Query 048267
Match_columns 109
No_of_seqs 103 out of 527
Neff 6.6
Searched_HMMs 46136
Date Fri Mar 29 07:56:41 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/048267.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/048267hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4747 Two-component phosphor 99.9 5.6E-24 1.2E-28 150.0 10.5 108 1-109 5-112 (150)
2 PF01627 Hpt: Hpt domain; Int 99.6 7.9E-15 1.7E-19 92.7 7.5 64 42-107 1-67 (90)
3 COG2198 ArcB FOG: HPt domain [ 99.6 1.3E-14 2.8E-19 98.6 8.8 78 25-105 11-88 (122)
4 smart00073 HPT Histidine Phosp 99.5 5E-14 1.1E-18 89.5 5.8 63 42-106 2-64 (87)
5 cd00088 HPT Histidine Phosphot 99.4 2.5E-13 5.5E-18 87.9 6.6 64 41-106 2-69 (94)
6 TIGR02956 TMAO_torS TMAO reduc 99.2 1.5E-10 3.2E-15 99.3 9.6 73 34-108 875-947 (968)
7 PRK10618 phosphotransfer inter 98.9 8.1E-09 1.8E-13 90.2 7.8 67 40-108 809-875 (894)
8 PRK11466 hybrid sensory histid 98.6 1.8E-07 3.9E-12 80.2 8.1 66 36-103 821-886 (914)
9 PRK11091 aerobic respiration c 98.5 5.1E-07 1.1E-11 76.5 7.8 76 29-106 672-747 (779)
10 PRK11107 hybrid sensory histid 98.3 5.1E-06 1.1E-10 70.9 9.1 69 36-106 822-890 (919)
11 COG0643 CheA Chemotaxis protei 98.1 1E-05 2.2E-10 69.7 7.4 64 38-101 4-73 (716)
12 PRK10547 chemotaxis protein Ch 98.0 2.2E-05 4.8E-10 67.2 8.0 62 41-102 4-71 (670)
13 PRK15347 two component system 97.0 0.0034 7.3E-08 53.9 7.7 62 42-107 837-898 (921)
14 PRK09959 hybrid sensory histid 96.8 0.019 4.2E-07 51.1 11.0 68 36-105 1098-1165(1197)
15 PF07743 HSCB_C: HSCB C-termin 83.4 8.2 0.00018 23.7 7.0 44 35-80 24-67 (78)
16 TIGR00714 hscB Fe-S protein as 79.7 19 0.00041 25.5 8.0 50 29-80 91-140 (157)
17 TIGR00984 3a0801s03tim44 mitoc 78.3 9.5 0.00021 31.1 6.5 80 7-105 213-293 (378)
18 cd08323 CARD_APAF1 Caspase act 74.9 15 0.00032 23.7 5.6 64 10-77 18-82 (86)
19 PF02845 CUE: CUE domain; Int 74.4 6.4 0.00014 21.6 3.4 35 24-58 4-38 (42)
20 PRK01356 hscB co-chaperone Hsc 74.0 30 0.00064 24.8 8.0 39 40-80 111-149 (166)
21 PRK03636 hypothetical protein; 72.6 15 0.00033 26.9 5.9 39 40-80 130-174 (179)
22 PRK03057 hypothetical protein; 72.0 15 0.00033 26.9 5.7 37 42-80 131-173 (180)
23 KOG2580 Mitochondrial import i 70.7 17 0.00036 30.4 6.2 67 2-78 282-350 (459)
24 smart00546 CUE Domain that may 66.6 12 0.00026 20.5 3.3 36 23-58 4-39 (43)
25 COG3046 Uncharacterized protei 61.7 14 0.00031 30.9 4.2 67 34-106 224-290 (505)
26 PRK03578 hscB co-chaperone Hsc 59.1 65 0.0014 23.3 6.9 43 36-80 115-158 (176)
27 PRK13916 plasmid segregation p 58.2 16 0.00034 24.0 3.1 28 25-52 21-48 (97)
28 COG2991 Uncharacterized protei 55.1 2.8 6.2E-05 26.6 -0.7 20 77-96 27-46 (77)
29 smart00188 IL10 Interleukin-10 55.0 53 0.0012 23.1 5.7 44 7-52 14-59 (137)
30 PRK01773 hscB co-chaperone Hsc 54.9 78 0.0017 22.8 6.9 38 40-79 116-153 (173)
31 PF08858 IDEAL: IDEAL domain; 54.2 34 0.00074 18.5 3.8 27 51-79 11-37 (37)
32 PF05396 Phage_T7_Capsid: Phag 51.1 81 0.0018 21.9 8.4 59 20-82 31-89 (123)
33 TIGR03042 PS_II_psbQ_bact phot 46.3 1E+02 0.0023 21.8 6.3 23 51-75 48-70 (142)
34 PRK10093 primosomal replicatio 46.1 1E+02 0.0022 22.5 6.1 34 42-77 40-73 (171)
35 KOG2833 Mevalonate pyrophospha 44.7 49 0.0011 26.9 4.6 30 44-75 224-254 (395)
36 KOG4747 Two-component phosphor 44.4 1.2E+02 0.0025 21.8 6.3 58 37-97 13-70 (150)
37 PF04280 Tim44: Tim44-like dom 44.2 41 0.0009 22.6 3.7 51 37-102 13-63 (147)
38 PLN02407 diphosphomevalonate d 43.9 47 0.001 26.8 4.4 32 43-76 224-256 (343)
39 COG3923 PriC Primosomal replic 43.3 65 0.0014 23.6 4.7 36 42-79 44-79 (175)
40 PF00619 CARD: Caspase recruit 41.2 81 0.0018 19.1 5.1 54 10-65 20-74 (85)
41 PF09280 XPC-binding: XPC-bind 40.2 54 0.0012 19.6 3.3 35 23-58 8-42 (59)
42 PLN00061 photosystem II protei 39.3 1.4E+02 0.0031 21.4 6.8 83 16-102 28-122 (150)
43 PF01322 Cytochrom_C_2: Cytoch 38.5 1.1E+02 0.0025 20.0 5.4 39 44-84 77-115 (122)
44 PF02203 TarH: Tar ligand bind 37.9 1.3E+02 0.0027 20.3 6.0 49 25-75 98-148 (171)
45 cd07298 PX_RICS The phosphoino 37.3 35 0.00076 23.4 2.4 39 12-50 53-95 (115)
46 PF13628 DUF4142: Domain of un 36.7 1.3E+02 0.0028 20.2 5.6 50 25-76 72-122 (139)
47 cd08326 CARD_CASP9 Caspase act 36.2 1.1E+02 0.0025 19.3 5.0 60 11-74 21-81 (84)
48 PF07014 Hs1pro-1_C: Hs1pro-1 35.9 1.2E+02 0.0027 23.3 5.4 38 39-78 54-91 (261)
49 PRK08582 hypothetical protein; 35.8 58 0.0013 22.5 3.4 27 39-65 104-130 (139)
50 TIGR03042 PS_II_psbQ_bact phot 35.1 64 0.0014 22.8 3.6 56 25-86 52-111 (142)
51 TIGR01220 Pmev_kin_Gr_pos phos 35.1 2.3E+02 0.0049 22.5 7.4 56 44-101 247-310 (358)
52 PRK08818 prephenate dehydrogen 35.0 1.7E+02 0.0036 23.7 6.4 42 36-84 226-267 (370)
53 PF07840 FadR_C: FadR C-termin 34.6 64 0.0014 23.4 3.6 40 25-64 122-161 (164)
54 PF04012 PspA_IM30: PspA/IM30 34.5 1.1E+02 0.0024 22.2 5.0 48 4-65 2-49 (221)
55 PF14493 HTH_40: Helix-turn-he 34.5 81 0.0018 19.8 3.8 37 37-74 52-88 (91)
56 TIGR01240 mevDPdecarb diphosph 34.5 81 0.0017 24.7 4.4 31 44-76 202-232 (305)
57 PF03981 Ubiq_cyt_C_chap: Ubiq 34.2 1.3E+02 0.0029 20.0 5.0 48 36-86 34-81 (141)
58 KOG1510 RNA polymerase II holo 33.7 1.7E+02 0.0038 20.7 5.7 56 6-63 70-126 (139)
59 PRK05014 hscB co-chaperone Hsc 33.2 1.8E+02 0.0039 20.7 6.8 39 40-80 115-153 (171)
60 TIGR02302 aProt_lowcomp conser 32.6 1.1E+02 0.0023 27.8 5.3 66 37-108 522-587 (851)
61 KOG4552 Vitamin-D-receptor int 31.9 2.4E+02 0.0051 21.7 6.8 41 42-83 102-142 (272)
62 PF02153 PDH: Prephenate dehyd 31.3 2.2E+02 0.0049 21.2 7.0 26 48-75 230-255 (258)
63 PHA02666 hypothetical protein; 29.7 78 0.0017 24.4 3.4 52 36-91 203-258 (287)
64 PF04400 DUF539: Protein of un 29.3 5.8 0.00012 22.9 -2.1 19 78-96 7-25 (45)
65 PF04840 Vps16_C: Vps16, C-ter 29.2 2.9E+02 0.0062 21.8 8.3 69 21-97 180-249 (319)
66 PF11563 Protoglobin: Protoglo 27.8 1.9E+02 0.0042 19.3 5.5 55 2-56 61-120 (158)
67 cd07299 PX_TCGAP The phosphoin 27.6 79 0.0017 21.6 2.9 38 13-50 52-93 (113)
68 COG4395 Uncharacterized protei 26.9 1E+02 0.0022 24.3 3.8 30 45-76 150-179 (281)
69 PF09130 DUF1932: Domain of un 26.7 1.5E+02 0.0033 17.9 5.8 47 18-64 4-50 (73)
70 PRK07417 arogenate dehydrogena 26.3 1.5E+02 0.0033 22.3 4.6 25 49-75 242-266 (279)
71 PF00726 IL10: Interleukin 10 25.8 1.7E+02 0.0036 21.2 4.5 47 7-55 46-94 (170)
72 PF03858 Crust_neuro_H: Crusta 25.4 59 0.0013 18.3 1.6 23 68-90 5-27 (41)
73 PF09209 DUF1956: Domain of un 25.4 1.9E+02 0.0041 18.4 8.9 83 3-87 4-87 (125)
74 PLN02956 PSII-Q subunit 25.4 2.9E+02 0.0062 20.5 6.7 66 27-106 98-163 (185)
75 KOG2716 Polymerase delta-inter 24.2 75 0.0016 24.2 2.5 52 46-97 48-99 (230)
76 cd07278 PX_RICS_like The phosp 23.9 80 0.0017 21.6 2.4 40 12-51 52-95 (114)
77 PF08822 DUF1804: Protein of u 23.7 1.9E+02 0.0042 21.0 4.5 34 27-60 55-88 (165)
78 PF09670 Cas_Cas02710: CRISPR- 23.6 3.7E+02 0.008 21.6 6.6 62 36-99 116-178 (379)
79 PF15605 Toxin_52: Putative to 23.5 2.4E+02 0.0052 19.0 5.6 10 38-47 47-56 (103)
80 PF02631 RecX: RecX family; I 23.5 2.2E+02 0.0048 18.6 6.0 34 16-49 6-39 (121)
81 COG1327 Predicted transcriptio 23.4 1.8E+02 0.0038 21.0 4.1 33 50-82 62-98 (156)
82 PF13779 DUF4175: Domain of un 23.1 2.8E+02 0.0061 25.0 6.2 67 37-108 491-557 (820)
83 PF01963 TraB: TraB family; I 22.6 1.5E+02 0.0032 21.6 3.8 25 49-75 170-194 (259)
84 COG5582 Uncharacterized conser 21.3 3E+02 0.0066 20.2 5.1 38 38-79 137-174 (182)
85 PRK03381 PII uridylyl-transfer 21.2 2.6E+02 0.0055 24.8 5.5 84 11-98 387-477 (774)
86 PF08332 CaMKII_AD: Calcium/ca 21.1 1.3E+02 0.0027 20.8 3.0 27 49-77 3-29 (128)
87 KOG3091 Nuclear pore complex, 21.0 5.4E+02 0.012 22.1 7.3 17 2-18 414-430 (508)
88 PHA01794 hypothetical protein 20.8 3.1E+02 0.0067 19.3 5.3 52 7-60 58-110 (134)
89 PF08747 DUF1788: Domain of un 20.6 2.3E+02 0.005 19.3 4.2 77 15-102 14-90 (126)
90 COG1842 PspA Phage shock prote 20.6 2.9E+02 0.0063 20.8 5.1 24 42-65 27-50 (225)
91 PF10768 FliX: Class II flagel 20.1 3.2E+02 0.007 19.2 9.5 78 26-103 54-131 (139)
No 1
>KOG4747 consensus Two-component phosphorelay intermediate involved in MAP kinase cascade regulation [Signal transduction mechanisms]
Probab=99.91 E-value=5.6e-24 Score=149.97 Aligned_cols=108 Identities=38% Similarity=0.635 Sum_probs=104.0
Q ss_pred ChHHHHHHHHHHhcccchhhhHHHHHHHHhhhccCCchhHHHHHHHHHHhHHHHHHHHHHHHhcCCcCHHHHHHHhHHhh
Q 048267 1 MEALRQQIAKMRQSFFDEEILDKYFLQLEQLEDISNPGFVKDVVTLYLRDSTKTLATIEDEMAKSPVDFMNLDKCFHQLK 80 (109)
Q Consensus 1 ~~~~~~~~~~~~~~~~~~~~lD~~~~~L~~L~~~~~~~f~~~li~~F~~d~~~~l~~L~~al~~~~~D~~~l~~~aH~LK 80 (109)
|..++.+..+|.+|++++|++|.+|.+|++|+++..|+|+.+++..|++++++.|.+|+.|+..+. |+.+++.+.|.+|
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 356889999999999999999999999999999999999999999999999999999999999864 9999999999999
Q ss_pred hhhhhhChHHHHHHHHHHHHHHhccCcCC
Q 048267 81 GSSASVGANKVLNEVNKAREHCKEGNLEA 109 (109)
Q Consensus 81 GSsasiGA~~l~~~c~~lE~~~~~~~~~g 109 (109)
|||++|||.++...|..+...|+.+|.+|
T Consensus 84 gssssIGa~kvk~~c~~~~~~~~~~n~eg 112 (150)
T KOG4747|consen 84 GSSSSIGALKVKKVCVGFNEFCEAGNIEG 112 (150)
T ss_pred CchhhhhHHHHHHHHHHHHHHHhhccchh
Confidence 99999999999999999999999999987
No 2
>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=7.9e-15 Score=92.67 Aligned_cols=64 Identities=22% Similarity=0.510 Sum_probs=61.1
Q ss_pred HHHHHHHHhHHHHHHHHHHHH---hcCCcCHHHHHHHhHHhhhhhhhhChHHHHHHHHHHHHHHhccCc
Q 048267 42 DVVTLYLRDSTKTLATIEDEM---AKSPVDFMNLDKCFHQLKGSSASVGANKVLNEVNKAREHCKEGNL 107 (109)
Q Consensus 42 ~li~~F~~d~~~~l~~L~~al---~~~~~D~~~l~~~aH~LKGSsasiGA~~l~~~c~~lE~~~~~~~~ 107 (109)
+++..|++++++.+..|..++ ..+ |++.+++.+|+|||+++++|+..+..+|..+|..++.++.
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 3
>COG2198 ArcB FOG: HPt domain [Signal transduction mechanisms]
Probab=99.58 E-value=1.3e-14 Score=98.59 Aligned_cols=78 Identities=23% Similarity=0.443 Sum_probs=70.3
Q ss_pred HHHHHhhhccCCchhHHHHHHHHHHhHHHHHHHHHHHHhcCCcCHHHHHHHhHHhhhhhhhhChHHHHHHHHHHHHHHhc
Q 048267 25 FLQLEQLEDISNPGFVKDVVTLYLRDSTKTLATIEDEMAKSPVDFMNLDKCFHQLKGSSASVGANKVLNEVNKAREHCKE 104 (109)
Q Consensus 25 ~~~L~~L~~~~~~~f~~~li~~F~~d~~~~l~~L~~al~~~~~D~~~l~~~aH~LKGSsasiGA~~l~~~c~~lE~~~~~ 104 (109)
+..+..+.. +.++++.+++..|+++.+..+..++.++..+ |+..+.+.||+||||++|+|+.+++.+|.++|..++.
T Consensus 11 ~~~~~~~~g-~~~~~~~~ll~~f~~~~~~~l~~l~~~l~~~--d~~~~~~~aH~lkg~a~~lg~~~L~~~~~~lE~~~~~ 87 (122)
T COG2198 11 IELLVRLIG-GDPDLLRELLAMFLEEAPAQLEQLESALAAE--DNDGLARLAHRLKGSAASLGLPALAQLCQQLEDALRS 87 (122)
T ss_pred HHHHHHHcC-CChHHHHHHHHHHHHHhHHHHHHHHHHHhcC--CcHHHHHHHHHHHhHHHhccHHHHHHHHHHHHHHHHc
Confidence 334444432 5699999999999999999999999999999 9999999999999999999999999999999999988
Q ss_pred c
Q 048267 105 G 105 (109)
Q Consensus 105 ~ 105 (109)
+
T Consensus 88 ~ 88 (122)
T COG2198 88 G 88 (122)
T ss_pred C
Confidence 3
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=99.50 E-value=5e-14 Score=89.50 Aligned_cols=63 Identities=17% Similarity=0.311 Sum_probs=59.4
Q ss_pred HHHHHHHHhHHHHHHHHHHHHhcCCcCHHHHHHHhHHhhhhhhhhChHHHHHHHHHHHHHHhccC
Q 048267 42 DVVTLYLRDSTKTLATIEDEMAKSPVDFMNLDKCFHQLKGSSASVGANKVLNEVNKAREHCKEGN 106 (109)
Q Consensus 42 ~li~~F~~d~~~~l~~L~~al~~~~~D~~~l~~~aH~LKGSsasiGA~~l~~~c~~lE~~~~~~~ 106 (109)
+++..|+++.++.+..|+.++..+ |++.+.+.+|+|||+++++|+..+..+|..+|..++...
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 688999999999999999999888 999999999999999999999999999999999887643
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=2.5e-13 Score=87.85 Aligned_cols=64 Identities=20% Similarity=0.392 Sum_probs=60.8
Q ss_pred HHHHHHHHHhHHHHHHHHHHHHh----cCCcCHHHHHHHhHHhhhhhhhhChHHHHHHHHHHHHHHhccC
Q 048267 41 KDVVTLYLRDSTKTLATIEDEMA----KSPVDFMNLDKCFHQLKGSSASVGANKVLNEVNKAREHCKEGN 106 (109)
Q Consensus 41 ~~li~~F~~d~~~~l~~L~~al~----~~~~D~~~l~~~aH~LKGSsasiGA~~l~~~c~~lE~~~~~~~ 106 (109)
.+++..|+++.+..+..|..++. .+ |+..+.+.+|+||||++++|+..+..+|..+|.+++.+.
T Consensus 2 ~~l~~~f~~~~~~~l~~l~~~~~~~~~~~--d~~~l~~~~H~LkGsa~~~G~~~l~~~~~~lE~~~~~~~ 69 (94)
T cd00088 2 EELLELFLEEAEELLEELERALLELEDAE--DLNEIFRAAHTLKGSAASLGLQRLAQLAHQLEDLLDALR 69 (94)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHcCCHH--HHHHHHHHHHhhhhHHhcCChHHHHHHHHHHHHHHHHHH
Confidence 47899999999999999999999 77 999999999999999999999999999999999998864
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=99.17 E-value=1.5e-10 Score=99.25 Aligned_cols=73 Identities=26% Similarity=0.377 Sum_probs=68.8
Q ss_pred cCCchhHHHHHHHHHHhHHHHHHHHHHHHhcCCcCHHHHHHHhHHhhhhhhhhChHHHHHHHHHHHHHHhccCcC
Q 048267 34 ISNPGFVKDVVTLYLRDSTKTLATIEDEMAKSPVDFMNLDKCFHQLKGSSASVGANKVLNEVNKAREHCKEGNLE 108 (109)
Q Consensus 34 ~~~~~f~~~li~~F~~d~~~~l~~L~~al~~~~~D~~~l~~~aH~LKGSsasiGA~~l~~~c~~lE~~~~~~~~~ 108 (109)
..+++.+.+++..|+++.+..+..|..++..+ |+..+++.+|+|||+++++|+..+..+|.+||.+++.++.+
T Consensus 875 ~~~~~~~~~~~~~f~~~~~~~~~~l~~~~~~~--d~~~~~~~~H~lkg~~~~~g~~~l~~~~~~le~~~~~~~~~ 947 (968)
T TIGR02956 875 VLGVEKVRQLVALFKTSSAEQLEELSAARAVD--DDAQIKKLAHKLKGSAGSLGLTQLTQLCQQLEKQGKTGALE 947 (968)
T ss_pred hcCcHHHHHHHHHHHHhhHHHHHHHHHHHhCC--CHHHHHHHHHHHHHHHHHhCHHHHHHHHHHHHHhcccCCcc
Confidence 34678999999999999999999999999999 99999999999999999999999999999999999988753
No 7
>PRK10618 phosphotransfer intermediate protein in two-component regulatory system with RcsBC; Provisional
Probab=98.85 E-value=8.1e-09 Score=90.21 Aligned_cols=67 Identities=21% Similarity=0.239 Sum_probs=62.7
Q ss_pred HHHHHHHHHHhHHHHHHHHHHHHhcCCcCHHHHHHHhHHhhhhhhhhChHHHHHHHHHHHHHHhccCcC
Q 048267 40 VKDVVTLYLRDSTKTLATIEDEMAKSPVDFMNLDKCFHQLKGSSASVGANKVLNEVNKAREHCKEGNLE 108 (109)
Q Consensus 40 ~~~li~~F~~d~~~~l~~L~~al~~~~~D~~~l~~~aH~LKGSsasiGA~~l~~~c~~lE~~~~~~~~~ 108 (109)
-..++..|++.++..+..|..++.++ |+.++++.||+|||+++.+|+..++.+|..||.+++.++..
T Consensus 809 ~s~~~~lF~~t~~~di~~L~~~~~~~--D~~~l~~~aHrLKG~~aml~l~~l~~~~~~LE~~i~~~~~~ 875 (894)
T PRK10618 809 ASDYYALFVDTVPDDVKRLYTEAATS--DFASLAQTAHRLKGVFAMLNLVPGKQLCETLEHLIREKDEP 875 (894)
T ss_pred hhhHHHHHHHhhHHHHHHHHHHHhcc--CHHHHHHHHHHHHHHHHHcChHHHHHHHHHHHHHHhhCChH
Confidence 34567899999999999999999999 99999999999999999999999999999999999988753
No 8
>PRK11466 hybrid sensory histidine kinase TorS; Provisional
Probab=98.59 E-value=1.8e-07 Score=80.17 Aligned_cols=66 Identities=18% Similarity=0.254 Sum_probs=61.8
Q ss_pred CchhHHHHHHHHHHhHHHHHHHHHHHHhcCCcCHHHHHHHhHHhhhhhhhhChHHHHHHHHHHHHHHh
Q 048267 36 NPGFVKDVVTLYLRDSTKTLATIEDEMAKSPVDFMNLDKCFHQLKGSSASVGANKVLNEVNKAREHCK 103 (109)
Q Consensus 36 ~~~f~~~li~~F~~d~~~~l~~L~~al~~~~~D~~~l~~~aH~LKGSsasiGA~~l~~~c~~lE~~~~ 103 (109)
+++.+.+++..|.+++...+..++.+...+ |+..+++.+|.|||+++++|+..+...|.++|..+.
T Consensus 821 ~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~--~~~~~~~~ah~lkg~~~~lg~~~l~~~~~~le~~~~ 886 (914)
T PRK11466 821 GTEKIHEWLALFKQHALPLLDEIDIARASQ--DSEKIKRAAHQLKSSCSSLGMRQASQACAQLEQQPL 886 (914)
T ss_pred CHHHHHHHHHHHHHhhHHHHHHHHHHHHCC--CHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhCCCC
Confidence 567788999999999999999999999999 999999999999999999999999999999998753
No 9
>PRK11091 aerobic respiration control sensor protein ArcB; Provisional
Probab=98.48 E-value=5.1e-07 Score=76.54 Aligned_cols=76 Identities=16% Similarity=0.284 Sum_probs=66.3
Q ss_pred HhhhccCCchhHHHHHHHHHHhHHHHHHHHHHHHhcCCcCHHHHHHHhHHhhhhhhhhChHHHHHHHHHHHHHHhccC
Q 048267 29 EQLEDISNPGFVKDVVTLYLRDSTKTLATIEDEMAKSPVDFMNLDKCFHQLKGSSASVGANKVLNEVNKAREHCKEGN 106 (109)
Q Consensus 29 ~~L~~~~~~~f~~~li~~F~~d~~~~l~~L~~al~~~~~D~~~l~~~aH~LKGSsasiGA~~l~~~c~~lE~~~~~~~ 106 (109)
..+.+..++..+.+.+..|.+..+..+..|..++..+ |+..+...+|+|||+++++|+..++.+|..+|.....+.
T Consensus 672 ~~~~~~~g~~~~~~~l~~~~~~~~~~~~~l~~~l~~~--d~~~~~~~ah~l~g~~~~~g~~~l~~~~~~le~~~~~~~ 747 (779)
T PRK11091 672 EQYVELVGPKLITDSLAVFEKMMPGYLSVLDSNLTAR--DQKGIVEEAHKIKGAAGSVGLRHLQQLAQQIQSPDLPAW 747 (779)
T ss_pred HHHHHhcCHHHHHHHHHHHHHhhHHHHHHHHHHHHCC--CHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHhCcCcccc
Confidence 3333333567888999999999999999999999999 999999999999999999999999999999998766544
No 10
>PRK11107 hybrid sensory histidine kinase BarA; Provisional
Probab=98.27 E-value=5.1e-06 Score=70.92 Aligned_cols=69 Identities=19% Similarity=0.331 Sum_probs=64.6
Q ss_pred CchhHHHHHHHHHHhHHHHHHHHHHHHhcCCcCHHHHHHHhHHhhhhhhhhChHHHHHHHHHHHHHHhccC
Q 048267 36 NPGFVKDVVTLYLRDSTKTLATIEDEMAKSPVDFMNLDKCFHQLKGSSASVGANKVLNEVNKAREHCKEGN 106 (109)
Q Consensus 36 ~~~f~~~li~~F~~d~~~~l~~L~~al~~~~~D~~~l~~~aH~LKGSsasiGA~~l~~~c~~lE~~~~~~~ 106 (109)
.++...+++..|.+..+..+..|..++... |...+...+|.+||+++++|+..+..+|..+|..++.+.
T Consensus 822 ~~~~~~~~l~~~~~~~~~~~~~l~~~~~~~--~~~~~~~~~h~l~g~~~~~g~~~l~~~~~~le~~~~~~~ 890 (919)
T PRK11107 822 KPDLARDMLQMLLDFLPEVRNKVEEALAGE--DPEGLLDLIHKLHGSCSYSGVPRLKKLCQLIEQQLRSGT 890 (919)
T ss_pred CHHHHHHHHHHHHHhHHHHHHHHHHHHHCC--CHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHcCC
Confidence 467888999999999999999999999998 999999999999999999999999999999999998653
No 11
>COG0643 CheA Chemotaxis protein histidine kinase and related kinases [Cell motility and secretion / Signal transduction mechanisms]
Probab=98.10 E-value=1e-05 Score=69.68 Aligned_cols=64 Identities=16% Similarity=0.339 Sum_probs=53.8
Q ss_pred hhHHHHHHHHHHhHHHHHHHHHHHHh---cCCcCH---HHHHHHhHHhhhhhhhhChHHHHHHHHHHHHH
Q 048267 38 GFVKDVVTLYLRDSTKTLATIEDEMA---KSPVDF---MNLDKCFHQLKGSSASVGANKVLNEVNKAREH 101 (109)
Q Consensus 38 ~f~~~li~~F~~d~~~~l~~L~~al~---~~~~D~---~~l~~~aH~LKGSsasiGA~~l~~~c~~lE~~ 101 (109)
.-..++...|++++++.+..|..++- ..+.|. .++.|.||+|||+++.+|...++.+|..+|..
T Consensus 4 ~~~~~~~~~F~~Ea~e~l~~l~~~Ll~LE~~~~d~~~ln~ifRaaHTlKG~a~~~g~~~l~~l~H~~E~~ 73 (716)
T COG0643 4 MDMEEILEDFLEEAEELLQALEQALLALEPDPEDLDLLNAIFRAAHTLKGGAGTLGLTTLAELAHAMEDL 73 (716)
T ss_pred hHHHHHHHHHHHhhHHHHHHHHHhHhhccCCCCCHHHHHHHHHHHHhhhhhhhhcChhHHHHHHHHHHHH
Confidence 45678999999999999999998653 222243 47889999999999999999999999999974
No 12
>PRK10547 chemotaxis protein CheA; Provisional
Probab=98.03 E-value=2.2e-05 Score=67.21 Aligned_cols=62 Identities=15% Similarity=0.262 Sum_probs=52.4
Q ss_pred HHHHHHHHHhHHHHHHHHHHHHh---cCCcCH---HHHHHHhHHhhhhhhhhChHHHHHHHHHHHHHH
Q 048267 41 KDVVTLYLRDSTKTLATIEDEMA---KSPVDF---MNLDKCFHQLKGSSASVGANKVLNEVNKAREHC 102 (109)
Q Consensus 41 ~~li~~F~~d~~~~l~~L~~al~---~~~~D~---~~l~~~aH~LKGSsasiGA~~l~~~c~~lE~~~ 102 (109)
.+++..|++++.+++..|+..+- ..+.|. ..+-|.+|+|||+|+.+|...+..+|..+|..-
T Consensus 4 ~~~l~~F~~Ea~E~l~~le~~Ll~LE~~p~d~e~in~lFRa~HTiKG~a~~~g~~~i~~l~H~~E~ll 71 (670)
T PRK10547 4 SDFYQTFFDEADELLADMEQHLLVLDPEAPDAEQLNAIFRAAHSIKGGAGTFGFTVLQETTHLMENLL 71 (670)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhccCCCCHHHHHHHHHHHHhhhhHHhhcCchHHHHHHHHHHHHH
Confidence 47899999999999999998774 332253 467789999999999999999999999999754
No 13
>PRK15347 two component system sensor kinase SsrA; Provisional
Probab=96.98 E-value=0.0034 Score=53.94 Aligned_cols=62 Identities=19% Similarity=0.303 Sum_probs=53.0
Q ss_pred HHHHHHHHhHHHHHHHHHHHHhcCCcCHHHHHHHhHHhhhhhhhhChHHHHHHHHHHHHHHhccCc
Q 048267 42 DVVTLYLRDSTKTLATIEDEMAKSPVDFMNLDKCFHQLKGSSASVGANKVLNEVNKAREHCKEGNL 107 (109)
Q Consensus 42 ~li~~F~~d~~~~l~~L~~al~~~~~D~~~l~~~aH~LKGSsasiGA~~l~~~c~~lE~~~~~~~~ 107 (109)
.+-..+.+.....+..+..++..+ | .+++.+|.+||+++.+|+..+...|.++|..++.+..
T Consensus 837 ~l~~~~~~~l~~~~~~~~~~~~~~--~--~l~~~~h~i~~~~~~~g~~~l~~~~~~~e~~~~~~~~ 898 (921)
T PRK15347 837 ALNSKLYQSLLLLLAQIEQAVENQ--E--VLSQLLHTLKGCAGQAGLTELQCAVIDLENALETGEI 898 (921)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhCH--H--HHHHHHHHHHHHHHHcCHHHHHHHHHHHHHHHhcCCC
Confidence 344555666778888999999887 6 8999999999999999999999999999999887653
No 14
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=96.77 E-value=0.019 Score=51.07 Aligned_cols=68 Identities=12% Similarity=0.309 Sum_probs=61.6
Q ss_pred CchhHHHHHHHHHHhHHHHHHHHHHHHhcCCcCHHHHHHHhHHhhhhhhhhChHHHHHHHHHHHHHHhcc
Q 048267 36 NPGFVKDVVTLYLRDSTKTLATIEDEMAKSPVDFMNLDKCFHQLKGSSASVGANKVLNEVNKAREHCKEG 105 (109)
Q Consensus 36 ~~~f~~~li~~F~~d~~~~l~~L~~al~~~~~D~~~l~~~aH~LKGSsasiGA~~l~~~c~~lE~~~~~~ 105 (109)
......+++..+...+...+..+..+...+ |...+..++|.+||++..+|+..+...|.++|......
T Consensus 1098 ~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~h~~~g~~~~l~~~~l~~~~~~~e~~~~~~ 1165 (1197)
T PRK09959 1098 DLQLMQEILMTFQHETHKDLPAAFHALEAG--DNRTFHQCIHRIHGAANILNLQKLINISHQLEITPVSD 1165 (1197)
T ss_pred CHHHHHHHHHHHHHhhHHHHHHHHHHHHcC--CHHHHHHHHHHHHHHHHHcCHHHHHHHHHHHHHhhhcC
Confidence 446788899999999999999999999999 99999999999999999999999999999999887654
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=83.36 E-value=8.2 Score=23.71 Aligned_cols=44 Identities=7% Similarity=0.191 Sum_probs=36.4
Q ss_pred CCchhHHHHHHHHHHhHHHHHHHHHHHHhcCCcCHHHHHHHhHHhh
Q 048267 35 SNPGFVKDVVTLYLRDSTKTLATIEDEMAKSPVDFMNLDKCFHQLK 80 (109)
Q Consensus 35 ~~~~f~~~li~~F~~d~~~~l~~L~~al~~~~~D~~~l~~~aH~LK 80 (109)
++.+-+..+....-......+..|..+++.+ ||.......+.||
T Consensus 24 ~~~~~L~~l~~~~~~~~~~~~~~l~~~f~~~--d~~~A~~~~~kLk 67 (78)
T PF07743_consen 24 DDEAELEELKKEIEERIKELIKELAEAFDAK--DWEEAKEALRKLK 67 (78)
T ss_dssp TSHHHHHHHHHHHHHHHHHHHHHHHHHHHTT---HHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHccC--cHHHHHHHHHHHH
Confidence 3446677888888888888999999999988 9999999999886
No 16
>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=79.70 E-value=19 Score=25.49 Aligned_cols=50 Identities=4% Similarity=0.144 Sum_probs=32.5
Q ss_pred HhhhccCCchhHHHHHHHHHHhHHHHHHHHHHHHhcCCcCHHHHHHHhHHhh
Q 048267 29 EQLEDISNPGFVKDVVTLYLRDSTKTLATIEDEMAKSPVDFMNLDKCFHQLK 80 (109)
Q Consensus 29 ~~L~~~~~~~f~~~li~~F~~d~~~~l~~L~~al~~~~~D~~~l~~~aH~LK 80 (109)
.++....+++-+..+....-.........|..+++.+ ||+........||
T Consensus 91 ee~~~~~d~~~L~~l~~~~~~~~~~~~~~l~~~~~~~--d~~~A~~~~~kLk 140 (157)
T TIGR00714 91 DEIEQAKDEARLESFIKRVKKMFQTRHQLLVEQLDNQ--TWAAAADYTRKLR 140 (157)
T ss_pred HHHHhCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcC--CHHHHHHHHHHHH
Confidence 3333333444555666666666666677778888888 8888887777665
No 17
>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=78.27 E-value=9.5 Score=31.14 Aligned_cols=80 Identities=18% Similarity=0.245 Sum_probs=56.0
Q ss_pred HHHHHHhcccchhhhHHHHHHHHhhhccCCchhHHHHHHHHHHhHHHH-HHHHHHHHhcCCcCHHHHHHHhHHhhhhhhh
Q 048267 7 QIAKMRQSFFDEEILDKYFLQLEQLEDISNPGFVKDVVTLYLRDSTKT-LATIEDEMAKSPVDFMNLDKCFHQLKGSSAS 85 (109)
Q Consensus 7 ~~~~~~~~~~~~~~lD~~~~~L~~L~~~~~~~f~~~li~~F~~d~~~~-l~~L~~al~~~~~D~~~l~~~aH~LKGSsas 85 (109)
.+...+.++|.+.-+-..+.+++++. |.|- +..|+..+... +..|-.|+..+ |.+.|+.+++.
T Consensus 213 kv~~~~~~lF~ete~a~~l~eIk~~D----PsFd---~~~Fl~gar~aI~p~ILeAf~kG--D~e~LK~~lse------- 276 (378)
T TIGR00984 213 KIGGVFSGMFSETEVSEVLTEFKKID----PTFD---KEHFLRFLREYIVPEILEAYVKG--DLEVLKSWCSE------- 276 (378)
T ss_pred hhhhhhhcccCCCHHHHHHHHHHHhC----CCCC---HHHHHHHHHHHHHHHHHHHHHcC--CHHHHHHhhCH-------
Confidence 34445556777777766677887775 4454 46788889988 69999999999 99999988653
Q ss_pred hChHHHHHHHHHHHHHHhcc
Q 048267 86 VGANKVLNEVNKAREHCKEG 105 (109)
Q Consensus 86 iGA~~l~~~c~~lE~~~~~~ 105 (109)
......|..+++..++|
T Consensus 277 ---~vy~~f~a~I~qr~~~G 293 (378)
T TIGR00984 277 ---APFSVYATVVKEYKKMG 293 (378)
T ss_pred ---HHHHHHHHHHHHHHHCC
Confidence 23445555565555544
No 18
>cd08323 CARD_APAF1 Caspase activation and recruitment domain similar to that found in Apoptotic Protease-Activating Factor 1. Caspase activation and recruitment domain (CARD) similar to that found in apoptotic protease-activating factor 1 (APAF-1), which is an activator of caspase-9. APAF-1 contains WD-40 repeats, a CARD, and an ATPase domain. Upon stimulation, APAF-1, together with caspase-9, forms the heptameric 'apoptosome', which leads to the processing and activation of caspase-9, starting a caspase cascade which leads to apoptosis. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and DED (Death Effect
Probab=74.91 E-value=15 Score=23.69 Aligned_cols=64 Identities=6% Similarity=0.144 Sum_probs=48.3
Q ss_pred HHHhcccchhhhHHH-HHHHHhhhccCCchhHHHHHHHHHHhHHHHHHHHHHHHhcCCcCHHHHHHHhH
Q 048267 10 KMRQSFFDEEILDKY-FLQLEQLEDISNPGFVKDVVTLYLRDSTKTLATIEDEMAKSPVDFMNLDKCFH 77 (109)
Q Consensus 10 ~~~~~~~~~~~lD~~-~~~L~~L~~~~~~~f~~~li~~F~~d~~~~l~~L~~al~~~~~D~~~l~~~aH 77 (109)
..+..++.+|+++.. .+.++.- ....+-...|+++-..-+++.+.....++... .|+.+..+.|
T Consensus 18 ~ild~L~~~gvlt~~~~e~I~~~--~t~~~qa~~Lld~L~trG~~Af~~F~~aL~~~--~~~~La~lL~ 82 (86)
T cd08323 18 YIMDHMISDGVLTLDEEEKVKSK--ATQKEKAVMLINMILTKDNHAYVSFYNALLHE--GYKDLALLLH 82 (86)
T ss_pred HHHHHHHhcCCCCHHHHHHHHcC--CChHHHHHHHHHHHHhcCHHHHHHHHHHHHhc--CChHHHHHHh
Confidence 355667777888875 6666663 33467788899999999999999999999865 6888877765
No 19
>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=74.40 E-value=6.4 Score=21.56 Aligned_cols=35 Identities=11% Similarity=0.132 Sum_probs=27.9
Q ss_pred HHHHHHhhhccCCchhHHHHHHHHHHhHHHHHHHH
Q 048267 24 YFLQLEQLEDISNPGFVKDVVTLYLRDSTKTLATI 58 (109)
Q Consensus 24 ~~~~L~~L~~~~~~~f~~~li~~F~~d~~~~l~~L 58 (109)
.+.+|+++.+.-+++++..++..+-.+.+..+..|
T Consensus 4 ~v~~L~~mFP~~~~~~I~~~L~~~~~~ve~ai~~L 38 (42)
T PF02845_consen 4 MVQQLQEMFPDLDREVIEAVLQANNGDVEAAIDAL 38 (42)
T ss_dssp HHHHHHHHSSSS-HHHHHHHHHHTTTTHHHHHHHH
T ss_pred HHHHHHHHCCCCCHHHHHHHHHHcCCCHHHHHHHH
Confidence 46789999988888999998888888887777655
No 20
>PRK01356 hscB co-chaperone HscB; Provisional
Probab=73.97 E-value=30 Score=24.78 Aligned_cols=39 Identities=8% Similarity=0.165 Sum_probs=22.5
Q ss_pred HHHHHHHHHHhHHHHHHHHHHHHhcCCcCHHHHHHHhHHhh
Q 048267 40 VKDVVTLYLRDSTKTLATIEDEMAKSPVDFMNLDKCFHQLK 80 (109)
Q Consensus 40 ~~~li~~F~~d~~~~l~~L~~al~~~~~D~~~l~~~aH~LK 80 (109)
+.++-...-......+..|..+++.+ ||+.....+-.||
T Consensus 111 L~~l~~~~~~~~~~~~~~l~~~f~~~--d~~~A~~~~~~L~ 149 (166)
T PRK01356 111 LEKIKNKYELMYKNEIDSLKQAFEEQ--NLSDATIKTSKLK 149 (166)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhcC--CHHHHHHHHHHHH
Confidence 44444444444445556677777777 7776666555543
No 21
>PRK03636 hypothetical protein; Provisional
Probab=72.56 E-value=15 Score=26.86 Aligned_cols=39 Identities=15% Similarity=0.282 Sum_probs=31.0
Q ss_pred HHHHHHHHHHh------HHHHHHHHHHHHhcCCcCHHHHHHHhHHhh
Q 048267 40 VKDVVTLYLRD------STKTLATIEDEMAKSPVDFMNLDKCFHQLK 80 (109)
Q Consensus 40 ~~~li~~F~~d------~~~~l~~L~~al~~~~~D~~~l~~~aH~LK 80 (109)
....++.+++. -.+++.+|..|++.+ |-+.+.+++..||
T Consensus 130 ~~~~ae~~L~~~~~~~r~~~L~~~ID~ALd~~--D~e~F~~Ls~~l~ 174 (179)
T PRK03636 130 DRLLAEQFLEQSVFQFRREKLLKQIDEALDRR--DKEAFHRLSDELN 174 (179)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcC--CHHHHHHHHHHHH
Confidence 34555566655 567889999999999 9999999988876
No 22
>PRK03057 hypothetical protein; Provisional
Probab=72.04 E-value=15 Score=26.92 Aligned_cols=37 Identities=14% Similarity=0.275 Sum_probs=29.9
Q ss_pred HHHHHHHHh------HHHHHHHHHHHHhcCCcCHHHHHHHhHHhh
Q 048267 42 DVVTLYLRD------STKTLATIEDEMAKSPVDFMNLDKCFHQLK 80 (109)
Q Consensus 42 ~li~~F~~d------~~~~l~~L~~al~~~~~D~~~l~~~aH~LK 80 (109)
+.++.|++. -.++..+|..|++.+ |.+.+.++.+.|+
T Consensus 131 ~~ae~~L~~~~~~~~~~~L~~~ID~ALd~~--D~e~F~~Lt~~L~ 173 (180)
T PRK03057 131 KETEQVLDEVLKRNEVSRLRMQIDQALDRK--DMEEFQRLTEKLK 173 (180)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHCC--CHHHHHHHHHHHH
Confidence 456666666 567788999999999 9999999888875
No 23
>KOG2580 consensus Mitochondrial import inner membrane translocase, subunit TIM44 [Intracellular trafficking, secretion, and vesicular transport]
Probab=70.69 E-value=17 Score=30.37 Aligned_cols=67 Identities=12% Similarity=0.339 Sum_probs=48.9
Q ss_pred hHHHHHHHHHHhcccchhhhHHHHHHHHhhhccCC-chhHHHHHHHHHHhHHH-HHHHHHHHHhcCCcCHHHHHHHhHH
Q 048267 2 EALRQQIAKMRQSFFDEEILDKYFLQLEQLEDISN-PGFVKDVVTLYLRDSTK-TLATIEDEMAKSPVDFMNLDKCFHQ 78 (109)
Q Consensus 2 ~~~~~~~~~~~~~~~~~~~lD~~~~~L~~L~~~~~-~~f~~~li~~F~~d~~~-~l~~L~~al~~~~~D~~~l~~~aH~ 78 (109)
..++..|.+.+.++|+.--.-+...++..+.+.-+ |+|+ .++++ .+.++-.|+-.+ |.+.|+..+|.
T Consensus 282 rdvtdki~~~~~g~fsktE~Sev~tei~~iDPsF~~~~Fl--------r~~ee~IiPnVLeAyvkG--D~evLK~wcse 350 (459)
T KOG2580|consen 282 RDVTDKITDVDGGLFSKTEMSEVLTEIKKIDPSFDKEDFL--------RECEEYIIPNVLEAYVKG--DLEVLKKWCSE 350 (459)
T ss_pred HHHHHhhhhcccccchhhHHHHHHHHHHhcCCCCCcHHHH--------HHHHHhhhHHHHHHHHhc--cHHHHHHHHhh
Confidence 45677888888888888777777888888865433 4455 33443 345588888999 99999988874
No 24
>smart00546 CUE Domain that may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two protein of the IL-1 signal transduction pathway, tollip and TAB2. Ponting (Biochem. J.) "Proteins of the Endoplasmic reticulum" (in press)
Probab=66.60 E-value=12 Score=20.47 Aligned_cols=36 Identities=11% Similarity=0.131 Sum_probs=28.6
Q ss_pred HHHHHHHhhhccCCchhHHHHHHHHHHhHHHHHHHH
Q 048267 23 KYFLQLEQLEDISNPGFVKDVVTLYLRDSTKTLATI 58 (109)
Q Consensus 23 ~~~~~L~~L~~~~~~~f~~~li~~F~~d~~~~l~~L 58 (109)
+.+..|+++.+.-+++.++.++..+-.+.+..+..|
T Consensus 4 ~~v~~L~~mFP~l~~~~I~~~L~~~~g~ve~~i~~L 39 (43)
T smart00546 4 EALHDLKDMFPNLDEEVIKAVLEANNGNVEATINNL 39 (43)
T ss_pred HHHHHHHHHCCCCCHHHHHHHHHHcCCCHHHHHHHH
Confidence 347899999988888888888888777877777655
No 25
>COG3046 Uncharacterized protein related to deoxyribodipyrimidine photolyase [General function prediction only]
Probab=61.71 E-value=14 Score=30.88 Aligned_cols=67 Identities=16% Similarity=0.245 Sum_probs=57.6
Q ss_pred cCCchhHHHHHHHHHHhHHHHHHHHHHHHhcCCcCHHHHHHHhHHhhhhhhhhChHHHHHHHHHHHHHHhccC
Q 048267 34 ISNPGFVKDVVTLYLRDSTKTLATIEDEMAKSPVDFMNLDKCFHQLKGSSASVGANKVLNEVNKAREHCKEGN 106 (109)
Q Consensus 34 ~~~~~f~~~li~~F~~d~~~~l~~L~~al~~~~~D~~~l~~~aH~LKGSsasiGA~~l~~~c~~lE~~~~~~~ 106 (109)
+.+++-....+.-|+++.-..+..-+.|+..+ |.. +=|+|=+++.|+|...=.++|+..+.+-+.|+
T Consensus 224 pvtr~~A~~~L~~Fi~~~L~nFG~yQDam~~d--~~~----L~HSllS~alNigLL~PleVi~Aa~~Ay~~g~ 290 (505)
T COG3046 224 PVTRTQALRALKHFIADRLPNFGSYQDAMSAD--DPH----LWHSLLSFALNIGLLTPLEVIRAALKAYREGD 290 (505)
T ss_pred CCCHHHHHHHHHHHHHHhhhcCCcHHHHHhcC--Cch----hHHHHHHHHhhccCCCHHHHHHHHHHhhccCC
Confidence 34455667889999999999999999999887 554 77999999999999999999999999988865
No 26
>PRK03578 hscB co-chaperone HscB; Provisional
Probab=59.13 E-value=65 Score=23.28 Aligned_cols=43 Identities=9% Similarity=0.093 Sum_probs=26.5
Q ss_pred CchhHHHHHHHHHHhHHHHHHHHHHHHhc-CCcCHHHHHHHhHHhh
Q 048267 36 NPGFVKDVVTLYLRDSTKTLATIEDEMAK-SPVDFMNLDKCFHQLK 80 (109)
Q Consensus 36 ~~~f~~~li~~F~~d~~~~l~~L~~al~~-~~~D~~~l~~~aH~LK 80 (109)
+++-+..+....-......+..|..+++. + ||.........||
T Consensus 115 d~~~L~~l~~e~~~~~~~~~~~l~~~~~~~~--d~~~A~~~~~kL~ 158 (176)
T PRK03578 115 DVDALDALLAELRDERRERYAELGALLDSRG--DDQAAAEAVRQLM 158 (176)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHccc--cHHHHHHHHHHHH
Confidence 34444455555555555566666777766 5 7777777766666
No 27
>PRK13916 plasmid segregation protein ParR; Provisional
Probab=58.21 E-value=16 Score=24.03 Aligned_cols=28 Identities=14% Similarity=0.320 Sum_probs=24.4
Q ss_pred HHHHHhhhccCCchhHHHHHHHHHHhHH
Q 048267 25 FLQLEQLEDISNPGFVKDVVTLYLRDST 52 (109)
Q Consensus 25 ~~~L~~L~~~~~~~f~~~li~~F~~d~~ 52 (109)
|+=|..+.++.-+.|++++++.|+++..
T Consensus 21 F~FL~~~P~GT~~~~iR~~L~rYI~~~G 48 (97)
T PRK13916 21 FDFLENVPRGTKTAHIREALRRYIEEIG 48 (97)
T ss_pred HHHHHHCCCCCccHHHHHHHHHHHHhcC
Confidence 7788888888779999999999999864
No 28
>COG2991 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=55.06 E-value=2.8 Score=26.61 Aligned_cols=20 Identities=20% Similarity=0.333 Sum_probs=17.6
Q ss_pred HHhhhhhhhhChHHHHHHHH
Q 048267 77 HQLKGSSASVGANKVLNEVN 96 (109)
Q Consensus 77 H~LKGSsasiGA~~l~~~c~ 96 (109)
-++|||++.|++..+...|.
T Consensus 27 k~I~GSCGGi~alGi~K~Cd 46 (77)
T COG2991 27 KSIKGSCGGIAALGIEKVCD 46 (77)
T ss_pred cccccccccHHhhccchhcC
Confidence 46899999999999988885
No 29
>smart00188 IL10 Interleukin-10 family. Interleukin-10 inhibits the synthesis of a number of cytokines, including IFN-gamma, IL-2, IL-3, TNF and GM-CSF produced by activated macrophages and by helper T cells.
Probab=54.95 E-value=53 Score=23.12 Aligned_cols=44 Identities=16% Similarity=0.291 Sum_probs=30.4
Q ss_pred HHHHHHhc--ccchhhhHHHHHHHHhhhccCCchhHHHHHHHHHHhHH
Q 048267 7 QIAKMRQS--FFDEEILDKYFLQLEQLEDISNPGFVKDVVTLYLRDST 52 (109)
Q Consensus 7 ~~~~~~~~--~~~~~~lD~~~~~L~~L~~~~~~~f~~~li~~F~~d~~ 52 (109)
++..+++. ..+..+|+. +-|+.+.+..+.-++.++++-|++.+=
T Consensus 14 ~Ik~~~q~kD~~~~vll~~--~ll~~~k~~~gC~~l~ell~FYLd~V~ 59 (137)
T smart00188 14 RVKTFFQMKDQLDNILLTE--SLLEDFKGYLGCQALSEMIQFYLEEVM 59 (137)
T ss_pred HHHHHHHccchHhhHhhhH--HHHHHhCCCcchHHHHHHHHHHHHHHH
Confidence 34445444 222245555 466777788889999999999999876
No 30
>PRK01773 hscB co-chaperone HscB; Provisional
Probab=54.94 E-value=78 Score=22.84 Aligned_cols=38 Identities=5% Similarity=0.139 Sum_probs=18.8
Q ss_pred HHHHHHHHHHhHHHHHHHHHHHHhcCCcCHHHHHHHhHHh
Q 048267 40 VKDVVTLYLRDSTKTLATIEDEMAKSPVDFMNLDKCFHQL 79 (109)
Q Consensus 40 ~~~li~~F~~d~~~~l~~L~~al~~~~~D~~~l~~~aH~L 79 (109)
+..+....-......+..|..+++.+ ||+.....+-.|
T Consensus 116 L~~l~~~v~~~~~~~~~~l~~~~~~~--d~~~A~~~~~rL 153 (173)
T PRK01773 116 LTAFSKEIKQEQQAILTELSTALNSQ--QWQQASQINDRL 153 (173)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhcC--CHHHHHHHHHHH
Confidence 33333333334444455566666666 666555444443
No 31
>PF08858 IDEAL: IDEAL domain; InterPro: IPR014957 This entry represents the C-terminal domain of Bacteriophage SPP1, p90. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. his domain may also be referred to as the IDEAL domain, after the sequence of the most conserved region of the domain.; PDB: 3DO9_A.
Probab=54.16 E-value=34 Score=18.48 Aligned_cols=27 Identities=15% Similarity=0.167 Sum_probs=21.0
Q ss_pred HHHHHHHHHHHHhcCCcCHHHHHHHhHHh
Q 048267 51 STKTLATIEDEMAKSPVDFMNLDKCFHQL 79 (109)
Q Consensus 51 ~~~~l~~L~~al~~~~~D~~~l~~~aH~L 79 (109)
-+++...|..|++.+ |-+.+.+++..|
T Consensus 11 ~~~L~~~ID~ALd~~--D~e~F~~Ls~eL 37 (37)
T PF08858_consen 11 KEQLLELIDEALDNR--DKEWFYELSEEL 37 (37)
T ss_dssp HHHHHHHHHHHHHTT---HHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHcC--CHHHHHHHHhhC
Confidence 356788899999999 999988877553
No 32
>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=51.06 E-value=81 Score=21.88 Aligned_cols=59 Identities=7% Similarity=0.149 Sum_probs=42.3
Q ss_pred hhHHHHHHHHhhhccCCchhHHHHHHHHHHhHHHHHHHHHHHHhcCCcCHHHHHHHhHHhhhh
Q 048267 20 ILDKYFLQLEQLEDISNPGFVKDVVTLYLRDSTKTLATIEDEMAKSPVDFMNLDKCFHQLKGS 82 (109)
Q Consensus 20 ~lD~~~~~L~~L~~~~~~~f~~~li~~F~~d~~~~l~~L~~al~~~~~D~~~l~~~aH~LKGS 82 (109)
+.|.....+..+. ||++-...|+.---...+..+..+..+++++ |..+++.+.-.+++|
T Consensus 31 L~~~yV~~V~~~A--GG~e~f~~i~~~~~~~~~~~~ea~~~Ai~~~--dla~vk~~vn~~~~s 89 (123)
T PF05396_consen 31 LAEQYVNSVKGYA--GGEEGFAAIMSHAEANSPAAAEAFNEAIESG--DLATVKAAVNLAGAS 89 (123)
T ss_pred HHHHHHHHHHHHh--cCHHHHHHHHHHHHhCCHHHHHHHHHHHHhC--CHHHHHHHHHHHHHH
Confidence 3443455555554 4666666666665677899999999999999 999999876555544
No 33
>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=46.31 E-value=1e+02 Score=21.77 Aligned_cols=23 Identities=17% Similarity=0.264 Sum_probs=11.5
Q ss_pred HHHHHHHHHHHHhcCCcCHHHHHHH
Q 048267 51 STKTLATIEDEMAKSPVDFMNLDKC 75 (109)
Q Consensus 51 ~~~~l~~L~~al~~~~~D~~~l~~~ 75 (109)
+.+++.+|+..++.+ ||..++..
T Consensus 48 ~~~r~~eLk~lI~kk--~W~~vrn~ 70 (142)
T TIGR03042 48 AKDRLPELASLVAKE--DWVFTRNL 70 (142)
T ss_pred HHHhhHHHHHHHhhc--chHHHHHH
Confidence 444555555555555 55555543
No 34
>PRK10093 primosomal replication protein N''; Provisional
Probab=46.09 E-value=1e+02 Score=22.54 Aligned_cols=34 Identities=12% Similarity=0.269 Sum_probs=27.4
Q ss_pred HHHHHHHHhHHHHHHHHHHHHhcCCcCHHHHHHHhH
Q 048267 42 DVVTLYLRDSTKTLATIEDEMAKSPVDFMNLDKCFH 77 (109)
Q Consensus 42 ~li~~F~~d~~~~l~~L~~al~~~~~D~~~l~~~aH 77 (109)
..+.-|+.++...++.|..++..+ +..++.-++=
T Consensus 40 ~~L~~yl~Ei~~~l~qL~~~~~~~--~~~~~~flaE 73 (171)
T PRK10093 40 TLLQAYLDEAGDNLAALRHAVEQQ--QLPQVAWLAE 73 (171)
T ss_pred cchHHHHHHHHHHHHHHHHHHhcC--cHHHHHHHHH
Confidence 467889999999999999999988 6666655543
No 35
>KOG2833 consensus Mevalonate pyrophosphate decarboxylase [Lipid transport and metabolism]
Probab=44.68 E-value=49 Score=26.94 Aligned_cols=30 Identities=10% Similarity=0.305 Sum_probs=24.5
Q ss_pred HHHHHHh-HHHHHHHHHHHHhcCCcCHHHHHHH
Q 048267 44 VTLYLRD-STKTLATIEDEMAKSPVDFMNLDKC 75 (109)
Q Consensus 44 i~~F~~d-~~~~l~~L~~al~~~~~D~~~l~~~ 75 (109)
+.-=+++ +|++|.+|++|+.++ ||+.+.++
T Consensus 224 ~qhRi~~vVP~Ri~~m~eaI~~r--DF~~FA~l 254 (395)
T KOG2833|consen 224 LQHRIESVVPQRIQQMREAIRER--DFESFAKL 254 (395)
T ss_pred HHHHHHhhhHHHHHHHHHHHHhc--CHHHHHHH
Confidence 3333444 899999999999999 99998876
No 36
>KOG4747 consensus Two-component phosphorelay intermediate involved in MAP kinase cascade regulation [Signal transduction mechanisms]
Probab=44.39 E-value=1.2e+02 Score=21.80 Aligned_cols=58 Identities=10% Similarity=0.162 Sum_probs=46.7
Q ss_pred chhHHHHHHHHHHhHHHHHHHHHHHHhcCCcCHHHHHHHhHHhhhhhhhhChHHHHHHHHH
Q 048267 37 PGFVKDVVTLYLRDSTKTLATIEDEMAKSPVDFMNLDKCFHQLKGSSASVGANKVLNEVNK 97 (109)
Q Consensus 37 ~~f~~~li~~F~~d~~~~l~~L~~al~~~~~D~~~l~~~aH~LKGSsasiGA~~l~~~c~~ 97 (109)
.+|-..++..++.| ..+.+|.+-.+....|+. ..-..|.+|+|+..+|-.+.+-.|..
T Consensus 13 ~d~~~sl~~qgild--~qF~qlq~lqD~~~p~fv-~ev~~~fF~~s~~~i~~~r~ald~~~ 70 (150)
T KOG4747|consen 13 SDYTKSLFDQGILD--SQFLQLQELQDDSSPDFV-EEVVGLFFEDSERLINNLRLALDCER 70 (150)
T ss_pred HHHHHHHHHHHhhH--HHHHHHHHHhcccCccHH-HHHHHHHHHHHHHHHHHHHHHHhhHh
Confidence 47888888888888 688899998876633443 35678999999999999999888874
No 37
>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=44.15 E-value=41 Score=22.59 Aligned_cols=51 Identities=18% Similarity=0.292 Sum_probs=34.9
Q ss_pred chhHHHHHHHHHHhHHHHHHHHHHHHhcCCcCHHHHHHHhHHhhhhhhhhChHHHHHHHHHHHHHH
Q 048267 37 PGFVKDVVTLYLRDSTKTLATIEDEMAKSPVDFMNLDKCFHQLKGSSASVGANKVLNEVNKAREHC 102 (109)
Q Consensus 37 ~~f~~~li~~F~~d~~~~l~~L~~al~~~~~D~~~l~~~aH~LKGSsasiGA~~l~~~c~~lE~~~ 102 (109)
|+|- ...|+..+.+.+..|..|...+ |.+.++.+. +-.-+..++.++....
T Consensus 13 p~Fd---~~~F~~~ak~~f~~i~~A~~~~--D~~~l~~~~----------t~~~~~~~~~~i~~~~ 63 (147)
T PF04280_consen 13 PGFD---PAAFLEEAKEAFLPIQEAWAKG--DLEALRPLL----------TEELYERLQAEIKARR 63 (147)
T ss_dssp TT-----HHHHHHHHHHTHHHHHHHHHHT---HHHHHHHB-----------HHHHHHHHHHHHHHH
T ss_pred CCCC---HHHHHHHHHHHHHHHHHHHHcC--CHHHHHHHh----------CHHHHHHHHHHHHHHH
Confidence 4554 5688999999999999999999 999988763 3334445555555543
No 38
>PLN02407 diphosphomevalonate decarboxylase
Probab=43.86 E-value=47 Score=26.82 Aligned_cols=32 Identities=16% Similarity=0.339 Sum_probs=26.7
Q ss_pred HHHHHHHh-HHHHHHHHHHHHhcCCcCHHHHHHHh
Q 048267 43 VVTLYLRD-STKTLATIEDEMAKSPVDFMNLDKCF 76 (109)
Q Consensus 43 li~~F~~d-~~~~l~~L~~al~~~~~D~~~l~~~a 76 (109)
++..-++. +++.+.+|+.|+..+ ||.++.+++
T Consensus 224 ~~~~w~~~~~~~~~~~~~~Ai~~~--Df~~~gei~ 256 (343)
T PLN02407 224 LLQHRAKEVVPKRILQMEEAIKNR--DFASFAKLT 256 (343)
T ss_pred hHHHHHHhhhHHHHHHHHHHHHhc--CHHHHHHHH
Confidence 45566676 899999999999999 999887764
No 39
>COG3923 PriC Primosomal replication protein N'' [DNA replication, recombination, and repair]
Probab=43.32 E-value=65 Score=23.58 Aligned_cols=36 Identities=14% Similarity=0.390 Sum_probs=29.6
Q ss_pred HHHHHHHHhHHHHHHHHHHHHhcCCcCHHHHHHHhHHh
Q 048267 42 DVVTLYLRDSTKTLATIEDEMAKSPVDFMNLDKCFHQL 79 (109)
Q Consensus 42 ~li~~F~~d~~~~l~~L~~al~~~~~D~~~l~~~aH~L 79 (109)
.+++-|++++.+.|+.|+.+.+++ -..++.-+|-.|
T Consensus 44 ~~ls~ylqEa~~tL~aL~~~~e~~--~l~q~afLAErL 79 (175)
T COG3923 44 QLLSFYLQEAGQTLTALKQAVEQD--RLPQVAFLAERL 79 (175)
T ss_pred chHHHHHHHHHHHHHHHHHHHhcc--chHHHHHHHHHH
Confidence 578899999999999999999998 566666665544
No 40
>PF00619 CARD: Caspase recruitment domain; InterPro: IPR001315 The caspase recruitment domain domain (CARD) is a homotypic protein interaction module composed of a bundle of six alpha-helices. CARD is related in sequence and structure to the death domain (DD, see IPR000488 from INTERPRO) and the death effector domain (DED, see IPR001875 from INTERPRO), which work in similar pathways and show similar interaction properties []. The CARD domain typically associates with other CARD-containing proteins, forming either dimers or trimers. CARD domains can be found in isolation, or in combination with other domains. Domains associated with CARD include: NACHT (IPR007111 from INTERPRO) (in Nal1 and Bir1), NB-ARC (IPR002182 from INTERPRO) (in Apaf-1), pyrin/dapin domains (IPR004020 from INTERPRO) (in Nal1), leucine-rich repeats () (in Nal1), WD repeats (IPR001680 from INTERPRO) (in Apaf1), Src homology domains (IPR001452 from INTERPRO), PDZ (IPR001478 from INTERPRO), RING, kinase and DD domains []. CARD-containing proteins are involved in apoptosis through their regulation of caspases that contain CARDs in their N-terminal pro-domains, including human caspases 1, 2, 9, 11 and 12 []. CARD-containing proteins are also involved in inflammation through their regulation of NF-kappaB []. The mechanisms by which CARDs activate caspases and NF-kappaB involve the assembly of multi-protein complexes, which can facilitate dimerisation or serve as scaffolds on which proteases and kinases are assembled and activated.; GO: 0005515 protein binding, 0042981 regulation of apoptosis, 0005622 intracellular; PDB: 2NSN_A 2NZ7_B 2DBD_A 4E9M_C 2B1W_A 3YGS_P 2KN6_A 3CRD_A 1DGN_A 3KAT_A ....
Probab=41.21 E-value=81 Score=19.06 Aligned_cols=54 Identities=4% Similarity=0.227 Sum_probs=35.2
Q ss_pred HHHhcccchhhhHHH-HHHHHhhhccCCchhHHHHHHHHHHhHHHHHHHHHHHHhcC
Q 048267 10 KMRQSFFDEEILDKY-FLQLEQLEDISNPGFVKDVVTLYLRDSTKTLATIEDEMAKS 65 (109)
Q Consensus 10 ~~~~~~~~~~~lD~~-~~~L~~L~~~~~~~f~~~li~~F~~d~~~~l~~L~~al~~~ 65 (109)
..+..++..++|.+. ...+.. ..+..+-+..+++....-++.....+-.++...
T Consensus 20 ~ild~L~~~~vlt~~e~e~I~~--~~t~~~k~~~LLd~l~~kg~~a~~~F~~~L~~~ 74 (85)
T PF00619_consen 20 DILDHLLSRGVLTEEEYEEIRS--EPTRQDKARKLLDILKRKGPEAFDIFCQALREN 74 (85)
T ss_dssp HHHHHHHHTTSSSHHHHHHHHT--SSSHHHHHHHHHHHHHHCCHHHHHHHHHHHHHH
T ss_pred HHHHHHHHCCCCCHHHHHHHHc--cCChHHHHHHHHHHHHHHCHHHHHHHHHHHHhh
Confidence 344445555666664 455554 233456788888888888888888888887764
No 41
>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=40.21 E-value=54 Score=19.62 Aligned_cols=35 Identities=26% Similarity=0.327 Sum_probs=24.0
Q ss_pred HHHHHHHhhhccCCchhHHHHHHHHHHhHHHHHHHH
Q 048267 23 KYFLQLEQLEDISNPGFVKDVVTLYLRDSTKTLATI 58 (109)
Q Consensus 23 ~~~~~L~~L~~~~~~~f~~~li~~F~~d~~~~l~~L 58 (109)
++|.+|+++-.. +|+.+..++..--..-|+.+..|
T Consensus 8 Pqf~~lR~~vq~-NP~lL~~lLqql~~~nP~l~q~I 42 (59)
T PF09280_consen 8 PQFQQLRQLVQQ-NPQLLPPLLQQLGQSNPQLLQLI 42 (59)
T ss_dssp HHHHHHHHHHHC--GGGHHHHHHHHHCCSHHHHHHH
T ss_pred hHHHHHHHHHHH-CHHHHHHHHHHHhccCHHHHHHH
Confidence 368888887544 78888888777776666665554
No 42
>PLN00061 photosystem II protein Psb27; Provisional
Probab=39.30 E-value=1.4e+02 Score=21.36 Aligned_cols=83 Identities=13% Similarity=0.224 Sum_probs=53.6
Q ss_pred cchhhhHHHHHHHHhhhccCCch-hHHHHHHHHHHhHHHHHHHHHHHHhcCCcCHHHHHHHhHH-----------hhhhh
Q 048267 16 FDEEILDKYFLQLEQLEDISNPG-FVKDVVTLYLRDSTKTLATIEDEMAKSPVDFMNLDKCFHQ-----------LKGSS 83 (109)
Q Consensus 16 ~~~~~lD~~~~~L~~L~~~~~~~-f~~~li~~F~~d~~~~l~~L~~al~~~~~D~~~l~~~aH~-----------LKGSs 83 (109)
.++|+++ .+..|.|++... -=..|-..|.+++...+..|+.+|+..+-|....++.+.. -+++.
T Consensus 28 ~~~~~~~----~~~~~fdp~e~tksg~~Lpg~Y~kdtr~VV~tLresl~l~p~D~~~~~~aa~~Ake~IndYisryR~~~ 103 (150)
T PLN00061 28 EGEGVVG----AIKSLFDPNEKTKSGKKLPKAYLKSAREVVKTLRESLKEDPKDEAKFRRTADAAKESIREYLGNWRGQK 103 (150)
T ss_pred ccccHHH----HHHHhcCccccccccccCchHHHHHHHHHHHHHHHHHccCCcchHHHHHHHHHHHHHHHHHHHHhcCCc
Confidence 3445554 667777653321 2235667899999999999999999754477665554433 34556
Q ss_pred hhhChHHHHHHHHHHHHHH
Q 048267 84 ASVGANKVLNEVNKAREHC 102 (109)
Q Consensus 84 asiGA~~l~~~c~~lE~~~ 102 (109)
..-|-.....+-..|..++
T Consensus 104 ~V~gl~SfttMqtALnsLA 122 (150)
T PLN00061 104 TVAEEESYVELEKAIRSLA 122 (150)
T ss_pred cccccchHHHHHHHHHHHH
Confidence 6666666666666665544
No 43
>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=38.45 E-value=1.1e+02 Score=20.00 Aligned_cols=39 Identities=13% Similarity=0.183 Sum_probs=29.9
Q ss_pred HHHHHHhHHHHHHHHHHHHhcCCcCHHHHHHHhHHhhhhhh
Q 048267 44 VTLYLRDSTKTLATIEDEMAKSPVDFMNLDKCFHQLKGSSA 84 (109)
Q Consensus 44 i~~F~~d~~~~l~~L~~al~~~~~D~~~l~~~aH~LKGSsa 84 (109)
...+.....+....|..+...+ |...+......+.++|.
T Consensus 77 F~~~~~~~~~aa~~L~~aa~~~--d~~~~~~a~~~v~~~C~ 115 (122)
T PF01322_consen 77 FKQLAQAFQKAAAALAAAAKSG--DLAAIKAAFGEVGKSCK 115 (122)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHT--SHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHhcC--CHHHHHHHHHHHHHHHH
Confidence 4455666667778888888888 99999988877777763
No 44
>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=37.88 E-value=1.3e+02 Score=20.32 Aligned_cols=49 Identities=8% Similarity=0.141 Sum_probs=33.3
Q ss_pred HHHHHhhhcc--CCchhHHHHHHHHHHhHHHHHHHHHHHHhcCCcCHHHHHHH
Q 048267 25 FLQLEQLEDI--SNPGFVKDVVTLYLRDSTKTLATIEDEMAKSPVDFMNLDKC 75 (109)
Q Consensus 25 ~~~L~~L~~~--~~~~f~~~li~~F~~d~~~~l~~L~~al~~~~~D~~~l~~~ 75 (109)
|......... .+.....++...|-.=....+..+..++..+ |+..+.++
T Consensus 98 ~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~~~~al~~~--d~~~~~~~ 148 (171)
T PF02203_consen 98 FDAFKALPHASPEERALADELEASFDAYLQQALDPLLAALRAG--DIAAFMQL 148 (171)
T ss_dssp HHHHHCS---GTGGHHHHHHHHHHHHH-HHHHHHHHHHHHHTT---HHHHHHS
T ss_pred HHHHHccCCCCcchHHHHHHHHHHHHHHHHHhHHHHHHHHHCC--CHHHHHHH
Confidence 5555555332 3457888888888877778889999999999 99877655
No 45
>cd07298 PX_RICS The phosphoinositide binding Phox Homology domain of PX-RICS. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions such as cell signaling, vesicular trafficking, protein sorting, and lipid modification, among others. RICS is a Rho GTPase-activating protein for cdc42 and Rac1. It is implicated in the regulation of postsynaptic signaling and neurite outgrowth. An N-terminal splicing variant of RICS containing additional PX and Src Homology 3 (SH3) domains, also called PX-RICS, is the main isoform expressed during neural development. PX-RICS is involved in neural functions including axon and dendrite extension, postnatal remodeling, and fine-tuning of neural circuits during early brain development. The PX domain is involved in targeting of proteins to PI-enriched membranes, and may also be involved in protein-protein interaction. The PX domain of PX-RICS specifically binds phosphatidylinositol 3-phosphate (PI3P), PI4P, and
Probab=37.25 E-value=35 Score=23.39 Aligned_cols=39 Identities=26% Similarity=0.358 Sum_probs=28.5
Q ss_pred HhcccchhhhHHHHHHHHhhhcc----CCchhHHHHHHHHHHh
Q 048267 12 RQSFFDEEILDKYFLQLEQLEDI----SNPGFVKDVVTLYLRD 50 (109)
Q Consensus 12 ~~~~~~~~~lD~~~~~L~~L~~~----~~~~f~~~li~~F~~d 50 (109)
+..+.+.=+-|..|++|.+|.+. .+|+++..++..|+.-
T Consensus 53 LD~~LHrCvyDRrfS~L~eLp~~~~l~~~~~~v~~~l~~YL~R 95 (115)
T cd07298 53 LDKHLHLCIYDRRFSQLPELPRSDSLKDSPESVTQMLMAYLSR 95 (115)
T ss_pred HHHHHHHHHHhhhhhccccCCCcccccccHHHHHHHHHHHHHH
Confidence 34456667788889999998652 2468888999988864
No 46
>PF13628 DUF4142: Domain of unknown function (DUF4142)
Probab=36.67 E-value=1.3e+02 Score=20.16 Aligned_cols=50 Identities=20% Similarity=0.246 Sum_probs=37.8
Q ss_pred HHHHHhhhccCCchhHHHHHHHHHHhHHHHHHHHHH-HHhcCCcCHHHHHHHh
Q 048267 25 FLQLEQLEDISNPGFVKDVVTLYLRDSTKTLATIED-EMAKSPVDFMNLDKCF 76 (109)
Q Consensus 25 ~~~L~~L~~~~~~~f~~~li~~F~~d~~~~l~~L~~-al~~~~~D~~~l~~~a 76 (109)
-..+..|....|++|=...++.-+..-.+.|..++. ....+ +-..++..+
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 445566665567899999999999999999999998 66665 556666554
No 47
>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=36.19 E-value=1.1e+02 Score=19.32 Aligned_cols=60 Identities=3% Similarity=0.101 Sum_probs=37.7
Q ss_pred HHhcccchhhhHHH-HHHHHhhhccCCchhHHHHHHHHHHhHHHHHHHHHHHHhcCCcCHHHHHH
Q 048267 11 MRQSFFDEEILDKY-FLQLEQLEDISNPGFVKDVVTLYLRDSTKTLATIEDEMAKSPVDFMNLDK 74 (109)
Q Consensus 11 ~~~~~~~~~~lD~~-~~~L~~L~~~~~~~f~~~li~~F~~d~~~~l~~L~~al~~~~~D~~~l~~ 74 (109)
.+..++..|+++.. .+.+..- ++..+-...+++.--.-+++.+.....|+... .+..+..
T Consensus 21 v~~~L~~~~Vlt~~~~e~I~~~--~tr~~q~~~LLd~L~~RG~~AF~~F~~aL~~~--~~~~LA~ 81 (84)
T cd08326 21 LWDHLLSRGVFTPDMIEEIQAA--GSRRDQARQLLIDLETRGKQAFPAFLSALRET--GQTDLAE 81 (84)
T ss_pred HHHHHHhcCCCCHHHHHHHHcC--CCHHHHHHHHHHHHHhcCHHHHHHHHHHHHhc--CchHHHH
Confidence 44445666777664 5555543 23456677777777777777777777777654 4544443
No 48
>PF07014 Hs1pro-1_C: Hs1pro-1 protein C-terminus; InterPro: IPR009743 This entry represents the C terminus (approximately 270 residues) of a number of plant Hs1pro-1 proteins, which are believed to confer nematode resistance [].
Probab=35.88 E-value=1.2e+02 Score=23.32 Aligned_cols=38 Identities=16% Similarity=0.249 Sum_probs=28.0
Q ss_pred hHHHHHHHHHHhHHHHHHHHHHHHhcCCcCHHHHHHHhHH
Q 048267 39 FVKDVVTLYLRDSTKTLATIEDEMAKSPVDFMNLDKCFHQ 78 (109)
Q Consensus 39 f~~~li~~F~~d~~~~l~~L~~al~~~~~D~~~l~~~aH~ 78 (109)
-+..+++.++.-+.++|..+...+..+ |+++..+-++.
T Consensus 54 t~hQIlEsWi~~a~~LL~ri~~~i~~~--~~ekAa~dc~~ 91 (261)
T PF07014_consen 54 TTHQILESWIHVARKLLERIEERIEAR--DFEKAASDCWI 91 (261)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHcc--cHHHHHhHHHH
Confidence 356777888888888888888888888 77765554443
No 49
>PRK08582 hypothetical protein; Provisional
Probab=35.76 E-value=58 Score=22.54 Aligned_cols=27 Identities=19% Similarity=0.338 Sum_probs=22.6
Q ss_pred hHHHHHHHHHHhHHHHHHHHHHHHhcC
Q 048267 39 FVKDVVTLYLRDSTKTLATIEDEMAKS 65 (109)
Q Consensus 39 f~~~li~~F~~d~~~~l~~L~~al~~~ 65 (109)
=+...+..|+.++++.|++|++-.+.+
T Consensus 104 ~fe~~l~~flk~s~~~~~~l~~~~~~~ 130 (139)
T PRK08582 104 DFEQKMSRFLKDSEDRLTSIKRNTESK 130 (139)
T ss_pred CHHHHHHHHHHHHHHHHHHHHhhcccC
Confidence 345899999999999999998776554
No 50
>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=35.10 E-value=64 Score=22.84 Aligned_cols=56 Identities=11% Similarity=0.107 Sum_probs=28.4
Q ss_pred HHHHHhhhccCCchhHHHHHHHHHHh----HHHHHHHHHHHHhcCCcCHHHHHHHhHHhhhhhhhh
Q 048267 25 FLQLEQLEDISNPGFVKDVVTLYLRD----STKTLATIEDEMAKSPVDFMNLDKCFHQLKGSSASV 86 (109)
Q Consensus 25 ~~~L~~L~~~~~~~f~~~li~~F~~d----~~~~l~~L~~al~~~~~D~~~l~~~aH~LKGSsasi 86 (109)
+.+|+.|-+..+.-++ +.|+.- ..+.+.-|...+-.. |-..+++++-.|+++=.++
T Consensus 52 ~~eLk~lI~kk~W~~v----rn~irgp~g~Lr~dl~~l~~sl~p~--dqk~a~~L~~~Lf~~L~~L 111 (142)
T TIGR03042 52 LPELASLVAKEDWVFT----RNLIHGPMGEVRREMTYLNQSLLPK--DQKEALALAKELKDDLEKL 111 (142)
T ss_pred hHHHHHHHhhcchHHH----HHHHhccHHHHHHHHHHHHHccCHH--hHHHHHHHHHHHHHHHHHH
Confidence 4455555444343332 455543 233333344444334 6777788877777665333
No 51
>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=35.06 E-value=2.3e+02 Score=22.45 Aligned_cols=56 Identities=16% Similarity=0.169 Sum_probs=37.3
Q ss_pred HHHHHHhHHHHHHHHHHHHhcCCcCHHHHHHHh---HHhhhhh---h--hhChHHHHHHHHHHHHH
Q 048267 44 VTLYLRDSTKTLATIEDEMAKSPVDFMNLDKCF---HQLKGSS---A--SVGANKVLNEVNKAREH 101 (109)
Q Consensus 44 i~~F~~d~~~~l~~L~~al~~~~~D~~~l~~~a---H~LKGSs---a--siGA~~l~~~c~~lE~~ 101 (109)
+..|++...+...++..++..+ |+..+.++. |.++-+= + .|--..+-.++...+..
T Consensus 247 ~~~~l~~~~~i~~~~~~al~~~--d~~~lg~~~~~~~~lL~~l~~~~~~~vs~~~l~~li~~a~~~ 310 (358)
T TIGR01220 247 YQRFLETSTDCVESAITAFETG--DITSLQKEIRRNRQELARLDDEVGVGIETEKLKALCDAAEAY 310 (358)
T ss_pred HHHHHHHHHHHHHHHHHHHHhC--CHHHHHHHHHHHHHHHHHhhcccCCCcCCHHHHHHHHHHhhc
Confidence 4567788888888999999999 888776654 4454332 1 23356666666555543
No 52
>PRK08818 prephenate dehydrogenase; Provisional
Probab=35.03 E-value=1.7e+02 Score=23.71 Aligned_cols=42 Identities=21% Similarity=0.287 Sum_probs=30.3
Q ss_pred CchhHHHHHHHHHHhHHHHHHHHHHHHhcCCcCHHHHHHHhHHhhhhhh
Q 048267 36 NPGFVKDVVTLYLRDSTKTLATIEDEMAKSPVDFMNLDKCFHQLKGSSA 84 (109)
Q Consensus 36 ~~~f~~~li~~F~~d~~~~l~~L~~al~~~~~D~~~l~~~aH~LKGSsa 84 (109)
|| .+.+.++.|.+ .+.++++++.++ |.+.+.+..|.++-+..
T Consensus 226 N~-~i~~~l~~~~~----~L~~l~~~i~~~--D~~~~~~~~~~f~~a~~ 267 (370)
T PRK08818 226 NP-YVGEMLDRLLA----QLQELRALVAQG--DDAARARFRAQFLHANA 267 (370)
T ss_pred CH-HHHHHHHHHHH----HHHHHHHHHHcC--CHHHHHHHHHHHHHHHh
Confidence 44 55566666554 566788888999 99999988777766544
No 53
>PF07840 FadR_C: FadR C-terminal domain; InterPro: IPR008920 Bacteria regulate membrane fluidity by manipulating the relative levels of saturated and unsaturated fatty acids within the phospholipids of their membrane bilayers. In Escherichia coli, the transcription factor, FadR, functions as a switch that co-ordinately regulates the machinery required for fatty acid beta-oxidation and the expression of a key enzyme in fatty acid biosynthesis. This single repressor controls the transcription of the whole fad regulon []. Binding of fadR is specifically inhibited by long chain fatty acyl-CoA compounds. The crystal structure of FadR reveals a two domain dimeric molecule where the N-terminal winged-helix domain binds DNA (IPR000524 from INTERPRO), and the C-terminal domain binds acyl-CoA []. The binding of acyl-CoA to the C-terminal domain results in a conformational change that affects the DNA binding affinity of the N-terminal domain []. FadR is a member of the GntR family of bacterial transcription regulators. The DNA-binding domain is well conserved for this family, whereas the C-terminal effector-binding domain (IPR011711 from INTERPRO) is more variable, and is consequently used to define the GntR subfamilies []. The FadR group is the largest subgroup, and is characterised by an all-helical C-terminal domain composed of 6 to 7 alpha helices []. This entry represents the C-terminal domain of FadR.; GO: 0000062 fatty-acyl-CoA binding, 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0019217 regulation of fatty acid metabolic process; PDB: 1HW1_B 1H9T_A 1HW2_A 1H9G_A 1E2X_A.
Probab=34.64 E-value=64 Score=23.36 Aligned_cols=40 Identities=20% Similarity=0.270 Sum_probs=31.7
Q ss_pred HHHHHhhhccCCchhHHHHHHHHHHhHHHHHHHHHHHHhc
Q 048267 25 FLQLEQLEDISNPGFVKDVVTLYLRDSTKTLATIEDEMAK 64 (109)
Q Consensus 25 ~~~L~~L~~~~~~~f~~~li~~F~~d~~~~l~~L~~al~~ 64 (109)
-.+|..+-..++.+-+..+++.|-.++.+.+..++..+.+
T Consensus 122 Y~~L~~~~~~~~~~~v~~~vr~yg~~Sg~iW~~~~~~lp~ 161 (164)
T PF07840_consen 122 YRELLEACEKGDYDQVPDVVRQYGIESGEIWQSMRDNLPE 161 (164)
T ss_dssp HHHHHHHHHCT-CCGHHHHHHHHHHHHHHHHHHHHTT---
T ss_pred HHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHhcch
Confidence 4578888778788999999999999999999999877654
No 54
>PF04012 PspA_IM30: PspA/IM30 family; InterPro: IPR007157 This family includes PspA a protein that suppresses sigma54-dependent transcription. The PspA protein, a negative regulator of the Escherichia coli phage shock psp operon, is produced when virulence factors are exported through secretins in many Gram-negative pathogenic bacteria and its homologue in plants, VIPP1, plays a critical role in thylakoid biogenesis, essential for photosynthesis. Activation of transcription by the enhancer-dependent bacterial sigma54-containing RNA polymerase occurs through ATP hydrolysis-driven protein conformational changes enabled by activator proteins that belong to the large AAA(+) mechanochemical protein family. It has been shown that PspA directly and specifically acts upon and binds to the AAA(+) domain of the PspF transcription activator [].
Probab=34.53 E-value=1.1e+02 Score=22.20 Aligned_cols=48 Identities=21% Similarity=0.422 Sum_probs=31.1
Q ss_pred HHHHHHHHHhcccchhhhHHHHHHHHhhhccCCchhHHHHHHHHHHhHHHHHHHHHHHHhcC
Q 048267 4 LRQQIAKMRQSFFDEEILDKYFLQLEQLEDISNPGFVKDVVTLYLRDSTKTLATIEDEMAKS 65 (109)
Q Consensus 4 ~~~~~~~~~~~~~~~~~lD~~~~~L~~L~~~~~~~f~~~li~~F~~d~~~~l~~L~~al~~~ 65 (109)
||.++.+.+++-++ .+|| .+. +|+ .+++.|+.+....+..++.++..-
T Consensus 2 lf~Rl~~~~~a~~~-~~ld-------~~E---DP~---~~l~q~ird~e~~l~~a~~~~a~~ 49 (221)
T PF04012_consen 2 LFKRLKTLVKANIN-ELLD-------KAE---DPE---KMLEQAIRDMEEQLRKARQALARV 49 (221)
T ss_pred HHHHHHHHHHHHHH-HHHH-------hhc---CHH---HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34555555555444 2232 333 454 788999999999998888888753
No 55
>PF14493 HTH_40: Helix-turn-helix domain
Probab=34.46 E-value=81 Score=19.80 Aligned_cols=37 Identities=8% Similarity=0.199 Sum_probs=26.1
Q ss_pred chhHHHHHHHHHHhHHHHHHHHHHHHhcCCcCHHHHHH
Q 048267 37 PGFVKDVVTLYLRDSTKTLATIEDEMAKSPVDFMNLDK 74 (109)
Q Consensus 37 ~~f~~~li~~F~~d~~~~l~~L~~al~~~~~D~~~l~~ 74 (109)
++....+...|-......+..+..++... +||..+|-
T Consensus 52 ~e~~~~I~~~~~~~~~~~lk~i~e~l~~~-~sy~~iRl 88 (91)
T PF14493_consen 52 EEEIKQIEDAIEKLGSEKLKPIKEALPGD-YSYFEIRL 88 (91)
T ss_pred HHHHHHHHHHHHHcCcccHHHHHHHCCCC-CCHHHHHH
Confidence 35566666777666667888888888765 58888764
No 56
>TIGR01240 mevDPdecarb diphosphomevalonate decarboxylase. Alternate names: mevalonate diphosphate decarboxylase; pyrophosphomevalonate decarboxylase
Probab=34.46 E-value=81 Score=24.70 Aligned_cols=31 Identities=10% Similarity=0.207 Sum_probs=25.5
Q ss_pred HHHHHHhHHHHHHHHHHHHhcCCcCHHHHHHHh
Q 048267 44 VTLYLRDSTKTLATIEDEMAKSPVDFMNLDKCF 76 (109)
Q Consensus 44 i~~F~~d~~~~l~~L~~al~~~~~D~~~l~~~a 76 (109)
+...++++++.+..|..|+.++ ||+.+.+.+
T Consensus 202 ~~~~v~~~~~~l~~~~~ai~~~--D~~~~g~~~ 232 (305)
T TIGR01240 202 FKEWIEHVVPDFEVXRKAIKTK--DFATFGKET 232 (305)
T ss_pred HHHHHHHHHHHHHHHHHHHHhc--cHHHHHHHH
Confidence 4556677887899999999999 999887764
No 57
>PF03981 Ubiq_cyt_C_chap: Ubiquinol-cytochrome C chaperone ; InterPro: IPR021150 Saccharomyces cerevisiae ubiquinol-cytochrome C chaperone is required for assembly of coenzyme QF-2-cytochrome C reductase. It appears to be found in a number of different organisms including Homo sapiens, Caenorhabditis elegans and Rhizobium meliloti. This entry also contains bacterial proteins belonging to the UPF0174 family.
Probab=34.22 E-value=1.3e+02 Score=20.05 Aligned_cols=48 Identities=13% Similarity=0.088 Sum_probs=32.2
Q ss_pred CchhHHHHHHHHHHhHHHHHHHHHHHHhcCCcCHHHHHHHhHHhhhhhhhh
Q 048267 36 NPGFVKDVVTLYLRDSTKTLATIEDEMAKSPVDFMNLDKCFHQLKGSSASV 86 (109)
Q Consensus 36 ~~~f~~~li~~F~~d~~~~l~~L~~al~~~~~D~~~l~~~aH~LKGSsasi 86 (109)
+..+-..|++.|.+|+...+.++..- +.. --..++.+...+-|....+
T Consensus 34 ~~~~~q~l~~~~~~d~~~~l~~~gv~-d~~--~~k~~k~l~~~~~g~~~ay 81 (141)
T PF03981_consen 34 GKELEQALFDKFFEDMDERLREMGVG-DLS--VGKRMKKLQEQFYGRLLAY 81 (141)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhcCc-chh--hhHHHHHHHHHHHHHHHHH
Confidence 56788889999999999988877531 111 2345666666666666544
No 58
>KOG1510 consensus RNA polymerase II holoenzyme and mediator subcomplex, subunit SURB7/SRB7 [Transcription]
Probab=33.71 E-value=1.7e+02 Score=20.67 Aligned_cols=56 Identities=14% Similarity=0.205 Sum_probs=38.4
Q ss_pred HHHHHHHhc-ccchhhhHHHHHHHHhhhccCCchhHHHHHHHHHHhHHHHHHHHHHHHh
Q 048267 6 QQIAKMRQS-FFDEEILDKYFLQLEQLEDISNPGFVKDVVTLYLRDSTKTLATIEDEMA 63 (109)
Q Consensus 6 ~~~~~~~~~-~~~~~~lD~~~~~L~~L~~~~~~~f~~~li~~F~~d~~~~l~~L~~al~ 63 (109)
.+++.++.| +-.+|-...|+..+.+|+.+ +.+...++.. -+..+++++..+...++
T Consensus 70 kqId~LIdsLP~~~~~~e~Ql~~i~kLq~e-n~e~~~el~~-~v~~~e~Ll~~vq~~le 126 (139)
T KOG1510|consen 70 KQIDTLIDSLPGEEGSAEAQLEKIKKLQEE-NEEVALELEE-LVSKGEKLLEQVQSLLE 126 (139)
T ss_pred HHHHHHHHhCCCcccCHHHHHHHHHHHHHH-HHHHHHHHHH-HHHHHHHHHHHHHHHHH
Confidence 467788888 55556677788888888765 4455555544 35667778877777765
No 59
>PRK05014 hscB co-chaperone HscB; Provisional
Probab=33.20 E-value=1.8e+02 Score=20.74 Aligned_cols=39 Identities=8% Similarity=0.160 Sum_probs=22.2
Q ss_pred HHHHHHHHHHhHHHHHHHHHHHHhcCCcCHHHHHHHhHHhh
Q 048267 40 VKDVVTLYLRDSTKTLATIEDEMAKSPVDFMNLDKCFHQLK 80 (109)
Q Consensus 40 ~~~li~~F~~d~~~~l~~L~~al~~~~~D~~~l~~~aH~LK 80 (109)
+.++....-......+..|..+++.+ ||+......-.||
T Consensus 115 l~~l~~~~~~~~~~~~~~l~~~~~~~--d~~~A~~~~~~Lk 153 (171)
T PRK05014 115 LESFIKRVKKMFKTRLQQMVEQLDNE--AWDAAADTVRKLK 153 (171)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhC--CHHHHHHHHHHHH
Confidence 33444444444444555566677666 7776666665555
No 60
>TIGR02302 aProt_lowcomp conserved hypothetical protein TIGR02302. Members of this family are long (~850 residue) bacterial proteins from the alpha Proteobacteria. Each has 2-3 predicted transmembrane helices near the N-terminus and a long C-terminal region that includes stretches of Gln/Gly-rich low complexity sequence, predicted by TMHMM to be outside the membrane. In Bradyrhizobium japonicum, two tandem reading frames are together homologous the single members found in other species; the cutoffs scores are set low enough that the longer scores above the trusted cutoff and the shorter above the noise cutoff for this model.
Probab=32.59 E-value=1.1e+02 Score=27.80 Aligned_cols=66 Identities=8% Similarity=0.203 Sum_probs=39.9
Q ss_pred chhHHHHHHHHHHhHHHHHHHHHHHHhcCCcCHHHHHHHhHHhhhhhhhhChHHHHHHHHHHHHHHhccCcC
Q 048267 37 PGFVKDVVTLYLRDSTKTLATIEDEMAKSPVDFMNLDKCFHQLKGSSASVGANKVLNEVNKAREHCKEGNLE 108 (109)
Q Consensus 37 ~~f~~~li~~F~~d~~~~l~~L~~al~~~~~D~~~l~~~aH~LKGSsasiGA~~l~~~c~~lE~~~~~~~~~ 108 (109)
++=+.+|+..+-+=....+.+|.+...+++ +-.. -..-+.+.+++-..|..+..+||++++.|+++
T Consensus 522 deEI~~Lm~eLR~Am~~ym~~LAeq~~~~~-~~~~-----~~~~~~~~~l~~~dLq~Mmd~ieela~~G~~~ 587 (851)
T TIGR02302 522 DEEIKQLTDKLRAAMQTYMRQLAQQLRNNP-QQLA-----RPLDPNTKVLRQQDLQNMMDQIENLARSGDRD 587 (851)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhhCc-cccc-----ccCCccccccCHHHHHHHHHHHHHHHHcCCHH
Confidence 445555555555555555555554443321 1000 00122357799999999999999999999875
No 61
>KOG4552 consensus Vitamin-D-receptor interacting protein complex component [Transcription]
Probab=31.92 E-value=2.4e+02 Score=21.70 Aligned_cols=41 Identities=20% Similarity=0.261 Sum_probs=29.4
Q ss_pred HHHHHHHHhHHHHHHHHHHHHhcCCcCHHHHHHHhHHhhhhh
Q 048267 42 DVVTLYLRDSTKTLATIEDEMAKSPVDFMNLDKCFHQLKGSS 83 (109)
Q Consensus 42 ~li~~F~~d~~~~l~~L~~al~~~~~D~~~l~~~aH~LKGSs 83 (109)
-++.+-+-.+.+.|..|.+|-.. +|.-+.+-++||.+-.+.
T Consensus 102 ~iLtta~fqA~qKLksi~~A~kr-pvsSEelIKyAHrIS~~N 142 (272)
T KOG4552|consen 102 VILTTACFQANQKLKSIKEAEKR-PVSSEELIKYAHRISKHN 142 (272)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcC-CCCHHHHHHHHHHhhhcc
Confidence 34555666677777778777544 678999999999985543
No 62
>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=31.29 E-value=2.2e+02 Score=21.23 Aligned_cols=26 Identities=19% Similarity=0.316 Sum_probs=19.6
Q ss_pred HHhHHHHHHHHHHHHhcCCcCHHHHHHH
Q 048267 48 LRDSTKTLATIEDEMAKSPVDFMNLDKC 75 (109)
Q Consensus 48 ~~d~~~~l~~L~~al~~~~~D~~~l~~~ 75 (109)
++.-.+.|.+++.+++++ |.+.+.+.
T Consensus 230 l~~~~~~L~~l~~~l~~~--d~~~l~~~ 255 (258)
T PF02153_consen 230 LDEFIKELNELREALEAG--DEEELEEL 255 (258)
T ss_dssp HHHHHHHHHHHHHHHHTT--SHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHcC--CHHHHHHH
Confidence 444456677888899999 99988765
No 63
>PHA02666 hypothetical protein; Provisional
Probab=29.71 E-value=78 Score=24.37 Aligned_cols=52 Identities=13% Similarity=0.305 Sum_probs=36.4
Q ss_pred CchhHHHHHHHHHHhHHHHHHHHHHHHhcCCcCHHHHHHHhHHhhh----hhhhhChHHH
Q 048267 36 NPGFVKDVVTLYLRDSTKTLATIEDEMAKSPVDFMNLDKCFHQLKG----SSASVGANKV 91 (109)
Q Consensus 36 ~~~f~~~li~~F~~d~~~~l~~L~~al~~~~~D~~~l~~~aH~LKG----SsasiGA~~l 91 (109)
.|++. .=|-+.+.|.++.|+.|++.++.. +.-.++..|.-|. -++|||-..|
T Consensus 203 kpNLQ-~DIcTLC~DIEtQLSALEKSLESE---lnFYrrYIqDTKsLLatRAANIgsKAL 258 (287)
T PHA02666 203 KPNLQ-SDICTLCHDIETQLSALEKSLESE---LNFYRRYIQDTKSLLATRAANIGSKAL 258 (287)
T ss_pred CCchh-hHHHHhhhhHHHHHHHHHHHHHHH---HHHHHHHHHhHHHHHHHHhhcccccee
Confidence 34544 556778888999999999998874 6666777777664 4666665443
No 64
>PF04400 DUF539: Protein of unknown function (DUF539); InterPro: IPR007495 This is a family of putative periplasmic proteins.
Probab=29.32 E-value=5.8 Score=22.86 Aligned_cols=19 Identities=32% Similarity=0.492 Sum_probs=14.6
Q ss_pred HhhhhhhhhChHHHHHHHH
Q 048267 78 QLKGSSASVGANKVLNEVN 96 (109)
Q Consensus 78 ~LKGSsasiGA~~l~~~c~ 96 (109)
.||||++-||+..+-..|.
T Consensus 7 ~I~GSCGGl~~lGi~~~C~ 25 (45)
T PF04400_consen 7 PIKGSCGGLGALGIDKECD 25 (45)
T ss_pred cccccchhhhhcCCCccCC
Confidence 5799999999977755543
No 65
>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=29.19 E-value=2.9e+02 Score=21.77 Aligned_cols=69 Identities=14% Similarity=0.158 Sum_probs=45.1
Q ss_pred hHHHHHHHHhhhccCCchhHHHHHHHHHH-hHHHHHHHHHHHHhcCCcCHHHHHHHhHHhhhhhhhhChHHHHHHHHH
Q 048267 21 LDKYFLQLEQLEDISNPGFVKDVVTLYLR-DSTKTLATIEDEMAKSPVDFMNLDKCFHQLKGSSASVGANKVLNEVNK 97 (109)
Q Consensus 21 lD~~~~~L~~L~~~~~~~f~~~li~~F~~-d~~~~l~~L~~al~~~~~D~~~l~~~aH~LKGSsasiGA~~l~~~c~~ 97 (109)
|+..+..|-.+. .......|...|.= |-.=.+-.|+.....+ ||+.+...+-+=| +-||-..+.+.|..
T Consensus 180 l~~Ti~~li~~~---~~k~A~kl~k~Fkv~dkrfw~lki~aLa~~~--~w~eL~~fa~skK---sPIGyepFv~~~~~ 249 (319)
T PF04840_consen 180 LNDTIRKLIEMG---QEKQAEKLKKEFKVPDKRFWWLKIKALAENK--DWDELEKFAKSKK---SPIGYEPFVEACLK 249 (319)
T ss_pred HHHHHHHHHHCC---CHHHHHHHHHHcCCcHHHHHHHHHHHHHhcC--CHHHHHHHHhCCC---CCCChHHHHHHHHH
Confidence 444444444443 33556677777732 2222344566677788 9999999987644 46999999999975
No 66
>PF11563 Protoglobin: Protoglobin; PDB: 2VEE_G 3QZZ_A 3R0G_A 3QZX_A 2VEB_A 1OR6_A 1OR4_B 2W31_B.
Probab=27.75 E-value=1.9e+02 Score=19.31 Aligned_cols=55 Identities=13% Similarity=0.187 Sum_probs=34.2
Q ss_pred hHHHHHHHHHHhcccchhhhHHHHHHHHhhhc-----cCCchhHHHHHHHHHHhHHHHHH
Q 048267 2 EALRQQIAKMRQSFFDEEILDKYFLQLEQLED-----ISNPGFVKDVVTLYLRDSTKTLA 56 (109)
Q Consensus 2 ~~~~~~~~~~~~~~~~~~~lD~~~~~L~~L~~-----~~~~~f~~~li~~F~~d~~~~l~ 56 (109)
+.|+..+..||..+++.++-+..+....++.. +-.|.++...+..|.+...+.|.
T Consensus 61 ~~lk~~q~~~~~~l~s~~~d~~y~~~~~~iG~~H~~igl~~~~~~~~~~~~~~~l~~~l~ 120 (158)
T PF11563_consen 61 ERLKATQRRHWRELFSGDFDEEYVERRRRIGQVHARIGLPPRWYIGAYSFLREFLLEALA 120 (158)
T ss_dssp HHHHHHHHHHHHHCTSS-CSHHHHHHHHHHHHHHHHCT--HHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHhCCCchHHHHHHHHHHHHHHhHcCCCHHHHHHHHHHHHHHHHHHHH
Confidence 56888899999999886633334666666543 34466776666666665555543
No 67
>cd07299 PX_TCGAP The phosphoinositide binding Phox Homology domain of Tc10/Cdc42 GTPase-activating protein. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions such as cell signaling, vesicular trafficking, protein sorting, and lipid modification, among others. TCGAP (Tc10/Cdc42 GTPase-activating protein) contains N-terminal PX and Src Homology 3 (SH3) domains, a central Rho GAP domain, and C-terminal proline-rich regions. It is widely expressed in the brain where it is involved in regulating the outgrowth of axons and dendrites and is regulated by the protein tyrosine kinase Fyn. It interacts with cdc42 and TC10beta through its GAP domain and with phosphatidylinositol-(4,5)-bisphosphate [PI(4,5)P2] through its PX domain. It is translocated to the plasma membrane in adipocytes in response to insulin and may be involved in the regulation of insulin-stimulated glucose transport. TCGAP has also been named sorting nexins 26 (SNX26). SNXs
Probab=27.61 E-value=79 Score=21.59 Aligned_cols=38 Identities=21% Similarity=0.380 Sum_probs=27.3
Q ss_pred hcccchhhhHHHHHHHHhhhcc----CCchhHHHHHHHHHHh
Q 048267 13 QSFFDEEILDKYFLQLEQLEDI----SNPGFVKDVVTLYLRD 50 (109)
Q Consensus 13 ~~~~~~~~lD~~~~~L~~L~~~----~~~~f~~~li~~F~~d 50 (109)
..+.+.=+-|..|++|.+|.+. ..++.+..++..|+.-
T Consensus 52 D~~LHrCiyDRr~S~L~eL~~~~~l~~~~~~~~~~l~~YL~R 93 (113)
T cd07299 52 DAHLHRCIFDRRFSQLLELPPLCEIGDRLQILTPLLSEYLNR 93 (113)
T ss_pred HHHHHHHHHhhhhhhhhccCccccccchHHHHHHHHHHHHHH
Confidence 3455667788889999998652 2346788899998864
No 68
>COG4395 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=26.94 E-value=1e+02 Score=24.29 Aligned_cols=30 Identities=13% Similarity=0.238 Sum_probs=27.1
Q ss_pred HHHHHhHHHHHHHHHHHHhcCCcCHHHHHHHh
Q 048267 45 TLYLRDSTKTLATIEDEMAKSPVDFMNLDKCF 76 (109)
Q Consensus 45 ~~F~~d~~~~l~~L~~al~~~~~D~~~l~~~a 76 (109)
..|++.++..+..|..+...+ |+++++.+.
T Consensus 150 ~~fl~~a~~a~~~Iq~a~~~~--D~~tL~~L~ 179 (281)
T COG4395 150 ARFLNGARAAYEMIQQAYGAG--DRKTLRELL 179 (281)
T ss_pred hHHHHHHHHHHHHHHHHhhhc--cHHHHHHhc
Confidence 478899999999999999999 999999873
No 69
>PF09130 DUF1932: Domain of unknown function (DUF1932); InterPro: IPR015814 This domain has been found in a number of eukaryotic and prokaryotic proteins, some of which are predicted to be 6-phosphogluconate dehydrogenase, NAD-binding proteins.; PDB: 3QSG_A 1I36_A 4EZB_A.
Probab=26.71 E-value=1.5e+02 Score=17.88 Aligned_cols=47 Identities=11% Similarity=0.045 Sum_probs=34.9
Q ss_pred hhhhHHHHHHHHhhhccCCchhHHHHHHHHHHhHHHHHHHHHHHHhc
Q 048267 18 EEILDKYFLQLEQLEDISNPGFVKDVVTLYLRDSTKTLATIEDEMAK 64 (109)
Q Consensus 18 ~~~lD~~~~~L~~L~~~~~~~f~~~li~~F~~d~~~~l~~L~~al~~ 64 (109)
-|+.|+-+..|.+..+....+++..+|..-...+.+...+|+...+.
T Consensus 4 ~Gv~~~ll~sl~~s~p~~~~~~~~~~v~~~~~hA~Rr~~EM~Eia~t 50 (73)
T PF09130_consen 4 YGVEDELLASLAESFPGLDWALAERLVPRMAPHAYRRAAEMEEIADT 50 (73)
T ss_dssp TT-HHHHHHHHHHHSCCSCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred cccHHHHHHHHHHHCCcchHHHHHHHcccchhhHHHHHHHHHHHHHH
Confidence 47777778888887654333788888888888888888888877654
No 70
>PRK07417 arogenate dehydrogenase; Reviewed
Probab=26.25 E-value=1.5e+02 Score=22.27 Aligned_cols=25 Identities=12% Similarity=0.328 Sum_probs=17.1
Q ss_pred HhHHHHHHHHHHHHhcCCcCHHHHHHH
Q 048267 49 RDSTKTLATIEDEMAKSPVDFMNLDKC 75 (109)
Q Consensus 49 ~d~~~~l~~L~~al~~~~~D~~~l~~~ 75 (109)
++..+.|.+++.+++.+ |.+.+.+.
T Consensus 242 ~~~~~~l~~~~~~l~~~--d~~~l~~~ 266 (279)
T PRK07417 242 ASYRQSLDQLEELIEQE--NWSALEQK 266 (279)
T ss_pred HHHHHHHHHHHHHHHcC--CHHHHHHH
Confidence 33445577788888888 87776654
No 71
>PF00726 IL10: Interleukin 10 This family is a subset of the SCOP family; InterPro: IPR020443 Interleukin-10 (IL-10) is a protein that inhibits the synthesis of a number of cytokines, including IFN-gamma, IL-2, IL-3, TNF and GM-CSF produced by activated macrophages and by helper T cells. Structurally, IL-10 is a protein of about 160 amino acids that contains four conserved cysteines involved in disulphide bonds []. IL-10 is highly similar to the Epstein-Barr virus (strain GD1) (HHV-4) (Human herpesvirus 4) BCRF1 protein which inhibits the synthesis of gamma-interferon and to Equid herpesvirus 2 (Equine herpesvirus 2) protein E7. It is also similar, but to a lesser degree, with human protein mda-7 [], a protein which has antiproliferative properties in human melanoma cells. Mda-7 only contains two of the four cysteines of IL-10.; PDB: 1VLK_A 1Y6N_L 1Y6M_L 2ILK_A 1LK3_A 2H24_A 1J7V_L 1ILK_A 1Y6K_L 1INR_A ....
Probab=25.79 E-value=1.7e+02 Score=21.19 Aligned_cols=47 Identities=21% Similarity=0.323 Sum_probs=30.8
Q ss_pred HHHHHHhc--ccchhhhHHHHHHHHhhhccCCchhHHHHHHHHHHhHHHHH
Q 048267 7 QIAKMRQS--FFDEEILDKYFLQLEQLEDISNPGFVKDVVTLYLRDSTKTL 55 (109)
Q Consensus 7 ~~~~~~~~--~~~~~~lD~~~~~L~~L~~~~~~~f~~~li~~F~~d~~~~l 55 (109)
++.+++++ .++.-+++.. -|+.+.+..+.-++.+|++-|++.+=+.-
T Consensus 46 ~Ik~~~q~~D~~~~iLl~~~--ll~~~k~~~~C~~~~~lL~FYLd~Vfp~~ 94 (170)
T PF00726_consen 46 EIKDFFQAKDDIDNILLDKS--LLQDFKGPDGCCFLSELLRFYLDRVFPNA 94 (170)
T ss_dssp HHHHHHHCCSSSTS-SSTHH--HHHHHHSTTHHHHHHHHHHHHHHTHHHHH
T ss_pred HHHHHhhccCchhhhhccHH--HHHhcCCCCccHHHHHHHHHHHHHHcccc
Confidence 45556655 2232356655 35667777788999999999998775443
No 72
>PF03858 Crust_neuro_H: Crustacean neurohormone H; InterPro: IPR005558 Arthropod express a family of neuropeptides [] which so far consist of the following types of neurohormones: Crustacean hyperglycemic hormone (CHH). CHH is primarily involved in blood sugar regulation, but also plays a role in the control of molting and reproduction. Molt-inhibiting hormone (MIH). MIH inhibits Y-organs where molting hormone (ecdysteroid) is secreted. A molting cycle is initiated when MIH secretion diminishes or stops. Gonad-inhibiting hormone (GIH), also known as vitellogenesis-inhibiting hormone (VIH) because of its role in inhibiting vitellogenesis in female animals. Mandibular organ-inhibiting hormone (MOIH). MOIH represses the synthesis of methyl farnesoate, the precursor of insect juvenile hormone III in the mandibular organ. Ion transport peptide (ITP) from locust. ITP stimulates salt and water reabsorption and inhibits acid secretion in the ileum of the locust. Caenorhabditis elegans hypothetical protein ZC168.2. These neurohormones are peptides of 70 to 80 residues which are processed from larger size precursors. They contain six conserved cysteines that are involved in disulphide bonds, as shown in the following schematic representation. Crustacean neurohormone H proteins are referred to as precursor-related peptides as they are typically co-transcribed and translated with the CHH neurohormone (IPR001166 from INTERPRO). However, in some species this neuropeptide is synthesized as a separate protein. Furthermore, neurohormone H can undergo proteolysis to give rise to 5 different neuropeptides [].
Probab=25.41 E-value=59 Score=18.31 Aligned_cols=23 Identities=22% Similarity=0.358 Sum_probs=18.7
Q ss_pred CHHHHHHHhHHhhhhhhhhChHH
Q 048267 68 DFMNLDKCFHQLKGSSASVGANK 90 (109)
Q Consensus 68 D~~~l~~~aH~LKGSsasiGA~~ 90 (109)
-|-++.++.-+|||++-+.++..
T Consensus 5 G~GRMerLLaSlrg~~~s~~plg 27 (41)
T PF03858_consen 5 GFGRMERLLASLRGSADSSTPLG 27 (41)
T ss_pred chhhHHHHHHHHhccCCCCcchh
Confidence 47789999999999988776643
No 73
>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=25.41 E-value=1.9e+02 Score=18.44 Aligned_cols=83 Identities=16% Similarity=0.198 Sum_probs=51.6
Q ss_pred HHHHHHHHHHhcccchhhhHHH-HHHHHhhhccCCchhHHHHHHHHHHhHHHHHHHHHHHHhcCCcCHHHHHHHhHHhhh
Q 048267 3 ALRQQIAKMRQSFFDEEILDKY-FLQLEQLEDISNPGFVKDVVTLYLRDSTKTLATIEDEMAKSPVDFMNLDKCFHQLKG 81 (109)
Q Consensus 3 ~~~~~~~~~~~~~~~~~~lD~~-~~~L~~L~~~~~~~f~~~li~~F~~d~~~~l~~L~~al~~~~~D~~~l~~~aH~LKG 81 (109)
.|+.=+..++..+++.+--.+. ---++++.++ + +.+..++..++.-..+.+..|-..+...++|-..+...+|++=|
T Consensus 4 ~L~~~i~~~~~~l~~~~~~~~~~~l~~RE~~~P-t-~~~~~i~~~~~~P~~~~l~~ll~~~~g~~~~~~~~~~~~~si~g 81 (125)
T PF09209_consen 4 RLRAFIRALLRRLLSDPESRWWLRLIAREMLNP-T-PAFDRIVEELIRPKHEALARLLAEILGEPADDPEVRLCAFSIVG 81 (125)
T ss_dssp HHHHHHHHHHHHTTSG-GGHHHHHHHHHHHHS----HHHHHHHHHTHHHHHHHHHHHHHHHHT--TTSHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHcccchhHHHHHHHHHhcCc-h-HHHHHHHHHHhhhHHHHHHHHHHHHhCcCCChHHHHHHHHHHHH
Confidence 3444455555555555333332 2345666554 3 46778888888777777777777665554578899999999988
Q ss_pred hhhhhC
Q 048267 82 SSASVG 87 (109)
Q Consensus 82 SsasiG 87 (109)
.+..+.
T Consensus 82 ~~~~~~ 87 (125)
T PF09209_consen 82 QCLFFR 87 (125)
T ss_dssp HHHHHH
T ss_pred HHHHHH
Confidence 876544
No 74
>PLN02956 PSII-Q subunit
Probab=25.35 E-value=2.9e+02 Score=20.51 Aligned_cols=66 Identities=14% Similarity=0.118 Sum_probs=33.6
Q ss_pred HHHhhhccCCchhHHHHHHHHHHhHHHHHHHHHHHHhcCCcCHHHHHHHhHHhhhhhhhhChHHHHHHHHHHHHHHhccC
Q 048267 27 QLEQLEDISNPGFVKDVVTLYLRDSTKTLATIEDEMAKSPVDFMNLDKCFHQLKGSSASVGANKVLNEVNKAREHCKEGN 106 (109)
Q Consensus 27 ~L~~L~~~~~~~f~~~li~~F~~d~~~~l~~L~~al~~~~~D~~~l~~~aH~LKGSsasiGA~~l~~~c~~lE~~~~~~~ 106 (109)
.|+.|-+.++.-++.-.|..=.....+.+..+..++-.+ |-..+++++-.|+.+ ..+|..++|.+|
T Consensus 98 ~LK~LI~k~~W~yvrn~LRgp~s~Lr~DL~~Ii~slpp~--Drk~a~~La~~LFd~------------l~~LD~AAR~kd 163 (185)
T PLN02956 98 RVKALIESESWKEAQKALRRSASNLKQDLYAIIQAKPGK--DRPQLRRLYSDLFNS------------VTKLDYAARDKD 163 (185)
T ss_pred HHHHHhhhccHHHHHHHHHccHHHHHHHHHHHHHhcCHh--HhHHHHHHHHHHHHH------------HHHHHHHHhcCC
Confidence 444444444444555555544444455555555554444 555555554444443 356666666654
No 75
>KOG2716 consensus Polymerase delta-interacting protein PDIP1 and related proteins, contain BTB/POZ domain [Inorganic ion transport and metabolism]
Probab=24.16 E-value=75 Score=24.23 Aligned_cols=52 Identities=17% Similarity=0.213 Sum_probs=43.4
Q ss_pred HHHHhHHHHHHHHHHHHhcCCcCHHHHHHHhHHhhhhhhhhChHHHHHHHHH
Q 048267 46 LYLRDSTKTLATIEDEMAKSPVDFMNLDKCFHQLKGSSASVGANKVLNEVNK 97 (109)
Q Consensus 46 ~F~~d~~~~l~~L~~al~~~~~D~~~l~~~aH~LKGSsasiGA~~l~~~c~~ 97 (109)
.|++-+|+++.-|=..+..|.|+.+.-.+..-.|+-=+--++...|+++|..
T Consensus 48 IFIDRSpKHF~~ILNfmRdGdv~LPe~~kel~El~~EA~fYlL~~Lv~~C~~ 99 (230)
T KOG2716|consen 48 IFIDRSPKHFDTILNFMRDGDVDLPESEKELKELLREAEFYLLDGLVELCQS 99 (230)
T ss_pred EEecCChhHHHHHHHhhhcccccCccchHHHHHHHHHHHHhhHHHHHHHHHH
Confidence 5788899999988888888866766666777777888889999999999987
No 76
>cd07278 PX_RICS_like The phosphoinositide binding Phox Homology domain of PX-RICS-like proteins. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions such as cell signaling, vesicular trafficking, protein sorting, and lipid modification, among others. Members of this family include PX-RICS, TCGAP (Tc10/Cdc42 GTPase-activating protein), and similar proteins. They contain N-terminal PX and Src Homology 3 (SH3) domains, a central Rho GAP domain, and C-terminal extensions. They act as Rho GTPase-activating proteins. PX-RICS is the main isoform expressed during neural development. It is involved in neural functions including axon and dendrite extension, postnatal remodeling, and fine-tuning of neural circuits during early brain development. The PX domain of PX-RICS specifically binds phosphatidylinositol 3-phosphate (PI3P), PI4P, and PI5P. TCGAP is widely expressed in the brain where it is involved in regulating the outgrowth of axons and d
Probab=23.93 E-value=80 Score=21.60 Aligned_cols=40 Identities=23% Similarity=0.340 Sum_probs=29.0
Q ss_pred HhcccchhhhHHHHHHHHhhhccC----CchhHHHHHHHHHHhH
Q 048267 12 RQSFFDEEILDKYFLQLEQLEDIS----NPGFVKDVVTLYLRDS 51 (109)
Q Consensus 12 ~~~~~~~~~lD~~~~~L~~L~~~~----~~~f~~~li~~F~~d~ 51 (109)
+..+.+.=+-|..|++|.+|.+.. .++.+..++..|++--
T Consensus 52 LD~~LHrCiyDRr~S~L~eL~~~~~~~~~~~~~~~~l~~YL~Rl 95 (114)
T cd07278 52 LDKHLHQCIYDRKFSQLTELPEECIEKREQQNLHQVLSDYLKRL 95 (114)
T ss_pred HHHHHHHHHHhhhhhccccCCccccccchHHHHHHHHHHHHHHH
Confidence 344566677888899999997532 3478889999988643
No 77
>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=23.65 E-value=1.9e+02 Score=20.97 Aligned_cols=34 Identities=6% Similarity=0.142 Sum_probs=27.0
Q ss_pred HHHhhhccCCchhHHHHHHHHHHhHHHHHHHHHH
Q 048267 27 QLEQLEDISNPGFVKDVVTLYLRDSTKTLATIED 60 (109)
Q Consensus 27 ~L~~L~~~~~~~f~~~li~~F~~d~~~~l~~L~~ 60 (109)
.-..|.+++-.+....++..|+-+...++.+|+.
T Consensus 55 aA~~laggg~e~v~~~~l~~f~~Q~~~tmeel~~ 88 (165)
T PF08822_consen 55 AAHTLAGGGIEDVARQMLEDFVVQYQATMEELKE 88 (165)
T ss_pred HHHHhccCcHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 3445555544689999999999999999999984
No 78
>PF09670 Cas_Cas02710: CRISPR-associated protein (Cas_Cas02710)
Probab=23.62 E-value=3.7e+02 Score=21.56 Aligned_cols=62 Identities=5% Similarity=0.044 Sum_probs=48.3
Q ss_pred CchhHHHHHHHHHHhHHHHHHHHHHHHhcCCcCHHHHHHHhHHhhhh-hhhhChHHHHHHHHHHH
Q 048267 36 NPGFVKDVVTLYLRDSTKTLATIEDEMAKSPVDFMNLDKCFHQLKGS-SASVGANKVLNEVNKAR 99 (109)
Q Consensus 36 ~~~f~~~li~~F~~d~~~~l~~L~~al~~~~~D~~~l~~~aH~LKGS-sasiGA~~l~~~c~~lE 99 (109)
|.+.+..+-+-|.--+...+.....+++.. ||....+..+.+... +.+.....+..+|..+.
T Consensus 116 Gte~l~~~~~p~~~~~~~~~~~a~~l~n~~--~y~aA~~~l~~l~~rl~~~~~~~~~~~l~~~y~ 178 (379)
T PF09670_consen 116 GTERLRELENPYEVFGDREWRRAKELFNRY--DYGAAARILEELLRRLPGREEYQRYKDLCEGYD 178 (379)
T ss_pred cchhhhhcCCHHHHHHHHHHHHHHHHHhcC--CHHHHHHHHHHHHHhCCchhhHHHHHHHHHHHH
Confidence 446777777777777788888889999999 999999999999886 55555667777777544
No 79
>PF15605 Toxin_52: Putative toxin 52
Probab=23.50 E-value=2.4e+02 Score=18.97 Aligned_cols=10 Identities=10% Similarity=0.424 Sum_probs=4.3
Q ss_pred hhHHHHHHHH
Q 048267 38 GFVKDVVTLY 47 (109)
Q Consensus 38 ~f~~~li~~F 47 (109)
+-+.||-+.|
T Consensus 47 dHlqEm~da~ 56 (103)
T PF15605_consen 47 DHLQEMQDAY 56 (103)
T ss_pred HHHHHHHHHH
Confidence 4444444443
No 80
>PF02631 RecX: RecX family; InterPro: IPR003783 RecX is a putative bacterial regulatory protein []. The gene encoding RecX is found downstream of recA, and it is suggested that the RecX protein might be regulator of RecA activity by interaction with the RecA protein or filament [].; GO: 0006282 regulation of DNA repair; PDB: 3DFG_A 3D5L_B 3C1D_B 3E3V_A.
Probab=23.46 E-value=2.2e+02 Score=18.56 Aligned_cols=34 Identities=26% Similarity=0.435 Sum_probs=17.6
Q ss_pred cchhhhHHHHHHHHhhhccCCchhHHHHHHHHHH
Q 048267 16 FDEEILDKYFLQLEQLEDISNPGFVKDVVTLYLR 49 (109)
Q Consensus 16 ~~~~~lD~~~~~L~~L~~~~~~~f~~~li~~F~~ 49 (109)
+++..|+..+..|.+..=-++..|....+...+.
T Consensus 6 ~~~e~I~~vi~~l~~~gyidD~~ya~~~v~~~~~ 39 (121)
T PF02631_consen 6 FSEEAIEEVIDRLKELGYIDDERYAESYVRSRLR 39 (121)
T ss_dssp --HHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHhcc
Confidence 4555566556666555433345566666666654
No 81
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=23.38 E-value=1.8e+02 Score=21.03 Aligned_cols=33 Identities=24% Similarity=0.321 Sum_probs=26.4
Q ss_pred hHHHHHHHHHHHHhcCCcCHHHHHHHh----HHhhhh
Q 048267 50 DSTKTLATIEDEMAKSPVDFMNLDKCF----HQLKGS 82 (109)
Q Consensus 50 d~~~~l~~L~~al~~~~~D~~~l~~~a----H~LKGS 82 (109)
+-.+++..|..|....||+.+++...+ |+|.++
T Consensus 62 ~r~Kl~~gl~~A~~KRpVs~e~ie~~v~~ie~~Lr~~ 98 (156)
T COG1327 62 DREKLRRGLIRACEKRPVSSEQIEEAVSHIERQLRSS 98 (156)
T ss_pred CHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHhc
Confidence 357889999999999999999887665 556555
No 82
>PF13779 DUF4175: Domain of unknown function (DUF4175)
Probab=23.12 E-value=2.8e+02 Score=25.03 Aligned_cols=67 Identities=7% Similarity=0.173 Sum_probs=39.7
Q ss_pred chhHHHHHHHHHHhHHHHHHHHHHHHhcCCcCHHHHHHHhHHhhhhhhhhChHHHHHHHHHHHHHHhccCcC
Q 048267 37 PGFVKDVVTLYLRDSTKTLATIEDEMAKSPVDFMNLDKCFHQLKGSSASVGANKVLNEVNKAREHCKEGNLE 108 (109)
Q Consensus 37 ~~f~~~li~~F~~d~~~~l~~L~~al~~~~~D~~~l~~~aH~LKGSsasiGA~~l~~~c~~lE~~~~~~~~~ 108 (109)
++=+.+++....+=..+.+..|.+-..+.+ +-. .-..--+.+.+++-..|..+..+||++++.|+++
T Consensus 491 ~eEI~rLm~eLR~A~~~ym~~LAeq~~~~~-~~~----~~p~~~~~~~~~~~~dL~~mmd~ie~la~~G~~~ 557 (820)
T PF13779_consen 491 DEEIARLMQELREAMQDYMQALAEQAQRNP-QQQ----DQPPDQGNSQMMSQQDLQRMMDRIEELARSGRMD 557 (820)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhHhCc-ccc----cCcccchhhhccCHHHHHHHHHHHHHHHHcCCHH
Confidence 344445555444444444444444443331 000 0011135567899999999999999999999875
No 83
>PF01963 TraB: TraB family; InterPro: IPR002816 In prokaryotes, for example Enterococcus faecalis (Streptococcus faecalis), the conjugative transfer of certain plasmids is controlled by peptide pheromones []. Plasmid free recipient cells secret plasmid specific oligopeptides, termed sex pheromones. They induce bacterial clumping and specifically activate the conjugative transfer of the corresponding plasmid. Once recipient cells acquire the plasmid they start to produce a pheromone inhibitor to block the activity of the pheromone and to prevent plasmid containing cells from clumping; they also become donor cells able to transfer the plasmid to plasmid free recipient cells. Examples of such plasmid-pheromone systems are bacteriocin plasmid pPD1 [], haemolysin/bacteriocin plasmid, pAD1 [], tetracycline-resistance plasmid, pCF10 [], and the haemolysin/bacteriocin plasmid, pOB1 []. TraB in combination with another factor contributes to pheromone shutdown in cells that have acquired a plasmid. It exact function has not yet been determined [, ]. This entry also contains plant and mammalian proteins, suggesting that these Trab-related proteins may have a somewhat wider or different function in eukaryotes.
Probab=22.65 E-value=1.5e+02 Score=21.61 Aligned_cols=25 Identities=20% Similarity=0.251 Sum_probs=13.8
Q ss_pred HhHHHHHHHHHHHHhcCCcCHHHHHHH
Q 048267 49 RDSTKTLATIEDEMAKSPVDFMNLDKC 75 (109)
Q Consensus 49 ~d~~~~l~~L~~al~~~~~D~~~l~~~ 75 (109)
++..+.+..+..++..+ |.+.+...
T Consensus 170 ~~~~~~~~~~~~~~~~g--d~~~l~~~ 194 (259)
T PF01963_consen 170 EDGEKMLEQLIEAWKNG--DLDALMEL 194 (259)
T ss_pred ccchHHHHHHHHHHHcc--CHHHHHHH
Confidence 44455555666666666 55554444
No 84
>COG5582 Uncharacterized conserved protein [Function unknown]
Probab=21.29 E-value=3e+02 Score=20.24 Aligned_cols=38 Identities=18% Similarity=0.289 Sum_probs=28.6
Q ss_pred hhHHHHHHHHHHhHHHHHHHHHHHHhcCCcCHHHHHHHhHHh
Q 048267 38 GFVKDVVTLYLRDSTKTLATIEDEMAKSPVDFMNLDKCFHQL 79 (109)
Q Consensus 38 ~f~~~li~~F~~d~~~~l~~L~~al~~~~~D~~~l~~~aH~L 79 (109)
.++.+.+..|.. ..+|.+|..|++.+ |-.++..+.-.|
T Consensus 137 ~~ie~~~~~f~~--~~LL~~IDeALd~~--Dk~~F~~L~q~L 174 (182)
T COG5582 137 ALIERSVHAFER--KKLLQQIDEALDMR--DKERFYQLVQIL 174 (182)
T ss_pred HHHHHHHHHHHH--HHHHHHHHHHHhhh--hHHHHHHHHHHH
Confidence 577777777765 47899999999998 877766665443
No 85
>PRK03381 PII uridylyl-transferase; Provisional
Probab=21.20 E-value=2.6e+02 Score=24.84 Aligned_cols=84 Identities=18% Similarity=0.244 Sum_probs=43.1
Q ss_pred HHhcccchhhhHHHHHHHHhhhccCCchhHHHHHHHHHHhHHHHHHHH---HHHHhcCCcCHHHHHHHhHHh-hhh---h
Q 048267 11 MRQSFFDEEILDKYFLQLEQLEDISNPGFVKDVVTLYLRDSTKTLATI---EDEMAKSPVDFMNLDKCFHQL-KGS---S 83 (109)
Q Consensus 11 ~~~~~~~~~~lD~~~~~L~~L~~~~~~~f~~~li~~F~~d~~~~l~~L---~~al~~~~~D~~~l~~~aH~L-KGS---s 83 (109)
.++-|.+.|+|..-|.++..+..-...+.... .+.+ +.+-..+..+ ...+..+ +.-.+.-+.|.+ ||. =
T Consensus 387 ~l~~m~~~GvL~~~iPE~~~i~~~~Q~~~~H~-ytVd-~Htl~~l~~~~~~~~~~~~~--~lL~lAaLlHDiGKg~~~~H 462 (774)
T PRK03381 387 VIEALDRTGLWGRLLPEWEAVRDLPPRDPVHR-WTVD-RHLVETAVRAAALTRRVARP--DLLLLGALLHDIGKGRGGDH 462 (774)
T ss_pred HHHHHHHhCCHHHhchhHHHhhCCCCCCCCcc-ChHH-HHHHHHHHHHHHHHhccCCH--HHHHHHHHHHhhcCCCCCCh
Confidence 45556777888775555555432111121110 0100 1122222222 2233333 556777788888 664 3
Q ss_pred hhhChHHHHHHHHHH
Q 048267 84 ASVGANKVLNEVNKA 98 (109)
Q Consensus 84 asiGA~~l~~~c~~l 98 (109)
+.+||.-...+|.++
T Consensus 463 s~~Ga~~a~~i~~RL 477 (774)
T PRK03381 463 SVVGAELARQIGARL 477 (774)
T ss_pred HHHHHHHHHHHHHHc
Confidence 567888888888765
No 86
>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=21.05 E-value=1.3e+02 Score=20.75 Aligned_cols=27 Identities=11% Similarity=0.181 Sum_probs=20.7
Q ss_pred HhHHHHHHHHHHHHhcCCcCHHHHHHHhH
Q 048267 49 RDSTKTLATIEDEMAKSPVDFMNLDKCFH 77 (109)
Q Consensus 49 ~d~~~~l~~L~~al~~~~~D~~~l~~~aH 77 (109)
++..+++..+-.||.++ |++++.++.+
T Consensus 3 ~eI~~l~~~w~~ai~tg--D~~~~~~ly~ 29 (128)
T PF08332_consen 3 QEIAALFDRWNDAIQTG--DPETYAKLYA 29 (128)
T ss_dssp HHHHHHHHHHHHHHHHT---HHHHHHHEE
T ss_pred HHHHHHHHHHHHHHHcC--CHHHHhhhcC
Confidence 34566778889999999 9999988754
No 87
>KOG3091 consensus Nuclear pore complex, p54 component (sc Nup57) [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=20.98 E-value=5.4e+02 Score=22.08 Aligned_cols=17 Identities=18% Similarity=0.294 Sum_probs=14.4
Q ss_pred hHHHHHHHHHHhcccch
Q 048267 2 EALRQQIAKMRQSFFDE 18 (109)
Q Consensus 2 ~~~~~~~~~~~~~~~~~ 18 (109)
|.||.++.++.+.+-+.
T Consensus 414 E~Lr~Kldtll~~ln~P 430 (508)
T KOG3091|consen 414 EELRAKLDTLLAQLNAP 430 (508)
T ss_pred HHHHHHHHHHHHHhcCh
Confidence 57899999999888776
No 88
>PHA01794 hypothetical protein
Probab=20.84 E-value=3.1e+02 Score=19.26 Aligned_cols=52 Identities=21% Similarity=0.355 Sum_probs=33.0
Q ss_pred HHHHHHhccc-chhhhHHHHHHHHhhhccCCchhHHHHHHHHHHhHHHHHHHHHH
Q 048267 7 QIAKMRQSFF-DEEILDKYFLQLEQLEDISNPGFVKDVVTLYLRDSTKTLATIED 60 (109)
Q Consensus 7 ~~~~~~~~~~-~~~~lD~~~~~L~~L~~~~~~~f~~~li~~F~~d~~~~l~~L~~ 60 (109)
.+.+++.+.+ ++|--..-|.+|++=.-+ ..|+..=+..|++..++.+.-|..
T Consensus 58 aI~d~v~~~~~Ee~~~e~lF~eleqEm~~--SGFF~~ki~kyien~EK~~~yl~~ 110 (134)
T PHA01794 58 AIADFVETFEDEEGTTEGLFAELEKEMVD--SGFFRAKIKKYIENMEKSARYLKA 110 (134)
T ss_pred HHHHHHHHhhhhcchHHHHHHHHHHHHHH--hhHHHHHHHHHHHHHHHHHHHhhc
Confidence 3555665554 334444446777653322 368888899999998888877655
No 89
>PF08747 DUF1788: Domain of unknown function (DUF1788); InterPro: IPR014858 This entry represents a putative uncharacterised protein of length around 200 amino acids.
Probab=20.64 E-value=2.3e+02 Score=19.32 Aligned_cols=77 Identities=16% Similarity=0.149 Sum_probs=53.6
Q ss_pred ccchhhhHHHHHHHHhhhccCCchhHHHHHHHHHHhHHHHHHHHHHHHhcCCcCHHHHHHHhHHhhhhhhhhChHHHHHH
Q 048267 15 FFDEEILDKYFLQLEQLEDISNPGFVKDVVTLYLRDSTKTLATIEDEMAKSPVDFMNLDKCFHQLKGSSASVGANKVLNE 94 (109)
Q Consensus 15 ~~~~~~lD~~~~~L~~L~~~~~~~f~~~li~~F~~d~~~~l~~L~~al~~~~~D~~~l~~~aH~LKGSsasiGA~~l~~~ 94 (109)
+.+.+++| .+-++....+.+.+.+-+..-+.........|...+... +.+ .=-|.|-.+..+..+.+.+
T Consensus 14 l~~~~~~d----~~~~~E~~~g~~~~~~~l~~~l~~~~~i~~~i~~~~~~~--~~~-----vv~ltGvG~l~P~~R~h~l 82 (126)
T PF08747_consen 14 LEERGILD----KIIEMEEKKGSDALLKQLQGILDMQEKIAEYIQEELEDD--DRD-----VVFLTGVGSLFPFIRSHEL 82 (126)
T ss_pred HHhcChHH----HHHHHHHhhhHHHHHHHHHHHhhhHHHHHHHHHHhccCC--CCc-----EEEEeCcchhcchhhHHHH
Confidence 34445554 555565555778888888888887666777777765544 222 2357899999999999999
Q ss_pred HHHHHHHH
Q 048267 95 VNKAREHC 102 (109)
Q Consensus 95 c~~lE~~~ 102 (109)
-..+....
T Consensus 83 L~~l~~~~ 90 (126)
T PF08747_consen 83 LNNLQPKF 90 (126)
T ss_pred HHHHHHHh
Confidence 98888654
No 90
>COG1842 PspA Phage shock protein A (IM30), suppresses sigma54-dependent transcription [Transcription / Signal transduction mechanisms]
Probab=20.57 E-value=2.9e+02 Score=20.80 Aligned_cols=24 Identities=21% Similarity=0.356 Sum_probs=21.3
Q ss_pred HHHHHHHHhHHHHHHHHHHHHhcC
Q 048267 42 DVVTLYLRDSTKTLATIEDEMAKS 65 (109)
Q Consensus 42 ~li~~F~~d~~~~l~~L~~al~~~ 65 (109)
.+|+.|+.+....+.+++..+++-
T Consensus 27 ~~l~Q~ird~~~~l~~ar~~~A~~ 50 (225)
T COG1842 27 KMLEQAIRDMESELAKARQALAQA 50 (225)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 899999999999999999888753
No 91
>PF10768 FliX: Class II flagellar assembly regulator; InterPro: IPR019704 The FliX protein is possibly a transient component of the flagellum that is required for the assembly process. FliX may contribute to the targeting or assembly of the P- and L-ring protein monomers at the cell pole. The family carries a potential N-terminal signal sequence and at least one transmembrane domain indicating that it might function either in or in association with the cell membrane [].
Probab=20.15 E-value=3.2e+02 Score=19.23 Aligned_cols=78 Identities=12% Similarity=0.122 Sum_probs=51.0
Q ss_pred HHHHhhhccCCchhHHHHHHHHHHhHHHHHHHHHHHHhcCCcCHHHHHHHhHHhhhhhhhhChHHHHHHHHHHHHHHh
Q 048267 26 LQLEQLEDISNPGFVKDVVTLYLRDSTKTLATIEDEMAKSPVDFMNLDKCFHQLKGSSASVGANKVLNEVNKAREHCK 103 (109)
Q Consensus 26 ~~L~~L~~~~~~~f~~~li~~F~~d~~~~l~~L~~al~~~~~D~~~l~~~aH~LKGSsasiGA~~l~~~c~~lE~~~~ 103 (109)
+.|..||+.++|.--++=...-=++.-..|++|+-++=.+.++-..+.+++-.+..--.+.|=++|-.+-.+||..++
T Consensus 54 DaLLALQ~vdd~~erRrRav~Rg~~lLD~Ld~Lk~~LL~G~v~~~~L~~L~~~~~~~r~~s~Dp~L~~vL~eIELRa~ 131 (139)
T PF10768_consen 54 DALLALQEVDDPTERRRRAVRRGHDLLDVLDELKIGLLSGTVPRGDLERLARAVRERRESSGDPRLDAVLDEIELRAE 131 (139)
T ss_pred HHHHHHhhccChHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhhccCCCchHHHHHHHHHHHHH
Confidence 355555554443222222222233444567788888888888888888888877776677788888888888887654
Done!