type I enzymes and the Res subunit of type III enzymes. The type I enzyme represented is EcoEI, which recognises 5'-GAGN(7)ATGC-3; the R protein (HsdR) is required for both nuclease and ATPase activity [, ]. ; GO: 0003677 DNA binding, 0003824 catalytic activity, 0006304 DNA modification
Probab=34.14 E-value=1.4e+02 Score=22.45 Aligned_cols=50 Identities=12% Similarity=0.225 Sum_probs=39.5
Q ss_pred HHhHHHHHhc-c------hhHHHHHHhHHHhcCCCCccchHHHHHHHHHHHHhhcCHHH
Q psy16704 59 FKAGLCHLCI-D------LLNCQQALSRYIDLSPAFQDTREYKFLLKLIESLEEEDSDA 110 (146)
Q Consensus 59 fkA~LC~L~~-D------~v~a~~ale~Y~~~DPsF~~SRE~klL~~LieAve~~D~e~ 110 (146)
+-..|||++. | ...|++++++|.+..+ -+...-++|..|++.+.++-...
T Consensus 68 l~~~ir~i~g~d~~l~tr~erv~~~~~~~l~~~~--~~~~Q~~~L~~i~~~~~~~G~~~ 124 (164)
T PF08463_consen 68 LFDFIRHILGLDTPLLTRRERVEEAFSKFLNQHQ--FNAEQREFLERILDYYAQNGIIE 124 (164)
T ss_pred HHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHhcC--CCHHHHHHHHHHHHHHHHhCccc
Confidence 5678999966 9 8899999998886555 45788889999999987765443
No 63
>KOG2003|consensus
Probab=33.95 E-value=1e+02 Score=29.79 Aligned_cols=91 Identities=18% Similarity=0.323 Sum_probs=60.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhcccchhhchhHHhHHhHHHHHhc-chhHHHHHHhHHHhcCCCCccchHH-HHHHHHHH
Q psy16704 24 MLMMTFRIVYSLLFYSTGKAATENSLMKYNSKEYFFKAGLCHLCI-DLLNCQQALSRYIDLSPAFQDTREY-KFLLKLIE 101 (146)
Q Consensus 24 ~~~~~~~~~A~eiyE~VA~~sl~n~LlKysaKeyffkA~LC~L~~-D~v~a~~ale~Y~~~DPsF~~SRE~-klL~~Lie 101 (146)
-+=-.|...|+..||+.+ -+.-+..||. +. ..-|- -.-+-++|++-|.+..-.|+..-|| +||..|.-
T Consensus 636 yidtqf~ekai~y~ekaa--liqp~~~kwq-----lm---iasc~rrsgnyqka~d~yk~~hrkfpedldclkflvri~~ 705 (840)
T KOG2003|consen 636 YIDTQFSEKAINYFEKAA--LIQPNQSKWQ-----LM---IASCFRRSGNYQKAFDLYKDIHRKFPEDLDCLKFLVRIAG 705 (840)
T ss_pred HHhhHHHHHHHHHHHHHH--hcCccHHHHH-----HH---HHHHHHhcccHHHHHHHHHHHHHhCccchHHHHHHHHHhc
Confidence 334456666777777654 2333334442 21 22344 6778899999999999999888887 78888877
Q ss_pred HHhhcCHHHHHHHHHhhhccCCc
Q psy16704 102 SLEEEDSDAFSETVKEFDSISRL 124 (146)
Q Consensus 102 Ave~~D~e~Ft~aV~eYD~isrL 124 (146)
-+--.|...|.+.+..-.+|..+
T Consensus 706 dlgl~d~key~~klek~eki~ei 728 (840)
T KOG2003|consen 706 DLGLKDAKEYADKLEKAEKIKEI 728 (840)
T ss_pred cccchhHHHHHHHHHHHHHHHHH
Confidence 77777788888777665555443
No 64
>KOG0545|consensus
Probab=33.95 E-value=2.2e+02 Score=25.36 Aligned_cols=82 Identities=18% Similarity=0.243 Sum_probs=60.2
Q ss_pred HHHHHHHHHHHHHHHHhhcccchhhchhHHhHHhHHHHHhc-chhHHHHHHhHHHhcCCCCc--cchHHHHHHHHHHHHh
Q psy16704 28 TFRIVYSLLFYSTGKAATENSLMKYNSKEYFFKAGLCHLCI-DLLNCQQALSRYIDLSPAFQ--DTREYKFLLKLIESLE 104 (146)
Q Consensus 28 ~~~~~A~eiyE~VA~~sl~n~LlKysaKeyffkA~LC~L~~-D~v~a~~ale~Y~~~DPsF~--~SRE~klL~~LieAve 104 (146)
.-+-.+.+.||-+-..|==-+.=--++|-||-+|- .|-+. ....|+.-+.+--++||+.. -|||-+++.+=..+=.
T Consensus 238 QC~L~~~e~yevleh~seiL~~~~~nvKA~frRak-Ahaa~Wn~~eA~~D~~~vL~ldpslasvVsrElr~le~r~~ek~ 316 (329)
T KOG0545|consen 238 QCLLKKEEYYEVLEHCSEILRHHPGNVKAYFRRAK-AHAAVWNEAEAKADLQKVLELDPSLASVVSRELRLLENRMAEKQ 316 (329)
T ss_pred HHHhhHHHHHHHHHHHHHHHhcCCchHHHHHHHHH-HHHhhcCHHHHHHHHHHHHhcChhhHHHHHHHHHHHHHHHHHhh
Confidence 34567788888765544333333458999987765 67777 99999999999999999995 5899999888666655
Q ss_pred hcCHHH
Q psy16704 105 EEDSDA 110 (146)
Q Consensus 105 ~~D~e~ 110 (146)
+.|--.
T Consensus 317 ~edr~~ 322 (329)
T KOG0545|consen 317 EEDRLR 322 (329)
T ss_pred hHHHHH
Confidence 554433
No 65
>PF14164 YqzH: YqzH-like protein
Probab=33.82 E-value=1.2e+02 Score=21.08 Aligned_cols=46 Identities=20% Similarity=0.213 Sum_probs=30.4
Q ss_pred HHHHHhHHHhc-CCCCccchHHHHHHHHHHHHhhcCHH-----HHHHHHHhh
Q psy16704 73 CQQALSRYIDL-SPAFQDTREYKFLLKLIESLEEEDSD-----AFSETVKEF 118 (146)
Q Consensus 73 a~~ale~Y~~~-DPsF~~SRE~klL~~LieAve~~D~e-----~Ft~aV~eY 118 (146)
++++|..|--- ....-+++|.+-|.+=|++..+.+.+ .-.++|++|
T Consensus 10 i~~~l~QYg~d~~~~pls~~E~~~L~~~i~~~~~~~~~~Dl~eiVeDvVY~y 61 (64)
T PF14164_consen 10 IINCLRQYGYDVECMPLSDEEWEELCKHIQERKNEEPDEDLHEIVEDVVYDY 61 (64)
T ss_pred HHHHHHHhCCcccCCCCCHHHHHHHHHHHHHHHhcCCCchHHHHHHHHHHHH
Confidence 57888888443 34446889988887777777666544 344556555
No 66
>PF04733 Coatomer_E: Coatomer epsilon subunit; InterPro: IPR006822 Proteins synthesised on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment. This traffic is bidirectional, to ensure that proteins required to form vesicles are recycled. Vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transfer []. While clathrin mediates endocytic protein transport, and transport from ER to Golgi, coatomers primarily mediate intra-Golgi transport, as well as the reverse Golgi to ER transport of dilysine-tagged proteins []. For example, the coatomer COP1 (coat protein complex 1) is responsible for reverse transport of recycled proteins from Golgi and pre-Golgi compartments back to the ER, while COPII buds vesicles from the ER to the Golgi []. Coatomers reversibly associate with Golgi (non-clathrin-coated) vesicles to mediate protein transport and for budding from Golgi membranes []. Activated small guanine triphosphatases (GTPases) attract coat proteins to specific membrane export sites, thereby linking coatomers to export cargos. As coat proteins polymerise, vesicles are formed and budded from membrane-bound organelles. Coatomer complexes also influence Golgi structural integrity, as well as the processing, activity, and endocytic recycling of LDL receptors. In mammals, coatomer complexes can only be recruited by membranes associated to ADP-ribosylation factors (ARFs), which are small GTP-binding proteins. Coatomer complexes are hetero-oligomers composed of at least an alpha, beta, beta', gamma, delta, epsilon and zeta subunits. This entry represents the epsilon subunit of the coatomer complex, which is involved in the regulation of intracellular protein trafficking between the endoplasmic reticulum and the Golgi complex []. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0005198 structural molecule activity, 0006890 retrograde vesicle-mediated transport, Golgi to ER, 0030126 COPI vesicle coat; PDB: 3MV2_B 3MV3_F 3MKR_A.
Probab=32.30 E-value=2.4e+02 Score=23.87 Aligned_cols=89 Identities=12% Similarity=0.141 Sum_probs=52.7
Q ss_pred HHHHHHHHHHHHHhhcccchhhchhHHhHHhHHHHHhc-chhHHHHHHhHHHhcCCCCccchHHHHHHHHHHH-HhhcCH
Q psy16704 31 IVYSLLFYSTGKAATENSLMKYNSKEYFFKAGLCHLCI-DLLNCQQALSRYIDLSPAFQDTREYKFLLKLIES-LEEEDS 108 (146)
Q Consensus 31 ~~A~eiyE~VA~~sl~n~LlKysaKeyffkA~LC~L~~-D~v~a~~ale~Y~~~DPsF~~SRE~klL~~LieA-ve~~D~ 108 (146)
.+|.-+||+++.+.=.++.+ +.--+.||+.. +..+|+..+++=.+.||.- ...|.+++-+ .-.|+.
T Consensus 184 ~~A~y~f~El~~~~~~t~~~-------lng~A~~~l~~~~~~eAe~~L~~al~~~~~~-----~d~LaNliv~~~~~gk~ 251 (290)
T PF04733_consen 184 QDAFYIFEELSDKFGSTPKL-------LNGLAVCHLQLGHYEEAEELLEEALEKDPND-----PDTLANLIVCSLHLGKP 251 (290)
T ss_dssp CHHHHHHHHHHCCS--SHHH-------HHHHHHHHHHCT-HHHHHHHHHHHCCC-CCH-----HHHHHHHHHHHHHTT-T
T ss_pred HHHHHHHHHHHhccCCCHHH-------HHHHHHHHHHhCCHHHHHHHHHHHHHhccCC-----HHHHHHHHHHHHHhCCC
Confidence 46889999988764333322 22345689998 9999999999988888764 4455555554 444444
Q ss_pred -HHHHHHHHhhhccCCchHHHHHH
Q psy16704 109 -DAFSETVKEFDSISRLDQWYTTM 131 (146)
Q Consensus 109 -e~Ft~aV~eYD~isrLD~WKT~m 131 (146)
+.-..-+.+..+..+=-+|-..+
T Consensus 252 ~~~~~~~l~qL~~~~p~h~~~~~~ 275 (290)
T PF04733_consen 252 TEAAERYLSQLKQSNPNHPLVKDL 275 (290)
T ss_dssp CHHHHHHHHHCHHHTTTSHHHHHH
T ss_pred hhHHHHHHHHHHHhCCCChHHHHH
Confidence 44555555554455545555544
No 67
>PRK07630 CobD/CbiB family protein; Provisional
Probab=31.80 E-value=3.3e+02 Score=23.37 Aligned_cols=54 Identities=15% Similarity=0.065 Sum_probs=41.9
Q ss_pred HhHHHHHhc-chhHHHHHHhHHHhcCCCCccchHHHHHHHHHHHHhhcCHHHHHHHH
Q psy16704 60 KAGLCHLCI-DLLNCQQALSRYIDLSPAFQDTREYKFLLKLIESLEEEDSDAFSETV 115 (146)
Q Consensus 60 kA~LC~L~~-D~v~a~~ale~Y~~~DPsF~~SRE~klL~~LieAve~~D~e~Ft~aV 115 (146)
++..-.+.. |...||+.+......|++ +--|.++.+..+|++-++..|.+..-+
T Consensus 99 ~~v~~al~~~dl~~AR~~l~~~v~rdt~--~l~~~~i~~a~iEs~~en~~d~~~apl 153 (312)
T PRK07630 99 TDIHLALRNDDLPRARELLGEWTGLDTV--DMPVSEIVRHTIEHALVASHRHVFGVF 153 (312)
T ss_pred HHHHHHHHcCCHHHHHHHHHHHhCCCcc--cCChhHHHHHHHHHHHHHhcccchHHH
Confidence 345566666 999999999999988888 455666889999999888888755443
No 68
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=30.53 E-value=1.5e+02 Score=24.46 Aligned_cols=43 Identities=19% Similarity=0.257 Sum_probs=32.3
Q ss_pred HHHhHHHhcCCCC--ccchHHHHHHHHHHHHhhcCHHHHHHHHHh
Q psy16704 75 QALSRYIDLSPAF--QDTREYKFLLKLIESLEEEDSDAFSETVKE 117 (146)
Q Consensus 75 ~ale~Y~~~DPsF--~~SRE~klL~~LieAve~~D~e~Ft~aV~e 117 (146)
+|..+-.+.-|.+ ...+..+++...++|++.||.+...+.+.+
T Consensus 154 RAr~~Lr~~~~~~~~~~~~~~~~v~~f~~A~~~gD~~~l~~Lla~ 198 (293)
T PRK09636 154 RARKHVRAARPRFPVSDEEGAELVEAFFAALASGDLDALVALLAP 198 (293)
T ss_pred HHHHHHHhhCCCCCCCchHHHHHHHHHHHHHHhCCHHHHHHHHhh
Confidence 4444445555655 455677799999999999999999887765
No 69
>smart00028 TPR Tetratricopeptide repeats. Repeats present in 4 or more copies in proteins. Contain a minimum of 34 amino acids each and self-associate via a "knobs and holes" mechanism.
Probab=30.51 E-value=69 Score=15.05 Aligned_cols=29 Identities=17% Similarity=0.353 Sum_probs=19.0
Q ss_pred hHHhHHHHHhc-chhHHHHHHhHHHhcCCC
Q psy16704 58 FFKAGLCHLCI-DLLNCQQALSRYIDLSPA 86 (146)
Q Consensus 58 ffkA~LC~L~~-D~v~a~~ale~Y~~~DPs 86 (146)
+++-|.|+.-. +...|...+++-.+.+|+
T Consensus 4 ~~~~a~~~~~~~~~~~a~~~~~~~~~~~~~ 33 (34)
T smart00028 4 LYNLGNAYLKLGDYDEALEYYEKALELDPN 33 (34)
T ss_pred HHHHHHHHHHHhhHHHHHHHHHHHHccCCC
Confidence 34555666655 777777777776666664
No 70
>COG1270 CbiB Cobalamin biosynthesis protein CobD/CbiB [Coenzyme metabolism]
Probab=30.11 E-value=3.9e+02 Score=23.67 Aligned_cols=95 Identities=20% Similarity=0.089 Sum_probs=63.5
Q ss_pred HHHHHHHHHHHHHHHhhcccchhhchhHHhHHhHHHHHhc-chhHHHHHHhHHHhcCCCCccchHHHHHHHHHHHHhhcC
Q psy16704 29 FRIVYSLLFYSTGKAATENSLMKYNSKEYFFKAGLCHLCI-DLLNCQQALSRYIDLSPAFQDTREYKFLLKLIESLEEED 107 (146)
Q Consensus 29 ~~~~A~eiyE~VA~~sl~n~LlKysaKeyffkA~LC~L~~-D~v~a~~ale~Y~~~DPsF~~SRE~klL~~LieAve~~D 107 (146)
+-+++.-+|-..|.+|+.+. .+...-.|.. |..+||++++.+..-||+= --|.+..+..||++-|+=
T Consensus 86 ~l~~~~~l~~tla~rsL~~~----------~~~v~~~L~~gdl~~aR~~ls~iV~RDts~--L~~~~i~~AaIES~aEN~ 153 (320)
T COG1270 86 FLIEVLLLKTTLAIRSLADH----------ARKVARALRRGDLEGARRALSMIVGRDTSK--LSEAEIASAAIESLAENL 153 (320)
T ss_pred HHHHHHHHHHHHHHHHHHHH----------HHHHHHHHHhCCHHHHHHHHHHHhcCCccc--CCHHHHHHHHHHHHHHhc
Confidence 34445555555555555443 2333445666 9999999999999999974 457889999999999999
Q ss_pred HHHHHHHHHhhhccCCchHHHHHHHHHHHhhc
Q psy16704 108 SDAFSETVKEFDSISRLDQWYTTMLLKIKRQI 139 (146)
Q Consensus 108 ~e~Ft~aV~eYD~isrLD~WKT~mLLkIKk~I 139 (146)
+|.+..-++=|=-. .|=-.++.|.-|++
T Consensus 154 ~DgvvaPLF~~~v~----G~pgA~~YRaiNTl 181 (320)
T COG1270 154 VDGVVAPLFWFLVG----GLPGALLYRAINTL 181 (320)
T ss_pred ccchHHHHHHHHHh----hhHHHHHHHHHHHH
Confidence 99888776654332 33344444444433
No 71
>COG0781 NusB Transcription termination factor [Transcription]
Probab=29.88 E-value=30 Score=27.15 Aligned_cols=62 Identities=16% Similarity=0.327 Sum_probs=45.0
Q ss_pred hcccchhhchhH--H----hHHhHHHHHhc-chhHHHHHHhHHHhcCCCCccchHHHHHHHHHHHHhhc
Q psy16704 45 TENSLMKYNSKE--Y----FFKAGLCHLCI-DLLNCQQALSRYIDLSPAFQDTREYKFLLKLIESLEEE 106 (146)
Q Consensus 45 l~n~LlKysaKe--y----ffkA~LC~L~~-D~v~a~~ale~Y~~~DPsF~~SRE~klL~~LieAve~~ 106 (146)
+.+.|.+|+.+. + .|+.+++.+-. +.+-.+-.++++.++--.|++.-++||+.++++.+-..
T Consensus 76 I~~~L~~w~~~rL~~verAILRla~yEl~~~~dvP~~VvInEaielaK~f~~e~s~kFINgVLd~i~~~ 144 (151)
T COG0781 76 ISPHLKKWSLERLDLVERAILRLALYELLFRDDVPYKVVINEAIELAKKFSGEDSHKFVNGVLDKIAKK 144 (151)
T ss_pred HHHHHccCCHHHhhHHHHHHHHHHHHHHHhcCCCCCcchHHHHHHHHHHhCCCCchHHHHHHHHHHHHH
Confidence 344444477664 3 34455555554 55777888889999999999999999999999887544
No 72
>PF02607 B12-binding_2: B12 binding domain; InterPro: IPR003759 Cobalamin-dependent methionine synthase (2.1.1.13 from EC) is a large modular protein that catalyses methyl transfer from methyltetrahydrofolate (CH3-H4folate) to homocysteine. During the catalytic cycle, it supports three distinct methyl transfer reactions, each involving the cobalamin (vitamin B12) cofactor and a substrate bound to its own functional unit []. The cobalamin cofactor plays an essential role in this reaction, accepting the methyl group from CH3-H4folate to form methylcob(III)alamin, and in turn donating the methyl group to homocysteine to generate methionine and cob(I)alamin. Methionine synthase is a large enzyme composed of four structurally and functionally distinct modules: the first two modules bind homocysteine and CH3-H4folate, the third module binds the cobalamin cofactor and the C-terminal module binds S-adenosylmethionine. The cobalamin-binding module is composed of two structurally distinct domains: a 4-helical bundle cap domain (residues 651-740 in the Escherichia coli enzyme) and an alpha/beta B12-binding domain (residues 741-896) (IPR006158 from INTERPRO). The 4-helical bundle forms a cap over the alpha/beta domain, which acts to shield the methyl ligand of cobalamin from solvent []. Furthermore, in the conversion to the active conformation of this enzyme, the 4-helical cap rotates to allow the cobalamin cofactor to bind the activation domain (IPR004223 from INTERPRO). The alpha/beta domain is a common cobalamin-binding motif, whereas the 4-helical bundle domain with its methyl cap is a distinctive feature of methionine synthases. This entry represents the 4-helical bundle cap domain. This domain is also present in other shorter proteins that bind to B12, and is always found N terminus to the alpha/beta B12-binding domain.; GO: 0008705 methionine synthase activity, 0031419 cobalamin binding, 0046872 metal ion binding, 0009086 methionine biosynthetic process; PDB: 3EZX_A 3BUL_A 1K7Y_A 1BMT_A 3IV9_A 1K98_A 3IVA_A 2I2X_P.
Probab=29.57 E-value=1.2e+02 Score=19.91 Aligned_cols=46 Identities=13% Similarity=0.212 Sum_probs=34.7
Q ss_pred HHHHHHHHHHhhcCHHHHHHHHHhhhcc-CCchHHHHHHHHHHHhhc
Q psy16704 94 KFLLKLIESLEEEDSDAFSETVKEFDSI-SRLDQWYTTMLLKIKRQI 139 (146)
Q Consensus 94 klL~~LieAve~~D~e~Ft~aV~eYD~i-srLD~WKT~mLLkIKk~I 139 (146)
.+++++.+|+-++|.+...+.+.+.=+- ......-..++..+-+.|
T Consensus 3 ~~~~~l~~al~~~d~~~~~~~~~~~l~~g~~~~~i~~~~l~p~m~~i 49 (79)
T PF02607_consen 3 ELIERLLDALLAGDEEEAEALLEEALAQGYPPEDIIEEILMPAMEEI 49 (79)
T ss_dssp HHHHHHHHHHHTT-CCHHHHHHHHHHHCSSSTTHHHHHTHHHHHHHH
T ss_pred HHHHHHHHHHHhCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHH
Confidence 4678899999999999999988887766 666677777666665555
No 73
>TIGR01951 nusB transcription antitermination factor NusB. A transcription antitermination complex active in many bacteria was designated N-utilization substance (Nus) in E. coli because of its interaction with phage lambda protein N. This model represents NusB. Other components are NusA and NusG. NusE is, in fact, ribosomal protein S10.
Probab=29.04 E-value=1e+02 Score=22.21 Aligned_cols=48 Identities=13% Similarity=0.261 Sum_probs=36.5
Q ss_pred HhHHhHHHHHhc-chhHHHHHHhHHHhcCCCCccchHHHHHHHHHHHHh
Q psy16704 57 YFFKAGLCHLCI-DLLNCQQALSRYIDLSPAFQDTREYKFLLKLIESLE 104 (146)
Q Consensus 57 yffkA~LC~L~~-D~v~a~~ale~Y~~~DPsF~~SRE~klL~~LieAve 104 (146)
..|+-|+|++.- |.+...-+++++.++-..|.+.+..+|+.+++..+.
T Consensus 79 ~iLr~a~~el~~~~~~p~~avineaV~lak~~~~~~~~~fVNaVLr~i~ 127 (129)
T TIGR01951 79 AILRLAAYELLYRPDVPYKVVINEAVELAKKFGDEDSHKFVNGVLDKIA 127 (129)
T ss_pred HHHHHHHHHHHhCCCCCCcchHHHHHHHHHHHCCCCchhhHHHHHHHHh
Confidence 357777788775 455777778888888888887888889988887654
No 74
>TIGR02785 addA_Gpos recombination helicase AddA, Firmicutes type. AddAB, also called RexAB, substitutes for RecBCD in several bacterial lineages. These DNA recombination proteins act before synapse and are particularly important for DNA repair of double-stranded breaks by homologous recombination. The term AddAB is used broadly, with AddA homologous between the Firmicutes (as modeled here) and the alphaproteobacteria, while the partner AddB proteins show no strong homology across the two groups of species.
Probab=29.00 E-value=1.9e+02 Score=29.60 Aligned_cols=113 Identities=19% Similarity=0.289 Sum_probs=58.2
Q ss_pred HHHHHHHHHHH-HHHHHHHHHhhcccchhhchhHHhHHhHHH----HHhc-chhHHHHHHhHH--HhcCCCC--ccchHH
Q psy16704 24 MLMMTFRIVYS-LLFYSTGKAATENSLMKYNSKEYFFKAGLC----HLCI-DLLNCQQALSRY--IDLSPAF--QDTREY 93 (146)
Q Consensus 24 ~~~~~~~~~A~-eiyE~VA~~sl~n~LlKysaKeyffkA~LC----~L~~-D~v~a~~ale~Y--~~~DPsF--~~SRE~ 93 (146)
+|.+||-..|+ |+=++|.+. ++..+-+-.-..|+-++... +..+ |.-..+..-+.| .++||+| .+.-|.
T Consensus 48 il~~tFt~~aa~e~~~ri~~~-l~~~~~~~p~~~~L~~q~~~~~~~~i~Tihsf~~~~~~~~~~~l~ldP~F~i~de~e~ 126 (1232)
T TIGR02785 48 LLVVTFTNAAAREMKERIEEA-LQKALQQEPNSKHLRRQLALLNTANISTLHSFCLKVIRKHYYLLDLDPSFRILTDTEQ 126 (1232)
T ss_pred EEEEeccHHHHHHHHHHHHHH-HHHHHhcCchhHHHHHHHhhccCCeEeeHHHHHHHHHHHhhhhcCCCCCceeCCHHHH
Confidence 35678866555 555555433 22222222223444433221 1123 444333333322 4789999 355555
Q ss_pred HHH-HHHHHHH-----hhcCHHHHHHHHHhhhccCCchHHHHHHHHHHHhh
Q psy16704 94 KFL-LKLIESL-----EEEDSDAFSETVKEFDSISRLDQWYTTMLLKIKRQ 138 (146)
Q Consensus 94 klL-~~LieAv-----e~~D~e~Ft~aV~eYD~isrLD~WKT~mLLkIKk~ 138 (146)
.+| ++.++.+ +++|.+.|..-+..|.. .|-|.=...+++++-+.
T Consensus 127 ~ll~~e~~~~~~e~~y~~~d~~~f~~l~~~f~~-~~~d~~l~~~i~~ly~~ 176 (1232)
T TIGR02785 127 LLLIKEVVDDVFEEEYYKEDNEGFFELTDNFSG-DRSDDGLRDLILKLYDF 176 (1232)
T ss_pred HHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcC-CCCHHHHHHHHHHHHHH
Confidence 444 4444433 23444889999999998 66665455566666543
No 75
>PF13877 RPAP3_C: Potential Monad-binding region of RPAP3
Probab=27.62 E-value=87 Score=21.68 Aligned_cols=39 Identities=31% Similarity=0.608 Sum_probs=25.8
Q ss_pred CccchHHHHHHHHHHHHhh----cCHHHHHHHHHhhhccCCch
Q psy16704 87 FQDTREYKFLLKLIESLEE----EDSDAFSETVKEFDSISRLD 125 (146)
Q Consensus 87 F~~SRE~klL~~LieAve~----~D~e~Ft~aV~eYD~isrLD 125 (146)
|...=|..+|.++++++.+ +|.+.=.+.+....+++|.|
T Consensus 40 f~~~l~~~~L~~il~~l~~~~~~~~~~~i~~~L~~L~~~~RF~ 82 (94)
T PF13877_consen 40 FKNSLEPEFLSEILEALNEHFIPEDPEFIFEILEALSKVKRFD 82 (94)
T ss_pred HHccCCHHHHHHHHHHHHHHHccCCHHHHHHHHHHhcCCCCHH
Confidence 5667778889999998887 56664444455555554444
No 76
>KOG2580|consensus
Probab=27.56 E-value=1.6e+02 Score=27.58 Aligned_cols=44 Identities=16% Similarity=0.357 Sum_probs=32.8
Q ss_pred HHHHHHhHHHhcCCCCccc---hHH--HHHHHHHHHHhhcCHHHHHHHH
Q psy16704 72 NCQQALSRYIDLSPAFQDT---REY--KFLLKLIESLEEEDSDAFSETV 115 (146)
Q Consensus 72 ~a~~ale~Y~~~DPsF~~S---RE~--klL~~LieAve~~D~e~Ft~aV 115 (146)
.+.+-+.+...+||+|+.. ||| ..+-+++||.-.||+|-..+=+
T Consensus 300 E~Sev~tei~~iDPsF~~~~Flr~~ee~IiPnVLeAyvkGD~evLK~wc 348 (459)
T KOG2580|consen 300 EMSEVLTEIKKIDPSFDKEDFLRECEEYIIPNVLEAYVKGDLEVLKKWC 348 (459)
T ss_pred HHHHHHHHHHhcCCCCCcHHHHHHHHHhhhHHHHHHHHhccHHHHHHHH
Confidence 4556788899999999754 444 3566799999999988755433
No 77
>KOG1962|consensus
Probab=27.53 E-value=2.8e+02 Score=23.35 Aligned_cols=57 Identities=19% Similarity=0.416 Sum_probs=33.1
Q ss_pred HHHHHHHHhhhhhhHHHH----------------------HHHHHHHHHHHHHHHHHHHHHH-H----hhcccchhhchh
Q psy16704 3 MVIFMLMLIPMAMPFRLM----------------------LIFMLMMTFRIVYSLLFYSTGK-A----ATENSLMKYNSK 55 (146)
Q Consensus 3 ~~~~~~~~~~~~~~~~~~----------------------~~~~~~~~~~~~A~eiyE~VA~-~----sl~n~LlKysaK 55 (146)
|++|.++++|. |.|.- .++++...|-....+++-.++. . ..+++.-.....
T Consensus 13 ial~~iL~Lpi--p~r~~~~~~~~~~~~~~~~~~~~~i~~~~~villlfiDsvr~i~~~~~~~~~~~n~~~~~~a~~~~~ 90 (216)
T KOG1962|consen 13 IALFLILLLPI--PPRRRRKIFKDRLKSGLAPQVLKTIATTMIVILLLFIDSVRRIQKYVSEYGSMANPTDQPLARTHLL 90 (216)
T ss_pred HHHHHHHHcCC--CHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhcccCCccchHHHHHHH
Confidence 56788888898 65532 2233444454555555544444 2 225555666677
Q ss_pred HHhHHh
Q psy16704 56 EYFFKA 61 (146)
Q Consensus 56 eyffkA 61 (146)
+-+|+|
T Consensus 91 ~~l~ra 96 (216)
T KOG1962|consen 91 EALFRA 96 (216)
T ss_pred HHHHHH
Confidence 777888
No 78
>PLN03088 SGT1, suppressor of G2 allele of SKP1; Provisional
Probab=26.55 E-value=2.8e+02 Score=23.86 Aligned_cols=65 Identities=14% Similarity=0.099 Sum_probs=42.4
Q ss_pred HHHHHHHHHHHHHhhcccchhhchhHHhHHhHHHHHhc-chhHHHHHHhHHHhcCCCCccchHHHHHHHHHHHHh
Q psy16704 31 IVYSLLFYSTGKAATENSLMKYNSKEYFFKAGLCHLCI-DLLNCQQALSRYIDLSPAFQDTREYKFLLKLIESLE 104 (146)
Q Consensus 31 ~~A~eiyE~VA~~sl~n~LlKysaKeyffkA~LC~L~~-D~v~a~~ale~Y~~~DPsF~~SRE~klL~~LieAve 104 (146)
.+|+..+++...-.=+ +++-|+.+ |.+++.. +...|...+++..+++|.....+.. +..+-+.+.
T Consensus 53 ~eAl~~~~~Al~l~P~------~~~a~~~l-g~~~~~lg~~~eA~~~~~~al~l~P~~~~~~~~--l~~~~~kl~ 118 (356)
T PLN03088 53 TEAVADANKAIELDPS------LAKAYLRK-GTACMKLEEYQTAKAALEKGASLAPGDSRFTKL--IKECDEKIA 118 (356)
T ss_pred HHHHHHHHHHHHhCcC------CHHHHHHH-HHHHHHhCCHHHHHHHHHHHHHhCCCCHHHHHH--HHHHHHHHH
Confidence 4677777777654322 34445555 4555555 9999999999999999998654433 455544443
No 79
>PRK11189 lipoprotein NlpI; Provisional
Probab=26.11 E-value=1.8e+02 Score=24.10 Aligned_cols=29 Identities=14% Similarity=0.327 Sum_probs=18.9
Q ss_pred HHHHHhc-chhHHHHHHhHHHhcCCCCccc
Q psy16704 62 GLCHLCI-DLLNCQQALSRYIDLSPAFQDT 90 (146)
Q Consensus 62 ~LC~L~~-D~v~a~~ale~Y~~~DPsF~~S 90 (146)
|..+... |...|..++++-.+++|.+...
T Consensus 105 g~~~~~~g~~~~A~~~~~~Al~l~P~~~~a 134 (296)
T PRK11189 105 GIYLTQAGNFDAAYEAFDSVLELDPTYNYA 134 (296)
T ss_pred HHHHHHCCCHHHHHHHHHHHHHhCCCCHHH
Confidence 3333333 7777777777777777777544
No 80
>PRK10987 regulatory protein AmpE; Provisional
Probab=25.88 E-value=4.1e+02 Score=22.47 Aligned_cols=50 Identities=22% Similarity=0.197 Sum_probs=36.5
Q ss_pred HhHHHHHhc-chhHHHHHHhHH---HhcCCCCccchHHHHHHHHHHHHhhcCHHHHH
Q psy16704 60 KAGLCHLCI-DLLNCQQALSRY---IDLSPAFQDTREYKFLLKLIESLEEEDSDAFS 112 (146)
Q Consensus 60 kA~LC~L~~-D~v~a~~ale~Y---~~~DPsF~~SRE~klL~~LieAve~~D~e~Ft 112 (146)
|+....++. |..+||+.+++. ...|++ . -|.+..+.++|++-++|.+.+.
T Consensus 92 ~~v~~AL~~gDl~aAR~~l~~l~~~~grd~~-l--~~~~i~~~~~e~~~~~~~~~~~ 145 (284)
T PRK10987 92 KAYLQAACRGDSQACYHMAEELTLIHGLPAD-V--SERELLRELQQALLWINYRYYL 145 (284)
T ss_pred HHHHHHHHCCCHHHHHHHHHHhhhccCCCCC-C--CHHHHHHHHHHHHHHHHhhHHH
Confidence 344566777 999999976665 778887 3 3446779999998777767654
No 81
>PRK11447 cellulose synthase subunit BcsC; Provisional
Probab=25.57 E-value=2.3e+02 Score=28.34 Aligned_cols=98 Identities=14% Similarity=0.039 Sum_probs=57.5
Q ss_pred HHHHHHHHHHHHHHHHHHhhcccchh--hchhHHhHHhHHHHHhc-chhHHHHHHhHHHhcCCCCccchHHHHHH-----
Q psy16704 26 MMTFRIVYSLLFYSTGKAATENSLMK--YNSKEYFFKAGLCHLCI-DLLNCQQALSRYIDLSPAFQDTREYKFLL----- 97 (146)
Q Consensus 26 ~~~~~~~A~eiyE~VA~~sl~n~LlK--ysaKeyffkA~LC~L~~-D~v~a~~ale~Y~~~DPsF~~SRE~klL~----- 97 (146)
...-|+.-..-=.+.|+.+++. ++. -+--+.+..++.+.+-. |...|.+.+++-.+.+|.....++....-
T Consensus 32 l~q~~~~~~~~~~d~a~~~l~k-l~~~~p~~p~~~~~~~~~~l~~g~~~~A~~~l~~l~~~~P~~~~~~~~~~~~~~~~~ 110 (1157)
T PRK11447 32 LEQVRLGEATHREDLVRQSLYR-LELIDPNNPDVIAARFRLLLRQGDSDGAQKLLDRLSQLAPDSNAYRSSRTTMLLSTP 110 (1157)
T ss_pred HHHHHHHHhhCChHHHHHHHHH-HHccCCCCHHHHHHHHHHHHhCCCHHHHHHHHHHHHhhCCCChHHHHHHHHHHhcCC
Confidence 3344444333333455555552 222 22346677777777777 99999999999999999987766533221
Q ss_pred ----HHHHHHhhcCHHHHHHHHHhhhccCCc
Q psy16704 98 ----KLIESLEEEDSDAFSETVKEFDSISRL 124 (146)
Q Consensus 98 ----~LieAve~~D~e~Ft~aV~eYD~isrL 124 (146)
.+..|-.-.....+.+++..|++.-+.
T Consensus 111 ~~~~~l~~A~ll~~~g~~~eA~~~~~~~l~~ 141 (1157)
T PRK11447 111 EGRQALQQARLLATTGRTEEALASYDKLFNG 141 (1157)
T ss_pred chhhHHHHHHHHHhCCCHHHHHHHHHHHccC
Confidence 122222222223456777777776554
No 82
>PRK07248 hypothetical protein; Provisional
Probab=25.53 E-value=2.1e+02 Score=19.74 Aligned_cols=35 Identities=17% Similarity=0.133 Sum_probs=26.4
Q ss_pred HhcCCCCccchHHHHHHHHHHHHhhcCHHHHHHHH
Q psy16704 81 IDLSPAFQDTREYKFLLKLIESLEEEDSDAFSETV 115 (146)
Q Consensus 81 ~~~DPsF~~SRE~klL~~LieAve~~D~e~Ft~aV 115 (146)
..--|-|...||.+.+..+.+..+++-.+.+...+
T Consensus 37 ~~~~~v~d~~RE~~vl~~~~~~~~~~~~~~~i~~i 71 (87)
T PRK07248 37 ATGKPVLDTKREQVILDKVSSLVENKAYQETIVAT 71 (87)
T ss_pred HcCCCCCChHHHHHHHHHHHHHcccCCCHHHHHHH
Confidence 33459999999999999999887665555555555
No 83
>PRK11447 cellulose synthase subunit BcsC; Provisional
Probab=24.94 E-value=3.4e+02 Score=27.16 Aligned_cols=89 Identities=11% Similarity=0.082 Sum_probs=54.8
Q ss_pred HHHHHHHHHHHHHhhcccchhhchhHHhHHhHHHHHhc-chhHHHHHHhHHHhcCCCCccchHH---------HHH-HHH
Q psy16704 31 IVYSLLFYSTGKAATENSLMKYNSKEYFFKAGLCHLCI-DLLNCQQALSRYIDLSPAFQDTREY---------KFL-LKL 99 (146)
Q Consensus 31 ~~A~eiyE~VA~~sl~n~LlKysaKeyffkA~LC~L~~-D~v~a~~ale~Y~~~DPsF~~SRE~---------klL-~~L 99 (146)
.+|.+.|++.-+..=+++ +-+..-|.+++.. |...|...+++..+.+|........ ..+ ..-
T Consensus 286 ~~A~~~l~~aL~~~P~~~-------~a~~~Lg~~~~~~g~~~eA~~~l~~Al~~~p~~~~~~~~~~ll~~~~~~~~~~~g 358 (1157)
T PRK11447 286 GKAIPELQQAVRANPKDS-------EALGALGQAYSQQGDRARAVAQFEKALALDPHSSNRDKWESLLKVNRYWLLIQQG 358 (1157)
T ss_pred HHHHHHHHHHHHhCCCCH-------HHHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCccchhHHHHHHHhhhHHHHHHHH
Confidence 577888887776544332 3444556777777 9999999999999999987654321 111 111
Q ss_pred HHHHhhcCHHHHHHHHHhhhccCCchHHHH
Q psy16704 100 IESLEEEDSDAFSETVKEFDSISRLDQWYT 129 (146)
Q Consensus 100 ieAve~~D~e~Ft~aV~eYD~isrLD~WKT 129 (146)
-.+.+.| .+.+++..|.+.-.+|+...
T Consensus 359 ~~~~~~g---~~~eA~~~~~~Al~~~P~~~ 385 (1157)
T PRK11447 359 DAALKAN---NLAQAERLYQQARQVDNTDS 385 (1157)
T ss_pred HHHHHCC---CHHHHHHHHHHHHHhCCCCH
Confidence 1223333 35566666666666655443
No 84
>PF08544 GHMP_kinases_C: GHMP kinases C terminal ; InterPro: IPR013750 This domain is found in homoserine kinases (2.7.1.39 from EC), galactokinases (2.7.1.6 from EC) and mevalonate kinases (2.7.1.36 from EC). These kinases make up the GHMP kinase superfamily of ATP-dependent enzymes []. These enzymes are involved in the biosynthesis of isoprenes and amino acids as well as in carbohydrate metabolism. The C-terminal domain of homoserine kinase has a central alpha-beta plait fold and an insertion of four helices, which, together with the N-terminal fold, create a novel nucleotide binding fold [].; PDB: 2R3V_C 4EMD_A 4DXL_A 4ED4_A 2GS8_A 1K47_E 3GON_A 3K17_B 1PIE_A 2AJ4_A ....
Probab=24.75 E-value=88 Score=20.35 Aligned_cols=22 Identities=27% Similarity=0.436 Sum_probs=18.7
Q ss_pred HHHHHhhcCHHHHHHHHHhhhc
Q psy16704 99 LIESLEEEDSDAFSETVKEFDS 120 (146)
Q Consensus 99 LieAve~~D~e~Ft~aV~eYD~ 120 (146)
+++|+.++|.+.|.+.+.+...
T Consensus 1 m~~al~~~d~~~~~~~~~~~~~ 22 (85)
T PF08544_consen 1 MIKALAEGDLELLGELMNENQE 22 (85)
T ss_dssp HHHHHHTTCHHHHHHHHHHHHH
T ss_pred CHHHHHCcCHHHHHHHHHHhhh
Confidence 5789999999999999986543
No 85
>TIGR01807 CM_P2 chorismate mutase domain of proteobacterial P-protein, clade 2. This model represents one of two separate clades of the chorismate mutase domain of the gamma and beta and epsilon proteobacterial "P-protein" which contains an N-terminal chorismate mutase domain and a C-terminal prephenate dehydratase domain. It is also found in Aquifex aolicus.
Probab=24.68 E-value=2.2e+02 Score=19.17 Aligned_cols=40 Identities=8% Similarity=0.046 Sum_probs=27.3
Q ss_pred HhHHHhc----CCCCccchHHHHHHHHHHHHhhcCHHHHHHHHH
Q psy16704 77 LSRYIDL----SPAFQDTREYKFLLKLIESLEEEDSDAFSETVK 116 (146)
Q Consensus 77 le~Y~~~----DPsF~~SRE~klL~~LieAve~~D~e~Ft~aV~ 116 (146)
+.+|+.. -|-|...||.+.+..+.+..+.+=.+.+...++
T Consensus 29 i~~~K~~~~~~~~i~d~~Re~~vl~~~~~~~~~~l~~~~i~~if 72 (76)
T TIGR01807 29 VGELKGSGASGASFYRPEREAQVIRRLQNLNKGPLDQEAIARIF 72 (76)
T ss_pred HHHHHHhccCCCCcCChHHHHHHHHHHHHhccCCCCHHHHHHHH
Confidence 3455544 578999999999999877654333555655554
No 86
>smart00830 CM_2 Chorismate mutase type II. Chorismate mutase, catalyses the conversion of chorismate to prephenate in the pathway of tyrosine and phenylalanine biosynthesis. This enzyme is negatively regulated by tyrosine, tryptophan and phenylalanine PUBMED:9642265, PUBMED:9497350.
Probab=24.52 E-value=2.1e+02 Score=18.73 Aligned_cols=37 Identities=19% Similarity=0.231 Sum_probs=27.3
Q ss_pred HHHhcCCCCccchHHHHHHHHHHHHhhcC-HHHHHHHH
Q psy16704 79 RYIDLSPAFQDTREYKFLLKLIESLEEED-SDAFSETV 115 (146)
Q Consensus 79 ~Y~~~DPsF~~SRE~klL~~LieAve~~D-~e~Ft~aV 115 (146)
|...--|-+...||..++..+.+...+.. ...|...+
T Consensus 29 K~~~~~~i~d~~Re~~vl~~~~~~a~~~~l~~~~~~~i 66 (79)
T smart00830 29 KAKNGLPIYDPEREAEVLERLRALAEGPGLDPELVERI 66 (79)
T ss_pred HHHCCCCCCChHHHHHHHHHHHHHcccCCcCHHHHHHH
Confidence 33334689999999999999998887765 44555554
No 87
>PF13010 pRN1_helical: Primase helical domain; PDB: 1RO0_A 1RNI_A 1RO2_A 3M1M_A.
Probab=24.35 E-value=41 Score=26.47 Aligned_cols=36 Identities=22% Similarity=0.412 Sum_probs=21.1
Q ss_pred hhcCHHHHHHHHHhhhcc--CCchHHHHHHHHHHHhhc
Q psy16704 104 EEEDSDAFSETVKEFDSI--SRLDQWYTTMLLKIKRQI 139 (146)
Q Consensus 104 e~~D~e~Ft~aV~eYD~i--srLD~WKT~mLLkIKk~I 139 (146)
++.|.|++.+-++.||+. ..+|.-+..+.-++|+++
T Consensus 9 t~~~~ekLkeEm~KydrfkGKtveair~evC~~~kk~~ 46 (135)
T PF13010_consen 9 TEEDFEKLKEEMAKYDRFKGKTVEAIREEVCKKIKKSL 46 (135)
T ss_dssp ------HHHHHHHHH-------HHHHHHHHHTS---HH
T ss_pred cHHHHHHHHHHHHHhccccCchHHHHHHHHHHhcchhh
Confidence 477899999999999997 899999999999999988
No 88
>PF02609 Exonuc_VII_S: Exonuclease VII small subunit; InterPro: IPR003761 Exonuclease VII is composed of two non-identical subunits; one large subunit and 4 small ones []. This enzyme catalyses exonucleolytic cleavage in either 5'-3' or 3'-5' direction to yield nucleoside 5'-phosphates.; GO: 0008855 exodeoxyribonuclease VII activity, 0006308 DNA catabolic process, 0009318 exodeoxyribonuclease VII complex; PDB: 1VP7_F.
Probab=23.59 E-value=88 Score=19.98 Aligned_cols=44 Identities=20% Similarity=0.266 Sum_probs=29.8
Q ss_pred HHHHHHHHHhhcCHHHHHHHHHhhhccCCchHHHHHHHHHHHhhc
Q psy16704 95 FLLKLIESLEEEDSDAFSETVKEFDSISRLDQWYTTMLLKIKRQI 139 (146)
Q Consensus 95 lL~~LieAve~~D~e~Ft~aV~eYD~isrLD~WKT~mLLkIKk~I 139 (146)
=|+++++.++++|.. ..+++..|.+=.+|=+--.+.|.++...|
T Consensus 7 ~Le~Iv~~Le~~~~s-Ldes~~lyeeg~~l~~~c~~~L~~~e~~i 50 (53)
T PF02609_consen 7 RLEEIVEKLESGELS-LDESLKLYEEGMELIKKCQERLEEAEQKI 50 (53)
T ss_dssp HHHHHHHHHHTT-S--HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHcCCCC-HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 377888888888766 67777777776666666666666666554
No 89
>PF10163 EnY2: Transcription factor e(y)2; InterPro: IPR018783 Enhancer of yellow 2 (EnY2) is a small transcription factor which is combined in a complex with the TAFII40 protein []. This protein is conserved from protozoa to humans.; PDB: 4DHX_C 3FWC_P 3M99_C 3KIK_A 3KJL_C 3FWB_C 3MHS_B 3MHH_B.
Probab=23.52 E-value=1.7e+02 Score=20.47 Aligned_cols=44 Identities=11% Similarity=0.152 Sum_probs=33.6
Q ss_pred HHHHHHH--HhhcCHHHHHHHHHhhhccCCchHHHHHHHHHHHhhc
Q psy16704 96 LLKLIES--LEEEDSDAFSETVKEFDSISRLDQWYTTMLLKIKRQI 139 (146)
Q Consensus 96 L~~LieA--ve~~D~e~Ft~aV~eYD~isrLD~WKT~mLLkIKk~I 139 (146)
..+.+.. .++-+++.-.+.|.---+-+-=|.+|+.++.+|++.+
T Consensus 40 ~re~i~~~g~~~~~~~~l~~~i~P~Ar~~VP~~vk~ell~~Ir~~L 85 (86)
T PF10163_consen 40 CREIIRERGIDNLTFEDLLEEITPKARAMVPDEVKKELLQRIRAFL 85 (86)
T ss_dssp HHHHHHHH-TTTSBHHHHHHHHHHHHHHCS-HHHHHHHHHHHHHHH
T ss_pred HHHHHHhhCCCCCCHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHh
Confidence 4455555 6666788888888888777778999999999999865
No 90
>PF13474 SnoaL_3: SnoaL-like domain; PDB: 2GXF_A 3KSP_A 3KE7_A 3BB9_E 3CNX_A 3F7S_A 3GWR_B.
Probab=23.41 E-value=98 Score=20.80 Aligned_cols=23 Identities=30% Similarity=0.381 Sum_probs=19.1
Q ss_pred HHHHHHHHHHhhcCHHHHHHHHH
Q psy16704 94 KFLLKLIESLEEEDSDAFSETVK 116 (146)
Q Consensus 94 klL~~LieAve~~D~e~Ft~aV~ 116 (146)
+++++..+|.+++|++.+.+...
T Consensus 3 ~~~~~~~~a~~~~D~~~~~~~~~ 25 (121)
T PF13474_consen 3 ALLEEWIEAFERGDIDALLSLFS 25 (121)
T ss_dssp HHHHHHHHHHHCT-HHHHHHHEE
T ss_pred HHHHHHHHHHHhCCHHHHHHhhC
Confidence 57899999999999999987665
No 91
>COG4105 ComL DNA uptake lipoprotein [General function prediction only]
Probab=22.73 E-value=5e+02 Score=22.36 Aligned_cols=65 Identities=12% Similarity=0.086 Sum_probs=45.3
Q ss_pred HHHHHHHHHHHHhhcccchhhchhHHhHHhHHHHHhc-chhHHHHHHhHHHhcCCCCccchHHHHHHHHH
Q psy16704 32 VYSLLFYSTGKAATENSLMKYNSKEYFFKAGLCHLCI-DLLNCQQALSRYIDLSPAFQDTREYKFLLKLI 100 (146)
Q Consensus 32 ~A~eiyE~VA~~sl~n~LlKysaKeyffkA~LC~L~~-D~v~a~~ale~Y~~~DPsF~~SRE~klL~~Li 100 (146)
+|++.||.+-+.--.++ |+ +.=.+--+=.|.=. |.+.|...+++|..+.|+-.+--..-.|++|.
T Consensus 52 ~A~~~fe~l~~~~p~s~---~~-~qa~l~l~yA~Yk~~~y~~A~~~~drFi~lyP~~~n~dY~~YlkgLs 117 (254)
T COG4105 52 EAIKYFEALDSRHPFSP---YS-EQAQLDLAYAYYKNGEYDLALAYIDRFIRLYPTHPNADYAYYLKGLS 117 (254)
T ss_pred HHHHHHHHHHHcCCCCc---cc-HHHHHHHHHHHHhcccHHHHHHHHHHHHHhCCCCCChhHHHHHHHHH
Confidence 56666666664433333 44 22222222333335 99999999999999999999999999999887
No 92
>PF12895 Apc3: Anaphase-promoting complex, cyclosome, subunit 3; PDB: 3KAE_D 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2XPI_A 3ULQ_A.
Probab=22.72 E-value=2.3e+02 Score=18.45 Aligned_cols=49 Identities=12% Similarity=0.213 Sum_probs=38.1
Q ss_pred HHHHHHHHHHHHHhhcccchhhchhHHhHHhHHHHHhc-chhHHHHHHhHHHhcCC
Q psy16704 31 IVYSLLFYSTGKAATENSLMKYNSKEYFFKAGLCHLCI-DLLNCQQALSRYIDLSP 85 (146)
Q Consensus 31 ~~A~eiyE~VA~~sl~n~LlKysaKeyffkA~LC~L~~-D~v~a~~ale~Y~~~DP 85 (146)
..|+..||++-...-.|+ -..|++.=+.|++-. +...|-..+++ .+.+|
T Consensus 6 ~~Ai~~~~k~~~~~~~~~-----~~~~~~~la~~~~~~~~y~~A~~~~~~-~~~~~ 55 (84)
T PF12895_consen 6 ENAIKYYEKLLELDPTNP-----NSAYLYNLAQCYFQQGKYEEAIELLQK-LKLDP 55 (84)
T ss_dssp HHHHHHHHHHHHHHCGTH-----HHHHHHHHHHHHHHTTHHHHHHHHHHC-HTHHH
T ss_pred HHHHHHHHHHHHHCCCCh-----hHHHHHHHHHHHHHCCCHHHHHHHHHH-hCCCC
Confidence 468899999988776533 455888889999998 88888888877 55555
No 93
>KOG2908|consensus
Probab=22.66 E-value=1.8e+02 Score=26.58 Aligned_cols=48 Identities=19% Similarity=0.236 Sum_probs=37.0
Q ss_pred ccchHHHHHHHHHHHHhhcCHHHHHHHHHhhhccCCchHHHHHHHHHHH
Q psy16704 88 QDTREYKFLLKLIESLEEEDSDAFSETVKEFDSISRLDQWYTTMLLKIK 136 (146)
Q Consensus 88 ~~SRE~klL~~LieAve~~D~e~Ft~aV~eYD~isrLD~WKT~mLLkIK 136 (146)
.+|+ ++=|.+++.|+..||+..|.+....+.++--|-.-...++-||.
T Consensus 230 ~gT~-~eWL~dll~Afn~Gdl~~f~~l~~~~~~~p~L~~~e~~L~qKI~ 277 (380)
T KOG2908|consen 230 KGTN-REWLKDLLIAFNSGDLKRFESLKGVWGKQPDLASNEDFLLQKIR 277 (380)
T ss_pred cCCc-HHHHHHHHHHhccCCHHHHHHHHHHhccCchHHHHHHHHHHHHH
Confidence 3443 34578999999999999999999999997767666666665554
No 94
>PF14649 Spatacsin_C: Spatacsin C-terminus
Probab=22.09 E-value=3.1e+02 Score=23.87 Aligned_cols=84 Identities=17% Similarity=0.231 Sum_probs=61.3
Q ss_pred hHHhHHhHHHHHhc-chhHHHHHHhHHHhcCCCCccchHHHHHHHHHH-------------HHhhcCHHHHHHHHHhhhc
Q psy16704 55 KEYFFKAGLCHLCI-DLLNCQQALSRYIDLSPAFQDTREYKFLLKLIE-------------SLEEEDSDAFSETVKEFDS 120 (146)
Q Consensus 55 KeyffkA~LC~L~~-D~v~a~~ale~Y~~~DPsF~~SRE~klL~~Lie-------------Ave~~D~e~Ft~aV~eYD~ 120 (146)
=|-+.+|=-|.-++ +..+..+-++.-+..=+.+...+|+.+|-.|+- ..-+++. |.--+..+.
T Consensus 23 VELLI~AH~cf~~~c~meGi~~vl~~~~~~~~~l~~~~~~~llvRLltGi~ry~em~yifd~L~~n~q--fE~LL~k~~- 99 (296)
T PF14649_consen 23 VELLIRAHDCFTLSCSMEGIAVVLQAAKSLVNHLAAEGDWSLLVRLLTGIGRYREMTYIFDILIENDQ--FELLLRKGI- 99 (296)
T ss_pred hhHHHHHHHHHHhhcchHHHHHHHHHHHHHHHHHhhcccHHHHHHHHHccCcHHHHHHHHHHHHHcCh--HHHHHhccc-
Confidence 47889999999888 888777777777777777778888888877764 3333433 666666654
Q ss_pred cCCchHHHHHHHHHHHhhcCCC
Q psy16704 121 ISRLDQWYTTMLLKIKRQISTN 142 (146)
Q Consensus 121 isrLD~WKT~mLLkIKk~I~~~ 142 (146)
.+-..+|+.++.=+|+.--++
T Consensus 100 -d~~~~lk~all~ylk~~~P~d 120 (296)
T PF14649_consen 100 -DKVNGLKMALLDYLKRCCPED 120 (296)
T ss_pred -cccchHHHHHHHHHHhcCCCC
Confidence 555779999999998875333
No 95
>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=21.91 E-value=6.1e+02 Score=23.07 Aligned_cols=87 Identities=15% Similarity=0.108 Sum_probs=47.3
Q ss_pred HHHHHHHHHHHHHhhcccchhhchhHHhHHhHHHHHhc-chhHHHHHHhHHHhcCCCCccchHHHHHHHHHHHHhhcCHH
Q psy16704 31 IVYSLLFYSTGKAATENSLMKYNSKEYFFKAGLCHLCI-DLLNCQQALSRYIDLSPAFQDTREYKFLLKLIESLEEEDSD 109 (146)
Q Consensus 31 ~~A~eiyE~VA~~sl~n~LlKysaKeyffkA~LC~L~~-D~v~a~~ale~Y~~~DPsF~~SRE~klL~~LieAve~~D~e 109 (146)
.+|.+.|++...-.=+++-...+.-...-+++.+.-.. |...|...+++-.++||..... ...+.++... .+
T Consensus 484 ~~A~~~~~~Al~l~p~~~~~~~~~~~l~~~a~~~~~~~~~~~eA~~~~~kAl~l~p~~~~a-----~~~la~~~~~--~g 556 (615)
T TIGR00990 484 DEAIEKFDTAIELEKETKPMYMNVLPLINKALALFQWKQDFIEAENLCEKALIIDPECDIA-----VATMAQLLLQ--QG 556 (615)
T ss_pred HHHHHHHHHHHhcCCccccccccHHHHHHHHHHHHHHhhhHHHHHHHHHHHHhcCCCcHHH-----HHHHHHHHHH--cc
Confidence 45777777765433222222233333444455554434 8888999999988999876432 2233333322 22
Q ss_pred HHHHHHHhhhccCCc
Q psy16704 110 AFSETVKEFDSISRL 124 (146)
Q Consensus 110 ~Ft~aV~eYD~isrL 124 (146)
.+.+|+..|++.-++
T Consensus 557 ~~~eAi~~~e~A~~l 571 (615)
T TIGR00990 557 DVDEALKLFERAAEL 571 (615)
T ss_pred CHHHHHHHHHHHHHH
Confidence 355666666654443
No 96
>cd00781 ketosteroid_isomerase ketosteroid isomerase: Many biological reactions proceed by enzymatic cleavage of a C-H bond adjacent to carbonyl or a carboxyl group, leading to an enol or a enolate intermediate that is subsequently re-protonated at the same or an adjacent carbon. Ketosteroid isomerases are important members of this class of enzymes which are the most proficient of all enzymes known and have served as a paradigm for enzymatic enolizations since its discovery in 1954. This CD includes members of this class that calalyze the isomerization of various beta,gamma-unsaturated isomers at nearly a diffusion-controlled rate. These enzymes are widely distributed in bacteria.
Probab=21.77 E-value=99 Score=21.31 Aligned_cols=25 Identities=8% Similarity=0.231 Sum_probs=20.7
Q ss_pred HHHHHHHHHHHhhcCHHHHHHHHHh
Q psy16704 93 YKFLLKLIESLEEEDSDAFSETVKE 117 (146)
Q Consensus 93 ~klL~~LieAve~~D~e~Ft~aV~e 117 (146)
..+++...+|++++|.+.+.+...+
T Consensus 6 ~~~v~~~~~a~~~~D~~~~~~l~ae 30 (122)
T cd00781 6 KAAVQRYVEAVNAGDPEGIVALFAD 30 (122)
T ss_pred HHHHHHHHHHHHCCCHHHHHHHcCC
Confidence 3578889999999999998877655
No 97
>KOG0548|consensus
Probab=21.52 E-value=5.5e+02 Score=24.59 Aligned_cols=93 Identities=14% Similarity=0.217 Sum_probs=64.0
Q ss_pred HHHHHHHHHHHHhhcccchhhchhHHhHHhHHHHHhc-chhHHHHHHhHHHhcCCCC--ccchHHHHHHHHHHHHhhcCH
Q psy16704 32 VYSLLFYSTGKAATENSLMKYNSKEYFFKAGLCHLCI-DLLNCQQALSRYIDLSPAF--QDTREYKFLLKLIESLEEEDS 108 (146)
Q Consensus 32 ~A~eiyE~VA~~sl~n~LlKysaKeyffkA~LC~L~~-D~v~a~~ale~Y~~~DPsF--~~SRE~klL~~LieAve~~D~ 108 (146)
.|++.|.+-.+..=++ --+|=+.++||+-. ..-.|=.-.++-.++||+| .-+|.+.-+.. .
T Consensus 376 ~Av~~YteAIkr~P~D-------a~lYsNRAac~~kL~~~~~aL~Da~~~ieL~p~~~kgy~RKg~al~~---------m 439 (539)
T KOG0548|consen 376 EAVKHYTEAIKRDPED-------ARLYSNRAACYLKLGEYPEALKDAKKCIELDPNFIKAYLRKGAALRA---------M 439 (539)
T ss_pred HHHHHHHHHHhcCCch-------hHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCchHHHHHHHHHHHHHH---------H
Confidence 5777887733333222 23566888999875 5555555566667779999 57888654444 4
Q ss_pred HHHHHHHHhhhccCCchHHHHHHHHHHHhhcC
Q psy16704 109 DAFSETVKEFDSISRLDQWYTTMLLKIKRQIS 140 (146)
Q Consensus 109 e~Ft~aV~eYD~isrLD~WKT~mLLkIKk~I~ 140 (146)
..|.++..-|..=..+|+=...++..+++-.+
T Consensus 440 k~ydkAleay~eale~dp~~~e~~~~~~rc~~ 471 (539)
T KOG0548|consen 440 KEYDKALEAYQEALELDPSNAEAIDGYRRCVE 471 (539)
T ss_pred HHHHHHHHHHHHHHhcCchhHHHHHHHHHHHH
Confidence 56777777777778888888888888888664
No 98
>PRK10049 pgaA outer membrane protein PgaA; Provisional
Probab=21.19 E-value=2.5e+02 Score=26.65 Aligned_cols=52 Identities=10% Similarity=-0.038 Sum_probs=32.6
Q ss_pred HHHHHHHHHHHHHhhcccchhhchhHHhHHhHHHHHhc-chhHHHHHHhHHHhcCCCCcc
Q psy16704 31 IVYSLLFYSTGKAATENSLMKYNSKEYFFKAGLCHLCI-DLLNCQQALSRYIDLSPAFQD 89 (146)
Q Consensus 31 ~~A~eiyE~VA~~sl~n~LlKysaKeyffkA~LC~L~~-D~v~a~~ale~Y~~~DPsF~~ 89 (146)
.+|.+.|+++-...=+|+ +..+..+.+.+.. +...|...+++..+.+|.-..
T Consensus 66 ~~A~~~~~~al~~~P~~~-------~a~~~la~~l~~~g~~~eA~~~l~~~l~~~P~~~~ 118 (765)
T PRK10049 66 QNSLTLWQKALSLEPQND-------DYQRGLILTLADAGQYDEALVKAKQLVSGAPDKAN 118 (765)
T ss_pred HHHHHHHHHHHHhCCCCH-------HHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCCCHH
Confidence 367777777655433332 3334555566666 777777778887777776654
No 99
>PF04048 Sec8_exocyst: Sec8 exocyst complex component specific domain; InterPro: IPR007191 Sec8 is a component of the exocyst complex involved in the docking of exocystic vesicles with a fusion site on the plasma membrane. The exocyst complex is composed of Sec3, Sec5, Sec6, Sec8, Sec10, Sec15, Exo70 and Exo84.; GO: 0006904 vesicle docking involved in exocytosis, 0015031 protein transport, 0000145 exocyst
Probab=20.47 E-value=1.4e+02 Score=22.56 Aligned_cols=46 Identities=13% Similarity=0.283 Sum_probs=33.4
Q ss_pred HHHHHHHHHHHhhcCHHHHHHHHHhhhccCC-chHHHHHHHHHHHhhc
Q psy16704 93 YKFLLKLIESLEEEDSDAFSETVKEFDSISR-LDQWYTTMLLKIKRQI 139 (146)
Q Consensus 93 ~klL~~LieAve~~D~e~Ft~aV~eYD~isr-LD~WKT~mLLkIKk~I 139 (146)
++-+.+-++.+=+.+-+.|.++|..|.+|.. +...+.++ ..+|+.+
T Consensus 49 ~~~~~~~L~~vV~eh~q~Fn~sI~sy~~i~~~i~~sq~~i-~~lK~~L 95 (142)
T PF04048_consen 49 KKRIEKALQEVVNEHYQGFNSSIGSYSQILSSISESQERI-RELKESL 95 (142)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHH
Confidence 4456777788888899999999999999864 45555443 4556555
No 100
>PF01875 Memo: Memo-like protein; InterPro: IPR002737 This entry contains proteins from all branches of life. The molecular function of these proteins are unknown, but Memo (mediator of ErbB2-driven cell motility) a human protein is included in this family []. It has been suggested that Memo controls cell migration by relaying extracellular chemotactic signals to the microtubule cytoskeleton [].; PDB: 3BD0_C 3BCZ_C.
Probab=20.43 E-value=1.3e+02 Score=25.24 Aligned_cols=36 Identities=22% Similarity=0.242 Sum_probs=26.3
Q ss_pred HHHHHHHhhcCHHHHHHHHHhhh-ccCCchHHHHHHH
Q psy16704 97 LKLIESLEEEDSDAFSETVKEFD-SISRLDQWYTTML 132 (146)
Q Consensus 97 ~~LieAve~~D~e~Ft~aV~eYD-~isrLD~WKT~mL 132 (146)
+..+++++++|.+.|.+.+.+++ ++|-.-+..+-|.
T Consensus 205 ~~~i~~i~~~d~~~~~~~~~~~~~t~CG~~pi~~~l~ 241 (276)
T PF01875_consen 205 REAIEAIEALDPEGFYEYLKETNNTACGRGPIAVLLE 241 (276)
T ss_dssp HHHHHHHHTT-HHHHHHHHHHH----TTHHHHHHHHH
T ss_pred HHHHHHHHccCHHHHHHHHHHcCCceechHHHHHHHH
Confidence 78899999999999999999885 4676666655543
No 101
>cd00447 NusB_Sun RNA binding domain of NusB (N protein-Utilization Substance B) and Sun (also known as RrmB or Fmu) proteins. This family includes two orthologous groups exemplified by the transcription termination factor NusB and the N-terminal domain of the rRNA-specific 5-methylcytidine transferase (m5C-methyltransferase) Sun. The NusB protein plays a key role in the regulation of ribosomal RNA biosynthesis in eubacteria by modulating the efficiency of transcriptional antitermination. NusB along with other Nus factors (NusA, NusE/S10 and NusG) forms the core complex with the boxA element of the nut site of the rRNA operons. These interactions help RNA polymerase to counteract polarity during transcription of rRNA operons and allow stable antitermination. The transcription antitermination system can be appropriated by some bacteriophages such as lambda, which use the system to switch between the lysogenic and lytic modes of phage propagation. The m5C-methyltransferase Sun shares the
Probab=20.43 E-value=2.9e+02 Score=19.73 Aligned_cols=71 Identities=14% Similarity=0.156 Sum_probs=46.3
Q ss_pred HHHHHHHHhhcccch-hh-chhHHhHHhHHHHHhc-c-hhHHHHHHhHHHhcCCCCccchHHHHHHHHHHHHhhc
Q psy16704 36 LFYSTGKAATENSLM-KY-NSKEYFFKAGLCHLCI-D-LLNCQQALSRYIDLSPAFQDTREYKFLLKLIESLEEE 106 (146)
Q Consensus 36 iyE~VA~~sl~n~Ll-Ky-saKeyffkA~LC~L~~-D-~v~a~~ale~Y~~~DPsF~~SRE~klL~~LieAve~~ 106 (146)
..+.+....++++.+ +- ...-..++.+.|.+.. . .+...-+++++.++--.|.+.+.++|+.+++..+..+
T Consensus 54 ~ld~~i~~~~~~~~~~r~~~~~~~il~l~~~el~~~~~~~p~~~vineaVelak~~~~~~~~~fVNaVLr~~~r~ 128 (129)
T cd00447 54 ELDDIISPLLKKWLLDRLDKVDRAILRLLLYELYQLLYDVPPPVAINEAVELAKRFGDDDSAKFVNGVLRRIAKE 128 (129)
T ss_pred HHHHHHHHHccCCChhhhhHHHHHHHHHHHHHHHhCcCCCCchhHHHHHHHHHHHHCCCCcchhHHHHHHHHhhc
Confidence 345555555555431 00 1345566777777765 3 2467778888888888888888889999998877543
No 102
>PRK00202 nusB transcription antitermination protein NusB; Reviewed
Probab=20.05 E-value=1.3e+02 Score=22.12 Aligned_cols=70 Identities=17% Similarity=0.266 Sum_probs=45.8
Q ss_pred HHHHHHHhh-cccchhhchhH-HhHHhHHHHHhc-chhHHHHHHhHHHhcCCCCccchHHHHHHHHHHHHhhc
Q psy16704 37 FYSTGKAAT-ENSLMKYNSKE-YFFKAGLCHLCI-DLLNCQQALSRYIDLSPAFQDTREYKFLLKLIESLEEE 106 (146)
Q Consensus 37 yE~VA~~sl-~n~LlKysaKe-yffkA~LC~L~~-D~v~a~~ale~Y~~~DPsF~~SRE~klL~~LieAve~~ 106 (146)
.+.+..+.+ +.++-+-+..+ -.|+-|+|++.. |.+...-+++++.++-..|.+....+|+.+++..+..+
T Consensus 59 lD~ii~~~l~~~~~~~l~~~~~~iLr~a~~Ell~~~~~p~~~vinEaV~lak~~~~~~~~~fVNaVLr~i~r~ 131 (137)
T PRK00202 59 LDELISPYLKDWTLERLDPVERAILRLALYELLFRDDVPYKVVINEAIELAKKFGDEDSHKFVNGVLDKIAKE 131 (137)
T ss_pred HHHHHHHHhcCCCHHHhhHHHHHHHHHHHHHHHhCCCCCCcchHHHHHHHHHHHCCCCcchhHHHHHHHHHHH
Confidence 344555555 22333322111 356666777766 55677778888888888888888889999988877654
No 103
>PF05529 Bap31: B-cell receptor-associated protein 31-like ; InterPro: IPR008417 Bap31 is a polytopic integral protein of the endoplasmic reticulum membrane and a substrate of caspase-8. Bap31 is cleaved within its cytosolic domain, generating pro-apoptotic p20 Bap31 [].; GO: 0006886 intracellular protein transport, 0005783 endoplasmic reticulum, 0016021 integral to membrane
Probab=20.02 E-value=2.5e+02 Score=21.96 Aligned_cols=16 Identities=25% Similarity=0.926 Sum_probs=13.7
Q ss_pred HHHHHHHHhhhhhhHH
Q psy16704 3 MVIFMLMLIPMAMPFR 18 (146)
Q Consensus 3 ~~~~~~~~~~~~~~~~ 18 (146)
|+++.++++|...|.|
T Consensus 16 i~~~~lL~lPlp~~~R 31 (192)
T PF05529_consen 16 IAVLLLLVLPLPSPIR 31 (192)
T ss_pred HHHHHHHHHhCCcHHH
Confidence 6788889999998887
Done!