Query 040572
Match_columns 142
No_of_seqs 102 out of 115
Neff 2.2
Searched_HMMs 46136
Date Fri Mar 29 09:42:31 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/040572.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/040572hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF12554 MOZART1: Mitotic-spin 99.9 3.3E-27 7.2E-32 155.1 6.0 48 78-125 1-48 (48)
2 PF12926 MOZART2: Mitotic-spin 97.0 0.0032 7E-08 46.4 7.0 58 84-141 29-86 (88)
3 cd04774 HTH_YfmP Helix-Turn-He 82.7 5.4 0.00012 28.1 5.8 48 80-127 41-91 (96)
4 PF05105 Phage_holin_4: Holin 79.8 3.4 7.4E-05 29.7 4.0 30 98-127 87-117 (118)
5 PF12169 DNA_pol3_gamma3: DNA 75.2 11 0.00023 26.8 5.4 44 83-126 16-60 (143)
6 cd00127 DSPc Dual specificity 73.9 15 0.00033 25.1 5.8 51 76-126 65-123 (139)
7 PF13817 DDE_Tnp_IS66_C: IS66 71.8 5.3 0.00012 25.0 2.9 19 108-126 7-26 (39)
8 PF10819 DUF2564: Protein of u 70.5 19 0.00041 26.5 5.8 41 69-109 25-68 (79)
9 cd04765 HTH_MlrA-like_sg2 Heli 69.5 18 0.00039 25.7 5.5 50 79-128 41-92 (99)
10 PTZ00242 protein tyrosine phos 63.8 24 0.00051 27.0 5.5 36 91-126 102-140 (166)
11 PRK11050 manganese transport r 63.5 49 0.0011 24.8 7.1 52 77-128 98-150 (152)
12 PLN03112 cytochrome P450 famil 62.8 16 0.00034 31.0 4.8 46 83-128 296-341 (514)
13 PTZ00393 protein tyrosine phos 61.7 15 0.00033 31.1 4.5 38 91-128 174-213 (241)
14 PF00067 p450: Cytochrome P450 60.0 6.7 0.00015 30.0 1.9 47 82-128 261-307 (463)
15 PF08809 DUF1799: Phage relate 59.1 18 0.0004 25.8 3.9 45 80-126 24-74 (83)
16 PLN02971 tryptophan N-hydroxyl 58.4 20 0.00043 31.1 4.7 48 82-129 326-373 (543)
17 COG2445 Uncharacterized conser 56.4 42 0.00092 25.9 5.8 49 77-125 40-92 (138)
18 KOG2836 Protein tyrosine phosp 55.9 16 0.00035 30.0 3.6 36 94-129 106-141 (173)
19 PF15297 CKAP2_C: Cytoskeleton 54.9 19 0.0004 32.3 4.1 30 99-128 104-133 (353)
20 TIGR00756 PPR pentatricopeptid 54.4 21 0.00046 18.4 2.8 28 88-115 7-34 (35)
21 COG0298 HypC Hydrogenase matur 53.8 15 0.00032 27.2 2.8 21 76-96 59-79 (82)
22 PTZ00404 cytochrome P450; Prov 53.1 31 0.00067 28.9 4.9 48 82-129 282-329 (482)
23 PF02627 CMD: Carboxymuconolac 52.2 56 0.0012 20.4 5.8 18 106-123 49-66 (85)
24 smart00422 HTH_MERR helix_turn 51.2 19 0.00041 22.5 2.7 19 104-122 50-68 (70)
25 TIGR02120 GspF general secreti 51.0 42 0.0009 28.1 5.4 49 79-130 61-109 (399)
26 smart00856 PMEI Plant invertas 50.5 53 0.0011 23.0 5.1 45 81-127 50-97 (148)
27 PRK06585 holA DNA polymerase I 50.5 49 0.0011 26.8 5.6 43 84-126 214-257 (343)
28 PRK10416 signal recognition pa 50.5 54 0.0012 27.7 6.0 44 86-129 33-78 (318)
29 PRK10161 transcriptional regul 50.0 18 0.0004 26.0 2.8 49 82-130 160-208 (229)
30 PF13032 DUF3893: Domain of un 48.8 3.6 7.7E-05 31.4 -1.1 33 95-127 64-96 (138)
31 PLN02169 fatty acid (omega-1)- 48.7 41 0.00089 29.0 5.1 45 83-127 301-345 (500)
32 TIGR02425 decarb_PcaC 4-carbox 48.7 63 0.0014 24.0 5.5 19 106-124 81-99 (123)
33 smart00845 GatB_Yqey GatB doma 48.2 1E+02 0.0022 22.9 6.6 44 84-127 19-71 (147)
34 PLN02936 epsilon-ring hydroxyl 47.3 35 0.00075 29.1 4.4 45 83-127 278-322 (489)
35 PF02885 Glycos_trans_3N: Glyc 45.6 31 0.00066 22.6 3.1 39 90-128 26-65 (66)
36 PLN00168 Cytochrome P450; Prov 45.5 46 0.001 28.5 4.9 47 83-129 306-352 (519)
37 PRK00771 signal recognition pa 44.8 57 0.0012 29.2 5.5 41 89-129 10-56 (437)
38 COG5012 Predicted cobalamin bi 44.7 39 0.00084 28.7 4.3 34 83-116 17-50 (227)
39 PLN00110 flavonoid 3',5'-hydro 44.4 42 0.00091 28.9 4.5 46 83-128 289-334 (504)
40 PLN02183 ferulate 5-hydroxylas 44.4 50 0.0011 28.2 5.0 46 83-128 304-349 (516)
41 PLN02655 ent-kaurene oxidase 44.3 40 0.00086 28.4 4.3 46 83-128 262-307 (466)
42 PLN02500 cytochrome P450 90B1 43.8 47 0.001 28.0 4.7 44 83-126 279-322 (490)
43 PF01314 AFOR_C: Aldehyde ferr 43.7 56 0.0012 28.1 5.2 45 81-125 109-172 (382)
44 PF13812 PPR_3: Pentatricopept 43.6 39 0.00085 17.8 2.9 24 103-126 6-29 (34)
45 PF02861 Clp_N: Clp amino term 43.4 25 0.00054 20.8 2.2 40 82-125 13-52 (53)
46 PRK00400 hisE phosphoribosyl-A 43.4 72 0.0016 23.7 5.1 32 83-122 58-89 (105)
47 COG3636 Predicted transcriptio 42.9 79 0.0017 24.1 5.3 56 67-125 31-89 (100)
48 cd04773 HTH_TioE_rpt2 Second H 42.8 1.2E+02 0.0026 21.5 6.5 47 79-125 41-87 (108)
49 cd04448 DEP_PIKfyve DEP (Dishe 42.8 32 0.0007 23.9 3.0 31 78-112 31-62 (81)
50 PLN02687 flavonoid 3'-monooxyg 42.7 49 0.0011 28.3 4.6 46 83-128 297-342 (517)
51 PRK09247 ATP-dependent DNA lig 42.3 74 0.0016 29.0 5.9 51 73-124 9-64 (539)
52 PRK11753 DNA-binding transcrip 42.2 1.3E+02 0.0029 21.9 6.5 20 110-129 178-197 (211)
53 PF01503 PRA-PH: Phosphoribosy 42.1 90 0.002 21.1 5.1 35 80-122 46-80 (83)
54 PF13877 RPAP3_C: Potential Mo 41.7 40 0.00086 23.0 3.3 39 86-124 34-75 (94)
55 TIGR01797 CM_P_1 chorismate mu 41.1 1.2E+02 0.0025 20.8 5.6 62 67-128 8-78 (83)
56 PRK14703 glutaminyl-tRNA synth 40.8 72 0.0016 31.0 5.9 43 84-126 644-693 (771)
57 cd06258 Peptidase_M3_like The 40.6 81 0.0017 25.9 5.4 44 79-126 5-48 (365)
58 PF01817 CM_2: Chorismate muta 40.6 34 0.00074 22.6 2.8 61 67-127 4-73 (81)
59 PRK08903 DnaA regulatory inact 40.6 1.3E+02 0.0029 22.7 6.3 45 81-127 162-206 (227)
60 cd04766 HTH_HspR Helix-Turn-He 40.3 87 0.0019 21.3 4.8 46 79-127 41-87 (91)
61 PLN03234 cytochrome P450 83B1; 40.0 64 0.0014 27.2 4.9 47 83-129 288-334 (499)
62 PRK02615 thiamine-phosphate py 39.6 32 0.00069 30.0 3.1 44 87-130 8-53 (347)
63 PLN03018 homomethionine N-hydr 39.5 60 0.0013 28.5 4.8 46 83-128 314-359 (534)
64 PF13041 PPR_2: PPR repeat fam 39.4 38 0.00082 20.1 2.6 29 88-116 10-38 (50)
65 PLN02290 cytokinin trans-hydro 39.2 53 0.0012 27.8 4.3 46 83-128 316-361 (516)
66 PLN02966 cytochrome P450 83A1 39.1 64 0.0014 27.4 4.8 46 83-128 289-334 (502)
67 PRK10573 type IV pilin biogene 38.4 84 0.0018 26.4 5.3 50 78-130 58-107 (399)
68 PRK13856 two-component respons 37.3 52 0.0011 24.3 3.5 56 75-130 154-209 (241)
69 COG1641 Uncharacterized conser 36.7 35 0.00076 31.1 3.0 24 103-126 16-39 (387)
70 PRK07914 hypothetical protein; 36.6 1E+02 0.0022 25.2 5.5 43 84-126 198-241 (320)
71 cd04778 HTH_MerR-like_sg2 Heli 36.6 76 0.0017 25.7 4.7 35 95-129 131-165 (219)
72 PF14840 DNA_pol3_delt_C: Proc 36.5 98 0.0021 23.0 4.9 40 86-125 2-42 (125)
73 PRK07452 DNA polymerase III su 35.5 92 0.002 25.0 4.9 43 83-125 201-244 (326)
74 PF04447 DUF550: Protein of un 35.4 73 0.0016 24.3 4.1 49 76-130 26-78 (100)
75 PF06207 DUF1002: Protein of u 35.3 84 0.0018 26.1 4.8 57 68-126 124-186 (225)
76 PRK05458 guanosine 5'-monophos 34.3 64 0.0014 28.0 4.1 37 93-129 91-139 (326)
77 PF02881 SRP54_N: SRP54-type p 34.2 82 0.0018 20.3 3.8 25 102-126 29-53 (75)
78 PF13411 MerR_1: MerR HTH fami 34.1 47 0.001 20.8 2.5 19 80-98 41-59 (69)
79 PRK12402 replication factor C 34.0 1.1E+02 0.0025 24.0 5.1 40 84-123 254-294 (337)
80 KOG0157 Cytochrome P450 CYP4/C 33.6 91 0.002 27.2 5.0 46 84-129 292-337 (497)
81 TIGR02154 PhoB phosphate regul 33.6 47 0.001 23.3 2.7 49 82-130 160-208 (226)
82 TIGR03499 FlhF flagellar biosy 33.1 2.5E+02 0.0055 22.9 7.2 33 95-127 131-163 (282)
83 PRK05629 hypothetical protein; 32.8 1.2E+02 0.0026 24.7 5.3 39 83-121 195-233 (318)
84 PF00550 PP-binding: Phosphopa 32.7 11 0.00024 23.2 -0.6 42 86-129 5-46 (67)
85 PF00782 DSPc: Dual specificit 32.6 82 0.0018 21.6 3.7 60 67-126 48-115 (133)
86 cd00383 trans_reg_C Effector d 32.6 1E+02 0.0022 19.9 4.0 52 79-130 26-77 (95)
87 cd04371 DEP DEP domain, named 32.5 79 0.0017 20.3 3.5 32 78-112 31-62 (81)
88 PLN02738 carotene beta-ring hy 32.3 1E+02 0.0022 28.3 5.2 47 83-129 391-437 (633)
89 PRK00188 trpD anthranilate pho 31.7 1.8E+02 0.0039 24.7 6.3 43 88-130 25-68 (339)
90 PRK14137 recX recombination re 31.0 2.4E+02 0.0053 22.6 6.7 48 82-129 39-86 (195)
91 TIGR01791 CM_archaeal chorisma 30.8 66 0.0014 21.7 3.0 61 67-127 8-77 (83)
92 PLN02394 trans-cinnamate 4-mon 30.7 1.1E+02 0.0024 25.8 4.9 44 85-128 295-338 (503)
93 PF13545 HTH_Crp_2: Crp-like h 30.0 63 0.0014 20.4 2.6 30 94-128 27-56 (76)
94 TIGR03420 DnaA_homol_Hda DnaA 29.7 2.3E+02 0.0051 20.9 6.5 46 79-126 162-207 (226)
95 TIGR01245 trpD anthranilate ph 29.4 2.1E+02 0.0046 24.2 6.4 43 88-130 19-62 (330)
96 TIGR00064 ftsY signal recognit 29.4 66 0.0014 26.4 3.3 25 103-127 10-34 (272)
97 PF14947 HTH_45: Winged helix- 29.1 1.6E+02 0.0034 19.7 4.6 42 82-128 5-47 (77)
98 COG0140 HisI Phosphoribosyl-AT 29.0 1.7E+02 0.0038 21.7 5.1 31 83-121 54-84 (92)
99 PF04566 RNA_pol_Rpb2_4: RNA p 28.8 59 0.0013 21.9 2.4 18 113-130 13-30 (63)
100 smart00657 RPOL4c DNA-directed 28.6 2.1E+02 0.0045 20.9 5.4 58 69-126 51-113 (118)
101 cd02436 Nodulin-21 Nodulin-21. 28.2 47 0.001 26.7 2.1 32 71-118 62-93 (152)
102 PF02082 Rrf2: Transcriptional 28.0 1.9E+02 0.004 19.3 4.8 48 78-130 7-55 (83)
103 TIGR02054 MerD mercuric resist 27.6 2.6E+02 0.0056 20.8 6.2 32 80-111 45-76 (120)
104 PRK02759 bifunctional phosphor 27.5 1.5E+02 0.0032 24.7 5.0 30 83-120 169-198 (203)
105 PRK14970 DNA polymerase III su 27.1 2.1E+02 0.0045 23.6 5.8 42 84-125 237-279 (367)
106 PF01535 PPR: PPR repeat; Int 27.1 87 0.0019 16.0 2.5 25 88-112 7-31 (31)
107 PF14069 SpoVIF: Stage VI spor 27.1 2E+02 0.0043 20.7 5.0 55 70-125 22-77 (79)
108 PRK10701 DNA-binding transcrip 26.8 86 0.0019 22.9 3.2 57 74-130 159-215 (240)
109 PLN03141 3-epi-6-deoxocathaste 26.8 1.4E+02 0.003 25.0 4.8 44 83-126 251-294 (452)
110 PF04137 ERO1: Endoplasmic Ret 26.8 2.2E+02 0.0048 25.2 6.2 62 63-126 269-348 (357)
111 TIGR00778 ahpD_dom alkylhydrop 26.7 1.5E+02 0.0032 17.6 4.7 34 87-122 14-47 (50)
112 smart00354 HTH_LACI helix_turn 26.6 1.9E+02 0.0041 18.8 4.6 40 86-128 4-43 (70)
113 PF00486 Trans_reg_C: Transcri 26.6 1.1E+02 0.0025 19.0 3.4 49 82-130 11-59 (77)
114 PF05796 Chordopox_G2: Chordop 26.6 1.2E+02 0.0026 25.8 4.4 36 84-120 7-43 (216)
115 PF02742 Fe_dep_repr_C: Iron d 26.5 1.9E+02 0.0042 18.9 6.8 51 75-125 5-57 (71)
116 PRK10710 DNA-binding transcrip 26.5 79 0.0017 22.7 2.9 49 82-130 166-214 (240)
117 PF01934 DUF86: Protein of unk 26.4 2.2E+02 0.0048 19.6 5.5 47 77-125 37-83 (119)
118 smart00049 DEP Domain found in 26.3 1.1E+02 0.0023 19.8 3.3 15 98-112 40-54 (77)
119 TIGR01614 PME_inhib pectineste 25.7 1.1E+02 0.0023 22.4 3.5 49 76-126 73-121 (178)
120 PF12802 MarR_2: MarR family; 25.6 1.2E+02 0.0025 18.4 3.2 18 111-128 32-49 (62)
121 TIGR03188 histidine_hisI phosp 25.5 1.7E+02 0.0037 20.9 4.4 29 83-119 54-82 (84)
122 smart00347 HTH_MARR helix_turn 25.4 1.6E+02 0.0035 18.6 4.0 19 111-129 35-53 (101)
123 PRK06843 inosine 5-monophospha 25.4 1E+02 0.0022 27.7 3.9 36 94-129 148-193 (404)
124 PLN03195 fatty acid omega-hydr 24.9 1.6E+02 0.0034 25.1 4.8 45 83-127 292-336 (516)
125 PRK07081 acyl carrier protein; 24.8 81 0.0018 21.6 2.6 40 91-130 12-51 (83)
126 PRK00440 rfc replication facto 24.8 2.4E+02 0.0051 22.0 5.4 39 84-122 230-269 (319)
127 PF06816 NOD: NOTCH protein; 24.7 55 0.0012 22.0 1.7 30 65-96 10-39 (57)
128 PF04906 Tweety: Tweety; Inte 24.6 63 0.0014 28.4 2.5 34 81-114 327-361 (406)
129 PRK14958 DNA polymerase III su 24.5 2E+02 0.0044 26.0 5.7 43 86-128 250-293 (509)
130 PF09748 Med10: Transcription 24.5 2.8E+02 0.0061 20.7 5.6 52 73-128 33-93 (128)
131 PRK11083 DNA-binding response 24.5 93 0.002 21.9 2.9 49 82-130 160-208 (228)
132 PRK14963 DNA polymerase III su 24.4 2.1E+02 0.0046 25.9 5.7 41 85-125 245-286 (504)
133 cd03572 ENTH_epsin_related ENT 24.2 2.3E+02 0.005 21.5 5.1 39 73-111 24-69 (122)
134 TIGR00152 dephospho-CoA kinase 24.1 3E+02 0.0066 20.4 6.3 34 94-127 61-101 (188)
135 TIGR03697 NtcA_cyano global ni 23.9 79 0.0017 22.7 2.5 20 110-129 153-172 (193)
136 cd00592 HTH_MerR-like Helix-Tu 23.5 2.4E+02 0.0052 19.0 4.7 35 79-113 40-74 (100)
137 PF04043 PMEI: Plant invertase 23.5 1.9E+02 0.0042 20.0 4.3 45 78-124 48-96 (152)
138 PRK02436 xerD site-specific ty 23.4 1.1E+02 0.0024 22.9 3.3 26 96-121 205-232 (245)
139 PF13443 HTH_26: Cro/C1-type H 23.4 89 0.0019 19.2 2.4 21 88-108 27-47 (63)
140 PF13833 EF-hand_8: EF-hand do 23.3 1.4E+02 0.003 17.7 3.2 14 96-109 22-35 (54)
141 PF02637 GatB_Yqey: GatB domai 23.2 1.7E+02 0.0036 21.5 4.1 35 93-127 37-72 (148)
142 PRK10766 DNA-binding transcrip 23.1 1.1E+02 0.0023 21.8 3.0 56 74-129 157-212 (221)
143 PF00589 Phage_integrase: Phag 23.0 2.5E+02 0.0054 19.0 6.5 39 83-121 113-155 (173)
144 KOG0591 NIMA (never in mitosis 22.7 78 0.0017 28.9 2.7 60 67-130 54-120 (375)
145 PRK00013 groEL chaperonin GroE 22.6 1.3E+02 0.0028 27.3 4.1 33 96-128 94-134 (542)
146 PRK11517 transcriptional regul 22.4 1.2E+02 0.0026 21.4 3.2 51 80-130 151-201 (223)
147 cd00194 UBA Ubiquitin Associat 22.4 1E+02 0.0022 17.5 2.4 25 87-111 4-28 (38)
148 cd05025 S-100A1 S-100A1: S-100 22.1 2.5E+02 0.0055 18.7 6.3 48 78-125 7-62 (92)
149 KOG3251 Golgi SNAP receptor co 22.1 66 0.0014 27.1 2.0 31 73-103 140-182 (213)
150 TIGR02348 GroEL chaperonin Gro 21.9 1.3E+02 0.0029 26.9 4.0 33 96-128 93-133 (524)
151 PRK09391 fixK transcriptional 21.9 87 0.0019 24.1 2.5 21 110-130 189-209 (230)
152 PLN02641 anthranilate phosphor 21.9 3.1E+02 0.0068 23.8 6.1 41 89-130 27-68 (343)
153 TIGR02684 dnstrm_HI1420 probab 21.9 89 0.0019 22.2 2.4 16 113-128 29-44 (89)
154 PRK07394 hypothetical protein; 21.9 3.3E+02 0.0072 23.5 6.2 42 88-129 31-73 (342)
155 PLN02302 ent-kaurenoic acid ox 21.8 1.7E+02 0.0036 24.3 4.3 45 83-127 287-331 (490)
156 PRK06585 holA DNA polymerase I 21.7 3.5E+02 0.0076 22.0 6.1 47 78-126 144-190 (343)
157 TIGR01807 CM_P2 chorismate mut 21.6 2.6E+02 0.0056 18.6 5.8 58 67-124 8-75 (76)
158 PLN02774 brassinosteroid-6-oxi 21.6 2E+02 0.0044 24.2 4.8 45 83-127 264-308 (463)
159 PRK13918 CRP/FNR family transc 21.6 91 0.002 22.7 2.5 21 110-130 159-179 (202)
160 PLN02346 histidine biosynthesi 21.6 2.2E+02 0.0047 24.8 5.1 32 83-122 221-252 (271)
161 TIGR01593 holin_tox_secr toxin 21.6 1.8E+02 0.0039 21.7 4.1 33 98-130 90-123 (128)
162 cd02259 Peptidase_C39_like Pep 21.6 2.5E+02 0.0054 18.4 5.3 46 80-125 7-52 (122)
163 PRK06645 DNA polymerase III su 21.5 2.5E+02 0.0053 25.7 5.6 36 84-119 260-295 (507)
164 PF06673 L_lactis_ph-MCP: Lact 21.3 86 0.0019 27.7 2.6 32 99-130 5-36 (347)
165 PRK11173 two-component respons 21.3 1.5E+02 0.0032 21.7 3.5 58 73-130 157-214 (237)
166 PRK08487 DNA polymerase III su 21.1 2.8E+02 0.006 22.9 5.4 41 84-126 204-245 (328)
167 PRK09071 hypothetical protein; 21.0 4.1E+02 0.0089 22.8 6.6 43 88-130 30-73 (323)
168 PRK08136 glycosyl transferase 21.0 5.4E+02 0.012 22.1 7.4 43 88-130 29-72 (317)
169 PRK14971 DNA polymerase III su 20.9 2.6E+02 0.0057 26.0 5.8 44 83-126 249-293 (614)
170 PF07865 DUF1652: Protein of u 20.9 1.2E+02 0.0027 21.1 2.9 27 92-128 42-68 (69)
171 cd00043 CYCLIN Cyclin box fold 20.9 2E+02 0.0044 17.2 6.2 40 81-122 5-52 (88)
172 PLN03025 replication factor C 20.9 3E+02 0.0065 22.4 5.6 29 95-123 238-266 (319)
173 cd04447 DEP_BRCC3 DEP (Disheve 20.7 1.8E+02 0.0039 21.6 3.9 35 78-112 32-70 (92)
174 smart00195 DSPc Dual specifici 20.7 2.3E+02 0.005 19.6 4.3 33 94-126 87-120 (138)
175 PRK00982 acpP acyl carrier pro 20.6 1.2E+02 0.0027 19.5 2.7 41 88-130 12-53 (78)
176 smart00404 PTPc_motif Protein 20.6 83 0.0018 19.9 1.9 37 94-130 48-88 (105)
177 smart00012 PTPc_DSPc Protein t 20.6 83 0.0018 19.9 1.9 37 94-130 48-88 (105)
178 PRK00080 ruvB Holliday junctio 20.4 3.4E+02 0.0073 22.2 5.7 45 80-126 184-228 (328)
179 PRK12850 groEL chaperonin GroE 20.4 1.5E+02 0.0034 26.8 4.1 31 98-128 97-135 (544)
180 PRK12849 groEL chaperonin GroE 20.2 1.6E+02 0.0034 26.8 4.1 33 96-128 94-134 (542)
181 cd00569 HTH_Hin_like Helix-tur 20.2 1.2E+02 0.0027 14.4 4.0 23 97-119 7-29 (42)
182 PRK09849 putative oxidoreducta 20.2 2.3E+02 0.0051 27.3 5.4 36 89-124 370-430 (702)
183 TIGR01387 cztR_silR_copR heavy 20.1 1.1E+02 0.0024 21.3 2.6 51 80-130 151-201 (218)
184 TIGR00959 ffh signal recogniti 20.0 1.1E+02 0.0024 27.3 3.1 28 102-129 32-59 (428)
185 COG1459 PulF Type II secretory 20.0 2.5E+02 0.0053 25.0 5.2 51 77-130 56-106 (397)
No 1
>PF12554 MOZART1: Mitotic-spindle organizing gamma-tubulin ring associated; InterPro: IPR022214 This family of proteins is found in eukaryotes. Proteins in this family are typically between 71 and 105 amino acids in length. There is a single completely conserved residue L that may be functionally important.
Probab=99.94 E-value=3.3e-27 Score=155.06 Aligned_cols=48 Identities=65% Similarity=1.007 Sum_probs=46.9
Q ss_pred HHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHhCCCCHHHHHHHHHHHH
Q 040572 78 ARESLDLAFHMSNILDTGLDRHTLSVLIALCDLGVNPEALAAVVKELQ 125 (142)
Q Consensus 78 ArEtLDiL~EIS~LLNTGLDReTLsICI~LcE~GVNPEALA~VIKELR 125 (142)
|+++||++|+||+||||||||+||+|||+|||+||||||||+||||||
T Consensus 1 a~~~~d~l~eiS~lLntgLd~etL~ici~L~e~GVnPeaLA~vI~elr 48 (48)
T PF12554_consen 1 ARETLDVLHEISDLLNTGLDRETLSICIELCENGVNPEALAAVIKELR 48 (48)
T ss_pred CchHHHHHHHHHHHHcCCCCHHHHHHHHHHHHCCCCHHHHHHHHHHhC
Confidence 579999999999999999999999999999999999999999999997
No 2
>PF12926 MOZART2: Mitotic-spindle organizing gamma-tubulin ring associated; InterPro: IPR024332 The MOZART2 family of proteins (also known as FAM128 and Mitotic-spindle organizing protein 2) operate as part of the gamma-tubulin ring complex, gamma-TuRC, one of the complexes necessary for chromosome segregation. This complex is located at centrosomes and mediates the formation of bipolar spindles in mitosis; it consists of six subunits. However, unlike the other four known subunits, the MOZART proteins, both 1 and 2, do not carry the conserved 'Spc97-Spc98' GCP domain, so the TUBGCP nomenclature cannot be used for it. The exact function of MOZART2 is not clear [].
Probab=97.04 E-value=0.0032 Score=46.42 Aligned_cols=58 Identities=16% Similarity=0.354 Sum_probs=48.7
Q ss_pred HHHHHHHHhcCCCCHHHHHHHHHHHhCCCCHHHHHHHHHHHHhCCCCCCCCCCCCCCC
Q 040572 84 LAFHMSNILDTGLDRHTLSVLIALCDLGVNPEALAAVVKELQREPSPSPPMSTAPSSI 141 (142)
Q Consensus 84 iL~EIS~LLNTGLDReTLsICI~LcE~GVNPEALA~VIKELRrE~~a~~~~~~~p~~~ 141 (142)
-|||+.++=..++|.+-+.|++.|+..+|.|+|+..+.|.|---.......+..|.++
T Consensus 29 EL~ELa~~AGv~~dp~VFriildLL~~nVsP~AI~qmLK~m~s~~~~~~~~~~~~~~~ 86 (88)
T PF12926_consen 29 ELYELAQLAGVPMDPEVFRIILDLLRLNVSPDAIFQMLKSMCSGSRLASTAPGDPASA 86 (88)
T ss_pred HHHHHHHHhCCCcChHHHHHHHHHHHcCCCHHHHHHHHHHHHcccccCccCCCCcccc
Confidence 6899999999999999999999999999999999999999976666544434444443
No 3
>cd04774 HTH_YfmP Helix-Turn-Helix DNA binding domain of the YfmP transcription regulator. Helix-turn-helix (HTH) transcription regulator, YfmP, and related proteins; N-terminal domain. YfmP regulates the multidrug efflux protein, YfmO, and indirectly regulates the expression of the Bacillus subtilis copZA operon encoding a metallochaperone, CopZ, and a CPx-type ATPase efflux protein, CopA. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=82.71 E-value=5.4 Score=28.10 Aligned_cols=48 Identities=13% Similarity=0.131 Sum_probs=39.4
Q ss_pred HHHHHHHHHHHHhc-CCCCHHHHHHHHHHHhCCCCHHH--HHHHHHHHHhC
Q 040572 80 ESLDLAFHMSNILD-TGLDRHTLSVLIALCDLGVNPEA--LAAVVKELQRE 127 (142)
Q Consensus 80 EtLDiL~EIS~LLN-TGLDReTLsICI~LcE~GVNPEA--LA~VIKELRrE 127 (142)
+.+..|..|-.|.+ .|++-+.+.-++++++.|++.+. ...++.+++..
T Consensus 41 ~dv~~l~~I~~L~~~~G~~l~ei~~~l~~~~~~~~~~~~~~~~~l~~~~~~ 91 (96)
T cd04774 41 EDLKRLERILRLREVLGFSLQEVTHFLERPLEPVDGGHRYSAESLREIHDA 91 (96)
T ss_pred HHHHHHHHHHHHHHHcCCCHHHHHHHHhccccccchhHHHHHHHHHHHHHH
Confidence 66788999999999 99999999999999999986665 55666666543
No 4
>PF05105 Phage_holin_4: Holin family ; InterPro: IPR006480 This group of sequences describe one of the many mutually dissimilar families of holins, phage proteins that act together with lytic enzymes in bacterial lysis. This family includes, besides phage holins, the protein TcdE/UtxA involved in toxin secretion in Clostridium difficile and related species []. This entry is represented by the Bacteriophage phi-29, Gp14 (holin). The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=79.78 E-value=3.4 Score=29.69 Aligned_cols=30 Identities=30% Similarity=0.547 Sum_probs=27.4
Q ss_pred HHHHHHHHHHHhCCCC-HHHHHHHHHHHHhC
Q 040572 98 RHTLSVLIALCDLGVN-PEALAAVVKELQRE 127 (142)
Q Consensus 98 ReTLsICI~LcE~GVN-PEALA~VIKELRrE 127 (142)
.|.+||+=+|.+.|++ |+.|.++++.|+++
T Consensus 87 ~E~~SI~EN~~~~G~~iP~~l~~~l~~l~~k 117 (118)
T PF05105_consen 87 NELISILENLAEMGVPIPKWLKKFLKQLKDK 117 (118)
T ss_pred HHHHHHHHHHHHhCCCchHHHHHHHHHHhcC
Confidence 5788999999999998 99999999999876
No 5
>PF12169 DNA_pol3_gamma3: DNA polymerase III subunits gamma and tau domain III; InterPro: IPR022754 This domain is found in bacteria and eukaryotes, and is approximately 110 amino acids in length. It is found in association with PF00004 from PFAM. This domain is also present in the tau subunit before it undergoes cleavage. Domains I-III are shared between the tau and the gamma subunits, while most of the DnaB-binding Domain IV and all of the alpha-interacting Domain V are unique to tau. ; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 1NJF_B 3GLG_G 1XXH_I 1NJG_A 3GLF_B 3GLI_G.
Probab=75.18 E-value=11 Score=26.81 Aligned_cols=44 Identities=18% Similarity=0.363 Sum_probs=31.3
Q ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHHhCCCCHHHH-HHHHHHHHh
Q 040572 83 DLAFHMSNILDTGLDRHTLSVLIALCDLGVNPEAL-AAVVKELQR 126 (142)
Q Consensus 83 DiL~EIS~LLNTGLDReTLsICI~LcE~GVNPEAL-A~VIKELRr 126 (142)
+.++++.+.+-.|=-.+.|.++=++++.|++|..+ ...+..+|.
T Consensus 16 ~~i~~l~~ai~~~d~~~~l~~~~~l~~~G~d~~~~l~~L~~~~R~ 60 (143)
T PF12169_consen 16 EQIFELLDAILEGDAAEALELLNELLEQGKDPKQFLDDLIEYLRD 60 (143)
T ss_dssp HHHHHHHHHHHTT-HHHHHHHHHHHHHCT--HHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHcCCHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 45677777777777789999999999999999984 445555553
No 6
>cd00127 DSPc Dual specificity phosphatases (DSP); Ser/Thr and Tyr protein phosphatases. Structurally similar to tyrosine-specific phosphatases but with a shallower active site cleft and a distinctive active site signature motif, HCxxGxxR. Characterized as VHR- or Cdc25-like.
Probab=73.91 E-value=15 Score=25.13 Aligned_cols=51 Identities=16% Similarity=0.230 Sum_probs=32.4
Q ss_pred HHHHHHHHHHHHHHH-----HhcC--CCCHHHHH-HHHHHHhCCCCHHHHHHHHHHHHh
Q 040572 76 RTARESLDLAFHMSN-----ILDT--GLDRHTLS-VLIALCDLGVNPEALAAVVKELQR 126 (142)
Q Consensus 76 ~aArEtLDiL~EIS~-----LLNT--GLDReTLs-ICI~LcE~GVNPEALA~VIKELRr 126 (142)
..-.++++.+...-+ ++.| |++|...- +++-+...|++++.--..|+++|-
T Consensus 65 ~~~~~~~~~i~~~~~~~~~vlVHC~~G~~Rs~~~~~~~l~~~~~~~~~~a~~~vr~~r~ 123 (139)
T cd00127 65 KYFDEAVDFIDDAREKGGKVLVHCLAGVSRSATLVIAYLMKTLGLSLREAYEFVKSRRP 123 (139)
T ss_pred HHHHHHHHHHHHHHhcCCcEEEECCCCCchhHHHHHHHHHHHcCCCHHHHHHHHHHHCC
Confidence 334445555544332 3344 99999844 556666789999887777777764
No 7
>PF13817 DDE_Tnp_IS66_C: IS66 C-terminal element
Probab=71.79 E-value=5.3 Score=25.03 Aligned_cols=19 Identities=37% Similarity=0.445 Sum_probs=16.3
Q ss_pred HhCCCCHHH-HHHHHHHHHh
Q 040572 108 CDLGVNPEA-LAAVVKELQR 126 (142)
Q Consensus 108 cE~GVNPEA-LA~VIKELRr 126 (142)
-.+||||++ |..|+.+|-.
T Consensus 7 K~ngv~P~~yL~~vL~~i~~ 26 (39)
T PF13817_consen 7 KLNGVNPYAYLTDVLERIPN 26 (39)
T ss_pred HHcCCCHHHHHHHHHHHHcc
Confidence 458999999 9999998865
No 8
>PF10819 DUF2564: Protein of unknown function (DUF2564) ; InterPro: IPR020314 This entry contains proteins with no known function.
Probab=70.47 E-value=19 Score=26.45 Aligned_cols=41 Identities=29% Similarity=0.336 Sum_probs=34.4
Q ss_pred CCCHHHHHHHHHHHHHHH-H--HHHHhcCCCCHHHHHHHHHHHh
Q 040572 69 DMDPEAARTARESLDLAF-H--MSNILDTGLDRHTLSVLIALCD 109 (142)
Q Consensus 69 ~md~d~~~aArEtLDiL~-E--IS~LLNTGLDReTLsICI~LcE 109 (142)
.||++-.+.|..+++... + .+.=+-||||..=|.-|-.|++
T Consensus 25 smdp~~Le~A~qAve~Ar~ql~~a~~~at~lD~~Fl~~~~~~L~ 68 (79)
T PF10819_consen 25 SMDPDQLEHATQAVEDAREQLSQAKSHATGLDEPFLQQSEQLLD 68 (79)
T ss_pred cCCHHHHHHHHHHHHHHHHHHHHHHHHHhCCcHHHHHHHHHHHH
Confidence 589999999999998877 4 4455679999999999998875
No 9
>cd04765 HTH_MlrA-like_sg2 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 2), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=69.52 E-value=18 Score=25.68 Aligned_cols=50 Identities=10% Similarity=0.137 Sum_probs=39.8
Q ss_pred HHHHHHHHHHHHHh-cCCCCHHHHHHHHHHHhCCCCHHH-HHHHHHHHHhCC
Q 040572 79 RESLDLAFHMSNIL-DTGLDRHTLSVLIALCDLGVNPEA-LAAVVKELQREP 128 (142)
Q Consensus 79 rEtLDiL~EIS~LL-NTGLDReTLsICI~LcE~GVNPEA-LA~VIKELRrE~ 128 (142)
.+.+..|..|-.+| +.|++-+.+.-++...+.|+.|.+ +-..+.++|+|.
T Consensus 41 ~~di~~l~~I~~llr~~G~~l~~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~ 92 (99)
T cd04765 41 PKDVELLLLIKHLLYEKGYTIEGAKQALKEDGAAAIREEEAEERLPSIRAEL 92 (99)
T ss_pred HHHHHHHHHHHHHHHHCCCCHHHHHHHHHhccccccchhhHHHHHHHHHHHH
Confidence 36677788888876 789999999999999999977655 667777777664
No 10
>PTZ00242 protein tyrosine phosphatase; Provisional
Probab=63.76 E-value=24 Score=27.02 Aligned_cols=36 Identities=28% Similarity=0.513 Sum_probs=29.2
Q ss_pred HhcC--CCCHHHHHHHHHHHhCC-CCHHHHHHHHHHHHh
Q 040572 91 ILDT--GLDRHTLSVLIALCDLG-VNPEALAAVVKELQR 126 (142)
Q Consensus 91 LLNT--GLDReTLsICI~LcE~G-VNPEALA~VIKELRr 126 (142)
++.| |+.|...-++.-|++.| ++|+.--..|+..|.
T Consensus 102 ~VHC~aGigRSgt~~a~yL~~~~~~s~~eAi~~vr~~R~ 140 (166)
T PTZ00242 102 AVHCVAGLGRAPILVALALVEYGGMEPLDAVGFVREKRK 140 (166)
T ss_pred EEECCCCCCHHHHHHHHHHHHhCCCCHHHHHHHHHHHCC
Confidence 5556 99999999999999988 888777777777664
No 11
>PRK11050 manganese transport regulator MntR; Provisional
Probab=63.51 E-value=49 Score=24.81 Aligned_cols=52 Identities=29% Similarity=0.174 Sum_probs=40.0
Q ss_pred HHHHHHHHHHHHHHHhc-CCCCHHHHHHHHHHHhCCCCHHHHHHHHHHHHhCC
Q 040572 77 TARESLDLAFHMSNILD-TGLDRHTLSVLIALCDLGVNPEALAAVVKELQREP 128 (142)
Q Consensus 77 aArEtLDiL~EIS~LLN-TGLDReTLsICI~LcE~GVNPEALA~VIKELRrE~ 128 (142)
-.....+....+.+++. -|+|.+....+-..+|..|.|+.++.+++-|++-.
T Consensus 98 l~~~~~~~~~~le~~l~~lg~~~~~~~~~a~~le~~is~~~i~r~~~~l~~~~ 150 (152)
T PRK11050 98 LAQESRERHQIVENFLLALGVSPETARRDAEGIEHHVSEETLAAFRRFLQRHG 150 (152)
T ss_pred HHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHhhhcCCHHHHHHHHHHHhccc
Confidence 33444555556666555 49999999888888999999999999999887643
No 12
>PLN03112 cytochrome P450 family protein; Provisional
Probab=62.78 E-value=16 Score=30.96 Aligned_cols=46 Identities=17% Similarity=0.292 Sum_probs=40.7
Q ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHHhCCCCHHHHHHHHHHHHhCC
Q 040572 83 DLAFHMSNILDTGLDRHTLSVLIALCDLGVNPEALAAVVKELQREP 128 (142)
Q Consensus 83 DiL~EIS~LLNTGLDReTLsICI~LcE~GVNPEALA~VIKELRrE~ 128 (142)
+++.++..++-.|.|-.+-.++..|.+.+-||+..+.+..|+..-.
T Consensus 296 ~i~~~~~~~~~AG~dTTa~~l~~~l~~L~~~P~vq~kl~~Ei~~~~ 341 (514)
T PLN03112 296 EIKALMQDMIAAATDTSAVTNEWAMAEVIKNPRVLRKIQEELDSVV 341 (514)
T ss_pred HHHHHHHHHhccccccHHHHHHHHHHHHHhChHHHHHHHHHHHHhc
Confidence 5677888889999999999999999999999999999999987643
No 13
>PTZ00393 protein tyrosine phosphatase; Provisional
Probab=61.75 E-value=15 Score=31.05 Aligned_cols=38 Identities=18% Similarity=0.424 Sum_probs=32.6
Q ss_pred HhcC--CCCHHHHHHHHHHHhCCCCHHHHHHHHHHHHhCC
Q 040572 91 ILDT--GLDRHTLSVLIALCDLGVNPEALAAVVKELQREP 128 (142)
Q Consensus 91 LLNT--GLDReTLsICI~LcE~GVNPEALA~VIKELRrE~ 128 (142)
++.| |+.|.-+-++..|++.|+.|+.--..|++.|.-+
T Consensus 174 aVHC~AGlGRTGtl~AayLI~~GmspeeAI~~VR~~RPgA 213 (241)
T PTZ00393 174 AVHCVAGLGRAPVLASIVLIEFGMDPIDAIVFIRDRRKGA 213 (241)
T ss_pred EEECCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHCCCC
Confidence 4555 9999999999999999999999888888888643
No 14
>PF00067 p450: Cytochrome P450 p450 superfamily signature b-class p450 signature mitochondrial p450 signature E-class p450 group I signature E-class p450 group II signature E-class p450 group IV signature; InterPro: IPR001128 Cytochrome P450 enzymes are a superfamily of haem-containing mono-oxygenases that are found in all kingdoms of life, and which show extraordinary diversity in their reaction chemistry. In mammals, these proteins are found primarily in microsomes of hepatocytes and other cell types, where they oxidise steroids, fatty acids and xenobiotics, and are important for the detoxification and clearance of various compounds, as well as for hormone synthesis and breakdown, cholesterol synthesis and vitamin D metabolism. In plants, these proteins are important for the biosynthesis of several compounds such as hormones, defensive compounds and fatty acids. In bacteria, they are important for several metabolic processes, such as the biosynthesis of antibiotic erythromycin in Saccharopolyspora erythraea (Streptomyces erythraeus). Cytochrome P450 enzymes use haem to oxidise their substrates, using protons derived from NADH or NADPH to split the oxygen so a single atom can be added to a substrate. They also require electrons, which they receive from a variety of redox partners. In certain cases, cytochrome P450 can be fused to its redox partner to produce a bi-functional protein, such as with P450BM-3 from Bacillus megaterium [], which has haem and flavin domains. Organisms produce many different cytochrome P450 enzymes (at least 58 in humans), which together with alternative splicing can provide a wide array of enzymes with different substrate and tissue specificities. Individual cytochrome P450 proteins follow the nomenclature: CYP, followed by a number (family), then a letter (subfamily), and another number (protein); e.g. CYP3A4 is the fourth protein in family 3, subfamily A. In general, family members should share >40% identity, while subfamily members should share >55% identity. Cytochrome P450 proteins can also be grouped by two different schemes. One scheme was based on a taxonomic split: class I (prokaryotic/mitochondrial) and class II (eukaryotic microsomes). The other scheme was based on the number of components in the system: class B (3-components) and class E (2-components). These classes merge to a certain degree. Most prokaryotes and mitochondria (and fungal CYP55) have 3-component systems (class I/class B) - a FAD-containing flavoprotein (NAD(P)H-dependent reductase), an iron-sulphur protein and P450. Most eukaryotic microsomes have 2-component systems (class II/class E) - NADPH:P450 reductase (FAD and FMN-containing flavoprotein) and P450. There are exceptions to this scheme, such as 1-component systems that resemble class E enzymes [, , ]. The class E enzymes can be further subdivided into five sequence clusters, groups I-V, each of which may contain more than one cytochrome P450 family (eg, CYP1 and CYP2 are both found in group I). The divergence of the cytochrome P450 superfamily into B- and E-classes, and further divergence into stable clusters within the E-class, appears to be very ancient, occurring before the appearance of eukaryotes. More information about these proteins can be found at Protein of the Month: Cytochrome P450 [].; GO: 0005506 iron ion binding, 0009055 electron carrier activity, 0016705 oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 0020037 heme binding, 0055114 oxidation-reduction process; PDB: 2RFC_B 2RFB_A 3EJB_H 3EJE_H 3EJD_H 1N6B_A 1NR6_A 1DT6_A 3EL3_A 3DBG_B ....
Probab=59.95 E-value=6.7 Score=29.98 Aligned_cols=47 Identities=21% Similarity=0.290 Sum_probs=38.6
Q ss_pred HHHHHHHHHHhcCCCCHHHHHHHHHHHhCCCCHHHHHHHHHHHHhCC
Q 040572 82 LDLAFHMSNILDTGLDRHTLSVLIALCDLGVNPEALAAVVKELQREP 128 (142)
Q Consensus 82 LDiL~EIS~LLNTGLDReTLsICI~LcE~GVNPEALA~VIKELRrE~ 128 (142)
-++..++..++=.|.|--+-.++..|.+.+-||+.+..+.+||..-.
T Consensus 261 ~~i~~~~~~~~~ag~dtt~~~l~~~l~~L~~~P~~~~kl~~Ei~~~~ 307 (463)
T PF00067_consen 261 EEIAAELLTLLFAGHDTTASTLSWTLYELAKNPEVQEKLREEIDSVL 307 (463)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSHHHHHHHHHHHHHHT
T ss_pred ccccccccccccccccccccccccccccccccccccccccccccccc
Confidence 35566677777778888888889999999999999999999988654
No 15
>PF08809 DUF1799: Phage related hypothetical protein (DUF1799); InterPro: IPR014915 This entry is represented by the Bacteriophage TLS, TfmB. The characteristics of the protein distribution suggest prophage matches.
Probab=59.14 E-value=18 Score=25.76 Aligned_cols=45 Identities=24% Similarity=0.428 Sum_probs=34.8
Q ss_pred HHHHHHHHHHHHh------cCCCCHHHHHHHHHHHhCCCCHHHHHHHHHHHHh
Q 040572 80 ESLDLAFHMSNIL------DTGLDRHTLSVLIALCDLGVNPEALAAVVKELQR 126 (142)
Q Consensus 80 EtLDiL~EIS~LL------NTGLDReTLsICI~LcE~GVNPEALA~VIKELRr 126 (142)
+++.++..|+.=. =+|||...|...+.++ ||.++...++...||-
T Consensus 24 ~A~~~f~~~~TQWR~g~~g~~GLDY~al~~~~~~~--gi~~~~~~~~~~~lrv 74 (83)
T PF08809_consen 24 PAVELFLAMQTQWRVGMGGPTGLDYGALPAVMDLM--GIDDEDRPELFDDLRV 74 (83)
T ss_pred HHHHHHHHccccceEcCCcCccccHHHHHHHHHHc--CCChhhHHHHHHHHHH
Confidence 5566666666533 4799999999999998 8988888777777763
No 16
>PLN02971 tryptophan N-hydroxylase
Probab=58.40 E-value=20 Score=31.12 Aligned_cols=48 Identities=17% Similarity=0.233 Sum_probs=41.2
Q ss_pred HHHHHHHHHHhcCCCCHHHHHHHHHHHhCCCCHHHHHHHHHHHHhCCC
Q 040572 82 LDLAFHMSNILDTGLDRHTLSVLIALCDLGVNPEALAAVVKELQREPS 129 (142)
Q Consensus 82 LDiL~EIS~LLNTGLDReTLsICI~LcE~GVNPEALA~VIKELRrE~~ 129 (142)
-++...+..++-.|.|-.+-.++..|....-|||....+-+||.+-..
T Consensus 326 ~~i~~~~~~l~~AG~dTTa~tl~~~l~~La~~Pevq~kl~~EI~~v~g 373 (543)
T PLN02971 326 DEIKPTIKELVMAAPDNPSNAVEWAMAEMINKPEILHKAMEEIDRVVG 373 (543)
T ss_pred HHHHHhHHHHheeccchHHHHHHHHHHHHHhCHHHHHHHHHHHHHHhC
Confidence 357778889999999999889999999999999999999999976543
No 17
>COG2445 Uncharacterized conserved protein [Function unknown]
Probab=56.43 E-value=42 Score=25.86 Aligned_cols=49 Identities=27% Similarity=0.349 Sum_probs=31.4
Q ss_pred HHHHHHHHHHHHHHHhcC--CC-CHHH-HHHHHHHHhCCCCHHHHHHHHHHHH
Q 040572 77 TARESLDLAFHMSNILDT--GL-DRHT-LSVLIALCDLGVNPEALAAVVKELQ 125 (142)
Q Consensus 77 aArEtLDiL~EIS~LLNT--GL-DReT-LsICI~LcE~GVNPEALA~VIKELR 125 (142)
+++-+++.+.+|++.+.. |+ +.++ ..+.-.|.+.||-|+..++.++.+-
T Consensus 40 ~lq~~ies~~Di~~~li~~~~~~~p~~y~d~~~~L~~~gvi~~e~~e~L~~~~ 92 (138)
T COG2445 40 ILQVAIESLIDIGNMLISKFGLRDPGTYDDCIDILVEEGVIPEEEAEELKKMV 92 (138)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHcCCCCHHHHHHHHHHH
Confidence 444555556666655544 44 4444 4455567889999999888887653
No 18
>KOG2836 consensus Protein tyrosine phosphatase IVA1 [Signal transduction mechanisms]
Probab=55.91 E-value=16 Score=30.02 Aligned_cols=36 Identities=25% Similarity=0.425 Sum_probs=32.1
Q ss_pred CCCCHHHHHHHHHHHhCCCCHHHHHHHHHHHHhCCC
Q 040572 94 TGLDRHTLSVLIALCDLGVNPEALAAVVKELQREPS 129 (142)
Q Consensus 94 TGLDReTLsICI~LcE~GVNPEALA~VIKELRrE~~ 129 (142)
.||-|.-.-+.++|||.|+.=|+-...|+.=|+-+-
T Consensus 106 aglgrapvlvalalie~gmkyedave~ir~krrga~ 141 (173)
T KOG2836|consen 106 AGLGRAPVLVALALIEAGMKYEDAVEMIRQKRRGAI 141 (173)
T ss_pred cccCcchHHHHHHHHHccccHHHHHHHHHHHhhccc
Confidence 399999999999999999999999999998887553
No 19
>PF15297 CKAP2_C: Cytoskeleton-associated protein 2 C-terminus
Probab=54.91 E-value=19 Score=32.33 Aligned_cols=30 Identities=27% Similarity=0.352 Sum_probs=25.7
Q ss_pred HHHHHHHHHHhCCCCHHHHHHHHHHHHhCC
Q 040572 99 HTLSVLIALCDLGVNPEALAAVVKELQREP 128 (142)
Q Consensus 99 eTLsICI~LcE~GVNPEALA~VIKELRrE~ 128 (142)
.||+=|+.||+-|..++.+.+++.+|.+-.
T Consensus 104 ~tlsECl~Li~eGcp~eei~~~L~~li~~I 133 (353)
T PF15297_consen 104 KTLSECLNLIEEGCPKEEILATLSDLIKNI 133 (353)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHHHHHhcC
Confidence 589999999999999998888888776654
No 20
>TIGR00756 PPR pentatricopeptide repeat domain (PPR motif). This family has a similar consensus to the TPR domain (tetratricopeptide), pfam pfam00515, a 33-residue repeat. It is predicted to form a pair of antiparallel helices similar to that of TPR.
Probab=54.38 E-value=21 Score=18.39 Aligned_cols=28 Identities=14% Similarity=0.445 Sum_probs=18.9
Q ss_pred HHHHhcCCCCHHHHHHHHHHHhCCCCHH
Q 040572 88 MSNILDTGLDRHTLSVLIALCDLGVNPE 115 (142)
Q Consensus 88 IS~LLNTGLDReTLsICI~LcE~GVNPE 115 (142)
|+.+...|.-.+++.++-.|.+.|+.|.
T Consensus 7 i~~~~~~~~~~~a~~~~~~M~~~g~~p~ 34 (35)
T TIGR00756 7 IDGLCKAGRVEEALELFKEMLERGIEPD 34 (35)
T ss_pred HHHHHHCCCHHHHHHHHHHHHHcCCCCC
Confidence 4455566666777777777777777663
No 21
>COG0298 HypC Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=53.78 E-value=15 Score=27.16 Aligned_cols=21 Identities=19% Similarity=0.249 Sum_probs=18.1
Q ss_pred HHHHHHHHHHHHHHHHhcCCC
Q 040572 76 RTARESLDLAFHMSNILDTGL 96 (142)
Q Consensus 76 ~aArEtLDiL~EIS~LLNTGL 96 (142)
++|+|+++++.+|++.++...
T Consensus 59 eeAketle~l~e~~~~~~~~~ 79 (82)
T COG0298 59 EEAKETLEALQEMFDAEGEDI 79 (82)
T ss_pred HHHHHHHHHHHHHHHhhcccc
Confidence 578999999999999997653
No 22
>PTZ00404 cytochrome P450; Provisional
Probab=53.06 E-value=31 Score=28.88 Aligned_cols=48 Identities=17% Similarity=0.189 Sum_probs=42.4
Q ss_pred HHHHHHHHHHhcCCCCHHHHHHHHHHHhCCCCHHHHHHHHHHHHhCCC
Q 040572 82 LDLAFHMSNILDTGLDRHTLSVLIALCDLGVNPEALAAVVKELQREPS 129 (142)
Q Consensus 82 LDiL~EIS~LLNTGLDReTLsICI~LcE~GVNPEALA~VIKELRrE~~ 129 (142)
.+++.++..++-.|.|-.+..++..|....-||+....+..||..-..
T Consensus 282 ~~i~~~~~~~~~AG~dTta~~l~~~l~~L~~~P~vq~kl~~Ei~~v~~ 329 (482)
T PTZ00404 282 LSILATILDFFLAGVDTSATSLEWMVLMLCNYPEIQEKAYNEIKSTVN 329 (482)
T ss_pred HHHHHHHHHHHHhccchHHHHHHHHHHHHHcCcHHHHHHHHHHHHHhc
Confidence 347788899999999999999999999999999999999999887544
No 23
>PF02627 CMD: Carboxymuconolactone decarboxylase family; InterPro: IPR003779 The catechol and protocatechuate branches of the 3-oxoadipate pathway, which are important for the bacterial degradation of aromatic compounds, converge at the common intermediate 3-oxoadipate enol-lactone. Carboxymuconolactone decarboxylase (CMD) is involved in protocatechuate catabolism. In some bacteria a gene fusion event leads to expression of CMD with a hydrolase involved in the same pathway [].; GO: 0051920 peroxiredoxin activity, 0055114 oxidation-reduction process; PDB: 2GMY_E 2CWQ_C 2QEU_B 1P8C_D 1VKE_C 2OUW_A 2AF7_G 3D7I_A 1ME5_B 1KNC_A ....
Probab=52.20 E-value=56 Score=20.39 Aligned_cols=18 Identities=28% Similarity=0.304 Sum_probs=13.9
Q ss_pred HHHhCCCCHHHHHHHHHH
Q 040572 106 ALCDLGVNPEALAAVVKE 123 (142)
Q Consensus 106 ~LcE~GVNPEALA~VIKE 123 (142)
.+.+.|+.++.+.+++.-
T Consensus 49 ~a~~~G~t~eei~~~~~~ 66 (85)
T PF02627_consen 49 AARKAGVTEEEIDEAVRW 66 (85)
T ss_dssp HHHHTTTHHHHHHHHHHH
T ss_pred HHHHcCCCHHHHHHHHHH
Confidence 456889998888887754
No 24
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=51.21 E-value=19 Score=22.46 Aligned_cols=19 Identities=21% Similarity=0.424 Sum_probs=9.7
Q ss_pred HHHHHhCCCCHHHHHHHHH
Q 040572 104 LIALCDLGVNPEALAAVVK 122 (142)
Q Consensus 104 CI~LcE~GVNPEALA~VIK 122 (142)
...|.+.|+++++++.++.
T Consensus 50 i~~lr~~g~~~~~i~~~l~ 68 (70)
T smart00422 50 IKRLKELGFSLEEIKELLE 68 (70)
T ss_pred HHHHHHcCCCHHHHHHHHh
Confidence 3344555555555555543
No 25
>TIGR02120 GspF general secretion pathway protein F. This membrane protein is a component of the terminal branch complex of the general secretion pathway (GSP), also known as the"Type II" secretion pathway. The GSP transports proteins (generally virulence-associated cell wall hydrolases) across the outer membrase of the bacterial cell. Transport across the inner membrane is often, but not exclusively handled by the Sec system. This model was constructed from the broader subfamily model, pfam00482 which includes components of pilin complexes (PilC) as well as other related genes. GspF is nearly always gene clustered with other GSP subunits. Some genes from Xylella and Xanthomonas strains score below the trusted cutoff due to excessive divergence from the family such that a sequence from Deinococcus which does not appear to be GspF scores higher.
Probab=51.00 E-value=42 Score=28.11 Aligned_cols=49 Identities=14% Similarity=0.115 Sum_probs=32.5
Q ss_pred HHHHHHHHHHHHHhcCCCCHHHHHHHHHHHhCCCCHHHHHHHHHHHHhCCCC
Q 040572 79 RESLDLAFHMSNILDTGLDRHTLSVLIALCDLGVNPEALAAVVKELQREPSP 130 (142)
Q Consensus 79 rEtLDiL~EIS~LLNTGLDReTLsICI~LcE~GVNPEALA~VIKELRrE~~a 130 (142)
++....+.+++.+|+.|++= .-+++++.....-..+..+++++++....
T Consensus 61 ~~~~~f~~~La~ll~sGi~l---~~aL~~l~~~~~~~~~~~~~~~i~~~l~~ 109 (399)
T TIGR02120 61 AELALFTRQLATLLGAGLPL---EEALAALLEQAEKPRLKSVLAAIRSRVLE 109 (399)
T ss_pred HHHHHHHHHHHHHHHcCCCH---HHHHHHHHHhCCChHHHHHHHHHHHHHHC
Confidence 46677999999999999983 33444444444444667777777655444
No 26
>smart00856 PMEI Plant invertase/pectin methylesterase inhibitor. This domain inhibits pectin methylesterases (PMEs) and invertases through formation of a non-covalent 1:1 complex PUBMED:8521860. It has been implicated in the regulation of fruit development, carbohydrate metabolism and cell wall extension. It may also be involved in inhibiting microbial pathogen PMEs. It has been observed that it is often expressed as a large inactive preprotein PUBMED:8521860. It is also found at the N-termini of PMEs predicted from DNA sequences, suggesting that both PMEs and their inhibitors are expressed as a single polyprotein and subsequently processed. It has two disulphide bridges and is mainly alpha-helical PUBMED:10880981.
Probab=50.54 E-value=53 Score=22.96 Aligned_cols=45 Identities=22% Similarity=0.302 Sum_probs=31.9
Q ss_pred HHHHHHHHHHHhcCCCC---HHHHHHHHHHHhCCCCHHHHHHHHHHHHhC
Q 040572 81 SLDLAFHMSNILDTGLD---RHTLSVLIALCDLGVNPEALAAVVKELQRE 127 (142)
Q Consensus 81 tLDiL~EIS~LLNTGLD---ReTLsICI~LcE~GVNPEALA~VIKELRrE 127 (142)
+-+.+..|+.|++.+.| +..|..|++|.+..++ .|...+..|...
T Consensus 50 a~~~~~~~~~l~~~~~~~~~~~al~~C~~~y~~a~~--~L~~a~~~l~~~ 97 (148)
T smart00856 50 ATKTLSFISSLLKKTKDPRLKAALKDCLELYDDAVD--SLEKALEELKSG 97 (148)
T ss_pred HHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHhc
Confidence 44455567777776665 5689999999998876 566666766543
No 27
>PRK06585 holA DNA polymerase III subunit delta; Reviewed
Probab=50.50 E-value=49 Score=26.85 Aligned_cols=43 Identities=19% Similarity=0.054 Sum_probs=33.9
Q ss_pred HHHHHHHHhcCCCCHHHHHHHHHHHhCCCCHHH-HHHHHHHHHh
Q 040572 84 LAFHMSNILDTGLDRHTLSVLIALCDLGVNPEA-LAAVVKELQR 126 (142)
Q Consensus 84 iL~EIS~LLNTGLDReTLsICI~LcE~GVNPEA-LA~VIKELRr 126 (142)
.+|++.+-+-.|=...++.++-.|++.|.+|-. |+.+++++|.
T Consensus 214 ~if~l~dai~~~~~~~a~~~l~~ll~~g~~p~~il~~L~~~~r~ 257 (343)
T PRK06585 214 SLDDAADAALAGDLAAFERALDRALAEGTAPVLILRAALRHFQR 257 (343)
T ss_pred cHHHHHHHHHCCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHH
Confidence 466777777777777899999999999999987 5666677664
No 28
>PRK10416 signal recognition particle-docking protein FtsY; Provisional
Probab=50.45 E-value=54 Score=27.73 Aligned_cols=44 Identities=16% Similarity=0.260 Sum_probs=34.6
Q ss_pred HHHHHHh-cCCCCHHHH-HHHHHHHhCCCCHHHHHHHHHHHHhCCC
Q 040572 86 FHMSNIL-DTGLDRHTL-SVLIALCDLGVNPEALAAVVKELQREPS 129 (142)
Q Consensus 86 ~EIS~LL-NTGLDReTL-sICI~LcE~GVNPEALA~VIKELRrE~~ 129 (142)
..|.+|. +..+|.+.+ .+...|+++||+++.-..++..|+++..
T Consensus 33 ~~~~~l~~~~~~~~~~~~~l~~~L~~~dv~~~~a~~i~~~~~~~~~ 78 (318)
T PRK10416 33 EGINGLFAKKKIDEDLLEELEELLIEADVGVETTEEIIEELRERVK 78 (318)
T ss_pred HHHHHHhCCCCCCHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHh
Confidence 3555555 457898888 5678899999999999999999987643
No 29
>PRK10161 transcriptional regulator PhoB; Provisional
Probab=49.98 E-value=18 Score=25.99 Aligned_cols=49 Identities=12% Similarity=0.156 Sum_probs=40.5
Q ss_pred HHHHHHHHHHhcCCCCHHHHHHHHHHHhCCCCHHHHHHHHHHHHhCCCC
Q 040572 82 LDLAFHMSNILDTGLDRHTLSVLIALCDLGVNPEALAAVVKELQREPSP 130 (142)
Q Consensus 82 LDiL~EIS~LLNTGLDReTLsICI~LcE~GVNPEALA~VIKELRrE~~a 130 (142)
+++|.-+..--|-+++++.|.-.+-=-+.++++.++...|+.||+....
T Consensus 160 ~~ll~~l~~~~~~~~s~~~l~~~~~~~~~~~~~~tv~~~i~rlr~Kl~~ 208 (229)
T PRK10161 160 FKLLHFFMTHPERVYSREQLLNHVWGTNVYVEDRTVDVHIRRLRKALEP 208 (229)
T ss_pred HHHHHHHHhCCCceEcHHHHHHHhcCCCCCCCCCCHHHHHHHHHHhhcc
Confidence 7888888888888999999876554446778899999999999998864
No 30
>PF13032 DUF3893: Domain of unknown function (DUF3893)
Probab=48.82 E-value=3.6 Score=31.44 Aligned_cols=33 Identities=30% Similarity=0.420 Sum_probs=28.3
Q ss_pred CCCHHHHHHHHHHHhCCCCHHHHHHHHHHHHhC
Q 040572 95 GLDRHTLSVLIALCDLGVNPEALAAVVKELQRE 127 (142)
Q Consensus 95 GLDReTLsICI~LcE~GVNPEALA~VIKELRrE 127 (142)
..-..-|.|+|..|..+.+|++||..|..||+-
T Consensus 64 ~~~~~ilEI~V~~~~~~d~~~~lA~~vh~LR~~ 96 (138)
T PF13032_consen 64 WQNPQILEITVLGCQPEDDPEALAKLVHYLRRS 96 (138)
T ss_pred ccCCCceEEEEeccCCCCCHHHHHHHHHHHHhC
Confidence 335566889999999999999999999999965
No 31
>PLN02169 fatty acid (omega-1)-hydroxylase/midchain alkane hydroxylase
Probab=48.70 E-value=41 Score=28.96 Aligned_cols=45 Identities=13% Similarity=0.175 Sum_probs=39.9
Q ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHHhCCCCHHHHHHHHHHHHhC
Q 040572 83 DLAFHMSNILDTGLDRHTLSVLIALCDLGVNPEALAAVVKELQRE 127 (142)
Q Consensus 83 DiL~EIS~LLNTGLDReTLsICI~LcE~GVNPEALA~VIKELRrE 127 (142)
++..++..++-.|-|-.+-.++..|.....||+....+..||...
T Consensus 301 ~i~~~~~~~l~AG~dTTa~tl~w~l~~La~~Pevq~kl~~Ei~~v 345 (500)
T PLN02169 301 FIRDVIFSLVLAGRDTTSSALTWFFWLLSKHPQVMAKIRHEINTK 345 (500)
T ss_pred HHHHHHHHHHHhchhHHHHHHHHHHHHHHCCHHHHHHHHHHHHhh
Confidence 467788899999999999999999999999999999999888653
No 32
>TIGR02425 decarb_PcaC 4-carboxymuconolactone decarboxylase. Members of this family are 4-carboxymuconolactone decarboxylase, which catalyzes the third step in the catabolism of protocatechuate (and therefore the fourth step in the catabolism of para-hydroxybenzoate, of 3-hydroxybenzoate, of vanillate, etc.). Most members of this family are encoded within protocatechuate catabolism operons. This protein is sometimes found as a fusion protein with other enzymes of the pathway, as in Rhodococcus opacus, Streptomyces avermitilis, and Caulobacter crescentus.
Probab=48.67 E-value=63 Score=23.98 Aligned_cols=19 Identities=21% Similarity=0.398 Sum_probs=14.5
Q ss_pred HHHhCCCCHHHHHHHHHHH
Q 040572 106 ALCDLGVNPEALAAVVKEL 124 (142)
Q Consensus 106 ~LcE~GVNPEALA~VIKEL 124 (142)
.-+.+|++|+.|.++|..+
T Consensus 81 ~Al~~G~T~~ei~Evl~q~ 99 (123)
T TIGR02425 81 ATANTGVTEDDIKEVLLHV 99 (123)
T ss_pred HHHHcCCCHHHHHHHHHHH
Confidence 4467888888888887764
No 33
>smart00845 GatB_Yqey GatB domain. This domain is found in GatB and proteins related to bacterial Yqey. It is about 140 amino acid residues long. This domain is found at the C terminus of GatB which transamidates Glu-tRNA to Gln-tRNA. The function of this domain is uncertain. It does however suggest that Yqey and its relatives have a role in tRNA metabolism.
Probab=48.16 E-value=1e+02 Score=22.90 Aligned_cols=44 Identities=20% Similarity=0.278 Sum_probs=32.3
Q ss_pred HHHHHHHHhc--------CCCCHHHHHHHHHHHhCC-CCHHHHHHHHHHHHhC
Q 040572 84 LAFHMSNILD--------TGLDRHTLSVLIALCDLG-VNPEALAAVVKELQRE 127 (142)
Q Consensus 84 iL~EIS~LLN--------TGLDReTLsICI~LcE~G-VNPEALA~VIKELRrE 127 (142)
+++++..+|| +.++.+.|.-+|.|++.| ++-++--.|+.++-.+
T Consensus 19 i~~el~~~l~~~~~~~~~~~i~~~~l~~li~lv~~g~It~~~ak~vl~~~~~~ 71 (147)
T smart00845 19 LLGELLGELNKEGLEIEESPITPEHLAELLKLIEDGTISGKIAKEVLEELLES 71 (147)
T ss_pred HHHHHHHHHHhCCCCHhhCCCCHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHc
Confidence 4566656664 457788999999999999 6777767777776554
No 34
>PLN02936 epsilon-ring hydroxylase
Probab=47.27 E-value=35 Score=29.07 Aligned_cols=45 Identities=29% Similarity=0.310 Sum_probs=38.7
Q ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHHhCCCCHHHHHHHHHHHHhC
Q 040572 83 DLAFHMSNILDTGLDRHTLSVLIALCDLGVNPEALAAVVKELQRE 127 (142)
Q Consensus 83 DiL~EIS~LLNTGLDReTLsICI~LcE~GVNPEALA~VIKELRrE 127 (142)
++..++..++-.|.|-.+..++..|....-||+++..+..||..-
T Consensus 278 ~i~~~~~~~~~aG~dTta~~l~~~l~~L~~~p~~~~kl~~Ei~~~ 322 (489)
T PLN02936 278 QLRDDLLSMLVAGHETTGSVLTWTLYLLSKNPEALRKAQEELDRV 322 (489)
T ss_pred HHHHHHHHHHHHhHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHH
Confidence 456677888889999999999988888888999999999998754
No 35
>PF02885 Glycos_trans_3N: Glycosyl transferase family, helical bundle domain Prosite entry for Thymidine and pyrimidine-nucleoside phosphorylases; InterPro: IPR017459 The biosynthesis of disaccharides, oligosaccharides and polysaccharides involves the action of hundreds of different glycosyltransferases. These enzymes catalyse the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. A classification of glycosyltransferases using nucleotide diphospho-sugar, nucleotide monophospho-sugar and sugar phosphates (2.4.1.- from EC) and related proteins into distinct sequence based families has been described []. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. The same three-dimensional fold is expected to occur within each of the families. Because 3-D structures are better conserved than sequences, several of the families defined on the basis of sequence similarities may have similar 3-D structures and therefore form 'clans'. The glycosyl transferase family includes anthranilate phosphoribosyltransferase (TrpD, 2.4.2.18 from EC) and thymidine phosphorylase (2.4.2.2 from EC). All these proteins can transfer a phosphorylated ribose substrate. Thymidine phosphorylase (2.4.2.2 from EC) catalyses the reversible phosphorolysis of thymidine, deoxyuridine and their analogues to their respective bases and 2-deoxyribose 1-phosphate. This enzyme regulates the availability of thymidine and is therefore essential to nucleic acid metabolism. This N-terminal domain is found in various family 3 glycosyl transferases, including anthranilate phosphoribosyltransferase (TrpD, 2.4.2.18 from EC) and thymidine phosphorylase (2.4.2.2 from EC). All these proteins can transfer a phosphorylated ribose substrate. Thymidine phosphorylase catalyses the reversible phosphorolysis of thymidine, deoxyuridine and their analogues to their respective bases and 2-deoxyribose 1-phosphate. This enzyme regulates the availability of thymidine and is therefore essential to nucleic acid metabolism.; PDB: 2DSJ_B 2ELC_B 2BPQ_A 1ZVW_B 3QR9_B 1V8G_B 2WK5_C 2J0F_C 2WK6_B 1UOU_A ....
Probab=45.58 E-value=31 Score=22.57 Aligned_cols=39 Identities=28% Similarity=0.447 Sum_probs=25.9
Q ss_pred HHhcCCCCHHHH-HHHHHHHhCCCCHHHHHHHHHHHHhCC
Q 040572 90 NILDTGLDRHTL-SVLIALCDLGVNPEALAAVVKELQREP 128 (142)
Q Consensus 90 ~LLNTGLDReTL-sICI~LcE~GVNPEALA~VIKELRrE~ 128 (142)
.|++=.++...+ ++++.|.-.|.+++.|+..++-+|.-+
T Consensus 26 ~i~~g~~s~~qiaAfL~al~~kget~~Eiag~~~am~~~a 65 (66)
T PF02885_consen 26 AILDGEVSDAQIAAFLMALRMKGETPEEIAGFAKAMREHA 65 (66)
T ss_dssp HHHTTSS-HHHHHHHHHHHHHH---HHHHHHHHHHHHHTS
T ss_pred HHHcCCCCHHHHHHHHHHHHHhCcCHHHHHHHHHHHHHhc
Confidence 345555555444 578888889999999999999998753
No 36
>PLN00168 Cytochrome P450; Provisional
Probab=45.49 E-value=46 Score=28.48 Aligned_cols=47 Identities=17% Similarity=0.308 Sum_probs=40.1
Q ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHHhCCCCHHHHHHHHHHHHhCCC
Q 040572 83 DLAFHMSNILDTGLDRHTLSVLIALCDLGVNPEALAAVVKELQREPS 129 (142)
Q Consensus 83 DiL~EIS~LLNTGLDReTLsICI~LcE~GVNPEALA~VIKELRrE~~ 129 (142)
+++.++..++-.|.|-.+-.++..|....-||+....+..||.....
T Consensus 306 ~i~~~~~~l~~AG~dTTa~~l~~~l~~L~~~P~~q~kl~~Ei~~v~~ 352 (519)
T PLN00168 306 EIVNLCSEFLNAGTDTTSTALQWIMAELVKNPSIQSKLHDEIKAKTG 352 (519)
T ss_pred HHHHHHHHHHHhcchHHHHHHHHHHHHHHhCHHHHHHHHHHHHHHhC
Confidence 57778888888999998888888888888999999999999976543
No 37
>PRK00771 signal recognition particle protein Srp54; Provisional
Probab=44.76 E-value=57 Score=29.16 Aligned_cols=41 Identities=17% Similarity=0.279 Sum_probs=30.9
Q ss_pred HHHhcCC-CCHHHHH-----HHHHHHhCCCCHHHHHHHHHHHHhCCC
Q 040572 89 SNILDTG-LDRHTLS-----VLIALCDLGVNPEALAAVVKELQREPS 129 (142)
Q Consensus 89 S~LLNTG-LDReTLs-----ICI~LcE~GVNPEALA~VIKELRrE~~ 129 (142)
..|...+ ||.+.+. ++.+|++++||++....++.++++...
T Consensus 10 ~~l~~~~~l~e~~i~~~l~ei~~aLl~adV~~~~~~~~~~~v~~~~~ 56 (437)
T PRK00771 10 KKLAGKSRIDEKTVKEVVKDIQRALLQADVNVKLVKELSKSIKERAL 56 (437)
T ss_pred HHHhCCCCCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHh
Confidence 3444444 7776554 888999999999999999999986543
No 38
>COG5012 Predicted cobalamin binding protein [General function prediction only]
Probab=44.65 E-value=39 Score=28.71 Aligned_cols=34 Identities=12% Similarity=0.258 Sum_probs=32.3
Q ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHHhCCCCHHH
Q 040572 83 DLAFHMSNILDTGLDRHTLSVLIALCDLGVNPEA 116 (142)
Q Consensus 83 DiL~EIS~LLNTGLDReTLsICI~LcE~GVNPEA 116 (142)
++++++++.+.-|....+.....+.+|.|+.|..
T Consensus 17 ~li~~~~~av~dg~~~~~~e~~~~al~~Gidp~~ 50 (227)
T COG5012 17 ELINEYADAVVDGEEEMAVELTQKALEAGIDPYD 50 (227)
T ss_pred HHHHHHHHHHhcchHHHHHHHHHHHHHcCCCHHH
Confidence 3899999999999999999999999999999976
No 39
>PLN00110 flavonoid 3',5'-hydroxylase (F3'5'H); Provisional
Probab=44.40 E-value=42 Score=28.85 Aligned_cols=46 Identities=17% Similarity=0.286 Sum_probs=39.8
Q ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHHhCCCCHHHHHHHHHHHHhCC
Q 040572 83 DLAFHMSNILDTGLDRHTLSVLIALCDLGVNPEALAAVVKELQREP 128 (142)
Q Consensus 83 DiL~EIS~LLNTGLDReTLsICI~LcE~GVNPEALA~VIKELRrE~ 128 (142)
+++.++..++-.|.|-.+..++..|....-||+....+.+|+..-.
T Consensus 289 ~i~~~~~~~~~Ag~dTta~~l~~~l~~L~~~P~~~~kl~~Ei~~~~ 334 (504)
T PLN00110 289 NIKALLLNLFTAGTDTSSSVIEWSLAEMLKNPSILKRAHEEMDQVI 334 (504)
T ss_pred HHHHHHHhhhcccccchHHHHHHHHHHHHhCHHHHHHHHHHHHHHh
Confidence 5777888889999999999999999999999999999999987543
No 40
>PLN02183 ferulate 5-hydroxylase
Probab=44.36 E-value=50 Score=28.23 Aligned_cols=46 Identities=20% Similarity=0.265 Sum_probs=39.7
Q ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHHhCCCCHHHHHHHHHHHHhCC
Q 040572 83 DLAFHMSNILDTGLDRHTLSVLIALCDLGVNPEALAAVVKELQREP 128 (142)
Q Consensus 83 DiL~EIS~LLNTGLDReTLsICI~LcE~GVNPEALA~VIKELRrE~ 128 (142)
++..++..++-.|.|-.+-.++..|....-||+..+.+..|+..-.
T Consensus 304 ~i~~~~~~~~~AG~dTTa~tl~~~l~~La~~Pevq~kl~~Ei~~v~ 349 (516)
T PLN02183 304 NIKAIIMDVMFGGTETVASAIEWAMAELMKSPEDLKRVQQELADVV 349 (516)
T ss_pred HHHHHHHHHHHcchhhHHHHHHHHHHHHHhCHHHHHHHHHHHHHHc
Confidence 4566777788889999999999999999999999999999998654
No 41
>PLN02655 ent-kaurene oxidase
Probab=44.33 E-value=40 Score=28.37 Aligned_cols=46 Identities=15% Similarity=0.210 Sum_probs=36.5
Q ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHHhCCCCHHHHHHHHHHHHhCC
Q 040572 83 DLAFHMSNILDTGLDRHTLSVLIALCDLGVNPEALAAVVKELQREP 128 (142)
Q Consensus 83 DiL~EIS~LLNTGLDReTLsICI~LcE~GVNPEALA~VIKELRrE~ 128 (142)
+++..+..++-.|.|-.+-.+...|....-||+..+.+..||++-.
T Consensus 262 ~i~~~~~~~~~ag~dtta~~l~~~~~~l~~~p~~~~~l~~Ei~~~~ 307 (466)
T PLN02655 262 QLMMLVWEPIIEAADTTLVTTEWAMYELAKNPDKQERLYREIREVC 307 (466)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCHHHHHHHHHHHHHHh
Confidence 3566778888889988777777777777779999999999888654
No 42
>PLN02500 cytochrome P450 90B1
Probab=43.81 E-value=47 Score=28.02 Aligned_cols=44 Identities=16% Similarity=0.218 Sum_probs=36.8
Q ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHHhCCCCHHHHHHHHHHHHh
Q 040572 83 DLAFHMSNILDTGLDRHTLSVLIALCDLGVNPEALAAVVKELQR 126 (142)
Q Consensus 83 DiL~EIS~LLNTGLDReTLsICI~LcE~GVNPEALA~VIKELRr 126 (142)
+++..+..++-.|.|-.+..+...|....-||+....+..|+.+
T Consensus 279 ~i~~~~~~ll~AG~dTta~tl~~~l~~L~~~Pevq~kl~~Ei~~ 322 (490)
T PLN02500 279 QILDLILSLLFAGHETSSVAIALAIFFLQGCPKAVQELREEHLE 322 (490)
T ss_pred HHHHHHHHHHHhhhhHHHHHHHHHHHHHhhCHHHHHHHHHHHHH
Confidence 56667778888888888888888888888899999999999875
No 43
>PF01314 AFOR_C: Aldehyde ferredoxin oxidoreductase, domains 2 & 3; InterPro: IPR001203 Enzymes of the aldehyde ferredoxin oxidoreductase (AOR) family [] contain a tungsten cofactor and an 4Fe4S cluster and catalyse the interconversion of aldehydes to carboxylates []. This family includes AOR, formaldehyde ferredoxin oxidoreductase (FOR), glyceraldehyde-3-phosphate ferredoxin oxidoreductase (GAPOR), all isolated from hyperthermophilic archea []; carboxylic acid reductase found in clostridia []; and hydroxycarboxylate viologen oxidoreductase from Proteus vulgaris, the sole member of the AOR family containing molybdenum []. GAPOR may be involved in glycolysis [], but the functions of the other proteins are not yet clear. AOR has been proposed to be the primary enzyme responsible for oxidising the aldehydes that are produced by the 2-keto acid oxidoreductases []. This entry represents the C-terminal region of these enzymes, containing the alpha-helical structural domains 2 and 3 [, ].; GO: 0009055 electron carrier activity, 0016491 oxidoreductase activity, 0016625 oxidoreductase activity, acting on the aldehyde or oxo group of donors, iron-sulfur protein as acceptor, 0051536 iron-sulfur cluster binding, 0055114 oxidation-reduction process; PDB: 1B25_C 1B4N_C 1AOR_B.
Probab=43.72 E-value=56 Score=28.14 Aligned_cols=45 Identities=24% Similarity=0.556 Sum_probs=34.1
Q ss_pred HHHHHHHHHHHhcC-CCCH----HHHHHHHHHHhCCC--------------CHHHHHHHHHHHH
Q 040572 81 SLDLAFHMSNILDT-GLDR----HTLSVLIALCDLGV--------------NPEALAAVVKELQ 125 (142)
Q Consensus 81 tLDiL~EIS~LLNT-GLDR----eTLsICI~LcE~GV--------------NPEALA~VIKELR 125 (142)
.++.+..+..|.|- |||- .++..+++|-|.|+ |++++...|..|=
T Consensus 109 D~~~~~~~~~lcd~~GlDtis~G~~ia~~me~~e~G~i~~~d~~g~~l~~Gd~e~~~~ll~~IA 172 (382)
T PF01314_consen 109 DLEAVIKANDLCDDYGLDTISAGNTIAWAMELYEKGLITKEDTDGLELRWGDPEAVLELLEKIA 172 (382)
T ss_dssp -HHHHHHHHHHHHHHTB-HHHHHHHHHHHHHHHHTTSSSCHHHTS-S--TT-CHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHhCCcHHHHHHHHHHHHHHHHCCCCChhhcCCCCCCCCCHHHHHHHHHHHH
Confidence 35566777777776 8885 57888999999999 9999999988874
No 44
>PF13812 PPR_3: Pentatricopeptide repeat domain
Probab=43.61 E-value=39 Score=17.80 Aligned_cols=24 Identities=21% Similarity=0.479 Sum_probs=10.4
Q ss_pred HHHHHHhCCCCHHHHHHHHHHHHh
Q 040572 103 VLIALCDLGVNPEALAAVVKELQR 126 (142)
Q Consensus 103 ICI~LcE~GVNPEALA~VIKELRr 126 (142)
++|..|-..-+++..-.++.++++
T Consensus 6 ~ll~a~~~~g~~~~a~~~~~~M~~ 29 (34)
T PF13812_consen 6 ALLRACAKAGDPDAALQLFDEMKE 29 (34)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHH
Confidence 334444444444444444444443
No 45
>PF02861 Clp_N: Clp amino terminal domain; InterPro: IPR004176 This short domain is found in one or two copies at the amino terminus of ClpA and ClpB proteins from bacteria and eukaryotes. The function of these domains is uncertain but they may form a protein binding site []. The proteins are thought to be subunits of ATP-dependent proteases which act as chaperones to target the proteases to substrates.; GO: 0019538 protein metabolic process; PDB: 3FH2_A 3ZRJ_A 3ZRI_A 1QVR_C 3FES_C 2Y1R_F 3PXG_D 2Y1Q_A 3PXI_C 2K77_A ....
Probab=43.40 E-value=25 Score=20.83 Aligned_cols=40 Identities=20% Similarity=0.294 Sum_probs=24.2
Q ss_pred HHHHHHHHHHhcCCCCHHHHHHHHHHHhCCCCHHHHHHHHHHHH
Q 040572 82 LDLAFHMSNILDTGLDRHTLSVLIALCDLGVNPEALAAVVKELQ 125 (142)
Q Consensus 82 LDiL~EIS~LLNTGLDReTLsICI~LcE~GVNPEALA~VIKELR 125 (142)
++.-|-+..||+.+=+ .+.--|-+.|||++.|...|++++
T Consensus 13 i~~eHlL~all~~~~~----~~~~il~~~~id~~~l~~~i~~~l 52 (53)
T PF02861_consen 13 ISPEHLLLALLEDPDS----IAARILKKLGIDPEQLKAAIEKAL 52 (53)
T ss_dssp E-HHHHHHHHHHHTTS----HHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred ccHHHHHHHHHhhhhH----HHHHHHHHcCCCHHHHHHHHHHHh
Confidence 3444555555543211 122235578999999999998876
No 46
>PRK00400 hisE phosphoribosyl-ATP pyrophosphatase; Validated
Probab=43.36 E-value=72 Score=23.74 Aligned_cols=32 Identities=22% Similarity=0.523 Sum_probs=23.1
Q ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHHhCCCCHHHHHHHHH
Q 040572 83 DLAFHMSNILDTGLDRHTLSVLIALCDLGVNPEALAAVVK 122 (142)
Q Consensus 83 DiL~EIS~LLNTGLDReTLsICI~LcE~GVNPEALA~VIK 122 (142)
++++|+++|| .-++|.|...||+|+.+..++.
T Consensus 58 ~~i~E~ADLl--------YHllVlL~~~gv~~~dV~~eL~ 89 (105)
T PRK00400 58 ELVYEIADLL--------YHLLVLLAARGISLEDVLAELE 89 (105)
T ss_pred HHHHHHHHHH--------HHHHHHHHHcCCCHHHHHHHHH
Confidence 4677777776 4578889999999876544443
No 47
>COG3636 Predicted transcriptional regulator [Transcription]
Probab=42.86 E-value=79 Score=24.12 Aligned_cols=56 Identities=29% Similarity=0.373 Sum_probs=44.4
Q ss_pred cCCCCHHHHHHHHHHHHHHHHHHHHh-cCCCCHHHHHHHHHHHhCCCCHH--HHHHHHHHHH
Q 040572 67 VDDMDPEAARTARESLDLAFHMSNIL-DTGLDRHTLSVLIALCDLGVNPE--ALAAVVKELQ 125 (142)
Q Consensus 67 ~~~md~d~~~aArEtLDiL~EIS~LL-NTGLDReTLsICI~LcE~GVNPE--ALA~VIKELR 125 (142)
.++-|++-+.++.-.+...-+||+|- ++||+||.| ++=+-.|=||. .+-+|+|-|=
T Consensus 31 le~~d~a~i~~alg~var~~GMsqvA~~aGlsRe~L---YkaLS~~GNPtf~Til~V~kAlG 89 (100)
T COG3636 31 LEEGDPALIAAALGVVARSRGMSQVARKAGLSREGL---YKALSPGGNPTFDTILAVLKALG 89 (100)
T ss_pred HHcCCHHHHHHHHHHHHHhcCHHHHHHHhCccHHHH---HHHhCCCCCCcHHHHHHHHHHcC
Confidence 35567888889999999999999997 689999987 45566788885 4777777653
No 48
>cd04773 HTH_TioE_rpt2 Second Helix-Turn-Helix DNA binding domain of the regulatory protein TioE. Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD mainly contains the C-terminal or second repeat (rpt2) of these tandem MerR-like domain proteins.
Probab=42.82 E-value=1.2e+02 Score=21.50 Aligned_cols=47 Identities=15% Similarity=0.101 Sum_probs=35.7
Q ss_pred HHHHHHHHHHHHHhcCCCCHHHHHHHHHHHhCCCCHHHHHHHHHHHH
Q 040572 79 RESLDLAFHMSNILDTGLDRHTLSVLIALCDLGVNPEALAAVVKELQ 125 (142)
Q Consensus 79 rEtLDiL~EIS~LLNTGLDReTLsICI~LcE~GVNPEALA~VIKELR 125 (142)
.+.+..|..|-.|.+.|++-..+.-++.+.+.|-+++.+.+.+.+-+
T Consensus 41 ~~dl~~l~~I~~lr~~G~~l~~I~~~l~~~~~~~~~~~~~~~l~~~~ 87 (108)
T cd04773 41 PSDVRDARLIHLLRRGGYLLEQIATVVEQLRHAGGTEALAAALEQRR 87 (108)
T ss_pred HHHHHHHHHHHHHHHCCCCHHHHHHHHHHhhcCCCHHHHHHHHHHHH
Confidence 36677888889999999999999999998877655555555554433
No 49
>cd04448 DEP_PIKfyve DEP (Dishevelled, Egl-10, and Pleckstrin) domain found in fungal RhoGEF (GDP/GTP exchange factor) PIKfyve-like proteins. PIKfyve contains N-terminal Fyve finger and DEP domains, a central chaperonin-like domain and a C-terminal PIPK (phosphatidylinositol phosphate kinase) domain. PIKfyve-like proteins are important phosphatidylinositol (3)-monophosphate (PtdIns(3)P)-5-kinases, producing PtdIns(3,5)P2, which plays a major role in multivesicular body (MVB) sorting and control of retrograde traffic from the vacuole back to the endosome and/or Golgi. PIKfyve itself has been shown to be play a role in regulating early-endosome-to-trans-Golgi network (TGN) retrograde trafficking.
Probab=42.80 E-value=32 Score=23.93 Aligned_cols=31 Identities=19% Similarity=0.290 Sum_probs=22.8
Q ss_pred HHHHHHHHHHHHHHhcCCCCH-HHHHHHHHHHhCCC
Q 040572 78 ARESLDLAFHMSNILDTGLDR-HTLSVLIALCDLGV 112 (142)
Q Consensus 78 ArEtLDiL~EIS~LLNTGLDR-eTLsICI~LcE~GV 112 (142)
..|.+|-|.+-. -..+| |++.+|-+|++.|+
T Consensus 31 GselVdWL~~~~----~~~~R~eAv~~gq~Ll~~g~ 62 (81)
T cd04448 31 GKELVNWLIRQG----KAATRVQAIAIGQALLDAGW 62 (81)
T ss_pred hHHHHHHHHHcC----CCCCHHHHHHHHHHHHHCCC
Confidence 346677766532 23777 89999999999997
No 50
>PLN02687 flavonoid 3'-monooxygenase
Probab=42.66 E-value=49 Score=28.30 Aligned_cols=46 Identities=22% Similarity=0.319 Sum_probs=38.9
Q ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHHhCCCCHHHHHHHHHHHHhCC
Q 040572 83 DLAFHMSNILDTGLDRHTLSVLIALCDLGVNPEALAAVVKELQREP 128 (142)
Q Consensus 83 DiL~EIS~LLNTGLDReTLsICI~LcE~GVNPEALA~VIKELRrE~ 128 (142)
++..++..++-.|.|-.+-.++..|.+..-||+.+..+..||.+-.
T Consensus 297 ~i~~~~~~~~~AG~eTta~~l~~~l~~L~~~P~~~~kl~~Ei~~~~ 342 (517)
T PLN02687 297 EIKALLLNLFTAGTDTTSSTVEWAIAELIRHPDILKKAQEELDAVV 342 (517)
T ss_pred HHHHHHHHHhccccCchHHHHHHHHHHHHhCHHHHHHHHHHHHHHc
Confidence 4666777888889998888888888888899999999999998654
No 51
>PRK09247 ATP-dependent DNA ligase; Validated
Probab=42.31 E-value=74 Score=28.95 Aligned_cols=51 Identities=10% Similarity=0.024 Sum_probs=40.9
Q ss_pred HHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHH-----hCCCCHHHHHHHHHHH
Q 040572 73 EAARTARESLDLAFHMSNILDTGLDRHTLSVLIALC-----DLGVNPEALAAVVKEL 124 (142)
Q Consensus 73 d~~~aArEtLDiL~EIS~LLNTGLDReTLsICI~Lc-----E~GVNPEALA~VIKEL 124 (142)
+++.+....++.+.-|+++|.+- +.+-+..++.|| +.||++..|..+|.++
T Consensus 9 ~~i~~t~~~~ek~~~l~~~~~~~-~~~d~~~~~~ll~g~~~~~~i~~~~l~k~~~~~ 64 (539)
T PRK09247 9 DRLDLTTSTNAKLALLADYFRSA-PDPDRAWALALLTGGLPRRLVKTRLLRELAAER 64 (539)
T ss_pred HHHHhccCHHHHHHHHHHHHHhC-CHHHHHHHHHHhcCCcccCCCCHHHHHHHHHHH
Confidence 45566666777778888888875 778888999999 8999999988888665
No 52
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=42.15 E-value=1.3e+02 Score=21.88 Aligned_cols=20 Identities=25% Similarity=0.381 Sum_probs=17.5
Q ss_pred CCCCHHHHHHHHHHHHhCCC
Q 040572 110 LGVNPEALAAVVKELQREPS 129 (142)
Q Consensus 110 ~GVNPEALA~VIKELRrE~~ 129 (142)
.|++++.+..++++|++|.-
T Consensus 178 lG~tr~tvsR~l~~l~~~gi 197 (211)
T PRK11753 178 VGCSREMVGRVLKMLEDQGL 197 (211)
T ss_pred hCCCHHHHHHHHHHHHHCCC
Confidence 47899999999999999874
No 53
>PF01503 PRA-PH: Phosphoribosyl-ATP pyrophosphohydrolase; InterPro: IPR021130 Phosphoribosyl-ATP pyrophosphatase, 3.6.1.31 from EC catalyses the second step in the histidine biosynthetic pathway: 5-phosphoribosyl-ATP + H2O = 5-phosphoribosyl-AMP + PPi The Neurospora crassa enzyme also catalyzes the reactions of histidinol dehydrogenase (1.1.1.23 from EC) and phosphoribosyl-AMP cyclohydrolase (3.5.4.19 from EC). This entry also includes the Bacillus subtilis Cof proteins, which catalyze the hydrolysis of 4-amino-2-methyl-5-hydroxymethylpyrimidine pyrophosphate to 4-amino-2-methyl-5-hydroxymethylpyrimidine phosphate []. ; PDB: 2A7W_K 3NL9_A 1YXB_D 1YVW_A 2YFD_C 2YFC_B 2YF3_C 2YF4_A 2YEU_E 2YF9_A ....
Probab=42.12 E-value=90 Score=21.08 Aligned_cols=35 Identities=17% Similarity=0.327 Sum_probs=22.7
Q ss_pred HHHHHHHHHHHHhcCCCCHHHHHHHHHHHhCCCCHHHHHHHHH
Q 040572 80 ESLDLAFHMSNILDTGLDRHTLSVLIALCDLGVNPEALAAVVK 122 (142)
Q Consensus 80 EtLDiL~EIS~LLNTGLDReTLsICI~LcE~GVNPEALA~VIK 122 (142)
...++++++++|+- -+++.|...||+|+.+.+.|.
T Consensus 46 d~~~~~~e~aDlly--------~~~~~~~~~gi~~~~v~~ev~ 80 (83)
T PF01503_consen 46 DKEEVADELADLLY--------HLLGLLASMGIDLDEVFDEVH 80 (83)
T ss_dssp HHHHHHHHHHHHHH--------HHHHHHHHTT--HHHHHHHHH
T ss_pred CHHHHHHHHHHHHH--------HHHHHHHHcCCCHHHHHHHHH
Confidence 34566777777753 456778899999888766654
No 54
>PF13877 RPAP3_C: Potential Monad-binding region of RPAP3
Probab=41.67 E-value=40 Score=22.98 Aligned_cols=39 Identities=18% Similarity=0.281 Sum_probs=28.6
Q ss_pred HHHHHHhcCCCCHHHHHHHHHHHhCCCCH---HHHHHHHHHH
Q 040572 86 FHMSNILDTGLDRHTLSVLIALCDLGVNP---EALAAVVKEL 124 (142)
Q Consensus 86 ~EIS~LLNTGLDReTLsICI~LcE~GVNP---EALA~VIKEL 124 (142)
..+.+|+..+||-+.|.-.+.-+...+.+ +....+++.|
T Consensus 34 ~~l~~if~~~l~~~~L~~il~~l~~~~~~~~~~~i~~~L~~L 75 (94)
T PF13877_consen 34 DSLPKIFKNSLEPEFLSEILEALNEHFIPEDPEFIFEILEAL 75 (94)
T ss_pred HHHHHHHHccCCHHHHHHHHHHHHHHHccCCHHHHHHHHHHh
Confidence 46788999999999999888888876654 3344444444
No 55
>TIGR01797 CM_P_1 chorismate mutase domain of proteobacterial P-protein, clade 1. This model represents the chorismate mutase domain of the gamma and beta proteobacterial "P-protein" which contains an N-terminal chorismate mutase domain and a C-terminal prephenate dehydratase domain.
Probab=41.15 E-value=1.2e+02 Score=20.81 Aligned_cols=62 Identities=16% Similarity=0.258 Sum_probs=48.6
Q ss_pred cCCCCHHHHHHHHHHHHHHHHHHHHh-cCCC-------CHHHHHHHHHHHh-CCCCHHHHHHHHHHHHhCC
Q 040572 67 VDDMDPEAARTARESLDLAFHMSNIL-DTGL-------DRHTLSVLIALCD-LGVNPEALAAVVKELQREP 128 (142)
Q Consensus 67 ~~~md~d~~~aArEtLDiL~EIS~LL-NTGL-------DReTLsICI~LcE-~GVNPEALA~VIKELRrE~ 128 (142)
+|..|.+-+.--.+-+.++.+|+.+= +.|+ .++-|.-+.++.+ .|++|+.+..+.+.|-.++
T Consensus 8 ID~ID~~lv~Ll~~R~~~~~~i~~~K~~~~~~v~dp~RE~~vl~~~~~~~~~~~l~~~~i~~if~~ii~~S 78 (83)
T TIGR01797 8 ISAIDEKLLKLLAERRELAFEVGKSKLLSHRPVRDIERERDLLQRLITLGKAYHLDAHYITRLFQLIIEDS 78 (83)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCChHHHHHHHHHHHHHhhhCCCCHHHHHHHHHHHHHHH
Confidence 57788888888889999999998886 3454 2455777788885 8999999999988886543
No 56
>PRK14703 glutaminyl-tRNA synthetase/YqeY domain fusion protein; Provisional
Probab=40.81 E-value=72 Score=31.00 Aligned_cols=43 Identities=23% Similarity=0.389 Sum_probs=34.6
Q ss_pred HHHHHHHHhcCC------CCHHHHHHHHHHHhCC-CCHHHHHHHHHHHHh
Q 040572 84 LAFHMSNILDTG------LDRHTLSVLIALCDLG-VNPEALAAVVKELQR 126 (142)
Q Consensus 84 iL~EIS~LLNTG------LDReTLsICI~LcE~G-VNPEALA~VIKELRr 126 (142)
++.|+..+||-+ |+.+.|.-+|.|++.| ++.++.-.|+.+|-.
T Consensus 644 l~~El~~~Lne~~i~~~~l~pe~LaeLv~lV~~g~IS~~~AK~VL~~m~~ 693 (771)
T PRK14703 644 VVNDLAGLLRDRELAALPFTPAALARLVALVDAGRISTRIAKDVLAELAA 693 (771)
T ss_pred HHHHHHHHHhcCCCccCCCCHHHHHHHHHHHHcCCccHHHHHHHHHHHHh
Confidence 567777888776 8899999999999999 677777777777754
No 57
>cd06258 Peptidase_M3_like The peptidase M3-like family, also called neurolysin-like family, is part of the "zincins" metallopeptidases, and includes M3, M2 and M32 families of metallopeptidases. The M3 family is subdivided into two subfamilies: the widespread M3A, which comprises a number of high-molecular mass endo- and exopeptidases from bacteria, archaea, protozoa, fungi, plants and animals, and the small M3B, whose members are enzymes primarily from bacteria. Well-known mammalian/eukaryotic M3A endopeptidases are the thimet oligopeptidase (TOP; endopeptidase 3.4.24.15), neurolysin (alias endopeptidase 3.4.24.16), and the mitochondrial intermediate peptidase. The first two are intracellular oligopeptidases, which act only on relatively short substrates of less than 20 amino acid residues, while the latter cleaves N-terminal octapeptides from proteins during their import into the mitochondria. The M3A subfamily also contains several bacterial endopeptidases, collectively called olig
Probab=40.63 E-value=81 Score=25.86 Aligned_cols=44 Identities=23% Similarity=0.378 Sum_probs=34.3
Q ss_pred HHHHHHHHHHHHHhcCCCCHHHHHHHHHHHhCCCCHHHHHHHHHHHHh
Q 040572 79 RESLDLAFHMSNILDTGLDRHTLSVLIALCDLGVNPEALAAVVKELQR 126 (142)
Q Consensus 79 rEtLDiL~EIS~LLNTGLDReTLsICI~LcE~GVNPEALA~VIKELRr 126 (142)
+|.+++-.+++++|+ . ..--..++..-+.| +||.+-..+.+|++
T Consensus 5 ~~lv~lr~e~A~~lG--y-~~~~d~~l~~~~~~-~~e~v~~f~~~l~~ 48 (365)
T cd06258 5 EELVSLRNQLARLLG--Y-ENFADYKLALQEAK-SPETVEGFFEELKR 48 (365)
T ss_pred HHHHHHHHHHHHHcC--C-CCHHHHHHHHHhcC-CHHHHHHHHHHHHH
Confidence 577888899999995 4 45566777888888 99998888777764
No 58
>PF01817 CM_2: Chorismate mutase type II; InterPro: IPR020822 Chorismate mutase, 5.4.99.5 from EC, catalyses the conversion of chorismate to prephenate in the pathway of tyrosine and phenylalanine biosynthesis. This enzyme is negatively regulated by tyrosine, tryptophan and phenylalanine [, ]. Prephenate dehydratase (IPR001086 from INTERPRO, 4.2.1.51 from EC, PDT) catalyses the decarboxylation of prephenate into phenylpyruvate. In microorganisms PDT is involved in the terminal pathway of the biosynthesis of phenylalanine. In some bacteria, such as Escherichia coli, PDT is part of a bifunctional enzyme (P-protein) that also catalyzes the transformation of chorismate into prephenate (chorismate mutase) while in other bacteria it is a monofunctional enzyme. The sequence of monofunctional chorismate mutase aligns well with the N-terminal part of P-proteins [].; GO: 0046417 chorismate metabolic process; PDB: 1YBZ_A 2GTV_X 2FP1_B 2F6L_B 2FP2_B 2AO2_A 3HGW_C 3HGX_B 2H9C_A 3RET_B ....
Probab=40.58 E-value=34 Score=22.59 Aligned_cols=61 Identities=26% Similarity=0.471 Sum_probs=45.2
Q ss_pred cCCCCHHHHHHHHHHHHHHHHHHHHhcC-CC---C----HHHHHHHHHHHh-CCCCHHHHHHHHHHHHhC
Q 040572 67 VDDMDPEAARTARESLDLAFHMSNILDT-GL---D----RHTLSVLIALCD-LGVNPEALAAVVKELQRE 127 (142)
Q Consensus 67 ~~~md~d~~~aArEtLDiL~EIS~LLNT-GL---D----ReTLsICI~LcE-~GVNPEALA~VIKELRrE 127 (142)
+|..|.+-+.--.+-++++.+|+.+=.. |+ | .+-+.-+.++++ .|++|+.+..+.+.|...
T Consensus 4 Id~iD~~i~~Ll~~R~~l~~~i~~~K~~~~~~i~d~~RE~~v~~~~~~~~~~~~l~~~~i~~if~~ii~~ 73 (81)
T PF01817_consen 4 IDEIDREIVDLLAERMDLVRKIAEYKKENGLPIFDPDREEEVLERLRELAEEGGLDPEFIERIFRAIIEE 73 (81)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCSSTHHHHHHHHHHHHHHHHHTTSEHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCcHHHHHHHHHHHHHhHhCCCCHHHHHHHHHHHHHH
Confidence 3555667777778888888888887433 34 2 345677778888 999999999999888654
No 59
>PRK08903 DnaA regulatory inactivator Hda; Validated
Probab=40.58 E-value=1.3e+02 Score=22.71 Aligned_cols=45 Identities=13% Similarity=0.105 Sum_probs=37.8
Q ss_pred HHHHHHHHHHHhcCCCCHHHHHHHHHHHhCCCCHHHHHHHHHHHHhC
Q 040572 81 SLDLAFHMSNILDTGLDRHTLSVLIALCDLGVNPEALAAVVKELQRE 127 (142)
Q Consensus 81 tLDiL~EIS~LLNTGLDReTLsICI~LcE~GVNPEALA~VIKELRrE 127 (142)
.+.+|.+++.-.+.+++.+.+..++. ..+=|+..|-.+|..|...
T Consensus 162 ~~~~l~~~~~~~~v~l~~~al~~L~~--~~~gn~~~l~~~l~~l~~~ 206 (227)
T PRK08903 162 KIAALKAAAAERGLQLADEVPDYLLT--HFRRDMPSLMALLDALDRY 206 (227)
T ss_pred HHHHHHHHHHHcCCCCCHHHHHHHHH--hccCCHHHHHHHHHHHHHH
Confidence 34577777777889999999999999 5778999999999998753
No 60
>cd04766 HTH_HspR Helix-Turn-Helix DNA binding domain of the HspR transcription regulator. Helix-turn-helix (HTH) transcription regulator HspR, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=40.32 E-value=87 Score=21.31 Aligned_cols=46 Identities=13% Similarity=0.224 Sum_probs=33.4
Q ss_pred HHHHHHHHHHHHHhc-CCCCHHHHHHHHHHHhCCCCHHHHHHHHHHHHhC
Q 040572 79 RESLDLAFHMSNILD-TGLDRHTLSVLIALCDLGVNPEALAAVVKELQRE 127 (142)
Q Consensus 79 rEtLDiL~EIS~LLN-TGLDReTLsICI~LcE~GVNPEALA~VIKELRrE 127 (142)
.+.+..|..|-.|.+ .|++-..+..++.|.+. =+.|..-|.+||+.
T Consensus 41 ~~dv~~l~~i~~L~~d~g~~l~~i~~~l~l~~~---~~~l~~~l~~l~~~ 87 (91)
T cd04766 41 ERDIERLRRIQRLTQELGVNLAGVKRILELEEE---LAELRAELDELRAR 87 (91)
T ss_pred HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHH---HHHHHHHHHHHHHH
Confidence 356777888888887 99999999999998875 34555555555543
No 61
>PLN03234 cytochrome P450 83B1; Provisional
Probab=40.04 E-value=64 Score=27.17 Aligned_cols=47 Identities=21% Similarity=0.232 Sum_probs=39.0
Q ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHHhCCCCHHHHHHHHHHHHhCCC
Q 040572 83 DLAFHMSNILDTGLDRHTLSVLIALCDLGVNPEALAAVVKELQREPS 129 (142)
Q Consensus 83 DiL~EIS~LLNTGLDReTLsICI~LcE~GVNPEALA~VIKELRrE~~ 129 (142)
++...+..++-.|-|-.+-.++..|....-||+.++.+..|+.....
T Consensus 288 ~i~~~~~~ll~AG~dTTa~tl~~~l~~L~~~P~v~~kl~~Ei~~~~~ 334 (499)
T PLN03234 288 NVKAMILDIVVPGTDTAAAVVVWAMTYLIKYPEAMKKAQDEVRNVIG 334 (499)
T ss_pred HHHHHHHHHHhcchhhHHHHHHHHHHHHHhCHHHHHHHHHHHHHHhC
Confidence 46677778888999988888888888888899999999999887543
No 62
>PRK02615 thiamine-phosphate pyrophosphorylase; Provisional
Probab=39.61 E-value=32 Score=29.98 Aligned_cols=44 Identities=36% Similarity=0.602 Sum_probs=39.3
Q ss_pred HHHHHhcCCCCH--HHHHHHHHHHhCCCCHHHHHHHHHHHHhCCCC
Q 040572 87 HMSNILDTGLDR--HTLSVLIALCDLGVNPEALAAVVKELQREPSP 130 (142)
Q Consensus 87 EIS~LLNTGLDR--eTLsICI~LcE~GVNPEALA~VIKELRrE~~a 130 (142)
.|..|||..||| |=|.++=..|--|.|-..|+.-+|+||.+...
T Consensus 8 ~~~r~~danl~r~reglrv~e~~~r~~~~~~~~~~~~k~~r~~~~~ 53 (347)
T PRK02615 8 RIARILDANLDRAREGLRVLEEWCRFGLENEDLVERCKDLRQELGR 53 (347)
T ss_pred HHHHHHhccchhhhcccHHHHHHHHHhcCcHHHHHHHHHHHHHHhh
Confidence 677889999995 78999999999999999999999999987654
No 63
>PLN03018 homomethionine N-hydroxylase
Probab=39.51 E-value=60 Score=28.51 Aligned_cols=46 Identities=20% Similarity=0.230 Sum_probs=38.5
Q ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHHhCCCCHHHHHHHHHHHHhCC
Q 040572 83 DLAFHMSNILDTGLDRHTLSVLIALCDLGVNPEALAAVVKELQREP 128 (142)
Q Consensus 83 DiL~EIS~LLNTGLDReTLsICI~LcE~GVNPEALA~VIKELRrE~ 128 (142)
+++..+..++-.|.|-.+-.++..|....-||+..+.+..||..-.
T Consensus 314 ~i~~~~~~~~~aG~dTta~~l~~~l~~L~~~P~~q~kl~~Ei~~v~ 359 (534)
T PLN03018 314 EIKAQCVEFCIAAIDNPANNMEWTLGEMLKNPEILRKALKELDEVV 359 (534)
T ss_pred HHHHHHHHHHHHhhhHHHHHHHHHHHHHHcCHHHHHHHHHHHHHHh
Confidence 4566777788889998888888888889999999999999987654
No 64
>PF13041 PPR_2: PPR repeat family
Probab=39.37 E-value=38 Score=20.09 Aligned_cols=29 Identities=17% Similarity=0.362 Sum_probs=18.5
Q ss_pred HHHHhcCCCCHHHHHHHHHHHhCCCCHHH
Q 040572 88 MSNILDTGLDRHTLSVLIALCDLGVNPEA 116 (142)
Q Consensus 88 IS~LLNTGLDReTLsICI~LcE~GVNPEA 116 (142)
|+.+...|--.+++.+.-+|.+.|+.|..
T Consensus 10 i~~~~~~~~~~~a~~l~~~M~~~g~~P~~ 38 (50)
T PF13041_consen 10 ISGYCKAGKFEEALKLFKEMKKRGIKPDS 38 (50)
T ss_pred HHHHHHCcCHHHHHHHHHHHHHcCCCCCH
Confidence 44455566666777777777777776654
No 65
>PLN02290 cytokinin trans-hydroxylase
Probab=39.15 E-value=53 Score=27.83 Aligned_cols=46 Identities=17% Similarity=0.083 Sum_probs=38.7
Q ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHHhCCCCHHHHHHHHHHHHhCC
Q 040572 83 DLAFHMSNILDTGLDRHTLSVLIALCDLGVNPEALAAVVKELQREP 128 (142)
Q Consensus 83 DiL~EIS~LLNTGLDReTLsICI~LcE~GVNPEALA~VIKELRrE~ 128 (142)
+++.++..++-.|.|-.+..++..|....-||+....+..||.+-.
T Consensus 316 ~i~~~~~~~~~AG~dTta~tl~~~l~~L~~~P~vq~kl~~Ei~~v~ 361 (516)
T PLN02290 316 LIMDECKTFFFAGHETTALLLTWTLMLLASNPTWQDKVRAEVAEVC 361 (516)
T ss_pred HHHHHHHHHHhhhHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHh
Confidence 4666777888899999999988888888899999999999987643
No 66
>PLN02966 cytochrome P450 83A1
Probab=39.09 E-value=64 Score=27.43 Aligned_cols=46 Identities=17% Similarity=0.210 Sum_probs=38.6
Q ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHHhCCCCHHHHHHHHHHHHhCC
Q 040572 83 DLAFHMSNILDTGLDRHTLSVLIALCDLGVNPEALAAVVKELQREP 128 (142)
Q Consensus 83 DiL~EIS~LLNTGLDReTLsICI~LcE~GVNPEALA~VIKELRrE~ 128 (142)
++..++..++-.|-|-.+..+...|.+..-||+....+..||..-.
T Consensus 289 ~i~~~~~~l~~AG~eTta~~l~~~l~~L~~~P~~q~kl~~Ei~~v~ 334 (502)
T PLN02966 289 NVKAVILDIVVAGTDTAAAAVVWGMTYLMKYPQVLKKAQAEVREYM 334 (502)
T ss_pred HHHHHHHHHHhccccchHHHHHHHHHHHHhCHHHHHHHHHHHHHHh
Confidence 4566778888899998888888888888889999999999988653
No 67
>PRK10573 type IV pilin biogenesis protein; Provisional
Probab=38.43 E-value=84 Score=26.39 Aligned_cols=50 Identities=18% Similarity=0.264 Sum_probs=34.1
Q ss_pred HHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHhCCCCHHHHHHHHHHHHhCCCC
Q 040572 78 ARESLDLAFHMSNILDTGLDRHTLSVLIALCDLGVNPEALAAVVKELQREPSP 130 (142)
Q Consensus 78 ArEtLDiL~EIS~LLNTGLDReTLsICI~LcE~GVNPEALA~VIKELRrE~~a 130 (142)
.++....+.+++.+|+.|++ |.-+++++....+-..+..++++++.....
T Consensus 58 ~~~~~~f~~~L~~ll~~G~~---l~~aL~~l~~~~~~~~~~~~~~~i~~~l~~ 107 (399)
T PRK10573 58 GEQSAEFIRQLATLLQAGLP---LSEGLQLLAEQHPSAQWQALLQDLAHQLEQ 107 (399)
T ss_pred HHHHHHHHHHHHHHHHcCCC---HHHHHHHHHhcCCCHHHHHHHHHHHHHHHC
Confidence 45677889999999999997 344455555444444677777777655444
No 68
>PRK13856 two-component response regulator VirG; Provisional
Probab=37.28 E-value=52 Score=24.34 Aligned_cols=56 Identities=13% Similarity=0.163 Sum_probs=44.7
Q ss_pred HHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHhCCCCHHHHHHHHHHHHhCCCC
Q 040572 75 ARTARESLDLAFHMSNILDTGLDRHTLSVLIALCDLGVNPEALAAVVKELQREPSP 130 (142)
Q Consensus 75 ~~aArEtLDiL~EIS~LLNTGLDReTLsICI~LcE~GVNPEALA~VIKELRrE~~a 130 (142)
+.-...=+++|.-+..--+--++|+.|.-.+---+..++..+|-..|..||+....
T Consensus 154 i~Lt~~E~~lL~~l~~~~~~v~sr~~l~~~~~~~~~~~~~~~l~~~i~rLR~Kl~~ 209 (241)
T PRK13856 154 VKLTAGEFNLLVAFLEKPRDVLSREQLLIASRVREEEVYDRSIDVLILRLRRKLEQ 209 (241)
T ss_pred eecCHHHHHHHHHHHhCCCCccCHHHHHHHhcCcCCCCCCccHhHHHHHHHHhccc
Confidence 44455667888888888888999999987665445667889999999999999864
No 69
>COG1641 Uncharacterized conserved protein [Function unknown]
Probab=36.66 E-value=35 Score=31.14 Aligned_cols=24 Identities=54% Similarity=0.715 Sum_probs=20.4
Q ss_pred HHHHHHhCCCCHHHHHHHHHHHHh
Q 040572 103 VLIALCDLGVNPEALAAVVKELQR 126 (142)
Q Consensus 103 ICI~LcE~GVNPEALA~VIKELRr 126 (142)
++=+|++.||+||.|..+|+.+--
T Consensus 16 ~LgaLidlGv~~e~~~e~v~~l~~ 39 (387)
T COG1641 16 ILGALIDLGVDPEYLKEVVEALGP 39 (387)
T ss_pred HHHHHHHcCCCHHHHHHHHHhcCc
Confidence 345799999999999999998754
No 70
>PRK07914 hypothetical protein; Reviewed
Probab=36.62 E-value=1e+02 Score=25.23 Aligned_cols=43 Identities=16% Similarity=0.077 Sum_probs=35.8
Q ss_pred HHHHHHHHhcCCCCHHHHHHHHHHHhCCCCHHHHH-HHHHHHHh
Q 040572 84 LAFHMSNILDTGLDRHTLSVLIALCDLGVNPEALA-AVVKELQR 126 (142)
Q Consensus 84 iL~EIS~LLNTGLDReTLsICI~LcE~GVNPEALA-~VIKELRr 126 (142)
.+|++.+-+-.|=..+++.++-.|.+.|..|-.|. .+.+++|.
T Consensus 198 ~vf~L~dAi~~g~~~~A~~~l~~L~~~ge~p~~il~~l~~~~r~ 241 (320)
T PRK07914 198 KGFDIADKAVAGDVAGAAEALRWAMMRGEPHVVLADALAEAVHT 241 (320)
T ss_pred hHHHHHHHHHCCCHHHHHHHHHHHHHCCCchHHHHHHHHHHHHH
Confidence 57788888888888999999999999999999865 56566665
No 71
>cd04778 HTH_MerR-like_sg2 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 2). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=36.55 E-value=76 Score=25.75 Aligned_cols=35 Identities=23% Similarity=0.305 Sum_probs=30.3
Q ss_pred CCCHHHHHHHHHHHhCCCCHHHHHHHHHHHHhCCC
Q 040572 95 GLDRHTLSVLIALCDLGVNPEALAAVVKELQREPS 129 (142)
Q Consensus 95 GLDReTLsICI~LcE~GVNPEALA~VIKELRrE~~ 129 (142)
.-|..-+.+..+|.+.|+.+.++..++..+|....
T Consensus 131 ~~~~~~~~~~~~L~~~Gi~~~~i~~~lr~~r~~ad 165 (219)
T cd04778 131 VPSPRLLEALAELVDAGIPLRAVLDLVAAVRRHAD 165 (219)
T ss_pred ccCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHH
Confidence 34678899999999999999999999999987554
No 72
>PF14840 DNA_pol3_delt_C: Processivity clamp loader gamma complex DNA pol III C-term; PDB: 3GLG_F 1XXH_A 3GLF_F 1JQJ_C 3GLI_F.
Probab=36.48 E-value=98 Score=22.97 Aligned_cols=40 Identities=33% Similarity=0.480 Sum_probs=28.0
Q ss_pred HHHHHHhcCCCCHHHHHHHHHHHhCCCCHHH-HHHHHHHHH
Q 040572 86 FHMSNILDTGLDRHTLSVLIALCDLGVNPEA-LAAVVKELQ 125 (142)
Q Consensus 86 ~EIS~LLNTGLDReTLsICI~LcE~GVNPEA-LA~VIKELR 125 (142)
|++++-+=.|=...++.|+-.|-..|++|-. |-.+.+|||
T Consensus 2 F~L~Da~L~G~~~ra~riL~~L~~Eg~ep~~lLw~L~rElr 42 (125)
T PF14840_consen 2 FQLIDALLAGDAKRALRILQGLQAEGVEPPILLWALQRELR 42 (125)
T ss_dssp HHHHHHHHTT-HHHHHHHHHHHHHTT--HHHHHHHHHHHHH
T ss_pred CcHHHHHHCCCHHHHHHHHHHHHHCCccHHHHHHHHHHHHH
Confidence 3444445567778899999999999999988 566777776
No 73
>PRK07452 DNA polymerase III subunit delta; Validated
Probab=35.49 E-value=92 Score=25.05 Aligned_cols=43 Identities=16% Similarity=0.229 Sum_probs=33.2
Q ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHHhCCCCHHH-HHHHHHHHH
Q 040572 83 DLAFHMSNILDTGLDRHTLSVLIALCDLGVNPEA-LAAVVKELQ 125 (142)
Q Consensus 83 DiL~EIS~LLNTGLDReTLsICI~LcE~GVNPEA-LA~VIKELR 125 (142)
+.+|++.+-+-.|=-..++.++-.|++.|.+|-. |+.+.+++|
T Consensus 201 ~~if~l~dai~~~~~~~A~~~l~~L~~~g~~p~~il~~l~~~~r 244 (326)
T PRK07452 201 QNSLQLADALLQGNTGKALALLDDLLDANEPALRIVATLTGQFR 244 (326)
T ss_pred CcHHHHHHHHHCCCHHHHHHHHHHHHHCCCcHHHHHHHHHHHHH
Confidence 3466777777777778899999999999999986 556656655
No 74
>PF04447 DUF550: Protein of unknown function (DUF550); InterPro: IPR007538 This entry represents the N terminus of a protein of unknown function, found in a range of Proteobacteria and a few P22-like dsDNA virus particles.
Probab=35.39 E-value=73 Score=24.26 Aligned_cols=49 Identities=16% Similarity=0.233 Sum_probs=34.3
Q ss_pred HHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHH----hCCCCHHHHHHHHHHHHhCCCC
Q 040572 76 RTARESLDLAFHMSNILDTGLDRHTLSVLIALC----DLGVNPEALAAVVKELQREPSP 130 (142)
Q Consensus 76 ~aArEtLDiL~EIS~LLNTGLDReTLsICI~Lc----E~GVNPEALA~VIKELRrE~~a 130 (142)
-.++|.+++.....++ .|-..+.|-|. ..|+.|+.|+..|.+=..-+.+
T Consensus 26 Hl~kE~~E~~~~p~Dl------~EwaDv~~Ll~D~~~RaGis~~~i~~A~~~K~~iN~a 78 (100)
T PF04447_consen 26 HLSKEALEAEAAPGDL------SEWADVQILLWDGARRAGISPEQIIDAMEAKLAINKA 78 (100)
T ss_pred HHHHHHHHHHhCCCCH------HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhccc
Confidence 3466777777666555 37788888777 7999999998887654443333
No 75
>PF06207 DUF1002: Protein of unknown function (DUF1002); InterPro: IPR009343 This protein family has no known function. Its members are about 300 amino acids in length. It has so far been detected in Firmicute bacteria and some archaebacteria.
Probab=35.30 E-value=84 Score=26.10 Aligned_cols=57 Identities=18% Similarity=0.306 Sum_probs=37.8
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHH-----HHhCC-CCHHHHHHHHHHHHh
Q 040572 68 DDMDPEAARTARESLDLAFHMSNILDTGLDRHTLSVLIA-----LCDLG-VNPEALAAVVKELQR 126 (142)
Q Consensus 68 ~~md~d~~~aArEtLDiL~EIS~LLNTGLDReTLsICI~-----LcE~G-VNPEALA~VIKELRr 126 (142)
...|.++.+.|+|=|...-+|++ +.|++.+-+.-+|. +.+.+ -+++.+..+|.+.-+
T Consensus 124 ~~l~~~~k~~A~eEl~~t~~i~~--~~~~~~~k~~~~i~~iK~~va~~~~~t~~eI~~IV~~~~~ 186 (225)
T PF06207_consen 124 EKLDEENKKVANEELVTTSEIAE--GDGIGDEKANAAIAEIKEEVAKQKPKTDEEIRNIVNNVLN 186 (225)
T ss_pred CCCCHHHHHHHHHHHHHHHhhcc--ccCCCHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHH
Confidence 46788999999999999999988 66666666655543 33333 245555555555443
No 76
>PRK05458 guanosine 5'-monophosphate oxidoreductase; Provisional
Probab=34.35 E-value=64 Score=27.98 Aligned_cols=37 Identities=8% Similarity=0.324 Sum_probs=31.3
Q ss_pred cCCCCHHHHHHHHHHHhCCC------------CHHHHHHHHHHHHhCCC
Q 040572 93 DTGLDRHTLSVLIALCDLGV------------NPEALAAVVKELQREPS 129 (142)
Q Consensus 93 NTGLDReTLsICI~LcE~GV------------NPEALA~VIKELRrE~~ 129 (142)
..|.+.+.+.-+.+|+|+|+ +-+.+.+.|++||+...
T Consensus 91 ~vg~~~~~~~~~~~Lv~ag~~~d~i~iD~a~gh~~~~~e~I~~ir~~~p 139 (326)
T PRK05458 91 SVGVKDDEYDFVDQLAAEGLTPEYITIDIAHGHSDSVINMIQHIKKHLP 139 (326)
T ss_pred EecCCHHHHHHHHHHHhcCCCCCEEEEECCCCchHHHHHHHHHHHhhCC
Confidence 34667899999999999987 77888889999998764
No 77
>PF02881 SRP54_N: SRP54-type protein, helical bundle domain; InterPro: IPR013822 The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes [, ]. SRP recognises the signal sequence of the nascent polypeptide on the ribosome, retards its elongation, and docks the SRP-ribosome-polypeptide complex to the RER membrane via the SR receptor. Eukaryotic SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor []. In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane. In archaea, the SRP complex contains 7S RNA like its eukaryotic counterpart, yet only includes two of the six protein subunits found in the eukarytic complex: SRP19 and SRP54 []. This entry represents the N-terminal helical bundle domain of the 54 kDa SRP54 component, a GTP-binding protein that interacts with the signal sequence when it emerges from the ribosome. SRP54 of the signal recognition particle has a three-domain structure: an N-terminal helical bundle domain, a GTPase domain, and the M-domain that binds the 7s RNA and also binds the signal sequence. The extreme C-terminal region is glycine-rich and lower in complexity and poorly conserved between species. These proteins include Escherichia coli and Bacillus subtilis ffh protein (P48), which seems to be the prokaryotic counterpart of SRP54; signal recognition particle receptor alpha subunit (docking protein), an integral membrane GTP-binding protein which ensures, in conjunction with SRP, the correct targeting of nascent secretory proteins to the endoplasmic reticulum membrane; bacterial FtsY protein, which is believed to play a similar role to that of the docking protein in eukaryotes; the pilA protein from Neisseria gonorrhoeae, the homologue of ftsY; and bacterial flagellar biosynthesis protein flhF.; GO: 0005525 GTP binding, 0006614 SRP-dependent cotranslational protein targeting to membrane; PDB: 1J8M_F 1J8Y_F 2J37_W 2OG2_A 3B9Q_A 2V3C_C 3NDB_B 1ZU5_B 1ZU4_A 1WGW_A ....
Probab=34.18 E-value=82 Score=20.31 Aligned_cols=25 Identities=16% Similarity=0.306 Sum_probs=22.1
Q ss_pred HHHHHHHhCCCCHHHHHHHHHHHHh
Q 040572 102 SVLIALCDLGVNPEALAAVVKELQR 126 (142)
Q Consensus 102 sICI~LcE~GVNPEALA~VIKELRr 126 (142)
.+...|+++-|++++-..++..||+
T Consensus 29 ele~~Li~aDVg~~~a~~i~~~ik~ 53 (75)
T PF02881_consen 29 ELEEALIEADVGVEVAEKIIENIKK 53 (75)
T ss_dssp HHHHHHHHTTTSHHHHHHHHHHHHH
T ss_pred HHHHHHHHcCcCHHHHHHHHHHHHH
Confidence 4667899999999999999999988
No 78
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=34.14 E-value=47 Score=20.75 Aligned_cols=19 Identities=11% Similarity=0.260 Sum_probs=8.6
Q ss_pred HHHHHHHHHHHHhcCCCCH
Q 040572 80 ESLDLAFHMSNILDTGLDR 98 (142)
Q Consensus 80 EtLDiL~EIS~LLNTGLDR 98 (142)
+.++.|..|-.|.+.|++-
T Consensus 41 ~dv~~l~~i~~l~~~G~sl 59 (69)
T PF13411_consen 41 EDVERLREIKELRKQGMSL 59 (69)
T ss_dssp HHHHHHHHHHHHHHTTTHH
T ss_pred HHHHHHHHHHHHHHCcCCH
Confidence 3444444444444444433
No 79
>PRK12402 replication factor C small subunit 2; Reviewed
Probab=33.98 E-value=1.1e+02 Score=24.01 Aligned_cols=40 Identities=13% Similarity=0.068 Sum_probs=28.6
Q ss_pred HHHHHHHHhcCCCCHHHHHHHHHHH-hCCCCHHHHHHHHHH
Q 040572 84 LAFHMSNILDTGLDRHTLSVLIALC-DLGVNPEALAAVVKE 123 (142)
Q Consensus 84 iL~EIS~LLNTGLDReTLsICI~Lc-E~GVNPEALA~VIKE 123 (142)
.+++|-+.+-.|=-++.+.++-.|+ +.|++|..++..+..
T Consensus 254 ~i~~l~~ai~~~~~~~a~~~l~~l~~~~g~~~~~i~~~l~~ 294 (337)
T PRK12402 254 VIESLLDAAEAGDFTDARKTLDDLLIDEGLSGGEVLEELLR 294 (337)
T ss_pred HHHHHHHHHHcCCHHHHHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 4555555555564456888888887 899999988877643
No 80
>KOG0157 consensus Cytochrome P450 CYP4/CYP19/CYP26 subfamilies [Secondary metabolites biosynthesis, transport and catabolism; Lipid transport and metabolism]
Probab=33.62 E-value=91 Score=27.22 Aligned_cols=46 Identities=15% Similarity=0.181 Sum_probs=40.0
Q ss_pred HHHHHHHHhcCCCCHHHHHHHHHHHhCCCCHHHHHHHHHHHHhCCC
Q 040572 84 LAFHMSNILDTGLDRHTLSVLIALCDLGVNPEALAAVVKELQREPS 129 (142)
Q Consensus 84 iL~EIS~LLNTGLDReTLsICI~LcE~GVNPEALA~VIKELRrE~~ 129 (142)
+..++-.++=.|-|-.+..+...|.-.+-||+.++.+..|++.-..
T Consensus 292 i~d~v~tf~faG~DTTss~ltw~l~~La~hP~vq~k~~eEi~~i~~ 337 (497)
T KOG0157|consen 292 IRDEVDTFMFAGHDTTSSALTWTLWLLAKHPEVQEKLREEVDEILG 337 (497)
T ss_pred HHHHHHHheeeccchHHHHHHHHHHHHhcCHHHHHHHHHHHHHHhC
Confidence 5666677777799999999999999999999999999999997554
No 81
>TIGR02154 PhoB phosphate regulon transcriptional regulatory protein PhoB. PhoB is a DNA-binding response regulator protein acting with PhoR in a 2-component system responding to phosphate ion. PhoB acts as a positive regulator of gene expression for phosphate-related genes such as phoA, phoS, phoE and ugpAB as well as itself. It is often found proximal to genes for the high-affinity phosphate ABC transporter (pstSCAB; GenProp0190) and presumably regulates these as well.
Probab=33.56 E-value=47 Score=23.27 Aligned_cols=49 Identities=14% Similarity=0.155 Sum_probs=36.5
Q ss_pred HHHHHHHHHHhcCCCCHHHHHHHHHHHhCCCCHHHHHHHHHHHHhCCCC
Q 040572 82 LDLAFHMSNILDTGLDRHTLSVLIALCDLGVNPEALAAVVKELQREPSP 130 (142)
Q Consensus 82 LDiL~EIS~LLNTGLDReTLsICI~LcE~GVNPEALA~VIKELRrE~~a 130 (142)
+++|.-+.+-.+-|++++.+.-.+-=-+.++++..+...|+.||+....
T Consensus 160 ~~il~~l~~~~~~~~s~~~i~~~~~~~~~~~~~~tv~~~i~~l~~Kl~~ 208 (226)
T TIGR02154 160 FRLLHFFMTHPERVYSREQLLDRVWGRDVYVEERTVDVHIRRLRKALNP 208 (226)
T ss_pred HHHHHHHHhCCCceEcHHHHHHHhcCCCCCCCCccHHHHHHHHHHhhcc
Confidence 5667777776667888877754443336788999999999999998764
No 82
>TIGR03499 FlhF flagellar biosynthetic protein FlhF.
Probab=33.09 E-value=2.5e+02 Score=22.93 Aligned_cols=33 Identities=24% Similarity=0.325 Sum_probs=27.6
Q ss_pred CCCHHHHHHHHHHHhCCCCHHHHHHHHHHHHhC
Q 040572 95 GLDRHTLSVLIALCDLGVNPEALAAVVKELQRE 127 (142)
Q Consensus 95 GLDReTLsICI~LcE~GVNPEALA~VIKELRrE 127 (142)
+++.+--.+.-.|+++||+++....++++|+..
T Consensus 131 ~~~~~l~~l~~~L~~~gv~~~la~~L~~~l~~~ 163 (282)
T TIGR03499 131 QRDPEGAKLLERLLRAGVSPELARELLEKLPER 163 (282)
T ss_pred ccCHHHHHHHHHHHHCCCCHHHHHHHHHHhhcc
Confidence 567777778889999999999999999988753
No 83
>PRK05629 hypothetical protein; Validated
Probab=32.76 E-value=1.2e+02 Score=24.74 Aligned_cols=39 Identities=26% Similarity=0.346 Sum_probs=30.7
Q ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHHhCCCCHHHHHHHH
Q 040572 83 DLAFHMSNILDTGLDRHTLSVLIALCDLGVNPEALAAVV 121 (142)
Q Consensus 83 DiL~EIS~LLNTGLDReTLsICI~LcE~GVNPEALA~VI 121 (142)
..+|++.+-+-.|=...++.++-.|+..|++|-.|..++
T Consensus 195 ~~iF~l~dAv~~g~~~~Al~~l~~l~~~g~~pi~il~~l 233 (318)
T PRK05629 195 VSGFDIADLACAGQVSKAVASTRRALQLGVSPVALAAAL 233 (318)
T ss_pred chHHHHHHHHHcCCHHHHHHHHHHHHHcCCCcHHHHHHH
Confidence 346777777777778889999999999999999864443
No 84
>PF00550 PP-binding: Phosphopantetheine attachment site; InterPro: IPR006163 Phosphopantetheine (or pantetheine 4' phosphate) is the prosthetic group of acyl carrier proteins (ACP) in some multienzyme complexes where it serves as a 'swinging arm' for the attachment of activated fatty acid and amino-acid groups []. The amino-terminal region of the ACP proteins is well defined and consists of alpha four helices arranged in a right-handed bundle held together by interhelical hydrophobic interactions. The Asp-Ser-Leu (DSL)motif is conserved in all of the ACP sequences, and the 4'-PP prosthetic group is covalently linked via a phosphodiester bond to the serine residue. The DSL sequence is present at the amino terminus of helix II, a domain of the protein referred to as the recognition helix and which is responsible for the interaction of ACPs with the enzymes of type II fatty acid synthesis [].; GO: 0048037 cofactor binding; PDB: 3EJB_E 3EJE_G 1L0I_A 2FHS_C 3EJD_E 2FAE_B 2FAD_B 2FAC_B 2K94_A 1ACP_A ....
Probab=32.66 E-value=11 Score=23.19 Aligned_cols=42 Identities=21% Similarity=0.312 Sum_probs=30.3
Q ss_pred HHHHHHhcCCCCHHHHHHHHHHHhCCCCHHHHHHHHHHHHhCCC
Q 040572 86 FHMSNILDTGLDRHTLSVLIALCDLGVNPEALAAVVKELQREPS 129 (142)
Q Consensus 86 ~EIS~LLNTGLDReTLsICI~LcE~GVNPEALA~VIKELRrE~~ 129 (142)
.-++++++ ++.+.+..--.|.+.|++.=.+..++..|+++-.
T Consensus 5 ~~~~~~l~--~~~~~i~~~~~~~~lG~DSl~~~~l~~~l~~~~g 46 (67)
T PF00550_consen 5 EIIAEVLG--VDPEEIDPDTDFFDLGLDSLDAIELVSELEEEFG 46 (67)
T ss_dssp HHHHHHHT--SSGGCTSTTSBTTTTTSSHHHHHHHHHHHHHHHT
T ss_pred HHHHHHHC--cCHhhCCCCCCHHHhCCchHHHHHHHHHHHHHHc
Confidence 33455553 5555555666778999999999999999988743
No 85
>PF00782 DSPc: Dual specificity phosphatase, catalytic domain; InterPro: IPR000340 Protein tyrosine (pTyr) phosphorylation is a common post-translational modification which can create novel recognition motifs for protein interactions and cellular localisation, affect protein stability, and regulate enzyme activity. Consequently, maintaining an appropriate level of protein tyrosine phosphorylation is essential for many cellular functions. Tyrosine-specific protein phosphatases (PTPase; 3.1.3.48 from EC) catalyse the removal of a phosphate group attached to a tyrosine residue, using a cysteinyl-phosphate enzyme intermediate. These enzymes are key regulatory components in signal transduction pathways (such as the MAP kinase pathway) and cell cycle control, and are important in the control of cell growth, proliferation, differentiation and transformation [, ]. The PTP superfamily can be divided into four subfamilies []: (1) pTyr-specific phosphatases (2) dual specificity phosphatases (dTyr and dSer/dThr) (3) Cdc25 phosphatases (dTyr and/or dThr) (4) LMW (low molecular weight) phosphatases Based on their cellular localisation, PTPases are also classified as: Receptor-like, which are transmembrane receptors that contain PTPase domains [] Non-receptor (intracellular) PTPases [] All PTPases carry the highly conserved active site motif C(X)5R (PTP signature motif), employ a common catalytic mechanism, and share a similar core structure made of a central parallel beta-sheet with flanking alpha-helices containing a beta-loop-alpha-loop that encompasses the PTP signature motif []. Functional diversity between PTPases is endowed by regulatory domains and subunits. This entry represents dual specificity protein-tyrosine phosphatases. Ser/Thr and Tyr dual specificity phosphatases are a group of enzymes with both Ser/Thr (3.1.3.16 from EC) and tyrosine specific protein phosphatase (3.1.3.48 from EC) activity able to remove both the serine/threonine or tyrosine-bound phosphate group from a wide range of phosphoproteins, including a number of enzymes which have been phosphorylated under the action of a kinase. Dual specificity protein phosphatases (DSPs) regulate mitogenic signal transduction and control the cell cycle. The crystal structure of a human DSP, vaccinia H1-related phosphatase (or VHR), has been determined at 2.1 angstrom resolution []. A shallow active site pocket in VHR allows for the hydrolysis of phosphorylated serine, threonine, or tyrosine protein residues, whereas the deeper active site of protein tyrosine phosphatases (PTPs) restricts substrate specificity to only phosphotyrosine. Positively charged crevices near the active site may explain the enzyme's preference for substrates with two phosphorylated residues. The VHR structure defines a conserved structural scaffold for both DSPs and PTPs. A "recognition region" connecting helix alpha1 to strand beta1, may determine differences in substrate specificity between VHR, the PTPs, and other DSPs. These proteins may also have inactive phosphatase domains, and dependent on the domain composition this loss of catalytic activity has different effects on protein function. Inactive single domain phosphatases can still specifically bind substrates, and protect again dephosphorylation, while the inactive domains of tandem phosphatases can be further subdivided into two classes. Those which bind phosphorylated tyrosine residues may recruit multi-phosphorylated substrates for the adjacent active domains and are more conserved, while the other class have accumulated several variable amino acid substitutions and have a complete loss of tyrosine binding capability. The second class shows a release of evolutionary constraint for the sites around the catalytic centre, which emphasises a difference in function from the first group. There is a region of higher conservation common to both classes, suggesting a new regulatory centre [].; GO: 0008138 protein tyrosine/serine/threonine phosphatase activity, 0006470 protein dephosphorylation; PDB: 2G6Z_A 1MKP_A 1YZ4_A 2P4D_A 1M3G_A 1ZZW_A 2OUD_A 2HXP_A 3LJ8_A 1OHD_A ....
Probab=32.64 E-value=82 Score=21.60 Aligned_cols=60 Identities=15% Similarity=0.179 Sum_probs=41.2
Q ss_pred cCCCCHHHHHHHHHHHHHHHHHHH-----HhcC--CCCHHHHHHHHHHHh-CCCCHHHHHHHHHHHHh
Q 040572 67 VDDMDPEAARTARESLDLAFHMSN-----ILDT--GLDRHTLSVLIALCD-LGVNPEALAAVVKELQR 126 (142)
Q Consensus 67 ~~~md~d~~~aArEtLDiL~EIS~-----LLNT--GLDReTLsICI~LcE-~GVNPEALA~VIKELRr 126 (142)
.|.+.......-.++++.++..-+ |+.| |++|...-+|.-|+. .|++++.=-+.|+..|-
T Consensus 48 ~D~~~~~~~~~~~~~~~~i~~~~~~~~~VlVHC~~G~~RS~~v~~ayLm~~~~~~~~~A~~~v~~~rp 115 (133)
T PF00782_consen 48 DDDPEEPILEHLDQAVEFIENAISEGGKVLVHCKAGLSRSGAVAAAYLMKKNGMSLEEAIEYVRSRRP 115 (133)
T ss_dssp ESSTTSHGGGGHHHHHHHHHHHHHTTSEEEEEESSSSSHHHHHHHHHHHHHHTSSHHHHHHHHHHHST
T ss_pred cCCCCcchHHHHHHHHHhhhhhhcccceeEEEeCCCcccchHHHHHHHHHHcCCCHHHHHHHHHHHCC
Confidence 344555555666667777776432 3444 999999888887777 79999866667777773
No 86
>cd00383 trans_reg_C Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and a response regulator. The former autophosphorylates in a histidine residue on detecting an external stimulus. The phosphate is then transferred to an invariant aspartate residue in a highly conserved receiver domain of the response regulator. Phosphorylation activates a variable effector domain of the response regulator, which triggers the cellular response. The C-terminal effector domain contains DNA and RNA polymerase binding sites. Several dimers or monomers bind head to tail to small tandem repeats upstream of the genes. The RNA polymerase binding sites interact with the alpha or sigma subunite of RNA polymerase.
Probab=32.57 E-value=1e+02 Score=19.86 Aligned_cols=52 Identities=13% Similarity=0.122 Sum_probs=37.4
Q ss_pred HHHHHHHHHHHHHhcCCCCHHHHHHHHHHHhCCCCHHHHHHHHHHHHhCCCC
Q 040572 79 RESLDLAFHMSNILDTGLDRHTLSVLIALCDLGVNPEALAAVVKELQREPSP 130 (142)
Q Consensus 79 rEtLDiL~EIS~LLNTGLDReTLsICI~LcE~GVNPEALA~VIKELRrE~~a 130 (142)
..-+.+|.-+..=-+..++++.|.-.+-=-+..++..+|...|..||+....
T Consensus 26 ~~e~~lL~~L~~~~~~~vs~~~l~~~lw~~~~~~~~~~l~~~I~rLRkkl~~ 77 (95)
T cd00383 26 PKEFELLELLARNPGRVLSREQLLEAVWGDDYDVDDRTVDVHISRLRKKLED 77 (95)
T ss_pred HHHHHHHHHHHhCCCCcCCHHHHHHHhcCCCCCCCcccHHHHHHHHHHHhcc
Confidence 3445666666666677899998876664222236788999999999998865
No 87
>cd04371 DEP DEP domain, named after Dishevelled, Egl-10, and Pleckstrin, where this domain was first discovered. The function of this domain is still not clear, but it is believed to be important for the membrane association of the signaling proteins in which it is present. New studies show that the DEP domain of Sst2, a yeast RGS protein is necessary and sufficient for receptor interaction.
Probab=32.50 E-value=79 Score=20.32 Aligned_cols=32 Identities=19% Similarity=0.196 Sum_probs=21.2
Q ss_pred HHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHhCCC
Q 040572 78 ARESLDLAFHMSNILDTGLDRHTLSVLIALCDLGV 112 (142)
Q Consensus 78 ArEtLDiL~EIS~LLNTGLDReTLsICI~LcE~GV 112 (142)
..|++|-|.+. .+..--.++..+|-.|++.|+
T Consensus 31 G~e~v~WL~~~---~~~~~r~ea~~~~~~ll~~g~ 62 (81)
T cd04371 31 GSELVDWLLDN---LEAITREEAVELGQALLKHGL 62 (81)
T ss_pred cHHHHHHHHHh---CCCCCHHHHHHHHHHHHHCCC
Confidence 34555555444 343445678999999999996
No 88
>PLN02738 carotene beta-ring hydroxylase
Probab=32.25 E-value=1e+02 Score=28.28 Aligned_cols=47 Identities=15% Similarity=0.191 Sum_probs=39.7
Q ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHHhCCCCHHHHHHHHHHHHhCCC
Q 040572 83 DLAFHMSNILDTGLDRHTLSVLIALCDLGVNPEALAAVVKELQREPS 129 (142)
Q Consensus 83 DiL~EIS~LLNTGLDReTLsICI~LcE~GVNPEALA~VIKELRrE~~ 129 (142)
++..++-.++-.|-|-.+-.++..|....-||+.+..+-.||..-..
T Consensus 391 ~L~~e~~~ll~AG~eTTA~tLt~~l~~L~~~Pevq~kLreEl~~v~~ 437 (633)
T PLN02738 391 QLRDDLMTMLIAGHETSAAVLTWTFYLLSKEPSVVAKLQEEVDSVLG 437 (633)
T ss_pred HHHHHHHHHHhcCCccHHHHHHHHHHHHHhCHHHHHHHHHHHHHhcC
Confidence 46677788888999999888888888889999999999999887543
No 89
>PRK00188 trpD anthranilate phosphoribosyltransferase; Provisional
Probab=31.75 E-value=1.8e+02 Score=24.67 Aligned_cols=43 Identities=19% Similarity=0.314 Sum_probs=34.6
Q ss_pred HHHHhcCCCCHHHH-HHHHHHHhCCCCHHHHHHHHHHHHhCCCC
Q 040572 88 MSNILDTGLDRHTL-SVLIALCDLGVNPEALAAVVKELQREPSP 130 (142)
Q Consensus 88 IS~LLNTGLDReTL-sICI~LcE~GVNPEALA~VIKELRrE~~a 130 (142)
|..||+-.++...+ ++++.|.-.|..|+.|+..++-+|+-...
T Consensus 25 ~~~il~g~~~~~q~~AfL~alr~kget~~El~g~~~a~~~~~~~ 68 (339)
T PRK00188 25 MDAIMSGEATPAQIAAFLTALRVKGETVDEIAGAARAMREHAVP 68 (339)
T ss_pred HHHHHcCCCCHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHhCCc
Confidence 45567777776555 67788999999999999999999987653
No 90
>PRK14137 recX recombination regulator RecX; Provisional
Probab=30.98 E-value=2.4e+02 Score=22.63 Aligned_cols=48 Identities=6% Similarity=-0.071 Sum_probs=34.8
Q ss_pred HHHHHHHHHHhcCCCCHHHHHHHHHHHhCCCCHHHHHHHHHHHHhCCC
Q 040572 82 LDLAFHMSNILDTGLDRHTLSVLIALCDLGVNPEALAAVVKELQREPS 129 (142)
Q Consensus 82 LDiL~EIS~LLNTGLDReTLsICI~LcE~GVNPEALA~VIKELRrE~~ 129 (142)
++.++..+--+=+.=++..-.+.-.|...|++++.+..||..|.....
T Consensus 39 ~~~~~~~Al~~Ls~R~rS~~ELr~KL~~kg~~~e~Ie~vI~rL~e~gy 86 (195)
T PRK14137 39 REALLAYAFRALAARAMTAAELRAKLERRSEDEALVTEVLERVQELGY 86 (195)
T ss_pred HHHHHHHHHHHHhcchhhHHHHHHHHHhcCCCHHHHHHHHHHHHHcCC
Confidence 333333333333455788888889999999999999999999987654
No 91
>TIGR01791 CM_archaeal chorismate mutase, archaeal type. This model represents a clade of archaeal chorismate mutases. Chorismate mutase catalyzes the conversion of chorismate into prephenate which is subsequently converted into either phenylalanine or tyrosine. In Sulfolobus this gene is found as a fusion with prephenate dehydrogenase (although the non-TIGR annotation contains a typographical error indicating it as a dehydratase) which is the next enzyme in the tyrosine biosynthesis pathway. The Archaeoglobus gene contains an N-terminal prephenate dehydrogenase domain and a C-terminal prephenate dehydratase domain followed by a regulatory amino acid-binding ACT domain. The Thermoplasma volcanium gene is adjacent to prephenate dehydratase.
Probab=30.76 E-value=66 Score=21.66 Aligned_cols=61 Identities=18% Similarity=0.314 Sum_probs=41.8
Q ss_pred cCCCCHHHHHHHHHHHHHHHHHHHHhcC-CC---CH----HHHHHHHHHHh-CCCCHHHHHHHHHHHHhC
Q 040572 67 VDDMDPEAARTARESLDLAFHMSNILDT-GL---DR----HTLSVLIALCD-LGVNPEALAAVVKELQRE 127 (142)
Q Consensus 67 ~~~md~d~~~aArEtLDiL~EIS~LLNT-GL---DR----eTLsICI~LcE-~GVNPEALA~VIKELRrE 127 (142)
+|..|.+-+.--.+-+.++.+|+.+=.. |+ |. +-+.-+.++.+ .|++|+.+..+.+.|-..
T Consensus 8 Id~iD~~i~~Ll~~R~~l~~~i~~~K~~~g~~i~d~~RE~~v~~~~~~~~~~~~l~~~~i~~if~~i~~~ 77 (83)
T TIGR01791 8 IEEIDKSILDLIEKRIKIARKIGEIKHNNGLPITDEEREERVIERLRNTARNLGLDVLKLKEIFEILMSL 77 (83)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCChHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHH
Confidence 5667777777888888888888877543 43 22 22444555554 789999988888777543
No 92
>PLN02394 trans-cinnamate 4-monooxygenase
Probab=30.74 E-value=1.1e+02 Score=25.75 Aligned_cols=44 Identities=18% Similarity=0.220 Sum_probs=34.7
Q ss_pred HHHHHHHhcCCCCHHHHHHHHHHHhCCCCHHHHHHHHHHHHhCC
Q 040572 85 AFHMSNILDTGLDRHTLSVLIALCDLGVNPEALAAVVKELQREP 128 (142)
Q Consensus 85 L~EIS~LLNTGLDReTLsICI~LcE~GVNPEALA~VIKELRrE~ 128 (142)
+..+..++=.|.|-.+-.++..|....-||+....+.+||+.-.
T Consensus 295 ~~~~~~~~~AG~dTTa~tl~~~l~~L~~~P~vq~kl~~Ei~~v~ 338 (503)
T PLN02394 295 LYIVENINVAAIETTLWSIEWGIAELVNHPEIQKKLRDELDTVL 338 (503)
T ss_pred HHHHHHHHHhchhhHHHHHHHHHHHHHcCHHHHHHHHHHHHHHh
Confidence 44455566678888888888888888889999999999998654
No 93
>PF13545 HTH_Crp_2: Crp-like helix-turn-helix domain; PDB: 3LA2_A 3LA3_B 3LA7_A 3B02_A 3E97_A 2H6C_B 1OMI_A 2BGC_H 2BEO_A 2GAU_A ....
Probab=30.00 E-value=63 Score=20.38 Aligned_cols=30 Identities=27% Similarity=0.478 Sum_probs=19.7
Q ss_pred CCCCHHHHHHHHHHHhCCCCHHHHHHHHHHHHhCC
Q 040572 94 TGLDRHTLSVLIALCDLGVNPEALAAVVKELQREP 128 (142)
Q Consensus 94 TGLDReTLsICI~LcE~GVNPEALA~VIKELRrE~ 128 (142)
..++++-|+-. .|++.+.+..++++|+++.
T Consensus 27 ~~lt~~~iA~~-----~g~sr~tv~r~l~~l~~~g 56 (76)
T PF13545_consen 27 LPLTQEEIADM-----LGVSRETVSRILKRLKDEG 56 (76)
T ss_dssp EESSHHHHHHH-----HTSCHHHHHHHHHHHHHTT
T ss_pred ecCCHHHHHHH-----HCCCHHHHHHHHHHHHHCC
Confidence 44556665544 3777777777777777765
No 94
>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda. Members of this protein family are Hda (Homologous to DnaA). These proteins are about half the length of DnaA and homologous over length of Hda. In the model species Escherichia coli, the initiation of DNA replication requires DnaA bound to ATP rather than ADP; Hda helps facilitate the conversion of DnaA-ATP to DnaA-ADP.
Probab=29.66 E-value=2.3e+02 Score=20.93 Aligned_cols=46 Identities=15% Similarity=0.114 Sum_probs=36.1
Q ss_pred HHHHHHHHHHHHHhcCCCCHHHHHHHHHHHhCCCCHHHHHHHHHHHHh
Q 040572 79 RESLDLAFHMSNILDTGLDRHTLSVLIALCDLGVNPEALAAVVKELQR 126 (142)
Q Consensus 79 rEtLDiL~EIS~LLNTGLDReTLsICI~LcE~GVNPEALA~VIKELRr 126 (142)
.+...+|..++.-.+-+++.+.+..+.+ ..+=|+..|-++|+++..
T Consensus 162 ~e~~~~l~~~~~~~~~~~~~~~l~~L~~--~~~gn~r~L~~~l~~~~~ 207 (226)
T TIGR03420 162 EEKIAALQSRAARRGLQLPDEVADYLLR--HGSRDMGSLMALLDALDR 207 (226)
T ss_pred HHHHHHHHHHHHHcCCCCCHHHHHHHHH--hccCCHHHHHHHHHHHHH
Confidence 3445556555555567899999999999 488899999999999875
No 95
>TIGR01245 trpD anthranilate phosphoribosyltransferase. In many widely different species, including E. coli, Thermotoga maritima, and Archaeoglobus fulgidus, this enzymatic domain (anthranilate phosphoribosyltransferase) is found C-terminal to glutamine amidotransferase; the fusion protein is designated anthranilate synthase component II (EC 4.1.3.27)
Probab=29.38 E-value=2.1e+02 Score=24.19 Aligned_cols=43 Identities=21% Similarity=0.345 Sum_probs=34.7
Q ss_pred HHHHhcCCCCHHHH-HHHHHHHhCCCCHHHHHHHHHHHHhCCCC
Q 040572 88 MSNILDTGLDRHTL-SVLIALCDLGVNPEALAAVVKELQREPSP 130 (142)
Q Consensus 88 IS~LLNTGLDReTL-sICI~LcE~GVNPEALA~VIKELRrE~~a 130 (142)
|..||+-.++...+ ++++.|--.|.+++.|+..++-+|.....
T Consensus 19 ~~~il~g~~~~~q~~AfL~alr~kget~~Elag~~~a~~~~~~~ 62 (330)
T TIGR01245 19 MKEIMSGEASPAQIAAILAALRIKGETPEEITGFAKAMREHAVK 62 (330)
T ss_pred HHHHHcCCCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhCCC
Confidence 45667777776555 67788889999999999999999977754
No 96
>TIGR00064 ftsY signal recognition particle-docking protein FtsY. There is a weak division between FtsY and SRP54; both are GTPases. In E.coli, ftsY is an essential gene located in an operon with cell division genes ftsE and ftsX, but its apparent function is as the signal recognition particle docking protein.
Probab=29.36 E-value=66 Score=26.42 Aligned_cols=25 Identities=20% Similarity=0.317 Sum_probs=16.2
Q ss_pred HHHHHHhCCCCHHHHHHHHHHHHhC
Q 040572 103 VLIALCDLGVNPEALAAVVKELQRE 127 (142)
Q Consensus 103 ICI~LcE~GVNPEALA~VIKELRrE 127 (142)
+...|+++||+++.--+++.+++++
T Consensus 10 l~~~L~~~dv~~~~~~~i~~~~~~~ 34 (272)
T TIGR00064 10 LEEILLESDVGYEVVEKIIEALKKE 34 (272)
T ss_pred HHHHHHHCCCCHHHHHHHHHHHHHH
Confidence 5566677777776666666666554
No 97
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=29.07 E-value=1.6e+02 Score=19.75 Aligned_cols=42 Identities=24% Similarity=0.423 Sum_probs=26.8
Q ss_pred HHHHHHHHHHh-cCCCCHHHHHHHHHHHhCCCCHHHHHHHHHHHHhCC
Q 040572 82 LDLAFHMSNIL-DTGLDRHTLSVLIALCDLGVNPEALAAVVKELQREP 128 (142)
Q Consensus 82 LDiL~EIS~LL-NTGLDReTLsICI~LcE~GVNPEALA~VIKELRrE~ 128 (142)
++|+++|=..+ +.|....-|. ...|+|...+...+++|.+..
T Consensus 5 ~~Ii~~IL~~l~~~~~~~t~i~-----~~~~L~~~~~~~yL~~L~~~g 47 (77)
T PF14947_consen 5 LEIIFDILKILSKGGAKKTEIM-----YKANLNYSTLKKYLKELEEKG 47 (77)
T ss_dssp THHHHHHHHHH-TT-B-HHHHH-----TTST--HHHHHHHHHHHHHTT
T ss_pred HHHHHHHHHHHHcCCCCHHHHH-----HHhCcCHHHHHHHHHHHHHCc
Confidence 45556655555 7777776654 567889999999999887654
No 98
>COG0140 HisI Phosphoribosyl-ATP pyrophosphohydrolase [Amino acid transport and metabolism]
Probab=29.03 E-value=1.7e+02 Score=21.70 Aligned_cols=31 Identities=19% Similarity=0.368 Sum_probs=22.7
Q ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHHhCCCCHHHHHHHH
Q 040572 83 DLAFHMSNILDTGLDRHTLSVLIALCDLGVNPEALAAVV 121 (142)
Q Consensus 83 DiL~EIS~LLNTGLDReTLsICI~LcE~GVNPEALA~VI 121 (142)
++++|+++|| .-++|-|...||+++.+....
T Consensus 54 ~l~~E~ADLl--------YH~lVlL~~~gv~l~dV~~eL 84 (92)
T COG0140 54 ELVSEAADLL--------YHLLVLLAAQGLSLEDVLREL 84 (92)
T ss_pred HHHHHHHHHH--------HHHHHHHHHcCCCHHHHHHHH
Confidence 4778888887 346788889999987655443
No 99
>PF04566 RNA_pol_Rpb2_4: RNA polymerase Rpb2, domain 4; InterPro: IPR007646 RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial and chloroplast polymerases). Domain 4, is also known as the external 2 domain [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3S17_B 1I6H_B 4A3B_B 3K1F_B 4A3I_B 1TWA_B 3S14_B 3S15_B 2NVX_B 3M3Y_B ....
Probab=28.84 E-value=59 Score=21.90 Aligned_cols=18 Identities=28% Similarity=0.534 Sum_probs=16.4
Q ss_pred CHHHHHHHHHHHHhCCCC
Q 040572 113 NPEALAAVVKELQREPSP 130 (142)
Q Consensus 113 NPEALA~VIKELRrE~~a 130 (142)
+|+.|+..++++|+...-
T Consensus 13 ~p~~l~~~lr~~RR~g~i 30 (63)
T PF04566_consen 13 DPEELVKTLRNLRRSGKI 30 (63)
T ss_dssp SHHHHHHHHHHHHHTTSS
T ss_pred CHHHHHHHHHHHhhccCC
Confidence 899999999999998764
No 100
>smart00657 RPOL4c DNA-directed RNA-polymerase II subunit.
Probab=28.59 E-value=2.1e+02 Score=20.85 Aligned_cols=58 Identities=17% Similarity=0.244 Sum_probs=43.2
Q ss_pred CCCHHHHHHHHHHHHHH----HHHHHHhcC-CCCHHHHHHHHHHHhCCCCHHHHHHHHHHHHh
Q 040572 69 DMDPEAARTARESLDLA----FHMSNILDT-GLDRHTLSVLIALCDLGVNPEALAAVVKELQR 126 (142)
Q Consensus 69 ~md~d~~~aArEtLDiL----~EIS~LLNT-GLDReTLsICI~LcE~GVNPEALA~VIKELRr 126 (142)
..+++.+.+-.+.|.-. +||.+|.|. ==+-+.+..||..|+.-.+-+.|..++.+|.+
T Consensus 51 ~~~~e~i~~~~~~L~~~~L~k~E~~~i~Nl~P~s~~E~~~lI~sl~~r~~ee~l~~iL~~i~~ 113 (118)
T smart00657 51 FKNREIVRAVRTLLKSKKLHKFEIAQLGNLRPETAEEAQLLIPSLEERIDEEELEELLDDLSS 113 (118)
T ss_pred CCCHHHHHHHHHHHHhcCCCHHHHHHHhCCCCCCHHHHHHHhhhhhccCCHHHHHHHHHHHHH
Confidence 45677777777766642 567778877 34667888899999888888888888887765
No 101
>cd02436 Nodulin-21 Nodulin-21. Nodulin-21: This is a family of proteins that may be unique to certain plants. The family member in soybean is found to be nodule-specific and is abundant during nodule development. The proteins of this family thus may play a role in symbiotic nitrogen fixation.
Probab=28.17 E-value=47 Score=26.69 Aligned_cols=32 Identities=6% Similarity=-0.076 Sum_probs=22.4
Q ss_pred CHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHhCCCCHHHHH
Q 040572 71 DPEAARTARESLDLAFHMSNILDTGLDRHTLSVLIALCDLGVNPEALA 118 (142)
Q Consensus 71 d~d~~~aArEtLDiL~EIS~LLNTGLDReTLsICI~LcE~GVNPEALA 118 (142)
|.+++.-.+|.-++ +-|||+++ |.|++++.++
T Consensus 62 d~e~a~i~~e~~el--------~rGl~~~l--------elgi~~~~~~ 93 (152)
T cd02436 62 RRPRAARCLRGRNR--------ARGPAPDS--------EPEGLRRQAP 93 (152)
T ss_pred chHHHHHHHHHHHh--------hcCCChhh--------hcCCCccccC
Confidence 45555555555544 88999998 8999887643
No 102
>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulfovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis sp. (strain PCC 6803) hypothetical protein slr0846. These are small proteins of 12 to 18kDa which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.; PDB: 3T8T_A 3T8R_A 3K69_A 3LWF_C 1XD7_A 2Y75_E 1YLF_C.
Probab=28.04 E-value=1.9e+02 Score=19.26 Aligned_cols=48 Identities=15% Similarity=0.300 Sum_probs=33.3
Q ss_pred HHHHHHHHHHHHHHhcCC-CCHHHHHHHHHHHhCCCCHHHHHHHHHHHHhCCCC
Q 040572 78 ARESLDLAFHMSNILDTG-LDRHTLSVLIALCDLGVNPEALAAVVKELQREPSP 130 (142)
Q Consensus 78 ArEtLDiL~EIS~LLNTG-LDReTLsICI~LcE~GVNPEALA~VIKELRrE~~a 130 (142)
.+-++.++..|+.-=+-+ ++-+.|+- ..|++|..|..++..|++..--
T Consensus 7 ~~~Al~~l~~la~~~~~~~~s~~eiA~-----~~~i~~~~l~kil~~L~~~Gli 55 (83)
T PF02082_consen 7 TDYALRILLYLARHPDGKPVSSKEIAE-----RLGISPSYLRKILQKLKKAGLI 55 (83)
T ss_dssp HHHHHHHHHHHHCTTTSC-BEHHHHHH-----HHTS-HHHHHHHHHHHHHTTSE
T ss_pred HHHHHHHHHHHHhCCCCCCCCHHHHHH-----HHCcCHHHHHHHHHHHhhCCee
Confidence 445667777776554444 66666554 5689999999999999997643
No 103
>TIGR02054 MerD mercuric resistence transcriptional repressor protein MerD. This model represents a transcriptional repressor protein of the MerR family (pfam00376) whose expression is regulated by the mercury-sensitive transcriptional activator, MerR. MerD has been shown to repress the transcription of the mer operon.
Probab=27.63 E-value=2.6e+02 Score=20.80 Aligned_cols=32 Identities=19% Similarity=0.195 Sum_probs=28.3
Q ss_pred HHHHHHHHHHHHhcCCCCHHHHHHHHHHHhCC
Q 040572 80 ESLDLAFHMSNILDTGLDRHTLSVLIALCDLG 111 (142)
Q Consensus 80 EtLDiL~EIS~LLNTGLDReTLsICI~LcE~G 111 (142)
+.++.|.-|-.+-++|++-+.+.-++.+.+.|
T Consensus 45 ~~l~rL~~I~~lr~~G~~L~eI~~ll~~~~~~ 76 (120)
T TIGR02054 45 ASLQRLRFVRAAFEAGIGLGELARLCRALDAA 76 (120)
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHHhhccC
Confidence 66778888999999999999999999998876
No 104
>PRK02759 bifunctional phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-ATP pyrophosphatase protein; Reviewed
Probab=27.54 E-value=1.5e+02 Score=24.70 Aligned_cols=30 Identities=23% Similarity=0.402 Sum_probs=22.6
Q ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHHhCCCCHHHHHHH
Q 040572 83 DLAFHMSNILDTGLDRHTLSVLIALCDLGVNPEALAAV 120 (142)
Q Consensus 83 DiL~EIS~LLNTGLDReTLsICI~LcE~GVNPEALA~V 120 (142)
++++|+++|| .-++|-|-..||+|+.+..+
T Consensus 169 ~li~E~ADLl--------YHllVlL~~~gv~l~dV~~e 198 (203)
T PRK02759 169 ELINEAADLL--------YHLLVLLADQGLSLSDVIAE 198 (203)
T ss_pred HHHHHHHHHH--------HHHHHHHHHcCCCHHHHHHH
Confidence 3778888886 45788899999998765443
No 105
>PRK14970 DNA polymerase III subunits gamma and tau; Provisional
Probab=27.14 E-value=2.1e+02 Score=23.60 Aligned_cols=42 Identities=7% Similarity=0.119 Sum_probs=28.8
Q ss_pred HHHHHHHHhcCCCCHHHHHHHHHHHhCCCCHHHHHH-HHHHHH
Q 040572 84 LAFHMSNILDTGLDRHTLSVLIALCDLGVNPEALAA-VVKELQ 125 (142)
Q Consensus 84 iL~EIS~LLNTGLDReTLsICI~LcE~GVNPEALA~-VIKELR 125 (142)
.+++|.+.+-.|=-.+.+.++-.|+..|.+|..+.. ++..+|
T Consensus 237 ~if~l~~ai~~~~~~~a~~~~~~l~~~~~~~~~il~~l~~~fr 279 (367)
T PRK14970 237 TYINVTDLILENKIPELLLAFNEILRKGFDGHHFIAGLASHFR 279 (367)
T ss_pred HHHHHHHHHHcCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHH
Confidence 455555666566566788888888999999998544 434444
No 106
>PF01535 PPR: PPR repeat; InterPro: IPR002885 This entry represents the PPR repeat. Pentatricopeptide repeat (PPR) proteins are characterised by tandem repeats of a degenerate 35 amino acid motif []. Most of PPR proteins have roles in mitochondria or plastid []. PPR repeats were discovered while screening Arabidopsis proteins for those predicted to be targeted to mitochondria or chloroplast [, ]. Some of these proteins have been shown to play a role in post-transcriptional processes within organelles and they are thought to be sequence-specific RNA-binding proteins [, , ]. Plant genomes have between one hundred to five hundred PPR genes per genome whereas non-plant genomes encode two to six PPR proteins. Although no PPR structures are yet known, the motif is predicted to fold into a helix-turn-helix structure similar to those found in the tetratricopeptide repeat (TPR) family (see PDOC50005 from PROSITEDOC) []. The plant PPR protein family has been divided in two subfamilies on the basis of their motif content and organisation [, ]. Examples of PPR repeat-containing proteins include PET309 P32522 from SWISSPROT, which may be involved in RNA stabilisation [], and crp1, which is involved in RNA processing []. The repeat is associated with a predicted plant protein O49549 from SWISSPROT that has a domain organisation similar to the human BRCA1 protein.
Probab=27.11 E-value=87 Score=15.96 Aligned_cols=25 Identities=20% Similarity=0.286 Sum_probs=14.2
Q ss_pred HHHHhcCCCCHHHHHHHHHHHhCCC
Q 040572 88 MSNILDTGLDRHTLSVLIALCDLGV 112 (142)
Q Consensus 88 IS~LLNTGLDReTLsICI~LcE~GV 112 (142)
|+.+-..|.-.+++.+.-++.+.|+
T Consensus 7 i~~~~~~~~~~~a~~~~~~M~~~g~ 31 (31)
T PF01535_consen 7 ISGYCKMGQFEEALEVFDEMRERGI 31 (31)
T ss_pred HHHHHccchHHHHHHHHHHHhHCcC
Confidence 3444455555666666666666654
No 107
>PF14069 SpoVIF: Stage VI sporulation protein F
Probab=27.07 E-value=2e+02 Score=20.69 Aligned_cols=55 Identities=9% Similarity=0.189 Sum_probs=42.3
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHhC-CCCHHHHHHHHHHHH
Q 040572 70 MDPEAARTARESLDLAFHMSNILDTGLDRHTLSVLIALCDL-GVNPEALAAVVKELQ 125 (142)
Q Consensus 70 md~d~~~aArEtLDiL~EIS~LLNTGLDReTLsICI~LcE~-GVNPEALA~VIKELR 125 (142)
......+.-...=+++..+|+++|--+++++..-+|..+-+ |+ |.-+.+++|.+-
T Consensus 22 v~~adlqdE~~vR~lIk~vs~~an~~Vs~~~ed~IV~~I~~~~~-p~d~~~l~Km~~ 77 (79)
T PF14069_consen 22 VQKADLQDEKKVRQLIKQVSQIANKPVSKEQEDQIVQAIINQKI-PNDMNHLMKMMN 77 (79)
T ss_pred cchhhcccHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhCCC-CcCHHHHHHHHc
Confidence 33344444556667999999999999999999999887655 56 888888887654
No 108
>PRK10701 DNA-binding transcriptional regulator RstA; Provisional
Probab=26.84 E-value=86 Score=22.90 Aligned_cols=57 Identities=11% Similarity=0.131 Sum_probs=43.8
Q ss_pred HHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHhCCCCHHHHHHHHHHHHhCCCC
Q 040572 74 AARTARESLDLAFHMSNILDTGLDRHTLSVLIALCDLGVNPEALAAVVKELQREPSP 130 (142)
Q Consensus 74 ~~~aArEtLDiL~EIS~LLNTGLDReTLsICI~LcE~GVNPEALA~VIKELRrE~~a 130 (142)
.+.-...-+++|..+..=-+-=++|+.|.-.|-=-+...+...|-..|+.||+....
T Consensus 159 ~i~Lt~~E~~lL~~l~~~~~~v~sr~~l~~~vw~~~~~~~~~~i~~~i~rlR~kl~~ 215 (240)
T PRK10701 159 EISLSTADFDLLWELATHAGQIMDRDALLKNLRGVSYDGLDRSVDVAISRLRKKLLD 215 (240)
T ss_pred EeecCHHHHHHHHHHHhCCCccCcHHHHHHHhcCCCCCCCCcCHHHHHHHHHHhccc
Confidence 344566678888888887777799999887775334445778999999999998864
No 109
>PLN03141 3-epi-6-deoxocathasterone 23-monooxygenase; Provisional
Probab=26.81 E-value=1.4e+02 Score=24.97 Aligned_cols=44 Identities=20% Similarity=0.197 Sum_probs=31.1
Q ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHHhCCCCHHHHHHHHHHHHh
Q 040572 83 DLAFHMSNILDTGLDRHTLSVLIALCDLGVNPEALAAVVKELQR 126 (142)
Q Consensus 83 DiL~EIS~LLNTGLDReTLsICI~LcE~GVNPEALA~VIKELRr 126 (142)
++++.+-.|+-.|.|-.+..++..+...--||+.+..+..|+.+
T Consensus 251 ~i~~~~~~ll~Ag~dTts~tl~~~~~~L~~~P~v~~kl~~Ei~~ 294 (452)
T PLN03141 251 LISDNMIDMMIPGEDSVPVLMTLAVKFLSDCPVALQQLTEENMK 294 (452)
T ss_pred HHHHHHHHHHHhcchhHHHHHHHHHHHHHhChHHHHHHHHHHHH
Confidence 45666777777787777666665555555689888888888754
No 110
>PF04137 ERO1: Endoplasmic Reticulum Oxidoreductin 1 (ERO1); InterPro: IPR007266 Members of this family are required for the formation of disulphide bonds in the endoplasmic reticulum [, ].; GO: 0016671 oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor, 0050660 flavin adenine dinucleotide binding, 0006467 protein thiol-disulfide exchange, 0055114 oxidation-reduction process, 0005789 endoplasmic reticulum membrane; PDB: 1RQ1_A 1RP4_A 3NVJ_A 3M31_A 3AHR_A 3AHQ_A.
Probab=26.78 E-value=2.2e+02 Score=25.21 Aligned_cols=62 Identities=24% Similarity=0.329 Sum_probs=42.9
Q ss_pred cccccCCCCHHHHHHHHHHHHHHHHHHHHhcC-CCCH-------------HHHHHHHHHHh----CCCCHHHHHHHHHHH
Q 040572 63 ESRLVDDMDPEAARTARESLDLAFHMSNILDT-GLDR-------------HTLSVLIALCD----LGVNPEALAAVVKEL 124 (142)
Q Consensus 63 ~~~~~~~md~d~~~aArEtLDiL~EIS~LLNT-GLDR-------------eTLsICI~LcE----~GVNPEALA~VIKEL 124 (142)
|+.+.... ++..-.+|--...+.||.|+|| |-|| .+|.|+.+.-+ .-.+...|.+.|.-+
T Consensus 269 E~~lf~~~--~~~~Lk~efr~~F~NIs~IMDCV~CeKCRLWGKlQt~GlgTALKILf~~~~~~~~~~L~R~E~VAL~Nt~ 346 (357)
T PF04137_consen 269 ESSLFKGD--EAPQLKEEFRQHFRNISRIMDCVGCEKCRLWGKLQTQGLGTALKILFSDDEKQNPFKLQRNELVALFNTF 346 (357)
T ss_dssp TTTTTTTT--CHHHHHHHHHHHHHHHHHHHCC-SSHHHHHHHHHHHHHHHHHHHHHCHHHCHHCCCTSBHHHHHHHHHHH
T ss_pred HHHHcCCc--cHHHHHHHHHHHHhhHHHHHcCcccchheeechhhhhhHHHHHHHHhCccCcCCcCcccHHHHHHHHHHH
Confidence 44454443 3344445666889999999999 9998 67788877776 235667777777766
Q ss_pred Hh
Q 040572 125 QR 126 (142)
Q Consensus 125 Rr 126 (142)
.|
T Consensus 347 ~r 348 (357)
T PF04137_consen 347 GR 348 (357)
T ss_dssp HH
T ss_pred HH
Confidence 54
No 111
>TIGR00778 ahpD_dom alkylhydroperoxidase AhpD family core domain. Members of the family include the alkylhydroperoxidase AhpD of Mycobacterium tuberculosis, a macrophage infectivity potentiator peptide of Legionella pneumophila, and an uncharacterized peptide in the tetrachloroethene reductive dehalogenase operon of Dehalospirillum multivorans. We suggest that many peptides containing this domain may have alkylhydroperoxidase or related antioxidant activity.
Probab=26.73 E-value=1.5e+02 Score=17.62 Aligned_cols=34 Identities=21% Similarity=0.088 Sum_probs=21.8
Q ss_pred HHHHHhcCCCCHHHHHHHHHHHhCCCCHHHHHHHHH
Q 040572 87 HMSNILDTGLDRHTLSVLIALCDLGVNPEALAAVVK 122 (142)
Q Consensus 87 EIS~LLNTGLDReTLsICI~LcE~GVNPEALA~VIK 122 (142)
.+|...+| +-..-.-.-.+.+.|+.++.+.+++.
T Consensus 14 ~~s~~~~C--~yc~~~H~~~a~~~G~~~~ei~~v~~ 47 (50)
T TIGR00778 14 AVSQINGC--GYCLDAHTKLARKAGVTAEELAEALA 47 (50)
T ss_pred HHHHHcCC--HHHHHHHHHHHHHcCCCHHHHHHHHH
Confidence 44444444 33333444467788999999998875
No 112
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=26.64 E-value=1.9e+02 Score=18.83 Aligned_cols=40 Identities=15% Similarity=0.205 Sum_probs=24.3
Q ss_pred HHHHHHhcCCCCHHHHHHHHHHHhCCCCHHHHHHHHHHHHhCC
Q 040572 86 FHMSNILDTGLDRHTLSVLIALCDLGVNPEALAAVVKELQREP 128 (142)
Q Consensus 86 ~EIS~LLNTGLDReTLsICI~LcE~GVNPEALA~VIKELRrE~ 128 (142)
.+|+..+ |+++.|++-+++- ..||+|+.-..|.+-+++-.
T Consensus 4 ~~iA~~~--gvS~~TVSr~ln~-~~~v~~~t~~~i~~~~~~~g 43 (70)
T smart00354 4 KDVARLA--GVSKATVSRVLNG-NGRVSEETREKVLAAMEELG 43 (70)
T ss_pred HHHHHHH--CCCHHHHHHHHCC-CCCCCHHHHHHHHHHHHHhC
Confidence 3445443 8899998887653 34677776555555444443
No 113
>PF00486 Trans_reg_C: Transcriptional regulatory protein, C terminal; InterPro: IPR001867 Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions []. Some bacteria can contain up to as many as 200 two-component systems that need tight regulation to prevent unwanted cross-talk []. These pathways have been adapted to response to a wide variety of stimuli, including nutrients, cellular redox state, changes in osmolarity, quorum signals, antibiotics, and more []. Two-component systems are comprised of a sensor histidine kinase (HK) and its cognate response regulator (RR) []. The HK catalyses its own auto-phosphorylation followed by the transfer of the phosphoryl group to the receiver domain on RR; phosphorylation of the RR usually activates an attached output domain, which can then effect changes in cellular physiology, often by regulating gene expression. Some HK are bifunctional, catalysing both the phosphorylation and dephosphorylation of their cognate RR. The input stimuli can regulate either the kinase or phosphatase activity of the bifunctional HK. A variant of the two-component system is the phospho-relay system. Here a hybrid HK auto-phosphorylates and then transfers the phosphoryl group to an internal receiver domain, rather than to a separate RR protein. The phosphoryl group is then shuttled to histidine phosphotransferase (HPT) and subsequently to a terminal RR, which can evoke the desired response [, ]. This entry represents a domain that is almost always found associated with the response regulator receiver domain (see IPR001789 from INTERPRO). It may play a role in DNA binding [].; GO: 0000156 two-component response regulator activity, 0003677 DNA binding, 0000160 two-component signal transduction system (phosphorelay), 0006355 regulation of transcription, DNA-dependent; PDB: 2K4J_A 2JPB_A 1ODD_A 1OPC_A 1KGS_A 2PMU_E 2JZY_A 1GXP_B 1QQI_A 2Z33_A ....
Probab=26.63 E-value=1.1e+02 Score=19.00 Aligned_cols=49 Identities=12% Similarity=0.049 Sum_probs=33.1
Q ss_pred HHHHHHHHHHhcCCCCHHHHHHHHHHHhCCCCHHHHHHHHHHHHhCCCC
Q 040572 82 LDLAFHMSNILDTGLDRHTLSVLIALCDLGVNPEALAAVVKELQREPSP 130 (142)
Q Consensus 82 LDiL~EIS~LLNTGLDReTLsICI~LcE~GVNPEALA~VIKELRrE~~a 130 (142)
+++|.-+..=-+--++++.|.-.|---+..++..+|...|..||+....
T Consensus 11 ~~lL~~L~~~~~~~vs~~~l~~~~w~~~~~~~~~~l~~~I~rLR~kL~~ 59 (77)
T PF00486_consen 11 FRLLELLLRNPGRVVSREELIEALWGDEEDVSDNSLDVHISRLRKKLED 59 (77)
T ss_dssp HHHHHHHHHTTTSEEEHHHHHHHHTSSSSTTCTHHHHHHHHHHHHHHHS
T ss_pred HHHHHHHHhCCCCCCCHHHhCChhhhcccccchhhHHHHHHHHHHHHhh
Confidence 4455555444455678887765444333347899999999999987665
No 114
>PF05796 Chordopox_G2: Chordopoxvirus protein G2; InterPro: IPR008446 This family consists of several Chordopoxvirus isatin-beta-thiosemicarbazone dependent protein (protein G2) sequences. Inactivation of the gene coding for this protein renders the virus dependent upon isatin-beta-thiosemicarbazone (IBT) for growth [].
Probab=26.58 E-value=1.2e+02 Score=25.78 Aligned_cols=36 Identities=33% Similarity=0.617 Sum_probs=30.8
Q ss_pred HHHHHHHHhcCCCCHHHHHHHHHHHhC-CCCHHHHHHH
Q 040572 84 LAFHMSNILDTGLDRHTLSVLIALCDL-GVNPEALAAV 120 (142)
Q Consensus 84 iL~EIS~LLNTGLDReTLsICI~LcE~-GVNPEALA~V 120 (142)
|||.+|..|-|| |.+.+...++||.. ||+.++|-.-
T Consensus 7 ILFhL~kfLlTe-d~~s~~~~~SLCrgF~id~~~li~~ 43 (216)
T PF05796_consen 7 ILFHLSKFLLTE-DEESMKMFISLCRGFGIDFEELISE 43 (216)
T ss_pred HHHHHHHHHhcC-CHHHHHHHHHHhcccCCCHHHHHHH
Confidence 689999999999 89999999999974 7888875443
No 115
>PF02742 Fe_dep_repr_C: Iron dependent repressor, metal binding and dimerisation domain; InterPro: IPR001367 The diphtheria toxin repressor protein (DTXR) is a member of this group []. In Corynebacterium diphtheriae where it has been studied in some detail this protein acts as an iron-binding repressor of dipheteria toxin gene expression and may serve as a global regulator of gene expression. The N terminus may be involved in iron binding and may associate with the Tox operator. Binding of DTXR to Tox operator requires a divalent metal ion such as cobalt, ferric, manganese and nickel whereas zinc shows weak activation [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0005506 iron ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2X4H_D 2H09_A 1ON1_B 2HYF_C 2F5E_A 3R60_B 1ON2_B 2F5F_A 2F5D_A 3R61_A ....
Probab=26.54 E-value=1.9e+02 Score=18.95 Aligned_cols=51 Identities=18% Similarity=0.200 Sum_probs=37.9
Q ss_pred HHHHHHHHHHHHHHHHHh-c-CCCCHHHHHHHHHHHhCCCCHHHHHHHHHHHH
Q 040572 75 ARTARESLDLAFHMSNIL-D-TGLDRHTLSVLIALCDLGVNPEALAAVVKELQ 125 (142)
Q Consensus 75 ~~aArEtLDiL~EIS~LL-N-TGLDReTLsICI~LcE~GVNPEALA~VIKELR 125 (142)
.+.|+..+.-=.-+..+| + -|+|.+...--..-+|..++++.+..+.+-|.
T Consensus 5 ~~~A~~i~~rH~~le~fl~~~lgv~~~~a~~~A~~iEH~is~e~~~~l~~~l~ 57 (71)
T PF02742_consen 5 REIAERILRRHRILEEFLVEVLGVDEEEAEEEACRIEHVISPETIERLCKFLG 57 (71)
T ss_dssp HHHHHHHHHHHHHHHHHHHHTTT--HHHHHHHHHHHGCCS-HHHHHHHHHHTT
T ss_pred HHHHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHccCCHHHHHHHHHHhc
Confidence 345666666666677788 4 59999998888899999999999998888774
No 116
>PRK10710 DNA-binding transcriptional regulator BaeR; Provisional
Probab=26.47 E-value=79 Score=22.65 Aligned_cols=49 Identities=16% Similarity=0.085 Sum_probs=35.1
Q ss_pred HHHHHHHHHHhcCCCCHHHHHHHHHHHhCCCCHHHHHHHHHHHHhCCCC
Q 040572 82 LDLAFHMSNILDTGLDRHTLSVLIALCDLGVNPEALAAVVKELQREPSP 130 (142)
Q Consensus 82 LDiL~EIS~LLNTGLDReTLsICI~LcE~GVNPEALA~VIKELRrE~~a 130 (142)
+++|.-+..--+-|++++.+.--+.=-+.++++.++-..|..||+....
T Consensus 166 ~~il~~l~~~~~~~~s~~~i~~~~~~~~~~~~~~tv~~~i~~lr~kl~~ 214 (240)
T PRK10710 166 FRLLKTLSHEPGKVFSREQLLNHLYDDYRVVTDRTIDSHIKNLRRKLES 214 (240)
T ss_pred HHHHHHHHhCCCceEcHHHHHHHhcCcCcCCCccCHHHHHHHHHHHhhc
Confidence 5555555554466788886655443334568999999999999999875
No 117
>PF01934 DUF86: Protein of unknown function DUF86; InterPro: IPR008201 This entry describes prokaryotic proteins of unknown function.; PDB: 1YLM_A.
Probab=26.45 E-value=2.2e+02 Score=19.56 Aligned_cols=47 Identities=17% Similarity=0.224 Sum_probs=28.5
Q ss_pred HHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHhCCCCHHHHHHHHHHHH
Q 040572 77 TARESLDLAFHMSNILDTGLDRHTLSVLIALCDLGVNPEALAAVVKELQ 125 (142)
Q Consensus 77 aArEtLDiL~EIS~LLNTGLDReTLsICI~LcE~GVNPEALA~VIKELR 125 (142)
..+..+|+..+|..-.+-+....- +...|.+.|+-++..+.-.+.+.
T Consensus 37 ~~e~~~di~~~i~~~~~~~~p~~~--~~~~L~~~~ii~~~~~~~l~~~~ 83 (119)
T PF01934_consen 37 IIEAIIDIAKHIISEEGLGKPGSY--IFEILAEHGIISEEPAEPLRKMV 83 (119)
T ss_dssp HHHHHHHHHHHHHHHTT----SSH--HHHHHHHTTSS-HHHHHHHHHHH
T ss_pred HHHHHhhhHHHHHHHhCCCCCccH--HHHHHHHcCCccchhHHHHHHHH
Confidence 344555555555555554444444 88889999998888887777664
No 118
>smart00049 DEP Domain found in Dishevelled, Egl-10, and Pleckstrin. Domain of unknown function present in signalling proteins that contain PH, rasGEF, rhoGEF, rhoGAP, RGS, PDZ domains. DEP domain in Drosophila dishevelled is essential to rescue planar polarity defects and induce JNK signalling (Cell 94, 109-118).
Probab=26.30 E-value=1.1e+02 Score=19.80 Aligned_cols=15 Identities=20% Similarity=0.226 Sum_probs=13.5
Q ss_pred HHHHHHHHHHHhCCC
Q 040572 98 RHTLSVLIALCDLGV 112 (142)
Q Consensus 98 ReTLsICI~LcE~GV 112 (142)
.+++.+|-.|++.|+
T Consensus 40 ~eA~~l~~~ll~~g~ 54 (77)
T smart00049 40 EEAVHLGQLLLDEGL 54 (77)
T ss_pred HHHHHHHHHHHHCCC
Confidence 688999999999996
No 119
>TIGR01614 PME_inhib pectinesterase inhibitor domain. This model describes a plant domain of about 200 amino acids, characterized by four conserved Cys residues, shown in a pectinesterase inhibitor from Kiwi to form two disulfide bonds: first to second and third to fourth. Roughly half the members of this family have the region described by this model followed immediately by a pectinesterase domain, pfam01095. This suggests that the pairing of the enzymatic domain and its inhibitor reflects a conserved regulatory mechanism for this enzyme family.
Probab=25.73 E-value=1.1e+02 Score=22.45 Aligned_cols=49 Identities=18% Similarity=0.201 Sum_probs=29.8
Q ss_pred HHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHhCCCCHHHHHHHHHHHHh
Q 040572 76 RTARESLDLAFHMSNILDTGLDRHTLSVLIALCDLGVNPEALAAVVKELQR 126 (142)
Q Consensus 76 ~aArEtLDiL~EIS~LLNTGLDReTLsICI~LcE~GVNPEALA~VIKELRr 126 (142)
.++.+++..+.++..--+....+..|..|.++.+..++- |...++.|..
T Consensus 73 ~~~~~~~~~i~~l~~~~~~~~~~~al~~C~~~y~~a~~~--L~~a~~~l~~ 121 (178)
T TIGR01614 73 SNASDTLDHISKLLLTKGDPRDKSALEDCVELYSDAVDA--LDKALASLKS 121 (178)
T ss_pred HHHHHHHHHHHHHHccCCCHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHh
Confidence 334444444443332112235688999999999988754 6666676664
No 120
>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B ....
Probab=25.63 E-value=1.2e+02 Score=18.37 Aligned_cols=18 Identities=22% Similarity=0.578 Sum_probs=10.1
Q ss_pred CCCHHHHHHHHHHHHhCC
Q 040572 111 GVNPEALAAVVKELQREP 128 (142)
Q Consensus 111 GVNPEALA~VIKELRrE~ 128 (142)
|+.+.++..+|+.|-+..
T Consensus 32 ~~~~~~vs~~v~~L~~~G 49 (62)
T PF12802_consen 32 GISKSTVSRIVKRLEKKG 49 (62)
T ss_dssp TS-HHHHHHHHHHHHHTT
T ss_pred CcCHHHHHHHHHHHHHCC
Confidence 345666666666665543
No 121
>TIGR03188 histidine_hisI phosphoribosyl-ATP pyrophosphohydrolase. This enzyme, phosphoribosyl-ATP pyrophosphohydrolase, catalyses the second step in the histidine biosynthesis pathway. It often occurs as a fusion protein. This model a somewhat narrower scope than Pfam model pfam01503, as some paralogs that appear to be functionally distinct are excluded from this model.
Probab=25.48 E-value=1.7e+02 Score=20.89 Aligned_cols=29 Identities=28% Similarity=0.537 Sum_probs=21.2
Q ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHHhCCCCHHHHHH
Q 040572 83 DLAFHMSNILDTGLDRHTLSVLIALCDLGVNPEALAA 119 (142)
Q Consensus 83 DiL~EIS~LLNTGLDReTLsICI~LcE~GVNPEALA~ 119 (142)
++++|+++|+ .-++|-|...||.|+.+..
T Consensus 54 ~~~~E~ADLl--------YHllVlL~~~gi~~~dV~~ 82 (84)
T TIGR03188 54 ELVYEAADLL--------YHLLVLLAAQGVSLEDVLA 82 (84)
T ss_pred HHHHHHHHHH--------HHHHHHHHHcCCCHHHHHh
Confidence 4677777776 3567888999999886543
No 122
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=25.41 E-value=1.6e+02 Score=18.55 Aligned_cols=19 Identities=26% Similarity=0.581 Sum_probs=11.9
Q ss_pred CCCHHHHHHHHHHHHhCCC
Q 040572 111 GVNPEALAAVVKELQREPS 129 (142)
Q Consensus 111 GVNPEALA~VIKELRrE~~ 129 (142)
|+++.++...|++|.+..-
T Consensus 35 ~~s~~~i~~~l~~L~~~g~ 53 (101)
T smart00347 35 GVSPSTVTRVLDRLEKKGL 53 (101)
T ss_pred CCCchhHHHHHHHHHHCCC
Confidence 4566666667777766543
No 123
>PRK06843 inosine 5-monophosphate dehydrogenase; Validated
Probab=25.38 E-value=1e+02 Score=27.73 Aligned_cols=36 Identities=17% Similarity=0.269 Sum_probs=31.8
Q ss_pred CCCCHHHHHHHHHHHhCCC----------CHHHHHHHHHHHHhCCC
Q 040572 94 TGLDRHTLSVLIALCDLGV----------NPEALAAVVKELQREPS 129 (142)
Q Consensus 94 TGLDReTLsICI~LcE~GV----------NPEALA~VIKELRrE~~ 129 (142)
.|.+.+++..+-+|+|+|| +++.+.+.|++||+...
T Consensus 148 vg~~~~~~~~v~~lv~aGvDvI~iD~a~g~~~~~~~~v~~ik~~~p 193 (404)
T PRK06843 148 VSIDIDTIERVEELVKAHVDILVIDSAHGHSTRIIELVKKIKTKYP 193 (404)
T ss_pred EeCCHHHHHHHHHHHhcCCCEEEEECCCCCChhHHHHHHHHHhhCC
Confidence 5778899999999999998 67899999999998753
No 124
>PLN03195 fatty acid omega-hydroxylase; Provisional
Probab=24.87 E-value=1.6e+02 Score=25.15 Aligned_cols=45 Identities=18% Similarity=0.158 Sum_probs=34.7
Q ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHHhCCCCHHHHHHHHHHHHhC
Q 040572 83 DLAFHMSNILDTGLDRHTLSVLIALCDLGVNPEALAAVVKELQRE 127 (142)
Q Consensus 83 DiL~EIS~LLNTGLDReTLsICI~LcE~GVNPEALA~VIKELRrE 127 (142)
++..++-.++-.|.|-.+-.+...|...--||+....+..||..-
T Consensus 292 ~i~~~~~~ll~AG~dTTa~tl~~~l~~L~~~P~vq~kl~~Ei~~~ 336 (516)
T PLN03195 292 SLRDIVLNFVIAGRDTTATTLSWFVYMIMMNPHVAEKLYSELKAL 336 (516)
T ss_pred HHHHHHHHHHHHhhHhHHHHHHHHHHHHhcCHHHHHHHHHHHHHh
Confidence 455666677788888777777777777778999999999998753
No 125
>PRK07081 acyl carrier protein; Provisional
Probab=24.82 E-value=81 Score=21.58 Aligned_cols=40 Identities=8% Similarity=0.080 Sum_probs=26.6
Q ss_pred HhcCCCCHHHHHHHHHHHhCCCCHHHHHHHHHHHHhCCCC
Q 040572 91 ILDTGLDRHTLSVLIALCDLGVNPEALAAVVKELQREPSP 130 (142)
Q Consensus 91 LLNTGLDReTLsICI~LcE~GVNPEALA~VIKELRrE~~a 130 (142)
.+..+++.+.+.--..|.+.|++.-.+..+|-+|-++-.-
T Consensus 12 ~~~~~~~~~~i~~d~~l~dlGlDSl~~v~li~~lE~~f~I 51 (83)
T PRK07081 12 VAKLEVPIDSIADDADLYEAGLSSLATVQLMLAIEDAFDI 51 (83)
T ss_pred HHcCCCCHHhcCCCCCHhhcCCCHHHHHHHHHHHHHHhCC
Confidence 3344666666666666777777777777777777666544
No 126
>PRK00440 rfc replication factor C small subunit; Reviewed
Probab=24.80 E-value=2.4e+02 Score=21.97 Aligned_cols=39 Identities=18% Similarity=0.123 Sum_probs=22.3
Q ss_pred HHHHHHHHhcCCCCHHHHHHHHHHH-hCCCCHHHHHHHHH
Q 040572 84 LAFHMSNILDTGLDRHTLSVLIALC-DLGVNPEALAAVVK 122 (142)
Q Consensus 84 iL~EIS~LLNTGLDReTLsICI~Lc-E~GVNPEALA~VIK 122 (142)
.+++|.+.+..+--.+++.++..|+ +.|.+|..++.-+.
T Consensus 230 ~i~~l~~~~~~~~~~~a~~~l~~ll~~~g~~~~~i~~~l~ 269 (319)
T PRK00440 230 EIREMIELALNGDFTEAREKLRDLMIDYGLSGEDIIKQIH 269 (319)
T ss_pred HHHHHHHHHHcCCHHHHHHHHHHHHHHcCCCHHHHHHHHH
Confidence 3444444444455566777777766 46777776554443
No 127
>PF06816 NOD: NOTCH protein; InterPro: IPR010660 NOTCH signalling plays a fundamental role during a great number of developmental processes in multicellular animals []. NOD (NOTCH protein domain) represents a region present in many NOTCH proteins and NOTCH homologues in multiple species such as 0, NOTCH2 and NOTCH3, LIN12, SC1 and TAN1. Role of NOD domain remains to be elucidated.; GO: 0030154 cell differentiation, 0016021 integral to membrane; PDB: 2OO4_A 3ETO_A 3I08_A 3L95_X.
Probab=24.66 E-value=55 Score=22.05 Aligned_cols=30 Identities=33% Similarity=0.440 Sum_probs=22.4
Q ss_pred cccCCCCHHHHHHHHHHHHHHHHHHHHhcCCC
Q 040572 65 RLVDDMDPEAARTARESLDLAFHMSNILDTGL 96 (142)
Q Consensus 65 ~~~~~md~d~~~aArEtLDiL~EIS~LLNTGL 96 (142)
.+|--|+++.... .....|.+||.+|.|.+
T Consensus 10 vivvl~~P~~f~~--~~~~FLr~Ls~~Lrt~V 39 (57)
T PF06816_consen 10 VIVVLMDPEEFRN--NSVQFLRELSRVLRTTV 39 (57)
T ss_dssp EEEESS-HHHHHH--THHHHHHHHHHHCTSEE
T ss_pred EEEEEeCHHHHHH--HHHHHHHHHHHHHeeeE
Confidence 3455688888765 66688999999999964
No 128
>PF04906 Tweety: Tweety; InterPro: IPR006990 None of the members of the tweety (tty) family have been functionally characterised. However, they are considered to be transmembrane proteins with five potential membrane-spanning regions. A number of potential functions have been suggested on the basis of homology to the yeast FTR1 and FTH1 iron transporter proteins and the mammalian neurotensin receptors 1 and 2 in that they have a similar hydrophobicity profiles although there is no detectable sequence homology to the tweety-related proteins. It has been proposed that the tweety-related proteins could be involved in transport of iron or other divalent cations or alternatively that they may be membrane-bound receptors [].
Probab=24.59 E-value=63 Score=28.40 Aligned_cols=34 Identities=24% Similarity=0.435 Sum_probs=30.1
Q ss_pred HHHHHHHHHHHhcC-CCCHHHHHHHHHHHhCCCCH
Q 040572 81 SLDLAFHMSNILDT-GLDRHTLSVLIALCDLGVNP 114 (142)
Q Consensus 81 tLDiL~EIS~LLNT-GLDReTLsICI~LcE~GVNP 114 (142)
+-..+|.++.+||| ||.+.=+.....+|+.|+.-
T Consensus 327 ~e~~l~~l~alldCr~lh~dY~~al~g~C~dg~eG 361 (406)
T PF04906_consen 327 TERSLHQLTALLDCRGLHKDYVDALRGLCYDGLEG 361 (406)
T ss_pred HHHHHHHHHhhcccccHHHHHHHHHHhhccchHhH
Confidence 34468999999999 99999999999999999964
No 129
>PRK14958 DNA polymerase III subunits gamma and tau; Provisional
Probab=24.53 E-value=2e+02 Score=25.98 Aligned_cols=43 Identities=21% Similarity=0.302 Sum_probs=28.3
Q ss_pred HHHHHHhcCCCCHHHHHHHHHHHhCCCCHHH-HHHHHHHHHhCC
Q 040572 86 FHMSNILDTGLDRHTLSVLIALCDLGVNPEA-LAAVVKELQREP 128 (142)
Q Consensus 86 ~EIS~LLNTGLDReTLsICI~LcE~GVNPEA-LA~VIKELRrE~ 128 (142)
++|-+-|-.|=-...+.++-.|++.|++|.. |++++..|++..
T Consensus 250 ~~ll~al~~~d~~~~l~~~~~l~~~g~~~~~il~~l~~~~~~~~ 293 (509)
T PRK14958 250 FDILEALAAKAGDRLLGCVTRLVEQGVDFSNALADLLSLLHQIA 293 (509)
T ss_pred HHHHHHHHcCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHH
Confidence 3333333334344578888899999999865 677777777653
No 130
>PF09748 Med10: Transcription factor subunit Med10 of Mediator complex; InterPro: IPR019145 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. Med10 is one of the protein subunits of the Mediator complex, tethered to Med14 (Rgr1) protein. Med10 specifically mediates basal-level HIS4 transcription via Gcn4. In addition, there is a putative requirement for Med10 in Bas2-mediated transcription []. ; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006357 regulation of transcription from RNA polymerase II promoter, 0016592 mediator complex
Probab=24.51 E-value=2.8e+02 Score=20.73 Aligned_cols=52 Identities=19% Similarity=0.220 Sum_probs=31.5
Q ss_pred HHHHHHHHHHHHHHHHHHH--------hcCCCCHHHHHHHHHHHhCCCCHHH-HHHHHHHHHhCC
Q 040572 73 EAARTARESLDLAFHMSNI--------LDTGLDRHTLSVLIALCDLGVNPEA-LAAVVKELQREP 128 (142)
Q Consensus 73 d~~~aArEtLDiL~EIS~L--------LNTGLDReTLsICI~LcE~GVNPEA-LA~VIKELRrE~ 128 (142)
.+++.--+.|+-|+.++.- -+.-+..+ +|..+|.|-||+- .-..|...+++.
T Consensus 33 ~ki~~lv~~L~~l~~~~~~~~~~~~~~~~~~IP~e----vl~yID~GrNPDiyTre~vE~~~~~N 93 (128)
T PF09748_consen 33 QKINQLVTSLQELDKLAQQTNDPDSPLQDIQIPLE----VLEYIDDGRNPDIYTREFVELVRREN 93 (128)
T ss_pred HHHHHHHHHHHHHHHHhcccCCCCcccccCCCCHH----HHHHHhCCCCchHHHHHHHHHHHHHh
Confidence 3445555556666666555 23345544 4688999999987 445555555544
No 131
>PRK11083 DNA-binding response regulator CreB; Provisional
Probab=24.46 E-value=93 Score=21.91 Aligned_cols=49 Identities=10% Similarity=-0.010 Sum_probs=37.9
Q ss_pred HHHHHHHHHHhcCCCCHHHHHHHHHHHhCCCCHHHHHHHHHHHHhCCCC
Q 040572 82 LDLAFHMSNILDTGLDRHTLSVLIALCDLGVNPEALAAVVKELQREPSP 130 (142)
Q Consensus 82 LDiL~EIS~LLNTGLDReTLsICI~LcE~GVNPEALA~VIKELRrE~~a 130 (142)
+++|.-+.+=-+-|++++.|.--+..-+..+++..+-..|+.||+....
T Consensus 160 ~~il~~l~~~~~~~~s~~~i~~~l~~~~~~~~~~tv~~~i~~l~~Kl~~ 208 (228)
T PRK11083 160 FLLLKTLLLSPGRVFSRQQLMDIVWEDAQDSYDRTVDTHIKTLRAKLRA 208 (228)
T ss_pred HHHHHHHHhCCCceECHHHHHHHhcCCCCCCCccCHHHHHHHHHHHhcc
Confidence 6677666665556799998887777666667788999999999998764
No 132
>PRK14963 DNA polymerase III subunits gamma and tau; Provisional
Probab=24.38 E-value=2.1e+02 Score=25.92 Aligned_cols=41 Identities=15% Similarity=0.175 Sum_probs=29.4
Q ss_pred HHHHHHHhcCCCCHHHHHHHHHHHhCCCCHHH-HHHHHHHHH
Q 040572 85 AFHMSNILDTGLDRHTLSVLIALCDLGVNPEA-LAAVVKELQ 125 (142)
Q Consensus 85 L~EIS~LLNTGLDReTLsICI~LcE~GVNPEA-LA~VIKELR 125 (142)
+|+|.+.+--|=-..++.++-.|++.|.+|.. ++.++..+|
T Consensus 245 if~Li~al~~~d~~~Al~~l~~Ll~~G~~~~~Il~~L~~~~r 286 (504)
T PRK14963 245 LRGIAAALAQGDAAEALSGAAQLYRDGFAARTLVEGLLEAFR 286 (504)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHH
Confidence 55555555445556788899999999999987 556667777
No 133
>cd03572 ENTH_epsin_related ENTH domain, Epsin Related family; composed of hypothetical proteins containing an ENTH-like domain. The epsin N-terminal homology (ENTH) domain is an evolutionarily conserved protein module found primarily in proteins that participate in clathrin-mediated endocytosis. A set of proteins previously designated as harboring an ENTH domain in fact contains a highly similar, yet unique module referred to as an AP180 N-terminal homology (ANTH) domain. ENTH and ANTH (E/ANTH) domains are structurally similar to the VHS domain and are composed of a superhelix of eight alpha helices. E/ANTH domains bind both inositol phospholipids and proteins and contribute to the nucleation and formation of clathrin coats on membranes. ENTH domains also function in the development of membrane curvature through lipid remodeling during the formation of clathrin-coated vesicles. E/ANTH-bearing proteins have recently been shown to function with adaptor protein-1 and GGA adaptors at the t
Probab=24.20 E-value=2.3e+02 Score=21.53 Aligned_cols=39 Identities=26% Similarity=0.395 Sum_probs=31.2
Q ss_pred HHHHHHHHHHHHHHHHHHHhcCCCC-------HHHHHHHHHHHhCC
Q 040572 73 EAARTARESLDLAFHMSNILDTGLD-------RHTLSVLIALCDLG 111 (142)
Q Consensus 73 d~~~aArEtLDiL~EIS~LLNTGLD-------ReTLsICI~LcE~G 111 (142)
|.++...+..+.+++|.+.|.-.|. -.+|.|+-.||+.|
T Consensus 24 Eia~~t~~s~~~~~ei~d~L~kRL~~~~~hVK~K~Lrilk~l~~~G 69 (122)
T cd03572 24 EIAKLTRKSVGSCQELLEYLLKRLKRSSPHVKLKVLKIIKHLCEKG 69 (122)
T ss_pred HHHHHHHcCHHHHHHHHHHHHHHhcCCCCcchHHHHHHHHHHHhhC
Confidence 6667777777778888888877665 46899999999999
No 134
>TIGR00152 dephospho-CoA kinase. This model produces scores in the range of 0-25 bits against adenylate, guanylate, uridine, and thymidylate kinases.
Probab=24.13 E-value=3e+02 Score=20.36 Aligned_cols=34 Identities=21% Similarity=0.112 Sum_probs=27.8
Q ss_pred CCCCHHHHHHHH-------HHHhCCCCHHHHHHHHHHHHhC
Q 040572 94 TGLDRHTLSVLI-------ALCDLGVNPEALAAVVKELQRE 127 (142)
Q Consensus 94 TGLDReTLsICI-------~LcE~GVNPEALA~VIKELRrE 127 (142)
=.+||..|.-+| .++|.+++|.....+.+.|++.
T Consensus 61 g~idr~~L~~~vf~~~~~~~~le~ilhP~i~~~i~~~i~~~ 101 (188)
T TIGR00152 61 GELDRKALGERVFNDPEELKWLNNLLHPLIREWMKKLLAQF 101 (188)
T ss_pred CCCCHHHHHHHHhCCHHHHHHHHHhhCHHHHHHHHHHHHHh
Confidence 369999999776 6789999999988887777654
No 135
>TIGR03697 NtcA_cyano global nitrogen regulator NtcA, cyanobacterial. Members of this protein family, found in the cyanobacteria, are the global nitrogen regulator NtcA. This DNA-binding transcriptional regulator is required for expressing many different ammonia-repressible genes. The consensus NtcA-binding site is G T A N(8)T A C.
Probab=23.88 E-value=79 Score=22.68 Aligned_cols=20 Identities=10% Similarity=0.358 Sum_probs=17.3
Q ss_pred CCCCHHHHHHHHHHHHhCCC
Q 040572 110 LGVNPEALAAVVKELQREPS 129 (142)
Q Consensus 110 ~GVNPEALA~VIKELRrE~~ 129 (142)
.|+.++.+..++++|+++.-
T Consensus 153 lG~tretvsR~l~~l~~~g~ 172 (193)
T TIGR03697 153 IGSTRVTITRLLGDLRKKKL 172 (193)
T ss_pred hCCcHHHHHHHHHHHHHCCC
Confidence 37899999999999999864
No 136
>cd00592 HTH_MerR-like Helix-Turn-Helix DNA binding domain of MerR-like transcription regulators. Helix-turn-helix (HTH) MerR-like transcription regulator, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=23.54 E-value=2.4e+02 Score=18.99 Aligned_cols=35 Identities=17% Similarity=0.233 Sum_probs=28.7
Q ss_pred HHHHHHHHHHHHHhcCCCCHHHHHHHHHHHhCCCC
Q 040572 79 RESLDLAFHMSNILDTGLDRHTLSVLIALCDLGVN 113 (142)
Q Consensus 79 rEtLDiL~EIS~LLNTGLDReTLsICI~LcE~GVN 113 (142)
.+.+..+..|-.|.+.|++-..+.-.+.+.+.|-.
T Consensus 40 ~~dv~~l~~i~~l~~~g~~~~~i~~~l~~~~~~~~ 74 (100)
T cd00592 40 EEDLERLRLIRRLRELGLSLKEIRELLDARDEELS 74 (100)
T ss_pred HHHHHHHHHHHHHHHcCCCHHHHHHHHhcccccch
Confidence 35667777777888899999999999999888853
No 137
>PF04043 PMEI: Plant invertase/pectin methylesterase inhibitor; InterPro: IPR006501 This entry represents a plant domain of about 200 amino acids, characterised by four conserved cysteine residues. This domain inhibits pectinesterase/pectin methylesterases (PMEs) and invertases through formation of a non-covalent 1:1 complex []. It has been implicated in the regulation of fruit development, carbohydrate metabolism and cell wall extension. It may also be involved in inhibiting microbial pathogen PMEs. It has been observed that it is often expressed as a large inactive preprotein []. This domain is also found at the N-termini of PMEs predicted from DNA sequences, suggesting that both PMEs and their inhibitors are expressed as a single polyprotein and subsequently processed. It has two disulphide bridges and is mainly alpha-helical in structure [].; GO: 0004857 enzyme inhibitor activity, 0030599 pectinesterase activity; PDB: 1X90_A 1X8Z_C 1X91_A 1XG2_B 1RJ4_D 2CJ4_B 2XQR_F 2CJ7_A 2CJ8_A 2CJ6_A ....
Probab=23.49 E-value=1.9e+02 Score=19.96 Aligned_cols=45 Identities=20% Similarity=0.281 Sum_probs=30.1
Q ss_pred HHHHHHHHHHHHHHhcC-CCC---HHHHHHHHHHHhCCCCHHHHHHHHHHH
Q 040572 78 ARESLDLAFHMSNILDT-GLD---RHTLSVLIALCDLGVNPEALAAVVKEL 124 (142)
Q Consensus 78 ArEtLDiL~EIS~LLNT-GLD---ReTLsICI~LcE~GVNPEALA~VIKEL 124 (142)
..++.+....++.++.. +.| +..|..|.++.+..+. .|...+..|
T Consensus 48 ~~~~~~a~~~~~~l~~~~~~~~~~~~~l~~C~~~y~~a~~--~l~~a~~~l 96 (152)
T PF04043_consen 48 LSNATSASAFISKLLKNPSKDPNAKQALQDCQELYDDAVD--SLQRALEAL 96 (152)
T ss_dssp HHHHHHHHHHHHHHHTC-S-THHHHHHHHHHHHHHHHHHH--HHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHhhccCCHHhhHHHHHHHHHHHHHHH--HHHHHHHhh
Confidence 34445555667777765 555 7789999999988765 555555555
No 138
>PRK02436 xerD site-specific tyrosine recombinase XerD-like protein; Reviewed
Probab=23.40 E-value=1.1e+02 Score=22.93 Aligned_cols=26 Identities=19% Similarity=0.275 Sum_probs=17.8
Q ss_pred CCHHHHH--HHHHHHhCCCCHHHHHHHH
Q 040572 96 LDRHTLS--VLIALCDLGVNPEALAAVV 121 (142)
Q Consensus 96 LDReTLs--ICI~LcE~GVNPEALA~VI 121 (142)
+..+.|. .+..|+++|+++.+|+.+.
T Consensus 205 ~t~H~lRHtfat~~~~~g~~~~~l~~~l 232 (245)
T PRK02436 205 LSAQKLREQFILKQKEAGKSIYELARLL 232 (245)
T ss_pred CCcchhHHHHHHHHHHcCCCHHHHHHHh
Confidence 3444443 3556889999999987753
No 139
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=23.38 E-value=89 Score=19.19 Aligned_cols=21 Identities=24% Similarity=0.333 Sum_probs=6.5
Q ss_pred HHHHhcCCCCHHHHHHHHHHH
Q 040572 88 MSNILDTGLDRHTLSVLIALC 108 (142)
Q Consensus 88 IS~LLNTGLDReTLsICI~Lc 108 (142)
|+.+++-....=++..+..||
T Consensus 27 l~~~~~~~~~~~~~~~l~~ia 47 (63)
T PF13443_consen 27 LSRILNGKPSNPSLDTLEKIA 47 (63)
T ss_dssp HHHHHTTT-----HHHHHHHH
T ss_pred HHHHHhcccccccHHHHHHHH
Confidence 344444333333333333443
No 140
>PF13833 EF-hand_8: EF-hand domain pair; PDB: 3KF9_A 1TTX_A 1WLZ_A 1ALV_A 1NX3_A 1ALW_A 1NX2_A 1NX1_A 1NX0_A 1DF0_A ....
Probab=23.33 E-value=1.4e+02 Score=17.71 Aligned_cols=14 Identities=21% Similarity=0.264 Sum_probs=6.9
Q ss_pred CCHHHHHHHHHHHh
Q 040572 96 LDRHTLSVLIALCD 109 (142)
Q Consensus 96 LDReTLsICI~LcE 109 (142)
++.+.+..++..++
T Consensus 22 ~s~~e~~~l~~~~D 35 (54)
T PF13833_consen 22 LSEEEVDRLFREFD 35 (54)
T ss_dssp SCHHHHHHHHHHHT
T ss_pred CCHHHHHHHHHhcc
Confidence 44555555554443
No 141
>PF02637 GatB_Yqey: GatB domain; InterPro: IPR018027 The GatB domain, the function of which is uncertain, is associated with aspartyl/glutamyl amidotransferase subunit B and glutamyl amidotransferase subunit E. These are involved in the formation of correctly charged Asn-tRNA(Asn) or Gln-tRNA(Gln) through the transamidation of misacylated Asp-tRNA(Asn) or Glu-tRNA(Gln) in organisms which lack either or both of asparaginyl-tRNA or glutaminyl-tRNA synthetases. The reaction takes place in the presence of glutamine and ATP through an activated phospho-Asp-tRNA(Asn) or phospho-Glu-tRNA(Gln). ; GO: 0016884 carbon-nitrogen ligase activity, with glutamine as amido-N-donor; PDB: 2D6F_D 3H0M_H 3H0R_K 3H0L_K 3KFU_F 3AL0_B 3IP4_B 2DF4_B 2G5I_B 2F2A_B ....
Probab=23.24 E-value=1.7e+02 Score=21.53 Aligned_cols=35 Identities=23% Similarity=0.415 Sum_probs=25.2
Q ss_pred cCCCCHHHHHHHHHHHhCC-CCHHHHHHHHHHHHhC
Q 040572 93 DTGLDRHTLSVLIALCDLG-VNPEALAAVVKELQRE 127 (142)
Q Consensus 93 NTGLDReTLsICI~LcE~G-VNPEALA~VIKELRrE 127 (142)
++.++.+.|.-+|.|++.| ++-...-.++.++-..
T Consensus 37 ~~~i~~~~l~~li~l~~~~~Is~~~ak~ll~~~~~~ 72 (148)
T PF02637_consen 37 DSPISPEHLAELINLLEDGKISKKSAKELLRELLEN 72 (148)
T ss_dssp TSSSTHHHHHHHHHHHHTTSSGHHHHHHHHHHHHHH
T ss_pred hcCCCHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHc
Confidence 4457889999999999888 5666666666666533
No 142
>PRK10766 DNA-binding transcriptional regulator TorR; Provisional
Probab=23.06 E-value=1.1e+02 Score=21.82 Aligned_cols=56 Identities=11% Similarity=0.165 Sum_probs=41.8
Q ss_pred HHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHhCCCCHHHHHHHHHHHHhCCC
Q 040572 74 AARTARESLDLAFHMSNILDTGLDRHTLSVLIALCDLGVNPEALAAVVKELQREPS 129 (142)
Q Consensus 74 ~~~aArEtLDiL~EIS~LLNTGLDReTLsICI~LcE~GVNPEALA~VIKELRrE~~ 129 (142)
.+.-...-+++|.-+..--|-=++|+.|.-.|.=-+..+++..|-..|..||+...
T Consensus 157 ~v~Lt~~E~~ll~~l~~~~~~v~sr~~l~~~v~~~~~~~~~~~~~~~i~~LR~Kl~ 212 (221)
T PRK10766 157 PIKLTKAEYELLVAFVTNPGQVLSRERLLRMLSHRVENPNDRTIDVLIRRLRHKLN 212 (221)
T ss_pred EecCCHHHHHHHHHHHHCCCceEcHHHHHHHhcCCCCCCCCccHHHHHHHHHHhCC
Confidence 34445566778887777666678999887777633445688999999999999874
No 143
>PF00589 Phage_integrase: Phage integrase family; InterPro: IPR002104 Phage integrase proteins cleave DNA substrates by a series of staggered cuts, during which the protein becomes covalently linked to the DNA through a catalytic tyrosine residue at the carboxy end of the alignment [, ]. The catalytic site residues in CRE recombinase (P06956 from SWISSPROT) are Arg-173, His-289, Arg-292 and Tyr-324.; GO: 0003677 DNA binding, 0006310 DNA recombination, 0015074 DNA integration; PDB: 1A0P_A 1Z1G_B 1Z19_A 1AE9_A 1Z1B_A 1P7D_B 2A3V_C 1Q3V_E 1Q3U_A 1OUQ_F ....
Probab=23.02 E-value=2.5e+02 Score=19.01 Aligned_cols=39 Identities=18% Similarity=0.223 Sum_probs=27.1
Q ss_pred HHHHHHHHHhcC--CCCHHHHH--HHHHHHhCCCCHHHHHHHH
Q 040572 83 DLAFHMSNILDT--GLDRHTLS--VLIALCDLGVNPEALAAVV 121 (142)
Q Consensus 83 DiL~EIS~LLNT--GLDReTLs--ICI~LcE~GVNPEALA~VI 121 (142)
..+..+..-++. ++.-+.|. .+..|++.|++++.++.+.
T Consensus 113 ~~~~~~~~~~~~~~~~~~h~lR~t~~t~l~~~g~~~~~i~~~~ 155 (173)
T PF00589_consen 113 KIFRRIIKKAGIEKKFTPHSLRHTFATNLARSGVPIEVIAKLM 155 (173)
T ss_dssp HHHHHHHHHTT-SSCTCHHHHHHHHHHHHHHTTTSHHHHHHHH
T ss_pred cccccccccccccccccccccccccccccccccccHHHHHHHc
Confidence 345555555444 47777775 6778999999999887764
No 144
>KOG0591 consensus NIMA (never in mitosis)-related G2-specific serine/threonine protein kinase [Cell cycle control, cell division, chromosome partitioning]
Probab=22.65 E-value=78 Score=28.87 Aligned_cols=60 Identities=20% Similarity=0.387 Sum_probs=39.9
Q ss_pred cCCCCHHHHHHHHHHHHHHHH-----HHHHhcC--CCCHHHHHHHHHHHhCCCCHHHHHHHHHHHHhCCCC
Q 040572 67 VDDMDPEAARTARESLDLAFH-----MSNILDT--GLDRHTLSVLIALCDLGVNPEALAAVVKELQREPSP 130 (142)
Q Consensus 67 ~~~md~d~~~aArEtLDiL~E-----IS~LLNT--GLDReTLsICI~LcE~GVNPEALA~VIKELRrE~~a 130 (142)
.+.||..+.++--.-+++|-+ |-+..+- -=|.+.|-|.++||++| .|+.+||.-+++..-
T Consensus 54 f~~md~k~rq~~v~Ei~lLkQL~HpNIVqYy~~~f~~~~evlnivmE~c~~G----DLsqmIk~~K~qkr~ 120 (375)
T KOG0591|consen 54 FGMMDAKARQDCVKEISLLKQLNHPNIVQYYAHSFIEDNEVLNIVMELCDAG----DLSQMIKHFKKQKRL 120 (375)
T ss_pred hhhccHHHHHHHHHHHHHHHhcCCchHHHHHHHhhhccchhhHHHHHhhccc----CHHHHHHHHHhcccc
Confidence 466776655554444444433 2223332 23566799999999999 699999999998754
No 145
>PRK00013 groEL chaperonin GroEL; Reviewed
Probab=22.63 E-value=1.3e+02 Score=27.35 Aligned_cols=33 Identities=27% Similarity=0.376 Sum_probs=25.4
Q ss_pred CCHHHHHHHHHHHhCCCCH--------HHHHHHHHHHHhCC
Q 040572 96 LDRHTLSVLIALCDLGVNP--------EALAAVVKELQREP 128 (142)
Q Consensus 96 LDReTLsICI~LcE~GVNP--------EALA~VIKELRrE~ 128 (142)
|-.+-|.-+..|++.|+|| .|+..+++.|.+..
T Consensus 94 La~~LL~~a~~li~~Gi~P~~I~~G~~~A~~~~~~~L~~~a 134 (542)
T PRK00013 94 LAQAIVREGLKNVAAGANPMDLKRGIDKAVEAAVEELKKIS 134 (542)
T ss_pred HHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHHHHhc
Confidence 3445577888999999999 67777888886644
No 146
>PRK11517 transcriptional regulatory protein YedW; Provisional
Probab=22.41 E-value=1.2e+02 Score=21.40 Aligned_cols=51 Identities=8% Similarity=0.173 Sum_probs=36.3
Q ss_pred HHHHHHHHHHHHhcCCCCHHHHHHHHHHHhCCCCHHHHHHHHHHHHhCCCC
Q 040572 80 ESLDLAFHMSNILDTGLDRHTLSVLIALCDLGVNPEALAAVVKELQREPSP 130 (142)
Q Consensus 80 EtLDiL~EIS~LLNTGLDReTLsICI~LcE~GVNPEALA~VIKELRrE~~a 130 (142)
.=+++|.-+..=-+--++++.|.-.|-=.+...++..+-..|+.||+....
T Consensus 151 ~E~~il~~l~~~~g~~~s~~~i~~~~w~~~~~~~~~tv~~~i~rlr~Kl~~ 201 (223)
T PRK11517 151 KEFQLLWLLASRAGEIIPRTVIASEIWGINFDSDTNTVDVAIRRLRAKVDD 201 (223)
T ss_pred HHHHHHHHHHhCCCccCCHHHHHHHhcCCCCCCCcCCHHHHHHHHHHhhcC
Confidence 445666666555555578888877765444456789999999999999853
No 147
>cd00194 UBA Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been suggested that UBA domains are involved in conferring protein target specificity. The domain, a compact three helix bundle, has a conserved GFP-loop and the proline is thought to be critical for binding. The UBA domain is distinct from the conserved three helical domain seen in the N-terminus of EF-TS and eukaryotic NAC proteins.
Probab=22.36 E-value=1e+02 Score=17.53 Aligned_cols=25 Identities=12% Similarity=0.310 Sum_probs=17.9
Q ss_pred HHHHHhcCCCCHHHHHHHHHHHhCC
Q 040572 87 HMSNILDTGLDRHTLSVLIALCDLG 111 (142)
Q Consensus 87 EIS~LLNTGLDReTLsICI~LcE~G 111 (142)
.|.+|++-|.+++...-.+..|...
T Consensus 4 ~v~~L~~mGf~~~~~~~AL~~~~~d 28 (38)
T cd00194 4 KLEQLLEMGFSREEARKALRATNNN 28 (38)
T ss_pred HHHHHHHcCCCHHHHHHHHHHhCCC
Confidence 3556677799988877777777653
No 148
>cd05025 S-100A1 S-100A1: S-100A1 domain found in proteins similar to S100A1. S100A1 is a calcium-binding protein belonging to a large S100 vertebrate-specific protein family within the EF-hand superfamily of calcium-binding proteins. Note that the S-100 hierarchy, to which this S-100A1 group belongs, contains only S-100 EF-hand domains, other EF-hands have been modeled separately. As is the case with many other members of S100 protein family, S100A1 is implicated in intracellular and extracellular regulatory activities, including interaction with myosin-associated twitchin kinase, actin-capping protein CapZ, sinapsin I, and tubulin. Structural data suggests that S100A1 proteins exist within cells as antiparallel homodimers, while heterodimers with S100A4 and S100B also has been reported. Upon binding calcium S100A1 changes conformation to expose a hydrophobic cleft which is the interaction site of S100A1 with its more that 20 known target proteins.
Probab=22.10 E-value=2.5e+02 Score=18.71 Aligned_cols=48 Identities=31% Similarity=0.424 Sum_probs=29.3
Q ss_pred HHHHHHHHHHHHH-HhcCC--CCHHHHHHHHH--HHh-C--CCCHHHHHHHHHHHH
Q 040572 78 ARESLDLAFHMSN-ILDTG--LDRHTLSVLIA--LCD-L--GVNPEALAAVVKELQ 125 (142)
Q Consensus 78 ArEtLDiL~EIS~-LLNTG--LDReTLsICI~--LcE-~--GVNPEALA~VIKELR 125 (142)
|.+.+.-+|.+=+ --+.| |+.+.|..++. |-+ . ..+.+.+..+++++-
T Consensus 7 ~~~~l~~~F~~fDd~dg~G~~Is~~El~~~l~~~lg~~~~~~~s~~~v~~i~~~~D 62 (92)
T cd05025 7 AMETLINVFHAHSGKEGDKYKLSKKELKDLLQTELSDFLDAQKDADAVDKIMKELD 62 (92)
T ss_pred HHHHHHHHHHHHhcccCCCCeECHHHHHHHHHHHHHHHccCCCCHHHHHHHHHHHC
Confidence 3333433444433 55577 99999998885 312 2 346677888888763
No 149
>KOG3251 consensus Golgi SNAP receptor complex member [Intracellular trafficking, secretion, and vesicular transport]
Probab=22.06 E-value=66 Score=27.12 Aligned_cols=31 Identities=23% Similarity=0.417 Sum_probs=22.5
Q ss_pred HHHHHHHHHHHHHH-----------HHHHHhcC-CCCHHHHHH
Q 040572 73 EAARTARESLDLAF-----------HMSNILDT-GLDRHTLSV 103 (142)
Q Consensus 73 d~~~aArEtLDiL~-----------EIS~LLNT-GLDReTLsI 103 (142)
|-...+...|+-|. .|.+++|| ||+++|+.+
T Consensus 140 d~l~~G~~ile~l~~Q~~~L~~~~~ki~~~~ntLGlSn~ti~l 182 (213)
T KOG3251|consen 140 DLLESGSAILENLVEQRLTLKGTQKKILDILNTLGLSNQTIRL 182 (213)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcHHHHHH
Confidence 44555566666554 48899999 999999764
No 150
>TIGR02348 GroEL chaperonin GroL. This family consists of GroEL, the larger subunit of the GroEL/GroES cytosolic chaperonin. It is found in bacteria, organelles derived from bacteria, and occasionally in the Archaea. The bacterial GroEL/GroES group I chaperonin is replaced a group II chaperonin, usually called the thermosome in the Archaeota and CCT (chaperone-containing TCP) in the Eukaryota. GroEL, thermosome subunits, and CCT subunits all fall under the scope of Pfam model pfam00118.
Probab=21.92 E-value=1.3e+02 Score=26.91 Aligned_cols=33 Identities=27% Similarity=0.378 Sum_probs=25.5
Q ss_pred CCHHHHHHHHHHHhCCCCH--------HHHHHHHHHHHhCC
Q 040572 96 LDRHTLSVLIALCDLGVNP--------EALAAVVKELQREP 128 (142)
Q Consensus 96 LDReTLsICI~LcE~GVNP--------EALA~VIKELRrE~ 128 (142)
|-.+-|.-+..|++.|+|| .|+..+++.|.+..
T Consensus 93 La~~Ll~~a~~li~~GihP~~Ii~G~~~A~~~~l~~L~~~s 133 (524)
T TIGR02348 93 LAQAIVKEGLKNVAAGANPIELKRGIEKAVEAAVEELKKLS 133 (524)
T ss_pred HHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHHHHHHHHHhc
Confidence 3355677788999999999 67888888886643
No 151
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=21.91 E-value=87 Score=24.08 Aligned_cols=21 Identities=24% Similarity=0.335 Sum_probs=18.2
Q ss_pred CCCCHHHHHHHHHHHHhCCCC
Q 040572 110 LGVNPEALAAVVKELQREPSP 130 (142)
Q Consensus 110 ~GVNPEALA~VIKELRrE~~a 130 (142)
.|+.++.|..++++|+++.--
T Consensus 189 lGisretlsR~L~~L~~~GlI 209 (230)
T PRK09391 189 LGLTIETVSRALSQLQDRGLI 209 (230)
T ss_pred HCCCHHHHHHHHHHHHHCCcE
Confidence 489999999999999998643
No 152
>PLN02641 anthranilate phosphoribosyltransferase
Probab=21.90 E-value=3.1e+02 Score=23.77 Aligned_cols=41 Identities=20% Similarity=0.328 Sum_probs=31.3
Q ss_pred HHHhcCCCCHHHH-HHHHHHHhCCCCHHHHHHHHHHHHhCCCC
Q 040572 89 SNILDTGLDRHTL-SVLIALCDLGVNPEALAAVVKELQREPSP 130 (142)
Q Consensus 89 S~LLNTGLDReTL-sICI~LcE~GVNPEALA~VIKELRrE~~a 130 (142)
..||+ |.+...+ ++++.|--.|..++.|+..++-+|.....
T Consensus 27 ~~il~-~~~~~qigAfL~alr~kget~eEiag~~~a~~~~~~~ 68 (343)
T PLN02641 27 DFLLD-DADEAQISAFLVLLRAKGETFEEIAGLARAMIKRARK 68 (343)
T ss_pred HHHHc-CCCHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHhCCC
Confidence 34455 5666555 66778889999999999999999977643
No 153
>TIGR02684 dnstrm_HI1420 probable addiction module antidote protein. gene pairs, when found on the bacterial chromosome, are located often with prophage regions, but also both in integrated plasmid regions and in housekeeping gene regions. Analysis suggests that the gene pair may serve as an addiction module.
Probab=21.85 E-value=89 Score=22.21 Aligned_cols=16 Identities=19% Similarity=0.345 Sum_probs=8.6
Q ss_pred CHHHHHHHHHHHHhCC
Q 040572 113 NPEALAAVVKELQREP 128 (142)
Q Consensus 113 NPEALA~VIKELRrE~ 128 (142)
+|+-+..-|+++|++.
T Consensus 29 ~~~~~~~~l~~~r~~~ 44 (89)
T TIGR02684 29 DPAYIAHALGYIARAR 44 (89)
T ss_pred CHHHHHHHHHHHHHHC
Confidence 5555555555555543
No 154
>PRK07394 hypothetical protein; Provisional
Probab=21.85 E-value=3.3e+02 Score=23.46 Aligned_cols=42 Identities=19% Similarity=0.152 Sum_probs=33.9
Q ss_pred HHHHhcCCCCHHHH-HHHHHHHhCCCCHHHHHHHHHHHHhCCC
Q 040572 88 MSNILDTGLDRHTL-SVLIALCDLGVNPEALAAVVKELQREPS 129 (142)
Q Consensus 88 IS~LLNTGLDReTL-sICI~LcE~GVNPEALA~VIKELRrE~~ 129 (142)
|..||+=..+...+ ++++.|--.|..|+.|+..++-+|+...
T Consensus 31 ~~~il~g~~~~~q~aAfL~alr~KGET~eEiaG~~~a~~~~~~ 73 (342)
T PRK07394 31 LKLMLLGEATPAQIGAFLIAHRIKRPTPEELAGMLDTYDELGP 73 (342)
T ss_pred HHHHHcCCCCHHHHHHHHHHHHhhCCCHHHHHHHHHHHHHhCC
Confidence 45667777776555 6788899999999999999999997553
No 155
>PLN02302 ent-kaurenoic acid oxidase
Probab=21.84 E-value=1.7e+02 Score=24.33 Aligned_cols=45 Identities=18% Similarity=0.133 Sum_probs=33.8
Q ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHHhCCCCHHHHHHHHHHHHhC
Q 040572 83 DLAFHMSNILDTGLDRHTLSVLIALCDLGVNPEALAAVVKELQRE 127 (142)
Q Consensus 83 DiL~EIS~LLNTGLDReTLsICI~LcE~GVNPEALA~VIKELRrE 127 (142)
+++..+-.++-.|.|-.+-.++..|....-||+....+-.|+.+.
T Consensus 287 ~i~~~~~~~~~Ag~dtta~~l~~~l~~L~~~P~~~~kl~~E~~~v 331 (490)
T PLN02302 287 EIIDLLLMYLNAGHESSGHLTMWATIFLQEHPEVLQKAKAEQEEI 331 (490)
T ss_pred HHHHHHHHHHHhhHHHHHHHHHHHHHHHHhCHHHHHHHHHHHHHH
Confidence 455666677788888777777777777777999888888887653
No 156
>PRK06585 holA DNA polymerase III subunit delta; Reviewed
Probab=21.72 E-value=3.5e+02 Score=21.96 Aligned_cols=47 Identities=15% Similarity=0.051 Sum_probs=37.6
Q ss_pred HHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHhCCCCHHHHHHHHHHHHh
Q 040572 78 ARESLDLAFHMSNILDTGLDRHTLSVLIALCDLGVNPEALAAVVKELQR 126 (142)
Q Consensus 78 ArEtLDiL~EIS~LLNTGLDReTLsICI~LcE~GVNPEALA~VIKELRr 126 (142)
.++..+.|.++.+-.+-.++.+++..+++.++. |..+|..-|..|--
T Consensus 144 ~~~l~~~i~~~~~~~g~~i~~~a~~~L~~~~g~--dl~~l~~EleKL~l 190 (343)
T PRK06585 144 ERDLARLIDDELAEAGLRITPDARALLVALLGG--DRLASRNEIEKLAL 190 (343)
T ss_pred HHHHHHHHHHHHHHCCCCCCHHHHHHHHHHhCC--CHHHHHHHHHHHHH
Confidence 456777889999999999999999999999864 77777666666543
No 157
>TIGR01807 CM_P2 chorismate mutase domain of proteobacterial P-protein, clade 2. This model represents one of two separate clades of the chorismate mutase domain of the gamma and beta and epsilon proteobacterial "P-protein" which contains an N-terminal chorismate mutase domain and a C-terminal prephenate dehydratase domain. It is also found in Aquifex aolicus.
Probab=21.61 E-value=2.6e+02 Score=18.64 Aligned_cols=58 Identities=19% Similarity=0.278 Sum_probs=40.9
Q ss_pred cCCCCHHHHHHHHHHHHHHHHHHHHhc---CCCC-------HHHHHHHHHHHhCCCCHHHHHHHHHHH
Q 040572 67 VDDMDPEAARTARESLDLAFHMSNILD---TGLD-------RHTLSVLIALCDLGVNPEALAAVVKEL 124 (142)
Q Consensus 67 ~~~md~d~~~aArEtLDiL~EIS~LLN---TGLD-------ReTLsICI~LcE~GVNPEALA~VIKEL 124 (142)
+|..|.+-+.--.+-++++.+|+.+=- .|+. .+-|.-+..+-+.|++|+.+..+.++|
T Consensus 8 ID~iD~~iv~Ll~~R~~~~~~i~~~K~~~~~~~~i~d~~Re~~vl~~~~~~~~~~l~~~~i~~if~~I 75 (76)
T TIGR01807 8 IDAIDDRILDLLSERATYAQAVGELKGSGASGASFYRPEREAQVIRRLQNLNKGPLDQEAIARIFREI 75 (76)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCcCChHHHHHHHHHHHHhccCCCCHHHHHHHHHHH
Confidence 567778888888888999999988754 3443 233444555555668888888887765
No 158
>PLN02774 brassinosteroid-6-oxidase
Probab=21.61 E-value=2e+02 Score=24.16 Aligned_cols=45 Identities=22% Similarity=0.273 Sum_probs=33.8
Q ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHHhCCCCHHHHHHHHHHHHhC
Q 040572 83 DLAFHMSNILDTGLDRHTLSVLIALCDLGVNPEALAAVVKELQRE 127 (142)
Q Consensus 83 DiL~EIS~LLNTGLDReTLsICI~LcE~GVNPEALA~VIKELRrE 127 (142)
++...+..|+-.|.|-.+-.+...|....-||+...++-.|+.+.
T Consensus 264 ei~~~~~~ll~Ag~dTt~~~l~w~l~~L~~~P~~q~kl~~Ei~~~ 308 (463)
T PLN02774 264 EIIDQIITILYSGYETVSTTSMMAVKYLHDHPKALQELRKEHLAI 308 (463)
T ss_pred HHHHHHHHHHHhcchhHHHHHHHHHHHHHcCHHHHHHHHHHHHHH
Confidence 456667777888888777777777777777999988887777654
No 159
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=21.60 E-value=91 Score=22.71 Aligned_cols=21 Identities=33% Similarity=0.412 Sum_probs=17.6
Q ss_pred CCCCHHHHHHHHHHHHhCCCC
Q 040572 110 LGVNPEALAAVVKELQREPSP 130 (142)
Q Consensus 110 ~GVNPEALA~VIKELRrE~~a 130 (142)
.|+.+|.+..++++|+++.--
T Consensus 159 lG~tretvsR~l~~l~~~g~I 179 (202)
T PRK13918 159 VGSVRETVTKVIGELSREGYI 179 (202)
T ss_pred hCccHHHHHHHHHHHHHCCCE
Confidence 378899999999999988644
No 160
>PLN02346 histidine biosynthesis bifunctional protein hisIE
Probab=21.60 E-value=2.2e+02 Score=24.84 Aligned_cols=32 Identities=25% Similarity=0.402 Sum_probs=22.7
Q ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHHhCCCCHHHHHHHHH
Q 040572 83 DLAFHMSNILDTGLDRHTLSVLIALCDLGVNPEALAAVVK 122 (142)
Q Consensus 83 DiL~EIS~LLNTGLDReTLsICI~LcE~GVNPEALA~VIK 122 (142)
++++|+++||- -+++-|-..||+++.+..++.
T Consensus 221 ~lieElADLLy--------HlLVLl~~~GIsleeV~~eL~ 252 (271)
T PLN02346 221 RTASEMADVLY--------HAMVLLAKQGVKMEDVLEVLR 252 (271)
T ss_pred HHHHHHHHHHH--------HHHHHHHHcCCCHHHHHHHHH
Confidence 46778888863 456677789999987665433
No 161
>TIGR01593 holin_tox_secr toxin secretion/phage lysis holin. This model describes one of the many mutally dissimilar families of holins, phage proteins that act together with lytic enzymes in bacterial lysis. This family includes, besides phage holins, the protein TcdE/UtxA involved in toxin secretion in Clostridium difficile and related species.
Probab=21.59 E-value=1.8e+02 Score=21.74 Aligned_cols=33 Identities=33% Similarity=0.554 Sum_probs=27.9
Q ss_pred HHHHHHHHHHHhCCCC-HHHHHHHHHHHHhCCCC
Q 040572 98 RHTLSVLIALCDLGVN-PEALAAVVKELQREPSP 130 (142)
Q Consensus 98 ReTLsICI~LcE~GVN-PEALA~VIKELRrE~~a 130 (142)
.|.+||+=++-+.|+. |+.|.++++.|+++.+.
T Consensus 90 nE~lSIlEN~~~~G~pvP~~l~~~l~~l~~~~~~ 123 (128)
T TIGR01593 90 NESLSILENLALLGVKVPEMLVDILETLKNKTKE 123 (128)
T ss_pred HHHHHHHHHHHHhCCCchHHHHHHHHHHHHhccc
Confidence 5778888888899985 79999999999887665
No 162
>cd02259 Peptidase_C39_like Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is not conserved in all sub-families.
Probab=21.56 E-value=2.5e+02 Score=18.43 Aligned_cols=46 Identities=13% Similarity=0.085 Sum_probs=38.0
Q ss_pred HHHHHHHHHHHHhcCCCCHHHHHHHHHHHhCCCCHHHHHHHHHHHH
Q 040572 80 ESLDLAFHMSNILDTGLDRHTLSVLIALCDLGVNPEALAAVVKELQ 125 (142)
Q Consensus 80 EtLDiL~EIS~LLNTGLDReTLsICI~LcE~GVNPEALA~VIKELR 125 (142)
..+..|..|...++...+.+.|..-+.+-+.|.+...|..+.+.+-
T Consensus 7 ~gl~~l~~i~~~~g~~~~~~~l~~~~~~~~~~~~~~~l~~~a~~~g 52 (122)
T cd02259 7 CGLACLQMLLRYFGIPVRRDVLLNAQQRRQQGLSLADLVSLANKLG 52 (122)
T ss_pred hHHHHHHHHHHHcCCCCCHHHHHHHHhhccCCCCHHHHHHHHHHcC
Confidence 5677888899999999999999877777778899998888876543
No 163
>PRK06645 DNA polymerase III subunits gamma and tau; Validated
Probab=21.48 E-value=2.5e+02 Score=25.74 Aligned_cols=36 Identities=11% Similarity=0.146 Sum_probs=26.1
Q ss_pred HHHHHHHHhcCCCCHHHHHHHHHHHhCCCCHHHHHH
Q 040572 84 LAFHMSNILDTGLDRHTLSVLIALCDLGVNPEALAA 119 (142)
Q Consensus 84 iL~EIS~LLNTGLDReTLsICI~LcE~GVNPEALA~ 119 (142)
.+++|-+.+-.|=-..+|.++-.|++.|.+|..+..
T Consensus 260 ~if~L~~ai~~~d~~~Al~~l~~L~~~g~~~~~~l~ 295 (507)
T PRK06645 260 VIIEFVEYIIHRETEKAINLINKLYGSSVNLEIFIE 295 (507)
T ss_pred HHHHHHHHHHcCCHHHHHHHHHHHHHcCCCHHHHHH
Confidence 344444444455566789999999999999998643
No 164
>PF06673 L_lactis_ph-MCP: Lactococcus lactis bacteriophage major capsid protein; InterPro: IPR009559 This family consists of several Lactococcus lactis bacteriophage major capsid proteins.
Probab=21.30 E-value=86 Score=27.68 Aligned_cols=32 Identities=28% Similarity=0.365 Sum_probs=25.8
Q ss_pred HHHHHHHHHHhCCCCHHHHHHHHHHHHhCCCC
Q 040572 99 HTLSVLIALCDLGVNPEALAAVVKELQREPSP 130 (142)
Q Consensus 99 eTLsICI~LcE~GVNPEALA~VIKELRrE~~a 130 (142)
||-.+.-.-||+||.-..|.+.|.||.+|.+.
T Consensus 5 etqemmkqaieagvkvreleakveelnkeree 36 (347)
T PF06673_consen 5 ETQEMMKQAIEAGVKVRELEAKVEELNKEREE 36 (347)
T ss_pred HHHHHHHHHHHhccchHHHHHHHHHHHHHHHH
Confidence 56677778899999999999999888776544
No 165
>PRK11173 two-component response regulator; Provisional
Probab=21.26 E-value=1.5e+02 Score=21.71 Aligned_cols=58 Identities=10% Similarity=0.138 Sum_probs=43.6
Q ss_pred HHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHhCCCCHHHHHHHHHHHHhCCCC
Q 040572 73 EAARTARESLDLAFHMSNILDTGLDRHTLSVLIALCDLGVNPEALAAVVKELQREPSP 130 (142)
Q Consensus 73 d~~~aArEtLDiL~EIS~LLNTGLDReTLsICI~LcE~GVNPEALA~VIKELRrE~~a 130 (142)
..+.-...-+++|.-+..=.+.=++|+.|.--|.=-+...+...|...|+.||+....
T Consensus 157 ~~~~Lt~~E~~ll~~l~~~~g~v~sr~~l~~~vw~~~~~~~~~~~~~~i~rlR~kl~~ 214 (237)
T PRK11173 157 EQYKLPRSEFRAMLHFCENPGKIQSRAELLKKMTGRELKPHDRTVDVTIRRIRKHFES 214 (237)
T ss_pred eEEeCCHHHHHHHHHHHhCCCccCcHHHHHHHhcCcCCCCCCccHHHHHHHHHHHhcc
Confidence 3344455567777777776778889999887775445556788999999999998764
No 166
>PRK08487 DNA polymerase III subunit delta; Validated
Probab=21.14 E-value=2.8e+02 Score=22.89 Aligned_cols=41 Identities=17% Similarity=0.007 Sum_probs=29.0
Q ss_pred HHHHHHHHhcCCCCHHHHHHHHHHHhCCCCHHH-HHHHHHHHHh
Q 040572 84 LAFHMSNILDTGLDRHTLSVLIALCDLGVNPEA-LAAVVKELQR 126 (142)
Q Consensus 84 iL~EIS~LLNTGLDReTLsICI~LcE~GVNPEA-LA~VIKELRr 126 (142)
.+|++.+.+-.|= ..+.++-.|.+.|.+|-. |+.+.+++|.
T Consensus 204 ~vF~l~dai~~g~--~a~~~l~~L~~~g~~pi~Il~~L~r~~~~ 245 (328)
T PRK08487 204 SFEDFFEKLLNKK--DIKDDLEKLLEEGFNEIALLNSLERFFYQ 245 (328)
T ss_pred cHHHHHHHHHCCC--cHHHHHHHHHHCCCCHHHHHHHHHHHHHH
Confidence 3555655555554 478888899999999988 4666666654
No 167
>PRK09071 hypothetical protein; Validated
Probab=21.01 E-value=4.1e+02 Score=22.83 Aligned_cols=43 Identities=26% Similarity=0.325 Sum_probs=34.5
Q ss_pred HHHHhcCCCCHHHH-HHHHHHHhCCCCHHHHHHHHHHHHhCCCC
Q 040572 88 MSNILDTGLDRHTL-SVLIALCDLGVNPEALAAVVKELQREPSP 130 (142)
Q Consensus 88 IS~LLNTGLDReTL-sICI~LcE~GVNPEALA~VIKELRrE~~a 130 (142)
|..||+=..+...+ ++++.|--.|..++.|+..++-||+.+..
T Consensus 30 ~~~il~g~~~~~q~aAfL~alr~kgeT~eEi~g~~~a~r~~~~~ 73 (323)
T PRK09071 30 MGMILDGEVEDDQLGAFLMLLRVKEETAEELAGFVEAIRERLQA 73 (323)
T ss_pred HHHHHcCCCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhccc
Confidence 34566777776554 67788999999999999999999988754
No 168
>PRK08136 glycosyl transferase family protein; Provisional
Probab=21.00 E-value=5.4e+02 Score=22.14 Aligned_cols=43 Identities=23% Similarity=0.336 Sum_probs=35.0
Q ss_pred HHHHhcCCCCHHHH-HHHHHHHhCCCCHHHHHHHHHHHHhCCCC
Q 040572 88 MSNILDTGLDRHTL-SVLIALCDLGVNPEALAAVVKELQREPSP 130 (142)
Q Consensus 88 IS~LLNTGLDReTL-sICI~LcE~GVNPEALA~VIKELRrE~~a 130 (142)
|..||+-..+...+ ++|+.|--.|-.+|.|+..++-+|+....
T Consensus 29 ~~~il~g~~~~~qi~AfL~alr~KgET~eElaG~~~a~~~~~~~ 72 (317)
T PRK08136 29 YGAMLDGRVPDLELGAILIALRIKGESEAEMLGFLDAMQAHTIP 72 (317)
T ss_pred HHHHHcCCCCHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHhCCc
Confidence 45667777887666 56777889999999999999999988764
No 169
>PRK14971 DNA polymerase III subunits gamma and tau; Provisional
Probab=20.94 E-value=2.6e+02 Score=25.97 Aligned_cols=44 Identities=14% Similarity=0.298 Sum_probs=31.5
Q ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHHhCCCCHHH-HHHHHHHHHh
Q 040572 83 DLAFHMSNILDTGLDRHTLSVLIALCDLGVNPEA-LAAVVKELQR 126 (142)
Q Consensus 83 DiL~EIS~LLNTGLDReTLsICI~LcE~GVNPEA-LA~VIKELRr 126 (142)
+.+|+|.+.+-.|=..++|.++-.|+..|.+|.. |+.++..+|.
T Consensus 249 ~~iF~L~dai~~~~~~~al~ll~~Ll~~g~~~~~iL~~L~~~fRd 293 (614)
T PRK14971 249 DYYFRLTDALLAGKVSDSLLLFDEILNKGFDGSHFITGLASHFRD 293 (614)
T ss_pred HHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHH
Confidence 3456666666667677889999999999999976 4555554443
No 170
>PF07865 DUF1652: Protein of unknown function (DUF1652); InterPro: IPR012448 The proteins in this entry have not been characterised.
Probab=20.94 E-value=1.2e+02 Score=21.13 Aligned_cols=27 Identities=22% Similarity=0.349 Sum_probs=18.5
Q ss_pred hcCCCCHHHHHHHHHHHhCCCCHHHHHHHHHHHHhCC
Q 040572 92 LDTGLDRHTLSVLIALCDLGVNPEALAAVVKELQREP 128 (142)
Q Consensus 92 LNTGLDReTLsICI~LcE~GVNPEALA~VIKELRrE~ 128 (142)
.-||+|-+.| .++.+++++|.+||.|.
T Consensus 42 ~vtGI~~~~l----------~s~rdI~~LI~eLr~el 68 (69)
T PF07865_consen 42 TVTGISTSAL----------NSSRDIVRLIAELRAEL 68 (69)
T ss_pred EEcCcCHHHc----------CCHHHHHHHHHHHHHhc
Confidence 3466666555 35677888888888764
No 171
>cd00043 CYCLIN Cyclin box fold. Protein binding domain functioning in cell-cycle and transcription control. Present in cyclins, TFIIB and Retinoblastoma (RB).The cyclins consist of 8 classes of cell cycle regulators that regulate cyclin dependent kinases (CDKs). TFIIB is a transcription factor that binds the TATA box. Cyclins, TFIIB and RB contain 2 copies of the domain.
Probab=20.93 E-value=2e+02 Score=17.16 Aligned_cols=40 Identities=33% Similarity=0.483 Sum_probs=25.7
Q ss_pred HHHHHHHHHHHhcCCCCHHHHHHHHHHHhC--------CCCHHHHHHHHH
Q 040572 81 SLDLAFHMSNILDTGLDRHTLSVLIALCDL--------GVNPEALAAVVK 122 (142)
Q Consensus 81 tLDiL~EIS~LLNTGLDReTLsICI~LcE~--------GVNPEALA~VIK 122 (142)
.++-+.++...+ +++.+++.+.+.++|. |.+|+.+|....
T Consensus 5 ~~~~l~~~~~~~--~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~ia~a~l 52 (88)
T cd00043 5 PLDFLRRVAKAL--GLSPETLTLAVNLLDRFLLDYSVLGRSPSLVAAAAL 52 (88)
T ss_pred HHHHHHHHHHHc--CCCHHHHHHHHHHHHHHHHhcccccCChHHHHHHHH
Confidence 345555666555 7788888887777663 567777655443
No 172
>PLN03025 replication factor C subunit; Provisional
Probab=20.91 E-value=3e+02 Score=22.44 Aligned_cols=29 Identities=24% Similarity=0.293 Sum_probs=19.9
Q ss_pred CCCHHHHHHHHHHHhCCCCHHHHHHHHHH
Q 040572 95 GLDRHTLSVLIALCDLGVNPEALAAVVKE 123 (142)
Q Consensus 95 GLDReTLsICI~LcE~GVNPEALA~VIKE 123 (142)
+=-..++.++..|++.|++|..+-..|.+
T Consensus 238 ~~~~~a~~~l~~ll~~g~~~~~Il~~l~~ 266 (319)
T PLN03025 238 GKFDDACDGLKQLYDLGYSPTDIITTLFR 266 (319)
T ss_pred CCHHHHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 33455778888899999999864444333
No 173
>cd04447 DEP_BRCC3 DEP (Dishevelled, Egl-10, and Pleckstrin) domain found in BBRC3-like proteins. BBRC3, also known as DEPDC1B, is a DEP containing protein of unknown function.
Probab=20.75 E-value=1.8e+02 Score=21.60 Aligned_cols=35 Identities=20% Similarity=0.263 Sum_probs=23.5
Q ss_pred HHHHHHHHHHHH---HHhcCCCCH-HHHHHHHHHHhCCC
Q 040572 78 ARESLDLAFHMS---NILDTGLDR-HTLSVLIALCDLGV 112 (142)
Q Consensus 78 ArEtLDiL~EIS---~LLNTGLDR-eTLsICI~LcE~GV 112 (142)
+.|++|.|++.= .-..-.++| +++++|=.|++++|
T Consensus 32 gsEAVDwL~~~l~~n~~fg~~vtR~~av~l~qkll~~hV 70 (92)
T cd04447 32 ASEAVDWLHELLRSNSNFGPEVTRQQTVQLLKKFLKNHV 70 (92)
T ss_pred hHHHHHHHHHHHHhccccCCCCCHHHHHHHHHHHHHcCC
Confidence 568888887651 112335666 57888888999887
No 174
>smart00195 DSPc Dual specificity phosphatase, catalytic domain.
Probab=20.75 E-value=2.3e+02 Score=19.64 Aligned_cols=33 Identities=15% Similarity=0.181 Sum_probs=24.6
Q ss_pred CCCCHHHHHHHHHHH-hCCCCHHHHHHHHHHHHh
Q 040572 94 TGLDRHTLSVLIALC-DLGVNPEALAAVVKELQR 126 (142)
Q Consensus 94 TGLDReTLsICI~Lc-E~GVNPEALA~VIKELRr 126 (142)
.|++|...-++.-|+ ..|.+++.--..|+..|.
T Consensus 87 ~G~~RS~~v~~~yl~~~~~~~~~~A~~~v~~~R~ 120 (138)
T smart00195 87 AGVSRSATLIIAYLMKYRNLSLNDAYDFVKDRRP 120 (138)
T ss_pred CCCchHHHHHHHHHHHHhCCCHHHHHHHHHHHCC
Confidence 399999876665554 689998887777777763
No 175
>PRK00982 acpP acyl carrier protein; Provisional
Probab=20.62 E-value=1.2e+02 Score=19.50 Aligned_cols=41 Identities=22% Similarity=0.305 Sum_probs=31.4
Q ss_pred HHHHhcCCCCHHHHHHHHHH-HhCCCCHHHHHHHHHHHHhCCCC
Q 040572 88 MSNILDTGLDRHTLSVLIAL-CDLGVNPEALAAVVKELQREPSP 130 (142)
Q Consensus 88 IS~LLNTGLDReTLsICI~L-cE~GVNPEALA~VIKELRrE~~a 130 (142)
+++.+ |++.+.+..=..| -+.|++-=....+|.+|.++-.-
T Consensus 12 l~~~l--~~~~~~i~~d~~l~~dlglDSl~~~~li~~le~~f~i 53 (78)
T PRK00982 12 IVEQL--GVDEEEVTPEASFVDDLGADSLDTVELVMALEEEFGI 53 (78)
T ss_pred HHHHH--CCCHHHCCCCcchHhhcCCCHHHHHHHHHHHHHHHCC
Confidence 34444 6777777777788 78999999999999999887654
No 176
>smart00404 PTPc_motif Protein tyrosine phosphatase, catalytic domain motif.
Probab=20.60 E-value=83 Score=19.91 Aligned_cols=37 Identities=19% Similarity=0.236 Sum_probs=26.5
Q ss_pred CCCCHHHHHHHHHHHhCCCC----HHHHHHHHHHHHhCCCC
Q 040572 94 TGLDRHTLSVLIALCDLGVN----PEALAAVVKELQREPSP 130 (142)
Q Consensus 94 TGLDReTLsICI~LcE~GVN----PEALA~VIKELRrE~~a 130 (142)
.|.+|...-+++.|+-.++. .-.+..++++||.....
T Consensus 48 ~G~gRtg~~~~~~~~~~~~~~~~~~~~~~~~~~~ir~~r~~ 88 (105)
T smart00404 48 AGVGRTGTFVALDILLQQLESETGEVDIFQTVKELRKQRPG 88 (105)
T ss_pred CCCChhhHHHHHHHHHHHHHhcCCCCCHHHHHHHHHhhhhh
Confidence 39999998777777766653 34577888888866543
No 177
>smart00012 PTPc_DSPc Protein tyrosine phosphatase, catalytic domain, undefined specificity. Protein tyrosine phosphatases. Homologues detected by this profile and not by those of "PTPc" or "DSPc" are predicted to be protein phosphatases with a similar fold to DSPs and PTPs, yet with unpredicted specificities.
Probab=20.60 E-value=83 Score=19.91 Aligned_cols=37 Identities=19% Similarity=0.236 Sum_probs=26.5
Q ss_pred CCCCHHHHHHHHHHHhCCCC----HHHHHHHHHHHHhCCCC
Q 040572 94 TGLDRHTLSVLIALCDLGVN----PEALAAVVKELQREPSP 130 (142)
Q Consensus 94 TGLDReTLsICI~LcE~GVN----PEALA~VIKELRrE~~a 130 (142)
.|.+|...-+++.|+-.++. .-.+..++++||.....
T Consensus 48 ~G~gRtg~~~~~~~~~~~~~~~~~~~~~~~~~~~ir~~r~~ 88 (105)
T smart00012 48 AGVGRTGTFVALDILLQQLESETGEVDIFQTVKELRKQRPG 88 (105)
T ss_pred CCCChhhHHHHHHHHHHHHHhcCCCCCHHHHHHHHHhhhhh
Confidence 39999998777777766653 34577888888866543
No 178
>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed
Probab=20.40 E-value=3.4e+02 Score=22.19 Aligned_cols=45 Identities=11% Similarity=0.140 Sum_probs=35.3
Q ss_pred HHHHHHHHHHHHhcCCCCHHHHHHHHHHHhCCCCHHHHHHHHHHHHh
Q 040572 80 ESLDLAFHMSNILDTGLDRHTLSVLIALCDLGVNPEALAAVVKELQR 126 (142)
Q Consensus 80 EtLDiL~EIS~LLNTGLDReTLsICI~LcE~GVNPEALA~VIKELRr 126 (142)
+..++|..+...++..++.+.+..+++.|+. +|..+..+++.++.
T Consensus 184 e~~~il~~~~~~~~~~~~~~~~~~ia~~~~G--~pR~a~~~l~~~~~ 228 (328)
T PRK00080 184 ELEKIVKRSARILGVEIDEEGALEIARRSRG--TPRIANRLLRRVRD 228 (328)
T ss_pred HHHHHHHHHHHHcCCCcCHHHHHHHHHHcCC--CchHHHHHHHHHHH
Confidence 4567777788888999999999999998874 66777777776553
No 179
>PRK12850 groEL chaperonin GroEL; Reviewed
Probab=20.39 E-value=1.5e+02 Score=26.79 Aligned_cols=31 Identities=35% Similarity=0.423 Sum_probs=23.6
Q ss_pred HHHHHHHHHHHhCCCCH--------HHHHHHHHHHHhCC
Q 040572 98 RHTLSVLIALCDLGVNP--------EALAAVVKELQREP 128 (142)
Q Consensus 98 ReTLsICI~LcE~GVNP--------EALA~VIKELRrE~ 128 (142)
.+-|.-+..|++.|+|| .|+..+++.|.+..
T Consensus 97 ~~LL~~a~~li~~GihP~~I~~G~~~a~~~~~~~L~~~s 135 (544)
T PRK12850 97 QAIVREGAKLVAAGMNPMDLKRGIDLAVAAVVDELKKIA 135 (544)
T ss_pred HHHHHHHHHHHHCCCChHHHHHHHHHHHHHHHHHHHHhc
Confidence 44567788999999999 67777888886654
No 180
>PRK12849 groEL chaperonin GroEL; Reviewed
Probab=20.23 E-value=1.6e+02 Score=26.81 Aligned_cols=33 Identities=30% Similarity=0.371 Sum_probs=24.9
Q ss_pred CCHHHHHHHHHHHhCCCCH--------HHHHHHHHHHHhCC
Q 040572 96 LDRHTLSVLIALCDLGVNP--------EALAAVVKELQREP 128 (142)
Q Consensus 96 LDReTLsICI~LcE~GVNP--------EALA~VIKELRrE~ 128 (142)
|-.+-|.-+..|++.|+|| .|+..+++.|.+..
T Consensus 94 LageLL~~a~~li~~GihP~~I~~G~~~A~~~~~~~L~~~s 134 (542)
T PRK12849 94 LAQALVQEGLKNVAAGANPMDLKRGIDKAVEAVVEELKALA 134 (542)
T ss_pred HHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHHHHHHhc
Confidence 3345577788999999999 67777888886643
No 181
>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D
Probab=20.21 E-value=1.2e+02 Score=14.44 Aligned_cols=23 Identities=13% Similarity=0.086 Sum_probs=11.8
Q ss_pred CHHHHHHHHHHHhCCCCHHHHHH
Q 040572 97 DRHTLSVLIALCDLGVNPEALAA 119 (142)
Q Consensus 97 DReTLsICI~LcE~GVNPEALA~ 119 (142)
+.+...+.+.+++.|.+...++.
T Consensus 7 ~~~~~~~i~~~~~~~~s~~~ia~ 29 (42)
T cd00569 7 TPEQIEEARRLLAAGESVAEIAR 29 (42)
T ss_pred CHHHHHHHHHHHHcCCCHHHHHH
Confidence 33444455555566665555543
No 182
>PRK09849 putative oxidoreductase; Provisional
Probab=20.17 E-value=2.3e+02 Score=27.29 Aligned_cols=36 Identities=22% Similarity=0.241 Sum_probs=26.6
Q ss_pred HHHhcC-CCCHH---HHHHHHHHHhCCC---------------------CHHHHHHHHHHH
Q 040572 89 SNILDT-GLDRH---TLSVLIALCDLGV---------------------NPEALAAVVKEL 124 (142)
Q Consensus 89 S~LLNT-GLDRe---TLsICI~LcE~GV---------------------NPEALA~VIKEL 124 (142)
.+|.|- |||-. ++...++|-|.|+ |+|++..+|..|
T Consensus 370 n~Lcn~lGlDtS~G~tIA~amEl~ekGil~~~~~~ed~~~l~~~~l~~Gd~e~~~~ll~~I 430 (702)
T PRK09849 370 LNLFDDYGLWCNYGQLHRDFTYCYSKGVFKRVLPAEEYAEIRWDQLEAGDPAFLKDFYYRI 430 (702)
T ss_pred HHHHHHhCCcccHHHHHHHHHHHHHCCCCCcccchhhccccccccccCCCHHHHHHHHHHH
Confidence 345554 77763 5888888888887 688888888777
No 183
>TIGR01387 cztR_silR_copR heavy metal response regulator. Members of this family contain a response regulator receiver domain (Pfam:PF00072) and an associated transcriptional regulatory region (Pfam:PF00486). This group is separated phylogenetically from related proteins with similar architecture and contains a number of proteins associated with heavy metal resistance efflux systems for copper, silver, cadmium, and/or zinc. Most members encoded by genes adjacent to genes for encoding a member of the heavy metal sensor histidine kinase family (TIGRFAMs:TIGR01386), its partner in the two-component response regulator system.
Probab=20.12 E-value=1.1e+02 Score=21.34 Aligned_cols=51 Identities=10% Similarity=0.204 Sum_probs=35.0
Q ss_pred HHHHHHHHHHHHhcCCCCHHHHHHHHHHHhCCCCHHHHHHHHHHHHhCCCC
Q 040572 80 ESLDLAFHMSNILDTGLDRHTLSVLIALCDLGVNPEALAAVVKELQREPSP 130 (142)
Q Consensus 80 EtLDiL~EIS~LLNTGLDReTLsICI~LcE~GVNPEALA~VIKELRrE~~a 130 (142)
.-+++|.-+..-.+.-++|+.|.--+.=-+...+...+...|..||+....
T Consensus 151 ~E~~il~~l~~~~~~~~sr~~i~~~~~~~~~~~~~~~~~~~i~~lr~kl~~ 201 (218)
T TIGR01387 151 KEFQLLWLLMRRTGEVLPRTVIASLVWGMNFDSDTNVVDVAIRRLRAKVDD 201 (218)
T ss_pred HHHHHHHHHHhCCCeeEcHHHHHHHhcCCCCCCCcCCHHHHHHHHHHhhcC
Confidence 345666666655555588888765553334456778999999999998764
No 184
>TIGR00959 ffh signal recognition particle protein. This model represents Ffh (Fifty-Four Homolog), the protein component that forms the bacterial (and organellar) signal recognition particle together with a 4.5S RNA. Ffh is a GTPase homologous to eukaryotic SRP54 and also to the GTPase FtsY (TIGR00064) that is the receptor for the signal recognition particle.
Probab=20.03 E-value=1.1e+02 Score=27.26 Aligned_cols=28 Identities=18% Similarity=0.345 Sum_probs=22.2
Q ss_pred HHHHHHHhCCCCHHHHHHHHHHHHhCCC
Q 040572 102 SVLIALCDLGVNPEALAAVVKELQREPS 129 (142)
Q Consensus 102 sICI~LcE~GVNPEALA~VIKELRrE~~ 129 (142)
.|..+|++++||.+..-.+++.+++...
T Consensus 32 ei~~~Ll~aDV~~~~v~~~~~~i~~~~~ 59 (428)
T TIGR00959 32 EIRLALLEADVNLQVVKDFIKKVKEKAL 59 (428)
T ss_pred HHHHHHHHCCCCHHHHHHHHHHHHHHhc
Confidence 4677889999999888888888876543
No 185
>COG1459 PulF Type II secretory pathway, component PulF [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=20.02 E-value=2.5e+02 Score=24.97 Aligned_cols=51 Identities=14% Similarity=0.195 Sum_probs=35.5
Q ss_pred HHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHhCCCCHHHHHHHHHHHHhCCCC
Q 040572 77 TARESLDLAFHMSNILDTGLDRHTLSVLIALCDLGVNPEALAAVVKELQREPSP 130 (142)
Q Consensus 77 aArEtLDiL~EIS~LLNTGLDReTLsICI~LcE~GVNPEALA~VIKELRrE~~a 130 (142)
..++......+++.||+.|+. |.-+++++..+-.=..+..++++++.+...
T Consensus 56 ~~~~l~~f~~qLa~Ll~aG~p---L~~aL~~l~~q~~~~~~~~~l~~i~~~l~~ 106 (397)
T COG1459 56 SKKDLALFTRQLATLLKAGLP---LYEALEILADQAPNPKLKQVLTSILEELES 106 (397)
T ss_pred CHHHHHHHHHHHHHHHHCCCc---HHHHHHHHHHhCCCHHHHHHHHHHHHHHHC
Confidence 356788899999999999996 444455555554446677777777765544
Done!