Query 042062
Match_columns 142
No_of_seqs 178 out of 635
Neff 7.5
Searched_HMMs 46136
Date Fri Mar 29 02:26:53 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/042062.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/042062hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4747 Two-component phosphor 99.9 2.1E-24 4.6E-29 154.1 12.8 139 2-141 6-146 (150)
2 COG2198 ArcB FOG: HPt domain [ 99.7 9.5E-17 2.1E-21 112.5 12.9 109 20-130 5-117 (122)
3 PF01627 Hpt: Hpt domain; Int 99.7 2.2E-16 4.8E-21 103.4 10.2 82 41-124 1-88 (90)
4 smart00073 HPT Histidine Phosp 99.6 5.3E-15 1.1E-19 97.1 5.0 84 41-127 2-85 (87)
5 cd00088 HPT Histidine Phosphot 99.5 3.5E-13 7.6E-18 89.9 8.6 64 40-105 2-69 (94)
6 TIGR02956 TMAO_torS TMAO reduc 99.4 2.9E-12 6.2E-17 114.7 11.0 105 20-130 863-968 (968)
7 PRK10618 phosphotransfer inter 99.2 2.4E-10 5.2E-15 103.0 10.5 83 40-124 810-892 (894)
8 PRK11091 aerobic respiration c 99.1 7.6E-10 1.6E-14 97.6 11.9 112 20-135 665-777 (779)
9 PRK11107 hybrid sensory histid 98.7 2E-07 4.3E-12 83.1 12.6 97 34-132 821-918 (919)
10 PRK11466 hybrid sensory histid 98.7 2.1E-07 4.5E-12 83.3 11.9 66 35-102 821-886 (914)
11 COG0643 CheA Chemotaxis protei 98.2 8.6E-06 1.9E-10 72.2 9.7 89 37-125 4-101 (716)
12 PRK10547 chemotaxis protein Ch 98.1 2.3E-05 4.9E-10 69.2 9.8 63 40-102 4-72 (670)
13 PRK09959 hybrid sensory histid 97.8 0.00073 1.6E-08 62.5 14.6 102 27-130 1090-1192(1197)
14 PRK15347 two component system 97.1 0.0022 4.7E-08 57.5 7.7 78 42-124 838-915 (921)
15 TIGR03042 PS_II_psbQ_bact phot 88.7 5.1 0.00011 28.9 8.2 79 43-133 38-140 (142)
16 PF13779 DUF4175: Domain of un 82.5 10 0.00022 34.9 8.8 85 35-124 490-574 (820)
17 cd08323 CARD_APAF1 Caspase act 82.0 8.6 0.00019 25.3 6.2 66 9-77 17-83 (86)
18 PF07743 HSCB_C: HSCB C-termin 81.8 10 0.00023 23.8 6.9 41 37-79 27-67 (78)
19 TIGR02302 aProt_lowcomp conser 81.7 13 0.00028 34.4 9.1 84 35-124 521-604 (851)
20 TIGR03042 PS_II_psbQ_bact phot 80.6 19 0.00041 26.0 9.1 61 25-87 52-113 (142)
21 TIGR00714 hscB Fe-S protein as 76.9 18 0.0004 26.2 7.3 66 55-131 88-153 (157)
22 PF05757 PsbQ: Oxygen evolving 72.0 20 0.00042 27.5 6.5 77 47-125 105-199 (202)
23 PLN02956 PSII-Q subunit 71.2 42 0.00091 25.3 9.1 77 44-125 86-183 (185)
24 PRK01773 hscB co-chaperone Hsc 66.2 46 0.001 24.6 7.4 77 35-130 90-166 (173)
25 COG3046 Uncharacterized protei 66.1 13 0.00028 31.7 4.8 76 35-116 226-303 (505)
26 PF08900 DUF1845: Domain of un 65.5 41 0.00088 25.8 7.2 53 80-133 32-84 (217)
27 PRK03578 hscB co-chaperone Hsc 64.5 48 0.001 24.6 7.2 77 35-130 93-170 (176)
28 TIGR00984 3a0801s03tim44 mitoc 63.9 27 0.00058 29.3 6.2 75 12-104 218-293 (378)
29 PRK01356 hscB co-chaperone Hsc 61.0 63 0.0014 23.7 7.3 53 67-128 107-159 (166)
30 PRK03057 hypothetical protein; 52.4 53 0.0012 24.6 5.6 37 41-79 131-173 (180)
31 PRK03636 hypothetical protein; 51.5 60 0.0013 24.3 5.8 37 41-79 132-174 (179)
32 PF09280 XPC-binding: XPC-bind 50.0 24 0.00051 21.5 2.9 36 24-59 9-44 (59)
33 TIGR03761 ICE_PFL4669 integrat 49.6 1.1E+02 0.0024 23.6 7.1 51 81-131 31-87 (216)
34 cd01671 CARD Caspase activatio 48.1 64 0.0014 19.9 5.5 57 7-64 14-71 (80)
35 PF02153 PDH: Prephenate dehyd 47.6 89 0.0019 24.2 6.6 48 25-74 201-255 (258)
36 PF14931 IFT20: Intraflagellar 47.5 95 0.0021 21.7 9.4 100 18-135 11-111 (120)
37 cd08325 CARD_CASP1-like Caspas 46.9 77 0.0017 20.4 5.9 60 7-68 17-77 (83)
38 PRK13916 plasmid segregation p 46.1 36 0.00077 22.5 3.4 26 25-50 21-47 (97)
39 PF02845 CUE: CUE domain; Int 45.4 43 0.00094 18.4 3.3 33 25-57 5-38 (42)
40 PRK05014 hscB co-chaperone Hsc 44.9 1.2E+02 0.0027 22.2 7.4 77 35-130 88-165 (171)
41 TIGR00465 ilvC ketol-acid redu 44.3 25 0.00054 28.5 3.0 74 20-108 173-248 (314)
42 PF05227 CHASE3: CHASE3 domain 44.1 97 0.0021 20.8 6.9 29 33-62 35-63 (138)
43 PF03670 UPF0184: Uncharacteri 43.5 93 0.002 20.4 5.2 35 103-137 32-66 (83)
44 cd08330 CARD_ASC_NALP1 Caspase 43.4 88 0.0019 20.1 5.8 56 8-64 17-73 (82)
45 PRK08818 prephenate dehydrogen 42.9 60 0.0013 27.0 5.1 38 39-82 229-266 (370)
46 PLN02407 diphosphomevalonate d 42.6 48 0.001 27.4 4.4 33 41-75 223-256 (343)
47 PRK05685 fliS flagellar protei 42.1 1.2E+02 0.0026 21.2 10.0 28 41-70 26-53 (132)
48 smart00388 HisKA His Kinase A 41.8 62 0.0013 17.9 7.3 56 71-134 6-61 (66)
49 PRK10093 primosomal replicatio 41.5 90 0.0019 23.3 5.3 36 41-78 40-75 (171)
50 PF03993 DUF349: Domain of Unk 41.5 57 0.0012 20.0 3.9 32 91-122 37-68 (77)
51 cd08326 CARD_CASP9 Caspase act 41.4 97 0.0021 20.0 5.4 61 9-72 19-80 (84)
52 KOG3232 Vacuolar assembly/sort 41.0 1.4E+02 0.0031 22.5 6.3 48 75-127 85-132 (203)
53 PF08858 IDEAL: IDEAL domain; 40.8 62 0.0014 17.6 5.5 25 51-77 12-36 (37)
54 COG2991 Uncharacterized protei 38.1 7.6 0.00017 24.9 -0.6 20 76-95 27-46 (77)
55 PF00619 CARD: Caspase recruit 38.0 99 0.0021 19.2 4.6 55 8-63 18-73 (85)
56 COG4842 Uncharacterized protei 37.7 1.2E+02 0.0026 20.0 7.2 69 66-135 7-78 (97)
57 PF14357 DUF4404: Domain of un 37.6 45 0.00097 21.7 2.9 28 4-31 2-30 (85)
58 KOG2424 Protein involved in tr 37.3 55 0.0012 24.8 3.7 23 82-106 147-169 (195)
59 smart00188 IL10 Interleukin-10 37.2 1.6E+02 0.0034 21.2 7.8 31 19-51 28-59 (137)
60 PF04282 DUF438: Family of unk 36.4 1.1E+02 0.0025 19.3 5.1 48 28-75 6-55 (71)
61 PF07445 priB_priC: Primosomal 36.3 1.7E+02 0.0038 21.5 7.7 23 42-64 41-63 (173)
62 PF04280 Tim44: Tim44-like dom 36.0 65 0.0014 22.3 3.8 36 35-75 12-47 (147)
63 PF06013 WXG100: Proteins of 1 35.9 1E+02 0.0022 18.6 5.7 27 108-134 48-74 (86)
64 PRK12491 pyrroline-5-carboxyla 35.2 64 0.0014 25.3 4.0 69 6-85 145-215 (272)
65 PF09403 FadA: Adhesion protei 35.0 1.2E+02 0.0025 21.4 4.9 10 80-89 12-21 (126)
66 PRK10807 paraquat-inducible pr 34.6 3.2E+02 0.0069 24.0 9.3 28 108-136 501-528 (547)
67 TIGR00208 fliS flagellar biosy 34.6 1.6E+02 0.0034 20.4 9.4 29 41-71 22-50 (124)
68 PF03847 TFIID_20kDa: Transcri 34.5 67 0.0014 20.1 3.3 46 5-60 2-47 (68)
69 smart00546 CUE Domain that may 33.9 85 0.0018 17.2 3.4 33 25-57 6-39 (43)
70 PF03194 LUC7: LUC7 N_terminus 33.7 2.3E+02 0.0051 22.2 8.3 73 40-117 85-159 (254)
71 PHA02845 hypothetical protein; 32.9 60 0.0013 21.6 2.9 43 8-50 5-49 (91)
72 PF05396 Phage_T7_Capsid: Phag 32.3 1.8E+02 0.0039 20.5 7.6 57 21-80 32-88 (123)
73 PRK08507 prephenate dehydrogen 32.0 1.8E+02 0.0039 22.5 6.1 48 25-74 210-264 (275)
74 cd08329 CARD_BIRC2_BIRC3 Caspa 31.9 1.5E+02 0.0033 19.5 6.6 60 10-72 27-87 (94)
75 cd08332 CARD_CASP2 Caspase act 31.7 1.5E+02 0.0032 19.3 5.9 54 10-64 24-78 (90)
76 KOG2833 Mevalonate pyrophospha 31.1 97 0.0021 25.7 4.4 31 42-74 223-254 (395)
77 PF12854 PPR_1: PPR repeat 30.8 61 0.0013 16.9 2.3 22 95-116 12-33 (34)
78 KOG1104 Nuclear cap-binding co 30.8 4.3E+02 0.0093 24.4 9.6 101 26-135 87-207 (759)
79 PF04840 Vps16_C: Vps16, C-ter 30.1 3E+02 0.0065 22.3 9.9 87 20-117 175-264 (319)
80 PF00512 HisKA: His Kinase A ( 30.0 1.2E+02 0.0026 17.7 8.6 58 70-135 5-64 (68)
81 cd08819 CARD_MDA5_2 Caspase ac 29.7 1.7E+02 0.0037 19.4 4.8 56 7-63 20-78 (88)
82 KOG4552 Vitamin-D-receptor int 29.6 2.6E+02 0.0056 21.8 6.3 36 45-81 106-141 (272)
83 PRK11199 tyrA bifunctional cho 29.5 2.9E+02 0.0062 22.8 7.1 48 28-77 292-345 (374)
84 TIGR01240 mevDPdecarb diphosph 28.7 1.1E+02 0.0023 24.7 4.4 31 43-75 202-232 (305)
85 PTZ00431 pyrroline carboxylate 28.7 66 0.0014 24.9 3.1 70 5-85 137-208 (260)
86 PF00435 Spectrin: Spectrin re 28.3 1.5E+02 0.0032 18.2 7.1 43 90-133 60-102 (105)
87 cd07298 PX_RICS The phosphoino 27.4 74 0.0016 22.1 2.7 38 14-51 55-97 (115)
88 COG3433 Aryl carrier domain [S 27.2 1.3E+02 0.0029 19.2 3.7 51 41-92 5-55 (74)
89 PF07870 DUF1657: Protein of u 27.1 1.4E+02 0.003 17.4 4.5 36 95-130 14-49 (50)
90 PF01535 PPR: PPR repeat; Int 26.5 86 0.0019 14.9 2.7 23 96-118 6-28 (31)
91 PRK10698 phage shock protein P 26.3 3E+02 0.0065 21.1 9.3 23 41-63 27-49 (222)
92 PF02203 TarH: Tar ligand bind 25.8 2.3E+02 0.0049 19.7 5.3 85 37-130 82-167 (171)
93 KOG2580 Mitochondrial import i 25.7 1.7E+02 0.0036 25.1 5.0 65 5-77 285-350 (459)
94 cd00082 HisKA Histidine Kinase 25.5 1.2E+02 0.0027 16.3 7.2 54 71-132 8-62 (65)
95 PRK07417 arogenate dehydrogena 25.3 1.5E+02 0.0033 23.1 4.6 26 47-74 241-266 (279)
96 PF14748 P5CR_dimer: Pyrroline 25.2 71 0.0015 21.4 2.4 54 21-85 1-56 (107)
97 PF04722 Ssu72: Ssu72-like pro 24.9 70 0.0015 24.3 2.5 36 82-118 145-181 (195)
98 PF09209 DUF1956: Domain of un 24.8 2.1E+02 0.0046 18.8 8.0 82 3-86 4-87 (125)
99 PF07361 Cytochrom_B562: Cytoc 24.7 1.4E+02 0.0031 20.0 3.8 38 84-121 59-99 (103)
100 PHA02666 hypothetical protein; 24.6 1.5E+02 0.0032 23.2 4.2 54 33-90 201-258 (287)
101 PHA03079 hypothetical protein; 24.6 1E+02 0.0022 20.3 2.8 63 8-72 4-70 (87)
102 TIGR00756 PPR pentatricopeptid 24.2 1E+02 0.0022 14.8 3.2 23 96-118 6-28 (35)
103 KOG2716 Polymerase delta-inter 24.1 56 0.0012 25.5 1.9 52 45-96 48-99 (230)
104 PF09851 SHOCT: Short C-termin 23.6 56 0.0012 17.0 1.3 19 11-29 7-26 (31)
105 PRK13858 type IV secretion sys 23.3 3E+02 0.0065 20.0 6.8 62 68-135 72-133 (147)
106 PF10018 Med4: Vitamin-D-recep 23.3 3.1E+02 0.0068 20.2 6.8 21 64-84 79-99 (188)
107 PF08657 DASH_Spc34: DASH comp 23.2 3.8E+02 0.0082 21.2 7.1 62 69-130 134-199 (259)
108 PF13812 PPR_3: Pentatricopept 23.2 1.1E+02 0.0024 14.9 3.3 22 97-118 8-29 (34)
109 COG0282 ackA Acetate kinase [E 23.2 2.3E+02 0.0051 23.9 5.4 46 43-105 248-293 (396)
110 TIGR00444 mazG MazG family pro 23.1 1.5E+02 0.0033 23.2 4.2 92 37-128 74-172 (248)
111 PF11563 Protoglobin: Protoglo 23.0 2.6E+02 0.0057 19.2 5.4 49 2-51 61-116 (158)
112 COG2178 Predicted RNA-binding 22.9 3.5E+02 0.0077 20.7 6.5 43 88-130 27-69 (204)
113 PF09577 Spore_YpjB: Sporulati 22.5 2.5E+02 0.0054 21.9 5.2 40 88-127 101-140 (232)
114 cd07278 PX_RICS_like The phosp 21.9 77 0.0017 22.0 2.0 37 14-50 54-95 (114)
115 PHA02649 hypothetical protein; 21.7 1.2E+02 0.0027 20.2 2.9 63 8-72 5-71 (95)
116 PRK07502 cyclohexadienyl dehyd 21.6 1.9E+02 0.0042 22.7 4.6 48 25-74 223-277 (307)
117 COG4623 Predicted soluble lyti 21.4 4.6E+02 0.0099 22.5 6.7 114 3-120 220-347 (473)
118 smart00114 CARD Caspase recrui 21.3 2.3E+02 0.005 17.9 5.6 54 10-64 24-78 (88)
119 PF11123 DNA_Packaging_2: DNA 21.1 2.5E+02 0.0053 18.2 5.1 54 37-102 14-70 (82)
120 KOG4747 Two-component phosphor 20.8 3E+02 0.0065 20.1 4.9 59 35-96 12-70 (150)
121 PF10923 DUF2791: P-loop Domai 20.5 5.4E+02 0.012 21.9 8.6 85 38-122 119-203 (416)
122 PF08332 CaMKII_AD: Calcium/ca 20.2 99 0.0021 21.7 2.3 26 49-76 4-29 (128)
123 PRK09613 thiH thiamine biosynt 20.0 2E+02 0.0044 24.8 4.6 64 16-79 8-74 (469)
No 1
>KOG4747 consensus Two-component phosphorelay intermediate involved in MAP kinase cascade regulation [Signal transduction mechanisms]
Probab=99.92 E-value=2.1e-24 Score=154.07 Aligned_cols=139 Identities=36% Similarity=0.575 Sum_probs=132.8
Q ss_pred hHHHHHHHHHHHhccCcchhhHHHHHHhhc-CCCChhhHHHHHHHHHHcHHHHHHHHHHHHhcCccCHHHHHHHHhHhhc
Q 042062 2 EALRQQIAEMRQSFFDEEILDRYFIQLEQL-GENNPGFVEDVLTVYFRDSTRTLANIEKELQKTEVNYVELDRYFYNLKG 80 (142)
Q Consensus 2 ~~~~~~~~~~~~~~~~~~~lD~~l~~L~~l-~~~~~~~~~eli~~F~~d~~~~l~~L~~al~~~~~D~~~l~~~aH~LKG 80 (142)
..+..+...+-+|++++|++|.+|.+|++| ++.+|+|+.+++..|++++.+.+..++.|+..+ .|+..+..+.|.+||
T Consensus 6 ~~~q~~~~d~~~sl~~qgild~qF~qlq~lqD~~~p~fv~ev~~~fF~~s~~~i~~~r~ald~~-~d~k~~~~~~hqlkg 84 (150)
T KOG4747|consen 6 ISMQRDVSDYTKSLFDQGILDSQFLQLQELQDDSSPDFVEEVVGLFFEDSERLINNLRLALDCE-RDFKKLGSHVHQLKG 84 (150)
T ss_pred HHHHHHHHHHHHHHHHHHhhHHHHHHHHHHhcccCccHHHHHHHHHHHHHHHHHHHHHHHHhhH-hHHHHHHHHHHHccC
Confidence 467889999999999999999889999999 999999999999999999999999999999974 499999999999999
Q ss_pred cccccChHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-hcccC
Q 042062 81 SSASIGANKVRNEVNKTRELCRAANWEEAKVSLEQLKVEHSTLKDKLTAYFELVAQ-LGTDS 141 (142)
Q Consensus 81 ss~~lGA~~L~~~c~~LE~~~~~~~~~~~~~~~~~l~~~~~~~~~~L~~~l~~~~~-~~~~~ 141 (142)
||++|||.++...|..+...|+.++.+++...+++++.+|..++..|+++.+++|| |.++|
T Consensus 85 ssssIGa~kvk~~c~~~~~~~~~~n~egcvr~l~~v~ie~~~lkkkL~~~f~L~rq~i~~~~ 146 (150)
T KOG4747|consen 85 SSSSIGALKVKKVCVGFNEFCEAGNIEGCVRCLQQVKIEYSLLKKKLETLFQLERQEILAAG 146 (150)
T ss_pred chhhhhHHHHHHHHHHHHHHHhhccchhHhhchHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 99999999999999999999999999999999999999999999999999999999 66654
No 2
>COG2198 ArcB FOG: HPt domain [Signal transduction mechanisms]
Probab=99.73 E-value=9.5e-17 Score=112.47 Aligned_cols=109 Identities=25% Similarity=0.350 Sum_probs=94.8
Q ss_pred hhhHH-HHHHhhcCCCChhhHHHHHHHHHHcHHHHHHHHHHHHhcCccCHHHHHHHHhHhhccccccChHHHHHHHHHHH
Q 042062 20 ILDRY-FIQLEQLGENNPGFVEDVLTVYFRDSTRTLANIEKELQKTEVNYVELDRYFYNLKGSSASIGANKVRNEVNKTR 98 (142)
Q Consensus 20 ~lD~~-l~~L~~l~~~~~~~~~eli~~F~~d~~~~l~~L~~al~~~~~D~~~l~~~aH~LKGss~~lGA~~L~~~c~~LE 98 (142)
.++.. +..+..+..++|+++++++..|+++.+..+..+..++..+ |+..+.+.||+|||+|+|+|+.+|+..|..+|
T Consensus 5 ~~~~~~~~~~~~~~g~~~~~~~~ll~~f~~~~~~~l~~l~~~l~~~--d~~~~~~~aH~lkg~a~~lg~~~L~~~~~~lE 82 (122)
T COG2198 5 PLSTSDIELLVRLIGGDPDLLRELLAMFLEEAPAQLEQLESALAAE--DNDGLARLAHRLKGSAASLGLPALAQLCQQLE 82 (122)
T ss_pred ccccccHHHHHHHcCCChHHHHHHHHHHHHHhHHHHHHHHHHHhcC--CcHHHHHHHHHHHhHHHhccHHHHHHHHHHHH
Confidence 34444 6677777447899999999999999999999999999999 99999999999999999999999999999999
Q ss_pred HHHHh-cCHHHHHHHHHHHHHH--HHHHHHHHHHH
Q 042062 99 ELCRA-ANWEEAKVSLEQLKVE--HSTLKDKLTAY 130 (142)
Q Consensus 99 ~~~~~-~~~~~~~~~~~~l~~~--~~~~~~~L~~~ 130 (142)
..++. ...+....++.+++.+ ...+...+.++
T Consensus 83 ~~~~~~~~~~~~~~~i~~l~~~~~~~~~~~~~~~~ 117 (122)
T COG2198 83 DALRSGASLEELEELIAELKDELQLDVLALELLTY 117 (122)
T ss_pred HHHHcCCcHHHHHHHHHHHHHHhcchHHHHHHHHH
Confidence 99999 6778899999999999 55555544444
No 3
>PF01627 Hpt: Hpt domain; InterPro: IPR008207 Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions []. Some bacteria can contain up to as many as 200 two-component systems that need tight regulation to prevent unwanted cross-talk []. These pathways have been adapted to response to a wide variety of stimuli, including nutrients, cellular redox state, changes in osmolarity, quorum signals, antibiotics, and more []. Two-component systems are comprised of a sensor histidine kinase (HK) and its cognate response regulator (RR) []. The HK catalyses its own auto-phosphorylation followed by the transfer of the phosphoryl group to the receiver domain on RR; phosphorylation of the RR usually activates an attached output domain, which can then effect changes in cellular physiology, often by regulating gene expression. Some HK are bifunctional, catalysing both the phosphorylation and dephosphorylation of their cognate RR. The input stimuli can regulate either the kinase or phosphatase activity of the bifunctional HK. A variant of the two-component system is the phospho-relay system. Here a hybrid HK auto-phosphorylates and then transfers the phosphoryl group to an internal receiver domain, rather than to a separate RR protein. The phosphoryl group is then shuttled to histidine phosphotransferase (HPT) and subsequently to a terminal RR, which can evoke the desired response [, ]. Signal transducing histidine kinases are the key elements in two-component signal transduction systems, which control complex processes such as the initiation of development in microorganisms [, ]. Examples of histidine kinases are EnvZ, which plays a central role in osmoregulation [], and CheA, which plays a central role in the chemotaxis system []. Histidine kinases usually have an N-terminal ligand-binding domain and a C-terminal kinase domain, but other domains may also be present. The kinase domain is responsible for the autophosphorylation of the histidine with ATP, the phosphotransfer from the kinase to an aspartate of the response regulator, and (with bifunctional enzymes) the phosphotransfer from aspartyl phosphate back to ADP or to water []. The kinase core has a unique fold, distinct from that of the Ser/Thr/Tyr kinase superfamily. HKs can be roughly divided into two classes: orthodox and hybrid kinases [, ]. Most orthodox HKs, typified by the Escherichia coli EnvZ protein, function as periplasmic membrane receptors and have a signal peptide and transmembrane segment(s) that separate the protein into a periplasmic N-terminal sensing domain and a highly conserved cytoplasmic C-terminal kinase core. Members of this family, however, have an integral membrane sensor domain. Not all orthodox kinases are membrane bound, e.g., the nitrogen regulatory kinase NtrB (GlnL) is a soluble cytoplasmic HK []. Hybrid kinases contain multiple phosphodonor and phosphoacceptor sites and use multi-step phospho-relay schemes instead of promoting a single phosphoryl transfer. In addition to the sensor domain and kinase core, they contain a CheY-like receiver domain and a His-containing phosphotransfer (HPt) domain. This entry represents a domain present at the N terminus in proteins which undergo autophosphorylation. The group includes, the gliding motility regulatory protein from Myxococcus xanthus and a number of bacterial chemotaxis proteins.; GO: 0004871 signal transducer activity, 0000160 two-component signal transduction system (phosphorelay); PDB: 3KYJ_A 3KYI_A 3IQT_A 1Y6D_A 2LD6_A 1TQG_A 2R25_A 1OXB_A 1QSP_B 1C03_B ....
Probab=99.70 E-value=2.2e-16 Score=103.45 Aligned_cols=82 Identities=21% Similarity=0.434 Sum_probs=72.0
Q ss_pred HHHHHHHHcHHHHHHHHHHHH---hcCccCHHHHHHHHhHhhccccccChHHHHHHHHHHHHHHHhcCHHH---HHHHHH
Q 042062 41 DVLTVYFRDSTRTLANIEKEL---QKTEVNYVELDRYFYNLKGSSASIGANKVRNEVNKTRELCRAANWEE---AKVSLE 114 (142)
Q Consensus 41 eli~~F~~d~~~~l~~L~~al---~~~~~D~~~l~~~aH~LKGss~~lGA~~L~~~c~~LE~~~~~~~~~~---~~~~~~ 114 (142)
++++.|+++.++.+..|..++ ..+ |++.+.+.+|+|||+++++|+.++..+|..+|..++.++... +...+.
T Consensus 1 ell~~f~~~~~~~~~~l~~~~~~~~~~--d~~~l~~~~H~lkG~a~~~g~~~l~~~~~~lE~~~~~~~~~~~~~~~~~~~ 78 (90)
T PF01627_consen 1 ELLDIFLEEAPEDLEQLEQALQALEQE--DWEELRRLAHRLKGSAGNLGAPRLAELAEQLEQALKSGDKPEAEELEQLLD 78 (90)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHCSSHHC--HHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTHHHHSHHHHHHHH
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHhHh--hHHHHHHHHHHHhhhHHhcCHHHHHHHHHHHHHHHHcCCccchhHHHHHHH
Confidence 579999999999999999999 888 999999999999999999999999999999999999998777 555555
Q ss_pred HHHHHHHHHH
Q 042062 115 QLKVEHSTLK 124 (142)
Q Consensus 115 ~l~~~~~~~~ 124 (142)
.+...+.++.
T Consensus 79 ~l~~~l~~l~ 88 (90)
T PF01627_consen 79 ELEAMLEQLR 88 (90)
T ss_dssp HHHHHHHHHH
T ss_pred HHHHHHHHHh
Confidence 5555555444
No 4
>smart00073 HPT Histidine Phosphotransfer domain. Contains an active histidine residue that mediates phosphotransfer reactions. Domain detected only in eubacteria. This alignment is an extension to that shown in the Cell structure paper.
Probab=99.56 E-value=5.3e-15 Score=97.09 Aligned_cols=84 Identities=24% Similarity=0.241 Sum_probs=71.9
Q ss_pred HHHHHHHHcHHHHHHHHHHHHhcCccCHHHHHHHHhHhhccccccChHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHH
Q 042062 41 DVLTVYFRDSTRTLANIEKELQKTEVNYVELDRYFYNLKGSSASIGANKVRNEVNKTRELCRAANWEEAKVSLEQLKVEH 120 (142)
Q Consensus 41 eli~~F~~d~~~~l~~L~~al~~~~~D~~~l~~~aH~LKGss~~lGA~~L~~~c~~LE~~~~~~~~~~~~~~~~~l~~~~ 120 (142)
+++..|+++.++.+..|..++..+ |+..+.+.+|+|||+|+++|+..|..+|..+|..++... .+...+...+...|
T Consensus 2 e~~~~f~~~~~~~l~~l~~~~~~~--~~~~l~~~~H~LKG~a~~~g~~~l~~~~~~lE~~~~~~~-~~~~~~~~~l~~~~ 78 (87)
T smart00073 2 EELAEFLQSLEEGLLELEKALDAQ--DVNEIFRAAHTLKGSAGSLGLQQLAQLCHQLENLLDAAR-SGEVELTPDLLDLL 78 (87)
T ss_pred hHHHHHHHHHHHHHHHHHhCcCHh--HHHHHHHHHHhhhhhHHhcCHHHHHHHHHHHHHHHHHHH-cCCCCCCHHHHHHH
Confidence 678999999999999999999888 999999999999999999999999999999999988644 22335666777777
Q ss_pred HHHHHHH
Q 042062 121 STLKDKL 127 (142)
Q Consensus 121 ~~~~~~L 127 (142)
..+...|
T Consensus 79 ~~~~~~l 85 (87)
T smart00073 79 LELVDVL 85 (87)
T ss_pred HHHHHHH
Confidence 6666654
No 5
>cd00088 HPT Histidine Phosphotransfer domain, involved in signalling through a two part component systems in which an autophosphorylating histidine protein kinase serves as a phosphoryl donor to a response regulator protein; the response regulator protein is modulated by phosphorylation and dephosphorylation of a conserved aspartic acid residue; two-component proteins are abundant in most eubacteria; In E. coli there are 62 two-component proteins involved in a variety of processes such as chemotaxis, osmoregulation, metabolism and transport 1; also present in both Gram positive and Gram negative pathogenic bacteria where they regulate basic housekeeping functions and control expression of toxins and other proteins important for pathogenesis; in archaea and eukaryotes, two-component pathways constitute a very small number of all signaling systems; in fungi they mediate environmental stress responses and, in pathogenic yeast, hyphal development. In Dictyostelium and in plants, they are i
Probab=99.47 E-value=3.5e-13 Score=89.91 Aligned_cols=64 Identities=25% Similarity=0.423 Sum_probs=60.6
Q ss_pred HHHHHHHHHcHHHHHHHHHHHHh----cCccCHHHHHHHHhHhhccccccChHHHHHHHHHHHHHHHhcC
Q 042062 40 EDVLTVYFRDSTRTLANIEKELQ----KTEVNYVELDRYFYNLKGSSASIGANKVRNEVNKTRELCRAAN 105 (142)
Q Consensus 40 ~eli~~F~~d~~~~l~~L~~al~----~~~~D~~~l~~~aH~LKGss~~lGA~~L~~~c~~LE~~~~~~~ 105 (142)
.+++..|+++.++.+..|..++. .+ |+..+.+.+|+|||+++++|+..|..+|..+|..++.+.
T Consensus 2 ~~l~~~f~~~~~~~l~~l~~~~~~~~~~~--d~~~l~~~~H~LkGsa~~~G~~~l~~~~~~lE~~~~~~~ 69 (94)
T cd00088 2 EELLELFLEEAEELLEELERALLELEDAE--DLNEIFRAAHTLKGSAASLGLQRLAQLAHQLEDLLDALR 69 (94)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHcCCHH--HHHHHHHHHHhhhhHHhcCChHHHHHHHHHHHHHHHHHH
Confidence 47899999999999999999999 77 999999999999999999999999999999999999854
No 6
>TIGR02956 TMAO_torS TMAO reductase sytem sensor TorS. This protein, TorS, is part of a regulatory system for the torCAD operon that encodes the pterin molybdenum cofactor-containing enzyme trimethylamine-N-oxide (TMAO) reductase (TorA), a cognate chaperone (TorD), and a penta-haem cytochrome (TorC). TorS works together with the inducer-binding protein TorT and the response regulator TorR. TorS contains histidine kinase ATPase (pfam02518), HAMP (pfam00672), phosphoacceptor (pfam00512), and phosphotransfer (pfam01627) domains and a response regulator receiver domain (pfam00072).
Probab=99.38 E-value=2.9e-12 Score=114.66 Aligned_cols=105 Identities=14% Similarity=0.231 Sum_probs=92.6
Q ss_pred hhhHH-HHHHhhcCCCChhhHHHHHHHHHHcHHHHHHHHHHHHhcCccCHHHHHHHHhHhhccccccChHHHHHHHHHHH
Q 042062 20 ILDRY-FIQLEQLGENNPGFVEDVLTVYFRDSTRTLANIEKELQKTEVNYVELDRYFYNLKGSSASIGANKVRNEVNKTR 98 (142)
Q Consensus 20 ~lD~~-l~~L~~l~~~~~~~~~eli~~F~~d~~~~l~~L~~al~~~~~D~~~l~~~aH~LKGss~~lGA~~L~~~c~~LE 98 (142)
++|.. +...... .+++.+.+++..|+++.+..+..|..++..+ |+..+++.+|+|||+++++|+..|..+|+.||
T Consensus 863 ll~~~~~~~~~~~--~~~~~~~~~~~~f~~~~~~~~~~l~~~~~~~--d~~~~~~~~H~lkg~~~~~g~~~l~~~~~~le 938 (968)
T TIGR02956 863 LLDEEQLQQDIEV--LGVEKVRQLVALFKTSSAEQLEELSAARAVD--DDAQIKKLAHKLKGSAGSLGLTQLTQLCQQLE 938 (968)
T ss_pred hcCHHHHHHHHHh--cCcHHHHHHHHHHHHhhHHHHHHHHHHHhCC--CHHHHHHHHHHHHHHHHHhCHHHHHHHHHHHH
Confidence 66666 5544333 4558899999999999999999999999999 99999999999999999999999999999999
Q ss_pred HHHHhcCHHHHHHHHHHHHHHHHHHHHHHHHH
Q 042062 99 ELCRAANWEEAKVSLEQLKVEHSTLKDKLTAY 130 (142)
Q Consensus 99 ~~~~~~~~~~~~~~~~~l~~~~~~~~~~L~~~ 130 (142)
..++.|+. ....+..++..|..+..+|+.|
T Consensus 939 ~~~~~~~~--~~~~~~~l~~~~~~~~~~l~~~ 968 (968)
T TIGR02956 939 KQGKTGAL--ELSDIDEIKQAWQASKTALDQW 968 (968)
T ss_pred HhcccCCc--chhHHHHHHHHHHHHHHHHHhC
Confidence 99999987 4577899999999999988764
No 7
>PRK10618 phosphotransfer intermediate protein in two-component regulatory system with RcsBC; Provisional
Probab=99.15 E-value=2.4e-10 Score=102.99 Aligned_cols=83 Identities=12% Similarity=0.139 Sum_probs=77.1
Q ss_pred HHHHHHHHHcHHHHHHHHHHHHhcCccCHHHHHHHHhHhhccccccChHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHH
Q 042062 40 EDVLTVYFRDSTRTLANIEKELQKTEVNYVELDRYFYNLKGSSASIGANKVRNEVNKTRELCRAANWEEAKVSLEQLKVE 119 (142)
Q Consensus 40 ~eli~~F~~d~~~~l~~L~~al~~~~~D~~~l~~~aH~LKGss~~lGA~~L~~~c~~LE~~~~~~~~~~~~~~~~~l~~~ 119 (142)
..++..|++.+|..+..|..++.++ |+..+...||+|||+++++|+..+..+|..||+.++.++..++...+.+|...
T Consensus 810 s~~~~lF~~t~~~di~~L~~~~~~~--D~~~l~~~aHrLKG~~aml~l~~l~~~~~~LE~~i~~~~~~~i~~~i~~id~~ 887 (894)
T PRK10618 810 SDYYALFVDTVPDDVKRLYTEAATS--DFASLAQTAHRLKGVFAMLNLVPGKQLCETLEHLIREKDEPGIENYISDIDSF 887 (894)
T ss_pred hhHHHHHHHhhHHHHHHHHHHHhcc--CHHHHHHHHHHHHHHHHHcChHHHHHHHHHHHHHHhhCChHHHHHHHHHHHHH
Confidence 4456899999999999999999999 99999999999999999999999999999999999999999999999988887
Q ss_pred HHHHH
Q 042062 120 HSTLK 124 (142)
Q Consensus 120 ~~~~~ 124 (142)
+.++.
T Consensus 888 v~~ll 892 (894)
T PRK10618 888 VKSLL 892 (894)
T ss_pred HHHHh
Confidence 76654
No 8
>PRK11091 aerobic respiration control sensor protein ArcB; Provisional
Probab=99.12 E-value=7.6e-10 Score=97.62 Aligned_cols=112 Identities=20% Similarity=0.274 Sum_probs=98.9
Q ss_pred hhhHH-HHHHhhcCCCChhhHHHHHHHHHHcHHHHHHHHHHHHhcCccCHHHHHHHHhHhhccccccChHHHHHHHHHHH
Q 042062 20 ILDRY-FIQLEQLGENNPGFVEDVLTVYFRDSTRTLANIEKELQKTEVNYVELDRYFYNLKGSSASIGANKVRNEVNKTR 98 (142)
Q Consensus 20 ~lD~~-l~~L~~l~~~~~~~~~eli~~F~~d~~~~l~~L~~al~~~~~D~~~l~~~aH~LKGss~~lGA~~L~~~c~~LE 98 (142)
.+|.. +..+.+. .++..+.+.+..|.+..+..+..+..++..+ |+..+...||+|||+++++|+..++.+|+.+|
T Consensus 665 ~l~~~~l~~~~~~--~g~~~~~~~l~~~~~~~~~~~~~l~~~l~~~--d~~~~~~~ah~l~g~~~~~g~~~l~~~~~~le 740 (779)
T PRK11091 665 LLDIPMLEQYVEL--VGPKLITDSLAVFEKMMPGYLSVLDSNLTAR--DQKGIVEEAHKIKGAAGSVGLRHLQQLAQQIQ 740 (779)
T ss_pred ccCHHHHHHHHHh--cCHHHHHHHHHHHHHhhHHHHHHHHHHHHCC--CHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHh
Confidence 45555 5555444 3346778899999999999999999999999 99999999999999999999999999999999
Q ss_pred HHHHhcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 042062 99 ELCRAANWEEAKVSLEQLKVEHSTLKDKLTAYFELVA 135 (142)
Q Consensus 99 ~~~~~~~~~~~~~~~~~l~~~~~~~~~~L~~~l~~~~ 135 (142)
.....+.++....++.++..+|......|+.|+...+
T Consensus 741 ~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~ 777 (779)
T PRK11091 741 SPDLPAWWDNVQDWVEELKNEWRHDVEVLKAWLAQAE 777 (779)
T ss_pred CcCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 9999989999999999999999999999999987643
No 9
>PRK11107 hybrid sensory histidine kinase BarA; Provisional
Probab=98.72 E-value=2e-07 Score=83.14 Aligned_cols=97 Identities=15% Similarity=0.197 Sum_probs=84.8
Q ss_pred CChhhHHHHHHHHHHcHHHHHHHHHHHHhcCccCHHHHHHHHhHhhccccccChHHHHHHHHHHHHHHHhc-CHHHHHHH
Q 042062 34 NNPGFVEDVLTVYFRDSTRTLANIEKELQKTEVNYVELDRYFYNLKGSSASIGANKVRNEVNKTRELCRAA-NWEEAKVS 112 (142)
Q Consensus 34 ~~~~~~~eli~~F~~d~~~~l~~L~~al~~~~~D~~~l~~~aH~LKGss~~lGA~~L~~~c~~LE~~~~~~-~~~~~~~~ 112 (142)
+.+....+++..|.+..+.....+..++... |+..+...+|++||+++++|+..+..+|..+|..++.+ ..+.+...
T Consensus 821 ~~~~~~~~~l~~~~~~~~~~~~~l~~~~~~~--~~~~~~~~~h~l~g~~~~~g~~~l~~~~~~le~~~~~~~~~~~~~~~ 898 (919)
T PRK11107 821 GKPDLARDMLQMLLDFLPEVRNKVEEALAGE--DPEGLLDLIHKLHGSCSYSGVPRLKKLCQLIEQQLRSGTSVEDLEPE 898 (919)
T ss_pred CCHHHHHHHHHHHHHhHHHHHHHHHHHHHCC--CHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHcCCChhhHHHH
Confidence 4567888999999999999999999999999 99999999999999999999999999999999999976 45667777
Q ss_pred HHHHHHHHHHHHHHHHHHHH
Q 042062 113 LEQLKVEHSTLKDKLTAYFE 132 (142)
Q Consensus 113 ~~~l~~~~~~~~~~L~~~l~ 132 (142)
+..+..++.++...+..+++
T Consensus 899 ~~~~~~~~~~~~~~~~~~~~ 918 (919)
T PRK11107 899 LLELLDEMENVARAAKKVLS 918 (919)
T ss_pred HHHHHHHHHHHHHHHHHHhh
Confidence 77777777777777776653
No 10
>PRK11466 hybrid sensory histidine kinase TorS; Provisional
Probab=98.70 E-value=2.1e-07 Score=83.33 Aligned_cols=66 Identities=14% Similarity=0.182 Sum_probs=61.5
Q ss_pred ChhhHHHHHHHHHHcHHHHHHHHHHHHhcCccCHHHHHHHHhHhhccccccChHHHHHHHHHHHHHHH
Q 042062 35 NPGFVEDVLTVYFRDSTRTLANIEKELQKTEVNYVELDRYFYNLKGSSASIGANKVRNEVNKTRELCR 102 (142)
Q Consensus 35 ~~~~~~eli~~F~~d~~~~l~~L~~al~~~~~D~~~l~~~aH~LKGss~~lGA~~L~~~c~~LE~~~~ 102 (142)
+++.+.+++..|.++.+..+..+..+...+ |+..+++.||+|||+++++|+..+...|..+|..+.
T Consensus 821 ~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~--~~~~~~~~ah~lkg~~~~lg~~~l~~~~~~le~~~~ 886 (914)
T PRK11466 821 GTEKIHEWLALFKQHALPLLDEIDIARASQ--DSEKIKRAAHQLKSSCSSLGMRQASQACAQLEQQPL 886 (914)
T ss_pred CHHHHHHHHHHHHHhhHHHHHHHHHHHHCC--CHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhCCCC
Confidence 446678899999999999999999999999 999999999999999999999999999999998764
No 11
>COG0643 CheA Chemotaxis protein histidine kinase and related kinases [Cell motility and secretion / Signal transduction mechanisms]
Probab=98.22 E-value=8.6e-06 Score=72.21 Aligned_cols=89 Identities=17% Similarity=0.238 Sum_probs=64.6
Q ss_pred hhHHHHHHHHHHcHHHHHHHHHHHHhc---CccC---HHHHHHHHhHhhccccccChHHHHHHHHHHHH---HHHhcCHH
Q 042062 37 GFVEDVLTVYFRDSTRTLANIEKELQK---TEVN---YVELDRYFYNLKGSSASIGANKVRNEVNKTRE---LCRAANWE 107 (142)
Q Consensus 37 ~~~~eli~~F~~d~~~~l~~L~~al~~---~~~D---~~~l~~~aH~LKGss~~lGA~~L~~~c~~LE~---~~~~~~~~ 107 (142)
....+++..|++++++.+..|...+-. .+.| ...+.+.||+|||+|+.+|...+..+|..+|. ..++|...
T Consensus 4 ~~~~~~~~~F~~Ea~e~l~~l~~~Ll~LE~~~~d~~~ln~ifRaaHTlKG~a~~~g~~~l~~l~H~~E~~ld~~r~g~~~ 83 (716)
T COG0643 4 MDMEEILEDFLEEAEELLQALEQALLALEPDPEDLDLLNAIFRAAHTLKGGAGTLGLTTLAELAHAMEDLLDALRNGELE 83 (716)
T ss_pred hHHHHHHHHHHHhhHHHHHHHHHhHhhccCCCCCHHHHHHHHHHHHhhhhhhhhcChhHHHHHHHHHHHHHHHHhcCCcc
Confidence 446688999999999999999985542 2223 45788999999999999999999999999997 45566543
Q ss_pred HHHHHHHHHHHHHHHHHH
Q 042062 108 EAKVSLEQLKVEHSTLKD 125 (142)
Q Consensus 108 ~~~~~~~~l~~~~~~~~~ 125 (142)
--..++..+-.+...+..
T Consensus 84 ~~~~l~d~~l~~~D~l~~ 101 (716)
T COG0643 84 LTSELLDLLLEALDALEE 101 (716)
T ss_pred CcHHHHHHHhhhhHHHHH
Confidence 323444444444333333
No 12
>PRK10547 chemotaxis protein CheA; Provisional
Probab=98.10 E-value=2.3e-05 Score=69.16 Aligned_cols=63 Identities=17% Similarity=0.317 Sum_probs=52.8
Q ss_pred HHHHHHHHHcHHHHHHHHHHHHh---cCccC---HHHHHHHHhHhhccccccChHHHHHHHHHHHHHHH
Q 042062 40 EDVLTVYFRDSTRTLANIEKELQ---KTEVN---YVELDRYFYNLKGSSASIGANKVRNEVNKTRELCR 102 (142)
Q Consensus 40 ~eli~~F~~d~~~~l~~L~~al~---~~~~D---~~~l~~~aH~LKGss~~lGA~~L~~~c~~LE~~~~ 102 (142)
.+++..|++++.+.++.|+..+- ..+.| ...+.+.+|+|||+|+.+|...+..+|..+|....
T Consensus 4 ~~~l~~F~~Ea~E~l~~le~~Ll~LE~~p~d~e~in~lFRa~HTiKG~a~~~g~~~i~~l~H~~E~lld 72 (670)
T PRK10547 4 SDFYQTFFDEADELLADMEQHLLVLDPEAPDAEQLNAIFRAAHSIKGGAGTFGFTVLQETTHLMENLLD 72 (670)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhccCCCCHHHHHHHHHHHHhhhhHHhhcCchHHHHHHHHHHHHHH
Confidence 47789999999999998888765 22224 45788999999999999999999999999996544
No 13
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=97.81 E-value=0.00073 Score=62.54 Aligned_cols=102 Identities=12% Similarity=0.200 Sum_probs=79.4
Q ss_pred HHhhcCCCChhhHHHHHHHHHHcHHHHHHHHHHHHhcCccCHHHHHHHHhHhhccccccChHHHHHHHHHHHHHHHhcC-
Q 042062 27 QLEQLGENNPGFVEDVLTVYFRDSTRTLANIEKELQKTEVNYVELDRYFYNLKGSSASIGANKVRNEVNKTRELCRAAN- 105 (142)
Q Consensus 27 ~L~~l~~~~~~~~~eli~~F~~d~~~~l~~L~~al~~~~~D~~~l~~~aH~LKGss~~lGA~~L~~~c~~LE~~~~~~~- 105 (142)
.+......+...+++++..+...+...+..+..+...+ |...+..++|++||++..+|+..+...|..+|......+
T Consensus 1090 ~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~h~~~g~~~~l~~~~l~~~~~~~e~~~~~~~~ 1167 (1197)
T PRK09959 1090 ALKNNTANDLQLMQEILMTFQHETHKDLPAAFHALEAG--DNRTFHQCIHRIHGAANILNLQKLINISHQLEITPVSDDS 1167 (1197)
T ss_pred HHHhHhCCCHHHHHHHHHHHHHhhHHHHHHHHHHHHcC--CHHHHHHHHHHHHHHHHHcCHHHHHHHHHHHHHhhhcCCc
Confidence 33333334557788999999999999999999999999 999999999999999999999999999999998887654
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Q 042062 106 WEEAKVSLEQLKVEHSTLKDKLTAY 130 (142)
Q Consensus 106 ~~~~~~~~~~l~~~~~~~~~~L~~~ 130 (142)
.+.+...+..+..........+..+
T Consensus 1168 ~~~l~~~~~~~~~~~~~~~~~~~~~ 1192 (1197)
T PRK09959 1168 KPEILQLLNSVKEHIAELDQEIAVF 1192 (1197)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 3455555666665555555444444
No 14
>PRK15347 two component system sensor kinase SsrA; Provisional
Probab=97.07 E-value=0.0022 Score=57.54 Aligned_cols=78 Identities=17% Similarity=0.200 Sum_probs=58.7
Q ss_pred HHHHHHHcHHHHHHHHHHHHhcCccCHHHHHHHHhHhhccccccChHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHH
Q 042062 42 VLTVYFRDSTRTLANIEKELQKTEVNYVELDRYFYNLKGSSASIGANKVRNEVNKTRELCRAANWEEAKVSLEQLKVEHS 121 (142)
Q Consensus 42 li~~F~~d~~~~l~~L~~al~~~~~D~~~l~~~aH~LKGss~~lGA~~L~~~c~~LE~~~~~~~~~~~~~~~~~l~~~~~ 121 (142)
+-..+.+.....+..+..+++.+ | .+.+.+|.+||+++.+|+..+...|..+|..++.+.... ...+..++..+.
T Consensus 838 l~~~~~~~l~~~~~~~~~~~~~~--~--~l~~~~h~i~~~~~~~g~~~l~~~~~~~e~~~~~~~~~~-~~~~~~~~~~~~ 912 (921)
T PRK15347 838 LNSKLYQSLLLLLAQIEQAVENQ--E--VLSQLLHTLKGCAGQAGLTELQCAVIDLENALETGEILS-LEELTDLRELIH 912 (921)
T ss_pred HHHHHHHHHHHHHHHHHHHHhCH--H--HHHHHHHHHHHHHHHcCHHHHHHHHHHHHHHHhcCCCCC-HHHHHHHHHHHH
Confidence 34455566677888889998887 5 899999999999999999999999999999998875432 222444444444
Q ss_pred HHH
Q 042062 122 TLK 124 (142)
Q Consensus 122 ~~~ 124 (142)
.+.
T Consensus 913 ~~~ 915 (921)
T PRK15347 913 ALF 915 (921)
T ss_pred HHh
Confidence 333
No 15
>TIGR03042 PS_II_psbQ_bact photosystem II protein PsbQ. This protein through the member sll1638 from Synechocystis sp. PCC 6803, was shown to be part of the cyanobacteria photosystem II. It is homologous to (but quite diverged from) the chloroplast PsbQ protein, called oxygen-evolving enhancer protein 3 (OEE3). We designate this cyanobacteria protein PsbQ by homology.
Probab=88.70 E-value=5.1 Score=28.94 Aligned_cols=79 Identities=13% Similarity=0.241 Sum_probs=49.9
Q ss_pred HHHHHHc---HHHHHHHHHHHHhcCccCHHHHHHHHhHhhccccccCh---------------------HHHHHHHHHHH
Q 042062 43 LTVYFRD---STRTLANIEKELQKTEVNYVELDRYFYNLKGSSASIGA---------------------NKVRNEVNKTR 98 (142)
Q Consensus 43 i~~F~~d---~~~~l~~L~~al~~~~~D~~~l~~~aH~LKGss~~lGA---------------------~~L~~~c~~LE 98 (142)
|..|.+. +.+.+.+|+..++++ ||..++...| |..+.++- ..|.+....|-
T Consensus 38 i~~~~~~i~~~~~r~~eLk~lI~kk--~W~~vrn~ir---gp~g~Lr~dl~~l~~sl~p~dqk~a~~L~~~Lf~~L~~LD 112 (142)
T TIGR03042 38 IQRQAEGIEAAKDRLPELASLVAKE--DWVFTRNLIH---GPMGEVRREMTYLNQSLLPKDQKEALALAKELKDDLEKLD 112 (142)
T ss_pred HHHHHHHHHHHHHhhHHHHHHHhhc--chHHHHHHHh---ccHHHHHHHHHHHHHccCHHhHHHHHHHHHHHHHHHHHHH
Confidence 5555444 778899999999999 9999998866 45554442 22333334444
Q ss_pred HHHHhcCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 042062 99 ELCRAANWEEAKVSLEQLKVEHSTLKDKLTAYFEL 133 (142)
Q Consensus 99 ~~~~~~~~~~~~~~~~~l~~~~~~~~~~L~~~l~~ 133 (142)
.+++.+|... ...+|..+...|+.|+++
T Consensus 113 ~AA~~kd~~~-------a~k~Y~~av~~~dafl~~ 140 (142)
T TIGR03042 113 EAARLQDGPQ-------AQKAYQKAAADFDAYLDL 140 (142)
T ss_pred HHHHhcCHHH-------HHHHHHHHHHHHHHHHhh
Confidence 5555555444 444566666666666654
No 16
>PF13779 DUF4175: Domain of unknown function (DUF4175)
Probab=82.49 E-value=10 Score=34.88 Aligned_cols=85 Identities=14% Similarity=0.198 Sum_probs=60.1
Q ss_pred ChhhHHHHHHHHHHcHHHHHHHHHHHHhcCccCHHHHHHHHhHhhccccccChHHHHHHHHHHHHHHHhcCHHHHHHHHH
Q 042062 35 NPGFVEDVLTVYFRDSTRTLANIEKELQKTEVNYVELDRYFYNLKGSSASIGANKVRNEVNKTRELCRAANWEEAKVSLE 114 (142)
Q Consensus 35 ~~~~~~eli~~F~~d~~~~l~~L~~al~~~~~D~~~l~~~aH~LKGss~~lGA~~L~~~c~~LE~~~~~~~~~~~~~~~~ 114 (142)
+++=+.+++..+.+-..+++.+|.+-..+. .-.. .-+.--+.+.+++-..|..+...||+.+++|+.+.+..+++
T Consensus 490 s~eEI~rLm~eLR~A~~~ym~~LAeq~~~~--~~~~---~~p~~~~~~~~~~~~dL~~mmd~ie~la~~G~~~~A~q~L~ 564 (820)
T PF13779_consen 490 SDEEIARLMQELREAMQDYMQALAEQAQRN--PQQQ---DQPPDQGNSQMMSQQDLQRMMDRIEELARSGRMDEARQLLE 564 (820)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHhHhC--cccc---cCcccchhhhccCHHHHHHHHHHHHHHHHcCCHHHHHHHHH
Confidence 344556666666666666676666665543 1110 00111356778999999999999999999999999999999
Q ss_pred HHHHHHHHHH
Q 042062 115 QLKVEHSTLK 124 (142)
Q Consensus 115 ~l~~~~~~~~ 124 (142)
++.+-++.++
T Consensus 565 qlq~mmenmq 574 (820)
T PF13779_consen 565 QLQQMMENMQ 574 (820)
T ss_pred HHHHHHHhcc
Confidence 9888776544
No 17
>cd08323 CARD_APAF1 Caspase activation and recruitment domain similar to that found in Apoptotic Protease-Activating Factor 1. Caspase activation and recruitment domain (CARD) similar to that found in apoptotic protease-activating factor 1 (APAF-1), which is an activator of caspase-9. APAF-1 contains WD-40 repeats, a CARD, and an ATPase domain. Upon stimulation, APAF-1, together with caspase-9, forms the heptameric 'apoptosome', which leads to the processing and activation of caspase-9, starting a caspase cascade which leads to apoptosis. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and DED (Death Effect
Probab=82.04 E-value=8.6 Score=25.27 Aligned_cols=66 Identities=6% Similarity=0.110 Sum_probs=51.7
Q ss_pred HHHHHhccCcchhhHH-HHHHhhcCCCChhhHHHHHHHHHHcHHHHHHHHHHHHhcCccCHHHHHHHHhH
Q 042062 9 AEMRQSFFDEEILDRY-FIQLEQLGENNPGFVEDVLTVYFRDSTRTLANIEKELQKTEVNYVELDRYFYN 77 (142)
Q Consensus 9 ~~~~~~~~~~~~lD~~-l~~L~~l~~~~~~~~~eli~~F~~d~~~~l~~L~~al~~~~~D~~~l~~~aH~ 77 (142)
..++..+..+|+++.+ .+.++.-+ ...+-...+|+....-.+.-+.....++... .|+.++.+.|.
T Consensus 17 ~~ild~L~~~gvlt~~~~e~I~~~~-t~~~qa~~Lld~L~trG~~Af~~F~~aL~~~--~~~~La~lL~~ 83 (86)
T cd08323 17 SYIMDHMISDGVLTLDEEEKVKSKA-TQKEKAVMLINMILTKDNHAYVSFYNALLHE--GYKDLALLLHD 83 (86)
T ss_pred HHHHHHHHhcCCCCHHHHHHHHcCC-ChHHHHHHHHHHHHhcCHHHHHHHHHHHHhc--CChHHHHHHhc
Confidence 4467778889999999 88888872 2245667888988888999999999998876 68888777653
No 18
>PF07743 HSCB_C: HSCB C-terminal oligomerisation domain; InterPro: IPR009073 This entry represents the C-terminal oligomerisation domain found in HscB (heat shock cognate protein B), which is also known as HSC20 (20K heat shock cognate protein). HscB acts as a co-chaperone to regulate the ATPase activity and peptide-binding specificity of the molecular chaperone HscA, also known as HSC66 (HSP70 class). HscB proteins contain two domains, an N-terminal J-domain, which is involved in interactions with HscA, connected by a short loop to the C-terminal oligomerisation domain; the two domains make contact through a hydrophobic interface. The core of the oligomerisation domain is thought to bind and target proteins to HscA and consists of an open, three-helical bundle []. HscB, along with HscA, has been shown to play a role in the biogenesis of iron-sulphur proteins.; GO: 0006457 protein folding; PDB: 1FPO_C 3BVO_B 3HHO_A 3UO2_B 3UO3_B.
Probab=81.83 E-value=10 Score=23.82 Aligned_cols=41 Identities=10% Similarity=0.157 Sum_probs=24.8
Q ss_pred hhHHHHHHHHHHcHHHHHHHHHHHHhcCccCHHHHHHHHhHhh
Q 042062 37 GFVEDVLTVYFRDSTRTLANIEKELQKTEVNYVELDRYFYNLK 79 (142)
Q Consensus 37 ~~~~eli~~F~~d~~~~l~~L~~al~~~~~D~~~l~~~aH~LK 79 (142)
.-+..+....-......+..|..++..+ ||.......+.||
T Consensus 27 ~~L~~l~~~~~~~~~~~~~~l~~~f~~~--d~~~A~~~~~kLk 67 (78)
T PF07743_consen 27 AELEELKKEIEERIKELIKELAEAFDAK--DWEEAKEALRKLK 67 (78)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHTT---HHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHccC--cHHHHHHHHHHHH
Confidence 4444555555555556666666666666 7777777666664
No 19
>TIGR02302 aProt_lowcomp conserved hypothetical protein TIGR02302. Members of this family are long (~850 residue) bacterial proteins from the alpha Proteobacteria. Each has 2-3 predicted transmembrane helices near the N-terminus and a long C-terminal region that includes stretches of Gln/Gly-rich low complexity sequence, predicted by TMHMM to be outside the membrane. In Bradyrhizobium japonicum, two tandem reading frames are together homologous the single members found in other species; the cutoffs scores are set low enough that the longer scores above the trusted cutoff and the shorter above the noise cutoff for this model.
Probab=81.72 E-value=13 Score=34.38 Aligned_cols=84 Identities=13% Similarity=0.221 Sum_probs=60.7
Q ss_pred ChhhHHHHHHHHHHcHHHHHHHHHHHHhcCccCHHHHHHHHhHhhccccccChHHHHHHHHHHHHHHHhcCHHHHHHHHH
Q 042062 35 NPGFVEDVLTVYFRDSTRTLANIEKELQKTEVNYVELDRYFYNLKGSSASIGANKVRNEVNKTRELCRAANWEEAKVSLE 114 (142)
Q Consensus 35 ~~~~~~eli~~F~~d~~~~l~~L~~al~~~~~D~~~l~~~aH~LKGss~~lGA~~L~~~c~~LE~~~~~~~~~~~~~~~~ 114 (142)
+++=+.+|+..+.+-..+++.+|.+...+++ +-.. -..-+.+.+++-..|.++...||+++++|+.+++..+++
T Consensus 521 sdeEI~~Lm~eLR~Am~~ym~~LAeq~~~~~-~~~~-----~~~~~~~~~l~~~dLq~Mmd~ieela~~G~~~~A~qlL~ 594 (851)
T TIGR02302 521 SDEEIKQLTDKLRAAMQTYMRQLAQQLRNNP-QQLA-----RPLDPNTKVLRQQDLQNMMDQIENLARSGDRDQAKQLLS 594 (851)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHhhhCc-cccc-----ccCCccccccCHHHHHHHHHHHHHHHHcCCHHHHHHHHH
Confidence 3455667777777777777777766555430 1000 111234578999999999999999999999999999999
Q ss_pred HHHHHHHHHH
Q 042062 115 QLKVEHSTLK 124 (142)
Q Consensus 115 ~l~~~~~~~~ 124 (142)
+|.+-++.++
T Consensus 595 qlq~mmenlq 604 (851)
T TIGR02302 595 QLQQMMNNLQ 604 (851)
T ss_pred HHHHHHHHHh
Confidence 9988887766
No 20
>TIGR03042 PS_II_psbQ_bact photosystem II protein PsbQ. This protein through the member sll1638 from Synechocystis sp. PCC 6803, was shown to be part of the cyanobacteria photosystem II. It is homologous to (but quite diverged from) the chloroplast PsbQ protein, called oxygen-evolving enhancer protein 3 (OEE3). We designate this cyanobacteria protein PsbQ by homology.
Probab=80.62 E-value=19 Score=26.02 Aligned_cols=61 Identities=13% Similarity=0.172 Sum_probs=43.0
Q ss_pred HHHHhhc-CCCChhhHHHHHHHHHHcHHHHHHHHHHHHhcCccCHHHHHHHHhHhhccccccCh
Q 042062 25 FIQLEQL-GENNPGFVEDVLTVYFRDSTRTLANIEKELQKTEVNYVELDRYFYNLKGSSASIGA 87 (142)
Q Consensus 25 l~~L~~l-~~~~~~~~~eli~~F~~d~~~~l~~L~~al~~~~~D~~~l~~~aH~LKGss~~lGA 87 (142)
+.+|+.+ +..+=.+++..|..=+.+....+..|.+.+-.. |-+.+++++-.|++.-.+++.
T Consensus 52 ~~eLk~lI~kk~W~~vrn~irgp~g~Lr~dl~~l~~sl~p~--dqk~a~~L~~~Lf~~L~~LD~ 113 (142)
T TIGR03042 52 LPELASLVAKEDWVFTRNLIHGPMGEVRREMTYLNQSLLPK--DQKEALALAKELKDDLEKLDE 113 (142)
T ss_pred hHHHHHHHhhcchHHHHHHHhccHHHHHHHHHHHHHccCHH--hHHHHHHHHHHHHHHHHHHHH
Confidence 6666666 555555566666666666777777777776666 888888888888887776664
No 21
>TIGR00714 hscB Fe-S protein assembly co-chaperone HscB. This model describes the small subunit, Hsc20 (20K heat shock cognate protein) of a pair of proteins Hsc66-Hsc20, related to the DnaK-DnaJ heat shock proteins, which also serve as molecular chaperones. Hsc20, unlike DnaJ, appears not to have chaperone activity on its own, but to act solely as a regulatory subunit for Hsc66 (i.e., to be a co-chaperone). The gene for Hsc20 in E. coli, hscB, is not induced by heat shock.
Probab=76.92 E-value=18 Score=26.23 Aligned_cols=66 Identities=12% Similarity=0.179 Sum_probs=44.4
Q ss_pred HHHHHHHhcCccCHHHHHHHHhHhhccccccChHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 042062 55 ANIEKELQKTEVNYVELDRYFYNLKGSSASIGANKVRNEVNKTRELCRAANWEEAKVSLEQLKVEHSTLKDKLTAYF 131 (142)
Q Consensus 55 ~~L~~al~~~~~D~~~l~~~aH~LKGss~~lGA~~L~~~c~~LE~~~~~~~~~~~~~~~~~l~~~~~~~~~~L~~~l 131 (142)
+.+..+-..+ |...+..+.+.++ ..+..+...++.+...++++.+...+.+|+= |..+...+..+.
T Consensus 88 E~lee~~~~~--d~~~L~~l~~~~~--------~~~~~~~~~l~~~~~~~d~~~A~~~~~kLky-~~kl~~~i~~~~ 153 (157)
T TIGR00714 88 EELDEIEQAK--DEARLESFIKRVK--------KMFQTRHQLLVEQLDNQTWAAAADYTRKLRF-LDKLRSSAEQLE 153 (157)
T ss_pred HHHHHHHhCC--CHHHHHHHHHHHH--------HHHHHHHHHHHHHHhcCCHHHHHHHHHHHHH-HHHHHHHHHHHH
Confidence 3444444455 7777777777665 3566677778877888888888888777764 566666665543
No 22
>PF05757 PsbQ: Oxygen evolving enhancer protein 3 (PsbQ); InterPro: IPR008797 Oxygenic photosynthesis uses two multi-subunit photosystems (I and II) located in the cell membranes of cyanobacteria and in the thylakoid membranes of chloroplasts in plants and algae. Photosystem II (PSII) has a P680 reaction centre containing chlorophyll 'a' that uses light energy to carry out the oxidation (splitting) of water molecules, and to produce ATP via a proton pump. Photosystem I (PSI) has a P700 reaction centre containing chlorophyll that takes the electron and associated hydrogen donated from PSII to reduce NADP+ to NADPH. Both ATP and NADPH are subsequently used in the light-independent reactions to convert carbon dioxide to glucose using the hydrogen atom extracted from water by PSII, releasing oxygen as a by-product. PSII is a multisubunit protein-pigment complex containing polypeptides both intrinsic and extrinsic to the photosynthetic membrane [, ]. Within the core of the complex, the chlorophyll and beta-carotene pigments are mainly bound to the antenna proteins CP43 (PsbC) and CP47 (PsbB), which pass the excitation energy on to the reaction centre proteins D1 (Qb, PsbA) and D2 (Qa, PsbD) that bind all the redox-active cofactors involved in the energy conversion process. The PSII oxygen-evolving complex (OEC) oxidises water to provide protons for use by PSI, and consists of OEE1 (PsbO), OEE2 (PsbP) and OEE3 (PsbQ). The remaining subunits in PSII are of low molecular weight (less than 10 kDa), and are involved in PSII assembly, stabilisation, dimerisation, and photo-protection []. In PSII, the oxygen-evolving complex (OEC) is responsible for catalysing the splitting of water to O(2) and 4H+. The OEC is composed of a cluster of manganese, calcium and chloride ions bound to extrinsic proteins. In cyanobacteria there are five extrinsic proteins in OEC (PsbO, PsbP-like, PsbQ-like, PsbU and PsbV), while in plants there are only three (PsbO, PsbP and PsbQ), PsbU and PsbV having been lost during the evolution of green plants []. This family represents the PSII OEC protein PsbQ. Both PsbQ and PsbP (IPR002683 from INTERPRO) are regulators that are necessary for the biogenesis of optically active PSII. The crystal structure of PsbQ from spinach revealed a 4-helical bundle polypeptide. The distribution of positive and negative charges on the protein surface might explain the ability of PsbQ to increase the binding of chloride and calcium ions and make them available to PSII [].; GO: 0005509 calcium ion binding, 0015979 photosynthesis, 0009523 photosystem II, 0009654 oxygen evolving complex, 0019898 extrinsic to membrane; PDB: 1VYK_A 1NZE_A 3LS1_A 3LS0_A.
Probab=72.00 E-value=20 Score=27.45 Aligned_cols=77 Identities=14% Similarity=0.185 Sum_probs=52.5
Q ss_pred HHcHHHHHHHHHHHHhcCccCHHHHHHHHhH--------hhccccccCh----------HHHHHHHHHHHHHHHhcCHHH
Q 042062 47 FRDSTRTLANIEKELQKTEVNYVELDRYFYN--------LKGSSASIGA----------NKVRNEVNKTRELCRAANWEE 108 (142)
Q Consensus 47 ~~d~~~~l~~L~~al~~~~~D~~~l~~~aH~--------LKGss~~lGA----------~~L~~~c~~LE~~~~~~~~~~ 108 (142)
+.++.+.|..++..++.. .|..++...|. |+....+.+- ..|..-..+|..+++.++...
T Consensus 105 ik~sa~~L~~lk~lIdk~--sW~~v~~~LRlka~~Lr~DL~~liss~p~~~kk~l~~La~~lf~~ie~LD~Aar~K~~~~ 182 (202)
T PF05757_consen 105 IKESAKRLLSLKELIDKK--SWPYVRNYLRLKAGYLRYDLNTLISSKPKDEKKALTDLANKLFDNIEELDYAARSKDVPE 182 (202)
T ss_dssp HHHHHHHHCCCHHHHHTT---HHHHHHHHHCCCCCHHHHHHHHHCCS-HHHHHHHHHHHHHHHHHHHHHHHHHHTT-HHH
T ss_pred HHHHHHHHHHHHHHHhhc--cHHHHHHHHHHHHhHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHH
Confidence 456777888999999999 99999988764 3333334432 456667777788888888887
Q ss_pred HHHHHHHHHHHHHHHHH
Q 042062 109 AKVSLEQLKVEHSTLKD 125 (142)
Q Consensus 109 ~~~~~~~l~~~~~~~~~ 125 (142)
+...++.....++.+..
T Consensus 183 a~~~Y~~t~~~Ldevla 199 (202)
T PF05757_consen 183 AEKYYADTVKALDEVLA 199 (202)
T ss_dssp HHHHHHHHHHHHHHHHC
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 77776666666655543
No 23
>PLN02956 PSII-Q subunit
Probab=71.17 E-value=42 Score=25.32 Aligned_cols=77 Identities=12% Similarity=0.116 Sum_probs=51.4
Q ss_pred HHHHHcHHHHHHHHHHHHhcCccCHHHHHHHHhHhhccccccC---------------------hHHHHHHHHHHHHHHH
Q 042062 44 TVYFRDSTRTLANIEKELQKTEVNYVELDRYFYNLKGSSASIG---------------------ANKVRNEVNKTRELCR 102 (142)
Q Consensus 44 ~~F~~d~~~~l~~L~~al~~~~~D~~~l~~~aH~LKGss~~lG---------------------A~~L~~~c~~LE~~~~ 102 (142)
..=+.++.+.|-.|+..++.+ +|..++...| |.++.++ +..|.+-...|..+++
T Consensus 86 ~ar~k~~A~~l~~LK~LI~k~--~W~yvrn~LR---gp~s~Lr~DL~~Ii~slpp~Drk~a~~La~~LFd~l~~LD~AAR 160 (185)
T PLN02956 86 ESGVRGHAENLLRVKALIESE--SWKEAQKALR---RSASNLKQDLYAIIQAKPGKDRPQLRRLYSDLFNSVTKLDYAAR 160 (185)
T ss_pred HHHHHHHHHHHHHHHHHhhhc--cHHHHHHHHH---ccHHHHHHHHHHHHHhcCHhHhHHHHHHHHHHHHHHHHHHHHHh
Confidence 334555666778889999988 9998887755 5666554 2445555666777777
Q ss_pred hcCHHHHHHHHHHHHHHHHHHHH
Q 042062 103 AANWEEAKVSLEQLKVEHSTLKD 125 (142)
Q Consensus 103 ~~~~~~~~~~~~~l~~~~~~~~~ 125 (142)
.++...+...+......|..+..
T Consensus 161 ~kd~~~a~k~Y~~tva~lD~Vl~ 183 (185)
T PLN02956 161 DKDETRVWEYYENIVASLDDIFS 183 (185)
T ss_pred cCCHHHHHHHHHHHHHHHHHHHh
Confidence 77777666666666655555543
No 24
>PRK01773 hscB co-chaperone HscB; Provisional
Probab=66.18 E-value=46 Score=24.64 Aligned_cols=77 Identities=12% Similarity=0.208 Sum_probs=49.1
Q ss_pred ChhhHHHHHHHHHHcHHHHHHHHHHHHhcCccCHHHHHHHHhHhhccccccChHHHHHHHHHHHHHHHhcCHHHHHHHHH
Q 042062 35 NPGFVEDVLTVYFRDSTRTLANIEKELQKTEVNYVELDRYFYNLKGSSASIGANKVRNEVNKTRELCRAANWEEAKVSLE 114 (142)
Q Consensus 35 ~~~~~~eli~~F~~d~~~~l~~L~~al~~~~~D~~~l~~~aH~LKGss~~lGA~~L~~~c~~LE~~~~~~~~~~~~~~~~ 114 (142)
+|+|+-++++ +.+ .|..+-..+ |...+..+...++ ..+..+...++.+-..++++.+...+.
T Consensus 90 d~~fLme~ME-~rE-------~lee~~~~~--d~~~L~~l~~~v~--------~~~~~~~~~l~~~~~~~d~~~A~~~~~ 151 (173)
T PRK01773 90 DMAFLMQQME-WRE-------QLEEIEQQQ--DEDALTAFSKEIK--------QEQQAILTELSTALNSQQWQQASQIND 151 (173)
T ss_pred CHHHHHHHHH-HHH-------HHHhhcccC--CHHHHHHHHHHHH--------HHHHHHHHHHHHHHhcCCHHHHHHHHH
Confidence 6777766443 222 233333456 7788877777665 356677788888888889888887777
Q ss_pred HHHHHHHHHHHHHHHH
Q 042062 115 QLKVEHSTLKDKLTAY 130 (142)
Q Consensus 115 ~l~~~~~~~~~~L~~~ 130 (142)
+++= |..+...+.+.
T Consensus 152 rL~y-~~kl~~ei~~~ 166 (173)
T PRK01773 152 RLRF-IKKLIIEIERV 166 (173)
T ss_pred HHHH-HHHHHHHHHHH
Confidence 6654 55555555433
No 25
>COG3046 Uncharacterized protein related to deoxyribodipyrimidine photolyase [General function prediction only]
Probab=66.15 E-value=13 Score=31.69 Aligned_cols=76 Identities=9% Similarity=0.095 Sum_probs=62.1
Q ss_pred ChhhHHHHHHHHHHcHHHHHHHHHHHHhcCccCHHHHHHHHhHhhccccccChHHHHHHHHHHHHHHHhcCHH--HHHHH
Q 042062 35 NPGFVEDVLTVYFRDSTRTLANIEKELQKTEVNYVELDRYFYNLKGSSASIGANKVRNEVNKTRELCRAANWE--EAKVS 112 (142)
Q Consensus 35 ~~~~~~eli~~F~~d~~~~l~~L~~al~~~~~D~~~l~~~aH~LKGss~~lGA~~L~~~c~~LE~~~~~~~~~--~~~~~ 112 (142)
++.-....+..|+++.-..+..-+.|+... |+. +=|+|=+++-|+|.-.-.+.|+..+.+-+.|+.+ .++.-
T Consensus 226 tr~~A~~~L~~Fi~~~L~nFG~yQDam~~d--~~~----L~HSllS~alNigLL~PleVi~Aa~~Ay~~g~ipLN~VEGF 299 (505)
T COG3046 226 TRTQALRALKHFIADRLPNFGSYQDAMSAD--DPH----LWHSLLSFALNIGLLTPLEVIRAALKAYREGDIPLNSVEGF 299 (505)
T ss_pred CHHHHHHHHHHHHHHhhhcCCcHHHHHhcC--Cch----hHHHHHHHHhhccCCCHHHHHHHHHHhhccCCCchHHHHHH
Confidence 455566889999999999999999999988 765 7799999999999999999999999999987642 34444
Q ss_pred HHHH
Q 042062 113 LEQL 116 (142)
Q Consensus 113 ~~~l 116 (142)
+.||
T Consensus 300 vRQi 303 (505)
T COG3046 300 VRQI 303 (505)
T ss_pred HHHH
Confidence 4443
No 26
>PF08900 DUF1845: Domain of unknown function (DUF1845); InterPro: IPR014996 Members of this protein family, such as PFL4669, are found in integrating conjugative elements (ICE) of the PFGI-1 class as in Pseudomonas fluorescens.
Probab=65.47 E-value=41 Score=25.82 Aligned_cols=53 Identities=17% Similarity=0.166 Sum_probs=35.2
Q ss_pred ccccccChHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 042062 80 GSSASIGANKVRNEVNKTRELCRAANWEEAKVSLEQLKVEHSTLKDKLTAYFEL 133 (142)
Q Consensus 80 Gss~~lGA~~L~~~c~~LE~~~~~~~~~~~~~~~~~l~~~~~~~~~~L~~~l~~ 133 (142)
|..+.+|.......+..+...+.+.|.= +...+-++++.+..+...++...+.
T Consensus 32 ~~~~I~Gm~~~~~~~~~i~~~a~~DdPy-AD~~L~~iEe~i~~~~~~l~~~~~~ 84 (217)
T PF08900_consen 32 GKPAIIGMPGFASRLNRIWRDARQDDPY-ADWWLLRIEEKINEARQELQELIAR 84 (217)
T ss_pred CCCCCcCHHHHHHHHHHHHHHHhcCCcH-HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4458999999999999999999987642 2334444555555544444444433
No 27
>PRK03578 hscB co-chaperone HscB; Provisional
Probab=64.54 E-value=48 Score=24.56 Aligned_cols=77 Identities=18% Similarity=0.252 Sum_probs=47.4
Q ss_pred ChhhHHHHHHHHHHcHHHHHHHHHHHHhcCccCHHHHHHHHhHhhccccccChHHHHHHHHHHHHHHHh-cCHHHHHHHH
Q 042062 35 NPGFVEDVLTVYFRDSTRTLANIEKELQKTEVNYVELDRYFYNLKGSSASIGANKVRNEVNKTRELCRA-ANWEEAKVSL 113 (142)
Q Consensus 35 ~~~~~~eli~~F~~d~~~~l~~L~~al~~~~~D~~~l~~~aH~LKGss~~lGA~~L~~~c~~LE~~~~~-~~~~~~~~~~ 113 (142)
+|+|+-++++ +.+ .|..+-..+ |...+..+...++ ..+..+...++.+... ++++.+...+
T Consensus 93 d~~fLme~mE-~rE-------~lee~~~~~--d~~~L~~l~~e~~--------~~~~~~~~~l~~~~~~~~d~~~A~~~~ 154 (176)
T PRK03578 93 PPAFLMQQME-WRE-------AIEDARAAR--DVDALDALLAELR--------DERRERYAELGALLDSRGDDQAAAEAV 154 (176)
T ss_pred CHHHHHHHHH-HHH-------HHHHhhccC--CHHHHHHHHHHHH--------HHHHHHHHHHHHHHHccccHHHHHHHH
Confidence 6778766544 222 233333455 7778888777774 4556666777776666 7888777777
Q ss_pred HHHHHHHHHHHHHHHHH
Q 042062 114 EQLKVEHSTLKDKLTAY 130 (142)
Q Consensus 114 ~~l~~~~~~~~~~L~~~ 130 (142)
.+++= |..+...+...
T Consensus 155 ~kL~y-~~kl~~ei~~~ 170 (176)
T PRK03578 155 RQLMF-IEKLAQEIGAA 170 (176)
T ss_pred HHHHH-HHHHHHHHHHH
Confidence 77663 55555555443
No 28
>TIGR00984 3a0801s03tim44 mitochondrial import inner membrane, translocase subunit. translocase (Tom) import receptor, five proteins of the Tom channel complex, five proteins of the inner membrane translocase (Tim) and three "motor" proteins. This family is specific for the Tim proteins.
Probab=63.86 E-value=27 Score=29.29 Aligned_cols=75 Identities=12% Similarity=0.187 Sum_probs=52.6
Q ss_pred HHhccCcchhhHHHHHHhhcCCCChhhHHHHHHHHHHcHHHH-HHHHHHHHhcCccCHHHHHHHHhHhhccccccChHHH
Q 042062 12 RQSFFDEEILDRYFIQLEQLGENNPGFVEDVLTVYFRDSTRT-LANIEKELQKTEVNYVELDRYFYNLKGSSASIGANKV 90 (142)
Q Consensus 12 ~~~~~~~~~lD~~l~~L~~l~~~~~~~~~eli~~F~~d~~~~-l~~L~~al~~~~~D~~~l~~~aH~LKGss~~lGA~~L 90 (142)
+-++|.+.-+-.-+.+++.+ +|.|- +..|++.+... ++.+-.|+..+ |.+.|+.+++. ...
T Consensus 218 ~~~lF~ete~a~~l~eIk~~---DPsFd---~~~Fl~gar~aI~p~ILeAf~kG--D~e~LK~~lse----------~vy 279 (378)
T TIGR00984 218 FSGMFSETEVSEVLTEFKKI---DPTFD---KEHFLRFLREYIVPEILEAYVKG--DLEVLKSWCSE----------APF 279 (378)
T ss_pred hhcccCCCHHHHHHHHHHHh---CCCCC---HHHHHHHHHHHHHHHHHHHHHcC--CHHHHHHhhCH----------HHH
Confidence 33366666555556666666 34664 68899999998 79999999999 99999988764 244
Q ss_pred HHHHHHHHHHHHhc
Q 042062 91 RNEVNKTRELCRAA 104 (142)
Q Consensus 91 ~~~c~~LE~~~~~~ 104 (142)
...|..+++..+.|
T Consensus 280 ~~f~a~I~qr~~~G 293 (378)
T TIGR00984 280 SVYATVVKEYKKMG 293 (378)
T ss_pred HHHHHHHHHHHHCC
Confidence 45555666665554
No 29
>PRK01356 hscB co-chaperone HscB; Provisional
Probab=61.04 E-value=63 Score=23.68 Aligned_cols=53 Identities=21% Similarity=0.315 Sum_probs=35.6
Q ss_pred CHHHHHHHHhHhhccccccChHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHH
Q 042062 67 NYVELDRYFYNLKGSSASIGANKVRNEVNKTRELCRAANWEEAKVSLEQLKVEHSTLKDKLT 128 (142)
Q Consensus 67 D~~~l~~~aH~LKGss~~lGA~~L~~~c~~LE~~~~~~~~~~~~~~~~~l~~~~~~~~~~L~ 128 (142)
|...+..+...++. .+..+...|+.+-..++++.+...+.+|+= |..+...++
T Consensus 107 ~~~~L~~l~~~~~~--------~~~~~~~~l~~~f~~~d~~~A~~~~~~L~y-~~kl~~~i~ 159 (166)
T PRK01356 107 LFSDLEKIKNKYEL--------MYKNEIDSLKQAFEEQNLSDATIKTSKLKY-IGTLLNKLQ 159 (166)
T ss_pred CHHHHHHHHHHHHH--------HHHHHHHHHHHHHhcCCHHHHHHHHHHHHH-HHHHHHHHH
Confidence 55666677666653 345666777777788888888888777764 555555554
No 30
>PRK03057 hypothetical protein; Provisional
Probab=52.36 E-value=53 Score=24.62 Aligned_cols=37 Identities=19% Similarity=0.281 Sum_probs=28.7
Q ss_pred HHHHHHHHc------HHHHHHHHHHHHhcCccCHHHHHHHHhHhh
Q 042062 41 DVLTVYFRD------STRTLANIEKELQKTEVNYVELDRYFYNLK 79 (142)
Q Consensus 41 eli~~F~~d------~~~~l~~L~~al~~~~~D~~~l~~~aH~LK 79 (142)
+.++.|++. -.+....|..|+..+ |.+.+.++.+.|+
T Consensus 131 ~~ae~~L~~~~~~~~~~~L~~~ID~ALd~~--D~e~F~~Lt~~L~ 173 (180)
T PRK03057 131 KETEQVLDEVLKRNEVSRLRMQIDQALDRK--DMEEFQRLTEKLK 173 (180)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHCC--CHHHHHHHHHHHH
Confidence 346666666 556678899999999 9998888887775
No 31
>PRK03636 hypothetical protein; Provisional
Probab=51.46 E-value=60 Score=24.32 Aligned_cols=37 Identities=14% Similarity=0.267 Sum_probs=28.9
Q ss_pred HHHHHHHHc------HHHHHHHHHHHHhcCccCHHHHHHHHhHhh
Q 042062 41 DVLTVYFRD------STRTLANIEKELQKTEVNYVELDRYFYNLK 79 (142)
Q Consensus 41 eli~~F~~d------~~~~l~~L~~al~~~~~D~~~l~~~aH~LK 79 (142)
..++.+++. -.+.+..|..|+.++ |-+.+.++...||
T Consensus 132 ~~ae~~L~~~~~~~r~~~L~~~ID~ALd~~--D~e~F~~Ls~~l~ 174 (179)
T PRK03636 132 LLAEQFLEQSVFQFRREKLLKQIDEALDRR--DKEAFHRLSDELN 174 (179)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHcC--CHHHHHHHHHHHH
Confidence 445555555 456789999999999 9999999888776
No 32
>PF09280 XPC-binding: XPC-binding domain; InterPro: IPR015360 Members of this entry adopt a structure consisting of four alpha helices, arranged in an array. They bind specifically and directly to the xeroderma pigmentosum group C protein (XPC) to initiate nucleotide excision repair []. ; GO: 0003684 damaged DNA binding, 0006289 nucleotide-excision repair, 0043161 proteasomal ubiquitin-dependent protein catabolic process; PDB: 1PVE_A 1QZE_A 1OQY_A 1TP4_A 1X3W_B 3ESW_B 2QSG_X 2QSF_X 1X3Z_B 2QSH_X ....
Probab=50.04 E-value=24 Score=21.53 Aligned_cols=36 Identities=28% Similarity=0.368 Sum_probs=27.6
Q ss_pred HHHHHhhcCCCChhhHHHHHHHHHHcHHHHHHHHHH
Q 042062 24 YFIQLEQLGENNPGFVEDVLTVYFRDSTRTLANIEK 59 (142)
Q Consensus 24 ~l~~L~~l~~~~~~~~~eli~~F~~d~~~~l~~L~~ 59 (142)
+|..+|++=..||+++..++...-++.|..+..+.+
T Consensus 9 qf~~lR~~vq~NP~lL~~lLqql~~~nP~l~q~I~~ 44 (59)
T PF09280_consen 9 QFQQLRQLVQQNPQLLPPLLQQLGQSNPQLLQLIQQ 44 (59)
T ss_dssp HHHHHHHHHHC-GGGHHHHHHHHHCCSHHHHHHHHH
T ss_pred HHHHHHHHHHHCHHHHHHHHHHHhccCHHHHHHHHH
Confidence 388999983457899999999988888877766653
No 33
>TIGR03761 ICE_PFL4669 integrating conjugative element protein, PFL_4669 family. Members of this protein family, such as PFL4669, are found in integrating conjugative elements (ICE) of the PFGI-1 class as in Pseudomonas fluorescens.
Probab=49.59 E-value=1.1e+02 Score=23.64 Aligned_cols=51 Identities=14% Similarity=0.158 Sum_probs=33.8
Q ss_pred cccccChHHHHHHHHHHHHHHHhcCHH------HHHHHHHHHHHHHHHHHHHHHHHH
Q 042062 81 SSASIGANKVRNEVNKTRELCRAANWE------EAKVSLEQLKVEHSTLKDKLTAYF 131 (142)
Q Consensus 81 ss~~lGA~~L~~~c~~LE~~~~~~~~~------~~~~~~~~l~~~~~~~~~~L~~~l 131 (142)
-.+.+|.......+..|...+.+.|.= .++..+.+....++.+...++..+
T Consensus 31 ~~~IiGl~~f~s~~~~i~~~a~~DdPyAD~~Ll~~E~~l~~~~~~l~~~~~~l~~~l 87 (216)
T TIGR03761 31 KPGIIGMPGFISRLNRINQASEQDDPYADWALLRIEEKLLSARQEMQALLQRLDDLL 87 (216)
T ss_pred CCCCcCcHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 356899999999999999999988742 334444444444444444444443
No 34
>cd01671 CARD Caspase activation and recruitment domain: a protein-protein interaction domain. Caspase activation and recruitment domains (CARDs) are death domains (DDs) found associated with caspases. Caspases are aspartate-specific cysteine proteases with functions in apoptosis, immune signaling, inflammation, and host-defense mechanisms. In addition to caspases, proteins containing CARDs include adaptor proteins such as RAIDD, CARD9, and RIG-I-like helicases, which can form mutliprotein complexes and play important roles in mediating the signals to induce immune and inflammatory responses. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and DED (Death Effector Domain). They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=48.13 E-value=64 Score=19.87 Aligned_cols=57 Identities=11% Similarity=0.280 Sum_probs=42.6
Q ss_pred HHHHHHHhccCcchhhHH-HHHHhhcCCCChhhHHHHHHHHHHcHHHHHHHHHHHHhcC
Q 042062 7 QIAEMRQSFFDEEILDRY-FIQLEQLGENNPGFVEDVLTVYFRDSTRTLANIEKELQKT 64 (142)
Q Consensus 7 ~~~~~~~~~~~~~~lD~~-l~~L~~l~~~~~~~~~eli~~F~~d~~~~l~~L~~al~~~ 64 (142)
....++..+...++|..+ .+.+..-+. .++-...+++.-..-.+..+..+-.++...
T Consensus 14 ~~~~il~~L~~~~vlt~~e~~~i~~~~~-~~~k~~~Lld~l~~kg~~af~~F~~~L~~~ 71 (80)
T cd01671 14 DVEDVLDHLLSDGVLTEEEYEKIRSEST-RQDKARKLLDILPRKGPKAFQSFLQALQET 71 (80)
T ss_pred cHHHHHHHHHHcCCCCHHHHHHHHcCCC-hHHHHHHHHHHHHhcChHHHHHHHHHHHhc
Confidence 456677778888888888 888877632 556777778877777777787877777765
No 35
>PF02153 PDH: Prephenate dehydrogenase; InterPro: IPR003099 Members of this family are prephenate dehydrogenases 1.3.1.12 from EC involved in tyrosine biosynthesis. ; GO: 0004665 prephenate dehydrogenase (NADP+) activity, 0008977 prephenate dehydrogenase activity, 0006571 tyrosine biosynthetic process, 0055114 oxidation-reduction process; PDB: 2F1K_B 2PV7_A 3DZB_B 3KTD_B 3B1F_A 2G5C_D 3GGP_C 3GGG_C 3GGO_D.
Probab=47.59 E-value=89 Score=24.19 Aligned_cols=48 Identities=15% Similarity=0.362 Sum_probs=28.5
Q ss_pred HHHHhhcCCCChhhHHHHH-------HHHHHcHHHHHHHHHHHHhcCccCHHHHHHH
Q 042062 25 FIQLEQLGENNPGFVEDVL-------TVYFRDSTRTLANIEKELQKTEVNYVELDRY 74 (142)
Q Consensus 25 l~~L~~l~~~~~~~~~eli-------~~F~~d~~~~l~~L~~al~~~~~D~~~l~~~ 74 (142)
|....++...+|++..+++ ...++...+.+.+++.+++++ |.+.+.++
T Consensus 201 frd~tRia~~~p~l~~~I~~~N~~~~~~~l~~~~~~L~~l~~~l~~~--d~~~l~~~ 255 (258)
T PF02153_consen 201 FRDMTRIASSDPELWADIFLSNPENLLEALDEFIKELNELREALEAG--DEEELEEL 255 (258)
T ss_dssp HHHHHGGGGS-HHHHHHHHHHTHHHHHHHHHHHHHHHHHHHHHHHTT--SHHHHHHH
T ss_pred HHhhcccccCChHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHcC--CHHHHHHH
Confidence 3444455345556555543 233444555677888888888 88887764
No 36
>PF14931 IFT20: Intraflagellar transport complex B, subunit 20
Probab=47.53 E-value=95 Score=21.66 Aligned_cols=100 Identities=18% Similarity=0.233 Sum_probs=61.9
Q ss_pred cchhhHH-HHHHhhcCCCChhhHHHHHHHHHHcHHHHHHHHHHHHhcCccCHHHHHHHHhHhhccccccChHHHHHHHHH
Q 042062 18 EEILDRY-FIQLEQLGENNPGFVEDVLTVYFRDSTRTLANIEKELQKTEVNYVELDRYFYNLKGSSASIGANKVRNEVNK 96 (142)
Q Consensus 18 ~~~lD~~-l~~L~~l~~~~~~~~~eli~~F~~d~~~~l~~L~~al~~~~~D~~~l~~~aH~LKGss~~lGA~~L~~~c~~ 96 (142)
=-+||+. .+.-.++.+...+|+.. |..|-.-+...+..+......- +-.+++. ||+..+...+..
T Consensus 11 iRVldp~~~~~t~~Lk~ec~~F~~k-i~~F~~iv~~~~~~~~~~A~~V--E~eKlkA-----------IG~RN~l~s~~k 76 (120)
T PF14931_consen 11 IRVLDPEKADQTQELKEECKEFVEK-ISEFQKIVKGFIEILDELAKRV--ENEKLKA-----------IGARNLLKSEAK 76 (120)
T ss_pred eeecChHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHH--HHHHHHH-----------HHhHHHHHHHHH
Confidence 3468888 88888774444577766 7777777766666666544332 4444442 455444433321
Q ss_pred HHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 042062 97 TRELCRAANWEEAKVSLEQLKVEHSTLKDKLTAYFELVA 135 (142)
Q Consensus 97 LE~~~~~~~~~~~~~~~~~l~~~~~~~~~~L~~~l~~~~ 135 (142)
-+......+...+..-+.++.+++..++.+...|+
T Consensus 77 ----~R~~~~q~lq~~I~Ek~~eLERl~~E~~sL~kve~ 111 (120)
T PF14931_consen 77 ----QREAQQQQLQALIAEKKMELERLRSEYESLQKVEQ 111 (120)
T ss_pred ----hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 12223445677788888888888888888777654
No 37
>cd08325 CARD_CASP1-like Caspase activation and recruitment domain found in Caspase-1 and related proteins. Caspase activation and recruitment domain (CARD) similar to those found in Caspase-1 (CASP1, ICE) and related proteins, including CARD-only proteins such as ICEBERG or CARD18, INCA (CARD17), CARD16 (COP1, PSEUDO-ICE), CARD8 (DACAR, NDPP1, TUCAN), and CARD12 (NLRC4), as well as ICE-like caspases such as CASP12, CASP5 (ICH-3) and CASP4 (TX, ICH-2). Caspases are aspartate-specific cysteine proteases with functions in apoptosis and immune signaling. CASP1 plays a central role in the cellular response to a wide variety of microbial and non-microbial stimuli, being activated by the inflammasome or the pyroptosome. CARD8 binds itself and the initiator caspase-9, interfering with the binding of APAF-1 and suppressing caspase-9 activation. CARD12 is a Nod-like receptor (NLR) that plays an important role in the innate immune response to Gram-negative bacteria. Caspase-4 (CASP4), -5 (CASP5),
Probab=46.89 E-value=77 Score=20.39 Aligned_cols=60 Identities=7% Similarity=0.073 Sum_probs=45.4
Q ss_pred HHHHHHHhccCcchhhHH-HHHHhhcCCCChhhHHHHHHHHHHcHHHHHHHHHHHHhcCccCH
Q 042062 7 QIAEMRQSFFDEEILDRY-FIQLEQLGENNPGFVEDVLTVYFRDSTRTLANIEKELQKTEVNY 68 (142)
Q Consensus 7 ~~~~~~~~~~~~~~lD~~-l~~L~~l~~~~~~~~~eli~~F~~d~~~~l~~L~~al~~~~~D~ 68 (142)
.+..++..+...++|+.+ .+.++.-.....+-.+.||+....-.+.-..-+..++.+. |.
T Consensus 17 ~i~~llD~Ll~~~Vl~~~E~e~i~~~~~t~~dkar~Lid~v~~KG~~A~~iF~~~L~~~--d~ 77 (83)
T cd08325 17 VINGLLDDLLEKNVLNEEEMEKIKEENNTIMDKARVLVDSVTEKGQEAGQIFIKHLLNR--DK 77 (83)
T ss_pred hHHHHHHHHHHcCCCCHHHHHHHHhccCCHHHHHHHHHHHHHHHhHHHHHHHHHHHHhc--Ch
Confidence 467777888888888888 7777764222346677888888888888888888888877 64
No 38
>PRK13916 plasmid segregation protein ParR; Provisional
Probab=46.12 E-value=36 Score=22.53 Aligned_cols=26 Identities=19% Similarity=0.372 Sum_probs=22.6
Q ss_pred HHHHhhc-CCCChhhHHHHHHHHHHcH
Q 042062 25 FIQLEQL-GENNPGFVEDVLTVYFRDS 50 (142)
Q Consensus 25 l~~L~~l-~~~~~~~~~eli~~F~~d~ 50 (142)
|+=|..+ ++.-+.|+++++..|+++.
T Consensus 21 F~FL~~~P~GT~~~~iR~~L~rYI~~~ 47 (97)
T PRK13916 21 FDFLENVPRGTKTAHIREALRRYIEEI 47 (97)
T ss_pred HHHHHHCCCCCccHHHHHHHHHHHHhc
Confidence 7788888 7777899999999999874
No 39
>PF02845 CUE: CUE domain; InterPro: IPR003892 This domain may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two proteins of the IL-1 signal transduction pathway, tollip and TAB2.; GO: 0005515 protein binding; PDB: 2EKF_A 1OTR_A 1P3Q_Q 1MN3_A 1WGL_A 2EJS_A 2DAE_A 2DHY_A 2DI0_A.
Probab=45.36 E-value=43 Score=18.41 Aligned_cols=33 Identities=18% Similarity=0.272 Sum_probs=23.3
Q ss_pred HHHHhhc-CCCChhhHHHHHHHHHHcHHHHHHHH
Q 042062 25 FIQLEQL-GENNPGFVEDVLTVYFRDSTRTLANI 57 (142)
Q Consensus 25 l~~L~~l-~~~~~~~~~eli~~F~~d~~~~l~~L 57 (142)
+..|+++ +.-+++++..++..+-.+....+..|
T Consensus 5 v~~L~~mFP~~~~~~I~~~L~~~~~~ve~ai~~L 38 (42)
T PF02845_consen 5 VQQLQEMFPDLDREVIEAVLQANNGDVEAAIDAL 38 (42)
T ss_dssp HHHHHHHSSSS-HHHHHHHHHHTTTTHHHHHHHH
T ss_pred HHHHHHHCCCCCHHHHHHHHHHcCCCHHHHHHHH
Confidence 7788888 88888888777777766666555544
No 40
>PRK05014 hscB co-chaperone HscB; Provisional
Probab=44.93 E-value=1.2e+02 Score=22.20 Aligned_cols=77 Identities=14% Similarity=0.304 Sum_probs=42.7
Q ss_pred ChhhHHHHHHHHHHcHHHHHHHHHHHHhcCccC-HHHHHHHHhHhhccccccChHHHHHHHHHHHHHHHhcCHHHHHHHH
Q 042062 35 NPGFVEDVLTVYFRDSTRTLANIEKELQKTEVN-YVELDRYFYNLKGSSASIGANKVRNEVNKTRELCRAANWEEAKVSL 113 (142)
Q Consensus 35 ~~~~~~eli~~F~~d~~~~l~~L~~al~~~~~D-~~~l~~~aH~LKGss~~lGA~~L~~~c~~LE~~~~~~~~~~~~~~~ 113 (142)
+|+|+-+++. .-+.|..+-... | -..+..+...++. .+..+...++.+...++++.+...+
T Consensus 88 d~efLme~me--------~rE~le~~~~~~--d~~~~l~~l~~~~~~--------~~~~~~~~l~~~~~~~d~~~A~~~~ 149 (171)
T PRK05014 88 DTAFLMEQME--------LREELEDIEQSK--DPEAALESFIKRVKK--------MFKTRLQQMVEQLDNEAWDAAADTV 149 (171)
T ss_pred CHHHHHHHHH--------HHHHHHhhcccc--CHHHHHHHHHHHHHH--------HHHHHHHHHHHHHhhCCHHHHHHHH
Confidence 5667666332 223333333334 5 2336666665553 3455666666666777888777776
Q ss_pred HHHHHHHHHHHHHHHHH
Q 042062 114 EQLKVEHSTLKDKLTAY 130 (142)
Q Consensus 114 ~~l~~~~~~~~~~L~~~ 130 (142)
.+++= |..+...+.+.
T Consensus 150 ~~Lky-~~kl~~ei~~~ 165 (171)
T PRK05014 150 RKLKF-LDKLRSEVEQL 165 (171)
T ss_pred HHHHH-HHHHHHHHHHH
Confidence 66653 45555555443
No 41
>TIGR00465 ilvC ketol-acid reductoisomerase. This is the second enzyme in the parallel isoleucine-valine biosynthetic pathway
Probab=44.31 E-value=25 Score=28.46 Aligned_cols=74 Identities=7% Similarity=-0.032 Sum_probs=45.5
Q ss_pred hhhHH-HHHHhhcCCCChhhHHHHHHHHHHcHHHHHHHHHHHHhcCccCH-HHHHHHHhHhhccccccChHHHHHHHHHH
Q 042062 20 ILDRY-FIQLEQLGENNPGFVEDVLTVYFRDSTRTLANIEKELQKTEVNY-VELDRYFYNLKGSSASIGANKVRNEVNKT 97 (142)
Q Consensus 20 ~lD~~-l~~L~~l~~~~~~~~~eli~~F~~d~~~~l~~L~~al~~~~~D~-~~l~~~aH~LKGss~~lGA~~L~~~c~~L 97 (142)
.++++ |+..-.|..+.|.|+...++.. ++.+ .+. ......+|++||++-.+.-..+..+...+
T Consensus 173 e~~edl~~~~t~l~Gs~pa~v~~~~eal--------------v~~G-~~~e~A~~~~~~~~~g~~~l~~e~g~~~l~~~V 237 (314)
T TIGR00465 173 ETESDLFGEQAVLCGGLTALIKAGFDTL--------------VEAG-YQPELAYFETVHELKLIVDLIYEGGITGMRDRI 237 (314)
T ss_pred hhhHHhcCcchhHHhHHHHHHHHHHHHH--------------HHcC-CCHHHHHHHHHHHHHHHHHHHHHhcHHHHHHHc
Confidence 45555 6666666445677765544333 3333 222 45566789999999888666566666666
Q ss_pred HHHHHhcCHHH
Q 042062 98 RELCRAANWEE 108 (142)
Q Consensus 98 E~~~~~~~~~~ 108 (142)
=.-++-|+...
T Consensus 238 sstaeyg~~~~ 248 (314)
T TIGR00465 238 SNTAEYGALTR 248 (314)
T ss_pred CCHHHcCcchh
Confidence 66667776643
No 42
>PF05227 CHASE3: CHASE3 domain; InterPro: IPR007891 CHASE3 is an extracellular sensory domain, which is present in various classes of transmembrane receptors that are upstream of signal transduction pathways in bacteria. Specifically, CHASE3 domains are found in histidine kinases, adenylate cyclases, methyl-accepting chemotaxis proteins and predicted diguanylate cyclases/phosphodiesterases. Environmental factors that are recognised by CHASE3 domains are not known at this time [].; PDB: 3VA9_A.
Probab=44.10 E-value=97 Score=20.79 Aligned_cols=29 Identities=21% Similarity=0.316 Sum_probs=19.9
Q ss_pred CCChhhHHHHHHHHHHcHHHHHHHHHHHHh
Q 042062 33 ENNPGFVEDVLTVYFRDSTRTLANIEKELQ 62 (142)
Q Consensus 33 ~~~~~~~~eli~~F~~d~~~~l~~L~~al~ 62 (142)
.++|.|+.. +..-..+.+..+..|...+.
T Consensus 35 tgd~~~l~~-y~~~~~~~~~~l~~L~~l~~ 63 (138)
T PF05227_consen 35 TGDPEFLEP-YQEARARLEKALAQLRQLVQ 63 (138)
T ss_dssp H--HHHHHH-HHHHHHHHHHHHHHHHHHTT
T ss_pred cCCHhhhch-HHHHHHHHHHHHHHHHHHhc
Confidence 367777755 66677778888888887764
No 43
>PF03670 UPF0184: Uncharacterised protein family (UPF0184); InterPro: IPR022788 This family of proteins has no known function.
Probab=43.54 E-value=93 Score=20.41 Aligned_cols=35 Identities=17% Similarity=0.291 Sum_probs=26.8
Q ss_pred hcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 042062 103 AANWEEAKVSLEQLKVEHSTLKDKLTAYFELVAQL 137 (142)
Q Consensus 103 ~~~~~~~~~~~~~l~~~~~~~~~~L~~~l~~~~~~ 137 (142)
+..++.+..++..|+.--..+...|..+|+.-||+
T Consensus 32 ns~LD~Lns~LD~LE~rnD~l~~~L~~LLesnrq~ 66 (83)
T PF03670_consen 32 NSMLDQLNSCLDHLEQRNDHLHAQLQELLESNRQI 66 (83)
T ss_pred HHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHH
Confidence 34566777888888888888888888888877765
No 44
>cd08330 CARD_ASC_NALP1 Caspase activation and recruitment domain found in Human ASC, NALP1, and similar proteins. Caspase activation and recruitment domain (CARD) similar to those found in human ASC (Apoptosis-associated speck-like protein containing a CARD) and NALP1 (CARD7, NLRP1). ASC, an adaptor molecule, and NALP1, a member of the Nod-like receptor (NLR) family, are involved in the assembly of the 'inflammasome', a multiprotein platform, which is responsible for caspase-1 activation and regulation of IL-1beta maturation. In general, CARDs are death domains (DDs) associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and DED (Death Effector Domain). They se
Probab=43.37 E-value=88 Score=20.06 Aligned_cols=56 Identities=4% Similarity=0.079 Sum_probs=41.9
Q ss_pred HHHHHHhccCcchhhHH-HHHHhhcCCCChhhHHHHHHHHHHcHHHHHHHHHHHHhcC
Q 042062 8 IAEMRQSFFDEEILDRY-FIQLEQLGENNPGFVEDVLTVYFRDSTRTLANIEKELQKT 64 (142)
Q Consensus 8 ~~~~~~~~~~~~~lD~~-l~~L~~l~~~~~~~~~eli~~F~~d~~~~l~~L~~al~~~ 64 (142)
...++..+...|+|.++ .+.++.-+ ..++-.+.|++.-..-.+.-...+..++...
T Consensus 17 v~~ilD~L~~~~Vit~e~~~~I~a~~-T~~~kar~Lld~l~~kG~~A~~~F~~~L~e~ 73 (82)
T cd08330 17 VDPILDKLHGKKVITQEQYSEVRAEK-TNQEKMRKLFSFVRSWGASCKDIFYQILREE 73 (82)
T ss_pred HHHHHHHHHHCCCCCHHHHHHHHcCC-CcHHHHHHHHHHHHccCHHHHHHHHHHHHHh
Confidence 45567778888888888 88888762 3457777888887777788888888888655
No 45
>PRK08818 prephenate dehydrogenase; Provisional
Probab=42.94 E-value=60 Score=27.01 Aligned_cols=38 Identities=11% Similarity=0.174 Sum_probs=26.7
Q ss_pred HHHHHHHHHHcHHHHHHHHHHHHhcCccCHHHHHHHHhHhhccc
Q 042062 39 VEDVLTVYFRDSTRTLANIEKELQKTEVNYVELDRYFYNLKGSS 82 (142)
Q Consensus 39 ~~eli~~F~~d~~~~l~~L~~al~~~~~D~~~l~~~aH~LKGss 82 (142)
+.+.++.|. +.+.+++.+++++ |+..+.+..|++.-+.
T Consensus 229 i~~~l~~~~----~~L~~l~~~i~~~--D~~~~~~~~~~f~~a~ 266 (370)
T PRK08818 229 VGEMLDRLL----AQLQELRALVAQG--DDAARARFRAQFLHAN 266 (370)
T ss_pred HHHHHHHHH----HHHHHHHHHHHcC--CHHHHHHHHHHHHHHH
Confidence 334444444 4577889999999 9999988877665543
No 46
>PLN02407 diphosphomevalonate decarboxylase
Probab=42.63 E-value=48 Score=27.43 Aligned_cols=33 Identities=6% Similarity=0.307 Sum_probs=28.5
Q ss_pred HHHHHHHHc-HHHHHHHHHHHHhcCccCHHHHHHHH
Q 042062 41 DVLTVYFRD-STRTLANIEKELQKTEVNYVELDRYF 75 (142)
Q Consensus 41 eli~~F~~d-~~~~l~~L~~al~~~~~D~~~l~~~a 75 (142)
.++...++. +++.+..++.|+.++ ||.++.+++
T Consensus 223 p~~~~w~~~~~~~~~~~~~~Ai~~~--Df~~~gei~ 256 (343)
T PLN02407 223 PLLQHRAKEVVPKRILQMEEAIKNR--DFASFAKLT 256 (343)
T ss_pred hhHHHHHHhhhHHHHHHHHHHHHhc--CHHHHHHHH
Confidence 346677888 899999999999999 999998775
No 47
>PRK05685 fliS flagellar protein FliS; Validated
Probab=42.06 E-value=1.2e+02 Score=21.21 Aligned_cols=28 Identities=7% Similarity=0.235 Sum_probs=20.9
Q ss_pred HHHHHHHHcHHHHHHHHHHHHhcCccCHHH
Q 042062 41 DVLTVYFRDSTRTLANIEKELQKTEVNYVE 70 (142)
Q Consensus 41 eli~~F~~d~~~~l~~L~~al~~~~~D~~~ 70 (142)
+++-...+-+-+.+.....++.++ |++.
T Consensus 26 ~Li~mLydgai~~l~~A~~ai~~~--~~~~ 53 (132)
T PRK05685 26 KLIQMLYEGALSFLAQAKLAIEQG--DIEA 53 (132)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHcC--CHHH
Confidence 566666677777777888888888 8773
No 48
>smart00388 HisKA His Kinase A (phosphoacceptor) domain. Dimerisation and phosphoacceptor domain of histidine kinases.
Probab=41.84 E-value=62 Score=17.89 Aligned_cols=56 Identities=14% Similarity=0.144 Sum_probs=30.3
Q ss_pred HHHHHhHhhccccccChHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 042062 71 LDRYFYNLKGSSASIGANKVRNEVNKTRELCRAANWEEAKVSLEQLKVEHSTLKDKLTAYFELV 134 (142)
Q Consensus 71 l~~~aH~LKGss~~lGA~~L~~~c~~LE~~~~~~~~~~~~~~~~~l~~~~~~~~~~L~~~l~~~ 134 (142)
+..++|.+|..=+.+. ..+..+.. ...+.+. ...+..+..+...+..-+..++...
T Consensus 6 ~~~i~Hel~~pl~~i~-----~~~~~l~~--~~~~~~~-~~~~~~~~~~~~~~~~~v~~l~~~~ 61 (66)
T smart00388 6 LANLSHELRTPLTAIR-----GYLELLED--TELSEEQ-REYLETILRSAERLLRLINDLLDLS 61 (66)
T ss_pred HHHHHHhccCcHHHHH-----HHHHHHHh--CCCChHH-HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4567899985544322 22222322 1112223 5666777777777766666665544
No 49
>PRK10093 primosomal replication protein N''; Provisional
Probab=41.54 E-value=90 Score=23.27 Aligned_cols=36 Identities=14% Similarity=0.315 Sum_probs=26.5
Q ss_pred HHHHHHHHcHHHHHHHHHHHHhcCccCHHHHHHHHhHh
Q 042062 41 DVLTVYFRDSTRTLANIEKELQKTEVNYVELDRYFYNL 78 (142)
Q Consensus 41 eli~~F~~d~~~~l~~L~~al~~~~~D~~~l~~~aH~L 78 (142)
..+.-|+.+....+..|..++..+ +...+.-++=+|
T Consensus 40 ~~L~~yl~Ei~~~l~qL~~~~~~~--~~~~~~flaEkL 75 (171)
T PRK10093 40 TLLQAYLDEAGDNLAALRHAVEQQ--QLPQVAWLAEHL 75 (171)
T ss_pred cchHHHHHHHHHHHHHHHHHHhcC--cHHHHHHHHHHH
Confidence 347788888999999999988887 766655554443
No 50
>PF03993 DUF349: Domain of Unknown Function (DUF349); InterPro: IPR007139 This motif is found singly or as up to five tandem repeats in a small set of bacterial proteins. There are two or three alpha-helices, and possibly a beta-strand.
Probab=41.50 E-value=57 Score=19.98 Aligned_cols=32 Identities=19% Similarity=0.454 Sum_probs=20.2
Q ss_pred HHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHH
Q 042062 91 RNEVNKTRELCRAANWEEAKVSLEQLKVEHST 122 (142)
Q Consensus 91 ~~~c~~LE~~~~~~~~~~~~~~~~~l~~~~~~ 122 (142)
-.+|..++....+.+.......+..|...|..
T Consensus 37 ~~Li~~~~~l~~~~d~~~~~~~~k~l~~~Wk~ 68 (77)
T PF03993_consen 37 EALIEEAEALAESEDWKEAAEEIKELQQEWKE 68 (77)
T ss_pred HHHHHHHHHhcccccHHHHHHHHHHHHHHHHH
Confidence 34667777777776666666666666666544
No 51
>cd08326 CARD_CASP9 Caspase activation and recruitment domain of Caspase-9. Caspase activation and recruitment domain (CARD) similar to that found in caspase-9 (CASP9, MCH6, APAF3), which interacts with the CARD of apoptotic protease-activating factor 1 (APAF-1). Caspases are aspartate-specific cysteine proteases with functions in apoptosis and immune signaling. Initiator caspases are the first to be activated following death- or inflammation-inducing signals. Caspase-9 is the initiator caspase associated with the intrinsic or mitochondrial pathway of apoptosis, induced by many pro-apoptotic signals. Together with APAF-1, it forms the heptameric 'apoptosome' in response to the release of cytochrome c from mitochondria. Activated caspase-9 cleaves and activates downstream effector caspases, like caspase-3, caspase-6, and caspase-7, resulting in apoptosis. In general, CARDs are death domains (DDs) associated with caspases. They are known to be important in the signaling pathways for apopt
Probab=41.43 E-value=97 Score=20.04 Aligned_cols=61 Identities=8% Similarity=0.157 Sum_probs=37.2
Q ss_pred HHHHHhccCcchhhHH-HHHHhhcCCCChhhHHHHHHHHHHcHHHHHHHHHHHHhcCccCHHHHH
Q 042062 9 AEMRQSFFDEEILDRY-FIQLEQLGENNPGFVEDVLTVYFRDSTRTLANIEKELQKTEVNYVELD 72 (142)
Q Consensus 9 ~~~~~~~~~~~~lD~~-l~~L~~l~~~~~~~~~eli~~F~~d~~~~l~~L~~al~~~~~D~~~l~ 72 (142)
+..+.-+...|+++.. .+.+..-+ ...+-...+++..-.-.+.-+...-.|+... .+..+.
T Consensus 19 ~~v~~~L~~~~Vlt~~~~e~I~~~~-tr~~q~~~LLd~L~~RG~~AF~~F~~aL~~~--~~~~LA 80 (84)
T cd08326 19 KYLWDHLLSRGVFTPDMIEEIQAAG-SRRDQARQLLIDLETRGKQAFPAFLSALRET--GQTDLA 80 (84)
T ss_pred HHHHHHHHhcCCCCHHHHHHHHcCC-CHHHHHHHHHHHHHhcCHHHHHHHHHHHHhc--CchHHH
Confidence 4455666777777777 77777652 1234456666666666666666666666654 444333
No 52
>KOG3232 consensus Vacuolar assembly/sorting protein DID2 [Intracellular trafficking, secretion, and vesicular transport]
Probab=41.03 E-value=1.4e+02 Score=22.48 Aligned_cols=48 Identities=10% Similarity=0.158 Sum_probs=37.7
Q ss_pred HhHhhccccccChHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHH
Q 042062 75 FYNLKGSSASIGANKVRNEVNKTRELCRAANWEEAKVSLEQLKVEHSTLKDKL 127 (142)
Q Consensus 75 aH~LKGss~~lGA~~L~~~c~~LE~~~~~~~~~~~~~~~~~l~~~~~~~~~~L 127 (142)
|-+.+-.++| ++..|+.++.+-+..+++.+..+++..+..|..+...-
T Consensus 85 avtmr~Vt~s-----M~gVvK~md~alktmNLekis~~MDkFE~qFedldvqt 132 (203)
T KOG3232|consen 85 AVTMRKVTKS-----MAGVVKSMDSALKTMNLEKISQLMDKFEKQFEDLDVQT 132 (203)
T ss_pred HHHHHHHHHH-----HHHHHHHHHHHHHhCCHHHHHHHHHHHHHHhhhhhhHH
Confidence 3444444443 56789999999999999999999999999998766543
No 53
>PF08858 IDEAL: IDEAL domain; InterPro: IPR014957 This entry represents the C-terminal domain of Bacteriophage SPP1, p90. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. his domain may also be referred to as the IDEAL domain, after the sequence of the most conserved region of the domain.; PDB: 3DO9_A.
Probab=40.83 E-value=62 Score=17.64 Aligned_cols=25 Identities=12% Similarity=0.048 Sum_probs=19.6
Q ss_pred HHHHHHHHHHHhcCccCHHHHHHHHhH
Q 042062 51 TRTLANIEKELQKTEVNYVELDRYFYN 77 (142)
Q Consensus 51 ~~~l~~L~~al~~~~~D~~~l~~~aH~ 77 (142)
.+....|..|+..+ |-..+.++...
T Consensus 12 ~~L~~~ID~ALd~~--D~e~F~~Ls~e 36 (37)
T PF08858_consen 12 EQLLELIDEALDNR--DKEWFYELSEE 36 (37)
T ss_dssp HHHHHHHHHHHHTT---HHHHHHHHHH
T ss_pred HHHHHHHHHHHHcC--CHHHHHHHHhh
Confidence 35678899999999 99998887654
No 54
>COG2991 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=38.12 E-value=7.6 Score=24.86 Aligned_cols=20 Identities=25% Similarity=0.368 Sum_probs=17.2
Q ss_pred hHhhccccccChHHHHHHHH
Q 042062 76 YNLKGSSASIGANKVRNEVN 95 (142)
Q Consensus 76 H~LKGss~~lGA~~L~~~c~ 95 (142)
-++|||+|-+++-.+...|.
T Consensus 27 k~I~GSCGGi~alGi~K~Cd 46 (77)
T COG2991 27 KSIKGSCGGIAALGIEKVCD 46 (77)
T ss_pred cccccccccHHhhccchhcC
Confidence 46899999999988888876
No 55
>PF00619 CARD: Caspase recruitment domain; InterPro: IPR001315 The caspase recruitment domain domain (CARD) is a homotypic protein interaction module composed of a bundle of six alpha-helices. CARD is related in sequence and structure to the death domain (DD, see IPR000488 from INTERPRO) and the death effector domain (DED, see IPR001875 from INTERPRO), which work in similar pathways and show similar interaction properties []. The CARD domain typically associates with other CARD-containing proteins, forming either dimers or trimers. CARD domains can be found in isolation, or in combination with other domains. Domains associated with CARD include: NACHT (IPR007111 from INTERPRO) (in Nal1 and Bir1), NB-ARC (IPR002182 from INTERPRO) (in Apaf-1), pyrin/dapin domains (IPR004020 from INTERPRO) (in Nal1), leucine-rich repeats () (in Nal1), WD repeats (IPR001680 from INTERPRO) (in Apaf1), Src homology domains (IPR001452 from INTERPRO), PDZ (IPR001478 from INTERPRO), RING, kinase and DD domains []. CARD-containing proteins are involved in apoptosis through their regulation of caspases that contain CARDs in their N-terminal pro-domains, including human caspases 1, 2, 9, 11 and 12 []. CARD-containing proteins are also involved in inflammation through their regulation of NF-kappaB []. The mechanisms by which CARDs activate caspases and NF-kappaB involve the assembly of multi-protein complexes, which can facilitate dimerisation or serve as scaffolds on which proteases and kinases are assembled and activated.; GO: 0005515 protein binding, 0042981 regulation of apoptosis, 0005622 intracellular; PDB: 2NSN_A 2NZ7_B 2DBD_A 4E9M_C 2B1W_A 3YGS_P 2KN6_A 3CRD_A 1DGN_A 3KAT_A ....
Probab=37.99 E-value=99 Score=19.19 Aligned_cols=55 Identities=7% Similarity=0.215 Sum_probs=35.0
Q ss_pred HHHHHHhccCcchhhHH-HHHHhhcCCCChhhHHHHHHHHHHcHHHHHHHHHHHHhc
Q 042062 8 IAEMRQSFFDEEILDRY-FIQLEQLGENNPGFVEDVLTVYFRDSTRTLANIEKELQK 63 (142)
Q Consensus 8 ~~~~~~~~~~~~~lD~~-l~~L~~l~~~~~~~~~eli~~F~~d~~~~l~~L~~al~~ 63 (142)
...++..++..++|.+. .+.++.. ....+-+..+++....-.+.-...+-.++.+
T Consensus 18 ~~~ild~L~~~~vlt~~e~e~I~~~-~t~~~k~~~LLd~l~~kg~~a~~~F~~~L~~ 73 (85)
T PF00619_consen 18 LDDILDHLLSRGVLTEEEYEEIRSE-PTRQDKARKLLDILKRKGPEAFDIFCQALRE 73 (85)
T ss_dssp HHHHHHHHHHTTSSSHHHHHHHHTS-SSHHHHHHHHHHHHHHCCHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHCCCCCHHHHHHHHcc-CChHHHHHHHHHHHHHHCHHHHHHHHHHHHh
Confidence 34455556667777777 7777663 2334556777777776777777777666665
No 56
>COG4842 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=37.73 E-value=1.2e+02 Score=20.00 Aligned_cols=69 Identities=20% Similarity=0.189 Sum_probs=37.8
Q ss_pred cCHHHHHHHHhHhhccccccChHHHHHHHHHHHHHHHh--c-CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 042062 66 VNYVELDRYFYNLKGSSASIGANKVRNEVNKTRELCRA--A-NWEEAKVSLEQLKVEHSTLKDKLTAYFELVA 135 (142)
Q Consensus 66 ~D~~~l~~~aH~LKGss~~lGA~~L~~~c~~LE~~~~~--~-~~~~~~~~~~~l~~~~~~~~~~L~~~l~~~~ 135 (142)
++++.+...|=.++|++..+-. -|.++...+...... | ........+.+..+....+...|..+-.--+
T Consensus 7 ~~~~~~~~~A~~~~~~~~~i~~-~l~~l~s~~~~l~~~W~G~a~~~f~~~~~~w~~~~~~l~~~l~~i~~~l~ 78 (97)
T COG4842 7 VNPEEMRATAKDYAGSSGEIQA-LLQDLASEIAKLQSAWEGDAAEAFQSEQQQWNQAATELNEALEQLADALR 78 (97)
T ss_pred CCHHHHHHHHHHHHhhhHHHHH-HHHHHHHHHHHHHhhcCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5778888888888888776655 444444444433332 2 2234445555555555555555544444333
No 57
>PF14357 DUF4404: Domain of unknown function (DUF4404)
Probab=37.59 E-value=45 Score=21.74 Aligned_cols=28 Identities=21% Similarity=0.302 Sum_probs=18.6
Q ss_pred HHHHHHHHHHhccCcchhhHH-HHHHhhc
Q 042062 4 LRQQIAEMRQSFFDEEILDRY-FIQLEQL 31 (142)
Q Consensus 4 ~~~~~~~~~~~~~~~~~lD~~-l~~L~~l 31 (142)
|+++++.+-.-+...+.+|.. -..|..+
T Consensus 2 L~~~L~~L~~eL~~~~~ld~~~~~~L~~l 30 (85)
T PF14357_consen 2 LQELLEKLHQELEQNPPLDEETRAELSSL 30 (85)
T ss_pred HHHHHHHHHHHHhcCCCCCHHHHHHHHHH
Confidence 566666666666666777776 6666555
No 58
>KOG2424 consensus Protein involved in transcription start site selection [Transcription]
Probab=37.30 E-value=55 Score=24.77 Aligned_cols=23 Identities=13% Similarity=0.175 Sum_probs=18.8
Q ss_pred ccccChHHHHHHHHHHHHHHHhcCH
Q 042062 82 SASIGANKVRNEVNKTRELCRAANW 106 (142)
Q Consensus 82 s~~lGA~~L~~~c~~LE~~~~~~~~ 106 (142)
-+++||.-+.++|..|+. ++.++
T Consensus 147 dA~~Gaf~I~elcq~l~~--~s~d~ 169 (195)
T KOG2424|consen 147 DATLGAFLILELCQCLQA--QSDDL 169 (195)
T ss_pred hhhhhHHHHHHHHHHHHh--ccccH
Confidence 578999999999999987 44443
No 59
>smart00188 IL10 Interleukin-10 family. Interleukin-10 inhibits the synthesis of a number of cytokines, including IFN-gamma, IL-2, IL-3, TNF and GM-CSF produced by activated macrophages and by helper T cells.
Probab=37.23 E-value=1.6e+02 Score=21.18 Aligned_cols=31 Identities=16% Similarity=0.291 Sum_probs=23.7
Q ss_pred chhhHHHHHHhhc-CCCChhhHHHHHHHHHHcHH
Q 042062 19 EILDRYFIQLEQL-GENNPGFVEDVLTVYFRDST 51 (142)
Q Consensus 19 ~~lD~~l~~L~~l-~~~~~~~~~eli~~F~~d~~ 51 (142)
.+|+.+ -|+.+ +..+.-++.+||.-|++++=
T Consensus 28 vll~~~--ll~~~k~~~gC~~l~ell~FYLd~V~ 59 (137)
T smart00188 28 ILLTES--LLEDFKGYLGCQALSEMIQFYLEEVM 59 (137)
T ss_pred HhhhHH--HHHHhCCCcchHHHHHHHHHHHHHHH
Confidence 345553 44556 77889999999999999874
No 60
>PF04282 DUF438: Family of unknown function (DUF438); InterPro: IPR007380 This is a a group of uncharacterised proteins.
Probab=36.37 E-value=1.1e+02 Score=19.32 Aligned_cols=48 Identities=21% Similarity=0.382 Sum_probs=28.4
Q ss_pred Hhhc-CCCChhhHHHHHHHHHHc-HHHHHHHHHHHHhcCccCHHHHHHHH
Q 042062 28 LEQL-GENNPGFVEDVLTVYFRD-STRTLANIEKELQKTEVNYVELDRYF 75 (142)
Q Consensus 28 L~~l-~~~~~~~~~eli~~F~~d-~~~~l~~L~~al~~~~~D~~~l~~~a 75 (142)
|++| .+.+++-+++-+...+.+ ++.-|..+.+.+=+..++...+.++|
T Consensus 6 i~~Lh~G~~~e~vk~~F~~~~~~Vs~~EI~~~Eq~Li~eG~~~eeiq~LC 55 (71)
T PF04282_consen 6 IKRLHEGEDPEEVKEEFKKLFSDVSASEISAAEQELIQEGMPVEEIQKLC 55 (71)
T ss_pred HHHHhCCCCHHHHHHHHHHHHCCCCHHHHHHHHHHHHHcCCCHHHHHHHh
Confidence 4556 555666665555554444 55566666665554446777777665
No 61
>PF07445 priB_priC: Primosomal replication protein priB and priC; InterPro: IPR010890 This family contains the bacterial primosomal replication proteins priB and priC (approximately 180 residues long). In Escherichia coli, these function in the assembly of the primosome [].
Probab=36.29 E-value=1.7e+02 Score=21.48 Aligned_cols=23 Identities=22% Similarity=0.537 Sum_probs=18.9
Q ss_pred HHHHHHHcHHHHHHHHHHHHhcC
Q 042062 42 VLTVYFRDSTRTLANIEKELQKT 64 (142)
Q Consensus 42 li~~F~~d~~~~l~~L~~al~~~ 64 (142)
.+.-|+.+....+..|......+
T Consensus 41 ~L~~yl~Ei~~~l~~L~~~~~~~ 63 (173)
T PF07445_consen 41 RLSDYLQEIEQTLAQLQQQVEQN 63 (173)
T ss_pred hHHHHHHHHHHHHHHHHHHHhcC
Confidence 36778888888899999888775
No 62
>PF04280 Tim44: Tim44-like domain; InterPro: IPR007379 Tim44 is an essential component of the machinery that mediates the translocation of nuclear-encoded proteins across the mitochondrial inner membrane []. Tim44 is thought to bind phospholipids of the mitochondrial inner membrane both by electrostatic interactions and by penetrating the polar head group region [].; GO: 0015450 P-P-bond-hydrolysis-driven protein transmembrane transporter activity, 0006886 intracellular protein transport, 0005744 mitochondrial inner membrane presequence translocase complex; PDB: 2CW9_A 2FXT_A 3QK9_A.
Probab=35.98 E-value=65 Score=22.32 Aligned_cols=36 Identities=17% Similarity=0.412 Sum_probs=27.8
Q ss_pred ChhhHHHHHHHHHHcHHHHHHHHHHHHhcCccCHHHHHHHH
Q 042062 35 NPGFVEDVLTVYFRDSTRTLANIEKELQKTEVNYVELDRYF 75 (142)
Q Consensus 35 ~~~~~~eli~~F~~d~~~~l~~L~~al~~~~~D~~~l~~~a 75 (142)
+|.|- ...|+..+.+.+..+..|..++ |...++.++
T Consensus 12 dp~Fd---~~~F~~~ak~~f~~i~~A~~~~--D~~~l~~~~ 47 (147)
T PF04280_consen 12 DPGFD---PAAFLEEAKEAFLPIQEAWAKG--DLEALRPLL 47 (147)
T ss_dssp -TT-----HHHHHHHHHHTHHHHHHHHHHT---HHHHHHHB
T ss_pred CCCCC---HHHHHHHHHHHHHHHHHHHHcC--CHHHHHHHh
Confidence 34664 6789999999999999999999 999888663
No 63
>PF06013 WXG100: Proteins of 100 residues with WXG; InterPro: IPR010310 ESAT-6 is a small protein appears to be of fundamental importance in virulence and protective immunity in Mycobacterium tuberculosis. Homologues have been detected in other Gram-positive bacterial species. It may represent a novel secretion system potentially driven by the PF01580 from PFAM domains in the YukA-like proteins []. Members of this protein family include secretion targets for type main variants of type VII secretion systems (T7SS), one found in the Actinobacteria, one found in the Firmicutes. This model was derived through iteration from PF06013 from PFAM. The best characterised member of this family is ESAT-6 from Mycobacterium tuberculosis. Members of this family usually are ~100 amino acids in length but occasionally have long C-terminal extension. ; PDB: 3FAV_A 1WA8_A 3Q4H_B 2KG7_A 2VRZ_B 2VS0_B 3OGI_A 3H6P_B 3GVM_B 3GWK_C ....
Probab=35.87 E-value=1e+02 Score=18.56 Aligned_cols=27 Identities=11% Similarity=0.156 Sum_probs=13.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 042062 108 EAKVSLEQLKVEHSTLKDKLTAYFELV 134 (142)
Q Consensus 108 ~~~~~~~~l~~~~~~~~~~L~~~l~~~ 134 (142)
.+...+.++...+..+...|..+.+..
T Consensus 48 af~~~~~~~~~~~~~~~~~L~~~~~~l 74 (86)
T PF06013_consen 48 AFQDKFEEWNQAFRQLNEALEELSQAL 74 (86)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344555555555555555555444443
No 64
>PRK12491 pyrroline-5-carboxylate reductase; Reviewed
Probab=35.19 E-value=64 Score=25.35 Aligned_cols=69 Identities=9% Similarity=0.182 Sum_probs=45.4
Q ss_pred HHHHHHHHhccCcchhhHH-HHHHhhcCCCChhhHHHHHHHHHHcHHHHHHHHHHHHhcCccCHHHHHHH-HhHhhcccc
Q 042062 6 QQIAEMRQSFFDEEILDRY-FIQLEQLGENNPGFVEDVLTVYFRDSTRTLANIEKELQKTEVNYVELDRY-FYNLKGSSA 83 (142)
Q Consensus 6 ~~~~~~~~~~~~~~~lD~~-l~~L~~l~~~~~~~~~eli~~F~~d~~~~l~~L~~al~~~~~D~~~l~~~-aH~LKGss~ 83 (142)
+.+..++..+=..-++++. |+.+-.+...+|.|+-.+++.+.+-. ++.+ .+.+..+++ +++++|++.
T Consensus 145 ~~v~~lf~~~G~~~~~~E~~~d~~talsgsgPAf~~~~~eal~~a~----------v~~G-l~~~~A~~l~~~t~~G~a~ 213 (272)
T PRK12491 145 KEVLNIFNIFGQTEVVNEKLMDVVTSISGSSPAYVYMFIEAMADAA----------VLGG-MPRKQAYKFAAQAVLGSAK 213 (272)
T ss_pred HHHHHHHHcCCCEEEEcHHHhhhHHHhccCcHHHHHHHHHHHHHHH----------HHcC-CCHHHHHHHHHHHHHHHHH
Confidence 4456666666666678888 99999997789999888777655433 2222 344444444 466888875
Q ss_pred cc
Q 042062 84 SI 85 (142)
Q Consensus 84 ~l 85 (142)
.+
T Consensus 214 ll 215 (272)
T PRK12491 214 MV 215 (272)
T ss_pred HH
Confidence 43
No 65
>PF09403 FadA: Adhesion protein FadA; InterPro: IPR018543 FadA (Fusobacterium adhesin A) is an adhesin which forms two alpha helices. ; PDB: 3ETZ_B 3ETY_A 2GL2_B 3ETX_C 3ETW_A.
Probab=35.04 E-value=1.2e+02 Score=21.44 Aligned_cols=10 Identities=40% Similarity=0.182 Sum_probs=0.0
Q ss_pred ccccccChHH
Q 042062 80 GSSASIGANK 89 (142)
Q Consensus 80 Gss~~lGA~~ 89 (142)
=||.+++|+.
T Consensus 12 lss~sfaA~~ 21 (126)
T PF09403_consen 12 LSSISFAATA 21 (126)
T ss_dssp ----------
T ss_pred HHHHHHHccc
Confidence 3566777766
No 66
>PRK10807 paraquat-inducible protein B; Provisional
Probab=34.62 E-value=3.2e+02 Score=24.00 Aligned_cols=28 Identities=7% Similarity=0.092 Sum_probs=14.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 042062 108 EAKVSLEQLKVEHSTLKDKLTAYFELVAQ 136 (142)
Q Consensus 108 ~~~~~~~~l~~~~~~~~~~L~~~l~~~~~ 136 (142)
++...+.++.+....++. |-.+|+.++.
T Consensus 501 ~l~~tl~~l~~~~r~lr~-l~~~L~~~P~ 528 (547)
T PRK10807 501 KMVADMQRLDQVLRELQP-VLKTLNEKSN 528 (547)
T ss_pred HHHHHHHHHHHHHHHHHH-HHHHHHhCch
Confidence 444555555555554444 4455555443
No 67
>TIGR00208 fliS flagellar biosynthetic protein FliS. The function of this protein in flagellar biosynthesis is unknown, but appears to be regulatory. The member of this family in Vibrio parahaemolyticus is designated FlaJ (creating a synonym for FliS) and was shown essential for flagellin biosynthesis.
Probab=34.60 E-value=1.6e+02 Score=20.42 Aligned_cols=29 Identities=0% Similarity=0.133 Sum_probs=22.2
Q ss_pred HHHHHHHHcHHHHHHHHHHHHhcCccCHHHH
Q 042062 41 DVLTVYFRDSTRTLANIEKELQKTEVNYVEL 71 (142)
Q Consensus 41 eli~~F~~d~~~~l~~L~~al~~~~~D~~~l 71 (142)
++|-...+..-+.+.....++.++ |++..
T Consensus 22 ~Li~mLydg~i~~l~~a~~ai~~~--d~~~~ 50 (124)
T TIGR00208 22 ELTLMLYNGCLKFIRLAAQAIEND--DIERK 50 (124)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHcC--CHHHH
Confidence 667777777777788888889988 87643
No 68
>PF03847 TFIID_20kDa: Transcription initiation factor TFIID subunit A; InterPro: IPR003228 Human transcription initiation factor TFIID is composed of the TATA-binding polypeptide (TBP) and at least 13 TBP-associated factors (TAFs) that collectively or individually are involved in activator-dependent transcription [].; GO: 0006352 transcription initiation, DNA-dependent, 0005669 transcription factor TFIID complex; PDB: 1H3O_B.
Probab=34.55 E-value=67 Score=20.06 Aligned_cols=46 Identities=13% Similarity=0.203 Sum_probs=26.6
Q ss_pred HHHHHHHHHhccCcchhhHHHHHHhhcCCCChhhHHHHHHHHHHcHHHHHHHHHHH
Q 042062 5 RQQIAEMRQSFFDEEILDRYFIQLEQLGENNPGFVEDVLTVYFRDSTRTLANIEKE 60 (142)
Q Consensus 5 ~~~~~~~~~~~~~~~~lD~~l~~L~~l~~~~~~~~~eli~~F~~d~~~~l~~L~~a 60 (142)
+.++..+++.+.-..-+|+. -.+++.++.+.|++++-..-..+...
T Consensus 2 K~~l~~Lv~~iDp~~~ld~~----------vee~Ll~laddFv~~v~~~ac~lAKh 47 (68)
T PF03847_consen 2 KRKLQELVKQIDPNEKLDPD----------VEELLLELADDFVDDVVSFACRLAKH 47 (68)
T ss_dssp HHHHHHHHHCC-SS----HH----------HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred hHHHHHHHHHcCCCCCCCHH----------HHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 45677788887665556654 22556677778888876665555544
No 69
>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=33.87 E-value=85 Score=17.20 Aligned_cols=33 Identities=15% Similarity=0.253 Sum_probs=22.6
Q ss_pred HHHHhhc-CCCChhhHHHHHHHHHHcHHHHHHHH
Q 042062 25 FIQLEQL-GENNPGFVEDVLTVYFRDSTRTLANI 57 (142)
Q Consensus 25 l~~L~~l-~~~~~~~~~eli~~F~~d~~~~l~~L 57 (142)
+..|+++ +.-++..++.++..+-.+....+..|
T Consensus 6 v~~L~~mFP~l~~~~I~~~L~~~~g~ve~~i~~L 39 (43)
T smart00546 6 LHDLKDMFPNLDEEVIKAVLEANNGNVEATINNL 39 (43)
T ss_pred HHHHHHHCCCCCHHHHHHHHHHcCCCHHHHHHHH
Confidence 7788888 87777777776666665665555443
No 70
>PF03194 LUC7: LUC7 N_terminus; InterPro: IPR004882 This family consists of several LUC7 protein homologues that are restricted to eukaryotes. LUC7 has been shown to be a U1 snRNA associated protein [] with a role in splice site recognition []. The entry contains human and mouse LUC7 like (LUC7L) proteins [] and human cisplatin resistance-associated overexpressed protein (CROP) [].
Probab=33.68 E-value=2.3e+02 Score=22.19 Aligned_cols=73 Identities=16% Similarity=0.236 Sum_probs=43.5
Q ss_pred HHHHHHHHHcHHHHHHHHHHHHhcCccCHHHHHHH--HhHhhccccccChHHHHHHHHHHHHHHHhcCHHHHHHHHHHHH
Q 042062 40 EDVLTVYFRDSTRTLANIEKELQKTEVNYVELDRY--FYNLKGSSASIGANKVRNEVNKTRELCRAANWEEAKVSLEQLK 117 (142)
Q Consensus 40 ~eli~~F~~d~~~~l~~L~~al~~~~~D~~~l~~~--aH~LKGss~~lGA~~L~~~c~~LE~~~~~~~~~~~~~~~~~l~ 117 (142)
-+.+..|+.++...|..-..-++..+.+....... +=.|..-. ..+..+....|.++..|+.+++..++..++
T Consensus 85 ~~~L~~~i~d~drrI~~~k~RL~~~~~~~~~~~~~~~~~~i~~l~-----~~I~~ll~~aE~LGeeG~VdeA~~~~~~~e 159 (254)
T PF03194_consen 85 LRYLQRLIRDCDRRIERAKERLEQTQEEQAKEADEEKAEKIDELD-----EKIGELLKEAEELGEEGDVDEAQKLMEEVE 159 (254)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhCccccccchhhhHHHHHHHHH-----HHHHHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence 36688999999998887777666431111111110 11111111 236677788999999999987766554443
No 71
>PHA02845 hypothetical protein; Provisional
Probab=32.93 E-value=60 Score=21.64 Aligned_cols=43 Identities=9% Similarity=0.023 Sum_probs=33.1
Q ss_pred HHHHHHhccCcchhhHH-HHHHhhc-CCCChhhHHHHHHHHHHcH
Q 042062 8 IAEMRQSFFDEEILDRY-FIQLEQL-GENNPGFVEDVLTVYFRDS 50 (142)
Q Consensus 8 ~~~~~~~~~~~~~lD~~-l~~L~~l-~~~~~~~~~eli~~F~~d~ 50 (142)
+-+.++|+..+...|+. ++.+..= ....+.+++.++..+++=.
T Consensus 5 L~~Kl~sIe~~N~~nek~LDcIi~~iE~~~~~llRP~~RLlfDl~ 49 (91)
T PHA02845 5 LFSKLKSIERENLLNESILDCIINEIENNHHYLFRPFIRLTIDLI 49 (91)
T ss_pred HHHHHHHHHHHhhhhhhHHHHHHHHHHhcccHHHHHHHHHHHHHH
Confidence 45778888888888888 8776655 6667778888888887753
No 72
>PF05396 Phage_T7_Capsid: Phage T7 capsid assembly protein; InterPro: IPR008768 This family contains the capsid assembly protein (scaffolding protein) of bacteriophage T7.; GO: 0019069 viral capsid assembly
Probab=32.27 E-value=1.8e+02 Score=20.48 Aligned_cols=57 Identities=4% Similarity=0.054 Sum_probs=34.1
Q ss_pred hhHHHHHHhhcCCCChhhHHHHHHHHHHcHHHHHHHHHHHHhcCccCHHHHHHHHhHhhc
Q 042062 21 LDRYFIQLEQLGENNPGFVEDVLTVYFRDSTRTLANIEKELQKTEVNYVELDRYFYNLKG 80 (142)
Q Consensus 21 lD~~l~~L~~l~~~~~~~~~eli~~F~~d~~~~l~~L~~al~~~~~D~~~l~~~aH~LKG 80 (142)
.|...+.+..+- |+++=...|+.---..+|..++.+..+++++ |...++-+.-.+.+
T Consensus 32 ~~~yV~~V~~~A-GG~e~f~~i~~~~~~~~~~~~ea~~~Ai~~~--dla~vk~~vn~~~~ 88 (123)
T PF05396_consen 32 AEQYVNSVKGYA-GGEEGFAAIMSHAEANSPAAAEAFNEAIESG--DLATVKAAVNLAGA 88 (123)
T ss_pred HHHHHHHHHHHh-cCHHHHHHHHHHHHhCCHHHHHHHHHHHHhC--CHHHHHHHHHHHHH
Confidence 333355555552 2234444544444456777888888888888 87777766544443
No 73
>PRK08507 prephenate dehydrogenase; Validated
Probab=31.97 E-value=1.8e+02 Score=22.49 Aligned_cols=48 Identities=15% Similarity=0.435 Sum_probs=27.4
Q ss_pred HHHHhhcCCCChhhHHHHHH-------HHHHcHHHHHHHHHHHHhcCccCHHHHHHH
Q 042062 25 FIQLEQLGENNPGFVEDVLT-------VYFRDSTRTLANIEKELQKTEVNYVELDRY 74 (142)
Q Consensus 25 l~~L~~l~~~~~~~~~eli~-------~F~~d~~~~l~~L~~al~~~~~D~~~l~~~ 74 (142)
|..+..+...+|.+..+++. .-+++..+.+.+++.++..+ |.+.+.+.
T Consensus 210 frd~tria~~~p~l~~~i~~~N~~~~~~~l~~~~~~l~~~~~~l~~~--d~~~~~~~ 264 (275)
T PRK08507 210 FRSMSRLAKSSPAMWSDIFKQNKENVLEAIDEFIKELEQFKQLIENE--DWEELEEW 264 (275)
T ss_pred hhhhhhcccCCHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHcC--CHHHHHHH
Confidence 44444554456777666542 23444455566777777777 76665543
No 74
>cd08329 CARD_BIRC2_BIRC3 Caspase activation and recruitment domain found in Baculoviral IAP repeat-containing proteins, BIRC2 (c-IAP1) and BIRC3 (c-IAP2). Caspase activation and recruitment domain (CARD) similar to those found in Baculoviral IAP repeat (BIR)-containing protein 2 (BIRC2) or cellular Inhibitor of Apoptosis Protein 1 (c-IAP1), and BIRC3 (or c-IAP2). IAPs are anti-apoptotic proteins that contain at least one BIR domain. Most IAPs also contain a C-terminal RING domain. In addition, both BIRC2 and BIRC3 contain a CARD. BIRC2 and BIRC3, through their binding with TRAF (TNF receptor-associated factor) 2, are recruited to TNFR-1/2 signaling complexes, where they regulate caspase-8 activity. They also play important roles in pro-survival NF-kB signaling pathways. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation and host-defense mechanisms. DDs are protein-protein interac
Probab=31.86 E-value=1.5e+02 Score=19.49 Aligned_cols=60 Identities=10% Similarity=0.177 Sum_probs=44.3
Q ss_pred HHHHhccCcchhhHH-HHHHhhcCCCChhhHHHHHHHHHHcHHHHHHHHHHHHhcCccCHHHHH
Q 042062 10 EMRQSFFDEEILDRY-FIQLEQLGENNPGFVEDVLTVYFRDSTRTLANIEKELQKTEVNYVELD 72 (142)
Q Consensus 10 ~~~~~~~~~~~lD~~-l~~L~~l~~~~~~~~~eli~~F~~d~~~~l~~L~~al~~~~~D~~~l~ 72 (142)
.++..+...|+|+.+ .+.++.-+. ..+-.+.||+....-.+.-...+..++... |..-..
T Consensus 27 ~ilD~Ll~~~Vlt~ee~e~I~~~~t-~~~qAr~Lld~l~~KG~~A~~~F~~~L~e~--~~~L~~ 87 (94)
T cd08329 27 PILDSLLSANVITEQEYDVIKQKTQ-TPLQARELIDTVLVKGNAAAEVFRNCLKKN--DPVLYR 87 (94)
T ss_pred HHHHHHHHcCCCCHHHHHHHHcCCC-hHHHHHHHHHHHHhhhHHHHHHHHHHHHhc--CHhHHH
Confidence 466677788888888 888887622 246778888888888888888888888765 544433
No 75
>cd08332 CARD_CASP2 Caspase activation and recruitment domain of Caspase-2. Caspase activation and recruitment domain (CARD) similar to that found in caspase-2. Caspases are aspartate-specific cysteine proteases with functions in apoptosis and immune signaling. Caspase-2 (also known as ICH1, NEDD2, or CASP2) is one of the most evolutionarily conserved caspases, and plays a role in apoptosis, DNA damage response, cell cycle regulation, and tumor suppression. It is localized in the nucleus and exhibits properties of both an initiator and an effector caspase. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and
Probab=31.68 E-value=1.5e+02 Score=19.32 Aligned_cols=54 Identities=13% Similarity=0.143 Sum_probs=28.5
Q ss_pred HHHHhccCcchhhHH-HHHHhhcCCCChhhHHHHHHHHHHcHHHHHHHHHHHHhcC
Q 042062 10 EMRQSFFDEEILDRY-FIQLEQLGENNPGFVEDVLTVYFRDSTRTLANIEKELQKT 64 (142)
Q Consensus 10 ~~~~~~~~~~~lD~~-l~~L~~l~~~~~~~~~eli~~F~~d~~~~l~~L~~al~~~ 64 (142)
..+..+...|+|... .+.+...+. ..+-...+++..-.-.|.-+..+-.|+...
T Consensus 24 ~v~~~L~~~gvlt~~~~~~I~~~~t-~~~k~~~Lld~L~~RG~~AF~~F~~aL~~~ 78 (90)
T cd08332 24 ELLIHLLQKDILTDSMAESIMAKPT-SFSQNVALLNLLPKRGPRAFSAFCEALRET 78 (90)
T ss_pred HHHHHHHHcCCCCHHHHHHHHcCCC-cHHHHHHHHHHHHHhChhHHHHHHHHHHhc
Confidence 344445555666666 666665511 123344555555555555555555555543
No 76
>KOG2833 consensus Mevalonate pyrophosphate decarboxylase [Lipid transport and metabolism]
Probab=31.09 E-value=97 Score=25.73 Aligned_cols=31 Identities=3% Similarity=0.292 Sum_probs=25.2
Q ss_pred HHHHHHHc-HHHHHHHHHHHHhcCccCHHHHHHH
Q 042062 42 VLTVYFRD-STRTLANIEKELQKTEVNYVELDRY 74 (142)
Q Consensus 42 li~~F~~d-~~~~l~~L~~al~~~~~D~~~l~~~ 74 (142)
++.-=++. +|++|.+|++|+.++ ||+.+.++
T Consensus 223 L~qhRi~~vVP~Ri~~m~eaI~~r--DF~~FA~l 254 (395)
T KOG2833|consen 223 LLQHRIESVVPQRIQQMREAIRER--DFESFAKL 254 (395)
T ss_pred HHHHHHHhhhHHHHHHHHHHHHhc--CHHHHHHH
Confidence 34444555 899999999999999 99998876
No 77
>PF12854 PPR_1: PPR repeat
Probab=30.83 E-value=61 Score=16.87 Aligned_cols=22 Identities=18% Similarity=0.336 Sum_probs=17.2
Q ss_pred HHHHHHHHhcCHHHHHHHHHHH
Q 042062 95 NKTRELCRAANWEEAKVSLEQL 116 (142)
Q Consensus 95 ~~LE~~~~~~~~~~~~~~~~~l 116 (142)
.-+...|+.|..+++..++.++
T Consensus 12 ~lI~~~Ck~G~~~~A~~l~~~M 33 (34)
T PF12854_consen 12 TLIDGYCKAGRVDEAFELFDEM 33 (34)
T ss_pred HHHHHHHHCCCHHHHHHHHHhC
Confidence 4466789999999988887764
No 78
>KOG1104 consensus Nuclear cap-binding complex, subunit NCBP1/CBP80 [RNA processing and modification]
Probab=30.83 E-value=4.3e+02 Score=24.36 Aligned_cols=101 Identities=16% Similarity=0.124 Sum_probs=73.5
Q ss_pred HHHhhc-CCCChhhHHHHHHHHHHcHHHHHHHHHHHHhcCccCHHHHHHHHhHhhccc--cccChHHHHHHHHHHHHHHH
Q 042062 26 IQLEQL-GENNPGFVEDVLTVYFRDSTRTLANIEKELQKTEVNYVELDRYFYNLKGSS--ASIGANKVRNEVNKTRELCR 102 (142)
Q Consensus 26 ~~L~~l-~~~~~~~~~eli~~F~~d~~~~l~~L~~al~~~~~D~~~l~~~aH~LKGss--~~lGA~~L~~~c~~LE~~~~ 102 (142)
..|-.+ ...|+.|..+++..|+.+. +..+..+ +|.+.+-++|-|---+ .-+-+..|..+...+=.++.
T Consensus 87 aTLvgllN~kn~~fg~~~v~~~~~~~-------q~sl~~~--~~n~ar~llrfL~dL~~~~vl~~~sli~l~esl~~~~~ 157 (759)
T KOG1104|consen 87 ATLVGLLNLKNFNFGGEFVEYMIEEL-------QESLKSG--NWNEARYLLRFLSDLSNCHVLQADSLINLFESLLDAAI 157 (759)
T ss_pred HHHHHHHhccchhhHHHHHHHHHHHH-------HHHhhcC--ChHHHHHHHHHHHHHhcCCccChHHHHHHHHHHHHHHH
Confidence 344444 4567788888888877654 5777888 9999999999887655 77888888888888777777
Q ss_pred hcCHHHH-----------------HHHHHHHHHHHHHHHHHHHHHHHHHH
Q 042062 103 AANWEEA-----------------KVSLEQLKVEHSTLKDKLTAYFELVA 135 (142)
Q Consensus 103 ~~~~~~~-----------------~~~~~~l~~~~~~~~~~L~~~l~~~~ 135 (142)
..+.+.. .++-++.+.+++++...++.|+..-+
T Consensus 158 e~~~Pqvr~D~~v~~vLs~lPw~g~el~e~~~~~~e~ll~~ie~Yl~~R~ 207 (759)
T KOG1104|consen 158 EENVPQVRRDYYVYCVLSSLPWFGRELNEKKPTEMEELLVYIEIYLKKRK 207 (759)
T ss_pred hhcCcchhhhHHHHHHHhccchhhhhhcccchHHHHHHHHHHHHHHHHhc
Confidence 6554322 24445567788888888888887543
No 79
>PF04840 Vps16_C: Vps16, C-terminal region; InterPro: IPR006925 This protein forms part of the Class C vacuolar protein sorting (Vps) complex. Vps16 is essential for vacuolar protein sorting, which is essential for viability in plants, but not yeast []. The Class C Vps complex is required for SNARE-mediated membrane fusion at the lysosome-like yeast vacuole. It is thought to play essential roles in membrane docking and fusion at the Golgi-to-endosome and endosome-to-vacuole stages of transport []. The role of VPS16 in this complex is not known.; GO: 0006886 intracellular protein transport, 0005737 cytoplasm
Probab=30.13 E-value=3e+02 Score=22.30 Aligned_cols=87 Identities=14% Similarity=0.110 Sum_probs=54.5
Q ss_pred hhhHH-HHHHhhc-CCCChhhHHHHHHHHHHc-HHHHHHHHHHHHhcCccCHHHHHHHHhHhhccccccChHHHHHHHHH
Q 042062 20 ILDRY-FIQLEQL-GENNPGFVEDVLTVYFRD-STRTLANIEKELQKTEVNYVELDRYFYNLKGSSASIGANKVRNEVNK 96 (142)
Q Consensus 20 ~lD~~-l~~L~~l-~~~~~~~~~eli~~F~~d-~~~~l~~L~~al~~~~~D~~~l~~~aH~LKGss~~lGA~~L~~~c~~ 96 (142)
+++.+ -+.+..+ .-+.......|...|.=. -.=.+-.++..+..+ +|+.+...+.+=| +-||-..+.+.|-.
T Consensus 175 f~~~Sl~~Ti~~li~~~~~k~A~kl~k~Fkv~dkrfw~lki~aLa~~~--~w~eL~~fa~skK---sPIGyepFv~~~~~ 249 (319)
T PF04840_consen 175 FVGLSLNDTIRKLIEMGQEKQAEKLKKEFKVPDKRFWWLKIKALAENK--DWDELEKFAKSKK---SPIGYEPFVEACLK 249 (319)
T ss_pred hhcCCHHHHHHHHHHCCCHHHHHHHHHHcCCcHHHHHHHHHHHHHhcC--CHHHHHHHHhCCC---CCCChHHHHHHHHH
Confidence 33434 3344444 334445566777777322 222456788888888 9999999998744 35999999999864
Q ss_pred HHHHHHhcCHHHHHHHHHHHH
Q 042062 97 TRELCRAANWEEAKVSLEQLK 117 (142)
Q Consensus 97 LE~~~~~~~~~~~~~~~~~l~ 117 (142)
.|+...+...+..+.
T Consensus 250 ------~~~~~eA~~yI~k~~ 264 (319)
T PF04840_consen 250 ------YGNKKEASKYIPKIP 264 (319)
T ss_pred ------CCCHHHHHHHHHhCC
Confidence 344445555555533
No 80
>PF00512 HisKA: His Kinase A (phospho-acceptor) domain; InterPro: IPR003661 Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions []. Some bacteria can contain up to as many as 200 two-component systems that need tight regulation to prevent unwanted cross-talk []. These pathways have been adapted to response to a wide variety of stimuli, including nutrients, cellular redox state, changes in osmolarity, quorum signals, antibiotics, and more []. Two-component systems are comprised of a sensor histidine kinase (HK) and its cognate response regulator (RR) []. The HK catalyses its own auto-phosphorylation followed by the transfer of the phosphoryl group to the receiver domain on RR; phosphorylation of the RR usually activates an attached output domain, which can then effect changes in cellular physiology, often by regulating gene expression. Some HK are bifunctional, catalysing both the phosphorylation and dephosphorylation of their cognate RR. The input stimuli can regulate either the kinase or phosphatase activity of the bifunctional HK. A variant of the two-component system is the phospho-relay system. Here a hybrid HK auto-phosphorylates and then transfers the phosphoryl group to an internal receiver domain, rather than to a separate RR protein. The phosphoryl group is then shuttled to histidine phosphotransferase (HPT) and subsequently to a terminal RR, which can evoke the desired response [, ]. Signal transducing histidine kinases are the key elements in two-component signal transduction systems, which control complex processes such as the initiation of development in microorganisms [, ]. Examples of histidine kinases are EnvZ, which plays a central role in osmoregulation [], and CheA, which plays a central role in the chemotaxis system []. Histidine kinases usually have an N-terminal ligand-binding domain and a C-terminal kinase domain, but other domains may also be present. The kinase domain is responsible for the autophosphorylation of the histidine with ATP, the phosphotransfer from the kinase to an aspartate of the response regulator, and (with bifunctional enzymes) the phosphotransfer from aspartyl phosphate back to ADP or to water []. The kinase core has a unique fold, distinct from that of the Ser/Thr/Tyr kinase superfamily. HKs can be roughly divided into two classes: orthodox and hybrid kinases [, ]. Most orthodox HKs, typified by the Escherichia coli EnvZ protein, function as periplasmic membrane receptors and have a signal peptide and transmembrane segment(s) that separate the protein into a periplasmic N-terminal sensing domain and a highly conserved cytoplasmic C-terminal kinase core. Members of this family, however, have an integral membrane sensor domain. Not all orthodox kinases are membrane bound, e.g., the nitrogen regulatory kinase NtrB (GlnL) is a soluble cytoplasmic HK []. Hybrid kinases contain multiple phosphodonor and phosphoacceptor sites and use multi-step phospho-relay schemes instead of promoting a single phosphoryl transfer. In addition to the sensor domain and kinase core, they contain a CheY-like receiver domain and a His-containing phosphotransfer (HPt) domain. This entry represents the dimerisation and phosphoacceptor domain found in histidine kinases. It has been found in bacterial sensor protein/histidine kinases. Signal transducing histidine kinases are the key elements in two-component signal transduction systems, which control complex processes such as the initiation of development in microorganisms []. Examples of histidine kinases are EnvZ, which plays a central role in osmoregulation [], and CheA, which plays a central role in the chemotaxis system []. Histidine kinases usually have an N-terminal ligand-binding domain and a C-terminal kinase domain, but other domains may also be present. The kinase domain is responsible for the autophosphorylation of the histidine with ATP, the phosphotransfer from the kinase to an aspartate of the response regulator, and the phosphotransfer from aspartyl phosphate back to ADP or to water []. The homodimeric domain includes the site of histidine autophosphorylation and phosphate transfer reactions. The structure of the homodimeric domain comprises a closed, four-helical bundle with a left-handed twist, formed by two identical alpha-hairpin subunits.; GO: 0000155 two-component sensor activity, 0007165 signal transduction, 0016020 membrane; PDB: 3DGE_A 2C2A_A 3A0R_A 4EW8_A 2LFS_B 2LFR_B 3JZ3_A 1JOY_B 3ZRW_C 3ZRV_A ....
Probab=29.97 E-value=1.2e+02 Score=17.69 Aligned_cols=58 Identities=12% Similarity=0.099 Sum_probs=38.3
Q ss_pred HHHHHHhHhhccccccChHHHHHHHHHHHHHHH-hcC-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 042062 70 ELDRYFYNLKGSSASIGANKVRNEVNKTRELCR-AAN-WEEAKVSLEQLKVEHSTLKDKLTAYFELVA 135 (142)
Q Consensus 70 ~l~~~aH~LKGss~~lGA~~L~~~c~~LE~~~~-~~~-~~~~~~~~~~l~~~~~~~~~~L~~~l~~~~ 135 (142)
-+...+|-||..= ..+...++.... ... .+.....+..+..+..++..-+..++.+-|
T Consensus 5 ~~~~isHelr~PL--------~~i~~~~~~l~~~~~~~~~~~~~~l~~i~~~~~~l~~li~~ll~~sr 64 (68)
T PF00512_consen 5 FLASISHELRNPL--------TAIRGYLELLERDSDLDPEQLREYLDRIRSAADRLNELINDLLDFSR 64 (68)
T ss_dssp HHHHHHHHHHHHH--------HHHHHHHHHHHCSSCC-HHHCHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHhHHHHHHH--------HHHHHHHHHHHHccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 3567888888653 333344444444 333 333478889999999888888888877654
No 81
>cd08819 CARD_MDA5_2 Caspase activation and recruitment domain found in MDA5, second repeat. Caspase activation and recruitment domain (CARD) found in MDA5 (melanoma-differentiation-associated gene 5), second repeat. MDA5, also known as IFIH1, contains two N-terminal CARD domains and a C-terminal RNA helicase domain. MDA5 is a cytoplasmic DEAD box RNA helicase that plays an important role in host antiviral response by sensing incoming viral RNA. Upon activation, the signal is transferred to downstream pathways via the adaptor molecule IPS-1 (MAVS, VISA, CARDIF), leading to the induction of type I interferons. Although very similar in sequence, MDA5 recognizes different sets of viruses compared to RIG-I, a related RNA helicase. MDA5 associates with IPS-1 through a CARD-CARD interaction. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. DDs are protei
Probab=29.67 E-value=1.7e+02 Score=19.37 Aligned_cols=56 Identities=9% Similarity=0.157 Sum_probs=30.2
Q ss_pred HHHHHHHhccCcchhhHH-HHHHhhc--CCCChhhHHHHHHHHHHcHHHHHHHHHHHHhc
Q 042062 7 QIAEMRQSFFDEEILDRY-FIQLEQL--GENNPGFVEDVLTVYFRDSTRTLANIEKELQK 63 (142)
Q Consensus 7 ~~~~~~~~~~~~~~lD~~-l~~L~~l--~~~~~~~~~eli~~F~~d~~~~l~~L~~al~~ 63 (142)
+....+..+...|++... .+.+..- ..++.+-+++++...- ..|.-++..-.++..
T Consensus 20 ~~~~v~d~ll~~~ilT~~d~e~I~aa~~~~g~~~~ar~LL~~L~-rg~~aF~~Fl~aLre 78 (88)
T cd08819 20 KTRDVCDKCLEQGLLTEEDRNRIEAATENHGNESGARELLKRIV-QKEGWFSKFLQALRE 78 (88)
T ss_pred hHHHHHHHHHhcCCCCHHHHHHHHHhccccCcHHHHHHHHHHhc-cCCcHHHHHHHHHHH
Confidence 344555556666666666 6666654 2344455555555554 555555555555543
No 82
>KOG4552 consensus Vitamin-D-receptor interacting protein complex component [Transcription]
Probab=29.61 E-value=2.6e+02 Score=21.79 Aligned_cols=36 Identities=19% Similarity=0.194 Sum_probs=24.0
Q ss_pred HHHHcHHHHHHHHHHHHhcCccCHHHHHHHHhHhhcc
Q 042062 45 VYFRDSTRTLANIEKELQKTEVNYVELDRYFYNLKGS 81 (142)
Q Consensus 45 ~F~~d~~~~l~~L~~al~~~~~D~~~l~~~aH~LKGs 81 (142)
+-+=.+.+.+..+++|- .++|.-+.+-.+||++-.+
T Consensus 106 ta~fqA~qKLksi~~A~-krpvsSEelIKyAHrIS~~ 141 (272)
T KOG4552|consen 106 TACFQANQKLKSIKEAE-KRPVSSEELIKYAHRISKH 141 (272)
T ss_pred HHHHHHHHHHHHHHHHh-cCCCCHHHHHHHHHHhhhc
Confidence 33334555566666663 4478889999999998544
No 83
>PRK11199 tyrA bifunctional chorismate mutase/prephenate dehydrogenase; Provisional
Probab=29.54 E-value=2.9e+02 Score=22.76 Aligned_cols=48 Identities=10% Similarity=0.186 Sum_probs=26.2
Q ss_pred HhhcCCCChhhHHHHHHH------HHHcHHHHHHHHHHHHhcCccCHHHHHHHHhH
Q 042062 28 LEQLGENNPGFVEDVLTV------YFRDSTRTLANIEKELQKTEVNYVELDRYFYN 77 (142)
Q Consensus 28 L~~l~~~~~~~~~eli~~------F~~d~~~~l~~L~~al~~~~~D~~~l~~~aH~ 77 (142)
...+..++|++..+++.. -+++..+.+..+..+++++ |++.+.++.-.
T Consensus 292 ~tRia~~~p~lw~dI~~~N~~~~~~l~~~~~~l~~l~~~l~~~--d~~~l~~~~~~ 345 (374)
T PRK11199 292 VGRLFAQDPQLYADIIMSSPENLALIKRYYQRFGEALELLEQG--DKQAFIDSFRK 345 (374)
T ss_pred HHHHHcCCHHHHHHHHHhChhHHHHHHHHHHHHHHHHHHHHcC--CHHHHHHHHHH
Confidence 444434555555554421 1233344566777777777 77777665444
No 84
>TIGR01240 mevDPdecarb diphosphomevalonate decarboxylase. Alternate names: mevalonate diphosphate decarboxylase; pyrophosphomevalonate decarboxylase
Probab=28.71 E-value=1.1e+02 Score=24.71 Aligned_cols=31 Identities=3% Similarity=0.196 Sum_probs=26.4
Q ss_pred HHHHHHcHHHHHHHHHHHHhcCccCHHHHHHHH
Q 042062 43 LTVYFRDSTRTLANIEKELQKTEVNYVELDRYF 75 (142)
Q Consensus 43 i~~F~~d~~~~l~~L~~al~~~~~D~~~l~~~a 75 (142)
+...++.++..+..+..++.++ |++.+.+.+
T Consensus 202 ~~~~v~~~~~~l~~~~~ai~~~--D~~~~g~~~ 232 (305)
T TIGR01240 202 FKEWIEHVVPDFEVXRKAIKTK--DFATFGKET 232 (305)
T ss_pred HHHHHHHHHHHHHHHHHHHHhc--cHHHHHHHH
Confidence 5667777887899999999999 999988765
No 85
>PTZ00431 pyrroline carboxylate reductase; Provisional
Probab=28.68 E-value=66 Score=24.90 Aligned_cols=70 Identities=7% Similarity=0.066 Sum_probs=48.6
Q ss_pred HHHHHHHHHhccCcchhhHH-HHHHhhcCCCChhhHHHHHHHHHHcHHHHHHHHHHHHhcCccCHHH-HHHHHhHhhccc
Q 042062 5 RQQIAEMRQSFFDEEILDRY-FIQLEQLGENNPGFVEDVLTVYFRDSTRTLANIEKELQKTEVNYVE-LDRYFYNLKGSS 82 (142)
Q Consensus 5 ~~~~~~~~~~~~~~~~lD~~-l~~L~~l~~~~~~~~~eli~~F~~d~~~~l~~L~~al~~~~~D~~~-l~~~aH~LKGss 82 (142)
...+..+|.++=..-.++++ |+..-.+...+|.|+..+++.+.+-.. ..+ .+.+. .+-.+++++|++
T Consensus 137 ~~~v~~l~~~~G~~~~v~E~~~d~~ta~~gsgPA~~~~~~~al~~~~v----------~~G-l~~~~a~~l~~~~~~G~a 205 (260)
T PTZ00431 137 KKKVIDIFSACGIIQEIKEKDMDIATAISGCGPAYVFLFIESLIDAGV----------KNG-LNRDVSKNLVLQTILGSV 205 (260)
T ss_pred HHHHHHHHHhCCcEEEEChHHcchhhhhcCCHHHHHHHHHHHHHHHHH----------HcC-CCHHHHHHHHHHHHHHHH
Confidence 34677888887777789988 999998877789999887776654332 222 34443 344568888887
Q ss_pred ccc
Q 042062 83 ASI 85 (142)
Q Consensus 83 ~~l 85 (142)
..+
T Consensus 206 ~ll 208 (260)
T PTZ00431 206 HMV 208 (260)
T ss_pred HHH
Confidence 643
No 86
>PF00435 Spectrin: Spectrin repeat; InterPro: IPR002017 Spectrin repeats [] are found in several proteins involved in cytoskeletal structure. These include spectrin alpha and beta subunits [, ], alpha-actinin [] and dystrophin. The spectrin repeat forms a three-helix bundle. The second helix is interrupted by proline in some sequences. The repeats are defined by a characteristic tryptophan (W) residue at position 17 in helix A and a leucine (L) at 2 residues from the carboxyl end of helix C.; GO: 0005515 protein binding; PDB: 1HCI_A 1QUU_A 3FB2_B 1S35_A 1U5P_A 1U4Q_A 1CUN_B 1YDI_B 3EDV_A 1AJ3_A ....
Probab=28.27 E-value=1.5e+02 Score=18.23 Aligned_cols=43 Identities=12% Similarity=0.108 Sum_probs=28.2
Q ss_pred HHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 042062 90 VRNEVNKTRELCRAANWEEAKVSLEQLKVEHSTLKDKLTAYFEL 133 (142)
Q Consensus 90 L~~~c~~LE~~~~~~~~~~~~~~~~~l~~~~~~~~~~L~~~l~~ 133 (142)
+...+..| ......+.+.+...+..|...|..++..+......
T Consensus 60 l~~~~~~L-~~~~~~~~~~i~~~~~~l~~~w~~l~~~~~~r~~~ 102 (105)
T PF00435_consen 60 LNEQAQQL-IDSGPEDSDEIQEKLEELNQRWEALCELVEERRQK 102 (105)
T ss_dssp HHHHHHHH-HHTTHTTHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHH-HHcCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33444555 22334466778888888888888888887665443
No 87
>cd07298 PX_RICS The phosphoinositide binding Phox Homology domain of PX-RICS. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions such as cell signaling, vesicular trafficking, protein sorting, and lipid modification, among others. RICS is a Rho GTPase-activating protein for cdc42 and Rac1. It is implicated in the regulation of postsynaptic signaling and neurite outgrowth. An N-terminal splicing variant of RICS containing additional PX and Src Homology 3 (SH3) domains, also called PX-RICS, is the main isoform expressed during neural development. PX-RICS is involved in neural functions including axon and dendrite extension, postnatal remodeling, and fine-tuning of neural circuits during early brain development. The PX domain is involved in targeting of proteins to PI-enriched membranes, and may also be involved in protein-protein interaction. The PX domain of PX-RICS specifically binds phosphatidylinositol 3-phosphate (PI3P), PI4P, and
Probab=27.37 E-value=74 Score=22.11 Aligned_cols=38 Identities=29% Similarity=0.436 Sum_probs=26.7
Q ss_pred hccCcchhhHHHHHHhhc-CC----CChhhHHHHHHHHHHcHH
Q 042062 14 SFFDEEILDRYFIQLEQL-GE----NNPGFVEDVLTVYFRDST 51 (142)
Q Consensus 14 ~~~~~~~lD~~l~~L~~l-~~----~~~~~~~eli~~F~~d~~ 51 (142)
.+-+.=+-|+.|++|.+| +. .+|+++..++..|++.-.
T Consensus 55 ~~LHrCvyDRrfS~L~eLp~~~~l~~~~~~v~~~l~~YL~RlS 97 (115)
T cd07298 55 KHLHLCIYDRRFSQLPELPRSDSLKDSPESVTQMLMAYLSRLS 97 (115)
T ss_pred HHHHHHHHhhhhhccccCCCcccccccHHHHHHHHHHHHHHHH
Confidence 334445678889999999 32 256888888888887543
No 88
>COG3433 Aryl carrier domain [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=27.23 E-value=1.3e+02 Score=19.24 Aligned_cols=51 Identities=10% Similarity=0.180 Sum_probs=32.5
Q ss_pred HHHHHHHHcHHHHHHHHHHHHhcCccCHHHHHHHHhHhhccccccChHHHHH
Q 042062 41 DVLTVYFRDSTRTLANIEKELQKTEVNYVELDRYFYNLKGSSASIGANKVRN 92 (142)
Q Consensus 41 eli~~F~~d~~~~l~~L~~al~~~~~D~~~l~~~aH~LKGss~~lGA~~L~~ 92 (142)
+++...+.++++.+..=...+..| .|.-.+..++|+.|-.-+.|+...|+.
T Consensus 5 ~~~~~Ll~e~~~~l~dqeNLi~~G-LDSiR~M~L~~~wR~~G~~i~F~~La~ 55 (74)
T COG3433 5 EQIAELLGESVEELDDQENLIDYG-LDSIRMMALLERWRKRGADIDFAQLAA 55 (74)
T ss_pred HHHHHHHcCChhhcCchhhHHHhc-hhHHHHHHHHHHHHHcCCcccHHHHHh
Confidence 344444455555554444455444 577778888888888888888777654
No 89
>PF07870 DUF1657: Protein of unknown function (DUF1657); InterPro: IPR012452 This domain appears to be restricted to the Bacillales.
Probab=27.08 E-value=1.4e+02 Score=17.41 Aligned_cols=36 Identities=17% Similarity=0.104 Sum_probs=25.8
Q ss_pred HHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHHHH
Q 042062 95 NKTRELCRAANWEEAKVSLEQLKVEHSTLKDKLTAY 130 (142)
Q Consensus 95 ~~LE~~~~~~~~~~~~~~~~~l~~~~~~~~~~L~~~ 130 (142)
..+|..+-.-+-+.+...+.+....+..+...|+.+
T Consensus 14 A~Le~fal~T~d~~AK~~y~~~a~~l~~ii~~L~~r 49 (50)
T PF07870_consen 14 ADLETFALQTQDQEAKQMYEQAAQQLEEIIQDLEPR 49 (50)
T ss_pred hhHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHhHcc
Confidence 457777776666677888888888888777776543
No 90
>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=26.53 E-value=86 Score=14.88 Aligned_cols=23 Identities=17% Similarity=0.424 Sum_probs=16.2
Q ss_pred HHHHHHHhcCHHHHHHHHHHHHH
Q 042062 96 KTRELCRAANWEEAKVSLEQLKV 118 (142)
Q Consensus 96 ~LE~~~~~~~~~~~~~~~~~l~~ 118 (142)
-+...++.|+.+++...+.++..
T Consensus 6 li~~~~~~~~~~~a~~~~~~M~~ 28 (31)
T PF01535_consen 6 LISGYCKMGQFEEALEVFDEMRE 28 (31)
T ss_pred HHHHHHccchHHHHHHHHHHHhH
Confidence 35667777888887777776653
No 91
>PRK10698 phage shock protein PspA; Provisional
Probab=26.31 E-value=3e+02 Score=21.06 Aligned_cols=23 Identities=9% Similarity=0.296 Sum_probs=14.3
Q ss_pred HHHHHHHHcHHHHHHHHHHHHhc
Q 042062 41 DVLTVYFRDSTRTLANIEKELQK 63 (142)
Q Consensus 41 eli~~F~~d~~~~l~~L~~al~~ 63 (142)
.+|+.|+.+..+.+..++.+++.
T Consensus 27 k~l~q~i~em~~~l~~~r~alA~ 49 (222)
T PRK10698 27 KLVRLMIQEMEDTLVEVRSTSAR 49 (222)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 35666666666666666666554
No 92
>PF02203 TarH: Tar ligand binding domain homologue; InterPro: IPR003122 Methyl-accepting chemotaxis proteins (MCPs) are a family of bacterial receptors that mediate chemotaxis to diverse signals, responding to changes in the concentration of attractants and repellents in the environment by altering swimming behaviour []. Environmental diversity gives rise to diversity in bacterial signalling receptors, and consequently there are many genes encoding MCPs []. For example, there are four well-characterised MCPs found in Escherichia coli: Tar (taxis towards aspartate and maltose, away from nickel and cobalt), Tsr (taxis towards serine, away from leucine, indole and weak acids), Trg (taxis towards galactose and ribose) and Tap (taxis towards dipeptides). MCPs share similar topology and signalling mechanisms. MCPs either bind ligands directly or interact with ligand-binding proteins, transducing the signal to downstream signalling proteins in the cytoplasm. MCPs undergo two covalent modifications: deamidation and reversible methylation at a number of glutamate residues. Attractants increase the level of methylation, while repellents decrease it. The methyl groups are added by the methyl-transferase cheR and are removed by the methylesterase cheB. Most MCPs are homodimers that contain the following organisation: an N-terminal signal sequence that acts as a transmembrane domain in the mature protein; a poorly-conserved periplasmic receptor (ligand-binding) domain; a second transmembrane domain; and a highly-conserved C-terminal cytoplasmic domain that interacts with downstream signalling components. The C-terminal domain contains the glycosylated glutamate residues. This entry represents the ligand-binding domain found in a number of methyl-accepting chemotaxis receptors.; GO: 0004888 transmembrane signaling receptor activity, 0006935 chemotaxis, 0007165 signal transduction, 0016020 membrane; PDB: 2ASR_A 3ATP_A 2D4U_A 2LIG_A 1VLS_A 1LIH_A 1WAT_B 1VLT_B 1WAS_A 1JMW_A.
Probab=25.80 E-value=2.3e+02 Score=19.70 Aligned_cols=85 Identities=6% Similarity=0.022 Sum_probs=45.8
Q ss_pred hhHHHHHHHHHHcHHHHHHHHHHHHhcCccCHHHHHHHHhHhhccccccChHHHHHHHHHHHHHHHhcCHHHHHHH-HHH
Q 042062 37 GFVEDVLTVYFRDSTRTLANIEKELQKTEVNYVELDRYFYNLKGSSASIGANKVRNEVNKTRELCRAANWEEAKVS-LEQ 115 (142)
Q Consensus 37 ~~~~eli~~F~~d~~~~l~~L~~al~~~~~D~~~l~~~aH~LKGss~~lGA~~L~~~c~~LE~~~~~~~~~~~~~~-~~~ 115 (142)
..+.. ++.+++++.+.+..........+.+......+.-...- -+...+..+..+.+.+|..+.... ..+
T Consensus 82 ~~l~~-~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~--------~~~~~l~~~~~al~~~d~~~~~~~~~~~ 152 (171)
T PF02203_consen 82 ELLAR-AEQNLEQAEQAFDAFKALPHASPEERALADELEASFDA--------YLQQALDPLLAALRAGDIAAFMQLPNEK 152 (171)
T ss_dssp HHHHH-HHHHHHHHHHHHHHHHCS---GTGGHHHHHHHHHHHHH---------HHHHHHHHHHHHHTT-HHHHHHSSHHH
T ss_pred HHHHH-HHHHHHHHHHHHHHHHccCCCCcchHHHHHHHHHHHHH--------HHHHhHHHHHHHHHCCCHHHHHHHHHHh
Confidence 44544 36666666666655554433221233334444333332 113445666666777888776555 777
Q ss_pred HHHHHHHHHHHHHHH
Q 042062 116 LKVEHSTLKDKLTAY 130 (142)
Q Consensus 116 l~~~~~~~~~~L~~~ 130 (142)
+...|......+..+
T Consensus 153 ~~~~~~~~~~~~~~~ 167 (171)
T PF02203_consen 153 IQPLFDAFTAAWQAQ 167 (171)
T ss_dssp HHHHHHHHHHHHHHH
T ss_pred cchhHHHHHHHHHHH
Confidence 777787777777664
No 93
>KOG2580 consensus Mitochondrial import inner membrane translocase, subunit TIM44 [Intracellular trafficking, secretion, and vesicular transport]
Probab=25.71 E-value=1.7e+02 Score=25.15 Aligned_cols=65 Identities=11% Similarity=0.314 Sum_probs=37.8
Q ss_pred HHHHHHHHHhccCcchhhHHHHHHhhcCCCChhhHHHHHHHHHHcHHHH-HHHHHHHHhcCccCHHHHHHHHhH
Q 042062 5 RQQIAEMRQSFFDEEILDRYFIQLEQLGENNPGFVEDVLTVYFRDSTRT-LANIEKELQKTEVNYVELDRYFYN 77 (142)
Q Consensus 5 ~~~~~~~~~~~~~~~~lD~~l~~L~~l~~~~~~~~~eli~~F~~d~~~~-l~~L~~al~~~~~D~~~l~~~aH~ 77 (142)
+.-|.+.+..+|.+-=.-+-+.+++.+++ .|- ...|+.++++. +.++-.|+-.+ |.+-|...||.
T Consensus 285 tdki~~~~~g~fsktE~Sev~tei~~iDP---sF~---~~~Flr~~ee~IiPnVLeAyvkG--D~evLK~wcse 350 (459)
T KOG2580|consen 285 TDKITDVDGGLFSKTEMSEVLTEIKKIDP---SFD---KEDFLRECEEYIIPNVLEAYVKG--DLEVLKKWCSE 350 (459)
T ss_pred HHhhhhcccccchhhHHHHHHHHHHhcCC---CCC---cHHHHHHHHHhhhHHHHHHHHhc--cHHHHHHHHhh
Confidence 34444444445543322222777777733 332 23344444443 45688888899 99999999885
No 94
>cd00082 HisKA Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via trans-autophosphorylation by the catalytic domain of the histidine kinase. They subsequently transfer the phosphoryl group to the Asp acceptor residue of a response regulator protein. Two-component signalling systems, consisting of a histidine protein kinase that senses a signal input and a response regulator that mediates the output, are ancient and evolutionarily conserved signaling mechanisms in prokaryotes and eukaryotes.
Probab=25.45 E-value=1.2e+02 Score=16.31 Aligned_cols=54 Identities=19% Similarity=0.178 Sum_probs=26.0
Q ss_pred HHHHHhHhhccccccChHHHHHHHHHHHHHHHhc-CHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 042062 71 LDRYFYNLKGSSASIGANKVRNEVNKTRELCRAA-NWEEAKVSLEQLKVEHSTLKDKLTAYFE 132 (142)
Q Consensus 71 l~~~aH~LKGss~~lGA~~L~~~c~~LE~~~~~~-~~~~~~~~~~~l~~~~~~~~~~L~~~l~ 132 (142)
+..++|.+|..-+.+ -..++...+.. ..+.....+..+.....++..-++.++.
T Consensus 8 ~~~~~hel~~pl~~i--------~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~ 62 (65)
T cd00082 8 LANVSHELRTPLTAI--------RGALELLEEELLDDEEQREYLERIREEAERLLRLINDLLD 62 (65)
T ss_pred HHHHhHHhcchHHHH--------HHHHHHHHhcccCcHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 456788888544322 12222222211 1334455566666666555555554443
No 95
>PRK07417 arogenate dehydrogenase; Reviewed
Probab=25.29 E-value=1.5e+02 Score=23.06 Aligned_cols=26 Identities=15% Similarity=0.397 Sum_probs=16.7
Q ss_pred HHcHHHHHHHHHHHHhcCccCHHHHHHH
Q 042062 47 FRDSTRTLANIEKELQKTEVNYVELDRY 74 (142)
Q Consensus 47 ~~d~~~~l~~L~~al~~~~~D~~~l~~~ 74 (142)
+++..+.+.+++.+++++ |.+.+.+.
T Consensus 241 l~~~~~~l~~~~~~l~~~--d~~~l~~~ 266 (279)
T PRK07417 241 LASYRQSLDQLEELIEQE--NWSALEQK 266 (279)
T ss_pred HHHHHHHHHHHHHHHHcC--CHHHHHHH
Confidence 344445567777888777 77666544
No 96
>PF14748 P5CR_dimer: Pyrroline-5-carboxylate reductase dimerisation; PDB: 2RCY_D 3TRI_A 2IZZ_B 2GR9_B 2GRA_B 2GER_C 1YQG_A 2AG8_A 3GT0_A 2AMF_E ....
Probab=25.21 E-value=71 Score=21.44 Aligned_cols=54 Identities=11% Similarity=0.118 Sum_probs=32.4
Q ss_pred hhHH-HHHHhhcCCCChhhHHHHHHHHHHcHHHHHHHHHHHHhcCccCHHHHH-HHHhHhhcccccc
Q 042062 21 LDRY-FIQLEQLGENNPGFVEDVLTVYFRDSTRTLANIEKELQKTEVNYVELD-RYFYNLKGSSASI 85 (142)
Q Consensus 21 lD~~-l~~L~~l~~~~~~~~~eli~~F~~d~~~~l~~L~~al~~~~~D~~~l~-~~aH~LKGss~~l 85 (142)
++++ |+-+-.+...+|.|+-.+++.+.+-.. ..+ ++.+..+ -.+++++|++.-+
T Consensus 1 V~E~~~d~~talsGsgpA~~~~~~eal~~a~v----------~~G-l~~~~A~~lv~~t~~G~a~ll 56 (107)
T PF14748_consen 1 VDEDQFDAATALSGSGPAYFFLFIEALADAAV----------AQG-LPREEARKLVAQTFIGAAKLL 56 (107)
T ss_dssp -SGGGHHHHHHHCTTHHHHHHHHHHHHHHHHH----------HTT---HHHHHHHHHHHHHHHHHHH
T ss_pred CCHHHHhHHHHHhccHHHHHHHHHHHHHHHHH----------HcC-CCHHHHHHHHHHHHHHHHHHH
Confidence 3566 788888866788998777776655432 222 3444333 4567888877544
No 97
>PF04722 Ssu72: Ssu72-like protein; InterPro: IPR006811 The highly conserved and essential protein Ssu72 has intrinsic phosphatase activity and plays an essential role in the transcription cycle. Ssu72 was originally identified in a yeast genetic screen as enhancer of a defect caused by a mutation in the transcription initiation factor TFIIB []. It binds to TFIIB and is also involved in mRNA elongation. Ssu72 is further involved in both poly(A) dependent and independent termination. It is a subunit of the yeast cleavage and polyadenylation factor (CPF), which is part of the machinery for mRNA 3'-end formation. Ssu72 is also essential for transcription termination of snRNAs [].; GO: 0004721 phosphoprotein phosphatase activity, 0006397 mRNA processing, 0005634 nucleus; PDB: 3O2S_B 3O2Q_E 3FMV_H 3OMW_D 3P9Y_B 3FDF_A 3OMX_A.
Probab=24.89 E-value=70 Score=24.35 Aligned_cols=36 Identities=22% Similarity=0.222 Sum_probs=22.8
Q ss_pred ccccChHHHHHHHHHHHHHHHhcCHH-HHHHHHHHHHH
Q 042062 82 SASIGANKVRNEVNKTRELCRAANWE-EAKVSLEQLKV 118 (142)
Q Consensus 82 s~~lGA~~L~~~c~~LE~~~~~~~~~-~~~~~~~~l~~ 118 (142)
-|.+||..+.++|..|+. ....+++ .+..++.+.+.
T Consensus 145 eA~~Ga~~ileLc~~l~~-~~~~d~e~~i~~il~~fe~ 181 (195)
T PF04722_consen 145 EATIGAFLILELCQMLEE-EASEDLEDEIDEILQEFEE 181 (195)
T ss_dssp HHHHHHHHHHHHHHHHH---TSSSHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHh-hccccHHHHHHHHHHHHHH
Confidence 468999999999999997 2334544 34444444443
No 98
>PF09209 DUF1956: Domain of unknown function (DUF1956); InterPro: IPR015292 This entry represents the C-terminal domain found in the hypothetical transcriptional regulator YbiH from bacteria such as Salmonella typhimurium and Escherichia coli. YbiH is a member of the TetR (tetracycline resistance) transcriptional regulator family of proteins. The C-terminal domains of YbiH and TetR share a multi-helical, interlocking structure.; PDB: 1T33_A.
Probab=24.78 E-value=2.1e+02 Score=18.80 Aligned_cols=82 Identities=11% Similarity=0.169 Sum_probs=53.2
Q ss_pred HHHHHHHHHHHhccCcchhhHH-HHHHhhc-CCCChhhHHHHHHHHHHcHHHHHHHHHHHHhcCccCHHHHHHHHhHhhc
Q 042062 3 ALRQQIAEMRQSFFDEEILDRY-FIQLEQL-GENNPGFVEDVLTVYFRDSTRTLANIEKELQKTEVNYVELDRYFYNLKG 80 (142)
Q Consensus 3 ~~~~~~~~~~~~~~~~~~lD~~-l~~L~~l-~~~~~~~~~eli~~F~~d~~~~l~~L~~al~~~~~D~~~l~~~aH~LKG 80 (142)
+|+.=+..++..+.+++--.+. ---++++ .+ + +.+..++..++.-..+.+..|-..+...+.|-..+...+|++=|
T Consensus 4 ~L~~~i~~~~~~l~~~~~~~~~~~l~~RE~~~P-t-~~~~~i~~~~~~P~~~~l~~ll~~~~g~~~~~~~~~~~~~si~g 81 (125)
T PF09209_consen 4 RLRAFIRALLRRLLSDPESRWWLRLIAREMLNP-T-PAFDRIVEELIRPKHEALARLLAEILGEPADDPEVRLCAFSIVG 81 (125)
T ss_dssp HHHHHHHHHHHHTTSG-GGHHHHHHHHHHHHS----HHHHHHHHHTHHHHHHHHHHHHHHHHT--TTSHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHcccchhHHHHHHHHHhcCc-h-HHHHHHHHHHhhhHHHHHHHHHHHHhCcCCChHHHHHHHHHHHH
Confidence 4566666777776666443333 3466777 44 2 55678888888777777777777666554567889999999888
Q ss_pred cccccC
Q 042062 81 SSASIG 86 (142)
Q Consensus 81 ss~~lG 86 (142)
.+..+.
T Consensus 82 ~~~~~~ 87 (125)
T PF09209_consen 82 QCLFFR 87 (125)
T ss_dssp HHHHHH
T ss_pred HHHHHH
Confidence 775543
No 99
>PF07361 Cytochrom_B562: Cytochrome b562; InterPro: IPR009155 Cytochrome b562 is a haem-containing protein that is expressed in the periplasm of Escherichia coli. In b-type cytochromes, the haem atom is not covalently attached to the polypeptide. Cytochrome b562 has a four-helical bundle structure that is structurally similar to that found in members of the cytochrome c family (IPR002321 from INTERPRO). Cytochrome b562 has a reduction potential of 167 mV, which sets the energy yield possible in metabolism and is also a key determinant of the rate at which redox reactions proceed [].; GO: 0005506 iron ion binding, 0009055 electron carrier activity, 0020037 heme binding, 0042597 periplasmic space; PDB: 4ER9_A 3IQ6_G 2QLA_B 3FOO_A 3M79_C 256B_A 3NMI_F 3HNK_A 3NMK_D 2BC5_A ....
Probab=24.68 E-value=1.4e+02 Score=19.96 Aligned_cols=38 Identities=29% Similarity=0.478 Sum_probs=27.1
Q ss_pred ccChHHHHHHHHHHHHHHHhcCHHHHHHHHH---HHHHHHH
Q 042062 84 SIGANKVRNEVNKTRELCRAANWEEAKVSLE---QLKVEHS 121 (142)
Q Consensus 84 ~lGA~~L~~~c~~LE~~~~~~~~~~~~~~~~---~l~~~~~ 121 (142)
.=|...|......++..+..|+.+++...+. .++.+|.
T Consensus 59 ~~Gl~~li~~id~a~~~~~~G~l~~AK~~l~~l~~lR~eyH 99 (103)
T PF07361_consen 59 QEGLDKLIDQIDKAEALAEAGKLDEAKAALKKLDDLRKEYH 99 (103)
T ss_dssp HHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 3466788888889999999999887765544 4444443
No 100
>PHA02666 hypothetical protein; Provisional
Probab=24.63 E-value=1.5e+02 Score=23.19 Aligned_cols=54 Identities=24% Similarity=0.425 Sum_probs=40.2
Q ss_pred CCChhhHHHHHHHHHHcHHHHHHHHHHHHhcCccCHHHHHHHHhHhhc----cccccChHHH
Q 042062 33 ENNPGFVEDVLTVYFRDSTRTLANIEKELQKTEVNYVELDRYFYNLKG----SSASIGANKV 90 (142)
Q Consensus 33 ~~~~~~~~eli~~F~~d~~~~l~~L~~al~~~~~D~~~l~~~aH~LKG----ss~~lGA~~L 90 (142)
.+.|.+-.. |-+.+.|.+.+|..|+..++. .+.=.+++.|.-|. -++|||-..|
T Consensus 201 agkpNLQ~D-IcTLC~DIEtQLSALEKSLES---ElnFYrrYIqDTKsLLatRAANIgsKAL 258 (287)
T PHA02666 201 AGKPNLQSD-ICTLCHDIETQLSALEKSLES---ELNFYRRYIQDTKSLLATRAANIGSKAL 258 (287)
T ss_pred CCCCchhhH-HHHhhhhHHHHHHHHHHHHHH---HHHHHHHHHHhHHHHHHHHhhcccccee
Confidence 345666544 889999999999999999987 56666788887665 4667776554
No 101
>PHA03079 hypothetical protein; Provisional
Probab=24.59 E-value=1e+02 Score=20.31 Aligned_cols=63 Identities=16% Similarity=0.166 Sum_probs=38.0
Q ss_pred HHHHHHhccCcchhhHH-HHHHh-hcCCCChhhHHHHHHHHHHcHHHH--HHHHHHHHhcCccCHHHHH
Q 042062 8 IAEMRQSFFDEEILDRY-FIQLE-QLGENNPGFVEDVLTVYFRDSTRT--LANIEKELQKTEVNYVELD 72 (142)
Q Consensus 8 ~~~~~~~~~~~~~lD~~-l~~L~-~l~~~~~~~~~eli~~F~~d~~~~--l~~L~~al~~~~~D~~~l~ 72 (142)
+-+.++|+..+..+|+. ++..- ++....+.+++.+++.|++=---. +..+-.-+-.+ ||..+-
T Consensus 4 l~~KLksIe~eN~~NEK~lDcII~eie~~~~~i~RPfiRL~iDvlil~iV~~~~~iRl~kR--Ny~~L~ 70 (87)
T PHA03079 4 IADRLDDIVKQNIADEKFVDFVIHGLEHQCPAILRPLIRLFIDILLFVIVIYIFTVRLVSR--NYQMLL 70 (87)
T ss_pred HHHHHHHHHHhhhhhhHHHHHHHHHHHHcCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHH
Confidence 45677888888888888 66543 335556788888888887652211 22333333345 666544
No 102
>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=24.25 E-value=1e+02 Score=14.84 Aligned_cols=23 Identities=26% Similarity=0.323 Sum_probs=16.7
Q ss_pred HHHHHHHhcCHHHHHHHHHHHHH
Q 042062 96 KTRELCRAANWEEAKVSLEQLKV 118 (142)
Q Consensus 96 ~LE~~~~~~~~~~~~~~~~~l~~ 118 (142)
-|...++.|+.+.+..++..+..
T Consensus 6 li~~~~~~~~~~~a~~~~~~M~~ 28 (35)
T TIGR00756 6 LIDGLCKAGRVEEALELFKEMLE 28 (35)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHH
Confidence 35567788888888888777654
No 103
>KOG2716 consensus Polymerase delta-interacting protein PDIP1 and related proteins, contain BTB/POZ domain [Inorganic ion transport and metabolism]
Probab=24.12 E-value=56 Score=25.47 Aligned_cols=52 Identities=10% Similarity=0.141 Sum_probs=39.6
Q ss_pred HHHHcHHHHHHHHHHHHhcCccCHHHHHHHHhHhhccccccChHHHHHHHHH
Q 042062 45 VYFRDSTRTLANIEKELQKTEVNYVELDRYFYNLKGSSASIGANKVRNEVNK 96 (142)
Q Consensus 45 ~F~~d~~~~l~~L~~al~~~~~D~~~l~~~aH~LKGss~~lGA~~L~~~c~~ 96 (142)
.|++.+|+.+.-+-..+..|.|+.+.-.+-.-.|+.-|--.+...|+++|..
T Consensus 48 IFIDRSpKHF~~ILNfmRdGdv~LPe~~kel~El~~EA~fYlL~~Lv~~C~~ 99 (230)
T KOG2716|consen 48 IFIDRSPKHFDTILNFMRDGDVDLPESEKELKELLREAEFYLLDGLVELCQS 99 (230)
T ss_pred EEecCChhHHHHHHHhhhcccccCccchHHHHHHHHHHHHhhHHHHHHHHHH
Confidence 4777788888888888887755555555555566777888888889999887
No 104
>PF09851 SHOCT: Short C-terminal domain; InterPro: IPR018649 This family of hypothetical prokaryotic proteins has no known function.
Probab=23.58 E-value=56 Score=16.98 Aligned_cols=19 Identities=11% Similarity=0.226 Sum_probs=14.1
Q ss_pred HHHhccCcchhhHH-HHHHh
Q 042062 11 MRQSFFDEEILDRY-FIQLE 29 (142)
Q Consensus 11 ~~~~~~~~~~lD~~-l~~L~ 29 (142)
.++.+++.|+|+.. |...+
T Consensus 7 ~L~~l~~~G~IseeEy~~~k 26 (31)
T PF09851_consen 7 KLKELYDKGEISEEEYEQKK 26 (31)
T ss_pred HHHHHHHcCCCCHHHHHHHH
Confidence 45677888888888 77654
No 105
>PRK13858 type IV secretion system T-DNA border endonuclease VirD1; Provisional
Probab=23.26 E-value=3e+02 Score=20.00 Aligned_cols=62 Identities=10% Similarity=0.115 Sum_probs=34.6
Q ss_pred HHHHHHHHhHhhccccccChHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 042062 68 YVELDRYFYNLKGSSASIGANKVRNEVNKTRELCRAANWEEAKVSLEQLKVEHSTLKDKLTAYFELVA 135 (142)
Q Consensus 68 ~~~l~~~aH~LKGss~~lGA~~L~~~c~~LE~~~~~~~~~~~~~~~~~l~~~~~~~~~~L~~~l~~~~ 135 (142)
.+.+..+...|.|-++|+ ++|+..|.. ....+.+.+..--..+-.+|..+-.-|..+|..-|
T Consensus 72 ~e~~~~lir~l~gianNL--NQLAr~aN~----~~~~~~~~l~~er~~~g~~~~~l~~~l~~~~~vsr 133 (147)
T PRK13858 72 REKMEAILQSIGTLSSNI--AALLSAYAE----NPRPDLEALRAERIAFGKEFADLDGLLRSILSVSR 133 (147)
T ss_pred HHHHHHHHHHHHHHHHHH--HHHHHHHhc----CCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344555666666666654 344444433 11123555555556666777777777777776654
No 106
>PF10018 Med4: Vitamin-D-receptor interacting Mediator subunit 4; InterPro: IPR019258 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. Members of this family represent the Med4 subunit of the Mediator (Med) complex [, ]. ; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006357 regulation of transcription from RNA polymerase II promoter, 0016592 mediator complex
Probab=23.25 E-value=3.1e+02 Score=20.22 Aligned_cols=21 Identities=24% Similarity=0.327 Sum_probs=18.3
Q ss_pred CccCHHHHHHHHhHhhccccc
Q 042062 64 TEVNYVELDRYFYNLKGSSAS 84 (142)
Q Consensus 64 ~~~D~~~l~~~aH~LKGss~~ 84 (142)
.+||+..|-.+||+|-..++.
T Consensus 79 ~~v~~~eLL~YA~rISk~t~~ 99 (188)
T PF10018_consen 79 RPVDYEELLSYAHRISKFTSA 99 (188)
T ss_pred CCCCHHHHHHHHHHHHHhcCC
Confidence 468999999999999887776
No 107
>PF08657 DASH_Spc34: DASH complex subunit Spc34 ; InterPro: IPR013966 The DASH complex is a ~10 subunit microtubule-binding complex that is transferred to the kinetochore prior to mitosis []. In Saccharomyces cerevisiae (Baker's yeast) DASH forms both rings and spiral structures on microtubules in vitro [, ]. Components of the DASH complex, including Dam1, Duo1, Spc34, Dad1 and Ask1, are essential and connect the centromere to the plus end of spindle microtubules [].
Probab=23.23 E-value=3.8e+02 Score=21.19 Aligned_cols=62 Identities=11% Similarity=0.112 Sum_probs=44.5
Q ss_pred HHHHHHHhHhhccccc----cChHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHHHH
Q 042062 69 VELDRYFYNLKGSSAS----IGANKVRNEVNKTRELCRAANWEEAKVSLEQLKVEHSTLKDKLTAY 130 (142)
Q Consensus 69 ~~l~~~aH~LKGss~~----lGA~~L~~~c~~LE~~~~~~~~~~~~~~~~~l~~~~~~~~~~L~~~ 130 (142)
...++.+|.+...+-. .|=..+-.+|+.+|..|.-=...++...+..+...|..+...+..|
T Consensus 134 ~~~~~~avA~vlG~~m~~e~~~d~dvevLL~~ae~L~~vYP~~ga~eki~~Lr~~y~~l~~~i~~l 199 (259)
T PF08657_consen 134 KQRRNTAVALVLGGVMHEEIVEDVDVEVLLRGAEKLCNVYPLPGAREKIAALRQRYNQLSNSIAYL 199 (259)
T ss_pred HHHHHHHHHHhccCcccccccccCCHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4555666555554422 3556777888889988887666688888899999998888877544
No 108
>PF13812 PPR_3: Pentatricopeptide repeat domain
Probab=23.22 E-value=1.1e+02 Score=14.91 Aligned_cols=22 Identities=18% Similarity=0.231 Sum_probs=15.5
Q ss_pred HHHHHHhcCHHHHHHHHHHHHH
Q 042062 97 TRELCRAANWEEAKVSLEQLKV 118 (142)
Q Consensus 97 LE~~~~~~~~~~~~~~~~~l~~ 118 (142)
|..+++.|+.+.+..++..++.
T Consensus 8 l~a~~~~g~~~~a~~~~~~M~~ 29 (34)
T PF13812_consen 8 LRACAKAGDPDAALQLFDEMKE 29 (34)
T ss_pred HHHHHHCCCHHHHHHHHHHHHH
Confidence 5566777888877777776654
No 109
>COG0282 ackA Acetate kinase [Energy production and conversion]
Probab=23.18 E-value=2.3e+02 Score=23.95 Aligned_cols=46 Identities=15% Similarity=0.261 Sum_probs=35.1
Q ss_pred HHHHHHcHHHHHHHHHHHHhcCccCHHHHHHHHhHhhccccccChHHHHHHHHHHHHHHHhcC
Q 042062 43 LTVYFRDSTRTLANIEKELQKTEVNYVELDRYFYNLKGSSASIGANKVRNEVNKTRELCRAAN 105 (142)
Q Consensus 43 i~~F~~d~~~~l~~L~~al~~~~~D~~~l~~~aH~LKGss~~lGA~~L~~~c~~LE~~~~~~~ 105 (142)
+.-..+......+++...+.++ ||-+|...++.-|+.+|.....|+
T Consensus 248 i~~l~~~~~~s~~~i~~~LNkk-----------------SGllGlSg~ssD~R~l~~~~~~g~ 293 (396)
T COG0282 248 ILYLMEQEGMSAEEIDTLLNKK-----------------SGLLGLSGLSSDMRDLEEAAAEGN 293 (396)
T ss_pred HHHHHHhcCCCHHHHHHHHhhh-----------------ccccccccccchHHHHHHHhccCc
Confidence 3334444445566777777666 999999999999999999999885
No 110
>TIGR00444 mazG MazG family protein. This family of prokaryotic proteins has no known function. It includes the uncharacterized protein MazG in E. coli.
Probab=23.07 E-value=1.5e+02 Score=23.23 Aligned_cols=92 Identities=8% Similarity=0.137 Sum_probs=55.6
Q ss_pred hhHHHHHHHHHHcHHHHHHHHHHH-HhcCccCHHHHHHHHhHhhcccc-----ccChHHHHHHHHHHHHHHHhc-CHHHH
Q 042062 37 GFVEDVLTVYFRDSTRTLANIEKE-LQKTEVNYVELDRYFYNLKGSSA-----SIGANKVRNEVNKTRELCRAA-NWEEA 109 (142)
Q Consensus 37 ~~~~eli~~F~~d~~~~l~~L~~a-l~~~~~D~~~l~~~aH~LKGss~-----~lGA~~L~~~c~~LE~~~~~~-~~~~~ 109 (142)
+.+..+...|+.--|-........ ++.-...|..+...-..=|+..+ .-+.+.|....+-.+.+++.| +++..
T Consensus 74 dvl~~~~~K~irRhphVf~~~~~~s~~e~~~~We~~K~~Ek~~~~~~s~ld~ip~~lPaL~~A~ki~~raa~~Gfdw~~~ 153 (248)
T TIGR00444 74 DVCAGISEKLVRRHPHVFADVKAEDESEVLARWEQIKAEEKAQKAQTSALDDVPRTLPALMRAAKIQKRCAKVGFDWEDV 153 (248)
T ss_pred HHHHHHHHHHHhhchhhhhccccCCHHHHHHHHHHHHHHHHhhcccCCccccCcccCCHHHHHHHHHHHHHHcCCCCCCc
Confidence 456666666776666555433210 00001145555544332222111 125567888888888889988 77788
Q ss_pred HHHHHHHHHHHHHHHHHHH
Q 042062 110 KVSLEQLKVEHSTLKDKLT 128 (142)
Q Consensus 110 ~~~~~~l~~~~~~~~~~L~ 128 (142)
...+.++..++.++..++.
T Consensus 154 ~~~~~k~~EE~~El~~a~~ 172 (248)
T TIGR00444 154 SPVWDKVYEELDEVMYEAR 172 (248)
T ss_pred HHHHHHHHHHHHHHHHHHh
Confidence 8889999999888888774
No 111
>PF11563 Protoglobin: Protoglobin; PDB: 2VEE_G 3QZZ_A 3R0G_A 3QZX_A 2VEB_A 1OR6_A 1OR4_B 2W31_B.
Probab=22.95 E-value=2.6e+02 Score=19.25 Aligned_cols=49 Identities=12% Similarity=0.157 Sum_probs=32.4
Q ss_pred hHHHHHHHHHHHhccCcchhhHH-HHHHhhcC------CCChhhHHHHHHHHHHcHH
Q 042062 2 EALRQQIAEMRQSFFDEEILDRY-FIQLEQLG------ENNPGFVEDVLTVYFRDST 51 (142)
Q Consensus 2 ~~~~~~~~~~~~~~~~~~~lD~~-l~~L~~l~------~~~~~~~~eli~~F~~d~~ 51 (142)
+.|+..+..+|..+++.+ +|.. +.....+| +-.|.++......+.+...
T Consensus 61 ~~lk~~q~~~~~~l~s~~-~d~~y~~~~~~iG~~H~~igl~~~~~~~~~~~~~~~l~ 116 (158)
T PF11563_consen 61 ERLKATQRRHWRELFSGD-FDEEYVERRRRIGQVHARIGLPPRWYIGAYSFLREFLL 116 (158)
T ss_dssp HHHHHHHHHHHHHCTSS--CSHHHHHHHHHHHHHHHHCT--HHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHhCCC-chHHHHHHHHHHHHHHhHcCCCHHHHHHHHHHHHHHHH
Confidence 568889999999999866 7777 87777774 2356666555555555443
No 112
>COG2178 Predicted RNA-binding protein of the translin family [Translation, ribosomal structure and biogenesis]
Probab=22.91 E-value=3.5e+02 Score=20.73 Aligned_cols=43 Identities=19% Similarity=0.234 Sum_probs=25.3
Q ss_pred HHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHHHH
Q 042062 88 NKVRNEVNKTRELCRAANWEEAKVSLEQLKVEHSTLKDKLTAY 130 (142)
Q Consensus 88 ~~L~~~c~~LE~~~~~~~~~~~~~~~~~l~~~~~~~~~~L~~~ 130 (142)
..+...|...-.+.+.|+.+.+...+.........++..|..|
T Consensus 27 Rei~r~s~~aI~~~H~~~~eeA~~~l~~a~~~v~~Lk~~l~~~ 69 (204)
T COG2178 27 REIVRLSGEAIFLLHRGDFEEAEKKLKKASEAVEKLKRLLAGF 69 (204)
T ss_pred HHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence 3445555555666666666666666666666665555555443
No 113
>PF09577 Spore_YpjB: Sporulation protein YpjB (SpoYpjB); InterPro: IPR014231 Proteins in thie entry, typified by YpjB, are restricted to a subset of the endospore-forming bacteria which includes Bacillus species, but not species. In Bacillus subtilis, ypjB was found to be part of the sigma-E regulon []. Sigma-E is a sporulation sigma factor that regulates expression in the mother cell compartment. Null mutants of ypjB show a sporulation defect, but this gene is not, however, a part of the endospore formation minimal gene set.
Probab=22.50 E-value=2.5e+02 Score=21.93 Aligned_cols=40 Identities=10% Similarity=0.251 Sum_probs=33.5
Q ss_pred HHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHH
Q 042062 88 NKVRNEVNKTRELCRAANWEEAKVSLEQLKVEHSTLKDKL 127 (142)
Q Consensus 88 ~~L~~~c~~LE~~~~~~~~~~~~~~~~~l~~~~~~~~~~L 127 (142)
..+......|++++..|+...+...++.+...|..+...+
T Consensus 101 ~~i~~~~~~mk~a~~~~~~~~f~~~~n~f~~~y~~I~Psl 140 (232)
T PF09577_consen 101 KPIMEDFQRMKQAAQKGDKEAFRASLNEFLSHYELIRPSL 140 (232)
T ss_pred HHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhcchh
Confidence 4567777889999999999999999999988888877765
No 114
>cd07278 PX_RICS_like The phosphoinositide binding Phox Homology domain of PX-RICS-like proteins. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions such as cell signaling, vesicular trafficking, protein sorting, and lipid modification, among others. Members of this family include PX-RICS, TCGAP (Tc10/Cdc42 GTPase-activating protein), and similar proteins. They contain N-terminal PX and Src Homology 3 (SH3) domains, a central Rho GAP domain, and C-terminal extensions. They act as Rho GTPase-activating proteins. PX-RICS is the main isoform expressed during neural development. It is involved in neural functions including axon and dendrite extension, postnatal remodeling, and fine-tuning of neural circuits during early brain development. The PX domain of PX-RICS specifically binds phosphatidylinositol 3-phosphate (PI3P), PI4P, and PI5P. TCGAP is widely expressed in the brain where it is involved in regulating the outgrowth of axons and d
Probab=21.87 E-value=77 Score=21.98 Aligned_cols=37 Identities=30% Similarity=0.422 Sum_probs=25.4
Q ss_pred hccCcchhhHHHHHHhhc-CCC----ChhhHHHHHHHHHHcH
Q 042062 14 SFFDEEILDRYFIQLEQL-GEN----NPGFVEDVLTVYFRDS 50 (142)
Q Consensus 14 ~~~~~~~lD~~l~~L~~l-~~~----~~~~~~eli~~F~~d~ 50 (142)
.+-+.=+-|+.|++|.+| ..+ .++.+..++..|++.-
T Consensus 54 ~~LHrCiyDRr~S~L~eL~~~~~~~~~~~~~~~~l~~YL~Rl 95 (114)
T cd07278 54 KHLHQCIYDRKFSQLTELPEECIEKREQQNLHQVLSDYLKRL 95 (114)
T ss_pred HHHHHHHHhhhhhccccCCccccccchHHHHHHHHHHHHHHH
Confidence 344446678889999999 321 4567778888887653
No 115
>PHA02649 hypothetical protein; Provisional
Probab=21.69 E-value=1.2e+02 Score=20.19 Aligned_cols=63 Identities=11% Similarity=0.030 Sum_probs=39.2
Q ss_pred HHHHHHhccCcchhhHH-HHHHh-hcCCCChhhHHHHHHHHHHcHHHH--HHHHHHHHhcCccCHHHHH
Q 042062 8 IAEMRQSFFDEEILDRY-FIQLE-QLGENNPGFVEDVLTVYFRDSTRT--LANIEKELQKTEVNYVELD 72 (142)
Q Consensus 8 ~~~~~~~~~~~~~lD~~-l~~L~-~l~~~~~~~~~eli~~F~~d~~~~--l~~L~~al~~~~~D~~~l~ 72 (142)
+-+.++++..+..+|+. ++.+- ++....+.+++.+++.|++=---. +..+-.-+-.+ +|..+-
T Consensus 5 L~~KL~~I~~eN~~NEK~lDcII~eie~~~~~i~RPfiRL~iDvlil~iV~~~~~iRl~kR--Ny~~Ll 71 (95)
T PHA02649 5 LINKLRNIELDNYGNEKIIDCIIYEIENTQYVIVRPILRLIVDLMILLIVLNDVIIRVIKR--NYKILL 71 (95)
T ss_pred HHHHHHHHHHHhhhhhHHHHHHHHHHHHcCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--hHHHHH
Confidence 45677888888888888 66543 335556788888888887653221 22333334445 776644
No 116
>PRK07502 cyclohexadienyl dehydrogenase; Validated
Probab=21.64 E-value=1.9e+02 Score=22.74 Aligned_cols=48 Identities=17% Similarity=0.253 Sum_probs=25.5
Q ss_pred HHHHhhcCCCChhhHHHHHH-------HHHHcHHHHHHHHHHHHhcCccCHHHHHHH
Q 042062 25 FIQLEQLGENNPGFVEDVLT-------VYFRDSTRTLANIEKELQKTEVNYVELDRY 74 (142)
Q Consensus 25 l~~L~~l~~~~~~~~~eli~-------~F~~d~~~~l~~L~~al~~~~~D~~~l~~~ 74 (142)
|..+..+...+|++..+++. .-+++..+.+..++.+++.+ |++.+.+.
T Consensus 223 frd~tRia~~~~~~w~~i~~~N~~~~~~~l~~~~~~l~~~~~~l~~~--d~~~l~~~ 277 (307)
T PRK07502 223 FRDFTRIAASDPTMWRDVFLHNKDAVLEMLGRFTEDLAALQRAIRWG--DGDALFDL 277 (307)
T ss_pred cccccccccCChHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHcC--CHHHHHHH
Confidence 33344454556666554432 12333444566777777777 77665544
No 117
>COG4623 Predicted soluble lytic transglycosylase fused to an ABC-type amino acid-binding protein [Cell envelope biogenesis, outer membrane]
Probab=21.36 E-value=4.6e+02 Score=22.54 Aligned_cols=114 Identities=11% Similarity=0.156 Sum_probs=67.0
Q ss_pred HHHHHHHHHHHhccCcchhhHHHHHHh-hcCCCChhhHHHHHHHHHHcHHHHHHHHHHHHhc--CccCHHHHHHHHh---
Q 042062 3 ALRQQIAEMRQSFFDEEILDRYFIQLE-QLGENNPGFVEDVLTVYFRDSTRTLANIEKELQK--TEVNYVELDRYFY--- 76 (142)
Q Consensus 3 ~~~~~~~~~~~~~~~~~~lD~~l~~L~-~l~~~~~~~~~eli~~F~~d~~~~l~~L~~al~~--~~~D~~~l~~~aH--- 76 (142)
-|+.-+.+|+.++..+|.++.-++.-- .+ +.-+++. -..|+.-....+.+++..+++ +..||..+...|.
T Consensus 220 tL~a~ll~F~~~~~e~g~larleeky~gH~--~~fdYvd--tr~f~~A~~~~Lp~~~pLfekya~e~dWrlLAAiaYQES 295 (473)
T COG4623 220 TLSAALLDFLNEAKEDGLLARLEEKYLGHG--DDFDYVD--TRTFLRAIDNRLPQLRPLFEKYAGELDWRLLAAIAYQES 295 (473)
T ss_pred HHHHHHHHHHHHhhcchHHHHHHHHHhccc--cccchhh--hHHHHHHHHhhhhhhhHHHHHhhccccHHHHHHHHHHHh
Confidence 477889999999999999986433221 11 1123332 366777777777777766663 3468988877664
Q ss_pred -HhhccccccChHHHHHHHHHHHHHHHhc-------CHHHHHHHHHHHHHHH
Q 042062 77 -NLKGSSASIGANKVRNEVNKTRELCRAA-------NWEEAKVSLEQLKVEH 120 (142)
Q Consensus 77 -~LKGss~~lGA~~L~~~c~~LE~~~~~~-------~~~~~~~~~~~l~~~~ 120 (142)
==-++.+.-|+..|+-+...-=+...=+ +..+....+.+|.+.+
T Consensus 296 HwnP~AtsptGvrGlMmLT~~TAqs~gv~dr~DpeqsI~ggs~YL~~i~~q~ 347 (473)
T COG4623 296 HWNPQATSPTGVRGLMMLTKATAQSMGVSDRTDPEQSISGGSRYLQDIMSQV 347 (473)
T ss_pred ccCCCCCCCccchhhhhhhHHHHHhcCCCccCChhhhhhHHHHHHHHHHHhC
Confidence 3445556666666665544322211111 2334455566665554
No 118
>smart00114 CARD Caspase recruitment domain. Motif contained in proteins involved in apoptotic signalling. Mediates homodimerisation. Structure consists of six antiparallel helices arranged in a topology homologue to the DEATH and the DED domain.
Probab=21.30 E-value=2.3e+02 Score=17.92 Aligned_cols=54 Identities=7% Similarity=0.139 Sum_probs=34.6
Q ss_pred HHHHhccCcchhhHH-HHHHhhcCCCChhhHHHHHHHHHHcHHHHHHHHHHHHhcC
Q 042062 10 EMRQSFFDEEILDRY-FIQLEQLGENNPGFVEDVLTVYFRDSTRTLANIEKELQKT 64 (142)
Q Consensus 10 ~~~~~~~~~~~lD~~-l~~L~~l~~~~~~~~~eli~~F~~d~~~~l~~L~~al~~~ 64 (142)
.++..+...++|+.. .+.++..+..- .=...+++....-.+.-+..+-.++...
T Consensus 24 ~vld~L~~~~Vlt~~e~e~i~~~~t~~-~~~~~Lld~l~~kG~~Af~~F~~~L~~~ 78 (88)
T smart00114 24 GLLDYLVEKNVLTEKEIEAIKAATTKL-RDKRELVDSLQKRGSQAFDTFLDSLQET 78 (88)
T ss_pred HHHHHHHHcCCCCHHHHHHHHccCChH-HHHHHHHHHHHhHhHHHHHHHHHHHHHc
Confidence 455566666777777 77777662211 2226677777777777777777777654
No 119
>PF11123 DNA_Packaging_2: DNA packaging protein ; InterPro: IPR024345 This entry represents Gp18 (gene 18 product), also known as DNA maturase A, from T7-like bacteriophages. In Bacteriophage T3, this protein is required for DNA packaging and functions in a complex with Gp19 [].
Probab=21.09 E-value=2.5e+02 Score=18.22 Aligned_cols=54 Identities=17% Similarity=0.126 Sum_probs=32.6
Q ss_pred hhHHHHHHHHHHc---HHHHHHHHHHHHhcCccCHHHHHHHHhHhhccccccChHHHHHHHHHHHHHHH
Q 042062 37 GFVEDVLTVYFRD---STRTLANIEKELQKTEVNYVELDRYFYNLKGSSASIGANKVRNEVNKTRELCR 102 (142)
Q Consensus 37 ~~~~eli~~F~~d---~~~~l~~L~~al~~~~~D~~~l~~~aH~LKGss~~lGA~~L~~~c~~LE~~~~ 102 (142)
++.+.|+.....+ +|+..+.+.+.+.. |.++=|+-..-..-|..++..+|+..+
T Consensus 14 EmA~~mL~DLr~dekRsPQLYnAI~k~L~R------------HkF~iskl~pd~~~LG~L~~aL~ey~~ 70 (82)
T PF11123_consen 14 EMAQQMLADLRDDEKRSPQLYNAIGKLLDR------------HKFQISKLQPDENILGELAAALEEYKK 70 (82)
T ss_pred HHHHHHHHHhcchhhcChHHHHHHHHHHHH------------ccchhhhcCccHHHHHHHHHHHHHHHH
Confidence 4555555555544 55566666666554 455555666666667777777776655
No 120
>KOG4747 consensus Two-component phosphorelay intermediate involved in MAP kinase cascade regulation [Signal transduction mechanisms]
Probab=20.82 E-value=3e+02 Score=20.08 Aligned_cols=59 Identities=5% Similarity=0.093 Sum_probs=45.5
Q ss_pred ChhhHHHHHHHHHHcHHHHHHHHHHHHhcCccCHHHHHHHHhHhhccccccChHHHHHHHHH
Q 042062 35 NPGFVEDVLTVYFRDSTRTLANIEKELQKTEVNYVELDRYFYNLKGSSASIGANKVRNEVNK 96 (142)
Q Consensus 35 ~~~~~~eli~~F~~d~~~~l~~L~~al~~~~~D~~~l~~~aH~LKGss~~lGA~~L~~~c~~ 96 (142)
..+|-..++..++.| .++.+|.+.......|+ -..-..|-+|+|+..+|-.+.+--|..
T Consensus 12 ~~d~~~sl~~qgild--~qF~qlq~lqD~~~p~f-v~ev~~~fF~~s~~~i~~~r~ald~~~ 70 (150)
T KOG4747|consen 12 VSDYTKSLFDQGILD--SQFLQLQELQDDSSPDF-VEEVVGLFFEDSERLINNLRLALDCER 70 (150)
T ss_pred HHHHHHHHHHHHhhH--HHHHHHHHHhcccCccH-HHHHHHHHHHHHHHHHHHHHHHHhhHh
Confidence 346777888888888 67889999888652233 234577999999999999988888885
No 121
>PF10923 DUF2791: P-loop Domain of unknown function (DUF2791); InterPro: IPR021228 This is a family of proteins found in archaea and bacteria. Some of the proteins in this family are annotated as being methyl-accepting chemotaxis proteins and ATP/GTP binding proteins.
Probab=20.51 E-value=5.4e+02 Score=21.90 Aligned_cols=85 Identities=12% Similarity=0.004 Sum_probs=56.2
Q ss_pred hHHHHHHHHHHcHHHHHHHHHHHHhcCccCHHHHHHHHhHhhccccccChHHHHHHHHHHHHHHHhcCHHHHHHHHHHHH
Q 042062 38 FVEDVLTVYFRDSTRTLANIEKELQKTEVNYVELDRYFYNLKGSSASIGANKVRNEVNKTRELCRAANWEEAKVSLEQLK 117 (142)
Q Consensus 38 ~~~eli~~F~~d~~~~l~~L~~al~~~~~D~~~l~~~aH~LKGss~~lGA~~L~~~c~~LE~~~~~~~~~~~~~~~~~l~ 117 (142)
-+..+++.|+....+....-...-.....+-..-..+.-.|...+..++...++..++.-=.+...||.+....++..|.
T Consensus 119 al~~ild~wi~~~~~~~~~~~~~~~~~~~~~~v~~~I~~~L~~l~~~~~~~~Fa~~l~~Y~~a~~~gd~~~~~~~l~WL~ 198 (416)
T PF10923_consen 119 ALRSILDRWIYNLEEEVAAEGGIEPDEGFEEAVEELIEERLASLSELVHGPDFAAALRAYYRAYVEGDEELADAALRWLR 198 (416)
T ss_pred HHHHHHHHHHHHHHHHHHhccCCCcchhhHHHHHHHHHHHHHHHHcccCChhHHHHHHHHHHHHhcCCHHHHHHHHHHHc
Confidence 47889999998887665433310000000011222344556666777788889999998888888899888888888888
Q ss_pred HHHHH
Q 042062 118 VEHST 122 (142)
Q Consensus 118 ~~~~~ 122 (142)
.++..
T Consensus 199 Ge~~~ 203 (416)
T PF10923_consen 199 GEYNT 203 (416)
T ss_pred CCCcc
Confidence 87744
No 122
>PF08332 CaMKII_AD: Calcium/calmodulin dependent protein kinase II Association; InterPro: IPR013543 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 domain is found at the C terminus of the Calcium/calmodulin dependent protein kinases II (CaMKII). These proteins also have a Ser/Thr protein kinase domain (IPR000719 from INTERPRO) at their N terminus []. The function of the CaMKII association domain is the assembly of the single proteins into large (8 to 14 subunits) multimers [] and is a prominent kinase in the central nervous system that may function in long-term potentiation and neurotransmitter release. ; GO: 0004683 calmodulin-dependent protein kinase activity, 0005516 calmodulin binding, 0006468 protein phosphorylation; PDB: 2W2C_F 3H51_B 3SOA_A 2UX0_A 1HKX_M 2F86_B.
Probab=20.18 E-value=99 Score=21.75 Aligned_cols=26 Identities=4% Similarity=0.106 Sum_probs=19.8
Q ss_pred cHHHHHHHHHHHHhcCccCHHHHHHHHh
Q 042062 49 DSTRTLANIEKELQKTEVNYVELDRYFY 76 (142)
Q Consensus 49 d~~~~l~~L~~al~~~~~D~~~l~~~aH 76 (142)
+..+.+..+..++..+ |++++..+.+
T Consensus 4 eI~~l~~~w~~ai~tg--D~~~~~~ly~ 29 (128)
T PF08332_consen 4 EIAALFDRWNDAIQTG--DPETYAKLYA 29 (128)
T ss_dssp HHHHHHHHHHHHHHHT---HHHHHHHEE
T ss_pred HHHHHHHHHHHHHHcC--CHHHHhhhcC
Confidence 3455678889999999 9999988765
No 123
>PRK09613 thiH thiamine biosynthesis protein ThiH; Reviewed
Probab=20.00 E-value=2e+02 Score=24.77 Aligned_cols=64 Identities=9% Similarity=-0.001 Sum_probs=41.0
Q ss_pred cCcchhhHH-HHHHhhc-CCCChhhHHHHHHHHHHcHHHHHHHHHHHHhcC-ccCHHHHHHHHhHhh
Q 042062 16 FDEEILDRY-FIQLEQL-GENNPGFVEDVLTVYFRDSTRTLANIEKELQKT-EVNYVELDRYFYNLK 79 (142)
Q Consensus 16 ~~~~~lD~~-l~~L~~l-~~~~~~~~~eli~~F~~d~~~~l~~L~~al~~~-~~D~~~l~~~aH~LK 79 (142)
..+.+||.. +..+.+- ...+++-+.+++..-++...-...+....+... +.+...+...|+.+|
T Consensus 8 ~~~~~i~~~~i~~~l~~~~~~~~~~v~~il~Kal~~~~Ls~eEal~LL~~~~~~~le~L~~~A~~ir 74 (469)
T PRK09613 8 NAADFIDDEEIEELLEKAKNPDKDEIREILEKAKEKKGLSPEEAAVLLNVEDPELLEEIFEAAREIK 74 (469)
T ss_pred hhhhhcCHHHHHHHHHhccCCCHHHHHHHHHHHHcCCCCCHHHHHHHHcCCChhHHHHHHHHHHHHH
Confidence 345678888 6666665 555666678888887765333344444455443 114678889999886
Done!