Query 031498
Match_columns 158
No_of_seqs 132 out of 785
Neff 8.3
Searched_HMMs 46136
Date Fri Mar 29 14:58:32 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031498.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031498hhsearch_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 2.4E-50 5.3E-55 291.5 17.0 155 4-158 4-162 (162)
2 COG5201 SKP1 SCF ubiquitin lig 100.0 9.7E-49 2.1E-53 268.1 14.9 153 6-158 3-157 (158)
3 PF01466 Skp1: Skp1 family, di 100.0 9.8E-32 2.1E-36 173.9 8.2 78 81-158 1-78 (78)
4 smart00512 Skp1 Found in Skp1 100.0 1.3E-29 2.8E-34 172.6 11.2 99 5-108 2-104 (104)
5 PF03931 Skp1_POZ: Skp1 family 99.8 6.1E-21 1.3E-25 118.1 6.1 61 5-65 1-62 (62)
6 KOG3473 RNA polymerase II tran 99.8 1.3E-19 2.9E-24 118.7 7.3 92 4-108 16-112 (112)
7 PHA02713 hypothetical protein; 99.0 1.6E-09 3.4E-14 93.0 10.4 102 6-133 27-133 (557)
8 PF00651 BTB: BTB/POZ domain; 99.0 6.5E-09 1.4E-13 70.2 9.6 93 5-121 11-109 (111)
9 PHA03098 kelch-like protein; P 98.9 1.7E-08 3.7E-13 85.9 10.1 100 6-130 11-112 (534)
10 PHA02790 Kelch-like protein; P 98.9 5.7E-09 1.2E-13 88.1 7.0 96 8-127 24-124 (480)
11 smart00225 BTB Broad-Complex, 98.7 4.3E-08 9.3E-13 62.8 6.4 82 11-116 5-90 (90)
12 KOG4441 Proteins containing BT 98.6 1.6E-07 3.4E-12 81.0 8.3 93 7-124 39-135 (571)
13 KOG4682 Uncharacterized conser 97.2 0.00055 1.2E-08 56.2 5.1 104 11-141 75-185 (488)
14 KOG2716 Polymerase delta-inter 97.0 0.012 2.6E-07 45.3 10.3 101 2-126 2-108 (230)
15 KOG4350 Uncharacterized conser 96.6 0.023 4.9E-07 47.2 9.2 119 6-132 46-181 (620)
16 PF11822 DUF3342: Domain of un 96.3 0.0047 1E-07 49.5 3.9 87 14-124 13-105 (317)
17 KOG0783 Uncharacterized conser 94.7 0.11 2.3E-06 46.9 6.6 107 7-133 713-825 (1267)
18 KOG3433 Protein involved in me 93.8 0.13 2.8E-06 38.1 4.6 31 107-142 170-200 (203)
19 PF02214 BTB_2: BTB/POZ domain 93.3 0.091 2E-06 34.3 2.9 80 13-115 6-94 (94)
20 COG5124 Protein predicted to b 91.3 0.2 4.3E-06 37.0 2.7 31 107-142 174-204 (209)
21 KOG2075 Topoisomerase TOP1-int 87.8 3 6.4E-05 35.6 7.3 48 15-62 129-180 (521)
22 KOG1665 AFH1-interacting prote 86.5 1.2 2.5E-05 34.5 4.0 88 5-117 9-105 (302)
23 PF03962 Mnd1: Mnd1 family; I 83.3 1.3 2.8E-05 33.1 3.0 41 97-142 145-187 (188)
24 PF05409 Peptidase_C30: Corona 83.1 3.7 8.1E-05 32.5 5.5 102 42-147 162-266 (293)
25 PF07928 Vps54: Vps54-like pro 80.4 0.53 1.2E-05 33.3 0.0 46 13-63 1-46 (135)
26 KOG0511 Ankyrin repeat protein 76.8 9.4 0.0002 31.9 6.1 110 12-124 298-431 (516)
27 KOG4591 Uncharacterized conser 66.8 14 0.0003 28.3 4.6 60 42-123 107-166 (280)
28 KOG4350 Uncharacterized conser 66.3 3.5 7.6E-05 34.7 1.5 37 90-126 112-148 (620)
29 PRK14981 DNA-directed RNA poly 59.8 52 0.0011 22.3 6.5 44 107-151 61-105 (112)
30 KOG2838 Uncharacterized conser 59.2 39 0.00084 27.1 6.0 29 92-120 357-385 (401)
31 PF03656 Pam16: Pam16; InterP 58.6 8 0.00017 27.1 2.0 31 122-155 51-81 (127)
32 PF10892 DUF2688: Protein of u 58.1 13 0.00028 22.2 2.5 24 128-151 30-55 (60)
33 PHA03098 kelch-like protein; P 57.6 37 0.0008 29.0 6.3 52 85-136 97-159 (534)
34 PF11978 MVP_shoulder: Shoulde 55.4 11 0.00025 25.9 2.3 40 100-139 37-89 (118)
35 PF11460 DUF3007: Protein of u 54.4 13 0.00028 25.1 2.3 24 127-153 79-102 (104)
36 PRK05365 malonic semialdehyde 53.4 10 0.00023 27.9 2.0 34 98-141 130-163 (195)
37 cd05029 S-100A6 S-100A6: S-100 52.5 30 0.00065 22.3 3.9 45 108-152 9-59 (88)
38 PF13921 Myb_DNA-bind_6: Myb-l 52.1 25 0.00055 20.4 3.3 33 117-149 21-60 (60)
39 smart00385 CYCLIN domain prese 50.9 51 0.0011 19.5 4.9 41 108-151 37-79 (83)
40 PF10075 PCI_Csn8: COP9 signal 50.6 34 0.00074 23.9 4.2 47 108-158 76-126 (143)
41 cd02148 Nitroreductase_5 Nitro 50.1 12 0.00026 27.3 1.9 33 99-141 124-156 (185)
42 PF05321 HHA: Haemolysin expre 50.1 39 0.00084 20.2 3.7 30 49-105 8-37 (57)
43 PF12556 CobS_N: Cobaltochelat 47.5 12 0.00025 20.3 1.1 12 131-142 14-25 (36)
44 PF02519 Auxin_inducible: Auxi 45.7 82 0.0018 21.0 5.2 53 6-60 40-99 (100)
45 smart00875 BACK BTB And C-term 43.4 81 0.0018 19.7 5.2 41 97-137 2-51 (101)
46 cd00167 SANT 'SWI3, ADA2, N-Co 41.5 29 0.00062 18.2 2.2 20 117-136 23-42 (45)
47 KOG3442 Uncharacterized conser 41.5 28 0.00061 24.3 2.5 31 124-157 54-84 (132)
48 PRK11053 dihydropteridine redu 41.2 25 0.00055 26.3 2.5 34 96-139 147-180 (217)
49 smart00717 SANT SANT SWI3, AD 39.5 32 0.0007 18.3 2.2 20 117-136 25-44 (49)
50 PF00382 TFIIB: Transcription 39.1 76 0.0017 19.1 4.1 29 110-138 37-67 (71)
51 PF11198 DUF2857: Protein of u 39.1 72 0.0016 23.5 4.6 60 90-149 57-131 (180)
52 PF01592 NifU_N: NifU-like N t 39.1 42 0.0009 23.1 3.1 24 110-133 62-85 (126)
53 PRK11325 scaffold protein; Pro 38.7 47 0.001 23.0 3.4 37 99-135 52-89 (127)
54 TIGR02698 CopY_TcrY copper tra 38.0 1.1E+02 0.0023 21.2 5.1 36 116-151 77-112 (130)
55 TIGR03419 NifU_clost FeS clust 37.6 56 0.0012 22.3 3.6 37 99-135 46-83 (121)
56 PF13518 HTH_28: Helix-turn-he 37.1 56 0.0012 18.0 3.0 20 119-138 6-25 (52)
57 PF00690 Cation_ATPase_N: Cati 36.8 54 0.0012 19.7 3.1 30 125-154 3-34 (69)
58 PF00134 Cyclin_N: Cyclin, N-t 36.3 57 0.0012 21.7 3.5 43 110-152 74-117 (127)
59 TIGR01999 iscU FeS cluster ass 36.0 57 0.0012 22.4 3.4 37 99-135 50-87 (124)
60 COG4957 Predicted transcriptio 34.8 35 0.00075 24.2 2.1 17 125-141 98-114 (148)
61 KOG2714 SETA binding protein S 33.7 1.8E+02 0.0039 24.8 6.4 83 5-113 11-102 (465)
62 PF10507 DUF2453: Protein of u 33.7 98 0.0021 21.2 4.1 38 110-147 34-79 (111)
63 PRK09296 cysteine desufuration 33.6 84 0.0018 22.2 4.0 34 111-144 77-118 (138)
64 PF13384 HTH_23: Homeodomain-l 33.2 46 0.001 18.4 2.2 15 124-138 16-30 (50)
65 cd00068 GGL G protein gamma su 33.1 52 0.0011 19.4 2.5 25 40-68 17-41 (57)
66 PHA02713 hypothetical protein; 33.0 97 0.0021 27.0 5.1 72 85-156 115-198 (557)
67 PF08671 SinI: Anti-repressor 32.6 28 0.00061 18.0 1.1 13 124-136 15-27 (30)
68 PF11338 DUF3140: Protein of u 32.1 52 0.0011 21.7 2.5 22 45-66 54-75 (92)
69 PF01726 LexA_DNA_bind: LexA D 32.1 86 0.0019 19.0 3.4 31 110-140 10-40 (65)
70 PF07707 BACK: BTB And C-termi 32.1 62 0.0013 20.5 3.0 41 97-137 2-51 (103)
71 COG2996 Predicted RNA-bindinin 31.7 30 0.00064 27.6 1.5 16 124-139 244-260 (287)
72 PRK15019 CsdA-binding activato 31.4 87 0.0019 22.5 3.8 34 111-144 87-128 (147)
73 PF15063 TC1: Thyroid cancer p 30.8 54 0.0012 20.9 2.3 12 129-140 56-67 (79)
74 TIGR03391 FeS_syn_CsdE cystein 30.7 94 0.002 22.0 3.9 34 111-144 82-123 (138)
75 PF07638 Sigma70_ECF: ECF sigm 30.7 2.1E+02 0.0046 20.7 6.4 47 91-139 118-165 (185)
76 PF03131 bZIP_Maf: bZIP Maf tr 30.3 68 0.0015 20.8 2.9 28 121-151 4-31 (92)
77 cd06664 IscU_like Iron-sulfur 30.1 86 0.0019 21.1 3.6 39 98-136 46-85 (123)
78 PF03883 DUF328: Protein of un 30.0 54 0.0012 25.3 2.7 31 115-145 30-60 (237)
79 PF10415 FumaraseC_C: Fumarase 29.4 1.2E+02 0.0027 17.7 3.7 23 124-149 24-46 (55)
80 PF07671 DUF1601: Protein of u 29.2 63 0.0014 17.5 2.1 30 105-134 7-36 (37)
81 PF13798 PCYCGC: Protein of un 29.0 86 0.0019 22.8 3.4 24 112-135 118-141 (158)
82 COG1460 Uncharacterized protei 28.6 2E+02 0.0043 19.8 6.0 60 88-150 45-105 (114)
83 PF00196 GerE: Bacterial regul 28.5 92 0.002 17.9 3.0 23 116-138 9-31 (58)
84 PRK13503 transcriptional activ 28.0 2.7E+02 0.0059 21.1 9.6 80 49-140 169-251 (278)
85 PF06945 DUF1289: Protein of u 27.9 1.1E+02 0.0024 17.6 3.2 23 125-151 21-43 (51)
86 PF13725 tRNA_bind_2: Possible 27.7 1.7E+02 0.0038 18.8 5.7 69 47-139 28-97 (101)
87 cd02140 Nitroreductase_4 Nitro 27.5 54 0.0012 24.0 2.3 38 96-141 127-164 (192)
88 PLN03212 Transcription repress 27.5 91 0.002 24.4 3.5 35 117-151 49-91 (249)
89 COG1710 Uncharacterized protei 27.4 45 0.00097 23.2 1.7 18 121-138 104-122 (139)
90 TIGR02476 BluB cob(II)yrinic a 27.4 56 0.0012 24.2 2.4 37 95-141 133-169 (205)
91 PF13542 HTH_Tnp_ISL3: Helix-t 27.4 1.2E+02 0.0026 16.8 3.6 29 111-139 12-41 (52)
92 TIGR03879 near_KaiC_dom probab 27.3 1.5E+02 0.0032 18.6 3.9 19 121-139 28-46 (73)
93 PF02736 Myosin_N: Myosin N-te 26.9 40 0.00087 18.5 1.2 19 4-22 23-41 (42)
94 COG0822 IscU NifU homolog invo 26.8 1.1E+02 0.0023 22.0 3.6 39 97-135 51-90 (150)
95 PF00249 Myb_DNA-binding: Myb- 26.7 1.2E+02 0.0026 16.7 4.6 38 93-135 6-44 (48)
96 COG0499 SAM1 S-adenosylhomocys 26.7 99 0.0021 25.9 3.8 62 3-64 337-402 (420)
97 smart00224 GGL G protein gamma 26.6 71 0.0015 19.3 2.3 25 40-68 17-41 (63)
98 smart00755 Grip golgin-97, Ran 26.5 68 0.0015 18.2 2.1 42 108-151 4-45 (46)
99 PF02657 SufE: Fe-S metabolism 26.2 1.4E+02 0.0031 20.5 4.1 32 113-144 70-108 (125)
100 TIGR01994 SUF_scaf_2 SUF syste 26.1 1.1E+02 0.0024 21.3 3.6 38 99-136 50-88 (137)
101 PF03750 DUF310: Protein of un 26.0 88 0.0019 21.4 3.0 31 107-138 9-41 (119)
102 COG0549 ArcC Carbamate kinase 26.0 49 0.0011 26.7 1.9 17 141-157 135-151 (312)
103 cd00043 CYCLIN Cyclin box fold 25.8 1.5E+02 0.0033 17.5 5.5 40 108-150 43-84 (88)
104 TIGR02603 CxxCH_TIGR02603 puta 25.6 2.1E+02 0.0045 19.7 4.9 51 4-62 79-132 (133)
105 PHA02790 Kelch-like protein; P 25.2 1.1E+02 0.0024 26.0 4.0 39 87-125 114-154 (480)
106 PF02796 HTH_7: Helix-turn-hel 25.1 1E+02 0.0022 16.9 2.7 15 124-138 20-34 (45)
107 cd02144 iodotyrosine_dehalogen 24.6 70 0.0015 23.0 2.5 35 97-141 130-165 (193)
108 PRK13696 hypothetical protein; 24.4 1.8E+02 0.0038 17.8 6.2 51 95-152 11-61 (62)
109 PF09116 gp45-slide_C: gp45 sl 24.3 38 0.00082 23.2 0.8 22 90-111 5-26 (112)
110 PRK13742 replication protein; 24.1 74 0.0016 24.7 2.6 33 110-142 164-199 (245)
111 KOG0028 Ca2+-binding protein ( 23.8 1.9E+02 0.0041 21.3 4.4 48 102-152 82-134 (172)
112 PF08154 NLE: NLE (NUC135) dom 23.4 1.2E+02 0.0025 18.3 2.9 29 6-34 3-39 (65)
113 smart00421 HTH_LUXR helix_turn 23.3 1.2E+02 0.0026 16.4 2.9 16 123-138 16-31 (58)
114 PF08299 Bac_DnaA_C: Bacterial 23.3 1.3E+02 0.0028 18.3 3.1 26 113-138 33-58 (70)
115 TIGR03147 cyt_nit_nrfF cytochr 23.1 83 0.0018 22.0 2.4 17 119-135 66-83 (126)
116 COG2445 Uncharacterized conser 22.9 2E+02 0.0043 20.4 4.3 46 106-151 43-90 (138)
117 COG4565 CitB Response regulato 22.9 1.6E+02 0.0034 22.8 4.0 22 40-61 146-168 (224)
118 smart00760 Bac_DnaA_C Bacteria 22.9 1.5E+02 0.0032 17.3 3.2 26 112-137 32-57 (60)
119 KOG0027 Calmodulin and related 22.7 2.1E+02 0.0046 19.9 4.6 48 105-152 60-113 (151)
120 PF08281 Sigma70_r4_2: Sigma-7 22.7 57 0.0012 18.3 1.3 18 121-138 22-39 (54)
121 PF09821 AAA_assoc_C: C-termin 22.7 69 0.0015 22.0 1.9 21 89-109 7-27 (120)
122 cd03370 NADH_oxidase NADPH_oxi 22.5 69 0.0015 22.5 2.0 32 98-139 97-128 (156)
123 PF03026 CM1: Influenza C viru 22.5 1.3E+02 0.0027 21.9 3.3 47 93-144 92-138 (235)
124 PRK13379 protocatechuate 4,5-d 22.2 1.8E+02 0.0038 20.2 3.8 24 116-139 94-117 (119)
125 PF08661 Rep_fac-A_3: Replicat 22.0 99 0.0022 20.6 2.6 61 3-64 33-106 (109)
126 PF11197 DUF2835: Protein of u 22.0 89 0.0019 19.4 2.1 22 4-25 20-41 (68)
127 PF11094 UL11: Membrane-associ 21.9 1E+02 0.0022 17.0 2.1 19 5-23 14-32 (39)
128 COG4680 Uncharacterized protei 21.9 64 0.0014 21.3 1.5 17 125-141 35-51 (98)
129 COG4049 Uncharacterized protei 21.8 81 0.0018 18.9 1.8 16 4-19 4-19 (65)
130 PF14098 SSPI: Small, acid-sol 21.8 1.1E+02 0.0023 18.9 2.4 19 117-135 5-23 (65)
131 PF11795 DUF3322: Uncharacteri 21.6 73 0.0016 23.6 2.0 47 48-100 142-188 (190)
132 PF05443 ROS_MUCR: ROS/MUCR tr 21.6 44 0.00096 23.5 0.8 17 125-141 94-110 (132)
133 TIGR01044 rplV_bact ribosomal 21.2 1.1E+02 0.0024 20.4 2.6 22 116-137 13-34 (103)
134 KOG4244 Failed axon connection 21.2 1.2E+02 0.0026 24.2 3.2 22 128-149 111-132 (281)
135 PF14407 Frankia_peptide: Ribo 21.1 84 0.0018 19.1 1.8 14 139-152 30-43 (61)
136 PF06514 PsbU: Photosystem II 20.8 37 0.0008 22.4 0.3 46 102-151 22-67 (93)
137 PRK10945 gene expression modul 20.6 2E+02 0.0042 18.1 3.4 15 91-105 35-49 (72)
138 PF04312 DUF460: Protein of un 20.6 1.4E+02 0.003 21.3 3.1 28 128-155 92-124 (138)
139 COG4754 Uncharacterized conser 20.5 3.4E+02 0.0074 19.6 5.3 56 43-110 4-59 (157)
140 PF10850 DUF2653: Protein of u 20.5 24 0.00052 23.2 -0.7 34 106-140 5-38 (91)
141 PF02084 Bindin: Bindin; Inte 20.3 1.8E+02 0.0039 22.5 3.8 46 13-65 95-142 (238)
142 PF12674 Zn_ribbon_2: Putative 20.2 1.6E+02 0.0035 18.7 3.1 28 108-136 44-71 (81)
No 1
>KOG1724 consensus SCF ubiquitin ligase, Skp1 component [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=2.4e-50 Score=291.50 Aligned_cols=155 Identities=66% Similarity=1.034 Sum_probs=140.4
Q ss_pred CCcEEEEcCCCCeEEecHHHHHHhHHHHHHHHhCC-CCC--ceecCCCCHHHHHHHHHHHHHhcccCCCCCCC-CCCCcc
Q 031498 4 EKKITLKSSDGETFEVEETVALESQTIKHMVEDDC-ADT--VIPLPNVTSTILSKVIEYCKKHVEAGSGDKKD-DKSTED 79 (158)
Q Consensus 4 ~~~i~l~s~DG~~f~v~~~~a~~S~~l~~~l~~~~-~~~--~Ipl~~i~~~~L~~Ii~~~~~~~~~~~~~~~~-~~~~~~ 79 (158)
.++|+|+|+||++|.|+.++|++|.+|++++.+.| ... +||||+|+|.+|++||+||+||+.+++...+. ..+...
T Consensus 4 ~~~ikL~SsDG~~f~ve~~~a~~s~~i~~~~~~~~~~~~~~~IPl~nV~~~iL~kVIewC~~Hk~d~~~~~~~~~~~~~~ 83 (162)
T KOG1724|consen 4 KKKIKLESSDGEIFEVEEEVARQSQTISAHMIEDGCADENDPIPLPNVTSKILKKVIEWCKKHKDDDPANPEDKELPEET 83 (162)
T ss_pred CCeEEEEccCCceeehhHHHHHHhHHHHHHHHHcCCCccCCccccCccCHHHHHHHHHHHHHcccccccccccccccccC
Confidence 67999999999999999999999999999998776 344 89999999999999999999999876532211 123444
Q ss_pred hhchHHHhhccCChHHHHHHHHhhhccCchhHHHHHHHHHHHHhcCCCHHHHHhHcCCCCCCCHHHHHHHHHhcccccC
Q 031498 80 DLKTWDADFVKVDQNTLFDLILAANYLNIKGLLDLTCQTVADMIKGKTPEEIRKTFNIKNDFSPDEEEEVRRENQWAFE 158 (158)
Q Consensus 80 ~~~~wd~~Fl~~~~~~l~~Ll~AA~~L~i~~L~~~~~~~ia~~i~~ks~eeir~~f~i~~d~t~eee~~i~~e~~w~~~ 158 (158)
.++.||++|++++..+||+|+.|||||+|++|+++||+.+|++++||||+|||..|||++|+||||+++++++|.|+|+
T Consensus 84 ~i~~WD~~Flk~d~~tLfdli~AAnyLdi~gLl~~~ck~va~mikgktpeEir~~f~I~~d~t~eE~~~~~~e~~~~~~ 162 (162)
T KOG1724|consen 84 DIPEWDAEFLKVDQGTLFDLILAANYLDIKGLLDLTCKTVANMIKGKTPEEIREIFNIENDETPEEEEAIRKENEWAFE 162 (162)
T ss_pred CccHHHHHHHhcCHHHHHHHHHHhhhcccHHHHHHHHHHHHHHHccCCHHHHHHHcCCCCCCChhHHHHHhhccccccC
Confidence 5999999999999999999999999999999999999999999999999999999999999999999999999999986
No 2
>COG5201 SKP1 SCF ubiquitin ligase, SKP1 component [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=9.7e-49 Score=268.13 Aligned_cols=153 Identities=49% Similarity=0.797 Sum_probs=138.4
Q ss_pred cEEEEcCCCCeEEecHHHHHHhHHHHHHHHhCC-CCCceecCCCCHHHHHHHHHHHHHhcccCCCCCCC-CCCCcchhch
Q 031498 6 KITLKSSDGETFEVEETVALESQTIKHMVEDDC-ADTVIPLPNVTSTILSKVIEYCKKHVEAGSGDKKD-DKSTEDDLKT 83 (158)
Q Consensus 6 ~i~l~s~DG~~f~v~~~~a~~S~~l~~~l~~~~-~~~~Ipl~~i~~~~L~~Ii~~~~~~~~~~~~~~~~-~~~~~~~~~~ 83 (158)
.|.|.|.||++|+|+..+|..|-+|++|+.+.+ ...|||+|+|+|.+|.+|++||+||.....++..+ .-....+...
T Consensus 3 ~i~l~s~dge~F~vd~~iAerSiLikN~l~d~~~~n~p~p~pnVrSsvl~kv~ew~ehh~~s~sede~d~~~rks~p~D~ 82 (158)
T COG5201 3 MIELESIDGEIFRVDENIAERSILIKNMLCDSTACNYPIPAPNVRSSVLMKVQEWMEHHTSSLSEDENDLEIRKSKPSDF 82 (158)
T ss_pred ceEEEecCCcEEEehHHHHHHHHHHHHHhccccccCCCCcccchhHHHHHHHHHHHHhccccCCCccChHhhhccCCccH
Confidence 799999999999999999999999999998765 47789999999999999999999998754433221 1223455678
Q ss_pred HHHhhccCChHHHHHHHHhhhccCchhHHHHHHHHHHHHhcCCCHHHHHhHcCCCCCCCHHHHHHHHHhcccccC
Q 031498 84 WDADFVKVDQNTLFDLILAANYLNIKGLLDLTCQTVADMIKGKTPEEIRKTFNIKNDFSPDEEEEVRRENQWAFE 158 (158)
Q Consensus 84 wd~~Fl~~~~~~l~~Ll~AA~~L~i~~L~~~~~~~ia~~i~~ks~eeir~~f~i~~d~t~eee~~i~~e~~w~~~ 158 (158)
||..|+.+|+++|+++++|||||+|++|+++||+.||.+|+|||++|||++|||++||||||+++++|||.|++|
T Consensus 83 wdr~Fm~vDqemL~eI~laaNYL~ikpLLd~gCKivaemirgkSpeeir~tfni~ndfTpEEe~~irkEnEWaed 157 (158)
T COG5201 83 WDRFFMEVDQEMLLEICLAANYLEIKPLLDLGCKIVAEMIRGKSPEEIRETFNIENDFTPEEERRIRKENEWAED 157 (158)
T ss_pred HHHHHHHhhHHHHHHHHHhhccccchHHHHHHHHHHHHHHccCCHHHHHHHhCCCCCCCHHHHHHHHHhcccccc
Confidence 999999999999999999999999999999999999999999999999999999999999999999999999986
No 3
>PF01466 Skp1: Skp1 family, dimerisation domain; InterPro: IPR016072 SKP1 (together with SKP2) was identified as an essential component of the cyclin A-CDK2 S phase kinase complex []. It was found to bind several F-box containing proteins (e.g., Cdc4, Skp2, cyclin F) and to be involved in the ubiquitin protein degradation pathway. A yeast homologue of SKP1 (P52286) was identified in the centromere bound kinetochore complex [] and is also involved in the ubiquitin pathway []. In Dictyostelium discoideum (Slime mold) FP21 was shown to be glycosylated in the cytosol and has homology to SKP1 []. This entry represents a dimerisation domain found at the C-terminal of SKP1 proteins [], as well as in subunit D of the centromere DNA-binding protein complex Cbf3 []. This domain is multi-helical in structure, and consists of an interlocked herterodimer in F-box proteins.; GO: 0006511 ubiquitin-dependent protein catabolic process; PDB: 2P1O_A 3OGL_G 3OGM_A 3C6O_A 2P1N_A 2P1Q_A 3OGK_I 3C6N_A 3C6P_A 2P1P_A ....
Probab=99.97 E-value=9.8e-32 Score=173.93 Aligned_cols=78 Identities=65% Similarity=1.193 Sum_probs=68.7
Q ss_pred hchHHHhhccCChHHHHHHHHhhhccCchhHHHHHHHHHHHHhcCCCHHHHHhHcCCCCCCCHHHHHHHHHhcccccC
Q 031498 81 LKTWDADFVKVDQNTLFDLILAANYLNIKGLLDLTCQTVADMIKGKTPEEIRKTFNIKNDFSPDEEEEVRRENQWAFE 158 (158)
Q Consensus 81 ~~~wd~~Fl~~~~~~l~~Ll~AA~~L~i~~L~~~~~~~ia~~i~~ks~eeir~~f~i~~d~t~eee~~i~~e~~w~~~ 158 (158)
+++||++|++++.+.|++|+.||+||+|++|+++||++||.+++|||++|||++|||++|+|+||+++++++|+|+||
T Consensus 1 l~~wD~~F~~~~~~~L~~l~~AA~yL~I~~L~~~~~~~iA~~i~gks~eeir~~fgi~~d~t~eee~~i~~e~~w~~~ 78 (78)
T PF01466_consen 1 LPEWDQEFLDVDNDELFDLLNAANYLDIKGLLDLCCKYIANMIKGKSPEEIRKYFGIENDLTPEEEEEIRKENEWAFE 78 (78)
T ss_dssp HHHHHHHHT-S-HHHHHHHHHHHHHHT-HHHHHHHHHHHHHHHTTS-HHHHHHHHT---TSSHHHHHHHHHHCCCTB-
T ss_pred CCHHHHHHHHcCHHHHHHHHHHHHHHcchHHHHHHHHHHHHHhcCCCHHHHHHHcCCCCCCCHHHHHHHHHHcchhcC
Confidence 478999999999999999999999999999999999999999999999999999999999999999999999999996
No 4
>smart00512 Skp1 Found in Skp1 protein family. Family of Skp1 (kinetochore protein required for cell cycle progression) and elongin C (subunit of RNA polymerase II transcription factor SIII) homologues.
Probab=99.96 E-value=1.3e-29 Score=172.57 Aligned_cols=99 Identities=63% Similarity=0.940 Sum_probs=88.1
Q ss_pred CcEEEEcCCCCeEEecHHHHHHhHHHHHHHHhCCC----CCceecCCCCHHHHHHHHHHHHHhcccCCCCCCCCCCCcch
Q 031498 5 KKITLKSSDGETFEVEETVALESQTIKHMVEDDCA----DTVIPLPNVTSTILSKVIEYCKKHVEAGSGDKKDDKSTEDD 80 (158)
Q Consensus 5 ~~i~l~s~DG~~f~v~~~~a~~S~~l~~~l~~~~~----~~~Ipl~~i~~~~L~~Ii~~~~~~~~~~~~~~~~~~~~~~~ 80 (158)
++|+|+|+||++|.|++++|++|++|++|+++.+. ..+||+|+|++.+|++|++||+||+.++.+... ...
T Consensus 2 ~~v~L~S~Dg~~f~v~~~~a~~S~~i~~~l~~~~~~~~~~~~Ipl~~v~~~~L~~Vi~yc~~h~~~~~~~~~-----~~~ 76 (104)
T smart00512 2 KYIKLISSDGEVFEVEREVARQSKTIKAMIEDLGVDDENNNPIPLPNVTSKILSKVIEYCEHHVDDPPSVAD-----KDD 76 (104)
T ss_pred CeEEEEeCCCCEEEecHHHHHHHHHHHHHHHccCcccCCCCCccCCCcCHHHHHHHHHHHHHcccCCCCccc-----ccc
Confidence 57999999999999999999999999999997662 148999999999999999999999987654321 146
Q ss_pred hchHHHhhccCChHHHHHHHHhhhccCc
Q 031498 81 LKTWDADFVKVDQNTLFDLILAANYLNI 108 (158)
Q Consensus 81 ~~~wd~~Fl~~~~~~l~~Ll~AA~~L~i 108 (158)
+++||.+|++++.+.|++|+.||+||+|
T Consensus 77 ~~~wD~~F~~~d~~~l~dLl~AAnyL~I 104 (104)
T smart00512 77 IPTWDAEFLKIDQETLFELILAANYLDI 104 (104)
T ss_pred ccHHHHHHHcCCHHHHHHHHHHHHhhCC
Confidence 8999999999999999999999999997
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=99.84 E-value=6.1e-21 Score=118.15 Aligned_cols=61 Identities=51% Similarity=0.756 Sum_probs=54.4
Q ss_pred CcEEEEcCCCCeEEecHHHHHHhHHHHHHHHhCCCCC-ceecCCCCHHHHHHHHHHHHHhcc
Q 031498 5 KKITLKSSDGETFEVEETVALESQTIKHMVEDDCADT-VIPLPNVTSTILSKVIEYCKKHVE 65 (158)
Q Consensus 5 ~~i~l~s~DG~~f~v~~~~a~~S~~l~~~l~~~~~~~-~Ipl~~i~~~~L~~Ii~~~~~~~~ 65 (158)
.+|+|+|+||++|.|++++|++|++|++|+++.+... +||||+|++++|++|++||+||++
T Consensus 1 ~~v~L~SsDg~~f~V~~~~a~~S~~i~~ml~~~~~~~~~Ipl~~v~~~~L~kViewc~~H~~ 62 (62)
T PF03931_consen 1 MYVKLVSSDGQEFEVSREAAKQSKTIKNMLEDLGDEDEPIPLPNVSSRILKKVIEWCEHHKN 62 (62)
T ss_dssp -EEEEEETTSEEEEEEHHHHTTSHHHHHHHHCTCCCGTEEEETTS-HHHHHHHHHHHHHHHH
T ss_pred CEEEEEcCCCCEEEeeHHHHHHhHHHHHHHhhhcccccccccCccCHHHHHHHHHHHHhcCC
Confidence 3699999999999999999999999999999877433 699999999999999999999963
No 6
>KOG3473 consensus RNA polymerase II transcription elongation factor Elongin/SIII, subunit elongin C [Transcription]
Probab=99.80 E-value=1.3e-19 Score=118.70 Aligned_cols=92 Identities=26% Similarity=0.414 Sum_probs=80.6
Q ss_pred CCcEEEEcCCCCeEEecHHHHHHhHHHHHHHHhCC-----CCCceecCCCCHHHHHHHHHHHHHhcccCCCCCCCCCCCc
Q 031498 4 EKKITLKSSDGETFEVEETVALESQTIKHMVEDDC-----ADTVIPLPNVTSTILSKVIEYCKKHVEAGSGDKKDDKSTE 78 (158)
Q Consensus 4 ~~~i~l~s~DG~~f~v~~~~a~~S~~l~~~l~~~~-----~~~~Ipl~~i~~~~L~~Ii~~~~~~~~~~~~~~~~~~~~~ 78 (158)
+.+|+|+|+||++|.+.+++|..|++||.|+.+.+ ..+.+.+++|+|-+|+||++|+.+...+.. ..
T Consensus 16 ~~yVkLvS~Ddhefiikre~AmtSgTiraml~gpg~~se~~~n~v~f~di~shiLeKvc~Yl~Yk~rY~~--------~s 87 (112)
T KOG3473|consen 16 SMYVKLVSSDDHEFIIKREHAMTSGTIRAMLSGPGVFSEAEKNEVYFRDIPSHILEKVCEYLAYKVRYTN--------SS 87 (112)
T ss_pred hhheEeecCCCcEEEEeehhhhhhhHHHHHHcCCccccccccceEEeccchHHHHHHHHHHhhheeeecc--------cc
Confidence 67999999999999999999999999999999765 356799999999999999999999766543 23
Q ss_pred chhchHHHhhccCChHHHHHHHHhhhccCc
Q 031498 79 DDLKTWDADFVKVDQNTLFDLILAANYLNI 108 (158)
Q Consensus 79 ~~~~~wd~~Fl~~~~~~l~~Ll~AA~~L~i 108 (158)
..+|+| .+.++..++||.|||||++
T Consensus 88 ~eiPeF-----~IppemaleLL~aAn~Lec 112 (112)
T KOG3473|consen 88 TEIPEF-----DIPPEMALELLMAANYLEC 112 (112)
T ss_pred ccCCCC-----CCCHHHHHHHHHHhhhhcC
Confidence 567776 5899999999999999974
No 7
>PHA02713 hypothetical protein; Provisional
Probab=99.04 E-value=1.6e-09 Score=93.01 Aligned_cols=102 Identities=17% Similarity=0.258 Sum_probs=85.7
Q ss_pred cEEEEcCCCCeEEecHHH-HHHhHHHHHHHHhCC----CCCceecCCCCHHHHHHHHHHHHHhcccCCCCCCCCCCCcch
Q 031498 6 KITLKSSDGETFEVEETV-ALESQTIKHMVEDDC----ADTVIPLPNVTSTILSKVIEYCKKHVEAGSGDKKDDKSTEDD 80 (158)
Q Consensus 6 ~i~l~s~DG~~f~v~~~~-a~~S~~l~~~l~~~~----~~~~Ipl~~i~~~~L~~Ii~~~~~~~~~~~~~~~~~~~~~~~ 80 (158)
.|+|...+|+.|.+++.+ |.+|++++.||...- ....|.|++++..+|+.|++|++...
T Consensus 27 DV~L~v~~~~~f~~Hr~vLaa~S~YF~amF~~~~~e~~~~~~v~l~~v~~~~~~~ll~y~Yt~~---------------- 90 (557)
T PHA02713 27 DVIITIGDGEEIKAHKTILAAGSKYFRTLFTTPMIIRDLVTRVNLQMFDKDAVKNIVQYLYNRH---------------- 90 (557)
T ss_pred CEEEEeCCCCEEeehHHHHhhcCHHHHHHhcCCchhhccCceEEeccCCHHHHHHHHHHhcCCC----------------
Confidence 578888779999999998 568999999997542 14568999999999999999999841
Q ss_pred hchHHHhhccCChHHHHHHHHhhhccCchhHHHHHHHHHHHHhcCCCHHHHHh
Q 031498 81 LKTWDADFVKVDQNTLFDLILAANYLNIKGLLDLTCQTVADMIKGKTPEEIRK 133 (158)
Q Consensus 81 ~~~wd~~Fl~~~~~~l~~Ll~AA~~L~i~~L~~~~~~~ia~~i~~ks~eeir~ 133 (158)
++.+.+.+|+.||++|+|+.|.+.||.++...+.-.+--+|..
T Consensus 91 ----------i~~~nv~~ll~aA~~lqi~~l~~~C~~~l~~~l~~~NCl~i~~ 133 (557)
T PHA02713 91 ----------ISSMNVIDVLKCADYLLIDDLVTDCESYIKDYTNHDTCIYMYH 133 (557)
T ss_pred ----------CCHHHHHHHHHHHHHHCHHHHHHHHHHHHHhhCCccchHHHHH
Confidence 3567899999999999999999999999998887766555543
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=98.98 E-value=6.5e-09 Score=70.23 Aligned_cols=93 Identities=20% Similarity=0.353 Sum_probs=76.1
Q ss_pred CcEEEEcCCCCeEEecHHHH-HHhHHHHHHHHhCC--CC--CceecCCCCHHHHHHHHHHHHHhcccCCCCCCCCCCCcc
Q 031498 5 KKITLKSSDGETFEVEETVA-LESQTIKHMVEDDC--AD--TVIPLPNVTSTILSKVIEYCKKHVEAGSGDKKDDKSTED 79 (158)
Q Consensus 5 ~~i~l~s~DG~~f~v~~~~a-~~S~~l~~~l~~~~--~~--~~Ipl~~i~~~~L~~Ii~~~~~~~~~~~~~~~~~~~~~~ 79 (158)
..++|+..||+.|.|++.++ .+|+++++++...+ .. ..|++++++...++.+++||+....
T Consensus 11 ~D~~i~v~d~~~~~vhk~iL~~~S~~F~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~l~~~Y~~~~-------------- 76 (111)
T PF00651_consen 11 SDVTIRVGDGKTFYVHKNILAARSPYFRNLFEGSKFKESTVPEISLPDVSPEAFEAFLEYMYTGEI-------------- 76 (111)
T ss_dssp --EEEEETTTEEEEE-HHHHHHHBHHHHHHHTTTTSTTSSEEEEEETTSCHHHHHHHHHHHHHSEE--------------
T ss_pred CCEEEEECCCEEEeechhhhhccchhhhhcccccccccccccccccccccccccccccccccCCcc--------------
Confidence 46889999999999999985 67999999999773 22 2588899999999999999966421
Q ss_pred hhchHHHhhccCC-hHHHHHHHHhhhccCchhHHHHHHHHHHH
Q 031498 80 DLKTWDADFVKVD-QNTLFDLILAANYLNIKGLLDLTCQTVAD 121 (158)
Q Consensus 80 ~~~~wd~~Fl~~~-~~~l~~Ll~AA~~L~i~~L~~~~~~~ia~ 121 (158)
.++ .+.+.+++.+|++|+++.|.+.|+.++..
T Consensus 77 ----------~~~~~~~~~~ll~lA~~~~~~~L~~~~~~~l~~ 109 (111)
T PF00651_consen 77 ----------EINSDENVEELLELADKLQIPELKKACEKFLQE 109 (111)
T ss_dssp ----------EEE-TTTHHHHHHHHHHTTBHHHHHHHHHHHHH
T ss_pred ----------cCCHHHHHHHHHHHHHHhCcHHHHHHHHHHHHh
Confidence 123 67799999999999999999999999864
No 9
>PHA03098 kelch-like protein; Provisional
Probab=98.87 E-value=1.7e-08 Score=85.91 Aligned_cols=100 Identities=20% Similarity=0.311 Sum_probs=81.5
Q ss_pred cEEEE-cCCCCeEEecHHHH-HHhHHHHHHHHhCCCCCceecCCCCHHHHHHHHHHHHHhcccCCCCCCCCCCCcchhch
Q 031498 6 KITLK-SSDGETFEVEETVA-LESQTIKHMVEDDCADTVIPLPNVTSTILSKVIEYCKKHVEAGSGDKKDDKSTEDDLKT 83 (158)
Q Consensus 6 ~i~l~-s~DG~~f~v~~~~a-~~S~~l~~~l~~~~~~~~Ipl~~i~~~~L~~Ii~~~~~~~~~~~~~~~~~~~~~~~~~~ 83 (158)
.++|. +.+|+.|.+++.++ ..|++++.|+...-....|.|+. +..+|+.|++|++...
T Consensus 11 Dv~l~~~~~~~~~~~Hk~vLaa~S~yF~~mf~~~~~~~~i~l~~-~~~~~~~~l~y~Ytg~------------------- 70 (534)
T PHA03098 11 DESIIIVNGGGIIKVHKIILSSSSEYFKKMFKNNFKENEINLNI-DYDSFNEVIKYIYTGK------------------- 70 (534)
T ss_pred CEEEEEEcCCEEEEeHHHHHHhhhHHHHHHHhCCCCCceEEecC-CHHHHHHHHHHhcCCc-------------------
Confidence 35555 46899999999995 56999999998653356788988 9999999999999853
Q ss_pred HHHhhccCChHHHHHHHHhhhccCchhHHHHHHHHHHHHhcCCCHHH
Q 031498 84 WDADFVKVDQNTLFDLILAANYLNIKGLLDLTCQTVADMIKGKTPEE 130 (158)
Q Consensus 84 wd~~Fl~~~~~~l~~Ll~AA~~L~i~~L~~~~~~~ia~~i~~ks~ee 130 (158)
+.++.+++.+|+.||++|+++.|.+.|++++...+.-.+.-+
T Consensus 71 -----~~i~~~~~~~ll~~A~~l~~~~l~~~C~~~l~~~l~~~nc~~ 112 (534)
T PHA03098 71 -----INITSNNVKDILSIANYLIIDFLINLCINYIIKIIDDNNCID 112 (534)
T ss_pred -----eEEcHHHHHHHHHHHHHhCcHHHHHHHHHHHHHhCCHhHHHH
Confidence 246778899999999999999999999999988776554333
No 10
>PHA02790 Kelch-like protein; Provisional
Probab=98.86 E-value=5.7e-09 Score=88.11 Aligned_cols=96 Identities=11% Similarity=0.150 Sum_probs=75.5
Q ss_pred EEEcCCCCeEEecHHH-HHHhHHHHHHHHhCC--CCCceec--CCCCHHHHHHHHHHHHHhcccCCCCCCCCCCCcchhc
Q 031498 8 TLKSSDGETFEVEETV-ALESQTIKHMVEDDC--ADTVIPL--PNVTSTILSKVIEYCKKHVEAGSGDKKDDKSTEDDLK 82 (158)
Q Consensus 8 ~l~s~DG~~f~v~~~~-a~~S~~l~~~l~~~~--~~~~Ipl--~~i~~~~L~~Ii~~~~~~~~~~~~~~~~~~~~~~~~~ 82 (158)
.+...-|++|.+++.+ |..|++++.||...- ....|.+ .+++..+|+.|++|++..+
T Consensus 24 ~~~~~~~~~~~~HR~VLAa~S~YFraMF~~~~~Es~~~v~~~~~~v~~~~l~~lldy~YTg~------------------ 85 (480)
T PHA02790 24 TIIEAIGGNIIVNSTILKKLSPYFRTHLRQKYTKNKDPVTRVCLDLDIHSLTSIVIYSYTGK------------------ 85 (480)
T ss_pred eEEEEcCcEEeeehhhhhhcCHHHHHHhcCCccccccceEEEecCcCHHHHHHHHHhheeee------------------
Confidence 3445678999999999 678999999997542 1223443 3899999999999997743
Q ss_pred hHHHhhccCChHHHHHHHHhhhccCchhHHHHHHHHHHHHhcCCC
Q 031498 83 TWDADFVKVDQNTLFDLILAANYLNIKGLLDLTCQTVADMIKGKT 127 (158)
Q Consensus 83 ~wd~~Fl~~~~~~l~~Ll~AA~~L~i~~L~~~~~~~ia~~i~~ks 127 (158)
+.++.+++.+|+.||++|+|+.+++.||+++...|.-.+
T Consensus 86 ------l~it~~nV~~ll~aA~~Lqi~~v~~~C~~fL~~~l~~~N 124 (480)
T PHA02790 86 ------VYIDSHNVVNLLRASILTSVEFIIYTCINFILRDFRKEY 124 (480)
T ss_pred ------EEEecccHHHHHHHHHHhChHHHHHHHHHHHHhhCCcch
Confidence 346778899999999999999999999998877665443
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=98.73 E-value=4.3e-08 Score=62.77 Aligned_cols=82 Identities=22% Similarity=0.335 Sum_probs=67.8
Q ss_pred cCCCCeEEecHHHHH-HhHHHHHHHHhCC---CCCceecCCCCHHHHHHHHHHHHHhcccCCCCCCCCCCCcchhchHHH
Q 031498 11 SSDGETFEVEETVAL-ESQTIKHMVEDDC---ADTVIPLPNVTSTILSKVIEYCKKHVEAGSGDKKDDKSTEDDLKTWDA 86 (158)
Q Consensus 11 s~DG~~f~v~~~~a~-~S~~l~~~l~~~~---~~~~Ipl~~i~~~~L~~Ii~~~~~~~~~~~~~~~~~~~~~~~~~~wd~ 86 (158)
..+|+.|.+++.++. .|++++.++.... ....|++++++..+++.+++|++...-
T Consensus 5 ~v~~~~~~~h~~iL~~~s~~f~~~~~~~~~~~~~~~i~l~~~~~~~f~~~l~~ly~~~~--------------------- 63 (90)
T smart00225 5 VVGGKKFKAHKAVLAACSPYFKALFSGDFKESKKSEIYLDDVSPEDFRALLEFLYTGKL--------------------- 63 (90)
T ss_pred EECCEEEehHHHHHhhcCHHHHHHHcCCCccCCCCEEEecCCCHHHHHHHHHeecCcee---------------------
Confidence 457799999999865 5899999998653 356788999999999999999997421
Q ss_pred hhccCChHHHHHHHHhhhccCchhHHHHHH
Q 031498 87 DFVKVDQNTLFDLILAANYLNIKGLLDLTC 116 (158)
Q Consensus 87 ~Fl~~~~~~l~~Ll~AA~~L~i~~L~~~~~ 116 (158)
.++...+.+++.+|++++++.|.+.|+
T Consensus 64 ---~~~~~~~~~l~~~a~~~~~~~l~~~c~ 90 (90)
T smart00225 64 ---DLPEENVEELLELADYLQIPGLVELCE 90 (90)
T ss_pred ---ecCHHHHHHHHHHHHHHCcHHHHhhhC
Confidence 234457899999999999999999874
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=98.61 E-value=1.6e-07 Score=80.99 Aligned_cols=93 Identities=20% Similarity=0.345 Sum_probs=78.5
Q ss_pred EEEEcCCCCeEEecHHH-HHHhHHHHHHHHhCC---CCCceecCCCCHHHHHHHHHHHHHhcccCCCCCCCCCCCcchhc
Q 031498 7 ITLKSSDGETFEVEETV-ALESQTIKHMVEDDC---ADTVIPLPNVTSTILSKVIEYCKKHVEAGSGDKKDDKSTEDDLK 82 (158)
Q Consensus 7 i~l~s~DG~~f~v~~~~-a~~S~~l~~~l~~~~---~~~~Ipl~~i~~~~L~~Ii~~~~~~~~~~~~~~~~~~~~~~~~~ 82 (158)
+.|.- +|+.|.+++.+ |.+|++++.|+...- ....|.+.+|+..+|+.+++|++...
T Consensus 39 v~L~v-~~~~~~aHR~VLAa~S~YFraMFt~~l~e~~~~~i~l~~v~~~~l~~ll~y~Yt~~------------------ 99 (571)
T KOG4441|consen 39 VTLLV-GDREFPAHRVVLAACSPYFRAMFTSGLKESKQKEINLEGVDPETLELLLDYAYTGK------------------ 99 (571)
T ss_pred EEEEE-CCeeechHHHHHHhccHHHHHHhcCCcccccceEEEEecCCHHHHHHHHHHhhcce------------------
Confidence 44444 44999999998 677999999998532 46778999999999999999999864
Q ss_pred hHHHhhccCChHHHHHHHHhhhccCchhHHHHHHHHHHHHhc
Q 031498 83 TWDADFVKVDQNTLFDLILAANYLNIKGLLDLTCQTVADMIK 124 (158)
Q Consensus 83 ~wd~~Fl~~~~~~l~~Ll~AA~~L~i~~L~~~~~~~ia~~i~ 124 (158)
+.++.+++-+|+.||.+|+|+.+.+.||.++...+.
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 357889999999999999999999999999876544
No 13
>KOG4682 consensus Uncharacterized conserved protein, contains BTB/POZ domain [General function prediction only]
Probab=97.24 E-value=0.00055 Score=56.20 Aligned_cols=104 Identities=16% Similarity=0.274 Sum_probs=82.4
Q ss_pred cCCCCeEEecHHHHHHhHHHHHHHHhCC---C----CCceecCCCCHHHHHHHHHHHHHhcccCCCCCCCCCCCcchhch
Q 031498 11 SSDGETFEVEETVALESQTIKHMVEDDC---A----DTVIPLPNVTSTILSKVIEYCKKHVEAGSGDKKDDKSTEDDLKT 83 (158)
Q Consensus 11 s~DG~~f~v~~~~a~~S~~l~~~l~~~~---~----~~~Ipl~~i~~~~L~~Ii~~~~~~~~~~~~~~~~~~~~~~~~~~ 83 (158)
..=|.+.++++--+.||+++..|+.+.- . .-.||=|+|+...|..++-=+++-.
T Consensus 75 ~alg~eWrlHk~yL~QS~yf~smf~Gtw~es~~~iIqleI~Dp~Id~~al~~a~gsLY~dE------------------- 135 (488)
T KOG4682|consen 75 EALGFEWRLHKPYLFQSEYFKSMFSGTWKESSMNIIQLEIPDPNIDVVALQVAFGSLYRDE------------------- 135 (488)
T ss_pred hhccceeeeeeeeeeccHHHHHHhccccChhhCceEEEEcCCCcccHHHHHHHHhhhhhhh-------------------
Confidence 4558999999999999999999998652 1 2246668999999999988776621
Q ss_pred HHHhhccCChHHHHHHHHhhhccCchhHHHHHHHHHHHHhcCCCHHHHHhHcCCCCCC
Q 031498 84 WDADFVKVDQNTLFDLILAANYLNIKGLLDLTCQTVADMIKGKTPEEIRKTFNIKNDF 141 (158)
Q Consensus 84 wd~~Fl~~~~~~l~~Ll~AA~~L~i~~L~~~~~~~ia~~i~~ks~eeir~~f~i~~d~ 141 (158)
+.|+.+.+..++.||.+|..++|.+-|...+.+.|+-+|+ .+++....-+
T Consensus 136 -----veI~l~dv~gvlAaA~~lqldgl~qrC~evMie~lspkta---~~yYea~ckY 185 (488)
T KOG4682|consen 136 -----VEIKLSDVVGVLAAACLLQLDGLIQRCGEVMIETLSPKTA---CGYYEAACKY 185 (488)
T ss_pred -----eeccHHHHHHHHHHHHHHHHhhHHHHHHHHHHHhcChhhh---hHhhhhhhhh
Confidence 3588999999999999999999999999998887766663 4455444333
No 14
>KOG2716 consensus Polymerase delta-interacting protein PDIP1 and related proteins, contain BTB/POZ domain [Inorganic ion transport and metabolism]
Probab=97.02 E-value=0.012 Score=45.25 Aligned_cols=101 Identities=19% Similarity=0.350 Sum_probs=79.1
Q ss_pred CCCCcEEEEcCCCCeEEecHHHH-HHhHHHHHHHHhCC-----CCCceecCCCCHHHHHHHHHHHHHhcccCCCCCCCCC
Q 031498 2 SSEKKITLKSSDGETFEVEETVA-LESQTIKHMVEDDC-----ADTVIPLPNVTSTILSKVIEYCKKHVEAGSGDKKDDK 75 (158)
Q Consensus 2 ~~~~~i~l~s~DG~~f~v~~~~a-~~S~~l~~~l~~~~-----~~~~Ipl~~i~~~~L~~Ii~~~~~~~~~~~~~~~~~~ 75 (158)
.++..++| --.|.+|.-++.-+ ++.+.++.|++..- ..+.|=+ +=+..-+..|+.||+-....
T Consensus 2 ~~~~~vkL-nvGG~~F~Tsk~TLtk~dg~fk~m~e~~i~~~~d~s~~IFI-DRSpKHF~~ILNfmRdGdv~--------- 70 (230)
T KOG2716|consen 2 SMSETVKL-NVGGTIFKTSKSTLTKFDGFFKTMLETDIPVEKDESGCIFI-DRSPKHFDTILNFMRDGDVD--------- 70 (230)
T ss_pred CccceEEE-ecCCeEEEeehhhhhhhhhHHHHHhhcCCccccCCcCcEEe-cCChhHHHHHHHhhhccccc---------
Confidence 44566775 34688999988875 67999999998652 2455666 67899999999999864221
Q ss_pred CCcchhchHHHhhccCChHHHHHHHHhhhccCchhHHHHHHHHHHHHhcCC
Q 031498 76 STEDDLKTWDADFVKVDQNTLFDLILAANYLNIKGLLDLTCQTVADMIKGK 126 (158)
Q Consensus 76 ~~~~~~~~wd~~Fl~~~~~~l~~Ll~AA~~L~i~~L~~~~~~~ia~~i~~k 126 (158)
+|+ +...|-+|+.-|.|..+++|+++|...++..+++.
T Consensus 71 -----LPe--------~~kel~El~~EA~fYlL~~Lv~~C~~~i~~~~~~~ 108 (230)
T KOG2716|consen 71 -----LPE--------SEKELKELLREAEFYLLDGLVELCQSAIARLIRGY 108 (230)
T ss_pred -----Ccc--------chHHHHHHHHHHHHhhHHHHHHHHHHHhhhcccCc
Confidence 222 56789999999999999999999999999988775
No 15
>KOG4350 consensus Uncharacterized conserved protein, contains BTB/POZ domain [General function prediction only]
Probab=96.58 E-value=0.023 Score=47.22 Aligned_cols=119 Identities=14% Similarity=0.249 Sum_probs=86.1
Q ss_pred cEEEEcCCCCeEEecHHH-HHHhHHHHHHHHhCC---CCCceecCCCCHHHHHHHHHHHHHhcccCCCCCCC------C-
Q 031498 6 KITLKSSDGETFEVEETV-ALESQTIKHMVEDDC---ADTVIPLPNVTSTILSKVIEYCKKHVEAGSGDKKD------D- 74 (158)
Q Consensus 6 ~i~l~s~DG~~f~v~~~~-a~~S~~l~~~l~~~~---~~~~Ipl~~i~~~~L~~Ii~~~~~~~~~~~~~~~~------~- 74 (158)
.++++-.| +.|..++-+ |..|.++|.|+=+.- ....|||+.-++..++.+++|++..+-+-.-..++ +
T Consensus 46 DVtfvve~-~rfpAHRvILAaRs~yFRAlLYgGm~Es~q~~ipLq~t~~eAF~~lLrYiYtg~~~l~~~~ed~lld~Lsl 124 (620)
T KOG4350|consen 46 DVTFVVED-TRFPAHRVILAARSSYFRALLYGGMQESHQQLIPLQETNSEAFRALLRYIYTGKIDLAGVEEDILLDYLSL 124 (620)
T ss_pred ceEEEEec-cccchhhhhHHHHHHHHHHHHhhhhhhhhhcccccccccHHHHHHHHHHHhhcceecccchHHHHHHHHHH
Confidence 47777766 889999988 567999999986542 35679998888999999999999876543221111 1
Q ss_pred ------CCCcchhchHHHhhccCChHHHHHHHHhhhccCchhHHHHHHHHHHHHhcCCCHHHHH
Q 031498 75 ------KSTEDDLKTWDADFVKVDQNTLFDLILAANYLNIKGLLDLTCQTVADMIKGKTPEEIR 132 (158)
Q Consensus 75 ------~~~~~~~~~wd~~Fl~~~~~~l~~Ll~AA~~L~i~~L~~~~~~~ia~~i~~ks~eeir 132 (158)
......++++-.+. +..++++-++.||.+.+.+.|.++||.++ ++.+.++.
T Consensus 125 Ah~Ygf~~Le~aiSeYl~~i--L~~~NvCmifdaA~ly~l~~Lt~~C~mfm-----DrnA~~lL 181 (620)
T KOG4350|consen 125 AHRYGFIQLETAISEYLKEI--LKNENVCMIFDAAYLYQLTDLTDYCMMFM-----DRNADQLL 181 (620)
T ss_pred HHhcCcHHHHHHHHHHHHHH--HcccceeeeeeHHHHhcchHHHHHHHHHH-----hcCHHhhh
Confidence 11223334443333 46678899999999999999999999887 56666663
No 16
>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=96.34 E-value=0.0047 Score=49.51 Aligned_cols=87 Identities=13% Similarity=0.253 Sum_probs=61.8
Q ss_pred CCeEEecHHHH-HHhHHHHHHHHh---C-CCCCceecC-CCCHHHHHHHHHHHHHhcccCCCCCCCCCCCcchhchHHHh
Q 031498 14 GETFEVEETVA-LESQTIKHMVED---D-CADTVIPLP-NVTSTILSKVIEYCKKHVEAGSGDKKDDKSTEDDLKTWDAD 87 (158)
Q Consensus 14 G~~f~v~~~~a-~~S~~l~~~l~~---~-~~~~~Ipl~-~i~~~~L~~Ii~~~~~~~~~~~~~~~~~~~~~~~~~~wd~~ 87 (158)
.+.|..+++.+ ...++++..+.. . ...++|+|. .-+=.|++=+++|++. ..+
T Consensus 13 ~rdF~C~~~lL~~~M~YF~~~l~~~~~~~~~~~~idisVhCDv~iF~WLm~yv~~----~~p------------------ 70 (317)
T PF11822_consen 13 KRDFTCPRDLLVSEMRYFAEYLSRYINDSQRWEEIDISVHCDVHIFEWLMRYVKG----EPP------------------ 70 (317)
T ss_pred ceeeeccHHHHHHhhHHHHHHHhhcccccCcCCCcceEEecChhHHHHHHHHhhc----CCC------------------
Confidence 36799999985 669999999964 2 234456652 2344455555555544 222
Q ss_pred hccCChHHHHHHHHhhhccCchhHHHHHHHHHHHHhc
Q 031498 88 FVKVDQNTLFDLILAANYLNIKGLLDLTCQTVADMIK 124 (158)
Q Consensus 88 Fl~~~~~~l~~Ll~AA~~L~i~~L~~~~~~~ia~~i~ 124 (158)
.++++++..++.-|+||+|++|++.|-+|+...+.
T Consensus 71 --~l~~~NvvsIliSS~FL~M~~Lve~cl~y~~~~~~ 105 (317)
T PF11822_consen 71 --SLTPSNVVSILISSEFLQMESLVEECLQYCHDHMS 105 (317)
T ss_pred --cCCcCcEEEeEehhhhhccHHHHHHHHHHHHHhHH
Confidence 36788899999999999999999999998865543
No 17
>KOG0783 consensus Uncharacterized conserved protein, contains ankyrin and BTB/POZ domains [Function unknown]
Probab=94.68 E-value=0.11 Score=46.90 Aligned_cols=107 Identities=18% Similarity=0.240 Sum_probs=77.0
Q ss_pred EEEEcCCCCeEEecHHHH-HHhHHHHHHHHhCC-CCCcee--cCCCCHHHHHHHHHHHHHhcccCCCCCCCCCCCcchhc
Q 031498 7 ITLKSSDGETFEVEETVA-LESQTIKHMVEDDC-ADTVIP--LPNVTSTILSKVIEYCKKHVEAGSGDKKDDKSTEDDLK 82 (158)
Q Consensus 7 i~l~s~DG~~f~v~~~~a-~~S~~l~~~l~~~~-~~~~Ip--l~~i~~~~L~~Ii~~~~~~~~~~~~~~~~~~~~~~~~~ 82 (158)
..++..||++|..++.++ ..+.++..|+...- +...|. +--++++.|+-|++|++.- +..
T Consensus 713 ~~i~~KDGkvl~aHkc~L~aRlEYF~smf~~~w~E~sS~t~~~~p~~~e~m~ivLdylYs~--d~~-------------- 776 (1267)
T KOG0783|consen 713 TVIKLKDGKVLKAHKCFLSARLEYFSSMFQFVWMESSSITVNLSPLTVEHMSIVLDYLYSD--DKV-------------- 776 (1267)
T ss_pred EEEEecCCcCcccceeEeeeHHHHHHHHHHHHHhhhccceeecCcchHHHHHHHHHHHHcc--chH--------------
Confidence 456667999999999984 56899999987532 111122 2235699999999998852 111
Q ss_pred hHHHhhcc--CChHHHHHHHHhhhccCchhHHHHHHHHHHHHhcCCCHHHHHh
Q 031498 83 TWDADFVK--VDQNTLFDLILAANYLNIKGLLDLTCQTVADMIKGKTPEEIRK 133 (158)
Q Consensus 83 ~wd~~Fl~--~~~~~l~~Ll~AA~~L~i~~L~~~~~~~ia~~i~~ks~eeir~ 133 (158)
+|++ ...+-++++|..|+-|=|..|-++|-+.+-+++.=|+...+-+
T Consensus 777 ----~~~k~~~~~dF~~~il~iaDqlli~~Lk~Ice~~ll~kl~lk~~~~lle 825 (1267)
T KOG0783|consen 777 ----ELFKDLKESDFMFEILSIADQLLILELKSICEQSLLRKLNLKTLPTLLE 825 (1267)
T ss_pred ----HHHhccchhhhhHHHHHHHHHHHHHHHHHHHHHHHHhHhcccchHHHHH
Confidence 1222 3456689999999999999999999999999888887655543
No 18
>KOG3433 consensus Protein involved in meiotic recombination/predicted coiled-coil protein [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=93.85 E-value=0.13 Score=38.07 Aligned_cols=31 Identities=42% Similarity=0.664 Sum_probs=27.0
Q ss_pred CchhHHHHHHHHHHHHhcCCCHHHHHhHcCCCCCCC
Q 031498 107 NIKGLLDLTCQTVADMIKGKTPEEIRKTFNIKNDFS 142 (158)
Q Consensus 107 ~i~~L~~~~~~~ia~~i~~ks~eeir~~f~i~~d~t 142 (158)
+|--|.++||+.. |.-+.+||+.||||+||.
T Consensus 170 nI~il~dy~~rkf-----~~e~nqi~~~fgIPed~d 200 (203)
T KOG3433|consen 170 NIFILIDYLYRKF-----GLEPNQIRKEFGIPEDFD 200 (203)
T ss_pred hHHHHHHHHHHhc-----CCCHHHHhHhcCCCcccc
Confidence 7778888888876 889999999999999874
No 19
>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=93.33 E-value=0.091 Score=34.33 Aligned_cols=80 Identities=13% Similarity=0.240 Sum_probs=54.6
Q ss_pred CCCeEEecHHHHHH--hHHHHHHHHhC------CCCCceecCCCCHHHHHHHHHHHHHhcccCCCCCCCCCCCcchhchH
Q 031498 13 DGETFEVEETVALE--SQTIKHMVEDD------CADTVIPLPNVTSTILSKVIEYCKKHVEAGSGDKKDDKSTEDDLKTW 84 (158)
Q Consensus 13 DG~~f~v~~~~a~~--S~~l~~~l~~~------~~~~~Ipl~~i~~~~L~~Ii~~~~~~~~~~~~~~~~~~~~~~~~~~w 84 (158)
.|+.|.++++.+.. ..++..++... ...+++-+ +=++..++.|+.|++.. ...+
T Consensus 6 GG~~f~~~~~tL~~~~~s~l~~~~~~~~~~~~~~~~~~~fi-DRdp~~F~~IL~ylr~~--~~l~--------------- 67 (94)
T PF02214_consen 6 GGTIFETSRSTLTRYPDSLLARLFSGERSDDYDDDDGEYFI-DRDPELFEYILNYLRTG--GKLP--------------- 67 (94)
T ss_dssp TTEEEEEEHHHHHTSTTSTTTSHHHTGHGGGEETTTTEEEE-SS-HHHHHHHHHHHHHT--SSB----------------
T ss_pred CCEEEEEcHHHHhhCCCChhhhHHhhccccccCCccceEEe-ccChhhhhHHHHHHhhc--CccC---------------
Confidence 58999999998763 45677777743 13455655 67999999999999995 1110
Q ss_pred HHhhccCChHHHHHHHHhhhccCchhH-HHHH
Q 031498 85 DADFVKVDQNTLFDLILAANYLNIKGL-LDLT 115 (158)
Q Consensus 85 d~~Fl~~~~~~l~~Ll~AA~~L~i~~L-~~~~ 115 (158)
.-+...+..++..|.|.+|+.| ++.|
T Consensus 68 -----~~~~~~~~~l~~Ea~fy~l~~l~i~~c 94 (94)
T PF02214_consen 68 -----IPDEICLEELLEEAEFYGLDELFIEDC 94 (94)
T ss_dssp -------TTS-HHHHHHHHHHHT-HHHHBHHC
T ss_pred -----CCCchhHHHHHHHHHHcCCCccccCCC
Confidence 0123456788999999999999 6654
No 20
>COG5124 Protein predicted to be involved in meiotic recombination [Cell division and chromosome partitioning / General function prediction only]
Probab=91.27 E-value=0.2 Score=37.00 Aligned_cols=31 Identities=42% Similarity=0.692 Sum_probs=24.8
Q ss_pred CchhHHHHHHHHHHHHhcCCCHHHHHhHcCCCCCCC
Q 031498 107 NIKGLLDLTCQTVADMIKGKTPEEIRKTFNIKNDFS 142 (158)
Q Consensus 107 ~i~~L~~~~~~~ia~~i~~ks~eeir~~f~i~~d~t 142 (158)
+|.-|.++.|+.. +.-++|||+.||||.||.
T Consensus 174 nI~ilidy~c~kf-----~~~~~qir~~fgIPedld 204 (209)
T COG5124 174 NIEILIDYLCKKF-----FLKPEQIRKEFGIPEDLD 204 (209)
T ss_pred hHHHHHHHHHHHc-----CCCHHHHHHhcCCCcchh
Confidence 5666777666665 788999999999999863
No 21
>KOG2075 consensus Topoisomerase TOP1-interacting protein BTBD1 [Function unknown]
Probab=87.75 E-value=3 Score=35.56 Aligned_cols=48 Identities=17% Similarity=0.200 Sum_probs=38.9
Q ss_pred CeEEecHHHH-HHhHHHHHHHHhCC---CCCceecCCCCHHHHHHHHHHHHH
Q 031498 15 ETFEVEETVA-LESQTIKHMVEDDC---ADTVIPLPNVTSTILSKVIEYCKK 62 (158)
Q Consensus 15 ~~f~v~~~~a-~~S~~l~~~l~~~~---~~~~Ipl~~i~~~~L~~Ii~~~~~ 62 (158)
+.+..++-+. .-|.++..|+.+.- ...+|.+|+|..+.+...++|++-
T Consensus 129 q~~paHk~vla~gS~VFdaMf~g~~a~~~s~ei~lpdvepaaFl~~L~flYs 180 (521)
T KOG2075|consen 129 QRIPAHKLVLADGSDVFDAMFYGGLAEDASLEIRLPDVEPAAFLAFLRFLYS 180 (521)
T ss_pred cccchhhhhhhcchHHHHHHhccCcccccCceeecCCcChhHhHHHHHHHhc
Confidence 6777888875 45999999997542 267899999999999999998876
No 22
>KOG1665 consensus AFH1-interacting protein FIP2, contains BTB/POZ domain and pentapeptide repeats [General function prediction only]
Probab=86.51 E-value=1.2 Score=34.49 Aligned_cols=88 Identities=14% Similarity=0.229 Sum_probs=60.4
Q ss_pred CcEEEEcCCCCeEEecHH--HHHH-hHHHHHHHHhCCC------CCceecCCCCHHHHHHHHHHHHHhcccCCCCCCCCC
Q 031498 5 KKITLKSSDGETFEVEET--VALE-SQTIKHMVEDDCA------DTVIPLPNVTSTILSKVIEYCKKHVEAGSGDKKDDK 75 (158)
Q Consensus 5 ~~i~l~s~DG~~f~v~~~--~a~~-S~~l~~~l~~~~~------~~~Ipl~~i~~~~L~~Ii~~~~~~~~~~~~~~~~~~ 75 (158)
++|+|- -.|+.|.-..+ +.+. -.++..|+.+.+. .+.+-| +=++.-++-|+.|+.+..
T Consensus 9 ~~vrln-igGk~f~TTidTlv~rEPDSMLa~MF~~~g~~~~~d~kGa~lI-DRsp~yFepIlNyLr~Gq----------- 75 (302)
T KOG1665|consen 9 SMVRLN-IGGKKFCTTIDTLVIREPDSMLAAMFSGRGAMCQEDKKGAVLI-DRSPKYFEPILNYLRDGQ----------- 75 (302)
T ss_pred hhheee-cCCeEEEEeehhhcccCchHHHHHHHccCCCccccccCceEEE-ccCchhhHHHHHHHhcCc-----------
Confidence 345553 45777765444 3333 5677888887651 233444 678889999999998843
Q ss_pred CCcchhchHHHhhccCChHHHHHHHHhhhccCchhHHHHHHH
Q 031498 76 STEDDLKTWDADFVKVDQNTLFDLILAANYLNIKGLLDLTCQ 117 (158)
Q Consensus 76 ~~~~~~~~wd~~Fl~~~~~~l~~Ll~AA~~L~i~~L~~~~~~ 117 (158)
|...+...+++++.+|.|++|.+|.+..-.
T Consensus 76 ------------~~~~s~i~~lgvLeeArff~i~sL~~hle~ 105 (302)
T KOG1665|consen 76 ------------IPSLSDIDCLGVLEEARFFQILSLKDHLED 105 (302)
T ss_pred ------------eeecCCccHHHHHHHhhHHhhHhHHhHHhh
Confidence 122456678999999999999999987643
No 23
>PF03962 Mnd1: Mnd1 family; InterPro: IPR005647 This family of proteins includes meiotic nuclear division protein 1 (MND1) from Saccharomyces cerevisiae (Baker's yeast). The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair [].
Probab=83.25 E-value=1.3 Score=33.09 Aligned_cols=41 Identities=37% Similarity=0.363 Sum_probs=30.1
Q ss_pred HHHHHhhhcc--CchhHHHHHHHHHHHHhcCCCHHHHHhHcCCCCCCC
Q 031498 97 FDLILAANYL--NIKGLLDLTCQTVADMIKGKTPEEIRKTFNIKNDFS 142 (158)
Q Consensus 97 ~~Ll~AA~~L--~i~~L~~~~~~~ia~~i~~ks~eeir~~f~i~~d~t 142 (158)
.....|||.- ||..|..+|+... |.+.+++++.||||+||.
T Consensus 145 ~~~~~~anrwTDNI~~l~~~~~~k~-----~~~~~~i~k~f~Ip~d~d 187 (188)
T PF03962_consen 145 KIAKEAANRWTDNIFSLKSYLKKKF-----GMDEEDIRKEFGIPEDFD 187 (188)
T ss_pred HHHHHHHHHHHhhHHHHHHHHHHhc-----CCCHHHHHHHcCCccccC
Confidence 3344466654 6677777776653 899999999999999873
No 24
>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=83.14 E-value=3.7 Score=32.49 Aligned_cols=102 Identities=18% Similarity=0.348 Sum_probs=59.5
Q ss_pred ceecCCCCHHHHHHHHHHHHHhcccCCC-CCCCCCCCcchhchHHHh--hccCChHHHHHHHHhhhccCchhHHHHHHHH
Q 031498 42 VIPLPNVTSTILSKVIEYCKKHVEAGSG-DKKDDKSTEDDLKTWDAD--FVKVDQNTLFDLILAANYLNIKGLLDLTCQT 118 (158)
Q Consensus 42 ~Ipl~~i~~~~L~~Ii~~~~~~~~~~~~-~~~~~~~~~~~~~~wd~~--Fl~~~~~~l~~Ll~AA~~L~i~~L~~~~~~~ 118 (158)
...++..+.-.-.-|+.|++-|--...+ =..........+.+|-.. |-++..+..++.|.|..-..+.+|+...-+
T Consensus 162 ~~Q~~~~~~~~T~NVvA~LYAalln~~~w~l~~~~~svedFN~WA~~N~ft~~~~~~~~~~Laa~TgVsV~rlLaaI~~- 240 (293)
T PF05409_consen 162 VAQLEGADQYITDNVVAWLYAALLNGCPWWLSSQRISVEDFNEWAMNNGFTSFSSDDAFDMLAAKTGVSVERLLAAIQR- 240 (293)
T ss_dssp SSTTTTS-SB-HHHHHHHHHHHHHTT--TTSSSS---HHHHHHHHHHTTB--SSHHHHHHHHHHHHT--HHHHHHHHHH-
T ss_pred hhhhcCccceeehhHHHHHHHHHHcCCCeeeccceecHHHHHHHHHhCCCcccchhhHHHHHHHHhCCcHHHHHHHHHH-
Confidence 3445444555667799999988544221 011122455667888554 555788899999999999999999987766
Q ss_pred HHHHhcCCCHHHHHhHcCCCCCCCHHHHH
Q 031498 119 VADMIKGKTPEEIRKTFNIKNDFSPDEEE 147 (158)
Q Consensus 119 ia~~i~~ks~eeir~~f~i~~d~t~eee~ 147 (158)
+..-..|++ |--...+++||||++--
T Consensus 241 L~~g~~G~~---IlG~~~ledE~Tp~~V~ 266 (293)
T PF05409_consen 241 LHKGFGGRT---ILGSCSLEDEFTPEMVY 266 (293)
T ss_dssp HHHTTTTT----BTTBSS--TSS-HHHHH
T ss_pred HhcCCCCCc---ccccccccccCCHHHHh
Confidence 566556665 44455577889998753
No 25
>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=80.37 E-value=0.53 Score=33.30 Aligned_cols=46 Identities=24% Similarity=0.356 Sum_probs=0.0
Q ss_pred CCCeEEecHHHHHHhHHHHHHHHhCCCCCceecCCCCHHHHHHHHHHHHHh
Q 031498 13 DGETFEVEETVALESQTIKHMVEDDCADTVIPLPNVTSTILSKVIEYCKKH 63 (158)
Q Consensus 13 DG~~f~v~~~~a~~S~~l~~~l~~~~~~~~Ipl~~i~~~~L~~Ii~~~~~~ 63 (158)
||+.|.|+..++...+.+.+.+.- ...+|.+..+++.+++++++..
T Consensus 1 d~e~f~vv~s~l~ll~~l~~Y~~~-----~~~~P~~a~di~~~l~elLk~f 46 (135)
T PF07928_consen 1 DNEKFVVVGSALLLLKMLSDYLQL-----ASNFPSLAPDILSRLLELLKLF 46 (135)
T ss_dssp ---------------------------------------------------
T ss_pred CCCceecHHHHHHHHHHHHHHHHH-----HHHCchhHHHHHHHHHHHHHHH
Confidence 788888888888877777776542 1245668889999999998775
No 26
>KOG0511 consensus Ankyrin repeat protein [General function prediction only]
Probab=76.79 E-value=9.4 Score=31.88 Aligned_cols=110 Identities=14% Similarity=0.175 Sum_probs=78.3
Q ss_pred CCCCeEEecHHHHHHhHHHHHHHHhCC----CCCce---ecCCCCHHHHHHHHHHHHHhcccCCCCC-CC----------
Q 031498 12 SDGETFEVEETVALESQTIKHMVEDDC----ADTVI---PLPNVTSTILSKVIEYCKKHVEAGSGDK-KD---------- 73 (158)
Q Consensus 12 ~DG~~f~v~~~~a~~S~~l~~~l~~~~----~~~~I---pl~~i~~~~L~~Ii~~~~~~~~~~~~~~-~~---------- 73 (158)
-....+.++...+....+++.|+.+.- .+..+ .+|+..+.+.+.+.+|++.|+.+-++.. .+
T Consensus 298 ~~~~RyP~hla~i~R~eyfk~mf~g~f~e~s~n~~~p~lslp~~~~~vveI~lr~lY~d~tdi~~~~A~dvll~ad~lal 377 (516)
T KOG0511|consen 298 PEEDRYPAHLARILRVEYFKSMFVGDFIESSVNDTRPGLSLPSLADVVVEIDLRNLYCDQTDIIFDVASDVLLFADKLAL 377 (516)
T ss_pred cccccccHHHHHHHHHHHHHHHhccchhhhcCCccccccccchHHHHHHHHHHHHhhcccccchHHHHhhHHHHhhHhhh
Confidence 344558888888888999999987542 13333 4788999999999999999987655421 00
Q ss_pred --C----CCCcchhchHHHhhccCChHHHHHHHHhhhccCchhHHHHHHHHHHHHhc
Q 031498 74 --D----KSTEDDLKTWDADFVKVDQNTLFDLILAANYLNIKGLLDLTCQTVADMIK 124 (158)
Q Consensus 74 --~----~~~~~~~~~wd~~Fl~~~~~~l~~Ll~AA~~L~i~~L~~~~~~~ia~~i~ 124 (158)
. ......+.+|. +| ++.-.+++++.-|.-+...+|=..+..++|..+.
T Consensus 378 ~~dr~Lkt~as~~itq~~-e~--id~y~V~dIl~~~wd~~~~rlEqfa~~~~a~hl~ 431 (516)
T KOG0511|consen 378 ADDRLLKTAASAEITQWL-EL--IDMYGVLDILEYCWDLVACRLEQFAETHEARHLL 431 (516)
T ss_pred hhhhhhhhhhhHHHHHHH-HH--HHhhhHHHHHHHHHHhhhHHHHHHHHHHHHHHHH
Confidence 0 01233455563 22 4555689999999999999999999999887764
No 27
>KOG4591 consensus Uncharacterized conserved protein, contains BTB/POZ domain [General function prediction only]
Probab=66.76 E-value=14 Score=28.25 Aligned_cols=60 Identities=15% Similarity=0.186 Sum_probs=36.9
Q ss_pred ceecCCCCHHHHHHHHHHHHHhcccCCCCCCCCCCCcchhchHHHhhccCChHHHHHHHHhhhccCchhHHHHHHHHHHH
Q 031498 42 VIPLPNVTSTILSKVIEYCKKHVEAGSGDKKDDKSTEDDLKTWDADFVKVDQNTLFDLILAANYLNIKGLLDLTCQTVAD 121 (158)
Q Consensus 42 ~Ipl~~i~~~~L~~Ii~~~~~~~~~~~~~~~~~~~~~~~~~~wd~~Fl~~~~~~l~~Ll~AA~~L~i~~L~~~~~~~ia~ 121 (158)
...+.+++..+.-..++|.+.-. .. +..++..|++|+.-|+.++++-|.+.|-+-+..
T Consensus 107 ~~~~dDad~Ea~~t~iRWIYTDE---id-------------------fk~dD~~L~el~e~An~FqLe~Lke~C~k~l~a 164 (280)
T KOG4591|consen 107 ELDLDDADFEAFHTAIRWIYTDE---ID-------------------FKEDDEFLLELCELANRFQLELLKERCEKGLGA 164 (280)
T ss_pred hhcccccCHHHHHHhheeeeccc---cc-------------------cccchHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 34456778888888888876521 10 134556666777777777777666666665544
Q ss_pred Hh
Q 031498 122 MI 123 (158)
Q Consensus 122 ~i 123 (158)
++
T Consensus 165 ~l 166 (280)
T KOG4591|consen 165 LL 166 (280)
T ss_pred Hh
Confidence 33
No 28
>KOG4350 consensus Uncharacterized conserved protein, contains BTB/POZ domain [General function prediction only]
Probab=66.34 E-value=3.5 Score=34.68 Aligned_cols=37 Identities=16% Similarity=0.291 Sum_probs=27.8
Q ss_pred cCChHHHHHHHHhhhccCchhHHHHHHHHHHHHhcCC
Q 031498 90 KVDQNTLFDLILAANYLNIKGLLDLTCQTVADMIKGK 126 (158)
Q Consensus 90 ~~~~~~l~~Ll~AA~~L~i~~L~~~~~~~ia~~i~~k 126 (158)
.++.+.+++.|.-|+-.|...|....+.|+-..++..
T Consensus 112 ~~~ed~lld~LslAh~Ygf~~Le~aiSeYl~~iL~~~ 148 (620)
T KOG4350|consen 112 GVEEDILLDYLSLAHRYGFIQLETAISEYLKEILKNE 148 (620)
T ss_pred cchHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHccc
Confidence 4667778888888888888888888777776666554
No 29
>PRK14981 DNA-directed RNA polymerase subunit F; Provisional
Probab=59.77 E-value=52 Score=22.32 Aligned_cols=44 Identities=25% Similarity=0.453 Sum_probs=30.0
Q ss_pred CchhHHHHHHHHHHHHhcCCCHHHHHhHcCCCC-CCCHHHHHHHHH
Q 031498 107 NIKGLLDLTCQTVADMIKGKTPEEIRKTFNIKN-DFSPDEEEEVRR 151 (158)
Q Consensus 107 ~i~~L~~~~~~~ia~~i~~ks~eeir~~f~i~~-d~t~eee~~i~~ 151 (158)
++..|-+.....||+. .=.|++|+|..|.-.. -+++|+.++|-.
T Consensus 61 ~~~~l~e~~a~~I~nL-~P~~~dElrai~~~~~~~~~~e~l~~ILd 105 (112)
T PRK14981 61 ELEKMKEKTAVKIADI-LPETRDELRAIFAKERYTLSPEELDEILD 105 (112)
T ss_pred HccCCCHHHHHHHHhc-CCCCHHHHHHHHHHhccCCCHHHHHHHHH
Confidence 3444555555555553 4578999999887663 388998888754
No 30
>KOG2838 consensus Uncharacterized conserved protein, contains BTB/POZ domain [General function prediction only]
Probab=59.22 E-value=39 Score=27.14 Aligned_cols=29 Identities=14% Similarity=0.194 Sum_probs=25.2
Q ss_pred ChHHHHHHHHhhhccCchhHHHHHHHHHH
Q 031498 92 DQNTLFDLILAANYLNIKGLLDLTCQTVA 120 (158)
Q Consensus 92 ~~~~l~~Ll~AA~~L~i~~L~~~~~~~ia 120 (158)
.....++|+.-|-|++.+.|...|...|-
T Consensus 357 qaaeAleL~~IAlFfEfemLaQa~e~Vir 385 (401)
T KOG2838|consen 357 QAAEALELIEIALFFEFEMLAQACEDVIR 385 (401)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45778999999999999999999987764
No 31
>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=58.55 E-value=8 Score=27.09 Aligned_cols=31 Identities=29% Similarity=0.517 Sum_probs=15.4
Q ss_pred HhcCCCHHHHHhHcCCCCCCCHHHHHHHHHhccc
Q 031498 122 MIKGKTPEEIRKTFNIKNDFSPDEEEEVRRENQW 155 (158)
Q Consensus 122 ~i~~ks~eeir~~f~i~~d~t~eee~~i~~e~~w 155 (158)
...|+|.+|-++++|++...++|+ |.+.|.-
T Consensus 51 ~~~~Mtl~EA~~ILnv~~~~~~ee---I~k~y~~ 81 (127)
T PF03656_consen 51 NSKGMTLDEARQILNVKEELSREE---IQKRYKH 81 (127)
T ss_dssp ------HHHHHHHHT--G--SHHH---HHHHHHH
T ss_pred hcCCCCHHHHHHHcCCCCccCHHH---HHHHHHH
Confidence 346899999999999998777665 4444443
No 32
>PF10892 DUF2688: Protein of unknown function (DUF2688); InterPro: IPR024392 Members of this protein family are annotated as KleB, and may play a role in the regulation of transcription in plasmids.
Probab=58.05 E-value=13 Score=22.22 Aligned_cols=24 Identities=25% Similarity=0.621 Sum_probs=18.6
Q ss_pred HHHHHhHcC-CCCC-CCHHHHHHHHH
Q 031498 128 PEEIRKTFN-IKND-FSPDEEEEVRR 151 (158)
Q Consensus 128 ~eeir~~f~-i~~d-~t~eee~~i~~ 151 (158)
.+++|..|| |=.+ +||||..+|.+
T Consensus 30 ad~lr~klG~IC~~CitpEE~~~I~e 55 (60)
T PF10892_consen 30 ADDLRVKLGGICGDCITPEEDREILE 55 (60)
T ss_pred hHHHHHHHcchhhccCCHHHHHHHHH
Confidence 678888887 4445 89999988865
No 33
>PHA03098 kelch-like protein; Provisional
Probab=57.62 E-value=37 Score=28.99 Aligned_cols=52 Identities=15% Similarity=0.250 Sum_probs=41.6
Q ss_pred HHhhcc--CChHHHHHHHHhhhccCchhHHHHHHHHHHHHhc---------CCCHHHHHhHcC
Q 031498 85 DADFVK--VDQNTLFDLILAANYLNIKGLLDLTCQTVADMIK---------GKTPEEIRKTFN 136 (158)
Q Consensus 85 d~~Fl~--~~~~~l~~Ll~AA~~L~i~~L~~~~~~~ia~~i~---------~ks~eeir~~f~ 136 (158)
-.+|+. ++.++.++++..|...+...|.+.|-++|+..+. .-+.+++.+++.
T Consensus 97 C~~~l~~~l~~~nc~~~~~~a~~~~~~~L~~~~~~~i~~nf~~v~~~~~f~~l~~~~l~~ll~ 159 (534)
T PHA03098 97 CINYIIKIIDDNNCIDIYRFSFFYGCKKLYSAAYNYIRNNIELIYNDPDFIYLSKNELIKILS 159 (534)
T ss_pred HHHHHHHhCCHhHHHHHHHHHHHcCcHHHHHHHHHHHHHHHHHHhcCchhhcCCHHHHHHHhc
Confidence 344543 7899999999999999999999999999986653 235788888765
No 34
>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=55.37 E-value=11 Score=25.93 Aligned_cols=40 Identities=25% Similarity=0.469 Sum_probs=30.6
Q ss_pred HHhhhccCchhHHHHHHHHHHHHhcCC----C--------HHHHHh-HcCCCC
Q 031498 100 ILAANYLNIKGLLDLTCQTVADMIKGK----T--------PEEIRK-TFNIKN 139 (158)
Q Consensus 100 l~AA~~L~i~~L~~~~~~~ia~~i~~k----s--------~eeir~-~f~i~~ 139 (158)
-.|+..+.++..+-.+|+.||.+|+|. + +.-||. .||...
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 378899999999999999999999984 3 444444 788654
No 35
>PF11460 DUF3007: Protein of unknown function (DUF3007); InterPro: IPR021562 This is a family of uncharacterised proteins found in bacteria and eukaryotes.
Probab=54.41 E-value=13 Score=25.11 Aligned_cols=24 Identities=38% Similarity=0.613 Sum_probs=17.5
Q ss_pred CHHHHHhHcCCCCCCCHHHHHHHHHhc
Q 031498 127 TPEEIRKTFNIKNDFSPDEEEEVRREN 153 (158)
Q Consensus 127 s~eeir~~f~i~~d~t~eee~~i~~e~ 153 (158)
+.+++.+.|. .+||||.+++.+|-
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 47899999888763
No 36
>PRK05365 malonic semialdehyde reductase; Provisional
Probab=53.45 E-value=10 Score=27.92 Aligned_cols=34 Identities=24% Similarity=0.277 Sum_probs=26.8
Q ss_pred HHHHhhhccCchhHHHHHHHHHHHHhcCCCHHHHHhHcCCCCCC
Q 031498 98 DLILAANYLNIKGLLDLTCQTVADMIKGKTPEEIRKTFNIKNDF 141 (158)
Q Consensus 98 ~Ll~AA~~L~i~~L~~~~~~~ia~~i~~ks~eeir~~f~i~~d~ 141 (158)
.|+.||.-||+... .+.|-..+.+++.|||++++
T Consensus 130 ~l~LaA~~~Glgs~----------~~~g~~~~~v~~~l~ip~~~ 163 (195)
T PRK05365 130 YLILAARALGLDAG----------PMSGFDAAAVDAEFFAGTTW 163 (195)
T ss_pred HHHHHHHHcCCccC----------CccccCHHHHHHHhCCCCCe
Confidence 38999999998872 33566789999999998664
No 37
>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=52.53 E-value=30 Score=22.28 Aligned_cols=45 Identities=13% Similarity=0.155 Sum_probs=28.0
Q ss_pred chhHHHHHHHHHHHHh-cC-CCHHHHHhHcC----CCCCCCHHHHHHHHHh
Q 031498 108 IKGLLDLTCQTVADMI-KG-KTPEEIRKTFN----IKNDFSPDEEEEVRRE 152 (158)
Q Consensus 108 i~~L~~~~~~~ia~~i-~~-ks~eeir~~f~----i~~d~t~eee~~i~~e 152 (158)
|..|+.+..+|-++-= .| -+.+|+|+.+. +.+.+|++|.+++.++
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 3456666666665321 23 27888888773 4455788888777654
No 38
>PF13921 Myb_DNA-bind_6: Myb-like DNA-binding domain; PDB: 1A5J_A 1MBH_A 1GV5_A 1H89_C 1IDY_A 1MBK_A 1IDZ_A 1H88_C 1GVD_A 1MBG_A ....
Probab=52.05 E-value=25 Score=20.43 Aligned_cols=33 Identities=15% Similarity=0.494 Sum_probs=21.7
Q ss_pred HHHHHHhcCCCHHHHHhHcCC------C-CCCCHHHHHHH
Q 031498 117 QTVADMIKGKTPEEIRKTFNI------K-NDFSPDEEEEV 149 (158)
Q Consensus 117 ~~ia~~i~~ks~eeir~~f~i------~-~d~t~eee~~i 149 (158)
..||..+..+|+.+++..|.- . ..+|+||.++|
T Consensus 21 ~~Ia~~l~~Rt~~~~~~r~~~~l~~~~~~~~wt~eEd~~L 60 (60)
T PF13921_consen 21 KKIAEHLGNRTPKQCRNRWRNHLRPKISRGPWTKEEDQRL 60 (60)
T ss_dssp HHHHHHSTTS-HHHHHHHHHHTTSTTSTSSSSSHHHHHHH
T ss_pred HHHHHHHCcCCHHHHHHHHHHHCcccccCCCcCHHHHhcC
Confidence 567888844999999875432 2 23888887764
No 39
>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=50.94 E-value=51 Score=19.51 Aligned_cols=41 Identities=12% Similarity=0.111 Sum_probs=27.4
Q ss_pred chhHHHHHHHHHHHHhcCC--CHHHHHhHcCCCCCCCHHHHHHHHH
Q 031498 108 IKGLLDLTCQTVADMIKGK--TPEEIRKTFNIKNDFSPDEEEEVRR 151 (158)
Q Consensus 108 i~~L~~~~~~~ia~~i~~k--s~eeir~~f~i~~d~t~eee~~i~~ 151 (158)
-+.++-.+|-++|.++.+. +..++..+.|. +|.++..+..+
T Consensus 37 ~~~~ia~a~l~lA~k~~~~~~~~~~~~~~~~~---~~~~~i~~~~~ 79 (83)
T smart00385 37 SPSLIAAAALYLAAKTEEIPPWTKELVHYTGY---FTEEEILRMEK 79 (83)
T ss_pred CHHHHHHHHHHHHHHHhcCCCCchhHhHhhCC---CCHHHHHHHHH
Confidence 3456667788888888774 56777777765 56666555443
No 40
>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=50.64 E-value=34 Score=23.89 Aligned_cols=47 Identities=11% Similarity=0.331 Sum_probs=29.1
Q ss_pred chhHHHHHHH----HHHHHhcCCCHHHHHhHcCCCCCCCHHHHHHHHHhcccccC
Q 031498 108 IKGLLDLTCQ----TVADMIKGKTPEEIRKTFNIKNDFSPDEEEEVRRENQWAFE 158 (158)
Q Consensus 108 i~~L~~~~~~----~ia~~i~~ks~eeir~~f~i~~d~t~eee~~i~~e~~w~~~ 158 (158)
|.+|.+..-. .|+.-...-+...+.+++|++ ++|..++-++..|..|
T Consensus 76 v~~~~~~iR~~i~~~i~~aY~sIs~~~la~~Lg~~----~~el~~~~~~~gW~~d 126 (143)
T PF10075_consen 76 VPGFEDTIRERIAHLISKAYSSISLSDLAEMLGLS----EEELEKFIKSRGWTVD 126 (143)
T ss_dssp STTHHHHHHHHHHHHHHHH-SEE-HHHHHHHTTS-----HHHHHHHHHHHT-EE-
T ss_pred HHHHHHHHHHHHHHHHHHHHhHcCHHHHHHHhCCC----HHHHHHHHHHcCCEEC
Confidence 4445554444 444445566899999999986 5677777777799754
No 41
>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=50.09 E-value=12 Score=27.32 Aligned_cols=33 Identities=21% Similarity=0.307 Sum_probs=26.0
Q ss_pred HHHhhhccCchhHHHHHHHHHHHHhcCCCHHHHHhHcCCCCCC
Q 031498 99 LILAANYLNIKGLLDLTCQTVADMIKGKTPEEIRKTFNIKNDF 141 (158)
Q Consensus 99 Ll~AA~~L~i~~L~~~~~~~ia~~i~~ks~eeir~~f~i~~d~ 141 (158)
++.||.-||+... ++.|-..+.+++.||+++++
T Consensus 124 l~LaA~~lGlgs~----------~~~g~d~~~~~~~L~lp~~~ 156 (185)
T cd02148 124 FILAARALGLDAG----------PMSGFDAAAVDAEFFADTRW 156 (185)
T ss_pred HHHHHHHcCCCcC----------CCcccCHHHHHHHhCCCCCe
Confidence 8888888888762 34566789999999998765
No 42
>PF05321 HHA: Haemolysin expression modulating protein; InterPro: IPR007985 This family consists of haemolysin expression modulating protein (Hha) from Escherichia coli and its enterobacterial homologues, such as YmoA from Yersinia enterocolitica, and RmoA encoded on the R100 plasmid. These proteins act as modulators of bacterial gene expression. Members of the Hha/YmoA/RmoA family act in conjunction with members of the H-NS family, participating in the thermoregulation of different virulence factors and in plasmid transfer []. Hha, along with the chromatin-associated protein H-NS, is involved in the regulation of expression of the toxin alpha-haemolysin in response to osmolarity and temperature []. YmoA modulates the expression of various virulence factors, such as Yop proteins and YadA adhesin, in response to temperature. RmoA is a plasmid R100 modulator involved in plasmid transfer []. The HHA family of proteins display striking similarity to the oligomerization domain of the H-NS proteins.; PDB: 1JW2_A 2K5S_A 2JQT_A.
Probab=50.07 E-value=39 Score=20.24 Aligned_cols=30 Identities=27% Similarity=0.234 Sum_probs=20.9
Q ss_pred CHHHHHHHHHHHHHhcccCCCCCCCCCCCcchhchHHHhhccCChHHHHHHHHhhhc
Q 031498 49 TSTILSKVIEYCKKHVEAGSGDKKDDKSTEDDLKTWDADFVKVDQNTLFDLILAANY 105 (158)
Q Consensus 49 ~~~~L~~Ii~~~~~~~~~~~~~~~~~~~~~~~~~~wd~~Fl~~~~~~l~~Ll~AA~~ 105 (158)
+.++|++|++...+. ++.+.+..+..||++
T Consensus 8 s~dtLEkv~e~~~~~---------------------------L~~~e~~~f~~AaDH 37 (57)
T PF05321_consen 8 SLDTLEKVIEHNRYK---------------------------LTDDELEAFNSAADH 37 (57)
T ss_dssp -HHHHHHHHHHHHHH---------------------------S-HHHHHHHHHHHHH
T ss_pred CHhhHHHHHHHhhCc---------------------------CCHHHHHHHHHHHHH
Confidence 457899999888773 456677777777774
No 43
>PF12556 CobS_N: Cobaltochelatase CobS subunit N terminal
Probab=47.50 E-value=12 Score=20.31 Aligned_cols=12 Identities=33% Similarity=0.783 Sum_probs=10.0
Q ss_pred HHhHcCCCCCCC
Q 031498 131 IRKTFNIKNDFS 142 (158)
Q Consensus 131 ir~~f~i~~d~t 142 (158)
+|+.|||..|++
T Consensus 14 vre~FGiDsDm~ 25 (36)
T PF12556_consen 14 VREVFGIDSDMK 25 (36)
T ss_pred HHHhcCCCcCCe
Confidence 588999998864
No 44
>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=45.67 E-value=82 Score=20.97 Aligned_cols=53 Identities=9% Similarity=0.202 Sum_probs=37.5
Q ss_pred cEEEEcC-CCCeEEecHHHHHHhHHHHHHHHhC----C--CCCceecCCCCHHHHHHHHHHH
Q 031498 6 KITLKSS-DGETFEVEETVALESQTIKHMVEDD----C--ADTVIPLPNVTSTILSKVIEYC 60 (158)
Q Consensus 6 ~i~l~s~-DG~~f~v~~~~a~~S~~l~~~l~~~----~--~~~~Ipl~~i~~~~L~~Ii~~~ 60 (158)
.+.+... +.+.|.|+...+. .++++.+++.. | .+++|.|| -+...++.|+..+
T Consensus 40 ~~~VyVG~~~~Rfvvp~~~L~-hp~f~~LL~~aeeEfG~~~~G~l~iP-C~~~~Fe~~l~~l 99 (100)
T PF02519_consen 40 HFAVYVGEERRRFVVPVSYLN-HPLFQELLEQAEEEFGFDQDGPLTIP-CDVVLFEHLLWLL 99 (100)
T ss_pred eEEEEeCccceEEEechHHcC-chhHHHHHHHHhhhcCcCCCCcEEee-CCHHHHHHHHHHh
Confidence 3444444 4889999999877 67788888753 2 36678776 7788888887654
No 45
>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=43.37 E-value=81 Score=19.66 Aligned_cols=41 Identities=10% Similarity=0.109 Sum_probs=27.5
Q ss_pred HHHHHhhhccCchhHHHHHHHHHHHHh---------cCCCHHHHHhHcCC
Q 031498 97 FDLILAANYLNIKGLLDLTCQTVADMI---------KGKTPEEIRKTFNI 137 (158)
Q Consensus 97 ~~Ll~AA~~L~i~~L~~~~~~~ia~~i---------~~ks~eeir~~f~i 137 (158)
+++...|...+.+.|.+.|.++++..+ ..-+.+++..+++=
T Consensus 2 ~~i~~~a~~~~~~~L~~~~~~~i~~nf~~~~~~~~f~~L~~~~l~~iL~~ 51 (101)
T smart00875 2 LGIRRFAELYGLEELLEKALRFILKNFLEVAQSEEFLELSLEQLLSLLSS 51 (101)
T ss_pred HhHHHHHHHhChHHHHHHHHHHHHHHHHHHhcCcHHhcCCHHHHHHHhCc
Confidence 345666777788888888888776532 33456777776653
No 46
>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=41.50 E-value=29 Score=18.18 Aligned_cols=20 Identities=25% Similarity=0.647 Sum_probs=15.8
Q ss_pred HHHHHHhcCCCHHHHHhHcC
Q 031498 117 QTVADMIKGKTPEEIRKTFN 136 (158)
Q Consensus 117 ~~ia~~i~~ks~eeir~~f~ 136 (158)
..||..+.++|..+++..+.
T Consensus 23 ~~Ia~~~~~rs~~~~~~~~~ 42 (45)
T cd00167 23 EKIAKELPGRTPKQCRERWR 42 (45)
T ss_pred HHHHhHcCCCCHHHHHHHHH
Confidence 56777778899999988763
No 47
>KOG3442 consensus Uncharacterized conserved protein [Function unknown]
Probab=41.49 E-value=28 Score=24.29 Aligned_cols=31 Identities=19% Similarity=0.381 Sum_probs=22.7
Q ss_pred cCCCHHHHHhHcCCCCCCCHHHHHHHHHhccccc
Q 031498 124 KGKTPEEIRKTFNIKNDFSPDEEEEVRRENQWAF 157 (158)
Q Consensus 124 ~~ks~eeir~~f~i~~d~t~eee~~i~~e~~w~~ 157 (158)
.+.|.+|-++++||.++++.|| |.+.|.-+|
T Consensus 54 ~~iTlqEa~qILnV~~~ln~ee---i~k~yehLF 84 (132)
T KOG3442|consen 54 GKITLQEAQQILNVKEPLNREE---IEKRYEHLF 84 (132)
T ss_pred ccccHHHHhhHhCCCCCCCHHH---HHHHHHHHH
Confidence 4578999999999998776554 555565554
No 48
>PRK11053 dihydropteridine reductase; Provisional
Probab=41.16 E-value=25 Score=26.27 Aligned_cols=34 Identities=26% Similarity=0.391 Sum_probs=25.5
Q ss_pred HHHHHHhhhccCchhHHHHHHHHHHHHhcCCCHHHHHhHcCCCC
Q 031498 96 LFDLILAANYLNIKGLLDLTCQTVADMIKGKTPEEIRKTFNIKN 139 (158)
Q Consensus 96 l~~Ll~AA~~L~i~~L~~~~~~~ia~~i~~ks~eeir~~f~i~~ 139 (158)
+..|+.||.-||+... .+.|-..+.+++.|||++
T Consensus 147 ~~~lmLaA~~~Glgs~----------~i~g~~~~~v~~~l~ip~ 180 (217)
T PRK11053 147 LGNLLLGAAALGIDAT----------PIEGFDAAILDAEFGLRE 180 (217)
T ss_pred HHHHHHHHHHcCCCCC----------CcCCcCHHHHHHHhCCCC
Confidence 4477777777777754 345667899999999984
No 49
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=39.54 E-value=32 Score=18.27 Aligned_cols=20 Identities=30% Similarity=0.624 Sum_probs=15.8
Q ss_pred HHHHHHhcCCCHHHHHhHcC
Q 031498 117 QTVADMIKGKTPEEIRKTFN 136 (158)
Q Consensus 117 ~~ia~~i~~ks~eeir~~f~ 136 (158)
..||..+.++|+.+++..+.
T Consensus 25 ~~Ia~~~~~rt~~~~~~~~~ 44 (49)
T smart00717 25 EKIAKELPGRTAEQCRERWN 44 (49)
T ss_pred HHHHHHcCCCCHHHHHHHHH
Confidence 45677778999999988764
No 50
>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=39.08 E-value=76 Score=19.13 Aligned_cols=29 Identities=21% Similarity=0.351 Sum_probs=23.4
Q ss_pred hHHHHHHHHHHHHhcC--CCHHHHHhHcCCC
Q 031498 110 GLLDLTCQTVADMIKG--KTPEEIRKTFNIK 138 (158)
Q Consensus 110 ~L~~~~~~~ia~~i~~--ks~eeir~~f~i~ 138 (158)
.-+-.+|-|+|.+..| +|..||.+..|++
T Consensus 37 ~~iaAA~iY~acr~~~~~~t~~eIa~~~~Vs 67 (71)
T PF00382_consen 37 ESIAAACIYLACRLNGVPRTLKEIAEAAGVS 67 (71)
T ss_dssp HHHHHHHHHHHHHHTTSSSSHHHHHHHCTSS
T ss_pred HHHHHHHHHHHHHHcCCCcCHHHHHHHhCCC
Confidence 4455678888988887 5899999999986
No 51
>PF11198 DUF2857: Protein of unknown function (DUF2857); InterPro: IPR021364 This is a bacterial family of uncharacterised proteins.
Probab=39.08 E-value=72 Score=23.52 Aligned_cols=60 Identities=22% Similarity=0.346 Sum_probs=37.1
Q ss_pred cCChHHHHHHHHhhh-----ccCchhHHHHH-HHHHHHHhcCCCHHHH---HhHcCCCCC------CCHHHHHHH
Q 031498 90 KVDQNTLFDLILAAN-----YLNIKGLLDLT-CQTVADMIKGKTPEEI---RKTFNIKND------FSPDEEEEV 149 (158)
Q Consensus 90 ~~~~~~l~~Ll~AA~-----~L~i~~L~~~~-~~~ia~~i~~ks~eei---r~~f~i~~d------~t~eee~~i 149 (158)
.+|.+.+-.++.-|. .--|+.++.++ +..+-..+-|.|..|+ |+.+|++.. .|+|++.+|
T Consensus 57 ~in~~~l~~~L~~~~~~~~~~~~idr~L~lGAS~~mm~~~FGls~~ev~~rR~llgi~~~~GR~~~~~ee~~~~i 131 (180)
T PF11198_consen 57 SINHDVLWRLLEQARREQQEQQLIDRALRLGASIEMMQRLFGLSSAEVAARRRLLGIPVRKGRPPALSEEEEAAI 131 (180)
T ss_pred eeCHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHhCCCCCCCCCCCcCHHHHHHH
Confidence 367777766666655 24455555555 3445666778887766 678888854 345555554
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=39.07 E-value=42 Score=23.08 Aligned_cols=24 Identities=33% Similarity=0.418 Sum_probs=17.9
Q ss_pred hHHHHHHHHHHHHhcCCCHHHHHh
Q 031498 110 GLLDLTCQTVADMIKGKTPEEIRK 133 (158)
Q Consensus 110 ~L~~~~~~~ia~~i~~ks~eeir~ 133 (158)
...-.++..++.+++|||++|+.+
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 344556677889999999888854
No 53
>PRK11325 scaffold protein; Provisional
Probab=38.68 E-value=47 Score=22.97 Aligned_cols=37 Identities=22% Similarity=0.211 Sum_probs=25.3
Q ss_pred HHHhhhccCchhHHHHH-HHHHHHHhcCCCHHHHHhHc
Q 031498 99 LILAANYLNIKGLLDLT-CQTVADMIKGKTPEEIRKTF 135 (158)
Q Consensus 99 Ll~AA~~L~i~~L~~~~-~~~ia~~i~~ks~eeir~~f 135 (158)
.+.-+.|-.-=.-...+ +..++.++.|||++|.+.+-
T Consensus 52 ~I~d~~f~~~GC~is~Asas~~~e~~~Gktl~ea~~i~ 89 (127)
T PRK11325 52 IIEDAKFKTYGCGSAIASSSLVTEWVKGKTLDEALAIK 89 (127)
T ss_pred eEEEEEEEeeCCHHHHHHHHHHHHHHcCCCHHHHHhcC
Confidence 55556666555555554 45567999999999987753
No 54
>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=37.95 E-value=1.1e+02 Score=21.19 Aligned_cols=36 Identities=11% Similarity=0.142 Sum_probs=21.3
Q ss_pred HHHHHHHhcCCCHHHHHhHcCCCCCCCHHHHHHHHH
Q 031498 116 CQTVADMIKGKTPEEIRKTFNIKNDFSPDEEEEVRR 151 (158)
Q Consensus 116 ~~~ia~~i~~ks~eeir~~f~i~~d~t~eee~~i~~ 151 (158)
.+.+.+.+-|-++..+-..|--.+.+++||.++|++
T Consensus 77 ~~~~~~~~f~gs~~~ll~~l~~~~~ls~eele~L~~ 112 (130)
T TIGR02698 77 AQELFSRICSRKVGAVIADLIEESPLSQTDIEKLEK 112 (130)
T ss_pred HHHHHHHHHCCCHHHHHHHHHhcCCCCHHHHHHHHH
Confidence 344444445555555544442245689999888876
No 55
>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=37.59 E-value=56 Score=22.34 Aligned_cols=37 Identities=24% Similarity=0.284 Sum_probs=25.1
Q ss_pred HHHhhhccCchhHHHHH-HHHHHHHhcCCCHHHHHhHc
Q 031498 99 LILAANYLNIKGLLDLT-CQTVADMIKGKTPEEIRKTF 135 (158)
Q Consensus 99 Ll~AA~~L~i~~L~~~~-~~~ia~~i~~ks~eeir~~f 135 (158)
.+.-+.|-.-=.....+ +..+++++.|||++|..++-
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 55556666555555444 45567999999999977654
No 56
>PF13518 HTH_28: Helix-turn-helix domain
Probab=37.13 E-value=56 Score=18.02 Aligned_cols=20 Identities=30% Similarity=0.537 Sum_probs=16.2
Q ss_pred HHHHhcCCCHHHHHhHcCCC
Q 031498 119 VADMIKGKTPEEIRKTFNIK 138 (158)
Q Consensus 119 ia~~i~~ks~eeir~~f~i~ 138 (158)
|.....|.|..++.+.|||+
T Consensus 6 v~~~~~g~s~~~~a~~~gis 25 (52)
T PF13518_consen 6 VELYLEGESVREIAREFGIS 25 (52)
T ss_pred HHHHHcCCCHHHHHHHHCCC
Confidence 44455789999999999995
No 57
>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=36.77 E-value=54 Score=19.70 Aligned_cols=30 Identities=30% Similarity=0.384 Sum_probs=20.5
Q ss_pred CCCHHHHHhHcCCCC--CCCHHHHHHHHHhcc
Q 031498 125 GKTPEEIRKTFNIKN--DFSPDEEEEVRRENQ 154 (158)
Q Consensus 125 ~ks~eeir~~f~i~~--d~t~eee~~i~~e~~ 154 (158)
.++++++.+.|+... -+|++|-++.+++|.
T Consensus 3 ~~~~~~v~~~l~t~~~~GLs~~ev~~r~~~~G 34 (69)
T PF00690_consen 3 QLSVEEVLKRLNTSSSQGLSSEEVEERRKKYG 34 (69)
T ss_dssp TSSHHHHHHHHTTBTSSBBTHHHHHHHHHHHS
T ss_pred CCCHHHHHHHHCcCCCCCCCHHHHHHHHHhcc
Confidence 357888888887332 288887777776653
No 58
>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=36.31 E-value=57 Score=21.66 Aligned_cols=43 Identities=26% Similarity=0.485 Sum_probs=29.2
Q ss_pred hHHHHHHHHHHHHhcCCCHHHHHhHcCCCC-CCCHHHHHHHHHh
Q 031498 110 GLLDLTCQTVADMIKGKTPEEIRKTFNIKN-DFSPDEEEEVRRE 152 (158)
Q Consensus 110 ~L~~~~~~~ia~~i~~ks~eeir~~f~i~~-d~t~eee~~i~~e 152 (158)
.|+-++|-.+|.++.+..+--+.....+.+ .+|+++..+++..
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 577888999999998875555666555544 4888877666543
No 59
>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=35.97 E-value=57 Score=22.41 Aligned_cols=37 Identities=24% Similarity=0.270 Sum_probs=24.9
Q ss_pred HHHhhhccCchhHHHHH-HHHHHHHhcCCCHHHHHhHc
Q 031498 99 LILAANYLNIKGLLDLT-CQTVADMIKGKTPEEIRKTF 135 (158)
Q Consensus 99 Ll~AA~~L~i~~L~~~~-~~~ia~~i~~ks~eeir~~f 135 (158)
.+.-+.|-.-=.-...+ +..+++++.|||++|.+.+-
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 45555565555444444 45678999999999887654
No 60
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=34.76 E-value=35 Score=24.25 Aligned_cols=17 Identities=35% Similarity=0.778 Sum_probs=16.0
Q ss_pred CCCHHHHHhHcCCCCCC
Q 031498 125 GKTPEEIRKTFNIKNDF 141 (158)
Q Consensus 125 ~ks~eeir~~f~i~~d~ 141 (158)
|+|++|-|..||++.|+
T Consensus 98 gmTPd~YR~KW~LP~dY 114 (148)
T COG4957 98 GLTPDEYRAKWGLPPDY 114 (148)
T ss_pred CCCHHHHHHhcCCCCCC
Confidence 89999999999999995
No 61
>KOG2714 consensus SETA binding protein SB1 and related proteins, contain BTB/POZ domain [General function prediction only]
Probab=33.69 E-value=1.8e+02 Score=24.82 Aligned_cols=83 Identities=11% Similarity=0.110 Sum_probs=54.1
Q ss_pred CcEEEEcCCCCeEEecHHHHHHhH---HHHHHHHhCC-----CCCceecCCCCHHHHHHHHHHHHHhcccCCCCCCCCCC
Q 031498 5 KKITLKSSDGETFEVEETVALESQ---TIKHMVEDDC-----ADTVIPLPNVTSTILSKVIEYCKKHVEAGSGDKKDDKS 76 (158)
Q Consensus 5 ~~i~l~s~DG~~f~v~~~~a~~S~---~l~~~l~~~~-----~~~~Ipl~~i~~~~L~~Ii~~~~~~~~~~~~~~~~~~~ 76 (158)
+.|+| --.|++|.-++.-+.-++ ++..++.+.- ..++|-+ +=+.+++.-|+.|++...-+. +
T Consensus 11 ~~V~l-NVGGriF~Ts~qTL~~~~~DSffsaL~s~~~~s~~~~~~~iFI-DRDPdlFaviLn~LRTg~L~~-~------- 80 (465)
T KOG2714|consen 11 DRVKL-NVGGRIFETSAQTLTWIPRDSFFSALLSGRINSLKDESGAIFI-DRDPDLFAVILNLLRTGDLDA-S------- 80 (465)
T ss_pred ceEEE-ecCceEEecchhhhhcCCcchHHHHHhcCccccccCCCCceEe-cCCchHHHHHHHHHhcCCCCC-c-------
Confidence 34444 356899999998876655 7788876321 2445655 567889999999998853221 1
Q ss_pred CcchhchHHHhhccCChHHH-HHHHHhhhccCchhHHH
Q 031498 77 TEDDLKTWDADFVKVDQNTL-FDLILAANYLNIKGLLD 113 (158)
Q Consensus 77 ~~~~~~~wd~~Fl~~~~~~l-~~Ll~AA~~L~i~~L~~ 113 (158)
.-.. -.|..-|.|.+|.+|+.
T Consensus 81 ----------------g~~~~~llhdEA~fYGl~~llr 102 (465)
T KOG2714|consen 81 ----------------GVFPERLLHDEAMFYGLTPLLR 102 (465)
T ss_pred ----------------cCchhhhhhhhhhhcCcHHHHH
Confidence 1111 12334788999999988
No 62
>PF10507 DUF2453: Protein of unknown function (DUF2453); InterPro: IPR019537 The function of these transmembrane protein is not known.
Probab=33.67 E-value=98 Score=21.16 Aligned_cols=38 Identities=11% Similarity=0.378 Sum_probs=28.6
Q ss_pred hHHHHHHHHHHHHhcC-------CCHHHHHhHcCCCCC-CCHHHHH
Q 031498 110 GLLDLTCQTVADMIKG-------KTPEEIRKTFNIKND-FSPDEEE 147 (158)
Q Consensus 110 ~L~~~~~~~ia~~i~~-------ks~eeir~~f~i~~d-~t~eee~ 147 (158)
+|--++++.+.+.+++ -.+|.+.+++|++.+ +|++|.+
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 4555666666666655 359999999999986 9998866
No 63
>PRK09296 cysteine desufuration protein SufE; Provisional
Probab=33.58 E-value=84 Score=22.22 Aligned_cols=34 Identities=15% Similarity=0.308 Sum_probs=24.0
Q ss_pred HHHHHHHHHHHHhcCCCHHHHHh--------HcCCCCCCCHH
Q 031498 111 LLDLTCQTVADMIKGKTPEEIRK--------TFNIKNDFSPD 144 (158)
Q Consensus 111 L~~~~~~~ia~~i~~ks~eeir~--------~f~i~~d~t~e 144 (158)
+++-.+..+...++|+|++||.+ .+|+...+||-
T Consensus 77 ivkGl~alL~~~~~g~tp~eIl~~d~~~~~~~lGL~~~LSps 118 (138)
T PRK09296 77 IVKGLIAVVFILYQQMTPQDIVNFDVRPWFEKLALTQHLTPS 118 (138)
T ss_pred HHHHHHHHHHHHHcCCCHHHHHhCChHHHHHHcCcccccCcc
Confidence 44445566677779999999864 45777777764
No 64
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=33.18 E-value=46 Score=18.41 Aligned_cols=15 Identities=27% Similarity=0.428 Sum_probs=10.7
Q ss_pred cCCCHHHHHhHcCCC
Q 031498 124 KGKTPEEIRKTFNIK 138 (158)
Q Consensus 124 ~~ks~eeir~~f~i~ 138 (158)
.|.|..+|.+.||++
T Consensus 16 ~G~s~~~ia~~lgvs 30 (50)
T PF13384_consen 16 EGWSIREIAKRLGVS 30 (50)
T ss_dssp HT--HHHHHHHHTS-
T ss_pred CCCCHHHHHHHHCcC
Confidence 499999999999986
No 65
>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=33.09 E-value=52 Score=19.44 Aligned_cols=25 Identities=16% Similarity=0.496 Sum_probs=19.0
Q ss_pred CCceecCCCCHHHHHHHHHHHHHhcccCC
Q 031498 40 DTVIPLPNVTSTILSKVIEYCKKHVEAGS 68 (158)
Q Consensus 40 ~~~Ipl~~i~~~~L~~Ii~~~~~~~~~~~ 68 (158)
...|++ |.....++.||+.|...++
T Consensus 17 ~~Rikv----S~a~~~l~~y~e~~~~~Dp 41 (57)
T cd00068 17 RERLKV----SKAAAELLKYCEQNAENDP 41 (57)
T ss_pred CchhhH----HHHHHHHHHHHHhcCCCCC
Confidence 345666 8899999999999965443
No 66
>PHA02713 hypothetical protein; Provisional
Probab=32.98 E-value=97 Score=26.97 Aligned_cols=72 Identities=10% Similarity=0.089 Sum_probs=46.2
Q ss_pred HHhhcc--CChHHHHHHHHhhhccCchhHHHHHHHHHHHHhcC---------CCHHHHHhHcCCCCCCC-HHHHHHHHHh
Q 031498 85 DADFVK--VDQNTLFDLILAANYLNIKGLLDLTCQTVADMIKG---------KTPEEIRKTFNIKNDFS-PDEEEEVRRE 152 (158)
Q Consensus 85 d~~Fl~--~~~~~l~~Ll~AA~~L~i~~L~~~~~~~ia~~i~~---------ks~eeir~~f~i~~d~t-~eee~~i~~e 152 (158)
-.+|+. ++.++.++++..|.-.....|.+.|.++++..+.. -+.+++.+++.=.+.+. +.|++-.+.=
T Consensus 115 C~~~l~~~l~~~NCl~i~~~~~~~~~~~L~~~a~~~i~~~f~~v~~~~ef~~L~~~~l~~lL~~d~~l~v~~Ee~v~eav 194 (557)
T PHA02713 115 CESYIKDYTNHDTCIYMYHRLYEMSHIPIVKYIKRMLMSNIPTLITTDAFKKTVFEILFDIISTNDNVYLYREGYKVTIL 194 (557)
T ss_pred HHHHHHhhCCccchHHHHHHHHhccchHHHHHHHHHHHHHHHHHhCChhhhhCCHHHHHHHhccccccCCCcHHHHHHHH
Confidence 344554 78888999986344444556999999988877642 46888888877544343 4454444444
Q ss_pred cccc
Q 031498 153 NQWA 156 (158)
Q Consensus 153 ~~w~ 156 (158)
-+|+
T Consensus 195 ~~W~ 198 (557)
T PHA02713 195 LKWL 198 (557)
T ss_pred HHHH
Confidence 4554
No 67
>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=32.61 E-value=28 Score=17.96 Aligned_cols=13 Identities=38% Similarity=0.598 Sum_probs=9.0
Q ss_pred cCCCHHHHHhHcC
Q 031498 124 KGKTPEEIRKTFN 136 (158)
Q Consensus 124 ~~ks~eeir~~f~ 136 (158)
.|-|.+|+|+++.
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 5889999999874
No 68
>PF11338 DUF3140: Protein of unknown function (DUF3140); InterPro: IPR021487 Some members in this family of proteins are annotated as DNA binding proteins. No function is currently known.
Probab=32.15 E-value=52 Score=21.72 Aligned_cols=22 Identities=27% Similarity=0.486 Sum_probs=17.6
Q ss_pred cCCCCHHHHHHHHHHHHHhccc
Q 031498 45 LPNVTSTILSKVIEYCKKHVEA 66 (158)
Q Consensus 45 l~~i~~~~L~~Ii~~~~~~~~~ 66 (158)
|..-.-..|++|+.||+.|...
T Consensus 54 ltddD~~hMrkVV~yv~rhlaq 75 (92)
T PF11338_consen 54 LTDDDYEHMRKVVGYVKRHLAQ 75 (92)
T ss_pred CCHHHHHHHHHHHHHHHHHHhc
Confidence 4344567899999999999876
No 69
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=32.10 E-value=86 Score=18.99 Aligned_cols=31 Identities=16% Similarity=0.224 Sum_probs=20.8
Q ss_pred hHHHHHHHHHHHHhcCCCHHHHHhHcCCCCC
Q 031498 110 GLLDLTCQTVADMIKGKTPEEIRKTFNIKND 140 (158)
Q Consensus 110 ~L~~~~~~~ia~~i~~ks~eeir~~f~i~~d 140 (158)
..+++.+.++...=..-|+.||.+.||+.+.
T Consensus 10 ~vL~~I~~~~~~~G~~Pt~rEIa~~~g~~S~ 40 (65)
T PF01726_consen 10 EVLEFIREYIEENGYPPTVREIAEALGLKST 40 (65)
T ss_dssp HHHHHHHHHHHHHSS---HHHHHHHHTSSSH
T ss_pred HHHHHHHHHHHHcCCCCCHHHHHHHhCCCCh
Confidence 3456677777765444589999999999854
No 70
>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=32.10 E-value=62 Score=20.53 Aligned_cols=41 Identities=7% Similarity=0.109 Sum_probs=30.9
Q ss_pred HHHHHhhhccCchhHHHHHHHHHHHHhc---------CCCHHHHHhHcCC
Q 031498 97 FDLILAANYLNIKGLLDLTCQTVADMIK---------GKTPEEIRKTFNI 137 (158)
Q Consensus 97 ~~Ll~AA~~L~i~~L~~~~~~~ia~~i~---------~ks~eeir~~f~i 137 (158)
++++..|..++...|.+.|-++++..+. .-+.+++..+++-
T Consensus 2 ~~i~~~A~~~~~~~L~~~~~~~i~~nf~~v~~~~~f~~L~~~~l~~iL~~ 51 (103)
T PF07707_consen 2 LSIYRLAEKYGLEELAEACLRFIAKNFNEVSKSDEFLELPFDQLIEILSS 51 (103)
T ss_dssp HHHHHHHHHTT-HHHHHHHHHHHHHTHHHHTTSHHHHCS-HHHHHHHHHT
T ss_pred hhHHHHHHHcChHHHHHHHHHHHHHHHHHHccchhhhcCCHHHHHHHHhc
Confidence 5788999999999999999999976553 2357777777763
No 71
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=31.72 E-value=30 Score=27.55 Aligned_cols=16 Identities=44% Similarity=0.846 Sum_probs=13.0
Q ss_pred cCC-CHHHHHhHcCCCC
Q 031498 124 KGK-TPEEIRKTFNIKN 139 (158)
Q Consensus 124 ~~k-s~eeir~~f~i~~ 139 (158)
++| |||+|++.||++.
T Consensus 244 ~DKSsPEdIk~~FgiSK 260 (287)
T COG2996 244 NDKSSPEDIKATFGISK 260 (287)
T ss_pred CCCCCHHHHHHHhCcCH
Confidence 345 5999999999973
No 72
>PRK15019 CsdA-binding activator; Provisional
Probab=31.43 E-value=87 Score=22.45 Aligned_cols=34 Identities=15% Similarity=0.341 Sum_probs=23.8
Q ss_pred HHHHHHHHHHHHhcCCCHHHHHh--------HcCCCCCCCHH
Q 031498 111 LLDLTCQTVADMIKGKTPEEIRK--------TFNIKNDFSPD 144 (158)
Q Consensus 111 L~~~~~~~ia~~i~~ks~eeir~--------~f~i~~d~t~e 144 (158)
+++-.+..+...++|+|++||.+ -+|+...+||-
T Consensus 87 IvkGl~alL~~~~~g~tp~eIl~~d~~~~~~~lGL~~~LSps 128 (147)
T PRK15019 87 IVRGLLAVLLTAVEGKTAAELQAQSPLALFDELGLRAQLSAS 128 (147)
T ss_pred HHHHHHHHHHHHHcCCCHHHHHhcCHHHHHHHCCchhhcCcc
Confidence 44444556667779999999865 45777777764
No 73
>PF15063 TC1: Thyroid cancer protein 1
Probab=30.84 E-value=54 Score=20.86 Aligned_cols=12 Identities=25% Similarity=0.379 Sum_probs=5.9
Q ss_pred HHHHhHcCCCCC
Q 031498 129 EEIRKTFNIKND 140 (158)
Q Consensus 129 eeir~~f~i~~d 140 (158)
|..|-+|++..|
T Consensus 56 eRA~iI~~~~~d 67 (79)
T PF15063_consen 56 ERARIIWECAQD 67 (79)
T ss_pred HHHHHHHhhCCC
Confidence 344445555544
No 74
>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=30.69 E-value=94 Score=21.97 Aligned_cols=34 Identities=18% Similarity=0.392 Sum_probs=23.3
Q ss_pred HHHHHHHHHHHHhcCCCHHHHHh--------HcCCCCCCCHH
Q 031498 111 LLDLTCQTVADMIKGKTPEEIRK--------TFNIKNDFSPD 144 (158)
Q Consensus 111 L~~~~~~~ia~~i~~ks~eeir~--------~f~i~~d~t~e 144 (158)
+++-.+..+...++|+|++||.+ .+|+...+||-
T Consensus 82 IvkGl~alL~~~~~g~tp~eI~~~d~~~~~~~lGL~~~LSps 123 (138)
T TIGR03391 82 IVRGLLAVLLTAVEGKTPEQLLAQDPLALFDELGLRAQLSAS 123 (138)
T ss_pred HHHHHHHHHHHHHcCCCHHHHHHCCHHHHHHHcCchhccCcc
Confidence 44444566667779999999874 45677667764
No 75
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=30.69 E-value=2.1e+02 Score=20.73 Aligned_cols=47 Identities=23% Similarity=0.213 Sum_probs=33.9
Q ss_pred CChHHHHHHHHhhhccCchhHHHHHHHHHHH-HhcCCCHHHHHhHcCCCC
Q 031498 91 VDQNTLFDLILAANYLNIKGLLDLTCQTVAD-MIKGKTPEEIRKTFNIKN 139 (158)
Q Consensus 91 ~~~~~l~~Ll~AA~~L~i~~L~~~~~~~ia~-~i~~ks~eeir~~f~i~~ 139 (158)
-+.+.+.++-.|..-|.- |-.-.++.|.- .+.|.|.+||-+.+||+.
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 55666777764 568999999999999974
No 76
>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=30.27 E-value=68 Score=20.77 Aligned_cols=28 Identities=7% Similarity=0.286 Sum_probs=20.1
Q ss_pred HHhcCCCHHHHHhHcCCCCCCCHHHHHHHHH
Q 031498 121 DMIKGKTPEEIRKTFNIKNDFSPDEEEEVRR 151 (158)
Q Consensus 121 ~~i~~ks~eeir~~f~i~~d~t~eee~~i~~ 151 (158)
+.|..++++|+..++ ..+|+++...|+.
T Consensus 4 eeL~~m~v~efn~~L---~~lt~~q~~~lK~ 31 (92)
T PF03131_consen 4 EELVSMSVREFNRLL---RGLTEEQIAELKQ 31 (92)
T ss_dssp HHHHHS-HHHHHHHC---TTS-HHHHHHHHH
T ss_pred HHHhhCCHHHHHHHH---HcCCHHHHHHHHH
Confidence 345678999999988 6789998887764
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=30.08 E-value=86 Score=21.15 Aligned_cols=39 Identities=26% Similarity=0.397 Sum_probs=26.7
Q ss_pred HHHHhhhccCchhHHHHH-HHHHHHHhcCCCHHHHHhHcC
Q 031498 98 DLILAANYLNIKGLLDLT-CQTVADMIKGKTPEEIRKTFN 136 (158)
Q Consensus 98 ~Ll~AA~~L~i~~L~~~~-~~~ia~~i~~ks~eeir~~f~ 136 (158)
+.+..+.|-.-=...-.+ +..+++++.|||.+|...+..
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 456666666555444444 455679999999999987653
No 78
>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=30.00 E-value=54 Score=25.28 Aligned_cols=31 Identities=16% Similarity=0.422 Sum_probs=19.8
Q ss_pred HHHHHHHHhcCCCHHHHHhHcCCCCCCCHHH
Q 031498 115 TCQTVADMIKGKTPEEIRKTFNIKNDFSPDE 145 (158)
Q Consensus 115 ~~~~ia~~i~~ks~eeir~~f~i~~d~t~ee 145 (158)
..+.++..++..|++|+++.|+|+..+..+.
T Consensus 30 ~~~~l~~~L~~~s~~el~~l~~is~~la~~~ 60 (237)
T PF03883_consen 30 KTEELLEALKSLSEEELKKLMKISDKLAEEN 60 (237)
T ss_pred HHHHHHHHHHhcCHHHHHHHHCCCHHHHHHH
Confidence 3455566667777777777777775544333
No 79
>PF10415 FumaraseC_C: Fumarase C C-terminus; InterPro: IPR018951 Fumarase C catalyses the stereo-specific interconversion of fumarate to L-malate as part of the Krebs cycle. The full-length protein forms a tetramer with visible globular shape. FumaraseC_C is the C-terminal 65 residues referred to as domain 3. The core of the molecule consists of a bundle of 20 alpha-helices from the five-helix bundle of domain 2. The projections from the core of the tetramer are generated from domains 1 and 3 of each subunit []. This entry does not appear to be part of either the active site or the activation site but is helical in structure forming a little bundle. ; GO: 0016829 lyase activity, 0006099 tricarboxylic acid cycle; PDB: 3RRP_A 3OCE_D 3OCF_D 3E04_B 3GTD_A 3R6V_F 3R6Q_F 1J3U_B 1FUR_A 1YFE_A ....
Probab=29.42 E-value=1.2e+02 Score=17.68 Aligned_cols=23 Identities=17% Similarity=0.393 Sum_probs=15.2
Q ss_pred cCCCHHHHHhHcCCCCCCCHHHHHHH
Q 031498 124 KGKTPEEIRKTFNIKNDFSPDEEEEV 149 (158)
Q Consensus 124 ~~ks~eeir~~f~i~~d~t~eee~~i 149 (158)
.|+|+.|+-.-.|+ +|++|.+++
T Consensus 24 ~g~svre~v~~~g~---lt~ee~d~l 46 (55)
T PF10415_consen 24 EGRSVREVVLEEGL---LTEEELDEL 46 (55)
T ss_dssp HT--HHHHHHHTTS---S-HHHHHHH
T ss_pred cCCCHHHHHHHcCC---CCHHHHHHH
Confidence 58999999887775 577777765
No 80
>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=29.24 E-value=63 Score=17.51 Aligned_cols=30 Identities=30% Similarity=0.336 Sum_probs=22.0
Q ss_pred ccCchhHHHHHHHHHHHHhcCCCHHHHHhH
Q 031498 105 YLNIKGLLDLTCQTVADMIKGKTPEEIRKT 134 (158)
Q Consensus 105 ~L~i~~L~~~~~~~ia~~i~~ks~eeir~~ 134 (158)
||.-.+|-+.....|+..+..-++++|-..
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 466667777777788877777888887653
No 81
>PF13798 PCYCGC: Protein of unknown function with PCYCGC motif
Probab=29.01 E-value=86 Score=22.81 Aligned_cols=24 Identities=42% Similarity=0.663 Sum_probs=17.1
Q ss_pred HHHHHHHHHHHhcCCCHHHHHhHc
Q 031498 112 LDLTCQTVADMIKGKTPEEIRKTF 135 (158)
Q Consensus 112 ~~~~~~~ia~~i~~ks~eeir~~f 135 (158)
++.+.+.+...=+|||+.|||++-
T Consensus 118 l~ia~~a~~~~~~Gks~~eIR~~I 141 (158)
T PF13798_consen 118 LDIAVQAVQMYQEGKSPKEIRQYI 141 (158)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHH
Confidence 444555556666799999999853
No 82
>COG1460 Uncharacterized protein conserved in archaea [Function unknown]
Probab=28.59 E-value=2e+02 Score=19.77 Aligned_cols=60 Identities=23% Similarity=0.401 Sum_probs=37.5
Q ss_pred hccCChHHHHHHHHhhhccCchhHHHHHHHHHHHHhcCCCHHHHHhHcCCCCC-CCHHHHHHHH
Q 031498 88 FVKVDQNTLFDLILAANYLNIKGLLDLTCQTVADMIKGKTPEEIRKTFNIKND-FSPDEEEEVR 150 (158)
Q Consensus 88 Fl~~~~~~l~~Ll~AA~~L~i~~L~~~~~~~ia~~i~~ks~eeir~~f~i~~d-~t~eee~~i~ 150 (158)
|..++++..-++..- .++|..+-+-.+..||+. .=.|+.|+|..|.-..- +|+|+..+|-
T Consensus 45 Fakldpe~a~e~veE--L~~i~~~~e~~avkIadI-~P~t~~ElRsIla~e~~~~s~E~l~~Il 105 (114)
T COG1460 45 FAKLDPEKARELVEE--LLSIVKMSEKIAVKIADI-MPRTPDELRSILAKERVMLSDEELDKIL 105 (114)
T ss_pred HhcCCHHHHHHHHHH--HHhhccccHHHHHHHHHh-CCCCHHHHHHHHHHccCCCCHHHHHHHH
Confidence 555666555544431 223333455555666654 45799999999987765 6788877663
No 83
>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=28.49 E-value=92 Score=17.89 Aligned_cols=23 Identities=17% Similarity=0.327 Sum_probs=17.0
Q ss_pred HHHHHHHhcCCCHHHHHhHcCCC
Q 031498 116 CQTVADMIKGKTPEEIRKTFNIK 138 (158)
Q Consensus 116 ~~~ia~~i~~ks~eeir~~f~i~ 138 (158)
...+.-+..|+|..||-+.+|++
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 44556667899999999998885
No 84
>PRK13503 transcriptional activator RhaS; Provisional
Probab=28.03 E-value=2.7e+02 Score=21.14 Aligned_cols=80 Identities=10% Similarity=0.168 Sum_probs=47.9
Q ss_pred CHHHHHHHHHHHHHhcccCCCCCCCCCCCcchhchHHHhhccCChHHHHHHHHhhhccCchhHHHHHHHHHH-HHhc--C
Q 031498 49 TSTILSKVIEYCKKHVEAGSGDKKDDKSTEDDLKTWDADFVKVDQNTLFDLILAANYLNIKGLLDLTCQTVA-DMIK--G 125 (158)
Q Consensus 49 ~~~~L~~Ii~~~~~~~~~~~~~~~~~~~~~~~~~~wd~~Fl~~~~~~l~~Ll~AA~~L~i~~L~~~~~~~ia-~~i~--~ 125 (158)
....++++++|++.|...+. .+.++-+. +.++...+..+.....-.-...++...--.-| .++. +
T Consensus 169 ~~~~i~~~~~~I~~~~~~~~-----------tl~~lA~~-~~lS~~~l~r~Fk~~~G~S~~~yi~~~Rl~~A~~LL~~~~ 236 (278)
T PRK13503 169 SDARLNQLLAWLEDHFAEEV-----------NWEALADQ-FSLSLRTLHRQLKQQTGLTPQRYLNRLRLLKARHLLRHSD 236 (278)
T ss_pred cHHHHHHHHHHHHHhhcCCC-----------CHHHHHHH-HCCCHHHHHHHHHHHhCcCHHHHHHHHHHHHHHHHHHcCC
Confidence 45557788888887754332 24444333 46788888888877655554444444322222 3332 4
Q ss_pred CCHHHHHhHcCCCCC
Q 031498 126 KTPEEIRKTFNIKND 140 (158)
Q Consensus 126 ks~eeir~~f~i~~d 140 (158)
.|+.||...+|..+.
T Consensus 237 ~sI~eIA~~~GF~~~ 251 (278)
T PRK13503 237 ASVTDIAYRCGFGDS 251 (278)
T ss_pred CCHHHHHHHhCCCCH
Confidence 688888888887754
No 85
>PF06945 DUF1289: Protein of unknown function (DUF1289); InterPro: IPR010710 This family consists of a number of hypothetical bacterial proteins. The aligned region spans around 56 residues and contains 4 highly conserved cysteine residues towards the N terminus. The function of this family is unknown.
Probab=27.89 E-value=1.1e+02 Score=17.58 Aligned_cols=23 Identities=35% Similarity=0.472 Sum_probs=17.1
Q ss_pred CCCHHHHHhHcCCCCCCCHHHHHHHHH
Q 031498 125 GKTPEEIRKTFNIKNDFSPDEEEEVRR 151 (158)
Q Consensus 125 ~ks~eeir~~f~i~~d~t~eee~~i~~ 151 (158)
++|.+||+..... +++|..+|.+
T Consensus 21 ~RT~dEI~~W~~~----s~~er~~i~~ 43 (51)
T PF06945_consen 21 GRTLDEIRDWKSM----SDDERRAILA 43 (51)
T ss_pred CCcHHHHHHHhhC----CHHHHHHHHH
Confidence 4799999998885 5667666644
No 86
>PF13725 tRNA_bind_2: Possible tRNA binding domain; PDB: 2ZPA_B.
Probab=27.67 E-value=1.7e+02 Score=18.79 Aligned_cols=69 Identities=19% Similarity=0.250 Sum_probs=32.1
Q ss_pred CCCHHHHHHHHHHHHHhcccCCCCCCCCCCCcchhchHHHhhccCChHHHHHHHHhhhccCchhHHHHH-HHHHHHHhcC
Q 031498 47 NVTSTILSKVIEYCKKHVEAGSGDKKDDKSTEDDLKTWDADFVKVDQNTLFDLILAANYLNIKGLLDLT-CQTVADMIKG 125 (158)
Q Consensus 47 ~i~~~~L~~Ii~~~~~~~~~~~~~~~~~~~~~~~~~~wd~~Fl~~~~~~l~~Ll~AA~~L~i~~L~~~~-~~~ia~~i~~ 125 (158)
.++..-++++-.|+..+..... -...+-.++.....-. ..|-... .-.|+.-+.+
T Consensus 28 ~ls~~d~~rL~~ya~g~~~y~~-----------------------v~~~l~~l~~~~~~~~-~~Ls~~q~~lLi~k~LQ~ 83 (101)
T PF13725_consen 28 SLSPIDLQRLERYARGGRDYES-----------------------VAPALWRLAFQYFLSP-VSLSELQQALLIAKGLQG 83 (101)
T ss_dssp ---HHHHHHHHHHHHS---TCC-----------------------CHHHHHHHHHH-----------S--HHHHHHHCS-
T ss_pred cCCHHHHHHHHHHHcCCCCHHH-----------------------HHHHHHHHHHHccccc-hhhHHHHHHHHHHHHHCC
Confidence 5789999999999977654332 1222333333332211 2333323 3346777889
Q ss_pred CCHHHHHhHcCCCC
Q 031498 126 KTPEEIRKTFNIKN 139 (158)
Q Consensus 126 ks~eeir~~f~i~~ 139 (158)
||.+++.+.||++.
T Consensus 84 ksw~~~a~~l~l~g 97 (101)
T PF13725_consen 84 KSWEEVAKELGLPG 97 (101)
T ss_dssp --HHHHHHHCT-SS
T ss_pred CCHHHHHHHcCCCC
Confidence 99999999999874
No 87
>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=27.49 E-value=54 Score=23.97 Aligned_cols=38 Identities=21% Similarity=0.194 Sum_probs=25.7
Q ss_pred HHHHHHhhhccCchhHHHHHHHHHHHHhcCCCHHHHHhHcCCCCCC
Q 031498 96 LFDLILAANYLNIKGLLDLTCQTVADMIKGKTPEEIRKTFNIKNDF 141 (158)
Q Consensus 96 l~~Ll~AA~~L~i~~L~~~~~~~ia~~i~~ks~eeir~~f~i~~d~ 141 (158)
+..|+.||.-+|+-..+... .....+.+|+.|||++++
T Consensus 127 ~~nl~LaA~~~GlGs~~~~~--------~~~~~~~v~~~l~ip~~~ 164 (192)
T cd02140 127 QIAVWTALAAEGIGANLQHY--------NPLIDEEVAKKWNIPSNW 164 (192)
T ss_pred HHHHHHHHHhCCCcccHHHh--------CccCCHHHHHhcCCCccc
Confidence 45888888888887632110 012358999999998764
No 88
>PLN03212 Transcription repressor MYB5; Provisional
Probab=27.46 E-value=91 Score=24.43 Aligned_cols=35 Identities=17% Similarity=0.271 Sum_probs=26.0
Q ss_pred HHHHHHh-cCCCHHHHHhHcC------CCCC-CCHHHHHHHHH
Q 031498 117 QTVADMI-KGKTPEEIRKTFN------IKND-FSPDEEEEVRR 151 (158)
Q Consensus 117 ~~ia~~i-~~ks~eeir~~f~------i~~d-~t~eee~~i~~ 151 (158)
..||..+ .++|..+.|+.|. |... +|+||.+.|.+
T Consensus 49 ~~IAk~~g~gRT~KQCReRW~N~L~P~I~kgpWT~EED~lLle 91 (249)
T PLN03212 49 RSLPKRAGLLRCGKSCRLRWMNYLRPSVKRGGITSDEEDLILR 91 (249)
T ss_pred HHHHHhhhcCCCcchHHHHHHHhhchhcccCCCChHHHHHHHH
Confidence 3467666 4899999999773 6654 99998886654
No 89
>COG1710 Uncharacterized protein conserved in archaea [Function unknown]
Probab=27.43 E-value=45 Score=23.20 Aligned_cols=18 Identities=50% Similarity=0.875 Sum_probs=15.2
Q ss_pred HHh-cCCCHHHHHhHcCCC
Q 031498 121 DMI-KGKTPEEIRKTFNIK 138 (158)
Q Consensus 121 ~~i-~~ks~eeir~~f~i~ 138 (158)
.++ +||++.||.+.+||+
T Consensus 104 emlr~gk~preIsk~lGIp 122 (139)
T COG1710 104 EMLRNGKTPREISKDLGIP 122 (139)
T ss_pred HHHHcCCCHHHHHHhhCCc
Confidence 444 489999999999997
No 90
>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=27.38 E-value=56 Score=24.18 Aligned_cols=37 Identities=16% Similarity=0.259 Sum_probs=26.6
Q ss_pred HHHHHHHhhhccCchhHHHHHHHHHHHHhcCCCHHHHHhHcCCCCCC
Q 031498 95 TLFDLILAANYLNIKGLLDLTCQTVADMIKGKTPEEIRKTFNIKNDF 141 (158)
Q Consensus 95 ~l~~Ll~AA~~L~i~~L~~~~~~~ia~~i~~ks~eeir~~f~i~~d~ 141 (158)
.+..++.||..+|+-... +.+-..+.+++.|||+.++
T Consensus 133 A~~nl~LaA~~~GlGs~~----------~~~~~~~~v~~~L~lp~~~ 169 (205)
T TIGR02476 133 AIQNLWLAARAEGLGVGW----------VSILDPDAVRRLLGVPEGW 169 (205)
T ss_pred HHHHHHHHHHHCCCccee----------ecccChHHHHHHhCcCCCc
Confidence 445788888888887631 2234568899999999764
No 91
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=27.37 E-value=1.2e+02 Score=16.79 Aligned_cols=29 Identities=3% Similarity=0.174 Sum_probs=22.1
Q ss_pred HHHHHHHHHHHHhcCC-CHHHHHhHcCCCC
Q 031498 111 LLDLTCQTVADMIKGK-TPEEIRKTFNIKN 139 (158)
Q Consensus 111 L~~~~~~~ia~~i~~k-s~eeir~~f~i~~ 139 (158)
+.....++|...+... |..++.+.+|++.
T Consensus 12 ~T~~~~~~i~~~~~~~~s~~~vA~~~~vs~ 41 (52)
T PF13542_consen 12 ITKRLEQYILKLLRESRSFKDVARELGVSW 41 (52)
T ss_pred HHHHHHHHHHHHHhhcCCHHHHHHHHCCCH
Confidence 3445566777777777 9999999999863
No 92
>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=27.34 E-value=1.5e+02 Score=18.64 Aligned_cols=19 Identities=26% Similarity=0.291 Sum_probs=16.0
Q ss_pred HHhcCCCHHHHHhHcCCCC
Q 031498 121 DMIKGKTPEEIRKTFNIKN 139 (158)
Q Consensus 121 ~~i~~ks~eeir~~f~i~~ 139 (158)
..+.|+|..||-+.+|++.
T Consensus 28 R~~eGlS~kEIAe~LGIS~ 46 (73)
T TIGR03879 28 REEAGKTASEIAEELGRTE 46 (73)
T ss_pred HHHcCCCHHHHHHHHCcCH
Confidence 4568999999999999873
No 93
>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=26.90 E-value=40 Score=18.50 Aligned_cols=19 Identities=32% Similarity=0.587 Sum_probs=15.2
Q ss_pred CCcEEEEcCCCCeEEecHH
Q 031498 4 EKKITLKSSDGETFEVEET 22 (158)
Q Consensus 4 ~~~i~l~s~DG~~f~v~~~ 22 (158)
...+++++.||+...|+++
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 4578999999999888753
No 94
>COG0822 IscU NifU homolog involved in Fe-S cluster formation [Energy production and conversion]
Probab=26.78 E-value=1.1e+02 Score=22.01 Aligned_cols=39 Identities=21% Similarity=0.319 Sum_probs=27.9
Q ss_pred HHHHHhhhccCchhHHHHH-HHHHHHHhcCCCHHHHHhHc
Q 031498 97 FDLILAANYLNIKGLLDLT-CQTVADMIKGKTPEEIRKTF 135 (158)
Q Consensus 97 ~~Ll~AA~~L~i~~L~~~~-~~~ia~~i~~ks~eeir~~f 135 (158)
-+.+..|.|.+.=.-...+ +-.+.+++.|||.+|.+++-
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 4566677777766555554 45567999999999988765
No 95
>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=26.71 E-value=1.2e+02 Score=16.67 Aligned_cols=38 Identities=16% Similarity=0.265 Sum_probs=26.1
Q ss_pred hHHHHHHHHhhhccCchhHHHHHHHHHHHHhc-CCCHHHHHhHc
Q 031498 93 QNTLFDLILAANYLNIKGLLDLTCQTVADMIK-GKTPEEIRKTF 135 (158)
Q Consensus 93 ~~~l~~Ll~AA~~L~i~~L~~~~~~~ia~~i~-~ks~eeir~~f 135 (158)
.++-..|+.|..-++-. -=..||..+. |+|+.+++..|
T Consensus 6 ~eE~~~l~~~v~~~g~~-----~W~~Ia~~~~~~Rt~~qc~~~~ 44 (48)
T PF00249_consen 6 EEEDEKLLEAVKKYGKD-----NWKKIAKRMPGGRTAKQCRSRY 44 (48)
T ss_dssp HHHHHHHHHHHHHSTTT-----HHHHHHHHHSSSSTHHHHHHHH
T ss_pred HHHHHHHHHHHHHhCCc-----HHHHHHHHcCCCCCHHHHHHHH
Confidence 44445555666555555 3467888888 99999998865
No 96
>COG0499 SAM1 S-adenosylhomocysteine hydrolase [Coenzyme metabolism]
Probab=26.66 E-value=99 Score=25.92 Aligned_cols=62 Identities=15% Similarity=0.210 Sum_probs=46.1
Q ss_pred CCCcEEEEcCCCCeEE-ecHHHHHHhHHHHHHHHhCC--CCCceecC-CCCHHHHHHHHHHHHHhc
Q 031498 3 SEKKITLKSSDGETFE-VEETVALESQTIKHMVEDDC--ADTVIPLP-NVTSTILSKVIEYCKKHV 64 (158)
Q Consensus 3 ~~~~i~l~s~DG~~f~-v~~~~a~~S~~l~~~l~~~~--~~~~Ipl~-~i~~~~L~~Ii~~~~~~~ 64 (158)
..+.+.|-+.+|+... .+..++.|.-....++.+.+ ..++.+|| .++..+.+..++.+--.-
T Consensus 337 eGRLvNLa~a~GHPs~VMd~SFanQaLa~~~L~~n~~~~~~~Vy~lP~~lD~~VArl~L~~~G~~i 402 (420)
T COG0499 337 EGRLVNLAAATGHPSEVMDMSFANQALAQIYLVKNHGKLEPGVYRLPKELDEEVARLKLEAMGIEL 402 (420)
T ss_pred cceeeeeccCCCCcHHHhhhhHHHHHHHHHHHHhcccccCCceeeCcHHHHHHHHHHHHHHhCcee
Confidence 3466788888898544 58888888888888887654 46778888 588888888877765543
No 97
>smart00224 GGL G protein gamma subunit-like motifs.
Probab=26.56 E-value=71 Score=19.27 Aligned_cols=25 Identities=24% Similarity=0.551 Sum_probs=19.3
Q ss_pred CCceecCCCCHHHHHHHHHHHHHhcccCC
Q 031498 40 DTVIPLPNVTSTILSKVIEYCKKHVEAGS 68 (158)
Q Consensus 40 ~~~Ipl~~i~~~~L~~Ii~~~~~~~~~~~ 68 (158)
...|++ |.....++.||+.|....+
T Consensus 17 ~~Rikv----S~a~~~li~y~e~~~~~DP 41 (63)
T smart00224 17 RERIKV----SKAAEELLAYCEQHAEEDP 41 (63)
T ss_pred CceehH----HHHHHHHHHHHHcCCCCCC
Confidence 345666 8899999999999866544
No 98
>smart00755 Grip golgin-97, RanBP2alpha,Imh1p and p230/golgin-245.
Probab=26.48 E-value=68 Score=18.18 Aligned_cols=42 Identities=17% Similarity=0.150 Sum_probs=23.4
Q ss_pred chhHHHHHHHHHHHHhcCCCHHHHHhHcCCCCCCCHHHHHHHHH
Q 031498 108 IKGLLDLTCQTVADMIKGKTPEEIRKTFNIKNDFSPDEEEEVRR 151 (158)
Q Consensus 108 i~~L~~~~~~~ia~~i~~ks~eeir~~f~i~~d~t~eee~~i~~ 151 (158)
++.|.+..-+++...= ....++-..++.--.|||+|++++..
T Consensus 4 ~eYLKNVll~fl~~~e--~~r~~ll~vi~tlL~fs~~e~~~~~~ 45 (46)
T smart00755 4 FEYLKNVLLQFLTLRE--SERETLLKVISTVLQLSPEEMQKLLE 45 (46)
T ss_pred HHHHHHHHHHHhccCc--chHHHHHHHHHHHhCCCHHHHHHHHh
Confidence 4455555555553221 11355555555555688888887753
No 99
>PF02657 SufE: Fe-S metabolism associated domain; InterPro: IPR003808 This entry represents the core domain of SufE and related proteins. This domain of SufE shows strong structural similarity to IscU, and the sulfur-acceptor site in SufE coincides with the location of the cysteine residues mediating Fe-S cluster assembly in IscU. Thus, a conserved core structure is implicated in mediating the interactions of both SufE and IscU with the mutually homologous cysteine desulfurase enzymes present in their respective operons [].; PDB: 1MZG_B 1WLO_A 3G0M_A 1NI7_A.
Probab=26.18 E-value=1.4e+02 Score=20.53 Aligned_cols=32 Identities=25% Similarity=0.478 Sum_probs=21.9
Q ss_pred HHHHHHHHHHhcCCCHHHHHh-------HcCCCCCCCHH
Q 031498 113 DLTCQTVADMIKGKTPEEIRK-------TFNIKNDFSPD 144 (158)
Q Consensus 113 ~~~~~~ia~~i~~ks~eeir~-------~f~i~~d~t~e 144 (158)
+-....+...++|+|++||.. .+|+...+||-
T Consensus 70 kGl~all~~~~~g~t~~eI~~~~~~fl~~lgl~~~Ls~s 108 (125)
T PF02657_consen 70 KGLLALLLEVLNGQTPEEILAFDPDFLEQLGLSQHLSPS 108 (125)
T ss_dssp HHHHHHHHHHTTT-BHHHHHHS-THHHHHHTSCCCSTHH
T ss_pred HHHHHHHHHHHcCCCHHHHHhCCHHHHHHcCcccccCch
Confidence 333444555669999999976 57888888875
No 100
>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=26.12 E-value=1.1e+02 Score=21.31 Aligned_cols=38 Identities=21% Similarity=0.211 Sum_probs=25.7
Q ss_pred HHHhhhccCchhHHHHHH-HHHHHHhcCCCHHHHHhHcC
Q 031498 99 LILAANYLNIKGLLDLTC-QTVADMIKGKTPEEIRKTFN 136 (158)
Q Consensus 99 Ll~AA~~L~i~~L~~~~~-~~ia~~i~~ks~eeir~~f~ 136 (158)
.+..+.|-+-=.-...+| ..+++++.|||++|+.....
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 455555555554444444 56789999999999877653
No 101
>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=26.02 E-value=88 Score=21.36 Aligned_cols=31 Identities=26% Similarity=0.341 Sum_probs=19.1
Q ss_pred CchhHHHHHHHHHHHHhc--CCCHHHHHhHcCCC
Q 031498 107 NIKGLLDLTCQTVADMIK--GKTPEEIRKTFNIK 138 (158)
Q Consensus 107 ~i~~L~~~~~~~ia~~i~--~ks~eeir~~f~i~ 138 (158)
+++.|.+.+.+. |..++ +-|..|||++|+--
T Consensus 9 ~~~~~~~~Ae~~-~k~l~~~~lttsQlRkf~~~v 41 (119)
T PF03750_consen 9 DIELLVDYAEKI-AKELKKNKLTTSQLRKFYDEV 41 (119)
T ss_pred CHHHHHHHHHHH-HHHHHhCCCCHHHHHHHHHHH
Confidence 344444444443 34444 46999999999854
No 102
>COG0549 ArcC Carbamate kinase [Amino acid transport and metabolism]
Probab=25.97 E-value=49 Score=26.65 Aligned_cols=17 Identities=41% Similarity=0.915 Sum_probs=15.7
Q ss_pred CCHHHHHHHHHhccccc
Q 031498 141 FSPDEEEEVRRENQWAF 157 (158)
Q Consensus 141 ~t~eee~~i~~e~~w~~ 157 (158)
||+||-+++.+++.|.|
T Consensus 135 Y~~eea~~l~~~~gw~~ 151 (312)
T COG0549 135 YSEEEAEELAKEYGWVF 151 (312)
T ss_pred cCHHHHHHHHhhcCcEE
Confidence 78999999999999987
No 103
>cd00043 CYCLIN Cyclin box fold. Protein binding domain functioning in cell-cycle and transcription control. Present in cyclins, TFIIB and Retinoblastoma (RB).The cyclins consist of 8 classes of cell cycle regulators that regulate cyclin dependent kinases (CDKs). TFIIB is a transcription factor that binds the TATA box. Cyclins, TFIIB and RB contain 2 copies of the domain.
Probab=25.79 E-value=1.5e+02 Score=17.47 Aligned_cols=40 Identities=8% Similarity=0.041 Sum_probs=27.2
Q ss_pred chhHHHHHHHHHHHHhcCC--CHHHHHhHcCCCCCCCHHHHHHHH
Q 031498 108 IKGLLDLTCQTVADMIKGK--TPEEIRKTFNIKNDFSPDEEEEVR 150 (158)
Q Consensus 108 i~~L~~~~~~~ia~~i~~k--s~eeir~~f~i~~d~t~eee~~i~ 150 (158)
-+.++-.+|-++|.++.+. +..++.+..+.. |.++..+..
T Consensus 43 ~~~~ia~a~l~lA~k~~~~~~~~~~~~~~~~~~---~~~~i~~~e 84 (88)
T cd00043 43 SPSLVAAAALYLAAKVEEIPPWLKDLVHVTGYA---TEEEILRME 84 (88)
T ss_pred ChHHHHHHHHHHHHHHcCCCCCHHHHhHHhCCC---CHHHHHHHH
Confidence 3467778888899888775 577777777653 555554443
No 104
>TIGR02603 CxxCH_TIGR02603 putative heme-binding domain, Pirellula/Verrucomicrobium type. This model represents a domain limited to very few species but expanded into large paralogous families in some species that conain it. We find it in over 20 copies each in Pirellula sp. strain 1 (phylum Planctomycetes) and Verrucomicrobium spinosum DSM 4136 (phylum Verrucomicrobia), and no matches above trusted cutoff an any other species so far. This domain, about 140 amino acids long, contains an absolutely conserved motif CxxCH, the cytochrome c family heme-binding site signature (PS00190).
Probab=25.62 E-value=2.1e+02 Score=19.70 Aligned_cols=51 Identities=16% Similarity=0.225 Sum_probs=33.8
Q ss_pred CCcEEEEcCCCCeEEecHHHHHHhHHHHHHHHhCCCCCcee---cCCCCHHHHHHHHHHHHH
Q 031498 4 EKKITLKSSDGETFEVEETVALESQTIKHMVEDDCADTVIP---LPNVTSTILSKVIEYCKK 62 (158)
Q Consensus 4 ~~~i~l~s~DG~~f~v~~~~a~~S~~l~~~l~~~~~~~~Ip---l~~i~~~~L~~Ii~~~~~ 62 (158)
...++|+..+|+.+.|.++-+..-.. . .....| +..++..-+.-++.|+..
T Consensus 79 ~~~~~l~~~~g~~~~i~~~~I~~~~~------~--~~S~MP~gl~~~Lt~~e~~dL~aYL~s 132 (133)
T TIGR02603 79 ADGVTVKMPGGVEQSVPREEIKSREA------L--PVSLMPEGLEMGLSDQDLADLVAYLKS 132 (133)
T ss_pred CCeEEEEcCCCcEEEEEHHHHHHhhc------C--CCCcCCchhhccCCHHHHHHHHHHHhh
Confidence 35688899999999998875432111 1 112233 235899999999999853
No 105
>PHA02790 Kelch-like protein; Provisional
Probab=25.15 E-value=1.1e+02 Score=25.97 Aligned_cols=39 Identities=13% Similarity=0.126 Sum_probs=34.0
Q ss_pred hhcc--CChHHHHHHHHhhhccCchhHHHHHHHHHHHHhcC
Q 031498 87 DFVK--VDQNTLFDLILAANYLNIKGLLDLTCQTVADMIKG 125 (158)
Q Consensus 87 ~Fl~--~~~~~l~~Ll~AA~~L~i~~L~~~~~~~ia~~i~~ 125 (158)
+|+. ++.++.+++...|...+.+.|.+.+-+++.+.+..
T Consensus 114 ~fL~~~l~~~NCl~i~~~A~~y~~~~L~~~a~~fi~~nF~~ 154 (480)
T PHA02790 114 NFILRDFRKEYCVECYMMGIEYGLSNLLCHTKDFIAKHFLE 154 (480)
T ss_pred HHHHhhCCcchHHHHHHHHHHhCHHHHHHHHHHHHHHhHHH
Confidence 3543 88999999999999999999999999999877764
No 106
>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=25.08 E-value=1e+02 Score=16.89 Aligned_cols=15 Identities=33% Similarity=0.581 Sum_probs=10.9
Q ss_pred cCCCHHHHHhHcCCC
Q 031498 124 KGKTPEEIRKTFNIK 138 (158)
Q Consensus 124 ~~ks~eeir~~f~i~ 138 (158)
.|.|+.+|.+.|||+
T Consensus 20 ~G~si~~IA~~~gvs 34 (45)
T PF02796_consen 20 EGMSIAEIAKQFGVS 34 (45)
T ss_dssp TT--HHHHHHHTTS-
T ss_pred CCCCHHHHHHHHCcC
Confidence 589999999999985
No 107
>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=24.65 E-value=70 Score=23.01 Aligned_cols=35 Identities=9% Similarity=-0.050 Sum_probs=25.0
Q ss_pred HHHHHhhhccCchhHHHHHHHHHHHHhcCCC-HHHHHhHcCCCCCC
Q 031498 97 FDLILAANYLNIKGLLDLTCQTVADMIKGKT-PEEIRKTFNIKNDF 141 (158)
Q Consensus 97 ~~Ll~AA~~L~i~~L~~~~~~~ia~~i~~ks-~eeir~~f~i~~d~ 141 (158)
-.++.||.-||+... .+.+.. .+.+++.|||+++.
T Consensus 130 ~~l~LaA~~~Glgs~----------~~~~~~~~~~v~~~l~ip~~~ 165 (193)
T cd02144 130 GLLLAALQNAGLGTV----------TTTPLNMGPFLRRLLGRPANE 165 (193)
T ss_pred HHHHHHHHHCCCcee----------ecCCcchhHHHHHHhCCCCCC
Confidence 458888888888862 122333 38999999999764
No 108
>PRK13696 hypothetical protein; Provisional
Probab=24.44 E-value=1.8e+02 Score=17.75 Aligned_cols=51 Identities=22% Similarity=0.354 Sum_probs=30.5
Q ss_pred HHHHHHHhhhccCchhHHHHHHHHHHHHhcCCCHHHHHhHcCCCCCCCHHHHHHHHHh
Q 031498 95 TLFDLILAANYLNIKGLLDLTCQTVADMIKGKTPEEIRKTFNIKNDFSPDEEEEVRRE 152 (158)
Q Consensus 95 ~l~~Ll~AA~~L~i~~L~~~~~~~ia~~i~~ks~eeir~~f~i~~d~t~eee~~i~~e 152 (158)
..++.|. +.- +=.+.-++.-..+ .-+..+...+.++||+- ++||-++++++
T Consensus 11 d~Y~~L~-~kk-~~~SFSevi~~L~--~~~~~~~~~l~~~~Gil---~dee~~e~~~~ 61 (62)
T PRK13696 11 DVYEKLL-EIK-GDKSFSEVIRELI--EKKKGNLDKLMKAFGIL---SEEEAEELKKE 61 (62)
T ss_pred HHHHHHH-HHh-CCCCHHHHHHHHH--HHhhccHHHHHHHHCCC---CHHHHHHHHhh
Confidence 3444444 333 2235555555555 22345688899999985 57777787765
No 109
>PF09116 gp45-slide_C: gp45 sliding clamp, C terminal; InterPro: IPR015200 This domain is essential for the interaction of the gp45 sliding clamp with the corresponding polymerase. It adopts a DNA clamp fold, consisting of two alpha helices and two beta sheets - the fold is duplicated and has internal pseudo two-fold symmetry []. ; PDB: 1B8H_A 1B77_B 3U61_F 3U60_G 3U5Z_R 1CZD_B.
Probab=24.28 E-value=38 Score=23.20 Aligned_cols=22 Identities=23% Similarity=0.357 Sum_probs=16.9
Q ss_pred cCChHHHHHHHHhhhccCchhH
Q 031498 90 KVDQNTLFDLILAANYLNIKGL 111 (158)
Q Consensus 90 ~~~~~~l~~Ll~AA~~L~i~~L 111 (158)
++..+.+-+|+.||.-|+++.|
T Consensus 5 ~L~~edl~ql~kas~~l~l~dl 26 (112)
T PF09116_consen 5 ELKAEDLQQLMKASRTLGLPDL 26 (112)
T ss_dssp EE-HHHHHHHHHHHHHCT--EE
T ss_pred EecHHHHHHHHHHHHhcCCCeE
Confidence 5788999999999999998865
No 110
>PRK13742 replication protein; Provisional
Probab=24.10 E-value=74 Score=24.71 Aligned_cols=33 Identities=15% Similarity=0.220 Sum_probs=24.5
Q ss_pred hHHHHHHHHHHHHhcC---CCHHHHHhHcCCCCCCC
Q 031498 110 GLLDLTCQTVADMIKG---KTPEEIRKTFNIKNDFS 142 (158)
Q Consensus 110 ~L~~~~~~~ia~~i~~---ks~eeir~~f~i~~d~t 142 (158)
+|.+++|++-...-.| -+++++|..||+++.+.
T Consensus 164 RLYelL~q~~~~~~~g~~~i~i~elr~~l~~~~~Y~ 199 (245)
T PRK13742 164 RLYESLCQYRKPDGSGIVSLKIDWIIERYQLPQSYQ 199 (245)
T ss_pred HHHHHHHHhhhhccCCeEEEEHHHHHHHhCCccccc
Confidence 6788888876542223 47999999999987663
No 111
>KOG0028 consensus Ca2+-binding protein (centrin/caltractin), EF-Hand superfamily protein [Cytoskeleton; Cell cycle control, cell division, chromosome partitioning]
Probab=23.81 E-value=1.9e+02 Score=21.29 Aligned_cols=48 Identities=21% Similarity=0.396 Sum_probs=30.4
Q ss_pred hhhccCchhHHHHHHHHHHHHhcCCCHHHHHhHcCCCCC-----CCHHHHHHHHHh
Q 031498 102 AANYLNIKGLLDLTCQTVADMIKGKTPEEIRKTFNIKND-----FSPDEEEEVRRE 152 (158)
Q Consensus 102 AA~~L~i~~L~~~~~~~ia~~i~~ks~eeir~~f~i~~d-----~t~eee~~i~~e 152 (158)
++-.+..+.++...+..++. ++ |-+||++.|.+-++ +++-+..++.+|
T Consensus 82 ~~g~i~fe~f~~~mt~k~~e--~d-t~eEi~~afrl~D~D~~Gkis~~~lkrvake 134 (172)
T KOG0028|consen 82 GSGKITFEDFRRVMTVKLGE--RD-TKEEIKKAFRLFDDDKTGKISQRNLKRVAKE 134 (172)
T ss_pred cCceechHHHHHHHHHHHhc--cC-cHHHHHHHHHcccccCCCCcCHHHHHHHHHH
Confidence 34556666777766666654 24 88999988885543 456666665554
No 112
>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=23.41 E-value=1.2e+02 Score=18.31 Aligned_cols=29 Identities=14% Similarity=0.370 Sum_probs=17.1
Q ss_pred cEEEEcCCC------CeEEecHHH--HHHhHHHHHHH
Q 031498 6 KITLKSSDG------ETFEVEETV--ALESQTIKHMV 34 (158)
Q Consensus 6 ~i~l~s~DG------~~f~v~~~~--a~~S~~l~~~l 34 (158)
.|+|.|++| ..+.|+..+ ...|.++..++
T Consensus 3 ~v~F~t~~~~~~~~~~~~~VP~~~t~~~Ls~LvN~LL 39 (65)
T PF08154_consen 3 QVQFVTEDGEYEVPGTPISVPSNITRKELSELVNQLL 39 (65)
T ss_pred EEEEEcCCCCccCCCCCEEEeCCCCHHHHHHHHHHHh
Confidence 356677666 345555444 34577777776
No 113
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=23.29 E-value=1.2e+02 Score=16.44 Aligned_cols=16 Identities=31% Similarity=0.464 Sum_probs=12.6
Q ss_pred hcCCCHHHHHhHcCCC
Q 031498 123 IKGKTPEEIRKTFNIK 138 (158)
Q Consensus 123 i~~ks~eeir~~f~i~ 138 (158)
..|+|..+|-+.+|++
T Consensus 16 ~~g~s~~eia~~l~is 31 (58)
T smart00421 16 AEGLTNKEIAERLGIS 31 (58)
T ss_pred HcCCCHHHHHHHHCCC
Confidence 4688888888888875
No 114
>PF08299 Bac_DnaA_C: Bacterial dnaA protein helix-turn-helix; InterPro: IPR013159 This entry represents the C-terminal domain of bacterial DnaA proteins [, , ] that play an important role in initiating and regulating chromosomal replication. DnaA is an ATP- and DNA-binding protein. It binds specifically to 9 bp nucleotide repeats known as dnaA boxes which are found in the chromosome origin of replication (oriC). DnaA is a protein of about 50 kDa that contains two conserved regions: the first is located in the N-terminal half and corresponds to the ATP-binding domain, the second is located in the C-terminal half and could be involved in DNA-binding. The protein may also bind the RNA polymerase beta subunit, the dnaB and dnaZ proteins, and the groE gene products (chaperonins) [].; GO: 0005524 ATP binding, 0043565 sequence-specific DNA binding, 0006270 DNA-dependent DNA replication initiation, 0006275 regulation of DNA replication; PDB: 2HCB_B 3R8F_C 1L8Q_A 3PVP_B 3PVV_A 1J1V_A.
Probab=23.25 E-value=1.3e+02 Score=18.32 Aligned_cols=26 Identities=19% Similarity=0.225 Sum_probs=18.0
Q ss_pred HHHHHHHHHHhcCCCHHHHHhHcCCC
Q 031498 113 DLTCQTVADMIKGKTPEEIRKTFNIK 138 (158)
Q Consensus 113 ~~~~~~ia~~i~~ks~eeir~~f~i~ 138 (158)
...+-|++....|.|..+|-++||--
T Consensus 33 R~va~yL~r~~~~~sl~~Ig~~fg~r 58 (70)
T PF08299_consen 33 RQVAMYLARELTGLSLSEIGRYFGGR 58 (70)
T ss_dssp HHHHHHHHHHHS---HHHHHHHCTSS
T ss_pred HHHHHHHHHHHhCCCHHHHHHHhCCC
Confidence 44566888888899999999999943
No 115
>TIGR03147 cyt_nit_nrfF cytochrome c nitrite reductase, accessory protein NrfF.
Probab=23.10 E-value=83 Score=22.00 Aligned_cols=17 Identities=29% Similarity=0.503 Sum_probs=12.1
Q ss_pred HHHHh-cCCCHHHHHhHc
Q 031498 119 VADMI-KGKTPEEIRKTF 135 (158)
Q Consensus 119 ia~~i-~~ks~eeir~~f 135 (158)
|..++ .|+|.+||+.+|
T Consensus 66 Vr~~i~~G~Sd~eI~~~~ 83 (126)
T TIGR03147 66 VYSMVNEGKSNQQIIDFM 83 (126)
T ss_pred HHHHHHcCCCHHHHHHHH
Confidence 33333 499999999865
No 116
>COG2445 Uncharacterized conserved protein [Function unknown]
Probab=22.95 E-value=2e+02 Score=20.35 Aligned_cols=46 Identities=15% Similarity=0.232 Sum_probs=33.6
Q ss_pred cCchhHHHHHHHHHHHHhc--CCCHHHHHhHcCCCCCCCHHHHHHHHH
Q 031498 106 LNIKGLLDLTCQTVADMIK--GKTPEEIRKTFNIKNDFSPDEEEEVRR 151 (158)
Q Consensus 106 L~i~~L~~~~~~~ia~~i~--~ks~eeir~~f~i~~d~t~eee~~i~~ 151 (158)
+-|+.++++|...++.... -.|..++-..++=.+-+++++-+.+++
T Consensus 43 ~~ies~~Di~~~li~~~~~~~p~~y~d~~~~L~~~gvi~~e~~e~L~~ 90 (138)
T COG2445 43 VAIESLIDIGNMLISKFGLRDPGTYDDCIDILVEEGVIPEEEAEELKK 90 (138)
T ss_pred HHHHHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHcCCCCHHHHHHHHH
Confidence 4578899999888887663 357888877777655567777677665
No 117
>COG4565 CitB Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]
Probab=22.93 E-value=1.6e+02 Score=22.75 Aligned_cols=22 Identities=32% Similarity=0.279 Sum_probs=19.4
Q ss_pred CCceecC-CCCHHHHHHHHHHHH
Q 031498 40 DTVIPLP-NVTSTILSKVIEYCK 61 (158)
Q Consensus 40 ~~~Ipl~-~i~~~~L~~Ii~~~~ 61 (158)
..+.+|| ++++.+|++|.+|.+
T Consensus 146 ~~~~~LPkGi~~~Tl~~i~~~~~ 168 (224)
T COG4565 146 QPPDDLPKGLDELTLQKVREALK 168 (224)
T ss_pred cCcccCCCCcCHHHHHHHHHHHh
Confidence 5567788 799999999999999
No 118
>smart00760 Bac_DnaA_C Bacterial dnaA protein helix-turn-helix domain. Could be involved in DNA-binding.
Probab=22.91 E-value=1.5e+02 Score=17.31 Aligned_cols=26 Identities=19% Similarity=0.098 Sum_probs=20.8
Q ss_pred HHHHHHHHHHHhcCCCHHHHHhHcCC
Q 031498 112 LDLTCQTVADMIKGKTPEEIRKTFNI 137 (158)
Q Consensus 112 ~~~~~~~ia~~i~~ks~eeir~~f~i 137 (158)
-...+-|++....|.|..+|-+.||-
T Consensus 32 aR~iamyla~~~~~~sl~~Ig~~fg~ 57 (60)
T smart00760 32 ARQIAMYLARELTDLSLPEIGKIFGG 57 (60)
T ss_pred HHHHHHHHHHHHHCCCHHHHHHHhCC
Confidence 34455588888899999999999984
No 119
>KOG0027 consensus Calmodulin and related proteins (EF-Hand superfamily) [Signal transduction mechanisms]
Probab=22.74 E-value=2.1e+02 Score=19.89 Aligned_cols=48 Identities=21% Similarity=0.358 Sum_probs=23.1
Q ss_pred ccCchhHHHHHHHHHHHHhcC-CCHHHHHhHcCCCC---C--CCHHHHHHHHHh
Q 031498 105 YLNIKGLLDLTCQTVADMIKG-KTPEEIRKTFNIKN---D--FSPDEEEEVRRE 152 (158)
Q Consensus 105 ~L~i~~L~~~~~~~ia~~i~~-ks~eeir~~f~i~~---d--~t~eee~~i~~e 152 (158)
.++...++.++.......-.. .+.+++++.|.+-+ + +|.+|...+...
T Consensus 60 ~I~~~eF~~l~~~~~~~~~~~~~~~~el~eaF~~fD~d~~G~Is~~el~~~l~~ 113 (151)
T KOG0027|consen 60 TIDFEEFLDLMEKLGEEKTDEEASSEELKEAFRVFDKDGDGFISASELKKVLTS 113 (151)
T ss_pred eEcHHHHHHHHHhhhcccccccccHHHHHHHHHHHccCCCCcCcHHHHHHHHHH
Confidence 355555555555544332222 24555655444332 2 556666555543
No 120
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=22.74 E-value=57 Score=18.35 Aligned_cols=18 Identities=22% Similarity=0.366 Sum_probs=11.7
Q ss_pred HHhcCCCHHHHHhHcCCC
Q 031498 121 DMIKGKTPEEIRKTFNIK 138 (158)
Q Consensus 121 ~~i~~ks~eeir~~f~i~ 138 (158)
..+.|+|..||.+.+|++
T Consensus 22 ~~~~g~s~~eIa~~l~~s 39 (54)
T PF08281_consen 22 RYFQGMSYAEIAEILGIS 39 (54)
T ss_dssp HHTS---HHHHHHHCTS-
T ss_pred HHHHCcCHHHHHHHHCcC
Confidence 345799999999999986
No 121
>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=22.67 E-value=69 Score=22.04 Aligned_cols=21 Identities=19% Similarity=0.419 Sum_probs=17.9
Q ss_pred ccCChHHHHHHHHhhhccCch
Q 031498 89 VKVDQNTLFDLILAANYLNIK 109 (158)
Q Consensus 89 l~~~~~~l~~Ll~AA~~L~i~ 109 (158)
++++.+.|+.++.||..||.-
T Consensus 7 l~~eiDdL~p~~eAaelLgf~ 27 (120)
T PF09821_consen 7 LHLEIDDLLPIVEAAELLGFA 27 (120)
T ss_pred hCCcHHHHHHHHHHHHHcCCe
Confidence 357889999999999999875
No 122
>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=22.50 E-value=69 Score=22.46 Aligned_cols=32 Identities=22% Similarity=0.349 Sum_probs=21.5
Q ss_pred HHHHhhhccCchhHHHHHHHHHHHHhcCCCHHHHHhHcCCCC
Q 031498 98 DLILAANYLNIKGLLDLTCQTVADMIKGKTPEEIRKTFNIKN 139 (158)
Q Consensus 98 ~Ll~AA~~L~i~~L~~~~~~~ia~~i~~ks~eeir~~f~i~~ 139 (158)
.++.||.-||+-.. ++.|...+.+++.||++.
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 35666666664433 334567889999999986
No 123
>PF03026 CM1: Influenza C virus M1 protein; InterPro: IPR004271 This family represents the matrix protein, M1, of Influenza C virus. The M1 protein is the product of a spliced mRNA. Small quantities of the unspliced mRNA are found in the cell additionally encoding the M2 protein (see IPR004267 from INTERPRO).; GO: 0019028 viral capsid
Probab=22.46 E-value=1.3e+02 Score=21.93 Aligned_cols=47 Identities=13% Similarity=0.398 Sum_probs=31.0
Q ss_pred hHHHHHHHHhhhccCchhHHHHHHHHHHHHhcCCCHHHHHhHcCCCCCCCHH
Q 031498 93 QNTLFDLILAANYLNIKGLLDLTCQTVADMIKGKTPEEIRKTFNIKNDFSPD 144 (158)
Q Consensus 93 ~~~l~~Ll~AA~~L~i~~L~~~~~~~ia~~i~~ks~eeir~~f~i~~d~t~e 144 (158)
.+.--++-.|.+||++++++.+-+..= +.-.+-+.+.+.-++|+||+
T Consensus 92 rdirkqmkaagdflgvesmmkmrafrd-----dqimemveevydhpddytpd 138 (235)
T PF03026_consen 92 RDIRKQMKAAGDFLGVESMMKMRAFRD-----DQIMEMVEEVYDHPDDYTPD 138 (235)
T ss_pred hhHHHHHHhhcchhhHHHHHHHHhhhh-----HHHHHHHHHHhcCCccCCCC
Confidence 345567788899999999887654211 11123345578888889886
No 124
>PRK13379 protocatechuate 4,5-dioxygenase subunit alpha; Provisional
Probab=22.18 E-value=1.8e+02 Score=20.17 Aligned_cols=24 Identities=25% Similarity=0.335 Sum_probs=19.6
Q ss_pred HHHHHHHhcCCCHHHHHhHcCCCC
Q 031498 116 CQTVADMIKGKTPEEIRKTFNIKN 139 (158)
Q Consensus 116 ~~~ia~~i~~ks~eeir~~f~i~~ 139 (158)
-+.|...++|+|.||.++.=+.++
T Consensus 94 ~q~i~a~mtG~t~eeF~~tr~~~~ 117 (119)
T PRK13379 94 NLQVYAIMRGETFEEFMQTRRVPD 117 (119)
T ss_pred HHHHHHHhcCCcHHHHHHHccCCC
Confidence 467888889999999998877653
No 125
>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=22.02 E-value=99 Score=20.55 Aligned_cols=61 Identities=18% Similarity=0.225 Sum_probs=30.1
Q ss_pred CCCcEEEEcCCCCeEEecHHHHHHhHHHHHHHHhCC---CCC---ce------ec-CCCCHHHHHHHHHHHHHhc
Q 031498 3 SEKKITLKSSDGETFEVEETVALESQTIKHMVEDDC---ADT---VI------PL-PNVTSTILSKVIEYCKKHV 64 (158)
Q Consensus 3 ~~~~i~l~s~DG~~f~v~~~~a~~S~~l~~~l~~~~---~~~---~I------pl-~~i~~~~L~~Ii~~~~~~~ 64 (158)
.+..++++|+||..+.|...--. ...+...++-.| .+. .| ++ .+++-+...+++++++.++
T Consensus 33 ~g~~~~l~~~d~~~V~v~l~~~~-~~~~~~~vEviG~V~~~~~~~~i~~~~~~~~g~~~D~~~y~~lv~l~~~~p 106 (109)
T PF08661_consen 33 DGGSATLSTSDGGQVTVSLNPPS-DEELSKYVEVIGKVNDDGTVLSIRYFSFTDFGDDFDMDLYNELVQLTHKFP 106 (109)
T ss_dssp TSSEEEEE-TTS-EEEEEESS---SS---SEEEEEEEE-TTS-EEEEEEEE---SSS---HHHHHHHHHHHHHSG
T ss_pred CCCEEEEEcCCCCEEEEEeCCCC-CCCCCCEEEEEEEEcCCCCceEEEEEEeccCCCCcCHHHHHHHHHHHhhCC
Confidence 36789999999998887544210 001222222111 111 11 33 3688888888888887654
No 126
>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=22.00 E-value=89 Score=19.35 Aligned_cols=22 Identities=18% Similarity=0.318 Sum_probs=18.3
Q ss_pred CCcEEEEcCCCCeEEecHHHHH
Q 031498 4 EKKITLKSSDGETFEVEETVAL 25 (158)
Q Consensus 4 ~~~i~l~s~DG~~f~v~~~~a~ 25 (158)
.+.|.++|.||..+.++....+
T Consensus 20 a~~V~v~s~~Gr~v~~Pa~~lR 41 (68)
T PF11197_consen 20 ASKVVVRSDDGRRVQFPARHLR 41 (68)
T ss_pred ccEEEEEecCCcEEEEeHHHCc
Confidence 3578999999999999987643
No 127
>PF11094 UL11: Membrane-associated tegument protein; InterPro: IPR024351 The UL11 gene product of herpes simplex virus is a membrane-associated tegument protein that is incorporated into the HSV virion and functions in viral envelopment []. UL11 is acylated, which is crucial for lipid raft association [].
Probab=21.92 E-value=1e+02 Score=16.96 Aligned_cols=19 Identities=21% Similarity=0.391 Sum_probs=15.5
Q ss_pred CcEEEEcCCCCeEEecHHH
Q 031498 5 KKITLKSSDGETFEVEETV 23 (158)
Q Consensus 5 ~~i~l~s~DG~~f~v~~~~ 23 (158)
+.-.|.|.+|+++.++.+.
T Consensus 14 R~N~LvT~~Ge~vsL~a~~ 32 (39)
T PF11094_consen 14 RRNVLVTHSGETVSLDAEE 32 (39)
T ss_pred ecCEEEccCCeEEEeChhh
Confidence 4568999999999988764
No 128
>COG4680 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.88 E-value=64 Score=21.35 Aligned_cols=17 Identities=35% Similarity=0.499 Sum_probs=14.3
Q ss_pred CCCHHHHHhHcCCCCCC
Q 031498 125 GKTPEEIRKTFNIKNDF 141 (158)
Q Consensus 125 ~ks~eeir~~f~i~~d~ 141 (158)
=++|++|+.+|+..+++
T Consensus 35 w~~P~diK~~f~~d~~~ 51 (98)
T COG4680 35 WKKPEDIKSVFPLDNFK 51 (98)
T ss_pred cCCHHHHHHhcCcccce
Confidence 37899999999987763
No 129
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=21.81 E-value=81 Score=18.88 Aligned_cols=16 Identities=38% Similarity=0.540 Sum_probs=12.9
Q ss_pred CCcEEEEcCCCCeEEe
Q 031498 4 EKKITLKSSDGETFEV 19 (158)
Q Consensus 4 ~~~i~l~s~DG~~f~v 19 (158)
-+-+++.+.||++|.-
T Consensus 4 ~KA~Kv~~RDGE~~lr 19 (65)
T COG4049 4 LKAIKVRDRDGEEFLR 19 (65)
T ss_pred ceeeEeeccCCceeee
Confidence 3568999999998864
No 130
>PF14098 SSPI: Small, acid-soluble spore protein I
Probab=21.78 E-value=1.1e+02 Score=18.86 Aligned_cols=19 Identities=32% Similarity=0.604 Sum_probs=14.9
Q ss_pred HHHHHHhcCCCHHHHHhHc
Q 031498 117 QTVADMIKGKTPEEIRKTF 135 (158)
Q Consensus 117 ~~ia~~i~~ks~eeir~~f 135 (158)
+.|...+.|+|.+|++.+-
T Consensus 5 ~AI~~nv~g~s~~el~~~I 23 (65)
T PF14098_consen 5 QAIIHNVKGSSKEELKDTI 23 (65)
T ss_pred HHHHHHccCCCHHHHHHHH
Confidence 4566778999999998864
No 131
>PF11795 DUF3322: Uncharacterized protein conserved in bacteria N-term (DUF3322); InterPro: IPR024537 This domain, found in various hypothetical bacterial proteins, has no known function. The family represents just the N terminus.
Probab=21.65 E-value=73 Score=23.59 Aligned_cols=47 Identities=17% Similarity=0.219 Sum_probs=29.5
Q ss_pred CCHHHHHHHHHHHHHhcccCCCCCCCCCCCcchhchHHHhhccCChHHHHHHH
Q 031498 48 VTSTILSKVIEYCKKHVEAGSGDKKDDKSTEDDLKTWDADFVKVDQNTLFDLI 100 (158)
Q Consensus 48 i~~~~L~~Ii~~~~~~~~~~~~~~~~~~~~~~~~~~wd~~Fl~~~~~~l~~Ll 100 (158)
....-|-.|+.|+..|-..+.. .....++-+|.+|++-....|-+|+
T Consensus 142 ~d~~~l~~vl~wl~~h~~~g~y------lRqlpi~GvDTKfiE~h~~ll~~Ll 188 (190)
T PF11795_consen 142 DDFERLLAVLDWLRPHPRSGLY------LRQLPIPGVDTKFIERHRGLLAALL 188 (190)
T ss_pred hhHHHHHHHHHHHhcCCCCCCc------hhhCCcCCcchHHHHHHHHHHHHHh
Confidence 3346788899999888554332 3455567778888874344444443
No 132
>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=21.57 E-value=44 Score=23.53 Aligned_cols=17 Identities=41% Similarity=0.829 Sum_probs=12.4
Q ss_pred CCCHHHHHhHcCCCCCC
Q 031498 125 GKTPEEIRKTFNIKNDF 141 (158)
Q Consensus 125 ~ks~eeir~~f~i~~d~ 141 (158)
|.|++|=|+.||++.|+
T Consensus 94 gltp~eYR~kwGlp~dy 110 (132)
T PF05443_consen 94 GLTPEEYRAKWGLPKDY 110 (132)
T ss_dssp -S-HHHHHHHTT-GGG-
T ss_pred CCCHHHHHHHhCcCCCC
Confidence 89999999999999874
No 133
>TIGR01044 rplV_bact ribosomal protein L22, bacterial type. This model decribes bacterial and chloroplast ribosomal protein L22.
Probab=21.20 E-value=1.1e+02 Score=20.37 Aligned_cols=22 Identities=27% Similarity=0.490 Sum_probs=17.6
Q ss_pred HHHHHHHhcCCCHHHHHhHcCC
Q 031498 116 CQTVADMIKGKTPEEIRKTFNI 137 (158)
Q Consensus 116 ~~~ia~~i~~ks~eeir~~f~i 137 (158)
+..+++.|+|+++++-..++..
T Consensus 13 ~~~va~~IrG~~v~~A~~~L~f 34 (103)
T TIGR01044 13 ARLVADLIRGKSVSQALDILRF 34 (103)
T ss_pred HHHHHHHHcCCcHHHHHHHHhh
Confidence 3568899999999988877764
No 134
>KOG4244 consensus Failed axon connections (fax) protein/glutathione S-transferase-like protein [Signal transduction mechanisms]
Probab=21.19 E-value=1.2e+02 Score=24.15 Aligned_cols=22 Identities=27% Similarity=0.623 Sum_probs=18.0
Q ss_pred HHHHHhHcCCCCCCCHHHHHHH
Q 031498 128 PEEIRKTFNIKNDFSPDEEEEV 149 (158)
Q Consensus 128 ~eeir~~f~i~~d~t~eee~~i 149 (158)
...+|+.|++++++++||+..-
T Consensus 111 ~~~L~~hf~~~~~L~~e~~a~s 132 (281)
T KOG4244|consen 111 EDRLRKHFKIPDDLSAEQRAQS 132 (281)
T ss_pred HHHHHHHcCCCCCCCHHHHHHH
Confidence 4567899999999999998754
No 135
>PF14407 Frankia_peptide: Ribosomally synthesized peptide prototyped by Frankia Franean1_4349.
Probab=21.12 E-value=84 Score=19.07 Aligned_cols=14 Identities=29% Similarity=0.565 Sum_probs=10.9
Q ss_pred CCCCHHHHHHHHHh
Q 031498 139 NDFSPDEEEEVRRE 152 (158)
Q Consensus 139 ~d~t~eee~~i~~e 152 (158)
-++||||.+.+++.
T Consensus 30 Y~Lt~eeL~al~~~ 43 (61)
T PF14407_consen 30 YDLTPEELQALERL 43 (61)
T ss_pred CCCCHHHHHHHHHH
Confidence 46899999988753
No 136
>PF06514 PsbU: Photosystem II 12 kDa extrinsic protein (PsbU); InterPro: IPR010527 Oxygenic photosynthesis uses two multi-subunit photosystems (I and II) located in the cell membranes of cyanobacteria and in the thylakoid membranes of chloroplasts in plants and algae. Photosystem II (PSII) has a P680 reaction centre containing chlorophyll 'a' that uses light energy to carry out the oxidation (splitting) of water molecules, and to produce ATP via a proton pump. Photosystem I (PSI) has a P700 reaction centre containing chlorophyll that takes the electron and associated hydrogen donated from PSII to reduce NADP+ to NADPH. Both ATP and NADPH are subsequently used in the light-independent reactions to convert carbon dioxide to glucose using the hydrogen atom extracted from water by PSII, releasing oxygen as a by-product. PSII is a multisubunit protein-pigment complex containing polypeptides both intrinsic and extrinsic to the photosynthetic membrane [, ]. Within the core of the complex, the chlorophyll and beta-carotene pigments are mainly bound to the antenna proteins CP43 (PsbC) and CP47 (PsbB), which pass the excitation energy on to the reaction centre proteins D1 (Qb, PsbA) and D2 (Qa, PsbD) that bind all the redox-active cofactors involved in the energy conversion process. The PSII oxygen-evolving complex (OEC) oxidises water to provide protons for use by PSI, and consists of OEE1 (PsbO), OEE2 (PsbP) and OEE3 (PsbQ). The remaining subunits in PSII are of low molecular weight (less than 10 kDa), and are involved in PSII assembly, stabilisation, dimerisation, and photo-protection []. In PSII, the oxygen-evolving complex (OEC) is responsible for catalysing the splitting of water to O(2) and 4H+. The OEC is composed of a cluster of manganese, calcium and chloride ions bound to extrinsic proteins. In cyanobacteria there are five extrinsic proteins in OEC (PsbO, PsbP-like, PsbQ-like, PsbU and PsbV), while in plants there are only three (PsbO, PsbP and PsbQ), PsbU and PsbV having been lost during the evolution of green plants []. This family represents the PSII extrinsic protein PsbU, which forms part of the OEC in cyanobacteria and red algae. PsbU acts to stabilise the oxygen-evolving machinery of PSII against heat-induced inactivation, which is crucial for cellular thermo-tolerance [].; GO: 0015979 photosynthesis, 0042549 photosystem II stabilization, 0009523 photosystem II, 0009654 oxygen evolving complex, 0019898 extrinsic to membrane; PDB: 3BZ1_U 3KZI_U 3PRQ_U 2AXT_u 3BZ2_U 4FBY_U 3PRR_U 1S5L_U 3A0H_U 3ARC_U ....
Probab=20.85 E-value=37 Score=22.44 Aligned_cols=46 Identities=13% Similarity=0.272 Sum_probs=28.5
Q ss_pred hhhccCchhHHHHHHHHHHHHhcCCCHHHHHhHcCCCCCCCHHHHHHHHH
Q 031498 102 AANYLNIKGLLDLTCQTVADMIKGKTPEEIRKTFNIKNDFSPDEEEEVRR 151 (158)
Q Consensus 102 AA~~L~i~~L~~~~~~~ia~~i~~ks~eeir~~f~i~~d~t~eee~~i~~ 151 (158)
...|-+.+++.--.+..|+..---+|++++ +.|+ +||+.|++.+++
T Consensus 22 vr~f~~~pGmYPtlA~kIv~naPY~sveDv---l~ip-gLse~qK~~lk~ 67 (93)
T PF06514_consen 22 VRAFRQFPGMYPTLAGKIVSNAPYKSVEDV---LNIP-GLSERQKALLKK 67 (93)
T ss_dssp GGGGCCSTTTTCCHHHHHHHS---SSGGGG---CCST-T--HHHHHHHHH
T ss_pred HHHHHHCCCCCHHHHHHHHhCCCCCCHHHH---Hhcc-CCCHHHHHHHHH
Confidence 456777788877777777665445777776 4454 368888777766
No 137
>PRK10945 gene expression modulator; Provisional
Probab=20.60 E-value=2e+02 Score=18.09 Aligned_cols=15 Identities=20% Similarity=0.182 Sum_probs=10.5
Q ss_pred CChHHHHHHHHhhhc
Q 031498 91 VDQNTLFDLILAANY 105 (158)
Q Consensus 91 ~~~~~l~~Ll~AA~~ 105 (158)
++.+.+..+..||++
T Consensus 35 L~~~E~~~f~~AaDH 49 (72)
T PRK10945 35 LSDDELAVFYSAADH 49 (72)
T ss_pred CCHHHHHHHHHHHHH
Confidence 556677777777774
No 138
>PF04312 DUF460: Protein of unknown function (DUF460); InterPro: IPR007408 This is an archaeal protein of unknown function.
Probab=20.55 E-value=1.4e+02 Score=21.26 Aligned_cols=28 Identities=32% Similarity=0.499 Sum_probs=20.0
Q ss_pred HHHHHhHcC-----CCCCCCHHHHHHHHHhccc
Q 031498 128 PEEIRKTFN-----IKNDFSPDEEEEVRRENQW 155 (158)
Q Consensus 128 ~eeir~~f~-----i~~d~t~eee~~i~~e~~w 155 (158)
++-|+..|| -..|++-||+.++-+++.|
T Consensus 92 V~Kia~~f~A~ly~P~~dlsveeK~~l~~~~~~ 124 (138)
T PF04312_consen 92 VKKIARSFNAVLYTPERDLSVEEKQELAREYSE 124 (138)
T ss_pred HHHHHHHhCCcccCCCCcCCHHHHHHHHHhhCC
Confidence 455555555 3357999999999998876
No 139
>COG4754 Uncharacterized conserved protein [Function unknown]
Probab=20.50 E-value=3.4e+02 Score=19.62 Aligned_cols=56 Identities=20% Similarity=0.315 Sum_probs=38.5
Q ss_pred eecCCCCHHHHHHHHHHHHHhcccCCCCCCCCCCCcchhchHHHhhccCChHHHHHHHHhhhccCchh
Q 031498 43 IPLPNVTSTILSKVIEYCKKHVEAGSGDKKDDKSTEDDLKTWDADFVKVDQNTLFDLILAANYLNIKG 110 (158)
Q Consensus 43 Ipl~~i~~~~L~~Ii~~~~~~~~~~~~~~~~~~~~~~~~~~wd~~Fl~~~~~~l~~Ll~AA~~L~i~~ 110 (158)
+.+|++...-|.-++.=+..-.+.. ..++...++ ++++.+.|+.+..||+.|+.-.
T Consensus 4 ~~~P~a~i~~l~GLL~~l~n~fnGr-----------aDl~~L~~e-~~vdidDL~piv~ta~~Lglv~ 59 (157)
T COG4754 4 MRLPNARIAQLVGLLYVLNNIFNGR-----------ADLPYLEKE-MEVDIDDLMPIVETASLLGLVT 59 (157)
T ss_pred eeCCCccHHHHHHHHHHHHHHhCCc-----------ccchhHHHH-hCCChhhHHHHHHHHHhcCcee
Confidence 5578888888888887777642211 123333333 4688899999999999998754
No 140
>PF10850 DUF2653: Protein of unknown function (DUF2653); InterPro: IPR020516 This entry contains proteins with no known function.
Probab=20.50 E-value=24 Score=23.23 Aligned_cols=34 Identities=24% Similarity=0.544 Sum_probs=24.3
Q ss_pred cCchhHHHHHHHHHHHHhcCCCHHHHHhHcCCCCC
Q 031498 106 LNIKGLLDLTCQTVADMIKGKTPEEIRKTFNIKND 140 (158)
Q Consensus 106 L~i~~L~~~~~~~ia~~i~~ks~eeir~~f~i~~d 140 (158)
|+-+.+++..|.++|.. +|-.|+++---+.-.+|
T Consensus 5 l~EqeIiNAvCl~~A~~-~~i~P~dVeVeL~yDdd 38 (91)
T PF10850_consen 5 LSEQEIINAVCLHIAER-KGIQPEDVEVELMYDDD 38 (91)
T ss_pred ccHHHHHHHHHHHHHHh-cCCCcccEEEEEEEecC
Confidence 66778899999999987 67777776544433333
No 141
>PF02084 Bindin: Bindin; InterPro: IPR000775 Bindin, the major protein component of the acrosome granule of sea urchin sperm, mediates species-specific adhesion of sperm to the egg surface during fertilisation [, ]. The protein coats the acrosomal process after externalisation by the acrosome reaction; it binds to sulphated, fucose-containing polysaccharides on the vitelline-layer receptor proteoglycans that cover the egg plasma membrane. Bindins from different genera show high levels of sequence similarity in both the mature bindin domain and in the probindin precursor region. The most highly conserved region is a 42-residue segment in the central portion of the mature bindin protein. This domain may be responsible for conserved functions of bindin, while the more highly divergent flanking regions may be responsible for its species-specific properties [].; GO: 0007342 fusion of sperm to egg plasma membrane
Probab=20.31 E-value=1.8e+02 Score=22.55 Aligned_cols=46 Identities=24% Similarity=0.332 Sum_probs=29.5
Q ss_pred CCCeEEecHHHHHHhHHHHHHHHhCCCCCceecC-CC-CHHHHHHHHHHHHHhcc
Q 031498 13 DGETFEVEETVALESQTIKHMVEDDCADTVIPLP-NV-TSTILSKVIEYCKKHVE 65 (158)
Q Consensus 13 DG~~f~v~~~~a~~S~~l~~~l~~~~~~~~Ipl~-~i-~~~~L~~Ii~~~~~~~~ 65 (158)
|+..=+|+.++.. -|+..|- ...|-|| +| +.--|-++++.++||..
T Consensus 95 ~EEetTISAKvm~---~ikavLg----aTKiDLPVDINDPYDlGLLLRhLRHHSN 142 (238)
T PF02084_consen 95 DEEETTISAKVME---DIKAVLG----ATKIDLPVDINDPYDLGLLLRHLRHHSN 142 (238)
T ss_pred cCCCccccHHHHH---HHHHHhc----ccccccccccCChhhHHHHHHHHHHHHH
Confidence 5556666666554 4555553 2335444 55 56679999999999964
No 142
>PF12674 Zn_ribbon_2: Putative zinc ribbon domain
Probab=20.15 E-value=1.6e+02 Score=18.75 Aligned_cols=28 Identities=25% Similarity=0.510 Sum_probs=18.7
Q ss_pred chhHHHHHHHHHHHHhcCCCHHHHHhHcC
Q 031498 108 IKGLLDLTCQTVADMIKGKTPEEIRKTFN 136 (158)
Q Consensus 108 i~~L~~~~~~~ia~~i~~ks~eeir~~f~ 136 (158)
++.+++.|...++..- +.+++++|+++.
T Consensus 44 ~eemie~~~~~~~~~~-~~~~~~a~~~~~ 71 (81)
T PF12674_consen 44 MEEMIEFCVPFMDEFN-GMTPEEARKMMP 71 (81)
T ss_pred HHHHHHHHHHHHHHhC-CCCHHHHHHHHH
Confidence 3455667777776653 378888887663
Done!