Query 038597
Match_columns 161
No_of_seqs 119 out of 759
Neff 8.0
Searched_HMMs 46136
Date Fri Mar 29 12:38:23 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/038597.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/038597hhsearch_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 6E-48 1.3E-52 284.5 15.9 152 4-160 4-162 (162)
2 COG5201 SKP1 SCF ubiquitin lig 100.0 1.1E-45 2.3E-50 258.6 15.2 151 5-160 2-157 (158)
3 PF01466 Skp1: Skp1 family, di 100.0 1.2E-30 2.6E-35 172.0 8.5 78 80-160 1-78 (78)
4 smart00512 Skp1 Found in Skp1 99.9 5E-27 1.1E-31 162.6 10.6 98 5-110 2-104 (104)
5 PF03931 Skp1_POZ: Skp1 family 99.8 5.1E-19 1.1E-23 111.5 4.5 59 5-65 1-61 (62)
6 KOG3473 RNA polymerase II tran 99.7 2.2E-16 4.7E-21 105.9 7.7 91 4-110 16-112 (112)
7 PHA02713 hypothetical protein; 98.7 8.4E-08 1.8E-12 83.9 10.2 101 5-134 26-132 (557)
8 PF00651 BTB: BTB/POZ domain; 98.7 2E-07 4.3E-12 63.8 8.4 92 5-123 11-109 (111)
9 PHA03098 kelch-like protein; P 98.4 1.8E-06 4E-11 74.7 10.2 97 6-129 11-109 (534)
10 PHA02790 Kelch-like protein; P 98.4 9.5E-07 2E-11 75.9 7.1 91 11-128 27-123 (480)
11 smart00225 BTB Broad-Complex, 98.4 1.7E-06 3.6E-11 56.0 6.3 81 11-118 5-90 (90)
12 KOG4441 Proteins containing BT 98.2 4.2E-06 9.1E-11 73.5 8.0 92 7-126 39-135 (571)
13 KOG4682 Uncharacterized conser 96.0 0.0096 2.1E-07 50.0 4.4 103 12-144 76-186 (488)
14 KOG2716 Polymerase delta-inter 95.7 0.18 4E-06 39.5 10.1 101 2-128 2-108 (230)
15 KOG4350 Uncharacterized conser 95.7 0.098 2.1E-06 44.4 9.0 117 6-135 46-182 (620)
16 KOG0783 Uncharacterized conser 94.5 0.1 2.2E-06 47.8 6.3 108 7-135 713-825 (1267)
17 KOG3433 Protein involved in me 93.6 0.14 3E-06 38.7 4.4 37 103-144 162-200 (203)
18 PF11822 DUF3342: Domain of un 91.8 0.36 7.8E-06 39.6 4.9 86 14-126 13-105 (317)
19 COG5124 Protein predicted to b 91.6 0.17 3.7E-06 38.0 2.7 31 109-144 174-204 (209)
20 PF02214 BTB_2: BTB/POZ domain 84.5 0.65 1.4E-05 30.7 1.7 79 13-117 6-94 (94)
21 PF03962 Mnd1: Mnd1 family; I 80.6 1.9 4.1E-05 32.8 3.1 41 99-144 145-187 (188)
22 KOG2075 Topoisomerase TOP1-int 65.5 30 0.00065 30.3 6.9 112 15-126 129-251 (521)
23 PF07928 Vps54: Vps54-like pro 63.4 2.4 5.1E-05 30.5 0.0 43 13-60 1-44 (135)
24 KOG1665 AFH1-interacting prote 59.4 14 0.00031 29.2 3.7 88 5-119 9-105 (302)
25 PRK05365 malonic semialdehyde 59.1 6.5 0.00014 29.5 1.8 34 100-143 130-163 (195)
26 PF02519 Auxin_inducible: Auxi 56.4 44 0.00095 22.7 5.3 54 6-60 40-100 (100)
27 cd02148 Nitroreductase_5 Nitro 56.2 7.3 0.00016 28.9 1.6 34 100-143 123-156 (185)
28 KOG0511 Ankyrin repeat protein 55.5 78 0.0017 27.1 7.5 104 15-126 301-431 (516)
29 PRK13503 transcriptional activ 52.6 1.1E+02 0.0023 23.8 9.2 78 49-141 170-250 (278)
30 KOG4350 Uncharacterized conser 52.4 31 0.00067 29.8 4.8 37 91-127 111-147 (620)
31 cd05029 S-100A6 S-100A6: S-100 51.1 31 0.00067 22.6 3.9 45 110-154 9-59 (88)
32 PF12556 CobS_N: Cobaltochelat 51.1 9.3 0.0002 21.1 1.1 12 133-144 14-25 (36)
33 PF11460 DUF3007: Protein of u 50.5 15 0.00033 25.2 2.3 24 129-155 79-102 (104)
34 PF03656 Pam16: Pam16; InterP 48.8 14 0.0003 26.4 1.9 25 124-148 51-75 (127)
35 PF13921 Myb_DNA-bind_6: Myb-l 48.5 29 0.00063 20.5 3.2 34 118-151 20-60 (60)
36 KOG4591 Uncharacterized conser 45.6 31 0.00067 26.9 3.5 19 42-60 107-126 (280)
37 PF05409 Peptidase_C30: Corona 44.8 42 0.00091 27.2 4.3 99 41-148 161-265 (293)
38 PF10075 PCI_Csn8: COP9 signal 44.8 45 0.00097 23.6 4.2 45 112-160 82-126 (143)
39 PRK11053 dihydropteridine redu 43.0 20 0.00043 27.3 2.2 36 98-143 147-183 (217)
40 PF04700 Baculo_gp41: Structur 41.4 1.1E+02 0.0023 23.3 5.7 45 21-68 57-102 (186)
41 PF11978 MVP_shoulder: Shoulde 41.1 24 0.00052 24.8 2.1 40 102-141 37-89 (118)
42 COG4957 Predicted transcriptio 41.1 25 0.00054 25.4 2.2 18 127-144 98-115 (148)
43 KOG3442 Uncharacterized conser 39.4 17 0.00036 25.9 1.1 32 126-160 54-85 (132)
44 PF10892 DUF2688: Protein of u 37.7 41 0.00089 20.5 2.5 24 130-153 30-55 (60)
45 PF09821 AAA_assoc_C: C-termin 37.4 29 0.00063 24.4 2.1 21 91-111 7-27 (120)
46 smart00385 CYCLIN domain prese 37.3 92 0.002 18.6 5.0 41 110-153 37-79 (83)
47 TIGR01999 iscU FeS cluster ass 35.2 45 0.00099 23.3 2.9 37 101-137 50-87 (124)
48 cd00167 SANT 'SWI3, ADA2, N-Co 35.2 40 0.00086 17.9 2.1 20 119-138 23-42 (45)
49 PF07671 DUF1601: Protein of u 35.1 38 0.00083 18.8 1.9 30 107-136 7-36 (37)
50 TIGR02476 BluB cob(II)yrinic a 35.0 32 0.00069 25.9 2.2 38 97-144 133-170 (205)
51 PF08154 NLE: NLE (NUC135) dom 34.3 61 0.0013 20.0 3.0 43 6-50 3-55 (65)
52 PF01592 NifU_N: NifU-like N t 34.3 56 0.0012 22.8 3.2 24 112-135 62-85 (126)
53 TIGR03419 NifU_clost FeS clust 33.9 70 0.0015 22.2 3.7 37 101-137 46-83 (121)
54 PRK11325 scaffold protein; Pro 33.7 64 0.0014 22.7 3.5 38 101-138 52-90 (127)
55 smart00717 SANT SANT SWI3, AD 33.5 44 0.00096 18.0 2.2 20 119-138 25-44 (49)
56 TIGR02698 CopY_TcrY copper tra 33.4 1.4E+02 0.003 21.0 5.2 38 117-154 76-113 (130)
57 PF08671 SinI: Anti-repressor 33.4 26 0.00056 18.5 1.0 13 126-138 15-27 (30)
58 PF13518 HTH_28: Helix-turn-he 32.7 71 0.0015 17.9 3.0 21 120-140 5-25 (52)
59 PF13798 PCYCGC: Protein of un 31.5 73 0.0016 23.6 3.5 24 113-136 117-140 (158)
60 smart00875 BACK BTB And C-term 31.1 1.4E+02 0.003 18.8 4.7 40 100-139 3-51 (101)
61 PF15063 TC1: Thyroid cancer p 30.4 53 0.0011 21.3 2.3 12 131-142 56-67 (79)
62 cd02144 iodotyrosine_dehalogen 29.8 44 0.00096 24.5 2.2 37 98-144 129-166 (193)
63 PHA03098 kelch-like protein; P 29.8 2.4E+02 0.0052 24.4 7.1 54 84-138 97-159 (534)
64 PF11198 DUF2857: Protein of u 29.6 1.1E+02 0.0023 23.0 4.2 51 92-142 57-116 (180)
65 PF05443 ROS_MUCR: ROS/MUCR tr 29.2 26 0.00057 25.1 0.8 18 127-144 94-111 (132)
66 PF00249 Myb_DNA-binding: Myb- 29.2 1.1E+02 0.0024 17.1 4.6 39 94-137 5-44 (48)
67 PF10507 DUF2453: Protein of u 28.5 1.3E+02 0.0029 20.9 4.1 38 112-149 34-79 (111)
68 cd02140 Nitroreductase_4 Nitro 27.7 50 0.0011 24.5 2.2 38 98-143 127-164 (192)
69 PF11197 DUF2835: Protein of u 27.5 68 0.0015 20.2 2.4 21 5-25 21-41 (68)
70 COG1710 Uncharacterized protei 27.2 45 0.00098 23.6 1.7 21 121-141 102-123 (139)
71 PRK09296 cysteine desufuration 26.7 1.3E+02 0.0028 21.6 4.1 34 112-145 76-117 (138)
72 PF02736 Myosin_N: Myosin N-te 26.6 62 0.0013 18.1 1.9 19 4-22 23-41 (42)
73 PF13384 HTH_23: Homeodomain-l 26.3 67 0.0014 18.0 2.1 15 126-140 16-30 (50)
74 PF09713 A_thal_3526: Plant pr 25.7 42 0.00091 20.3 1.1 33 127-159 12-48 (54)
75 COG0822 IscU NifU homolog invo 25.4 1.2E+02 0.0025 22.2 3.7 39 99-137 51-90 (150)
76 PRK13696 hypothetical protein; 25.4 1.8E+02 0.0038 18.1 4.1 38 112-154 24-61 (62)
77 cd06664 IscU_like Iron-sulfur 25.3 1.2E+02 0.0026 20.8 3.7 39 100-138 46-85 (123)
78 PRK15019 CsdA-binding activato 25.2 1.3E+02 0.0028 21.9 3.9 34 112-145 86-127 (147)
79 PF09382 RQC: RQC domain; Int 25.1 1.4E+02 0.0031 19.6 3.9 39 115-153 19-64 (106)
80 COG4049 Uncharacterized protei 25.0 56 0.0012 20.0 1.6 15 5-19 5-19 (65)
81 PF03750 DUF310: Protein of un 24.7 95 0.0021 21.6 3.0 32 108-140 8-41 (119)
82 PF03131 bZIP_Maf: bZIP Maf tr 24.5 97 0.0021 20.4 2.9 27 124-153 5-31 (92)
83 KOG4244 Failed axon connection 24.4 93 0.002 25.2 3.2 23 130-152 111-133 (281)
84 TIGR01589 A_thal_3526 uncharac 24.1 58 0.0012 19.9 1.5 30 130-159 22-51 (57)
85 PF00690 Cation_ATPase_N: Cati 24.0 1.2E+02 0.0026 18.4 3.1 29 127-155 3-33 (69)
86 cd03370 NADH_oxidase NADPH_oxi 23.6 55 0.0012 23.3 1.7 32 100-141 97-128 (156)
87 TIGR03391 FeS_syn_CsdE cystein 23.5 1.5E+02 0.0033 21.3 3.9 34 112-145 81-122 (138)
88 PF07707 BACK: BTB And C-termi 22.9 1.1E+02 0.0023 19.7 2.9 40 99-138 2-50 (103)
89 COG4224 Uncharacterized protei 22.9 79 0.0017 20.4 2.1 18 139-156 57-74 (77)
90 TIGR03147 cyt_nit_nrfF cytochr 22.9 80 0.0017 22.5 2.3 19 119-137 64-83 (126)
91 TIGR01994 SUF_scaf_2 SUF syste 22.9 1.4E+02 0.0031 21.1 3.7 38 101-138 50-88 (137)
92 PF06540 GMAP: Galanin message 22.8 56 0.0012 20.2 1.3 20 47-66 21-40 (62)
93 COG2996 Predicted RNA-bindinin 22.8 52 0.0011 26.7 1.5 16 126-141 244-260 (287)
94 PF00134 Cyclin_N: Cyclin, N-t 22.6 1.3E+02 0.0029 20.1 3.5 43 112-154 74-117 (127)
95 PF03883 DUF328: Protein of un 22.6 83 0.0018 24.6 2.6 29 117-145 30-58 (237)
96 PF00196 GerE: Bacterial regul 22.4 1.2E+02 0.0026 17.7 2.8 23 118-140 9-31 (58)
97 PF08661 Rep_fac-A_3: Replicat 22.3 1E+02 0.0023 20.8 2.8 57 3-60 33-103 (109)
98 PRK07394 hypothetical protein; 22.1 1.3E+02 0.0028 25.0 3.8 33 127-159 128-161 (342)
99 cd02138 Nitroreductase_2 Nitro 21.9 76 0.0016 23.3 2.2 38 97-144 107-144 (181)
100 TIGR03879 near_KaiC_dom probab 21.8 2.2E+02 0.0047 18.2 3.9 19 123-141 28-46 (73)
101 smart00421 HTH_LUXR helix_turn 21.7 1.3E+02 0.0029 16.5 2.9 18 124-141 15-32 (58)
102 PF02796 HTH_7: Helix-turn-hel 21.6 1.3E+02 0.0029 16.8 2.7 16 125-140 19-34 (45)
103 cd00068 GGL G protein gamma su 20.9 1.1E+02 0.0024 18.3 2.4 22 41-67 18-39 (57)
104 PF00382 TFIIB: Transcription 20.7 2.1E+02 0.0047 17.4 5.9 44 97-140 17-67 (71)
105 TIGR03553 F420_FbiB_CTERM F420 20.4 63 0.0014 23.8 1.5 38 97-144 126-165 (194)
106 COG0549 ArcC Carbamate kinase 20.2 70 0.0015 26.2 1.7 18 143-160 135-152 (312)
107 cd02145 BluB Subfamily of the 20.2 63 0.0014 24.0 1.4 36 98-143 125-160 (196)
108 PF07638 Sigma70_ECF: ECF sigm 20.1 1.9E+02 0.0042 21.3 4.1 47 93-141 118-165 (185)
No 1
>KOG1724 consensus SCF ubiquitin ligase, Skp1 component [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=6e-48 Score=284.52 Aligned_cols=152 Identities=49% Similarity=0.830 Sum_probs=138.1
Q ss_pred CCeEEEEeCCCCEEEecHHHHHHHHHHHHHhhhcc-CCC--ccccc-ccHHHHHHHHHHhhcccccCCCCCCCCc---ch
Q 038597 4 TSTVKLRSGDNEVFEVEKQVMIQSGTIRNMIEDDA-ADG--EIPLQ-ISSRNLAKVVEWCKCMQHRDRNNNNDNK---EE 76 (161)
Q Consensus 4 ~~~i~l~s~Dg~~~~v~~~~a~~S~~l~~~~~~~~-~~~--~I~l~-v~s~~L~~Ii~y~~~~~h~~~~~~~~~~---~~ 76 (161)
.++|+|+|+||++|+|+.++|++|.+|++++.+.| ... +|||| |+|.||++||+||+ ||+++++...+. +.
T Consensus 4 ~~~ikL~SsDG~~f~ve~~~a~~s~~i~~~~~~~~~~~~~~~IPl~nV~~~iL~kVIewC~--~Hk~d~~~~~~~~~~~~ 81 (162)
T KOG1724|consen 4 KKKIKLESSDGEIFEVEEEVARQSQTISAHMIEDGCADENDPIPLPNVTSKILKKVIEWCK--KHKDDDPANPEDKELPE 81 (162)
T ss_pred CCeEEEEccCCceeehhHHHHHHhHHHHHHHHHcCCCccCCccccCccCHHHHHHHHHHHH--Hcccccccccccccccc
Confidence 37999999999999999999999999999998764 334 89999 99999999999999 999876543321 23
Q ss_pred hhhHHHHHHhhhhhhcCChHHHHHHHHhhccCCchHHHHHHHHHHHHHHcCCCHHHHHhHcCCCCCCCHHHHHHHHHhcC
Q 038597 77 EEEEEEWEKKFDEEVSEDKDLHFGLLLAANYLEIPALLHRLCQLAADIVKGKTPEEIRRTFNIKKDFTPEEEEAVMDEHG 156 (161)
Q Consensus 77 ~~~~~~wd~~F~~~~~~~~~~l~~Ll~AA~~L~I~~L~~l~~~~ia~~i~gks~eeir~~f~i~~d~t~eee~~i~~e~~ 156 (161)
...++.||++| ++++...||+|+.||+||+|++|+++||+.+|++++||||+|||+.|||++|+||||+++++++|.
T Consensus 82 ~~~i~~WD~~F---lk~d~~tLfdli~AAnyLdi~gLl~~~ck~va~mikgktpeEir~~f~I~~d~t~eE~~~~~~e~~ 158 (162)
T KOG1724|consen 82 ETDIPEWDAEF---LKVDQGTLFDLILAANYLDIKGLLDLTCKTVANMIKGKTPEEIREIFNIENDETPEEEEAIRKENE 158 (162)
T ss_pred cCCccHHHHHH---HhcCHHHHHHHHHHhhhcccHHHHHHHHHHHHHHHccCCHHHHHHHcCCCCCCChhHHHHHhhccc
Confidence 44599999999 889999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCC
Q 038597 157 WAFH 160 (161)
Q Consensus 157 w~~~ 160 (161)
|+|+
T Consensus 159 ~~~~ 162 (162)
T KOG1724|consen 159 WAFE 162 (162)
T ss_pred cccC
Confidence 9985
No 2
>COG5201 SKP1 SCF ubiquitin ligase, SKP1 component [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=1.1e-45 Score=258.57 Aligned_cols=151 Identities=38% Similarity=0.688 Sum_probs=136.7
Q ss_pred CeEEEEeCCCCEEEecHHHHHHHHHHHHHhhhcc-CCCccccc-ccHHHHHHHHHHhhcccccCCCCCCCCc---chhhh
Q 038597 5 STVKLRSGDNEVFEVEKQVMIQSGTIRNMIEDDA-ADGEIPLQ-ISSRNLAKVVEWCKCMQHRDRNNNNDNK---EEEEE 79 (161)
Q Consensus 5 ~~i~l~s~Dg~~~~v~~~~a~~S~~l~~~~~~~~-~~~~I~l~-v~s~~L~~Ii~y~~~~~h~~~~~~~~~~---~~~~~ 79 (161)
++|.|.|.||++|.|+..+|..|-+|++|+.+.+ .+.|||+| |+|.+|.+|++||+ ||.....+.... .....
T Consensus 2 s~i~l~s~dge~F~vd~~iAerSiLikN~l~d~~~~n~p~p~pnVrSsvl~kv~ew~e--hh~~s~sede~d~~~rks~p 79 (158)
T COG5201 2 SMIELESIDGEIFRVDENIAERSILIKNMLCDSTACNYPIPAPNVRSSVLMKVQEWME--HHTSSLSEDENDLEIRKSKP 79 (158)
T ss_pred CceEEEecCCcEEEehHHHHHHHHHHHHHhccccccCCCCcccchhHHHHHHHHHHHH--hccccCCCccChHhhhccCC
Confidence 4799999999999999999999999999998764 46889999 99999999999999 998754433321 22345
Q ss_pred HHHHHHhhhhhhcCChHHHHHHHHhhccCCchHHHHHHHHHHHHHHcCCCHHHHHhHcCCCCCCCHHHHHHHHHhcCCCC
Q 038597 80 EEEWEKKFDEEVSEDKDLHFGLLLAANYLEIPALLHRLCQLAADIVKGKTPEEIRRTFNIKKDFTPEEEEAVMDEHGWAF 159 (161)
Q Consensus 80 ~~~wd~~F~~~~~~~~~~l~~Ll~AA~~L~I~~L~~l~~~~ia~~i~gks~eeir~~f~i~~d~t~eee~~i~~e~~w~~ 159 (161)
.+.||+.| +.+|++.|++++.|||||+|++|+++||+.||++|+||||+|||++|||++||||||+++|++||.|+.
T Consensus 80 ~D~wdr~F---m~vDqemL~eI~laaNYL~ikpLLd~gCKivaemirgkSpeeir~tfni~ndfTpEEe~~irkEnEWae 156 (158)
T COG5201 80 SDFWDRFF---MEVDQEMLLEICLAANYLEIKPLLDLGCKIVAEMIRGKSPEEIRETFNIENDFTPEEERRIRKENEWAE 156 (158)
T ss_pred ccHHHHHH---HHhhHHHHHHHHHhhccccchHHHHHHHHHHHHHHccCCHHHHHHHhCCCCCCCHHHHHHHHHhccccc
Confidence 67899999 899999999999999999999999999999999999999999999999999999999999999999997
Q ss_pred C
Q 038597 160 H 160 (161)
Q Consensus 160 ~ 160 (161)
+
T Consensus 157 d 157 (158)
T COG5201 157 D 157 (158)
T ss_pred c
Confidence 6
No 3
>PF01466 Skp1: Skp1 family, dimerisation domain; InterPro: IPR016072 SKP1 (together with SKP2) was identified as an essential component of the cyclin A-CDK2 S phase kinase complex []. It was found to bind several F-box containing proteins (e.g., Cdc4, Skp2, cyclin F) and to be involved in the ubiquitin protein degradation pathway. A yeast homologue of SKP1 (P52286) was identified in the centromere bound kinetochore complex [] and is also involved in the ubiquitin pathway []. In Dictyostelium discoideum (Slime mold) FP21 was shown to be glycosylated in the cytosol and has homology to SKP1 []. This entry represents a dimerisation domain found at the C-terminal of SKP1 proteins [], as well as in subunit D of the centromere DNA-binding protein complex Cbf3 []. This domain is multi-helical in structure, and consists of an interlocked herterodimer in F-box proteins.; GO: 0006511 ubiquitin-dependent protein catabolic process; PDB: 2P1O_A 3OGL_G 3OGM_A 3C6O_A 2P1N_A 2P1Q_A 3OGK_I 3C6N_A 3C6P_A 2P1P_A ....
Probab=99.97 E-value=1.2e-30 Score=171.97 Aligned_cols=78 Identities=50% Similarity=0.907 Sum_probs=68.5
Q ss_pred HHHHHHhhhhhhcCChHHHHHHHHhhccCCchHHHHHHHHHHHHHHcCCCHHHHHhHcCCCCCCCHHHHHHHHHhcCCCC
Q 038597 80 EEEWEKKFDEEVSEDKDLHFGLLLAANYLEIPALLHRLCQLAADIVKGKTPEEIRRTFNIKKDFTPEEEEAVMDEHGWAF 159 (161)
Q Consensus 80 ~~~wd~~F~~~~~~~~~~l~~Ll~AA~~L~I~~L~~l~~~~ia~~i~gks~eeir~~f~i~~d~t~eee~~i~~e~~w~~ 159 (161)
+++||++| ++++.+.|++|+.||+||+|++|+++||++||.+++|||++|||++|||++|+|+||+++++++|+|+|
T Consensus 1 l~~wD~~F---~~~~~~~L~~l~~AA~yL~I~~L~~~~~~~iA~~i~gks~eeir~~fgi~~d~t~eee~~i~~e~~w~~ 77 (78)
T PF01466_consen 1 LPEWDQEF---LDVDNDELFDLLNAANYLDIKGLLDLCCKYIANMIKGKSPEEIRKYFGIENDLTPEEEEEIRKENEWAF 77 (78)
T ss_dssp HHHHHHHH---T-S-HHHHHHHHHHHHHHT-HHHHHHHHHHHHHHHTTS-HHHHHHHHT---TSSHHHHHHHHHHCCCTB
T ss_pred CCHHHHHH---HHcCHHHHHHHHHHHHHHcchHHHHHHHHHHHHHhcCCCHHHHHHHcCCCCCCCHHHHHHHHHHcchhc
Confidence 57999999 789999999999999999999999999999999999999999999999999999999999999999998
Q ss_pred C
Q 038597 160 H 160 (161)
Q Consensus 160 ~ 160 (161)
+
T Consensus 78 ~ 78 (78)
T PF01466_consen 78 E 78 (78)
T ss_dssp -
T ss_pred C
Confidence 6
No 4
>smart00512 Skp1 Found in Skp1 protein family. Family of Skp1 (kinetochore protein required for cell cycle progression) and elongin C (subunit of RNA polymerase II transcription factor SIII) homologues.
Probab=99.94 E-value=5e-27 Score=162.63 Aligned_cols=98 Identities=44% Similarity=0.736 Sum_probs=86.7
Q ss_pred CeEEEEeCCCCEEEecHHHHHHHHHHHHHhhhccCC----Cccccc-ccHHHHHHHHHHhhcccccCCCCCCCCcchhhh
Q 038597 5 STVKLRSGDNEVFEVEKQVMIQSGTIRNMIEDDAAD----GEIPLQ-ISSRNLAKVVEWCKCMQHRDRNNNNDNKEEEEE 79 (161)
Q Consensus 5 ~~i~l~s~Dg~~~~v~~~~a~~S~~l~~~~~~~~~~----~~I~l~-v~s~~L~~Ii~y~~~~~h~~~~~~~~~~~~~~~ 79 (161)
++++|+|+||++|.|++.+|++|++|++|+++.|.. .+||+| |++.+|++|++||+ ||+.++.+... ...
T Consensus 2 ~~v~L~S~Dg~~f~v~~~~a~~S~~i~~~l~~~~~~~~~~~~Ipl~~v~~~~L~~Vi~yc~--~h~~~~~~~~~---~~~ 76 (104)
T smart00512 2 KYIKLISSDGEVFEVEREVARQSKTIKAMIEDLGVDDENNNPIPLPNVTSKILSKVIEYCE--HHVDDPPSVAD---KDD 76 (104)
T ss_pred CeEEEEeCCCCEEEecHHHHHHHHHHHHHHHccCcccCCCCCccCCCcCHHHHHHHHHHHH--HcccCCCCccc---ccc
Confidence 589999999999999999999999999999976532 489999 99999999999999 99987654321 145
Q ss_pred HHHHHHhhhhhhcCChHHHHHHHHhhccCCc
Q 038597 80 EEEWEKKFDEEVSEDKDLHFGLLLAANYLEI 110 (161)
Q Consensus 80 ~~~wd~~F~~~~~~~~~~l~~Ll~AA~~L~I 110 (161)
+++||.+| ++++.+.|++|+.||+||+|
T Consensus 77 ~~~wD~~F---~~~d~~~l~dLl~AAnyL~I 104 (104)
T smart00512 77 IPTWDAEF---LKIDQETLFELILAANYLDI 104 (104)
T ss_pred ccHHHHHH---HcCCHHHHHHHHHHHHhhCC
Confidence 89999999 78999999999999999997
No 5
>PF03931 Skp1_POZ: Skp1 family, tetramerisation domain; InterPro: IPR016073 SKP1 (together with SKP2) was identified as an essential component of the cyclin A-CDK2 S phase kinase complex []. It was found to bind several F-box containing proteins (e.g., Cdc4, Skp2, cyclin F) and to be involved in the ubiquitin protein degradation pathway. A yeast homologue of SKP1 (P52286) was identified in the centromere bound kinetochore complex [] and is also involved in the ubiquitin pathway []. In Dictyostelium discoideum (Slime mold) FP21 was shown to be glycosylated in the cytosol and has homology to SKP1 []. This entry represents a POZ domain with a core structure consisting of beta(2)/alpha(2)/beta(2)/alpha(2) in two layers, alpha/beta. This domain is found at the N-terminal of SKP1 proteins [] as well as in subunit D of the centromere DNA-binding protein complex Cbf3 []. ; GO: 0006511 ubiquitin-dependent protein catabolic process; PDB: 1LM8_C 2XAI_E 1VCB_E 3ZRC_K 3ZRF_E 3DCG_B 2C9W_C 1LQB_B 2IZV_C 1HV2_A ....
Probab=99.76 E-value=5.1e-19 Score=111.54 Aligned_cols=59 Identities=49% Similarity=0.779 Sum_probs=53.0
Q ss_pred CeEEEEeCCCCEEEecHHHHHHHHHHHHHhhhccCCC-ccccc-ccHHHHHHHHHHhhccccc
Q 038597 5 STVKLRSGDNEVFEVEKQVMIQSGTIRNMIEDDAADG-EIPLQ-ISSRNLAKVVEWCKCMQHR 65 (161)
Q Consensus 5 ~~i~l~s~Dg~~~~v~~~~a~~S~~l~~~~~~~~~~~-~I~l~-v~s~~L~~Ii~y~~~~~h~ 65 (161)
.+|+|+|+||++|.|++++|++|++|++|+++.+... +||+| |++++|++|++||+ ||+
T Consensus 1 ~~v~L~SsDg~~f~V~~~~a~~S~~i~~ml~~~~~~~~~Ipl~~v~~~~L~kViewc~--~H~ 61 (62)
T PF03931_consen 1 MYVKLVSSDGQEFEVSREAAKQSKTIKNMLEDLGDEDEPIPLPNVSSRILKKVIEWCE--HHK 61 (62)
T ss_dssp -EEEEEETTSEEEEEEHHHHTTSHHHHHHHHCTCCCGTEEEETTS-HHHHHHHHHHHH--HHH
T ss_pred CEEEEEcCCCCEEEeeHHHHHHhHHHHHHHhhhcccccccccCccCHHHHHHHHHHHH--hcC
Confidence 3689999999999999999999999999999876544 59999 99999999999999 986
No 6
>KOG3473 consensus RNA polymerase II transcription elongation factor Elongin/SIII, subunit elongin C [Transcription]
Probab=99.67 E-value=2.2e-16 Score=105.86 Aligned_cols=91 Identities=32% Similarity=0.460 Sum_probs=76.0
Q ss_pred CCeEEEEeCCCCEEEecHHHHHHHHHHHHHhhhcc-----CCCccccc-ccHHHHHHHHHHhhcccccCCCCCCCCcchh
Q 038597 4 TSTVKLRSGDNEVFEVEKQVMIQSGTIRNMIEDDA-----ADGEIPLQ-ISSRNLAKVVEWCKCMQHRDRNNNNDNKEEE 77 (161)
Q Consensus 4 ~~~i~l~s~Dg~~~~v~~~~a~~S~~l~~~~~~~~-----~~~~I~l~-v~s~~L~~Ii~y~~~~~h~~~~~~~~~~~~~ 77 (161)
+.+++|+|+||.+|.|.+.+|..|++||.|+.+.+ ..+.+.++ |+|.+|+||++|+.|+..+....
T Consensus 16 ~~yVkLvS~Ddhefiikre~AmtSgTiraml~gpg~~se~~~n~v~f~di~shiLeKvc~Yl~Yk~rY~~~s-------- 87 (112)
T KOG3473|consen 16 SMYVKLVSSDDHEFIIKREHAMTSGTIRAMLSGPGVFSEAEKNEVYFRDIPSHILEKVCEYLAYKVRYTNSS-------- 87 (112)
T ss_pred hhheEeecCCCcEEEEeehhhhhhhHHHHHHcCCccccccccceEEeccchHHHHHHHHHHhhheeeecccc--------
Confidence 47999999999999999999999999999999754 45789999 99999999999999663332211
Q ss_pred hhHHHHHHhhhhhhcCChHHHHHHHHhhccCCc
Q 038597 78 EEEEEWEKKFDEEVSEDKDLHFGLLLAANYLEI 110 (161)
Q Consensus 78 ~~~~~wd~~F~~~~~~~~~~l~~Ll~AA~~L~I 110 (161)
..++ +| .+.++..++|+.||+||++
T Consensus 88 ~eiP----eF----~IppemaleLL~aAn~Lec 112 (112)
T KOG3473|consen 88 TEIP----EF----DIPPEMALELLMAANYLEC 112 (112)
T ss_pred ccCC----CC----CCCHHHHHHHHHHhhhhcC
Confidence 2233 35 8999999999999999974
No 7
>PHA02713 hypothetical protein; Provisional
Probab=98.73 E-value=8.4e-08 Score=83.86 Aligned_cols=101 Identities=18% Similarity=0.201 Sum_probs=82.3
Q ss_pred CeEEEEeCCCCEEEecHHHH-HHHHHHHHHhhhc-c---CCCccccc-ccHHHHHHHHHHhhcccccCCCCCCCCcchhh
Q 038597 5 STVKLRSGDNEVFEVEKQVM-IQSGTIRNMIEDD-A---ADGEIPLQ-ISSRNLAKVVEWCKCMQHRDRNNNNDNKEEEE 78 (161)
Q Consensus 5 ~~i~l~s~Dg~~~~v~~~~a-~~S~~l~~~~~~~-~---~~~~I~l~-v~s~~L~~Ii~y~~~~~h~~~~~~~~~~~~~~ 78 (161)
..++|...+|+.|.+++.++ ..|++++.|+.+. . ....|.|. ++..+|+.|++|++ ..
T Consensus 26 ~DV~L~v~~~~~f~~Hr~vLaa~S~YF~amF~~~~~e~~~~~~v~l~~v~~~~~~~ll~y~Y--t~-------------- 89 (557)
T PHA02713 26 CDVIITIGDGEEIKAHKTILAAGSKYFRTLFTTPMIIRDLVTRVNLQMFDKDAVKNIVQYLY--NR-------------- 89 (557)
T ss_pred CCEEEEeCCCCEEeehHHHHhhcCHHHHHHhcCCchhhccCceEEeccCCHHHHHHHHHHhc--CC--------------
Confidence 35788887899999999994 5899999999753 1 24579999 99999999999999 41
Q ss_pred hHHHHHHhhhhhhcCChHHHHHHHHhhccCCchHHHHHHHHHHHHHHcCCCHHHHH
Q 038597 79 EEEEWEKKFDEEVSEDKDLHFGLLLAANYLEIPALLHRLCQLAADIVKGKTPEEIR 134 (161)
Q Consensus 79 ~~~~wd~~F~~~~~~~~~~l~~Ll~AA~~L~I~~L~~l~~~~ia~~i~gks~eeir 134 (161)
.++.+.+.+|+.||++|+|+.|.+.||.++...+.-.+-=+|.
T Consensus 90 -------------~i~~~nv~~ll~aA~~lqi~~l~~~C~~~l~~~l~~~NCl~i~ 132 (557)
T PHA02713 90 -------------HISSMNVIDVLKCADYLLIDDLVTDCESYIKDYTNHDTCIYMY 132 (557)
T ss_pred -------------CCCHHHHHHHHHHHHHHCHHHHHHHHHHHHHhhCCccchHHHH
Confidence 1345678999999999999999999999998877765544444
No 8
>PF00651 BTB: BTB/POZ domain; InterPro: IPR013069 The BTB (for BR-C, ttk and bab) [] or POZ (for Pox virus and Zinc finger) [] domain is present near the N terminus of a fraction of zinc finger (IPR007087 from INTERPRO) proteins and in proteins that contain the IPR006652 from INTERPRO motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerisation and in some instances heteromeric dimerisation []. The structure of the dimerised PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule []. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT [, , ]. The POZ or BTB domain is also known as BR-C/Ttk or ZiN.; GO: 0005515 protein binding; PDB: 3M5B_A 1R28_B 3LBZ_A 3E4U_F 3BIM_B 1R2B_A 1R29_A 2VPK_A 2YY9_B 3GA1_A ....
Probab=98.66 E-value=2e-07 Score=63.85 Aligned_cols=92 Identities=26% Similarity=0.383 Sum_probs=74.5
Q ss_pred CeEEEEeCCCCEEEecHHHH-HHHHHHHHHhhhcc--CC--Cccccc-ccHHHHHHHHHHhhcccccCCCCCCCCcchhh
Q 038597 5 STVKLRSGDNEVFEVEKQVM-IQSGTIRNMIEDDA--AD--GEIPLQ-ISSRNLAKVVEWCKCMQHRDRNNNNDNKEEEE 78 (161)
Q Consensus 5 ~~i~l~s~Dg~~~~v~~~~a-~~S~~l~~~~~~~~--~~--~~I~l~-v~s~~L~~Ii~y~~~~~h~~~~~~~~~~~~~~ 78 (161)
..++|+..||+.|.|++.++ ..|+++++++...+ .. ..|+++ ++...++.+++||+ ...
T Consensus 11 ~D~~i~v~d~~~~~vhk~iL~~~S~~F~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~l~~~Y--~~~------------- 75 (111)
T PF00651_consen 11 SDVTIRVGDGKTFYVHKNILAARSPYFRNLFEGSKFKESTVPEISLPDVSPEAFEAFLEYMY--TGE------------- 75 (111)
T ss_dssp --EEEEETTTEEEEE-HHHHHHHBHHHHHHHTTTTSTTSSEEEEEETTSCHHHHHHHHHHHH--HSE-------------
T ss_pred CCEEEEECCCEEEeechhhhhccchhhhhccccccccccccccccccccccccccccccccc--CCc-------------
Confidence 56899999999999999995 67999999998762 22 358888 99999999999998 311
Q ss_pred hHHHHHHhhhhhhcCC-hHHHHHHHHhhccCCchHHHHHHHHHHHH
Q 038597 79 EEEEWEKKFDEEVSED-KDLHFGLLLAANYLEIPALLHRLCQLAAD 123 (161)
Q Consensus 79 ~~~~wd~~F~~~~~~~-~~~l~~Ll~AA~~L~I~~L~~l~~~~ia~ 123 (161)
+.++ .+.+.+++.+|++|+++.|.+.|+..+..
T Consensus 76 ------------~~~~~~~~~~~ll~lA~~~~~~~L~~~~~~~l~~ 109 (111)
T PF00651_consen 76 ------------IEINSDENVEELLELADKLQIPELKKACEKFLQE 109 (111)
T ss_dssp ------------EEEE-TTTHHHHHHHHHHTTBHHHHHHHHHHHHH
T ss_pred ------------ccCCHHHHHHHHHHHHHHhCcHHHHHHHHHHHHh
Confidence 1233 66789999999999999999999998865
No 9
>PHA03098 kelch-like protein; Provisional
Probab=98.43 E-value=1.8e-06 Score=74.66 Aligned_cols=97 Identities=18% Similarity=0.280 Sum_probs=75.4
Q ss_pred eEEEE-eCCCCEEEecHHHH-HHHHHHHHHhhhccCCCcccccccHHHHHHHHHHhhcccccCCCCCCCCcchhhhHHHH
Q 038597 6 TVKLR-SGDNEVFEVEKQVM-IQSGTIRNMIEDDAADGEIPLQISSRNLAKVVEWCKCMQHRDRNNNNDNKEEEEEEEEW 83 (161)
Q Consensus 6 ~i~l~-s~Dg~~~~v~~~~a-~~S~~l~~~~~~~~~~~~I~l~v~s~~L~~Ii~y~~~~~h~~~~~~~~~~~~~~~~~~w 83 (161)
.++|. ..+|+.|.+++.++ ..|++++.|+.+.-....|.++.+..+|+.|++|++ . +.
T Consensus 11 Dv~l~~~~~~~~~~~Hk~vLaa~S~yF~~mf~~~~~~~~i~l~~~~~~~~~~l~y~Y--t---g~--------------- 70 (534)
T PHA03098 11 DESIIIVNGGGIIKVHKIILSSSSEYFKKMFKNNFKENEINLNIDYDSFNEVIKYIY--T---GK--------------- 70 (534)
T ss_pred CEEEEEEcCCEEEEeHHHHHHhhhHHHHHHHhCCCCCceEEecCCHHHHHHHHHHhc--C---Cc---------------
Confidence 35555 46899999999995 569999999976422456777678999999999999 4 11
Q ss_pred HHhhhhhhcCChHHHHHHHHhhccCCchHHHHHHHHHHHHHHcCCC
Q 038597 84 EKKFDEEVSEDKDLHFGLLLAANYLEIPALLHRLCQLAADIVKGKT 129 (161)
Q Consensus 84 d~~F~~~~~~~~~~l~~Ll~AA~~L~I~~L~~l~~~~ia~~i~gks 129 (161)
+.++.+.+.+|+.||++|+++.|.++|+.++...+.-.+
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 345667788999999999999999999888877665444
No 10
>PHA02790 Kelch-like protein; Provisional
Probab=98.38 E-value=9.5e-07 Score=75.94 Aligned_cols=91 Identities=11% Similarity=0.090 Sum_probs=70.3
Q ss_pred eCCCCEEEecHHH-HHHHHHHHHHhhhc-cC-CCcccc---cccHHHHHHHHHHhhcccccCCCCCCCCcchhhhHHHHH
Q 038597 11 SGDNEVFEVEKQV-MIQSGTIRNMIEDD-AA-DGEIPL---QISSRNLAKVVEWCKCMQHRDRNNNNDNKEEEEEEEEWE 84 (161)
Q Consensus 11 s~Dg~~~~v~~~~-a~~S~~l~~~~~~~-~~-~~~I~l---~v~s~~L~~Ii~y~~~~~h~~~~~~~~~~~~~~~~~~wd 84 (161)
.--|+.|.+++.+ |..|++++.|+.+. .+ ...|.+ .|+..+|+.|++|++ . ..
T Consensus 27 ~~~~~~~~~HR~VLAa~S~YFraMF~~~~~Es~~~v~~~~~~v~~~~l~~lldy~Y--T---g~---------------- 85 (480)
T PHA02790 27 EAIGGNIIVNSTILKKLSPYFRTHLRQKYTKNKDPVTRVCLDLDIHSLTSIVIYSY--T---GK---------------- 85 (480)
T ss_pred EEcCcEEeeehhhhhhcCHHHHHHhcCCccccccceEEEecCcCHHHHHHHHHhhe--e---ee----------------
Confidence 3458899999999 66799999999753 11 223443 399999999999998 3 11
Q ss_pred HhhhhhhcCChHHHHHHHHhhccCCchHHHHHHHHHHHHHHcCC
Q 038597 85 KKFDEEVSEDKDLHFGLLLAANYLEIPALLHRLCQLAADIVKGK 128 (161)
Q Consensus 85 ~~F~~~~~~~~~~l~~Ll~AA~~L~I~~L~~l~~~~ia~~i~gk 128 (161)
+.++.+.+.+|+.||++|+|+.+++.||+++...+.-.
T Consensus 86 ------l~it~~nV~~ll~aA~~Lqi~~v~~~C~~fL~~~l~~~ 123 (480)
T PHA02790 86 ------VYIDSHNVVNLLRASILTSVEFIIYTCINFILRDFRKE 123 (480)
T ss_pred ------EEEecccHHHHHHHHHHhChHHHHHHHHHHHHhhCCcc
Confidence 45677789999999999999999999998887766543
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=1.7e-06 Score=55.99 Aligned_cols=81 Identities=22% Similarity=0.304 Sum_probs=65.5
Q ss_pred eCCCCEEEecHHHHH-HHHHHHHHhhhcc---CCCccccc-ccHHHHHHHHHHhhcccccCCCCCCCCcchhhhHHHHHH
Q 038597 11 SGDNEVFEVEKQVMI-QSGTIRNMIEDDA---ADGEIPLQ-ISSRNLAKVVEWCKCMQHRDRNNNNDNKEEEEEEEEWEK 85 (161)
Q Consensus 11 s~Dg~~~~v~~~~a~-~S~~l~~~~~~~~---~~~~I~l~-v~s~~L~~Ii~y~~~~~h~~~~~~~~~~~~~~~~~~wd~ 85 (161)
..+|+.|.+++.++. .|++++.++.... ....|+++ ++..+++.+++|++ .-.
T Consensus 5 ~v~~~~~~~h~~iL~~~s~~f~~~~~~~~~~~~~~~i~l~~~~~~~f~~~l~~ly--~~~-------------------- 62 (90)
T smart00225 5 VVGGKKFKAHKAVLAACSPYFKALFSGDFKESKKSEIYLDDVSPEDFRALLEFLY--TGK-------------------- 62 (90)
T ss_pred EECCEEEehHHHHHhhcCHHHHHHHcCCCccCCCCEEEecCCCHHHHHHHHHeec--Cce--------------------
Confidence 446799999999965 5999999998643 35678898 99999999999998 411
Q ss_pred hhhhhhcCChHHHHHHHHhhccCCchHHHHHHH
Q 038597 86 KFDEEVSEDKDLHFGLLLAANYLEIPALLHRLC 118 (161)
Q Consensus 86 ~F~~~~~~~~~~l~~Ll~AA~~L~I~~L~~l~~ 118 (161)
+.++...+.+++.+|++++++.|.+.|+
T Consensus 63 -----~~~~~~~~~~l~~~a~~~~~~~l~~~c~ 90 (90)
T smart00225 63 -----LDLPEENVEELLELADYLQIPGLVELCE 90 (90)
T ss_pred -----eecCHHHHHHHHHHHHHHCcHHHHhhhC
Confidence 2334447889999999999999999874
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=98.23 E-value=4.2e-06 Score=73.50 Aligned_cols=92 Identities=24% Similarity=0.377 Sum_probs=76.1
Q ss_pred EEEEeCCCCEEEecHHH-HHHHHHHHHHhhhc---cCCCccccc-ccHHHHHHHHHHhhcccccCCCCCCCCcchhhhHH
Q 038597 7 VKLRSGDNEVFEVEKQV-MIQSGTIRNMIEDD---AADGEIPLQ-ISSRNLAKVVEWCKCMQHRDRNNNNDNKEEEEEEE 81 (161)
Q Consensus 7 i~l~s~Dg~~~~v~~~~-a~~S~~l~~~~~~~---~~~~~I~l~-v~s~~L~~Ii~y~~~~~h~~~~~~~~~~~~~~~~~ 81 (161)
+.|...+ +.|.+++.+ |..|++++.|+... .....|.+. |+..+|+.+++|++ ...
T Consensus 39 v~L~v~~-~~~~aHR~VLAa~S~YFraMFt~~l~e~~~~~i~l~~v~~~~l~~ll~y~Y--t~~---------------- 99 (571)
T KOG4441|consen 39 VTLLVGD-REFPAHRVVLAACSPYFRAMFTSGLKESKQKEINLEGVDPETLELLLDYAY--TGK---------------- 99 (571)
T ss_pred EEEEECC-eeechHHHHHHhccHHHHHHhcCCcccccceEEEEecCCHHHHHHHHHHhh--cce----------------
Confidence 4455444 999999999 56799999999853 245789999 99999999999999 411
Q ss_pred HHHHhhhhhhcCChHHHHHHHHhhccCCchHHHHHHHHHHHHHHc
Q 038597 82 EWEKKFDEEVSEDKDLHFGLLLAANYLEIPALLHRLCQLAADIVK 126 (161)
Q Consensus 82 ~wd~~F~~~~~~~~~~l~~Ll~AA~~L~I~~L~~l~~~~ia~~i~ 126 (161)
+.++.+.+.+|+.||.+|+|..+++.||.++...+.
T Consensus 100 ---------i~i~~~nVq~ll~aA~~lQi~~v~~~C~~fL~~~l~ 135 (571)
T KOG4441|consen 100 ---------LEISEDNVQELLEAASLLQIPEVVDACCEFLESQLD 135 (571)
T ss_pred ---------EEechHhHHHHHHHHHHhhhHHHHHHHHHHHHhcCC
Confidence 567888999999999999999999999998876543
No 13
>KOG4682 consensus Uncharacterized conserved protein, contains BTB/POZ domain [General function prediction only]
Probab=96.02 E-value=0.0096 Score=50.05 Aligned_cols=103 Identities=19% Similarity=0.175 Sum_probs=77.9
Q ss_pred CCCCEEEecHHHHHHHHHHHHHhhhcc---CC----Cccccc-ccHHHHHHHHHHhhcccccCCCCCCCCcchhhhHHHH
Q 038597 12 GDNEVFEVEKQVMIQSGTIRNMIEDDA---AD----GEIPLQ-ISSRNLAKVVEWCKCMQHRDRNNNNDNKEEEEEEEEW 83 (161)
Q Consensus 12 ~Dg~~~~v~~~~a~~S~~l~~~~~~~~---~~----~~I~l~-v~s~~L~~Ii~y~~~~~h~~~~~~~~~~~~~~~~~~w 83 (161)
.=|.+..+++-.+.||+++..|+.+.- .. -.||=| |+...|..++-=++ + +
T Consensus 76 alg~eWrlHk~yL~QS~yf~smf~Gtw~es~~~iIqleI~Dp~Id~~al~~a~gsLY--~---d---------------- 134 (488)
T KOG4682|consen 76 ALGFEWRLHKPYLFQSEYFKSMFSGTWKESSMNIIQLEIPDPNIDVVALQVAFGSLY--R---D---------------- 134 (488)
T ss_pred hccceeeeeeeeeeccHHHHHHhccccChhhCceEEEEcCCCcccHHHHHHHHhhhh--h---h----------------
Confidence 348899999999999999999998752 11 245556 88888888777666 3 1
Q ss_pred HHhhhhhhcCChHHHHHHHHhhccCCchHHHHHHHHHHHHHHcCCCHHHHHhHcCCCCCCC
Q 038597 84 EKKFDEEVSEDKDLHFGLLLAANYLEIPALLHRLCQLAADIVKGKTPEEIRRTFNIKKDFT 144 (161)
Q Consensus 84 d~~F~~~~~~~~~~l~~Ll~AA~~L~I~~L~~l~~~~ia~~i~gks~eeir~~f~i~~d~t 144 (161)
++.++.+.+..++.||.+|..++|++-|...+...++-+| +.+++....-+.
T Consensus 135 ------EveI~l~dv~gvlAaA~~lqldgl~qrC~evMie~lspkt---a~~yYea~ckYg 186 (488)
T KOG4682|consen 135 ------EVEIKLSDVVGVLAAACLLQLDGLIQRCGEVMIETLSPKT---ACGYYEAACKYG 186 (488)
T ss_pred ------heeccHHHHHHHHHHHHHHHHhhHHHHHHHHHHHhcChhh---hhHhhhhhhhhh
Confidence 1578899999999999999999999999988877666555 455555544443
No 14
>KOG2716 consensus Polymerase delta-interacting protein PDIP1 and related proteins, contain BTB/POZ domain [Inorganic ion transport and metabolism]
Probab=95.70 E-value=0.18 Score=39.54 Aligned_cols=101 Identities=20% Similarity=0.344 Sum_probs=76.2
Q ss_pred CCCCeEEEEeCCCCEEEecHHHH-HHHHHHHHHhhhcc-----CCCcccccccHHHHHHHHHHhhcccccCCCCCCCCcc
Q 038597 2 ATTSTVKLRSGDNEVFEVEKQVM-IQSGTIRNMIEDDA-----ADGEIPLQISSRNLAKVVEWCKCMQHRDRNNNNDNKE 75 (161)
Q Consensus 2 ~~~~~i~l~s~Dg~~~~v~~~~a-~~S~~l~~~~~~~~-----~~~~I~l~v~s~~L~~Ii~y~~~~~h~~~~~~~~~~~ 75 (161)
..+..++|- --|.+|.-.+.-+ ++.+.++.|++..- ..+.|=+.=+..-+..|+.||+ - +..
T Consensus 2 ~~~~~vkLn-vGG~~F~Tsk~TLtk~dg~fk~m~e~~i~~~~d~s~~IFIDRSpKHF~~ILNfmR--d---Gdv------ 69 (230)
T KOG2716|consen 2 SMSETVKLN-VGGTIFKTSKSTLTKFDGFFKTMLETDIPVEKDESGCIFIDRSPKHFDTILNFMR--D---GDV------ 69 (230)
T ss_pred CccceEEEe-cCCeEEEeehhhhhhhhhHHHHHhhcCCccccCCcCcEEecCChhHHHHHHHhhh--c---ccc------
Confidence 445667753 3477999888884 67999999998641 2244555567889999999999 2 211
Q ss_pred hhhhHHHHHHhhhhhhcCChHHHHHHHHhhccCCchHHHHHHHHHHHHHHcCC
Q 038597 76 EEEEEEEWEKKFDEEVSEDKDLHFGLLLAANYLEIPALLHRLCQLAADIVKGK 128 (161)
Q Consensus 76 ~~~~~~~wd~~F~~~~~~~~~~l~~Ll~AA~~L~I~~L~~l~~~~ia~~i~gk 128 (161)
. +--+..++-+|+.-|.|..+++|+++|...++..+++.
T Consensus 70 ---~-----------LPe~~kel~El~~EA~fYlL~~Lv~~C~~~i~~~~~~~ 108 (230)
T KOG2716|consen 70 ---D-----------LPESEKELKELLREAEFYLLDGLVELCQSAIARLIRGY 108 (230)
T ss_pred ---c-----------CccchHHHHHHHHHHHHhhHHHHHHHHHHHhhhcccCc
Confidence 1 22356778999999999999999999999999998775
No 15
>KOG4350 consensus Uncharacterized conserved protein, contains BTB/POZ domain [General function prediction only]
Probab=95.69 E-value=0.098 Score=44.37 Aligned_cols=117 Identities=14% Similarity=0.183 Sum_probs=83.0
Q ss_pred eEEEEeCCCCEEEecHHH-HHHHHHHHHHhhhc---cCCCccccc-ccHHHHHHHHHHhhcccccCCCCCCCC-------
Q 038597 6 TVKLRSGDNEVFEVEKQV-MIQSGTIRNMIEDD---AADGEIPLQ-ISSRNLAKVVEWCKCMQHRDRNNNNDN------- 73 (161)
Q Consensus 6 ~i~l~s~Dg~~~~v~~~~-a~~S~~l~~~~~~~---~~~~~I~l~-v~s~~L~~Ii~y~~~~~h~~~~~~~~~------- 73 (161)
.++++-.| +.|...+-+ |..|.++|.|+-+. .....|||+ -++..++.+++|++ .-+-+-....+
T Consensus 46 DVtfvve~-~rfpAHRvILAaRs~yFRAlLYgGm~Es~q~~ipLq~t~~eAF~~lLrYiY--tg~~~l~~~~ed~lld~L 122 (620)
T KOG4350|consen 46 DVTFVVED-TRFPAHRVILAARSSYFRALLYGGMQESHQQLIPLQETNSEAFRALLRYIY--TGKIDLAGVEEDILLDYL 122 (620)
T ss_pred ceEEEEec-cccchhhhhHHHHHHHHHHHHhhhhhhhhhcccccccccHHHHHHHHHHHh--hcceecccchHHHHHHHH
Confidence 46666666 788888877 56799999999643 245779999 77999999999998 53322111111
Q ss_pred c--------chhhhHHHHHHhhhhhhcCChHHHHHHHHhhccCCchHHHHHHHHHHHHHHcCCCHHHHHh
Q 038597 74 K--------EEEEEEEEWEKKFDEEVSEDKDLHFGLLLAANYLEIPALLHRLCQLAADIVKGKTPEEIRR 135 (161)
Q Consensus 74 ~--------~~~~~~~~wd~~F~~~~~~~~~~l~~Ll~AA~~L~I~~L~~l~~~~ia~~i~gks~eeir~ 135 (161)
+ .....++++-++. +..+.++-++.||.+.+...|.++||.++ +++.+++..
T Consensus 123 slAh~Ygf~~Le~aiSeYl~~i-----L~~~NvCmifdaA~ly~l~~Lt~~C~mfm-----DrnA~~lL~ 182 (620)
T KOG4350|consen 123 SLAHRYGFIQLETAISEYLKEI-----LKNENVCMIFDAAYLYQLTDLTDYCMMFM-----DRNADQLLE 182 (620)
T ss_pred HHHHhcCcHHHHHHHHHHHHHH-----HcccceeeeeeHHHHhcchHHHHHHHHHH-----hcCHHhhhc
Confidence 0 2334455555554 35677899999999999999999999665 666666654
No 16
>KOG0783 consensus Uncharacterized conserved protein, contains ankyrin and BTB/POZ domains [Function unknown]
Probab=94.55 E-value=0.1 Score=47.84 Aligned_cols=108 Identities=16% Similarity=0.153 Sum_probs=77.9
Q ss_pred EEEEeCCCCEEEecHHHH-HHHHHHHHHhhhcc-CCCcc---cccccHHHHHHHHHHhhcccccCCCCCCCCcchhhhHH
Q 038597 7 VKLRSGDNEVFEVEKQVM-IQSGTIRNMIEDDA-ADGEI---PLQISSRNLAKVVEWCKCMQHRDRNNNNDNKEEEEEEE 81 (161)
Q Consensus 7 i~l~s~Dg~~~~v~~~~a-~~S~~l~~~~~~~~-~~~~I---~l~v~s~~L~~Ii~y~~~~~h~~~~~~~~~~~~~~~~~ 81 (161)
..++..||+++..++..+ ..+.++..|+.-.- +..-| -+|++++.|+-|++|++ . .+.
T Consensus 713 ~~i~~KDGkvl~aHkc~L~aRlEYF~smf~~~w~E~sS~t~~~~p~~~e~m~ivLdylY--s--~d~------------- 775 (1267)
T KOG0783|consen 713 TVIKLKDGKVLKAHKCFLSARLEYFSSMFQFVWMESSSITVNLSPLTVEHMSIVLDYLY--S--DDK------------- 775 (1267)
T ss_pred EEEEecCCcCcccceeEeeeHHHHHHHHHHHHHhhhccceeecCcchHHHHHHHHHHHH--c--cch-------------
Confidence 456677999999998884 45888888887531 11223 23367999999999988 3 221
Q ss_pred HHHHhhhhhhcCChHHHHHHHHhhccCCchHHHHHHHHHHHHHHcCCCHHHHHh
Q 038597 82 EWEKKFDEEVSEDKDLHFGLLLAANYLEIPALLHRLCQLAADIVKGKTPEEIRR 135 (161)
Q Consensus 82 ~wd~~F~~~~~~~~~~l~~Ll~AA~~L~I~~L~~l~~~~ia~~i~gks~eeir~ 135 (161)
.+||++ ..+.+.+|+++..|+.|-|..|-++|-+.+-+++.=|+..++.+
T Consensus 776 ---~~~~k~-~~~~dF~~~il~iaDqlli~~Lk~Ice~~ll~kl~lk~~~~lle 825 (1267)
T KOG0783|consen 776 ---VELFKD-LKESDFMFEILSIADQLLILELKSICEQSLLRKLNLKTLPTLLE 825 (1267)
T ss_pred ---HHHHhc-cchhhhhHHHHHHHHHHHHHHHHHHHHHHHHhHhcccchHHHHH
Confidence 135332 24567799999999999999999999998888888777655544
No 17
>KOG3433 consensus Protein involved in meiotic recombination/predicted coiled-coil protein [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=93.58 E-value=0.14 Score=38.69 Aligned_cols=37 Identities=38% Similarity=0.504 Sum_probs=29.5
Q ss_pred Hhhcc--CCchHHHHHHHHHHHHHHcCCCHHHHHhHcCCCCCCC
Q 038597 103 LAANY--LEIPALLHRLCQLAADIVKGKTPEEIRRTFNIKKDFT 144 (161)
Q Consensus 103 ~AA~~--L~I~~L~~l~~~~ia~~i~gks~eeir~~f~i~~d~t 144 (161)
.|||. =+|--|.++||+.. |.-+.+||+.||||+||.
T Consensus 162 eaanrwtDnI~il~dy~~rkf-----~~e~nqi~~~fgIPed~d 200 (203)
T KOG3433|consen 162 EAANRWTDNIFILIDYLYRKF-----GLEPNQIRKEFGIPEDFD 200 (203)
T ss_pred HHHhhhhhhHHHHHHHHHHhc-----CCCHHHHhHhcCCCcccc
Confidence 44443 27778888888765 899999999999999874
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=91.76 E-value=0.36 Score=39.61 Aligned_cols=86 Identities=13% Similarity=0.224 Sum_probs=63.3
Q ss_pred CCEEEecHHHH-HHHHHHHHHhhh---c-cCCCccccc--ccHHHHHHHHHHhhcccccCCCCCCCCcchhhhHHHHHHh
Q 038597 14 NEVFEVEKQVM-IQSGTIRNMIED---D-AADGEIPLQ--ISSRNLAKVVEWCKCMQHRDRNNNNDNKEEEEEEEEWEKK 86 (161)
Q Consensus 14 g~~~~v~~~~a-~~S~~l~~~~~~---~-~~~~~I~l~--v~s~~L~~Ii~y~~~~~h~~~~~~~~~~~~~~~~~~wd~~ 86 (161)
.+.|..+.+.+ ...++++..+.. . ...++|++- -+-.|++=+.+|++ . ..|
T Consensus 13 ~rdF~C~~~lL~~~M~YF~~~l~~~~~~~~~~~~idisVhCDv~iF~WLm~yv~--~--~~p------------------ 70 (317)
T PF11822_consen 13 KRDFTCPRDLLVSEMRYFAEYLSRYINDSQRWEEIDISVHCDVHIFEWLMRYVK--G--EPP------------------ 70 (317)
T ss_pred ceeeeccHHHHHHhhHHHHHHHhhcccccCcCCCcceEEecChhHHHHHHHHhh--c--CCC------------------
Confidence 45799999995 569999999953 2 234566666 46777887788877 4 111
Q ss_pred hhhhhcCChHHHHHHHHhhccCCchHHHHHHHHHHHHHHc
Q 038597 87 FDEEVSEDKDLHFGLLLAANYLEIPALLHRLCQLAADIVK 126 (161)
Q Consensus 87 F~~~~~~~~~~l~~Ll~AA~~L~I~~L~~l~~~~ia~~i~ 126 (161)
.+++..+..|+.-|+||+|++|++.|-.++...+.
T Consensus 71 -----~l~~~NvvsIliSS~FL~M~~Lve~cl~y~~~~~~ 105 (317)
T PF11822_consen 71 -----SLTPSNVVSILISSEFLQMESLVEECLQYCHDHMS 105 (317)
T ss_pred -----cCCcCcEEEeEehhhhhccHHHHHHHHHHHHHhHH
Confidence 24566678889999999999999999888855443
No 19
>COG5124 Protein predicted to be involved in meiotic recombination [Cell division and chromosome partitioning / General function prediction only]
Probab=91.65 E-value=0.17 Score=38.04 Aligned_cols=31 Identities=35% Similarity=0.616 Sum_probs=25.2
Q ss_pred CchHHHHHHHHHHHHHHcCCCHHHHHhHcCCCCCCC
Q 038597 109 EIPALLHRLCQLAADIVKGKTPEEIRRTFNIKKDFT 144 (161)
Q Consensus 109 ~I~~L~~l~~~~ia~~i~gks~eeir~~f~i~~d~t 144 (161)
+|.-|.++.|+.+ +.-++|||+.||||+|+.
T Consensus 174 nI~ilidy~c~kf-----~~~~~qir~~fgIPedld 204 (209)
T COG5124 174 NIEILIDYLCKKF-----FLKPEQIRKEFGIPEDLD 204 (209)
T ss_pred hHHHHHHHHHHHc-----CCCHHHHHHhcCCCcchh
Confidence 5667778777655 889999999999999864
No 20
>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=84.50 E-value=0.65 Score=30.68 Aligned_cols=79 Identities=13% Similarity=0.265 Sum_probs=52.0
Q ss_pred CCCEEEecHHHHHH--HHHHHHHhhhc------cCCCcccccccHHHHHHHHHHhhcccccCCCCCCCCcchhhhHHHHH
Q 038597 13 DNEVFEVEKQVMIQ--SGTIRNMIEDD------AADGEIPLQISSRNLAKVVEWCKCMQHRDRNNNNDNKEEEEEEEEWE 84 (161)
Q Consensus 13 Dg~~~~v~~~~a~~--S~~l~~~~~~~------~~~~~I~l~v~s~~L~~Ii~y~~~~~h~~~~~~~~~~~~~~~~~~wd 84 (161)
-|+.|.++...+.. ...+..++... ....++=+.=++..++.|+.|++ .- ..
T Consensus 6 GG~~f~~~~~tL~~~~~s~l~~~~~~~~~~~~~~~~~~~fiDRdp~~F~~IL~ylr--~~--~~---------------- 65 (94)
T PF02214_consen 6 GGTIFETSRSTLTRYPDSLLARLFSGERSDDYDDDDGEYFIDRDPELFEYILNYLR--TG--GK---------------- 65 (94)
T ss_dssp TTEEEEEEHHHHHTSTTSTTTSHHHTGHGGGEETTTTEEEESS-HHHHHHHHHHHH--HT--SS----------------
T ss_pred CCEEEEEcHHHHhhCCCChhhhHHhhccccccCCccceEEeccChhhhhHHHHHHh--hc--Cc----------------
Confidence 48999999998763 44667777642 13345545579999999999999 42 11
Q ss_pred HhhhhhhcC-ChHHHHHHHHhhccCCchHH-HHHH
Q 038597 85 KKFDEEVSE-DKDLHFGLLLAANYLEIPAL-LHRL 117 (161)
Q Consensus 85 ~~F~~~~~~-~~~~l~~Ll~AA~~L~I~~L-~~l~ 117 (161)
+.. +...+..+...|.|.+|+.| ++.|
T Consensus 66 ------l~~~~~~~~~~l~~Ea~fy~l~~l~i~~c 94 (94)
T PF02214_consen 66 ------LPIPDEICLEELLEEAEFYGLDELFIEDC 94 (94)
T ss_dssp ------B---TTS-HHHHHHHHHHHT-HHHHBHHC
T ss_pred ------cCCCCchhHHHHHHHHHHcCCCccccCCC
Confidence 111 23456788899999999998 6654
No 21
>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=80.59 E-value=1.9 Score=32.80 Aligned_cols=41 Identities=34% Similarity=0.307 Sum_probs=30.5
Q ss_pred HHHHHhhccC--CchHHHHHHHHHHHHHHcCCCHHHHHhHcCCCCCCC
Q 038597 99 FGLLLAANYL--EIPALLHRLCQLAADIVKGKTPEEIRRTFNIKKDFT 144 (161)
Q Consensus 99 ~~Ll~AA~~L--~I~~L~~l~~~~ia~~i~gks~eeir~~f~i~~d~t 144 (161)
..+..||+.- +|..|..+|+.. -|.+.++|++.||||+||-
T Consensus 145 ~~~~~~anrwTDNI~~l~~~~~~k-----~~~~~~~i~k~f~Ip~d~d 187 (188)
T PF03962_consen 145 KIAKEAANRWTDNIFSLKSYLKKK-----FGMDEEDIRKEFGIPEDFD 187 (188)
T ss_pred HHHHHHHHHHHhhHHHHHHHHHHh-----cCCCHHHHHHHcCCccccC
Confidence 3344466654 677777777764 3899999999999999873
No 22
>KOG2075 consensus Topoisomerase TOP1-interacting protein BTBD1 [Function unknown]
Probab=65.49 E-value=30 Score=30.25 Aligned_cols=112 Identities=14% Similarity=0.087 Sum_probs=68.0
Q ss_pred CEEEecHHHH-HHHHHHHHHhhhcc---CCCccccc-ccHHHHHHHHHHhhcccccCCCCCCCC------cchhhhHHHH
Q 038597 15 EVFEVEKQVM-IQSGTIRNMIEDDA---ADGEIPLQ-ISSRNLAKVVEWCKCMQHRDRNNNNDN------KEEEEEEEEW 83 (161)
Q Consensus 15 ~~~~v~~~~a-~~S~~l~~~~~~~~---~~~~I~l~-v~s~~L~~Ii~y~~~~~h~~~~~~~~~------~~~~~~~~~w 83 (161)
|.+..++-+. .-|.++..|+.+.- ...+|.+| |.-+++....+|+++.+-+..+.-... +-....+..=
T Consensus 129 q~~paHk~vla~gS~VFdaMf~g~~a~~~s~ei~lpdvepaaFl~~L~flYsdev~~~~dtvi~tl~~AkKY~VpaLer~ 208 (521)
T KOG2075|consen 129 QRIPAHKLVLADGSDVFDAMFYGGLAEDASLEIRLPDVEPAAFLAFLRFLYSDEVKLAADTVITTLYAAKKYLVPALERQ 208 (521)
T ss_pred cccchhhhhhhcchHHHHHHhccCcccccCceeecCCcChhHhHHHHHHHhcchhhhhHHHHHHHHHHHHHhhhHHHHHH
Confidence 4556666664 44889999987542 36789999 999999999999883221111100000 0001111122
Q ss_pred HHhhhhhhcCChHHHHHHHHhhccCCchHHHHHHHHHHHHHHc
Q 038597 84 EKKFDEEVSEDKDLHFGLLLAANYLEIPALLHRLCQLAADIVK 126 (161)
Q Consensus 84 d~~F~~~~~~~~~~l~~Ll~AA~~L~I~~L~~l~~~~ia~~i~ 126 (161)
--+|+...-.+...++.|...|..++=+.|+..|...+.....
T Consensus 209 CVkflr~~l~~~naf~~L~q~A~lf~ep~Li~~c~e~id~~~~ 251 (521)
T KOG2075|consen 209 CVKFLRKNLMADNAFLELFQRAKLFDEPSLISICLEVIDKSFE 251 (521)
T ss_pred HHHHHHHhcCChHHHHHHHHHHHhhcCHHHHHHHHHHhhhHHH
Confidence 2235321125667777777779999999999999888765444
No 23
>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=63.38 E-value=2.4 Score=30.55 Aligned_cols=43 Identities=19% Similarity=0.292 Sum_probs=0.0
Q ss_pred CCCEEEecHHHHHHHHHHHHHhhhccCCCccccc-ccHHHHHHHHHHhh
Q 038597 13 DNEVFEVEKQVMIQSGTIRNMIEDDAADGEIPLQ-ISSRNLAKVVEWCK 60 (161)
Q Consensus 13 Dg~~~~v~~~~a~~S~~l~~~~~~~~~~~~I~l~-v~s~~L~~Ii~y~~ 60 (161)
||+.|.|+..++..-+.+.+.+.-. ..+| +..+++.++++|++
T Consensus 1 d~e~f~vv~s~l~ll~~l~~Y~~~~-----~~~P~~a~di~~~l~elLk 44 (135)
T PF07928_consen 1 DNEKFVVVGSALLLLKMLSDYLQLA-----SNFPSLAPDILSRLLELLK 44 (135)
T ss_dssp -------------------------------------------------
T ss_pred CCCceecHHHHHHHHHHHHHHHHHH-----HHCchhHHHHHHHHHHHHH
Confidence 6788888888877777777765432 3455 78888888888887
No 24
>KOG1665 consensus AFH1-interacting protein FIP2, contains BTB/POZ domain and pentapeptide repeats [General function prediction only]
Probab=59.42 E-value=14 Score=29.19 Aligned_cols=88 Identities=17% Similarity=0.290 Sum_probs=58.1
Q ss_pred CeEEEEeCCCCEEE--ecHHHHHH-HHHHHHHhhhcc------CCCcccccccHHHHHHHHHHhhcccccCCCCCCCCcc
Q 038597 5 STVKLRSGDNEVFE--VEKQVMIQ-SGTIRNMIEDDA------ADGEIPLQISSRNLAKVVEWCKCMQHRDRNNNNDNKE 75 (161)
Q Consensus 5 ~~i~l~s~Dg~~~~--v~~~~a~~-S~~l~~~~~~~~------~~~~I~l~v~s~~L~~Ii~y~~~~~h~~~~~~~~~~~ 75 (161)
+.++|- -.|+.|. ++.-+.+. -.++..|+.+.+ ..+.+-+.=+..-++-|+.|+. + ..
T Consensus 9 ~~vrln-igGk~f~TTidTlv~rEPDSMLa~MF~~~g~~~~~d~kGa~lIDRsp~yFepIlNyLr--~-Gq--------- 75 (302)
T KOG1665|consen 9 SMVRLN-IGGKKFCTTIDTLVIREPDSMLAAMFSGRGAMCQEDKKGAVLIDRSPKYFEPILNYLR--D-GQ--------- 75 (302)
T ss_pred hhheee-cCCeEEEEeehhhcccCchHHHHHHHccCCCccccccCceEEEccCchhhHHHHHHHh--c-Cc---------
Confidence 445553 3577765 44444443 556777776653 2244555567888999999998 3 21
Q ss_pred hhhhHHHHHHhhhhhhcCChHHHHHHHHhhccCCchHHHHHHHH
Q 038597 76 EEEEEEEWEKKFDEEVSEDKDLHFGLLLAANYLEIPALLHRLCQ 119 (161)
Q Consensus 76 ~~~~~~~wd~~F~~~~~~~~~~l~~Ll~AA~~L~I~~L~~l~~~ 119 (161)
| ...+...++.++.+|.|++|.+|.+..-.
T Consensus 76 -----------~---~~~s~i~~lgvLeeArff~i~sL~~hle~ 105 (302)
T KOG1665|consen 76 -----------I---PSLSDIDCLGVLEEARFFQILSLKDHLED 105 (302)
T ss_pred -----------e---eecCCccHHHHHHHhhHHhhHhHHhHHhh
Confidence 2 23445568899999999999999987643
No 25
>PRK05365 malonic semialdehyde reductase; Provisional
Probab=59.05 E-value=6.5 Score=29.49 Aligned_cols=34 Identities=24% Similarity=0.276 Sum_probs=27.7
Q ss_pred HHHHhhccCCchHHHHHHHHHHHHHHcCCCHHHHHhHcCCCCCC
Q 038597 100 GLLLAANYLEIPALLHRLCQLAADIVKGKTPEEIRRTFNIKKDF 143 (161)
Q Consensus 100 ~Ll~AA~~L~I~~L~~l~~~~ia~~i~gks~eeir~~f~i~~d~ 143 (161)
.|+.||.-+|+.. .++.|-..+.+++.|||++++
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 4899999999887 245577889999999998765
No 26
>PF02519 Auxin_inducible: Auxin responsive protein; InterPro: IPR003676 This family consists of the protein products of a gene cluster that encodes a group of auxin-regulated RNAs (small auxin up RNAs, SAURs) []. Proteins from this ARG7 auxin responsive genes family have no identified functional role [].
Probab=56.36 E-value=44 Score=22.69 Aligned_cols=54 Identities=11% Similarity=0.204 Sum_probs=39.8
Q ss_pred eEEEEeCC-CCEEEecHHHHHHHHHHHHHhhhc----c--CCCcccccccHHHHHHHHHHhh
Q 038597 6 TVKLRSGD-NEVFEVEKQVMIQSGTIRNMIEDD----A--ADGEIPLQISSRNLAKVVEWCK 60 (161)
Q Consensus 6 ~i~l~s~D-g~~~~v~~~~a~~S~~l~~~~~~~----~--~~~~I~l~v~s~~L~~Ii~y~~ 60 (161)
.+.+-..+ .+.|.|+...+. .++++.+++.. | .+++|.||-+...++.|+..++
T Consensus 40 ~~~VyVG~~~~Rfvvp~~~L~-hp~f~~LL~~aeeEfG~~~~G~l~iPC~~~~Fe~~l~~le 100 (100)
T PF02519_consen 40 HFAVYVGEERRRFVVPVSYLN-HPLFQELLEQAEEEFGFDQDGPLTIPCDVVLFEHLLWLLE 100 (100)
T ss_pred eEEEEeCccceEEEechHHcC-chhHHHHHHHHhhhcCcCCCCcEEeeCCHHHHHHHHHHhC
Confidence 44555555 889999999876 67788888642 2 4578888888889998887653
No 27
>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=56.24 E-value=7.3 Score=28.93 Aligned_cols=34 Identities=21% Similarity=0.269 Sum_probs=27.5
Q ss_pred HHHHhhccCCchHHHHHHHHHHHHHHcCCCHHHHHhHcCCCCCC
Q 038597 100 GLLLAANYLEIPALLHRLCQLAADIVKGKTPEEIRRTFNIKKDF 143 (161)
Q Consensus 100 ~Ll~AA~~L~I~~L~~l~~~~ia~~i~gks~eeir~~f~i~~d~ 143 (161)
.|+.||.-||+.. .++.|-..+++++.||+++++
T Consensus 123 ~l~LaA~~lGlgs----------~~~~g~d~~~~~~~L~lp~~~ 156 (185)
T cd02148 123 YFILAARALGLDA----------GPMSGFDAAAVDAEFFADTRW 156 (185)
T ss_pred HHHHHHHHcCCCc----------CCCcccCHHHHHHHhCCCCCe
Confidence 3888999888876 255677889999999998765
No 28
>KOG0511 consensus Ankyrin repeat protein [General function prediction only]
Probab=55.51 E-value=78 Score=27.15 Aligned_cols=104 Identities=10% Similarity=0.015 Sum_probs=71.6
Q ss_pred CEEEecHHHHHHHHHHHHHhhhc----cCC---Cccccc-ccHHHHHHHHHHhhcccccCCCCCCCCc------------
Q 038597 15 EVFEVEKQVMIQSGTIRNMIEDD----AAD---GEIPLQ-ISSRNLAKVVEWCKCMQHRDRNNNNDNK------------ 74 (161)
Q Consensus 15 ~~~~v~~~~a~~S~~l~~~~~~~----~~~---~~I~l~-v~s~~L~~Ii~y~~~~~h~~~~~~~~~~------------ 74 (161)
..+.++...+....+++.|+.+. ..+ ....+| ..+.+.+.+.+|++ -|+.+.++..-+
T Consensus 301 ~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 301 DRYPAHLARILRVEYFKSMFVGDFIESSVNDTRPGLSLPSLADVVVEIDLRNLY--CDQTDIIFDVASDVLLFADKLALA 378 (516)
T ss_pred ccccHHHHHHHHHHHHHHHhccchhhhcCCccccccccchHHHHHHHHHHHHhh--cccccchHHHHhhHHHHhhHhhhh
Confidence 34677777777788899888653 112 334577 78999999999999 777765432210
Q ss_pred -------chhhhHHHHHHhhhhhhcCChHHHHHHHHhhccCCchHHHHHHHHHHHHHHc
Q 038597 75 -------EEEEEEEEWEKKFDEEVSEDKDLHFGLLLAANYLEIPALLHRLCQLAADIVK 126 (161)
Q Consensus 75 -------~~~~~~~~wd~~F~~~~~~~~~~l~~Ll~AA~~L~I~~L~~l~~~~ia~~i~ 126 (161)
.....+.+|.. | ++.-.+++++.-|.-+....|=.++..++|..+.
T Consensus 379 ~dr~Lkt~as~~itq~~e-~-----id~y~V~dIl~~~wd~~~~rlEqfa~~~~a~hl~ 431 (516)
T KOG0511|consen 379 DDRLLKTAASAEITQWLE-L-----IDMYGVLDILEYCWDLVACRLEQFAETHEARHLL 431 (516)
T ss_pred hhhhhhhhhhHHHHHHHH-H-----HHhhhHHHHHHHHHHhhhHHHHHHHHHHHHHHHH
Confidence 11233444432 3 3445588999999999999999999988888765
No 29
>PRK13503 transcriptional activator RhaS; Provisional
Probab=52.58 E-value=1.1e+02 Score=23.75 Aligned_cols=78 Identities=17% Similarity=0.208 Sum_probs=48.6
Q ss_pred HHHHHHHHHHhhcccccCCCCCCCCcchhhhHHHHHHhhhhhhcCChHHHHHHHHhhccCCchHHHHHHHHHH-HHHHc-
Q 038597 49 SRNLAKVVEWCKCMQHRDRNNNNDNKEEEEEEEEWEKKFDEEVSEDKDLHFGLLLAANYLEIPALLHRLCQLA-ADIVK- 126 (161)
Q Consensus 49 s~~L~~Ii~y~~~~~h~~~~~~~~~~~~~~~~~~wd~~F~~~~~~~~~~l~~Ll~AA~~L~I~~L~~l~~~~i-a~~i~- 126 (161)
...++++++|++ .|...+. .+.+|-+.| +++...+..++....-.-...++.-.=-.- ..++.
T Consensus 170 ~~~i~~~~~~I~--~~~~~~~---------tl~~lA~~~----~lS~~~l~r~Fk~~~G~S~~~yi~~~Rl~~A~~LL~~ 234 (278)
T PRK13503 170 DARLNQLLAWLE--DHFAEEV---------NWEALADQF----SLSLRTLHRQLKQQTGLTPQRYLNRLRLLKARHLLRH 234 (278)
T ss_pred HHHHHHHHHHHH--HhhcCCC---------CHHHHHHHH----CCCHHHHHHHHHHHhCcCHHHHHHHHHHHHHHHHHHc
Confidence 344677777777 6554432 345555554 788888888888776666555555442222 23333
Q ss_pred -CCCHHHHHhHcCCCC
Q 038597 127 -GKTPEEIRRTFNIKK 141 (161)
Q Consensus 127 -gks~eeir~~f~i~~ 141 (161)
+.|+.||...+|-.+
T Consensus 235 ~~~sI~eIA~~~GF~~ 250 (278)
T PRK13503 235 SDASVTDIAYRCGFGD 250 (278)
T ss_pred CCCCHHHHHHHhCCCC
Confidence 578888888888765
No 30
>KOG4350 consensus Uncharacterized conserved protein, contains BTB/POZ domain [General function prediction only]
Probab=52.37 E-value=31 Score=29.80 Aligned_cols=37 Identities=16% Similarity=0.231 Sum_probs=25.6
Q ss_pred hcCChHHHHHHHHhhccCCchHHHHHHHHHHHHHHcC
Q 038597 91 VSEDKDLHFGLLLAANYLEIPALLHRLCQLAADIVKG 127 (161)
Q Consensus 91 ~~~~~~~l~~Ll~AA~~L~I~~L~~l~~~~ia~~i~g 127 (161)
.+.+.+.+++.+.-|+..|...|....+.++-..++.
T Consensus 111 ~~~~ed~lld~LslAh~Ygf~~Le~aiSeYl~~iL~~ 147 (620)
T KOG4350|consen 111 AGVEEDILLDYLSLAHRYGFIQLETAISEYLKEILKN 147 (620)
T ss_pred ccchHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHcc
Confidence 3466677777777777777777777777766665554
No 31
>cd05029 S-100A6 S-100A6: S-100A6 domain found in proteins similar to S100A6. S100A6 is a member of the S100 domain family within EF-hand Ca2+-binding proteins superfamily. Note that the S-100 hierarchy, to which this S-100A6 group belongs, contains only S-100 EF-hand domains, other EF-hands have been modeled separately. S100 proteins exhibit unique patterns of tissue- and cell type-specific expression and have been implicated in the Ca2+-dependent regulation of diverse physiological processes, including cell cycle regulation, differentiation, growth, and metabolic control . S100A6 is normally expressed in the G1 phase of the cell cycle in neuronal cells. The function of S100A6 remains unclear, but evidence suggests that it is involved in cell cycle regulation and exocytosis. S100A6 may also be involved in tumorigenesis; the protein is overexpressed in several tumors. Ca2+ binding to S100A6 leads to a conformational change in the protein, which exposes a hydrophobic surface for interact
Probab=51.15 E-value=31 Score=22.59 Aligned_cols=45 Identities=16% Similarity=0.252 Sum_probs=27.7
Q ss_pred chHHHHHHHHHHHHHH-cCC-CHHHHHhHcC----CCCCCCHHHHHHHHHh
Q 038597 110 IPALLHRLCQLAADIV-KGK-TPEEIRRTFN----IKKDFTPEEEEAVMDE 154 (161)
Q Consensus 110 I~~L~~l~~~~ia~~i-~gk-s~eeir~~f~----i~~d~t~eee~~i~~e 154 (161)
|..|+.+..++.+.-= +|. +.+|+|+.+. +.+.+|++|..++.++
T Consensus 9 ~~~~i~~F~~y~~~~~~~g~Is~~EL~~~l~~~~~lg~k~t~~ev~~m~~~ 59 (88)
T cd05029 9 IGLLVAIFHKYSGREGDKNTLSKKELKELIQKELTIGSKLQDAEIAKLMED 59 (88)
T ss_pred HHHHHHHHHHHHccCCCCCEECHHHHHHHHHHHHhcCCCCCHHHHHHHHHH
Confidence 3455666666665321 332 7888888773 4455788777777654
No 32
>PF12556 CobS_N: Cobaltochelatase CobS subunit N terminal
Probab=51.09 E-value=9.3 Score=21.12 Aligned_cols=12 Identities=33% Similarity=0.739 Sum_probs=10.3
Q ss_pred HHhHcCCCCCCC
Q 038597 133 IRRTFNIKKDFT 144 (161)
Q Consensus 133 ir~~f~i~~d~t 144 (161)
+|+.|||..|++
T Consensus 14 vre~FGiDsDm~ 25 (36)
T PF12556_consen 14 VREVFGIDSDMK 25 (36)
T ss_pred HHHhcCCCcCCe
Confidence 689999999875
No 33
>PF11460 DUF3007: Protein of unknown function (DUF3007); InterPro: IPR021562 This is a family of uncharacterised proteins found in bacteria and eukaryotes.
Probab=50.52 E-value=15 Score=25.21 Aligned_cols=24 Identities=38% Similarity=0.620 Sum_probs=17.7
Q ss_pred CHHHHHhHcCCCCCCCHHHHHHHHHhc
Q 038597 129 TPEEIRRTFNIKKDFTPEEEEAVMDEH 155 (161)
Q Consensus 129 s~eeir~~f~i~~d~t~eee~~i~~e~ 155 (161)
+.+++.++|. .+||||.+++.+|-
T Consensus 79 ~~~~lqkRle---~l~~eE~~~L~~ei 102 (104)
T PF11460_consen 79 TNEELQKRLE---ELSPEELEALQAEI 102 (104)
T ss_pred hHHHHHHHHH---hCCHHHHHHHHHHh
Confidence 4556777775 68899988887763
No 34
>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=48.84 E-value=14 Score=26.38 Aligned_cols=25 Identities=36% Similarity=0.521 Sum_probs=13.0
Q ss_pred HHcCCCHHHHHhHcCCCCCCCHHHH
Q 038597 124 IVKGKTPEEIRRTFNIKKDFTPEEE 148 (161)
Q Consensus 124 ~i~gks~eeir~~f~i~~d~t~eee 148 (161)
..+|+|.+|-++++|++...++|+.
T Consensus 51 ~~~~Mtl~EA~~ILnv~~~~~~eeI 75 (127)
T PF03656_consen 51 NSKGMTLDEARQILNVKEELSREEI 75 (127)
T ss_dssp ------HHHHHHHHT--G--SHHHH
T ss_pred hcCCCCHHHHHHHcCCCCccCHHHH
Confidence 4468999999999999997777654
No 35
>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=48.47 E-value=29 Score=20.54 Aligned_cols=34 Identities=21% Similarity=0.435 Sum_probs=22.5
Q ss_pred HHHHHHHHcCCCHHHHHhHcC--C----C-CCCCHHHHHHH
Q 038597 118 CQLAADIVKGKTPEEIRRTFN--I----K-KDFTPEEEEAV 151 (161)
Q Consensus 118 ~~~ia~~i~gks~eeir~~f~--i----~-~d~t~eee~~i 151 (161)
=..||..+..+|+.+++..|. + . ..+|+||.+.+
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 357788884499999987543 2 2 25888887654
No 36
>KOG4591 consensus Uncharacterized conserved protein, contains BTB/POZ domain [General function prediction only]
Probab=45.61 E-value=31 Score=26.91 Aligned_cols=19 Identities=16% Similarity=0.413 Sum_probs=13.1
Q ss_pred ccccc-ccHHHHHHHHHHhh
Q 038597 42 EIPLQ-ISSRNLAKVVEWCK 60 (161)
Q Consensus 42 ~I~l~-v~s~~L~~Ii~y~~ 60 (161)
...+. ++..++-..++|.+
T Consensus 107 ~~~~dDad~Ea~~t~iRWIY 126 (280)
T KOG4591|consen 107 ELDLDDADFEAFHTAIRWIY 126 (280)
T ss_pred hhcccccCHHHHHHhheeee
Confidence 34455 77777777888866
No 37
>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=44.79 E-value=42 Score=27.22 Aligned_cols=99 Identities=21% Similarity=0.261 Sum_probs=55.6
Q ss_pred Cccccc-ccHHHHHHHHHHhhcccccCCC-C-CCCCc-chhhhHHHHHHh--hhhhhcCChHHHHHHHHhhccCCchHHH
Q 038597 41 GEIPLQ-ISSRNLAKVVEWCKCMQHRDRN-N-NNDNK-EEEEEEEEWEKK--FDEEVSEDKDLHFGLLLAANYLEIPALL 114 (161)
Q Consensus 41 ~~I~l~-v~s~~L~~Ii~y~~~~~h~~~~-~-~~~~~-~~~~~~~~wd~~--F~~~~~~~~~~l~~Ll~AA~~L~I~~L~ 114 (161)
+...++ .+.-.-.-|+.|++ -|--.. + ..... ...+...+|-.. | -++..+..++.+.|..-..+..|+
T Consensus 161 ~~~Q~~~~~~~~T~NVvA~LY--Aalln~~~w~l~~~~~svedFN~WA~~N~f---t~~~~~~~~~~Laa~TgVsV~rlL 235 (293)
T PF05409_consen 161 EVAQLEGADQYITDNVVAWLY--AALLNGCPWWLSSQRISVEDFNEWAMNNGF---TSFSSDDAFDMLAAKTGVSVERLL 235 (293)
T ss_dssp SSSTTTTS-SB-HHHHHHHHH--HHHHTT--TTSSSS---HHHHHHHHHHTTB-----SSHHHHHHHHHHHHT--HHHHH
T ss_pred hhhhhcCccceeehhHHHHHH--HHHHcCCCeeeccceecHHHHHHHHHhCCC---cccchhhHHHHHHHHhCCcHHHHH
Confidence 344455 44445567788887 554321 1 11111 234567888655 4 346778899999999999999998
Q ss_pred HHHHHHHHHHHcCCCHHHHHhHcCCCCCCCHHHH
Q 038597 115 HRLCQLAADIVKGKTPEEIRRTFNIKKDFTPEEE 148 (161)
Q Consensus 115 ~l~~~~ia~~i~gks~eeir~~f~i~~d~t~eee 148 (161)
...-+ +..-..|+ .|.-...+++||||++-
T Consensus 236 aaI~~-L~~g~~G~---~IlG~~~ledE~Tp~~V 265 (293)
T PF05409_consen 236 AAIQR-LHKGFGGR---TILGSCSLEDEFTPEMV 265 (293)
T ss_dssp HHHHH-HHHTTTTT----BTTBSS--TSS-HHHH
T ss_pred HHHHH-HhcCCCCC---cccccccccccCCHHHH
Confidence 76655 44444444 45666678889999875
No 38
>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=44.79 E-value=45 Score=23.64 Aligned_cols=45 Identities=16% Similarity=0.404 Sum_probs=28.1
Q ss_pred HHHHHHHHHHHHHHcCCCHHHHHhHcCCCCCCCHHHHHHHHHhcCCCCC
Q 038597 112 ALLHRLCQLAADIVKGKTPEEIRRTFNIKKDFTPEEEEAVMDEHGWAFH 160 (161)
Q Consensus 112 ~L~~l~~~~ia~~i~gks~eeir~~f~i~~d~t~eee~~i~~e~~w~~~ 160 (161)
...+..+..|+.-...-+...+.+++|++ .+|..++-+...|..+
T Consensus 82 ~iR~~i~~~i~~aY~sIs~~~la~~Lg~~----~~el~~~~~~~gW~~d 126 (143)
T PF10075_consen 82 TIRERIAHLISKAYSSISLSDLAEMLGLS----EEELEKFIKSRGWTVD 126 (143)
T ss_dssp HHHHHHHHHHHHH-SEE-HHHHHHHTTS-----HHHHHHHHHHHT-EE-
T ss_pred HHHHHHHHHHHHHHhHcCHHHHHHHhCCC----HHHHHHHHHHcCCEEC
Confidence 34444455555555667999999999987 3666777677799765
No 39
>PRK11053 dihydropteridine reductase; Provisional
Probab=42.97 E-value=20 Score=27.27 Aligned_cols=36 Identities=25% Similarity=0.315 Sum_probs=26.8
Q ss_pred HHHHHHhhccCCchHHHHHHHHHHHHHHcCCCHHHHHhHcCCCC-CC
Q 038597 98 HFGLLLAANYLEIPALLHRLCQLAADIVKGKTPEEIRRTFNIKK-DF 143 (161)
Q Consensus 98 l~~Ll~AA~~L~I~~L~~l~~~~ia~~i~gks~eeir~~f~i~~-d~ 143 (161)
+..|+.||.-||+... .+.|-..+.+++.|||++ ++
T Consensus 147 ~~~lmLaA~~~Glgs~----------~i~g~~~~~v~~~l~ip~~~~ 183 (217)
T PRK11053 147 LGNLLLGAAALGIDAT----------PIEGFDAAILDAEFGLREKGL 183 (217)
T ss_pred HHHHHHHHHHcCCCCC----------CcCCcCHHHHHHHhCCCCcCc
Confidence 4567777777777654 455678899999999985 45
No 40
>PF04700 Baculo_gp41: Structural glycoprotein p40/gp41 conserved region; InterPro: IPR006790 This is a family of viral structural glycoproteins [] from the baculoviridae.; GO: 0005198 structural molecule activity, 0019012 virion
Probab=41.37 E-value=1.1e+02 Score=23.30 Aligned_cols=45 Identities=13% Similarity=0.216 Sum_probs=29.6
Q ss_pred HHHHHHHHHHHHHhhh-ccCCCcccccccHHHHHHHHHHhhcccccCCC
Q 038597 21 KQVMIQSGTIRNMIED-DAADGEIPLQISSRNLAKVVEWCKCMQHRDRN 68 (161)
Q Consensus 21 ~~~a~~S~~l~~~~~~-~~~~~~I~l~v~s~~L~~Ii~y~~~~~h~~~~ 68 (161)
+++...|-.++-++.+ .-.+.|||+|++..+.. +|+...+|+.+-
T Consensus 57 eAA~hLs~~vkYQiA~AVT~n~PiPlp~~~~~~n---eYl~lL~~ka~i 102 (186)
T PF04700_consen 57 EAARHLSDVVKYQIAEAVTQNKPIPLPFNQQLAN---EYLTLLLQKAQI 102 (186)
T ss_pred HHHHHHHHHHHHHHHHHHHcCCCcCcchhhHHHH---HHHHHHHHhccC
Confidence 3444457777766654 23578999998888777 677655566543
No 41
>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=41.12 E-value=24 Score=24.84 Aligned_cols=40 Identities=25% Similarity=0.473 Sum_probs=30.4
Q ss_pred HHhhccCCchHHHHHHHHHHHHHHcCC----C--------HHHHHh-HcCCCC
Q 038597 102 LLAANYLEIPALLHRLCQLAADIVKGK----T--------PEEIRR-TFNIKK 141 (161)
Q Consensus 102 l~AA~~L~I~~L~~l~~~~ia~~i~gk----s--------~eeir~-~f~i~~ 141 (161)
-.|+..+.++..+-.+|+.+|.+|+|. + ..-||. .||...
T Consensus 37 ~~~~k~F~VpDFVGd~Ck~iaSRIR~aVa~~~Fd~FHknSa~iiR~aVFg~~~ 89 (118)
T PF11978_consen 37 EDAAKLFSVPDFVGDACKAIASRIRGAVASVTFDDFHKNSARIIRQAVFGFDE 89 (118)
T ss_dssp HHHHHTTSSTTHHHHHHHHHHHHHHHHHHTSHHHHHHHHHHHHHHHHHSTS--
T ss_pred hHHHHhcCCcchHHHHHHHHHHHHHHHHhcCcHHHHcccHHHHHHHHhcCCCC
Confidence 378889999999999999999999983 2 444544 677654
No 42
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=41.06 E-value=25 Score=25.45 Aligned_cols=18 Identities=33% Similarity=0.739 Sum_probs=16.7
Q ss_pred CCCHHHHHhHcCCCCCCC
Q 038597 127 GKTPEEIRRTFNIKKDFT 144 (161)
Q Consensus 127 gks~eeir~~f~i~~d~t 144 (161)
|.||+|-|..+|++.||.
T Consensus 98 gmTPd~YR~KW~LP~dYP 115 (148)
T COG4957 98 GLTPDEYRAKWGLPPDYP 115 (148)
T ss_pred CCCHHHHHHhcCCCCCCC
Confidence 899999999999999974
No 43
>KOG3442 consensus Uncharacterized conserved protein [Function unknown]
Probab=39.40 E-value=17 Score=25.90 Aligned_cols=32 Identities=22% Similarity=0.299 Sum_probs=23.1
Q ss_pred cCCCHHHHHhHcCCCCCCCHHHHHHHHHhcCCCCC
Q 038597 126 KGKTPEEIRRTFNIKKDFTPEEEEAVMDEHGWAFH 160 (161)
Q Consensus 126 ~gks~eeir~~f~i~~d~t~eee~~i~~e~~w~~~ 160 (161)
.|.|.+|-++++||.++++.|| |.+.|.-+|+
T Consensus 54 ~~iTlqEa~qILnV~~~ln~ee---i~k~yehLFe 85 (132)
T KOG3442|consen 54 GKITLQEAQQILNVKEPLNREE---IEKRYEHLFE 85 (132)
T ss_pred ccccHHHHhhHhCCCCCCCHHH---HHHHHHHHHh
Confidence 4578999999999998776644 5555555553
No 44
>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=37.74 E-value=41 Score=20.50 Aligned_cols=24 Identities=25% Similarity=0.566 Sum_probs=18.3
Q ss_pred HHHHHhHcCCC-CC-CCHHHHHHHHH
Q 038597 130 PEEIRRTFNIK-KD-FTPEEEEAVMD 153 (161)
Q Consensus 130 ~eeir~~f~i~-~d-~t~eee~~i~~ 153 (161)
.+++|..||=- .+ +||||..+|.+
T Consensus 30 ad~lr~klG~IC~~CitpEE~~~I~e 55 (60)
T PF10892_consen 30 ADDLRVKLGGICGDCITPEEDREILE 55 (60)
T ss_pred hHHHHHHHcchhhccCCHHHHHHHHH
Confidence 67888888733 34 89999988865
No 45
>PF09821 AAA_assoc_C: C-terminal AAA-associated domain; InterPro: IPR018632 Members of this family are found in various prokaryotic ABC transporters, predominantly involved in nitrate, sulphonate and bicarbonate translocation.
Probab=37.42 E-value=29 Score=24.36 Aligned_cols=21 Identities=19% Similarity=0.170 Sum_probs=18.7
Q ss_pred hcCChHHHHHHHHhhccCCch
Q 038597 91 VSEDKDLHFGLLLAANYLEIP 111 (161)
Q Consensus 91 ~~~~~~~l~~Ll~AA~~L~I~ 111 (161)
++++.+.|+.++.||..||.-
T Consensus 7 l~~eiDdL~p~~eAaelLgf~ 27 (120)
T PF09821_consen 7 LHLEIDDLLPIVEAAELLGFA 27 (120)
T ss_pred hCCcHHHHHHHHHHHHHcCCe
Confidence 678899999999999999875
No 46
>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=37.32 E-value=92 Score=18.58 Aligned_cols=41 Identities=20% Similarity=0.130 Sum_probs=28.4
Q ss_pred chHHHHHHHHHHHHHHcCC--CHHHHHhHcCCCCCCCHHHHHHHHH
Q 038597 110 IPALLHRLCQLAADIVKGK--TPEEIRRTFNIKKDFTPEEEEAVMD 153 (161)
Q Consensus 110 I~~L~~l~~~~ia~~i~gk--s~eeir~~f~i~~d~t~eee~~i~~ 153 (161)
-+.++-.+|-++|.++.+. +..++....|. +|.++..+..+
T Consensus 37 ~~~~ia~a~l~lA~k~~~~~~~~~~~~~~~~~---~~~~~i~~~~~ 79 (83)
T smart00385 37 SPSLIAAAALYLAAKTEEIPPWTKELVHYTGY---FTEEEILRMEK 79 (83)
T ss_pred CHHHHHHHHHHHHHHHhcCCCCchhHhHhhCC---CCHHHHHHHHH
Confidence 3466777788889988874 56777777765 67766655544
No 47
>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=35.24 E-value=45 Score=23.28 Aligned_cols=37 Identities=22% Similarity=0.260 Sum_probs=24.8
Q ss_pred HHHhhccCCchHHHHHH-HHHHHHHHcCCCHHHHHhHc
Q 038597 101 LLLAANYLEIPALLHRL-CQLAADIVKGKTPEEIRRTF 137 (161)
Q Consensus 101 Ll~AA~~L~I~~L~~l~-~~~ia~~i~gks~eeir~~f 137 (161)
.+.-+.|-.-=.-...+ +..++++++|||.+|.+.+-
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 45555555554444444 46678899999999888654
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=35.19 E-value=40 Score=17.91 Aligned_cols=20 Identities=25% Similarity=0.504 Sum_probs=16.0
Q ss_pred HHHHHHHcCCCHHHHHhHcC
Q 038597 119 QLAADIVKGKTPEEIRRTFN 138 (161)
Q Consensus 119 ~~ia~~i~gks~eeir~~f~ 138 (161)
..||..+.++|..+++.++.
T Consensus 23 ~~Ia~~~~~rs~~~~~~~~~ 42 (45)
T cd00167 23 EKIAKELPGRTPKQCRERWR 42 (45)
T ss_pred HHHHhHcCCCCHHHHHHHHH
Confidence 56788888899999988763
No 49
>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=35.14 E-value=38 Score=18.76 Aligned_cols=30 Identities=33% Similarity=0.380 Sum_probs=23.5
Q ss_pred cCCchHHHHHHHHHHHHHHcCCCHHHHHhH
Q 038597 107 YLEIPALLHRLCQLAADIVKGKTPEEIRRT 136 (161)
Q Consensus 107 ~L~I~~L~~l~~~~ia~~i~gks~eeir~~ 136 (161)
||.-++|-+.....|+..+..-++++|...
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 566778888888888888888888887654
No 50
>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=34.98 E-value=32 Score=25.92 Aligned_cols=38 Identities=21% Similarity=0.213 Sum_probs=27.2
Q ss_pred HHHHHHHhhccCCchHHHHHHHHHHHHHHcCCCHHHHHhHcCCCCCCC
Q 038597 97 LHFGLLLAANYLEIPALLHRLCQLAADIVKGKTPEEIRRTFNIKKDFT 144 (161)
Q Consensus 97 ~l~~Ll~AA~~L~I~~L~~l~~~~ia~~i~gks~eeir~~f~i~~d~t 144 (161)
-+..++.||..+|+-.. ++.+-..+.+++.|||+.+++
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 44577888888888752 223445789999999997654
No 51
>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=34.32 E-value=61 Score=19.96 Aligned_cols=43 Identities=16% Similarity=0.381 Sum_probs=28.4
Q ss_pred eEEEEeCCC------CEEEecHHH--HHHHHHHHHHhhhccCCCccccc--ccHH
Q 038597 6 TVKLRSGDN------EVFEVEKQV--MIQSGTIRNMIEDDAADGEIPLQ--ISSR 50 (161)
Q Consensus 6 ~i~l~s~Dg------~~~~v~~~~--a~~S~~l~~~~~~~~~~~~I~l~--v~s~ 50 (161)
.|+|.|.+| ..+.||..+ ...|.+++.++.+ ...++|+. |++.
T Consensus 3 ~v~F~t~~~~~~~~~~~~~VP~~~t~~~Ls~LvN~LL~~--~~~~vpfdF~i~~~ 55 (65)
T PF08154_consen 3 QVQFVTEDGEYEVPGTPISVPSNITRKELSELVNQLLDD--EEEPVPFDFLINGE 55 (65)
T ss_pred EEEEEcCCCCccCCCCCEEEeCCCCHHHHHHHHHHHhcc--CCCCCcEEEEECCE
Confidence 366777776 467777766 3469999999822 35667766 5543
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=34.25 E-value=56 Score=22.80 Aligned_cols=24 Identities=29% Similarity=0.421 Sum_probs=18.2
Q ss_pred HHHHHHHHHHHHHHcCCCHHHHHh
Q 038597 112 ALLHRLCQLAADIVKGKTPEEIRR 135 (161)
Q Consensus 112 ~L~~l~~~~ia~~i~gks~eeir~ 135 (161)
...-.++..++++++|||++|+.+
T Consensus 62 ~~~~Asas~~~~~i~gk~l~ea~~ 85 (126)
T PF01592_consen 62 AISIASASMMCELIKGKTLEEALK 85 (126)
T ss_dssp HHHHHHHHHHHHHHTTSBHHHHHC
T ss_pred hHHHHHHHHHHHHHcCCCHHHHHH
Confidence 344556778889999999888854
No 53
>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=33.92 E-value=70 Score=22.22 Aligned_cols=37 Identities=19% Similarity=0.238 Sum_probs=24.9
Q ss_pred HHHhhccCCchHHHHHH-HHHHHHHHcCCCHHHHHhHc
Q 038597 101 LLLAANYLEIPALLHRL-CQLAADIVKGKTPEEIRRTF 137 (161)
Q Consensus 101 Ll~AA~~L~I~~L~~l~-~~~ia~~i~gks~eeir~~f 137 (161)
.+..+.|-.-=.-+..+ +..++++++|||++|..++-
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 55556666555444444 45668899999999977654
No 54
>PRK11325 scaffold protein; Provisional
Probab=33.68 E-value=64 Score=22.66 Aligned_cols=38 Identities=24% Similarity=0.186 Sum_probs=25.3
Q ss_pred HHHhhccCCchHHHHHH-HHHHHHHHcCCCHHHHHhHcC
Q 038597 101 LLLAANYLEIPALLHRL-CQLAADIVKGKTPEEIRRTFN 138 (161)
Q Consensus 101 Ll~AA~~L~I~~L~~l~-~~~ia~~i~gks~eeir~~f~ 138 (161)
.+.-+.|-.-=.-...+ +..++++++|||++|.+.+-+
T Consensus 52 ~I~d~~f~~~GC~is~Asas~~~e~~~Gktl~ea~~i~~ 90 (127)
T PRK11325 52 IIEDAKFKTYGCGSAIASSSLVTEWVKGKTLDEALAIKN 90 (127)
T ss_pred eEEEEEEEeeCCHHHHHHHHHHHHHHcCCCHHHHHhcCH
Confidence 55556666555444444 456678999999999886533
No 55
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=33.53 E-value=44 Score=18.01 Aligned_cols=20 Identities=30% Similarity=0.481 Sum_probs=16.0
Q ss_pred HHHHHHHcCCCHHHHHhHcC
Q 038597 119 QLAADIVKGKTPEEIRRTFN 138 (161)
Q Consensus 119 ~~ia~~i~gks~eeir~~f~ 138 (161)
..||..+.++|+.+++.++.
T Consensus 25 ~~Ia~~~~~rt~~~~~~~~~ 44 (49)
T smart00717 25 EKIAKELPGRTAEQCRERWN 44 (49)
T ss_pred HHHHHHcCCCCHHHHHHHHH
Confidence 56777788999999988764
No 56
>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=33.39 E-value=1.4e+02 Score=20.97 Aligned_cols=38 Identities=5% Similarity=-0.034 Sum_probs=22.6
Q ss_pred HHHHHHHHHcCCCHHHHHhHcCCCCCCCHHHHHHHHHh
Q 038597 117 LCQLAADIVKGKTPEEIRRTFNIKKDFTPEEEEAVMDE 154 (161)
Q Consensus 117 ~~~~ia~~i~gks~eeir~~f~i~~d~t~eee~~i~~e 154 (161)
..+.+.+.+-|.++..+-..|--.+.+++||.+++++-
T Consensus 76 ~~~~~~~~~f~gs~~~ll~~l~~~~~ls~eele~L~~l 113 (130)
T TIGR02698 76 AAQELFSRICSRKVGAVIADLIEESPLSQTDIEKLEKL 113 (130)
T ss_pred HHHHHHHHHHCCCHHHHHHHHHhcCCCCHHHHHHHHHH
Confidence 34444554555555555444432466888888888763
No 57
>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=33.37 E-value=26 Score=18.51 Aligned_cols=13 Identities=38% Similarity=0.577 Sum_probs=9.0
Q ss_pred cCCCHHHHHhHcC
Q 038597 126 KGKTPEEIRRTFN 138 (161)
Q Consensus 126 ~gks~eeir~~f~ 138 (161)
.|-|.+|+|+++.
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 5889999999864
No 58
>PF13518 HTH_28: Helix-turn-helix domain
Probab=32.71 E-value=71 Score=17.89 Aligned_cols=21 Identities=29% Similarity=0.512 Sum_probs=16.6
Q ss_pred HHHHHHcCCCHHHHHhHcCCC
Q 038597 120 LAADIVKGKTPEEIRRTFNIK 140 (161)
Q Consensus 120 ~ia~~i~gks~eeir~~f~i~ 140 (161)
.|.....|.|..++.+.|||.
T Consensus 5 iv~~~~~g~s~~~~a~~~gis 25 (52)
T PF13518_consen 5 IVELYLEGESVREIAREFGIS 25 (52)
T ss_pred HHHHHHcCCCHHHHHHHHCCC
Confidence 344455789999999999994
No 59
>PF13798 PCYCGC: Protein of unknown function with PCYCGC motif
Probab=31.46 E-value=73 Score=23.63 Aligned_cols=24 Identities=33% Similarity=0.400 Sum_probs=18.0
Q ss_pred HHHHHHHHHHHHHcCCCHHHHHhH
Q 038597 113 LLHRLCQLAADIVKGKTPEEIRRT 136 (161)
Q Consensus 113 L~~l~~~~ia~~i~gks~eeir~~ 136 (161)
-++.+...+...=+|||+.|||+.
T Consensus 117 Cl~ia~~a~~~~~~Gks~~eIR~~ 140 (158)
T PF13798_consen 117 CLDIAVQAVQMYQEGKSPKEIRQY 140 (158)
T ss_pred HHHHHHHHHHHHHcCCCHHHHHHH
Confidence 355566666666789999999985
No 60
>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=31.08 E-value=1.4e+02 Score=18.79 Aligned_cols=40 Identities=13% Similarity=0.126 Sum_probs=25.0
Q ss_pred HHHHhhccCCchHHHHHHHHHHHHH---------HcCCCHHHHHhHcCC
Q 038597 100 GLLLAANYLEIPALLHRLCQLAADI---------VKGKTPEEIRRTFNI 139 (161)
Q Consensus 100 ~Ll~AA~~L~I~~L~~l~~~~ia~~---------i~gks~eeir~~f~i 139 (161)
++...|...+.+.|.+.|.++++.. +...+.+++...++-
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 4555666677777777777776553 233456666666653
No 61
>PF15063 TC1: Thyroid cancer protein 1
Probab=30.41 E-value=53 Score=21.31 Aligned_cols=12 Identities=25% Similarity=0.393 Sum_probs=5.3
Q ss_pred HHHHhHcCCCCC
Q 038597 131 EEIRRTFNIKKD 142 (161)
Q Consensus 131 eeir~~f~i~~d 142 (161)
|.-|-.|++..|
T Consensus 56 eRA~iI~~~~~d 67 (79)
T PF15063_consen 56 ERARIIWECAQD 67 (79)
T ss_pred HHHHHHHhhCCC
Confidence 333444554444
No 62
>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=29.85 E-value=44 Score=24.46 Aligned_cols=37 Identities=14% Similarity=-0.035 Sum_probs=25.8
Q ss_pred HHHHHHhhccCCchHHHHHHHHHHHHHHcCCCH-HHHHhHcCCCCCCC
Q 038597 98 HFGLLLAANYLEIPALLHRLCQLAADIVKGKTP-EEIRRTFNIKKDFT 144 (161)
Q Consensus 98 l~~Ll~AA~~L~I~~L~~l~~~~ia~~i~gks~-eeir~~f~i~~d~t 144 (161)
+..++.||.-||+... .+.+... +.+++.|||++++.
T Consensus 129 ~~~l~LaA~~~Glgs~----------~~~~~~~~~~v~~~l~ip~~~~ 166 (193)
T cd02144 129 CGLLLAALQNAGLGTV----------TTTPLNMGPFLRRLLGRPANEK 166 (193)
T ss_pred HHHHHHHHHHCCCcee----------ecCCcchhHHHHHHhCCCCCCc
Confidence 3457888888888762 2234333 89999999998654
No 63
>PHA03098 kelch-like protein; Provisional
Probab=29.85 E-value=2.4e+02 Score=24.35 Aligned_cols=54 Identities=6% Similarity=0.020 Sum_probs=41.9
Q ss_pred HHhhhhhhcCChHHHHHHHHhhccCCchHHHHHHHHHHHHHHc---------CCCHHHHHhHcC
Q 038597 84 EKKFDEEVSEDKDLHFGLLLAANYLEIPALLHRLCQLAADIVK---------GKTPEEIRRTFN 138 (161)
Q Consensus 84 d~~F~~~~~~~~~~l~~Ll~AA~~L~I~~L~~l~~~~ia~~i~---------gks~eeir~~f~ 138 (161)
-.+|+.+ .++.+..++++..|...+...|.+.|-++|+..+. ..+.+++.+.+.
T Consensus 97 C~~~l~~-~l~~~nc~~~~~~a~~~~~~~L~~~~~~~i~~nf~~v~~~~~f~~l~~~~l~~ll~ 159 (534)
T PHA03098 97 CINYIIK-IIDDNNCIDIYRFSFFYGCKKLYSAAYNYIRNNIELIYNDPDFIYLSKNELIKILS 159 (534)
T ss_pred HHHHHHH-hCCHhHHHHHHHHHHHcCcHHHHHHHHHHHHHHHHHHhcCchhhcCCHHHHHHHhc
Confidence 3456321 37889999999999999999999999999886553 236778887765
No 64
>PF11198 DUF2857: Protein of unknown function (DUF2857); InterPro: IPR021364 This is a bacterial family of uncharacterised proteins.
Probab=29.55 E-value=1.1e+02 Score=23.03 Aligned_cols=51 Identities=24% Similarity=0.176 Sum_probs=31.9
Q ss_pred cCChHHHHHHHHhhc-----cCCchHHHHHH-HHHHHHHHcCCCHHHH---HhHcCCCCC
Q 038597 92 SEDKDLHFGLLLAAN-----YLEIPALLHRL-CQLAADIVKGKTPEEI---RRTFNIKKD 142 (161)
Q Consensus 92 ~~~~~~l~~Ll~AA~-----~L~I~~L~~l~-~~~ia~~i~gks~eei---r~~f~i~~d 142 (161)
.+|.+.+-.++.-|. .--|+.++.++ +..+-..+-|.|+.|+ |+.+|++..
T Consensus 57 ~in~~~l~~~L~~~~~~~~~~~~idr~L~lGAS~~mm~~~FGls~~ev~~rR~llgi~~~ 116 (180)
T PF11198_consen 57 SINHDVLWRLLEQARREQQEQQLIDRALRLGASIEMMQRLFGLSSAEVAARRRLLGIPVR 116 (180)
T ss_pred eeCHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHhCCCCC
Confidence 466776666666554 23444555554 4555666678887776 668888853
No 65
>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=29.24 E-value=26 Score=25.13 Aligned_cols=18 Identities=44% Similarity=0.826 Sum_probs=12.5
Q ss_pred CCCHHHHHhHcCCCCCCC
Q 038597 127 GKTPEEIRRTFNIKKDFT 144 (161)
Q Consensus 127 gks~eeir~~f~i~~d~t 144 (161)
|.|++|=|+.||++.|+.
T Consensus 94 gltp~eYR~kwGlp~dyp 111 (132)
T PF05443_consen 94 GLTPEEYRAKWGLPKDYP 111 (132)
T ss_dssp -S-HHHHHHHTT-GGG--
T ss_pred CCCHHHHHHHhCcCCCCc
Confidence 899999999999998853
No 66
>PF00249 Myb_DNA-binding: Myb-like DNA-binding domain; InterPro: IPR014778 The retroviral oncogene v-myb, and its cellular counterpart c-myb, encode nuclear DNA-binding proteins. These belong to the SANT domain family that specifically recognise the sequence YAAC(G/T)G [, ]. In myb, one of the most conserved regions consisting of three tandem repeats has been shown to be involved in DNA-binding [].; PDB: 1X41_A 2XAF_B 2XAG_B 2XAH_B 2UXN_B 2Y48_B 2XAQ_B 2X0L_B 2IW5_B 2XAJ_B ....
Probab=29.24 E-value=1.1e+02 Score=17.13 Aligned_cols=39 Identities=18% Similarity=0.162 Sum_probs=27.1
Q ss_pred ChHHHHHHHHhhccCCchHHHHHHHHHHHHHHc-CCCHHHHHhHc
Q 038597 94 DKDLHFGLLLAANYLEIPALLHRLCQLAADIVK-GKTPEEIRRTF 137 (161)
Q Consensus 94 ~~~~l~~Ll~AA~~L~I~~L~~l~~~~ia~~i~-gks~eeir~~f 137 (161)
+.++-..|+.|..-++-. -=..||..+. |+|+.+++..|
T Consensus 5 t~eE~~~l~~~v~~~g~~-----~W~~Ia~~~~~~Rt~~qc~~~~ 44 (48)
T PF00249_consen 5 TEEEDEKLLEAVKKYGKD-----NWKKIAKRMPGGRTAKQCRSRY 44 (48)
T ss_dssp -HHHHHHHHHHHHHSTTT-----HHHHHHHHHSSSSTHHHHHHHH
T ss_pred CHHHHHHHHHHHHHhCCc-----HHHHHHHHcCCCCCHHHHHHHH
Confidence 344455566666666655 4567888888 99999999865
No 67
>PF10507 DUF2453: Protein of unknown function (DUF2453); InterPro: IPR019537 The function of these transmembrane protein is not known.
Probab=28.45 E-value=1.3e+02 Score=20.93 Aligned_cols=38 Identities=13% Similarity=0.218 Sum_probs=28.7
Q ss_pred HHHHHHHHHHHHHHcC-------CCHHHHHhHcCCCC-CCCHHHHH
Q 038597 112 ALLHRLCQLAADIVKG-------KTPEEIRRTFNIKK-DFTPEEEE 149 (161)
Q Consensus 112 ~L~~l~~~~ia~~i~g-------ks~eeir~~f~i~~-d~t~eee~ 149 (161)
+|-.++++.+.+.+++ ..+|.+.+++|++. ++|++|.+
T Consensus 34 giStmAAAalGN~vSDv~Gi~~~~~vE~~~~rlg~~~P~Lt~~Q~~ 79 (111)
T PF10507_consen 34 GISTMAAAALGNLVSDVAGIGLGGYVERLAQRLGLKAPVLTPAQLN 79 (111)
T ss_pred hHHHHHHHHHhhhhhhhhhhHHHHHHHHHHHHhCCCCCCCCHHHHh
Confidence 4556667777776665 35999999999997 59998865
No 68
>cd02140 Nitroreductase_4 Nitroreductase-like family 4. A subfamily of the nitroreductase family containing uncharacterized proteins that are similar to nitroreductase. Nitroreductase catalyzes the reduction of nitroaromatic compounds such as nitrotoluenes, nitrofurans and nitroimidazoles. This process requires NAD(P)H as electron donor in an obligatory two-electron transfer and uses FMN as cofactor. The enzyme is typically a homodimer. Members of this family are also called NADH dehydrogenase, oxygen-insensitive NAD(P)H nitrogenase or dihydropteridine reductase.
Probab=27.70 E-value=50 Score=24.53 Aligned_cols=38 Identities=21% Similarity=0.257 Sum_probs=25.7
Q ss_pred HHHHHHhhccCCchHHHHHHHHHHHHHHcCCCHHHHHhHcCCCCCC
Q 038597 98 HFGLLLAANYLEIPALLHRLCQLAADIVKGKTPEEIRRTFNIKKDF 143 (161)
Q Consensus 98 l~~Ll~AA~~L~I~~L~~l~~~~ia~~i~gks~eeir~~f~i~~d~ 143 (161)
+..|+.||.-+|+-..... ......+.+|+.|||++++
T Consensus 127 ~~nl~LaA~~~GlGs~~~~--------~~~~~~~~v~~~l~ip~~~ 164 (192)
T cd02140 127 QIAVWTALAAEGIGANLQH--------YNPLIDEEVAKKWNIPSNW 164 (192)
T ss_pred HHHHHHHHHhCCCcccHHH--------hCccCCHHHHHhcCCCccc
Confidence 4688888888888763211 0012358999999999765
No 69
>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=27.50 E-value=68 Score=20.25 Aligned_cols=21 Identities=24% Similarity=0.275 Sum_probs=18.2
Q ss_pred CeEEEEeCCCCEEEecHHHHH
Q 038597 5 STVKLRSGDNEVFEVEKQVMI 25 (161)
Q Consensus 5 ~~i~l~s~Dg~~~~v~~~~a~ 25 (161)
+.|.++|.||..+.+|....+
T Consensus 21 ~~V~v~s~~Gr~v~~Pa~~lR 41 (68)
T PF11197_consen 21 SKVVVRSDDGRRVQFPARHLR 41 (68)
T ss_pred cEEEEEecCCcEEEEeHHHCc
Confidence 578999999999999987654
No 70
>COG1710 Uncharacterized protein conserved in archaea [Function unknown]
Probab=27.18 E-value=45 Score=23.64 Aligned_cols=21 Identities=33% Similarity=0.643 Sum_probs=16.4
Q ss_pred HHHHH-cCCCHHHHHhHcCCCC
Q 038597 121 AADIV-KGKTPEEIRRTFNIKK 141 (161)
Q Consensus 121 ia~~i-~gks~eeir~~f~i~~ 141 (161)
|-.++ +||++.||.+.+||+=
T Consensus 102 i~emlr~gk~preIsk~lGIpi 123 (139)
T COG1710 102 IREMLRNGKTPREISKDLGIPI 123 (139)
T ss_pred HHHHHHcCCCHHHHHHhhCCch
Confidence 33444 4999999999999973
No 71
>PRK09296 cysteine desufuration protein SufE; Provisional
Probab=26.68 E-value=1.3e+02 Score=21.63 Aligned_cols=34 Identities=21% Similarity=0.407 Sum_probs=24.0
Q ss_pred HHHHHHHHHHHHHHcCCCHHHHHh--------HcCCCCCCCH
Q 038597 112 ALLHRLCQLAADIVKGKTPEEIRR--------TFNIKKDFTP 145 (161)
Q Consensus 112 ~L~~l~~~~ia~~i~gks~eeir~--------~f~i~~d~t~ 145 (161)
.++.-.+..+...++|+|++||.+ .+|+..-+||
T Consensus 76 ~ivkGl~alL~~~~~g~tp~eIl~~d~~~~~~~lGL~~~LSp 117 (138)
T PRK09296 76 AIVKGLIAVVFILYQQMTPQDIVNFDVRPWFEKLALTQHLTP 117 (138)
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHhCChHHHHHHcCcccccCc
Confidence 344455666777889999999874 4577766776
No 72
>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=26.63 E-value=62 Score=18.07 Aligned_cols=19 Identities=21% Similarity=0.375 Sum_probs=15.3
Q ss_pred CCeEEEEeCCCCEEEecHH
Q 038597 4 TSTVKLRSGDNEVFEVEKQ 22 (161)
Q Consensus 4 ~~~i~l~s~Dg~~~~v~~~ 22 (161)
...+++++.||+...|+++
T Consensus 23 g~~vtV~~~~G~~~tv~~d 41 (42)
T PF02736_consen 23 GDKVTVKTEDGKEVTVKKD 41 (42)
T ss_dssp SSEEEEEETTTEEEEEEGG
T ss_pred CCEEEEEECCCCEEEeCCC
Confidence 3578999999999988753
No 73
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=26.33 E-value=67 Score=18.04 Aligned_cols=15 Identities=20% Similarity=0.417 Sum_probs=10.7
Q ss_pred cCCCHHHHHhHcCCC
Q 038597 126 KGKTPEEIRRTFNIK 140 (161)
Q Consensus 126 ~gks~eeir~~f~i~ 140 (161)
.|+|..+|.+.||++
T Consensus 16 ~G~s~~~ia~~lgvs 30 (50)
T PF13384_consen 16 EGWSIREIAKRLGVS 30 (50)
T ss_dssp HT--HHHHHHHHTS-
T ss_pred CCCCHHHHHHHHCcC
Confidence 499999999999976
No 74
>PF09713 A_thal_3526: Plant protein 1589 of unknown function (A_thal_3526); InterPro: IPR006476 This plant-specific family of proteins are defined by an uncharacterised region 57 residues in length. It is found toward the N terminus of most proteins that contain it. Examples include at least several proteins from Arabidopsis thaliana (Mouse-ear cress) and Oryza sativa (Rice). The function of the proteins are unknown.
Probab=25.66 E-value=42 Score=20.26 Aligned_cols=33 Identities=24% Similarity=0.182 Sum_probs=24.2
Q ss_pred CCCHHHH----HhHcCCCCCCCHHHHHHHHHhcCCCC
Q 038597 127 GKTPEEI----RRTFNIKKDFTPEEEEAVMDEHGWAF 159 (161)
Q Consensus 127 gks~eei----r~~f~i~~d~t~eee~~i~~e~~w~~ 159 (161)
.+|.+|+ .+..||+..+|.-=..+++++|+=.|
T Consensus 12 yMsk~E~v~~L~~~a~I~P~~T~~VW~~Le~eN~eFF 48 (54)
T PF09713_consen 12 YMSKEECVRALQKQANIEPVFTSTVWQKLEKENPEFF 48 (54)
T ss_pred cCCHHHHHHHHHHHcCCChHHHHHHHHHHHHHCHHHH
Confidence 4555554 44558998999988999999987444
No 75
>COG0822 IscU NifU homolog involved in Fe-S cluster formation [Energy production and conversion]
Probab=25.44 E-value=1.2e+02 Score=22.17 Aligned_cols=39 Identities=21% Similarity=0.313 Sum_probs=27.8
Q ss_pred HHHHHhhccCCchHHHHHH-HHHHHHHHcCCCHHHHHhHc
Q 038597 99 FGLLLAANYLEIPALLHRL-CQLAADIVKGKTPEEIRRTF 137 (161)
Q Consensus 99 ~~Ll~AA~~L~I~~L~~l~-~~~ia~~i~gks~eeir~~f 137 (161)
-+.+..|.|.+.=.=+..+ +..+.++++|||.+|.++.-
T Consensus 51 ~~~I~d~~F~~~GC~is~ASss~~te~v~Gkti~EAl~i~ 90 (150)
T COG0822 51 NGVIEDAKFKGFGCAISIASSSMMTELVKGKTLDEALKIT 90 (150)
T ss_pred CCEEEEEEeeecCcHHHHHHHHHHHHHHcCCCHHHHHHHH
Confidence 4566677777766444444 45667899999999998765
No 76
>PRK13696 hypothetical protein; Provisional
Probab=25.38 E-value=1.8e+02 Score=18.10 Aligned_cols=38 Identities=21% Similarity=0.284 Sum_probs=24.7
Q ss_pred HHHHHHHHHHHHHHcCCCHHHHHhHcCCCCCCCHHHHHHHHHh
Q 038597 112 ALLHRLCQLAADIVKGKTPEEIRRTFNIKKDFTPEEEEAVMDE 154 (161)
Q Consensus 112 ~L~~l~~~~ia~~i~gks~eeir~~f~i~~d~t~eee~~i~~e 154 (161)
++-++.-..+ .-+..+...+.++||+-+ +||-++++++
T Consensus 24 SFSevi~~L~--~~~~~~~~~l~~~~Gil~---dee~~e~~~~ 61 (62)
T PRK13696 24 SFSEVIRELI--EKKKGNLDKLMKAFGILS---EEEAEELKKE 61 (62)
T ss_pred CHHHHHHHHH--HHhhccHHHHHHHHCCCC---HHHHHHHHhh
Confidence 4444444444 223456888999999964 4777787765
No 77
>cd06664 IscU_like Iron-sulfur cluster scaffold-like proteins. IscU_like and NifU_like proteins. IscU and NifU function as a scaffold for the assembly of [2Fe-2S] clusters before they are transferred to apo target proteins. They are highly conserved and play vital roles in the ISC and NIF systems of Fe-S protein maturation. NIF genes participate in nitrogen fixation in several isolated bacterial species. The NifU domain, however, is also found in bacteria that do not fix nitrogen, so it may have wider significance in the cell. Human IscU interacts with frataxin, the Friedreich ataxia gene product, and incorrectly spliced IscU has been shown to disrupt iron homeostasis in skeletal muscle and cause myopathy.
Probab=25.25 E-value=1.2e+02 Score=20.75 Aligned_cols=39 Identities=23% Similarity=0.391 Sum_probs=26.4
Q ss_pred HHHHhhccCCchHHHHHH-HHHHHHHHcCCCHHHHHhHcC
Q 038597 100 GLLLAANYLEIPALLHRL-CQLAADIVKGKTPEEIRRTFN 138 (161)
Q Consensus 100 ~Ll~AA~~L~I~~L~~l~-~~~ia~~i~gks~eeir~~f~ 138 (161)
+.+..+.|-.-=..+-.+ +..++++++||+.+|+..+..
T Consensus 46 ~~I~d~~f~~~GC~i~~Asas~~~~~~~Gk~~~ea~~i~~ 85 (123)
T cd06664 46 GRITDAKFQGFGCAISIASASLLTELIKGKTLDEALKLLN 85 (123)
T ss_pred CEEEEEEEEecCcHHHHHHHHHHHHHHcCCcHHHHHHHHH
Confidence 455666665555444444 456688999999999987653
No 78
>PRK15019 CsdA-binding activator; Provisional
Probab=25.18 E-value=1.3e+02 Score=21.92 Aligned_cols=34 Identities=18% Similarity=0.404 Sum_probs=23.9
Q ss_pred HHHHHHHHHHHHHHcCCCHHHHHh--------HcCCCCCCCH
Q 038597 112 ALLHRLCQLAADIVKGKTPEEIRR--------TFNIKKDFTP 145 (161)
Q Consensus 112 ~L~~l~~~~ia~~i~gks~eeir~--------~f~i~~d~t~ 145 (161)
.++.-.++.+...++|+|++||.+ .+|+..-+||
T Consensus 86 ~IvkGl~alL~~~~~g~tp~eIl~~d~~~~~~~lGL~~~LSp 127 (147)
T PRK15019 86 RIVRGLLAVLLTAVEGKTAAELQAQSPLALFDELGLRAQLSA 127 (147)
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHhcCHHHHHHHCCchhhcCc
Confidence 344555566677789999999875 4577766776
No 79
>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=25.08 E-value=1.4e+02 Score=19.62 Aligned_cols=39 Identities=23% Similarity=0.427 Sum_probs=27.3
Q ss_pred HHHHHHHHHHHcCCCHHHHHh-------HcCCCCCCCHHHHHHHHH
Q 038597 115 HRLCQLAADIVKGKTPEEIRR-------TFNIKKDFTPEEEEAVMD 153 (161)
Q Consensus 115 ~l~~~~ia~~i~gks~eeir~-------~f~i~~d~t~eee~~i~~ 153 (161)
.++...+++.++|.....|++ .||+-.+++..+.+++-+
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 567788888999987777665 599999999988877654
No 80
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=25.03 E-value=56 Score=19.99 Aligned_cols=15 Identities=33% Similarity=0.490 Sum_probs=12.4
Q ss_pred CeEEEEeCCCCEEEe
Q 038597 5 STVKLRSGDNEVFEV 19 (161)
Q Consensus 5 ~~i~l~s~Dg~~~~v 19 (161)
+-+++.+.||++|--
T Consensus 5 KA~Kv~~RDGE~~lr 19 (65)
T COG4049 5 KAIKVRDRDGEEFLR 19 (65)
T ss_pred eeeEeeccCCceeee
Confidence 568999999998863
No 81
>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=24.72 E-value=95 Score=21.56 Aligned_cols=32 Identities=22% Similarity=0.323 Sum_probs=20.4
Q ss_pred CCchHHHHHHHHHHHHHHc--CCCHHHHHhHcCCC
Q 038597 108 LEIPALLHRLCQLAADIVK--GKTPEEIRRTFNIK 140 (161)
Q Consensus 108 L~I~~L~~l~~~~ia~~i~--gks~eeir~~f~i~ 140 (161)
+++..|.+.+.+.. ..++ +.|+.+||++|+--
T Consensus 8 ~~~~~~~~~Ae~~~-k~l~~~~lttsQlRkf~~~v 41 (119)
T PF03750_consen 8 LDIELLVDYAEKIA-KELKKNKLTTSQLRKFYDEV 41 (119)
T ss_pred cCHHHHHHHHHHHH-HHHHhCCCCHHHHHHHHHHH
Confidence 44555555555444 4344 47999999999843
No 82
>PF03131 bZIP_Maf: bZIP Maf transcription factor; InterPro: IPR004826 There are several different types of Maf transcription factors with different roles in the cell. MafG and MafH are small Mafs which lack a putative transactivation domain. They behave as transcriptional repressors when they dimerize among themselves. However they also serve as transcriptional activators by dimerizing with other (usually larger) basic-zipper proteins and recruiting them to specific DNA-binding sites. Maf transcription factors contain a conserved basic region leucine zipper (bZIP) domain, which mediates their dimerization and DNA binding property. Neural retina-specific leucine zipper proteins also belong to this family. Together with the basic region, the Maf extended homology region (EHR), conserved only within the Maf family, defines the DNA binding specific to Mafs. This structure enables Mafs to make a broader area of contact with DNA and to recognise longer DNA sequences. In particular, the two residues at the beginning of helix H2 are positioned to recognise the flanking region []. Small Maf proteins heterodimerize with Fos and may act as competitive repressors of the NF2-E2 transcription factor. In mouse, Maf1 may play an early role in axial patterning. Defects in these proteins are a cause of autosomal dominant retinitis pigmentosa. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 2KZ5_A 3A5T_A 1K1V_A 1SKN_P 2WT7_B 2WTY_B.
Probab=24.51 E-value=97 Score=20.39 Aligned_cols=27 Identities=15% Similarity=0.218 Sum_probs=19.8
Q ss_pred HHcCCCHHHHHhHcCCCCCCCHHHHHHHHH
Q 038597 124 IVKGKTPEEIRRTFNIKKDFTPEEEEAVMD 153 (161)
Q Consensus 124 ~i~gks~eeir~~f~i~~d~t~eee~~i~~ 153 (161)
.|...+++|+..++ ..+|+++...+++
T Consensus 5 eL~~m~v~efn~~L---~~lt~~q~~~lK~ 31 (92)
T PF03131_consen 5 ELVSMSVREFNRLL---RGLTEEQIAELKQ 31 (92)
T ss_dssp HHHHS-HHHHHHHC---TTS-HHHHHHHHH
T ss_pred HHhhCCHHHHHHHH---HcCCHHHHHHHHH
Confidence 45678899999988 6799998877754
No 83
>KOG4244 consensus Failed axon connections (fax) protein/glutathione S-transferase-like protein [Signal transduction mechanisms]
Probab=24.41 E-value=93 Score=25.19 Aligned_cols=23 Identities=22% Similarity=0.515 Sum_probs=18.9
Q ss_pred HHHHHhHcCCCCCCCHHHHHHHH
Q 038597 130 PEEIRRTFNIKKDFTPEEEEAVM 152 (161)
Q Consensus 130 ~eeir~~f~i~~d~t~eee~~i~ 152 (161)
...+|+.|++++++++||+...+
T Consensus 111 ~~~L~~hf~~~~~L~~e~~a~s~ 133 (281)
T KOG4244|consen 111 EDRLRKHFKIPDDLSAEQRAQSR 133 (281)
T ss_pred HHHHHHHcCCCCCCCHHHHHHHH
Confidence 45678999999999999987544
No 84
>TIGR01589 A_thal_3526 uncharacterized plant-specific domain TIGR01589. This model represents an uncharacterized plant-specific domain 57 residues in length. It is found toward the N-terminus of most proteins that contain it. Examples include at least 10 proteins from Arabidopsis thaliana and at least one from Oryza sativa.
Probab=24.13 E-value=58 Score=19.91 Aligned_cols=30 Identities=17% Similarity=-0.033 Sum_probs=23.1
Q ss_pred HHHHHhHcCCCCCCCHHHHHHHHHhcCCCC
Q 038597 130 PEEIRRTFNIKKDFTPEEEEAVMDEHGWAF 159 (161)
Q Consensus 130 ~eeir~~f~i~~d~t~eee~~i~~e~~w~~ 159 (161)
+.-+.+..||+..+|.-=..++++||+=.|
T Consensus 22 v~~L~~~a~I~P~~T~~VW~~LekeN~eFF 51 (57)
T TIGR01589 22 VSFLFENAGISPKFTRFVWYLLEKENADFF 51 (57)
T ss_pred HHHHHHHcCCCchhHHHHHHHHHHHHHHHH
Confidence 334456789999999998999999987444
No 85
>PF00690 Cation_ATPase_N: Cation transporter/ATPase, N-terminus; InterPro: IPR004014 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. P-ATPases (sometime known as E1-E2 ATPases) (3.6.3.- from EC) are found in bacteria and in a number of eukaryotic plasma membranes and organelles []. P-ATPases function to transport a variety of different compounds, including ions and phospholipids, across a membrane using ATP hydrolysis for energy. There are many different classes of P-ATPases, each of which transports a specific type of ion: H+, Na+, K+, Mg2+, Ca2+, Ag+ and Ag2+, Zn2+, Co2+, Pb2+, Ni2+, Cd2+, Cu+ and Cu2+. P-ATPases can be composed of one or two polypeptides, and can usually assume two main conformations called E1 and E2. This entry represents the conserved N-terminal region found in several classes of cation-transporting P-type ATPases, including those that transport H+ (3.6.3.6 from EC), Na+ (3.6.3.7 from EC), Ca2+ (3.6.3.8 from EC), Na+/K+ (3.6.3.9 from EC), and H+/K+ (3.6.3.10 from EC). In the H+/K+- and Na+/K+-exchange P-ATPases, this domain is found in the catalytic alpha chain. In gastric H+/K+-ATPases, this domain undergoes reversible sequential phosphorylation inducing conformational changes that may be important for regulating the function of these ATPases [, ]. More information about this protein can be found at Protein of the Month: ATP Synthases [].; PDB: 3KDP_C 3N2F_A 3B8E_A 3N23_A 2XZB_A 1MHS_B 3A3Y_A 2ZXE_A 3B8C_A 3B9B_A ....
Probab=23.98 E-value=1.2e+02 Score=18.42 Aligned_cols=29 Identities=21% Similarity=0.249 Sum_probs=20.0
Q ss_pred CCCHHHHHhHcC--CCCCCCHHHHHHHHHhc
Q 038597 127 GKTPEEIRRTFN--IKKDFTPEEEEAVMDEH 155 (161)
Q Consensus 127 gks~eeir~~f~--i~~d~t~eee~~i~~e~ 155 (161)
.++++++.+.|+ .+..+|++|-++-+++|
T Consensus 3 ~~~~~~v~~~l~t~~~~GLs~~ev~~r~~~~ 33 (69)
T PF00690_consen 3 QLSVEEVLKRLNTSSSQGLSSEEVEERRKKY 33 (69)
T ss_dssp TSSHHHHHHHHTTBTSSBBTHHHHHHHHHHH
T ss_pred CCCHHHHHHHHCcCCCCCCCHHHHHHHHHhc
Confidence 357888888887 33458887777666654
No 86
>cd03370 NADH_oxidase NADPH_oxidase. Nitroreductase family containing NADH oxidase and other, uncharacterized proteins that are similar to nitroreductase. Nitroreductase catalyzes the reduction of nitroaromatic compounds such as nitrotoluenes, nitrofurans and nitroimidazoles. This process requires NAD(P)H as electron donor in an obligatory two-electron transfer and uses FMN as cofactor. The enzyme is typically a homodimer. Members of this family are also called NADH dehydrogenase, oxygen-insensitive NAD(P)H nitrogenase or dihydropteridine reductase.
Probab=23.56 E-value=55 Score=23.34 Aligned_cols=32 Identities=25% Similarity=0.332 Sum_probs=23.2
Q ss_pred HHHHhhccCCchHHHHHHHHHHHHHHcCCCHHHHHhHcCCCC
Q 038597 100 GLLLAANYLEIPALLHRLCQLAADIVKGKTPEEIRRTFNIKK 141 (161)
Q Consensus 100 ~Ll~AA~~L~I~~L~~l~~~~ia~~i~gks~eeir~~f~i~~ 141 (161)
.++.||.-||+-.. ++.|...+.+++.||++.
T Consensus 97 ~l~L~A~~lGlgs~----------~i~~~~~~~v~~~l~l~~ 128 (156)
T cd03370 97 FLLLAATALGLATS----------PMTGFDEEKVKEALGLPG 128 (156)
T ss_pred HHHHHHHHcCCCcc----------cCcCcCHHHHHHHhCcCC
Confidence 46777777775433 445667889999999986
No 87
>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=23.46 E-value=1.5e+02 Score=21.26 Aligned_cols=34 Identities=21% Similarity=0.456 Sum_probs=23.3
Q ss_pred HHHHHHHHHHHHHHcCCCHHHHHh--------HcCCCCCCCH
Q 038597 112 ALLHRLCQLAADIVKGKTPEEIRR--------TFNIKKDFTP 145 (161)
Q Consensus 112 ~L~~l~~~~ia~~i~gks~eeir~--------~f~i~~d~t~ 145 (161)
.++.-.+..+...++|+|++||.+ .+|+..-+||
T Consensus 81 ~IvkGl~alL~~~~~g~tp~eI~~~d~~~~~~~lGL~~~LSp 122 (138)
T TIGR03391 81 RIVRGLLAVLLTAVEGKTPEQLLAQDPLALFDELGLRAQLSA 122 (138)
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHHCCHHHHHHHcCchhccCc
Confidence 344445566667789999999874 4566666666
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=22.91 E-value=1.1e+02 Score=19.69 Aligned_cols=40 Identities=8% Similarity=0.075 Sum_probs=29.6
Q ss_pred HHHHHhhccCCchHHHHHHHHHHHHHHcC---------CCHHHHHhHcC
Q 038597 99 FGLLLAANYLEIPALLHRLCQLAADIVKG---------KTPEEIRRTFN 138 (161)
Q Consensus 99 ~~Ll~AA~~L~I~~L~~l~~~~ia~~i~g---------ks~eeir~~f~ 138 (161)
+++...|..++...|.+.|-++++..+.. .+.+++...++
T Consensus 2 ~~i~~~A~~~~~~~L~~~~~~~i~~nf~~v~~~~~f~~L~~~~l~~iL~ 50 (103)
T PF07707_consen 2 LSIYRLAEKYGLEELAEACLRFIAKNFNEVSKSDEFLELPFDQLIEILS 50 (103)
T ss_dssp HHHHHHHHHTT-HHHHHHHHHHHHHTHHHHTTSHHHHCS-HHHHHHHHH
T ss_pred hhHHHHHHHcChHHHHHHHHHHHHHHHHHHccchhhhcCCHHHHHHHHh
Confidence 57888999999999999999999765542 35666666666
No 89
>COG4224 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.89 E-value=79 Score=20.40 Aligned_cols=18 Identities=28% Similarity=0.477 Sum_probs=14.8
Q ss_pred CCCCCCHHHHHHHHHhcC
Q 038597 139 IKKDFTPEEEEAVMDEHG 156 (161)
Q Consensus 139 i~~d~t~eee~~i~~e~~ 156 (161)
..+|+||+-..++++++.
T Consensus 57 ~GnDVTP~Klk~~q~~~~ 74 (77)
T COG4224 57 KGNDVTPEKLKQIQRKKG 74 (77)
T ss_pred CCCCCChHHHHHHHHHhc
Confidence 457999999999988764
No 90
>TIGR03147 cyt_nit_nrfF cytochrome c nitrite reductase, accessory protein NrfF.
Probab=22.87 E-value=80 Score=22.48 Aligned_cols=19 Identities=21% Similarity=0.324 Sum_probs=13.6
Q ss_pred HHHHHHH-cCCCHHHHHhHc
Q 038597 119 QLAADIV-KGKTPEEIRRTF 137 (161)
Q Consensus 119 ~~ia~~i-~gks~eeir~~f 137 (161)
..|..++ .|+|.+||+.+|
T Consensus 64 ~~Vr~~i~~G~Sd~eI~~~~ 83 (126)
T TIGR03147 64 HEVYSMVNEGKSNQQIIDFM 83 (126)
T ss_pred HHHHHHHHcCCCHHHHHHHH
Confidence 4455555 499999999865
No 91
>TIGR01994 SUF_scaf_2 SUF system FeS assembly protein, NifU family. Three iron-sulfur cluster assembly systems are known so far. ISC is broadly distributed while NIF tends to be associated with nitrogenase in nitrogen-fixing bacteria. The most recently described is SUF, believed to be important to maintain the function during aerobic stress of enzymes with labile Fe-S clusters. It is fairly widely distributed. This family represents one of two different proteins proposed to act as a scaffold on which the Fe-S cluster is built and from which it is transferred.
Probab=22.86 E-value=1.4e+02 Score=21.12 Aligned_cols=38 Identities=16% Similarity=0.215 Sum_probs=25.5
Q ss_pred HHHhhccCCchHHHHHH-HHHHHHHHcCCCHHHHHhHcC
Q 038597 101 LLLAANYLEIPALLHRL-CQLAADIVKGKTPEEIRRTFN 138 (161)
Q Consensus 101 Ll~AA~~L~I~~L~~l~-~~~ia~~i~gks~eeir~~f~ 138 (161)
.+..+.|-+-=.-+..+ +..++++++|||.+|+.....
T Consensus 50 ~I~d~~f~~~GCais~Asas~~~e~i~Gk~~~ea~~l~~ 88 (137)
T TIGR01994 50 RIEDIAFEGEGCSISQASASMMTELIKGKTVEEALSLVE 88 (137)
T ss_pred eEEEEEEEecccHHHHHHHHHHHHHHcCCCHHHHHHHHH
Confidence 45555555555444444 466788999999999987653
No 92
>PF06540 GMAP: Galanin message associated peptide (GMAP); InterPro: IPR013068 Galanin is a peptide hormone that controls various biological activities []. Galanin-like immuno-reactivity has been found in the central and peripheral nervous systems of mammals, with high concentrations demonstrated in discrete regions of the central nervous system, including the median eminence, hypothalamus, arcuate nucleus, septum, neuro-intermediate lobe of the pituitary, and the spinal cord. Its localisation within neurosecretory granules suggests that galanin may function as a neurotransmitter, and it has been shown to coexist with a variety of other peptide and amine neurotransmitters within individual neurons []. Although the precise physiological role of galanin is uncertain, it has a number of pharmacological properties: it stimulates food intake, when injected into the third ventricle of rats; it increases levels of plasma growth hormone and prolactin, and decreases dopamine levels in the median eminence []; and infusion into humans results in hyperglycemia and glucose intolerance, and inhibits pancreatic release of insulin, somatostatin and pancreatic peptide. Galanin also modulates smooth muscle contractility within the gastro-intestinal and genito-urinary tracts, all such activities suggesting that the hormone may play an important role in the nervous modulation of endocrine and smooth muscle function []. This domain represents the galanin message-associated peptide (GMAP) domain which is found C-terminal to the galanin domain in the preprogalanin precursor protein. GMAP sequences in different species show a high degree of homology, but the biological function of the GMAP peptide is not known [].
Probab=22.80 E-value=56 Score=20.22 Aligned_cols=20 Identities=5% Similarity=0.296 Sum_probs=16.4
Q ss_pred ccHHHHHHHHHHhhcccccC
Q 038597 47 ISSRNLAKVVEWCKCMQHRD 66 (161)
Q Consensus 47 v~s~~L~~Ii~y~~~~~h~~ 66 (161)
-...+++.|++|+.|.|-+.
T Consensus 21 ~d~nivrTiiEFLtfLhLKE 40 (62)
T PF06540_consen 21 ADDNIVRTIIEFLTFLHLKE 40 (62)
T ss_pred chhHHHHHHHHHHHHHHHHH
Confidence 47899999999999775444
No 93
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=22.78 E-value=52 Score=26.66 Aligned_cols=16 Identities=50% Similarity=0.891 Sum_probs=13.2
Q ss_pred cCC-CHHHHHhHcCCCC
Q 038597 126 KGK-TPEEIRRTFNIKK 141 (161)
Q Consensus 126 ~gk-s~eeir~~f~i~~ 141 (161)
++| |||+|++.||++.
T Consensus 244 ~DKSsPEdIk~~FgiSK 260 (287)
T COG2996 244 NDKSSPEDIKATFGISK 260 (287)
T ss_pred CCCCCHHHHHHHhCcCH
Confidence 345 6999999999875
No 94
>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=22.60 E-value=1.3e+02 Score=20.08 Aligned_cols=43 Identities=21% Similarity=0.331 Sum_probs=29.0
Q ss_pred HHHHHHHHHHHHHHcCCCHHHHHhHcCCCC-CCCHHHHHHHHHh
Q 038597 112 ALLHRLCQLAADIVKGKTPEEIRRTFNIKK-DFTPEEEEAVMDE 154 (161)
Q Consensus 112 ~L~~l~~~~ia~~i~gks~eeir~~f~i~~-d~t~eee~~i~~e 154 (161)
.|+-++|-.+|.++.+..+-.+.....+.+ .+|+++..+++..
T Consensus 74 ~li~~~cl~lA~K~~e~~~~~~~~~~~~~~~~~~~~~i~~~E~~ 117 (127)
T PF00134_consen 74 QLIALACLFLASKMEEDNPPSISDLIRISDNTFTKKDILEMERE 117 (127)
T ss_dssp HHHHHHHHHHHHHHHTSS--HHHHHHHHTTTSSHHHHHHHHHHH
T ss_pred hhhhhhHHHHhhhhhccccchHHHHHHHHcCCCCHHHHHHHHHH
Confidence 577788999999998875555666555544 5888776665543
No 95
>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=22.56 E-value=83 Score=24.64 Aligned_cols=29 Identities=14% Similarity=0.275 Sum_probs=18.0
Q ss_pred HHHHHHHHHcCCCHHHHHhHcCCCCCCCH
Q 038597 117 LCQLAADIVKGKTPEEIRRTFNIKKDFTP 145 (161)
Q Consensus 117 ~~~~ia~~i~gks~eeir~~f~i~~d~t~ 145 (161)
..+.++..++..|.+|+++.|+|...+..
T Consensus 30 ~~~~l~~~L~~~s~~el~~l~~is~~la~ 58 (237)
T PF03883_consen 30 KTEELLEALKSLSEEELKKLMKISDKLAE 58 (237)
T ss_pred HHHHHHHHHHhcCHHHHHHHHCCCHHHHH
Confidence 34555566666777777777777654433
No 96
>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=22.38 E-value=1.2e+02 Score=17.67 Aligned_cols=23 Identities=17% Similarity=0.312 Sum_probs=16.7
Q ss_pred HHHHHHHHcCCCHHHHHhHcCCC
Q 038597 118 CQLAADIVKGKTPEEIRRTFNIK 140 (161)
Q Consensus 118 ~~~ia~~i~gks~eeir~~f~i~ 140 (161)
...+.-+..|++..||-+.+|++
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 34555667899999999988875
No 97
>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=22.27 E-value=1e+02 Score=20.80 Aligned_cols=57 Identities=12% Similarity=0.142 Sum_probs=28.2
Q ss_pred CCCeEEEEeCCCCEEEecHHHHHHHHHHHHHhhhcc---CCC---c------cccc--ccHHHHHHHHHHhh
Q 038597 3 TTSTVKLRSGDNEVFEVEKQVMIQSGTIRNMIEDDA---ADG---E------IPLQ--ISSRNLAKVVEWCK 60 (161)
Q Consensus 3 ~~~~i~l~s~Dg~~~~v~~~~a~~S~~l~~~~~~~~---~~~---~------I~l~--v~s~~L~~Ii~y~~ 60 (161)
.+..++++|+||..+.|...--. ...+...++-.| .+. . +++- ++-+...+++++++
T Consensus 33 ~g~~~~l~~~d~~~V~v~l~~~~-~~~~~~~vEviG~V~~~~~~~~i~~~~~~~~g~~~D~~~y~~lv~l~~ 103 (109)
T PF08661_consen 33 DGGSATLSTSDGGQVTVSLNPPS-DEELSKYVEVIGKVNDDGTVLSIRYFSFTDFGDDFDMDLYNELVQLTH 103 (109)
T ss_dssp TSSEEEEE-TTS-EEEEEESS---SS---SEEEEEEEE-TTS-EEEEEEEE---SSS---HHHHHHHHHHHH
T ss_pred CCCEEEEEcCCCCEEEEEeCCCC-CCCCCCEEEEEEEEcCCCCceEEEEEEeccCCCCcCHHHHHHHHHHHh
Confidence 35789999999998888654211 111233443222 111 1 1333 77778888888877
No 98
>PRK07394 hypothetical protein; Provisional
Probab=22.05 E-value=1.3e+02 Score=24.98 Aligned_cols=33 Identities=18% Similarity=0.271 Sum_probs=27.9
Q ss_pred CCCHHHHHhHcCCCCCC-CHHHHHHHHHhcCCCC
Q 038597 127 GKTPEEIRRTFNIKKDF-TPEEEEAVMDEHGWAF 159 (161)
Q Consensus 127 gks~eeir~~f~i~~d~-t~eee~~i~~e~~w~~ 159 (161)
|-+..++-+.+|++-+. ||++-.+.-++..|+|
T Consensus 128 GvtsaDvLe~LGv~~~~~~~~~~~~~l~~~g~~F 161 (342)
T PRK07394 128 GVPLVELWQGLGVDLTGLSLEQVQEGFEQTGLAF 161 (342)
T ss_pred CchHHHHHHHCCCCCCCCCHHHHHHHHHHcCcee
Confidence 34578999999999887 9999988888887775
No 99
>cd02138 Nitroreductase_2 Nitroreductase-like family 2. A subfamily of the nitroreductase family containing uncharacterized proteins that are similar to nitroreductase. Nitroreductase catalyzes the reduction of nitroaromatic compounds such as nitrotoluenes, nitrofurans and nitroimidazoles. This process requires NAD(P)H as electron donor in an obligatory two-electron transfer and uses FMN as cofactor. The enzyme is typically a homodimer. Members of this family are also called NADH dehydrogenase, oxygen-insensitive NAD(P)H nitrogenase or dihydropteridine reductase.
Probab=21.89 E-value=76 Score=23.27 Aligned_cols=38 Identities=24% Similarity=0.322 Sum_probs=28.0
Q ss_pred HHHHHHHhhccCCchHHHHHHHHHHHHHHcCCCHHHHHhHcCCCCCCC
Q 038597 97 LHFGLLLAANYLEIPALLHRLCQLAADIVKGKTPEEIRRTFNIKKDFT 144 (161)
Q Consensus 97 ~l~~Ll~AA~~L~I~~L~~l~~~~ia~~i~gks~eeir~~f~i~~d~t 144 (161)
.+..++.||.-||+... ++.|....++++.||++++..
T Consensus 107 a~~nl~Laa~~lGlgt~----------~~~~~~~~~l~~~l~l~~~~~ 144 (181)
T cd02138 107 AWGNLALQATAMGLAAH----------QMGGFDADKAREELNIPEDYE 144 (181)
T ss_pred HHHHHHHHHHHcCcccc----------eecCcCHHHHHHHhCCCCCce
Confidence 45678888888888742 334567789999999997643
No 100
>TIGR03879 near_KaiC_dom probable regulatory domain. This model describes a common domain shared by two different families of proteins, each of which occurs regularly next to its corresponding partner family, a probable regulatory with homology to KaiC. By implication, this protein family likely is also involved in sensory transduction and/or regulation.
Probab=21.78 E-value=2.2e+02 Score=18.24 Aligned_cols=19 Identities=26% Similarity=0.284 Sum_probs=16.0
Q ss_pred HHHcCCCHHHHHhHcCCCC
Q 038597 123 DIVKGKTPEEIRRTFNIKK 141 (161)
Q Consensus 123 ~~i~gks~eeir~~f~i~~ 141 (161)
..+.|+|..||-+.+|++.
T Consensus 28 R~~eGlS~kEIAe~LGIS~ 46 (73)
T TIGR03879 28 REEAGKTASEIAEELGRTE 46 (73)
T ss_pred HHHcCCCHHHHHHHHCcCH
Confidence 4568999999999999874
No 101
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=21.72 E-value=1.3e+02 Score=16.54 Aligned_cols=18 Identities=28% Similarity=0.488 Sum_probs=13.4
Q ss_pred HHcCCCHHHHHhHcCCCC
Q 038597 124 IVKGKTPEEIRRTFNIKK 141 (161)
Q Consensus 124 ~i~gks~eeir~~f~i~~ 141 (161)
...|++..+|-+.+|++.
T Consensus 15 ~~~g~s~~eia~~l~is~ 32 (58)
T smart00421 15 LAEGLTNKEIAERLGISE 32 (58)
T ss_pred HHcCCCHHHHHHHHCCCH
Confidence 346888888888888753
No 102
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=21.55 E-value=1.3e+02 Score=16.76 Aligned_cols=16 Identities=25% Similarity=0.536 Sum_probs=11.2
Q ss_pred HcCCCHHHHHhHcCCC
Q 038597 125 VKGKTPEEIRRTFNIK 140 (161)
Q Consensus 125 i~gks~eeir~~f~i~ 140 (161)
-.|.|..+|.+.|||.
T Consensus 19 ~~G~si~~IA~~~gvs 34 (45)
T PF02796_consen 19 AEGMSIAEIAKQFGVS 34 (45)
T ss_dssp HTT--HHHHHHHTTS-
T ss_pred HCCCCHHHHHHHHCcC
Confidence 3589999999999985
No 103
>cd00068 GGL G protein gamma subunit-like motifs, the alpha-helical G-gamma chain dimerizes with the G-beta propeller subunit as part of the heterotrimeric G-protein complex; involved in signal transduction via G-protein-coupled receptors
Probab=20.94 E-value=1.1e+02 Score=18.32 Aligned_cols=22 Identities=18% Similarity=0.584 Sum_probs=17.1
Q ss_pred CcccccccHHHHHHHHHHhhcccccCC
Q 038597 41 GEIPLQISSRNLAKVVEWCKCMQHRDR 67 (161)
Q Consensus 41 ~~I~l~v~s~~L~~Ii~y~~~~~h~~~ 67 (161)
..|++ |.....++.||+ .|...
T Consensus 18 ~Rikv---S~a~~~l~~y~e--~~~~~ 39 (57)
T cd00068 18 ERLKV---SKAAAELLKYCE--QNAEN 39 (57)
T ss_pred chhhH---HHHHHHHHHHHH--hcCCC
Confidence 44555 888899999999 88654
No 104
>PF00382 TFIIB: Transcription factor TFIIB repeat; InterPro: IPR013150 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. In eukaryotes, transcription initiation of all protein encoding genes involves the polymerase II system. This sytem is modulated by both general and specific transcription factors. The general factors (which include TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIG and TFIIH) operate through common promoter elements, such as the TATA box. Transcription factor IIB (TFIIB) is of central importance in transcription of class II genes. It associates with TFIID-TFIIA bound to DNA (the DA complex) to form a ternary TFIID-IIA-IBB (DAB) complex, which is recognised by RNA polymerase II [, ]. TFIIB comprises ~315-340 residues and contains an imperfect C-terminal repeat of a 75-residue domain that may contribute to the symmetry of the folded protein. The basal archaeal transcription machinery resembles that of the eukaryotic polymerase II system and includes a homologue of TFIIB []. This entry represents a cyclin-like domain which is found repeated in the C-terminal region of a variety of eukaryotic TFIIB's and their archaeal counterparts. These domains individually form the typical cyclin fold, and in the transcription complex they straddle the C-terminal region of the TATA-binding protein - an interaction essential for the formation of the transcription initiation complex [, ].; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2PHG_A 1C9B_Q 1TFB_A 1VOL_A 3K7A_M 1AIS_B 1D3U_B.
Probab=20.66 E-value=2.1e+02 Score=17.36 Aligned_cols=44 Identities=18% Similarity=0.206 Sum_probs=31.6
Q ss_pred HHHHHHHhhccCCc-----hHHHHHHHHHHHHHHcC--CCHHHHHhHcCCC
Q 038597 97 LHFGLLLAANYLEI-----PALLHRLCQLAADIVKG--KTPEEIRRTFNIK 140 (161)
Q Consensus 97 ~l~~Ll~AA~~L~I-----~~L~~l~~~~ia~~i~g--ks~eeir~~f~i~ 140 (161)
...+|...|.-.++ +.-+-.+|-++|.+..| +|..||.+..|++
T Consensus 17 ~A~~i~~~~~~~~~~~Gr~~~~iaAA~iY~acr~~~~~~t~~eIa~~~~Vs 67 (71)
T PF00382_consen 17 RAKEIYKKAQERGLLKGRSPESIAAACIYLACRLNGVPRTLKEIAEAAGVS 67 (71)
T ss_dssp HHHHHHHHHHHTTTSTTS-HHHHHHHHHHHHHHHTTSSSSHHHHHHHCTSS
T ss_pred HHHHHHHHHHHcCCcccCCHHHHHHHHHHHHHHHcCCCcCHHHHHHHhCCC
Confidence 44555555544443 34556678889999887 5899999999986
No 105
>TIGR03553 F420_FbiB_CTERM F420 biosynthesis protein FbiB, C-terminal domain. Coenzyme F420 differs between the Archaea and the Actinobacteria, where the numbers of glutamate residues attached are 2 (Archaea) or 5-6 (Mycobacterium). The enzyme in the Archaea is homologous to the N-terminal domain of FbiB from Mycobacterium bovis, and is responsible for glutamate ligation. Therefore it seems likely that the C-terminal domain of FbiB, modeled by this alignment, is involved in additional glutamate ligation.
Probab=20.39 E-value=63 Score=23.85 Aligned_cols=38 Identities=16% Similarity=0.205 Sum_probs=24.6
Q ss_pred HHHHHHHhhccCCchHHHHHHHHHHHHHHcC--CCHHHHHhHcCCCCCCC
Q 038597 97 LHFGLLLAANYLEIPALLHRLCQLAADIVKG--KTPEEIRRTFNIKKDFT 144 (161)
Q Consensus 97 ~l~~Ll~AA~~L~I~~L~~l~~~~ia~~i~g--ks~eeir~~f~i~~d~t 144 (161)
-+..++.||.-||+-... +.| ...+.+++.|||+.++.
T Consensus 126 a~qnl~LaA~~~Glgt~~----------~~~~~~~~~~v~~~l~lp~~~~ 165 (194)
T TIGR03553 126 AVQNLLVALAVEGLGSCW----------VGSTIFAADVVRAELDLPADWE 165 (194)
T ss_pred HHHHHHHHHHHcCCCeEE----------ecCcccCHHHHHHHhCcCCCce
Confidence 345566777777765432 122 35688999999998754
No 106
>COG0549 ArcC Carbamate kinase [Amino acid transport and metabolism]
Probab=20.24 E-value=70 Score=26.25 Aligned_cols=18 Identities=39% Similarity=0.896 Sum_probs=15.9
Q ss_pred CCHHHHHHHHHhcCCCCC
Q 038597 143 FTPEEEEAVMDEHGWAFH 160 (161)
Q Consensus 143 ~t~eee~~i~~e~~w~~~ 160 (161)
||+||-+++.+++.|.|.
T Consensus 135 Y~~eea~~l~~~~gw~~k 152 (312)
T COG0549 135 YSEEEAEELAKEYGWVFK 152 (312)
T ss_pred cCHHHHHHHHhhcCcEEE
Confidence 678888999999999874
No 107
>cd02145 BluB Subfamily of the nitroreductase family that includes BluB protein in Rhodobacter capsulatus is involved in the conversion of cobinamide to cobalamin in Cobalamin (vitamin B12) biosynthesis. Nitroreductases typically reduce their substrates by using NAD(P)H as electron donor and often use FMN as a cofactor.
Probab=20.16 E-value=63 Score=23.97 Aligned_cols=36 Identities=28% Similarity=0.245 Sum_probs=25.2
Q ss_pred HHHHHHhhccCCchHHHHHHHHHHHHHHcCCCHHHHHhHcCCCCCC
Q 038597 98 HFGLLLAANYLEIPALLHRLCQLAADIVKGKTPEEIRRTFNIKKDF 143 (161)
Q Consensus 98 l~~Ll~AA~~L~I~~L~~l~~~~ia~~i~gks~eeir~~f~i~~d~ 143 (161)
+..|+.||.-+|+-.. ++.+-..+++++.|||++++
T Consensus 125 ~~nl~LaA~~~Glgt~----------~~~~~~~~~v~~~l~lp~~~ 160 (196)
T cd02145 125 IQNLWLAARAEGLGVG----------WVSILDPEALARLLGIPEDW 160 (196)
T ss_pred HHHHHHHHHHcCCceE----------EecccChHHHHHHcCcCCCc
Confidence 4467777777777642 23355679999999999764
No 108
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=20.15 E-value=1.9e+02 Score=21.28 Aligned_cols=47 Identities=21% Similarity=0.157 Sum_probs=33.8
Q ss_pred CChHHHHHHHHhhccCCchHHHHHHHHHHHH-HHcCCCHHHHHhHcCCCC
Q 038597 93 EDKDLHFGLLLAANYLEIPALLHRLCQLAAD-IVKGKTPEEIRRTFNIKK 141 (161)
Q Consensus 93 ~~~~~l~~Ll~AA~~L~I~~L~~l~~~~ia~-~i~gks~eeir~~f~i~~ 141 (161)
-+++.+.++-.+..-|.- |-.-.++.|.- .+.|.|.+||-+.+||+.
T Consensus 118 ~~~~~~~~l~e~l~~L~~--l~~~~~~~v~l~~~~Gls~~EIA~~lgiS~ 165 (185)
T PF07638_consen 118 PSPEELLELEEALERLLA--LDPRQRRVVELRFFEGLSVEEIAERLGISE 165 (185)
T ss_pred CCHHHHHHHHHHHHHHHc--cCHHHHHHHHHHHHCCCCHHHHHHHHCcCH
Confidence 355667777666665433 55566777765 468999999999999975
Done!