Query 034402
Match_columns 95
No_of_seqs 89 out of 106
Neff 3.5
Searched_HMMs 46136
Date Fri Mar 29 02:29:14 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034402.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/034402hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR01589 A_thal_3526 uncharac 100.0 1.3E-36 2.7E-41 194.1 6.7 56 9-64 1-56 (57)
2 PF09713 A_thal_3526: Plant pr 100.0 1.1E-35 2.3E-40 187.9 6.2 53 12-64 1-53 (54)
3 PF08986 DUF1889: Domain of un 91.8 0.21 4.6E-06 36.0 3.3 40 30-69 69-117 (119)
4 PF13565 HTH_32: Homeodomain-l 81.9 4.9 0.00011 24.5 4.7 43 9-51 33-77 (77)
5 smart00411 BHL bacterial (prok 80.7 3.7 8.1E-05 26.0 4.1 30 24-53 1-30 (90)
6 COG1725 Predicted transcriptio 78.3 4.3 9.3E-05 29.3 4.1 50 5-54 10-62 (125)
7 PF14775 NYD-SP28_assoc: Sperm 77.0 16 0.00034 23.1 6.0 47 35-85 5-56 (60)
8 PF08145 BOP1NT: BOP1NT (NUC16 72.9 2.8 6.1E-05 33.8 2.2 32 7-42 213-244 (260)
9 PF00216 Bac_DNA_binding: Bact 71.2 7.8 0.00017 24.4 3.6 30 24-53 1-30 (90)
10 PF14420 Clr5: Clr5 domain 68.1 15 0.00032 22.3 4.2 36 7-42 3-39 (54)
11 TIGR00988 hip integration host 65.0 16 0.00034 23.7 4.2 30 24-53 1-31 (94)
12 PF08020 DUF1706: Protein of u 63.5 13 0.00029 27.5 4.0 54 36-89 68-123 (166)
13 TIGR00987 himA integration hos 63.4 16 0.00035 24.0 4.0 30 24-53 2-31 (96)
14 smart00139 MyTH4 Domain in Myo 61.8 22 0.00047 25.4 4.7 53 1-53 33-91 (144)
15 COG4399 Uncharacterized protei 60.5 45 0.00097 28.5 7.0 79 7-85 83-169 (376)
16 PRK00285 ihfA integration host 60.2 20 0.00042 23.6 4.0 31 23-53 2-32 (99)
17 PF06570 DUF1129: Protein of u 60.1 10 0.00022 28.1 2.9 35 50-85 1-35 (206)
18 PRK05617 3-hydroxyisobutyryl-C 59.8 90 0.0019 25.0 8.4 57 6-66 222-278 (342)
19 PRK00199 ihfB integration host 59.7 22 0.00048 23.1 4.2 30 24-53 1-31 (94)
20 PRK10664 transcriptional regul 59.6 21 0.00045 23.6 4.1 26 24-49 1-26 (90)
21 PLN02814 beta-glucosidase 58.5 11 0.00023 32.3 3.0 49 5-68 112-171 (504)
22 PRK14552 C/D box methylation g 56.2 21 0.00046 30.1 4.4 49 1-49 222-272 (414)
23 PF05402 PqqD: Coenzyme PQQ sy 56.1 38 0.00082 20.2 4.5 33 18-50 24-57 (68)
24 PLN02849 beta-glucosidase 53.3 13 0.00029 31.7 2.9 48 6-68 115-173 (503)
25 PRK10753 transcriptional regul 53.0 31 0.00068 22.6 4.1 26 24-49 1-26 (90)
26 COG3415 Transposase and inacti 52.5 32 0.0007 25.0 4.4 52 3-55 60-111 (138)
27 PLN02998 beta-glucosidase 51.3 15 0.00032 31.4 2.8 47 6-67 118-175 (497)
28 PRK10963 hypothetical protein; 50.8 13 0.00028 28.1 2.2 22 23-63 2-23 (223)
29 PF04340 DUF484: Protein of un 48.5 5.8 0.00013 29.6 0.0 10 53-62 16-25 (225)
30 TIGR01795 CM_mono_cladeE monof 48.1 28 0.0006 23.5 3.3 25 31-55 58-82 (94)
31 PF00325 Crp: Bacterial regula 47.6 38 0.00082 19.1 3.3 29 23-55 2-30 (32)
32 PF02082 Rrf2: Transcriptional 47.3 27 0.00059 22.1 3.0 27 29-55 27-53 (83)
33 PF03918 CcmH: Cytochrome C bi 46.9 44 0.00096 24.3 4.4 37 2-38 52-88 (148)
34 TIGR01201 HU_rel DNA-binding p 46.8 39 0.00085 24.1 4.0 31 24-54 31-61 (145)
35 PF03979 Sigma70_r1_1: Sigma-7 45.5 60 0.0013 20.9 4.4 51 7-58 4-55 (82)
36 PF13545 HTH_Crp_2: Crp-like h 45.3 44 0.00096 20.0 3.6 31 21-55 26-56 (76)
37 TIGR03356 BGL beta-galactosida 44.4 31 0.00068 28.5 3.6 39 28-67 98-146 (427)
38 PF12776 Myb_DNA-bind_3: Myb/S 44.2 79 0.0017 19.8 5.4 49 40-88 26-75 (96)
39 COG4359 Uncharacterized conser 43.9 27 0.00057 27.9 3.0 27 21-47 56-82 (220)
40 PRK08091 ribulose-phosphate 3- 43.6 15 0.00033 28.6 1.6 33 24-57 1-33 (228)
41 PF04433 SWIRM: SWIRM domain; 43.4 32 0.0007 22.0 2.9 46 5-54 32-81 (86)
42 PF00232 Glyco_hydro_1: Glycos 42.5 9.9 0.00021 31.4 0.5 47 5-66 94-150 (455)
43 TIGR03147 cyt_nit_nrfF cytochr 41.4 60 0.0013 23.5 4.3 46 3-48 53-105 (126)
44 PF07527 Hairy_orange: Hairy O 40.5 59 0.0013 18.6 3.5 27 27-53 12-38 (43)
45 KOG2211 Predicted Golgi transp 40.2 37 0.0008 31.4 3.7 17 38-54 361-377 (797)
46 COG1725 Predicted transcriptio 40.1 52 0.0011 23.7 3.8 29 7-35 90-118 (125)
47 PRK11753 DNA-binding transcrip 39.8 82 0.0018 22.0 4.7 30 22-55 167-196 (211)
48 PRK05686 fliG flagellar motor 39.1 1.8E+02 0.004 23.2 7.1 60 1-62 171-237 (339)
49 PRK15014 6-phospho-beta-glucos 38.9 37 0.0008 28.8 3.3 47 5-66 105-162 (477)
50 PF00784 MyTH4: MyTH4 domain; 38.8 1.1E+02 0.0025 20.4 5.2 46 8-53 2-49 (114)
51 PRK13511 6-phospho-beta-galact 38.4 22 0.00048 29.8 1.9 47 5-66 89-145 (469)
52 PF14164 YqzH: YqzH-like prote 37.8 41 0.00089 22.1 2.7 14 10-23 4-17 (64)
53 cd00591 HU_IHF Integration hos 37.5 76 0.0017 19.7 3.9 29 25-53 1-29 (87)
54 smart00345 HTH_GNTR helix_turn 37.4 56 0.0012 18.1 3.0 26 30-55 23-48 (60)
55 PF14769 CLAMP: Flagellar C1a 37.2 1.2E+02 0.0027 20.0 6.8 56 7-62 19-84 (101)
56 TIGR02894 DNA_bind_RsfA transc 35.0 2E+02 0.0044 21.8 7.7 62 22-84 78-148 (161)
57 TIGR00269 conserved hypothetic 34.4 1.4E+02 0.0031 19.9 5.1 41 22-63 8-61 (104)
58 TIGR01233 lacG 6-phospho-beta- 34.3 62 0.0013 27.3 3.9 38 29-67 98-145 (467)
59 PF09280 XPC-binding: XPC-bind 34.2 42 0.0009 21.1 2.3 28 35-62 15-42 (59)
60 COG1510 Predicted transcriptio 34.0 2.2E+02 0.0048 22.0 7.1 59 24-89 42-121 (177)
61 PF13720 Acetyltransf_11: Udp 33.8 1.4E+02 0.003 19.5 5.4 43 5-47 29-71 (83)
62 PRK10144 formate-dependent nit 33.6 95 0.0021 22.5 4.3 46 3-48 53-105 (126)
63 PF05295 Luciferase_N: Lucifer 33.3 1.2E+02 0.0027 20.8 4.6 45 28-72 4-53 (82)
64 smart00511 ORANGE Orange domai 32.3 87 0.0019 17.9 3.3 27 27-53 12-38 (45)
65 KOG3973 Uncharacterized conser 32.3 43 0.00092 29.1 2.7 56 12-67 141-220 (465)
66 PF11417 Inhibitor_G39P: Loade 31.6 50 0.0011 21.5 2.4 30 24-53 1-41 (71)
67 PF13936 HTH_38: Helix-turn-he 31.4 79 0.0017 18.1 3.0 33 14-53 11-43 (44)
68 PRK09589 celA 6-phospho-beta-g 31.3 58 0.0012 27.6 3.3 48 5-67 103-161 (476)
69 PF05960 DUF885: Bacterial pro 30.9 3.1E+02 0.0066 22.7 7.7 59 3-62 432-499 (549)
70 PF11333 DUF3135: Protein of u 30.4 1.7E+02 0.0037 19.6 5.2 27 46-72 7-33 (83)
71 smart00760 Bac_DnaA_C Bacteria 30.3 51 0.0011 19.8 2.2 18 25-42 1-18 (60)
72 PRK10820 DNA-binding transcrip 29.9 1.4E+02 0.003 25.3 5.3 37 10-53 473-509 (520)
73 PF02954 HTH_8: Bacterial regu 29.7 1.1E+02 0.0024 17.2 4.7 34 13-53 7-41 (42)
74 TIGR00207 fliG flagellar motor 29.6 3E+02 0.0066 22.2 7.3 59 2-62 170-234 (338)
75 PRK07194 fliG flagellar motor 29.6 2.8E+02 0.0062 22.3 6.8 58 1-61 166-230 (334)
76 smart00830 CM_2 Chorismate mut 29.4 73 0.0016 19.5 2.8 9 56-64 60-68 (79)
77 PRK09239 chorismate mutase; Pr 29.3 95 0.0021 21.3 3.6 18 55-72 74-91 (104)
78 PRK14137 recX recombination re 29.1 1.6E+02 0.0034 22.3 5.0 52 10-62 37-96 (195)
79 PF13305 WHG: WHG domain; PDB: 28.9 1.3E+02 0.0028 17.7 4.3 18 51-68 10-27 (81)
80 PF08004 DUF1699: Protein of u 28.5 1.4E+02 0.003 22.2 4.5 40 6-49 91-130 (131)
81 cd07377 WHTH_GntR Winged helix 28.5 93 0.002 17.5 3.0 26 30-55 28-53 (66)
82 TIGR02010 IscR iron-sulfur clu 28.4 73 0.0016 21.9 2.9 26 30-55 28-53 (135)
83 PRK11361 acetoacetate metaboli 28.3 1.7E+02 0.0036 23.3 5.2 37 11-54 417-454 (457)
84 PF03965 Penicillinase_R: Peni 28.2 63 0.0014 21.5 2.5 30 24-53 18-47 (115)
85 PF13592 HTH_33: Winged helix- 28.1 1.1E+02 0.0025 18.4 3.5 38 9-47 7-44 (60)
86 COG0776 HimA Bacterial nucleoi 28.0 1.3E+02 0.0027 20.7 4.0 18 24-41 2-19 (94)
87 COG5104 PRP40 Splicing factor 27.7 2.2E+02 0.0048 25.6 6.3 36 55-90 189-228 (590)
88 TIGR01803 CM-like chorismate m 27.6 79 0.0017 20.2 2.8 20 34-53 57-76 (82)
89 PF09012 FeoC: FeoC like trans 27.2 87 0.0019 19.2 2.9 24 30-53 17-40 (69)
90 PF12383 SARS_3b: Severe acute 26.9 63 0.0014 24.0 2.5 35 14-48 114-148 (153)
91 PRK00117 recX recombination re 26.7 2.2E+02 0.0048 19.7 5.5 47 18-65 20-70 (157)
92 cd05062 PTKc_IGF-1R Catalytic 25.9 75 0.0016 22.6 2.7 25 10-34 248-276 (277)
93 PRK04182 cytidylate kinase; Pr 25.7 2.1E+02 0.0046 19.2 4.9 69 22-90 98-176 (180)
94 smart00419 HTH_CRP helix_turn_ 25.1 99 0.0021 16.6 2.6 30 22-55 7-36 (48)
95 COG4283 Uncharacterized conser 25.0 1.1E+02 0.0025 23.5 3.6 54 35-88 67-122 (170)
96 PLN02350 phosphogluconate dehy 24.7 1.6E+02 0.0035 25.3 4.9 45 1-47 178-223 (493)
97 KOG1199 Short-chain alcohol de 24.5 56 0.0012 26.3 2.0 17 2-19 227-243 (260)
98 PF10045 DUF2280: Uncharacteri 24.5 2.7E+02 0.0058 19.9 7.1 54 11-64 7-68 (104)
99 PF14123 DUF4290: Domain of un 24.5 1.7E+02 0.0037 22.5 4.5 46 6-52 13-68 (176)
100 PF05066 HARE-HTH: HB1, ASXL, 24.4 1.3E+02 0.0029 18.4 3.3 30 24-54 1-30 (72)
101 PTZ00398 phosphoenolpyruvate c 24.3 77 0.0017 29.8 3.1 33 12-45 155-187 (974)
102 PF11349 DUF3151: Protein of u 24.3 1.3E+02 0.0028 22.3 3.7 38 54-91 87-124 (129)
103 PF00735 Septin: Septin; Inte 24.0 68 0.0015 25.1 2.3 54 7-60 81-180 (281)
104 KOG0451 Predicted 2-oxoglutara 24.0 87 0.0019 29.1 3.2 47 40-86 435-481 (913)
105 TIGR03697 NtcA_cyano global ni 23.5 1E+02 0.0022 21.0 3.0 30 22-55 142-171 (193)
106 cd04787 HTH_HMRTR_unk Helix-Tu 23.4 2.5E+02 0.0055 19.3 9.6 71 5-86 40-110 (133)
107 cd07765 KRAB_A-box KRAB (Krupp 23.4 35 0.00076 14.6 0.4 25 38-62 5-29 (40)
108 PF14039 YusW: YusW-like prote 23.4 73 0.0016 21.6 2.1 37 8-44 45-82 (92)
109 cd05094 PTKc_TrkC Catalytic do 23.2 1E+02 0.0022 22.2 3.0 29 10-38 252-284 (291)
110 PRK09852 cryptic 6-phospho-bet 23.2 1.8E+02 0.0038 24.8 4.8 48 5-67 107-165 (474)
111 PF07531 TAFH: NHR1 homology t 23.2 1.5E+02 0.0033 20.6 3.7 37 5-41 22-58 (96)
112 TIGR02915 PEP_resp_reg putativ 23.1 1.9E+02 0.0042 22.9 4.7 37 11-54 405-442 (445)
113 TIGR02173 cyt_kin_arch cytidyl 22.6 2.4E+02 0.0053 18.8 4.8 41 25-65 101-141 (171)
114 PRK00009 phosphoenolpyruvate c 22.6 89 0.0019 29.2 3.1 33 12-45 109-141 (911)
115 PRK10857 DNA-binding transcrip 22.6 1E+02 0.0022 22.4 2.9 25 30-54 28-52 (164)
116 PF11626 Rap1_C: TRF2-interact 22.5 1.1E+02 0.0023 20.0 2.7 38 16-53 1-38 (87)
117 COG1438 ArgR Arginine represso 22.1 1.1E+02 0.0024 22.8 3.0 30 22-53 19-48 (150)
118 PF13625 Helicase_C_3: Helicas 22.0 1.2E+02 0.0026 20.6 3.1 48 14-69 45-94 (129)
119 COG1498 SIK1 Protein implicate 21.9 1.6E+02 0.0034 25.3 4.2 51 1-51 200-252 (395)
120 PRK14135 recX recombination re 21.8 2E+02 0.0043 21.7 4.4 47 7-54 105-152 (263)
121 PRK09391 fixK transcriptional 21.7 1.4E+02 0.003 21.8 3.5 31 21-55 177-207 (230)
122 PF02847 MA3: MA3 domain; Int 21.4 2.3E+02 0.0051 18.1 7.7 73 13-86 2-83 (113)
123 PRK15115 response regulator Gl 21.1 2.2E+02 0.0048 22.6 4.7 37 11-54 398-435 (444)
124 COG2963 Transposase and inacti 20.9 1.1E+02 0.0024 20.1 2.6 41 19-59 16-57 (116)
125 KOG2150 CCR4-NOT transcription 20.9 5.1E+02 0.011 23.5 7.3 66 10-89 4-69 (575)
126 KOG2431 1, 2-alpha-mannosidase 20.8 1E+02 0.0023 27.4 3.0 21 5-25 390-411 (546)
127 smart00543 MIF4G Middle domain 20.8 2.9E+02 0.0062 18.8 7.4 52 11-62 15-73 (200)
128 PRK10696 tRNA 2-thiocytidine b 20.7 2.7E+02 0.0058 21.1 4.9 43 22-65 179-235 (258)
129 COG2443 Sss1 Preprotein transl 20.7 2.1E+02 0.0045 18.8 3.8 31 51-81 7-37 (65)
130 PF00538 Linker_histone: linke 20.4 1.5E+02 0.0032 18.6 3.0 47 7-53 4-54 (77)
131 KOG0019 Molecular chaperone (H 20.4 2.4E+02 0.0053 25.8 5.3 41 54-94 378-422 (656)
132 cd01106 HTH_TipAL-Mta Helix-Tu 20.3 2.6E+02 0.0056 18.2 7.9 61 5-84 40-102 (103)
133 PF06711 DUF1198: Protein of u 20.3 1.9E+02 0.0041 21.9 3.9 37 28-64 26-62 (148)
134 TIGR01797 CM_P_1 chorismate mu 20.2 1.5E+02 0.0032 19.0 3.0 18 37-54 60-77 (83)
135 PF14076 DUF4258: Domain of un 20.1 1.6E+02 0.0035 17.3 3.0 23 13-35 4-26 (73)
No 1
>TIGR01589 A_thal_3526 uncharacterized plant-specific domain TIGR01589. This model represents an uncharacterized plant-specific domain 57 residues in length. It is found toward the N-terminus of most proteins that contain it. Examples include at least 10 proteins from Arabidopsis thaliana and at least one from Oryza sativa.
Probab=100.00 E-value=1.3e-36 Score=194.11 Aligned_cols=56 Identities=45% Similarity=0.681 Sum_probs=54.6
Q ss_pred HHHHHHHHHHHHHhhCCHHHHHHHHHhhcCCCchhHHHHHHHHHHhcHHHHHHHHH
Q 034402 9 IHMVQHLIEKCLIFRMTKEECMEALSKHANIKPVITSTVWNELEKENKEFFEAYAQ 64 (95)
Q Consensus 9 I~~VQ~LIErCLqlyMsk~E~v~~L~~~a~I~P~fT~~VW~~LE~eN~eFFkaY~~ 64 (95)
|++|||||||||++|||++|||++|++||||+|+||++||++||+||||||+||+.
T Consensus 1 i~~Vq~lIE~Cl~~yMsk~E~v~~L~~~a~I~P~~T~~VW~~LekeN~eFF~aY~~ 56 (57)
T TIGR01589 1 IDLVQNRIETCIQGYMSKEETVSFLFENAGISPKFTRFVWYLLEKENADFFRCYKT 56 (57)
T ss_pred CHHHHHHHHHHHHHHCCHHHHHHHHHHHcCCCchhHHHHHHHHHHHHHHHHHHHhc
Confidence 68999999999999999999999999999999999999999999999999999964
No 2
>PF09713 A_thal_3526: Plant protein 1589 of unknown function (A_thal_3526); InterPro: IPR006476 This plant-specific family of proteins are defined by an uncharacterised region 57 residues in length. It is found toward the N terminus of most proteins that contain it. Examples include at least several proteins from Arabidopsis thaliana (Mouse-ear cress) and Oryza sativa (Rice). The function of the proteins are unknown.
Probab=100.00 E-value=1.1e-35 Score=187.90 Aligned_cols=53 Identities=66% Similarity=1.072 Sum_probs=51.8
Q ss_pred HHHHHHHHHHhhCCHHHHHHHHHhhcCCCchhHHHHHHHHHHhcHHHHHHHHH
Q 034402 12 VQHLIEKCLIFRMTKEECMEALSKHANIKPVITSTVWNELEKENKEFFEAYAQ 64 (95)
Q Consensus 12 VQ~LIErCLqlyMsk~E~v~~L~~~a~I~P~fT~~VW~~LE~eN~eFFkaY~~ 64 (95)
||+||||||++|||++|||++|++||||+|+||++||++||+||||||+||+.
T Consensus 1 Vq~lIErCl~~yMsk~E~v~~L~~~a~I~P~~T~~VW~~Le~eN~eFF~aY~~ 53 (54)
T PF09713_consen 1 VQNLIERCLQLYMSKEECVRALQKQANIEPVFTSTVWQKLEKENPEFFKAYYT 53 (54)
T ss_pred CchHHHHHHHHcCCHHHHHHHHHHHcCCChHHHHHHHHHHHHHCHHHHHHhhc
Confidence 79999999999999999999999999999999999999999999999999965
No 3
>PF08986 DUF1889: Domain of unknown function (DUF1889); InterPro: IPR015079 This family consist of hypothetical bacterial proteins. ; PDB: 2JN8_A 2ES9_A.
Probab=91.83 E-value=0.21 Score=36.04 Aligned_cols=40 Identities=28% Similarity=0.393 Sum_probs=26.5
Q ss_pred HHHHHhhcCCCchhHHHHHHHHHH---------hcHHHHHHHHHhhhHH
Q 034402 30 MEALSKHANIKPVITSTVWNELEK---------ENKEFFEAYAQSQSKE 69 (95)
Q Consensus 30 v~~L~~~a~I~P~fT~~VW~~LE~---------eN~eFFkaY~~~~lk~ 69 (95)
|.+=-++-|-+|+||..|-.--++ .|||||..|.|-+||.
T Consensus 69 v~aRg~qeGWn~gFT~k~agwaeki~sG~rivIKnPEyFs~YMreqLra 117 (119)
T PF08986_consen 69 VTARGEQEGWNPGFTEKVAGWAEKIASGERIVIKNPEYFSSYMREQLRA 117 (119)
T ss_dssp HHHHHHHCT--HHHHHHHHHHHHHHHCT-----SSGGGS-HHHHHHHHH
T ss_pred HHHhcccccCChhHHHHHHHHHHHHhcCCeeeecChHHHHHHHHHHHHH
Confidence 444456779999999987333333 7999999998876663
No 4
>PF13565 HTH_32: Homeodomain-like domain
Probab=81.86 E-value=4.9 Score=24.54 Aligned_cols=43 Identities=28% Similarity=0.201 Sum_probs=29.3
Q ss_pred HHHHHHHHHHHHHh-hCCHHHHHHHHHhhcCCCc-hhHHHHHHHH
Q 034402 9 IHMVQHLIEKCLIF-RMTKEECMEALSKHANIKP-VITSTVWNEL 51 (95)
Q Consensus 9 I~~VQ~LIErCLql-yMsk~E~v~~L~~~a~I~P-~fT~~VW~~L 51 (95)
-.+.+.+++-.... .+|..++...|..++||.. .=-++||+-|
T Consensus 33 ~e~~~~i~~~~~~~p~wt~~~i~~~L~~~~g~~~~~S~~tv~R~L 77 (77)
T PF13565_consen 33 PEQRERIIALIEEHPRWTPREIAEYLEEEFGISVRVSRSTVYRIL 77 (77)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHHHHHhCCCCCccHhHHHHhC
Confidence 34445555544444 7999999999999999864 3345777643
No 5
>smart00411 BHL bacterial (prokaryotic) histone like domain.
Probab=80.74 E-value=3.7 Score=26.03 Aligned_cols=30 Identities=20% Similarity=0.297 Sum_probs=26.6
Q ss_pred CCHHHHHHHHHhhcCCCchhHHHHHHHHHH
Q 034402 24 MTKEECMEALSKHANIKPVITSTVWNELEK 53 (95)
Q Consensus 24 Msk~E~v~~L~~~a~I~P~fT~~VW~~LE~ 53 (95)
||++|+++.++++.++.+.-...|++.|.+
T Consensus 1 mtk~eli~~ia~~~~~~~~~v~~vl~~l~~ 30 (90)
T smart00411 1 MTKSELIDAIAEKAGLSKKDAKAAVDAFLE 30 (90)
T ss_pred CCHHHHHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 899999999999999999888888877654
No 6
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=78.27 E-value=4.3 Score=29.29 Aligned_cols=50 Identities=18% Similarity=0.345 Sum_probs=44.8
Q ss_pred hHHHHHHHHHHHHHHHHhhCCHHH---HHHHHHhhcCCCchhHHHHHHHHHHh
Q 034402 5 SASYIHMVQHLIEKCLIFRMTKEE---CMEALSKHANIKPVITSTVWNELEKE 54 (95)
Q Consensus 5 s~~~I~~VQ~LIErCLqlyMsk~E---~v~~L~~~a~I~P~fT~~VW~~LE~e 54 (95)
..-|.+.++.+.+.+..--+...| -|+.|..+.+|+|..++-++++||++
T Consensus 10 ~PIY~QI~~qIk~~I~~g~l~pGdkLPSvRelA~~~~VNpnTv~raY~eLE~e 62 (125)
T COG1725 10 KPIYEQIANQIKEQIASGELKPGDKLPSVRELAKDLGVNPNTVQRAYQELERE 62 (125)
T ss_pred CCHHHHHHHHHHHHHHhCCcCCCCCCCcHHHHHHHhCCCHHHHHHHHHHHHHC
Confidence 466788899999999999988887 47999999999999999999999985
No 7
>PF14775 NYD-SP28_assoc: Sperm tail C-terminal domain
Probab=77.02 E-value=16 Score=23.09 Aligned_cols=47 Identities=23% Similarity=0.521 Sum_probs=34.1
Q ss_pred hhcCCCchhHHHHHHHHHHhcHHHHHHHH-----HhhhHHhhhhHHHHHHHHHHHH
Q 034402 35 KHANIKPVITSTVWNELEKENKEFFEAYA-----QSQSKEDRMSEEETNQMIQKMI 85 (95)
Q Consensus 35 ~~a~I~P~fT~~VW~~LE~eN~eFFkaY~-----~~~lk~qi~s~~~~~~~iq~~~ 85 (95)
+-++|=|.=+.-+|+-|+. |++.|. |..+..+..+.++.|.-.+.++
T Consensus 5 ~~~~vip~~~~~~W~~L~~----~l~rY~~vL~~R~~l~~e~~~L~~qN~eLr~lL 56 (60)
T PF14775_consen 5 RLANVIPDEKIRLWDALEN----FLKRYNKVLLDRAALIQEKESLEQQNEELRSLL 56 (60)
T ss_pred HHhhcCChHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3468889999999999985 666663 3445555667777777777665
No 8
>PF08145 BOP1NT: BOP1NT (NUC169) domain; InterPro: IPR012953 WD-40 repeats (also known as WD or beta-transducin repeats) are short ~40 amino acid motifs, often terminating in a Trp-Asp (W-D) dipeptide. WD40 repeats usually assume a 7-8 bladed beta-propeller fold, but proteins have been found with 4 to 16 repeated units, which also form a circularised beta-propeller structure. WD-repeat proteins are a large family found in all eukaryotes and are implicated in a variety of functions ranging from signal transduction and transcription regulation to cell cycle control and apoptosis. Repeated WD40 motifs act as a site for protein-protein interaction, and proteins containing WD40 repeats are known to serve as platforms for the assembly of protein complexes or mediators of transient interplay among other proteins. The specificity of the proteins is determined by the sequences outside the repeats themselves. Examples of such complexes are G proteins (beta subunit is a beta-propeller), TAFII transcription factor, and E3 ubiquitin ligase [, ]. In Arabidopsis spp., several WD40-containing proteins act as key regulators of plant-specific developmental events. This N-terminal domain is found in BOP1-like WD40 proteins. Bop1 is a nucleolar protein involved in rRNA processing, thereby controlling the cell cycle []. It is required for the maturation of the 25S and 5.8S ribosomal RNAs. It may serve as an essential factor in ribosome formation that coordinates processing of the spacer regions in pre-rRNA. The Pes1-Bop1 complex has several components: BOP1, GRWD1, PES1, ORC6L, and RPL3 and is involved in ribosome biogenesis and altered chromosome segregation. The overexpression of BOP1 increases the percentage of multipolar spindles in human cells. Deregulation of the BOP1 pathway may contribute to colorectal tumourigenesis in humans []. Elevated levels of Bop1 induces Bop1/WDR12 and Bop1/Pes1 subcomplexes and the assembly and integrity of the PeBoW complex is highly sensitive to changes in Bop1 protein levels []. Nop7p-Erb1p-Ytm1p, found in yeast, is potentially the homologous complex of Pes1-Bop1-WDR12 as it is involved in the control of ribosome biogenesis and S phase entry. The integrity of the PeBoW complex is required for ribosome biogenesis and cell proliferation in mammalian cells []. In Giardia, the species specific cytoskeleton protein, beta-giardin, interacts with Bop1 []. ; GO: 0006364 rRNA processing, 0005634 nucleus
Probab=72.91 E-value=2.8 Score=33.76 Aligned_cols=32 Identities=25% Similarity=0.498 Sum_probs=25.4
Q ss_pred HHHHHHHHHHHHHHHhhCCHHHHHHHHHhhcCCCch
Q 034402 7 SYIHMVQHLIEKCLIFRMTKEECMEALSKHANIKPV 42 (95)
Q Consensus 7 ~~I~~VQ~LIErCLqlyMsk~E~v~~L~~~a~I~P~ 42 (95)
.|=..|+..-||||.|||-. ++.....||+|.
T Consensus 213 ~Y~~~i~ErFeRCLDLYLcP----R~~k~rlnidPe 244 (260)
T PF08145_consen 213 AYENFIKERFERCLDLYLCP----RVRKKRLNIDPE 244 (260)
T ss_pred hHHHHHHHHHHHhhhhhcCc----HhhcccCCCCHH
Confidence 45688999999999999954 455667788884
No 9
>PF00216 Bac_DNA_binding: Bacterial DNA-binding protein; InterPro: IPR000119 Bacteria synthesise a set of small, usually basic proteins of about 90 residues that bind DNA and are known as histone-like proteins [, ]. Examples include the HU protein in Escherichia coli is a dimer of closely related alpha and beta chains and in other bacteria can be a dimer of identical chains. HU-type proteins have been found in a variety of eubacteria, cyanobacteria and archaebacteria, and are also encoded in the chloroplast genome of some algae []. The integration host factor (IHF), a dimer of closely related chains which seem to function in genetic recombination as well as in translational and transcriptional control [] is found in enterobacteria and viral proteins include the African Swine fever virus protein A104R (or LMW5-AR) []. The exact function of these proteins is not yet clear but they are capable of wrapping DNA and stabilising it from denaturation under extreme environmental conditions. The structure is known for one of these proteins []. The protein exists as a dimer and two "beta-arms" function as the non-specific binding site for bacterial DNA. ; GO: 0003677 DNA binding; PDB: 3C4I_B 2O97_A 1MUL_A 1P78_A 1P51_C 1P71_B 2HT0_A 1OWG_A 2IIF_A 1OUZ_A ....
Probab=71.21 E-value=7.8 Score=24.38 Aligned_cols=30 Identities=20% Similarity=0.293 Sum_probs=24.8
Q ss_pred CCHHHHHHHHHhhcCCCchhHHHHHHHHHH
Q 034402 24 MTKEECMEALSKHANIKPVITSTVWNELEK 53 (95)
Q Consensus 24 Msk~E~v~~L~~~a~I~P~fT~~VW~~LE~ 53 (95)
||+.|+++.+++..++...-...|-..|.+
T Consensus 1 Mtk~eli~~ia~~~~~s~~~v~~vl~~~~~ 30 (90)
T PF00216_consen 1 MTKKELIKRIAEKTGLSKKDVEAVLDALFD 30 (90)
T ss_dssp EBHHHHHHHHHHHHTSSHHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHhcCCCHHHHHHHHHHHHH
Confidence 899999999999999988877777665543
No 10
>PF14420 Clr5: Clr5 domain
Probab=68.07 E-value=15 Score=22.34 Aligned_cols=36 Identities=22% Similarity=0.132 Sum_probs=28.3
Q ss_pred HHHHHHHHHHHHHH-HhhCCHHHHHHHHHhhcCCCch
Q 034402 7 SYIHMVQHLIEKCL-IFRMTKEECMEALSKHANIKPV 42 (95)
Q Consensus 7 ~~I~~VQ~LIErCL-qlyMsk~E~v~~L~~~a~I~P~ 42 (95)
++-...+..|++.- .-.+|.+||++.|..+.|..+.
T Consensus 3 ~~We~~K~~I~~LY~~e~~tl~~v~~~M~~~~~F~at 39 (54)
T PF14420_consen 3 EDWEPHKEEIERLYIDENKTLEEVMEIMKEEHGFKAT 39 (54)
T ss_pred chHHHHHHHHHHHHHhCCCcHHHHHHHHHHHhCCCcC
Confidence 44556677777644 5788999999999999999886
No 11
>TIGR00988 hip integration host factor, beta subunit. This protein forms a site-specific DNA-binding heterodimer with the homologous integration host factor alpha subunit. It is closely related to the DNA-binding protein HU.
Probab=65.04 E-value=16 Score=23.73 Aligned_cols=30 Identities=17% Similarity=0.245 Sum_probs=24.5
Q ss_pred CCHHHHHHHHHhh-cCCCchhHHHHHHHHHH
Q 034402 24 MTKEECMEALSKH-ANIKPVITSTVWNELEK 53 (95)
Q Consensus 24 Msk~E~v~~L~~~-a~I~P~fT~~VW~~LE~ 53 (95)
||+.|+++.+.++ .++.+.-...|++.+-+
T Consensus 1 m~k~eli~~i~~~~~~~s~~~v~~vv~~~~~ 31 (94)
T TIGR00988 1 MTKSELIERIATQQSHLPAKDVEDAVKTMLE 31 (94)
T ss_pred CCHHHHHHHHHHHcCCCCHHHHHHHHHHHHH
Confidence 8999999999875 57899888888876543
No 12
>PF08020 DUF1706: Protein of unknown function (DUF1706) ; InterPro: IPR012550 This family contains many hypothetical proteins from bacteria and yeast.
Probab=63.46 E-value=13 Score=27.52 Aligned_cols=54 Identities=24% Similarity=0.382 Sum_probs=42.5
Q ss_pred hcCCCchhHH--HHHHHHHHhcHHHHHHHHHhhhHHhhhhHHHHHHHHHHHHhhcc
Q 034402 36 HANIKPVITS--TVWNELEKENKEFFEAYAQSQSKEDRMSEEETNQMIQKMISTNS 89 (95)
Q Consensus 36 ~a~I~P~fT~--~VW~~LE~eN~eFFkaY~~~~lk~qi~s~~~~~~~iq~~~~~~~ 89 (95)
.+|-.|.|.. .=|+.|-.=|..|++.|-...+.+.+.-..++-+.|-.+|..-|
T Consensus 68 ~~G~~~~fp~~gykWn~lg~Ln~~f~~~y~~~sl~e~~~~l~~s~~~v~~lI~~~s 123 (166)
T PF08020_consen 68 QAGEEVDFPAPGYKWNQLGELNQSFYEKYQDTSLEELKALLKESHQKVIALIESFS 123 (166)
T ss_pred cCCCCCCCCCCCCChhhhhHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHhCc
Confidence 5677777754 56999999999999999777778888777777777777776544
No 13
>TIGR00987 himA integration host factor, alpha subunit. This protein forms a site-specific DNA-binding heterodimer with the integration host factor beta subunit. It is closely related to the DNA-binding protein HU.
Probab=63.37 E-value=16 Score=23.99 Aligned_cols=30 Identities=17% Similarity=0.083 Sum_probs=25.0
Q ss_pred CCHHHHHHHHHhhcCCCchhHHHHHHHHHH
Q 034402 24 MTKEECMEALSKHANIKPVITSTVWNELEK 53 (95)
Q Consensus 24 Msk~E~v~~L~~~a~I~P~fT~~VW~~LE~ 53 (95)
||+.|+++.++++.++...-...|.+.+.+
T Consensus 2 mtk~eli~~ia~~~~~s~~~v~~vv~~~~~ 31 (96)
T TIGR00987 2 LTKAEMSEYLFDELGLSKREAKELVELFFE 31 (96)
T ss_pred CCHHHHHHHHHHHhCcCHHHHHHHHHHHHH
Confidence 899999999999999988887777665543
No 14
>smart00139 MyTH4 Domain in Myosin and Kinesin Tails. Domain present twice in myosin-VIIa, and also present in 3 other myosins.
Probab=61.82 E-value=22 Score=25.42 Aligned_cols=53 Identities=25% Similarity=0.340 Sum_probs=41.3
Q ss_pred CCC-c---hHHHHHHHHHHHHHHHHhhCCHHHHHHHHHhhcCCCch--hHHHHHHHHHH
Q 034402 1 MGE-S---SASYIHMVQHLIEKCLIFRMTKEECMEALSKHANIKPV--ITSTVWNELEK 53 (95)
Q Consensus 1 ~~~-~---s~~~I~~VQ~LIErCLqlyMsk~E~v~~L~~~a~I~P~--fT~~VW~~LE~ 53 (95)
||| + +...+..+|++++.|+..--=++|+.-.|-+|-.=+|. -..-.|+-|-=
T Consensus 33 mgd~~~~~~~~~~~l~~~i~~~~~~~~~LrDEiy~QLiKQtt~Np~~~s~~rgW~Ll~l 91 (144)
T smart00139 33 MGDLPLPKPDSHLDLVQFILQKGLAHPELRDEIYCQLIKQLTDNPSRQSEERGWELLYL 91 (144)
T ss_pred hcCCCCCCcchHHHHHHHHHHHHhccHHHHHHHHHHHHHHHhCCCCchHHHHHHHHHHH
Confidence 788 2 35678999999999999888899999888887665555 44567887753
No 15
>COG4399 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=60.47 E-value=45 Score=28.47 Aligned_cols=79 Identities=22% Similarity=0.117 Sum_probs=57.1
Q ss_pred HHHHHHHHHHHHHHHhhCCHHHHH-HHHHhh--cCCCchhHHHHHHHHHHhcHHHHHHHHHhhhHHhhh-----hHHHHH
Q 034402 7 SYIHMVQHLIEKCLIFRMTKEECM-EALSKH--ANIKPVITSTVWNELEKENKEFFEAYAQSQSKEDRM-----SEEETN 78 (95)
Q Consensus 7 ~~I~~VQ~LIErCLqlyMsk~E~v-~~L~~~--a~I~P~fT~~VW~~LE~eN~eFFkaY~~~~lk~qi~-----s~~~~~ 78 (95)
.--+.|...|.+-||..|..+-.. ..|..+ ++++-..-.-+-+-|+.++.++|..|.-..+.++|. ++++.+
T Consensus 83 ~~~~rv~~~i~~~lqk~lk~~~t~k~~l~~~~~~d~e~~~i~~~~~~l~~~l~e~f~e~qsn~i~e~Ip~el~~s~eq~~ 162 (376)
T COG4399 83 LFQERVTEAIDQLLQKLLKSEVTDKEQLHQQIFADIEKDLIGNSERWLEKELAEKFTEAQSNTIFELIPLELVESLEQSL 162 (376)
T ss_pred HHHHHHHHHHHHHHHHHHHhhcchHHHHHHHHHhhHHHHHHHhhHHHHHHHHHHHHHHHHhhHHHHhccHHHHHHHHhcc
Confidence 345679999999999998877663 344433 344445555666789999999999996666777765 667777
Q ss_pred HHHHHHH
Q 034402 79 QMIQKMI 85 (95)
Q Consensus 79 ~~iq~~~ 85 (95)
..+..++
T Consensus 163 ~~~~~ll 169 (376)
T COG4399 163 PSADWLL 169 (376)
T ss_pred hhHHHHH
Confidence 7777766
No 16
>PRK00285 ihfA integration host factor subunit alpha; Reviewed
Probab=60.25 E-value=20 Score=23.60 Aligned_cols=31 Identities=16% Similarity=0.143 Sum_probs=25.9
Q ss_pred hCCHHHHHHHHHhhcCCCchhHHHHHHHHHH
Q 034402 23 RMTKEECMEALSKHANIKPVITSTVWNELEK 53 (95)
Q Consensus 23 yMsk~E~v~~L~~~a~I~P~fT~~VW~~LE~ 53 (95)
.||++|+++.+..+.++...-...|++.+.+
T Consensus 2 tmtk~el~~~ia~~~~~s~~~v~~vl~~~~~ 32 (99)
T PRK00285 2 TLTKADLAEALFEKVGLSKREAKELVELFFE 32 (99)
T ss_pred CcCHHHHHHHHHHHhCcCHHHHHHHHHHHHH
Confidence 4899999999999999988888888776543
No 17
>PF06570 DUF1129: Protein of unknown function (DUF1129); InterPro: IPR009214 There are currently no experimental data for members of this group or their homologues. However, these proteins contain predicted integral membrane proteins (with several transmembrane segments).
Probab=60.05 E-value=10 Score=28.15 Aligned_cols=35 Identities=23% Similarity=0.466 Sum_probs=22.6
Q ss_pred HHHHhcHHHHHHHHHhhhHHhhhhHHHHHHHHHHHH
Q 034402 50 ELEKENKEFFEAYAQSQSKEDRMSEEETNQMIQKMI 85 (95)
Q Consensus 50 ~LE~eN~eFFkaY~~~~lk~qi~s~~~~~~~iq~~~ 85 (95)
+|.++|.||..--. ..|+..-.++++..+++.+|+
T Consensus 1 ~LTkkN~~y~~~l~-~~L~~~~~~e~~~e~~L~eil 35 (206)
T PF06570_consen 1 KLTKKNQEYIFDLR-KYLRSSGVSEEEIEELLEEIL 35 (206)
T ss_pred CCchHHHHHHHHHH-HHHHHcCCCHHHHHHHHHHHH
Confidence 47899999976552 223555556666666666665
No 18
>PRK05617 3-hydroxyisobutyryl-CoA hydrolase; Provisional
Probab=59.79 E-value=90 Score=25.02 Aligned_cols=57 Identities=16% Similarity=0.170 Sum_probs=44.4
Q ss_pred HHHHHHHHHHHHHHHHhhCCHHHHHHHHHhhcCCCchhHHHHHHHHHHhcHHHHHHHHHhh
Q 034402 6 ASYIHMVQHLIEKCLIFRMTKEECMEALSKHANIKPVITSTVWNELEKENKEFFEAYAQSQ 66 (95)
Q Consensus 6 ~~~I~~VQ~LIErCLqlyMsk~E~v~~L~~~a~I~P~fT~~VW~~LE~eN~eFFkaY~~~~ 66 (95)
...++.....|.+|+.. -+-++++.+|.++ .+.|....-++|.+..|.=.++.+++.
T Consensus 222 ~~~~~~~~~~i~~~~~~-~~~~~~~~~l~~~---~~~~a~~~a~~i~~~sp~a~~~~k~~l 278 (342)
T PRK05617 222 ASELAAQRAWIDECFAG-DTVEDIIAALEAD---GGEFAAKTADTLRSRSPTSLKVTLEQL 278 (342)
T ss_pred cchhHHHHHHHHHHhCC-CCHHHHHHHHHhc---cHHHHHHHHHHHHhCCcHHHHHHHHHH
Confidence 34567888999999977 5999999999887 457877778888888887666665543
No 19
>PRK00199 ihfB integration host factor subunit beta; Reviewed
Probab=59.73 E-value=22 Score=23.13 Aligned_cols=30 Identities=23% Similarity=0.292 Sum_probs=23.6
Q ss_pred CCHHHHHHHHHhh-cCCCchhHHHHHHHHHH
Q 034402 24 MTKEECMEALSKH-ANIKPVITSTVWNELEK 53 (95)
Q Consensus 24 Msk~E~v~~L~~~-a~I~P~fT~~VW~~LE~ 53 (95)
||+.|+++.+.++ .++...-...|++.+.+
T Consensus 1 mtk~eli~~ia~~~~~~s~~~~~~vv~~~~~ 31 (94)
T PRK00199 1 MTKSELIERLAARNPHLSAKDVENAVKEILE 31 (94)
T ss_pred CCHHHHHHHHHHHcCCCCHHHHHHHHHHHHH
Confidence 8999999999874 67888887777766543
No 20
>PRK10664 transcriptional regulator HU subunit beta; Provisional
Probab=59.62 E-value=21 Score=23.60 Aligned_cols=26 Identities=15% Similarity=0.323 Sum_probs=20.4
Q ss_pred CCHHHHHHHHHhhcCCCchhHHHHHH
Q 034402 24 MTKEECMEALSKHANIKPVITSTVWN 49 (95)
Q Consensus 24 Msk~E~v~~L~~~a~I~P~fT~~VW~ 49 (95)
|||.|+++.|.+..++...-...+-+
T Consensus 1 MtK~eli~~ia~~~~~s~~~~~~~v~ 26 (90)
T PRK10664 1 MNKSQLIDKIAAGADISKAAAGRALD 26 (90)
T ss_pred CCHHHHHHHHHHHhCCCHHHHHHHHH
Confidence 89999999999988887765554443
No 21
>PLN02814 beta-glucosidase
Probab=58.46 E-value=11 Score=32.33 Aligned_cols=49 Identities=22% Similarity=0.292 Sum_probs=32.8
Q ss_pred hHHHHHHHHHHHHHHHHhhCCHHHHHHHHHhhcCCCchhHHHHHH---HHH--------HhcHHHHHHHHHhhhH
Q 034402 5 SASYIHMVQHLIEKCLIFRMTKEECMEALSKHANIKPVITSTVWN---ELE--------KENKEFFEAYAQSQSK 68 (95)
Q Consensus 5 s~~~I~~VQ~LIErCLqlyMsk~E~v~~L~~~a~I~P~fT~~VW~---~LE--------~eN~eFFkaY~~~~lk 68 (95)
..+-|+.=.++|..|+. +||+|.+|..=|. -|+ ++..++|..|.+...+
T Consensus 112 N~~Gl~fY~~lId~l~~---------------~GI~P~VTL~H~dlP~~L~~~yGGW~n~~~i~~F~~YA~~~f~ 171 (504)
T PLN02814 112 NPKGLLFYKNLIKELRS---------------HGIEPHVTLYHYDLPQSLEDEYGGWINRKIIEDFTAFADVCFR 171 (504)
T ss_pred CHHHHHHHHHHHHHHHH---------------cCCceEEEecCCCCCHHHHHhcCCcCChhHHHHHHHHHHHHHH
Confidence 44556666667766665 4999999987662 333 4677889999655443
No 22
>PRK14552 C/D box methylation guide ribonucleoprotein complex aNOP56 subunit; Provisional
Probab=56.20 E-value=21 Score=30.09 Aligned_cols=49 Identities=22% Similarity=0.264 Sum_probs=41.0
Q ss_pred CCCc-hHHHHHHHHHHHHHHHHhhCCHHHHHHHHHhhcC-CCchhHHHHHH
Q 034402 1 MGES-SASYIHMVQHLIEKCLIFRMTKEECMEALSKHAN-IKPVITSTVWN 49 (95)
Q Consensus 1 ~~~~-s~~~I~~VQ~LIErCLqlyMsk~E~v~~L~~~a~-I~P~fT~~VW~ 49 (95)
||-. |..++..|++++++-+.++=.++++.++|...+. |.|.+|..|=.
T Consensus 222 ~G~~lse~dl~~I~~~a~~I~~L~e~R~~L~~yI~~~M~~iAPNLtaLVG~ 272 (414)
T PRK14552 222 MGADLSEFDLEAIKKLANEILDLYKLREELEDYLETVMKEVAPNLTALVGP 272 (414)
T ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccHHHHHHhh
Confidence 4543 7788999999999999999999999999998765 48988887543
No 23
>PF05402 PqqD: Coenzyme PQQ synthesis protein D (PqqD); InterPro: IPR008792 This family contains several bacterial coenzyme PQQ synthesis protein D (PqqD) sequences. This protein is required for coenzyme pyrrolo-quinoline-quinone (PQQ) biosynthesis.; PDB: 3G2B_A.
Probab=56.11 E-value=38 Score=20.20 Aligned_cols=33 Identities=24% Similarity=0.175 Sum_probs=20.9
Q ss_pred HHHHhhCCHHHHHHHHHhhcCCCch-hHHHHHHH
Q 034402 18 KCLIFRMTKEECMEALSKHANIKPV-ITSTVWNE 50 (95)
Q Consensus 18 rCLqlyMsk~E~v~~L~~~a~I~P~-fT~~VW~~ 50 (95)
+++.--.|.+|+++.|.++++++|. ...-|..-
T Consensus 24 ~~~~g~~t~~ei~~~l~~~y~~~~~~~~~dv~~f 57 (68)
T PF05402_consen 24 ELLDGPRTVEEIVDALAEEYDVDPEEAEEDVEEF 57 (68)
T ss_dssp HH--SSS-HHHHHHHHHHHTT--HHHHHHHHHHH
T ss_pred HHccCCCCHHHHHHHHHHHcCCCHHHHHHHHHHH
Confidence 3346678999999999999999998 44444433
No 24
>PLN02849 beta-glucosidase
Probab=53.28 E-value=13 Score=31.69 Aligned_cols=48 Identities=21% Similarity=0.288 Sum_probs=29.6
Q ss_pred HHHHHHHHHHHHHHHHhhCCHHHHHHHHHhhcCCCchhHHHHHH---HHHH--------hcHHHHHHHHHhhhH
Q 034402 6 ASYIHMVQHLIEKCLIFRMTKEECMEALSKHANIKPVITSTVWN---ELEK--------ENKEFFEAYAQSQSK 68 (95)
Q Consensus 6 ~~~I~~VQ~LIErCLqlyMsk~E~v~~L~~~a~I~P~fT~~VW~---~LE~--------eN~eFFkaY~~~~lk 68 (95)
.+-|+.=.++|..|+. +||+|.+|..=|. .|++ +..++|..|.+...+
T Consensus 115 ~~gl~fY~~lid~l~~---------------~GI~P~VTL~H~dlP~~L~~~yGGW~nr~~v~~F~~YA~~~f~ 173 (503)
T PLN02849 115 PKGLQFYKNFIQELVK---------------HGIEPHVTLFHYDHPQYLEDDYGGWINRRIIKDFTAYADVCFR 173 (503)
T ss_pred HHHHHHHHHHHHHHHH---------------cCCeEEEeecCCCCcHHHHHhcCCcCCchHHHHHHHHHHHHHH
Confidence 3445555555555544 4999999986552 2443 556788888554433
No 25
>PRK10753 transcriptional regulator HU subunit alpha; Provisional
Probab=53.03 E-value=31 Score=22.64 Aligned_cols=26 Identities=12% Similarity=0.305 Sum_probs=19.6
Q ss_pred CCHHHHHHHHHhhcCCCchhHHHHHH
Q 034402 24 MTKEECMEALSKHANIKPVITSTVWN 49 (95)
Q Consensus 24 Msk~E~v~~L~~~a~I~P~fT~~VW~ 49 (95)
|||.|+++.|.++.++...-...|-+
T Consensus 1 M~K~eli~~ia~~~~~s~~~~~~~v~ 26 (90)
T PRK10753 1 MNKTQLIDVIADKAELSKTQAKAALE 26 (90)
T ss_pred CCHHHHHHHHHHHhCCCHHHHHHHHH
Confidence 89999999999988877665544443
No 26
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=52.54 E-value=32 Score=25.04 Aligned_cols=52 Identities=15% Similarity=0.030 Sum_probs=42.5
Q ss_pred CchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHhhcCCCchhHHHHHHHHHHhc
Q 034402 3 ESSASYIHMVQHLIEKCLIFRMTKEECMEALSKHANIKPVITSTVWNELEKEN 55 (95)
Q Consensus 3 ~~s~~~I~~VQ~LIErCLqlyMsk~E~v~~L~~~a~I~P~fT~~VW~~LE~eN 55 (95)
.|+.-.-..++-+.|.|=+.+.|..+++..|..++||.=+-. .||..|.+.-
T Consensus 60 rP~kl~~~q~~~l~e~~~~k~wTl~~~~~~l~~e~gv~y~~~-~v~~~l~~~G 111 (138)
T COG3415 60 RPRKLSEEQLEILLERLREKDWTLKELVEELGLEFGVWYHAS-AVRRLLHELG 111 (138)
T ss_pred CCcccCHHHHHHHHHHHhcccchHHHHHHHHhhhcCeEEeHH-HHHHHHHHcC
Confidence 344445567888999999999999999999999999987655 8999988753
No 27
>PLN02998 beta-glucosidase
Probab=51.31 E-value=15 Score=31.38 Aligned_cols=47 Identities=23% Similarity=0.347 Sum_probs=29.9
Q ss_pred HHHHHHHHHHHHHHHHhhCCHHHHHHHHHhhcCCCchhHHHHHH---H--------HHHhcHHHHHHHHHhhh
Q 034402 6 ASYIHMVQHLIEKCLIFRMTKEECMEALSKHANIKPVITSTVWN---E--------LEKENKEFFEAYAQSQS 67 (95)
Q Consensus 6 ~~~I~~VQ~LIErCLqlyMsk~E~v~~L~~~a~I~P~fT~~VW~---~--------LE~eN~eFFkaY~~~~l 67 (95)
.+-|+.=.++|..|+. .||+|.+|..=|. - |-++..++|..|.+...
T Consensus 118 ~~gl~~Y~~lid~L~~---------------~GIeP~VTL~H~dlP~~L~~~yGGW~n~~~v~~F~~YA~~~~ 175 (497)
T PLN02998 118 PKGLQYYNNLIDELIT---------------HGIQPHVTLHHFDLPQALEDEYGGWLSQEIVRDFTAYADTCF 175 (497)
T ss_pred HHHHHHHHHHHHHHHH---------------cCCceEEEecCCCCCHHHHHhhCCcCCchHHHHHHHHHHHHH
Confidence 3445555555555544 4999999986662 2 33466788999965544
No 28
>PRK10963 hypothetical protein; Provisional
Probab=50.79 E-value=13 Score=28.14 Aligned_cols=22 Identities=23% Similarity=0.416 Sum_probs=15.9
Q ss_pred hCCHHHHHHHHHhhcCCCchhHHHHHHHHHHhcHHHHHHHH
Q 034402 23 RMTKEECMEALSKHANIKPVITSTVWNELEKENKEFFEAYA 63 (95)
Q Consensus 23 yMsk~E~v~~L~~~a~I~P~fT~~VW~~LE~eN~eFFkaY~ 63 (95)
.||-++|+.+| ++|||||.-+-
T Consensus 2 ~l~~~~V~~yL-------------------~~~PdFf~~h~ 23 (223)
T PRK10963 2 ELDDRAVVDYL-------------------LQNPDFFIRNA 23 (223)
T ss_pred CCCHHHHHHHH-------------------HHCchHHhhCH
Confidence 36677777777 45799998873
No 29
>PF04340 DUF484: Protein of unknown function, DUF484; InterPro: IPR007435 This family consists of several proteins of uncharacterised function.; PDB: 3E98_B.
Probab=48.54 E-value=5.8 Score=29.59 Aligned_cols=10 Identities=30% Similarity=0.750 Sum_probs=0.0
Q ss_pred HhcHHHHHHH
Q 034402 53 KENKEFFEAY 62 (95)
Q Consensus 53 ~eN~eFFkaY 62 (95)
.+|||||.-|
T Consensus 16 ~~~PdFf~~~ 25 (225)
T PF04340_consen 16 RQHPDFFERH 25 (225)
T ss_dssp ----------
T ss_pred HhCcHHHHhC
Confidence 3578888887
No 30
>TIGR01795 CM_mono_cladeE monofunctional chorismate mutase, alpha proteobacterial type. The alpha proteobacterial members are trusted because the pathways of CM are evident and there is only one plausible CM in the genome. In S. coelicolor, however, there is another aparrent monofunctional CM.
Probab=48.14 E-value=28 Score=23.46 Aligned_cols=25 Identities=20% Similarity=0.250 Sum_probs=19.4
Q ss_pred HHHHhhcCCCchhHHHHHHHHHHhc
Q 034402 31 EALSKHANIKPVITSTVWNELEKEN 55 (95)
Q Consensus 31 ~~L~~~a~I~P~fT~~VW~~LE~eN 55 (95)
..+..+.|++|.|...+|+.+-.+.
T Consensus 58 ~~~a~~~gl~p~~~e~i~~~i~~es 82 (94)
T TIGR01795 58 RRLAIDAGLDPEFAEKFLNFIVTEV 82 (94)
T ss_pred HHHHHHCCCCHHHHHHHHHHHHHHH
Confidence 3445778999999999998886654
No 31
>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. This family groups together a range of proteins, including anr, crp, clp, cysR, fixK, flp, fnr, fnrN, hlyX and ntcA [, ]. Within this family, the HTH motif is situated towards the C terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2OZ6_A 1CGP_B 2GZW_C 1O3T_B 3ROU_A 2CGP_A 3RDI_A 1I5Z_A 3IYD_H 3FWE_B ....
Probab=47.59 E-value=38 Score=19.15 Aligned_cols=29 Identities=21% Similarity=0.397 Sum_probs=21.2
Q ss_pred hCCHHHHHHHHHhhcCCCchhHHHHHHHHHHhc
Q 034402 23 RMTKEECMEALSKHANIKPVITSTVWNELEKEN 55 (95)
Q Consensus 23 yMsk~E~v~~L~~~a~I~P~fT~~VW~~LE~eN 55 (95)
.||+.|+.+.| |..|..-+-+..+|+++.
T Consensus 2 ~mtr~diA~~l----G~t~ETVSR~l~~l~~~g 30 (32)
T PF00325_consen 2 PMTRQDIADYL----GLTRETVSRILKKLERQG 30 (32)
T ss_dssp E--HHHHHHHH----TS-HHHHHHHHHHHHHTT
T ss_pred CcCHHHHHHHh----CCcHHHHHHHHHHHHHcC
Confidence 58888888887 888888888888888763
No 32
>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulfovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis sp. (strain PCC 6803) hypothetical protein slr0846. These are small proteins of 12 to 18kDa which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.; PDB: 3T8T_A 3T8R_A 3K69_A 3LWF_C 1XD7_A 2Y75_E 1YLF_C.
Probab=47.32 E-value=27 Score=22.05 Aligned_cols=27 Identities=15% Similarity=0.329 Sum_probs=21.5
Q ss_pred HHHHHHhhcCCCchhHHHHHHHHHHhc
Q 034402 29 CMEALSKHANIKPVITSTVWNELEKEN 55 (95)
Q Consensus 29 ~v~~L~~~a~I~P~fT~~VW~~LE~eN 55 (95)
.++.|.+..+|.|.+..-|-+.|++.+
T Consensus 27 s~~eiA~~~~i~~~~l~kil~~L~~~G 53 (83)
T PF02082_consen 27 SSKEIAERLGISPSYLRKILQKLKKAG 53 (83)
T ss_dssp EHHHHHHHHTS-HHHHHHHHHHHHHTT
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHhhCC
Confidence 456677777999999999999999864
No 33
>PF03918 CcmH: Cytochrome C biogenesis protein; InterPro: IPR005616 Members of this family include NrfF, CcmH, CycL, Ccl2.; PDB: 2KW0_A 2HL7_A.
Probab=46.94 E-value=44 Score=24.33 Aligned_cols=37 Identities=16% Similarity=0.180 Sum_probs=28.1
Q ss_pred CCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHhhcC
Q 034402 2 GESSASYIHMVQHLIEKCLIFRMTKEECMEALSKHAN 38 (95)
Q Consensus 2 ~~~s~~~I~~VQ~LIErCLqlyMsk~E~v~~L~~~a~ 38 (95)
+||.+..-.-..+.|.+=+.--+|++||++++-.++|
T Consensus 52 ~~s~a~~A~dmR~~I~~~l~~G~s~~eI~~~~v~rYG 88 (148)
T PF03918_consen 52 ADSNAPIARDMRREIREMLAEGKSDEEIIDYFVERYG 88 (148)
T ss_dssp TT--SHHHHHHHHHHHHHHHHT--HHHHHHHHHHHHT
T ss_pred hhcCcHHHHHHHHHHHHHHHcCCCHHHHHHHHHHhcC
Confidence 3455666677888899999999999999999999888
No 34
>TIGR01201 HU_rel DNA-binding protein, histone-like, putative. This model describes a set of proteins related to but longer than DNA-binding protein HU. Its distinctive domain architecture compared to HU and related histone-like DNA-binding proteins justifies the designation as superfamily. Members include, so far, one from Bacteroides fragilis, a gut bacterium, and ten from Porphyromonas gingivalis, an oral anaerobe.
Probab=46.77 E-value=39 Score=24.12 Aligned_cols=31 Identities=16% Similarity=0.226 Sum_probs=28.2
Q ss_pred CCHHHHHHHHHhhcCCCchhHHHHHHHHHHh
Q 034402 24 MTKEECMEALSKHANIKPVITSTVWNELEKE 54 (95)
Q Consensus 24 Msk~E~v~~L~~~a~I~P~fT~~VW~~LE~e 54 (95)
||++|+++.++++.++.+.-...|+..|.+.
T Consensus 31 mt~~el~~~Ia~~s~~s~~dv~~vl~~l~~~ 61 (145)
T TIGR01201 31 IDFEEIAELIAEESSLSPGDVKGIIDRLAYV 61 (145)
T ss_pred cCHHHHHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 8999999999999999999999999887664
No 35
>PF03979 Sigma70_r1_1: Sigma-70 factor, region 1.1; InterPro: IPR007127 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. This entry represents Region 1.1 which modulates DNA binding by region 2 and 4 when sigma is unbound by the core RNA polymerase [, ]. Region 1.1 is also involved in promoter binding.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2K6X_A.
Probab=45.54 E-value=60 Score=20.87 Aligned_cols=51 Identities=27% Similarity=0.391 Sum_probs=33.7
Q ss_pred HHHHHHHHHHHHH-HHhhCCHHHHHHHHHhhcCCCchhHHHHHHHHHHhcHHH
Q 034402 7 SYIHMVQHLIEKC-LIFRMTKEECMEALSKHANIKPVITSTVWNELEKENKEF 58 (95)
Q Consensus 7 ~~I~~VQ~LIErC-LqlyMsk~E~v~~L~~~a~I~P~fT~~VW~~LE~eN~eF 58 (95)
.+...|+.||++- =+-|+|-+|+.++|. ...+.|.--..|...|+..+=+.
T Consensus 4 ~~~~~i~~Li~~gK~~G~lT~~eI~~~L~-~~~~~~e~id~i~~~L~~~gI~V 55 (82)
T PF03979_consen 4 QYEEAIKKLIEKGKKKGYLTYDEINDALP-EDDLDPEQIDEIYDTLEDEGIEV 55 (82)
T ss_dssp HHHHHHHHHHHHHHHHSS-BHHHHHHH-S--S---HHHHHHHHHHHHTT----
T ss_pred hhHHHHHHHHHHHhhcCcCCHHHHHHHcC-ccCCCHHHHHHHHHHHHHCCCEE
Confidence 3556788899865 478999999999997 46799988888888888766443
No 36
>PF13545 HTH_Crp_2: Crp-like helix-turn-helix domain; PDB: 3LA2_A 3LA3_B 3LA7_A 3B02_A 3E97_A 2H6C_B 1OMI_A 2BGC_H 2BEO_A 2GAU_A ....
Probab=45.26 E-value=44 Score=19.99 Aligned_cols=31 Identities=23% Similarity=0.348 Sum_probs=26.4
Q ss_pred HhhCCHHHHHHHHHhhcCCCchhHHHHHHHHHHhc
Q 034402 21 IFRMTKEECMEALSKHANIKPVITSTVWNELEKEN 55 (95)
Q Consensus 21 qlyMsk~E~v~~L~~~a~I~P~fT~~VW~~LE~eN 55 (95)
.+.+|++++.+.+ |+.+...+-+.++|++++
T Consensus 26 ~~~lt~~~iA~~~----g~sr~tv~r~l~~l~~~g 56 (76)
T PF13545_consen 26 PLPLTQEEIADML----GVSRETVSRILKRLKDEG 56 (76)
T ss_dssp EEESSHHHHHHHH----TSCHHHHHHHHHHHHHTT
T ss_pred EecCCHHHHHHHH----CCCHHHHHHHHHHHHHCC
Confidence 4678888887776 999999999999999864
No 37
>TIGR03356 BGL beta-galactosidase.
Probab=44.43 E-value=31 Score=28.51 Aligned_cols=39 Identities=31% Similarity=0.632 Sum_probs=23.9
Q ss_pred HHHHHHHhhcCCCchhHHHHHH---HHH-------HhcHHHHHHHHHhhh
Q 034402 28 ECMEALSKHANIKPVITSTVWN---ELE-------KENKEFFEAYAQSQS 67 (95)
Q Consensus 28 E~v~~L~~~a~I~P~fT~~VW~---~LE-------~eN~eFFkaY~~~~l 67 (95)
++++.|.+ .||+|.+|..=|. .|. .+..+.|..|-+...
T Consensus 98 ~~i~~l~~-~gi~pivtL~Hfd~P~~l~~~gGw~~~~~~~~f~~ya~~~~ 146 (427)
T TIGR03356 98 RLVDELLE-AGIEPFVTLYHWDLPQALEDRGGWLNRDTAEWFAEYAAVVA 146 (427)
T ss_pred HHHHHHHH-cCCeeEEeeccCCccHHHHhcCCCCChHHHHHHHHHHHHHH
Confidence 34444433 4999998874443 343 566789999955433
No 38
>PF12776 Myb_DNA-bind_3: Myb/SANT-like DNA-binding domain; InterPro: IPR024752 This domain, found in a range of uncharacterised proteins, may be related to Myb/SANT-like DNA binding domains.
Probab=44.21 E-value=79 Score=19.80 Aligned_cols=49 Identities=12% Similarity=0.162 Sum_probs=39.1
Q ss_pred CchhHHHHHHHHHHhcHHHHHHH-HHhhhHHhhhhHHHHHHHHHHHHhhc
Q 034402 40 KPVITSTVWNELEKENKEFFEAY-AQSQSKEDRMSEEETNQMIQKMISTN 88 (95)
Q Consensus 40 ~P~fT~~VW~~LE~eN~eFFkaY-~~~~lk~qi~s~~~~~~~iq~~~~~~ 88 (95)
...|+...|+.+.++=.++|... -+.++|.........=..+..++..+
T Consensus 26 ~~~fk~~~w~~i~~~~~~~~~~~~t~~qlknk~~~lk~~y~~~~~l~~~s 75 (96)
T PF12776_consen 26 NGGFKKEGWNNIAEEFNEKTGLNYTKKQLKNKWKTLKKDYRIWKELRNHS 75 (96)
T ss_pred CCCcCHHHHHHHHHHHHHHhCCcccHHHHHHHHHHHHHHHHHHHHHHcCC
Confidence 46999999999999877788777 56778888888888878888877544
No 39
>COG4359 Uncharacterized conserved protein [Function unknown]
Probab=43.93 E-value=27 Score=27.85 Aligned_cols=27 Identities=30% Similarity=0.308 Sum_probs=23.5
Q ss_pred HhhCCHHHHHHHHHhhcCCCchhHHHH
Q 034402 21 IFRMTKEECMEALSKHANIKPVITSTV 47 (95)
Q Consensus 21 qlyMsk~E~v~~L~~~a~I~P~fT~~V 47 (95)
..+.|-+||.+.|.+.++|+|.|-..|
T Consensus 56 ~i~~s~~Eile~llk~i~Idp~fKef~ 82 (220)
T COG4359 56 SIHSSLEEILEFLLKDIKIDPGFKEFV 82 (220)
T ss_pred hcCCCHHHHHHHHHhhcccCccHHHHH
Confidence 356788999999999999999998765
No 40
>PRK08091 ribulose-phosphate 3-epimerase; Validated
Probab=43.57 E-value=15 Score=28.55 Aligned_cols=33 Identities=21% Similarity=0.322 Sum_probs=26.1
Q ss_pred CCHHHHHHHHHhhcCCCchhHHHHHHHHHHhcHH
Q 034402 24 MTKEECMEALSKHANIKPVITSTVWNELEKENKE 57 (95)
Q Consensus 24 Msk~E~v~~L~~~a~I~P~fT~~VW~~LE~eN~e 57 (95)
||+.+||..| ++.-|.|++-+.=|-+|+++=..
T Consensus 1 ~~~~~~~~~~-~~~~I~pSil~ad~~~l~~el~~ 33 (228)
T PRK08091 1 MSKLSLIQQL-KQQPISVGILASNWLKFNETLTT 33 (228)
T ss_pred CCHHHHHHHh-cCCeEEeehhhcCHHHHHHHHHH
Confidence 8999999988 56799999988777777665433
No 41
>PF04433 SWIRM: SWIRM domain; InterPro: IPR007526 The SWIRM domain is a small alpha-helical domain of about 85 amino acid residues found in eukaryotic chromosomal proteins. It is named after the proteins SWI3, RSC8 and MOIRA in which it was first recognised. This domain is predicted to mediate protein-protein interactions in the assembly of chromatin-protein complexes. The SWIRM domain can be linked to different domains, such as the ZZ-type zinc finger (IPR000433 from INTERPRO), the Myb DNA-binding domain (IPR001005 from INTERPRO), the HORMA domain (IPR003511 from INTERPRO), the amino-oxidase domain, the chromo domain (IPR000953 from INTERPRO), and the JAB1/PAD1 domain.; GO: 0005515 protein binding; PDB: 2Z3Y_A 2UXN_A 2Y48_A 2HKO_A 2XAF_A 2X0L_A 2XAJ_A 2UXX_A 2V1D_A 2L3D_A ....
Probab=43.44 E-value=32 Score=21.99 Aligned_cols=46 Identities=15% Similarity=0.176 Sum_probs=30.3
Q ss_pred hHHHHHHHHHHHHHH----HHhhCCHHHHHHHHHhhcCCCchhHHHHHHHHHHh
Q 034402 5 SASYIHMVQHLIEKC----LIFRMTKEECMEALSKHANIKPVITSTVWNELEKE 54 (95)
Q Consensus 5 s~~~I~~VQ~LIErC----LqlyMsk~E~v~~L~~~a~I~P~fT~~VW~~LE~e 54 (95)
+..|+ .++|.|=.. -..|+++++|-..+. |+++..+.-||.-|+..
T Consensus 32 p~~Yl-~iRn~il~~w~~n~~~~lt~~~~~~~i~---~~d~~~~~ri~~FL~~~ 81 (86)
T PF04433_consen 32 PEQYL-KIRNTILAEWRKNPNKYLTKTDARKLIK---GIDVNKIRRIYDFLERW 81 (86)
T ss_dssp HHHHH-HHHHHHHHHHHHHTTS---HHHHHHHTT---SSSHHHHHHHHHHHHHT
T ss_pred hHHHH-HHHHHHHHHHHHCCCCcccHHHHHHHcc---ccCHHHHHHHHHHHHHc
Confidence 34454 345555333 267899999977774 79999999999988763
No 42
>PF00232 Glyco_hydro_1: Glycosyl hydrolase family 1; InterPro: IPR001360 O-Glycosyl hydrolases 3.2.1. from EC are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families [, ]. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. Glycoside hydrolase family 1 GH1 from CAZY comprises enzymes with a number of known activities; beta-glucosidase (3.2.1.21 from EC); beta-galactosidase (3.2.1.23 from EC); 6-phospho-beta-galactosidase (3.2.1.85 from EC); 6-phospho-beta-glucosidase (3.2.1.86 from EC); lactase-phlorizin hydrolase (3.2.1.62 from EC), (3.2.1.108 from EC); beta-mannosidase (3.2.1.25 from EC); myrosinase (3.2.1.147 from EC). ; GO: 0004553 hydrolase activity, hydrolyzing O-glycosyl compounds, 0005975 carbohydrate metabolic process; PDB: 1QVB_A 3AHY_D 2E9L_A 2ZOX_A 2JFE_X 2E9M_A 3FIZ_A 3FIY_A 3CMJ_A 3FJ0_A ....
Probab=42.48 E-value=9.9 Score=31.36 Aligned_cols=47 Identities=26% Similarity=0.458 Sum_probs=28.3
Q ss_pred hHHHHHHHHHHHHHHHHhhCCHHHHHHHHHhhcCCCchhHHHHH-----HH-----HHHhcHHHHHHHHHhh
Q 034402 5 SASYIHMVQHLIEKCLIFRMTKEECMEALSKHANIKPVITSTVW-----NE-----LEKENKEFFEAYAQSQ 66 (95)
Q Consensus 5 s~~~I~~VQ~LIErCLqlyMsk~E~v~~L~~~a~I~P~fT~~VW-----~~-----LE~eN~eFFkaY~~~~ 66 (95)
..+-++.=.++|+.|+. +||+|.+|..=| =. +-++++++|..|.+..
T Consensus 94 n~~~~~~Y~~~i~~l~~---------------~gi~P~vtL~H~~~P~~l~~~ggw~~~~~~~~F~~Ya~~~ 150 (455)
T PF00232_consen 94 NEEGLDFYRDLIDELLE---------------NGIEPIVTLYHFDLPLWLEDYGGWLNRETVDWFARYAEFV 150 (455)
T ss_dssp -HHHHHHHHHHHHHHHH---------------TT-EEEEEEESS--BHHHHHHTGGGSTHHHHHHHHHHHHH
T ss_pred CHhHhhhhHHHHHHHHh---------------hccceeeeeeecccccceeecccccCHHHHHHHHHHHHHH
Confidence 34455555555555543 599998876433 32 2357889999995543
No 43
>TIGR03147 cyt_nit_nrfF cytochrome c nitrite reductase, accessory protein NrfF.
Probab=41.39 E-value=60 Score=23.53 Aligned_cols=46 Identities=13% Similarity=0.193 Sum_probs=36.0
Q ss_pred CchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHhhcCC----Cch---hHHHHH
Q 034402 3 ESSASYIHMVQHLIEKCLIFRMTKEECMEALSKHANI----KPV---ITSTVW 48 (95)
Q Consensus 3 ~~s~~~I~~VQ~LIErCLqlyMsk~E~v~~L~~~a~I----~P~---fT~~VW 48 (95)
||.+....-..+.|-+=+.--+|.+||++++-++.|= +|- +|..+|
T Consensus 53 dS~a~iA~dmR~~Vr~~i~~G~Sd~eI~~~~v~RYG~~Vly~Pp~~~~t~~LW 105 (126)
T TIGR03147 53 ESNSPIAYDLRHEVYSMVNEGKSNQQIIDFMTARFGDFVLYNPPFKWQTLLLW 105 (126)
T ss_pred hcCCHHHHHHHHHHHHHHHcCCCHHHHHHHHHHhcCCeEEecCCCCcchHHHH
Confidence 5666666777888888899999999999999999883 444 355566
No 44
>PF07527 Hairy_orange: Hairy Orange; InterPro: IPR003650 This domain confers specificity among members of the Hairy/E(SPL) family. HES-2 (hairy and enhancer of split 2) is a transcription factor, and the hairy protein is a pair-rule protein that regulates embryonic segmentation and adult bristle patterning. These proteins are transcriptional repressors of genes that require the BHLH protein for their transcription.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DB7_A.
Probab=40.54 E-value=59 Score=18.60 Aligned_cols=27 Identities=19% Similarity=0.320 Sum_probs=20.3
Q ss_pred HHHHHHHHhhcCCCchhHHHHHHHHHH
Q 034402 27 EECMEALSKHANIKPVITSTVWNELEK 53 (95)
Q Consensus 27 ~E~v~~L~~~a~I~P~fT~~VW~~LE~ 53 (95)
.||.+.|....+++|.+..-+-+.|..
T Consensus 12 ~Ev~~fL~~~~~~~~~~~~rLl~HL~~ 38 (43)
T PF07527_consen 12 NEVSRFLSSVEGVDPGVRARLLSHLQS 38 (43)
T ss_dssp HHHHHHHHHTS---THHHHHHHHHHHH
T ss_pred HHHHHHHhcCCCCChHHHHHHHHHHHH
Confidence 589999999999999998888887765
No 45
>KOG2211 consensus Predicted Golgi transport complex 1 protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=40.18 E-value=37 Score=31.43 Aligned_cols=17 Identities=29% Similarity=0.563 Sum_probs=15.9
Q ss_pred CCCchhHHHHHHHHHHh
Q 034402 38 NIKPVITSTVWNELEKE 54 (95)
Q Consensus 38 ~I~P~fT~~VW~~LE~e 54 (95)
+++|.++..+|++|++.
T Consensus 361 ~gd~cI~~rfw~~l~qa 377 (797)
T KOG2211|consen 361 NGDKCIPERFWKKLEQA 377 (797)
T ss_pred ccchhHHHHHHHHHHHH
Confidence 79999999999999984
No 46
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=40.07 E-value=52 Score=23.69 Aligned_cols=29 Identities=21% Similarity=0.272 Sum_probs=25.1
Q ss_pred HHHHHHHHHHHHHHHhhCCHHHHHHHHHh
Q 034402 7 SYIHMVQHLIEKCLIFRMTKEECMEALSK 35 (95)
Q Consensus 7 ~~I~~VQ~LIErCLqlyMsk~E~v~~L~~ 35 (95)
.....++++|+.|..+.+|++|+.+.|.+
T Consensus 90 ~~~~~l~~~I~~~~~~G~s~eei~~~~~~ 118 (125)
T COG1725 90 LAEEELEEFIEEAKALGLSLEEILELLKE 118 (125)
T ss_pred HHHHHHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 34567899999999999999999998865
No 47
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=39.84 E-value=82 Score=21.95 Aligned_cols=30 Identities=17% Similarity=0.255 Sum_probs=21.2
Q ss_pred hhCCHHHHHHHHHhhcCCCchhHHHHHHHHHHhc
Q 034402 22 FRMTKEECMEALSKHANIKPVITSTVWNELEKEN 55 (95)
Q Consensus 22 lyMsk~E~v~~L~~~a~I~P~fT~~VW~~LE~eN 55 (95)
+.+|++|+... .|+.|.-.+-+.++|++++
T Consensus 167 ~~~t~~~lA~~----lG~tr~tvsR~l~~l~~~g 196 (211)
T PRK11753 167 IKITRQEIGRI----VGCSREMVGRVLKMLEDQG 196 (211)
T ss_pred cCCCHHHHHHH----hCCCHHHHHHHHHHHHHCC
Confidence 34555655444 4888888888888888875
No 48
>PRK05686 fliG flagellar motor switch protein G; Validated
Probab=39.10 E-value=1.8e+02 Score=23.23 Aligned_cols=60 Identities=20% Similarity=0.258 Sum_probs=42.9
Q ss_pred CCCchHHHHHHHHHHHHHHHHhhC-CH------HHHHHHHHhhcCCCchhHHHHHHHHHHhcHHHHHHH
Q 034402 1 MGESSASYIHMVQHLIEKCLIFRM-TK------EECMEALSKHANIKPVITSTVWNELEKENKEFFEAY 62 (95)
Q Consensus 1 ~~~~s~~~I~~VQ~LIErCLqlyM-sk------~E~v~~L~~~a~I~P~fT~~VW~~LE~eN~eFFkaY 62 (95)
||.-+.+-++.|-..+++||..-. +. -+.+-.+.+ ++++.-...|...|++.+|++.+.=
T Consensus 171 l~~v~~~~~~~i~~~L~~~l~~~~~~~~~~~~g~~~~a~Iln--~~~~~~~~~il~~L~~~d~~~a~~I 237 (339)
T PRK05686 171 LEGVSPEALKEVEEVLEKKLSSMANADRTKMGGVKTVAEILN--NLDRQTEKTILESLEEEDPELAEKI 237 (339)
T ss_pred cCCCCHHHHHHHHHHHHHHHhhcccccccccCcHHHHHHHHh--cCCchHHHHHHHHHHhhCHHHHHHH
Confidence 455678888899899999997522 11 132333333 5677777899999999999999875
No 49
>PRK15014 6-phospho-beta-glucosidase BglA; Provisional
Probab=38.94 E-value=37 Score=28.78 Aligned_cols=47 Identities=23% Similarity=0.461 Sum_probs=31.8
Q ss_pred hHHHHHHHHHHHHHHHHhhCCHHHHHHHHHhhcCCCchhHHHHHHH---HH--------HhcHHHHHHHHHhh
Q 034402 5 SASYIHMVQHLIEKCLIFRMTKEECMEALSKHANIKPVITSTVWNE---LE--------KENKEFFEAYAQSQ 66 (95)
Q Consensus 5 s~~~I~~VQ~LIErCLqlyMsk~E~v~~L~~~a~I~P~fT~~VW~~---LE--------~eN~eFFkaY~~~~ 66 (95)
..+-++.-.++|+.|+.. ||+|.+|..=|.- |+ ++..+.|..|.+..
T Consensus 105 N~~gl~~Y~~lid~l~~~---------------GI~P~vTL~H~dlP~~L~~~yGGW~n~~~~~~F~~Ya~~~ 162 (477)
T PRK15014 105 NEEGLKFYDDMFDELLKY---------------NIEPVITLSHFEMPLHLVQQYGSWTNRKVVDFFVRFAEVV 162 (477)
T ss_pred CHHHHHHHHHHHHHHHHc---------------CCEEEEEeeCCCCCHHHHHhcCCCCChHHHHHHHHHHHHH
Confidence 456677777777777654 9999999854432 33 34567788885543
No 50
>PF00784 MyTH4: MyTH4 domain; InterPro: IPR000857 The microtubule-based kinesin motors and actin-based myosin motors generate movements required for intracellular trafficking, cell division, and muscle contraction. In general, these proteins consist of a motor domain that generates movement and a tail region that varies widely from class to class and is thought to mediate many of the regulatory or cargo binding functions specific to each class of motor []. The Myosin Tail Homology 4 (MyTH4) domain has been identified as a conserved domain in the tail domains of several different unconventional myosins [] and a plant kinesin-like protein [], but has more recently been found in several non-motor proteins []. Although the function is not yet fully understood, there is an evidence that the MyTH4 domain of Myosin-X (Myo10) binds to microtubules and thus could provide a link between an actin-based motor protein and the microtubule cytoskeleton []. The MyTH4 domain is found in one or two copies associated with other domains, such as myosin head, kinesin motor, FERM, PH, SH3 and IQ. The domain is predicted to be largely alpha-helical, interrupted by three or four turns. The MyTH4 domain contains four highly conserved regions designated MGD (consensus sequence L(K/R)(F/Y)MGDhP, LRDE (consensus LRDEhYCQhhKQHxxxN), RGW (consensus RGWxLh), and ELEA (RxxPPSxhELEA), where h indicates a hydrophobic residue and x is any residue [].; GO: 0005856 cytoskeleton; PDB: 3AU5_A 3AU4_A 3PZD_A 3PVL_A.
Probab=38.79 E-value=1.1e+02 Score=20.36 Aligned_cols=46 Identities=22% Similarity=0.271 Sum_probs=36.9
Q ss_pred HHHHHHHHHHHHHHhhCCHHHHHHHHHhhcCCCch--hHHHHHHHHHH
Q 034402 8 YIHMVQHLIEKCLIFRMTKEECMEALSKHANIKPV--ITSTVWNELEK 53 (95)
Q Consensus 8 ~I~~VQ~LIErCLqlyMsk~E~v~~L~~~a~I~P~--fT~~VW~~LE~ 53 (95)
.++.+|++|..|+.---=++|+.-.|-+|-+=+|. ...-.|+-|--
T Consensus 2 ~~~l~~~Il~~~l~~~~LrDEiy~QliKQtt~np~~~s~~r~W~Ll~~ 49 (114)
T PF00784_consen 2 EIDLIQNILQKGLENPELRDEIYCQLIKQTTNNPSPDSCIRGWQLLAL 49 (114)
T ss_dssp HHHHHHHHHHHHHH-CCHHHHHHHHHHHHTSS-SSCHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHcchhhHHHHHHHHHHHHHCCCchhhHHHHHHHHHH
Confidence 46789999999999999999999999998777665 45678998864
No 51
>PRK13511 6-phospho-beta-galactosidase; Provisional
Probab=38.38 E-value=22 Score=29.80 Aligned_cols=47 Identities=21% Similarity=0.432 Sum_probs=30.9
Q ss_pred hHHHHHHHHHHHHHHHHhhCCHHHHHHHHHhhcCCCchhHHHHHH---HHH-------HhcHHHHHHHHHhh
Q 034402 5 SASYIHMVQHLIEKCLIFRMTKEECMEALSKHANIKPVITSTVWN---ELE-------KENKEFFEAYAQSQ 66 (95)
Q Consensus 5 s~~~I~~VQ~LIErCLqlyMsk~E~v~~L~~~a~I~P~fT~~VW~---~LE-------~eN~eFFkaY~~~~ 66 (95)
..+-|+.-.+||..|+. +||+|.+|..=|. -|+ ++..++|..|.+..
T Consensus 89 N~~gl~~Y~~lid~l~~---------------~GI~P~VTL~H~dlP~~L~~~GGW~n~~~v~~F~~YA~~~ 145 (469)
T PRK13511 89 NPKGVEYYHRLFAECHK---------------RHVEPFVTLHHFDTPEALHSNGDWLNRENIDHFVRYAEFC 145 (469)
T ss_pred CHHHHHHHHHHHHHHHH---------------cCCEEEEEecCCCCcHHHHHcCCCCCHHHHHHHHHHHHHH
Confidence 34556666666666654 4999999986553 343 36678899995543
No 52
>PF14164 YqzH: YqzH-like protein
Probab=37.85 E-value=41 Score=22.06 Aligned_cols=14 Identities=21% Similarity=0.534 Sum_probs=12.2
Q ss_pred HHHHHHHHHHHHhh
Q 034402 10 HMVQHLIEKCLIFR 23 (95)
Q Consensus 10 ~~VQ~LIErCLqly 23 (95)
..++.+|-+||+.|
T Consensus 4 k~I~Kmi~~~l~QY 17 (64)
T PF14164_consen 4 KLIEKMIINCLRQY 17 (64)
T ss_pred HHHHHHHHHHHHHh
Confidence 46788999999999
No 53
>cd00591 HU_IHF Integration host factor (IHF) and HU are small heterodimeric members of the DNABII protein family that bind and bend DNA, functioning as architectural factors in many cellular processes including transcription, site-specific recombination, and higher-order nucleoprotein complex assembly. The dimer subunits associate to form a compact globular core from which two beta ribbon arms (one from each subunit) protrude. The beta arms track and bind the DNA minor groove. Despite sequence and structural similarity, IHF and HU can be distinguished by their different DNA substrate preferences.
Probab=37.54 E-value=76 Score=19.70 Aligned_cols=29 Identities=17% Similarity=0.241 Sum_probs=23.1
Q ss_pred CHHHHHHHHHhhcCCCchhHHHHHHHHHH
Q 034402 25 TKEECMEALSKHANIKPVITSTVWNELEK 53 (95)
Q Consensus 25 sk~E~v~~L~~~a~I~P~fT~~VW~~LE~ 53 (95)
||+|+++.|+...++.+.-...|-..|..
T Consensus 1 ~K~~l~~~ia~~~~~~~~~v~~vl~~~~~ 29 (87)
T cd00591 1 TKSELIEAIAEKTGLSKKDAEAAVDAFLD 29 (87)
T ss_pred CHHHHHHHHHHHhCcCHHHHHHHHHHHHH
Confidence 68899999999998888877777665544
No 54
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=37.37 E-value=56 Score=18.15 Aligned_cols=26 Identities=15% Similarity=0.217 Sum_probs=20.2
Q ss_pred HHHHHhhcCCCchhHHHHHHHHHHhc
Q 034402 30 MEALSKHANIKPVITSTVWNELEKEN 55 (95)
Q Consensus 30 v~~L~~~a~I~P~fT~~VW~~LE~eN 55 (95)
+..|.++.+|.+..-.-..+.|++++
T Consensus 23 ~~~la~~~~vs~~tv~~~l~~L~~~g 48 (60)
T smart00345 23 ERELAAQLGVSRTTVREALSRLEAEG 48 (60)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHCC
Confidence 56677888999888777888887753
No 55
>PF14769 CLAMP: Flagellar C1a complex subunit C1a-32
Probab=37.19 E-value=1.2e+02 Score=20.02 Aligned_cols=56 Identities=13% Similarity=0.342 Sum_probs=39.7
Q ss_pred HHHHHHHHHHHHHHHhhCCHHHHHHHHHhh---cCCC------chhHHHHHHHHHH-hcHHHHHHH
Q 034402 7 SYIHMVQHLIEKCLIFRMTKEECMEALSKH---ANIK------PVITSTVWNELEK-ENKEFFEAY 62 (95)
Q Consensus 7 ~~I~~VQ~LIErCLqlyMsk~E~v~~L~~~---a~I~------P~fT~~VW~~LE~-eN~eFFkaY 62 (95)
.-...++.+.+.|+...||.+++++.+.+- .++. |.|+..-.+.+-+ =.-.||+-|
T Consensus 19 ~~~~i~~~ll~~~i~~~~~~~~~~~~fk~~l~~~sv~rpp~~~~iFs~~~~~~i~~y~~~t~frHy 84 (101)
T PF14769_consen 19 AFLSILKELLEKNIEKGMSLEDSFKYFKELLLRHSVQRPPFSIGIFSVDQVKAIIDYFHNTYFRHY 84 (101)
T ss_pred HHHHHHHHHHHHHHHccCCHHHHHHHHHHHHHHhccCCCCcccCcCCHHHHHHHHHHHHHHHHHHH
Confidence 345678889999999999999999988763 3444 3477776666654 334466666
No 56
>TIGR02894 DNA_bind_RsfA transcription factor, RsfA family. In a subset of endospore-forming members of the Firmcutes, members of this protein family are found, several to a genome. Two very strongly conserved sequences regions are separated by a highly variable linker region. Much of the linker region was excised from the seed alignment for this model. A characterized member is the prespore-specific transcription RsfA from Bacillus subtilis, previously called YwfN, which is controlled by sigma factor F and seems to fine-tune expression of some genes in the sigma-F regulon. A paralog in Bacillus subtilis is designated YlbO.
Probab=35.02 E-value=2e+02 Score=21.83 Aligned_cols=62 Identities=15% Similarity=0.169 Sum_probs=35.8
Q ss_pred hhCCHHHHHHHHHhhcCCCchhHH--HHHHHHHHhcHH-------HHHHHHHhhhHHhhhhHHHHHHHHHHH
Q 034402 22 FRMTKEECMEALSKHANIKPVITS--TVWNELEKENKE-------FFEAYAQSQSKEDRMSEEETNQMIQKM 84 (95)
Q Consensus 22 lyMsk~E~v~~L~~~a~I~P~fT~--~VW~~LE~eN~e-------FFkaY~~~~lk~qi~s~~~~~~~iq~~ 84 (95)
.-||-++||.+|+....-.|.... .=++.|++++.+ -=+.+.++ .++..+-++++..+|+=|
T Consensus 78 ~~ltl~~vI~fLq~l~~~~~~~~~~~~e~~~l~~e~~~l~~~~e~Le~e~~~L-~~~~~~~~eDY~~L~~Im 148 (161)
T TIGR02894 78 GSLTLQDVISFLQNLKTTNPSDQALQKENERLKNQNESLQKRNEELEKELEKL-RQRLSTIEEDYQTLIDIM 148 (161)
T ss_pred ccCCHHHHHHHHHHHHhcchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHH
Confidence 358999999999998777776643 234444444433 33333222 233344566777776644
No 57
>TIGR00269 conserved hypothetical protein TIGR00269.
Probab=34.40 E-value=1.4e+02 Score=19.93 Aligned_cols=41 Identities=10% Similarity=-0.040 Sum_probs=27.9
Q ss_pred hhCCHHHHHHHHHhhcCCCch-------------hHHHHHHHHHHhcHHHHHHHH
Q 034402 22 FRMTKEECMEALSKHANIKPV-------------ITSTVWNELEKENKEFFEAYA 63 (95)
Q Consensus 22 lyMsk~E~v~~L~~~a~I~P~-------------fT~~VW~~LE~eN~eFFkaY~ 63 (95)
.|.+.+|++.+- ...||... ....+.+.||+.||.+....+
T Consensus 8 ~~v~E~ei~~ya-~~~~lp~~~~~CP~~~~a~R~~~k~~L~~LE~~~P~~k~~i~ 61 (104)
T TIGR00269 8 RYIPEKEVVLYA-FLNELKVHLDECPYSSLSVRARIRDFLYDLENKKPGVKFSVL 61 (104)
T ss_pred ccCCHHHHHHHH-HHcCCCcCCCCCCCCCCCchHHHHHHHHHHHHHCcChHHHHH
Confidence 356677777544 44577643 556789999999998755443
No 58
>TIGR01233 lacG 6-phospho-beta-galactosidase. This enzyme is part of the tagatose-6-phosphate pathway of galactose-6-phosphate degradation.
Probab=34.28 E-value=62 Score=27.28 Aligned_cols=38 Identities=26% Similarity=0.379 Sum_probs=24.1
Q ss_pred HHHHHHhhcCCCchhHHHHHH---HHH-------HhcHHHHHHHHHhhh
Q 034402 29 CMEALSKHANIKPVITSTVWN---ELE-------KENKEFFEAYAQSQS 67 (95)
Q Consensus 29 ~v~~L~~~a~I~P~fT~~VW~---~LE-------~eN~eFFkaY~~~~l 67 (95)
+++.|.+ +||+|.+|..=|. .|+ ++..++|..|.+...
T Consensus 98 lid~l~~-~GI~P~VTL~H~dlP~~L~~~GGW~n~~~v~~F~~YA~~~f 145 (467)
T TIGR01233 98 LFAECHK-RHVEPFVTLHHFDTPEALHSNGDFLNRENIEHFIDYAAFCF 145 (467)
T ss_pred HHHHHHH-cCCEEEEeccCCCCcHHHHHcCCCCCHHHHHHHHHHHHHHH
Confidence 3344433 4999999986553 233 467889999955433
No 59
>PF09280 XPC-binding: XPC-binding domain; InterPro: IPR015360 Members of this entry adopt a structure consisting of four alpha helices, arranged in an array. They bind specifically and directly to the xeroderma pigmentosum group C protein (XPC) to initiate nucleotide excision repair []. ; GO: 0003684 damaged DNA binding, 0006289 nucleotide-excision repair, 0043161 proteasomal ubiquitin-dependent protein catabolic process; PDB: 1PVE_A 1QZE_A 1OQY_A 1TP4_A 1X3W_B 3ESW_B 2QSG_X 2QSF_X 1X3Z_B 2QSH_X ....
Probab=34.20 E-value=42 Score=21.13 Aligned_cols=28 Identities=11% Similarity=0.293 Sum_probs=22.3
Q ss_pred hhcCCCchhHHHHHHHHHHhcHHHHHHH
Q 034402 35 KHANIKPVITSTVWNELEKENKEFFEAY 62 (95)
Q Consensus 35 ~~a~I~P~fT~~VW~~LE~eN~eFFkaY 62 (95)
....=+|..-..|.+.|...||+.|+.-
T Consensus 15 ~~vq~NP~lL~~lLqql~~~nP~l~q~I 42 (59)
T PF09280_consen 15 QLVQQNPQLLPPLLQQLGQSNPQLLQLI 42 (59)
T ss_dssp HHHHC-GGGHHHHHHHHHCCSHHHHHHH
T ss_pred HHHHHCHHHHHHHHHHHhccCHHHHHHH
Confidence 3334479999999999999999998764
No 60
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=34.03 E-value=2.2e+02 Score=21.99 Aligned_cols=59 Identities=22% Similarity=0.291 Sum_probs=35.4
Q ss_pred CCHHHHHHHHHhhcCCCchhHHHHHHHHHHhc------------------HHHHHHH---HHhhhHHhhhhHHHHHHHHH
Q 034402 24 MTKEECMEALSKHANIKPVITSTVWNELEKEN------------------KEFFEAY---AQSQSKEDRMSEEETNQMIQ 82 (95)
Q Consensus 24 Msk~E~v~~L~~~a~I~P~fT~~VW~~LE~eN------------------~eFFkaY---~~~~lk~qi~s~~~~~~~iq 82 (95)
||.+|++++| |+.-.=-+.+-++|+..| ++||+-+ ..-+.+++|. .+.+.+.
T Consensus 42 mtl~Ei~E~l----g~Sks~vS~~lkkL~~~~lV~~~~~~G~Rk~~F~a~~df~~~f~t~f~ek~~ReId---~t~e~l~ 114 (177)
T COG1510 42 LTLDEIAEAL----GMSKSNVSMGLKKLQDWNLVKKVFEKGDRKDYFEAEKDFSQIFRTLFEEKWKREID---PTKEALK 114 (177)
T ss_pred ccHHHHHHHH----CCCcchHHHHHHHHHhcchHHhhhccCcchhhhcccchHHHHHHHHHHHHHHHHhh---hHHHHHH
Confidence 3667777776 666555566667777654 3454444 2344566676 6666666
Q ss_pred HHHhhcc
Q 034402 83 KMISTNS 89 (95)
Q Consensus 83 ~~~~~~~ 89 (95)
+.+....
T Consensus 115 k~~~e~~ 121 (177)
T COG1510 115 KLLEELN 121 (177)
T ss_pred HHHHHcc
Confidence 6655443
No 61
>PF13720 Acetyltransf_11: Udp N-acetylglucosamine O-acyltransferase; Domain 2; PDB: 3I3A_A 3I3X_A 3HSQ_B 2JF2_A 1LXA_A 2AQ9_A 2QIV_X 2QIA_A 2JF3_A 4EQY_F ....
Probab=33.77 E-value=1.4e+02 Score=19.52 Aligned_cols=43 Identities=21% Similarity=0.195 Sum_probs=29.9
Q ss_pred hHHHHHHHHHHHHHHHHhhCCHHHHHHHHHhhcCCCchhHHHH
Q 034402 5 SASYIHMVQHLIEKCLIFRMTKEECMEALSKHANIKPVITSTV 47 (95)
Q Consensus 5 s~~~I~~VQ~LIErCLqlyMsk~E~v~~L~~~a~I~P~fT~~V 47 (95)
|.++|..++.....=+...++.+|.++.|.+...=.|.+...|
T Consensus 29 s~~~i~~l~~ayr~l~~~~~~~~~a~~~l~~~~~~~~~v~~~~ 71 (83)
T PF13720_consen 29 SKEEISALRRAYRILFRSGLTLEEALEELEEEYPDSPEVREIV 71 (83)
T ss_dssp -HHHHHHHHHHHHHHHTSSS-HHHHHHHHHHHTTSCHHHHHHH
T ss_pred CHHHHHHHHHHHHHHHhCCCCHHHHHHHHHHhccCCHHHHHHH
Confidence 4677777777777777777788888888877666677666544
No 62
>PRK10144 formate-dependent nitrite reductase complex subunit NrfF; Provisional
Probab=33.58 E-value=95 Score=22.54 Aligned_cols=46 Identities=17% Similarity=0.212 Sum_probs=35.8
Q ss_pred CchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHhhcCC----Cch---hHHHHH
Q 034402 3 ESSASYIHMVQHLIEKCLIFRMTKEECMEALSKHANI----KPV---ITSTVW 48 (95)
Q Consensus 3 ~~s~~~I~~VQ~LIErCLqlyMsk~E~v~~L~~~a~I----~P~---fT~~VW 48 (95)
||.+....-..+.|-+=+.--+|++||++++-.+.|= +|- .|..+|
T Consensus 53 dSna~iA~dmR~~Vr~~i~~G~sd~eI~~~~v~RYG~~Vl~~Pp~~~~t~~LW 105 (126)
T PRK10144 53 ESNAPVAVSMRHQVYSMVAEGKSEVEIIGWMTERYGDFVRYNPPLTGQTLVLW 105 (126)
T ss_pred hcCCHHHHHHHHHHHHHHHcCCCHHHHHHHHHHhcCCeEEecCCCCcchHHHH
Confidence 5656666677788888899999999999999999883 454 355666
No 63
>PF05295 Luciferase_N: Luciferase/LBP N-terminal domain; InterPro: IPR007959 Proteins in this entry belong to a family of dinoflagellate luciferase and luciferin binding proteins. Luciferase is involved in catalysing the light emitting reaction in bioluminescence and luciferin binding protein (LBP) is known to bind to luciferin (the substrate for luciferase) to stop it reacting with the enzyme and therefore switching off the bioluminescence function. The expression of these two proteins is controlled by a circadian clock at the translational level, with synthesis and degradation occurring on a daily basis []. This entry consists of a presumed N-terminal domain that is conserved between dinoflagellate luciferase and luciferin binding proteins. This domain is not, however, the catalytic part of the protein. It has been suggested that this region may mediate an interaction between LBP and Luciferase or their association with the vacuolar membrane []. More information about these proteins can be found at Protein of the Month: Luciferase [].
Probab=33.28 E-value=1.2e+02 Score=20.81 Aligned_cols=45 Identities=18% Similarity=0.330 Sum_probs=34.9
Q ss_pred HHHHHHHhhcCCCchhHHHHHHHHHHhcHHHHHHH-----HHhhhHHhhh
Q 034402 28 ECMEALSKHANIKPVITSTVWNELEKENKEFFEAY-----AQSQSKEDRM 72 (95)
Q Consensus 28 E~v~~L~~~a~I~P~fT~~VW~~LE~eN~eFFkaY-----~~~~lk~qi~ 72 (95)
|....|.+.++++|.+-..+=+.|.-|+-.=|--| |..-.++.|+
T Consensus 4 ql~~FLt~dakvD~~vv~ymTk~L~lesvsDFAn~WTs~eyE~GvqdDIi 53 (82)
T PF05295_consen 4 QLAQFLTNDAKVDPKVVAYMTKQLQLESVSDFANYWTSAEYEKGVQDDII 53 (82)
T ss_pred HHHHHHhcccccCHHHHHHHHhhcchhhHHHHHhhhhHHHHHhhhHHHHH
Confidence 67788999999999999999999998886666555 3334455555
No 64
>smart00511 ORANGE Orange domain. This domain confers specificity among members of the Hairy/E(SPL) family.
Probab=32.35 E-value=87 Score=17.90 Aligned_cols=27 Identities=19% Similarity=0.302 Sum_probs=23.0
Q ss_pred HHHHHHHHhhcCCCchhHHHHHHHHHH
Q 034402 27 EECMEALSKHANIKPVITSTVWNELEK 53 (95)
Q Consensus 27 ~E~v~~L~~~a~I~P~fT~~VW~~LE~ 53 (95)
.||++.|...-+++|.+...+-+.|..
T Consensus 12 ~Ev~~fLs~~~~~~~~~~~~Ll~HL~~ 38 (45)
T smart00511 12 NEVSRFLSQLPGTDPDVRARLLSHLQT 38 (45)
T ss_pred HHHHHHHhcCCCCChHHHHHHHHHHHH
Confidence 589999998888999988888888764
No 65
>KOG3973 consensus Uncharacterized conserved glycine-rich protein [Function unknown]
Probab=32.33 E-value=43 Score=29.09 Aligned_cols=56 Identities=21% Similarity=0.439 Sum_probs=36.5
Q ss_pred HHHHHH-HHHHhhCCHH-------HHHHHHHh-----hcCCCchh----------HHHHHHHHHHhcHHHHHHH-HHhhh
Q 034402 12 VQHLIE-KCLIFRMTKE-------ECMEALSK-----HANIKPVI----------TSTVWNELEKENKEFFEAY-AQSQS 67 (95)
Q Consensus 12 VQ~LIE-rCLqlyMsk~-------E~v~~L~~-----~a~I~P~f----------T~~VW~~LE~eN~eFFkaY-~~~~l 67 (95)
|+.+|+ -|..|.|+|- ...+++.. -+++.|.. +..-|.++|+.|.+|=+.| .|++|
T Consensus 141 v~q~i~~~~~~L~~~k~p~Nin~~~lfe~i~~kl~~ai~kv~p~~~~~PLlKkpl~~a~w~~iE~~~~~~~~ey~~Rr~l 220 (465)
T KOG3973|consen 141 VTQLIDSALRTLNFPKQPGNINEWKLFETIRQKLDGAIKKVSPSQRSHPLLKKPLDEATWPEIEKQCESFSREYYNRRLL 220 (465)
T ss_pred HHHHHHHHHHHcCCCCCCCCchHHHHHHHHHHHHHhHHhcCCHhhcCCchhcCcCChhhHHHHHHHHHHHHHHHHHHHHH
Confidence 566666 5777877652 22222221 23565543 4678999999999999999 55443
No 66
>PF11417 Inhibitor_G39P: Loader and inhibitor of phage G40P; InterPro: IPR024424 G39P inhibits the initiation of DNA replication by blocking G40P replicative helicase. G39P has a bipartite stricture consisting of a folded N-terminal domain and an unfolded C-terminal domain. The C-terminal is essential for helicase interaction [].; PDB: 1NO1_B.
Probab=31.55 E-value=50 Score=21.51 Aligned_cols=30 Identities=33% Similarity=0.411 Sum_probs=19.3
Q ss_pred CCHHHHHHHHHhhcCCCc----h-------hHHHHHHHHHH
Q 034402 24 MTKEECMEALSKHANIKP----V-------ITSTVWNELEK 53 (95)
Q Consensus 24 Msk~E~v~~L~~~a~I~P----~-------fT~~VW~~LE~ 53 (95)
|+++|+++-|..-...=| . -+..+|..+-+
T Consensus 1 Mtk~E~~~ll~~I~~aYP~~~~~f~~~~~k~~v~~W~~~L~ 41 (71)
T PF11417_consen 1 MTKEETAKLLKLIKAAYPQWAGNFKPTDSKETVDLWYDMLK 41 (71)
T ss_dssp --HHHHHHHHHHHHHHST---TT---STHHHHHHHHHHHHT
T ss_pred CCHHHHHHHHHHHHHHCCcchhccchhhHHHHHHHHHHHHH
Confidence 899999999987666666 2 24567766543
No 67
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=31.42 E-value=79 Score=18.12 Aligned_cols=33 Identities=33% Similarity=0.277 Sum_probs=19.5
Q ss_pred HHHHHHHHhhCCHHHHHHHHHhhcCCCchhHHHHHHHHHH
Q 034402 14 HLIEKCLIFRMTKEECMEALSKHANIKPVITSTVWNELEK 53 (95)
Q Consensus 14 ~LIErCLqlyMsk~E~v~~L~~~a~I~P~fT~~VW~~LE~ 53 (95)
..|+..+...||..|+.+.| |+.| ++|.+.|..
T Consensus 11 ~~I~~l~~~G~s~~~IA~~l----g~s~---sTV~relkR 43 (44)
T PF13936_consen 11 NQIEALLEQGMSIREIAKRL----GRSR---STVSRELKR 43 (44)
T ss_dssp -HHHHHHCS---HHHHHHHT----T--H---HHHHHHHHH
T ss_pred HHHHHHHHcCCCHHHHHHHH----CcCc---HHHHHHHhc
Confidence 34777788889988888777 5555 377777753
No 68
>PRK09589 celA 6-phospho-beta-glucosidase; Reviewed
Probab=31.28 E-value=58 Score=27.58 Aligned_cols=48 Identities=23% Similarity=0.459 Sum_probs=31.9
Q ss_pred hHHHHHHHHHHHHHHHHhhCCHHHHHHHHHhhcCCCchhHHHHHH---HHHH--------hcHHHHHHHHHhhh
Q 034402 5 SASYIHMVQHLIEKCLIFRMTKEECMEALSKHANIKPVITSTVWN---ELEK--------ENKEFFEAYAQSQS 67 (95)
Q Consensus 5 s~~~I~~VQ~LIErCLqlyMsk~E~v~~L~~~a~I~P~fT~~VW~---~LE~--------eN~eFFkaY~~~~l 67 (95)
..+-|+.=.+||..|+. .||+|.+|..=|. -|+. +..+.|..|.+...
T Consensus 103 N~~gl~~Y~~lid~L~~---------------~GI~P~VTL~H~dlP~~L~~~yGGW~n~~~i~~F~~YA~~~f 161 (476)
T PRK09589 103 NEEGLQFYDDLFDECLK---------------QGIEPVVTLSHFEMPYHLVTEYGGWRNRKLIDFFVRFAEVVF 161 (476)
T ss_pred CHHHHHHHHHHHHHHHH---------------cCCEEEEEecCCCCCHHHHHhcCCcCChHHHHHHHHHHHHHH
Confidence 34556666666666654 3999999987665 4543 45678999955433
No 69
>PF05960 DUF885: Bacterial protein of unknown function (DUF885); InterPro: IPR010281 This family consists of hypothetical bacterial proteins.; PDB: 3O0Y_B 3U24_A 3IUK_A.
Probab=30.92 E-value=3.1e+02 Score=22.66 Aligned_cols=59 Identities=7% Similarity=0.085 Sum_probs=47.2
Q ss_pred CchHHHHHHHHHHHHHHHHh---------hCCHHHHHHHHHhhcCCCchhHHHHHHHHHHhcHHHHHHH
Q 034402 3 ESSASYIHMVQHLIEKCLIF---------RMTKEECMEALSKHANIKPVITSTVWNELEKENKEFFEAY 62 (95)
Q Consensus 3 ~~s~~~I~~VQ~LIErCLql---------yMsk~E~v~~L~~~a~I~P~fT~~VW~~LE~eN~eFFkaY 62 (95)
+.+...+-+.+..+-||+.+ -||.+|+++.|.++.+..+.....-|...-. +|..+-+|
T Consensus 432 ~~p~~~lg~l~~~l~ra~r~vvD~glH~~~wt~e~a~~~l~~~~~~~~~~a~~ev~ry~~-~Pgq~~sY 499 (549)
T PF05960_consen 432 DDPLDRLGQLNDELWRAARLVVDTGLHYGGWTREQAIDYLVENTGFSEEEAESEVDRYIS-SPGQALSY 499 (549)
T ss_dssp CSHHHHHHHHHHHHHHHHHHHHHHHHHCCB--HHHHHHHHHHHS-S-HHHHHHHHHHHHH-STTGGGHH
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCHHHHHHHHHHhcCCChHHHHHHHHHHHh-CcHHHHHH
Confidence 45677888888888899875 5899999999999999999888888877776 99999999
No 70
>PF11333 DUF3135: Protein of unknown function (DUF3135); InterPro: IPR021482 This family of proteins with unkown function appears to be restricted to Proteobacteria.
Probab=30.42 E-value=1.7e+02 Score=19.56 Aligned_cols=27 Identities=26% Similarity=0.222 Sum_probs=21.1
Q ss_pred HHHHHHHHhcHHHHHHHHHhhhHHhhh
Q 034402 46 TVWNELEKENKEFFEAYAQSQSKEDRM 72 (95)
Q Consensus 46 ~VW~~LE~eN~eFFkaY~~~~lk~qi~ 72 (95)
.-|..|-++|||=|++..+..+++=|.
T Consensus 7 D~L~~LA~~dPe~fe~lr~~~~ee~I~ 33 (83)
T PF11333_consen 7 DELKELAQNDPEAFEQLRQELIEEMIE 33 (83)
T ss_pred HHHHHHHHhCHHHHHHHHHHHHHHHHH
Confidence 456679999999999997766665555
No 71
>smart00760 Bac_DnaA_C Bacterial dnaA protein helix-turn-helix domain. Could be involved in DNA-binding.
Probab=30.33 E-value=51 Score=19.80 Aligned_cols=18 Identities=39% Similarity=0.501 Sum_probs=14.8
Q ss_pred CHHHHHHHHHhhcCCCch
Q 034402 25 TKEECMEALSKHANIKPV 42 (95)
Q Consensus 25 sk~E~v~~L~~~a~I~P~ 42 (95)
|.+++++...+.+||+|.
T Consensus 1 ~~~~I~~~Va~~~~i~~~ 18 (60)
T smart00760 1 TIEEIIEAVAEYFGVKPE 18 (60)
T ss_pred CHHHHHHHHHHHhCCCHH
Confidence 457888999999999875
No 72
>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional
Probab=29.90 E-value=1.4e+02 Score=25.27 Aligned_cols=37 Identities=8% Similarity=0.163 Sum_probs=29.7
Q ss_pred HHHHHHHHHHHHhhCCHHHHHHHHHhhcCCCchhHHHHHHHHHH
Q 034402 10 HMVQHLIEKCLIFRMTKEECMEALSKHANIKPVITSTVWNELEK 53 (95)
Q Consensus 10 ~~VQ~LIErCLqlyMsk~E~v~~L~~~a~I~P~fT~~VW~~LE~ 53 (95)
+.-+.+|++.+..|.|..++.+.| ||.+ .++|++|.+
T Consensus 473 ~~E~~~i~~~l~~~~~~~~aA~~L----Gisr---~tL~rkl~~ 509 (520)
T PRK10820 473 RFERSVLTRLYRNYPSTRKLAKRL----GVSH---TAIANKLRE 509 (520)
T ss_pred HHHHHHHHHHHHHCCCHHHHHHHh----CCCH---HHHHHHHHH
Confidence 345788999999999988766655 8887 489999986
No 73
>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences [,]. It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli []. Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion. In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor []. The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution [,]. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as `feelers' suitable for DNA or protein (invertase) recognition []. Other proteins belonging to this subfamily include: E. coli: atoC, hydG, ntrC, fhlA, tyrR, Rhizobium spp.: ntrC, nifA, dctD ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NTC_A 3JRH_A 3JRB_A 3IV5_A 3JRI_A 1ETQ_A 1ETW_B 1ETY_A 3JRF_A 3JRA_A ....
Probab=29.71 E-value=1.1e+02 Score=17.20 Aligned_cols=34 Identities=24% Similarity=0.282 Sum_probs=23.0
Q ss_pred HHHHHHHHHhhC-CHHHHHHHHHhhcCCCchhHHHHHHHHHH
Q 034402 13 QHLIEKCLIFRM-TKEECMEALSKHANIKPVITSTVWNELEK 53 (95)
Q Consensus 13 Q~LIErCLqlyM-sk~E~v~~L~~~a~I~P~fT~~VW~~LE~ 53 (95)
..+|+.+|..+= |..++.+.| ||.|. ++|.+|++
T Consensus 7 ~~~i~~aL~~~~gn~~~aA~~L----gisr~---tL~~klkk 41 (42)
T PF02954_consen 7 KQLIRQALERCGGNVSKAARLL----GISRR---TLYRKLKK 41 (42)
T ss_dssp HHHHHHHHHHTTT-HHHHHHHH----TS-HH---HHHHHHHH
T ss_pred HHHHHHHHHHhCCCHHHHHHHH----CCCHH---HHHHHHHh
Confidence 567777776554 788777777 88775 78888765
No 74
>TIGR00207 fliG flagellar motor switch protein FliG. The fliG protein along with fliM and fliN interact to form the switch complex of the bacterial flagellar motor located at the base of the basal body. This complex interacts with chemotaxis proteins (eg CHEY). In addition the complex interacts with other components of the motor that determine the direction of flagellar rotation. The model contains putative members of the fliG family at scores of less than 100 from Agrobacterium radiobacter and Sinorhizobium meliloti as well as fliG-like genes from treponema pallidum and Borrelia burgdorferi. That is why the suggested cutoff is set at 20 but was set at 100 to construct the family.
Probab=29.58 E-value=3e+02 Score=22.22 Aligned_cols=59 Identities=17% Similarity=0.182 Sum_probs=41.0
Q ss_pred CCchHHHHHHHHHHHHHHHHhhCCH------HHHHHHHHhhcCCCchhHHHHHHHHHHhcHHHHHHH
Q 034402 2 GESSASYIHMVQHLIEKCLIFRMTK------EECMEALSKHANIKPVITSTVWNELEKENKEFFEAY 62 (95)
Q Consensus 2 ~~~s~~~I~~VQ~LIErCLqlyMsk------~E~v~~L~~~a~I~P~fT~~VW~~LE~eN~eFFkaY 62 (95)
|.-|.+.+..|-..+++|+..+-+. -+.+..+.+ +.++.-...|...|++.+|++...=
T Consensus 170 ~~vs~~~i~~ie~~L~~~~~~~~~~~~~~gG~~~~a~ILN--~~~~~~~~~il~~L~~~dp~la~~I 234 (338)
T TIGR00207 170 GRTSPEVVAEVERVLEGKLDSLNSDYTKMGGVRAVAEIIN--LMDRKTEKTIITSLEEFDPELAEEI 234 (338)
T ss_pred CCCCHHHHHHHHHHHHHHHHhhccccccCChHHHHHHHHH--hCCchHHHHHHHHHHHhCHHHHHHH
Confidence 4457788888888999998866531 122222323 3555666699999999999998765
No 75
>PRK07194 fliG flagellar motor switch protein G; Reviewed
Probab=29.57 E-value=2.8e+02 Score=22.29 Aligned_cols=58 Identities=12% Similarity=0.225 Sum_probs=40.6
Q ss_pred CCCchHHHHHHHHHHHHHHHHhhCC-------HHHHHHHHHhhcCCCchhHHHHHHHHHHhcHHHHHH
Q 034402 1 MGESSASYIHMVQHLIEKCLIFRMT-------KEECMEALSKHANIKPVITSTVWNELEKENKEFFEA 61 (95)
Q Consensus 1 ~~~~s~~~I~~VQ~LIErCLqlyMs-------k~E~v~~L~~~a~I~P~fT~~VW~~LE~eN~eFFka 61 (95)
||.-|.+.+..|-..+++|+..+.+ -.+.+..+.++.. ... ..+|..|++.+|++...
T Consensus 166 l~~Vs~e~~~~V~e~l~~~~~~~~~~~~~~~~G~~~aa~ILn~l~-~~~--~~il~~L~~~dp~~a~~ 230 (334)
T PRK07194 166 LDDVDRDVVDELDELIERCLAVLSEQSHTKVIGVKQAADIINRFP-GDR--QQLMEMLKEHDEEVVNE 230 (334)
T ss_pred cCCCCHHHHHHHHHHHHHHHHhhhhcccccCCCHHHHHHHHHhCc-hhH--HHHHHHHHhhCHHHHHH
Confidence 3455778888888888999876432 2334555555544 222 58999999999999887
No 76
>smart00830 CM_2 Chorismate mutase type II. Chorismate mutase, catalyses the conversion of chorismate to prephenate in the pathway of tyrosine and phenylalanine biosynthesis. This enzyme is negatively regulated by tyrosine, tryptophan and phenylalanine PUBMED:9642265, PUBMED:9497350.
Probab=29.38 E-value=73 Score=19.50 Aligned_cols=9 Identities=22% Similarity=0.246 Sum_probs=4.0
Q ss_pred HHHHHHHHH
Q 034402 56 KEFFEAYAQ 64 (95)
Q Consensus 56 ~eFFkaY~~ 64 (95)
|+|.+..++
T Consensus 60 ~~~~~~if~ 68 (79)
T smart00830 60 PELVERIFR 68 (79)
T ss_pred HHHHHHHHH
Confidence 444444433
No 77
>PRK09239 chorismate mutase; Provisional
Probab=29.34 E-value=95 Score=21.27 Aligned_cols=18 Identities=22% Similarity=0.189 Sum_probs=8.5
Q ss_pred cHHHHHHHHHhhhHHhhh
Q 034402 55 NKEFFEAYAQSQSKEDRM 72 (95)
Q Consensus 55 N~eFFkaY~~~~lk~qi~ 72 (95)
.|+|.+..++..+..-+-
T Consensus 74 ~p~~~~~i~~~ii~esir 91 (104)
T PRK09239 74 DPDFAEKFLNFIIKEVIR 91 (104)
T ss_pred CHHHHHHHHHHHHHHHHH
Confidence 345555555554444333
No 78
>PRK14137 recX recombination regulator RecX; Provisional
Probab=29.08 E-value=1.6e+02 Score=22.31 Aligned_cols=52 Identities=13% Similarity=0.146 Sum_probs=42.7
Q ss_pred HHHHHHHHHHHHh----hCCHHHHHHHHHhhcCCCchhHHHHHHHHHHhc----HHHHHHH
Q 034402 10 HMVQHLIEKCLIF----RMTKEECMEALSKHANIKPVITSTVWNELEKEN----KEFFEAY 62 (95)
Q Consensus 10 ~~VQ~LIErCLql----yMsk~E~v~~L~~~a~I~P~fT~~VW~~LE~eN----~eFFkaY 62 (95)
..-+.+...||.+ -.|..|+-+-|.++ +++|.+-..|-..|.+.| ..|=++|
T Consensus 37 e~~~~~~~~Al~~Ls~R~rS~~ELr~KL~~k-g~~~e~Ie~vI~rL~e~gyLDD~rfAe~~ 96 (195)
T PRK14137 37 EAREALLAYAFRALAARAMTAAELRAKLERR-SEDEALVTEVLERVQELGYQDDAQVARAE 96 (195)
T ss_pred HHHHHHHHHHHHHHhcchhhHHHHHHHHHhc-CCCHHHHHHHHHHHHHcCCCCHHHHHHHH
Confidence 5567888899988 88999999999886 999999999999999954 3444444
No 79
>PF13305 WHG: WHG domain; PDB: 1ZK8_B 3ON2_B 3CJD_B.
Probab=28.86 E-value=1.3e+02 Score=17.72 Aligned_cols=18 Identities=22% Similarity=0.305 Sum_probs=13.0
Q ss_pred HHHhcHHHHHHHHHhhhH
Q 034402 51 LEKENKEFFEAYAQSQSK 68 (95)
Q Consensus 51 LE~eN~eFFkaY~~~~lk 68 (95)
.-.+||++|++.+.....
T Consensus 10 Fa~~~p~~f~~mf~~~~~ 27 (81)
T PF13305_consen 10 FAREHPELFRLMFMSDII 27 (81)
T ss_dssp HHHHSHHHHHHHHHSCHS
T ss_pred HHHHHHHHHHHHhcCCCC
Confidence 456899999999655444
No 80
>PF08004 DUF1699: Protein of unknown function (DUF1699); InterPro: IPR012546 This family contains many archaeal proteins which have very conserved sequences.
Probab=28.55 E-value=1.4e+02 Score=22.20 Aligned_cols=40 Identities=20% Similarity=0.287 Sum_probs=30.5
Q ss_pred HHHHHHHHHHHHHHHHhhCCHHHHHHHHHhhcCCCchhHHHHHH
Q 034402 6 ASYIHMVQHLIEKCLIFRMTKEECMEALSKHANIKPVITSTVWN 49 (95)
Q Consensus 6 ~~~I~~VQ~LIErCLqlyMsk~E~v~~L~~~a~I~P~fT~~VW~ 49 (95)
.+.|..+..| ..-.+|.+|+++.+++..++.|.|-..+.+
T Consensus 91 ~~vi~~I~el----~~eG~s~eei~~ki~~e~kl~pd~i~yi~~ 130 (131)
T PF08004_consen 91 ESVIERIKEL----KSEGKSEEEIAEKISRETKLSPDMIKYILK 130 (131)
T ss_pred HHHHHHHHHH----HHcCCCHHHHHHHHHHhhcCCHHHHHHHhc
Confidence 4444444444 456899999999999999999999876643
No 81
>cd07377 WHTH_GntR Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators. This CD represents the winged HTH DNA-binding domain of the GntR (named after the gluconate operon repressor in Bacillus subtilis) family of bacterial transcriptional regulators and their putative homologs found in eukaryota and archaea. The GntR family has over 6000 members distributed among almost all bacterial species, which is comprised of FadR, HutC, MocR, YtrA, AraR, PlmA, and other subfamilies for the regulation of the most varied biological process. The monomeric proteins of the GntR family are characterized by two function domains: a small highly conserved winged helix-turn-helix prokaryotic DNA binding domain in the N-terminus, and a very diverse regulatory ligand-binding domain in the C-terminus for effector-binding/oligomerization, which provides the basis for the subfamily classifications. Binding of the effector to GntR-like transcriptional regulators is
Probab=28.50 E-value=93 Score=17.54 Aligned_cols=26 Identities=19% Similarity=0.261 Sum_probs=19.1
Q ss_pred HHHHHhhcCCCchhHHHHHHHHHHhc
Q 034402 30 MEALSKHANIKPVITSTVWNELEKEN 55 (95)
Q Consensus 30 v~~L~~~a~I~P~fT~~VW~~LE~eN 55 (95)
+..|.++++|.+.--..+.++|++++
T Consensus 28 ~~~la~~~~is~~~v~~~l~~L~~~G 53 (66)
T cd07377 28 ERELAEELGVSRTTVREALRELEAEG 53 (66)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHCC
Confidence 66788888999876666666666654
No 82
>TIGR02010 IscR iron-sulfur cluster assembly transcription factor IscR. This model describes IscR, an iron-sulfur binding transcription factor of the ISC iron-sulfur cluster assembly system.
Probab=28.41 E-value=73 Score=21.88 Aligned_cols=26 Identities=15% Similarity=0.294 Sum_probs=21.8
Q ss_pred HHHHHhhcCCCchhHHHHHHHHHHhc
Q 034402 30 MEALSKHANIKPVITSTVWNELEKEN 55 (95)
Q Consensus 30 v~~L~~~a~I~P~fT~~VW~~LE~eN 55 (95)
++.|+++.+|.|.+..-|.++|.+.+
T Consensus 28 ~~~ia~~~~ip~~~l~kil~~L~~~g 53 (135)
T TIGR02010 28 LADISERQGISLSYLEQLFAKLRKAG 53 (135)
T ss_pred HHHHHHHHCcCHHHHHHHHHHHHHCC
Confidence 45667777999999999999999854
No 83
>PRK11361 acetoacetate metabolism regulatory protein AtoC; Provisional
Probab=28.32 E-value=1.7e+02 Score=23.26 Aligned_cols=37 Identities=14% Similarity=0.147 Sum_probs=30.2
Q ss_pred HHHHHHHHHHHhh-CCHHHHHHHHHhhcCCCchhHHHHHHHHHHh
Q 034402 11 MVQHLIEKCLIFR-MTKEECMEALSKHANIKPVITSTVWNELEKE 54 (95)
Q Consensus 11 ~VQ~LIErCLqly-Msk~E~v~~L~~~a~I~P~fT~~VW~~LE~e 54 (95)
.-+.+|+++|..+ .|+.+..+.| ||.+ .++|++|++-
T Consensus 417 ~E~~~i~~al~~~~gn~~~aA~~L----Gisr---~tL~rkl~~~ 454 (457)
T PRK11361 417 VEKRIIMEVLEQQEGNRTRTALML----GISR---RALMYKLQEY 454 (457)
T ss_pred HHHHHHHHHHHHhCCCHHHHHHHH----CCCH---HHHHHHHHHh
Confidence 4577899999875 9999998887 8885 4899999863
No 84
>PF03965 Penicillinase_R: Penicillinase repressor; InterPro: IPR005650 Proteins in this entry are transcriptional regulators found in a variety of bacteria and a small number of archaea. Many are BlaI/MecI proteins which regulate resistance to penicillins (beta-lactams), though at least one protein (Q47839 from SWISSPROT) appears to be involved in the regulation of copper homeostasis []. BlaI regulators repress the expression of penicillin-degrading enzymes (penicillinases) until the cell encounters the antiobiotic, at which point repression ceases and penicillinase expression occurs, allowing cell growth []. MecI regulators repress the expression of MecA, a cell-wall biosynthetic enzyme not inhibited by penicillins at clinically achievable concentrations, until the presence of the antibiotic is detected []. At this point repression ends and MecA expression occurs which, together with the switching off of the penicillin-sensitive enzymes, allows the cell to grow despite the presence of antibiotic.; GO: 0003677 DNA binding, 0045892 negative regulation of transcription, DNA-dependent; PDB: 2G9W_A 2K4B_A 1XSD_A 1SD4_A 1SD7_A 1SD6_A 2P7C_B 1P6R_A 1OKR_B 2D45_B ....
Probab=28.18 E-value=63 Score=21.53 Aligned_cols=30 Identities=27% Similarity=0.206 Sum_probs=26.3
Q ss_pred CCHHHHHHHHHhhcCCCchhHHHHHHHHHH
Q 034402 24 MTKEECMEALSKHANIKPVITSTVWNELEK 53 (95)
Q Consensus 24 Msk~E~v~~L~~~a~I~P~fT~~VW~~LE~ 53 (95)
++-.||++.|.+..++.|.-+.++.+.|.+
T Consensus 18 ~t~~eI~~~l~~~~~~~~sTv~t~L~rL~~ 47 (115)
T PF03965_consen 18 ATVREIHEALPEERSWAYSTVQTLLNRLVE 47 (115)
T ss_dssp EEHHHHHHHHCTTSS--HHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHhccccchhHHHHHHHHHHh
Confidence 788999999999889999999999999998
No 85
>PF13592 HTH_33: Winged helix-turn helix
Probab=28.09 E-value=1.1e+02 Score=18.35 Aligned_cols=38 Identities=8% Similarity=0.046 Sum_probs=28.7
Q ss_pred HHHHHHHHHHHHHhhCCHHHHHHHHHhhcCCCchhHHHH
Q 034402 9 IHMVQHLIEKCLIFRMTKEECMEALSKHANIKPVITSTV 47 (95)
Q Consensus 9 I~~VQ~LIErCLqlyMsk~E~v~~L~~~a~I~P~fT~~V 47 (95)
...|+.+|++++---+|..-|-+.|. +.|..+.-...+
T Consensus 7 ~~~i~~~I~~~fgv~ys~~~v~~lL~-r~G~s~~kp~~~ 44 (60)
T PF13592_consen 7 LKEIAAYIEEEFGVKYSPSGVYRLLK-RLGFSYQKPRPR 44 (60)
T ss_pred HHHHHHHHHHHHCCEEcHHHHHHHHH-HcCCccccCCCC
Confidence 46788999999998888888888775 457776655544
No 86
>COG0776 HimA Bacterial nucleoid DNA-binding protein [DNA replication, recombination, and repair]
Probab=27.95 E-value=1.3e+02 Score=20.72 Aligned_cols=18 Identities=33% Similarity=0.569 Sum_probs=16.3
Q ss_pred CCHHHHHHHHHhhcCCCc
Q 034402 24 MTKEECMEALSKHANIKP 41 (95)
Q Consensus 24 Msk~E~v~~L~~~a~I~P 41 (95)
|||.|+++.|.+++++..
T Consensus 2 mtKseli~~ia~~~~l~k 19 (94)
T COG0776 2 MTKSELIDAIAEKAGLSK 19 (94)
T ss_pred CCHHHHHHHHHHHcCCCH
Confidence 899999999999998665
No 87
>COG5104 PRP40 Splicing factor [RNA processing and modification]
Probab=27.68 E-value=2.2e+02 Score=25.58 Aligned_cols=36 Identities=33% Similarity=0.499 Sum_probs=26.1
Q ss_pred cHHHHHHHHHhhhHHhhhhHH----HHHHHHHHHHhhccc
Q 034402 55 NKEFFEAYAQSQSKEDRMSEE----ETNQMIQKMISTNSS 90 (95)
Q Consensus 55 N~eFFkaY~~~~lk~qi~s~~----~~~~~iq~~~~~~~~ 90 (95)
-++-|++|+--.+++|...++ ....-+++|+..+|.
T Consensus 189 rK~~f~kY~~n~~~dq~~~e~n~~~k~~~ef~kml~~n~~ 228 (590)
T COG5104 189 RKDLFKKYFENQEKDQREEEENKQRKYINEFCKMLAGNSH 228 (590)
T ss_pred HHHHHHHHHHhhhhhhhHHHHhHHHHHHHHHHHHhcCCCc
Confidence 468999998888889877443 244567889876653
No 88
>TIGR01803 CM-like chorismate mutase related enzymes. This subfamily includes two enzymes which are variants on the mechanism of chorismate mutase and are likely to have evolved from an ancestral chorismate mutase enzyme. 4-amino-4-deoxy-chorismate mutase produces amino-deoxy-prephenate which is subsequently converted to para-dimethylamino-phenylalanine, a component of the natural product pristinamycin. Isochorismate-pyruvate lyase presumably catalyzes the same type of 2+2+2 cyclo-rearrangement as chorismate mutase, but acting on isochorismate, this results in two broken bonds instead of one broken and one made. The product of this reaction is salicylate (2-hydroxy-benzoate) which is also incorporated into various natural products.
Probab=27.64 E-value=79 Score=20.25 Aligned_cols=20 Identities=5% Similarity=0.327 Sum_probs=15.6
Q ss_pred HhhcCCCchhHHHHHHHHHH
Q 034402 34 SKHANIKPVITSTVWNELEK 53 (95)
Q Consensus 34 ~~~a~I~P~fT~~VW~~LE~ 53 (95)
..+.|++|.+...+|+.+=.
T Consensus 57 a~~~gl~~~~~~~if~~ii~ 76 (82)
T TIGR01803 57 AEENGLDPPFVEGLFAQIIH 76 (82)
T ss_pred HHHcCCCHHHHHHHHHHHHH
Confidence 34578999999999987754
No 89
>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.
Probab=27.24 E-value=87 Score=19.18 Aligned_cols=24 Identities=17% Similarity=0.368 Sum_probs=17.5
Q ss_pred HHHHHhhcCCCchhHHHHHHHHHH
Q 034402 30 MEALSKHANIKPVITSTVWNELEK 53 (95)
Q Consensus 30 v~~L~~~a~I~P~fT~~VW~~LE~ 53 (95)
+..|+++++++|..-..+...|++
T Consensus 17 ~~eLa~~~~~s~~~ve~mL~~l~~ 40 (69)
T PF09012_consen 17 LAELAREFGISPEAVEAMLEQLIR 40 (69)
T ss_dssp HHHHHHHTT--HHHHHHHHHHHHC
T ss_pred HHHHHHHHCcCHHHHHHHHHHHHH
Confidence 356788899999999888888765
No 90
>PF12383 SARS_3b: Severe acute respiratory syndrome coronavirus 3b protein; InterPro: IPR022117 This family of proteins is found in viruses. Proteins in this family are typically between 32 and 154 amino acids in length. This family contains the SARS coronavirus 3b protein which is predominantly localized in the nucleolus, and induces G0/G1 arrest and apoptosis in transfected cells.
Probab=26.87 E-value=63 Score=23.98 Aligned_cols=35 Identities=23% Similarity=0.450 Sum_probs=29.4
Q ss_pred HHHHHHHHhhCCHHHHHHHHHhhcCCCchhHHHHH
Q 034402 14 HLIEKCLIFRMTKEECMEALSKHANIKPVITSTVW 48 (95)
Q Consensus 14 ~LIErCLqlyMsk~E~v~~L~~~a~I~P~fT~~VW 48 (95)
-||.+-+||-||+.....-|.+|-++....-+.-+
T Consensus 114 lliqqwiqfmmsrrrllaclckhkkvstnlcshsf 148 (153)
T PF12383_consen 114 LLIQQWIQFMMSRRRLLACLCKHKKVSTNLCSHSF 148 (153)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcccccccccchhhh
Confidence 36889999999999999999999998877655443
No 91
>PRK00117 recX recombination regulator RecX; Reviewed
Probab=26.73 E-value=2.2e+02 Score=19.73 Aligned_cols=47 Identities=17% Similarity=0.274 Sum_probs=36.7
Q ss_pred HHHHhhCCHHHHHHHHHhhcCCCchhHHHHHHHHHHh----cHHHHHHHHHh
Q 034402 18 KCLIFRMTKEECMEALSKHANIKPVITSTVWNELEKE----NKEFFEAYAQS 65 (95)
Q Consensus 18 rCLqlyMsk~E~v~~L~~~a~I~P~fT~~VW~~LE~e----N~eFFkaY~~~ 65 (95)
.|=..-.|..|+.+.|.+. |++|.+...|-..|.+. ...|-+.|.+.
T Consensus 20 ~L~~r~~s~~el~~kL~~k-g~~~~~i~~vl~~l~~~~~ldD~~~a~~~~~~ 70 (157)
T PRK00117 20 LLARREHSRAELRRKLAAK-GFSEEVIEAVLDRLKEEGLLDDERFAESFVRS 70 (157)
T ss_pred HHccchhHHHHHHHHHHhc-CCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHH
Confidence 3334456889999999886 99999999999999983 35777787443
No 92
>cd05062 PTKc_IGF-1R Catalytic domain of the Protein Tyrosine Kinase, Insulin-like Growth Factor-1 Receptor. Protein Tyrosine Kinase (PTK) family; Insulin-like Growth Factor-1 Receptor (IGF-1R); catalytic (c) domain. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. IGF-1R is a receptor tyr kinases (RTK) that is composed of two alphabeta heterodimers. Binding of the ligand (IGF-1 or IGF-2) to the extracellular alpha subunit activates the intracellular tyr kinase domain of the transmembrane beta subunit. Receptor activation leads to autophosphorylation, which stimulates downstream kinase activities and biological function. IGF-1R signaling is important in the differentiation, growth, and survival of normal cells. In cancer cells, wh
Probab=25.95 E-value=75 Score=22.63 Aligned_cols=25 Identities=16% Similarity=0.352 Sum_probs=18.0
Q ss_pred HHHHHHHHHHHHhh----CCHHHHHHHHH
Q 034402 10 HMVQHLIEKCLIFR----MTKEECMEALS 34 (95)
Q Consensus 10 ~~VQ~LIErCLqly----Msk~E~v~~L~ 34 (95)
..++++|.+||+.. .|-.|++..|.
T Consensus 248 ~~~~~li~~~l~~~p~~Rps~~e~l~~l~ 276 (277)
T cd05062 248 DMLFELMRMCWQYNPKMRPSFLEIISSIK 276 (277)
T ss_pred HHHHHHHHHHcCCChhhCcCHHHHHHHhh
Confidence 35788999999875 56666666553
No 93
>PRK04182 cytidylate kinase; Provisional
Probab=25.71 E-value=2.1e+02 Score=19.16 Aligned_cols=69 Identities=14% Similarity=0.087 Sum_probs=38.6
Q ss_pred hhCCHHHHHHHHHhhcCCCchhHHHHHHHHHHhcHHHHHHHHH----------hhhHHhhhhHHHHHHHHHHHHhhccc
Q 034402 22 FRMTKEECMEALSKHANIKPVITSTVWNELEKENKEFFEAYAQ----------SQSKEDRMSEEETNQMIQKMISTNSS 90 (95)
Q Consensus 22 lyMsk~E~v~~L~~~a~I~P~fT~~VW~~LE~eN~eFFkaY~~----------~~lk~qi~s~~~~~~~iq~~~~~~~~ 90 (95)
++.+.+.+++-+..+.+..+.-......+......++|+.|+. +.+=....+.+++.+.|.+++..-++
T Consensus 98 l~a~~e~~~~Rl~~r~~~~~~~a~~~~~~~d~~~~~~~~~~~~~~~~~~~~~d~~idt~~~~~~~~~~~I~~~~~~~~~ 176 (180)
T PRK04182 98 LKAPLEVRAERIAEREGISVEEALEETIEREESEAKRYKEYYGIDIDDLSIYDLVINTSRWDPEGVFDIILTAIDKLLK 176 (180)
T ss_pred EECCHHHHHHHHHhccCCCHHHHHHHHHHHHHHHHHHHHHHhCCCccccccccEEEECCCCCHHHHHHHHHHHHHHHhc
Confidence 4556777888887766654332223333344444556655532 11112233678888899888865443
No 94
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=25.10 E-value=99 Score=16.58 Aligned_cols=30 Identities=30% Similarity=0.403 Sum_probs=18.6
Q ss_pred hhCCHHHHHHHHHhhcCCCchhHHHHHHHHHHhc
Q 034402 22 FRMTKEECMEALSKHANIKPVITSTVWNELEKEN 55 (95)
Q Consensus 22 lyMsk~E~v~~L~~~a~I~P~fT~~VW~~LE~eN 55 (95)
+.++..|+.+.+ ++.+.-..-.-+.|++++
T Consensus 7 ~~~s~~~la~~l----~~s~~tv~~~l~~L~~~g 36 (48)
T smart00419 7 LPLTRQEIAELL----GLTRETVSRTLKRLEKEG 36 (48)
T ss_pred eccCHHHHHHHH----CCCHHHHHHHHHHHHHCC
Confidence 445666555554 777776666666666643
No 95
>COG4283 Uncharacterized conserved protein [Function unknown]
Probab=25.03 E-value=1.1e+02 Score=23.52 Aligned_cols=54 Identities=20% Similarity=0.323 Sum_probs=37.6
Q ss_pred hhcCCCchhHH--HHHHHHHHhcHHHHHHHHHhhhHHhhhhHHHHHHHHHHHHhhc
Q 034402 35 KHANIKPVITS--TVWNELEKENKEFFEAYAQSQSKEDRMSEEETNQMIQKMISTN 88 (95)
Q Consensus 35 ~~a~I~P~fT~--~VW~~LE~eN~eFFkaY~~~~lk~qi~s~~~~~~~iq~~~~~~ 88 (95)
+++|-+|..-+ .=|+.|-+=|..|.+.|-.+.|++...-..++-.-|=.||++-
T Consensus 67 e~~G~~~f~Ps~~ykWn~~geln~~F~kkyq~~SL~e~~~~L~k~h~~v~~lI~~~ 122 (170)
T COG4283 67 EKRGLKVFTPSPGYKWNNLGELNQWFWKKYQHLSLKELKAKLNKNHNDVYELIDEF 122 (170)
T ss_pred hhcCCcCCCCCCCCcccccHHHHHHHHHHhhhccHHHHHHHHHHHHHHHHHHHHHh
Confidence 35666644333 3699999999999999988888887665555555555555543
No 96
>PLN02350 phosphogluconate dehydrogenase (decarboxylating)
Probab=24.67 E-value=1.6e+02 Score=25.30 Aligned_cols=45 Identities=18% Similarity=0.242 Sum_probs=33.1
Q ss_pred CCCc-hHHHHHHHHHHHHHHHHhhCCHHHHHHHHHhhcCCCchhHHHH
Q 034402 1 MGES-SASYIHMVQHLIEKCLIFRMTKEECMEALSKHANIKPVITSTV 47 (95)
Q Consensus 1 ~~~~-s~~~I~~VQ~LIErCLqlyMsk~E~v~~L~~~a~I~P~fT~~V 47 (95)
+|+. +..++.+|+|.|+=+.-. --.|.+..+.+..|++|.--..|
T Consensus 178 vG~~GaG~~vKlv~N~i~~~~m~--~iaEA~~l~~~~~Gld~~~l~~v 223 (493)
T PLN02350 178 IGPGGAGNFVKMVHNGIEYGDMQ--LISEAYDVLKSVGGLSNEELAEV 223 (493)
T ss_pred eCCcCHHHHHHHHHHHHHHHHHH--HHHHHHHHHHhhCCCCHHHHHHH
Confidence 4653 789999999999965543 24677777766569999877766
No 97
>KOG1199 consensus Short-chain alcohol dehydrogenase/3-hydroxyacyl-CoA dehydrogenase [Secondary metabolites biosynthesis, transport and catabolism]
Probab=24.54 E-value=56 Score=26.26 Aligned_cols=17 Identities=41% Similarity=0.706 Sum_probs=14.1
Q ss_pred CCchHHHHHHHHHHHHHH
Q 034402 2 GESSASYIHMVQHLIEKC 19 (95)
Q Consensus 2 ~~~s~~~I~~VQ~LIErC 19 (95)
|++ ++|-++||+.||.-
T Consensus 227 g~p-~eyahlvqaiienp 243 (260)
T KOG1199|consen 227 GHP-HEYAHLVQAIIENP 243 (260)
T ss_pred CCh-HHHHHHHHHHHhCc
Confidence 454 89999999999963
No 98
>PF10045 DUF2280: Uncharacterized conserved protein (DUF2280); InterPro: IPR018738 This entry is represented by Burkholderia phage Bups phi1, Orf2.36. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=24.48 E-value=2.7e+02 Score=19.87 Aligned_cols=54 Identities=24% Similarity=0.205 Sum_probs=44.3
Q ss_pred HHHHHHHHHHHhhCCHHHHHHHHHhhcCCCc--------hhHHHHHHHHHHhcHHHHHHHHH
Q 034402 11 MVQHLIEKCLIFRMTKEECMEALSKHANIKP--------VITSTVWNELEKENKEFFEAYAQ 64 (95)
Q Consensus 11 ~VQ~LIErCLqlyMsk~E~v~~L~~~a~I~P--------~fT~~VW~~LE~eN~eFFkaY~~ 64 (95)
-|+--|=+-|--|.|..||+++..+.+||+- .=|...=+.|-++-.+.|+..-+
T Consensus 7 ~vK~FIVQ~LAcfdTPs~v~~aVk~eFgi~vsrQqve~yDPTK~aG~~Ls~k~~~lF~~TR~ 68 (104)
T PF10045_consen 7 EVKAFIVQSLACFDTPSEVAEAVKEEFGIDVSRQQVESYDPTKRAGRDLSKKWVDLFEETRK 68 (104)
T ss_pred HHHHHHHHHHHhhCCHHHHHHHHHHHhCCccCHHHHHHcCchHHHHHHHHHHHHHHHHHHHH
Confidence 4667777888899999999999999998863 34677778888899999988733
No 99
>PF14123 DUF4290: Domain of unknown function (DUF4290)
Probab=24.46 E-value=1.7e+02 Score=22.47 Aligned_cols=46 Identities=22% Similarity=0.408 Sum_probs=34.7
Q ss_pred HHHHHHHHHHHHHHHHhhCCHHH----------HHHHHHhhcCCCchhHHHHHHHHH
Q 034402 6 ASYIHMVQHLIEKCLIFRMTKEE----------CMEALSKHANIKPVITSTVWNELE 52 (95)
Q Consensus 6 ~~~I~~VQ~LIErCLqlyMsk~E----------~v~~L~~~a~I~P~fT~~VW~~LE 52 (95)
.+|=+.||++|+-|+.+ =+++| +|..|.=|..=.|.|..-+|..|-
T Consensus 13 pEYGR~IQ~MVd~~~ti-eDreeR~~~A~~II~iM~~l~P~lRd~~Df~hKLWDhL~ 68 (176)
T PF14123_consen 13 PEYGRNIQKMVDYAVTI-EDREERNRCAETIIEIMGNLNPHLRDVPDFKHKLWDHLF 68 (176)
T ss_pred chhhHHHHHHHHHHHhC-CCHHHHHHHHHHHHHHHHhcCCccCCChhHHHHHHHHHH
Confidence 46778999999999987 24443 455555566777889999999884
No 100
>PF05066 HARE-HTH: HB1, ASXL, restriction endonuclease HTH domain; InterPro: IPR007759 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. The delta protein is a dispensable subunit of Bacillus subtilis RNA polymerase (RNAP) that has major effects on the biochemical properties of the purified enzyme. In the presence of delta, RNAP displays an increased specificity of transcription, a decreased affinity for nucleic acids, and an increased efficiency of RNA synthesis because of enhanced recycling []. The delta protein, contains two distinct regions, an N-terminal domain and a glutamate and aspartate residue-rich C-terminal region [].; GO: 0003677 DNA binding, 0006351 transcription, DNA-dependent; PDB: 2KRC_A.
Probab=24.41 E-value=1.3e+02 Score=18.36 Aligned_cols=30 Identities=23% Similarity=0.518 Sum_probs=20.5
Q ss_pred CCHHHHHHHHHhhcCCCchhHHHHHHHHHHh
Q 034402 24 MTKEECMEALSKHANIKPVITSTVWNELEKE 54 (95)
Q Consensus 24 Msk~E~v~~L~~~a~I~P~fT~~VW~~LE~e 54 (95)
||--|.+..+.+++| .|.=..-+|++..+.
T Consensus 1 mt~~eaa~~vL~~~~-~pm~~~eI~~~i~~~ 30 (72)
T PF05066_consen 1 MTFKEAAYEVLEEAG-RPMTFKEIWEEIQER 30 (72)
T ss_dssp S-HHHHHHHHHHHH--S-EEHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHhcC-CCcCHHHHHHHHHHh
Confidence 666677777777778 888888888887763
No 101
>PTZ00398 phosphoenolpyruvate carboxylase; Provisional
Probab=24.34 E-value=77 Score=29.77 Aligned_cols=33 Identities=30% Similarity=0.365 Sum_probs=29.0
Q ss_pred HHHHHHHHHHhhCCHHHHHHHHHhhcCCCchhHH
Q 034402 12 VQHLIEKCLIFRMTKEECMEALSKHANIKPVITS 45 (95)
Q Consensus 12 VQ~LIErCLqlyMsk~E~v~~L~~~a~I~P~fT~ 45 (95)
+.+.+.++.+..++.+++.++|.+ ..|.|+||.
T Consensus 155 l~~~l~~L~~~g~~~e~i~~~L~~-~~i~pVlTA 187 (974)
T PTZ00398 155 LKNTIEMLLQAGFDKEEIYKQLCN-QEIDLVLTA 187 (974)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHhc-Cceeeeecc
Confidence 567889999999999999999955 799999995
No 102
>PF11349 DUF3151: Protein of unknown function (DUF3151); InterPro: IPR014487 This group represents an uncharacterised conserved protein.
Probab=24.27 E-value=1.3e+02 Score=22.29 Aligned_cols=38 Identities=13% Similarity=0.287 Sum_probs=30.1
Q ss_pred hcHHHHHHHHHhhhHHhhhhHHHHHHHHHHHHhhcccc
Q 034402 54 ENKEFFEAYAQSQSKEDRMSEEETNQMIQKMISTNSSK 91 (95)
Q Consensus 54 eN~eFFkaY~~~~lk~qi~s~~~~~~~iq~~~~~~~~~ 91 (95)
-|..|+++-.-+-.-.+.|-|.+--++..++|++++..
T Consensus 87 PNrGfLRal~aLa~AA~~IGE~dE~~Rc~~~L~Dsdp~ 124 (129)
T PF11349_consen 87 PNRGFLRALAALARAAQAIGETDEYDRCRQFLRDSDPE 124 (129)
T ss_pred CccHHHHHHHHHHHHHHHhCChhHHHHHHHHHHhCCHH
Confidence 59999999977666677776777778889999988743
No 103
>PF00735 Septin: Septin; InterPro: IPR000038 Septins constitute a eukaryotic family of guanine nucleotide-binding proteins, most of which polymerise to form filaments []. Members of the family were first identified by genetic screening for Saccharomyces cerevisiae (Baker's yeast) mutants defective in cytokinesis []. Temperature-sensitive mutations in four genes, CDC3, CDC10, CDC11 and CDC12, were found to cause cell-cycle arrest and defects in bud growth and cytokinesis. The protein products of these genes localise at the division plane between mother and daughter cells, indicating a role in mother-daughter separation during cytokinesis []. Members of the family were therefore termed septins to reflect their role in septation and cell division. The identification of septin homologues in higher eukaryotes, which localise to the cleavage furrow in dividing cells, supports an orthologous function in cytokinesis. Septins have since been identified in most eukaryotes, except plants []. Septins are approximately 40-50 kDa in molecular mass, and typically comprise a conserved central core domain (more than 35% sequence identity between mammalian and yeast homologues) flanked by more divergent N- and C-termini. Most septins possess a P-loop motif in their N-terminal domain (which is characteristic of GTP-binding proteins), and a predicted C-terminal coiled-coil domain []. A number of septin interaction partners have been identified in yeast, many of which are components of the budding site selection machinery, kinase cascades or of the ubiquitination pathway. It has been proposed that septins may act as a scaffold that provides an interaction matrix for other proteins [, ]. In mammals, septins have been shown to regulate vesicle dynamics []. Mammalian septins have also been implicated in a variety of other cellular processes, including apoptosis, carcinogenesis and neurodegeneration []. This entry represents a variety of septins and homologous sequences involved in the cell division process.; GO: 0005525 GTP binding, 0007049 cell cycle; PDB: 2QAG_B 3FTQ_D 2QA5_A 2QNR_B 3TW4_A 3T5D_C.
Probab=24.00 E-value=68 Score=25.15 Aligned_cols=54 Identities=30% Similarity=0.440 Sum_probs=38.1
Q ss_pred HHHHHHHHHHHHHHHhhCCHH--------------------------------HHHHHHHhhcCCCchhHH---------
Q 034402 7 SYIHMVQHLIEKCLIFRMTKE--------------------------------ECMEALSKHANIKPVITS--------- 45 (95)
Q Consensus 7 ~~I~~VQ~LIErCLqlyMsk~--------------------------------E~v~~L~~~a~I~P~fT~--------- 45 (95)
.....|.+-|+..+..||..+ ++|+.|++..||=|++..
T Consensus 81 ~~~~~I~~yI~~qf~~~l~eE~~~~R~~~~D~RVH~cLYfI~pt~~~L~~~Di~~mk~Ls~~vNvIPvIaKaD~lt~~el 160 (281)
T PF00735_consen 81 DCWEPIVDYIESQFDSYLEEESKINRPRIEDTRVHACLYFIPPTGHGLKPLDIEFMKRLSKRVNVIPVIAKADTLTPEEL 160 (281)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHTSSS-TTS----EEEEEEEE-TTSSSS-HHHHHHHHHHTTTSEEEEEESTGGGS-HHHH
T ss_pred hhhHHHHHHHHHHHHHHHHHhhcccccCcCCCCcceEEEEEcCCCccchHHHHHHHHHhcccccEEeEEecccccCHHHH
Confidence 344566677777777776655 788999999999998754
Q ss_pred -----HHHHHHHHhcHHHHH
Q 034402 46 -----TVWNELEKENKEFFE 60 (95)
Q Consensus 46 -----~VW~~LE~eN~eFFk 60 (95)
.|.+.|++.|-.+|.
T Consensus 161 ~~~k~~i~~~l~~~~I~~f~ 180 (281)
T PF00735_consen 161 QAFKQRIREDLEENNIKIFD 180 (281)
T ss_dssp HHHHHHHHHHHHHTT--S--
T ss_pred HHHHHHHHHHHHHcCceeec
Confidence 688889888888887
No 104
>KOG0451 consensus Predicted 2-oxoglutarate dehydrogenase, E1 subunit [Carbohydrate transport and metabolism]
Probab=23.99 E-value=87 Score=29.12 Aligned_cols=47 Identities=26% Similarity=0.364 Sum_probs=40.8
Q ss_pred CchhHHHHHHHHHHhcHHHHHHHHHhhhHHhhhhHHHHHHHHHHHHh
Q 034402 40 KPVITSTVWNELEKENKEFFEAYAQSQSKEDRMSEEETNQMIQKMIS 86 (95)
Q Consensus 40 ~P~fT~~VW~~LE~eN~eFFkaY~~~~lk~qi~s~~~~~~~iq~~~~ 86 (95)
+|-||+.|-.+.-+.-..-=+.|.+...+++..++++..+|-+++..
T Consensus 435 dp~ftspvmyk~v~aReSvPdlya~~L~~eg~~tee~vkE~~~~y~~ 481 (913)
T KOG0451|consen 435 DPTFTSPVMYKEVEARESVPDLYAQQLAKEGVLTEEKVKEMRDEYMK 481 (913)
T ss_pred CccccChhHHHHHHhhhcccHHHHHHHHhcccccHHHHHHHHHHHHH
Confidence 79999999888888777777889888899999999999999997653
No 105
>TIGR03697 NtcA_cyano global nitrogen regulator NtcA, cyanobacterial. Members of this protein family, found in the cyanobacteria, are the global nitrogen regulator NtcA. This DNA-binding transcriptional regulator is required for expressing many different ammonia-repressible genes. The consensus NtcA-binding site is G T A N(8)T A C.
Probab=23.53 E-value=1e+02 Score=21.04 Aligned_cols=30 Identities=20% Similarity=0.395 Sum_probs=24.4
Q ss_pred hhCCHHHHHHHHHhhcCCCchhHHHHHHHHHHhc
Q 034402 22 FRMTKEECMEALSKHANIKPVITSTVWNELEKEN 55 (95)
Q Consensus 22 lyMsk~E~v~~L~~~a~I~P~fT~~VW~~LE~eN 55 (95)
+.+|++|+...| |+.|.-.+-+.++|++++
T Consensus 142 ~~~t~~~iA~~l----G~tretvsR~l~~l~~~g 171 (193)
T TIGR03697 142 LRLSHQAIAEAI----GSTRVTITRLLGDLRKKK 171 (193)
T ss_pred CCCCHHHHHHHh----CCcHHHHHHHHHHHHHCC
Confidence 457888777776 899999999999998864
No 106
>cd04787 HTH_HMRTR_unk Helix-Turn-Helix DNA binding domain of putative Heavy Metal Resistance transcription regulators. Putative helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR), unknown subgroup. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules, such as, metal ions, drugs, and organic substrates. This subgroup lacks one of the c
Probab=23.45 E-value=2.5e+02 Score=19.26 Aligned_cols=71 Identities=13% Similarity=0.106 Sum_probs=41.8
Q ss_pred hHHHHHHHHHHHHHHHHhhCCHHHHHHHHHhhcCCCchhHHHHHHHHHHhcHHHHHHHHHhhhHHhhhhHHHHHHHHHHH
Q 034402 5 SASYIHMVQHLIEKCLIFRMTKEECMEALSKHANIKPVITSTVWNELEKENKEFFEAYAQSQSKEDRMSEEETNQMIQKM 84 (95)
Q Consensus 5 s~~~I~~VQ~LIErCLqlyMsk~E~v~~L~~~a~I~P~fT~~VW~~LE~eN~eFFkaY~~~~lk~qi~s~~~~~~~iq~~ 84 (95)
+.+++..+ .+|-++-.+.||.+|+-..|... .-.+.-...+..-|+++ ...+.+||....+..+.++..
T Consensus 40 ~~~~~~~l-~~I~~lr~~G~sL~eI~~~l~~~-~~~~~~~~~~~~~l~~~---------~~~l~~~i~~l~~~~~~l~~~ 108 (133)
T cd04787 40 SEKDLSRL-RFILSARQLGFSLKDIKEILSHA-DQGESPCPMVRRLIEQR---------LAETERRIKELLKLRDRMQQA 108 (133)
T ss_pred CHHHHHHH-HHHHHHHHcCCCHHHHHHHHhhh-ccCCCcHHHHHHHHHHH---------HHHHHHHHHHHHHHHHHHHHH
Confidence 45666666 57888899999999999888643 22221122233333222 133456666666666666665
Q ss_pred Hh
Q 034402 85 IS 86 (95)
Q Consensus 85 ~~ 86 (95)
++
T Consensus 109 ~~ 110 (133)
T cd04787 109 VS 110 (133)
T ss_pred HH
Confidence 54
No 107
>cd07765 KRAB_A-box KRAB (Kruppel-associated box) domain -A box. The KRAB domain is a transcription repression module, found in a subgroup of the zinc finger proteins (ZFPs) of the C2H2 family, KRAB-ZFPs. KRAB-ZFPs comprise the largest group of transcriptional regulators in mammals, and are only found in tetrapods. These proteins have been shown to play important roles in cell differentiation and organ development, and in regulating viral replication and transcription. A KRAB domain may consist of an A-box, or of an A-box plus either a B-box, a divergent B-box (b), or a C-box. Only the A-box is included in this model. The A-box is needed for repression, the B- and C- boxes are not. KRAB-ZFPs have one or two KRAB domains at their amino-terminal end, and multiple C2H2 zinc finger motifs at their C-termini. Some KRAB-ZFPs also contain a SCAN domain which mediates homo- and hetero-oligomerization. The KRAB domain is a protein-protein interaction module which represses transcription through
Probab=23.41 E-value=35 Score=14.65 Aligned_cols=25 Identities=8% Similarity=0.445 Sum_probs=17.2
Q ss_pred CCCchhHHHHHHHHHHhcHHHHHHH
Q 034402 38 NIKPVITSTVWNELEKENKEFFEAY 62 (95)
Q Consensus 38 ~I~P~fT~~VW~~LE~eN~eFFkaY 62 (95)
++...++..-|..++....++|+.-
T Consensus 5 ~~~~~~~~~~~~~~~~~~~~~~~~~ 29 (40)
T cd07765 5 DVAVYFSQEEWELLDPAQRDLYRDV 29 (40)
T ss_pred eeeeecCHHHHhcCCHHHHHHHHHH
Confidence 3445667778888887777777643
No 108
>PF14039 YusW: YusW-like protein
Probab=23.38 E-value=73 Score=21.60 Aligned_cols=37 Identities=16% Similarity=0.256 Sum_probs=27.5
Q ss_pred HHHHHHHHHHH-HHHhhCCHHHHHHHHHhhcCCCchhH
Q 034402 8 YIHMVQHLIEK-CLIFRMTKEECMEALSKHANIKPVIT 44 (95)
Q Consensus 8 ~I~~VQ~LIEr-CLqlyMsk~E~v~~L~~~a~I~P~fT 44 (95)
-++.++.++.+ -|.-.|+.++||..+-+.+|++|.+.
T Consensus 45 A~~~l~~~l~~L~~~~~t~~~evi~~Vl~~f~Ld~dy~ 82 (92)
T PF14039_consen 45 AFDELEPLLSELSFDSDTSEEEVIDQVLKAFNLDPDYQ 82 (92)
T ss_pred HHHHHHHHHHhCCCCCCCChHHHHHHHHHHhCCCccce
Confidence 34455555543 35668999999999999999998653
No 109
>cd05094 PTKc_TrkC Catalytic domain of the Protein Tyrosine Kinase, Tropomyosin Related Kinase C. Protein Tyrosine Kinase (PTK) family; Tropomyosin Related Kinase C (TrkC); catalytic (c) domain. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. TrkC is a member of the Trk subfamily of proteins, which are receptor tyr kinases (RTKs) containing an extracellular region with arrays of leucine-rich motifs flanked by two cysteine-rich clusters followed by two immunoglobulin-like domains, a transmembrane segment, and an intracellular catalytic domain. Binding of TrkC to its ligand, neurotrophin 3 (NT3), results in receptor oligomerization and activation of the catalytic domain. TrkC is broadly expressed in the nervous system and in some n
Probab=23.24 E-value=1e+02 Score=22.23 Aligned_cols=29 Identities=17% Similarity=0.236 Sum_probs=21.7
Q ss_pred HHHHHHHHHHHHh----hCCHHHHHHHHHhhcC
Q 034402 10 HMVQHLIEKCLIF----RMTKEECMEALSKHAN 38 (95)
Q Consensus 10 ~~VQ~LIErCLql----yMsk~E~v~~L~~~a~ 38 (95)
..++++|.+||+. ..|-+|+++.|.+-.+
T Consensus 252 ~~~~~li~~~l~~~P~~Rpt~~~v~~~l~~~~~ 284 (291)
T cd05094 252 KEVYDIMLGCWQREPQQRLNIKEIYKILHALGK 284 (291)
T ss_pred HHHHHHHHHHcccChhhCcCHHHHHHHHHHHHh
Confidence 4588999999985 4667888888866433
No 110
>PRK09852 cryptic 6-phospho-beta-glucosidase; Provisional
Probab=23.21 E-value=1.8e+02 Score=24.81 Aligned_cols=48 Identities=25% Similarity=0.497 Sum_probs=31.6
Q ss_pred hHHHHHHHHHHHHHHHHhhCCHHHHHHHHHhhcCCCchhHHHHHH---HHH--------HhcHHHHHHHHHhhh
Q 034402 5 SASYIHMVQHLIEKCLIFRMTKEECMEALSKHANIKPVITSTVWN---ELE--------KENKEFFEAYAQSQS 67 (95)
Q Consensus 5 s~~~I~~VQ~LIErCLqlyMsk~E~v~~L~~~a~I~P~fT~~VW~---~LE--------~eN~eFFkaY~~~~l 67 (95)
..+-++....+|+.|+.. ||+|.+|..=|. -|+ ++..+.|..|.+...
T Consensus 107 n~~~~~~Y~~~i~~l~~~---------------gi~p~VtL~H~~~P~~l~~~~GGW~~~~~~~~F~~ya~~~~ 165 (474)
T PRK09852 107 NQQGIAFYRSVFEECKKY---------------GIEPLVTLCHFDVPMHLVTEYGSWRNRKMVEFFSRYARTCF 165 (474)
T ss_pred CHHHHHHHHHHHHHHHHc---------------CCEEEEEeeCCCCCHHHHHhcCCCCCHHHHHHHHHHHHHHH
Confidence 456677777778777654 999987765441 143 355677888855433
No 111
>PF07531 TAFH: NHR1 homology to TAF; InterPro: IPR003894 The TAF homology (TAFH) or Nervy homology region 1 (NHR1) domain is a domain of 95-100 amino acids present in eukaryotic proteins of the MTG/ETO family and whereof the core ~75-80 residues occur in TAF proteins. The transcription initiation TFIID complex is composed of TATA binding protein (TBP) and a number of TBP-associated factors (TAFs). The TAFH/NHR1 domain is named after fruit fly TATA-box-associated factor 110 (TAF110), human TAF105 and TAF130, and the fruit fly protein Nervy, which is a homologue of human MTG8/ETO [, ]. The human eight twenty-one (ETO or MTG8) and related myeloid transforming gene products MTGR1 and MTG16 as well as the Nervy protein contain the NHR1-4 domains. The NHR1/TAFH domain occurs in the N-terminal part of these proteins, while a MYND-type zinc finger forms the NHR4 domain []. The TAFH/NHR1 domain can be involved in protein-protein interactions, e.g in MTG8/ETO with HSP90 and Gfi-1 []. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2P6V_A 2KNH_A 2PP4_A 2H7B_A.
Probab=23.15 E-value=1.5e+02 Score=20.63 Aligned_cols=37 Identities=22% Similarity=0.237 Sum_probs=30.1
Q ss_pred hHHHHHHHHHHHHHHHHhhCCHHHHHHHHHhhcCCCc
Q 034402 5 SASYIHMVQHLIEKCLIFRMTKEECMEALSKHANIKP 41 (95)
Q Consensus 5 s~~~I~~VQ~LIErCLqlyMsk~E~v~~L~~~a~I~P 41 (95)
|.+....|+.||..++..-++-||--..|++..|-.|
T Consensus 22 spev~~~Vr~LV~~L~~~~i~~EeF~~~Lq~~lns~p 58 (96)
T PF07531_consen 22 SPEVGENVRELVQNLVDGKIEAEEFTSKLQEELNSSP 58 (96)
T ss_dssp -CCHHHHHHHHHHHHHTTSS-HHHHHHHHHHHCTSS-
T ss_pred ChHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHhcCCC
Confidence 5677889999999999999999999999998666555
No 112
>TIGR02915 PEP_resp_reg putative PEP-CTERM system response regulator. Members of this protein family share full-length homology with (but do not include) the acetoacetate metabolism regulatory protein AtoC. These proteins have a Fis family DNA binding sequence (pfam02954), a response regulator receiver domain (pfam00072), and sigma-54 interaction domain (pfam00158).
Probab=23.11 E-value=1.9e+02 Score=22.94 Aligned_cols=37 Identities=16% Similarity=0.209 Sum_probs=29.7
Q ss_pred HHHHHHHHHHHhh-CCHHHHHHHHHhhcCCCchhHHHHHHHHHHh
Q 034402 11 MVQHLIEKCLIFR-MTKEECMEALSKHANIKPVITSTVWNELEKE 54 (95)
Q Consensus 11 ~VQ~LIErCLqly-Msk~E~v~~L~~~a~I~P~fT~~VW~~LE~e 54 (95)
.-+.+|++.|..+ .|+.++.+.| ||.+ .++|++|++-
T Consensus 405 ~E~~~i~~al~~~~gn~~~aA~~L----gisr---~tl~rkl~~~ 442 (445)
T TIGR02915 405 AEREAVRKAIARVDGNIARAAELL----GITR---PTLYDLMKKH 442 (445)
T ss_pred HHHHHHHHHHHHhCCCHHHHHHHh----CCCH---HHHHHHHHHh
Confidence 3467899999887 7998888777 8887 4899999863
No 113
>TIGR02173 cyt_kin_arch cytidylate kinase, putative. Proteins in this family are believed to be cytidylate kinase. Members of this family are found in the archaea and in spirochaetes, and differ considerably from the common bacterial form of cytidylate kinase described by TIGR00017.
Probab=22.64 E-value=2.4e+02 Score=18.76 Aligned_cols=41 Identities=12% Similarity=0.058 Sum_probs=29.7
Q ss_pred CHHHHHHHHHhhcCCCchhHHHHHHHHHHhcHHHHHHHHHh
Q 034402 25 TKEECMEALSKHANIKPVITSTVWNELEKENKEFFEAYAQS 65 (95)
Q Consensus 25 sk~E~v~~L~~~a~I~P~fT~~VW~~LE~eN~eFFkaY~~~ 65 (95)
+.+.+++-+.++.++++.-...-|..-.+....||+.|+..
T Consensus 101 ~~~~r~~R~~~R~~~s~~~a~~~~~~~d~~~~~~~~~~~~~ 141 (171)
T TIGR02173 101 PLEVRARRIAKREGKSLTVARSETIEREESEKRRYLKFYGI 141 (171)
T ss_pred CHHHHHHHHHHccCCCHHHHHHHHHHHHHHHHHHHHHHhCC
Confidence 55667777777777877777666777777778888877554
No 114
>PRK00009 phosphoenolpyruvate carboxylase; Reviewed
Probab=22.63 E-value=89 Score=29.15 Aligned_cols=33 Identities=24% Similarity=0.387 Sum_probs=28.4
Q ss_pred HHHHHHHHHHhhCCHHHHHHHHHhhcCCCchhHH
Q 034402 12 VQHLIEKCLIFRMTKEECMEALSKHANIKPVITS 45 (95)
Q Consensus 12 VQ~LIErCLqlyMsk~E~v~~L~~~a~I~P~fT~ 45 (95)
+.+.+.++.+..++++++.+.|.+ ..|.|+||.
T Consensus 109 l~~~~~~l~~~g~~~e~i~~~L~~-~~i~pVlTA 141 (911)
T PRK00009 109 LAETLRRLKAAGVSPEELARALEE-LDIEPVLTA 141 (911)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHhh-Ccceeeeec
Confidence 567788888888999999999955 699999995
No 115
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=22.61 E-value=1e+02 Score=22.44 Aligned_cols=25 Identities=16% Similarity=0.317 Sum_probs=20.6
Q ss_pred HHHHHhhcCCCchhHHHHHHHHHHh
Q 034402 30 MEALSKHANIKPVITSTVWNELEKE 54 (95)
Q Consensus 30 v~~L~~~a~I~P~fT~~VW~~LE~e 54 (95)
++.|++..+|.|.+..-|++.|.+.
T Consensus 28 ~~eIA~~~~ip~~~l~kIl~~L~~a 52 (164)
T PRK10857 28 LADISERQGISLSYLEQLFSRLRKN 52 (164)
T ss_pred HHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 3455666799999999999999984
No 116
>PF11626 Rap1_C: TRF2-interacting telomeric protein/Rap1 - C terminal domain; InterPro: IPR021661 This family of proteins represents the C-terminal domain of the protein Rap-1, which plays a distinct role in silencing at the silent mating-type loci and telomeres []. The Rap-1 C terminus adopts an all-helical fold. Rap1 carries out its function by recruiting the Sir3 and Sir4 proteins to chromatin via its C-terminal domain []. ; PDB: 3K6G_C 3CZ6_A 3OWT_A.
Probab=22.48 E-value=1.1e+02 Score=19.96 Aligned_cols=38 Identities=18% Similarity=0.099 Sum_probs=25.1
Q ss_pred HHHHHHhhCCHHHHHHHHHhhcCCCchhHHHHHHHHHH
Q 034402 16 IEKCLIFRMTKEECMEALSKHANIKPVITSTVWNELEK 53 (95)
Q Consensus 16 IErCLqlyMsk~E~v~~L~~~a~I~P~fT~~VW~~LE~ 53 (95)
|.+|..+..++..|+.+|....+-.+.+...|-+.|..
T Consensus 1 i~~~~~~g~~~~~v~~aL~~tSgd~~~a~~~vl~~l~~ 38 (87)
T PF11626_consen 1 IKHYEELGYSREFVTHALYATSGDPELARRFVLNFLQA 38 (87)
T ss_dssp -HHHHHHTB-HHHHHHHHHHTTTBHHHHHHHHHHCHCH
T ss_pred CchHHHhCCCHHHHHHHHHHhCCCHHHHHHHHHHHHHc
Confidence 67788889999999999987655444444446666554
No 117
>COG1438 ArgR Arginine repressor [Transcription]
Probab=22.15 E-value=1.1e+02 Score=22.79 Aligned_cols=30 Identities=33% Similarity=0.378 Sum_probs=24.5
Q ss_pred hhCCHHHHHHHHHhhcCCCchhHHHHHHHHHH
Q 034402 22 FRMTKEECMEALSKHANIKPVITSTVWNELEK 53 (95)
Q Consensus 22 lyMsk~E~v~~L~~~a~I~P~fT~~VW~~LE~ 53 (95)
..-|++|+++.|+++ ||+ .--.+|-+-|.+
T Consensus 19 ~i~TQ~Elv~~L~~~-Gi~-vTQaTvSRDlke 48 (150)
T COG1438 19 KISTQEELVELLQEE-GIE-VTQATVSRDLKE 48 (150)
T ss_pred CCCCHHHHHHHHHHc-CCe-EehHHHHHHHHH
Confidence 467999999999886 999 666678877776
No 118
>PF13625 Helicase_C_3: Helicase conserved C-terminal domain
Probab=22.01 E-value=1.2e+02 Score=20.60 Aligned_cols=48 Identities=15% Similarity=0.246 Sum_probs=31.5
Q ss_pred HHHHHHHHhhCCHHHHHHHHHhhcC--CCchhHHHHHHHHHHhcHHHHHHHHHhhhHH
Q 034402 14 HLIEKCLIFRMTKEECMEALSKHAN--IKPVITSTVWNELEKENKEFFEAYAQSQSKE 69 (95)
Q Consensus 14 ~LIErCLqlyMsk~E~v~~L~~~a~--I~P~fT~~VW~~LE~eN~eFFkaY~~~~lk~ 69 (95)
.-+-+++...|+.+++++.|.++++ |.+.+. ..|+ +..+.|-+..+.+
T Consensus 45 ~Sl~~A~~~G~~~e~i~~~L~~~S~~~lP~~v~----~~i~----~w~~~~g~v~l~~ 94 (129)
T PF13625_consen 45 ASLWRAASAGLTAEEIIEFLERYSKNPLPQNVE----QSIE----DWARRYGRVRLYK 94 (129)
T ss_pred HHHHHHHHcCCCHHHHHHHHHHHcCCCCCHHHH----HHHH----HHHHhcCCEEEec
Confidence 4567899999999999999999763 443333 3333 3445565544433
No 119
>COG1498 SIK1 Protein implicated in ribosomal biogenesis, Nop56p homolog [Translation, ribosomal structure and biogenesis]
Probab=21.86 E-value=1.6e+02 Score=25.32 Aligned_cols=51 Identities=27% Similarity=0.292 Sum_probs=43.5
Q ss_pred CCCc-hHHHHHHHHHHHHHHHHhhCCHHHHHHHHHhhc-CCCchhHHHHHHHH
Q 034402 1 MGES-SASYIHMVQHLIEKCLIFRMTKEECMEALSKHA-NIKPVITSTVWNEL 51 (95)
Q Consensus 1 ~~~~-s~~~I~~VQ~LIErCLqlyMsk~E~v~~L~~~a-~I~P~fT~~VW~~L 51 (95)
||.. +..||+.|+.+.|.-..+|==++++-+++.... .|-|.+|.+|=-.|
T Consensus 200 mG~~~~~~Di~~i~~~ae~i~~L~~~R~~l~~Yi~~~M~~vAPNlt~LVG~~l 252 (395)
T COG1498 200 MGADLSEEDIDNIRELAEIILELYELREQLEEYIESKMSEIAPNLTALVGPVL 252 (395)
T ss_pred cccCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCccHHHHHhHHH
Confidence 5653 789999999999999999999999999998854 58999999885544
No 120
>PRK14135 recX recombination regulator RecX; Provisional
Probab=21.81 E-value=2e+02 Score=21.67 Aligned_cols=47 Identities=11% Similarity=0.073 Sum_probs=37.3
Q ss_pred HHHHHHHHHHHHHHHh-hCCHHHHHHHHHhhcCCCchhHHHHHHHHHHh
Q 034402 7 SYIHMVQHLIEKCLIF-RMTKEECMEALSKHANIKPVITSTVWNELEKE 54 (95)
Q Consensus 7 ~~I~~VQ~LIErCLql-yMsk~E~v~~L~~~a~I~P~fT~~VW~~LE~e 54 (95)
+|.+.+...+...+.. ..++.++...|..+ ||++.+...|...+.++
T Consensus 105 dD~~~a~~~~~~~~~~~~~g~~~I~~kL~~k-Gi~~~~Ie~~l~~l~~~ 152 (263)
T PRK14135 105 DDKEYAESYVRTNINTGDKGPRVIKQKLLQK-GIEDEIIEEALSEYTEE 152 (263)
T ss_pred CHHHHHHHHHHHHHhccccchHHHHHHHHHc-CCCHHHHHHHHHhCChh
Confidence 4567778888877764 46888999999765 99999999999988543
No 121
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=21.74 E-value=1.4e+02 Score=21.84 Aligned_cols=31 Identities=13% Similarity=0.258 Sum_probs=25.5
Q ss_pred HhhCCHHHHHHHHHhhcCCCchhHHHHHHHHHHhc
Q 034402 21 IFRMTKEECMEALSKHANIKPVITSTVWNELEKEN 55 (95)
Q Consensus 21 qlyMsk~E~v~~L~~~a~I~P~fT~~VW~~LE~eN 55 (95)
.+.+|++++...| |+.|.-.+-+.++|++++
T Consensus 177 ~i~lt~~~IA~~l----GisretlsR~L~~L~~~G 207 (230)
T PRK09391 177 ALPMSRRDIADYL----GLTIETVSRALSQLQDRG 207 (230)
T ss_pred EecCCHHHHHHHH----CCCHHHHHHHHHHHHHCC
Confidence 4567777777776 999999999999999876
No 122
>PF02847 MA3: MA3 domain; InterPro: IPR003891 This entry represents the MI domain (after MA-3 and eIF4G), it is a protein-protein interaction module of ~130 amino acids [, , ]. It appears in several translation factors and is found in: One copy in plant and animal eIF4G 1 and 2 (DAP-5/NAT1/p97) Two copies in the animal programmed cell death protein 4 (PDCD4) or MA-3 that is induced during programmed cell death and inhibits neoplastic transformation Four tandem-repeated copies in a group of uncharacterised plant proteins The MI domain consists of seven alpha-helices, which pack into a globular form. The packing arrangement consists of repeating pairs of antiparallel helices packed one upon the other such that a superhelical axis is generated perpendicular to the alpha-helical axes []. The MI domain has also been named MA3 domain.; PDB: 2ION_A 2IOL_B 2NSZ_A 3EIQ_C 2HM8_A 2KZT_B 2IOS_A 2RG8_B 2ZU6_E 3EIJ_A ....
Probab=21.45 E-value=2.3e+02 Score=18.09 Aligned_cols=73 Identities=16% Similarity=0.240 Sum_probs=47.2
Q ss_pred HHHHHHHHHhhC---CHHHHHHHHHhhcCCC---chhHHHHHHHHHHhcHHHHHHH---HHhhhHHhhhhHHHHHHHHHH
Q 034402 13 QHLIEKCLIFRM---TKEECMEALSKHANIK---PVITSTVWNELEKENKEFFEAY---AQSQSKEDRMSEEETNQMIQK 83 (95)
Q Consensus 13 Q~LIErCLqlyM---sk~E~v~~L~~~a~I~---P~fT~~VW~~LE~eN~eFFkaY---~~~~lk~qi~s~~~~~~~iq~ 83 (95)
+..|..+|.-|+ +.+|.+..|.+ .++. |.|...+-...-++++.+=+.| .....+....+.+....-+++
T Consensus 2 rk~i~~~l~ey~~~~d~~ea~~~l~e-l~~~~~~~~vv~~~l~~~le~~~~~r~~~~~Ll~~L~~~~~~~~~~~~~gf~~ 80 (113)
T PF02847_consen 2 RKKIFSILMEYFSSGDVDEAVECLKE-LKLPSQHHEVVKVILECALEEKKSYREYYSKLLSHLCKRKLISKEQFQEGFED 80 (113)
T ss_dssp HHHHHHHHHHHHHHT-HHHHHHHHHH-TT-GGGHHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHTTSS-HHHHHHHHHH
T ss_pred hHHHHHHHHHHhcCCCHHHHHHHHHH-hCCCccHHHHHHHHHHHHhhccHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHH
Confidence 345666677777 99999999966 3444 5566556666556677776766 334555667777777777777
Q ss_pred HHh
Q 034402 84 MIS 86 (95)
Q Consensus 84 ~~~ 86 (95)
++.
T Consensus 81 ~l~ 83 (113)
T PF02847_consen 81 LLE 83 (113)
T ss_dssp HHH
T ss_pred HHh
Confidence 665
No 123
>PRK15115 response regulator GlrR; Provisional
Probab=21.06 E-value=2.2e+02 Score=22.57 Aligned_cols=37 Identities=8% Similarity=0.103 Sum_probs=28.8
Q ss_pred HHHHHHHHHHHh-hCCHHHHHHHHHhhcCCCchhHHHHHHHHHHh
Q 034402 11 MVQHLIEKCLIF-RMTKEECMEALSKHANIKPVITSTVWNELEKE 54 (95)
Q Consensus 11 ~VQ~LIErCLql-yMsk~E~v~~L~~~a~I~P~fT~~VW~~LE~e 54 (95)
.-+.+|++.|.. ..|+.++.+.| ||... ++|++|++-
T Consensus 398 ~E~~~i~~al~~~~gn~~~aA~~L----gisr~---tL~rkl~~~ 435 (444)
T PRK15115 398 FELNYLRKLLQITKGNVTHAARMA----GRNRT---EFYKLLSRH 435 (444)
T ss_pred HHHHHHHHHHHHhCCCHHHHHHHh----CCCHH---HHHHHHHHh
Confidence 356788888888 47888887777 88764 899999863
No 124
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=20.93 E-value=1.1e+02 Score=20.09 Aligned_cols=41 Identities=10% Similarity=0.115 Sum_probs=29.4
Q ss_pred HHHhhCCHHHHHHHHHhhcCC-CchhHHHHHHHHHHhcHHHH
Q 034402 19 CLIFRMTKEECMEALSKHANI-KPVITSTVWNELEKENKEFF 59 (95)
Q Consensus 19 CLqlyMsk~E~v~~L~~~a~I-~P~fT~~VW~~LE~eN~eFF 59 (95)
..++|......|..+.+++|| .|..-..=|.++.+.....|
T Consensus 16 iv~~~~~~g~sv~~vAr~~gv~~~~~l~~W~~~~~~~~~~~~ 57 (116)
T COG2963 16 AVALYLRGGDTVSEVAREFGIVSATQLYKWRIQLQKGGGLAF 57 (116)
T ss_pred HHHHHHhcCccHHHHHHHhCCCChHHHHHHHHHHHHcccccc
Confidence 345555566678888999996 88887777778877664443
No 125
>KOG2150 consensus CCR4-NOT transcriptional regulation complex, NOT5 subunit [Transcription]
Probab=20.92 E-value=5.1e+02 Score=23.47 Aligned_cols=66 Identities=20% Similarity=0.266 Sum_probs=39.7
Q ss_pred HHHHHHHHHHHHhhCCHHHHHHHHHhhcCCCchhHHHHHHHHHHhcHHHHHHHHHhhhHHhhhhHHHHHHHHHHHHhhcc
Q 034402 10 HMVQHLIEKCLIFRMTKEECMEALSKHANIKPVITSTVWNELEKENKEFFEAYAQSQSKEDRMSEEETNQMIQKMISTNS 89 (95)
Q Consensus 10 ~~VQ~LIErCLqlyMsk~E~v~~L~~~a~I~P~fT~~VW~~LE~eN~eFFkaY~~~~lk~qi~s~~~~~~~iq~~~~~~~ 89 (95)
+.+|.-|.|||..- .|=|+ +-.-+|++|..-|-.==+.=+..-||++|--+-+.+.-|..-++.+.
T Consensus 4 RKLq~eIdr~lkKv---~Egve-----------~Fd~i~ek~~~~~n~sqkeK~e~DLKkEIKKLQRlRdQIKtW~ss~d 69 (575)
T KOG2150|consen 4 RKLQQEIDRCLKKV---DEGVE-----------IFDEIYEKLHSANNVSQKEKLESDLKKEIKKLQRLRDQIKTWQSSSD 69 (575)
T ss_pred hHHHHHHHHHHHHh---hhhHH-----------HHHHHHHHHHhcCChhHHHHHHHHHHHHHHHHHHHHHHHHhhhcccc
Confidence 67899999999752 12222 22368999988552211222334457777766677777766665443
No 126
>KOG2431 consensus 1, 2-alpha-mannosidase [Carbohydrate transport and metabolism]
Probab=20.78 E-value=1e+02 Score=27.38 Aligned_cols=21 Identities=24% Similarity=0.453 Sum_probs=18.6
Q ss_pred hHHHHHHHHHHHHHHHHhh-CC
Q 034402 5 SASYIHMVQHLIEKCLIFR-MT 25 (95)
Q Consensus 5 s~~~I~~VQ~LIErCLqly-Ms 25 (95)
+.++..+.|+|-+.|.+.| ||
T Consensus 390 ~~~hl~lA~~l~~TCyqMY~~~ 411 (546)
T KOG2431|consen 390 SEEHLELAQELMETCYQMYRQN 411 (546)
T ss_pred chHHHHHHHHHHHHHHHHHccC
Confidence 4679999999999999999 44
No 127
>smart00543 MIF4G Middle domain of eukaryotic initiation factor 4G (eIF4G). Also occurs in NMD2p and CBP80. The domain is rich in alpha-helices and may contain multiple alpha-helical repeats. In eIF4G, this domain binds eIF4A, eIF3, RNA and DNA. Ponting (TiBS) "Novel eIF4G domain homologues (in press)
Probab=20.76 E-value=2.9e+02 Score=18.82 Aligned_cols=52 Identities=15% Similarity=0.215 Sum_probs=37.4
Q ss_pred HHHHHHHHHHHhhCC----HHHHHHHHHhhcCCCchhH---HHHHHHHHHhcHHHHHHH
Q 034402 11 MVQHLIEKCLIFRMT----KEECMEALSKHANIKPVIT---STVWNELEKENKEFFEAY 62 (95)
Q Consensus 11 ~VQ~LIErCLqlyMs----k~E~v~~L~~~a~I~P~fT---~~VW~~LE~eN~eFFkaY 62 (95)
.+...++.....+++ .+++++.+.+.+..+|.+. ..+...|...+++|...-
T Consensus 15 n~~~~~~~l~~~~~~~~~~~~~l~~~i~~~~~~~~~~~~~ya~L~~~l~~~~~~f~~~l 73 (200)
T smart00543 15 NFESIIKELLKLNNSDKNLRKYILELIFEKAVEEPNFIPAYARLCALLNAKNPDFGSLL 73 (200)
T ss_pred HHHHHHHHHHHHHccCHHHHHHHHHHHHHHHHcCcchHHHHHHHHHHHHHHHHHHHHHH
Confidence 344555555556655 5678888999999999887 566777777888877665
No 128
>PRK10696 tRNA 2-thiocytidine biosynthesis protein TtcA; Provisional
Probab=20.71 E-value=2.7e+02 Score=21.10 Aligned_cols=43 Identities=9% Similarity=0.118 Sum_probs=28.3
Q ss_pred hhCCHHHHHHHHHhhcCCCc----------hh----HHHHHHHHHHhcHHHHHHHHHh
Q 034402 22 FRMTKEECMEALSKHANIKP----------VI----TSTVWNELEKENKEFFEAYAQS 65 (95)
Q Consensus 22 lyMsk~E~v~~L~~~a~I~P----------~f----T~~VW~~LE~eN~eFFkaY~~~ 65 (95)
++++++|+..+...+ ||.+ .+ ...+-..|++.||.|-....+.
T Consensus 179 l~~~k~eI~~y~~~~-~lp~~~~~~~~~~~~~~R~~ir~~l~~L~~~~P~~~~~i~~~ 235 (258)
T PRK10696 179 AYVAEKDIIKFAEAK-EFPIIPCNLCGSQENLQRQVVKEMLRDWEKEYPGRIETMFRA 235 (258)
T ss_pred ccCCHHHHHHHHHHc-CCCEeeCCCCCCCchhHHHHHHHHHHHHHHHCccHHHHHHHH
Confidence 468999999998764 6653 11 1234577788888776666443
No 129
>COG2443 Sss1 Preprotein translocase subunit Sss1 [Intracellular trafficking and secretion]
Probab=20.66 E-value=2.1e+02 Score=18.77 Aligned_cols=31 Identities=19% Similarity=0.279 Sum_probs=23.2
Q ss_pred HHHhcHHHHHHHHHhhhHHhhhhHHHHHHHH
Q 034402 51 LEKENKEFFEAYAQSQSKEDRMSEEETNQMI 81 (95)
Q Consensus 51 LE~eN~eFFkaY~~~~lk~qi~s~~~~~~~i 81 (95)
+-++=.+|+++|.|...+---.+.+|+....
T Consensus 7 ~~e~~~~~lke~~rvl~~arKP~~eEy~~~a 37 (65)
T COG2443 7 KPEELREFLKEYRRVLKVARKPDWEEYSKIA 37 (65)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCCHHHHHHHH
Confidence 3455678999998877777778888876543
No 130
>PF00538 Linker_histone: linker histone H1 and H5 family; InterPro: IPR005818 Histone proteins have central roles in both chromatin organisation (as structural units of the nucleosome) and gene regulation (as dynamic components that have a direct impact on DNA transcription and replication). Eukaryotic DNA wraps around a histone octamer to form a nucleosome, the first order of compaction of eukaryotic chromatin. The core histone octamer is composed of a central H3-H4 tetramer and two flanking H2A-H2B dimers. Each of the core histone contains a common structural motif, called the histone fold, which facilitates the interactions between the individual core histones. In addition to the core histones, there is a "linker histone" called H1 (or H5 in avian species). The linker histones present in all multicellular eukaryotes are the most divergent group of histones, with numerous cell type- and stage-specific variant. Linker histone H1 is an essential component of chromatin structure. H1 links nucleosomes into higher order structures. Histone H5 performs the same function as histone H1, and replaces H1 in certain cells. The structure of GH5, the globular domain of the linker histone H5 is known [, ]. The fold is similar to the DNA-binding domain of the catabolite gene activator protein, CAP, thus providing a possible model for the binding of GH5 to DNA. The linker histones, which do not contain the histone fold motif, are critical to the higher-order compaction of chromatin, because they bind to internucleosomal DNA and facilitate interactions between individual nucleosomes. In addition, H1 variants have been shown to be involved in the regulation of developmental genes. A common feature of this protein family is a tripartite structure in which a globular (H15) domain of about 80 amino acids is flanked by two less structured N- and C-terminal tails. The H15 domain is also characterised by high sequence homology among the family of linker histones. The highly conserved H15 domain is essential for the binding of H1 or H5 to the nucleosome. It consists of a three helix bundle (I-III), with a beta-hairpin at the C terminus. There is also a short three-residue stretch between helices I and II that is in the beta-strand conformation. Together with the C-terminal beta-hairpin, this strand forms the third strand of an antiparallel beta-sheet [, , , ]. Proteins known to contain a H15 domain are: - Eukaryotic histone H1. The histones H1 constitute a family with many variants, differing in their affinity for chromatin. Several variants are simultaneously present in a single cell. For example, the nucleated erythrocytes of birds contain both H1 and H5, the latter being an extreme variant of H1. - Eukaryotic MHYST family of histone acetyltransferase. Histone acetyltransferases transfer an acetyl group from acetyl-CoA to the epsylon- amino group of lysine within the basic NH2-termini of histones, which bind the acidic phosphates of DNA []. This entry represents the H15 domain.; GO: 0003677 DNA binding, 0006334 nucleosome assembly, 0000786 nucleosome, 0005634 nucleus; PDB: 2LSO_A 2RQP_A 1UHM_A 1UST_A 1GHC_A 1HST_A 1YQA_A 1USS_A.
Probab=20.41 E-value=1.5e+02 Score=18.61 Aligned_cols=47 Identities=13% Similarity=0.162 Sum_probs=31.5
Q ss_pred HHHHHHHHHHHHHHH-hhCCHHHHHHHHHhhcC--CCc-hhHHHHHHHHHH
Q 034402 7 SYIHMVQHLIEKCLI-FRMTKEECMEALSKHAN--IKP-VITSTVWNELEK 53 (95)
Q Consensus 7 ~~I~~VQ~LIErCLq-lyMsk~E~v~~L~~~a~--I~P-~fT~~VW~~LE~ 53 (95)
.+.+||...|..+=. ---|...+..++..+.+ ++| .|...|..-|.+
T Consensus 4 ~y~~mI~eAI~~l~er~GsS~~aI~kyI~~~y~~~~~~~~~~~~l~~aLk~ 54 (77)
T PF00538_consen 4 PYSDMILEAIKALKERKGSSLQAIKKYIKAKYKVDLNPANFKSRLKRALKR 54 (77)
T ss_dssp CHHHHHHHHHHHCCSSSSEEHHHHHHHHHHHSSCCCCHTTHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHcCCCCCCCHHHHHHHHHHhcCcCCChHHHHHHHHHHHHH
Confidence 456677777764422 45677788888888875 555 677777766654
No 131
>KOG0019 consensus Molecular chaperone (HSP90 family) [Posttranslational modification, protein turnover, chaperones]
Probab=20.36 E-value=2.4e+02 Score=25.84 Aligned_cols=41 Identities=24% Similarity=0.282 Sum_probs=24.1
Q ss_pred hcHHHHHHHH---HhhhHHhhhhHHHHHHH-HHHHHhhccccccC
Q 034402 54 ENKEFFEAYA---QSQSKEDRMSEEETNQM-IQKMISTNSSKSQN 94 (95)
Q Consensus 54 eN~eFFkaY~---~~~lk~qi~s~~~~~~~-iq~~~~~~~~~~~~ 94 (95)
+|+|+|+.|+ .+-+|.-|....+.... |-+.++-.|+.|++
T Consensus 378 ~d~e~Y~kFy~~f~~~lk~gi~e~s~~~~k~~a~lLry~ss~s~~ 422 (656)
T KOG0019|consen 378 KDAEKYKKFFKNYGLFLKEGIVTASEQQVKEIAKLLRYESSKSGE 422 (656)
T ss_pred hhHHHHHHHHHHHhhhhhhcccchhhhhhhHHHHHhhhhcccccc
Confidence 5666655552 24467777655555555 88888754444443
No 132
>cd01106 HTH_TipAL-Mta Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA. Helix-turn-helix (HTH) TipAL, Mta, and SkgA transcription regulators, and related proteins, N-terminal domain. TipAL regulates resistance to and activation by numerous cyclic thiopeptide antibiotics, such as thiostrepton. Mta is a global transcriptional regulator; the N-terminal DNA-binding domain of Mta interacts directly with the promoters of mta, bmr, blt, and ydfK, and induces transcription of these multidrug-efflux transport genes. SkgA has been shown to control stationary-phase expression of catalase-peroxidase in Caulobacter crescentus. These proteins are comprised of distinct domains that harbor an N-terminal active (DNA-binding) site and a regulatory (effector-binding) site. The conserved N-terminal domain of these transcription regulators contains winged HTH motifs that mediate DNA binding. These proteins share the N-terminal DNA binding domain with other transcrip
Probab=20.33 E-value=2.6e+02 Score=18.19 Aligned_cols=61 Identities=13% Similarity=0.196 Sum_probs=36.5
Q ss_pred hHHHHHHHHHHHHHHHHhhCCHHHHHHHHHhhcCCCchhHHHHHHHHHHhcHHHHHHH--HHhhhHHhhhhHHHHHHHHH
Q 034402 5 SASYIHMVQHLIEKCLIFRMTKEECMEALSKHANIKPVITSTVWNELEKENKEFFEAY--AQSQSKEDRMSEEETNQMIQ 82 (95)
Q Consensus 5 s~~~I~~VQ~LIErCLqlyMsk~E~v~~L~~~a~I~P~fT~~VW~~LE~eN~eFFkaY--~~~~lk~qi~s~~~~~~~iq 82 (95)
+.++|..++.+. .+-...|+-+++-..|... ++++-..+ .+..|.+|+.-.....+.|+
T Consensus 40 ~~~di~~l~~i~-~lr~~g~~l~~i~~~~~~~------------------~~~~~~~l~~~~~~l~~~i~~l~~~~~~l~ 100 (103)
T cd01106 40 TEEDLERLQQIL-FLKELGFSLKEIKELLKDP------------------SEDLLEALREQKELLEEKKERLDKLIKTID 100 (103)
T ss_pred CHHHHHHHHHHH-HHHHcCCCHHHHHHHHHcC------------------cHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 456666665543 4566788888888777432 14444444 33445666765666666665
Q ss_pred HH
Q 034402 83 KM 84 (95)
Q Consensus 83 ~~ 84 (95)
++
T Consensus 101 ~~ 102 (103)
T cd01106 101 RT 102 (103)
T ss_pred Hh
Confidence 54
No 133
>PF06711 DUF1198: Protein of unknown function (DUF1198); InterPro: IPR009587 This family consists of several bacterial proteins of around 150 residues in length which are specific to Escherichia coli, Salmonella species and Yersinia pestis. The function of this family is unknown.
Probab=20.28 E-value=1.9e+02 Score=21.88 Aligned_cols=37 Identities=27% Similarity=0.449 Sum_probs=32.7
Q ss_pred HHHHHHHhhcCCCchhHHHHHHHHHHhcHHHHHHHHH
Q 034402 28 ECMEALSKHANIKPVITSTVWNELEKENKEFFEAYAQ 64 (95)
Q Consensus 28 E~v~~L~~~a~I~P~fT~~VW~~LE~eN~eFFkaY~~ 64 (95)
-.++.|++..||+|+--+.+-.++-+++.+=|--|..
T Consensus 26 ~A~~~Ls~rL~I~Pv~iESMl~qMGk~~~~~Firyl~ 62 (148)
T PF06711_consen 26 RAIRRLSERLNIKPVYIESMLDQMGKRAGQEFIRYLS 62 (148)
T ss_pred HHHHHHHHHhCCCceeHHHHHHHHhHhHHHHHHHHHc
Confidence 3578899999999999999999999999988888843
No 134
>TIGR01797 CM_P_1 chorismate mutase domain of proteobacterial P-protein, clade 1. This model represents the chorismate mutase domain of the gamma and beta proteobacterial "P-protein" which contains an N-terminal chorismate mutase domain and a C-terminal prephenate dehydratase domain.
Probab=20.15 E-value=1.5e+02 Score=19.04 Aligned_cols=18 Identities=0% Similarity=0.148 Sum_probs=12.1
Q ss_pred cCCCchhHHHHHHHHHHh
Q 034402 37 ANIKPVITSTVWNELEKE 54 (95)
Q Consensus 37 a~I~P~fT~~VW~~LE~e 54 (95)
.+++|.+...+|+.+=+.
T Consensus 60 ~~l~~~~i~~if~~ii~~ 77 (83)
T TIGR01797 60 YHLDAHYITRLFQLIIED 77 (83)
T ss_pred CCCCHHHHHHHHHHHHHH
Confidence 567777777777766544
No 135
>PF14076 DUF4258: Domain of unknown function (DUF4258)
Probab=20.11 E-value=1.6e+02 Score=17.28 Aligned_cols=23 Identities=22% Similarity=0.281 Sum_probs=20.3
Q ss_pred HHHHHHHHHhhCCHHHHHHHHHh
Q 034402 13 QHLIEKCLIFRMTKEECMEALSK 35 (95)
Q Consensus 13 Q~LIErCLqlyMsk~E~v~~L~~ 35 (95)
.|.++|..+-..|.+++..+|..
T Consensus 4 ~Ha~~rm~eR~Is~~~I~~~l~~ 26 (73)
T PF14076_consen 4 KHARERMQERGISEEDIEDALEN 26 (73)
T ss_pred HHHHHHHHhCCCCHHHHHHHHhc
Confidence 47889999999999999999965
Done!