Query psy3153
Match_columns 89
No_of_seqs 88 out of 109
Neff 3.0
Searched_HMMs 46136
Date Fri Aug 16 17:45:33 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy3153.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/3153hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF02284 COX5A: Cytochrome c o 100.0 4.2E-52 9.2E-57 291.0 6.2 76 1-77 33-108 (108)
2 cd00923 Cyt_c_Oxidase_Va Cytoc 100.0 3.6E-50 7.8E-55 279.5 6.0 74 1-75 30-103 (103)
3 KOG4077|consensus 100.0 1.6E-46 3.4E-51 274.2 6.3 78 1-79 72-149 (149)
4 PF08542 Rep_fac_C: Replicatio 90.1 2.1 4.6E-05 26.6 6.3 53 10-68 2-54 (89)
5 PF08822 DUF1804: Protein of u 87.8 1.2 2.7E-05 33.3 4.7 46 17-66 109-158 (165)
6 PF13812 PPR_3: Pentatricopept 87.7 1.4 3E-05 22.2 3.6 26 16-41 4-29 (34)
7 PF13041 PPR_2: PPR repeat fam 85.3 4.6 9.9E-05 22.6 5.2 46 11-56 1-46 (50)
8 KOG2908|consensus 82.9 3.7 8E-05 34.6 5.7 35 12-46 74-108 (380)
9 PF00617 RasGEF: RasGEF domain 80.9 2.1 4.6E-05 29.2 3.1 50 15-65 80-129 (188)
10 PF13089 PP_kinase_N: Polyphos 80.3 1.1 2.3E-05 30.5 1.5 39 30-68 68-106 (109)
11 PF01535 PPR: PPR repeat; Int 79.3 4 8.7E-05 19.9 3.1 27 16-42 3-29 (31)
12 TIGR00756 PPR pentatricopeptid 79.2 4.8 0.0001 19.7 3.4 27 16-42 3-29 (35)
13 PF13174 TPR_6: Tetratricopept 76.9 5.9 0.00013 19.5 3.4 24 22-45 9-32 (33)
14 TIGR01837 PHA_granule_1 poly(h 76.0 5.2 0.00011 27.6 3.9 26 48-73 73-98 (118)
15 PF14559 TPR_19: Tetratricopep 75.8 6.9 0.00015 22.2 3.8 44 12-57 24-67 (68)
16 PF14853 Fis1_TPR_C: Fis1 C-te 72.8 15 0.00033 22.3 5.0 43 22-66 10-52 (53)
17 PF09597 IGR: IGR protein moti 72.3 3.5 7.6E-05 26.1 2.1 40 27-70 2-42 (57)
18 cd08183 Fe-ADH2 Iron-containin 70.2 8.1 0.00018 30.4 4.2 32 49-80 313-344 (374)
19 PF13176 TPR_7: Tetratricopept 70.0 5.4 0.00012 21.4 2.3 18 21-38 7-24 (36)
20 PF13428 TPR_14: Tetratricopep 67.3 18 0.00039 19.8 4.2 32 15-46 3-34 (44)
21 PF02637 GatB_Yqey: GatB domai 66.4 4.6 0.0001 27.9 1.9 35 34-69 1-35 (148)
22 PF12192 CBP: Fungal calcium b 66.0 14 0.0003 24.0 3.9 43 26-72 8-57 (59)
23 PF00627 UBA: UBA/TS-N domain; 65.4 8.3 0.00018 21.2 2.5 23 12-36 15-37 (37)
24 PF12921 ATP13: Mitochondrial 65.2 18 0.0004 25.0 4.7 51 6-56 45-96 (126)
25 PF15469 Sec5: Exocyst complex 62.2 19 0.00042 25.4 4.5 49 18-66 91-141 (182)
26 PF05597 Phasin: Poly(hydroxya 59.1 21 0.00045 25.6 4.2 39 35-73 73-111 (132)
27 cd00620 Methyltransferase_Sun 56.1 17 0.00036 24.3 3.2 36 6-43 87-122 (126)
28 PF07261 DnaB_2: Replication i 53.2 14 0.00031 22.1 2.3 22 51-73 50-71 (77)
29 PF13925 Katanin_con80: con80 52.6 30 0.00066 24.7 4.2 29 16-44 30-60 (164)
30 smart00147 RasGEF Guanine nucl 51.2 19 0.00041 26.2 3.0 24 20-43 85-108 (242)
31 PF12854 PPR_1: PPR repeat 50.6 38 0.00083 18.1 3.5 32 8-39 2-33 (34)
32 PF14726 RTTN_N: Rotatin, an a 50.0 32 0.00068 23.5 3.8 41 5-46 39-86 (98)
33 PF01029 NusB: NusB family; I 50.0 17 0.00038 24.1 2.5 36 7-43 97-132 (134)
34 PLN03081 pentatricopeptide (PP 49.4 29 0.00063 29.0 4.1 51 5-55 418-469 (697)
35 PRK00117 recX recombination re 49.2 58 0.0013 22.4 5.1 28 12-39 41-71 (157)
36 PF14663 RasGEF_N_2: Rapamycin 46.5 37 0.00081 23.0 3.7 16 51-66 41-56 (115)
37 PF05854 MC1: Non-histone chro 46.0 9.3 0.0002 26.7 0.7 9 17-25 26-34 (93)
38 PF12374 Dmrt1: Double-sex mab 45.3 11 0.00023 24.7 0.9 19 64-84 1-19 (71)
39 PF15564 Imm13: Immunity prote 44.3 18 0.00039 26.5 2.0 39 50-88 4-42 (131)
40 PF03634 TCP: TCP family trans 43.3 39 0.00085 23.3 3.5 44 24-68 20-65 (138)
41 PLN03077 Protein ECB2; Provisi 42.9 40 0.00086 28.9 4.1 50 6-55 582-632 (857)
42 PRK04016 DNA-directed RNA poly 42.2 21 0.00045 23.2 1.8 27 42-68 9-41 (62)
43 KOG3103|consensus 41.5 12 0.00025 30.1 0.7 10 59-68 82-91 (249)
44 PF14337 DUF4393: Domain of un 41.5 70 0.0015 22.5 4.6 51 10-60 13-68 (186)
45 PF08626 TRAPPC9-Trs120: Trans 40.9 27 0.00059 32.1 3.0 26 14-39 524-549 (1185)
46 PLN00032 DNA-directed RNA poly 40.9 22 0.00048 23.7 1.9 27 42-68 9-41 (71)
47 PRK12451 arginyl-tRNA syntheta 40.8 22 0.00047 30.1 2.2 58 14-73 505-562 (562)
48 cd00194 UBA Ubiquitin Associat 40.3 46 0.001 17.7 2.8 22 13-36 15-36 (38)
49 PF05746 DALR_1: DALR anticodo 40.2 9.9 0.00022 24.3 0.1 52 22-73 61-119 (119)
50 PF02037 SAP: SAP domain; Int 40.2 21 0.00045 19.8 1.4 18 53-70 4-21 (35)
51 cd08171 GlyDH-like2 Glycerol d 39.7 15 0.00033 28.5 1.1 28 53-80 285-313 (345)
52 PLN03081 pentatricopeptide (PP 39.2 79 0.0017 26.5 5.2 60 8-68 489-560 (697)
53 smart00165 UBA Ubiquitin assoc 38.7 50 0.0011 17.5 2.8 22 13-36 15-36 (37)
54 TIGR00456 argS arginyl-tRNA sy 38.7 15 0.00032 30.9 0.9 59 14-73 507-566 (566)
55 cd00155 RasGEF Guanine nucleot 38.1 34 0.00074 24.6 2.6 24 18-41 83-106 (237)
56 PF03368 Dicer_dimer: Dicer di 38.0 22 0.00048 23.1 1.5 12 16-27 61-72 (90)
57 PF10602 RPN7: 26S proteasome 37.9 40 0.00087 24.2 3.0 33 25-58 48-80 (177)
58 cd08193 HVD 5-hydroxyvalerate 37.8 33 0.00073 26.9 2.7 31 50-80 314-345 (376)
59 PF04289 DUF447: Protein of un 37.6 81 0.0018 22.8 4.5 42 14-55 130-176 (177)
60 cd06101 citrate_synt Citrate s 37.6 98 0.0021 23.9 5.2 61 5-68 159-228 (265)
61 PF09986 DUF2225: Uncharacteri 37.2 29 0.00063 25.9 2.2 36 21-59 173-208 (214)
62 PF01194 RNA_pol_N: RNA polyme 36.9 37 0.00081 21.8 2.4 27 42-68 9-41 (60)
63 PF05138 PaaA_PaaC: Phenylacet 36.4 22 0.00048 27.6 1.5 24 48-71 204-227 (263)
64 PRK10304 ferritin; Provisional 36.2 79 0.0017 22.7 4.3 43 15-59 100-142 (165)
65 cd08194 Fe-ADH6 Iron-containin 35.9 25 0.00053 27.7 1.7 29 51-79 312-340 (375)
66 PRK15138 aldehyde reductase; P 35.7 28 0.00061 27.8 2.0 31 49-79 321-352 (387)
67 PF06293 Kdo: Lipopolysacchari 35.2 15 0.00031 26.3 0.3 17 61-77 67-83 (206)
68 PLN02522 ATP citrate (pro-S)-l 35.1 1E+02 0.0023 27.2 5.5 58 10-68 495-552 (608)
69 cd07956 Anticodon_Ia_Arg Antic 34.7 27 0.00058 24.0 1.6 24 50-73 133-156 (156)
70 PF04336 DUF479: Protein of un 34.3 39 0.00085 22.4 2.3 42 14-55 59-104 (106)
71 PLN03218 maturation of RBCL 1; 34.2 63 0.0014 29.9 4.2 34 8-41 502-535 (1060)
72 smart00386 HAT HAT (Half-A-TPR 34.1 59 0.0013 15.4 3.1 29 27-56 1-29 (33)
73 PF13419 HAD_2: Haloacid dehal 34.0 14 0.00031 23.4 0.1 50 29-79 79-135 (176)
74 smart00513 SAP Putative DNA-bi 33.5 33 0.00071 18.7 1.5 16 55-70 6-21 (35)
75 TIGR02158 PA_CoA_Oxy3 phenylac 33.2 38 0.00082 26.3 2.3 26 48-73 178-203 (237)
76 TIGR02795 tol_pal_ybgF tol-pal 33.1 1.1E+02 0.0024 18.2 4.5 27 19-45 45-71 (119)
77 COG3888 Predicted transcriptio 32.9 40 0.00088 28.0 2.5 35 37-72 282-316 (321)
78 PF07980 SusD: SusD family; I 32.6 1.6E+02 0.0035 20.4 5.3 31 15-45 135-165 (266)
79 PF03530 SK_channel: Calcium-a 32.6 43 0.00092 23.9 2.3 20 19-38 8-27 (119)
80 TIGR02552 LcrH_SycD type III s 32.2 1.3E+02 0.0028 18.8 6.0 25 22-46 94-118 (135)
81 PF07721 TPR_4: Tetratricopept 32.0 53 0.0012 16.5 2.1 17 21-37 9-25 (26)
82 PRK05443 polyphosphate kinase; 31.5 32 0.0007 30.5 1.9 40 30-69 83-122 (691)
83 smart00546 CUE Domain that may 31.4 69 0.0015 17.8 2.7 22 13-36 18-39 (43)
84 KOG4281|consensus 31.2 71 0.0015 25.6 3.6 42 32-76 4-45 (236)
85 PF02631 RecX: RecX family; I 30.4 1.6E+02 0.0035 19.3 5.8 49 12-68 7-58 (121)
86 cd01041 Rubrerythrin Rubreryth 29.9 1.1E+02 0.0023 20.5 3.8 30 14-43 91-120 (134)
87 cd08176 LPO Lactadehyde:propan 29.9 28 0.00061 27.4 1.2 29 52-80 318-347 (377)
88 PF08967 DUF1884: Domain of un 29.8 24 0.00052 24.3 0.7 43 32-77 7-63 (85)
89 COG1644 RPB10 DNA-directed RNA 29.7 39 0.00084 22.2 1.6 27 42-68 9-41 (63)
90 PF13743 Thioredoxin_5: Thiore 28.8 1.9E+02 0.0042 20.5 5.2 57 8-68 59-116 (176)
91 PF13766 ECH_C: 2-enoyl-CoA Hy 28.5 23 0.0005 24.2 0.4 49 2-57 10-58 (118)
92 PF03705 CheR_N: CheR methyltr 28.2 84 0.0018 17.9 2.7 40 34-73 7-47 (57)
93 TIGR00198 cat_per_HPI catalase 28.0 50 0.0011 29.9 2.5 19 28-46 121-139 (716)
94 PF05843 Suf: Suppressor of fo 27.7 1.3E+02 0.0028 22.8 4.3 30 26-56 49-78 (280)
95 TIGR01951 nusB transcription a 27.7 61 0.0013 21.3 2.3 34 9-43 93-126 (129)
96 PF08405 Calici_PP_N: Viral po 27.6 1.4E+02 0.003 25.3 4.8 41 16-59 250-290 (358)
97 COG3629 DnrI DNA-binding trans 27.5 1.1E+02 0.0025 24.4 4.2 29 14-42 188-216 (280)
98 smart00836 DALR_1 DALR anticod 27.5 42 0.0009 21.6 1.5 24 50-73 99-122 (122)
99 KOG2005|consensus 27.5 73 0.0016 29.7 3.4 29 8-36 231-262 (878)
100 PLN03077 Protein ECB2; Provisi 27.1 3.1E+02 0.0068 23.6 7.0 61 7-68 651-723 (857)
101 cd00619 Terminator_NusB Transc 27.0 68 0.0015 21.2 2.5 36 7-43 91-126 (130)
102 cd08175 G1PDH Glycerol-1-phosp 26.7 28 0.0006 27.0 0.6 27 54-80 295-322 (348)
103 TIGR02058 lin0512_fam conserve 26.7 54 0.0012 23.5 2.1 23 2-30 11-36 (116)
104 PRK10947 global DNA-binding tr 26.4 1.2E+02 0.0027 21.8 3.8 22 51-73 54-75 (135)
105 cd08186 Fe-ADH8 Iron-containin 26.3 36 0.00079 26.9 1.2 28 52-79 317-345 (383)
106 PRK06224 citrate synthase; Pro 26.3 1.6E+02 0.0035 22.6 4.7 58 11-69 155-213 (263)
107 PF00378 ECH: Enoyl-CoA hydrat 26.2 96 0.0021 22.5 3.3 37 7-43 173-210 (245)
108 PF07442 Ponericin: Ponericin; 26.1 39 0.00085 19.2 1.0 12 12-23 17-28 (29)
109 KOG4204|consensus 26.1 78 0.0017 24.4 3.0 51 28-80 18-74 (231)
110 COG5304 Uncharacterized protei 25.8 68 0.0015 22.4 2.4 26 32-58 59-84 (92)
111 PRK10586 putative oxidoreducta 25.8 59 0.0013 26.0 2.3 26 52-77 292-318 (362)
112 PF06267 DUF1028: Family of un 25.7 68 0.0015 24.4 2.5 33 10-42 118-150 (190)
113 PF03704 BTAD: Bacterial trans 25.7 2E+02 0.0042 18.7 5.1 29 16-44 65-93 (146)
114 smart00138 MeTrc Methyltransfe 25.7 1E+02 0.0022 23.3 3.5 40 34-73 6-46 (264)
115 cd00913 PCD_DCoH_subfamily_a P 25.5 33 0.00072 21.5 0.7 26 26-53 17-42 (76)
116 PF13646 HEAT_2: HEAT repeats; 25.4 1.4E+02 0.003 17.5 3.4 25 11-36 43-67 (88)
117 PF02607 B12-binding_2: B12 bi 25.4 62 0.0014 19.4 1.9 34 28-66 16-50 (79)
118 TIGR01428 HAD_type_II 2-haloal 25.3 1.5E+02 0.0033 20.2 4.0 65 11-79 76-150 (198)
119 PF08869 XisI: XisI protein; 25.2 46 0.00099 23.5 1.4 24 57-81 78-103 (111)
120 PF08385 DHC_N1: Dynein heavy 24.8 1.2E+02 0.0027 24.3 4.0 59 11-73 61-120 (579)
121 COG3179 Predicted chitinase [G 24.7 34 0.00073 26.9 0.8 24 51-74 20-43 (206)
122 cd08185 Fe-ADH1 Iron-containin 24.7 35 0.00077 26.8 0.9 29 52-80 319-348 (380)
123 cd08188 Fe-ADH4 Iron-containin 24.5 42 0.0009 26.5 1.2 29 52-80 318-347 (377)
124 PLN03218 maturation of RBCL 1; 24.4 2.1E+02 0.0046 26.6 5.8 33 8-40 537-569 (1060)
125 cd08182 HEPD Hydroxyethylphosp 23.3 44 0.00095 26.1 1.2 28 52-79 308-336 (367)
126 TIGR03405 Phn_Fe-ADH phosphona 23.2 47 0.001 26.1 1.3 28 53-80 308-336 (355)
127 cd08180 PDD 1,3-propanediol de 23.1 54 0.0012 25.3 1.6 28 52-79 269-297 (332)
128 cd08191 HHD 6-hydroxyhexanoate 23.0 46 0.001 26.4 1.2 30 50-79 325-355 (386)
129 PF12933 FTO_NTD: FTO catalyti 22.8 62 0.0013 26.1 1.9 26 15-40 97-124 (253)
130 PRK09248 putative hydrolase; V 22.7 1.1E+02 0.0023 22.5 3.0 60 11-81 173-244 (246)
131 PF12827 Peroxin-22: Peroxisom 22.7 46 0.001 23.4 1.1 31 42-74 73-108 (117)
132 PRK09634 nusB transcription an 22.6 87 0.0019 24.0 2.6 37 7-45 164-200 (207)
133 TIGR01870 cas_TM1810_Csm2 CRIS 22.6 1.6E+02 0.0035 19.4 3.6 27 13-39 57-88 (97)
134 PF12525 DUF3726: Protein of u 22.6 1.6E+02 0.0035 19.4 3.6 49 14-73 6-61 (80)
135 PRK13778 paaA phenylacetate-Co 22.6 77 0.0017 25.9 2.4 29 48-76 231-260 (314)
136 PF01329 Pterin_4a: Pterin 4 a 22.6 49 0.0011 21.6 1.1 22 25-46 33-54 (95)
137 PRK00464 nrdR transcriptional 22.5 2.1E+02 0.0046 20.9 4.5 47 13-59 64-117 (154)
138 PF09585 Lin0512_fam: Conserve 22.5 74 0.0016 22.6 2.1 23 2-30 11-36 (113)
139 PF13623 SurA_N_2: SurA N-term 22.3 1.4E+02 0.0031 21.2 3.5 47 27-73 52-111 (145)
140 PF04994 TfoX_C: TfoX C-termin 22.3 29 0.00063 22.6 -0.0 18 56-73 13-30 (81)
141 PF14528 LAGLIDADG_3: LAGLIDAD 22.2 58 0.0013 19.5 1.3 18 52-69 31-48 (77)
142 PRK10015 oxidoreductase; Provi 22.2 1.3E+02 0.0028 24.1 3.6 40 1-40 388-427 (429)
143 smart00860 SMI1_KNR4 SMI1 / KN 22.1 51 0.0011 19.3 1.0 18 56-73 5-22 (129)
144 PF11342 DUF3144: Protein of u 21.8 1.6E+02 0.0034 19.6 3.4 49 14-64 24-72 (78)
145 KOG1953|consensus 21.7 94 0.002 30.1 3.1 30 14-43 563-592 (1235)
146 smart00544 MA3 Domain in DAP-5 21.2 2.3E+02 0.005 18.0 4.4 22 19-40 8-29 (113)
147 cd00447 NusB_Sun RNA binding d 21.2 1.1E+02 0.0025 19.9 2.7 33 10-43 93-125 (129)
148 PF05965 FYRC: F/Y rich C-term 21.1 28 0.00061 22.0 -0.3 35 46-80 22-64 (86)
149 PF07719 TPR_2: Tetratricopept 21.1 1.2E+02 0.0026 14.7 4.8 25 19-43 7-31 (34)
150 TIGR03504 FimV_Cterm FimV C-te 21.0 1E+02 0.0022 18.1 2.2 21 21-41 7-27 (44)
151 PF06368 Met_asp_mut_E: Methyl 20.9 3.7E+02 0.0081 23.3 6.2 52 10-63 28-96 (441)
152 PRK04452 acetyl-CoA decarbonyl 20.6 68 0.0015 26.1 1.8 66 10-76 136-209 (319)
153 cd06111 DsCS_like Cold-active 20.6 1.7E+02 0.0036 23.8 4.0 57 12-69 263-319 (362)
154 PF12688 TPR_5: Tetratrico pep 20.5 2.7E+02 0.0058 19.1 4.5 26 20-45 45-70 (120)
155 KOG3584|consensus 20.5 2.1E+02 0.0045 24.2 4.6 43 18-67 301-343 (348)
156 TIGR03290 CoB_CoM_SS_C CoB--Co 20.5 1.9E+02 0.0041 19.8 3.8 34 35-68 104-141 (144)
157 PF00465 Fe-ADH: Iron-containi 20.4 80 0.0017 24.5 2.0 30 49-78 309-339 (366)
158 PF10865 DUF2703: Domain of un 20.3 72 0.0016 22.5 1.7 20 49-68 23-42 (120)
159 PF11817 Foie-gras_1: Foie gra 20.1 1.5E+02 0.0032 22.1 3.3 35 25-62 190-224 (247)
160 PF13424 TPR_12: Tetratricopep 20.0 1.3E+02 0.0028 17.4 2.5 19 21-39 54-72 (78)
161 smart00845 GatB_Yqey GatB doma 20.0 72 0.0016 22.1 1.6 33 36-69 2-34 (147)
No 1
>PF02284 COX5A: Cytochrome c oxidase subunit Va; InterPro: IPR003204 Cytochrome c oxidase (1.9.3.1 from EC) is an oligomeric enzymatic complex which is a component of the respiratory chain complex and is involved in the transfer of electrons from cytochrome c to oxygen []. In eukaryotes this enzyme complex is located in the mitochondrial inner membrane; in aerobic prokaryotes it is found in the plasma membrane. In eukaryotes, in addition to the three large subunits, I, II and III, that form the catalytic centre of the enzyme complex, there are a variable number of small polypeptidic subunits. One of these subunits is known as Va.; GO: 0004129 cytochrome-c oxidase activity; PDB: 2DYR_R 3AG1_E 3ABL_E 1V54_R 2EIJ_R 1OCR_E 2DYS_E 2EIM_E 2OCC_E 3ASN_R ....
Probab=100.00 E-value=4.2e-52 Score=290.98 Aligned_cols=76 Identities=62% Similarity=1.055 Sum_probs=65.7
Q ss_pred CcccccCCCCCCHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHhcCCcccchHHHHHhhhhhhhhhCCCCccccCCCC
Q psy3153 1 MNDLAQDDGVPDPVIIIAALKAARRLNDYALTIRLLEMVQEKCGKKKKVIWPYILGEIRPTLTELGIETPEDLGYDK 77 (89)
Q Consensus 1 lN~l~~~DlVP~P~ii~AALrAcRRvND~alAVR~lE~iK~K~~~~~~~iY~~~lqElkPtl~ELGI~t~EeLgydk 77 (89)
|||||||||||+|+||+|||||||||||||+||||||+||+|||++ ++|||||+|||||||+||||+|||||||||
T Consensus 33 lN~l~~~DlVP~P~ii~aALrAcRRvND~a~AVR~lE~iK~K~~~~-~~~Y~~~lqElkPtl~ELGI~t~EeLg~dk 108 (108)
T PF02284_consen 33 LNNLFGYDLVPEPKIIEAALRACRRVNDFALAVRILEGIKDKCGNK-KEIYPYILQELKPTLEELGIPTPEELGYDK 108 (108)
T ss_dssp HHHHTTSSB---HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHTTT--TTHHHHHHHHHHHHHHHHT---TTTTTTT-
T ss_pred HHHHhccccCCChHHHHHHHHHHHHhhhHHHHHHHHHHHHHHccCh-HHHHHHHHHHHhhHHHHhCCCCHHHhCCCC
Confidence 7999999999999999999999999999999999999999999998 569999999999999999999999999997
No 2
>cd00923 Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. Found only in eukaryotes, subunit Va is one of three mammalian subunits that lacks a transmembrane region. Subunit Va is located on the matrix side of the membrane and binds thyroid hormone T2, releasing allosteric inhibition caused by the binding of ATP to subunit IV and allowing high turnover at elevated intramitochondrial ATP/ADP ratios.
Probab=100.00 E-value=3.6e-50 Score=279.48 Aligned_cols=74 Identities=59% Similarity=1.048 Sum_probs=72.4
Q ss_pred CcccccCCCCCCHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHhcCCcccchHHHHHhhhhhhhhhCCCCccccCC
Q psy3153 1 MNDLAQDDGVPDPVIIIAALKAARRLNDYALTIRLLEMVQEKCGKKKKVIWPYILGEIRPTLTELGIETPEDLGY 75 (89)
Q Consensus 1 lN~l~~~DlVP~P~ii~AALrAcRRvND~alAVR~lE~iK~K~~~~~~~iY~~~lqElkPtl~ELGI~t~EeLgy 75 (89)
|||||||||||+|+||+|||||||||||||+||||||+||+|||++ ++|||||+|||||||+||||+|||||||
T Consensus 30 mN~l~~~DlVP~P~ii~aaLrAcRRvND~alAVR~lE~vK~K~~~~-~~~y~~~lqeikp~l~ELGI~t~EeLgy 103 (103)
T cd00923 30 LNNLFGYDLVPEPKVIEAALRACRRVNDFALAVRILEAIKDKCGAH-KEIYPYILQEIKPTLKELGISTPEELGY 103 (103)
T ss_pred HHHHhccccCCCcHHHHHHHHHHHHhhhHHHHHHHHHHHHHHccCc-hhhHHHHHHHHhHHHHHHCCCCHHHhCc
Confidence 7999999999999999999999999999999999999999999985 6899999999999999999999999998
No 3
>KOG4077|consensus
Probab=100.00 E-value=1.6e-46 Score=274.20 Aligned_cols=78 Identities=49% Similarity=0.919 Sum_probs=75.4
Q ss_pred CcccccCCCCCCHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHhcCCcccchHHHHHhhhhhhhhhCCCCccccCCCCCc
Q psy3153 1 MNDLAQDDGVPDPVIIIAALKAARRLNDYALTIRLLEMVQEKCGKKKKVIWPYILGEIRPTLTELGIETPEDLGYDKPE 79 (89)
Q Consensus 1 lN~l~~~DlVP~P~ii~AALrAcRRvND~alAVR~lE~iK~K~~~~~~~iY~~~lqElkPtl~ELGI~t~EeLgydkpE 79 (89)
|||||+||+||+|+||+|||||||||||||+||||||+||+|||++ +++||||++||||||.||||+||||||++++|
T Consensus 72 lN~l~~yDlVP~pkvIEaaLRA~RRvNDfa~aVRilE~iK~K~g~~-k~~Y~y~v~elkpvl~ELGI~t~EeLg~~~~~ 149 (149)
T KOG4077|consen 72 LNNLFDYDLVPSPKVIEAALRACRRVNDFATAVRILEAIKDKCGAQ-KQVYPYYVKELKPVLNELGIPTPEELGFPSVE 149 (149)
T ss_pred HHhhhccccCCChHHHHHHHHHHHHhccHHHHHHHHHHHHHhcccH-HHHHHHHHHHHHHHHHHhCCCCHHHhCCCCCC
Confidence 6999999999999999999999999999999999999999999998 66899999999999999999999999988875
No 4
>PF08542 Rep_fac_C: Replication factor C C-terminal domain; InterPro: IPR013748 Replication factor C (RFC) is a multimeric AAA+ protein complex that loads the DNA polymerase processivity clamp PCNA (Proliferating Cell Nuclear Antigen) onto DNA using ATP to drive the reaction []. PCNA functions at multiple levels in directing DNA metabolic pathways []. When bound to DNA, PCNA organises various proteins involved in DNA replication, DNA repair, DNA modification, and chromatin modelling. Replication factor C consists of five subunits in a spiral arrangement: Rfc1, Rfc2, Rfc3, Rfc4, and Rfc5 subunits. Rfc1 and Rfc2 load the PCNA sliding clamp onto DNA, while Rfc3 binds ATP and also acts as a checkpoint sensor. The RFC complex contains four ATP sites (sites A, B, C, and D) located at subunit interfaces. In each ATP site, an arginine residue from one subunit is located near the gamma-phosphate of ATP bound in the adjacent subunit. These arginine residues act as "arginine fingers" that can potentially perform two functions: sensing that ATP is bound and catalyzing ATP hydrolysis []. This entry represents the core domain found in Rfc1-5.; GO: 0003689 DNA clamp loader activity, 0005524 ATP binding, 0006260 DNA replication, 0005663 DNA replication factor C complex; PDB: 1SXJ_B 2CHG_B 2CHV_F 2CHQ_C 1IQP_A.
Probab=90.10 E-value=2.1 Score=26.57 Aligned_cols=53 Identities=23% Similarity=0.268 Sum_probs=38.8
Q ss_pred CCCHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHhcCCcccchHHHHHhhhhhhhhhCCC
Q psy3153 10 VPDPVIIIAALKAARRLNDYALTIRLLEMVQEKCGKKKKVIWPYILGEIRPTLTELGIE 68 (89)
Q Consensus 10 VP~P~ii~AALrAcRRvND~alAVR~lE~iK~K~~~~~~~iY~~~lqElkPtl~ELGI~ 68 (89)
+|.|+.|..-++.|+. ++|..+-..++.+... |=. ...++++|-..+-+..++
T Consensus 2 ~p~~~~i~~i~~~~~~-~~~~~~~~~~~~l~~~-G~s----~~~Il~~l~~~l~~~~~~ 54 (89)
T PF08542_consen 2 WPPPEVIEEILESCLN-GDFKEARKKLYELLVE-GYS----ASDILKQLHEVLVESDIP 54 (89)
T ss_dssp S--HHHHHHHHHHHHH-TCHHHHHHHHHHHHHT-T------HHHHHHHHHHHHHTSTSS
T ss_pred CCCHHHHHHHHHHHHh-CCHHHHHHHHHHHHHc-CCC----HHHHHHHHHHHHHHhhcc
Confidence 5899999999999988 6999999999999888 544 455666666666555443
No 5
>PF08822 DUF1804: Protein of unknown function (DUF1804); InterPro: IPR014926 This entry is represented by Bacteriophage D3112, Orf24. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=87.81 E-value=1.2 Score=33.33 Aligned_cols=46 Identities=20% Similarity=0.379 Sum_probs=37.9
Q ss_pred HHHHHHHHhh----hhHHHHHHHHHHHHHHhcCCcccchHHHHHhhhhhhhhhC
Q psy3153 17 IAALKAARRL----NDYALTIRLLEMVQEKCGKKKKVIWPYILGEIRPTLTELG 66 (89)
Q Consensus 17 ~AALrAcRRv----ND~alAVR~lE~iK~K~~~~~~~iY~~~lqElkPtl~ELG 66 (89)
..+..|+||+ +..++|++++|.+-.-. ++.||.-++.+-.+|++.|
T Consensus 109 ~K~vaaskr~lPets~LavA~~vl~~l~~fv----~e~~P~h~~af~eiLepFg 158 (165)
T PF08822_consen 109 SKMVAASKRVLPETSELAVAMEVLELLAAFV----QERYPQHLAAFLEILEPFG 158 (165)
T ss_pred HHHHHHHhhcCchHHHHHHHHHHHHHHHHHH----HhcCHHHHHHHHHHHHHHH
Confidence 4567889998 99999999999766555 4559999998888888887
No 6
>PF13812 PPR_3: Pentatricopeptide repeat domain
Probab=87.65 E-value=1.4 Score=22.19 Aligned_cols=26 Identities=23% Similarity=0.347 Sum_probs=23.5
Q ss_pred HHHHHHHHHhhhhHHHHHHHHHHHHH
Q psy3153 16 IIAALKAARRLNDYALTIRLLEMVQE 41 (89)
Q Consensus 16 i~AALrAcRRvND~alAVR~lE~iK~ 41 (89)
.++.++||.+-+|+..|.++|+..+.
T Consensus 4 y~~ll~a~~~~g~~~~a~~~~~~M~~ 29 (34)
T PF13812_consen 4 YNALLRACAKAGDPDAALQLFDEMKE 29 (34)
T ss_pred HHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 46789999999999999999998876
No 7
>PF13041 PPR_2: PPR repeat family
Probab=85.31 E-value=4.6 Score=22.59 Aligned_cols=46 Identities=11% Similarity=0.253 Sum_probs=33.6
Q ss_pred CCHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHhcCCcccchHHHHH
Q psy3153 11 PDPVIIIAALKAARRLNDYALTIRLLEMVQEKCGKKKKVIWPYILG 56 (89)
Q Consensus 11 P~P~ii~AALrAcRRvND~alAVR~lE~iK~K~~~~~~~iY~~~lq 56 (89)
|+-..-.+.++++-|-+++..|.++|+..+.+--..-...|.-+++
T Consensus 1 P~~~~yn~li~~~~~~~~~~~a~~l~~~M~~~g~~P~~~Ty~~li~ 46 (50)
T PF13041_consen 1 PDVVTYNTLISGYCKAGKFEEALKLFKEMKKRGIKPDSYTYNILIN 46 (50)
T ss_pred CchHHHHHHHHHHHHCcCHHHHHHHHHHHHHcCCCCCHHHHHHHHH
Confidence 5556778899999999999999999999886522221345555554
No 8
>KOG2908|consensus
Probab=82.93 E-value=3.7 Score=34.63 Aligned_cols=35 Identities=17% Similarity=0.214 Sum_probs=31.1
Q ss_pred CHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHhcCC
Q psy3153 12 DPVIIIAALKAARRLNDYALTIRLLEMVQEKCGKK 46 (89)
Q Consensus 12 ~P~ii~AALrAcRRvND~alAVR~lE~iK~K~~~~ 46 (89)
.=+.|+-+|...|+.||...|++|||.|++|....
T Consensus 74 plslvei~l~~~~~~~D~~~al~~Le~i~~~~~~~ 108 (380)
T KOG2908|consen 74 PLSLVEILLVVSEQISDKDEALEFLEKIIEKLKEY 108 (380)
T ss_pred hHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHhh
Confidence 34678889999999999999999999999998754
No 9
>PF00617 RasGEF: RasGEF domain; InterPro: IPR001895 Ras proteins are membrane-associated molecular switches that bind GTP and GDP and slowly hydrolyze GTP to GDP []. The balance between the GTP bound (active) and GDP bound (inactive) states is regulated by the opposite action of proteins activating the GTPase activity and that of proteins which promote the loss of bound GDP and the uptake of fresh GTP [, ]. The latter proteins are known as guanine-nucleotide dissociation stimulators (GDSs) (or also as guanine-nucleotide releasing (or exchange) factors (GRFs)). Proteins that act as GDS can be classified into at least two families, on the basis of sequence similarities, the CDC24 family (see IPR001331 from INTERPRO) and the CDC25 family. The size of the proteins of the CDC25 family range from 309 residues (LTE1) to 1596 residues (sos). The sequence similarity shared by all these proteins is limited to a region of about 250 amino acids generally located in their C-terminal section (currently the only exceptions are sos and ralGDS where this domain makes up the central part of the protein). This domain has been shown, in CDC25 an SCD25, to be essential for the activity of these proteins.; GO: 0005085 guanyl-nucleotide exchange factor activity, 0007264 small GTPase mediated signal transduction, 0005622 intracellular; PDB: 2IJE_S 3T6G_A 1NVW_S 1BKD_S 1XDV_A 2II0_A 1NVU_S 1NVX_S 1NVV_S 1XD4_B ....
Probab=80.89 E-value=2.1 Score=29.22 Aligned_cols=50 Identities=20% Similarity=0.311 Sum_probs=32.2
Q ss_pred HHHHHHHHHHhhhhHHHHHHHHHHHHHHhcCCcccchHHHHHhhhhhhhhh
Q psy3153 15 IIIAALKAARRLNDYALTIRLLEMVQEKCGKKKKVIWPYILGEIRPTLTEL 65 (89)
Q Consensus 15 ii~AALrAcRRvND~alAVR~lE~iK~K~~~~~~~iY~~~lqElkPtl~EL 65 (89)
.|.-|.. |+.+|||..+.-|+-|+....-.+.+..|..+-++.+-++++|
T Consensus 80 ~I~va~~-l~~l~Nf~s~~aI~~~L~s~~i~rL~~tw~~l~~~~~~~~~~l 129 (188)
T PF00617_consen 80 FIQVAKK-LYELGNFNSLMAILSALNSSSIQRLKKTWKSLSKKSKKTFEEL 129 (188)
T ss_dssp HHHHHHH-HHHTTBHHHHHHHHHHHTSHHHHT-HHHHHTSHHHHHHHHHHH
T ss_pred HHhHHHH-HHHhcCchHHHHHHHHhccccccchhhhhhhhHHHHHHHHHHH
Confidence 4444554 9999999999999999886654333445555544444444443
No 10
>PF13089 PP_kinase_N: Polyphosphate kinase N-terminal domain; PDB: 2O8R_A 1XDP_A 1XDO_B.
Probab=80.29 E-value=1.1 Score=30.52 Aligned_cols=39 Identities=18% Similarity=0.249 Sum_probs=33.5
Q ss_pred HHHHHHHHHHHHHhcCCcccchHHHHHhhhhhhhhhCCC
Q psy3153 30 ALTIRLLEMVQEKCGKKKKVIWPYILGEIRPTLTELGIE 68 (89)
Q Consensus 30 alAVR~lE~iK~K~~~~~~~iY~~~lqElkPtl~ELGI~ 68 (89)
-++-..|+.|..++...++++|..+-++|.|-|++=||-
T Consensus 68 ~tP~eqL~~I~~~v~~l~~~q~~~~~~~Llp~L~~~GI~ 106 (109)
T PF13089_consen 68 LTPQEQLDAIRKRVHELVEEQYEIYNEELLPELAEEGIH 106 (109)
T ss_dssp --HHHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHCTTEE
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCE
Confidence 346678999999999988899999999999999999983
No 11
>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=79.28 E-value=4 Score=19.91 Aligned_cols=27 Identities=4% Similarity=0.276 Sum_probs=23.1
Q ss_pred HHHHHHHHHhhhhHHHHHHHHHHHHHH
Q psy3153 16 IIAALKAARRLNDYALTIRLLEMVQEK 42 (89)
Q Consensus 16 i~AALrAcRRvND~alAVR~lE~iK~K 42 (89)
..+-+++|.+.+++..|.++++.++.+
T Consensus 3 y~~li~~~~~~~~~~~a~~~~~~M~~~ 29 (31)
T PF01535_consen 3 YNSLISGYCKMGQFEEALEVFDEMRER 29 (31)
T ss_pred HHHHHHHHHccchHHHHHHHHHHHhHC
Confidence 356789999999999999999988753
No 12
>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=79.15 E-value=4.8 Score=19.66 Aligned_cols=27 Identities=7% Similarity=0.117 Sum_probs=23.3
Q ss_pred HHHHHHHHHhhhhHHHHHHHHHHHHHH
Q psy3153 16 IIAALKAARRLNDYALTIRLLEMVQEK 42 (89)
Q Consensus 16 i~AALrAcRRvND~alAVR~lE~iK~K 42 (89)
..+.++++-|.+++..|+++|..++.+
T Consensus 3 ~n~li~~~~~~~~~~~a~~~~~~M~~~ 29 (35)
T TIGR00756 3 YNTLIDGLCKAGRVEEALELFKEMLER 29 (35)
T ss_pred HHHHHHHHHHCCCHHHHHHHHHHHHHc
Confidence 356788999999999999999998764
No 13
>PF13174 TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_A 3URZ_B 2Q7F_A.
Probab=76.90 E-value=5.9 Score=19.54 Aligned_cols=24 Identities=17% Similarity=0.310 Sum_probs=19.6
Q ss_pred HHHhhhhHHHHHHHHHHHHHHhcC
Q psy3153 22 AARRLNDYALTIRLLEMVQEKCGK 45 (89)
Q Consensus 22 AcRRvND~alAVR~lE~iK~K~~~ 45 (89)
+.++.+|+..|++.|+.+..+..+
T Consensus 9 ~~~~~g~~~~A~~~~~~~~~~~P~ 32 (33)
T PF13174_consen 9 CYYKLGDYDEAIEYFQRLIKRYPD 32 (33)
T ss_dssp HHHHHCHHHHHHHHHHHHHHHSTT
T ss_pred HHHHccCHHHHHHHHHHHHHHCcC
Confidence 345789999999999999887654
No 14
>TIGR01837 PHA_granule_1 poly(hydroxyalkanoate) granule-associated protein. This model describes a domain found in some proteins associated with polyhydroxyalkanoate (PHA) granules in a subset of species that have PHA inclusion granules. Included are two tandem proteins of Pseudomonas oleovorans, PhaI and PhaF, and their homologs in related species. PhaF proteins have a low-complexity C-terminal region with repeats similar to AAAKP.
Probab=75.96 E-value=5.2 Score=27.63 Aligned_cols=26 Identities=15% Similarity=0.226 Sum_probs=22.3
Q ss_pred ccchHHHHHhhhhhhhhhCCCCcccc
Q psy3153 48 KVIWPYILGEIRPTLTELGIETPEDL 73 (89)
Q Consensus 48 ~~iY~~~lqElkPtl~ELGI~t~EeL 73 (89)
..+-+.+-+.++-+|..|||+|.+|+
T Consensus 73 ~~le~~~~~~v~~~L~~lg~~tk~ev 98 (118)
T TIGR01837 73 DKLEKAFDERVEQALNRLNIPSREEI 98 (118)
T ss_pred HHHHHHHHHHHHHHHHHcCCCCHHHH
Confidence 45667788889999999999999986
No 15
>PF14559 TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN_B 3QOU_A 3ASG_A 3ASD_A 3AS5_A 3AS4_A 3ASH_B 3FP3_A 3LCA_A ....
Probab=75.76 E-value=6.9 Score=22.21 Aligned_cols=44 Identities=14% Similarity=0.175 Sum_probs=30.4
Q ss_pred CHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHhcCCcccchHHHHHh
Q psy3153 12 DPVIIIAALKAARRLNDYALTIRLLEMVQEKCGKKKKVIWPYILGE 57 (89)
Q Consensus 12 ~P~ii~AALrAcRRvND~alAVR~lE~iK~K~~~~~~~iY~~~lqE 57 (89)
.+++.-.--+++-+.+++..|.++|+.+.....+. ..|..++.+
T Consensus 24 ~~~~~~~la~~~~~~g~~~~A~~~l~~~~~~~~~~--~~~~~l~a~ 67 (68)
T PF14559_consen 24 NPEARLLLAQCYLKQGQYDEAEELLERLLKQDPDN--PEYQQLLAQ 67 (68)
T ss_dssp SHHHHHHHHHHHHHTT-HHHHHHHHHCCHGGGTTH--HHHHHHHHH
T ss_pred CHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCcCH--HHHHHHHhc
Confidence 45566666677788899999999998888877764 445555443
No 16
>PF14853 Fis1_TPR_C: Fis1 C-terminal tetratricopeptide repeat; PDB: 1IYG_A 1PC2_A 1NZN_A 3UUX_C 1Y8M_A 2PQR_A 2PQN_A 3O48_A.
Probab=72.83 E-value=15 Score=22.29 Aligned_cols=43 Identities=14% Similarity=0.104 Sum_probs=31.5
Q ss_pred HHHhhhhHHHHHHHHHHHHHHhcCCcccchHHHHHhhhhhhhhhC
Q psy3153 22 AARRLNDYALTIRLLEMVQEKCGKKKKVIWPYILGEIRPTLTELG 66 (89)
Q Consensus 22 AcRRvND~alAVR~lE~iK~K~~~~~~~iY~~~lqElkPtl~ELG 66 (89)
++-|++||..|.|.++.+=..=.+. .|...+.+.|+-.+..=|
T Consensus 10 g~ykl~~Y~~A~~~~~~lL~~eP~N--~Qa~~L~~~i~~~i~kdg 52 (53)
T PF14853_consen 10 GHYKLGEYEKARRYCDALLEIEPDN--RQAQSLKELIEDKIQKDG 52 (53)
T ss_dssp HHHHTT-HHHHHHHHHHHHHHTTS---HHHHHHHHHHHHHHHHTT
T ss_pred HHHHhhhHHHHHHHHHHHHhhCCCc--HHHHHHHHHHHHHHhccC
Confidence 5679999999999999987655444 788888887776655433
No 17
>PF09597 IGR: IGR protein motif; InterPro: IPR019083 This entry is found in fungal and plant proteins and contains a conserved IGR motif. Its function is unknown.
Probab=72.33 E-value=3.5 Score=26.06 Aligned_cols=40 Identities=28% Similarity=0.359 Sum_probs=26.8
Q ss_pred hhHHHHH-HHHHHHHHHhcCCcccchHHHHHhhhhhhhhhCCCCc
Q psy3153 27 NDYALTI-RLLEMVQEKCGKKKKVIWPYILGEIRPTLTELGIETP 70 (89)
Q Consensus 27 ND~alAV-R~lE~iK~K~~~~~~~iY~~~lqElkPtl~ELGI~t~ 70 (89)
.+|=++| |=.|.-.+|.++. |+.++.-=...|+|+|||..
T Consensus 2 ~tFL~~IGR~~~~~~~kf~~~----w~~lf~~~s~~LK~~GIp~r 42 (57)
T PF09597_consen 2 ETFLKLIGRGCEEHAEKFESD----WEKLFTTSSKQLKELGIPVR 42 (57)
T ss_pred HHHHHHHcccHHHHHHHHHHH----HHHHHhcCHHHHHHCCCCHH
Confidence 3444444 4455555666554 78888877888999999754
No 18
>cd08183 Fe-ADH2 Iron-containing alcohol dehydrogenases-like. Iron-containing alcohol dehydrogenases (Fe-ADH). Alcohol dehydrogenase catalyzes the reduction of acetaldehyde to alcohol with NADP as cofactor. Its activity requires iron ions. The protein structure represents a dehydroquinate synthase-like fold and is a member of the iron-activated alcohol dehydrogenase-like family. They are distinct from other alcohol dehydrogenases which contains different protein domain. Proteins of this family have not been characterized. Their specific function is unknown. They are mainly found in bacteria.
Probab=70.18 E-value=8.1 Score=30.37 Aligned_cols=32 Identities=19% Similarity=0.241 Sum_probs=26.4
Q ss_pred cchHHHHHhhhhhhhhhCCCCccccCCCCCcc
Q psy3153 49 VIWPYILGEIRPTLTELGIETPEDLGYDKPEL 80 (89)
Q Consensus 49 ~iY~~~lqElkPtl~ELGI~t~EeLgydkpEl 80 (89)
+.-...+++++..+++||+|+..|+|.++.++
T Consensus 313 ~~a~~~~~~l~~l~~~lglP~L~e~gv~~~~~ 344 (374)
T cd08183 313 AAADDLVEWLEHWVDELGLPRLSDYGLTPDDL 344 (374)
T ss_pred HHHHHHHHHHHHHHHHcCCCChhhcCCCHHHH
Confidence 44567889999999999999889999877554
No 19
>PF13176 TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_A 3RO2_A.
Probab=70.03 E-value=5.4 Score=21.39 Aligned_cols=18 Identities=28% Similarity=0.421 Sum_probs=15.5
Q ss_pred HHHHhhhhHHHHHHHHHH
Q psy3153 21 KAARRLNDYALTIRLLEM 38 (89)
Q Consensus 21 rAcRRvND~alAVR~lE~ 38 (89)
+++++.+||..|+.++|.
T Consensus 7 ~~~~~~g~~~~Ai~~y~~ 24 (36)
T PF13176_consen 7 RIYRQQGDYEKAIEYYEQ 24 (36)
T ss_dssp HHHHHCT-HHHHHHHHHH
T ss_pred HHHHHcCCHHHHHHHHHH
Confidence 578999999999999987
No 20
>PF13428 TPR_14: Tetratricopeptide repeat
Probab=67.26 E-value=18 Score=19.82 Aligned_cols=32 Identities=25% Similarity=0.143 Sum_probs=25.8
Q ss_pred HHHHHHHHHHhhhhHHHHHHHHHHHHHHhcCC
Q psy3153 15 IIIAALKAARRLNDYALTIRLLEMVQEKCGKK 46 (89)
Q Consensus 15 ii~AALrAcRRvND~alAVR~lE~iK~K~~~~ 46 (89)
+...-=++-++.+++..|++.|+.+-....+.
T Consensus 3 ~~~~la~~~~~~G~~~~A~~~~~~~l~~~P~~ 34 (44)
T PF13428_consen 3 AWLALARAYRRLGQPDEAERLLRRALALDPDD 34 (44)
T ss_pred HHHHHHHHHHHcCCHHHHHHHHHHHHHHCcCC
Confidence 33444567789999999999999998888776
No 21
>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=66.42 E-value=4.6 Score=27.85 Aligned_cols=35 Identities=26% Similarity=0.338 Sum_probs=28.6
Q ss_pred HHHHHHHHHhcCCcccchHHHHHhhhhhhhhhCCCC
Q psy3153 34 RLLEMVQEKCGKKKKVIWPYILGEIRPTLTELGIET 69 (89)
Q Consensus 34 R~lE~iK~K~~~~~~~iY~~~lqElkPtl~ELGI~t 69 (89)
++||.+-.++.+. +....|++.|+-+.+...|++.
T Consensus 1 d~Fe~~~~~~~~~-k~~anwi~~el~~~l~~~~~~~ 35 (148)
T PF02637_consen 1 DYFEEVVKKGKNP-KLAANWILNELLGLLNKKGLDI 35 (148)
T ss_dssp HHHHHHHCHSS-H-HHHHHHHHTHHHHHHHHHT--T
T ss_pred CHHHHHHHhcCCH-HHHHHHHHHHHHHHHHHCCCCh
Confidence 4799999999774 7899999999999999999854
No 22
>PF12192 CBP: Fungal calcium binding protein; InterPro: IPR022013 This domain is found in eukaryotes, and is approximately 60 amino acids in length. There is a single completely conserved residue C that may be functionally important. This is a calcium binding domain from the fungal protein CBP (calcium binding protein). This protein is a virulence factor with unknown virulence mechanisms. CBP complexes as a highly intertwined homodimer. Each monomer is comprised of four alpha helices which adopt the saposin fold, characteristic of a protein family that binds to membranes and lipids. ; PDB: 2JV7_A.
Probab=65.99 E-value=14 Score=24.05 Aligned_cols=43 Identities=23% Similarity=0.548 Sum_probs=31.6
Q ss_pred hhhHHHHHHHHHHHHHHhcCCcccchHHHHHhhhhh-------hhhhCCCCccc
Q psy3153 26 LNDYALTIRLLEMVQEKCGKKKKVIWPYILGEIRPT-------LTELGIETPED 72 (89)
Q Consensus 26 vND~alAVR~lE~iK~K~~~~~~~iY~~~lqElkPt-------l~ELGI~t~Ee 72 (89)
+|+|-.+|+.|+..|.-.+=. |..-+.-|-++ +.|||++.|-+
T Consensus 8 ~~~~n~~v~~F~kak~AA~Cd----Wl~CissLa~~sAaCaAA~~Elgl~~~~d 57 (59)
T PF12192_consen 8 LDMYNNAVTVFTKAKSAAGCD----WLACISSLAASSAACAAALAELGLNPPAD 57 (59)
T ss_dssp HHHHHHHHHHHHHHHHHHT--------HHHHHHTT--HHHHHHHHSSSSTTTTH
T ss_pred HHHHHHHHHHHHHHHhccCCC----hHHHHHHHhhhHHHHHHHHHHhCCCcccc
Confidence 688999999999999888766 88888887764 77888876644
No 23
>PF00627 UBA: UBA/TS-N domain; InterPro: IPR000449 UBA domains are a commonly occurring sequence motif of approximately 45 amino acid residues that are found in diverse proteins involved in the ubiquitin/proteasome pathway, DNA excision-repair, and cell signalling via protein kinases []. The human homologue of yeast Rad23A is one example of a nucleotide excision-repair protein that contains both an internal and a C-terminal UBA domain. The solution structure of human Rad23A UBA(2) showed that the domain forms a compact three-helix bundle []. Comparison of the structures of UBA(1) and UBA(2) reveals that both form very similar folds and have a conserved large hydrophobic surface patch which may be a common protein-interacting surface present in diverse UBA domains. Evidence that ubiquitin binds to UBA domains leads to the prediction that the hydrophobic surface patch of UBA domains interacts with the hydrophobic surface on the five-stranded beta-sheet of ubiquitin []. This domain is similar in sequence to the N-terminal domain of translation elongation factor EF1B (or EF-Ts) from bacteria, mitochondria and chloroplasts. More information about EF1B (EF-Ts) proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0005515 protein binding; PDB: 2DAI_A 2OO9_C 2JUJ_A 1WHC_A 1YLA_A 2O25_B 3K9O_A 3K9P_A 3F92_A 3E46_A ....
Probab=65.36 E-value=8.3 Score=21.16 Aligned_cols=23 Identities=17% Similarity=0.140 Sum_probs=17.1
Q ss_pred CHHHHHHHHHHHHhhhhHHHHHHHH
Q psy3153 12 DPVIIIAALKAARRLNDYALTIRLL 36 (89)
Q Consensus 12 ~P~ii~AALrAcRRvND~alAVR~l 36 (89)
+..-+..||++|.- |...|+.+|
T Consensus 15 ~~~~~~~AL~~~~~--nve~A~~~L 37 (37)
T PF00627_consen 15 SREQAREALRACNG--NVERAVDWL 37 (37)
T ss_dssp -HHHHHHHHHHTTT--SHHHHHHHH
T ss_pred CHHHHHHHHHHcCC--CHHHHHHhC
Confidence 45567788888875 899998876
No 24
>PF12921 ATP13: Mitochondrial ATPase expression; InterPro: IPR024319 ATPase expression protein 2 (also known as ATP13 in some species) is necessary for the expression of subunit 9 of mitochondrial ATPase. The protein has a basic amino terminal signal sequence that is cleaved upon import into mitochondria [].
Probab=65.24 E-value=18 Score=24.99 Aligned_cols=51 Identities=18% Similarity=0.264 Sum_probs=39.8
Q ss_pred cCCCCCCHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHhcCCc-ccchHHHHH
Q psy3153 6 QDDGVPDPVIIIAALKAARRLNDYALTIRLLEMVQEKCGKKK-KVIWPYILG 56 (89)
Q Consensus 6 ~~DlVP~P~ii~AALrAcRRvND~alAVR~lE~iK~K~~~~~-~~iY~~~lq 56 (89)
+.-+-|.+.++.|-+.|==.-||+..|+++++.+-.+-+-.. +..|..+++
T Consensus 45 ~spl~Pt~~lL~AIv~sf~~n~~i~~al~~vd~fs~~Y~I~i~~~~W~~Ll~ 96 (126)
T PF12921_consen 45 SSPLYPTSRLLIAIVHSFGYNGDIFSALKLVDFFSRKYPIPIPKEFWRRLLE 96 (126)
T ss_pred CCCCCCCHHHHHHHHHHHHhcccHHHHHHHHHHHHHHcCCCCCHHHHHHHHH
Confidence 345789999999999998888999999999999988876321 345555443
No 25
>PF15469 Sec5: Exocyst complex component Sec5
Probab=62.16 E-value=19 Score=25.36 Aligned_cols=49 Identities=14% Similarity=0.243 Sum_probs=38.7
Q ss_pred HHHHHHHhhhhHHHHHHHHHHHHHHhcCC--cccchHHHHHhhhhhhhhhC
Q psy3153 18 AALKAARRLNDYALTIRLLEMVQEKCGKK--KKVIWPYILGEIRPTLTELG 66 (89)
Q Consensus 18 AALrAcRRvND~alAVR~lE~iK~K~~~~--~~~iY~~~lqElkPtl~ELG 66 (89)
+-|+.|-.-|||+.||+-....|.-.+.. ...++..+.+|+..+++++=
T Consensus 91 ~~L~~~i~~~dy~~~i~dY~kak~l~~~~~~~~~vf~~v~~eve~ii~~~r 141 (182)
T PF15469_consen 91 SNLRECIKKGDYDQAINDYKKAKSLFEKYKQQVPVFQKVWSEVEKIIEEFR 141 (182)
T ss_pred HHHHHHHHcCcHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHH
Confidence 45677778899999999998888877765 45788888888888777653
No 26
>PF05597 Phasin: Poly(hydroxyalcanoate) granule associated protein (phasin); InterPro: IPR008769 Polyhydroxyalkanoates (PHAs) are storage polyesters synthesised by various bacteria as intracellular carbon and energy reserve material. PHAs are accumulated as water-insoluble inclusions within the cells. This family consists of the phasins PhaF and PhaI which act as a transcriptional regulator of PHA biosynthesis genes. PhaF has been proposed to repress expression of the phaC1 gene and the phaIF operon.
Probab=59.09 E-value=21 Score=25.59 Aligned_cols=39 Identities=15% Similarity=0.232 Sum_probs=25.0
Q ss_pred HHHHHHHHhcCCcccchHHHHHhhhhhhhhhCCCCcccc
Q psy3153 35 LLEMVQEKCGKKKKVIWPYILGEIRPTLTELGIETPEDL 73 (89)
Q Consensus 35 ~lE~iK~K~~~~~~~iY~~~lqElkPtl~ELGI~t~EeL 73 (89)
..+.++.+.......+=..+=+-+.-.|.-|||||.+++
T Consensus 73 ~~~~~~~~~~~~~dklE~~fd~rV~~aL~rLgvPs~~dv 111 (132)
T PF05597_consen 73 RVDDVKERATGQWDKLEQAFDERVARALNRLGVPSRKDV 111 (132)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCHHHH
Confidence 556666666554222222233358899999999998875
No 27
>cd00620 Methyltransferase_Sun N-terminal RNA binding domain of the methyltransferase Sun. The rRNA-specific 5-methylcytidine transferase Sun, also known as RrmB or Fmu shares the RNA-binding non-catalytic domain with the transcription termination factor NusB. The precise biological role of this domain in Sun is unknown, although it is likely to be involved in sequence-specific RNA binding. The C-terminal methyltransferase domain of Sun has been shown to catalyze formation of m5C at position 967 of 16S rRNA in Escherichia coli.
Probab=56.11 E-value=17 Score=24.27 Aligned_cols=36 Identities=19% Similarity=0.170 Sum_probs=28.1
Q ss_pred cCCCCCCHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHh
Q psy3153 6 QDDGVPDPVIIIAALKAARRLNDYALTIRLLEMVQEKC 43 (89)
Q Consensus 6 ~~DlVP~P~ii~AALrAcRRvND~alAVR~lE~iK~K~ 43 (89)
-.| +|...+|..|...|++..+ +.+-+|.-||=.+.
T Consensus 87 ~~~-~p~~avvneaVelak~~~~-~~~~~fVNaVLr~i 122 (126)
T cd00620 87 YLD-VPPHAAVDETVEIAKIRKD-LGRAGLVNAVLRRF 122 (126)
T ss_pred hcC-CCchHHHHHHHHHHHHhCC-CchhhHHHHHHHHH
Confidence 357 8999999999999998865 46677777775554
No 28
>PF07261 DnaB_2: Replication initiation and membrane attachment; InterPro: IPR006343 This entry represents a domain found in several bacterial replication initiation and membrane attachment proteins, DnaB and DnaD. The DnaD protein is a component of the PriA primosome. The PriA primosome functions to recruit the replication fork helicase onto the DNA []. Members, both chromosomal or phage-associated, are found in the Bacillus/Clostridium group of Gram-positive bacteria []. The DnaB protein is essential for both replication initiation and membrane attachment of the origin region of the chromosome and Plasmid pUB110 in Bacillus subtilis. It is known that there are two different classes (DnaBI and DnaBII) in the DnaB mutants; DnaBI is essential for both chromosome and pUB110 replication, whereas DnaBII is necessary only for chromosome replication []. This domain tends to be found towards the C terminus of DnaB and DnaD proteins and is alpha helical in nature.; PDB: 2I5U_A 2ZC2_A.
Probab=53.21 E-value=14 Score=22.08 Aligned_cols=22 Identities=32% Similarity=0.436 Sum_probs=10.4
Q ss_pred hHHHHHhhhhhhhhhCCCCcccc
Q psy3153 51 WPYILGEIRPTLTELGIETPEDL 73 (89)
Q Consensus 51 Y~~~lqElkPtl~ELGI~t~EeL 73 (89)
+.|+..-++- -.+-||.|.|+.
T Consensus 50 ~~Yi~~Il~~-W~~~gi~t~e~~ 71 (77)
T PF07261_consen 50 FNYIEKILNN-WKQKGIKTVEDA 71 (77)
T ss_dssp HHHHHHHHHH-HHHCT--SCCCC
T ss_pred HHHHHHHHHH-HHHcCCCCHHHH
Confidence 4444444433 344677777764
No 29
>PF13925 Katanin_con80: con80 domain of Katanin
Probab=52.60 E-value=30 Score=24.69 Aligned_cols=29 Identities=28% Similarity=0.356 Sum_probs=24.8
Q ss_pred HHHHHHHHHhhhhHHHHHHHHHHHH--HHhc
Q psy3153 16 IIAALKAARRLNDYALTIRLLEMVQ--EKCG 44 (89)
Q Consensus 16 i~AALrAcRRvND~alAVR~lE~iK--~K~~ 44 (89)
+.+|+.+++|.||.+..+-+|-.+. .|-+
T Consensus 30 ~k~ai~~~~~~~D~svlvD~L~vl~~~~~~~ 60 (164)
T PF13925_consen 30 IKGAIEYAVRMNDPSVLVDVLSVLNQSLKPE 60 (164)
T ss_pred HHHHHHHHHhcCCchHHHHHHHHHHHhcCcC
Confidence 5689999999999999999999988 5543
No 30
>smart00147 RasGEF Guanine nucleotide exchange factor for Ras-like small GTPases.
Probab=51.22 E-value=19 Score=26.16 Aligned_cols=24 Identities=17% Similarity=0.326 Sum_probs=19.5
Q ss_pred HHHHHhhhhHHHHHHHHHHHHHHh
Q psy3153 20 LKAARRLNDYALTIRLLEMVQEKC 43 (89)
Q Consensus 20 LrAcRRvND~alAVR~lE~iK~K~ 43 (89)
-..|+.+|||..+.-|+-|+..-+
T Consensus 85 a~~l~~l~Nfns~~aI~~~L~~~~ 108 (242)
T smart00147 85 AKHCRELNNFNSLMAIVSALSSSP 108 (242)
T ss_pred HHHHHHhCCHHHHHHHHHHhCChH
Confidence 367889999999999998886533
No 31
>PF12854 PPR_1: PPR repeat
Probab=50.60 E-value=38 Score=18.09 Aligned_cols=32 Identities=13% Similarity=0.132 Sum_probs=27.7
Q ss_pred CCCCCHHHHHHHHHHHHhhhhHHHHHHHHHHH
Q psy3153 8 DGVPDPVIIIAALKAARRLNDYALTIRLLEMV 39 (89)
Q Consensus 8 DlVP~P~ii~AALrAcRRvND~alAVR~lE~i 39 (89)
.+.|+......-+.+.=|.+++..|.++|+..
T Consensus 2 G~~Pd~~ty~~lI~~~Ck~G~~~~A~~l~~~M 33 (34)
T PF12854_consen 2 GCEPDVVTYNTLIDGYCKAGRVDEAFELFDEM 33 (34)
T ss_pred CCCCcHhHHHHHHHHHHHCCCHHHHHHHHHhC
Confidence 35788888889999999999999999999854
No 32
>PF14726 RTTN_N: Rotatin, an armadillo repeat protein, centriole functioning
Probab=50.05 E-value=32 Score=23.49 Aligned_cols=41 Identities=24% Similarity=0.264 Sum_probs=28.5
Q ss_pred ccCCCCCCHHHHHHHHH-------HHHhhhhHHHHHHHHHHHHHHhcCC
Q psy3153 5 AQDDGVPDPVIIIAALK-------AARRLNDYALTIRLLEMVQEKCGKK 46 (89)
Q Consensus 5 ~~~DlVP~P~ii~AALr-------AcRRvND~alAVR~lE~iK~K~~~~ 46 (89)
|++.=+|.++-|=+-|+ |+..++++. |+|||..+|...++.
T Consensus 39 Fnf~~~~~~~~VL~Ll~~L~~~~~a~~~l~~iG-~~~fL~klr~~~~~~ 86 (98)
T PF14726_consen 39 FNFPPVPMKEEVLALLLRLLKSPYAAQILRDIG-AVRFLSKLRPNVEPN 86 (98)
T ss_pred hCCCCCccHHHHHHHHHHHHhCcHHHHHHHHcc-HHHHHHHHHhcCCHH
Confidence 66777777765544442 666777764 788899999777665
No 33
>PF01029 NusB: NusB family; InterPro: IPR006027 This domain is found in a number of functionally different proteins: NusB a prokaryotic transcription factor involved in antitermination TIM44, the mitochondrial inner membrane translocase subunit RsmB, the 16S rRNA m5C967 methyltransferase NusB is a prokaryotic transcription factor involved in antitermination processes, during which it interacts with the boxA portion of the mRNA nut site. Previous studies have shown that NusB exhibits an all-helical fold, and that the protein from Escherichia coli forms monomers, while Mycobacterium tuberculosis NusB is a dimer. The functional significance of NusB dimerization is unknown. An N-terminal arginine-rich sequence is the probable RNA binding site, exhibiting aromatic residues as potential stacking partners for the RNA bases. The RNA binding region is hidden in the subunit interface of dimeric NusB proteins, such as NusB from M. tuberculosis, suggesting that such dimers have to undergo a considerable conformational change or dissociate for engagement with RNA. In certain organisms, dimerization may be employed to package NusB in an inactive form until recruitment into antitermination complexes [, ]. The antitermination proteins of E. coli are recruited in the replication cycle of Bacteriophage lambda, where they play an important role in switching from the lysogenic to the lytic cycle.; GO: 0003723 RNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1SQG_A 1SQF_A 3IMQ_A 3D3C_C 3D3B_A 1EY1_A 1EYV_A 1TZV_A 1TZT_B 1TZX_B ....
Probab=49.97 E-value=17 Score=24.05 Aligned_cols=36 Identities=19% Similarity=0.263 Sum_probs=27.8
Q ss_pred CCCCCCHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHh
Q psy3153 7 DDGVPDPVIIIAALKAARRLNDYALTIRLLEMVQEKC 43 (89)
Q Consensus 7 ~DlVP~P~ii~AALrAcRRvND~alAVR~lE~iK~K~ 43 (89)
.|=+|.+.+|..|.+.|++. .-.-+.+|.-||=.+.
T Consensus 97 ~~~~p~~v~InEaVelak~~-~~~~~~~fVNaVL~~~ 132 (134)
T PF01029_consen 97 LDDIPPHVAINEAVELAKKY-GDEKSAGFVNAVLRRI 132 (134)
T ss_dssp STTSHHHHHHHHHHHHHHHH-S-TTHHHHHHHHHHHH
T ss_pred cCCCCccchHHHHHHHHHHh-CCCCcchhHHHHHHHh
Confidence 45689999999999999998 4456677877776553
No 34
>PLN03081 pentatricopeptide (PPR) repeat-containing protein; Provisional
Probab=49.36 E-value=29 Score=29.02 Aligned_cols=51 Identities=16% Similarity=0.213 Sum_probs=39.8
Q ss_pred ccCCCCCCHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHhcCCc-ccchHHHH
Q psy3153 5 AQDDGVPDPVIIIAALKAARRLNDYALTIRLLEMVQEKCGKKK-KVIWPYIL 55 (89)
Q Consensus 5 ~~~DlVP~P~ii~AALrAcRRvND~alAVR~lE~iK~K~~~~~-~~iY~~~l 55 (89)
....+.|+.....+.|.||.+.+++..|.++|+.++.+.+... ...|..++
T Consensus 418 ~~~g~~Pd~~T~~~ll~a~~~~g~~~~a~~~f~~m~~~~g~~p~~~~y~~li 469 (697)
T PLN03081 418 IAEGVAPNHVTFLAVLSACRYSGLSEQGWEIFQSMSENHRIKPRAMHYACMI 469 (697)
T ss_pred HHhCCCCCHHHHHHHHHHHhcCCcHHHHHHHHHHHHHhcCCCCCccchHhHH
Confidence 3456789999999999999999999999999999987644321 24565554
No 35
>PRK00117 recX recombination regulator RecX; Reviewed
Probab=49.19 E-value=58 Score=22.38 Aligned_cols=28 Identities=18% Similarity=0.227 Sum_probs=24.0
Q ss_pred CHHHHHHHHHHHHh---hhhHHHHHHHHHHH
Q psy3153 12 DPVIIIAALKAARR---LNDYALTIRLLEMV 39 (89)
Q Consensus 12 ~P~ii~AALrAcRR---vND~alAVR~lE~i 39 (89)
++.+|+.+|.-+.. +||...|-.++..-
T Consensus 41 ~~~~i~~vl~~l~~~~~ldD~~~a~~~~~~~ 71 (157)
T PRK00117 41 SEEVIEAVLDRLKEEGLLDDERFAESFVRSR 71 (157)
T ss_pred CHHHHHHHHHHHHHcCCCCHHHHHHHHHHHH
Confidence 57899999999888 99998888888775
No 36
>PF14663 RasGEF_N_2: Rapamycin-insensitive companion of mTOR RasGEF_N domain
Probab=46.55 E-value=37 Score=22.98 Aligned_cols=16 Identities=38% Similarity=0.644 Sum_probs=10.7
Q ss_pred hHHHHHhhhhhhhhhC
Q psy3153 51 WPYILGEIRPTLTELG 66 (89)
Q Consensus 51 Y~~~lqElkPtl~ELG 66 (89)
|-..+=.++|.+.-||
T Consensus 41 ~le~~v~~~p~l~~L~ 56 (115)
T PF14663_consen 41 YLEYLVSLRPSLDHLG 56 (115)
T ss_pred hHHHHHHcCcHHHHHH
Confidence 4445556788887776
No 37
>PF05854 MC1: Non-histone chromosomal protein MC1; InterPro: IPR008674 This family consists of archaeal chromosomal protein MC1 sequences which protect DNA against thermal denaturation [].; GO: 0042262 DNA protection; PDB: 1T23_A 2KHL_A.
Probab=45.99 E-value=9.3 Score=26.75 Aligned_cols=9 Identities=89% Similarity=0.900 Sum_probs=8.4
Q ss_pred HHHHHHHHh
Q psy3153 17 IAALKAARR 25 (89)
Q Consensus 17 ~AALrAcRR 25 (89)
+||||||||
T Consensus 26 qAAlKAA~R 34 (93)
T PF05854_consen 26 QAALKAARR 34 (93)
T ss_dssp HHHHHHHCC
T ss_pred HHHHHHhhc
Confidence 699999999
No 38
>PF12374 Dmrt1: Double-sex mab3 related transcription factor 1; InterPro: IPR022114 This domain family is found in eukaryotes, and is typically between 61 and 73 amino acids in length. The family is found in association with PF00751 from PFAM. This family is a transcription factor involved in sex determination. The proteins in this family contain a zinc finger-like DNA-binding motif, DM domain.
Probab=45.32 E-value=11 Score=24.65 Aligned_cols=19 Identities=47% Similarity=0.691 Sum_probs=15.9
Q ss_pred hhCCCCccccCCCCCcccccC
Q psy3153 64 ELGIETPEDLGYDKPELWCKS 84 (89)
Q Consensus 64 ELGI~t~EeLgydkpEla~~~ 84 (89)
||||..|.-| --+|.-+++
T Consensus 1 ElGi~~pv~l--s~~e~~VKn 19 (71)
T PF12374_consen 1 ELGICHPVPL--SGPEVMVKN 19 (71)
T ss_pred CccccccccC--CCccccccc
Confidence 8999999998 668887764
No 39
>PF15564 Imm13: Immunity protein 13
Probab=44.26 E-value=18 Score=26.49 Aligned_cols=39 Identities=21% Similarity=0.345 Sum_probs=29.9
Q ss_pred chHHHHHhhhhhhhhhCCCCccccCCCCCcccccCCccc
Q psy3153 50 IWPYILGEIRPTLTELGIETPEDLGYDKPELWCKSTDEF 88 (89)
Q Consensus 50 iY~~~lqElkPtl~ELGI~t~EeLgydkpEla~~~~~d~ 88 (89)
-+..++.|..-++.+.|.+-||.|.|+--=---+++.|+
T Consensus 4 df~svv~ef~~lind~~f~cp~klwy~~li~lsk~v~di 42 (131)
T PF15564_consen 4 DFHSVVAEFGNLINDFGFSCPEKLWYDNLISLSKNVIDI 42 (131)
T ss_pred HHHHHHHHHHHHHHhhCCCCchHhcccchhhhhhcccee
Confidence 366788899999999999999999998633333555554
No 40
>PF03634 TCP: TCP family transcription factor; InterPro: IPR005333 The TCP transcription factor family was named after: teosinte branched 1 (tb1, Zea mays (Maize)) [], cycloidea (cyc) (Antirrhinum majus) (Garden snapdragon) [] and PCF in rice (Oryza sativa) [, ]. The TCP proteins code for structurally related proteins implicated in the evolution of key morphological traits []. However, the biochemical function of CYC and TB1 proteins remains to be demonstrated. One of the conserved regions is predicted to form a non-canonical basic-Helix-Loop-Helix (bHLP) structure. This domain is also found in two rice DNA-binding proteins, PCF1 and PCF2, where it has been shown to be involved in DNA-binding and dimerization. This family of transcription factors are exclusive to higher plants. They can be divided into two groups, TCP-C and TCP-P, that appear to have separated following an early gene duplication event []. This duplication event may have led to functional divergence and it has been proposed that that the TCP-P subfamily are transcriptional repressors, while the TPC-C subfamily are transcription activators [].
Probab=43.26 E-value=39 Score=23.27 Aligned_cols=44 Identities=18% Similarity=0.387 Sum_probs=35.2
Q ss_pred Hhhh-hHHHHHHHHHHHHHHhc-CCcccchHHHHHhhhhhhhhhCCC
Q psy3153 24 RRLN-DYALTIRLLEMVQEKCG-KKKKVIWPYILGEIRPTLTELGIE 68 (89)
Q Consensus 24 RRvN-D~alAVR~lE~iK~K~~-~~~~~iY~~~lqElkPtl~ELGI~ 68 (89)
|||- ....|.|||- +.+..| ++....-+|+|..=|+.++||--.
T Consensus 20 RRvRLs~~~Ar~FFd-LQDmLGfDKaSKTveWLL~kSk~AIkeL~~~ 65 (138)
T PF03634_consen 20 RRVRLSLEIARKFFD-LQDMLGFDKASKTVEWLLTKSKKAIKELTQS 65 (138)
T ss_pred CceecCHHHHHHHHH-HHHHhcCCCCCchHHHHHHhCHHHHHHHHHh
Confidence 4555 6778999996 888888 455678999999999999999654
No 41
>PLN03077 Protein ECB2; Provisional
Probab=42.93 E-value=40 Score=28.90 Aligned_cols=50 Identities=18% Similarity=0.211 Sum_probs=39.0
Q ss_pred cCCCCCCHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHhcCCc-ccchHHHH
Q psy3153 6 QDDGVPDPVIIIAALKAARRLNDYALTIRLLEMVQEKCGKKK-KVIWPYIL 55 (89)
Q Consensus 6 ~~DlVP~P~ii~AALrAcRRvND~alAVR~lE~iK~K~~~~~-~~iY~~~l 55 (89)
...+.|+.....+.|.||-+-+++..|.++|+.++.+-|-.. .+.|..++
T Consensus 582 ~~g~~Pd~~T~~~ll~a~~~~g~v~ea~~~f~~M~~~~gi~P~~~~y~~lv 632 (857)
T PLN03077 582 ESGVNPDEVTFISLLCACSRSGMVTQGLEYFHSMEEKYSITPNLKHYACVV 632 (857)
T ss_pred HcCCCCCcccHHHHHHHHhhcChHHHHHHHHHHHHHHhCCCCchHHHHHHH
Confidence 356788988999999999999999999999999986554321 24666655
No 42
>PRK04016 DNA-directed RNA polymerase subunit N; Provisional
Probab=42.24 E-value=21 Score=23.18 Aligned_cols=27 Identities=26% Similarity=0.583 Sum_probs=19.0
Q ss_pred HhcCCcccchHHHHHhhh------hhhhhhCCC
Q psy3153 42 KCGKKKKVIWPYILGEIR------PTLTELGIE 68 (89)
Q Consensus 42 K~~~~~~~iY~~~lqElk------Ptl~ELGI~ 68 (89)
-||....+-|..|.+-++ -+|++||+.
T Consensus 9 TCGkvi~~~we~y~~~~~~g~~~~~vLd~Lg~~ 41 (62)
T PRK04016 9 TCGKVIAEKWEEFKERVEAGEDPGKVLDDLGVK 41 (62)
T ss_pred CCCCChHHHHHHHHHHHHcCCCHHHHHHHcCCc
Confidence 466666666777776663 689999985
No 43
>KOG3103|consensus
Probab=41.54 E-value=12 Score=30.14 Aligned_cols=10 Identities=60% Similarity=0.946 Sum_probs=9.2
Q ss_pred hhhhhhhCCC
Q psy3153 59 RPTLTELGIE 68 (89)
Q Consensus 59 kPtl~ELGI~ 68 (89)
.|+||||||+
T Consensus 82 pPLLEELgIn 91 (249)
T KOG3103|consen 82 PPLLEELGIN 91 (249)
T ss_pred CchHHHhCCC
Confidence 7999999997
No 44
>PF14337 DUF4393: Domain of unknown function (DUF4393)
Probab=41.48 E-value=70 Score=22.52 Aligned_cols=51 Identities=25% Similarity=0.326 Sum_probs=39.4
Q ss_pred CCCHHHHHHHHHHHHhh-hhHHHHHHHHHHHHHHhcCCcc----cchHHHHHhhhh
Q psy3153 10 VPDPVIIIAALKAARRL-NDYALTIRLLEMVQEKCGKKKK----VIWPYILGEIRP 60 (89)
Q Consensus 10 VP~P~ii~AALrAcRRv-ND~alAVR~lE~iK~K~~~~~~----~iY~~~lqElkP 60 (89)
.|.|+|+.-||.+++-. +|=.+.=+|-+-+-.-+....+ -.|-.|+++|.|
T Consensus 13 ~~~~~i~~p~le~~~~~~~~e~Lremfa~LLass~d~~~~~~~hp~fv~Ii~qLsp 68 (186)
T PF14337_consen 13 EPPPKIAGPALEAASYEIDDEELREMFANLLASSMDKRKNDDVHPSFVEIIKQLSP 68 (186)
T ss_pred CCChhhhHHHHHhccCcCCcHHHHHHHHHHHHHHhCcCccccccHHHHHHHHhCCH
Confidence 36799999999999987 8888888888877766665422 367777888777
No 45
>PF08626 TRAPPC9-Trs120: Transport protein Trs120 or TRAPPC9, TRAPP II complex subunit; InterPro: IPR013935 The trafficking protein particle complex TRAPP is a multi-protein complex needed in the early stages of the secretory pathway. To date, two kinds of TRAPP complexes have been studied, TRAPPI and TRAPP II. These complexes differ in subunit composition []. TRAPP I binds vesicles derived from the endoplasmic reticulum bringing them closer to the acceptor membrane. Trs120 is a subunit specific to the TRAPP II complex [] along with Trs65p and Trs130p(TRAPPC10). It is suggested that Trs120p is required for the stability of the Trs130p subunit, suggesting that these two proteins might interact in some way []. It is likely that there is a complex function for TRAPP II in multiple pathways [].
Probab=40.90 E-value=27 Score=32.12 Aligned_cols=26 Identities=19% Similarity=0.396 Sum_probs=22.7
Q ss_pred HHHHHHHHHHHhhhhHHHHHHHHHHH
Q psy3153 14 VIIIAALKAARRLNDYALTIRLLEMV 39 (89)
Q Consensus 14 ~ii~AALrAcRRvND~alAVR~lE~i 39 (89)
.|+..++.+|+|++|++.++|+.=.+
T Consensus 524 ~vL~~~I~~ae~l~D~~~~~~~~~~L 549 (1185)
T PF08626_consen 524 DVLKECINIAEALGDFAGVLRFSSLL 549 (1185)
T ss_pred HHHHHHHHHHHhcCCHHHHHHHHHHH
Confidence 47889999999999999999987654
No 46
>PLN00032 DNA-directed RNA polymerase; Provisional
Probab=40.86 E-value=22 Score=23.67 Aligned_cols=27 Identities=30% Similarity=0.545 Sum_probs=20.1
Q ss_pred HhcCCcccchHHHHHhhh------hhhhhhCCC
Q psy3153 42 KCGKKKKVIWPYILGEIR------PTLTELGIE 68 (89)
Q Consensus 42 K~~~~~~~iY~~~lqElk------Ptl~ELGI~ 68 (89)
-||.-+..-|..|++-++ -+|++||+.
T Consensus 9 TCGkvig~~we~y~~~~~~g~~~~~~LD~LG~~ 41 (71)
T PLN00032 9 TCGKVIGNKWDTYLDLLQADYSEGDALDALGLV 41 (71)
T ss_pred CCCCCcHHHHHHHHHHHhcCCCHHHHHHHhCch
Confidence 477766677888887774 578899874
No 47
>PRK12451 arginyl-tRNA synthetase; Reviewed
Probab=40.75 E-value=22 Score=30.12 Aligned_cols=58 Identities=26% Similarity=0.365 Sum_probs=39.2
Q ss_pred HHHHHHHHHHHhhhhHHHHHHHHHHHHHHhcCCcccchHHHHHhhhhhhhhhCCCCcccc
Q psy3153 14 VIIIAALKAARRLNDYALTIRLLEMVQEKCGKKKKVIWPYILGEIRPTLTELGIETPEDL 73 (89)
Q Consensus 14 ~ii~AALrAcRRvND~alAVR~lE~iK~K~~~~~~~iY~~~lqElkPtl~ELGI~t~EeL 73 (89)
.++......|+..|.|=...++++.= ..-..+ =......-+-|+-.|+=|||++||.|
T Consensus 505 ~~~~yl~~LA~~fN~fy~~~~Vl~~~-~~~~~R-L~L~~a~~~vL~~gL~LLGI~~~erM 562 (562)
T PRK12451 505 VISKYVLDVAQSFNKYYGNVRILEES-AEKDSR-LALVYAVTVVLKEGLRLLGVEAPEEM 562 (562)
T ss_pred HHHHHHHHHHHHHHHHHHhCCCCCCH-HHHHHH-HHHHHHHHHHHHHHHHhcCCCccccC
Confidence 45666777788888887777777310 000011 13566777888899999999999976
No 48
>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=40.34 E-value=46 Score=17.70 Aligned_cols=22 Identities=23% Similarity=0.205 Sum_probs=17.2
Q ss_pred HHHHHHHHHHHHhhhhHHHHHHHH
Q psy3153 13 PVIIIAALKAARRLNDYALTIRLL 36 (89)
Q Consensus 13 P~ii~AALrAcRRvND~alAVR~l 36 (89)
..-+..||++|. ||...|+.+|
T Consensus 15 ~~~~~~AL~~~~--~d~~~A~~~L 36 (38)
T cd00194 15 REEARKALRATN--NNVERAVEWL 36 (38)
T ss_pred HHHHHHHHHHhC--CCHHHHHHHH
Confidence 566778888888 5888888775
No 49
>PF05746 DALR_1: DALR anticodon binding domain; InterPro: IPR008909 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. This all alpha helical domain is the anticodon binding domain of Arginyl tRNA synthetase. This domain is known as the DALR domain after characteristic conserved amino acids [].; GO: 0004814 arginine-tRNA ligase activity, 0005524 ATP binding, 0006420 arginyl-tRNA aminoacylation; PDB: 2ZUE_A 2ZUF_A 3FNR_A 1F7V_A 1F7U_A 1BS2_A 1IQ0_A.
Probab=40.20 E-value=9.9 Score=24.33 Aligned_cols=52 Identities=17% Similarity=0.188 Sum_probs=27.0
Q ss_pred HHHhhhhHHHHH-HHHHHHHHHhcCCcc------cchHHHHHhhhhhhhhhCCCCcccc
Q psy3153 22 AARRLNDYALTI-RLLEMVQEKCGKKKK------VIWPYILGEIRPTLTELGIETPEDL 73 (89)
Q Consensus 22 AcRRvND~alAV-R~lE~iK~K~~~~~~------~iY~~~lqElkPtl~ELGI~t~EeL 73 (89)
.|+-+.+++.++ +|+..++...++... .....+.+-++-.|+=|||++||.|
T Consensus 61 l~~yL~~La~~f~~fy~~~~I~~~~~~~~~~~RL~Ll~~v~~vl~~~l~llgi~~~~~M 119 (119)
T PF05746_consen 61 LCDYLYELAQAFNSFYDNVRILDEDEEIRKNNRLALLKAVRQVLKNGLDLLGIEPLEKM 119 (119)
T ss_dssp HHHHHHHHHHHHHHHHHHS-STTSTTCHH-HHHHHHHHHHHHHHHHHHHHTT----S--
T ss_pred HHHHHHHHHHHHHHHHhhccccccchHHHHHHHHHHHHHHHHHHHHHHHHcCCCccccC
Confidence 344555555444 455655555555411 1456667778888889999999875
No 50
>PF02037 SAP: SAP domain; InterPro: IPR003034 The SAP (after SAF-A/B, Acinus and PIAS) motif is a putative DNA binding domain found in diverse nuclear proteins involved in chromosomal organisation [], including in apoptosis []. In yeast, SAP is found in the most distal N-terminal region of E3 SUMO-protein ligase SIZ1, where it is involved in nuclear localization [].; GO: 0003676 nucleic acid binding; PDB: 2RNN_A 1JEQ_A 2KW9_A 2KVU_A 2DO1_A 1ZBU_B 1ZBH_A 2DO5_A 2RNO_A 1H1J_S ....
Probab=40.17 E-value=21 Score=19.77 Aligned_cols=18 Identities=28% Similarity=0.523 Sum_probs=14.2
Q ss_pred HHHHhhhhhhhhhCCCCc
Q psy3153 53 YILGEIRPTLTELGIETP 70 (89)
Q Consensus 53 ~~lqElkPtl~ELGI~t~ 70 (89)
+-+.|||-.+.++|+++-
T Consensus 4 l~v~eLk~~l~~~gL~~~ 21 (35)
T PF02037_consen 4 LTVAELKEELKERGLSTS 21 (35)
T ss_dssp SHHHHHHHHHHHTTS-ST
T ss_pred CcHHHHHHHHHHCCCCCC
Confidence 357899999999999864
No 51
>cd08171 GlyDH-like2 Glycerol dehydrogenase-like. Glycerol dehydrogenases-like. The proteins in this family have not been characterized, but they show sequence homology with glycerol dehydrogenase. Glycerol dehydrogenases (GlyDH) is a key enzyme in the glycerol dissimilation pathway. In anaerobic conditions, many microorganisms utilize glycerol as a source of carbon through coupled oxidative and reductive pathways. One of the pathways involves the oxidation of glycerol to dihydroxyacetone with the reduction of NAD+ to NADH catalyzed by glycerol dehydrogenases. Dihydroxyacetone is then phosphorylated by dihydroxyacetone kinase and enters the glycolytic pathway for further degradation. The activity of GlyDH is zinc-dependent. The zinc ion plays a role in stabilizing an alkoxide intermediate at the active site.
Probab=39.68 E-value=15 Score=28.55 Aligned_cols=28 Identities=32% Similarity=0.460 Sum_probs=23.6
Q ss_pred HHHHhhhhhhhhhCCCC-ccccCCCCCcc
Q psy3153 53 YILGEIRPTLTELGIET-PEDLGYDKPEL 80 (89)
Q Consensus 53 ~~lqElkPtl~ELGI~t-~EeLgydkpEl 80 (89)
..+++|+..++++|+|+ ..++|.++.++
T Consensus 285 ~~i~~i~~l~~~lglP~~L~~~gv~~~~l 313 (345)
T cd08171 285 EELERIYPFNKSIGLPVCLEDLGLTEDDL 313 (345)
T ss_pred HHHHHHHHHHHHcCCCCcHHHcCCCHHHH
Confidence 56899999999999984 79999887554
No 52
>PLN03081 pentatricopeptide (PPR) repeat-containing protein; Provisional
Probab=39.24 E-value=79 Score=26.49 Aligned_cols=60 Identities=22% Similarity=0.180 Sum_probs=42.9
Q ss_pred CCCCCHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHhcCCcccchHHHH------------HhhhhhhhhhCCC
Q psy3153 8 DGVPDPVIIIAALKAARRLNDYALTIRLLEMVQEKCGKKKKVIWPYIL------------GEIRPTLTELGIE 68 (89)
Q Consensus 8 DlVP~P~ii~AALrAcRRvND~alAVR~lE~iK~K~~~~~~~iY~~~l------------qElkPtl~ELGI~ 68 (89)
-..|+..+..+-|.|||+.+++..|.+++|.+.. .+......|-.++ .++.-.+.+-|+.
T Consensus 489 ~~~p~~~~~~~Ll~a~~~~g~~~~a~~~~~~l~~-~~p~~~~~y~~L~~~y~~~G~~~~A~~v~~~m~~~g~~ 560 (697)
T PLN03081 489 PFKPTVNMWAALLTACRIHKNLELGRLAAEKLYG-MGPEKLNNYVVLLNLYNSSGRQAEAAKVVETLKRKGLS 560 (697)
T ss_pred CCCCCHHHHHHHHHHHHHcCCcHHHHHHHHHHhC-CCCCCCcchHHHHHHHHhCCCHHHHHHHHHHHHHcCCc
Confidence 4568899999999999999999999999998753 3332123444333 3456667777875
No 53
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=38.69 E-value=50 Score=17.54 Aligned_cols=22 Identities=23% Similarity=0.211 Sum_probs=15.7
Q ss_pred HHHHHHHHHHHHhhhhHHHHHHHH
Q psy3153 13 PVIIIAALKAARRLNDYALTIRLL 36 (89)
Q Consensus 13 P~ii~AALrAcRRvND~alAVR~l 36 (89)
..-+..||++|. ||...|+.+|
T Consensus 15 ~~~a~~aL~~~~--~d~~~A~~~L 36 (37)
T smart00165 15 REEALKALRAAN--GNVERAAEYL 36 (37)
T ss_pred HHHHHHHHHHhC--CCHHHHHHHH
Confidence 446677888886 5788887765
No 54
>TIGR00456 argS arginyl-tRNA synthetase. This model recognizes arginyl-tRNA synthetase in every completed genome to date. An interesting feature of the alignment of all arginyl-tRNA synthetases is a fairly deep split between two families. One family includes archaeal, eukaryotic and organellar, spirochete, E. coli, and Synechocystis sp. The second, sharing a deletion of about 25 residues in the central region relative to the first, includes Bacillus subtilis, Aquifex aeolicus, the Mycoplasmas and Mycobacteria, and the Gram-negative bacterium Helicobacter pylori.
Probab=38.66 E-value=15 Score=30.94 Aligned_cols=59 Identities=19% Similarity=0.249 Sum_probs=33.6
Q ss_pred HHHHHHHHHHHhhhhHHHHHHHHHHHHH-HhcCCcccchHHHHHhhhhhhhhhCCCCcccc
Q psy3153 14 VIIIAALKAARRLNDYALTIRLLEMVQE-KCGKKKKVIWPYILGEIRPTLTELGIETPEDL 73 (89)
Q Consensus 14 ~ii~AALrAcRRvND~alAVR~lE~iK~-K~~~~~~~iY~~~lqElkPtl~ELGI~t~EeL 73 (89)
.++..++.-|+.+|.|=..-|++..=.. ....+ =......-+-|+-.|.=|||++||.|
T Consensus 507 ~~~~~l~~La~~~N~yy~~~~Vl~~~~~~~~~~R-L~L~~a~~~vl~~gL~lLGI~~~e~M 566 (566)
T TIGR00456 507 VLTNYLYELASLFSSFYKACPVLDAENENLAAAR-LALLKATRQTLKNGLQLLGIEPPERM 566 (566)
T ss_pred HHHHHHHHHHHHHHHHHhcCccCCCCCHHHHHHH-HHHHHHHHHHHHHHHHhcCCCccccC
Confidence 3455555566666666544455421000 00000 12455677788888999999999976
No 55
>cd00155 RasGEF Guanine nucleotide exchange factor for Ras-like small GTPases. Small GTP-binding proteins of the Ras superfamily function as molecular switches in fundamental events such as signal transduction, cytoskeleton dynamics and intracellular trafficking. Guanine-nucleotide-exchange factors (GEFs) positively regulate these GTP-binding proteins in response to a variety of signals. GEFs catalyze the dissociation of GDP from the inactive GTP-binding proteins. GTP can then bind and induce structural changes that allow interaction with effectors.
Probab=38.12 E-value=34 Score=24.60 Aligned_cols=24 Identities=17% Similarity=0.367 Sum_probs=19.6
Q ss_pred HHHHHHHhhhhHHHHHHHHHHHHH
Q psy3153 18 AALKAARRLNDYALTIRLLEMVQE 41 (89)
Q Consensus 18 AALrAcRRvND~alAVR~lE~iK~ 41 (89)
.....|+.+|||..+.-|+-|+..
T Consensus 83 ~ia~~l~~l~Nfns~~aI~~~L~~ 106 (237)
T cd00155 83 QVAKHCRELNNFNSLMAIVSALSS 106 (237)
T ss_pred HHHHHHHHhCCHHHHHHHHHHhCC
Confidence 344788999999999999988854
No 56
>PF03368 Dicer_dimer: Dicer dimerisation domain; InterPro: IPR005034 This domain is found in members of the Dicer protein family of dsRNA nucleases. This entry represents a dsRNA-binding domain. RNA interference (RNAi) is an ancient gene-silencing process that plays a fundamental role in diverse eukaryotic functions including viral defence, chromatin remodelling, genome rearrangement, developmental timing, brain morphogenesis, and stem cell maintenance. All RNAi pathways require the multidomain ribonuclease Dicer, which initiates RNAi by cleaving double-stranded RNA (dsRNA) substrates into small fragments ~25 nuleotides in length. A typical eukaryotic Dicer consists of a helicase domain (PDOC51192 from PROSITEDOC), a domain of unknown function, and a PAZ domain (PDOC50821 from PROSITEDOC) at the amino (N)-terminus as well as two ribonuclease III domains (PDOC00448 from PROSITEDOC) and a dsRNA-binding domain (dsRBD) (PDOC50137 from PROSITEDOC) at the carboxy (C)-terminus. The domain of unknown function of ~100 amino acids is predicted to adopt the canonical alpha-beta-beta-beta-alpha-fold found in all dsRBDs [, , , ].; GO: 0016891 endoribonuclease activity, producing 5'-phosphomonoesters; PDB: 2KOU_A.
Probab=38.00 E-value=22 Score=23.13 Aligned_cols=12 Identities=33% Similarity=0.481 Sum_probs=9.5
Q ss_pred HHHHHHHHHhhh
Q psy3153 16 IIAALKAARRLN 27 (89)
Q Consensus 16 i~AALrAcRRvN 27 (89)
-.||++||+++=
T Consensus 61 ~sAAf~Ac~~L~ 72 (90)
T PF03368_consen 61 RSAAFEACKKLH 72 (90)
T ss_dssp HHHHHHHHHHHH
T ss_pred HHHHHHHHHHHH
Confidence 368999999873
No 57
>PF10602 RPN7: 26S proteasome subunit RPN7; InterPro: IPR019585 This entry represents the regulatory subunit RPN7 (known as the non-ATPase regulatory subunit 6 in higher eukaryotes) of the 26S proteasome. This entry also matches the evolutionarily related subunit 1 of the COP9 signalosome complex (CSN) from Arabidopsis []. The 26S proteasome plays a major role in ATP-dependent degradation of ubiquitinated proteins. Substrate specificity is conferred by the regulatory particle (RP), which can dissociate into stable lid and base subcomplexes. The regulatory subunit RPN7 is one of the lid subunits of the 26S proteasome and has been shown in Saccharomyces cerevisiae (Baker's yeast) to be required for structural integrity []. The COP9 signalosome is a conserved protein complex composed of eight subunits, where Individual subunits of the complex have been linked to various signal transduction pathways leading to gene expression and cell cycle control []. The overall organisation and the amino acid sequences of the COP9 signalosome subunits resemble the lid subcomplex of the 19 S regulatory particle for the 26 S proteasome []. COP9 subunit 1 (CSN1 or GPS1) of the COP9 complex is an essential subunit of the complex with regard to both structural integrity and functionality. The N-terminal region of subunit 1 (CSN1-N) can inhibit c-fos expression from either a transfected template or a chromosomal transgene (fos-lacZ), and may contain the activity domain that confers most of the repression functions of CSN1. The C-terminal region of subunit 1 (CSN1-C) allows integration of the protein into the COP9 signalosome.
Probab=37.87 E-value=40 Score=24.23 Aligned_cols=33 Identities=12% Similarity=0.212 Sum_probs=25.0
Q ss_pred hhhhHHHHHHHHHHHHHHhcCCcccchHHHHHhh
Q psy3153 25 RLNDYALTIRLLEMVQEKCGKKKKVIWPYILGEI 58 (89)
Q Consensus 25 RvND~alAVR~lE~iK~K~~~~~~~iY~~~lqEl 58 (89)
+..|+..|++.++..+++|-+. +.+..-.+.-|
T Consensus 48 ~~Gd~~~A~k~y~~~~~~~~~~-~~~id~~l~~i 80 (177)
T PF10602_consen 48 KIGDLEEALKAYSRARDYCTSP-GHKIDMCLNVI 80 (177)
T ss_pred HhhhHHHHHHHHHHHhhhcCCH-HHHHHHHHHHH
Confidence 7889999999999999999765 44455444433
No 58
>cd08193 HVD 5-hydroxyvalerate dehydrogenase (HVD) catalyzes the oxidation of 5-hydroxyvalerate to 5-oxovalerate with NAD+ as cofactor. 5-hydroxyvalerate dehydrogenase (HVD) is an iron-containing (type III) NAD-dependent alcohol dehydrogenase. It plays a role in the cyclopentanol metabolism biochemical pathway. It catalyzes the oxidation of 5-hydroxyvalerate to 5-oxovalerate with NAD+ as cofactor. This cyclopentanol (cpn) degradation pathway is present in some bacteria which can use cyclopentanol as sole carbon source. In Comamonas sp. strain NCIMB 9872, this enzyme is encoded by the CpnD gene.
Probab=37.76 E-value=33 Score=26.90 Aligned_cols=31 Identities=16% Similarity=0.378 Sum_probs=24.4
Q ss_pred chHHHHHhhhhhhhhhCCCC-ccccCCCCCcc
Q psy3153 50 IWPYILGEIRPTLTELGIET-PEDLGYDKPEL 80 (89)
Q Consensus 50 iY~~~lqElkPtl~ELGI~t-~EeLgydkpEl 80 (89)
.-...++.++..+++||+|+ ..|+|.++.++
T Consensus 314 ~~~~~~~~~~~l~~~lglp~~L~e~gi~~~~~ 345 (376)
T cd08193 314 AAEALIDAMEALVADLGIPQRLREVGVTEDDL 345 (376)
T ss_pred HHHHHHHHHHHHHHHcCCCCCHHHcCCCHHHH
Confidence 34577888999999999984 78889876544
No 59
>PF04289 DUF447: Protein of unknown function (DUF447); InterPro: IPR007386 This entry contains archaeal and bacterial proteins of unknown function.; PDB: 2IML_A 3B5M_C 2PTF_A 2NR4_A.
Probab=37.62 E-value=81 Score=22.83 Aligned_cols=42 Identities=21% Similarity=0.297 Sum_probs=29.6
Q ss_pred HHHHHHHHHHH----hhhhHHHHHHHHHHHHHHhcCC-cccchHHHH
Q psy3153 14 VIIIAALKAAR----RLNDYALTIRLLEMVQEKCGKK-KKVIWPYIL 55 (89)
Q Consensus 14 ~ii~AALrAcR----RvND~alAVR~lE~iK~K~~~~-~~~iY~~~l 55 (89)
.||+||..|.| +-.++-.-++-+..+=.|||++ .++.|.++.
T Consensus 130 avIEaaV~~TRl~~~~~~~~~~~i~~~~~iv~K~gg~~e~ea~~~l~ 176 (177)
T PF04289_consen 130 AVIEAAVLATRLHMLPKEKLLEEIKYLYIIVKKTGGPREREAMELLM 176 (177)
T ss_dssp HHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHH
T ss_pred HHHHHHHHHHHhccCCHHHHHHHHHHHHHHHhhhCCHHHHHHHHHHh
Confidence 68999999999 4566777778888888999985 234565554
No 60
>cd06101 citrate_synt Citrate synthase (CS) catalyzes the condensation of acetyl coenzyme A (AcCoA) and oxalacetate (OAA) to form citrate and coenzyme A (CoA), the first step in the oxidative citric acid cycle (TCA or Krebs cycle). Peroxisomal CS is involved in the glyoxylate cycle. This group also includes CS proteins which functions as a 2-methylcitrate synthase (2MCS). 2MCS catalyzes the condensation of propionyl-CoA (PrCoA) and OAA to form 2-methylcitrate and CoA during propionate metabolism. This group contains proteins which functions exclusively as either a CS or a 2MCS, as well as those with relaxed specificity which have dual functions as both a CS and a 2MCS. The overall CS reaction is thought to proceed through three partial reactions and involves both closed and open conformational forms of the enzyme: a) the carbanion or equivalent is generated from AcCoA by base abstraction of a proton, b) the nucleophilic attack of this carbanion on OAA to generate citryl-CoA, and c) the
Probab=37.61 E-value=98 Score=23.92 Aligned_cols=61 Identities=18% Similarity=0.133 Sum_probs=35.5
Q ss_pred ccCCC--CCCHHHHHHHHHHHHhhhh-------HHHHHHHHHHHHHHhcCCcccchHHHHHhhhhhhhhhCCC
Q psy3153 5 AQDDG--VPDPVIIIAALKAARRLND-------YALTIRLLEMVQEKCGKKKKVIWPYILGEIRPTLTELGIE 68 (89)
Q Consensus 5 ~~~Dl--VP~P~ii~AALrAcRRvND-------~alAVR~lE~iK~K~~~~~~~iY~~~lqElkPtl~ELGI~ 68 (89)
|||-+ ..+|.. ..-++.|+.+-. +..|.++-+.+..+... +.+|+-+-=-.--++..||||
T Consensus 159 FGH~vy~~~DPRa-~~L~~~~~~l~~~~~~~~~~~~a~~~e~~~~~~~~~--k~l~pNvd~~~a~v~~~lG~p 228 (265)
T cd06101 159 FGHRVYKKYDPRA-TVLKKFAEKLLKEKGLDPMFELAAELEKIAPEVLYE--KKLYPNVDFYSGVLYKAMGFP 228 (265)
T ss_pred CCCCCCCCCCCCh-HHHHHHHHHHHHhhCCCHHHHHHHHHHHHHHHHhhc--cCCCCChHHHHHHHHHHhCCC
Confidence 44444 245554 334445555422 45555555555544323 377887777777788899997
No 61
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=37.18 E-value=29 Score=25.93 Aligned_cols=36 Identities=22% Similarity=0.208 Sum_probs=24.9
Q ss_pred HHHHhhhhHHHHHHHHHHHHHHhcCCcccchHHHHHhhh
Q psy3153 21 KAARRLNDYALTIRLLEMVQEKCGKKKKVIWPYILGEIR 59 (89)
Q Consensus 21 rAcRRvND~alAVR~lE~iK~K~~~~~~~iY~~~lqElk 59 (89)
.-.||++++..|+|+|..|=..-+.. . .+.+++-.|
T Consensus 173 eL~rrlg~~~eA~~~fs~vi~~~~~s--~-~~~l~~~AR 208 (214)
T PF09986_consen 173 ELNRRLGNYDEAKRWFSRVIGSKKAS--K-EPKLKDMAR 208 (214)
T ss_pred HHHHHhCCHHHHHHHHHHHHcCCCCC--C-cHHHHHHHH
Confidence 35899999999999999886544443 2 445554433
No 62
>PF01194 RNA_pol_N: RNA polymerases N / 8 kDa subunit; InterPro: IPR000268 In eukaryotes, there are three different forms of DNA-dependent RNA polymerases (2.7.7.6 from EC) transcribing different sets of genes. Each class of RNA polymerase is an assemblage of ten to twelve different polypeptides. In archaebacteria, there is generally a single form of RNA polymerase which also consists of an oligomeric assemblage of 10 to 13 polypeptides. Archaebacterial subunit N (gene rpoN) [] is a small protein of about 8 kDa, it is evolutionary related [] to a 8.3 kDa component shared by all three forms of eukaryotic RNA polymerases (gene RPB10 in yeast and POLR2J in mammals) as well as to African swine fever virus (ASFV) protein CP80R []. There is a conserved region which is located at the N-terminal extremity of these polymerase subunits; this region contains two cysteines that binds a zinc ion [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_N 3HKZ_N 1EF4_A 3H0G_V 2Y0S_N 2R92_J 3M4O_J 3S2D_J 1R9S_J 1Y1W_J ....
Probab=36.91 E-value=37 Score=21.81 Aligned_cols=27 Identities=30% Similarity=0.607 Sum_probs=18.6
Q ss_pred HhcCCcccchHHHHHhh------hhhhhhhCCC
Q psy3153 42 KCGKKKKVIWPYILGEI------RPTLTELGIE 68 (89)
Q Consensus 42 K~~~~~~~iY~~~lqEl------kPtl~ELGI~ 68 (89)
-||.-+..-|+.|++.+ +-+|++||+.
T Consensus 9 TCGkvi~~~~e~y~~~~~~~~~~~~~Ld~LG~~ 41 (60)
T PF01194_consen 9 TCGKVIGNKWEEYLERLENGEDPGDALDDLGLK 41 (60)
T ss_dssp TTTSBTCGHHHHHHHHHHTTS-HHHHHHHTT-S
T ss_pred CCCCChhHhHHHHHHHHHcCCCHHHHHHHhCCc
Confidence 36766667788888777 3478888874
No 63
>PF05138 PaaA_PaaC: Phenylacetic acid catabolic protein; InterPro: IPR007814 This family includes proteins such as PaaA and PaaC that are part of a catabolic pathway of phenylacetic acid []. These proteins may form part of a dioxygenase complex.; PDB: 3PWQ_K 3PVT_B 1OTK_B 3PW1_B 3PW8_B 3PVR_B 3PVY_B 3Q1G_A 3PF7_B 3PM5_C ....
Probab=36.39 E-value=22 Score=27.55 Aligned_cols=24 Identities=38% Similarity=0.612 Sum_probs=18.4
Q ss_pred ccchHHHHHhhhhhhhhhCCCCcc
Q psy3153 48 KVIWPYILGEIRPTLTELGIETPE 71 (89)
Q Consensus 48 ~~iY~~~lqElkPtl~ELGI~t~E 71 (89)
.+..+..+++++|+++++|+..|+
T Consensus 204 ~~lr~~w~~~v~~~l~~~gL~~P~ 227 (263)
T PF05138_consen 204 EELRQRWLAEVVPVLEEAGLEVPE 227 (263)
T ss_dssp HHHHHHHHHHHHHHHHHTT---S-
T ss_pred HHHHHHHHHHHHHHHHHcCCCCCC
Confidence 478889999999999999999998
No 64
>PRK10304 ferritin; Provisional
Probab=36.20 E-value=79 Score=22.75 Aligned_cols=43 Identities=21% Similarity=0.165 Sum_probs=29.1
Q ss_pred HHHHHHHHHHhhhhHHHHHHHHHHHHHHhcCCcccchHHHHHhhh
Q psy3153 15 IIIAALKAARRLNDYALTIRLLEMVQEKCGKKKKVIWPYILGEIR 59 (89)
Q Consensus 15 ii~AALrAcRRvND~alAVR~lE~iK~K~~~~~~~iY~~~lqElk 59 (89)
-|..+.+.|++.+||++..=+-.-+++-++.. .--.++++.++
T Consensus 100 ~i~~l~~~A~~~~D~~t~~fl~~fl~EQveEe--~~~~~l~~~l~ 142 (165)
T PRK10304 100 KINELAHAAMTNQDYPTFNFLQWYVSEQHEEE--KLFKSIIDKLS 142 (165)
T ss_pred HHHHHHHHHHHcCCHhHHHHHHHHHHHHHHHH--HHHHHHHHHHH
Confidence 35566778999999998876656666655443 34556666665
No 65
>cd08194 Fe-ADH6 Iron-containing alcohol dehydrogenases-like. Iron-containing alcohol dehydrogenase-like. Proteins of this family have not been characterized. Their specific function is unknown. The protein structure represents a dehydroquinate synthase-like fold and belongs to the alcohol dehydrogenase-like superfamily. They are distinct from other alcohol dehydrogenases which contain different protein domains. Alcohol dehydrogenase catalyzes the reduction of acetaldehyde to alcohol with NADP as cofactor. Its activity requires iron ions.
Probab=35.89 E-value=25 Score=27.71 Aligned_cols=29 Identities=21% Similarity=0.288 Sum_probs=24.8
Q ss_pred hHHHHHhhhhhhhhhCCCCccccCCCCCc
Q psy3153 51 WPYILGEIRPTLTELGIETPEDLGYDKPE 79 (89)
Q Consensus 51 Y~~~lqElkPtl~ELGI~t~EeLgydkpE 79 (89)
=...+++|+-.++++|+|+..++|.++.+
T Consensus 312 ~~~~~~~i~~l~~~~glP~L~~~gv~~~~ 340 (375)
T cd08194 312 AEKLIEALKELNRELEVPTLREYGIDKDA 340 (375)
T ss_pred HHHHHHHHHHHHHHcCCCCHHhcCCChHh
Confidence 35678889999999999999999988765
No 66
>PRK15138 aldehyde reductase; Provisional
Probab=35.67 E-value=28 Score=27.83 Aligned_cols=31 Identities=19% Similarity=0.281 Sum_probs=24.9
Q ss_pred cchHHHHHhhhhhhhhhCCCC-ccccCCCCCc
Q psy3153 49 VIWPYILGEIRPTLTELGIET-PEDLGYDKPE 79 (89)
Q Consensus 49 ~iY~~~lqElkPtl~ELGI~t-~EeLgydkpE 79 (89)
+.-...++.++-.+++||+|+ ..|+|.++-+
T Consensus 321 ~~~~~~i~~i~~l~~~lg~p~~L~~~gv~~~d 352 (387)
T PRK15138 321 ERIDAAIAATRNFFEQMGVPTRLSDYGLDGSS 352 (387)
T ss_pred HHHHHHHHHHHHHHHHcCCCCcHHHcCCCHHH
Confidence 445678899999999999996 7889987643
No 67
>PF06293 Kdo: Lipopolysaccharide kinase (Kdo/WaaP) family; InterPro: IPR010440 Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases. Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. Phosphoprotein phosphatases catalyse the reverse process. Protein kinases fall into three broad classes, characterised with respect to substrate specificity []: Serine/threonine-protein kinases Tyrosine-protein kinases Dual specific protein kinases (e.g. MEK - phosphorylates both Thr and Tyr on target proteins) Protein kinase function has been evolutionarily conserved from Escherichia coli to human []. Protein kinases play a role in a multitude of cellular processes, including division, proliferation, apoptosis, and differentiation []. Phosphorylation usually results in a functional change of the target protein by changing enzyme activity, cellular location, or association with other proteins. The catalytic subunits of protein kinases are highly conserved, and several structures have been solved [], leading to large screens to develop kinase-specific inhibitors for the treatments of a number of diseases []. This entry represents lipopolysaccharide kinases which are related to protein kinases IPR000719 from INTERPRO. This family includes waaP (rfaP) gene product is required for the addition of phosphate to O-4 of the first heptose residue of the lipopolysaccharide (LPS) inner core region. It has previously been shown that WaaP is necessary for resistance to hydrophobic and polycationic antimicrobials in E. coli and that it is required for virulence in invasive strains of Salmonella enterica [].; GO: 0005524 ATP binding, 0016773 phosphotransferase activity, alcohol group as acceptor, 0009103 lipopolysaccharide biosynthetic process, 0016020 membrane
Probab=35.23 E-value=15 Score=26.27 Aligned_cols=17 Identities=47% Similarity=0.794 Sum_probs=14.2
Q ss_pred hhhhhCCCCccccCCCC
Q psy3153 61 TLTELGIETPEDLGYDK 77 (89)
Q Consensus 61 tl~ELGI~t~EeLgydk 77 (89)
.|.++||+||+=++|..
T Consensus 67 ~L~~~Gi~tP~pva~~~ 83 (206)
T PF06293_consen 67 RLREAGIPTPEPVAYGE 83 (206)
T ss_pred HHHHcCCCCCcEEEEEE
Confidence 46789999999988864
No 68
>PLN02522 ATP citrate (pro-S)-lyase
Probab=35.05 E-value=1e+02 Score=27.21 Aligned_cols=58 Identities=16% Similarity=-0.022 Sum_probs=31.5
Q ss_pred CCCHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHhcCCcccchHHHHHhhhhhhhhhCCC
Q psy3153 10 VPDPVIIIAALKAARRLNDYALTIRLLEMVQEKCGKKKKVIWPYILGEIRPTLTELGIE 68 (89)
Q Consensus 10 VP~P~ii~AALrAcRRvND~alAVR~lE~iK~K~~~~~~~iY~~~lqElkPtl~ELGI~ 68 (89)
.++|.+ ...++.++.+-.....+++.+.|..-...+.+.+|+-+==-+--++.+||++
T Consensus 495 ~~DpRa-~~L~~~~~~~~~~~~~~~~a~~vE~~~~~~~k~L~~NVDga~a~i~~~lg~p 552 (608)
T PLN02522 495 NRDKRV-ELLQKYARTHFPSVKYMEYAVQVETYTLSKANNLVLNVDGAIGSLFLDLLAG 552 (608)
T ss_pred CCChhH-HHHHHHHHHhccccHHHHHHHHHHHHHhhccCCCCcCcHhHHHHHHHHcCCC
Confidence 346776 4444455544212223333444433222222567777777777789999998
No 69
>cd07956 Anticodon_Ia_Arg Anticodon-binding domain of arginyl tRNA synthetases. This domain is found in arginyl tRNA synthetases (ArgRS), which belong to the class Ia aminoacyl tRNA synthetases. It lies C-terminal to the catalytic core domain, and recognizes and specifically binds to the tRNA anticodon. ArgRS catalyzes the transfer of arginine to the 3'-end of its tRNA.
Probab=34.74 E-value=27 Score=23.98 Aligned_cols=24 Identities=29% Similarity=0.367 Sum_probs=18.0
Q ss_pred chHHHHHhhhhhhhhhCCCCcccc
Q psy3153 50 IWPYILGEIRPTLTELGIETPEDL 73 (89)
Q Consensus 50 iY~~~lqElkPtl~ELGI~t~EeL 73 (89)
+...+.+-++-.|+=|||++|+.|
T Consensus 133 Ll~~v~~vl~~~l~llgi~~~~~m 156 (156)
T cd07956 133 LVAAARQVLANGLDLLGIEAPERM 156 (156)
T ss_pred HHHHHHHHHHHHHHhcCCCccccC
Confidence 344556667778888999999875
No 70
>PF04336 DUF479: Protein of unknown function, DUF479; InterPro: IPR007431 This entry contains the Escherichia coli gene yajB, now renamed acpH, which encodes an ACP hydrolase. AcpH converts holo-ACP to apo-ACP by hydrolytic cleavage of the phosphopantetheine prosthetic group from ACP []. A mutant E. coli strain having a total deletion of the acpH grows normally, showing that phosphodiesterase activity is not essential for growth, although it is required for turnover of the ACP prosthetic group in vivo. AcpH is found only in Gram-negative organisms suggesting that it plays a role in some aspect of lipid metabolism that is unique to these organisms. The most obvious of which is biosynthesis of lipid A. Because AcpH is a hydrolase, it could possibly be an editing enzyme that intercepts acyl-ACPs that would give an inappropriate lipid A structure if used as acyl donors []. ; GO: 0008770 [acyl-carrier-protein] phosphodiesterase activity, 0006633 fatty acid biosynthetic process
Probab=34.28 E-value=39 Score=22.44 Aligned_cols=42 Identities=26% Similarity=0.146 Sum_probs=29.5
Q ss_pred HHHHHHH----HHHHhhhhHHHHHHHHHHHHHHhcCCcccchHHHH
Q psy3153 14 VIIIAAL----KAARRLNDYALTIRLLEMVQEKCGKKKKVIWPYIL 55 (89)
Q Consensus 14 ~ii~AAL----rAcRRvND~alAVR~lE~iK~K~~~~~~~iY~~~l 55 (89)
+-|+.|| +-.||.|+++.|+..|+.-....+..-.+.||.++
T Consensus 59 egi~~al~~m~~R~~~~~~l~~a~~~l~~~y~~le~~F~~FfpdL~ 104 (106)
T PF04336_consen 59 EGIERALQRMSRRLRRPNPLAGAIEELEEHYAELEQDFLEFFPDLQ 104 (106)
T ss_pred HHHHHHHHHHHhccCchhhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4444454 33457899999999999888887776556666554
No 71
>PLN03218 maturation of RBCL 1; Provisional
Probab=34.16 E-value=63 Score=29.92 Aligned_cols=34 Identities=9% Similarity=0.030 Sum_probs=18.3
Q ss_pred CCCCCHHHHHHHHHHHHhhhhHHHHHHHHHHHHH
Q psy3153 8 DGVPDPVIIIAALKAARRLNDYALTIRLLEMVQE 41 (89)
Q Consensus 8 DlVP~P~ii~AALrAcRRvND~alAVR~lE~iK~ 41 (89)
++.|+.....+.+.++.|.+++..|+++|+.++.
T Consensus 502 Gv~PdvvTynaLI~gy~k~G~~eeAl~lf~~M~~ 535 (1060)
T PLN03218 502 GVEANVHTFGALIDGCARAGQVAKAFGAYGIMRS 535 (1060)
T ss_pred CCCCCHHHHHHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 3445555555555555555555555555555543
No 72
>smart00386 HAT HAT (Half-A-TPR) repeats. Present in several RNA-binding proteins. Structurally and sequentially thought to be similar to TPRs.
Probab=34.13 E-value=59 Score=15.37 Aligned_cols=29 Identities=21% Similarity=0.235 Sum_probs=20.8
Q ss_pred hhHHHHHHHHHHHHHHhcCCcccchHHHHH
Q psy3153 27 NDYALTIRLLEMVQEKCGKKKKVIWPYILG 56 (89)
Q Consensus 27 ND~alAVR~lE~iK~K~~~~~~~iY~~~lq 56 (89)
+|+..|-.++|..-.+|... ..+|-.+++
T Consensus 1 ~~~~~~r~i~e~~l~~~~~~-~~~W~~y~~ 29 (33)
T smart00386 1 GDIERARKIYERALEKFPKS-VELWLKYAE 29 (33)
T ss_pred CcHHHHHHHHHHHHHHCCCC-hHHHHHHHH
Confidence 46777888888877777654 577776664
No 73
>PF13419 HAD_2: Haloacid dehalogenase-like hydrolase; PDB: 2FI1_A 2I6X_A 3SD7_A 4F71_A 4DFD_B 4F72_B 4DCC_A 3DDH_A 3KZX_A 2B0C_A ....
Probab=33.96 E-value=14 Score=23.44 Aligned_cols=50 Identities=28% Similarity=0.432 Sum_probs=29.2
Q ss_pred HHHHHHHHHHHHHHhcCCcccchHHHHHhhhhhhhhhCCC-------CccccCCCCCc
Q psy3153 29 YALTIRLLEMVQEKCGKKKKVIWPYILGEIRPTLTELGIE-------TPEDLGYDKPE 79 (89)
Q Consensus 29 ~alAVR~lE~iK~K~~~~~~~iY~~~lqElkPtl~ELGI~-------t~EeLgydkpE 79 (89)
++-+..+|+.+|.+ +-+.--.=..-.+.++..++.+|+. +.++.|..||+
T Consensus 79 ~~~~~~~L~~l~~~-~~~~~i~Sn~~~~~~~~~l~~~~~~~~f~~i~~~~~~~~~Kp~ 135 (176)
T PF13419_consen 79 YPGVRELLERLKAK-GIPLVIVSNGSRERIERVLERLGLDDYFDEIISSDDVGSRKPD 135 (176)
T ss_dssp STTHHHHHHHHHHT-TSEEEEEESSEHHHHHHHHHHTTHGGGCSEEEEGGGSSSSTTS
T ss_pred hhhhhhhhhhcccc-cceeEEeecCCcccccccccccccccccccccccchhhhhhhH
Confidence 56678888888854 2211000011235566777777766 45677887874
No 74
>smart00513 SAP Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation.
Probab=33.53 E-value=33 Score=18.67 Aligned_cols=16 Identities=25% Similarity=0.545 Sum_probs=13.7
Q ss_pred HHhhhhhhhhhCCCCc
Q psy3153 55 LGEIRPTLTELGIETP 70 (89)
Q Consensus 55 lqElkPtl~ELGI~t~ 70 (89)
.+|||-.+.++|+++.
T Consensus 6 ~~~Lk~~l~~~gl~~~ 21 (35)
T smart00513 6 VSELKDELKKRGLSTS 21 (35)
T ss_pred HHHHHHHHHHcCCCCC
Confidence 6789999999999863
No 75
>TIGR02158 PA_CoA_Oxy3 phenylacetate-CoA oxygenase, PaaI subunit. Phenylacetate-CoA oxygenase is comprised of a five gene complex responsible for the hydroxylation of phenylacetate-CoA (PA-CoA) as the second catabolic step in phenylacetic acid (PA) degradation. Although the exact function of this enzyme has not been determined, it has been shown to be required for phenylacetic acid degradation and has been proposed to function in a multicomponent oxygenase acting on phenylacetate-CoA.
Probab=33.18 E-value=38 Score=26.32 Aligned_cols=26 Identities=15% Similarity=0.201 Sum_probs=22.5
Q ss_pred ccchHHHHHhhhhhhhhhCCCCcccc
Q psy3153 48 KVIWPYILGEIRPTLTELGIETPEDL 73 (89)
Q Consensus 48 ~~iY~~~lqElkPtl~ELGI~t~EeL 73 (89)
.+.-+..++.+.|+++++|+..|+.-
T Consensus 178 ~~Lr~~w~~~v~~~l~~agL~~P~~~ 203 (237)
T TIGR02158 178 ATLQAAWEKEVNAVLNEATLTLPQQT 203 (237)
T ss_pred HHHHHHHHHHHHHHHHHhCCCCCCCc
Confidence 46788899999999999999999753
No 76
>TIGR02795 tol_pal_ybgF tol-pal system protein YbgF. Members of this protein family are the product of one of seven genes regularly clustered in operons to encode the proteins of the tol-pal system, which is critical for maintaining the integrity of the bacterial outer membrane. The gene for this periplasmic protein has been designated orf2 and ybgF. All members of the seed alignment were from unique tol-pal gene regions from completed bacterial genomes. The architecture of this protein is a signal sequence, a low-complexity region usually rich in Asn and Gln, a well-conserved region with tandem repeats that resemble the tetratricopeptide (TPR) repeat, involved in protein-protein interaction.
Probab=33.11 E-value=1.1e+02 Score=18.19 Aligned_cols=27 Identities=22% Similarity=0.078 Sum_probs=18.2
Q ss_pred HHHHHHhhhhHHHHHHHHHHHHHHhcC
Q psy3153 19 ALKAARRLNDYALTIRLLEMVQEKCGK 45 (89)
Q Consensus 19 ALrAcRRvND~alAVR~lE~iK~K~~~ 45 (89)
.-++..+.+++..|+..++.+-....+
T Consensus 45 l~~~~~~~~~~~~A~~~~~~~~~~~p~ 71 (119)
T TIGR02795 45 LGEAYYAQGKYADAAKAFLAVVKKYPK 71 (119)
T ss_pred HHHHHHhhccHHHHHHHHHHHHHHCCC
Confidence 345566777888888888876665544
No 77
>COG3888 Predicted transcriptional regulator [Transcription]
Probab=32.87 E-value=40 Score=28.01 Aligned_cols=35 Identities=23% Similarity=0.299 Sum_probs=25.7
Q ss_pred HHHHHHhcCCcccchHHHHHhhhhhhhhhCCCCccc
Q psy3153 37 EMVQEKCGKKKKVIWPYILGEIRPTLTELGIETPED 72 (89)
Q Consensus 37 E~iK~K~~~~~~~iY~~~lqElkPtl~ELGI~t~Ee 72 (89)
+.+|.-.++- .--|.+.+|++|--|+++|++.||+
T Consensus 282 ~~v~~S~esY-~f~~k~d~~~~k~~le~igy~~~e~ 316 (321)
T COG3888 282 NIVKESLESY-EFDYKLDLKEFKNYLEFIGYPIPEG 316 (321)
T ss_pred HHHHHHHhcc-ccchhhcHHHHHHHHHhcCCCChhh
Confidence 4455555554 2345568999999999999998886
No 78
>PF07980 SusD: SusD family; InterPro: IPR012944 This domain occurs in several hypothetical proteins. It also occurs in RagB, Q9ZA59 from SWISSPROT, a protein involved in signalling [] and SusD, Q8A1G2 from SWISSPROT, an outer membrane protein involved in nutrient binding [].; PDB: 3IHV_A 3LEW_A 3JQ1_A 3JQ0_A 3NQP_B 3SNX_A 3L22_A 3OTN_A 3IV0_A 3QNK_C ....
Probab=32.65 E-value=1.6e+02 Score=20.45 Aligned_cols=31 Identities=23% Similarity=0.359 Sum_probs=24.6
Q ss_pred HHHHHHHHHHhhhhHHHHHHHHHHHHHHhcC
Q psy3153 15 IIIAALKAARRLNDYALTIRLLEMVQEKCGK 45 (89)
Q Consensus 15 ii~AALrAcRRvND~alAVR~lE~iK~K~~~ 45 (89)
|.=-.-.|+=|+|+.+.|+-.|-.||..++.
T Consensus 135 vyL~~AEA~~~~g~~~~A~~~lN~vR~Rag~ 165 (266)
T PF07980_consen 135 VYLIYAEALARLGNTAEALEYLNQVRKRAGL 165 (266)
T ss_dssp HHHHHHHHHHHTTSHHHHHHHHHHHHHHTTT
T ss_pred HHHHHHHHHHHhCCHHHHHHHHHHHHHHcCC
Confidence 3333446777999999999999999998864
No 79
>PF03530 SK_channel: Calcium-activated SK potassium channel; InterPro: IPR011996 Potassium channels are the most diverse group of the ion channel family [, ]. They are important in shaping the action potential, and in neuronal excitability and plasticity []. The potassium channel family is composed of several functionally distinct isoforms, which can be broadly separated into 2 groups []: the practically non-inactivating 'delayed' group and the rapidly inactivating 'transient' group. These are all highly similar proteins, with only small amino acid changes causing the diversity of the voltage-dependent gating mechanism, channel conductance and toxin binding properties. Each type of K+ channel is activated by different signals and conditions depending on their type of regulation: some open in response to depolarisation of the plasma membrane; others in response to hyperpolarisation or an increase in intracellular calcium concentration; some can be regulated by binding of a transmitter, together with intracellular kinases; while others are regulated by GTP-binding proteins or other second messengers []. In eukaryotic cells, K+ channels are involved in neural signalling and generation of the cardiac rhythm, act as effectors in signal transduction pathways involving G protein-coupled receptors (GPCRs) and may have a role in target cell lysis by cytotoxic T-lymphocytes []. In prokaryotic cells, they play a role in the maintenance of ionic homeostasis []. All K+ channels discovered so far possess a core of alpha subunits, each comprising either one or two copies of a highly conserved pore loop domain (P-domain). The P-domain contains the sequence (T/SxxTxGxG), which has been termed the K+ selectivity sequence. In families that contain one P-domain, four subunits assemble to form a selective pathway for K+ across the membrane. However, it remains unclear how the 2 P-domain subunits assemble to form a selective pore. The functional diversity of these families can arise through homo- or hetero-associations of alpha subunits or association with auxiliary cytoplasmic beta subunits. K+ channel subunits containing one pore domain can be assigned into one of two superfamilies: those that possess six transmembrane (TM) domains and those that possess only two TM domains. The six TM domain superfamily can be further subdivided into conserved gene families: the voltage-gated (Kv) channels; the KCNQ channels (originally known as KvLQT channels); the EAG-like K+ channels; and three types of calcium (Ca)-activated K+ channels (BK, IK and SK) []. The 2TM domain family comprises inward-rectifying K+ channels. In addition, there are K+ channel alpha-subunits that possess two P-domains. These are usually highly regulated K+ selective leak channels. Ca2+-activated K+ channels are a diverse group of channels that are activated by an increase in intracellular Ca2+ concentration. They are found in the majority of nerve cells, where they modulate cell excitability and action potential. Three types of Ca2+-activated K+ channel have been characterised, termed small-conductance (SK), intermediate conductance (IK) and large conductance (BK) respectively []. SK channels are thought to play an important role in the functioning of all excitable tissues. To date, 3 subtypes (designated SK1-SK3) have been cloned, each of which possesses a different tissue expression profile: SK1 channels are expressed in the heart; SK2 channels are found in the adrenal gland; and SK3 channels are known to be present in skeletal muscle []. SK channels have a single-channel conductance of 2-20 pS and are activated by rises in cytosolic calcium with half maximal activation in the 400-800 nM range [, ]. Unlike BK channels, they are voltage insensitive and unaffected by low concentrations of TEA, charybdotoxin, or iberiotoxin. However, they are potently blocked by the bee venom apamin [, ], tubocurarine, and quaternary salts of bicuculline [, ]. A new series of compounds that block SK channels include dequalinium Synonym(s): SK Channel This entry represents a conserved region, found in proteins of SK channels family.
Probab=32.62 E-value=43 Score=23.90 Aligned_cols=20 Identities=30% Similarity=0.615 Sum_probs=16.1
Q ss_pred HHHHHHhhhhHHHHHHHHHH
Q psy3153 19 ALKAARRLNDYALTIRLLEM 38 (89)
Q Consensus 19 ALrAcRRvND~alAVR~lE~ 38 (89)
-+...||++|||++.-+|--
T Consensus 8 L~e~R~rlsD~aL~~a~~GI 27 (119)
T PF03530_consen 8 LFEKRKRLSDYALFFAMFGI 27 (119)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 35678999999999887643
No 80
>TIGR02552 LcrH_SycD type III secretion low calcium response chaperone LcrH/SycD. ScyD/LcrH contains three central tetratricopeptide-like repeats that are predicted to fold into an all-alpha-helical array.
Probab=32.23 E-value=1.3e+02 Score=18.80 Aligned_cols=25 Identities=20% Similarity=0.436 Sum_probs=13.2
Q ss_pred HHHhhhhHHHHHHHHHHHHHHhcCC
Q psy3153 22 AARRLNDYALTIRLLEMVQEKCGKK 46 (89)
Q Consensus 22 AcRRvND~alAVR~lE~iK~K~~~~ 46 (89)
.....+|+..|+.+|+.+-....+.
T Consensus 94 ~~~~~g~~~~A~~~~~~al~~~p~~ 118 (135)
T TIGR02552 94 CLLALGEPESALKALDLAIEICGEN 118 (135)
T ss_pred HHHHcCCHHHHHHHHHHHHHhcccc
Confidence 3344555555555555555555443
No 81
>PF07721 TPR_4: Tetratricopeptide repeat; InterPro: IPR011717 This entry includes tetratricopeptide-like repeats not detected by the IPR001440 from INTERPRO, IPR013105 from INTERPRO and IPR011716 from INTERPRO models. The tetratricopeptide repeat (TPR) motif is a protein-protein interaction module found in multiple copies in a number of functionally different proteins that facilitates specific interactions with a partner protein(s) [].; GO: 0042802 identical protein binding
Probab=31.99 E-value=53 Score=16.48 Aligned_cols=17 Identities=29% Similarity=0.186 Sum_probs=14.4
Q ss_pred HHHHhhhhHHHHHHHHH
Q psy3153 21 KAARRLNDYALTIRLLE 37 (89)
Q Consensus 21 rAcRRvND~alAVR~lE 37 (89)
++..+.+|++.|.+++|
T Consensus 9 ~~~~~~G~~~eA~~~l~ 25 (26)
T PF07721_consen 9 RALLAQGDPDEAERLLR 25 (26)
T ss_pred HHHHHcCCHHHHHHHHh
Confidence 56678899999999886
No 82
>PRK05443 polyphosphate kinase; Provisional
Probab=31.48 E-value=32 Score=30.50 Aligned_cols=40 Identities=18% Similarity=0.248 Sum_probs=33.2
Q ss_pred HHHHHHHHHHHHHhcCCcccchHHHHHhhhhhhhhhCCCC
Q psy3153 30 ALTIRLLEMVQEKCGKKKKVIWPYILGEIRPTLTELGIET 69 (89)
Q Consensus 30 alAVR~lE~iK~K~~~~~~~iY~~~lqElkPtl~ELGI~t 69 (89)
-++...|+.|..++....+.+|..+-++|.|.|++-||-.
T Consensus 83 ~~~~~ql~~I~~~v~~~~~~~~~i~~~~llpeL~~~GI~l 122 (691)
T PRK05443 83 LTPREQLDAISERAHRLVEEQYRLYNEELLPALAKEGIRI 122 (691)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCcEE
Confidence 4677889999999988767888888778999999999753
No 83
>smart00546 CUE Domain that may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two protein of the IL-1 signal transduction pathway, tollip and TAB2. Ponting (Biochem. J.) "Proteins of the Endoplasmic reticulum" (in press)
Probab=31.36 E-value=69 Score=17.84 Aligned_cols=22 Identities=32% Similarity=0.317 Sum_probs=17.5
Q ss_pred HHHHHHHHHHHHhhhhHHHHHHHH
Q psy3153 13 PVIIIAALKAARRLNDYALTIRLL 36 (89)
Q Consensus 13 P~ii~AALrAcRRvND~alAVR~l 36 (89)
+.+|...|+++. ||...||..|
T Consensus 18 ~~~I~~~L~~~~--g~ve~~i~~L 39 (43)
T smart00546 18 EEVIKAVLEANN--GNVEATINNL 39 (43)
T ss_pred HHHHHHHHHHcC--CCHHHHHHHH
Confidence 678889999866 8999998544
No 84
>KOG4281|consensus
Probab=31.20 E-value=71 Score=25.63 Aligned_cols=42 Identities=29% Similarity=0.413 Sum_probs=32.0
Q ss_pred HHHHHHHHHHHhcCCcccchHHHHHhhhhhhhhhCCCCccccCCC
Q psy3153 32 TIRLLEMVQEKCGKKKKVIWPYILGEIRPTLTELGIETPEDLGYD 76 (89)
Q Consensus 32 AVR~lE~iK~K~~~~~~~iY~~~lqElkPtl~ELGI~t~EeLgyd 76 (89)
+-|++...|.-..+..-+..+.-+|.||-+|+|| +||++|..
T Consensus 4 vq~l~ntck~~fs~~~pg~~~~nlqkLr~vLd~l---kp~Dvgl~ 45 (236)
T KOG4281|consen 4 VQRLFNTCKEVFSTGGPGPFEENLQKLRSVLDEL---KPEDVGLE 45 (236)
T ss_pred hHHHHHHHHHHhcCCCCCccHHHHHHHHHHHhhC---CHhhcCcC
Confidence 4578888888777654458999999999999987 36666654
No 85
>PF02631 RecX: RecX family; InterPro: IPR003783 RecX is a putative bacterial regulatory protein []. The gene encoding RecX is found downstream of recA, and it is suggested that the RecX protein might be regulator of RecA activity by interaction with the RecA protein or filament [].; GO: 0006282 regulation of DNA repair; PDB: 3DFG_A 3D5L_B 3C1D_B 3E3V_A.
Probab=30.37 E-value=1.6e+02 Score=19.32 Aligned_cols=49 Identities=14% Similarity=0.148 Sum_probs=28.9
Q ss_pred CHHHHHHHHHHHH---hhhhHHHHHHHHHHHHHHhcCCcccchHHHHHhhhhhhhhhCCC
Q psy3153 12 DPVIIIAALKAAR---RLNDYALTIRLLEMVQEKCGKKKKVIWPYILGEIRPTLTELGIE 68 (89)
Q Consensus 12 ~P~ii~AALrAcR---RvND~alAVR~lE~iK~K~~~~~~~iY~~~lqElkPtl~ELGI~ 68 (89)
++++|+.+|..|. =+||..-|-.+++.-....+.. -..|.++| .+-||+
T Consensus 7 ~~e~I~~vi~~l~~~gyidD~~ya~~~v~~~~~~~~~G----~~~I~~~L----~~kGi~ 58 (121)
T PF02631_consen 7 SEEAIEEVIDRLKELGYIDDERYAESYVRSRLRRKGKG----PRRIRQKL----KQKGID 58 (121)
T ss_dssp -HHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHHHTT------HHHHHHHH----HHTT--
T ss_pred CHHHHHHHHHHHHHcCCCCHHHHHHHHHHHhccccccc----HHHHHHHH----HHHCCC
Confidence 5677888877775 4799999999988766522222 23455554 345665
No 86
>cd01041 Rubrerythrin Rubrerythrin, ferritin-like diiron-binding domain. Rubrerythrin domain is a nonheme iron binding domain found in many air-sensitive bacteria and archaea and member of a broad superfamily of ferritin-like diiron-carboxylate proteins. The homodimeric rubrerythrin protein contains a binuclear metal center located within a four helix bundle. Many, but not all, rubrerythrin proteins have a second domain with a rubredoxin-like hexacoordinated iron center. Rubrerythrin is thought to reduce hydrogen peroxide as part of an oxidative stress protection system but its function is still poorly understood.
Probab=29.93 E-value=1.1e+02 Score=20.51 Aligned_cols=30 Identities=3% Similarity=-0.130 Sum_probs=24.1
Q ss_pred HHHHHHHHHHHhhhhHHHHHHHHHHHHHHh
Q psy3153 14 VIIIAALKAARRLNDYALTIRLLEMVQEKC 43 (89)
Q Consensus 14 ~ii~AALrAcRRvND~alAVR~lE~iK~K~ 43 (89)
+.+....+.|++.+|+.+|.-|-+.+++..
T Consensus 91 ~~y~~~~~~A~~e~d~~~~~~f~~i~~~E~ 120 (134)
T cd01041 91 EMYPEFAEVAEEEGFKEAARSFEAIAEAEK 120 (134)
T ss_pred HHHHHHHHHHHHcCCHHHHHHHHHHHHHHH
Confidence 456778889999999999887777777754
No 87
>cd08176 LPO Lactadehyde:propanediol oxidoreductase (LPO) catalyzes the interconversion between L-lactaldehyde and L-1,2-propanediol in Escherichia coli and other enterobacteria. Lactadehyde:propanediol oxidoreductase (LPO) is a member of the group III iron-activated dehydrogenases which catalyze the interconversion between L-lactaldehyde and L-1,2-propanediol in Escherichia coli and other enterobacteria. L-Fucose and L-rhamnose is used by Escherichia coli through an inducible pathway mediated by the fucose regulon comprising four linked oeprons fucO, fucA, fucPIK, and fucR. The fucA-encoded aldolase catalyzes the formation of dihydroxyacetone phosphate and L-lactaldehyde. Under anaerobic conditions, with NADH as a cofactor, lactaldehyde is converted by a fucO-encoded Lactadehyde:propanediol oxidoreductase (LPO) to L-1,2-propanediol, which is excreted as a fermentation product. In mutant strains, E. coli adapted to grow on L-1,2-propanediol, FucO catalyzes the oxidation of the polyol to
Probab=29.86 E-value=28 Score=27.38 Aligned_cols=29 Identities=17% Similarity=0.389 Sum_probs=23.6
Q ss_pred HHHHHhhhhhhhhhCCC-CccccCCCCCcc
Q psy3153 52 PYILGEIRPTLTELGIE-TPEDLGYDKPEL 80 (89)
Q Consensus 52 ~~~lqElkPtl~ELGI~-t~EeLgydkpEl 80 (89)
+..++.|+..++++|+| +..|+|.++.++
T Consensus 318 ~~~~~~i~~l~~~lglP~~L~e~gv~~~~~ 347 (377)
T cd08176 318 EAAIDAVRALSEDVGIPAGLRELGVKEEDF 347 (377)
T ss_pred HHHHHHHHHHHHHcCCCCCHHHcCCCHHHH
Confidence 45788899999999998 578899876554
No 88
>PF08967 DUF1884: Domain of unknown function (DUF1884); InterPro: IPR014418 This group represents an uncharacterised conserved protein.; PDB: 2PK8_A.
Probab=29.79 E-value=24 Score=24.34 Aligned_cols=43 Identities=28% Similarity=0.464 Sum_probs=24.8
Q ss_pred HHHHHHHHHHHhcCC------------cccchHHHHHhhhhhhhhhC--CCCccccCCCC
Q psy3153 32 TIRLLEMVQEKCGKK------------KKVIWPYILGEIRPTLTELG--IETPEDLGYDK 77 (89)
Q Consensus 32 AVR~lE~iK~K~~~~------------~~~iY~~~lqElkPtl~ELG--I~t~EeLgydk 77 (89)
-+|+++.|..|..-- -.+-|.|+-. ++++.+| |-..||||+|-
T Consensus 7 li~il~~ie~~inELk~dG~ePDivL~G~ef~e~~~~---~~l~~~~lkvy~i~ELg~DA 63 (85)
T PF08967_consen 7 LIRILELIEEKINELKEDGFEPDIVLVGPEFYEFLSE---EVLEVSGLKVYVIEELGSDA 63 (85)
T ss_dssp HHHHHHHHHHHHHHHHHTT----EEEE-HHHHHHHHH------EETTEEEEE-GGGTTEE
T ss_pred HHHHHHHHHHHHHHHHhcCCCCCEEEEcHHHHHHHHH---HHHHhhCceEEEHHhcCCce
Confidence 367888887775310 0245666655 5666666 55678999884
No 89
>COG1644 RPB10 DNA-directed RNA polymerase, subunit N (RpoN/RPB10) [Transcription]
Probab=29.74 E-value=39 Score=22.19 Aligned_cols=27 Identities=26% Similarity=0.534 Sum_probs=18.5
Q ss_pred HhcCCcccchHHHHHhh------hhhhhhhCCC
Q psy3153 42 KCGKKKKVIWPYILGEI------RPTLTELGIE 68 (89)
Q Consensus 42 K~~~~~~~iY~~~lqEl------kPtl~ELGI~ 68 (89)
-||.....-|+.|.+-+ +-+|++|||.
T Consensus 9 sCGkvi~~~w~~y~~rv~~ge~p~~vLDdLGv~ 41 (63)
T COG1644 9 SCGKVIGHKWEEYKRRVEEGEDPGEVLDDLGVK 41 (63)
T ss_pred cCCCCHHHHHHHHHHHHHcCCCHHHHHHHhCcH
Confidence 46666666677666544 5689999984
No 90
>PF13743 Thioredoxin_5: Thioredoxin; PDB: 3KZQ_C.
Probab=28.78 E-value=1.9e+02 Score=20.52 Aligned_cols=57 Identities=26% Similarity=0.181 Sum_probs=32.2
Q ss_pred CCCCCHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHhcCCcccchH-HHHHhhhhhhhhhCCC
Q psy3153 8 DGVPDPVIIIAALKAARRLNDYALTIRLLEMVQEKCGKKKKVIWP-YILGEIRPTLTELGIE 68 (89)
Q Consensus 8 DlVP~P~ii~AALrAcRRvND~alAVR~lE~iK~K~~~~~~~iY~-~~lqElkPtl~ELGI~ 68 (89)
+..+++-...-|.+||+ +=.-..|.|||-.++...-...+.+-. ..+.+ +.+++|++
T Consensus 59 ~~~~~~y~a~la~kAA~-~qg~k~~~~fL~~lQ~a~~~~~~~~s~~~~l~~---iA~~~gLD 116 (176)
T PF13743_consen 59 EPRSSSYPACLAYKAAQ-LQGKKKARRFLRALQEALFLEGKNYSDEELLLE---IAEELGLD 116 (176)
T ss_dssp --BS--HHHHHHHHHHH-TTT-H--HHHHHHHHHHHHTS---TTSHHHHHH---HHHHTT--
T ss_pred CCCCCchHHHHHHHHHH-HhChhhHHHHHHHHHHHHHhcCCCCCHHHHHHH---HHHHhCCC
Confidence 34566777778899996 667888999999999998655344444 44444 34566665
No 91
>PF13766 ECH_C: 2-enoyl-CoA Hydratase C-terminal region; PDB: 3JU1_A 3BPT_A.
Probab=28.55 E-value=23 Score=24.19 Aligned_cols=49 Identities=20% Similarity=0.163 Sum_probs=32.3
Q ss_pred cccccCCCCCCHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHhcCCcccchHHHHHh
Q psy3153 2 NDLAQDDGVPDPVIIIAALKAARRLNDYALTIRLLEMVQEKCGKKKKVIWPYILGE 57 (89)
Q Consensus 2 N~l~~~DlVP~P~ii~AALrAcRRvND~alAVR~lE~iK~K~~~~~~~iY~~~lqE 57 (89)
+.||+.| +.+=|.++|++ .+-.-|-..++.++.+|.-..+-.|..+-+-
T Consensus 10 ~~~F~~~---s~~eI~~~L~~----~~~~~a~~~~~~l~~~SP~Sl~vt~~~l~~~ 58 (118)
T PF13766_consen 10 DRCFSAD---SVEEIIEALEA----DGDEWAQKTLETLRSGSPLSLKVTFEQLRRG 58 (118)
T ss_dssp HHHTTSS---SHHHHHHHHHH----HS-HHHHHHHHHHCCS-HHHHHHHHHHHHCC
T ss_pred HHHhCCC---CHHHHHHHHHc----cCcHHHHHHHHHHHHCCHHHHHHHHHHHHHh
Confidence 4677754 66778888888 4456677888888888876655566555443
No 92
>PF03705 CheR_N: CheR methyltransferase, all-alpha domain; InterPro: IPR022641 CheR proteins are part of the chemotaxis signaling mechanism which methylates the chemotaxis receptor at specific glutamate residues. This entry refers to the N-terminal domain of the CherR-type MCP methyltransferases, which are found in bacteria, archaea and green plants. This entry is found in association with PF01739 from PFAM. Methyl transfer from the ubiquitous S-adenosyl-L-methionine (AdoMet) to either nitrogen, oxygen or carbon atoms is frequently employed in diverse organisms ranging from bacteria to plants and mammals. The reaction is catalysed by methyltransferases (Mtases) and modifies DNA, RNA, proteins and small molecules, such as catechol for regulatory purposes. The various aspects of the role of DNA methylation in prokaryotic restriction-modification systems and in a number of cellular processes in eukaryotes including gene regulation and differentiation is well documented. Three classes of DNA Mtases transfer the methyl group from AdoMet to the target base to form either N-6-methyladenine, or N-4-methylcytosine, or C-5- methylcytosine. In C-5-cytosine Mtases, ten conserved motifs are arranged in the same order []. Motif I (a glycine-rich or closely related consensus sequence; FAGxGG in M.HhaI []), shared by other AdoMet-Mtases [], is part of the cofactor binding site and motif IV (PCQ) is part of the catalytic site. In contrast, sequence comparison among N-6-adenine and N-4-cytosine Mtases indicated two of the conserved segments [], although more conserved segments may be present. One of them corresponds to motif I in C-5-cytosine Mtases, and the other is named (D/N/S)PP(Y/F). Crystal structures are known for a number of Mtases [, , , ]. The cofactor binding sites are almost identical and the essential catalytic amino acids coincide. The comparable protein folding and the existence of equivalent amino acids in similar secondary and tertiary positions indicate that many (if not all) AdoMet-Mtases have a common catalytic domain structure. This permits tertiary structure prediction of other DNA, RNA, protein, and small-molecule AdoMet-Mtases from their amino acid sequences []. Flagellated bacteria swim towards favourable chemicals and away from deleterious ones. Sensing of chemoeffector gradients involves chemotaxis receptors, transmembrane (TM) proteins that detect stimuli through their periplasmic domains and transduce the signals via their cytoplasmic domains []. Signalling outputs from these receptors are influenced both by the binding of the chemoeffector ligand to their periplasmic domains and by methylation of specific glutamate residues on their cytoplasmic domains. Methylation is catalysed by CheR, an S-adenosylmethionine-dependent methyltransferase [], which reversibly methylates specific glutamate residues within a coiled coil region, to form gamma-glutamyl methyl ester residues [, ]. The structure of the Salmonella typhimurium chemotaxis receptor methyltransferase CheR, bound to S-adenosylhomocysteine, has been determined to a resolution of 2.0 A []. The structure reveals CheR to be a two-domain protein, with a smaller N-terminal helical domain linked via a single polypeptide connection to a larger C-terminal alpha/beta domain. The C-terminal domain has the characteristics of a nucleotide-binding fold, with an insertion of a small anti-parallel beta-sheet subdomain. The S-adenosylhomocysteine-binding site is formed mainly by the large domain, with contributions from residues within the N-terminal domain and the linker region [].; PDB: 1AF7_A 1BC5_A.
Probab=28.22 E-value=84 Score=17.89 Aligned_cols=40 Identities=13% Similarity=0.244 Sum_probs=23.5
Q ss_pred HHHHHHHHHhcCCccc-chHHHHHhhhhhhhhhCCCCcccc
Q psy3153 34 RLLEMVQEKCGKKKKV-IWPYILGEIRPTLTELGIETPEDL 73 (89)
Q Consensus 34 R~lE~iK~K~~~~~~~-iY~~~lqElkPtl~ELGI~t~EeL 73 (89)
+|.+-|+.++|-...+ --..+..-|.+.+..+|+++.+++
T Consensus 7 ~~~~~i~~~~Gi~l~~~K~~~l~rRl~~rm~~~~~~~~~~y 47 (57)
T PF03705_consen 7 RFRELIYRRTGIDLSEYKRSLLERRLARRMRALGLPSFAEY 47 (57)
T ss_dssp HHHHHHHHHH-----GGGHHHHHHHHHHHHHHHT---HHHH
T ss_pred HHHHHHHHHHCCCCchhhHHHHHHHHHHHHHHcCCCCHHHH
Confidence 5677788899865333 124566789999999999887653
No 93
>TIGR00198 cat_per_HPI catalase/peroxidase HPI. Note that the translation PID:g296476 from accession X71420 from Rhodobacter capsulatus B10 contains extensive frameshift differences from the rest of the orthologous family.
Probab=27.98 E-value=50 Score=29.92 Aligned_cols=19 Identities=32% Similarity=0.406 Sum_probs=16.7
Q ss_pred hHHHHHHHHHHHHHHhcCC
Q psy3153 28 DYALTIRLLEMVQEKCGKK 46 (89)
Q Consensus 28 D~alAVR~lE~iK~K~~~~ 46 (89)
....|.|+||-||.||+++
T Consensus 121 ~Ldka~~lL~pIk~kyp~~ 139 (716)
T TIGR00198 121 NLDKARRLLWPIKKKYGNK 139 (716)
T ss_pred hHHHHHHHHHHHHHHCCCc
Confidence 4678999999999999875
No 94
>PF05843 Suf: Suppressor of forked protein (Suf); InterPro: IPR008847 This domain consists of several eukaryotic suppressor of forked (Suf) like proteins. The Drosophila melanogaster suppressor of forked [Su(f)] protein shares homology with the Saccharomyces cerevisiae RNA14 protein and the 77 kDa subunit of Homo sapiens cleavage stimulation factor, which are proteins involved in mRNA 3' end formation. This suggests a role for Su(f) in mRNA 3' end formation in Drosophila. The su(f) gene produces three transcripts; two of them are polyadenylated at the end of the transcription unit, and one is a truncated transcript, polyadenylated in intron 4. It is thought that su(f) plays a role in the regulation of poly(A) site utilisation and the GU-rich sequence is important for this regulation to occur [].; GO: 0006397 mRNA processing, 0005634 nucleus; PDB: 2L9B_B 2OND_B 2OOE_A 4E85_B 4EBA_C 4E6H_A 2UY1_B.
Probab=27.69 E-value=1.3e+02 Score=22.78 Aligned_cols=30 Identities=17% Similarity=0.138 Sum_probs=14.2
Q ss_pred hhhHHHHHHHHHHHHHHhcCCcccchHHHHH
Q psy3153 26 LNDYALTIRLLEMVQEKCGKKKKVIWPYILG 56 (89)
Q Consensus 26 vND~alAVR~lE~iK~K~~~~~~~iY~~~lq 56 (89)
-+|...|.+|||..-.+.+.. ...|-.|++
T Consensus 49 ~~d~~~A~~Ife~glk~f~~~-~~~~~~Y~~ 78 (280)
T PF05843_consen 49 NKDPKRARKIFERGLKKFPSD-PDFWLEYLD 78 (280)
T ss_dssp CS-HHHHHHHHHHHHHHHTT--HHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHHCCCC-HHHHHHHHH
Confidence 355555666666555555544 344444443
No 95
>TIGR01951 nusB transcription antitermination factor NusB. A transcription antitermination complex active in many bacteria was designated N-utilization substance (Nus) in E. coli because of its interaction with phage lambda protein N. This model represents NusB. Other components are NusA and NusG. NusE is, in fact, ribosomal protein S10.
Probab=27.65 E-value=61 Score=21.35 Aligned_cols=34 Identities=26% Similarity=0.396 Sum_probs=25.9
Q ss_pred CCCCHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHh
Q psy3153 9 GVPDPVIIIAALKAARRLNDYALTIRLLEMVQEKC 43 (89)
Q Consensus 9 lVP~P~ii~AALrAcRRvND~alAVR~lE~iK~K~ 43 (89)
=+|...+|..|.+.|++.++ +-+.+|.-||=.+.
T Consensus 93 ~~p~~avineaV~lak~~~~-~~~~~fVNaVLr~i 126 (129)
T TIGR01951 93 DVPYKVVINEAVELAKKFGD-EDSHKFVNGVLDKI 126 (129)
T ss_pred CCCCcchHHHHHHHHHHHCC-CCchhhHHHHHHHH
Confidence 37999999999999998754 35677777765543
No 96
>PF08405 Calici_PP_N: Viral polyprotein N-terminal; InterPro: IPR013614 This domain is found at the N terminus of non-structural viral polyproteins of the Caliciviridae subfamily. ; GO: 0003968 RNA-directed RNA polymerase activity, 0004197 cysteine-type endopeptidase activity, 0017111 nucleoside-triphosphatase activity, 0044419 interspecies interaction between organisms
Probab=27.64 E-value=1.4e+02 Score=25.32 Aligned_cols=41 Identities=27% Similarity=0.372 Sum_probs=28.0
Q ss_pred HHHHHHHHHhhhhHHHHHHHHHHHHHHhcCCcccchHHHHHhhh
Q psy3153 16 IIAALKAARRLNDYALTIRLLEMVQEKCGKKKKVIWPYILGEIR 59 (89)
Q Consensus 16 i~AALrAcRRvND~alAVR~lE~iK~K~~~~~~~iY~~~lqElk 59 (89)
-.++||||+-+..| +++||.-|+.-.-.+...+ +..+.-|.
T Consensus 250 a~~~Lra~~~lG~y--giei~~~i~kw~fp~~~~~-~~~l~~iE 290 (358)
T PF08405_consen 250 AASGLRAATELGQY--GIEIFKLIMKWFFPKKDPE-PATLRNIE 290 (358)
T ss_pred HHHHHHHHHHHHHH--HHHHHHHHHHHcCCCCccH-HHHHHHHH
Confidence 35789999999977 4688888887665543333 45554443
No 97
>COG3629 DnrI DNA-binding transcriptional activator of the SARP family [Signal transduction mechanisms]
Probab=27.51 E-value=1.1e+02 Score=24.40 Aligned_cols=29 Identities=10% Similarity=0.061 Sum_probs=24.2
Q ss_pred HHHHHHHHHHHhhhhHHHHHHHHHHHHHH
Q psy3153 14 VIIIAALKAARRLNDYALTIRLLEMVQEK 42 (89)
Q Consensus 14 ~ii~AALrAcRRvND~alAVR~lE~iK~K 42 (89)
++-.+.+++.-+.++.+.|+|.++.++..
T Consensus 188 ~~~~~lm~~y~~~g~~~~ai~~y~~l~~~ 216 (280)
T COG3629 188 PAYLRLMEAYLVNGRQSAAIRAYRQLKKT 216 (280)
T ss_pred HHHHHHHHHHHHcCCchHHHHHHHHHHHH
Confidence 35567788888899999999999999885
No 98
>smart00836 DALR_1 DALR anticodon binding domain. This all alpha helical domain is the anticodon binding domain of Arginyl tRNA synthetase. This domain is known as the DALR domain after characteristic conserved amino acids PUBMED:10447505.
Probab=27.49 E-value=42 Score=21.65 Aligned_cols=24 Identities=25% Similarity=0.385 Sum_probs=18.7
Q ss_pred chHHHHHhhhhhhhhhCCCCcccc
Q psy3153 50 IWPYILGEIRPTLTELGIETPEDL 73 (89)
Q Consensus 50 iY~~~lqElkPtl~ELGI~t~EeL 73 (89)
+...+.+-++-.++=|||+++|.|
T Consensus 99 Ll~~~~~~l~~~~~llgi~~~~~m 122 (122)
T smart00836 99 LLKAVRQVLANGLRLLGISAPERM 122 (122)
T ss_pred HHHHHHHHHHHHHHHcCCCccccC
Confidence 456666777788888999999864
No 99
>KOG2005|consensus
Probab=27.46 E-value=73 Score=29.69 Aligned_cols=29 Identities=24% Similarity=0.348 Sum_probs=24.2
Q ss_pred CCCCCHH---HHHHHHHHHHhhhhHHHHHHHH
Q psy3153 8 DGVPDPV---IIIAALKAARRLNDYALTIRLL 36 (89)
Q Consensus 8 DlVP~P~---ii~AALrAcRRvND~alAVR~l 36 (89)
-++|.|+ ++.-|++--+..|+|+.|+|..
T Consensus 231 ~~lP~Pdd~~ll~~a~~IYlKf~~~~~al~~a 262 (878)
T KOG2005|consen 231 PLLPGPDDVALLRTALKIYLKFNEYPRALVGA 262 (878)
T ss_pred hcCCCchhhHHHHHHHHHHHHHHHhHHHHHHH
Confidence 4789999 8888998888888888888763
No 100
>PLN03077 Protein ECB2; Provisional
Probab=27.13 E-value=3.1e+02 Score=23.60 Aligned_cols=61 Identities=21% Similarity=0.217 Sum_probs=42.1
Q ss_pred CCCCCCHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHhcCCcccchHHH------------HHhhhhhhhhhCCC
Q psy3153 7 DDGVPDPVIIIAALKAARRLNDYALTIRLLEMVQEKCGKKKKVIWPYI------------LGEIRPTLTELGIE 68 (89)
Q Consensus 7 ~DlVP~P~ii~AALrAcRRvND~alAVR~lE~iK~K~~~~~~~iY~~~------------lqElkPtl~ELGI~ 68 (89)
+.+-|++.+..+-|.|||.-++..+|-+..+.+-.- +......|-.+ ..+++-.|++-|+.
T Consensus 651 m~~~pd~~~~~aLl~ac~~~~~~e~~e~~a~~l~~l-~p~~~~~y~ll~n~ya~~g~~~~a~~vr~~M~~~g~~ 723 (857)
T PLN03077 651 MPITPDPAVWGALLNACRIHRHVELGELAAQHIFEL-DPNSVGYYILLCNLYADAGKWDEVARVRKTMRENGLT 723 (857)
T ss_pred CCCCCCHHHHHHHHHHHHHcCChHHHHHHHHHHHhh-CCCCcchHHHHHHHHHHCCChHHHHHHHHHHHHcCCC
Confidence 456799999999999999999998888777666533 33212223221 24777888888875
No 101
>cd00619 Terminator_NusB Transcription termination factor NusB (N protein-Utilization Substance B). NusB plays a key role in the regulation of ribosomal RNA biosynthesis in eubacteria by modulating the efficiency of transcriptional antitermination. NusB along with other Nus factors (NusA, NusE/S10 and NusG) forms the core complex with the boxA element of the nut site of the rRNA operons. These interactions help RNA polymerase to counteract polarity during transcription of rRNA operons and allow stable antitermination. The transcription antitermination system can be appropriated by some bacteriophages such as lambda, which use the system to switch between the lysogenic and lytic modes of phage propagation.
Probab=26.97 E-value=68 Score=21.21 Aligned_cols=36 Identities=28% Similarity=0.419 Sum_probs=27.4
Q ss_pred CCCCCCHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHh
Q psy3153 7 DDGVPDPVIIIAALKAARRLNDYALTIRLLEMVQEKC 43 (89)
Q Consensus 7 ~DlVP~P~ii~AALrAcRRvND~alAVR~lE~iK~K~ 43 (89)
.|=+|...+|..|...|++..+ ..+.+|.-||=.+.
T Consensus 91 ~~~~p~~~vinEaV~lak~~~~-~~~~~fVNaVLr~i 126 (130)
T cd00619 91 LPDVPHPVVINEAIELAKRFGG-DDSHKFVNGVLDKI 126 (130)
T ss_pred CCCCCCcchHHHHHHHHHHHCC-CcchhHHHHHHHHH
Confidence 3447999999999999998765 46677777776554
No 102
>cd08175 G1PDH Glycerol-1-phosphate dehydrogenase (G1PDH) catalyzes the reversible reduction of dihydroxyacetone phosphate (DHAP) to glycerol-1-phosphate (G1P) in an NADH-dependent manner. Glycerol-1-phosphate dehydrogenase (G1PDH) plays a role in the synthesis of phosphoglycerolipids in Gram-positive bacterial species. It catalyzes the reversibly reduction of dihydroxyacetone phosphate (DHAP) to glycerol-1-phosphate (G1P) in a NADH-dependent manner. Its activity requires a Ni++ ion. In Bacillus subtilis, it has been described as AraM gene in L-arabinose (ara) operon. AraM protein forms homodimer. This family is bacteria specific.
Probab=26.74 E-value=28 Score=27.01 Aligned_cols=27 Identities=33% Similarity=0.562 Sum_probs=21.5
Q ss_pred HHHhhhhhhhhhCCCC-ccccCCCCCcc
Q psy3153 54 ILGEIRPTLTELGIET-PEDLGYDKPEL 80 (89)
Q Consensus 54 ~lqElkPtl~ELGI~t-~EeLgydkpEl 80 (89)
.++.++..++++|+|+ .+++|.+..++
T Consensus 295 ~~~~i~~l~~~lglP~~l~~~gv~~~~l 322 (348)
T cd08175 295 ASAKIEELLKKVGAPTHPEEIGIDKELF 322 (348)
T ss_pred cHHHHHHHHHHCCCCCCHHHcCCCHHHH
Confidence 4677899999999995 58899876544
No 103
>TIGR02058 lin0512_fam conserved hypothetical protein. This family consists of few members, broadly distributed. It occurs so far in several Firmicutes (twice in Oceanobacillus), one Cyanobacterium, one alpha Proteobacterium, and (with a long prefix) in plants. The function is unknown. The alignment includes a perfectly conserved motif GxGxDxHG near the N-terminus.
Probab=26.72 E-value=54 Score=23.49 Aligned_cols=23 Identities=30% Similarity=0.330 Sum_probs=15.9
Q ss_pred cccccCCCCCCHHHHHHHHHHHH---hhhhHH
Q psy3153 2 NDLAQDDGVPDPVIIIAALKAAR---RLNDYA 30 (89)
Q Consensus 2 N~l~~~DlVP~P~ii~AALrAcR---RvND~a 30 (89)
|+++|.| +-.||.|||| +-|..+
T Consensus 11 ~DlhGqD------~TkAA~RAvrDAI~hnsip 36 (116)
T TIGR02058 11 VDQHGQN------ITKAAMRAVRNAIASNSMP 36 (116)
T ss_pred ccccCcc------HHHHHHHHHHHHHhhccch
Confidence 5667776 4689999998 445444
No 104
>PRK10947 global DNA-binding transcriptional dual regulator H-NS; Provisional
Probab=26.39 E-value=1.2e+02 Score=21.75 Aligned_cols=22 Identities=32% Similarity=0.457 Sum_probs=18.2
Q ss_pred hHHHHHhhhhhhhhhCCCCcccc
Q psy3153 51 WPYILGEIRPTLTELGIETPEDL 73 (89)
Q Consensus 51 Y~~~lqElkPtl~ELGI~t~EeL 73 (89)
...-+++++-.|.+.||+ ++||
T Consensus 54 r~~kl~~~r~~m~~~Gis-~~eL 75 (135)
T PRK10947 54 RTRKLQQYREMLIADGID-PNEL 75 (135)
T ss_pred HHHHHHHHHHHHHHcCCC-HHHH
Confidence 344689999999999997 7888
No 105
>cd08186 Fe-ADH8 Iron-containing alcohol dehydrogenase. Type III Iron-containing alcohol dehydrogenases (ADH). Alcohol dehydrogenase catalyzes the reduction of acetaldehyde to alcohol with NADP as cofactor. The ADH of hyperthermophilic archaeon Thermococcus hydrothermalis oxidizes a series of primary aliphatic and aromatic alcohols preferentially from C2 to C8 but is also active towards methanol and glycerol and stereospecific for monoterpenes. It was suggested that the type III ADHs in microorganisms are involved in acetaldehyde detoxication rather than in alcohol turnover.
Probab=26.33 E-value=36 Score=26.90 Aligned_cols=28 Identities=18% Similarity=0.308 Sum_probs=22.7
Q ss_pred HHHHHhhhhhhhhhCCC-CccccCCCCCc
Q psy3153 52 PYILGEIRPTLTELGIE-TPEDLGYDKPE 79 (89)
Q Consensus 52 ~~~lqElkPtl~ELGI~-t~EeLgydkpE 79 (89)
...++.|+..++++|+| +..|+|.++.+
T Consensus 317 ~~~i~~l~~l~~~lglP~~L~~~gv~~~~ 345 (383)
T cd08186 317 EKAAKAVEKWLFSIGITEKLSDYGFTEGD 345 (383)
T ss_pred HHHHHHHHHHHHHCCCCCCHHHcCCCHHH
Confidence 45688899999999998 57889987644
No 106
>PRK06224 citrate synthase; Provisional
Probab=26.31 E-value=1.6e+02 Score=22.57 Aligned_cols=58 Identities=24% Similarity=0.218 Sum_probs=33.7
Q ss_pred CCHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHhcCC-cccchHHHHHhhhhhhhhhCCCC
Q psy3153 11 PDPVIIIAALKAARRLNDYALTIRLLEMVQEKCGKK-KKVIWPYILGEIRPTLTELGIET 69 (89)
Q Consensus 11 P~P~ii~AALrAcRRvND~alAVR~lE~iK~K~~~~-~~~iY~~~lqElkPtl~ELGI~t 69 (89)
++|.. ..-+..++++.+....+++.+.|..-.... .+.+|+-+-=-.--++.+||++.
T Consensus 155 ~DPRa-~~L~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~l~~Nvd~~~a~l~~~lG~p~ 213 (263)
T PRK06224 155 VDPRA-PRLLALAREAGVAGRHCRLAEALEAALAAAKGKPLPLNVDGAIAAILADLGFPP 213 (263)
T ss_pred CCchH-HHHHHHHHHhccCCHHHHHHHHHHHHHHHhcCCCCCccHHHHHHHHHHHcCCCh
Confidence 46654 344455566654434455555544333221 13588887777888889999863
No 107
>PF00378 ECH: Enoyl-CoA hydratase/isomerase family; InterPro: IPR001753 The crotonase superfamily is comprised of mechanistically diverse proteins that share a conserved trimeric quaternary structure (sometimes a hexamer consisting of a dimer of trimers), the core of which consists of 4 turns of a (beta/beta/alpha)n superhelix. Some enzymes in the superfamily have been shown to display dehalogenase, hydratase, and isomerase activities, while others have been implicated in carbon-carbon bond formation and cleavage as well as the hydrolysis of thioesters []. However, these different enzymes share the need to stabilise an enolate anion intermediate derived from an acyl-CoA substrate. This is accomplished by two structurally conserved peptidic NH groups that provide hydrogen bonds to the carbonyl moieties of the acyl-CoA substrates and form an "oxyanion hole". The CoA thioester derivatives bind in a characteristic hooked shape and a conserved tunnel binds the pantetheine group of CoA, which links the 3'-phosphate ADP binding site to the site of reaction []. Enzymes in the crotonase superfamily include: Enoyl-CoA hydratase (crotonase; 4.2.1.17 from EC), which catalyses the hydratation of 2-trans-enoyl-CoA into 3-hydroxyacyl-CoA []. 3-2trans-enoyl-CoA isomerase (or dodecenoyl-CoA isomerise; 5.3.3.8 from EC), which shifts the 3-double bond of the intermediates of unsaturated fatty acid oxidation to the 2-trans position []. 3-hydroxbutyryl-CoA dehydratase (crotonase; 4.2.1.55 from EC), a bacterial enzyme involved in the butyrate/butanol-producing pathway. 4-Chlorobenzoyl-CoA dehalogenase (3.8.1.6 from EC), a Pseudomonas enzyme which catalyses the conversion of 4-chlorobenzoate-CoA to 4-hydroxybenzoate-CoA []. Dienoyl-CoA isomerise, which catalyses the isomerisation of 3-trans,5-cis-dienoyl-CoA to 2-trans,4-trans-dienoyl-CoA []. Naphthoate synthase (MenB, or DHNA synthetase; 4.1.3.36 from EC), a bacterial enzyme involved in the biosynthesis of menaquinone (vitamin K2) []. Carnitine racemase (gene caiD), which catalyses the reversible conversion of crotonobetaine to L-carnitine in Escherichia coli []. Methylmalonyl CoA decarboxylase (MMCD; 4.1.1.41 from EC), which has a hexameric structure (dimer of trimers) []. Carboxymethylproline synthase (CarB), which is involved in carbapenem biosynthesis []. 6-oxo camphor hydrolase, which catalyses the desymmetrisation of bicyclic beta-diketones to optically active keto acids []. The alpha subunit of fatty oxidation complex, a multi-enzyme complex that catalyses the last three reactions in the fatty acid beta-oxidation cycle []. AUH protein, a bifunctional RNA-binding homologue of enoyl-CoA hydratase []. This entry represents the core domain found in crotonase superfamily members.; GO: 0003824 catalytic activity, 0008152 metabolic process; PDB: 2VRE_B 3RSI_A 1HZD_F 2ZQR_E 2ZQQ_D 3R9S_C 1O8U_E 1SZO_C 3MOY_A 2UZF_A ....
Probab=26.24 E-value=96 Score=22.47 Aligned_cols=37 Identities=27% Similarity=0.338 Sum_probs=31.0
Q ss_pred CCCCCCHHHHHHHHHHHHhhhhH-HHHHHHHHHHHHHh
Q psy3153 7 DDGVPDPVIIIAALKAARRLNDY-ALTIRLLEMVQEKC 43 (89)
Q Consensus 7 ~DlVP~P~ii~AALrAcRRvND~-alAVR~lE~iK~K~ 43 (89)
..+||+.++.+.|++.|+|+... +.|+|.....-.+.
T Consensus 173 ~~v~~~~~l~~~a~~~a~~l~~~~~~a~~~~K~~~~~~ 210 (245)
T PF00378_consen 173 DEVVPDEELDEEALELAKRLAAKPPSALRATKKALNRA 210 (245)
T ss_dssp SEEESGGGHHHHHHHHHHHHHTSCHHHHHHHHHHHHHH
T ss_pred eEEcCchhhhHHHHHHHHHHhcCCHHHHHHHHHHHHHH
Confidence 45689999999999999999999 78888877766654
No 108
>PF07442 Ponericin: Ponericin; InterPro: IPR010002 This family contains a number of ponericin peptides (approximately 30 residues long) from the venom of the predatory ant Pachycondyla goeldii (Ponerine ant). These peptides exhibit antibacterial and insecticidal properties, and may adopt an amphipathic alpha-helical structure in polar environments such as cell membranes [].; GO: 0005576 extracellular region
Probab=26.15 E-value=39 Score=19.22 Aligned_cols=12 Identities=67% Similarity=0.720 Sum_probs=10.1
Q ss_pred CHHHHHHHHHHH
Q psy3153 12 DPVIIIAALKAA 23 (89)
Q Consensus 12 ~P~ii~AALrAc 23 (89)
-|-|+.|||+|+
T Consensus 17 gpgi~kaal~aa 28 (29)
T PF07442_consen 17 GPGILKAALKAA 28 (29)
T ss_pred CchHHHHHHHhc
Confidence 378999999986
No 109
>KOG4204|consensus
Probab=26.12 E-value=78 Score=24.39 Aligned_cols=51 Identities=20% Similarity=0.272 Sum_probs=36.1
Q ss_pred hHHHHHHHHHHHHHHhcCCcccchHHHHHhhhhhhhhhCCCCcc------ccCCCCCcc
Q psy3153 28 DYALTIRLLEMVQEKCGKKKKVIWPYILGEIRPTLTELGIETPE------DLGYDKPEL 80 (89)
Q Consensus 28 D~alAVR~lE~iK~K~~~~~~~iY~~~lqElkPtl~ELGI~t~E------eLgydkpEl 80 (89)
...-|..+|.+||.+..++ -++|..-++=++-.-.+ +|+|++ ||=-+.|+|
T Consensus 18 t~~DAlsYl~~VK~~f~d~-p~kY~~FL~im~d~ka~-~iD~~~vi~rv~eLfK~h~~L 74 (231)
T KOG4204|consen 18 TLDDALAYLKAVKEAFQDE-PEKYDEFLEIMKDFKAQ-RIDTPGVIARVKELLKGHPDL 74 (231)
T ss_pred ChHHHHHHHHHHHHHHhcC-hHHHHHHHHHHHHHHhc-cCCHHHHHHHHHHHHccCHHH
Confidence 3456899999999999996 78999988877665544 555543 455555544
No 110
>COG5304 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=25.84 E-value=68 Score=22.43 Aligned_cols=26 Identities=19% Similarity=0.289 Sum_probs=20.2
Q ss_pred HHHHHHHHHHHhcCCcccchHHHHHhh
Q psy3153 32 TIRLLEMVQEKCGKKKKVIWPYILGEI 58 (89)
Q Consensus 32 AVR~lE~iK~K~~~~~~~iY~~~lqEl 58 (89)
+---||+||.|+..+ .==|+-|+.|+
T Consensus 59 ss~dLeaIK~kaSa~-GlpYQtyIrei 84 (92)
T COG5304 59 SSSDLEAIKQKASAE-GLPYQTYIREI 84 (92)
T ss_pred CHHHHHHHHHHHhhc-CCcHHHHHHHH
Confidence 334599999999876 44699998876
No 111
>PRK10586 putative oxidoreductase; Provisional
Probab=25.77 E-value=59 Score=25.96 Aligned_cols=26 Identities=15% Similarity=0.220 Sum_probs=21.5
Q ss_pred HHHHHhhhhhhhhhCCCC-ccccCCCC
Q psy3153 52 PYILGEIRPTLTELGIET-PEDLGYDK 77 (89)
Q Consensus 52 ~~~lqElkPtl~ELGI~t-~EeLgydk 77 (89)
+..+++|+..++++|+|+ ..+||+++
T Consensus 292 ~~~~~~l~~~l~~lGLP~~L~dlGi~~ 318 (362)
T PRK10586 292 DDVLAQLIGAYQRFHLPTTLAELDVDI 318 (362)
T ss_pred HHHHHHHHHHHHHcCCCCCHHHCCCCC
Confidence 346788999999999976 68999975
No 112
>PF06267 DUF1028: Family of unknown function (DUF1028); InterPro: IPR010430 This is a family of bacterial and archaeal proteins with unknown function.; PDB: 2IMH_A.
Probab=25.75 E-value=68 Score=24.36 Aligned_cols=33 Identities=18% Similarity=0.203 Sum_probs=24.1
Q ss_pred CCCHHHHHHHHHHHHhhhhHHHHHHHHHHHHHH
Q psy3153 10 VPDPVIIIAALKAARRLNDYALTIRLLEMVQEK 42 (89)
Q Consensus 10 VP~P~ii~AALrAcRRvND~alAVR~lE~iK~K 42 (89)
.=.+.|++|+.+|-..-.+.+++-|.|.+++.-
T Consensus 118 La~~~V~~Am~~af~~~~~~~L~eRLl~AL~Ag 150 (190)
T PF06267_consen 118 LAGEEVLEAMADAFEAATGLPLAERLLAALEAG 150 (190)
T ss_dssp -S-TCHHHHHHHHHHH--S--HHHHHHHHHHHH
T ss_pred CCChhHHHHHHHHHHhccCccHHHHHHHHHHHH
Confidence 346789999999999999999999999999853
No 113
>PF03704 BTAD: Bacterial transcriptional activator domain; InterPro: IPR005158 Found in the DNRI/REDD/AFSR family of regulators, this region of AFSR (P25941 from SWISSPROT) along with the C-terminal region is capable of independently directing actinorhodin production. It is important for the formation of secondary metabolites.; PDB: 2FF4_B 2FEZ_A.
Probab=25.69 E-value=2e+02 Score=18.73 Aligned_cols=29 Identities=21% Similarity=0.166 Sum_probs=17.1
Q ss_pred HHHHHHHHHhhhhHHHHHHHHHHHHHHhc
Q psy3153 16 IIAALKAARRLNDYALTIRLLEMVQEKCG 44 (89)
Q Consensus 16 i~AALrAcRRvND~alAVR~lE~iK~K~~ 44 (89)
+.....++.+.+++..|++.++..-..-.
T Consensus 65 ~~~l~~~~~~~~~~~~a~~~~~~~l~~dP 93 (146)
T PF03704_consen 65 LERLAEALLEAGDYEEALRLLQRALALDP 93 (146)
T ss_dssp HHHHHHHHHHTT-HHHHHHHHHHHHHHST
T ss_pred HHHHHHHHHhccCHHHHHHHHHHHHhcCC
Confidence 33444455577788888887776554433
No 114
>smart00138 MeTrc Methyltransferase, chemotaxis proteins. Methylates methyl-accepting chemotaxis proteins to form gamma-glutamyl methyl ester residues.
Probab=25.68 E-value=1e+02 Score=23.31 Aligned_cols=40 Identities=13% Similarity=0.234 Sum_probs=29.4
Q ss_pred HHHHHHHHHhcCCccc-chHHHHHhhhhhhhhhCCCCcccc
Q psy3153 34 RLLEMVQEKCGKKKKV-IWPYILGEIRPTLTELGIETPEDL 73 (89)
Q Consensus 34 R~lE~iK~K~~~~~~~-iY~~~lqElkPtl~ELGI~t~EeL 73 (89)
+|.+.|+.++|-.... ....+...|++.+.++|+++++++
T Consensus 6 ~~~~~i~~~~Gi~~~~~k~~~l~~rl~~r~~~~~~~~~~~y 46 (264)
T smart00138 6 RFCDLIYSRTGIVLTDYKRTLLQSRLSRRLRVLGLKDFSEY 46 (264)
T ss_pred HHHHHHHHHhCCCCCcchHHHHHHHHHHHHHHcCCCCHHHH
Confidence 5777788888864333 445677888889999998888764
No 115
>cd00913 PCD_DCoH_subfamily_a PCD_DCoH: The bifunctional protein pterin-4alpha-carbinolamine dehydratase (PCD), also known as DCoH (dimerization cofactor of hepatocyte nuclear factor-1), is both a transcription activator and a metabolic enzyme. DCoH stimulates gene expression by associating with specific DNA binding proteins such as HNF-1alpha (hepatocyte nuclear factor-1) and Xenopus enhancer of rudimentary homologue (XERH). DCoH also catalyzes the dehydration of 4alpha- hydroxy- tetrahydrobiopterin (4alpha-OH-BH4) to quinoiddihydrobiopterin, a percursor of the phenylalanine hydroxylase cofactor BH4 (tetrahydrobiopterin). The DCoH homodimer has a saddle-shaped structure similar to that of TBP (TATA binding protein).
Probab=25.48 E-value=33 Score=21.54 Aligned_cols=26 Identities=12% Similarity=0.234 Sum_probs=20.5
Q ss_pred hhhHHHHHHHHHHHHHHhcCCcccchHH
Q psy3153 26 LNDYALTIRLLEMVQEKCGKKKKVIWPY 53 (89)
Q Consensus 26 vND~alAVR~lE~iK~K~~~~~~~iY~~ 53 (89)
+.||+.|++|+..|-..|+.. .-+|-
T Consensus 17 f~~f~~a~~f~~~va~~ae~~--~HHP~ 42 (76)
T cd00913 17 FKNFVEALEFVNAVGEIAEAE--GHHPD 42 (76)
T ss_pred cCCHHHHHHHHHHHHHHHHHc--CCCCC
Confidence 579999999999999988754 44543
No 116
>PF13646 HEAT_2: HEAT repeats; PDB: 1OYZ_A 3FGA_A 2PF4_C 2IAE_A 3B2A_A.
Probab=25.40 E-value=1.4e+02 Score=17.49 Aligned_cols=25 Identities=36% Similarity=0.465 Sum_probs=18.7
Q ss_pred CCHHHHHHHHHHHHhhhhHHHHHHHH
Q psy3153 11 PDPVIIIAALKAARRLNDYALTIRLL 36 (89)
Q Consensus 11 P~P~ii~AALrAcRRvND~alAVR~l 36 (89)
|+|.|-.+|.+|..++++ ..++..|
T Consensus 43 ~~~~vr~~a~~aL~~i~~-~~~~~~L 67 (88)
T PF13646_consen 43 EDPMVRRAAARALGRIGD-PEAIPAL 67 (88)
T ss_dssp SSHHHHHHHHHHHHCCHH-HHTHHHH
T ss_pred CCHHHHHHHHHHHHHhCC-HHHHHHH
Confidence 788999999999999986 3344433
No 117
>PF02607 B12-binding_2: B12 binding domain; InterPro: IPR003759 Cobalamin-dependent methionine synthase (2.1.1.13 from EC) is a large modular protein that catalyses methyl transfer from methyltetrahydrofolate (CH3-H4folate) to homocysteine. During the catalytic cycle, it supports three distinct methyl transfer reactions, each involving the cobalamin (vitamin B12) cofactor and a substrate bound to its own functional unit []. The cobalamin cofactor plays an essential role in this reaction, accepting the methyl group from CH3-H4folate to form methylcob(III)alamin, and in turn donating the methyl group to homocysteine to generate methionine and cob(I)alamin. Methionine synthase is a large enzyme composed of four structurally and functionally distinct modules: the first two modules bind homocysteine and CH3-H4folate, the third module binds the cobalamin cofactor and the C-terminal module binds S-adenosylmethionine. The cobalamin-binding module is composed of two structurally distinct domains: a 4-helical bundle cap domain (residues 651-740 in the Escherichia coli enzyme) and an alpha/beta B12-binding domain (residues 741-896) (IPR006158 from INTERPRO). The 4-helical bundle forms a cap over the alpha/beta domain, which acts to shield the methyl ligand of cobalamin from solvent []. Furthermore, in the conversion to the active conformation of this enzyme, the 4-helical cap rotates to allow the cobalamin cofactor to bind the activation domain (IPR004223 from INTERPRO). The alpha/beta domain is a common cobalamin-binding motif, whereas the 4-helical bundle domain with its methyl cap is a distinctive feature of methionine synthases. This entry represents the 4-helical bundle cap domain. This domain is also present in other shorter proteins that bind to B12, and is always found N terminus to the alpha/beta B12-binding domain.; GO: 0008705 methionine synthase activity, 0031419 cobalamin binding, 0046872 metal ion binding, 0009086 methionine biosynthetic process; PDB: 3EZX_A 3BUL_A 1K7Y_A 1BMT_A 3IV9_A 1K98_A 3IVA_A 2I2X_P.
Probab=25.37 E-value=62 Score=19.41 Aligned_cols=34 Identities=29% Similarity=0.357 Sum_probs=20.0
Q ss_pred hHHHHHHHHHHHHHHhcCCcccchHHHHHh-hhhhhhhhC
Q psy3153 28 DYALTIRLLEMVQEKCGKKKKVIWPYILGE-IRPTLTELG 66 (89)
Q Consensus 28 D~alAVR~lE~iK~K~~~~~~~iY~~~lqE-lkPtl~ELG 66 (89)
|-..+.++++..-.+ |-. ...++++ +.|.|.++|
T Consensus 16 d~~~~~~~~~~~l~~-g~~----~~~i~~~~l~p~m~~iG 50 (79)
T PF02607_consen 16 DEEEAEALLEEALAQ-GYP----PEDIIEEILMPAMEEIG 50 (79)
T ss_dssp -CCHHHHHHHHHHHC-SSS----TTHHHHHTHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHc-CCC----HHHHHHHHHHHHHHHHH
Confidence 445566666665555 322 2334444 889999988
No 118
>TIGR01428 HAD_type_II 2-haloalkanoic acid dehalogenase, type II. Note that the Type I HAD enzymes have not yet been fully characterized, but clearly utilize a substantially different catalytic mechanism and are thus unlikely to be related.
Probab=25.26 E-value=1.5e+02 Score=20.24 Aligned_cols=65 Identities=14% Similarity=0.068 Sum_probs=35.8
Q ss_pred CCHHHHHHHHHHHHhhhhHHHHHHHHHHHHHH---hcCCcccchHHHHHhhhhhhhhhCCC-------CccccCCCCCc
Q psy3153 11 PDPVIIIAALKAARRLNDYALTIRLLEMVQEK---CGKKKKVIWPYILGEIRPTLTELGIE-------TPEDLGYDKPE 79 (89)
Q Consensus 11 P~P~ii~AALrAcRRvND~alAVR~lE~iK~K---~~~~~~~iY~~~lqElkPtl~ELGI~-------t~EeLgydkpE 79 (89)
+++..+.....+-+++.=++-+..+|+.+|.+ ++--.+... ..++..++.+|+. +.++.|.-||.
T Consensus 76 ~~~~~~~~~~~~~~~~~~~~~~~~~L~~L~~~g~~~~i~Sn~~~----~~~~~~l~~~gl~~~fd~i~~s~~~~~~KP~ 150 (198)
T TIGR01428 76 DDESAADRLAEAYLRLPPHPDVPAGLRALKERGYRLAILSNGSP----AMLKSLVKHAGLDDPFDAVLSADAVRAYKPA 150 (198)
T ss_pred CCHHHHHHHHHHHhcCCCCCCHHHHHHHHHHCCCeEEEEeCCCH----HHHHHHHHHCCChhhhheeEehhhcCCCCCC
Confidence 34444444444445555567888889998876 221111111 2333455666653 45677877875
No 119
>PF08869 XisI: XisI protein; InterPro: IPR014968 The fdxN element, along with two other DNA elements, is excised from the chromosome during heterocyst differentiation in cyanobacteria. The xisH as well as the xisF and xisI genes are required []. ; PDB: 3D7Q_A 2NWV_A 2NVM_A 2NLV_B.
Probab=25.24 E-value=46 Score=23.49 Aligned_cols=24 Identities=42% Similarity=0.725 Sum_probs=15.3
Q ss_pred hhhhhhhhhCCCCccc--cCCCCCccc
Q psy3153 57 EIRPTLTELGIETPED--LGYDKPELW 81 (89)
Q Consensus 57 ElkPtl~ELGI~t~Ee--LgydkpEla 81 (89)
-|..-|-|+||| +|+ |||+.|+.-
T Consensus 78 gIa~eLve~GVp-k~dIVLgF~~P~~R 103 (111)
T PF08869_consen 78 GIAEELVEAGVP-KEDIVLGFHPPEVR 103 (111)
T ss_dssp HHHHHHHHTT---GGGEEETTS-GGGG
T ss_pred HHHHHHHHcCCC-HHHEEEccCCcccc
Confidence 455667899998 665 899999753
No 120
>PF08385 DHC_N1: Dynein heavy chain, N-terminal region 1; InterPro: IPR013594 Dynein heavy chains interact with other heavy chains to form dimers, and with intermediate chain-light chain complexes to form a basal cargo binding unit []. The region featured in this family includes the sequences implicated in mediating these interactions []. It is thought to be flexible and not to adopt a rigid conformation [].
Probab=24.84 E-value=1.2e+02 Score=24.32 Aligned_cols=59 Identities=17% Similarity=0.258 Sum_probs=40.7
Q ss_pred CCHHHHHHHHHHHHhhhhHHHHHHHHH-HHHHHhcCCcccchHHHHHhhhhhhhhhCCCCcccc
Q psy3153 11 PDPVIIIAALKAARRLNDYALTIRLLE-MVQEKCGKKKKVIWPYILGEIRPTLTELGIETPEDL 73 (89)
Q Consensus 11 P~P~ii~AALrAcRRvND~alAVR~lE-~iK~K~~~~~~~iY~~~lqElkPtl~ELGI~t~EeL 73 (89)
|+-..+..-|++++| + +....+-+. +|++...-. .-|-.+++.|+|..+.|.-..++++
T Consensus 61 ~~v~~~~~iL~~~~s-~-~~~~f~~~~~~l~~~~~ea--~d~~~fL~~l~~~~~~l~~~~~~~i 120 (579)
T PF08385_consen 61 PEVQKILEILEKAKS-S-YTKSFKNLTRELKEALNEA--KDNNKFLKPLEPPFELLEASDLSEI 120 (579)
T ss_pred hHHHHHHHHHHHhcc-h-hhHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHhhccCCHHHH
Confidence 566778888999988 4 444444443 777777544 4478888999888888866655544
No 121
>COG3179 Predicted chitinase [General function prediction only]
Probab=24.72 E-value=34 Score=26.92 Aligned_cols=24 Identities=29% Similarity=0.513 Sum_probs=19.2
Q ss_pred hHHHHHhhhhhhhhhCCCCccccC
Q psy3153 51 WPYILGEIRPTLTELGIETPEDLG 74 (89)
Q Consensus 51 Y~~~lqElkPtl~ELGI~t~EeLg 74 (89)
.--.+.-|.|.|+|-||+||..++
T Consensus 20 ~~~v~~al~~~l~~~gi~~p~r~A 43 (206)
T COG3179 20 FVDVIVALQPALDEAGITTPLRQA 43 (206)
T ss_pred hHHHHHHHHHHHHHhcCCCHHHHH
Confidence 344567899999999999998654
No 122
>cd08185 Fe-ADH1 Iron-containing alcohol dehydrogenases-like. Iron-containing alcohol dehydrogenases-like (ADH). Alcohol dehydrogenase catalyzes the reduction of acetaldehyde to alcohol with NADP as cofactor. Its activity requires iron ions. The protein structure represents a dehydroquinate synthase fold and is a member of the iron-containing alcohol dehydrogenase-like family. They are distinct from other alcohol dehydrogenases which contain different protein domains. Proteins of this family have not been characterized. Their specific function is unknown. They are present in bacteria and archaea.
Probab=24.66 E-value=35 Score=26.80 Aligned_cols=29 Identities=24% Similarity=0.518 Sum_probs=23.6
Q ss_pred HHHHHhhhhhhhhhCCCC-ccccCCCCCcc
Q psy3153 52 PYILGEIRPTLTELGIET-PEDLGYDKPEL 80 (89)
Q Consensus 52 ~~~lqElkPtl~ELGI~t-~EeLgydkpEl 80 (89)
...++.++..+++||+|+ ..|+|.++.++
T Consensus 319 ~~~~~~i~~~~~~lglP~~L~e~gv~~~~~ 348 (380)
T cd08185 319 EDFIEALRKLLKRIGLDDLLSDLGVTKEDI 348 (380)
T ss_pred HHHHHHHHHHHHHcCCCCCHHHcCCCHHHH
Confidence 456888999999999984 78999887654
No 123
>cd08188 Fe-ADH4 Iron-containing alcohol dehydrogenases-like. Iron-containing alcohol dehydrogenase-like. Alcohol dehydrogenase catalyzes the reduction of acetaldehyde to alcohol with NADP as cofactor. Its activity requires iron ions. The protein structure represents a dehydroquinate synthase-like fold and is belonged to the alcohol dehydrogenase-like superfamily. They are distinct from other alcohol dehydrogenases which contain different protein domains. Proteins of this family have not been characterized. Their specific function is unknown.
Probab=24.47 E-value=42 Score=26.52 Aligned_cols=29 Identities=24% Similarity=0.456 Sum_probs=23.7
Q ss_pred HHHHHhhhhhhhhhCCC-CccccCCCCCcc
Q psy3153 52 PYILGEIRPTLTELGIE-TPEDLGYDKPEL 80 (89)
Q Consensus 52 ~~~lqElkPtl~ELGI~-t~EeLgydkpEl 80 (89)
...+++|+-.++++|+| +..|+|.++.++
T Consensus 318 ~~~~~~i~~l~~~lglp~~L~e~gv~~~~~ 347 (377)
T cd08188 318 LAVIEAVRRLRAALGVPETLGDLGVKREDI 347 (377)
T ss_pred HHHHHHHHHHHHHcCCCCCHHHcCCCHHHH
Confidence 56789999999999998 578889876554
No 124
>PLN03218 maturation of RBCL 1; Provisional
Probab=24.38 E-value=2.1e+02 Score=26.62 Aligned_cols=33 Identities=18% Similarity=0.238 Sum_probs=17.4
Q ss_pred CCCCCHHHHHHHHHHHHhhhhHHHHHHHHHHHH
Q psy3153 8 DGVPDPVIIIAALKAARRLNDYALTIRLLEMVQ 40 (89)
Q Consensus 8 DlVP~P~ii~AALrAcRRvND~alAVR~lE~iK 40 (89)
.+.|+..+..+.+++|-+.+++..|.++|+.++
T Consensus 537 Gv~PD~vTYnsLI~a~~k~G~~deA~~lf~eM~ 569 (1060)
T PLN03218 537 NVKPDRVVFNALISACGQSGAVDRAFDVLAEMK 569 (1060)
T ss_pred CCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence 344555555555555555555555555555544
No 125
>cd08182 HEPD Hydroxyethylphosphoate dehydrogenase (HEPD) catalyzes the reduction of phosphonoacetaldehyde (PnAA) to hydroxyethylphosphoate (HEP). Hydroxyethylphosphoate dehydrogenase (HEPD) catalyzes the reduction of phosphonoacetaldehyde (PnAA) to hydroxyethylphosphoate (HEP) with either NADH or NADPH as a cofactor. NADH is the preferred cofactor. PnAA is a biosynthetic intermediate for several phosphonates such as the antibiotic fosfomycin, phosphinothricin tripeptide (PTT), and 2-aminoethylphosphonate (AEP). This enzyme is named PhpC in PTT biosynthesis pathway in Streptomyces hygroscopicus and S. viridochromogenes. Members of this family are only found in bacteria.
Probab=23.35 E-value=44 Score=26.09 Aligned_cols=28 Identities=21% Similarity=0.272 Sum_probs=22.3
Q ss_pred HHHHHhhhhhhhhhCCCC-ccccCCCCCc
Q psy3153 52 PYILGEIRPTLTELGIET-PEDLGYDKPE 79 (89)
Q Consensus 52 ~~~lqElkPtl~ELGI~t-~EeLgydkpE 79 (89)
...+++|+..++++|+|+ ..|+|.++.+
T Consensus 308 ~~~~~~i~~l~~~~glp~~L~e~gv~~~~ 336 (367)
T cd08182 308 AEAAARIEALLKELGLPTRLAEYIVTRED 336 (367)
T ss_pred HHHHHHHHHHHHHcCCCCCHHHcCCCHHH
Confidence 346888999999999985 7888876544
No 126
>TIGR03405 Phn_Fe-ADH phosphonate metabolism-associated iron-containing alcohol dehydrogenase. 2-hydroxyethylphosphonate (2-HEP), the presumed product of the reaction of Pald with an alcohol dehydrogenase, is a biologically novel but reasonable analog of 2-AEP and may be a constituent of as-yet undescribed natural products. In the case of Azoarcus, downstream of the dehydrogenase is a CDP-glycerol:glycerophosphate transferase homolog that may indicate the existence of a pathway for 2-HEP-derived phosphonolipid biosynthesis.
Probab=23.24 E-value=47 Score=26.08 Aligned_cols=28 Identities=29% Similarity=0.407 Sum_probs=22.9
Q ss_pred HHHHhhhhhhhhhCCCC-ccccCCCCCcc
Q psy3153 53 YILGEIRPTLTELGIET-PEDLGYDKPEL 80 (89)
Q Consensus 53 ~~lqElkPtl~ELGI~t-~EeLgydkpEl 80 (89)
..++.|+-.+++||+|+ ..++|.++-++
T Consensus 308 ~~~~~i~~l~~~lglP~~L~~~gv~~~~~ 336 (355)
T TIGR03405 308 SAPARLRAFLDTLGVKTRFADYGVSRDEA 336 (355)
T ss_pred HHHHHHHHHHHHcCCCCCHHHcCCCHHHH
Confidence 57889999999999985 78999876443
No 127
>cd08180 PDD 1,3-propanediol dehydrogenase (PPD) catalyzes the reduction of 3-hydroxypropionaldehyde (3-HPA) to 1,3-propanediol in glycerol metabolism. 1,3-propanediol dehydrogenase (PPD) plays a role in glycerol metabolism of some bacteria in anaerobic conditions. In this degradation pathway, glycerol is converted in a two-step process to 1,3-propanediol (1,3-PD) which is then excreted into the extracellular medium. The first reaction involves the transformation of glycerol into 3-hydroxypropionaldehyde (3-HPA) by a coenzyme B-12-dependent dehydratase. The second reaction involves the dismutation of the 3-hydroxypropionaldehyde (3-HPA) to 1,3-propanediol by the NADH-linked 1,3-propanediol dehydrogenase (PPD). The enzyme require iron ion for its function. Because many genes in this pathway are present in the pdu (propanediol utilisation) operon, they are also named pdu genes. PPD is a member of the iron-containing alcohol dehydrogenase superfamily. The PPD structure has a dehydroquinat
Probab=23.13 E-value=54 Score=25.31 Aligned_cols=28 Identities=29% Similarity=0.521 Sum_probs=22.6
Q ss_pred HHHHHhhhhhhhhhCCCC-ccccCCCCCc
Q psy3153 52 PYILGEIRPTLTELGIET-PEDLGYDKPE 79 (89)
Q Consensus 52 ~~~lqElkPtl~ELGI~t-~EeLgydkpE 79 (89)
.|..++++-.++++|+|+ ..++|+++.+
T Consensus 269 ~~~~~~i~~l~~~lglp~~L~~~gi~~~~ 297 (332)
T cd08180 269 EFLIEAIKQLKKKLNIPETLKELGVDKEE 297 (332)
T ss_pred HHHHHHHHHHHHHcCCCCCHHHcCCCHHH
Confidence 336778999999999985 7899998764
No 128
>cd08191 HHD 6-hydroxyhexanoate dehydrogenase (HHD) catalyzes the oxidation of 6-hydroxyhexanoate to 6-oxohexanoate. 6-hydroxyhexanoate dehydrogenase (HHD). The 6-hydroxyhexanoate dehydrogenase catalyzes the oxidation of 6-hydroxyhexanoate to 6-oxohexanoate. Some bacteria can grow on cyclic ketones, cyclohexylamine, and alcohols as sole carbon source. Cyclohexylamine is an insecticide and antiseptic in various industries and is considered a possible environmental pollutant. The degradation of these chemical compounds are through the cyclohexanol and cyclohexanone biological oxidation pathway. The intermediates of this pathway include cyclohexanol, cyclohexanone, e-caprolactone, 6-hydroxyhexanoate, 6-oxohexanoate and adipate. The 6-hydroxyhexanoate dehydrogenase catalyzes the oxidation of 6-hydroxyhexanoate to 6-oxohexanoate.
Probab=22.99 E-value=46 Score=26.37 Aligned_cols=30 Identities=20% Similarity=0.307 Sum_probs=23.6
Q ss_pred chHHHHHhhhhhhhhhCCC-CccccCCCCCc
Q psy3153 50 IWPYILGEIRPTLTELGIE-TPEDLGYDKPE 79 (89)
Q Consensus 50 iY~~~lqElkPtl~ELGI~-t~EeLgydkpE 79 (89)
.-...+++|+..+++||+| +..|+|.++.+
T Consensus 325 ~~~~~~~~l~~l~~~lglP~~L~e~gv~~~~ 355 (386)
T cd08191 325 QAAAAITRVEALLAAIGIPTTLAALGVTEAD 355 (386)
T ss_pred HHHHHHHHHHHHHHHcCCCCCHHHcCCCHHH
Confidence 3456788999999999998 46889986644
No 129
>PF12933 FTO_NTD: FTO catalytic domain; InterPro: IPR024367 Alpha-ketoglutarate-dependent dioxygenase FTO, also known as Fat mass and obesity-associated protein, is a nucleus protein which belongs to the FTO family. This enzyme is a dioxygenase that repairs alkylated DNA and RNA by oxidative demethylation []. FTO activity is highest towards single-stranded RNA containing 3-methyluracil, followed by single-stranded DNA containing 3-methylthymine. FTO has low demethylase activity towards single-stranded DNA containing 1-methyladenine or 3-methylcytosine []. FTO has no activity towards 1-methylguanine. It has no detectable activity towards double-stranded DNA. FTO requires molecular oxygen, alpha-ketoglutarate and iron. FTO contributes to the regulation of the global metabolic rate, energy expenditure and energy homeostasis. It contributes to the regulation of body size and body fat accumulation as well []. This domain is the catalytic AlkB-like domain from the FTO protein []. This domain catalyses a demethylase activity with a preference for 3-methylthymidine.; PDB: 3LFM_A.
Probab=22.84 E-value=62 Score=26.12 Aligned_cols=26 Identities=38% Similarity=0.434 Sum_probs=19.4
Q ss_pred HHHHHHHHHHhhhhH--HHHHHHHHHHH
Q psy3153 15 IIIAALKAARRLNDY--ALTIRLLEMVQ 40 (89)
Q Consensus 15 ii~AALrAcRRvND~--alAVR~lE~iK 40 (89)
=|.+|++|-+|+||| ..++..||+-.
T Consensus 97 ~i~~a~~al~~LN~~L~~~~~~~l~~~~ 124 (253)
T PF12933_consen 97 EIRSACKALGKLNDYLCSRAVQALEGRR 124 (253)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 367899999999998 44566666544
No 130
>PRK09248 putative hydrolase; Validated
Probab=22.71 E-value=1.1e+02 Score=22.50 Aligned_cols=60 Identities=17% Similarity=0.145 Sum_probs=36.7
Q ss_pred CCHHHHHHHHH------------HHHhhhhHHHHHHHHHHHHHHhcCCcccchHHHHHhhhhhhhhhCCCCccccCCCCC
Q psy3153 11 PDPVIIIAALK------------AARRLNDYALTIRLLEMVQEKCGKKKKVIWPYILGEIRPTLTELGIETPEDLGYDKP 78 (89)
Q Consensus 11 P~P~ii~AALr------------AcRRvND~alAVR~lE~iK~K~~~~~~~iY~~~lqElkPtl~ELGI~t~EeLgydkp 78 (89)
|..+++..|.+ .+..|++|..|+++++. +|-+...++....+.|.++|.-=|+ |..|
T Consensus 173 ~~~~~~~~~~~~g~~~~~gSDAH~~~~vg~~~~~~~~~~~----~g~~~~~~~~~~~~~~~~~~~~~~~-------~~~~ 241 (246)
T PRK09248 173 NCRAIAALCKKAGVWVALGSDAHIAFDIGNFEEALKILDE----VGFPEERILNVSPRRLLDFLESRGK-------APIP 241 (246)
T ss_pred hHHHHHHHHHHcCCeEEEeCCCCChhhhccHHHHHHHHHH----cCCCHHHeeeCCHHHHHHHHHHcCC-------ccch
Confidence 55555555554 33456667777776663 4433334555556788888877777 6667
Q ss_pred ccc
Q psy3153 79 ELW 81 (89)
Q Consensus 79 Ela 81 (89)
|+|
T Consensus 242 ~~~ 244 (246)
T PRK09248 242 EFA 244 (246)
T ss_pred hhc
Confidence 765
No 131
>PF12827 Peroxin-22: Peroxisomal biogenesis protein family; InterPro: IPR024359 Peroxin-22 is an integral peroxisomal membrane protein. The N terminus of peroxin-22 is located in the matrix, while the C terminus is located in the cytosol. Peroxin-22 interacts with the ubiquitin-conjugating enzyme Pex4p, anchoring it at the peroxisomal membrane. Both proteins may act at the same step in peroxisome biogenesis [].; PDB: 2Y9O_B 2Y9M_B 2Y9P_B.
Probab=22.69 E-value=46 Score=23.45 Aligned_cols=31 Identities=29% Similarity=0.557 Sum_probs=19.3
Q ss_pred HhcCCcccchHHHHHhhhhh-----hhhhCCCCccccC
Q psy3153 42 KCGKKKKVIWPYILGEIRPT-----LTELGIETPEDLG 74 (89)
Q Consensus 42 K~~~~~~~iY~~~lqElkPt-----l~ELGI~t~EeLg 74 (89)
+|.+- +=|=..++.|||- .+|||+..|++||
T Consensus 73 ~Cdt~--~G~~~~vK~Lk~d~llv~~ddl~~~ip~Di~ 108 (117)
T PF12827_consen 73 KCDTM--QGYWSCVKHLKPDQLLVCSDDLGISIPEDIN 108 (117)
T ss_dssp EESSH--HHHHHHHHHH--SEEEE-GGGT-SSS-GGGG
T ss_pred Eecch--hhHHHHHHhcCCCceEEehhhccccCHHHHH
Confidence 45554 3456678889984 6899999999875
No 132
>PRK09634 nusB transcription antitermination protein NusB; Provisional
Probab=22.64 E-value=87 Score=23.98 Aligned_cols=37 Identities=24% Similarity=0.283 Sum_probs=28.9
Q ss_pred CCCCCCHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHhcC
Q psy3153 7 DDGVPDPVIIIAALKAARRLNDYALTIRLLEMVQEKCGK 45 (89)
Q Consensus 7 ~DlVP~P~ii~AALrAcRRvND~alAVR~lE~iK~K~~~ 45 (89)
.| +|.+.+|..|...|++..+- -+-+|.-||=.+...
T Consensus 164 l~-~P~~vaINEAVeLAK~~~~~-~~~~FVNaVLrri~r 200 (207)
T PRK09634 164 LN-TPAAVAINEAVELAKRYSDE-QGRRFINGVLRRLQD 200 (207)
T ss_pred cC-CCchhHHHHHHHHHHHhCCC-cccchHHHHHHHHHH
Confidence 35 79999999999999999874 445888887666543
No 133
>TIGR01870 cas_TM1810_Csm2 CRISPR-associated protein, Csm2 family. These proteins are found adjacent to a characteristic short, palidromic repeat cluster termed CRISPR, a probable mobile DNA element. This model represents the C-terminal domain of a minor family of CRISPR-associated protein from the Mtube subtype of CRISPR/Cas locus. The family is designated Csm2, for CRISPR/Cas Subtype Mtube Protein 2.
Probab=22.64 E-value=1.6e+02 Score=19.43 Aligned_cols=27 Identities=7% Similarity=0.282 Sum_probs=17.0
Q ss_pred HHHHHHHHHHHHhh-----hhHHHHHHHHHHH
Q psy3153 13 PVIIIAALKAARRL-----NDYALTIRLLEMV 39 (89)
Q Consensus 13 P~ii~AALrAcRRv-----ND~alAVR~lE~i 39 (89)
-+++..++...... ++|-.-++|||+|
T Consensus 57 ~~~~~~~~~~i~~~~~~~~~~f~~F~~ffEAi 88 (97)
T TIGR01870 57 VELLEDLLDKIDKIDNDDRRAFERFVKFFEAI 88 (97)
T ss_pred HHHHHHHHHHHhcccchHHHHHHHHHHHHHHH
Confidence 34555555555555 6677777777776
No 134
>PF12525 DUF3726: Protein of unknown function (DUF3726) ; InterPro: IPR022201 This domain family is found in bacteria and eukaryotes, and is approximately 80 amino acids in length. There is a single completely conserved residue E that may be functionally important.
Probab=22.59 E-value=1.6e+02 Score=19.42 Aligned_cols=49 Identities=27% Similarity=0.161 Sum_probs=30.8
Q ss_pred HHHHHHHHHHHh-------hhhHHHHHHHHHHHHHHhcCCcccchHHHHHhhhhhhhhhCCCCcccc
Q psy3153 14 VIIIAALKAARR-------LNDYALTIRLLEMVQEKCGKKKKVIWPYILGEIRPTLTELGIETPEDL 73 (89)
Q Consensus 14 ~ii~AALrAcRR-------vND~alAVR~lE~iK~K~~~~~~~iY~~~lqElkPtl~ELGI~t~EeL 73 (89)
+|...+.||+|= =-|.|.+||+||..= -. . ++.+.-+|+.++-..+..+
T Consensus 6 Ei~a~~~kA~~Gag~~~G~Ae~aa~~v~wL~~~G----l~--G-----~~~L~~~L~~~~~~~~~~~ 61 (80)
T PF12525_consen 6 EIEALAKKAFRGAGLSWGEAEEAANMVAWLEMHG----LD--G-----VRHLNNALEFLDAEPDSPL 61 (80)
T ss_pred HHHHHHHHHHHhcCCCcchHHHHHHHHHHHHHcC----Cc--h-----HHHHHHHHHHhcCCCCCcc
Confidence 567778888883 358899999998642 22 1 3455555665655544444
No 135
>PRK13778 paaA phenylacetate-CoA oxygenase subunit PaaA; Provisional
Probab=22.58 E-value=77 Score=25.86 Aligned_cols=29 Identities=21% Similarity=0.444 Sum_probs=23.6
Q ss_pred ccchHHHHHhhhhhhhhhCCCCcc-ccCCC
Q psy3153 48 KVIWPYILGEIRPTLTELGIETPE-DLGYD 76 (89)
Q Consensus 48 ~~iY~~~lqElkPtl~ELGI~t~E-eLgyd 76 (89)
.+.-+..++.+.|+++++|+..|+ .|-||
T Consensus 231 ~eLR~~w~~~v~~~l~~~gL~vP~~~~~~~ 260 (314)
T PRK13778 231 DELRQKFVDATVPQAEVLGLTLPDPDLRWN 260 (314)
T ss_pred HHHHHHHHHHHHHHHHHcCCCCCCCcCCcc
Confidence 378888999999999999999885 44444
No 136
>PF01329 Pterin_4a: Pterin 4 alpha carbinolamine dehydratase; InterPro: IPR001533 DCoH is the dimerisation cofactor of hepatocyte nuclear factor 1 (HNF-1) that functions as both a transcriptional coactivator and a pterin dehydratase []. X-ray crystallographic studies have shown that the ligand binds at four sites per tetrameric enzyme, with little apparent conformational change in the protein.; GO: 0008124 4-alpha-hydroxytetrahydrobiopterin dehydratase activity, 0006729 tetrahydrobiopterin biosynthetic process; PDB: 2V6T_B 2V6U_A 2V6S_B 2EBB_A 1USM_A 1F93_B 1DCP_C 1DCH_E 3HXA_E 1DCO_C ....
Probab=22.57 E-value=49 Score=21.63 Aligned_cols=22 Identities=14% Similarity=0.383 Sum_probs=17.7
Q ss_pred hhhhHHHHHHHHHHHHHHhcCC
Q psy3153 25 RLNDYALTIRLLEMVQEKCGKK 46 (89)
Q Consensus 25 RvND~alAVR~lE~iK~K~~~~ 46 (89)
++.||+.|++|+..|-.-|+..
T Consensus 33 ~f~~f~~a~~f~~~Va~~ae~~ 54 (95)
T PF01329_consen 33 KFKDFAEAVEFVNRVAALAEEE 54 (95)
T ss_dssp E-SSHHHHHHHHHHHHHHHHHH
T ss_pred EeCCHHHHHHHHHHHHHHHHHh
Confidence 4678999999999998887653
No 137
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=22.45 E-value=2.1e+02 Score=20.91 Aligned_cols=47 Identities=9% Similarity=0.066 Sum_probs=26.0
Q ss_pred HHHHHHHHHHHHhhh-hHHHHHHHHHHHHHHhcC------CcccchHHHHHhhh
Q psy3153 13 PVIIIAALKAARRLN-DYALTIRLLEMVQEKCGK------KKKVIWPYILGEIR 59 (89)
Q Consensus 13 P~ii~AALrAcRRvN-D~alAVR~lE~iK~K~~~------~~~~iY~~~lqElk 59 (89)
-+|..|-.+|.+.+. +...+-.+.+.|.....+ .+.+|+..+.++|.
T Consensus 64 ~KI~~AI~kA~~a~~~~~~~~~~i~~~V~~~l~~~~~~~IsveEIqDiVE~~L~ 117 (154)
T PRK00464 64 EKLRRGLRRACEKRPVSSEQIEAAVSRIERQLRASGEREVPSKEIGELVMEELK 117 (154)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHH
Confidence 367777778888775 444444444444444432 23456666655543
No 138
>PF09585 Lin0512_fam: Conserved hypothetical protein (Lin0512_fam); InterPro: IPR011719 This family consists of few members, broadly distributed. It occurs so far in several Firmicutes (twice in Oceanobacillus), one Cyanobacterium, one alpha Proteobacterium, and (with a long prefix) in plants. The function is unknown. The alignment includes a perfectly conserved motif GxGxDxHG near the N terminus.
Probab=22.45 E-value=74 Score=22.65 Aligned_cols=23 Identities=39% Similarity=0.463 Sum_probs=15.9
Q ss_pred cccccCCCCCCHHHHHHHHHHHH---hhhhHH
Q psy3153 2 NDLAQDDGVPDPVIIIAALKAAR---RLNDYA 30 (89)
Q Consensus 2 N~l~~~DlVP~P~ii~AALrAcR---RvND~a 30 (89)
|+++|.| .-.||.|||| +-|..+
T Consensus 11 ~DlhGqD------~TkAA~RAv~DAI~~nslp 36 (113)
T PF09585_consen 11 NDLHGQD------YTKAAVRAVRDAISHNSLP 36 (113)
T ss_pred ccccCCc------HHHHHHHHHHHHHhhcchH
Confidence 4667766 4689999998 555554
No 139
>PF13623 SurA_N_2: SurA N-terminal domain
Probab=22.32 E-value=1.4e+02 Score=21.23 Aligned_cols=47 Identities=13% Similarity=0.481 Sum_probs=30.4
Q ss_pred hhHHHHHHHHH-HHHHHhcCC---------cccchHHHHHh--hhhhhhhhCCC-Ccccc
Q psy3153 27 NDYALTIRLLE-MVQEKCGKK---------KKVIWPYILGE--IRPTLTELGIE-TPEDL 73 (89)
Q Consensus 27 ND~alAVR~lE-~iK~K~~~~---------~~~iY~~~lqE--lkPtl~ELGI~-t~EeL 73 (89)
.||...|--.+ .+|...|.. .+..|..++++ |+.-.++|||. +++|+
T Consensus 52 ~ef~~~v~~~~~~~k~~~g~~~~~~~~~q~~~qvW~~~V~~~ll~~e~eklGi~Vs~~El 111 (145)
T PF13623_consen 52 QEFQQRVEQATENYKQQNGRSPTEQEQNQIRNQVWNQMVQNILLEQEFEKLGITVSDDEL 111 (145)
T ss_pred HHHHHHHHHHHHHHHHHcCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCCccCHHHH
Confidence 35555555554 455544432 24568888877 57888999998 66664
No 140
>PF04994 TfoX_C: TfoX C-terminal domain; InterPro: IPR007077 This domain is found in a number of bacterial proteins including the TfoX gene product of Haemophilus influenzae. TfoX may play a key role in the development of genetic competence by regulating the expression of late competence-specific genes []. This family corresponds to the C-terminal presumed domain of TfoX. The domain is found in association with the N-terminal domain in some, but not all members of this group, suggesting this is an autonomous and functionally unrelated domain. For example it is found associated with Q9JZR1 from SWISSPROT in IPR002125 from INTERPRO.; PDB: 3BQT_A 3MAB_A.
Probab=22.28 E-value=29 Score=22.56 Aligned_cols=18 Identities=39% Similarity=0.525 Sum_probs=12.0
Q ss_pred HhhhhhhhhhCCCCcccc
Q psy3153 56 GEIRPTLTELGIETPEDL 73 (89)
Q Consensus 56 qElkPtl~ELGI~t~EeL 73 (89)
..+.-.|.+.||.|+|+|
T Consensus 13 ~~~e~~L~~vGI~t~~~L 30 (81)
T PF04994_consen 13 PKSERMLAKVGIHTVEDL 30 (81)
T ss_dssp HHHHHHHHHTT--SHHHH
T ss_pred HHHHHHHHHcCCCCHHHH
Confidence 345556889999999986
No 141
>PF14528 LAGLIDADG_3: LAGLIDADG-like domain; PDB: 2CW7_A 2CW8_A 2VS8_F 2VS7_G 1B24_A 1DQ3_A 2DCH_X.
Probab=22.25 E-value=58 Score=19.53 Aligned_cols=18 Identities=28% Similarity=0.512 Sum_probs=14.1
Q ss_pred HHHHHhhhhhhhhhCCCC
Q psy3153 52 PYILGEIRPTLTELGIET 69 (89)
Q Consensus 52 ~~~lqElkPtl~ELGI~t 69 (89)
..++++++-+|.+|||.+
T Consensus 31 ~~ll~~v~~lL~~lGi~~ 48 (77)
T PF14528_consen 31 KELLEDVQKLLLRLGIKA 48 (77)
T ss_dssp HHHHHHHHHHHHHTT--E
T ss_pred HHHHHHHHHHHHHCCCee
Confidence 568899999999999986
No 142
>PRK10015 oxidoreductase; Provisional
Probab=22.21 E-value=1.3e+02 Score=24.09 Aligned_cols=40 Identities=20% Similarity=0.230 Sum_probs=30.4
Q ss_pred CcccccCCCCCCHHHHHHHHHHHHhhhhHHHHHHHHHHHH
Q psy3153 1 MNDLAQDDGVPDPVIIIAALKAARRLNDYALTIRLLEMVQ 40 (89)
Q Consensus 1 lN~l~~~DlVP~P~ii~AALrAcRRvND~alAVR~lE~iK 40 (89)
|+++|..|-.|.+.+....+++.++..-+.++--.+.++|
T Consensus 388 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 427 (429)
T PRK10015 388 MNDMFTIDGKPNQPVRKMIMGHAKKIGLINLLKDGIKGAT 427 (429)
T ss_pred HHHhcccCCccchHHHHHHHHHHHhccHHHHHHHHHHHHh
Confidence 3578889999999999999999887776666655555544
No 143
>smart00860 SMI1_KNR4 SMI1 / KNR4 family. Proteins in this family are involved in the regulation of 1,3-beta-glucan synthase activity and cell-wall formation.
Probab=22.10 E-value=51 Score=19.32 Aligned_cols=18 Identities=44% Similarity=0.617 Sum_probs=12.4
Q ss_pred HhhhhhhhhhCCCCcccc
Q psy3153 56 GEIRPTLTELGIETPEDL 73 (89)
Q Consensus 56 qElkPtl~ELGI~t~EeL 73 (89)
++|.-.=++||+..|+++
T Consensus 5 ~~i~~~e~~lg~~LP~~y 22 (129)
T smart00860 5 EEIAELEKKLGIKLPEDY 22 (129)
T ss_pred HHHHHHHHHHCCCCCHHH
Confidence 345555558899888876
No 144
>PF11342 DUF3144: Protein of unknown function (DUF3144); InterPro: IPR021490 This family of proteins with unknown function appears to be restricted to Proteobacteria.
Probab=21.85 E-value=1.6e+02 Score=19.57 Aligned_cols=49 Identities=22% Similarity=0.242 Sum_probs=30.9
Q ss_pred HHHHHHHHHHHhhhhHHHHHHHHHHHHHHhcCCcccchHHHHHhhhhhhhh
Q psy3153 14 VIIIAALKAARRLNDYALTIRLLEMVQEKCGKKKKVIWPYILGEIRPTLTE 64 (89)
Q Consensus 14 ~ii~AALrAcRRvND~alAVR~lE~iK~K~~~~~~~iY~~~lqElkPtl~E 64 (89)
+|=.|-|.|+-|.|=|-.|.-+--+=..+. .+ .+.-.|+.+|-|-.|++
T Consensus 24 ~VsaallyAaARfnAf~~a~~~~~~~~~~~-~k-e~~i~~f~~qy~~mL~~ 72 (78)
T PF11342_consen 24 QVSAALLYAAARFNAFVAASSFESKADMAA-EK-EEAIDYFTEQYRKMLEE 72 (78)
T ss_pred hHHHHHHHHHHHHHHHHHHHccCcHHHHHH-hH-HHHHHHHHHHHHHHHHH
Confidence 455566789999999988877642111111 11 35667777777766654
No 145
>KOG1953|consensus
Probab=21.74 E-value=94 Score=30.05 Aligned_cols=30 Identities=17% Similarity=0.301 Sum_probs=25.2
Q ss_pred HHHHHHHHHHHhhhhHHHHHHHHHHHHHHh
Q psy3153 14 VIIIAALKAARRLNDYALTIRLLEMVQEKC 43 (89)
Q Consensus 14 ~ii~AALrAcRRvND~alAVR~lE~iK~K~ 43 (89)
+|+.--+.+|+|.|||.-|.|++--+=.+.
T Consensus 563 kvL~eii~~a~ragd~~aa~~~~s~Ll~~y 592 (1235)
T KOG1953|consen 563 KVLNEIISLADRAGDYRAALLLISLLLLTY 592 (1235)
T ss_pred HHHHHHHHHHHhcCCHHHHHHHHHHHHHHh
Confidence 678889999999999999999887665544
No 146
>smart00544 MA3 Domain in DAP-5, eIF4G, MA-3 and other proteins. Highly alpha-helical. May contain repeats and/or regions similar to MIF4G domains Ponting (TIBS) "Novel eIF4G domain homologues" in press
Probab=21.24 E-value=2.3e+02 Score=17.97 Aligned_cols=22 Identities=9% Similarity=0.031 Sum_probs=10.5
Q ss_pred HHHHHHhhhhHHHHHHHHHHHH
Q psy3153 19 ALKAARRLNDYALTIRLLEMVQ 40 (89)
Q Consensus 19 ALrAcRRvND~alAVR~lE~iK 40 (89)
.++-.-...|+..|++-|..++
T Consensus 8 ~l~ey~~~~D~~ea~~~l~~L~ 29 (113)
T smart00544 8 IIEEYLSSGDTDEAVHCLLELK 29 (113)
T ss_pred HHHHHHHcCCHHHHHHHHHHhC
Confidence 3333344445555555555444
No 147
>cd00447 NusB_Sun RNA binding domain of NusB (N protein-Utilization Substance B) and Sun (also known as RrmB or Fmu) proteins. This family includes two orthologous groups exemplified by the transcription termination factor NusB and the N-terminal domain of the rRNA-specific 5-methylcytidine transferase (m5C-methyltransferase) Sun. The NusB protein plays a key role in the regulation of ribosomal RNA biosynthesis in eubacteria by modulating the efficiency of transcriptional antitermination. NusB along with other Nus factors (NusA, NusE/S10 and NusG) forms the core complex with the boxA element of the nut site of the rRNA operons. These interactions help RNA polymerase to counteract polarity during transcription of rRNA operons and allow stable antitermination. The transcription antitermination system can be appropriated by some bacteriophages such as lambda, which use the system to switch between the lysogenic and lytic modes of phage propagation. The m5C-methyltransferase Sun shares the
Probab=21.19 E-value=1.1e+02 Score=19.91 Aligned_cols=33 Identities=30% Similarity=0.449 Sum_probs=23.3
Q ss_pred CCCHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHh
Q psy3153 10 VPDPVIIIAALKAARRLNDYALTIRLLEMVQEKC 43 (89)
Q Consensus 10 VP~P~ii~AALrAcRRvND~alAVR~lE~iK~K~ 43 (89)
+|.+.+|..|...|++..+- .+-+|.-||=.+.
T Consensus 93 ~p~~~vineaVelak~~~~~-~~~~fVNaVLr~~ 125 (129)
T cd00447 93 VPPPVAINEAVELAKRFGDD-DSAKFVNGVLRRI 125 (129)
T ss_pred CCchhHHHHHHHHHHHHCCC-CcchhHHHHHHHH
Confidence 69999999999999876542 3456666655443
No 148
>PF05965 FYRC: F/Y rich C-terminus; InterPro: IPR003889 The "FY-rich" domain C-terminal region is sometimes closely juxtaposed with the N-terminal region (IPR003888 from INTERPRO), but sometimes is far distant. It is of unknown function, but occurs frequently in chromatin-associated proteins like trithorax and its homologues.; GO: 0005634 nucleus; PDB: 2WZO_A.
Probab=21.07 E-value=28 Score=22.05 Aligned_cols=35 Identities=26% Similarity=0.521 Sum_probs=22.6
Q ss_pred CcccchHHHHHhhhhhhhhhC--------CCCccccCCCCCcc
Q psy3153 46 KKKVIWPYILGEIRPTLTELG--------IETPEDLGYDKPEL 80 (89)
Q Consensus 46 ~~~~iY~~~lqElkPtl~ELG--------I~t~EeLgydkpEl 80 (89)
...+.|..+++.|...+...+ |+.++=+|+..|-.
T Consensus 22 s~~~~W~~i~~~v~~~r~~~~~~~~~~~~isG~~~FGls~p~V 64 (86)
T PF05965_consen 22 SPTEAWSEILERVNEARKQSGLLKLPPNSISGPEMFGLSNPAV 64 (86)
T ss_dssp SHHHHHHHHHHHHHHHHT-------TT----HHHHHSTTSHHH
T ss_pred CHHHHHHHHHHHHHHHHhhccccccCCCCCCHhHhcCCCCHHH
Confidence 345678889988888877766 77777788877653
No 149
>PF07719 TPR_2: Tetratricopeptide repeat; InterPro: IPR013105 The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [, , ]. It mediates protein-protein interactions and the assembly of multiprotein complexes []. The TPR motif consists of 3-16 tandem-repeats of 34 amino acids residues, although individual TPR motifs can be dispersed in the protein sequence. Sequence alignment of the TPR domains reveals a consensus sequence defined by a pattern of small and large amino acids. TPR motifs have been identified in various different organisms, ranging from bacteria to humans. Proteins containing TPRs are involved in a variety of biological processes, such as cell cycle regulation, transcriptional control, mitochondrial and peroxisomal protein transport, neurogenesis and protein folding. This repeat includes outlying Tetratricopeptide-like repeats (TPR) that are not matched by IPR001440 from INTERPRO.; PDB: 1XNF_B 3Q15_A 4ABN_A 1OUV_A 3U4T_A 3MA5_C 2KCV_A 2KCL_A 2XEV_A 3NF1_A ....
Probab=21.06 E-value=1.2e+02 Score=14.68 Aligned_cols=25 Identities=24% Similarity=0.180 Sum_probs=17.7
Q ss_pred HHHHHHhhhhHHHHHHHHHHHHHHh
Q psy3153 19 ALKAARRLNDYALTIRLLEMVQEKC 43 (89)
Q Consensus 19 ALrAcRRvND~alAVR~lE~iK~K~ 43 (89)
.=.+..+.++|..|++.++..-...
T Consensus 7 lg~~~~~~~~~~~A~~~~~~al~l~ 31 (34)
T PF07719_consen 7 LGQAYYQLGNYEEAIEYFEKALELD 31 (34)
T ss_dssp HHHHHHHTT-HHHHHHHHHHHHHHS
T ss_pred HHHHHHHhCCHHHHHHHHHHHHHHC
Confidence 3356778999999999988765443
No 150
>TIGR03504 FimV_Cterm FimV C-terminal domain. This protein is found at the extreme C-terminus of FimV from Pseudomonas aeruginosa, and of TspA of Neisseria meningitidis. Disruption of the former blocks twitching motility from type IV pili; Semmler, et al. suggest a role in peptidoglycan layer remodelling required by type IV fimbrial systems.
Probab=21.02 E-value=1e+02 Score=18.08 Aligned_cols=21 Identities=33% Similarity=0.283 Sum_probs=18.5
Q ss_pred HHHHhhhhHHHHHHHHHHHHH
Q psy3153 21 KAARRLNDYALTIRLLEMVQE 41 (89)
Q Consensus 21 rAcRRvND~alAVR~lE~iK~ 41 (89)
+|....+|+..|-.+||.|-.
T Consensus 7 ~ayie~Gd~e~Ar~lL~evl~ 27 (44)
T TIGR03504 7 RAYIEMGDLEGARELLEEVIE 27 (44)
T ss_pred HHHHHcCChHHHHHHHHHHHH
Confidence 677889999999999999884
No 151
>PF06368 Met_asp_mut_E: Methylaspartate mutase E chain (MutE); InterPro: IPR006396 Glutamate mutase (methylaspartate mutase) catalyses the reversible interconversion of L-glutamate and L-threo-3-methylaspartate, the first step in the pathway of glutamate fermentation []. Catalysis is initiated using the cobalamin cofactor. The E subunit is the catalytic subunit (MutE) []. ; GO: 0016866 intramolecular transferase activity, 0031419 cobalamin binding, 0019670 anaerobic glutamate catabolic process; PDB: 1CB7_D 1I9C_B 1CCW_D.
Probab=20.85 E-value=3.7e+02 Score=23.32 Aligned_cols=52 Identities=25% Similarity=0.269 Sum_probs=29.2
Q ss_pred CCCHHHHHHHHHHHH----------------hhhhHHHHHHHH-HHHHHHhcCCcccchHHHHHhhhhhhh
Q psy3153 10 VPDPVIIIAALKAAR----------------RLNDYALTIRLL-EMVQEKCGKKKKVIWPYILGEIRPTLT 63 (89)
Q Consensus 10 VP~P~ii~AALrAcR----------------RvND~alAVR~l-E~iK~K~~~~~~~iY~~~lqElkPtl~ 63 (89)
||.|+=..+.|++-+ |+|||+.|-+-| |+++..... -|+ ||-+-.-.+-+++
T Consensus 28 v~~~~~~i~lL~~l~~~g~~d~lp~TiDSyTR~n~y~~A~~~l~~s~~~~~s~-LNG-fP~VnhG~~~~R~ 96 (441)
T PF06368_consen 28 VALPEEMIELLQYLRDEGGADVLPLTIDSYTRQNDYEEAERGLEESIETGRSM-LNG-FPLVNHGVETCRK 96 (441)
T ss_dssp -SSHHHHHHHHHHHHHTT--SSEEEEB-HHHHTT-HHHHHHHHHHHHHHTS---SSS-B-HHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHhccCCCeeceeeecccccccHHHHHHHHHhchhcCccc-ccC-CccccccHHHHHH
Confidence 455555566565554 899999999988 455533322 133 7776655555544
No 152
>PRK04452 acetyl-CoA decarbonylase/synthase complex subunit delta; Provisional
Probab=20.63 E-value=68 Score=26.06 Aligned_cols=66 Identities=17% Similarity=0.108 Sum_probs=36.7
Q ss_pred CCCHHHHHHHHHHHH-h---hhhHHHH--HHHHHHHH-HHhcCCccc-chHHHHHhhhhhhhhhCCCCccccCCC
Q psy3153 10 VPDPVIIIAALKAAR-R---LNDYALT--IRLLEMVQ-EKCGKKKKV-IWPYILGEIRPTLTELGIETPEDLGYD 76 (89)
Q Consensus 10 VP~P~ii~AALrAcR-R---vND~alA--VR~lE~iK-~K~~~~~~~-iY~~~lqElkPtl~ELGI~t~EeLgyd 76 (89)
=|+|++++|||++|. | +|..... -++++..| .+|.--+.. .==.+.++|--.+.++||+ +|++-+|
T Consensus 136 ~kD~evleaale~~~g~~pLInSat~en~~~i~~lA~~y~~~Vva~s~~Dln~ak~L~~~l~~~Gi~-~edIviD 209 (319)
T PRK04452 136 EKDAEVLEKVAEAAEGERCLLGSAEEDNYKKIAAAAMAYGHAVIAWSPLDINLAKQLNILLTELGVP-RERIVMD 209 (319)
T ss_pred CCCHHHHHHHHHHhCCCCCEEEECCHHHHHHHHHHHHHhCCeEEEEcHHHHHHHHHHHHHHHHcCCC-HHHEEEe
Confidence 478999999999998 4 3332221 22333332 222211011 0124677788888999995 4444444
No 153
>cd06111 DsCS_like Cold-active citrate synthase (CS) from an Antarctic bacterial strain DS2-3R (Ds)-like. CS catalyzes the condensation of acetyl coenzyme A (AcCoA) and oxalacetate (OAA) to form citrate and coenzyme A (CoA), the first step in the citric acid cycle (TCA or Krebs cycle). 2-methylcitrate synthase (2MCS) catalyzes the condensation of propionyl-coenzyme A (PrCoA) and OAA to form 2-methylcitrate and coenzyme A (CoA) during propionate metabolism. The overall CS reaction is thought to proceed through three partial reactions: a) the carbanion or equivalent is generated from AcCoA by base abstraction of a proton, b) the nucleophilic attack of this carbanion on OAA to generate citryl-CoA, and c) the hydrolysis of citryl-CoA to produce citrate and CoA. DsCS, compared with CS from the hyperthermophile Pyrococcus furiosus (not included in this group), has an increase in the size of surface loops, a higher proline content in the loop regions, a more accessible active site, and a highe
Probab=20.61 E-value=1.7e+02 Score=23.83 Aligned_cols=57 Identities=14% Similarity=0.130 Sum_probs=30.1
Q ss_pred CHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHhcCCcccchHHHHHhhhhhhhhhCCCC
Q psy3153 12 DPVIIIAALKAARRLNDYALTIRLLEMVQEKCGKKKKVIWPYILGEIRPTLTELGIET 69 (89)
Q Consensus 12 ~P~ii~AALrAcRRvND~alAVR~lE~iK~K~~~~~~~iY~~~lqElkPtl~ELGI~t 69 (89)
-.+++..+++.--+-+.....+++.+.|.+..... +++|+-+==-.--++..||||.
T Consensus 263 Ra~~L~~~l~~l~~~~~~~~~~~~~~~i~~~~~~~-~~l~pNvD~~~a~l~~~lG~p~ 319 (362)
T cd06111 263 RVPTMEKALRRVAAVHDGQKWLAMYDALEDAMVAA-KGIKPNLDFPAGPAYYLMGFDI 319 (362)
T ss_pred hHHHHHHHHHHHHhhcCccHHHHHHHHHHHHHHHh-cCCCCChHHHHHHHHHHcCcCh
Confidence 33444444443211122334455555554444333 4567766666667788899863
No 154
>PF12688 TPR_5: Tetratrico peptide repeat
Probab=20.52 E-value=2.7e+02 Score=19.06 Aligned_cols=26 Identities=27% Similarity=0.334 Sum_probs=21.0
Q ss_pred HHHHHhhhhHHHHHHHHHHHHHHhcC
Q psy3153 20 LKAARRLNDYALTIRLLEMVQEKCGK 45 (89)
Q Consensus 20 LrAcRRvND~alAVR~lE~iK~K~~~ 45 (89)
=.+.|.++++..|+++|+.......+
T Consensus 45 astlr~LG~~deA~~~L~~~~~~~p~ 70 (120)
T PF12688_consen 45 ASTLRNLGRYDEALALLEEALEEFPD 70 (120)
T ss_pred HHHHHHcCCHHHHHHHHHHHHHHCCC
Confidence 35678999999999999988776554
No 155
>KOG3584|consensus
Probab=20.52 E-value=2.1e+02 Score=24.16 Aligned_cols=43 Identities=23% Similarity=0.203 Sum_probs=23.4
Q ss_pred HHHHHHHhhhhHHHHHHHHHHHHHHhcCCcccchHHHHHhhhhhhhhhCC
Q psy3153 18 AALKAARRLNDYALTIRLLEMVQEKCGKKKKVIWPYILGEIRPTLTELGI 67 (89)
Q Consensus 18 AALrAcRRvND~alAVR~lE~iK~K~~~~~~~iY~~~lqElkPtl~ELGI 67 (89)
.|-|-|||=-. .=|.-||.=-.-.+| |-+.+++||| +|+||=.
T Consensus 301 EAARECRRKKK--EYVKCLENRVAVLEN----QNKaLIEELK-tLKeLYc 343 (348)
T KOG3584|consen 301 EAARECRRKKK--EYVKCLENRVAVLEN----QNKALIEELK-TLKELYC 343 (348)
T ss_pred HHHHHHHHhHh--HHHHHHHhHHHHHhc----ccHHHHHHHH-HHHHHhh
Confidence 36688988431 223333322222233 4678999998 5677643
No 156
>TIGR03290 CoB_CoM_SS_C CoB--CoM heterodisulfide reductase, subunit C. The last step in methanogenesis leaves two coenzymes of methanogenesis, CoM and CoB, linked by a disulfide bond. Members of this protein family are the C subunit of the enzyme that reduces the heterodisulfide to CoB-SH and CoM-SH. Similar enzyme complex subunits are found in various other species, but likely act on a different substrate.
Probab=20.45 E-value=1.9e+02 Score=19.81 Aligned_cols=34 Identities=15% Similarity=0.315 Sum_probs=21.5
Q ss_pred HHHHHHHHhcCC----cccchHHHHHhhhhhhhhhCCC
Q psy3153 35 LLEMVQEKCGKK----KKVIWPYILGEIRPTLTELGIE 68 (89)
Q Consensus 35 ~lE~iK~K~~~~----~~~iY~~~lqElkPtl~ELGI~ 68 (89)
+.+.++.+++.. ....||.-+.|+.-+|+-+|++
T Consensus 104 ~~~~lr~~~g~~~~p~~~~~~p~~~~~~~~il~~~~~~ 141 (144)
T TIGR03290 104 EIKELRKELGLDEIPPTTHKYPEALEEVQKLIKALEFD 141 (144)
T ss_pred HHHHHHHHcCCCCCCCccccCHHHHHHHHHHHHHhChh
Confidence 445666776651 1335677777777777777763
No 157
>PF00465 Fe-ADH: Iron-containing alcohol dehydrogenase ; InterPro: IPR001670 Alcohol dehydrogenase (1.1.1.1 from EC) (ADH) catalyzes the reversible oxidation of ethanol to acetaldehyde with the concomitant reduction of NAD. Currently three, structurally and catalytically, different types of alcohol dehydrogenases are known: Zinc-containing 'long-chain' alcohol dehydrogenases. Insect-type, or 'short-chain' alcohol dehydrogenases. Iron-containing alcohol dehydrogenases. Iron-containing ADH's have been found in yeast (gene ADH4) [], as well as in Zymomonas mobilis (gene adhB) []. These two iron-containing ADH's are closely related to the following enzymes: Escherichia coli propanediol oxidoreductase (1.1.1.77 from EC) (gene fucO) [], an enzyme involved in the metabolism of fucose and which also seems to contain ferrous ion(s). Clostridium acetobutylicum NADPH- and NADH-dependent butanol dehydrogenases (1.1.1 from EC) (genes adh1, bdhA and bdhB) [], an enzyme which has activity using butanol and ethanol as substrates. E. coli adhE [], an iron-dependent enzyme which harbor three different activities: alcohol dehydrogenase, acetaldehyde dehydrogenase (acetylating) (1.2.1.10 from EC) and pyruvate-formate-lyase deactivase. Bacterial glycerol dehydrogenase (1.1.1.6 from EC) (gene gldA or dhaD) []. Clostridium kluyveri NAD-dependent 4-hydroxybutyrate dehydrogenase (4hbd) (1.1.1.61 from EC). Citrobacter freundii and Klebsiella pneumoniae 1,3-propanediol dehydrogenase (1.1.1.202 from EC) (gene dhaT). Bacillus methanolicus NAD-dependent methanol dehydrogenase (1.1.1.244 from EC) []. E. coli and Salmonella typhimurium ethanolamine utilization protein eutG. E. coli hypothetical protein yiaY. ; GO: 0016491 oxidoreductase activity, 0046872 metal ion binding, 0055114 oxidation-reduction process; PDB: 1RRM_A 2BL4_A 2BI4_A 3BFJ_R 1KQ3_A 1JQ5_A 1JPU_A 1JQA_A 3JZD_A 3UHJ_A ....
Probab=20.40 E-value=80 Score=24.53 Aligned_cols=30 Identities=33% Similarity=0.442 Sum_probs=23.0
Q ss_pred cchHHHHHhhhhhhhhhCCCC-ccccCCCCC
Q psy3153 49 VIWPYILGEIRPTLTELGIET-PEDLGYDKP 78 (89)
Q Consensus 49 ~iY~~~lqElkPtl~ELGI~t-~EeLgydkp 78 (89)
+.-...+++|+-.+++||+|+ ..++|++.-
T Consensus 309 ~~a~~~~~~l~~l~~~lglp~~l~~~gi~~~ 339 (366)
T PF00465_consen 309 EAADDAIDELRALLRSLGLPTRLSDLGIDEE 339 (366)
T ss_dssp HHHHHHHHHHHHHHHHTT--SSGGGGT-TGG
T ss_pred HHHHHHHHHHHHHHHHhCCCCCHHHcCCCHH
Confidence 456788999999999999998 899999873
No 158
>PF10865 DUF2703: Domain of unknown function (DUF2703); InterPro: IPR021219 This family of protein has no known function.
Probab=20.34 E-value=72 Score=22.55 Aligned_cols=20 Identities=35% Similarity=0.481 Sum_probs=17.1
Q ss_pred cchHHHHHhhhhhhhhhCCC
Q psy3153 49 VIWPYILGEIRPTLTELGIE 68 (89)
Q Consensus 49 ~iY~~~lqElkPtl~ELGI~ 68 (89)
..-...+++|+|.|+.+||.
T Consensus 23 ~~L~~av~~l~~~L~~~Gie 42 (120)
T PF10865_consen 23 ETLREAVKELAPVLAPLGIE 42 (120)
T ss_pred HHHHHHHHHHHHHHHhCCcE
Confidence 44677899999999999985
No 159
>PF11817 Foie-gras_1: Foie gras liver health family 1; InterPro: IPR021773 Mutating the gene foie gras in zebrafish has been shown to affect development; the mutants develop large, lipid-filled hepatocytes in the liver, resembling those in individuals with fatty liver disease []. Foie-gras protein is long and has several well-defined domains though none of them has a known function. We have annotated this one as the first []. THe C terminus of this region contains TPR repeats.
Probab=20.08 E-value=1.5e+02 Score=22.11 Aligned_cols=35 Identities=31% Similarity=0.440 Sum_probs=22.1
Q ss_pred hhhhHHHHHHHHHHHHHHhcCCcccchHHHHHhhhhhh
Q psy3153 25 RLNDYALTIRLLEMVQEKCGKKKKVIWPYILGEIRPTL 62 (89)
Q Consensus 25 RvND~alAVR~lE~iK~K~~~~~~~iY~~~lqElkPtl 62 (89)
+.+||..|+++|+.+ .+.-.+ +-|.-++.++-..+
T Consensus 190 ~~g~~~~A~~~l~~~-~~~yr~--egW~~l~~~~l~~l 224 (247)
T PF11817_consen 190 RLGDYDKALKLLEPA-ASSYRR--EGWWSLLTEVLWRL 224 (247)
T ss_pred HCCCHHHHHHHHHHH-HHHHHh--CCcHHHHHHHHHHH
Confidence 568888999999888 333222 44666665554444
No 160
>PF13424 TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15_A 3ASG_A 3ASD_A 3AS5_A 3AS4_A 3ASH_B 4A1S_B 3CEQ_B 3EDT_H ....
Probab=20.04 E-value=1.3e+02 Score=17.43 Aligned_cols=19 Identities=21% Similarity=0.364 Sum_probs=14.6
Q ss_pred HHHHhhhhHHHHHHHHHHH
Q psy3153 21 KAARRLNDYALTIRLLEMV 39 (89)
Q Consensus 21 rAcRRvND~alAVR~lE~i 39 (89)
...++.+|+..|+.+++-.
T Consensus 54 ~~~~~~g~~~~A~~~~~~a 72 (78)
T PF13424_consen 54 ECYYRLGDYEEALEYYQKA 72 (78)
T ss_dssp HHHHHTTHHHHHHHHHHHH
T ss_pred HHHHHcCCHHHHHHHHHHH
Confidence 4567888888888888754
No 161
>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=20.00 E-value=72 Score=22.11 Aligned_cols=33 Identities=27% Similarity=0.402 Sum_probs=23.2
Q ss_pred HHHHHHHhcCCcccchHHHHHhhhhhhhhhCCCC
Q psy3153 36 LEMVQEKCGKKKKVIWPYILGEIRPTLTELGIET 69 (89)
Q Consensus 36 lE~iK~K~~~~~~~iY~~~lqElkPtl~ELGI~t 69 (89)
||.+-.++.+. +.+..|++.|+-..|.+.|++.
T Consensus 2 fe~~~~~~~~~-k~~anwi~~el~~~l~~~~~~~ 34 (147)
T smart00845 2 FEEVVKAGADP-KLAANWLLGELLGELNKEGLEI 34 (147)
T ss_pred HHHHHHcCCCH-HHHHHHHHHHHHHHHHhCCCCH
Confidence 44443333332 5789999999999999988763
Done!