Query 030077
Match_columns 183
No_of_seqs 56 out of 58
Neff 2.9
Searched_HMMs 46136
Date Fri Mar 29 08:09:40 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030077.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030077hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG2608 CopZ Copper chaperone 99.7 5.4E-17 1.2E-21 114.2 7.6 68 99-171 3-70 (71)
2 PF00403 HMA: Heavy-metal-asso 99.7 2.3E-16 4.9E-21 104.9 6.4 62 101-167 1-62 (62)
3 PRK10671 copA copper exporting 98.6 4.6E-08 9.9E-13 93.9 6.5 63 99-171 4-66 (834)
4 TIGR00003 copper ion binding p 98.6 3.6E-07 7.7E-12 53.9 6.8 65 99-168 3-67 (68)
5 PLN02957 copper, zinc superoxi 98.3 2.3E-06 5E-11 72.1 7.9 66 98-172 6-71 (238)
6 COG2217 ZntA Cation transport 98.3 1.1E-06 2.5E-11 85.2 6.5 66 100-170 4-69 (713)
7 KOG4656 Copper chaperone for s 98.3 1.9E-06 4.1E-11 75.2 6.7 64 96-168 5-68 (247)
8 KOG1603 Copper chaperone [Inor 98.2 5.8E-06 1.2E-10 58.3 6.0 59 105-171 11-70 (73)
9 KOG0207 Cation transport ATPas 97.9 1.4E-05 3E-10 80.1 6.0 66 99-169 70-135 (951)
10 KOG0207 Cation transport ATPas 97.9 1.7E-05 3.7E-10 79.5 5.0 61 105-171 1-61 (951)
11 PRK11033 zntA zinc/cadmium/mer 97.7 0.0001 2.3E-09 70.9 7.4 70 94-170 49-118 (741)
12 PRK10671 copA copper exporting 97.4 0.0003 6.4E-09 68.1 6.7 64 98-169 99-162 (834)
13 TIGR02052 MerP mercuric transp 96.2 0.038 8.3E-07 36.3 7.1 65 99-168 24-88 (92)
14 TIGR00268 conserved hypothetic 94.6 0.062 1.3E-06 45.3 4.8 61 113-174 187-247 (252)
15 PRK13748 putative mercuric red 91.8 0.44 9.6E-06 43.4 6.2 63 102-170 4-66 (561)
16 PF01206 TusA: Sulfurtransfera 90.4 0.49 1.1E-05 32.2 3.8 57 101-172 2-58 (70)
17 cd00371 HMA Heavy-metal-associ 89.1 2 4.3E-05 22.1 5.6 41 103-143 3-43 (63)
18 PRK11018 hypothetical protein; 84.1 3.4 7.4E-05 29.6 5.3 56 101-171 10-65 (78)
19 PF13732 DUF4162: Domain of un 81.2 7 0.00015 26.9 5.9 46 120-173 26-71 (84)
20 cd03421 SirA_like_N SirA_like_ 78.0 3.9 8.5E-05 27.7 3.7 53 102-170 2-54 (67)
21 cd03423 SirA SirA (also known 77.8 8.1 0.00018 26.7 5.3 56 102-172 2-57 (69)
22 cd03422 YedF YedF is a bacteri 77.4 5.3 0.00011 27.8 4.3 56 102-172 2-57 (69)
23 cd00291 SirA_YedF_YeeD SirA, Y 76.7 6.8 0.00015 26.1 4.6 55 102-171 2-56 (69)
24 PF02120 Flg_hook: Flagellar h 76.6 5.6 0.00012 27.6 4.3 52 127-178 27-81 (85)
25 COG1606 ATP-utilizing enzymes 76.1 4 8.6E-05 36.9 4.2 56 118-174 198-253 (269)
26 smart00362 RRM_2 RNA recogniti 75.7 15 0.00033 22.2 6.1 46 102-147 2-51 (72)
27 cd04883 ACT_AcuB C-terminal AC 74.9 21 0.00045 23.4 7.2 63 102-170 4-70 (72)
28 PF09580 Spore_YhcN_YlaJ: Spor 74.9 9.7 0.00021 30.1 5.7 35 111-145 75-109 (177)
29 cd04888 ACT_PheB-BS C-terminal 72.9 9.3 0.0002 25.3 4.5 36 96-131 39-74 (76)
30 cd03420 SirA_RHOD_Pry_redox Si 72.4 10 0.00022 26.3 4.6 56 102-172 2-57 (69)
31 PRK09577 multidrug efflux prot 70.7 9.4 0.0002 38.8 5.8 57 112-168 157-213 (1032)
32 PF01883 DUF59: Domain of unkn 67.7 4.8 0.00011 27.5 2.2 36 96-131 34-72 (72)
33 TIGR02990 ectoine_eutA ectoine 66.9 8.9 0.00019 32.9 4.2 59 106-179 101-160 (239)
34 COG0425 SirA Predicted redox p 66.4 34 0.00074 24.9 6.5 59 99-172 5-64 (78)
35 PF02680 DUF211: Uncharacteriz 65.9 43 0.00093 26.2 7.3 56 109-171 15-77 (95)
36 cd04909 ACT_PDH-BS C-terminal 65.0 35 0.00075 22.4 5.9 60 102-168 4-69 (69)
37 PRK00299 sulfur transfer prote 64.6 30 0.00066 24.9 6.0 58 100-172 10-67 (81)
38 PF01709 Transcrip_reg: Transc 64.4 11 0.00024 32.4 4.3 50 115-175 148-197 (234)
39 COG2151 PaaD Predicted metal-s 64.1 6.6 0.00014 30.9 2.6 21 113-133 69-89 (111)
40 PRK10503 multidrug efflux syst 61.9 19 0.00042 36.7 6.1 81 85-165 134-221 (1040)
41 PRK00435 ef1B elongation facto 60.6 17 0.00037 27.5 4.2 39 93-133 46-84 (88)
42 TIGR03527 selenium_YedF seleni 60.6 12 0.00026 31.4 3.7 54 103-171 2-55 (194)
43 PF03927 NapD: NapD protein; 58.9 32 0.00068 25.0 5.2 57 112-176 16-74 (79)
44 PF08777 RRM_3: RNA binding mo 58.4 27 0.00058 26.5 5.0 58 101-164 3-60 (105)
45 TIGR00489 aEF-1_beta translati 56.8 23 0.0005 26.8 4.3 39 93-133 46-84 (88)
46 COG1888 Uncharacterized protei 55.4 64 0.0014 25.5 6.6 62 102-170 10-78 (97)
47 PF14437 MafB19-deam: MafB19-l 55.3 23 0.00049 29.4 4.4 38 99-137 101-139 (146)
48 PF11210 DUF2996: Protein of u 54.2 12 0.00026 30.2 2.6 29 107-136 10-38 (119)
49 PRK10555 aminoglycoside/multid 53.8 17 0.00038 37.0 4.2 55 110-164 156-210 (1037)
50 PF03698 UPF0180: Uncharacteri 53.1 11 0.00024 28.2 2.1 20 153-172 9-28 (80)
51 cd04874 ACT_Af1403 N-terminal 52.8 41 0.00088 21.3 4.5 33 96-131 39-71 (72)
52 TIGR02945 SUF_assoc FeS assemb 52.6 34 0.00073 24.8 4.5 39 96-134 37-78 (99)
53 PF08262 Lem_TRP: Leucophaea m 52.1 5.4 0.00012 20.0 0.2 7 51-57 4-10 (10)
54 COG0217 Uncharacterized conser 51.0 17 0.00036 32.4 3.2 47 115-172 152-198 (241)
55 TIGR02898 spore_YhcN_YlaJ spor 50.9 47 0.001 27.4 5.6 51 111-162 54-104 (158)
56 PRK03094 hypothetical protein; 49.2 15 0.00032 27.8 2.2 21 153-173 9-29 (80)
57 PF00873 ACR_tran: AcrB/AcrD/A 48.9 12 0.00027 37.4 2.3 85 86-170 123-216 (1021)
58 PRK04435 hypothetical protein; 48.4 35 0.00076 27.1 4.4 36 96-131 108-143 (147)
59 PRK10553 assembly protein for 47.8 44 0.00096 25.1 4.6 56 113-175 19-76 (87)
60 cd04902 ACT_3PGDH-xct C-termin 47.3 44 0.00096 21.7 4.1 33 95-131 38-70 (73)
61 PRK15127 multidrug efflux syst 47.2 44 0.00095 34.3 5.9 56 109-164 155-210 (1049)
62 PRK00110 hypothetical protein; 46.8 33 0.00072 30.0 4.4 50 116-176 151-200 (245)
63 TIGR03406 FeS_long_SufT probab 46.0 20 0.00042 29.9 2.7 22 113-134 133-154 (174)
64 cd04882 ACT_Bt0572_2 C-termina 45.3 41 0.0009 21.3 3.7 50 111-168 11-64 (65)
65 cd04886 ACT_ThrD-II-like C-ter 45.0 77 0.0017 19.9 6.8 62 105-169 4-72 (73)
66 cd02410 archeal_CPSF_KH The ar 44.8 58 0.0012 27.1 5.2 60 109-169 51-110 (145)
67 cd04908 ACT_Bt0572_1 N-termina 43.6 95 0.0021 20.5 6.3 58 104-169 6-65 (66)
68 cd00292 EF1B Elongation factor 42.3 52 0.0011 24.7 4.3 39 93-133 46-84 (88)
69 PF08002 DUF1697: Protein of u 42.3 42 0.0009 26.5 3.9 59 113-176 21-80 (137)
70 TIGR00915 2A0602 The (Largely 42.1 31 0.00067 35.3 3.9 54 111-164 157-210 (1044)
71 TIGR02830 spore_III_AG stage I 41.7 22 0.00047 30.2 2.4 29 112-140 62-92 (186)
72 cd04879 ACT_3PGDH-like ACT_3PG 40.0 56 0.0012 20.3 3.6 31 96-130 39-69 (71)
73 PRK09579 multidrug efflux prot 39.1 88 0.0019 32.1 6.5 78 87-164 126-210 (1017)
74 COG2092 EFB1 Translation elong 39.0 47 0.001 25.6 3.6 29 104-132 55-83 (88)
75 PRK14054 methionine sulfoxide 38.2 69 0.0015 26.8 4.8 44 111-159 11-73 (172)
76 cd04906 ACT_ThrD-I_1 First of 38.0 1.3E+02 0.0027 21.3 5.5 18 154-171 55-72 (85)
77 COG0841 AcrB Cation/multidrug 38.0 1.1E+02 0.0024 31.9 7.1 83 85-167 123-212 (1009)
78 PF00736 EF1_GNE: EF-1 guanine 37.1 85 0.0018 23.5 4.7 39 93-133 46-85 (89)
79 PF13399 LytR_C: LytR cell env 36.8 43 0.00093 23.6 3.0 21 151-171 15-35 (90)
80 PRK10614 multidrug efflux syst 36.2 1.4E+02 0.0029 30.7 7.3 80 87-166 127-213 (1025)
81 PF03780 Asp23: Asp23 family; 35.9 69 0.0015 23.1 4.0 50 128-177 49-106 (108)
82 PF00564 PB1: PB1 domain; Int 34.4 45 0.00097 22.8 2.7 48 128-181 3-52 (84)
83 cd01812 BAG1_N Ubiquitin-like 34.2 69 0.0015 21.1 3.5 43 129-177 3-46 (71)
84 PF01514 YscJ_FliF: Secretory 33.9 43 0.00094 28.1 3.0 21 114-134 118-138 (206)
85 PRK10614 multidrug efflux syst 32.0 78 0.0017 32.3 4.9 64 99-164 46-115 (1025)
86 PRK13558 bacterio-opsin activa 31.1 3E+02 0.0064 25.7 8.1 63 96-170 485-548 (665)
87 PF04324 Fer2_BFD: BFD-like [2 31.0 17 0.00036 24.0 0.1 17 106-122 37-53 (55)
88 PRK13835 conjugal transfer pro 30.8 27 0.0006 28.9 1.3 41 126-170 47-87 (145)
89 cd00590 RRM RRM (RNA recogniti 30.8 1.3E+02 0.0027 18.2 6.4 46 102-147 2-52 (74)
90 PRK07334 threonine dehydratase 29.6 3.9E+02 0.0085 24.2 8.5 70 97-169 324-400 (403)
91 cd04878 ACT_AHAS N-terminal AC 29.0 1.1E+02 0.0023 19.1 3.6 32 96-129 40-71 (72)
92 TIGR02544 III_secr_YscJ type I 28.1 54 0.0012 27.4 2.6 21 114-134 110-130 (193)
93 TIGR00119 acolac_sm acetolacta 27.7 3.4E+02 0.0074 22.2 9.1 70 96-172 41-115 (157)
94 TIGR01709 typeII_sec_gspL gene 27.6 1.6E+02 0.0036 26.1 5.7 60 114-178 313-374 (384)
95 PF13489 Methyltransf_23: Meth 27.4 61 0.0013 23.6 2.5 18 153-170 143-160 (161)
96 cd04903 ACT_LSD C-terminal ACT 27.2 1.4E+02 0.003 18.6 3.9 29 99-131 42-70 (71)
97 TIGR01033 DNA-binding regulato 26.7 96 0.0021 27.0 4.0 51 116-177 153-203 (238)
98 TIGR03028 EpsE polysaccharide 26.7 2.9E+02 0.0062 23.3 6.7 76 89-165 23-109 (239)
99 PF13893 RRM_5: RNA recognitio 26.7 1.4E+02 0.003 18.9 3.8 50 117-172 2-52 (56)
100 PRK12378 hypothetical protein; 26.6 85 0.0018 27.4 3.6 51 117-176 149-199 (235)
101 TIGR03675 arCOG00543 arCOG0054 26.4 1.2E+02 0.0027 29.8 5.0 61 108-169 67-127 (630)
102 PF00873 ACR_tran: AcrB/AcrD/A 26.2 40 0.00087 33.9 1.8 68 96-163 669-741 (1021)
103 PF14794 DUF4479: Domain of un 25.7 31 0.00067 25.2 0.7 25 137-168 43-67 (73)
104 PF09122 DUF1930: Domain of un 25.7 94 0.002 23.2 3.2 43 99-141 20-62 (68)
105 PRK15078 polysaccharide export 25.3 1.5E+02 0.0032 27.3 5.0 76 91-166 119-203 (379)
106 PF08478 POTRA_1: POTRA domain 24.8 90 0.002 20.5 2.8 30 112-141 35-65 (69)
107 COG1251 NirB NAD(P)H-nitrite r 24.7 61 0.0013 33.4 2.7 50 106-167 447-496 (793)
108 cd04876 ACT_RelA-SpoT ACT dom 24.6 1.5E+02 0.0032 17.4 3.5 32 98-130 39-70 (71)
109 PF11873 DUF3393: Domain of un 24.1 1.3E+02 0.0028 25.9 4.2 32 127-163 88-119 (204)
110 PRK10629 EnvZ/OmpR regulon mod 24.0 3.6E+02 0.0078 21.4 6.5 36 111-147 50-85 (127)
111 PF11543 UN_NPL4: Nuclear pore 23.5 93 0.002 22.6 2.8 42 129-176 7-49 (80)
112 PRK11152 ilvM acetolactate syn 23.4 2.4E+02 0.0053 20.5 5.0 33 96-131 43-75 (76)
113 smart00213 UBQ Ubiquitin homol 23.4 1.4E+02 0.0031 18.7 3.4 42 129-176 3-45 (64)
114 PF00076 RRM_1: RNA recognitio 22.7 2E+02 0.0044 17.9 6.3 44 104-147 3-51 (70)
115 TIGR00914 2A0601 heavy metal e 22.3 76 0.0017 32.4 2.9 63 100-163 684-752 (1051)
116 PRK05528 methionine sulfoxide 22.1 2E+02 0.0043 23.8 4.8 37 111-147 9-59 (156)
117 smart00360 RRM RNA recognition 21.8 1.9E+02 0.0041 17.1 4.9 43 105-147 2-50 (71)
118 cd01808 hPLIC_N Ubiquitin-like 21.7 1.1E+02 0.0025 20.6 2.9 43 129-177 3-46 (71)
119 PRK00194 hypothetical protein; 21.6 1.3E+02 0.0027 21.0 3.1 40 95-134 40-79 (90)
120 PRK15348 type III secretion sy 21.5 85 0.0018 27.8 2.7 21 114-134 110-130 (249)
121 TIGR02374 nitri_red_nirB nitri 21.2 59 0.0013 32.1 1.8 51 106-167 445-495 (785)
122 cd01804 midnolin_N Ubiquitin-l 21.2 1.3E+02 0.0028 21.1 3.1 43 129-177 4-48 (78)
123 PF02682 AHS1: Allophanate hyd 21.2 2.2E+02 0.0049 23.8 5.0 61 111-178 25-97 (202)
124 PRK10598 lipoprotein; Provisio 21.1 62 0.0013 27.6 1.7 53 122-176 47-99 (186)
125 PRK10509 bacterioferritin-asso 21.0 62 0.0013 22.8 1.4 18 106-123 36-53 (64)
126 TIGR00412 redox_disulf_2 small 20.9 1.5E+02 0.0032 20.4 3.3 25 100-124 1-28 (76)
127 PF01625 PMSR: Peptide methion 20.7 3.5E+02 0.0076 22.0 6.0 37 111-147 8-63 (155)
128 cd01806 Nedd8 Nebb8-like ubiq 20.5 1.1E+02 0.0025 20.2 2.6 44 129-178 3-48 (76)
129 COG0527 LysC Aspartokinases [A 20.3 4.3E+02 0.0094 25.1 7.2 74 95-172 345-418 (447)
130 PF10865 DUF2703: Domain of un 20.1 1.6E+02 0.0035 23.4 3.7 20 102-121 8-27 (120)
No 1
>COG2608 CopZ Copper chaperone [Inorganic ion transport and metabolism]
Probab=99.70 E-value=5.4e-17 Score=114.18 Aligned_cols=68 Identities=21% Similarity=0.458 Sum_probs=62.1
Q ss_pred EEEEEEecCCCcccHHHHHHhhccCCCceeeEEEEeccEEEEEeccceeeecccchHHHHHHHHhcCceeEee
Q 030077 99 TMYFQADGAMNETAIPAVTQALQGTEGISDLKVQVIEGIATVELKKQTTVQATGVAANLVEIIQGSGFKLQTL 171 (183)
Q Consensus 99 tM~FKaEGM~Ce~Ci~~VtkALE~ieGVsdVkV~LeeG~AtVe~dkqttvqatgvas~LvEaIe~aGFkVq~l 171 (183)
.+.|+++||+|+||+.+|+++|++++||.+++|+|+.|.+.|.++.... ....|+++|+++||++...
T Consensus 3 ~~~l~v~~MtC~~C~~~V~~al~~v~gv~~v~v~l~~~~~~V~~d~~~~-----~~~~i~~ai~~aGy~~~~~ 70 (71)
T COG2608 3 KTTLKVEGMTCGHCVKTVEKALEEVDGVASVDVDLEKGTATVTFDSNKV-----DIEAIIEAIEDAGYKVEEI 70 (71)
T ss_pred eEEEEECCcCcHHHHHHHHHHHhcCCCeeEEEEEcccCeEEEEEcCCcC-----CHHHHHHHHHHcCCCeeec
Confidence 3569999999999999999999999999999999999999999999544 3699999999999998653
No 2
>PF00403 HMA: Heavy-metal-associated domain; InterPro: IPR006121 Proteins that transport heavy metals in micro-organisms and mammals share similarities in their sequences and structures. These proteins provide an important focus for research, some being involved in bacterial resistance to toxic metals, such as lead and cadmium, while others are involved in inherited human syndromes, such as Wilson's and Menke's diseases []. A conserved domain has been found in a number of these heavy metal transport or detoxification proteins []. The domain, which has been termed Heavy-Metal-Associated (HMA), contains two conserved cysteines that are probably involved in metal binding. Structure solution of the fourth HMA domain of the Menke's copper transporting ATPase shows a well-defined structure comprising a four-stranded antiparallel beta-sheet and two alpha helices packed in an alpha-beta sandwich fold []. This fold is common to other domains and is classified as "ferredoxin-like".; GO: 0046872 metal ion binding, 0030001 metal ion transport; PDB: 2VOY_A 1P6T_A 1KQK_A 2RML_A 1JWW_A 3K7R_F 1FES_A 1CC8_A 1FD8_A 2GGP_A ....
Probab=99.66 E-value=2.3e-16 Score=104.90 Aligned_cols=62 Identities=24% Similarity=0.387 Sum_probs=58.8
Q ss_pred EEEEecCCCcccHHHHHHhhccCCCceeeEEEEeccEEEEEeccceeeecccchHHHHHHHHhcCce
Q 030077 101 YFQADGAMNETAIPAVTQALQGTEGISDLKVQVIEGIATVELKKQTTVQATGVAANLVEIIQGSGFK 167 (183)
Q Consensus 101 ~FKaEGM~Ce~Ci~~VtkALE~ieGVsdVkV~LeeG~AtVe~dkqttvqatgvas~LvEaIe~aGFk 167 (183)
+|+|+||.|++|+.+|+++|.+++||.+++|++..+.++|.++++.. .++.|+++|+++||+
T Consensus 1 t~~v~~m~C~~C~~~v~~~l~~~~GV~~v~vd~~~~~v~v~~~~~~~-----~~~~i~~~i~~~Gy~ 62 (62)
T PF00403_consen 1 TFKVPGMTCEGCAKKVEKALSKLPGVKSVKVDLETKTVTVTYDPDKT-----SIEKIIEAIEKAGYE 62 (62)
T ss_dssp EEEEESTTSHHHHHHHHHHHHTSTTEEEEEEETTTTEEEEEESTTTS-----CHHHHHHHHHHTTSE
T ss_pred CEEECCcccHHHHHHHHHHHhcCCCCcEEEEECCCCEEEEEEecCCC-----CHHHHHHHHHHhCcC
Confidence 58999999999999999999999999999999999999999998874 469999999999996
No 3
>PRK10671 copA copper exporting ATPase; Provisional
Probab=98.64 E-value=4.6e-08 Score=93.93 Aligned_cols=63 Identities=22% Similarity=0.332 Sum_probs=53.5
Q ss_pred EEEEEEecCCCcccHHHHHHhhccCCCceeeEEEEeccEEEEEeccceeeecccchHHHHHHHHhcCceeEee
Q 030077 99 TMYFQADGAMNETAIPAVTQALQGTEGISDLKVQVIEGIATVELKKQTTVQATGVAANLVEIIQGSGFKLQTL 171 (183)
Q Consensus 99 tM~FKaEGM~Ce~Ci~~VtkALE~ieGVsdVkV~LeeG~AtVe~dkqttvqatgvas~LvEaIe~aGFkVq~l 171 (183)
+..|+|+||+|.+|+.+|+++|++++||.+++|++.. +.++.+ . ....|.++|+++||++..+
T Consensus 4 ~~~l~V~gmtC~~C~~~i~~al~~~~gv~~v~v~~~~--~~v~~~--~------~~~~i~~~i~~~Gy~~~~~ 66 (834)
T PRK10671 4 TIDLTLDGLSCGHCVKRVKESLEQRPDVEQADVSITE--AHVTGT--A------SAEALIETIKQAGYDASVS 66 (834)
T ss_pred EEEEEECCcccHHHHHHHHHHHhcCCCcceEEEeeeE--EEEEec--C------CHHHHHHHHHhcCCccccc
Confidence 5679999999999999999999999999999999954 444331 2 4589999999999998764
No 4
>TIGR00003 copper ion binding protein. This model describes an apparently copper-specific subfamily of the metal-binding domain HMA (Pfam family pfam00403). Closely related sequences outside this model include mercury resistance proteins and repeated domains of eukaryotic eukaryotic copper transport proteins. Members of this family are strictly prokaryotic. The model identifies both small proteins consisting of just this domain and N-terminal regions of cation (probably copper) transporting ATPases.
Probab=98.58 E-value=3.6e-07 Score=53.88 Aligned_cols=65 Identities=15% Similarity=0.289 Sum_probs=56.0
Q ss_pred EEEEEEecCCCcccHHHHHHhhccCCCceeeEEEEeccEEEEEeccceeeecccchHHHHHHHHhcCcee
Q 030077 99 TMYFQADGAMNETAIPAVTQALQGTEGISDLKVQVIEGIATVELKKQTTVQATGVAANLVEIIQGSGFKL 168 (183)
Q Consensus 99 tM~FKaEGM~Ce~Ci~~VtkALE~ieGVsdVkV~LeeG~AtVe~dkqttvqatgvas~LvEaIe~aGFkV 168 (183)
++.|.++||.|..|...+++++...+|+....+++..+.+.+.+++... ....+...+++.||.+
T Consensus 3 ~~~~~v~~~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~g~~~ 67 (68)
T TIGR00003 3 KFTVQVMSMTCQHCVDKIEKFVGELEGVSKVQVKLEKASVKVEFDAPQA-----TEICIAEAILDAGYEV 67 (68)
T ss_pred EEEEEECCeEcHHHHHHHHHHHhcCCCEEEEEEEcCCCEEEEEeCCCCC-----CHHHHHHHHHHcCCCc
Confidence 4569999999999999999999999999999999999999999875432 2467778889999975
No 5
>PLN02957 copper, zinc superoxide dismutase
Probab=98.31 E-value=2.3e-06 Score=72.14 Aligned_cols=66 Identities=18% Similarity=0.265 Sum_probs=57.3
Q ss_pred eEEEEEEecCCCcccHHHHHHhhccCCCceeeEEEEeccEEEEEeccceeeecccchHHHHHHHHhcCceeEeee
Q 030077 98 LTMYFQADGAMNETAIPAVTQALQGTEGISDLKVQVIEGIATVELKKQTTVQATGVAANLVEIIQGSGFKLQTLN 172 (183)
Q Consensus 98 ltM~FKaEGM~Ce~Ci~~VtkALE~ieGVsdVkV~LeeG~AtVe~dkqttvqatgvas~LvEaIe~aGFkVq~l~ 172 (183)
..|.|++ ||.|+.|+.+|+++|.+++||..+.+++..+.+.|++. . ....+.++|++.||++.-+.
T Consensus 6 ~~~~~~V-gMsC~~Ca~~Iek~L~~~~GV~~v~vn~~~~~v~V~~~--~------~~~~I~~aIe~~Gy~a~~~~ 71 (238)
T PLN02957 6 LLTEFMV-DMKCEGCVAAVKNKLETLEGVKAVEVDLSNQVVRVLGS--S------PVKAMTAALEQTGRKARLIG 71 (238)
T ss_pred EEEEEEE-CccCHHHHHHHHHHHhcCCCeEEEEEEcCCCEEEEEec--C------CHHHHHHHHHHcCCcEEEec
Confidence 4566888 79999999999999999999999999999999999872 1 35789999999999975443
No 6
>COG2217 ZntA Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=98.30 E-value=1.1e-06 Score=85.22 Aligned_cols=66 Identities=17% Similarity=0.314 Sum_probs=59.5
Q ss_pred EEEEEecCCCcccHHHHHHhhccCCCceeeEEEEeccEEEEEeccceeeecccchHHHHHHHHhcCceeEe
Q 030077 100 MYFQADGAMNETAIPAVTQALQGTEGISDLKVQVIEGIATVELKKQTTVQATGVAANLVEIIQGSGFKLQT 170 (183)
Q Consensus 100 M~FKaEGM~Ce~Ci~~VtkALE~ieGVsdVkV~LeeG~AtVe~dkqttvqatgvas~LvEaIe~aGFkVq~ 170 (183)
..|.++||+|..|+.+|+ +|.+++||.++.|++....+.|.+++.... ..+.+..+|++.||....
T Consensus 4 ~~l~v~Gm~Ca~C~~~ie-~l~~~~gV~~~~vn~~t~~~~v~~~~~~~~----~~~~~~~~v~~~gy~~~~ 69 (713)
T COG2217 4 TSLSVEGMTCAACASRIE-ALNKLPGVEEARVNLATERATVVYDPEEVD----LPADIVAAVEKAGYSARL 69 (713)
T ss_pred eEEeecCcCcHHHHHHHH-HHhcCCCeeEEEeecccceEEEEecccccc----cHHHHHHHHHhcCccccc
Confidence 469999999999999999 999999999999999999999999976541 268999999999998764
No 7
>KOG4656 consensus Copper chaperone for superoxide dismutase [Inorganic ion transport and metabolism]
Probab=98.28 E-value=1.9e-06 Score=75.19 Aligned_cols=64 Identities=22% Similarity=0.374 Sum_probs=54.4
Q ss_pred CceEEEEEEecCCCcccHHHHHHhhccCCCceeeEEEEeccEEEEEeccceeeecccchHHHHHHHHhcCcee
Q 030077 96 DKLTMYFQADGAMNETAIPAVTQALQGTEGISDLKVQVIEGIATVELKKQTTVQATGVAANLVEIIQGSGFKL 168 (183)
Q Consensus 96 ~~ltM~FKaEGM~Ce~Ci~~VtkALE~ieGVsdVkV~LeeG~AtVe~dkqttvqatgvas~LvEaIe~aGFkV 168 (183)
|.+...|-|. |+||.|+..|+++|++++||.+|.|+|+++.+.|+-.- ..+.|.++|+..|=+.
T Consensus 5 ~~~~~efaV~-M~cescvnavk~~L~~V~Gi~~vevdle~q~v~v~ts~--------p~s~i~~~le~tGr~A 68 (247)
T KOG4656|consen 5 DTYEAEFAVQ-MTCESCVNAVKACLKGVPGINSVEVDLEQQIVSVETSV--------PPSEIQNTLENTGRDA 68 (247)
T ss_pred CceeEEEEEe-chhHHHHHHHHHHhccCCCcceEEEEhhhcEEEEEccC--------ChHHHHHHHHhhChhe
Confidence 5677778775 89999999999999999999999999999999977532 3578888888888654
No 8
>KOG1603 consensus Copper chaperone [Inorganic ion transport and metabolism]
Probab=98.17 E-value=5.8e-06 Score=58.27 Aligned_cols=59 Identities=15% Similarity=0.211 Sum_probs=51.4
Q ss_pred ecCCCcccHHHHHHhhccCCCceeeEEEEeccEEEEEeccceeeecccchHHHHHHHHhcC-ceeEee
Q 030077 105 DGAMNETAIPAVTQALQGTEGISDLKVQVIEGIATVELKKQTTVQATGVAANLVEIIQGSG-FKLQTL 171 (183)
Q Consensus 105 EGM~Ce~Ci~~VtkALE~ieGVsdVkV~LeeG~AtVe~dkqttvqatgvas~LvEaIe~aG-FkVq~l 171 (183)
=.|.|++|..+|+++|..++||.++++++.+++.+|.-. . .++.|.+.|++.| .+...+
T Consensus 11 v~~~C~gc~~kV~~~l~~~~GV~~v~id~~~~kvtV~g~--~------~p~~vl~~l~k~~~k~~~~~ 70 (73)
T KOG1603|consen 11 VNMHCEGCARKVKRVLQKLKGVESVDIDIKKQKVTVKGN--V------DPVKLLKKLKKTGGKRAELW 70 (73)
T ss_pred ECcccccHHHHHHHHhhccCCeEEEEecCCCCEEEEEEe--c------CHHHHHHHHHhcCCCceEEe
Confidence 379999999999999999999999999999999998776 2 4689999999988 665543
No 9
>KOG0207 consensus Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=97.94 E-value=1.4e-05 Score=80.15 Aligned_cols=66 Identities=20% Similarity=0.351 Sum_probs=63.3
Q ss_pred EEEEEEecCCCcccHHHHHHhhccCCCceeeEEEEeccEEEEEeccceeeecccchHHHHHHHHhcCceeE
Q 030077 99 TMYFQADGAMNETAIPAVTQALQGTEGISDLKVQVIEGIATVELKKQTTVQATGVAANLVEIIQGSGFKLQ 169 (183)
Q Consensus 99 tM~FKaEGM~Ce~Ci~~VtkALE~ieGVsdVkV~LeeG~AtVe~dkqttvqatgvas~LvEaIe~aGFkVq 169 (183)
+-+|.+.||+|-.|+..+++-|+.++||..+.|.|..+.+.+.+|+.++ ..+.+.+.|++.||+..
T Consensus 70 ~~~l~v~GmtC~scv~~i~~~l~~~~gv~~~~val~~~~~~v~~dp~v~-----s~~~~~e~ie~~gf~a~ 135 (951)
T KOG0207|consen 70 KCYLSVNGMTCASCVATIERNLRKIEGVESAVVALSASKAEVIYDPAVT-----SPDSIAESIEDLGFSAE 135 (951)
T ss_pred eeEEEecCceeHHHHHHHHHHhhccCCcceEEEEeeccceeEEECCccc-----CchhHHHHHHhcCccce
Confidence 7789999999999999999999999999999999999999999999998 79999999999999765
No 10
>KOG0207 consensus Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=97.86 E-value=1.7e-05 Score=79.54 Aligned_cols=61 Identities=18% Similarity=0.339 Sum_probs=56.1
Q ss_pred ecCCCcccHHHHHHhhccCCCceeeEEEEeccEEEEEeccceeeecccchHHHHHHHHhcCceeEee
Q 030077 105 DGAMNETAIPAVTQALQGTEGISDLKVQVIEGIATVELKKQTTVQATGVAANLVEIIQGSGFKLQTL 171 (183)
Q Consensus 105 EGM~Ce~Ci~~VtkALE~ieGVsdVkV~LeeG~AtVe~dkqttvqatgvas~LvEaIe~aGFkVq~l 171 (183)
.||+|..|+..+.+++...+||.++.|+|..+.+.|.|+ ... .++.|+++|+++||+..-+
T Consensus 1 ~gmtc~ac~~si~~~~~~~~g~~~i~vsl~~~~~~v~~~-~~~-----~~~~i~~~ied~gf~~~~~ 61 (951)
T KOG0207|consen 1 KGMTCSACSNSIEKAISRKPGVQKIEVSLAQKRANVSYD-NIV-----SPESIKETIEDMGFEASLL 61 (951)
T ss_pred CCccHHHHhhhHHHHHhcCCCceeEEEEeccccceEEEe-ecc-----CHHHHHHHhhcccceeeec
Confidence 599999999999999999999999999999999999999 444 5899999999999987644
No 11
>PRK11033 zntA zinc/cadmium/mercury/lead-transporting ATPase; Provisional
Probab=97.69 E-value=0.0001 Score=70.95 Aligned_cols=70 Identities=16% Similarity=0.238 Sum_probs=59.6
Q ss_pred CCCceEEEEEEecCCCcccHHHHHHhhccCCCceeeEEEEeccEEEEEeccceeeecccchHHHHHHHHhcCceeEe
Q 030077 94 PSDKLTMYFQADGAMNETAIPAVTQALQGTEGISDLKVQVIEGIATVELKKQTTVQATGVAANLVEIIQGSGFKLQT 170 (183)
Q Consensus 94 ~~~~ltM~FKaEGM~Ce~Ci~~VtkALE~ieGVsdVkV~LeeG~AtVe~dkqttvqatgvas~LvEaIe~aGFkVq~ 170 (183)
+++.-+..|+++||.|.+|+.+++++|+.++||.+++|++..+.+.+.+++.. . +.+.+++++.||.+..
T Consensus 49 ~~~~~r~~l~V~Gm~C~sCa~~Ie~aL~~~~GV~~v~Vn~at~k~~V~~d~~~------~-~~I~~aI~~~Gy~a~~ 118 (741)
T PRK11033 49 LVSGTRYSWKVSGMDCPSCARKVENAVRQLAGVNQVQVLFATEKLVVDADNDI------R-AQVESAVQKAGFSLRD 118 (741)
T ss_pred cCCCceEEEEECCCCcHHHHHHHHHHHhcCCCeeeEEEEcCCCeEEEEecccc------h-HHHHHHHHhccccccc
Confidence 34455677889999999999999999999999999999999999998886541 2 6788899999998754
No 12
>PRK10671 copA copper exporting ATPase; Provisional
Probab=97.44 E-value=0.0003 Score=68.10 Aligned_cols=64 Identities=20% Similarity=0.316 Sum_probs=55.4
Q ss_pred eEEEEEEecCCCcccHHHHHHhhccCCCceeeEEEEeccEEEEEeccceeeecccchHHHHHHHHhcCceeE
Q 030077 98 LTMYFQADGAMNETAIPAVTQALQGTEGISDLKVQVIEGIATVELKKQTTVQATGVAANLVEIIQGSGFKLQ 169 (183)
Q Consensus 98 ltM~FKaEGM~Ce~Ci~~VtkALE~ieGVsdVkV~LeeG~AtVe~dkqttvqatgvas~LvEaIe~aGFkVq 169 (183)
-++.+.++||.|.+|+..++++|+.++||.+++|++..+.+.+.. .. ....+.+.|++.||...
T Consensus 99 ~~~~l~V~Gm~Ca~Ca~~Ie~~L~~~~GV~~a~vnl~t~~~~V~~--~~------s~~~I~~~I~~~Gy~a~ 162 (834)
T PRK10671 99 DSQQLLLSGMSCASCVSRVQNALQSVPGVTQARVNLAERTALVMG--SA------SPQDLVQAVEKAGYGAE 162 (834)
T ss_pred ceEEEEeCCcCcHHHHHHHHHHHhcCCCceeeeeecCCCeEEEEc--cC------CHHHHHHHHHhcCCCcc
Confidence 367899999999999999999999999999999999999988762 11 35778899999999864
No 13
>TIGR02052 MerP mercuric transport protein periplasmic component. This model represents the periplasmic mercury (II) binding protein of the bacterial mercury detoxification system which passes mercuric ion to the MerT transporter for subsequent reduction to Hg(0) by the mercuric reductase MerA. MerP contains a distinctive GMTCXXC motif associated with metal binding. MerP is related to a larger family of metal binding proteins (pfam00403).
Probab=96.19 E-value=0.038 Score=36.29 Aligned_cols=65 Identities=22% Similarity=0.288 Sum_probs=50.1
Q ss_pred EEEEEEecCCCcccHHHHHHhhccCCCceeeEEEEeccEEEEEeccceeeecccchHHHHHHHHhcCcee
Q 030077 99 TMYFQADGAMNETAIPAVTQALQGTEGISDLKVQVIEGIATVELKKQTTVQATGVAANLVEIIQGSGFKL 168 (183)
Q Consensus 99 tM~FKaEGM~Ce~Ci~~VtkALE~ieGVsdVkV~LeeG~AtVe~dkqttvqatgvas~LvEaIe~aGFkV 168 (183)
++.+.+.|+.|..|...++..+...+|+....+....+...+.++... .....+...+++.||.+
T Consensus 24 ~~~~~~~~~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~g~~~ 88 (92)
T TIGR02052 24 TVTLEVPGMTCVACPITVETALQKVDGVSKAEVTFKTKLAVVTFDDEK-----TNVKALTEATTDAGYPS 88 (92)
T ss_pred EEEEEECCeEcHHHHHHHHHHHhcCCCEEEEEEEecCCEEEEEECCCC-----CCHHHHHHHHHhcCCCe
Confidence 445778999999999999999999999999999988887666653321 23455666678888873
No 14
>TIGR00268 conserved hypothetical protein TIGR00268. The N-terminal region of the model shows similarity to Argininosuccinate synthase proteins using PSI-blast and using the recognize protein identification server.
Probab=94.57 E-value=0.062 Score=45.26 Aligned_cols=61 Identities=15% Similarity=0.366 Sum_probs=51.0
Q ss_pred HHHHHHhhccCCCceeeEEEEeccEEEEEeccceeeecccchHHHHHHHHhcCceeEeeecc
Q 030077 113 IPAVTQALQGTEGISDLKVQVIEGIATVELKKQTTVQATGVAANLVEIIQGSGFKLQTLNLS 174 (183)
Q Consensus 113 i~~VtkALE~ieGVsdVkV~LeeG~AtVe~dkqttvqatgvas~LvEaIe~aGFkVq~l~l~ 174 (183)
+....+.|..+ |.+++.|-..++.|++|+++.--..+......|...+.+.||+-++|.|.
T Consensus 187 v~~~E~~l~~~-g~~~~rvr~~~~~a~ie~~~~~~~~~~~~~~~i~~~~~~~gf~~v~ldl~ 247 (252)
T TIGR00268 187 VDEAEEVLRNA-GVGQVRVRNYDNLAVIEVPEDELSKLLNEAEEVRDKFKDIGFRKVLIDLE 247 (252)
T ss_pred HHHHHHHHHHc-CCCeEEEEecCCeEEEEECHHHHHHHHhhHHHHHHHHHHcCCCeEEEccC
Confidence 55677888886 99999999999999999988655444444688999999999999999874
No 15
>PRK13748 putative mercuric reductase; Provisional
Probab=91.84 E-value=0.44 Score=43.43 Aligned_cols=63 Identities=19% Similarity=0.347 Sum_probs=51.0
Q ss_pred EEEecCCCcccHHHHHHhhccCCCceeeEEEEeccEEEEEeccceeeecccchHHHHHHHHhcCceeEe
Q 030077 102 FQADGAMNETAIPAVTQALQGTEGISDLKVQVIEGIATVELKKQTTVQATGVAANLVEIIQGSGFKLQT 170 (183)
Q Consensus 102 FKaEGM~Ce~Ci~~VtkALE~ieGVsdVkV~LeeG~AtVe~dkqttvqatgvas~LvEaIe~aGFkVq~ 170 (183)
+.++||.|.+|..++++.+...+|+....+++..+...+.+.... ....+...+++.||....
T Consensus 4 i~i~g~~C~~c~~~ie~~l~~~~gv~~a~~~~~~~~~~v~~~~~~------~~~~i~~~i~~~g~~~~~ 66 (561)
T PRK13748 4 LKITGMTCDSCAAHVKDALEKVPGVQSADVSYPKGSAQLAIEVGT------SPDALTAAVAGLGYRATL 66 (561)
T ss_pred EEECCeecHHHHHHHHHHHhcCCCeeEEEEEcCCCEEEEEECCCC------CHHHHHHHHHHcCCeeec
Confidence 668999999999999999999999999999999988777764321 345666778889987543
No 16
>PF01206 TusA: Sulfurtransferase TusA; InterPro: IPR001455 SirA functions as a response regulator as part of a two-component system, where BarA is the sensor kinase. This system increases the expression of virulence genes and decreases the expression of motility genes []. BarA phosphorylates SirA, thereby activating the protein. Phosphorylated SirA directly activates virulence expression by interacting with hilA and hilC promoters, while repressing the flagellar regulon indirectly by binding to the csrB promoter, which in turn affects flagellar gene expression. Orthologues of SirA from Salmonella spp. can be found throughout proteobacteria, such as GacA in Psuedomonas spp., VarA in Vibrio cholerae, ExpA in Erwinia carotovora, LetA in Legionella pneumophila, and UvrY in Escherichia coli []. A sensor kinase for SirA is present in each of these organisms as well; the sensor kinase is known as BarA in E. coli and Salmonella spp., but has different names in other genera. In different species, SirA/BarA orthologues are required for virulence gene expression, exoenzyme and antibiotic production, motility, and biofilm formation. The structure of SirA consists of an alpha/beta sandwich with a beta-alpha-beta-alpha-beta(2) fold, comprising a mixed four-stranded beta-sheet stacked against two alpha-helices, both of which are nearly parallel to the strands of the beta-sheet []. Several uncharacterised bacterial proteins (73 to 81 amino-acid residues in length) that contain a well-conserved region in their N-terminal region show structural similarity to the SirA protein, including the E. coli protein YedF (P0AA31 from SWISSPROT), and other members of the UPF0033 family.; GO: 0016783 sulfurtransferase activity, 0008033 tRNA processing, 0005737 cytoplasm; PDB: 3LVJ_D 3LVK_B 1DCJ_A 3HZ7_A 1JDQ_A 1JE3_A 1PAV_A.
Probab=90.35 E-value=0.49 Score=32.20 Aligned_cols=57 Identities=9% Similarity=0.152 Sum_probs=44.0
Q ss_pred EEEEecCCCcccHHHHHHhhccCCCceeeEEEEeccEEEEEeccceeeecccchHHHHHHHHhcCceeEeee
Q 030077 101 YFQADGAMNETAIPAVTQALQGTEGISDLKVQVIEGIATVELKKQTTVQATGVAANLVEIIQGSGFKLQTLN 172 (183)
Q Consensus 101 ~FKaEGM~Ce~Ci~~VtkALE~ieGVsdVkV~LeeG~AtVe~dkqttvqatgvas~LvEaIe~aGFkVq~l~ 172 (183)
.+.+-|..|...+-+++++|++++.= ....|..+.+.. ...|....+..||++..++
T Consensus 2 ~lD~rg~~CP~Pll~~~~~l~~l~~G---------~~l~v~~d~~~~------~~di~~~~~~~g~~~~~~~ 58 (70)
T PF01206_consen 2 TLDLRGLSCPMPLLKAKKALKELPPG---------EVLEVLVDDPAA------VEDIPRWCEENGYEVVEVE 58 (70)
T ss_dssp EEECSS-STTHHHHHHHHHHHTSGTT----------EEEEEESSTTH------HHHHHHHHHHHTEEEEEEE
T ss_pred EEeCCCCCCCHHHHHHHHHHHhcCCC---------CEEEEEECCccH------HHHHHHHHHHCCCEEEEEE
Confidence 46788999999999999999998522 234455666655 3899999999999987764
No 17
>cd00371 HMA Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain contains two cysteine residues that are important in binding and transfer of metal ions, such as copper, cadmium, cobalt and zinc. In the case of copper, stoichiometry of binding is one Cu+ ion per binding domain. Repeats of the HMA domain in copper chaperone has been associated with Menkes/Wilson disease due to binding of multiple copper ions.
Probab=89.10 E-value=2 Score=22.12 Aligned_cols=41 Identities=24% Similarity=0.426 Sum_probs=32.6
Q ss_pred EEecCCCcccHHHHHHhhccCCCceeeEEEEeccEEEEEec
Q 030077 103 QADGAMNETAIPAVTQALQGTEGISDLKVQVIEGIATVELK 143 (183)
Q Consensus 103 KaEGM~Ce~Ci~~VtkALE~ieGVsdVkV~LeeG~AtVe~d 143 (183)
.+.|+.|..|...+..-+...+|+....+.+......+.+.
T Consensus 3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 43 (63)
T cd00371 3 SVEGMTCAGCVSKIEKALEKLPGVESVEVDLETGKATVEYD 43 (63)
T ss_pred eECCeEcHHHHHHHHHHHhcCCCEeEEEEEccCCEEEEEEC
Confidence 36789999999999999999999887777776666555543
No 18
>PRK11018 hypothetical protein; Provisional
Probab=84.06 E-value=3.4 Score=29.60 Aligned_cols=56 Identities=14% Similarity=0.056 Sum_probs=43.5
Q ss_pred EEEEecCCCcccHHHHHHhhccCCCceeeEEEEeccEEEEEeccceeeecccchHHHHHHHHhcCceeEee
Q 030077 101 YFQADGAMNETAIPAVTQALQGTEGISDLKVQVIEGIATVELKKQTTVQATGVAANLVEIIQGSGFKLQTL 171 (183)
Q Consensus 101 ~FKaEGM~Ce~Ci~~VtkALE~ieGVsdVkV~LeeG~AtVe~dkqttvqatgvas~LvEaIe~aGFkVq~l 171 (183)
.+.+-|..|..-+-+.+++|++++.=..+ .|..+.+.. ...|....+..||++...
T Consensus 10 ~lD~rG~~CP~Pvl~~kk~l~~l~~G~~L---------~V~~d~~~a------~~di~~~~~~~G~~v~~~ 65 (78)
T PRK11018 10 RLDMVGEPCPYPAVATLEALPQLKKGEIL---------EVVSDCPQS------INNIPLDARNHGYTVLDI 65 (78)
T ss_pred eEECCCCcCCHHHHHHHHHHHhCCCCCEE---------EEEeCCccH------HHHHHHHHHHcCCEEEEE
Confidence 47889999999999999999998632333 444444444 389999999999998654
No 19
>PF13732 DUF4162: Domain of unknown function (DUF4162)
Probab=81.21 E-value=7 Score=26.93 Aligned_cols=46 Identities=17% Similarity=0.356 Sum_probs=38.2
Q ss_pred hccCCCceeeEEEEeccEEEEEeccceeeecccchHHHHHHHHhcCceeEeeec
Q 030077 120 LQGTEGISDLKVQVIEGIATVELKKQTTVQATGVAANLVEIIQGSGFKLQTLNL 173 (183)
Q Consensus 120 LE~ieGVsdVkV~LeeG~AtVe~dkqttvqatgvas~LvEaIe~aGFkVq~l~l 173 (183)
|+.++||..++- ..+|.+.+.+.+..+ +..|-+.+.+.|+ +..++.
T Consensus 26 l~~~~~v~~v~~-~~~~~~~i~l~~~~~------~~~ll~~l~~~g~-I~~f~~ 71 (84)
T PF13732_consen 26 LEELPGVESVEQ-DGDGKLRIKLEDEET------ANELLQELIEKGI-IRSFEE 71 (84)
T ss_pred HhhCCCeEEEEE-eCCcEEEEEECCccc------HHHHHHHHHhCCC-eeEEEE
Confidence 888899999974 367779999998766 5889999999999 887665
No 20
>cd03421 SirA_like_N SirA_like_N, a protein of unknown function with an N-terminal SirA-like domain. The SirA, YedF, YeeD protein family is present in bacteria as well as archaea. SirA (also known as UvrY, and YhhP) belongs to a family of a two-component response regulators that controls secondary metabolism and virulence. The other member of this two-component system is a sensor kinase called BarA which phosphorylates SirA. A variety of microorganisms have similar proteins, all of which contain a common CPxP sequence motif in the N-terminal region. YhhP is suggested to be important for normal cell division and growth in rich nutrient medium. Moreover, despite a low primary sequence similarity, the YccP structure closely resembles the non-homologous C-terminal RNA-binding domain of E. coli translation initiation factor IF3. The signature CPxP motif serves to stabilize the N-terminal helix as part of the N-capping box and might be important in mRNA-binding.
Probab=78.03 E-value=3.9 Score=27.73 Aligned_cols=53 Identities=15% Similarity=0.289 Sum_probs=38.6
Q ss_pred EEEecCCCcccHHHHHHhhccCCCceeeEEEEeccEEEEEeccceeeecccchHHHHHHHHhcCceeEe
Q 030077 102 FQADGAMNETAIPAVTQALQGTEGISDLKVQVIEGIATVELKKQTTVQATGVAANLVEIIQGSGFKLQT 170 (183)
Q Consensus 102 FKaEGM~Ce~Ci~~VtkALE~ieGVsdVkV~LeeG~AtVe~dkqttvqatgvas~LvEaIe~aGFkVq~ 170 (183)
+.+-|+.|..-+-++++|| +++.=..+ .|..+.+.. ...|....+..||++..
T Consensus 2 lD~rG~~CP~P~l~~k~al-~~~~g~~l---------~v~~d~~~s------~~~i~~~~~~~G~~~~~ 54 (67)
T cd03421 2 IDARGLACPQPVIKTKKAL-ELEAGGEI---------EVLVDNEVA------KENVSRFAESRGYEVSV 54 (67)
T ss_pred cccCCCCCCHHHHHHHHHH-hcCCCCEE---------EEEEcChhH------HHHHHHHHHHcCCEEEE
Confidence 3567999999999999999 65422233 344444444 37899999999999943
No 21
>cd03423 SirA SirA (also known as UvrY, and YhhP) belongs to a family of two-component response regulators that controls secondary metabolism and virulence. The other member of this two-component system is a sensor kinase called BarA which phosphorylates SirA. A variety of microorganisms have similar proteins, all of which contain a common CPxP sequence motif in the N-terminal region. YhhP is thought to be important for normal cell division and growth in rich nutrient medium. Moreover, despite a low primary sequence similarity, the YccP structure closely resembles the non-homologous C-terminal RNA-binding domain of E. coli translation initiation factor IF3. The signature CPxP motif serves to stabilize the N-terminal helix as part of the N-capping box and might be important in mRNA-binding.
Probab=77.84 E-value=8.1 Score=26.68 Aligned_cols=56 Identities=9% Similarity=0.095 Sum_probs=42.5
Q ss_pred EEEecCCCcccHHHHHHhhccCCCceeeEEEEeccEEEEEeccceeeecccchHHHHHHHHhcCceeEeee
Q 030077 102 FQADGAMNETAIPAVTQALQGTEGISDLKVQVIEGIATVELKKQTTVQATGVAANLVEIIQGSGFKLQTLN 172 (183)
Q Consensus 102 FKaEGM~Ce~Ci~~VtkALE~ieGVsdVkV~LeeG~AtVe~dkqttvqatgvas~LvEaIe~aGFkVq~l~ 172 (183)
+.+-|..|..=+-+++++|++++- ++...|..+.+.. ...|....+..||++....
T Consensus 2 lD~~G~~CP~P~i~~k~~l~~l~~---------G~~l~V~~dd~~s------~~di~~~~~~~g~~~~~~~ 57 (69)
T cd03423 2 LDTRGLRCPEPVMMLHKKVRKMKP---------GDTLLVLATDPST------TRDIPKFCTFLGHELLAQE 57 (69)
T ss_pred ccccCCcCCHHHHHHHHHHHcCCC---------CCEEEEEeCCCch------HHHHHHHHHHcCCEEEEEE
Confidence 356799999999999999999851 1234555555554 4899999999999987654
No 22
>cd03422 YedF YedF is a bacterial SirA-like protein of unknown function. SirA (also known as UvrY, and YhhP) belongs to a family of a two-component response regulators that controls secondary metabolism and virulence. The other member of this two-component system is a sensor kinase called BarA which phosphorylates SirA. A variety of microorganisms have similar proteins, all of which contain a common CPxP sequence motif in the N-terminal region. YhhP is suggested to be important for normal cell division and growth in rich nutrient medium. Moreover, despite a low primary sequence similarity, the YccP structure closely resembles the non-homologous C-terminal RNA-binding domain of E. coli translation initiation factor IF3. The signature CPxP motif serves to stabilize the N-terminal helix as part of the N-capping box and might be important in mRNA-binding.
Probab=77.44 E-value=5.3 Score=27.78 Aligned_cols=56 Identities=16% Similarity=0.103 Sum_probs=42.6
Q ss_pred EEEecCCCcccHHHHHHhhccCCCceeeEEEEeccEEEEEeccceeeecccchHHHHHHHHhcCceeEeee
Q 030077 102 FQADGAMNETAIPAVTQALQGTEGISDLKVQVIEGIATVELKKQTTVQATGVAANLVEIIQGSGFKLQTLN 172 (183)
Q Consensus 102 FKaEGM~Ce~Ci~~VtkALE~ieGVsdVkV~LeeG~AtVe~dkqttvqatgvas~LvEaIe~aGFkVq~l~ 172 (183)
+.+-|..|..=+-+.++||++++-=..+ .|..+.+.. ...|....+..||++....
T Consensus 2 lD~rG~~CP~Pvi~~kkal~~l~~G~~l---------~V~~d~~~s------~~ni~~~~~~~g~~v~~~~ 57 (69)
T cd03422 2 LDLRGEPCPYPAIATLEALPSLKPGEIL---------EVISDCPQS------INNIPIDARNHGYKVLAIE 57 (69)
T ss_pred cccCCCcCCHHHHHHHHHHHcCCCCCEE---------EEEecCchH------HHHHHHHHHHcCCEEEEEE
Confidence 3567999999999999999998633333 444444444 4899999999999997654
No 23
>cd00291 SirA_YedF_YeeD SirA, YedF, and YeeD. Two-layered alpha/beta sandwich domain. SirA (also known as UvrY, and YhhP) belongs to a family of bacterial two-component response regulators that controls secondary metabolism and virulence. The other member of this two-component system is a sensor kinase called BarA which phosphorylates SirA. A variety of microorganisms have similar proteins, all of which contain a common CPxP sequence motif in the N-terminal region. YhhP is suggested to be important for normal cell division and growth in rich nutrient medium. Moreover, despite a low primary sequence similarity, the YccP structure closely resembles the non-homologous C-terminal RNA-binding domain of E. coli translation initiation factor IF3. The signature CPxP motif serves to stabilize the N-terminal helix as part of the N-capping box and might be important in mRNA-binding.
Probab=76.73 E-value=6.8 Score=26.11 Aligned_cols=55 Identities=11% Similarity=0.119 Sum_probs=40.7
Q ss_pred EEEecCCCcccHHHHHHhhccCCCceeeEEEEeccEEEEEeccceeeecccchHHHHHHHHhcCceeEee
Q 030077 102 FQADGAMNETAIPAVTQALQGTEGISDLKVQVIEGIATVELKKQTTVQATGVAANLVEIIQGSGFKLQTL 171 (183)
Q Consensus 102 FKaEGM~Ce~Ci~~VtkALE~ieGVsdVkV~LeeG~AtVe~dkqttvqatgvas~LvEaIe~aGFkVq~l 171 (183)
+.+-|+.|..=..+++++|..++.=.. ..|..+.+.. ...|.+..+..||++...
T Consensus 2 lD~rg~~CP~Pl~~~~~~l~~l~~g~~---------l~v~~d~~~~------~~~i~~~~~~~g~~~~~~ 56 (69)
T cd00291 2 LDLRGLPCPLPVLKTKKALEKLKSGEV---------LEVLLDDPGA------VEDIPAWAKETGHEVLEV 56 (69)
T ss_pred ccccCCcCCHHHHHHHHHHhcCCCCCE---------EEEEecCCcH------HHHHHHHHHHcCCEEEEE
Confidence 356799999999999999999763222 3444444443 489999999999997554
No 24
>PF02120 Flg_hook: Flagellar hook-length control protein FliK; InterPro: IPR021136 This entry represents the C-terminal domain of the flagellar hook-length control protein FliK. This entry also includes YscP of the Yersinia type III secretion system, and equivalent proteins in other pathogenic bacterial type III secretion systems. During flagellar morphogenesis in Salmonella typhimurium and Escherichia coli, flagellar hook-length control protein (FliK) controls the length of the hook by directly measuring the hook length [, ]. It is considered unlikely that FliK functions as a molecular ruler for determining hook length, but that it is more likely to be employing a novel mechanism. The deduced amino acid sequences of FliK proteins from S. typhimurium and E. coli have molecular masses of 41,748 and 39,246 Da, respectively, and are fairly hydrophilic []. Sequence comparison reveals around 50% identity, with greatest conservation in the C-terminal region, with 71% identity in the last 154 amino acids - mutagenesis of this conserved region completely abolishes motility. The central and C-terminal regions are rich in proline and glutamine respectively; it is thought that they may constitute distinct domains [].; PDB: 2RRL_A.
Probab=76.59 E-value=5.6 Score=27.57 Aligned_cols=52 Identities=17% Similarity=0.268 Sum_probs=35.6
Q ss_pred eeeEEEEeccEEEEEecccee---eecccchHHHHHHHHhcCceeEeeeccccCc
Q 030077 127 SDLKVQVIEGIATVELKKQTT---VQATGVAANLVEIIQGSGFKLQTLNLSFDDE 178 (183)
Q Consensus 127 sdVkV~LeeG~AtVe~dkqtt---vqatgvas~LvEaIe~aGFkVq~l~l~f~d~ 178 (183)
=.|++.+.++..++.+.-+.. ...-.....|+++++..||++..++.+..+.
T Consensus 27 v~v~l~~~~~~l~v~~~~~~~~~~~~L~~~~~~L~~~L~~~G~~~~~~~v~~~~~ 81 (85)
T PF02120_consen 27 VEVKLRLQGGNLSVQFTAENPETKELLRQNLPELKERLQAQGLEVVNLSVSQGSS 81 (85)
T ss_dssp EEEEEEEETTEEEEEEE--SSHHHHHHHHTHHHHHHHHHTTT-EEEEEEEESS--
T ss_pred EEEEEEEeCCEEEEEEEECCHHHHHHHHHHHHHHHHHHHHCCCCeEEEEEEECCC
Confidence 468888899988877755332 2223456789999999999999988876554
No 25
>COG1606 ATP-utilizing enzymes of the PP-loop superfamily [General function prediction only]
Probab=76.07 E-value=4 Score=36.87 Aligned_cols=56 Identities=18% Similarity=0.368 Sum_probs=46.7
Q ss_pred HhhccCCCceeeEEEEeccEEEEEeccceeeecccchHHHHHHHHhcCceeEeeecc
Q 030077 118 QALQGTEGISDLKVQVIEGIATVELKKQTTVQATGVAANLVEIIQGSGFKLQTLNLS 174 (183)
Q Consensus 118 kALE~ieGVsdVkV~LeeG~AtVe~dkqttvqatgvas~LvEaIe~aGFkVq~l~l~ 174 (183)
..|-.+ |+..+.|--+.+.|.++..+.-.-..-+....|...|++.||+.++|+|.
T Consensus 198 ~~l~~l-~~~~irvr~~~~~A~iEv~~ee~~k~~~~~~~i~~~lk~~Gf~~VtldLe 253 (269)
T COG1606 198 EFLREL-GVRQIRVRSEDNLAVIEVGPEEPEKLLNEVEEIDDKLKKVGFRKVTLDLE 253 (269)
T ss_pred HHHHHh-hhceeeeeecCceeEEecCccCHHHHhhhHHHHHHHHHHhccceEEechh
Confidence 345555 59999999999999999987665556667788999999999999999984
No 26
>smart00362 RRM_2 RNA recognition motif.
Probab=75.66 E-value=15 Score=22.24 Aligned_cols=46 Identities=13% Similarity=0.154 Sum_probs=39.7
Q ss_pred EEEecCCCcccHHHHHHhhccCCCceeeEEEEec----cEEEEEecccee
Q 030077 102 FQADGAMNETAIPAVTQALQGTEGISDLKVQVIE----GIATVELKKQTT 147 (183)
Q Consensus 102 FKaEGM~Ce~Ci~~VtkALE~ieGVsdVkV~Lee----G~AtVe~dkqtt 147 (183)
+.|.|..+...-..|.+.++....|.++.+.... |.+.|++.....
T Consensus 2 v~i~~l~~~~~~~~l~~~~~~~g~v~~~~~~~~~~~~~~~~~v~f~~~~~ 51 (72)
T smart00362 2 LFVGNLPPDVTEEDLKELFSKFGPIESVKIPKDTGKSKGFAFVEFESEED 51 (72)
T ss_pred EEEcCCCCcCCHHHHHHHHHhcCCEEEEEEecCCCCCCceEEEEeCCHHH
Confidence 4577888888889999999999999999999887 999999987655
No 27
>cd04883 ACT_AcuB C-terminal ACT domain of the Bacillus subtilis acetoin utilization protein, AcuB. This CD includes the C-terminal ACT domain of the Bacillus subtilis acetoin utilization protein, AcuB. AcuB is putatively involved in the anaerobic catabolism of acetoin, and related proteins. Studies report the induction of AcuB by nitrate respiration and also by fermentation. Since acetoin can be secreted and later serve as a source of carbon, it has been proposed that, during anaerobic growth when other carbon sources are exhausted, the induction of the AcuB protein results in acetoin catabolism. AcuB-like proteins have two N-terminal tandem CBS domains and a single C-terminal ACT domain. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=74.95 E-value=21 Score=23.44 Aligned_cols=63 Identities=11% Similarity=0.185 Sum_probs=38.9
Q ss_pred EEEecCCCcccHHHHHHhhccCCCceeeEEE--Ee--ccEEEEEeccceeeecccchHHHHHHHHhcCceeEe
Q 030077 102 FQADGAMNETAIPAVTQALQGTEGISDLKVQ--VI--EGIATVELKKQTTVQATGVAANLVEIIQGSGFKLQT 170 (183)
Q Consensus 102 FKaEGM~Ce~Ci~~VtkALE~ieGVsdVkV~--Le--eG~AtVe~dkqttvqatgvas~LvEaIe~aGFkVq~ 170 (183)
|.++--...+...+|.+.|.+- |+.=.++. .. .+.+.+.+.=.+. ..+.++++|++.||++.-
T Consensus 4 ~~v~~~d~pG~l~~i~~~l~~~-~inI~~i~~~~~~~~~~~~v~i~v~~~-----~~~~~~~~L~~~G~~v~~ 70 (72)
T cd04883 4 IEVRVPDRPGQLADIAAIFKDR-GVNIVSVLVYPSKEEDNKILVFRVQTM-----NPRPIIEDLRRAGYEVLW 70 (72)
T ss_pred EEEEECCCCCHHHHHHHHHHHc-CCCEEEEEEeccCCCCeEEEEEEEecC-----CHHHHHHHHHHCCCeeeC
Confidence 4444445567888999999875 55444443 22 2344333332222 246999999999999864
No 28
>PF09580 Spore_YhcN_YlaJ: Sporulation lipoprotein YhcN/YlaJ (Spore_YhcN_YlaJ); InterPro: IPR019076 This entry contains YhcN and YlaJ, which are predicted lipoproteins that have been detected as spore proteins but not vegetative proteins in Bacillus subtilis. Both appear to be expressed under control of the RNA polymerase sigma-G factor. The YlaJ-like members of this family have a low-complexity, strongly acidic, 40-residue C-terminal domain.
Probab=74.92 E-value=9.7 Score=30.08 Aligned_cols=35 Identities=17% Similarity=0.244 Sum_probs=31.7
Q ss_pred ccHHHHHHhhccCCCceeeEEEEeccEEEEEeccc
Q 030077 111 TAIPAVTQALQGTEGISDLKVQVIEGIATVELKKQ 145 (183)
Q Consensus 111 ~Ci~~VtkALE~ieGVsdVkV~LeeG~AtVe~dkq 145 (183)
.=+..|.+.+..++||.++.|-+.+..|.|-+...
T Consensus 75 ~~a~~i~~~v~~~~~V~~A~vvv~~~~a~Vav~~~ 109 (177)
T PF09580_consen 75 QLADRIANRVKKVPGVEDATVVVTDDNAYVAVDLD 109 (177)
T ss_pred HHHHHHHHHHhcCCCceEEEEEEECCEEEEEEEec
Confidence 34678999999999999999999999999988776
No 29
>cd04888 ACT_PheB-BS C-terminal ACT domain of a small (~147 a.a.) putative phenylalanine biosynthetic pathway protein described in Bacillus subtilis (BS) PheB (PheB-BS) and related domains. This CD includes the C-terminal ACT domain of a small (~147 a.a.) putative phenylalanine biosynthetic pathway protein described in Bacillus subtilis (BS) PheB (PheB-BS) and other related ACT domains. In B. subtilis, the upstream gene of pheB, pheA encodes prephenate dehydratase (PDT). The presumed product of the pheB gene is chorismate mutase (CM). The deduced product of the B. subtilis pheB gene, however, has no significant homology to the CM portion of the bifunctional CM-PDT of Escherichia coli. The presence of an ACT domain lends support to the prediction that these proteins function as a phenylalanine-binding regulatory protein. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=72.88 E-value=9.3 Score=25.31 Aligned_cols=36 Identities=11% Similarity=0.290 Sum_probs=29.4
Q ss_pred CceEEEEEEecCCCcccHHHHHHhhccCCCceeeEE
Q 030077 96 DKLTMYFQADGAMNETAIPAVTQALQGTEGISDLKV 131 (183)
Q Consensus 96 ~~ltM~FKaEGM~Ce~Ci~~VtkALE~ieGVsdVkV 131 (183)
...++.|.++--.=+.....+-++|.+++||.+|.+
T Consensus 39 ~~~~i~~~v~v~~~~~~l~~l~~~L~~i~~V~~v~~ 74 (76)
T cd04888 39 GRANVTISIDTSTMNGDIDELLEELREIDGVEKVEL 74 (76)
T ss_pred CeEEEEEEEEcCchHHHHHHHHHHHhcCCCeEEEEE
Confidence 456777878775556688999999999999999876
No 30
>cd03420 SirA_RHOD_Pry_redox SirA_RHOD_Pry_redox. SirA-like domain located within a multidomain protein of unknown function. Other domains include RHOD (rhodanese homology domain), and Pry_redox (pyridine nucleotide-disulphide oxidoreductase) as well as a C-terminal domain that corresponds to COG2210. This fold is referred to as a two-layered alpha/beta sandwich, structurally similar to that of translation initiation factor 3.
Probab=72.37 E-value=10 Score=26.31 Aligned_cols=56 Identities=14% Similarity=0.115 Sum_probs=43.4
Q ss_pred EEEecCCCcccHHHHHHhhccCCCceeeEEEEeccEEEEEeccceeeecccchHHHHHHHHhcCceeEeee
Q 030077 102 FQADGAMNETAIPAVTQALQGTEGISDLKVQVIEGIATVELKKQTTVQATGVAANLVEIIQGSGFKLQTLN 172 (183)
Q Consensus 102 FKaEGM~Ce~Ci~~VtkALE~ieGVsdVkV~LeeG~AtVe~dkqttvqatgvas~LvEaIe~aGFkVq~l~ 172 (183)
+.+-|+.|..=+-+.++||.+++. ++...|..+.+.. ...|....+..||++....
T Consensus 2 lD~rG~~CP~Pvl~~kkal~~l~~---------G~~l~V~~d~~~a------~~di~~~~~~~G~~~~~~~ 57 (69)
T cd03420 2 VDACGLQCPGPILKLKKEIDKLQD---------GEQLEVKASDPGF------ARDAQAWCKSTGNTLISLE 57 (69)
T ss_pred cccCCCcCCHHHHHHHHHHHcCCC---------CCEEEEEECCccH------HHHHHHHHHHcCCEEEEEE
Confidence 456799999999999999999862 2334555555555 3899999999999998554
No 31
>PRK09577 multidrug efflux protein; Reviewed
Probab=70.73 E-value=9.4 Score=38.80 Aligned_cols=57 Identities=16% Similarity=0.139 Sum_probs=41.3
Q ss_pred cHHHHHHhhccCCCceeeEEEEeccEEEEEeccceeeecccchHHHHHHHHhcCcee
Q 030077 112 AIPAVTQALQGTEGISDLKVQVIEGIATVELKKQTTVQATGVAANLVEIIQGSGFKL 168 (183)
Q Consensus 112 Ci~~VtkALE~ieGVsdVkV~LeeG~AtVe~dkqttvqatgvas~LvEaIe~aGFkV 168 (183)
....|+..|+.+|||.+|++.=.+-+..|++|++.-.+--=+.+.|.++|+..+.+.
T Consensus 157 ~~~~l~~~L~~v~GV~~V~~~G~e~~v~V~vD~~kl~~~Gls~~~V~~~l~~~n~~~ 213 (1032)
T PRK09577 157 ASANVLQALRRVEGVGKVQFWGAEYAMRIWPDPVKLAALGLTASDIASAVRAHNARV 213 (1032)
T ss_pred HHHHHHHHHhcCCCcEEEEecCCceEEEEEeCHHHHHHcCCCHHHHHHHHHHhCCcC
Confidence 567899999999999999998655566666676543222224688999998876543
No 32
>PF01883 DUF59: Domain of unknown function DUF59; InterPro: IPR002744 This family includes prokaryotic proteins of unknown function. The family also includes PhaH (O84984 from SWISSPROT) from Pseudomonas putida. PhaH forms a complex with PhaF (O84982 from SWISSPROT), PhaG (O84983 from SWISSPROT) and PhaI (O84985 from SWISSPROT), which hydroxylates phenylacetic acid to 2-hydroxyphenylacetic acid []. So members of this family may all be components of ring hydroxylating complexes.; PDB: 3LNO_C 3CQ3_A 3CQ2_D 2CU6_B 3CQ1_A 3UX3_B 3UX2_A 1WCJ_A 1UWD_A.
Probab=67.67 E-value=4.8 Score=27.47 Aligned_cols=36 Identities=17% Similarity=0.281 Sum_probs=23.6
Q ss_pred CceEEEEEEecCCCc---ccHHHHHHhhccCCCceeeEE
Q 030077 96 DKLTMYFQADGAMNE---TAIPAVTQALQGTEGISDLKV 131 (183)
Q Consensus 96 ~~ltM~FKaEGM~Ce---~Ci~~VtkALE~ieGVsdVkV 131 (183)
+++++.+..-...|. .=...++++|.+++||++|+|
T Consensus 34 ~~V~v~l~l~~~~~~~~~~l~~~i~~~l~~l~gv~~V~V 72 (72)
T PF01883_consen 34 GKVSVSLELPTPACPAAEPLREEIREALKALPGVKSVKV 72 (72)
T ss_dssp CEEEEEE--SSTTHTTHHHHHHHHHHHHHTSTT-SEEEE
T ss_pred CEEEEEEEECCCCchHHHHHHHHHHHHHHhCCCCceEeC
Confidence 445555665555565 234678899999999999987
No 33
>TIGR02990 ectoine_eutA ectoine utilization protein EutA. Members of this protein family are EutA, a predicted arylmalonate decarboxylase found in a conserved ectoine utilization operon of species that include Sinorhizobium meliloti 1021 (where it is known to be induced by ectoine), Mesorhizobium loti and Silicibacter pomeroyi. It is missing from two other species with the other ectoine transport and utilization genes: Pseudomonas putida and Agrobacterium tumefaciens.
Probab=66.87 E-value=8.9 Score=32.94 Aligned_cols=59 Identities=17% Similarity=0.310 Sum_probs=45.5
Q ss_pred cCCCcccHHHHHHhhccCCCceeeEEEEeccEEEEEeccceeeecccchHHHHHHHHhcCceeEee-eccccCcc
Q 030077 106 GAMNETAIPAVTQALQGTEGISDLKVQVIEGIATVELKKQTTVQATGVAANLVEIIQGSGFKLQTL-NLSFDDEE 179 (183)
Q Consensus 106 GM~Ce~Ci~~VtkALE~ieGVsdVkV~LeeG~AtVe~dkqttvqatgvas~LvEaIe~aGFkVq~l-~l~f~d~~ 179 (183)
|.-+-..+.++-.||.++ ||+.+-|-.- |.+.++ ..+++-+++.||+|... +|..+|..
T Consensus 101 g~p~tt~~~A~~~AL~al-g~~RIalvTP-------Y~~~v~-------~~~~~~l~~~G~eV~~~~~~~~~~~~ 160 (239)
T TIGR02990 101 GTPVVTPSSAAVDGLAAL-GVRRISLLTP-------YTPETS-------RPMAQYFAVRGFEIVNFTCLGLTDDR 160 (239)
T ss_pred CCCeeCHHHHHHHHHHHc-CCCEEEEECC-------CcHHHH-------HHHHHHHHhCCcEEeeeeccCCCCCc
Confidence 566777888999999999 9998766431 555555 89999999999999887 66665544
No 34
>COG0425 SirA Predicted redox protein, regulator of disulfide bond formation [Posttranslational modification, protein turnover, chaperones]
Probab=66.38 E-value=34 Score=24.86 Aligned_cols=59 Identities=12% Similarity=0.119 Sum_probs=44.5
Q ss_pred EEEEEEecCCCcccHHHHHHhhccCCCceeeEEEEeccEEEEEeccceeeecccchHHHHHHHHhcC-ceeEeee
Q 030077 99 TMYFQADGAMNETAIPAVTQALQGTEGISDLKVQVIEGIATVELKKQTTVQATGVAANLVEIIQGSG-FKLQTLN 172 (183)
Q Consensus 99 tM~FKaEGM~Ce~Ci~~VtkALE~ieGVsdVkV~LeeG~AtVe~dkqttvqatgvas~LvEaIe~aG-FkVq~l~ 172 (183)
...+.+-|..|-.=+..++++|+.++= +....|..+++... ..|....+..| +++....
T Consensus 5 ~~~LD~rG~~CP~Pv~~~kk~l~~m~~---------Ge~LeV~~ddp~~~------~dIp~~~~~~~~~~ll~~e 64 (78)
T COG0425 5 DKVLDLRGLRCPGPVVETKKALAKLKP---------GEILEVIADDPAAK------EDIPAWAKKEGGHELLEVE 64 (78)
T ss_pred ceEEeccCCcCCccHHHHHHHHHcCCC---------CCEEEEEecCcchH------HHHHHHHHHcCCcEEEEEE
Confidence 556999999999999999999999973 33445555555553 88899999555 8876653
No 35
>PF02680 DUF211: Uncharacterized ArCR, COG1888; InterPro: IPR003831 This entry describes proteins of unknown function.; PDB: 3BPD_I 2RAQ_F 2X3D_E.
Probab=65.94 E-value=43 Score=26.17 Aligned_cols=56 Identities=23% Similarity=0.351 Sum_probs=38.3
Q ss_pred CcccHHHHHHhhccCCCceeeEEEEecc-------EEEEEeccceeeecccchHHHHHHHHhcCceeEee
Q 030077 109 NETAIPAVTQALQGTEGISDLKVQVIEG-------IATVELKKQTTVQATGVAANLVEIIQGSGFKLQTL 171 (183)
Q Consensus 109 Ce~Ci~~VtkALE~ieGVsdVkV~LeeG-------~AtVe~dkqttvqatgvas~LvEaIe~aGFkVq~l 171 (183)
-+.-+--+.++|.+++||..|.+.+.+= +.+++- ...+ -+.|+++|++.|=-++.+
T Consensus 15 ~~p~i~e~A~~l~~~~gV~gVnitv~EvD~ete~lkitiEG-~~id------~d~i~~~Ie~~Gg~IHSI 77 (95)
T PF02680_consen 15 HEPSIVELAKALSELEGVDGVNITVVEVDVETENLKITIEG-DDID------FDEIKEAIEELGGVIHSI 77 (95)
T ss_dssp SSS-HHHHHHHHHTSTTEEEEEEEEEEE-SSEEEEEEEEEE-SSE-------HHHHHHHHHHTT-EEEEE
T ss_pred CCCCHHHHHHHHHhCCCcceEEEEEEEeeccccEEEEEEEe-CCCC------HHHHHHHHHHcCCeEEee
Confidence 3556778899999999999999887541 122222 2233 599999999999766644
No 36
>cd04909 ACT_PDH-BS C-terminal ACT domain of the monofunctional, NAD dependent, prephenate dehydrogenase (PDH). The C-terminal ACT domain of the monofunctional, NAD dependent, prephenate dehydrogenase (PDH) enzyme that catalyzes the formation of 4-hydroxyphenylpyruvate from prephenate, found in Bacillus subtilis (BS) and other Firmicutes, Deinococci, and Bacteroidetes. PDH is the first enzyme in the aromatic amino acid pathway specific for the biosynthesis of tyrosine. This enzyme is feedback-inhibited by tyrosine in B. subtilis and other microorganisms. Both phenylalanine and tryptophan have been shown to be inhibitors of this activity in B. subtilis. Bifunctional chorismate mutase-PDH (TyrA) enzymes such as those seen in Escherichia coli do not contain an ACT domain. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=65.05 E-value=35 Score=22.41 Aligned_cols=60 Identities=28% Similarity=0.386 Sum_probs=38.2
Q ss_pred EEEecCCCcccHHHHHHhhccCCCceeeEEE--Ee----ccEEEEEeccceeeecccchHHHHHHHHhcCcee
Q 030077 102 FQADGAMNETAIPAVTQALQGTEGISDLKVQ--VI----EGIATVELKKQTTVQATGVAANLVEIIQGSGFKL 168 (183)
Q Consensus 102 FKaEGM~Ce~Ci~~VtkALE~ieGVsdVkV~--Le----eG~AtVe~dkqttvqatgvas~LvEaIe~aGFkV 168 (183)
|.++.-.=.|...+|.+.|.+- |+.=..+. -. .+...+....+. ..+.+++.++++||+|
T Consensus 4 ~~v~~~d~~G~L~~l~~~l~~~-~i~i~~~~~~~~~~~~~~~~~i~v~~~~------~~~~~~~~L~~~G~~v 69 (69)
T cd04909 4 LYVDVPDEPGVIAEVTQILGDA-GISIKNIEILEIREGIGGILRISFKTQE------DRERAKEILKEAGYEV 69 (69)
T ss_pred EEEEcCCCCCHHHHHHHHHHHc-CCCceeeEeEEeecCCcEEEEEEECCHH------HHHHHHHHHHHcCCcC
Confidence 4445555567888999999874 55433333 22 344445554222 3589999999999975
No 37
>PRK00299 sulfur transfer protein SirA; Reviewed
Probab=64.60 E-value=30 Score=24.86 Aligned_cols=58 Identities=9% Similarity=0.029 Sum_probs=44.7
Q ss_pred EEEEEecCCCcccHHHHHHhhccCCCceeeEEEEeccEEEEEeccceeeecccchHHHHHHHHhcCceeEeee
Q 030077 100 MYFQADGAMNETAIPAVTQALQGTEGISDLKVQVIEGIATVELKKQTTVQATGVAANLVEIIQGSGFKLQTLN 172 (183)
Q Consensus 100 M~FKaEGM~Ce~Ci~~VtkALE~ieGVsdVkV~LeeG~AtVe~dkqttvqatgvas~LvEaIe~aGFkVq~l~ 172 (183)
..+.+-|..|..=+-+++++|+.++-= +...|..+.+.. ...|....+..|+++....
T Consensus 10 ~~lD~~Gl~CP~Pll~~kk~l~~l~~G---------~~l~V~~dd~~~------~~di~~~~~~~G~~~~~~~ 67 (81)
T PRK00299 10 HTLDALGLRCPEPVMMVRKTVRNMQPG---------ETLLIIADDPAT------TRDIPSFCRFMDHELLAQE 67 (81)
T ss_pred eEEecCCCCCCHHHHHHHHHHHcCCCC---------CEEEEEeCCccH------HHHHHHHHHHcCCEEEEEE
Confidence 358899999999999999999998622 234455555444 5899999999999997643
No 38
>PF01709 Transcrip_reg: Transcriptional regulator; InterPro: IPR002876 This entry represents the core region of several hypothetical proteins found in bacteria, plants, and yeast proteins. This core region can be subdivided into three domains: a 3-helical bundle domain, and two alpha+beta domains with different folds, where domain 3 (ferredoxin-like fold) is inserted within domain 2. This core region is found in the following hypothetical proteins: YebC from Escherichia coli, HP0162 from Helicobacter pylori (Campylobacter pylori) and aq1575 from Aquifex aeolicus []. The crystal structure of a conserved hypothetical protein, Aq1575, from Aquifex aeolicus has been determined. A structural homology search reveals that this protein has a new fold with no obvious similarity to those of other proteins of known three-dimensional structure. The protein reveals a monomer consisting of three domains arranged along a pseudo threefold symmetry axis. There is a large cleft with approximate dimensions of 10 A x 10 A x 20 A in the centre of the three domains along the symmetry axis. Two possible active sites are suggested based on the structure and multiple sequence alignment. There are several highly conserved residues in these putative active sites [].; PDB: 1LFP_A 1MW7_A 1KON_A.
Probab=64.44 E-value=11 Score=32.40 Aligned_cols=50 Identities=12% Similarity=0.354 Sum_probs=36.6
Q ss_pred HHHHhhccCCCceeeEEEEeccEEEEEeccceeeecccchHHHHHHHHhcCceeEeeeccc
Q 030077 115 AVTQALQGTEGISDLKVQVIEGIATVELKKQTTVQATGVAANLVEIIQGSGFKLQTLNLSF 175 (183)
Q Consensus 115 ~VtkALE~ieGVsdVkV~LeeG~AtVe~dkqttvqatgvas~LvEaIe~aGFkVq~l~l~f 175 (183)
-+.-|||. |+.||..+ +|...|-.++.-. ..+++++++.||++..-.+.|
T Consensus 148 ~~e~aIe~--GaeDve~~--d~~~~~~c~p~~~-------~~v~~~L~~~g~~i~~~e~~~ 197 (234)
T PF01709_consen 148 LMEDAIEA--GAEDVEED--DGEFEFICDPSDL-------SAVKKALEKKGYEIESAELEY 197 (234)
T ss_dssp HHHHHHHH--TESEEEEC--TSEEEEEEEGGGH-------HHHHHHHHHTT---SEEEEEE
T ss_pred HHHHHHhC--CCcEeeec--CCeEEEEECHHHH-------HHHHHHHHHcCCCeeEEEEEE
Confidence 45667776 99999843 7887777766655 899999999999988777765
No 39
>COG2151 PaaD Predicted metal-sulfur cluster biosynthetic enzyme [General function prediction only]
Probab=64.05 E-value=6.6 Score=30.86 Aligned_cols=21 Identities=29% Similarity=0.510 Sum_probs=19.5
Q ss_pred HHHHHHhhccCCCceeeEEEE
Q 030077 113 IPAVTQALQGTEGISDLKVQV 133 (183)
Q Consensus 113 i~~VtkALE~ieGVsdVkV~L 133 (183)
...|+.||++++||++++|++
T Consensus 69 ~~~v~~al~~~~~v~~v~V~l 89 (111)
T COG2151 69 ADQVEAALEEIPGVEDVEVEL 89 (111)
T ss_pred HHHHHHHHHhcCCcceEEEEE
Confidence 578999999999999999987
No 40
>PRK10503 multidrug efflux system subunit MdtB; Provisional
Probab=61.91 E-value=19 Score=36.71 Aligned_cols=81 Identities=17% Similarity=0.229 Sum_probs=53.3
Q ss_pred CCceeeecCCCCceEEEEEEecCC------CcccHHHHHHhhccCCCceeeEEEE-eccEEEEEeccceeeecccchHHH
Q 030077 85 QQPVAVPVSPSDKLTMYFQADGAM------NETAIPAVTQALQGTEGISDLKVQV-IEGIATVELKKQTTVQATGVAANL 157 (183)
Q Consensus 85 ~~~~~~~~~~~~~ltM~FKaEGM~------Ce~Ci~~VtkALE~ieGVsdVkV~L-eeG~AtVe~dkqttvqatgvas~L 157 (183)
++|+....++++.-.|.+.+.|.. .+..-..|+..|+.+|||.+|++.= .+.+..|++|++.-.+--=+...+
T Consensus 134 ~~p~~~~~~~~~~pv~~~~l~~~~~~~~~L~~~~~~~l~~~L~~i~gV~~V~~~G~~~~ei~V~vd~~kl~~~gls~~~v 213 (1040)
T PRK10503 134 NPPVYSKVNPADPPIMTLAVTSTAMPMTQVEDMVETRVAQKISQVSGVGLVTLSGGQRPAVRVKLNAQAIAALGLTSETV 213 (1040)
T ss_pred CCCEEEEeCCCCCceEEEEEEcCCCCHHHHHHHHHHHHHHHhcCCCCceEEEecCCCceEEEEEECHHHHHHcCCCHHHH
Confidence 345555677777667777776531 1123357999999999999887663 245788999886543222245788
Q ss_pred HHHHHhcC
Q 030077 158 VEIIQGSG 165 (183)
Q Consensus 158 vEaIe~aG 165 (183)
.++|+..-
T Consensus 214 ~~ai~~~n 221 (1040)
T PRK10503 214 RTAITGAN 221 (1040)
T ss_pred HHHHHHhC
Confidence 88887654
No 41
>PRK00435 ef1B elongation factor 1-beta; Validated
Probab=60.63 E-value=17 Score=27.49 Aligned_cols=39 Identities=21% Similarity=0.319 Sum_probs=33.4
Q ss_pred CCCCceEEEEEEecCCCcccHHHHHHhhccCCCceeeEEEE
Q 030077 93 SPSDKLTMYFQADGAMNETAIPAVTQALQGTEGISDLKVQV 133 (183)
Q Consensus 93 ~~~~~ltM~FKaEGM~Ce~Ci~~VtkALE~ieGVsdVkV~L 133 (183)
+---.|.+.+-++.- ++-...+..++.+++||+.++|.-
T Consensus 46 FGLkaL~i~~vv~D~--~~~td~lee~i~~~e~Vqsvei~~ 84 (88)
T PRK00435 46 FGLKALKLYVIMPDE--EGGTEPVEEAFANVEGVESVEVEE 84 (88)
T ss_pred ccceeEEEEEEEEcC--CcCcHHHHHHHhccCCCcEEEEEE
Confidence 556788888888776 688899999999999999999853
No 42
>TIGR03527 selenium_YedF selenium metabolism protein YedF. Members of this protein family are about 200 amino acids in size, and include the uncharacterized YedF protein of Escherichia coli. This family shares an N-terminal domain, modeled by pfam01206, with the sulfurtransferase TusA (also called SirA). The C-terminal domain includes a typical redox-active disulfide motif, CGXC. This protein family found only among those genomes that also carry the selenium donor protein SelD, and its connection to selenium metabolism is indicated by the method of partial phylogenetic profiling vs. SelD. Its gene typically is found next to selD. Members of this family are found even when selenocysteine and selenouridine biosynthesis pathways are, except for SelD, completely absent, as in Enterococcus faecalis. Its role in selenium metabolism is unclear, but may include either detoxification or a role in labile selenoprotein biosynthesis.
Probab=60.57 E-value=12 Score=31.42 Aligned_cols=54 Identities=19% Similarity=0.304 Sum_probs=41.1
Q ss_pred EEecCCCcccHHHHHHhhccCCCceeeEEEEeccEEEEEeccceeeecccchHHHHHHHHhcCceeEee
Q 030077 103 QADGAMNETAIPAVTQALQGTEGISDLKVQVIEGIATVELKKQTTVQATGVAANLVEIIQGSGFKLQTL 171 (183)
Q Consensus 103 KaEGM~Ce~Ci~~VtkALE~ieGVsdVkV~LeeG~AtVe~dkqttvqatgvas~LvEaIe~aGFkVq~l 171 (183)
.+-|..|..-+-+.+|||++++. ++...|..|.+.. ...|.+..+..||++...
T Consensus 2 D~rGl~CP~Pvi~tKkal~~l~~---------g~~L~VlvD~~~a------~~nV~~~~~~~G~~v~~~ 55 (194)
T TIGR03527 2 DARGLACPQPVILTKKALDELGE---------EGVLTVIVDNEAA------KENVSKFATSLGYEVEVE 55 (194)
T ss_pred CCCCCCCCHHHHHHHHHHHcCCC---------CCEEEEEECCccH------HHHHHHHHHHcCCEEEEE
Confidence 35799999999999999999963 1234444555544 388999999999998643
No 43
>PF03927 NapD: NapD protein; InterPro: IPR005623 This entry represents NapD, the twin-arginine signal-peptide-binding chaperone for NapA, functioning as an assembly protein for the periplasmic nitrate reductase NapABC. The periplasmic NapABC enzyme likely functions during growth in nitrate-limited environments [].; PDB: 2JSX_A 2PQ4_A.
Probab=58.94 E-value=32 Score=24.96 Aligned_cols=57 Identities=16% Similarity=0.331 Sum_probs=35.9
Q ss_pred cHHHHHHhhccCCCceeeEEEEeccEEEEEeccceeeecccchHHHHHHHHhcCc--eeEeeecccc
Q 030077 112 AIPAVTQALQGTEGISDLKVQVIEGIATVELKKQTTVQATGVAANLVEIIQGSGF--KLQTLNLSFD 176 (183)
Q Consensus 112 Ci~~VtkALE~ieGVsdVkV~LeeG~AtVe~dkqttvqatgvas~LvEaIe~aGF--kVq~l~l~f~ 176 (183)
-...|.++|.++||| +|.-.=.+|+..|.++.+.. ..+.+.|...-= .|-..+|-|.
T Consensus 16 ~~~~v~~~l~~~~gv-EVh~~~~~GKiVVtiE~~~~-------~~~~~~~~~i~~l~GVlsa~lvYh 74 (79)
T PF03927_consen 16 RLEEVAEALAAIPGV-EVHAVDEDGKIVVTIEAESS-------EEEVDLIDAINALPGVLSASLVYH 74 (79)
T ss_dssp CHHHHHHHHCCSTTE-EEEEEETTTEEEEEEEESSH-------HHHHHHHHHHCCSTTEEEEEESSE
T ss_pred hHHHHHHHHHcCCCc-EEEeeCCCCeEEEEEEeCCh-------HHHHHHHHHHHcCCCceEEEEEEE
Confidence 467899999999999 44444444888888877666 455555544221 2444444443
No 44
>PF08777 RRM_3: RNA binding motif; InterPro: IPR014886 This domain is found in protein La which functions as an RNA chaperone during RNA polymerase III transcription, and can also stimulate translation initiation. It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.
Probab=58.40 E-value=27 Score=26.50 Aligned_cols=58 Identities=12% Similarity=0.131 Sum_probs=37.2
Q ss_pred EEEEecCCCcccHHHHHHhhccCCCceeeEEEEeccEEEEEeccceeeecccchHHHHHHHHhc
Q 030077 101 YFQADGAMNETAIPAVTQALQGTEGISDLKVQVIEGIATVELKKQTTVQATGVAANLVEIIQGS 164 (183)
Q Consensus 101 ~FKaEGM~Ce~Ci~~VtkALE~ieGVsdVkV~LeeG~AtVe~dkqttvqatgvas~LvEaIe~a 164 (183)
.++++|+.-+.+...|+.+|.....|.-|++.--...+.|.+..+-. |..+.+++...
T Consensus 3 il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G~~~g~VRf~~~~~------A~~a~~~~~~~ 60 (105)
T PF08777_consen 3 ILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRGDTEGYVRFKTPEA------AQKALEKLKEA 60 (105)
T ss_dssp EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT-SEEEEEESS---------HHHHHHHHHHT
T ss_pred EEEEecCCCCcCHHHHHHHHHhcCCcceEEecCCCCEEEEEECCcch------HHHHHHHHHhc
Confidence 47888888888899999999999999998888888899999988766 46666666665
No 45
>TIGR00489 aEF-1_beta translation elongation factor aEF-1 beta. This model describes the archaeal translation elongation factor aEF-1 beta. The member from Sulfolobus solfataricus was demonstrated experimentally. It is a dimer that catalyzes the exchange of GDP for GTP on aEF-1 alpha.
Probab=56.78 E-value=23 Score=26.76 Aligned_cols=39 Identities=18% Similarity=0.212 Sum_probs=31.2
Q ss_pred CCCCceEEEEEEecCCCcccHHHHHHhhccCCCceeeEEEE
Q 030077 93 SPSDKLTMYFQADGAMNETAIPAVTQALQGTEGISDLKVQV 133 (183)
Q Consensus 93 ~~~~~ltM~FKaEGM~Ce~Ci~~VtkALE~ieGVsdVkV~L 133 (183)
.---.|.+++-++.-. +-...|..++.+++||+.++|.-
T Consensus 46 FGLkaL~~~~vv~D~~--g~td~lee~i~~ve~V~svev~~ 84 (88)
T TIGR00489 46 FGLVAINVMVVMGDAE--GGTEAAEESLSGIEGVESVEVTD 84 (88)
T ss_pred ccceeeEEEEEEecCC--cChHHHHHHHhcCCCccEEEEEE
Confidence 4456788888887665 44599999999999999998854
No 46
>COG1888 Uncharacterized protein conserved in archaea [Function unknown]
Probab=55.38 E-value=64 Score=25.46 Aligned_cols=62 Identities=18% Similarity=0.216 Sum_probs=42.4
Q ss_pred EEEecCCCcccHHHHHHhhccCCCceeeEEEEecc-------EEEEEeccceeeecccchHHHHHHHHhcCceeEe
Q 030077 102 FQADGAMNETAIPAVTQALQGTEGISDLKVQVIEG-------IATVELKKQTTVQATGVAANLVEIIQGSGFKLQT 170 (183)
Q Consensus 102 FKaEGM~Ce~Ci~~VtkALE~ieGVsdVkV~LeeG-------~AtVe~dkqttvqatgvas~LvEaIe~aGFkVq~ 170 (183)
+.+-=.+.+.-+.-+.+.|.+++||..|.+.+.+= ..+++- ...+ -+.|+++|++.|=-++.
T Consensus 10 LDvlKP~~~p~ive~A~~lskl~gVegVNItv~eiD~et~~~~itIeG-~~ld------ydei~~~iE~~Gg~IHS 78 (97)
T COG1888 10 LDVLKPHRGPTIVELALELSKLEGVEGVNITVTEIDVETENLKITIEG-TNLD------YDEIEEVIEELGGAIHS 78 (97)
T ss_pred eeecCCcCCCcHHHHHHHHhhcCCcceEEEEEEEeeehhcceEEEEEc-CCCC------HHHHHHHHHHcCCeeee
Confidence 34444556667788899999999999888877542 222222 2223 48999999999976654
No 47
>PF14437 MafB19-deam: MafB19-like deaminase
Probab=55.27 E-value=23 Score=29.39 Aligned_cols=38 Identities=13% Similarity=0.159 Sum_probs=33.2
Q ss_pred EEEEEEecCCCcccHHHHHHhhccCCCceeeEEEEe-ccE
Q 030077 99 TMYFQADGAMNETAIPAVTQALQGTEGISDLKVQVI-EGI 137 (183)
Q Consensus 99 tM~FKaEGM~Ce~Ci~~VtkALE~ieGVsdVkV~Le-eG~ 137 (183)
.|.+.|+=-.|..|-.-|..+.+++ |++.+.|.-. .|.
T Consensus 101 ~~tm~Vdr~vC~~C~~~i~~~a~~l-Gl~~L~I~~~~sG~ 139 (146)
T PF14437_consen 101 SMTMYVDRDVCGYCGGDIPSMAEKL-GLKSLTIHEPDSGK 139 (146)
T ss_pred eEEEEECcccchHHHHHHHHHHHHc-CCCeEEEEecCCCc
Confidence 4666677899999999999999998 9999999988 773
No 48
>PF11210 DUF2996: Protein of unknown function (DUF2996); InterPro: IPR021374 This family of proteins has no known function.
Probab=54.20 E-value=12 Score=30.25 Aligned_cols=29 Identities=31% Similarity=0.541 Sum_probs=26.4
Q ss_pred CCCcccHHHHHHhhccCCCceeeEEEEecc
Q 030077 107 AMNETAIPAVTQALQGTEGISDLKVQVIEG 136 (183)
Q Consensus 107 M~Ce~Ci~~VtkALE~ieGVsdVkV~LeeG 136 (183)
++.++=+|+++++|++- |++|+++++.++
T Consensus 10 fi~ed~lPaL~~~l~~~-Gi~d~~L~f~~~ 38 (119)
T PF11210_consen 10 FIEEDFLPALKKALEKE-GISDVELSFEKN 38 (119)
T ss_pred HHHHhhhHHHHHHHHHc-CCCcceEEeccC
Confidence 46678899999999996 999999999998
No 49
>PRK10555 aminoglycoside/multidrug efflux system; Provisional
Probab=53.77 E-value=17 Score=36.98 Aligned_cols=55 Identities=9% Similarity=0.129 Sum_probs=41.7
Q ss_pred cccHHHHHHhhccCCCceeeEEEEeccEEEEEeccceeeecccchHHHHHHHHhc
Q 030077 110 ETAIPAVTQALQGTEGISDLKVQVIEGIATVELKKQTTVQATGVAANLVEIIQGS 164 (183)
Q Consensus 110 e~Ci~~VtkALE~ieGVsdVkV~LeeG~AtVe~dkqttvqatgvas~LvEaIe~a 164 (183)
+.....++..|+.++||++|++.-.+.+..|++|++.-.+--=+.+.+..+|+..
T Consensus 156 ~~~~~~l~~~L~~v~GV~~V~~~G~~~ei~V~vD~~kl~~~gls~~~v~~al~~~ 210 (1037)
T PRK10555 156 DYVASNIQDPLSRVNGVGDIDAYGSQYSMRIWLDPAKLNSFQMTTKDVTDAIESQ 210 (1037)
T ss_pred HHHHHHHHHHhhcCCCeEEEEEcCCceEEEEEECHHHHHHcCCCHHHHHHHHHHh
Confidence 3455779999999999999999866667889998865433333568888888854
No 50
>PF03698 UPF0180: Uncharacterised protein family (UPF0180); InterPro: IPR005370 The members of this family are small uncharacterised proteins.
Probab=53.13 E-value=11 Score=28.17 Aligned_cols=20 Identities=20% Similarity=0.418 Sum_probs=18.0
Q ss_pred chHHHHHHHHhcCceeEeee
Q 030077 153 VAANLVEIIQGSGFKLQTLN 172 (183)
Q Consensus 153 vas~LvEaIe~aGFkVq~l~ 172 (183)
..+.|++++++.||+|+.|.
T Consensus 9 ~Ls~v~~~L~~~GyeVv~l~ 28 (80)
T PF03698_consen 9 GLSNVKEALREKGYEVVDLE 28 (80)
T ss_pred CchHHHHHHHHCCCEEEecC
Confidence 35789999999999999997
No 51
>cd04874 ACT_Af1403 N-terminal ACT domain of the yet uncharacterized, small (~133 a.a.), putative amino acid binding protein, Af1403, and related domains. This CD includes the N-terminal ACT domain of the yet uncharacterized, small (~133 a.a.), putative amino acid binding protein, Af1403, from Archaeoglobus fulgidus and other related archeal ACT domains. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=52.83 E-value=41 Score=21.28 Aligned_cols=33 Identities=15% Similarity=0.411 Sum_probs=25.4
Q ss_pred CceEEEEEEecCCCcccHHHHHHhhccCCCceeeEE
Q 030077 96 DKLTMYFQADGAMNETAIPAVTQALQGTEGISDLKV 131 (183)
Q Consensus 96 ~~ltM~FKaEGM~Ce~Ci~~VtkALE~ieGVsdVkV 131 (183)
+.-.|.|.+++. .-...+.+.|++++||..+.+
T Consensus 39 ~~~~~~i~~~~~---~~~~~~~~~L~~~~~v~~v~~ 71 (72)
T cd04874 39 GKARIYMELEGV---GDIEELVEELRSLPIVREVEI 71 (72)
T ss_pred CeEEEEEEEecc---ccHHHHHHHHhCCCCeEEEEe
Confidence 344567888875 455588899999999998875
No 52
>TIGR02945 SUF_assoc FeS assembly SUF system protein. Members of this family belong to the broader Pfam family pfam01883, or Domain of Unknown Function DUF59. Many members of DUF59 are candidate ring hydroxylating complex subunits. However, members of the narrower family defined here all are found in genomes that carry the FeS assembly SUF system. For 70 % of these species, the member of this protein family is found as part of the SUF locus, usually immediately downstream of the sufS gene.
Probab=52.58 E-value=34 Score=24.77 Aligned_cols=39 Identities=13% Similarity=0.262 Sum_probs=28.4
Q ss_pred CceEEEEEEecCCCccc---HHHHHHhhccCCCceeeEEEEe
Q 030077 96 DKLTMYFQADGAMNETA---IPAVTQALQGTEGISDLKVQVI 134 (183)
Q Consensus 96 ~~ltM~FKaEGM~Ce~C---i~~VtkALE~ieGVsdVkV~Le 134 (183)
+.++..+..-...|.-. ...++++|.+++|+++|+|++.
T Consensus 37 ~~v~i~l~l~~p~~~~~~~l~~~i~~al~~l~gv~~v~v~i~ 78 (99)
T TIGR02945 37 GHVDIQMTLTAPNCPVAGSMPGEVENAVRAVPGVGSVTVELV 78 (99)
T ss_pred CeEEEEEEECCCCCChHHHHHHHHHHHHHhCCCCceEEEEEE
Confidence 35666666655555533 3568889999999999999985
No 53
>PF08262 Lem_TRP: Leucophaea maderae tachykinin-related peptide ; InterPro: IPR013206 These peptides are designated Leucophaea maderae (Madeira cockroach) tachykinin-related peptides (Lem TRPs). Some were isolated from the midgut of L. maderae, whereas others appear to be brain specific. The Lem TRPs of the brain are myotropic and induce increases in the amplitude and frequency of spontaneous contractions and tonus of hindgut muscle in L. maderae []. They were also isolated from brain-corpora, cardiaca-corpora, allata-suboesophageal ganglion extracts of Locusta migratoria (Migratory locust). They stimulate visceral muscle contractions of the oviduct and the foregut of L. migratoria [].
Probab=52.05 E-value=5.4 Score=20.01 Aligned_cols=7 Identities=71% Similarity=1.398 Sum_probs=5.4
Q ss_pred cccccce
Q 030077 51 WGFNGMR 57 (183)
Q Consensus 51 ~~~~~~r 57 (183)
-||||+|
T Consensus 4 mgf~g~r 10 (10)
T PF08262_consen 4 MGFHGMR 10 (10)
T ss_pred ccccccC
Confidence 4789886
No 54
>COG0217 Uncharacterized conserved protein [Function unknown]
Probab=50.98 E-value=17 Score=32.45 Aligned_cols=47 Identities=17% Similarity=0.395 Sum_probs=35.3
Q ss_pred HHHHhhccCCCceeeEEEEeccEEEEEeccceeeecccchHHHHHHHHhcCceeEeee
Q 030077 115 AVTQALQGTEGISDLKVQVIEGIATVELKKQTTVQATGVAANLVEIIQGSGFKLQTLN 172 (183)
Q Consensus 115 ~VtkALE~ieGVsdVkV~LeeG~AtVe~dkqttvqatgvas~LvEaIe~aGFkVq~l~ 172 (183)
-..-+||+ |+.||..+ +|..+|-..+..- ..++++++++||+...--
T Consensus 152 l~e~~iea--gaeDv~~~--~~~~~V~t~p~~~-------~~V~~~L~~~g~~~~~ae 198 (241)
T COG0217 152 LLEAAIEA--GAEDVEED--EGSIEVYTEPEDF-------NKVKEALEAAGYEIESAE 198 (241)
T ss_pred HHHHHHHC--CchhhhcC--CCeEEEEEChHHH-------HHHHHHHHHcCCceeeee
Confidence 34556676 99999998 6666666655444 899999999999877633
No 55
>TIGR02898 spore_YhcN_YlaJ sporulation lipoprotein, YhcN/YlaJ family. YhcN and YlaJ are predicted lipoproteins that have been detected as spore proteins but not vegetative proteins in Bacillus subtilis. Both appear to be expressed under control of the RNA polymerase sigma-G factor. The YlaJ-like members of this family have a low-complexity, strongly acidic 40-residue C-terminal domain that is not included in the seed alignment for this model. A portion of the low-complexity region between the lipoprotein signal sequence and the main conserved region of the protein family was also excised from the seed alignment.
Probab=50.94 E-value=47 Score=27.42 Aligned_cols=51 Identities=16% Similarity=0.218 Sum_probs=37.7
Q ss_pred ccHHHHHHhhccCCCceeeEEEEeccEEEEEeccceeeecccchHHHHHHHH
Q 030077 111 TAIPAVTQALQGTEGISDLKVQVIEGIATVELKKQTTVQATGVAANLVEIIQ 162 (183)
Q Consensus 111 ~Ci~~VtkALE~ieGVsdVkV~LeeG~AtVe~dkqttvqatgvas~LvEaIe 162 (183)
.=+.+|.+.+.+++||+++.|-+.+..|.|-++-.... -......|+..|.
T Consensus 54 ~~A~~Ia~~v~~v~~V~dA~vvVtg~~A~Vgv~~~~~~-~~~~~~~iK~~Va 104 (158)
T TIGR02898 54 DVADEIASEAAKVKGVKDATVVITGNYAYVGVDLTNGL-EGSVTDELKEKVA 104 (158)
T ss_pred HHHHHHHHHHhcCCCCceEEEEEECCEEEEEEEcCCCc-chhhHHHHHHHHH
Confidence 56788999999999999999999999999999754331 0112345555554
No 56
>PRK03094 hypothetical protein; Provisional
Probab=49.24 E-value=15 Score=27.76 Aligned_cols=21 Identities=10% Similarity=0.328 Sum_probs=18.3
Q ss_pred chHHHHHHHHhcCceeEeeec
Q 030077 153 VAANLVEIIQGSGFKLQTLNL 173 (183)
Q Consensus 153 vas~LvEaIe~aGFkVq~l~l 173 (183)
..+.|+++++..||+|+.|+-
T Consensus 9 ~Ls~i~~~L~~~GYeVv~l~~ 29 (80)
T PRK03094 9 SLTDVQQALKQKGYEVVQLRS 29 (80)
T ss_pred CcHHHHHHHHHCCCEEEecCc
Confidence 357899999999999999974
No 57
>PF00873 ACR_tran: AcrB/AcrD/AcrF family; InterPro: IPR001036 The Escherichia coli acrA and acrB genes encode a multi-drug efflux system that is believed to protect the bacterium against hydrophobic inhibitors []. The E. coli AcrB protein is a transporter that is energized by proton-motive force and that shows the widest substrate specificity among all known multidrug pumps, ranging from most of the currently used antibiotics, disinfectants, dyes, and detergents to simple solvents. The structure of ligand-free AcrB shows that it is a homotrimer of 110kDa per subunit. Each subunit contains 12 transmembrane helices and two large periplasmic domains (each exceeding 300 residues) between helices 1 and 2, and helices 7 and 8. X-ray analysis of the overexpressed AcrB protein demonstrated that the three periplasmic domains form, in the centre, a funnel-like structure and a connected narrow (or closed) pore. The pore is opened to the periplasm through three vestibules located at subunit interfaces. These vestibules were proposed to allow direct access of drugs from the periplasm as well as the outer leaflet of the cytoplasmic membrane. The three transmembrane domains of AcrB protomers form a large, 30A-wide central cavity that spans the cytoplasmic membrane and extends to the cytoplasm X-ray crystallographic structures of the trimeric AcrB pump from E. coli with four structurally diverse ligands demonstrated that three molecules of ligand bind simultaneously to the extremely large central cavity of 5000 cubic angstroms, primarily by hydrophobic, aromatic stacking and van der Waals interactions. Each ligand uses a slightly different subset of AcrB residues for binding. The bound ligand molecules often interact with each other, stabilising the binding. ; GO: 0005215 transporter activity, 0006810 transport, 0016020 membrane; PDB: 2V50_B 1T9U_A 2HRT_B 3NOC_A 3NOG_A 4DX7_A 1OYD_A 3AOB_A 1T9V_A 4DX6_B ....
Probab=48.91 E-value=12 Score=37.39 Aligned_cols=85 Identities=14% Similarity=0.215 Sum_probs=58.6
Q ss_pred CceeeecCCCCceEEEEEEecC--------CCcccHHHHHHhhccCCCceeeEEEE-eccEEEEEeccceeeecccchHH
Q 030077 86 QPVAVPVSPSDKLTMYFQADGA--------MNETAIPAVTQALQGTEGISDLKVQV-IEGIATVELKKQTTVQATGVAAN 156 (183)
Q Consensus 86 ~~~~~~~~~~~~ltM~FKaEGM--------~Ce~Ci~~VtkALE~ieGVsdVkV~L-eeG~AtVe~dkqttvqatgvas~ 156 (183)
+|...+.++++.=.|.+.+.|. ..+.+-..++..|+.++||.+|++.= .+.+..|++|++.-.+.-=+.+.
T Consensus 123 ~p~i~~~~~~~~~i~~~~l~~~~~~~~~~~l~~~~~~~l~~~L~~i~gV~~v~~~G~~~~ei~i~~d~~kl~~~gls~~~ 202 (1021)
T PF00873_consen 123 EPQIFKFDPSDSPIMILALTSDDGTLDLKELRDYAEEQLKPRLERIPGVARVDISGGREREIQIELDPEKLAAYGLSLSD 202 (1021)
T ss_dssp HHEEEEEEEECCEEEEEEEEESSSSS-HHHHHHHHHHCTHHHHHTSTTEEEEEESSS--EEEEEEE-HHHHHHTT--HHH
T ss_pred CCceeeccCCCceeEEEEeccCCCCCCHHHHHHHHHHHHHHhccceeEEEEEEeccchhhhhhheechhhhhhhCCCHHH
Confidence 4555677778877788777777 12334567899999999999999864 45678889988654333335688
Q ss_pred HHHHHHhcCceeEe
Q 030077 157 LVEIIQGSGFKLQT 170 (183)
Q Consensus 157 LvEaIe~aGFkVq~ 170 (183)
|.++|+....+.-.
T Consensus 203 v~~~l~~~n~~~~~ 216 (1021)
T PF00873_consen 203 VAQALQANNVNQPA 216 (1021)
T ss_dssp HHHHHHHHSCEEEE
T ss_pred HHHHHHHhhhhccC
Confidence 99999988876543
No 58
>PRK04435 hypothetical protein; Provisional
Probab=48.39 E-value=35 Score=27.13 Aligned_cols=36 Identities=14% Similarity=0.308 Sum_probs=29.2
Q ss_pred CceEEEEEEecCCCcccHHHHHHhhccCCCceeeEE
Q 030077 96 DKLTMYFQADGAMNETAIPAVTQALQGTEGISDLKV 131 (183)
Q Consensus 96 ~~ltM~FKaEGM~Ce~Ci~~VtkALE~ieGVsdVkV 131 (183)
...++.|.++-..-+..+..+-..|++++||.+|++
T Consensus 108 g~a~vs~tVevs~~~~~L~~Li~~L~~i~gV~~V~i 143 (147)
T PRK04435 108 GRANVTISIDTSSMEGDIDELLEKLRNLDGVEKVEL 143 (147)
T ss_pred CEEEEEEEEEeCChHHHHHHHHHHHHcCCCcEEEEE
Confidence 345666777776667789999999999999999876
No 59
>PRK10553 assembly protein for periplasmic nitrate reductase; Provisional
Probab=47.81 E-value=44 Score=25.10 Aligned_cols=56 Identities=14% Similarity=0.226 Sum_probs=37.5
Q ss_pred HHHHHHhhccCCCceeeEEEEeccEEEEEeccceeeecccchHHHHHHHHhcCc--eeEeeeccc
Q 030077 113 IPAVTQALQGTEGISDLKVQVIEGIATVELKKQTTVQATGVAANLVEIIQGSGF--KLQTLNLSF 175 (183)
Q Consensus 113 i~~VtkALE~ieGVsdVkV~LeeG~AtVe~dkqttvqatgvas~LvEaIe~aGF--kVq~l~l~f 175 (183)
...|+++|.++||+.=--.+-++|+..|.++.+.. ..+.+.|...-- .|...+|-|
T Consensus 19 ~~~V~~~l~~ipg~Evh~~d~~~GKiVVtiE~~~~-------~~~~~~i~~I~~l~GVlsa~lVY 76 (87)
T PRK10553 19 ISDISTQLNAFPGCEVAVSDAPSGQLIVVVEAEDS-------ETLLQTIESVRNVEGVLAVSLVY 76 (87)
T ss_pred HHHHHHHHHcCCCcEEEeecCCCCeEEEEEEeCCh-------HHHHHHHHHHHcCCCceEEEEEE
Confidence 67899999999998766666677998888877666 444444433221 355555555
No 60
>cd04902 ACT_3PGDH-xct C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH). The C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH), with an extended C-terminal (xct) region from bacteria, archaea, fungi, and plants. 3PGDH is an enzyme that belongs to the D-isomer specific, 2-hydroxyacid dehydrogenase family and catalyzes the oxidation of D-3-phosphoglycerate to 3- phosphohydroxypyruvate, which is the first step in the biosynthesis of L-serine, using NAD+ as the oxidizing agent. In bacteria, 3PGDH is feedback-controlled by the end product L-serine in an allosteric manner. Some 3PGDH enzymes have an additional domain formed by an extended C-terminal region. This additional domain introduces significant asymmetry to the homotetramer. Adjacent ACT (regulatory) domains interact, creating two serine-binding sites, however, this asymmetric arrangement results in the formation of two different and distinct domain interfaces between iden
Probab=47.26 E-value=44 Score=21.65 Aligned_cols=33 Identities=24% Similarity=0.301 Sum_probs=26.2
Q ss_pred CCceEEEEEEecCCCcccHHHHHHhhccCCCceeeEE
Q 030077 95 SDKLTMYFQADGAMNETAIPAVTQALQGTEGISDLKV 131 (183)
Q Consensus 95 ~~~ltM~FKaEGM~Ce~Ci~~VtkALE~ieGVsdVkV 131 (183)
.+.-.|.|.+++.. ...+-+.|.+++||..+.+
T Consensus 38 ~~~~~~~i~v~~~~----~~~~~~~l~~~~~v~~v~~ 70 (73)
T cd04902 38 GGEALMVLSVDEPV----PDEVLEELRALPGILSAKV 70 (73)
T ss_pred CCEEEEEEEeCCCC----CHHHHHHHHcCCCccEEEE
Confidence 35556889999955 3488999999999988875
No 61
>PRK15127 multidrug efflux system protein AcrB; Provisional
Probab=47.23 E-value=44 Score=34.30 Aligned_cols=56 Identities=7% Similarity=0.147 Sum_probs=40.9
Q ss_pred CcccHHHHHHhhccCCCceeeEEEEeccEEEEEeccceeeecccchHHHHHHHHhc
Q 030077 109 NETAIPAVTQALQGTEGISDLKVQVIEGIATVELKKQTTVQATGVAANLVEIIQGS 164 (183)
Q Consensus 109 Ce~Ci~~VtkALE~ieGVsdVkV~LeeG~AtVe~dkqttvqatgvas~LvEaIe~a 164 (183)
++.....|+..|+.++||.+|++.=...+..|++|++.-.+--=+.+.|.++|+..
T Consensus 155 ~~~~~~~l~~~L~~v~GV~~V~~~G~~~ei~V~vDp~kl~~~gls~~~V~~~l~~~ 210 (1049)
T PRK15127 155 SDYVAANMKDPISRTSGVGDVQLFGSQYAMRIWMNPNELNKFQLTPVDVINAIKAQ 210 (1049)
T ss_pred HHHHHHHHHHHHhcCCCceEEEEcCCceEEEEEeCHHHHHHcCCCHHHHHHHHHHh
Confidence 33455679999999999999998755667888888865432222567888888854
No 62
>PRK00110 hypothetical protein; Validated
Probab=46.75 E-value=33 Score=30.02 Aligned_cols=50 Identities=12% Similarity=0.239 Sum_probs=36.2
Q ss_pred HHHhhccCCCceeeEEEEeccEEEEEeccceeeecccchHHHHHHHHhcCceeEeeecccc
Q 030077 116 VTQALQGTEGISDLKVQVIEGIATVELKKQTTVQATGVAANLVEIIQGSGFKLQTLNLSFD 176 (183)
Q Consensus 116 VtkALE~ieGVsdVkV~LeeG~AtVe~dkqttvqatgvas~LvEaIe~aGFkVq~l~l~f~ 176 (183)
..-|||+ |+.|+++ ++|...|-.++.-. ..+++++++.||++..-.+.|-
T Consensus 151 ~e~aiea--GaeDv~~--e~~~~~i~~~p~~~-------~~v~~~L~~~g~~~~~sei~~~ 200 (245)
T PRK00110 151 MEAALEA--GAEDVET--DDESFEVITAPEDF-------EAVRDALEAAGLEAESAEVTMI 200 (245)
T ss_pred HHHHHhC--CCCEeec--cCCeEEEEECHHHH-------HHHHHHHHHcCCCeeeeEEEEe
Confidence 3456765 9998764 66765555555444 8999999999999887777664
No 63
>TIGR03406 FeS_long_SufT probable FeS assembly SUF system protein SufT. The function is unknown for this protein family, but members are found almost always in operons for the the SUF system of iron-sulfur cluster biosynthesis. The SUF system is present elsewhere on the chromosome for those few species where SUF genes are not adjacent. This family shares this property of association with the SUF system with a related family, TIGR02945. TIGR02945 consists largely of a DUF59 domain (see Pfam family pfam01883), while this protein is about double the length, with a unique N-terminal domain and DUF59 C-terminal domain. A location immediately downstream of the cysteine desulfurase gene sufS in many contexts suggests the gene symbol sufT. Note that some other homologs of this family and of TIGR02945, but no actual members of this family, are found in operons associated with phenylacetic acid (or other ring-hydroxylating) degradation pathways.
Probab=46.03 E-value=20 Score=29.93 Aligned_cols=22 Identities=9% Similarity=0.395 Sum_probs=18.9
Q ss_pred HHHHHHhhccCCCceeeEEEEe
Q 030077 113 IPAVTQALQGTEGISDLKVQVI 134 (183)
Q Consensus 113 i~~VtkALE~ieGVsdVkV~Le 134 (183)
...|+++|.+++||++|+|++.
T Consensus 133 ~~dV~~aL~~l~gV~~V~V~l~ 154 (174)
T TIGR03406 133 VEDVEDKVLAVPNVDEVEVELV 154 (174)
T ss_pred HHHHHHHHHhCCCceeEEEEEE
Confidence 3569999999999999999873
No 64
>cd04882 ACT_Bt0572_2 C-terminal ACT domain of a novel protein composed of just two ACT domains. Included in this CD is the C-terminal ACT domain of a novel protein composed of just two ACT domains, as seen in the yet uncharacterized structure (pdb 2F06) of the Bt0572 protein from Bacteroides thetaiotaomicron and related proteins. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=45.35 E-value=41 Score=21.30 Aligned_cols=50 Identities=22% Similarity=0.349 Sum_probs=28.8
Q ss_pred ccHHHHHHhhccCCCcee--eEEEEec--cEEEEEeccceeeecccchHHHHHHHHhcCcee
Q 030077 111 TAIPAVTQALQGTEGISD--LKVQVIE--GIATVELKKQTTVQATGVAANLVEIIQGSGFKL 168 (183)
Q Consensus 111 ~Ci~~VtkALE~ieGVsd--VkV~Lee--G~AtVe~dkqttvqatgvas~LvEaIe~aGFkV 168 (183)
|-..++.+.|.+- |+.= +...... |.+.+.+.-+. .+.+.+.++++||++
T Consensus 11 G~L~~i~~~l~~~-~~nI~~i~~~~~~~~~~~~v~~~ve~-------~~~~~~~L~~~G~~v 64 (65)
T cd04882 11 GGLHEILQILSEE-GINIEYMYAFVEKKGGKALLIFRTED-------IEKAIEVLQERGVEL 64 (65)
T ss_pred cHHHHHHHHHHHC-CCChhheEEEccCCCCeEEEEEEeCC-------HHHHHHHHHHCCceE
Confidence 4455666667664 4433 2222222 34444443332 479999999999986
No 65
>cd04886 ACT_ThrD-II-like C-terminal ACT domain of biodegradative (catabolic) threonine dehydratase II (ThrD-II) and other related ACT domains. This CD includes the C-terminal ACT domain of biodegradative (catabolic) threonine dehydratase II (ThrD-II) and other related ACT domains. The Escherichia coli tdcB gene product, ThrD-II, anaerobically catalyzes the pyridoxal phosphate-dependent dehydration of L-threonine and L-serine to ammonia and to alpha-ketobutyrate and pyruvate, respectively. Tetrameric ThrD-II is subject to allosteric activation by AMP, inhibition by alpha-keto acids, and catabolite inactivation by several metabolites of glycolysis and the citric acid cycle. Also included in this CD are N-terminal ACT domains present in smaller (~170 a.a.) archaeal proteins of unknown function. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=44.98 E-value=77 Score=19.86 Aligned_cols=62 Identities=13% Similarity=0.228 Sum_probs=37.6
Q ss_pred ecCCCcccHHHHHHhhccCCCceeeEEEEe-------ccEEEEEeccceeeecccchHHHHHHHHhcCceeE
Q 030077 105 DGAMNETAIPAVTQALQGTEGISDLKVQVI-------EGIATVELKKQTTVQATGVAANLVEIIQGSGFKLQ 169 (183)
Q Consensus 105 EGM~Ce~Ci~~VtkALE~ieGVsdVkV~Le-------eG~AtVe~dkqttvqatgvas~LvEaIe~aGFkVq 169 (183)
+.-.=.|-...|.++|.+. |+.=..+... .+.+.+.+.=.+. .......+.+.|++.||++.
T Consensus 4 ~~~d~~G~L~~i~~~i~~~-~~nI~~i~~~~~~~~~~~~~~~~~i~v~~~--~~~~l~~l~~~l~~~g~~~~ 72 (73)
T cd04886 4 ELPDRPGQLAKLLAVIAEA-GANIIEVSHDRAFKTLPLGEVEVELTLETR--GAEHIEEIIAALREAGYDVR 72 (73)
T ss_pred EeCCCCChHHHHHHHHHHc-CCCEEEEEEEeccCCCCCceEEEEEEEEeC--CHHHHHHHHHHHHHcCCEEe
Confidence 3334456778888999774 5555555443 3555555432211 11234699999999999874
No 66
>cd02410 archeal_CPSF_KH The archaeal cleavage and polyadenylation specificity factor (CPSF) contains an N-terminal K homology RNA-binding domain (KH). The archeal CPSFs are predicted to be metal-dependent RNases belonging to the beta-CASP family, a subgroup enzymes within the metallo-beta-lactamase fold. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH domains are known to bind single-stranded RNA or DNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=44.81 E-value=58 Score=27.05 Aligned_cols=60 Identities=25% Similarity=0.359 Sum_probs=47.9
Q ss_pred CcccHHHHHHhhccCCCceeeEEEEeccEEEEEeccceeeecccchHHHHHHHHhcCceeE
Q 030077 109 NETAIPAVTQALQGTEGISDLKVQVIEGIATVELKKQTTVQATGVAANLVEIIQGSGFKLQ 169 (183)
Q Consensus 109 Ce~Ci~~VtkALE~ieGVsdVkV~LeeG~AtVe~dkqttvqatgvas~LvEaIe~aGFkVq 169 (183)
-+-+...|.+.+-+-.||.|+..+=..|++.++..++--+..-| -..+++...+.|+...
T Consensus 51 ~e~A~~~I~~ivP~ea~i~di~Fd~~tGEV~IeaeKPG~ViGk~-g~~~reI~~~tgW~p~ 110 (145)
T cd02410 51 PEEAIKIILEIVPEEAGITDIYFDDDTGEVIIEAEKPGLVIGKG-GSTLREITRETGWAPK 110 (145)
T ss_pred HHHHHHHHHHhCCCccCceeeEecCCCcEEEEEEcCCeEEEecC-chhHHHHHHHhCCeeE
Confidence 45577788888876679999999999999999999987654444 4567888889998643
No 67
>cd04908 ACT_Bt0572_1 N-terminal ACT domain of a novel protein composed almost entirely of two tandem ACT domains. Included in this CD is the N-terminal ACT domain of a novel protein composed almost entirely of two tandem ACT domains as seen in the uncharacterized structure (pdb 2F06) of the Bt0572 protein from Bacteroides thetaiotaomicron and related ACT domains. These tandem ACT domain proteins belong to the superfamily of ACT regulatory domains.
Probab=43.64 E-value=95 Score=20.53 Aligned_cols=58 Identities=19% Similarity=0.241 Sum_probs=34.9
Q ss_pred EecCCCcccHHHHHHhhccCCCce--eeEEEEeccEEEEEeccceeeecccchHHHHHHHHhcCceeE
Q 030077 104 ADGAMNETAIPAVTQALQGTEGIS--DLKVQVIEGIATVELKKQTTVQATGVAANLVEIIQGSGFKLQ 169 (183)
Q Consensus 104 aEGM~Ce~Ci~~VtkALE~ieGVs--dVkV~LeeG~AtVe~dkqttvqatgvas~LvEaIe~aGFkVq 169 (183)
|+=....|-..+|.++|.+- |+. .+-+.-.++.+.+.+.- + ..+.+++.+++.||++.
T Consensus 6 v~v~d~pG~La~v~~~l~~~-~inI~~i~~~~~~~~~~~rl~~--~-----~~~~~~~~L~~~G~~v~ 65 (66)
T cd04908 6 VFLENKPGRLAAVTEILSEA-GINIRALSIADTSEFGILRLIV--S-----DPDKAKEALKEAGFAVK 65 (66)
T ss_pred EEEcCCCChHHHHHHHHHHC-CCCEEEEEEEecCCCCEEEEEE--C-----CHHHHHHHHHHCCCEEE
Confidence 33334567778888888773 553 33332222234444432 1 34789999999999974
No 68
>cd00292 EF1B Elongation factor 1 beta (EF1B) guanine nucleotide exchange domain. EF1B catalyzes the exchange of GDP bound to the G-protein, EF1A, for GTP, an important step in the elongation cycle of the protein biosynthesis. EF1A binds to and delivers the aminoacyl tRNA to the ribosome. The guanine nucleotide exchange domain of EF1B, which is the alpha subunit in yeast, is responsible for the catalysis of this exchange reaction.
Probab=42.29 E-value=52 Score=24.67 Aligned_cols=39 Identities=13% Similarity=0.282 Sum_probs=31.9
Q ss_pred CCCCceEEEEEEecCCCcccHHHHHHhhccCCCceeeEEEE
Q 030077 93 SPSDKLTMYFQADGAMNETAIPAVTQALQGTEGISDLKVQV 133 (183)
Q Consensus 93 ~~~~~ltM~FKaEGM~Ce~Ci~~VtkALE~ieGVsdVkV~L 133 (183)
+---.|.+.+-++.-- +-...+..++.+++||+.++|.-
T Consensus 46 FGlk~L~i~~vv~D~~--~~td~lee~i~~~d~VqsveI~~ 84 (88)
T cd00292 46 FGLKALQIYCVVEDDE--GGTDELEEAISEEDGVQSVDVEA 84 (88)
T ss_pred eEeeEEEEEEEEEeCC--cCcHHHHHHHhccCCceEEEEEE
Confidence 5567788888887664 55699999999999999999864
No 69
>PF08002 DUF1697: Protein of unknown function (DUF1697); InterPro: IPR012545 This family contains many hypothetical bacterial proteins.; PDB: 2HIY_B.
Probab=42.26 E-value=42 Score=26.48 Aligned_cols=59 Identities=17% Similarity=0.364 Sum_probs=36.0
Q ss_pred HHHHHHhhccCCCceeeEEEEeccEEEEEeccceeeecccchHHHHHHHH-hcCceeEeeecccc
Q 030077 113 IPAVTQALQGTEGISDLKVQVIEGIATVELKKQTTVQATGVAANLVEIIQ-GSGFKLQTLNLSFD 176 (183)
Q Consensus 113 i~~VtkALE~ieGVsdVkV~LeeG~AtVe~dkqttvqatgvas~LvEaIe-~aGFkVq~l~l~f~ 176 (183)
-..++++|+++ |-++|+-.+.+|-+.|+ ..... ...+..|.++|+ ..||++..+-++-+
T Consensus 21 MaeLr~~l~~~-Gf~~V~Tyi~SGNvvf~-~~~~~---~~l~~~ie~~l~~~fG~~v~v~vrs~~ 80 (137)
T PF08002_consen 21 MAELREALEDL-GFTNVRTYIQSGNVVFE-SDRDP---AELAAKIEKALEERFGFDVPVIVRSAE 80 (137)
T ss_dssp HHHHHHHHHHC-T-EEEEEETTTTEEEEE-ESS-H---HHHHHHHHHHHHHH-TT---EEEEEHH
T ss_pred HHHHHHHHHHc-CCCCceEEEeeCCEEEe-cCCCh---HHHHHHHHHHHHHhcCCCeEEEEeeHH
Confidence 35689999998 99999999999999999 22222 112333444443 36998776665544
No 70
>TIGR00915 2A0602 The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family. This family is one of several subfamilies within the scope of pfam model pfam00873.
Probab=42.12 E-value=31 Score=35.29 Aligned_cols=54 Identities=13% Similarity=0.133 Sum_probs=41.3
Q ss_pred ccHHHHHHhhccCCCceeeEEEEeccEEEEEeccceeeecccchHHHHHHHHhc
Q 030077 111 TAIPAVTQALQGTEGISDLKVQVIEGIATVELKKQTTVQATGVAANLVEIIQGS 164 (183)
Q Consensus 111 ~Ci~~VtkALE~ieGVsdVkV~LeeG~AtVe~dkqttvqatgvas~LvEaIe~a 164 (183)
.....|+..|+.++||.+|++.-.+.+..|++|++.-.+--=+.+.+.++|+..
T Consensus 157 ~~~~~l~~~L~~v~GV~~V~~~G~~~ei~V~vD~~kl~~~gls~~dV~~~i~~~ 210 (1044)
T TIGR00915 157 YIASNMVDPISRLEGVGDVQLFGSQYAMRIWLDPAKLNSYQLTPADVISAIQAQ 210 (1044)
T ss_pred HHHHHHHHHHhCCCCceEEEecCCceEEEEEECHHHHHHcCCCHHHHHHHHHHh
Confidence 344679999999999999999877777889998854432222468888888874
No 71
>TIGR02830 spore_III_AG stage III sporulation protein AG. CC A comparative genome analysis of all sequenced genomes of shows a number of proteins conserved strictly among the endospore-forming subset of the Firmicutes. This protein, a member of this panel, is found in a spore formation operon and is designated stage III sporulation protein AG.
Probab=41.74 E-value=22 Score=30.25 Aligned_cols=29 Identities=21% Similarity=0.287 Sum_probs=22.8
Q ss_pred cHHHHHHhhccCCCceeeEE--EEeccEEEE
Q 030077 112 AIPAVTQALQGTEGISDLKV--QVIEGIATV 140 (183)
Q Consensus 112 Ci~~VtkALE~ieGVsdVkV--~LeeG~AtV 140 (183)
--.+++..|+.|+||.+|+| +|+.+.-.+
T Consensus 62 lE~~L~~iL~~I~GvG~V~VmItl~s~~e~v 92 (186)
T TIGR02830 62 YENELKEILEKIEGVGDVTVMVNLDSSEEKV 92 (186)
T ss_pred HHHHHHHHHHhccCcceeEEEEEECCCceEE
Confidence 35789999999999999987 556665554
No 72
>cd04879 ACT_3PGDH-like ACT_3PGDH-like CD includes the C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH). ACT_3PGDH-like: The ACT_3PGDH-like CD includes the C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH), with or without an extended C-terminal (xct) region found in various bacteria, archaea, fungi, and plants. 3PGDH is an enzyme that belongs to the D-isomer specific, 2-hydroxyacid dehydrogenase family and catalyzes the oxidation of D-3-phosphoglycerate to 3- phosphohydroxypyruvate, which is the first step in the biosynthesis of L-serine, using NAD+ as the oxidizing agent. In bacteria, 3PGDH is feedback controlled by the end product L-serine in an allosteric manner. In the Escherichia coli homotetrameric enzyme, the interface at adjacent ACT (regulatory) domains couples to create an extended beta-sheet. Each regulatory interface forms two serine-binding sites. The mechanism by which serine transmits inhibition to the active
Probab=39.97 E-value=56 Score=20.29 Aligned_cols=31 Identities=19% Similarity=0.281 Sum_probs=24.4
Q ss_pred CceEEEEEEecCCCcccHHHHHHhhccCCCceeeE
Q 030077 96 DKLTMYFQADGAMNETAIPAVTQALQGTEGISDLK 130 (183)
Q Consensus 96 ~~ltM~FKaEGM~Ce~Ci~~VtkALE~ieGVsdVk 130 (183)
+.-.+.|.+++.. ...+.+.|.+++||..|.
T Consensus 39 ~~~~~~~~v~~~~----~~~l~~~l~~~~~V~~v~ 69 (71)
T cd04879 39 GIAYMVLDVDSPV----PEEVLEELKALPGIIRVR 69 (71)
T ss_pred CEEEEEEEcCCCC----CHHHHHHHHcCCCeEEEE
Confidence 4556778887742 668999999999999876
No 73
>PRK09579 multidrug efflux protein; Reviewed
Probab=39.15 E-value=88 Score=32.08 Aligned_cols=78 Identities=10% Similarity=0.053 Sum_probs=46.6
Q ss_pred ceeeecCCCCceEEEEEEecCC------CcccHHHHHHhhccCCCceeeEEEE-eccEEEEEeccceeeecccchHHHHH
Q 030077 87 PVAVPVSPSDKLTMYFQADGAM------NETAIPAVTQALQGTEGISDLKVQV-IEGIATVELKKQTTVQATGVAANLVE 159 (183)
Q Consensus 87 ~~~~~~~~~~~ltM~FKaEGM~------Ce~Ci~~VtkALE~ieGVsdVkV~L-eeG~AtVe~dkqttvqatgvas~LvE 159 (183)
|.....++++...|.+.+.|-. .+.....|+..|+.++||.+|++.= .+.+..|++|++.-.+.-=+.+.|.+
T Consensus 126 P~i~~~~~~~~~v~~~~~~~~~~~~~~L~~~~~~~i~~~L~~i~GV~~V~~~G~~~~ei~V~vd~~kl~~~gls~~dV~~ 205 (1017)
T PRK09579 126 PVLSKEAADASALMYISFYSEEMSNPQITDYLSRVIQPKLATLPGMAEAEILGNQVFAMRLWLDPVKLAGFGLSAGDVTQ 205 (1017)
T ss_pred CeEEeCCCCCcceEEEEEECCCCCHHHHHHHHHHHHHHHhhcCCCceEEEecCCCceEEEEEeCHHHHHHcCCCHHHHHH
Confidence 3433433444445566655421 2224466999999999999987631 22245677776443222224688889
Q ss_pred HHHhc
Q 030077 160 IIQGS 164 (183)
Q Consensus 160 aIe~a 164 (183)
+|+..
T Consensus 206 al~~~ 210 (1017)
T PRK09579 206 AVRRY 210 (1017)
T ss_pred HHHHh
Confidence 99874
No 74
>COG2092 EFB1 Translation elongation factor EF-1beta [Translation, ribosomal structure and biogenesis]
Probab=39.03 E-value=47 Score=25.63 Aligned_cols=29 Identities=24% Similarity=0.330 Sum_probs=23.6
Q ss_pred EecCCCcccHHHHHHhhccCCCceeeEEE
Q 030077 104 ADGAMNETAIPAVTQALQGTEGISDLKVQ 132 (183)
Q Consensus 104 aEGM~Ce~Ci~~VtkALE~ieGVsdVkV~ 132 (183)
+-.-.=++-...++++|++++||..++|-
T Consensus 55 vvv~D~Eg~td~~ee~l~~vegV~sveve 83 (88)
T COG2092 55 VVVEDKEGGTDALEEALEEVEGVESVEVE 83 (88)
T ss_pred EEEcccccCcHHHHHHHhhccCcceEEEE
Confidence 33345577889999999999999999875
No 75
>PRK14054 methionine sulfoxide reductase A; Provisional
Probab=38.19 E-value=69 Score=26.77 Aligned_cols=44 Identities=11% Similarity=0.179 Sum_probs=34.4
Q ss_pred ccHHHHHHhhccCCCceeeEEEEeccE-------------------EEEEeccceeeecccchHHHHH
Q 030077 111 TAIPAVTQALQGTEGISDLKVQVIEGI-------------------ATVELKKQTTVQATGVAANLVE 159 (183)
Q Consensus 111 ~Ci~~VtkALE~ieGVsdVkV~LeeG~-------------------AtVe~dkqttvqatgvas~LvE 159 (183)
||-=.++..++.++||.++.|=+..|. +.|.+|+..+ +-+.|.+
T Consensus 11 GCFWg~E~~f~~~~GV~~t~vGYagG~~~~PtY~~Vcsg~tgh~E~V~V~yDp~~i-----sy~~Ll~ 73 (172)
T PRK14054 11 GCFWGMEAPFDRVKGVISTRVGYTGGHVENPTYEQVCSGTTGHAEAVEITYDPAVI-----SYRELLE 73 (172)
T ss_pred CChhhhHHHHccCCCEEEEEeeecCCCCCCCChhhcccCCCCCeEEEEEEECCCcC-----CHHHHHH
Confidence 444456777889999999999999987 7888988877 4555654
No 76
>cd04906 ACT_ThrD-I_1 First of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase). This CD includes the first of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase) which catalyzes the committed step in branched chain amino acid biosynthesis in plants and microorganisms, the pyridoxal 5'-phosphate (PLP)-dependent dehydration/deamination of L-threonine (or L-serine) to 2-ketobutyrate (or pyruvate). ThrD-I is a cooperative, feedback-regulated (isoleucine and valine) allosteric enzyme that forms a tetramer and contains four pyridoxal phosphate moieties. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=37.97 E-value=1.3e+02 Score=21.33 Aligned_cols=18 Identities=28% Similarity=0.569 Sum_probs=15.2
Q ss_pred hHHHHHHHHhcCceeEee
Q 030077 154 AANLVEIIQGSGFKLQTL 171 (183)
Q Consensus 154 as~LvEaIe~aGFkVq~l 171 (183)
.+.+.+++++.||++..+
T Consensus 55 ~~~i~~~L~~~G~~~~~~ 72 (85)
T cd04906 55 LAELLEDLKSAGYEVVDL 72 (85)
T ss_pred HHHHHHHHHHCCCCeEEC
Confidence 478999999999998654
No 77
>COG0841 AcrB Cation/multidrug efflux pump [Defense mechanisms]
Probab=37.96 E-value=1.1e+02 Score=31.87 Aligned_cols=83 Identities=13% Similarity=0.121 Sum_probs=60.2
Q ss_pred CCceeeecCCCCceEEEEEEec--CC----CcccHHHHHHhhccCCCceeeEEEEe-ccEEEEEeccceeeecccchHHH
Q 030077 85 QQPVAVPVSPSDKLTMYFQADG--AM----NETAIPAVTQALQGTEGISDLKVQVI-EGIATVELKKQTTVQATGVAANL 157 (183)
Q Consensus 85 ~~~~~~~~~~~~~ltM~FKaEG--M~----Ce~Ci~~VtkALE~ieGVsdVkV~Le-eG~AtVe~dkqttvqatgvas~L 157 (183)
++|......++|...|.+-+.+ +. -+.....|+..|+.++||.+|++.=. +-..+|++|++.-..--=.++.+
T Consensus 123 ~~p~v~~~~~~~~~i~~~al~s~~~~~~~l~~~~~~~l~~~L~~v~GV~~V~~~G~~~~~~rI~ldp~kLa~~gLt~~dV 202 (1009)
T COG0841 123 QQPGVTVEKSSSNPLLILALTSTTDSSSDLTDYAASNVRDELSRVPGVGSVQLFGAQEYAMRIWLDPAKLAAYGLTPSDV 202 (1009)
T ss_pred CCCceEeccCCCceEEEEEEEcCCCChHHHHHHHHHHHHHHHhcCCCceEEEEcCCCceeEEEEeCHHHHHHcCCCHHHH
Confidence 5555556678998888877666 43 34566779999999999999988765 67889999985432111146889
Q ss_pred HHHHHhcCce
Q 030077 158 VEIIQGSGFK 167 (183)
Q Consensus 158 vEaIe~aGFk 167 (183)
..+|+.....
T Consensus 203 ~~ai~~qN~~ 212 (1009)
T COG0841 203 QSAIRAQNVQ 212 (1009)
T ss_pred HHHHHHhCcc
Confidence 9999875543
No 78
>PF00736 EF1_GNE: EF-1 guanine nucleotide exchange domain; InterPro: IPR014038 Translation elongation factors are responsible for two main processes during protein synthesis on the ribosome [, , ]. EF1A (or EF-Tu) is responsible for the selection and binding of the cognate aminoacyl-tRNA to the A-site (acceptor site) of the ribosome. EF2 (or EF-G) is responsible for the translocation of the peptidyl-tRNA from the A-site to the P-site (peptidyl-tRNA site) of the ribosome, thereby freeing the A-site for the next aminoacyl-tRNA to bind. Elongation factors are responsible for achieving accuracy of translation and both EF1A and EF2 are remarkably conserved throughout evolution. Elongation factor EF1B (also known as EF-Ts or EF-1beta/gamma/delta) is a nucleotide exchange factor that is required to regenerate EF1A from its inactive form (EF1A-GDP) to its active form (EF1A-GTP). EF1A is then ready to interact with a new aminoacyl-tRNA to begin the cycle again. EF1B is more complex in eukaryotes than in bacteria, and can consist of three subunits: EF1B-alpha (or EF-1beta), EF1B-gamma (or EF-1gamma) and EF1B-beta (or EF-1delta) []. This entry represents the guanine nucleotide exchange domain of the beta (EF-1beta, also known as EF1B-alpha) and delta (EF-1delta, also known as EF1B-beta) chains of EF1B proteins from eukaryotes and archaea. The beta and delta chains have exchange activity, which mainly resides in their homologous guanine nucleotide exchange domains, found in the C-terminal region of the peptides. Their N-terminal regions may be involved in interactions with the gamma chain (EF-1gamma). More information about these proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0003746 translation elongation factor activity, 0006414 translational elongation, 0005853 eukaryotic translation elongation factor 1 complex; PDB: 2YY3_B 1GH8_A 1B64_A 1IJE_B 1IJF_B 1F60_B 1G7C_B 2B7B_B 2B7C_B.
Probab=37.08 E-value=85 Score=23.47 Aligned_cols=39 Identities=13% Similarity=0.227 Sum_probs=32.4
Q ss_pred CCCCceEEEEEEecCCCcccHHHHHHhh-ccCCCceeeEEEE
Q 030077 93 SPSDKLTMYFQADGAMNETAIPAVTQAL-QGTEGISDLKVQV 133 (183)
Q Consensus 93 ~~~~~ltM~FKaEGM~Ce~Ci~~VtkAL-E~ieGVsdVkV~L 133 (183)
+---.|.|.+-++. =++-...|..++ ..++||+.++|.-
T Consensus 46 FGlk~L~v~~vv~D--~~~~~d~lee~i~~~~e~Vqsvei~~ 85 (89)
T PF00736_consen 46 FGLKALQVSCVVED--DEGSTDDLEEAIESFEEGVQSVEIES 85 (89)
T ss_dssp TTEEEEEEEEEECT--TTCGHHHHHHHHTTCTTTEEEEEEEE
T ss_pred ccEEEEEEEEEEEc--CccChHHHHHHHHhcCCCccEEEEEE
Confidence 55677888899988 345789999999 9999999999864
No 79
>PF13399 LytR_C: LytR cell envelope-related transcriptional attenuator
Probab=36.78 E-value=43 Score=23.56 Aligned_cols=21 Identities=24% Similarity=0.620 Sum_probs=18.0
Q ss_pred ccchHHHHHHHHhcCceeEee
Q 030077 151 TGVAANLVEIIQGSGFKLQTL 171 (183)
Q Consensus 151 tgvas~LvEaIe~aGFkVq~l 171 (183)
.|-+..+.+.+++.||.+...
T Consensus 15 ~GlA~~~a~~L~~~Gf~v~~~ 35 (90)
T PF13399_consen 15 SGLAARVADALRNRGFTVVEV 35 (90)
T ss_pred cCHHHHHHHHHHHCCCceeec
Confidence 578999999999999998643
No 80
>PRK10614 multidrug efflux system subunit MdtC; Provisional
Probab=36.20 E-value=1.4e+02 Score=30.69 Aligned_cols=80 Identities=18% Similarity=0.211 Sum_probs=49.9
Q ss_pred ceeeecCCCCceEEEEEEecC--CC----cccHHHHHHhhccCCCceeeEEEEe-ccEEEEEeccceeeecccchHHHHH
Q 030077 87 PVAVPVSPSDKLTMYFQADGA--MN----ETAIPAVTQALQGTEGISDLKVQVI-EGIATVELKKQTTVQATGVAANLVE 159 (183)
Q Consensus 87 ~~~~~~~~~~~ltM~FKaEGM--~C----e~Ci~~VtkALE~ieGVsdVkV~Le-eG~AtVe~dkqttvqatgvas~LvE 159 (183)
|.....++++.-.|.+.+.|- .- +.....|++.|+.+|||++|++.=. +.+..|++|++.-.+.-=+.+.+.+
T Consensus 127 p~~~~~~~~~~pv~~~~~~~~~~~~~~L~~~~~~~l~~~L~~i~GV~~V~~~G~~~~ei~V~vd~~kl~~~gls~~dV~~ 206 (1025)
T PRK10614 127 PTYRKANPSDAPIMILTLTSDTYSQGQLYDFASTQLAQTISQIDGVGDVDVGGSSLPAVRVGLNPQALFNQGVSLDDVRQ 206 (1025)
T ss_pred CEEEecCCCccceeEEEEEcCCCCHHHHHHHHHHHHHHHhcCCCCceEEEecCCCceEEEEEeCHHHHHHcCCCHHHHHH
Confidence 333445666543455554442 11 1234679999999999999988632 2368888888654333235688888
Q ss_pred HHHhcCc
Q 030077 160 IIQGSGF 166 (183)
Q Consensus 160 aIe~aGF 166 (183)
+|+..-.
T Consensus 207 al~~~~~ 213 (1025)
T PRK10614 207 AISNANV 213 (1025)
T ss_pred HHHHhCc
Confidence 8887644
No 81
>PF03780 Asp23: Asp23 family; InterPro: IPR005531 This entry represents the alkaline shock protein 23 family. These small proteins are involved in alkaline pH tolerance of Staphylococcus aureus [,].
Probab=35.88 E-value=69 Score=23.05 Aligned_cols=50 Identities=24% Similarity=0.409 Sum_probs=28.1
Q ss_pred eeEEEEe-ccEEEEEecc------ceeeecccchHHHHHHHHh-cCceeEeeeccccC
Q 030077 128 DLKVQVI-EGIATVELKK------QTTVQATGVAANLVEIIQG-SGFKLQTLNLSFDD 177 (183)
Q Consensus 128 dVkV~Le-eG~AtVe~dk------qttvqatgvas~LvEaIe~-aGFkVq~l~l~f~d 177 (183)
.++|... ++...|.+.= +..--+--....++++|+. .|+++...|..++|
T Consensus 49 ~v~v~~~~~~~i~v~l~v~v~~g~~i~~v~~~iq~~V~~~v~~~tg~~v~~V~V~V~~ 106 (108)
T PF03780_consen 49 GVKVEVDEDGGITVDLHVVVEYGVNIPEVAEEIQEKVKEAVEEMTGIEVSEVNVHVED 106 (108)
T ss_pred CeEEEEccCcceEEEEEEEEECCccHHHHHHHHHHHHHHHHHHHHCCeeEEEEEEEEe
Confidence 3566666 6666555432 1111111123455556666 49999999987765
No 82
>PF00564 PB1: PB1 domain; InterPro: IPR000270 The Phox and Bem1p domain, is present in many eukaryotic cytoplasmic signalling proteins. The domain adopts a beta-grasp fold, similar to that found in ubiquitin and Ras-binding domains. A motif, variously termed OPR, PC and AID, represents the most conserved region of the majority of PB1 domains, and is necessary for PB1 domain function. This function is the formation of PB1 domain heterodimers, although not all PB1 domain pairs associate.; GO: 0005515 protein binding; PDB: 1IPG_A 1IP9_A 2KFK_A 1WMH_A 1VD2_A 1WI0_A 1OEY_C 1PQS_A 1Q1O_A 1TZ1_A ....
Probab=34.40 E-value=45 Score=22.80 Aligned_cols=48 Identities=21% Similarity=0.288 Sum_probs=34.6
Q ss_pred eeEEEEeccEEE-EEeccceeeecccchHHHHHHHHh-cCceeEeeeccccCcccc
Q 030077 128 DLKVQVIEGIAT-VELKKQTTVQATGVAANLVEIIQG-SGFKLQTLNLSFDDEEEV 181 (183)
Q Consensus 128 dVkV~LeeG~At-Ve~dkqttvqatgvas~LvEaIe~-aGFkVq~l~l~f~d~~~~ 181 (183)
.+++.+.++.-. +.+....+ -+.|++.|.. .|..-..+.|.+.|+|..
T Consensus 3 ~vK~~~~~~~~~~~~~~~~~s------~~~L~~~i~~~~~~~~~~~~l~Y~D~dgD 52 (84)
T PF00564_consen 3 RVKVRYGGDIRRIISLPSDVS------FDDLRSKIREKFGLLDEDFQLKYKDEDGD 52 (84)
T ss_dssp EEEEEETTEEEEEEEECSTSH------HHHHHHHHHHHHTTSTSSEEEEEEETTSS
T ss_pred EEEEEECCeeEEEEEcCCCCC------HHHHHHHHHHHhCCCCccEEEEeeCCCCC
Confidence 467888887777 77777666 3788877766 555557788888887754
No 83
>cd01812 BAG1_N Ubiquitin-like domain of BAG1. BAG1_N N-terminal ubiquitin-like (Ubl) domain of the BAG1 protein. This domain occurs together with the BAG domain and is closely related to the Ubl domain of a family of deubiquitinases that includes Rpn11, UBP6 (USP14), USP7 (HAUSP).
Probab=34.24 E-value=69 Score=21.14 Aligned_cols=43 Identities=16% Similarity=0.268 Sum_probs=30.5
Q ss_pred eEEEEeccEEEEEeccceeeecccchHHHHHHHHhc-CceeEeeeccccC
Q 030077 129 LKVQVIEGIATVELKKQTTVQATGVAANLVEIIQGS-GFKLQTLNLSFDD 177 (183)
Q Consensus 129 VkV~LeeG~AtVe~dkqttvqatgvas~LvEaIe~a-GFkVq~l~l~f~d 177 (183)
|.|...+....+++++..++ ..|++.|+.. |+......|-|.+
T Consensus 3 i~vk~~g~~~~i~v~~~~tv------~~lK~~i~~~~gi~~~~q~L~~~g 46 (71)
T cd01812 3 VRVKHGGESHDLSISSQATF------GDLKKMLAPVTGVEPRDQKLIFKG 46 (71)
T ss_pred EEEEECCEEEEEEECCCCcH------HHHHHHHHHhhCCChHHeEEeeCC
Confidence 55666655667888887775 8999999654 7777666666653
No 84
>PF01514 YscJ_FliF: Secretory protein of YscJ/FliF family; InterPro: IPR006182 This domain is found in proteins that are related to the YscJ lipoprotein, where it covers most of the sequence, and the flagellar M-ring protein FliF, where it covers the N-terminal region. The members of the YscJ family are thought to be involved in secretion of several proteins. The FliF protein ring is thought to be part of the export apparatus for flagellar proteins, based on the similarity to YscJ proteins [].; PDB: 1YJ7_A 2Y9J_d.
Probab=33.88 E-value=43 Score=28.05 Aligned_cols=21 Identities=10% Similarity=0.487 Sum_probs=18.0
Q ss_pred HHHHHhhccCCCceeeEEEEe
Q 030077 114 PAVTQALQGTEGISDLKVQVI 134 (183)
Q Consensus 114 ~~VtkALE~ieGVsdVkV~Le 134 (183)
..+.+.|+.++||++++|.|.
T Consensus 118 ~eL~~tI~~i~gV~~A~V~l~ 138 (206)
T PF01514_consen 118 GELERTIESIDGVESARVHLV 138 (206)
T ss_dssp HHHHHHHTTSTTEEEEEEEEE
T ss_pred HHHHHHHHcCCCeeEEEEEEe
Confidence 357788999999999999974
No 85
>PRK10614 multidrug efflux system subunit MdtC; Provisional
Probab=32.01 E-value=78 Score=32.34 Aligned_cols=64 Identities=17% Similarity=0.267 Sum_probs=41.1
Q ss_pred EEEEEEecCCCccc----HHHHHHhhccCCCceeeEEEEeccEEEEEec--cceeeecccchHHHHHHHHhc
Q 030077 99 TMYFQADGAMNETA----IPAVTQALQGTEGISDLKVQVIEGIATVELK--KQTTVQATGVAANLVEIIQGS 164 (183)
Q Consensus 99 tM~FKaEGM~Ce~C----i~~VtkALE~ieGVsdVkV~LeeG~AtVe~d--kqttvqatgvas~LvEaIe~a 164 (183)
+....--|.+-+-. ...++++|.+++||++++-.-.+|.+.+.+. ..+++ .-..+.+++.|.++
T Consensus 46 ~V~~~~pGas~~~ve~~vt~piE~~l~~i~gv~~i~S~s~~G~s~i~l~f~~~~d~--~~a~~~v~~~v~~~ 115 (1025)
T PRK10614 46 MVSASLPGASPETMASSVATPLERSLGRIAGVNEMTSSSSLGSTRIILQFDFDRDI--NGAARDVQAAINAA 115 (1025)
T ss_pred EEEEEcCCCCHHHHHHHHHHHHHHHhcCCCCceEEEEEecCCeEEEEEEEECCCCh--HHHHHHHHHHHHHH
Confidence 33333445544333 3677899999999999998888888776554 44442 11346677777653
No 86
>PRK13558 bacterio-opsin activator; Provisional
Probab=31.05 E-value=3e+02 Score=25.73 Aligned_cols=63 Identities=19% Similarity=0.322 Sum_probs=48.2
Q ss_pred CceEEEEEEecCCCcccHHHHHHhhccCCCceeeEE-EEeccEEEEEeccceeeecccchHHHHHHHHhcCceeEe
Q 030077 96 DKLTMYFQADGAMNETAIPAVTQALQGTEGISDLKV-QVIEGIATVELKKQTTVQATGVAANLVEIIQGSGFKLQT 170 (183)
Q Consensus 96 ~~ltM~FKaEGM~Ce~Ci~~VtkALE~ieGVsdVkV-~LeeG~AtVe~dkqttvqatgvas~LvEaIe~aGFkVq~ 170 (183)
+...++|.++|-. ...|..+|++.++|.++.+ +-.++.+.+++.. . ...+..++.+.|.-+..
T Consensus 485 ~~~~~~~~~~~~~----~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~--~------~~~~~~~~~~~g~~~~~ 548 (665)
T PRK13558 485 GGVLVLFTVPGDD----ATALVDAAADYDAVQDVRVLVSTDDECLVEFTL--S------GDSLVRLLSERGGRVQD 548 (665)
T ss_pred CCEEEEEEEeCCC----HHHHHHhhhccCCcceEEEEEecCCceEEEEEe--c------CCcHhHhhHhcCCEEEE
Confidence 4588889999864 4789999999999999988 4566667777652 1 13678888888887765
No 87
>PF04324 Fer2_BFD: BFD-like [2Fe-2S] binding domain; InterPro: IPR007419 The two Fe ions are each coordinated by two conserved cysteine residues. This domain occurs alone in small proteins such as bacterioferritin-associated ferredoxin (BFD, P13655 from SWISSPROT). The function of BFD is not known, but it may be a general redox and/or regulatory component involved in the iron storage or mobilisation functions of bacterioferritin in bacteria []. This domain is also found in nitrate reductase proteins in association with the nitrite and sulphite reductase 4Fe-4S domain (IPR006067 from INTERPRO), nitrite/sulphite reductase ferredoxin-like half domain (IPR005117 from INTERPRO) and pyridine nucleotide-disulphide oxidoreductase (IPR001327 from INTERPRO). It is also found in NifU nitrogen fixation proteins, in association with NifU-like N-terminal domain (IPR002871 from INTERPRO) and C-terminal domain (IPR001075 from INTERPRO).; PDB: 2HU9_A.
Probab=30.97 E-value=17 Score=23.96 Aligned_cols=17 Identities=24% Similarity=0.393 Sum_probs=3.9
Q ss_pred cCCCcccHHHHHHhhcc
Q 030077 106 GAMNETAIPAVTQALQG 122 (183)
Q Consensus 106 GM~Ce~Ci~~VtkALE~ 122 (183)
|..|..|++.|++.|++
T Consensus 37 g~~Cg~C~~~v~~ll~e 53 (55)
T PF04324_consen 37 GTGCGSCVPEVKDLLAE 53 (55)
T ss_dssp SS-TH------------
T ss_pred CCCCCCccccccccccc
Confidence 99999999999988875
No 88
>PRK13835 conjugal transfer protein TrbH; Provisional
Probab=30.80 E-value=27 Score=28.94 Aligned_cols=41 Identities=32% Similarity=0.468 Sum_probs=30.9
Q ss_pred ceeeEEEEeccEEEEEeccceeeecccchHHHHHHHHhcCceeEe
Q 030077 126 ISDLKVQVIEGIATVELKKQTTVQATGVAANLVEIIQGSGFKLQT 170 (183)
Q Consensus 126 VsdVkV~LeeG~AtVe~dkqttvqatgvas~LvEaIe~aGFkVq~ 170 (183)
|+.+.-.+-.+..+|.+.++++. =...|++++++.||-|++
T Consensus 47 vsqLae~~pPa~tt~~l~q~~d~----Fg~aL~~aLr~~GYaVvt 87 (145)
T PRK13835 47 VSRLAEQIGPGTTTIKLKKDTSP----FGQALEAALKGWGYAVVT 87 (145)
T ss_pred HHHHHHhcCCCceEEEEeecCcH----HHHHHHHHHHhcCeEEee
Confidence 44444445567788888777752 557899999999999987
No 89
>cd00590 RRM RRM (RNA recognition motif), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).
Probab=30.79 E-value=1.3e+02 Score=18.16 Aligned_cols=46 Identities=9% Similarity=0.146 Sum_probs=37.8
Q ss_pred EEEecCCCcccHHHHHHhhccCCCceeeEEEEe-----ccEEEEEecccee
Q 030077 102 FQADGAMNETAIPAVTQALQGTEGISDLKVQVI-----EGIATVELKKQTT 147 (183)
Q Consensus 102 FKaEGM~Ce~Ci~~VtkALE~ieGVsdVkV~Le-----eG~AtVe~dkqtt 147 (183)
+.|.|......-..|.+.++...+|.++.+... .|.+.|++.....
T Consensus 2 i~i~~l~~~~~~~~i~~~~~~~g~i~~~~~~~~~~~~~~~~~~v~f~s~~~ 52 (74)
T cd00590 2 LFVGNLPPDVTEEDLRELFSKFGKVESVRIVRDKDTKSKGFAFVEFEDEED 52 (74)
T ss_pred EEEeCCCCccCHHHHHHHHHhcCCEEEEEEeeCCCCCcceEEEEEECCHHH
Confidence 457788888888999999999988999999986 4789999875443
No 90
>PRK07334 threonine dehydratase; Provisional
Probab=29.60 E-value=3.9e+02 Score=24.17 Aligned_cols=70 Identities=17% Similarity=0.188 Sum_probs=49.5
Q ss_pred ceEEEEEEecCCCcccHHHHHHhhccCCCceeeEEEEe-------ccEEEEEeccceeeecccchHHHHHHHHhcCceeE
Q 030077 97 KLTMYFQADGAMNETAIPAVTQALQGTEGISDLKVQVI-------EGIATVELKKQTTVQATGVAANLVEIIQGSGFKLQ 169 (183)
Q Consensus 97 ~ltM~FKaEGM~Ce~Ci~~VtkALE~ieGVsdVkV~Le-------eG~AtVe~dkqttvqatgvas~LvEaIe~aGFkVq 169 (183)
.....|.|+...-.+-...|.+.|.+. |+.=.+|+.. .|.+.+.+.=.+. -.--...|.+.|++.||++.
T Consensus 324 ~y~v~l~I~~~dr~GlL~dI~~~is~~-~~nI~~v~~~~~~~~~~~~~~~i~l~i~V~--d~~~L~~vi~~Lr~~g~~~~ 400 (403)
T PRK07334 324 GRLARLRVDIRDRPGALARVTALIGEA-GANIIEVSHQRLFTDLPAKGAELELVIETR--DAAHLQEVIAALRAAGFEAR 400 (403)
T ss_pred CCEEEEEEEeCCCCCHHHHHHHHHhhC-CCceEEEEEEecccCCCCCeEEEEEEEEeC--CHHHHHHHHHHHHHcCCeeE
Confidence 455789999999999999999999874 6655555543 4666665443322 01124688999999999875
No 91
>cd04878 ACT_AHAS N-terminal ACT domain of the Escherichia coli IlvH-like regulatory subunit of acetohydroxyacid synthase (AHAS). ACT_AHAS: N-terminal ACT domain of the Escherichia coli IlvH-like regulatory subunit of acetohydroxyacid synthase (AHAS). AHAS catalyses the first common step in the biosynthesis of the three branched-chain amino acids. The first step involves the condensation of either pyruvate or 2-ketobutyrate with the two-carbon hydroxyethyl fragment derived from another pyruvate molecule, covalently bound to the coenzyme thiamine diphosphate. Bacterial AHASs generally consist of regulatory and catalytic subunits. The effector (valine) binding sites are proposed to be located in two symmetrically related positions in the interface between a pair of N-terminal ACT domains with the C-terminal domain of IlvH contacting the catalytic dimer. Plants Arabidopsis and Oryza have tandem IlvH subunits; both the first and second ACT domain sequences are present in this CD. Members of
Probab=29.03 E-value=1.1e+02 Score=19.13 Aligned_cols=32 Identities=9% Similarity=0.143 Sum_probs=24.3
Q ss_pred CceEEEEEEecCCCcccHHHHHHhhccCCCceee
Q 030077 96 DKLTMYFQADGAMNETAIPAVTQALQGTEGISDL 129 (183)
Q Consensus 96 ~~ltM~FKaEGM~Ce~Ci~~VtkALE~ieGVsdV 129 (183)
+...+.|.++... .=...+.+.|++++||.+|
T Consensus 40 ~~~~~~~~~~~~~--~~~~~l~~~l~~~~~v~~v 71 (72)
T cd04878 40 GISRITIVVEGDD--DVIEQIVKQLNKLVDVLKV 71 (72)
T ss_pred CeEEEEEEEECCH--HHHHHHHHHHhCCccEEEe
Confidence 3445778888643 5578888999999999876
No 92
>TIGR02544 III_secr_YscJ type III secretion apparatus lipoprotein, YscJ/HrcJ family. All members of this protein family are predicted lipoproteins with a conserved Cys near the N-terminus for cleavage and modification, and are part of known or predicted type III secretion systems. Members are found in both plant and animal pathogens, including the obligately intracellular chlamydial species and (non-pathogenic) root nodule bacteria. The most closely related proteins outside this family are examples of the flagellar M-ring protein FliF.
Probab=28.14 E-value=54 Score=27.43 Aligned_cols=21 Identities=24% Similarity=0.485 Sum_probs=17.6
Q ss_pred HHHHHhhccCCCceeeEEEEe
Q 030077 114 PAVTQALQGTEGISDLKVQVI 134 (183)
Q Consensus 114 ~~VtkALE~ieGVsdVkV~Le 134 (183)
..+.+.|+.++||++++|.|.
T Consensus 110 ~EL~rtI~~i~~V~~ArVhl~ 130 (193)
T TIGR02544 110 QRLEQTLSQIDGVISARVHVV 130 (193)
T ss_pred HHHHHHHHhcCCeeeeEEEEE
Confidence 356778889999999999983
No 93
>TIGR00119 acolac_sm acetolactate synthase, small subunit. acetohydroxyacid synthase is a synonym.
Probab=27.75 E-value=3.4e+02 Score=22.21 Aligned_cols=70 Identities=10% Similarity=0.120 Sum_probs=45.3
Q ss_pred CceEEEEEEecCCCcccHHHHHHhhccCCCceeeEEEEeccE-----EEEEeccceeeecccchHHHHHHHHhcCceeEe
Q 030077 96 DKLTMYFQADGAMNETAIPAVTQALQGTEGISDLKVQVIEGI-----ATVELKKQTTVQATGVAANLVEIIQGSGFKLQT 170 (183)
Q Consensus 96 ~~ltM~FKaEGM~Ce~Ci~~VtkALE~ieGVsdVkV~LeeG~-----AtVe~dkqttvqatgvas~LvEaIe~aGFkVq~ 170 (183)
+...|.|.++| .+..+..+.|-|+++-.|-.|..--.+.. +-+...-... ....|.+.++-.+-++++
T Consensus 41 ~~sriti~V~~--d~~~i~qi~kQl~Kli~V~~V~~~~~~~~v~rEl~LiKv~~~~~-----~r~~i~~i~~~f~a~ivd 113 (157)
T TIGR00119 41 DLSRMTIVVVG--DDKVLEQITKQLNKLVDVIKVSDLTESAIVERELCLVKVSAPGE-----GRDEIIRLTNIFRGRIVD 113 (157)
T ss_pred CEEEEEEEEEC--CHHHHHHHHHHHhcCccEEEEEecCCCcceeeEEEEEEEECCcc-----CHHHHHHHHHHhCCEEEE
Confidence 45668899999 58999999999999999988776333322 2222211111 245666666666666665
Q ss_pred ee
Q 030077 171 LN 172 (183)
Q Consensus 171 l~ 172 (183)
++
T Consensus 114 v~ 115 (157)
T TIGR00119 114 VS 115 (157)
T ss_pred ec
Confidence 54
No 94
>TIGR01709 typeII_sec_gspL general secretion pathway protein L. This model represents GspL, protein L of the main terminal branch of the general secretion pathway, also called type II secretion. It transports folded proteins across the bacterial outer membrane and is widely distributed in Gram-negative pathogens.
Probab=27.63 E-value=1.6e+02 Score=26.13 Aligned_cols=60 Identities=15% Similarity=0.201 Sum_probs=41.7
Q ss_pred HHHHHhhccCCCceeeEEEEe--ccEEEEEeccceeeecccchHHHHHHHHhcCceeEeeeccccCc
Q 030077 114 PAVTQALQGTEGISDLKVQVI--EGIATVELKKQTTVQATGVAANLVEIIQGSGFKLQTLNLSFDDE 178 (183)
Q Consensus 114 ~~VtkALE~ieGVsdVkV~Le--eG~AtVe~dkqttvqatgvas~LvEaIe~aGFkVq~l~l~f~d~ 178 (183)
..+..+|...+|++=-.+++. .+..+++++....- ..+.+++.++ .||.|.--+.+=+++
T Consensus 313 ~~l~~al~~~~~~~l~sL~y~~~~~~L~l~l~a~~~~----~le~l~~~l~-~g~~v~~~~~~~~~~ 374 (384)
T TIGR01709 313 AALATALGQLPGLQLQSLDFDGARGELRLKLEAPSDA----DLEQLRSRLA-RGFQVALGQAGAEGD 374 (384)
T ss_pred HHHHHHhccCCCCceeEEeEcCCCCEEEEEEecCChH----HHHHHHHHHh-hhceecccccccCCC
Confidence 445667777777776667777 46666666544432 5688999999 999998877765553
No 95
>PF13489 Methyltransf_23: Methyltransferase domain; PDB: 3JWJ_A 3JWH_B 2AOV_B 2AOT_A 1JQD_B 2AOX_A 1JQE_A 2AOU_B 2AOW_A 3DLI_C ....
Probab=27.42 E-value=61 Score=23.56 Aligned_cols=18 Identities=17% Similarity=0.501 Sum_probs=15.9
Q ss_pred chHHHHHHHHhcCceeEe
Q 030077 153 VAANLVEIIQGSGFKLQT 170 (183)
Q Consensus 153 vas~LvEaIe~aGFkVq~ 170 (183)
.++.+++.++++||++++
T Consensus 143 ~~~~~~~ll~~~G~~iv~ 160 (161)
T PF13489_consen 143 SPDELRQLLEQAGFEIVE 160 (161)
T ss_dssp BHHHHHHHHHHTTEEEEE
T ss_pred CHHHHHHHHHHCCCEEEE
Confidence 468999999999999875
No 96
>cd04903 ACT_LSD C-terminal ACT domain of the L-serine dehydratase (LSD), iron-sulfur-dependent, beta subunit. The C-terminal ACT domain of the L-serine dehydratase (LSD), iron-sulfur-dependent, beta subunit, found in various bacterial anaerobes such as Clostridium, Bacillis, and Treponema species. These enzymes catalyze the deamination of L-serine, producing pyruvate and ammonia. Unlike the eukaryotic L-serine dehydratase, which requires the pyridoxal-5'-phosphate (PLP) cofactor, the prokaryotic L-serine dehydratase contains an [4Fe-4S] cluster instead of a PLP active site. The LSD alpha and beta subunits of the 'clostridial' enzyme are encoded by the sdhA and sdhB genes. The single subunit bacterial homologs of L-serine dehydratase (LSD1, LSD2, TdcG) present in Escherichia coli, and other enterobacterials, lack the ACT domain described here. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=27.20 E-value=1.4e+02 Score=18.63 Aligned_cols=29 Identities=14% Similarity=0.195 Sum_probs=22.8
Q ss_pred EEEEEEecCCCcccHHHHHHhhccCCCceeeEE
Q 030077 99 TMYFQADGAMNETAIPAVTQALQGTEGISDLKV 131 (183)
Q Consensus 99 tM~FKaEGM~Ce~Ci~~VtkALE~ieGVsdVkV 131 (183)
.+.|.+++. -...+-+.|++++||.+|..
T Consensus 42 ~i~i~v~~~----~~~~~i~~l~~~~~v~~v~~ 70 (71)
T cd04903 42 LMVIEVDQP----IDEEVIEEIKKIPNIHQVIL 70 (71)
T ss_pred EEEEEeCCC----CCHHHHHHHHcCCCceEEEE
Confidence 455777775 46788899999999998863
No 97
>TIGR01033 DNA-binding regulatory protein, YebC/PmpR family. This model describes a minimally characterized protein family, restricted to bacteria excepting for some eukaryotic sequences that have possible transit peptides. YebC from E. coli is crystallized, and PA0964 from Pseudomonas aeruginosa has been shown to be a sequence-specific DNA-binding regulatory protein.
Probab=26.72 E-value=96 Score=26.99 Aligned_cols=51 Identities=16% Similarity=0.343 Sum_probs=34.4
Q ss_pred HHHhhccCCCceeeEEEEeccEEEEEeccceeeecccchHHHHHHHHhcCceeEeeeccccC
Q 030077 116 VTQALQGTEGISDLKVQVIEGIATVELKKQTTVQATGVAANLVEIIQGSGFKLQTLNLSFDD 177 (183)
Q Consensus 116 VtkALE~ieGVsdVkV~LeeG~AtVe~dkqttvqatgvas~LvEaIe~aGFkVq~l~l~f~d 177 (183)
..-|||+ |+.|++.+ ++...|-.++... ..++++++..||++..-.+.|--
T Consensus 153 ~e~aiea--GAedv~~~--~~~~~v~~~~~~~-------~~v~~~L~~~g~~i~~sei~~~P 203 (238)
T TIGR01033 153 MEAAIEA--GAEDIDVD--DDEFEVYTAPEEL-------EKVKEALEAKGFPIESAEITMIP 203 (238)
T ss_pred HHHHHhC--CCceeecc--CCcEEEEECHHHH-------HHHHHHHHHcCCCceeeEEEEec
Confidence 3445654 88988643 3334444444333 89999999999998877776643
No 98
>TIGR03028 EpsE polysaccharide export protein EpsE. Sequences in this family of proteins are members of a polysaccharide export protein family (pfam02563) which includes the wza protein from E.coli. This family of proteins are homologous to the EpsE protein of the methanolan biosynthesis operon of Methylobacillus species strain 12S. The distribution of this protein appears to be restricted to a subset of exopolysaccharide operons containing a syntenic grouping of genes including a variant of the EpsH exosortase protein. Exosortase has been proposed to be involved in the targetting and processing of proteins containing the PEP-CTERM domain to the exopolysaccharide layer.
Probab=26.70 E-value=2.9e+02 Score=23.26 Aligned_cols=76 Identities=13% Similarity=0.184 Sum_probs=49.2
Q ss_pred eeecCCCCceEEE----EEEecCCCcccHHHHHHhhccCCCce--eeEEEEecc---EEEEE--eccceeeecccchHHH
Q 030077 89 AVPVSPSDKLTMY----FQADGAMNETAIPAVTQALQGTEGIS--DLKVQVIEG---IATVE--LKKQTTVQATGVAANL 157 (183)
Q Consensus 89 ~~~~~~~~~ltM~----FKaEGM~Ce~Ci~~VtkALE~ieGVs--dVkV~LeeG---~AtVe--~dkqttvqatgvas~L 157 (183)
.+.|+|.-++++= ++|.||+.+-....|++.|..-.=+. +|.|++.+- .++|. ...+-....++. ..|
T Consensus 23 ~~~V~~dG~I~~P~iG~v~v~G~T~~e~~~~I~~~l~~~~~~~~p~V~V~v~~~~~~~V~V~GeV~~PG~~~l~~~-~tl 101 (239)
T TIGR03028 23 DTRVSESGSITFPLIGEVKLGGETPAAAERKIASRLSKGGFVKQPQVTINVLQYRGQQVSVLGQVNRPGRYPLETA-GRV 101 (239)
T ss_pred eEEECCCCeEEeeecceEEECCCCHHHHHHHHHHHHhhcCcccCCEEEEEEEeccceEEEEEEEecCCceEEcCCC-CcH
Confidence 3567777777776 89999999999999999998621223 466666542 22221 122223333333 678
Q ss_pred HHHHHhcC
Q 030077 158 VEIIQGSG 165 (183)
Q Consensus 158 vEaIe~aG 165 (183)
.++|..+|
T Consensus 102 ~~ai~~AG 109 (239)
T TIGR03028 102 SDVLALAG 109 (239)
T ss_pred HHHHHHcC
Confidence 88998877
No 99
>PF13893 RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); PDB: 2PE8_A 2PEH_A 2D9O_A 1A9N_D 2DIT_A 3S6E_A 2LQ5_A 1SJQ_A 2AD9_A 1X4D_A ....
Probab=26.66 E-value=1.4e+02 Score=18.87 Aligned_cols=50 Identities=20% Similarity=0.292 Sum_probs=33.4
Q ss_pred HHhhccCCCceeeEEEEec-cEEEEEeccceeeecccchHHHHHHHHhcCceeEeee
Q 030077 117 TQALQGTEGISDLKVQVIE-GIATVELKKQTTVQATGVAANLVEIIQGSGFKLQTLN 172 (183)
Q Consensus 117 tkALE~ieGVsdVkV~Lee-G~AtVe~dkqttvqatgvas~LvEaIe~aGFkVq~l~ 172 (183)
.+.++.-.-|.++.+.-.. +.|-|++....+ |...++.+.+.=|.=..|.
T Consensus 2 ~~~f~~fG~V~~i~~~~~~~~~a~V~f~~~~~------A~~a~~~l~~~~~~g~~l~ 52 (56)
T PF13893_consen 2 YKLFSKFGEVKKIKIFKKKRGFAFVEFASVED------AQKAIEQLNGRQFNGRPLK 52 (56)
T ss_dssp HHHHTTTS-EEEEEEETTSTTEEEEEESSHHH------HHHHHHHHTTSEETTEEEE
T ss_pred hHHhCCcccEEEEEEEeCCCCEEEEEECCHHH------HHHHHHHhCCCEECCcEEE
Confidence 4566777778888887777 999999987666 4666666655544333333
No 100
>PRK12378 hypothetical protein; Provisional
Probab=26.60 E-value=85 Score=27.41 Aligned_cols=51 Identities=14% Similarity=0.182 Sum_probs=32.4
Q ss_pred HHhhccCCCceeeEEEEeccEEEEEeccceeeecccchHHHHHHHHhcCceeEeeecccc
Q 030077 117 TQALQGTEGISDLKVQVIEGIATVELKKQTTVQATGVAANLVEIIQGSGFKLQTLNLSFD 176 (183)
Q Consensus 117 tkALE~ieGVsdVkV~LeeG~AtVe~dkqttvqatgvas~LvEaIe~aGFkVq~l~l~f~ 176 (183)
.-|||+ |+.+-+|.-+++.-.|-.++..- ..+++++++.||++..-.|.|-
T Consensus 149 e~aiea--Ga~~edv~~~~~~~~i~t~p~~~-------~~v~~~L~~~g~~~~~sei~~~ 199 (235)
T PRK12378 149 EALIDA--DVDVEDVEEEEGTITVYTDPTDF-------HKVKKALEAAGIEFLVAELEMI 199 (235)
T ss_pred HHHHhC--CCCcccccccCCeEEEEECHHHH-------HHHHHHHHHcCCCceeeEEEEe
Confidence 345664 66333344456654444444333 8999999999999887777664
No 101
>TIGR03675 arCOG00543 arCOG00543 universal archaeal KH-domain/beta-lactamase-domain protein. This family of proteins is universal in the archaea and consistsof an N-terminal type-1 KH-domain (pfam00013) a central beta-lactamase-domain (pfam00753) with a C-terminal motif associated with RNA metabolism (pfam07521). KH-domains are associated with RNA-binding, so taken together, this protein is a likely metal-dependent RNAase. This family was defined in as arCOG01782.
Probab=26.43 E-value=1.2e+02 Score=29.76 Aligned_cols=61 Identities=25% Similarity=0.382 Sum_probs=50.0
Q ss_pred CCcccHHHHHHhhccCCCceeeEEEEeccEEEEEeccceeeecccchHHHHHHHHhcCceeE
Q 030077 108 MNETAIPAVTQALQGTEGISDLKVQVIEGIATVELKKQTTVQATGVAANLVEIIQGSGFKLQ 169 (183)
Q Consensus 108 ~Ce~Ci~~VtkALE~ieGVsdVkV~LeeG~AtVe~dkqttvqatgvas~LvEaIe~aGFkVq 169 (183)
.-+-++..|++.+-+-.||+|+..+-..|++.++..|+--+.--+ -+.+++...+.|+...
T Consensus 67 ~~~~~~~~i~~~~~~~~~~~~~~f~~~~~~v~i~~~~p~~~~~~~-~~~~~~i~~~~~w~~~ 127 (630)
T TIGR03675 67 PPEEAIEKIKEIVPEEAGITDIYFDDVTGEVIIEAEKPGLVIGKG-GSTLREITAETGWTPK 127 (630)
T ss_pred CHHHHHHHHHHhCCCcCCceeEEecCCCceEEEEEcCCeEEEecC-cchHHHHHHHhCCeee
Confidence 345678889999887789999999999999999999987654333 5678899999998644
No 102
>PF00873 ACR_tran: AcrB/AcrD/AcrF family; InterPro: IPR001036 The Escherichia coli acrA and acrB genes encode a multi-drug efflux system that is believed to protect the bacterium against hydrophobic inhibitors []. The E. coli AcrB protein is a transporter that is energized by proton-motive force and that shows the widest substrate specificity among all known multidrug pumps, ranging from most of the currently used antibiotics, disinfectants, dyes, and detergents to simple solvents. The structure of ligand-free AcrB shows that it is a homotrimer of 110kDa per subunit. Each subunit contains 12 transmembrane helices and two large periplasmic domains (each exceeding 300 residues) between helices 1 and 2, and helices 7 and 8. X-ray analysis of the overexpressed AcrB protein demonstrated that the three periplasmic domains form, in the centre, a funnel-like structure and a connected narrow (or closed) pore. The pore is opened to the periplasm through three vestibules located at subunit interfaces. These vestibules were proposed to allow direct access of drugs from the periplasm as well as the outer leaflet of the cytoplasmic membrane. The three transmembrane domains of AcrB protomers form a large, 30A-wide central cavity that spans the cytoplasmic membrane and extends to the cytoplasm X-ray crystallographic structures of the trimeric AcrB pump from E. coli with four structurally diverse ligands demonstrated that three molecules of ligand bind simultaneously to the extremely large central cavity of 5000 cubic angstroms, primarily by hydrophobic, aromatic stacking and van der Waals interactions. Each ligand uses a slightly different subset of AcrB residues for binding. The bound ligand molecules often interact with each other, stabilising the binding. ; GO: 0005215 transporter activity, 0006810 transport, 0016020 membrane; PDB: 2V50_B 1T9U_A 2HRT_B 3NOC_A 3NOG_A 4DX7_A 1OYD_A 3AOB_A 1T9V_A 4DX6_B ....
Probab=26.18 E-value=40 Score=33.89 Aligned_cols=68 Identities=15% Similarity=0.234 Sum_probs=47.0
Q ss_pred CceEEEEEEecCCCcc---cHHHHHHhhccCCCceeeEEEEeccEEEEEecccee-eeccc-chHHHHHHHHh
Q 030077 96 DKLTMYFQADGAMNET---AIPAVTQALQGTEGISDLKVQVIEGIATVELKKQTT-VQATG-VAANLVEIIQG 163 (183)
Q Consensus 96 ~~ltM~FKaEGM~Ce~---Ci~~VtkALE~ieGVsdVkV~LeeG~AtVe~dkqtt-vqatg-vas~LvEaIe~ 163 (183)
......+++.|-.-+. .+.+|++.|+++||+.+++.+...+.-.+.++.+.. .+.-| +.+.|..+|+.
T Consensus 669 ~~~~i~v~i~G~d~~~L~~~a~~v~~~l~~~pgv~dv~~~~~~~~~el~i~~dreka~~~Gls~~~va~~l~~ 741 (1021)
T PF00873_consen 669 SSAPIQVEIYGDDLEELRKAAEKVKAKLAEIPGVTDVRDDWEDGQPELRIDPDREKAARLGLSPADVARTLRT 741 (1021)
T ss_dssp EEEEEEEECSSSCHHHHHHHHHHHHHHHHHSTTEEEEEESSSSBEEEEEEEE-HHHHHHTTB-HHHHHHHHHH
T ss_pred cceeeeeccCCCCHHHHHHHHHHHHHHHHhCCCcccccccccccCcceEEEecHHHHHHcCCCHHHHHHHHHH
Confidence 3455667778876554 578899999999999999999999999888877533 22233 23444444443
No 103
>PF14794 DUF4479: Domain of unknown function (DUF4479); PDB: 3BU2_C.
Probab=25.75 E-value=31 Score=25.16 Aligned_cols=25 Identities=28% Similarity=0.360 Sum_probs=13.0
Q ss_pred EEEEEeccceeeecccchHHHHHHHHhcCcee
Q 030077 137 IATVELKKQTTVQATGVAANLVEIIQGSGFKL 168 (183)
Q Consensus 137 ~AtVe~dkqttvqatgvas~LvEaIe~aGFkV 168 (183)
...|.+++... +.|.++|+++||+-
T Consensus 43 ~G~V~Lt~eqv-------~~LN~~l~~~Gf~~ 67 (73)
T PF14794_consen 43 NGQVFLTEEQV-------AKLNQALQKAGFDE 67 (73)
T ss_dssp -------HHHH-------HHHHHHHHHTT---
T ss_pred CcCEEcCHHHH-------HHHHHHHHHcCCCc
Confidence 44455666655 89999999999973
No 104
>PF09122 DUF1930: Domain of unknown function (DUF1930); InterPro: IPR015206 This entry represents a domain found in 3-mercaptopyruvate sulphurtransferase which has no known function. This domain adopts a structure consisting of a four-stranded antiparallel beta-sheet and an alpha-helix, arranged in a beta(2)-alpha-beta(2) fashion, and bearing a remarkable structural similarity to the FK506-binding protein class of peptidylprolyl cis/trans-isomerase []. ; PDB: 1OKG_A.
Probab=25.72 E-value=94 Score=23.15 Aligned_cols=43 Identities=16% Similarity=0.036 Sum_probs=30.2
Q ss_pred EEEEEEecCCCcccHHHHHHhhccCCCceeeEEEEeccEEEEE
Q 030077 99 TMYFQADGAMNETAIPAVTQALQGTEGISDLKVQVIEGIATVE 141 (183)
Q Consensus 99 tM~FKaEGM~Ce~Ci~~VtkALE~ieGVsdVkV~LeeG~AtVe 141 (183)
+|++++||-.|+.=-.-+..|+.-+-==...+|.++.+...+-
T Consensus 20 ~~tl~vDg~~v~~PD~El~sA~~HlH~GEkA~V~FkS~Rv~~i 62 (68)
T PF09122_consen 20 NATLIVDGEIVENPDAELKSALVHLHIGEKAQVFFKSQRVAVI 62 (68)
T ss_dssp T--EEETTEEESS--HHHHHHHTT-BTT-EEEEEETTS-EEEE
T ss_pred ceEEEEcCeEcCCCCHHHHHHHHHhhcCceeEEEEecCcEEEE
Confidence 5779999999999999999999988666788888888765443
No 105
>PRK15078 polysaccharide export protein Wza; Provisional
Probab=25.25 E-value=1.5e+02 Score=27.27 Aligned_cols=76 Identities=16% Similarity=0.090 Sum_probs=50.5
Q ss_pred ecCCCCceEEE----EEEecCCCcccHHHHHHhhccCCCceeeEEEEecc---EEEEEe--ccceeeecccchHHHHHHH
Q 030077 91 PVSPSDKLTMY----FQADGAMNETAIPAVTQALQGTEGISDLKVQVIEG---IATVEL--KKQTTVQATGVAANLVEII 161 (183)
Q Consensus 91 ~~~~~~~ltM~----FKaEGM~Ce~Ci~~VtkALE~ieGVsdVkV~LeeG---~AtVe~--dkqttvqatgvas~LvEaI 161 (183)
.|.+.-++++= ++|.|++.+-.-..|++.|.+.=-=-+|.|.+.+- .++|.- .++.....++....|.++|
T Consensus 119 ~V~~dG~I~~P~vG~V~vaG~T~~e~~~~I~~~L~~~~~~PqV~V~v~~~~s~~V~V~GeV~~PG~~~l~~~~~tlldaI 198 (379)
T PRK15078 119 WVHADGTIFYPYIGKVHVAGKTVTEIRSDITGRLAKYIESPQVDVNIAAFRSQKAYVTGEVNKSGQQAITNVPLTILDAI 198 (379)
T ss_pred EECCCCeEeeccCceEEECCCCHHHHHHHHHHHHHHhccCCeEEEEEccCCceEEEEEceecCCeEEEecCCCccHHHHH
Confidence 36666666664 89999999999999999998742113455555543 233322 2334444455567899999
Q ss_pred HhcCc
Q 030077 162 QGSGF 166 (183)
Q Consensus 162 e~aGF 166 (183)
..+|=
T Consensus 199 a~AGG 203 (379)
T PRK15078 199 NAAGG 203 (379)
T ss_pred HHccC
Confidence 98863
No 106
>PF08478 POTRA_1: POTRA domain, FtsQ-type; InterPro: IPR013685 FtsQ/DivIB bacterial division proteins (IPR005548 from INTERPRO) contain an N-terminal POTRA domain (for polypeptide-transport-associated domain). This is found in different types of proteins, usually associated with a transmembrane beta-barrel. FtsQ/DivIB may have chaperone-like roles, which has also been postulated for the POTRA domain in other contexts []. ; PDB: 2ALJ_A 2VH1_B 3J00_Z 2VH2_B.
Probab=24.82 E-value=90 Score=20.53 Aligned_cols=30 Identities=10% Similarity=0.179 Sum_probs=22.7
Q ss_pred cHHHHHHhhccCCCceeeEEEE-eccEEEEE
Q 030077 112 AIPAVTQALQGTEGISDLKVQV-IEGIATVE 141 (183)
Q Consensus 112 Ci~~VtkALE~ieGVsdVkV~L-eeG~AtVe 141 (183)
=...+++.|++.|.|++++|.. ..+...|.
T Consensus 35 ~~~~~~~~l~~~p~V~~v~V~r~~P~~l~I~ 65 (69)
T PF08478_consen 35 DLKKIEQRLEKLPWVKSVSVSRRFPNTLEIK 65 (69)
T ss_dssp HHHHHHHCCCCTTTEEEEEEEEETTTEEEEE
T ss_pred CHHHHHHHHHcCCCEEEEEEEEeCCCEEEEE
Confidence 3678999999999999999984 34444443
No 107
>COG1251 NirB NAD(P)H-nitrite reductase [Energy production and conversion]
Probab=24.74 E-value=61 Score=33.40 Aligned_cols=50 Identities=24% Similarity=0.318 Sum_probs=33.6
Q ss_pred cCCCcccHHHHHHhhccCCCceeeEEEEeccEEEEEeccceeeecccchHHHHHHHHhcCce
Q 030077 106 GAMNETAIPAVTQALQGTEGISDLKVQVIEGIATVELKKQTTVQATGVAANLVEIIQGSGFK 167 (183)
Q Consensus 106 GM~Ce~Ci~~VtkALE~ieGVsdVkV~LeeG~AtVe~dkqttvqatgvas~LvEaIe~aGFk 167 (183)
|.+|.+|+|-|++.|...=| ++.+ ...+.-+..+. +.+.+++.|+.-|++
T Consensus 447 ~tsCGsC~plveqlL~~~~~-~~~~----~~~~~c~~~~~-------~~~~~~~~i~~~~~~ 496 (793)
T COG1251 447 GTSCGSCKPLVEQLLAATLG-DQFA----VNNAICGCTDL-------SRDEVVHLIRAKGLK 496 (793)
T ss_pred CCCCcCcHHHHHHHHHhhcc-cccc----cccccccCcCC-------CHHHHHHHHHHhccC
Confidence 89999999999999998643 2222 12222233322 358888888888774
No 108
>cd04876 ACT_RelA-SpoT ACT domain found C-terminal of the RelA/SpoT domains. ACT_RelA-SpoT: the ACT domain found C-terminal of the RelA/SpoT domains. Enzymes of the Rel/Spo family enable bacteria to survive prolonged periods of nutrient limitation by controlling guanosine-3'-diphosphate-5'-(tri)diphosphate ((p)ppGpp) production and subsequent rRNA repression (stringent response). Both the synthesis of (p)ppGpp from ATP and GDP(GTP), and its hydrolysis to GDP(GTP) and pyrophosphate, are catalyzed by Rel/Spo proteins. In Escherichia coli and its close relatives, the metabolism of (p)ppGpp is governed by two homologous proteins, RelA and SpoT. The RelA protein catalyzes (p)ppGpp synthesis in a reaction requiring its binding to ribosomes bearing codon-specified uncharged tRNA. The major role of the SpoT protein is the breakdown of (p)ppGpp by a manganese-dependent (p)ppGpp pyrophosphohydrolase activity. Although the stringent response appears to be tightly regulated by these two enzymes i
Probab=24.60 E-value=1.5e+02 Score=17.43 Aligned_cols=32 Identities=16% Similarity=0.262 Sum_probs=22.4
Q ss_pred eEEEEEEecCCCcccHHHHHHhhccCCCceeeE
Q 030077 98 LTMYFQADGAMNETAIPAVTQALQGTEGISDLK 130 (183)
Q Consensus 98 ltM~FKaEGM~Ce~Ci~~VtkALE~ieGVsdVk 130 (183)
..+.|.++-.... =...+.+.|.+++||..+.
T Consensus 39 ~~~~~~~~~~~~~-~~~~~~~~l~~~~~v~~v~ 70 (71)
T cd04876 39 ATIRLTLEVRDLE-HLARIMRKLRQIPGVIDVR 70 (71)
T ss_pred EEEEEEEEECCHH-HHHHHHHHHhCCCCcEEEE
Confidence 4455666655444 3788899999999987653
No 109
>PF11873 DUF3393: Domain of unknown function (DUF3393); InterPro: IPR024570 Membrane-bound lytic murein transglycosylase C (also known as murein hydrolase C), is a murein-degrading enzyme that may play a role in the recycling of muropeptides during cell elongation and/or cell division. This entry represents the N-terminal domain, whose function is currently not known.
Probab=24.07 E-value=1.3e+02 Score=25.92 Aligned_cols=32 Identities=31% Similarity=0.257 Sum_probs=27.5
Q ss_pred eeeEEEEeccEEEEEeccceeeecccchHHHHHHHHh
Q 030077 127 SDLKVQVIEGIATVELKKQTTVQATGVAANLVEIIQG 163 (183)
Q Consensus 127 sdVkV~LeeG~AtVe~dkqttvqatgvas~LvEaIe~ 163 (183)
+...|+.+.|..+||.-.+.. ....|++||-.
T Consensus 88 tRa~VdFd~G~I~VETi~~~~-----p~~~Lk~AIv~ 119 (204)
T PF11873_consen 88 TRAHVDFDKGTITVETIAQTD-----PKAHLKQAIVT 119 (204)
T ss_pred eEEEEEeeCCeEEEEecCCcC-----HHHHHHHHHHH
Confidence 567899999999999988766 68999999964
No 110
>PRK10629 EnvZ/OmpR regulon moderator; Provisional
Probab=23.95 E-value=3.6e+02 Score=21.43 Aligned_cols=36 Identities=14% Similarity=0.046 Sum_probs=31.6
Q ss_pred ccHHHHHHhhccCCCceeeEEEEeccEEEEEecccee
Q 030077 111 TAIPAVTQALQGTEGISDLKVQVIEGIATVELKKQTT 147 (183)
Q Consensus 111 ~Ci~~VtkALE~ieGVsdVkV~LeeG~AtVe~dkqtt 147 (183)
.-...|.++|++ .||.--.+.++++...|.++.+..
T Consensus 50 ~~~~~v~~~L~~-~gI~~ksi~~~~~~~~irf~~~~~ 85 (127)
T PRK10629 50 PDGFYVYQHLDA-NGIHIKSITPENDSLLIRFDSPEQ 85 (127)
T ss_pred chHHHHHHHHHH-CCCCcceEEeeCCEEEEEECCHHH
Confidence 556799999999 699999999999999999987555
No 111
>PF11543 UN_NPL4: Nuclear pore localisation protein NPL4; InterPro: IPR024682 Npl4, along with Ufd1, forms the heterodimer adaptor complex UN, which is involved in the recruitment of p97, an AAA ATPase, for tasks involving the ubiquitin pathway. Npl4 has a N-terminal ubiquitin-like domain which has within its structure a beta-grasp fold with a helical insert []. This entry represents the ubiquitin-like domain.; PDB: 2PJH_A 1WF9_A.
Probab=23.51 E-value=93 Score=22.61 Aligned_cols=42 Identities=26% Similarity=0.378 Sum_probs=25.8
Q ss_pred eEEEEeccEEEEEeccceeeecccchHHHHHHHHh-cCceeEeeecccc
Q 030077 129 LKVQVIEGIATVELKKQTTVQATGVAANLVEIIQG-SGFKLQTLNLSFD 176 (183)
Q Consensus 129 VkV~LeeG~AtVe~dkqttvqatgvas~LvEaIe~-aGFkVq~l~l~f~ 176 (183)
+.|.=.+|.-+|+.++..++ ..|++.|.+ .++......|+-+
T Consensus 7 lRvrS~dG~~Rie~~~~~t~------~~L~~kI~~~l~~~~~~~~L~~~ 49 (80)
T PF11543_consen 7 LRVRSKDGMKRIEVSPSSTL------SDLKEKISEQLSIPDSSQSLSKD 49 (80)
T ss_dssp EEEE-SSEEEEEEE-TTSBH------HHHHHHHHHHS---TTT---BSS
T ss_pred EEEECCCCCEEEEcCCcccH------HHHHHHHHHHcCCCCcceEEEec
Confidence 57778899999999988774 888888876 6665555555443
No 112
>PRK11152 ilvM acetolactate synthase 2 regulatory subunit; Provisional
Probab=23.41 E-value=2.4e+02 Score=20.54 Aligned_cols=33 Identities=9% Similarity=0.282 Sum_probs=28.3
Q ss_pred CceEEEEEEecCCCcccHHHHHHhhccCCCceeeEE
Q 030077 96 DKLTMYFQADGAMNETAIPAVTQALQGTEGISDLKV 131 (183)
Q Consensus 96 ~~ltM~FKaEGM~Ce~Ci~~VtkALE~ieGVsdVkV 131 (183)
+...|.+-++ -+.++..|.|-|+++.+|..|+|
T Consensus 43 ~~sriti~v~---~~~~i~ql~kQL~KL~dV~~V~~ 75 (76)
T PRK11152 43 QNINIELTVA---SERPIDLLSSQLNKLVDVAHVEI 75 (76)
T ss_pred CEEEEEEEEC---CCchHHHHHHHHhcCcCeEEEEE
Confidence 4567888885 39999999999999999999887
No 113
>smart00213 UBQ Ubiquitin homologues. Ubiquitin-mediated proteolysis is involved in the regulated turnover of proteins required for controlling cell cycle progression
Probab=23.40 E-value=1.4e+02 Score=18.70 Aligned_cols=42 Identities=31% Similarity=0.491 Sum_probs=27.9
Q ss_pred eEEEEeccEEEEEeccceeeecccchHHHHHHHH-hcCceeEeeecccc
Q 030077 129 LKVQVIEGIATVELKKQTTVQATGVAANLVEIIQ-GSGFKLQTLNLSFD 176 (183)
Q Consensus 129 VkV~LeeG~AtVe~dkqttvqatgvas~LvEaIe-~aGFkVq~l~l~f~ 176 (183)
|.|....+...+++++..++ ..|++.|+ ..|+......|-|.
T Consensus 3 i~vk~~~~~~~~~v~~~~tv------~~lk~~i~~~~~~~~~~~~L~~~ 45 (64)
T smart00213 3 LTVKTLDGTITLEVKPSDTV------SELKEKIAELTGIPVEQQRLIYK 45 (64)
T ss_pred EEEEECCceEEEEECCCCcH------HHHHHHHHHHHCCCHHHEEEEEC
Confidence 44555555677777777775 89999996 45766555555554
No 114
>PF00076 RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); InterPro: IPR000504 Many eukaryotic proteins containing one or more copies of a putative RNA-binding domain of about 90 amino acids are known to bind single-stranded RNAs [, , ]. The largest group of single strand RNA-binding proteins is the eukaryotic RNA recognition motif (RRM) family that contains an eight amino acid RNP-1 consensus sequence [, ]. RRM proteins have a variety of RNA binding preferences and functions, and include heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing (SR, U2AF, Sxl), protein components of small nuclear ribonucleoproteins (U1 and U2 snRNPs), and proteins that regulate RNA stability and translation (PABP, La, Hu) [, , ]. The RRM in heterodimeric splicing factor U2 snRNP auxiliary factor (U2AF) appears to have two RRM-like domains with specialised features for protein recognition []. The motif also appears in a few single stranded DNA binding proteins. The typical RRM consists of four anti-parallel beta-strands and two alpha-helices arranged in a beta-alpha-beta-beta-alpha-beta fold with side chains that stack with RNA bases. Specificity of RNA binding is determined by multiple contacts with surrounding amino acids. A third helix is present during RNA binding in some cases []. The RRM is reviewed in a number of publications [, , ].; GO: 0003676 nucleic acid binding; PDB: 2RNE_A 2DGO_A 2DO4_A 1YTY_B 2VOO_B 2VOP_A 2VON_B 1ZH5_B 2VOD_A 1S79_A ....
Probab=22.74 E-value=2e+02 Score=17.86 Aligned_cols=44 Identities=16% Similarity=0.161 Sum_probs=35.9
Q ss_pred EecCCCcccHHHHHHhhccCCCceeeEEEEe-----ccEEEEEecccee
Q 030077 104 ADGAMNETAIPAVTQALQGTEGISDLKVQVI-----EGIATVELKKQTT 147 (183)
Q Consensus 104 aEGM~Ce~Ci~~VtkALE~ieGVsdVkV~Le-----eG~AtVe~dkqtt 147 (183)
|.|...+.=-..|++.++....|..+++... .|-|-|++.....
T Consensus 3 v~nlp~~~t~~~l~~~f~~~g~i~~~~~~~~~~~~~~~~a~V~F~~~~~ 51 (70)
T PF00076_consen 3 VGNLPPDVTEEELRDFFSQFGKIESIKVMRNSSGKSKGYAFVEFESEED 51 (70)
T ss_dssp EESETTTSSHHHHHHHHHTTSTEEEEEEEEETTSSEEEEEEEEESSHHH
T ss_pred EcCCCCcCCHHHHHHHHHHhhhcccccccccccccccceEEEEEcCHHH
Confidence 4455555556789999999999999999995 8999999987655
No 115
>TIGR00914 2A0601 heavy metal efflux pump (cobalt-zinc-cadmium). This model represents a family of H+/heavy metal cation antiporters. This family is one of several subfamilies within the scope of pfam model pfam00873.
Probab=22.30 E-value=76 Score=32.41 Aligned_cols=63 Identities=19% Similarity=0.381 Sum_probs=39.7
Q ss_pred EEEEEecCCCc---ccHHHHHHhhccCCCceeeEEEEeccE--EEEEeccceeeeccc-chHHHHHHHHh
Q 030077 100 MYFQADGAMNE---TAIPAVTQALQGTEGISDLKVQVIEGI--ATVELKKQTTVQATG-VAANLVEIIQG 163 (183)
Q Consensus 100 M~FKaEGM~Ce---~Ci~~VtkALE~ieGVsdVkV~LeeG~--AtVe~dkqttvqatg-vas~LvEaIe~ 163 (183)
..+++.|..=+ .-+..|++.|+++|||++|+.++..|. ..+++|++.- ++-| +++.|-++++.
T Consensus 684 i~i~l~G~d~~~L~~~a~~v~~~l~~~pgv~~v~~~~~~~~~e~~i~id~~~~-~~~Glt~~~v~~~l~~ 752 (1051)
T TIGR00914 684 VAVKVFGDDLDDLDATAEKISAVLKGVPGAADVKVEQTTGLPYLTVEIDREKA-ARYGLTVGDVQDTVAT 752 (1051)
T ss_pred eEEEEECCCHHHHHHHHHHHHHHHhcCCCceeeeccccCCCceEEEEECHHHH-HHcCCCHHHHHHHHHH
Confidence 45677775332 346789999999999999999987654 4555555322 1222 34555555553
No 116
>PRK05528 methionine sulfoxide reductase A; Provisional
Probab=22.06 E-value=2e+02 Score=23.76 Aligned_cols=37 Identities=8% Similarity=0.112 Sum_probs=27.4
Q ss_pred ccHHHHHHhhccCCCceeeEEEEeccE--------------EEEEecccee
Q 030077 111 TAIPAVTQALQGTEGISDLKVQVIEGI--------------ATVELKKQTT 147 (183)
Q Consensus 111 ~Ci~~VtkALE~ieGVsdVkV~LeeG~--------------AtVe~dkqtt 147 (183)
||-=-++..+..++||.++.|=...|. +.|.+|+..+
T Consensus 9 GCFWg~E~~f~~l~GV~~t~vGYagG~~~~p~~~~tgH~E~V~V~yDp~~i 59 (156)
T PRK05528 9 GCLWGVQAFFKTLPGVIHTEAGRANGRTSTLDGPYDGYAECVKTHFDPRMV 59 (156)
T ss_pred CCchhhHHHHhcCCCEEEEEEEcCCCCCCCCCCCCCCcEEEEEEEECCCcC
Confidence 444446677888899999999888765 5567777666
No 117
>smart00360 RRM RNA recognition motif.
Probab=21.82 E-value=1.9e+02 Score=17.12 Aligned_cols=43 Identities=12% Similarity=0.156 Sum_probs=32.9
Q ss_pred ecCCCcccHHHHHHhhccCCCceeeEEEEec------cEEEEEecccee
Q 030077 105 DGAMNETAIPAVTQALQGTEGISDLKVQVIE------GIATVELKKQTT 147 (183)
Q Consensus 105 EGM~Ce~Ci~~VtkALE~ieGVsdVkV~Lee------G~AtVe~dkqtt 147 (183)
.|......-.-|++.++....|.++.+.... |.|.|++.....
T Consensus 2 ~~l~~~~~~~~l~~~f~~~g~v~~~~i~~~~~~~~~~~~a~v~f~~~~~ 50 (71)
T smart00360 2 GNLPPDVTEEELRELFSKFGKIESVRLVRDKDTGKSKGFAFVEFESEED 50 (71)
T ss_pred CCCCcccCHHHHHHHHHhhCCEeEEEEEeCCCCCCCCceEEEEeCCHHH
Confidence 3455566777899999998889999998864 589999965443
No 118
>cd01808 hPLIC_N Ubiquitin-like domain of hPLIC-1 and hPLIC2. hPLIC-1 and hPLIC-2 (human homologs of the yeast ubiquitin-like Dsk2 protein) are type2 UBL's (ubiquitin-like) proteins that are thought to serve as adaptors that link the ubiquitination machinery to the proteasome. The hPLIC's have an N-terminal UBL domain that binds the S5a subunit of the proteasome and a C-terminal UBA (ubiquitin-associated) domain that binds a ubiquitylated protein.
Probab=21.68 E-value=1.1e+02 Score=20.64 Aligned_cols=43 Identities=16% Similarity=0.254 Sum_probs=29.7
Q ss_pred eEEEEeccEEEEEeccceeeecccchHHHHHHHH-hcCceeEeeeccccC
Q 030077 129 LKVQVIEGIATVELKKQTTVQATGVAANLVEIIQ-GSGFKLQTLNLSFDD 177 (183)
Q Consensus 129 VkV~LeeG~AtVe~dkqttvqatgvas~LvEaIe-~aGFkVq~l~l~f~d 177 (183)
+.|....|...++.++..++ ..|++.|+ ..|.....+.|-|..
T Consensus 3 i~vk~~~g~~~l~v~~~~TV------~~lK~~I~~~~~i~~~~~~Li~~G 46 (71)
T cd01808 3 VTVKTPKDKEEIEIAEDASV------KDFKEAVSKKFKANQEQLVLIFAG 46 (71)
T ss_pred EEEEcCCCCEEEEECCCChH------HHHHHHHHHHhCCCHHHEEEEECC
Confidence 44555567778888887775 89999995 447766666666543
No 119
>PRK00194 hypothetical protein; Validated
Probab=21.61 E-value=1.3e+02 Score=21.03 Aligned_cols=40 Identities=13% Similarity=0.174 Sum_probs=31.5
Q ss_pred CCceEEEEEEecCCCcccHHHHHHhhccCCCceeeEEEEe
Q 030077 95 SDKLTMYFQADGAMNETAIPAVTQALQGTEGISDLKVQVI 134 (183)
Q Consensus 95 ~~~ltM~FKaEGM~Ce~Ci~~VtkALE~ieGVsdVkV~Le 134 (183)
.+.+.|.+.+++..+...+..+++.|+++.+.-.+++.+.
T Consensus 40 ~~~~~~~~~v~~~~~~~~~~~l~~~l~~l~~~~~~~~~~~ 79 (90)
T PRK00194 40 DGYFTMIMLVDISESKKDFAELKEELEELGKELGVKIRIQ 79 (90)
T ss_pred CCeeEEEEEEEecCCCCCHHHHHHHHHHHHHHcCCEEEEE
Confidence 4577888888887555668899999999988888887663
No 120
>PRK15348 type III secretion system lipoprotein SsaJ; Provisional
Probab=21.51 E-value=85 Score=27.78 Aligned_cols=21 Identities=24% Similarity=0.390 Sum_probs=19.2
Q ss_pred HHHHHhhccCCCceeeEEEEe
Q 030077 114 PAVTQALQGTEGISDLKVQVI 134 (183)
Q Consensus 114 ~~VtkALE~ieGVsdVkV~Le 134 (183)
..+.+.|+.++||.+++|.|.
T Consensus 110 gELarTI~~idgV~~ArVhL~ 130 (249)
T PRK15348 110 QRIEGMLSQMEGVINAKVTIA 130 (249)
T ss_pred HHHHHHHHhCCCeeEeEEEEE
Confidence 568899999999999999987
No 121
>TIGR02374 nitri_red_nirB nitrite reductase [NAD(P)H], large subunit.
Probab=21.23 E-value=59 Score=32.13 Aligned_cols=51 Identities=25% Similarity=0.200 Sum_probs=31.1
Q ss_pred cCCCcccHHHHHHhhccCCCceeeEEEEeccEEEEEeccceeeecccchHHHHHHHHhcCce
Q 030077 106 GAMNETAIPAVTQALQGTEGISDLKVQVIEGIATVELKKQTTVQATGVAANLVEIIQGSGFK 167 (183)
Q Consensus 106 GM~Ce~Ci~~VtkALE~ieGVsdVkV~LeeG~AtVe~dkqttvqatgvas~LvEaIe~aGFk 167 (183)
|+.|.+|.+-|++.|+..-+..-..| ...--+..+- +.+.|.+.|+..|++
T Consensus 445 g~~Cg~C~~~~~~il~~~~~~~~~~~----~~~~c~~~~~-------~~~~~~~~~~~~~~~ 495 (785)
T TIGR02374 445 GTSCGGCKPLVEQLLRAELNSQYTAS----TPALCECTDF-------SRDELFEEIQARGFT 495 (785)
T ss_pred CCCCcCHHHHHHHHHHHHHhhccccc----cCcccCCcCC-------CHHHHHHHHHHcCCC
Confidence 58999999999999986543322211 1122222222 347888888877664
No 122
>cd01804 midnolin_N Ubiquitin-like domain of midnolin. midnolin_N Midnolin (midbrain nucleolar protein) is expressed in the nucleolus and is thought to regulate genes involved in neurogenesis. Midnolin contains an amino-terminal ubiquitin-like domain.
Probab=21.18 E-value=1.3e+02 Score=21.11 Aligned_cols=43 Identities=19% Similarity=0.170 Sum_probs=29.2
Q ss_pred eEEEEec-cEEEEEeccceeeecccchHHHHHHH-HhcCceeEeeeccccC
Q 030077 129 LKVQVIE-GIATVELKKQTTVQATGVAANLVEII-QGSGFKLQTLNLSFDD 177 (183)
Q Consensus 129 VkV~Lee-G~AtVe~dkqttvqatgvas~LvEaI-e~aGFkVq~l~l~f~d 177 (183)
+.|.... ....++.++..++ ..|++.| ++.|+....+.|.|..
T Consensus 4 I~Vk~~~G~~~~l~v~~~~TV------~~LK~~I~~~~~~~~~~qrL~~~G 48 (78)
T cd01804 4 LNIHSTTGTRFDLSVPPDETV------EGLKKRISQRLKVPKERLALLHRE 48 (78)
T ss_pred EEEEECCCCEEEEEECCcCHH------HHHHHHHHHHhCCChHHEEEEECC
Confidence 3344433 3446777777665 9999999 4558888877777763
No 123
>PF02682 AHS1: Allophanate hydrolase subunit 1; InterPro: IPR003833 Allophanate hydrolase catalyses the second reaction in an ATP-dependent, two-step degradation of urea to ammonia and C02. This follows the action of the biotin-containing urea carboxylase. Saccharomyces cerevisiae can use urea as a sole nitrogen source via this degradation pathway []. In yeast, the fusion of allophanate hydrolase to urea carboxylase is called urea amidolyase. In bacteria, the second step in the urea degradation pathway is also the ATP-dependent allophanate hydrolase. The gene encoding this enzyme is found adjacent to the urea carboxylase gene []. Allophanate hydrolase has strict substrate specificity, as analogues of allophanate are not hydrolysed by it []. This domain represents subunit 1 of allophanate hydrolase (AHS1), which is found in urea carboxylase.; PDB: 3VA7_A 3MML_H 3OEP_A 3OPF_C 3ORE_A 2ZP2_A 2KWA_A 2PHC_B.
Probab=21.17 E-value=2.2e+02 Score=23.84 Aligned_cols=61 Identities=18% Similarity=0.205 Sum_probs=43.1
Q ss_pred ccHHHHHHhhcc--CCCceeeEEEEeccEEEEEeccceeeecccchHHHHHHHHhcC----------ceeEeeeccccCc
Q 030077 111 TAIPAVTQALQG--TEGISDLKVQVIEGIATVELKKQTTVQATGVAANLVEIIQGSG----------FKLQTLNLSFDDE 178 (183)
Q Consensus 111 ~Ci~~VtkALE~--ieGVsdVkV~LeeG~AtVe~dkqttvqatgvas~LvEaIe~aG----------FkVq~l~l~f~d~ 178 (183)
..+.++.++|++ ++||.++--.+ ....|.||+..+ ....|++.|++.- =+..++-..||++
T Consensus 25 ~~v~al~~~l~~~~~~gi~e~vp~~--~sllV~fdp~~~-----~~~~l~~~l~~~~~~~~~~~~~~~r~~~iPV~Y~~~ 97 (202)
T PF02682_consen 25 ARVLALARALRAAPLPGIVEVVPAY--RSLLVHFDPLRI-----DRAALRAALEELLASPQPSEKPPSRLIEIPVCYDGE 97 (202)
T ss_dssp HHHHHHHHHHHHHT-TTEEEEEEES--SEEEEEESTTTS-----HHHHHHHHHHHHHCCCCSSCCCCEEEEEEEEEESTT
T ss_pred HHHHHHHHHHhcCCCCCeEEeeccc--cEEEEEEcCCcC-----CHHHHHHHHHHhhhhccccccCCCceEEEEEEECCC
Confidence 567788899999 99999988887 689999998775 4567777666431 1355566666643
No 124
>PRK10598 lipoprotein; Provisional
Probab=21.12 E-value=62 Score=27.61 Aligned_cols=53 Identities=17% Similarity=0.266 Sum_probs=38.0
Q ss_pred cCCCceeeEEEEeccEEEEEeccceeeecccchHHHHHHHHhcCceeEeeecccc
Q 030077 122 GTEGISDLKVQVIEGIATVELKKQTTVQATGVAANLVEIIQGSGFKLQTLNLSFD 176 (183)
Q Consensus 122 ~ieGVsdVkV~LeeG~AtVe~dkqttvqatgvas~LvEaIe~aGFkVq~l~l~f~ 176 (183)
+++|+-+++++|.+..+.+=-+.+-.+..+|.+..-.... .|=--.+++|.|+
T Consensus 47 G~~gl~~a~i~l~~l~~~IGr~~~~~v~l~g~a~v~v~~~--~g~~~a~l~l~~~ 99 (186)
T PRK10598 47 GLPGVADAHIVLTNLTSQIGREEPNKVTLTGDANLDISSL--FGSQKADMKLTLK 99 (186)
T ss_pred CCCceeeeEEEeeeceeecCCCCCCEEEEeceeeeeeecc--CCCcCcEEEEEEE
Confidence 6899999999999988888877777778888776655555 3322344555543
No 125
>PRK10509 bacterioferritin-associated ferredoxin; Provisional
Probab=20.97 E-value=62 Score=22.76 Aligned_cols=18 Identities=22% Similarity=0.298 Sum_probs=15.6
Q ss_pred cCCCcccHHHHHHhhccC
Q 030077 106 GAMNETAIPAVTQALQGT 123 (183)
Q Consensus 106 GM~Ce~Ci~~VtkALE~i 123 (183)
|+.|..|.+.+++.|.+.
T Consensus 36 g~~CG~C~~~i~~il~~~ 53 (64)
T PRK10509 36 GNQCGKCIRAAREVMQDE 53 (64)
T ss_pred CCCccchHHHHHHHHHHH
Confidence 889999999999988653
No 126
>TIGR00412 redox_disulf_2 small redox-active disulfide protein 2. This small protein is found in three archaeal species so far (Methanococcus jannaschii, Archeoglobus fulgidus, and Methanobacterium thermoautotrophicum) as well as in Anabaena PCC7120. It is homologous to thioredoxins, glutaredoxins, and protein disulfide isomerases, and shares with them a redox-active disulfide. The redox active disulfide region CXXC motif resembles neither thioredoxin nor glutaredoxin. A closely related protein found in the same three Archaea, described by redox_disulf_1, has a glutaredoxin-like CP[YH]C sequence; it has been characterized in functional assays as redox-active but unlikely to be a thioredoxin or glutaredoxin.
Probab=20.94 E-value=1.5e+02 Score=20.45 Aligned_cols=25 Identities=20% Similarity=0.129 Sum_probs=18.3
Q ss_pred EEEEEecCCCcccHHH---HHHhhccCC
Q 030077 100 MYFQADGAMNETAIPA---VTQALQGTE 124 (183)
Q Consensus 100 M~FKaEGM~Ce~Ci~~---VtkALE~ie 124 (183)
|.+++-+.-|..|-.. +++++++.+
T Consensus 1 m~i~~~a~~C~~C~~~~~~~~~~~~e~~ 28 (76)
T TIGR00412 1 MKIQIYGTGCANCQMTEKNVKKAVEELG 28 (76)
T ss_pred CEEEEECCCCcCHHHHHHHHHHHHHHcC
Confidence 4566667889999765 677777764
No 127
>PF01625 PMSR: Peptide methionine sulfoxide reductase; InterPro: IPR002569 Peptide methionine sulphoxide reductase (Msr) reverses the inactivation of many proteins due to the oxidation of critical methionine residues by reducing methionine sulphoxide, Met(O), to methionine []. It is present in most living organisms, and the cognate structural gene belongs to the so-called minimum gene set [, ]. The domains: MsrA and MsrB, reduce different epimeric forms of methionine sulphoxide. This group represent MsrA, the crystal structure of which has been determined in a number of organisms. In Mycobacterium tuberculosis, the MsrA structure has been determined to 1.5 Angstrom resolution []. In contrast to the three catalytic cysteine residues found in previously characterised MsrA structures, M. tuberculosis MsrA represents a class containing only two functional cysteine residues. The overall structure shows no resemblance to the structures of MsrB (IPR002579 from INTERPRO) from other organisms; though the active sites show approximate mirror symmetry. In each case, conserved amino acid motifs mediate the stereo-specific recognition and reduction of the substrate. In a number of pathogenic bacteria including Neisseria gonorrhoeae, the MsrA and MsrB domains are fused; the MsrA being N-terminal to MsrB. This arrangement is reversed in Treponema pallidum. In N. gonorrhoeae and Neisseria meningitidis a thioredoxin domain is fused to the N terminus. This may function to reduce the active sites of the downstream MsrA and MsrB domains. ; GO: 0016671 oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor, 0019538 protein metabolic process, 0055114 oxidation-reduction process; PDB: 2GT3_A 1FF3_B 2IEM_A 3E0M_D 2J89_A 3PIN_B 3PIM_B 3PIL_B 2L90_A 3BQF_A ....
Probab=20.74 E-value=3.5e+02 Score=22.05 Aligned_cols=37 Identities=16% Similarity=0.183 Sum_probs=30.4
Q ss_pred ccHHHHHHhhccCCCceeeEEEEecc-------------------EEEEEecccee
Q 030077 111 TAIPAVTQALQGTEGISDLKVQVIEG-------------------IATVELKKQTT 147 (183)
Q Consensus 111 ~Ci~~VtkALE~ieGVsdVkV~LeeG-------------------~AtVe~dkqtt 147 (183)
||-=.++.+.+.++||.++.|=+..| .+.|.+|+..+
T Consensus 8 GCFW~~e~~f~~~~GV~~t~vGYagG~~~~PtY~~v~~g~tgh~E~V~V~yD~~~i 63 (155)
T PF01625_consen 8 GCFWGVEAAFRRLPGVISTRVGYAGGTTPNPTYRQVCSGRTGHAEAVRVTYDPSVI 63 (155)
T ss_dssp SSHHHHHHHHHTSTTEEEEEEEEESSSSSS--HHHHHTTTTT-EEEEEEEEETTTS
T ss_pred CCCeEhHHHHhhCCCEEEEEecccCCCCCCCcceeeecCCCCCeEEEEEEECCCcc
Confidence 56667788899999999999999988 45677777666
No 128
>cd01806 Nedd8 Nebb8-like ubiquitin protein. Nedd8 (also known as Rub1) has a single conserved ubiquitin-like domain that is part of a protein modification pathway similar to that of ubiquitin. Nedd8 modifies a family of molecular scaffold proteins called cullins that are responsible for assembling the ROC1/Rbx1 RING-based E3 ubiquitin ligases, of which several play a direct role in tumorigenesis.
Probab=20.48 E-value=1.1e+02 Score=20.20 Aligned_cols=44 Identities=16% Similarity=0.331 Sum_probs=29.9
Q ss_pred eEEEEec-cEEEEEeccceeeecccchHHHHHHHHhc-CceeEeeeccccCc
Q 030077 129 LKVQVIE-GIATVELKKQTTVQATGVAANLVEIIQGS-GFKLQTLNLSFDDE 178 (183)
Q Consensus 129 VkV~Lee-G~AtVe~dkqttvqatgvas~LvEaIe~a-GFkVq~l~l~f~d~ 178 (183)
+.|.... ....+++++..++ ..|++.|+.. |+......|-|+..
T Consensus 3 i~v~~~~g~~~~~~v~~~~tv------~~lK~~i~~~~g~~~~~qrL~~~g~ 48 (76)
T cd01806 3 IKVKTLTGKEIEIDIEPTDKV------ERIKERVEEKEGIPPQQQRLIYSGK 48 (76)
T ss_pred EEEEeCCCCEEEEEECCCCCH------HHHHHHHhHhhCCChhhEEEEECCe
Confidence 4455543 3445677766664 9999999554 88888888877653
No 129
>COG0527 LysC Aspartokinases [Amino acid transport and metabolism]
Probab=20.29 E-value=4.3e+02 Score=25.06 Aligned_cols=74 Identities=18% Similarity=0.250 Sum_probs=60.4
Q ss_pred CCceEEEEEEecCCCcccHHHHHHhhccCCCceeeEEEEeccEEEEEeccceeeecccchHHHHHHHHhcCceeEeee
Q 030077 95 SDKLTMYFQADGAMNETAIPAVTQALQGTEGISDLKVQVIEGIATVELKKQTTVQATGVAANLVEIIQGSGFKLQTLN 172 (183)
Q Consensus 95 ~~~ltM~FKaEGM~Ce~Ci~~VtkALE~ieGVsdVkV~LeeG~AtVe~dkqttvqatgvas~LvEaIe~aGFkVq~l~ 172 (183)
.+..++.|.+++...+.....+.++..+..+ .|.++++.|.|-..-.--...-|+++.+-+++.+.|..+.-.+
T Consensus 345 ~~~~~i~~~v~~~~~~~a~~~l~~~~~~~~~----~v~~~~~~a~vsiVG~gm~~~~gvaa~~f~aL~~~~ini~~is 418 (447)
T COG0527 345 ISEVSISFTVPESDAPRALRALLEEKLELLA----EVEVEEGLALVSIVGAGMRSNPGVAARIFQALAEENINIIMIS 418 (447)
T ss_pred cCCCeEEEEEchhhHHHHHHHHHHHHhhhcc----eEEeeCCeeEEEEEccccccCcCHHHHHHHHHHhCCCcEEEEE
Confidence 3345589999999988888888888876544 8888889999988877776777999999999999998776544
No 130
>PF10865 DUF2703: Domain of unknown function (DUF2703); InterPro: IPR021219 This family of protein has no known function.
Probab=20.08 E-value=1.6e+02 Score=23.44 Aligned_cols=20 Identities=15% Similarity=0.076 Sum_probs=13.7
Q ss_pred EEEecCCCcccHHHHHHhhc
Q 030077 102 FQADGAMNETAIPAVTQALQ 121 (183)
Q Consensus 102 FKaEGM~Ce~Ci~~VtkALE 121 (183)
+-.+|-+|+.|..+-+...+
T Consensus 8 l~~~g~tC~RC~~Tg~~L~~ 27 (120)
T PF10865_consen 8 LDLDGKTCERCGDTGETLRE 27 (120)
T ss_pred eecCCCcCCchhhHHHHHHH
Confidence 55668899999876544433
Done!