Query 038532
Match_columns 164
No_of_seqs 132 out of 756
Neff 8.0
Searched_HMMs 46136
Date Fri Mar 29 12:02:19 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/038532.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/038532hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1724 SCF ubiquitin ligase, 100.0 3.3E-49 7.2E-54 291.8 16.1 154 5-163 5-162 (162)
2 COG5201 SKP1 SCF ubiquitin lig 100.0 8.1E-47 1.7E-51 264.6 14.7 154 5-163 2-157 (158)
3 PF01466 Skp1: Skp1 family, di 100.0 4.6E-31 1E-35 174.3 8.7 78 83-163 1-78 (78)
4 smart00512 Skp1 Found in Skp1 99.9 1.6E-27 3.4E-32 165.5 10.6 98 5-113 2-104 (104)
5 PF03931 Skp1_POZ: Skp1 family 99.8 3.3E-19 7.1E-24 112.7 4.3 59 5-65 1-61 (62)
6 KOG3473 RNA polymerase II tran 99.7 3E-16 6.4E-21 105.3 7.8 91 4-113 16-112 (112)
7 PHA02713 hypothetical protein; 98.6 2.2E-07 4.7E-12 81.5 10.0 101 6-138 27-133 (557)
8 PF00651 BTB: BTB/POZ domain; 98.5 5.1E-07 1.1E-11 62.0 8.0 92 5-126 11-109 (111)
9 PHA03098 kelch-like protein; P 98.3 4.3E-06 9.3E-11 72.6 10.3 100 7-136 12-113 (534)
10 PHA02790 Kelch-like protein; P 98.3 1.9E-06 4.2E-11 74.3 7.3 98 9-136 25-128 (480)
11 smart00225 BTB Broad-Complex, 98.2 3.5E-06 7.5E-11 54.6 5.8 81 11-121 5-90 (90)
12 KOG4441 Proteins containing BT 98.1 1.2E-05 2.7E-10 70.8 7.9 95 7-132 39-138 (571)
13 KOG4350 Uncharacterized conser 95.9 0.021 4.5E-07 48.4 5.7 111 6-124 46-173 (620)
14 KOG4682 Uncharacterized conser 95.1 0.041 8.9E-07 46.5 4.9 103 12-147 76-186 (488)
15 KOG2716 Polymerase delta-inter 95.0 0.42 9.2E-06 37.6 10.0 101 2-131 2-108 (230)
16 KOG3433 Protein involved in me 93.9 0.12 2.6E-06 39.1 4.6 37 106-147 162-200 (203)
17 COG5124 Protein predicted to b 93.0 0.087 1.9E-06 39.7 2.6 31 112-147 174-204 (209)
18 KOG0783 Uncharacterized conser 93.0 0.29 6.3E-06 45.1 6.3 108 7-138 713-825 (1267)
19 PF11822 DUF3342: Domain of un 92.3 0.15 3.3E-06 41.9 3.3 85 14-128 13-104 (317)
20 PF03962 Mnd1: Mnd1 family; I 81.8 1.5 3.3E-05 33.4 3.0 42 101-147 144-187 (188)
21 PF02214 BTB_2: BTB/POZ domain 75.9 1.9 4E-05 28.5 1.7 80 13-120 6-94 (94)
22 PF07928 Vps54: Vps54-like pro 73.7 1.1 2.3E-05 32.4 0.0 43 13-60 1-44 (135)
23 PF05409 Peptidase_C30: Corona 66.2 10 0.00022 30.7 4.0 102 41-151 161-265 (293)
24 PF03656 Pam16: Pam16; InterP 61.2 6.6 0.00014 28.1 2.0 26 127-152 51-76 (127)
25 PRK05365 malonic semialdehyde 60.9 6.3 0.00014 29.6 2.0 35 103-147 130-164 (195)
26 cd02148 Nitroreductase_5 Nitro 58.5 7 0.00015 29.1 1.8 35 103-147 123-157 (185)
27 KOG3442 Uncharacterized conser 54.9 7.2 0.00016 27.8 1.3 32 128-162 53-84 (132)
28 PF11978 MVP_shoulder: Shoulde 54.2 12 0.00027 26.3 2.3 28 104-131 36-63 (118)
29 PF12556 CobS_N: Cobaltochelat 53.7 8.1 0.00017 21.4 1.1 12 136-147 14-25 (36)
30 PF13921 Myb_DNA-bind_6: Myb-l 52.2 24 0.00052 21.0 3.2 34 121-154 20-60 (60)
31 cd05029 S-100A6 S-100A6: S-100 49.8 32 0.0007 22.5 3.8 44 114-157 10-59 (88)
32 PF10892 DUF2688: Protein of u 49.7 20 0.00044 21.9 2.4 25 133-157 30-56 (60)
33 PRK11053 dihydropteridine redu 47.2 16 0.00035 27.8 2.3 36 101-146 147-183 (217)
34 PF11198 DUF2857: Protein of u 46.6 44 0.00096 25.1 4.5 60 95-154 57-131 (180)
35 COG4957 Predicted transcriptio 46.4 19 0.0004 26.1 2.3 18 130-147 98-115 (148)
36 PF11460 DUF3007: Protein of u 45.9 20 0.00044 24.7 2.3 23 132-157 79-101 (104)
37 KOG4591 Uncharacterized conser 45.5 30 0.00064 27.0 3.4 17 44-60 109-126 (280)
38 PRK13503 transcriptional activ 43.4 1.5E+02 0.0033 22.9 9.3 78 49-144 170-250 (278)
39 PF10075 PCI_Csn8: COP9 signal 42.3 54 0.0012 23.3 4.3 47 113-163 76-126 (143)
40 PF08154 NLE: NLE (NUC135) dom 42.2 21 0.00046 22.1 1.8 43 6-50 3-55 (65)
41 KOG2075 Topoisomerase TOP1-int 41.8 1.2E+02 0.0025 26.8 6.7 114 15-130 129-252 (521)
42 smart00385 CYCLIN domain prese 41.0 80 0.0017 18.9 5.0 43 112-157 36-80 (83)
43 cd00167 SANT 'SWI3, ADA2, N-Co 40.0 31 0.00067 18.4 2.2 20 122-141 23-42 (45)
44 KOG1665 AFH1-interacting prote 39.5 35 0.00075 27.1 3.0 87 5-121 9-104 (302)
45 PF09713 A_thal_3526: Plant pr 38.3 63 0.0014 19.5 3.4 32 130-161 12-47 (54)
46 smart00717 SANT SANT SWI3, AD 38.0 35 0.00075 18.5 2.2 20 122-141 25-44 (49)
47 PF02519 Auxin_inducible: Auxi 37.8 1.3E+02 0.0028 20.4 5.5 54 6-60 40-100 (100)
48 PRK09296 cysteine desufuration 37.3 60 0.0013 23.4 3.8 31 118-148 79-117 (138)
49 TIGR02476 BluB cob(II)yrinic a 37.1 31 0.00066 26.1 2.4 38 100-147 133-170 (205)
50 PHA03098 kelch-like protein; P 36.9 2E+02 0.0043 24.9 7.7 55 86-141 96-159 (534)
51 COG1926 Predicted phosphoribos 36.1 1.7E+02 0.0037 22.9 6.3 29 81-112 187-215 (220)
52 PF09821 AAA_assoc_C: C-termin 35.8 34 0.00073 24.1 2.3 22 94-115 7-28 (120)
53 PRK15019 CsdA-binding activato 34.9 64 0.0014 23.6 3.7 32 118-149 89-128 (147)
54 TIGR03419 NifU_clost FeS clust 34.6 68 0.0015 22.4 3.7 37 104-140 46-83 (121)
55 PRK11325 scaffold protein; Pro 34.5 61 0.0013 22.8 3.5 38 104-141 52-90 (127)
56 PF08671 SinI: Anti-repressor 34.1 25 0.00055 18.6 1.0 13 129-141 15-27 (30)
57 PF05443 ROS_MUCR: ROS/MUCR tr 34.0 20 0.00043 25.8 0.9 18 130-147 94-111 (132)
58 PF01592 NifU_N: NifU-like N t 34.0 57 0.0012 22.8 3.3 21 118-138 65-85 (126)
59 TIGR03391 FeS_syn_CsdE cystein 34.0 69 0.0015 23.1 3.7 31 118-148 84-122 (138)
60 TIGR01999 iscU FeS cluster ass 33.7 66 0.0014 22.5 3.5 37 104-140 50-87 (124)
61 cd02140 Nitroreductase_4 Nitro 33.5 41 0.0009 25.0 2.6 39 101-147 127-165 (192)
62 PF13798 PCYCGC: Protein of un 33.4 65 0.0014 23.9 3.5 23 117-139 118-140 (158)
63 smart00875 BACK BTB And C-term 32.9 1.3E+02 0.0028 19.0 4.9 39 103-141 3-50 (101)
64 PF11543 UN_NPL4: Nuclear pore 32.6 23 0.0005 23.0 0.9 21 1-21 1-22 (80)
65 cd02144 iodotyrosine_dehalogen 32.5 41 0.00089 24.7 2.4 38 101-148 129-167 (193)
66 PRK13696 hypothetical protein; 30.9 1.4E+02 0.003 18.6 4.6 38 115-157 24-61 (62)
67 TIGR02698 CopY_TcrY copper tra 30.3 1.7E+02 0.0036 20.6 5.2 36 122-157 78-113 (130)
68 PF11116 DUF2624: Protein of u 29.7 1.5E+02 0.0032 19.7 4.4 10 122-131 37-46 (85)
69 COG1710 Uncharacterized protei 28.9 41 0.00088 23.9 1.7 16 129-144 108-123 (139)
70 PF13518 HTH_28: Helix-turn-he 28.5 93 0.002 17.4 3.1 20 124-143 6-25 (52)
71 PF07671 DUF1601: Protein of u 28.4 57 0.0012 18.1 1.9 30 110-139 7-36 (37)
72 PF11197 DUF2835: Protein of u 28.0 63 0.0014 20.5 2.3 21 5-25 21-41 (68)
73 PF02736 Myosin_N: Myosin N-te 27.8 53 0.0011 18.4 1.8 19 4-22 23-41 (42)
74 PRK14981 DNA-directed RNA poly 27.4 2.1E+02 0.0046 19.7 6.6 43 114-157 63-106 (112)
75 PF08661 Rep_fac-A_3: Replicat 26.7 75 0.0016 21.6 2.8 20 3-22 33-52 (109)
76 PHA02713 hypothetical protein; 26.5 1.3E+02 0.0028 26.7 4.9 75 88-163 116-200 (557)
77 PF02657 SufE: Fe-S metabolism 26.5 1.2E+02 0.0026 21.4 3.8 28 122-149 74-108 (125)
78 cd03370 NADH_oxidase NADPH_oxi 26.3 49 0.0011 23.7 1.9 36 101-146 95-131 (156)
79 PF11103 DUF2887: Protein of u 26.1 97 0.0021 23.9 3.5 28 113-140 173-200 (200)
80 PF09010 AsiA: Anti-Sigma Fact 25.7 22 0.00049 23.8 -0.0 31 129-162 46-78 (91)
81 cd06664 IscU_like Iron-sulfur 25.4 1.2E+02 0.0026 20.8 3.7 39 103-141 46-85 (123)
82 COG4049 Uncharacterized protei 25.0 65 0.0014 19.7 1.9 15 5-19 5-19 (65)
83 PRK13742 replication protein; 24.9 73 0.0016 25.2 2.7 34 114-147 163-199 (245)
84 COG0822 IscU NifU homolog invo 24.5 1.3E+02 0.0027 22.1 3.7 39 102-140 51-90 (150)
85 PF15063 TC1: Thyroid cancer p 24.0 82 0.0018 20.5 2.3 12 134-145 56-67 (79)
86 COG4224 Uncharacterized protei 24.0 73 0.0016 20.6 2.1 18 142-159 57-74 (77)
87 PF03750 DUF310: Protein of un 24.0 95 0.0021 21.6 2.9 32 112-144 9-42 (119)
88 TIGR03147 cyt_nit_nrfF cytochr 23.8 76 0.0016 22.7 2.3 17 124-140 66-83 (126)
89 COG2996 Predicted RNA-bindinin 23.5 51 0.0011 26.8 1.6 16 129-144 244-260 (287)
90 PF13384 HTH_23: Homeodomain-l 23.4 82 0.0018 17.7 2.1 15 129-143 16-30 (50)
91 KOG4244 Failed axon connection 23.2 89 0.0019 25.4 2.9 23 133-155 111-133 (281)
92 PF00134 Cyclin_N: Cyclin, N-t 23.0 1.3E+02 0.0028 20.2 3.5 43 115-157 74-117 (127)
93 PF03131 bZIP_Maf: bZIP Maf tr 22.7 1.1E+02 0.0024 20.2 2.9 27 127-156 5-31 (92)
94 cd02145 BluB Subfamily of the 22.6 58 0.0012 24.3 1.7 37 100-146 124-160 (196)
95 TIGR01994 SUF_scaf_2 SUF syste 22.6 1.5E+02 0.0032 21.1 3.7 37 105-141 51-88 (137)
96 PF00249 Myb_DNA-binding: Myb- 22.2 1.6E+02 0.0035 16.5 4.8 37 99-140 7-44 (48)
97 COG4680 Uncharacterized protei 22.0 63 0.0014 21.8 1.5 17 130-146 35-51 (98)
98 PF14098 SSPI: Small, acid-sol 21.9 1.1E+02 0.0023 19.3 2.5 19 122-140 5-23 (65)
99 PRK13379 protocatechuate 4,5-d 21.3 1.2E+02 0.0026 21.4 2.9 24 121-144 94-117 (119)
100 PF03883 DUF328: Protein of un 21.3 88 0.0019 24.6 2.6 26 122-147 32-57 (237)
101 PLN03212 Transcription repress 21.3 1.3E+02 0.0029 24.0 3.5 35 122-156 49-91 (249)
102 TIGR01044 rplV_bact ribosomal 21.2 1.1E+02 0.0023 20.8 2.6 22 121-142 13-34 (103)
103 cd02138 Nitroreductase_2 Nitro 21.2 87 0.0019 23.0 2.4 38 100-147 107-144 (181)
104 cd00068 GGL G protein gamma su 20.7 1.1E+02 0.0024 18.4 2.3 23 41-68 18-40 (57)
105 TIGR01669 phage_XkdX phage unc 20.5 1.5E+02 0.0032 17.0 2.7 24 131-155 18-41 (45)
106 TIGR03553 F420_FbiB_CTERM F420 20.4 59 0.0013 24.1 1.3 38 100-147 126-165 (194)
107 PF03918 CcmH: Cytochrome C bi 20.4 84 0.0018 22.9 2.1 12 129-140 72-83 (148)
108 PF10507 DUF2453: Protein of u 20.2 2.4E+02 0.0052 19.7 4.2 36 117-152 36-79 (111)
109 PF00382 TFIIB: Transcription 20.1 2.2E+02 0.0048 17.3 4.2 29 115-143 37-67 (71)
110 PF00196 GerE: Bacterial regul 20.1 1.4E+02 0.0029 17.5 2.7 22 122-143 10-31 (58)
No 1
>KOG1724 consensus SCF ubiquitin ligase, Skp1 component [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=3.3e-49 Score=291.76 Aligned_cols=154 Identities=47% Similarity=0.817 Sum_probs=138.0
Q ss_pred CeEEEEcCCCCEEEecHHHHHHHHHHHHHHHhcC-CCC--cccce-ecHHHHHHHHHHhcccccCCCCCCCCCCCCchhh
Q 038532 5 STVKLRSSDNEVFEVEKQVMIQSGTIRNMIEDDA-ADG--EIPVQ-ISSRNLAKIVEWCKCMQHRDRNNNNNDNNKEEEE 80 (164)
Q Consensus 5 ~~i~l~s~DG~~f~v~~~~a~~S~~l~~~~~~~~-~~~--~I~l~-v~s~~L~~Ii~~~~~~~h~~~~~~~~~~~~~~~~ 80 (164)
++|+|+|+||++|.|+.++|++|.+|++++.+.| ..+ +|||| |+|.||++|++||+ ||+++++...+....+..
T Consensus 5 ~~ikL~SsDG~~f~ve~~~a~~s~~i~~~~~~~~~~~~~~~IPl~nV~~~iL~kVIewC~--~Hk~d~~~~~~~~~~~~~ 82 (162)
T KOG1724|consen 5 KKIKLESSDGEIFEVEEEVARQSQTISAHMIEDGCADENDPIPLPNVTSKILKKVIEWCK--KHKDDDPANPEDKELPEE 82 (162)
T ss_pred CeEEEEccCCceeehhHHHHHHhHHHHHHHHHcCCCccCCccccCccCHHHHHHHHHHHH--Hccccccccccccccccc
Confidence 7999999999999999999999999999998765 334 89999 99999999999999 999886543321101233
Q ss_pred hhHHHHHHHhhhhhcCcHHHHHHHHHhhhcCCChhHHHHHHHHHHHHhcCCCHHHHHhHcCCCCCCCHHHHHHHHHHcCC
Q 038532 81 EEEEEWEKKFDEEVSEDKDLHFGLLLAANYLEIPALLDRLCQLAADIVKGKTPEEIRRTFNIKKDFTPEEEKAVMDEHGW 160 (164)
Q Consensus 81 ~~~~~wd~~F~~~l~~~~~~l~~Ll~AA~~L~I~~L~~l~~~~ia~~i~gks~eeir~~f~i~~d~t~eee~~i~~e~~W 160 (164)
..+++||++| ++++...||+|+.|||||+|++|+++||+.+|++++||||+|||+.|||++|+||||++++++++.|
T Consensus 83 ~~i~~WD~~F---lk~d~~tLfdli~AAnyLdi~gLl~~~ck~va~mikgktpeEir~~f~I~~d~t~eE~~~~~~e~~~ 159 (162)
T KOG1724|consen 83 TDIPEWDAEF---LKVDQGTLFDLILAANYLDIKGLLDLTCKTVANMIKGKTPEEIREIFNIENDETPEEEEAIRKENEW 159 (162)
T ss_pred CCccHHHHHH---HhcCHHHHHHHHHHhhhcccHHHHHHHHHHHHHHHccCCHHHHHHHcCCCCCCChhHHHHHhhcccc
Confidence 4499999999 8899999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccC
Q 038532 161 ALH 163 (164)
Q Consensus 161 ~~~ 163 (164)
+++
T Consensus 160 ~~~ 162 (162)
T KOG1724|consen 160 AFE 162 (162)
T ss_pred ccC
Confidence 985
No 2
>COG5201 SKP1 SCF ubiquitin ligase, SKP1 component [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=8.1e-47 Score=264.57 Aligned_cols=154 Identities=37% Similarity=0.686 Sum_probs=136.3
Q ss_pred CeEEEEcCCCCEEEecHHHHHHHHHHHHHHHhcC-CCCcccce-ecHHHHHHHHHHhcccccCCCCCCCCCCCCchhhhh
Q 038532 5 STVKLRSSDNEVFEVEKQVMIQSGTIRNMIEDDA-ADGEIPVQ-ISSRNLAKIVEWCKCMQHRDRNNNNNDNNKEEEEEE 82 (164)
Q Consensus 5 ~~i~l~s~DG~~f~v~~~~a~~S~~l~~~~~~~~-~~~~I~l~-v~s~~L~~Ii~~~~~~~h~~~~~~~~~~~~~~~~~~ 82 (164)
.+|.|.|.||++|.|+..+|..|-+|++|+.+.+ .+.|||+| |+|.+|.+|++||+ ||.....+...+.-......
T Consensus 2 s~i~l~s~dge~F~vd~~iAerSiLikN~l~d~~~~n~p~p~pnVrSsvl~kv~ew~e--hh~~s~sede~d~~~rks~p 79 (158)
T COG5201 2 SMIELESIDGEIFRVDENIAERSILIKNMLCDSTACNYPIPAPNVRSSVLMKVQEWME--HHTSSLSEDENDLEIRKSKP 79 (158)
T ss_pred CceEEEecCCcEEEehHHHHHHHHHHHHHhccccccCCCCcccchhHHHHHHHHHHHH--hccccCCCccChHhhhccCC
Confidence 3799999999999999999999999999998875 35789999 99999999999999 99874333221111112345
Q ss_pred HHHHHHHhhhhhcCcHHHHHHHHHhhhcCCChhHHHHHHHHHHHHhcCCCHHHHHhHcCCCCCCCHHHHHHHHHHcCCcc
Q 038532 83 EEEWEKKFDEEVSEDKDLHFGLLLAANYLEIPALLDRLCQLAADIVKGKTPEEIRRTFNIKKDFTPEEEKAVMDEHGWAL 162 (164)
Q Consensus 83 ~~~wd~~F~~~l~~~~~~l~~Ll~AA~~L~I~~L~~l~~~~ia~~i~gks~eeir~~f~i~~d~t~eee~~i~~e~~W~~ 162 (164)
.+.||+.| +.+|++.|+++++|||||+|++|+++||+.||++|+||||+|||++|||++||||||+++||+||+|++
T Consensus 80 ~D~wdr~F---m~vDqemL~eI~laaNYL~ikpLLd~gCKivaemirgkSpeeir~tfni~ndfTpEEe~~irkEnEWae 156 (158)
T COG5201 80 SDFWDRFF---MEVDQEMLLEICLAANYLEIKPLLDLGCKIVAEMIRGKSPEEIRETFNIENDFTPEEERRIRKENEWAE 156 (158)
T ss_pred ccHHHHHH---HHhhHHHHHHHHHhhccccchHHHHHHHHHHHHHHccCCHHHHHHHhCCCCCCCHHHHHHHHHhccccc
Confidence 67899999 899999999999999999999999999999999999999999999999999999999999999999997
Q ss_pred C
Q 038532 163 H 163 (164)
Q Consensus 163 ~ 163 (164)
+
T Consensus 157 d 157 (158)
T COG5201 157 D 157 (158)
T ss_pred c
Confidence 6
No 3
>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=99.97 E-value=4.6e-31 Score=174.29 Aligned_cols=78 Identities=49% Similarity=0.894 Sum_probs=68.3
Q ss_pred HHHHHHHhhhhhcCcHHHHHHHHHhhhcCCChhHHHHHHHHHHHHhcCCCHHHHHhHcCCCCCCCHHHHHHHHHHcCCcc
Q 038532 83 EEEWEKKFDEEVSEDKDLHFGLLLAANYLEIPALLDRLCQLAADIVKGKTPEEIRRTFNIKKDFTPEEEKAVMDEHGWAL 162 (164)
Q Consensus 83 ~~~wd~~F~~~l~~~~~~l~~Ll~AA~~L~I~~L~~l~~~~ia~~i~gks~eeir~~f~i~~d~t~eee~~i~~e~~W~~ 162 (164)
+++||++| ++++.+.|++|+.||+||+|++|+++||++||.+++|||++|||++|||++|+|+||++++|+||+|+|
T Consensus 1 l~~wD~~F---~~~~~~~L~~l~~AA~yL~I~~L~~~~~~~iA~~i~gks~eeir~~fgi~~d~t~eee~~i~~e~~w~~ 77 (78)
T PF01466_consen 1 LPEWDQEF---LDVDNDELFDLLNAANYLDIKGLLDLCCKYIANMIKGKSPEEIRKYFGIENDLTPEEEEEIRKENEWAF 77 (78)
T ss_dssp HHHHHHHH---T-S-HHHHHHHHHHHHHHT-HHHHHHHHHHHHHHHTTS-HHHHHHHHT---TSSHHHHHHHHHHCCCTB
T ss_pred CCHHHHHH---HHcCHHHHHHHHHHHHHHcchHHHHHHHHHHHHHhcCCCHHHHHHHcCCCCCCCHHHHHHHHHHcchhc
Confidence 57999999 788999999999999999999999999999999999999999999999999999999999999999998
Q ss_pred C
Q 038532 163 H 163 (164)
Q Consensus 163 ~ 163 (164)
+
T Consensus 78 ~ 78 (78)
T PF01466_consen 78 E 78 (78)
T ss_dssp -
T ss_pred C
Confidence 6
No 4
>smart00512 Skp1 Found in Skp1 protein family. Family of Skp1 (kinetochore protein required for cell cycle progression) and elongin C (subunit of RNA polymerase II transcription factor SIII) homologues.
Probab=99.95 E-value=1.6e-27 Score=165.50 Aligned_cols=98 Identities=44% Similarity=0.742 Sum_probs=86.7
Q ss_pred CeEEEEcCCCCEEEecHHHHHHHHHHHHHHHhcCCC----Ccccce-ecHHHHHHHHHHhcccccCCCCCCCCCCCCchh
Q 038532 5 STVKLRSSDNEVFEVEKQVMIQSGTIRNMIEDDAAD----GEIPVQ-ISSRNLAKIVEWCKCMQHRDRNNNNNDNNKEEE 79 (164)
Q Consensus 5 ~~i~l~s~DG~~f~v~~~~a~~S~~l~~~~~~~~~~----~~I~l~-v~s~~L~~Ii~~~~~~~h~~~~~~~~~~~~~~~ 79 (164)
++++|+|+||++|.|++++|++|++|++|+++.+.. .+||+| |+|.+|++|++||+ ||+.++.+...
T Consensus 2 ~~v~L~S~Dg~~f~v~~~~a~~S~~i~~~l~~~~~~~~~~~~Ipl~~v~~~~L~~Vi~yc~--~h~~~~~~~~~------ 73 (104)
T smart00512 2 KYIKLISSDGEVFEVEREVARQSKTIKAMIEDLGVDDENNNPIPLPNVTSKILSKVIEYCE--HHVDDPPSVAD------ 73 (104)
T ss_pred CeEEEEeCCCCEEEecHHHHHHHHHHHHHHHccCcccCCCCCccCCCcCHHHHHHHHHHHH--HcccCCCCccc------
Confidence 589999999999999999999999999999986532 489999 99999999999999 99987654321
Q ss_pred hhhHHHHHHHhhhhhcCcHHHHHHHHHhhhcCCC
Q 038532 80 EEEEEEWEKKFDEEVSEDKDLHFGLLLAANYLEI 113 (164)
Q Consensus 80 ~~~~~~wd~~F~~~l~~~~~~l~~Ll~AA~~L~I 113 (164)
...+++||.+| ++++.+.|++|+.||+||+|
T Consensus 74 ~~~~~~wD~~F---~~~d~~~l~dLl~AAnyL~I 104 (104)
T smart00512 74 KDDIPTWDAEF---LKIDQETLFELILAANYLDI 104 (104)
T ss_pred cccccHHHHHH---HcCCHHHHHHHHHHHHhhCC
Confidence 14579999999 78999999999999999997
No 5
>PF03931 Skp1_POZ: Skp1 family, tetramerisation domain; InterPro: IPR016073 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 POZ domain with a core structure consisting of beta(2)/alpha(2)/beta(2)/alpha(2) in two layers, alpha/beta. This domain is found at the N-terminal of SKP1 proteins [] as well as in subunit D of the centromere DNA-binding protein complex Cbf3 []. ; GO: 0006511 ubiquitin-dependent protein catabolic process; PDB: 1LM8_C 2XAI_E 1VCB_E 3ZRC_K 3ZRF_E 3DCG_B 2C9W_C 1LQB_B 2IZV_C 1HV2_A ....
Probab=99.77 E-value=3.3e-19 Score=112.66 Aligned_cols=59 Identities=47% Similarity=0.775 Sum_probs=53.0
Q ss_pred CeEEEEcCCCCEEEecHHHHHHHHHHHHHHHhcCCCC-cccce-ecHHHHHHHHHHhcccccC
Q 038532 5 STVKLRSSDNEVFEVEKQVMIQSGTIRNMIEDDAADG-EIPVQ-ISSRNLAKIVEWCKCMQHR 65 (164)
Q Consensus 5 ~~i~l~s~DG~~f~v~~~~a~~S~~l~~~~~~~~~~~-~I~l~-v~s~~L~~Ii~~~~~~~h~ 65 (164)
++|+|+|+||++|.|++++|++|++|++|+++.+... +|||| |++++|++|++||+ ||+
T Consensus 1 ~~v~L~SsDg~~f~V~~~~a~~S~~i~~ml~~~~~~~~~Ipl~~v~~~~L~kViewc~--~H~ 61 (62)
T PF03931_consen 1 MYVKLVSSDGQEFEVSREAAKQSKTIKNMLEDLGDEDEPIPLPNVSSRILKKVIEWCE--HHK 61 (62)
T ss_dssp -EEEEEETTSEEEEEEHHHHTTSHHHHHHHHCTCCCGTEEEETTS-HHHHHHHHHHHH--HHH
T ss_pred CEEEEEcCCCCEEEeeHHHHHHhHHHHHHHhhhcccccccccCccCHHHHHHHHHHHH--hcC
Confidence 3799999999999999999999999999999876544 59999 99999999999999 885
No 6
>KOG3473 consensus RNA polymerase II transcription elongation factor Elongin/SIII, subunit elongin C [Transcription]
Probab=99.67 E-value=3e-16 Score=105.34 Aligned_cols=91 Identities=32% Similarity=0.456 Sum_probs=74.4
Q ss_pred CCeEEEEcCCCCEEEecHHHHHHHHHHHHHHHhcC-----CCCcccce-ecHHHHHHHHHHhcccccCCCCCCCCCCCCc
Q 038532 4 TSTVKLRSSDNEVFEVEKQVMIQSGTIRNMIEDDA-----ADGEIPVQ-ISSRNLAKIVEWCKCMQHRDRNNNNNDNNKE 77 (164)
Q Consensus 4 ~~~i~l~s~DG~~f~v~~~~a~~S~~l~~~~~~~~-----~~~~I~l~-v~s~~L~~Ii~~~~~~~h~~~~~~~~~~~~~ 77 (164)
+.+++|+|+||++|.+.+++|..|++||.|+.+.+ ..+.+.++ |+|-+|+||++|+.|...+.+ .
T Consensus 16 ~~yVkLvS~Ddhefiikre~AmtSgTiraml~gpg~~se~~~n~v~f~di~shiLeKvc~Yl~Yk~rY~~-~-------- 86 (112)
T KOG3473|consen 16 SMYVKLVSSDDHEFIIKREHAMTSGTIRAMLSGPGVFSEAEKNEVYFRDIPSHILEKVCEYLAYKVRYTN-S-------- 86 (112)
T ss_pred hhheEeecCCCcEEEEeehhhhhhhHHHHHHcCCccccccccceEEeccchHHHHHHHHHHhhheeeecc-c--------
Confidence 47999999999999999999999999999999654 35789999 999999999999994322221 1
Q ss_pred hhhhhHHHHHHHhhhhhcCcHHHHHHHHHhhhcCCC
Q 038532 78 EEEEEEEEWEKKFDEEVSEDKDLHFGLLLAANYLEI 113 (164)
Q Consensus 78 ~~~~~~~~wd~~F~~~l~~~~~~l~~Ll~AA~~L~I 113 (164)
...+| +| .+..+..++|+.|||||++
T Consensus 87 --s~eiP----eF----~IppemaleLL~aAn~Lec 112 (112)
T KOG3473|consen 87 --STEIP----EF----DIPPEMALELLMAANYLEC 112 (112)
T ss_pred --cccCC----CC----CCCHHHHHHHHHHhhhhcC
Confidence 12334 34 7889999999999999974
No 7
>PHA02713 hypothetical protein; Provisional
Probab=98.64 E-value=2.2e-07 Score=81.53 Aligned_cols=101 Identities=17% Similarity=0.179 Sum_probs=83.0
Q ss_pred eEEEEcCCCCEEEecHHHH-HHHHHHHHHHHhc-C---CCCcccce-ecHHHHHHHHHHhcccccCCCCCCCCCCCCchh
Q 038532 6 TVKLRSSDNEVFEVEKQVM-IQSGTIRNMIEDD-A---ADGEIPVQ-ISSRNLAKIVEWCKCMQHRDRNNNNNDNNKEEE 79 (164)
Q Consensus 6 ~i~l~s~DG~~f~v~~~~a-~~S~~l~~~~~~~-~---~~~~I~l~-v~s~~L~~Ii~~~~~~~h~~~~~~~~~~~~~~~ 79 (164)
.++|...+|+.|.+.+.++ ..|.+++.|+... . ....|.|. |+..+|+.|++|++ ..
T Consensus 27 DV~L~v~~~~~f~~Hr~vLaa~S~YF~amF~~~~~e~~~~~~v~l~~v~~~~~~~ll~y~Y--t~--------------- 89 (557)
T PHA02713 27 DVIITIGDGEEIKAHKTILAAGSKYFRTLFTTPMIIRDLVTRVNLQMFDKDAVKNIVQYLY--NR--------------- 89 (557)
T ss_pred CEEEEeCCCCEEeehHHHHhhcCHHHHHHhcCCchhhccCceEEeccCCHHHHHHHHHHhc--CC---------------
Confidence 4788877799999999995 5899999999753 1 24568999 99999999999999 41
Q ss_pred hhhHHHHHHHhhhhhcCcHHHHHHHHHhhhcCCChhHHHHHHHHHHHHhcCCCHHHHHh
Q 038532 80 EEEEEEWEKKFDEEVSEDKDLHFGLLLAANYLEIPALLDRLCQLAADIVKGKTPEEIRR 138 (164)
Q Consensus 80 ~~~~~~wd~~F~~~l~~~~~~l~~Ll~AA~~L~I~~L~~l~~~~ia~~i~gks~eeir~ 138 (164)
.++.+.+.+|+.||++|+|+.|.+.||.++...+.-.+.=+|+.
T Consensus 90 ---------------~i~~~nv~~ll~aA~~lqi~~l~~~C~~~l~~~l~~~NCl~i~~ 133 (557)
T PHA02713 90 ---------------HISSMNVIDVLKCADYLLIDDLVTDCESYIKDYTNHDTCIYMYH 133 (557)
T ss_pred ---------------CCCHHHHHHHHHHHHHHCHHHHHHHHHHHHHhhCCccchHHHHH
Confidence 12345689999999999999999999999988887777666654
No 8
>PF00651 BTB: BTB/POZ domain; InterPro: IPR013069 The BTB (for BR-C, ttk and bab) [] or POZ (for Pox virus and Zinc finger) [] domain is present near the N terminus of a fraction of zinc finger (IPR007087 from INTERPRO) proteins and in proteins that contain the IPR006652 from INTERPRO motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation []. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule []. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT [, , ]. The POZ or BTB domain is also known as BR-C/Ttk or ZiN.; GO: 0005515 protein binding; PDB: 3M5B_A 1R28_B 3LBZ_A 3E4U_F 3BIM_B 1R2B_A 1R29_A 2VPK_A 2YY9_B 3GA1_A ....
Probab=98.55 E-value=5.1e-07 Score=61.95 Aligned_cols=92 Identities=24% Similarity=0.363 Sum_probs=74.1
Q ss_pred CeEEEEcCCCCEEEecHHHH-HHHHHHHHHHHhcC-CC---Ccccce-ecHHHHHHHHHHhcccccCCCCCCCCCCCCch
Q 038532 5 STVKLRSSDNEVFEVEKQVM-IQSGTIRNMIEDDA-AD---GEIPVQ-ISSRNLAKIVEWCKCMQHRDRNNNNNDNNKEE 78 (164)
Q Consensus 5 ~~i~l~s~DG~~f~v~~~~a-~~S~~l~~~~~~~~-~~---~~I~l~-v~s~~L~~Ii~~~~~~~h~~~~~~~~~~~~~~ 78 (164)
..++|+..||+.|.|++.++ ..|+++++++...+ .+ ..|+++ ++...++.+++||+ ...
T Consensus 11 ~D~~i~v~d~~~~~vhk~iL~~~S~~F~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~l~~~Y--~~~------------- 75 (111)
T PF00651_consen 11 SDVTIRVGDGKTFYVHKNILAARSPYFRNLFEGSKFKESTVPEISLPDVSPEAFEAFLEYMY--TGE------------- 75 (111)
T ss_dssp --EEEEETTTEEEEE-HHHHHHHBHHHHHHHTTTTSTTSSEEEEEETTSCHHHHHHHHHHHH--HSE-------------
T ss_pred CCEEEEECCCEEEeechhhhhccchhhhhccccccccccccccccccccccccccccccccc--CCc-------------
Confidence 46889999999999999995 68999999999862 22 257888 99999999999998 311
Q ss_pred hhhhHHHHHHHhhhhhcCc-HHHHHHHHHhhhcCCChhHHHHHHHHHHH
Q 038532 79 EEEEEEEWEKKFDEEVSED-KDLHFGLLLAANYLEIPALLDRLCQLAAD 126 (164)
Q Consensus 79 ~~~~~~~wd~~F~~~l~~~-~~~l~~Ll~AA~~L~I~~L~~l~~~~ia~ 126 (164)
+.++ .+.+.+++.+|++|+++.|.+.|+..+..
T Consensus 76 ---------------~~~~~~~~~~~ll~lA~~~~~~~L~~~~~~~l~~ 109 (111)
T PF00651_consen 76 ---------------IEINSDENVEELLELADKLQIPELKKACEKFLQE 109 (111)
T ss_dssp ---------------EEEE-TTTHHHHHHHHHHTTBHHHHHHHHHHHHH
T ss_pred ---------------ccCCHHHHHHHHHHHHHHhCcHHHHHHHHHHHHh
Confidence 1233 56689999999999999999999998864
No 9
>PHA03098 kelch-like protein; Provisional
Probab=98.33 E-value=4.3e-06 Score=72.59 Aligned_cols=100 Identities=16% Similarity=0.271 Sum_probs=76.4
Q ss_pred EEEE-cCCCCEEEecHHHH-HHHHHHHHHHHhcCCCCcccceecHHHHHHHHHHhcccccCCCCCCCCCCCCchhhhhHH
Q 038532 7 VKLR-SSDNEVFEVEKQVM-IQSGTIRNMIEDDAADGEIPVQISSRNLAKIVEWCKCMQHRDRNNNNNDNNKEEEEEEEE 84 (164)
Q Consensus 7 i~l~-s~DG~~f~v~~~~a-~~S~~l~~~~~~~~~~~~I~l~v~s~~L~~Ii~~~~~~~h~~~~~~~~~~~~~~~~~~~~ 84 (164)
++|. +.+|+.|.+++.++ ..|++++.|+...-....|.++.+..+|+.|++|++ . +.
T Consensus 12 v~l~~~~~~~~~~~Hk~vLaa~S~yF~~mf~~~~~~~~i~l~~~~~~~~~~l~y~Y--t---g~---------------- 70 (534)
T PHA03098 12 ESIIIVNGGGIIKVHKIILSSSSEYFKKMFKNNFKENEINLNIDYDSFNEVIKYIY--T---GK---------------- 70 (534)
T ss_pred EEEEEEcCCEEEEeHHHHHHhhhHHHHHHHhCCCCCceEEecCCHHHHHHHHHHhc--C---Cc----------------
Confidence 4555 46899999999995 579999999986422456777678999999999999 3 10
Q ss_pred HHHHHhhhhhcCcHHHHHHHHHhhhcCCChhHHHHHHHHHHHHhcCCCHHHH
Q 038532 85 EWEKKFDEEVSEDKDLHFGLLLAANYLEIPALLDRLCQLAADIVKGKTPEEI 136 (164)
Q Consensus 85 ~wd~~F~~~l~~~~~~l~~Ll~AA~~L~I~~L~~l~~~~ia~~i~gks~eei 136 (164)
+.++.+.+.+|+.||++|+++.|.++|++++...+.-.+.-++
T Consensus 71 ---------~~i~~~~~~~ll~~A~~l~~~~l~~~C~~~l~~~l~~~nc~~~ 113 (534)
T PHA03098 71 ---------INITSNNVKDILSIANYLIIDFLINLCINYIIKIIDDNNCIDI 113 (534)
T ss_pred ---------eEEcHHHHHHHHHHHHHhCcHHHHHHHHHHHHHhCCHhHHHHH
Confidence 3456667889999999999999999999888777655444333
No 10
>PHA02790 Kelch-like protein; Provisional
Probab=98.30 E-value=1.9e-06 Score=74.26 Aligned_cols=98 Identities=12% Similarity=0.075 Sum_probs=73.7
Q ss_pred EEcCCCCEEEecHHH-HHHHHHHHHHHHhc-C-CCCcccc---eecHHHHHHHHHHhcccccCCCCCCCCCCCCchhhhh
Q 038532 9 LRSSDNEVFEVEKQV-MIQSGTIRNMIEDD-A-ADGEIPV---QISSRNLAKIVEWCKCMQHRDRNNNNNDNNKEEEEEE 82 (164)
Q Consensus 9 l~s~DG~~f~v~~~~-a~~S~~l~~~~~~~-~-~~~~I~l---~v~s~~L~~Ii~~~~~~~h~~~~~~~~~~~~~~~~~~ 82 (164)
+..--|+.|.+.+.+ |..|++++.|+... . ....|.+ .|+..+|+.|++|++ . ..
T Consensus 25 ~~~~~~~~~~~HR~VLAa~S~YFraMF~~~~~Es~~~v~~~~~~v~~~~l~~lldy~Y--T---g~-------------- 85 (480)
T PHA02790 25 IIEAIGGNIIVNSTILKKLSPYFRTHLRQKYTKNKDPVTRVCLDLDIHSLTSIVIYSY--T---GK-------------- 85 (480)
T ss_pred EEEEcCcEEeeehhhhhhcCHHHHHHhcCCccccccceEEEecCcCHHHHHHHHHhhe--e---ee--------------
Confidence 334568899999999 56899999999753 1 1223433 399999999999998 3 10
Q ss_pred HHHHHHHhhhhhcCcHHHHHHHHHhhhcCCChhHHHHHHHHHHHHhcCCCHHHH
Q 038532 83 EEEWEKKFDEEVSEDKDLHFGLLLAANYLEIPALLDRLCQLAADIVKGKTPEEI 136 (164)
Q Consensus 83 ~~~wd~~F~~~l~~~~~~l~~Ll~AA~~L~I~~L~~l~~~~ia~~i~gks~eei 136 (164)
+.++.+++.+|+.||++|+|+.+++.||+++...+.-.+.=+|
T Consensus 86 -----------l~it~~nV~~ll~aA~~Lqi~~v~~~C~~fL~~~l~~~NCl~i 128 (480)
T PHA02790 86 -----------VYIDSHNVVNLLRASILTSVEFIIYTCINFILRDFRKEYCVEC 128 (480)
T ss_pred -----------EEEecccHHHHHHHHHHhChHHHHHHHHHHHHhhCCcchHHHH
Confidence 4566778999999999999999999999988776665543333
No 11
>smart00225 BTB Broad-Complex, Tramtrack and Bric a brac. Domain in Broad-Complex, Tramtrack and Bric a brac. Also known as POZ (poxvirus and zinc finger) domain. Known to be a protein-protein interaction motif found at the N-termini of several C2H2-type transcription factors as well as Shaw-type potassium channels. Known structure reveals a tightly intertwined dimer formed via interactions between N-terminal strand and helix structures. However in a subset of BTB/POZ domains, these two secondary structures appear to be missing. Be aware SMART predicts BTB/POZ domains without the beta1- and alpha1-secondary structures.
Probab=98.24 E-value=3.5e-06 Score=54.64 Aligned_cols=81 Identities=21% Similarity=0.317 Sum_probs=65.2
Q ss_pred cCCCCEEEecHHHHH-HHHHHHHHHHhcC---CCCcccce-ecHHHHHHHHHHhcccccCCCCCCCCCCCCchhhhhHHH
Q 038532 11 SSDNEVFEVEKQVMI-QSGTIRNMIEDDA---ADGEIPVQ-ISSRNLAKIVEWCKCMQHRDRNNNNNDNNKEEEEEEEEE 85 (164)
Q Consensus 11 s~DG~~f~v~~~~a~-~S~~l~~~~~~~~---~~~~I~l~-v~s~~L~~Ii~~~~~~~h~~~~~~~~~~~~~~~~~~~~~ 85 (164)
..+|+.|.+++.++. .|..++.++.... ....|+++ ++...++.+++|++ .-.
T Consensus 5 ~v~~~~~~~h~~iL~~~s~~f~~~~~~~~~~~~~~~i~l~~~~~~~f~~~l~~ly--~~~-------------------- 62 (90)
T smart00225 5 VVGGKKFKAHKAVLAACSPYFKALFSGDFKESKKSEIYLDDVSPEDFRALLEFLY--TGK-------------------- 62 (90)
T ss_pred EECCEEEehHHHHHhhcCHHHHHHHcCCCccCCCCEEEecCCCHHHHHHHHHeec--Cce--------------------
Confidence 457799999999965 6899999998643 34678898 99999999999999 411
Q ss_pred HHHHhhhhhcCcHHHHHHHHHhhhcCCChhHHHHHH
Q 038532 86 WEKKFDEEVSEDKDLHFGLLLAANYLEIPALLDRLC 121 (164)
Q Consensus 86 wd~~F~~~l~~~~~~l~~Ll~AA~~L~I~~L~~l~~ 121 (164)
+.++...+.+++.+|++++++.|.+.|+
T Consensus 63 --------~~~~~~~~~~l~~~a~~~~~~~l~~~c~ 90 (90)
T smart00225 63 --------LDLPEENVEELLELADYLQIPGLVELCE 90 (90)
T ss_pred --------eecCHHHHHHHHHHHHHHCcHHHHhhhC
Confidence 1233446889999999999999999874
No 12
>KOG4441 consensus Proteins containing BTB/POZ and Kelch domains, involved in regulatory/signal transduction processes [Signal transduction mechanisms; General function prediction only]
Probab=98.09 E-value=1.2e-05 Score=70.80 Aligned_cols=95 Identities=21% Similarity=0.341 Sum_probs=76.7
Q ss_pred EEEEcCCCCEEEecHHH-HHHHHHHHHHHHhc---CCCCcccce-ecHHHHHHHHHHhcccccCCCCCCCCCCCCchhhh
Q 038532 7 VKLRSSDNEVFEVEKQV-MIQSGTIRNMIEDD---AADGEIPVQ-ISSRNLAKIVEWCKCMQHRDRNNNNNDNNKEEEEE 81 (164)
Q Consensus 7 i~l~s~DG~~f~v~~~~-a~~S~~l~~~~~~~---~~~~~I~l~-v~s~~L~~Ii~~~~~~~h~~~~~~~~~~~~~~~~~ 81 (164)
+.|.- +|+.|...+.+ |..|++++.|+... .....|.+. |+..+|..+++|++ ...
T Consensus 39 v~L~v-~~~~~~aHR~VLAa~S~YFraMFt~~l~e~~~~~i~l~~v~~~~l~~ll~y~Y--t~~---------------- 99 (571)
T KOG4441|consen 39 VTLLV-GDREFPAHRVVLAACSPYFRAMFTSGLKESKQKEINLEGVDPETLELLLDYAY--TGK---------------- 99 (571)
T ss_pred EEEEE-CCeeechHHHHHHhccHHHHHHhcCCcccccceEEEEecCCHHHHHHHHHHhh--cce----------------
Confidence 34444 44999999999 56899999999853 245789999 99999999999999 411
Q ss_pred hHHHHHHHhhhhhcCcHHHHHHHHHhhhcCCChhHHHHHHHHHHHHhcCCC
Q 038532 82 EEEEWEKKFDEEVSEDKDLHFGLLLAANYLEIPALLDRLCQLAADIVKGKT 132 (164)
Q Consensus 82 ~~~~wd~~F~~~l~~~~~~l~~Ll~AA~~L~I~~L~~l~~~~ia~~i~gks 132 (164)
+.++.+.+.+|+.||++|+|+.+.+.||.++...+--.+
T Consensus 100 ------------i~i~~~nVq~ll~aA~~lQi~~v~~~C~~fL~~~l~~~N 138 (571)
T KOG4441|consen 100 ------------LEISEDNVQELLEAASLLQIPEVVDACCEFLESQLDPSN 138 (571)
T ss_pred ------------EEechHhHHHHHHHHHHhhhHHHHHHHHHHHHhcCCHHH
Confidence 557788899999999999999999999998876544333
No 13
>KOG4350 consensus Uncharacterized conserved protein, contains BTB/POZ domain [General function prediction only]
Probab=95.86 E-value=0.021 Score=48.39 Aligned_cols=111 Identities=14% Similarity=0.168 Sum_probs=76.1
Q ss_pred eEEEEcCCCCEEEecHHH-HHHHHHHHHHHHhc---CCCCcccce-ecHHHHHHHHHHhcccccCCCCCCCCCC-----C
Q 038532 6 TVKLRSSDNEVFEVEKQV-MIQSGTIRNMIEDD---AADGEIPVQ-ISSRNLAKIVEWCKCMQHRDRNNNNNDN-----N 75 (164)
Q Consensus 6 ~i~l~s~DG~~f~v~~~~-a~~S~~l~~~~~~~---~~~~~I~l~-v~s~~L~~Ii~~~~~~~h~~~~~~~~~~-----~ 75 (164)
.++++-.| +.|...+-+ |..|.++|.|+=.. .....|||+ -++..++.+++|++ .-+-+-....++ -
T Consensus 46 DVtfvve~-~rfpAHRvILAaRs~yFRAlLYgGm~Es~q~~ipLq~t~~eAF~~lLrYiY--tg~~~l~~~~ed~lld~L 122 (620)
T KOG4350|consen 46 DVTFVVED-TRFPAHRVILAARSSYFRALLYGGMQESHQQLIPLQETNSEAFRALLRYIY--TGKIDLAGVEEDILLDYL 122 (620)
T ss_pred ceEEEEec-cccchhhhhHHHHHHHHHHHHhhhhhhhhhcccccccccHHHHHHHHHHHh--hcceecccchHHHHHHHH
Confidence 46666655 778888777 56899999998653 135789999 77999999999998 432221111111 0
Q ss_pred C-------chhhhhHHHHHHHhhhhhcCcHHHHHHHHHhhhcCCChhHHHHHHHHH
Q 038532 76 K-------EEEEEEEEEWEKKFDEEVSEDKDLHFGLLLAANYLEIPALLDRLCQLA 124 (164)
Q Consensus 76 ~-------~~~~~~~~~wd~~F~~~l~~~~~~l~~Ll~AA~~L~I~~L~~l~~~~i 124 (164)
+ ......++++-++. +..+.++-++.||.+.+.+.|.++||.++
T Consensus 123 slAh~Ygf~~Le~aiSeYl~~i-----L~~~NvCmifdaA~ly~l~~Lt~~C~mfm 173 (620)
T KOG4350|consen 123 SLAHRYGFIQLETAISEYLKEI-----LKNENVCMIFDAAYLYQLTDLTDYCMMFM 173 (620)
T ss_pred HHHHhcCcHHHHHHHHHHHHHH-----HcccceeeeeeHHHHhcchHHHHHHHHHH
Confidence 0 11233345444444 35667899999999999999999999876
No 14
>KOG4682 consensus Uncharacterized conserved protein, contains BTB/POZ domain [General function prediction only]
Probab=95.08 E-value=0.041 Score=46.48 Aligned_cols=103 Identities=19% Similarity=0.186 Sum_probs=75.3
Q ss_pred CCCCEEEecHHHHHHHHHHHHHHHhcC---CC----Ccccce-ecHHHHHHHHHHhcccccCCCCCCCCCCCCchhhhhH
Q 038532 12 SDNEVFEVEKQVMIQSGTIRNMIEDDA---AD----GEIPVQ-ISSRNLAKIVEWCKCMQHRDRNNNNNDNNKEEEEEEE 83 (164)
Q Consensus 12 ~DG~~f~v~~~~a~~S~~l~~~~~~~~---~~----~~I~l~-v~s~~L~~Ii~~~~~~~h~~~~~~~~~~~~~~~~~~~ 83 (164)
.=|.++.+.+--+.||+++..|+.+.- .. -.||=| |+...|..++-=++ +
T Consensus 76 alg~eWrlHk~yL~QS~yf~smf~Gtw~es~~~iIqleI~Dp~Id~~al~~a~gsLY--~-------------------- 133 (488)
T KOG4682|consen 76 ALGFEWRLHKPYLFQSEYFKSMFSGTWKESSMNIIQLEIPDPNIDVVALQVAFGSLY--R-------------------- 133 (488)
T ss_pred hccceeeeeeeeeeccHHHHHHhccccChhhCceEEEEcCCCcccHHHHHHHHhhhh--h--------------------
Confidence 447888898888899999999988642 11 234555 77777877776665 3
Q ss_pred HHHHHHhhhhhcCcHHHHHHHHHhhhcCCChhHHHHHHHHHHHHhcCCCHHHHHhHcCCCCCCC
Q 038532 84 EEWEKKFDEEVSEDKDLHFGLLLAANYLEIPALLDRLCQLAADIVKGKTPEEIRRTFNIKKDFT 147 (164)
Q Consensus 84 ~~wd~~F~~~l~~~~~~l~~Ll~AA~~L~I~~L~~l~~~~ia~~i~gks~eeir~~f~i~~d~t 147 (164)
+++.++.+.+..++.||.+|+.++|.+-|...+.+.++-|| +.+++....-|-
T Consensus 134 --------dEveI~l~dv~gvlAaA~~lqldgl~qrC~evMie~lspkt---a~~yYea~ckYg 186 (488)
T KOG4682|consen 134 --------DEVEIKLSDVVGVLAAACLLQLDGLIQRCGEVMIETLSPKT---ACGYYEAACKYG 186 (488)
T ss_pred --------hheeccHHHHHHHHHHHHHHHHhhHHHHHHHHHHHhcChhh---hhHhhhhhhhhh
Confidence 11567888999999999999999999999988877666555 455555444443
No 15
>KOG2716 consensus Polymerase delta-interacting protein PDIP1 and related proteins, contain BTB/POZ domain [Inorganic ion transport and metabolism]
Probab=94.98 E-value=0.42 Score=37.60 Aligned_cols=101 Identities=21% Similarity=0.345 Sum_probs=75.8
Q ss_pred CCCCeEEEEcCCCCEEEecHHHH-HHHHHHHHHHHhcC-----CCCcccceecHHHHHHHHHHhcccccCCCCCCCCCCC
Q 038532 2 ATTSTVKLRSSDNEVFEVEKQVM-IQSGTIRNMIEDDA-----ADGEIPVQISSRNLAKIVEWCKCMQHRDRNNNNNDNN 75 (164)
Q Consensus 2 ~~~~~i~l~s~DG~~f~v~~~~a-~~S~~l~~~~~~~~-----~~~~I~l~v~s~~L~~Ii~~~~~~~h~~~~~~~~~~~ 75 (164)
.++..++|- --|.+|.-+...+ ++.++++.|++..- ..+.|=+.=+.+=+..|+.||+ - +..
T Consensus 2 ~~~~~vkLn-vGG~~F~Tsk~TLtk~dg~fk~m~e~~i~~~~d~s~~IFIDRSpKHF~~ILNfmR--d---Gdv------ 69 (230)
T KOG2716|consen 2 SMSETVKLN-VGGTIFKTSKSTLTKFDGFFKTMLETDIPVEKDESGCIFIDRSPKHFDTILNFMR--D---GDV------ 69 (230)
T ss_pred CccceEEEe-cCCeEEEeehhhhhhhhhHHHHHhhcCCccccCCcCcEEecCChhHHHHHHHhhh--c---ccc------
Confidence 445667754 3578999888885 68999999999641 1233555567888999999999 2 111
Q ss_pred CchhhhhHHHHHHHhhhhhcCcHHHHHHHHHhhhcCCChhHHHHHHHHHHHHhcCC
Q 038532 76 KEEEEEEEEEWEKKFDEEVSEDKDLHFGLLLAANYLEIPALLDRLCQLAADIVKGK 131 (164)
Q Consensus 76 ~~~~~~~~~~wd~~F~~~l~~~~~~l~~Ll~AA~~L~I~~L~~l~~~~ia~~i~gk 131 (164)
.+| -+..++-+|+.-|.|..+++|+++|...++..+++.
T Consensus 70 ------~LP-----------e~~kel~El~~EA~fYlL~~Lv~~C~~~i~~~~~~~ 108 (230)
T KOG2716|consen 70 ------DLP-----------ESEKELKELLREAEFYLLDGLVELCQSAIARLIRGY 108 (230)
T ss_pred ------cCc-----------cchHHHHHHHHHHHHhhHHHHHHHHHHHhhhcccCc
Confidence 122 245678999999999999999999999999998875
No 16
>KOG3433 consensus Protein involved in meiotic recombination/predicted coiled-coil protein [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=93.90 E-value=0.12 Score=39.05 Aligned_cols=37 Identities=41% Similarity=0.573 Sum_probs=29.6
Q ss_pred HhhhcC--CChhHHHHHHHHHHHHhcCCCHHHHHhHcCCCCCCC
Q 038532 106 LAANYL--EIPALLDRLCQLAADIVKGKTPEEIRRTFNIKKDFT 147 (164)
Q Consensus 106 ~AA~~L--~I~~L~~l~~~~ia~~i~gks~eeir~~f~i~~d~t 147 (164)
.|||.- +|--|.++||+.. |.-+.+||+.||||+||-
T Consensus 162 eaanrwtDnI~il~dy~~rkf-----~~e~nqi~~~fgIPed~d 200 (203)
T KOG3433|consen 162 EAANRWTDNIFILIDYLYRKF-----GLEPNQIRKEFGIPEDFD 200 (203)
T ss_pred HHHhhhhhhHHHHHHHHHHhc-----CCCHHHHhHhcCCCcccc
Confidence 445432 7788888888765 899999999999999874
No 17
>COG5124 Protein predicted to be involved in meiotic recombination [Cell division and chromosome partitioning / General function prediction only]
Probab=93.04 E-value=0.087 Score=39.67 Aligned_cols=31 Identities=39% Similarity=0.663 Sum_probs=25.2
Q ss_pred CChhHHHHHHHHHHHHhcCCCHHHHHhHcCCCCCCC
Q 038532 112 EIPALLDRLCQLAADIVKGKTPEEIRRTFNIKKDFT 147 (164)
Q Consensus 112 ~I~~L~~l~~~~ia~~i~gks~eeir~~f~i~~d~t 147 (164)
+|.-|.++.|+.+ +..++|||+.||||+|+-
T Consensus 174 nI~ilidy~c~kf-----~~~~~qir~~fgIPedld 204 (209)
T COG5124 174 NIEILIDYLCKKF-----FLKPEQIRKEFGIPEDLD 204 (209)
T ss_pred hHHHHHHHHHHHc-----CCCHHHHHHhcCCCcchh
Confidence 5667777777654 889999999999999864
No 18
>KOG0783 consensus Uncharacterized conserved protein, contains ankyrin and BTB/POZ domains [Function unknown]
Probab=93.00 E-value=0.29 Score=45.12 Aligned_cols=108 Identities=15% Similarity=0.169 Sum_probs=73.6
Q ss_pred EEEEcCCCCEEEecHHHH-HHHHHHHHHHHhcC-CCCccc---ceecHHHHHHHHHHhcccccCCCCCCCCCCCCchhhh
Q 038532 7 VKLRSSDNEVFEVEKQVM-IQSGTIRNMIEDDA-ADGEIP---VQISSRNLAKIVEWCKCMQHRDRNNNNNDNNKEEEEE 81 (164)
Q Consensus 7 i~l~s~DG~~f~v~~~~a-~~S~~l~~~~~~~~-~~~~I~---l~v~s~~L~~Ii~~~~~~~h~~~~~~~~~~~~~~~~~ 81 (164)
..++..||+++.....++ ..+.++..|+...- ....|. .|++++.|+.|++|++ . .+.
T Consensus 713 ~~i~~KDGkvl~aHkc~L~aRlEYF~smf~~~w~E~sS~t~~~~p~~~e~m~ivLdylY--s--~d~------------- 775 (1267)
T KOG0783|consen 713 TVIKLKDGKVLKAHKCFLSARLEYFSSMFQFVWMESSSITVNLSPLTVEHMSIVLDYLY--S--DDK------------- 775 (1267)
T ss_pred EEEEecCCcCcccceeEeeeHHHHHHHHHHHHHhhhccceeecCcchHHHHHHHHHHHH--c--cch-------------
Confidence 456677999999888774 46777877777531 112233 3367999999999998 3 111
Q ss_pred hHHHHHHHhhhhhcCcHHHHHHHHHhhhcCCChhHHHHHHHHHHHHhcCCCHHHHHh
Q 038532 82 EEEEWEKKFDEEVSEDKDLHFGLLLAANYLEIPALLDRLCQLAADIVKGKTPEEIRR 138 (164)
Q Consensus 82 ~~~~wd~~F~~~l~~~~~~l~~Ll~AA~~L~I~~L~~l~~~~ia~~i~gks~eeir~ 138 (164)
..||++ ....+-+++++..|+-|=|..|-++|-+.+-+++.=|+..++-+
T Consensus 776 ------~~~~k~-~~~~dF~~~il~iaDqlli~~Lk~Ice~~ll~kl~lk~~~~lle 825 (1267)
T KOG0783|consen 776 ------VELFKD-LKESDFMFEILSIADQLLILELKSICEQSLLRKLNLKTLPTLLE 825 (1267)
T ss_pred ------HHHHhc-cchhhhhHHHHHHHHHHHHHHHHHHHHHHHHhHhcccchHHHHH
Confidence 134332 13456688888888888888888888888888877776555543
No 19
>PF11822 DUF3342: Domain of unknown function (DUF3342); InterPro: IPR021777 This family of proteins are functionally uncharacterised. This family is found in bacteria. This presumed domain is typically between 170 to 303 amino acids in length. The N-terminal half of this family is a BTB-like domain.
Probab=92.25 E-value=0.15 Score=41.86 Aligned_cols=85 Identities=13% Similarity=0.250 Sum_probs=59.8
Q ss_pred CCEEEecHHHH-HHHHHHHHHHHh---c-CCCCccccee--cHHHHHHHHHHhcccccCCCCCCCCCCCCchhhhhHHHH
Q 038532 14 NEVFEVEKQVM-IQSGTIRNMIED---D-AADGEIPVQI--SSRNLAKIVEWCKCMQHRDRNNNNNDNNKEEEEEEEEEW 86 (164)
Q Consensus 14 G~~f~v~~~~a-~~S~~l~~~~~~---~-~~~~~I~l~v--~s~~L~~Ii~~~~~~~h~~~~~~~~~~~~~~~~~~~~~w 86 (164)
.+.|..+...+ ...+++++.+.. . ...++|+|.| +-.|++=+++|++ . ..+
T Consensus 13 ~rdF~C~~~lL~~~M~YF~~~l~~~~~~~~~~~~idisVhCDv~iF~WLm~yv~--~----~~p---------------- 70 (317)
T PF11822_consen 13 KRDFTCPRDLLVSEMRYFAEYLSRYINDSQRWEEIDISVHCDVHIFEWLMRYVK--G----EPP---------------- 70 (317)
T ss_pred ceeeeccHHHHHHhhHHHHHHHhhcccccCcCCCcceEEecChhHHHHHHHHhh--c----CCC----------------
Confidence 45688999985 579999999954 1 2336677775 4455666666666 3 111
Q ss_pred HHHhhhhhcCcHHHHHHHHHhhhcCCChhHHHHHHHHHHHHh
Q 038532 87 EKKFDEEVSEDKDLHFGLLLAANYLEIPALLDRLCQLAADIV 128 (164)
Q Consensus 87 d~~F~~~l~~~~~~l~~Ll~AA~~L~I~~L~~l~~~~ia~~i 128 (164)
.++...+..|+..|+||++++|++-|..++...+
T Consensus 71 --------~l~~~NvvsIliSS~FL~M~~Lve~cl~y~~~~~ 104 (317)
T PF11822_consen 71 --------SLTPSNVVSILISSEFLQMESLVEECLQYCHDHM 104 (317)
T ss_pred --------cCCcCcEEEeEehhhhhccHHHHHHHHHHHHHhH
Confidence 1355667888999999999999999988874444
No 20
>PF03962 Mnd1: Mnd1 family; InterPro: IPR005647 This family of proteins includes meiotic nuclear division protein 1 (MND1) from Saccharomyces cerevisiae (Baker's yeast). The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair [].
Probab=81.85 E-value=1.5 Score=33.37 Aligned_cols=42 Identities=33% Similarity=0.288 Sum_probs=30.5
Q ss_pred HHHHHHhhhcC--CChhHHHHHHHHHHHHhcCCCHHHHHhHcCCCCCCC
Q 038532 101 HFGLLLAANYL--EIPALLDRLCQLAADIVKGKTPEEIRRTFNIKKDFT 147 (164)
Q Consensus 101 l~~Ll~AA~~L--~I~~L~~l~~~~ia~~i~gks~eeir~~f~i~~d~t 147 (164)
+..+..|||.- +|..|...|++. -|.+.+++++.||||+||-
T Consensus 144 ~~~~~~~anrwTDNI~~l~~~~~~k-----~~~~~~~i~k~f~Ip~d~d 187 (188)
T PF03962_consen 144 IKIAKEAANRWTDNIFSLKSYLKKK-----FGMDEEDIRKEFGIPEDFD 187 (188)
T ss_pred HHHHHHHHHHHHhhHHHHHHHHHHh-----cCCCHHHHHHHcCCccccC
Confidence 34444566654 566666666664 3899999999999999873
No 21
>PF02214 BTB_2: BTB/POZ domain; InterPro: IPR003131 Potassium channels are the most diverse group of the ion channel family [, ]. They are important in shaping the action potential, and in neuronal excitability and plasticity []. The potassium channel family is composed of several functionally distinct isoforms, which can be broadly separated into 2 groups []: the practically non-inactivating 'delayed' group and the rapidly inactivating 'transient' group. These are all highly similar proteins, with only small amino acid changes causing the diversity of the voltage-dependent gating mechanism, channel conductance and toxin binding properties. Each type of K+ channel is activated by different signals and conditions depending on their type of regulation: some open in response to depolarisation of the plasma membrane; others in response to hyperpolarisation or an increase in intracellular calcium concentration; some can be regulated by binding of a transmitter, together with intracellular kinases; while others are regulated by GTP-binding proteins or other second messengers []. In eukaryotic cells, K+ channels are involved in neural signalling and generation of the cardiac rhythm, act as effectors in signal transduction pathways involving G protein-coupled receptors (GPCRs) and may have a role in target cell lysis by cytotoxic T-lymphocytes []. In prokaryotic cells, they play a role in the maintenance of ionic homeostasis []. All K+ channels discovered so far possess a core of alpha subunits, each comprising either one or two copies of a highly conserved pore loop domain (P-domain). The P-domain contains the sequence (T/SxxTxGxG), which has been termed the K+ selectivity sequence. In families that contain one P-domain, four subunits assemble to form a selective pathway for K+ across the membrane. However, it remains unclear how the 2 P-domain subunits assemble to form a selective pore. The functional diversity of these families can arise through homo- or hetero-associations of alpha subunits or association with auxiliary cytoplasmic beta subunits. K+ channel subunits containing one pore domain can be assigned into one of two superfamilies: those that possess six transmembrane (TM) domains and those that possess only two TM domains. The six TM domain superfamily can be further subdivided into conserved gene families: the voltage-gated (Kv) channels; the KCNQ channels (originally known as KvLQT channels); the EAG-like K+ channels; and three types of calcium (Ca)-activated K+ channels (BK, IK and SK) []. The 2TM domain family comprises inward-rectifying K+ channels. In addition, there are K+ channel alpha-subunits that possess two P-domains. These are usually highly regulated K+ selective leak channels. The Kv family can be divided into several subfamilies on the basis of sequence similarity and function. Four of these subfamilies, Kv1 (Shaker), Kv2 (Shab), Kv3 (Shaw) and Kv4 (Shal), consist of pore-forming alpha subunits that associate with different types of beta subunit. Each alpha subunit comprises six hydrophobic TM domains with a P-domain between the fifth and sixth, which partially resides in the membrane. The fourth TM domain has positively charged residues at every third residue and acts as a voltage sensor, which triggers the conformational change that opens the channel pore in response to a displacement in membrane potential []. More recently, 4 new electrically-silent alpha subunits have been cloned: Kv5 (KCNF), Kv6 (KCNG), Kv8 and Kv9 (KCNS). These subunits do not themselves possess any functional activity, but appear to form heteromeric channels with Kv2 subunits, and thus modulate Shab channel activity []. When highly expressed, they inhibit channel activity, but at lower levels show more specific modulatory actions. The N-terminal, cytoplasmic tetramerization domain (T1) of voltage-gated potassium channels encodes molecular determinants for subfamily-specific assembly of alpha-subunits into functional tetrameric channels []. This domain is found in a subset of a larger group of proteins that contain the BTB/POZ domain.; GO: 0005249 voltage-gated potassium channel activity, 0006813 potassium ion transport, 0008076 voltage-gated potassium channel complex, 0016020 membrane; PDB: 1NN7_A 3KVT_A 1EXB_E 1QDV_A 1DSX_E 1QDW_F 3LUT_B 3LNM_B 2A79_B 3DRY_C ....
Probab=75.95 E-value=1.9 Score=28.51 Aligned_cols=80 Identities=14% Similarity=0.239 Sum_probs=51.0
Q ss_pred CCCEEEecHHHHH-H-HHHHHHHHHhc------CCCCcccceecHHHHHHHHHHhcccccCCCCCCCCCCCCchhhhhHH
Q 038532 13 DNEVFEVEKQVMI-Q-SGTIRNMIEDD------AADGEIPVQISSRNLAKIVEWCKCMQHRDRNNNNNDNNKEEEEEEEE 84 (164)
Q Consensus 13 DG~~f~v~~~~a~-~-S~~l~~~~~~~------~~~~~I~l~v~s~~L~~Ii~~~~~~~h~~~~~~~~~~~~~~~~~~~~ 84 (164)
-|+.|.++...+. . ..++..++... .....+=+.=++..++.|+.|++ .. ...+
T Consensus 6 GG~~f~~~~~tL~~~~~s~l~~~~~~~~~~~~~~~~~~~fiDRdp~~F~~IL~ylr--~~--~~l~-------------- 67 (94)
T PF02214_consen 6 GGTIFETSRSTLTRYPDSLLARLFSGERSDDYDDDDGEYFIDRDPELFEYILNYLR--TG--GKLP-------------- 67 (94)
T ss_dssp TTEEEEEEHHHHHTSTTSTTTSHHHTGHGGGEETTTTEEEESS-HHHHHHHHHHHH--HT--SSB---------------
T ss_pred CCEEEEEcHHHHhhCCCChhhhHHhhccccccCCccceEEeccChhhhhHHHHHHh--hc--CccC--------------
Confidence 5899999999876 2 34567776642 12344544479999999999999 42 1110
Q ss_pred HHHHHhhhhhcCcHHHHHHHHHhhhcCCChhH-HHHH
Q 038532 85 EWEKKFDEEVSEDKDLHFGLLLAANYLEIPAL-LDRL 120 (164)
Q Consensus 85 ~wd~~F~~~l~~~~~~l~~Ll~AA~~L~I~~L-~~l~ 120 (164)
..+...+..+...|.|.+|+.| ++.|
T Consensus 68 ----------~~~~~~~~~l~~Ea~fy~l~~l~i~~c 94 (94)
T PF02214_consen 68 ----------IPDEICLEELLEEAEFYGLDELFIEDC 94 (94)
T ss_dssp ------------TTS-HHHHHHHHHHHT-HHHHBHHC
T ss_pred ----------CCCchhHHHHHHHHHHcCCCccccCCC
Confidence 0122346778888999999988 6654
No 22
>PF07928 Vps54: Vps54-like protein; InterPro: IPR012501 This family contains various proteins that are homologues of the yeast Vps54 protein, such as the rat homologue (Q9JMK8 from SWISSPROT), the human homologue (Q86YF7 from SWISSPROT), and the mouse homologue (Q8R3X1 from SWISSPROT). In yeast, Vps54 associates with Vps52 and Vps53 proteins to form a trimolecular complex that is involved in protein transport between Golgi, endosomal, and vacuolar compartments []. All Vps54 homologues contain a coiled coil region (not found in the region featured in this family) and multiple dileucine motifs []. ; GO: 0042147 retrograde transport, endosome to Golgi; PDB: 3N1E_B 3N1B_B.
Probab=73.66 E-value=1.1 Score=32.41 Aligned_cols=43 Identities=19% Similarity=0.285 Sum_probs=0.0
Q ss_pred CCCEEEecHHHHHHHHHHHHHHHhcCCCCcccce-ecHHHHHHHHHHhc
Q 038532 13 DNEVFEVEKQVMIQSGTIRNMIEDDAADGEIPVQ-ISSRNLAKIVEWCK 60 (164)
Q Consensus 13 DG~~f~v~~~~a~~S~~l~~~~~~~~~~~~I~l~-v~s~~L~~Ii~~~~ 60 (164)
||+.|.|+..++..-+.+.+.+.-. -.+| +..+++.+++++++
T Consensus 1 d~e~f~vv~s~l~ll~~l~~Y~~~~-----~~~P~~a~di~~~l~elLk 44 (135)
T PF07928_consen 1 DNEKFVVVGSALLLLKMLSDYLQLA-----SNFPSLAPDILSRLLELLK 44 (135)
T ss_dssp -------------------------------------------------
T ss_pred CCCceecHHHHHHHHHHHHHHHHHH-----HHCchhHHHHHHHHHHHHH
Confidence 6777888887777777666665432 3556 77788888888877
No 23
>PF05409 Peptidase_C30: Coronavirus endopeptidase C30; InterPro: IPR008740 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of cysteine peptidases correspond to MEROPS peptidase family C30 (clan PA(C)). These peptidases are related to serine endopeptidases of family S1 and are restricted to RNA viruses, where they are involved in viral polyprotein processing during replication [, , ]. This entry represents the CoV M-pro which comprises three domains. Domains I and II are six-stranded antiparallel beta barrels and together resemble the architecture of chymotrypsin and of picornaviruses 3C proteinases. The substrate-binding site is located in a cleft between these two domains. The catalytic site is situated at the centre of the cleft. A long loop connects domain II to the C-terminal domain (domain III). This latter domain, a globular cluster of five helices, has been implicated in the proteolytic activity of M-pro. In the active site of M-pro, Cys and His form a catalytic dyad. In contrast to serine proteinases and other cysteine proteinases, which have a catalytic triad, there is no third catalytic residue present [, , , ]. ; GO: 0019082 viral protein processing; PDB: 2VJ1_B 2K7X_A 2Q6D_B 2Q6F_A 1P9U_E 1LVO_B 2AMP_B 1P9S_A 2ZU2_A 3D23_A ....
Probab=66.23 E-value=10 Score=30.74 Aligned_cols=102 Identities=20% Similarity=0.237 Sum_probs=54.9
Q ss_pred Ccccce-ecHHHHHHHHHHhcccccCCCCCCCCCCCCchhhhhHHHHHHH--hhhhhcCcHHHHHHHHHhhhcCCChhHH
Q 038532 41 GEIPVQ-ISSRNLAKIVEWCKCMQHRDRNNNNNDNNKEEEEEEEEEWEKK--FDEEVSEDKDLHFGLLLAANYLEIPALL 117 (164)
Q Consensus 41 ~~I~l~-v~s~~L~~Ii~~~~~~~h~~~~~~~~~~~~~~~~~~~~~wd~~--F~~~l~~~~~~l~~Ll~AA~~L~I~~L~ 117 (164)
+...++ -+.-.=..|+.|++ -|--...+---......-+.+.+|-.. | -++..+..++.|.|..-..+..|+
T Consensus 161 ~~~Q~~~~~~~~T~NVvA~LY--Aalln~~~w~l~~~~~svedFN~WA~~N~f---t~~~~~~~~~~Laa~TgVsV~rlL 235 (293)
T PF05409_consen 161 EVAQLEGADQYITDNVVAWLY--AALLNGCPWWLSSQRISVEDFNEWAMNNGF---TSFSSDDAFDMLAAKTGVSVERLL 235 (293)
T ss_dssp SSSTTTTS-SB-HHHHHHHHH--HHHHTT--TTSSSS---HHHHHHHHHHTTB-----SSHHHHHHHHHHHHT--HHHHH
T ss_pred hhhhhcCccceeehhHHHHHH--HHHHcCCCeeeccceecHHHHHHHHHhCCC---cccchhhHHHHHHHHhCCcHHHHH
Confidence 334444 34444456788877 544221100000112345677888554 4 346777899999999999999998
Q ss_pred HHHHHHHHHHhcCCCHHHHHhHcCCCCCCCHHHH
Q 038532 118 DRLCQLAADIVKGKTPEEIRRTFNIKKDFTPEEE 151 (164)
Q Consensus 118 ~l~~~~ia~~i~gks~eeir~~f~i~~d~t~eee 151 (164)
...-+ +..-+.|++ |--...+++||||++-
T Consensus 236 aaI~~-L~~g~~G~~---IlG~~~ledE~Tp~~V 265 (293)
T PF05409_consen 236 AAIQR-LHKGFGGRT---ILGSCSLEDEFTPEMV 265 (293)
T ss_dssp HHHHH-HHHTTTTT----BTTBSS--TSS-HHHH
T ss_pred HHHHH-HhcCCCCCc---ccccccccccCCHHHH
Confidence 86665 555555654 4445567788999864
No 24
>PF03656 Pam16: Pam16; InterPro: IPR005341 The Pam16 protein is the fifth essential subunit of the pre-sequence translocase-associated protein import motor (PAM) []. In Saccharomyces cerevisiae (Baker's yeast), Pam16 is required for preprotein translocation into the matrix, but not for protein insertion into the inner membrane [].; PDB: 2GUZ_J.
Probab=61.23 E-value=6.6 Score=28.07 Aligned_cols=26 Identities=35% Similarity=0.520 Sum_probs=13.4
Q ss_pred HhcCCCHHHHHhHcCCCCCCCHHHHH
Q 038532 127 IVKGKTPEEIRRTFNIKKDFTPEEEK 152 (164)
Q Consensus 127 ~i~gks~eeir~~f~i~~d~t~eee~ 152 (164)
..+|+|.+|-++++|++...++|+..
T Consensus 51 ~~~~Mtl~EA~~ILnv~~~~~~eeI~ 76 (127)
T PF03656_consen 51 NSKGMTLDEARQILNVKEELSREEIQ 76 (127)
T ss_dssp ------HHHHHHHHT--G--SHHHHH
T ss_pred hcCCCCHHHHHHHcCCCCccCHHHHH
Confidence 34689999999999999988876543
No 25
>PRK05365 malonic semialdehyde reductase; Provisional
Probab=60.93 E-value=6.3 Score=29.64 Aligned_cols=35 Identities=23% Similarity=0.269 Sum_probs=28.3
Q ss_pred HHHHhhhcCCChhHHHHHHHHHHHHhcCCCHHHHHhHcCCCCCCC
Q 038532 103 GLLLAANYLEIPALLDRLCQLAADIVKGKTPEEIRRTFNIKKDFT 147 (164)
Q Consensus 103 ~Ll~AA~~L~I~~L~~l~~~~ia~~i~gks~eeir~~f~i~~d~t 147 (164)
.|+.||..||+.. .++.|-..+.+++.|||++++.
T Consensus 130 ~l~LaA~~~Glgs----------~~~~g~~~~~v~~~l~ip~~~~ 164 (195)
T PRK05365 130 YLILAARALGLDA----------GPMSGFDAAAVDAEFFAGTTWK 164 (195)
T ss_pred HHHHHHHHcCCcc----------CCccccCHHHHHHHhCCCCCee
Confidence 4999999999987 2445678899999999997653
No 26
>cd02148 Nitroreductase_5 Nitroreductase-like family 5. A subfamily of the nitroreductase family containing uncharacterized proteins that are similar to nitroreductase. Nitroreductase catalyzes the reduction of nitroaromatic compounds such as nitrotoluenes, nitrofurans and nitroimidazoles. This process requires NAD(P)H as electron donor in an obligatory two-electron transfer and uses FMN as cofactor. The enzyme is typically a homodimer. Members of this family are also called NADH dehydrogenase, oxygen-insensitive NAD(P)H nitrogenase or dihydropteridine reductase.
Probab=58.53 E-value=7 Score=29.11 Aligned_cols=35 Identities=20% Similarity=0.260 Sum_probs=28.1
Q ss_pred HHHHhhhcCCChhHHHHHHHHHHHHhcCCCHHHHHhHcCCCCCCC
Q 038532 103 GLLLAANYLEIPALLDRLCQLAADIVKGKTPEEIRRTFNIKKDFT 147 (164)
Q Consensus 103 ~Ll~AA~~L~I~~L~~l~~~~ia~~i~gks~eeir~~f~i~~d~t 147 (164)
.++.||.-||+.. .++.|-..+++++.|||++++.
T Consensus 123 ~l~LaA~~lGlgs----------~~~~g~d~~~~~~~L~lp~~~~ 157 (185)
T cd02148 123 YFILAARALGLDA----------GPMSGFDAAAVDAEFFADTRWR 157 (185)
T ss_pred HHHHHHHHcCCCc----------CCCcccCHHHHHHHhCCCCCeE
Confidence 4899999999876 3455678899999999998763
No 27
>KOG3442 consensus Uncharacterized conserved protein [Function unknown]
Probab=54.94 E-value=7.2 Score=27.76 Aligned_cols=32 Identities=19% Similarity=0.221 Sum_probs=23.0
Q ss_pred hcCCCHHHHHhHcCCCCCCCHHHHHHHHHHcCCcc
Q 038532 128 VKGKTPEEIRRTFNIKKDFTPEEEKAVMDEHGWAL 162 (164)
Q Consensus 128 i~gks~eeir~~f~i~~d~t~eee~~i~~e~~W~~ 162 (164)
.-|.|.+|-++++||.+++..|| |.+.|.-+|
T Consensus 53 ~~~iTlqEa~qILnV~~~ln~ee---i~k~yehLF 84 (132)
T KOG3442|consen 53 NGKITLQEAQQILNVKEPLNREE---IEKRYEHLF 84 (132)
T ss_pred cccccHHHHhhHhCCCCCCCHHH---HHHHHHHHH
Confidence 34579999999999999887664 444444443
No 28
>PF11978 MVP_shoulder: Shoulder domain; InterPro: IPR021870 This domain is found in the Major Vault Protein and has been called the shoulder domain []. This family includes two bacterial proteins A6FXE2 from SWISSPROT and A1ZGE7 from SWISSPROT. This suggests that some bacteria may possess vault particles. ; PDB: 2ZUO_G 2QZV_B 2ZV5_c 2ZV4_Y.
Probab=54.21 E-value=12 Score=26.32 Aligned_cols=28 Identities=21% Similarity=0.418 Sum_probs=25.2
Q ss_pred HHHhhhcCCChhHHHHHHHHHHHHhcCC
Q 038532 104 LLLAANYLEIPALLDRLCQLAADIVKGK 131 (164)
Q Consensus 104 Ll~AA~~L~I~~L~~l~~~~ia~~i~gk 131 (164)
.-.|+....++..+-.+|+.+|.++||.
T Consensus 36 ~~~~~k~F~VpDFVGd~Ck~iaSRIR~a 63 (118)
T PF11978_consen 36 PEDAAKLFSVPDFVGDACKAIASRIRGA 63 (118)
T ss_dssp HHHHHHTTSSTTHHHHHHHHHHHHHHHH
T ss_pred hhHHHHhcCCcchHHHHHHHHHHHHHHH
Confidence 3478899999999999999999999985
No 29
>PF12556 CobS_N: Cobaltochelatase CobS subunit N terminal
Probab=53.70 E-value=8.1 Score=21.40 Aligned_cols=12 Identities=33% Similarity=0.739 Sum_probs=10.3
Q ss_pred HHhHcCCCCCCC
Q 038532 136 IRRTFNIKKDFT 147 (164)
Q Consensus 136 ir~~f~i~~d~t 147 (164)
+|+.|||..|++
T Consensus 14 vre~FGiDsDm~ 25 (36)
T PF12556_consen 14 VREVFGIDSDMK 25 (36)
T ss_pred HHHhcCCCcCCe
Confidence 589999999975
No 30
>PF13921 Myb_DNA-bind_6: Myb-like DNA-binding domain; PDB: 1A5J_A 1MBH_A 1GV5_A 1H89_C 1IDY_A 1MBK_A 1IDZ_A 1H88_C 1GVD_A 1MBG_A ....
Probab=52.20 E-value=24 Score=20.96 Aligned_cols=34 Identities=21% Similarity=0.433 Sum_probs=22.2
Q ss_pred HHHHHHHhcCCCHHHHHhHcC--C----C-CCCCHHHHHHH
Q 038532 121 CQLAADIVKGKTPEEIRRTFN--I----K-KDFTPEEEKAV 154 (164)
Q Consensus 121 ~~~ia~~i~gks~eeir~~f~--i----~-~d~t~eee~~i 154 (164)
=..||..+..+|+.+++..|. + . ..+|++|.+.+
T Consensus 20 W~~Ia~~l~~Rt~~~~~~r~~~~l~~~~~~~~wt~eEd~~L 60 (60)
T PF13921_consen 20 WKKIAEHLGNRTPKQCRNRWRNHLRPKISRGPWTKEEDQRL 60 (60)
T ss_dssp HHHHHHHSTTS-HHHHHHHHHHTTSTTSTSSSSSHHHHHHH
T ss_pred HHHHHHHHCcCCHHHHHHHHHHHCcccccCCCcCHHHHhcC
Confidence 356788883499999987643 2 2 24888877654
No 31
>cd05029 S-100A6 S-100A6: S-100A6 domain found in proteins similar to S100A6. S100A6 is a member of the S100 domain family within EF-hand Ca2+-binding proteins superfamily. Note that the S-100 hierarchy, to which this S-100A6 group belongs, contains only S-100 EF-hand domains, other EF-hands have been modeled separately. S100 proteins exhibit unique patterns of tissue- and cell type-specific expression and have been implicated in the Ca2+-dependent regulation of diverse physiological processes, including cell cycle regulation, differentiation, growth, and metabolic control . S100A6 is normally expressed in the G1 phase of the cell cycle in neuronal cells. The function of S100A6 remains unclear, but evidence suggests that it is involved in cell cycle regulation and exocytosis. S100A6 may also be involved in tumorigenesis; the protein is overexpressed in several tumors. Ca2+ binding to S100A6 leads to a conformational change in the protein, which exposes a hydrophobic surface for interact
Probab=49.84 E-value=32 Score=22.55 Aligned_cols=44 Identities=14% Similarity=0.228 Sum_probs=26.2
Q ss_pred hhHHHHHHHHHHHHh-cCC-CHHHHHhHcC----CCCCCCHHHHHHHHHH
Q 038532 114 PALLDRLCQLAADIV-KGK-TPEEIRRTFN----IKKDFTPEEEKAVMDE 157 (164)
Q Consensus 114 ~~L~~l~~~~ia~~i-~gk-s~eeir~~f~----i~~d~t~eee~~i~~e 157 (164)
..|+.+..++.+.-= +|. +.+|+|+.+. +-+.+|+++.+++.++
T Consensus 10 ~~~i~~F~~y~~~~~~~g~Is~~EL~~~l~~~~~lg~k~t~~ev~~m~~~ 59 (88)
T cd05029 10 GLLVAIFHKYSGREGDKNTLSKKELKELIQKELTIGSKLQDAEIAKLMED 59 (88)
T ss_pred HHHHHHHHHHHccCCCCCEECHHHHHHHHHHHHhcCCCCCHHHHHHHHHH
Confidence 345555566655221 332 7888888773 4455777777777654
No 32
>PF10892 DUF2688: Protein of unknown function (DUF2688); InterPro: IPR024392 Members of this protein family are annotated as KleB, and may play a role in the regulation of transcription in plasmids.
Probab=49.69 E-value=20 Score=21.86 Aligned_cols=25 Identities=28% Similarity=0.678 Sum_probs=18.8
Q ss_pred HHHHHhHcC-CCCC-CCHHHHHHHHHH
Q 038532 133 PEEIRRTFN-IKKD-FTPEEEKAVMDE 157 (164)
Q Consensus 133 ~eeir~~f~-i~~d-~t~eee~~i~~e 157 (164)
.+++|..|| |=.+ +||||..+|.+-
T Consensus 30 ad~lr~klG~IC~~CitpEE~~~I~e~ 56 (60)
T PF10892_consen 30 ADDLRVKLGGICGDCITPEEDREILEA 56 (60)
T ss_pred hHHHHHHHcchhhccCCHHHHHHHHHH
Confidence 578888887 4445 899999888653
No 33
>PRK11053 dihydropteridine reductase; Provisional
Probab=47.20 E-value=16 Score=27.83 Aligned_cols=36 Identities=25% Similarity=0.315 Sum_probs=27.5
Q ss_pred HHHHHHhhhcCCChhHHHHHHHHHHHHhcCCCHHHHHhHcCCCC-CC
Q 038532 101 HFGLLLAANYLEIPALLDRLCQLAADIVKGKTPEEIRRTFNIKK-DF 146 (164)
Q Consensus 101 l~~Ll~AA~~L~I~~L~~l~~~~ia~~i~gks~eeir~~f~i~~-d~ 146 (164)
+..|+.||.-||+... .+.|-..+.+++.|||++ ++
T Consensus 147 ~~~lmLaA~~~Glgs~----------~i~g~~~~~v~~~l~ip~~~~ 183 (217)
T PRK11053 147 LGNLLLGAAALGIDAT----------PIEGFDAAILDAEFGLREKGL 183 (217)
T ss_pred HHHHHHHHHHcCCCCC----------CcCCcCHHHHHHHhCCCCcCc
Confidence 5577888888887754 445678899999999985 45
No 34
>PF11198 DUF2857: Protein of unknown function (DUF2857); InterPro: IPR021364 This is a bacterial family of uncharacterised proteins.
Probab=46.57 E-value=44 Score=25.14 Aligned_cols=60 Identities=27% Similarity=0.249 Sum_probs=38.6
Q ss_pred cCcHHHHHHHHHhhh-----cCCChhHHHHH-HHHHHHHhcCCCHHHH---HhHcCCCCC------CCHHHHHHH
Q 038532 95 SEDKDLHFGLLLAAN-----YLEIPALLDRL-CQLAADIVKGKTPEEI---RRTFNIKKD------FTPEEEKAV 154 (164)
Q Consensus 95 ~~~~~~l~~Ll~AA~-----~L~I~~L~~l~-~~~ia~~i~gks~eei---r~~f~i~~d------~t~eee~~i 154 (164)
.+|.+.+-.++.-|. .--|+.++.++ +..+-..+-|.|+.|+ |+.+|++.. .|+|++..|
T Consensus 57 ~in~~~l~~~L~~~~~~~~~~~~idr~L~lGAS~~mm~~~FGls~~ev~~rR~llgi~~~~GR~~~~~ee~~~~i 131 (180)
T PF11198_consen 57 SINHDVLWRLLEQARREQQEQQLIDRALRLGASIEMMQRLFGLSSAEVAARRRLLGIPVRKGRPPALSEEEEAAI 131 (180)
T ss_pred eeCHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHhCCCCCCCCCCCcCHHHHHHH
Confidence 456666666665554 34555666666 5667777789998887 677888864 344555454
No 35
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=46.36 E-value=19 Score=26.12 Aligned_cols=18 Identities=33% Similarity=0.739 Sum_probs=16.8
Q ss_pred CCCHHHHHhHcCCCCCCC
Q 038532 130 GKTPEEIRRTFNIKKDFT 147 (164)
Q Consensus 130 gks~eeir~~f~i~~d~t 147 (164)
|+||+|-|..+|++.||.
T Consensus 98 gmTPd~YR~KW~LP~dYP 115 (148)
T COG4957 98 GLTPDEYRAKWGLPPDYP 115 (148)
T ss_pred CCCHHHHHHhcCCCCCCC
Confidence 899999999999999974
No 36
>PF11460 DUF3007: Protein of unknown function (DUF3007); InterPro: IPR021562 This is a family of uncharacterised proteins found in bacteria and eukaryotes.
Probab=45.95 E-value=20 Score=24.68 Aligned_cols=23 Identities=35% Similarity=0.644 Sum_probs=17.5
Q ss_pred CHHHHHhHcCCCCCCCHHHHHHHHHH
Q 038532 132 TPEEIRRTFNIKKDFTPEEEKAVMDE 157 (164)
Q Consensus 132 s~eeir~~f~i~~d~t~eee~~i~~e 157 (164)
+.+++.+.|. .+||||.+++..|
T Consensus 79 ~~~~lqkRle---~l~~eE~~~L~~e 101 (104)
T PF11460_consen 79 TNEELQKRLE---ELSPEELEALQAE 101 (104)
T ss_pred hHHHHHHHHH---hCCHHHHHHHHHH
Confidence 4567777775 6888988888776
No 37
>KOG4591 consensus Uncharacterized conserved protein, contains BTB/POZ domain [General function prediction only]
Probab=45.53 E-value=30 Score=27.05 Aligned_cols=17 Identities=6% Similarity=0.276 Sum_probs=10.9
Q ss_pred cce-ecHHHHHHHHHHhc
Q 038532 44 PVQ-ISSRNLAKIVEWCK 60 (164)
Q Consensus 44 ~l~-v~s~~L~~Ii~~~~ 60 (164)
-+. ++....-..++|.+
T Consensus 109 ~~dDad~Ea~~t~iRWIY 126 (280)
T KOG4591|consen 109 DLDDADFEAFHTAIRWIY 126 (280)
T ss_pred cccccCHHHHHHhheeee
Confidence 344 66666667777765
No 38
>PRK13503 transcriptional activator RhaS; Provisional
Probab=43.41 E-value=1.5e+02 Score=22.92 Aligned_cols=78 Identities=15% Similarity=0.176 Sum_probs=46.0
Q ss_pred HHHHHHHHHHhcccccCCCCCCCCCCCCchhhhhHHHHHHHhhhhhcCcHHHHHHHHHhhhcCCChhHHHHH-HHHHHHH
Q 038532 49 SRNLAKIVEWCKCMQHRDRNNNNNDNNKEEEEEEEEEWEKKFDEEVSEDKDLHFGLLLAANYLEIPALLDRL-CQLAADI 127 (164)
Q Consensus 49 s~~L~~Ii~~~~~~~h~~~~~~~~~~~~~~~~~~~~~wd~~F~~~l~~~~~~l~~Ll~AA~~L~I~~L~~l~-~~~ia~~ 127 (164)
...+.++++|++ .|...+. .+.++-+. ++++...+..++....-.-...++.-. -.....+
T Consensus 170 ~~~i~~~~~~I~--~~~~~~~------------tl~~lA~~----~~lS~~~l~r~Fk~~~G~S~~~yi~~~Rl~~A~~L 231 (278)
T PRK13503 170 DARLNQLLAWLE--DHFAEEV------------NWEALADQ----FSLSLRTLHRQLKQQTGLTPQRYLNRLRLLKARHL 231 (278)
T ss_pred HHHHHHHHHHHH--HhhcCCC------------CHHHHHHH----HCCCHHHHHHHHHHHhCcCHHHHHHHHHHHHHHHH
Confidence 344666677766 6554332 23333333 367777788888777666665555555 2333344
Q ss_pred hc--CCCHHHHHhHcCCCC
Q 038532 128 VK--GKTPEEIRRTFNIKK 144 (164)
Q Consensus 128 i~--gks~eeir~~f~i~~ 144 (164)
+. +.|+.||-..+|-.+
T Consensus 232 L~~~~~sI~eIA~~~GF~~ 250 (278)
T PRK13503 232 LRHSDASVTDIAYRCGFGD 250 (278)
T ss_pred HHcCCCCHHHHHHHhCCCC
Confidence 43 468888888887765
No 39
>PF10075 PCI_Csn8: COP9 signalosome, subunit CSN8; InterPro: IPR019280 The photomorphogenic 9 (COP9) signalosome or CSN complex is composed of eight subunits: Cops1/GPS1, Cops2, Cops3, Cops4, Cops5, Cop6, Cops7 (Cops7A or Cops7B) and Cops8. In the complex, Cops8, which is the smallest subunit, probably interacts directly with Cops3, Cops4 and Cops7 (Cops7A or Cops7B). This signalosome is homologous to the lid subcomplex of the 26S proteasome and regulates the ubiquitin-proteasome pathway. It functions as a structural scaffold for subunit-subunit interactions within the complex and is a key regulator of photomorphogenic development [].; PDB: 1RZ4_A.
Probab=42.34 E-value=54 Score=23.27 Aligned_cols=47 Identities=15% Similarity=0.443 Sum_probs=29.5
Q ss_pred ChhHHHHH----HHHHHHHhcCCCHHHHHhHcCCCCCCCHHHHHHHHHHcCCccC
Q 038532 113 IPALLDRL----CQLAADIVKGKTPEEIRRTFNIKKDFTPEEEKAVMDEHGWALH 163 (164)
Q Consensus 113 I~~L~~l~----~~~ia~~i~gks~eeir~~f~i~~d~t~eee~~i~~e~~W~~~ 163 (164)
|.+|.+.. +..++.-...-+...+.+++|+. ++|..++-+...|-.+
T Consensus 76 v~~~~~~iR~~i~~~i~~aY~sIs~~~la~~Lg~~----~~el~~~~~~~gW~~d 126 (143)
T PF10075_consen 76 VPGFEDTIRERIAHLISKAYSSISLSDLAEMLGLS----EEELEKFIKSRGWTVD 126 (143)
T ss_dssp STTHHHHHHHHHHHHHHHH-SEE-HHHHHHHTTS-----HHHHHHHHHHHT-EE-
T ss_pred HHHHHHHHHHHHHHHHHHHHhHcCHHHHHHHhCCC----HHHHHHHHHHcCCEEC
Confidence 44555544 44455555567999999999986 4677777777899754
No 40
>PF08154 NLE: NLE (NUC135) domain; InterPro: IPR012972 This domain is located N-terminal to WD40 repeats(IPR001680 from INTERPRO). It is found in the microtubule-associated protein Q12024 from SWISSPROT [].
Probab=42.17 E-value=21 Score=22.12 Aligned_cols=43 Identities=16% Similarity=0.374 Sum_probs=29.0
Q ss_pred eEEEEcCCC------CEEEecHHH--HHHHHHHHHHHHhcCCCCcccce--ecHH
Q 038532 6 TVKLRSSDN------EVFEVEKQV--MIQSGTIRNMIEDDAADGEIPVQ--ISSR 50 (164)
Q Consensus 6 ~i~l~s~DG------~~f~v~~~~--a~~S~~l~~~~~~~~~~~~I~l~--v~s~ 50 (164)
.+++.|++| ..+.||..+ ...|.+++.++.+ ..+++|.. |++.
T Consensus 3 ~v~F~t~~~~~~~~~~~~~VP~~~t~~~Ls~LvN~LL~~--~~~~vpfdF~i~~~ 55 (65)
T PF08154_consen 3 QVQFVTEDGEYEVPGTPISVPSNITRKELSELVNQLLDD--EEEPVPFDFLINGE 55 (65)
T ss_pred EEEEEcCCCCccCCCCCEEEeCCCCHHHHHHHHHHHhcc--CCCCCcEEEEECCE
Confidence 367777776 456677666 4579999999822 35677776 5554
No 41
>KOG2075 consensus Topoisomerase TOP1-interacting protein BTBD1 [Function unknown]
Probab=41.77 E-value=1.2e+02 Score=26.80 Aligned_cols=114 Identities=13% Similarity=0.076 Sum_probs=67.5
Q ss_pred CEEEecHHH-HHHHHHHHHHHHhcC---CCCcccce-ecHHHHHHHHHHhcccccCCCCCCC-CC--C--CCchhhhhHH
Q 038532 15 EVFEVEKQV-MIQSGTIRNMIEDDA---ADGEIPVQ-ISSRNLAKIVEWCKCMQHRDRNNNN-ND--N--NKEEEEEEEE 84 (164)
Q Consensus 15 ~~f~v~~~~-a~~S~~l~~~~~~~~---~~~~I~l~-v~s~~L~~Ii~~~~~~~h~~~~~~~-~~--~--~~~~~~~~~~ 84 (164)
+.+...+-+ +.-|.++..|+-..- ...+|.+| |....+...++|+++- |......+ .. + .+. .-..+.
T Consensus 129 q~~paHk~vla~gS~VFdaMf~g~~a~~~s~ei~lpdvepaaFl~~L~flYsd-ev~~~~dtvi~tl~~AkKY-~VpaLe 206 (521)
T KOG2075|consen 129 QRIPAHKLVLADGSDVFDAMFYGGLAEDASLEIRLPDVEPAAFLAFLRFLYSD-EVKLAADTVITTLYAAKKY-LVPALE 206 (521)
T ss_pred cccchhhhhhhcchHHHHHHhccCcccccCceeecCCcChhHhHHHHHHHhcc-hhhhhHHHHHHHHHHHHHh-hhHHHH
Confidence 444455555 345888888887532 25789999 9999999999998831 11111000 00 0 000 000111
Q ss_pred HHHHHhhhhhcCcHHHHHHHHHhhhcCCChhHHHHHHHHHHHHhcC
Q 038532 85 EWEKKFDEEVSEDKDLHFGLLLAANYLEIPALLDRLCQLAADIVKG 130 (164)
Q Consensus 85 ~wd~~F~~~l~~~~~~l~~Ll~AA~~L~I~~L~~l~~~~ia~~i~g 130 (164)
.---+|++..-+....++.|...|..++=+.|+..|...++..+..
T Consensus 207 r~CVkflr~~l~~~naf~~L~q~A~lf~ep~Li~~c~e~id~~~~~ 252 (521)
T KOG2075|consen 207 RQCVKFLRKNLMADNAFLELFQRAKLFDEPSLISICLEVIDKSFED 252 (521)
T ss_pred HHHHHHHHHhcCChHHHHHHHHHHHhhcCHHHHHHHHHHhhhHHHh
Confidence 1122353322256777888888899999999999998887655543
No 42
>smart00385 CYCLIN domain present in cyclins, TFIIB and Retinoblastoma. A helical domain present in cyclins and TFIIB (twice) and Retinoblastoma (once). A protein recognition domain functioning in cell-cycle and transcription control.
Probab=41.01 E-value=80 Score=18.93 Aligned_cols=43 Identities=19% Similarity=0.091 Sum_probs=29.0
Q ss_pred CChhHHHHHHHHHHHHhcCC--CHHHHHhHcCCCCCCCHHHHHHHHHH
Q 038532 112 EIPALLDRLCQLAADIVKGK--TPEEIRRTFNIKKDFTPEEEKAVMDE 157 (164)
Q Consensus 112 ~I~~L~~l~~~~ia~~i~gk--s~eeir~~f~i~~d~t~eee~~i~~e 157 (164)
.-+.++-.+|-++|.++.+. +..++....|. +|.++..+..++
T Consensus 36 ~~~~~ia~a~l~lA~k~~~~~~~~~~~~~~~~~---~~~~~i~~~~~~ 80 (83)
T smart00385 36 YSPSLIAAAALYLAAKTEEIPPWTKELVHYTGY---FTEEEILRMEKL 80 (83)
T ss_pred CCHHHHHHHHHHHHHHHhcCCCCchhHhHhhCC---CCHHHHHHHHHH
Confidence 34455666788889888874 56777777775 677766655443
No 43
>cd00167 SANT 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA.
Probab=40.02 E-value=31 Score=18.43 Aligned_cols=20 Identities=25% Similarity=0.504 Sum_probs=16.2
Q ss_pred HHHHHHhcCCCHHHHHhHcC
Q 038532 122 QLAADIVKGKTPEEIRRTFN 141 (164)
Q Consensus 122 ~~ia~~i~gks~eeir~~f~ 141 (164)
..||..+.++|+.+++..+.
T Consensus 23 ~~Ia~~~~~rs~~~~~~~~~ 42 (45)
T cd00167 23 EKIAKELPGRTPKQCRERWR 42 (45)
T ss_pred HHHHhHcCCCCHHHHHHHHH
Confidence 56788888899999988763
No 44
>KOG1665 consensus AFH1-interacting protein FIP2, contains BTB/POZ domain and pentapeptide repeats [General function prediction only]
Probab=39.48 E-value=35 Score=27.15 Aligned_cols=87 Identities=21% Similarity=0.305 Sum_probs=54.2
Q ss_pred CeEEEEcCCCCEEEec--HHHHH-HHHHHHHHHHhcCC------CCcccceecHHHHHHHHHHhcccccCCCCCCCCCCC
Q 038532 5 STVKLRSSDNEVFEVE--KQVMI-QSGTIRNMIEDDAA------DGEIPVQISSRNLAKIVEWCKCMQHRDRNNNNNDNN 75 (164)
Q Consensus 5 ~~i~l~s~DG~~f~v~--~~~a~-~S~~l~~~~~~~~~------~~~I~l~v~s~~L~~Ii~~~~~~~h~~~~~~~~~~~ 75 (164)
++++|- -.|+.|.-. .-+.+ --.++..|+.+.+. ...+-+.=++.-++-|+.|+. + .
T Consensus 9 ~~vrln-igGk~f~TTidTlv~rEPDSMLa~MF~~~g~~~~~d~kGa~lIDRsp~yFepIlNyLr--~-G---------- 74 (302)
T KOG1665|consen 9 SMVRLN-IGGKKFCTTIDTLVIREPDSMLAAMFSGRGAMCQEDKKGAVLIDRSPKYFEPILNYLR--D-G---------- 74 (302)
T ss_pred hhheee-cCCeEEEEeehhhcccCchHHHHHHHccCCCccccccCceEEEccCchhhHHHHHHHh--c-C----------
Confidence 344443 356666533 33333 24566777776541 234444467788888888888 3 1
Q ss_pred CchhhhhHHHHHHHhhhhhcCcHHHHHHHHHhhhcCCChhHHHHHH
Q 038532 76 KEEEEEEEEEWEKKFDEEVSEDKDLHFGLLLAANYLEIPALLDRLC 121 (164)
Q Consensus 76 ~~~~~~~~~~wd~~F~~~l~~~~~~l~~Ll~AA~~L~I~~L~~l~~ 121 (164)
+| ...+...++.++.+|.|.+|-+|.+..-
T Consensus 75 -------------q~---~~~s~i~~lgvLeeArff~i~sL~~hle 104 (302)
T KOG1665|consen 75 -------------QI---PSLSDIDCLGVLEEARFFQILSLKDHLE 104 (302)
T ss_pred -------------ce---eecCCccHHHHHHHhhHHhhHhHHhHHh
Confidence 12 2234456899999999999999998653
No 45
>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=38.34 E-value=63 Score=19.53 Aligned_cols=32 Identities=25% Similarity=0.097 Sum_probs=23.6
Q ss_pred CCCHHHHHh----HcCCCCCCCHHHHHHHHHHcCCc
Q 038532 130 GKTPEEIRR----TFNIKKDFTPEEEKAVMDEHGWA 161 (164)
Q Consensus 130 gks~eeir~----~f~i~~d~t~eee~~i~~e~~W~ 161 (164)
.+|.+|+-. ..||+-.+|.-=..+++++|+=.
T Consensus 12 yMsk~E~v~~L~~~a~I~P~~T~~VW~~Le~eN~eF 47 (54)
T PF09713_consen 12 YMSKEECVRALQKQANIEPVFTSTVWQKLEKENPEF 47 (54)
T ss_pred cCCHHHHHHHHHHHcCCChHHHHHHHHHHHHHCHHH
Confidence 456555544 45898889988889999998643
No 46
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=38.05 E-value=35 Score=18.52 Aligned_cols=20 Identities=30% Similarity=0.481 Sum_probs=16.2
Q ss_pred HHHHHHhcCCCHHHHHhHcC
Q 038532 122 QLAADIVKGKTPEEIRRTFN 141 (164)
Q Consensus 122 ~~ia~~i~gks~eeir~~f~ 141 (164)
..||..+.++|+.+++..+.
T Consensus 25 ~~Ia~~~~~rt~~~~~~~~~ 44 (49)
T smart00717 25 EKIAKELPGRTAEQCRERWN 44 (49)
T ss_pred HHHHHHcCCCCHHHHHHHHH
Confidence 56778888999999988764
No 47
>PF02519 Auxin_inducible: Auxin responsive protein; InterPro: IPR003676 This family consists of the protein products of a gene cluster that encodes a group of auxin-regulated RNAs (small auxin up RNAs, SAURs) []. Proteins from this ARG7 auxin responsive genes family have no identified functional role [].
Probab=37.83 E-value=1.3e+02 Score=20.41 Aligned_cols=54 Identities=9% Similarity=0.174 Sum_probs=38.0
Q ss_pred eEEEEcCC-CCEEEecHHHHHHHHHHHHHHHhc----C--CCCcccceecHHHHHHHHHHhc
Q 038532 6 TVKLRSSD-NEVFEVEKQVMIQSGTIRNMIEDD----A--ADGEIPVQISSRNLAKIVEWCK 60 (164)
Q Consensus 6 ~i~l~s~D-G~~f~v~~~~a~~S~~l~~~~~~~----~--~~~~I~l~v~s~~L~~Ii~~~~ 60 (164)
.+.+...+ .+.|.|+...+. .++++.+++.. | .+++|.||-+...++.|+..++
T Consensus 40 ~~~VyVG~~~~Rfvvp~~~L~-hp~f~~LL~~aeeEfG~~~~G~l~iPC~~~~Fe~~l~~le 100 (100)
T PF02519_consen 40 HFAVYVGEERRRFVVPVSYLN-HPLFQELLEQAEEEFGFDQDGPLTIPCDVVLFEHLLWLLE 100 (100)
T ss_pred eEEEEeCccceEEEechHHcC-chhHHHHHHHHhhhcCcCCCCcEEeeCCHHHHHHHHHHhC
Confidence 34444444 899999998876 46677777743 2 3578888878888888876653
No 48
>PRK09296 cysteine desufuration protein SufE; Provisional
Probab=37.32 E-value=60 Score=23.44 Aligned_cols=31 Identities=19% Similarity=0.370 Sum_probs=22.3
Q ss_pred HHHHHHHHHHhcCCCHHHHHh--------HcCCCCCCCH
Q 038532 118 DRLCQLAADIVKGKTPEEIRR--------TFNIKKDFTP 148 (164)
Q Consensus 118 ~l~~~~ia~~i~gks~eeir~--------~f~i~~d~t~ 148 (164)
.-.+..+...+.|+||+||.+ .+|+..-+||
T Consensus 79 kGl~alL~~~~~g~tp~eIl~~d~~~~~~~lGL~~~LSp 117 (138)
T PRK09296 79 KGLIAVVFILYQQMTPQDIVNFDVRPWFEKLALTQHLTP 117 (138)
T ss_pred HHHHHHHHHHHcCCCHHHHHhCChHHHHHHcCcccccCc
Confidence 333556677789999999874 2677777776
No 49
>TIGR02476 BluB cob(II)yrinic acid a,c-diamide reductase. The BluB protein is related to the nitroreductase family (pfam0881), and is found to substitute for the FldA cobalt reductase in aerobic species (by phylogenetic profiling). BluB is also found to be preceded by B12 promoter elements elements. The gene in R. capsulatus has been shown to be essential for cobalamin biosynthesis.
Probab=37.10 E-value=31 Score=26.08 Aligned_cols=38 Identities=21% Similarity=0.213 Sum_probs=28.1
Q ss_pred HHHHHHHhhhcCCChhHHHHHHHHHHHHhcCCCHHHHHhHcCCCCCCC
Q 038532 100 LHFGLLLAANYLEIPALLDRLCQLAADIVKGKTPEEIRRTFNIKKDFT 147 (164)
Q Consensus 100 ~l~~Ll~AA~~L~I~~L~~l~~~~ia~~i~gks~eeir~~f~i~~d~t 147 (164)
.+..++.||..||+-.. ++.+-..+.+++.|||+.+++
T Consensus 133 A~~nl~LaA~~~GlGs~----------~~~~~~~~~v~~~L~lp~~~~ 170 (205)
T TIGR02476 133 AIQNLWLAARAEGLGVG----------WVSILDPDAVRRLLGVPEGWR 170 (205)
T ss_pred HHHHHHHHHHHCCCcce----------eecccChHHHHHHhCcCCCce
Confidence 45688889999888763 122445789999999998754
No 50
>PHA03098 kelch-like protein; Provisional
Probab=36.94 E-value=2e+02 Score=24.92 Aligned_cols=55 Identities=5% Similarity=0.020 Sum_probs=42.1
Q ss_pred HHHHhhhhhcCcHHHHHHHHHhhhcCCChhHHHHHHHHHHHHhc---------CCCHHHHHhHcC
Q 038532 86 WEKKFDEEVSEDKDLHFGLLLAANYLEIPALLDRLCQLAADIVK---------GKTPEEIRRTFN 141 (164)
Q Consensus 86 wd~~F~~~l~~~~~~l~~Ll~AA~~L~I~~L~~l~~~~ia~~i~---------gks~eeir~~f~ 141 (164)
--.+|+.+ .++.+..++++..|...+.+.|.+.|-++|+..+. ..+.+++.+.+.
T Consensus 96 ~C~~~l~~-~l~~~nc~~~~~~a~~~~~~~L~~~~~~~i~~nf~~v~~~~~f~~l~~~~l~~ll~ 159 (534)
T PHA03098 96 LCINYIIK-IIDDNNCIDIYRFSFFYGCKKLYSAAYNYIRNNIELIYNDPDFIYLSKNELIKILS 159 (534)
T ss_pred HHHHHHHH-hCCHhHHHHHHHHHHHcCcHHHHHHHHHHHHHHHHHHhcCchhhcCCHHHHHHHhc
Confidence 33466422 37889999999999999999999999888876543 236888887765
No 51
>COG1926 Predicted phosphoribosyltransferases [General function prediction only]
Probab=36.07 E-value=1.7e+02 Score=22.91 Aligned_cols=29 Identities=24% Similarity=0.185 Sum_probs=23.5
Q ss_pred hhHHHHHHHhhhhhcCcHHHHHHHHHhhhcCC
Q 038532 81 EEEEEWEKKFDEEVSEDKDLHFGLLLAANYLE 112 (164)
Q Consensus 81 ~~~~~wd~~F~~~l~~~~~~l~~Ll~AA~~L~ 112 (164)
..+..|..+| -+++++++..+|..|+--+
T Consensus 187 ~AVg~~Y~dF---~q~sdeEV~~lL~~a~~~~ 215 (220)
T COG1926 187 EAVGEFYRDF---RQVSDEEVRALLRRANAPN 215 (220)
T ss_pred HHHHHHHHHH---hhcCHHHHHHHHHhccCCC
Confidence 3467888999 6789999999999987544
No 52
>PF09821 AAA_assoc_C: C-terminal AAA-associated domain; InterPro: IPR018632 Members of this family are found in various prokaryotic ABC transporters, predominantly involved in nitrate, sulphonate and bicarbonate translocation.
Probab=35.84 E-value=34 Score=24.07 Aligned_cols=22 Identities=18% Similarity=0.163 Sum_probs=18.8
Q ss_pred hcCcHHHHHHHHHhhhcCCChh
Q 038532 94 VSEDKDLHFGLLLAANYLEIPA 115 (164)
Q Consensus 94 l~~~~~~l~~Ll~AA~~L~I~~ 115 (164)
++++.+.|+.++.||..|+.-.
T Consensus 7 l~~eiDdL~p~~eAaelLgf~~ 28 (120)
T PF09821_consen 7 LHLEIDDLLPIVEAAELLGFAE 28 (120)
T ss_pred hCCcHHHHHHHHHHHHHcCCee
Confidence 5778899999999999998743
No 53
>PRK15019 CsdA-binding activator; Provisional
Probab=34.86 E-value=64 Score=23.59 Aligned_cols=32 Identities=19% Similarity=0.380 Sum_probs=22.5
Q ss_pred HHHHHHHHHHhcCCCHHHHHh--------HcCCCCCCCHH
Q 038532 118 DRLCQLAADIVKGKTPEEIRR--------TFNIKKDFTPE 149 (164)
Q Consensus 118 ~l~~~~ia~~i~gks~eeir~--------~f~i~~d~t~e 149 (164)
.-.++.+...+.|+||+||.+ .+|+..-+||-
T Consensus 89 kGl~alL~~~~~g~tp~eIl~~d~~~~~~~lGL~~~LSps 128 (147)
T PRK15019 89 RGLLAVLLTAVEGKTAAELQAQSPLALFDELGLRAQLSAS 128 (147)
T ss_pred HHHHHHHHHHHcCCCHHHHHhcCHHHHHHHCCchhhcCcc
Confidence 333455666779999999875 26777777763
No 54
>TIGR03419 NifU_clost FeS cluster assembly scaffold protein NifU, Clostridium type. NifU and NifS form a pair of iron-sulfur (FeS) cluster biosynthesis proteins much simpler than the ISC and SUF systems. Members of this protein family are a distinct group of NifU-like proteins, found always to a NifS-like protein and restricted to species that lack a SUF system. Typically, NIF systems service a smaller number of FeS-containing proteins than do ISC or SUF. Members of this particular branch typically are found, almost half the time, near the mnmA gene, involved in the carboxymethylaminomethyl modification of U34 in some tRNAs (see GenProp0704). While other NifU proteins are associated with nitrogen fixation, this family is not.
Probab=34.61 E-value=68 Score=22.35 Aligned_cols=37 Identities=19% Similarity=0.242 Sum_probs=23.7
Q ss_pred HHHhhhcCCChhHHHHH-HHHHHHHhcCCCHHHHHhHc
Q 038532 104 LLLAANYLEIPALLDRL-CQLAADIVKGKTPEEIRRTF 140 (164)
Q Consensus 104 Ll~AA~~L~I~~L~~l~-~~~ia~~i~gks~eeir~~f 140 (164)
.+.-+.|-.-=--.-.+ +..++++++|||++|..++-
T Consensus 46 ~I~d~~f~~~GC~is~Asas~~~e~i~Gk~l~ea~~i~ 83 (121)
T TIGR03419 46 IIKDVKFKTFGCGAAIASSSMATEMIKGKTLEEAWELT 83 (121)
T ss_pred EEEEEEEEEeccHHHHHHHHHHHHHHcCCCHHHHHHhh
Confidence 34444444444344444 56779999999999977664
No 55
>PRK11325 scaffold protein; Provisional
Probab=34.51 E-value=61 Score=22.82 Aligned_cols=38 Identities=24% Similarity=0.190 Sum_probs=24.2
Q ss_pred HHHhhhcCCChhHHHHH-HHHHHHHhcCCCHHHHHhHcC
Q 038532 104 LLLAANYLEIPALLDRL-CQLAADIVKGKTPEEIRRTFN 141 (164)
Q Consensus 104 Ll~AA~~L~I~~L~~l~-~~~ia~~i~gks~eeir~~f~ 141 (164)
.+.-+.|-.-=--.-.+ +..++++++|||++|.+.+-+
T Consensus 52 ~I~d~~f~~~GC~is~Asas~~~e~~~Gktl~ea~~i~~ 90 (127)
T PRK11325 52 IIEDAKFKTYGCGSAIASSSLVTEWVKGKTLDEALAIKN 90 (127)
T ss_pred eEEEEEEEeeCCHHHHHHHHHHHHHHcCCCHHHHHhcCH
Confidence 34444444444444444 567789999999999886633
No 56
>PF08671 SinI: Anti-repressor SinI; InterPro: IPR010981 The SinR repressor is part of a group of Sin (sporulation inhibition) proteins in Bacillus subtilis that regulate the commitment to sporulation in response to extreme adversity []. SinR is a tetrameric repressor protein that binds to the promoters of genes essential for entry into sporulation and prevents their transcription. This repression is overcome through the activity of SinI, which disrupts the SinR tetramer through the formation of a SinI-SinR heterodimer, thereby allowing sporulation to proceed. The SinR structure consists of two domains: a dimerisation domain stabilised by a hydrophobic core, and a DNA-binding domain that is identical to domains of the bacteriophage 434 CI and Cro proteins that regulate prophage induction. The dimerisation domain is a four-helical bundle formed from two helices from the C-terminal residues of SinR and two helices from the central residues of SinI. These regions in SinR and SinI are similar in both structure and sequence. The interaction of SinR monomers to form tetramers is weaker than between SinR and SinI, since SinI can effectively disrupt SinR tetramers. This entry represents the dimerisation domain in both SinI and SinR proteins.; GO: 0005488 binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1B0N_A 2YAL_A.
Probab=34.06 E-value=25 Score=18.57 Aligned_cols=13 Identities=38% Similarity=0.577 Sum_probs=9.0
Q ss_pred cCCCHHHHHhHcC
Q 038532 129 KGKTPEEIRRTFN 141 (164)
Q Consensus 129 ~gks~eeir~~f~ 141 (164)
.|-|.+|+|+++.
T Consensus 15 ~Gls~eeir~FL~ 27 (30)
T PF08671_consen 15 SGLSKEEIREFLE 27 (30)
T ss_dssp TT--HHHHHHHHH
T ss_pred cCCCHHHHHHHHH
Confidence 5889999999863
No 57
>PF05443 ROS_MUCR: ROS/MUCR transcriptional regulator protein; InterPro: IPR008807 This family consists of several ROS/MUCR transcriptional regulator proteins. The ros chromosomal gene is present in octopine and nopaline strains of Agrobacterium tumefaciens as well as in Rhizobium meliloti (Sinorhizobium meliloti). This gene encodes a 15.5 kDa protein that specifically represses the virC and virD operons in the virulence region of the Ti plasmid [] and is necessary for succinoglycan production []. S. meliloti can produce two types of acidic exopolysaccharides, succinoglycan and galactoglucan, that are interchangeable for infection of Medicago sativa (Alfalfa) nodules. MucR from S. meliloti acts as a transcriptional repressor that blocks the expression of the exp genes responsible for galactoglucan production therefore allowing the exclusive production of succinoglycan [].; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2JSP_A.
Probab=34.03 E-value=20 Score=25.81 Aligned_cols=18 Identities=44% Similarity=0.826 Sum_probs=12.6
Q ss_pred CCCHHHHHhHcCCCCCCC
Q 038532 130 GKTPEEIRRTFNIKKDFT 147 (164)
Q Consensus 130 gks~eeir~~f~i~~d~t 147 (164)
|.|++|=|+.||++.|+.
T Consensus 94 gltp~eYR~kwGlp~dyp 111 (132)
T PF05443_consen 94 GLTPEEYRAKWGLPKDYP 111 (132)
T ss_dssp -S-HHHHHHHTT-GGG--
T ss_pred CCCHHHHHHHhCcCCCCc
Confidence 899999999999998853
No 58
>PF01592 NifU_N: NifU-like N terminal domain; InterPro: IPR002871 Iron-sulphur (FeS) clusters are important cofactors for numerous proteins involved in electron transfer, in redox and non-redox catalysis, in gene regulation, and as sensors of oxygen and iron. These functions depend on the various FeS cluster prosthetic groups, the most common being [2Fe-2S] and [4Fe-4S] []. FeS cluster assembly is a complex process involving the mobilisation of Fe and S atoms from storage sources, their assembly into [Fe-S] form, their transport to specific cellular locations, and their transfer to recipient apoproteins. So far, three FeS assembly machineries have been identified, which are capable of synthesising all types of [Fe-S] clusters: ISC (iron-sulphur cluster), SUF (sulphur assimilation), and NIF (nitrogen fixation) systems. The ISC system is conserved in eubacteria and eukaryotes (mitochondria), and has broad specificity, targeting general FeS proteins [, ]. It is encoded by the isc operon (iscRSUA-hscBA-fdx-iscX). IscS is a cysteine desulphurase, which obtains S from cysteine (converting it to alanine) and serves as a S donor for FeS cluster assembly. IscU and IscA act as scaffolds to accept S and Fe atoms, assembling clusters and transfering them to recipient apoproteins. HscA is a molecular chaperone and HscB is a co-chaperone. Fdx is a [2Fe-2S]-type ferredoxin. IscR is a transcription factor that regulates expression of the isc operon. IscX (also known as YfhJ) appears to interact with IscS and may function as an Fe donor during cluster assembly []. The SUF system is an alternative pathway to the ISC system that operates under iron starvation and oxidative stress. It is found in eubacteria, archaea and eukaryotes (plastids). The SUF system is encoded by the suf operon (sufABCDSE), and the six encoded proteins are arranged into two complexes (SufSE and SufBCD) and one protein (SufA). SufS is a pyridoxal-phosphate (PLP) protein displaying cysteine desulphurase activity. SufE acts as a scaffold protein that accepts S from SufS and donates it to SufA []. SufC is an ATPase with an unorthodox ATP-binding cassette (ABC)-like component. No specific functions have been assigned to SufB and SufD. SufA is homologous to IscA [], acting as a scaffold protein in which Fe and S atoms are assembled into [FeS] cluster forms, which can then easily be transferred to apoproteins targets. In the NIF system, NifS and NifU are required for the formation of metalloclusters of nitrogenase in Azotobacter vinelandii, and other organisms, as well as in the maturation of other FeS proteins. Nitrogenase catalyses the fixation of nitrogen. It contains a complex cluster, the FeMo cofactor, which contains molybdenum, Fe and S. NifS is a cysteine desulphurase. NifU binds one Fe atom at its N-terminal, assembling an FeS cluster that is transferred to nitrogenase apoproteins []. Nif proteins involved in the formation of FeS clusters can also be found in organisms that do not fix nitrogen []. This entry represents the N-terminal of NifU and homologous proteins. NifU contains two domains: an N-terminal and a C-terminal domain (IPR001075 from INTERPRO) []. These domains exist either together or on different polypeptides, both domains being found in organisms that do not fix nitrogen (e.g. yeast), so they have a broader significance in the cell than nitrogen fixation. ; GO: 0005506 iron ion binding, 0051536 iron-sulfur cluster binding, 0016226 iron-sulfur cluster assembly; PDB: 3LVL_A 4EB5_C 4EB7_C 1WFZ_A 2Z7E_C 2AZH_A 1XJS_A 1Q48_A 1R9P_A 2KQK_A ....
Probab=34.01 E-value=57 Score=22.81 Aligned_cols=21 Identities=29% Similarity=0.406 Sum_probs=16.5
Q ss_pred HHHHHHHHHHhcCCCHHHHHh
Q 038532 118 DRLCQLAADIVKGKTPEEIRR 138 (164)
Q Consensus 118 ~l~~~~ia~~i~gks~eeir~ 138 (164)
-.++..++.+++|||++|+.+
T Consensus 65 ~Asas~~~~~i~gk~l~ea~~ 85 (126)
T PF01592_consen 65 IASASMMCELIKGKTLEEALK 85 (126)
T ss_dssp HHHHHHHHHHHTTSBHHHHHC
T ss_pred HHHHHHHHHHHcCCCHHHHHH
Confidence 345677899999999888864
No 59
>TIGR03391 FeS_syn_CsdE cysteine desulfurase, sulfur acceptor subunit CsdE. Members of this protein family are CsdE, formerly called YgdK. This protein, found as a paralog to SufE in Escherichia coli, Yersinia pestis, Photorhabdus luminescens, and related species, works together and physically interacts with CsdA (a paralog of SufS). CsdA has cysteine desulfurase activity that is enhanced by this protein (CsdE), in which Cys-61 (numbered as in E. coli) is a sulfur acceptor site. This gene pair, although involved in FeS cluster biosynthesis, is not found next to other such genes as are its paralogs from the Suf or Isc systems.
Probab=33.98 E-value=69 Score=23.12 Aligned_cols=31 Identities=23% Similarity=0.448 Sum_probs=21.7
Q ss_pred HHHHHHHHHHhcCCCHHHHHhH--------cCCCCCCCH
Q 038532 118 DRLCQLAADIVKGKTPEEIRRT--------FNIKKDFTP 148 (164)
Q Consensus 118 ~l~~~~ia~~i~gks~eeir~~--------f~i~~d~t~ 148 (164)
.-.++.+...+.|+||+||.++ +|+...+||
T Consensus 84 kGl~alL~~~~~g~tp~eI~~~d~~~~~~~lGL~~~LSp 122 (138)
T TIGR03391 84 RGLLAVLLTAVEGKTPEQLLAQDPLALFDELGLRAQLSA 122 (138)
T ss_pred HHHHHHHHHHHcCCCHHHHHHCCHHHHHHHcCchhccCc
Confidence 3335556667799999998743 577777776
No 60
>TIGR01999 iscU FeS cluster assembly scaffold IscU. This model represents IscU, a homolog of the N-terminal region of NifU, an Fe-S cluster assembly protein found mostly in nitrogen-fixing bacteria. IscU is considered part of the IscSUA-hscAB-fdx system of Fe-S assembly, whereas NifU is found in nitrogenase-containing (nitrogen-fixing) species. A NifU-type protein is also found in Helicobacter and Campylobacter. IscU and NifU are considered scaffold proteins on which Fe-S clusters are assembled before transfer to apoproteins. This model excludes true NifU proteins as in Klebsiella pneumoniae and Anabaena sp. as well as archaeal homologs. It includes largely proteobacterial and eukaryotic forms.
Probab=33.72 E-value=66 Score=22.50 Aligned_cols=37 Identities=22% Similarity=0.265 Sum_probs=23.7
Q ss_pred HHHhhhcCCChhHHHHH-HHHHHHHhcCCCHHHHHhHc
Q 038532 104 LLLAANYLEIPALLDRL-CQLAADIVKGKTPEEIRRTF 140 (164)
Q Consensus 104 Ll~AA~~L~I~~L~~l~-~~~ia~~i~gks~eeir~~f 140 (164)
.+.-+.|-.-=.-.-.+ +..++++++|||.+|.+.+-
T Consensus 50 ~I~d~~f~~~GC~~s~Asas~~~e~i~Gktl~ea~~i~ 87 (124)
T TIGR01999 50 IIEDAKFKTFGCGSAIASSSLATELIKGKSLEEALKIK 87 (124)
T ss_pred eEEEEEEEecCcHHHHHHHHHHHHHHcCCCHHHHHhcc
Confidence 34444444443333334 56789999999999988664
No 61
>cd02140 Nitroreductase_4 Nitroreductase-like family 4. A subfamily of the nitroreductase family containing uncharacterized proteins that are similar to nitroreductase. Nitroreductase catalyzes the reduction of nitroaromatic compounds such as nitrotoluenes, nitrofurans and nitroimidazoles. This process requires NAD(P)H as electron donor in an obligatory two-electron transfer and uses FMN as cofactor. The enzyme is typically a homodimer. Members of this family are also called NADH dehydrogenase, oxygen-insensitive NAD(P)H nitrogenase or dihydropteridine reductase.
Probab=33.50 E-value=41 Score=25.02 Aligned_cols=39 Identities=21% Similarity=0.249 Sum_probs=26.8
Q ss_pred HHHHHHhhhcCCChhHHHHHHHHHHHHhcCCCHHHHHhHcCCCCCCC
Q 038532 101 HFGLLLAANYLEIPALLDRLCQLAADIVKGKTPEEIRRTFNIKKDFT 147 (164)
Q Consensus 101 l~~Ll~AA~~L~I~~L~~l~~~~ia~~i~gks~eeir~~f~i~~d~t 147 (164)
+..|+.||.-+|+-....- ......+.+|+.|||++++.
T Consensus 127 ~~nl~LaA~~~GlGs~~~~--------~~~~~~~~v~~~l~ip~~~~ 165 (192)
T cd02140 127 QIAVWTALAAEGIGANLQH--------YNPLIDEEVAKKWNIPSNWK 165 (192)
T ss_pred HHHHHHHHHhCCCcccHHH--------hCccCCHHHHHhcCCCccce
Confidence 5688889999998763211 00123589999999998753
No 62
>PF13798 PCYCGC: Protein of unknown function with PCYCGC motif
Probab=33.38 E-value=65 Score=23.92 Aligned_cols=23 Identities=39% Similarity=0.501 Sum_probs=16.5
Q ss_pred HHHHHHHHHHHhcCCCHHHHHhH
Q 038532 117 LDRLCQLAADIVKGKTPEEIRRT 139 (164)
Q Consensus 117 ~~l~~~~ia~~i~gks~eeir~~ 139 (164)
++.+...+...=+|||+.|||++
T Consensus 118 l~ia~~a~~~~~~Gks~~eIR~~ 140 (158)
T PF13798_consen 118 LDIAVQAVQMYQEGKSPKEIRQY 140 (158)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHH
Confidence 34444555666679999999986
No 63
>smart00875 BACK BTB And C-terminal Kelch. The BACK domain is found juxtaposed to the BTB domain; they are separated by as little as two residues.
Probab=32.90 E-value=1.3e+02 Score=19.00 Aligned_cols=39 Identities=13% Similarity=0.164 Sum_probs=23.7
Q ss_pred HHHHhhhcCCChhHHHHHHHHHHHH---------hcCCCHHHHHhHcC
Q 038532 103 GLLLAANYLEIPALLDRLCQLAADI---------VKGKTPEEIRRTFN 141 (164)
Q Consensus 103 ~Ll~AA~~L~I~~L~~l~~~~ia~~---------i~gks~eeir~~f~ 141 (164)
++...|...+.+.|.+.|.++++.. +...+.++++.+++
T Consensus 3 ~i~~~a~~~~~~~L~~~~~~~i~~nf~~~~~~~~f~~L~~~~l~~iL~ 50 (101)
T smart00875 3 GIRRFAELYGLEELLEKALRFILKNFLEVAQSEEFLELSLEQLLSLLS 50 (101)
T ss_pred hHHHHHHHhChHHHHHHHHHHHHHHHHHHhcCcHHhcCCHHHHHHHhC
Confidence 4455566667777777776666542 33445666666655
No 64
>PF11543 UN_NPL4: Nuclear pore localisation protein NPL4; InterPro: IPR024682 Npl4, along with Ufd1, forms the heterodimer adaptor complex UN, which is involved in the recruitment of p97, an AAA ATPase, for tasks involving the ubiquitin pathway. Npl4 has a N-terminal ubiquitin-like domain which has within its structure a beta-grasp fold with a helical insert []. This entry represents the ubiquitin-like domain.; PDB: 2PJH_A 1WF9_A.
Probab=32.55 E-value=23 Score=23.00 Aligned_cols=21 Identities=33% Similarity=0.472 Sum_probs=10.4
Q ss_pred CCCCCeEEEEcCCCC-EEEecH
Q 038532 1 MATTSTVKLRSSDNE-VFEVEK 21 (164)
Q Consensus 1 m~~~~~i~l~s~DG~-~f~v~~ 21 (164)
|+++-.|+++|.||. .+.++.
T Consensus 1 ~~~~milRvrS~dG~~Rie~~~ 22 (80)
T PF11543_consen 1 MASSMILRVRSKDGMKRIEVSP 22 (80)
T ss_dssp -----EEEEE-SSEEEEEEE-T
T ss_pred CCccEEEEEECCCCCEEEEcCC
Confidence 788888999999985 344543
No 65
>cd02144 iodotyrosine_dehalogenase Iodotyrosine dehalogenase catalyzes the removal of iodine from the 3, 5 positions of L-tyosine in thyroid, liver and kidney, using NADPH as electron donor. This enzyme is a homolog of the nitroreductase family. These enzymes are usually homodimers.
Probab=32.49 E-value=41 Score=24.71 Aligned_cols=38 Identities=13% Similarity=-0.054 Sum_probs=26.8
Q ss_pred HHHHHHhhhcCCChhHHHHHHHHHHHHhcCCCH-HHHHhHcCCCCCCCH
Q 038532 101 HFGLLLAANYLEIPALLDRLCQLAADIVKGKTP-EEIRRTFNIKKDFTP 148 (164)
Q Consensus 101 l~~Ll~AA~~L~I~~L~~l~~~~ia~~i~gks~-eeir~~f~i~~d~t~ 148 (164)
+..++.||.-||+... .+.+... +.+++.|||++++.+
T Consensus 129 ~~~l~LaA~~~Glgs~----------~~~~~~~~~~v~~~l~ip~~~~~ 167 (193)
T cd02144 129 CGLLLAALQNAGLGTV----------TTTPLNMGPFLRRLLGRPANEKL 167 (193)
T ss_pred HHHHHHHHHHCCCcee----------ecCCcchhHHHHHHhCCCCCCce
Confidence 4458888888888862 1234344 899999999987543
No 66
>PRK13696 hypothetical protein; Provisional
Probab=30.95 E-value=1.4e+02 Score=18.63 Aligned_cols=38 Identities=18% Similarity=0.283 Sum_probs=24.9
Q ss_pred hHHHHHHHHHHHHhcCCCHHHHHhHcCCCCCCCHHHHHHHHHH
Q 038532 115 ALLDRLCQLAADIVKGKTPEEIRRTFNIKKDFTPEEEKAVMDE 157 (164)
Q Consensus 115 ~L~~l~~~~ia~~i~gks~eeir~~f~i~~d~t~eee~~i~~e 157 (164)
++-++.-+.+ .-+..+...+.++||+-+ +||.++++++
T Consensus 24 SFSevi~~L~--~~~~~~~~~l~~~~Gil~---dee~~e~~~~ 61 (62)
T PRK13696 24 SFSEVIRELI--EKKKGNLDKLMKAFGILS---EEEAEELKKE 61 (62)
T ss_pred CHHHHHHHHH--HHhhccHHHHHHHHCCCC---HHHHHHHHhh
Confidence 4555444444 223456888999999854 5777787765
No 67
>TIGR02698 CopY_TcrY copper transport repressor, CopY/TcrY family. This family includes metal-fist type transcriptional repressors of copper transport systems such as copYZAB of Enterococcus hirae and tcrYAZB (transferble copper resistance) of an Enterocuccus faecium plasmid. High levels of copper can displace zinc and prevent binding by the repressor, activating efflux by copper resistance transporters. The most closely related proteins excluded by this model are antibiotic resistance regulators including the methicillin resistance regulatory protein MecI.
Probab=30.28 E-value=1.7e+02 Score=20.61 Aligned_cols=36 Identities=3% Similarity=-0.052 Sum_probs=20.9
Q ss_pred HHHHHHhcCCCHHHHHhHcCCCCCCCHHHHHHHHHH
Q 038532 122 QLAADIVKGKTPEEIRRTFNIKKDFTPEEEKAVMDE 157 (164)
Q Consensus 122 ~~ia~~i~gks~eeir~~f~i~~d~t~eee~~i~~e 157 (164)
+.+.+.+-|-++..+-..|--.+.+++||.+++++-
T Consensus 78 ~~~~~~~f~gs~~~ll~~l~~~~~ls~eele~L~~l 113 (130)
T TIGR02698 78 QELFSRICSRKVGAVIADLIEESPLSQTDIEKLEKL 113 (130)
T ss_pred HHHHHHHHCCCHHHHHHHHHhcCCCCHHHHHHHHHH
Confidence 344444445555555444422456888888888763
No 68
>PF11116 DUF2624: Protein of unknown function (DUF2624); InterPro: IPR020277 This entry contains proteins with no known function.
Probab=29.67 E-value=1.5e+02 Score=19.68 Aligned_cols=10 Identities=40% Similarity=0.740 Sum_probs=4.7
Q ss_pred HHHHHHhcCC
Q 038532 122 QLAADIVKGK 131 (164)
Q Consensus 122 ~~ia~~i~gk 131 (164)
..|+..++|+
T Consensus 37 ~~I~~~lr~k 46 (85)
T PF11116_consen 37 EQIANILRGK 46 (85)
T ss_pred HHHHHHHhcC
Confidence 3444444554
No 69
>COG1710 Uncharacterized protein conserved in archaea [Function unknown]
Probab=28.88 E-value=41 Score=23.90 Aligned_cols=16 Identities=44% Similarity=0.727 Sum_probs=14.4
Q ss_pred cCCCHHHHHhHcCCCC
Q 038532 129 KGKTPEEIRRTFNIKK 144 (164)
Q Consensus 129 ~gks~eeir~~f~i~~ 144 (164)
+||+|.||.+.+||+=
T Consensus 108 ~gk~preIsk~lGIpi 123 (139)
T COG1710 108 NGKTPREISKDLGIPI 123 (139)
T ss_pred cCCCHHHHHHhhCCch
Confidence 5999999999999973
No 70
>PF13518 HTH_28: Helix-turn-helix domain
Probab=28.50 E-value=93 Score=17.41 Aligned_cols=20 Identities=30% Similarity=0.491 Sum_probs=16.1
Q ss_pred HHHHhcCCCHHHHHhHcCCC
Q 038532 124 AADIVKGKTPEEIRRTFNIK 143 (164)
Q Consensus 124 ia~~i~gks~eeir~~f~i~ 143 (164)
|.....|.|..++.+.|||.
T Consensus 6 v~~~~~g~s~~~~a~~~gis 25 (52)
T PF13518_consen 6 VELYLEGESVREIAREFGIS 25 (52)
T ss_pred HHHHHcCCCHHHHHHHHCCC
Confidence 44455789999999999994
No 71
>PF07671 DUF1601: Protein of unknown function (DUF1601); InterPro: IPR011632 This repeat is found in a small number of proteins and is apparently limited to Coxiella burnetii.
Probab=28.36 E-value=57 Score=18.08 Aligned_cols=30 Identities=37% Similarity=0.428 Sum_probs=21.9
Q ss_pred cCCChhHHHHHHHHHHHHhcCCCHHHHHhH
Q 038532 110 YLEIPALLDRLCQLAADIVKGKTPEEIRRT 139 (164)
Q Consensus 110 ~L~I~~L~~l~~~~ia~~i~gks~eeir~~ 139 (164)
||.-++|.+.....|+..+..-++++|-.+
T Consensus 7 ~l~~q~L~~~L~~aV~~~a~~Fn~QeiaNt 36 (37)
T PF07671_consen 7 YLEEQRLSDRLLDAVRRNAEQFNPQEIANT 36 (37)
T ss_pred hhhhccchHHHHHHHHHHHHHcCHHHHhhc
Confidence 566677777777778877777788877543
No 72
>PF11197 DUF2835: Protein of unknown function (DUF2835); InterPro: IPR021363 This is a bacterial family of uncharacterised proteins. One member of this family (A4VM42 from SWISSPROT) is annotated as the A subunit of Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV).
Probab=28.02 E-value=63 Score=20.45 Aligned_cols=21 Identities=24% Similarity=0.281 Sum_probs=18.1
Q ss_pred CeEEEEcCCCCEEEecHHHHH
Q 038532 5 STVKLRSSDNEVFEVEKQVMI 25 (164)
Q Consensus 5 ~~i~l~s~DG~~f~v~~~~a~ 25 (164)
+.|.++|.||..+.+|....+
T Consensus 21 ~~V~v~s~~Gr~v~~Pa~~lR 41 (68)
T PF11197_consen 21 SKVVVRSDDGRRVQFPARHLR 41 (68)
T ss_pred cEEEEEecCCcEEEEeHHHCc
Confidence 579999999999999987654
No 73
>PF02736 Myosin_N: Myosin N-terminal SH3-like domain; InterPro: IPR004009 This domain has an SH3-like fold. It is found at the N terminus of many but not all myosins. The function of this domain is unknown.; GO: 0003774 motor activity, 0005524 ATP binding, 0016459 myosin complex; PDB: 2EC6_A 2W4H_M 1O1E_P 1O1D_D 1O18_A 1O1C_P 1O1B_D 1O1F_A 2W4A_M 2W4G_M ....
Probab=27.77 E-value=53 Score=18.39 Aligned_cols=19 Identities=21% Similarity=0.393 Sum_probs=15.5
Q ss_pred CCeEEEEcCCCCEEEecHH
Q 038532 4 TSTVKLRSSDNEVFEVEKQ 22 (164)
Q Consensus 4 ~~~i~l~s~DG~~f~v~~~ 22 (164)
+..+++++.||+...|+++
T Consensus 23 g~~vtV~~~~G~~~tv~~d 41 (42)
T PF02736_consen 23 GDKVTVKTEDGKEVTVKKD 41 (42)
T ss_dssp SSEEEEEETTTEEEEEEGG
T ss_pred CCEEEEEECCCCEEEeCCC
Confidence 4578999999999988753
No 74
>PRK14981 DNA-directed RNA polymerase subunit F; Provisional
Probab=27.43 E-value=2.1e+02 Score=19.69 Aligned_cols=43 Identities=26% Similarity=0.429 Sum_probs=29.7
Q ss_pred hhHHHHHHHHHHHHhcCCCHHHHHhHcCCCC-CCCHHHHHHHHHH
Q 038532 114 PALLDRLCQLAADIVKGKTPEEIRRTFNIKK-DFTPEEEKAVMDE 157 (164)
Q Consensus 114 ~~L~~l~~~~ia~~i~gks~eeir~~f~i~~-d~t~eee~~i~~e 157 (164)
..|-+.....||+. .=.|++|+|..|.-.. -+++|+.++|-+.
T Consensus 63 ~~l~e~~a~~I~nL-~P~~~dElrai~~~~~~~~~~e~l~~ILd~ 106 (112)
T PRK14981 63 EKMKEKTAVKIADI-LPETRDELRAIFAKERYTLSPEELDEILDI 106 (112)
T ss_pred cCCCHHHHHHHHhc-CCCCHHHHHHHHHHhccCCCHHHHHHHHHH
Confidence 33445555556653 5679999999987663 4889988887653
No 75
>PF08661 Rep_fac-A_3: Replication factor A protein 3; InterPro: IPR013970 Replication factor A is involved in eukaryotic DNA replication, recombination and repair. ; PDB: 2PI2_H 1L1O_D 3KDF_A 2Z6K_D 1QUQ_D 2PQA_D.
Probab=26.75 E-value=75 Score=21.57 Aligned_cols=20 Identities=20% Similarity=0.227 Sum_probs=14.4
Q ss_pred CCCeEEEEcCCCCEEEecHH
Q 038532 3 TTSTVKLRSSDNEVFEVEKQ 22 (164)
Q Consensus 3 ~~~~i~l~s~DG~~f~v~~~ 22 (164)
++..+++.|+||..+.|...
T Consensus 33 ~g~~~~l~~~d~~~V~v~l~ 52 (109)
T PF08661_consen 33 DGGSATLSTSDGGQVTVSLN 52 (109)
T ss_dssp TSSEEEEE-TTS-EEEEEES
T ss_pred CCCEEEEEcCCCCEEEEEeC
Confidence 46789999999998887654
No 76
>PHA02713 hypothetical protein; Provisional
Probab=26.52 E-value=1.3e+02 Score=26.66 Aligned_cols=75 Identities=7% Similarity=0.013 Sum_probs=44.7
Q ss_pred HHhhhhhcCcHHHHHHHHHhhhcCCChhHHHHHHHHHHHHhc---------CCCHHHHHhHcCCCCCCC-HHHHHHHHHH
Q 038532 88 KKFDEEVSEDKDLHFGLLLAANYLEIPALLDRLCQLAADIVK---------GKTPEEIRRTFNIKKDFT-PEEEKAVMDE 157 (164)
Q Consensus 88 ~~F~~~l~~~~~~l~~Ll~AA~~L~I~~L~~l~~~~ia~~i~---------gks~eeir~~f~i~~d~t-~eee~~i~~e 157 (164)
.+|+.+ .++.+..++++..|.-..-..|.+.+.++++..+. ..+.+++.+++.=.+.+. +.|+.-.+-=
T Consensus 116 ~~~l~~-~l~~~NCl~i~~~~~~~~~~~L~~~a~~~i~~~f~~v~~~~ef~~L~~~~l~~lL~~d~~l~v~~Ee~v~eav 194 (557)
T PHA02713 116 ESYIKD-YTNHDTCIYMYHRLYEMSHIPIVKYIKRMLMSNIPTLITTDAFKKTVFEILFDIISTNDNVYLYREGYKVTIL 194 (557)
T ss_pred HHHHHh-hCCccchHHHHHHHHhccchHHHHHHHHHHHHHHHHHhCChhhhhCCHHHHHHHhccccccCCCcHHHHHHHH
Confidence 467321 36777888888633334445588888888777664 346888888877544343 2333333333
Q ss_pred cCCccC
Q 038532 158 HGWALH 163 (164)
Q Consensus 158 ~~W~~~ 163 (164)
.+|+.+
T Consensus 195 ~~W~~~ 200 (557)
T PHA02713 195 LKWLEY 200 (557)
T ss_pred HHHHhc
Confidence 566544
No 77
>PF02657 SufE: Fe-S metabolism associated domain; InterPro: IPR003808 This entry represents the core domain of SufE and related proteins. This domain of SufE shows strong structural similarity to IscU, and the sulfur-acceptor site in SufE coincides with the location of the cysteine residues mediating Fe-S cluster assembly in IscU. Thus, a conserved core structure is implicated in mediating the interactions of both SufE and IscU with the mutually homologous cysteine desulfurase enzymes present in their respective operons [].; PDB: 1MZG_B 1WLO_A 3G0M_A 1NI7_A.
Probab=26.51 E-value=1.2e+02 Score=21.37 Aligned_cols=28 Identities=29% Similarity=0.628 Sum_probs=20.0
Q ss_pred HHHHHHhcCCCHHHHHhH-------cCCCCCCCHH
Q 038532 122 QLAADIVKGKTPEEIRRT-------FNIKKDFTPE 149 (164)
Q Consensus 122 ~~ia~~i~gks~eeir~~-------f~i~~d~t~e 149 (164)
+.+...++|+||+||..+ +|+...+||-
T Consensus 74 all~~~~~g~t~~eI~~~~~~fl~~lgl~~~Ls~s 108 (125)
T PF02657_consen 74 ALLLEVLNGQTPEEILAFDPDFLEQLGLSQHLSPS 108 (125)
T ss_dssp HHHHHHTTT-BHHHHHHS-THHHHHHTSCCCSTHH
T ss_pred HHHHHHHcCCCHHHHHhCCHHHHHHcCcccccCch
Confidence 344456699999999765 7888888874
No 78
>cd03370 NADH_oxidase NADPH_oxidase. Nitroreductase family containing NADH oxidase and other, uncharacterized proteins that are similar to nitroreductase. Nitroreductase catalyzes the reduction of nitroaromatic compounds such as nitrotoluenes, nitrofurans and nitroimidazoles. This process requires NAD(P)H as electron donor in an obligatory two-electron transfer and uses FMN as cofactor. The enzyme is typically a homodimer. Members of this family are also called NADH dehydrogenase, oxygen-insensitive NAD(P)H nitrogenase or dihydropteridine reductase.
Probab=26.32 E-value=49 Score=23.67 Aligned_cols=36 Identities=25% Similarity=0.253 Sum_probs=25.6
Q ss_pred HHHHHHhhhcCCChhHHHHHHHHHHHHhcCCCHHHHHhHcCCCC-CC
Q 038532 101 HFGLLLAANYLEIPALLDRLCQLAADIVKGKTPEEIRRTFNIKK-DF 146 (164)
Q Consensus 101 l~~Ll~AA~~L~I~~L~~l~~~~ia~~i~gks~eeir~~f~i~~-d~ 146 (164)
...++.||.-||+-.. ++.|...+.+++.||++. ++
T Consensus 95 ~~~l~L~A~~lGlgs~----------~i~~~~~~~v~~~l~l~~~~~ 131 (156)
T cd03370 95 AGFLLLAATALGLATS----------PMTGFDEEKVKEALGLPGRDR 131 (156)
T ss_pred HHHHHHHHHHcCCCcc----------cCcCcCHHHHHHHhCcCCcCc
Confidence 3357778888876543 344567889999999986 53
No 79
>PF11103 DUF2887: Protein of unknown function (DUF2887); InterPro: IPR022573 This bacterial group of proteins has no known function.
Probab=26.15 E-value=97 Score=23.89 Aligned_cols=28 Identities=18% Similarity=0.141 Sum_probs=24.7
Q ss_pred ChhHHHHHHHHHHHHhcCCCHHHHHhHc
Q 038532 113 IPALLDRLCQLAADIVKGKTPEEIRRTF 140 (164)
Q Consensus 113 I~~L~~l~~~~ia~~i~gks~eeir~~f 140 (164)
=..++++.-..+.-++..+|.+||.+||
T Consensus 173 ~~~lleLIEtIlvyKfp~lSreEIeaMl 200 (200)
T PF11103_consen 173 QRELLELIETILVYKFPQLSREEIEAML 200 (200)
T ss_pred HHHHHHHHHHHHHHHccccCHHHHHHhC
Confidence 4578888889999999999999999886
No 80
>PF09010 AsiA: Anti-Sigma Factor A; InterPro: IPR015100 Anti-sigma factor A is a transcriptional inhibitor that inhibits sigma 70-directed transcription by weakening its interaction with the core of the host's RNA polymerase. It is an all-helical protein, composed of six helical segments and intervening loops and turns, as well as a helix-turn-helix DNA binding motif, although neither free anti-sigma factor nor anti-sigma factor bound to sigma-70 has been shown to interact directly with DNA. In solution, the protein forms a symmetric dimer of small (10.59 kDa) protomers, which are composed of helix and coil regions and are devoid of beta-strand/sheet secondary structural elements []. ; PDB: 1TKV_A 1JR5_B 1TLH_A 1TL6_A.
Probab=25.67 E-value=22 Score=23.79 Aligned_cols=31 Identities=29% Similarity=0.470 Sum_probs=21.8
Q ss_pred cCC--CHHHHHhHcCCCCCCCHHHHHHHHHHcCCcc
Q 038532 129 KGK--TPEEIRRTFNIKKDFTPEEEKAVMDEHGWAL 162 (164)
Q Consensus 129 ~gk--s~eeir~~f~i~~d~t~eee~~i~~e~~W~~ 162 (164)
.|+ |..-+|++++ ++|++|.+++.+|+.|-+
T Consensus 46 ~G~~~t~~sfr~m~~---~lt~~ek~elieeFn~G~ 78 (91)
T PF09010_consen 46 TGKEFTQMSFRQMFK---RLTQEEKEELIEEFNEGH 78 (91)
T ss_dssp SSSE--HHHHHHHHH---TS-HHHHHHHHHHSHHHH
T ss_pred CCcchhHHHHHHHHH---HcCHHHHHHHHHHHhhhh
Confidence 455 5666777776 789999999999887754
No 81
>cd06664 IscU_like Iron-sulfur cluster scaffold-like proteins. IscU_like and NifU_like proteins. IscU and NifU function as a scaffold for the assembly of [2Fe-2S] clusters before they are transferred to apo target proteins. They are highly conserved and play vital roles in the ISC and NIF systems of Fe-S protein maturation. NIF genes participate in nitrogen fixation in several isolated bacterial species. The NifU domain, however, is also found in bacteria that do not fix nitrogen, so it may have wider significance in the cell. Human IscU interacts with frataxin, the Friedreich ataxia gene product, and incorrectly spliced IscU has been shown to disrupt iron homeostasis in skeletal muscle and cause myopathy.
Probab=25.40 E-value=1.2e+02 Score=20.81 Aligned_cols=39 Identities=23% Similarity=0.397 Sum_probs=25.1
Q ss_pred HHHHhhhcCCChhHHHHH-HHHHHHHhcCCCHHHHHhHcC
Q 038532 103 GLLLAANYLEIPALLDRL-CQLAADIVKGKTPEEIRRTFN 141 (164)
Q Consensus 103 ~Ll~AA~~L~I~~L~~l~-~~~ia~~i~gks~eeir~~f~ 141 (164)
+.+..+.|-.-=-.+-.+ +..++++++|||.+|+..+.+
T Consensus 46 ~~I~d~~f~~~GC~i~~Asas~~~~~~~Gk~~~ea~~i~~ 85 (123)
T cd06664 46 GRITDAKFQGFGCAISIASASLLTELIKGKTLDEALKLLN 85 (123)
T ss_pred CEEEEEEEEecCcHHHHHHHHHHHHHHcCCcHHHHHHHHH
Confidence 344444444444444444 567789999999999987653
No 82
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=25.04 E-value=65 Score=19.72 Aligned_cols=15 Identities=33% Similarity=0.508 Sum_probs=12.6
Q ss_pred CeEEEEcCCCCEEEe
Q 038532 5 STVKLRSSDNEVFEV 19 (164)
Q Consensus 5 ~~i~l~s~DG~~f~v 19 (164)
+.+++.|.||++|-=
T Consensus 5 KA~Kv~~RDGE~~lr 19 (65)
T COG4049 5 KAIKVRDRDGEEFLR 19 (65)
T ss_pred eeeEeeccCCceeee
Confidence 568999999999863
No 83
>PRK13742 replication protein; Provisional
Probab=24.92 E-value=73 Score=25.22 Aligned_cols=34 Identities=18% Similarity=0.299 Sum_probs=24.8
Q ss_pred hhHHHHHHHHHHHHhcC---CCHHHHHhHcCCCCCCC
Q 038532 114 PALLDRLCQLAADIVKG---KTPEEIRRTFNIKKDFT 147 (164)
Q Consensus 114 ~~L~~l~~~~ia~~i~g---ks~eeir~~f~i~~d~t 147 (164)
..|.+++|++-...-.| -+.+++|..||+++.|.
T Consensus 163 ~RLYelL~q~~~~~~~g~~~i~i~elr~~l~~~~~Y~ 199 (245)
T PRK13742 163 MRLYESLCQYRKPDGSGIVSLKIDWIIERYQLPQSYQ 199 (245)
T ss_pred HHHHHHHHHhhhhccCCeEEEEHHHHHHHhCCccccc
Confidence 35778888765542224 47999999999998775
No 84
>COG0822 IscU NifU homolog involved in Fe-S cluster formation [Energy production and conversion]
Probab=24.55 E-value=1.3e+02 Score=22.06 Aligned_cols=39 Identities=21% Similarity=0.319 Sum_probs=26.4
Q ss_pred HHHHHhhhcCCChhHHHHH-HHHHHHHhcCCCHHHHHhHc
Q 038532 102 FGLLLAANYLEIPALLDRL-CQLAADIVKGKTPEEIRRTF 140 (164)
Q Consensus 102 ~~Ll~AA~~L~I~~L~~l~-~~~ia~~i~gks~eeir~~f 140 (164)
-+.+..|.|.+.=-=+-.+ +..++++++|||.+|.+++-
T Consensus 51 ~~~I~d~~F~~~GC~is~ASss~~te~v~Gkti~EAl~i~ 90 (150)
T COG0822 51 NGVIEDAKFKGFGCAISIASSSMMTELVKGKTLDEALKIT 90 (150)
T ss_pred CCEEEEEEeeecCcHHHHHHHHHHHHHHcCCCHHHHHHHH
Confidence 3445555555555444444 45678999999999998775
No 85
>PF15063 TC1: Thyroid cancer protein 1
Probab=24.03 E-value=82 Score=20.48 Aligned_cols=12 Identities=25% Similarity=0.393 Sum_probs=5.2
Q ss_pred HHHHhHcCCCCC
Q 038532 134 EEIRRTFNIKKD 145 (164)
Q Consensus 134 eeir~~f~i~~d 145 (164)
|..|-+|+...|
T Consensus 56 eRA~iI~~~~~d 67 (79)
T PF15063_consen 56 ERARIIWECAQD 67 (79)
T ss_pred HHHHHHHhhCCC
Confidence 333444554443
No 86
>COG4224 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.98 E-value=73 Score=20.60 Aligned_cols=18 Identities=33% Similarity=0.514 Sum_probs=14.8
Q ss_pred CCCCCCHHHHHHHHHHcC
Q 038532 142 IKKDFTPEEEKAVMDEHG 159 (164)
Q Consensus 142 i~~d~t~eee~~i~~e~~ 159 (164)
.-+|+||+-..++++++.
T Consensus 57 ~GnDVTP~Klk~~q~~~~ 74 (77)
T COG4224 57 KGNDVTPEKLKQIQRKKG 74 (77)
T ss_pred CCCCCChHHHHHHHHHhc
Confidence 447999999999988764
No 87
>PF03750 DUF310: Protein of unknown function (DUF310); InterPro: IPR010149 Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) are a family of DNA direct repeats separated by regularly sized non-repetitive spacer sequences that are found in most bacterial and archaeal genomes []. CRISPRs appear to provide acquired resistance against bacteriophages, possibly acting with an RNA interference-like mechanism to inhibit gene functions of invasive DNA elements [, ]. Differences in the number and type of spacers between CRISPR repeats correlate with phage sensitivity. It is thought that following phage infection, bacteria integrate new spacers derived from phage genomic sequences, and that the removal or addition of particular spacers modifies the phage-resistance phenotype of the cell. Therefore, the specificity of CRISPRs may be determined by spacer-phage sequence similarity. In addition, there are many protein families known as CRISPR-associated sequences (Cas), which are encoded in the vicinity of CRISPR loci []. CRISPR/cas gene regions can be quite large, with up to 20 different, tandem-arranged cas genes next to a CRISPR cluster or filling the region between two repeat clusters. Cas genes and CRISPRs are found on mobile genetic elements such as plasmids, and have undergone extensive horizontal transfer. Cas proteins are thought to be involved in the propagation and functioning of CRISPRs. Some Cas proteins show similarity to helicases and repair proteins, although the functions of most are unknown. Cas families can be divided into subtypes according to operon organisation and phylogeny. This entry represents the C-terminal domain of a minor family of CRISPR-associated proteins. These proteins are found adjacent to a characteristic short, palindromic repeat cluster termed CRISPR, a probable mobile DNA element.
Probab=23.98 E-value=95 Score=21.61 Aligned_cols=32 Identities=25% Similarity=0.322 Sum_probs=19.2
Q ss_pred CChhHHHHHHHHHHHHhc--CCCHHHHHhHcCCCC
Q 038532 112 EIPALLDRLCQLAADIVK--GKTPEEIRRTFNIKK 144 (164)
Q Consensus 112 ~I~~L~~l~~~~ia~~i~--gks~eeir~~f~i~~ 144 (164)
+++.|.+.+.+ +|..++ +.|+.|||++|+--.
T Consensus 9 ~~~~~~~~Ae~-~~k~l~~~~lttsQlRkf~~~v~ 42 (119)
T PF03750_consen 9 DIELLVDYAEK-IAKELKKNKLTTSQLRKFYDEVK 42 (119)
T ss_pred CHHHHHHHHHH-HHHHHHhCCCCHHHHHHHHHHHH
Confidence 33444444433 334444 479999999998443
No 88
>TIGR03147 cyt_nit_nrfF cytochrome c nitrite reductase, accessory protein NrfF.
Probab=23.80 E-value=76 Score=22.66 Aligned_cols=17 Identities=24% Similarity=0.393 Sum_probs=12.5
Q ss_pred HHHHh-cCCCHHHHHhHc
Q 038532 124 AADIV-KGKTPEEIRRTF 140 (164)
Q Consensus 124 ia~~i-~gks~eeir~~f 140 (164)
|..++ .|+|.+||+.+|
T Consensus 66 Vr~~i~~G~Sd~eI~~~~ 83 (126)
T TIGR03147 66 VYSMVNEGKSNQQIIDFM 83 (126)
T ss_pred HHHHHHcCCCHHHHHHHH
Confidence 44444 499999999875
No 89
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=23.53 E-value=51 Score=26.79 Aligned_cols=16 Identities=50% Similarity=0.891 Sum_probs=13.0
Q ss_pred cCC-CHHHHHhHcCCCC
Q 038532 129 KGK-TPEEIRRTFNIKK 144 (164)
Q Consensus 129 ~gk-s~eeir~~f~i~~ 144 (164)
+.| |||+|+++|||.-
T Consensus 244 ~DKSsPEdIk~~FgiSK 260 (287)
T COG2996 244 NDKSSPEDIKATFGISK 260 (287)
T ss_pred CCCCCHHHHHHHhCcCH
Confidence 455 6999999999864
No 90
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=23.37 E-value=82 Score=17.67 Aligned_cols=15 Identities=20% Similarity=0.417 Sum_probs=10.6
Q ss_pred cCCCHHHHHhHcCCC
Q 038532 129 KGKTPEEIRRTFNIK 143 (164)
Q Consensus 129 ~gks~eeir~~f~i~ 143 (164)
.|+|..+|-+.||++
T Consensus 16 ~G~s~~~ia~~lgvs 30 (50)
T PF13384_consen 16 EGWSIREIAKRLGVS 30 (50)
T ss_dssp HT--HHHHHHHHTS-
T ss_pred CCCCHHHHHHHHCcC
Confidence 499999999999976
No 91
>KOG4244 consensus Failed axon connections (fax) protein/glutathione S-transferase-like protein [Signal transduction mechanisms]
Probab=23.16 E-value=89 Score=25.35 Aligned_cols=23 Identities=22% Similarity=0.510 Sum_probs=18.6
Q ss_pred HHHHHhHcCCCCCCCHHHHHHHH
Q 038532 133 PEEIRRTFNIKKDFTPEEEKAVM 155 (164)
Q Consensus 133 ~eeir~~f~i~~d~t~eee~~i~ 155 (164)
...+|+.|++++++++||+..-+
T Consensus 111 ~~~L~~hf~~~~~L~~e~~a~s~ 133 (281)
T KOG4244|consen 111 EDRLRKHFKIPDDLSAEQRAQSR 133 (281)
T ss_pred HHHHHHHcCCCCCCCHHHHHHHH
Confidence 35678999999999999887654
No 92
>PF00134 Cyclin_N: Cyclin, N-terminal domain; InterPro: IPR006671 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. Cyclins contain two domains of similar all-alpha fold, of which this entry is associated with the N-terminal domain.; PDB: 2W2H_B 3RGF_B 1KXU_A 1JKW_A 1URC_D 2WMB_D 1H26_D 1GY3_B 2UUE_D 1E9H_D ....
Probab=23.01 E-value=1.3e+02 Score=20.21 Aligned_cols=43 Identities=21% Similarity=0.340 Sum_probs=28.6
Q ss_pred hHHHHHHHHHHHHhcCCCHHHHHhHcCCCC-CCCHHHHHHHHHH
Q 038532 115 ALLDRLCQLAADIVKGKTPEEIRRTFNIKK-DFTPEEEKAVMDE 157 (164)
Q Consensus 115 ~L~~l~~~~ia~~i~gks~eeir~~f~i~~-d~t~eee~~i~~e 157 (164)
.|+-++|-.+|.++.+..+-.+.....+.+ .+|+++..+.+.+
T Consensus 74 ~li~~~cl~lA~K~~e~~~~~~~~~~~~~~~~~~~~~i~~~E~~ 117 (127)
T PF00134_consen 74 QLIALACLFLASKMEEDNPPSISDLIRISDNTFTKKDILEMERE 117 (127)
T ss_dssp HHHHHHHHHHHHHHHTSS--HHHHHHHHTTTSSHHHHHHHHHHH
T ss_pred hhhhhhHHHHhhhhhccccchHHHHHHHHcCCCCHHHHHHHHHH
Confidence 466778999999998875555666555444 4888776666553
No 93
>PF03131 bZIP_Maf: bZIP Maf transcription factor; InterPro: IPR004826 There are several different types of Maf transcription factors with different roles in the cell. MafG and MafH are small Mafs which lack a putative transactivation domain. They behave as transcriptional repressors when they dimerize among themselves. However they also serve as transcriptional activators by dimerizing with other (usually larger) basic-zipper proteins and recruiting them to specific DNA-binding sites. Maf transcription factors contain a conserved basic region leucine zipper (bZIP) domain, which mediates their dimerization and DNA binding property. Neural retina-specific leucine zipper proteins also belong to this family. Together with the basic region, the Maf extended homology region (EHR), conserved only within the Maf family, defines the DNA binding specific to Mafs. This structure enables Mafs to make a broader area of contact with DNA and to recognise longer DNA sequences. In particular, the two residues at the beginning of helix H2 are positioned to recognise the flanking region []. Small Maf proteins heterodimerize with Fos and may act as competitive repressors of the NF2-E2 transcription factor. In mouse, Maf1 may play an early role in axial patterning. Defects in these proteins are a cause of autosomal dominant retinitis pigmentosa. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 2KZ5_A 3A5T_A 1K1V_A 1SKN_P 2WT7_B 2WTY_B.
Probab=22.72 E-value=1.1e+02 Score=20.16 Aligned_cols=27 Identities=15% Similarity=0.213 Sum_probs=19.4
Q ss_pred HhcCCCHHHHHhHcCCCCCCCHHHHHHHHH
Q 038532 127 IVKGKTPEEIRRTFNIKKDFTPEEEKAVMD 156 (164)
Q Consensus 127 ~i~gks~eeir~~f~i~~d~t~eee~~i~~ 156 (164)
.|..++++|+..++ ..+|+++...|++
T Consensus 5 eL~~m~v~efn~~L---~~lt~~q~~~lK~ 31 (92)
T PF03131_consen 5 ELVSMSVREFNRLL---RGLTEEQIAELKQ 31 (92)
T ss_dssp HHHHS-HHHHHHHC---TTS-HHHHHHHHH
T ss_pred HHhhCCHHHHHHHH---HcCCHHHHHHHHH
Confidence 45567899998888 6799988887764
No 94
>cd02145 BluB Subfamily of the nitroreductase family that includes BluB protein in Rhodobacter capsulatus is involved in the conversion of cobinamide to cobalamin in Cobalamin (vitamin B12) biosynthesis. Nitroreductases typically reduce their substrates by using NAD(P)H as electron donor and often use FMN as a cofactor.
Probab=22.61 E-value=58 Score=24.25 Aligned_cols=37 Identities=27% Similarity=0.228 Sum_probs=26.5
Q ss_pred HHHHHHHhhhcCCChhHHHHHHHHHHHHhcCCCHHHHHhHcCCCCCC
Q 038532 100 LHFGLLLAANYLEIPALLDRLCQLAADIVKGKTPEEIRRTFNIKKDF 146 (164)
Q Consensus 100 ~l~~Ll~AA~~L~I~~L~~l~~~~ia~~i~gks~eeir~~f~i~~d~ 146 (164)
.+..|+.||.-+|+-.. ++.+-..+++++.|||++++
T Consensus 124 a~~nl~LaA~~~Glgt~----------~~~~~~~~~v~~~l~lp~~~ 160 (196)
T cd02145 124 AIQNLWLAARAEGLGVG----------WVSILDPEALARLLGIPEDW 160 (196)
T ss_pred HHHHHHHHHHHcCCceE----------EecccChHHHHHHcCcCCCc
Confidence 34577788888877642 23355689999999999764
No 95
>TIGR01994 SUF_scaf_2 SUF system FeS assembly protein, NifU family. Three iron-sulfur cluster assembly systems are known so far. ISC is broadly distributed while NIF tends to be associated with nitrogenase in nitrogen-fixing bacteria. The most recently described is SUF, believed to be important to maintain the function during aerobic stress of enzymes with labile Fe-S clusters. It is fairly widely distributed. This family represents one of two different proteins proposed to act as a scaffold on which the Fe-S cluster is built and from which it is transferred.
Probab=22.57 E-value=1.5e+02 Score=21.11 Aligned_cols=37 Identities=16% Similarity=0.247 Sum_probs=23.8
Q ss_pred HHhhhcCCChhHHHHH-HHHHHHHhcCCCHHHHHhHcC
Q 038532 105 LLAANYLEIPALLDRL-CQLAADIVKGKTPEEIRRTFN 141 (164)
Q Consensus 105 l~AA~~L~I~~L~~l~-~~~ia~~i~gks~eeir~~f~ 141 (164)
+..+.|-+----+-.+ +..++++++|||.+|+.....
T Consensus 51 I~d~~f~~~GCais~Asas~~~e~i~Gk~~~ea~~l~~ 88 (137)
T TIGR01994 51 IEDIAFEGEGCSISQASASMMTELIKGKTVEEALSLVE 88 (137)
T ss_pred EEEEEEEecccHHHHHHHHHHHHHHcCCCHHHHHHHHH
Confidence 3444444443334444 467799999999999977753
No 96
>PF00249 Myb_DNA-binding: Myb-like DNA-binding domain; InterPro: IPR014778 The retroviral oncogene v-myb, and its cellular counterpart c-myb, encode nuclear DNA-binding proteins. These belong to the SANT domain family that specifically recognise the sequence YAAC(G/T)G [, ]. In myb, one of the most conserved regions consisting of three tandem repeats has been shown to be involved in DNA-binding [].; PDB: 1X41_A 2XAF_B 2XAG_B 2XAH_B 2UXN_B 2Y48_B 2XAQ_B 2X0L_B 2IW5_B 2XAJ_B ....
Probab=22.24 E-value=1.6e+02 Score=16.49 Aligned_cols=37 Identities=19% Similarity=0.160 Sum_probs=24.8
Q ss_pred HHHHHHHHhhhcCCChhHHHHHHHHHHHHhc-CCCHHHHHhHc
Q 038532 99 DLHFGLLLAANYLEIPALLDRLCQLAADIVK-GKTPEEIRRTF 140 (164)
Q Consensus 99 ~~l~~Ll~AA~~L~I~~L~~l~~~~ia~~i~-gks~eeir~~f 140 (164)
++-..|+.|..-++-. -=..||..+. |+|+.++|..|
T Consensus 7 eE~~~l~~~v~~~g~~-----~W~~Ia~~~~~~Rt~~qc~~~~ 44 (48)
T PF00249_consen 7 EEDEKLLEAVKKYGKD-----NWKKIAKRMPGGRTAKQCRSRY 44 (48)
T ss_dssp HHHHHHHHHHHHSTTT-----HHHHHHHHHSSSSTHHHHHHHH
T ss_pred HHHHHHHHHHHHhCCc-----HHHHHHHHcCCCCCHHHHHHHH
Confidence 3344455555555544 3467888888 99999999775
No 97
>COG4680 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.00 E-value=63 Score=21.83 Aligned_cols=17 Identities=29% Similarity=0.434 Sum_probs=14.2
Q ss_pred CCCHHHHHhHcCCCCCC
Q 038532 130 GKTPEEIRRTFNIKKDF 146 (164)
Q Consensus 130 gks~eeir~~f~i~~d~ 146 (164)
=++|++|+.+|+..+++
T Consensus 35 w~~P~diK~~f~~d~~~ 51 (98)
T COG4680 35 WKKPEDIKSVFPLDNFK 51 (98)
T ss_pred cCCHHHHHHhcCcccce
Confidence 37999999999987763
No 98
>PF14098 SSPI: Small, acid-soluble spore protein I
Probab=21.90 E-value=1.1e+02 Score=19.31 Aligned_cols=19 Identities=37% Similarity=0.485 Sum_probs=14.9
Q ss_pred HHHHHHhcCCCHHHHHhHc
Q 038532 122 QLAADIVKGKTPEEIRRTF 140 (164)
Q Consensus 122 ~~ia~~i~gks~eeir~~f 140 (164)
+.|...++|+|.+|++.+-
T Consensus 5 ~AI~~nv~g~s~~el~~~I 23 (65)
T PF14098_consen 5 QAIIHNVKGSSKEELKDTI 23 (65)
T ss_pred HHHHHHccCCCHHHHHHHH
Confidence 3456678999999999874
No 99
>PRK13379 protocatechuate 4,5-dioxygenase subunit alpha; Provisional
Probab=21.35 E-value=1.2e+02 Score=21.40 Aligned_cols=24 Identities=25% Similarity=0.252 Sum_probs=19.6
Q ss_pred HHHHHHHhcCCCHHHHHhHcCCCC
Q 038532 121 CQLAADIVKGKTPEEIRRTFNIKK 144 (164)
Q Consensus 121 ~~~ia~~i~gks~eeir~~f~i~~ 144 (164)
-+.|...++|+|.||.+++=+.++
T Consensus 94 ~q~i~a~mtG~t~eeF~~tr~~~~ 117 (119)
T PRK13379 94 NLQVYAIMRGETFEEFMQTRRVPD 117 (119)
T ss_pred HHHHHHHhcCCcHHHHHHHccCCC
Confidence 467788889999999999877764
No 100
>PF03883 DUF328: Protein of unknown function (DUF328); InterPro: IPR005583 The members of this family are functionally uncharacterised. They are about 250 amino acids in length.
Probab=21.34 E-value=88 Score=24.55 Aligned_cols=26 Identities=15% Similarity=0.346 Sum_probs=13.8
Q ss_pred HHHHHHhcCCCHHHHHhHcCCCCCCC
Q 038532 122 QLAADIVKGKTPEEIRRTFNIKKDFT 147 (164)
Q Consensus 122 ~~ia~~i~gks~eeir~~f~i~~d~t 147 (164)
+.++..++..|.+|+++.|+|...+.
T Consensus 32 ~~l~~~L~~~s~~el~~l~~is~~la 57 (237)
T PF03883_consen 32 EELLEALKSLSEEELKKLMKISDKLA 57 (237)
T ss_pred HHHHHHHHhcCHHHHHHHHCCCHHHH
Confidence 33444455556666666666554433
No 101
>PLN03212 Transcription repressor MYB5; Provisional
Probab=21.27 E-value=1.3e+02 Score=24.00 Aligned_cols=35 Identities=14% Similarity=0.247 Sum_probs=26.2
Q ss_pred HHHHHHh-cCCCHHHHHhHc------CCCC-CCCHHHHHHHHH
Q 038532 122 QLAADIV-KGKTPEEIRRTF------NIKK-DFTPEEEKAVMD 156 (164)
Q Consensus 122 ~~ia~~i-~gks~eeir~~f------~i~~-d~t~eee~~i~~ 156 (164)
..||..+ .|+|..+.|+.+ +|.. .||+||.+.|.+
T Consensus 49 ~~IAk~~g~gRT~KQCReRW~N~L~P~I~kgpWT~EED~lLle 91 (249)
T PLN03212 49 RSLPKRAGLLRCGKSCRLRWMNYLRPSVKRGGITSDEEDLILR 91 (249)
T ss_pred HHHHHhhhcCCCcchHHHHHHHhhchhcccCCCChHHHHHHHH
Confidence 3467766 489999999986 3665 499998886654
No 102
>TIGR01044 rplV_bact ribosomal protein L22, bacterial type. This model decribes bacterial and chloroplast ribosomal protein L22.
Probab=21.18 E-value=1.1e+02 Score=20.82 Aligned_cols=22 Identities=23% Similarity=0.495 Sum_probs=18.0
Q ss_pred HHHHHHHhcCCCHHHHHhHcCC
Q 038532 121 CQLAADIVKGKTPEEIRRTFNI 142 (164)
Q Consensus 121 ~~~ia~~i~gks~eeir~~f~i 142 (164)
+..+|+.|+|+++++-..++..
T Consensus 13 ~~~va~~IrG~~v~~A~~~L~f 34 (103)
T TIGR01044 13 ARLVADLIRGKSVSQALDILRF 34 (103)
T ss_pred HHHHHHHHcCCcHHHHHHHHhh
Confidence 4568999999999998887763
No 103
>cd02138 Nitroreductase_2 Nitroreductase-like family 2. A subfamily of the nitroreductase family containing uncharacterized proteins that are similar to nitroreductase. Nitroreductase catalyzes the reduction of nitroaromatic compounds such as nitrotoluenes, nitrofurans and nitroimidazoles. This process requires NAD(P)H as electron donor in an obligatory two-electron transfer and uses FMN as cofactor. The enzyme is typically a homodimer. Members of this family are also called NADH dehydrogenase, oxygen-insensitive NAD(P)H nitrogenase or dihydropteridine reductase.
Probab=21.18 E-value=87 Score=22.99 Aligned_cols=38 Identities=24% Similarity=0.322 Sum_probs=28.6
Q ss_pred HHHHHHHhhhcCCChhHHHHHHHHHHHHhcCCCHHHHHhHcCCCCCCC
Q 038532 100 LHFGLLLAANYLEIPALLDRLCQLAADIVKGKTPEEIRRTFNIKKDFT 147 (164)
Q Consensus 100 ~l~~Ll~AA~~L~I~~L~~l~~~~ia~~i~gks~eeir~~f~i~~d~t 147 (164)
.+..++.||.-||+... ++.|...+++++.||++++..
T Consensus 107 a~~nl~Laa~~lGlgt~----------~~~~~~~~~l~~~l~l~~~~~ 144 (181)
T cd02138 107 AWGNLALQATAMGLAAH----------QMGGFDADKAREELNIPEDYE 144 (181)
T ss_pred HHHHHHHHHHHcCcccc----------eecCcCHHHHHHHhCCCCCce
Confidence 46688889988888742 233567789999999998644
No 104
>cd00068 GGL G protein gamma subunit-like motifs, the alpha-helical G-gamma chain dimerizes with the G-beta propeller subunit as part of the heterotrimeric G-protein complex; involved in signal transduction via G-protein-coupled receptors
Probab=20.69 E-value=1.1e+02 Score=18.39 Aligned_cols=23 Identities=22% Similarity=0.628 Sum_probs=17.2
Q ss_pred CcccceecHHHHHHHHHHhcccccCCCC
Q 038532 41 GEIPVQISSRNLAKIVEWCKCMQHRDRN 68 (164)
Q Consensus 41 ~~I~l~v~s~~L~~Ii~~~~~~~h~~~~ 68 (164)
..|++ |.....++.||+ .|....
T Consensus 18 ~Rikv---S~a~~~l~~y~e--~~~~~D 40 (57)
T cd00068 18 ERLKV---SKAAAELLKYCE--QNAEND 40 (57)
T ss_pred chhhH---HHHHHHHHHHHH--hcCCCC
Confidence 34555 888899999999 886543
No 105
>TIGR01669 phage_XkdX phage uncharacterized protein, XkdX family. This model represents a family of small (about 50 amino acid) phage proteins, found in at least 12 different phage and prophage regions of Gram-positive bacteria. In a number of these phage, the gene for this protein is found near the holin and endolysin genes.
Probab=20.48 E-value=1.5e+02 Score=17.05 Aligned_cols=24 Identities=21% Similarity=0.249 Sum_probs=16.4
Q ss_pred CCHHHHHhHcCCCCCCCHHHHHHHH
Q 038532 131 KTPEEIRRTFNIKKDFTPEEEKAVM 155 (164)
Q Consensus 131 ks~eeir~~f~i~~d~t~eee~~i~ 155 (164)
-|.++++.+-... =.|+||-++|-
T Consensus 18 ~t~e~v~~~V~~~-~IT~eey~eIT 41 (45)
T TIGR01669 18 YSNEDVNKFVEKK-LITREQYKVIT 41 (45)
T ss_pred CCHHHHHHHhhcC-ccCHHHHHHHh
Confidence 4788888765542 37888887763
No 106
>TIGR03553 F420_FbiB_CTERM F420 biosynthesis protein FbiB, C-terminal domain. Coenzyme F420 differs between the Archaea and the Actinobacteria, where the numbers of glutamate residues attached are 2 (Archaea) or 5-6 (Mycobacterium). The enzyme in the Archaea is homologous to the N-terminal domain of FbiB from Mycobacterium bovis, and is responsible for glutamate ligation. Therefore it seems likely that the C-terminal domain of FbiB, modeled by this alignment, is involved in additional glutamate ligation.
Probab=20.41 E-value=59 Score=24.06 Aligned_cols=38 Identities=13% Similarity=0.149 Sum_probs=25.8
Q ss_pred HHHHHHHhhhcCCChhHHHHHHHHHHHHhcC--CCHHHHHhHcCCCCCCC
Q 038532 100 LHFGLLLAANYLEIPALLDRLCQLAADIVKG--KTPEEIRRTFNIKKDFT 147 (164)
Q Consensus 100 ~l~~Ll~AA~~L~I~~L~~l~~~~ia~~i~g--ks~eeir~~f~i~~d~t 147 (164)
.+..++.||.-||+-...- .| ...+.+++.|||+.++.
T Consensus 126 a~qnl~LaA~~~Glgt~~~----------~~~~~~~~~v~~~l~lp~~~~ 165 (194)
T TIGR03553 126 AVQNLLVALAVEGLGSCWV----------GSTIFAADVVRAELDLPADWE 165 (194)
T ss_pred HHHHHHHHHHHcCCCeEEe----------cCcccCHHHHHHHhCcCCCce
Confidence 4556777777777654321 12 35688999999998754
No 107
>PF03918 CcmH: Cytochrome C biogenesis protein; InterPro: IPR005616 Members of this family include NrfF, CcmH, CycL, Ccl2.; PDB: 2KW0_A 2HL7_A.
Probab=20.40 E-value=84 Score=22.94 Aligned_cols=12 Identities=50% Similarity=0.706 Sum_probs=8.3
Q ss_pred cCCCHHHHHhHc
Q 038532 129 KGKTPEEIRRTF 140 (164)
Q Consensus 129 ~gks~eeir~~f 140 (164)
.|+|.+||+++|
T Consensus 72 ~G~s~~eI~~~~ 83 (148)
T PF03918_consen 72 EGKSDEEIIDYF 83 (148)
T ss_dssp HT--HHHHHHHH
T ss_pred cCCCHHHHHHHH
Confidence 599999998874
No 108
>PF10507 DUF2453: Protein of unknown function (DUF2453); InterPro: IPR019537 The function of these transmembrane protein is not known.
Probab=20.22 E-value=2.4e+02 Score=19.68 Aligned_cols=36 Identities=14% Similarity=0.222 Sum_probs=24.8
Q ss_pred HHHHHHHHHHHhcC-------CCHHHHHhHcCCCCC-CCHHHHH
Q 038532 117 LDRLCQLAADIVKG-------KTPEEIRRTFNIKKD-FTPEEEK 152 (164)
Q Consensus 117 ~~l~~~~ia~~i~g-------ks~eeir~~f~i~~d-~t~eee~ 152 (164)
.-++++.+.+.+.+ -.+|.+.+.+|++.. +|++|.+
T Consensus 36 StmAAAalGN~vSDv~Gi~~~~~vE~~~~rlg~~~P~Lt~~Q~~ 79 (111)
T PF10507_consen 36 STMAAAALGNLVSDVAGIGLGGYVERLAQRLGLKAPVLTPAQLN 79 (111)
T ss_pred HHHHHHHHhhhhhhhhhhHHHHHHHHHHHHhCCCCCCCCHHHHh
Confidence 33444555444443 469999999999975 9998766
No 109
>PF00382 TFIIB: Transcription factor TFIIB repeat; InterPro: IPR013150 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. In eukaryotes, transcription initiation of all protein encoding genes involves the polymerase II system. This sytem is modulated by both general and specific transcription factors. The general factors (which include TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIG and TFIIH) operate through common promoter elements, such as the TATA box. Transcription factor IIB (TFIIB) is of central importance in transcription of class II genes. It associates with TFIID-TFIIA bound to DNA (the DA complex) to form a ternary TFIID-IIA-IBB (DAB) complex, which is recognised by RNA polymerase II [, ]. TFIIB comprises ~315-340 residues and contains an imperfect C-terminal repeat of a 75-residue domain that may contribute to the symmetry of the folded protein. The basal archaeal transcription machinery resembles that of the eukaryotic polymerase II system and includes a homologue of TFIIB []. This entry represents a cyclin-like domain which is found repeated in the C-terminal region of a variety of eukaryotic TFIIB's and their archaeal counterparts. These domains individually form the typical cyclin fold, and in the transcription complex they straddle the C-terminal region of the TATA-binding protein - an interaction essential for the formation of the transcription initiation complex [, ].; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2PHG_A 1C9B_Q 1TFB_A 1VOL_A 3K7A_M 1AIS_B 1D3U_B.
Probab=20.12 E-value=2.2e+02 Score=17.33 Aligned_cols=29 Identities=21% Similarity=0.305 Sum_probs=23.0
Q ss_pred hHHHHHHHHHHHHhcC--CCHHHHHhHcCCC
Q 038532 115 ALLDRLCQLAADIVKG--KTPEEIRRTFNIK 143 (164)
Q Consensus 115 ~L~~l~~~~ia~~i~g--ks~eeir~~f~i~ 143 (164)
.-+-.+|-++|.+..| +|..||.+..|+.
T Consensus 37 ~~iaAA~iY~acr~~~~~~t~~eIa~~~~Vs 67 (71)
T PF00382_consen 37 ESIAAACIYLACRLNGVPRTLKEIAEAAGVS 67 (71)
T ss_dssp HHHHHHHHHHHHHHTTSSSSHHHHHHHCTSS
T ss_pred HHHHHHHHHHHHHHcCCCcCHHHHHHHhCCC
Confidence 3444558888999887 5899999999986
No 110
>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators. The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....
Probab=20.06 E-value=1.4e+02 Score=17.50 Aligned_cols=22 Identities=18% Similarity=0.348 Sum_probs=15.7
Q ss_pred HHHHHHhcCCCHHHHHhHcCCC
Q 038532 122 QLAADIVKGKTPEEIRRTFNIK 143 (164)
Q Consensus 122 ~~ia~~i~gks~eeir~~f~i~ 143 (164)
..+.-+..|+|+.||-..+||.
T Consensus 10 ~vl~~l~~G~~~~eIA~~l~is 31 (58)
T PF00196_consen 10 EVLRLLAQGMSNKEIAEELGIS 31 (58)
T ss_dssp HHHHHHHTTS-HHHHHHHHTSH
T ss_pred HHHHHHHhcCCcchhHHhcCcc
Confidence 4455566789998888888875
Done!