Query 033824
Match_columns 111
No_of_seqs 193 out of 1017
Neff 7.4
Searched_HMMs 46136
Date Fri Mar 29 06:42:41 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033824.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033824hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4747 Two-component phosphor 99.8 4.7E-19 1E-23 121.5 10.9 108 3-111 5-112 (150)
2 COG2198 ArcB FOG: HPt domain [ 99.6 9.3E-15 2E-19 97.5 9.1 69 37-107 20-88 (122)
3 PF01627 Hpt: Hpt domain; Int 99.6 8E-15 1.7E-19 91.4 7.0 64 44-109 1-67 (90)
4 smart00073 HPT Histidine Phosp 99.5 6.7E-14 1.4E-18 87.5 6.8 63 44-108 2-64 (87)
5 cd00088 HPT Histidine Phosphot 99.5 3.6E-13 7.8E-18 85.6 7.3 64 43-108 2-69 (94)
6 TIGR02956 TMAO_torS TMAO reduc 99.2 8.7E-11 1.9E-15 99.2 9.6 74 35-110 874-947 (968)
7 PRK10618 phosphotransfer inter 99.0 1.5E-09 3.2E-14 92.9 7.9 64 44-109 811-874 (894)
8 PRK11466 hybrid sensory histid 98.6 2.6E-07 5.6E-12 78.1 8.7 68 36-105 819-886 (914)
9 PRK11091 aerobic respiration c 98.6 2.9E-07 6.3E-12 76.9 8.5 77 30-108 671-747 (779)
10 COG0643 CheA Chemotaxis protei 98.4 1E-06 2.3E-11 74.1 8.7 66 39-104 3-74 (716)
11 PRK10547 chemotaxis protein Ch 98.4 1.4E-06 3E-11 72.9 8.8 63 43-105 4-72 (670)
12 PRK11107 hybrid sensory histid 98.4 3E-06 6.6E-11 71.3 9.5 71 36-108 820-890 (919)
13 PRK09959 hybrid sensory histid 97.0 0.0054 1.2E-07 53.7 9.4 69 37-107 1097-1165(1197)
14 PRK15347 two component system 97.0 0.0034 7.4E-08 53.2 7.7 61 45-109 838-898 (921)
15 PF07743 HSCB_C: HSCB C-termin 91.7 1.9 4E-05 26.1 7.6 51 30-82 17-67 (78)
16 PF05396 Phage_T7_Capsid: Phag 90.2 4 8.7E-05 27.5 8.0 61 20-84 29-89 (123)
17 PRK01356 hscB co-chaperone Hsc 87.7 5.1 0.00011 28.1 7.6 59 22-82 91-149 (166)
18 TIGR00714 hscB Fe-S protein as 86.8 6.1 0.00013 27.4 7.5 52 29-82 89-140 (157)
19 cd08323 CARD_APAF1 Caspase act 84.3 8.1 0.00017 24.3 6.7 67 10-80 16-83 (86)
20 PRK03578 hscB co-chaperone Hsc 79.5 16 0.00035 25.9 7.3 45 36-82 113-158 (176)
21 PRK01773 hscB co-chaperone Hsc 78.9 17 0.00038 25.7 7.4 45 36-82 110-154 (173)
22 PF04840 Vps16_C: Vps16, C-ter 72.5 39 0.00085 26.1 8.4 65 30-99 184-249 (319)
23 COG3046 Uncharacterized protei 70.7 4.3 9.3E-05 33.0 2.8 67 37-109 225-291 (505)
24 TIGR00984 3a0801s03tim44 mitoc 65.9 68 0.0015 25.7 9.6 50 46-107 243-293 (378)
25 PHA00435 capsid assembly prote 65.1 29 0.00063 26.7 6.1 56 20-79 182-237 (306)
26 PF09280 XPC-binding: XPC-bind 63.6 18 0.00039 21.1 3.8 37 25-62 8-44 (59)
27 PRK05014 hscB co-chaperone Hsc 62.7 51 0.0011 23.1 7.2 41 40-82 113-153 (171)
28 PF03847 TFIID_20kDa: Transcri 62.6 25 0.00053 21.1 4.4 49 7-66 2-50 (68)
29 PF14615 Rsa3: Ribosome-assemb 61.8 26 0.00055 19.6 4.1 42 44-88 5-46 (47)
30 KOG1142 Transcription initiati 58.3 18 0.00038 27.5 3.9 49 7-66 157-205 (258)
31 PF04280 Tim44: Tim44-like dom 55.2 58 0.0013 21.5 5.9 50 46-107 17-66 (147)
32 TIGR03042 PS_II_psbQ_bact phot 51.8 25 0.00055 24.3 3.5 28 51-80 46-73 (142)
33 TIGR00601 rad23 UV excision re 49.4 58 0.0013 26.0 5.7 45 25-77 255-299 (378)
34 PRK08818 prephenate dehydrogen 48.9 92 0.002 24.7 6.8 35 50-86 233-267 (370)
35 KOG4552 Vitamin-D-receptor int 46.6 1.2E+02 0.0026 22.7 6.5 40 44-84 102-141 (272)
36 PF02153 PDH: Prephenate dehyd 46.3 1.2E+02 0.0025 22.4 7.1 39 37-77 210-255 (258)
37 PF04282 DUF438: Family of unk 44.1 73 0.0016 19.4 4.8 50 29-78 5-55 (71)
38 COG2991 Uncharacterized protei 44.1 4.6 9.9E-05 24.9 -0.9 20 79-98 27-46 (77)
39 PLN02407 diphosphomevalonate d 43.8 44 0.00096 26.4 4.2 32 45-78 224-256 (343)
40 PRK03057 hypothetical protein; 42.7 1.1E+02 0.0024 21.9 5.8 37 44-82 131-173 (180)
41 PF09209 DUF1956: Domain of un 38.9 1E+02 0.0022 19.4 8.9 83 8-92 3-90 (125)
42 PRK03636 hypothetical protein; 38.9 1.4E+02 0.0031 21.3 6.0 28 53-82 147-174 (179)
43 cd08326 CARD_CASP9 Caspase act 38.3 98 0.0021 19.2 5.9 56 10-67 18-74 (84)
44 PF07014 Hs1pro-1_C: Hs1pro-1 37.5 1.2E+02 0.0025 22.9 5.3 39 41-81 54-92 (261)
45 COG3433 Aryl carrier domain [S 36.2 62 0.0014 19.9 3.2 51 44-95 5-55 (74)
46 KOG2833 Mevalonate pyrophospha 35.9 73 0.0016 25.3 4.2 32 44-77 222-254 (395)
47 PF14276 DUF4363: Domain of un 35.6 1.2E+02 0.0027 19.5 5.1 37 43-81 18-54 (121)
48 PF10018 Med4: Vitamin-D-recep 35.0 1.6E+02 0.0035 20.7 9.5 58 28-87 29-99 (188)
49 PRK11199 tyrA bifunctional cho 34.4 2.3E+02 0.0049 22.2 9.3 64 37-102 298-367 (374)
50 cd01671 CARD Caspase activatio 34.0 1E+02 0.0022 18.0 6.4 57 9-67 14-71 (80)
51 PF01322 Cytochrom_C_2: Cytoch 33.6 1.3E+02 0.0029 19.3 5.0 39 47-87 78-116 (122)
52 TIGR01220 Pmev_kin_Gr_pos phos 32.6 2.4E+02 0.0052 21.9 7.2 55 45-101 246-308 (358)
53 PF10431 ClpB_D2-small: C-term 32.2 82 0.0018 18.7 3.3 56 38-98 2-57 (81)
54 KOG3192 Mitochondrial J-type c 32.2 1.9E+02 0.004 20.6 7.3 48 32-81 107-154 (168)
55 PRK08507 prephenate dehydrogen 31.9 2.1E+02 0.0045 21.0 6.1 48 27-77 210-264 (275)
56 PF11563 Protoglobin: Protoglo 31.2 1.6E+02 0.0034 19.4 7.0 57 2-58 59-120 (158)
57 TIGR01240 mevDPdecarb diphosph 30.9 98 0.0021 23.8 4.3 31 46-78 202-232 (305)
58 PRK13916 plasmid segregation p 29.5 90 0.002 19.9 3.2 28 27-54 21-48 (97)
59 KOG4559 Uncharacterized conser 29.0 1.2E+02 0.0026 20.0 3.8 47 39-89 39-85 (120)
60 COG3923 PriC Primosomal replic 28.3 1.6E+02 0.0035 21.0 4.6 37 44-82 44-80 (175)
61 PF03398 Ist1: Regulator of Vp 27.9 2.1E+02 0.0046 19.8 5.6 88 8-99 23-111 (165)
62 PF09670 Cas_Cas02710: CRISPR- 27.0 3.2E+02 0.0069 21.6 6.7 65 37-103 115-180 (379)
63 PF13779 DUF4175: Domain of un 26.7 2.3E+02 0.005 25.1 6.2 70 36-110 488-557 (820)
64 PF08858 IDEAL: IDEAL domain; 26.4 1.1E+02 0.0023 16.0 5.5 24 55-80 13-36 (37)
65 PF14674 FANCI_S1-cap: FANCI s 26.4 1.4E+02 0.003 17.2 4.4 37 46-85 6-42 (53)
66 PF02845 CUE: CUE domain; Int 25.1 1.2E+02 0.0025 15.9 3.6 34 27-60 5-38 (42)
67 PF04400 DUF539: Protein of un 24.9 6.9 0.00015 21.8 -2.2 18 80-97 7-24 (45)
68 KOG2280 Vacuolar assembly/sort 24.5 3E+02 0.0065 24.4 6.3 66 29-99 690-756 (829)
69 PF13628 DUF4142: Domain of un 24.3 2.1E+02 0.0047 18.7 6.2 50 27-78 72-122 (139)
70 PRK10093 primosomal replicatio 23.5 2.8E+02 0.0061 19.8 6.4 36 44-81 40-75 (171)
71 PRK08582 hypothetical protein; 22.6 1.6E+02 0.0034 19.9 3.7 28 40-67 103-130 (139)
72 PF02203 TarH: Tar ligand bind 21.9 2.5E+02 0.0053 18.5 5.4 38 38-77 111-148 (171)
73 PF08822 DUF1804: Protein of u 21.0 3.1E+02 0.0068 19.4 6.5 50 10-62 36-88 (165)
74 PF08637 NCA2: ATP synthase re 21.0 3.9E+02 0.0084 20.4 7.5 45 38-84 73-126 (290)
75 PF08112 ATP-synt_E_2: ATP syn 20.9 1.8E+02 0.004 16.7 3.5 11 5-15 15-25 (56)
76 PF05168 HEPN: HEPN domain; I 20.7 2.1E+02 0.0047 17.4 4.9 31 47-79 2-32 (118)
77 PF08332 CaMKII_AD: Calcium/ca 20.4 86 0.0019 21.1 2.0 26 52-79 4-29 (128)
78 TIGR02606 antidote_CC2985 puta 20.1 2.1E+02 0.0045 16.9 3.5 47 6-65 6-52 (69)
No 1
>KOG4747 consensus Two-component phosphorelay intermediate involved in MAP kinase cascade regulation [Signal transduction mechanisms]
Probab=99.81 E-value=4.7e-19 Score=121.48 Aligned_cols=108 Identities=66% Similarity=1.016 Sum_probs=104.4
Q ss_pred hHHHHHHHHHHHHhhhhhcchhHHHHHHHhhhccCCHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhh
Q 033824 3 VGQMQRRLLEYTKSLFMEGVLDNQFLQLQQLQDESNPDFVAEVVSLFFADSERLLNDLTRALDQPTIDFKMVDSHVHQLK 82 (111)
Q Consensus 3 ~~~~~~~~~~~~~~~~~~~~ld~~~~~L~~L~~~~~~~~~~~ll~~F~~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~LK 82 (111)
|.+|+++...+.+|++++|++|.+|.+|++|.++..|+|+.+++..|++++...+..++.|+..+. |+..+....|.+|
T Consensus 5 i~~~q~~~~d~~~sl~~qgild~qF~qlq~lqD~~~p~fv~ev~~~fF~~s~~~i~~~r~ald~~~-d~k~~~~~~hqlk 83 (150)
T KOG4747|consen 5 IISMQRDVSDYTKSLFDQGILDSQFLQLQELQDDSSPDFVEEVVGLFFEDSERLINNLRLALDCER-DFKKLGSHVHQLK 83 (150)
T ss_pred HHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHhcccCccHHHHHHHHHHHHHHHHHHHHHHHHhhHh-HHHHHHHHHHHcc
Confidence 678999999999999999999999999999999999999999999999999999999999998875 9999999999999
Q ss_pred hhhhhhChHHHHHHHHHHHHHHHhhccCC
Q 033824 83 GSSSSIGAERIKNACVAFRNFCEEQNIEG 111 (111)
Q Consensus 83 Gsa~~lGa~~L~~~~~~lE~~~~~gd~~g 111 (111)
||+.++||.++...|..+...|+.++.+|
T Consensus 84 gssssIGa~kvk~~c~~~~~~~~~~n~eg 112 (150)
T KOG4747|consen 84 GSSSSIGALKVKKVCVGFNEFCEAGNIEG 112 (150)
T ss_pred CchhhhhHHHHHHHHHHHHHHHhhccchh
Confidence 99999999999999999999999999886
No 2
>COG2198 ArcB FOG: HPt domain [Signal transduction mechanisms]
Probab=99.59 E-value=9.3e-15 Score=97.49 Aligned_cols=69 Identities=25% Similarity=0.481 Sum_probs=67.0
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhhhhhhhChHHHHHHHHHHHHHHHhh
Q 033824 37 SNPDFVAEVVSLFFADSERLLNDLTRALDQPTIDFKMVDSHVHQLKGSSSSIGAERIKNACVAFRNFCEEQ 107 (111)
Q Consensus 37 ~~~~~~~~ll~~F~~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~LKGsa~~lGa~~L~~~~~~lE~~~~~g 107 (111)
++++++.+++..|+++.++.+..+..++..+ |+..+.+.||+|||+|+++|+.+|...|..+|..++.+
T Consensus 20 ~~~~~~~~ll~~f~~~~~~~l~~l~~~l~~~--d~~~~~~~aH~lkg~a~~lg~~~L~~~~~~lE~~~~~~ 88 (122)
T COG2198 20 GDPDLLRELLAMFLEEAPAQLEQLESALAAE--DNDGLARLAHRLKGSAASLGLPALAQLCQQLEDALRSG 88 (122)
T ss_pred CChHHHHHHHHHHHHHhHHHHHHHHHHHhcC--CcHHHHHHHHHHHhHHHhccHHHHHHHHHHHHHHHHcC
Confidence 6799999999999999999999999999999 99999999999999999999999999999999999874
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=99.58 E-value=8e-15 Score=91.36 Aligned_cols=64 Identities=25% Similarity=0.474 Sum_probs=61.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHh---cCCCCCHHHHHHHHHHhhhhhhhhChHHHHHHHHHHHHHHHhhcc
Q 033824 44 EVVSLFFADSERLLNDLTRAL---DQPTIDFKMVDSHVHQLKGSSSSIGAERIKNACVAFRNFCEEQNI 109 (111)
Q Consensus 44 ~ll~~F~~~~~~~l~~L~~a~---~~~~~D~~~l~~~aH~LKGsa~~lGa~~L~~~~~~lE~~~~~gd~ 109 (111)
+++..|+++.++.+..|++++ ..+ |++.+.+.+|+|||+++++|+.++..+|..+|..++.++.
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=99.51 E-value=6.7e-14 Score=87.48 Aligned_cols=63 Identities=29% Similarity=0.470 Sum_probs=59.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhhhhhhhChHHHHHHHHHHHHHHHhhc
Q 033824 44 EVVSLFFADSERLLNDLTRALDQPTIDFKMVDSHVHQLKGSSSSIGAERIKNACVAFRNFCEEQN 108 (111)
Q Consensus 44 ~ll~~F~~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~LKGsa~~lGa~~L~~~~~~lE~~~~~gd 108 (111)
+++..|+++.+..+..|..++..+ |+..+.+.+|+|||+|+++|+..|..+|..+|..++...
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 678999999999999999999988 999999999999999999999999999999999988654
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=99.45 E-value=3.6e-13 Score=85.64 Aligned_cols=64 Identities=30% Similarity=0.527 Sum_probs=60.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhc----CCCCCHHHHHHHHHHhhhhhhhhChHHHHHHHHHHHHHHHhhc
Q 033824 43 AEVVSLFFADSERLLNDLTRALD----QPTIDFKMVDSHVHQLKGSSSSIGAERIKNACVAFRNFCEEQN 108 (111)
Q Consensus 43 ~~ll~~F~~~~~~~l~~L~~a~~----~~~~D~~~l~~~aH~LKGsa~~lGa~~L~~~~~~lE~~~~~gd 108 (111)
.+++..|+++.++.+..|.+++. .. |+..+.+.+|+|||+++++|+.++...|..+|.+++.+.
T Consensus 2 ~~l~~~f~~~~~~~l~~l~~~~~~~~~~~--d~~~l~~~~H~LkGsa~~~G~~~l~~~~~~lE~~~~~~~ 69 (94)
T cd00088 2 EELLELFLEEAEELLEELERALLELEDAE--DLNEIFRAAHTLKGSAASLGLQRLAQLAHQLEDLLDALR 69 (94)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHcCCHH--HHHHHHHHHHhhhhHHhcCChHHHHHHHHHHHHHHHHHH
Confidence 47899999999999999999999 78 999999999999999999999999999999999999864
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=99.20 E-value=8.7e-11 Score=99.24 Aligned_cols=74 Identities=24% Similarity=0.371 Sum_probs=69.7
Q ss_pred ccCCHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhhhhhhhChHHHHHHHHHHHHHHHhhccC
Q 033824 35 DESNPDFVAEVVSLFFADSERLLNDLTRALDQPTIDFKMVDSHVHQLKGSSSSIGAERIKNACVAFRNFCEEQNIE 110 (111)
Q Consensus 35 ~~~~~~~~~~ll~~F~~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~LKGsa~~lGa~~L~~~~~~lE~~~~~gd~~ 110 (111)
...+++.+.+++..|+++.+..+..|..++..+ |+..+++.+|+|||+++++|+.+++.+|..||..++.|++.
T Consensus 874 ~~~~~~~~~~~~~~f~~~~~~~~~~l~~~~~~~--d~~~~~~~~H~lkg~~~~~g~~~l~~~~~~le~~~~~~~~~ 947 (968)
T TIGR02956 874 EVLGVEKVRQLVALFKTSSAEQLEELSAARAVD--DDAQIKKLAHKLKGSAGSLGLTQLTQLCQQLEKQGKTGALE 947 (968)
T ss_pred HhcCcHHHHHHHHHHHHhhHHHHHHHHHHHhCC--CHHHHHHHHHHHHHHHHHhCHHHHHHHHHHHHHhcccCCcc
Confidence 446788999999999999999999999999999 99999999999999999999999999999999999988753
No 7
>PRK10618 phosphotransfer intermediate protein in two-component regulatory system with RcsBC; Provisional
Probab=98.99 E-value=1.5e-09 Score=92.91 Aligned_cols=64 Identities=19% Similarity=0.290 Sum_probs=61.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhhhhhhhChHHHHHHHHHHHHHHHhhcc
Q 033824 44 EVVSLFFADSERLLNDLTRALDQPTIDFKMVDSHVHQLKGSSSSIGAERIKNACVAFRNFCEEQNI 109 (111)
Q Consensus 44 ~ll~~F~~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~LKGsa~~lGa~~L~~~~~~lE~~~~~gd~ 109 (111)
.+...|++..|.++..|..++..+ |+..+.+.||+|||+++++|+..+.++|..||+.++.+|.
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=98.58 E-value=2.6e-07 Score=78.07 Aligned_cols=68 Identities=25% Similarity=0.329 Sum_probs=62.8
Q ss_pred cCCHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhhhhhhhChHHHHHHHHHHHHHHH
Q 033824 36 ESNPDFVAEVVSLFFADSERLLNDLTRALDQPTIDFKMVDSHVHQLKGSSSSIGAERIKNACVAFRNFCE 105 (111)
Q Consensus 36 ~~~~~~~~~ll~~F~~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~LKGsa~~lGa~~L~~~~~~lE~~~~ 105 (111)
..+++.+.+++..|..+.+..+..+..+...+ |+..+.+++|+|||+++++|+..+..+|..+|.++.
T Consensus 819 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~--~~~~~~~~ah~lkg~~~~lg~~~l~~~~~~le~~~~ 886 (914)
T PRK11466 819 LMGTEKIHEWLALFKQHALPLLDEIDIARASQ--DSEKIKRAAHQLKSSCSSLGMRQASQACAQLEQQPL 886 (914)
T ss_pred hcCHHHHHHHHHHHHHhhHHHHHHHHHHHHCC--CHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhCCCC
Confidence 34667788999999999999999999999999 999999999999999999999999999999998653
No 9
>PRK11091 aerobic respiration control sensor protein ArcB; Provisional
Probab=98.57 E-value=2.9e-07 Score=76.86 Aligned_cols=77 Identities=18% Similarity=0.264 Sum_probs=67.5
Q ss_pred HHhhhccCCHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhhhhhhhChHHHHHHHHHHHHHHHhhc
Q 033824 30 LQQLQDESNPDFVAEVVSLFFADSERLLNDLTRALDQPTIDFKMVDSHVHQLKGSSSSIGAERIKNACVAFRNFCEEQN 108 (111)
Q Consensus 30 L~~L~~~~~~~~~~~ll~~F~~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~LKGsa~~lGa~~L~~~~~~lE~~~~~gd 108 (111)
+..+.+..+...+...+..|.+..+..++.+..++..+ |+..+...+|+|||+++++|+..++.+|..+|.....+.
T Consensus 671 l~~~~~~~g~~~~~~~l~~~~~~~~~~~~~l~~~l~~~--d~~~~~~~ah~l~g~~~~~g~~~l~~~~~~le~~~~~~~ 747 (779)
T PRK11091 671 LEQYVELVGPKLITDSLAVFEKMMPGYLSVLDSNLTAR--DQKGIVEEAHKIKGAAGSVGLRHLQQLAQQIQSPDLPAW 747 (779)
T ss_pred HHHHHHhcCHHHHHHHHHHHHHhhHHHHHHHHHHHHCC--CHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHhCcCcccc
Confidence 33444445667888999999999999999999999999 999999999999999999999999999999998766554
No 10
>COG0643 CheA Chemotaxis protein histidine kinase and related kinases [Cell motility and secretion / Signal transduction mechanisms]
Probab=98.44 E-value=1e-06 Score=74.09 Aligned_cols=66 Identities=23% Similarity=0.399 Sum_probs=55.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHh---cCCCCCH---HHHHHHHHHhhhhhhhhChHHHHHHHHHHHHHH
Q 033824 39 PDFVAEVVSLFFADSERLLNDLTRAL---DQPTIDF---KMVDSHVHQLKGSSSSIGAERIKNACVAFRNFC 104 (111)
Q Consensus 39 ~~~~~~ll~~F~~~~~~~l~~L~~a~---~~~~~D~---~~l~~~aH~LKGsa~~lGa~~L~~~~~~lE~~~ 104 (111)
.....+++..|+.++++.++.|.+.+ +..+.|. ..+.+.||+|||+||++|+..+..+|+.+|...
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 45678899999999999999999864 3322244 477999999999999999999999999999753
No 11
>PRK10547 chemotaxis protein CheA; Provisional
Probab=98.42 E-value=1.4e-06 Score=72.89 Aligned_cols=63 Identities=21% Similarity=0.429 Sum_probs=53.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHh---cCCCCCH---HHHHHHHHHhhhhhhhhChHHHHHHHHHHHHHHH
Q 033824 43 AEVVSLFFADSERLLNDLTRAL---DQPTIDF---KMVDSHVHQLKGSSSSIGAERIKNACVAFRNFCE 105 (111)
Q Consensus 43 ~~ll~~F~~~~~~~l~~L~~a~---~~~~~D~---~~l~~~aH~LKGsa~~lGa~~L~~~~~~lE~~~~ 105 (111)
.+++..|++++.+.++.|++.+ +..+.|. ..+.+.+|+|||+|+++|+..+..+|+.+|....
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 5789999999999999998874 4333353 5778999999999999999999999999997653
No 12
>PRK11107 hybrid sensory histidine kinase BarA; Provisional
Probab=98.36 E-value=3e-06 Score=71.34 Aligned_cols=71 Identities=21% Similarity=0.343 Sum_probs=66.3
Q ss_pred cCCHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhhhhhhhChHHHHHHHHHHHHHHHhhc
Q 033824 36 ESNPDFVAEVVSLFFADSERLLNDLTRALDQPTIDFKMVDSHVHQLKGSSSSIGAERIKNACVAFRNFCEEQN 108 (111)
Q Consensus 36 ~~~~~~~~~ll~~F~~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~LKGsa~~lGa~~L~~~~~~lE~~~~~gd 108 (111)
.+.++...+++..|.++.+..+..|..++... |+..+...+|++||+++++|+.++..+|..+|+.++.+.
T Consensus 820 ~~~~~~~~~~l~~~~~~~~~~~~~l~~~~~~~--~~~~~~~~~h~l~g~~~~~g~~~l~~~~~~le~~~~~~~ 890 (919)
T PRK11107 820 AGKPDLARDMLQMLLDFLPEVRNKVEEALAGE--DPEGLLDLIHKLHGSCSYSGVPRLKKLCQLIEQQLRSGT 890 (919)
T ss_pred CCCHHHHHHHHHHHHHhHHHHHHHHHHHHHCC--CHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHcCC
Confidence 35778889999999999999999999999999 999999999999999999999999999999999998653
No 13
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=97.01 E-value=0.0054 Score=53.73 Aligned_cols=69 Identities=13% Similarity=0.251 Sum_probs=63.0
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhhhhhhhChHHHHHHHHHHHHHHHhh
Q 033824 37 SNPDFVAEVVSLFFADSERLLNDLTRALDQPTIDFKMVDSHVHQLKGSSSSIGAERIKNACVAFRNFCEEQ 107 (111)
Q Consensus 37 ~~~~~~~~ll~~F~~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~LKGsa~~lGa~~L~~~~~~lE~~~~~g 107 (111)
.+...+.+++..|.......+..+..+...+ |...+...+|+++|++..+|+..+...|.++|......
T Consensus 1097 ~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~h~~~g~~~~l~~~~l~~~~~~~e~~~~~~ 1165 (1197)
T PRK09959 1097 NDLQLMQEILMTFQHETHKDLPAAFHALEAG--DNRTFHQCIHRIHGAANILNLQKLINISHQLEITPVSD 1165 (1197)
T ss_pred CCHHHHHHHHHHHHHhhHHHHHHHHHHHHcC--CHHHHHHHHHHHHHHHHHcCHHHHHHHHHHHHHhhhcC
Confidence 5667889999999999999999999999999 99999999999999999999999999999999877644
No 14
>PRK15347 two component system sensor kinase SsrA; Provisional
Probab=96.98 E-value=0.0034 Score=53.19 Aligned_cols=61 Identities=21% Similarity=0.389 Sum_probs=51.4
Q ss_pred HHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhhhhhhhChHHHHHHHHHHHHHHHhhcc
Q 033824 45 VVSLFFADSERLLNDLTRALDQPTIDFKMVDSHVHQLKGSSSSIGAERIKNACVAFRNFCEEQNI 109 (111)
Q Consensus 45 ll~~F~~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~LKGsa~~lGa~~L~~~~~~lE~~~~~gd~ 109 (111)
+...+.+.....+..+..++..+ | .+.+.+|++||+++.+|+.++...|..+|..++.+..
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 34455556677888888888887 6 8999999999999999999999999999999887653
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=91.74 E-value=1.9 Score=26.11 Aligned_cols=51 Identities=20% Similarity=0.334 Sum_probs=40.8
Q ss_pred HHhhhccCCHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhh
Q 033824 30 LQQLQDESNPDFVAEVVSLFFADSERLLNDLTRALDQPTIDFKMVDSHVHQLK 82 (111)
Q Consensus 30 L~~L~~~~~~~~~~~ll~~F~~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~LK 82 (111)
|......++.+-+..+....-......+..|..++..+ ||..+....++||
T Consensus 17 le~~~~~~~~~~L~~l~~~~~~~~~~~~~~l~~~f~~~--d~~~A~~~~~kLk 67 (78)
T PF07743_consen 17 LEEAQNSDDEAELEELKKEIEERIKELIKELAEAFDAK--DWEEAKEALRKLK 67 (78)
T ss_dssp HHHHCCCTSHHHHHHHHHHHHHHHHHHHHHHHHHHHTT---HHHHHHHHHHHH
T ss_pred HHHhhcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHccC--cHHHHHHHHHHHH
Confidence 33433335667888888888888899999999999999 9999999999985
No 16
>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=90.20 E-value=4 Score=27.54 Aligned_cols=61 Identities=16% Similarity=0.175 Sum_probs=47.1
Q ss_pred hcchhHHHHHHHhhhccCCHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhhh
Q 033824 20 EGVLDNQFLQLQQLQDESNPDFVAEVVSLFFADSERLLNDLTRALDQPTIDFKMVDSHVHQLKGS 84 (111)
Q Consensus 20 ~~~ld~~~~~L~~L~~~~~~~~~~~ll~~F~~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~LKGs 84 (111)
+-++|.-++.+... .|+++-+..++...-...|+.++.+..+++.+ |..+++.+.--+.++
T Consensus 29 eAL~~~yV~~V~~~--AGG~e~f~~i~~~~~~~~~~~~ea~~~Ai~~~--dla~vk~~vn~~~~s 89 (123)
T PF05396_consen 29 EALAEQYVNSVKGY--AGGEEGFAAIMSHAEANSPAAAEAFNEAIESG--DLATVKAAVNLAGAS 89 (123)
T ss_pred HHHHHHHHHHHHHH--hcCHHHHHHHHHHHHhCCHHHHHHHHHHHHhC--CHHHHHHHHHHHHHH
Confidence 34455434455555 48899999999998888999999999999999 999988876655543
No 17
>PRK01356 hscB co-chaperone HscB; Provisional
Probab=87.71 E-value=5.1 Score=28.12 Aligned_cols=59 Identities=8% Similarity=0.137 Sum_probs=36.2
Q ss_pred chhHHHHHHHhhhccCCHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhh
Q 033824 22 VLDNQFLQLQQLQDESNPDFVAEVVSLFFADSERLLNDLTRALDQPTIDFKMVDSHVHQLK 82 (111)
Q Consensus 22 ~ld~~~~~L~~L~~~~~~~~~~~ll~~F~~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~LK 82 (111)
.|.+.+..-+.+.+..+.+-+.++....-......+..|.+++..+ ||+.+...+-+||
T Consensus 91 fLme~me~rE~le~~~~~~~L~~l~~~~~~~~~~~~~~l~~~f~~~--d~~~A~~~~~~L~ 149 (166)
T PRK01356 91 ELSIFWDEMERIENTILFSDLEKIKNKYELMYKNEIDSLKQAFEEQ--NLSDATIKTSKLK 149 (166)
T ss_pred HHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcC--CHHHHHHHHHHHH
Confidence 3334333333444444555556666666666667777888888888 9887777665554
No 18
>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=86.75 E-value=6.1 Score=27.44 Aligned_cols=52 Identities=10% Similarity=0.147 Sum_probs=39.2
Q ss_pred HHHhhhccCCHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhh
Q 033824 29 QLQQLQDESNPDFVAEVVSLFFADSERLLNDLTRALDQPTIDFKMVDSHVHQLK 82 (111)
Q Consensus 29 ~L~~L~~~~~~~~~~~ll~~F~~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~LK 82 (111)
.+.++....+.+-+..+....-.........|..++..+ ||..+...+.+||
T Consensus 89 ~lee~~~~~d~~~L~~l~~~~~~~~~~~~~~l~~~~~~~--d~~~A~~~~~kLk 140 (157)
T TIGR00714 89 ELDEIEQAKDEARLESFIKRVKKMFQTRHQLLVEQLDNQ--TWAAAADYTRKLR 140 (157)
T ss_pred HHHHHHhCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcC--CHHHHHHHHHHHH
Confidence 344444455667777777777777777888888999999 9998888877765
No 19
>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=84.26 E-value=8.1 Score=24.30 Aligned_cols=67 Identities=10% Similarity=0.210 Sum_probs=50.3
Q ss_pred HHHHHHhhhhhcchhHHHHHHHhhhc-cCCHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHH
Q 033824 10 LLEYTKSLFMEGVLDNQFLQLQQLQD-ESNPDFVAEVVSLFFADSERLLNDLTRALDQPTIDFKMVDSHVHQ 80 (111)
Q Consensus 10 ~~~~~~~~~~~~~ld~~~~~L~~L~~-~~~~~~~~~ll~~F~~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~ 80 (111)
....+..++.+|++++. ..+.+.. ....+-..+++.......+.-...+..++... .+..++.+.|.
T Consensus 16 v~~ild~L~~~gvlt~~--~~e~I~~~~t~~~qa~~Lld~L~trG~~Af~~F~~aL~~~--~~~~La~lL~~ 83 (86)
T cd08323 16 TSYIMDHMISDGVLTLD--EEEKVKSKATQKEKAVMLINMILTKDNHAYVSFYNALLHE--GYKDLALLLHD 83 (86)
T ss_pred HHHHHHHHHhcCCCCHH--HHHHHHcCCChHHHHHHHHHHHHhcCHHHHHHHHHHHHhc--CChHHHHHHhc
Confidence 45577888889999974 3444443 34577788999999999999999999998765 67777777653
No 20
>PRK03578 hscB co-chaperone HscB; Provisional
Probab=79.50 E-value=16 Score=25.88 Aligned_cols=45 Identities=18% Similarity=0.194 Sum_probs=34.9
Q ss_pred cCCHHHHHHHHHHHHHHHHHHHHHHHHHhcC-CCCCHHHHHHHHHHhh
Q 033824 36 ESNPDFVAEVVSLFFADSERLLNDLTRALDQ-PTIDFKMVDSHVHQLK 82 (111)
Q Consensus 36 ~~~~~~~~~ll~~F~~~~~~~l~~L~~a~~~-~~~D~~~l~~~aH~LK 82 (111)
.++++-+..+....-......+..|..++.. + ||..+...+.+||
T Consensus 113 ~~d~~~L~~l~~e~~~~~~~~~~~l~~~~~~~~--d~~~A~~~~~kL~ 158 (176)
T PRK03578 113 ARDVDALDALLAELRDERRERYAELGALLDSRG--DDQAAAEAVRQLM 158 (176)
T ss_pred cCCHHHHHHHHHHHHHHHHHHHHHHHHHHHccc--cHHHHHHHHHHHH
Confidence 3466677777777777777778888888877 7 8998888887776
No 21
>PRK01773 hscB co-chaperone HscB; Provisional
Probab=78.89 E-value=17 Score=25.67 Aligned_cols=45 Identities=13% Similarity=0.299 Sum_probs=31.8
Q ss_pred cCCHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhh
Q 033824 36 ESNPDFVAEVVSLFFADSERLLNDLTRALDQPTIDFKMVDSHVHQLK 82 (111)
Q Consensus 36 ~~~~~~~~~ll~~F~~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~LK 82 (111)
..+.+-+..+....-....+.+..|..++..+ ||+.+...+-+||
T Consensus 110 ~~d~~~L~~l~~~v~~~~~~~~~~l~~~~~~~--d~~~A~~~~~rL~ 154 (173)
T PRK01773 110 QQDEDALTAFSKEIKQEQQAILTELSTALNSQ--QWQQASQINDRLR 154 (173)
T ss_pred cCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcC--CHHHHHHHHHHHH
Confidence 34566666666666666677778888888888 8887777665544
No 22
>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=72.54 E-value=39 Score=26.10 Aligned_cols=65 Identities=15% Similarity=0.265 Sum_probs=46.0
Q ss_pred HHhhhccCCHHHHHHHHHHHH-HHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhhhhhhhChHHHHHHHHH
Q 033824 30 LQQLQDESNPDFVAEVVSLFF-ADSERLLNDLTRALDQPTIDFKMVDSHVHQLKGSSSSIGAERIKNACVA 99 (111)
Q Consensus 30 L~~L~~~~~~~~~~~ll~~F~-~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~LKGsa~~lGa~~L~~~~~~ 99 (111)
+..|-..|......++...|- .+-.=..-.++..+..+ +|+++...+-+=|+ -+|..++.+.|..
T Consensus 184 i~~li~~~~~k~A~kl~k~Fkv~dkrfw~lki~aLa~~~--~w~eL~~fa~skKs---PIGyepFv~~~~~ 249 (319)
T PF04840_consen 184 IRKLIEMGQEKQAEKLKKEFKVPDKRFWWLKIKALAENK--DWDELEKFAKSKKS---PIGYEPFVEACLK 249 (319)
T ss_pred HHHHHHCCCHHHHHHHHHHcCCcHHHHHHHHHHHHHhcC--CHHHHHHHHhCCCC---CCChHHHHHHHHH
Confidence 344433455666777777772 33333455678888899 99999999987554 5999999999864
No 23
>COG3046 Uncharacterized protein related to deoxyribodipyrimidine photolyase [General function prediction only]
Probab=70.70 E-value=4.3 Score=33.05 Aligned_cols=67 Identities=18% Similarity=0.093 Sum_probs=57.7
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhhhhhhhChHHHHHHHHHHHHHHHhhcc
Q 033824 37 SNPDFVAEVVSLFFADSERLLNDLTRALDQPTIDFKMVDSHVHQLKGSSSSIGAERIKNACVAFRNFCEEQNI 109 (111)
Q Consensus 37 ~~~~~~~~ll~~F~~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~LKGsa~~lGa~~L~~~~~~lE~~~~~gd~ 109 (111)
-+.+-....+..|+++.-.....-+.++..+ |+. +=|++-+.+-|+|...=.+.|+..+.+-++|+.
T Consensus 225 vtr~~A~~~L~~Fi~~~L~nFG~yQDam~~d--~~~----L~HSllS~alNigLL~PleVi~Aa~~Ay~~g~i 291 (505)
T COG3046 225 VTRTQALRALKHFIADRLPNFGSYQDAMSAD--DPH----LWHSLLSFALNIGLLTPLEVIRAALKAYREGDI 291 (505)
T ss_pred CCHHHHHHHHHHHHHHhhhcCCcHHHHHhcC--Cch----hHHHHHHHHhhccCCCHHHHHHHHHHhhccCCC
Confidence 4566678899999999988888888888887 765 789999999999999999999999998887664
No 24
>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=65.89 E-value=68 Score=25.69 Aligned_cols=50 Identities=8% Similarity=0.124 Sum_probs=39.2
Q ss_pred HHHHHHHHHHH-HHHHHHHhcCCCCCHHHHHHHHHHhhhhhhhhChHHHHHHHHHHHHHHHhh
Q 033824 46 VSLFFADSERL-LNDLTRALDQPTIDFKMVDSHVHQLKGSSSSIGAERIKNACVAFRNFCEEQ 107 (111)
Q Consensus 46 l~~F~~~~~~~-l~~L~~a~~~~~~D~~~l~~~aH~LKGsa~~lGa~~L~~~~~~lE~~~~~g 107 (111)
+..|+..+... +..+-.|...+ |.+.|+.++ +-......+..+++..+.|
T Consensus 243 ~~~Fl~gar~aI~p~ILeAf~kG--D~e~LK~~l----------se~vy~~f~a~I~qr~~~G 293 (378)
T TIGR00984 243 KEHFLRFLREYIVPEILEAYVKG--DLEVLKSWC----------SEAPFSVYATVVKEYKKMG 293 (378)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcC--CHHHHHHhh----------CHHHHHHHHHHHHHHHHCC
Confidence 67788888888 68899999999 999999884 4456666777777666555
No 25
>PHA00435 capsid assembly protein
Probab=65.06 E-value=29 Score=26.74 Aligned_cols=56 Identities=13% Similarity=0.204 Sum_probs=42.6
Q ss_pred hcchhHHHHHHHhhhccCCHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHH
Q 033824 20 EGVLDNQFLQLQQLQDESNPDFVAEVVSLFFADSERLLNDLTRALDQPTIDFKMVDSHVH 79 (111)
Q Consensus 20 ~~~ld~~~~~L~~L~~~~~~~~~~~ll~~F~~~~~~~l~~L~~a~~~~~~D~~~l~~~aH 79 (111)
+-|+++-.+.+... .|+++-+..|....-.+.+...+.|..++..+ |..+++.+.-
T Consensus 182 EAL~eQyV~sv~~y--AGG~E~F~~i~shl~atnp~~~eal~~Ave~~--dl~t~K~ivn 237 (306)
T PHA00435 182 EALVEQYVESVVEY--AGGRERFQAIYSHLEATNPSAAESLEAAIENR--DLATVKAIIN 237 (306)
T ss_pred HHHHHHHHHHHHHH--hccHHHHHHHHHHHHhcChhHHHHHHHHHHcC--CHHHHHHHHH
Confidence 34555434455444 47888889998888778999999999999999 9988876543
No 26
>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=63.59 E-value=18 Score=21.13 Aligned_cols=37 Identities=27% Similarity=0.432 Sum_probs=29.3
Q ss_pred HHHHHHHhhhccCCHHHHHHHHHHHHHHHHHHHHHHHH
Q 033824 25 NQFLQLQQLQDESNPDFVAEVVSLFFADSERLLNDLTR 62 (111)
Q Consensus 25 ~~~~~L~~L~~~~~~~~~~~ll~~F~~~~~~~l~~L~~ 62 (111)
++|.+++++.. .+|+++..++...-.+.|+.+..|.+
T Consensus 8 Pqf~~lR~~vq-~NP~lL~~lLqql~~~nP~l~q~I~~ 44 (59)
T PF09280_consen 8 PQFQQLRQLVQ-QNPQLLPPLLQQLGQSNPQLLQLIQQ 44 (59)
T ss_dssp HHHHHHHHHHH-C-GGGHHHHHHHHHCCSHHHHHHHHH
T ss_pred hHHHHHHHHHH-HCHHHHHHHHHHHhccCHHHHHHHHH
Confidence 56788888775 68899999999988888888887765
No 27
>PRK05014 hscB co-chaperone HscB; Provisional
Probab=62.72 E-value=51 Score=23.13 Aligned_cols=41 Identities=15% Similarity=0.191 Sum_probs=28.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhh
Q 033824 40 DFVAEVVSLFFADSERLLNDLTRALDQPTIDFKMVDSHVHQLK 82 (111)
Q Consensus 40 ~~~~~ll~~F~~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~LK 82 (111)
..+.++....-.........|..++..+ ||..+...+-+||
T Consensus 113 ~~l~~l~~~~~~~~~~~~~~l~~~~~~~--d~~~A~~~~~~Lk 153 (171)
T PRK05014 113 AALESFIKRVKKMFKTRLQQMVEQLDNE--AWDAAADTVRKLK 153 (171)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhC--CHHHHHHHHHHHH
Confidence 3355555555556666667788888888 9988887776665
No 28
>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=62.61 E-value=25 Score=21.11 Aligned_cols=49 Identities=20% Similarity=0.257 Sum_probs=32.3
Q ss_pred HHHHHHHHHhhhhhcchhHHHHHHHhhhccCCHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Q 033824 7 QRRLLEYTKSLFMEGVLDNQFLQLQQLQDESNPDFVAEVVSLFFADSERLLNDLTRALDQ 66 (111)
Q Consensus 7 ~~~~~~~~~~~~~~~~ld~~~~~L~~L~~~~~~~~~~~ll~~F~~~~~~~l~~L~~a~~~ 66 (111)
|.++.++++.+....-+|+ .-.+++.++.+.|++++-...-.|...=..
T Consensus 2 K~~l~~Lv~~iDp~~~ld~-----------~vee~Ll~laddFv~~v~~~ac~lAKhR~s 50 (68)
T PF03847_consen 2 KRKLQELVKQIDPNEKLDP-----------DVEELLLELADDFVDDVVSFACRLAKHRKS 50 (68)
T ss_dssp HHHHHHHHHCC-SS----H-----------HHHHHHHHHHHHHHHHHHHHHHHHHHHTT-
T ss_pred hHHHHHHHHHcCCCCCCCH-----------HHHHHHHHHHHHHHHHHHHHHHHHHhccCC
Confidence 5678888888877777775 234678899999999998877777665333
No 29
>PF14615 Rsa3: Ribosome-assembly protein 3
Probab=61.80 E-value=26 Score=19.63 Aligned_cols=42 Identities=14% Similarity=0.089 Sum_probs=28.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhhhhhhh
Q 033824 44 EVVSLFFADSERLLNDLTRALDQPTIDFKMVDSHVHQLKGSSSSI 88 (111)
Q Consensus 44 ~ll~~F~~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~LKGsa~~l 88 (111)
..+....++-.++|++|+++-.= .-..+.-++|.|+..+..+
T Consensus 5 ~yl~~~t~efgdDLd~lR~~~dF---~~~sl~~Li~aL~~G~~~F 46 (47)
T PF14615_consen 5 FYLQRLTDEFGDDLDELRKAPDF---TDKSLPLLIDALQQGTDMF 46 (47)
T ss_pred HHHHHHHHHHHHHHHHHhcCCCC---CchhHHHHHHHHHhccccc
Confidence 44556666667778888854222 2367888999999877543
No 30
>KOG1142 consensus Transcription initiation factor TFIID, subunit TAF12 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=58.30 E-value=18 Score=27.46 Aligned_cols=49 Identities=16% Similarity=0.197 Sum_probs=37.4
Q ss_pred HHHHHHHHHhhhhhcchhHHHHHHHhhhccCCHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Q 033824 7 QRRLLEYTKSLFMEGVLDNQFLQLQQLQDESNPDFVAEVVSLFFADSERLLNDLTRALDQ 66 (111)
Q Consensus 7 ~~~~~~~~~~~~~~~~ld~~~~~L~~L~~~~~~~~~~~ll~~F~~~~~~~l~~L~~a~~~ 66 (111)
+.++.++++.+.-++.||+ .-++++.++.+.|+++.-...-.|...-..
T Consensus 157 k~kl~dLvqqId~~~~LD~-----------dVedlLleiADdFV~sii~~sC~LAKHRKs 205 (258)
T KOG1142|consen 157 KRKLDDLVQQIDGTTKLDD-----------DVEDLLLEIADDFVSSIIHRSCKLAKHRKS 205 (258)
T ss_pred ccchhHHHHhhcCcccccH-----------HHHHHHHHHHHHHHHHHHHHHHHHHHhccc
Confidence 4577888888877777775 245688999999999998888877766433
No 31
>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=55.17 E-value=58 Score=21.45 Aligned_cols=50 Identities=8% Similarity=0.131 Sum_probs=37.9
Q ss_pred HHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhhhhhhhChHHHHHHHHHHHHHHHhh
Q 033824 46 VSLFFADSERLLNDLTRALDQPTIDFKMVDSHVHQLKGSSSSIGAERIKNACVAFRNFCEEQ 107 (111)
Q Consensus 46 l~~F~~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~LKGsa~~lGa~~L~~~~~~lE~~~~~g 107 (111)
...|+..+.+.+..+..|...+ |++.++.+ ++-.-+..++..+......|
T Consensus 17 ~~~F~~~ak~~f~~i~~A~~~~--D~~~l~~~----------~t~~~~~~~~~~i~~~~~~g 66 (147)
T PF04280_consen 17 PAAFLEEAKEAFLPIQEAWAKG--DLEALRPL----------LTEELYERLQAEIKARRSRG 66 (147)
T ss_dssp HHHHHHHHHHTHHHHHHHHHHT---HHHHHHH----------B-HHHHHHHHHHHHHHHHTT
T ss_pred HHHHHHHHHHHHHHHHHHHHcC--CHHHHHHH----------hCHHHHHHHHHHHHHHHHcC
Confidence 6678888888899999999999 99999887 56666677777777664444
No 32
>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=51.76 E-value=25 Score=24.28 Aligned_cols=28 Identities=14% Similarity=0.311 Sum_probs=22.0
Q ss_pred HHHHHHHHHHHHHhcCCCCCHHHHHHHHHH
Q 033824 51 ADSERLLNDLTRALDQPTIDFKMVDSHVHQ 80 (111)
Q Consensus 51 ~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~ 80 (111)
+.+.+.+.+|+..++++ ||..++...|.
T Consensus 46 ~~~~~r~~eLk~lI~kk--~W~~vrn~irg 73 (142)
T TIGR03042 46 EAAKDRLPELASLVAKE--DWVFTRNLIHG 73 (142)
T ss_pred HHHHHhhHHHHHHHhhc--chHHHHHHHhc
Confidence 34667788888889999 99988887664
No 33
>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=49.40 E-value=58 Score=25.96 Aligned_cols=45 Identities=20% Similarity=0.335 Sum_probs=35.2
Q ss_pred HHHHHHHhhhccCCHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHH
Q 033824 25 NQFLQLQQLQDESNPDFVAEVVSLFFADSERLLNDLTRALDQPTIDFKMVDSH 77 (111)
Q Consensus 25 ~~~~~L~~L~~~~~~~~~~~ll~~F~~~~~~~l~~L~~a~~~~~~D~~~l~~~ 77 (111)
++|.+|+++.. .+|+++..++...-+..|+.++.|.+ |.+.+.++
T Consensus 255 pqf~~lR~~vq-~NP~~L~~lLqql~~~nP~l~q~I~~-------n~e~Fl~l 299 (378)
T TIGR00601 255 PQFQQLRQVVQ-QNPQLLPPLLQQIGQENPQLLQQISQ-------HPEQFLQM 299 (378)
T ss_pred HHHHHHHHHHH-HCHHHHHHHHHHHHhhCHHHHHHHHH-------CHHHHHHH
Confidence 56888888775 69999999999999999988887765 45555444
No 34
>PRK08818 prephenate dehydrogenase; Provisional
Probab=48.94 E-value=92 Score=24.67 Aligned_cols=35 Identities=14% Similarity=0.043 Sum_probs=25.4
Q ss_pred HHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhhhhh
Q 033824 50 FADSERLLNDLTRALDQPTIDFKMVDSHVHQLKGSSS 86 (111)
Q Consensus 50 ~~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~LKGsa~ 86 (111)
++...+.+..+++++.++ |++.+.+..|++.-+-.
T Consensus 233 l~~~~~~L~~l~~~i~~~--D~~~~~~~~~~f~~a~~ 267 (370)
T PRK08818 233 LDRLLAQLQELRALVAQG--DDAARARFRAQFLHANA 267 (370)
T ss_pred HHHHHHHHHHHHHHHHcC--CHHHHHHHHHHHHHHHh
Confidence 344445567788889999 99999988777665443
No 35
>KOG4552 consensus Vitamin-D-receptor interacting protein complex component [Transcription]
Probab=46.56 E-value=1.2e+02 Score=22.67 Aligned_cols=40 Identities=8% Similarity=0.120 Sum_probs=28.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhhh
Q 033824 44 EVVSLFFADSERLLNDLTRALDQPTIDFKMVDSHVHQLKGS 84 (111)
Q Consensus 44 ~ll~~F~~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~LKGs 84 (111)
.++.+-+-++.+.+..|++|- .+++.-+.+-.+||+|-.+
T Consensus 102 ~iLtta~fqA~qKLksi~~A~-krpvsSEelIKyAHrIS~~ 141 (272)
T KOG4552|consen 102 VILTTACFQANQKLKSIKEAE-KRPVSSEELIKYAHRISKH 141 (272)
T ss_pred HHHHHHHHHHHHHHHHHHHHh-cCCCCHHHHHHHHHHhhhc
Confidence 345555666677777777763 4457888999999998654
No 36
>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=46.28 E-value=1.2e+02 Score=22.36 Aligned_cols=39 Identities=23% Similarity=0.333 Sum_probs=26.0
Q ss_pred CCHHHHHHHH-------HHHHHHHHHHHHHHHHHhcCCCCCHHHHHHH
Q 033824 37 SNPDFVAEVV-------SLFFADSERLLNDLTRALDQPTIDFKMVDSH 77 (111)
Q Consensus 37 ~~~~~~~~ll-------~~F~~~~~~~l~~L~~a~~~~~~D~~~l~~~ 77 (111)
.+|+++.+++ ...+++..+.+..++.++.++ |.+.+.++
T Consensus 210 ~~p~l~~~I~~~N~~~~~~~l~~~~~~L~~l~~~l~~~--d~~~l~~~ 255 (258)
T PF02153_consen 210 SDPELWADIFLSNPENLLEALDEFIKELNELREALEAG--DEEELEEL 255 (258)
T ss_dssp S-HHHHHHHHHHTHHHHHHHHHHHHHHHHHHHHHHHTT--SHHHHHHH
T ss_pred CChHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHcC--CHHHHHHH
Confidence 4555555553 234555566678888899999 99988765
No 37
>PF04282 DUF438: Family of unknown function (DUF438); InterPro: IPR007380 This is a a group of uncharacterised proteins.
Probab=44.13 E-value=73 Score=19.36 Aligned_cols=50 Identities=16% Similarity=0.279 Sum_probs=32.3
Q ss_pred HHHhhhccCCHHHHHHHHHHHHHHH-HHHHHHHHHHhcCCCCCHHHHHHHH
Q 033824 29 QLQQLQDESNPDFVAEVVSLFFADS-ERLLNDLTRALDQPTIDFKMVDSHV 78 (111)
Q Consensus 29 ~L~~L~~~~~~~~~~~ll~~F~~~~-~~~l~~L~~a~~~~~~D~~~l~~~a 78 (111)
-|..|-.+.+++-+++-+...+.+. +..+..+++.+=....+.+.+.++|
T Consensus 5 ii~~Lh~G~~~e~vk~~F~~~~~~Vs~~EI~~~Eq~Li~eG~~~eeiq~LC 55 (71)
T PF04282_consen 5 IIKRLHEGEDPEEVKEEFKKLFSDVSASEISAAEQELIQEGMPVEEIQKLC 55 (71)
T ss_pred HHHHHhCCCCHHHHHHHHHHHHCCCCHHHHHHHHHHHHHcCCCHHHHHHHh
Confidence 3556666777777666655555544 7777777776544446778877765
No 38
>COG2991 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=44.08 E-value=4.6 Score=24.88 Aligned_cols=20 Identities=35% Similarity=0.572 Sum_probs=16.7
Q ss_pred HHhhhhhhhhChHHHHHHHH
Q 033824 79 HQLKGSSSSIGAERIKNACV 98 (111)
Q Consensus 79 H~LKGsa~~lGa~~L~~~~~ 98 (111)
-++|||+|-+++..+...|.
T Consensus 27 k~I~GSCGGi~alGi~K~Cd 46 (77)
T COG2991 27 KSIKGSCGGIAALGIEKVCD 46 (77)
T ss_pred cccccccccHHhhccchhcC
Confidence 46899999999988888764
No 39
>PLN02407 diphosphomevalonate decarboxylase
Probab=43.82 E-value=44 Score=26.37 Aligned_cols=32 Identities=9% Similarity=0.157 Sum_probs=27.2
Q ss_pred HHHHHHHH-HHHHHHHHHHHhcCCCCCHHHHHHHH
Q 033824 45 VVSLFFAD-SERLLNDLTRALDQPTIDFKMVDSHV 78 (111)
Q Consensus 45 ll~~F~~~-~~~~l~~L~~a~~~~~~D~~~l~~~a 78 (111)
++...++. +++++..+++++..+ |+..+.+++
T Consensus 224 ~~~~w~~~~~~~~~~~~~~Ai~~~--Df~~~gei~ 256 (343)
T PLN02407 224 LLQHRAKEVVPKRILQMEEAIKNR--DFASFAKLT 256 (343)
T ss_pred hHHHHHHhhhHHHHHHHHHHHHhc--CHHHHHHHH
Confidence 46677777 899999999999999 999887664
No 40
>PRK03057 hypothetical protein; Provisional
Probab=42.74 E-value=1.1e+02 Score=21.93 Aligned_cols=37 Identities=22% Similarity=0.331 Sum_probs=27.6
Q ss_pred HHHHHHHHH------HHHHHHHHHHHhcCCCCCHHHHHHHHHHhh
Q 033824 44 EVVSLFFAD------SERLLNDLTRALDQPTIDFKMVDSHVHQLK 82 (111)
Q Consensus 44 ~ll~~F~~~------~~~~l~~L~~a~~~~~~D~~~l~~~aH~LK 82 (111)
..++.|++. .......|..|+..+ |.+...++.+.|+
T Consensus 131 ~~ae~~L~~~~~~~~~~~L~~~ID~ALd~~--D~e~F~~Lt~~L~ 173 (180)
T PRK03057 131 KETEQVLDEVLKRNEVSRLRMQIDQALDRK--DMEEFQRLTEKLK 173 (180)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHCC--CHHHHHHHHHHHH
Confidence 335555555 455678888999999 9998888887775
No 41
>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=38.88 E-value=1e+02 Score=19.45 Aligned_cols=83 Identities=14% Similarity=0.159 Sum_probs=52.0
Q ss_pred HHHHHHHHhhhhhcchh---HHHHH--HHhhhccCCHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhh
Q 033824 8 RRLLEYTKSLFMEGVLD---NQFLQ--LQQLQDESNPDFVAEVVSLFFADSERLLNDLTRALDQPTIDFKMVDSHVHQLK 82 (111)
Q Consensus 8 ~~~~~~~~~~~~~~~ld---~~~~~--L~~L~~~~~~~~~~~ll~~F~~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~LK 82 (111)
+++..++..+...-+-+ ..+.+ ++++. ...+.+..++..++.-..+.+..|-..+...+.|-..+...+|++=
T Consensus 3 ~~L~~~i~~~~~~l~~~~~~~~~~~l~~RE~~--~Pt~~~~~i~~~~~~P~~~~l~~ll~~~~g~~~~~~~~~~~~~si~ 80 (125)
T PF09209_consen 3 ERLRAFIRALLRRLLSDPESRWWLRLIAREML--NPTPAFDRIVEELIRPKHEALARLLAEILGEPADDPEVRLCAFSIV 80 (125)
T ss_dssp HHHHHHHHHHHHHTTSG-GGHHHHHHHHHHHH--S--HHHHHHHHHTHHHHHHHHHHHHHHHHT--TTSHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHcccchhHHHHHHHHHhc--CchHHHHHHHHHHhhhHHHHHHHHHHHHhCcCCChHHHHHHHHHHH
Confidence 56677777777754443 12322 34443 3456778888888877777776666655444346678899999999
Q ss_pred hhhhhhChHH
Q 033824 83 GSSSSIGAER 92 (111)
Q Consensus 83 Gsa~~lGa~~ 92 (111)
|.+..+...+
T Consensus 81 g~~~~~~~~r 90 (125)
T PF09209_consen 81 GQCLFFRIAR 90 (125)
T ss_dssp HHHHHHHHTH
T ss_pred HHHHHHHHhH
Confidence 9887665443
No 42
>PRK03636 hypothetical protein; Provisional
Probab=38.85 E-value=1.4e+02 Score=21.27 Aligned_cols=28 Identities=29% Similarity=0.440 Sum_probs=23.8
Q ss_pred HHHHHHHHHHHhcCCCCCHHHHHHHHHHhh
Q 033824 53 SERLLNDLTRALDQPTIDFKMVDSHVHQLK 82 (111)
Q Consensus 53 ~~~~l~~L~~a~~~~~~D~~~l~~~aH~LK 82 (111)
-......|..|+..+ |-+...+++..||
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 356778899999999 9999999888776
No 43
>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=38.32 E-value=98 Score=19.16 Aligned_cols=56 Identities=14% Similarity=0.134 Sum_probs=35.4
Q ss_pred HHHHHHhhhhhcchhHH-HHHHHhhhccCCHHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Q 033824 10 LLEYTKSLFMEGVLDNQ-FLQLQQLQDESNPDFVAEVVSLFFADSERLLNDLTRALDQP 67 (111)
Q Consensus 10 ~~~~~~~~~~~~~ld~~-~~~L~~L~~~~~~~~~~~ll~~F~~~~~~~l~~L~~a~~~~ 67 (111)
....+.-++..|++++. +..|..- ....+-..+++...-+-.+.-...+-.++...
T Consensus 18 ~~~v~~~L~~~~Vlt~~~~e~I~~~--~tr~~q~~~LLd~L~~RG~~AF~~F~~aL~~~ 74 (84)
T cd08326 18 PKYLWDHLLSRGVFTPDMIEEIQAA--GSRRDQARQLLIDLETRGKQAFPAFLSALRET 74 (84)
T ss_pred HHHHHHHHHhcCCCCHHHHHHHHcC--CCHHHHHHHHHHHHHhcCHHHHHHHHHHHHhc
Confidence 45566777778888863 3444322 34456667777777777777777777666544
No 44
>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=37.51 E-value=1.2e+02 Score=22.85 Aligned_cols=39 Identities=13% Similarity=0.303 Sum_probs=33.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHh
Q 033824 41 FVAEVVSLFFADSERLLNDLTRALDQPTIDFKMVDSHVHQL 81 (111)
Q Consensus 41 ~~~~ll~~F~~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~L 81 (111)
...++++.++.-+...++.+...+..+ +++....-++.+
T Consensus 54 t~hQIlEsWi~~a~~LL~ri~~~i~~~--~~ekAa~dc~~v 92 (261)
T PF07014_consen 54 TTHQILESWIHVARKLLERIEERIEAR--DFEKAASDCWIV 92 (261)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHcc--cHHHHHhHHHHH
Confidence 467899999999999999999999999 998877666653
No 45
>COG3433 Aryl carrier domain [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=36.23 E-value=62 Score=19.90 Aligned_cols=51 Identities=14% Similarity=0.208 Sum_probs=34.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhhhhhhhChHHHHH
Q 033824 44 EVVSLFFADSERLLNDLTRALDQPTIDFKMVDSHVHQLKGSSSSIGAERIKN 95 (111)
Q Consensus 44 ~ll~~F~~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~LKGsa~~lGa~~L~~ 95 (111)
+++...+.+.++.+..=.+.+..+ .|--.+..++|+.|--.+.+++..|++
T Consensus 5 ~~~~~Ll~e~~~~l~dqeNLi~~G-LDSiR~M~L~~~wR~~G~~i~F~~La~ 55 (74)
T COG3433 5 EQIAELLGESVEELDDQENLIDYG-LDSIRMMALLERWRKRGADIDFAQLAA 55 (74)
T ss_pred HHHHHHHcCChhhcCchhhHHHhc-hhHHHHHHHHHHHHHcCCcccHHHHHh
Confidence 444444555555555555555555 466677888999998888888887765
No 46
>KOG2833 consensus Mevalonate pyrophosphate decarboxylase [Lipid transport and metabolism]
Probab=35.88 E-value=73 Score=25.32 Aligned_cols=32 Identities=9% Similarity=0.234 Sum_probs=25.6
Q ss_pred HHHHHHHHH-HHHHHHHHHHHhcCCCCCHHHHHHH
Q 033824 44 EVVSLFFAD-SERLLNDLTRALDQPTIDFKMVDSH 77 (111)
Q Consensus 44 ~ll~~F~~~-~~~~l~~L~~a~~~~~~D~~~l~~~ 77 (111)
.++..=+++ .|+++.+|++++..+ |++.+.++
T Consensus 222 ~L~qhRi~~vVP~Ri~~m~eaI~~r--DF~~FA~l 254 (395)
T KOG2833|consen 222 QLLQHRIESVVPQRIQQMREAIRER--DFESFAKL 254 (395)
T ss_pred HHHHHHHHhhhHHHHHHHHHHHHhc--CHHHHHHH
Confidence 345555556 699999999999999 99988766
No 47
>PF14276 DUF4363: Domain of unknown function (DUF4363)
Probab=35.57 E-value=1.2e+02 Score=19.50 Aligned_cols=37 Identities=14% Similarity=0.218 Sum_probs=24.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHh
Q 033824 43 AEVVSLFFADSERLLNDLTRALDQPTIDFKMVDSHVHQL 81 (111)
Q Consensus 43 ~~ll~~F~~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~L 81 (111)
...+..+.++.++.++.+.+.+..+ ||+.+....=.+
T Consensus 18 ~~~l~~~~~~i~~~l~~i~~~i~~~--dW~~A~~~~~~l 54 (121)
T PF14276_consen 18 NNYLNNSTDSIEEQLEQIEEAIENE--DWEKAYKETEEL 54 (121)
T ss_pred HhhhhhHHHHHHHHHHHHHHHHHhC--CHHHHHHHHHHH
Confidence 4445556677777777777777777 777666554443
No 48
>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=34.96 E-value=1.6e+02 Score=20.74 Aligned_cols=58 Identities=16% Similarity=0.239 Sum_probs=34.7
Q ss_pred HHHHhhhccCCHHHHHHHHHHHHHHHHHHHHHHHHHh-------------cCCCCCHHHHHHHHHHhhhhhhh
Q 033824 28 LQLQQLQDESNPDFVAEVVSLFFADSERLLNDLTRAL-------------DQPTIDFKMVDSHVHQLKGSSSS 87 (111)
Q Consensus 28 ~~L~~L~~~~~~~~~~~ll~~F~~~~~~~l~~L~~a~-------------~~~~~D~~~l~~~aH~LKGsa~~ 87 (111)
.+|..|.. ...-+..-+..++....+.-..|..++ ...++|++.+..+||+|-.....
T Consensus 29 ~~I~~L~~--e~~~ld~~i~~~~~~L~~~~~~L~~~~~~~~~~~~~~~~~~~~~v~~~eLL~YA~rISk~t~~ 99 (188)
T PF10018_consen 29 ARIQQLRA--EIEELDEQIRDILKQLKEARKELRTLPDQADEKLKSIPKAEKRPVDYEELLSYAHRISKFTSA 99 (188)
T ss_pred HHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccccccccccCCCCHHHHHHHHHHHHHhcCC
Confidence 34555543 222334445555555555555555554 23467899999999999877655
No 49
>PRK11199 tyrA bifunctional chorismate mutase/prephenate dehydrogenase; Provisional
Probab=34.40 E-value=2.3e+02 Score=22.22 Aligned_cols=64 Identities=9% Similarity=0.157 Sum_probs=38.8
Q ss_pred CCHHHHHHHHHH------HHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhhhhhhhChHHHHHHHHHHHH
Q 033824 37 SNPDFVAEVVSL------FFADSERLLNDLTRALDQPTIDFKMVDSHVHQLKGSSSSIGAERIKNACVAFRN 102 (111)
Q Consensus 37 ~~~~~~~~ll~~------F~~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~LKGsa~~lGa~~L~~~~~~lE~ 102 (111)
++|+++..++.. -+++..+.+..++.++.++ |.+.+.+..-+-+..=|...=..+-..-..+|.
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 566666655432 2344456677788889999 999998887666555444433444444444443
No 50
>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=34.02 E-value=1e+02 Score=18.05 Aligned_cols=57 Identities=12% Similarity=0.339 Sum_probs=38.2
Q ss_pred HHHHHHHhhhhhcchhHHHHHHHhhhc-cCCHHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Q 033824 9 RLLEYTKSLFMEGVLDNQFLQLQQLQD-ESNPDFVAEVVSLFFADSERLLNDLTRALDQP 67 (111)
Q Consensus 9 ~~~~~~~~~~~~~~ld~~~~~L~~L~~-~~~~~~~~~ll~~F~~~~~~~l~~L~~a~~~~ 67 (111)
....++..+...++++.. ....+.. ....+-..+++.......+.....+-.++...
T Consensus 14 ~~~~il~~L~~~~vlt~~--e~~~i~~~~~~~~k~~~Lld~l~~kg~~af~~F~~~L~~~ 71 (80)
T cd01671 14 DVEDVLDHLLSDGVLTEE--EYEKIRSESTRQDKARKLLDILPRKGPKAFQSFLQALQET 71 (80)
T ss_pred cHHHHHHHHHHcCCCCHH--HHHHHHcCCChHHHHHHHHHHHHhcChHHHHHHHHHHHhc
Confidence 455667777778888853 3333333 23567777777777777777777777777665
No 51
>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=33.61 E-value=1.3e+02 Score=19.30 Aligned_cols=39 Identities=10% Similarity=0.118 Sum_probs=27.1
Q ss_pred HHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhhhhhh
Q 033824 47 SLFFADSERLLNDLTRALDQPTIDFKMVDSHVHQLKGSSSS 87 (111)
Q Consensus 47 ~~F~~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~LKGsa~~ 87 (111)
..+..........|..+...+ |+..+......+.++|..
T Consensus 78 ~~~~~~~~~aa~~L~~aa~~~--d~~~~~~a~~~v~~~C~a 116 (122)
T PF01322_consen 78 KQLAQAFQKAAAALAAAAKSG--DLAAIKAAFGEVGKSCKA 116 (122)
T ss_dssp HHHHHHHHHHHHHHHHHHHHT--SHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHhcC--CHHHHHHHHHHHHHHHHH
Confidence 334444455566777778788 898888887777777654
No 52
>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=32.58 E-value=2.4e+02 Score=21.94 Aligned_cols=55 Identities=16% Similarity=0.318 Sum_probs=35.2
Q ss_pred HHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhhhhhhh------C--hHHHHHHHHHHH
Q 033824 45 VVSLFFADSERLLNDLTRALDQPTIDFKMVDSHVHQLKGSSSSI------G--AERIKNACVAFR 101 (111)
Q Consensus 45 ll~~F~~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~LKGsa~~l------G--a~~L~~~~~~lE 101 (111)
....|++...+...++..++..+ |+..+.++.+.-...-..+ | -..+-+++...+
T Consensus 246 ~~~~~l~~~~~i~~~~~~al~~~--d~~~lg~~~~~~~~lL~~l~~~~~~~vs~~~l~~li~~a~ 308 (358)
T TIGR01220 246 SYQRFLETSTDCVESAITAFETG--DITSLQKEIRRNRQELARLDDEVGVGIETEKLKALCDAAE 308 (358)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhC--CHHHHHHHHHHHHHHHHHhhcccCCCcCCHHHHHHHHHHh
Confidence 35667888888888999999999 9887765544433333322 3 455555554444
No 53
>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=32.23 E-value=82 Score=18.71 Aligned_cols=56 Identities=14% Similarity=0.240 Sum_probs=33.2
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhhhhhhhChHHHHHHHH
Q 033824 38 NPDFVAEVVSLFFADSERLLNDLTRALDQPTIDFKMVDSHVHQLKGSSSSIGAERIKNACV 98 (111)
Q Consensus 38 ~~~~~~~ll~~F~~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~LKGsa~~lGa~~L~~~~~ 98 (111)
+++.+.+++...+.+..+.+.. .. +.=. .|-+.+..++.. |....+||.+|.....
T Consensus 2 ~~~~l~~I~~~~l~~l~~~l~~-~~-i~l~-~~~~~~~~l~~~--~~~~~~GAR~l~r~i~ 57 (81)
T PF10431_consen 2 SEEDLEKIADLQLKKLNERLKE-KG-IELE-FDDAVVDYLAEK--GYDPEYGARPLRRIIE 57 (81)
T ss_dssp -HHHHHHHHHSHHHHHHHHHHH-TT-EEEE-E-HHHHHHHHHH--HHHTTTTTTCHHHHHH
T ss_pred CHHHHHHHHHHHHHHHHHHHHH-CC-CeEE-ecHHHHHHHHHh--CcccCCCHHHHHHHHH
Confidence 3456777788777777776654 22 1111 134444555443 6778899999887654
No 54
>KOG3192 consensus Mitochondrial J-type chaperone [Posttranslational modification, protein turnover, chaperones]
Probab=32.20 E-value=1.9e+02 Score=20.57 Aligned_cols=48 Identities=8% Similarity=0.120 Sum_probs=32.6
Q ss_pred hhhccCCHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHh
Q 033824 32 QLQDESNPDFVAEVVSLFFADSERLLNDLTRALDQPTIDFKMVDSHVHQL 81 (111)
Q Consensus 32 ~L~~~~~~~~~~~ll~~F~~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~L 81 (111)
+++...|..-+..+-..-.+...+..++|.++.+.. +|.......-++
T Consensus 107 ~IS~~~De~~l~~lk~q~q~ri~q~~~qlge~~esk--~~~~Al~~i~rl 154 (168)
T KOG3192|consen 107 AISEMDDEEDLKQLKSQNQERIAQCKQQLGEAFESK--KYDEALKKILRL 154 (168)
T ss_pred HHHhccCcHHHHHHHHHHHHHHHHHHHHHHHHHhhc--cHHHHHHHHHHH
Confidence 333334444467777777777778888899999999 888776654443
No 55
>PRK08507 prephenate dehydrogenase; Validated
Probab=31.89 E-value=2.1e+02 Score=21.04 Aligned_cols=48 Identities=13% Similarity=0.342 Sum_probs=30.0
Q ss_pred HHHHHhhhccCCHHHHHHHHH-------HHHHHHHHHHHHHHHHhcCCCCCHHHHHHH
Q 033824 27 FLQLQQLQDESNPDFVAEVVS-------LFFADSERLLNDLTRALDQPTIDFKMVDSH 77 (111)
Q Consensus 27 ~~~L~~L~~~~~~~~~~~ll~-------~F~~~~~~~l~~L~~a~~~~~~D~~~l~~~ 77 (111)
|..+..+. ..+|+++.+++. .-+++..+.+..+++++..+ |.+.+.+.
T Consensus 210 frd~tria-~~~p~l~~~i~~~N~~~~~~~l~~~~~~l~~~~~~l~~~--d~~~~~~~ 264 (275)
T PRK08507 210 FRSMSRLA-KSSPAMWSDIFKQNKENVLEAIDEFIKELEQFKQLIENE--DWEELEEW 264 (275)
T ss_pred hhhhhhcc-cCCHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHcC--CHHHHHHH
Confidence 44444443 356777766642 33555566677888888888 88776654
No 56
>PF11563 Protoglobin: Protoglobin; PDB: 2VEE_G 3QZZ_A 3R0G_A 3QZX_A 2VEB_A 1OR6_A 1OR4_B 2W31_B.
Probab=31.20 E-value=1.6e+02 Score=19.41 Aligned_cols=57 Identities=9% Similarity=0.061 Sum_probs=38.1
Q ss_pred chHHHHHHHHHHHHhhhhhcchhHHHHHHHhhhc-----cCCHHHHHHHHHHHHHHHHHHHH
Q 033824 2 EVGQMQRRLLEYTKSLFMEGVLDNQFLQLQQLQD-----ESNPDFVAEVVSLFFADSERLLN 58 (111)
Q Consensus 2 ~~~~~~~~~~~~~~~~~~~~~ld~~~~~L~~L~~-----~~~~~~~~~ll~~F~~~~~~~l~ 58 (111)
.+..|+..+..|+..+++.++.+.-+.....+.. +-++..+......+.+...+.+.
T Consensus 59 ~~~~lk~~q~~~~~~l~s~~~d~~y~~~~~~iG~~H~~igl~~~~~~~~~~~~~~~l~~~l~ 120 (158)
T PF11563_consen 59 TIERLKATQRRHWRELFSGDFDEEYVERRRRIGQVHARIGLPPRWYIGAYSFLREFLLEALA 120 (158)
T ss_dssp CHHHHHHHHHHHHHHCTSS-CSHHHHHHHHHHHHHHHHCT--HHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHhCCCchHHHHHHHHHHHHHHhHcCCCHHHHHHHHHHHHHHHHHHHH
Confidence 4678999999999999887755543444444333 56788888888877777655444
No 57
>TIGR01240 mevDPdecarb diphosphomevalonate decarboxylase. Alternate names: mevalonate diphosphate decarboxylase; pyrophosphomevalonate decarboxylase
Probab=30.87 E-value=98 Score=23.76 Aligned_cols=31 Identities=10% Similarity=0.144 Sum_probs=25.7
Q ss_pred HHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHH
Q 033824 46 VSLFFADSERLLNDLTRALDQPTIDFKMVDSHV 78 (111)
Q Consensus 46 l~~F~~~~~~~l~~L~~a~~~~~~D~~~l~~~a 78 (111)
+...+++.+.++..+..++.++ |++.+.+++
T Consensus 202 ~~~~v~~~~~~l~~~~~ai~~~--D~~~~g~~~ 232 (305)
T TIGR01240 202 FKEWIEHVVPDFEVXRKAIKTK--DFATFGKET 232 (305)
T ss_pred HHHHHHHHHHHHHHHHHHHHhc--cHHHHHHHH
Confidence 5667777887899999999999 999887654
No 58
>PRK13916 plasmid segregation protein ParR; Provisional
Probab=29.51 E-value=90 Score=19.85 Aligned_cols=28 Identities=11% Similarity=0.253 Sum_probs=23.9
Q ss_pred HHHHHhhhccCCHHHHHHHHHHHHHHHH
Q 033824 27 FLQLQQLQDESNPDFVAEVVSLFFADSE 54 (111)
Q Consensus 27 ~~~L~~L~~~~~~~~~~~ll~~F~~~~~ 54 (111)
|.-|..+-++.-+.+++++++.|+++..
T Consensus 21 F~FL~~~P~GT~~~~iR~~L~rYI~~~G 48 (97)
T PRK13916 21 FDFLENVPRGTKTAHIREALRRYIEEIG 48 (97)
T ss_pred HHHHHHCCCCCccHHHHHHHHHHHHhcC
Confidence 6678888887789999999999999863
No 59
>KOG4559 consensus Uncharacterized conserved protein [Function unknown]
Probab=29.02 E-value=1.2e+02 Score=19.97 Aligned_cols=47 Identities=17% Similarity=0.343 Sum_probs=32.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhhhhhhhC
Q 033824 39 PDFVAEVVSLFFADSERLLNDLTRALDQPTIDFKMVDSHVHQLKGSSSSIG 89 (111)
Q Consensus 39 ~~~~~~ll~~F~~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~LKGsa~~lG 89 (111)
.+|+.--++.=+++. +.++.+..+-.++ |..++.+|-.+.|+-.++.
T Consensus 39 ~ef~qHeLe~~iEdY-KLLEeMNkaTaak---Y~DMk~iAEkla~k~deLn 85 (120)
T KOG4559|consen 39 EEFFQHELEAPIEDY-KLLEEMNKATAAK---YKDMKQIAEKLAGKLDELN 85 (120)
T ss_pred HHHHHHHHcCcHHHH-HHHHHHHHHHHHH---HHHHHHHHHHHccchHHHH
Confidence 344444444444444 4677788877775 8888999999999877665
No 60
>COG3923 PriC Primosomal replication protein N'' [DNA replication, recombination, and repair]
Probab=28.26 E-value=1.6e+02 Score=20.98 Aligned_cols=37 Identities=19% Similarity=0.368 Sum_probs=31.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhh
Q 033824 44 EVVSLFFADSERLLNDLTRALDQPTIDFKMVDSHVHQLK 82 (111)
Q Consensus 44 ~ll~~F~~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~LK 82 (111)
.++.-|+++..+.+..|+++.+.+ -..++.-+|-+|-
T Consensus 44 ~~ls~ylqEa~~tL~aL~~~~e~~--~l~q~afLAErLl 80 (175)
T COG3923 44 QLLSFYLQEAGQTLTALKQAVEQD--RLPQVAFLAERLL 80 (175)
T ss_pred chHHHHHHHHHHHHHHHHHHHhcc--chHHHHHHHHHHH
Confidence 568899999999999999999998 6667777776653
No 61
>PF03398 Ist1: Regulator of Vps4 activity in the MVB pathway; InterPro: IPR005061 This is a eukaryotic protein family of unknown function.; PDB: 3GGZ_B 3GGY_B 3FRR_A 3FRS_A.
Probab=27.95 E-value=2.1e+02 Score=19.85 Aligned_cols=88 Identities=9% Similarity=0.070 Sum_probs=56.3
Q ss_pred HHHHHHHHhhhhhcchhHHHHHHHhhhccCCHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhhhhhh
Q 033824 8 RRLLEYTKSLFMEGVLDNQFLQLQQLQDESNPDFVAEVVSLFFADSERLLNDLTRALDQPTIDFKMVDSHVHQLKGSSSS 87 (111)
Q Consensus 8 ~~~~~~~~~~~~~~~ld~~~~~L~~L~~~~~~~~~~~ll~~F~~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~LKGsa~~ 87 (111)
.++.+=++.++..|-.+....+.+.+......-...++++.|++-.-..+..|...-. -.+.+...+.+|==++.-
T Consensus 23 ~~~rkdIa~LL~~g~~~~Ar~rvE~li~ed~~~e~~e~Le~yce~l~~r~~~i~~~k~----~p~~l~eAi~siiyAa~r 98 (165)
T PF03398_consen 23 KQARKDIAQLLKNGKEESARIRVEQLIREDNMIEAYEILELYCELLLARFSLIEKSKE----CPPELKEAISSIIYAAPR 98 (165)
T ss_dssp HHHHHHHHHHHCCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHCT-TS----SSCCHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccC----CCHHHHHHHHHHHHHhhh
Confidence 3455556667777888876667777776666666788999999999888888876522 234555666666555555
Q ss_pred h-ChHHHHHHHHH
Q 033824 88 I-GAERIKNACVA 99 (111)
Q Consensus 88 l-Ga~~L~~~~~~ 99 (111)
+ -..-|..+...
T Consensus 99 ~~elpEL~~vr~~ 111 (165)
T PF03398_consen 99 CGELPELQEVRKQ 111 (165)
T ss_dssp HTTTCCHHHHHHH
T ss_pred ccCChhHHHHHHH
Confidence 5 44444444433
No 62
>PF09670 Cas_Cas02710: CRISPR-associated protein (Cas_Cas02710)
Probab=26.95 E-value=3.2e+02 Score=21.56 Aligned_cols=65 Identities=11% Similarity=0.199 Sum_probs=48.7
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhhh-hhhhChHHHHHHHHHHHHH
Q 033824 37 SNPDFVAEVVSLFFADSERLLNDLTRALDQPTIDFKMVDSHVHQLKGS-SSSIGAERIKNACVAFRNF 103 (111)
Q Consensus 37 ~~~~~~~~ll~~F~~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~LKGs-a~~lGa~~L~~~~~~lE~~ 103 (111)
.|.+.+..+-+-|.--....+.....+.... ||....++.+.+... ++......+..+|.....+
T Consensus 115 ~Gte~l~~~~~p~~~~~~~~~~~a~~l~n~~--~y~aA~~~l~~l~~rl~~~~~~~~~~~l~~~y~~W 180 (379)
T PF09670_consen 115 PGTERLRELENPYEVFGDREWRRAKELFNRY--DYGAAARILEELLRRLPGREEYQRYKDLCEGYDAW 180 (379)
T ss_pred CcchhhhhcCCHHHHHHHHHHHHHHHHHhcC--CHHHHHHHHHHHHHhCCchhhHHHHHHHHHHHHHH
Confidence 4566666666666666667778888889999 999999998888886 6655567778887776644
No 63
>PF13779 DUF4175: Domain of unknown function (DUF4175)
Probab=26.72 E-value=2.3e+02 Score=25.08 Aligned_cols=70 Identities=6% Similarity=0.131 Sum_probs=43.4
Q ss_pred cCCHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhhhhhhhChHHHHHHHHHHHHHHHhhccC
Q 033824 36 ESNPDFVAEVVSLFFADSERLLNDLTRALDQPTIDFKMVDSHVHQLKGSSSSIGAERIKNACVAFRNFCEEQNIE 110 (111)
Q Consensus 36 ~~~~~~~~~ll~~F~~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~LKGsa~~lGa~~L~~~~~~lE~~~~~gd~~ 110 (111)
+-+.+-+.++...+.+-..+.+..|.+-.... .-.. ..+.--+.+.+++-..|......||+.+++|+.+
T Consensus 488 gAs~eEI~rLm~eLR~A~~~ym~~LAeq~~~~--~~~~---~~p~~~~~~~~~~~~dL~~mmd~ie~la~~G~~~ 557 (820)
T PF13779_consen 488 GASDEEIARLMQELREAMQDYMQALAEQAQRN--PQQQ---DQPPDQGNSQMMSQQDLQRMMDRIEELARSGRMD 557 (820)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHhHhC--cccc---cCcccchhhhccCHHHHHHHHHHHHHHHHcCCHH
Confidence 33455556666666666666666655544433 1110 0011135567899999999999999999999864
No 64
>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=26.44 E-value=1.1e+02 Score=15.98 Aligned_cols=24 Identities=25% Similarity=0.263 Sum_probs=17.3
Q ss_pred HHHHHHHHHhcCCCCCHHHHHHHHHH
Q 033824 55 RLLNDLTRALDQPTIDFKMVDSHVHQ 80 (111)
Q Consensus 55 ~~l~~L~~a~~~~~~D~~~l~~~aH~ 80 (111)
.....|..|+..+ |-+...+++..
T Consensus 13 ~L~~~ID~ALd~~--D~e~F~~Ls~e 36 (37)
T PF08858_consen 13 QLLELIDEALDNR--DKEWFYELSEE 36 (37)
T ss_dssp HHHHHHHHHHHTT---HHHHHHHHHH
T ss_pred HHHHHHHHHHHcC--CHHHHHHHHhh
Confidence 4667788888888 88888777654
No 65
>PF14674 FANCI_S1-cap: FANCI solenoid 1 cap; PDB: 3S51_A 3S4Z_A 3S4W_A.
Probab=26.39 E-value=1.4e+02 Score=17.18 Aligned_cols=37 Identities=22% Similarity=0.346 Sum_probs=17.6
Q ss_pred HHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhhhh
Q 033824 46 VSLFFADSERLLNDLTRALDQPTIDFKMVDSHVHQLKGSS 85 (111)
Q Consensus 46 l~~F~~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~LKGsa 85 (111)
+..--++.++.++..-+.+... |+..+... |.+||-.
T Consensus 6 lsLa~~~t~e~LQ~~Lq~L~ed--eLt~~lt~-~AlKGk~ 42 (53)
T PF14674_consen 6 LSLAAEDTTEELQKFLQTLKED--ELTDLLTN-QALKGKD 42 (53)
T ss_dssp HHHHHH-TTHHHHHHHHHH-S---SHHHHHHH-HHH-HHH
T ss_pred HHHhhcCCHHHHHHHHHHcchh--HHHHHHHH-HhhcchH
Confidence 3333344444455544555566 66666554 6777754
No 66
>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=25.07 E-value=1.2e+02 Score=15.88 Aligned_cols=34 Identities=21% Similarity=0.292 Sum_probs=20.3
Q ss_pred HHHHHhhhccCCHHHHHHHHHHHHHHHHHHHHHH
Q 033824 27 FLQLQQLQDESNPDFVAEVVSLFFADSERLLNDL 60 (111)
Q Consensus 27 ~~~L~~L~~~~~~~~~~~ll~~F~~~~~~~l~~L 60 (111)
+.+|.++...-+++++...+..+-.+.+..+..|
T Consensus 5 v~~L~~mFP~~~~~~I~~~L~~~~~~ve~ai~~L 38 (42)
T PF02845_consen 5 VQQLQEMFPDLDREVIEAVLQANNGDVEAAIDAL 38 (42)
T ss_dssp HHHHHHHSSSS-HHHHHHHHHHTTTTHHHHHHHH
T ss_pred HHHHHHHCCCCCHHHHHHHHHHcCCCHHHHHHHH
Confidence 4567777777777777777666555555444443
No 67
>PF04400 DUF539: Protein of unknown function (DUF539); InterPro: IPR007495 This is a family of putative periplasmic proteins.
Probab=24.92 E-value=6.9 Score=21.83 Aligned_cols=18 Identities=39% Similarity=0.746 Sum_probs=13.2
Q ss_pred HhhhhhhhhChHHHHHHH
Q 033824 80 QLKGSSSSIGAERIKNAC 97 (111)
Q Consensus 80 ~LKGsa~~lGa~~L~~~~ 97 (111)
.|+||+|-|++..+-..|
T Consensus 7 ~I~GSCGGl~~lGi~~~C 24 (45)
T PF04400_consen 7 PIKGSCGGLGALGIDKEC 24 (45)
T ss_pred cccccchhhhhcCCCccC
Confidence 589999999886654443
No 68
>KOG2280 consensus Vacuolar assembly/sorting protein VPS16 [Intracellular trafficking, secretion, and vesicular transport]
Probab=24.54 E-value=3e+02 Score=24.40 Aligned_cols=66 Identities=18% Similarity=0.176 Sum_probs=46.9
Q ss_pred HHHhhhccCCHHHHHHHHHHHH-HHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhhhhhhhChHHHHHHHHH
Q 033824 29 QLQQLQDESNPDFVAEVVSLFF-ADSERLLNDLTRALDQPTIDFKMVDSHVHQLKGSSSSIGAERIKNACVA 99 (111)
Q Consensus 29 ~L~~L~~~~~~~~~~~ll~~F~-~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~LKGsa~~lGa~~L~~~~~~ 99 (111)
.+.+|.-.|...-..++...|. .+-.=..=.+..+...+ ||+++.+.|-+-|+ -+|..++.+.|..
T Consensus 690 Tv~~li~~g~~k~a~ql~~~FkipdKr~~wLk~~aLa~~~--kweeLekfAkskks---PIGy~PFVe~c~~ 756 (829)
T KOG2280|consen 690 TVTTLILIGQNKRAEQLKSDFKIPDKRLWWLKLTALADIK--KWEELEKFAKSKKS---PIGYLPFVEACLK 756 (829)
T ss_pred HHHHHHHccchHHHHHHHHhcCCcchhhHHHHHHHHHhhh--hHHHHHHHHhccCC---CCCchhHHHHHHh
Confidence 3445554456666677777773 33333444567777888 99999999988776 7999999998864
No 69
>PF13628 DUF4142: Domain of unknown function (DUF4142)
Probab=24.32 E-value=2.1e+02 Score=18.71 Aligned_cols=50 Identities=14% Similarity=0.099 Sum_probs=38.0
Q ss_pred HHHHHhhhccCCHHHHHHHHHHHHHHHHHHHHHHHH-HhcCCCCCHHHHHHHH
Q 033824 27 FLQLQQLQDESNPDFVAEVVSLFFADSERLLNDLTR-ALDQPTIDFKMVDSHV 78 (111)
Q Consensus 27 ~~~L~~L~~~~~~~~~~~ll~~F~~~~~~~l~~L~~-a~~~~~~D~~~l~~~a 78 (111)
-..+..|....|++|=...+...+..-.+.+..++. ....+ +-..++..+
T Consensus 72 ~~~l~~L~~~~g~~FD~~yl~~~i~~h~~~l~~~~~~~~~~~--~~~~lk~~a 122 (139)
T PF13628_consen 72 QAELDRLQKLSGSAFDRAYLDAQIKAHEKALALFEKQLAASG--KDPELKAFA 122 (139)
T ss_pred HHHHHHHHcCchhHHHHHHHHHHHHHHHHHHHHHHHHhhccC--CCHHHHHHH
Confidence 445666666677899999999999999999999998 66666 556666554
No 70
>PRK10093 primosomal replication protein N''; Provisional
Probab=23.53 E-value=2.8e+02 Score=19.76 Aligned_cols=36 Identities=17% Similarity=0.289 Sum_probs=29.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHh
Q 033824 44 EVVSLFFADSERLLNDLTRALDQPTIDFKMVDSHVHQL 81 (111)
Q Consensus 44 ~ll~~F~~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~L 81 (111)
..+..|+.+....+..|..++..+ +...+.-++=+|
T Consensus 40 ~~L~~yl~Ei~~~l~qL~~~~~~~--~~~~~~flaEkL 75 (171)
T PRK10093 40 TLLQAYLDEAGDNLAALRHAVEQQ--QLPQVAWLAEHL 75 (171)
T ss_pred cchHHHHHHHHHHHHHHHHHHhcC--cHHHHHHHHHHH
Confidence 458889999999999999999888 887776665544
No 71
>PRK08582 hypothetical protein; Provisional
Probab=22.56 E-value=1.6e+02 Score=19.90 Aligned_cols=28 Identities=25% Similarity=0.356 Sum_probs=23.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhcCC
Q 033824 40 DFVAEVVSLFFADSERLLNDLTRALDQP 67 (111)
Q Consensus 40 ~~~~~ll~~F~~~~~~~l~~L~~a~~~~ 67 (111)
.-+...+..|+.++.+.++.|+.-.+.+
T Consensus 103 ~~fe~~l~~flk~s~~~~~~l~~~~~~~ 130 (139)
T PRK08582 103 EDFEQKMSRFLKDSEDRLTSIKRNTESK 130 (139)
T ss_pred cCHHHHHHHHHHHHHHHHHHHHhhcccC
Confidence 4568999999999999999998765543
No 72
>PF02203 TarH: Tar ligand binding domain homologue; InterPro: IPR003122 Methyl-accepting chemotaxis proteins (MCPs) are a family of bacterial receptors that mediate chemotaxis to diverse signals, responding to changes in the concentration of attractants and repellents in the environment by altering swimming behaviour []. Environmental diversity gives rise to diversity in bacterial signalling receptors, and consequently there are many genes encoding MCPs []. For example, there are four well-characterised MCPs found in Escherichia coli: Tar (taxis towards aspartate and maltose, away from nickel and cobalt), Tsr (taxis towards serine, away from leucine, indole and weak acids), Trg (taxis towards galactose and ribose) and Tap (taxis towards dipeptides). MCPs share similar topology and signalling mechanisms. MCPs either bind ligands directly or interact with ligand-binding proteins, transducing the signal to downstream signalling proteins in the cytoplasm. MCPs undergo two covalent modifications: deamidation and reversible methylation at a number of glutamate residues. Attractants increase the level of methylation, while repellents decrease it. The methyl groups are added by the methyl-transferase cheR and are removed by the methylesterase cheB. Most MCPs are homodimers that contain the following organisation: an N-terminal signal sequence that acts as a transmembrane domain in the mature protein; a poorly-conserved periplasmic receptor (ligand-binding) domain; a second transmembrane domain; and a highly-conserved C-terminal cytoplasmic domain that interacts with downstream signalling components. The C-terminal domain contains the glycosylated glutamate residues. This entry represents the ligand-binding domain found in a number of methyl-accepting chemotaxis receptors.; GO: 0004888 transmembrane signaling receptor activity, 0006935 chemotaxis, 0007165 signal transduction, 0016020 membrane; PDB: 2ASR_A 3ATP_A 2D4U_A 2LIG_A 1VLS_A 1LIH_A 1WAT_B 1VLT_B 1WAS_A 1JMW_A.
Probab=21.93 E-value=2.5e+02 Score=18.54 Aligned_cols=38 Identities=21% Similarity=0.159 Sum_probs=26.0
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHH
Q 033824 38 NPDFVAEVVSLFFADSERLLNDLTRALDQPTIDFKMVDSH 77 (111)
Q Consensus 38 ~~~~~~~ll~~F~~~~~~~l~~L~~a~~~~~~D~~~l~~~ 77 (111)
+..+..++...|-.=....+..+..++..+ |+..+.++
T Consensus 111 ~~~l~~~~~~~~~~~~~~~l~~~~~al~~~--d~~~~~~~ 148 (171)
T PF02203_consen 111 ERALADELEASFDAYLQQALDPLLAALRAG--DIAAFMQL 148 (171)
T ss_dssp GHHHHHHHHHHHHH-HHHHHHHHHHHHHTT---HHHHHHS
T ss_pred hHHHHHHHHHHHHHHHHHhHHHHHHHHHCC--CHHHHHHH
Confidence 456777777777665666777788888888 88877655
No 73
>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=21.02 E-value=3.1e+02 Score=19.39 Aligned_cols=50 Identities=10% Similarity=0.161 Sum_probs=36.4
Q ss_pred HHHHHHhhhhhcchhHHHHHHH---hhhccCCHHHHHHHHHHHHHHHHHHHHHHHH
Q 033824 10 LLEYTKSLFMEGVLDNQFLQLQ---QLQDESNPDFVAEVVSLFFADSERLLNDLTR 62 (111)
Q Consensus 10 ~~~~~~~~~~~~~ld~~~~~L~---~L~~~~~~~~~~~ll~~F~~~~~~~l~~L~~ 62 (111)
..+|.+.-.+.|=. |+.++ .|.+++-.++...++..|+-+....+++|+.
T Consensus 36 arrWK~~Ak~~GDD---WDk~RaA~~laggg~e~v~~~~l~~f~~Q~~~tmeel~~ 88 (165)
T PF08822_consen 36 ARRWKREAKAKGDD---WDKARAAHTLAGGGIEDVARQMLEDFVVQYQATMEELKE 88 (165)
T ss_pred HHHHHHHHHHcCCc---HHHHHHHHHhccCcHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 35666666666722 44544 4555556789999999999999999999984
No 74
>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=21.00 E-value=3.9e+02 Score=20.44 Aligned_cols=45 Identities=20% Similarity=0.276 Sum_probs=35.5
Q ss_pred CHHHHHHHHHHHHHHHH----HHHHHHHHHhcCCCCCHHHH-----HHHHHHhhhh
Q 033824 38 NPDFVAEVVSLFFADSE----RLLNDLTRALDQPTIDFKMV-----DSHVHQLKGS 84 (111)
Q Consensus 38 ~~~~~~~ll~~F~~~~~----~~l~~L~~a~~~~~~D~~~l-----~~~aH~LKGs 84 (111)
+.+-+.+|+..|..+.. ..++.|.+.+..+ |...+ .++-|-+||.
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 56678999999999986 5789999999999 98766 3455666665
No 75
>PF08112 ATP-synt_E_2: ATP synthase epsilon subunit; InterPro: IPR012508 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. A-ATPases (or A1A0-ATPase) (3.6.3.14 from EC) are found exclusively in Archaea and display a close resemblance in structure and subunit composition with V-ATPases, although their function in both ATP synthesis and ATP hydrolysis is closer to that of F-ATPases []. A-ATPases are composed of two linked complexes: the A1 complex consisting of seven subunits contains the catalytic core that synthesizes/hydrolyses ATP, while the A0 complex consisting of at least two subunits forms the membrane-spanning pore []. The rotary motor in A-ATPases is composed of only two subunits, the stator subunit I and the rotor subunit C []. A-ATPases may have arisen as an adaptation to the different cellular needs and the more extreme environmental conditions faced by Archaeal species. The epsilon subunit is the smallest (7 kDa) of those found in the A1 complex. Unlike the A, B and C subunits, the epsilon subunit does not have a homologous counterpart in F- or V-ATPases []. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0016820 hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances, 0042626 ATPase activity, coupled to transmembrane movement of substances, 0015986 ATP synthesis coupled proton transport, 0033178 proton-transporting two-sector ATPase complex, catalytic domain
Probab=20.95 E-value=1.8e+02 Score=16.72 Aligned_cols=11 Identities=18% Similarity=0.202 Sum_probs=4.7
Q ss_pred HHHHHHHHHHH
Q 033824 5 QMQRRLLEYTK 15 (111)
Q Consensus 5 ~~~~~~~~~~~ 15 (111)
.|+.+|++...
T Consensus 15 ~Lk~kLd~Kk~ 25 (56)
T PF08112_consen 15 ILKSKLDEKKS 25 (56)
T ss_pred HHHHHHHHHHH
Confidence 34444444433
No 76
>PF05168 HEPN: HEPN domain; InterPro: IPR007842 The HEPN (higher eukaryotes and prokaryotes nucleotide-binding) domain is a region of 110 residues found in the C terminus of sacsin, a chaperonin implicated in an early-onset neurodegenerative disease in human, and in many bacterial and archeabacterial proteins. There are three classes of proteins with HEPN domain: Single-domain HEPN proteins found in many bacteria. Two-domain proteins with N-terminal nucleotidyltransferase (NT) and C- terminal HEPN domains. This N-terminal NT domain belongs to a large family of NTs, which includes several classes of enzymes that are responsible for some types of bacterial resistance to aminoglycosides. These enzymes deactivate various antibiotics by transferring a nucleotidyl group to the drug. A multidomain sacsin protein in genomes of fish and mammals. The HEPN domain is located at the C terminus of the protein, directly after the DnaJ domain (see PDOC00553 from PROSITEDOC). The crystal structure of the HEPN domain from the TM0613 protein of Thermotoga maritima indicates that it is structurally similar to the C-terminal all- alpha-helical domain of kanamycin nucleotidyltransferases (KNTases). It is composed of five alpha helices, three of which form an up- and-down helical bundle, with a pair of short helices on the side. The distant structural similarity suggests that the HEPN domain might be involved in nucleotide binding [].; PDB: 1O3U_A 1WOL_A 3O10_D 2HSB_A 1UFB_A.
Probab=20.65 E-value=2.1e+02 Score=17.36 Aligned_cols=31 Identities=16% Similarity=0.192 Sum_probs=18.8
Q ss_pred HHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHH
Q 033824 47 SLFFADSERLLNDLTRALDQPTIDFKMVDSHVH 79 (111)
Q Consensus 47 ~~F~~~~~~~l~~L~~a~~~~~~D~~~l~~~aH 79 (111)
..|++.+...+...+..++.+ ++......+|
T Consensus 2 ~~~~~~A~~~l~~A~~~~~~~--~~~~a~~~a~ 32 (118)
T PF05168_consen 2 QDWLEKAEEDLKAAEILLEEG--DYNWAVFHAY 32 (118)
T ss_dssp HHHHHHHHHHHHHHHHHHHTT---HHHHHHHHH
T ss_pred hHHHHHHHHHHHHHHHHHHCC--CHHHHHHHHH
Confidence 345666666666666667766 6666555554
No 77
>PF08332 CaMKII_AD: Calcium/calmodulin dependent protein kinase II Association; InterPro: IPR013543 Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases. Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. Phosphoprotein phosphatases catalyse the reverse process. Protein kinases fall into three broad classes, characterised with respect to substrate specificity []: Serine/threonine-protein kinases Tyrosine-protein kinases Dual specific protein kinases (e.g. MEK - phosphorylates both Thr and Tyr on target proteins) Protein kinase function has been evolutionarily conserved from Escherichia coli to human []. Protein kinases play a role in a multitude of cellular processes, including division, proliferation, apoptosis, and differentiation []. Phosphorylation usually results in a functional change of the target protein by changing enzyme activity, cellular location, or association with other proteins. The catalytic subunits of protein kinases are highly conserved, and several structures have been solved [], leading to large screens to develop kinase-specific inhibitors for the treatments of a number of diseases []. This domain is found at the C terminus of the Calcium/calmodulin dependent protein kinases II (CaMKII). These proteins also have a Ser/Thr protein kinase domain (IPR000719 from INTERPRO) at their N terminus []. The function of the CaMKII association domain is the assembly of the single proteins into large (8 to 14 subunits) multimers [] and is a prominent kinase in the central nervous system that may function in long-term potentiation and neurotransmitter release. ; GO: 0004683 calmodulin-dependent protein kinase activity, 0005516 calmodulin binding, 0006468 protein phosphorylation; PDB: 2W2C_F 3H51_B 3SOA_A 2UX0_A 1HKX_M 2F86_B.
Probab=20.42 E-value=86 Score=21.07 Aligned_cols=26 Identities=12% Similarity=0.112 Sum_probs=19.4
Q ss_pred HHHHHHHHHHHHhcCCCCCHHHHHHHHH
Q 033824 52 DSERLLNDLTRALDQPTIDFKMVDSHVH 79 (111)
Q Consensus 52 ~~~~~l~~L~~a~~~~~~D~~~l~~~aH 79 (111)
+..+..+.+..++..+ |++.+..+.+
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 4456677888889999 9999988764
No 78
>TIGR02606 antidote_CC2985 putative addiction module antidote protein, CC2985 family. This bacterial protein family has a very similar seed alignment to that of Pfam model pfam03693 but is a more stringent model with higher cutoff scores. Proteins that score above the trusted cutoff to this model almost invariably are found adjacent to a ParE family protein (pfam05016), where ParE is the killing partner of an addiction module for plasmid stabilization. Members of this family, therefore, are putative addiction module antidote proteins. Some are encoded on plasmids or in prophage regions, but others appear chromosomal. A genome may contain several identical copies, such as the four in Magnetococcus sp. MC-1. This family is named for one member, CC2985 of Caulobacter crescentus CB15.
Probab=20.08 E-value=2.1e+02 Score=16.93 Aligned_cols=47 Identities=19% Similarity=0.293 Sum_probs=25.4
Q ss_pred HHHHHHHHHHhhhhhcchhHHHHHHHhhhccCCHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 033824 6 MQRRLLEYTKSLFMEGVLDNQFLQLQQLQDESNPDFVAEVVSLFFADSERLLNDLTRALD 65 (111)
Q Consensus 6 ~~~~~~~~~~~~~~~~~ld~~~~~L~~L~~~~~~~~~~~ll~~F~~~~~~~l~~L~~a~~ 65 (111)
|..++..|++..++.|--. +..+.++..+..+.+.. ..+..|+..+.
T Consensus 6 L~~~~~~~i~~~V~sG~Y~------------s~SEVir~aLR~le~~e-~~~~~Lr~~i~ 52 (69)
T TIGR02606 6 LGEHLESFIRSQVQSGRYG------------SASEVVRAALRLLEERE-TKLQALRDAIE 52 (69)
T ss_pred cCHHHHHHHHHHHHCCCCC------------CHHHHHHHHHHHHHHHH-HHHHHHHHHHH
Confidence 4455666666666555433 23455666666555543 34555655543
Done!