Query 043345
Match_columns 80
No_of_seqs 126 out of 574
Neff 7.7
Searched_HMMs 46136
Date Fri Mar 29 04:07:20 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/043345.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/043345hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF01627 Hpt: Hpt domain; Int 99.5 1.4E-13 3E-18 78.4 7.7 60 4-63 26-88 (90)
2 KOG4747 Two-component phosphor 99.5 1.3E-13 2.8E-18 86.8 7.8 75 4-78 69-143 (150)
3 COG2198 ArcB FOG: HPt domain [ 99.4 1.9E-12 4.2E-17 78.8 8.3 67 4-70 49-118 (122)
4 smart00073 HPT Histidine Phosp 99.4 1.3E-12 2.8E-17 74.6 4.6 64 3-67 23-86 (87)
5 cd00088 HPT Histidine Phosphot 99.2 4.9E-11 1.1E-15 69.3 5.8 41 4-44 29-69 (94)
6 TIGR02956 TMAO_torS TMAO reduc 99.0 5.9E-10 1.3E-14 85.1 6.6 64 4-69 905-968 (968)
7 PRK10618 phosphotransfer inter 99.0 2E-09 4.4E-14 83.3 7.6 61 3-63 832-892 (894)
8 PRK11091 aerobic respiration c 98.9 8.9E-09 1.9E-13 77.6 7.3 70 3-72 706-775 (779)
9 PRK11107 hybrid sensory histid 98.2 7.8E-06 1.7E-10 62.3 8.7 67 4-70 850-917 (919)
10 PRK11466 hybrid sensory histid 98.2 3.6E-06 7.8E-11 64.4 5.3 38 4-41 849-886 (914)
11 COG0643 CheA Chemotaxis protei 97.9 6.2E-05 1.4E-09 57.8 6.9 63 6-68 40-105 (716)
12 PRK10547 chemotaxis protein Ch 97.8 8.7E-05 1.9E-09 56.6 7.2 59 6-64 37-98 (670)
13 PRK09959 hybrid sensory histid 97.1 0.0049 1.1E-07 48.9 8.5 67 4-70 1126-1193(1197)
14 PRK15347 two component system 96.7 0.0049 1.1E-07 47.3 5.9 54 9-63 862-915 (921)
15 PF08900 DUF1845: Domain of un 83.9 10 0.00022 25.4 7.2 54 19-72 32-91 (217)
16 PF13779 DUF4175: Domain of un 81.7 4.6 9.9E-05 32.2 5.5 45 19-63 530-574 (820)
17 PF14276 DUF4363: Domain of un 78.2 5.3 0.00012 23.9 3.9 49 13-66 17-65 (121)
18 TIGR02302 aProt_lowcomp conser 77.2 9 0.00019 30.8 5.8 44 21-64 562-605 (851)
19 PLN02956 PSII-Q subunit 72.9 24 0.00053 23.3 6.3 39 27-65 146-184 (185)
20 smart00388 HisKA His Kinase A 72.3 10 0.00022 18.6 6.9 58 9-74 5-62 (66)
21 COG2991 Uncharacterized protei 70.8 0.8 1.7E-05 25.9 -0.9 26 16-42 28-53 (77)
22 TIGR03761 ICE_PFL4669 integrat 69.4 32 0.00069 23.2 7.3 51 21-71 32-88 (216)
23 PF03670 UPF0184: Uncharacteri 69.1 20 0.00043 20.7 5.2 37 41-77 31-67 (83)
24 PF03993 DUF349: Domain of Unk 68.7 13 0.00028 20.1 3.8 32 30-61 37-68 (77)
25 PF07361 Cytochrom_B562: Cytoc 65.2 16 0.00036 21.5 3.9 33 24-56 60-92 (103)
26 PF00512 HisKA: His Kinase A ( 65.1 18 0.00039 18.7 8.7 58 9-74 5-64 (68)
27 KOG2424 Protein involved in tr 64.6 15 0.00033 24.3 3.9 24 21-46 147-170 (195)
28 PF04837 MbeB_N: MbeB-like, N- 64.4 19 0.00042 18.9 7.1 48 28-79 3-50 (52)
29 KOG3232 Vacuolar assembly/sort 63.5 41 0.00088 22.3 6.2 40 28-67 94-133 (203)
30 PF04722 Ssu72: Ssu72-like pro 58.6 23 0.00049 23.6 4.0 36 21-57 145-181 (195)
31 PRK13858 type IV secretion sys 56.8 49 0.0011 21.1 7.6 62 8-77 73-136 (147)
32 PF05757 PsbQ: Oxygen evolving 55.8 42 0.00092 22.4 4.9 38 27-64 162-199 (202)
33 PF12854 PPR_1: PPR repeat 55.7 15 0.00033 16.9 2.2 22 34-55 12-33 (34)
34 PF09577 Spore_YpjB: Sporulati 53.9 58 0.0013 22.2 5.5 40 28-67 102-141 (232)
35 PF04400 DUF539: Protein of un 52.2 1.1 2.4E-05 23.0 -2.3 19 16-34 7-25 (45)
36 PF07870 DUF1657: Protein of u 52.2 33 0.00071 17.7 5.0 36 34-69 14-49 (50)
37 PF14077 WD40_alt: Alternative 49.9 29 0.00063 17.9 2.7 36 43-78 11-46 (48)
38 COG2178 Predicted RNA-binding 48.3 83 0.0018 21.2 6.5 43 27-69 27-69 (204)
39 cd00082 HisKA Histidine Kinase 46.1 35 0.00076 16.2 7.5 55 9-71 7-62 (65)
40 PF09403 FadA: Adhesion protei 45.1 74 0.0016 19.7 5.0 9 20-28 13-21 (126)
41 PF01535 PPR: PPR repeat; Int 44.7 28 0.0006 14.7 2.7 22 36-57 7-28 (31)
42 PF00435 Spectrin: Spectrin re 44.4 52 0.0011 17.7 7.2 45 26-71 57-101 (105)
43 PRK10548 flagellar biosynthesi 43.5 76 0.0016 19.4 7.8 23 27-49 12-34 (121)
44 PF13812 PPR_3: Pentatricopept 42.4 33 0.00071 14.8 3.3 22 36-57 8-29 (34)
45 PF15300 INT_SG_DDX_CT_C: INTS 41.8 20 0.00044 19.7 1.5 20 2-21 17-36 (65)
46 PF11173 DUF2960: Protein of u 41.6 22 0.00047 20.4 1.6 15 66-80 38-52 (79)
47 PF10180 DUF2373: Uncharacteri 37.9 67 0.0014 17.5 3.2 29 3-35 35-63 (65)
48 PRK10987 regulatory protein Am 37.9 63 0.0014 22.3 3.8 35 21-55 79-113 (284)
49 PF08738 Gon7: Gon7 family; I 37.4 92 0.002 18.6 4.0 26 47-72 51-76 (103)
50 PRK00068 hypothetical protein; 37.4 1.2E+02 0.0027 25.0 5.7 39 26-64 930-968 (970)
51 PRK10265 chaperone-modulator p 37.3 58 0.0013 19.0 3.1 23 49-71 77-99 (101)
52 TIGR00756 PPR pentatricopeptid 37.3 39 0.00085 14.3 3.2 22 36-57 7-28 (35)
53 KOG4182 Uncharacterized conser 37.1 2E+02 0.0044 22.5 7.8 58 4-61 73-166 (828)
54 PF01044 Vinculin: Vinculin fa 37.0 1.6E+02 0.0035 24.1 6.3 61 8-68 411-480 (968)
55 PF05190 MutS_IV: MutS family 36.6 66 0.0014 17.5 3.2 26 50-75 4-29 (92)
56 PF14756 Pdase_C33_assoc: Pept 35.9 1.1E+02 0.0024 19.0 4.6 21 24-44 70-90 (147)
57 PRK15058 cytochrome b562; Prov 35.0 1.1E+02 0.0025 19.0 4.6 32 25-56 86-117 (128)
58 TIGR00444 mazG MazG family pro 34.0 1.1E+02 0.0023 21.1 4.3 43 25-67 129-172 (248)
59 PRK11107 hybrid sensory histid 33.4 2.3E+02 0.0051 22.1 6.7 55 10-72 297-351 (919)
60 COG1270 CbiB Cobalamin biosynt 32.9 1E+02 0.0022 22.1 4.2 35 21-55 94-128 (320)
61 PF09686 Plasmid_RAQPRD: Plasm 32.7 53 0.0012 18.8 2.3 23 52-74 46-68 (81)
62 PLN02999 photosystem II oxygen 31.9 1.6E+02 0.0034 19.6 5.7 38 27-64 150-187 (190)
63 PRK03170 dihydrodipicolinate s 31.8 1.7E+02 0.0036 19.9 5.2 41 18-58 197-239 (292)
64 PF13041 PPR_2: PPR repeat fam 31.8 69 0.0015 15.5 3.2 24 34-57 8-31 (50)
65 PF09660 DUF2397: Protein of u 31.5 2.3E+02 0.0049 21.3 9.2 64 14-77 105-174 (486)
66 PF07891 DUF1666: Protein of u 31.2 1.8E+02 0.0039 20.2 5.4 47 27-74 7-62 (247)
67 PLN02729 PSII-Q subunit 31.2 1.7E+02 0.0037 19.9 5.4 37 27-63 180-216 (220)
68 COG4354 Predicted bile acid be 31.1 1.9E+02 0.0041 22.9 5.6 56 14-73 501-556 (721)
69 PRK01209 cobD cobalamin biosyn 30.3 1.1E+02 0.0024 21.4 4.1 33 23-55 92-124 (312)
70 TIGR00674 dapA dihydrodipicoli 29.7 1.8E+02 0.004 19.7 5.1 42 17-58 193-236 (285)
71 TIGR02878 spore_ypjB sporulati 27.7 1.5E+02 0.0033 20.4 4.2 33 29-61 104-136 (233)
72 PRK10722 hypothetical protein; 27.5 2.1E+02 0.0047 19.8 4.9 32 45-76 178-209 (247)
73 cd00408 DHDPS-like Dihydrodipi 27.5 1.8E+02 0.0039 19.5 4.6 43 18-60 193-237 (281)
74 PF13047 DUF3907: Protein of u 27.3 1.2E+02 0.0026 19.4 3.5 26 44-69 117-142 (148)
75 PF13747 DUF4164: Domain of un 27.1 1.3E+02 0.0029 17.2 4.2 23 47-69 36-58 (89)
76 PHA02585 16 small terminase pr 27.0 1.8E+02 0.0039 18.8 7.6 64 4-76 45-109 (161)
77 PF00701 DHDPS: Dihydrodipicol 26.5 1.6E+02 0.0035 19.9 4.3 42 19-60 198-241 (289)
78 PF08657 DASH_Spc34: DASH comp 25.0 2.4E+02 0.0052 19.5 6.6 62 8-69 134-199 (259)
79 cd00950 DHDPS Dihydrodipicolin 24.9 2.3E+02 0.0049 19.2 5.2 41 18-58 196-238 (284)
80 TIGR01690 ICE_RAQPRD integrati 24.9 61 0.0013 19.1 1.7 23 52-74 59-81 (94)
81 PF08581 Tup_N: Tup N-terminal 24.7 1.4E+02 0.0031 16.8 3.8 17 50-66 4-20 (79)
82 cd05136 RasGAP_DAB2IP The DAB2 24.2 2.3E+02 0.0049 20.0 4.7 46 28-73 13-58 (309)
83 COG0783 Dps DNA-binding ferrit 24.0 2E+02 0.0044 18.3 5.2 66 7-72 57-124 (156)
84 PF02870 Methyltransf_1N: 6-O- 23.9 1.1E+02 0.0024 16.4 2.6 17 59-75 52-68 (77)
85 PRK10841 hybrid sensory kinase 23.9 4E+02 0.0086 21.6 8.0 56 10-73 451-506 (924)
86 TIGR02956 TMAO_torS TMAO reduc 23.9 3.7E+02 0.0079 21.2 7.8 55 10-72 468-522 (968)
87 PF01231 IDO: Indoleamine 2,3- 23.7 2.8E+02 0.0061 20.4 5.3 34 38-71 181-214 (422)
88 PF13942 Lipoprotein_20: YfhG 23.4 2.3E+02 0.005 18.7 4.6 32 45-76 132-163 (179)
89 TIGR03042 PS_II_psbQ_bact phot 23.4 2E+02 0.0044 18.1 6.7 37 29-72 104-140 (142)
90 PF01322 Cytochrom_C_2: Cytoch 23.4 1.7E+02 0.0037 17.2 6.4 36 28-63 83-118 (122)
91 PF11855 DUF3375: Protein of u 23.4 3.2E+02 0.007 20.4 7.4 64 5-69 100-163 (478)
92 cd00089 HR1 Protein kinase C-r 23.4 1.4E+02 0.0029 16.1 4.1 29 43-71 42-70 (72)
93 COG1220 HslU ATP-dependent pro 22.9 1.2E+02 0.0026 22.6 3.2 31 7-37 374-404 (444)
94 PRK06342 transcription elongat 22.9 2.1E+02 0.0046 18.2 6.2 46 7-67 36-81 (160)
95 KOG3612 PHD Zn-finger protein 22.9 2.6E+02 0.0056 21.8 5.0 36 29-64 491-526 (588)
96 PF10481 CENP-F_N: Cenp-F N-te 22.6 2.9E+02 0.0064 19.7 5.6 42 27-68 70-127 (307)
97 COG5214 POL12 DNA polymerase a 22.5 1.3E+02 0.0028 22.9 3.3 45 27-80 23-68 (581)
98 COG5613 Uncharacterized conser 22.1 3.3E+02 0.0072 20.1 5.7 43 25-67 319-361 (400)
99 TIGR00465 ilvC ketol-acid redu 22.1 2.7E+02 0.0058 19.6 4.8 38 9-46 210-247 (314)
100 PF10191 COG7: Golgi complex c 22.0 3.1E+02 0.0067 21.9 5.5 38 25-62 126-163 (766)
101 PRK04778 septation ring format 22.0 3.6E+02 0.0079 20.5 6.5 42 28-69 176-217 (569)
102 PF07743 HSCB_C: HSCB C-termin 21.6 1.5E+02 0.0033 16.0 6.6 25 31-55 42-66 (78)
103 PF10069 DICT: Sensory domain 21.5 56 0.0012 19.9 1.2 50 19-72 22-72 (129)
104 PF03858 Crust_neuro_H: Crusta 21.5 93 0.002 15.6 1.7 22 6-27 5-26 (41)
105 COG1598 Predicted nuclease of 21.5 66 0.0014 17.6 1.3 28 46-73 24-51 (73)
106 PF04428 Choline_kin_N: Cholin 21.4 97 0.0021 16.3 1.9 11 8-18 30-40 (53)
107 PF05465 Halo_GVPC: Halobacter 21.0 1.1E+02 0.0024 14.2 3.7 23 48-70 4-26 (32)
108 PF06160 EzrA: Septation ring 20.9 3.9E+02 0.0084 20.4 6.7 42 27-68 171-212 (560)
109 PRK14158 heat shock protein Gr 20.8 2.6E+02 0.0057 18.5 5.4 15 28-42 95-109 (194)
110 cd04751 Commd3 COMM_Domain con 20.8 96 0.0021 17.9 2.0 16 6-21 72-87 (95)
111 PF14989 CCDC32: Coiled-coil d 20.8 99 0.0021 19.7 2.2 71 9-79 60-133 (148)
112 PF13779 DUF4175: Domain of un 20.8 4.7E+02 0.01 21.3 6.4 21 53-73 492-512 (820)
113 COG2841 Uncharacterized protei 20.8 1.7E+02 0.0038 16.4 6.7 65 7-73 2-69 (72)
114 PF04782 DUF632: Protein of un 20.5 1.7E+02 0.0037 20.8 3.5 36 21-56 271-306 (312)
115 PRK08655 prephenate dehydrogen 20.3 3.6E+02 0.0078 19.8 5.7 35 28-62 240-274 (437)
No 1
>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=99.51 E-value=1.4e-13 Score=78.44 Aligned_cols=60 Identities=20% Similarity=0.347 Sum_probs=50.7
Q ss_pred chhHHHHHHHHHHhhhhhhccChHHHHHHHHHHHHHHhhcCHHH---HHHHHHHHHHHHHHHH
Q 043345 4 NVDFTKVGGHVHQLKGSSSSIGAQRVNNVCTAFRSFCEERNIEG---CQQYLQHLKQEYYLVK 63 (80)
Q Consensus 4 ~~D~~~~~~laH~LKGss~nlGa~~L~~~c~~lE~~~~~~~~~~---~~~~~~~l~~~~~~l~ 63 (80)
..|++.+.+.+|+|||+++++|+..+..+|..+|..++.++.+. +...++.|...++.+.
T Consensus 26 ~~d~~~l~~~~H~lkG~a~~~g~~~l~~~~~~lE~~~~~~~~~~~~~~~~~~~~l~~~l~~l~ 88 (90)
T PF01627_consen 26 QEDWEELRRLAHRLKGSAGNLGAPRLAELAEQLEQALKSGDKPEAEELEQLLDELEAMLEQLR 88 (90)
T ss_dssp HCHHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTHHHHSHHHHHHHHHHHHHHHHHH
T ss_pred HhhHHHHHHHHHHHhhhHHhcCHHHHHHHHHHHHHHHHcCCccchhHHHHHHHHHHHHHHHHh
Confidence 57999999999999999999999999999999999999988877 5555555555555544
No 2
>KOG4747 consensus Two-component phosphorelay intermediate involved in MAP kinase cascade regulation [Signal transduction mechanisms]
Probab=99.50 E-value=1.3e-13 Score=86.76 Aligned_cols=75 Identities=57% Similarity=0.936 Sum_probs=71.9
Q ss_pred chhHHHHHHHHHHhhhhhhccChHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 043345 4 NVDFTKVGGHVHQLKGSSSSIGAQRVNNVCTAFRSFCEERNIEGCQQYLQHLKQEYYLVKNKLQTLFQVCLKSLA 78 (80)
Q Consensus 4 ~~D~~~~~~laH~LKGss~nlGa~~L~~~c~~lE~~~~~~~~~~~~~~~~~l~~~~~~l~~~L~~~l~~~~~~~~ 78 (80)
++|+..++...|.+||||.+|||.++...|..+...|+.+|.+++...+++++.+|..++.+|++++++|||.+.
T Consensus 69 ~~d~k~~~~~~hqlkgssssIGa~kvk~~c~~~~~~~~~~n~egcvr~l~~v~ie~~~lkkkL~~~f~L~rq~i~ 143 (150)
T KOG4747|consen 69 ERDFKKLGSHVHQLKGSSSSIGALKVKKVCVGFNEFCEAGNIEGCVRCLQQVKIEYSLLKKKLETLFQLERQEIL 143 (150)
T ss_pred HhHHHHHHHHHHHccCchhhhhHHHHHHHHHHHHHHHhhccchhHhhchHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 349999999999999999999999999999999999999999999999999999999999999999999999554
No 3
>COG2198 ArcB FOG: HPt domain [Signal transduction mechanisms]
Probab=99.41 E-value=1.9e-12 Score=78.76 Aligned_cols=67 Identities=22% Similarity=0.380 Sum_probs=58.2
Q ss_pred chhHHHHHHHHHHhhhhhhccChHHHHHHHHHHHHHHhh-cCHHHHHHHHHHHHHH--HHHHHHHHHHHH
Q 043345 4 NVDFTKVGGHVHQLKGSSSSIGAQRVNNVCTAFRSFCEE-RNIEGCQQYLQHLKQE--YYLVKNKLQTLF 70 (80)
Q Consensus 4 ~~D~~~~~~laH~LKGss~nlGa~~L~~~c~~lE~~~~~-~~~~~~~~~~~~l~~~--~~~l~~~L~~~l 70 (80)
..|+..+.+++|+|||+++++|+..|...|.+||..++. ...+....++.++..+ +..+...+.++.
T Consensus 49 ~~d~~~~~~~aH~lkg~a~~lg~~~L~~~~~~lE~~~~~~~~~~~~~~~i~~l~~~~~~~~~~~~~~~~~ 118 (122)
T COG2198 49 AEDNDGLARLAHRLKGSAASLGLPALAQLCQQLEDALRSGASLEELEELIAELKDELQLDVLALELLTYL 118 (122)
T ss_pred cCCcHHHHHHHHHHHhHHHhccHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHhcchHHHHHHHHHh
Confidence 568899999999999999999999999999999999988 5677889999999999 666666665554
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=99.36 E-value=1.3e-12 Score=74.63 Aligned_cols=64 Identities=20% Similarity=0.352 Sum_probs=52.1
Q ss_pred CchhHHHHHHHHHHhhhhhhccChHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHHHHHH
Q 043345 3 QNVDFTKVGGHVHQLKGSSSSIGAQRVNNVCTAFRSFCEERNIEGCQQYLQHLKQEYYLVKNKLQ 67 (80)
Q Consensus 3 ~~~D~~~~~~laH~LKGss~nlGa~~L~~~c~~lE~~~~~~~~~~~~~~~~~l~~~~~~l~~~L~ 67 (80)
...|+..+.+.+|+|||+++++|+..|..+|..+|..++... ++...+++.+...|..+...|.
T Consensus 23 ~~~~~~~l~~~~H~LKG~a~~~g~~~l~~~~~~lE~~~~~~~-~~~~~~~~~l~~~~~~~~~~l~ 86 (87)
T smart00073 23 DAQDVNEIFRAAHTLKGSAGSLGLQQLAQLCHQLENLLDAAR-SGEVELTPDLLDLLLELVDVLK 86 (87)
T ss_pred CHhHHHHHHHHHHhhhhhHHhcCHHHHHHHHHHHHHHHHHHH-cCCCCCCHHHHHHHHHHHHHHc
Confidence 357899999999999999999999999999999999987644 3334566777777777766553
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=99.21 E-value=4.9e-11 Score=69.25 Aligned_cols=41 Identities=24% Similarity=0.429 Sum_probs=38.9
Q ss_pred chhHHHHHHHHHHhhhhhhccChHHHHHHHHHHHHHHhhcC
Q 043345 4 NVDFTKVGGHVHQLKGSSSSIGAQRVNNVCTAFRSFCEERN 44 (80)
Q Consensus 4 ~~D~~~~~~laH~LKGss~nlGa~~L~~~c~~lE~~~~~~~ 44 (80)
+.|+..+...+|+|||+++++|+..|...|..+|..++.+.
T Consensus 29 ~~d~~~l~~~~H~LkGsa~~~G~~~l~~~~~~lE~~~~~~~ 69 (94)
T cd00088 29 AEDLNEIFRAAHTLKGSAASLGLQRLAQLAHQLEDLLDALR 69 (94)
T ss_pred HHHHHHHHHHHHhhhhHHhcCChHHHHHHHHHHHHHHHHHH
Confidence 68999999999999999999999999999999999998754
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=99.03 E-value=5.9e-10 Score=85.10 Aligned_cols=64 Identities=20% Similarity=0.330 Sum_probs=58.3
Q ss_pred chhHHHHHHHHHHhhhhhhccChHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHHHHHHHH
Q 043345 4 NVDFTKVGGHVHQLKGSSSSIGAQRVNNVCTAFRSFCEERNIEGCQQYLQHLKQEYYLVKNKLQTL 69 (80)
Q Consensus 4 ~~D~~~~~~laH~LKGss~nlGa~~L~~~c~~lE~~~~~~~~~~~~~~~~~l~~~~~~l~~~L~~~ 69 (80)
.+|+..++..+|+|||+++++|+..|...|.+||..++.+++ ....++.|...|..+...|+.|
T Consensus 905 ~~d~~~~~~~~H~lkg~~~~~g~~~l~~~~~~le~~~~~~~~--~~~~~~~l~~~~~~~~~~l~~~ 968 (968)
T TIGR02956 905 VDDDAQIKKLAHKLKGSAGSLGLTQLTQLCQQLEKQGKTGAL--ELSDIDEIKQAWQASKTALDQW 968 (968)
T ss_pred CCCHHHHHHHHHHHHHHHHHhCHHHHHHHHHHHHHhcccCCc--chhHHHHHHHHHHHHHHHHHhC
Confidence 579999999999999999999999999999999999999887 4567899999999999988764
No 7
>PRK10618 phosphotransfer intermediate protein in two-component regulatory system with RcsBC; Provisional
Probab=98.98 E-value=2e-09 Score=83.32 Aligned_cols=61 Identities=16% Similarity=0.348 Sum_probs=55.8
Q ss_pred CchhHHHHHHHHHHhhhhhhccChHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHH
Q 043345 3 QNVDFTKVGGHVHQLKGSSSSIGAQRVNNVCTAFRSFCEERNIEGCQQYLQHLKQEYYLVK 63 (80)
Q Consensus 3 ~~~D~~~~~~laH~LKGss~nlGa~~L~~~c~~lE~~~~~~~~~~~~~~~~~l~~~~~~l~ 63 (80)
..+||..+...||+|||+++++|+..+.++|..||+.++.++..++...+.+|...+..+.
T Consensus 832 ~~~D~~~l~~~aHrLKG~~aml~l~~l~~~~~~LE~~i~~~~~~~i~~~i~~id~~v~~ll 892 (894)
T PRK10618 832 ATSDFASLAQTAHRLKGVFAMLNLVPGKQLCETLEHLIREKDEPGIENYISDIDSFVKSLL 892 (894)
T ss_pred hccCHHHHHHHHHHHHHHHHHcChHHHHHHHHHHHHHHhhCChHHHHHHHHHHHHHHHHHh
Confidence 3579999999999999999999999999999999999999999999888888888776654
No 8
>PRK11091 aerobic respiration control sensor protein ArcB; Provisional
Probab=98.86 E-value=8.9e-09 Score=77.65 Aligned_cols=70 Identities=17% Similarity=0.261 Sum_probs=65.7
Q ss_pred CchhHHHHHHHHHHhhhhhhccChHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 043345 3 QNVDFTKVGGHVHQLKGSSSSIGAQRVNNVCTAFRSFCEERNIEGCQQYLQHLKQEYYLVKNKLQTLFQV 72 (80)
Q Consensus 3 ~~~D~~~~~~laH~LKGss~nlGa~~L~~~c~~lE~~~~~~~~~~~~~~~~~l~~~~~~l~~~L~~~l~~ 72 (80)
+..|+..+...+|+|||+++++|+..|..+|..+|.....+.++....++++|..+|......|+.|+..
T Consensus 706 ~~~d~~~~~~~ah~l~g~~~~~g~~~l~~~~~~le~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~ 775 (779)
T PRK11091 706 TARDQKGIVEEAHKIKGAAGSVGLRHLQQLAQQIQSPDLPAWWDNVQDWVEELKNEWRHDVEVLKAWLAQ 775 (779)
T ss_pred HCCCHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHhCcCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3578899999999999999999999999999999999888889999999999999999999999999875
No 9
>PRK11107 hybrid sensory histidine kinase BarA; Provisional
Probab=98.25 E-value=7.8e-06 Score=62.30 Aligned_cols=67 Identities=21% Similarity=0.276 Sum_probs=55.4
Q ss_pred chhHHHHHHHHHHhhhhhhccChHHHHHHHHHHHHHHhhcC-HHHHHHHHHHHHHHHHHHHHHHHHHH
Q 043345 4 NVDFTKVGGHVHQLKGSSSSIGAQRVNNVCTAFRSFCEERN-IEGCQQYLQHLKQEYYLVKNKLQTLF 70 (80)
Q Consensus 4 ~~D~~~~~~laH~LKGss~nlGa~~L~~~c~~lE~~~~~~~-~~~~~~~~~~l~~~~~~l~~~L~~~l 70 (80)
..|+..+..++|++||+++++|+..+...|..+|..++.+. .+.+...+..+..++..+...+..++
T Consensus 850 ~~~~~~~~~~~h~l~g~~~~~g~~~l~~~~~~le~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 917 (919)
T PRK11107 850 GEDPEGLLDLIHKLHGSCSYSGVPRLKKLCQLIEQQLRSGTSVEDLEPELLELLDEMENVARAAKKVL 917 (919)
T ss_pred CCCHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHcCCChhhHHHHHHHHHHHHHHHHHHHHHHh
Confidence 46788999999999999999999999999999999998764 45666667777777777777776665
No 10
>PRK11466 hybrid sensory histidine kinase TorS; Provisional
Probab=98.17 E-value=3.6e-06 Score=64.40 Aligned_cols=38 Identities=29% Similarity=0.415 Sum_probs=35.4
Q ss_pred chhHHHHHHHHHHhhhhhhccChHHHHHHHHHHHHHHh
Q 043345 4 NVDFTKVGGHVHQLKGSSSSIGAQRVNNVCTAFRSFCE 41 (80)
Q Consensus 4 ~~D~~~~~~laH~LKGss~nlGa~~L~~~c~~lE~~~~ 41 (80)
.+|+..+...+|+|||+++++|+..+...|.++|..+.
T Consensus 849 ~~~~~~~~~~ah~lkg~~~~lg~~~l~~~~~~le~~~~ 886 (914)
T PRK11466 849 SQDSEKIKRAAHQLKSSCSSLGMRQASQACAQLEQQPL 886 (914)
T ss_pred CCCHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhCCCC
Confidence 47899999999999999999999999999999999764
No 11
>COG0643 CheA Chemotaxis protein histidine kinase and related kinases [Cell motility and secretion / Signal transduction mechanisms]
Probab=97.85 E-value=6.2e-05 Score=57.76 Aligned_cols=63 Identities=16% Similarity=0.269 Sum_probs=46.6
Q ss_pred hHHHHHHHHHHhhhhhhccChHHHHHHHHHHHHH---HhhcCHHHHHHHHHHHHHHHHHHHHHHHH
Q 043345 6 DFTKVGGHVHQLKGSSSSIGAQRVNNVCTAFRSF---CEERNIEGCQQYLQHLKQEYYLVKNKLQT 68 (80)
Q Consensus 6 D~~~~~~laH~LKGss~nlGa~~L~~~c~~lE~~---~~~~~~~~~~~~~~~l~~~~~~l~~~L~~ 68 (80)
....+.+.+|+|||+++.+|+..+..+|..+|.. .+++...--..++..+-.+.+.+...++.
T Consensus 40 ~ln~ifRaaHTlKG~a~~~g~~~l~~l~H~~E~~ld~~r~g~~~~~~~l~d~~l~~~D~l~~~~~~ 105 (716)
T COG0643 40 LLNAIFRAAHTLKGGAGTLGLTTLAELAHAMEDLLDALRNGELELTSELLDLLLEALDALEEMLDA 105 (716)
T ss_pred HHHHHHHHHHhhhhhhhhcChhHHHHHHHHHHHHHHHHhcCCccCcHHHHHHHhhhhHHHHHHHHh
Confidence 3567899999999999999999999999999975 46666554455555555555555554443
No 12
>PRK10547 chemotaxis protein CheA; Provisional
Probab=97.82 E-value=8.7e-05 Score=56.61 Aligned_cols=59 Identities=7% Similarity=0.191 Sum_probs=41.8
Q ss_pred hHHHHHHHHHHhhhhhhccChHHHHHHHHHHHHHH---hhcCHHHHHHHHHHHHHHHHHHHH
Q 043345 6 DFTKVGGHVHQLKGSSSSIGAQRVNNVCTAFRSFC---EERNIEGCQQYLQHLKQEYYLVKN 64 (80)
Q Consensus 6 D~~~~~~laH~LKGss~nlGa~~L~~~c~~lE~~~---~~~~~~~~~~~~~~l~~~~~~l~~ 64 (80)
....+.+.+|+|||+|+.+|+..|..+|..+|... |+|...-...++.-+-.+++.+..
T Consensus 37 ~in~lFRa~HTiKG~a~~~g~~~i~~l~H~~E~lld~vR~g~l~~~~~~~dlll~~~D~l~~ 98 (670)
T PRK10547 37 QLNAIFRAAHSIKGGAGTFGFTVLQETTHLMENLLDEARRGEMQLNTDIINLFLETKDIMQE 98 (670)
T ss_pred HHHHHHHHHHhhhhHHhhcCchHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHH
Confidence 35678899999999999999999999999999766 555433223344444444444433
No 13
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=97.06 E-value=0.0049 Score=48.90 Aligned_cols=67 Identities=12% Similarity=0.177 Sum_probs=53.6
Q ss_pred chhHHHHHHHHHHhhhhhhccChHHHHHHHHHHHHHHhhcC-HHHHHHHHHHHHHHHHHHHHHHHHHH
Q 043345 4 NVDFTKVGGHVHQLKGSSSSIGAQRVNNVCTAFRSFCEERN-IEGCQQYLQHLKQEYYLVKNKLQTLF 70 (80)
Q Consensus 4 ~~D~~~~~~laH~LKGss~nlGa~~L~~~c~~lE~~~~~~~-~~~~~~~~~~l~~~~~~l~~~L~~~l 70 (80)
.+|...+..++|+++|++..+|+..|...|.++|......+ .+.+...++.+...+..+...+..|+
T Consensus 1126 ~~~~~~~~~~~h~~~g~~~~l~~~~l~~~~~~~e~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~ 1193 (1197)
T PRK09959 1126 AGDNRTFHQCIHRIHGAANILNLQKLINISHQLEITPVSDDSKPEILQLLNSVKEHIAELDQEIAVFC 1193 (1197)
T ss_pred cCCHHHHHHHHHHHHHHHHHcCHHHHHHHHHHHHHhhhcCCchHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 35667889999999999999999999999999998886655 45667777777777766666666654
No 14
>PRK15347 two component system sensor kinase SsrA; Provisional
Probab=96.71 E-value=0.0049 Score=47.32 Aligned_cols=54 Identities=17% Similarity=0.201 Sum_probs=41.5
Q ss_pred HHHHHHHHhhhhhhccChHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHH
Q 043345 9 KVGGHVHQLKGSSSSIGAQRVNNVCTAFRSFCEERNIEGCQQYLQHLKQEYYLVK 63 (80)
Q Consensus 9 ~~~~laH~LKGss~nlGa~~L~~~c~~lE~~~~~~~~~~~~~~~~~l~~~~~~l~ 63 (80)
.+..++|.+||+++.+|+..+...|.++|..++.+...... .+..++..+..+.
T Consensus 862 ~l~~~~h~i~~~~~~~g~~~l~~~~~~~e~~~~~~~~~~~~-~~~~~~~~~~~~~ 915 (921)
T PRK15347 862 VLSQLLHTLKGCAGQAGLTELQCAVIDLENALETGEILSLE-ELTDLRELIHALF 915 (921)
T ss_pred HHHHHHHHHHHHHHHcCHHHHHHHHHHHHHHHhcCCCCCHH-HHHHHHHHHHHHh
Confidence 78899999999999999999999999999999876644322 2455555444433
No 15
>PF08900 DUF1845: Domain of unknown function (DUF1845); InterPro: IPR014996 Members of this protein family, such as PFL4669, are found in integrating conjugative elements (ICE) of the PFGI-1 class as in Pseudomonas fluorescens.
Probab=83.90 E-value=10 Score=25.36 Aligned_cols=54 Identities=13% Similarity=0.159 Sum_probs=36.6
Q ss_pred hhhhccChHHHHHHHHHHHHHHhhcCHHH------HHHHHHHHHHHHHHHHHHHHHHHHH
Q 043345 19 GSSSSIGAQRVNNVCTAFRSFCEERNIEG------CQQYLQHLKQEYYLVKNKLQTLFQV 72 (80)
Q Consensus 19 Gss~nlGa~~L~~~c~~lE~~~~~~~~~~------~~~~~~~l~~~~~~l~~~L~~~l~~ 72 (80)
|..+.+|.......+..|.+.+.+.|+-. +.+.++.+...+......|+..+..
T Consensus 32 ~~~~I~Gm~~~~~~~~~i~~~a~~DdPyAD~~L~~iEe~i~~~~~~l~~~~~~l~~~l~~ 91 (217)
T PF08900_consen 32 GKPAIIGMPGFASRLNRIWRDARQDDPYADWWLLRIEEKINEARQELQELIARLDALLAE 91 (217)
T ss_pred CCCCCcCHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 34488999999999999999998887432 3444555555555555555544443
No 16
>PF13779 DUF4175: Domain of unknown function (DUF4175)
Probab=81.71 E-value=4.6 Score=32.19 Aligned_cols=45 Identities=16% Similarity=0.297 Sum_probs=39.9
Q ss_pred hhhhccChHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHH
Q 043345 19 GSSSSIGAQRVNNVCTAFRSFCEERNIEGCQQYLQHLKQEYYLVK 63 (80)
Q Consensus 19 Gss~nlGa~~L~~~c~~lE~~~~~~~~~~~~~~~~~l~~~~~~l~ 63 (80)
+.+.+++-..|.++..+||+.+++|+.+++..++++|++-++.++
T Consensus 530 ~~~~~~~~~dL~~mmd~ie~la~~G~~~~A~q~L~qlq~mmenmq 574 (820)
T PF13779_consen 530 GNSQMMSQQDLQRMMDRIEELARSGRMDEARQLLEQLQQMMENMQ 574 (820)
T ss_pred hhhhccCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHhcc
Confidence 456689999999999999999999999999999999988877654
No 17
>PF14276 DUF4363: Domain of unknown function (DUF4363)
Probab=78.16 E-value=5.3 Score=23.87 Aligned_cols=49 Identities=14% Similarity=0.179 Sum_probs=39.2
Q ss_pred HHHHhhhhhhccChHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHHHHH
Q 043345 13 HVHQLKGSSSSIGAQRVNNVCTAFRSFCEERNIEGCQQYLQHLKQEYYLVKNKL 66 (80)
Q Consensus 13 laH~LKGss~nlGa~~L~~~c~~lE~~~~~~~~~~~~~~~~~l~~~~~~l~~~L 66 (80)
..|.+++++ ..+...+..+|+...++|++.+...++.+...+......+
T Consensus 17 ~~~~l~~~~-----~~i~~~l~~i~~~i~~~dW~~A~~~~~~l~~~W~k~~~~~ 65 (121)
T PF14276_consen 17 SNNYLNNST-----DSIEEQLEQIEEAIENEDWEKAYKETEELEKEWDKNKKRW 65 (121)
T ss_pred HHhhhhhHH-----HHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhhchhe
Confidence 346666664 5667889999999999999999999999999988765543
No 18
>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=77.21 E-value=9 Score=30.78 Aligned_cols=44 Identities=14% Similarity=0.230 Sum_probs=39.7
Q ss_pred hhccChHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHHH
Q 043345 21 SSSIGAQRVNNVCTAFRSFCEERNIEGCQQYLQHLKQEYYLVKN 64 (80)
Q Consensus 21 s~nlGa~~L~~~c~~lE~~~~~~~~~~~~~~~~~l~~~~~~l~~ 64 (80)
+.+|+-..|-++..+||+.+++|+.+++.+++++|++-++.++.
T Consensus 562 ~~~l~~~dLq~Mmd~ieela~~G~~~~A~qlL~qlq~mmenlq~ 605 (851)
T TIGR02302 562 TKVLRQQDLQNMMDQIENLARSGDRDQAKQLLSQLQQMMNNLQM 605 (851)
T ss_pred ccccCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHhc
Confidence 45688999999999999999999999999999999998888763
No 19
>PLN02956 PSII-Q subunit
Probab=72.92 E-value=24 Score=23.32 Aligned_cols=39 Identities=8% Similarity=0.114 Sum_probs=27.1
Q ss_pred HHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHHHH
Q 043345 27 QRVNNVCTAFRSFCEERNIEGCQQYLQHLKQEYYLVKNK 65 (80)
Q Consensus 27 ~~L~~~c~~lE~~~~~~~~~~~~~~~~~l~~~~~~l~~~ 65 (80)
..|.+...+|..+++..|.......+......|+.+..+
T Consensus 146 ~~LFd~l~~LD~AAR~kd~~~a~k~Y~~tva~lD~Vl~~ 184 (185)
T PLN02956 146 SDLFNSVTKLDYAARDKDETRVWEYYENIVASLDDIFSR 184 (185)
T ss_pred HHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHhc
Confidence 445566678888888888777777777666666666543
No 20
>smart00388 HisKA His Kinase A (phosphoacceptor) domain. Dimerisation and phosphoacceptor domain of histidine kinases.
Probab=72.34 E-value=10 Score=18.61 Aligned_cols=58 Identities=12% Similarity=0.174 Sum_probs=31.8
Q ss_pred HHHHHHHHhhhhhhccChHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 043345 9 KVGGHVHQLKGSSSSIGAQRVNNVCTAFRSFCEERNIEGCQQYLQHLKQEYYLVKNKLQTLFQVCL 74 (80)
Q Consensus 9 ~~~~laH~LKGss~nlGa~~L~~~c~~lE~~~~~~~~~~~~~~~~~l~~~~~~l~~~L~~~l~~~~ 74 (80)
-+..++|.||..-+.+ ...+..+.. ....+.....+..+......+..-+..++...+
T Consensus 5 ~~~~i~Hel~~pl~~i-----~~~~~~l~~---~~~~~~~~~~~~~~~~~~~~~~~~v~~l~~~~~ 62 (66)
T smart00388 5 FLANLSHELRTPLTAI-----RGYLELLED---TELSEEQREYLETILRSAERLLRLINDLLDLSR 62 (66)
T ss_pred HHHHHHHhccCcHHHH-----HHHHHHHHh---CCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3566889999544322 122222322 122222266677777777777777766665543
No 21
>COG2991 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=70.81 E-value=0.8 Score=25.91 Aligned_cols=26 Identities=31% Similarity=0.632 Sum_probs=20.9
Q ss_pred HhhhhhhccChHHHHHHHHHHHHHHhh
Q 043345 16 QLKGSSSSIGAQRVNNVCTAFRSFCEE 42 (80)
Q Consensus 16 ~LKGss~nlGa~~L~~~c~~lE~~~~~ 42 (80)
.||||+|-|++..+...|. -++-|.+
T Consensus 28 ~I~GSCGGi~alGi~K~Cd-C~~pCDt 53 (77)
T COG2991 28 SIKGSCGGIAALGIEKVCD-CDEPCDT 53 (77)
T ss_pred ccccccccHHhhccchhcC-CCCchHH
Confidence 6899999999999999887 4555544
No 22
>TIGR03761 ICE_PFL4669 integrating conjugative element protein, PFL_4669 family. Members of this protein family, such as PFL4669, are found in integrating conjugative elements (ICE) of the PFGI-1 class as in Pseudomonas fluorescens.
Probab=69.37 E-value=32 Score=23.21 Aligned_cols=51 Identities=16% Similarity=0.165 Sum_probs=35.6
Q ss_pred hhccChHHHHHHHHHHHHHHhhcCHHH------HHHHHHHHHHHHHHHHHHHHHHHH
Q 043345 21 SSSIGAQRVNNVCTAFRSFCEERNIEG------CQQYLQHLKQEYYLVKNKLQTLFQ 71 (80)
Q Consensus 21 s~nlGa~~L~~~c~~lE~~~~~~~~~~------~~~~~~~l~~~~~~l~~~L~~~l~ 71 (80)
.+.+|.+.....+..|.+.+.+.|+-. +...++.+...++.+...++..+.
T Consensus 32 ~~IiGl~~f~s~~~~i~~~a~~DdPyAD~~Ll~~E~~l~~~~~~l~~~~~~l~~~l~ 88 (216)
T TIGR03761 32 PGIIGMPGFISRLNRINQASEQDDPYADWALLRIEEKLLSARQEMQALLQRLDDLLA 88 (216)
T ss_pred CCCcCcHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 468999999999999999999888532 344455555555555555555444
No 23
>PF03670 UPF0184: Uncharacterised protein family (UPF0184); InterPro: IPR022788 This family of proteins has no known function.
Probab=69.06 E-value=20 Score=20.72 Aligned_cols=37 Identities=19% Similarity=0.206 Sum_probs=29.1
Q ss_pred hhcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 043345 41 EERNIEGCQQYLQHLKQEYYLVKNKLQTLFQVCLKSL 77 (80)
Q Consensus 41 ~~~~~~~~~~~~~~l~~~~~~l~~~L~~~l~~~~~~~ 77 (80)
-+...+.+..+++.|++--..|...|..+|+..||+-
T Consensus 31 ins~LD~Lns~LD~LE~rnD~l~~~L~~LLesnrq~R 67 (83)
T PF03670_consen 31 INSMLDQLNSCLDHLEQRNDHLHAQLQELLESNRQIR 67 (83)
T ss_pred HHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHH
Confidence 3344667777888888888889999999999888864
No 24
>PF03993 DUF349: Domain of Unknown Function (DUF349); InterPro: IPR007139 This motif is found singly or as up to five tandem repeats in a small set of bacterial proteins. There are two or three alpha-helices, and possibly a beta-strand.
Probab=68.75 E-value=13 Score=20.05 Aligned_cols=32 Identities=13% Similarity=0.240 Sum_probs=18.3
Q ss_pred HHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHH
Q 043345 30 NNVCTAFRSFCEERNIEGCQQYLQHLKQEYYL 61 (80)
Q Consensus 30 ~~~c~~lE~~~~~~~~~~~~~~~~~l~~~~~~ 61 (80)
-.+|.+++......++......+..|...|..
T Consensus 37 ~~Li~~~~~l~~~~d~~~~~~~~k~l~~~Wk~ 68 (77)
T PF03993_consen 37 EALIEEAEALAESEDWKEAAEEIKELQQEWKE 68 (77)
T ss_pred HHHHHHHHHhcccccHHHHHHHHHHHHHHHHH
Confidence 35666666666666655555555555555543
No 25
>PF07361 Cytochrom_B562: Cytochrome b562; InterPro: IPR009155 Cytochrome b562 is a haem-containing protein that is expressed in the periplasm of Escherichia coli. In b-type cytochromes, the haem atom is not covalently attached to the polypeptide. Cytochrome b562 has a four-helical bundle structure that is structurally similar to that found in members of the cytochrome c family (IPR002321 from INTERPRO). Cytochrome b562 has a reduction potential of 167 mV, which sets the energy yield possible in metabolism and is also a key determinant of the rate at which redox reactions proceed [].; GO: 0005506 iron ion binding, 0009055 electron carrier activity, 0020037 heme binding, 0042597 periplasmic space; PDB: 4ER9_A 3IQ6_G 2QLA_B 3FOO_A 3M79_C 256B_A 3NMI_F 3HNK_A 3NMK_D 2BC5_A ....
Probab=65.15 E-value=16 Score=21.53 Aligned_cols=33 Identities=12% Similarity=0.249 Sum_probs=24.5
Q ss_pred cChHHHHHHHHHHHHHHhhcCHHHHHHHHHHHH
Q 043345 24 IGAQRVNNVCTAFRSFCEERNIEGCQQYLQHLK 56 (80)
Q Consensus 24 lGa~~L~~~c~~lE~~~~~~~~~~~~~~~~~l~ 56 (80)
=|...|......++..+.+|+.+++...+..|.
T Consensus 60 ~Gl~~li~~id~a~~~~~~G~l~~AK~~l~~l~ 92 (103)
T PF07361_consen 60 EGLDKLIDQIDKAEALAEAGKLDEAKAALKKLD 92 (103)
T ss_dssp HHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence 467778888888888888888887766654443
No 26
>PF00512 HisKA: His Kinase A (phospho-acceptor) domain; InterPro: IPR003661 Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions []. Some bacteria can contain up to as many as 200 two-component systems that need tight regulation to prevent unwanted cross-talk []. These pathways have been adapted to response to a wide variety of stimuli, including nutrients, cellular redox state, changes in osmolarity, quorum signals, antibiotics, and more []. Two-component systems are comprised of a sensor histidine kinase (HK) and its cognate response regulator (RR) []. The HK catalyses its own auto-phosphorylation followed by the transfer of the phosphoryl group to the receiver domain on RR; phosphorylation of the RR usually activates an attached output domain, which can then effect changes in cellular physiology, often by regulating gene expression. Some HK are bifunctional, catalysing both the phosphorylation and dephosphorylation of their cognate RR. The input stimuli can regulate either the kinase or phosphatase activity of the bifunctional HK. A variant of the two-component system is the phospho-relay system. Here a hybrid HK auto-phosphorylates and then transfers the phosphoryl group to an internal receiver domain, rather than to a separate RR protein. The phosphoryl group is then shuttled to histidine phosphotransferase (HPT) and subsequently to a terminal RR, which can evoke the desired response [, ]. Signal transducing histidine kinases are the key elements in two-component signal transduction systems, which control complex processes such as the initiation of development in microorganisms [, ]. Examples of histidine kinases are EnvZ, which plays a central role in osmoregulation [], and CheA, which plays a central role in the chemotaxis system []. Histidine kinases usually have an N-terminal ligand-binding domain and a C-terminal kinase domain, but other domains may also be present. The kinase domain is responsible for the autophosphorylation of the histidine with ATP, the phosphotransfer from the kinase to an aspartate of the response regulator, and (with bifunctional enzymes) the phosphotransfer from aspartyl phosphate back to ADP or to water []. The kinase core has a unique fold, distinct from that of the Ser/Thr/Tyr kinase superfamily. HKs can be roughly divided into two classes: orthodox and hybrid kinases [, ]. Most orthodox HKs, typified by the Escherichia coli EnvZ protein, function as periplasmic membrane receptors and have a signal peptide and transmembrane segment(s) that separate the protein into a periplasmic N-terminal sensing domain and a highly conserved cytoplasmic C-terminal kinase core. Members of this family, however, have an integral membrane sensor domain. Not all orthodox kinases are membrane bound, e.g., the nitrogen regulatory kinase NtrB (GlnL) is a soluble cytoplasmic HK []. Hybrid kinases contain multiple phosphodonor and phosphoacceptor sites and use multi-step phospho-relay schemes instead of promoting a single phosphoryl transfer. In addition to the sensor domain and kinase core, they contain a CheY-like receiver domain and a His-containing phosphotransfer (HPt) domain. This entry represents the dimerisation and phosphoacceptor domain found in histidine kinases. It has been found in bacterial sensor protein/histidine kinases. Signal transducing histidine kinases are the key elements in two-component signal transduction systems, which control complex processes such as the initiation of development in microorganisms []. Examples of histidine kinases are EnvZ, which plays a central role in osmoregulation [], and CheA, which plays a central role in the chemotaxis system []. Histidine kinases usually have an N-terminal ligand-binding domain and a C-terminal kinase domain, but other domains may also be present. The kinase domain is responsible for the autophosphorylation of the histidine with ATP, the phosphotransfer from the kinase to an aspartate of the response regulator, and the phosphotransfer from aspartyl phosphate back to ADP or to water []. The homodimeric domain includes the site of histidine autophosphorylation and phosphate transfer reactions. The structure of the homodimeric domain comprises a closed, four-helical bundle with a left-handed twist, formed by two identical alpha-hairpin subunits.; GO: 0000155 two-component sensor activity, 0007165 signal transduction, 0016020 membrane; PDB: 3DGE_A 2C2A_A 3A0R_A 4EW8_A 2LFS_B 2LFR_B 3JZ3_A 1JOY_B 3ZRW_C 3ZRV_A ....
Probab=65.13 E-value=18 Score=18.73 Aligned_cols=58 Identities=9% Similarity=0.143 Sum_probs=39.6
Q ss_pred HHHHHHHHhhhhhhccChHHHHHHHHHHHHHHh-hcCHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 043345 9 KVGGHVHQLKGSSSSIGAQRVNNVCTAFRSFCE-ERNIEG-CQQYLQHLKQEYYLVKNKLQTLFQVCL 74 (80)
Q Consensus 9 ~~~~laH~LKGss~nlGa~~L~~~c~~lE~~~~-~~~~~~-~~~~~~~l~~~~~~l~~~L~~~l~~~~ 74 (80)
-+..++|-||. +|..+...++.... ....++ ....+..+..+..++..-++.++.+-|
T Consensus 5 ~~~~isHelr~--------PL~~i~~~~~~l~~~~~~~~~~~~~~l~~i~~~~~~l~~li~~ll~~sr 64 (68)
T PF00512_consen 5 FLASISHELRN--------PLTAIRGYLELLERDSDLDPEQLREYLDRIRSAADRLNELINDLLDFSR 64 (68)
T ss_dssp HHHHHHHHHHH--------HHHHHHHHHHHHHCSSCC-HHHCHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHhHHHHH--------HHHHHHHHHHHHHHccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 45678888885 44444455555444 333333 488899999999999998888887654
No 27
>KOG2424 consensus Protein involved in transcription start site selection [Transcription]
Probab=64.56 E-value=15 Score=24.34 Aligned_cols=24 Identities=17% Similarity=0.552 Sum_probs=18.7
Q ss_pred hhccChHHHHHHHHHHHHHHhhcCHH
Q 043345 21 SSSIGAQRVNNVCTAFRSFCEERNIE 46 (80)
Q Consensus 21 s~nlGa~~L~~~c~~lE~~~~~~~~~ 46 (80)
-+.+||.-+.++|..|+. ++.+++
T Consensus 147 dA~~Gaf~I~elcq~l~~--~s~d~E 170 (195)
T KOG2424|consen 147 DATLGAFLILELCQCLQA--QSDDLE 170 (195)
T ss_pred hhhhhHHHHHHHHHHHHh--ccccHH
Confidence 467999999999999987 444433
No 28
>PF04837 MbeB_N: MbeB-like, N-term conserved region; InterPro: IPR006922 This family consists of Mbe/Mob proteins defined by an N-terminal conserved region. These proteins are essential for specific plasmid transfer.
Probab=64.36 E-value=19 Score=18.91 Aligned_cols=48 Identities=13% Similarity=0.202 Sum_probs=36.3
Q ss_pred HHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhc
Q 043345 28 RVNNVCTAFRSFCEERNIEGCQQYLQHLKQEYYLVKNKLQTLFQVCLKSLAS 79 (80)
Q Consensus 28 ~L~~~c~~lE~~~~~~~~~~~~~~~~~l~~~~~~l~~~L~~~l~~~~~~~~~ 79 (80)
.+..++..+|+..+. .....=..|+.+|.+....|..-|....+.+.+
T Consensus 3 ~il~LA~~feqkske----qa~ste~~vk~af~~~E~~l~~~L~~s~~~is~ 50 (52)
T PF04837_consen 3 EILNLAKDFEQKSKE----QAESTEQMVKNAFEQHEKSLSAALKESEQKISD 50 (52)
T ss_pred HHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHhHHHhhh
Confidence 467788888887765 455566778889999999888888876666653
No 29
>KOG3232 consensus Vacuolar assembly/sorting protein DID2 [Intracellular trafficking, secretion, and vesicular transport]
Probab=63.50 E-value=41 Score=22.31 Aligned_cols=40 Identities=13% Similarity=0.228 Sum_probs=33.9
Q ss_pred HHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHHHHHH
Q 043345 28 RVNNVCTAFRSFCEERNIEGCQQYLQHLKQEYYLVKNKLQ 67 (80)
Q Consensus 28 ~L~~~c~~lE~~~~~~~~~~~~~~~~~l~~~~~~l~~~L~ 67 (80)
.|...|..++.+.+..|.+.+..+++..+..|..+...-.
T Consensus 94 sM~gVvK~md~alktmNLekis~~MDkFE~qFedldvqt~ 133 (203)
T KOG3232|consen 94 SMAGVVKSMDSALKTMNLEKISQLMDKFEKQFEDLDVQTE 133 (203)
T ss_pred HHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHhhhhhhHHH
Confidence 3677899999999999999999999999999988765433
No 30
>PF04722 Ssu72: Ssu72-like protein; InterPro: IPR006811 The highly conserved and essential protein Ssu72 has intrinsic phosphatase activity and plays an essential role in the transcription cycle. Ssu72 was originally identified in a yeast genetic screen as enhancer of a defect caused by a mutation in the transcription initiation factor TFIIB []. It binds to TFIIB and is also involved in mRNA elongation. Ssu72 is further involved in both poly(A) dependent and independent termination. It is a subunit of the yeast cleavage and polyadenylation factor (CPF), which is part of the machinery for mRNA 3'-end formation. Ssu72 is also essential for transcription termination of snRNAs [].; GO: 0004721 phosphoprotein phosphatase activity, 0006397 mRNA processing, 0005634 nucleus; PDB: 3O2S_B 3O2Q_E 3FMV_H 3OMW_D 3P9Y_B 3FDF_A 3OMX_A.
Probab=58.61 E-value=23 Score=23.64 Aligned_cols=36 Identities=19% Similarity=0.422 Sum_probs=22.7
Q ss_pred hhccChHHHHHHHHHHHHHHhhcCHH-HHHHHHHHHHH
Q 043345 21 SSSIGAQRVNNVCTAFRSFCEERNIE-GCQQYLQHLKQ 57 (80)
Q Consensus 21 s~nlGa~~L~~~c~~lE~~~~~~~~~-~~~~~~~~l~~ 57 (80)
-+.+||..+.++|..|+. ....+++ .+..++.+.+.
T Consensus 145 eA~~Ga~~ileLc~~l~~-~~~~d~e~~i~~il~~fe~ 181 (195)
T PF04722_consen 145 EATIGAFLILELCQMLEE-EASEDLEDEIDEILQEFEE 181 (195)
T ss_dssp HHHHHHHHHHHHHHHHH---TSSSHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHh-hccccHHHHHHHHHHHHHH
Confidence 367899999999999997 3344544 34444444443
No 31
>PRK13858 type IV secretion system T-DNA border endonuclease VirD1; Provisional
Probab=56.82 E-value=49 Score=21.10 Aligned_cols=62 Identities=13% Similarity=0.205 Sum_probs=40.8
Q ss_pred HHHHHHHHHhhhhhhccChHHHHHHHHHHHHHHhhc--CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 043345 8 TKVGGHVHQLKGSSSSIGAQRVNNVCTAFRSFCEER--NIEGCQQYLQHLKQEYYLVKNKLQTLFQVCLKSL 77 (80)
Q Consensus 8 ~~~~~laH~LKGss~nlGa~~L~~~c~~lE~~~~~~--~~~~~~~~~~~l~~~~~~l~~~L~~~l~~~~~~~ 77 (80)
+.+..+...|.|-++|| ++|+..|.+ .+ +.+.+..--..+-.+|..+..-|...|...|..+
T Consensus 73 e~~~~lir~l~gianNL--NQLAr~aN~------~~~~~~~~l~~er~~~g~~~~~l~~~l~~~~~vsrrr~ 136 (147)
T PRK13858 73 EKMEAILQSIGTLSSNI--AALLSAYAE------NPRPDLEALRAERIAFGKEFADLDGLLRSILSVSRRRI 136 (147)
T ss_pred HHHHHHHHHHHHHHHHH--HHHHHHHhc------CCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence 34556777777777775 444444444 22 2555666667778888888888888888877654
No 32
>PF05757 PsbQ: Oxygen evolving enhancer protein 3 (PsbQ); InterPro: IPR008797 Oxygenic photosynthesis uses two multi-subunit photosystems (I and II) located in the cell membranes of cyanobacteria and in the thylakoid membranes of chloroplasts in plants and algae. Photosystem II (PSII) has a P680 reaction centre containing chlorophyll 'a' that uses light energy to carry out the oxidation (splitting) of water molecules, and to produce ATP via a proton pump. Photosystem I (PSI) has a P700 reaction centre containing chlorophyll that takes the electron and associated hydrogen donated from PSII to reduce NADP+ to NADPH. Both ATP and NADPH are subsequently used in the light-independent reactions to convert carbon dioxide to glucose using the hydrogen atom extracted from water by PSII, releasing oxygen as a by-product. PSII is a multisubunit protein-pigment complex containing polypeptides both intrinsic and extrinsic to the photosynthetic membrane [, ]. Within the core of the complex, the chlorophyll and beta-carotene pigments are mainly bound to the antenna proteins CP43 (PsbC) and CP47 (PsbB), which pass the excitation energy on to the reaction centre proteins D1 (Qb, PsbA) and D2 (Qa, PsbD) that bind all the redox-active cofactors involved in the energy conversion process. The PSII oxygen-evolving complex (OEC) oxidises water to provide protons for use by PSI, and consists of OEE1 (PsbO), OEE2 (PsbP) and OEE3 (PsbQ). The remaining subunits in PSII are of low molecular weight (less than 10 kDa), and are involved in PSII assembly, stabilisation, dimerisation, and photo-protection []. In PSII, the oxygen-evolving complex (OEC) is responsible for catalysing the splitting of water to O(2) and 4H+. The OEC is composed of a cluster of manganese, calcium and chloride ions bound to extrinsic proteins. In cyanobacteria there are five extrinsic proteins in OEC (PsbO, PsbP-like, PsbQ-like, PsbU and PsbV), while in plants there are only three (PsbO, PsbP and PsbQ), PsbU and PsbV having been lost during the evolution of green plants []. This family represents the PSII OEC protein PsbQ. Both PsbQ and PsbP (IPR002683 from INTERPRO) are regulators that are necessary for the biogenesis of optically active PSII. The crystal structure of PsbQ from spinach revealed a 4-helical bundle polypeptide. The distribution of positive and negative charges on the protein surface might explain the ability of PsbQ to increase the binding of chloride and calcium ions and make them available to PSII [].; GO: 0005509 calcium ion binding, 0015979 photosynthesis, 0009523 photosystem II, 0009654 oxygen evolving complex, 0019898 extrinsic to membrane; PDB: 1VYK_A 1NZE_A 3LS1_A 3LS0_A.
Probab=55.77 E-value=42 Score=22.42 Aligned_cols=38 Identities=5% Similarity=0.106 Sum_probs=27.5
Q ss_pred HHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHHH
Q 043345 27 QRVNNVCTAFRSFCEERNIEGCQQYLQHLKQEYYLVKN 64 (80)
Q Consensus 27 ~~L~~~c~~lE~~~~~~~~~~~~~~~~~l~~~~~~l~~ 64 (80)
..|.....+|..+++..|...+...++.....++.+..
T Consensus 162 ~~lf~~ie~LD~Aar~K~~~~a~~~Y~~t~~~Ldevla 199 (202)
T PF05757_consen 162 NKLFDNIEELDYAARSKDVPEAEKYYADTVKALDEVLA 199 (202)
T ss_dssp HHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHC
T ss_pred HHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 56777788888888998888777777766666666544
No 33
>PF12854 PPR_1: PPR repeat
Probab=55.66 E-value=15 Score=16.91 Aligned_cols=22 Identities=9% Similarity=0.459 Sum_probs=17.2
Q ss_pred HHHHHHHhhcCHHHHHHHHHHH
Q 043345 34 TAFRSFCEERNIEGCQQYLQHL 55 (80)
Q Consensus 34 ~~lE~~~~~~~~~~~~~~~~~l 55 (80)
.-|.-.|+.|..+++..+++++
T Consensus 12 ~lI~~~Ck~G~~~~A~~l~~~M 33 (34)
T PF12854_consen 12 TLIDGYCKAGRVDEAFELFDEM 33 (34)
T ss_pred HHHHHHHHCCCHHHHHHHHHhC
Confidence 3456688999999988888764
No 34
>PF09577 Spore_YpjB: Sporulation protein YpjB (SpoYpjB); InterPro: IPR014231 Proteins in thie entry, typified by YpjB, are restricted to a subset of the endospore-forming bacteria which includes Bacillus species, but not species. In Bacillus subtilis, ypjB was found to be part of the sigma-E regulon []. Sigma-E is a sporulation sigma factor that regulates expression in the mother cell compartment. Null mutants of ypjB show a sporulation defect, but this gene is not, however, a part of the endospore formation minimal gene set.
Probab=53.85 E-value=58 Score=22.20 Aligned_cols=40 Identities=13% Similarity=0.233 Sum_probs=31.6
Q ss_pred HHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHHHHHH
Q 043345 28 RVNNVCTAFRSFCEERNIEGCQQYLQHLKQEYYLVKNKLQ 67 (80)
Q Consensus 28 ~L~~~c~~lE~~~~~~~~~~~~~~~~~l~~~~~~l~~~L~ 67 (80)
.|.+....+++++..|+.......++.+...|..+...+.
T Consensus 102 ~i~~~~~~mk~a~~~~~~~~f~~~~n~f~~~y~~I~Psl~ 141 (232)
T PF09577_consen 102 PIMEDFQRMKQAAQKGDKEAFRASLNEFLSHYELIRPSLT 141 (232)
T ss_pred HHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhcchhh
Confidence 4667778888989888988888888888888877765543
No 35
>PF04400 DUF539: Protein of unknown function (DUF539); InterPro: IPR007495 This is a family of putative periplasmic proteins.
Probab=52.23 E-value=1.1 Score=23.00 Aligned_cols=19 Identities=32% Similarity=0.709 Sum_probs=15.5
Q ss_pred HhhhhhhccChHHHHHHHH
Q 043345 16 QLKGSSSSIGAQRVNNVCT 34 (80)
Q Consensus 16 ~LKGss~nlGa~~L~~~c~ 34 (80)
.|+||+|-|++..+-..|.
T Consensus 7 ~I~GSCGGl~~lGi~~~C~ 25 (45)
T PF04400_consen 7 PIKGSCGGLGALGIDKECD 25 (45)
T ss_pred cccccchhhhhcCCCccCC
Confidence 5899999999887766666
No 36
>PF07870 DUF1657: Protein of unknown function (DUF1657); InterPro: IPR012452 This domain appears to be restricted to the Bacillales.
Probab=52.20 E-value=33 Score=17.66 Aligned_cols=36 Identities=11% Similarity=0.175 Sum_probs=27.7
Q ss_pred HHHHHHHhhcCHHHHHHHHHHHHHHHHHHHHHHHHH
Q 043345 34 TAFRSFCEERNIEGCQQYLQHLKQEYYLVKNKLQTL 69 (80)
Q Consensus 34 ~~lE~~~~~~~~~~~~~~~~~l~~~~~~l~~~L~~~ 69 (80)
..+|.++-.-+-+.+..++.+....+..+...|+.+
T Consensus 14 A~Le~fal~T~d~~AK~~y~~~a~~l~~ii~~L~~r 49 (50)
T PF07870_consen 14 ADLETFALQTQDQEAKQMYEQAAQQLEEIIQDLEPR 49 (50)
T ss_pred hhHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHhHcc
Confidence 667888866666677888999888888888877644
No 37
>PF14077 WD40_alt: Alternative WD40 repeat motif
Probab=49.94 E-value=29 Score=17.89 Aligned_cols=36 Identities=14% Similarity=0.225 Sum_probs=28.4
Q ss_pred cCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 043345 43 RNIEGCQQYLQHLKQEYYLVKNKLQTLFQVCLKSLA 78 (80)
Q Consensus 43 ~~~~~~~~~~~~l~~~~~~l~~~L~~~l~~~~~~~~ 78 (80)
|+-+.....+..|+.++..++..=...+.+.-+|++
T Consensus 11 G~~e~l~vrv~eLEeEV~~LrKINrdLfdFSt~iiT 46 (48)
T PF14077_consen 11 GDQEQLRVRVSELEEEVRTLRKINRDLFDFSTRIIT 46 (48)
T ss_pred CCcchheeeHHHHHHHHHHHHHHhHHHHhhhhhhcc
Confidence 455566677889999999988866788888888876
No 38
>COG2178 Predicted RNA-binding protein of the translin family [Translation, ribosomal structure and biogenesis]
Probab=48.33 E-value=83 Score=21.18 Aligned_cols=43 Identities=9% Similarity=0.103 Sum_probs=34.1
Q ss_pred HHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHHHHHHHH
Q 043345 27 QRVNNVCTAFRSFCEERNIEGCQQYLQHLKQEYYLVKNKLQTL 69 (80)
Q Consensus 27 ~~L~~~c~~lE~~~~~~~~~~~~~~~~~l~~~~~~l~~~L~~~ 69 (80)
..+...|...--+.+.++.+.+...+......+..++..|..|
T Consensus 27 Rei~r~s~~aI~~~H~~~~eeA~~~l~~a~~~v~~Lk~~l~~~ 69 (204)
T COG2178 27 REIVRLSGEAIFLLHRGDFEEAEKKLKKASEAVEKLKRLLAGF 69 (204)
T ss_pred HHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence 4566777777788888998888888888888888888777655
No 39
>cd00082 HisKA Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via trans-autophosphorylation by the catalytic domain of the histidine kinase. They subsequently transfer the phosphoryl group to the Asp acceptor residue of a response regulator protein. Two-component signalling systems, consisting of a histidine protein kinase that senses a signal input and a response regulator that mediates the output, are ancient and evolutionarily conserved signaling mechanisms in prokaryotes and eukaryotes.
Probab=46.13 E-value=35 Score=16.25 Aligned_cols=55 Identities=20% Similarity=0.250 Sum_probs=28.4
Q ss_pred HHHHHHHHhhhhhhccChHHHHHHHHHHHHHHhhcC-HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 043345 9 KVGGHVHQLKGSSSSIGAQRVNNVCTAFRSFCEERN-IEGCQQYLQHLKQEYYLVKNKLQTLFQ 71 (80)
Q Consensus 9 ~~~~laH~LKGss~nlGa~~L~~~c~~lE~~~~~~~-~~~~~~~~~~l~~~~~~l~~~L~~~l~ 71 (80)
-+..++|.||..-+.+ -..++....... .+.....+..+......+..-++.++.
T Consensus 7 ~~~~~~hel~~pl~~i--------~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~ 62 (65)
T cd00082 7 FLANVSHELRTPLTAI--------RGALELLEEELLDDEEQREYLERIREEAERLLRLINDLLD 62 (65)
T ss_pred HHHHHhHHhcchHHHH--------HHHHHHHHhcccCcHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3566889998543322 222222221111 344556666666666666665555544
No 40
>PF09403 FadA: Adhesion protein FadA; InterPro: IPR018543 FadA (Fusobacterium adhesin A) is an adhesin which forms two alpha helices. ; PDB: 3ETZ_B 3ETY_A 2GL2_B 3ETX_C 3ETW_A.
Probab=45.08 E-value=74 Score=19.68 Aligned_cols=9 Identities=44% Similarity=0.302 Sum_probs=0.0
Q ss_pred hhhccChHH
Q 043345 20 SSSSIGAQR 28 (80)
Q Consensus 20 ss~nlGa~~ 28 (80)
||.+++|+.
T Consensus 13 ss~sfaA~~ 21 (126)
T PF09403_consen 13 SSISFAATA 21 (126)
T ss_dssp ---------
T ss_pred HHHHHHccc
Confidence 455666666
No 41
>PF01535 PPR: PPR repeat; InterPro: IPR002885 This entry represents the PPR repeat. Pentatricopeptide repeat (PPR) proteins are characterised by tandem repeats of a degenerate 35 amino acid motif []. Most of PPR proteins have roles in mitochondria or plastid []. PPR repeats were discovered while screening Arabidopsis proteins for those predicted to be targeted to mitochondria or chloroplast [, ]. Some of these proteins have been shown to play a role in post-transcriptional processes within organelles and they are thought to be sequence-specific RNA-binding proteins [, , ]. Plant genomes have between one hundred to five hundred PPR genes per genome whereas non-plant genomes encode two to six PPR proteins. Although no PPR structures are yet known, the motif is predicted to fold into a helix-turn-helix structure similar to those found in the tetratricopeptide repeat (TPR) family (see PDOC50005 from PROSITEDOC) []. The plant PPR protein family has been divided in two subfamilies on the basis of their motif content and organisation [, ]. Examples of PPR repeat-containing proteins include PET309 P32522 from SWISSPROT, which may be involved in RNA stabilisation [], and crp1, which is involved in RNA processing []. The repeat is associated with a predicted plant protein O49549 from SWISSPROT that has a domain organisation similar to the human BRCA1 protein.
Probab=44.72 E-value=28 Score=14.67 Aligned_cols=22 Identities=9% Similarity=0.463 Sum_probs=16.1
Q ss_pred HHHHHhhcCHHHHHHHHHHHHH
Q 043345 36 FRSFCEERNIEGCQQYLQHLKQ 57 (80)
Q Consensus 36 lE~~~~~~~~~~~~~~~~~l~~ 57 (80)
|.-.++.++.+++..++.++.+
T Consensus 7 i~~~~~~~~~~~a~~~~~~M~~ 28 (31)
T PF01535_consen 7 ISGYCKMGQFEEALEVFDEMRE 28 (31)
T ss_pred HHHHHccchHHHHHHHHHHHhH
Confidence 5566788888888888777654
No 42
>PF00435 Spectrin: Spectrin repeat; InterPro: IPR002017 Spectrin repeats [] are found in several proteins involved in cytoskeletal structure. These include spectrin alpha and beta subunits [, ], alpha-actinin [] and dystrophin. The spectrin repeat forms a three-helix bundle. The second helix is interrupted by proline in some sequences. The repeats are defined by a characteristic tryptophan (W) residue at position 17 in helix A and a leucine (L) at 2 residues from the carboxyl end of helix C.; GO: 0005515 protein binding; PDB: 1HCI_A 1QUU_A 3FB2_B 1S35_A 1U5P_A 1U4Q_A 1CUN_B 1YDI_B 3EDV_A 1AJ3_A ....
Probab=44.42 E-value=52 Score=17.74 Aligned_cols=45 Identities=13% Similarity=0.126 Sum_probs=30.9
Q ss_pred hHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 043345 26 AQRVNNVCTAFRSFCEERNIEGCQQYLQHLKQEYYLVKNKLQTLFQ 71 (80)
Q Consensus 26 a~~L~~~c~~lE~~~~~~~~~~~~~~~~~l~~~~~~l~~~L~~~l~ 71 (80)
...|...+..| ......+.+.+...+..|...|..+...+..+..
T Consensus 57 l~~l~~~~~~L-~~~~~~~~~~i~~~~~~l~~~w~~l~~~~~~r~~ 101 (105)
T PF00435_consen 57 LESLNEQAQQL-IDSGPEDSDEIQEKLEELNQRWEALCELVEERRQ 101 (105)
T ss_dssp HHHHHHHHHHH-HHTTHTTHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHH-HHcCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34455666666 3333456677888889999999998888866544
No 43
>PRK10548 flagellar biosynthesis protein FliT; Provisional
Probab=43.46 E-value=76 Score=19.38 Aligned_cols=23 Identities=9% Similarity=0.138 Sum_probs=17.5
Q ss_pred HHHHHHHHHHHHHHhhcCHHHHH
Q 043345 27 QRVNNVCTAFRSFCEERNIEGCQ 49 (80)
Q Consensus 27 ~~L~~~c~~lE~~~~~~~~~~~~ 49 (80)
..|..+..++=.+++.|+|+.+.
T Consensus 12 q~I~~lS~~ML~aA~~g~Wd~Li 34 (121)
T PRK10548 12 QQILTLSQSMLRLATEGQWDELI 34 (121)
T ss_pred HHHHHHHHHHHHHHHHCCHHHHH
Confidence 35667778888888999988753
No 44
>PF13812 PPR_3: Pentatricopeptide repeat domain
Probab=42.37 E-value=33 Score=14.84 Aligned_cols=22 Identities=14% Similarity=0.351 Sum_probs=16.1
Q ss_pred HHHHHhhcCHHHHHHHHHHHHH
Q 043345 36 FRSFCEERNIEGCQQYLQHLKQ 57 (80)
Q Consensus 36 lE~~~~~~~~~~~~~~~~~l~~ 57 (80)
|...++.|+.+.+..++..++.
T Consensus 8 l~a~~~~g~~~~a~~~~~~M~~ 29 (34)
T PF13812_consen 8 LRACAKAGDPDAALQLFDEMKE 29 (34)
T ss_pred HHHHHHCCCHHHHHHHHHHHHH
Confidence 4455688888888888777764
No 45
>PF15300 INT_SG_DDX_CT_C: INTS6/SAGE1/DDX26B/CT45 C-terminus
Probab=41.84 E-value=20 Score=19.70 Aligned_cols=20 Identities=15% Similarity=0.303 Sum_probs=16.6
Q ss_pred cCchhHHHHHHHHHHhhhhh
Q 043345 2 QQNVDFTKVGGHVHQLKGSS 21 (80)
Q Consensus 2 ~~~~D~~~~~~laH~LKGss 21 (80)
.|.+||+.+-.+...++|+-
T Consensus 17 rpGr~ye~iF~lL~~vqG~~ 36 (65)
T PF15300_consen 17 RPGRNYEKIFKLLEQVQGPL 36 (65)
T ss_pred ccCCcHHHHHHHHHHccCCH
Confidence 37789999999888888875
No 46
>PF11173 DUF2960: Protein of unknown function (DUF2960); InterPro: IPR021343 This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
Probab=41.56 E-value=22 Score=20.35 Aligned_cols=15 Identities=13% Similarity=0.160 Sum_probs=11.8
Q ss_pred HHHHHHHHHhhhhcC
Q 043345 66 LQTLFQVCLKSLASS 80 (80)
Q Consensus 66 L~~~l~~~~~~~~~~ 80 (80)
|..|+.+|+|+...|
T Consensus 38 lt~fl~ME~Qv~~~s 52 (79)
T PF11173_consen 38 LTEFLKMEQQVEMTS 52 (79)
T ss_pred HHHHHHHHHHHHHHh
Confidence 678999999986543
No 47
>PF10180 DUF2373: Uncharacterised conserved protein (DUF2373); InterPro: IPR019327 This is a conserved family of proteins found from fungi to humans. The function is not known.
Probab=37.92 E-value=67 Score=17.47 Aligned_cols=29 Identities=17% Similarity=0.232 Sum_probs=20.7
Q ss_pred CchhHHHHHHHHHHhhhhhhccChHHHHHHHHH
Q 043345 3 QNVDFTKVGGHVHQLKGSSSSIGAQRVNNVCTA 35 (80)
Q Consensus 3 ~~~D~~~~~~laH~LKGss~nlGa~~L~~~c~~ 35 (80)
|..+++.+..+.-.|||++. .+|.+.|.+
T Consensus 35 P~~~~~~ll~Yl~glkG~aR----~rl~~~a~~ 63 (65)
T PF10180_consen 35 PSEYFPILLEYLKGLKGGAR----ERLREEAKE 63 (65)
T ss_pred CHHHHHHHHHHHHhCcchHH----HHHHHHHHh
Confidence 56778889999999999664 345555543
No 48
>PRK10987 regulatory protein AmpE; Provisional
Probab=37.87 E-value=63 Score=22.34 Aligned_cols=35 Identities=17% Similarity=0.215 Sum_probs=30.1
Q ss_pred hhccChHHHHHHHHHHHHHHhhcCHHHHHHHHHHH
Q 043345 21 SSSIGAQRVNNVCTAFRSFCEERNIEGCQQYLQHL 55 (80)
Q Consensus 21 s~nlGa~~L~~~c~~lE~~~~~~~~~~~~~~~~~l 55 (80)
...+|...+.+...++.++.++||.+.+...+.++
T Consensus 79 ~~~lg~r~L~~~~~~v~~AL~~gDl~aAR~~l~~l 113 (284)
T PRK10987 79 LLCIGAGKQRLHYKAYLQAACRGDSQACYHMAEEL 113 (284)
T ss_pred HHHhCCchHHHHHHHHHHHHHCCCHHHHHHHHHHh
Confidence 34589999999999999999999999888876666
No 49
>PF08738 Gon7: Gon7 family; InterPro: IPR014849 In Saccharomyces cerevisiae Gon7 is a member of the KEOPS protein complex. A protein complex proposed to be involved in transcription and promoting telomere uncapping and telomere elongation [].
Probab=37.43 E-value=92 Score=18.61 Aligned_cols=26 Identities=12% Similarity=0.349 Sum_probs=21.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Q 043345 47 GCQQYLQHLKQEYYLVKNKLQTLFQV 72 (80)
Q Consensus 47 ~~~~~~~~l~~~~~~l~~~L~~~l~~ 72 (80)
.-...|..|+..+..++..|+.||.-
T Consensus 51 ~K~t~L~~LR~~lt~lQddIN~fLTe 76 (103)
T PF08738_consen 51 DKDTYLSELRAQLTTLQDDINEFLTE 76 (103)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33467899999999999999999864
No 50
>PRK00068 hypothetical protein; Validated
Probab=37.41 E-value=1.2e+02 Score=25.01 Aligned_cols=39 Identities=5% Similarity=0.031 Sum_probs=30.8
Q ss_pred hHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHHH
Q 043345 26 AQRVNNVCTAFRSFCEERNIEGCQQYLQHLKQEYYLVKN 64 (80)
Q Consensus 26 a~~L~~~c~~lE~~~~~~~~~~~~~~~~~l~~~~~~l~~ 64 (80)
+....++..+.+++.++||+.+..+.+++|++.++++..
T Consensus 930 l~~a~~a~~~a~~Alk~GDw~~yG~a~~~L~~al~~~~~ 968 (970)
T PRK00068 930 LKEAQDAYNKAIEAQKSGDFAEYGEALKELDDALNKYNK 968 (970)
T ss_pred HHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHh
Confidence 445667777788888999999999988888888776643
No 51
>PRK10265 chaperone-modulator protein CbpM; Provisional
Probab=37.33 E-value=58 Score=18.99 Aligned_cols=23 Identities=30% Similarity=0.483 Sum_probs=15.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Q 043345 49 QQYLQHLKQEYYLVKNKLQTLFQ 71 (80)
Q Consensus 49 ~~~~~~l~~~~~~l~~~L~~~l~ 71 (80)
.+.+++|++++..++..|..|++
T Consensus 77 Ld~i~~Lr~el~~L~~~l~~~~~ 99 (101)
T PRK10265 77 LDEIAHLKQENRLLRQRLSRFVA 99 (101)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhc
Confidence 34456667777777777777764
No 52
>TIGR00756 PPR pentatricopeptide repeat domain (PPR motif). This family has a similar consensus to the TPR domain (tetratricopeptide), pfam pfam00515, a 33-residue repeat. It is predicted to form a pair of antiparallel helices similar to that of TPR.
Probab=37.29 E-value=39 Score=14.32 Aligned_cols=22 Identities=9% Similarity=0.424 Sum_probs=16.5
Q ss_pred HHHHHhhcCHHHHHHHHHHHHH
Q 043345 36 FRSFCEERNIEGCQQYLQHLKQ 57 (80)
Q Consensus 36 lE~~~~~~~~~~~~~~~~~l~~ 57 (80)
|...++.++.+++..++..+..
T Consensus 7 i~~~~~~~~~~~a~~~~~~M~~ 28 (35)
T TIGR00756 7 IDGLCKAGRVEEALELFKEMLE 28 (35)
T ss_pred HHHHHHCCCHHHHHHHHHHHHH
Confidence 4556788888888888877754
No 53
>KOG4182 consensus Uncharacterized conserved protein [Function unknown]
Probab=37.09 E-value=2e+02 Score=22.46 Aligned_cols=58 Identities=16% Similarity=0.200 Sum_probs=35.5
Q ss_pred chhHHHHHHHHHHhhhhhhccC------------------------------------hHHHHHHHHHHHHHHhhcCHHH
Q 043345 4 NVDFTKVGGHVHQLKGSSSSIG------------------------------------AQRVNNVCTAFRSFCEERNIEG 47 (80)
Q Consensus 4 ~~D~~~~~~laH~LKGss~nlG------------------------------------a~~L~~~c~~lE~~~~~~~~~~ 47 (80)
..|...++.=+|+|.|+.+.|- +..+..+...+|.-...||..+
T Consensus 73 akd~~~Lq~Da~~Lq~kma~il~el~~aegesadCiAaLaRldn~kQkleaA~esLQdaaGl~nL~a~lED~Fa~gDL~~ 152 (828)
T KOG4182|consen 73 AKDSAALQADAHRLQEKMAAILLELAAAEGESADCIAALARLDNKKQKLEAAKESLQDAAGLGNLLAELEDGFARGDLKG 152 (828)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHhCChHHHHHHHHHhccHHHHHHHHHHHHHhhccHHHHHHHHHHHhhcCCchh
Confidence 3566777888888888765431 2233444555666666666666
Q ss_pred HHHHHHHHHHHHHH
Q 043345 48 CQQYLQHLKQEYYL 61 (80)
Q Consensus 48 ~~~~~~~l~~~~~~ 61 (80)
+...+..++.++..
T Consensus 153 aadkLaalqkcL~A 166 (828)
T KOG4182|consen 153 AADKLAALQKCLHA 166 (828)
T ss_pred HHHHHHHHHHHHHH
Confidence 66666666666543
No 54
>PF01044 Vinculin: Vinculin family; InterPro: IPR006077 Vinculin is a eukaryotic protein that seems to be involved in the attachment of the actin-based microfilaments to the plasma membrane. Vinculin is located at the cytoplasmic side of focal contacts or adhesion plaques []. In addition to actin, vinculin interacts with other structural proteins such as talin and alpha-actinins. Vinculin is a large protein of 116 kDa (about a 1000 residues). Structurally the protein consists of an acidic N-terminal domain of about 90 kDa separated from a basic C-terminal domain of about 25 kDa by a proline-rich region of about 50 residues. The central part of the N-terminal domain consists of a variable number (3 in vertebrates, 2 in Caenorhabditis elegans) of repeats of a 110 amino acids domain. Alpha-catenins are evolutionary related to vinculin IPR001033 from INTERPRO []. Catenins are proteins that associate with the cytoplasmic domain of a variety of cadherins. The association of catenins to cadherins produces a complex which is linked to the actin filament network, and which seems to be of primary importance for cadherins cell-adhesion properties. Three different types of catenins seem to exist: alpha, beta, and gamma. Alpha-catenins are proteins of about 100 kDa which are evolutionary related to vinculin. In terms of their structure the most significant differences are the absence, in alpha-catenin, of the repeated domain and of the proline-rich segment.; GO: 0005198 structural molecule activity, 0007155 cell adhesion, 0015629 actin cytoskeleton; PDB: 3S90_B 1TR2_B 2IBF_A 1RKC_A 3TJ5_A 3RF3_B 4DJ9_A 2GWW_A 2HSQ_A 3TJ6_A ....
Probab=36.97 E-value=1.6e+02 Score=24.11 Aligned_cols=61 Identities=15% Similarity=0.231 Sum_probs=38.2
Q ss_pred HHHHHHHHHhhhhhhccChHHHHHHHHHHHH---------HHhhcCHHHHHHHHHHHHHHHHHHHHHHHH
Q 043345 8 TKVGGHVHQLKGSSSSIGAQRVNNVCTAFRS---------FCEERNIEGCQQYLQHLKQEYYLVKNKLQT 68 (80)
Q Consensus 8 ~~~~~laH~LKGss~nlGa~~L~~~c~~lE~---------~~~~~~~~~~~~~~~~l~~~~~~l~~~L~~ 68 (80)
..+..-+..+-+++..=--..+..+|.++++ ....++.++......+|...+..|+..|..
T Consensus 411 ~~lv~e~~~~A~~~~~~~R~~Il~lc~~i~~l~~qL~dL~~~~~~~spea~~la~~L~~~l~~L~~~l~~ 480 (968)
T PF01044_consen 411 RDLVEEARKLADSSDPEEREEILELCDEIEQLTNQLADLEMRGEGDSPEAKALAEQLSQKLDDLRQQLQK 480 (968)
T ss_dssp HHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHHHHHHHHHCHCSCCSSHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHhccccchHHhHHHHHHHHHHhcchhhhhhhccCCCcccccccccchhhhHHHHHHHHHH
Confidence 3445555566666654445577888888888 333445456666667777777777666653
No 55
>PF05190 MutS_IV: MutS family domain IV C-terminus.; InterPro: IPR007861 Mismatch repair contributes to the overall fidelity of DNA replication and is essential for combating the adverse effects of damage to the genome. It involves the correction of mismatched base pairs that have been missed by the proofreading element of the DNA polymerase complex. The post-replicative Mismatch Repair System (MMRS) of Escherichia coli involves MutS (Mutator S), MutL and MutH proteins, and acts to correct point mutations or small insertion/deletion loops produced during DNA replication []. MutS and MutL are involved in preventing recombination between partially homologous DNA sequences. The assembly of MMRS is initiated by MutS, which recognises and binds to mispaired nucleotides and allows further action of MutL and MutH to eliminate a portion of newly synthesized DNA strand containing the mispaired base []. MutS can also collaborate with methyltransferases in the repair of O(6)-methylguanine damage, which would otherwise pair with thymine during replication to create an O(6)mG:T mismatch []. MutS exists as a dimer, where the two monomers have different conformations and form a heterodimer at the structural level []. Only one monomer recognises the mismatch specifically and has ADP bound. Non-specific major groove DNA-binding domains from both monomers embrace the DNA in a clamp-like structure. Mismatch binding induces ATP uptake and a conformational change in the MutS protein, resulting in a clamp that translocates on DNA. MutS is a modular protein with a complex structure [], and is composed of: N-terminal mismatch-recognition domain, which is similar in structure to tRNA endonuclease. Connector domain, which is similar in structure to Holliday junction resolvase ruvC. Core domain, which is composed of two separate subdomains that join together to form a helical bundle; from within the core domain, two helices act as levers that extend towards (but do not touch) the DNA. Clamp domain, which is inserted between the two subdomains of the core domain at the top of the lever helices; the clamp domain has a beta-sheet structure. ATPase domain (connected to the core domain), which has a classical Walker A motif. HTH (helix-turn-helix) domain, which is involved in dimer contacts. The MutS family of proteins is named after the Salmonella typhimurium MutS protein involved in mismatch repair. Homologues of MutS have been found in many species including eukaryotes (MSH 1, 2, 3, 4, 5, and 6 proteins), archaea and bacteria, and together these proteins have been grouped into the MutS family. Although many of these proteins have similar activities to the E. coli MutS, there is significant diversity of function among the MutS family members. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein [].This diversity is even seen within species, where many species encode multiple MutS homologues with distinct functions []. Inter-species homologues may have arisen through frequent ancient horizontal gene transfer of MutS (and MutL) from bacteria to archaea and eukaryotes via endosymbiotic ancestors of mitochondria and chloroplasts []. This entry represents the clamp domain (domain 4) found in proteins of the MutS family. The clamp domain is inserted within the core domain at the top of the lever helices. It has a beta-sheet structure [].; GO: 0005524 ATP binding, 0030983 mismatched DNA binding, 0006298 mismatch repair; PDB: 2WTU_A 1OH7_A 1OH5_B 1W7A_B 1NG9_A 1OH8_B 1WBD_A 1WB9_A 3K0S_A 1OH6_A ....
Probab=36.59 E-value=66 Score=17.51 Aligned_cols=26 Identities=27% Similarity=0.466 Sum_probs=15.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHh
Q 043345 50 QYLQHLKQEYYLVKNKLQTLFQVCLK 75 (80)
Q Consensus 50 ~~~~~l~~~~~~l~~~L~~~l~~~~~ 75 (80)
..++.+...+..+...|..++.-.++
T Consensus 4 ~~Ld~~~~~~~~~~~~l~~~~~~~~~ 29 (92)
T PF05190_consen 4 EELDELREEYEEIEEELEELLEEIRK 29 (92)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34566666666666666666655544
No 56
>PF14756 Pdase_C33_assoc: Peptidase_C33-associated domain
Probab=35.87 E-value=1.1e+02 Score=19.05 Aligned_cols=21 Identities=14% Similarity=0.493 Sum_probs=16.3
Q ss_pred cChHHHHHHHHHHHHHHhhcC
Q 043345 24 IGAQRVNNVCTAFRSFCEERN 44 (80)
Q Consensus 24 lGa~~L~~~c~~lE~~~~~~~ 44 (80)
+-.-++..+|+-||..|-..|
T Consensus 70 ~~lgkiislcqvie~ccc~qn 90 (147)
T PF14756_consen 70 VCLGKIISLCQVIEECCCSQN 90 (147)
T ss_pred hHHHHHHHHHHHHHHHHcccC
Confidence 345578999999999995554
No 57
>PRK15058 cytochrome b562; Provisional
Probab=35.04 E-value=1.1e+02 Score=18.97 Aligned_cols=32 Identities=16% Similarity=0.172 Sum_probs=25.2
Q ss_pred ChHHHHHHHHHHHHHHhhcCHHHHHHHHHHHH
Q 043345 25 GAQRVNNVCTAFRSFCEERNIEGCQQYLQHLK 56 (80)
Q Consensus 25 Ga~~L~~~c~~lE~~~~~~~~~~~~~~~~~l~ 56 (80)
|...|...-...+..+.+|+.+++.....+|.
T Consensus 86 G~d~Li~qID~a~~la~~GkL~eAK~~a~~l~ 117 (128)
T PRK15058 86 GFDILVGQIDGALKLANEGKVKEAQAAAEQLK 117 (128)
T ss_pred HHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHH
Confidence 67888888888889999999998776654443
No 58
>TIGR00444 mazG MazG family protein. This family of prokaryotic proteins has no known function. It includes the uncharacterized protein MazG in E. coli.
Probab=33.98 E-value=1.1e+02 Score=21.09 Aligned_cols=43 Identities=7% Similarity=0.002 Sum_probs=30.5
Q ss_pred ChHHHHHHHHHHHHHHhhc-CHHHHHHHHHHHHHHHHHHHHHHH
Q 043345 25 GAQRVNNVCTAFRSFCEER-NIEGCQQYLQHLKQEYYLVKNKLQ 67 (80)
Q Consensus 25 Ga~~L~~~c~~lE~~~~~~-~~~~~~~~~~~l~~~~~~l~~~L~ 67 (80)
+.+.|.....-...+++.| +++.....+..+..++.++..++.
T Consensus 129 ~lPaL~~A~ki~~raa~~Gfdw~~~~~~~~k~~EE~~El~~a~~ 172 (248)
T TIGR00444 129 TLPALMRAAKIQKRCAKVGFDWEDVSPVWDKVYEELDEVMYEAR 172 (248)
T ss_pred cCCHHHHHHHHHHHHHHcCCCCCCcHHHHHHHHHHHHHHHHHHh
Confidence 4456666666677777777 566777788888888877777663
No 59
>PRK11107 hybrid sensory histidine kinase BarA; Provisional
Probab=33.36 E-value=2.3e+02 Score=22.06 Aligned_cols=55 Identities=15% Similarity=0.201 Sum_probs=26.4
Q ss_pred HHHHHHHhhhhhhccChHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 043345 10 VGGHVHQLKGSSSSIGAQRVNNVCTAFRSFCEERNIEGCQQYLQHLKQEYYLVKNKLQTLFQV 72 (80)
Q Consensus 10 ~~~laH~LKGss~nlGa~~L~~~c~~lE~~~~~~~~~~~~~~~~~l~~~~~~l~~~L~~~l~~ 72 (80)
+..++|-||-- |..+-..++...+....+.....+..+......+..-++..+.+
T Consensus 297 l~~isHelrtP--------L~~i~~~~~~l~~~~~~~~~~~~l~~i~~~~~~l~~li~~ll~~ 351 (919)
T PRK11107 297 LANMSHELRTP--------LNGVIGFTRQTLKTPLTPTQRDYLQTIERSANNLLAIINDILDF 351 (919)
T ss_pred HHHhhHhhccc--------HHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45677887743 22222223322322222334445566666665555555555443
No 60
>COG1270 CbiB Cobalamin biosynthesis protein CobD/CbiB [Coenzyme metabolism]
Probab=32.90 E-value=1e+02 Score=22.15 Aligned_cols=35 Identities=9% Similarity=0.249 Sum_probs=29.1
Q ss_pred hhccChHHHHHHHHHHHHHHhhcCHHHHHHHHHHH
Q 043345 21 SSSIGAQRVNNVCTAFRSFCEERNIEGCQQYLQHL 55 (80)
Q Consensus 21 s~nlGa~~L~~~c~~lE~~~~~~~~~~~~~~~~~l 55 (80)
...++...|.+.+.++.+..+++|.++....+..+
T Consensus 94 ~~tla~rsL~~~~~~v~~~L~~gdl~~aR~~ls~i 128 (320)
T COG1270 94 KTTLAIRSLADHARKVARALRRGDLEGARRALSMI 128 (320)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH
Confidence 45688999999999999999999988877666543
No 61
>PF09686 Plasmid_RAQPRD: Plasmid protein of unknown function (Plasmid_RAQPRD); InterPro: IPR019110 This entry identifies a family of proteins, around 100 amino acids in length, that include a predicted signal sequence and a perfectly conserved motif, RAQPRD, towards the C terminus. They are found in the Pseudomonas putida TOL plasmid pWW0 and in cryptic plasmid regions of Salmonella enterica subsp. enterica serovar Typhi and Pseudomonas syringae pv. tomato str. DC3000. The function of these proteins is unknown.
Probab=32.66 E-value=53 Score=18.76 Aligned_cols=23 Identities=9% Similarity=0.196 Sum_probs=20.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Q 043345 52 LQHLKQEYYLVKNKLQTLFQVCL 74 (80)
Q Consensus 52 ~~~l~~~~~~l~~~L~~~l~~~~ 74 (80)
..+|...+..++.-|+.||...|
T Consensus 46 Y~rl~~Dl~~ir~GI~~YL~psR 68 (81)
T PF09686_consen 46 YPRLRADLERIRAGIQDYLNPSR 68 (81)
T ss_pred HHHHHHHHHHHHHHHHHHcCccc
Confidence 68899999999999999998766
No 62
>PLN02999 photosystem II oxygen-evolving enhancer 3 protein (PsbQ)
Probab=31.86 E-value=1.6e+02 Score=19.62 Aligned_cols=38 Identities=5% Similarity=0.055 Sum_probs=26.7
Q ss_pred HHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHHH
Q 043345 27 QRVNNVCTAFRSFCEERNIEGCQQYLQHLKQEYYLVKN 64 (80)
Q Consensus 27 ~~L~~~c~~lE~~~~~~~~~~~~~~~~~l~~~~~~l~~ 64 (80)
..|.+-...|+.+++..+..+.....+..-..++.+..
T Consensus 150 nkLFdnvt~LDyAAR~K~~~eae~yY~~Tv~slddVl~ 187 (190)
T PLN02999 150 NELVENMSELDYYVRTPKVYESYLYYEKTLKSIDNVVE 187 (190)
T ss_pred HHHhhhHHHHHHHHhcCChHHHHHHHHHHHHHHHHHHH
Confidence 56777778888899888877766666665555555544
No 63
>PRK03170 dihydrodipicolinate synthase; Provisional
Probab=31.84 E-value=1.7e+02 Score=19.94 Aligned_cols=41 Identities=7% Similarity=0.032 Sum_probs=30.6
Q ss_pred hhhhhccChHH--HHHHHHHHHHHHhhcCHHHHHHHHHHHHHH
Q 043345 18 KGSSSSIGAQR--VNNVCTAFRSFCEERNIEGCQQYLQHLKQE 58 (80)
Q Consensus 18 KGss~nlGa~~--L~~~c~~lE~~~~~~~~~~~~~~~~~l~~~ 58 (80)
-|+.|.++... +.+.+.++-++.++||.+.+.++..++...
T Consensus 197 ~G~~G~is~~~n~~P~~~~~l~~~~~~gd~~~a~~l~~~l~~~ 239 (292)
T PRK03170 197 LGGVGVISVAANVAPKEMAEMCDAALAGDFAEAREIHRRLLPL 239 (292)
T ss_pred cCCCEEEEhHHhhhHHHHHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 46677666544 779999999999999998877766555543
No 64
>PF13041 PPR_2: PPR repeat family
Probab=31.83 E-value=69 Score=15.49 Aligned_cols=24 Identities=17% Similarity=0.497 Sum_probs=18.7
Q ss_pred HHHHHHHhhcCHHHHHHHHHHHHH
Q 043345 34 TAFRSFCEERNIEGCQQYLQHLKQ 57 (80)
Q Consensus 34 ~~lE~~~~~~~~~~~~~~~~~l~~ 57 (80)
.-|...++.|+.+++..++.++..
T Consensus 8 ~li~~~~~~~~~~~a~~l~~~M~~ 31 (50)
T PF13041_consen 8 TLISGYCKAGKFEEALKLFKEMKK 31 (50)
T ss_pred HHHHHHHHCcCHHHHHHHHHHHHH
Confidence 345667888999998888888775
No 65
>PF09660 DUF2397: Protein of unknown function (DUF2397); InterPro: IPR013493 Proteins in this family are encoded within a conserved gene four-gene neighbourhood found sporadically in a phylogenetically broad range of bacteria including: Nocardia farcinica, Symbiobacterium thermophilum, Streptomyces avermitilis (Actinobacteria), Geobacillus kaustophilus (Firmicutes), Azoarcus sp. (strain EbN1) (Aromatoleum aromaticum (strain EbN1)) and Ralstonia solanacearum (Betaproteobacteria).
Probab=31.46 E-value=2.3e+02 Score=21.35 Aligned_cols=64 Identities=13% Similarity=0.256 Sum_probs=48.1
Q ss_pred HHHhhhhhhccChHHHHHHHHHHHHHHh------hcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 043345 14 VHQLKGSSSSIGAQRVNNVCTAFRSFCE------ERNIEGCQQYLQHLKQEYYLVKNKLQTLFQVCLKSL 77 (80)
Q Consensus 14 aH~LKGss~nlGa~~L~~~c~~lE~~~~------~~~~~~~~~~~~~l~~~~~~l~~~L~~~l~~~~~~~ 77 (80)
...+.|.++++--..|-.+...|..... .++.+.+...+..|...|..+...-..|+......+
T Consensus 105 le~~~~~~gsL~~~~l~~I~~~L~~L~~~~~~~~~~d~~~~~~~w~~L~~~f~~L~~na~df~~~L~~~~ 174 (486)
T PF09660_consen 105 LENLLGERGSLQRTLLERILERLRALAELAESPREGDAAEVYEWWRDLFEDFERLAQNAQDFYASLQSVK 174 (486)
T ss_pred HHhhcccccccchhHHHHHHHHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence 3444578888887777777777765553 457778888999999999999999998887755443
No 66
>PF07891 DUF1666: Protein of unknown function (DUF1666); InterPro: IPR012870 These sequences are derived from hypothetical plant proteins of unknown function. The region in question is approximately 250 residues long.
Probab=31.20 E-value=1.8e+02 Score=20.15 Aligned_cols=47 Identities=13% Similarity=0.224 Sum_probs=32.0
Q ss_pred HHHHHHHHHHHHHHhh---------cCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 043345 27 QRVNNVCTAFRSFCEE---------RNIEGCQQYLQHLKQEYYLVKNKLQTLFQVCL 74 (80)
Q Consensus 27 ~~L~~~c~~lE~~~~~---------~~~~~~~~~~~~l~~~~~~l~~~L~~~l~~~~ 74 (80)
.=++.+|-..|-..-+ .+.. -....+.+.++|+.++.-|++|++-|+
T Consensus 7 vYVaQiCLSWEaL~wqY~k~~~l~~~~~~-~~~~yn~VA~eFQqFQVLLQRFiENEP 62 (247)
T PF07891_consen 7 VYVAQICLSWEALHWQYKKASELWESDPQ-NPHCYNHVAGEFQQFQVLLQRFIENEP 62 (247)
T ss_pred HHHHHHHhhHHHHHhHHHHHHHHHhcCCC-CCCChHHHHHHHHHHHHHHHHHHhCCC
Confidence 3467778877743311 1111 123578999999999999999998764
No 67
>PLN02729 PSII-Q subunit
Probab=31.18 E-value=1.7e+02 Score=19.88 Aligned_cols=37 Identities=11% Similarity=0.108 Sum_probs=24.4
Q ss_pred HHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHH
Q 043345 27 QRVNNVCTAFRSFCEERNIEGCQQYLQHLKQEYYLVK 63 (80)
Q Consensus 27 ~~L~~~c~~lE~~~~~~~~~~~~~~~~~l~~~~~~l~ 63 (80)
..|.+-..+|..+++..+..+....+......++.|.
T Consensus 180 nkLFdn~~eLD~AaR~Ks~~eae~yY~~Tv~aLdeVl 216 (220)
T PLN02729 180 NRLFDNFEKLEDASKRKNLSETESSYKDTKTLLQEVM 216 (220)
T ss_pred HHHHhhHHHHHHHHhCCChHHHHHHHHHHHHHHHHHH
Confidence 5677777888888888876666665555555544443
No 68
>COG4354 Predicted bile acid beta-glucosidase [Carbohydrate transport and metabolism]
Probab=31.10 E-value=1.9e+02 Score=22.93 Aligned_cols=56 Identities=14% Similarity=0.076 Sum_probs=33.1
Q ss_pred HHHhhhhhhccChHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 043345 14 VHQLKGSSSSIGAQRVNNVCTAFRSFCEERNIEGCQQYLQHLKQEYYLVKNKLQTLFQVC 73 (80)
Q Consensus 14 aH~LKGss~nlGa~~L~~~c~~lE~~~~~~~~~~~~~~~~~l~~~~~~l~~~L~~~l~~~ 73 (80)
+|+|+|.++-.|-..++.+..-++-.--=++. ..++.+..+........+++|..-
T Consensus 501 a~~i~G~ssy~~sl~iaal~A~l~is~~l~~~----~~~~a~~e~~~~~~~~y~~~L~~~ 556 (721)
T COG4354 501 ATRIQGHSSYCGSLFIAALIAALEISKYLLDN----AQLEALNEASKNYVDFYNTWLKEA 556 (721)
T ss_pred cceeechhhhhhHHHHHHHHHHHHHHHHHhhh----hhhhhhHHHHHHHHHHHHHHHHHH
Confidence 68999999999998888888877743322111 233334444444444444444433
No 69
>PRK01209 cobD cobalamin biosynthesis protein; Provisional
Probab=30.34 E-value=1.1e+02 Score=21.42 Aligned_cols=33 Identities=6% Similarity=0.185 Sum_probs=27.9
Q ss_pred ccChHHHHHHHHHHHHHHhhcCHHHHHHHHHHH
Q 043345 23 SIGAQRVNNVCTAFRSFCEERNIEGCQQYLQHL 55 (80)
Q Consensus 23 nlGa~~L~~~c~~lE~~~~~~~~~~~~~~~~~l 55 (80)
.+|...+.+.+.++.++.+++|.+.+...+..+
T Consensus 92 ~l~~~~l~~~~~~v~~al~~gd~~~AR~~l~~~ 124 (312)
T PRK01209 92 ALAGRSLADHARAVARALRAGDLEEARRAVSMI 124 (312)
T ss_pred HHhhhhHHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence 478889999999999999999988887777665
No 70
>TIGR00674 dapA dihydrodipicolinate synthase. Dihydrodipicolinate synthase is a homotetrameric enzyme of lysine biosynthesis. E. coli has several paralogs closely related to dihydrodipicoline synthase (DapA), as well as the more distant N-acetylneuraminate lyase. In Pyrococcus horikoshii, the bidirectional best hit with E. coli is to an uncharacterized paralog of DapA, not DapA itself, and it is omitted from the seed. The putative members from the Chlamydias (pathogens with a parasitic metabolism) are easily the most divergent members of the multiple alignment.
Probab=29.72 E-value=1.8e+02 Score=19.73 Aligned_cols=42 Identities=12% Similarity=0.099 Sum_probs=30.8
Q ss_pred hhhhhhccChHH--HHHHHHHHHHHHhhcCHHHHHHHHHHHHHH
Q 043345 17 LKGSSSSIGAQR--VNNVCTAFRSFCEERNIEGCQQYLQHLKQE 58 (80)
Q Consensus 17 LKGss~nlGa~~--L~~~c~~lE~~~~~~~~~~~~~~~~~l~~~ 58 (80)
.-|..|.++... +.+.+.++=++..+||.+.+.++..++..-
T Consensus 193 ~~G~~G~i~~~~~~~P~~~~~l~~a~~~gd~~~A~~lq~~l~~l 236 (285)
T TIGR00674 193 ALGGKGVISVTANVAPKLMKEMVNNALEGDFAEAREIHQKLMPL 236 (285)
T ss_pred HcCCCEEEehHHHhhHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence 446777765444 668999999999999998877765555543
No 71
>TIGR02878 spore_ypjB sporulation protein YpjB. Members of this protein, YpjB, family are restricted to a subset of endospore-forming bacteria, including Bacillus species but not CLostridium or some others. In Bacillus subtilis, ypjB was found to be part of the sigma-E regulon, where sigma-E is a sporulation sigma factor that regulates expression in the mother cell compartment. Null mutants of ypjB show a sporulation defect. This protein family is not, however, a part of the endospore formation minimal gene set.
Probab=27.67 E-value=1.5e+02 Score=20.35 Aligned_cols=33 Identities=18% Similarity=0.238 Sum_probs=17.9
Q ss_pred HHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHH
Q 043345 29 VNNVCTAFRSFCEERNIEGCQQYLQHLKQEYYL 61 (80)
Q Consensus 29 L~~~c~~lE~~~~~~~~~~~~~~~~~l~~~~~~ 61 (80)
|......+++++..++.......++..-..|.-
T Consensus 104 im~~f~~mk~a~~~~~~~~f~~~ln~Fl~~Y~~ 136 (233)
T TIGR02878 104 VMEAFTELEKAAQKEDSQAFQEKLNEFLSLYDL 136 (233)
T ss_pred HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhhh
Confidence 444555566666666655555555555554443
No 72
>PRK10722 hypothetical protein; Provisional
Probab=27.49 E-value=2.1e+02 Score=19.81 Aligned_cols=32 Identities=22% Similarity=0.265 Sum_probs=26.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 043345 45 IEGCQQYLQHLKQEYYLVKNKLQTLFQVCLKS 76 (80)
Q Consensus 45 ~~~~~~~~~~l~~~~~~l~~~L~~~l~~~~~~ 76 (80)
.+...+....|+..+..+..+|+..-.+|||.
T Consensus 178 lD~lrqq~~~Lq~~L~~t~rKLEnLTdIERqL 209 (247)
T PRK10722 178 LDALRQQQQRLQYQLELTTRKLENLTDIERQL 209 (247)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 45566777888889999999999999999986
No 73
>cd00408 DHDPS-like Dihydrodipicolinate synthase family. A member of the class I aldolases, which use an active-site lysine which stablilzes a reaction intermediate via Schiff base formation, and have TIM beta/alpha barrel fold. The dihydrodipicolinate synthase family comprises several pyruvate-dependent class I aldolases that use the same catalytic step to catalyze different reactions in different pathways and includes such proteins as N-acetylneuraminate lyase, MosA protein, 5-keto-4-deoxy-glucarate dehydratase, trans-o-hydroxybenzylidenepyruvate hydratase-aldolase, trans-2'-carboxybenzalpyruvate hydratase-aldolase, and 2-keto-3-deoxy- gluconate aldolase. The family is also referred to as the N-acetylneuraminate lyase (NAL) family.
Probab=27.46 E-value=1.8e+02 Score=19.55 Aligned_cols=43 Identities=12% Similarity=0.149 Sum_probs=31.1
Q ss_pred hhhhhccCh--HHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHH
Q 043345 18 KGSSSSIGA--QRVNNVCTAFRSFCEERNIEGCQQYLQHLKQEYY 60 (80)
Q Consensus 18 KGss~nlGa--~~L~~~c~~lE~~~~~~~~~~~~~~~~~l~~~~~ 60 (80)
-|..|.++. +-+.+.+..+-++.++|+.+.+.++...+..-..
T Consensus 193 ~G~~G~i~~~~n~~p~~~~~~~~~~~~g~~~~a~~~~~~~~~~~~ 237 (281)
T cd00408 193 LGADGAISGAANVAPKLAVALYEAARAGDLEEARALQDRLLPLIE 237 (281)
T ss_pred cCCCEEEehHHhhCHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHH
Confidence 355555555 6678999999999999998887776665555433
No 74
>PF13047 DUF3907: Protein of unknown function (DUF3907)
Probab=27.35 E-value=1.2e+02 Score=19.36 Aligned_cols=26 Identities=8% Similarity=0.181 Sum_probs=21.7
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHH
Q 043345 44 NIEGCQQYLQHLKQEYYLVKNKLQTL 69 (80)
Q Consensus 44 ~~~~~~~~~~~l~~~~~~l~~~L~~~ 69 (80)
-.+++..++..|...|..++..|+=|
T Consensus 117 ~~~~l~~l~~~le~~Fq~mREEL~YY 142 (148)
T PF13047_consen 117 PPRSLKDLMLSLEKIFQEMREELEYY 142 (148)
T ss_pred CChHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34678889999999999999998754
No 75
>PF13747 DUF4164: Domain of unknown function (DUF4164)
Probab=27.06 E-value=1.3e+02 Score=17.23 Aligned_cols=23 Identities=13% Similarity=0.185 Sum_probs=10.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Q 043345 47 GCQQYLQHLKQEYYLVKNKLQTL 69 (80)
Q Consensus 47 ~~~~~~~~l~~~~~~l~~~L~~~ 69 (80)
....-++.|.....++-..|...
T Consensus 36 ~~e~ei~~l~~dr~rLa~eLD~~ 58 (89)
T PF13747_consen 36 ELEEEIQRLDADRSRLAQELDQA 58 (89)
T ss_pred hHHHHHHHHHhhHHHHHHHHHhH
Confidence 33444455555545555555433
No 76
>PHA02585 16 small terminase protein; Provisional
Probab=27.02 E-value=1.8e+02 Score=18.80 Aligned_cols=64 Identities=9% Similarity=0.125 Sum_probs=40.2
Q ss_pred chhHHHHHHHHHHhhhhhhccChHHHHHHHH-HHHHHHhhcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 043345 4 NVDFTKVGGHVHQLKGSSSSIGAQRVNNVCT-AFRSFCEERNIEGCQQYLQHLKQEYYLVKNKLQTLFQVCLKS 76 (80)
Q Consensus 4 ~~D~~~~~~laH~LKGss~nlGa~~L~~~c~-~lE~~~~~~~~~~~~~~~~~l~~~~~~l~~~L~~~l~~~~~~ 76 (80)
..||+.+|+-.|..- ..+.+... .||. +++.+.+..-+++..|-..+..+...|-..-.-+|.+
T Consensus 45 e~DY~~vR~~~h~q~--------Qm~mda~~iaLE~-AknSesPR~~EVf~~Lm~qm~~~nk~Ll~lhK~MK~i 109 (161)
T PHA02585 45 EDDYSLVRRNMHFQQ--------QMLMDAAKIALEN-AKNSESPRHVEVFATLMGQMTNTNKEILKIHKEMKDI 109 (161)
T ss_pred HHHHHHHHHHHHHHH--------HHHHHHHHHHHHh-ccccCCchHHHHHHHHHHHHHhhHHHHHHHHHHHHHh
Confidence 368999999999821 11222223 3444 5555666677778888888877777776555544443
No 77
>PF00701 DHDPS: Dihydrodipicolinate synthetase family; InterPro: IPR002220 Dihydropicolinate synthase (DHDPS) is the key enzyme in lysine biosynthesis via the diaminopimelate pathway of prokaryotes, some phycomycetes and higher plants. The enzyme catalyses the condensation of L-aspartate-beta- semialdehyde and pyruvate to dihydropicolinic acid via a ping-pong mechanism in which pyruvate binds to the enzyme by forming a Schiff-base with a lysine residue []. Three other proteins are structurally related to DHDPS and probably also act via a similar catalytic mechanism. These are Escherichia coli N-acetylneuraminate lyase (4.1.3.3 from EC) (gene nanA), which catalyzes the condensation of N-acetyl-D-mannosamine and pyruvate to form N-acetylneuraminate; Rhizobium meliloti (Sinorhizobium meliloti) protein mosA [], which is involved in the biosynthesis of the rhizopine 3-o-methyl-scyllo-inosamine; and E. coli hypothetical protein yjhH. The sequences of DHDPS from different sources are well-conserved. The structure takes the form of a homotetramer, in which 2 monomers are related by an approximate 2-fold symmetry []. Each monomer comprises 2 domains: an 8-fold alpha-/beta-barrel, and a C-terminal alpha-helical domain. The fold resembles that of N-acetylneuraminate lyase. The active site lysine is located in the barrel domain, and has access via 2 channels on the C-terminal side of the barrel.; GO: 0016829 lyase activity, 0008152 metabolic process; PDB: 3B4U_B 3S8H_A 3QZE_B 1XXX_F 3L21_F 3IRD_A 3A5F_B 3G0S_B 3DAQ_C 3UQN_A ....
Probab=26.54 E-value=1.6e+02 Score=19.93 Aligned_cols=42 Identities=14% Similarity=0.063 Sum_probs=29.0
Q ss_pred hhhhcc--ChHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHH
Q 043345 19 GSSSSI--GAQRVNNVCTAFRSFCEERNIEGCQQYLQHLKQEYY 60 (80)
Q Consensus 19 Gss~nl--Ga~~L~~~c~~lE~~~~~~~~~~~~~~~~~l~~~~~ 60 (80)
|+.|.+ .++-+.+.+.++-+++.+|+.+.+..+.+++..-+.
T Consensus 198 G~~G~is~~~n~~P~~~~~i~~~~~~Gd~~~A~~l~~~l~~~~~ 241 (289)
T PF00701_consen 198 GADGFISGLANVFPELIVEIYDAFQAGDWEEARELQQRLLPLRE 241 (289)
T ss_dssp TSSEEEESGGGTHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHH
T ss_pred cCCEEEEcccccChHHHHHHHHHHHcCcHHHHHHHHHHHhHHHH
Confidence 444433 233477899999999999999887766665555433
No 78
>PF08657 DASH_Spc34: DASH complex subunit Spc34 ; InterPro: IPR013966 The DASH complex is a ~10 subunit microtubule-binding complex that is transferred to the kinetochore prior to mitosis []. In Saccharomyces cerevisiae (Baker's yeast) DASH forms both rings and spiral structures on microtubules in vitro [, ]. Components of the DASH complex, including Dam1, Duo1, Spc34, Dad1 and Ask1, are essential and connect the centromere to the plus end of spindle microtubules [].
Probab=25.04 E-value=2.4e+02 Score=19.51 Aligned_cols=62 Identities=15% Similarity=0.195 Sum_probs=42.7
Q ss_pred HHHHHHHHHhhhhhhcc----ChHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHHHHHHHH
Q 043345 8 TKVGGHVHQLKGSSSSI----GAQRVNNVCTAFRSFCEERNIEGCQQYLQHLKQEYYLVKNKLQTL 69 (80)
Q Consensus 8 ~~~~~laH~LKGss~nl----Ga~~L~~~c~~lE~~~~~~~~~~~~~~~~~l~~~~~~l~~~L~~~ 69 (80)
...++.++.+..++-.+ |=..+-.+|..+|..|..=...++..-+..|...|..+...|..|
T Consensus 134 ~~~~~~avA~vlG~~m~~e~~~d~dvevLL~~ae~L~~vYP~~ga~eki~~Lr~~y~~l~~~i~~l 199 (259)
T PF08657_consen 134 KQRRNTAVALVLGGVMHEEIVEDVDVEVLLRGAEKLCNVYPLPGAREKIAALRQRYNQLSNSIAYL 199 (259)
T ss_pred HHHHHHHHHHhccCcccccccccCCHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34455665555554322 444566778888888876566688888888888888888877655
No 79
>cd00950 DHDPS Dihydrodipicolinate synthase (DHDPS) is a key enzyme in lysine biosynthesis. It catalyzes the aldol condensation of L-aspartate-beta- semialdehyde and pyruvate to dihydropicolinic acid via a Schiff base formation between pyruvate and a lysine residue. The functional enzyme is a homotetramer consisting of a dimer of dimers. DHDPS is member of dihydrodipicolinate synthase family that comprises several pyruvate-dependent class I aldolases that use the same catalytic step to catalyze different reactions in different pathways.
Probab=24.90 E-value=2.3e+02 Score=19.15 Aligned_cols=41 Identities=10% Similarity=0.105 Sum_probs=30.4
Q ss_pred hhhhhccChHH--HHHHHHHHHHHHhhcCHHHHHHHHHHHHHH
Q 043345 18 KGSSSSIGAQR--VNNVCTAFRSFCEERNIEGCQQYLQHLKQE 58 (80)
Q Consensus 18 KGss~nlGa~~--L~~~c~~lE~~~~~~~~~~~~~~~~~l~~~ 58 (80)
-|..|.+.... +.+.+.++=++.++|+.+++.++..++..-
T Consensus 196 ~G~~G~~s~~~n~~p~~~~~~~~~~~~g~~~~a~~l~~~l~~~ 238 (284)
T cd00950 196 LGGVGVISVAANVAPKLMAEMVRAALAGDLEKARELHRKLLPL 238 (284)
T ss_pred CCCCEEEehHHHhhHHHHHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 37777765554 778999999999999998877766555543
No 80
>TIGR01690 ICE_RAQPRD integrative conjugative element protein, RAQPRD family. This model represents a small family of proteins about 100 amino acids in length, including a predicted signal sequence and a perfectly conserved motif RAQPRD towards the C-terminus. Members are found in the Pseudomonas putida TOL plasmid pWW0 and in cryptic plasmid regions of Salmonella enterica subsp. enterica serovar Typhi and Pseudomonas syringae DC3000. The function is unknown.
Probab=24.88 E-value=61 Score=19.14 Aligned_cols=23 Identities=9% Similarity=0.209 Sum_probs=19.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Q 043345 52 LQHLKQEYYLVKNKLQTLFQVCL 74 (80)
Q Consensus 52 ~~~l~~~~~~l~~~L~~~l~~~~ 74 (80)
+.++...+.+++.-|+.||...|
T Consensus 59 Y~rl~~Dl~~ir~GI~~YL~PsR 81 (94)
T TIGR01690 59 YPRLRADLKRIRQGIQQYLTPSR 81 (94)
T ss_pred HHHHHHHHHHHHHHHHHhCCCcc
Confidence 46699999999999999998765
No 81
>PF08581 Tup_N: Tup N-terminal; InterPro: IPR013890 The N-terminal region of the Tup protein has been shown to interact with the Ssn6 transcriptional co-repressor []. ; PDB: 3VP9_B 3VP8_B.
Probab=24.66 E-value=1.4e+02 Score=16.83 Aligned_cols=17 Identities=18% Similarity=0.386 Sum_probs=9.2
Q ss_pred HHHHHHHHHHHHHHHHH
Q 043345 50 QYLQHLKQEYYLVKNKL 66 (80)
Q Consensus 50 ~~~~~l~~~~~~l~~~L 66 (80)
++++.|+.+|..+...+
T Consensus 4 elLd~ir~Ef~~~~~e~ 20 (79)
T PF08581_consen 4 ELLDAIRQEFENLSQEA 20 (79)
T ss_dssp HHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 45555666665555433
No 82
>cd05136 RasGAP_DAB2IP The DAB2IP family of Ras GTPase-activating proteins includes DAB2IP, nGAP, and Syn GAP. Disabled 2 interactive protein, (DAB2IP; also known as ASK-interacting protein 1 (AIP1)), is a member of the GTPase-activating proteins, down-regulates Ras-mediated signal pathways, and mediates TNF-induced activation of ASK1-JNK signaling pathways. The mechanism by which TNF signaling is coupled to DAB2IP is not known.
Probab=24.15 E-value=2.3e+02 Score=20.05 Aligned_cols=46 Identities=20% Similarity=0.151 Sum_probs=33.4
Q ss_pred HHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 043345 28 RVNNVCTAFRSFCEERNIEGCQQYLQHLKQEYYLVKNKLQTLFQVC 73 (80)
Q Consensus 28 ~L~~~c~~lE~~~~~~~~~~~~~~~~~l~~~~~~l~~~L~~~l~~~ 73 (80)
....+|..||......+.+++...+-.+-+........|...+..|
T Consensus 13 ~~~~l~~~l~~~~~~~~~~ela~~Lv~if~~~~~~~~~l~~Li~~E 58 (309)
T cd05136 13 NYARLCEVLEPVLSVRAKEELACALVHVLQSTGKAKDFLTDLVMAE 58 (309)
T ss_pred hHHHHHHHHHhhCCchhHHHHHHHHHHHHHhcChHHHHHHHHHHHH
Confidence 4568899999988888888877777777666666666665555443
No 83
>COG0783 Dps DNA-binding ferritin-like protein (oxidative damage protectant) [Inorganic ion transport and metabolism]
Probab=24.04 E-value=2e+02 Score=18.32 Aligned_cols=66 Identities=12% Similarity=0.274 Sum_probs=43.2
Q ss_pred HHHHHHHHHHhhhhhhccChHHHHHHHHHHHHHH-hhcCH-HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 043345 7 FTKVGGHVHQLKGSSSSIGAQRVNNVCTAFRSFC-EERNI-EGCQQYLQHLKQEYYLVKNKLQTLFQV 72 (80)
Q Consensus 7 ~~~~~~laH~LKGss~nlGa~~L~~~c~~lE~~~-~~~~~-~~~~~~~~~l~~~~~~l~~~L~~~l~~ 72 (80)
|..+......+---...+|..++.....-++... +..+. ....+.+..|...|..+...++..+..
T Consensus 57 y~el~~~~DeiAERi~~LGg~p~~t~~~~~~~s~ike~~~~~~~~~~l~~l~~~~~~l~~~~r~~~~~ 124 (156)
T COG0783 57 YEELAEHVDEIAERIRALGGVPLGTLSEYLKLSSIKEEPGDYTAREMLKELVEDYEYLIKELRKGIEL 124 (156)
T ss_pred HHHHHHHHHHHHHHHHHcCCCCcccHHHHHHhCCCcccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 3444445555555556678888888888777766 22221 357778888888888887777766554
No 84
>PF02870 Methyltransf_1N: 6-O-methylguanine DNA methyltransferase, ribonuclease-like domain; InterPro: IPR008332 Synonym(s): 6-O-methylguanine-DNA methyltransferase, O-6-methylguanine-DNA-alkyltransferase The repair of DNA containing O6-alkylated guanine is carried out by DNA-[protein]-cysteine S-methyltransferase (2.1.1.63 from EC). The major mutagenic and carcinogenic effect of methylating agents in DNA is the formation of O6-alkylguanine. The alkyl group at the O-6 position is transferred to a cysteine residue in the enzyme []. This is a suicide reaction since the enzyme is irreversibly inactivated and the methylated protein accumulates as a dead-end product. Most, but not all of the methyltransferases are also able to repair O-4-methylthymine. DNA-[protein]-cysteine S-methyltransferases are widely distributed and are found in various prokaryotic and eukaryotic sources []. This group of proteins are characterised by having an N-terminal ribonuclease-like domain associated with 6-O-methylguanine DNA methyltransferase activity (IPR001497 from INTERPRO).; GO: 0003908 methylated-DNA-[protein]-cysteine S-methyltransferase activity, 0006281 DNA repair; PDB: 1SFE_A 1T39_B 1T38_A 1EH7_A 1EH6_A 1YFH_C 1EH8_A 1QNT_A.
Probab=23.94 E-value=1.1e+02 Score=16.35 Aligned_cols=17 Identities=18% Similarity=0.075 Sum_probs=12.5
Q ss_pred HHHHHHHHHHHHHHHHh
Q 043345 59 YYLVKNKLQTLFQVCLK 75 (80)
Q Consensus 59 ~~~l~~~L~~~l~~~~~ 75 (80)
+..+...|+.|+..+|+
T Consensus 52 ~~~~~~qL~eYF~G~r~ 68 (77)
T PF02870_consen 52 LAEAKQQLDEYFAGERT 68 (77)
T ss_dssp HHHHHHHHHHHHHHHHS
T ss_pred HHHHHHHHHHHHcCCCC
Confidence 45566778888888776
No 85
>PRK10841 hybrid sensory kinase in two-component regulatory system with RcsB and YojN; Provisional
Probab=23.93 E-value=4e+02 Score=21.64 Aligned_cols=56 Identities=7% Similarity=0.182 Sum_probs=30.5
Q ss_pred HHHHHHHhhhhhhccChHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 043345 10 VGGHVHQLKGSSSSIGAQRVNNVCTAFRSFCEERNIEGCQQYLQHLKQEYYLVKNKLQTLFQVC 73 (80)
Q Consensus 10 ~~~laH~LKGss~nlGa~~L~~~c~~lE~~~~~~~~~~~~~~~~~l~~~~~~l~~~L~~~l~~~ 73 (80)
+...+|-||- +|..+...+|........++....+..+...-..+..-++..+.+-
T Consensus 451 la~iSHELRT--------PL~~I~g~lelL~~~~~~~~~~~~l~~i~~~~~~L~~lI~dlLd~s 506 (924)
T PRK10841 451 LATVSHELRT--------PLYGIIGNLDLLQTKELPKGVDRLVTAMNNSSSLLLKIISDILDFS 506 (924)
T ss_pred HHHhHHHHHH--------HHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4667888874 3333334444433333334555666666666666666555555543
No 86
>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=23.91 E-value=3.7e+02 Score=21.24 Aligned_cols=55 Identities=15% Similarity=0.219 Sum_probs=29.2
Q ss_pred HHHHHHHhhhhhhccChHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 043345 10 VGGHVHQLKGSSSSIGAQRVNNVCTAFRSFCEERNIEGCQQYLQHLKQEYYLVKNKLQTLFQV 72 (80)
Q Consensus 10 ~~~laH~LKGss~nlGa~~L~~~c~~lE~~~~~~~~~~~~~~~~~l~~~~~~l~~~L~~~l~~ 72 (80)
+..++|-||. +|..+...++........+.....++.+......+...++..+..
T Consensus 468 ~~~~sHelrt--------PL~~i~~~~~ll~~~~~~~~~~~~l~~i~~~~~~l~~~i~~ll~~ 522 (968)
T TIGR02956 468 LATMSHEIRT--------PLNGILGTLELLGDTGLTSQQQQYLQVINRSGESLLDILNDILDY 522 (968)
T ss_pred HHHhHHHhhh--------HHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3566777774 333333344433333333444556666666666666666555544
No 87
>PF01231 IDO: Indoleamine 2,3-dioxygenase; InterPro: IPR000898 Indoleamine 2,3-dioxgyenase (IDO, 1.13.11.42 from EC) [] is a cytosolic haem protein which, together with the hepatic enzyme tryptophan 2,3-dioxygenase, catalyzes the conversion of tryptophan and other indole derivatives to kynurenines. The physiological role of IDO is not fully understood but is of great interest, because IDO is widely distributed in human tissues, can be up-regulated via cytokines such as interferon-gamma, and can thereby modulate the levels of tryptophan, which is vital for cell growth. The degradative action of IDO on tryptophan leads to cell death by starvation of this essential and relatively scarce amino acid. IDO is a haem-containing enzyme of about 400 amino acids. Site-directed mutagenesis showed His346 (P14902 from SWISSPROT) to be essential for haem binding, indicating that this histidine residue may be the proximal ligand. Mutation of Asp274 also compromised the ability of IDO to bind haem, suggesting that Asp274 may coordinate to haem directly as the distal ligand or is essential in maintaining the conformation of the haem pocket []. Other proteins that are evolutionarily related to IDO include yeast hypothetical protein YJR078w; and myoglobin from the red muscle of the archaeogastropodic molluscs, Nordotis madaka (Giant abalone) and Sulculus diversicolor [, ]. These unusual globins lack enzymatic activity but have kept the haem group.; GO: 0020037 heme binding; PDB: 2D0U_A 2D0T_A.
Probab=23.66 E-value=2.8e+02 Score=20.43 Aligned_cols=34 Identities=6% Similarity=0.192 Sum_probs=25.1
Q ss_pred HHHhhcCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 043345 38 SFCEERNIEGCQQYLQHLKQEYYLVKNKLQTLFQ 71 (80)
Q Consensus 38 ~~~~~~~~~~~~~~~~~l~~~~~~l~~~L~~~l~ 71 (80)
.++..+|...+...+..|...+..+...|.++-+
T Consensus 181 ~a~~~~d~~~i~~~L~~i~~~i~~i~~~l~rm~e 214 (422)
T PF01231_consen 181 DAVKAGDSDRITEALRRIAEAIERITALLERMYE 214 (422)
T ss_dssp HHHHTT-HHHHHHHHHHHHHHHHHHHHHHTTHHH
T ss_pred HHHHhcCHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 4456788888888888888888888877765544
No 88
>PF13942 Lipoprotein_20: YfhG lipoprotein
Probab=23.40 E-value=2.3e+02 Score=18.70 Aligned_cols=32 Identities=19% Similarity=0.209 Sum_probs=26.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 043345 45 IEGCQQYLQHLKQEYYLVKNKLQTLFQVCLKS 76 (80)
Q Consensus 45 ~~~~~~~~~~l~~~~~~l~~~L~~~l~~~~~~ 76 (80)
.+.+...-..|+.++..+..+|+..-.+|||.
T Consensus 132 lD~Lr~qq~~Lq~qL~~T~RKLEnLTDIERQL 163 (179)
T PF13942_consen 132 LDALRQQQQRLQYQLDTTTRKLENLTDIERQL 163 (179)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHH
Confidence 34566667788888899999999999999985
No 89
>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=23.38 E-value=2e+02 Score=18.14 Aligned_cols=37 Identities=3% Similarity=0.085 Sum_probs=20.1
Q ss_pred HHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 043345 29 VNNVCTAFRSFCEERNIEGCQQYLQHLKQEYYLVKNKLQTLFQV 72 (80)
Q Consensus 29 L~~~c~~lE~~~~~~~~~~~~~~~~~l~~~~~~l~~~L~~~l~~ 72 (80)
|.+....|-.+++.+|... ...+|..+...++.|+++
T Consensus 104 Lf~~L~~LD~AA~~kd~~~-------a~k~Y~~av~~~dafl~~ 140 (142)
T TIGR03042 104 LKDDLEKLDEAARLQDGPQ-------AQKAYQKAAADFDAYLDL 140 (142)
T ss_pred HHHHHHHHHHHHHhcCHHH-------HHHHHHHHHHHHHHHHhh
Confidence 3344455555666655443 445566666666666653
No 90
>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=23.38 E-value=1.7e+02 Score=17.17 Aligned_cols=36 Identities=3% Similarity=0.093 Sum_probs=25.0
Q ss_pred HHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHH
Q 043345 28 RVNNVCTAFRSFCEERNIEGCQQYLQHLKQEYYLVK 63 (80)
Q Consensus 28 ~L~~~c~~lE~~~~~~~~~~~~~~~~~l~~~~~~l~ 63 (80)
.+......|..+++.+|.+.+...+..|...-....
T Consensus 83 ~~~~aa~~L~~aa~~~d~~~~~~a~~~v~~~C~aCH 118 (122)
T PF01322_consen 83 AFQKAAAALAAAAKSGDLAAIKAAFGEVGKSCKACH 118 (122)
T ss_dssp HHHHHHHHHHHHHHHTSHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHH
Confidence 344555778888888888888877777766554443
No 91
>PF11855 DUF3375: Protein of unknown function (DUF3375); InterPro: IPR021804 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 479 to 499 amino acids in length.
Probab=23.37 E-value=3.2e+02 Score=20.42 Aligned_cols=64 Identities=17% Similarity=0.217 Sum_probs=48.3
Q ss_pred hhHHHHHHHHHHhhhhhhccChHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHHHHHHHH
Q 043345 5 VDFTKVGGHVHQLKGSSSSIGAQRVNNVCTAFRSFCEERNIEGCQQYLQHLKQEYYLVKNKLQTL 69 (80)
Q Consensus 5 ~D~~~~~~laH~LKGss~nlGa~~L~~~c~~lE~~~~~~~~~~~~~~~~~l~~~~~~l~~~L~~~ 69 (80)
......-+.+.+|.+.....-..+|..+...|++.+..-+.+. ..-+..|+.+...+..+|.+.
T Consensus 100 ~~a~~Al~~l~~L~~~~~~~TeSRl~tv~~~l~~la~~~~~Dp-~~Ri~~Le~e~~~i~~EI~~l 163 (478)
T PF11855_consen 100 PAAEKALRFLERLEERRFVGTESRLNTVFDALRQLAEGTDPDP-ERRIAELEREIAEIDAEIDRL 163 (478)
T ss_pred HHHHHHHHHHHHcCCCcccccHHHHHHHHHHHHHHHHhcCCCH-HHHHHHHHHHHHHHHHHHHHH
Confidence 3455677788899999999999999999999999997766554 344566666666666666544
No 92
>cd00089 HR1 Protein kinase C-related kinase homology region 1 domain; also known as the ACC (antiparallel coiled-coil) finger domain or Rho-binding domain. Found in vertebrate PRK1 and yeast PKC1 protein kinases C; those found in rhophilin bind RhoGTP; those in PRK1 bind RhoA and RhoB. Rho family members function as molecular switches, cycling between inactive and active forms, controlling a variety of cellular processes. HR1 repeats often occur in tandem repeat arrangments, seperated by a short linker region.
Probab=23.36 E-value=1.4e+02 Score=16.08 Aligned_cols=29 Identities=31% Similarity=0.370 Sum_probs=20.7
Q ss_pred cCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 043345 43 RNIEGCQQYLQHLKQEYYLVKNKLQTLFQ 71 (80)
Q Consensus 43 ~~~~~~~~~~~~l~~~~~~l~~~L~~~l~ 71 (80)
++...+...+......++.++..|..|..
T Consensus 42 ~~~~~~~~~l~es~~ki~~Lr~~L~k~~~ 70 (72)
T cd00089 42 KLLAEAEQMLRESKQKLELLKMQLEKLKQ 70 (72)
T ss_pred cCHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 44566777777777777888888877753
No 93
>COG1220 HslU ATP-dependent protease HslVU (ClpYQ), ATPase subunit [Posttranslational modification, protein turnover, chaperones]
Probab=22.91 E-value=1.2e+02 Score=22.59 Aligned_cols=31 Identities=19% Similarity=0.358 Sum_probs=26.1
Q ss_pred HHHHHHHHHHhhhhhhccChHHHHHHHHHHH
Q 043345 7 FTKVGGHVHQLKGSSSSIGAQRVNNVCTAFR 37 (80)
Q Consensus 7 ~~~~~~laH~LKGss~nlGa~~L~~~c~~lE 37 (80)
.+.+...|..+-...-||||.+|......+=
T Consensus 374 I~~iAeiA~~vN~~~ENIGARRLhTvlErlL 404 (444)
T COG1220 374 IKRIAEIAYQVNEKTENIGARRLHTVLERLL 404 (444)
T ss_pred HHHHHHHHHHhcccccchhHHHHHHHHHHHH
Confidence 3577888999999999999999998876653
No 94
>PRK06342 transcription elongation factor regulatory protein; Validated
Probab=22.89 E-value=2.1e+02 Score=18.18 Aligned_cols=46 Identities=4% Similarity=0.151 Sum_probs=29.4
Q ss_pred HHHHHHHHHHhhhhhhccChHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHHHHHH
Q 043345 7 FTKVGGHVHQLKGSSSSIGAQRVNNVCTAFRSFCEERNIEGCQQYLQHLKQEYYLVKNKLQ 67 (80)
Q Consensus 7 ~~~~~~laH~LKGss~nlGa~~L~~~c~~lE~~~~~~~~~~~~~~~~~l~~~~~~l~~~L~ 67 (80)
|..+..-.+.|| ..+..+...||..+.......+...+..+...|.
T Consensus 36 ~~~L~~El~~L~---------------~~i~~Ar~~GDlsEak~~~~~~e~rI~~L~~~L~ 81 (160)
T PRK06342 36 LKALEDQLAQAR---------------AAYEAAQAIEDVNERRRQMARPLRDLRYLAARRR 81 (160)
T ss_pred HHHHHHHHHHHH---------------HHHHHHHHCCChhHHHHHHHHHHHHHHHHHHHHc
Confidence 556666666666 3566777788888766566666666665555543
No 95
>KOG3612 consensus PHD Zn-finger protein [General function prediction only]
Probab=22.88 E-value=2.6e+02 Score=21.83 Aligned_cols=36 Identities=8% Similarity=0.049 Sum_probs=22.0
Q ss_pred HHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHHH
Q 043345 29 VNNVCTAFRSFCEERNIEGCQQYLQHLKQEYYLVKN 64 (80)
Q Consensus 29 L~~~c~~lE~~~~~~~~~~~~~~~~~l~~~~~~l~~ 64 (80)
|.+.+..+|+..+....+.+..+..+.+.++..++.
T Consensus 491 m~~~r~tlE~k~~~n~~e~~kkl~~~~qr~l~etKk 526 (588)
T KOG3612|consen 491 MAEMRKTLEQKHAENIKEEIKKLAEEHQRALAETKK 526 (588)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 566677777777666666666655555555555443
No 96
>PF10481 CENP-F_N: Cenp-F N-terminal domain; InterPro: IPR018463 Mitosin or centromere-associated protein-F (Cenp-F) is found bound across the centromere as one of the proteins of the outer layer of the kinetochore []. Most of the kinetochore/centromere functions appear to depend upon binding of the C-terminal part of the molecule, whereas the N-terminal part, here, may be a cytoplasmic player in controlling the function of microtubules and dynein [].
Probab=22.59 E-value=2.9e+02 Score=19.67 Aligned_cols=42 Identities=21% Similarity=0.411 Sum_probs=24.7
Q ss_pred HHHHHHHHHHHHHH----------------hhcCHHHHHHHHHHHHHHHHHHHHHHHH
Q 043345 27 QRVNNVCTAFRSFC----------------EERNIEGCQQYLQHLKQEYYLVKNKLQT 68 (80)
Q Consensus 27 ~~L~~~c~~lE~~~----------------~~~~~~~~~~~~~~l~~~~~~l~~~L~~ 68 (80)
..|.+.|..+|..- -.|....+...++.|..++.++...|++
T Consensus 70 q~l~e~c~~lek~rqKlshdlq~Ke~qv~~lEgQl~s~Kkqie~Leqelkr~KsELEr 127 (307)
T PF10481_consen 70 QSLMESCENLEKTRQKLSHDLQVKESQVNFLEGQLNSCKKQIEKLEQELKRCKSELER 127 (307)
T ss_pred hhHHHHHHHHHHHHHHhhHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45677777777533 2233344555666677777777666654
No 97
>COG5214 POL12 DNA polymerase alpha-primase complex, polymerase-associated subunit B [DNA replication, recombination, and repair]
Probab=22.53 E-value=1.3e+02 Score=22.87 Aligned_cols=45 Identities=16% Similarity=0.200 Sum_probs=23.9
Q ss_pred HHHHHHHHHHHHHH-hhcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhcC
Q 043345 27 QRVNNVCTAFRSFC-EERNIEGCQQYLQHLKQEYYLVKNKLQTLFQVCLKSLASS 80 (80)
Q Consensus 27 ~~L~~~c~~lE~~~-~~~~~~~~~~~~~~l~~~~~~l~~~L~~~l~~~~~~~~~~ 80 (80)
.....+..++|..| +.|++.-- +.. |..+... ..+++|||+++++
T Consensus 23 m~~q~mf~kwes~~~qr~~t~~d---l~t----~~~f~k~--mk~qmerqv~at~ 68 (581)
T COG5214 23 MDEQTMFYKWESWCLQRGNTKLD---LDT----FKAFAKD--MKFQMERQVKATL 68 (581)
T ss_pred ccHHHHHHHHHHHHHhcCCcccc---cHH----HHHHHHH--HHHHHHHHHHHHh
Confidence 34456667889988 45554211 111 2222221 2367888988753
No 98
>COG5613 Uncharacterized conserved protein [Function unknown]
Probab=22.11 E-value=3.3e+02 Score=20.13 Aligned_cols=43 Identities=12% Similarity=0.107 Sum_probs=17.1
Q ss_pred ChHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHHHHHH
Q 043345 25 GAQRVNNVCTAFRSFCEERNIEGCQQYLQHLKQEYYLVKNKLQ 67 (80)
Q Consensus 25 Ga~~L~~~c~~lE~~~~~~~~~~~~~~~~~l~~~~~~l~~~L~ 67 (80)
|+.+...-.-+-|.+-.+.+.+....-+..|+.-++++.+.+.
T Consensus 319 Gi~Qa~t~~~nae~a~~qad~q~~~ad~~~Lq~iierlkeelk 361 (400)
T COG5613 319 GIRQAGTTALNAEAAQLQADSQLAAADVQNLQRIIERLKEELK 361 (400)
T ss_pred hHHHhcchhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3333333333444443444443333333444444444444333
No 99
>TIGR00465 ilvC ketol-acid reductoisomerase. This is the second enzyme in the parallel isoleucine-valine biosynthetic pathway
Probab=22.05 E-value=2.7e+02 Score=19.61 Aligned_cols=38 Identities=16% Similarity=0.044 Sum_probs=25.3
Q ss_pred HHHHHHHHhhhhhhccChHHHHHHHHHHHHHHhhcCHH
Q 043345 9 KVGGHVHQLKGSSSSIGAQRVNNVCTAFRSFCEERNIE 46 (80)
Q Consensus 9 ~~~~laH~LKGss~nlGa~~L~~~c~~lE~~~~~~~~~ 46 (80)
.....+|++||++-.+.-..+..+...+=.-++=|+..
T Consensus 210 A~~~~~~~~~g~~~l~~e~g~~~l~~~Vsstaeyg~~~ 247 (314)
T TIGR00465 210 AYFETVHELKLIVDLIYEGGITGMRDRISNTAEYGALT 247 (314)
T ss_pred HHHHHHHHHHHHHHHHHHhcHHHHHHHcCCHHHcCcch
Confidence 34566899999999886665655555555555556543
No 100
>PF10191 COG7: Golgi complex component 7 (COG7); InterPro: IPR019335 The conserved oligomeric Golgi (COG) complex is an eight-subunit (Cog1-8) peripheral Golgi protein involved in membrane trafficking and glycoconjugate synthesis []. COG7 is required for normal Golgi morphology and trafficking. Mutation in COG7 causes a congenital disorder of glycosylation [].
Probab=22.01 E-value=3.1e+02 Score=21.89 Aligned_cols=38 Identities=11% Similarity=0.203 Sum_probs=31.7
Q ss_pred ChHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHH
Q 043345 25 GAQRVNNVCTAFRSFCEERNIEGCQQYLQHLKQEYYLV 62 (80)
Q Consensus 25 Ga~~L~~~c~~lE~~~~~~~~~~~~~~~~~l~~~~~~l 62 (80)
.|..+..++.+++.....+|.+.+...+..++..+..+
T Consensus 126 EA~~w~~l~~~v~~~~~~~d~~~~a~~l~~m~~sL~~l 163 (766)
T PF10191_consen 126 EADNWSTLSAEVDDLFESGDIAKIADRLAEMQRSLAVL 163 (766)
T ss_pred HHHhHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHH
Confidence 46678889999999999999999888888888877654
No 101
>PRK04778 septation ring formation regulator EzrA; Provisional
Probab=21.99 E-value=3.6e+02 Score=20.52 Aligned_cols=42 Identities=12% Similarity=0.286 Sum_probs=32.7
Q ss_pred HHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHHHHHHHH
Q 043345 28 RVNNVCTAFRSFCEERNIEGCQQYLQHLKQEYYLVKNKLQTL 69 (80)
Q Consensus 28 ~L~~~c~~lE~~~~~~~~~~~~~~~~~l~~~~~~l~~~L~~~ 69 (80)
.+-....+++....+||...+...+..++.....+...++..
T Consensus 176 ~~e~~f~~f~~l~~~Gd~~~A~e~l~~l~~~~~~l~~~~~~i 217 (569)
T PRK04778 176 NLEEEFSQFVELTESGDYVEAREILDQLEEELAALEQIMEEI 217 (569)
T ss_pred HHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 455556677788889999999999999998888887766544
No 102
>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=21.55 E-value=1.5e+02 Score=15.96 Aligned_cols=25 Identities=12% Similarity=0.274 Sum_probs=12.5
Q ss_pred HHHHHHHHHHhhcCHHHHHHHHHHH
Q 043345 31 NVCTAFRSFCEERNIEGCQQYLQHL 55 (80)
Q Consensus 31 ~~c~~lE~~~~~~~~~~~~~~~~~l 55 (80)
.....|..+...++++.+...+.+|
T Consensus 42 ~~~~~l~~~f~~~d~~~A~~~~~kL 66 (78)
T PF07743_consen 42 ELIKELAEAFDAKDWEEAKEALRKL 66 (78)
T ss_dssp HHHHHHHHHHHTT-HHHHHHHHHHH
T ss_pred HHHHHHHHHHccCcHHHHHHHHHHH
Confidence 3344444555555555555555555
No 103
>PF10069 DICT: Sensory domain found in DIguanylate Cyclases & Two-component systems; InterPro: IPR019278 This entry, found in various cyanobacterial sensor proteins that catalyse the reaction [ATP + protein L-histidine = ADP + protein N- phospho-L-histidine], has no known function.
Probab=21.54 E-value=56 Score=19.86 Aligned_cols=50 Identities=10% Similarity=0.046 Sum_probs=31.4
Q ss_pred hhhhccChHHHHHHHHHHHHHHhhcC-HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 043345 19 GSSSSIGAQRVNNVCTAFRSFCEERN-IEGCQQYLQHLKQEYYLVKNKLQTLFQV 72 (80)
Q Consensus 19 Gss~nlGa~~L~~~c~~lE~~~~~~~-~~~~~~~~~~l~~~~~~l~~~L~~~l~~ 72 (80)
+...++--..|..+|..||..+-... ..-+..-|++... ....+.+|.++
T Consensus 22 ~~~~~~~k~~L~alsr~iEd~a~~~~~~~~v~a~FQ~~s~----~~~e~~rY~~l 72 (129)
T PF10069_consen 22 PPFTSYSKRLLVALSRAIEDRAWRAGISGTVWAGFQRLSR----FRQEIDRYRQL 72 (129)
T ss_pred CCcceecHHHHHHHHHHHHHHHHhcCCCCEEEEeCCChhh----hHHHHHHHHHH
Confidence 47788899999999999999985544 2233333333333 33333555544
No 104
>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=21.53 E-value=93 Score=15.56 Aligned_cols=22 Identities=23% Similarity=0.348 Sum_probs=17.2
Q ss_pred hHHHHHHHHHHhhhhhhccChH
Q 043345 6 DFTKVGGHVHQLKGSSSSIGAQ 27 (80)
Q Consensus 6 D~~~~~~laH~LKGss~nlGa~ 27 (80)
-|-.+.++.-+|||++-+.+..
T Consensus 5 G~GRMerLLaSlrg~~~s~~pl 26 (41)
T PF03858_consen 5 GFGRMERLLASLRGSADSSTPL 26 (41)
T ss_pred chhhHHHHHHHHhccCCCCcch
Confidence 4677888999999998876543
No 105
>COG1598 Predicted nuclease of the RNAse H fold, HicB family [General function prediction only]
Probab=21.52 E-value=66 Score=17.59 Aligned_cols=28 Identities=14% Similarity=0.286 Sum_probs=18.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 043345 46 EGCQQYLQHLKQEYYLVKNKLQTLFQVC 73 (80)
Q Consensus 46 ~~~~~~~~~l~~~~~~l~~~L~~~l~~~ 73 (80)
++|...-..++..+..+..+|+-|+..+
T Consensus 24 pgc~s~G~T~eea~~n~~eai~l~~e~~ 51 (73)
T COG1598 24 PGCHSQGETLEEALQNAKEAIELHLEAL 51 (73)
T ss_pred CCccccCCCHHHHHHHHHHHHHHHHHHH
Confidence 3444555666777777777777777653
No 106
>PF04428 Choline_kin_N: Choline kinase N terminus; InterPro: IPR007521 This domain is found N-terminal to choline/ethanolamine kinase regions (IPR002573 from INTERPRO) in some plant and fungal choline kinase enzymes (2.7.1.32 from EC). This region is only found in some members of the choline kinase family, and is therefore unlikely to contribute to catalysis.; GO: 0016773 phosphotransferase activity, alcohol group as acceptor
Probab=21.38 E-value=97 Score=16.28 Aligned_cols=11 Identities=27% Similarity=0.383 Sum_probs=9.2
Q ss_pred HHHHHHHHHhh
Q 043345 8 TKVGGHVHQLK 18 (80)
Q Consensus 8 ~~~~~laH~LK 18 (80)
..+.+++|+||
T Consensus 30 ~di~~l~htL~ 40 (53)
T PF04428_consen 30 QDILRLIHTLK 40 (53)
T ss_pred HHHHHHHHHhc
Confidence 57888999987
No 107
>PF05465 Halo_GVPC: Halobacterial gas vesicle protein C (GVPC) repeat; InterPro: IPR008639 This family consists of Halobacterium gas vesicle protein C sequences which are thought to confer stability to the gas vesicle membranes [,].; GO: 0031412 gas vesicle organization, 0031411 gas vesicle
Probab=20.98 E-value=1.1e+02 Score=14.23 Aligned_cols=23 Identities=4% Similarity=0.163 Sum_probs=17.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Q 043345 48 CQQYLQHLKQEYYLVKNKLQTLF 70 (80)
Q Consensus 48 ~~~~~~~l~~~~~~l~~~L~~~l 70 (80)
+...+..++.+|..++.....|-
T Consensus 4 l~a~I~~~r~~f~~~~~aF~aY~ 26 (32)
T PF05465_consen 4 LLAAIAEFREEFDDTQDAFEAYA 26 (32)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 44567778888888888887774
No 108
>PF06160 EzrA: Septation ring formation regulator, EzrA ; InterPro: IPR010379 During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerises into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation [].; GO: 0000921 septin ring assembly, 0005940 septin ring, 0016021 integral to membrane
Probab=20.88 E-value=3.9e+02 Score=20.41 Aligned_cols=42 Identities=14% Similarity=0.294 Sum_probs=32.8
Q ss_pred HHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHHHHHHH
Q 043345 27 QRVNNVCTAFRSFCEERNIEGCQQYLQHLKQEYYLVKNKLQT 68 (80)
Q Consensus 27 ~~L~~~c~~lE~~~~~~~~~~~~~~~~~l~~~~~~l~~~L~~ 68 (80)
..+-.....++....+||...+...+..++.....+...++.
T Consensus 171 ~~ie~~F~~f~~lt~~GD~~~A~eil~~l~~~~~~l~~~~e~ 212 (560)
T PF06160_consen 171 ENIEEEFSEFEELTENGDYLEAREILEKLKEETDELEEIMED 212 (560)
T ss_pred HHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345556677778889999999999999999888887776653
No 109
>PRK14158 heat shock protein GrpE; Provisional
Probab=20.82 E-value=2.6e+02 Score=18.48 Aligned_cols=15 Identities=0% Similarity=0.014 Sum_probs=7.8
Q ss_pred HHHHHHHHHHHHHhh
Q 043345 28 RVNNVCTAFRSFCEE 42 (80)
Q Consensus 28 ~L~~~c~~lE~~~~~ 42 (80)
.|...+..||.+...
T Consensus 95 ~lLpV~DnLerAl~~ 109 (194)
T PRK14158 95 EILPAVDNMERALDH 109 (194)
T ss_pred HHHhHHhHHHHHHhc
Confidence 344555556655543
No 110
>cd04751 Commd3 COMM_Domain containing protein 3. The COMM Domain is found at the C-terminus of a variety of proteins; presumably all COMM_Domain containing proteins are located in the nucleus and the COMM domain plays a role in protein-protein interactions. Several family members have been shown to bind and inhibit NF-kappaB.
Probab=20.81 E-value=96 Score=17.89 Aligned_cols=16 Identities=19% Similarity=0.376 Sum_probs=8.5
Q ss_pred hHHHHHHHHHHhhhhh
Q 043345 6 DFTKVGGHVHQLKGSS 21 (80)
Q Consensus 6 D~~~~~~laH~LKGss 21 (80)
|.+++..+.+.||...
T Consensus 72 ~~e~L~~Li~~Lk~A~ 87 (95)
T cd04751 72 TLEQLQDLVNKLKDAA 87 (95)
T ss_pred CHHHHHHHHHHHHHHH
Confidence 4455555555555444
No 111
>PF14989 CCDC32: Coiled-coil domain containing 32
Probab=20.79 E-value=99 Score=19.74 Aligned_cols=71 Identities=10% Similarity=0.251 Sum_probs=43.3
Q ss_pred HHHHHHHHhhhhhhccChHHHHHHHHHHHHHHhhcCHHH--HHHHH-HHHHHHHHHHHHHHHHHHHHHHhhhhc
Q 043345 9 KVGGHVHQLKGSSSSIGAQRVNNVCTAFRSFCEERNIEG--CQQYL-QHLKQEYYLVKNKLQTLFQVCLKSLAS 79 (80)
Q Consensus 9 ~~~~laH~LKGss~nlGa~~L~~~c~~lE~~~~~~~~~~--~~~~~-~~l~~~~~~l~~~L~~~l~~~~~~~~~ 79 (80)
.+.+-.-+|||.+..|-...|...-.+.-+.|-..=..+ ....+ ..+...-..+...|.++|..|+|++++
T Consensus 60 sLE~KL~rik~~~~~vtsKemL~sL~~aK~d~~~rlL~~~~~~~~~~~~~~~D~p~~~~~l~R~L~Pe~qAls~ 133 (148)
T PF14989_consen 60 SLERKLKRIKGKNREVTSKEMLRSLSQAKEDCWDRLLSSGNPSEFFEDDLDSDEPILEHYLKRWLAPEKQALSK 133 (148)
T ss_pred HHHHHHHHHhCCCccCCHHHHHHHHHHHHHHHHHHHHcCCCcchhccCccccccchhhhhHHhhhCchhhcccH
Confidence 455557889999999999888887777666553221111 11111 112222233455588999999998764
No 112
>PF13779 DUF4175: Domain of unknown function (DUF4175)
Probab=20.79 E-value=4.7e+02 Score=21.32 Aligned_cols=21 Identities=10% Similarity=0.191 Sum_probs=12.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHH
Q 043345 53 QHLKQEYYLVKNKLQTLFQVC 73 (80)
Q Consensus 53 ~~l~~~~~~l~~~L~~~l~~~ 73 (80)
++|+.-++.++.+++.||+..
T Consensus 492 eEI~rLm~eLR~A~~~ym~~L 512 (820)
T PF13779_consen 492 EEIARLMQELREAMQDYMQAL 512 (820)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 445555556666666666653
No 113
>COG2841 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.79 E-value=1.7e+02 Score=16.37 Aligned_cols=65 Identities=17% Similarity=0.276 Sum_probs=46.7
Q ss_pred HHHHHHHHHHhhhhhhccChHHHHHHHHHHHHHHh--hcC-HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 043345 7 FTKVGGHVHQLKGSSSSIGAQRVNNVCTAFRSFCE--ERN-IEGCQQYLQHLKQEYYLVKNKLQTLFQVC 73 (80)
Q Consensus 7 ~~~~~~laH~LKGss~nlGa~~L~~~c~~lE~~~~--~~~-~~~~~~~~~~l~~~~~~l~~~L~~~l~~~ 73 (80)
+..++.+.|.|||-- -.+.+|.+--.+|-.... .++ ......-+..|+.+=-.+..+|-.+|+-.
T Consensus 2 ~~Efr~~is~Lk~~d--ahF~rLfd~hn~LDd~I~~~E~n~~~~s~~ev~~LKKqkL~LKDEi~~~L~~a 69 (72)
T COG2841 2 FHEFRDLISKLKAND--AHFARLFDKHNELDDRIKRAEGNRQPGSDAEVSNLKKQKLQLKDEIASILQKA 69 (72)
T ss_pred chhHHHHHHHHhccc--hHHHHHHHHHhHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHhHHHHHHHHHHH
Confidence 456789999999875 467888888888876552 222 33455567888888888888888877643
No 114
>PF04782 DUF632: Protein of unknown function (DUF632); InterPro: IPR006867 This conserved region contains a leucine zipper-like domain. The proteins are found only in plants and their functions are unknown.
Probab=20.46 E-value=1.7e+02 Score=20.80 Aligned_cols=36 Identities=8% Similarity=0.180 Sum_probs=25.6
Q ss_pred hhccChHHHHHHHHHHHHHHhhcCHHHHHHHHHHHH
Q 043345 21 SSSIGAQRVNNVCTAFRSFCEERNIEGCQQYLQHLK 56 (80)
Q Consensus 21 s~nlGa~~L~~~c~~lE~~~~~~~~~~~~~~~~~l~ 56 (80)
-+.+|+++++.+|.+.-++...-....+...+..+.
T Consensus 271 p~~~~aPpIf~lC~~W~~aLd~lp~k~v~~AIk~f~ 306 (312)
T PF04782_consen 271 PRRSGAPPIFVLCNDWSQALDRLPDKEVSEAIKSFA 306 (312)
T ss_pred ccccCCCcHHHHHHHHHHHHHcCChHHHHHHHHHHH
Confidence 456899999999999999887655445444444333
No 115
>PRK08655 prephenate dehydrogenase; Provisional
Probab=20.28 E-value=3.6e+02 Score=19.80 Aligned_cols=35 Identities=6% Similarity=0.143 Sum_probs=20.3
Q ss_pred HHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHH
Q 043345 28 RVNNVCTAFRSFCEERNIEGCQQYLQHLKQEYYLV 62 (80)
Q Consensus 28 ~L~~~c~~lE~~~~~~~~~~~~~~~~~l~~~~~~l 62 (80)
.+...+.++.....++|.+.+...+.+-...+..+
T Consensus 240 ~~~~~l~~l~~~l~~~D~~~l~~~~~~a~~~~~~~ 274 (437)
T PRK08655 240 TFIKECEELSELVKNGDREEFVERMKEAAKHFGDT 274 (437)
T ss_pred HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHhccc
Confidence 34445566666666677666666666555544433
Done!