Query 047910
Match_columns 135
No_of_seqs 111 out of 384
Neff 6.8
Searched_HMMs 46136
Date Fri Mar 29 04:30:00 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/047910.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/047910hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4747 Two-component phosphor 100.0 1.7E-27 3.7E-32 172.9 12.4 133 1-134 5-137 (150)
2 COG2198 ArcB FOG: HPt domain [ 99.7 3.7E-16 8E-21 110.3 11.2 103 26-131 12-117 (122)
3 PF01627 Hpt: Hpt domain; Int 99.7 2.8E-16 6.2E-21 103.4 8.9 83 42-126 1-89 (90)
4 smart00073 HPT Histidine Phosp 99.6 5E-15 1.1E-19 97.8 5.1 85 42-129 2-86 (87)
5 cd00088 HPT Histidine Phosphot 99.5 1.6E-13 3.4E-18 92.3 6.5 64 41-106 2-69 (94)
6 TIGR02956 TMAO_torS TMAO reduc 99.4 9.6E-13 2.1E-17 118.0 10.3 93 35-131 876-968 (968)
7 PRK11091 aerobic respiration c 99.1 3.6E-10 7.8E-15 100.0 10.3 97 35-133 678-774 (779)
8 PRK10618 phosphotransfer inter 99.0 2.7E-09 5.9E-14 97.1 9.7 83 40-124 809-891 (894)
9 PRK11466 hybrid sensory histid 98.7 8.6E-08 1.9E-12 86.0 8.7 67 35-103 820-886 (914)
10 PRK11107 hybrid sensory histid 98.7 2.6E-07 5.6E-12 82.5 11.4 97 35-133 821-918 (919)
11 COG0643 CheA Chemotaxis protei 98.0 4.7E-05 1E-09 68.3 9.9 79 39-117 5-92 (716)
12 PRK10547 chemotaxis protein Ch 98.0 5.6E-05 1.2E-09 67.4 9.8 66 41-106 4-78 (670)
13 PRK09959 hybrid sensory histid 97.1 0.013 2.8E-07 54.6 13.7 95 36-132 1098-1193(1197)
14 PRK15347 two component system 96.8 0.0038 8.3E-08 56.1 6.6 61 43-107 838-898 (921)
15 TIGR02302 aProt_lowcomp conser 86.8 5.1 0.00011 37.3 9.0 82 38-125 523-604 (851)
16 TIGR00984 3a0801s03tim44 mitoc 83.4 12 0.00026 31.7 9.0 81 7-106 213-294 (378)
17 PF13779 DUF4175: Domain of un 73.2 27 0.00057 32.5 8.8 81 39-124 493-573 (820)
18 cd08323 CARD_APAF1 Caspase act 71.0 22 0.00047 23.7 5.9 66 8-77 16-82 (86)
19 PF14276 DUF4363: Domain of un 67.9 13 0.00027 25.8 4.4 48 76-128 18-65 (121)
20 PRK03636 hypothetical protein; 63.3 24 0.00052 26.8 5.5 38 41-80 131-174 (179)
21 TIGR00714 hscB Fe-S protein as 62.8 52 0.0011 24.1 7.1 54 68-130 98-151 (157)
22 PRK03057 hypothetical protein; 62.5 25 0.00054 26.7 5.4 37 42-80 131-173 (180)
23 PF04280 Tim44: Tim44-like dom 60.7 48 0.001 23.2 6.5 55 36-105 12-66 (147)
24 PF08893 DUF1839: Domain of un 57.4 51 0.0011 27.3 6.7 44 87-130 271-318 (319)
25 PF07743 HSCB_C: HSCB C-termin 57.2 47 0.001 21.0 6.8 40 38-79 27-66 (78)
26 PRK01356 hscB co-chaperone Hsc 57.1 76 0.0016 23.5 7.2 53 68-129 107-159 (166)
27 KOG4747 Two-component phosphor 54.3 87 0.0019 23.2 7.7 58 37-97 13-70 (150)
28 PF03993 DUF349: Domain of Unk 50.8 34 0.00073 21.3 3.9 61 42-124 9-69 (77)
29 PF13326 PSII_Pbs27: Photosyst 48.7 1E+02 0.0023 22.4 7.0 86 42-128 44-145 (145)
30 PLN00061 photosystem II protei 47.5 47 0.001 24.6 4.6 59 15-77 27-86 (150)
31 PF08858 IDEAL: IDEAL domain; 47.3 50 0.0011 18.4 5.7 26 52-79 12-37 (37)
32 KOG2424 Protein involved in tr 46.9 31 0.00067 26.5 3.7 24 83-108 147-170 (195)
33 TIGR03044 PS_II_psb27 photosys 46.9 70 0.0015 23.3 5.3 88 42-130 32-134 (135)
34 PF08900 DUF1845: Domain of un 46.5 1.3E+02 0.0029 23.2 7.3 51 81-131 32-88 (217)
35 PF12854 PPR_1: PPR repeat 44.6 24 0.00053 18.8 2.1 21 97-117 13-33 (34)
36 PF09280 XPC-binding: XPC-bind 44.2 38 0.00083 20.9 3.2 36 24-60 9-44 (59)
37 KOG2580 Mitochondrial import i 43.5 60 0.0013 28.1 5.2 66 4-78 284-350 (459)
38 COG2991 Uncharacterized protei 43.4 6.4 0.00014 25.7 -0.4 20 77-96 27-46 (77)
39 KOG0796 Spliceosome subunit [R 43.3 1.9E+02 0.0042 24.0 10.8 74 38-120 83-160 (319)
40 PF04722 Ssu72: Ssu72-like pro 42.6 26 0.00056 27.1 2.7 38 83-121 145-183 (195)
41 PF03194 LUC7: LUC7 N_terminus 42.1 1.7E+02 0.0038 23.1 7.8 79 40-126 84-170 (254)
42 TIGR03042 PS_II_psbQ_bact phot 41.2 1.4E+02 0.0031 21.8 11.0 73 50-134 47-140 (142)
43 PRK15178 Vi polysaccharide exp 40.3 81 0.0018 27.2 5.6 121 5-132 183-306 (434)
44 PF04840 Vps16_C: Vps16, C-ter 40.0 2.1E+02 0.0045 23.4 8.7 68 21-97 180-249 (319)
45 PF11827 DUF3347: Protein of u 39.9 1.6E+02 0.0034 21.9 8.4 81 38-128 44-128 (174)
46 PF02153 PDH: Prephenate dehyd 39.7 1.1E+02 0.0024 23.8 6.0 24 50-75 232-255 (258)
47 PLN02407 diphosphomevalonate d 39.0 58 0.0012 27.3 4.4 32 43-76 224-256 (343)
48 PF03847 TFIID_20kDa: Transcri 38.6 1E+02 0.0022 19.5 4.7 46 5-61 2-47 (68)
49 COG4865 Glutamate mutase epsil 38.2 18 0.0004 30.6 1.4 40 11-50 62-101 (485)
50 PF02845 CUE: CUE domain; Int 37.6 56 0.0012 18.2 3.0 34 25-58 5-38 (42)
51 PRK01773 hscB co-chaperone Hsc 37.2 1.8E+02 0.0038 21.8 7.2 65 36-118 90-154 (173)
52 COG5490 Uncharacterized conser 37.0 1.7E+02 0.0038 21.7 7.1 67 36-102 24-91 (158)
53 PF13812 PPR_3: Pentatricopept 35.7 62 0.0013 16.1 3.2 22 98-119 8-29 (34)
54 PRK03578 hscB co-chaperone Hsc 35.5 1.8E+02 0.0039 21.7 6.3 65 36-118 93-158 (176)
55 COG2178 Predicted RNA-binding 34.9 1.7E+02 0.0036 22.8 6.1 45 88-132 26-70 (204)
56 smart00388 HisKA His Kinase A 34.8 84 0.0018 17.4 5.7 53 72-132 6-58 (66)
57 TIGR03761 ICE_PFL4669 integrat 34.7 2.2E+02 0.0047 22.3 6.8 49 83-131 32-86 (216)
58 PF01535 PPR: PPR repeat; Int 34.7 60 0.0013 15.7 2.7 23 97-119 6-28 (31)
59 PRK08818 prephenate dehydrogen 34.4 1.4E+02 0.0031 25.0 6.1 39 36-81 226-264 (370)
60 KOG3232 Vacuolar assembly/sort 34.3 1.9E+02 0.0041 22.2 6.2 37 91-127 95-131 (203)
61 TIGR00756 PPR pentatricopeptid 33.8 65 0.0014 15.8 3.0 22 98-119 7-28 (35)
62 COG0783 Dps DNA-binding ferrit 33.6 1.4E+02 0.0031 22.0 5.4 29 35-63 42-72 (156)
63 PF08657 DASH_Spc34: DASH comp 33.5 2E+02 0.0044 23.0 6.6 62 70-131 134-199 (259)
64 cd08326 CARD_CASP9 Caspase act 32.6 1.5E+02 0.0032 19.5 5.1 54 8-63 18-72 (84)
65 cd07298 PX_RICS The phosphoino 32.4 45 0.00098 23.6 2.4 39 11-49 52-94 (115)
66 PRK13916 plasmid segregation p 32.3 73 0.0016 21.5 3.3 28 25-52 21-48 (97)
67 PF00619 CARD: Caspase recruit 30.0 1.4E+02 0.0031 18.6 4.5 55 8-64 18-73 (85)
68 COG3046 Uncharacterized protei 29.7 94 0.002 27.1 4.3 64 37-106 227-290 (505)
69 KOG1142 Transcription initiati 29.5 81 0.0018 25.4 3.7 48 6-64 158-205 (258)
70 PF07304 SRA1: Steroid recepto 29.0 2.3E+02 0.0051 20.7 7.6 66 45-126 64-140 (157)
71 PF08581 Tup_N: Tup N-terminal 28.3 1.3E+02 0.0028 19.8 3.9 21 110-130 2-22 (79)
72 PRK12791 flbT flagellar biosyn 27.9 2.3E+02 0.0051 20.3 7.7 52 6-66 54-105 (131)
73 PF14493 HTH_40: Helix-turn-he 27.0 1.4E+02 0.003 19.4 4.0 37 37-74 52-88 (91)
74 PF04012 PspA_IM30: PspA/IM30 25.9 2.9E+02 0.0063 20.8 7.6 27 35-64 22-48 (221)
75 KOG2833 Mevalonate pyrophospha 25.8 1.3E+02 0.0029 25.3 4.4 29 45-75 225-254 (395)
76 TIGR01240 mevDPdecarb diphosph 25.5 1.3E+02 0.0028 24.4 4.4 32 43-76 201-232 (305)
77 PF04049 APC8: Anaphase promot 25.5 2.6E+02 0.0056 20.0 5.8 81 2-86 7-104 (142)
78 PRK10548 flagellar biosynthesi 25.2 2.5E+02 0.0054 19.8 5.8 35 90-128 13-47 (121)
79 smart00546 CUE Domain that may 25.2 1.2E+02 0.0027 16.8 3.1 35 24-58 5-39 (43)
80 cd07299 PX_TCGAP The phosphoin 25.1 90 0.0019 22.0 2.9 38 12-49 51-92 (113)
81 PF03858 Crust_neuro_H: Crusta 24.8 73 0.0016 18.4 2.0 22 69-90 6-27 (41)
82 PF05218 DUF713: Protein of un 24.7 3.1E+02 0.0067 20.7 7.2 91 5-96 73-167 (182)
83 PF06248 Zw10: Centromere/kine 24.6 4.9E+02 0.011 22.9 9.1 18 47-64 77-94 (593)
84 cd00225 API3 Ascaris pepsin in 24.2 1.1E+02 0.0024 22.7 3.4 43 41-86 36-78 (159)
85 COG2603 Predicted ATPase [Gene 24.1 2.1E+02 0.0046 23.8 5.2 80 40-123 243-326 (334)
86 PRK05014 hscB co-chaperone Hsc 23.9 3E+02 0.0066 20.3 7.2 30 89-118 124-153 (171)
87 PRK10987 regulatory protein Am 23.7 1.1E+02 0.0025 24.4 3.7 35 83-117 79-113 (284)
88 PF13041 PPR_2: PPR repeat fam 23.6 1.4E+02 0.003 16.6 3.2 24 96-119 8-31 (50)
89 PF05465 Halo_GVPC: Halobacter 23.3 1.4E+02 0.003 16.1 3.6 23 110-132 4-26 (32)
90 PF00512 HisKA: His Kinase A ( 23.3 1.7E+02 0.0037 17.2 6.8 55 71-133 5-61 (68)
91 PRK10698 phage shock protein P 23.2 3.5E+02 0.0077 20.8 6.5 23 42-64 27-49 (222)
92 PF00435 Spectrin: Spectrin re 23.1 1.9E+02 0.0042 17.8 6.3 40 91-131 60-99 (105)
93 PF05396 Phage_T7_Capsid: Phag 22.9 2.9E+02 0.0063 19.8 7.0 30 94-123 63-92 (123)
94 PF13628 DUF4142: Domain of un 22.8 2.7E+02 0.0058 19.3 5.2 49 26-76 73-122 (139)
95 PF14612 Ino80_Iec3: IEC3 subu 22.7 2.3E+02 0.0051 22.5 5.1 50 49-98 92-141 (232)
96 TIGR00465 ilvC ketol-acid redu 22.5 1.3E+02 0.0029 24.4 3.9 55 70-124 209-263 (314)
97 cd07278 PX_RICS_like The phosp 22.5 88 0.0019 22.1 2.4 39 11-49 51-93 (114)
98 PF07014 Hs1pro-1_C: Hs1pro-1 22.3 2.6E+02 0.0057 22.3 5.2 32 39-72 54-85 (261)
99 PF05757 PsbQ: Oxygen evolving 21.9 2.3E+02 0.0051 21.9 4.9 74 48-126 105-199 (202)
100 COG1270 CbiB Cobalamin biosynt 21.6 1.3E+02 0.0029 24.9 3.7 34 84-117 95-128 (320)
101 cd08812 CARD_RIG-I_like Caspas 21.4 2.5E+02 0.0054 18.4 5.2 36 94-129 36-77 (88)
102 PLN02956 PSII-Q subunit 21.4 3.8E+02 0.0083 20.5 9.4 40 88-127 145-184 (185)
103 PF06160 EzrA: Septation ring 21.2 5.8E+02 0.013 22.5 14.0 108 21-131 173-297 (560)
104 cd00089 HR1 Protein kinase C-r 20.6 2.3E+02 0.0049 17.6 4.1 45 87-134 27-71 (72)
105 PRK07417 arogenate dehydrogena 20.5 2.1E+02 0.0046 22.4 4.6 21 52-74 245-265 (279)
106 PHA02666 hypothetical protein; 20.5 1E+02 0.0022 24.5 2.7 53 35-91 202-258 (287)
107 COG1327 Predicted transcriptio 20.4 3.7E+02 0.0081 20.0 6.0 46 50-95 62-117 (156)
108 COG1220 HslU ATP-dependent pro 20.3 1.4E+02 0.003 25.7 3.5 29 70-98 375-403 (444)
109 PF02203 TarH: Tar ligand bind 20.2 3.1E+02 0.0068 19.1 5.6 40 92-131 127-167 (171)
110 PRK10337 sensor protein QseC; 20.0 4.8E+02 0.01 21.2 9.6 43 37-86 213-255 (449)
No 1
>KOG4747 consensus Two-component phosphorelay intermediate involved in MAP kinase cascade regulation [Signal transduction mechanisms]
Probab=99.95 E-value=1.7e-27 Score=172.94 Aligned_cols=133 Identities=28% Similarity=0.506 Sum_probs=128.3
Q ss_pred ChHHHHHHHHHHHhccchhhhhHHHHHHHhccccCCcchHHHHHHHHHHcHHHHHHHHHHHHhcCCCCHHHHHHHHhhhc
Q 047910 1 MEALRQQISAMRQSFFDEDILDTHIFQLEQVEHISDPSLFEDFVNVYLRDSTKTLAIIEEEIANNPVNYMDLDKYFHQLK 80 (135)
Q Consensus 1 ~~~~~~~~~~~~~~~~d~~~lD~~~~~L~~L~~~~~~df~~~li~~fl~d~~~~l~~L~~al~~~~~D~~~l~~~aH~LK 80 (135)
|.+++++..+|.+|++++|++|++|.+|++|+++..|+|+.+++..|++++.+.+..|+.|+..+. |+.+++.+-|.||
T Consensus 5 i~~~q~~~~d~~~sl~~qgild~qF~qlq~lqD~~~p~fv~ev~~~fF~~s~~~i~~~r~ald~~~-d~k~~~~~~hqlk 83 (150)
T KOG4747|consen 5 IISMQRDVSDYTKSLFDQGILDSQFLQLQELQDDSSPDFVEEVVGLFFEDSERLINNLRLALDCER-DFKKLGSHVHQLK 83 (150)
T ss_pred HHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHhcccCccHHHHHHHHHHHHHHHHHHHHHHHHhhHh-HHHHHHHHHHHcc
Confidence 457899999999999999999999999999999999999999999999999999999999999864 9999999999999
Q ss_pred ccccccChHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Q 047910 81 SSSNCIGANKVVNEAKKAIELCKEENLEAAKASFEKMKVEHTTLKTKLQAYLEV 134 (135)
Q Consensus 81 GSSa~iGA~~l~~~c~~lE~~~~~~~~~~~~~~l~~l~~ef~~~~~~L~~~l~~ 134 (135)
|||++|||.++...|..+...|+.++.++|...+++++.||..++.+|++|.++
T Consensus 84 gssssIGa~kvk~~c~~~~~~~~~~n~egcvr~l~~v~ie~~~lkkkL~~~f~L 137 (150)
T KOG4747|consen 84 GSSSSIGALKVKKVCVGFNEFCEAGNIEGCVRCLQQVKIEYSLLKKKLETLFQL 137 (150)
T ss_pred CchhhhhHHHHHHHHHHHHHHHhhccchhHhhchHHHHHHHHHHHHHHHHHHHH
Confidence 999999999999999999999999999999999999999999999999998753
No 2
>COG2198 ArcB FOG: HPt domain [Signal transduction mechanisms]
Probab=99.69 E-value=3.7e-16 Score=110.35 Aligned_cols=103 Identities=20% Similarity=0.350 Sum_probs=90.0
Q ss_pred HHHHhccccCCcchHHHHHHHHHHcHHHHHHHHHHHHhcCCCCHHHHHHHHhhhcccccccChHHHHHHHHHHHHHHhh-
Q 047910 26 FQLEQVEHISDPSLFEDFVNVYLRDSTKTLAIIEEEIANNPVNYMDLDKYFHQLKSSSNCIGANKVVNEAKKAIELCKE- 104 (135)
Q Consensus 26 ~~L~~L~~~~~~df~~~li~~fl~d~~~~l~~L~~al~~~~~D~~~l~~~aH~LKGSSa~iGA~~l~~~c~~lE~~~~~- 104 (135)
..+..+.. +.|+++.+++.+|+++++..+..++.++..+ |+..+.+.||+||||++|+|+.+++.+|.++|..++.
T Consensus 12 ~~~~~~~g-~~~~~~~~ll~~f~~~~~~~l~~l~~~l~~~--d~~~~~~~aH~lkg~a~~lg~~~L~~~~~~lE~~~~~~ 88 (122)
T COG2198 12 ELLVRLIG-GDPDLLRELLAMFLEEAPAQLEQLESALAAE--DNDGLARLAHRLKGSAASLGLPALAQLCQQLEDALRSG 88 (122)
T ss_pred HHHHHHcC-CChHHHHHHHHHHHHHhHHHHHHHHHHHhcC--CcHHHHHHHHHHHhHHHhccHHHHHHHHHHHHHHHHcC
Confidence 34444432 5699999999999999999999999999998 8899999999999999999999999999999999998
Q ss_pred cCHHHHHHHHHHHHHH--HHHHHHHHHHH
Q 047910 105 ENLEAAKASFEKMKVE--HTTLKTKLQAY 131 (135)
Q Consensus 105 ~~~~~~~~~l~~l~~e--f~~~~~~L~~~ 131 (135)
...+....++..++.+ ...+...+.++
T Consensus 89 ~~~~~~~~~i~~l~~~~~~~~~~~~~~~~ 117 (122)
T COG2198 89 ASLEELEELIAELKDELQLDVLALELLTY 117 (122)
T ss_pred CcHHHHHHHHHHHHHHhcchHHHHHHHHH
Confidence 6889999999999999 55555555554
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=99.68 E-value=2.8e-16 Score=103.39 Aligned_cols=83 Identities=16% Similarity=0.385 Sum_probs=73.8
Q ss_pred HHHHHHHHcHHHHHHHHHHHH---hcCCCCHHHHHHHHhhhcccccccChHHHHHHHHHHHHHHhhcCHHH---HHHHHH
Q 047910 42 DFVNVYLRDSTKTLAIIEEEI---ANNPVNYMDLDKYFHQLKSSSNCIGANKVVNEAKKAIELCKEENLEA---AKASFE 115 (135)
Q Consensus 42 ~li~~fl~d~~~~l~~L~~al---~~~~~D~~~l~~~aH~LKGSSa~iGA~~l~~~c~~lE~~~~~~~~~~---~~~~l~ 115 (135)
+++..|++++++.+..|++++ ..+ |++.+++.+|+|||+++++|+.++..+|..+|..++.++.+. +...+.
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 589999999999999999999 766 999999999999999999999999999999999999998888 666666
Q ss_pred HHHHHHHHHHH
Q 047910 116 KMKVEHTTLKT 126 (135)
Q Consensus 116 ~l~~ef~~~~~ 126 (135)
.+...++++.+
T Consensus 79 ~l~~~l~~l~~ 89 (90)
T PF01627_consen 79 ELEAMLEQLRQ 89 (90)
T ss_dssp HHHHHHHHHHH
T ss_pred HHHHHHHHHhC
Confidence 66666665544
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=5e-15 Score=97.84 Aligned_cols=85 Identities=13% Similarity=0.155 Sum_probs=74.6
Q ss_pred HHHHHHHHcHHHHHHHHHHHHhcCCCCHHHHHHHHhhhcccccccChHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHH
Q 047910 42 DFVNVYLRDSTKTLAIIEEEIANNPVNYMDLDKYFHQLKSSSNCIGANKVVNEAKKAIELCKEENLEAAKASFEKMKVEH 121 (135)
Q Consensus 42 ~li~~fl~d~~~~l~~L~~al~~~~~D~~~l~~~aH~LKGSSa~iGA~~l~~~c~~lE~~~~~~~~~~~~~~l~~l~~ef 121 (135)
+++..|+++.+..+..|..++..+ |+..+++.+|+||||++|+|+..|..+|..+|...+... ++...++..+...|
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 678999999999999999999766 899999999999999999999999999999999988644 34446788888888
Q ss_pred HHHHHHHH
Q 047910 122 TTLKTKLQ 129 (135)
Q Consensus 122 ~~~~~~L~ 129 (135)
..+...|.
T Consensus 79 ~~~~~~l~ 86 (87)
T smart00073 79 LELVDVLK 86 (87)
T ss_pred HHHHHHHc
Confidence 88877764
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=99.46 E-value=1.6e-13 Score=92.30 Aligned_cols=64 Identities=17% Similarity=0.352 Sum_probs=60.1
Q ss_pred HHHHHHHHHcHHHHHHHHHHHHh----cCCCCHHHHHHHHhhhcccccccChHHHHHHHHHHHHHHhhcC
Q 047910 41 EDFVNVYLRDSTKTLAIIEEEIA----NNPVNYMDLDKYFHQLKSSSNCIGANKVVNEAKKAIELCKEEN 106 (135)
Q Consensus 41 ~~li~~fl~d~~~~l~~L~~al~----~~~~D~~~l~~~aH~LKGSSa~iGA~~l~~~c~~lE~~~~~~~ 106 (135)
.+++..|+++.+..+..|..++. .+ |+..++..+|+||||++++|+.+|..+|..+|..++.+.
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 47899999999999999999998 55 899999999999999999999999999999999998764
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=99.42 E-value=9.6e-13 Score=117.98 Aligned_cols=93 Identities=17% Similarity=0.254 Sum_probs=88.1
Q ss_pred CCcchHHHHHHHHHHcHHHHHHHHHHHHhcCCCCHHHHHHHHhhhcccccccChHHHHHHHHHHHHHHhhcCHHHHHHHH
Q 047910 35 SDPSLFEDFVNVYLRDSTKTLAIIEEEIANNPVNYMDLDKYFHQLKSSSNCIGANKVVNEAKKAIELCKEENLEAAKASF 114 (135)
Q Consensus 35 ~~~df~~~li~~fl~d~~~~l~~L~~al~~~~~D~~~l~~~aH~LKGSSa~iGA~~l~~~c~~lE~~~~~~~~~~~~~~l 114 (135)
.|++.+.+++..|+++++..+..|..++..+ |+..++..+|.|||+++++||.+++.+|+.||..++.|+. ....+
T Consensus 876 ~~~~~~~~~~~~f~~~~~~~~~~l~~~~~~~--d~~~~~~~~H~lkg~~~~~g~~~l~~~~~~le~~~~~~~~--~~~~~ 951 (968)
T TIGR02956 876 LGVEKVRQLVALFKTSSAEQLEELSAARAVD--DDAQIKKLAHKLKGSAGSLGLTQLTQLCQQLEKQGKTGAL--ELSDI 951 (968)
T ss_pred cCcHHHHHHHHHHHHhhHHHHHHHHHHHhCC--CHHHHHHHHHHHHHHHHHhCHHHHHHHHHHHHHhcccCCc--chhHH
Confidence 5788999999999999999999999999987 9999999999999999999999999999999999999988 45789
Q ss_pred HHHHHHHHHHHHHHHHH
Q 047910 115 EKMKVEHTTLKTKLQAY 131 (135)
Q Consensus 115 ~~l~~ef~~~~~~L~~~ 131 (135)
+.++..|.++..+|++|
T Consensus 952 ~~l~~~~~~~~~~l~~~ 968 (968)
T TIGR02956 952 DEIKQAWQASKTALDQW 968 (968)
T ss_pred HHHHHHHHHHHHHHHhC
Confidence 99999999999999875
No 7
>PRK11091 aerobic respiration control sensor protein ArcB; Provisional
Probab=99.12 E-value=3.6e-10 Score=100.03 Aligned_cols=97 Identities=15% Similarity=0.223 Sum_probs=92.1
Q ss_pred CCcchHHHHHHHHHHcHHHHHHHHHHHHhcCCCCHHHHHHHHhhhcccccccChHHHHHHHHHHHHHHhhcCHHHHHHHH
Q 047910 35 SDPSLFEDFVNVYLRDSTKTLAIIEEEIANNPVNYMDLDKYFHQLKSSSNCIGANKVVNEAKKAIELCKEENLEAAKASF 114 (135)
Q Consensus 35 ~~~df~~~li~~fl~d~~~~l~~L~~al~~~~~D~~~l~~~aH~LKGSSa~iGA~~l~~~c~~lE~~~~~~~~~~~~~~l 114 (135)
.++..+.+.+..|.+..+..+..|..++..+ |...+...+|.|||+++++|+..++.+|..+|.....+.++....++
T Consensus 678 ~g~~~~~~~l~~~~~~~~~~~~~l~~~l~~~--d~~~~~~~ah~l~g~~~~~g~~~l~~~~~~le~~~~~~~~~~~~~~~ 755 (779)
T PRK11091 678 VGPKLITDSLAVFEKMMPGYLSVLDSNLTAR--DQKGIVEEAHKIKGAAGSVGLRHLQQLAQQIQSPDLPAWWDNVQDWV 755 (779)
T ss_pred cCHHHHHHHHHHHHHhhHHHHHHHHHHHHCC--CHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHhCcCccccHHHHHHHH
Confidence 4667888999999999999999999999987 89999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHhc
Q 047910 115 EKMKVEHTTLKTKLQAYLE 133 (135)
Q Consensus 115 ~~l~~ef~~~~~~L~~~l~ 133 (135)
+++..+|+....+|+.|+.
T Consensus 756 ~~l~~~~~~~~~~~~~~~~ 774 (779)
T PRK11091 756 EELKNEWRHDVEVLKAWLA 774 (779)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 9999999999999999985
No 8
>PRK10618 phosphotransfer intermediate protein in two-component regulatory system with RcsBC; Provisional
Probab=98.97 E-value=2.7e-09 Score=97.08 Aligned_cols=83 Identities=12% Similarity=0.162 Sum_probs=77.2
Q ss_pred HHHHHHHHHHcHHHHHHHHHHHHhcCCCCHHHHHHHHhhhcccccccChHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHH
Q 047910 40 FEDFVNVYLRDSTKTLAIIEEEIANNPVNYMDLDKYFHQLKSSSNCIGANKVVNEAKKAIELCKEENLEAAKASFEKMKV 119 (135)
Q Consensus 40 ~~~li~~fl~d~~~~l~~L~~al~~~~~D~~~l~~~aH~LKGSSa~iGA~~l~~~c~~lE~~~~~~~~~~~~~~l~~l~~ 119 (135)
...+...|++.+|.-+..|..++.++ |+..+++.||.|||+++++|+..++.+|+.||..++.++..++...+.+|..
T Consensus 809 ~s~~~~lF~~t~~~di~~L~~~~~~~--D~~~l~~~aHrLKG~~aml~l~~l~~~~~~LE~~i~~~~~~~i~~~i~~id~ 886 (894)
T PRK10618 809 ASDYYALFVDTVPDDVKRLYTEAATS--DFASLAQTAHRLKGVFAMLNLVPGKQLCETLEHLIREKDEPGIENYISDIDS 886 (894)
T ss_pred hhhHHHHHHHhhHHHHHHHHHHHhcc--CHHHHHHHHHHHHHHHHHcChHHHHHHHHHHHHHHhhCChHHHHHHHHHHHH
Confidence 34567899999999999999999998 9999999999999999999999999999999999999999999999999998
Q ss_pred HHHHH
Q 047910 120 EHTTL 124 (135)
Q Consensus 120 ef~~~ 124 (135)
.+.++
T Consensus 887 ~v~~l 891 (894)
T PRK10618 887 FVKSL 891 (894)
T ss_pred HHHHH
Confidence 76654
No 9
>PRK11466 hybrid sensory histidine kinase TorS; Provisional
Probab=98.67 E-value=8.6e-08 Score=85.98 Aligned_cols=67 Identities=15% Similarity=0.210 Sum_probs=62.1
Q ss_pred CCcchHHHHHHHHHHcHHHHHHHHHHHHhcCCCCHHHHHHHHhhhcccccccChHHHHHHHHHHHHHHh
Q 047910 35 SDPSLFEDFVNVYLRDSTKTLAIIEEEIANNPVNYMDLDKYFHQLKSSSNCIGANKVVNEAKKAIELCK 103 (135)
Q Consensus 35 ~~~df~~~li~~fl~d~~~~l~~L~~al~~~~~D~~~l~~~aH~LKGSSa~iGA~~l~~~c~~lE~~~~ 103 (135)
.+++.+.+++..|.+.++..+..++.+...+ |+..+++.||.|||+++++|+.+++.+|.++|..+.
T Consensus 820 ~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~--~~~~~~~~ah~lkg~~~~lg~~~l~~~~~~le~~~~ 886 (914)
T PRK11466 820 MGTEKIHEWLALFKQHALPLLDEIDIARASQ--DSEKIKRAAHQLKSSCSSLGMRQASQACAQLEQQPL 886 (914)
T ss_pred cCHHHHHHHHHHHHHhhHHHHHHHHHHHHCC--CHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhCCCC
Confidence 4667788999999999999999999999987 899999999999999999999999999999998753
No 10
>PRK11107 hybrid sensory histidine kinase BarA; Provisional
Probab=98.66 E-value=2.6e-07 Score=82.54 Aligned_cols=97 Identities=15% Similarity=0.205 Sum_probs=85.0
Q ss_pred CCcchHHHHHHHHHHcHHHHHHHHHHHHhcCCCCHHHHHHHHhhhcccccccChHHHHHHHHHHHHHHhhc-CHHHHHHH
Q 047910 35 SDPSLFEDFVNVYLRDSTKTLAIIEEEIANNPVNYMDLDKYFHQLKSSSNCIGANKVVNEAKKAIELCKEE-NLEAAKAS 113 (135)
Q Consensus 35 ~~~df~~~li~~fl~d~~~~l~~L~~al~~~~~D~~~l~~~aH~LKGSSa~iGA~~l~~~c~~lE~~~~~~-~~~~~~~~ 113 (135)
+.++...+++..|++..+..+..|..++..+ |...++..+|.+||+++++|+.++..+|..+|...+.+ ..+.....
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 4567788999999999999999999999987 89999999999999999999999999999999998876 46777777
Q ss_pred HHHHHHHHHHHHHHHHHHhc
Q 047910 114 FEKMKVEHTTLKTKLQAYLE 133 (135)
Q Consensus 114 l~~l~~ef~~~~~~L~~~l~ 133 (135)
+..+..++.++..+++++++
T Consensus 899 ~~~~~~~~~~~~~~~~~~~~ 918 (919)
T PRK11107 899 LLELLDEMENVARAAKKVLS 918 (919)
T ss_pred HHHHHHHHHHHHHHHHHHhh
Confidence 77888888888888777653
No 11
>COG0643 CheA Chemotaxis protein histidine kinase and related kinases [Cell motility and secretion / Signal transduction mechanisms]
Probab=98.00 E-value=4.7e-05 Score=68.31 Aligned_cols=79 Identities=16% Similarity=0.319 Sum_probs=60.7
Q ss_pred hHHHHHHHHHHcHHHHHHHHHHHHh---cCCCCHH---HHHHHHhhhcccccccChHHHHHHHHHHHHH---HhhcCHHH
Q 047910 39 LFEDFVNVYLRDSTKTLAIIEEEIA---NNPVNYM---DLDKYFHQLKSSSNCIGANKVVNEAKKAIEL---CKEENLEA 109 (135)
Q Consensus 39 f~~~li~~fl~d~~~~l~~L~~al~---~~~~D~~---~l~~~aH~LKGSSa~iGA~~l~~~c~~lE~~---~~~~~~~~ 109 (135)
-..++...|++++++++..|..++- .++.|.+ ++.+.||+|||+|+.+|...++.+|-.+|.. .++|...-
T Consensus 5 ~~~~~~~~F~~Ea~e~l~~l~~~Ll~LE~~~~d~~~ln~ifRaaHTlKG~a~~~g~~~l~~l~H~~E~~ld~~r~g~~~~ 84 (716)
T COG0643 5 DMEEILEDFLEEAEELLQALEQALLALEPDPEDLDLLNAIFRAAHTLKGGAGTLGLTTLAELAHAMEDLLDALRNGELEL 84 (716)
T ss_pred HHHHHHHHHHHhhHHHHHHHHHhHhhccCCCCCHHHHHHHHHHHHhhhhhhhhcChhHHHHHHHHHHHHHHHHhcCCccC
Confidence 4568899999999999999998753 3233444 6788999999999999999999999999985 56665433
Q ss_pred HHHHHHHH
Q 047910 110 AKASFEKM 117 (135)
Q Consensus 110 ~~~~l~~l 117 (135)
-..++..+
T Consensus 85 ~~~l~d~~ 92 (716)
T COG0643 85 TSELLDLL 92 (716)
T ss_pred cHHHHHHH
Confidence 33333333
No 12
>PRK10547 chemotaxis protein CheA; Provisional
Probab=97.97 E-value=5.6e-05 Score=67.38 Aligned_cols=66 Identities=14% Similarity=0.256 Sum_probs=54.7
Q ss_pred HHHHHHHHHcHHHHHHHHHHHHh---cCCCCH---HHHHHHHhhhcccccccChHHHHHHHHHHHHH---HhhcC
Q 047910 41 EDFVNVYLRDSTKTLAIIEEEIA---NNPVNY---MDLDKYFHQLKSSSNCIGANKVVNEAKKAIEL---CKEEN 106 (135)
Q Consensus 41 ~~li~~fl~d~~~~l~~L~~al~---~~~~D~---~~l~~~aH~LKGSSa~iGA~~l~~~c~~lE~~---~~~~~ 106 (135)
.+++..|++++.++|+.|+..+- ..+.|. ..+-+.+|+|||+|+.+|...+..+|-.+|.. .|.|.
T Consensus 4 ~~~l~~F~~Ea~E~l~~le~~Ll~LE~~p~d~e~in~lFRa~HTiKG~a~~~g~~~i~~l~H~~E~lld~vR~g~ 78 (670)
T PRK10547 4 SDFYQTFFDEADELLADMEQHLLVLDPEAPDAEQLNAIFRAAHSIKGGAGTFGFTVLQETTHLMENLLDEARRGE 78 (670)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhccCCCCHHHHHHHHHHHHhhhhHHhhcCchHHHHHHHHHHHHHHHHHCCC
Confidence 47899999999999999999863 333353 36778999999999999999999999999987 35553
No 13
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=97.14 E-value=0.013 Score=54.57 Aligned_cols=95 Identities=11% Similarity=0.221 Sum_probs=75.8
Q ss_pred CcchHHHHHHHHHHcHHHHHHHHHHHHhcCCCCHHHHHHHHhhhcccccccChHHHHHHHHHHHHHHhhcC-HHHHHHHH
Q 047910 36 DPSLFEDFVNVYLRDSTKTLAIIEEEIANNPVNYMDLDKYFHQLKSSSNCIGANKVVNEAKKAIELCKEEN-LEAAKASF 114 (135)
Q Consensus 36 ~~df~~~li~~fl~d~~~~l~~L~~al~~~~~D~~~l~~~aH~LKGSSa~iGA~~l~~~c~~lE~~~~~~~-~~~~~~~l 114 (135)
......+++..+...+...+..+..+...+ |...++..+|.+||++..+|+..+...|.++|......+ .+.....+
T Consensus 1098 ~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~h~~~g~~~~l~~~~l~~~~~~~e~~~~~~~~~~~l~~~~ 1175 (1197)
T PRK09959 1098 DLQLMQEILMTFQHETHKDLPAAFHALEAG--DNRTFHQCIHRIHGAANILNLQKLINISHQLEITPVSDDSKPEILQLL 1175 (1197)
T ss_pred CHHHHHHHHHHHHHhhHHHHHHHHHHHHcC--CHHHHHHHHHHHHHHHHHcCHHHHHHHHHHHHHhhhcCCchHHHHHHH
Confidence 445678888999999999998998999988 789999999999999999999999999999998876554 34455556
Q ss_pred HHHHHHHHHHHHHHHHHh
Q 047910 115 EKMKVEHTTLKTKLQAYL 132 (135)
Q Consensus 115 ~~l~~ef~~~~~~L~~~l 132 (135)
..+..........++.++
T Consensus 1176 ~~~~~~~~~~~~~~~~~~ 1193 (1197)
T PRK09959 1176 NSVKEHIAELDQEIAVFC 1193 (1197)
T ss_pred HHHHHHHHHHHHHHHHhc
Confidence 666655555555555554
No 14
>PRK15347 two component system sensor kinase SsrA; Provisional
Probab=96.76 E-value=0.0038 Score=56.11 Aligned_cols=61 Identities=16% Similarity=0.199 Sum_probs=51.8
Q ss_pred HHHHHHHcHHHHHHHHHHHHhcCCCCHHHHHHHHhhhcccccccChHHHHHHHHHHHHHHhhcCH
Q 047910 43 FVNVYLRDSTKTLAIIEEEIANNPVNYMDLDKYFHQLKSSSNCIGANKVVNEAKKAIELCKEENL 107 (135)
Q Consensus 43 li~~fl~d~~~~l~~L~~al~~~~~D~~~l~~~aH~LKGSSa~iGA~~l~~~c~~lE~~~~~~~~ 107 (135)
+-..+.+.....+..+..++..+ | .++..+|.+||+++++|+.++...|.++|...+.+..
T Consensus 838 l~~~~~~~l~~~~~~~~~~~~~~--~--~l~~~~h~i~~~~~~~g~~~l~~~~~~~e~~~~~~~~ 898 (921)
T PRK15347 838 LNSKLYQSLLLLLAQIEQAVENQ--E--VLSQLLHTLKGCAGQAGLTELQCAVIDLENALETGEI 898 (921)
T ss_pred HHHHHHHHHHHHHHHHHHHHhCH--H--HHHHHHHHHHHHHHHcCHHHHHHHHHHHHHHHhcCCC
Confidence 44555566678888899999876 4 8999999999999999999999999999999877653
No 15
>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=86.79 E-value=5.1 Score=37.25 Aligned_cols=82 Identities=11% Similarity=0.231 Sum_probs=54.9
Q ss_pred chHHHHHHHHHHcHHHHHHHHHHHHhcCCCCHHHHHHHHhhhcccccccChHHHHHHHHHHHHHHhhcCHHHHHHHHHHH
Q 047910 38 SLFEDFVNVYLRDSTKTLAIIEEEIANNPVNYMDLDKYFHQLKSSSNCIGANKVVNEAKKAIELCKEENLEAAKASFEKM 117 (135)
Q Consensus 38 df~~~li~~fl~d~~~~l~~L~~al~~~~~D~~~l~~~aH~LKGSSa~iGA~~l~~~c~~lE~~~~~~~~~~~~~~l~~l 117 (135)
+=+.+|+..+-+-...+|.+|.+...+++ +-.. -..-+.+.+++-.-|..+...||+++++|+.+.+.++|++|
T Consensus 523 eEI~~Lm~eLR~Am~~ym~~LAeq~~~~~-~~~~-----~~~~~~~~~l~~~dLq~Mmd~ieela~~G~~~~A~qlL~ql 596 (851)
T TIGR02302 523 EEIKQLTDKLRAAMQTYMRQLAQQLRNNP-QQLA-----RPLDPNTKVLRQQDLQNMMDQIENLARSGDRDQAKQLLSQL 596 (851)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhhCc-cccc-----ccCCccccccCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence 34445555555555555555555444321 1000 11123357799999999999999999999999999999999
Q ss_pred HHHHHHHH
Q 047910 118 KVEHTTLK 125 (135)
Q Consensus 118 ~~ef~~~~ 125 (135)
++-.+..+
T Consensus 597 q~mmenlq 604 (851)
T TIGR02302 597 QQMMNNLQ 604 (851)
T ss_pred HHHHHHHh
Confidence 88666554
No 16
>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=83.40 E-value=12 Score=31.68 Aligned_cols=81 Identities=16% Similarity=0.174 Sum_probs=60.2
Q ss_pred HHHHHHHhccchhhhhHHHHHHHhccccCCcchHHHHHHHHHHcHHHH-HHHHHHHHhcCCCCHHHHHHHHhhhcccccc
Q 047910 7 QISAMRQSFFDEDILDTHIFQLEQVEHISDPSLFEDFVNVYLRDSTKT-LAIIEEEIANNPVNYMDLDKYFHQLKSSSNC 85 (135)
Q Consensus 7 ~~~~~~~~~~d~~~lD~~~~~L~~L~~~~~~df~~~li~~fl~d~~~~-l~~L~~al~~~~~D~~~l~~~aH~LKGSSa~ 85 (135)
.+..++-++|.+.=+-..+.+++.+ +|+|- +..|+..+... +..|-.|...| |.+.|+.+
T Consensus 213 kv~~~~~~lF~ete~a~~l~eIk~~----DPsFd---~~~Fl~gar~aI~p~ILeAf~kG--D~e~LK~~---------- 273 (378)
T TIGR00984 213 KIGGVFSGMFSETEVSEVLTEFKKI----DPTFD---KEHFLRFLREYIVPEILEAYVKG--DLEVLKSW---------- 273 (378)
T ss_pred hhhhhhhcccCCCHHHHHHHHHHHh----CCCCC---HHHHHHHHHHHHHHHHHHHHHcC--CHHHHHHh----------
Confidence 4444555577777777667788877 45554 46788889998 68999999998 89999988
Q ss_pred cChHHHHHHHHHHHHHHhhcC
Q 047910 86 IGANKVVNEAKKAIELCKEEN 106 (135)
Q Consensus 86 iGA~~l~~~c~~lE~~~~~~~ 106 (135)
++-......|..+......|.
T Consensus 274 lse~vy~~f~a~I~qr~~~G~ 294 (378)
T TIGR00984 274 CSEAPFSVYATVVKEYKKMGV 294 (378)
T ss_pred hCHHHHHHHHHHHHHHHHCCC
Confidence 455667777778877776663
No 17
>PF13779 DUF4175: Domain of unknown function (DUF4175)
Probab=73.15 E-value=27 Score=32.53 Aligned_cols=81 Identities=10% Similarity=0.159 Sum_probs=53.1
Q ss_pred hHHHHHHHHHHcHHHHHHHHHHHHhcCCCCHHHHHHHHhhhcccccccChHHHHHHHHHHHHHHhhcCHHHHHHHHHHHH
Q 047910 39 LFEDFVNVYLRDSTKTLAIIEEEIANNPVNYMDLDKYFHQLKSSSNCIGANKVVNEAKKAIELCKEENLEAAKASFEKMK 118 (135)
Q Consensus 39 f~~~li~~fl~d~~~~l~~L~~al~~~~~D~~~l~~~aH~LKGSSa~iGA~~l~~~c~~lE~~~~~~~~~~~~~~l~~l~ 118 (135)
=+.+++.-..+-..+.|.+|.+...+++ +.. ..+.--+.+.+++..-|.....+||+++++|+.+.+.++|++|+
T Consensus 493 EI~rLm~eLR~A~~~ym~~LAeq~~~~~-~~~----~~p~~~~~~~~~~~~dL~~mmd~ie~la~~G~~~~A~q~L~qlq 567 (820)
T PF13779_consen 493 EIARLMQELREAMQDYMQALAEQAQRNP-QQQ----DQPPDQGNSQMMSQQDLQRMMDRIEELARSGRMDEARQLLEQLQ 567 (820)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhHhCc-ccc----cCcccchhhhccCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence 3444555554445555555554444331 100 00111355678999999999999999999999999999999988
Q ss_pred HHHHHH
Q 047910 119 VEHTTL 124 (135)
Q Consensus 119 ~ef~~~ 124 (135)
+-.+..
T Consensus 568 ~mmenm 573 (820)
T PF13779_consen 568 QMMENM 573 (820)
T ss_pred HHHHhc
Confidence 755543
No 18
>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=70.99 E-value=22 Score=23.67 Aligned_cols=66 Identities=12% Similarity=0.207 Sum_probs=48.7
Q ss_pred HHHHHHhccchhhhhHH-HHHHHhccccCCcchHHHHHHHHHHcHHHHHHHHHHHHhcCCCCHHHHHHHHh
Q 047910 8 ISAMRQSFFDEDILDTH-IFQLEQVEHISDPSLFEDFVNVYLRDSTKTLAIIEEEIANNPVNYMDLDKYFH 77 (135)
Q Consensus 8 ~~~~~~~~~d~~~lD~~-~~~L~~L~~~~~~df~~~li~~fl~d~~~~l~~L~~al~~~~~D~~~l~~~aH 77 (135)
...++..|+.+|+++.. .+.++.-. ...+=...||++-..-++.-+.....|+... .|+.+..+.|
T Consensus 16 v~~ild~L~~~gvlt~~~~e~I~~~~--t~~~qa~~Lld~L~trG~~Af~~F~~aL~~~--~~~~La~lL~ 82 (86)
T cd08323 16 TSYIMDHMISDGVLTLDEEEKVKSKA--TQKEKAVMLINMILTKDNHAYVSFYNALLHE--GYKDLALLLH 82 (86)
T ss_pred HHHHHHHHHhcCCCCHHHHHHHHcCC--ChHHHHHHHHHHHHhcCHHHHHHHHHHHHhc--CChHHHHHHh
Confidence 45678888899999987 77777643 3345567888888888888888888888753 4667766654
No 19
>PF14276 DUF4363: Domain of unknown function (DUF4363)
Probab=67.91 E-value=13 Score=25.78 Aligned_cols=48 Identities=19% Similarity=0.223 Sum_probs=33.4
Q ss_pred HhhhcccccccChHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHHHHH
Q 047910 76 FHQLKSSSNCIGANKVVNEAKKAIELCKEENLEAAKASFEKMKVEHTTLKTKL 128 (135)
Q Consensus 76 aH~LKGSSa~iGA~~l~~~c~~lE~~~~~~~~~~~~~~l~~l~~ef~~~~~~L 128 (135)
.|.+++++ ..+...+..+++..+.++++.+...++.+...|.+.+..+
T Consensus 18 ~~~l~~~~-----~~i~~~l~~i~~~i~~~dW~~A~~~~~~l~~~W~k~~~~~ 65 (121)
T PF14276_consen 18 NNYLNNST-----DSIEEQLEQIEEAIENEDWEKAYKETEELEKEWDKNKKRW 65 (121)
T ss_pred HhhhhhHH-----HHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhhchhe
Confidence 35555553 4556677778888888888888888888888777665543
No 20
>PRK03636 hypothetical protein; Provisional
Probab=63.33 E-value=24 Score=26.77 Aligned_cols=38 Identities=16% Similarity=0.282 Sum_probs=30.0
Q ss_pred HHHHHHHHHc------HHHHHHHHHHHHhcCCCCHHHHHHHHhhhc
Q 047910 41 EDFVNVYLRD------STKTLAIIEEEIANNPVNYMDLDKYFHQLK 80 (135)
Q Consensus 41 ~~li~~fl~d------~~~~l~~L~~al~~~~~D~~~l~~~aH~LK 80 (135)
...++++++. -.+++.+|.+|++++ |.+.+.+++..||
T Consensus 131 ~~~ae~~L~~~~~~~r~~~L~~~ID~ALd~~--D~e~F~~Ls~~l~ 174 (179)
T PRK03636 131 RLLAEQFLEQSVFQFRREKLLKQIDEALDRR--DKEAFHRLSDELN 174 (179)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHcC--CHHHHHHHHHHHH
Confidence 3455566655 467889999999998 8999999988776
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=62.77 E-value=52 Score=24.12 Aligned_cols=54 Identities=13% Similarity=0.232 Sum_probs=35.7
Q ss_pred CHHHHHHHHhhhcccccccChHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHHHHHHH
Q 047910 68 NYMDLDKYFHQLKSSSNCIGANKVVNEAKKAIELCKEENLEAAKASFEKMKVEHTTLKTKLQA 130 (135)
Q Consensus 68 D~~~l~~~aH~LKGSSa~iGA~~l~~~c~~lE~~~~~~~~~~~~~~l~~l~~ef~~~~~~L~~ 130 (135)
|...+..+.+.++ .++..+...++.+-..++++.+...+.+|+= |.++...+++
T Consensus 98 d~~~L~~l~~~~~--------~~~~~~~~~l~~~~~~~d~~~A~~~~~kLky-~~kl~~~i~~ 151 (157)
T TIGR00714 98 DEARLESFIKRVK--------KMFQTRHQLLVEQLDNQTWAAAADYTRKLRF-LDKLRSSAEQ 151 (157)
T ss_pred CHHHHHHHHHHHH--------HHHHHHHHHHHHHHhcCCHHHHHHHHHHHHH-HHHHHHHHHH
Confidence 5566766666554 4667777777777777888888877766654 4445444443
No 22
>PRK03057 hypothetical protein; Provisional
Probab=62.45 E-value=25 Score=26.71 Aligned_cols=37 Identities=11% Similarity=0.232 Sum_probs=29.4
Q ss_pred HHHHHHHHc------HHHHHHHHHHHHhcCCCCHHHHHHHHhhhc
Q 047910 42 DFVNVYLRD------STKTLAIIEEEIANNPVNYMDLDKYFHQLK 80 (135)
Q Consensus 42 ~li~~fl~d------~~~~l~~L~~al~~~~~D~~~l~~~aH~LK 80 (135)
..++.|++. -.+++..|..|++.+ |.+.+.++++.|+
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 456666666 567788999999998 8999999888775
No 23
>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=60.74 E-value=48 Score=23.18 Aligned_cols=55 Identities=13% Similarity=0.146 Sum_probs=41.8
Q ss_pred CcchHHHHHHHHHHcHHHHHHHHHHHHhcCCCCHHHHHHHHhhhcccccccChHHHHHHHHHHHHHHhhc
Q 047910 36 DPSLFEDFVNVYLRDSTKTLAIIEEEIANNPVNYMDLDKYFHQLKSSSNCIGANKVVNEAKKAIELCKEE 105 (135)
Q Consensus 36 ~~df~~~li~~fl~d~~~~l~~L~~al~~~~~D~~~l~~~aH~LKGSSa~iGA~~l~~~c~~lE~~~~~~ 105 (135)
.|+|- ...|+..+.+.+..|..|..++ |...++.+ ++-.-+..++..+......|
T Consensus 12 dp~Fd---~~~F~~~ak~~f~~i~~A~~~~--D~~~l~~~----------~t~~~~~~~~~~i~~~~~~g 66 (147)
T PF04280_consen 12 DPGFD---PAAFLEEAKEAFLPIQEAWAKG--DLEALRPL----------LTEELYERLQAEIKARRSRG 66 (147)
T ss_dssp -TT-----HHHHHHHHHHTHHHHHHHHHHT---HHHHHHH----------B-HHHHHHHHHHHHHHHHTT
T ss_pred CCCCC---HHHHHHHHHHHHHHHHHHHHcC--CHHHHHHH----------hCHHHHHHHHHHHHHHHHcC
Confidence 45554 5688999999999999999998 89999988 77788888888888775544
No 24
>PF08893 DUF1839: Domain of unknown function (DUF1839); InterPro: IPR014989 This group of proteins are functionally uncharacterised.
Probab=57.36 E-value=51 Score=27.33 Aligned_cols=44 Identities=11% Similarity=0.173 Sum_probs=32.6
Q ss_pred ChHHHHHHHHHHH----HHHhhcCHHHHHHHHHHHHHHHHHHHHHHHH
Q 047910 87 GANKVVNEAKKAI----ELCKEENLEAAKASFEKMKVEHTTLKTKLQA 130 (135)
Q Consensus 87 GA~~l~~~c~~lE----~~~~~~~~~~~~~~l~~l~~ef~~~~~~L~~ 130 (135)
.+..++.-|+.++ .++..+..+++...|+.++..|+.+...|.+
T Consensus 271 a~~~ias~Ak~~QFrLARAv~r~r~~~~~~~Ld~~~~ay~~~~~~L~~ 318 (319)
T PF08893_consen 271 ACRTIASEAKVVQFRLARAVARGRFDDCEDCLDPMEAAYDRAMDGLAR 318 (319)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCCCCchhHHHHHHHHHHHHHHHHhc
Confidence 3455666666555 2234578889999999999999999988753
No 25
>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=57.23 E-value=47 Score=20.97 Aligned_cols=40 Identities=8% Similarity=0.179 Sum_probs=21.1
Q ss_pred chHHHHHHHHHHcHHHHHHHHHHHHhcCCCCHHHHHHHHhhh
Q 047910 38 SLFEDFVNVYLRDSTKTLAIIEEEIANNPVNYMDLDKYFHQL 79 (135)
Q Consensus 38 df~~~li~~fl~d~~~~l~~L~~al~~~~~D~~~l~~~aH~L 79 (135)
+=+..+....-.....++..|..++..+ |+.......+.|
T Consensus 27 ~~L~~l~~~~~~~~~~~~~~l~~~f~~~--d~~~A~~~~~kL 66 (78)
T PF07743_consen 27 AELEELKKEIEERIKELIKELAEAFDAK--DWEEAKEALRKL 66 (78)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHTT---HHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHccC--cHHHHHHHHHHH
Confidence 3344455555555555555666666544 566665555554
No 26
>PRK01356 hscB co-chaperone HscB; Provisional
Probab=57.08 E-value=76 Score=23.51 Aligned_cols=53 Identities=30% Similarity=0.286 Sum_probs=34.0
Q ss_pred CHHHHHHHHhhhcccccccChHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHHHHHH
Q 047910 68 NYMDLDKYFHQLKSSSNCIGANKVVNEAKKAIELCKEENLEAAKASFEKMKVEHTTLKTKLQ 129 (135)
Q Consensus 68 D~~~l~~~aH~LKGSSa~iGA~~l~~~c~~lE~~~~~~~~~~~~~~l~~l~~ef~~~~~~L~ 129 (135)
|...+..+...++ .++..+...|+.+-..++++.+...+.+|+= |.++...++
T Consensus 107 ~~~~L~~l~~~~~--------~~~~~~~~~l~~~f~~~d~~~A~~~~~~L~y-~~kl~~~i~ 159 (166)
T PRK01356 107 LFSDLEKIKNKYE--------LMYKNEIDSLKQAFEEQNLSDATIKTSKLKY-IGTLLNKLQ 159 (166)
T ss_pred CHHHHHHHHHHHH--------HHHHHHHHHHHHHHhcCCHHHHHHHHHHHHH-HHHHHHHHH
Confidence 4456666666665 3456667777777777888888887777654 444444444
No 27
>KOG4747 consensus Two-component phosphorelay intermediate involved in MAP kinase cascade regulation [Signal transduction mechanisms]
Probab=54.27 E-value=87 Score=23.19 Aligned_cols=58 Identities=7% Similarity=0.087 Sum_probs=47.3
Q ss_pred cchHHHHHHHHHHcHHHHHHHHHHHHhcCCCCHHHHHHHHhhhcccccccChHHHHHHHHH
Q 047910 37 PSLFEDFVNVYLRDSTKTLAIIEEEIANNPVNYMDLDKYFHQLKSSSNCIGANKVVNEAKK 97 (135)
Q Consensus 37 ~df~~~li~~fl~d~~~~l~~L~~al~~~~~D~~~l~~~aH~LKGSSa~iGA~~l~~~c~~ 97 (135)
.+|-..++..++.| ..+.+|.+-.....+|+ -..-..|.+|+|+..||-.+.+--|..
T Consensus 13 ~d~~~sl~~qgild--~qF~qlq~lqD~~~p~f-v~ev~~~fF~~s~~~i~~~r~ald~~~ 70 (150)
T KOG4747|consen 13 SDYTKSLFDQGILD--SQFLQLQELQDDSSPDF-VEEVVGLFFEDSERLINNLRLALDCER 70 (150)
T ss_pred HHHHHHHHHHHhhH--HHHHHHHHHhcccCccH-HHHHHHHHHHHHHHHHHHHHHHHhhHh
Confidence 45777788888888 78889999888765554 456678999999999999999999985
No 28
>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=50.79 E-value=34 Score=21.29 Aligned_cols=61 Identities=13% Similarity=0.199 Sum_probs=40.9
Q ss_pred HHHHHHHHcHHHHHHHHHHHHhcCCCCHHHHHHHHhhhcccccccChHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHH
Q 047910 42 DFVNVYLRDSTKTLAIIEEEIANNPVNYMDLDKYFHQLKSSSNCIGANKVVNEAKKAIELCKEENLEAAKASFEKMKVEH 121 (135)
Q Consensus 42 ~li~~fl~d~~~~l~~L~~al~~~~~D~~~l~~~aH~LKGSSa~iGA~~l~~~c~~lE~~~~~~~~~~~~~~l~~l~~ef 121 (135)
.+.+.|..-.......+......+ + ..=..+|.+++.+....++..+...+..|..+|
T Consensus 9 ~a~~~~~~~~~~~~~~~~~~~~~n---~-------------------~~K~~Li~~~~~l~~~~d~~~~~~~~k~l~~~W 66 (77)
T PF03993_consen 9 AACDAFFDRRKEFFEEQDAEREEN---L-------------------EKKEALIEEAEALAESEDWKEAAEEIKELQQEW 66 (77)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH---H-------------------HHHHHHHHHHHHhcccccHHHHHHHHHHHHHHH
Confidence 556666666666666655555432 1 222467888888888888888888888888887
Q ss_pred HHH
Q 047910 122 TTL 124 (135)
Q Consensus 122 ~~~ 124 (135)
..+
T Consensus 67 k~i 69 (77)
T PF03993_consen 67 KEI 69 (77)
T ss_pred HHc
Confidence 653
No 29
>PF13326 PSII_Pbs27: Photosystem II Pbs27; PDB: 2KND_A 2KMF_A 2Y6X_A.
Probab=48.70 E-value=1e+02 Score=22.44 Aligned_cols=86 Identities=10% Similarity=0.101 Sum_probs=56.3
Q ss_pred HHHHHHHHcHHHHHHHHHHHHhcCCCCHHHHHHHHhhhcc-----------cccccChHHHHHHHHHHHHHH----hhcC
Q 047910 42 DFVNVYLRDSTKTLAIIEEEIANNPVNYMDLDKYFHQLKS-----------SSNCIGANKVVNEAKKAIELC----KEEN 106 (135)
Q Consensus 42 ~li~~fl~d~~~~l~~L~~al~~~~~D~~~l~~~aH~LKG-----------SSa~iGA~~l~~~c~~lE~~~----~~~~ 106 (135)
.+-..|.+|+.+.+..|+.+++.+ .|.+..++.+-.+|- ..+--|=.....+-..|..++ ..|+
T Consensus 44 ~l~~~Y~~dt~~vv~~lr~~l~l~-~d~~~~~~~~~~ar~~in~~vs~YRr~~~v~g~~Sf~~m~tAln~LaghY~s~g~ 122 (145)
T PF13326_consen 44 GLTGDYVKDTRAVVKTLREALELD-KDDPNRAEAAAEARELINDYVSRYRRGPSVSGLPSFTTMYTALNALAGHYSSYGN 122 (145)
T ss_dssp S--S-CHHHHHHHHHHHHHHHCS--TT-TTHHHHHHHHHHHHHHHHCCCCCCHHCCTSHHHHHHHHHHHHHHHHCHHHTT
T ss_pred cccchHHHHHHHHHHHHHHHHcCC-CCCccHHHHHHHHHHHHHHHHHHhCCCCCcCCcchHHHHHHHHHHHHHHHHhCCC
Confidence 344679999999999999999765 366666666666653 333345455566666666553 5566
Q ss_pred H-HHHHHHHHHHHHHHHHHHHHH
Q 047910 107 L-EAAKASFEKMKVEHTTLKTKL 128 (135)
Q Consensus 107 ~-~~~~~~l~~l~~ef~~~~~~L 128 (135)
. +--....+.|.++|.++..+|
T Consensus 123 raPlP~k~k~rll~el~~Ae~aL 145 (145)
T PF13326_consen 123 RAPLPEKLKERLLKELDQAEKAL 145 (145)
T ss_dssp S-S--HHHHHHHHHHHHHHHHHH
T ss_pred CCCCCHHHHHHHHHHHHHHHhcC
Confidence 6 555678889999999888765
No 30
>PLN00061 photosystem II protein Psb27; Provisional
Probab=47.54 E-value=47 Score=24.56 Aligned_cols=59 Identities=8% Similarity=0.210 Sum_probs=40.6
Q ss_pred ccchhhhhHHHHHHHhccccCCcc-hHHHHHHHHHHcHHHHHHHHHHHHhcCCCCHHHHHHHHh
Q 047910 15 FFDEDILDTHIFQLEQVEHISDPS-LFEDFVNVYLRDSTKTLAIIEEEIANNPVNYMDLDKYFH 77 (135)
Q Consensus 15 ~~d~~~lD~~~~~L~~L~~~~~~d-f~~~li~~fl~d~~~~l~~L~~al~~~~~D~~~l~~~aH 77 (135)
=.++|+++ -+..|-|++..- -=..|=..|.+|+-..+..|+++|+..+-|...+++.+.
T Consensus 27 ~~~~~~~~----~~~~~fdp~e~tksg~~Lpg~Y~kdtr~VV~tLresl~l~p~D~~~~~~aa~ 86 (150)
T PLN00061 27 EEGEGVVG----AIKSLFDPNEKTKSGKKLPKAYLKSAREVVKTLRESLKEDPKDEAKFRRTAD 86 (150)
T ss_pred cccccHHH----HHHHhcCccccccccccCchHHHHHHHHHHHHHHHHHccCCcchHHHHHHHH
Confidence 34567777 677776654321 112466889999999999999999985557676655443
No 31
>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=47.33 E-value=50 Score=18.38 Aligned_cols=26 Identities=19% Similarity=0.263 Sum_probs=20.6
Q ss_pred HHHHHHHHHHHhcCCCCHHHHHHHHhhh
Q 047910 52 TKTLAIIEEEIANNPVNYMDLDKYFHQL 79 (135)
Q Consensus 52 ~~~l~~L~~al~~~~~D~~~l~~~aH~L 79 (135)
+++...|..|+.++ |-+.+.+++..|
T Consensus 12 ~~L~~~ID~ALd~~--D~e~F~~Ls~eL 37 (37)
T PF08858_consen 12 EQLLELIDEALDNR--DKEWFYELSEEL 37 (37)
T ss_dssp HHHHHHHHHHHHTT---HHHHHHHHHHH
T ss_pred HHHHHHHHHHHHcC--CHHHHHHHHhhC
Confidence 57888999999998 889988877543
No 32
>KOG2424 consensus Protein involved in transcription start site selection [Transcription]
Probab=46.95 E-value=31 Score=26.49 Aligned_cols=24 Identities=17% Similarity=0.274 Sum_probs=19.0
Q ss_pred ccccChHHHHHHHHHHHHHHhhcCHH
Q 047910 83 SNCIGANKVVNEAKKAIELCKEENLE 108 (135)
Q Consensus 83 Sa~iGA~~l~~~c~~lE~~~~~~~~~ 108 (135)
-|++||..+.++|..|+. ++.+++
T Consensus 147 dA~~Gaf~I~elcq~l~~--~s~d~E 170 (195)
T KOG2424|consen 147 DATLGAFLILELCQCLQA--QSDDLE 170 (195)
T ss_pred hhhhhHHHHHHHHHHHHh--ccccHH
Confidence 467999999999999997 444443
No 33
>TIGR03044 PS_II_psb27 photosystem II protein Psb27. Members of this family are the Psb27 protein of the cyanobacterial photosynthetic supracomplex, photosystem II. Although most protein components of both cyanobacterial and chloroplast versions of photosystem II are closely related and described together by single model families, this family is strictly bacterial. Some uncharacterized proteins with highly divergent sequences, from Arabidopsis, score between trusted and noise cutoffs for this model but are not at this time assigned as functionally equivalent photosystem II proteins.
Probab=46.92 E-value=70 Score=23.29 Aligned_cols=88 Identities=11% Similarity=0.100 Sum_probs=59.4
Q ss_pred HHHHHHHHcHHHHHHHHHHHHhcCCCCHHHHHHHHhhh-----------cccccccChHHHHHHHHHHHHHH----hhcC
Q 047910 42 DFVNVYLRDSTKTLAIIEEEIANNPVNYMDLDKYFHQL-----------KSSSNCIGANKVVNEAKKAIELC----KEEN 106 (135)
Q Consensus 42 ~li~~fl~d~~~~l~~L~~al~~~~~D~~~l~~~aH~L-----------KGSSa~iGA~~l~~~c~~lE~~~----~~~~ 106 (135)
.|-..|.+|+-..+..|+.+++-+. |-+...+..... .+-..--|-.....+-..|+..+ ..++
T Consensus 32 ~Ltg~Y~~DT~~Vi~tlr~~i~lpk-d~p~~~~a~~~ar~~indyvsrYRr~~~v~g~~SFttm~TALNsLAGHY~sy~~ 110 (135)
T TIGR03044 32 RLTGDYVEDTLAVIQTLREAIDLPD-DDPNKSEAQAEARQLINDYISRYRRRPRVNGLSSFTTMQTALNSLAGHYKSYAN 110 (135)
T ss_pred cccchHHHHHHHHHHHHHHHHcCCC-CCccHHHHHHHHHHHHHHHHHHhcCCCCcCCcccHHHHHHHHHHHHHHhccCCC
Confidence 5778999999999999999998642 434333333332 33344556666666666666553 3344
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Q 047910 107 LEAAKASFEKMKVEHTTLKTKLQA 130 (135)
Q Consensus 107 ~~~~~~~l~~l~~ef~~~~~~L~~ 130 (135)
.+--..+-++|.+||.++..+|.+
T Consensus 111 rPlPeklk~Rl~~El~~AE~al~R 134 (135)
T TIGR03044 111 RPLPEKLKERLEKELKKAEKALLR 134 (135)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHhc
Confidence 455567888999999999888764
No 34
>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=46.46 E-value=1.3e+02 Score=23.23 Aligned_cols=51 Identities=14% Similarity=0.221 Sum_probs=32.7
Q ss_pred ccccccChHHHHHHHHHHHHHHhhcC------HHHHHHHHHHHHHHHHHHHHHHHHH
Q 047910 81 SSSNCIGANKVVNEAKKAIELCKEEN------LEAAKASFEKMKVEHTTLKTKLQAY 131 (135)
Q Consensus 81 GSSa~iGA~~l~~~c~~lE~~~~~~~------~~~~~~~l~~l~~ef~~~~~~L~~~ 131 (135)
|..+=+|...+...+..+...++..| +-..++.+..+.+++......|++.
T Consensus 32 ~~~~I~Gm~~~~~~~~~i~~~a~~DdPyAD~~L~~iEe~i~~~~~~l~~~~~~l~~~ 88 (217)
T PF08900_consen 32 GKPAIIGMPGFASRLNRIWRDARQDDPYADWWLLRIEEKINEARQELQELIARLDAL 88 (217)
T ss_pred CCCCCcCHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34478999999999999999877765 2223344444444444444444443
No 35
>PF12854 PPR_1: PPR repeat
Probab=44.60 E-value=24 Score=18.80 Aligned_cols=21 Identities=24% Similarity=0.373 Sum_probs=17.4
Q ss_pred HHHHHHhhcCHHHHHHHHHHH
Q 047910 97 KAIELCKEENLEAAKASFEKM 117 (135)
Q Consensus 97 ~lE~~~~~~~~~~~~~~l~~l 117 (135)
-+.-+|+.|..+.+..+++++
T Consensus 13 lI~~~Ck~G~~~~A~~l~~~M 33 (34)
T PF12854_consen 13 LIDGYCKAGRVDEAFELFDEM 33 (34)
T ss_pred HHHHHHHCCCHHHHHHHHHhC
Confidence 456679999999999998875
No 36
>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=44.24 E-value=38 Score=20.93 Aligned_cols=36 Identities=19% Similarity=0.384 Sum_probs=28.1
Q ss_pred HHHHHHhccccCCcchHHHHHHHHHHcHHHHHHHHHH
Q 047910 24 HIFQLEQVEHISDPSLFEDFVNVYLRDSTKTLAIIEE 60 (135)
Q Consensus 24 ~~~~L~~L~~~~~~df~~~li~~fl~d~~~~l~~L~~ 60 (135)
+|.+++++-. .+|+.+..++...-..-|.++..|.+
T Consensus 9 qf~~lR~~vq-~NP~lL~~lLqql~~~nP~l~q~I~~ 44 (59)
T PF09280_consen 9 QFQQLRQLVQ-QNPQLLPPLLQQLGQSNPQLLQLIQQ 44 (59)
T ss_dssp HHHHHHHHHH-C-GGGHHHHHHHHHCCSHHHHHHHHH
T ss_pred HHHHHHHHHH-HCHHHHHHHHHHHhccCHHHHHHHHH
Confidence 5888888766 58999989988888888888777654
No 37
>KOG2580 consensus Mitochondrial import inner membrane translocase, subunit TIM44 [Intracellular trafficking, secretion, and vesicular transport]
Probab=43.46 E-value=60 Score=28.08 Aligned_cols=66 Identities=11% Similarity=0.269 Sum_probs=42.1
Q ss_pred HHHHHHHHHHhccchhhhhHHHHHHHhccccCCcchHHHHHHHHHHcHHHHHH-HHHHHHhcCCCCHHHHHHHHhh
Q 047910 4 LRQQISAMRQSFFDEDILDTHIFQLEQVEHISDPSLFEDFVNVYLRDSTKTLA-IIEEEIANNPVNYMDLDKYFHQ 78 (135)
Q Consensus 4 ~~~~~~~~~~~~~d~~~lD~~~~~L~~L~~~~~~df~~~li~~fl~d~~~~l~-~L~~al~~~~~D~~~l~~~aH~ 78 (135)
++..+.+.+..|+.+--..+.+.++..+++. |- ...|+.++++.|- .+-+|.-.| |.+-|...||.
T Consensus 284 vtdki~~~~~g~fsktE~Sev~tei~~iDPs----F~---~~~Flr~~ee~IiPnVLeAyvkG--D~evLK~wcse 350 (459)
T KOG2580|consen 284 VTDKITDVDGGLFSKTEMSEVLTEIKKIDPS----FD---KEDFLRECEEYIIPNVLEAYVKG--DLEVLKKWCSE 350 (459)
T ss_pred HHHhhhhcccccchhhHHHHHHHHHHhcCCC----CC---cHHHHHHHHHhhhHHHHHHHHhc--cHHHHHHHHhh
Confidence 4555666666666665555557778777543 22 2344555555444 477888888 89999999885
No 38
>COG2991 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=43.36 E-value=6.4 Score=25.74 Aligned_cols=20 Identities=20% Similarity=0.199 Sum_probs=18.3
Q ss_pred hhhcccccccChHHHHHHHH
Q 047910 77 HQLKSSSNCIGANKVVNEAK 96 (135)
Q Consensus 77 H~LKGSSa~iGA~~l~~~c~ 96 (135)
-++|||.+-|+|..+...|.
T Consensus 27 k~I~GSCGGi~alGi~K~Cd 46 (77)
T COG2991 27 KSIKGSCGGIAALGIEKVCD 46 (77)
T ss_pred cccccccccHHhhccchhcC
Confidence 57999999999999999987
No 39
>KOG0796 consensus Spliceosome subunit [RNA processing and modification]
Probab=43.27 E-value=1.9e+02 Score=24.00 Aligned_cols=74 Identities=19% Similarity=0.298 Sum_probs=47.2
Q ss_pred chHHHHHHHHHHcHHHHHHHHHHHHhcC---CCCHHHHH-HHHhhhcccccccChHHHHHHHHHHHHHHhhcCHHHHHHH
Q 047910 38 SLFEDFVNVYLRDSTKTLAIIEEEIANN---PVNYMDLD-KYFHQLKSSSNCIGANKVVNEAKKAIELCKEENLEAAKAS 113 (135)
Q Consensus 38 df~~~li~~fl~d~~~~l~~L~~al~~~---~~D~~~l~-~~aH~LKGSSa~iGA~~l~~~c~~lE~~~~~~~~~~~~~~ 113 (135)
+|+ ++|..|+.|+...+...++-++.. .++..... ...|.|- ..+-.+-.++|.++.+|+.+.+..+
T Consensus 83 d~~-~~l~~~v~d~~rri~~~kerL~e~~ee~~~e~~~k~~~v~~l~--------e~I~~~l~~~E~LG~eG~Veeaq~~ 153 (319)
T KOG0796|consen 83 DAL-EILERFVADVDRRIEKAKERLAETVEERSEEAARKAEKVHELE--------EKIGKLLEKAEELGEEGNVEEAQKA 153 (319)
T ss_pred HHH-HHHHHHHHHHHHHHHHHHHHHHhhhhhhhhHHHHHHHHHHHHH--------HHHHHHHHHHHHHhhcCCHHHHHHH
Confidence 344 788888999888877777666542 11111111 1122221 5566677888999999999999887
Q ss_pred HHHHHHH
Q 047910 114 FEKMKVE 120 (135)
Q Consensus 114 l~~l~~e 120 (135)
+..++.-
T Consensus 154 ~~e~E~l 160 (319)
T KOG0796|consen 154 MKEVEEL 160 (319)
T ss_pred HHHHHHH
Confidence 7766653
No 40
>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=42.62 E-value=26 Score=27.05 Aligned_cols=38 Identities=21% Similarity=0.279 Sum_probs=24.6
Q ss_pred ccccChHHHHHHHHHHHHHHhhcCHH-HHHHHHHHHHHHH
Q 047910 83 SNCIGANKVVNEAKKAIELCKEENLE-AAKASFEKMKVEH 121 (135)
Q Consensus 83 Sa~iGA~~l~~~c~~lE~~~~~~~~~-~~~~~l~~l~~ef 121 (135)
.|.+||..+.++|..|+. ....+++ .+...+...+..+
T Consensus 145 eA~~Ga~~ileLc~~l~~-~~~~d~e~~i~~il~~fe~k~ 183 (195)
T PF04722_consen 145 EATIGAFLILELCQMLEE-EASEDLEDEIDEILQEFEEKH 183 (195)
T ss_dssp HHHHHHHHHHHHHHHHH---TSSSHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHh-hccccHHHHHHHHHHHHHHHc
Confidence 356999999999999997 3344443 3445565555544
No 41
>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=42.07 E-value=1.7e+02 Score=23.14 Aligned_cols=79 Identities=20% Similarity=0.314 Sum_probs=47.6
Q ss_pred HHHHHHHHHHcHHHHHHHHHHHHhcCCCCHHHH-----HHHHhhhcccccccChHHHHHHHHHHHHHHhhcCHHHHHHHH
Q 047910 40 FEDFVNVYLRDSTKTLAIIEEEIANNPVNYMDL-----DKYFHQLKSSSNCIGANKVVNEAKKAIELCKEENLEAAKASF 114 (135)
Q Consensus 40 ~~~li~~fl~d~~~~l~~L~~al~~~~~D~~~l-----~~~aH~LKGSSa~iGA~~l~~~c~~lE~~~~~~~~~~~~~~l 114 (135)
+-+.+..|+.|+...|..=..-++..+.+.... ....+.| -..+..+-.+.|.++.+|+.+.+...+
T Consensus 84 ~~~~L~~~i~d~drrI~~~k~RL~~~~~~~~~~~~~~~~~~i~~l--------~~~I~~ll~~aE~LGeeG~VdeA~~~~ 155 (254)
T PF03194_consen 84 FLRYLQRLIRDCDRRIERAKERLEQTQEEQAKEADEEKAEKIDEL--------DEKIGELLKEAEELGEEGDVDEAQKLM 155 (254)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhCccccccchhhhHHHHHHHH--------HHHHHHHHHHHHHHHHCCCHHHHHHHH
Confidence 347888999999998887777665531111000 0111111 123666777889999999999887765
Q ss_pred HHH---HHHHHHHHH
Q 047910 115 EKM---KVEHTTLKT 126 (135)
Q Consensus 115 ~~l---~~ef~~~~~ 126 (135)
..+ +.+-..+..
T Consensus 156 ~~~e~Lk~ek~~le~ 170 (254)
T PF03194_consen 156 EEVEKLKEEKEELEK 170 (254)
T ss_pred HHHHHHHHHHHHHHh
Confidence 544 444444444
No 42
>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=41.15 E-value=1.4e+02 Score=21.82 Aligned_cols=73 Identities=11% Similarity=0.203 Sum_probs=43.1
Q ss_pred cHHHHHHHHHHHHhcCCCCHHHHHHHHhhhcccccccChH---------------------HHHHHHHHHHHHHhhcCHH
Q 047910 50 DSTKTLAIIEEEIANNPVNYMDLDKYFHQLKSSSNCIGAN---------------------KVVNEAKKAIELCKEENLE 108 (135)
Q Consensus 50 d~~~~l~~L~~al~~~~~D~~~l~~~aH~LKGSSa~iGA~---------------------~l~~~c~~lE~~~~~~~~~ 108 (135)
.+.+++.+++..++.+ |+..++...| |+.++++-. .|..--..|-.+++.+|
T Consensus 47 ~~~~r~~eLk~lI~kk--~W~~vrn~ir---gp~g~Lr~dl~~l~~sl~p~dqk~a~~L~~~Lf~~L~~LD~AA~~kd-- 119 (142)
T TIGR03042 47 AAKDRLPELASLVAKE--DWVFTRNLIH---GPMGEVRREMTYLNQSLLPKDQKEALALAKELKDDLEKLDEAARLQD-- 119 (142)
T ss_pred HHHHhhHHHHHHHhhc--chHHHHHHHh---ccHHHHHHHHHHHHHccCHHhHHHHHHHHHHHHHHHHHHHHHHHhcC--
Confidence 3566777777777776 7777776544 555554422 12222223333344444
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhcC
Q 047910 109 AAKASFEKMKVEHTTLKTKLQAYLEV 134 (135)
Q Consensus 109 ~~~~~l~~l~~ef~~~~~~L~~~l~~ 134 (135)
-.+.++.|.++.+.|+.|+++
T Consensus 120 -----~~~a~k~Y~~av~~~dafl~~ 140 (142)
T TIGR03042 120 -----GPQAQKAYQKAAADFDAYLDL 140 (142)
T ss_pred -----HHHHHHHHHHHHHHHHHHHhh
Confidence 345567788888888888764
No 43
>PRK15178 Vi polysaccharide export inner membrane protein VexD; Provisional
Probab=40.32 E-value=81 Score=27.23 Aligned_cols=121 Identities=11% Similarity=0.068 Sum_probs=75.7
Q ss_pred HHHHHHHHHhccchhhhhHH-HHHHHhccccCCcchHHHHHHHHHHcHHHHHHHHHHHHhcCCCCHHHHHHHHhhhcccc
Q 047910 5 RQQISAMRQSFFDEDILDTH-IFQLEQVEHISDPSLFEDFVNVYLRDSTKTLAIIEEEIANNPVNYMDLDKYFHQLKSSS 83 (135)
Q Consensus 5 ~~~~~~~~~~~~d~~~lD~~-~~~L~~L~~~~~~df~~~li~~fl~d~~~~l~~L~~al~~~~~D~~~l~~~aH~LKGSS 83 (135)
.+.++++|+++.+-.+=... +-.|+.- .-+|+.-..+-..-+..+++.+.+|-.-+.. ++++..-..++.+-
T Consensus 183 ~E~l~~Yy~~~V~V~~D~~sGIi~l~V~--AF~PedA~~ia~aLL~~sE~~VN~Ls~rar~-----D~v~~Ae~ev~~Ae 255 (434)
T PRK15178 183 NDDPYRYYLSKVSVAVDIQQGMLRLNVK--ARSAKQAEFFAQRILSFAEQHVNTVSARMQK-----ERILWLENDVKSAQ 255 (434)
T ss_pred HHHHHHHHHhceEEeecCCCCeEEEEEE--ecCHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHH
Confidence 35566777777665443322 2222211 2478888899999999999999999988875 36666666666655
Q ss_pred cccChHHHHHHHHHHHHH--HhhcCHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 047910 84 NCIGANKVVNEAKKAIEL--CKEENLEAAKASFEKMKVEHTTLKTKLQAYL 132 (135)
Q Consensus 84 a~iGA~~l~~~c~~lE~~--~~~~~~~~~~~~l~~l~~ef~~~~~~L~~~l 132 (135)
..+.+.+.+-..-+=++. -+..........+..|+.+...++..|..+.
T Consensus 256 ~rl~~Ar~aL~~fRn~~gvlDP~~~a~~~~~lI~~Le~qLa~~~aeL~~L~ 306 (434)
T PRK15178 256 ENLGAARLELLKIQHIQKDIDPKETITAIYQLIAGFETQLAEAKAEYAQLM 306 (434)
T ss_pred HHHHHHHHHHHHHHHhCCCcChHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 444443333222221111 1233455566789999999999888887653
No 44
>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=39.99 E-value=2.1e+02 Score=23.42 Aligned_cols=68 Identities=22% Similarity=0.284 Sum_probs=44.0
Q ss_pred hhHHHHHHHhccccCCcchHHHHHHHHHHcHHHH--HHHHHHHHhcCCCCHHHHHHHHhhhcccccccChHHHHHHHHH
Q 047910 21 LDTHIFQLEQVEHISDPSLFEDFVNVYLRDSTKT--LAIIEEEIANNPVNYMDLDKYFHQLKSSSNCIGANKVVNEAKK 97 (135)
Q Consensus 21 lD~~~~~L~~L~~~~~~df~~~li~~fl~d~~~~--l~~L~~al~~~~~D~~~l~~~aH~LKGSSa~iGA~~l~~~c~~ 97 (135)
|+..+..|-.+ |...-+.+|...|-- ++++ .-.|+..+..+ ||+.+...+-+=|++ ||-..+.+.|..
T Consensus 180 l~~Ti~~li~~---~~~k~A~kl~k~Fkv-~dkrfw~lki~aLa~~~--~w~eL~~fa~skKsP---IGyepFv~~~~~ 249 (319)
T PF04840_consen 180 LNDTIRKLIEM---GQEKQAEKLKKEFKV-PDKRFWWLKIKALAENK--DWDELEKFAKSKKSP---IGYEPFVEACLK 249 (319)
T ss_pred HHHHHHHHHHC---CCHHHHHHHHHHcCC-cHHHHHHHHHHHHHhcC--CHHHHHHHHhCCCCC---CChHHHHHHHHH
Confidence 44445555555 334456677777743 2333 23445555655 999999999885654 999999999964
No 45
>PF11827 DUF3347: Protein of unknown function (DUF3347); InterPro: IPR021782 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 169 to 570 amino acids in length.
Probab=39.95 E-value=1.6e+02 Score=21.95 Aligned_cols=81 Identities=15% Similarity=0.302 Sum_probs=55.4
Q ss_pred chHHHHHHHHHHcHHHHHHHHHHHHhcCCCCHHHHHHHHhhhcccccccChHHH-HHHHHHHHHHHh---hcCHHHHHHH
Q 047910 38 SLFEDFVNVYLRDSTKTLAIIEEEIANNPVNYMDLDKYFHQLKSSSNCIGANKV-VNEAKKAIELCK---EENLEAAKAS 113 (135)
Q Consensus 38 df~~~li~~fl~d~~~~l~~L~~al~~~~~D~~~l~~~aH~LKGSSa~iGA~~l-~~~c~~lE~~~~---~~~~~~~~~~ 113 (135)
+.+..|+.-|+ .|+.||..+ |.......|=.|..+-..+....+ ......+..... ..+++..+..
T Consensus 44 ~~l~~v~~~Yl--------~lk~ALv~d--d~~~a~~aA~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~di~~qR~~ 113 (174)
T PF11827_consen 44 DSLQQVLNAYL--------ALKDALVAD--DLKAAKAAAKALLAALKAVDMAELSASLAKALMEAAEDAKEHDIEHQREA 113 (174)
T ss_pred HHHHHHHHHHH--------HHHHHHHhc--CHHHHHHHHHHHHHHHHhcccccccHHHHHHHHHHHHhhhhCCHHHHHHH
Confidence 34555666664 699999988 899999999888888888776633 333444444332 2288888888
Q ss_pred HHHHHHHHHHHHHHH
Q 047910 114 FEKMKVEHTTLKTKL 128 (135)
Q Consensus 114 l~~l~~ef~~~~~~L 128 (135)
|..|-..+-.+...+
T Consensus 114 F~~lS~~~~~l~~~~ 128 (174)
T PF11827_consen 114 FESLSEAMIDLVKAF 128 (174)
T ss_pred HHHHHHHHHHHHHhc
Confidence 888877776665543
No 46
>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=39.71 E-value=1.1e+02 Score=23.82 Aligned_cols=24 Identities=17% Similarity=0.296 Sum_probs=17.7
Q ss_pred cHHHHHHHHHHHHhcCCCCHHHHHHH
Q 047910 50 DSTKTLAIIEEEIANNPVNYMDLDKY 75 (135)
Q Consensus 50 d~~~~l~~L~~al~~~~~D~~~l~~~ 75 (135)
.-.+.|.++++++.++ |.+.+.++
T Consensus 232 ~~~~~L~~l~~~l~~~--d~~~l~~~ 255 (258)
T PF02153_consen 232 EFIKELNELREALEAG--DEEELEEL 255 (258)
T ss_dssp HHHHHHHHHHHHHHTT--SHHHHHHH
T ss_pred HHHHHHHHHHHHHHcC--CHHHHHHH
Confidence 3366778888888887 78887754
No 47
>PLN02407 diphosphomevalonate decarboxylase
Probab=38.95 E-value=58 Score=27.26 Aligned_cols=32 Identities=19% Similarity=0.354 Sum_probs=27.3
Q ss_pred HHHHHHHc-HHHHHHHHHHHHhcCCCCHHHHHHHH
Q 047910 43 FVNVYLRD-STKTLAIIEEEIANNPVNYMDLDKYF 76 (135)
Q Consensus 43 li~~fl~d-~~~~l~~L~~al~~~~~D~~~l~~~a 76 (135)
+....++. +++.+..|++|+.++ |+.++.+.+
T Consensus 224 ~~~~w~~~~~~~~~~~~~~Ai~~~--Df~~~gei~ 256 (343)
T PLN02407 224 LLQHRAKEVVPKRILQMEEAIKNR--DFASFAKLT 256 (343)
T ss_pred hHHHHHHhhhHHHHHHHHHHHHhc--CHHHHHHHH
Confidence 56677888 899999999999998 999887654
No 48
>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=38.55 E-value=1e+02 Score=19.51 Aligned_cols=46 Identities=9% Similarity=0.229 Sum_probs=27.8
Q ss_pred HHHHHHHHHhccchhhhhHHHHHHHhccccCCcchHHHHHHHHHHcHHHHHHHHHHH
Q 047910 5 RQQISAMRQSFFDEDILDTHIFQLEQVEHISDPSLFEDFVNVYLRDSTKTLAIIEEE 61 (135)
Q Consensus 5 ~~~~~~~~~~~~d~~~lD~~~~~L~~L~~~~~~df~~~li~~fl~d~~~~l~~L~~a 61 (135)
+.+|.++++++--..-+|.. -.+++.++.+.|++++-..--.+...
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 46778888887444455533 23467788888888887766666554
No 49
>COG4865 Glutamate mutase epsilon subunit [Amino acid transport and metabolism]
Probab=38.19 E-value=18 Score=30.62 Aligned_cols=40 Identities=23% Similarity=0.316 Sum_probs=33.6
Q ss_pred HHHhccchhhhhHHHHHHHhccccCCcchHHHHHHHHHHc
Q 047910 11 MRQSFFDEDILDTHIFQLEQVEHISDPSLFEDFVNVYLRD 50 (135)
Q Consensus 11 ~~~~~~d~~~lD~~~~~L~~L~~~~~~df~~~li~~fl~d 50 (135)
+.|+-.....||+.+.-|.-|+++|+.||+...|+.|-++
T Consensus 62 l~Qpragv~lLdehielL~tl~eeGqADlLp~tIDSyTR~ 101 (485)
T COG4865 62 LSQPRAGVALLDEHIELLKTLQEEGQADLLPSTIDSYTRL 101 (485)
T ss_pred ecccccCcchHHHHHHHHHHHHHhccccccchhhhhhhhh
Confidence 3455556678999999999999999999999999999654
No 50
>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=37.59 E-value=56 Score=18.24 Aligned_cols=34 Identities=15% Similarity=0.169 Sum_probs=23.6
Q ss_pred HHHHHhccccCCcchHHHHHHHHHHcHHHHHHHH
Q 047910 25 IFQLEQVEHISDPSLFEDFVNVYLRDSTKTLAII 58 (135)
Q Consensus 25 ~~~L~~L~~~~~~df~~~li~~fl~d~~~~l~~L 58 (135)
+..|+++-+.-+++++..++..+-.|.+..+..|
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 6688888877788888777777766666665544
No 51
>PRK01773 hscB co-chaperone HscB; Provisional
Probab=37.22 E-value=1.8e+02 Score=21.77 Aligned_cols=65 Identities=9% Similarity=0.113 Sum_probs=40.1
Q ss_pred CcchHHHHHHHHHHcHHHHHHHHHHHHhcCCCCHHHHHHHHhhhcccccccChHHHHHHHHHHHHHHhhcCHHHHHHHHH
Q 047910 36 DPSLFEDFVNVYLRDSTKTLAIIEEEIANNPVNYMDLDKYFHQLKSSSNCIGANKVVNEAKKAIELCKEENLEAAKASFE 115 (135)
Q Consensus 36 ~~df~~~li~~fl~d~~~~l~~L~~al~~~~~D~~~l~~~aH~LKGSSa~iGA~~l~~~c~~lE~~~~~~~~~~~~~~l~ 115 (135)
+|+|+.++++. .+ .|..+-..+ |..++..+...++ .++..+...++.+-..++++.+...+.
T Consensus 90 d~~fLme~ME~-----rE---~lee~~~~~--d~~~L~~l~~~v~--------~~~~~~~~~l~~~~~~~d~~~A~~~~~ 151 (173)
T PRK01773 90 DMAFLMQQMEW-----RE---QLEEIEQQQ--DEDALTAFSKEIK--------QEQQAILTELSTALNSQQWQQASQIND 151 (173)
T ss_pred CHHHHHHHHHH-----HH---HHHhhcccC--CHHHHHHHHHHHH--------HHHHHHHHHHHHHHhcCCHHHHHHHHH
Confidence 56777666652 22 222222233 6677777766554 467777778888778888888877555
Q ss_pred HHH
Q 047910 116 KMK 118 (135)
Q Consensus 116 ~l~ 118 (135)
+|+
T Consensus 152 rL~ 154 (173)
T PRK01773 152 RLR 154 (173)
T ss_pred HHH
Confidence 544
No 52
>COG5490 Uncharacterized conserved protein [Function unknown]
Probab=37.05 E-value=1.7e+02 Score=21.66 Aligned_cols=67 Identities=12% Similarity=0.199 Sum_probs=43.4
Q ss_pred CcchHHHHHHHHH-HcHHHHHHHHHHHHhcCCCCHHHHHHHHhhhcccccccChHHHHHHHHHHHHHH
Q 047910 36 DPSLFEDFVNVYL-RDSTKTLAIIEEEIANNPVNYMDLDKYFHQLKSSSNCIGANKVVNEAKKAIELC 102 (135)
Q Consensus 36 ~~df~~~li~~fl-~d~~~~l~~L~~al~~~~~D~~~l~~~aH~LKGSSa~iGA~~l~~~c~~lE~~~ 102 (135)
+++-+...+.-|- .++++-............-+.+++...+-+=+..+.++|+.....+=...|...
T Consensus 24 da~~f~d~f~~Faekgveqs~~a~a~~~th~~knleAleasv~aa~~ga~~Lg~kt~a~lr~~ae~~~ 91 (158)
T COG5490 24 DADKFMDMFRRFAEKGVEQSKEAYAKIKTHHEKNLEALEASVEAAAAGATSLGLKTIAALRDNAEEIA 91 (158)
T ss_pred chHHHHHHHHHHHHhhhhhhHHHHHHHHHhhHHHHHHHHHHHHHHHhhHHHHhHHHHHHHHHHHHHHH
Confidence 3444456677776 444444444444333222267888888888888899999998888777777653
No 53
>PF13812 PPR_3: Pentatricopeptide repeat domain
Probab=35.67 E-value=62 Score=16.12 Aligned_cols=22 Identities=27% Similarity=0.264 Sum_probs=17.6
Q ss_pred HHHHHhhcCHHHHHHHHHHHHH
Q 047910 98 AIELCKEENLEAAKASFEKMKV 119 (135)
Q Consensus 98 lE~~~~~~~~~~~~~~l~~l~~ 119 (135)
|...++.|+.+.+...+..++.
T Consensus 8 l~a~~~~g~~~~a~~~~~~M~~ 29 (34)
T PF13812_consen 8 LRACAKAGDPDAALQLFDEMKE 29 (34)
T ss_pred HHHHHHCCCHHHHHHHHHHHHH
Confidence 4566788999998888888775
No 54
>PRK03578 hscB co-chaperone HscB; Provisional
Probab=35.49 E-value=1.8e+02 Score=21.72 Aligned_cols=65 Identities=14% Similarity=0.187 Sum_probs=40.0
Q ss_pred CcchHHHHHHHHHHcHHHHHHHHHHHHhcCCCCHHHHHHHHhhhcccccccChHHHHHHHHHHHHHHhh-cCHHHHHHHH
Q 047910 36 DPSLFEDFVNVYLRDSTKTLAIIEEEIANNPVNYMDLDKYFHQLKSSSNCIGANKVVNEAKKAIELCKE-ENLEAAKASF 114 (135)
Q Consensus 36 ~~df~~~li~~fl~d~~~~l~~L~~al~~~~~D~~~l~~~aH~LKGSSa~iGA~~l~~~c~~lE~~~~~-~~~~~~~~~l 114 (135)
+|+|+.++++. .+.| ..+-..+ |...+..+...+ ..++..+...+..+-.. ++++.+...+
T Consensus 93 d~~fLme~mE~-----rE~l---ee~~~~~--d~~~L~~l~~e~--------~~~~~~~~~~l~~~~~~~~d~~~A~~~~ 154 (176)
T PRK03578 93 PPAFLMQQMEW-----REAI---EDARAAR--DVDALDALLAEL--------RDERRERYAELGALLDSRGDDQAAAEAV 154 (176)
T ss_pred CHHHHHHHHHH-----HHHH---HHhhccC--CHHHHHHHHHHH--------HHHHHHHHHHHHHHHHccccHHHHHHHH
Confidence 57788777652 2222 2222333 667777777666 35666777777776655 7888877766
Q ss_pred HHHH
Q 047910 115 EKMK 118 (135)
Q Consensus 115 ~~l~ 118 (135)
.+++
T Consensus 155 ~kL~ 158 (176)
T PRK03578 155 RQLM 158 (176)
T ss_pred HHHH
Confidence 5554
No 55
>COG2178 Predicted RNA-binding protein of the translin family [Translation, ribosomal structure and biogenesis]
Probab=34.92 E-value=1.7e+02 Score=22.80 Aligned_cols=45 Identities=22% Similarity=0.283 Sum_probs=36.7
Q ss_pred hHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 047910 88 ANKVVNEAKKAIELCKEENLEAAKASFEKMKVEHTTLKTKLQAYL 132 (135)
Q Consensus 88 A~~l~~~c~~lE~~~~~~~~~~~~~~l~~l~~ef~~~~~~L~~~l 132 (135)
+..+...|...-.....|+++.+...+..+......++..|..|-
T Consensus 26 sRei~r~s~~aI~~~H~~~~eeA~~~l~~a~~~v~~Lk~~l~~~p 70 (204)
T COG2178 26 SREIVRLSGEAIFLLHRGDFEEAEKKLKKASEAVEKLKRLLAGFP 70 (204)
T ss_pred HHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHHHHHHhhhH
Confidence 466788888888888999999998888888888888887776653
No 56
>smart00388 HisKA His Kinase A (phosphoacceptor) domain. Dimerisation and phosphoacceptor domain of histidine kinases.
Probab=34.79 E-value=84 Score=17.39 Aligned_cols=53 Identities=17% Similarity=0.171 Sum_probs=28.0
Q ss_pred HHHHHhhhcccccccChHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 047910 72 LDKYFHQLKSSSNCIGANKVVNEAKKAIELCKEENLEAAKASFEKMKVEHTTLKTKLQAYL 132 (135)
Q Consensus 72 l~~~aH~LKGSSa~iGA~~l~~~c~~lE~~~~~~~~~~~~~~l~~l~~ef~~~~~~L~~~l 132 (135)
+...+|.+|.+=+.+. ..|..+.. ....+.....+..++.+...+..-++.++
T Consensus 6 ~~~i~Hel~~pl~~i~-----~~~~~l~~---~~~~~~~~~~~~~~~~~~~~~~~~v~~l~ 58 (66)
T smart00388 6 LANLSHELRTPLTAIR-----GYLELLED---TELSEEQREYLETILRSAERLLRLINDLL 58 (66)
T ss_pred HHHHHHhccCcHHHHH-----HHHHHHHh---CCCChHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5567899997655332 22233332 12122225666777766666666555544
No 57
>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=34.67 E-value=2.2e+02 Score=22.26 Aligned_cols=49 Identities=12% Similarity=0.221 Sum_probs=30.6
Q ss_pred ccccChHHHHHHHHHHHHHHhhcC------HHHHHHHHHHHHHHHHHHHHHHHHH
Q 047910 83 SNCIGANKVVNEAKKAIELCKEEN------LEAAKASFEKMKVEHTTLKTKLQAY 131 (135)
Q Consensus 83 Sa~iGA~~l~~~c~~lE~~~~~~~------~~~~~~~l~~l~~ef~~~~~~L~~~ 131 (135)
.+=+|..++...+..|...+...| +-..+..+..+..+.++....+++.
T Consensus 32 ~~IiGl~~f~s~~~~i~~~a~~DdPyAD~~Ll~~E~~l~~~~~~l~~~~~~l~~~ 86 (216)
T TIGR03761 32 PGIIGMPGFISRLNRINQASEQDDPYADWALLRIEEKLLSARQEMQALLQRLDDL 86 (216)
T ss_pred CCCcCcHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345999999999999999887765 2223334444444444444444433
No 58
>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=34.67 E-value=60 Score=15.71 Aligned_cols=23 Identities=26% Similarity=0.407 Sum_probs=17.8
Q ss_pred HHHHHHhhcCHHHHHHHHHHHHH
Q 047910 97 KAIELCKEENLEAAKASFEKMKV 119 (135)
Q Consensus 97 ~lE~~~~~~~~~~~~~~l~~l~~ 119 (135)
-+...++.|+.+++...+.++..
T Consensus 6 li~~~~~~~~~~~a~~~~~~M~~ 28 (31)
T PF01535_consen 6 LISGYCKMGQFEEALEVFDEMRE 28 (31)
T ss_pred HHHHHHccchHHHHHHHHHHHhH
Confidence 35667888889998888887764
No 59
>PRK08818 prephenate dehydrogenase; Provisional
Probab=34.36 E-value=1.4e+02 Score=25.01 Aligned_cols=39 Identities=10% Similarity=0.206 Sum_probs=27.7
Q ss_pred CcchHHHHHHHHHHcHHHHHHHHHHHHhcCCCCHHHHHHHHhhhcc
Q 047910 36 DPSLFEDFVNVYLRDSTKTLAIIEEEIANNPVNYMDLDKYFHQLKS 81 (135)
Q Consensus 36 ~~df~~~li~~fl~d~~~~l~~L~~al~~~~~D~~~l~~~aH~LKG 81 (135)
|| .+.+.++.| .+.|.++++++.++ |...+.+..|.+.-
T Consensus 226 N~-~i~~~l~~~----~~~L~~l~~~i~~~--D~~~~~~~~~~f~~ 264 (370)
T PRK08818 226 NP-YVGEMLDRL----LAQLQELRALVAQG--DDAARARFRAQFLH 264 (370)
T ss_pred CH-HHHHHHHHH----HHHHHHHHHHHHcC--CHHHHHHHHHHHHH
Confidence 55 566677777 56777888888887 88888777555543
No 60
>KOG3232 consensus Vacuolar assembly/sorting protein DID2 [Intracellular trafficking, secretion, and vesicular transport]
Probab=34.31 E-value=1.9e+02 Score=22.19 Aligned_cols=37 Identities=19% Similarity=0.198 Sum_probs=33.0
Q ss_pred HHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHHHH
Q 047910 91 VVNEAKKAIELCKEENLEAAKASFEKMKVEHTTLKTK 127 (135)
Q Consensus 91 l~~~c~~lE~~~~~~~~~~~~~~l~~l~~ef~~~~~~ 127 (135)
++.+|+.++.+-+..+++.+..+++..+..|+.+-..
T Consensus 95 M~gVvK~md~alktmNLekis~~MDkFE~qFedldvq 131 (203)
T KOG3232|consen 95 MAGVVKSMDSALKTMNLEKISQLMDKFEKQFEDLDVQ 131 (203)
T ss_pred HHHHHHHHHHHHHhCCHHHHHHHHHHHHHHhhhhhhH
Confidence 5678999999999999999999999999999876544
No 61
>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=33.75 E-value=65 Score=15.78 Aligned_cols=22 Identities=32% Similarity=0.397 Sum_probs=17.8
Q ss_pred HHHHHhhcCHHHHHHHHHHHHH
Q 047910 98 AIELCKEENLEAAKASFEKMKV 119 (135)
Q Consensus 98 lE~~~~~~~~~~~~~~l~~l~~ 119 (135)
|...++.|+.+.+...+..++.
T Consensus 7 i~~~~~~~~~~~a~~~~~~M~~ 28 (35)
T TIGR00756 7 IDGLCKAGRVEEALELFKEMLE 28 (35)
T ss_pred HHHHHHCCCHHHHHHHHHHHHH
Confidence 5567889999999998888765
No 62
>COG0783 Dps DNA-binding ferritin-like protein (oxidative damage protectant) [Inorganic ion transport and metabolism]
Probab=33.65 E-value=1.4e+02 Score=21.99 Aligned_cols=29 Identities=17% Similarity=0.358 Sum_probs=16.3
Q ss_pred CCcchH--HHHHHHHHHcHHHHHHHHHHHHh
Q 047910 35 SDPSLF--EDFVNVYLRDSTKTLAIIEEEIA 63 (135)
Q Consensus 35 ~~~df~--~~li~~fl~d~~~~l~~L~~al~ 63 (135)
.||+|. .++.+.+.++....+..+.+-+.
T Consensus 42 ~G~~F~~lHe~~ee~y~el~~~~DeiAERi~ 72 (156)
T COG0783 42 KGPNFFALHEKLEELYEELAEHVDEIAERIR 72 (156)
T ss_pred eCccHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 478775 34555555555555555555543
No 63
>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=33.48 E-value=2e+02 Score=23.00 Aligned_cols=62 Identities=13% Similarity=0.087 Sum_probs=47.0
Q ss_pred HHHHHHHhhhcccccc----cChHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHHHHHHHH
Q 047910 70 MDLDKYFHQLKSSSNC----IGANKVVNEAKKAIELCKEENLEAAKASFEKMKVEHTTLKTKLQAY 131 (135)
Q Consensus 70 ~~l~~~aH~LKGSSa~----iGA~~l~~~c~~lE~~~~~~~~~~~~~~l~~l~~ef~~~~~~L~~~ 131 (135)
...++.++++..++-- .|=..+-.+|+.+|..|.-=...++...+..+...|..+...+..|
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 3556666666555522 4666778899999999988788899999999999999888887654
No 64
>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=32.61 E-value=1.5e+02 Score=19.48 Aligned_cols=54 Identities=4% Similarity=0.074 Sum_probs=30.9
Q ss_pred HHHHHHhccchhhhhHH-HHHHHhccccCCcchHHHHHHHHHHcHHHHHHHHHHHHh
Q 047910 8 ISAMRQSFFDEDILDTH-IFQLEQVEHISDPSLFEDFVNVYLRDSTKTLAIIEEEIA 63 (135)
Q Consensus 8 ~~~~~~~~~d~~~lD~~-~~~L~~L~~~~~~df~~~li~~fl~d~~~~l~~L~~al~ 63 (135)
.+..+.-++..|+++.. .+.|..-. ...+=...+++.--.-+|.-+...-.|+.
T Consensus 18 ~~~v~~~L~~~~Vlt~~~~e~I~~~~--tr~~q~~~LLd~L~~RG~~AF~~F~~aL~ 72 (84)
T cd08326 18 PKYLWDHLLSRGVFTPDMIEEIQAAG--SRRDQARQLLIDLETRGKQAFPAFLSALR 72 (84)
T ss_pred HHHHHHHHHhcCCCCHHHHHHHHcCC--CHHHHHHHHHHHHHhcCHHHHHHHHHHHH
Confidence 45566667777777775 66666542 23344555555555555555555555554
No 65
>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=32.41 E-value=45 Score=23.58 Aligned_cols=39 Identities=18% Similarity=0.279 Sum_probs=27.9
Q ss_pred HHHhccchhhhhHHHHHHHhccccC----CcchHHHHHHHHHH
Q 047910 11 MRQSFFDEDILDTHIFQLEQVEHIS----DPSLFEDFVNVYLR 49 (135)
Q Consensus 11 ~~~~~~d~~~lD~~~~~L~~L~~~~----~~df~~~li~~fl~ 49 (135)
+...+.+.=+-|..|++|.+|.+.+ +|+++..++..|+.
T Consensus 52 ~LD~~LHrCvyDRrfS~L~eLp~~~~l~~~~~~v~~~l~~YL~ 94 (115)
T cd07298 52 VLDKHLHLCIYDRRFSQLPELPRSDSLKDSPESVTQMLMAYLS 94 (115)
T ss_pred HHHHHHHHHHHhhhhhccccCCCcccccccHHHHHHHHHHHHH
Confidence 3456666677888888999887632 45788888888854
No 66
>PRK13916 plasmid segregation protein ParR; Provisional
Probab=32.25 E-value=73 Score=21.50 Aligned_cols=28 Identities=14% Similarity=0.183 Sum_probs=24.0
Q ss_pred HHHHHhccccCCcchHHHHHHHHHHcHH
Q 047910 25 IFQLEQVEHISDPSLFEDFVNVYLRDST 52 (135)
Q Consensus 25 ~~~L~~L~~~~~~df~~~li~~fl~d~~ 52 (135)
|+-|..+.+..-|.||.+++..|+++..
T Consensus 21 F~FL~~~P~GT~~~~iR~~L~rYI~~~G 48 (97)
T PRK13916 21 FDFLENVPRGTKTAHIREALRRYIEEIG 48 (97)
T ss_pred HHHHHHCCCCCccHHHHHHHHHHHHhcC
Confidence 7788899887778999999999998753
No 67
>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=30.00 E-value=1.4e+02 Score=18.59 Aligned_cols=55 Identities=5% Similarity=0.204 Sum_probs=36.6
Q ss_pred HHHHHHhccchhhhhHH-HHHHHhccccCCcchHHHHHHHHHHcHHHHHHHHHHHHhc
Q 047910 8 ISAMRQSFFDEDILDTH-IFQLEQVEHISDPSLFEDFVNVYLRDSTKTLAIIEEEIAN 64 (135)
Q Consensus 8 ~~~~~~~~~d~~~lD~~-~~~L~~L~~~~~~df~~~li~~fl~d~~~~l~~L~~al~~ 64 (135)
+..++..++..|+|+.. .+.+... ....+=+..|++....-++.-...+-.++..
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 34555566667777775 6666662 2334567778888777777777777777765
No 68
>COG3046 Uncharacterized protein related to deoxyribodipyrimidine photolyase [General function prediction only]
Probab=29.74 E-value=94 Score=27.07 Aligned_cols=64 Identities=13% Similarity=0.194 Sum_probs=54.0
Q ss_pred cchHHHHHHHHHHcHHHHHHHHHHHHhcCCCCHHHHHHHHhhhcccccccChHHHHHHHHHHHHHHhhcC
Q 047910 37 PSLFEDFVNVYLRDSTKTLAIIEEEIANNPVNYMDLDKYFHQLKSSSNCIGANKVVNEAKKAIELCKEEN 106 (135)
Q Consensus 37 ~df~~~li~~fl~d~~~~l~~L~~al~~~~~D~~~l~~~aH~LKGSSa~iGA~~l~~~c~~lE~~~~~~~ 106 (135)
+.=....+.-|+++.-..+..-..|+..++. . +=|+|=|++-|||-..=.++|+.-+.+=++|+
T Consensus 227 r~~A~~~L~~Fi~~~L~nFG~yQDam~~d~~---~---L~HSllS~alNigLL~PleVi~Aa~~Ay~~g~ 290 (505)
T COG3046 227 RTQALRALKHFIADRLPNFGSYQDAMSADDP---H---LWHSLLSFALNIGLLTPLEVIRAALKAYREGD 290 (505)
T ss_pred HHHHHHHHHHHHHHhhhcCCcHHHHHhcCCc---h---hHHHHHHHHhhccCCCHHHHHHHHHHhhccCC
Confidence 3345578899999999999999999988732 2 56999999999999999999999999877774
No 69
>KOG1142 consensus Transcription initiation factor TFIID, subunit TAF12 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=29.48 E-value=81 Score=25.40 Aligned_cols=48 Identities=8% Similarity=0.145 Sum_probs=32.9
Q ss_pred HHHHHHHHhccchhhhhHHHHHHHhccccCCcchHHHHHHHHHHcHHHHHHHHHHHHhc
Q 047910 6 QQISAMRQSFFDEDILDTHIFQLEQVEHISDPSLFEDFVNVYLRDSTKTLAIIEEEIAN 64 (135)
Q Consensus 6 ~~~~~~~~~~~d~~~lD~~~~~L~~L~~~~~~df~~~li~~fl~d~~~~l~~L~~al~~ 64 (135)
..|.++++.+--.+.||.. -.||+.+|.+.|+++....--.|..-=..
T Consensus 158 ~kl~dLvqqId~~~~LD~d-----------VedlLleiADdFV~sii~~sC~LAKHRKs 205 (258)
T KOG1142|consen 158 RKLDDLVQQIDGTTKLDDD-----------VEDLLLEIADDFVSSIIHRSCKLAKHRKS 205 (258)
T ss_pred cchhHHHHhhcCcccccHH-----------HHHHHHHHHHHHHHHHHHHHHHHHHhccc
Confidence 4567777777666777732 34577788888888887776666655443
No 70
>PF07304 SRA1: Steroid receptor RNA activator (SRA1); InterPro: IPR009917 This entry consists of several hypothetical mammalian steroid receptor RNA activator proteins. The SRA-RNAs encode stable proteins that are widely expressed and upregulated in breast cancer cell lines. SRA-RNA is a steroid receptor co-activator which acts as a functional RNA. This domain is also found at the C terminus of Sec31, a component of the coat protein complex II (COPII, which promotes the formation of transport vesicles from the endoplasmic reticulum (ER). COPII has two main functions, the physical deformation of the endoplasmic reticulum membrane into vesicles and the selection of cargo molecules. ; PDB: 2YRU_A.
Probab=28.97 E-value=2.3e+02 Score=20.70 Aligned_cols=66 Identities=12% Similarity=0.097 Sum_probs=39.1
Q ss_pred HHHHHcHHHHHHHHHHHHhcCCCCHHHHHHHHhhhcccccccChHHHHHHHHHHHHH-----------HhhcCHHHHHHH
Q 047910 45 NVYLRDSTKTLAIIEEEIANNPVNYMDLDKYFHQLKSSSNCIGANKVVNEAKKAIEL-----------CKEENLEAAKAS 113 (135)
Q Consensus 45 ~~fl~d~~~~l~~L~~al~~~~~D~~~l~~~aH~LKGSSa~iGA~~l~~~c~~lE~~-----------~~~~~~~~~~~~ 113 (135)
...++|+.++|.-|...+.+|.+.-... .+|..+|..|+.- --..+.+.|..|
T Consensus 64 kr~~~D~~KRL~iLfd~ln~g~Ls~~v~----------------~~L~~L~~aL~~~d~~~A~~Ih~~L~t~h~~E~~~W 127 (157)
T PF07304_consen 64 KRVVDDIEKRLNILFDHLNNGKLSKPVV----------------DKLHQLAQALQARDYDAADEIHVDLMTDHVDECGNW 127 (157)
T ss_dssp HHHHHHHHHHHHHHHHHHHHT-S-HHHH----------------HHHHHHHHHHHHT-HHHHHHHHHHHHHSSHHHHTTT
T ss_pred hhHHHHHHHHHHHHHHHHhcCCCCHHHH----------------HHHHHHHHHHHcCCHHHHHHHHHHHHhccHHHhhhH
Confidence 3446899999999999998875433322 3455566555431 122355666666
Q ss_pred HHHHHHHHHHHHH
Q 047910 114 FEKMKVEHTTLKT 126 (135)
Q Consensus 114 l~~l~~ef~~~~~ 126 (135)
+-.++.-...++.
T Consensus 128 mvGVKRLI~~~r~ 140 (157)
T PF07304_consen 128 MVGVKRLIAMARN 140 (157)
T ss_dssp HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHh
Confidence 6666665554443
No 71
>PF08581 Tup_N: Tup N-terminal; InterPro: IPR013890 The N-terminal region of the Tup protein has been shown to interact with the Ssn6 transcriptional co-repressor []. ; PDB: 3VP9_B 3VP8_B.
Probab=28.29 E-value=1.3e+02 Score=19.75 Aligned_cols=21 Identities=10% Similarity=0.245 Sum_probs=15.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHH
Q 047910 110 AKASFEKMKVEHTTLKTKLQA 130 (135)
Q Consensus 110 ~~~~l~~l~~ef~~~~~~L~~ 130 (135)
...+|+.|+.||+.+...++.
T Consensus 2 l~elLd~ir~Ef~~~~~e~~~ 22 (79)
T PF08581_consen 2 LNELLDAIRQEFENLSQEANS 22 (79)
T ss_dssp HHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 456888889998888776544
No 72
>PRK12791 flbT flagellar biosynthesis repressor FlbT; Reviewed
Probab=27.87 E-value=2.3e+02 Score=20.34 Aligned_cols=52 Identities=10% Similarity=0.107 Sum_probs=31.9
Q ss_pred HHHHHHHHhccchhhhhHHHHHHHhccccCCcchHHHHHHHHHHcHHHHHHHHHHHHhcCC
Q 047910 6 QQISAMRQSFFDEDILDTHIFQLEQVEHISDPSLFEDFVNVYLRDSTKTLAIIEEEIANNP 66 (135)
Q Consensus 6 ~~~~~~~~~~~d~~~lD~~~~~L~~L~~~~~~df~~~li~~fl~d~~~~l~~L~~al~~~~ 66 (135)
+|++..+|-|+-.+--+....... ..+.+++..| .++...+..+..++..|+
T Consensus 54 rrlYf~vQ~m~l~~~~~~~~~~~~--------~~~~~l~~~~-p~~~~~l~~~~~~v~~g~ 105 (131)
T PRK12791 54 KRVYLCVQLMYLSNDIPAYHGTYL--------GLIRELIEAV-PSAWPIIEAINNHILNGD 105 (131)
T ss_pred HHHHHHHHHHHhCCchHHHHHHHH--------HHHHHHHHHh-HHHHHHHHHHHHHHhCCC
Confidence 477888887765442111111111 1255677777 678888888889998883
No 73
>PF14493 HTH_40: Helix-turn-helix domain
Probab=27.01 E-value=1.4e+02 Score=19.39 Aligned_cols=37 Identities=11% Similarity=0.250 Sum_probs=25.7
Q ss_pred cchHHHHHHHHHHcHHHHHHHHHHHHhcCCCCHHHHHH
Q 047910 37 PSLFEDFVNVYLRDSTKTLAIIEEEIANNPVNYMDLDK 74 (135)
Q Consensus 37 ~df~~~li~~fl~d~~~~l~~L~~al~~~~~D~~~l~~ 74 (135)
++....+...|-......|..+.+++... +||..+|-
T Consensus 52 ~e~~~~I~~~~~~~~~~~lk~i~e~l~~~-~sy~~iRl 88 (91)
T PF14493_consen 52 EEEIKQIEDAIEKLGSEKLKPIKEALPGD-YSYFEIRL 88 (91)
T ss_pred HHHHHHHHHHHHHcCcccHHHHHHHCCCC-CCHHHHHH
Confidence 34556666666666667888888888764 68887763
No 74
>PF04012 PspA_IM30: PspA/IM30 family; InterPro: IPR007157 This family includes PspA a protein that suppresses sigma54-dependent transcription. The PspA protein, a negative regulator of the Escherichia coli phage shock psp operon, is produced when virulence factors are exported through secretins in many Gram-negative pathogenic bacteria and its homologue in plants, VIPP1, plays a critical role in thylakoid biogenesis, essential for photosynthesis. Activation of transcription by the enhancer-dependent bacterial sigma54-containing RNA polymerase occurs through ATP hydrolysis-driven protein conformational changes enabled by activator proteins that belong to the large AAA(+) mechanochemical protein family. It has been shown that PspA directly and specifically acts upon and binds to the AAA(+) domain of the PspF transcription activator [].
Probab=25.93 E-value=2.9e+02 Score=20.78 Aligned_cols=27 Identities=22% Similarity=0.419 Sum_probs=22.7
Q ss_pred CCcchHHHHHHHHHHcHHHHHHHHHHHHhc
Q 047910 35 SDPSLFEDFVNVYLRDSTKTLAIIEEEIAN 64 (135)
Q Consensus 35 ~~~df~~~li~~fl~d~~~~l~~L~~al~~ 64 (135)
.+|. .+++.|+.|....+..++.++..
T Consensus 22 EDP~---~~l~q~ird~e~~l~~a~~~~a~ 48 (221)
T PF04012_consen 22 EDPE---KMLEQAIRDMEEQLRKARQALAR 48 (221)
T ss_pred cCHH---HHHHHHHHHHHHHHHHHHHHHHH
Confidence 4565 88999999999999999988875
No 75
>KOG2833 consensus Mevalonate pyrophosphate decarboxylase [Lipid transport and metabolism]
Probab=25.77 E-value=1.3e+02 Score=25.28 Aligned_cols=29 Identities=10% Similarity=0.272 Sum_probs=23.3
Q ss_pred HHHHHc-HHHHHHHHHHHHhcCCCCHHHHHHH
Q 047910 45 NVYLRD-STKTLAIIEEEIANNPVNYMDLDKY 75 (135)
Q Consensus 45 ~~fl~d-~~~~l~~L~~al~~~~~D~~~l~~~ 75 (135)
.-=++. +|+++.+|++|+.+. ||+.+.++
T Consensus 225 qhRi~~vVP~Ri~~m~eaI~~r--DF~~FA~l 254 (395)
T KOG2833|consen 225 QHRIESVVPQRIQQMREAIRER--DFESFAKL 254 (395)
T ss_pred HHHHHhhhHHHHHHHHHHHHhc--CHHHHHHH
Confidence 333444 799999999999998 99988765
No 76
>TIGR01240 mevDPdecarb diphosphomevalonate decarboxylase. Alternate names: mevalonate diphosphate decarboxylase; pyrophosphomevalonate decarboxylase
Probab=25.54 E-value=1.3e+02 Score=24.44 Aligned_cols=32 Identities=6% Similarity=0.257 Sum_probs=26.4
Q ss_pred HHHHHHHcHHHHHHHHHHHHhcCCCCHHHHHHHH
Q 047910 43 FVNVYLRDSTKTLAIIEEEIANNPVNYMDLDKYF 76 (135)
Q Consensus 43 li~~fl~d~~~~l~~L~~al~~~~~D~~~l~~~a 76 (135)
.....++.++..+..|..|+.++ |++.+.+.+
T Consensus 201 ~~~~~v~~~~~~l~~~~~ai~~~--D~~~~g~~~ 232 (305)
T TIGR01240 201 LFKEWIEHVVPDFEVXRKAIKTK--DFATFGKET 232 (305)
T ss_pred cHHHHHHHHHHHHHHHHHHHHhc--cHHHHHHHH
Confidence 45677888888899999999998 898887654
No 77
>PF04049 APC8: Anaphase promoting complex subunit 8 / Cdc23 ; InterPro: IPR007192 The anaphase-promoting complex is composed of eight protein subunits, including BimE (APC1), CDC27 (APC3), CDC16 (APC6), and CDC23 (APC8). This entry is for CDC23.; GO: 0030071 regulation of mitotic metaphase/anaphase transition, 0005680 anaphase-promoting complex
Probab=25.48 E-value=2.6e+02 Score=20.04 Aligned_cols=81 Identities=10% Similarity=0.068 Sum_probs=47.8
Q ss_pred hHHHHHHHHHHHhccchhhhhHH-H--HHHHhccccCC-------------cchHHH-HHHHHHHcHHHHHHHHHHHHhc
Q 047910 2 EALRQQISAMRQSFFDEDILDTH-I--FQLEQVEHISD-------------PSLFED-FVNVYLRDSTKTLAIIEEEIAN 64 (135)
Q Consensus 2 ~~~~~~~~~~~~~~~d~~~lD~~-~--~~L~~L~~~~~-------------~df~~~-li~~fl~d~~~~l~~L~~al~~ 64 (135)
..++.+|..-++...+.|+++.. | ..|..|.+... +.+-.. ......+..+.-.=-+...+-
T Consensus 7 ~~ir~~L~~a~~~~s~RgL~~saKWaaElL~gL~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~d~yllAksyF- 85 (142)
T PF04049_consen 7 KEIRSELRQAIRECSERGLYQSAKWAAELLNGLPPPWRDDTPDDPSSSPSSSQLSPSSPSEDQLESKEYDKYLLAKSYF- 85 (142)
T ss_pred HHHHHHHHHHHHHHHHhcHHHHHHHHHHHHHcCCCCcccccccccccCCCccccCCCChhhhhhhhhHHHHHHHHHHHh-
Confidence 45788889999999999999985 3 34666662111 111100 111111112222223555554
Q ss_pred CCCCHHHHHHHHhhhccccccc
Q 047910 65 NPVNYMDLDKYFHQLKSSSNCI 86 (135)
Q Consensus 65 ~~~D~~~l~~~aH~LKGSSa~i 86 (135)
|...+++.||.||+..+..
T Consensus 86 ---D~kEy~RaA~~L~~~~s~~ 104 (142)
T PF04049_consen 86 ---DCKEYDRAAHVLKDCKSPK 104 (142)
T ss_pred ---chhHHHHHHHHHccCCCch
Confidence 6789999999999988443
No 78
>PRK10548 flagellar biosynthesis protein FliT; Provisional
Probab=25.22 E-value=2.5e+02 Score=19.78 Aligned_cols=35 Identities=9% Similarity=0.190 Sum_probs=22.9
Q ss_pred HHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHHHHH
Q 047910 90 KVVNEAKKAIELCKEENLEAAKASFEKMKVEHTTLKTKL 128 (135)
Q Consensus 90 ~l~~~c~~lE~~~~~~~~~~~~~~l~~l~~ef~~~~~~L 128 (135)
.+..+..++=.+++.|+|+... .++.+|......|
T Consensus 13 ~I~~lS~~ML~aA~~g~Wd~Li----~lE~~y~~~Ve~l 47 (121)
T PRK10548 13 QILTLSQSMLRLATEGQWDELI----EQEVAYVQAVEEI 47 (121)
T ss_pred HHHHHHHHHHHHHHHCCHHHHH----HHHHHHHHHHHHH
Confidence 4667777888888888887743 3455555554444
No 79
>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=25.16 E-value=1.2e+02 Score=16.77 Aligned_cols=35 Identities=9% Similarity=0.116 Sum_probs=22.8
Q ss_pred HHHHHHhccccCCcchHHHHHHHHHHcHHHHHHHH
Q 047910 24 HIFQLEQVEHISDPSLFEDFVNVYLRDSTKTLAII 58 (135)
Q Consensus 24 ~~~~L~~L~~~~~~df~~~li~~fl~d~~~~l~~L 58 (135)
.+..|.++-+.-+++.+...+..+-.+.+..+..|
T Consensus 5 ~v~~L~~mFP~l~~~~I~~~L~~~~g~ve~~i~~L 39 (43)
T smart00546 5 ALHDLKDMFPNLDEEVIKAVLEANNGNVEATINNL 39 (43)
T ss_pred HHHHHHHHCCCCCHHHHHHHHHHcCCCHHHHHHHH
Confidence 36678888777777777666666655655555443
No 80
>cd07299 PX_TCGAP The phosphoinositide binding Phox Homology domain of Tc10/Cdc42 GTPase-activating protein. 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. TCGAP (Tc10/Cdc42 GTPase-activating protein) contains N-terminal PX and Src Homology 3 (SH3) domains, a central Rho GAP domain, and C-terminal proline-rich regions. It is widely expressed in the brain where it is involved in regulating the outgrowth of axons and dendrites and is regulated by the protein tyrosine kinase Fyn. It interacts with cdc42 and TC10beta through its GAP domain and with phosphatidylinositol-(4,5)-bisphosphate [PI(4,5)P2] through its PX domain. It is translocated to the plasma membrane in adipocytes in response to insulin and may be involved in the regulation of insulin-stimulated glucose transport. TCGAP has also been named sorting nexins 26 (SNX26). SNXs
Probab=25.09 E-value=90 Score=21.98 Aligned_cols=38 Identities=16% Similarity=0.301 Sum_probs=26.9
Q ss_pred HHhccchhhhhHHHHHHHhcccc----CCcchHHHHHHHHHH
Q 047910 12 RQSFFDEDILDTHIFQLEQVEHI----SDPSLFEDFVNVYLR 49 (135)
Q Consensus 12 ~~~~~d~~~lD~~~~~L~~L~~~----~~~df~~~li~~fl~ 49 (135)
...+.+.=+-|..|++|.+|.+. ..++.+..++..|+.
T Consensus 51 LD~~LHrCiyDRr~S~L~eL~~~~~l~~~~~~~~~~l~~YL~ 92 (113)
T cd07299 51 LDAHLHRCIFDRRFSQLLELPPLCEIGDRLQILTPLLSEYLN 92 (113)
T ss_pred HHHHHHHHHHhhhhhhhhccCccccccchHHHHHHHHHHHHH
Confidence 45566677788888889888762 223577888888864
No 81
>PF03858 Crust_neuro_H: Crustacean neurohormone H; InterPro: IPR005558 Arthropod express a family of neuropeptides [] which so far consist of the following types of neurohormones: Crustacean hyperglycemic hormone (CHH). CHH is primarily involved in blood sugar regulation, but also plays a role in the control of molting and reproduction. Molt-inhibiting hormone (MIH). MIH inhibits Y-organs where molting hormone (ecdysteroid) is secreted. A molting cycle is initiated when MIH secretion diminishes or stops. Gonad-inhibiting hormone (GIH), also known as vitellogenesis-inhibiting hormone (VIH) because of its role in inhibiting vitellogenesis in female animals. Mandibular organ-inhibiting hormone (MOIH). MOIH represses the synthesis of methyl farnesoate, the precursor of insect juvenile hormone III in the mandibular organ. Ion transport peptide (ITP) from locust. ITP stimulates salt and water reabsorption and inhibits acid secretion in the ileum of the locust. Caenorhabditis elegans hypothetical protein ZC168.2. These neurohormones are peptides of 70 to 80 residues which are processed from larger size precursors. They contain six conserved cysteines that are involved in disulphide bonds, as shown in the following schematic representation. Crustacean neurohormone H proteins are referred to as precursor-related peptides as they are typically co-transcribed and translated with the CHH neurohormone (IPR001166 from INTERPRO). However, in some species this neuropeptide is synthesized as a separate protein. Furthermore, neurohormone H can undergo proteolysis to give rise to 5 different neuropeptides [].
Probab=24.79 E-value=73 Score=18.43 Aligned_cols=22 Identities=9% Similarity=0.258 Sum_probs=18.3
Q ss_pred HHHHHHHHhhhcccccccChHH
Q 047910 69 YMDLDKYFHQLKSSSNCIGANK 90 (135)
Q Consensus 69 ~~~l~~~aH~LKGSSa~iGA~~ 90 (135)
|.++.++.-+|||++.+.++..
T Consensus 6 ~GRMerLLaSlrg~~~s~~plg 27 (41)
T PF03858_consen 6 FGRMERLLASLRGSADSSTPLG 27 (41)
T ss_pred hhhHHHHHHHHhccCCCCcchh
Confidence 7789999999999988877643
No 82
>PF05218 DUF713: Protein of unknown function (DUF713); InterPro: IPR007883 This family contains proteins of unknown function from Caenorhabditis species.
Probab=24.73 E-value=3.1e+02 Score=20.66 Aligned_cols=91 Identities=16% Similarity=0.247 Sum_probs=55.8
Q ss_pred HHHHHHHHHhccch-hhhhHHHHHHHhccccCCcchHHHHHHHHHHcHHHHHHHHHHHHhcC---CCCHHHHHHHHhhhc
Q 047910 5 RQQISAMRQSFFDE-DILDTHIFQLEQVEHISDPSLFEDFVNVYLRDSTKTLAIIEEEIANN---PVNYMDLDKYFHQLK 80 (135)
Q Consensus 5 ~~~~~~~~~~~~d~-~~lD~~~~~L~~L~~~~~~df~~~li~~fl~d~~~~l~~L~~al~~~---~~D~~~l~~~aH~LK 80 (135)
+.++..|.++.... ..+-..|..|..|.+.-...++.+|+...+.+....|-.+-..+..- ..+|..++..-=.|+
T Consensus 73 ~~E~~~l~~~v~~a~~~l~~~f~~L~~L~~~~~D~iFlkvLqK~i~~va~~L~~il~~l~~~~~~~~~~~~L~~~~s~l~ 152 (182)
T PF05218_consen 73 QSEISNLHKSVMSAYNMLENAFENLKKLSEKFPDKIFLKVLQKCISDVANKLLEILESLDELENDKDWFQKLREAFSRLD 152 (182)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCcchHHHHHHHHHHHHHHHHHHHHHHHhhcCChHHHHHHHHHHHcCC
Confidence 33444444444333 44555688888887654445556899999999888888888887432 225666776666666
Q ss_pred ccccccChHHHHHHHH
Q 047910 81 SSSNCIGANKVVNEAK 96 (135)
Q Consensus 81 GSSa~iGA~~l~~~c~ 96 (135)
.|+ =-.-.+|..+|.
T Consensus 153 ~~~-IptT~~Lr~ic~ 167 (182)
T PF05218_consen 153 PSD-IPTTSQLRRICK 167 (182)
T ss_pred ccc-CCCHHHHHHHhc
Confidence 633 234445555554
No 83
>PF06248 Zw10: Centromere/kinetochore Zw10; InterPro: IPR009361 Zeste white 10 (ZW10) was initially identified as a mitotic checkpoint protein involved in chromosome segregation, and then implicated in targeting cytoplasmic dynein and dynactin to mitotic kinetochores, but it is also important in non-dividing cells. These include cytoplasmic dynein targeting to Golgi and other membranes, and SNARE-mediated ER-Golgi trafficking [, ]. Dominant-negative ZW10, anti-ZW10 antibody, and ZW10 RNA interference (RNAi) cause Golgi dispersal. ZW10 RNAi also disperse endosomes and lysosomes []. Drosophila kinetochore components Rough deal (Rod) and Zw10 are required for the proper functioning of the metaphase checkpoint in flies []. The eukaryotic spindle assembly checkpoint (SAC) monitors microtubule attachment to kinetochores and prevents anaphase onset until all kinetochores are aligned on the metaphase plate. It is an essential surveillance mechanism that ensures high fidelity chromosome segregation during mitosis. In higher eukaryotes, cytoplasmic dynein is involved in silencing the SAC by removing the checkpoint proteins Mad2 and the Rod-Zw10-Zwilch complex (RZZ) from aligned kinetochores [, , ].; GO: 0007067 mitosis, 0000775 chromosome, centromeric region, 0005634 nucleus
Probab=24.58 E-value=4.9e+02 Score=22.92 Aligned_cols=18 Identities=28% Similarity=0.506 Sum_probs=9.8
Q ss_pred HHHcHHHHHHHHHHHHhc
Q 047910 47 YLRDSTKTLAIIEEEIAN 64 (135)
Q Consensus 47 fl~d~~~~l~~L~~al~~ 64 (135)
=+.++...+..+++.+..
T Consensus 77 ~l~~a~~e~~~L~~eL~~ 94 (593)
T PF06248_consen 77 QLRDAAEELQELKRELEE 94 (593)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 344555555566655553
No 84
>cd00225 API3 Ascaris pepsin inhibitor-3 (API3); protein inhibitor that reversibly inhibits aspartic proteinase cathepsin E, and gastric enzymes pepsin and gastricsin.
Probab=24.21 E-value=1.1e+02 Score=22.72 Aligned_cols=43 Identities=9% Similarity=0.087 Sum_probs=33.6
Q ss_pred HHHHHHHHHcHHHHHHHHHHHHhcCCCCHHHHHHHHhhhccccccc
Q 047910 41 EDFVNVYLRDSTKTLAIIEEEIANNPVNYMDLDKYFHQLKSSSNCI 86 (135)
Q Consensus 41 ~~li~~fl~d~~~~l~~L~~al~~~~~D~~~l~~~aH~LKGSSa~i 86 (135)
...+..|.+|+...=.++++++..+ -+.++..-|+=|++++++
T Consensus 36 q~el~~y~~d~~~yK~~~k~~l~er---~~~~~~~~~~~~~~~~~~ 78 (159)
T cd00225 36 QQELAQYVEDVADYKEEVKQALKER---QEGLKLRRAGKKKKAVTL 78 (159)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH---HHhhhhhhhccccccccc
Confidence 3667799999999999999999986 356666667777775554
No 85
>COG2603 Predicted ATPase [General function prediction only]
Probab=24.15 E-value=2.1e+02 Score=23.79 Aligned_cols=80 Identities=13% Similarity=0.160 Sum_probs=54.3
Q ss_pred HHHHHHHHHHcHHHHHHHHHHHHhcCCCCHHHHHHHHhhhcccccccChHHHHHHHHHHH----HHHhhcCHHHHHHHHH
Q 047910 40 FEDFVNVYLRDSTKTLAIIEEEIANNPVNYMDLDKYFHQLKSSSNCIGANKVVNEAKKAI----ELCKEENLEAAKASFE 115 (135)
Q Consensus 40 ~~~li~~fl~d~~~~l~~L~~al~~~~~D~~~l~~~aH~LKGSSa~iGA~~l~~~c~~lE----~~~~~~~~~~~~~~l~ 115 (135)
|.++++.|...-.+. .-..++.... -|.++. +-|.|-++---+|-.+...++..+- +....|+.++-..++.
T Consensus 243 v~RIi~ey~~kkh~~--df~~~~~~~~-~~~~~~-l~~~l~~~~~r~~~qr~~~l~~~~~~~~~~q~~~~~~d~~~~~i~ 318 (334)
T COG2603 243 VERIIEEYFKKKHKH--DFTHAVGDEQ-GWQAYS-LHHGLSAIKRRLGLQRYNELAARLDAALTEQLTTGSTDGHLAWIV 318 (334)
T ss_pred HHHHHHHHHHHhhhh--hhhhhhccch-hHHHHH-HhhhHHHHHHHHhHHHHHHHHHHHHHHHHhcCCcCCccchHHHHH
Confidence 566777776544321 2223333221 255665 6799999999999999988887654 4456778888888888
Q ss_pred HHHHHHHH
Q 047910 116 KMKVEHTT 123 (135)
Q Consensus 116 ~l~~ef~~ 123 (135)
.+..||-.
T Consensus 319 ~~~~e~~d 326 (334)
T COG2603 319 PLLEEYYD 326 (334)
T ss_pred HHHHHHHH
Confidence 88888754
No 86
>PRK05014 hscB co-chaperone HscB; Provisional
Probab=23.93 E-value=3e+02 Score=20.31 Aligned_cols=30 Identities=20% Similarity=0.284 Sum_probs=19.4
Q ss_pred HHHHHHHHHHHHHHhhcCHHHHHHHHHHHH
Q 047910 89 NKVVNEAKKAIELCKEENLEAAKASFEKMK 118 (135)
Q Consensus 89 ~~l~~~c~~lE~~~~~~~~~~~~~~l~~l~ 118 (135)
.++..+...|..+-..++++.+...+.+++
T Consensus 124 ~~~~~~~~~l~~~~~~~d~~~A~~~~~~Lk 153 (171)
T PRK05014 124 KMFKTRLQQMVEQLDNEAWDAAADTVRKLK 153 (171)
T ss_pred HHHHHHHHHHHHHHhhCCHHHHHHHHHHHH
Confidence 355566666666666778887776555554
No 87
>PRK10987 regulatory protein AmpE; Provisional
Probab=23.70 E-value=1.1e+02 Score=24.41 Aligned_cols=35 Identities=23% Similarity=0.208 Sum_probs=30.9
Q ss_pred ccccChHHHHHHHHHHHHHHhhcCHHHHHHHHHHH
Q 047910 83 SNCIGANKVVNEAKKAIELCKEENLEAAKASFEKM 117 (135)
Q Consensus 83 Sa~iGA~~l~~~c~~lE~~~~~~~~~~~~~~l~~l 117 (135)
..++|...+.+..+.+.++.++||.+.+...+.++
T Consensus 79 ~~~lg~r~L~~~~~~v~~AL~~gDl~aAR~~l~~l 113 (284)
T PRK10987 79 LLCIGAGKQRLHYKAYLQAACRGDSQACYHMAEEL 113 (284)
T ss_pred HHHhCCchHHHHHHHHHHHHHCCCHHHHHHHHHHh
Confidence 45699999999999999999999999999987776
No 88
>PF13041 PPR_2: PPR repeat family
Probab=23.62 E-value=1.4e+02 Score=16.65 Aligned_cols=24 Identities=29% Similarity=0.389 Sum_probs=19.6
Q ss_pred HHHHHHHhhcCHHHHHHHHHHHHH
Q 047910 96 KKAIELCKEENLEAAKASFEKMKV 119 (135)
Q Consensus 96 ~~lE~~~~~~~~~~~~~~l~~l~~ 119 (135)
.-|...++.|+.+.+..++.+++.
T Consensus 8 ~li~~~~~~~~~~~a~~l~~~M~~ 31 (50)
T PF13041_consen 8 TLISGYCKAGKFEEALKLFKEMKK 31 (50)
T ss_pred HHHHHHHHCcCHHHHHHHHHHHHH
Confidence 345677899999999999998875
No 89
>PF05465 Halo_GVPC: Halobacterial gas vesicle protein C (GVPC) repeat; InterPro: IPR008639 This family consists of Halobacterium gas vesicle protein C sequences which are thought to confer stability to the gas vesicle membranes [,].; GO: 0031412 gas vesicle organization, 0031411 gas vesicle
Probab=23.34 E-value=1.4e+02 Score=16.15 Aligned_cols=23 Identities=17% Similarity=0.303 Sum_probs=17.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHh
Q 047910 110 AKASFEKMKVEHTTLKTKLQAYL 132 (135)
Q Consensus 110 ~~~~l~~l~~ef~~~~~~L~~~l 132 (135)
....+...+.+|..+..++..|-
T Consensus 4 l~a~I~~~r~~f~~~~~aF~aY~ 26 (32)
T PF05465_consen 4 LLAAIAEFREEFDDTQDAFEAYA 26 (32)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 34557778888888888888874
No 90
>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=23.26 E-value=1.7e+02 Score=17.17 Aligned_cols=55 Identities=11% Similarity=0.133 Sum_probs=34.7
Q ss_pred HHHHHHhhhcccccccChHHHHHHHHHHHHHHh-hcCHHH-HHHHHHHHHHHHHHHHHHHHHHhc
Q 047910 71 DLDKYFHQLKSSSNCIGANKVVNEAKKAIELCK-EENLEA-AKASFEKMKVEHTTLKTKLQAYLE 133 (135)
Q Consensus 71 ~l~~~aH~LKGSSa~iGA~~l~~~c~~lE~~~~-~~~~~~-~~~~l~~l~~ef~~~~~~L~~~l~ 133 (135)
-+...+|.||.+ |..+-..++.... ....+. ....+..+..+..++..-++.+++
T Consensus 5 ~~~~isHelr~P--------L~~i~~~~~~l~~~~~~~~~~~~~~l~~i~~~~~~l~~li~~ll~ 61 (68)
T PF00512_consen 5 FLASISHELRNP--------LTAIRGYLELLERDSDLDPEQLREYLDRIRSAADRLNELINDLLD 61 (68)
T ss_dssp HHHHHHHHHHHH--------HHHHHHHHHHHHCSSCC-HHHCHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHhHHHHHH--------HHHHHHHHHHHHHccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 356788888865 3444444444444 333333 478888888888888777776654
No 91
>PRK10698 phage shock protein PspA; Provisional
Probab=23.22 E-value=3.5e+02 Score=20.84 Aligned_cols=23 Identities=17% Similarity=0.323 Sum_probs=17.2
Q ss_pred HHHHHHHHcHHHHHHHHHHHHhc
Q 047910 42 DFVNVYLRDSTKTLAIIEEEIAN 64 (135)
Q Consensus 42 ~li~~fl~d~~~~l~~L~~al~~ 64 (135)
.+|+.|+.+....+..++.+++.
T Consensus 27 k~l~q~i~em~~~l~~~r~alA~ 49 (222)
T PRK10698 27 KLVRLMIQEMEDTLVEVRSTSAR 49 (222)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 57777888888777777777664
No 92
>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=23.13 E-value=1.9e+02 Score=17.78 Aligned_cols=40 Identities=10% Similarity=0.128 Sum_probs=26.8
Q ss_pred HHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHHHHHHHH
Q 047910 91 VVNEAKKAIELCKEENLEAAKASFEKMKVEHTTLKTKLQAY 131 (135)
Q Consensus 91 l~~~c~~lE~~~~~~~~~~~~~~l~~l~~ef~~~~~~L~~~ 131 (135)
+...|..| ......+.+.+...+..|...|..++..+..+
T Consensus 60 l~~~~~~L-~~~~~~~~~~i~~~~~~l~~~w~~l~~~~~~r 99 (105)
T PF00435_consen 60 LNEQAQQL-IDSGPEDSDEIQEKLEELNQRWEALCELVEER 99 (105)
T ss_dssp HHHHHHHH-HHTTHTTHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHH-HHcCCCcHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34555555 22334566778888888888888888877654
No 93
>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=22.95 E-value=2.9e+02 Score=19.76 Aligned_cols=30 Identities=17% Similarity=0.099 Sum_probs=16.0
Q ss_pred HHHHHHHHHhhcCHHHHHHHHHHHHHHHHH
Q 047910 94 EAKKAIELCKEENLEAAKASFEKMKVEHTT 123 (135)
Q Consensus 94 ~c~~lE~~~~~~~~~~~~~~l~~l~~ef~~ 123 (135)
....++.+..++|+..+..++..+...|..
T Consensus 63 ~~ea~~~Ai~~~dla~vk~~vn~~~~s~~~ 92 (123)
T PF05396_consen 63 AAEAFNEAIESGDLATVKAAVNLAGASYRK 92 (123)
T ss_pred HHHHHHHHHHhCCHHHHHHHHHHHHHHHHH
Confidence 344555555555555555555555555543
No 94
>PF13628 DUF4142: Domain of unknown function (DUF4142)
Probab=22.84 E-value=2.7e+02 Score=19.32 Aligned_cols=49 Identities=16% Similarity=0.358 Sum_probs=34.4
Q ss_pred HHHHhccccCCcchHHHHHHHHHHcHHHHHHHHHH-HHhcCCCCHHHHHHHH
Q 047910 26 FQLEQVEHISDPSLFEDFVNVYLRDSTKTLAIIEE-EIANNPVNYMDLDKYF 76 (135)
Q Consensus 26 ~~L~~L~~~~~~df~~~li~~fl~d~~~~l~~L~~-al~~~~~D~~~l~~~a 76 (135)
..+..|+...|++|=...+..-+.+-.+.+..++. ...++ +-..++.++
T Consensus 73 ~~l~~L~~~~g~~FD~~yl~~~i~~h~~~l~~~~~~~~~~~--~~~~lk~~a 122 (139)
T PF13628_consen 73 AELDRLQKLSGSAFDRAYLDAQIKAHEKALALFEKQLAASG--KDPELKAFA 122 (139)
T ss_pred HHHHHHHcCchhHHHHHHHHHHHHHHHHHHHHHHHHhhccC--CCHHHHHHH
Confidence 34445555578888888888888888888888888 56554 335666553
No 95
>PF14612 Ino80_Iec3: IEC3 subunit of the Ino80 complex, chromatin re-modelling
Probab=22.70 E-value=2.3e+02 Score=22.45 Aligned_cols=50 Identities=10% Similarity=0.117 Sum_probs=40.0
Q ss_pred HcHHHHHHHHHHHHhcCCCCHHHHHHHHhhhcccccccChHHHHHHHHHH
Q 047910 49 RDSTKTLAIIEEEIANNPVNYMDLDKYFHQLKSSSNCIGANKVVNEAKKA 98 (135)
Q Consensus 49 ~d~~~~l~~L~~al~~~~~D~~~l~~~aH~LKGSSa~iGA~~l~~~c~~l 98 (135)
+-+...|...+..+..|...+...+.+.+++|.|.+-=.+..+..+-..+
T Consensus 92 ~~a~~~L~~ak~~l~aG~i~~~~~~~le~~~~~~~~faP~~~~~~Ll~~V 141 (232)
T PF14612_consen 92 ETARQMLREAKAQLAAGEITADEYRRLEESIKRSNAFAPTKSYASLLKEV 141 (232)
T ss_pred HHHHHHHHHHHHHhccCCCCHHHHHHHHHHHHhcccccchhhHHHHHhhC
Confidence 34566777888888999999999999999999999887777666665543
No 96
>TIGR00465 ilvC ketol-acid reductoisomerase. This is the second enzyme in the parallel isoleucine-valine biosynthetic pathway
Probab=22.53 E-value=1.3e+02 Score=24.44 Aligned_cols=55 Identities=15% Similarity=0.124 Sum_probs=34.5
Q ss_pred HHHHHHHhhhcccccccChHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHH
Q 047910 70 MDLDKYFHQLKSSSNCIGANKVVNEAKKAIELCKEENLEAAKASFEKMKVEHTTL 124 (135)
Q Consensus 70 ~~l~~~aH~LKGSSa~iGA~~l~~~c~~lE~~~~~~~~~~~~~~l~~l~~ef~~~ 124 (135)
.+....+|++||+.--+.-..+..+...+=.-++.|+.......-+..+..+.++
T Consensus 209 ~A~~~~~~~~~g~~~l~~e~g~~~l~~~Vsstaeyg~~~~~~~~~~~~~~~~~~~ 263 (314)
T TIGR00465 209 LAYFETVHELKLIVDLIYEGGITGMRDRISNTAEYGALTRRRIIKEELKPEMQKI 263 (314)
T ss_pred HHHHHHHHHHHHHHHHHHHhcHHHHHHHcCCHHHcCcchhHHHhhHHHHHHHHHH
Confidence 4777889999999988866666655555555567776654433333344444433
No 97
>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=22.50 E-value=88 Score=22.07 Aligned_cols=39 Identities=18% Similarity=0.309 Sum_probs=28.2
Q ss_pred HHHhccchhhhhHHHHHHHhccccC----CcchHHHHHHHHHH
Q 047910 11 MRQSFFDEDILDTHIFQLEQVEHIS----DPSLFEDFVNVYLR 49 (135)
Q Consensus 11 ~~~~~~d~~~lD~~~~~L~~L~~~~----~~df~~~li~~fl~ 49 (135)
+...+.+.=+-|..|++|.+|.+.. .++.+..++..|++
T Consensus 51 ~LD~~LHrCiyDRr~S~L~eL~~~~~~~~~~~~~~~~l~~YL~ 93 (114)
T cd07278 51 MLDKHLHQCIYDRKFSQLTELPEECIEKREQQNLHQVLSDYLK 93 (114)
T ss_pred HHHHHHHHHHHhhhhhccccCCccccccchHHHHHHHHHHHHH
Confidence 3456666777888899999997742 34677788888854
No 98
>PF07014 Hs1pro-1_C: Hs1pro-1 protein C-terminus; InterPro: IPR009743 This entry represents the C terminus (approximately 270 residues) of a number of plant Hs1pro-1 proteins, which are believed to confer nematode resistance [].
Probab=22.35 E-value=2.6e+02 Score=22.30 Aligned_cols=32 Identities=19% Similarity=0.311 Sum_probs=25.1
Q ss_pred hHHHHHHHHHHcHHHHHHHHHHHHhcCCCCHHHH
Q 047910 39 LFEDFVNVYLRDSTKTLAIIEEEIANNPVNYMDL 72 (135)
Q Consensus 39 f~~~li~~fl~d~~~~l~~L~~al~~~~~D~~~l 72 (135)
-+..+++.++.-+.++|..|.+.+..+ |+++.
T Consensus 54 t~hQIlEsWi~~a~~LL~ri~~~i~~~--~~ekA 85 (261)
T PF07014_consen 54 TTHQILESWIHVARKLLERIEERIEAR--DFEKA 85 (261)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHcc--cHHHH
Confidence 456788888889999999988888877 55544
No 99
>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=21.85 E-value=2.3e+02 Score=21.86 Aligned_cols=74 Identities=14% Similarity=0.246 Sum_probs=43.4
Q ss_pred HHcHHHHHHHHHHHHhcCCCCHHHHHHHHhhhccccccc-----------C----------hHHHHHHHHHHHHHHhhcC
Q 047910 48 LRDSTKTLAIIEEEIANNPVNYMDLDKYFHQLKSSSNCI-----------G----------ANKVVNEAKKAIELCKEEN 106 (135)
Q Consensus 48 l~d~~~~l~~L~~al~~~~~D~~~l~~~aH~LKGSSa~i-----------G----------A~~l~~~c~~lE~~~~~~~ 106 (135)
+.++.+.|..|+..|+.. .+..++...| +.++++ + |..|..--.+|..+++.++
T Consensus 105 ik~sa~~L~~lk~lIdk~--sW~~v~~~LR---lka~~Lr~DL~~liss~p~~~kk~l~~La~~lf~~ie~LD~Aar~K~ 179 (202)
T PF05757_consen 105 IKESAKRLLSLKELIDKK--SWPYVRNYLR---LKAGYLRYDLNTLISSKPKDEKKALTDLANKLFDNIEELDYAARSKD 179 (202)
T ss_dssp HHHHHHHHCCCHHHHHTT---HHHHHHHHH---CCCCCHHHHHHHHHCCS-HHHHHHHHHHHHHHHHHHHHHHHHHHTT-
T ss_pred HHHHHHHHHHHHHHHhhc--cHHHHHHHHH---HHHhHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCC
Confidence 345566667777777765 5666654433 333333 2 2456666667777788888
Q ss_pred HHHHHHHHHHHHHHHHHHHH
Q 047910 107 LEAAKASFEKMKVEHTTLKT 126 (135)
Q Consensus 107 ~~~~~~~l~~l~~ef~~~~~ 126 (135)
...+....+.....++.+..
T Consensus 180 ~~~a~~~Y~~t~~~Ldevla 199 (202)
T PF05757_consen 180 VPEAEKYYADTVKALDEVLA 199 (202)
T ss_dssp HHHHHHHHHHHHHHHHHHHC
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 88777666666665555543
No 100
>COG1270 CbiB Cobalamin biosynthesis protein CobD/CbiB [Coenzyme metabolism]
Probab=21.61 E-value=1.3e+02 Score=24.87 Aligned_cols=34 Identities=15% Similarity=0.337 Sum_probs=30.1
Q ss_pred cccChHHHHHHHHHHHHHHhhcCHHHHHHHHHHH
Q 047910 84 NCIGANKVVNEAKKAIELCKEENLEAAKASFEKM 117 (135)
Q Consensus 84 a~iGA~~l~~~c~~lE~~~~~~~~~~~~~~l~~l 117 (135)
++++...|.+.|+++.+.-++||+++++..+..+
T Consensus 95 ~tla~rsL~~~~~~v~~~L~~gdl~~aR~~ls~i 128 (320)
T COG1270 95 TTLAIRSLADHARKVARALRRGDLEGARRALSMI 128 (320)
T ss_pred HHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH
Confidence 4588899999999999999999999999887755
No 101
>cd08812 CARD_RIG-I_like Caspase activation and recruitment domains found in RIG-I-like DEAD box helicases. Caspase activation and recruitment domains (CARDs) found in Retinoic acid Inducible Gene I (RIG-I)-like DEAD box helicases. These helicases, including MDA5 and RIG-I, contain two N-terminal CARD domains and a C-terminal DEAD box RNA helicase domain. They are cytoplasmic RNA helicases that play 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, RIG-I and MDA5 have been shown to recognize different sets of viruses. MDA5 and RIG-I associate 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 mec
Probab=21.40 E-value=2.5e+02 Score=18.40 Aligned_cols=36 Identities=11% Similarity=0.234 Sum_probs=20.4
Q ss_pred HHHHHHHHHhh-cCHHHHHHHHHHHHH-----HHHHHHHHHH
Q 047910 94 EAKKAIELCKE-ENLEAAKASFEKMKV-----EHTTLKTKLQ 129 (135)
Q Consensus 94 ~c~~lE~~~~~-~~~~~~~~~l~~l~~-----ef~~~~~~L~ 129 (135)
.|.+|.....+ |+.+++..++..|.. -|...+.+|+
T Consensus 36 ~~e~I~a~~~~~g~~~aa~~Ll~~L~~~r~~~wf~~Fl~AL~ 77 (88)
T cd08812 36 DKEQILAEERNKGNIAAAEELLDRLERCDKPGWFQAFLDALR 77 (88)
T ss_pred HHHHHHHHHhccChHHHHHHHHHHHHHhccCCcHHHHHHHHH
Confidence 44455544433 566666666666664 3555555554
No 102
>PLN02956 PSII-Q subunit
Probab=21.38 E-value=3.8e+02 Score=20.52 Aligned_cols=40 Identities=8% Similarity=0.106 Sum_probs=27.7
Q ss_pred hHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHHHH
Q 047910 88 ANKVVNEAKKAIELCKEENLEAAKASFEKMKVEHTTLKTK 127 (135)
Q Consensus 88 A~~l~~~c~~lE~~~~~~~~~~~~~~l~~l~~ef~~~~~~ 127 (135)
|..|.+--..|..+++.++...+..........|+.+.+.
T Consensus 145 a~~LFd~l~~LD~AAR~kd~~~a~k~Y~~tva~lD~Vl~~ 184 (185)
T PLN02956 145 YSDLFNSVTKLDYAARDKDETRVWEYYENIVASLDDIFSR 184 (185)
T ss_pred HHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHhc
Confidence 3556666677788888888877777766666666666543
No 103
>PF06160 EzrA: Septation ring formation regulator, EzrA ; InterPro: IPR010379 During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerises into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation [].; GO: 0000921 septin ring assembly, 0005940 septin ring, 0016021 integral to membrane
Probab=21.15 E-value=5.8e+02 Score=22.51 Aligned_cols=108 Identities=12% Similarity=0.201 Sum_probs=63.5
Q ss_pred hhHHHHHHHhccccCCcchHHH----------HHHHHHHcHHHHHHHHHHHHhcCCCCHHHHHHHHhhhcccccccChH-
Q 047910 21 LDTHIFQLEQVEHISDPSLFED----------FVNVYLRDSTKTLAIIEEEIANNPVNYMDLDKYFHQLKSSSNCIGAN- 89 (135)
Q Consensus 21 lD~~~~~L~~L~~~~~~df~~~----------li~~fl~d~~~~l~~L~~al~~~~~D~~~l~~~aH~LKGSSa~iGA~- 89 (135)
++..|+...+|...|++.=..+ -+...+++.|.++..+..-+-. -...++.--..++..-=.+.-.
T Consensus 173 ie~~F~~f~~lt~~GD~~~A~eil~~l~~~~~~l~~~~e~IP~l~~~l~~~~P~---ql~eL~~gy~~m~~~gy~l~~~~ 249 (560)
T PF06160_consen 173 IEEEFSEFEELTENGDYLEAREILEKLKEETDELEEIMEDIPKLYKELQKEFPD---QLEELKEGYREMEEEGYYLEHLD 249 (560)
T ss_pred HHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHhHH---HHHHHHHHHHHHHHCCCCCCCCC
Confidence 3334667777777676542222 3455667777777777766654 2455665556666555445442
Q ss_pred ------HHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHHHHHHHH
Q 047910 90 ------KVVNEAKKAIELCKEENLEAAKASFEKMKVEHTTLKTKLQAY 131 (135)
Q Consensus 90 ------~l~~~c~~lE~~~~~~~~~~~~~~l~~l~~ef~~~~~~L~~~ 131 (135)
.+.+.+......-.+++++.+...+..|....+.+-..|++.
T Consensus 250 i~~~i~~i~~~l~~~~~~L~~l~l~~~~~~~~~i~~~Id~lYd~le~E 297 (560)
T PF06160_consen 250 IEEEIEQIEEQLEEALALLKNLELDEVEEENEEIEERIDQLYDILEKE 297 (560)
T ss_pred HHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 233333333344466788888887777777776666666544
No 104
>cd00089 HR1 Protein kinase C-related kinase homology region 1 domain; also known as the ACC (antiparallel coiled-coil) finger domain or Rho-binding domain. Found in vertebrate PRK1 and yeast PKC1 protein kinases C; those found in rhophilin bind RhoGTP; those in PRK1 bind RhoA and RhoB. Rho family members function as molecular switches, cycling between inactive and active forms, controlling a variety of cellular processes. HR1 repeats often occur in tandem repeat arrangments, seperated by a short linker region.
Probab=20.64 E-value=2.3e+02 Score=17.61 Aligned_cols=45 Identities=20% Similarity=0.195 Sum_probs=30.8
Q ss_pred ChHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Q 047910 87 GANKVVNEAKKAIELCKEENLEAAKASFEKMKVEHTTLKTKLQAYLEV 134 (135)
Q Consensus 87 GA~~l~~~c~~lE~~~~~~~~~~~~~~l~~l~~ef~~~~~~L~~~l~~ 134 (135)
||..|..++.. -...++...+...+.......+.++..|..|...
T Consensus 27 Gaenm~~~~~~---~~~~~~~~~~~~~l~es~~ki~~Lr~~L~k~~~~ 71 (72)
T cd00089 27 GAENLLRLYSD---EKKKKLLAEAEQMLRESKQKLELLKMQLEKLKQE 71 (72)
T ss_pred HHHHHHHHHhc---CCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 55555544331 1122578888888899999999999999888653
No 105
>PRK07417 arogenate dehydrogenase; Reviewed
Probab=20.54 E-value=2.1e+02 Score=22.36 Aligned_cols=21 Identities=29% Similarity=0.506 Sum_probs=11.9
Q ss_pred HHHHHHHHHHHhcCCCCHHHHHH
Q 047910 52 TKTLAIIEEEIANNPVNYMDLDK 74 (135)
Q Consensus 52 ~~~l~~L~~al~~~~~D~~~l~~ 74 (135)
.+.|..++.+++++ |.+.+.+
T Consensus 245 ~~~l~~~~~~l~~~--d~~~l~~ 265 (279)
T PRK07417 245 RQSLDQLEELIEQE--NWSALEQ 265 (279)
T ss_pred HHHHHHHHHHHHcC--CHHHHHH
Confidence 44566666666665 5555443
No 106
>PHA02666 hypothetical protein; Provisional
Probab=20.47 E-value=1e+02 Score=24.46 Aligned_cols=53 Identities=19% Similarity=0.344 Sum_probs=38.4
Q ss_pred CCcchHHHHHHHHHHcHHHHHHHHHHHHhcCCCCHHHHHHHHhhhcc----cccccChHHH
Q 047910 35 SDPSLFEDFVNVYLRDSTKTLAIIEEEIANNPVNYMDLDKYFHQLKS----SSNCIGANKV 91 (135)
Q Consensus 35 ~~~df~~~li~~fl~d~~~~l~~L~~al~~~~~D~~~l~~~aH~LKG----SSa~iGA~~l 91 (135)
|.|++ ..=|.+.+.|-+.+|..|++.++.. +.=.+++.|.-|+ -++|||-..|
T Consensus 202 gkpNL-Q~DIcTLC~DIEtQLSALEKSLESE---lnFYrrYIqDTKsLLatRAANIgsKAL 258 (287)
T PHA02666 202 GKPNL-QSDICTLCHDIETQLSALEKSLESE---LNFYRRYIQDTKSLLATRAANIGSKAL 258 (287)
T ss_pred CCCch-hhHHHHhhhhHHHHHHHHHHHHHHH---HHHHHHHHHhHHHHHHHHhhcccccee
Confidence 34554 3567788899999999999999874 5667788887765 4667775543
No 107
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=20.41 E-value=3.7e+02 Score=20.02 Aligned_cols=46 Identities=24% Similarity=0.224 Sum_probs=32.6
Q ss_pred cHHHHHHHHHHHHhcCCCCHHHHHHHH----hhhccc------ccccChHHHHHHH
Q 047910 50 DSTKTLAIIEEEIANNPVNYMDLDKYF----HQLKSS------SNCIGANKVVNEA 95 (135)
Q Consensus 50 d~~~~l~~L~~al~~~~~D~~~l~~~a----H~LKGS------Sa~iGA~~l~~~c 95 (135)
|-.+++..|..|....+++.+++...+ |.|.++ |.-||-.-|-.|-
T Consensus 62 ~r~Kl~~gl~~A~~KRpVs~e~ie~~v~~ie~~Lr~~g~~EV~S~~IG~~VM~~Lk 117 (156)
T COG1327 62 DREKLRRGLIRACEKRPVSSEQIEEAVSHIERQLRSSGEREVPSKEIGELVMEELK 117 (156)
T ss_pred CHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHH
Confidence 457889999999999999998876554 566554 4556655554443
No 108
>COG1220 HslU ATP-dependent protease HslVU (ClpYQ), ATPase subunit [Posttranslational modification, protein turnover, chaperones]
Probab=20.32 E-value=1.4e+02 Score=25.68 Aligned_cols=29 Identities=14% Similarity=0.219 Sum_probs=24.9
Q ss_pred HHHHHHHhhhcccccccChHHHHHHHHHH
Q 047910 70 MDLDKYFHQLKSSSNCIGANKVVNEAKKA 98 (135)
Q Consensus 70 ~~l~~~aH~LKGSSa~iGA~~l~~~c~~l 98 (135)
+++...|-.+-.++-||||.||..+...+
T Consensus 375 ~~iAeiA~~vN~~~ENIGARRLhTvlErl 403 (444)
T COG1220 375 KRIAEIAYQVNEKTENIGARRLHTVLERL 403 (444)
T ss_pred HHHHHHHHHhcccccchhHHHHHHHHHHH
Confidence 47778888889999999999999988764
No 109
>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=20.18 E-value=3.1e+02 Score=19.07 Aligned_cols=40 Identities=13% Similarity=0.075 Sum_probs=26.2
Q ss_pred HHHHHHHHHHHhhcCHHHHHHH-HHHHHHHHHHHHHHHHHH
Q 047910 92 VNEAKKAIELCKEENLEAAKAS-FEKMKVEHTTLKTKLQAY 131 (135)
Q Consensus 92 ~~~c~~lE~~~~~~~~~~~~~~-l~~l~~ef~~~~~~L~~~ 131 (135)
...+..+..+.+.||.+..... .+++...|......++.|
T Consensus 127 ~~~l~~~~~al~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~ 167 (171)
T PF02203_consen 127 QQALDPLLAALRAGDIAAFMQLPNEKIQPLFDAFTAAWQAQ 167 (171)
T ss_dssp HHHHHHHHHHHHTT-HHHHHHSSHHHHHHHHHHHHHHHHHH
T ss_pred HHhHHHHHHHHHCCCHHHHHHHHHHhcchhHHHHHHHHHHH
Confidence 4455566666677777776555 777777777777776664
No 110
>PRK10337 sensor protein QseC; Provisional
Probab=20.04 E-value=4.8e+02 Score=21.18 Aligned_cols=43 Identities=16% Similarity=0.177 Sum_probs=26.9
Q ss_pred cchHHHHHHHHHHcHHHHHHHHHHHHhcCCCCHHHHHHHHhhhccccccc
Q 047910 37 PSLFEDFVNVYLRDSTKTLAIIEEEIANNPVNYMDLDKYFHQLKSSSNCI 86 (135)
Q Consensus 37 ~df~~~li~~fl~d~~~~l~~L~~al~~~~~D~~~l~~~aH~LKGSSa~i 86 (135)
|+=+..+...| ...+..+++.+... -.-+...+|.||.+.+.+
T Consensus 213 ~~Ei~~l~~~~----n~~~~~l~~~~~~~---~~~~~~~ahelrtpl~~i 255 (449)
T PRK10337 213 PSEVRPLVEAL----NQLFARTHAMMVRE---RRFTSDAAHELRSPLAAL 255 (449)
T ss_pred ChHHHHHHHHH----HHHHHHHHHHHHHH---HHHHHHHHHHhcCHHHHH
Confidence 44445555555 45566666666542 234788999999887643
Done!