Query 030962
Match_columns 168
No_of_seqs 115 out of 764
Neff 8.0
Searched_HMMs 46136
Date Fri Mar 29 07:10:55 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030962.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030962hhsearch_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 1.9E-48 4.1E-53 289.7 16.4 156 4-168 4-162 (162)
2 COG5201 SKP1 SCF ubiquitin lig 100.0 4.9E-45 1.1E-49 257.3 14.6 154 6-168 3-157 (158)
3 PF01466 Skp1: Skp1 family, di 100.0 9.9E-31 2.1E-35 173.9 6.2 78 91-168 1-78 (78)
4 smart00512 Skp1 Found in Skp1 100.0 1.6E-28 3.6E-33 171.6 10.4 99 5-118 2-104 (104)
5 PF03931 Skp1_POZ: Skp1 family 99.8 1.5E-20 3.2E-25 119.6 5.0 60 6-65 2-62 (62)
6 KOG3473 RNA polymerase II tran 99.7 2E-17 4.3E-22 111.7 7.5 92 4-118 16-112 (112)
7 PF00651 BTB: BTB/POZ domain; 98.7 2.5E-07 5.4E-12 64.0 9.4 93 5-131 11-109 (111)
8 PHA02713 hypothetical protein; 98.6 2.6E-07 5.6E-12 81.6 9.8 101 6-142 27-132 (557)
9 PHA03098 kelch-like protein; P 98.5 1.1E-06 2.3E-11 76.9 10.3 96 7-137 12-109 (534)
10 PHA02790 Kelch-like protein; P 98.4 7.1E-07 1.5E-11 77.5 6.8 93 9-135 25-122 (480)
11 smart00225 BTB Broad-Complex, 98.4 1E-06 2.3E-11 57.5 5.4 82 11-126 5-90 (90)
12 KOG4441 Proteins containing BT 98.1 7.6E-06 1.7E-10 72.6 7.4 89 11-133 42-134 (571)
13 KOG4682 Uncharacterized conser 95.2 0.036 7.7E-07 47.1 4.8 104 11-151 75-185 (488)
14 KOG4350 Uncharacterized conser 94.9 0.25 5.4E-06 42.4 9.1 128 6-143 46-182 (620)
15 KOG3433 Protein involved in me 94.2 0.059 1.3E-06 41.0 3.5 39 109-152 160-200 (203)
16 COG5124 Protein predicted to b 93.7 0.061 1.3E-06 40.7 2.7 31 117-152 174-204 (209)
17 KOG2716 Polymerase delta-inter 93.0 1.5 3.3E-05 34.7 9.7 102 1-136 1-108 (230)
18 PF11822 DUF3342: Domain of un 89.7 0.64 1.4E-05 38.5 4.7 86 14-134 13-105 (317)
19 KOG0783 Uncharacterized conser 88.6 1.4 2.9E-05 41.2 6.3 105 7-141 713-823 (1267)
20 PF03962 Mnd1: Mnd1 family; I 83.1 1.3 2.8E-05 34.0 3.0 43 105-152 143-187 (188)
21 PF02214 BTB_2: BTB/POZ domain 78.1 2.5 5.5E-05 28.0 2.8 80 13-125 6-94 (94)
22 PF03656 Pam16: Pam16; InterP 75.2 1.2 2.6E-05 32.1 0.6 32 133-167 52-83 (127)
23 KOG3442 Uncharacterized conser 72.0 2.7 5.9E-05 30.1 1.7 32 134-168 54-85 (132)
24 KOG4350 Uncharacterized conser 56.3 6.8 0.00015 33.9 1.6 37 100-136 112-148 (620)
25 PF11978 MVP_shoulder: Shoulde 52.9 12 0.00025 26.6 2.1 41 110-150 37-90 (118)
26 PF12556 CobS_N: Cobaltochelat 50.3 9.7 0.00021 21.2 1.1 12 141-152 14-25 (36)
27 PRK05365 malonic semialdehyde 49.3 11 0.00025 28.4 1.7 34 108-151 130-163 (195)
28 KOG0511 Ankyrin repeat protein 47.7 37 0.0008 29.2 4.6 118 13-134 299-431 (516)
29 cd02148 Nitroreductase_5 Nitro 47.3 12 0.00026 28.0 1.6 33 109-151 124-156 (185)
30 KOG2075 Topoisomerase TOP1-int 46.8 86 0.0019 27.8 6.7 48 15-62 129-180 (521)
31 PRK13503 transcriptional activ 46.8 1.4E+02 0.003 23.3 8.0 80 49-150 169-251 (278)
32 PF10892 DUF2688: Protein of u 45.8 25 0.00055 21.6 2.5 24 138-161 30-55 (60)
33 smart00385 CYCLIN domain prese 44.7 70 0.0015 19.3 4.9 41 118-161 37-79 (83)
34 PF07928 Vps54: Vps54-like pro 41.4 8.8 0.00019 27.8 0.0 48 13-65 1-48 (135)
35 PHA03098 kelch-like protein; P 41.4 72 0.0016 27.9 5.7 47 101-147 105-160 (534)
36 cd00068 GGL G protein gamma su 40.5 35 0.00077 20.7 2.6 25 40-68 17-41 (57)
37 COG4957 Predicted transcriptio 39.6 27 0.00059 25.5 2.3 18 135-152 98-115 (148)
38 cd05029 S-100A6 S-100A6: S-100 39.6 60 0.0013 21.4 3.9 44 119-162 10-59 (88)
39 PRK14981 DNA-directed RNA poly 39.4 70 0.0015 22.3 4.3 44 117-161 61-105 (112)
40 PF11198 DUF2857: Protein of u 38.6 69 0.0015 24.3 4.5 60 100-159 57-131 (180)
41 smart00224 GGL G protein gamma 35.2 45 0.00098 20.7 2.5 25 40-68 17-41 (63)
42 PF05409 Peptidase_C30: Corona 34.9 44 0.00095 27.4 3.0 103 41-157 161-266 (293)
43 PF11460 DUF3007: Protein of u 33.8 41 0.00088 23.4 2.3 24 137-163 79-102 (104)
44 PF10075 PCI_Csn8: COP9 signal 33.7 90 0.0019 22.3 4.3 47 118-168 76-126 (143)
45 PRK11053 dihydropteridine redu 32.0 37 0.0008 26.0 2.2 35 107-151 148-183 (217)
46 KOG4591 Uncharacterized conser 31.8 1.1E+02 0.0024 24.2 4.6 31 101-131 134-164 (280)
47 PF15063 TC1: Thyroid cancer p 31.4 49 0.0011 21.6 2.3 42 107-157 31-72 (79)
48 cd00167 SANT 'SWI3, ADA2, N-Co 30.9 51 0.0011 17.6 2.2 19 127-145 23-41 (45)
49 PF00382 TFIIB: Transcription 30.9 1.2E+02 0.0027 18.7 4.1 29 120-148 37-67 (71)
50 PF13921 Myb_DNA-bind_6: Myb-l 29.8 88 0.0019 18.5 3.2 34 126-159 20-60 (60)
51 KOG1665 AFH1-interacting prote 29.3 28 0.0006 27.9 1.0 89 5-127 9-105 (302)
52 PF01592 NifU_N: NifU-like N t 29.2 74 0.0016 22.4 3.2 23 121-143 63-85 (126)
53 PF11197 DUF2835: Protein of u 28.9 63 0.0014 20.6 2.4 22 4-25 20-41 (68)
54 smart00717 SANT SANT SWI3, AD 28.9 59 0.0013 17.6 2.2 20 127-146 25-44 (49)
55 PF05443 ROS_MUCR: ROS/MUCR tr 28.7 27 0.00059 25.3 0.8 17 135-151 94-110 (132)
56 PF08671 SinI: Anti-repressor 28.5 35 0.00076 18.1 1.0 13 134-146 15-27 (30)
57 TIGR01999 iscU FeS cluster ass 28.5 88 0.0019 22.0 3.5 37 109-145 50-87 (124)
58 COG1710 Uncharacterized protei 28.5 41 0.0009 24.0 1.7 16 134-149 108-123 (139)
59 PF08154 NLE: NLE (NUC135) dom 28.4 94 0.002 19.2 3.2 29 6-34 3-39 (65)
60 PRK11325 scaffold protein; Pro 28.4 87 0.0019 22.2 3.4 37 109-145 52-89 (127)
61 TIGR03419 NifU_clost FeS clust 28.3 96 0.0021 21.7 3.6 37 109-145 46-83 (121)
62 PF07671 DUF1601: Protein of u 28.2 66 0.0014 18.0 2.2 30 115-144 7-36 (37)
63 COG1460 Uncharacterized protei 27.7 2E+02 0.0043 20.3 5.0 39 121-160 66-105 (114)
64 smart00875 BACK BTB And C-term 27.5 1.7E+02 0.0037 18.6 5.0 40 108-147 3-51 (101)
65 PF06514 PsbU: Photosystem II 27.2 35 0.00076 23.2 1.1 46 112-161 22-67 (93)
66 PRK09296 cysteine desufuration 26.1 1.3E+02 0.0028 21.8 4.0 33 121-153 77-117 (138)
67 PF13798 PCYCGC: Protein of un 26.1 1E+02 0.0022 23.1 3.4 20 125-144 121-140 (158)
68 PF13518 HTH_28: Helix-turn-he 25.8 1.1E+02 0.0024 17.2 3.0 20 129-148 6-25 (52)
69 TIGR02476 BluB cob(II)yrinic a 25.7 54 0.0012 24.9 2.1 38 105-152 133-170 (205)
70 PF00134 Cyclin_N: Cyclin, N-t 25.7 1E+02 0.0023 20.8 3.4 42 120-161 74-116 (127)
71 TIGR02698 CopY_TcrY copper tra 24.7 2.3E+02 0.0051 20.0 5.1 34 127-161 78-112 (130)
72 PF03750 DUF310: Protein of un 24.4 95 0.0021 21.8 3.0 34 116-150 8-43 (119)
73 PF08661 Rep_fac-A_3: Replicat 23.4 92 0.002 21.3 2.7 61 3-64 33-106 (109)
74 PF13384 HTH_23: Homeodomain-l 23.3 84 0.0018 17.8 2.2 15 134-148 16-30 (50)
75 PF05871 ESCRT-II: ESCRT-II co 22.9 56 0.0012 23.8 1.6 15 54-68 27-41 (139)
76 PF03883 DUF328: Protein of un 22.8 85 0.0018 24.8 2.7 26 126-151 31-56 (237)
77 TIGR03391 FeS_syn_CsdE cystein 22.6 1.6E+02 0.0034 21.4 3.9 32 122-153 83-122 (138)
78 PHA02713 hypothetical protein; 22.5 1.5E+02 0.0033 26.4 4.6 71 96-166 116-198 (557)
79 COG4049 Uncharacterized protei 22.5 78 0.0017 19.5 1.9 18 4-21 4-22 (65)
80 cd02144 iodotyrosine_dehalogen 22.5 71 0.0015 23.6 2.1 37 106-152 129-166 (193)
81 PF02736 Myosin_N: Myosin N-te 22.4 59 0.0013 18.3 1.3 18 4-21 23-40 (42)
82 PRK15019 CsdA-binding activato 22.4 1.6E+02 0.0034 21.7 3.8 32 122-153 88-127 (147)
83 PF11094 UL11: Membrane-associ 22.0 91 0.002 17.7 2.0 19 5-23 14-32 (39)
84 KOG0028 Ca2+-binding protein ( 22.0 2.2E+02 0.0047 21.5 4.5 49 112-163 82-135 (172)
85 PF09116 gp45-slide_C: gp45 sl 21.5 43 0.00093 23.6 0.7 22 100-121 5-26 (112)
86 KOG4244 Failed axon connection 21.3 1.1E+02 0.0023 25.0 3.0 22 138-159 111-132 (281)
87 PF11399 DUF3192: Protein of u 21.3 93 0.002 21.5 2.3 26 127-153 26-51 (102)
88 PF07707 BACK: BTB And C-termi 21.2 1E+02 0.0022 20.0 2.5 41 107-147 2-51 (103)
89 PF11338 DUF3140: Protein of u 20.8 75 0.0016 21.5 1.7 22 45-66 54-75 (92)
90 PF00196 GerE: Bacterial regul 20.7 1.5E+02 0.0032 17.4 3.0 23 126-148 9-31 (58)
91 PF09382 RQC: RQC domain; Int 20.7 1.5E+02 0.0033 19.6 3.4 39 123-161 19-64 (106)
92 PF10507 DUF2453: Protein of u 20.6 2.3E+02 0.0049 19.9 4.2 39 120-158 34-80 (111)
93 cd06664 IscU_like Iron-sulfur 20.2 1.7E+02 0.0036 20.2 3.6 38 108-145 46-84 (123)
94 PHA02790 Kelch-like protein; P 20.1 82 0.0018 27.4 2.3 40 97-136 114-155 (480)
No 1
>KOG1724 consensus SCF ubiquitin ligase, Skp1 component [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=1.9e-48 Score=289.70 Aligned_cols=156 Identities=63% Similarity=0.971 Sum_probs=139.5
Q ss_pred CCeEEEEcCCCCeEEecHHHHHHhHHHHHHHHhCC-CCC--CcccCCCCHHHHHHHHHHHHhccCCCCCCCCCCCCCCCC
Q 030962 4 PKMIVLKSCDGESFEVEEAVALESTTIKHMIEDDC-ADN--GIPLPNVTGKILAKVVEYCKKHVEVPTTQDSNTSGANSN 80 (168)
Q Consensus 4 ~~~i~l~S~DG~~~~v~~~~a~~S~~l~~~l~~~~-~~~--~Ipl~~i~s~~L~~Ii~wc~~h~~~~~~~~~~~~~~~~~ 80 (168)
.++|+|+|+||++|.|+.++|++|.+|++++.+.+ ... +||||+|+|.+|++||+||+||+++++...+.+
T Consensus 4 ~~~ikL~SsDG~~f~ve~~~a~~s~~i~~~~~~~~~~~~~~~IPl~nV~~~iL~kVIewC~~Hk~d~~~~~~~~------ 77 (162)
T KOG1724|consen 4 KKKIKLESSDGEIFEVEEEVARQSQTISAHMIEDGCADENDPIPLPNVTSKILKKVIEWCKKHKDDDPANPEDK------ 77 (162)
T ss_pred CCeEEEEccCCceeehhHHHHHHhHHHHHHHHHcCCCccCCccccCccCHHHHHHHHHHHHHcccccccccccc------
Confidence 47999999999999999999999999999988765 334 899999999999999999999998865221100
Q ss_pred CCCCCCCcccccccchhccccchHHHHHHHhhhcccCchhHHHHHHHHHHHHhcCCCHHHHHhhcCCCCCCCHHHHHHHH
Q 030962 81 GAATNGGEEDLKSWDTDFVKVDQATLFDLILAANYLNIKGLLDLTCQTVADMIKGKTPEEIRKTFNIKNDFTPEEEEEVR 160 (168)
Q Consensus 81 ~~~~~~~~~~~~~wd~eFl~~~~~~l~~Ll~AA~~L~I~~L~~~~~~~ia~~i~~ks~eeir~~f~i~~d~t~ee~~~i~ 160 (168)
..+....+++||++|++++..+||+|+.|||||+|++|+++||+.+|++++||||+|||..|||++|+|+||+++++
T Consensus 78 ---~~~~~~~i~~WD~~Flk~d~~tLfdli~AAnyLdi~gLl~~~ck~va~mikgktpeEir~~f~I~~d~t~eE~~~~~ 154 (162)
T KOG1724|consen 78 ---ELPEETDIPEWDAEFLKVDQGTLFDLILAANYLDIKGLLDLTCKTVANMIKGKTPEEIREIFNIENDETPEEEEAIR 154 (162)
T ss_pred ---cccccCCccHHHHHHHhcCHHHHHHHHHHhhhcccHHHHHHHHHHHHHHHccCCHHHHHHHcCCCCCCChhHHHHHh
Confidence 01234459999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhcccccC
Q 030962 161 RENQWAFE 168 (168)
Q Consensus 161 ~e~~w~~~ 168 (168)
+++.|+|+
T Consensus 155 ~e~~~~~~ 162 (162)
T KOG1724|consen 155 KENEWAFE 162 (162)
T ss_pred hccccccC
Confidence 99999986
No 2
>COG5201 SKP1 SCF ubiquitin ligase, SKP1 component [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=4.9e-45 Score=257.27 Aligned_cols=154 Identities=49% Similarity=0.791 Sum_probs=136.7
Q ss_pred eEEEEcCCCCeEEecHHHHHHhHHHHHHHHhCC-CCCCcccCCCCHHHHHHHHHHHHhccCCCCCCCCCCCCCCCCCCCC
Q 030962 6 MIVLKSCDGESFEVEEAVALESTTIKHMIEDDC-ADNGIPLPNVTGKILAKVVEYCKKHVEVPTTQDSNTSGANSNGAAT 84 (168)
Q Consensus 6 ~i~l~S~DG~~~~v~~~~a~~S~~l~~~l~~~~-~~~~Ipl~~i~s~~L~~Ii~wc~~h~~~~~~~~~~~~~~~~~~~~~ 84 (168)
.|.|.|.||++|.|+..+|..|-+|++++.+.+ .+-+||+|+|+|.+|.+|++||+||+.... +++ ++...
T Consensus 3 ~i~l~s~dge~F~vd~~iAerSiLikN~l~d~~~~n~p~p~pnVrSsvl~kv~ew~ehh~~s~s-ede-------~d~~~ 74 (158)
T COG5201 3 MIELESIDGEIFRVDENIAERSILIKNMLCDSTACNYPIPAPNVRSSVLMKVQEWMEHHTSSLS-EDE-------NDLEI 74 (158)
T ss_pred ceEEEecCCcEEEehHHHHHHHHHHHHHhccccccCCCCcccchhHHHHHHHHHHHHhccccCC-Ccc-------ChHhh
Confidence 699999999999999999999999999988765 467899999999999999999999987543 222 11110
Q ss_pred CCCcccccccchhccccchHHHHHHHhhhcccCchhHHHHHHHHHHHHhcCCCHHHHHhhcCCCCCCCHHHHHHHHHhcc
Q 030962 85 NGGEEDLKSWDTDFVKVDQATLFDLILAANYLNIKGLLDLTCQTVADMIKGKTPEEIRKTFNIKNDFTPEEEEEVRRENQ 164 (168)
Q Consensus 85 ~~~~~~~~~wd~eFl~~~~~~l~~Ll~AA~~L~I~~L~~~~~~~ia~~i~~ks~eeir~~f~i~~d~t~ee~~~i~~e~~ 164 (168)
......+.||+.|+.+|+++|++++.|||||+|++|+++||+.||.+|+||||+|||++|||++||||||+++|++|++
T Consensus 75 -rks~p~D~wdr~Fm~vDqemL~eI~laaNYL~ikpLLd~gCKivaemirgkSpeeir~tfni~ndfTpEEe~~irkEnE 153 (158)
T COG5201 75 -RKSKPSDFWDRFFMEVDQEMLLEICLAANYLEIKPLLDLGCKIVAEMIRGKSPEEIRETFNIENDFTPEEERRIRKENE 153 (158)
T ss_pred -hccCCccHHHHHHHHhhHHHHHHHHHhhccccchHHHHHHHHHHHHHHccCCHHHHHHHhCCCCCCCHHHHHHHHHhcc
Confidence 1234567899999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccC
Q 030962 165 WAFE 168 (168)
Q Consensus 165 w~~~ 168 (168)
|+.+
T Consensus 154 Waed 157 (158)
T COG5201 154 WAED 157 (158)
T ss_pred cccc
Confidence 9864
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=9.9e-31 Score=173.86 Aligned_cols=78 Identities=68% Similarity=1.193 Sum_probs=68.5
Q ss_pred ccccchhccccchHHHHHHHhhhcccCchhHHHHHHHHHHHHhcCCCHHHHHhhcCCCCCCCHHHHHHHHHhcccccC
Q 030962 91 LKSWDTDFVKVDQATLFDLILAANYLNIKGLLDLTCQTVADMIKGKTPEEIRKTFNIKNDFTPEEEEEVRRENQWAFE 168 (168)
Q Consensus 91 ~~~wd~eFl~~~~~~l~~Ll~AA~~L~I~~L~~~~~~~ia~~i~~ks~eeir~~f~i~~d~t~ee~~~i~~e~~w~~~ 168 (168)
+++||++|++++.+.|++|+.||+||+|++|+++||++||.+++|||++|||++|||++|+|+||++++++||+|+||
T Consensus 1 l~~wD~~F~~~~~~~L~~l~~AA~yL~I~~L~~~~~~~iA~~i~gks~eeir~~fgi~~d~t~eee~~i~~e~~w~~~ 78 (78)
T PF01466_consen 1 LPEWDQEFLDVDNDELFDLLNAANYLDIKGLLDLCCKYIANMIKGKSPEEIRKYFGIENDLTPEEEEEIRKENEWAFE 78 (78)
T ss_dssp HHHHHHHHT-S-HHHHHHHHHHHHHHT-HHHHHHHHHHHHHHHTTS-HHHHHHHHT---TSSHHHHHHHHHHCCCTB-
T ss_pred CCHHHHHHHHcCHHHHHHHHHHHHHHcchHHHHHHHHHHHHHhcCCCHHHHHHHcCCCCCCCHHHHHHHHHHcchhcC
Confidence 468999999999999999999999999999999999999999999999999999999999999999999999999997
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=99.96 E-value=1.6e-28 Score=171.59 Aligned_cols=99 Identities=61% Similarity=0.957 Sum_probs=87.7
Q ss_pred CeEEEEcCCCCeEEecHHHHHHhHHHHHHHHhCCCC----CCcccCCCCHHHHHHHHHHHHhccCCCCCCCCCCCCCCCC
Q 030962 5 KMIVLKSCDGESFEVEEAVALESTTIKHMIEDDCAD----NGIPLPNVTGKILAKVVEYCKKHVEVPTTQDSNTSGANSN 80 (168)
Q Consensus 5 ~~i~l~S~DG~~~~v~~~~a~~S~~l~~~l~~~~~~----~~Ipl~~i~s~~L~~Ii~wc~~h~~~~~~~~~~~~~~~~~ 80 (168)
++++|+|+||++|.|++++|++|++|++++++.+.. .+||+|+|+|.+|++|++||+||+.++.+...
T Consensus 2 ~~v~L~S~Dg~~f~v~~~~a~~S~~i~~~l~~~~~~~~~~~~Ipl~~v~~~~L~~Vi~yc~~h~~~~~~~~~-------- 73 (104)
T smart00512 2 KYIKLISSDGEVFEVEREVARQSKTIKAMIEDLGVDDENNNPIPLPNVTSKILSKVIEYCEHHVDDPPSVAD-------- 73 (104)
T ss_pred CeEEEEeCCCCEEEecHHHHHHHHHHHHHHHccCcccCCCCCccCCCcCHHHHHHHHHHHHHcccCCCCccc--------
Confidence 589999999999999999999999999999976532 48999999999999999999999987652211
Q ss_pred CCCCCCCcccccccchhccccchHHHHHHHhhhcccCc
Q 030962 81 GAATNGGEEDLKSWDTDFVKVDQATLFDLILAANYLNI 118 (168)
Q Consensus 81 ~~~~~~~~~~~~~wd~eFl~~~~~~l~~Ll~AA~~L~I 118 (168)
...+++||.+|++++.+.|++|+.||+||+|
T Consensus 74 -------~~~~~~wD~~F~~~d~~~l~dLl~AAnyL~I 104 (104)
T smart00512 74 -------KDDIPTWDAEFLKIDQETLFELILAANYLDI 104 (104)
T ss_pred -------cccccHHHHHHHcCCHHHHHHHHHHHHhhCC
Confidence 1457999999999999999999999999997
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=99.82 E-value=1.5e-20 Score=119.60 Aligned_cols=60 Identities=47% Similarity=0.777 Sum_probs=54.6
Q ss_pred eEEEEcCCCCeEEecHHHHHHhHHHHHHHHhCCCCC-CcccCCCCHHHHHHHHHHHHhccC
Q 030962 6 MIVLKSCDGESFEVEEAVALESTTIKHMIEDDCADN-GIPLPNVTGKILAKVVEYCKKHVE 65 (168)
Q Consensus 6 ~i~l~S~DG~~~~v~~~~a~~S~~l~~~l~~~~~~~-~Ipl~~i~s~~L~~Ii~wc~~h~~ 65 (168)
+++|+|+||+.|.|++++|++|++|++|+++.+... +||||+|+|++|++|++||+||++
T Consensus 2 ~v~L~SsDg~~f~V~~~~a~~S~~i~~ml~~~~~~~~~Ipl~~v~~~~L~kViewc~~H~~ 62 (62)
T PF03931_consen 2 YVKLVSSDGQEFEVSREAAKQSKTIKNMLEDLGDEDEPIPLPNVSSRILKKVIEWCEHHKN 62 (62)
T ss_dssp EEEEEETTSEEEEEEHHHHTTSHHHHHHHHCTCCCGTEEEETTS-HHHHHHHHHHHHHHHH
T ss_pred EEEEEcCCCCEEEeeHHHHHHhHHHHHHHhhhcccccccccCccCHHHHHHHHHHHHhcCC
Confidence 689999999999999999999999999999877544 599999999999999999999973
No 6
>KOG3473 consensus RNA polymerase II transcription elongation factor Elongin/SIII, subunit elongin C [Transcription]
Probab=99.72 E-value=2e-17 Score=111.72 Aligned_cols=92 Identities=25% Similarity=0.429 Sum_probs=78.7
Q ss_pred CCeEEEEcCCCCeEEecHHHHHHhHHHHHHHHhCC-----CCCCcccCCCCHHHHHHHHHHHHhccCCCCCCCCCCCCCC
Q 030962 4 PKMIVLKSCDGESFEVEEAVALESTTIKHMIEDDC-----ADNGIPLPNVTGKILAKVVEYCKKHVEVPTTQDSNTSGAN 78 (168)
Q Consensus 4 ~~~i~l~S~DG~~~~v~~~~a~~S~~l~~~l~~~~-----~~~~Ipl~~i~s~~L~~Ii~wc~~h~~~~~~~~~~~~~~~ 78 (168)
+.+++|+|+||++|.|.+.+|..|+|||.|+.+.+ ..+.+.+++|+|.+|++|++|+.+...+..
T Consensus 16 ~~yVkLvS~Ddhefiikre~AmtSgTiraml~gpg~~se~~~n~v~f~di~shiLeKvc~Yl~Yk~rY~~---------- 85 (112)
T KOG3473|consen 16 SMYVKLVSSDDHEFIIKREHAMTSGTIRAMLSGPGVFSEAEKNEVYFRDIPSHILEKVCEYLAYKVRYTN---------- 85 (112)
T ss_pred hhheEeecCCCcEEEEeehhhhhhhHHHHHHcCCccccccccceEEeccchHHHHHHHHHHhhheeeecc----------
Confidence 47999999999999999999999999999998654 256789999999999999999998766544
Q ss_pred CCCCCCCCCcccccccchhccccchHHHHHHHhhhcccCc
Q 030962 79 SNGAATNGGEEDLKSWDTDFVKVDQATLFDLILAANYLNI 118 (168)
Q Consensus 79 ~~~~~~~~~~~~~~~wd~eFl~~~~~~l~~Ll~AA~~L~I 118 (168)
....+|+| .+.++..++|+.||+||++
T Consensus 86 --------~s~eiPeF-----~IppemaleLL~aAn~Lec 112 (112)
T KOG3473|consen 86 --------SSTEIPEF-----DIPPEMALELLMAANYLEC 112 (112)
T ss_pred --------ccccCCCC-----CCCHHHHHHHHHHhhhhcC
Confidence 11345665 6899999999999999974
No 7
>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=98.68 E-value=2.5e-07 Score=63.95 Aligned_cols=93 Identities=18% Similarity=0.332 Sum_probs=74.4
Q ss_pred CeEEEEcCCCCeEEecHHHH-HHhHHHHHHHHhCC-CC---CCcccCCCCHHHHHHHHHHHHhccCCCCCCCCCCCCCCC
Q 030962 5 KMIVLKSCDGESFEVEEAVA-LESTTIKHMIEDDC-AD---NGIPLPNVTGKILAKVVEYCKKHVEVPTTQDSNTSGANS 79 (168)
Q Consensus 5 ~~i~l~S~DG~~~~v~~~~a-~~S~~l~~~l~~~~-~~---~~Ipl~~i~s~~L~~Ii~wc~~h~~~~~~~~~~~~~~~~ 79 (168)
.-++|+..||+.|.|++.++ ..|+++++++...+ .. ..|++++++...++.+++||+...
T Consensus 11 ~D~~i~v~d~~~~~vhk~iL~~~S~~F~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~l~~~Y~~~--------------- 75 (111)
T PF00651_consen 11 SDVTIRVGDGKTFYVHKNILAARSPYFRNLFEGSKFKESTVPEISLPDVSPEAFEAFLEYMYTGE--------------- 75 (111)
T ss_dssp --EEEEETTTEEEEE-HHHHHHHBHHHHHHHTTTTSTTSSEEEEEETTSCHHHHHHHHHHHHHSE---------------
T ss_pred CCEEEEECCCEEEeechhhhhccchhhhhcccccccccccccccccccccccccccccccccCCc---------------
Confidence 35788889999999999985 68999999999762 22 247889999999999999996321
Q ss_pred CCCCCCCCcccccccchhcccc-chHHHHHHHhhhcccCchhHHHHHHHHHHH
Q 030962 80 NGAATNGGEEDLKSWDTDFVKV-DQATLFDLILAANYLNIKGLLDLTCQTVAD 131 (168)
Q Consensus 80 ~~~~~~~~~~~~~~wd~eFl~~-~~~~l~~Ll~AA~~L~I~~L~~~~~~~ia~ 131 (168)
+.+ +.+.+.+++.+|++|+++.|.+.|+..+..
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 012 266789999999999999999999998864
No 8
>PHA02713 hypothetical protein; Provisional
Probab=98.61 E-value=2.6e-07 Score=81.64 Aligned_cols=101 Identities=15% Similarity=0.231 Sum_probs=81.8
Q ss_pred eEEEEcCCCCeEEecHHHH-HHhHHHHHHHHhCC----CCCCcccCCCCHHHHHHHHHHHHhccCCCCCCCCCCCCCCCC
Q 030962 6 MIVLKSCDGESFEVEEAVA-LESTTIKHMIEDDC----ADNGIPLPNVTGKILAKVVEYCKKHVEVPTTQDSNTSGANSN 80 (168)
Q Consensus 6 ~i~l~S~DG~~~~v~~~~a-~~S~~l~~~l~~~~----~~~~Ipl~~i~s~~L~~Ii~wc~~h~~~~~~~~~~~~~~~~~ 80 (168)
-++|...+|+.|.+++.++ ..|.+++.|+...- ....|.|.+++..+|+.|++|++...
T Consensus 27 DV~L~v~~~~~f~~Hr~vLaa~S~YF~amF~~~~~e~~~~~~v~l~~v~~~~~~~ll~y~Yt~~---------------- 90 (557)
T PHA02713 27 DVIITIGDGEEIKAHKTILAAGSKYFRTLFTTPMIIRDLVTRVNLQMFDKDAVKNIVQYLYNRH---------------- 90 (557)
T ss_pred CEEEEeCCCCEEeehHHHHhhcCHHHHHHhcCCchhhccCceEEeccCCHHHHHHHHHHhcCCC----------------
Confidence 3677777799999999985 58999999997532 13468899999999999999998521
Q ss_pred CCCCCCCcccccccchhccccchHHHHHHHhhhcccCchhHHHHHHHHHHHHhcCCCHHHHH
Q 030962 81 GAATNGGEEDLKSWDTDFVKVDQATLFDLILAANYLNIKGLLDLTCQTVADMIKGKTPEEIR 142 (168)
Q Consensus 81 ~~~~~~~~~~~~~wd~eFl~~~~~~l~~Ll~AA~~L~I~~L~~~~~~~ia~~i~~ks~eeir 142 (168)
++.+++.+|+.||++|+|+.|.+.||.++...+.-.+-=+|.
T Consensus 91 --------------------i~~~nv~~ll~aA~~lqi~~l~~~C~~~l~~~l~~~NCl~i~ 132 (557)
T PHA02713 91 --------------------ISSMNVIDVLKCADYLLIDDLVTDCESYIKDYTNHDTCIYMY 132 (557)
T ss_pred --------------------CCHHHHHHHHHHHHHHCHHHHHHHHHHHHHhhCCccchHHHH
Confidence 245679999999999999999999999998877655544443
No 9
>PHA03098 kelch-like protein; Provisional
Probab=98.48 E-value=1.1e-06 Score=76.89 Aligned_cols=96 Identities=20% Similarity=0.295 Sum_probs=77.4
Q ss_pred EEEE-cCCCCeEEecHHHH-HHhHHHHHHHHhCCCCCCcccCCCCHHHHHHHHHHHHhccCCCCCCCCCCCCCCCCCCCC
Q 030962 7 IVLK-SCDGESFEVEEAVA-LESTTIKHMIEDDCADNGIPLPNVTGKILAKVVEYCKKHVEVPTTQDSNTSGANSNGAAT 84 (168)
Q Consensus 7 i~l~-S~DG~~~~v~~~~a-~~S~~l~~~l~~~~~~~~Ipl~~i~s~~L~~Ii~wc~~h~~~~~~~~~~~~~~~~~~~~~ 84 (168)
++|. +.+|+.|.+++.++ ..|.+++.|+.+......|.|+. +..+|+.|++|++..+
T Consensus 12 v~l~~~~~~~~~~~Hk~vLaa~S~yF~~mf~~~~~~~~i~l~~-~~~~~~~~l~y~Ytg~-------------------- 70 (534)
T PHA03098 12 ESIIIVNGGGIIKVHKIILSSSSEYFKKMFKNNFKENEINLNI-DYDSFNEVIKYIYTGK-------------------- 70 (534)
T ss_pred EEEEEEcCCEEEEeHHHHHHhhhHHHHHHHhCCCCCceEEecC-CHHHHHHHHHHhcCCc--------------------
Confidence 3444 46899999999985 57999999998643356788888 9999999999998532
Q ss_pred CCCcccccccchhccccchHHHHHHHhhhcccCchhHHHHHHHHHHHHhcCCC
Q 030962 85 NGGEEDLKSWDTDFVKVDQATLFDLILAANYLNIKGLLDLTCQTVADMIKGKT 137 (168)
Q Consensus 85 ~~~~~~~~~wd~eFl~~~~~~l~~Ll~AA~~L~I~~L~~~~~~~ia~~i~~ks 137 (168)
+.++.+++.+|+.||++|+++.|.+.|+.++...+.-.+
T Consensus 71 --------------~~i~~~~~~~ll~~A~~l~~~~l~~~C~~~l~~~l~~~n 109 (534)
T PHA03098 71 --------------INITSNNVKDILSIANYLIIDFLINLCINYIIKIIDDNN 109 (534)
T ss_pred --------------eEEcHHHHHHHHHHHHHhCcHHHHHHHHHHHHHhCCHhH
Confidence 235677799999999999999999999999887765444
No 10
>PHA02790 Kelch-like protein; Provisional
Probab=98.39 E-value=7.1e-07 Score=77.46 Aligned_cols=93 Identities=11% Similarity=0.141 Sum_probs=71.9
Q ss_pred EEcCCCCeEEecHHH-HHHhHHHHHHHHhCCC--CCCccc--CCCCHHHHHHHHHHHHhccCCCCCCCCCCCCCCCCCCC
Q 030962 9 LKSCDGESFEVEEAV-ALESTTIKHMIEDDCA--DNGIPL--PNVTGKILAKVVEYCKKHVEVPTTQDSNTSGANSNGAA 83 (168)
Q Consensus 9 l~S~DG~~~~v~~~~-a~~S~~l~~~l~~~~~--~~~Ipl--~~i~s~~L~~Ii~wc~~h~~~~~~~~~~~~~~~~~~~~ 83 (168)
+..--|+.|.+++.+ |..|++++.|+...-. ...+.+ .+++..+|+.|++|++.-+
T Consensus 25 ~~~~~~~~~~~HR~VLAa~S~YFraMF~~~~~Es~~~v~~~~~~v~~~~l~~lldy~YTg~------------------- 85 (480)
T PHA02790 25 IIEAIGGNIIVNSTILKKLSPYFRTHLRQKYTKNKDPVTRVCLDLDIHSLTSIVIYSYTGK------------------- 85 (480)
T ss_pred EEEEcCcEEeeehhhhhhcCHHHHHHhcCCccccccceEEEecCcCHHHHHHHHHhheeee-------------------
Confidence 334568899999998 6789999999975321 223433 3899999999999996321
Q ss_pred CCCCcccccccchhccccchHHHHHHHhhhcccCchhHHHHHHHHHHHHhcC
Q 030962 84 TNGGEEDLKSWDTDFVKVDQATLFDLILAANYLNIKGLLDLTCQTVADMIKG 135 (168)
Q Consensus 84 ~~~~~~~~~~wd~eFl~~~~~~l~~Ll~AA~~L~I~~L~~~~~~~ia~~i~~ 135 (168)
+.++.+++.+|+.||++|+|+.+++.||.++...+.-
T Consensus 86 ---------------l~it~~nV~~ll~aA~~Lqi~~v~~~C~~fL~~~l~~ 122 (480)
T PHA02790 86 ---------------VYIDSHNVVNLLRASILTSVEFIIYTCINFILRDFRK 122 (480)
T ss_pred ---------------EEEecccHHHHHHHHHHhChHHHHHHHHHHHHhhCCc
Confidence 3467778999999999999999999999997665543
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=98.35 E-value=1e-06 Score=57.53 Aligned_cols=82 Identities=23% Similarity=0.347 Sum_probs=66.1
Q ss_pred cCCCCeEEecHHHHH-HhHHHHHHHHhCC---CCCCcccCCCCHHHHHHHHHHHHhccCCCCCCCCCCCCCCCCCCCCCC
Q 030962 11 SCDGESFEVEEAVAL-ESTTIKHMIEDDC---ADNGIPLPNVTGKILAKVVEYCKKHVEVPTTQDSNTSGANSNGAATNG 86 (168)
Q Consensus 11 S~DG~~~~v~~~~a~-~S~~l~~~l~~~~---~~~~Ipl~~i~s~~L~~Ii~wc~~h~~~~~~~~~~~~~~~~~~~~~~~ 86 (168)
..+|+.|.+++.++. .|.+++.++.... ....+++++++..+++.+++|++... .
T Consensus 5 ~v~~~~~~~h~~iL~~~s~~f~~~~~~~~~~~~~~~i~l~~~~~~~f~~~l~~ly~~~---~------------------ 63 (90)
T smart00225 5 VVGGKKFKAHKAVLAACSPYFKALFSGDFKESKKSEIYLDDVSPEDFRALLEFLYTGK---L------------------ 63 (90)
T ss_pred EECCEEEehHHHHHhhcCHHHHHHHcCCCccCCCCEEEecCCCHHHHHHHHHeecCce---e------------------
Confidence 457799999998864 6899999998643 35578899999999999999998532 1
Q ss_pred CcccccccchhccccchHHHHHHHhhhcccCchhHHHHHH
Q 030962 87 GEEDLKSWDTDFVKVDQATLFDLILAANYLNIKGLLDLTC 126 (168)
Q Consensus 87 ~~~~~~~wd~eFl~~~~~~l~~Ll~AA~~L~I~~L~~~~~ 126 (168)
.++...+.+++.+|.+++++.|.+.|+
T Consensus 64 -------------~~~~~~~~~l~~~a~~~~~~~l~~~c~ 90 (90)
T smart00225 64 -------------DLPEENVEELLELADYLQIPGLVELCE 90 (90)
T ss_pred -------------ecCHHHHHHHHHHHHHHCcHHHHhhhC
Confidence 123347899999999999999998874
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=98.12 E-value=7.6e-06 Score=72.60 Aligned_cols=89 Identities=19% Similarity=0.323 Sum_probs=74.6
Q ss_pred cCCCCeEEecHHH-HHHhHHHHHHHHhCC---CCCCcccCCCCHHHHHHHHHHHHhccCCCCCCCCCCCCCCCCCCCCCC
Q 030962 11 SCDGESFEVEEAV-ALESTTIKHMIEDDC---ADNGIPLPNVTGKILAKVVEYCKKHVEVPTTQDSNTSGANSNGAATNG 86 (168)
Q Consensus 11 S~DG~~~~v~~~~-a~~S~~l~~~l~~~~---~~~~Ipl~~i~s~~L~~Ii~wc~~h~~~~~~~~~~~~~~~~~~~~~~~ 86 (168)
.-+|+.|..++.+ |..|.+++.|+...- ....|.+.+++..+|+.+++|++...
T Consensus 42 ~v~~~~~~aHR~VLAa~S~YFraMFt~~l~e~~~~~i~l~~v~~~~l~~ll~y~Yt~~---------------------- 99 (571)
T KOG4441|consen 42 LVGDREFPAHRVVLAACSPYFRAMFTSGLKESKQKEINLEGVDPETLELLLDYAYTGK---------------------- 99 (571)
T ss_pred EECCeeechHHHHHHhccHHHHHHhcCCcccccceEEEEecCCHHHHHHHHHHhhcce----------------------
Confidence 3455999999998 568999999998532 35678899999999999999998543
Q ss_pred CcccccccchhccccchHHHHHHHhhhcccCchhHHHHHHHHHHHHh
Q 030962 87 GEEDLKSWDTDFVKVDQATLFDLILAANYLNIKGLLDLTCQTVADMI 133 (168)
Q Consensus 87 ~~~~~~~wd~eFl~~~~~~l~~Ll~AA~~L~I~~L~~~~~~~ia~~i 133 (168)
+.++.+++-+|+.||++|+|+.++++||.++...+
T Consensus 100 ------------i~i~~~nVq~ll~aA~~lQi~~v~~~C~~fL~~~l 134 (571)
T KOG4441|consen 100 ------------LEISEDNVQELLEAASLLQIPEVVDACCEFLESQL 134 (571)
T ss_pred ------------EEechHhHHHHHHHHHHhhhHHHHHHHHHHHHhcC
Confidence 24688899999999999999999999999986543
No 13
>KOG4682 consensus Uncharacterized conserved protein, contains BTB/POZ domain [General function prediction only]
Probab=95.18 E-value=0.036 Score=47.13 Aligned_cols=104 Identities=16% Similarity=0.248 Sum_probs=78.4
Q ss_pred cCCCCeEEecHHHHHHhHHHHHHHHhCCC-------CCCcccCCCCHHHHHHHHHHHHhccCCCCCCCCCCCCCCCCCCC
Q 030962 11 SCDGESFEVEEAVALESTTIKHMIEDDCA-------DNGIPLPNVTGKILAKVVEYCKKHVEVPTTQDSNTSGANSNGAA 83 (168)
Q Consensus 11 S~DG~~~~v~~~~a~~S~~l~~~l~~~~~-------~~~Ipl~~i~s~~L~~Ii~wc~~h~~~~~~~~~~~~~~~~~~~~ 83 (168)
..=|.++.+++--+.||+++..|+.+.-. .-.||=|+|+...|..++-=+++- .
T Consensus 75 ~alg~eWrlHk~yL~QS~yf~smf~Gtw~es~~~iIqleI~Dp~Id~~al~~a~gsLY~d---E---------------- 135 (488)
T KOG4682|consen 75 EALGFEWRLHKPYLFQSEYFKSMFSGTWKESSMNIIQLEIPDPNIDVVALQVAFGSLYRD---E---------------- 135 (488)
T ss_pred hhccceeeeeeeeeeccHHHHHHhccccChhhCceEEEEcCCCcccHHHHHHHHhhhhhh---h----------------
Confidence 34588899999889999999999886421 123555789999999988766541 1
Q ss_pred CCCCcccccccchhccccchHHHHHHHhhhcccCchhHHHHHHHHHHHHhcCCCHHHHHhhcCCCCCC
Q 030962 84 TNGGEEDLKSWDTDFVKVDQATLFDLILAANYLNIKGLLDLTCQTVADMIKGKTPEEIRKTFNIKNDF 151 (168)
Q Consensus 84 ~~~~~~~~~~wd~eFl~~~~~~l~~Ll~AA~~L~I~~L~~~~~~~ia~~i~~ks~eeir~~f~i~~d~ 151 (168)
+.++.+.+..++.||.+|...+|++-|...+...++-+| +.+++....-+
T Consensus 136 ---------------veI~l~dv~gvlAaA~~lqldgl~qrC~evMie~lspkt---a~~yYea~ckY 185 (488)
T KOG4682|consen 136 ---------------VEIKLSDVVGVLAAACLLQLDGLIQRCGEVMIETLSPKT---ACGYYEAACKY 185 (488)
T ss_pred ---------------eeccHHHHHHHHHHHHHHHHhhHHHHHHHHHHHhcChhh---hhHhhhhhhhh
Confidence 257889999999999999999999999998877665555 45555544333
No 14
>KOG4350 consensus Uncharacterized conserved protein, contains BTB/POZ domain [General function prediction only]
Probab=94.90 E-value=0.25 Score=42.37 Aligned_cols=128 Identities=10% Similarity=0.154 Sum_probs=83.1
Q ss_pred eEEEEcCCCCeEEecHHH-HHHhHHHHHHHHhCC---CCCCcccCCCCHHHHHHHHHHHHhccCCCCCCCCCCCCCCCCC
Q 030962 6 MIVLKSCDGESFEVEEAV-ALESTTIKHMIEDDC---ADNGIPLPNVTGKILAKVVEYCKKHVEVPTTQDSNTSGANSNG 81 (168)
Q Consensus 6 ~i~l~S~DG~~~~v~~~~-a~~S~~l~~~l~~~~---~~~~Ipl~~i~s~~L~~Ii~wc~~h~~~~~~~~~~~~~~~~~~ 81 (168)
-++|+-.| +.|..++-+ |..|.++|.||=+.- ....|||..-++..++.+++|++.-+-+-...++ +..-....
T Consensus 46 DVtfvve~-~rfpAHRvILAaRs~yFRAlLYgGm~Es~q~~ipLq~t~~eAF~~lLrYiYtg~~~l~~~~e-d~lld~Ls 123 (620)
T KOG4350|consen 46 DVTFVVED-TRFPAHRVILAARSSYFRALLYGGMQESHQQLIPLQETNSEAFRALLRYIYTGKIDLAGVEE-DILLDYLS 123 (620)
T ss_pred ceEEEEec-cccchhhhhHHHHHHHHHHHHhhhhhhhhhcccccccccHHHHHHHHHHHhhcceecccchH-HHHHHHHH
Confidence 35666656 888888876 568999999986542 2567999888899999999999876644321111 00000000
Q ss_pred CCCCCCcccccccc---hhccc--cchHHHHHHHhhhcccCchhHHHHHHHHHHHHhcCCCHHHHHh
Q 030962 82 AATNGGEEDLKSWD---TDFVK--VDQATLFDLILAANYLNIKGLLDLTCQTVADMIKGKTPEEIRK 143 (168)
Q Consensus 82 ~~~~~~~~~~~~wd---~eFl~--~~~~~l~~Ll~AA~~L~I~~L~~~~~~~ia~~i~~ks~eeir~ 143 (168)
. ...-.+++.+ .+++. +..+++|-+++||.+.+.+.|.++||.++ ++.+.|+-.
T Consensus 124 l---Ah~Ygf~~Le~aiSeYl~~iL~~~NvCmifdaA~ly~l~~Lt~~C~mfm-----DrnA~~lL~ 182 (620)
T KOG4350|consen 124 L---AHRYGFIQLETAISEYLKEILKNENVCMIFDAAYLYQLTDLTDYCMMFM-----DRNADQLLE 182 (620)
T ss_pred H---HHhcCcHHHHHHHHHHHHHHHcccceeeeeeHHHHhcchHHHHHHHHHH-----hcCHHhhhc
Confidence 0 0011111111 13333 56788899999999999999999999876 666776644
No 15
>KOG3433 consensus Protein involved in meiotic recombination/predicted coiled-coil protein [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=94.19 E-value=0.059 Score=40.99 Aligned_cols=39 Identities=41% Similarity=0.569 Sum_probs=31.3
Q ss_pred HHhhhccc--CchhHHHHHHHHHHHHhcCCCHHHHHhhcCCCCCCC
Q 030962 109 LILAANYL--NIKGLLDLTCQTVADMIKGKTPEEIRKTFNIKNDFT 152 (168)
Q Consensus 109 Ll~AA~~L--~I~~L~~~~~~~ia~~i~~ks~eeir~~f~i~~d~t 152 (168)
...|||.- +|--|.++||+.. |.-+.+||+.||||+||.
T Consensus 160 ~~eaanrwtDnI~il~dy~~rkf-----~~e~nqi~~~fgIPed~d 200 (203)
T KOG3433|consen 160 MAEAANRWTDNIFILIDYLYRKF-----GLEPNQIRKEFGIPEDFD 200 (203)
T ss_pred HHHHHhhhhhhHHHHHHHHHHhc-----CCCHHHHhHhcCCCcccc
Confidence 34455543 7888899998876 899999999999999973
No 16
>COG5124 Protein predicted to be involved in meiotic recombination [Cell division and chromosome partitioning / General function prediction only]
Probab=93.69 E-value=0.061 Score=40.73 Aligned_cols=31 Identities=42% Similarity=0.686 Sum_probs=26.1
Q ss_pred CchhHHHHHHHHHHHHhcCCCHHHHHhhcCCCCCCC
Q 030962 117 NIKGLLDLTCQTVADMIKGKTPEEIRKTFNIKNDFT 152 (168)
Q Consensus 117 ~I~~L~~~~~~~ia~~i~~ks~eeir~~f~i~~d~t 152 (168)
+|.-|.++.|+.. +..++|||+.||||.||.
T Consensus 174 nI~ilidy~c~kf-----~~~~~qir~~fgIPedld 204 (209)
T COG5124 174 NIEILIDYLCKKF-----FLKPEQIRKEFGIPEDLD 204 (209)
T ss_pred hHHHHHHHHHHHc-----CCCHHHHHHhcCCCcchh
Confidence 6777888777765 789999999999999873
No 17
>KOG2716 consensus Polymerase delta-interacting protein PDIP1 and related proteins, contain BTB/POZ domain [Inorganic ion transport and metabolism]
Probab=93.00 E-value=1.5 Score=34.71 Aligned_cols=102 Identities=20% Similarity=0.339 Sum_probs=74.5
Q ss_pred CCCCCeEEEEcCCCCeEEecHHH-HHHhHHHHHHHHhCC-----CCCCcccCCCCHHHHHHHHHHHHhccCCCCCCCCCC
Q 030962 1 MSSPKMIVLKSCDGESFEVEEAV-ALESTTIKHMIEDDC-----ADNGIPLPNVTGKILAKVVEYCKKHVEVPTTQDSNT 74 (168)
Q Consensus 1 m~~~~~i~l~S~DG~~~~v~~~~-a~~S~~l~~~l~~~~-----~~~~Ipl~~i~s~~L~~Ii~wc~~h~~~~~~~~~~~ 74 (168)
|.+++.++|- --|..|.-++.- .++.+.++.|++..- ..+.|=+ +=+..=+..|+.||+--...
T Consensus 1 ~~~~~~vkLn-vGG~~F~Tsk~TLtk~dg~fk~m~e~~i~~~~d~s~~IFI-DRSpKHF~~ILNfmRdGdv~-------- 70 (230)
T KOG2716|consen 1 LSMSETVKLN-VGGTIFKTSKSTLTKFDGFFKTMLETDIPVEKDESGCIFI-DRSPKHFDTILNFMRDGDVD-------- 70 (230)
T ss_pred CCccceEEEe-cCCeEEEeehhhhhhhhhHHHHHhhcCCccccCCcCcEEe-cCChhHHHHHHHhhhccccc--------
Confidence 3455667753 347788887765 568999999998642 1223433 66788899999999832111
Q ss_pred CCCCCCCCCCCCCcccccccchhccccchHHHHHHHhhhcccCchhHHHHHHHHHHHHhcCC
Q 030962 75 SGANSNGAATNGGEEDLKSWDTDFVKVDQATLFDLILAANYLNIKGLLDLTCQTVADMIKGK 136 (168)
Q Consensus 75 ~~~~~~~~~~~~~~~~~~~wd~eFl~~~~~~l~~Ll~AA~~L~I~~L~~~~~~~ia~~i~~k 136 (168)
+|+ +...+-+|+.-|.|..+.+|+++|...++..+++.
T Consensus 71 ----------------LPe--------~~kel~El~~EA~fYlL~~Lv~~C~~~i~~~~~~~ 108 (230)
T KOG2716|consen 71 ----------------LPE--------SEKELKELLREAEFYLLDGLVELCQSAIARLIRGY 108 (230)
T ss_pred ----------------Ccc--------chHHHHHHHHHHHHhhHHHHHHHHHHHhhhcccCc
Confidence 111 46778999999999999999999999999987774
No 18
>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=89.74 E-value=0.64 Score=38.49 Aligned_cols=86 Identities=14% Similarity=0.264 Sum_probs=59.0
Q ss_pred CCeEEecHHHH-HHhHHHHHHHHh---C-CCCCCcccCCC--CHHHHHHHHHHHHhccCCCCCCCCCCCCCCCCCCCCCC
Q 030962 14 GESFEVEEAVA-LESTTIKHMIED---D-CADNGIPLPNV--TGKILAKVVEYCKKHVEVPTTQDSNTSGANSNGAATNG 86 (168)
Q Consensus 14 G~~~~v~~~~a-~~S~~l~~~l~~---~-~~~~~Ipl~~i--~s~~L~~Ii~wc~~h~~~~~~~~~~~~~~~~~~~~~~~ 86 (168)
.+.|..+++.+ ...+++++.+.. . ...++|+| .| +-.|++=+++|++. .. |
T Consensus 13 ~rdF~C~~~lL~~~M~YF~~~l~~~~~~~~~~~~idi-sVhCDv~iF~WLm~yv~~----~~------------p----- 70 (317)
T PF11822_consen 13 KRDFTCPRDLLVSEMRYFAEYLSRYINDSQRWEEIDI-SVHCDVHIFEWLMRYVKG----EP------------P----- 70 (317)
T ss_pred ceeeeccHHHHHHhhHHHHHHHhhcccccCcCCCcce-EEecChhHHHHHHHHhhc----CC------------C-----
Confidence 45789999885 679999999853 2 22345555 33 33445555555554 21 0
Q ss_pred CcccccccchhccccchHHHHHHHhhhcccCchhHHHHHHHHHHHHhc
Q 030962 87 GEEDLKSWDTDFVKVDQATLFDLILAANYLNIKGLLDLTCQTVADMIK 134 (168)
Q Consensus 87 ~~~~~~~wd~eFl~~~~~~l~~Ll~AA~~L~I~~L~~~~~~~ia~~i~ 134 (168)
.++++++..++--|+||+|++|++.|-.++...+.
T Consensus 71 -------------~l~~~NvvsIliSS~FL~M~~Lve~cl~y~~~~~~ 105 (317)
T PF11822_consen 71 -------------SLTPSNVVSILISSEFLQMESLVEECLQYCHDHMS 105 (317)
T ss_pred -------------cCCcCcEEEeEehhhhhccHHHHHHHHHHHHHhHH
Confidence 24667788899999999999999999888755543
No 19
>KOG0783 consensus Uncharacterized conserved protein, contains ankyrin and BTB/POZ domains [Function unknown]
Probab=88.59 E-value=1.4 Score=41.23 Aligned_cols=105 Identities=17% Similarity=0.205 Sum_probs=71.4
Q ss_pred EEEEcCCCCeEEecHHHH-HHhHHHHHHHHhCC-C--CCCcccCCCCHHHHHHHHHHHHhccCCCCCCCCCCCCCCCCCC
Q 030962 7 IVLKSCDGESFEVEEAVA-LESTTIKHMIEDDC-A--DNGIPLPNVTGKILAKVVEYCKKHVEVPTTQDSNTSGANSNGA 82 (168)
Q Consensus 7 i~l~S~DG~~~~v~~~~a-~~S~~l~~~l~~~~-~--~~~Ipl~~i~s~~L~~Ii~wc~~h~~~~~~~~~~~~~~~~~~~ 82 (168)
..++.+||+++..++.++ ..+.++..|+...- . .-.+.+-.++++.|+.|++|++-- +..
T Consensus 713 ~~i~~KDGkvl~aHkc~L~aRlEYF~smf~~~w~E~sS~t~~~~p~~~e~m~ivLdylYs~--d~~-------------- 776 (1267)
T KOG0783|consen 713 TVIKLKDGKVLKAHKCFLSARLEYFSSMFQFVWMESSSITVNLSPLTVEHMSIVLDYLYSD--DKV-------------- 776 (1267)
T ss_pred EEEEecCCcCcccceeEeeeHHHHHHHHHHHHHhhhccceeecCcchHHHHHHHHHHHHcc--chH--------------
Confidence 456677999999999874 45888888876432 1 111222235699999999998731 111
Q ss_pred CCCCCcccccccchhccc--cchHHHHHHHhhhcccCchhHHHHHHHHHHHHhcCCCHHHH
Q 030962 83 ATNGGEEDLKSWDTDFVK--VDQATLFDLILAANYLNIKGLLDLTCQTVADMIKGKTPEEI 141 (168)
Q Consensus 83 ~~~~~~~~~~~wd~eFl~--~~~~~l~~Ll~AA~~L~I~~L~~~~~~~ia~~i~~ks~eei 141 (168)
+|++ .+.+-+|+++-.|+-|=|..|.+.|-+.+-+++.=|+.-++
T Consensus 777 --------------~~~k~~~~~dF~~~il~iaDqlli~~Lk~Ice~~ll~kl~lk~~~~l 823 (1267)
T KOG0783|consen 777 --------------ELFKDLKESDFMFEILSIADQLLILELKSICEQSLLRKLNLKTLPTL 823 (1267)
T ss_pred --------------HHHhccchhhhhHHHHHHHHHHHHHHHHHHHHHHHHhHhcccchHHH
Confidence 1122 23455888999999999999999888888887776665443
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=83.14 E-value=1.3 Score=33.96 Aligned_cols=43 Identities=35% Similarity=0.337 Sum_probs=31.6
Q ss_pred HHHHHHhhhccc--CchhHHHHHHHHHHHHhcCCCHHHHHhhcCCCCCCC
Q 030962 105 TLFDLILAANYL--NIKGLLDLTCQTVADMIKGKTPEEIRKTFNIKNDFT 152 (168)
Q Consensus 105 ~l~~Ll~AA~~L--~I~~L~~~~~~~ia~~i~~ks~eeir~~f~i~~d~t 152 (168)
.+..+..||+.. ||..|..+|+.. -|.+.++|++.||||+||.
T Consensus 143 ~~~~~~~~anrwTDNI~~l~~~~~~k-----~~~~~~~i~k~f~Ip~d~d 187 (188)
T PF03962_consen 143 EIKIAKEAANRWTDNIFSLKSYLKKK-----FGMDEEDIRKEFGIPEDFD 187 (188)
T ss_pred HHHHHHHHHHHHHhhHHHHHHHHHHh-----cCCCHHHHHHHcCCccccC
Confidence 334445566654 666777777664 3899999999999999973
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=78.14 E-value=2.5 Score=28.05 Aligned_cols=80 Identities=13% Similarity=0.237 Sum_probs=51.7
Q ss_pred CCCeEEecHHHHH-H-hHHHHHHHHhC--C----CCCCcccCCCCHHHHHHHHHHHHhccCCCCCCCCCCCCCCCCCCCC
Q 030962 13 DGESFEVEEAVAL-E-STTIKHMIEDD--C----ADNGIPLPNVTGKILAKVVEYCKKHVEVPTTQDSNTSGANSNGAAT 84 (168)
Q Consensus 13 DG~~~~v~~~~a~-~-S~~l~~~l~~~--~----~~~~Ipl~~i~s~~L~~Ii~wc~~h~~~~~~~~~~~~~~~~~~~~~ 84 (168)
-|+.|.+++..+. . ...+..++... . ....+=+ +=++...+.|+.|++.. ... .
T Consensus 6 GG~~f~~~~~tL~~~~~s~l~~~~~~~~~~~~~~~~~~~fi-DRdp~~F~~IL~ylr~~--~~l-~-------------- 67 (94)
T PF02214_consen 6 GGTIFETSRSTLTRYPDSLLARLFSGERSDDYDDDDGEYFI-DRDPELFEYILNYLRTG--GKL-P-------------- 67 (94)
T ss_dssp TTEEEEEEHHHHHTSTTSTTTSHHHTGHGGGEETTTTEEEE-SS-HHHHHHHHHHHHHT--SSB----------------
T ss_pred CCEEEEEcHHHHhhCCCChhhhHHhhccccccCCccceEEe-ccChhhhhHHHHHHhhc--Ccc-C--------------
Confidence 4889999998765 2 34566666632 1 2344434 78999999999999984 111 0
Q ss_pred CCCcccccccchhccccchHHHHHHHhhhcccCchhH-HHHH
Q 030962 85 NGGEEDLKSWDTDFVKVDQATLFDLILAANYLNIKGL-LDLT 125 (168)
Q Consensus 85 ~~~~~~~~~wd~eFl~~~~~~l~~Ll~AA~~L~I~~L-~~~~ 125 (168)
.-+...+..+...|.|.+|+.| ++.|
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 0023346788999999999999 6654
No 22
>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=75.21 E-value=1.2 Score=32.11 Aligned_cols=32 Identities=31% Similarity=0.586 Sum_probs=17.4
Q ss_pred hcCCCHHHHHhhcCCCCCCCHHHHHHHHHhccccc
Q 030962 133 IKGKTPEEIRKTFNIKNDFTPEEEEEVRRENQWAF 167 (168)
Q Consensus 133 i~~ks~eeir~~f~i~~d~t~ee~~~i~~e~~w~~ 167 (168)
..|+|.+|-++++|++...++|+ |.+.|.-+|
T Consensus 52 ~~~Mtl~EA~~ILnv~~~~~~ee---I~k~y~~Lf 83 (127)
T PF03656_consen 52 SKGMTLDEARQILNVKEELSREE---IQKRYKHLF 83 (127)
T ss_dssp -----HHHHHHHHT--G--SHHH---HHHHHHHHH
T ss_pred cCCCCHHHHHHHcCCCCccCHHH---HHHHHHHHH
Confidence 45899999999999998777644 666665554
No 23
>KOG3442 consensus Uncharacterized conserved protein [Function unknown]
Probab=71.98 E-value=2.7 Score=30.05 Aligned_cols=32 Identities=25% Similarity=0.412 Sum_probs=24.9
Q ss_pred cCCCHHHHHhhcCCCCCCCHHHHHHHHHhcccccC
Q 030962 134 KGKTPEEIRKTFNIKNDFTPEEEEEVRRENQWAFE 168 (168)
Q Consensus 134 ~~ks~eeir~~f~i~~d~t~ee~~~i~~e~~w~~~ 168 (168)
.++|.+|-++++||.++++. ++|.+.|.-+|+
T Consensus 54 ~~iTlqEa~qILnV~~~ln~---eei~k~yehLFe 85 (132)
T KOG3442|consen 54 GKITLQEAQQILNVKEPLNR---EEIEKRYEHLFE 85 (132)
T ss_pred ccccHHHHhhHhCCCCCCCH---HHHHHHHHHHHh
Confidence 35789999999999987766 456677777764
No 24
>KOG4350 consensus Uncharacterized conserved protein, contains BTB/POZ domain [General function prediction only]
Probab=56.27 E-value=6.8 Score=33.90 Aligned_cols=37 Identities=16% Similarity=0.268 Sum_probs=32.1
Q ss_pred ccchHHHHHHHhhhcccCchhHHHHHHHHHHHHhcCC
Q 030962 100 KVDQATLFDLILAANYLNIKGLLDLTCQTVADMIKGK 136 (168)
Q Consensus 100 ~~~~~~l~~Ll~AA~~L~I~~L~~~~~~~ia~~i~~k 136 (168)
.++.+.+++.+.-|+..+...|...++.++-..++-.
T Consensus 112 ~~~ed~lld~LslAh~Ygf~~Le~aiSeYl~~iL~~~ 148 (620)
T KOG4350|consen 112 GVEEDILLDYLSLAHRYGFIQLETAISEYLKEILKNE 148 (620)
T ss_pred cchHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHccc
Confidence 4688999999999999999999999998887766643
No 25
>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=52.90 E-value=12 Score=26.60 Aligned_cols=41 Identities=24% Similarity=0.476 Sum_probs=30.6
Q ss_pred HhhhcccCchhHHHHHHHHHHHHhcCC----C--------HHHHHh-hcCCCCC
Q 030962 110 ILAANYLNIKGLLDLTCQTVADMIKGK----T--------PEEIRK-TFNIKND 150 (168)
Q Consensus 110 l~AA~~L~I~~L~~~~~~~ia~~i~~k----s--------~eeir~-~f~i~~d 150 (168)
-.|+..+.++..+..+|+.||..++|. + ..-||. .||....
T Consensus 37 ~~~~k~F~VpDFVGd~Ck~iaSRIR~aVa~~~Fd~FHknSa~iiR~aVFg~~~~ 90 (118)
T PF11978_consen 37 EDAAKLFSVPDFVGDACKAIASRIRGAVASVTFDDFHKNSARIIRQAVFGFDEN 90 (118)
T ss_dssp HHHHHTTSSTTHHHHHHHHHHHHHHHHHHTSHHHHHHHHHHHHHHHHHSTS---
T ss_pred hHHHHhcCCcchHHHHHHHHHHHHHHHHhcCcHHHHcccHHHHHHHHhcCCCCC
Confidence 478999999999999999999999973 2 344444 7887643
No 26
>PF12556 CobS_N: Cobaltochelatase CobS subunit N terminal
Probab=50.35 E-value=9.7 Score=21.22 Aligned_cols=12 Identities=33% Similarity=0.783 Sum_probs=10.1
Q ss_pred HHhhcCCCCCCC
Q 030962 141 IRKTFNIKNDFT 152 (168)
Q Consensus 141 ir~~f~i~~d~t 152 (168)
+|+.|||..|++
T Consensus 14 vre~FGiDsDm~ 25 (36)
T PF12556_consen 14 VREVFGIDSDMK 25 (36)
T ss_pred HHHhcCCCcCCe
Confidence 588999999864
No 27
>PRK05365 malonic semialdehyde reductase; Provisional
Probab=49.27 E-value=11 Score=28.42 Aligned_cols=34 Identities=24% Similarity=0.321 Sum_probs=26.5
Q ss_pred HHHhhhcccCchhHHHHHHHHHHHHhcCCCHHHHHhhcCCCCCC
Q 030962 108 DLILAANYLNIKGLLDLTCQTVADMIKGKTPEEIRKTFNIKNDF 151 (168)
Q Consensus 108 ~Ll~AA~~L~I~~L~~~~~~~ia~~i~~ks~eeir~~f~i~~d~ 151 (168)
.|+.||.-+++.. .++.|...+.+++.|||++++
T Consensus 130 ~l~LaA~~~Glgs----------~~~~g~~~~~v~~~l~ip~~~ 163 (195)
T PRK05365 130 YLILAARALGLDA----------GPMSGFDAAAVDAEFFAGTTW 163 (195)
T ss_pred HHHHHHHHcCCcc----------CCccccCHHHHHHHhCCCCCe
Confidence 3888888888876 234567889999999999764
No 28
>KOG0511 consensus Ankyrin repeat protein [General function prediction only]
Probab=47.75 E-value=37 Score=29.25 Aligned_cols=118 Identities=12% Similarity=0.135 Sum_probs=74.3
Q ss_pred CCCeEEecHHHHHHhHHHHHHHHhCC----CCCCc---ccCCCCHHHHHHHHHHHHhccCCCCCCCC-------CCC-CC
Q 030962 13 DGESFEVEEAVALESTTIKHMIEDDC----ADNGI---PLPNVTGKILAKVVEYCKKHVEVPTTQDS-------NTS-GA 77 (168)
Q Consensus 13 DG~~~~v~~~~a~~S~~l~~~l~~~~----~~~~I---pl~~i~s~~L~~Ii~wc~~h~~~~~~~~~-------~~~-~~ 77 (168)
....+.++.+++..+.++..|+-+.. .+..+ .+|+..+.+.+.+++|+..|+++-+.... .+. .+
T Consensus 299 ~~~RyP~hla~i~R~eyfk~mf~g~f~e~s~n~~~p~lslp~~~~~vveI~lr~lY~d~tdi~~~~A~dvll~ad~lal~ 378 (516)
T KOG0511|consen 299 EEDRYPAHLARILRVEYFKSMFVGDFIESSVNDTRPGLSLPSLADVVVEIDLRNLYCDQTDIIFDVASDVLLFADKLALA 378 (516)
T ss_pred ccccccHHHHHHHHHHHHHHHhccchhhhcCCccccccccchHHHHHHHHHHHHhhcccccchHHHHhhHHHHhhHhhhh
Confidence 33457788888888888888776432 13333 47889999999999999999987652111 000 00
Q ss_pred CCCCCCCCCCcccccccchhccccchHHHHHHHhhhcccCchhHHHHHHHHHHHHhc
Q 030962 78 NSNGAATNGGEEDLKSWDTDFVKVDQATLFDLILAANYLNIKGLLDLTCQTVADMIK 134 (168)
Q Consensus 78 ~~~~~~~~~~~~~~~~wd~eFl~~~~~~l~~Ll~AA~~L~I~~L~~~~~~~ia~~i~ 134 (168)
. ..+..-.....+..| .+| ++.-.+++++.-|=-+...+|=.++..++|.++.
T Consensus 379 ~-dr~Lkt~as~~itq~-~e~--id~y~V~dIl~~~wd~~~~rlEqfa~~~~a~hl~ 431 (516)
T KOG0511|consen 379 D-DRLLKTAASAEITQW-LEL--IDMYGVLDILEYCWDLVACRLEQFAETHEARHLL 431 (516)
T ss_pred h-hhhhhhhhhHHHHHH-HHH--HHhhhHHHHHHHHHHhhhHHHHHHHHHHHHHHHH
Confidence 0 000000122334555 222 3455688888888888888888888888887664
No 29
>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=47.34 E-value=12 Score=28.01 Aligned_cols=33 Identities=21% Similarity=0.352 Sum_probs=25.8
Q ss_pred HHhhhcccCchhHHHHHHHHHHHHhcCCCHHHHHhhcCCCCCC
Q 030962 109 LILAANYLNIKGLLDLTCQTVADMIKGKTPEEIRKTFNIKNDF 151 (168)
Q Consensus 109 Ll~AA~~L~I~~L~~~~~~~ia~~i~~ks~eeir~~f~i~~d~ 151 (168)
|+.||.-|++.. .++.|...+++++.||+++++
T Consensus 124 l~LaA~~lGlgs----------~~~~g~d~~~~~~~L~lp~~~ 156 (185)
T cd02148 124 FILAARALGLDA----------GPMSGFDAAAVDAEFFADTRW 156 (185)
T ss_pred HHHHHHHcCCCc----------CCCcccCHHHHHHHhCCCCCe
Confidence 788888888765 244567889999999999765
No 30
>KOG2075 consensus Topoisomerase TOP1-interacting protein BTBD1 [Function unknown]
Probab=46.82 E-value=86 Score=27.76 Aligned_cols=48 Identities=17% Similarity=0.181 Sum_probs=35.7
Q ss_pred CeEEecHHH-HHHhHHHHHHHHhCC--C-CCCcccCCCCHHHHHHHHHHHHh
Q 030962 15 ESFEVEEAV-ALESTTIKHMIEDDC--A-DNGIPLPNVTGKILAKVVEYCKK 62 (168)
Q Consensus 15 ~~~~v~~~~-a~~S~~l~~~l~~~~--~-~~~Ipl~~i~s~~L~~Ii~wc~~ 62 (168)
|.+..++-+ +.-|.++..|+-..- . ..+|-+|++.-+.....++|++-
T Consensus 129 q~~paHk~vla~gS~VFdaMf~g~~a~~~s~ei~lpdvepaaFl~~L~flYs 180 (521)
T KOG2075|consen 129 QRIPAHKLVLADGSDVFDAMFYGGLAEDASLEIRLPDVEPAAFLAFLRFLYS 180 (521)
T ss_pred cccchhhhhhhcchHHHHHHhccCcccccCceeecCCcChhHhHHHHHHHhc
Confidence 456667766 456888888876532 2 45788999999999999988874
No 31
>PRK13503 transcriptional activator RhaS; Provisional
Probab=46.80 E-value=1.4e+02 Score=23.35 Aligned_cols=80 Identities=11% Similarity=0.155 Sum_probs=48.4
Q ss_pred CHHHHHHHHHHHHhccCCCCCCCCCCCCCCCCCCCCCCCcccccccchhccccchHHHHHHHhhhcccCchhHHHHHHHH
Q 030962 49 TGKILAKVVEYCKKHVEVPTTQDSNTSGANSNGAATNGGEEDLKSWDTDFVKVDQATLFDLILAANYLNIKGLLDLTCQT 128 (168)
Q Consensus 49 ~s~~L~~Ii~wc~~h~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~wd~eFl~~~~~~l~~Ll~AA~~L~I~~L~~~~~~~ 128 (168)
....++++++|++.|...+. .++++- +-+.++...+..++....-.-...++...=-.
T Consensus 169 ~~~~i~~~~~~I~~~~~~~~---------------------tl~~lA-~~~~lS~~~l~r~Fk~~~G~S~~~yi~~~Rl~ 226 (278)
T PRK13503 169 SDARLNQLLAWLEDHFAEEV---------------------NWEALA-DQFSLSLRTLHRQLKQQTGLTPQRYLNRLRLL 226 (278)
T ss_pred cHHHHHHHHHHHHHhhcCCC---------------------CHHHHH-HHHCCCHHHHHHHHHHHhCcCHHHHHHHHHHH
Confidence 34557777777777654332 234442 22467888888888877655555555444322
Q ss_pred HH-HHhc--CCCHHHHHhhcCCCCC
Q 030962 129 VA-DMIK--GKTPEEIRKTFNIKND 150 (168)
Q Consensus 129 ia-~~i~--~ks~eeir~~f~i~~d 150 (168)
-| .++. +.|..||...+|..+-
T Consensus 227 ~A~~LL~~~~~sI~eIA~~~GF~~~ 251 (278)
T PRK13503 227 KARHLLRHSDASVTDIAYRCGFGDS 251 (278)
T ss_pred HHHHHHHcCCCCHHHHHHHhCCCCH
Confidence 22 3332 5788999888888754
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=45.78 E-value=25 Score=21.59 Aligned_cols=24 Identities=33% Similarity=0.648 Sum_probs=18.5
Q ss_pred HHHHHhhcC-CCCC-CCHHHHHHHHH
Q 030962 138 PEEIRKTFN-IKND-FTPEEEEEVRR 161 (168)
Q Consensus 138 ~eeir~~f~-i~~d-~t~ee~~~i~~ 161 (168)
.+++|..|| |=.+ +||||..+|.+
T Consensus 30 ad~lr~klG~IC~~CitpEE~~~I~e 55 (60)
T PF10892_consen 30 ADDLRVKLGGICGDCITPEEDREILE 55 (60)
T ss_pred hHHHHHHHcchhhccCCHHHHHHHHH
Confidence 578888887 4455 89999888765
No 33
>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=44.66 E-value=70 Score=19.33 Aligned_cols=41 Identities=17% Similarity=0.127 Sum_probs=27.5
Q ss_pred chhHHHHHHHHHHHHhcCC--CHHHHHhhcCCCCCCCHHHHHHHHH
Q 030962 118 IKGLLDLTCQTVADMIKGK--TPEEIRKTFNIKNDFTPEEEEEVRR 161 (168)
Q Consensus 118 I~~L~~~~~~~ia~~i~~k--s~eeir~~f~i~~d~t~ee~~~i~~ 161 (168)
=+.++-.+|-++|.++.+. +..++..+.|. +|.++..+..+
T Consensus 37 ~~~~ia~a~l~lA~k~~~~~~~~~~~~~~~~~---~~~~~i~~~~~ 79 (83)
T smart00385 37 SPSLIAAAALYLAAKTEEIPPWTKELVHYTGY---FTEEEILRMEK 79 (83)
T ss_pred CHHHHHHHHHHHHHHHhcCCCCchhHhHhhCC---CCHHHHHHHHH
Confidence 3456677888889888874 45777777766 56666555443
No 34
>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=41.42 E-value=8.8 Score=27.82 Aligned_cols=48 Identities=21% Similarity=0.294 Sum_probs=0.0
Q ss_pred CCCeEEecHHHHHHhHHHHHHHHhCCCCCCcccCCCCHHHHHHHHHHHHhccC
Q 030962 13 DGESFEVEEAVALESTTIKHMIEDDCADNGIPLPNVTGKILAKVVEYCKKHVE 65 (168)
Q Consensus 13 DG~~~~v~~~~a~~S~~l~~~l~~~~~~~~Ipl~~i~s~~L~~Ii~wc~~h~~ 65 (168)
||+.|.|+..++..-+.+.+.+.-. ..+|.+..+++.++++++..++.
T Consensus 1 d~e~f~vv~s~l~ll~~l~~Y~~~~-----~~~P~~a~di~~~l~elLk~fNS 48 (135)
T PF07928_consen 1 DNEKFVVVGSALLLLKMLSDYLQLA-----SNFPSLAPDILSRLLELLKLFNS 48 (135)
T ss_dssp -----------------------------------------------------
T ss_pred CCCceecHHHHHHHHHHHHHHHHHH-----HHCchhHHHHHHHHHHHHHHHHH
Confidence 7888888888887777777765421 23566888888888888877653
No 35
>PHA03098 kelch-like protein; Provisional
Probab=41.41 E-value=72 Score=27.89 Aligned_cols=47 Identities=15% Similarity=0.190 Sum_probs=39.3
Q ss_pred cchHHHHHHHhhhcccCchhHHHHHHHHHHHHhc---------CCCHHHHHhhcCC
Q 030962 101 VDQATLFDLILAANYLNIKGLLDLTCQTVADMIK---------GKTPEEIRKTFNI 147 (168)
Q Consensus 101 ~~~~~l~~Ll~AA~~L~I~~L~~~~~~~ia~~i~---------~ks~eeir~~f~i 147 (168)
++.++.++++..|...+...|.+.|-.+|+..+. ..+.+++..++.=
T Consensus 105 l~~~nc~~~~~~a~~~~~~~L~~~~~~~i~~nf~~v~~~~~f~~l~~~~l~~ll~~ 160 (534)
T PHA03098 105 IDDNNCIDIYRFSFFYGCKKLYSAAYNYIRNNIELIYNDPDFIYLSKNELIKILSD 160 (534)
T ss_pred CCHhHHHHHHHHHHHcCcHHHHHHHHHHHHHHHHHHhcCchhhcCCHHHHHHHhcC
Confidence 7889999999999999999999999999886653 3467888887653
No 36
>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=40.53 E-value=35 Score=20.73 Aligned_cols=25 Identities=20% Similarity=0.503 Sum_probs=19.2
Q ss_pred CCCcccCCCCHHHHHHHHHHHHhccCCCC
Q 030962 40 DNGIPLPNVTGKILAKVVEYCKKHVEVPT 68 (168)
Q Consensus 40 ~~~Ipl~~i~s~~L~~Ii~wc~~h~~~~~ 68 (168)
...|++ |.....++.||+.|..+++
T Consensus 17 ~~Rikv----S~a~~~l~~y~e~~~~~Dp 41 (57)
T cd00068 17 RERLKV----SKAAAELLKYCEQNAENDP 41 (57)
T ss_pred CchhhH----HHHHHHHHHHHHhcCCCCC
Confidence 345665 8899999999999966554
No 37
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=39.59 E-value=27 Score=25.46 Aligned_cols=18 Identities=33% Similarity=0.737 Sum_probs=16.7
Q ss_pred CCCHHHHHhhcCCCCCCC
Q 030962 135 GKTPEEIRKTFNIKNDFT 152 (168)
Q Consensus 135 ~ks~eeir~~f~i~~d~t 152 (168)
|+||+|-|..+|++.|+.
T Consensus 98 gmTPd~YR~KW~LP~dYP 115 (148)
T COG4957 98 GLTPDEYRAKWGLPPDYP 115 (148)
T ss_pred CCCHHHHHHhcCCCCCCC
Confidence 899999999999999964
No 38
>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=39.58 E-value=60 Score=21.40 Aligned_cols=44 Identities=11% Similarity=0.129 Sum_probs=25.7
Q ss_pred hhHHHHHHHHHHHHh-cC-CCHHHHHhhcC----CCCCCCHHHHHHHHHh
Q 030962 119 KGLLDLTCQTVADMI-KG-KTPEEIRKTFN----IKNDFTPEEEEEVRRE 162 (168)
Q Consensus 119 ~~L~~~~~~~ia~~i-~~-ks~eeir~~f~----i~~d~t~ee~~~i~~e 162 (168)
..|+....++-+.-- .| -+.+|+|+.+. +...+|++|.+++.++
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 345555555554211 22 37788888773 4445777777776654
No 39
>PRK14981 DNA-directed RNA polymerase subunit F; Provisional
Probab=39.40 E-value=70 Score=22.27 Aligned_cols=44 Identities=25% Similarity=0.454 Sum_probs=30.8
Q ss_pred CchhHHHHHHHHHHHHhcCCCHHHHHhhcCCCC-CCCHHHHHHHHH
Q 030962 117 NIKGLLDLTCQTVADMIKGKTPEEIRKTFNIKN-DFTPEEEEEVRR 161 (168)
Q Consensus 117 ~I~~L~~~~~~~ia~~i~~ks~eeir~~f~i~~-d~t~ee~~~i~~ 161 (168)
++..|-......|++. .=.|++|+|.+|.-.. -+++|+.++|-.
T Consensus 61 ~~~~l~e~~a~~I~nL-~P~~~dElrai~~~~~~~~~~e~l~~ILd 105 (112)
T PRK14981 61 ELEKMKEKTAVKIADI-LPETRDELRAIFAKERYTLSPEELDEILD 105 (112)
T ss_pred HccCCCHHHHHHHHhc-CCCCHHHHHHHHHHhccCCCHHHHHHHHH
Confidence 3444556666666663 5679999999887653 388998888755
No 40
>PF11198 DUF2857: Protein of unknown function (DUF2857); InterPro: IPR021364 This is a bacterial family of uncharacterised proteins.
Probab=38.61 E-value=69 Score=24.26 Aligned_cols=60 Identities=22% Similarity=0.334 Sum_probs=39.8
Q ss_pred ccchHHHHHHHhhhc-----ccCchhHHHHH-HHHHHHHhcCCCHHHH---HhhcCCCCC------CCHHHHHHH
Q 030962 100 KVDQATLFDLILAAN-----YLNIKGLLDLT-CQTVADMIKGKTPEEI---RKTFNIKND------FTPEEEEEV 159 (168)
Q Consensus 100 ~~~~~~l~~Ll~AA~-----~L~I~~L~~~~-~~~ia~~i~~ks~eei---r~~f~i~~d------~t~ee~~~i 159 (168)
.+|.+.+-.++.-|. .--|+.++.++ +..+-..+-|.|+.|+ |.++|++.. .|+|++.+|
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 467777777776665 34555666555 4457777889998887 678999854 345555544
No 41
>smart00224 GGL G protein gamma subunit-like motifs.
Probab=35.18 E-value=45 Score=20.72 Aligned_cols=25 Identities=24% Similarity=0.539 Sum_probs=19.5
Q ss_pred CCCcccCCCCHHHHHHHHHHHHhccCCCC
Q 030962 40 DNGIPLPNVTGKILAKVVEYCKKHVEVPT 68 (168)
Q Consensus 40 ~~~Ipl~~i~s~~L~~Ii~wc~~h~~~~~ 68 (168)
...|++ |.....++.||+.|....+
T Consensus 17 ~~Rikv----S~a~~~li~y~e~~~~~DP 41 (63)
T smart00224 17 RERIKV----SKAAEELLAYCEQHAEEDP 41 (63)
T ss_pred CceehH----HHHHHHHHHHHHcCCCCCC
Confidence 345666 8899999999999876655
No 42
>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=34.87 E-value=44 Score=27.36 Aligned_cols=103 Identities=20% Similarity=0.273 Sum_probs=57.5
Q ss_pred CCcccCCCCHHHHHHHHHHHHhccCCCCCC-CCCCCCCCCCCCCCCCCcccccccch--hccccchHHHHHHHhhhcccC
Q 030962 41 NGIPLPNVTGKILAKVVEYCKKHVEVPTTQ-DSNTSGANSNGAATNGGEEDLKSWDT--DFVKVDQATLFDLILAANYLN 117 (168)
Q Consensus 41 ~~Ipl~~i~s~~L~~Ii~wc~~h~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~wd~--eFl~~~~~~l~~Ll~AA~~L~ 117 (168)
+...++.-+.-.-..|+.|++-|--...+. ..+ ....-..+.+|-. .|-++..+..++.|.|..-..
T Consensus 161 ~~~Q~~~~~~~~T~NVvA~LYAalln~~~w~l~~----------~~~svedFN~WA~~N~ft~~~~~~~~~~Laa~TgVs 230 (293)
T PF05409_consen 161 EVAQLEGADQYITDNVVAWLYAALLNGCPWWLSS----------QRISVEDFNEWAMNNGFTSFSSDDAFDMLAAKTGVS 230 (293)
T ss_dssp SSSTTTTS-SB-HHHHHHHHHHHHHTT--TTSSS----------S---HHHHHHHHHHTTB--SSHHHHHHHHHHHHT--
T ss_pred hhhhhcCccceeehhHHHHHHHHHHcCCCeeecc----------ceecHHHHHHHHHhCCCcccchhhHHHHHHHHhCCc
Confidence 344555555566778999998875332211 110 0123445566743 354577788999999999999
Q ss_pred chhHHHHHHHHHHHHhcCCCHHHHHhhcCCCCCCCHHHHH
Q 030962 118 IKGLLDLTCQTVADMIKGKTPEEIRKTFNIKNDFTPEEEE 157 (168)
Q Consensus 118 I~~L~~~~~~~ia~~i~~ks~eeir~~f~i~~d~t~ee~~ 157 (168)
+.+|+...-+ +..-+.|++ |-....+++||||++--
T Consensus 231 V~rlLaaI~~-L~~g~~G~~---IlG~~~ledE~Tp~~V~ 266 (293)
T PF05409_consen 231 VERLLAAIQR-LHKGFGGRT---ILGSCSLEDEFTPEMVY 266 (293)
T ss_dssp HHHHHHHHHH-HHHTTTTT----BTTBSS--TSS-HHHHH
T ss_pred HHHHHHHHHH-HhcCCCCCc---ccccccccccCCHHHHh
Confidence 9999886655 565556665 44445577889998743
No 43
>PF11460 DUF3007: Protein of unknown function (DUF3007); InterPro: IPR021562 This is a family of uncharacterised proteins found in bacteria and eukaryotes.
Probab=33.79 E-value=41 Score=23.37 Aligned_cols=24 Identities=38% Similarity=0.616 Sum_probs=16.4
Q ss_pred CHHHHHhhcCCCCCCCHHHHHHHHHhc
Q 030962 137 TPEEIRKTFNIKNDFTPEEEEEVRREN 163 (168)
Q Consensus 137 s~eeir~~f~i~~d~t~ee~~~i~~e~ 163 (168)
+.+++.+.| +.+||||.+++..|-
T Consensus 79 ~~~~lqkRl---e~l~~eE~~~L~~ei 102 (104)
T PF11460_consen 79 TNEELQKRL---EELSPEELEALQAEI 102 (104)
T ss_pred hHHHHHHHH---HhCCHHHHHHHHHHh
Confidence 445666665 347899988887764
No 44
>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=33.68 E-value=90 Score=22.27 Aligned_cols=47 Identities=13% Similarity=0.338 Sum_probs=28.0
Q ss_pred chhHHHHHHH----HHHHHhcCCCHHHHHhhcCCCCCCCHHHHHHHHHhcccccC
Q 030962 118 IKGLLDLTCQ----TVADMIKGKTPEEIRKTFNIKNDFTPEEEEEVRRENQWAFE 168 (168)
Q Consensus 118 I~~L~~~~~~----~ia~~i~~ks~eeir~~f~i~~d~t~ee~~~i~~e~~w~~~ 168 (168)
|.+|.+..-. .|+.-...-+...+.+++|++ ++|..++-+...|-.+
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 4444444444 444444567999999999997 5566777667788653
No 45
>PRK11053 dihydropteridine reductase; Provisional
Probab=32.02 E-value=37 Score=26.02 Aligned_cols=35 Identities=23% Similarity=0.362 Sum_probs=23.6
Q ss_pred HHHHhhhcccCchhHHHHHHHHHHHHhcCCCHHHHHhhcCCCC-CC
Q 030962 107 FDLILAANYLNIKGLLDLTCQTVADMIKGKTPEEIRKTFNIKN-DF 151 (168)
Q Consensus 107 ~~Ll~AA~~L~I~~L~~~~~~~ia~~i~~ks~eeir~~f~i~~-d~ 151 (168)
..|+.||.-|++..- ++.|...+.+++.|||++ ++
T Consensus 148 ~~lmLaA~~~Glgs~----------~i~g~~~~~v~~~l~ip~~~~ 183 (217)
T PRK11053 148 GNLLLGAAALGIDAT----------PIEGFDAAILDAEFGLREKGL 183 (217)
T ss_pred HHHHHHHHHcCCCCC----------CcCCcCHHHHHHHhCCCCcCc
Confidence 355556666655532 345678899999999985 44
No 46
>KOG4591 consensus Uncharacterized conserved protein, contains BTB/POZ domain [General function prediction only]
Probab=31.78 E-value=1.1e+02 Score=24.16 Aligned_cols=31 Identities=19% Similarity=0.186 Sum_probs=19.6
Q ss_pred cchHHHHHHHhhhcccCchhHHHHHHHHHHH
Q 030962 101 VDQATLFDLILAANYLNIKGLLDLTCQTVAD 131 (168)
Q Consensus 101 ~~~~~l~~Ll~AA~~L~I~~L~~~~~~~ia~ 131 (168)
.++.-|++|+.-|+.++.+.|.+.|-+-+..
T Consensus 134 ~dD~~L~el~e~An~FqLe~Lke~C~k~l~a 164 (280)
T KOG4591|consen 134 EDDEFLLELCELANRFQLELLKERCEKGLGA 164 (280)
T ss_pred cchHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 4555666777777777776666666555443
No 47
>PF15063 TC1: Thyroid cancer protein 1
Probab=31.41 E-value=49 Score=21.63 Aligned_cols=42 Identities=21% Similarity=0.340 Sum_probs=21.5
Q ss_pred HHHHhhhcccCchhHHHHHHHHHHHHhcCCCHHHHHhhcCCCCCCCHHHHH
Q 030962 107 FDLILAANYLNIKGLLDLTCQTVADMIKGKTPEEIRKTFNIKNDFTPEEEE 157 (168)
Q Consensus 107 ~~Ll~AA~~L~I~~L~~~~~~~ia~~i~~ks~eeir~~f~i~~d~t~ee~~ 157 (168)
-+++.-+|...+.+|+...... +..|..|-+|++..| +||..
T Consensus 31 aNIFe~vn~~qlqrLF~~sGD~-------kAEeRA~iI~~~~~d--~ee~a 72 (79)
T PF15063_consen 31 ANIFENVNLDQLQRLFQKSGDK-------KAEERARIIWECAQD--PEEKA 72 (79)
T ss_pred hhhhhccCHHHHHHHHHHccch-------hHHHHHHHHHhhCCC--HHHHH
Confidence 3444455555555555543321 334555667777665 44433
No 48
>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=30.94 E-value=51 Score=17.59 Aligned_cols=19 Identities=26% Similarity=0.676 Sum_probs=15.1
Q ss_pred HHHHHHhcCCCHHHHHhhc
Q 030962 127 QTVADMIKGKTPEEIRKTF 145 (168)
Q Consensus 127 ~~ia~~i~~ks~eeir~~f 145 (168)
..||..+.++|..+++.++
T Consensus 23 ~~Ia~~~~~rs~~~~~~~~ 41 (45)
T cd00167 23 EKIAKELPGRTPKQCRERW 41 (45)
T ss_pred HHHHhHcCCCCHHHHHHHH
Confidence 4577777889999998765
No 49
>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=30.88 E-value=1.2e+02 Score=18.68 Aligned_cols=29 Identities=21% Similarity=0.351 Sum_probs=23.4
Q ss_pred hHHHHHHHHHHHHhcC--CCHHHHHhhcCCC
Q 030962 120 GLLDLTCQTVADMIKG--KTPEEIRKTFNIK 148 (168)
Q Consensus 120 ~L~~~~~~~ia~~i~~--ks~eeir~~f~i~ 148 (168)
.-+-.+|-|+|....| +|..||.+..|+.
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 4455678889988887 6899999999986
No 50
>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=29.78 E-value=88 Score=18.51 Aligned_cols=34 Identities=21% Similarity=0.543 Sum_probs=21.2
Q ss_pred HHHHHHHhcCCCHHHHHhhcC--C----C-CCCCHHHHHHH
Q 030962 126 CQTVADMIKGKTPEEIRKTFN--I----K-NDFTPEEEEEV 159 (168)
Q Consensus 126 ~~~ia~~i~~ks~eeir~~f~--i----~-~d~t~ee~~~i 159 (168)
=..||..+..+|+.+++..|. + . ..+|+||.+.+
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 346788884499999987543 2 2 23788776653
No 51
>KOG1665 consensus AFH1-interacting protein FIP2, contains BTB/POZ domain and pentapeptide repeats [General function prediction only]
Probab=29.31 E-value=28 Score=27.85 Aligned_cols=89 Identities=17% Similarity=0.276 Sum_probs=52.9
Q ss_pred CeEEEEcCCCCeEE--ecHHHHHH-hHHHHHHHHhCC-----CCCCcccCCCCHHHHHHHHHHHHhccCCCCCCCCCCCC
Q 030962 5 KMIVLKSCDGESFE--VEEAVALE-STTIKHMIEDDC-----ADNGIPLPNVTGKILAKVVEYCKKHVEVPTTQDSNTSG 76 (168)
Q Consensus 5 ~~i~l~S~DG~~~~--v~~~~a~~-S~~l~~~l~~~~-----~~~~Ipl~~i~s~~L~~Ii~wc~~h~~~~~~~~~~~~~ 76 (168)
++++|- -.|+.|. ++.-+.+. -..+..|+...+ +...--+-+=+..-++-|+.|+.+-.-
T Consensus 9 ~~vrln-igGk~f~TTidTlv~rEPDSMLa~MF~~~g~~~~~d~kGa~lIDRsp~yFepIlNyLr~Gq~----------- 76 (302)
T KOG1665|consen 9 SMVRLN-IGGKKFCTTIDTLVIREPDSMLAAMFSGRGAMCQEDKKGAVLIDRSPKYFEPILNYLRDGQI----------- 76 (302)
T ss_pred hhheee-cCCeEEEEeehhhcccCchHHHHHHHccCCCccccccCceEEEccCchhhHHHHHHHhcCce-----------
Confidence 344442 3466663 33333332 445566665543 112222336677778888888875321
Q ss_pred CCCCCCCCCCCcccccccchhccccchHHHHHHHhhhcccCchhHHHHHHH
Q 030962 77 ANSNGAATNGGEEDLKSWDTDFVKVDQATLFDLILAANYLNIKGLLDLTCQ 127 (168)
Q Consensus 77 ~~~~~~~~~~~~~~~~~wd~eFl~~~~~~l~~Ll~AA~~L~I~~L~~~~~~ 127 (168)
...+...++.++.+|.|++|-+|++..-.
T Consensus 77 ----------------------~~~s~i~~lgvLeeArff~i~sL~~hle~ 105 (302)
T KOG1665|consen 77 ----------------------PSLSDIDCLGVLEEARFFQILSLKDHLED 105 (302)
T ss_pred ----------------------eecCCccHHHHHHHhhHHhhHhHHhHHhh
Confidence 12345568999999999999999986543
No 52
>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=29.21 E-value=74 Score=22.40 Aligned_cols=23 Identities=35% Similarity=0.429 Sum_probs=17.2
Q ss_pred HHHHHHHHHHHHhcCCCHHHHHh
Q 030962 121 LLDLTCQTVADMIKGKTPEEIRK 143 (168)
Q Consensus 121 L~~~~~~~ia~~i~~ks~eeir~ 143 (168)
..-.++..++.+++|||.+|+.+
T Consensus 63 ~~~Asas~~~~~i~gk~l~ea~~ 85 (126)
T PF01592_consen 63 ISIASASMMCELIKGKTLEEALK 85 (126)
T ss_dssp HHHHHHHHHHHHHTTSBHHHHHC
T ss_pred HHHHHHHHHHHHHcCCCHHHHHH
Confidence 34455667889999999888853
No 53
>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=28.92 E-value=63 Score=20.60 Aligned_cols=22 Identities=18% Similarity=0.243 Sum_probs=18.6
Q ss_pred CCeEEEEcCCCCeEEecHHHHH
Q 030962 4 PKMIVLKSCDGESFEVEEAVAL 25 (168)
Q Consensus 4 ~~~i~l~S~DG~~~~v~~~~a~ 25 (168)
.+.|.+.|.||..+.+|....+
T Consensus 20 a~~V~v~s~~Gr~v~~Pa~~lR 41 (68)
T PF11197_consen 20 ASKVVVRSDDGRRVQFPARHLR 41 (68)
T ss_pred ccEEEEEecCCcEEEEeHHHCc
Confidence 3679999999999999987654
No 54
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=28.91 E-value=59 Score=17.63 Aligned_cols=20 Identities=30% Similarity=0.624 Sum_probs=15.5
Q ss_pred HHHHHHhcCCCHHHHHhhcC
Q 030962 127 QTVADMIKGKTPEEIRKTFN 146 (168)
Q Consensus 127 ~~ia~~i~~ks~eeir~~f~ 146 (168)
..||..+.++|+.+++..+.
T Consensus 25 ~~Ia~~~~~rt~~~~~~~~~ 44 (49)
T smart00717 25 EKIAKELPGRTAEQCRERWN 44 (49)
T ss_pred HHHHHHcCCCCHHHHHHHHH
Confidence 45777778899999988653
No 55
>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=28.70 E-value=27 Score=25.26 Aligned_cols=17 Identities=41% Similarity=0.829 Sum_probs=12.6
Q ss_pred CCCHHHHHhhcCCCCCC
Q 030962 135 GKTPEEIRKTFNIKNDF 151 (168)
Q Consensus 135 ~ks~eeir~~f~i~~d~ 151 (168)
|.|++|=|+.||++.|+
T Consensus 94 gltp~eYR~kwGlp~dy 110 (132)
T PF05443_consen 94 GLTPEEYRAKWGLPKDY 110 (132)
T ss_dssp -S-HHHHHHHTT-GGG-
T ss_pred CCCHHHHHHHhCcCCCC
Confidence 89999999999999884
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=28.55 E-value=35 Score=18.14 Aligned_cols=13 Identities=38% Similarity=0.598 Sum_probs=9.1
Q ss_pred cCCCHHHHHhhcC
Q 030962 134 KGKTPEEIRKTFN 146 (168)
Q Consensus 134 ~~ks~eeir~~f~ 146 (168)
.|.|.+|+|+++.
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 5899999999864
No 57
>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=28.48 E-value=88 Score=22.00 Aligned_cols=37 Identities=24% Similarity=0.270 Sum_probs=24.8
Q ss_pred HHhhhcccCchhHHHHHH-HHHHHHhcCCCHHHHHhhc
Q 030962 109 LILAANYLNIKGLLDLTC-QTVADMIKGKTPEEIRKTF 145 (168)
Q Consensus 109 Ll~AA~~L~I~~L~~~~~-~~ia~~i~~ks~eeir~~f 145 (168)
.+.-+.|-.-=.-...+| ..++.++.|||.+|...+-
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 455556655554444444 5678999999998887653
No 58
>COG1710 Uncharacterized protein conserved in archaea [Function unknown]
Probab=28.47 E-value=41 Score=24.02 Aligned_cols=16 Identities=50% Similarity=0.723 Sum_probs=14.5
Q ss_pred cCCCHHHHHhhcCCCC
Q 030962 134 KGKTPEEIRKTFNIKN 149 (168)
Q Consensus 134 ~~ks~eeir~~f~i~~ 149 (168)
+||+|.||.+.+||+-
T Consensus 108 ~gk~preIsk~lGIpi 123 (139)
T COG1710 108 NGKTPREISKDLGIPI 123 (139)
T ss_pred cCCCHHHHHHhhCCch
Confidence 4899999999999984
No 59
>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=28.43 E-value=94 Score=19.24 Aligned_cols=29 Identities=14% Similarity=0.273 Sum_probs=19.8
Q ss_pred eEEEEcCCC------CeEEecHHH--HHHhHHHHHHH
Q 030962 6 MIVLKSCDG------ESFEVEEAV--ALESTTIKHMI 34 (168)
Q Consensus 6 ~i~l~S~DG------~~~~v~~~~--a~~S~~l~~~l 34 (168)
.++|.|++| ..+.||..+ ...|.+++.++
T Consensus 3 ~v~F~t~~~~~~~~~~~~~VP~~~t~~~Ls~LvN~LL 39 (65)
T PF08154_consen 3 QVQFVTEDGEYEVPGTPISVPSNITRKELSELVNQLL 39 (65)
T ss_pred EEEEEcCCCCccCCCCCEEEeCCCCHHHHHHHHHHHh
Confidence 467777777 356666554 45788888887
No 60
>PRK11325 scaffold protein; Provisional
Probab=28.36 E-value=87 Score=22.19 Aligned_cols=37 Identities=22% Similarity=0.211 Sum_probs=25.4
Q ss_pred HHhhhcccCchhHHHHHHH-HHHHHhcCCCHHHHHhhc
Q 030962 109 LILAANYLNIKGLLDLTCQ-TVADMIKGKTPEEIRKTF 145 (168)
Q Consensus 109 Ll~AA~~L~I~~L~~~~~~-~ia~~i~~ks~eeir~~f 145 (168)
.+.-+.|-.-=.-...+|. .++.+++|||++|.+.+-
T Consensus 52 ~I~d~~f~~~GC~is~Asas~~~e~~~Gktl~ea~~i~ 89 (127)
T PRK11325 52 IIEDAKFKTYGCGSAIASSSLVTEWVKGKTLDEALAIK 89 (127)
T ss_pred eEEEEEEEeeCCHHHHHHHHHHHHHHcCCCHHHHHhcC
Confidence 5556666655555555544 667999999999887653
No 61
>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=28.34 E-value=96 Score=21.73 Aligned_cols=37 Identities=24% Similarity=0.284 Sum_probs=25.0
Q ss_pred HHhhhcccCchhHHHHHHH-HHHHHhcCCCHHHHHhhc
Q 030962 109 LILAANYLNIKGLLDLTCQ-TVADMIKGKTPEEIRKTF 145 (168)
Q Consensus 109 Ll~AA~~L~I~~L~~~~~~-~ia~~i~~ks~eeir~~f 145 (168)
.+..+.|-.-=.-+..+|. .++.++.|||.+|..++-
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 5555666655555555544 677999999999876653
No 62
>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=28.16 E-value=66 Score=17.96 Aligned_cols=30 Identities=30% Similarity=0.336 Sum_probs=22.3
Q ss_pred ccCchhHHHHHHHHHHHHhcCCCHHHHHhh
Q 030962 115 YLNIKGLLDLTCQTVADMIKGKTPEEIRKT 144 (168)
Q Consensus 115 ~L~I~~L~~~~~~~ia~~i~~ks~eeir~~ 144 (168)
||.-++|-+.....|+..+...++++|-.+
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 456667777777888887888888887654
No 63
>COG1460 Uncharacterized protein conserved in archaea [Function unknown]
Probab=27.67 E-value=2e+02 Score=20.33 Aligned_cols=39 Identities=23% Similarity=0.405 Sum_probs=26.9
Q ss_pred HHHHHHHHHHHHhcCCCHHHHHhhcCCCCC-CCHHHHHHHH
Q 030962 121 LLDLTCQTVADMIKGKTPEEIRKTFNIKND-FTPEEEEEVR 160 (168)
Q Consensus 121 L~~~~~~~ia~~i~~ks~eeir~~f~i~~d-~t~ee~~~i~ 160 (168)
+-+-.+.+||+ |.=.|++|+|.+|.-..- +|+|+..+|-
T Consensus 66 ~~e~~avkIad-I~P~t~~ElRsIla~e~~~~s~E~l~~Il 105 (114)
T COG1460 66 MSEKIAVKIAD-IMPRTPDELRSILAKERVMLSDEELDKIL 105 (114)
T ss_pred ccHHHHHHHHH-hCCCCHHHHHHHHHHccCCCCHHHHHHHH
Confidence 35555566666 356899999999876654 5777776653
No 64
>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=27.47 E-value=1.7e+02 Score=18.57 Aligned_cols=40 Identities=10% Similarity=0.095 Sum_probs=26.7
Q ss_pred HHHhhhcccCchhHHHHHHHHHHHH---------hcCCCHHHHHhhcCC
Q 030962 108 DLILAANYLNIKGLLDLTCQTVADM---------IKGKTPEEIRKTFNI 147 (168)
Q Consensus 108 ~Ll~AA~~L~I~~L~~~~~~~ia~~---------i~~ks~eeir~~f~i 147 (168)
++...|...+.+.|.+.|..+++.. +...+.+++..+++=
T Consensus 3 ~i~~~a~~~~~~~L~~~~~~~i~~nf~~~~~~~~f~~L~~~~l~~iL~~ 51 (101)
T smart00875 3 GIRRFAELYGLEELLEKALRFILKNFLEVAQSEEFLELSLEQLLSLLSS 51 (101)
T ss_pred hHHHHHHHhChHHHHHHHHHHHHHHHHHHhcCcHHhcCCHHHHHHHhCc
Confidence 4556667778888888887776653 234566777776654
No 65
>PF06514 PsbU: Photosystem II 12 kDa extrinsic protein (PsbU); InterPro: IPR010527 Oxygenic photosynthesis uses two multi-subunit photosystems (I and II) located in the cell membranes of cyanobacteria and in the thylakoid membranes of chloroplasts in plants and algae. Photosystem II (PSII) has a P680 reaction centre containing chlorophyll 'a' that uses light energy to carry out the oxidation (splitting) of water molecules, and to produce ATP via a proton pump. Photosystem I (PSI) has a P700 reaction centre containing chlorophyll that takes the electron and associated hydrogen donated from PSII to reduce NADP+ to NADPH. Both ATP and NADPH are subsequently used in the light-independent reactions to convert carbon dioxide to glucose using the hydrogen atom extracted from water by PSII, releasing oxygen as a by-product. PSII is a multisubunit protein-pigment complex containing polypeptides both intrinsic and extrinsic to the photosynthetic membrane [, ]. Within the core of the complex, the chlorophyll and beta-carotene pigments are mainly bound to the antenna proteins CP43 (PsbC) and CP47 (PsbB), which pass the excitation energy on to the reaction centre proteins D1 (Qb, PsbA) and D2 (Qa, PsbD) that bind all the redox-active cofactors involved in the energy conversion process. The PSII oxygen-evolving complex (OEC) oxidises water to provide protons for use by PSI, and consists of OEE1 (PsbO), OEE2 (PsbP) and OEE3 (PsbQ). The remaining subunits in PSII are of low molecular weight (less than 10 kDa), and are involved in PSII assembly, stabilisation, dimerisation, and photo-protection []. In PSII, the oxygen-evolving complex (OEC) is responsible for catalysing the splitting of water to O(2) and 4H+. The OEC is composed of a cluster of manganese, calcium and chloride ions bound to extrinsic proteins. In cyanobacteria there are five extrinsic proteins in OEC (PsbO, PsbP-like, PsbQ-like, PsbU and PsbV), while in plants there are only three (PsbO, PsbP and PsbQ), PsbU and PsbV having been lost during the evolution of green plants []. This family represents the PSII extrinsic protein PsbU, which forms part of the OEC in cyanobacteria and red algae. PsbU acts to stabilise the oxygen-evolving machinery of PSII against heat-induced inactivation, which is crucial for cellular thermo-tolerance [].; GO: 0015979 photosynthesis, 0042549 photosystem II stabilization, 0009523 photosystem II, 0009654 oxygen evolving complex, 0019898 extrinsic to membrane; PDB: 3BZ1_U 3KZI_U 3PRQ_U 2AXT_u 3BZ2_U 4FBY_U 3PRR_U 1S5L_U 3A0H_U 3ARC_U ....
Probab=27.19 E-value=35 Score=23.18 Aligned_cols=46 Identities=11% Similarity=0.272 Sum_probs=27.9
Q ss_pred hhcccCchhHHHHHHHHHHHHhcCCCHHHHHhhcCCCCCCCHHHHHHHHH
Q 030962 112 AANYLNIKGLLDLTCQTVADMIKGKTPEEIRKTFNIKNDFTPEEEEEVRR 161 (168)
Q Consensus 112 AA~~L~I~~L~~~~~~~ia~~i~~ks~eeir~~f~i~~d~t~ee~~~i~~ 161 (168)
...|-+.+++.--.+..|+...--+|++++ +.|+ +||+.|++.+++
T Consensus 22 vr~f~~~pGmYPtlA~kIv~naPY~sveDv---l~ip-gLse~qK~~lk~ 67 (93)
T PF06514_consen 22 VRAFRQFPGMYPTLAGKIVSNAPYKSVEDV---LNIP-GLSERQKALLKK 67 (93)
T ss_dssp GGGGCCSTTTTCCHHHHHHHS---SSGGGG---CCST-T--HHHHHHHHH
T ss_pred HHHHHHCCCCCHHHHHHHHhCCCCCCHHHH---Hhcc-CCCHHHHHHHHH
Confidence 466777888877777766654444666654 6665 478888777765
No 66
>PRK09296 cysteine desufuration protein SufE; Provisional
Probab=26.15 E-value=1.3e+02 Score=21.81 Aligned_cols=33 Identities=18% Similarity=0.323 Sum_probs=22.6
Q ss_pred HHHHHHHHHHHHhcCCCHHHHHh--------hcCCCCCCCH
Q 030962 121 LLDLTCQTVADMIKGKTPEEIRK--------TFNIKNDFTP 153 (168)
Q Consensus 121 L~~~~~~~ia~~i~~ks~eeir~--------~f~i~~d~t~ 153 (168)
++.-.+..+...++|+||+||.+ .+|+..-+||
T Consensus 77 ivkGl~alL~~~~~g~tp~eIl~~d~~~~~~~lGL~~~LSp 117 (138)
T PRK09296 77 IVKGLIAVVFILYQQMTPQDIVNFDVRPWFEKLALTQHLTP 117 (138)
T ss_pred HHHHHHHHHHHHHcCCCHHHHHhCChHHHHHHcCcccccCc
Confidence 33444555666779999999864 4577777776
No 67
>PF13798 PCYCGC: Protein of unknown function with PCYCGC motif
Probab=26.06 E-value=1e+02 Score=23.07 Aligned_cols=20 Identities=40% Similarity=0.587 Sum_probs=14.2
Q ss_pred HHHHHHHHhcCCCHHHHHhh
Q 030962 125 TCQTVADMIKGKTPEEIRKT 144 (168)
Q Consensus 125 ~~~~ia~~i~~ks~eeir~~ 144 (168)
+...+...=+|||+.|||++
T Consensus 121 a~~a~~~~~~Gks~~eIR~~ 140 (158)
T PF13798_consen 121 AVQAVQMYQEGKSPKEIRQY 140 (158)
T ss_pred HHHHHHHHHcCCCHHHHHHH
Confidence 33444455579999999985
No 68
>PF13518 HTH_28: Helix-turn-helix domain
Probab=25.78 E-value=1.1e+02 Score=17.22 Aligned_cols=20 Identities=30% Similarity=0.537 Sum_probs=16.2
Q ss_pred HHHHhcCCCHHHHHhhcCCC
Q 030962 129 VADMIKGKTPEEIRKTFNIK 148 (168)
Q Consensus 129 ia~~i~~ks~eeir~~f~i~ 148 (168)
|.....|.|..++.+.|||.
T Consensus 6 v~~~~~g~s~~~~a~~~gis 25 (52)
T PF13518_consen 6 VELYLEGESVREIAREFGIS 25 (52)
T ss_pred HHHHHcCCCHHHHHHHHCCC
Confidence 44455789999999999994
No 69
>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=25.72 E-value=54 Score=24.87 Aligned_cols=38 Identities=16% Similarity=0.248 Sum_probs=27.0
Q ss_pred HHHHHHhhhcccCchhHHHHHHHHHHHHhcCCCHHHHHhhcCCCCCCC
Q 030962 105 TLFDLILAANYLNIKGLLDLTCQTVADMIKGKTPEEIRKTFNIKNDFT 152 (168)
Q Consensus 105 ~l~~Ll~AA~~L~I~~L~~~~~~~ia~~i~~ks~eeir~~f~i~~d~t 152 (168)
.+-.|+.||..+++-.- ++.+-..+++++.|||+.++.
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 44578888888888752 223445789999999997643
No 70
>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=25.70 E-value=1e+02 Score=20.83 Aligned_cols=42 Identities=26% Similarity=0.481 Sum_probs=28.2
Q ss_pred hHHHHHHHHHHHHhcCCCHHHHHhhcCCCC-CCCHHHHHHHHH
Q 030962 120 GLLDLTCQTVADMIKGKTPEEIRKTFNIKN-DFTPEEEEEVRR 161 (168)
Q Consensus 120 ~L~~~~~~~ia~~i~~ks~eeir~~f~i~~-d~t~ee~~~i~~ 161 (168)
.|+-++|-.+|.++....+-.+.....+.+ .+|.++.-+.+.
T Consensus 74 ~li~~~cl~lA~K~~e~~~~~~~~~~~~~~~~~~~~~i~~~E~ 116 (127)
T PF00134_consen 74 QLIALACLFLASKMEEDNPPSISDLIRISDNTFTKKDILEMER 116 (127)
T ss_dssp HHHHHHHHHHHHHHHTSS--HHHHHHHHTTTSSHHHHHHHHHH
T ss_pred hhhhhhHHHHhhhhhccccchHHHHHHHHcCCCCHHHHHHHHH
Confidence 578889999999998875555555555443 478877665554
No 71
>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=24.68 E-value=2.3e+02 Score=20.00 Aligned_cols=34 Identities=9% Similarity=0.204 Sum_probs=19.5
Q ss_pred HHHHHHhcCCCHHHH-HhhcCCCCCCCHHHHHHHHH
Q 030962 127 QTVADMIKGKTPEEI-RKTFNIKNDFTPEEEEEVRR 161 (168)
Q Consensus 127 ~~ia~~i~~ks~eei-r~~f~i~~d~t~ee~~~i~~ 161 (168)
+.+.+.+-|.++..+ ..+++ .+.+++||.+++++
T Consensus 78 ~~~~~~~f~gs~~~ll~~l~~-~~~ls~eele~L~~ 112 (130)
T TIGR02698 78 QELFSRICSRKVGAVIADLIE-ESPLSQTDIEKLEK 112 (130)
T ss_pred HHHHHHHHCCCHHHHHHHHHh-cCCCCHHHHHHHHH
Confidence 334443444454444 33433 45688998888876
No 72
>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=24.42 E-value=95 Score=21.76 Aligned_cols=34 Identities=26% Similarity=0.355 Sum_probs=20.5
Q ss_pred cCchhHHHHHHHHHHHHhc--CCCHHHHHhhcCCCCC
Q 030962 116 LNIKGLLDLTCQTVADMIK--GKTPEEIRKTFNIKND 150 (168)
Q Consensus 116 L~I~~L~~~~~~~ia~~i~--~ks~eeir~~f~i~~d 150 (168)
+++..|.+.+... |..++ +.|+.|||++|+--..
T Consensus 8 ~~~~~~~~~Ae~~-~k~l~~~~lttsQlRkf~~~v~~ 43 (119)
T PF03750_consen 8 LDIELLVDYAEKI-AKELKKNKLTTSQLRKFYDEVKR 43 (119)
T ss_pred cCHHHHHHHHHHH-HHHHHhCCCCHHHHHHHHHHHHH
Confidence 3444455544443 33343 4799999999985543
No 73
>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=23.37 E-value=92 Score=21.27 Aligned_cols=61 Identities=15% Similarity=0.175 Sum_probs=30.3
Q ss_pred CCCeEEEEcCCCCeEEecHHHHHHhHHHHHHHHhCC---CCC---Cc------cc-CCCCHHHHHHHHHHHHhcc
Q 030962 3 SPKMIVLKSCDGESFEVEEAVALESTTIKHMIEDDC---ADN---GI------PL-PNVTGKILAKVVEYCKKHV 64 (168)
Q Consensus 3 ~~~~i~l~S~DG~~~~v~~~~a~~S~~l~~~l~~~~---~~~---~I------pl-~~i~s~~L~~Ii~wc~~h~ 64 (168)
+++.++++|+||..+.|...--. ...+...+|-.| .+. .| ++ .+++-+....+++.++.++
T Consensus 33 ~g~~~~l~~~d~~~V~v~l~~~~-~~~~~~~vEviG~V~~~~~~~~i~~~~~~~~g~~~D~~~y~~lv~l~~~~p 106 (109)
T PF08661_consen 33 DGGSATLSTSDGGQVTVSLNPPS-DEELSKYVEVIGKVNDDGTVLSIRYFSFTDFGDDFDMDLYNELVQLTHKFP 106 (109)
T ss_dssp TSSEEEEE-TTS-EEEEEESS---SS---SEEEEEEEE-TTS-EEEEEEEE---SSS---HHHHHHHHHHHHHSG
T ss_pred CCCEEEEEcCCCCEEEEEeCCCC-CCCCCCEEEEEEEEcCCCCceEEEEEEeccCCCCcCHHHHHHHHHHHhhCC
Confidence 35789999999999988654210 111222333111 111 11 22 3688888888888887764
No 74
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=23.31 E-value=84 Score=17.77 Aligned_cols=15 Identities=27% Similarity=0.428 Sum_probs=10.8
Q ss_pred cCCCHHHHHhhcCCC
Q 030962 134 KGKTPEEIRKTFNIK 148 (168)
Q Consensus 134 ~~ks~eeir~~f~i~ 148 (168)
.|.|..+|.+.||++
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 499999999999986
No 75
>PF05871 ESCRT-II: ESCRT-II complex subunit; InterPro: IPR008570 This entry represents the vps25 subunit (vacuolar protein sorting-associated protein 25) of the endosome-associated complex ESCRT-II (Endosomal Sorting Complexes Required for Transport protein II). ESCRT (ESCRT-I, -II, -III) complexes orchestrate efficient sorting of ubiquitinated transmembrane receptors to lysosomes via multivesicular bodies (MVBs) []. ESCRT-II recruits the transport machinery for protein sorting at MVB []. In addition, the human ESCRT-II has been shown to form a complex with RNA polymerase II elongation factor ELL in order to exert transcriptional control activity. ESCRT-II transiently associates with the endosomal membrane and thereby initiates the formation of ESCRT-III, a membrane-associated protein complex that functions immediately downstream of ESCRT-II during sorting of MVB cargo. ESCRT-II in turn functions downstream of ESCRT-I, a protein complex that binds to ubiquitinated endosomal cargo []. ESCRT-II is a trilobal complex composed of two copies of vps25, one copy of vps22 and the C-terminal region of vps36. The crystal structure of vps25 revealed two winged-helix domains, the N-terminal domain of vps25 interacting with vps22 and vps35 [].; PDB: 1W7P_B 1U5T_D 1XB4_D 3HTU_E 3CUQ_C 2ZME_D.
Probab=22.86 E-value=56 Score=23.80 Aligned_cols=15 Identities=20% Similarity=0.607 Sum_probs=11.0
Q ss_pred HHHHHHHHhccCCCC
Q 030962 54 AKVVEYCKKHVEVPT 68 (168)
Q Consensus 54 ~~Ii~wc~~h~~~~~ 68 (168)
..|++||.||+-...
T Consensus 27 ~lIl~y~~~~k~~~l 41 (139)
T PF05871_consen 27 DLILDYCRHHKIFRL 41 (139)
T ss_dssp HHHHHHHHHTT-SEE
T ss_pred HHHHHHHHHhceeee
Confidence 359999999987544
No 76
>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=22.84 E-value=85 Score=24.82 Aligned_cols=26 Identities=19% Similarity=0.447 Sum_probs=15.7
Q ss_pred HHHHHHHhcCCCHHHHHhhcCCCCCC
Q 030962 126 CQTVADMIKGKTPEEIRKTFNIKNDF 151 (168)
Q Consensus 126 ~~~ia~~i~~ks~eeir~~f~i~~d~ 151 (168)
...++..++..|.+|+++.|+|...+
T Consensus 31 ~~~l~~~L~~~s~~el~~l~~is~~l 56 (237)
T PF03883_consen 31 TEELLEALKSLSEEELKKLMKISDKL 56 (237)
T ss_pred HHHHHHHHHhcCHHHHHHHHCCCHHH
Confidence 44455555666667777777766544
No 77
>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=22.62 E-value=1.6e+02 Score=21.37 Aligned_cols=32 Identities=16% Similarity=0.375 Sum_probs=21.4
Q ss_pred HHHHHHHHHHHhcCCCHHHHHh--------hcCCCCCCCH
Q 030962 122 LDLTCQTVADMIKGKTPEEIRK--------TFNIKNDFTP 153 (168)
Q Consensus 122 ~~~~~~~ia~~i~~ks~eeir~--------~f~i~~d~t~ 153 (168)
+.-.+..+...++|+|++||.+ .+|+..-+||
T Consensus 83 vkGl~alL~~~~~g~tp~eI~~~d~~~~~~~lGL~~~LSp 122 (138)
T TIGR03391 83 VRGLLAVLLTAVEGKTPEQLLAQDPLALFDELGLRAQLSA 122 (138)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHCCHHHHHHHcCchhccCc
Confidence 3334445556679999999874 4567766776
No 78
>PHA02713 hypothetical protein; Provisional
Probab=22.54 E-value=1.5e+02 Score=26.38 Aligned_cols=71 Identities=10% Similarity=0.096 Sum_probs=44.8
Q ss_pred hhccc--cchHHHHHHHhhhcccCchhHHHHHHHHHHHHhc---------CCCHHHHHhhcCCCCCCC-HHHHHHHHHhc
Q 030962 96 TDFVK--VDQATLFDLILAANYLNIKGLLDLTCQTVADMIK---------GKTPEEIRKTFNIKNDFT-PEEEEEVRREN 163 (168)
Q Consensus 96 ~eFl~--~~~~~l~~Ll~AA~~L~I~~L~~~~~~~ia~~i~---------~ks~eeir~~f~i~~d~t-~ee~~~i~~e~ 163 (168)
.+|+. ++.++-++++..|.-.....|.+.+.++++..+. ..+.+++.+++.=.+.+. +.|++-.+--.
T Consensus 116 ~~~l~~~l~~~NCl~i~~~~~~~~~~~L~~~a~~~i~~~f~~v~~~~ef~~L~~~~l~~lL~~d~~l~v~~Ee~v~eav~ 195 (557)
T PHA02713 116 ESYIKDYTNHDTCIYMYHRLYEMSHIPIVKYIKRMLMSNIPTLITTDAFKKTVFEILFDIISTNDNVYLYREGYKVTILL 195 (557)
T ss_pred HHHHHhhCCccchHHHHHHHHhccchHHHHHHHHHHHHHHHHHhCChhhhhCCHHHHHHHhccccccCCCcHHHHHHHHH
Confidence 34544 6777888888633334445699988888887764 357788888877654343 34444444444
Q ss_pred ccc
Q 030962 164 QWA 166 (168)
Q Consensus 164 ~w~ 166 (168)
+|+
T Consensus 196 ~W~ 198 (557)
T PHA02713 196 KWL 198 (557)
T ss_pred HHH
Confidence 564
No 79
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=22.49 E-value=78 Score=19.50 Aligned_cols=18 Identities=33% Similarity=0.455 Sum_probs=13.8
Q ss_pred CCeEEEEcCCCCeEE-ecH
Q 030962 4 PKMIVLKSCDGESFE-VEE 21 (168)
Q Consensus 4 ~~~i~l~S~DG~~~~-v~~ 21 (168)
-+-+++.|.||++|. .|+
T Consensus 4 ~KA~Kv~~RDGE~~lrCPR 22 (65)
T COG4049 4 LKAIKVRDRDGEEFLRCPR 22 (65)
T ss_pred ceeeEeeccCCceeeeCCc
Confidence 356899999999884 454
No 80
>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=22.46 E-value=71 Score=23.58 Aligned_cols=37 Identities=8% Similarity=-0.067 Sum_probs=25.9
Q ss_pred HHHHHhhhcccCchhHHHHHHHHHHHHhcCCCH-HHHHhhcCCCCCCC
Q 030962 106 LFDLILAANYLNIKGLLDLTCQTVADMIKGKTP-EEIRKTFNIKNDFT 152 (168)
Q Consensus 106 l~~Ll~AA~~L~I~~L~~~~~~~ia~~i~~ks~-eeir~~f~i~~d~t 152 (168)
+-.|+.||.-|++-.. ++.+... +.+++.|||++++.
T Consensus 129 ~~~l~LaA~~~Glgs~----------~~~~~~~~~~v~~~l~ip~~~~ 166 (193)
T cd02144 129 CGLLLAALQNAGLGTV----------TTTPLNMGPFLRRLLGRPANEK 166 (193)
T ss_pred HHHHHHHHHHCCCcee----------ecCCcchhHHHHHHhCCCCCCc
Confidence 3458888888888762 1234344 89999999997643
No 81
>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=22.42 E-value=59 Score=18.32 Aligned_cols=18 Identities=22% Similarity=0.420 Sum_probs=14.8
Q ss_pred CCeEEEEcCCCCeEEecH
Q 030962 4 PKMIVLKSCDGESFEVEE 21 (168)
Q Consensus 4 ~~~i~l~S~DG~~~~v~~ 21 (168)
...+++++.||+...|++
T Consensus 23 g~~vtV~~~~G~~~tv~~ 40 (42)
T PF02736_consen 23 GDKVTVKTEDGKEVTVKK 40 (42)
T ss_dssp SSEEEEEETTTEEEEEEG
T ss_pred CCEEEEEECCCCEEEeCC
Confidence 357899999999998875
No 82
>PRK15019 CsdA-binding activator; Provisional
Probab=22.35 E-value=1.6e+02 Score=21.71 Aligned_cols=32 Identities=13% Similarity=0.320 Sum_probs=21.5
Q ss_pred HHHHHHHHHHHhcCCCHHHHHh--------hcCCCCCCCH
Q 030962 122 LDLTCQTVADMIKGKTPEEIRK--------TFNIKNDFTP 153 (168)
Q Consensus 122 ~~~~~~~ia~~i~~ks~eeir~--------~f~i~~d~t~ 153 (168)
+.-.+..+...++|+||+||.+ -+|+..-+||
T Consensus 88 vkGl~alL~~~~~g~tp~eIl~~d~~~~~~~lGL~~~LSp 127 (147)
T PRK15019 88 VRGLLAVLLTAVEGKTAAELQAQSPLALFDELGLRAQLSA 127 (147)
T ss_pred HHHHHHHHHHHHcCCCHHHHHhcCHHHHHHHCCchhhcCc
Confidence 3333445555669999999865 4577777776
No 83
>PF11094 UL11: Membrane-associated tegument protein; InterPro: IPR024351 The UL11 gene product of herpes simplex virus is a membrane-associated tegument protein that is incorporated into the HSV virion and functions in viral envelopment []. UL11 is acylated, which is crucial for lipid raft association [].
Probab=22.05 E-value=91 Score=17.65 Aligned_cols=19 Identities=21% Similarity=0.338 Sum_probs=15.5
Q ss_pred CeEEEEcCCCCeEEecHHH
Q 030962 5 KMIVLKSCDGESFEVEEAV 23 (168)
Q Consensus 5 ~~i~l~S~DG~~~~v~~~~ 23 (168)
|.-+|.|++|+++.++...
T Consensus 14 R~N~LvT~~Ge~vsL~a~~ 32 (39)
T PF11094_consen 14 RRNVLVTHSGETVSLDAEE 32 (39)
T ss_pred ecCEEEccCCeEEEeChhh
Confidence 4568999999999988753
No 84
>KOG0028 consensus Ca2+-binding protein (centrin/caltractin), EF-Hand superfamily protein [Cytoskeleton; Cell cycle control, cell division, chromosome partitioning]
Probab=21.96 E-value=2.2e+02 Score=21.55 Aligned_cols=49 Identities=18% Similarity=0.368 Sum_probs=32.6
Q ss_pred hhcccCchhHHHHHHHHHHHHhcCCCHHHHHhhcCCCCC-----CCHHHHHHHHHhc
Q 030962 112 AANYLNIKGLLDLTCQTVADMIKGKTPEEIRKTFNIKND-----FTPEEEEEVRREN 163 (168)
Q Consensus 112 AA~~L~I~~L~~~~~~~ia~~i~~ks~eeir~~f~i~~d-----~t~ee~~~i~~e~ 163 (168)
++..+..+.++...+.++.. ++ |-+||++.|.+-++ +++-+..++.+|.
T Consensus 82 ~~g~i~fe~f~~~mt~k~~e--~d-t~eEi~~afrl~D~D~~Gkis~~~lkrvakeL 135 (172)
T KOG0028|consen 82 GSGKITFEDFRRVMTVKLGE--RD-TKEEIKKAFRLFDDDKTGKISQRNLKRVAKEL 135 (172)
T ss_pred cCceechHHHHHHHHHHHhc--cC-cHHHHHHHHHcccccCCCCcCHHHHHHHHHHh
Confidence 45667777888777776654 34 88999998886543 3455666555543
No 85
>PF09116 gp45-slide_C: gp45 sliding clamp, C terminal; InterPro: IPR015200 This domain is essential for the interaction of the gp45 sliding clamp with the corresponding polymerase. It adopts a DNA clamp fold, consisting of two alpha helices and two beta sheets - the fold is duplicated and has internal pseudo two-fold symmetry []. ; PDB: 1B8H_A 1B77_B 3U61_F 3U60_G 3U5Z_R 1CZD_B.
Probab=21.53 E-value=43 Score=23.57 Aligned_cols=22 Identities=23% Similarity=0.344 Sum_probs=17.0
Q ss_pred ccchHHHHHHHhhhcccCchhH
Q 030962 100 KVDQATLFDLILAANYLNIKGL 121 (168)
Q Consensus 100 ~~~~~~l~~Ll~AA~~L~I~~L 121 (168)
++..+.+-+|++||.-|+++.|
T Consensus 5 ~L~~edl~ql~kas~~l~l~dl 26 (112)
T PF09116_consen 5 ELKAEDLQQLMKASRTLGLPDL 26 (112)
T ss_dssp EE-HHHHHHHHHHHHHCT--EE
T ss_pred EecHHHHHHHHHHHHhcCCCeE
Confidence 5788999999999999998865
No 86
>KOG4244 consensus Failed axon connections (fax) protein/glutathione S-transferase-like protein [Signal transduction mechanisms]
Probab=21.34 E-value=1.1e+02 Score=25.04 Aligned_cols=22 Identities=27% Similarity=0.626 Sum_probs=17.7
Q ss_pred HHHHHhhcCCCCCCCHHHHHHH
Q 030962 138 PEEIRKTFNIKNDFTPEEEEEV 159 (168)
Q Consensus 138 ~eeir~~f~i~~d~t~ee~~~i 159 (168)
...+|+.|++++++++||+..-
T Consensus 111 ~~~L~~hf~~~~~L~~e~~a~s 132 (281)
T KOG4244|consen 111 EDRLRKHFKIPDDLSAEQRAQS 132 (281)
T ss_pred HHHHHHHcCCCCCCCHHHHHHH
Confidence 3567899999999999987653
No 87
>PF11399 DUF3192: Protein of unknown function (DUF3192); InterPro: IPR021534 Some members in this family of proteins are annotated as lipoproteins however this cannot be confirmed.
Probab=21.27 E-value=93 Score=21.51 Aligned_cols=26 Identities=19% Similarity=0.405 Sum_probs=20.1
Q ss_pred HHHHHHhcCCCHHHHHhhcCCCCCCCH
Q 030962 127 QTVADMIKGKTPEEIRKTFNIKNDFTP 153 (168)
Q Consensus 127 ~~ia~~i~~ks~eeir~~f~i~~d~t~ 153 (168)
+.|+.+--|+|-++++..+|-| |||+
T Consensus 26 ~~i~~L~lg~s~~~V~~~lG~p-dfsE 51 (102)
T PF11399_consen 26 QNIAKLSLGMSKDQVIALLGTP-DFSE 51 (102)
T ss_pred HHHHhcCCCCCHHHHHHHhCCC-Cchh
Confidence 4556666799999999999998 4543
No 88
>PF07707 BACK: BTB And C-terminal Kelch; InterPro: IPR011705 This domain is found associated with (IPR000210 from INTERPRO) and (IPR006652 from INTERPRO). BTB (broad-complex, tramtrack and bric a brac) is a Kelch related domain, also known as the POZ domain []. BTB proteins are divided into subgroups depending on what domain lies at the C terminus. Despite the divergence in sequences, the BTB fold is highly conserved. BTB-Kelch proteins have Kelch repeats that form a beta-propeller that can interact with actin filaments []. BTB and C-terminal Kelch (BACK) together constitute a novel conserved domain, which is thought to have a possible role in substrate orientation in Cullin3-based E3 ligase complexes. Four domains, namely the BTB domain, a kelch domain, a BACK domain, and an intervening region (IVR) make up the aryl hydrocarbon receptor (AHR); a ligand-activated transcription factor []. This entry represents the domain associated with BTB and Kelch.; PDB: 3HVE_A 2EQX_A 3I3N_A 4AP2_A 4APF_A.
Probab=21.22 E-value=1e+02 Score=20.01 Aligned_cols=41 Identities=7% Similarity=0.109 Sum_probs=31.2
Q ss_pred HHHHhhhcccCchhHHHHHHHHHHHHhc---------CCCHHHHHhhcCC
Q 030962 107 FDLILAANYLNIKGLLDLTCQTVADMIK---------GKTPEEIRKTFNI 147 (168)
Q Consensus 107 ~~Ll~AA~~L~I~~L~~~~~~~ia~~i~---------~ks~eeir~~f~i 147 (168)
+++...|..++...|.+.|-++|+..+. ..+.+++..+++=
T Consensus 2 ~~i~~~A~~~~~~~L~~~~~~~i~~nf~~v~~~~~f~~L~~~~l~~iL~~ 51 (103)
T PF07707_consen 2 LSIYRLAEKYGLEELAEACLRFIAKNFNEVSKSDEFLELPFDQLIEILSS 51 (103)
T ss_dssp HHHHHHHHHTT-HHHHHHHHHHHHHTHHHHTTSHHHHCS-HHHHHHHHHT
T ss_pred hhHHHHHHHcChHHHHHHHHHHHHHHHHHHccchhhhcCCHHHHHHHHhc
Confidence 5788899999999999999999886554 3567777777764
No 89
>PF11338 DUF3140: Protein of unknown function (DUF3140); InterPro: IPR021487 Some members in this family of proteins are annotated as DNA binding proteins. No function is currently known.
Probab=20.80 E-value=75 Score=21.55 Aligned_cols=22 Identities=32% Similarity=0.452 Sum_probs=18.0
Q ss_pred cCCCCHHHHHHHHHHHHhccCC
Q 030962 45 LPNVTGKILAKVVEYCKKHVEV 66 (168)
Q Consensus 45 l~~i~s~~L~~Ii~wc~~h~~~ 66 (168)
|.+=.-..|++|+.||+.|...
T Consensus 54 ltddD~~hMrkVV~yv~rhlaq 75 (92)
T PF11338_consen 54 LTDDDYEHMRKVVGYVKRHLAQ 75 (92)
T ss_pred CCHHHHHHHHHHHHHHHHHHhc
Confidence 4455667899999999999876
No 90
>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=20.74 E-value=1.5e+02 Score=17.43 Aligned_cols=23 Identities=17% Similarity=0.327 Sum_probs=16.5
Q ss_pred HHHHHHHhcCCCHHHHHhhcCCC
Q 030962 126 CQTVADMIKGKTPEEIRKTFNIK 148 (168)
Q Consensus 126 ~~~ia~~i~~ks~eeir~~f~i~ 148 (168)
...+.-+..|++..||-..+|+.
T Consensus 9 ~~vl~~l~~G~~~~eIA~~l~is 31 (58)
T PF00196_consen 9 LEVLRLLAQGMSNKEIAEELGIS 31 (58)
T ss_dssp HHHHHHHHTTS-HHHHHHHHTSH
T ss_pred HHHHHHHHhcCCcchhHHhcCcc
Confidence 34455667899999998888885
No 91
>PF09382 RQC: RQC domain; InterPro: IPR018982 This entry represents the RQC domain, which is a DNA-binding domain found only in RecQ family enzymes. RecQ family helicases can unwind G4 DNA, and play important roles at G-rich domains of the genome, including the telomeres, rDNA, and immunoglobulin switch regions. This domain has a helix-turn-helix structure and acts as a high affinity G4 DNA binding domain []. Binding of RecQ to Holliday junctions involves both the RQC and the HRDC domains.; GO: 0043140 ATP-dependent 3'-5' DNA helicase activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1OYW_A 1OYY_A 3AAF_A 2AXL_A 2V1X_B 2WWY_B.
Probab=20.74 E-value=1.5e+02 Score=19.62 Aligned_cols=39 Identities=23% Similarity=0.530 Sum_probs=27.2
Q ss_pred HHHHHHHHHHhcCCCHHHHHh-------hcCCCCCCCHHHHHHHHH
Q 030962 123 DLTCQTVADMIKGKTPEEIRK-------TFNIKNDFTPEEEEEVRR 161 (168)
Q Consensus 123 ~~~~~~ia~~i~~ks~eeir~-------~f~i~~d~t~ee~~~i~~ 161 (168)
.++...+++.++|.....|++ .||+-.+++..+.+++-.
T Consensus 19 ~~~~~~ivdvlrGs~~~~i~~~~~~~l~~yG~gk~~~~~~~~~li~ 64 (106)
T PF09382_consen 19 RFGLSQIVDVLRGSKSKKIREKGHDQLPTYGIGKDMSKDDWERLIR 64 (106)
T ss_dssp -S-HHHHHHHHTT-S-CCCHHTTGGGSTTTTTTTTS-HHHHHHHHH
T ss_pred cccHHHHHHHHHhccchhhhhcCCCcCcccCCcccCCHHHHHHHHH
Confidence 567778888999987777665 599999999888887654
No 92
>PF10507 DUF2453: Protein of unknown function (DUF2453); InterPro: IPR019537 The function of these transmembrane protein is not known.
Probab=20.60 E-value=2.3e+02 Score=19.94 Aligned_cols=39 Identities=13% Similarity=0.381 Sum_probs=29.1
Q ss_pred hHHHHHHHHHHHHhcC-------CCHHHHHhhcCCCCC-CCHHHHHH
Q 030962 120 GLLDLTCQTVADMIKG-------KTPEEIRKTFNIKND-FTPEEEEE 158 (168)
Q Consensus 120 ~L~~~~~~~ia~~i~~-------ks~eeir~~f~i~~d-~t~ee~~~ 158 (168)
+|-.++++.+.+.+++ ...|.+.+.+|++.. +|++|.+.
T Consensus 34 giStmAAAalGN~vSDv~Gi~~~~~vE~~~~rlg~~~P~Lt~~Q~~~ 80 (111)
T PF10507_consen 34 GISTMAAAALGNLVSDVAGIGLGGYVERLAQRLGLKAPVLTPAQLNS 80 (111)
T ss_pred hHHHHHHHHHhhhhhhhhhhHHHHHHHHHHHHhCCCCCCCCHHHHhC
Confidence 4555677777777765 458999999999976 99988654
No 93
>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=20.21 E-value=1.7e+02 Score=20.21 Aligned_cols=38 Identities=24% Similarity=0.367 Sum_probs=26.2
Q ss_pred HHHhhhcccCchhHHHHHHH-HHHHHhcCCCHHHHHhhc
Q 030962 108 DLILAANYLNIKGLLDLTCQ-TVADMIKGKTPEEIRKTF 145 (168)
Q Consensus 108 ~Ll~AA~~L~I~~L~~~~~~-~ia~~i~~ks~eeir~~f 145 (168)
+.+..+.|-.-=..+..++. .+++++.||+.+|+..+.
T Consensus 46 ~~I~d~~f~~~GC~i~~Asas~~~~~~~Gk~~~ea~~i~ 84 (123)
T cd06664 46 GRITDAKFQGFGCAISIASASLLTELIKGKTLDEALKLL 84 (123)
T ss_pred CEEEEEEEEecCcHHHHHHHHHHHHHHcCCcHHHHHHHH
Confidence 45666666655555555544 667999999999998754
No 94
>PHA02790 Kelch-like protein; Provisional
Probab=20.11 E-value=82 Score=27.44 Aligned_cols=40 Identities=13% Similarity=0.098 Sum_probs=34.0
Q ss_pred hccc--cchHHHHHHHhhhcccCchhHHHHHHHHHHHHhcCC
Q 030962 97 DFVK--VDQATLFDLILAANYLNIKGLLDLTCQTVADMIKGK 136 (168)
Q Consensus 97 eFl~--~~~~~l~~Ll~AA~~L~I~~L~~~~~~~ia~~i~~k 136 (168)
+|+. ++.++-+++...|...+.+.|.+.+-++|.+.+..-
T Consensus 114 ~fL~~~l~~~NCl~i~~~A~~y~~~~L~~~a~~fi~~nF~~v 155 (480)
T PHA02790 114 NFILRDFRKEYCVECYMMGIEYGLSNLLCHTKDFIAKHFLEL 155 (480)
T ss_pred HHHHhhCCcchHHHHHHHHHHhCHHHHHHHHHHHHHHhHHHH
Confidence 4443 788999999999999999999999999988777653
Done!