Query 030912
Match_columns 169
No_of_seqs 113 out of 583
Neff 7.2
Searched_HMMs 46136
Date Fri Mar 29 06:27:44 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030912.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030912hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2659 LisH motif-containing 100.0 3.8E-35 8.1E-40 234.1 15.3 152 2-153 56-211 (228)
2 PF10607 CLTH: CTLH/CRA C-term 100.0 3.1E-34 6.8E-39 215.5 14.0 138 10-149 1-144 (145)
3 KOG0396 Uncharacterized conser 99.9 8.7E-22 1.9E-26 165.5 13.1 134 6-141 148-285 (389)
4 smart00757 CRA CT11-RanBPM. pr 99.8 4.9E-19 1.1E-23 124.6 10.7 91 64-154 2-98 (99)
5 KOG2817 Predicted E3 ubiquitin 99.7 9.2E-17 2E-21 136.5 12.2 137 9-147 154-308 (394)
6 smart00668 CTLH C-terminal to 99.5 4.8E-14 1E-18 90.0 5.4 56 11-66 2-57 (58)
7 KOG1477 SPRY domain-containing 99.0 2E-10 4.3E-15 101.5 1.5 154 14-168 308-468 (469)
8 KOG0293 WD40 repeat-containing 96.5 0.03 6.5E-07 49.1 9.9 129 14-147 53-187 (519)
9 PF14559 TPR_19: Tetratricopep 85.7 3.8 8.2E-05 25.5 5.7 59 20-83 1-59 (68)
10 COG3071 HemY Uncharacterized e 80.6 21 0.00046 31.4 9.8 95 15-133 268-362 (400)
11 PF04494 TFIID_90kDa: WD40 ass 73.4 6.3 0.00014 29.3 4.2 48 45-94 38-85 (142)
12 KOG2910 Uncharacterized conser 68.2 19 0.00041 28.7 5.8 53 12-64 41-106 (209)
13 PF13838 Clathrin_H_link: Clat 66.8 9.7 0.00021 25.0 3.4 41 50-90 7-47 (66)
14 cd08044 TAF5_NTD2 TAF5_NTD2 is 66.2 2.4 5.1E-05 31.3 0.5 52 46-99 28-79 (133)
15 PF04157 EAP30: EAP30/Vps36 fa 64.3 51 0.0011 26.3 7.9 80 65-144 39-125 (223)
16 COG5516 Conserved protein cont 61.2 27 0.00059 27.4 5.5 58 111-168 41-99 (196)
17 KOG0396 Uncharacterized conser 60.3 30 0.00066 30.2 6.2 86 12-100 118-206 (389)
18 PF10607 CLTH: CTLH/CRA C-term 58.3 36 0.00079 24.7 5.7 30 8-37 38-67 (145)
19 PF04121 Nup84_Nup100: Nuclear 55.8 17 0.00036 34.1 4.2 29 8-36 131-159 (697)
20 PF10827 DUF2552: Protein of u 55.1 8.2 0.00018 25.8 1.5 17 25-41 60-76 (79)
21 PF14973 TINF2_N: TERF1-intera 49.6 54 0.0012 24.8 5.4 76 16-95 46-129 (145)
22 PF01158 Ribosomal_L36e: Ribos 49.3 37 0.0008 24.1 4.1 46 49-97 48-93 (98)
23 PTZ00196 60S ribosomal protein 48.3 40 0.00088 23.9 4.2 32 49-80 48-79 (98)
24 KOG2235 Uncharacterized conser 48.1 42 0.0009 31.5 5.3 66 86-152 87-157 (776)
25 PRK04984 fatty acid metabolism 47.9 40 0.00087 26.6 4.8 27 10-36 189-215 (239)
26 PF07035 Mic1: Colon cancer-as 47.7 33 0.00072 26.5 4.1 62 14-75 49-115 (167)
27 PF12854 PPR_1: PPR repeat 47.2 30 0.00066 19.0 2.9 25 11-35 8-32 (34)
28 PF12895 Apc3: Anaphase-promot 46.9 19 0.0004 23.5 2.3 50 17-72 32-81 (84)
29 PF07721 TPR_4: Tetratricopept 44.3 29 0.00062 17.8 2.3 17 18-34 9-25 (26)
30 PF12931 Sec16_C: Sec23-bindin 43.2 25 0.00055 29.1 3.0 21 16-36 1-21 (284)
31 PRK10421 DNA-binding transcrip 43.0 59 0.0013 26.0 5.1 31 9-39 189-219 (253)
32 PRK10225 DNA-binding transcrip 42.4 43 0.00093 26.9 4.2 23 54-76 202-224 (257)
33 PF14691 Fer4_20: Dihydroprymi 42.2 33 0.0007 24.6 3.1 27 49-75 38-64 (111)
34 KOG1156 N-terminal acetyltrans 41.5 3.2E+02 0.0068 26.0 13.5 129 8-141 183-332 (700)
35 COG0268 RpsT Ribosomal protein 40.4 48 0.001 23.0 3.5 29 15-43 33-61 (88)
36 TIGR02812 fadR_gamma fatty aci 40.2 62 0.0013 25.5 4.8 24 54-77 193-216 (235)
37 PF12793 SgrR_N: Sugar transpo 40.2 50 0.0011 23.8 3.8 25 14-39 74-98 (115)
38 COG5109 Uncharacterized conser 40.1 65 0.0014 27.8 4.9 88 8-99 136-225 (396)
39 TIGR00083 ribF riboflavin kina 39.4 30 0.00065 29.0 2.9 25 14-38 146-170 (288)
40 PF14689 SPOB_a: Sensor_kinase 39.4 88 0.0019 19.8 4.5 32 11-42 24-55 (62)
41 PF14691 Fer4_20: Dihydroprymi 39.3 43 0.00093 24.0 3.3 24 15-38 43-66 (111)
42 PRK07143 hypothetical protein; 37.9 22 0.00048 29.7 1.9 24 14-37 152-175 (279)
43 PF03398 Ist1: Regulator of Vp 37.6 1.8E+02 0.004 22.1 6.8 27 10-36 22-48 (165)
44 PRK11523 DNA-binding transcrip 36.6 76 0.0016 25.4 4.8 28 10-37 191-218 (253)
45 PF15391 DUF4614: Domain of un 36.3 44 0.00095 26.3 3.2 50 27-76 113-179 (181)
46 PRK09464 pdhR transcriptional 36.1 81 0.0017 25.2 4.9 29 10-38 197-226 (254)
47 PF00627 UBA: UBA/TS-N domain; 35.8 29 0.00064 19.4 1.6 19 15-33 17-37 (37)
48 COG5443 FlbT Flagellar biosynt 35.8 63 0.0014 24.2 3.7 32 7-38 91-122 (148)
49 TIGR01470 cysG_Nterm siroheme 34.7 76 0.0016 25.0 4.4 64 12-76 135-204 (205)
50 PRK09990 DNA-binding transcrip 34.5 77 0.0017 25.2 4.5 23 54-76 203-225 (251)
51 TIGR00756 PPR pentatricopeptid 31.4 78 0.0017 16.0 2.9 22 15-36 5-26 (35)
52 PRK05627 bifunctional riboflav 31.3 38 0.00081 28.6 2.2 25 14-38 163-187 (305)
53 PRK00239 rpsT 30S ribosomal pr 31.3 82 0.0018 21.7 3.6 28 15-42 33-60 (88)
54 PF13432 TPR_16: Tetratricopep 30.6 1.3E+02 0.0027 18.1 5.1 56 17-77 4-59 (65)
55 PRK00794 flbT flagellar biosyn 30.0 1.1E+02 0.0024 22.7 4.3 30 9-38 92-121 (132)
56 PF07378 FlbT: Flagellar prote 29.5 1.2E+02 0.0025 22.4 4.3 32 7-38 88-119 (126)
57 PF12862 Apc5: Anaphase-promot 28.7 1.9E+02 0.004 19.5 5.8 28 18-45 6-33 (94)
58 KOG3452 60S ribosomal protein 28.3 1.1E+02 0.0024 21.7 3.8 45 49-96 50-94 (102)
59 PF07208 DUF1414: Protein of u 28.1 79 0.0017 19.1 2.6 18 110-127 24-41 (44)
60 PF13934 ELYS: Nuclear pore co 28.0 1.1E+02 0.0024 24.5 4.4 107 20-140 88-197 (226)
61 PF13934 ELYS: Nuclear pore co 27.5 3.2E+02 0.007 21.8 7.4 55 16-77 114-168 (226)
62 PF12169 DNA_pol3_gamma3: DNA 27.0 1.1E+02 0.0024 21.9 4.0 22 15-36 19-40 (143)
63 COG5051 RPL36A Ribosomal prote 27.0 1.7E+02 0.0037 20.3 4.4 44 50-96 51-94 (97)
64 KOG0989 Replication factor C, 26.3 2.5E+02 0.0055 24.3 6.3 73 20-93 218-299 (346)
65 KOG2659 LisH motif-containing 26.2 2.3E+02 0.0049 23.2 5.8 73 6-81 24-96 (228)
66 PF01649 Ribosomal_S20p: Ribos 26.1 1.1E+02 0.0025 20.7 3.5 28 15-42 32-59 (84)
67 PF14498 Glyco_hyd_65N_2: Glyc 25.4 46 0.001 26.6 1.7 33 5-37 49-81 (236)
68 PRK13754 conjugal transfer fer 25.0 1.2E+02 0.0027 23.8 3.9 26 20-45 67-92 (186)
69 cd00194 UBA Ubiquitin Associat 24.8 58 0.0013 18.0 1.6 21 14-34 15-37 (38)
70 PF01399 PCI: PCI domain; Int 24.8 2.1E+02 0.0046 18.8 6.2 46 14-62 3-48 (105)
71 KOG3850 Predicted membrane pro 24.4 90 0.002 27.6 3.3 47 6-59 331-377 (455)
72 KOG2817 Predicted E3 ubiquitin 24.1 3.4E+02 0.0073 24.0 6.8 86 15-101 122-210 (394)
73 KOG3239 Density-regulated prot 23.7 64 0.0014 25.3 2.1 21 23-43 28-48 (193)
74 TIGR00029 S20 ribosomal protei 23.4 1.4E+02 0.003 20.6 3.5 28 15-42 33-60 (87)
75 KOG3341 RNA polymerase II tran 23.4 4.2E+02 0.009 21.7 6.7 97 51-147 26-131 (249)
76 smart00165 UBA Ubiquitin assoc 23.4 63 0.0014 17.7 1.6 18 16-33 17-36 (37)
77 PF10475 DUF2450: Protein of u 23.2 1.1E+02 0.0024 25.3 3.7 29 12-40 129-157 (291)
78 PF13041 PPR_2: PPR repeat fam 23.0 1.2E+02 0.0025 17.6 2.8 22 15-36 8-29 (50)
79 PF06100 Strep_67kDa_ant: Stre 22.8 31 0.00067 31.3 0.2 54 10-63 123-192 (500)
80 TIGR03504 FimV_Cterm FimV C-te 22.4 1.2E+02 0.0027 17.9 2.8 19 18-36 7-25 (44)
81 PHA00780 hypothetical protein 22.2 1.7E+02 0.0036 19.9 3.6 56 12-76 12-73 (80)
82 PF09551 Spore_II_R: Stage II 22.0 2.2E+02 0.0048 21.1 4.6 37 7-43 19-60 (130)
83 TIGR01159 DRP1 density-regulat 22.0 80 0.0017 24.6 2.4 21 23-43 20-40 (173)
84 PF13812 PPR_3: Pentatricopept 21.1 1.4E+02 0.0029 15.2 2.9 21 15-35 6-26 (34)
85 PF06910 MEA1: Male enhanced a 21.1 1.8E+02 0.004 22.7 4.2 38 82-119 123-160 (174)
86 PF01535 PPR: PPR repeat; Int 21.0 1.2E+02 0.0027 15.0 2.4 20 16-35 6-25 (31)
87 PF13428 TPR_14: Tetratricopep 20.7 1.4E+02 0.003 16.9 2.8 17 19-35 10-26 (44)
88 TIGR03147 cyt_nit_nrfF cytochr 20.6 93 0.002 23.0 2.4 29 11-39 60-89 (126)
89 PF12569 NARP1: NMDA receptor- 20.5 4.2E+02 0.009 24.2 7.0 70 20-94 14-83 (517)
90 PRK12791 flbT flagellar biosyn 20.5 2E+02 0.0044 21.3 4.2 27 12-38 92-118 (131)
91 PF08283 Gemini_AL1_M: Geminiv 20.4 1.2E+02 0.0025 21.8 2.8 25 15-39 7-31 (106)
92 KOG2027 Spindle pole body prot 20.4 1.3E+02 0.0029 26.4 3.7 117 12-144 19-155 (388)
93 PF02607 B12-binding_2: B12 bi 20.3 1E+02 0.0022 19.7 2.4 23 14-36 5-27 (79)
94 KOG2051 Nonsense-mediated mRNA 20.1 9.1E+02 0.02 24.4 9.3 80 45-124 517-601 (1128)
95 TIGR03362 VI_chp_7 type VI sec 20.0 1.8E+02 0.0039 24.6 4.3 62 10-73 213-274 (301)
No 1
>KOG2659 consensus LisH motif-containing protein [Cytoskeleton]
Probab=100.00 E-value=3.8e-35 Score=234.08 Aligned_cols=152 Identities=38% Similarity=0.529 Sum_probs=145.4
Q ss_pred CCchhhHHhHHHHHHHHHHHHcCCHHHHHHHHHHhchHHHccCCcceehhchHHHHHHHhhhchHHHHHHHHhhcCCcCC
Q 030912 2 KQPANCLEDMEMRKRILHFALEGNALKAIELTEELAQDLLEKNKDLHFDLLSLHFVELVCSRKCTEALEFAQTKLTPFGK 81 (169)
Q Consensus 2 ~~p~~~~~~~~~R~~I~~~I~~G~i~~Ai~~i~~~~p~ll~~~~~L~F~L~~q~fIElir~~~~~eAi~~ar~~l~~~~~ 81 (169)
+.|..|+++++.|.+|+++|.+|+|+.||+.+++++|++|++|.+|.|+|++|+||||||.|..++||+|||+++++++.
T Consensus 56 ~~~~~d~~~~~eR~~Ir~~I~~G~Ie~Aie~in~l~PeiLd~n~~l~F~Lq~q~lIEliR~~~~eeal~F~q~~LA~~a~ 135 (228)
T KOG2659|consen 56 KPPSIDLDSMDERLQIRRAIEEGQIEEAIEKVNQLNPEILDTNRELFFHLQQLHLIELIREGKTEEALEFAQTKLAPFAE 135 (228)
T ss_pred CCccCchhhHhHHHHHHHHHHhccHHHHHHHHHHhChHHHccchhHHHHHHHHHHHHHHHhhhHHHHHHHHHHHcccccc
Confidence 45789999999999999999999999999999999999999999999999999999999999999999999999999997
Q ss_pred -chhhHHHHHHHHHHhccCCCCCCchhhhCCHHHHHHHHHHHHHHHhc---CCCchHHHHHHHHHHHHHHHHHHhc
Q 030912 82 -VQKYVEKLEDFMALLAYEEPEKSPMFHLLSLEYRQHVADNLNRAILE---RPRYAAMERLIQQTTAVRQCLSQEL 153 (169)
Q Consensus 82 -~~~~~~el~~~~~LLay~~p~~sp~~~Ll~~~rr~~lA~~vn~aIL~---~~~~s~Le~l~k~~~~~~~~l~~~~ 153 (169)
++.++.+++++|++|+|++|..||++++++.++|+++|+.||+|||. .+..+.|..+++...|.+..+..+.
T Consensus 136 e~~~~~~elE~~l~lLvf~~~~~sp~~~l~~~s~R~kvA~~vN~aiL~~~~~~~~~~l~~llk~~~~~~~~~~~~~ 211 (228)
T KOG2659|consen 136 ENPKKMEELERTLALLVFELSQESPSAELLSQSLRQKVASEVNSAILASQEHESEPKLPFLLKLISWAQEELDREK 211 (228)
T ss_pred ccHHHHHHHHHHHHHHHcCCcccCcHHHHHHHHHHHHHHHHHHHHHHHHhcccccchHHHHHHHHHHHHHHHhHhh
Confidence 77899999999999999999999999999999999999999999999 5578999999999999998887654
No 2
>PF10607 CLTH: CTLH/CRA C-terminal to LisH motif domain; InterPro: IPR019589 This entry represents the CRA (or CT11-RanBPM) domain, which is a protein-protein interaction domain present in crown eukaryotes (plants, animals, fungi) and which is found in Ran-binding proteins such as Ran-binding protein 9 (RanBP9 or RanBPM) and RanBP10. RanBPM is a scaffolding protein important in regulating cellular function in both the immune system and the nervous system, and may act as an adapter protein to couple membrane receptors to intracellular signaling pathways. This domain is at the C terminus of the proteins and is the binding domain for the CRA motif, which is comprised of approximately 100 amino acids at the C-terminal of RanBPM. It was found to be important for the interaction of RanBPM with fragile X mental retardation protein (FMRP), but its functional significance has yet to be determined [].
Probab=100.00 E-value=3.1e-34 Score=215.51 Aligned_cols=138 Identities=36% Similarity=0.598 Sum_probs=130.2
Q ss_pred hHHHHHHHHHHHHcCCHHHHHHHHHHhchHHHccCCcceehhchHHHHHHHhhhchHHHHHHHHhhcCCcCCchhhHHHH
Q 030912 10 DMEMRKRILHFALEGNALKAIELTEELAQDLLEKNKDLHFDLLSLHFVELVCSRKCTEALEFAQTKLTPFGKVQKYVEKL 89 (169)
Q Consensus 10 ~~~~R~~I~~~I~~G~i~~Ai~~i~~~~p~ll~~~~~L~F~L~~q~fIElir~~~~~eAi~~ar~~l~~~~~~~~~~~el 89 (169)
++..|+.|+++|++||+++|++||++++|.+++.++.|+|.|++|+|||||++|++.+||+|||+++.++. ..+.+++
T Consensus 1 ~~~~r~~I~~~I~~g~i~~Ai~w~~~~~~~l~~~~~~L~f~L~~q~fiell~~~~~~~Ai~y~r~~l~~~~--~~~~~~l 78 (145)
T PF10607_consen 1 SFKERKKIRQAILNGDIDPAIEWLNENFPELLKRNSSLEFELRCQQFIELLREGDIMEAIEYARKHLSPFN--DEFLEEL 78 (145)
T ss_pred CHHHHHHHHHHHHcCCHHHHHHHHHHcCHHHHhcCCchhHHHHHHHHHHHHHHHhHHHHHHHHHHHhhhhH--HHHHHHH
Confidence 47899999999999999999999999999999999999999999999999999999999999999997665 3588999
Q ss_pred HHHHHHhccCCCCC---CchhhhCCHHHHHHHHHHHHHHHhc---CCCchHHHHHHHHHHHHHHHH
Q 030912 90 EDFMALLAYEEPEK---SPMFHLLSLEYRQHVADNLNRAILE---RPRYAAMERLIQQTTAVRQCL 149 (169)
Q Consensus 90 ~~~~~LLay~~p~~---sp~~~Ll~~~rr~~lA~~vn~aIL~---~~~~s~Le~l~k~~~~~~~~l 149 (169)
+++|+||||++|++ +||++++++++|+.||+.||++|+. .|..|+|+.++++..++...+
T Consensus 79 ~~~~~lL~~~~~~~~~~s~~~~l~~~~~~~~la~~~~~~~l~~~~~~~~s~L~~~~~~g~~~l~~l 144 (145)
T PF10607_consen 79 KKLMSLLAYPDPEEPLPSPYKELLSPERREELAEEFNSAILKSYGLPKESPLEVILKAGLSALKTL 144 (145)
T ss_pred HHHHHHHHcCCcccccchHHHHHhChHHHHHHHHHHHHHHHHHhCcCCCCHHHHHHHHHHHHhhhc
Confidence 99999999999987 7999999999999999999999999 788999999999999887664
No 3
>KOG0396 consensus Uncharacterized conserved protein [Function unknown]
Probab=99.87 E-value=8.7e-22 Score=165.53 Aligned_cols=134 Identities=23% Similarity=0.283 Sum_probs=123.6
Q ss_pred hhHHhHHHHHHHHHHHHcCCHHHHHHHHHHhchHHHccCCcceehhchHHHHHHHhhhchHHHHHHHHhhcCCcCCchhh
Q 030912 6 NCLEDMEMRKRILHFALEGNALKAIELTEELAQDLLEKNKDLHFDLLSLHFVELVCSRKCTEALEFAQTKLTPFGKVQKY 85 (169)
Q Consensus 6 ~~~~~~~~R~~I~~~I~~G~i~~Ai~~i~~~~p~ll~~~~~L~F~L~~q~fIElir~~~~~eAi~~ar~~l~~~~~~~~~ 85 (169)
+|.|.++.-..|+++|+.|++.+|+.||++|.-.|-+.++.|+|.++.|+|||||+.++..+||+||+++|+++++ ++
T Consensus 148 vD~Dv~~~~~~I~~sll~~~l~~~Lswc~ehk~~LkK~~S~lEf~lRlQefIELi~~~~~~~Ai~~akk~f~~~~~--~~ 225 (389)
T KOG0396|consen 148 VDSDVYKRAYGIRDSLLAGELEPALSWCKEHKVELKKEESSLEFQLRLQEFIELIKVDNYDKAIAFAKKHFAPWAK--SH 225 (389)
T ss_pred HhHHHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHHhccchhhhHHHHHHHHHHHHhccHHHHHHHHHHHHhhhhh--hh
Confidence 6788889999999999999999999999999999999999999999999999999999999999999999999994 78
Q ss_pred HHHHHHHHHHhccCCC-CCCchhhhCCHHHHHHHHHHHHHHHhc---CCCchHHHHHHHH
Q 030912 86 VEKLEDFMALLAYEEP-EKSPMFHLLSLEYRQHVADNLNRAILE---RPRYAAMERLIQQ 141 (169)
Q Consensus 86 ~~el~~~~~LLay~~p-~~sp~~~Ll~~~rr~~lA~~vn~aIL~---~~~~s~Le~l~k~ 141 (169)
.++++.+||+|||+.- +.++|..+++..||+.+++.+-+.-+. .|..++|-..+..
T Consensus 226 ~~~Lk~a~g~laF~~~t~~sky~~l~~~~rw~~l~~lF~s~a~~l~~i~~~~~L~~~l~~ 285 (389)
T KOG0396|consen 226 KSDLKLAMGLLAFPKYTSSSKYLNLLTADRWSVLADLFLSEALKLFGIPINPALTIYLQA 285 (389)
T ss_pred HHHHHHHHHhhcCccccCcccccCcccHHHHHHHHHHhhHHHHHHhCCCCCcHHHHHHHh
Confidence 9999999999999975 566799999999999999998885444 7888888887776
No 4
>smart00757 CRA CT11-RanBPM. protein-protein interaction domain present in crown eukaryotes (plants, animals, fungi)
Probab=99.80 E-value=4.9e-19 Score=124.65 Aligned_cols=91 Identities=42% Similarity=0.606 Sum_probs=83.1
Q ss_pred chHHHHHHHHhhcCCcCC-chhhHHHHHHHHHHhccCCC-CCCchhhhCCHHHHHHHHHHHHHHHhc----CCCchHHHH
Q 030912 64 KCTEALEFAQTKLTPFGK-VQKYVEKLEDFMALLAYEEP-EKSPMFHLLSLEYRQHVADNLNRAILE----RPRYAAMER 137 (169)
Q Consensus 64 ~~~eAi~~ar~~l~~~~~-~~~~~~el~~~~~LLay~~p-~~sp~~~Ll~~~rr~~lA~~vn~aIL~----~~~~s~Le~ 137 (169)
++.+||+|||+++++|.. ++.++++|+++||||||++| +.+||++++++++|+.||++||++||. .+..|.|+.
T Consensus 2 ~~~eAi~yar~~l~~~~~~~~~~~~el~~~m~llaf~~~~~~sp~~~ll~~~~~~~la~~~n~~~l~~~~~~~~~s~L~~ 81 (99)
T smart00757 2 KIEEALAYARELLAPFAKEHEKFLKELEKTMALLAYPDPTEPSPYKELLSPSQREKLAEELNSAILELLHGKSSESPLEI 81 (99)
T ss_pred cHHHHHHHHHHHHhhhcccCHHHHHHHHHHHHHHhcCCCCCCccHHHHCCHHHHHHHHHHHHHHHHHHccCCCCCChHHH
Confidence 578999999999999996 55568899999999999999 899999999999999999999999997 456899999
Q ss_pred HHHHHHHHHHHHHHhcC
Q 030912 138 LIQQTTAVRQCLSQELG 154 (169)
Q Consensus 138 l~k~~~~~~~~l~~~~~ 154 (169)
++++..|+...+...++
T Consensus 82 ~~~~~~~~~~~l~~~~~ 98 (99)
T smart00757 82 LLSAGLAALKTLLEKGG 98 (99)
T ss_pred HHHHHHHHHHHHHHhcC
Confidence 99999999999887664
No 5
>KOG2817 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.71 E-value=9.2e-17 Score=136.48 Aligned_cols=137 Identities=28% Similarity=0.435 Sum_probs=122.8
Q ss_pred HhHHHHHHHHHHHHcCCHHHHHHHHHHhchHHHccCCcceehhchHHHHHHHhhhchH--HHHHHHHhhcCCcCCchhhH
Q 030912 9 EDMEMRKRILHFALEGNALKAIELTEELAQDLLEKNKDLHFDLLSLHFVELVCSRKCT--EALEFAQTKLTPFGKVQKYV 86 (169)
Q Consensus 9 ~~~~~R~~I~~~I~~G~i~~Ai~~i~~~~p~ll~~~~~L~F~L~~q~fIElir~~~~~--eAi~~ar~~l~~~~~~~~~~ 86 (169)
..+-+-++|.++|..||+++|++|+..+.-.|.+.++.|+|+|+.++|+++++.|+-. +||.|||++++||+ ..+.
T Consensus 154 ~~F~el~~Iv~~lke~Dl~~aLeWa~~~~~~L~~~~s~LE~~Lh~l~fl~l~~~g~~~~~eAl~Yar~~~~~F~--~~~~ 231 (394)
T KOG2817|consen 154 TEFVELNQIVEALKERDLEPALEWAESNRQKLKEKSSSLEFKLHSLHFLSLIRGGKSDQREALRYARTHFAPFV--ADHL 231 (394)
T ss_pred hhHHHHHHHHHHHHhccchhHHHHHHHhhhhhccccccHHHHHHHHHHHHHHhcCCcCcHHHHHHHHHhcCccc--cchH
Confidence 4455678999999999999999999999999999999999999999999999998766 99999999999998 4568
Q ss_pred HHHHHHHHHhccCCC--CCCchhhhCCHHHHHHHHHHHHH---HHhc-----------CCCchHHHHHHHHHHHHHH
Q 030912 87 EKLEDFMALLAYEEP--EKSPMFHLLSLEYRQHVADNLNR---AILE-----------RPRYAAMERLIQQTTAVRQ 147 (169)
Q Consensus 87 ~el~~~~~LLay~~p--~~sp~~~Ll~~~rr~~lA~~vn~---aIL~-----------~~~~s~Le~l~k~~~~~~~ 147 (169)
.|||.+|++|.|-.- ++|||.+++++..|..+...+-+ +.|. ..|+.+|+.++++..++..
T Consensus 232 ~eIQklm~sl~~l~~gl~~spy~~~ls~~~w~~~~~~f~r~ycallg~s~eSPL~v~v~aG~~Alp~Llk~~~v~~~ 308 (394)
T KOG2817|consen 232 REIQKLMGSLLYLRNGLEKSPYSEILSPKLWKELTEEFTREYCALLGISVESPLSVLVNAGCIALPQLLKYKSVMEL 308 (394)
T ss_pred HHHHHHHHHHHHHHcCCCCCChHHHhCHHHHHHHHHHHHHHHHHHcCCCccCcHHHHHHhhHHHHHHHHHHHHHHHH
Confidence 999999999998754 79999999999999999999888 5555 2378899999999888777
No 6
>smart00668 CTLH C-terminal to LisH motif. Alpha-helical motif of unknown function.
Probab=99.49 E-value=4.8e-14 Score=89.96 Aligned_cols=56 Identities=38% Similarity=0.524 Sum_probs=52.9
Q ss_pred HHHHHHHHHHHHcCCHHHHHHHHHHhchHHHccCCcceehhchHHHHHHHhhhchH
Q 030912 11 MEMRKRILHFALEGNALKAIELTEELAQDLLEKNKDLHFDLLSLHFVELVCSRKCT 66 (169)
Q Consensus 11 ~~~R~~I~~~I~~G~i~~Ai~~i~~~~p~ll~~~~~L~F~L~~q~fIElir~~~~~ 66 (169)
+..|..|+++|+.|++++|++|+++++|.+.++++.+.|.|++|+|||+++.|+..
T Consensus 2 ~~~~~~i~~~i~~g~~~~a~~~~~~~~~~l~~~~~~l~f~L~~q~~lell~~~~~~ 57 (58)
T smart00668 2 FDERKRIRELILKGDWDEALEWLSSLKPPLLERNSKLEFELRKQKFLELVRQGKLE 57 (58)
T ss_pred hHHHHHHHHHHHcCCHHHHHHHHHHcCHHHhccCCCchhHHHHHHHHHHHHcCCcC
Confidence 57899999999999999999999999999999999999999999999999988653
No 7
>KOG1477 consensus SPRY domain-containing proteins [General function prediction only]
Probab=98.95 E-value=2e-10 Score=101.49 Aligned_cols=154 Identities=25% Similarity=0.175 Sum_probs=125.0
Q ss_pred HHHHHHHHHcCCHHHHHHHHHHhchHHHc-cCCcceehhchHHHHHHHhhhchHHHHHHHHhhcCCcCC---chhhHHHH
Q 030912 14 RKRILHFALEGNALKAIELTEELAQDLLE-KNKDLHFDLLSLHFVELVCSRKCTEALEFAQTKLTPFGK---VQKYVEKL 89 (169)
Q Consensus 14 R~~I~~~I~~G~i~~Ai~~i~~~~p~ll~-~~~~L~F~L~~q~fIElir~~~~~eAi~~ar~~l~~~~~---~~~~~~el 89 (169)
|+.+.....+|....|+.-....+..+.+ ..+...+.+.|+.+|++.+-|.+...+++.+..+++... +.....++
T Consensus 308 ~~g~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~g~v~~e~~~~k~~l~~~~g~~~~~~~~~~~ 387 (469)
T KOG1477|consen 308 RKGRGQFTRNGAYNAALIPTYRKVGQVFEVDYPQRGAKDPCGLHVNLGRAGFVFIEANAKKWELAKDYGIKKNSAAVGML 387 (469)
T ss_pred hcCcceeechhhhcccccccccccceeecccccchhhccchhhhhhHHHHHHHHHHHHHHHHhhhhhhCcCccccccccc
Confidence 33344444455544444444443332222 457899999999999999999999999999988888765 66788999
Q ss_pred HHHHHHhccCCCCCCchhhhCCHHHHHHHHHHHHHHHhc---CCCchHHHHHHHHHHHHHHHHHHhcCCCCCCCcChhhh
Q 030912 90 EDFMALLAYEEPEKSPMFHLLSLEYRQHVADNLNRAILE---RPRYAAMERLIQQTTAVRQCLSQELGKDVHPPFSLKDF 166 (169)
Q Consensus 90 ~~~~~LLay~~p~~sp~~~Ll~~~rr~~lA~~vn~aIL~---~~~~s~Le~l~k~~~~~~~~l~~~~~~~~~~~~~l~~~ 166 (169)
..+|+||+|.+|++||..+++++.+|+-+|+.+|.+||. .+..+.|++++.++.++...+...+.+++ .++++.+.
T Consensus 388 ~~s~~Llays~p~~s~~g~~~~~~~~e~v~~~~n~~il~t~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~-~~~~~~~~ 466 (469)
T KOG1477|consen 388 SDSSSLLAYSDPEESPVGYLLDPIQREPVAEALNSAILETDNNSKDPDLERVLSQTPAELSLYARDNPPRN-DFVRDRDY 466 (469)
T ss_pred cchHHHHHhcCcccCccccccCcccchhHHhhhcccccccCCCCccchhhhhhccchhhHhhhhhcCCCcc-ceecchhh
Confidence 999999999999999999999999999999999999999 56778899999999999999998887766 78888776
Q ss_pred hc
Q 030912 167 MK 168 (169)
Q Consensus 167 l~ 168 (169)
+.
T Consensus 467 ~~ 468 (469)
T KOG1477|consen 467 FH 468 (469)
T ss_pred hc
Confidence 54
No 8
>KOG0293 consensus WD40 repeat-containing protein [Function unknown]
Probab=96.47 E-value=0.03 Score=49.08 Aligned_cols=129 Identities=17% Similarity=0.164 Sum_probs=91.0
Q ss_pred HHHHHHHHHcCCHHHHHHHHHHh-chHHHccCCcceehhchHHHHHHHhhhchHHHHHHHHhhcCCcCCchhhHHHHHHH
Q 030912 14 RKRILHFALEGNALKAIELTEEL-AQDLLEKNKDLHFDLLSLHFVELVCSRKCTEALEFAQTKLTPFGKVQKYVEKLEDF 92 (169)
Q Consensus 14 R~~I~~~I~~G~i~~Ai~~i~~~-~p~ll~~~~~L~F~L~~q~fIElir~~~~~eAi~~ar~~l~~~~~~~~~~~el~~~ 92 (169)
-+...+.++.|+.+.++.-.... ++. ..+.....|.+..|.|+|..+.|++.+|+..-|..+.... -.++.+.++
T Consensus 53 ~klf~q~vlqg~w~q~v~~~~~i~~~d-e~~~~ea~fLv~kQ~fLEf~k~~~is~al~~l~~~~~~lr---~~~kk~~el 128 (519)
T KOG0293|consen 53 TKLFDQQVLQGQWDQQVMSLVRISFED-ERNRKEAMFLVNKQIFLEFLKTGSISHALPVLRNPVLYLR---KNKKKFHEL 128 (519)
T ss_pred HHHHHHHHHcccHHHHHHHHhhccCcc-hhhhHHHHHHHHHHHHHHHHhhccHhhhhHhhhcchhhhh---hhHHHHHHH
Confidence 34567889999999987776665 666 4555678999999999999999999999998886555553 345678888
Q ss_pred HHHhccCCCCCC-c--hhhhCCHHHHHHHHHHHHHHHhc--CCCchHHHHHHHHHHHHHH
Q 030912 93 MALLAYEEPEKS-P--MFHLLSLEYRQHVADNLNRAILE--RPRYAAMERLIQQTTAVRQ 147 (169)
Q Consensus 93 ~~LLay~~p~~s-p--~~~Ll~~~rr~~lA~~vn~aIL~--~~~~s~Le~l~k~~~~~~~ 147 (169)
...|.+++...+ . -...+ -..|.++-+++..-|=- .=+.-.||.+++|+...|.
T Consensus 129 ~~sll~sn~~~~ne~~~~~~~-~n~R~~ll~elskyi~p~illP~rRLehLl~qAv~~Q~ 187 (519)
T KOG0293|consen 129 ASSLLVSNDQFSNEENTTAQL-NNERDKLLDELSKYIPPNILLPKRRLEHLLEQAVKYQR 187 (519)
T ss_pred HHHHhccccccccccchhhhh-chhHHHHHHHHHhhCCHhhcCChHHHHHHHHHHHHHHH
Confidence 888888875322 1 11222 23455666666554422 2356689999999876543
No 9
>PF14559 TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN_B 3QOU_A 3ASG_A 3ASD_A 3AS5_A 3AS4_A 3ASH_B 3FP3_A 3LCA_A ....
Probab=85.75 E-value=3.8 Score=25.47 Aligned_cols=59 Identities=20% Similarity=0.113 Sum_probs=36.1
Q ss_pred HHHcCCHHHHHHHHHHhchHHHccCCcceehhchHHHHHHHhhhchHHHHHHHHhhcCCcCCch
Q 030912 20 FALEGNALKAIELTEELAQDLLEKNKDLHFDLLSLHFVELVCSRKCTEALEFAQTKLTPFGKVQ 83 (169)
Q Consensus 20 ~I~~G~i~~Ai~~i~~~~p~ll~~~~~L~F~L~~q~fIElir~~~~~eAi~~ar~~l~~~~~~~ 83 (169)
++..|+.+.|++.+++.. .....+..+.+ .--.=+++.|+.++|...-.+.+....+++
T Consensus 1 ll~~~~~~~A~~~~~~~l-~~~p~~~~~~~----~la~~~~~~g~~~~A~~~l~~~~~~~~~~~ 59 (68)
T PF14559_consen 1 LLKQGDYDEAIELLEKAL-QRNPDNPEARL----LLAQCYLKQGQYDEAEELLERLLKQDPDNP 59 (68)
T ss_dssp HHHTTHHHHHHHHHHHHH-HHTTTSHHHHH----HHHHHHHHTT-HHHHHHHHHCCHGGGTTHH
T ss_pred ChhccCHHHHHHHHHHHH-HHCCCCHHHHH----HHHHHHHHcCCHHHHHHHHHHHHHHCcCHH
Confidence 478899999999997643 11112223333 222234678999999988887666654333
No 10
>COG3071 HemY Uncharacterized enzyme of heme biosynthesis [Coenzyme metabolism]
Probab=80.61 E-value=21 Score=31.39 Aligned_cols=95 Identities=14% Similarity=0.107 Sum_probs=70.4
Q ss_pred HHHHHHHHcCCHHHHHHHHHHhchHHHccCCcceehhchHHHHHHHhhhchHHHHHHHHhhcCCcCCchhhHHHHHHHHH
Q 030912 15 KRILHFALEGNALKAIELTEELAQDLLEKNKDLHFDLLSLHFVELVCSRKCTEALEFAQTKLTPFGKVQKYVEKLEDFMA 94 (169)
Q Consensus 15 ~~I~~~I~~G~i~~Ai~~i~~~~p~ll~~~~~L~F~L~~q~fIElir~~~~~eAi~~ar~~l~~~~~~~~~~~el~~~~~ 94 (169)
.-+.++|.+|+-++|.+|+.+..+.-.+.+ ...||.-++-++...-++-+++-+....++| .+-.+.|
T Consensus 268 ~~a~~li~l~~~~~A~~~i~~~Lk~~~D~~--------L~~~~~~l~~~d~~~l~k~~e~~l~~h~~~p----~L~~tLG 335 (400)
T COG3071 268 AYAERLIRLGDHDEAQEIIEDALKRQWDPR--------LCRLIPRLRPGDPEPLIKAAEKWLKQHPEDP----LLLSTLG 335 (400)
T ss_pred HHHHHHHHcCChHHHHHHHHHHHHhccChh--------HHHHHhhcCCCCchHHHHHHHHHHHhCCCCh----hHHHHHH
Confidence 356789999999999999999887777664 6678888888888888888887777776555 5677788
Q ss_pred HhccCCCCCCchhhhCCHHHHHHHHHHHHHHHhcCCCch
Q 030912 95 LLAYEEPEKSPMFHLLSLEYRQHVADNLNRAILERPRYA 133 (169)
Q Consensus 95 LLay~~p~~sp~~~Ll~~~rr~~lA~~vn~aIL~~~~~s 133 (169)
-|||.+ ..|.+-.+.+-.||-..|+.+
T Consensus 336 ~L~~k~------------~~w~kA~~~leaAl~~~~s~~ 362 (400)
T COG3071 336 RLALKN------------KLWGKASEALEAALKLRPSAS 362 (400)
T ss_pred HHHHHh------------hHHHHHHHHHHHHHhcCCChh
Confidence 888875 556665555655555444433
No 11
>PF04494 TFIID_90kDa: WD40 associated region in TFIID subunit; InterPro: IPR007582 This region, possibly a domain is found in subunits of transcription factor TFIID. The function of this region is unknown.; GO: 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 2J4B_D 2J49_A 2NXP_F.
Probab=73.44 E-value=6.3 Score=29.32 Aligned_cols=48 Identities=19% Similarity=0.297 Sum_probs=38.0
Q ss_pred CcceehhchHHHHHHHhhhchHHHHHHHHhhcCCcCCchhhHHHHHHHHH
Q 030912 45 KDLHFDLLSLHFVELVCSRKCTEALEFAQTKLTPFGKVQKYVEKLEDFMA 94 (169)
Q Consensus 45 ~~L~F~L~~q~fIElir~~~~~eAi~~ar~~l~~~~~~~~~~~el~~~~~ 94 (169)
..+.|=+-+.-|++||.+|..++|-.|-.++-..+. ..+..+|+++.+
T Consensus 38 ~~lLyPvFvh~YL~Lv~~~~~~~A~~F~~kf~~~~~--~~~~~~i~~L~~ 85 (142)
T PF04494_consen 38 SRLLYPVFVHSYLDLVSKGHPEEAKSFLEKFSPDFE--DSHQEDIEKLSS 85 (142)
T ss_dssp GGGHHHHHHHHHHHHHHTT-HHHHHHHHHHHGGGGH--GHGHHHHHHHTT
T ss_pred HHHHHHHHHHHHHHHHHCCChHHHHHHHHHHHHHHh--HHHHHHHHHHHh
Confidence 357899999999999999999999999998777775 345666666654
No 12
>KOG2910 consensus Uncharacterized conserved protein predicted to be involved in protein sorting [General function prediction only]
Probab=68.21 E-value=19 Score=28.68 Aligned_cols=53 Identities=17% Similarity=0.234 Sum_probs=41.8
Q ss_pred HHHHHHHHHHHcCCHHHHHHHHHHh--chHHHcc-----------CCcceehhchHHHHHHHhhhc
Q 030912 12 EMRKRILHFALEGNALKAIELTEEL--AQDLLEK-----------NKDLHFDLLSLHFVELVCSRK 64 (169)
Q Consensus 12 ~~R~~I~~~I~~G~i~~Ai~~i~~~--~p~ll~~-----------~~~L~F~L~~q~fIElir~~~ 64 (169)
.+|...|++|+.|+=+.|+-++... .-+|+.. -++++|.....+|++=++.|+
T Consensus 41 ~Er~~Ar~lird~rKdrAlllLKkKryQE~Ll~qt~~qL~nlEqmvsdiEft~vqk~V~~gLk~GN 106 (209)
T KOG2910|consen 41 AERQLARDLIRDGRKDRALLLLKKKRYQEELLTQTDNQLINLEQMVSDIEFTQVQKKVMEGLKQGN 106 (209)
T ss_pred HHHHHHHHHHHhChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3578889999999999998777543 3345543 268999999999999999883
No 13
>PF13838 Clathrin_H_link: Clathrin-H-link; PDB: 2XZG_A 3GD1_I 1BPO_C 1C9I_B 1C9L_A.
Probab=66.79 E-value=9.7 Score=25.01 Aligned_cols=41 Identities=20% Similarity=0.271 Sum_probs=26.7
Q ss_pred hhchHHHHHHHhhhchHHHHHHHHhhcCCcCCchhhHHHHH
Q 030912 50 DLLSLHFVELVCSRKCTEALEFAQTKLTPFGKVQKYVEKLE 90 (169)
Q Consensus 50 ~L~~q~fIElir~~~~~eAi~~ar~~l~~~~~~~~~~~el~ 90 (169)
.|.+++|-+++..|+..+|-..|-..=...-.+++.+..++
T Consensus 7 ~l~~~~F~~l~~~g~y~eAA~~AA~sP~giLRt~~Ti~rFk 47 (66)
T PF13838_consen 7 DLYVQQFNELFSQGQYEEAAKVAANSPRGILRTPETINRFK 47 (66)
T ss_dssp HHHHHHHHHHHHTT-HHHHHHHHHHSGGGTT-SHHHHHHHH
T ss_pred HHHHHHHHHHHHcCCHHHHHHHHHhCccchhcCHHHHHHHH
Confidence 46789999999999999998888743222222444444444
No 14
>cd08044 TAF5_NTD2 TAF5_NTD2 is the second conserved N-terminal region of TATA Binding Protein (TBP) Associated Factor 5 (TAF5), involved in forming Transcription Factor IID (TFIID). The TATA Binding Protein (TBP) Associated Factor 5 (TAF5) is one of several TAFs that bind TBP and are involved in forming Transcription Factor IID (TFIID) complex. TAF5 contains three domains, two conserved sequence motifs at the N-terminal and one at the C-terminal region. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the preinitiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. In yeast and human cells, TAFs have been found as components of other complexes besides TFIID. TAF5 may play a major role in forming TFIID and its related complexes. TAFs from various
Probab=66.22 E-value=2.4 Score=31.27 Aligned_cols=52 Identities=19% Similarity=0.301 Sum_probs=40.0
Q ss_pred cceehhchHHHHHHHhhhchHHHHHHHHhhcCCcCCchhhHHHHHHHHHHhccC
Q 030912 46 DLHFDLLSLHFVELVCSRKCTEALEFAQTKLTPFGKVQKYVEKLEDFMALLAYE 99 (169)
Q Consensus 46 ~L~F~L~~q~fIElir~~~~~eAi~~ar~~l~~~~~~~~~~~el~~~~~LLay~ 99 (169)
.+.|=+-+--|++||.+|...+|..|-.+.-..+. +.+.+.|+...++.--.
T Consensus 28 ~lLyPiFvh~yL~lv~~~~~~~A~~F~~~f~~~~~--~~~~~~i~~L~~i~~p~ 79 (133)
T cd08044 28 QLLYPIFVHSYLDLVASGHLEEAKSFFERFSGDFE--DSHSEDIKKLSSITTPE 79 (133)
T ss_pred HHHHHHHHHHHHHHHHCCCHHHHHHHHHHhhHhhH--HHHHHHHHHHHccCCHH
Confidence 47888999999999999999999999887666554 56677777775544333
No 15
>PF04157 EAP30: EAP30/Vps36 family; InterPro: IPR007286 EAP30 is a subunit of the ELL complex. The ELL is an 80kDa RNA polymerase II transcription factor. ELL interacts with three other proteins to form the complex known as ELL complex. The ELL complex is capable of increasing that catalytic rate of transcription elongation, but is unable to repress initiation of transcription by RNA polymerase II as is the case of ELL. EAP30 is thought to lead to the derepression of ELL's transcriptional inhibitory activity. ; PDB: 2ZME_A 3CUQ_A 1W7P_D 1U5T_B.
Probab=64.32 E-value=51 Score=26.28 Aligned_cols=80 Identities=11% Similarity=0.063 Sum_probs=58.6
Q ss_pred hHHHHHHHHhhcCCcCCchhhHHHHHHHHHHhccCCCCCCc-hhhhC-CHHHH-HHHHHHHHHHHhc----CCCchHHHH
Q 030912 65 CTEALEFAQTKLTPFGKVQKYVEKLEDFMALLAYEEPEKSP-MFHLL-SLEYR-QHVADNLNRAILE----RPRYAAMER 137 (169)
Q Consensus 65 ~~eAi~~ar~~l~~~~~~~~~~~el~~~~~LLay~~p~~sp-~~~Ll-~~~rr-~~lA~~vn~aIL~----~~~~s~Le~ 137 (169)
..-+-+|+++|-.....+|++..+++..+.-|.-++|...+ ++..+ +...+ .+||.+|-..++. ..+.-+|..
T Consensus 39 ~~~l~~fa~k~~~~i~~~~~~r~~f~~~~~~lGvdp~~s~~~~s~~l~~~~~f~~ELa~qi~e~c~~~~~~~GGii~L~d 118 (223)
T PF04157_consen 39 VELLENFARKHKSEIKSDPEFRSQFQSMCASLGVDPLASSKFWSESLKGSGDFYYELAVQIAEVCLATRSKNGGIISLSD 118 (223)
T ss_dssp HHHHHHHHHHHCCCCCCSHHHHHHHHHHHHHHT--CHCCTTCCCCCCSCHHHHHHHHHHHHHHHHHHHCCTTTSEEEHHH
T ss_pred HHHHHHHHHHhhccccCCchHHHHHHHHHHHcCCCcccchhhhhhccccchhHHHHHHHHHHHHHHHHHhcCCCEEEHHH
Confidence 34566899998888877899999999999999999987666 44555 66544 8999999887777 334566777
Q ss_pred HHHHHHH
Q 030912 138 LIQQTTA 144 (169)
Q Consensus 138 l~k~~~~ 144 (169)
++.....
T Consensus 119 l~~~~nr 125 (223)
T PF04157_consen 119 LYCRYNR 125 (223)
T ss_dssp HHHHHHH
T ss_pred HHHHHHH
Confidence 6665543
No 16
>COG5516 Conserved protein containing a Zn-ribbon-like motif, possibly RNA-binding [General function prediction only]
Probab=61.18 E-value=27 Score=27.40 Aligned_cols=58 Identities=9% Similarity=0.079 Sum_probs=40.1
Q ss_pred CHHHHHHHHHHHHHHHhcCCCchHHHHHHHHH-HHHHHHHHHhcCCCCCCCcChhhhhc
Q 030912 111 SLEYRQHVADNLNRAILERPRYAAMERLIQQT-TAVRQCLSQELGKDVHPPFSLKDFMK 168 (169)
Q Consensus 111 ~~~rr~~lA~~vn~aIL~~~~~s~Le~l~k~~-~~~~~~l~~~~~~~~~~~~~l~~~l~ 168 (169)
+.+++.+.|.+++.-....+...+|-....++ .++.+.+....++..+..-||.+||.
T Consensus 41 ~isr~~~aA~e~~~~~~~v~ap~al~~vai~LRE~i~~l~~~r~~g~~~rt~dl~~flr 99 (196)
T COG5516 41 DISRFAMAAGEVDETLAGVYAPGALLAVAIHLREVIDRLFRTRKAGKRVRTDDLPDFLR 99 (196)
T ss_pred HHHHHHHHhhhhhhhhcCCCCchhHHHHHHHHHHHHHHHHHHHhccCcCChhhHHHHHH
Confidence 35788999999998877744444454555554 55666666555555779999999974
No 17
>KOG0396 consensus Uncharacterized conserved protein [Function unknown]
Probab=60.34 E-value=30 Score=30.19 Aligned_cols=86 Identities=15% Similarity=0.147 Sum_probs=65.4
Q ss_pred HHHHHHHHHHHcCCHHHHHHHHHHhchHHHccCCcceehhchHHHHHHHhhhchHHHHHHHHhhcCCcCC---chhhHHH
Q 030912 12 EMRKRILHFALEGNALKAIELTEELAQDLLEKNKDLHFDLLSLHFVELVCSRKCTEALEFAQTKLTPFGK---VQKYVEK 88 (169)
Q Consensus 12 ~~R~~I~~~I~~G~i~~Ai~~i~~~~p~ll~~~~~L~F~L~~q~fIElir~~~~~eAi~~ar~~l~~~~~---~~~~~~e 88 (169)
-+|..+..++++|.++.|..++++.-- ++=.++-+..+-+....-+..|.+++||.|-.+|-....+ .=++.-.
T Consensus 118 l~r~vvdhmlr~gy~~~A~~L~K~s~l---edlvD~Dv~~~~~~I~~sll~~~l~~~Lswc~ehk~~LkK~~S~lEf~lR 194 (389)
T KOG0396|consen 118 LDRFVVDHMLRNGYFGAAVLLGKKSQL---EDLVDSDVYKRAYGIRDSLLAGELEPALSWCKEHKVELKKEESSLEFQLR 194 (389)
T ss_pred HHHHHHHHHHHcCchhHHHHHHHhhhh---hhhHhHHHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHHhccchhhhHHH
Confidence 357788899999999999999977432 2224555777778888889999999999999988776664 2256677
Q ss_pred HHHHHHHhccCC
Q 030912 89 LEDFMALLAYEE 100 (169)
Q Consensus 89 l~~~~~LLay~~ 100 (169)
+|+...|+=-++
T Consensus 195 lQefIELi~~~~ 206 (389)
T KOG0396|consen 195 LQEFIELIKVDN 206 (389)
T ss_pred HHHHHHHHHhcc
Confidence 888888876554
No 18
>PF10607 CLTH: CTLH/CRA C-terminal to LisH motif domain; InterPro: IPR019589 This entry represents the CRA (or CT11-RanBPM) domain, which is a protein-protein interaction domain present in crown eukaryotes (plants, animals, fungi) and which is found in Ran-binding proteins such as Ran-binding protein 9 (RanBP9 or RanBPM) and RanBP10. RanBPM is a scaffolding protein important in regulating cellular function in both the immune system and the nervous system, and may act as an adapter protein to couple membrane receptors to intracellular signaling pathways. This domain is at the C terminus of the proteins and is the binding domain for the CRA motif, which is comprised of approximately 100 amino acids at the C-terminal of RanBPM. It was found to be important for the interaction of RanBPM with fragile X mental retardation protein (FMRP), but its functional significance has yet to be determined [].
Probab=58.26 E-value=36 Score=24.66 Aligned_cols=30 Identities=23% Similarity=0.278 Sum_probs=24.5
Q ss_pred HHhHHHHHHHHHHHHcCCHHHHHHHHHHhc
Q 030912 8 LEDMEMRKRILHFALEGNALKAIELTEELA 37 (169)
Q Consensus 8 ~~~~~~R~~I~~~I~~G~i~~Ai~~i~~~~ 37 (169)
+..-=.+.+..+.|+.|++.+|+++++++.
T Consensus 38 L~f~L~~q~fiell~~~~~~~Ai~y~r~~l 67 (145)
T PF10607_consen 38 LEFELRCQQFIELLREGDIMEAIEYARKHL 67 (145)
T ss_pred hhHHHHHHHHHHHHHHHhHHHHHHHHHHHh
Confidence 444445778889999999999999999965
No 19
>PF04121 Nup84_Nup100: Nuclear pore protein 84 / 107 ; InterPro: IPR007252 Nup84p forms a complex with five proteins, including Nup120p, Nup85p, Sec13p, and a Sec13p homolog. This Nup84p complex in conjunction with Sec13-type proteins is required for correct nuclear pore biogenesis [].; GO: 0006810 transport, 0005643 nuclear pore; PDB: 3CQC_A 3CQG_A 3I4R_A 3IKO_I 3JRO_C.
Probab=55.75 E-value=17 Score=34.14 Aligned_cols=29 Identities=24% Similarity=0.252 Sum_probs=22.4
Q ss_pred HHhHHHHHHHHHHHHcCCHHHHHHHHHHh
Q 030912 8 LEDMEMRKRILHFALEGNALKAIELTEEL 36 (169)
Q Consensus 8 ~~~~~~R~~I~~~I~~G~i~~Ai~~i~~~ 36 (169)
...-..-+.|..+|++|++++|++||++.
T Consensus 131 ~~e~~~~~~i~~llR~G~~~eA~~lc~~~ 159 (697)
T PF04121_consen 131 EDERALLKYIFELLRAGRIEEAQELCRER 159 (697)
T ss_dssp HHHHHHHHHHHHHHHTT-HHHHHHHHHHT
T ss_pred HHHHHHHHHHHHHHHCCCHHHHHHHHHHC
Confidence 33344457889999999999999999875
No 20
>PF10827 DUF2552: Protein of unknown function (DUF2552) ; InterPro: IPR020157 This entry contains proteins with no known function.
Probab=55.14 E-value=8.2 Score=25.78 Aligned_cols=17 Identities=18% Similarity=0.007 Sum_probs=14.7
Q ss_pred CHHHHHHHHHHhchHHH
Q 030912 25 NALKAIELTEELAQDLL 41 (169)
Q Consensus 25 ~i~~Ai~~i~~~~p~ll 41 (169)
.+|.|++|+.++.|++-
T Consensus 60 tld~Ai~Wi~e~M~~iT 76 (79)
T PF10827_consen 60 TLDLAIAWIGEHMPHIT 76 (79)
T ss_pred cHHHHHHHHHhcccchh
Confidence 47999999999998764
No 21
>PF14973 TINF2_N: TERF1-interacting nuclear factor 2 N-terminus
Probab=49.62 E-value=54 Score=24.76 Aligned_cols=76 Identities=17% Similarity=0.267 Sum_probs=46.7
Q ss_pred HHHHHHHcCCHHHHHHHHHHhchHHHccC-----CcceehhchHHHHHHHhh--hchHHHHHHHHhhcC-CcCCchhhHH
Q 030912 16 RILHFALEGNALKAIELTEELAQDLLEKN-----KDLHFDLLSLHFVELVCS--RKCTEALEFAQTKLT-PFGKVQKYVE 87 (169)
Q Consensus 16 ~I~~~I~~G~i~~Ai~~i~~~~p~ll~~~-----~~L~F~L~~q~fIElir~--~~~~eAi~~ar~~l~-~~~~~~~~~~ 87 (169)
.|-++++.|.... +..|+.|+|.+ ..+ ++..-.=-...|..+|++ .+..+--.|-++.|. .|+ +.|..
T Consensus 46 lILELc~~~~~~d-l~~I~~Hl~~~-~~~~~~~~~D~~~~~~~~~F~~LV~~Ll~dp~~r~~f~qe~f~~eYG--~~f~~ 121 (145)
T PF14973_consen 46 LILELCRQERPWD-LKAIQPHLPRI-PQDPNATSKDHKMEEAHENFCQLVQNLLEDPEERENFFQEVFPQEYG--EPFDA 121 (145)
T ss_pred HHHHHHhCCCCch-HHHHHHhcccc-cccccccccHHHHHHHHHHHHHHHHHHHhChHHHHHHHHHHHHHHHC--hHHHH
Confidence 4678888776555 99999999999 322 233334445667777765 344555556665553 343 55666
Q ss_pred HHHHHHHH
Q 030912 88 KLEDFMAL 95 (169)
Q Consensus 88 el~~~~~L 95 (169)
.+++.+.=
T Consensus 122 ~Le~L~~e 129 (145)
T PF14973_consen 122 ALEKLLWE 129 (145)
T ss_pred HHHHHHHH
Confidence 66666553
No 22
>PF01158 Ribosomal_L36e: Ribosomal protein L36e; InterPro: IPR000509 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic ribosomal proteins can be grouped on the basis of sequence similarities. The L36E ribosomal family consists of mammalian, Caenorhabditis elegans and Drosophila L36, Candida albicans L39, and yeast YL39 ribosomal proteins [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1B_Q 4A1D_Q 4A19_Q 4A18_Q 3IZS_k 3IZR_k.
Probab=49.28 E-value=37 Score=24.05 Aligned_cols=46 Identities=28% Similarity=0.313 Sum_probs=32.9
Q ss_pred ehhchHHHHHHHhhhchHHHHHHHHhhcCCcCCchhhHHHHHHHHHHhc
Q 030912 49 FDLLSLHFVELVCSRKCTEALEFAQTKLTPFGKVQKYVEKLEDFMALLA 97 (169)
Q Consensus 49 F~L~~q~fIElir~~~~~eAi~~ar~~l~~~~~~~~~~~el~~~~~LLa 97 (169)
|-=+-.+-+||++.++--.|+.|+++.+..+. +-....+++..+|+
T Consensus 48 faPYEkr~mELlkv~kdKrAlKf~KKRlGth~---RAKrKrEel~~vl~ 93 (98)
T PF01158_consen 48 FAPYEKRAMELLKVSKDKRALKFAKKRLGTHI---RAKRKREELSNVLA 93 (98)
T ss_dssp HCHHHHHHHHHHHHCCHHHHHHHHHHHHCHHH---HHHHHHHHHHHHHH
T ss_pred CChHHHHHHHHHhcchhHHHHHHHHHHhhhhH---HHHHHHHHHHHHHH
Confidence 44456788999999999999999999997765 33444444444443
No 23
>PTZ00196 60S ribosomal protein L36; Provisional
Probab=48.28 E-value=40 Score=23.85 Aligned_cols=32 Identities=25% Similarity=0.364 Sum_probs=27.5
Q ss_pred ehhchHHHHHHHhhhchHHHHHHHHhhcCCcC
Q 030912 49 FDLLSLHFVELVCSRKCTEALEFAQTKLTPFG 80 (169)
Q Consensus 49 F~L~~q~fIElir~~~~~eAi~~ar~~l~~~~ 80 (169)
|-=+-.+.+||++.|.--.|+.||++.+..+.
T Consensus 48 faPYErr~mELLkv~kdKrAlKfaKkRlGth~ 79 (98)
T PTZ00196 48 FSPYERRMIELLKVGKDKRALKYAKKRLGTHK 79 (98)
T ss_pred ccHHHHHHHHHHHhcchHHHHHHHHHHhhhHH
Confidence 45566788999999999999999999998775
No 24
>KOG2235 consensus Uncharacterized conserved protein [Function unknown]
Probab=48.09 E-value=42 Score=31.47 Aligned_cols=66 Identities=15% Similarity=0.265 Sum_probs=46.7
Q ss_pred HHHHHHHHHHhccCCCCCC-chhhhCCHHHHHHHHHHHHHHHhcCCCchHHHHHHHHH----HHHHHHHHHh
Q 030912 86 VEKLEDFMALLAYEEPEKS-PMFHLLSLEYRQHVADNLNRAILERPRYAAMERLIQQT----TAVRQCLSQE 152 (169)
Q Consensus 86 ~~el~~~~~LLay~~p~~s-p~~~Ll~~~rr~~lA~~vn~aIL~~~~~s~Le~l~k~~----~~~~~~l~~~ 152 (169)
...|+.....+.-.+++-. -.+++++++.|.++|++||.-+-+ .++-+.-.+-+|. ..++..+-+.
T Consensus 87 l~hIEk~a~dIv~~d~~v~Lv~geiide~Y~d~iaeEinekLqE-~gqvtiaeLakq~dl~sellqs~l~ek 157 (776)
T KOG2235|consen 87 LDHIEKTARDIVSTDDEVTLVLGEIIDEEYVDRIAEEINEKLQE-QGQVTIAELAKQWDLPSELLQSLLIEK 157 (776)
T ss_pred HHHHHHHHHHHhhcCCceEEehhhhhhHHHHHHHHHHHHHHHHH-hcchHHHHHHHhcCCcHHHHHHHHHHH
Confidence 4578999999998888744 468999999999999999976554 2333444455553 3355555555
No 25
>PRK04984 fatty acid metabolism regulator; Provisional
Probab=47.86 E-value=40 Score=26.62 Aligned_cols=27 Identities=15% Similarity=0.209 Sum_probs=14.2
Q ss_pred hHHHHHHHHHHHHcCCHHHHHHHHHHh
Q 030912 10 DMEMRKRILHFALEGNALKAIELTEEL 36 (169)
Q Consensus 10 ~~~~R~~I~~~I~~G~i~~Ai~~i~~~ 36 (169)
++.....|.++|..||.+.|.+.+.+|
T Consensus 189 ~~~~H~~I~~Ai~~~D~~~a~~~~~~H 215 (239)
T PRK04984 189 ALGFYHKLSALCEEGNHDQVPECVRQY 215 (239)
T ss_pred HHHHHHHHHHHHHhCCHHHHHHHHHHH
Confidence 444455555555555555555555444
No 26
>PF07035 Mic1: Colon cancer-associated protein Mic1-like; InterPro: IPR009755 This entry represents the C terminus (approximately 160 residues) of a number of proteins that resemble colon cancer-associated protein Mic1.
Probab=47.69 E-value=33 Score=26.50 Aligned_cols=62 Identities=16% Similarity=0.110 Sum_probs=42.1
Q ss_pred HHHHHHHHHcCCHHHHHHHHHH--hchHHHccCCcceehhc--hHHHHH-HHhhhchHHHHHHHHhh
Q 030912 14 RKRILHFALEGNALKAIELTEE--LAQDLLEKNKDLHFDLL--SLHFVE-LVCSRKCTEALEFAQTK 75 (169)
Q Consensus 14 R~~I~~~I~~G~i~~Ai~~i~~--~~p~ll~~~~~L~F~L~--~q~fIE-lir~~~~~eAi~~ar~~ 75 (169)
++-|+..+..-...-|..++.- .+|....-.-|+..+|. .-..+| |+..|++.+|+.|+|+.
T Consensus 49 ~qllq~~Vi~DSk~lA~~LLs~~~~~~~~~Ql~lDMLkRL~~~~~~iievLL~~g~vl~ALr~ar~~ 115 (167)
T PF07035_consen 49 HQLLQYHVIPDSKPLACQLLSLGNQYPPAYQLGLDMLKRLGTAYEEIIEVLLSKGQVLEALRYARQY 115 (167)
T ss_pred HHHHhhcccCCcHHHHHHHHHhHccChHHHHHHHHHHHHhhhhHHHHHHHHHhCCCHHHHHHHHHHc
Confidence 4445555555566666666644 56777766656666665 445556 77899999999999974
No 27
>PF12854 PPR_1: PPR repeat
Probab=47.24 E-value=30 Score=18.96 Aligned_cols=25 Identities=24% Similarity=0.280 Sum_probs=19.6
Q ss_pred HHHHHHHHHHHHcCCHHHHHHHHHH
Q 030912 11 MEMRKRILHFALEGNALKAIELTEE 35 (169)
Q Consensus 11 ~~~R~~I~~~I~~G~i~~Ai~~i~~ 35 (169)
+.--.-|.-.-++|++++|+++.++
T Consensus 8 ~ty~~lI~~~Ck~G~~~~A~~l~~~ 32 (34)
T PF12854_consen 8 VTYNTLIDGYCKAGRVDEAFELFDE 32 (34)
T ss_pred hHHHHHHHHHHHCCCHHHHHHHHHh
Confidence 3344567888899999999998865
No 28
>PF12895 Apc3: Anaphase-promoting complex, cyclosome, subunit 3; PDB: 3KAE_D 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2XPI_A 3ULQ_A.
Probab=46.91 E-value=19 Score=23.53 Aligned_cols=50 Identities=28% Similarity=0.357 Sum_probs=25.4
Q ss_pred HHHHHHcCCHHHHHHHHHHhchHHHccCCcceehhchHHHHHHHhhhchHHHHHHH
Q 030912 17 ILHFALEGNALKAIELTEELAQDLLEKNKDLHFDLLSLHFVELVCSRKCTEALEFA 72 (169)
Q Consensus 17 I~~~I~~G~i~~Ai~~i~~~~p~ll~~~~~L~F~L~~q~fIElir~~~~~eAi~~a 72 (169)
-.-....|+.+.|++++++ ..+-..+....+.+ -+-++++ |+.++|++.-
T Consensus 32 a~~~~~~~~y~~A~~~~~~--~~~~~~~~~~~~l~-a~~~~~l---~~y~eAi~~l 81 (84)
T PF12895_consen 32 AQCYFQQGKYEEAIELLQK--LKLDPSNPDIHYLL-ARCLLKL---GKYEEAIKAL 81 (84)
T ss_dssp HHHHHHTTHHHHHHHHHHC--HTHHHCHHHHHHHH-HHHHHHT---T-HHHHHHHH
T ss_pred HHHHHHCCCHHHHHHHHHH--hCCCCCCHHHHHHH-HHHHHHh---CCHHHHHHHH
Confidence 3445667777777777766 33333332333322 3444433 5666666543
No 29
>PF07721 TPR_4: Tetratricopeptide repeat; InterPro: IPR011717 This entry includes tetratricopeptide-like repeats not detected by the IPR001440 from INTERPRO, IPR013105 from INTERPRO and IPR011716 from INTERPRO models. The tetratricopeptide repeat (TPR) motif is a protein-protein interaction module found in multiple copies in a number of functionally different proteins that facilitates specific interactions with a partner protein(s) [].; GO: 0042802 identical protein binding
Probab=44.35 E-value=29 Score=17.76 Aligned_cols=17 Identities=18% Similarity=0.155 Sum_probs=13.7
Q ss_pred HHHHHcCCHHHHHHHHH
Q 030912 18 LHFALEGNALKAIELTE 34 (169)
Q Consensus 18 ~~~I~~G~i~~Ai~~i~ 34 (169)
+-+...|+.++|..++.
T Consensus 9 ~~~~~~G~~~eA~~~l~ 25 (26)
T PF07721_consen 9 RALLAQGDPDEAERLLR 25 (26)
T ss_pred HHHHHcCCHHHHHHHHh
Confidence 45678899999998875
No 30
>PF12931 Sec16_C: Sec23-binding domain of Sec16; PDB: 3MZK_C.
Probab=43.22 E-value=25 Score=29.15 Aligned_cols=21 Identities=33% Similarity=0.445 Sum_probs=16.5
Q ss_pred HHHHHHHcCCHHHHHHHHHHh
Q 030912 16 RILHFALEGNALKAIELTEEL 36 (169)
Q Consensus 16 ~I~~~I~~G~i~~Ai~~i~~~ 36 (169)
+|+++|+.|++++|+++|-+.
T Consensus 1 ~I~~~Ll~G~~~~Av~~al~~ 21 (284)
T PF12931_consen 1 KIQQLLLVGNREEAVELALDN 21 (284)
T ss_dssp HHHHHHHTT-HHHHHHHHHHT
T ss_pred CHHHHHhCCCHHHHHHHHHHC
Confidence 588999999999999988554
No 31
>PRK10421 DNA-binding transcriptional repressor LldR; Provisional
Probab=42.95 E-value=59 Score=26.04 Aligned_cols=31 Identities=16% Similarity=0.064 Sum_probs=22.9
Q ss_pred HhHHHHHHHHHHHHcCCHHHHHHHHHHhchH
Q 030912 9 EDMEMRKRILHFALEGNALKAIELTEELAQD 39 (169)
Q Consensus 9 ~~~~~R~~I~~~I~~G~i~~Ai~~i~~~~p~ 39 (169)
.++.....|.++|..||.+.|..++.+|.-.
T Consensus 189 ~~~~~H~~I~~AI~~~D~~~A~~~~~~H~~~ 219 (253)
T PRK10421 189 QLTEQHQAVMDAILAGDAEGARKAMMAHLSF 219 (253)
T ss_pred HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence 4566777788888888888888887776543
No 32
>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional
Probab=42.37 E-value=43 Score=26.87 Aligned_cols=23 Identities=9% Similarity=0.023 Sum_probs=12.1
Q ss_pred HHHHHHHhhhchHHHHHHHHhhc
Q 030912 54 LHFVELVCSRKCTEALEFAQTKL 76 (169)
Q Consensus 54 q~fIElir~~~~~eAi~~ar~~l 76 (169)
.+.++.|++|+.+.|-+..+.|+
T Consensus 202 ~~I~~Ai~~~D~~~A~~~m~~Hi 224 (257)
T PRK10225 202 KQILAALIKKDARAAKLAMWQHL 224 (257)
T ss_pred HHHHHHHHhCCHHHHHHHHHHHH
Confidence 44455555555555555555555
No 33
>PF14691 Fer4_20: Dihydroprymidine dehydrogenase domain II, 4Fe-4S cluster; PDB: 2VDC_G 1H7X_C 1H7W_A 1GT8_A 1GTE_B 1GTH_B.
Probab=42.21 E-value=33 Score=24.62 Aligned_cols=27 Identities=15% Similarity=0.233 Sum_probs=20.6
Q ss_pred ehhchHHHHHHHhhhchHHHHHHHHhh
Q 030912 49 FDLLSLHFVELVCSRKCTEALEFAQTK 75 (169)
Q Consensus 49 F~L~~q~fIElir~~~~~eAi~~ar~~ 75 (169)
.++..+.||.+|+.|+..+|++..++.
T Consensus 38 ~~~dip~~i~~i~~g~~~~A~~~i~~~ 64 (111)
T PF14691_consen 38 AHIDIPEYIRLIREGNFKEAYELIRED 64 (111)
T ss_dssp T---HHHHHHHHHCT-HHHHHHHHHHH
T ss_pred CCCcHHHHHHHHHCCCHHHHHHHHHHh
Confidence 467789999999999999999998854
No 34
>KOG1156 consensus N-terminal acetyltransferase [Chromatin structure and dynamics]
Probab=41.52 E-value=3.2e+02 Score=25.96 Aligned_cols=129 Identities=18% Similarity=0.193 Sum_probs=84.8
Q ss_pred HHhHHHHHHHHHHHHcCCHHHHHHHHHHhchHHHccCCcceehhchHHHHHHHhhhchHHHHHHHHhhcCCcCCchhhHH
Q 030912 8 LEDMEMRKRILHFALEGNALKAIELTEELAQDLLEKNKDLHFDLLSLHFVELVCSRKCTEALEFAQTKLTPFGKVQKYVE 87 (169)
Q Consensus 8 ~~~~~~R~~I~~~I~~G~i~~Ai~~i~~~~p~ll~~~~~L~F~L~~q~fIElir~~~~~eAi~~ar~~l~~~~~~~~~~~ 87 (169)
..+...--+++..+.+|..+.|++.+...-|.++++- .|....-.+ +++-+++++|+...+..+....+|-.+..
T Consensus 183 e~se~~Ly~n~i~~E~g~~q~ale~L~~~e~~i~Dkl---a~~e~ka~l--~~kl~~lEeA~~~y~~Ll~rnPdn~~Yy~ 257 (700)
T KOG1156|consen 183 EHSELLLYQNQILIEAGSLQKALEHLLDNEKQIVDKL---AFEETKADL--LMKLGQLEEAVKVYRRLLERNPDNLDYYE 257 (700)
T ss_pred HHHHHHHHHHHHHHHcccHHHHHHHHHhhhhHHHHHH---HHhhhHHHH--HHHHhhHHhHHHHHHHHHhhCchhHHHHH
Confidence 3344445678889999999999999999999988762 232222222 33457889999999999888876555566
Q ss_pred HHHHHHH--------H-hccCC-----C-CCCc----hhhhCCHHHHHHHHHHHHHHHhc--CCCchHHHHHHHH
Q 030912 88 KLEDFMA--------L-LAYEE-----P-EKSP----MFHLLSLEYRQHVADNLNRAILE--RPRYAAMERLIQQ 141 (169)
Q Consensus 88 el~~~~~--------L-Lay~~-----p-~~sp----~~~Ll~~~rr~~lA~~vn~aIL~--~~~~s~Le~l~k~ 141 (169)
.++.++| + .+|.. | ..|| ..-+-..+-++.|..-++.-+-. .+-.+.|+.+.+.
T Consensus 258 ~l~~~lgk~~d~~~~lk~ly~~ls~~y~r~e~p~Rlplsvl~~eel~~~vdkyL~~~l~Kg~p~vf~dl~SLyk~ 332 (700)
T KOG1156|consen 258 GLEKALGKIKDMLEALKALYAILSEKYPRHECPRRLPLSVLNGEELKEIVDKYLRPLLSKGVPSVFKDLRSLYKD 332 (700)
T ss_pred HHHHHHHHHhhhHHHHHHHHHHHhhcCcccccchhccHHHhCcchhHHHHHHHHHHHhhcCCCchhhhhHHHHhc
Confidence 6666665 1 22322 1 2344 44455677888888888876655 3334555555555
No 35
>COG0268 RpsT Ribosomal protein S20 [Translation, ribosomal structure and biogenesis]
Probab=40.40 E-value=48 Score=22.99 Aligned_cols=29 Identities=14% Similarity=0.088 Sum_probs=24.2
Q ss_pred HHHHHHHHcCCHHHHHHHHHHhchHHHcc
Q 030912 15 KRILHFALEGNALKAIELTEELAQDLLEK 43 (169)
Q Consensus 15 ~~I~~~I~~G~i~~Ai~~i~~~~p~ll~~ 43 (169)
+....+|..||.+.|.+.+..-+|.|-..
T Consensus 33 Kk~~~ai~~gd~~~A~~~l~~a~~~idka 61 (88)
T COG0268 33 KKVEAAIEAGDKEAAKAALKEAQKKIDKA 61 (88)
T ss_pred HHHHHHHHcCCHHHHHHHHHHHHHHHHHH
Confidence 34568899999999999999999887654
No 36
>TIGR02812 fadR_gamma fatty acid metabolism transcriptional regulator FadR. Members of this family are FadR, a transcriptional regulator of fatty acid metabolism, including both biosynthesis and beta-oxidation. It is found exclusively in a subset of Gammaproteobacteria, with strictly one copy per genome. It has an N-terminal DNA-binding domain and a less well conserved C-terminal long chain acyl-CoA-binding domain. FadR from this family heterologously expressed in Escherichia coli show differences in regulatory response and fatty acid binding profiles. The family is nevertheless designated equivalog, as all member proteins have at least nominally the same function.
Probab=40.23 E-value=62 Score=25.50 Aligned_cols=24 Identities=8% Similarity=-0.046 Sum_probs=12.2
Q ss_pred HHHHHHHhhhchHHHHHHHHhhcC
Q 030912 54 LHFVELVCSRKCTEALEFAQTKLT 77 (169)
Q Consensus 54 q~fIElir~~~~~eAi~~ar~~l~ 77 (169)
++.++.|+.|+.+.|-...+.|+.
T Consensus 193 ~~I~~Ai~~~d~~~A~~~m~~H~~ 216 (235)
T TIGR02812 193 KELQALCKAGNHDEVPDCIRQYGI 216 (235)
T ss_pred HHHHHHHHcCCHHHHHHHHHHHHH
Confidence 344555555555555555555553
No 37
>PF12793 SgrR_N: Sugar transport-related sRNA regulator N-term
Probab=40.20 E-value=50 Score=23.79 Aligned_cols=25 Identities=16% Similarity=0.271 Sum_probs=20.6
Q ss_pred HHHHHHHHHcCCHHHHHHHHHHhchH
Q 030912 14 RKRILHFALEGNALKAIELTEELAQD 39 (169)
Q Consensus 14 R~~I~~~I~~G~i~~Ai~~i~~~~p~ 39 (169)
...+.+.|..|+++.|++++. .++.
T Consensus 74 ~~~~~~~l~~g~~~~a~~ll~-~~~~ 98 (115)
T PF12793_consen 74 EQQAEELLEQGKYEQALQLLD-FDQR 98 (115)
T ss_pred HHHHHHHHHcCCHHHHHHHHH-hCHH
Confidence 457889999999999999998 4443
No 38
>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=40.13 E-value=65 Score=27.79 Aligned_cols=88 Identities=19% Similarity=0.285 Sum_probs=60.5
Q ss_pred HHhHHHHHHHHHHHHcCCHHHHHHHHHHhchHHHccCCcceehh--chHHHHHHHhhhchHHHHHHHHhhcCCcCCchhh
Q 030912 8 LEDMEMRKRILHFALEGNALKAIELTEELAQDLLEKNKDLHFDL--LSLHFVELVCSRKCTEALEFAQTKLTPFGKVQKY 85 (169)
Q Consensus 8 ~~~~~~R~~I~~~I~~G~i~~Ai~~i~~~~p~ll~~~~~L~F~L--~~q~fIElir~~~~~eAi~~ar~~l~~~~~~~~~ 85 (169)
.+-+..-+.|...|.+.+...-|+|. +..-.+-+.++.+++.| ....+.-++-+ ++.+|+-+-++.++.|. +.+
T Consensus 136 ~~~f~~lK~v~~gI~~k~~~l~iE~~-Qi~gyl~kgdtesel~l~~~~~esl~l~hk-~~~~a~r~c~t~~a~f~--~kh 211 (396)
T COG5109 136 RDGFVKLKKVISGISEKSTFLLIEFL-QIEGYLSKGDTESELELYLVSHESLLLIHK-RYDEALRLCFTKLASFV--PKH 211 (396)
T ss_pred HHHHHHHHHHHHhhccchhHhHHHHH-HhcCccccCCchhhhHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHH--HHh
Confidence 34455566777888888888888888 43333444444444444 44444444443 89999999999999998 677
Q ss_pred HHHHHHHHHHhccC
Q 030912 86 VEKLEDFMALLAYE 99 (169)
Q Consensus 86 ~~el~~~~~LLay~ 99 (169)
...++..|-.+.+-
T Consensus 212 ~~dv~~~~~~l~na 225 (396)
T COG5109 212 IQDVKPLLRFLVNA 225 (396)
T ss_pred ccchHHHHHHHHcC
Confidence 78888888777663
No 39
>TIGR00083 ribF riboflavin kinase/FMN adenylyltransferase. multifunctional enzyme: riboflavin kinase (EC 2.7.1.26) (flavokinase) / FMN adenylyltransferase (EC 2.7.7.2) (FAD pyrophosphorylase) (FAD synthetase).
Probab=39.38 E-value=30 Score=29.00 Aligned_cols=25 Identities=16% Similarity=-0.047 Sum_probs=21.8
Q ss_pred HHHHHHHHHcCCHHHHHHHHHHhch
Q 030912 14 RKRILHFALEGNALKAIELTEELAQ 38 (169)
Q Consensus 14 R~~I~~~I~~G~i~~Ai~~i~~~~p 38 (169)
-..||++|..|+++.|-+++...|.
T Consensus 146 ST~IR~~l~~G~i~~A~~lLGr~y~ 170 (288)
T TIGR00083 146 SSAIRQALKNGDLELANKLLGRPYF 170 (288)
T ss_pred HHHHHHHHHcCCHHHHHHhhhhhhc
Confidence 4689999999999999999987653
No 40
>PF14689 SPOB_a: Sensor_kinase_SpoOB-type, alpha-helical domain; PDB: 1F51_C 2FTK_B 1IXM_B.
Probab=39.37 E-value=88 Score=19.77 Aligned_cols=32 Identities=25% Similarity=0.270 Sum_probs=22.9
Q ss_pred HHHHHHHHHHHHcCCHHHHHHHHHHhchHHHc
Q 030912 11 MEMRKRILHFALEGNALKAIELTEELAQDLLE 42 (169)
Q Consensus 11 ~~~R~~I~~~I~~G~i~~Ai~~i~~~~p~ll~ 42 (169)
++.-+-|.-.|..|++++|.+.+++..-++-.
T Consensus 24 ~NhLqvI~gllqlg~~~~a~eYi~~~~~~~~~ 55 (62)
T PF14689_consen 24 LNHLQVIYGLLQLGKYEEAKEYIKELSKDLQQ 55 (62)
T ss_dssp HHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 44456677888999999999999877655443
No 41
>PF14691 Fer4_20: Dihydroprymidine dehydrogenase domain II, 4Fe-4S cluster; PDB: 2VDC_G 1H7X_C 1H7W_A 1GT8_A 1GTE_B 1GTH_B.
Probab=39.30 E-value=43 Score=24.00 Aligned_cols=24 Identities=29% Similarity=0.286 Sum_probs=18.7
Q ss_pred HHHHHHHHcCCHHHHHHHHHHhch
Q 030912 15 KRILHFALEGNALKAIELTEELAQ 38 (169)
Q Consensus 15 ~~I~~~I~~G~i~~Ai~~i~~~~p 38 (169)
....++|..|++++|++++.+..|
T Consensus 43 p~~i~~i~~g~~~~A~~~i~~~np 66 (111)
T PF14691_consen 43 PEYIRLIREGNFKEAYELIREDNP 66 (111)
T ss_dssp HHHHHHHHCT-HHHHHHHHHHH-T
T ss_pred HHHHHHHHCCCHHHHHHHHHHhCC
Confidence 345688999999999999988755
No 42
>PRK07143 hypothetical protein; Provisional
Probab=37.93 E-value=22 Score=29.67 Aligned_cols=24 Identities=13% Similarity=-0.141 Sum_probs=21.0
Q ss_pred HHHHHHHHHcCCHHHHHHHHHHhc
Q 030912 14 RKRILHFALEGNALKAIELTEELA 37 (169)
Q Consensus 14 R~~I~~~I~~G~i~~Ai~~i~~~~ 37 (169)
-..||++|.+|+++.|=+++-..|
T Consensus 152 ST~IR~~l~~G~i~~A~~lLGr~y 175 (279)
T PRK07143 152 TSLLKEFIEFGDIELLNSLLLYNY 175 (279)
T ss_pred HHHHHHHHHcCCHHHHHHHcCCCc
Confidence 468999999999999999987765
No 43
>PF03398 Ist1: Regulator of Vps4 activity in the MVB pathway; InterPro: IPR005061 This is a eukaryotic protein family of unknown function.; PDB: 3GGZ_B 3GGY_B 3FRR_A 3FRS_A.
Probab=37.62 E-value=1.8e+02 Score=22.12 Aligned_cols=27 Identities=26% Similarity=0.244 Sum_probs=21.9
Q ss_pred hHHHHHHHHHHHHcCCHHHHHHHHHHh
Q 030912 10 DMEMRKRILHFALEGNALKAIELTEEL 36 (169)
Q Consensus 10 ~~~~R~~I~~~I~~G~i~~Ai~~i~~~ 36 (169)
.-..|++|-++|..|+.+.|.-.+...
T Consensus 22 ~~~~rkdIa~LL~~g~~~~Ar~rvE~l 48 (165)
T PF03398_consen 22 AKQARKDIAQLLKNGKEESARIRVEQL 48 (165)
T ss_dssp HHHHHHHHHHHHCCT-HHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHCCCHHHHHHHHHHH
Confidence 346799999999999999999888653
No 44
>PRK11523 DNA-binding transcriptional repressor ExuR; Provisional
Probab=36.58 E-value=76 Score=25.38 Aligned_cols=28 Identities=11% Similarity=-0.073 Sum_probs=17.6
Q ss_pred hHHHHHHHHHHHHcCCHHHHHHHHHHhc
Q 030912 10 DMEMRKRILHFALEGNALKAIELTEELA 37 (169)
Q Consensus 10 ~~~~R~~I~~~I~~G~i~~Ai~~i~~~~ 37 (169)
++.....|.++|.+||.+.|.+.+.+|.
T Consensus 191 ~~~eH~~I~~Ai~~~D~~~A~~~~~~Hi 218 (253)
T PRK11523 191 WCDDHDQILKALIRKDPHAAKLAMWQHL 218 (253)
T ss_pred HHHHHHHHHHHHHhCCHHHHHHHHHHHH
Confidence 3455666666666666666666666654
No 45
>PF15391 DUF4614: Domain of unknown function (DUF4614)
Probab=36.25 E-value=44 Score=26.30 Aligned_cols=50 Identities=26% Similarity=0.266 Sum_probs=37.6
Q ss_pred HHHHHHHHHhchHHHccCCcceehh-chHHHHHHHhhh----------------chHHHHHHHHhhc
Q 030912 27 LKAIELTEELAQDLLEKNKDLHFDL-LSLHFVELVCSR----------------KCTEALEFAQTKL 76 (169)
Q Consensus 27 ~~Ai~~i~~~~p~ll~~~~~L~F~L-~~q~fIElir~~----------------~~~eAi~~ar~~l 76 (169)
.+||+-+....|.+|.-|..|.=+| ..|+|||.-|.- .++++-+|.|.|-
T Consensus 113 ~dAiEALTaYSPA~lALnDMLkQQL~LTqqFve~sr~LH~Sll~SL~~~~~hY~TLEetKeyIr~hr 179 (181)
T PF15391_consen 113 ADAIEALTAYSPAVLALNDMLKQQLSLTQQFVEASRHLHQSLLQSLDADSFHYHTLEETKEYIRRHR 179 (181)
T ss_pred HHHHHHHhccChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcceeeHHHHHHHHHHcC
Confidence 3689999999999998876665544 468999987652 3778888887653
No 46
>PRK09464 pdhR transcriptional regulator PdhR; Reviewed
Probab=36.13 E-value=81 Score=25.16 Aligned_cols=29 Identities=21% Similarity=0.272 Sum_probs=17.7
Q ss_pred hHHHHH-HHHHHHHcCCHHHHHHHHHHhch
Q 030912 10 DMEMRK-RILHFALEGNALKAIELTEELAQ 38 (169)
Q Consensus 10 ~~~~R~-~I~~~I~~G~i~~Ai~~i~~~~p 38 (169)
++.... .|.++|.+||.+.|...+.+|.-
T Consensus 197 ~~~~H~~~I~~Ai~~~D~~~A~~~~~~Hl~ 226 (254)
T PRK09464 197 KVSSHRARIFEAIVAGKPEKAREASHRHLA 226 (254)
T ss_pred HHHHHHHHHHHHHHhCCHHHHHHHHHHHHH
Confidence 344443 66666777776666666666553
No 47
>PF00627 UBA: UBA/TS-N domain; InterPro: IPR000449 UBA domains are a commonly occurring sequence motif of approximately 45 amino acid residues that are found in diverse proteins involved in the ubiquitin/proteasome pathway, DNA excision-repair, and cell signalling via protein kinases []. The human homologue of yeast Rad23A is one example of a nucleotide excision-repair protein that contains both an internal and a C-terminal UBA domain. The solution structure of human Rad23A UBA(2) showed that the domain forms a compact three-helix bundle []. Comparison of the structures of UBA(1) and UBA(2) reveals that both form very similar folds and have a conserved large hydrophobic surface patch which may be a common protein-interacting surface present in diverse UBA domains. Evidence that ubiquitin binds to UBA domains leads to the prediction that the hydrophobic surface patch of UBA domains interacts with the hydrophobic surface on the five-stranded beta-sheet of ubiquitin []. This domain is similar in sequence to the N-terminal domain of translation elongation factor EF1B (or EF-Ts) from bacteria, mitochondria and chloroplasts. More information about EF1B (EF-Ts) proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0005515 protein binding; PDB: 2DAI_A 2OO9_C 2JUJ_A 1WHC_A 1YLA_A 2O25_B 3K9O_A 3K9P_A 3F92_A 3E46_A ....
Probab=35.79 E-value=29 Score=19.42 Aligned_cols=19 Identities=16% Similarity=0.211 Sum_probs=13.1
Q ss_pred HHHHHHHH--cCCHHHHHHHH
Q 030912 15 KRILHFAL--EGNALKAIELT 33 (169)
Q Consensus 15 ~~I~~~I~--~G~i~~Ai~~i 33 (169)
...++++. .||++.|++|+
T Consensus 17 ~~~~~AL~~~~~nve~A~~~L 37 (37)
T PF00627_consen 17 EQAREALRACNGNVERAVDWL 37 (37)
T ss_dssp HHHHHHHHHTTTSHHHHHHHH
T ss_pred HHHHHHHHHcCCCHHHHHHhC
Confidence 34555554 45899999986
No 48
>COG5443 FlbT Flagellar biosynthesis regulator FlbT [Cell motility and secretion]
Probab=35.78 E-value=63 Score=24.23 Aligned_cols=32 Identities=25% Similarity=0.262 Sum_probs=28.2
Q ss_pred hHHhHHHHHHHHHHHHcCCHHHHHHHHHHhch
Q 030912 7 CLEDMEMRKRILHFALEGNALKAIELTEELAQ 38 (169)
Q Consensus 7 ~~~~~~~R~~I~~~I~~G~i~~Ai~~i~~~~p 38 (169)
+-+-+...+.|-.++.+|.+-+|++.+...||
T Consensus 91 ~~eil~~lk~Id~lV~~~~~feALkaiR~lyp 122 (148)
T COG5443 91 DAEILAALKRIDGLVMAGRAFEALKAIRGLYP 122 (148)
T ss_pred CHHHHHHHHHHHHHHhccHHHHHHHHHhhhch
Confidence 34567788999999999999999999999998
No 49
>TIGR01470 cysG_Nterm siroheme synthase, N-terminal domain. This model represents a subfamily of CysG N-terminal region-related sequences. All sequences in the seed alignment for this model are N-terminal regions of known or predicted siroheme synthases. The C-terminal region of each is uroporphyrin-III C-methyltransferase (EC 2.1.1.107), which catalyzes the first step committed to the biosynthesis of either siroheme or cobalamin (vitamin B12) rather than protoheme (heme). The region represented by this model completes the process of oxidation and iron insertion to yield siroheme. Siroheme is a cofactor for nitrite and sulfite reductases, so siroheme synthase is CysG of cysteine biosynthesis in some organisms.
Probab=34.71 E-value=76 Score=25.00 Aligned_cols=64 Identities=16% Similarity=0.125 Sum_probs=42.8
Q ss_pred HHHHHHHHHHHcCCHHHHHHHHHHhchHHHccCC------cceehhchHHHHHHHhhhchHHHHHHHHhhc
Q 030912 12 EMRKRILHFALEGNALKAIELTEELAQDLLEKNK------DLHFDLLSLHFVELVCSRKCTEALEFAQTKL 76 (169)
Q Consensus 12 ~~R~~I~~~I~~G~i~~Ai~~i~~~~p~ll~~~~------~L~F~L~~q~fIElir~~~~~eAi~~ar~~l 76 (169)
..|.+|.+.+-. +++.-++++.+....+.+..+ .+...+.--.|.+++++|+.++|.+.+.+.+
T Consensus 135 ~lr~~ie~~l~~-~~~~~~~~~~~~R~~~k~~~~~~~~r~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~ 204 (205)
T TIGR01470 135 LLRERIETLLPP-SLGDLATLAATWRDAVKKRLPNGAARRRFWEKFFDGAFAERVLAGREEQAERVLATRL 204 (205)
T ss_pred HHHHHHHHhcch-hHHHHHHHHHHHHHHHHhhCCCHHHHHHHHHHHhccHHHHHHHcCCHHHHHHHHHHhh
Confidence 457777777644 456667888777777765433 2233344456788899999988888877654
No 50
>PRK09990 DNA-binding transcriptional regulator GlcC; Provisional
Probab=34.48 E-value=77 Score=25.22 Aligned_cols=23 Identities=17% Similarity=0.138 Sum_probs=11.7
Q ss_pred HHHHHHHhhhchHHHHHHHHhhc
Q 030912 54 LHFVELVCSRKCTEALEFAQTKL 76 (169)
Q Consensus 54 q~fIElir~~~~~eAi~~ar~~l 76 (169)
...++.|++|+.+.|....+.|+
T Consensus 203 ~~I~~Ai~~~D~~~A~~~~~~Hi 225 (251)
T PRK09990 203 ARLYNAVLQRLPEQAQRAARDHI 225 (251)
T ss_pred HHHHHHHHhCCHHHHHHHHHHHH
Confidence 44455555555555555555555
No 51
>TIGR00756 PPR pentatricopeptide repeat domain (PPR motif). This family has a similar consensus to the TPR domain (tetratricopeptide), pfam pfam00515, a 33-residue repeat. It is predicted to form a pair of antiparallel helices similar to that of TPR.
Probab=31.37 E-value=78 Score=16.01 Aligned_cols=22 Identities=27% Similarity=0.312 Sum_probs=17.7
Q ss_pred HHHHHHHHcCCHHHHHHHHHHh
Q 030912 15 KRILHFALEGNALKAIELTEEL 36 (169)
Q Consensus 15 ~~I~~~I~~G~i~~Ai~~i~~~ 36 (169)
..|.-..+.|++++|.++.++.
T Consensus 5 ~li~~~~~~~~~~~a~~~~~~M 26 (35)
T TIGR00756 5 TLIDGLCKAGRVEEALELFKEM 26 (35)
T ss_pred HHHHHHHHCCCHHHHHHHHHHH
Confidence 3567788999999999988764
No 52
>PRK05627 bifunctional riboflavin kinase/FMN adenylyltransferase; Reviewed
Probab=31.30 E-value=38 Score=28.62 Aligned_cols=25 Identities=20% Similarity=0.038 Sum_probs=21.6
Q ss_pred HHHHHHHHHcCCHHHHHHHHHHhch
Q 030912 14 RKRILHFALEGNALKAIELTEELAQ 38 (169)
Q Consensus 14 R~~I~~~I~~G~i~~Ai~~i~~~~p 38 (169)
-..||++|.+|+++.|-+++...|-
T Consensus 163 ST~IR~~I~~G~i~~A~~lLg~~y~ 187 (305)
T PRK05627 163 STAIRQALAEGDLELANKLLGRPYS 187 (305)
T ss_pred hHHHHHHHHcCCHHHHHhhhcCCCc
Confidence 3679999999999999999977653
No 53
>PRK00239 rpsT 30S ribosomal protein S20; Reviewed
Probab=31.25 E-value=82 Score=21.68 Aligned_cols=28 Identities=14% Similarity=0.093 Sum_probs=21.2
Q ss_pred HHHHHHHHcCCHHHHHHHHHHhchHHHc
Q 030912 15 KRILHFALEGNALKAIELTEELAQDLLE 42 (169)
Q Consensus 15 ~~I~~~I~~G~i~~Ai~~i~~~~p~ll~ 42 (169)
+.+..+|..||.++|.+.+...++.|-+
T Consensus 33 Kk~~~ai~~~~~~~a~~~~~~a~s~iDk 60 (88)
T PRK00239 33 KKVEAAIAAGDKEAAEEALKAAQSKIDK 60 (88)
T ss_pred HHHHHHHHcCCHHHHHHHHHHHHHHHHH
Confidence 3456788889999999988887766544
No 54
>PF13432 TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL_A 3CVQ_A 3CV0_A 2GW1_B 3CVN_A 3QKY_A 2PL2_B.
Probab=30.63 E-value=1.3e+02 Score=18.14 Aligned_cols=56 Identities=21% Similarity=0.188 Sum_probs=31.8
Q ss_pred HHHHHHcCCHHHHHHHHHHhchHHHccCCcceehhchHHHHHHHhhhchHHHHHHHHhhcC
Q 030912 17 ILHFALEGNALKAIELTEELAQDLLEKNKDLHFDLLSLHFVELVCSRKCTEALEFAQTKLT 77 (169)
Q Consensus 17 I~~~I~~G~i~~Ai~~i~~~~p~ll~~~~~L~F~L~~q~fIElir~~~~~eAi~~ar~~l~ 77 (169)
-..++..|+.+.|++.+++ +++.++.-.--+...-.+ +...|+.++|+.+-++.+.
T Consensus 4 a~~~~~~g~~~~A~~~~~~----~l~~~P~~~~a~~~lg~~-~~~~g~~~~A~~~~~~a~~ 59 (65)
T PF13432_consen 4 ARALYQQGDYDEAIAAFEQ----ALKQDPDNPEAWYLLGRI-LYQQGRYDEALAYYERALE 59 (65)
T ss_dssp HHHHHHCTHHHHHHHHHHH----HHCCSTTHHHHHHHHHHH-HHHTT-HHHHHHHHHHHHH
T ss_pred HHHHHHcCCHHHHHHHHHH----HHHHCCCCHHHHHHHHHH-HHHcCCHHHHHHHHHHHHH
Confidence 3567888999999888754 455544311111111111 2356888888888776543
No 55
>PRK00794 flbT flagellar biosynthesis repressor FlbT; Reviewed
Probab=30.05 E-value=1.1e+02 Score=22.69 Aligned_cols=30 Identities=17% Similarity=0.106 Sum_probs=24.0
Q ss_pred HhHHHHHHHHHHHHcCCHHHHHHHHHHhch
Q 030912 9 EDMEMRKRILHFALEGNALKAIELTEELAQ 38 (169)
Q Consensus 9 ~~~~~R~~I~~~I~~G~i~~Ai~~i~~~~p 38 (169)
+....-..|.++|.+|++-.|++.+...+|
T Consensus 92 ~~~~~l~~i~~~V~~g~~y~ALk~lR~L~~ 121 (132)
T PRK00794 92 DILAGLKAIDELVEAGRYYEALKALRGLYP 121 (132)
T ss_pred HHHHHHHHHHHHHHCCcHHHHHHHHHHhhH
Confidence 344556678889999999999999988776
No 56
>PF07378 FlbT: Flagellar protein FlbT; InterPro: IPR009967 This family consists of several FlbT proteins. FlbT is a post-transcriptional repressor function in flagellum biogenesis. FlbT is associated with the 5' untranslated region (UTR) of fljK (25 kDa flagellin) mRNA and that this association requires a predicted loop structure in the transcript. Mutations within this loop abolish FlbT association and result in increased mRNA stability. It is therefore thought that FlbT promotes the degradation of flagellin mRNA by associating with the 5' UTR [].; GO: 0048027 mRNA 5'-UTR binding, 0006402 mRNA catabolic process, 0045718 negative regulation of flagellum assembly
Probab=29.46 E-value=1.2e+02 Score=22.41 Aligned_cols=32 Identities=16% Similarity=0.068 Sum_probs=26.3
Q ss_pred hHHhHHHHHHHHHHHHcCCHHHHHHHHHHhch
Q 030912 7 CLEDMEMRKRILHFALEGNALKAIELTEELAQ 38 (169)
Q Consensus 7 ~~~~~~~R~~I~~~I~~G~i~~Ai~~i~~~~p 38 (169)
+.+....-..|.++|.+|++-.|++.+...+|
T Consensus 88 ~p~~~~~l~~~~~~v~~g~~y~ALk~~R~L~~ 119 (126)
T PF07378_consen 88 DPDAREGLDEANELVEAGRYYKALKALRKLIP 119 (126)
T ss_pred CHHHHHHHHHHHHHHHCCcHHHHHHHHHHhHH
Confidence 44556666788899999999999999988776
No 57
>PF12862 Apc5: Anaphase-promoting complex subunit 5
Probab=28.68 E-value=1.9e+02 Score=19.46 Aligned_cols=28 Identities=14% Similarity=0.127 Sum_probs=21.9
Q ss_pred HHHHHcCCHHHHHHHHHHhchHHHccCC
Q 030912 18 LHFALEGNALKAIELTEELAQDLLEKNK 45 (169)
Q Consensus 18 ~~~I~~G~i~~Ai~~i~~~~p~ll~~~~ 45 (169)
-++++.||+..|++-+.+.+---..++.
T Consensus 6 ~~~~~~~dy~~A~d~L~~~fD~~~~~~~ 33 (94)
T PF12862_consen 6 LNALRSGDYSEALDALHRYFDYAKQSNN 33 (94)
T ss_pred HHHHHcCCHHHHHHHHHHHHHHHhhccc
Confidence 4689999999999999888855555443
No 58
>KOG3452 consensus 60S ribosomal protein L36 [Translation, ribosomal structure and biogenesis]
Probab=28.27 E-value=1.1e+02 Score=21.66 Aligned_cols=45 Identities=22% Similarity=0.263 Sum_probs=31.8
Q ss_pred ehhchHHHHHHHhhhchHHHHHHHHhhcCCcCCchhhHHHHHHHHHHh
Q 030912 49 FDLLSLHFVELVCSRKCTEALEFAQTKLTPFGKVQKYVEKLEDFMALL 96 (169)
Q Consensus 49 F~L~~q~fIElir~~~~~eAi~~ar~~l~~~~~~~~~~~el~~~~~LL 96 (169)
|-=+-.+-+||++..+-..|+.++++.+..+. +-....++....|
T Consensus 50 ~aPyErr~meLlkvskdkrA~K~lKkRlGth~---RAk~KrEELsnvl 94 (102)
T KOG3452|consen 50 FAPYERRAMELLKVSKDKRALKLLKKRLGTHK---RAKRKREELSNVL 94 (102)
T ss_pred CChHHHHHHHHHHHcccHHHHHHHHHHhhHHH---HHHHHHHHHHHHH
Confidence 34455678999999999999999999998875 2333444444433
No 59
>PF07208 DUF1414: Protein of unknown function (DUF1414); InterPro: IPR009857 This family consists of several hypothetical bacterial proteins of around 70 residues in length. Members of this family are often referred to as YejL. The function of this family is unknown.; PDB: 2JPQ_A 2JUZ_B 2JUW_B 2QTI_A 2OTA_A 2JR2_A 2JRX_A.
Probab=28.09 E-value=79 Score=19.08 Aligned_cols=18 Identities=22% Similarity=0.373 Sum_probs=14.8
Q ss_pred CCHHHHHHHHHHHHHHHh
Q 030912 110 LSLEYRQHVADNLNRAIL 127 (169)
Q Consensus 110 l~~~rr~~lA~~vn~aIL 127 (169)
+.+++|+.+|+.+..|+.
T Consensus 24 V~~~qR~~iAe~Fa~AL~ 41 (44)
T PF07208_consen 24 VPPAQRQAIAEKFAQALK 41 (44)
T ss_dssp S-HHHHHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHHHH
Confidence 467999999999998875
No 60
>PF13934 ELYS: Nuclear pore complex assembly
Probab=28.03 E-value=1.1e+02 Score=24.46 Aligned_cols=107 Identities=20% Similarity=0.246 Sum_probs=53.3
Q ss_pred HHHcCCHHHHHHHHHHhchHHHccCCcceehhchHHHHH-HHhhhchHHHHHHHHhhcCCcCCchhhHHHHHHHHHHhcc
Q 030912 20 FALEGNALKAIELTEELAQDLLEKNKDLHFDLLSLHFVE-LVCSRKCTEALEFAQTKLTPFGKVQKYVEKLEDFMALLAY 98 (169)
Q Consensus 20 ~I~~G~i~~Ai~~i~~~~p~ll~~~~~L~F~L~~q~fIE-lir~~~~~eAi~~ar~~l~~~~~~~~~~~el~~~~~LLay 98 (169)
++-.|+++.|++.+.+ |.+..+ | ..+.+. |+++|+...|+.|.|..-.+... + +.+.-.+.+||.
T Consensus 88 ~LD~~~~~~A~~~L~~--ps~~~~-----~---~~~Il~~L~~~~~~~lAL~y~~~~~p~l~s-~---~~~~~~~~~La~ 153 (226)
T PF13934_consen 88 LLDHGDFEEALELLSH--PSLIPW-----F---PDKILQALLRRGDPKLALRYLRAVGPPLSS-P---EALTLYFVALAN 153 (226)
T ss_pred HhChHhHHHHHHHhCC--CCCCcc-----c---HHHHHHHHHHCCChhHHHHHHHhcCCCCCC-H---HHHHHHHHHHHc
Confidence 3445778888887733 322211 1 112222 33467777788888865555554 4 344555555666
Q ss_pred CCCCCC-chhhhCCHHHHHHHHHHHHHHHhc-CCCchHHHHHHH
Q 030912 99 EEPEKS-PMFHLLSLEYRQHVADNLNRAILE-RPRYAAMERLIQ 140 (169)
Q Consensus 99 ~~p~~s-p~~~Ll~~~rr~~lA~~vn~aIL~-~~~~s~Le~l~k 140 (169)
....+. -+.--...+.|..+.+.+-..++. .+....+..++.
T Consensus 154 ~~v~EAf~~~R~~~~~~~~~l~e~l~~~~~~~~~~~~~~~~Ll~ 197 (226)
T PF13934_consen 154 GLVTEAFSFQRSYPDELRRRLFEQLLEHCLEECARSGRLDELLS 197 (226)
T ss_pred CCHHHHHHHHHhCchhhhHHHHHHHHHHHHHHhhhhhHHHHHHh
Confidence 543211 122223334445556665556655 333334444443
No 61
>PF13934 ELYS: Nuclear pore complex assembly
Probab=27.48 E-value=3.2e+02 Score=21.80 Aligned_cols=55 Identities=13% Similarity=0.114 Sum_probs=32.3
Q ss_pred HHHHHHHcCCHHHHHHHHHHhchHHHccCCcceehhchHHHHHHHhhhchHHHHHHHHhhcC
Q 030912 16 RILHFALEGNALKAIELTEELAQDLLEKNKDLHFDLLSLHFVELVCSRKCTEALEFAQTKLT 77 (169)
Q Consensus 16 ~I~~~I~~G~i~~Ai~~i~~~~p~ll~~~~~L~F~L~~q~fIElir~~~~~eAi~~ar~~l~ 77 (169)
-|+-++..|+.+-|+..+....|.+-.. --..-++..+-++.+.||..|+|++-.
T Consensus 114 Il~~L~~~~~~~lAL~y~~~~~p~l~s~-------~~~~~~~~~La~~~v~EAf~~~R~~~~ 168 (226)
T PF13934_consen 114 ILQALLRRGDPKLALRYLRAVGPPLSSP-------EALTLYFVALANGLVTEAFSFQRSYPD 168 (226)
T ss_pred HHHHHHHCCChhHHHHHHHhcCCCCCCH-------HHHHHHHHHHHcCCHHHHHHHHHhCch
Confidence 3445555677777777777666555444 112223334556777777777776544
No 62
>PF12169 DNA_pol3_gamma3: DNA polymerase III subunits gamma and tau domain III; InterPro: IPR022754 This domain is found in bacteria and eukaryotes, and is approximately 110 amino acids in length. It is found in association with PF00004 from PFAM. This domain is also present in the tau subunit before it undergoes cleavage. Domains I-III are shared between the tau and the gamma subunits, while most of the DnaB-binding Domain IV and all of the alpha-interacting Domain V are unique to tau. ; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 1NJF_B 3GLG_G 1XXH_I 1NJG_A 3GLF_B 3GLI_G.
Probab=26.98 E-value=1.1e+02 Score=21.92 Aligned_cols=22 Identities=45% Similarity=0.607 Sum_probs=12.6
Q ss_pred HHHHHHHHcCCHHHHHHHHHHh
Q 030912 15 KRILHFALEGNALKAIELTEEL 36 (169)
Q Consensus 15 ~~I~~~I~~G~i~~Ai~~i~~~ 36 (169)
..+-++|.+||...|+..+++.
T Consensus 19 ~~l~~ai~~~d~~~~l~~~~~l 40 (143)
T PF12169_consen 19 FELLDAILEGDAAEALELLNEL 40 (143)
T ss_dssp HHHHHHHHTT-HHHHHHHHHHH
T ss_pred HHHHHHHHcCCHHHHHHHHHHH
Confidence 3455666666666666666553
No 63
>COG5051 RPL36A Ribosomal protein L36E [Translation, ribosomal structure and biogenesis]
Probab=26.95 E-value=1.7e+02 Score=20.35 Aligned_cols=44 Identities=16% Similarity=0.301 Sum_probs=33.0
Q ss_pred hhchHHHHHHHhhhchHHHHHHHHhhcCCcCCchhhHHHHHHHHHHh
Q 030912 50 DLLSLHFVELVCSRKCTEALEFAQTKLTPFGKVQKYVEKLEDFMALL 96 (169)
Q Consensus 50 ~L~~q~fIElir~~~~~eAi~~ar~~l~~~~~~~~~~~el~~~~~LL 96 (169)
.=+-.+.|+||++.+-..|=..|++.|..+. +-...+++.-..|
T Consensus 51 sPyErr~i~Lirns~~krArKlakKRLGs~k---RAkaKvEel~~~i 94 (97)
T COG5051 51 SPYERRVIELIRNSQDKRARKLAKKRLGSLK---RAKAKVEELTSVI 94 (97)
T ss_pred CHHHHHHHHHHHhcccHHHHHHHHHHhhhHH---HHHHHHHHHHHHH
Confidence 3355788999999888889999999998874 4556666665554
No 64
>KOG0989 consensus Replication factor C, subunit RFC4 [Replication, recombination and repair]
Probab=26.28 E-value=2.5e+02 Score=24.29 Aligned_cols=73 Identities=15% Similarity=0.135 Sum_probs=49.7
Q ss_pred HHHcCCHHHHHHHHHHhchHHHccC---------CcceehhchHHHHHHHhhhchHHHHHHHHhhcCCcCCchhhHHHHH
Q 030912 20 FALEGNALKAIELTEELAQDLLEKN---------KDLHFDLLSLHFVELVCSRKCTEALEFAQTKLTPFGKVQKYVEKLE 90 (169)
Q Consensus 20 ~I~~G~i~~Ai~~i~~~~p~ll~~~---------~~L~F~L~~q~fIElir~~~~~eAi~~ar~~l~~~~~~~~~~~el~ 90 (169)
.+-.|+.-.|+..+++..+ +-+.= ..+.-.-....+.|+.++++..+.++++|+.+..-..--..+..+.
T Consensus 218 ~~S~GdLR~Ait~Lqsls~-~gk~It~~~~~e~~~GvVp~~~l~~lle~a~S~d~~~~v~~~Rei~~sg~~~~~lmsQLa 296 (346)
T KOG0989|consen 218 KISDGDLRRAITTLQSLSL-LGKRITTSLVNEELAGVVPDEKLLDLLELALSADTPNTVKRVREIMRSGYSPLQLMSQLA 296 (346)
T ss_pred HHcCCcHHHHHHHHHHhhc-cCcccchHHHHHHHhccCCHHHHHHHHHHHHccChHHHHHHHHHHHHhccCHHHHHHHHH
Confidence 3457999999999999988 22210 1244455678899999999999999999987765432113344444
Q ss_pred HHH
Q 030912 91 DFM 93 (169)
Q Consensus 91 ~~~ 93 (169)
+++
T Consensus 297 ~vi 299 (346)
T KOG0989|consen 297 EVI 299 (346)
T ss_pred HHH
Confidence 433
No 65
>KOG2659 consensus LisH motif-containing protein [Cytoskeleton]
Probab=26.23 E-value=2.3e+02 Score=23.15 Aligned_cols=73 Identities=18% Similarity=0.075 Sum_probs=45.6
Q ss_pred hhHHhHHHHHHHHHHHHcCCHHHHHHHHHHhchHHHccCCcceehhchHHHHHHHhhhchHHHHHHHHhhcCCcCC
Q 030912 6 NCLEDMEMRKRILHFALEGNALKAIELTEELAQDLLEKNKDLHFDLLSLHFVELVCSRKCTEALEFAQTKLTPFGK 81 (169)
Q Consensus 6 ~~~~~~~~R~~I~~~I~~G~i~~Ai~~i~~~~p~ll~~~~~L~F~L~~q~fIElir~~~~~eAi~~ar~~l~~~~~ 81 (169)
++-++++ |--|-..+-.|..+.|....++. ++-....++.+.=.+.+..++|+.|++++||+...++....-+
T Consensus 24 ~~~~d~n-~LVmnylv~eg~~EaA~~Fa~e~--~i~~~~~d~~~~~eR~~Ir~~I~~G~Ie~Aie~in~l~PeiLd 96 (228)
T KOG2659|consen 24 VMREDLN-RLVMNYLVHEGYVEAAEKFAKES--GIKPPSIDLDSMDERLQIRRAIEEGQIEEAIEKVNQLNPEILD 96 (228)
T ss_pred cchhhHH-HHHHHHHHhccHHHHHHHhcccc--CCCCccCchhhHhHHHHHHHHHHhccHHHHHHHHHHhChHHHc
Confidence 3334444 55555666677777665555442 1111134555655666777788999999999999976654443
No 66
>PF01649 Ribosomal_S20p: Ribosomal protein S20; InterPro: IPR002583 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This family consists of bacterial (and chloroplast) examples of the ribosomal small subunit protein S20. Bacterial ribosomal protein S20 forms part of the 30S ribosomal subunit, and interacts with 16S rRNA.; GO: 0003723 RNA binding, 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1I94_T 1FJG_T 4DH9_T 3KNJ_T 3TVG_W 3UYF_W 3V28_T 3KIS_t 3HUY_T 1HNX_T ....
Probab=26.15 E-value=1.1e+02 Score=20.73 Aligned_cols=28 Identities=18% Similarity=0.129 Sum_probs=21.3
Q ss_pred HHHHHHHHcCCHHHHHHHHHHhchHHHc
Q 030912 15 KRILHFALEGNALKAIELTEELAQDLLE 42 (169)
Q Consensus 15 ~~I~~~I~~G~i~~Ai~~i~~~~p~ll~ 42 (169)
+.+..+|..|+-+.|.+.+...++.|-.
T Consensus 32 Kk~~~ai~~~~~~~a~~~l~~a~s~iDk 59 (84)
T PF01649_consen 32 KKFREAIEAGDKEEAKELLRKAYSAIDK 59 (84)
T ss_dssp HHHHHHHHTT-HHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHccChHHHHHHHHHHHHHHHH
Confidence 4567888899999999999887776644
No 67
>PF14498 Glyco_hyd_65N_2: Glycosyl hydrolase family 65, N-terminal domain; PDB: 2EAE_A 2EAB_B 2EAC_A 2EAD_B 2RDY_A.
Probab=25.36 E-value=46 Score=26.59 Aligned_cols=33 Identities=27% Similarity=0.210 Sum_probs=24.0
Q ss_pred hhhHHhHHHHHHHHHHHHcCCHHHHHHHHHHhc
Q 030912 5 ANCLEDMEMRKRILHFALEGNALKAIELTEELA 37 (169)
Q Consensus 5 ~~~~~~~~~R~~I~~~I~~G~i~~Ai~~i~~~~ 37 (169)
.........=.+||++|..|+.++|-+++++++
T Consensus 49 ~~~~~~~~~L~~iR~l~~~g~~~~A~~l~~~~~ 81 (236)
T PF14498_consen 49 RTPPDAAEYLPEIRELLFEGDYEEAEELAEENF 81 (236)
T ss_dssp SSSHHHHHHHHHHHHHHHTT-CCHHHHHHCCS-
T ss_pred ccCccHHHHHHHHHHHHHcCChhHHHHHHHHhc
Confidence 334445666778999999999999999886553
No 68
>PRK13754 conjugal transfer fertility inhibition protein FinO; Provisional
Probab=24.95 E-value=1.2e+02 Score=23.85 Aligned_cols=26 Identities=8% Similarity=0.023 Sum_probs=21.6
Q ss_pred HHHcCCHHHHHHHHHHhchHHHccCC
Q 030912 20 FALEGNALKAIELTEELAQDLLEKNK 45 (169)
Q Consensus 20 ~I~~G~i~~Ai~~i~~~~p~ll~~~~ 45 (169)
...--+..+||+++.+.||.+|..+.
T Consensus 67 y~Kl~~~keaI~~Lae~wP~lF~~g~ 92 (186)
T PRK13754 67 YLNLPPLDEAVNTLKPWWPGLFDGDT 92 (186)
T ss_pred hhhcCCHHHHHHHHHHhhHHhcCCCC
Confidence 34556789999999999999998753
No 69
>cd00194 UBA Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been suggested that UBA domains are involved in conferring protein target specificity. The domain, a compact three helix bundle, has a conserved GFP-loop and the proline is thought to be critical for binding. The UBA domain is distinct from the conserved three helical domain seen in the N-terminus of EF-TS and eukaryotic NAC proteins.
Probab=24.82 E-value=58 Score=17.97 Aligned_cols=21 Identities=19% Similarity=0.137 Sum_probs=14.6
Q ss_pred HHHHHHHH--HcCCHHHHHHHHH
Q 030912 14 RKRILHFA--LEGNALKAIELTE 34 (169)
Q Consensus 14 R~~I~~~I--~~G~i~~Ai~~i~ 34 (169)
+..++.++ -.||++.|+.|+-
T Consensus 15 ~~~~~~AL~~~~~d~~~A~~~L~ 37 (38)
T cd00194 15 REEARKALRATNNNVERAVEWLL 37 (38)
T ss_pred HHHHHHHHHHhCCCHHHHHHHHh
Confidence 45555554 3579999999973
No 70
>PF01399 PCI: PCI domain; InterPro: IPR000717 A homology domain of unclear function, occurs in the C-terminal region of several regulatory components of the 26S proteasome as well as in other proteins. This domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15) []. Apparently, all of the characterised proteins containing PCI domains are parts of larger multi-protein complexes. Proteins with PCI domains include budding yeast proteasome regulatory components Rpn3(Sun2), Rpn5, Rpn6, Rpn7and Rpn9 []; mammalian proteasome regulatory components p55, p58 and p44.5, and translation initiation factor 3 complex subunits p110 and INT6 [, ]; Arabidopsis COP9 and FUS6/COP11 []; mammalian G-protein pathway suppressor GPS1, and several uncharacterised ORFs from plant, nematodes and mammals. The complete homology domain comprises approx. 200 residues, the highest conservation is found in the C-terminal half. Several of the proteins mentioned above have no detectable homology to the N-terminal half of the domain.; GO: 0005515 protein binding; PDB: 3TXM_A 3TXN_A 1UFM_A 3CHM_A 3T5X_A 3T5V_B.
Probab=24.80 E-value=2.1e+02 Score=18.79 Aligned_cols=46 Identities=13% Similarity=0.130 Sum_probs=31.7
Q ss_pred HHHHHHHHHcCCHHHHHHHHHHhchHHHccCCcceehhchHHHHHHHhh
Q 030912 14 RKRILHFALEGNALKAIELTEELAQDLLEKNKDLHFDLLSLHFVELVCS 62 (169)
Q Consensus 14 R~~I~~~I~~G~i~~Ai~~i~~~~p~ll~~~~~L~F~L~~q~fIElir~ 62 (169)
..++.+++..|++....++++.+...++.+. .+......+.+.++.
T Consensus 3 ~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~---~l~~~~~~l~~~i~~ 48 (105)
T PF01399_consen 3 YSELLRAFRSGDLQEFEEFLEKHSESLFKDP---FLAEYVEQLKEKIRR 48 (105)
T ss_dssp HHHHHHHHHCT-HHHHHHHHHHTCHHHHHCT---THHHHHHHHHHHHHH
T ss_pred HHHHHHHHHhCCHHHHHHHHHHHHHHHHcCc---cHHHHHHHHHHHHHH
Confidence 4678899999999999999999867777653 233344455555543
No 71
>KOG3850 consensus Predicted membrane protein [Function unknown]
Probab=24.41 E-value=90 Score=27.60 Aligned_cols=47 Identities=19% Similarity=0.210 Sum_probs=37.5
Q ss_pred hhHHhHHHHHHHHHHHHcCCHHHHHHHHHHhchHHHccCCcceehhchHHHHHH
Q 030912 6 NCLEDMEMRKRILHFALEGNALKAIELTEELAQDLLEKNKDLHFDLLSLHFVEL 59 (169)
Q Consensus 6 ~~~~~~~~R~~I~~~I~~G~i~~Ai~~i~~~~p~ll~~~~~L~F~L~~q~fIEl 59 (169)
+.+.+|++|..-+..=+..||.+|++-|..+- +.|+...++|+.+.+
T Consensus 331 qElasmeervaYQsyERaRdIqEalEscqtri-------sKlEl~qq~qqv~Q~ 377 (455)
T KOG3850|consen 331 QELASMEERVAYQSYERARDIQEALESCQTRI-------SKLELQQQQQQVVQL 377 (455)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHH
Confidence 35778999999999999999999999998766 456666676676554
No 72
>KOG2817 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=24.06 E-value=3.4e+02 Score=24.04 Aligned_cols=86 Identities=17% Similarity=0.132 Sum_probs=54.3
Q ss_pred HHHHHHHHcCCHHHHHHHHHHhchHHHccCCcceehhchHHHHHHHhhhchHHHHHHHHhhcCCcCC-ch--hhHHHHHH
Q 030912 15 KRILHFALEGNALKAIELTEELAQDLLEKNKDLHFDLLSLHFVELVCSRKCTEALEFAQTKLTPFGK-VQ--KYVEKLED 91 (169)
Q Consensus 15 ~~I~~~I~~G~i~~Ai~~i~~~~p~ll~~~~~L~F~L~~q~fIElir~~~~~eAi~~ar~~l~~~~~-~~--~~~~el~~ 91 (169)
-.+....+.|..|-|..++++-.-..-+..+. .=-+...+-++-++.+++..|++||..+-..... +. ++.-.=..
T Consensus 122 ai~~h~~rqGm~dv~~~l~~Ea~~~~~~~~~~-~~F~el~~Iv~~lke~Dl~~aLeWa~~~~~~L~~~~s~LE~~Lh~l~ 200 (394)
T KOG2817|consen 122 AIVYHFYRQGMDDVGECLIKEAGLSEDESKSR-TEFVELNQIVEALKERDLEPALEWAESNRQKLKEKSSSLEFKLHSLH 200 (394)
T ss_pred HHHHHHHHcCchHHHHHHHHHhcCCCcchhhh-hhHHHHHHHHHHHHhccchhHHHHHHHhhhhhccccccHHHHHHHHH
Confidence 34567778999999999998865332211111 1223445677789999999999999977655443 22 33333345
Q ss_pred HHHHhccCCC
Q 030912 92 FMALLAYEEP 101 (169)
Q Consensus 92 ~~~LLay~~p 101 (169)
.+.++.....
T Consensus 201 fl~l~~~g~~ 210 (394)
T KOG2817|consen 201 FLSLIRGGKS 210 (394)
T ss_pred HHHHHhcCCc
Confidence 5666666543
No 73
>KOG3239 consensus Density-regulated protein related to translation initiation factor 1 (eIF-1/SUI1) [General function prediction only]
Probab=23.66 E-value=64 Score=25.34 Aligned_cols=21 Identities=38% Similarity=0.382 Sum_probs=19.1
Q ss_pred cCCHHHHHHHHHHhchHHHcc
Q 030912 23 EGNALKAIELTEELAQDLLEK 43 (169)
Q Consensus 23 ~G~i~~Ai~~i~~~~p~ll~~ 43 (169)
.|++..+-.|+.+++|+++..
T Consensus 28 ~~~~~kCk~WL~~n~pdly~k 48 (193)
T KOG3239|consen 28 SGDLKKCKEWLEENHPDLYAK 48 (193)
T ss_pred cccHHHHHHHHHhcChhHHHh
Confidence 689999999999999999875
No 74
>TIGR00029 S20 ribosomal protein S20. This family consists of bacterial (and chloroplast) examples of the bacteria ribosomal small subunit protein S20.
Probab=23.40 E-value=1.4e+02 Score=20.55 Aligned_cols=28 Identities=29% Similarity=0.247 Sum_probs=20.9
Q ss_pred HHHHHHHHcCCHHHHHHHHHHhchHHHc
Q 030912 15 KRILHFALEGNALKAIELTEELAQDLLE 42 (169)
Q Consensus 15 ~~I~~~I~~G~i~~Ai~~i~~~~p~ll~ 42 (169)
+.+..+|..||.+.|.+.+..-++.|-+
T Consensus 33 Kk~~~ai~~~d~~~a~~~l~~a~s~iDk 60 (87)
T TIGR00029 33 KKVYAAIAAGDKDKAQEAFKEAAKKLDR 60 (87)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 3466788889999888888777765544
No 75
>KOG3341 consensus RNA polymerase II transcription factor complex subunit [Transcription]
Probab=23.39 E-value=4.2e+02 Score=21.72 Aligned_cols=97 Identities=13% Similarity=0.203 Sum_probs=60.2
Q ss_pred hchHHHHHHHhhhc-hH-HHHHHHHhhcCCcCCchhhHHHHHHHHHHhccCCCCCC-c-hhhhCCH-HHHHHHHHHHHHH
Q 030912 51 LLSLHFVELVCSRK-CT-EALEFAQTKLTPFGKVQKYVEKLEDFMALLAYEEPEKS-P-MFHLLSL-EYRQHVADNLNRA 125 (169)
Q Consensus 51 L~~q~fIElir~~~-~~-eAi~~ar~~l~~~~~~~~~~~el~~~~~LLay~~p~~s-p-~~~Ll~~-~rr~~lA~~vn~a 125 (169)
|.-+|..|+-+.-. .. .--+||++|-.+...||+|...+++.|+.+.-++..+. . .+.++.. +-.-.++-+|-..
T Consensus 26 l~e~Ql~q~~~Ql~~f~~~LeeFA~kH~~ei~knsqFR~~Fq~Mca~IGvDPlas~kgfw~~~lgvgdFYYelgVqviEv 105 (249)
T KOG3341|consen 26 LAEQQLVQMSKQLEVFQEALEEFARKHKTEIRKNSQFRNQFQEMCASIGVDPLASGKGFWAELLGVGDFYYELGVQVIEV 105 (249)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCHHHHHHHHHHHHHcCCCccccCcchHHHHhhhHHHHHHHhhHHHHH
Confidence 44455566544322 23 34479999988888899999999999999988775432 2 3445544 3445555555554
Q ss_pred Hhc----CCCchHHHHHHHHHHHHHH
Q 030912 126 ILE----RPRYAAMERLIQQTTAVRQ 147 (169)
Q Consensus 126 IL~----~~~~s~Le~l~k~~~~~~~ 147 (169)
.+. ..+--+|+.+-+++...++
T Consensus 106 C~at~~~nGGlislqel~~~l~~~R~ 131 (249)
T KOG3341|consen 106 CLATKHTNGGLISLQELCNHLLQRRK 131 (249)
T ss_pred HHHhhcccCCeeeHHHHHHHHHHHhc
Confidence 444 3345567766666554443
No 76
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=23.35 E-value=63 Score=17.74 Aligned_cols=18 Identities=28% Similarity=0.274 Sum_probs=12.3
Q ss_pred HHHHHH--HcCCHHHHHHHH
Q 030912 16 RILHFA--LEGNALKAIELT 33 (169)
Q Consensus 16 ~I~~~I--~~G~i~~Ai~~i 33 (169)
.++.++ ..||++.|+.|+
T Consensus 17 ~a~~aL~~~~~d~~~A~~~L 36 (37)
T smart00165 17 EALKALRAANGNVERAAEYL 36 (37)
T ss_pred HHHHHHHHhCCCHHHHHHHH
Confidence 444443 357899999986
No 77
>PF10475 DUF2450: Protein of unknown function N-terminal domain (DUF2450) ; InterPro: IPR019515 This entry represents Vacuolar protein sorting-associated protein 54, and is thought to be involved in retrograde transport from early and late endosomes to late Golgi found in eukaryotes, but its function is not known.
Probab=23.19 E-value=1.1e+02 Score=25.32 Aligned_cols=29 Identities=31% Similarity=0.384 Sum_probs=24.4
Q ss_pred HHHHHHHHHHHcCCHHHHHHHHHHhchHH
Q 030912 12 EMRKRILHFALEGNALKAIELTEELAQDL 40 (169)
Q Consensus 12 ~~R~~I~~~I~~G~i~~Ai~~i~~~~p~l 40 (169)
+....|+.++.+||+..|+++|.+..--+
T Consensus 129 ~~~~~l~~ll~~~dy~~Al~li~~~~~~l 157 (291)
T PF10475_consen 129 QTQSRLQELLEEGDYPGALDLIEECQQLL 157 (291)
T ss_pred HHHHHHHHHHhcCCHHHHHHHHHHHHHHH
Confidence 44678899999999999999998876544
No 78
>PF13041 PPR_2: PPR repeat family
Probab=22.97 E-value=1.2e+02 Score=17.60 Aligned_cols=22 Identities=23% Similarity=0.323 Sum_probs=17.2
Q ss_pred HHHHHHHHcCCHHHHHHHHHHh
Q 030912 15 KRILHFALEGNALKAIELTEEL 36 (169)
Q Consensus 15 ~~I~~~I~~G~i~~Ai~~i~~~ 36 (169)
..|.-..+.|++++|+++.++.
T Consensus 8 ~li~~~~~~~~~~~a~~l~~~M 29 (50)
T PF13041_consen 8 TLISGYCKAGKFEEALKLFKEM 29 (50)
T ss_pred HHHHHHHHCcCHHHHHHHHHHH
Confidence 3567778899999999888664
No 79
>PF06100 Strep_67kDa_ant: Streptococcal 67 kDa myosin-cross-reactive antigen like family ; InterPro: IPR010354 Members of this family are thought to have structural features in common with the beta chain of the class II antigens, as well as myosin, and may play an important role in the pathogenesis [].
Probab=22.78 E-value=31 Score=31.35 Aligned_cols=54 Identities=11% Similarity=0.135 Sum_probs=42.3
Q ss_pred hHHHHHHHHHHHHcCCHHHHHHHHHHhch-HHHcc---------------CCcceehhchHHHHHHHhhh
Q 030912 10 DMEMRKRILHFALEGNALKAIELTEELAQ-DLLEK---------------NKDLHFDLLSLHFVELVCSR 63 (169)
Q Consensus 10 ~~~~R~~I~~~I~~G~i~~Ai~~i~~~~p-~ll~~---------------~~~L~F~L~~q~fIElir~~ 63 (169)
+.+.|..|-+++...+-+-.=..|++.|+ +.|++ ||-++|+.+.++||..+..-
T Consensus 123 s~k~r~eL~kL~l~~E~~L~~~~I~d~F~~~FF~SnFW~~W~T~FAFqpWhSa~E~rRyl~Rf~h~~~~l 192 (500)
T PF06100_consen 123 SEKDRMELIKLLLTPEEDLGDKRIEDWFSESFFESNFWYMWSTMFAFQPWHSAVEFRRYLHRFIHEIPGL 192 (500)
T ss_pred CHHHHHHHHHHhcCCHHHhCcccHHHhcchhhhcCchhHhHHHhhccCcchhHHHHHHHHHHHHHhcCCC
Confidence 35788999999988876665666777765 56666 47899999999999998753
No 80
>TIGR03504 FimV_Cterm FimV C-terminal domain. This protein is found at the extreme C-terminus of FimV from Pseudomonas aeruginosa, and of TspA of Neisseria meningitidis. Disruption of the former blocks twitching motility from type IV pili; Semmler, et al. suggest a role in peptidoglycan layer remodelling required by type IV fimbrial systems.
Probab=22.39 E-value=1.2e+02 Score=17.92 Aligned_cols=19 Identities=32% Similarity=0.274 Sum_probs=14.5
Q ss_pred HHHHHcCCHHHHHHHHHHh
Q 030912 18 LHFALEGNALKAIELTEEL 36 (169)
Q Consensus 18 ~~~I~~G~i~~Ai~~i~~~ 36 (169)
+-.|.-||.+.|.+++++.
T Consensus 7 ~ayie~Gd~e~Ar~lL~ev 25 (44)
T TIGR03504 7 RAYIEMGDLEGARELLEEV 25 (44)
T ss_pred HHHHHcCChHHHHHHHHHH
Confidence 4567888888888888663
No 81
>PHA00780 hypothetical protein
Probab=22.17 E-value=1.7e+02 Score=19.86 Aligned_cols=56 Identities=20% Similarity=0.367 Sum_probs=35.6
Q ss_pred HHHHHHHHHHHcCC--HHHHHHHHHHhchHHHccCCcceehhchHHHHHHHhhh----chHHHHHHHHhhc
Q 030912 12 EMRKRILHFALEGN--ALKAIELTEELAQDLLEKNKDLHFDLLSLHFVELVCSR----KCTEALEFAQTKL 76 (169)
Q Consensus 12 ~~R~~I~~~I~~G~--i~~Ai~~i~~~~p~ll~~~~~L~F~L~~q~fIElir~~----~~~eAi~~ar~~l 76 (169)
+.|..|.+++.+-. -.+||.++.. +.|.|.|..++|-.--.++ +..+||+-+.+-+
T Consensus 12 q~~Ldil~lv~~DTAAAk~AI~FV~d---------~~Lk~ElF~~q~~~~~~E~~~vart~kAIq~akEAL 73 (80)
T PHA00780 12 KFQLEIYKLVMNQNAAAEEAFQFIGT---------DELKLELFKIHFQSGGANSDITTRTIEAVRKSKEAL 73 (80)
T ss_pred HHHHHHHHHHhcchHHHHHHHHHhcc---------hHHHHHHHHHHHHHccccchHHHHHHHHHHHHHHHH
Confidence 45677777766554 4567777754 6788899888887654332 2345555555443
No 82
>PF09551 Spore_II_R: Stage II sporulation protein R (spore_II_R); InterPro: IPR014202 This entry is designated stage II sporulation protein R. A comparative genome analysis of all sequenced genomes of Firmicutes shows that the proteins are strictly conserved among the sub-set of endospore-forming species. SpoIIR is a signalling protein that links the activation of sigma E to the transcriptional activity of sigma F during sporulation [, ].
Probab=22.03 E-value=2.2e+02 Score=21.13 Aligned_cols=37 Identities=14% Similarity=0.165 Sum_probs=27.4
Q ss_pred hHHhHHHHHHHHHHHH-----cCCHHHHHHHHHHhchHHHcc
Q 030912 7 CLEDMEMRKRILHFAL-----EGNALKAIELTEELAQDLLEK 43 (169)
Q Consensus 7 ~~~~~~~R~~I~~~I~-----~G~i~~Ai~~i~~~~p~ll~~ 43 (169)
..-.++-|-.|...+. .++.++|.+++.++.|+|-+.
T Consensus 19 Q~lKl~VRD~Vl~~l~~~~~~~~~~~ea~~~i~~~~~~Ie~~ 60 (130)
T PF09551_consen 19 QALKLKVRDAVLEYLSPWLSQAKSKEEAREVIRENLPEIEQI 60 (130)
T ss_pred HHHHHHHHHHHHHHHHHHhccCCCHHHHHHHHHHhHHHHHHH
Confidence 3344556667776666 678999999999998887665
No 83
>TIGR01159 DRP1 density-regulated protein DRP1. This protein family shows weak but suggestive similarity to translation initiation factor SUI1 and its prokaryotic homologs.
Probab=22.01 E-value=80 Score=24.61 Aligned_cols=21 Identities=29% Similarity=0.284 Sum_probs=18.3
Q ss_pred cCCHHHHHHHHHHhchHHHcc
Q 030912 23 EGNALKAIELTEELAQDLLEK 43 (169)
Q Consensus 23 ~G~i~~Ai~~i~~~~p~ll~~ 43 (169)
.|..+.+-+|+.+++|+++..
T Consensus 20 ~~~~~kCk~WL~~n~p~l~~~ 40 (173)
T TIGR01159 20 SGDLKRCKVWLSENAPDLYAK 40 (173)
T ss_pred CCCHHHHHHHHHHhChHHHHH
Confidence 467899999999999999964
No 84
>PF13812 PPR_3: Pentatricopeptide repeat domain
Probab=21.11 E-value=1.4e+02 Score=15.24 Aligned_cols=21 Identities=24% Similarity=0.262 Sum_probs=16.7
Q ss_pred HHHHHHHHcCCHHHHHHHHHH
Q 030912 15 KRILHFALEGNALKAIELTEE 35 (169)
Q Consensus 15 ~~I~~~I~~G~i~~Ai~~i~~ 35 (169)
..|+-....|+.+.|..+.++
T Consensus 6 ~ll~a~~~~g~~~~a~~~~~~ 26 (34)
T PF13812_consen 6 ALLRACAKAGDPDAALQLFDE 26 (34)
T ss_pred HHHHHHHHCCCHHHHHHHHHH
Confidence 456778889999999888765
No 85
>PF06910 MEA1: Male enhanced antigen 1 (MEA1); InterPro: IPR009685 This family consists of several mammalian male enhanced antigen 1 (MEA1) proteins. The Mea-1 gene is found to be localised in primary and secondary spermatocytes and spermatids, but the protein products are detected only in spermatids. Intensive transcription of Mea-1 gene and specific localisation of the gene product suggest that Mea-1 may play a important role in the late stage of spermatogenesis [].; GO: 0007283 spermatogenesis
Probab=21.10 E-value=1.8e+02 Score=22.66 Aligned_cols=38 Identities=18% Similarity=0.059 Sum_probs=31.5
Q ss_pred chhhHHHHHHHHHHhccCCCCCCchhhhCCHHHHHHHH
Q 030912 82 VQKYVEKLEDFMALLAYEEPEKSPMFHLLSLEYRQHVA 119 (169)
Q Consensus 82 ~~~~~~el~~~~~LLay~~p~~sp~~~Ll~~~rr~~lA 119 (169)
++.+.+.|+++|+-+.-+.......+.-++.++|..+-
T Consensus 123 D~~~ve~Vk~~Ma~i~LP~~~vP~WA~~IseeqWk~~l 160 (174)
T PF06910_consen 123 DAEHVELVKRTMAGITLPSSAVPEWAKEISEEQWKDVL 160 (174)
T ss_pred CHHHHHHHHHHHhcccCCCCCCcHHHhhCCHHHHHHHH
Confidence 57788999999999888876666689999999997653
No 86
>PF01535 PPR: PPR repeat; InterPro: IPR002885 This entry represents the PPR repeat. Pentatricopeptide repeat (PPR) proteins are characterised by tandem repeats of a degenerate 35 amino acid motif []. Most of PPR proteins have roles in mitochondria or plastid []. PPR repeats were discovered while screening Arabidopsis proteins for those predicted to be targeted to mitochondria or chloroplast [, ]. Some of these proteins have been shown to play a role in post-transcriptional processes within organelles and they are thought to be sequence-specific RNA-binding proteins [, , ]. Plant genomes have between one hundred to five hundred PPR genes per genome whereas non-plant genomes encode two to six PPR proteins. Although no PPR structures are yet known, the motif is predicted to fold into a helix-turn-helix structure similar to those found in the tetratricopeptide repeat (TPR) family (see PDOC50005 from PROSITEDOC) []. The plant PPR protein family has been divided in two subfamilies on the basis of their motif content and organisation [, ]. Examples of PPR repeat-containing proteins include PET309 P32522 from SWISSPROT, which may be involved in RNA stabilisation [], and crp1, which is involved in RNA processing []. The repeat is associated with a predicted plant protein O49549 from SWISSPROT that has a domain organisation similar to the human BRCA1 protein.
Probab=20.99 E-value=1.2e+02 Score=14.98 Aligned_cols=20 Identities=25% Similarity=0.300 Sum_probs=15.6
Q ss_pred HHHHHHHcCCHHHHHHHHHH
Q 030912 16 RILHFALEGNALKAIELTEE 35 (169)
Q Consensus 16 ~I~~~I~~G~i~~Ai~~i~~ 35 (169)
.|.-....|++++|.++.++
T Consensus 6 li~~~~~~~~~~~a~~~~~~ 25 (31)
T PF01535_consen 6 LISGYCKMGQFEEALEVFDE 25 (31)
T ss_pred HHHHHHccchHHHHHHHHHH
Confidence 45667788999999888765
No 87
>PF13428 TPR_14: Tetratricopeptide repeat
Probab=20.70 E-value=1.4e+02 Score=16.89 Aligned_cols=17 Identities=18% Similarity=0.141 Sum_probs=11.0
Q ss_pred HHHHcCCHHHHHHHHHH
Q 030912 19 HFALEGNALKAIELTEE 35 (169)
Q Consensus 19 ~~I~~G~i~~Ai~~i~~ 35 (169)
-....|+.+.|+++.++
T Consensus 10 ~~~~~G~~~~A~~~~~~ 26 (44)
T PF13428_consen 10 AYRRLGQPDEAERLLRR 26 (44)
T ss_pred HHHHcCCHHHHHHHHHH
Confidence 45566777777776654
No 88
>TIGR03147 cyt_nit_nrfF cytochrome c nitrite reductase, accessory protein NrfF.
Probab=20.62 E-value=93 Score=22.99 Aligned_cols=29 Identities=17% Similarity=0.348 Sum_probs=22.6
Q ss_pred HHHHHHHHHHHHcCCHHHH-HHHHHHhchH
Q 030912 11 MEMRKRILHFALEGNALKA-IELTEELAQD 39 (169)
Q Consensus 11 ~~~R~~I~~~I~~G~i~~A-i~~i~~~~p~ 39 (169)
-+.|..|++.|.+|+.++. +++..+.|-+
T Consensus 60 ~dmR~~Vr~~i~~G~Sd~eI~~~~v~RYG~ 89 (126)
T TIGR03147 60 YDLRHEVYSMVNEGKSNQQIIDFMTARFGD 89 (126)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHHHHhcCC
Confidence 4679999999999998877 5666666644
No 89
>PF12569 NARP1: NMDA receptor-regulated protein 1 ; InterPro: IPR021183 This group represents N-terminal acetyltransferase A (NatA) auxiliary subunit and represents a non-catalytic component of the NatA N-terminal acetyltransferase, which catalyzes acetylation of proteins beginning with Met-Ser, Met-Gly and Met-Ala. N-terminal acetylation plays a role in normal eukaryotic translation and processing, protect against proteolytic degradation and protein turnover. NAT1 anchors ARD1 and NAT5 to the ribosome and may present the N- terminal of nascent polypeptides for acetylation [], [].
Probab=20.53 E-value=4.2e+02 Score=24.19 Aligned_cols=70 Identities=19% Similarity=0.145 Sum_probs=43.1
Q ss_pred HHHcCCHHHHHHHHHHhchHHHccCCcceehhchHHHHHHHhhhchHHHHHHHHhhcCCcCCchhhHHHHHHHHH
Q 030912 20 FALEGNALKAIELTEELAQDLLEKNKDLHFDLLSLHFVELVCSRKCTEALEFAQTKLTPFGKVQKYVEKLEDFMA 94 (169)
Q Consensus 20 ~I~~G~i~~Ai~~i~~~~p~ll~~~~~L~F~L~~q~fIElir~~~~~eAi~~ar~~l~~~~~~~~~~~el~~~~~ 94 (169)
....|+.+.|++.++++-..++..-+-++ .+--=+++-|+.++|...-+..+..-.+|..+..-++.++|
T Consensus 14 l~e~g~~~~AL~~L~~~~~~I~Dk~~~~E-----~rA~ll~kLg~~~eA~~~y~~Li~rNPdn~~Yy~~L~~~~g 83 (517)
T PF12569_consen 14 LEEAGDYEEALEHLEKNEKQILDKLAVLE-----KRAELLLKLGRKEEAEKIYRELIDRNPDNYDYYRGLEEALG 83 (517)
T ss_pred HHHCCCHHHHHHHHHhhhhhCCCHHHHHH-----HHHHHHHHcCCHHHHHHHHHHHHHHCCCcHHHHHHHHHHHh
Confidence 46789999999999998777766522111 11111334467777777777666554444455555555553
No 90
>PRK12791 flbT flagellar biosynthesis repressor FlbT; Reviewed
Probab=20.52 E-value=2e+02 Score=21.33 Aligned_cols=27 Identities=22% Similarity=0.299 Sum_probs=20.5
Q ss_pred HHHHHHHHHHHcCCHHHHHHHHHHhch
Q 030912 12 EMRKRILHFALEGNALKAIELTEELAQ 38 (169)
Q Consensus 12 ~~R~~I~~~I~~G~i~~Ai~~i~~~~p 38 (169)
..-..|.++|.+|++-.|++.+...+|
T Consensus 92 ~~l~~~~~~v~~g~~Y~ALK~~R~Li~ 118 (131)
T PRK12791 92 PIIEAINNHILNGDLYKALKELRKLIA 118 (131)
T ss_pred HHHHHHHHHHhCCCHHHHHHHHHHhHH
Confidence 444557788888888888888877766
No 91
>PF08283 Gemini_AL1_M: Geminivirus rep protein central domain; InterPro: IPR022692 Geminiviruses are characterised by a genome of circular single-stranded DNA encapsidated in twinned (geminate) quasi-isometric particles, from which the group derives its name []. Most geminiviruses can be divided into two subgroups on the basis of host range and/or insect vector: i.e. those that infect dicotyledenous plants and are transmitted by the same whitefly species, and those that infect monocotyledenous plants and are transmitted by different leafhopper vectors. The genomes of the whitefly-transmitted African cassava mosaic virus, Tomato golden mosaic virus (TGMV) and Bean golden mosaic virus (BGMV) possess a bipartite genome. By contrast, only a single DNA component has been identified for the leafhopper-transmitted Maize streak virus (MSV) and Wheat dwarf virus (WDV) [, ]. Beet curly top virus (BCTV), and Tobacco yellow dwarf virus belong to a third possible subgroup. Like MSV and WDV, BCTV is transmitted by a specific leafhopper species, yet like the whitefly-transmitted geminiviruses it has a host range confined to dicotyledenous plants. Sequence comparison of the whitefly-transmitted Squash leaf curl virus (SqLCV) and Tomato yellow leaf curl virus (TYLCV) with the genomic components of TGMV and BGMV reveals a close evolutionary relationship [, , ]. Amino acid sequence alignments of Potato yellow mosaic virus (PYMV) proteins with those encoded by other geminiviruses show that PYMV is closely related to geminiviruses isolated from the New World, especially in the putative coat protein gene regions []. Comparison of MSV DNA-encoded proteins with those of other geminiviruses infecting monocotyledonous plants, including Panicum streak virus [] and Miscanthus streak virus (MiSV) [], reveal high levels of similarity. This is the central region of the geminivirus rep proteins []. It is found C-terminal to PF00799 from PFAM and is thought to be responsible for oligomerisation.; GO: 0016888 endodeoxyribonuclease activity, producing 5'-phosphomonoesters
Probab=20.39 E-value=1.2e+02 Score=21.78 Aligned_cols=25 Identities=20% Similarity=0.230 Sum_probs=20.8
Q ss_pred HHHHHHHHcCCHHHHHHHHHHhchH
Q 030912 15 KRILHFALEGNALKAIELTEELAQD 39 (169)
Q Consensus 15 ~~I~~~I~~G~i~~Ai~~i~~~~p~ 39 (169)
-..-++|-+|.-++|+..+++.+|.
T Consensus 7 Da~a~aina~sk~EaL~iike~~P~ 31 (106)
T PF08283_consen 7 DAYARAINAGSKEEALSIIKELAPK 31 (106)
T ss_pred HHHHHHHhcCCHHHHHHHHHhcCch
Confidence 3456778899999999999999886
No 92
>KOG2027 consensus Spindle pole body protein [Cytoskeleton]
Probab=20.37 E-value=1.3e+02 Score=26.41 Aligned_cols=117 Identities=21% Similarity=0.313 Sum_probs=61.0
Q ss_pred HHHHHHHHHHHcCCHHHHHHHHHHhchHHHccCCcceehhchHHHHHHHhhhchHHHHHHHHhhcCCcCCchhhHHHHHH
Q 030912 12 EMRKRILHFALEGNALKAIELTEELAQDLLEKNKDLHFDLLSLHFVELVCSRKCTEALEFAQTKLTPFGKVQKYVEKLED 91 (169)
Q Consensus 12 ~~R~~I~~~I~~G~i~~Ai~~i~~~~p~ll~~~~~L~F~L~~q~fIElir~~~~~eAi~~ar~~l~~~~~~~~~~~el~~ 91 (169)
+.|..|-++|.+|.-+.|.-.+.... .....+.-.=....|.|+|-. | ++......+.-.++.+
T Consensus 19 q~RrdIA~lL~sg~~~~A~~RvE~li----~ee~~~~a~e~le~fCelll~----------R--~~~i~~~~~cp~~l~E 82 (388)
T KOG2027|consen 19 QLRRDIADLLKSGQDERARIRVEHLI----REENLLEAYEILELFCELLLA----------R--LSLIEKQKECPDDLKE 82 (388)
T ss_pred HHHHHHHHHHHcCCchhhHHHHHHHH----HHHHHHHHHHHHHHHHHHHHH----------H--hhHHhhcccCCHHHHH
Confidence 56999999999999999988886532 322222222222334444321 1 1111111233457788
Q ss_pred HHHHhccCCCCCCc------hhhhCCHHHHHHHHHH---------HHHHHhc-----CCCchHHHHHHHHHHH
Q 030912 92 FMALLAYEEPEKSP------MFHLLSLEYRQHVADN---------LNRAILE-----RPRYAAMERLIQQTTA 144 (169)
Q Consensus 92 ~~~LLay~~p~~sp------~~~Ll~~~rr~~lA~~---------vn~aIL~-----~~~~s~Le~l~k~~~~ 144 (169)
+++.|.|--|--+. .+.+|....=...+.. ||..|.+ .|+...-+++++.+..
T Consensus 83 AVsSlifAA~R~~EvpEL~~i~~~f~~kYGk~f~~~a~~l~p~~~Vn~kiiekLs~~~P~~e~k~k~lkEIA~ 155 (388)
T KOG2027|consen 83 AVSSLIFAAPRLSEVPELREIRDLFVKKYGKEFVKAAIELRPGNGVNRKIIEKLSVEAPPKELKEKYLKEIAK 155 (388)
T ss_pred HHHHHHHHhccccccHHHHHHHHHHHHHHhHHHHHHHHhccccCCcCHHHHHHhcCCCCcHHHHHHHHHHHHH
Confidence 88888887764332 2344444433444444 4444555 2333333555555543
No 93
>PF02607 B12-binding_2: B12 binding domain; InterPro: IPR003759 Cobalamin-dependent methionine synthase (2.1.1.13 from EC) is a large modular protein that catalyses methyl transfer from methyltetrahydrofolate (CH3-H4folate) to homocysteine. During the catalytic cycle, it supports three distinct methyl transfer reactions, each involving the cobalamin (vitamin B12) cofactor and a substrate bound to its own functional unit []. The cobalamin cofactor plays an essential role in this reaction, accepting the methyl group from CH3-H4folate to form methylcob(III)alamin, and in turn donating the methyl group to homocysteine to generate methionine and cob(I)alamin. Methionine synthase is a large enzyme composed of four structurally and functionally distinct modules: the first two modules bind homocysteine and CH3-H4folate, the third module binds the cobalamin cofactor and the C-terminal module binds S-adenosylmethionine. The cobalamin-binding module is composed of two structurally distinct domains: a 4-helical bundle cap domain (residues 651-740 in the Escherichia coli enzyme) and an alpha/beta B12-binding domain (residues 741-896) (IPR006158 from INTERPRO). The 4-helical bundle forms a cap over the alpha/beta domain, which acts to shield the methyl ligand of cobalamin from solvent []. Furthermore, in the conversion to the active conformation of this enzyme, the 4-helical cap rotates to allow the cobalamin cofactor to bind the activation domain (IPR004223 from INTERPRO). The alpha/beta domain is a common cobalamin-binding motif, whereas the 4-helical bundle domain with its methyl cap is a distinctive feature of methionine synthases. This entry represents the 4-helical bundle cap domain. This domain is also present in other shorter proteins that bind to B12, and is always found N terminus to the alpha/beta B12-binding domain.; GO: 0008705 methionine synthase activity, 0031419 cobalamin binding, 0046872 metal ion binding, 0009086 methionine biosynthetic process; PDB: 3EZX_A 3BUL_A 1K7Y_A 1BMT_A 3IV9_A 1K98_A 3IVA_A 2I2X_P.
Probab=20.29 E-value=1e+02 Score=19.74 Aligned_cols=23 Identities=35% Similarity=0.390 Sum_probs=14.6
Q ss_pred HHHHHHHHHcCCHHHHHHHHHHh
Q 030912 14 RKRILHFALEGNALKAIELTEEL 36 (169)
Q Consensus 14 R~~I~~~I~~G~i~~Ai~~i~~~ 36 (169)
..++.+++.+||.+.|.+++++.
T Consensus 5 ~~~l~~al~~~d~~~~~~~~~~~ 27 (79)
T PF02607_consen 5 IERLLDALLAGDEEEAEALLEEA 27 (79)
T ss_dssp HHHHHHHHHTT-CCHHHHHHHHH
T ss_pred HHHHHHHHHhCCHHHHHHHHHHH
Confidence 45666777777777777776554
No 94
>KOG2051 consensus Nonsense-mediated mRNA decay 2 protein [RNA processing and modification]
Probab=20.12 E-value=9.1e+02 Score=24.42 Aligned_cols=80 Identities=19% Similarity=0.159 Sum_probs=58.5
Q ss_pred CcceehhchHHHH-HHHhhh--chHHHHHHHHhhcCCcCC-chhhHHHHHHHHHHhccCCCCCCc-hhhhCCHHHHHHHH
Q 030912 45 KDLHFDLLSLHFV-ELVCSR--KCTEALEFAQTKLTPFGK-VQKYVEKLEDFMALLAYEEPEKSP-MFHLLSLEYRQHVA 119 (169)
Q Consensus 45 ~~L~F~L~~q~fI-Elir~~--~~~eAi~~ar~~l~~~~~-~~~~~~el~~~~~LLay~~p~~sp-~~~Ll~~~rr~~lA 119 (169)
..++-+|.+-.|| ||++=+ ...+++..-+..+..|.. +=+..-.+-+.+|...|..|+..- ...+++.-+|...|
T Consensus 517 ~~ietk~~~VrfIsEL~KF~lv~~~~if~cLk~ll~dF~~hnIEm~c~lLE~~GrfLlr~pEt~lrM~~~Le~i~rkK~a 596 (1128)
T KOG2051|consen 517 INIETKLKIVRFISELCKFQLVPKFEIFSCLKMLLNDFTHHNIEMACVLLESCGRFLLRSPETKLRMRVFLEQIKRKKRA 596 (1128)
T ss_pred hhhhhhhhhhhhHHhhhhhCccChHHHHHHHHHHHHhcccccHHHHHHHHHhcchhhhcChhHHHHHHHHHHHHHHHHHH
Confidence 4577788888887 566655 345566667777667764 345556678888999999988664 57888888988888
Q ss_pred HHHHH
Q 030912 120 DNLNR 124 (169)
Q Consensus 120 ~~vn~ 124 (169)
..+++
T Consensus 597 ~~lDs 601 (1128)
T KOG2051|consen 597 SALDS 601 (1128)
T ss_pred hhhch
Confidence 88777
No 95
>TIGR03362 VI_chp_7 type VI secretion-associated protein, VC_A0119 family. This protein family is one of two related families in type VI secretion systems that contain an ImpA-related N-terminal domain (pfam06812).
Probab=20.01 E-value=1.8e+02 Score=24.55 Aligned_cols=62 Identities=21% Similarity=0.224 Sum_probs=41.3
Q ss_pred hHHHHHHHHHHHHcCCHHHHHHHHHHhchHHHccCCcceehhchHHHHHHHhhhchHHHHHHHH
Q 030912 10 DMEMRKRILHFALEGNALKAIELTEELAQDLLEKNKDLHFDLLSLHFVELVCSRKCTEALEFAQ 73 (169)
Q Consensus 10 ~~~~R~~I~~~I~~G~i~~Ai~~i~~~~p~ll~~~~~L~F~L~~q~fIElir~~~~~eAi~~ar 73 (169)
....+.+.+..+.+|.++.|+.|+++..|..-......+.+|..-++.+- .|..+-|+.+-+
T Consensus 213 ~~~~~~eA~~l~~~~gl~~Al~~L~~~~~~~~s~R~rf~~rL~~A~l~~~--~g~~~lA~~ll~ 274 (301)
T TIGR03362 213 WEELREEARALAAEGGLEAALQRLQQRLAQAREPRERFHWRLLLARLLEQ--AGKAELAQQLYA 274 (301)
T ss_pred HHHHHHHHHHHHHcCCHHHHHHHHHhhcccCCChHHHHHHHHHHHHHHHH--cCCHHHHHHHHH
Confidence 34556778999999999999999998777665554555556555555543 344344443333
Done!