Query 034494
Match_columns 93
No_of_seqs 91 out of 104
Neff 3.5
Searched_HMMs 46136
Date Fri Mar 29 03:28:12 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034494.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/034494hhsearch_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 3E-37 6.6E-42 196.3 6.8 57 9-65 1-57 (57)
2 PF09713 A_thal_3526: Plant pr 100.0 2.9E-36 6.4E-41 189.8 6.3 54 12-65 1-54 (54)
3 PF13565 HTH_32: Homeodomain-l 83.3 3.8 8.2E-05 24.9 4.6 43 8-50 32-76 (77)
4 PF08986 DUF1889: Domain of un 82.2 1.5 3.3E-05 31.6 2.8 37 29-65 68-113 (119)
5 smart00411 BHL bacterial (prok 81.0 3.8 8.1E-05 25.9 4.1 30 24-53 1-30 (90)
6 COG1725 Predicted transcriptio 79.8 4 8.6E-05 29.3 4.3 51 5-55 10-63 (125)
7 PF08145 BOP1NT: BOP1NT (NUC16 75.2 2.4 5.2E-05 34.0 2.3 32 7-42 213-244 (260)
8 PF00216 Bac_DNA_binding: Bact 71.8 7.6 0.00016 24.3 3.6 30 24-53 1-30 (90)
9 PF14420 Clr5: Clr5 domain 71.4 11 0.00023 22.8 4.1 36 7-42 3-39 (54)
10 TIGR00988 hip integration host 65.9 15 0.00033 23.7 4.2 30 24-53 1-31 (94)
11 TIGR00987 himA integration hos 63.7 16 0.00035 23.9 4.1 30 24-53 2-31 (96)
12 PRK10664 transcriptional regul 60.6 20 0.00044 23.6 4.1 24 24-47 1-24 (90)
13 PRK00199 ihfB integration host 60.2 23 0.00049 23.0 4.2 30 24-53 1-31 (94)
14 PRK00285 ihfA integration host 60.1 20 0.00044 23.4 4.1 31 23-53 2-32 (99)
15 smart00139 MyTH4 Domain in Myo 60.0 23 0.0005 25.2 4.6 52 1-52 33-90 (144)
16 PF06570 DUF1129: Protein of u 59.3 7.8 0.00017 28.6 2.1 34 50-83 1-35 (206)
17 PRK14552 C/D box methylation g 58.7 18 0.00038 30.5 4.3 47 1-47 222-270 (414)
18 PF05402 PqqD: Coenzyme PQQ sy 57.5 37 0.0008 20.2 4.6 32 18-49 24-56 (68)
19 COG3415 Transposase and inacti 54.4 27 0.00059 25.3 4.2 55 3-58 60-114 (138)
20 PRK10753 transcriptional regul 54.3 30 0.00066 22.6 4.1 25 24-48 1-25 (90)
21 PF04340 DUF484: Protein of un 53.1 4.5 9.7E-05 30.1 0.0 10 54-63 17-26 (225)
22 PF10045 DUF2280: Uncharacteri 51.7 85 0.0018 22.3 7.0 55 11-65 7-69 (104)
23 PF03979 Sigma70_r1_1: Sigma-7 51.0 52 0.0011 21.1 4.8 52 7-59 4-56 (82)
24 PF03918 CcmH: Cytochrome C bi 51.0 34 0.00074 24.8 4.3 37 2-38 52-88 (148)
25 PRK10963 hypothetical protein; 50.5 13 0.00028 28.0 2.1 22 23-63 2-23 (223)
26 TIGR01201 HU_rel DNA-binding p 47.6 39 0.00084 24.0 4.1 31 24-54 31-61 (145)
27 PF02082 Rrf2: Transcriptional 47.4 29 0.00062 21.9 3.1 27 29-55 27-53 (83)
28 TIGR01795 CM_mono_cladeE monof 46.6 37 0.00081 22.7 3.7 25 31-55 58-82 (94)
29 COG4359 Uncharacterized conser 46.4 23 0.0005 28.1 3.0 26 22-47 57-82 (220)
30 TIGR03147 cyt_nit_nrfF cytochr 46.1 44 0.00096 24.1 4.2 38 2-39 52-89 (126)
31 KOG3973 Uncharacterized conser 44.8 35 0.00076 29.5 4.0 60 12-71 141-223 (465)
32 PLN02814 beta-glucosidase 44.6 16 0.00035 31.1 2.0 46 5-65 112-168 (504)
33 PF04433 SWIRM: SWIRM domain; 42.5 36 0.00078 21.7 3.0 45 6-54 33-81 (86)
34 PF13720 Acetyltransf_11: Udp 41.3 1E+02 0.0022 20.1 5.5 43 5-47 29-71 (83)
35 COG1725 Predicted transcriptio 41.3 49 0.0011 23.8 3.8 29 7-35 90-118 (125)
36 PF14164 YqzH: YqzH-like prote 41.2 34 0.00073 22.4 2.7 14 10-23 4-17 (64)
37 PF07527 Hairy_orange: Hairy O 40.7 62 0.0013 18.5 3.6 27 27-53 12-38 (43)
38 PF00784 MyTH4: MyTH4 domain; 40.3 1E+02 0.0022 20.6 5.0 46 8-53 2-49 (114)
39 PRK05686 fliG flagellar motor 40.0 1.7E+02 0.0038 23.3 7.1 63 1-65 171-240 (339)
40 PLN02849 beta-glucosidase 39.3 20 0.00044 30.5 1.8 45 6-65 115-170 (503)
41 PLN02998 beta-glucosidase 38.1 22 0.00047 30.3 1.8 45 6-65 118-173 (497)
42 PF14769 CLAMP: Flagellar C1a 38.0 1.2E+02 0.0026 20.0 6.7 56 7-62 19-84 (101)
43 PF05295 Luciferase_N: Lucifer 37.7 63 0.0014 22.2 3.7 38 28-65 4-41 (82)
44 cd00591 HU_IHF Integration hos 37.1 81 0.0018 19.5 4.0 29 25-53 1-29 (87)
45 PRK10144 formate-dependent nit 36.9 77 0.0017 22.9 4.3 46 3-48 53-105 (126)
46 smart00345 HTH_GNTR helix_turn 36.8 62 0.0013 17.9 3.1 27 29-55 22-48 (60)
47 PF00938 Lipoprotein_3: Lipopr 35.9 1.4E+02 0.0031 20.6 5.2 56 25-90 27-84 (87)
48 PF09280 XPC-binding: XPC-bind 35.5 44 0.00095 20.9 2.5 33 32-64 12-44 (59)
49 COG0776 HimA Bacterial nucleoi 35.1 53 0.0012 22.5 3.1 18 24-41 2-19 (94)
50 PF08006 DUF1700: Protein of u 34.5 94 0.002 22.2 4.4 34 24-64 1-34 (181)
51 PF05960 DUF885: Bacterial pro 33.8 1.6E+02 0.0035 24.2 6.2 62 3-65 432-502 (549)
52 PF08004 DUF1699: Protein of u 33.4 1.1E+02 0.0023 22.7 4.6 36 14-49 95-130 (131)
53 PF00232 Glyco_hydro_1: Glycos 33.0 12 0.00026 30.8 -0.5 46 5-65 94-149 (455)
54 PF12685 SpoIIIAH: SpoIIIAH-li 32.9 40 0.00087 24.8 2.4 33 54-88 83-115 (196)
55 smart00511 ORANGE Orange domai 32.7 91 0.002 17.8 3.4 27 27-53 12-38 (45)
56 TIGR02173 cyt_kin_arch cytidyl 32.6 1.5E+02 0.0033 19.7 5.0 41 25-65 101-141 (171)
57 TIGR03356 BGL beta-galactosida 32.1 43 0.00093 27.6 2.6 37 28-65 98-144 (427)
58 PRK07194 fliG flagellar motor 31.9 2.5E+02 0.0054 22.5 6.8 58 1-61 166-230 (334)
59 smart00760 Bac_DnaA_C Bacteria 31.7 49 0.0011 19.8 2.2 19 25-43 1-19 (60)
60 TIGR00207 fliG flagellar motor 31.5 2.8E+02 0.006 22.4 7.3 62 2-65 170-237 (338)
61 PF03965 Penicillinase_R: Peni 31.4 56 0.0012 21.7 2.7 31 24-54 18-48 (115)
62 PF11417 Inhibitor_G39P: Loade 30.8 55 0.0012 21.2 2.5 18 24-41 1-18 (71)
63 PRK09239 chorismate mutase; Pr 30.3 93 0.002 21.2 3.7 19 34-52 68-86 (104)
64 smart00830 CM_2 Chorismate mut 30.3 73 0.0016 19.4 2.9 16 36-51 55-70 (79)
65 PRK14137 recX recombination re 30.2 1.6E+02 0.0034 22.2 5.2 45 10-55 37-85 (195)
66 KOG2211 Predicted Golgi transp 30.1 1.7E+02 0.0037 27.3 6.1 19 38-56 361-379 (797)
67 PRK08091 ribulose-phosphate 3- 29.9 32 0.0007 26.7 1.5 34 24-58 1-34 (228)
68 PF09012 FeoC: FeoC like trans 28.9 69 0.0015 19.6 2.6 24 30-53 17-40 (69)
69 cd05062 PTKc_IGF-1R Catalytic 28.8 62 0.0013 23.0 2.7 25 10-34 248-276 (277)
70 TIGR02010 IscR iron-sulfur clu 28.7 76 0.0016 21.7 3.0 27 29-55 27-53 (135)
71 TIGR01803 CM-like chorismate m 28.7 79 0.0017 20.2 2.9 20 34-53 57-76 (82)
72 COG4399 Uncharacterized protei 28.6 2.9E+02 0.0064 23.6 7.0 62 7-68 83-148 (376)
73 smart00543 MIF4G Middle domain 28.3 1.9E+02 0.0042 19.6 6.2 52 11-62 15-73 (200)
74 PF05066 HARE-HTH: HB1, ASXL, 28.0 97 0.0021 18.9 3.2 30 24-54 1-30 (72)
75 cd07377 WHTH_GntR Winged helix 27.8 1E+02 0.0023 17.3 3.1 26 30-55 28-53 (66)
76 PRK12461 UDP-N-acetylglucosami 27.5 2.7E+02 0.0058 21.5 6.1 43 5-47 201-243 (255)
77 PRK05289 UDP-N-acetylglucosami 27.0 2.8E+02 0.0061 21.1 6.1 43 5-47 205-247 (262)
78 PF12383 SARS_3b: Severe acute 26.4 65 0.0014 23.8 2.5 34 14-47 114-147 (153)
79 cd05094 PTKc_TrkC Catalytic do 26.2 82 0.0018 22.7 3.0 29 10-38 252-284 (291)
80 TIGR02894 DNA_bind_RsfA transc 26.0 2.9E+02 0.0064 20.9 7.3 60 22-81 78-147 (161)
81 TIGR00461 gcvP glycine dehydro 25.8 1.1E+02 0.0025 28.6 4.4 61 24-85 46-120 (939)
82 PF03081 Exo70: Exo70 exocyst 25.6 3.2E+02 0.007 21.2 6.4 77 7-83 248-331 (371)
83 PF07531 TAFH: NHR1 homology t 25.4 1.3E+02 0.0028 20.9 3.7 37 5-41 22-58 (96)
84 PLN02350 phosphogluconate dehy 25.3 1.6E+02 0.0036 25.2 5.0 45 1-47 178-223 (493)
85 COG1498 SIK1 Protein implicate 25.2 1.2E+02 0.0025 25.9 4.1 51 1-51 200-252 (395)
86 COG3159 Uncharacterized protei 24.9 63 0.0014 25.6 2.3 9 54-62 15-23 (218)
87 PTZ00398 phosphoenolpyruvate c 24.6 73 0.0016 29.8 2.9 33 12-45 155-187 (974)
88 PF11626 Rap1_C: TRF2-interact 24.3 98 0.0021 20.0 2.8 38 16-53 1-38 (87)
89 TIGR00269 conserved hypothetic 24.3 2.2E+02 0.0047 19.0 4.6 40 22-62 8-60 (104)
90 PF01466 Skp1: Skp1 family, di 24.2 88 0.0019 19.8 2.5 23 34-56 52-74 (78)
91 PF13936 HTH_38: Helix-turn-he 24.0 1.3E+02 0.0028 17.1 3.0 33 14-53 11-43 (44)
92 PF13625 Helicase_C_3: Helicas 23.7 1.1E+02 0.0023 20.8 3.0 34 14-47 45-80 (129)
93 PF09278 MerR-DNA-bind: MerR, 23.6 1.7E+02 0.0036 17.2 5.0 36 14-51 5-40 (65)
94 PF14039 YusW: YusW-like prote 23.5 70 0.0015 21.6 2.1 37 8-44 45-82 (92)
95 PF07954 DUF1689: Protein of u 23.5 46 0.001 24.7 1.2 22 44-65 108-129 (152)
96 KOG1199 Short-chain alcohol de 23.4 61 0.0013 26.0 2.0 17 2-19 227-243 (260)
97 PRK00009 phosphoenolpyruvate c 23.1 82 0.0018 29.2 3.0 34 11-45 108-141 (911)
98 PRK10857 DNA-binding transcrip 22.9 1.1E+02 0.0023 22.3 3.0 27 29-55 27-53 (164)
99 PF14123 DUF4290: Domain of un 22.8 2E+02 0.0044 22.0 4.6 46 6-52 13-68 (176)
100 PF10364 NKWYS: Putative capsu 22.7 75 0.0016 23.4 2.2 33 3-35 7-39 (141)
101 smart00337 BCL BCL (B-Cell lym 22.5 1.8E+02 0.0038 19.2 3.8 38 49-86 6-45 (100)
102 COG1412 Uncharacterized protei 22.4 2.1E+02 0.0047 20.7 4.5 40 15-55 19-58 (136)
103 PF08970 Sda: Sporulation inhi 22.3 2E+02 0.0043 17.6 3.9 33 23-55 3-37 (46)
104 PF00735 Septin: Septin; Inte 22.3 71 0.0015 25.0 2.1 75 7-83 81-201 (281)
105 cd02433 Nodulin-21_like_2 Nodu 22.1 1.9E+02 0.0041 22.3 4.4 52 10-65 86-137 (234)
106 PRK00117 recX recombination re 22.1 2.8E+02 0.006 19.2 5.6 43 21-64 23-69 (157)
107 KOG2431 1, 2-alpha-mannosidase 22.0 94 0.002 27.6 3.0 21 5-25 390-411 (546)
108 PF13833 EF-hand_8: EF-hand do 22.0 1.2E+02 0.0025 17.0 2.5 49 23-80 4-52 (54)
109 TIGR01797 CM_P_1 chorismate mu 21.9 1.4E+02 0.003 19.1 3.1 20 36-55 59-78 (83)
110 PF14076 DUF4258: Domain of un 21.9 1.4E+02 0.003 17.5 3.0 23 13-35 4-26 (73)
111 PRK11675 LexA regulated protei 21.9 1.7E+02 0.0038 20.1 3.8 25 10-34 60-84 (90)
112 PF13518 HTH_28: Helix-turn-he 21.8 1.4E+02 0.0031 16.4 2.8 27 29-55 14-40 (52)
113 PF12980 DUF3864: Domain of Un 21.4 26 0.00056 23.9 -0.4 29 36-64 50-78 (82)
114 cd05093 PTKc_TrkB Catalytic do 21.4 96 0.0021 22.3 2.5 29 11-39 250-282 (288)
115 cd05049 PTKc_Trk Catalytic dom 21.3 1.1E+02 0.0023 21.6 2.7 25 10-34 251-279 (280)
116 cd04763 HTH_MlrA-like Helix-Tu 21.2 2E+02 0.0042 17.1 3.6 28 5-33 40-67 (68)
117 cd07765 KRAB_A-box KRAB (Krupp 20.9 39 0.00084 14.4 0.3 25 38-62 5-29 (40)
118 KOG2939 Uncharacterized conser 20.9 1.3E+02 0.0029 26.6 3.6 44 28-71 122-169 (502)
119 PF08020 DUF1706: Protein of u 20.8 1.6E+02 0.0035 21.7 3.6 30 36-65 68-99 (166)
120 PF00452 Bcl-2: Apoptosis regu 20.7 1.9E+02 0.0041 18.4 3.6 38 48-85 5-45 (101)
121 COG2963 Transposase and inacti 20.7 1.2E+02 0.0026 19.9 2.7 41 19-59 16-57 (116)
122 PF13551 HTH_29: Winged helix- 20.6 2.3E+02 0.0049 17.6 5.5 31 23-54 80-111 (112)
123 PF07882 Fucose_iso_N2: L-fuco 20.6 23 0.0005 27.3 -0.9 29 55-83 19-47 (181)
124 PF12415 rpo132: Poxvirus DNA 20.5 1.1E+02 0.0024 17.6 2.2 16 4-19 11-26 (33)
125 cd05116 PTKc_Syk Catalytic dom 20.5 1.3E+02 0.0027 21.1 2.9 26 10-35 225-254 (257)
126 COG1438 ArgR Arginine represso 20.1 1.2E+02 0.0027 22.4 2.9 30 22-53 19-48 (150)
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=3e-37 Score=196.30 Aligned_cols=57 Identities=46% Similarity=0.673 Sum_probs=55.7
Q ss_pred HHHHHHHHHHHHHhhCCHHHHHHHHHhhcCCChhhHHHHHHHHHHhcHHHHHHHHhc
Q 034494 9 IHLVHHLIEECLVFNMSKEECMEALSKHANIKPVITSTVWKELEKENKEFFEAYARK 65 (93)
Q Consensus 9 I~~VQ~LIErCLqlyMsk~Evv~~L~~~a~I~P~fT~~VW~~Le~eNpeFF~aY~~~ 65 (93)
|++|||||||||++|||++|||++|++||||+|+||++||++||+||||||+|||.+
T Consensus 1 i~~Vq~lIE~Cl~~yMsk~E~v~~L~~~a~I~P~~T~~VW~~LekeN~eFF~aY~~~ 57 (57)
T TIGR01589 1 IDLVQNRIETCIQGYMSKEETVSFLFENAGISPKFTRFVWYLLEKENADFFRCYKTH 57 (57)
T ss_pred CHHHHHHHHHHHHHHCCHHHHHHHHHHHcCCCchhHHHHHHHHHHHHHHHHHHHhcC
Confidence 689999999999999999999999999999999999999999999999999999975
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=2.9e-36 Score=189.79 Aligned_cols=54 Identities=65% Similarity=1.058 Sum_probs=52.9
Q ss_pred HHHHHHHHHHhhCCHHHHHHHHHhhcCCChhhHHHHHHHHHHhcHHHHHHHHhc
Q 034494 12 VHHLIEECLVFNMSKEECMEALSKHANIKPVITSTVWKELEKENKEFFEAYARK 65 (93)
Q Consensus 12 VQ~LIErCLqlyMsk~Evv~~L~~~a~I~P~fT~~VW~~Le~eNpeFF~aY~~~ 65 (93)
||+||||||++|||++|||++|++||||+|+||++||++||+||||||+||++|
T Consensus 1 Vq~lIErCl~~yMsk~E~v~~L~~~a~I~P~~T~~VW~~Le~eN~eFF~aY~~r 54 (54)
T PF09713_consen 1 VQNLIERCLQLYMSKEECVRALQKQANIEPVFTSTVWQKLEKENPEFFKAYYTR 54 (54)
T ss_pred CchHHHHHHHHcCCHHHHHHHHHHHcCCChHHHHHHHHHHHHHCHHHHHHhhcC
Confidence 799999999999999999999999999999999999999999999999999975
No 3
>PF13565 HTH_32: Homeodomain-like domain
Probab=83.25 E-value=3.8 Score=24.94 Aligned_cols=43 Identities=21% Similarity=0.112 Sum_probs=29.3
Q ss_pred HHHHHHHHHHHHHHh-hCCHHHHHHHHHhhcCCCh-hhHHHHHHH
Q 034494 8 YIHLVHHLIEECLVF-NMSKEECMEALSKHANIKP-VITSTVWKE 50 (93)
Q Consensus 8 ~I~~VQ~LIErCLql-yMsk~Evv~~L~~~a~I~P-~fT~~VW~~ 50 (93)
+-++.+.+++-.... .+|..++...|..++||.. .=-++||+-
T Consensus 32 ~~e~~~~i~~~~~~~p~wt~~~i~~~L~~~~g~~~~~S~~tv~R~ 76 (77)
T PF13565_consen 32 DPEQRERIIALIEEHPRWTPREIAEYLEEEFGISVRVSRSTVYRI 76 (77)
T ss_pred cHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhCCCCCccHhHHHHh
Confidence 334445555554444 7999999999999999864 334567654
No 4
>PF08986 DUF1889: Domain of unknown function (DUF1889); InterPro: IPR015079 This family consist of hypothetical bacterial proteins. ; PDB: 2JN8_A 2ES9_A.
Probab=82.17 E-value=1.5 Score=31.57 Aligned_cols=37 Identities=30% Similarity=0.515 Sum_probs=23.5
Q ss_pred HHHHHHhhcCCChhhHHHH--HHHHH-------HhcHHHHHHHHhc
Q 034494 29 CMEALSKHANIKPVITSTV--WKELE-------KENKEFFEAYARK 65 (93)
Q Consensus 29 vv~~L~~~a~I~P~fT~~V--W~~Le-------~eNpeFF~aY~~~ 65 (93)
-|.+=-++-|-+|+||..| |.+-- =.|||||..|..-
T Consensus 68 dv~aRg~qeGWn~gFT~k~agwaeki~sG~rivIKnPEyFs~YMre 113 (119)
T PF08986_consen 68 DVTARGEQEGWNPGFTEKVAGWAEKIASGERIVIKNPEYFSSYMRE 113 (119)
T ss_dssp HHHHHHHHCT--HHHHHHHHHHHHHHHCT-----SSGGGS-HHHHH
T ss_pred HHHHhcccccCChhHHHHHHHHHHHHhcCCeeeecChHHHHHHHHH
Confidence 3444556779999999987 54322 2799999999754
No 5
>smart00411 BHL bacterial (prokaryotic) histone like domain.
Probab=81.01 E-value=3.8 Score=25.92 Aligned_cols=30 Identities=17% Similarity=0.267 Sum_probs=26.4
Q ss_pred CCHHHHHHHHHhhcCCChhhHHHHHHHHHH
Q 034494 24 MSKEECMEALSKHANIKPVITSTVWKELEK 53 (93)
Q Consensus 24 Msk~Evv~~L~~~a~I~P~fT~~VW~~Le~ 53 (93)
||++|+++.++++.++.+.-...|++.|..
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=79.81 E-value=4 Score=29.35 Aligned_cols=51 Identities=18% Similarity=0.361 Sum_probs=45.5
Q ss_pred hHHHHHHHHHHHHHHHHhhCCHHH---HHHHHHhhcCCChhhHHHHHHHHHHhc
Q 034494 5 SASYIHLVHHLIEECLVFNMSKEE---CMEALSKHANIKPVITSTVWKELEKEN 55 (93)
Q Consensus 5 s~~~I~~VQ~LIErCLqlyMsk~E---vv~~L~~~a~I~P~fT~~VW~~Le~eN 55 (93)
..-|.+.++.+.+.+..--+...| -|+.|..+.+|+|..++-++++||++.
T Consensus 10 ~PIY~QI~~qIk~~I~~g~l~pGdkLPSvRelA~~~~VNpnTv~raY~eLE~eG 63 (125)
T COG1725 10 KPIYEQIANQIKEQIASGELKPGDKLPSVRELAKDLGVNPNTVQRAYQELEREG 63 (125)
T ss_pred CCHHHHHHHHHHHHHHhCCcCCCCCCCcHHHHHHHhCCCHHHHHHHHHHHHHCC
Confidence 466888999999999999998887 479999999999999999999999863
No 7
>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=75.17 E-value=2.4 Score=34.01 Aligned_cols=32 Identities=25% Similarity=0.488 Sum_probs=25.6
Q ss_pred HHHHHHHHHHHHHHHhhCCHHHHHHHHHhhcCCChh
Q 034494 7 SYIHLVHHLIEECLVFNMSKEECMEALSKHANIKPV 42 (93)
Q Consensus 7 ~~I~~VQ~LIErCLqlyMsk~Evv~~L~~~a~I~P~ 42 (93)
.|=..|+..-||||.|||-. ++.....||+|.
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 35578999999999999955 455667899884
No 8
>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=71.84 E-value=7.6 Score=24.35 Aligned_cols=30 Identities=17% Similarity=0.263 Sum_probs=24.3
Q ss_pred CCHHHHHHHHHhhcCCChhhHHHHHHHHHH
Q 034494 24 MSKEECMEALSKHANIKPVITSTVWKELEK 53 (93)
Q Consensus 24 Msk~Evv~~L~~~a~I~P~fT~~VW~~Le~ 53 (93)
||++|+++.+++..++...-...|-..|.+
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 899999999999999988877766555443
No 9
>PF14420 Clr5: Clr5 domain
Probab=71.42 E-value=11 Score=22.82 Aligned_cols=36 Identities=22% Similarity=0.134 Sum_probs=28.5
Q ss_pred HHHHHHHHHHHHHH-HhhCCHHHHHHHHHhhcCCChh
Q 034494 7 SYIHLVHHLIEECL-VFNMSKEECMEALSKHANIKPV 42 (93)
Q Consensus 7 ~~I~~VQ~LIErCL-qlyMsk~Evv~~L~~~a~I~P~ 42 (93)
++-...+..|.+.- ...+|.+||++.|..++|..+.
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 5788999999999999998886
No 10
>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=65.89 E-value=15 Score=23.67 Aligned_cols=30 Identities=17% Similarity=0.261 Sum_probs=24.2
Q ss_pred CCHHHHHHHHHhh-cCCChhhHHHHHHHHHH
Q 034494 24 MSKEECMEALSKH-ANIKPVITSTVWKELEK 53 (93)
Q Consensus 24 Msk~Evv~~L~~~-a~I~P~fT~~VW~~Le~ 53 (93)
||++|+++.+.++ .++.+.-...|++.+-.
T Consensus 1 m~k~eli~~i~~~~~~~s~~~v~~vv~~~~~ 31 (94)
T TIGR00988 1 MTKSELIERIATQQSHLPAKDVEDAVKTMLE 31 (94)
T ss_pred CCHHHHHHHHHHHcCCCCHHHHHHHHHHHHH
Confidence 8999999999975 57888888888776544
No 11
>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=63.75 E-value=16 Score=23.88 Aligned_cols=30 Identities=13% Similarity=0.076 Sum_probs=24.6
Q ss_pred CCHHHHHHHHHhhcCCChhhHHHHHHHHHH
Q 034494 24 MSKEECMEALSKHANIKPVITSTVWKELEK 53 (93)
Q Consensus 24 Msk~Evv~~L~~~a~I~P~fT~~VW~~Le~ 53 (93)
||+.|+++.++++.++...-...|.+.+..
T Consensus 2 mtk~eli~~ia~~~~~s~~~v~~vv~~~~~ 31 (96)
T TIGR00987 2 LTKAEMSEYLFDELGLSKREAKELVELFFE 31 (96)
T ss_pred CCHHHHHHHHHHHhCcCHHHHHHHHHHHHH
Confidence 899999999999999988877777655443
No 12
>PRK10664 transcriptional regulator HU subunit beta; Provisional
Probab=60.55 E-value=20 Score=23.56 Aligned_cols=24 Identities=17% Similarity=0.335 Sum_probs=19.3
Q ss_pred CCHHHHHHHHHhhcCCChhhHHHH
Q 034494 24 MSKEECMEALSKHANIKPVITSTV 47 (93)
Q Consensus 24 Msk~Evv~~L~~~a~I~P~fT~~V 47 (93)
|||.|+++.|.+..++...-...+
T Consensus 1 MtK~eli~~ia~~~~~s~~~~~~~ 24 (90)
T PRK10664 1 MNKSQLIDKIAAGADISKAAAGRA 24 (90)
T ss_pred CCHHHHHHHHHHHhCCCHHHHHHH
Confidence 899999999999888877655544
No 13
>PRK00199 ihfB integration host factor subunit beta; Reviewed
Probab=60.16 E-value=23 Score=23.00 Aligned_cols=30 Identities=23% Similarity=0.307 Sum_probs=23.1
Q ss_pred CCHHHHHHHHHhh-cCCChhhHHHHHHHHHH
Q 034494 24 MSKEECMEALSKH-ANIKPVITSTVWKELEK 53 (93)
Q Consensus 24 Msk~Evv~~L~~~-a~I~P~fT~~VW~~Le~ 53 (93)
||+.|+++.+..+ .++...-...|++.+.+
T Consensus 1 mtk~eli~~ia~~~~~~s~~~~~~vv~~~~~ 31 (94)
T PRK00199 1 MTKSELIERLAARNPHLSAKDVENAVKEILE 31 (94)
T ss_pred CCHHHHHHHHHHHcCCCCHHHHHHHHHHHHH
Confidence 8999999999874 67888777777665543
No 14
>PRK00285 ihfA integration host factor subunit alpha; Reviewed
Probab=60.12 E-value=20 Score=23.42 Aligned_cols=31 Identities=13% Similarity=0.143 Sum_probs=25.7
Q ss_pred hCCHHHHHHHHHhhcCCChhhHHHHHHHHHH
Q 034494 23 NMSKEECMEALSKHANIKPVITSTVWKELEK 53 (93)
Q Consensus 23 yMsk~Evv~~L~~~a~I~P~fT~~VW~~Le~ 53 (93)
.||++|+++.+..+.++...-...|++.+.+
T Consensus 2 tmtk~el~~~ia~~~~~s~~~v~~vl~~~~~ 32 (99)
T PRK00285 2 TLTKADLAEALFEKVGLSKREAKELVELFFE 32 (99)
T ss_pred CcCHHHHHHHHHHHhCcCHHHHHHHHHHHHH
Confidence 4899999999999999988888777766544
No 15
>smart00139 MyTH4 Domain in Myosin and Kinesin Tails. Domain present twice in myosin-VIIa, and also present in 3 other myosins.
Probab=59.99 E-value=23 Score=25.16 Aligned_cols=52 Identities=23% Similarity=0.303 Sum_probs=40.0
Q ss_pred CCCc----hHHHHHHHHHHHHHHHHhhCCHHHHHHHHHhhcCCChh--hHHHHHHHHH
Q 034494 1 MDDS----SASYIHLVHHLIEECLVFNMSKEECMEALSKHANIKPV--ITSTVWKELE 52 (93)
Q Consensus 1 ~~~~----s~~~I~~VQ~LIErCLqlyMsk~Evv~~L~~~a~I~P~--fT~~VW~~Le 52 (93)
|||. +...++.+|++++.|+..--=+||+.-.|-+|-.=+|. -..-.|+-|-
T Consensus 33 mgd~~~~~~~~~~~l~~~i~~~~~~~~~LrDEiy~QLiKQtt~Np~~~s~~rgW~Ll~ 90 (144)
T smart00139 33 MGDLPLPKPDSHLDLVQFILQKGLAHPELRDEIYCQLIKQLTDNPSRQSEERGWELLY 90 (144)
T ss_pred hcCCCCCCcchHHHHHHHHHHHHhccHHHHHHHHHHHHHHHhCCCCchHHHHHHHHHH
Confidence 7882 35678999999999999888899998888887655554 4456787664
No 16
>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=59.30 E-value=7.8 Score=28.63 Aligned_cols=34 Identities=24% Similarity=0.369 Sum_probs=21.1
Q ss_pred HHHHhcHHHHHHHHhc-hhhhhhHHHHHHHHHHHH
Q 034494 50 ELEKENKEFFEAYARK-NAERATVMETRERIEKML 83 (93)
Q Consensus 50 ~Le~eNpeFF~aY~~~-~~e~~se~~~~~~iq~m~ 83 (93)
+|.++|.||...-.+. ++.-.+|++..+.+..|+
T Consensus 1 ~LTkkN~~y~~~l~~~L~~~~~~e~~~e~~L~eil 35 (206)
T PF06570_consen 1 KLTKKNQEYIFDLRKYLRSSGVSEEEIEELLEEIL 35 (206)
T ss_pred CCchHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHH
Confidence 4778999998766544 444445555555555444
No 17
>PRK14552 C/D box methylation guide ribonucleoprotein complex aNOP56 subunit; Provisional
Probab=58.65 E-value=18 Score=30.46 Aligned_cols=47 Identities=23% Similarity=0.273 Sum_probs=40.2
Q ss_pred CCCc-hHHHHHHHHHHHHHHHHhhCCHHHHHHHHHhhcC-CChhhHHHH
Q 034494 1 MDDS-SASYIHLVHHLIEECLVFNMSKEECMEALSKHAN-IKPVITSTV 47 (93)
Q Consensus 1 ~~~~-s~~~I~~VQ~LIErCLqlyMsk~Evv~~L~~~a~-I~P~fT~~V 47 (93)
||-. |..++..|++++++-+.++=.++++.++|...++ |.|.+|..|
T Consensus 222 ~G~~lse~dl~~I~~~a~~I~~L~e~R~~L~~yI~~~M~~iAPNLtaLV 270 (414)
T PRK14552 222 MGADLSEFDLEAIKKLANEILDLYKLREELEDYLETVMKEVAPNLTALV 270 (414)
T ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccHHHHHH
Confidence 4543 7789999999999999999999999999998765 489888876
No 18
>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=57.49 E-value=37 Score=20.18 Aligned_cols=32 Identities=25% Similarity=0.248 Sum_probs=20.5
Q ss_pred HHHHhhCCHHHHHHHHHhhcCCChh-hHHHHHH
Q 034494 18 ECLVFNMSKEECMEALSKHANIKPV-ITSTVWK 49 (93)
Q Consensus 18 rCLqlyMsk~Evv~~L~~~a~I~P~-fT~~VW~ 49 (93)
+++.--.|.+|+++.|.++++++|. ...-|..
T Consensus 24 ~~~~g~~t~~ei~~~l~~~y~~~~~~~~~dv~~ 56 (68)
T PF05402_consen 24 ELLDGPRTVEEIVDALAEEYDVDPEEAEEDVEE 56 (68)
T ss_dssp HH--SSS-HHHHHHHHHHHTT--HHHHHHHHHH
T ss_pred HHccCCCCHHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 3346678999999999999999998 4444433
No 19
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=54.40 E-value=27 Score=25.32 Aligned_cols=55 Identities=13% Similarity=0.047 Sum_probs=43.9
Q ss_pred CchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHhhcCCChhhHHHHHHHHHHhcHHH
Q 034494 3 DSSASYIHLVHHLIEECLVFNMSKEECMEALSKHANIKPVITSTVWKELEKENKEF 58 (93)
Q Consensus 3 ~~s~~~I~~VQ~LIErCLqlyMsk~Evv~~L~~~a~I~P~fT~~VW~~Le~eNpeF 58 (93)
.++.-+-..++-+.|.|=+.+.+..+++..|..++||.=+-. .||.-|.+.-=.|
T Consensus 60 rP~kl~~~q~~~l~e~~~~k~wTl~~~~~~l~~e~gv~y~~~-~v~~~l~~~Glsy 114 (138)
T COG3415 60 RPRKLSEEQLEILLERLREKDWTLKELVEELGLEFGVWYHAS-AVRRLLHELGLSY 114 (138)
T ss_pred CCcccCHHHHHHHHHHHhcccchHHHHHHHHhhhcCeEEeHH-HHHHHHHHcCCCc
Confidence 344445567888899999999999999999999999987655 8999998754333
No 20
>PRK10753 transcriptional regulator HU subunit alpha; Provisional
Probab=54.28 E-value=30 Score=22.62 Aligned_cols=25 Identities=12% Similarity=0.311 Sum_probs=18.9
Q ss_pred CCHHHHHHHHHhhcCCChhhHHHHH
Q 034494 24 MSKEECMEALSKHANIKPVITSTVW 48 (93)
Q Consensus 24 Msk~Evv~~L~~~a~I~P~fT~~VW 48 (93)
||+.|+++.|.++.++...-...|-
T Consensus 1 M~K~eli~~ia~~~~~s~~~~~~~v 25 (90)
T PRK10753 1 MNKTQLIDVIADKAELSKTQAKAAL 25 (90)
T ss_pred CCHHHHHHHHHHHhCCCHHHHHHHH
Confidence 8999999999988777665544443
No 21
>PF04340 DUF484: Protein of unknown function, DUF484; InterPro: IPR007435 This family consists of several proteins of uncharacterised function.; PDB: 3E98_B.
Probab=53.09 E-value=4.5 Score=30.08 Aligned_cols=10 Identities=30% Similarity=0.670 Sum_probs=0.0
Q ss_pred hcHHHHHHHH
Q 034494 54 ENKEFFEAYA 63 (93)
Q Consensus 54 eNpeFF~aY~ 63 (93)
+|||||..|-
T Consensus 17 ~~PdFf~~~~ 26 (225)
T PF04340_consen 17 QHPDFFERHP 26 (225)
T ss_dssp ----------
T ss_pred hCcHHHHhCH
Confidence 5788888774
No 22
>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=51.71 E-value=85 Score=22.31 Aligned_cols=55 Identities=22% Similarity=0.230 Sum_probs=45.8
Q ss_pred HHHHHHHHHHHhhCCHHHHHHHHHhhcCCCh--------hhHHHHHHHHHHhcHHHHHHHHhc
Q 034494 11 LVHHLIEECLVFNMSKEECMEALSKHANIKP--------VITSTVWKELEKENKEFFEAYARK 65 (93)
Q Consensus 11 ~VQ~LIErCLqlyMsk~Evv~~L~~~a~I~P--------~fT~~VW~~Le~eNpeFF~aY~~~ 65 (93)
-|+--|=+-|--|.++.||+++..+.+||+- .=|...=+.|-++-.+.|+....+
T Consensus 7 ~vK~FIVQ~LAcfdTPs~v~~aVk~eFgi~vsrQqve~yDPTK~aG~~Ls~k~~~lF~~TR~~ 69 (104)
T PF10045_consen 7 EVKAFIVQSLACFDTPSEVAEAVKEEFGIDVSRQQVESYDPTKRAGRDLSKKWVDLFEETRKR 69 (104)
T ss_pred HHHHHHHHHHHhhCCHHHHHHHHHHHhCCccCHHHHHHcCchHHHHHHHHHHHHHHHHHHHHH
Confidence 4677777888899999999999999998863 346777788889999999888766
No 23
>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=51.03 E-value=52 Score=21.09 Aligned_cols=52 Identities=23% Similarity=0.351 Sum_probs=34.4
Q ss_pred HHHHHHHHHHHHH-HHhhCCHHHHHHHHHhhcCCChhhHHHHHHHHHHhcHHHH
Q 034494 7 SYIHLVHHLIEEC-LVFNMSKEECMEALSKHANIKPVITSTVWKELEKENKEFF 59 (93)
Q Consensus 7 ~~I~~VQ~LIErC-LqlyMsk~Evv~~L~~~a~I~P~fT~~VW~~Le~eNpeFF 59 (93)
.+...|+.||++- =+-|+|-+|+.++|. ...+.|.--..|...|+..+=+..
T Consensus 4 ~~~~~i~~Li~~gK~~G~lT~~eI~~~L~-~~~~~~e~id~i~~~L~~~gI~Vv 56 (82)
T PF03979_consen 4 QYEEAIKKLIEKGKKKGYLTYDEINDALP-EDDLDPEQIDEIYDTLEDEGIEVV 56 (82)
T ss_dssp HHHHHHHHHHHHHHHHSS-BHHHHHHH-S--S---HHHHHHHHHHHHTT----B
T ss_pred hhHHHHHHHHHHHhhcCcCCHHHHHHHcC-ccCCCHHHHHHHHHHHHHCCCEEe
Confidence 3557788899865 478999999999999 567999988888888887664443
No 24
>PF03918 CcmH: Cytochrome C biogenesis protein; InterPro: IPR005616 Members of this family include NrfF, CcmH, CycL, Ccl2.; PDB: 2KW0_A 2HL7_A.
Probab=50.96 E-value=34 Score=24.82 Aligned_cols=37 Identities=24% Similarity=0.223 Sum_probs=28.0
Q ss_pred CCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHhhcC
Q 034494 2 DDSSASYIHLVHHLIEECLVFNMSKEECMEALSKHAN 38 (93)
Q Consensus 2 ~~~s~~~I~~VQ~LIErCLqlyMsk~Evv~~L~~~a~ 38 (93)
+||.+..-.-..+.|.+=|.-.+|++||++++-.++|
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 3555566667788899999999999999999999888
No 25
>PRK10963 hypothetical protein; Provisional
Probab=50.53 E-value=13 Score=28.03 Aligned_cols=22 Identities=23% Similarity=0.431 Sum_probs=15.8
Q ss_pred hCCHHHHHHHHHhhcCCChhhHHHHHHHHHHhcHHHHHHHH
Q 034494 23 NMSKEECMEALSKHANIKPVITSTVWKELEKENKEFFEAYA 63 (93)
Q Consensus 23 yMsk~Evv~~L~~~a~I~P~fT~~VW~~Le~eNpeFF~aY~ 63 (93)
.||.++|+.+|. +|||||..+-
T Consensus 2 ~l~~~~V~~yL~-------------------~~PdFf~~h~ 23 (223)
T PRK10963 2 ELDDRAVVDYLL-------------------QNPDFFIRNA 23 (223)
T ss_pred CCCHHHHHHHHH-------------------HCchHHhhCH
Confidence 367777777775 5788887763
No 26
>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=47.56 E-value=39 Score=24.04 Aligned_cols=31 Identities=16% Similarity=0.213 Sum_probs=27.9
Q ss_pred CCHHHHHHHHHhhcCCChhhHHHHHHHHHHh
Q 034494 24 MSKEECMEALSKHANIKPVITSTVWKELEKE 54 (93)
Q Consensus 24 Msk~Evv~~L~~~a~I~P~fT~~VW~~Le~e 54 (93)
||++|+++.++++.++.+.-...|+..|...
T Consensus 31 mt~~el~~~Ia~~s~~s~~dv~~vl~~l~~~ 61 (145)
T TIGR01201 31 IDFEEIAELIAEESSLSPGDVKGIIDRLAYV 61 (145)
T ss_pred cCHHHHHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 8999999999999999999999998887654
No 27
>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=47.37 E-value=29 Score=21.86 Aligned_cols=27 Identities=15% Similarity=0.339 Sum_probs=22.5
Q ss_pred HHHHHHhhcCCChhhHHHHHHHHHHhc
Q 034494 29 CMEALSKHANIKPVITSTVWKELEKEN 55 (93)
Q Consensus 29 vv~~L~~~a~I~P~fT~~VW~~Le~eN 55 (93)
.++.|.+..+|.|.+..-|-+.|++.+
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 467788889999999999999999864
No 28
>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=46.58 E-value=37 Score=22.75 Aligned_cols=25 Identities=16% Similarity=0.210 Sum_probs=19.6
Q ss_pred HHHHhhcCCChhhHHHHHHHHHHhc
Q 034494 31 EALSKHANIKPVITSTVWKELEKEN 55 (93)
Q Consensus 31 ~~L~~~a~I~P~fT~~VW~~Le~eN 55 (93)
..+..+.|++|.|...+|+.+-.+.
T Consensus 58 ~~~a~~~gl~p~~~e~i~~~i~~es 82 (94)
T TIGR01795 58 RRLAIDAGLDPEFAEKFLNFIVTEV 82 (94)
T ss_pred HHHHHHCCCCHHHHHHHHHHHHHHH
Confidence 3446678999999999999886653
No 29
>COG4359 Uncharacterized conserved protein [Function unknown]
Probab=46.41 E-value=23 Score=28.10 Aligned_cols=26 Identities=35% Similarity=0.359 Sum_probs=22.9
Q ss_pred hhCCHHHHHHHHHhhcCCChhhHHHH
Q 034494 22 FNMSKEECMEALSKHANIKPVITSTV 47 (93)
Q Consensus 22 lyMsk~Evv~~L~~~a~I~P~fT~~V 47 (93)
.+.|-+||.+.|.+.++|+|+|-..|
T Consensus 57 i~~s~~Eile~llk~i~Idp~fKef~ 82 (220)
T COG4359 57 IHSSLEEILEFLLKDIKIDPGFKEFV 82 (220)
T ss_pred cCCCHHHHHHHHHhhcccCccHHHHH
Confidence 46788999999999999999997765
No 30
>TIGR03147 cyt_nit_nrfF cytochrome c nitrite reductase, accessory protein NrfF.
Probab=46.13 E-value=44 Score=24.13 Aligned_cols=38 Identities=8% Similarity=0.035 Sum_probs=31.6
Q ss_pred CCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHhhcCC
Q 034494 2 DDSSASYIHLVHHLIEECLVFNMSKEECMEALSKHANI 39 (93)
Q Consensus 2 ~~~s~~~I~~VQ~LIErCLqlyMsk~Evv~~L~~~a~I 39 (93)
.||.+..-.-..+.|-+=+.--+|.+||++++-++.|-
T Consensus 52 adS~a~iA~dmR~~Vr~~i~~G~Sd~eI~~~~v~RYG~ 89 (126)
T TIGR03147 52 VESNSPIAYDLRHEVYSMVNEGKSNQQIIDFMTARFGD 89 (126)
T ss_pred hhcCCHHHHHHHHHHHHHHHcCCCHHHHHHHHHHhcCC
Confidence 35666666777888888899999999999999999883
No 31
>KOG3973 consensus Uncharacterized conserved glycine-rich protein [Function unknown]
Probab=44.76 E-value=35 Score=29.49 Aligned_cols=60 Identities=22% Similarity=0.429 Sum_probs=40.1
Q ss_pred HHHHHH-HHHHhhCCHH-------HHHHHHHh-----hcCCChhh----------HHHHHHHHHHhcHHHHHHHHhchhh
Q 034494 12 VHHLIE-ECLVFNMSKE-------ECMEALSK-----HANIKPVI----------TSTVWKELEKENKEFFEAYARKNAE 68 (93)
Q Consensus 12 VQ~LIE-rCLqlyMsk~-------Evv~~L~~-----~a~I~P~f----------T~~VW~~Le~eNpeFF~aY~~~~~e 68 (93)
|+.+|+ -|..|.|++- ...+++.. -+++.|.. +..-|.++|++|.+|=+.||.|++-
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 22233322 23565543 4678999999999999999999654
Q ss_pred hhh
Q 034494 69 RAT 71 (93)
Q Consensus 69 ~~s 71 (93)
-++
T Consensus 221 l~s 223 (465)
T KOG3973|consen 221 LNS 223 (465)
T ss_pred HHH
Confidence 433
No 32
>PLN02814 beta-glucosidase
Probab=44.58 E-value=16 Score=31.12 Aligned_cols=46 Identities=26% Similarity=0.322 Sum_probs=31.6
Q ss_pred hHHHHHHHHHHHHHHHHhhCCHHHHHHHHHhhcCCChhhHHHHHH---HHH--------HhcHHHHHHHHhc
Q 034494 5 SASYIHLVHHLIEECLVFNMSKEECMEALSKHANIKPVITSTVWK---ELE--------KENKEFFEAYARK 65 (93)
Q Consensus 5 s~~~I~~VQ~LIErCLqlyMsk~Evv~~L~~~a~I~P~fT~~VW~---~Le--------~eNpeFF~aY~~~ 65 (93)
..+-|+.=.+||..|+. +||+|.+|..=|. -|+ ++..++|..|-..
T Consensus 112 N~~Gl~fY~~lId~l~~---------------~GI~P~VTL~H~dlP~~L~~~yGGW~n~~~i~~F~~YA~~ 168 (504)
T PLN02814 112 NPKGLLFYKNLIKELRS---------------HGIEPHVTLYHYDLPQSLEDEYGGWINRKIIEDFTAFADV 168 (504)
T ss_pred CHHHHHHHHHHHHHHHH---------------cCCceEEEecCCCCCHHHHHhcCCcCChhHHHHHHHHHHH
Confidence 45556666777777765 4999999987662 333 4667888888654
No 33
>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=42.53 E-value=36 Score=21.68 Aligned_cols=45 Identities=13% Similarity=0.155 Sum_probs=30.0
Q ss_pred HHHHHHHHHHHHHH----HHhhCCHHHHHHHHHhhcCCChhhHHHHHHHHHHh
Q 034494 6 ASYIHLVHHLIEEC----LVFNMSKEECMEALSKHANIKPVITSTVWKELEKE 54 (93)
Q Consensus 6 ~~~I~~VQ~LIErC----LqlyMsk~Evv~~L~~~a~I~P~fT~~VW~~Le~e 54 (93)
..|+ .++|.|=.. -..|+++++|-..+. |+++..+.-||.-|+..
T Consensus 33 ~~Yl-~iRn~il~~w~~n~~~~lt~~~~~~~i~---~~d~~~~~ri~~FL~~~ 81 (86)
T PF04433_consen 33 EQYL-KIRNTILAEWRKNPNKYLTKTDARKLIK---GIDVNKIRRIYDFLERW 81 (86)
T ss_dssp HHHH-HHHHHHHHHHHHHTTS---HHHHHHHTT---SSSHHHHHHHHHHHHHT
T ss_pred HHHH-HHHHHHHHHHHHCCCCcccHHHHHHHcc---ccCHHHHHHHHHHHHHc
Confidence 3444 455555333 267899999977766 89999999999988763
No 34
>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=41.27 E-value=1e+02 Score=20.11 Aligned_cols=43 Identities=19% Similarity=0.186 Sum_probs=34.0
Q ss_pred hHHHHHHHHHHHHHHHHhhCCHHHHHHHHHhhcCCChhhHHHH
Q 034494 5 SASYIHLVHHLIEECLVFNMSKEECMEALSKHANIKPVITSTV 47 (93)
Q Consensus 5 s~~~I~~VQ~LIErCLqlyMsk~Evv~~L~~~a~I~P~fT~~V 47 (93)
|.++|..++.....=+...++.+|.++.|.+...=.|.+...|
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 5678888888888777788899999999988777788887766
No 35
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=41.25 E-value=49 Score=23.75 Aligned_cols=29 Identities=28% Similarity=0.310 Sum_probs=25.2
Q ss_pred HHHHHHHHHHHHHHHhhCCHHHHHHHHHh
Q 034494 7 SYIHLVHHLIEECLVFNMSKEECMEALSK 35 (93)
Q Consensus 7 ~~I~~VQ~LIErCLqlyMsk~Evv~~L~~ 35 (93)
.....++++|+.|..+.+|++|+.+.|.+
T Consensus 90 ~~~~~l~~~I~~~~~~G~s~eei~~~~~~ 118 (125)
T COG1725 90 LAEEELEEFIEEAKALGLSLEEILELLKE 118 (125)
T ss_pred HHHHHHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 34567899999999999999999998875
No 36
>PF14164 YqzH: YqzH-like protein
Probab=41.18 E-value=34 Score=22.37 Aligned_cols=14 Identities=29% Similarity=0.553 Sum_probs=12.3
Q ss_pred HHHHHHHHHHHHhh
Q 034494 10 HLVHHLIEECLVFN 23 (93)
Q Consensus 10 ~~VQ~LIErCLqly 23 (93)
.+++.+|-+||+.|
T Consensus 4 k~I~Kmi~~~l~QY 17 (64)
T PF14164_consen 4 KLIEKMIINCLRQY 17 (64)
T ss_pred HHHHHHHHHHHHHh
Confidence 56888999999999
No 37
>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=40.71 E-value=62 Score=18.46 Aligned_cols=27 Identities=19% Similarity=0.310 Sum_probs=20.3
Q ss_pred HHHHHHHHhhcCCChhhHHHHHHHHHH
Q 034494 27 EECMEALSKHANIKPVITSTVWKELEK 53 (93)
Q Consensus 27 ~Evv~~L~~~a~I~P~fT~~VW~~Le~ 53 (93)
.||.++|....+++|.+..-+-+.|..
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 38
>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=40.32 E-value=1e+02 Score=20.55 Aligned_cols=46 Identities=20% Similarity=0.260 Sum_probs=36.6
Q ss_pred HHHHHHHHHHHHHHhhCCHHHHHHHHHhhcCCChh--hHHHHHHHHHH
Q 034494 8 YIHLVHHLIEECLVFNMSKEECMEALSKHANIKPV--ITSTVWKELEK 53 (93)
Q Consensus 8 ~I~~VQ~LIErCLqlyMsk~Evv~~L~~~a~I~P~--fT~~VW~~Le~ 53 (93)
.++.+|++|..|+..--=++|+.-.|-+|-+=+|. ...-.|+-|--
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 46789999999999999999999999998776664 45678988753
No 39
>PRK05686 fliG flagellar motor switch protein G; Validated
Probab=40.04 E-value=1.7e+02 Score=23.26 Aligned_cols=63 Identities=17% Similarity=0.230 Sum_probs=44.7
Q ss_pred CCCchHHHHHHHHHHHHHHHHhhC-C------HHHHHHHHHhhcCCChhhHHHHHHHHHHhcHHHHHHHHhc
Q 034494 1 MDDSSASYIHLVHHLIEECLVFNM-S------KEECMEALSKHANIKPVITSTVWKELEKENKEFFEAYARK 65 (93)
Q Consensus 1 ~~~~s~~~I~~VQ~LIErCLqlyM-s------k~Evv~~L~~~a~I~P~fT~~VW~~Le~eNpeFF~aY~~~ 65 (93)
||..+.+-++.|-..+++||..-. + --+.+-.+.+ ++++.-...|...|++.+|++.+.=..+
T Consensus 171 l~~v~~~~~~~i~~~L~~~l~~~~~~~~~~~~g~~~~a~Iln--~~~~~~~~~il~~L~~~d~~~a~~Ir~~ 240 (339)
T PRK05686 171 LEGVSPEALKEVEEVLEKKLSSMANADRTKMGGVKTVAEILN--NLDRQTEKTILESLEEEDPELAEKIKDL 240 (339)
T ss_pred cCCCCHHHHHHHHHHHHHHHhhcccccccccCcHHHHHHHHh--cCCchHHHHHHHHHHhhCHHHHHHHHHH
Confidence 455678888889899999997522 1 1133333333 5677778899999999999999865444
No 40
>PLN02849 beta-glucosidase
Probab=39.27 E-value=20 Score=30.53 Aligned_cols=45 Identities=24% Similarity=0.315 Sum_probs=28.4
Q ss_pred HHHHHHHHHHHHHHHHhhCCHHHHHHHHHhhcCCChhhHHHHHH---HHHH--------hcHHHHHHHHhc
Q 034494 6 ASYIHLVHHLIEECLVFNMSKEECMEALSKHANIKPVITSTVWK---ELEK--------ENKEFFEAYARK 65 (93)
Q Consensus 6 ~~~I~~VQ~LIErCLqlyMsk~Evv~~L~~~a~I~P~fT~~VW~---~Le~--------eNpeFF~aY~~~ 65 (93)
.+-|+.=.++|..|+. +||+|.+|..=|. .|++ +..++|..|-..
T Consensus 115 ~~gl~fY~~lid~l~~---------------~GI~P~VTL~H~dlP~~L~~~yGGW~nr~~v~~F~~YA~~ 170 (503)
T PLN02849 115 PKGLQFYKNFIQELVK---------------HGIEPHVTLFHYDHPQYLEDDYGGWINRRIIKDFTAYADV 170 (503)
T ss_pred HHHHHHHHHHHHHHHH---------------cCCeEEEeecCCCCcHHHHHhcCCcCCchHHHHHHHHHHH
Confidence 4445555556655554 4999999986552 2433 456788888554
No 41
>PLN02998 beta-glucosidase
Probab=38.12 E-value=22 Score=30.28 Aligned_cols=45 Identities=27% Similarity=0.396 Sum_probs=29.1
Q ss_pred HHHHHHHHHHHHHHHHhhCCHHHHHHHHHhhcCCChhhHHHHHH---H--------HHHhcHHHHHHHHhc
Q 034494 6 ASYIHLVHHLIEECLVFNMSKEECMEALSKHANIKPVITSTVWK---E--------LEKENKEFFEAYARK 65 (93)
Q Consensus 6 ~~~I~~VQ~LIErCLqlyMsk~Evv~~L~~~a~I~P~fT~~VW~---~--------Le~eNpeFF~aY~~~ 65 (93)
.+-|+.=.++|..|+. .||+|.+|..=|. - |-++..++|..|-..
T Consensus 118 ~~gl~~Y~~lid~L~~---------------~GIeP~VTL~H~dlP~~L~~~yGGW~n~~~v~~F~~YA~~ 173 (497)
T PLN02998 118 PKGLQYYNNLIDELIT---------------HGIQPHVTLHHFDLPQALEDEYGGWLSQEIVRDFTAYADT 173 (497)
T ss_pred HHHHHHHHHHHHHHHH---------------cCCceEEEecCCCCCHHHHHhhCCcCCchHHHHHHHHHHH
Confidence 3445555566665554 4999999986652 2 334667888888554
No 42
>PF14769 CLAMP: Flagellar C1a complex subunit C1a-32
Probab=37.98 E-value=1.2e+02 Score=20.04 Aligned_cols=56 Identities=14% Similarity=0.358 Sum_probs=37.9
Q ss_pred HHHHHHHHHHHHHHHhhCCHHHHHHHHHhh---cCCC------hhhHHHHHHHHHH-hcHHHHHHH
Q 034494 7 SYIHLVHHLIEECLVFNMSKEECMEALSKH---ANIK------PVITSTVWKELEK-ENKEFFEAY 62 (93)
Q Consensus 7 ~~I~~VQ~LIErCLqlyMsk~Evv~~L~~~---a~I~------P~fT~~VW~~Le~-eNpeFF~aY 62 (93)
.-...++.+.+.|+...||.+++++.+.+- .++. |.|+..-.+.+-+ =.-.||+-|
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 345678889999999999999999988773 3444 3377666555543 233455544
No 43
>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=37.65 E-value=63 Score=22.17 Aligned_cols=38 Identities=21% Similarity=0.322 Sum_probs=33.7
Q ss_pred HHHHHHHhhcCCChhhHHHHHHHHHHhcHHHHHHHHhc
Q 034494 28 ECMEALSKHANIKPVITSTVWKELEKENKEFFEAYARK 65 (93)
Q Consensus 28 Evv~~L~~~a~I~P~fT~~VW~~Le~eNpeFF~aY~~~ 65 (93)
|....|.+.|+++|.+-..+=+.|.-++-.=|..|.+.
T Consensus 4 ql~~FLt~dakvD~~vv~ymTk~L~lesvsDFAn~WTs 41 (82)
T PF05295_consen 4 QLAQFLTNDAKVDPKVVAYMTKQLQLESVSDFANYWTS 41 (82)
T ss_pred HHHHHHhcccccCHHHHHHHHhhcchhhHHHHHhhhhH
Confidence 67788999999999999999999999998888777665
No 44
>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=37.13 E-value=81 Score=19.51 Aligned_cols=29 Identities=14% Similarity=0.210 Sum_probs=22.6
Q ss_pred CHHHHHHHHHhhcCCChhhHHHHHHHHHH
Q 034494 25 SKEECMEALSKHANIKPVITSTVWKELEK 53 (93)
Q Consensus 25 sk~Evv~~L~~~a~I~P~fT~~VW~~Le~ 53 (93)
|++|+++.|+...++.+.-...|-..|..
T Consensus 1 ~K~~l~~~ia~~~~~~~~~v~~vl~~~~~ 29 (87)
T cd00591 1 TKSELIEAIAEKTGLSKKDAEAAVDAFLD 29 (87)
T ss_pred CHHHHHHHHHHHhCcCHHHHHHHHHHHHH
Confidence 68899999999988888877777555543
No 45
>PRK10144 formate-dependent nitrite reductase complex subunit NrfF; Provisional
Probab=36.89 E-value=77 Score=22.93 Aligned_cols=46 Identities=17% Similarity=0.216 Sum_probs=35.4
Q ss_pred CchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHhhcCC----Chh---hHHHHH
Q 034494 3 DSSASYIHLVHHLIEECLVFNMSKEECMEALSKHANI----KPV---ITSTVW 48 (93)
Q Consensus 3 ~~s~~~I~~VQ~LIErCLqlyMsk~Evv~~L~~~a~I----~P~---fT~~VW 48 (93)
||.+....-..+.|-+=+.-.+|++||+++|-.+.|= +|- .|..+|
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 5656666667788888899999999999999998883 444 355555
No 46
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=36.78 E-value=62 Score=17.88 Aligned_cols=27 Identities=15% Similarity=0.201 Sum_probs=21.1
Q ss_pred HHHHHHhhcCCChhhHHHHHHHHHHhc
Q 034494 29 CMEALSKHANIKPVITSTVWKELEKEN 55 (93)
Q Consensus 29 vv~~L~~~a~I~P~fT~~VW~~Le~eN 55 (93)
.+..|.++.+|.+..-.-..+.|++++
T Consensus 22 s~~~la~~~~vs~~tv~~~l~~L~~~g 48 (60)
T smart00345 22 SERELAAQLGVSRTTVREALSRLEAEG 48 (60)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCC
Confidence 367788888999988888888887754
No 47
>PF00938 Lipoprotein_3: Lipoprotein This Pfam family is a subset of the Prosite family.; InterPro: IPR001595 This family of lipoproteins is Mycoplasma specific, and includes a variety of hypothetical proteins []. They all have a prokaryotic membrane lipoprotein lipid attachment site which is probable acts as a membrane anchor.
Probab=35.86 E-value=1.4e+02 Score=20.56 Aligned_cols=56 Identities=14% Similarity=0.318 Sum_probs=42.1
Q ss_pred CHHHHHHHHHhhcCCChhhHHHHHHHHHHhcHHHHHHHHhc-hhhhhhHHHHHHHHHHHH-hcccccc
Q 034494 25 SKEECMEALSKHANIKPVITSTVWKELEKENKEFFEAYARK-NAERATVMETRERIEKML-ANSTTIR 90 (93)
Q Consensus 25 sk~Evv~~L~~~a~I~P~fT~~VW~~Le~eNpeFF~aY~~~-~~e~~se~~~~~~iq~m~-s~~~~~~ 90 (93)
.|..+|..|.+-++++|.=|--| -|.|+... -+.+|-+...++|+-+-+ |++++.+
T Consensus 27 ~KknlItsLKksYe~np~~Tt~~----------LL~aWK~Sl~d~kile~~~dsrF~kafgs~~~k~d 84 (87)
T PF00938_consen 27 GKKNLITSLKKSYEVNPKKTTNL----------LLDAWKQSLEDQKILEKDLDSRFAKAFGSGKSKED 84 (87)
T ss_pred hHHHHHHHHHHHhccChHHHHHH----------HHHHHHHHHHHhhhccccchhHHHHHHcCCCCccc
Confidence 39999999999999999877755 36677655 555777777778877766 5666554
No 48
>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=35.47 E-value=44 Score=20.95 Aligned_cols=33 Identities=12% Similarity=0.307 Sum_probs=24.6
Q ss_pred HHHhhcCCChhhHHHHHHHHHHhcHHHHHHHHh
Q 034494 32 ALSKHANIKPVITSTVWKELEKENKEFFEAYAR 64 (93)
Q Consensus 32 ~L~~~a~I~P~fT~~VW~~Le~eNpeFF~aY~~ 64 (93)
.|.....=+|..-..|.+.|...||+.++.-..
T Consensus 12 ~lR~~vq~NP~lL~~lLqql~~~nP~l~q~I~~ 44 (59)
T PF09280_consen 12 QLRQLVQQNPQLLPPLLQQLGQSNPQLLQLIQQ 44 (59)
T ss_dssp HHHHHHHC-GGGHHHHHHHHHCCSHHHHHHHHH
T ss_pred HHHHHHHHCHHHHHHHHHHHhccCHHHHHHHHH
Confidence 344444457999999999999999999987543
No 49
>COG0776 HimA Bacterial nucleoid DNA-binding protein [DNA replication, recombination, and repair]
Probab=35.13 E-value=53 Score=22.48 Aligned_cols=18 Identities=28% Similarity=0.551 Sum_probs=16.3
Q ss_pred CCHHHHHHHHHhhcCCCh
Q 034494 24 MSKEECMEALSKHANIKP 41 (93)
Q Consensus 24 Msk~Evv~~L~~~a~I~P 41 (93)
|||.|+++.|.+++++..
T Consensus 2 mtKseli~~ia~~~~l~k 19 (94)
T COG0776 2 MTKSELIDAIAEKAGLSK 19 (94)
T ss_pred CCHHHHHHHHHHHcCCCH
Confidence 899999999999998665
No 50
>PF08006 DUF1700: Protein of unknown function (DUF1700); InterPro: IPR012963 This family contains many hypothetical bacterial proteins and two putative membrane proteins (Q6GFD0 from SWISSPROT and Q6G806 from SWISSPROT).
Probab=34.45 E-value=94 Score=22.18 Aligned_cols=34 Identities=29% Similarity=0.415 Sum_probs=20.9
Q ss_pred CCHHHHHHHHHhhcCCChhhHHHHHHHHHHhcHHHHHHHHh
Q 034494 24 MSKEECMEALSKHANIKPVITSTVWKELEKENKEFFEAYAR 64 (93)
Q Consensus 24 Msk~Evv~~L~~~a~I~P~fT~~VW~~Le~eNpeFF~aY~~ 64 (93)
|||+|-++.|.++.+-=|.=. .++.=+||+.|..
T Consensus 1 M~k~efL~~L~~~L~~lp~~e-------~~e~l~~Y~e~f~ 34 (181)
T PF08006_consen 1 MNKNEFLNELEKYLKKLPEEE-------REEILEYYEEYFD 34 (181)
T ss_pred CCHHHHHHHHHHHHHcCCHHH-------HHHHHHHHHHHHH
Confidence 889999999988765323211 1344556666644
No 51
>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=33.76 E-value=1.6e+02 Score=24.18 Aligned_cols=62 Identities=6% Similarity=0.055 Sum_probs=48.7
Q ss_pred CchHHHHHHHHHHHHHHHHh---------hCCHHHHHHHHHhhcCCChhhHHHHHHHHHHhcHHHHHHHHhc
Q 034494 3 DSSASYIHLVHHLIEECLVF---------NMSKEECMEALSKHANIKPVITSTVWKELEKENKEFFEAYARK 65 (93)
Q Consensus 3 ~~s~~~I~~VQ~LIErCLql---------yMsk~Evv~~L~~~a~I~P~fT~~VW~~Le~eNpeFF~aY~~~ 65 (93)
+.+...+-+.+..+-||+.+ -||.+|+++.|.++.+..+.....-|...-. +|..+-+|+.-
T Consensus 432 ~~p~~~lg~l~~~l~ra~r~vvD~glH~~~wt~e~a~~~l~~~~~~~~~~a~~ev~ry~~-~Pgq~~sY~~G 502 (549)
T PF05960_consen 432 DDPLDRLGQLNDELWRAARLVVDTGLHYGGWTREQAIDYLVENTGFSEEEAESEVDRYIS-SPGQALSYKVG 502 (549)
T ss_dssp CSHHHHHHHHHHHHHHHHHHHHHHHHHCCB--HHHHHHHHHHHS-S-HHHHHHHHHHHHH-STTGGGHHHHH
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCHHHHHHHHHHhcCCChHHHHHHHHHHHh-CcHHHHHHHHH
Confidence 45677788888888888875 5899999999999999999888888877766 99999999765
No 52
>PF08004 DUF1699: Protein of unknown function (DUF1699); InterPro: IPR012546 This family contains many archaeal proteins which have very conserved sequences.
Probab=33.35 E-value=1.1e+02 Score=22.68 Aligned_cols=36 Identities=25% Similarity=0.301 Sum_probs=28.5
Q ss_pred HHHHHHHHhhCCHHHHHHHHHhhcCCChhhHHHHHH
Q 034494 14 HLIEECLVFNMSKEECMEALSKHANIKPVITSTVWK 49 (93)
Q Consensus 14 ~LIErCLqlyMsk~Evv~~L~~~a~I~P~fT~~VW~ 49 (93)
+-|+.-..-.+|.+|+++.+++..++.|.|-..+.+
T Consensus 95 ~~I~el~~eG~s~eei~~ki~~e~kl~pd~i~yi~~ 130 (131)
T PF08004_consen 95 ERIKELKSEGKSEEEIAEKISRETKLSPDMIKYILK 130 (131)
T ss_pred HHHHHHHHcCCCHHHHHHHHHHhhcCCHHHHHHHhc
Confidence 334444566899999999999999999999877643
No 53
>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=33.02 E-value=12 Score=30.77 Aligned_cols=46 Identities=30% Similarity=0.569 Sum_probs=28.6
Q ss_pred hHHHHHHHHHHHHHHHHhhCCHHHHHHHHHhhcCCChhhHHHH-----HHH-----HHHhcHHHHHHHHhc
Q 034494 5 SASYIHLVHHLIEECLVFNMSKEECMEALSKHANIKPVITSTV-----WKE-----LEKENKEFFEAYARK 65 (93)
Q Consensus 5 s~~~I~~VQ~LIErCLqlyMsk~Evv~~L~~~a~I~P~fT~~V-----W~~-----Le~eNpeFF~aY~~~ 65 (93)
..+-++.=.++|+.|+. +||+|.+|..= |=. +-++++++|..|-..
T Consensus 94 n~~~~~~Y~~~i~~l~~---------------~gi~P~vtL~H~~~P~~l~~~ggw~~~~~~~~F~~Ya~~ 149 (455)
T PF00232_consen 94 NEEGLDFYRDLIDELLE---------------NGIEPIVTLYHFDLPLWLEDYGGWLNRETVDWFARYAEF 149 (455)
T ss_dssp -HHHHHHHHHHHHHHHH---------------TT-EEEEEEESS--BHHHHHHTGGGSTHHHHHHHHHHHH
T ss_pred CHhHhhhhHHHHHHHHh---------------hccceeeeeeecccccceeecccccCHHHHHHHHHHHHH
Confidence 44555556666666554 49999887643 332 335788999999665
No 54
>PF12685 SpoIIIAH: SpoIIIAH-like protein; InterPro: IPR024232 Stage III sporulation protein AH (SpoIIIAH) is a protein that is involved in forespore engulfment. It forms a channel with SpoIIIAH that is open on the forespore end and closed (or gated) on the mother cell end. This allows sigma-E-directed gene expression in the mother-cell compartment of the sporangium to trigger the activation of sigma-G forespore-specific gene expression by a pathway of intercellular signaling. This family of proteins is found in bacteria, archaea and eukaryotes and so must have a wider function than in sporulation. Proteins in this family are typically between 174 and 223 amino acids in length.; PDB: 3UZ0_A 3TUF_A.
Probab=32.90 E-value=40 Score=24.83 Aligned_cols=33 Identities=9% Similarity=0.324 Sum_probs=21.7
Q ss_pred hcHHHHHHHHhchhhhhhHHHHHHHHHHHHhcccc
Q 034494 54 ENKEFFEAYARKNAERATVMETRERIEKMLANSTT 88 (93)
Q Consensus 54 eNpeFF~aY~~~~~e~~se~~~~~~iq~m~s~~~~ 88 (93)
...+||..|...|...-+ +..+.++.++.+...
T Consensus 83 ~~~~~f~~~rl~Re~~r~--~~~e~L~~ii~~~~~ 115 (196)
T PF12685_consen 83 SGSDYFAEARLEREQSRS--KQIETLKEIINNENA 115 (196)
T ss_dssp ----HHHHHHHHHHHHHH--HHHHHHHHHHT-TTS
T ss_pred chHHHHHHHHHHHHHHHH--HHHHHHHHHHhCCCC
Confidence 445799999888777666 667788888876543
No 55
>smart00511 ORANGE Orange domain. This domain confers specificity among members of the Hairy/E(SPL) family.
Probab=32.73 E-value=91 Score=17.76 Aligned_cols=27 Identities=19% Similarity=0.292 Sum_probs=22.9
Q ss_pred HHHHHHHHhhcCCChhhHHHHHHHHHH
Q 034494 27 EECMEALSKHANIKPVITSTVWKELEK 53 (93)
Q Consensus 27 ~Evv~~L~~~a~I~P~fT~~VW~~Le~ 53 (93)
.||++.|...-+++|.+...+-..|..
T Consensus 12 ~Ev~~fLs~~~~~~~~~~~~Ll~HL~~ 38 (45)
T smart00511 12 NEVSRFLSQLPGTDPDVRARLLSHLQT 38 (45)
T ss_pred HHHHHHHhcCCCCChHHHHHHHHHHHH
Confidence 589999998888999988888888764
No 56
>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=32.56 E-value=1.5e+02 Score=19.69 Aligned_cols=41 Identities=12% Similarity=0.064 Sum_probs=31.1
Q ss_pred CHHHHHHHHHhhcCCChhhHHHHHHHHHHhcHHHHHHHHhc
Q 034494 25 SKEECMEALSKHANIKPVITSTVWKELEKENKEFFEAYARK 65 (93)
Q Consensus 25 sk~Evv~~L~~~a~I~P~fT~~VW~~Le~eNpeFF~aY~~~ 65 (93)
+.+.+++-+.++.++++.-...-|..-.+....||+.|+..
T Consensus 101 ~~~~r~~R~~~R~~~s~~~a~~~~~~~d~~~~~~~~~~~~~ 141 (171)
T TIGR02173 101 PLEVRARRIAKREGKSLTVARSETIEREESEKRRYLKFYGI 141 (171)
T ss_pred CHHHHHHHHHHccCCCHHHHHHHHHHHHHHHHHHHHHHhCC
Confidence 55667777777778888777777777777888888888765
No 57
>TIGR03356 BGL beta-galactosidase.
Probab=32.06 E-value=43 Score=27.61 Aligned_cols=37 Identities=32% Similarity=0.644 Sum_probs=22.7
Q ss_pred HHHHHHHhhcCCChhhHHHHHH---HHH-------HhcHHHHHHHHhc
Q 034494 28 ECMEALSKHANIKPVITSTVWK---ELE-------KENKEFFEAYARK 65 (93)
Q Consensus 28 Evv~~L~~~a~I~P~fT~~VW~---~Le-------~eNpeFF~aY~~~ 65 (93)
++++.|.+ .||+|.+|..=|. .|. .+..+.|..|-..
T Consensus 98 ~~i~~l~~-~gi~pivtL~Hfd~P~~l~~~gGw~~~~~~~~f~~ya~~ 144 (427)
T TIGR03356 98 RLVDELLE-AGIEPFVTLYHWDLPQALEDRGGWLNRDTAEWFAEYAAV 144 (427)
T ss_pred HHHHHHHH-cCCeeEEeeccCCccHHHHhcCCCCChHHHHHHHHHHHH
Confidence 33444443 4999998874443 333 4566888888655
No 58
>PRK07194 fliG flagellar motor switch protein G; Reviewed
Probab=31.86 E-value=2.5e+02 Score=22.53 Aligned_cols=58 Identities=16% Similarity=0.244 Sum_probs=40.9
Q ss_pred CCCchHHHHHHHHHHHHHHHHhhCC-------HHHHHHHHHhhcCCChhhHHHHHHHHHHhcHHHHHH
Q 034494 1 MDDSSASYIHLVHHLIEECLVFNMS-------KEECMEALSKHANIKPVITSTVWKELEKENKEFFEA 61 (93)
Q Consensus 1 ~~~~s~~~I~~VQ~LIErCLqlyMs-------k~Evv~~L~~~a~I~P~fT~~VW~~Le~eNpeFF~a 61 (93)
||.-|.+.+..|-..+++|+..+.+ -.+.+..+.++.. .. - ..+|..|++.+|++...
T Consensus 166 l~~Vs~e~~~~V~e~l~~~~~~~~~~~~~~~~G~~~aa~ILn~l~-~~-~-~~il~~L~~~dp~~a~~ 230 (334)
T PRK07194 166 LDDVDRDVVDELDELIERCLAVLSEQSHTKVIGVKQAADIINRFP-GD-R-QQLMEMLKEHDEEVVNE 230 (334)
T ss_pred cCCCCHHHHHHHHHHHHHHHHhhhhcccccCCCHHHHHHHHHhCc-hh-H-HHHHHHHHhhCHHHHHH
Confidence 3455778888888888999876432 2345556655544 22 2 58999999999999877
No 59
>smart00760 Bac_DnaA_C Bacterial dnaA protein helix-turn-helix domain. Could be involved in DNA-binding.
Probab=31.66 E-value=49 Score=19.79 Aligned_cols=19 Identities=32% Similarity=0.391 Sum_probs=15.3
Q ss_pred CHHHHHHHHHhhcCCChhh
Q 034494 25 SKEECMEALSKHANIKPVI 43 (93)
Q Consensus 25 sk~Evv~~L~~~a~I~P~f 43 (93)
|.+++++...+.+||+|.=
T Consensus 1 ~~~~I~~~Va~~~~i~~~~ 19 (60)
T smart00760 1 TIEEIIEAVAEYFGVKPED 19 (60)
T ss_pred CHHHHHHHHHHHhCCCHHH
Confidence 4678889999999998753
No 60
>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=31.54 E-value=2.8e+02 Score=22.36 Aligned_cols=62 Identities=16% Similarity=0.146 Sum_probs=42.9
Q ss_pred CCchHHHHHHHHHHHHHHHHhhCCH------HHHHHHHHhhcCCChhhHHHHHHHHHHhcHHHHHHHHhc
Q 034494 2 DDSSASYIHLVHHLIEECLVFNMSK------EECMEALSKHANIKPVITSTVWKELEKENKEFFEAYARK 65 (93)
Q Consensus 2 ~~~s~~~I~~VQ~LIErCLqlyMsk------~Evv~~L~~~a~I~P~fT~~VW~~Le~eNpeFF~aY~~~ 65 (93)
|..|.+.+..|-..+++|+..+-+. -+.+..+.+ ++++.-...|...|++.+|++...=..+
T Consensus 170 ~~vs~~~i~~ie~~L~~~~~~~~~~~~~~gG~~~~a~ILN--~~~~~~~~~il~~L~~~dp~la~~Ir~~ 237 (338)
T TIGR00207 170 GRTSPEVVAEVERVLEGKLDSLNSDYTKMGGVRAVAEIIN--LMDRKTEKTIITSLEEFDPELAEEIKKE 237 (338)
T ss_pred CCCCHHHHHHHHHHHHHHHHhhccccccCChHHHHHHHHH--hCCchHHHHHHHHHHHhCHHHHHHHHHH
Confidence 4457788888888999998865531 123333333 4566666699999999999998765444
No 61
>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=31.37 E-value=56 Score=21.70 Aligned_cols=31 Identities=19% Similarity=0.170 Sum_probs=26.8
Q ss_pred CCHHHHHHHHHhhcCCChhhHHHHHHHHHHh
Q 034494 24 MSKEECMEALSKHANIKPVITSTVWKELEKE 54 (93)
Q Consensus 24 Msk~Evv~~L~~~a~I~P~fT~~VW~~Le~e 54 (93)
++-.||++.|.+..++.|.-+.++.+.|.+.
T Consensus 18 ~t~~eI~~~l~~~~~~~~sTv~t~L~rL~~K 48 (115)
T PF03965_consen 18 ATVREIHEALPEERSWAYSTVQTLLNRLVEK 48 (115)
T ss_dssp EEHHHHHHHHCTTSS--HHHHHHHHHHHHHT
T ss_pred CCHHHHHHHHHhccccchhHHHHHHHHHHhC
Confidence 7889999999998899999999999999983
No 62
>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=30.76 E-value=55 Score=21.22 Aligned_cols=18 Identities=33% Similarity=0.350 Sum_probs=12.6
Q ss_pred CCHHHHHHHHHhhcCCCh
Q 034494 24 MSKEECMEALSKHANIKP 41 (93)
Q Consensus 24 Msk~Evv~~L~~~a~I~P 41 (93)
|+++|+++.|..-...=|
T Consensus 1 Mtk~E~~~ll~~I~~aYP 18 (71)
T PF11417_consen 1 MTKEETAKLLKLIKAAYP 18 (71)
T ss_dssp --HHHHHHHHHHHHHHST
T ss_pred CCHHHHHHHHHHHHHHCC
Confidence 899999999987655555
No 63
>PRK09239 chorismate mutase; Provisional
Probab=30.32 E-value=93 Score=21.22 Aligned_cols=19 Identities=21% Similarity=0.303 Sum_probs=10.3
Q ss_pred HhhcCCChhhHHHHHHHHH
Q 034494 34 SKHANIKPVITSTVWKELE 52 (93)
Q Consensus 34 ~~~a~I~P~fT~~VW~~Le 52 (93)
....|++|.|...+|+.+-
T Consensus 68 a~~~gl~p~~~~~i~~~ii 86 (104)
T PRK09239 68 AKDANLDPDFAEKFLNFII 86 (104)
T ss_pred HHHCCCCHHHHHHHHHHHH
Confidence 3445666666655555443
No 64
>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=30.28 E-value=73 Score=19.41 Aligned_cols=16 Identities=13% Similarity=0.561 Sum_probs=7.4
Q ss_pred hcCCChhhHHHHHHHH
Q 034494 36 HANIKPVITSTVWKEL 51 (93)
Q Consensus 36 ~a~I~P~fT~~VW~~L 51 (93)
..+++|.+...||+.+
T Consensus 55 ~~~l~~~~~~~if~~i 70 (79)
T smart00830 55 GPGLDPELVERIFREI 70 (79)
T ss_pred cCCcCHHHHHHHHHHH
Confidence 3344444444444444
No 65
>PRK14137 recX recombination regulator RecX; Provisional
Probab=30.24 E-value=1.6e+02 Score=22.23 Aligned_cols=45 Identities=11% Similarity=0.156 Sum_probs=39.5
Q ss_pred HHHHHHHHHHHHh----hCCHHHHHHHHHhhcCCChhhHHHHHHHHHHhc
Q 034494 10 HLVHHLIEECLVF----NMSKEECMEALSKHANIKPVITSTVWKELEKEN 55 (93)
Q Consensus 10 ~~VQ~LIErCLql----yMsk~Evv~~L~~~a~I~P~fT~~VW~~Le~eN 55 (93)
..-+.+...||.+ -.|..|+-+-|.++ +++|.+-..|-..|.+.|
T Consensus 37 e~~~~~~~~Al~~Ls~R~rS~~ELr~KL~~k-g~~~e~Ie~vI~rL~e~g 85 (195)
T PRK14137 37 EAREALLAYAFRALAARAMTAAELRAKLERR-SEDEALVTEVLERVQELG 85 (195)
T ss_pred HHHHHHHHHHHHHHhcchhhHHHHHHHHHhc-CCCHHHHHHHHHHHHHcC
Confidence 5567888899988 88999999999986 999999999999999954
No 66
>KOG2211 consensus Predicted Golgi transport complex 1 protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=30.10 E-value=1.7e+02 Score=27.25 Aligned_cols=19 Identities=32% Similarity=0.504 Sum_probs=16.6
Q ss_pred CCChhhHHHHHHHHHHhcH
Q 034494 38 NIKPVITSTVWKELEKENK 56 (93)
Q Consensus 38 ~I~P~fT~~VW~~Le~eNp 56 (93)
+++|.++..+|++|++.=.
T Consensus 361 ~gd~cI~~rfw~~l~qal~ 379 (797)
T KOG2211|consen 361 NGDKCIPERFWKKLEQALH 379 (797)
T ss_pred ccchhHHHHHHHHHHHHHH
Confidence 8999999999999998533
No 67
>PRK08091 ribulose-phosphate 3-epimerase; Validated
Probab=29.93 E-value=32 Score=26.68 Aligned_cols=34 Identities=21% Similarity=0.317 Sum_probs=26.5
Q ss_pred CCHHHHHHHHHhhcCCChhhHHHHHHHHHHhcHHH
Q 034494 24 MSKEECMEALSKHANIKPVITSTVWKELEKENKEF 58 (93)
Q Consensus 24 Msk~Evv~~L~~~a~I~P~fT~~VW~~Le~eNpeF 58 (93)
||+.+||..|. +.-|.|++-..=|-+|+++=...
T Consensus 1 ~~~~~~~~~~~-~~~I~pSil~ad~~~l~~el~~l 34 (228)
T PRK08091 1 MSKLSLIQQLK-QQPISVGILASNWLKFNETLTTL 34 (228)
T ss_pred CCHHHHHHHhc-CCeEEeehhhcCHHHHHHHHHHH
Confidence 89999998876 57999999887777777654443
No 68
>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=28.94 E-value=69 Score=19.56 Aligned_cols=24 Identities=17% Similarity=0.372 Sum_probs=17.8
Q ss_pred HHHHHhhcCCChhhHHHHHHHHHH
Q 034494 30 MEALSKHANIKPVITSTVWKELEK 53 (93)
Q Consensus 30 v~~L~~~a~I~P~fT~~VW~~Le~ 53 (93)
+..|+.+++++|..-..+...|++
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 356788999999999988888875
No 69
>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=28.83 E-value=62 Score=22.97 Aligned_cols=25 Identities=20% Similarity=0.418 Sum_probs=18.0
Q ss_pred HHHHHHHHHHHHhh----CCHHHHHHHHH
Q 034494 10 HLVHHLIEECLVFN----MSKEECMEALS 34 (93)
Q Consensus 10 ~~VQ~LIErCLqly----Msk~Evv~~L~ 34 (93)
..++++|.+||+.. .|-.|++..|.
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 70
>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=28.74 E-value=76 Score=21.72 Aligned_cols=27 Identities=15% Similarity=0.276 Sum_probs=23.1
Q ss_pred HHHHHHhhcCCChhhHHHHHHHHHHhc
Q 034494 29 CMEALSKHANIKPVITSTVWKELEKEN 55 (93)
Q Consensus 29 vv~~L~~~a~I~P~fT~~VW~~Le~eN 55 (93)
-++.|+++.+|.|.+..-|.++|.+.+
T Consensus 27 s~~~ia~~~~ip~~~l~kil~~L~~~g 53 (135)
T TIGR02010 27 TLADISERQGISLSYLEQLFAKLRKAG 53 (135)
T ss_pred cHHHHHHHHCcCHHHHHHHHHHHHHCC
Confidence 456778889999999999999999854
No 71
>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=28.67 E-value=79 Score=20.17 Aligned_cols=20 Identities=5% Similarity=0.325 Sum_probs=15.7
Q ss_pred HhhcCCChhhHHHHHHHHHH
Q 034494 34 SKHANIKPVITSTVWKELEK 53 (93)
Q Consensus 34 ~~~a~I~P~fT~~VW~~Le~ 53 (93)
..+.|++|.+...+|+.+-.
T Consensus 57 a~~~gl~~~~~~~if~~ii~ 76 (82)
T TIGR01803 57 AEENGLDPPFVEGLFAQIIH 76 (82)
T ss_pred HHHcCCCHHHHHHHHHHHHH
Confidence 34578999999999988754
No 72
>COG4399 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=28.61 E-value=2.9e+02 Score=23.61 Aligned_cols=62 Identities=24% Similarity=0.180 Sum_probs=44.1
Q ss_pred HHHHHHHHHHHHHHHhhCCHHHHH-HHHHhh--cCCChhhHHHHHHHHHHhcHHHHHHHHhc-hhh
Q 034494 7 SYIHLVHHLIEECLVFNMSKEECM-EALSKH--ANIKPVITSTVWKELEKENKEFFEAYARK-NAE 68 (93)
Q Consensus 7 ~~I~~VQ~LIErCLqlyMsk~Evv-~~L~~~--a~I~P~fT~~VW~~Le~eNpeFF~aY~~~-~~e 68 (93)
.--+.|...|.+-||..|..+-.. ..|..+ ++++-..-.-+-+-|+.++.++|..+.-. +.+
T Consensus 83 ~~~~rv~~~i~~~lqk~lk~~~t~k~~l~~~~~~d~e~~~i~~~~~~l~~~l~e~f~e~qsn~i~e 148 (376)
T COG4399 83 LFQERVTEAIDQLLQKLLKSEVTDKEQLHQQIFADIEKDLIGNSERWLEKELAEKFTEAQSNTIFE 148 (376)
T ss_pred HHHHHHHHHHHHHHHHHHHhhcchHHHHHHHHHhhHHHHHHHhhHHHHHHHHHHHHHHHHhhHHHH
Confidence 344679999999999998877663 344443 34455555566678999999999988666 555
No 73
>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=28.30 E-value=1.9e+02 Score=19.57 Aligned_cols=52 Identities=21% Similarity=0.245 Sum_probs=36.1
Q ss_pred HHHHHHHHHHHhhCC----HHHHHHHHHhhcCCChhhH---HHHHHHHHHhcHHHHHHH
Q 034494 11 LVHHLIEECLVFNMS----KEECMEALSKHANIKPVIT---STVWKELEKENKEFFEAY 62 (93)
Q Consensus 11 ~VQ~LIErCLqlyMs----k~Evv~~L~~~a~I~P~fT---~~VW~~Le~eNpeFF~aY 62 (93)
.+...++.....+++ .+++++.+.+.+..+|.+. ..+...|...+++|...-
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 344555555566665 5678888889999999877 456677777777766554
No 74
>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=28.03 E-value=97 Score=18.93 Aligned_cols=30 Identities=20% Similarity=0.510 Sum_probs=21.0
Q ss_pred CCHHHHHHHHHhhcCCChhhHHHHHHHHHHh
Q 034494 24 MSKEECMEALSKHANIKPVITSTVWKELEKE 54 (93)
Q Consensus 24 Msk~Evv~~L~~~a~I~P~fT~~VW~~Le~e 54 (93)
||--|.+..+.+++| .|.=..-+|++..+.
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 666777777777778 888888888888764
No 75
>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=27.79 E-value=1e+02 Score=17.25 Aligned_cols=26 Identities=19% Similarity=0.291 Sum_probs=19.6
Q ss_pred HHHHHhhcCCChhhHHHHHHHHHHhc
Q 034494 30 MEALSKHANIKPVITSTVWKELEKEN 55 (93)
Q Consensus 30 v~~L~~~a~I~P~fT~~VW~~Le~eN 55 (93)
+..|.++++|.+.--..+.++|++++
T Consensus 28 ~~~la~~~~is~~~v~~~l~~L~~~G 53 (66)
T cd07377 28 ERELAEELGVSRTTVREALRELEAEG 53 (66)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHCC
Confidence 67788899999876666667776654
No 76
>PRK12461 UDP-N-acetylglucosamine acyltransferase; Provisional
Probab=27.52 E-value=2.7e+02 Score=21.45 Aligned_cols=43 Identities=12% Similarity=0.121 Sum_probs=34.5
Q ss_pred hHHHHHHHHHHHHHHHHhhCCHHHHHHHHHhhcCCChhhHHHH
Q 034494 5 SASYIHLVHHLIEECLVFNMSKEECMEALSKHANIKPVITSTV 47 (93)
Q Consensus 5 s~~~I~~VQ~LIErCLqlyMsk~Evv~~L~~~a~I~P~fT~~V 47 (93)
|.+.|+.++.....-+..-++.+|.++.|.++..-.|.+-..+
T Consensus 201 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 243 (255)
T PRK12461 201 SSRAIRALKRAYKIIYRSGLSVQQAVAELELQQFESPEVEELI 243 (255)
T ss_pred CHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHhccCCHHHHHHH
Confidence 5678888888888888888899999999988777777765544
No 77
>PRK05289 UDP-N-acetylglucosamine acyltransferase; Provisional
Probab=26.98 E-value=2.8e+02 Score=21.11 Aligned_cols=43 Identities=19% Similarity=0.219 Sum_probs=31.6
Q ss_pred hHHHHHHHHHHHHHHHHhhCCHHHHHHHHHhhcCCChhhHHHH
Q 034494 5 SASYIHLVHHLIEECLVFNMSKEECMEALSKHANIKPVITSTV 47 (93)
Q Consensus 5 s~~~I~~VQ~LIErCLqlyMsk~Evv~~L~~~a~I~P~fT~~V 47 (93)
+.+.+..++....-.|..-.+.+|.++.|.+...-.|.+...+
T Consensus 205 ~~~~~~~i~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 247 (262)
T PRK05289 205 SREEIHALRRAYKLLYRSGLTLEEALEELAEEYPDSPEVKEIL 247 (262)
T ss_pred CHHHHHHHHHHHHHHHHcCccHHHHHHHHHhhccCCHHHHHHH
Confidence 5677777888887777777888888888877766666654443
No 78
>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=26.39 E-value=65 Score=23.84 Aligned_cols=34 Identities=26% Similarity=0.436 Sum_probs=28.9
Q ss_pred HHHHHHHHhhCCHHHHHHHHHhhcCCChhhHHHH
Q 034494 14 HLIEECLVFNMSKEECMEALSKHANIKPVITSTV 47 (93)
Q Consensus 14 ~LIErCLqlyMsk~Evv~~L~~~a~I~P~fT~~V 47 (93)
-||.+-+||-||+.....-|.+|-++....-+.-
T Consensus 114 lliqqwiqfmmsrrrllaclckhkkvstnlcshs 147 (153)
T PF12383_consen 114 LLIQQWIQFMMSRRRLLACLCKHKKVSTNLCSHS 147 (153)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcccccccccchhh
Confidence 4688999999999999999999998887665543
No 79
>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=26.16 E-value=82 Score=22.66 Aligned_cols=29 Identities=14% Similarity=0.184 Sum_probs=21.7
Q ss_pred HHHHHHHHHHHHh----hCCHHHHHHHHHhhcC
Q 034494 10 HLVHHLIEECLVF----NMSKEECMEALSKHAN 38 (93)
Q Consensus 10 ~~VQ~LIErCLql----yMsk~Evv~~L~~~a~ 38 (93)
..++++|.+||+. ..+-+|+++.|.+-.+
T Consensus 252 ~~~~~li~~~l~~~P~~Rpt~~~v~~~l~~~~~ 284 (291)
T cd05094 252 KEVYDIMLGCWQREPQQRLNIKEIYKILHALGK 284 (291)
T ss_pred HHHHHHHHHHcccChhhCcCHHHHHHHHHHHHh
Confidence 4588999999985 5667888888876433
No 80
>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=26.05 E-value=2.9e+02 Score=20.88 Aligned_cols=60 Identities=12% Similarity=0.121 Sum_probs=33.6
Q ss_pred hhCCHHHHHHHHHhhcCCChhhHH--HHHHHHH-------HhcHHHHHHHHhc-hhhhhhHHHHHHHHHH
Q 034494 22 FNMSKEECMEALSKHANIKPVITS--TVWKELE-------KENKEFFEAYARK-NAERATVMETRERIEK 81 (93)
Q Consensus 22 lyMsk~Evv~~L~~~a~I~P~fT~--~VW~~Le-------~eNpeFF~aY~~~-~~e~~se~~~~~~iq~ 81 (93)
.-||.++||.+|+....-.|.... .=++.|+ ++|..-=+.+..- .+.++.++.+..+++=
T Consensus 78 ~~ltl~~vI~fLq~l~~~~~~~~~~~~e~~~l~~e~~~l~~~~e~Le~e~~~L~~~~~~~~eDY~~L~~I 147 (161)
T TIGR02894 78 GSLTLQDVISFLQNLKTTNPSDQALQKENERLKNQNESLQKRNEELEKELEKLRQRLSTIEEDYQTLIDI 147 (161)
T ss_pred ccCCHHHHHHHHHHHHhcchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 358999999999987777776643 2233333 3343333333222 3335556666655543
No 81
>TIGR00461 gcvP glycine dehydrogenase (decarboxylating). This apparently ubiquitous enzyme is found in bacterial, mammalian and plant sources. The enzyme catalyzes the reaction: GLYCINE + LIPOYLPROTEIN = S-AMINOMETHYL-DIHYDROLIPOYLPROTEIN + CO2. It is part of the glycine decarboxylase multienzyme complex (GDC) consisting of four proteins P, H, L and T. Active site in E.coli is located as the (K) residues at position 713 of the SEED alignment.
Probab=25.81 E-value=1.1e+02 Score=28.57 Aligned_cols=61 Identities=18% Similarity=0.194 Sum_probs=35.6
Q ss_pred CCHHHHHHHHHhhc------------CCChhhHHHHHHHHHHhcHHHHHHHHhchhhhhhHHHHHHH--HHHHHhc
Q 034494 24 MSKEECMEALSKHA------------NIKPVITSTVWKELEKENKEFFEAYARKNAERATVMETRER--IEKMLAN 85 (93)
Q Consensus 24 Msk~Evv~~L~~~a------------~I~P~fT~~VW~~Le~eNpeFF~aY~~~~~e~~se~~~~~~--iq~m~s~ 85 (93)
||--|+++.|.+-+ |.-|.++-.|-+.=--+||+||-+|.--.-| +||-....+ +|.|+++
T Consensus 46 ~sE~e~~~~~~~la~~N~~~~~fig~G~y~~~~p~~i~r~v~~~p~~~TaytPyQ~E-isQG~Le~l~e~Qt~i~e 120 (939)
T TIGR00461 46 SKEYEALAHLKKIASKNHKFKSYIGMGYYGTILPPVIQRNLLENPGWYTAYTPYQPE-ISQGRLEALLNFQTVVSD 120 (939)
T ss_pred CCHHHHHHHHHHHHhcCCCccccCCCCcCCCcCChHHHHHHHhCchhhhcCCCCChh-hhhHHHHHHHHHHHHHHH
Confidence 56677777754432 2223333333332225899999999433544 777665555 7888764
No 82
>PF03081 Exo70: Exo70 exocyst complex subunit; InterPro: IPR004140 The Exo70 protein forms one subunit of the exocyst complex. First discovered in Saccharomyces cerevisiae [], Exo70 and other exocyst proteins have been observed in several other eukaryotes, including humans. In S. cerevisiae, the exocyst complex is involved in the late stages of exocytosis, and is localized at the tip of the bud, the major site of exocytosis in yeast []. Exo70 interacts with the Rho3 GTPase []. This interaction mediates one of the three known functions of Rho3 in cell polarity: vesicle docking and fusion with the plasma membrane (the other two functions are regulation of actin polarity and transport of exocytic vesicles from the mother cell to the bud) []. In humans, the functions of Exo70 and the exocyst complex are less well characterised: Exo70 is expressed in several tissues and is thought to also be involved in exocytosis [].; GO: 0006887 exocytosis, 0000145 exocyst; PDB: 2PFV_A 2B7M_B 2B1E_A 2PFT_A.
Probab=25.60 E-value=3.2e+02 Score=21.18 Aligned_cols=77 Identities=16% Similarity=0.220 Sum_probs=48.7
Q ss_pred HHHHHHHHHHHHHHHhhCCH--HHHHHHHHhh-----cCCChhhHHHHHHHHHHhcHHHHHHHHhchhhhhhHHHHHHHH
Q 034494 7 SYIHLVHHLIEECLVFNMSK--EECMEALSKH-----ANIKPVITSTVWKELEKENKEFFEAYARKNAERATVMETRERI 79 (93)
Q Consensus 7 ~~I~~VQ~LIErCLqlyMsk--~Evv~~L~~~-----a~I~P~fT~~VW~~Le~eNpeFF~aY~~~~~e~~se~~~~~~i 79 (93)
+-++.....|++|...||.- .-|+..|... .+....--..+=.++.+=|.+|=++|...+.=-+.+.+.++.+
T Consensus 248 ~~~~~~~~~~~~~~~~Y~~~sW~~v~~~L~~~~~~~~~~~~~~~~~~~ke~f~~Fn~~fee~~~~q~~~~vpD~~LR~~L 327 (371)
T PF03081_consen 248 DWEQRLSSKIEQYIKSYLRSSWGPVLSCLSDDSSSSGGKLSSKERELLKEKFKKFNSAFEEIYKAQKTWKVPDPELREEL 327 (371)
T ss_dssp CHHHHHHHHHHHHHHHHHCHHHHHHHCTCCHHCC-T-SSS-HHHHHHHHHHHHHHHHHHHHHHHHHTT---S-HHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhccccCCCCCccHHHHHHHHHHHHHHHHHHHHcCcceecCCHHHHHHH
Confidence 34566779999999999976 5566666652 3444445556667777778888888877644444555555555
Q ss_pred HHHH
Q 034494 80 EKML 83 (93)
Q Consensus 80 q~m~ 83 (93)
.+-+
T Consensus 328 r~~i 331 (371)
T PF03081_consen 328 RREI 331 (371)
T ss_dssp HHHH
T ss_pred HHHH
Confidence 4443
No 83
>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=25.44 E-value=1.3e+02 Score=20.90 Aligned_cols=37 Identities=22% Similarity=0.216 Sum_probs=30.1
Q ss_pred hHHHHHHHHHHHHHHHHhhCCHHHHHHHHHhhcCCCh
Q 034494 5 SASYIHLVHHLIEECLVFNMSKEECMEALSKHANIKP 41 (93)
Q Consensus 5 s~~~I~~VQ~LIErCLqlyMsk~Evv~~L~~~a~I~P 41 (93)
|.+....|+.||..++..-++-||--..|+...|-.|
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 5677889999999999999999999999998666554
No 84
>PLN02350 phosphogluconate dehydrogenase (decarboxylating)
Probab=25.29 E-value=1.6e+02 Score=25.17 Aligned_cols=45 Identities=16% Similarity=0.200 Sum_probs=33.0
Q ss_pred CCCc-hHHHHHHHHHHHHHHHHhhCCHHHHHHHHHhhcCCChhhHHHH
Q 034494 1 MDDS-SASYIHLVHHLIEECLVFNMSKEECMEALSKHANIKPVITSTV 47 (93)
Q Consensus 1 ~~~~-s~~~I~~VQ~LIErCLqlyMsk~Evv~~L~~~a~I~P~fT~~V 47 (93)
+|+. +.....+|+|.|+=+.-. --.|.+..+.+..|++|.--..|
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 3553 788999999999965544 24677777776579999877766
No 85
>COG1498 SIK1 Protein implicated in ribosomal biogenesis, Nop56p homolog [Translation, ribosomal structure and biogenesis]
Probab=25.20 E-value=1.2e+02 Score=25.93 Aligned_cols=51 Identities=25% Similarity=0.238 Sum_probs=43.1
Q ss_pred CCCc-hHHHHHHHHHHHHHHHHhhCCHHHHHHHHHhhc-CCChhhHHHHHHHH
Q 034494 1 MDDS-SASYIHLVHHLIEECLVFNMSKEECMEALSKHA-NIKPVITSTVWKEL 51 (93)
Q Consensus 1 ~~~~-s~~~I~~VQ~LIErCLqlyMsk~Evv~~L~~~a-~I~P~fT~~VW~~L 51 (93)
||.. +..||+.|+.+.|+-..+|==++++-+++.... .|-|.+|.+|=-.|
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 5553 789999999999999999999999999998854 58999999884433
No 86
>COG3159 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.86 E-value=63 Score=25.60 Aligned_cols=9 Identities=33% Similarity=0.549 Sum_probs=6.3
Q ss_pred hcHHHHHHH
Q 034494 54 ENKEFFEAY 62 (93)
Q Consensus 54 eNpeFF~aY 62 (93)
+|||||.-.
T Consensus 15 ~hPeFf~~h 23 (218)
T COG3159 15 QHPEFFIQH 23 (218)
T ss_pred hCcHHHHhC
Confidence 468888754
No 87
>PTZ00398 phosphoenolpyruvate carboxylase; Provisional
Probab=24.59 E-value=73 Score=29.80 Aligned_cols=33 Identities=30% Similarity=0.373 Sum_probs=29.2
Q ss_pred HHHHHHHHHHhhCCHHHHHHHHHhhcCCChhhHH
Q 034494 12 VHHLIEECLVFNMSKEECMEALSKHANIKPVITS 45 (93)
Q Consensus 12 VQ~LIErCLqlyMsk~Evv~~L~~~a~I~P~fT~ 45 (93)
+.+.+.++.+..++++++.++|.+ ..|.|+||.
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 567899999999999999999975 799999995
No 88
>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=24.34 E-value=98 Score=20.05 Aligned_cols=38 Identities=18% Similarity=0.096 Sum_probs=25.0
Q ss_pred HHHHHHhhCCHHHHHHHHHhhcCCChhhHHHHHHHHHH
Q 034494 16 IEECLVFNMSKEECMEALSKHANIKPVITSTVWKELEK 53 (93)
Q Consensus 16 IErCLqlyMsk~Evv~~L~~~a~I~P~fT~~VW~~Le~ 53 (93)
|.+|..+..++..|+.+|....+-.+.+...|-+.|..
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 67788899999999999988655444444446665543
No 89
>TIGR00269 conserved hypothetical protein TIGR00269.
Probab=24.28 E-value=2.2e+02 Score=18.96 Aligned_cols=40 Identities=10% Similarity=-0.027 Sum_probs=26.8
Q ss_pred hhCCHHHHHHHHHhhcCCChh-------------hHHHHHHHHHHhcHHHHHHH
Q 034494 22 FNMSKEECMEALSKHANIKPV-------------ITSTVWKELEKENKEFFEAY 62 (93)
Q Consensus 22 lyMsk~Evv~~L~~~a~I~P~-------------fT~~VW~~Le~eNpeFF~aY 62 (93)
.|.+.+|++.+-. ..||... ....+.+.||+.||.+....
T Consensus 8 ~~v~E~ei~~ya~-~~~lp~~~~~CP~~~~a~R~~~k~~L~~LE~~~P~~k~~i 60 (104)
T TIGR00269 8 RYIPEKEVVLYAF-LNELKVHLDECPYSSLSVRARIRDFLYDLENKKPGVKFSV 60 (104)
T ss_pred ccCCHHHHHHHHH-HcCCCcCCCCCCCCCCCchHHHHHHHHHHHHHCcChHHHH
Confidence 3566677764443 4577643 55678999999999865444
No 90
>PF01466 Skp1: Skp1 family, dimerisation domain; InterPro: IPR016072 SKP1 (together with SKP2) was identified as an essential component of the cyclin A-CDK2 S phase kinase complex []. It was found to bind several F-box containing proteins (e.g., Cdc4, Skp2, cyclin F) and to be involved in the ubiquitin protein degradation pathway. A yeast homologue of SKP1 (P52286) was identified in the centromere bound kinetochore complex [] and is also involved in the ubiquitin pathway []. In Dictyostelium discoideum (Slime mold) FP21 was shown to be glycosylated in the cytosol and has homology to SKP1 []. This entry represents a dimerisation domain found at the C-terminal of SKP1 proteins [], as well as in subunit D of the centromere DNA-binding protein complex Cbf3 []. This domain is multi-helical in structure, and consists of an interlocked herterodimer in F-box proteins.; GO: 0006511 ubiquitin-dependent protein catabolic process; PDB: 2P1O_A 3OGL_G 3OGM_A 3C6O_A 2P1N_A 2P1Q_A 3OGK_I 3C6N_A 3C6P_A 2P1P_A ....
Probab=24.22 E-value=88 Score=19.76 Aligned_cols=23 Identities=30% Similarity=0.284 Sum_probs=12.3
Q ss_pred HhhcCCChhhHHHHHHHHHHhcH
Q 034494 34 SKHANIKPVITSTVWKELEKENK 56 (93)
Q Consensus 34 ~~~a~I~P~fT~~VW~~Le~eNp 56 (93)
.+.+||+-.+|.--=.+++++|+
T Consensus 52 r~~fgi~~d~t~eee~~i~~e~~ 74 (78)
T PF01466_consen 52 RKYFGIENDLTPEEEEEIRKENE 74 (78)
T ss_dssp HHHHT---TSSHHHHHHHHHHCC
T ss_pred HHHcCCCCCCCHHHHHHHHHHcc
Confidence 33457777777666666777665
No 91
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=24.00 E-value=1.3e+02 Score=17.11 Aligned_cols=33 Identities=36% Similarity=0.335 Sum_probs=18.5
Q ss_pred HHHHHHHHhhCCHHHHHHHHHhhcCCChhhHHHHHHHHHH
Q 034494 14 HLIEECLVFNMSKEECMEALSKHANIKPVITSTVWKELEK 53 (93)
Q Consensus 14 ~LIErCLqlyMsk~Evv~~L~~~a~I~P~fT~~VW~~Le~ 53 (93)
..|+..+...||..|+.+.|- +.| ++|.+.|..
T Consensus 11 ~~I~~l~~~G~s~~~IA~~lg----~s~---sTV~relkR 43 (44)
T PF13936_consen 11 NQIEALLEQGMSIREIAKRLG----RSR---STVSRELKR 43 (44)
T ss_dssp -HHHHHHCS---HHHHHHHTT------H---HHHHHHHHH
T ss_pred HHHHHHHHcCCCHHHHHHHHC----cCc---HHHHHHHhc
Confidence 347777788888888777654 444 477777653
No 92
>PF13625 Helicase_C_3: Helicase conserved C-terminal domain
Probab=23.66 E-value=1.1e+02 Score=20.80 Aligned_cols=34 Identities=12% Similarity=0.185 Sum_probs=25.9
Q ss_pred HHHHHHHHhhCCHHHHHHHHHhhc--CCChhhHHHH
Q 034494 14 HLIEECLVFNMSKEECMEALSKHA--NIKPVITSTV 47 (93)
Q Consensus 14 ~LIErCLqlyMsk~Evv~~L~~~a--~I~P~fT~~V 47 (93)
.-+-+++...|+.+++++.|.+++ +|.+.+...+
T Consensus 45 ~Sl~~A~~~G~~~e~i~~~L~~~S~~~lP~~v~~~i 80 (129)
T PF13625_consen 45 ASLWRAASAGLTAEEIIEFLERYSKNPLPQNVEQSI 80 (129)
T ss_pred HHHHHHHHcCCCHHHHHHHHHHHcCCCCCHHHHHHH
Confidence 456789999999999999999976 3555555443
No 93
>PF09278 MerR-DNA-bind: MerR, DNA binding; InterPro: IPR015358 This entry represents a family of DNA-binding domains that are predominantly found in the prokaryotic transcriptional regulator MerR. They adopt a structure consisting of a core of three alpha helices, with an architecture that is similar to that of the 'winged helix' fold []. ; PDB: 3QAO_A 1R8D_B 1JBG_A 2VZ4_A 2ZHH_A 2ZHG_A 1Q09_A 1Q08_B 1Q0A_B 1Q07_A ....
Probab=23.58 E-value=1.7e+02 Score=17.15 Aligned_cols=36 Identities=19% Similarity=0.090 Sum_probs=25.7
Q ss_pred HHHHHHHHhhCCHHHHHHHHHhhcCCChhhHHHHHHHH
Q 034494 14 HLIEECLVFNMSKEECMEALSKHANIKPVITSTVWKEL 51 (93)
Q Consensus 14 ~LIErCLqlyMsk~Evv~~L~~~a~I~P~fT~~VW~~L 51 (93)
+.|-+|=.+.||.+||-..|.-..+ |.-+..-|..+
T Consensus 5 ~~I~~~r~lGfsL~eI~~~l~l~~~--~~~~~~~~~~~ 40 (65)
T PF09278_consen 5 QFIRRLRELGFSLEEIRELLELYDQ--GDPPCADRRAL 40 (65)
T ss_dssp HHHHHHHHTT--HHHHHHHHHHCCS--HCHHHHHHHHH
T ss_pred HHHHHHHHcCCCHHHHHHHHhccCC--CCCCHHHHHHH
Confidence 4788999999999999999954444 66666666643
No 94
>PF14039 YusW: YusW-like protein
Probab=23.55 E-value=70 Score=21.60 Aligned_cols=37 Identities=22% Similarity=0.295 Sum_probs=27.7
Q ss_pred HHHHHHHHHHH-HHHhhCCHHHHHHHHHhhcCCChhhH
Q 034494 8 YIHLVHHLIEE-CLVFNMSKEECMEALSKHANIKPVIT 44 (93)
Q Consensus 8 ~I~~VQ~LIEr-CLqlyMsk~Evv~~L~~~a~I~P~fT 44 (93)
-++.++.++.+ -|.--|+.++||..+.+.+|++|.+.
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 34555555543 45668999999999999999998653
No 95
>PF07954 DUF1689: Protein of unknown function (DUF1689) ; InterPro: IPR012470 Family of fungal proteins with unknown function. A member of this family has been found to localise in the mitochondria [].
Probab=23.52 E-value=46 Score=24.67 Aligned_cols=22 Identities=27% Similarity=0.501 Sum_probs=20.1
Q ss_pred HHHHHHHHHHhcHHHHHHHHhc
Q 034494 44 TSTVWKELEKENKEFFEAYARK 65 (93)
Q Consensus 44 T~~VW~~Le~eNpeFF~aY~~~ 65 (93)
-.-||+.|+-.|+.+|-.||.+
T Consensus 108 q~~vwk~m~~~~~~~~~~Yy~~ 129 (152)
T PF07954_consen 108 QYEVWKLMDYGSASFWYLYYYK 129 (152)
T ss_pred HHHHHHhcccCCchHHHHHHHH
Confidence 3479999999999999999988
No 96
>KOG1199 consensus Short-chain alcohol dehydrogenase/3-hydroxyacyl-CoA dehydrogenase [Secondary metabolites biosynthesis, transport and catabolism]
Probab=23.41 E-value=61 Score=25.96 Aligned_cols=17 Identities=35% Similarity=0.575 Sum_probs=13.9
Q ss_pred CCchHHHHHHHHHHHHHH
Q 034494 2 DDSSASYIHLVHHLIEEC 19 (93)
Q Consensus 2 ~~~s~~~I~~VQ~LIErC 19 (93)
|+ +++|-++||++||.-
T Consensus 227 g~-p~eyahlvqaiienp 243 (260)
T KOG1199|consen 227 GH-PHEYAHLVQAIIENP 243 (260)
T ss_pred CC-hHHHHHHHHHHHhCc
Confidence 44 489999999999963
No 97
>PRK00009 phosphoenolpyruvate carboxylase; Reviewed
Probab=23.11 E-value=82 Score=29.24 Aligned_cols=34 Identities=26% Similarity=0.356 Sum_probs=28.9
Q ss_pred HHHHHHHHHHHhhCCHHHHHHHHHhhcCCChhhHH
Q 034494 11 LVHHLIEECLVFNMSKEECMEALSKHANIKPVITS 45 (93)
Q Consensus 11 ~VQ~LIErCLqlyMsk~Evv~~L~~~a~I~P~fT~ 45 (93)
.+.+.+.++.+..++++++.+.|.+ ..|.|+||.
T Consensus 108 sl~~~~~~l~~~g~~~e~i~~~L~~-~~i~pVlTA 141 (911)
T PRK00009 108 SLAETLRRLKAAGVSPEELARALEE-LDIEPVLTA 141 (911)
T ss_pred cHHHHHHHHHHcCCCHHHHHHHHhh-Ccceeeeec
Confidence 3567888888888999999999975 799999995
No 98
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=22.86 E-value=1.1e+02 Score=22.27 Aligned_cols=27 Identities=15% Similarity=0.251 Sum_probs=22.4
Q ss_pred HHHHHHhhcCCChhhHHHHHHHHHHhc
Q 034494 29 CMEALSKHANIKPVITSTVWKELEKEN 55 (93)
Q Consensus 29 vv~~L~~~a~I~P~fT~~VW~~Le~eN 55 (93)
-++.|++..+|.|.+..-|++.|.+.+
T Consensus 27 s~~eIA~~~~ip~~~l~kIl~~L~~aG 53 (164)
T PRK10857 27 PLADISERQGISLSYLEQLFSRLRKNG 53 (164)
T ss_pred cHHHHHHHHCcCHHHHHHHHHHHHHCC
Confidence 346677888999999999999999843
No 99
>PF14123 DUF4290: Domain of unknown function (DUF4290)
Probab=22.80 E-value=2e+02 Score=22.03 Aligned_cols=46 Identities=20% Similarity=0.382 Sum_probs=34.1
Q ss_pred HHHHHHHHHHHHHHHHhhCCHHH----------HHHHHHhhcCCChhhHHHHHHHHH
Q 034494 6 ASYIHLVHHLIEECLVFNMSKEE----------CMEALSKHANIKPVITSTVWKELE 52 (93)
Q Consensus 6 ~~~I~~VQ~LIErCLqlyMsk~E----------vv~~L~~~a~I~P~fT~~VW~~Le 52 (93)
.+|=+.||++|+-|+.+ =+++| +|..|.=|..=.|.|..-+|..|-
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 455555566667889999999884
No 100
>PF10364 NKWYS: Putative capsular polysaccharide synthesis protein; InterPro: IPR018831 This entry contains proteins of no known function. They are found predominantly in Vibrio and cyanobacterial species and are characterised by having a NKWYS sequence motif.
Probab=22.70 E-value=75 Score=23.40 Aligned_cols=33 Identities=15% Similarity=0.220 Sum_probs=28.6
Q ss_pred CchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHh
Q 034494 3 DSSASYIHLVHHLIEECLVFNMSKEECMEALSK 35 (93)
Q Consensus 3 ~~s~~~I~~VQ~LIErCLqlyMsk~Evv~~L~~ 35 (93)
|+++.+|..-|.+.|.|+..+|+.+-...-+-+
T Consensus 7 d~~~~~~e~~~~l~e~~F~~~~~~~~~~~WFD~ 39 (141)
T PF10364_consen 7 DDIHIDIERTQLLLEHCFENHFNHNYPLNWFDN 39 (141)
T ss_pred hhhhhcchHHHHHHHHHHhccCCcchhhhHHHH
Confidence 567889999999999999999999988776654
No 101
>smart00337 BCL BCL (B-Cell lymphoma); contains BH1, BH2 regions. (BH1, BH2, (BH3 (one helix only)) and not BH4(one helix only)). Involved in apoptosis regulation
Probab=22.53 E-value=1.8e+02 Score=19.21 Aligned_cols=38 Identities=13% Similarity=0.260 Sum_probs=25.7
Q ss_pred HHHHHhcHHHHHHHHhc--hhhhhhHHHHHHHHHHHHhcc
Q 034494 49 KELEKENKEFFEAYARK--NAERATVMETRERIEKMLANS 86 (93)
Q Consensus 49 ~~Le~eNpeFF~aY~~~--~~e~~se~~~~~~iq~m~s~~ 86 (93)
.+|+++.+.+|+..-.+ +.+......+.+....++++.
T Consensus 6 dele~~~~~~f~~~~~~l~~~~~~~~~~f~~Va~~lf~dg 45 (100)
T smart00337 6 DELNKRYERAFSSFSAQLHVTPGTAIELFGEVATELFSDG 45 (100)
T ss_pred HHHHHHHHHHHHHHHHHhCCCcccHHHHHHHHHHHHHccC
Confidence 57888899999888665 434444456666667776653
No 102
>COG1412 Uncharacterized proteins of PilT N-term./Vapc superfamily [General function prediction only]
Probab=22.37 E-value=2.1e+02 Score=20.70 Aligned_cols=40 Identities=35% Similarity=0.346 Sum_probs=27.5
Q ss_pred HHHHHHHhhCCHHHHHHHHHhhcCCChhhHHHHHHHHHHhc
Q 034494 15 LIEECLVFNMSKEECMEALSKHANIKPVITSTVWKELEKEN 55 (93)
Q Consensus 15 LIErCLqlyMsk~Evv~~L~~~a~I~P~fT~~VW~~Le~eN 55 (93)
.|-=|.|.-.+..+-+..+. .++.+|.+|+.|-.+|++--
T Consensus 19 fl~~~~q~~vdi~~~l~r~l-~~~~~~~Ip~~Vi~EL~~l~ 58 (136)
T COG1412 19 FLLYPYQFKVDIFEELERLL-GAKYKPAIPSCVIRELEKLK 58 (136)
T ss_pred HHHHHHHccCCHHHHHHHHh-cccccccchHHHHHHHHHHH
Confidence 34445666666555555544 25689999999999998743
No 103
>PF08970 Sda: Sporulation inhibitor A; InterPro: IPR015064 Members of this protein group contain two antiparallel alpha helices that are linked by a highly structured inter-helix loop to form a helical hairpin; the structure is stabilised by numerous hydrophobic and electrostatic interactions. These sporulation inhibitors are antikinases that bind to the histidine kinase KinA phosphotransfer domain and act as a molecular barricade that inhibit productive interaction between the ATP binding site and the phosphorylatable KinA His residue. This results in the inhibition of sporulation (by preventing phosphorylation of spo0A) []. ; PDB: 3FYR_B 1PV0_A.
Probab=22.30 E-value=2e+02 Score=17.58 Aligned_cols=33 Identities=21% Similarity=0.370 Sum_probs=20.5
Q ss_pred hCCHHHHHHHHHh--hcCCChhhHHHHHHHHHHhc
Q 034494 23 NMSKEECMEALSK--HANIKPVITSTVWKELEKEN 55 (93)
Q Consensus 23 yMsk~Evv~~L~~--~a~I~P~fT~~VW~~Le~eN 55 (93)
+||.+-.+++-.+ .-|.+|.|..++-+++++-+
T Consensus 3 ~LSDe~LiesY~~A~el~L~~dFI~Ll~~Ei~rR~ 37 (46)
T PF08970_consen 3 KLSDELLIESYHKAIELNLDPDFIRLLEEEIQRRS 37 (46)
T ss_dssp TS-HHHHHHHHHHHHHTT--HHHHHHHHHHHHHCT
T ss_pred cccHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHcC
Confidence 3555555555443 56899999999988887654
No 104
>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=22.30 E-value=71 Score=24.96 Aligned_cols=75 Identities=27% Similarity=0.404 Sum_probs=44.4
Q ss_pred HHHHHHHHHHHHHHHhhCCHH--------------------------------HHHHHHHhhcCCChhhH----------
Q 034494 7 SYIHLVHHLIEECLVFNMSKE--------------------------------ECMEALSKHANIKPVIT---------- 44 (93)
Q Consensus 7 ~~I~~VQ~LIErCLqlyMsk~--------------------------------Evv~~L~~~a~I~P~fT---------- 44 (93)
.....|.+-|+..+..||..+ ++|+.|++..||=|++.
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 444566677777777776655 78899999999988765
Q ss_pred ----HHHHHHHHHhcHHHHHHHHhchhhhhhHHHHHHHHHHHH
Q 034494 45 ----STVWKELEKENKEFFEAYARKNAERATVMETRERIEKML 83 (93)
Q Consensus 45 ----~~VW~~Le~eNpeFF~aY~~~~~e~~se~~~~~~iq~m~ 83 (93)
..|.+.|++.|-.+|.-....-. -.+.+.++.++.++
T Consensus 161 ~~~k~~i~~~l~~~~I~~f~f~~~~~~--~~e~~~~~~~~~~~ 201 (281)
T PF00735_consen 161 QAFKQRIREDLEENNIKIFDFPEDDDD--DEEIEENQKIRSML 201 (281)
T ss_dssp HHHHHHHHHHHHHTT--S------------HCHHHHHHHHHC-
T ss_pred HHHHHHHHHHHHHcCceeecccccccc--ccccccccccccce
Confidence 46899999999988872221111 12234555566655
No 105
>cd02433 Nodulin-21_like_2 Nodulin-21 and CCC1-related protein family. Nodulin-21_like_2: This is a family of proteins closely related to nodulin-21, a plant nodule-specific protein that may be involved in symbiotic nitrogen fixation. This family is also related to CCC1, a yeast vacuole transmembrane protein that functions as an iron and manganese transporter.
Probab=22.08 E-value=1.9e+02 Score=22.31 Aligned_cols=52 Identities=8% Similarity=-0.066 Sum_probs=38.0
Q ss_pred HHHHHHHHHHHHhhCCHHHHHHHHHhhcCCChhhHHHHHHHHHHhcHHHHHHHHhc
Q 034494 10 HLVHHLIEECLVFNMSKEECMEALSKHANIKPVITSTVWKELEKENKEFFEAYARK 65 (93)
Q Consensus 10 ~~VQ~LIErCLqlyMsk~Evv~~L~~~a~I~P~fT~~VW~~Le~eNpeFF~aY~~~ 65 (93)
+.-+..|+.|.. .-++|+++.+.++ |++|.--..|=+.|.+ ||++|-....+
T Consensus 86 ~re~~~i~~~p~--~e~~el~~iy~~~-G~~~~~a~~~~~~l~~-~~~~~~~~~~~ 137 (234)
T cd02433 86 PDERRELRKHPL--EEAAELALIYRAK-GLDEEEAKRVASQLMN-DPEQALDTLAR 137 (234)
T ss_pred HHHHHHhhhCcH--HHHHHHHHHHHHc-CCCHHHHHHHHHHHHh-CcchhHHHHHH
Confidence 344555666655 4568888888766 9999999999999965 78888665544
No 106
>PRK00117 recX recombination regulator RecX; Reviewed
Probab=22.07 E-value=2.8e+02 Score=19.17 Aligned_cols=43 Identities=21% Similarity=0.343 Sum_probs=33.6
Q ss_pred HhhCCHHHHHHHHHhhcCCChhhHHHHHHHHHHh----cHHHHHHHHh
Q 034494 21 VFNMSKEECMEALSKHANIKPVITSTVWKELEKE----NKEFFEAYAR 64 (93)
Q Consensus 21 qlyMsk~Evv~~L~~~a~I~P~fT~~VW~~Le~e----NpeFF~aY~~ 64 (93)
..-.|..|+...|.+. |++|.+...|-..|.+. ...|-+.|-.
T Consensus 23 ~r~~s~~el~~kL~~k-g~~~~~i~~vl~~l~~~~~ldD~~~a~~~~~ 69 (157)
T PRK00117 23 RREHSRAELRRKLAAK-GFSEEVIEAVLDRLKEEGLLDDERFAESFVR 69 (157)
T ss_pred cchhHHHHHHHHHHhc-CCCHHHHHHHHHHHHHcCCCCHHHHHHHHHH
Confidence 3456889999999976 99999999999999983 2456566543
No 107
>KOG2431 consensus 1, 2-alpha-mannosidase [Carbohydrate transport and metabolism]
Probab=22.04 E-value=94 Score=27.56 Aligned_cols=21 Identities=24% Similarity=0.464 Sum_probs=18.6
Q ss_pred hHHHHHHHHHHHHHHHHhh-CC
Q 034494 5 SASYIHLVHHLIEECLVFN-MS 25 (93)
Q Consensus 5 s~~~I~~VQ~LIErCLqly-Ms 25 (93)
+.++..+.|+|-+.|.|.| ||
T Consensus 390 ~~~hl~lA~~l~~TCyqMY~~~ 411 (546)
T KOG2431|consen 390 SEEHLELAQELMETCYQMYRQN 411 (546)
T ss_pred chHHHHHHHHHHHHHHHHHccC
Confidence 4679999999999999999 54
No 108
>PF13833 EF-hand_8: EF-hand domain pair; PDB: 3KF9_A 1TTX_A 1WLZ_A 1ALV_A 1NX3_A 1ALW_A 1NX2_A 1NX1_A 1NX0_A 1DF0_A ....
Probab=22.02 E-value=1.2e+02 Score=16.99 Aligned_cols=49 Identities=18% Similarity=0.307 Sum_probs=26.3
Q ss_pred hCCHHHHHHHHHhhcCCChhhHHHHHHHHHHhcHHHHHHHHhchhhhhhHHHHHHHHH
Q 034494 23 NMSKEECMEALSKHANIKPVITSTVWKELEKENKEFFEAYARKNAERATVMETRERIE 80 (93)
Q Consensus 23 yMsk~Evv~~L~~~a~I~P~fT~~VW~~Le~eNpeFF~aY~~~~~e~~se~~~~~~iq 80 (93)
+++++|...+| ...|+.+ ++. ++=...|+.+-......++-.++....+
T Consensus 4 ~i~~~~~~~~l-~~~g~~~-~s~-------~e~~~l~~~~D~~~~G~I~~~EF~~~~~ 52 (54)
T PF13833_consen 4 KITREEFRRAL-SKLGIKD-LSE-------EEVDRLFREFDTDGDGYISFDEFISMMQ 52 (54)
T ss_dssp EEEHHHHHHHH-HHTTSSS-SCH-------HHHHHHHHHHTTSSSSSEEHHHHHHHHH
T ss_pred EECHHHHHHHH-HHhCCCC-CCH-------HHHHHHHHhcccCCCCCCCHHHHHHHHH
Confidence 56778888888 4445553 222 2223445555544555666555555443
No 109
>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=21.93 E-value=1.4e+02 Score=19.12 Aligned_cols=20 Identities=0% Similarity=0.149 Sum_probs=13.7
Q ss_pred hcCCChhhHHHHHHHHHHhc
Q 034494 36 HANIKPVITSTVWKELEKEN 55 (93)
Q Consensus 36 ~a~I~P~fT~~VW~~Le~eN 55 (93)
..+++|.+...+|+.+=+..
T Consensus 59 ~~~l~~~~i~~if~~ii~~S 78 (83)
T TIGR01797 59 AYHLDAHYITRLFQLIIEDS 78 (83)
T ss_pred hCCCCHHHHHHHHHHHHHHH
Confidence 35688888888877765543
No 110
>PF14076 DUF4258: Domain of unknown function (DUF4258)
Probab=21.92 E-value=1.4e+02 Score=17.49 Aligned_cols=23 Identities=26% Similarity=0.277 Sum_probs=20.4
Q ss_pred HHHHHHHHHhhCCHHHHHHHHHh
Q 034494 13 HHLIEECLVFNMSKEECMEALSK 35 (93)
Q Consensus 13 Q~LIErCLqlyMsk~Evv~~L~~ 35 (93)
.|.++|..+-..|.+++..+|..
T Consensus 4 ~Ha~~rm~eR~Is~~~I~~~l~~ 26 (73)
T PF14076_consen 4 KHARERMQERGISEEDIEDALEN 26 (73)
T ss_pred HHHHHHHHhCCCCHHHHHHHHhc
Confidence 47889999999999999999975
No 111
>PRK11675 LexA regulated protein; Provisional
Probab=21.91 E-value=1.7e+02 Score=20.06 Aligned_cols=25 Identities=32% Similarity=0.325 Sum_probs=21.8
Q ss_pred HHHHHHHHHHHHhhCCHHHHHHHHH
Q 034494 10 HLVHHLIEECLVFNMSKEECMEALS 34 (93)
Q Consensus 10 ~~VQ~LIErCLqlyMsk~Evv~~L~ 34 (93)
+.++.|-+-|-+..||+.|+|+..-
T Consensus 60 dl~ekL~eyAe~~nitRSElIr~~I 84 (90)
T PRK11675 60 DLVDALNELAEARNISRSELIEEIL 84 (90)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHHH
Confidence 5788999999999999999997644
No 112
>PF13518 HTH_28: Helix-turn-helix domain
Probab=21.75 E-value=1.4e+02 Score=16.35 Aligned_cols=27 Identities=7% Similarity=0.090 Sum_probs=15.5
Q ss_pred HHHHHHhhcCCChhhHHHHHHHHHHhc
Q 034494 29 CMEALSKHANIKPVITSTVWKELEKEN 55 (93)
Q Consensus 29 vv~~L~~~a~I~P~fT~~VW~~Le~eN 55 (93)
-+..+..++||.|.--...++..++.-
T Consensus 14 s~~~~a~~~gis~~tv~~w~~~y~~~G 40 (52)
T PF13518_consen 14 SVREIAREFGISRSTVYRWIKRYREGG 40 (52)
T ss_pred CHHHHHHHHCCCHhHHHHHHHHHHhcC
Confidence 455567788997754444444444433
No 113
>PF12980 DUF3864: Domain of Unknown Function with PDB structure (DUF3864); InterPro: IPR024335 This entry represents a functionally uncharacterised domain found in bacterial sequences. The structure of one of the sequences, A6LGL1 from SWISSPROT from Parabacteroides distasonis atcc 8503, has been determined.; PDB: 3LM3_A.
Probab=21.40 E-value=26 Score=23.92 Aligned_cols=29 Identities=17% Similarity=0.434 Sum_probs=19.5
Q ss_pred hcCCChhhHHHHHHHHHHhcHHHHHHHHh
Q 034494 36 HANIKPVITSTVWKELEKENKEFFEAYAR 64 (93)
Q Consensus 36 ~a~I~P~fT~~VW~~Le~eNpeFF~aY~~ 64 (93)
|-|..|.=+-.+..+|..+|.+|-++||-
T Consensus 50 qkglrpqd~pvll~~l~~~~q~li~kyyp 78 (82)
T PF12980_consen 50 QKGLRPQDKPVLLSELSQEDQDLIRKYYP 78 (82)
T ss_dssp TT--SGGGS-B-GGGS-HHHHHHHHHH-G
T ss_pred hccCCCcCcchHHHHHhHHHHHHHHHHhH
Confidence 45677777777889999999999999984
No 114
>cd05093 PTKc_TrkB Catalytic domain of the Protein Tyrosine Kinase, Tropomyosin Related Kinase B. Protein Tyrosine Kinase (PTK) family; Tropomyosin Related Kinase B (TrkB); 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. TrkB 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 TrkB to its ligands, brain-derived neurotrophic factor (BDNF) or neurotrophin 4 (NT4), results in receptor oligomerization and activation of the catalytic domain. TrkB is broadly
Probab=21.39 E-value=96 Score=22.28 Aligned_cols=29 Identities=21% Similarity=0.200 Sum_probs=21.5
Q ss_pred HHHHHHHHHHHhh----CCHHHHHHHHHhhcCC
Q 034494 11 LVHHLIEECLVFN----MSKEECMEALSKHANI 39 (93)
Q Consensus 11 ~VQ~LIErCLqly----Msk~Evv~~L~~~a~I 39 (93)
-+.++|.+||+.- .|-+|+...|.+-++.
T Consensus 250 ~l~~li~~~l~~~p~~Rpt~~~v~~~l~~~~~~ 282 (288)
T cd05093 250 EVYDLMLGCWQREPHMRLNIKEIHSLLQNLAKA 282 (288)
T ss_pred HHHHHHHHHccCChhhCCCHHHHHHHHHHHHHh
Confidence 4788999999864 7778888887765443
No 115
>cd05049 PTKc_Trk Catalytic domain of the Protein Tyrosine Kinases, Tropomyosin Related Kinases. Protein Tyrosine Kinase (PTK) family; Tropomyosin Related Kinase (Trk) subfamily; catalytic (c) domain. The Trk subfamily consists of TrkA, TrkB, TrkC, and similar proteins. 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. Trk subfamily members 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 to their ligands, the nerve growth factor (NGF) family of neutrotrophins, leads to Trk receptor oligomerization and activation of the catalyt
Probab=21.34 E-value=1.1e+02 Score=21.59 Aligned_cols=25 Identities=16% Similarity=0.247 Sum_probs=18.2
Q ss_pred HHHHHHHHHHHHhh----CCHHHHHHHHH
Q 034494 10 HLVHHLIEECLVFN----MSKEECMEALS 34 (93)
Q Consensus 10 ~~VQ~LIErCLqly----Msk~Evv~~L~ 34 (93)
..+.++|.+||+.- .+-+|+.+.|.
T Consensus 251 ~~~~~li~~~l~~~p~~Rp~~~eil~~l~ 279 (280)
T cd05049 251 SEVYDIMLGCWKRDPQQRINIKDIHERLQ 279 (280)
T ss_pred HHHHHHHHHHcCCCcccCCCHHHHHHHhh
Confidence 46788999999874 66667766653
No 116
>cd04763 HTH_MlrA-like Helix-Turn-Helix DNA binding domain of MlrA-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A) and related proteins, N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen
Probab=21.24 E-value=2e+02 Score=17.11 Aligned_cols=28 Identities=11% Similarity=0.105 Sum_probs=20.6
Q ss_pred hHHHHHHHHHHHHHHHHhhCCHHHHHHHH
Q 034494 5 SASYIHLVHHLIEECLVFNMSKEECMEAL 33 (93)
Q Consensus 5 s~~~I~~VQ~LIErCLqlyMsk~Evv~~L 33 (93)
+.++|..++. |-...+..||.+||...|
T Consensus 40 t~~di~~l~~-i~~l~~~g~~l~~i~~~l 67 (68)
T cd04763 40 NDADIDRILE-IKRWIDNGVQVSKVKKLL 67 (68)
T ss_pred CHHHHHHHHH-HHHHHHcCCCHHHHHHHh
Confidence 4567776654 666677899999998776
No 117
>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=20.92 E-value=39 Score=14.44 Aligned_cols=25 Identities=8% Similarity=0.449 Sum_probs=16.6
Q ss_pred CCChhhHHHHHHHHHHhcHHHHHHH
Q 034494 38 NIKPVITSTVWKELEKENKEFFEAY 62 (93)
Q Consensus 38 ~I~P~fT~~VW~~Le~eNpeFF~aY 62 (93)
++...++.--|..++....++|+.-
T Consensus 5 ~~~~~~~~~~~~~~~~~~~~~~~~~ 29 (40)
T cd07765 5 DVAVYFSQEEWELLDPAQRDLYRDV 29 (40)
T ss_pred eeeeecCHHHHhcCCHHHHHHHHHH
Confidence 3445566778888877777776543
No 118
>KOG2939 consensus Uncharacterized conserved protein [Function unknown]
Probab=20.87 E-value=1.3e+02 Score=26.55 Aligned_cols=44 Identities=18% Similarity=0.445 Sum_probs=29.4
Q ss_pred HHHHHHHhhcCCChhh----HHHHHHHHHHhcHHHHHHHHhchhhhhh
Q 034494 28 ECMEALSKHANIKPVI----TSTVWKELEKENKEFFEAYARKNAERAT 71 (93)
Q Consensus 28 Evv~~L~~~a~I~P~f----T~~VW~~Le~eNpeFF~aY~~~~~e~~s 71 (93)
.++++++.--+|--.| +..+=..++++.++||++|+..+-+++.
T Consensus 122 qive~isrf~~vGeeFcg~ese~l~Esi~k~se~YFkrYH~q~meel~ 169 (502)
T KOG2939|consen 122 QIVETISRFYYVGEEFCGFESEKLHESIKKQSEEYFKRYHRQRMEELN 169 (502)
T ss_pred HHHHHHHHHHhhhhhhccchHHHHHHHHHhhhHHHHHHHHHHHHHHHH
Confidence 5666666544444333 3445567889999999999988555443
No 119
>PF08020 DUF1706: Protein of unknown function (DUF1706) ; InterPro: IPR012550 This family contains many hypothetical proteins from bacteria and yeast.
Probab=20.80 E-value=1.6e+02 Score=21.72 Aligned_cols=30 Identities=23% Similarity=0.478 Sum_probs=24.8
Q ss_pred hcCCChhhHH--HHHHHHHHhcHHHHHHHHhc
Q 034494 36 HANIKPVITS--TVWKELEKENKEFFEAYARK 65 (93)
Q Consensus 36 ~a~I~P~fT~--~VW~~Le~eNpeFF~aY~~~ 65 (93)
.+|-.|.|.. .=|+.|-.=|..|++.|...
T Consensus 68 ~~G~~~~fp~~gykWn~lg~Ln~~f~~~y~~~ 99 (166)
T PF08020_consen 68 QAGEEVDFPAPGYKWNQLGELNQSFYEKYQDT 99 (166)
T ss_pred cCCCCCCCCCCCCChhhhhHHHHHHHHHHcCC
Confidence 5677777754 56999999999999999776
No 120
>PF00452 Bcl-2: Apoptosis regulator proteins, Bcl-2 family; InterPro: IPR000712 Apoptosis, or programmed cell death (PCD), is a common and evolutionarily conserved property of all metazoans []. In many biological processes, apoptosis is required to eliminate supernumerary or dangerous (such as pre-cancerous) cells and to promote normal development. Dysregulation of apoptosis can, therefore, contribute to the development of many major diseases including cancer, autoimmunity and neurodegenerative disorders. In most cases, proteins of the caspase family execute the genetic programme that leads to cell death. Bcl-2 proteins are central regulators of caspase activation, and play a key role in cell death by regulating the integrity of the mitochondrial and endoplasmic reticulum (ER) membranes []. At least 20 Bcl-2 proteins have been reported in mammals, and several others have been identified in viruses. Bcl-2 family proteins fall roughly into three subtypes, which either promote cell survival (anti-apoptotic) or trigger cell death (pro-apoptotic). All members contain at least one of four conserved motifs, termed Bcl-2 Homology (BH) domains. Bcl-2 subfamily proteins, which contain at least BH1 and BH2, promote cell survival by inhibiting the adapters needed for the activation of caspases. Pro-apoptotic members potentially exert their effects by displacing the adapters from the pro-survival proteins; these proteins belong either to the Bax subfamily, which contain BH1-BH3, or to the BH3 subfamily, which mostly only feature BH3 []. Thus, the balance between antagonistic family members is believed to play a role in determining cell fate. Members of the wider Bcl-2 family, which also includes Bcl-x, Bcl-w and Mcl-1, are described by their similarity to Bcl-2 protein, a member of the pro-survival Bcl-2 subfamily []. Full-length Bcl-2 proteins feature all four BH domains, seven alpha-helices, and a C-terminal hydrophobic motif that targets the protein to the outer mitochondrial membrane, ER and nuclear envelope. Active cell suicide (apoptosis) is induced by events such as growth factor withdrawal and toxins. It is controlled by regulators, which have either an inhibitory effect on programmed cell death (anti-apoptotic) or block the protective effect of inhibitors (pro-apoptotic) [, ]. Many viruses have found a way of countering defensive apoptosis by encoding their own anti-apoptosis genes preventing their target-cells from dying too soon. All proteins belonging to the Bcl-2 family [] contain either a BH1, BH2, BH3, or BH4 domain. All anti-apoptotic proteins contain BH1 and BH2 domains, some of them contain an additional N-terminal BH4 domain (Bcl-2, Bcl-x(L), Bcl-w), which is never seen in pro-apoptotic proteins, except for Bcl-x(S). On the other hand, all pro-apoptotic proteins contain a BH3 domain (except for Bad) necessary for dimerisation with other proteins of Bcl-2 family and crucial for their killing activity, some of them also contain BH1 and BH2 domains (Bax, Bak). The BH3 domain is also present in some anti-apoptotic protein, such as Bcl-2 or Bcl-x(L). Proteins that are known to contain these domains include vertebrate Bcl-2 (alpha and beta isoforms) and Bcl-x (isoforms (Bcl-x(L) and Bcl-x(S)); mammalian proteins Bax and Bak; mouse protein Bid; Xenopus laevis proteins Xr1 and Xr11; human induced myeloid leukemia cell differentiation protein MCL1 and Caenorhabditis elegans protein ced-9.; GO: 0042981 regulation of apoptosis; PDB: 2WH6_A 1K3K_A 1AF3_A 3PK1_B 2K7W_A 1F16_A 3PL7_C 2VM6_A 3I1H_A 3MQP_A ....
Probab=20.75 E-value=1.9e+02 Score=18.35 Aligned_cols=38 Identities=21% Similarity=0.326 Sum_probs=26.8
Q ss_pred HHHHHHhcHHHHHHHHhc--h-hhhhhHHHHHHHHHHHHhc
Q 034494 48 WKELEKENKEFFEAYARK--N-AERATVMETRERIEKMLAN 85 (93)
Q Consensus 48 W~~Le~eNpeFF~aY~~~--~-~e~~se~~~~~~iq~m~s~ 85 (93)
=.++++.++++|+..... . .+..+...+.+....++++
T Consensus 5 ~~~~e~~~~~~f~~~~~~l~~~~~~~~~~~f~~v~~~lf~d 45 (101)
T PF00452_consen 5 ADELERKYEDFFENMLNQLNINTPDNAYETFNEVAEELFED 45 (101)
T ss_dssp HHHHHHHHHHHHHHHHHHHCSSSTTTHHHHHHHHHHHHTTT
T ss_pred HHHHHHHHHHHHHHHHHHhCCCCcchHHHHHHHHHHHHhcc
Confidence 357889999999998776 2 3334555677777777765
No 121
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=20.70 E-value=1.2e+02 Score=19.85 Aligned_cols=41 Identities=10% Similarity=0.131 Sum_probs=29.5
Q ss_pred HHHhhCCHHHHHHHHHhhcCC-ChhhHHHHHHHHHHhcHHHH
Q 034494 19 CLVFNMSKEECMEALSKHANI-KPVITSTVWKELEKENKEFF 59 (93)
Q Consensus 19 CLqlyMsk~Evv~~L~~~a~I-~P~fT~~VW~~Le~eNpeFF 59 (93)
..++|......|..+..++|| .|..-..=|.++.+.....|
T Consensus 16 iv~~~~~~g~sv~~vAr~~gv~~~~~l~~W~~~~~~~~~~~~ 57 (116)
T COG2963 16 AVALYLRGGDTVSEVAREFGIVSATQLYKWRIQLQKGGGLAF 57 (116)
T ss_pred HHHHHHhcCccHHHHHHHhCCCChHHHHHHHHHHHHcccccc
Confidence 445566666688889999996 88887777777777664443
No 122
>PF13551 HTH_29: Winged helix-turn helix
Probab=20.64 E-value=2.3e+02 Score=17.61 Aligned_cols=31 Identities=26% Similarity=0.226 Sum_probs=23.7
Q ss_pred hCCHHHHHHHH-HhhcCCChhhHHHHHHHHHHh
Q 034494 23 NMSKEECMEAL-SKHANIKPVITSTVWKELEKE 54 (93)
Q Consensus 23 yMsk~Evv~~L-~~~a~I~P~fT~~VW~~Le~e 54 (93)
..+.+++...| .+..++.+.. .+||+-|.+.
T Consensus 80 ~~t~~~l~~~l~~~~~~~~~s~-~ti~r~L~~~ 111 (112)
T PF13551_consen 80 RWTLEELAEWLIEEEFGIDVSP-STIRRILKRA 111 (112)
T ss_pred cccHHHHHHHHHHhccCccCCH-HHHHHHHHHC
Confidence 47889999987 7777887766 5788887764
No 123
>PF07882 Fucose_iso_N2: L-fucose isomerase, second N-terminal domain; InterPro: IPR012889 Proteins containing this domain are similar to L-fucose isomerase expressed by Escherichia coli (P11552 from SWISSPROT, 5.3.1.3 from EC). This enzyme corresponds to glucose-6-phosphate isomerase in glycolysis, and converts an aldo-hexose to a ketose to prepare it for aldol cleavage. The enzyme is a hexamer, with each subunit being wedge-shaped and composed of three domains. Both domains 1 and 2 contain central parallel beta- sheets with surrounding alpha helices. The active centre is shared between pairs of subunits related along the molecular three-fold axis, with domains 2 and 3 from one subunit providing most of the substrate-contacting residues []. ; GO: 0008736 L-fucose isomerase activity, 0006004 fucose metabolic process, 0005737 cytoplasm; PDB: 3A9R_A 3A9T_C 3A9S_C 1FUI_E.
Probab=20.55 E-value=23 Score=27.29 Aligned_cols=29 Identities=24% Similarity=0.449 Sum_probs=19.4
Q ss_pred cHHHHHHHHhchhhhhhHHHHHHHHHHHH
Q 034494 55 NKEFFEAYARKNAERATVMETRERIEKML 83 (93)
Q Consensus 55 NpeFF~aY~~~~~e~~se~~~~~~iq~m~ 83 (93)
||+||+.|..-+.|.+.+.+...|++..|
T Consensus 19 d~~f~~~ylGmr~E~VD~~Ei~RR~e~~i 47 (181)
T PF07882_consen 19 DPDFFQEYLGMRVEYVDMSEIIRRMEEGI 47 (181)
T ss_dssp -HHHHHHCT--EEEEE-THHHHHHHHCT-
T ss_pred CHHHHHHHhCCCceeecHHHHHHHHHccC
Confidence 89999999887777777777777777654
No 124
>PF12415 rpo132: Poxvirus DNA dependent RNA polymerase; InterPro: IPR024390 All three classes of poxvirus genes - early, intermediate and late - are transcribed by the viral RNA polymerase compex []. This complex is composed of nine distinct subunits which total more than 500kDa in mass. The two largest subunits (147 and 136kDa) are homologous to the largest subunits of eukaryotic and prokaryotic RNA polymerases and, like them, are thought to form a claw-shaped structure whose cleft is the site of template interaction and phosphodiester bond formation. While the smaller subunits of poxvirus RNA polymerase show much less similarity, if any, to the smaller subunits of the eukaryotic and prokaryotic enzymes, it is thought that they may play a similar role in interacting with transcription factors. The 132kDa subunit is the second largest subunit of the poxvirus DNA dependent RNA polymerase and shows structural similarity to the second-largest RNA polymerase subunits of eubacteria, archaebacteria, and eukaryotes.
Probab=20.53 E-value=1.1e+02 Score=17.57 Aligned_cols=16 Identities=38% Similarity=0.412 Sum_probs=13.2
Q ss_pred chHHHHHHHHHHHHHH
Q 034494 4 SSASYIHLVHHLIEEC 19 (93)
Q Consensus 4 ~s~~~I~~VQ~LIErC 19 (93)
-|.+-+.+|+.+||.-
T Consensus 11 mp~ei~ylvnalIest 26 (33)
T PF12415_consen 11 MPPEIIYLVNALIEST 26 (33)
T ss_pred CCHHHHHHHHHHHHHH
Confidence 3678899999999963
No 125
>cd05116 PTKc_Syk Catalytic domain of the Protein Tyrosine Kinase, Spleen tyrosine kinase. Protein Tyrosine Kinase (PTK) family; Spleen tyrosine kinase (Syk); 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. Syk, together with Zap-70, form the Syk subfamily of kinases which are cytoplasmic (or nonreceptor) tyr kinases containing two Src homology 2 (SH2) domains N-terminal to the catalytic tyr kinase domain. Syk was first cloned from the spleen, and its function in hematopoietic cells is well-established. Syk is involved in the signaling downstream of activated receptors (including B-cell and Fc receptors) that contain ITAMs (immunoreceptor tyr activation motifs), leading to processes such as cell proliferatio
Probab=20.51 E-value=1.3e+02 Score=21.11 Aligned_cols=26 Identities=12% Similarity=0.117 Sum_probs=19.2
Q ss_pred HHHHHHHHHHHHh----hCCHHHHHHHHHh
Q 034494 10 HLVHHLIEECLVF----NMSKEECMEALSK 35 (93)
Q Consensus 10 ~~VQ~LIErCLql----yMsk~Evv~~L~~ 35 (93)
..++++|.+|++. ..+-++|+..|.+
T Consensus 225 ~~l~~li~~~~~~~p~~Rp~~~~i~~~l~~ 254 (257)
T cd05116 225 PEMYDLMKLCWTYGVDERPGFAVVELRLRN 254 (257)
T ss_pred HHHHHHHHHHhccCchhCcCHHHHHHHHhc
Confidence 4567899999964 5677777777764
No 126
>COG1438 ArgR Arginine repressor [Transcription]
Probab=20.06 E-value=1.2e+02 Score=22.39 Aligned_cols=30 Identities=30% Similarity=0.389 Sum_probs=24.6
Q ss_pred hhCCHHHHHHHHHhhcCCChhhHHHHHHHHHH
Q 034494 22 FNMSKEECMEALSKHANIKPVITSTVWKELEK 53 (93)
Q Consensus 22 lyMsk~Evv~~L~~~a~I~P~fT~~VW~~Le~ 53 (93)
..-|++|+++.|+++ ||+ .--.+|-+-|.+
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 467999999999985 999 666678777776
Done!