Query 033727
Match_columns 112
No_of_seqs 226 out of 1016
Neff 7.6
Searched_HMMs 46136
Date Fri Mar 29 05:36:19 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033727.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033727hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4747 Two-component phosphor 99.7 6E-17 1.3E-21 110.3 8.3 106 5-112 7-112 (150)
2 COG2198 ArcB FOG: HPt domain [ 99.6 2.2E-15 4.8E-20 100.0 10.1 78 28-108 11-88 (122)
3 PF01627 Hpt: Hpt domain; Int 99.6 3.3E-15 7.1E-20 92.8 7.1 64 45-110 1-67 (90)
4 smart00073 HPT Histidine Phosp 99.5 3.2E-14 6.8E-19 88.6 6.3 63 45-109 2-64 (87)
5 cd00088 HPT Histidine Phosphot 99.5 1.6E-13 3.4E-18 86.9 7.0 64 44-109 2-69 (94)
6 TIGR02956 TMAO_torS TMAO reduc 99.3 3.1E-11 6.7E-16 101.5 12.7 85 22-111 863-947 (968)
7 PRK10618 phosphotransfer inter 99.0 1.1E-09 2.5E-14 93.1 8.0 64 45-110 811-874 (894)
8 PRK11466 hybrid sensory histid 98.8 4.3E-08 9.3E-13 82.5 11.7 99 3-106 787-886 (914)
9 PRK11091 aerobic respiration c 98.8 6.4E-08 1.4E-12 80.5 11.4 103 2-109 631-747 (779)
10 PRK11107 hybrid sensory histid 98.5 2.2E-06 4.7E-11 71.9 13.0 69 39-109 822-890 (919)
11 COG0643 CheA Chemotaxis protei 98.5 7.1E-07 1.5E-11 74.7 8.3 66 40-105 3-74 (716)
12 PRK10547 chemotaxis protein Ch 98.5 7.9E-07 1.7E-11 73.9 8.5 63 44-106 4-72 (670)
13 PRK09959 hybrid sensory histid 97.5 0.0023 5E-08 55.8 12.2 68 39-108 1098-1165(1197)
14 PRK15347 two component system 97.2 0.0018 3.8E-08 54.7 8.0 61 46-110 838-898 (921)
15 PF07743 HSCB_C: HSCB C-termin 88.6 3.7 8E-05 24.6 7.3 43 39-83 25-67 (78)
16 cd08323 CARD_APAF1 Caspase act 86.0 6.4 0.00014 24.6 6.8 67 10-80 16-82 (86)
17 TIGR00714 hscB Fe-S protein as 82.5 13 0.00029 25.6 7.6 43 39-83 98-140 (157)
18 PRK01773 hscB co-chaperone Hsc 76.2 22 0.00048 25.0 7.2 43 39-83 112-154 (173)
19 PRK03578 hscB co-chaperone Hsc 71.4 33 0.00071 24.2 8.3 43 39-83 115-158 (176)
20 TIGR03042 PS_II_psbQ_bact phot 68.3 36 0.00078 23.4 6.9 34 52-90 46-79 (142)
21 PF05396 Phage_T7_Capsid: Phag 67.5 21 0.00045 24.0 5.1 54 27-84 35-88 (123)
22 PF03847 TFIID_20kDa: Transcri 66.1 26 0.00056 20.9 5.0 46 7-64 2-47 (68)
23 COG2991 Uncharacterized protei 59.1 2.1 4.5E-05 26.2 -0.7 20 80-99 27-46 (77)
24 PRK03057 hypothetical protein; 58.8 44 0.00096 23.8 5.8 35 47-83 133-173 (180)
25 cd08326 CARD_CASP9 Caspase act 57.6 43 0.00093 20.7 6.0 56 11-68 19-74 (84)
26 TIGR00984 3a0801s03tim44 mitoc 57.5 42 0.00092 26.7 6.0 76 13-108 217-293 (378)
27 KOG4552 Vitamin-D-receptor int 57.2 72 0.0016 23.6 6.7 39 46-85 103-141 (272)
28 PRK08818 prephenate dehydrogen 57.1 61 0.0013 25.6 6.9 39 42-86 228-266 (370)
29 PRK05014 hscB co-chaperone Hsc 57.1 64 0.0014 22.5 7.1 39 43-83 115-153 (171)
30 PRK03636 hypothetical protein; 56.1 58 0.0013 23.2 6.0 28 54-83 147-174 (179)
31 TIGR03042 PS_II_psbQ_bact phot 55.8 21 0.00046 24.5 3.6 20 71-90 93-112 (142)
32 PF14357 DUF4404: Domain of un 55.6 37 0.00081 21.0 4.5 30 6-35 2-31 (85)
33 TIGR01220 Pmev_kin_Gr_pos phos 54.7 90 0.0019 24.2 7.4 57 46-104 246-310 (358)
34 PF09209 DUF1956: Domain of un 52.0 58 0.0013 20.5 8.2 87 4-92 3-89 (125)
35 COG3046 Uncharacterized protei 51.2 37 0.0008 27.7 4.8 66 39-110 226-291 (505)
36 PF08858 IDEAL: IDEAL domain; 51.1 35 0.00077 17.7 5.7 34 44-81 3-36 (37)
37 PF04840 Vps16_C: Vps16, C-ter 50.0 1.2E+02 0.0025 23.4 7.8 66 27-100 183-249 (319)
38 PF02153 PDH: Prephenate dehyd 49.7 1E+02 0.0022 22.6 7.2 28 49-78 228-255 (258)
39 PLN02407 diphosphomevalonate d 48.9 37 0.00079 26.7 4.4 32 46-79 224-256 (343)
40 cd08330 CARD_ASC_NALP1 Caspase 46.6 66 0.0014 19.6 6.9 56 11-68 18-73 (82)
41 PRK13916 plasmid segregation p 45.4 49 0.0011 20.9 3.8 29 27-55 20-48 (97)
42 PF09280 XPC-binding: XPC-bind 45.3 16 0.00034 21.2 1.5 39 24-63 6-44 (59)
43 PF11563 Protoglobin: Protoglo 44.0 92 0.002 20.5 6.9 55 3-58 60-119 (158)
44 PF00619 CARD: Caspase recruit 43.6 66 0.0014 19.0 4.2 57 10-68 18-74 (85)
45 PF02845 CUE: CUE domain; Int 43.4 48 0.001 17.3 3.2 32 27-58 4-35 (42)
46 cd08329 CARD_BIRC2_BIRC3 Caspa 43.0 84 0.0018 19.7 8.2 65 2-68 14-81 (94)
47 PRK01356 hscB co-chaperone Hsc 42.9 1.1E+02 0.0024 21.2 7.7 42 40-83 108-149 (166)
48 PF07014 Hs1pro-1_C: Hs1pro-1 41.9 97 0.0021 23.1 5.4 51 42-103 54-104 (261)
49 cd08332 CARD_CASP2 Caspase act 41.7 86 0.0019 19.5 6.7 55 12-68 24-78 (90)
50 PF04400 DUF539: Protein of un 41.6 2.7 5.9E-05 23.3 -2.0 18 81-98 7-24 (45)
51 PF14615 Rsa3: Ribosome-assemb 39.8 68 0.0015 17.8 4.8 39 47-88 7-45 (47)
52 PRK09613 thiH thiamine biosynt 39.6 64 0.0014 26.3 4.6 68 17-84 7-75 (469)
53 PF07818 HCNGP: HCNGP-like pro 39.3 55 0.0012 20.8 3.5 44 3-50 10-53 (96)
54 PF04280 Tim44: Tim44-like dom 39.0 47 0.001 21.8 3.3 47 47-105 17-63 (147)
55 PRK12491 pyrroline-5-carboxyla 37.8 74 0.0016 23.7 4.5 71 7-89 144-215 (272)
56 PF14276 DUF4363: Domain of un 37.0 1.1E+02 0.0025 19.6 5.3 41 42-84 16-56 (121)
57 PF01322 Cytochrom_C_2: Cytoch 36.5 1.2E+02 0.0025 19.5 5.4 40 47-88 77-116 (122)
58 PF08822 DUF1804: Protein of u 36.4 1.5E+02 0.0033 20.8 7.5 41 23-63 48-88 (165)
59 PRK11199 tyrA bifunctional cho 35.6 2.1E+02 0.0046 22.3 9.7 64 38-103 298-367 (374)
60 TIGR01240 mevDPdecarb diphosph 35.4 81 0.0018 24.1 4.4 32 46-79 201-232 (305)
61 KOG2833 Mevalonate pyrophospha 34.5 88 0.0019 24.7 4.5 32 46-79 223-255 (395)
62 cd01671 CARD Caspase activatio 34.2 98 0.0021 18.0 6.3 58 9-68 14-71 (80)
63 COG3433 Aryl carrier domain [S 32.3 77 0.0017 19.3 3.1 26 71-96 30-55 (74)
64 PTZ00431 pyrroline carboxylate 32.2 96 0.0021 22.7 4.3 71 7-89 137-208 (260)
65 PRK07417 arogenate dehydrogena 31.7 1.3E+02 0.0028 22.2 5.0 26 51-78 241-266 (279)
66 COG1577 ERG12 Mevalonate kinas 31.0 2.5E+02 0.0054 21.6 6.9 59 44-105 199-260 (307)
67 PF14165 YtzH: YtzH-like prote 30.3 65 0.0014 20.3 2.6 27 8-34 29-55 (87)
68 PF14821 Thr_synth_N: Threonin 29.9 30 0.00065 21.0 1.1 32 21-55 35-67 (79)
69 PF14748 P5CR_dimer: Pyrroline 29.8 81 0.0018 20.1 3.1 30 24-54 2-31 (107)
70 PRK08507 prephenate dehydrogen 29.1 2.3E+02 0.005 20.7 6.4 39 38-78 219-264 (275)
71 PHA01794 hypothetical protein 28.8 1.4E+02 0.0031 20.2 4.2 51 10-63 59-110 (134)
72 PF14942 Muted: Organelle biog 28.5 2E+02 0.0043 19.7 5.3 61 3-63 16-77 (145)
73 KOG1142 Transcription initiati 28.4 1.1E+02 0.0023 23.2 3.9 44 9-64 159-202 (258)
74 PF05974 DUF892: Domain of unk 28.1 87 0.0019 21.4 3.3 59 6-68 2-61 (159)
75 KOG4747 Two-component phosphor 27.5 2.1E+02 0.0047 19.8 7.4 59 39-100 12-70 (150)
76 PRK07502 cyclohexadienyl dehyd 27.3 1.7E+02 0.0037 21.8 5.0 25 52-78 253-277 (307)
77 TIGR00601 rad23 UV excision re 26.9 90 0.002 24.8 3.5 37 26-63 255-291 (378)
78 PF13779 DUF4175: Domain of un 26.7 2.4E+02 0.0051 24.9 6.2 68 39-111 490-557 (820)
79 PF11277 Med24_N: Mediator com 26.6 2.2E+02 0.0049 25.7 6.1 47 4-50 705-752 (990)
80 COG3923 PriC Primosomal replic 26.5 2E+02 0.0043 20.4 4.8 35 46-82 45-79 (175)
81 cd08327 CARD_RAIDD Caspase act 25.3 1.8E+02 0.004 18.3 5.6 52 13-66 26-77 (94)
82 PRK10093 primosomal replicatio 24.8 2.6E+02 0.0056 19.8 6.5 35 46-82 41-75 (171)
83 KOG2280 Vacuolar assembly/sort 24.6 2.7E+02 0.006 24.5 6.1 66 27-100 690-756 (829)
84 PF15112 DUF4559: Domain of un 24.5 3.1E+02 0.0067 21.3 5.8 24 3-26 231-254 (307)
85 COG5162 Transcription initiati 24.1 1.9E+02 0.0041 20.5 4.3 27 26-52 73-99 (197)
86 KOG2702 Predicted panthothenat 24.0 64 0.0014 24.6 2.1 26 77-102 180-205 (323)
87 PRK15431 ferrous iron transpor 23.7 81 0.0018 19.4 2.2 32 58-91 4-35 (78)
88 COG3685 Uncharacterized protei 23.5 2.5E+02 0.0054 19.8 4.8 63 1-67 1-64 (167)
89 PLN02956 PSII-Q subunit 23.3 2.9E+02 0.0063 19.9 7.2 36 50-90 88-123 (185)
90 PF13801 Metal_resist: Heavy-m 23.2 1.9E+02 0.0041 17.6 10.0 70 23-97 42-111 (125)
91 PF10018 Med4: Vitamin-D-recep 23.0 2.7E+02 0.006 19.5 7.2 44 45-88 43-99 (188)
92 PHA00435 capsid assembly prote 23.0 2E+02 0.0044 22.1 4.5 49 27-79 188-236 (306)
93 PF08332 CaMKII_AD: Calcium/ca 22.8 96 0.0021 20.7 2.6 26 53-80 4-29 (128)
94 PF10431 ClpB_D2-small: C-term 22.6 1.2E+02 0.0026 17.8 2.8 56 40-100 3-58 (81)
95 PF05153 DUF706: Family of unk 22.5 1.5E+02 0.0032 22.4 3.7 58 26-89 43-100 (253)
96 PF11221 Med21: Subunit 21 of 22.5 2.5E+02 0.0054 18.8 5.6 54 10-65 85-138 (144)
97 COG4997 Uncharacterized conser 21.6 2.2E+02 0.0049 17.9 6.3 52 58-111 42-93 (95)
98 PF08637 NCA2: ATP synthase re 21.3 1.5E+02 0.0032 22.6 3.7 45 39-85 73-126 (290)
99 PF05974 DUF892: Domain of unk 21.0 1.6E+02 0.0034 20.1 3.5 73 28-107 7-79 (159)
100 COG4395 Uncharacterized protei 20.9 1.7E+02 0.0036 22.4 3.8 30 48-79 150-179 (281)
101 COG3388 Predicted transcriptio 20.5 2.2E+02 0.0047 18.4 3.7 36 7-45 42-77 (101)
102 TIGR00112 proC pyrroline-5-car 20.1 2E+02 0.0043 20.9 4.0 71 7-89 124-195 (245)
No 1
>KOG4747 consensus Two-component phosphorelay intermediate involved in MAP kinase cascade regulation [Signal transduction mechanisms]
Probab=99.71 E-value=6e-17 Score=110.30 Aligned_cols=106 Identities=55% Similarity=0.901 Sum_probs=100.8
Q ss_pred HHHHHHHHHHhcccCCCCCCHHHHHHHHccccCCChHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHhhhh
Q 033727 5 QLQHQVLYMRRSLFDQGYLDSEQLIQLEDLQDDANPNFVEEVVSLFYSDSARLIQNIEQTLSNRPVDFSRLDDILHQFKG 84 (112)
Q Consensus 5 ~l~~~~~~~~~~~~~~~~lD~~~l~~L~~l~~~~~~~~~~eli~~F~~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~LKG 84 (112)
.++.....|..|++.++++| ++|.+|+++.++..|.|+.+++..|++++.+.+..++.|+..+. |+..+....|.+||
T Consensus 7 ~~q~~~~d~~~sl~~qgild-~qF~qlq~lqD~~~p~fv~ev~~~fF~~s~~~i~~~r~ald~~~-d~k~~~~~~hqlkg 84 (150)
T KOG4747|consen 7 SMQRDVSDYTKSLFDQGILD-SQFLQLQELQDDSSPDFVEEVVGLFFEDSERLINNLRLALDCER-DFKKLGSHVHQLKG 84 (150)
T ss_pred HHHHHHHHHHHHHHHHHhhH-HHHHHHHHHhcccCccHHHHHHHHHHHHHHHHHHHHHHHHhhHh-HHHHHHHHHHHccC
Confidence 57788899999999999999 99999999999999999999999999999999999999988753 99999999999999
Q ss_pred hhhhhcHHHHHHHHHHHHHHHHccCCCC
Q 033727 85 SCSSIGAKKVKDACSQFREYCNAGNAEG 112 (112)
Q Consensus 85 sa~~lGa~~l~~~~~~lE~~~~~~~~~g 112 (112)
|+.++||.++...|..+...|+.++.+|
T Consensus 85 ssssIGa~kvk~~c~~~~~~~~~~n~eg 112 (150)
T KOG4747|consen 85 SSSSIGALKVKKVCVGFNEFCEAGNIEG 112 (150)
T ss_pred chhhhhHHHHHHHHHHHHHHHhhccchh
Confidence 9999999999999999999999999886
No 2
>COG2198 ArcB FOG: HPt domain [Signal transduction mechanisms]
Probab=99.65 E-value=2.2e-15 Score=100.01 Aligned_cols=78 Identities=23% Similarity=0.516 Sum_probs=71.1
Q ss_pred HHHHHccccCCChHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHhhhhhhhhhcHHHHHHHHHHHHHHHHc
Q 033727 28 LIQLEDLQDDANPNFVEEVVSLFYSDSARLIQNIEQTLSNRPVDFSRLDDILHQFKGSCSSIGAKKVKDACSQFREYCNA 107 (112)
Q Consensus 28 l~~L~~l~~~~~~~~~~eli~~F~~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~LKGsa~~lGa~~l~~~~~~lE~~~~~ 107 (112)
+..+..+.+ +.++++.+++..|+++.+..+..++.++..+ |+..+.+.||+|||+|+++|+.+|+.+|+++|..++.
T Consensus 11 ~~~~~~~~g-~~~~~~~~ll~~f~~~~~~~l~~l~~~l~~~--d~~~~~~~aH~lkg~a~~lg~~~L~~~~~~lE~~~~~ 87 (122)
T COG2198 11 IELLVRLIG-GDPDLLRELLAMFLEEAPAQLEQLESALAAE--DNDGLARLAHRLKGSAASLGLPALAQLCQQLEDALRS 87 (122)
T ss_pred HHHHHHHcC-CChHHHHHHHHHHHHHhHHHHHHHHHHHhcC--CcHHHHHHHHHHHhHHHhccHHHHHHHHHHHHHHHHc
Confidence 455555542 4799999999999999999999999999999 9999999999999999999999999999999999988
Q ss_pred c
Q 033727 108 G 108 (112)
Q Consensus 108 ~ 108 (112)
+
T Consensus 88 ~ 88 (122)
T COG2198 88 G 88 (122)
T ss_pred C
Confidence 4
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=99.60 E-value=3.3e-15 Score=92.78 Aligned_cols=64 Identities=23% Similarity=0.555 Sum_probs=60.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHh---hCCCCCHHHHHHHHHhhhhhhhhhcHHHHHHHHHHHHHHHHccCC
Q 033727 45 EVVSLFYSDSARLIQNIEQTL---SNRPVDFSRLDDILHQFKGSCSSIGAKKVKDACSQFREYCNAGNA 110 (112)
Q Consensus 45 eli~~F~~~~~~~l~~L~~a~---~~~~~D~~~l~~~aH~LKGsa~~lGa~~l~~~~~~lE~~~~~~~~ 110 (112)
+++..|+++.++.+..|++++ ..+ |+..+.+.+|+|||+++++|+.+++.+|..+|+.++.++.
T Consensus 1 ell~~f~~~~~~~~~~l~~~~~~~~~~--d~~~l~~~~H~lkG~a~~~g~~~l~~~~~~lE~~~~~~~~ 67 (90)
T PF01627_consen 1 ELLDIFLEEAPEDLEQLEQALQALEQE--DWEELRRLAHRLKGSAGNLGAPRLAELAEQLEQALKSGDK 67 (90)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHCSSHHC--HHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTHH
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHhHh--hHHHHHHHHHHHhhhHHhcCHHHHHHHHHHHHHHHHcCCc
Confidence 589999999999999999999 888 9999999999999999999999999999999999998764
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=99.52 E-value=3.2e-14 Score=88.57 Aligned_cols=63 Identities=22% Similarity=0.416 Sum_probs=59.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHhhhhhhhhhcHHHHHHHHHHHHHHHHccC
Q 033727 45 EVVSLFYSDSARLIQNIEQTLSNRPVDFSRLDDILHQFKGSCSSIGAKKVKDACSQFREYCNAGN 109 (112)
Q Consensus 45 eli~~F~~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~LKGsa~~lGa~~l~~~~~~lE~~~~~~~ 109 (112)
+++..|+++.+..+..|.+++..+ |+..+.+.+|+|||+|+++|+..|..+|..+|..++...
T Consensus 2 e~~~~f~~~~~~~l~~l~~~~~~~--~~~~l~~~~H~LKG~a~~~g~~~l~~~~~~lE~~~~~~~ 64 (87)
T smart00073 2 EELAEFLQSLEEGLLELEKALDAQ--DVNEIFRAAHTLKGSAGSLGLQQLAQLCHQLENLLDAAR 64 (87)
T ss_pred hHHHHHHHHHHHHHHHHHhCcCHh--HHHHHHHHHHhhhhhHHhcCHHHHHHHHHHHHHHHHHHH
Confidence 578999999999999999999888 999999999999999999999999999999999888643
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=99.48 E-value=1.6e-13 Score=86.89 Aligned_cols=64 Identities=25% Similarity=0.494 Sum_probs=60.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhh----CCCCCHHHHHHHHHhhhhhhhhhcHHHHHHHHHHHHHHHHccC
Q 033727 44 EEVVSLFYSDSARLIQNIEQTLS----NRPVDFSRLDDILHQFKGSCSSIGAKKVKDACSQFREYCNAGN 109 (112)
Q Consensus 44 ~eli~~F~~~~~~~l~~L~~a~~----~~~~D~~~l~~~aH~LKGsa~~lGa~~l~~~~~~lE~~~~~~~ 109 (112)
.+++..|+++.++.+..|.+++. .. |+..+.+.+|+|||+++++|+.++..+|..+|.+++.+.
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 46899999999999999999998 77 999999999999999999999999999999999998764
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=99.32 E-value=3.1e-11 Score=101.55 Aligned_cols=85 Identities=27% Similarity=0.441 Sum_probs=75.1
Q ss_pred CCCHHHHHHHHccccCCChHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHhhhhhhhhhcHHHHHHHHHHH
Q 033727 22 YLDSEQLIQLEDLQDDANPNFVEEVVSLFYSDSARLIQNIEQTLSNRPVDFSRLDDILHQFKGSCSSIGAKKVKDACSQF 101 (112)
Q Consensus 22 ~lD~~~l~~L~~l~~~~~~~~~~eli~~F~~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~LKGsa~~lGa~~l~~~~~~l 101 (112)
++|...+....... +++.+.+++..|+++.+..+..|..++..+ |+..+++.+|+|||+++++|+.++..+|..|
T Consensus 863 ll~~~~~~~~~~~~---~~~~~~~~~~~f~~~~~~~~~~l~~~~~~~--d~~~~~~~~H~lkg~~~~~g~~~l~~~~~~l 937 (968)
T TIGR02956 863 LLDEEQLQQDIEVL---GVEKVRQLVALFKTSSAEQLEELSAARAVD--DDAQIKKLAHKLKGSAGSLGLTQLTQLCQQL 937 (968)
T ss_pred hcCHHHHHHHHHhc---CcHHHHHHHHHHHHhhHHHHHHHHHHHhCC--CHHHHHHHHHHHHHHHHHhCHHHHHHHHHHH
Confidence 66655555443333 678899999999999999999999999999 9999999999999999999999999999999
Q ss_pred HHHHHccCCC
Q 033727 102 REYCNAGNAE 111 (112)
Q Consensus 102 E~~~~~~~~~ 111 (112)
|+.++.|+..
T Consensus 938 e~~~~~~~~~ 947 (968)
T TIGR02956 938 EKQGKTGALE 947 (968)
T ss_pred HHhcccCCcc
Confidence 9999988753
No 7
>PRK10618 phosphotransfer intermediate protein in two-component regulatory system with RcsBC; Provisional
Probab=99.01 E-value=1.1e-09 Score=93.08 Aligned_cols=64 Identities=16% Similarity=0.308 Sum_probs=61.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHhhhhhhhhhcHHHHHHHHHHHHHHHHccCC
Q 033727 45 EVVSLFYSDSARLIQNIEQTLSNRPVDFSRLDDILHQFKGSCSSIGAKKVKDACSQFREYCNAGNA 110 (112)
Q Consensus 45 eli~~F~~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~LKGsa~~lGa~~l~~~~~~lE~~~~~~~~ 110 (112)
.+...|++..+..+..|..++..+ |+..+.+.||+|||+++++|+..++++|..||+.++.++.
T Consensus 811 ~~~~lF~~t~~~di~~L~~~~~~~--D~~~l~~~aHrLKG~~aml~l~~l~~~~~~LE~~i~~~~~ 874 (894)
T PRK10618 811 DYYALFVDTVPDDVKRLYTEAATS--DFASLAQTAHRLKGVFAMLNLVPGKQLCETLEHLIREKDE 874 (894)
T ss_pred hHHHHHHHhhHHHHHHHHHHHhcc--CHHHHHHHHHHHHHHHHHcChHHHHHHHHHHHHHHhhCCh
Confidence 456899999999999999999999 9999999999999999999999999999999999998875
No 8
>PRK11466 hybrid sensory histidine kinase TorS; Provisional
Probab=98.85 E-value=4.3e-08 Score=82.46 Aligned_cols=99 Identities=23% Similarity=0.346 Sum_probs=75.5
Q ss_pred hHHHHHHHHHHHhccc-CCCCCCHHHHHHHHccccCCChHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHh
Q 033727 3 SNQLQHQVLYMRRSLF-DQGYLDSEQLIQLEDLQDDANPNFVEEVVSLFYSDSARLIQNIEQTLSNRPVDFSRLDDILHQ 81 (112)
Q Consensus 3 ~~~l~~~~~~~~~~~~-~~~~lD~~~l~~L~~l~~~~~~~~~~eli~~F~~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~ 81 (112)
.+.|...+..++.... ....++...+....... ++..+.+++..|.++....+..++.+...+ |+..++++||+
T Consensus 787 ~~~L~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~--~~~~~~~~ah~ 861 (914)
T PRK11466 787 REVLGQLLAHYLQLQVNNDQPLDVSQLNEDAALM---GTEKIHEWLALFKQHALPLLDEIDIARASQ--DSEKIKRAAHQ 861 (914)
T ss_pred HHHHHHHHHHHhhhccccccCCCHHHHHHHHHhc---CHHHHHHHHHHHHHhhHHHHHHHHHHHHCC--CHHHHHHHHHH
Confidence 3455555555554311 12334544444333222 567788999999999999999999999999 99999999999
Q ss_pred hhhhhhhhcHHHHHHHHHHHHHHHH
Q 033727 82 FKGSCSSIGAKKVKDACSQFREYCN 106 (112)
Q Consensus 82 LKGsa~~lGa~~l~~~~~~lE~~~~ 106 (112)
|||+++++|+..+..+|.++|..+.
T Consensus 862 lkg~~~~lg~~~l~~~~~~le~~~~ 886 (914)
T PRK11466 862 LKSSCSSLGMRQASQACAQLEQQPL 886 (914)
T ss_pred HHHHHHHhHHHHHHHHHHHHhCCCC
Confidence 9999999999999999999998653
No 9
>PRK11091 aerobic respiration control sensor protein ArcB; Provisional
Probab=98.81 E-value=6.4e-08 Score=80.46 Aligned_cols=103 Identities=17% Similarity=0.260 Sum_probs=81.6
Q ss_pred ChHHHHHHHHHHHhccc--------------CCCCCCHHHHHHHHccccCCChHHHHHHHHHHHHHHHHHHHHHHHHhhC
Q 033727 2 NSNQLQHQVLYMRRSLF--------------DQGYLDSEQLIQLEDLQDDANPNFVEEVVSLFYSDSARLIQNIEQTLSN 67 (112)
Q Consensus 2 ~~~~l~~~~~~~~~~~~--------------~~~~lD~~~l~~L~~l~~~~~~~~~~eli~~F~~~~~~~l~~L~~a~~~ 67 (112)
+.+.|...+..++.... ...++|.+.+..+.+.. ++..+.+.+..|.+..+..+..|..++..
T Consensus 631 ~~~~L~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~l~~~~~~~---g~~~~~~~l~~~~~~~~~~~~~l~~~l~~ 707 (779)
T PRK11091 631 SVPALTAMIKKFWDTQDDEESTVTTEESSKANEALLDIPMLEQYVELV---GPKLITDSLAVFEKMMPGYLSVLDSNLTA 707 (779)
T ss_pred CHHHHHHHHHHHhcccccccccccccccccccccccCHHHHHHHHHhc---CHHHHHHHHHHHHHhhHHHHHHHHHHHHC
Confidence 34566666666663321 12356666556555544 56778889999999999999999999999
Q ss_pred CCCCHHHHHHHHHhhhhhhhhhcHHHHHHHHHHHHHHHHccC
Q 033727 68 RPVDFSRLDDILHQFKGSCSSIGAKKVKDACSQFREYCNAGN 109 (112)
Q Consensus 68 ~~~D~~~l~~~aH~LKGsa~~lGa~~l~~~~~~lE~~~~~~~ 109 (112)
+ |+..+...+|+|||+++++|+..++.+|..+|.....+.
T Consensus 708 ~--d~~~~~~~ah~l~g~~~~~g~~~l~~~~~~le~~~~~~~ 747 (779)
T PRK11091 708 R--DQKGIVEEAHKIKGAAGSVGLRHLQQLAQQIQSPDLPAW 747 (779)
T ss_pred C--CHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHhCcCcccc
Confidence 9 999999999999999999999999999999997665543
No 10
>PRK11107 hybrid sensory histidine kinase BarA; Provisional
Probab=98.54 E-value=2.2e-06 Score=71.94 Aligned_cols=69 Identities=22% Similarity=0.510 Sum_probs=65.0
Q ss_pred ChHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHhhhhhhhhhcHHHHHHHHHHHHHHHHccC
Q 033727 39 NPNFVEEVVSLFYSDSARLIQNIEQTLSNRPVDFSRLDDILHQFKGSCSSIGAKKVKDACSQFREYCNAGN 109 (112)
Q Consensus 39 ~~~~~~eli~~F~~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~LKGsa~~lGa~~l~~~~~~lE~~~~~~~ 109 (112)
.+....+++..|.+..+.....|..++... |+..+..++|++||+++++|+.++..+|..+|+.++.+.
T Consensus 822 ~~~~~~~~l~~~~~~~~~~~~~l~~~~~~~--~~~~~~~~~h~l~g~~~~~g~~~l~~~~~~le~~~~~~~ 890 (919)
T PRK11107 822 KPDLARDMLQMLLDFLPEVRNKVEEALAGE--DPEGLLDLIHKLHGSCSYSGVPRLKKLCQLIEQQLRSGT 890 (919)
T ss_pred CHHHHHHHHHHHHHhHHHHHHHHHHHHHCC--CHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHcCC
Confidence 678888999999999999999999999999 999999999999999999999999999999999998763
No 11
>COG0643 CheA Chemotaxis protein histidine kinase and related kinases [Cell motility and secretion / Signal transduction mechanisms]
Probab=98.47 E-value=7.1e-07 Score=74.66 Aligned_cols=66 Identities=21% Similarity=0.409 Sum_probs=54.9
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHh---hCCCCCH---HHHHHHHHhhhhhhhhhcHHHHHHHHHHHHHHH
Q 033727 40 PNFVEEVVSLFYSDSARLIQNIEQTL---SNRPVDF---SRLDDILHQFKGSCSSIGAKKVKDACSQFREYC 105 (112)
Q Consensus 40 ~~~~~eli~~F~~~~~~~l~~L~~a~---~~~~~D~---~~l~~~aH~LKGsa~~lGa~~l~~~~~~lE~~~ 105 (112)
+....++...|+.++++++..|.+.+ +..|.|. ..+.+.||+|||+|+++|+..+..+|+.+|...
T Consensus 3 ~~~~~~~~~~F~~Ea~e~l~~l~~~Ll~LE~~~~d~~~ln~ifRaaHTlKG~a~~~g~~~l~~l~H~~E~~l 74 (716)
T COG0643 3 SMDMEEILEDFLEEAEELLQALEQALLALEPDPEDLDLLNAIFRAAHTLKGGAGTLGLTTLAELAHAMEDLL 74 (716)
T ss_pred hhHHHHHHHHHHHhhHHHHHHHHHhHhhccCCCCCHHHHHHHHHHHHhhhhhhhhcChhHHHHHHHHHHHHH
Confidence 34567899999999999999999853 3333454 567899999999999999999999999999743
No 12
>PRK10547 chemotaxis protein CheA; Provisional
Probab=98.47 E-value=7.9e-07 Score=73.94 Aligned_cols=63 Identities=16% Similarity=0.357 Sum_probs=53.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHH---hhCCCCCH---HHHHHHHHhhhhhhhhhcHHHHHHHHHHHHHHHH
Q 033727 44 EEVVSLFYSDSARLIQNIEQT---LSNRPVDF---SRLDDILHQFKGSCSSIGAKKVKDACSQFREYCN 106 (112)
Q Consensus 44 ~eli~~F~~~~~~~l~~L~~a---~~~~~~D~---~~l~~~aH~LKGsa~~lGa~~l~~~~~~lE~~~~ 106 (112)
.+++..|++++.+.++.|++. +++.|.|. ..+.+.+|+|||+|+.+|+..+..+|+.+|....
T Consensus 4 ~~~l~~F~~Ea~E~l~~le~~Ll~LE~~p~d~e~in~lFRa~HTiKG~a~~~g~~~i~~l~H~~E~lld 72 (670)
T PRK10547 4 SDFYQTFFDEADELLADMEQHLLVLDPEAPDAEQLNAIFRAAHSIKGGAGTFGFTVLQETTHLMENLLD 72 (670)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhccCCCCHHHHHHHHHHHHhhhhHHhhcCchHHHHHHHHHHHHHH
Confidence 368999999999999999887 44444454 5678999999999999999999999999997653
No 13
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=97.49 E-value=0.0023 Score=55.78 Aligned_cols=68 Identities=12% Similarity=0.237 Sum_probs=61.6
Q ss_pred ChHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHhhhhhhhhhcHHHHHHHHHHHHHHHHcc
Q 033727 39 NPNFVEEVVSLFYSDSARLIQNIEQTLSNRPVDFSRLDDILHQFKGSCSSIGAKKVKDACSQFREYCNAG 108 (112)
Q Consensus 39 ~~~~~~eli~~F~~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~LKGsa~~lGa~~l~~~~~~lE~~~~~~ 108 (112)
+...+.+++..+.......+..+..+...+ |...+...+|++||++..+|+..+...|.++|......
T Consensus 1098 ~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~h~~~g~~~~l~~~~l~~~~~~~e~~~~~~ 1165 (1197)
T PRK09959 1098 DLQLMQEILMTFQHETHKDLPAAFHALEAG--DNRTFHQCIHRIHGAANILNLQKLINISHQLEITPVSD 1165 (1197)
T ss_pred CHHHHHHHHHHHHHhhHHHHHHHHHHHHcC--CHHHHHHHHHHHHHHHHHcCHHHHHHHHHHHHHhhhcC
Confidence 567788899999999999998888899999 99999999999999999999999999999999877654
No 14
>PRK15347 two component system sensor kinase SsrA; Provisional
Probab=97.21 E-value=0.0018 Score=54.71 Aligned_cols=61 Identities=25% Similarity=0.424 Sum_probs=51.9
Q ss_pred HHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHhhhhhhhhhcHHHHHHHHHHHHHHHHccCC
Q 033727 46 VVSLFYSDSARLIQNIEQTLSNRPVDFSRLDDILHQFKGSCSSIGAKKVKDACSQFREYCNAGNA 110 (112)
Q Consensus 46 li~~F~~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~LKGsa~~lGa~~l~~~~~~lE~~~~~~~~ 110 (112)
+...+.+.....+..+..++..+ | .+.+++|++||+++.+|+.++...|.++|..++.+..
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 44555666677788888888877 6 8899999999999999999999999999999987653
No 15
>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=88.59 E-value=3.7 Score=24.63 Aligned_cols=43 Identities=16% Similarity=0.328 Sum_probs=35.4
Q ss_pred ChHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHhhh
Q 033727 39 NPNFVEEVVSLFYSDSARLIQNIEQTLSNRPVDFSRLDDILHQFK 83 (112)
Q Consensus 39 ~~~~~~eli~~F~~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~LK 83 (112)
+..-+.++....-......+..|..++... ||..+...+++||
T Consensus 25 ~~~~L~~l~~~~~~~~~~~~~~l~~~f~~~--d~~~A~~~~~kLk 67 (78)
T PF07743_consen 25 DEAELEELKKEIEERIKELIKELAEAFDAK--DWEEAKEALRKLK 67 (78)
T ss_dssp SHHHHHHHHHHHHHHHHHHHHHHHHHHHTT---HHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHccC--cHHHHHHHHHHHH
Confidence 456677777777778888888999999999 9999999999986
No 16
>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=85.99 E-value=6.4 Score=24.60 Aligned_cols=67 Identities=10% Similarity=0.227 Sum_probs=53.3
Q ss_pred HHHHHhcccCCCCCCHHHHHHHHccccCCChHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHH
Q 033727 10 VLYMRRSLFDQGYLDSEQLIQLEDLQDDANPNFVEEVVSLFYSDSARLIQNIEQTLSNRPVDFSRLDDILH 80 (112)
Q Consensus 10 ~~~~~~~~~~~~~lD~~~l~~L~~l~~~~~~~~~~eli~~F~~~~~~~l~~L~~a~~~~~~D~~~l~~~aH 80 (112)
....+..+..+++++.+..+.++... ...+-...+|+....-.+.-...+..++... .+..++.+.|
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 45577788899999988888888754 3567778899999999999999999998866 6777777665
No 17
>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=82.49 E-value=13 Score=25.56 Aligned_cols=43 Identities=12% Similarity=0.131 Sum_probs=31.3
Q ss_pred ChHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHhhh
Q 033727 39 NPNFVEEVVSLFYSDSARLIQNIEQTLSNRPVDFSRLDDILHQFK 83 (112)
Q Consensus 39 ~~~~~~eli~~F~~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~LK 83 (112)
+.+-+..+....-.........|.++++.+ ||+.+...+.+||
T Consensus 98 d~~~L~~l~~~~~~~~~~~~~~l~~~~~~~--d~~~A~~~~~kLk 140 (157)
T TIGR00714 98 DEARLESFIKRVKKMFQTRHQLLVEQLDNQ--TWAAAADYTRKLR 140 (157)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHhcC--CHHHHHHHHHHHH
Confidence 455556666666666666777788888888 9988888777765
No 18
>PRK01773 hscB co-chaperone HscB; Provisional
Probab=76.16 E-value=22 Score=25.00 Aligned_cols=43 Identities=5% Similarity=0.252 Sum_probs=28.7
Q ss_pred ChHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHhhh
Q 033727 39 NPNFVEEVVSLFYSDSARLIQNIEQTLSNRPVDFSRLDDILHQFK 83 (112)
Q Consensus 39 ~~~~~~eli~~F~~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~LK 83 (112)
+++-+..+....-......+..|.++++.+ ||..+...+-+||
T Consensus 112 d~~~L~~l~~~v~~~~~~~~~~l~~~~~~~--d~~~A~~~~~rL~ 154 (173)
T PRK01773 112 DEDALTAFSKEIKQEQQAILTELSTALNSQ--QWQQASQINDRLR 154 (173)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHhcC--CHHHHHHHHHHHH
Confidence 455555555555556666677788888888 8877776655554
No 19
>PRK03578 hscB co-chaperone HscB; Provisional
Probab=71.41 E-value=33 Score=24.16 Aligned_cols=43 Identities=7% Similarity=0.144 Sum_probs=31.8
Q ss_pred ChHHHHHHHHHHHHHHHHHHHHHHHHhhC-CCCCHHHHHHHHHhhh
Q 033727 39 NPNFVEEVVSLFYSDSARLIQNIEQTLSN-RPVDFSRLDDILHQFK 83 (112)
Q Consensus 39 ~~~~~~eli~~F~~~~~~~l~~L~~a~~~-~~~D~~~l~~~aH~LK 83 (112)
+++-+..+....-......+..|.++++. + ||..+...+.+||
T Consensus 115 d~~~L~~l~~e~~~~~~~~~~~l~~~~~~~~--d~~~A~~~~~kL~ 158 (176)
T PRK03578 115 DVDALDALLAELRDERRERYAELGALLDSRG--DDQAAAEAVRQLM 158 (176)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHccc--cHHHHHHHHHHHH
Confidence 55556666666666666777778888877 7 8998888887777
No 20
>TIGR03042 PS_II_psbQ_bact photosystem II protein PsbQ. This protein through the member sll1638 from Synechocystis sp. PCC 6803, was shown to be part of the cyanobacteria photosystem II. It is homologous to (but quite diverged from) the chloroplast PsbQ protein, called oxygen-evolving enhancer protein 3 (OEE3). We designate this cyanobacteria protein PsbQ by homology.
Probab=68.27 E-value=36 Score=23.37 Aligned_cols=34 Identities=9% Similarity=0.320 Sum_probs=23.7
Q ss_pred HHHHHHHHHHHHHhhCCCCCHHHHHHHHHhhhhhhhhhc
Q 033727 52 SDSARLIQNIEQTLSNRPVDFSRLDDILHQFKGSCSSIG 90 (112)
Q Consensus 52 ~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~LKGsa~~lG 90 (112)
+.+.+.+.+|+..++++ ||..++...| |..|.++
T Consensus 46 ~~~~~r~~eLk~lI~kk--~W~~vrn~ir---gp~g~Lr 79 (142)
T TIGR03042 46 EAAKDRLPELASLVAKE--DWVFTRNLIH---GPMGEVR 79 (142)
T ss_pred HHHHHhhHHHHHHHhhc--chHHHHHHHh---ccHHHHH
Confidence 34566777788888888 8888887755 4455444
No 21
>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=67.50 E-value=21 Score=23.96 Aligned_cols=54 Identities=6% Similarity=0.099 Sum_probs=40.5
Q ss_pred HHHHHHccccCCChHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHhhhh
Q 033727 27 QLIQLEDLQDDANPNFVEEVVSLFYSDSARLIQNIEQTLSNRPVDFSRLDDILHQFKG 84 (112)
Q Consensus 27 ~l~~L~~l~~~~~~~~~~eli~~F~~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~LKG 84 (112)
.++.+.... ++++-+..|+.-.-...+..++.+..+++.+ |...++.+.--+.+
T Consensus 35 yV~~V~~~A--GG~e~f~~i~~~~~~~~~~~~ea~~~Ai~~~--dla~vk~~vn~~~~ 88 (123)
T PF05396_consen 35 YVNSVKGYA--GGEEGFAAIMSHAEANSPAAAEAFNEAIESG--DLATVKAAVNLAGA 88 (123)
T ss_pred HHHHHHHHh--cCHHHHHHHHHHHHhCCHHHHHHHHHHHHhC--CHHHHHHHHHHHHH
Confidence 355666554 3788888877776677799999999999999 99888776544433
No 22
>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=66.11 E-value=26 Score=20.89 Aligned_cols=46 Identities=11% Similarity=0.155 Sum_probs=26.4
Q ss_pred HHHHHHHHhcccCCCCCCHHHHHHHHccccCCChHHHHHHHHHHHHHHHHHHHHHHHH
Q 033727 7 QHQVLYMRRSLFDQGYLDSEQLIQLEDLQDDANPNFVEEVVSLFYSDSARLIQNIEQT 64 (112)
Q Consensus 7 ~~~~~~~~~~~~~~~~lD~~~l~~L~~l~~~~~~~~~~eli~~F~~~~~~~l~~L~~a 64 (112)
+.++..+++.+.+..-+|+++-+ ++.++.+.|++++-...-.|...
T Consensus 2 K~~l~~Lv~~iDp~~~ld~~vee------------~Ll~laddFv~~v~~~ac~lAKh 47 (68)
T PF03847_consen 2 KRKLQELVKQIDPNEKLDPDVEE------------LLLELADDFVDDVVSFACRLAKH 47 (68)
T ss_dssp HHHHHHHHHCC-SS----HHHHH------------HHHHHHHHHHHHHHHHHHHHHHH
T ss_pred hHHHHHHHHHcCCCCCCCHHHHH------------HHHHHHHHHHHHHHHHHHHHHhc
Confidence 46788899999888888865544 34455666777666555555443
No 23
>COG2991 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=59.09 E-value=2.1 Score=26.15 Aligned_cols=20 Identities=35% Similarity=0.778 Sum_probs=17.0
Q ss_pred HhhhhhhhhhcHHHHHHHHH
Q 033727 80 HQFKGSCSSIGAKKVKDACS 99 (112)
Q Consensus 80 H~LKGsa~~lGa~~l~~~~~ 99 (112)
-.||||+|-+++..+...|.
T Consensus 27 k~I~GSCGGi~alGi~K~Cd 46 (77)
T COG2991 27 KSIKGSCGGIAALGIEKVCD 46 (77)
T ss_pred cccccccccHHhhccchhcC
Confidence 36899999999998888775
No 24
>PRK03057 hypothetical protein; Provisional
Probab=58.79 E-value=44 Score=23.78 Aligned_cols=35 Identities=20% Similarity=0.416 Sum_probs=26.6
Q ss_pred HHHHHHH------HHHHHHHHHHHhhCCCCCHHHHHHHHHhhh
Q 033727 47 VSLFYSD------SARLIQNIEQTLSNRPVDFSRLDDILHQFK 83 (112)
Q Consensus 47 i~~F~~~------~~~~l~~L~~a~~~~~~D~~~l~~~aH~LK 83 (112)
++.|++. -.....+|..|++.+ |.+...++.+.|+
T Consensus 133 ae~~L~~~~~~~~~~~L~~~ID~ALd~~--D~e~F~~Lt~~L~ 173 (180)
T PRK03057 133 TEQVLDEVLKRNEVSRLRMQIDQALDRK--DMEEFQRLTEKLK 173 (180)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHCC--CHHHHHHHHHHHH
Confidence 5555555 456678899999999 9988888887765
No 25
>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=57.59 E-value=43 Score=20.66 Aligned_cols=56 Identities=7% Similarity=0.197 Sum_probs=36.7
Q ss_pred HHHHhcccCCCCCCHHHHHHHHccccCCChHHHHHHHHHHHHHHHHHHHHHHHHhhCC
Q 033727 11 LYMRRSLFDQGYLDSEQLIQLEDLQDDANPNFVEEVVSLFYSDSARLIQNIEQTLSNR 68 (112)
Q Consensus 11 ~~~~~~~~~~~~lD~~~l~~L~~l~~~~~~~~~~eli~~F~~~~~~~l~~L~~a~~~~ 68 (112)
...+.-+.+.++++.+..+.+.... ...+-...+++..-.-.+.-+..+-.++...
T Consensus 19 ~~v~~~L~~~~Vlt~~~~e~I~~~~--tr~~q~~~LLd~L~~RG~~AF~~F~~aL~~~ 74 (84)
T cd08326 19 KYLWDHLLSRGVFTPDMIEEIQAAG--SRRDQARQLLIDLETRGKQAFPAFLSALRET 74 (84)
T ss_pred HHHHHHHHhcCCCCHHHHHHHHcCC--CHHHHHHHHHHHHHhcCHHHHHHHHHHHHhc
Confidence 3445556677888877777777543 2456666777777777777777777666554
No 26
>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=57.47 E-value=42 Score=26.69 Aligned_cols=76 Identities=16% Similarity=0.268 Sum_probs=48.8
Q ss_pred HHhcccCCCCCCHHHHHHHHccccCCChHHHHHHHHHHHHHHHHH-HHHHHHHhhCCCCCHHHHHHHHHhhhhhhhhhcH
Q 033727 13 MRRSLFDQGYLDSEQLIQLEDLQDDANPNFVEEVVSLFYSDSARL-IQNIEQTLSNRPVDFSRLDDILHQFKGSCSSIGA 91 (112)
Q Consensus 13 ~~~~~~~~~~lD~~~l~~L~~l~~~~~~~~~~eli~~F~~~~~~~-l~~L~~a~~~~~~D~~~l~~~aH~LKGsa~~lGa 91 (112)
++..+|.+.-+- ..+.+++.+ +|.|- +..|+..+... +..|-.|...+ |.+.|+.+++.
T Consensus 217 ~~~~lF~ete~a-~~l~eIk~~----DPsFd---~~~Fl~gar~aI~p~ILeAf~kG--D~e~LK~~lse---------- 276 (378)
T TIGR00984 217 VFSGMFSETEVS-EVLTEFKKI----DPTFD---KEHFLRFLREYIVPEILEAYVKG--DLEVLKSWCSE---------- 276 (378)
T ss_pred hhhcccCCCHHH-HHHHHHHHh----CCCCC---HHHHHHHHHHHHHHHHHHHHHcC--CHHHHHHhhCH----------
Confidence 333344443333 345555544 34443 57899999888 79999999999 99988877643
Q ss_pred HHHHHHHHHHHHHHHcc
Q 033727 92 KKVKDACSQFREYCNAG 108 (112)
Q Consensus 92 ~~l~~~~~~lE~~~~~~ 108 (112)
......|..+++..++|
T Consensus 277 ~vy~~f~a~I~qr~~~G 293 (378)
T TIGR00984 277 APFSVYATVVKEYKKMG 293 (378)
T ss_pred HHHHHHHHHHHHHHHCC
Confidence 34455556666555554
No 27
>KOG4552 consensus Vitamin-D-receptor interacting protein complex component [Transcription]
Probab=57.25 E-value=72 Score=23.63 Aligned_cols=39 Identities=15% Similarity=0.296 Sum_probs=28.4
Q ss_pred HHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHhhhhh
Q 033727 46 VVSLFYSDSARLIQNIEQTLSNRPVDFSRLDDILHQFKGS 85 (112)
Q Consensus 46 li~~F~~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~LKGs 85 (112)
++.+-+=++.+.+..|++| ..+|+.-+.+..+||+|-.+
T Consensus 103 iLtta~fqA~qKLksi~~A-~krpvsSEelIKyAHrIS~~ 141 (272)
T KOG4552|consen 103 ILTTACFQANQKLKSIKEA-EKRPVSSEELIKYAHRISKH 141 (272)
T ss_pred HHHHHHHHHHHHHHHHHHH-hcCCCCHHHHHHHHHHhhhc
Confidence 4555556666777777776 45578889999999998654
No 28
>PRK08818 prephenate dehydrogenase; Provisional
Probab=57.07 E-value=61 Score=25.57 Aligned_cols=39 Identities=15% Similarity=0.229 Sum_probs=27.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHhhhhhh
Q 033727 42 FVEEVVSLFYSDSARLIQNIEQTLSNRPVDFSRLDDILHQFKGSC 86 (112)
Q Consensus 42 ~~~eli~~F~~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~LKGsa 86 (112)
.+.+.++.|.+ .+.++++++.++ |++.+.+..|++.-+-
T Consensus 228 ~i~~~l~~~~~----~L~~l~~~i~~~--D~~~~~~~~~~f~~a~ 266 (370)
T PRK08818 228 YVGEMLDRLLA----QLQELRALVAQG--DDAARARFRAQFLHAN 266 (370)
T ss_pred HHHHHHHHHHH----HHHHHHHHHHcC--CHHHHHHHHHHHHHHH
Confidence 34444555544 467788889999 9999888877766543
No 29
>PRK05014 hscB co-chaperone HscB; Provisional
Probab=57.06 E-value=64 Score=22.49 Aligned_cols=39 Identities=15% Similarity=0.244 Sum_probs=24.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHhhh
Q 033727 43 VEEVVSLFYSDSARLIQNIEQTLSNRPVDFSRLDDILHQFK 83 (112)
Q Consensus 43 ~~eli~~F~~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~LK 83 (112)
+.++....-.........|.++++.+ ||..+...+-+||
T Consensus 115 l~~l~~~~~~~~~~~~~~l~~~~~~~--d~~~A~~~~~~Lk 153 (171)
T PRK05014 115 LESFIKRVKKMFKTRLQQMVEQLDNE--AWDAAADTVRKLK 153 (171)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhC--CHHHHHHHHHHHH
Confidence 44444444444455556677778778 8887777766665
No 30
>PRK03636 hypothetical protein; Provisional
Probab=56.12 E-value=58 Score=23.15 Aligned_cols=28 Identities=18% Similarity=0.462 Sum_probs=23.7
Q ss_pred HHHHHHHHHHHhhCCCCCHHHHHHHHHhhh
Q 033727 54 SARLIQNIEQTLSNRPVDFSRLDDILHQFK 83 (112)
Q Consensus 54 ~~~~l~~L~~a~~~~~~D~~~l~~~aH~LK 83 (112)
-.+...+|..|++.+ |-+...+++..||
T Consensus 147 ~~~L~~~ID~ALd~~--D~e~F~~Ls~~l~ 174 (179)
T PRK03636 147 REKLLKQIDEALDRR--DKEAFHRLSDELN 174 (179)
T ss_pred HHHHHHHHHHHHHcC--CHHHHHHHHHHHH
Confidence 356788999999999 9999988887776
No 31
>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=55.79 E-value=21 Score=24.51 Aligned_cols=20 Identities=10% Similarity=0.144 Sum_probs=15.0
Q ss_pred CHHHHHHHHHhhhhhhhhhc
Q 033727 71 DFSRLDDILHQFKGSCSSIG 90 (112)
Q Consensus 71 D~~~l~~~aH~LKGsa~~lG 90 (112)
|-..+++++-.|++.-..+.
T Consensus 93 dqk~a~~L~~~Lf~~L~~LD 112 (142)
T TIGR03042 93 DQKEALALAKELKDDLEKLD 112 (142)
T ss_pred hHHHHHHHHHHHHHHHHHHH
Confidence 77888888888887765554
No 32
>PF14357 DUF4404: Domain of unknown function (DUF4404)
Probab=55.59 E-value=37 Score=21.01 Aligned_cols=30 Identities=27% Similarity=0.283 Sum_probs=21.2
Q ss_pred HHHHHHHHHhcccCCCCCCHHHHHHHHccc
Q 033727 6 LQHQVLYMRRSLFDQGYLDSEQLIQLEDLQ 35 (112)
Q Consensus 6 l~~~~~~~~~~~~~~~~lD~~~l~~L~~l~ 35 (112)
|++.|..+-.-+.+.+-+|.+.-..|..+.
T Consensus 2 L~~~L~~L~~eL~~~~~ld~~~~~~L~~l~ 31 (85)
T PF14357_consen 2 LQELLEKLHQELEQNPPLDEETRAELSSLD 31 (85)
T ss_pred HHHHHHHHHHHHhcCCCCCHHHHHHHHHHH
Confidence 566677777777777788877766666665
No 33
>TIGR01220 Pmev_kin_Gr_pos phosphomevalonate kinase, ERG8-type, Gram-positive branch. This enzyme is part of the mevalonate pathway, one of two alternative pathways for the biosynthesis of IPP. In an example of nonorthologous gene displacement, two different types of phosphomevalonate kinase are found - the animal type and this ERG8 type. This model represents the low GC Gram-positive organism forms of the ERG8 type of phosphomevalonate kinase.
Probab=54.68 E-value=90 Score=24.20 Aligned_cols=57 Identities=16% Similarity=0.299 Sum_probs=37.6
Q ss_pred HHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHhhhhhhhh--------hcHHHHHHHHHHHHHH
Q 033727 46 VVSLFYSDSARLIQNIEQTLSNRPVDFSRLDDILHQFKGSCSS--------IGAKKVKDACSQFREY 104 (112)
Q Consensus 46 li~~F~~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~LKGsa~~--------lGa~~l~~~~~~lE~~ 104 (112)
..+.|++...+...++.+++..+ |+..+.++.+.-...-.. +--..+.+++...++.
T Consensus 246 ~~~~~l~~~~~i~~~~~~al~~~--d~~~lg~~~~~~~~lL~~l~~~~~~~vs~~~l~~li~~a~~~ 310 (358)
T TIGR01220 246 SYQRFLETSTDCVESAITAFETG--DITSLQKEIRRNRQELARLDDEVGVGIETEKLKALCDAAEAY 310 (358)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhC--CHHHHHHHHHHHHHHHHHhhcccCCCcCCHHHHHHHHHHhhc
Confidence 45678888888889999999999 988776554443333332 2255666666555543
No 34
>PF09209 DUF1956: Domain of unknown function (DUF1956); InterPro: IPR015292 This entry represents the C-terminal domain found in the hypothetical transcriptional regulator YbiH from bacteria such as Salmonella typhimurium and Escherichia coli. YbiH is a member of the TetR (tetracycline resistance) transcriptional regulator family of proteins. The C-terminal domains of YbiH and TetR share a multi-helical, interlocking structure.; PDB: 1T33_A.
Probab=51.96 E-value=58 Score=20.49 Aligned_cols=87 Identities=9% Similarity=0.100 Sum_probs=51.3
Q ss_pred HHHHHHHHHHHhcccCCCCCCHHHHHHHHccccCCChHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHhhh
Q 033727 4 NQLQHQVLYMRRSLFDQGYLDSEQLIQLEDLQDDANPNFVEEVVSLFYSDSARLIQNIEQTLSNRPVDFSRLDDILHQFK 83 (112)
Q Consensus 4 ~~l~~~~~~~~~~~~~~~~lD~~~l~~L~~l~~~~~~~~~~eli~~F~~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~LK 83 (112)
+.|+.=+..++..+..++--.+-.-=-++++.+ ....+..+++.++.-..+.+..|-..+...+.|-..+...+|++=
T Consensus 3 ~~L~~~i~~~~~~l~~~~~~~~~~~l~~RE~~~--Pt~~~~~i~~~~~~P~~~~l~~ll~~~~g~~~~~~~~~~~~~si~ 80 (125)
T PF09209_consen 3 ERLRAFIRALLRRLLSDPESRWWLRLIAREMLN--PTPAFDRIVEELIRPKHEALARLLAEILGEPADDPEVRLCAFSIV 80 (125)
T ss_dssp HHHHHHHHHHHHHTTSG-GGHHHHHHHHHHHHS----HHHHHHHHHTHHHHHHHHHHHHHHHHT--TTSHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHcccchhHHHHHHHHHhcC--chHHHHHHHHHHhhhHHHHHHHHHHHHhCcCCChHHHHHHHHHHH
Confidence 344444555555555442222111123466654 346677888888877777777766655555446678899999999
Q ss_pred hhhhhhcHH
Q 033727 84 GSCSSIGAK 92 (112)
Q Consensus 84 Gsa~~lGa~ 92 (112)
|.+..+...
T Consensus 81 g~~~~~~~~ 89 (125)
T PF09209_consen 81 GQCLFFRIA 89 (125)
T ss_dssp HHHHHHHHT
T ss_pred HHHHHHHHh
Confidence 988766544
No 35
>COG3046 Uncharacterized protein related to deoxyribodipyrimidine photolyase [General function prediction only]
Probab=51.16 E-value=37 Score=27.68 Aligned_cols=66 Identities=12% Similarity=0.117 Sum_probs=55.4
Q ss_pred ChHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHhhhhhhhhhcHHHHHHHHHHHHHHHHccCC
Q 033727 39 NPNFVEEVVSLFYSDSARLIQNIEQTLSNRPVDFSRLDDILHQFKGSCSSIGAKKVKDACSQFREYCNAGNA 110 (112)
Q Consensus 39 ~~~~~~eli~~F~~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~LKGsa~~lGa~~l~~~~~~lE~~~~~~~~ 110 (112)
.+.-....+..|+++.-.....-+.|+... |+. +=|++=+.+.|+|.-.=.+.|+..+.+-++|+.
T Consensus 226 tr~~A~~~L~~Fi~~~L~nFG~yQDam~~d--~~~----L~HSllS~alNigLL~PleVi~Aa~~Ay~~g~i 291 (505)
T COG3046 226 TRTQALRALKHFIADRLPNFGSYQDAMSAD--DPH----LWHSLLSFALNIGLLTPLEVIRAALKAYREGDI 291 (505)
T ss_pred CHHHHHHHHHHHHHHhhhcCCcHHHHHhcC--Cch----hHHHHHHHHhhccCCCHHHHHHHHHHhhccCCC
Confidence 455566788999998877788888888887 663 889999999999999999999999999888763
No 36
>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=51.06 E-value=35 Score=17.74 Aligned_cols=34 Identities=24% Similarity=0.450 Sum_probs=22.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHh
Q 033727 44 EEVVSLFYSDSARLIQNIEQTLSNRPVDFSRLDDILHQ 81 (112)
Q Consensus 44 ~eli~~F~~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~ 81 (112)
.+.+..|..+ .....|..|++.+ |-+.+.+++..
T Consensus 3 ~~~~~~~~~~--~L~~~ID~ALd~~--D~e~F~~Ls~e 36 (37)
T PF08858_consen 3 DESLREFRKE--QLLELIDEALDNR--DKEWFYELSEE 36 (37)
T ss_dssp HHHHHHHHHH--HHHHHHHHHHHTT---HHHHHHHHHH
T ss_pred HHHHHHHHHH--HHHHHHHHHHHcC--CHHHHHHHHhh
Confidence 3344444333 5677899999999 99888887654
No 37
>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=50.00 E-value=1.2e+02 Score=23.39 Aligned_cols=66 Identities=21% Similarity=0.322 Sum_probs=46.2
Q ss_pred HHHHHHccccCCChHHHHHHHHHHH-HHHHHHHHHHHHHhhCCCCCHHHHHHHHHhhhhhhhhhcHHHHHHHHHH
Q 033727 27 QLIQLEDLQDDANPNFVEEVVSLFY-SDSARLIQNIEQTLSNRPVDFSRLDDILHQFKGSCSSIGAKKVKDACSQ 100 (112)
Q Consensus 27 ~l~~L~~l~~~~~~~~~~eli~~F~-~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~LKGsa~~lGa~~l~~~~~~ 100 (112)
++..|..++ .......+...|. .|-.=..-.++.....+ +|+.+...+-.=| +-||..++.+.|..
T Consensus 183 Ti~~li~~~---~~k~A~kl~k~Fkv~dkrfw~lki~aLa~~~--~w~eL~~fa~skK---sPIGyepFv~~~~~ 249 (319)
T PF04840_consen 183 TIRKLIEMG---QEKQAEKLKKEFKVPDKRFWWLKIKALAENK--DWDELEKFAKSKK---SPIGYEPFVEACLK 249 (319)
T ss_pred HHHHHHHCC---CHHHHHHHHHHcCCcHHHHHHHHHHHHHhcC--CHHHHHHHHhCCC---CCCChHHHHHHHHH
Confidence 444554444 4566667777773 23333456678888899 9999999987644 35999999999975
No 38
>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=49.68 E-value=1e+02 Score=22.61 Aligned_cols=28 Identities=11% Similarity=0.249 Sum_probs=19.9
Q ss_pred HHHHHHHHHHHHHHHHhhCCCCCHHHHHHH
Q 033727 49 LFYSDSARLIQNIEQTLSNRPVDFSRLDDI 78 (112)
Q Consensus 49 ~F~~~~~~~l~~L~~a~~~~~~D~~~l~~~ 78 (112)
..+++..+.+.+++++++++ |.+.+.++
T Consensus 228 ~~l~~~~~~L~~l~~~l~~~--d~~~l~~~ 255 (258)
T PF02153_consen 228 EALDEFIKELNELREALEAG--DEEELEEL 255 (258)
T ss_dssp HHHHHHHHHHHHHHHHHHTT--SHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHcC--CHHHHHHH
Confidence 33444455577888889999 99887754
No 39
>PLN02407 diphosphomevalonate decarboxylase
Probab=48.90 E-value=37 Score=26.68 Aligned_cols=32 Identities=19% Similarity=0.400 Sum_probs=28.0
Q ss_pred HHHHHHHH-HHHHHHHHHHHhhCCCCCHHHHHHHH
Q 033727 46 VVSLFYSD-SARLIQNIEQTLSNRPVDFSRLDDIL 79 (112)
Q Consensus 46 li~~F~~~-~~~~l~~L~~a~~~~~~D~~~l~~~a 79 (112)
+.+..++. +++.+..+++|+.++ |+..+.+++
T Consensus 224 ~~~~w~~~~~~~~~~~~~~Ai~~~--Df~~~gei~ 256 (343)
T PLN02407 224 LLQHRAKEVVPKRILQMEEAIKNR--DFASFAKLT 256 (343)
T ss_pred hHHHHHHhhhHHHHHHHHHHHHhc--CHHHHHHHH
Confidence 56777888 899999999999999 999988765
No 40
>cd08330 CARD_ASC_NALP1 Caspase activation and recruitment domain found in Human ASC, NALP1, and similar proteins. Caspase activation and recruitment domain (CARD) similar to those found in human ASC (Apoptosis-associated speck-like protein containing a CARD) and NALP1 (CARD7, NLRP1). ASC, an adaptor molecule, and NALP1, a member of the Nod-like receptor (NLR) family, are involved in the assembly of the 'inflammasome', a multiprotein platform, which is responsible for caspase-1 activation and regulation of IL-1beta maturation. In general, CARDs are death domains (DDs) associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and DED (Death Effector Domain). They se
Probab=46.60 E-value=66 Score=19.60 Aligned_cols=56 Identities=16% Similarity=0.092 Sum_probs=42.6
Q ss_pred HHHHhcccCCCCCCHHHHHHHHccccCCChHHHHHHHHHHHHHHHHHHHHHHHHhhCC
Q 033727 11 LYMRRSLFDQGYLDSEQLIQLEDLQDDANPNFVEEVVSLFYSDSARLIQNIEQTLSNR 68 (112)
Q Consensus 11 ~~~~~~~~~~~~lD~~~l~~L~~l~~~~~~~~~~eli~~F~~~~~~~l~~L~~a~~~~ 68 (112)
...+..+...++|..+..+.++.-. ..++-..+|++.-..-.+.....+.+++...
T Consensus 18 ~~ilD~L~~~~Vit~e~~~~I~a~~--T~~~kar~Lld~l~~kG~~A~~~F~~~L~e~ 73 (82)
T cd08330 18 DPILDKLHGKKVITQEQYSEVRAEK--TNQEKMRKLFSFVRSWGASCKDIFYQILREE 73 (82)
T ss_pred HHHHHHHHHCCCCCHHHHHHHHcCC--CcHHHHHHHHHHHHccCHHHHHHHHHHHHHh
Confidence 5567778888899988888887643 4677778888887777788778888877655
No 41
>PRK13916 plasmid segregation protein ParR; Provisional
Probab=45.41 E-value=49 Score=20.88 Aligned_cols=29 Identities=10% Similarity=0.216 Sum_probs=23.3
Q ss_pred HHHHHHccccCCChHHHHHHHHHHHHHHH
Q 033727 27 QLIQLEDLQDDANPNFVEEVVSLFYSDSA 55 (112)
Q Consensus 27 ~l~~L~~l~~~~~~~~~~eli~~F~~~~~ 55 (112)
.|+-|..+-++.-+.|++++++.|+++..
T Consensus 20 iF~FL~~~P~GT~~~~iR~~L~rYI~~~G 48 (97)
T PRK13916 20 IFDFLENVPRGTKTAHIREALRRYIEEIG 48 (97)
T ss_pred HHHHHHHCCCCCccHHHHHHHHHHHHhcC
Confidence 36667777766789999999999998864
No 42
>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=45.34 E-value=16 Score=21.22 Aligned_cols=39 Identities=26% Similarity=0.428 Sum_probs=28.5
Q ss_pred CHHHHHHHHccccCCChHHHHHHHHHHHHHHHHHHHHHHH
Q 033727 24 DSEQLIQLEDLQDDANPNFVEEVVSLFYSDSARLIQNIEQ 63 (112)
Q Consensus 24 D~~~l~~L~~l~~~~~~~~~~eli~~F~~~~~~~l~~L~~ 63 (112)
+..+|..++++.. .+|+++..++...-.+.|..+..|.+
T Consensus 6 ~~Pqf~~lR~~vq-~NP~lL~~lLqql~~~nP~l~q~I~~ 44 (59)
T PF09280_consen 6 NNPQFQQLRQLVQ-QNPQLLPPLLQQLGQSNPQLLQLIQQ 44 (59)
T ss_dssp TSHHHHHHHHHHH-C-GGGHHHHHHHHHCCSHHHHHHHHH
T ss_pred cChHHHHHHHHHH-HCHHHHHHHHHHHhccCHHHHHHHHH
Confidence 3356888888753 38888888888888888887776665
No 43
>PF11563 Protoglobin: Protoglobin; PDB: 2VEE_G 3QZZ_A 3R0G_A 3QZX_A 2VEB_A 1OR6_A 1OR4_B 2W31_B.
Probab=44.04 E-value=92 Score=20.49 Aligned_cols=55 Identities=15% Similarity=0.154 Sum_probs=37.9
Q ss_pred hHHHHHHHHHHHhcccCCCCCCHHHHHHHHcccc-----CCChHHHHHHHHHHHHHHHHHH
Q 033727 3 SNQLQHQVLYMRRSLFDQGYLDSEQLIQLEDLQD-----DANPNFVEEVVSLFYSDSARLI 58 (112)
Q Consensus 3 ~~~l~~~~~~~~~~~~~~~~lD~~~l~~L~~l~~-----~~~~~~~~eli~~F~~~~~~~l 58 (112)
.+.|+..+..|+..+++.+ +|.+.+.....++. +-+|.++......+.+...+.+
T Consensus 60 ~~~lk~~q~~~~~~l~s~~-~d~~y~~~~~~iG~~H~~igl~~~~~~~~~~~~~~~l~~~l 119 (158)
T PF11563_consen 60 IERLKATQRRHWRELFSGD-FDEEYVERRRRIGQVHARIGLPPRWYIGAYSFLREFLLEAL 119 (158)
T ss_dssp HHHHHHHHHHHHHHCTSS--CSHHHHHHHHHHHHHHHHCT--HHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHhCCC-chHHHHHHHHHHHHHHhHcCCCHHHHHHHHHHHHHHHHHHH
Confidence 4789999999999999976 88787777766643 4467777666666666554433
No 44
>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=43.63 E-value=66 Score=18.99 Aligned_cols=57 Identities=11% Similarity=0.184 Sum_probs=37.1
Q ss_pred HHHHHhcccCCCCCCHHHHHHHHccccCCChHHHHHHHHHHHHHHHHHHHHHHHHhhCC
Q 033727 10 VLYMRRSLFDQGYLDSEQLIQLEDLQDDANPNFVEEVVSLFYSDSARLIQNIEQTLSNR 68 (112)
Q Consensus 10 ~~~~~~~~~~~~~lD~~~l~~L~~l~~~~~~~~~~eli~~F~~~~~~~l~~L~~a~~~~ 68 (112)
+...+..+...++|..+..+.+.... ...+-...+++......+.....+-.++...
T Consensus 18 ~~~ild~L~~~~vlt~~e~e~I~~~~--t~~~k~~~LLd~l~~kg~~a~~~F~~~L~~~ 74 (85)
T PF00619_consen 18 LDDILDHLLSRGVLTEEEYEEIRSEP--TRQDKARKLLDILKRKGPEAFDIFCQALREN 74 (85)
T ss_dssp HHHHHHHHHHTTSSSHHHHHHHHTSS--SHHHHHHHHHHHHHHCCHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHCCCCCHHHHHHHHccC--ChHHHHHHHHHHHHHHCHHHHHHHHHHHHhh
Confidence 33455556677888877777777632 3456677777777766666666666666543
No 45
>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=43.35 E-value=48 Score=17.32 Aligned_cols=32 Identities=22% Similarity=0.293 Sum_probs=15.2
Q ss_pred HHHHHHccccCCChHHHHHHHHHHHHHHHHHH
Q 033727 27 QLIQLEDLQDDANPNFVEEVVSLFYSDSARLI 58 (112)
Q Consensus 27 ~l~~L~~l~~~~~~~~~~eli~~F~~~~~~~l 58 (112)
.+..|+++-++-+++++..++..+-.+.+..+
T Consensus 4 ~v~~L~~mFP~~~~~~I~~~L~~~~~~ve~ai 35 (42)
T PF02845_consen 4 MVQQLQEMFPDLDREVIEAVLQANNGDVEAAI 35 (42)
T ss_dssp HHHHHHHHSSSS-HHHHHHHHHHTTTTHHHHH
T ss_pred HHHHHHHHCCCCCHHHHHHHHHHcCCCHHHHH
Confidence 45555555544455555555444444444333
No 46
>cd08329 CARD_BIRC2_BIRC3 Caspase activation and recruitment domain found in Baculoviral IAP repeat-containing proteins, BIRC2 (c-IAP1) and BIRC3 (c-IAP2). Caspase activation and recruitment domain (CARD) similar to those found in Baculoviral IAP repeat (BIR)-containing protein 2 (BIRC2) or cellular Inhibitor of Apoptosis Protein 1 (c-IAP1), and BIRC3 (or c-IAP2). IAPs are anti-apoptotic proteins that contain at least one BIR domain. Most IAPs also contain a C-terminal RING domain. In addition, both BIRC2 and BIRC3 contain a CARD. BIRC2 and BIRC3, through their binding with TRAF (TNF receptor-associated factor) 2, are recruited to TNFR-1/2 signaling complexes, where they regulate caspase-8 activity. They also play important roles in pro-survival NF-kB signaling pathways. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation and host-defense mechanisms. DDs are protein-protein interac
Probab=43.01 E-value=84 Score=19.73 Aligned_cols=65 Identities=11% Similarity=0.151 Sum_probs=47.7
Q ss_pred ChHHHHHHHH---HHHhcccCCCCCCHHHHHHHHccccCCChHHHHHHHHHHHHHHHHHHHHHHHHhhCC
Q 033727 2 NSNQLQHQVL---YMRRSLFDQGYLDSEQLIQLEDLQDDANPNFVEEVVSLFYSDSARLIQNIEQTLSNR 68 (112)
Q Consensus 2 ~~~~l~~~~~---~~~~~~~~~~~lD~~~l~~L~~l~~~~~~~~~~eli~~F~~~~~~~l~~L~~a~~~~ 68 (112)
|+.+|-..+. ..+..+...++|+.+..+.++.-.. ..+-..+||+....-.+.-...+.+++.+.
T Consensus 14 ~R~~Lv~~l~~v~~ilD~Ll~~~Vlt~ee~e~I~~~~t--~~~qAr~Lld~l~~KG~~A~~~F~~~L~e~ 81 (94)
T cd08329 14 NRMALFQHLTSVLPILDSLLSANVITEQEYDVIKQKTQ--TPLQARELIDTVLVKGNAAAEVFRNCLKKN 81 (94)
T ss_pred hHHHHHHHHhhhHHHHHHHHHcCCCCHHHHHHHHcCCC--hHHHHHHHHHHHHhhhHHHHHHHHHHHHhc
Confidence 3455555552 3667778889999887888876432 457778888888888888888888888765
No 47
>PRK01356 hscB co-chaperone HscB; Provisional
Probab=42.92 E-value=1.1e+02 Score=21.19 Aligned_cols=42 Identities=12% Similarity=0.112 Sum_probs=25.6
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHhhh
Q 033727 40 PNFVEEVVSLFYSDSARLIQNIEQTLSNRPVDFSRLDDILHQFK 83 (112)
Q Consensus 40 ~~~~~eli~~F~~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~LK 83 (112)
.+-+.++....-......+..|.++++.+ ||+.+...+-+||
T Consensus 108 ~~~L~~l~~~~~~~~~~~~~~l~~~f~~~--d~~~A~~~~~~L~ 149 (166)
T PRK01356 108 FSDLEKIKNKYELMYKNEIDSLKQAFEEQ--NLSDATIKTSKLK 149 (166)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhcC--CHHHHHHHHHHHH
Confidence 33344444444444455666777888888 8877776665554
No 48
>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=41.89 E-value=97 Score=23.12 Aligned_cols=51 Identities=12% Similarity=0.296 Sum_probs=38.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHhhhhhhhhhcHHHHHHHHHHHHH
Q 033727 42 FVEEVVSLFYSDSARLIQNIEQTLSNRPVDFSRLDDILHQFKGSCSSIGAKKVKDACSQFRE 103 (112)
Q Consensus 42 ~~~eli~~F~~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~LKGsa~~lGa~~l~~~~~~lE~ 103 (112)
-..++++.++.-+...++.+...+..+ +++....-++.+ .++-.+..++|.
T Consensus 54 t~hQIlEsWi~~a~~LL~ri~~~i~~~--~~ekAa~dc~~v---------ERiWKLL~eieD 104 (261)
T PF07014_consen 54 TTHQILESWIHVARKLLERIEERIEAR--DFEKAASDCWIV---------ERIWKLLAEIED 104 (261)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHcc--cHHHHHhHHHHH---------HHHHHHHHHHHH
Confidence 356789999999999999999999999 988777666554 344555555443
No 49
>cd08332 CARD_CASP2 Caspase activation and recruitment domain of Caspase-2. Caspase activation and recruitment domain (CARD) similar to that found in caspase-2. Caspases are aspartate-specific cysteine proteases with functions in apoptosis and immune signaling. Caspase-2 (also known as ICH1, NEDD2, or CASP2) is one of the most evolutionarily conserved caspases, and plays a role in apoptosis, DNA damage response, cell cycle regulation, and tumor suppression. It is localized in the nucleus and exhibits properties of both an initiator and an effector caspase. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and
Probab=41.65 E-value=86 Score=19.46 Aligned_cols=55 Identities=9% Similarity=0.061 Sum_probs=35.2
Q ss_pred HHHhcccCCCCCCHHHHHHHHccccCCChHHHHHHHHHHHHHHHHHHHHHHHHhhCC
Q 033727 12 YMRRSLFDQGYLDSEQLIQLEDLQDDANPNFVEEVVSLFYSDSARLIQNIEQTLSNR 68 (112)
Q Consensus 12 ~~~~~~~~~~~lD~~~l~~L~~l~~~~~~~~~~eli~~F~~~~~~~l~~L~~a~~~~ 68 (112)
..+..+...+++..+..+.+..... ..+-...+++..-.-.+.-...+-.++...
T Consensus 24 ~v~~~L~~~gvlt~~~~~~I~~~~t--~~~k~~~Lld~L~~RG~~AF~~F~~aL~~~ 78 (90)
T cd08332 24 ELLIHLLQKDILTDSMAESIMAKPT--SFSQNVALLNLLPKRGPRAFSAFCEALRET 78 (90)
T ss_pred HHHHHHHHcCCCCHHHHHHHHcCCC--cHHHHHHHHHHHHHhChhHHHHHHHHHHhc
Confidence 3444556667888777777766532 455566677776666677777777766554
No 50
>PF04400 DUF539: Protein of unknown function (DUF539); InterPro: IPR007495 This is a family of putative periplasmic proteins.
Probab=41.57 E-value=2.7 Score=23.28 Aligned_cols=18 Identities=39% Similarity=0.912 Sum_probs=13.6
Q ss_pred hhhhhhhhhcHHHHHHHH
Q 033727 81 QFKGSCSSIGAKKVKDAC 98 (112)
Q Consensus 81 ~LKGsa~~lGa~~l~~~~ 98 (112)
.||||+|-+++..+...|
T Consensus 7 ~I~GSCGGl~~lGi~~~C 24 (45)
T PF04400_consen 7 PIKGSCGGLGALGIDKEC 24 (45)
T ss_pred cccccchhhhhcCCCccC
Confidence 589999999987664443
No 51
>PF14615 Rsa3: Ribosome-assembly protein 3
Probab=39.79 E-value=68 Score=17.76 Aligned_cols=39 Identities=3% Similarity=0.061 Sum_probs=24.3
Q ss_pred HHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHhhhhhhhh
Q 033727 47 VSLFYSDSARLIQNIEQTLSNRPVDFSRLDDILHQFKGSCSS 88 (112)
Q Consensus 47 i~~F~~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~LKGsa~~ 88 (112)
+....++..+.+.+|+++ +.-.-..+.-++|.||..+..
T Consensus 7 l~~~t~efgdDLd~lR~~---~dF~~~sl~~Li~aL~~G~~~ 45 (47)
T PF14615_consen 7 LQRLTDEFGDDLDELRKA---PDFTDKSLPLLIDALQQGTDM 45 (47)
T ss_pred HHHHHHHHHHHHHHHhcC---CCCCchhHHHHHHHHHhcccc
Confidence 444445555557778754 311236788899999987654
No 52
>PRK09613 thiH thiamine biosynthesis protein ThiH; Reviewed
Probab=39.59 E-value=64 Score=26.32 Aligned_cols=68 Identities=10% Similarity=0.147 Sum_probs=42.4
Q ss_pred ccCCCCCCHHHHHHHHccccCCChHHHHHHHHHHHHHHHHHHHHHHHHhhCC-CCCHHHHHHHHHhhhh
Q 033727 17 LFDQGYLDSEQLIQLEDLQDDANPNFVEEVVSLFYSDSARLIQNIEQTLSNR-PVDFSRLDDILHQFKG 84 (112)
Q Consensus 17 ~~~~~~lD~~~l~~L~~l~~~~~~~~~~eli~~F~~~~~~~l~~L~~a~~~~-~~D~~~l~~~aH~LKG 84 (112)
...+.+||.+.|..+.+-....+++.+.++++.-+....-..++....+... +.++..+.+.|+++|=
T Consensus 7 ~~~~~~i~~~~i~~~l~~~~~~~~~~v~~il~Kal~~~~Ls~eEal~LL~~~~~~~le~L~~~A~~ir~ 75 (469)
T PRK09613 7 ENAADFIDDEEIEELLEKAKNPDKDEIREILEKAKEKKGLSPEEAAVLLNVEDPELLEEIFEAAREIKE 75 (469)
T ss_pred hhhhhhcCHHHHHHHHHhccCCCHHHHHHHHHHHHcCCCCCHHHHHHHHcCCChhHHHHHHHHHHHHHH
Confidence 3345788988877776664444666678888877654333334444444443 1146788888888873
No 53
>PF07818 HCNGP: HCNGP-like protein; InterPro: IPR012479 This family comprises sequences bearing significant similarity to the mouse transcriptional regulator protein HCNGP (Q02614 from SWISSPROT). This protein is localised to the nucleus and is thought to be involved in the regulation of beta-2-microglobulin genes.
Probab=39.26 E-value=55 Score=20.79 Aligned_cols=44 Identities=16% Similarity=0.323 Sum_probs=29.0
Q ss_pred hHHHHHHHHHHHhcccCCCCCCHHHHHHHHccccCCChHHHHHHHHHH
Q 033727 3 SNQLQHQVLYMRRSLFDQGYLDSEQLIQLEDLQDDANPNFVEEVVSLF 50 (112)
Q Consensus 3 ~~~l~~~~~~~~~~~~~~~~lD~~~l~~L~~l~~~~~~~~~~eli~~F 50 (112)
.++|+++...|..-...---++ +.|..=..+. +|.++..|++.|
T Consensus 10 ~~~l~~Ki~~fl~lk~~G~~fN-~~L~~s~~fr---NP~i~ekLi~~~ 53 (96)
T PF07818_consen 10 DPELQAKIAKFLELKRQGIHFN-DRLQNSKSFR---NPSILEKLIEFF 53 (96)
T ss_pred CHHHHHHHHHHHHHHHcCCCHH-HHHHHccccC---ChHHHHHHHHHc
Confidence 3678999999988776432344 3344444444 899888877655
No 54
>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=39.03 E-value=47 Score=21.80 Aligned_cols=47 Identities=11% Similarity=0.196 Sum_probs=33.2
Q ss_pred HHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHhhhhhhhhhcHHHHHHHHHHHHHHH
Q 033727 47 VSLFYSDSARLIQNIEQTLSNRPVDFSRLDDILHQFKGSCSSIGAKKVKDACSQFREYC 105 (112)
Q Consensus 47 i~~F~~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~LKGsa~~lGa~~l~~~~~~lE~~~ 105 (112)
...|+..+.+.+..+..|..++ |...++.++ +-.-+..++.++....
T Consensus 17 ~~~F~~~ak~~f~~i~~A~~~~--D~~~l~~~~----------t~~~~~~~~~~i~~~~ 63 (147)
T PF04280_consen 17 PAAFLEEAKEAFLPIQEAWAKG--DLEALRPLL----------TEELYERLQAEIKARR 63 (147)
T ss_dssp HHHHHHHHHHTHHHHHHHHHHT---HHHHHHHB-----------HHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHcC--CHHHHHHHh----------CHHHHHHHHHHHHHHH
Confidence 5789999999999999999999 998877653 3344445555555543
No 55
>PRK12491 pyrroline-5-carboxylate reductase; Reviewed
Probab=37.83 E-value=74 Score=23.67 Aligned_cols=71 Identities=8% Similarity=0.120 Sum_probs=43.5
Q ss_pred HHHHHHHHhcccCCCCCCHHHHHHHHccccCCChHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHH-HHhhhhh
Q 033727 7 QHQVLYMRRSLFDQGYLDSEQLIQLEDLQDDANPNFVEEVVSLFYSDSARLIQNIEQTLSNRPVDFSRLDDI-LHQFKGS 85 (112)
Q Consensus 7 ~~~~~~~~~~~~~~~~lD~~~l~~L~~l~~~~~~~~~~eli~~F~~~~~~~l~~L~~a~~~~~~D~~~l~~~-aH~LKGs 85 (112)
++.+..++.++=..-+++.+.++.+-.+. ..+|.|+-.+++.+.+-..+ . -.+.+..+++ +++++|+
T Consensus 144 ~~~v~~lf~~~G~~~~~~E~~~d~~tals-gsgPAf~~~~~eal~~a~v~----------~-Gl~~~~A~~l~~~t~~G~ 211 (272)
T PRK12491 144 IKEVLNIFNIFGQTEVVNEKLMDVVTSIS-GSSPAYVYMFIEAMADAAVL----------G-GMPRKQAYKFAAQAVLGS 211 (272)
T ss_pred HHHHHHHHHcCCCEEEEcHHHhhhHHHhc-cCcHHHHHHHHHHHHHHHHH----------c-CCCHHHHHHHHHHHHHHH
Confidence 34445555554444667878888888886 35899888877766654432 1 1244444444 4557777
Q ss_pred hhhh
Q 033727 86 CSSI 89 (112)
Q Consensus 86 a~~l 89 (112)
+..+
T Consensus 212 a~ll 215 (272)
T PRK12491 212 AKMV 215 (272)
T ss_pred HHHH
Confidence 7554
No 56
>PF14276 DUF4363: Domain of unknown function (DUF4363)
Probab=37.01 E-value=1.1e+02 Score=19.56 Aligned_cols=41 Identities=12% Similarity=0.245 Sum_probs=29.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHhhhh
Q 033727 42 FVEEVVSLFYSDSARLIQNIEQTLSNRPVDFSRLDDILHQFKG 84 (112)
Q Consensus 42 ~~~eli~~F~~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~LKG 84 (112)
+....+..+.++....++.+++.+.++ ||+......=.+..
T Consensus 16 ~~~~~l~~~~~~i~~~l~~i~~~i~~~--dW~~A~~~~~~l~~ 56 (121)
T PF14276_consen 16 FSNNYLNNSTDSIEEQLEQIEEAIENE--DWEKAYKETEELEK 56 (121)
T ss_pred HHHhhhhhHHHHHHHHHHHHHHHHHhC--CHHHHHHHHHHHHH
Confidence 334456677788888888888888888 88877765544433
No 57
>PF01322 Cytochrom_C_2: Cytochrome C'; InterPro: IPR002321 Cytochromes c (cytC) can be defined as electron-transfer proteins having one or several haem c groups, bound to the protein by one or, more generally, two thioether bonds involving sulphydryl groups of cysteine residues. The fifth haem iron ligand is always provided by a histidine residue. CytC possess a wide range of properties and function in a large number of different redox processes. Ambler [] recognised four classes of cytC. Class II includes the high-spin cytC' and a number of low-spin cytochromes, e.g. cyt c-556. The haem-attachment site is close to the C terminus. The cytC' are capable of binding such ligands as CO, NO or CN(-), albeit with rate and equilibrium constants 100 to 1,000,000-fold smaller than other high-spin haemoproteins []. This, coupled with its relatively low redox potential, makes it unlikely that cytC' is a terminal oxidase. Thus cytC' probably functions as an electron transfer protein []. The 3D structures of a number of cytC' have been determined. The molecule usually exists as a dimer, each monomer folding as a four-alpha-helix bundle incorporating a covalently-bound haem group at the core []. The Chromatium vinosum cytC' exhibits dimer dissociation upon ligand binding [].; GO: 0005506 iron ion binding, 0009055 electron carrier activity, 0020037 heme binding, 0005746 mitochondrial respiratory chain; PDB: 1BBH_A 2J9B_B 2J8W_A 1JAF_B 3ZTM_A 2XLD_A 2XL6_A 1E86_A 2YLD_A 2YKZ_A ....
Probab=36.45 E-value=1.2e+02 Score=19.48 Aligned_cols=40 Identities=8% Similarity=0.185 Sum_probs=28.4
Q ss_pred HHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHhhhhhhhh
Q 033727 47 VSLFYSDSARLIQNIEQTLSNRPVDFSRLDDILHQFKGSCSS 88 (112)
Q Consensus 47 i~~F~~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~LKGsa~~ 88 (112)
+..+..........|..+...+ |...+......+.++|..
T Consensus 77 F~~~~~~~~~aa~~L~~aa~~~--d~~~~~~a~~~v~~~C~a 116 (122)
T PF01322_consen 77 FKQLAQAFQKAAAALAAAAKSG--DLAAIKAAFGEVGKSCKA 116 (122)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHT--SHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHhcC--CHHHHHHHHHHHHHHHHH
Confidence 3444455555667788888888 999888888777777754
No 58
>PF08822 DUF1804: Protein of unknown function (DUF1804); InterPro: IPR014926 This entry is represented by Bacteriophage D3112, Orf24. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=36.42 E-value=1.5e+02 Score=20.84 Aligned_cols=41 Identities=7% Similarity=0.123 Sum_probs=34.0
Q ss_pred CCHHHHHHHHccccCCChHHHHHHHHHHHHHHHHHHHHHHH
Q 033727 23 LDSEQLIQLEDLQDDANPNFVEEVVSLFYSDSARLIQNIEQ 63 (112)
Q Consensus 23 lD~~~l~~L~~l~~~~~~~~~~eli~~F~~~~~~~l~~L~~ 63 (112)
=||+.+..-..+.+++-.++...++..|+-+....+++|+.
T Consensus 48 DDWDk~RaA~~laggg~e~v~~~~l~~f~~Q~~~tmeel~~ 88 (165)
T PF08822_consen 48 DDWDKARAAHTLAGGGIEDVARQMLEDFVVQYQATMEELKE 88 (165)
T ss_pred CcHHHHHHHHHhccCcHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 57777777777776666789999999999999999999984
No 59
>PRK11199 tyrA bifunctional chorismate mutase/prephenate dehydrogenase; Provisional
Probab=35.64 E-value=2.1e+02 Score=22.27 Aligned_cols=64 Identities=9% Similarity=0.147 Sum_probs=36.7
Q ss_pred CChHHHHHHHHH------HHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHhhhhhhhhhcHHHHHHHHHHHHH
Q 033727 38 ANPNFVEEVVSL------FYSDSARLIQNIEQTLSNRPVDFSRLDDILHQFKGSCSSIGAKKVKDACSQFRE 103 (112)
Q Consensus 38 ~~~~~~~eli~~------F~~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~LKGsa~~lGa~~l~~~~~~lE~ 103 (112)
++|.++.+++.. -+++..+.+..++.++.++ |.+.+.+.--+-|..-|...=..+...-.-+|.
T Consensus 298 ~~p~lw~dI~~~N~~~~~~l~~~~~~l~~l~~~l~~~--d~~~l~~~~~~a~~~~~~~~~~~~~~~~~~~~~ 367 (374)
T PRK11199 298 QDPQLYADIIMSSPENLALIKRYYQRFGEALELLEQG--DKQAFIDSFRKVEHWFGDYAEQFLKESRSLLQQ 367 (374)
T ss_pred CCHHHHHHHHHhChhHHHHHHHHHHHHHHHHHHHHcC--CHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHH
Confidence 356666655421 1344445577788889889 999988876655554443333333333333443
No 60
>TIGR01240 mevDPdecarb diphosphomevalonate decarboxylase. Alternate names: mevalonate diphosphate decarboxylase; pyrophosphomevalonate decarboxylase
Probab=35.41 E-value=81 Score=24.09 Aligned_cols=32 Identities=6% Similarity=0.169 Sum_probs=26.9
Q ss_pred HHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHH
Q 033727 46 VVSLFYSDSARLIQNIEQTLSNRPVDFSRLDDIL 79 (112)
Q Consensus 46 li~~F~~~~~~~l~~L~~a~~~~~~D~~~l~~~a 79 (112)
++...+++....+..+.+++.++ |++.+.+++
T Consensus 201 ~~~~~v~~~~~~l~~~~~ai~~~--D~~~~g~~~ 232 (305)
T TIGR01240 201 LFKEWIEHVVPDFEVXRKAIKTK--DFATFGKET 232 (305)
T ss_pred cHHHHHHHHHHHHHHHHHHHHhc--cHHHHHHHH
Confidence 46677888887899999999999 999887765
No 61
>KOG2833 consensus Mevalonate pyrophosphate decarboxylase [Lipid transport and metabolism]
Probab=34.54 E-value=88 Score=24.72 Aligned_cols=32 Identities=16% Similarity=0.350 Sum_probs=25.3
Q ss_pred HHHHHHHH-HHHHHHHHHHHhhCCCCCHHHHHHHH
Q 033727 46 VVSLFYSD-SARLIQNIEQTLSNRPVDFSRLDDIL 79 (112)
Q Consensus 46 li~~F~~~-~~~~l~~L~~a~~~~~~D~~~l~~~a 79 (112)
++..=+++ .|+++.+|++++.++ ||+.+.++.
T Consensus 223 L~qhRi~~vVP~Ri~~m~eaI~~r--DF~~FA~lT 255 (395)
T KOG2833|consen 223 LLQHRIESVVPQRIQQMREAIRER--DFESFAKLT 255 (395)
T ss_pred HHHHHHHhhhHHHHHHHHHHHHhc--CHHHHHHHH
Confidence 44444555 689999999999999 999887763
No 62
>cd01671 CARD Caspase activation and recruitment domain: a protein-protein interaction domain. Caspase activation and recruitment domains (CARDs) are death domains (DDs) found associated with caspases. Caspases are aspartate-specific cysteine proteases with functions in apoptosis, immune signaling, inflammation, and host-defense mechanisms. In addition to caspases, proteins containing CARDs include adaptor proteins such as RAIDD, CARD9, and RIG-I-like helicases, which can form mutliprotein complexes and play important roles in mediating the signals to induce immune and inflammatory responses. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and DED (Death Effector Domain). They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=34.25 E-value=98 Score=18.00 Aligned_cols=58 Identities=14% Similarity=0.231 Sum_probs=42.9
Q ss_pred HHHHHHhcccCCCCCCHHHHHHHHccccCCChHHHHHHHHHHHHHHHHHHHHHHHHhhCC
Q 033727 9 QVLYMRRSLFDQGYLDSEQLIQLEDLQDDANPNFVEEVVSLFYSDSARLIQNIEQTLSNR 68 (112)
Q Consensus 9 ~~~~~~~~~~~~~~lD~~~l~~L~~l~~~~~~~~~~eli~~F~~~~~~~l~~L~~a~~~~ 68 (112)
....++..+...++++.+..+.+..... ..+-..++++.-..-.+.....+-.++...
T Consensus 14 ~~~~il~~L~~~~vlt~~e~~~i~~~~~--~~~k~~~Lld~l~~kg~~af~~F~~~L~~~ 71 (80)
T cd01671 14 DVEDVLDHLLSDGVLTEEEYEKIRSEST--RQDKARKLLDILPRKGPKAFQSFLQALQET 71 (80)
T ss_pred cHHHHHHHHHHcCCCCHHHHHHHHcCCC--hHHHHHHHHHHHHhcChHHHHHHHHHHHhc
Confidence 4466777788889999877777776542 567777777777777777777777777665
No 63
>COG3433 Aryl carrier domain [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=32.26 E-value=77 Score=19.34 Aligned_cols=26 Identities=15% Similarity=0.279 Sum_probs=19.5
Q ss_pred CHHHHHHHHHhhhhhhhhhcHHHHHH
Q 033727 71 DFSRLDDILHQFKGSCSSIGAKKVKD 96 (112)
Q Consensus 71 D~~~l~~~aH~LKGsa~~lGa~~l~~ 96 (112)
|--.+..++|+.|--.+.+++..|++
T Consensus 30 DSiR~M~L~~~wR~~G~~i~F~~La~ 55 (74)
T COG3433 30 DSIRMMALLERWRKRGADIDFAQLAA 55 (74)
T ss_pred hHHHHHHHHHHHHHcCCcccHHHHHh
Confidence 55566788888888888888777764
No 64
>PTZ00431 pyrroline carboxylate reductase; Provisional
Probab=32.18 E-value=96 Score=22.69 Aligned_cols=71 Identities=10% Similarity=0.129 Sum_probs=46.8
Q ss_pred HHHHHHHHhcccCCCCCCHHHHHHHHccccCCChHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHH-HHHHHhhhhh
Q 033727 7 QHQVLYMRRSLFDQGYLDSEQLIQLEDLQDDANPNFVEEVVSLFYSDSARLIQNIEQTLSNRPVDFSRL-DDILHQFKGS 85 (112)
Q Consensus 7 ~~~~~~~~~~~~~~~~lD~~~l~~L~~l~~~~~~~~~~eli~~F~~~~~~~l~~L~~a~~~~~~D~~~l-~~~aH~LKGs 85 (112)
.+.+..+++++=..-+++.+.++..-.+. ..+|.|+-.+++.|.+-..+ .+ .+.+.. .-.+++++|+
T Consensus 137 ~~~v~~l~~~~G~~~~v~E~~~d~~ta~~-gsgPA~~~~~~~al~~~~v~----------~G-l~~~~a~~l~~~~~~G~ 204 (260)
T PTZ00431 137 KKKVIDIFSACGIIQEIKEKDMDIATAIS-GCGPAYVFLFIESLIDAGVK----------NG-LNRDVSKNLVLQTILGS 204 (260)
T ss_pred HHHHHHHHHhCCcEEEEChHHcchhhhhc-CCHHHHHHHHHHHHHHHHHH----------cC-CCHHHHHHHHHHHHHHH
Confidence 45677778877777778877788888776 34799988888777654332 11 233333 3445777777
Q ss_pred hhhh
Q 033727 86 CSSI 89 (112)
Q Consensus 86 a~~l 89 (112)
+..+
T Consensus 205 a~ll 208 (260)
T PTZ00431 205 VHMV 208 (260)
T ss_pred HHHH
Confidence 7654
No 65
>PRK07417 arogenate dehydrogenase; Reviewed
Probab=31.72 E-value=1.3e+02 Score=22.17 Aligned_cols=26 Identities=12% Similarity=0.344 Sum_probs=17.1
Q ss_pred HHHHHHHHHHHHHHhhCCCCCHHHHHHH
Q 033727 51 YSDSARLIQNIEQTLSNRPVDFSRLDDI 78 (112)
Q Consensus 51 ~~~~~~~l~~L~~a~~~~~~D~~~l~~~ 78 (112)
+++..+.+.+++.+++.+ |.+.+.+.
T Consensus 241 l~~~~~~l~~~~~~l~~~--d~~~l~~~ 266 (279)
T PRK07417 241 LASYRQSLDQLEELIEQE--NWSALEQK 266 (279)
T ss_pred HHHHHHHHHHHHHHHHcC--CHHHHHHH
Confidence 334444467788888888 87766544
No 66
>COG1577 ERG12 Mevalonate kinase [Lipid metabolism]
Probab=30.97 E-value=2.5e+02 Score=21.64 Aligned_cols=59 Identities=17% Similarity=0.259 Sum_probs=44.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhCCCCC---HHHHHHHHHhhhhhhhhhcHHHHHHHHHHHHHHH
Q 033727 44 EEVVSLFYSDSARLIQNIEQTLSNRPVD---FSRLDDILHQFKGSCSSIGAKKVKDACSQFREYC 105 (112)
Q Consensus 44 ~eli~~F~~~~~~~l~~L~~a~~~~~~D---~~~l~~~aH~LKGsa~~lGa~~l~~~~~~lE~~~ 105 (112)
.+.+..|++...+...++..++.++ | +.++...+|.|=.+-+ +--..|..++...+.+.
T Consensus 199 ~~~~~~~~~~ig~~~~~a~~al~~~--d~e~lgelm~~nq~LL~~Lg-Vs~~~L~~lv~~a~~~G 260 (307)
T COG1577 199 PEVIDPILDAIGELVQEAEAALQTG--DFEELGELMNINQGLLKALG-VSTPELDELVEAARSLG 260 (307)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHhcc--cHHHHHHHHHHHHHHHHhcC-cCcHHHHHHHHHHHhcC
Confidence 3467888888889999999999999 9 4556778888766655 66667777666666443
No 67
>PF14165 YtzH: YtzH-like protein
Probab=30.28 E-value=65 Score=20.30 Aligned_cols=27 Identities=22% Similarity=0.357 Sum_probs=21.0
Q ss_pred HHHHHHHhcccCCCCCCHHHHHHHHcc
Q 033727 8 HQVLYMRRSLFDQGYLDSEQLIQLEDL 34 (112)
Q Consensus 8 ~~~~~~~~~~~~~~~lD~~~l~~L~~l 34 (112)
+|+.+.++||...+-||.+.-..|.++
T Consensus 29 EQieRLvksLm~n~~i~~~ik~~L~~I 55 (87)
T PF14165_consen 29 EQIERLVKSLMANPNIDADIKQTLEEI 55 (87)
T ss_pred HHHHHHHHHHHcCCCcCHHHHHHHHHH
Confidence 789999999999999996655555544
No 68
>PF14821 Thr_synth_N: Threonine synthase N terminus; PDB: 3V7N_A 1VB3_A 1KL7_A.
Probab=29.86 E-value=30 Score=20.97 Aligned_cols=32 Identities=28% Similarity=0.396 Sum_probs=19.4
Q ss_pred CCCCHHHHHHHHccccCCChHHHHHHHHHHH-HHHH
Q 033727 21 GYLDSEQLIQLEDLQDDANPNFVEEVVSLFY-SDSA 55 (112)
Q Consensus 21 ~~lD~~~l~~L~~l~~~~~~~~~~eli~~F~-~~~~ 55 (112)
|-++.+.|..+..+. -+++..+++..|+ .+.+
T Consensus 35 P~l~~~~l~~l~~~s---y~elA~~il~~f~~~di~ 67 (79)
T PF14821_consen 35 PKLSKEELEELKNLS---YAELAFEILSPFLGDDIP 67 (79)
T ss_dssp ----HHHHHHHTTS----HHHHHHHHHHHHCCCCS-
T ss_pred CCCCHHHHHHHHCCC---HHHHHHHHHHHHHccCCC
Confidence 456756666776664 6888889999998 5543
No 69
>PF14748 P5CR_dimer: Pyrroline-5-carboxylate reductase dimerisation; PDB: 2RCY_D 3TRI_A 2IZZ_B 2GR9_B 2GRA_B 2GER_C 1YQG_A 2AG8_A 3GT0_A 2AMF_E ....
Probab=29.75 E-value=81 Score=20.06 Aligned_cols=30 Identities=13% Similarity=0.242 Sum_probs=19.1
Q ss_pred CHHHHHHHHccccCCChHHHHHHHHHHHHHH
Q 033727 24 DSEQLIQLEDLQDDANPNFVEEVVSLFYSDS 54 (112)
Q Consensus 24 D~~~l~~L~~l~~~~~~~~~~eli~~F~~~~ 54 (112)
+.++|+.+-.+. +.+|.|+-.+++.+.+-.
T Consensus 2 ~E~~~d~~tals-GsgpA~~~~~~eal~~a~ 31 (107)
T PF14748_consen 2 DEDQFDAATALS-GSGPAYFFLFIEALADAA 31 (107)
T ss_dssp SGGGHHHHHHHC-TTHHHHHHHHHHHHHHHH
T ss_pred CHHHHhHHHHHh-ccHHHHHHHHHHHHHHHH
Confidence 445566666665 347888777777666543
No 70
>PRK08507 prephenate dehydrogenase; Validated
Probab=29.08 E-value=2.3e+02 Score=20.70 Aligned_cols=39 Identities=13% Similarity=0.349 Sum_probs=24.4
Q ss_pred CChHHHHHHHH-------HHHHHHHHHHHHHHHHhhCCCCCHHHHHHH
Q 033727 38 ANPNFVEEVVS-------LFYSDSARLIQNIEQTLSNRPVDFSRLDDI 78 (112)
Q Consensus 38 ~~~~~~~eli~-------~F~~~~~~~l~~L~~a~~~~~~D~~~l~~~ 78 (112)
.+|.++.+++. .-+++..+.+.++++++..+ |.+.+.+.
T Consensus 219 ~~p~l~~~i~~~N~~~~~~~l~~~~~~l~~~~~~l~~~--d~~~~~~~ 264 (275)
T PRK08507 219 SSPAMWSDIFKQNKENVLEAIDEFIKELEQFKQLIENE--DWEELEEW 264 (275)
T ss_pred CCHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHcC--CHHHHHHH
Confidence 36666666542 23445555577788888888 87766543
No 71
>PHA01794 hypothetical protein
Probab=28.81 E-value=1.4e+02 Score=20.23 Aligned_cols=51 Identities=8% Similarity=0.199 Sum_probs=32.4
Q ss_pred HHHHHhccc-CCCCCCHHHHHHHHccccCCChHHHHHHHHHHHHHHHHHHHHHHH
Q 033727 10 VLYMRRSLF-DQGYLDSEQLIQLEDLQDDANPNFVEEVVSLFYSDSARLIQNIEQ 63 (112)
Q Consensus 10 ~~~~~~~~~-~~~~lD~~~l~~L~~l~~~~~~~~~~eli~~F~~~~~~~l~~L~~ 63 (112)
..+||.... +++-.. ..|.+|++-+- ...|+..=+..|++..++.+.-|..
T Consensus 59 I~d~v~~~~~Ee~~~e-~lF~eleqEm~--~SGFF~~ki~kyien~EK~~~yl~~ 110 (134)
T PHA01794 59 IADFVETFEDEEGTTE-GLFAELEKEMV--DSGFFRAKIKKYIENMEKSARYLKA 110 (134)
T ss_pred HHHHHHHhhhhcchHH-HHHHHHHHHHH--HhhHHHHHHHHHHHHHHHHHHHhhc
Confidence 455665554 333322 45667754332 5678888888999988888777765
No 72
>PF14942 Muted: Organelle biogenesis, Muted-like protein
Probab=28.48 E-value=2e+02 Score=19.69 Aligned_cols=61 Identities=13% Similarity=0.325 Sum_probs=33.0
Q ss_pred hHHHHHHHHHHHhccc-CCCCCCHHHHHHHHccccCCChHHHHHHHHHHHHHHHHHHHHHHH
Q 033727 3 SNQLQHQVLYMRRSLF-DQGYLDSEQLIQLEDLQDDANPNFVEEVVSLFYSDSARLIQNIEQ 63 (112)
Q Consensus 3 ~~~l~~~~~~~~~~~~-~~~~lD~~~l~~L~~l~~~~~~~~~~eli~~F~~~~~~~l~~L~~ 63 (112)
++-++.+..+|++-+. ..+.=+...|..+..+..+.+...+...+..--+..+.....|..
T Consensus 16 rpvIqgEI~~FvkEFE~KRgdRE~~~L~~~~~~~~e~~e~~lp~~~~~~~~~L~~l~~~l~~ 77 (145)
T PF14942_consen 16 RPVIQGEIRYFVKEFEEKRGDREVRVLENLTEMISETNEHILPRCIELMQQNLEQLLERLQA 77 (145)
T ss_pred hHHHHHHHHHHHHHHHHccCcHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHH
Confidence 4667888888888866 445555555666665543334444444444433333333333333
No 73
>KOG1142 consensus Transcription initiation factor TFIID, subunit TAF12 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=28.43 E-value=1.1e+02 Score=23.23 Aligned_cols=44 Identities=11% Similarity=0.120 Sum_probs=27.7
Q ss_pred HHHHHHhcccCCCCCCHHHHHHHHccccCCChHHHHHHHHHHHHHHHHHHHHHHHH
Q 033727 9 QVLYMRRSLFDQGYLDSEQLIQLEDLQDDANPNFVEEVVSLFYSDSARLIQNIEQT 64 (112)
Q Consensus 9 ~~~~~~~~~~~~~~lD~~~l~~L~~l~~~~~~~~~~eli~~F~~~~~~~l~~L~~a 64 (112)
++.+++.-+..+..||.++ .+++.++.+.|+++.....-.|...
T Consensus 159 kl~dLvqqId~~~~LD~dV------------edlLleiADdFV~sii~~sC~LAKH 202 (258)
T KOG1142|consen 159 KLDDLVQQIDGTTKLDDDV------------EDLLLEIADDFVSSIIHRSCKLAKH 202 (258)
T ss_pred chhHHHHhhcCcccccHHH------------HHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 4566666666667777433 4555667777777776666665553
No 74
>PF05974 DUF892: Domain of unknown function (DUF892); InterPro: IPR010287 This domain is found in several hypothetical bacterial proteins of unknown function.; PDB: 4ERU_B 3OGH_A 2GS4_B 2GYQ_B 3HIU_A.
Probab=28.08 E-value=87 Score=21.41 Aligned_cols=59 Identities=17% Similarity=0.345 Sum_probs=36.0
Q ss_pred HHHHHHHHHhcccCCCCCCHHHHHHHHccccC-CChHHHHHHHHHHHHHHHHHHHHHHHHhhCC
Q 033727 6 LQHQVLYMRRSLFDQGYLDSEQLIQLEDLQDD-ANPNFVEEVVSLFYSDSARLIQNIEQTLSNR 68 (112)
Q Consensus 6 l~~~~~~~~~~~~~~~~lD~~~l~~L~~l~~~-~~~~~~~eli~~F~~~~~~~l~~L~~a~~~~ 68 (112)
|++.+..+++.+..- ....+..|..+... .+|+ +...+...++++..++..|++.+..-
T Consensus 2 l~~~~~~~L~d~y~a---E~q~~~~l~~~~~~a~~~~-L~~~l~~h~~eT~~q~~rLe~~~~~l 61 (159)
T PF05974_consen 2 LRDLFIDELRDLYSA---EKQLLKALPKLAEAASSPE-LKAALEEHLEETEQQIERLEQIFEAL 61 (159)
T ss_dssp HHHHHHHHHHHHHHH---HHHHHHHHHHHHHH-SSHH-HHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred HHHHHHHHHHHHHHH---HHHHHHHHHHHHhhCCCHH-HHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence 444455555554442 11224455544321 2454 57779999999999999999887654
No 75
>KOG4747 consensus Two-component phosphorelay intermediate involved in MAP kinase cascade regulation [Signal transduction mechanisms]
Probab=27.54 E-value=2.1e+02 Score=19.81 Aligned_cols=59 Identities=12% Similarity=0.161 Sum_probs=45.0
Q ss_pred ChHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHhhhhhhhhhcHHHHHHHHHH
Q 033727 39 NPNFVEEVVSLFYSDSARLIQNIEQTLSNRPVDFSRLDDILHQFKGSCSSIGAKKVKDACSQ 100 (112)
Q Consensus 39 ~~~~~~eli~~F~~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~LKGsa~~lGa~~l~~~~~~ 100 (112)
..+|-..++..++.+ +...+|++..+...+++ ...-+.|-+++|+..+|-.+.+--|..
T Consensus 12 ~~d~~~sl~~qgild--~qF~qlq~lqD~~~p~f-v~ev~~~fF~~s~~~i~~~r~ald~~~ 70 (150)
T KOG4747|consen 12 VSDYTKSLFDQGILD--SQFLQLQELQDDSSPDF-VEEVVGLFFEDSERLINNLRLALDCER 70 (150)
T ss_pred HHHHHHHHHHHHhhH--HHHHHHHHHhcccCccH-HHHHHHHHHHHHHHHHHHHHHHHhhHh
Confidence 456777778888887 67888999888764444 234567999999999999888877774
No 76
>PRK07502 cyclohexadienyl dehydrogenase; Validated
Probab=27.32 E-value=1.7e+02 Score=21.82 Aligned_cols=25 Identities=12% Similarity=0.104 Sum_probs=16.7
Q ss_pred HHHHHHHHHHHHHhhCCCCCHHHHHHH
Q 033727 52 SDSARLIQNIEQTLSNRPVDFSRLDDI 78 (112)
Q Consensus 52 ~~~~~~l~~L~~a~~~~~~D~~~l~~~ 78 (112)
++..+.+..+++++..+ |++.+.+.
T Consensus 253 ~~~~~~l~~~~~~l~~~--d~~~l~~~ 277 (307)
T PRK07502 253 GRFTEDLAALQRAIRWG--DGDALFDL 277 (307)
T ss_pred HHHHHHHHHHHHHHHcC--CHHHHHHH
Confidence 33444566778888888 88766544
No 77
>TIGR00601 rad23 UV excision repair protein Rad23. All proteins in this family for which functions are known are components of a multiprotein complex used for targeting nucleotide excision repair to specific parts of the genome. In humans, Rad23 complexes with the XPC protein. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=26.94 E-value=90 Score=24.75 Aligned_cols=37 Identities=24% Similarity=0.434 Sum_probs=28.7
Q ss_pred HHHHHHHccccCCChHHHHHHHHHHHHHHHHHHHHHHH
Q 033727 26 EQLIQLEDLQDDANPNFVEEVVSLFYSDSARLIQNIEQ 63 (112)
Q Consensus 26 ~~l~~L~~l~~~~~~~~~~eli~~F~~~~~~~l~~L~~ 63 (112)
.+|..|+++.. .+|+++..|+...-+..|+.++.|.+
T Consensus 255 pqf~~lR~~vq-~NP~~L~~lLqql~~~nP~l~q~I~~ 291 (378)
T TIGR00601 255 PQFQQLRQVVQ-QNPQLLPPLLQQIGQENPQLLQQISQ 291 (378)
T ss_pred HHHHHHHHHHH-HCHHHHHHHHHHHHhhCHHHHHHHHH
Confidence 56888888753 38998888888888888887776655
No 78
>PF13779 DUF4175: Domain of unknown function (DUF4175)
Probab=26.70 E-value=2.4e+02 Score=24.92 Aligned_cols=68 Identities=6% Similarity=0.138 Sum_probs=45.1
Q ss_pred ChHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHhhhhhhhhhcHHHHHHHHHHHHHHHHccCCC
Q 033727 39 NPNFVEEVVSLFYSDSARLIQNIEQTLSNRPVDFSRLDDILHQFKGSCSSIGAKKVKDACSQFREYCNAGNAE 111 (112)
Q Consensus 39 ~~~~~~eli~~F~~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~LKGsa~~lGa~~l~~~~~~lE~~~~~~~~~ 111 (112)
+.+=+.++++.+.+-..+++.+|.+-..+. .-.. ..+..-+.+.+++-..|.....+||+.+++|+.+
T Consensus 490 s~eEI~rLm~eLR~A~~~ym~~LAeq~~~~--~~~~---~~p~~~~~~~~~~~~dL~~mmd~ie~la~~G~~~ 557 (820)
T PF13779_consen 490 SDEEIARLMQELREAMQDYMQALAEQAQRN--PQQQ---DQPPDQGNSQMMSQQDLQRMMDRIEELARSGRMD 557 (820)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHhHhC--cccc---cCcccchhhhccCHHHHHHHHHHHHHHHHcCCHH
Confidence 455566666666666666666666654443 1100 0111245677899999999999999999999864
No 79
>PF11277 Med24_N: Mediator complex subunit 24 N-terminal; InterPro: IPR021429 This subunit of the Mediator complex appears to be conserved only from insects to humans. It is essential for correct retinal development in fish. Subunit composition of the mediator contributes to the control of differentiation in the vertebrate CNS as there are divergent functions of the mediator subunits Crsp34/Med27, Trap100/Med24, and Crsp150/Med14 [].
Probab=26.56 E-value=2.2e+02 Score=25.69 Aligned_cols=47 Identities=15% Similarity=0.227 Sum_probs=33.3
Q ss_pred HHHHHHHHHHHhcccCCCCCCHHHHHHHHccccCCChH-HHHHHHHHH
Q 033727 4 NQLQHQVLYMRRSLFDQGYLDSEQLIQLEDLQDDANPN-FVEEVVSLF 50 (112)
Q Consensus 4 ~~l~~~~~~~~~~~~~~~~lD~~~l~~L~~l~~~~~~~-~~~eli~~F 50 (112)
..+.|++...|+...+.|++|.+.+..+..+...+|+. |...++...
T Consensus 705 ~p~~E~l~~~f~~~~~~Gw~~~~~~~~~d~ll~~gG~~W~~~~lvkel 752 (990)
T PF11277_consen 705 TPILEQLRSVFSAARQRGWLDIRAIQLFDSLLNMGGVFWFCTNLVKEL 752 (990)
T ss_pred CchHHHHHHHHHHHHHcCCcCHHHHHHHHHHHHccchhHHHHHHHHHH
Confidence 34689999999999999999999877776664444543 333444444
No 80
>COG3923 PriC Primosomal replication protein N'' [DNA replication, recombination, and repair]
Probab=26.54 E-value=2e+02 Score=20.41 Aligned_cols=35 Identities=6% Similarity=0.343 Sum_probs=28.8
Q ss_pred HHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHhh
Q 033727 46 VVSLFYSDSARLIQNIEQTLSNRPVDFSRLDDILHQF 82 (112)
Q Consensus 46 li~~F~~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~L 82 (112)
++..|++++...+..|+++.+.+ -...+.-+|-+|
T Consensus 45 ~ls~ylqEa~~tL~aL~~~~e~~--~l~q~afLAErL 79 (175)
T COG3923 45 LLSFYLQEAGQTLTALKQAVEQD--RLPQVAFLAERL 79 (175)
T ss_pred hHHHHHHHHHHHHHHHHHHHhcc--chHHHHHHHHHH
Confidence 68999999999999999999887 555666666555
No 81
>cd08327 CARD_RAIDD Caspase activation and recruitment domain of RIP-associated ICH-1 homologous protein with a death domain. Caspase activation and recruitment domain (CARD) of RAIDD (RIP-associated ICH-1 homologous protein with a death domain), also known as CRADD (Caspase and RIP adaptor). RAIDD is an adaptor protein that together with the p53-inducible protein PIDD and caspase-2, forms the PIDDosome complex, which is required for caspase-2 activation and plays a role in mediating stress-induced apoptosis. RAIDD contains an N-terminal CARD, which interacts with the caspase-2 CARD, and a C-terminal Death domain (DD), which interacts with the DD of PIDD. In general, CARDs are DDs associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodime
Probab=25.34 E-value=1.8e+02 Score=18.28 Aligned_cols=52 Identities=12% Similarity=0.268 Sum_probs=37.6
Q ss_pred HHhcccCCCCCCHHHHHHHHccccCCChHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 033727 13 MRRSLFDQGYLDSEQLIQLEDLQDDANPNFVEEVVSLFYSDSARLIQNIEQTLS 66 (112)
Q Consensus 13 ~~~~~~~~~~lD~~~l~~L~~l~~~~~~~~~~eli~~F~~~~~~~l~~L~~a~~ 66 (112)
+...+.+.++|..+..+.+.... ...+-...+++..-.-.+.-...+-+++.
T Consensus 26 v~~~L~~~gIlT~~~~e~I~a~~--T~~~k~~~LLdiLp~RG~~AF~~F~~aL~ 77 (94)
T cd08327 26 VIQYLYQEGILTESHVEEIESQT--TSRRKTMKLLDILPSRGPKAFHAFLDSLE 77 (94)
T ss_pred HHHHHHhCCCCCHHHHHHHHccC--ChHHHHHHHHHHHHhhChhHHHHHHHHHH
Confidence 44457888899988888887654 35667777777777777777777777764
No 82
>PRK10093 primosomal replication protein N''; Provisional
Probab=24.80 E-value=2.6e+02 Score=19.81 Aligned_cols=35 Identities=0% Similarity=0.259 Sum_probs=27.9
Q ss_pred HHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHhh
Q 033727 46 VVSLFYSDSARLIQNIEQTLSNRPVDFSRLDDILHQF 82 (112)
Q Consensus 46 li~~F~~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~L 82 (112)
.+..|+.+....+..|..+...+ +...+..++=+|
T Consensus 41 ~L~~yl~Ei~~~l~qL~~~~~~~--~~~~~~flaEkL 75 (171)
T PRK10093 41 LLQAYLDEAGDNLAALRHAVEQQ--QLPQVAWLAEHL 75 (171)
T ss_pred chHHHHHHHHHHHHHHHHHHhcC--cHHHHHHHHHHH
Confidence 57889999999999999998888 776666555444
No 83
>KOG2280 consensus Vacuolar assembly/sorting protein VPS16 [Intracellular trafficking, secretion, and vesicular transport]
Probab=24.65 E-value=2.7e+02 Score=24.49 Aligned_cols=66 Identities=17% Similarity=0.188 Sum_probs=44.7
Q ss_pred HHHHHHccccCCChHHHHHHHHHHHH-HHHHHHHHHHHHhhCCCCCHHHHHHHHHhhhhhhhhhcHHHHHHHHHH
Q 033727 27 QLIQLEDLQDDANPNFVEEVVSLFYS-DSARLIQNIEQTLSNRPVDFSRLDDILHQFKGSCSSIGAKKVKDACSQ 100 (112)
Q Consensus 27 ~l~~L~~l~~~~~~~~~~eli~~F~~-~~~~~l~~L~~a~~~~~~D~~~l~~~aH~LKGsa~~lGa~~l~~~~~~ 100 (112)
++..|...+ ...-..++...|.= |-.-..-.+..+.+.+ ||+++...|-+-|+ -+|..++.+.|..
T Consensus 690 Tv~~li~~g---~~k~a~ql~~~FkipdKr~~wLk~~aLa~~~--kweeLekfAkskks---PIGy~PFVe~c~~ 756 (829)
T KOG2280|consen 690 TVTTLILIG---QNKRAEQLKSDFKIPDKRLWWLKLTALADIK--KWEELEKFAKSKKS---PIGYLPFVEACLK 756 (829)
T ss_pred HHHHHHHcc---chHHHHHHHHhcCCcchhhHHHHHHHHHhhh--hHHHHHHHHhccCC---CCCchhHHHHHHh
Confidence 344444333 44556666666642 3233445577778888 99999999966555 8999999999865
No 84
>PF15112 DUF4559: Domain of unknown function (DUF4559)
Probab=24.49 E-value=3.1e+02 Score=21.33 Aligned_cols=24 Identities=17% Similarity=0.104 Sum_probs=17.5
Q ss_pred hHHHHHHHHHHHhcccCCCCCCHH
Q 033727 3 SNQLQHQVLYMRRSLFDQGYLDSE 26 (112)
Q Consensus 3 ~~~l~~~~~~~~~~~~~~~~lD~~ 26 (112)
.+.|++++.+....+.+..+.+.+
T Consensus 231 ~e~Lke~lqel~~~~e~~~~~~ee 254 (307)
T PF15112_consen 231 MELLKEKLQELYLQAEEQEVLPEE 254 (307)
T ss_pred HHHHHHHHHHHHHHHhhccccchh
Confidence 367888888888887777766533
No 85
>COG5162 Transcription initiation factor TFIID, subunit TAF10 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=24.06 E-value=1.9e+02 Score=20.55 Aligned_cols=27 Identities=19% Similarity=0.270 Sum_probs=11.6
Q ss_pred HHHHHHHccccCCChHHHHHHHHHHHH
Q 033727 26 EQLIQLEDLQDDANPNFVEEVVSLFYS 52 (112)
Q Consensus 26 ~~l~~L~~l~~~~~~~~~~eli~~F~~ 52 (112)
++|++|.+.++...|-+-..+++.|++
T Consensus 73 ktlee~l~~mDsy~PliPd~v~DYyl~ 99 (197)
T COG5162 73 KTLEELLQNMDSYTPLIPDSVTDYYLE 99 (197)
T ss_pred HHHHHHHHhcccCCCCccHHHHHHHHH
Confidence 345555555543333333333444443
No 86
>KOG2702 consensus Predicted panthothenate kinase/uridine kinase-related protein [Nucleotide transport and metabolism; Coenzyme transport and metabolism]
Probab=23.98 E-value=64 Score=24.59 Aligned_cols=26 Identities=12% Similarity=0.261 Sum_probs=24.2
Q ss_pred HHHHhhhhhhhhhcHHHHHHHHHHHH
Q 033727 77 DILHQFKGSCSSIGAKKVKDACSQFR 102 (112)
Q Consensus 77 ~~aH~LKGsa~~lGa~~l~~~~~~lE 102 (112)
+.||+.+|+-.++.+.-+..+|+.|-
T Consensus 180 ~~AharRGapwTFD~~lfl~l~k~lk 205 (323)
T KOG2702|consen 180 QTAHARRGAPWTFDSNLFLQLCKILK 205 (323)
T ss_pred HHHHhhcCCCcccCHHHHHHHHHHHh
Confidence 68999999999999999999999875
No 87
>PRK15431 ferrous iron transport protein FeoC; Provisional
Probab=23.67 E-value=81 Score=19.44 Aligned_cols=32 Identities=16% Similarity=0.162 Sum_probs=22.3
Q ss_pred HHHHHHHhhCCCCCHHHHHHHHHhhhhhhhhhcH
Q 033727 58 IQNIEQTLSNRPVDFSRLDDILHQFKGSCSSIGA 91 (112)
Q Consensus 58 l~~L~~a~~~~~~D~~~l~~~aH~LKGsa~~lGa 91 (112)
+.+++.++... -...+.+++|.+..+...+-|
T Consensus 4 L~qlRd~l~~~--gr~s~~~Ls~~~~~p~~~Vea 35 (78)
T PRK15431 4 LIQVRDLLALR--GRMEAAQISQTLNTPQPMINA 35 (78)
T ss_pred HHHHHHHHHHc--CcccHHHHHHHHCcCHHHHHH
Confidence 45677777766 566778888888877765544
No 88
>COG3685 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.49 E-value=2.5e+02 Score=19.84 Aligned_cols=63 Identities=14% Similarity=0.309 Sum_probs=42.1
Q ss_pred CChHHHHHHHHHHHhcccCCCCCCHHHHHHHHccccC-CChHHHHHHHHHHHHHHHHHHHHHHHHhhC
Q 033727 1 MNSNQLQHQVLYMRRSLFDQGYLDSEQLIQLEDLQDD-ANPNFVEEVVSLFYSDSARLIQNIEQTLSN 67 (112)
Q Consensus 1 ~~~~~l~~~~~~~~~~~~~~~~lD~~~l~~L~~l~~~-~~~~~~~eli~~F~~~~~~~l~~L~~a~~~ 67 (112)
|+-.++.+....|++.+..- ....+..|..+... .+|+ +..-++..++++..+++.|++-++.
T Consensus 1 ~~~kt~~d~f~~~LrD~y~a---Ekq~~kaL~kma~~~~~~~-Lka~~E~Hl~ET~~qi~rLe~Vfe~ 64 (167)
T COG3685 1 MAMKTLEDLFIDTLRDIYAA---EKQILKALPKMARRAQYPE-LKAAIEKHLEETKGQIERLEQVFER 64 (167)
T ss_pred CCcccHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHhcCHH-HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34456777788888876553 22335566655332 2454 5556899999999999999988776
No 89
>PLN02956 PSII-Q subunit
Probab=23.34 E-value=2.9e+02 Score=19.86 Aligned_cols=36 Identities=11% Similarity=0.178 Sum_probs=20.8
Q ss_pred HHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHhhhhhhhhhc
Q 033727 50 FYSDSARLIQNIEQTLSNRPVDFSRLDDILHQFKGSCSSIG 90 (112)
Q Consensus 50 F~~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~LKGsa~~lG 90 (112)
=+.+..+.|-.|+..++++ +|..++... +|.++.++
T Consensus 88 r~k~~A~~l~~LK~LI~k~--~W~yvrn~L---Rgp~s~Lr 123 (185)
T PLN02956 88 GVRGHAENLLRVKALIESE--SWKEAQKAL---RRSASNLK 123 (185)
T ss_pred HHHHHHHHHHHHHHHhhhc--cHHHHHHHH---HccHHHHH
Confidence 3444555566677777777 776666554 34444444
No 90
>PF13801 Metal_resist: Heavy-metal resistance; PDB: 3EPV_C 2Y3D_A 2Y3H_D 2Y3G_B 2Y3B_A 2Y39_A 3LAY_H.
Probab=23.24 E-value=1.9e+02 Score=17.64 Aligned_cols=70 Identities=19% Similarity=0.336 Sum_probs=45.2
Q ss_pred CCHHHHHHHHccccCCChHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHhhhhhhhhhcHHHHHHH
Q 033727 23 LDSEQLIQLEDLQDDANPNFVEEVVSLFYSDSARLIQNIEQTLSNRPVDFSRLDDILHQFKGSCSSIGAKKVKDA 97 (112)
Q Consensus 23 lD~~~l~~L~~l~~~~~~~~~~eli~~F~~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~LKGsa~~lGa~~l~~~ 97 (112)
++.++...++.+.. ++..+ ......+....-.+|..++.+.++|...+..+.-.+......+-...+...
T Consensus 42 Lt~eQ~~~l~~~~~----~~~~~-~~~~r~~~~~~r~~l~~ll~~~~~D~~~i~a~~~~~~~~~~~l~~~~~~~~ 111 (125)
T PF13801_consen 42 LTPEQQAKLRALMD----EFRQE-MRALRQELRAARQELRALLAAPPPDEAAIEALLEEIREAQAELRQERLEHL 111 (125)
T ss_dssp TTHHHHHHHHHHHH----HHHHH-HHHHHHHHHHHHHHHHHHHCCSSS-HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHH----HHHHH-HHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 55566777776652 33333 445556666677778888888888999888887777666655555444433
No 91
>PF10018 Med4: Vitamin-D-receptor interacting Mediator subunit 4; InterPro: IPR019258 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. Members of this family represent the Med4 subunit of the Mediator (Med) complex [, ]. ; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006357 regulation of transcription from RNA polymerase II promoter, 0016592 mediator complex
Probab=22.95 E-value=2.7e+02 Score=19.46 Aligned_cols=44 Identities=18% Similarity=0.248 Sum_probs=28.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHh-------------hCCCCCHHHHHHHHHhhhhhhhh
Q 033727 45 EVVSLFYSDSARLIQNIEQTL-------------SNRPVDFSRLDDILHQFKGSCSS 88 (112)
Q Consensus 45 eli~~F~~~~~~~l~~L~~a~-------------~~~~~D~~~l~~~aH~LKGsa~~ 88 (112)
+-+..++......-..|..++ ...++|+..|...||+|-.....
T Consensus 43 ~~i~~~~~~L~~~~~~L~~~~~~~~~~~~~~~~~~~~~v~~~eLL~YA~rISk~t~~ 99 (188)
T PF10018_consen 43 EQIRDILKQLKEARKELRTLPDQADEKLKSIPKAEKRPVDYEELLSYAHRISKFTSA 99 (188)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhhccccccccccCCCCHHHHHHHHHHHHHhcCC
Confidence 345555555555555555554 23468899999999999776654
No 92
>PHA00435 capsid assembly protein
Probab=22.95 E-value=2e+02 Score=22.14 Aligned_cols=49 Identities=12% Similarity=0.264 Sum_probs=33.4
Q ss_pred HHHHHHccccCCChHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHH
Q 033727 27 QLIQLEDLQDDANPNFVEEVVSLFYSDSARLIQNIEQTLSNRPVDFSRLDDIL 79 (112)
Q Consensus 27 ~l~~L~~l~~~~~~~~~~eli~~F~~~~~~~l~~L~~a~~~~~~D~~~l~~~a 79 (112)
.++.+.... ++++-+..|..-.-...+...+.|..++..+ |..+++.+.
T Consensus 188 yV~sv~~yA--GG~E~F~~i~shl~atnp~~~eal~~Ave~~--dl~t~K~iv 236 (306)
T PHA00435 188 YVESVVEYA--GGRERFQAIYSHLEATNPSAAESLEAAIENR--DLATVKAII 236 (306)
T ss_pred HHHHHHHHh--ccHHHHHHHHHHHHhcChhHHHHHHHHHHcC--CHHHHHHHH
Confidence 345555544 3777777755555457788888899999988 887776543
No 93
>PF08332 CaMKII_AD: Calcium/calmodulin dependent protein kinase II Association; InterPro: IPR013543 Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases. Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. Phosphoprotein phosphatases catalyse the reverse process. Protein kinases fall into three broad classes, characterised with respect to substrate specificity []: Serine/threonine-protein kinases Tyrosine-protein kinases Dual specific protein kinases (e.g. MEK - phosphorylates both Thr and Tyr on target proteins) Protein kinase function has been evolutionarily conserved from Escherichia coli to human []. Protein kinases play a role in a multitude of cellular processes, including division, proliferation, apoptosis, and differentiation []. Phosphorylation usually results in a functional change of the target protein by changing enzyme activity, cellular location, or association with other proteins. The catalytic subunits of protein kinases are highly conserved, and several structures have been solved [], leading to large screens to develop kinase-specific inhibitors for the treatments of a number of diseases []. This domain is found at the C terminus of the Calcium/calmodulin dependent protein kinases II (CaMKII). These proteins also have a Ser/Thr protein kinase domain (IPR000719 from INTERPRO) at their N terminus []. The function of the CaMKII association domain is the assembly of the single proteins into large (8 to 14 subunits) multimers [] and is a prominent kinase in the central nervous system that may function in long-term potentiation and neurotransmitter release. ; GO: 0004683 calmodulin-dependent protein kinase activity, 0005516 calmodulin binding, 0006468 protein phosphorylation; PDB: 2W2C_F 3H51_B 3SOA_A 2UX0_A 1HKX_M 2F86_B.
Probab=22.75 E-value=96 Score=20.70 Aligned_cols=26 Identities=12% Similarity=0.196 Sum_probs=19.7
Q ss_pred HHHHHHHHHHHHhhCCCCCHHHHHHHHH
Q 033727 53 DSARLIQNIEQTLSNRPVDFSRLDDILH 80 (112)
Q Consensus 53 ~~~~~l~~L~~a~~~~~~D~~~l~~~aH 80 (112)
+..+..+++..++..+ |++.+.++.+
T Consensus 4 eI~~l~~~w~~ai~tg--D~~~~~~ly~ 29 (128)
T PF08332_consen 4 EIAALFDRWNDAIQTG--DPETYAKLYA 29 (128)
T ss_dssp HHHHHHHHHHHHHHHT---HHHHHHHEE
T ss_pred HHHHHHHHHHHHHHcC--CHHHHhhhcC
Confidence 4456677888999999 9999988764
No 94
>PF10431 ClpB_D2-small: C-terminal, D2-small domain, of ClpB protein ; InterPro: IPR019489 Most Clp ATPases form complexes with peptidase subunits and are involved in protein degradation, though some, such as ClpB, do not associate with peptidases and are involved in protein disaggregation []. This entry represents the C-terminal domain of Clp ATPases, often referred to as the D2-small domain, which forms a mixed alpha-beta structure. Compared with the adjacent AAA D1-small domain (IPR003959 from INTERPRO) it lacks the long coiled-coil insertion, and instead of helix C4 contains a beta-strand (e3) that is part of a three stranded beta-pleated sheet. In Thermophilus the whole protein forms a hexamer with the D1-small and D2-small domains located on the outside of the hexamer, with the long coiled-coil being exposed on the surface. The D2-small domain is essential for oligomerisation, forming a tight interface with the D2-large domain of a neighbouring subunit, thereby providing enough binding energy to stabilise the functional assembly [].; PDB: 3HWS_A 3HTE_F 1KYI_T 1G3I_S 1OFH_B 1OFI_A 1G41_A 1IM2_A 3PXI_A 1R6B_X ....
Probab=22.56 E-value=1.2e+02 Score=17.83 Aligned_cols=56 Identities=14% Similarity=0.202 Sum_probs=32.0
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHhhhhhhhhhcHHHHHHHHHH
Q 033727 40 PNFVEEVVSLFYSDSARLIQNIEQTLSNRPVDFSRLDDILHQFKGSCSSIGAKKVKDACSQ 100 (112)
Q Consensus 40 ~~~~~eli~~F~~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~LKGsa~~lGa~~l~~~~~~ 100 (112)
.+.+.+++...+++..+.+.. .. +.= ..|-..+..++. +|-...+||..|......
T Consensus 3 ~~~l~~I~~~~l~~l~~~l~~-~~-i~l-~~~~~~~~~l~~--~~~~~~~GAR~l~r~i~~ 58 (81)
T PF10431_consen 3 EEDLEKIADLQLKKLNERLKE-KG-IEL-EFDDAVVDYLAE--KGYDPEYGARPLRRIIER 58 (81)
T ss_dssp HHHHHHHHHSHHHHHHHHHHH-TT-EEE-EE-HHHHHHHHH--HHHHTTTTTTCHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHH-CC-CeE-EecHHHHHHHHH--hCcccCCCHHHHHHHHHH
Confidence 455667777777777666644 21 111 112233344443 367789999998876544
No 95
>PF05153 DUF706: Family of unknown function (DUF706) ; InterPro: IPR007828 Inositol oxygenase (1.13.99.1 from EC) is involved in the biosynthesis of UDP-glucuronic acid (UDP-GlcA), providing nucleotide sugars for cell-wall polymers. It may be also involved in plant ascorbate biosynthesis [, ].; GO: 0005506 iron ion binding, 0050113 inositol oxygenase activity, 0019310 inositol catabolic process, 0055114 oxidation-reduction process, 0005737 cytoplasm; PDB: 2HUO_A 3BXD_A 2IBN_A.
Probab=22.48 E-value=1.5e+02 Score=22.37 Aligned_cols=58 Identities=17% Similarity=0.294 Sum_probs=33.1
Q ss_pred HHHHHHHccccCCChHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHhhhhhhhhh
Q 033727 26 EQLIQLEDLQDDANPNFVEEVVSLFYSDSARLIQNIEQTLSNRPVDFSRLDDILHQFKGSCSSI 89 (112)
Q Consensus 26 ~~l~~L~~l~~~~~~~~~~eli~~F~~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~LKGsa~~l 89 (112)
+.+..|..+.++.+|+.-.--|.--++.+ +.+++..... ||-.+.-+.|-|--.-..+
T Consensus 43 eA~~~L~~LvDeSDPD~d~~~i~H~lQTA----EaiR~d~~~~--dW~~LtGLiHDLGKvl~~~ 100 (253)
T PF05153_consen 43 EALELLNTLVDESDPDTDLPQIQHALQTA----EAIRRDHPDP--DWMQLTGLIHDLGKVLALF 100 (253)
T ss_dssp HHHHHGGG---TT-TT--S-HHHHHHHHH----HHHHHHSTT---HHHHHHHHHTTGGGHHHHC
T ss_pred HHHHHHHHhccCccCCCchhHHHHHHHHH----HHHHHhCCCc--chhhheehhccchhhhhhh
Confidence 56677777777777776443444444444 4567765666 9999999999885544444
No 96
>PF11221 Med21: Subunit 21 of Mediator complex; InterPro: IPR021384 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. Med21 has been known as Srb7 in yeasts, hSrb7 in humans and Trap 19 in Drosophila. The heterodimer of the two subunits Med7 and Med21 appears to act as a hinge between the middle and the tail regions of Mediator []. ; PDB: 1YKE_B 1YKH_B.
Probab=22.45 E-value=2.5e+02 Score=18.83 Aligned_cols=54 Identities=19% Similarity=0.322 Sum_probs=21.3
Q ss_pred HHHHHhcccCCCCCCHHHHHHHHccccCCChHHHHHHHHHHHHHHHHHHHHHHHHh
Q 033727 10 VLYMRRSLFDQGYLDSEQLIQLEDLQDDANPNFVEEVVSLFYSDSARLIQNIEQTL 65 (112)
Q Consensus 10 ~~~~~~~~~~~~~lD~~~l~~L~~l~~~~~~~~~~eli~~F~~~~~~~l~~L~~a~ 65 (112)
.+.++.++...+.=..++...|++|.. ...-+.+-+..-+.+....+..++.++
T Consensus 85 Ie~LIdsLPg~~~see~Q~~~i~~L~~--E~~~~~~el~~~v~e~e~ll~~v~~~i 138 (144)
T PF11221_consen 85 IEYLIDSLPGIEVSEEEQLKRIKELEE--ENEEAEEELQEAVKEAEELLKQVQELI 138 (144)
T ss_dssp HHHHHHHSTTSSS-HHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHhCCCCCCCHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344444444433322233444444432 112222234444444444444444443
No 97
>COG4997 Uncharacterized conserved protein [Function unknown]
Probab=21.59 E-value=2.2e+02 Score=17.95 Aligned_cols=52 Identities=17% Similarity=0.319 Sum_probs=38.6
Q ss_pred HHHHHHHhhCCCCCHHHHHHHHHhhhhhhhhhcHHHHHHHHHHHHHHHHccCCC
Q 033727 58 IQNIEQTLSNRPVDFSRLDDILHQFKGSCSSIGAKKVKDACSQFREYCNAGNAE 111 (112)
Q Consensus 58 l~~L~~a~~~~~~D~~~l~~~aH~LKGsa~~lGa~~l~~~~~~lE~~~~~~~~~ 111 (112)
++++...+... +.+.+..+.--+-+-+..+|+..=--...+++...+.|..+
T Consensus 42 ~EE~~E~ledk--~lEeLadllEvi~~ia~a~gfske~l~~~R~~Kk~e~Ggf~ 93 (95)
T COG4997 42 LEEVEEFLEDK--NLEELADLLEVISRIAEARGFSKENLEALRLQKKLEKGGFE 93 (95)
T ss_pred HHHHHHHHhcc--cHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHhcCcc
Confidence 34445556666 78888888888888888888888777778888887777653
No 98
>PF08637 NCA2: ATP synthase regulation protein NCA2; InterPro: IPR013946 NCA2 (Nuclear Control of ATPase), is one of the two nuclear genes involved in the control of mitochondrial expression of subunits 6 and 8 of the Fo-F1 ATP synthase in Saccharomyces cerevisiae (Baker's yeast). Mutations in either NCA2 or NCA3 (IPR005556 from INTERPRO) dramatically lower the level of the co-transcript encoding subunits 6 and 8 [, ].
Probab=21.32 E-value=1.5e+02 Score=22.57 Aligned_cols=45 Identities=18% Similarity=0.335 Sum_probs=34.0
Q ss_pred ChHHHHHHHHHHHHHHH----HHHHHHHHHhhCCCCCHHHH-----HHHHHhhhhh
Q 033727 39 NPNFVEEVVSLFYSDSA----RLIQNIEQTLSNRPVDFSRL-----DDILHQFKGS 85 (112)
Q Consensus 39 ~~~~~~eli~~F~~~~~----~~l~~L~~a~~~~~~D~~~l-----~~~aH~LKGs 85 (112)
+.+=+.+|+..|..|.. ..++.|.+.+..+ |...+ .++-|.+||.
T Consensus 73 d~~SLeRMv~dF~~d~~~~~~~~~~~l~~~v~~G--dlt~Vm~~YE~el~~Pik~~ 126 (290)
T PF08637_consen 73 DMESLERMVVDFAKDNSPNMPADLEELRQQVREG--DLTPVMKRYEKELKHPIKNI 126 (290)
T ss_pred HHHHHHHHHHHHHhcCCCCCcchHHHHHHHHHcC--CcHHHHHHHHHHHHhHHHHH
Confidence 34567789999999985 4688999999999 87655 3566777765
No 99
>PF05974 DUF892: Domain of unknown function (DUF892); InterPro: IPR010287 This domain is found in several hypothetical bacterial proteins of unknown function.; PDB: 4ERU_B 3OGH_A 2GS4_B 2GYQ_B 3HIU_A.
Probab=20.97 E-value=1.6e+02 Score=20.11 Aligned_cols=73 Identities=10% Similarity=0.260 Sum_probs=42.1
Q ss_pred HHHHHccccCCChHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHhhhhhhhhhcHHHHHHHHHHHHHHHHc
Q 033727 28 LIQLEDLQDDANPNFVEEVVSLFYSDSARLIQNIEQTLSNRPVDFSRLDDILHQFKGSCSSIGAKKVKDACSQFREYCNA 107 (112)
Q Consensus 28 l~~L~~l~~~~~~~~~~eli~~F~~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~LKGsa~~lGa~~l~~~~~~lE~~~~~ 107 (112)
+..|+++.. -..-+.+.+......+.. ..|+.++.. ......+...+|...-..+|..+=..-|..++-....
T Consensus 7 ~~~L~d~y~--aE~q~~~~l~~~~~~a~~--~~L~~~l~~---h~~eT~~q~~rLe~~~~~lg~~p~~~~c~~~~gl~~e 79 (159)
T PF05974_consen 7 IDELRDLYS--AEKQLLKALPKLAEAASS--PELKAALEE---HLEETEQQIERLEQIFEALGADPSAEKCDAMEGLVAE 79 (159)
T ss_dssp HHHHHHHHH--HHHHHHHHHHHHHHH-SS--HHHHHHHHH---HHHHHHHHHHHHHHHHHHTTS-S-CHH-HHHHHHHHH
T ss_pred HHHHHHHHH--HHHHHHHHHHHHHhhCCC--HHHHHHHHH---HHHHHHHHHHHHHHHHHHccCCCccCcchHHHHHHHH
Confidence 345555531 223334445555555443 566666665 3667788888888888888888777777776655443
No 100
>COG4395 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.89 E-value=1.7e+02 Score=22.44 Aligned_cols=30 Identities=20% Similarity=0.303 Sum_probs=26.8
Q ss_pred HHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHH
Q 033727 48 SLFYSDSARLIQNIEQTLSNRPVDFSRLDDIL 79 (112)
Q Consensus 48 ~~F~~~~~~~l~~L~~a~~~~~~D~~~l~~~a 79 (112)
..|+...+..++.|..+...+ |+++++++.
T Consensus 150 ~~fl~~a~~a~~~Iq~a~~~~--D~~tL~~L~ 179 (281)
T COG4395 150 ARFLNGARAAYEMIQQAYGAG--DRKTLRELL 179 (281)
T ss_pred hHHHHHHHHHHHHHHHHhhhc--cHHHHHHhc
Confidence 578999999999999999999 999998774
No 101
>COG3388 Predicted transcriptional regulator [Transcription]
Probab=20.52 E-value=2.2e+02 Score=18.37 Aligned_cols=36 Identities=28% Similarity=0.446 Sum_probs=22.7
Q ss_pred HHHHHHHHhcccCCCCCCHHHHHHHHccccCCChHHHHH
Q 033727 7 QHQVLYMRRSLFDQGYLDSEQLIQLEDLQDDANPNFVEE 45 (112)
Q Consensus 7 ~~~~~~~~~~~~~~~~lD~~~l~~L~~l~~~~~~~~~~e 45 (112)
+++..+.++-+.++++|-+++--.+ ..+..++|+.+
T Consensus 42 ~HKVRYSLRVLEq~~iI~PS~~GAi---~td~~~e~ie~ 77 (101)
T COG3388 42 EHKVRYSLRVLEQENIISPSRQGAI---LTDDFPEFIEE 77 (101)
T ss_pred hhhhhhhhhhhhhcCccCccccCCc---cCccHHHHHHH
Confidence 4677788888888888887653332 32345555444
No 102
>TIGR00112 proC pyrroline-5-carboxylate reductase. This enzyme catalyzes the final step in proline biosynthesis. Among the four paralogs in Bacillus subtilis (proG, proH, proI, and comER), ComER is the most divergent and does not prevent proline auxotrophy from mutation of the other three. It is excluded from the seed and scores between the trusted and noise cutoffs.
Probab=20.07 E-value=2e+02 Score=20.86 Aligned_cols=71 Identities=11% Similarity=0.095 Sum_probs=42.5
Q ss_pred HHHHHHHHhcccCCCCCCHHHHHHHHccccCCChHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCHHHHH-HHHHhhhhh
Q 033727 7 QHQVLYMRRSLFDQGYLDSEQLIQLEDLQDDANPNFVEEVVSLFYSDSARLIQNIEQTLSNRPVDFSRLD-DILHQFKGS 85 (112)
Q Consensus 7 ~~~~~~~~~~~~~~~~lD~~~l~~L~~l~~~~~~~~~~eli~~F~~~~~~~l~~L~~a~~~~~~D~~~l~-~~aH~LKGs 85 (112)
++.+..+++++=..-+++.+.++..-.+. +.+|.|+-.+++.+.+-..+ .+ .+.+..+ -.++.++|+
T Consensus 124 ~~~v~~lf~~~G~~~~v~E~~~~~~tals-gsgPA~~~~~~~al~~~~v~----------~G-l~~~~A~~lv~~~~~G~ 191 (245)
T TIGR00112 124 RALVLALFKAVGEVVELPEALMDAVTALS-GSGPAYVFLFIEALADAGVK----------QG-LPRELALELAAQTVKGA 191 (245)
T ss_pred HHHHHHHHHhCCCEEEECHHHcchHHhhc-cCcHHHHHHHHHHHHHHHHH----------cC-CCHHHHHHHHHHHHHHH
Confidence 34555566665555667877788787775 35899888877776664322 11 2333333 345677777
Q ss_pred hhhh
Q 033727 86 CSSI 89 (112)
Q Consensus 86 a~~l 89 (112)
+..+
T Consensus 192 a~l~ 195 (245)
T TIGR00112 192 AKLL 195 (245)
T ss_pred HHHH
Confidence 6654
Done!