Query 027999
Match_columns 215
No_of_seqs 130 out of 744
Neff 8.0
Searched_HMMs 46136
Date Fri Mar 29 04:43:15 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/027999.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/027999hhsearch_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 3.7E-41 8E-46 272.7 20.4 197 3-199 14-211 (228)
2 PF10607 CLTH: CTLH/CRA C-term 100.0 1.9E-32 4.1E-37 211.7 15.3 140 54-195 2-144 (145)
3 KOG0396 Uncharacterized conser 100.0 6.7E-30 1.5E-34 217.5 16.2 176 9-187 109-285 (389)
4 KOG2817 Predicted E3 ubiquitin 99.9 1.8E-26 4E-31 198.5 18.0 175 10-186 110-290 (394)
5 smart00757 CRA CT11-RanBPM. pr 99.8 1.1E-17 2.4E-22 120.9 11.7 94 107-200 2-98 (99)
6 smart00668 CTLH C-terminal to 99.5 1.8E-13 3.9E-18 89.2 6.4 56 54-109 2-57 (58)
7 KOG0293 WD40 repeat-containing 99.4 1.4E-12 2.9E-17 113.5 11.3 170 12-192 14-186 (519)
8 KOG1477 SPRY domain-containing 98.9 4.9E-10 1.1E-14 101.4 2.2 195 19-214 253-468 (469)
9 PF08513 LisH: LisH; InterPro 98.6 5.4E-08 1.2E-12 53.5 3.8 27 16-42 1-27 (27)
10 smart00667 LisH Lissencephaly 98.4 6.8E-07 1.5E-11 51.2 4.6 32 14-45 2-33 (34)
11 COG5109 Uncharacterized conser 98.3 1.4E-05 3E-10 68.0 11.5 185 6-193 91-300 (396)
12 KOG0275 Conserved WD40 repeat- 97.8 0.00025 5.4E-09 61.1 10.9 168 11-197 3-176 (508)
13 KOG1333 Uncharacterized conser 94.0 0.28 6E-06 39.8 7.2 137 16-157 6-151 (241)
14 PF09398 FOP_dimer: FOP N term 93.2 0.19 4.2E-06 34.8 4.4 31 17-47 20-50 (81)
15 PF14559 TPR_19: Tetratricopep 86.6 4 8.6E-05 26.0 6.3 56 63-123 1-56 (68)
16 PF10607 CLTH: CTLH/CRA C-term 82.9 9.4 0.0002 28.7 7.8 59 21-80 7-67 (145)
17 TIGR03362 VI_chp_7 type VI sec 79.3 21 0.00046 30.9 9.5 98 17-116 134-274 (301)
18 PF04494 TFIID_90kDa: WD40 ass 78.9 4.8 0.0001 30.7 4.9 48 88-137 38-85 (142)
19 KOG0273 Beta-transducin family 78.3 0.82 1.8E-05 41.5 0.5 105 11-116 1-115 (524)
20 cd08044 TAF5_NTD2 TAF5_NTD2 is 78.1 1.3 2.8E-05 33.5 1.5 48 89-138 28-75 (133)
21 PF04053 Coatomer_WDAD: Coatom 77.1 11 0.00025 34.3 7.6 76 17-116 296-371 (443)
22 PF13838 Clathrin_H_link: Clat 60.6 28 0.0006 23.1 4.7 41 93-133 7-47 (66)
23 PF01726 LexA_DNA_bind: LexA D 60.3 25 0.00054 23.1 4.5 48 14-67 7-54 (65)
24 PF09295 ChAPs: ChAPs (Chs5p-A 58.8 1.4E+02 0.003 26.9 11.0 97 10-117 163-259 (395)
25 KOG2910 Uncharacterized conser 56.6 74 0.0016 25.8 7.3 63 55-119 41-116 (209)
26 PRK02289 4-oxalocrotonate taut 53.4 23 0.00049 22.5 3.4 26 153-178 12-37 (60)
27 PRK10564 maltose regulon perip 53.3 16 0.00035 31.6 3.4 24 56-79 260-283 (303)
28 PF10602 RPN7: 26S proteasome 52.4 1.1E+02 0.0025 24.0 11.8 112 11-123 31-144 (177)
29 PF14276 DUF4363: Domain of un 52.2 31 0.00067 25.2 4.4 47 55-101 30-76 (121)
30 PTZ00196 60S ribosomal protein 50.8 32 0.0007 24.7 4.1 44 92-135 48-91 (98)
31 PF07729 FCD: FCD domain; Int 50.7 33 0.00071 23.9 4.3 29 52-80 95-123 (125)
32 KOG2437 Muskelin [Signal trans 50.1 62 0.0014 30.3 6.7 62 18-85 168-229 (723)
33 KOG0292 Vesicle coat complex C 50.0 5.3 0.00011 39.4 -0.1 48 18-79 622-669 (1202)
34 PRK00794 flbT flagellar biosyn 49.5 92 0.002 23.6 6.6 31 52-82 92-122 (132)
35 PF12895 Apc3: Anaphase-promot 49.3 30 0.00064 23.1 3.7 52 59-116 31-82 (84)
36 PF07035 Mic1: Colon cancer-as 48.0 1.1E+02 0.0023 24.2 7.0 88 11-118 25-115 (167)
37 PF06794 UPF0270: Uncharacteri 47.3 59 0.0013 21.8 4.7 44 12-68 7-50 (70)
38 KOG0640 mRNA cleavage stimulat 46.8 35 0.00076 29.9 4.4 33 14-46 10-42 (430)
39 KOG2659 LisH motif-containing 45.8 1.1E+02 0.0023 25.5 7.0 68 13-80 60-130 (228)
40 PF13432 TPR_16: Tetratricopep 45.1 74 0.0016 19.7 6.1 55 60-119 4-58 (65)
41 PF07079 DUF1347: Protein of u 45.1 97 0.0021 28.7 7.1 54 54-107 129-190 (549)
42 PF14689 SPOB_a: Sensor_kinase 43.7 72 0.0016 20.5 4.7 34 51-84 21-54 (62)
43 COG4105 ComL DNA uptake lipopr 42.3 2.1E+02 0.0046 24.2 9.0 65 54-124 35-103 (254)
44 PF04840 Vps16_C: Vps16, C-ter 41.6 1.3E+02 0.0028 26.2 7.3 77 24-117 185-262 (319)
45 PF01158 Ribosomal_L36e: Ribos 40.7 50 0.0011 23.7 3.8 32 92-123 48-79 (98)
46 KOG1156 N-terminal acetyltrans 38.2 3.8E+02 0.0083 26.0 14.5 79 54-137 186-264 (700)
47 KOG3060 Uncharacterized conser 37.7 2.6E+02 0.0057 23.9 10.6 106 17-133 53-161 (289)
48 PF07721 TPR_4: Tetratricopept 37.7 42 0.00091 17.3 2.4 17 61-77 9-25 (26)
49 COG5443 FlbT Flagellar biosynt 37.2 58 0.0013 24.7 3.8 58 25-82 65-123 (148)
50 COG5051 RPL36A Ribosomal prote 36.8 87 0.0019 22.0 4.3 43 95-140 53-95 (97)
51 TIGR02531 yecD_yerC TrpR-relat 36.7 1.2E+02 0.0027 21.1 5.2 56 18-76 4-59 (88)
52 PF10827 DUF2552: Protein of u 36.3 24 0.00051 23.8 1.4 16 68-83 60-75 (79)
53 PF03477 ATP-cone: ATP cone do 36.1 35 0.00077 23.3 2.5 28 12-39 55-82 (90)
54 PF00627 UBA: UBA/TS-N domain; 35.8 56 0.0012 18.5 2.9 18 59-76 18-37 (37)
55 PRK01271 4-oxalocrotonate taut 35.2 65 0.0014 21.9 3.5 26 153-178 13-38 (76)
56 PF13371 TPR_9: Tetratricopept 34.5 1.2E+02 0.0026 19.1 6.9 53 63-120 5-57 (73)
57 PF07378 FlbT: Flagellar prote 34.1 2E+02 0.0044 21.5 6.6 30 52-81 90-119 (126)
58 PF07208 DUF1414: Protein of u 33.2 76 0.0016 19.3 3.1 20 153-172 24-43 (44)
59 PRK02220 4-oxalocrotonate taut 33.2 66 0.0014 20.1 3.2 26 153-178 12-37 (61)
60 smart00299 CLH Clathrin heavy 33.0 1.9E+02 0.0041 21.1 6.2 11 67-77 110-120 (140)
61 KOG4594 Sequence-specific sing 32.4 57 0.0012 28.1 3.4 28 15-42 17-44 (354)
62 PF09312 SurA_N: SurA N-termin 32.3 93 0.002 22.6 4.3 48 9-65 63-113 (118)
63 PRK09239 chorismate mutase; Pr 32.1 1.9E+02 0.0041 20.8 5.8 50 151-201 50-102 (104)
64 cd00491 4Oxalocrotonate_Tautom 31.7 84 0.0018 19.2 3.5 25 154-178 12-36 (58)
65 PF01361 Tautomerase: Tautomer 31.6 62 0.0013 20.2 2.9 25 154-178 12-36 (60)
66 PRK01964 4-oxalocrotonate taut 31.0 77 0.0017 20.1 3.3 26 153-178 12-37 (64)
67 TIGR01470 cysG_Nterm siroheme 30.9 1.5E+02 0.0032 24.0 5.6 64 55-119 135-204 (205)
68 PF15658 Latrotoxin_C: Latroto 30.7 2E+02 0.0043 21.6 5.7 52 27-78 43-94 (127)
69 cd00194 UBA Ubiquitin Associat 30.6 82 0.0018 17.6 3.0 13 65-77 25-37 (38)
70 TIGR00083 ribF riboflavin kina 30.6 35 0.00077 29.3 2.0 51 29-80 115-169 (288)
71 PRK11534 DNA-binding transcrip 30.3 87 0.0019 25.2 4.2 28 53-80 183-210 (224)
72 TIGR00013 taut 4-oxalocrotonat 29.6 96 0.0021 19.4 3.5 26 153-178 12-37 (63)
73 PF09976 TPR_21: Tetratricopep 29.1 2.4E+02 0.0051 20.8 9.8 60 55-117 50-110 (145)
74 PF13424 TPR_12: Tetratricopep 28.5 1.6E+02 0.0036 18.8 5.6 56 63-119 15-73 (78)
75 COG0268 RpsT Ribosomal protein 28.5 1E+02 0.0022 21.7 3.7 29 57-85 32-60 (88)
76 PF04840 Vps16_C: Vps16, C-ter 28.4 2.2E+02 0.0048 24.7 6.6 62 9-78 201-262 (319)
77 TIGR03338 phnR_burk phosphonat 28.3 1.1E+02 0.0024 24.2 4.5 29 52-80 178-206 (212)
78 PF14691 Fer4_20: Dihydroprymi 28.3 80 0.0017 23.0 3.3 25 57-81 42-66 (111)
79 PRK10225 DNA-binding transcrip 27.9 98 0.0021 25.5 4.2 24 97-120 202-225 (257)
80 PF12931 Sec16_C: Sec23-bindin 27.7 62 0.0014 27.5 3.0 21 59-79 1-21 (284)
81 PRK12791 flbT flagellar biosyn 27.2 1.3E+02 0.0027 22.8 4.2 30 53-82 90-119 (131)
82 COG3492 Uncharacterized protei 26.6 1.7E+02 0.0037 20.7 4.5 45 153-197 6-50 (104)
83 KOG0396 Uncharacterized conser 26.4 2.6E+02 0.0055 25.1 6.5 65 21-86 158-224 (389)
84 PRK00745 4-oxalocrotonate taut 26.2 1.1E+02 0.0023 19.1 3.3 25 153-177 12-36 (62)
85 PF09048 Cro: Cro; InterPro: 26.1 1.4E+02 0.003 19.4 3.6 17 22-38 6-22 (59)
86 KOG1920 IkappaB kinase complex 25.8 7.9E+02 0.017 25.8 11.0 85 18-119 941-1026(1265)
87 PF10075 PCI_Csn8: COP9 signal 25.6 2.1E+02 0.0045 21.4 5.3 55 59-116 10-64 (143)
88 PRK04984 fatty acid metabolism 25.6 1.2E+02 0.0026 24.6 4.3 29 52-80 188-216 (239)
89 smart00550 Zalpha Z-DNA-bindin 25.4 1.4E+02 0.0029 19.5 3.7 50 13-69 2-52 (68)
90 smart00165 UBA Ubiquitin assoc 25.3 1.1E+02 0.0024 16.9 3.0 12 65-76 25-36 (37)
91 TIGR02812 fadR_gamma fatty aci 24.9 1.3E+02 0.0027 24.4 4.3 28 53-80 188-215 (235)
92 PF13934 ELYS: Nuclear pore co 24.8 3.9E+02 0.0084 21.9 10.4 49 20-76 48-101 (226)
93 PF14691 Fer4_20: Dihydroprymi 24.8 88 0.0019 22.8 3.0 30 92-122 38-67 (111)
94 COG3071 HemY Uncharacterized e 24.7 5.3E+02 0.011 23.4 8.9 123 8-142 179-340 (400)
95 PF12854 PPR_1: PPR repeat 24.7 1.2E+02 0.0025 16.7 2.9 21 58-78 12-32 (34)
96 PRK10421 DNA-binding transcrip 24.2 1.5E+02 0.0032 24.4 4.6 30 52-81 189-218 (253)
97 TIGR00756 PPR pentatricopeptid 23.9 1.2E+02 0.0026 15.6 3.0 21 59-79 6-26 (35)
98 COG1802 GntR Transcriptional r 23.9 3.3E+02 0.0072 21.9 6.6 29 53-81 184-212 (230)
99 PRK00239 rpsT 30S ribosomal pr 23.7 1.4E+02 0.003 20.9 3.7 29 57-85 32-60 (88)
100 cd02064 FAD_synthetase_N FAD s 23.6 55 0.0012 25.7 1.8 50 29-79 116-170 (180)
101 PRK07143 hypothetical protein; 23.5 55 0.0012 28.0 1.9 23 58-80 153-175 (279)
102 KOG3452 60S ribosomal protein 23.2 2.2E+02 0.0048 20.4 4.6 45 92-139 50-94 (102)
103 PRK11414 colanic acid/biofilm 23.2 1.3E+02 0.0029 24.1 4.1 29 52-80 180-208 (221)
104 KOG1538 Uncharacterized conser 22.9 2E+02 0.0043 28.1 5.5 56 61-117 781-842 (1081)
105 PRK11788 tetratricopeptide rep 22.9 4.8E+02 0.01 22.3 10.6 20 60-79 148-167 (389)
106 TIGR01159 DRP1 density-regulat 22.4 73 0.0016 25.3 2.3 21 66-86 20-40 (173)
107 PF01671 ASFV_360: African swi 22.2 1.8E+02 0.004 23.8 4.5 87 35-122 3-111 (215)
108 PRK04966 hypothetical protein; 22.2 88 0.0019 21.1 2.3 45 12-69 7-51 (72)
109 PRK03837 transcriptional regul 22.2 1.7E+02 0.0037 23.7 4.6 30 52-81 198-227 (241)
110 PF06910 MEA1: Male enhanced a 22.0 1.8E+02 0.004 23.0 4.4 39 125-163 123-161 (174)
111 PRK09990 DNA-binding transcrip 22.0 1.5E+02 0.0032 24.3 4.2 27 54-80 199-225 (251)
112 KOG3239 Density-regulated prot 22.0 70 0.0015 25.5 2.0 22 65-86 27-48 (193)
113 PF12862 Apc5: Anaphase-promot 21.7 2.8E+02 0.006 19.0 6.9 29 59-87 4-32 (94)
114 PRK11523 DNA-binding transcrip 21.5 1.7E+02 0.0037 24.0 4.5 28 53-80 191-218 (253)
115 PF14498 Glyco_hyd_65N_2: Glyc 21.3 77 0.0017 26.0 2.3 30 51-80 52-81 (236)
116 PRK00304 hypothetical protein; 21.2 94 0.002 21.2 2.3 43 13-69 8-50 (75)
117 PF01649 Ribosomal_S20p: Ribos 20.9 1.7E+02 0.0038 20.2 3.7 29 57-85 31-59 (84)
118 PF09862 DUF2089: Protein of u 20.8 2.1E+02 0.0045 21.1 4.2 54 19-75 39-111 (113)
119 PRK09464 pdhR transcriptional 20.7 1.9E+02 0.0041 23.7 4.6 27 54-80 198-225 (254)
120 PF12793 SgrR_N: Sugar transpo 20.2 1.6E+02 0.0036 21.5 3.6 23 56-78 73-95 (115)
No 1
>KOG2659 consensus LisH motif-containing protein [Cytoskeleton]
Probab=100.00 E-value=3.7e-41 Score=272.73 Aligned_cols=197 Identities=36% Similarity=0.530 Sum_probs=187.6
Q ss_pred CChhhhhcCCCCHHHHHHHHHHHHHhhcHHHHHHHHHHhhCCCCCCCCHHhHHHHHHHHHHHHcCCHHHHHHHHHHhcHH
Q 027999 3 VDPRQYEHIAINDNDIHNIVLSYLVHNCYKETVDSFISCTGMKQPANCLEDMEMRKRILHFALEGNALKAIELTEELAQD 82 (215)
Q Consensus 3 ~~~~~~~~~~~~~~~l~~lI~~yL~~~Gy~eta~~f~~e~~~~~~~~~~~~~~~r~~I~~~I~~G~i~~Ai~~~~~~~p~ 82 (215)
.+.+.+.++++..+++|+||++||+|+||.|+|+.|.+|+|++.|..+.+.+..|.+|+.+|..|+|..||+.+++++|.
T Consensus 14 ~w~~~~~~~~~~~~d~n~LVmnylv~eg~~EaA~~Fa~e~~i~~~~~d~~~~~eR~~Ir~~I~~G~Ie~Aie~in~l~Pe 93 (228)
T KOG2659|consen 14 EWEEQLMKVSVMREDLNRLVMNYLVHEGYVEAAEKFAKESGIKPPSIDLDSMDERLQIRRAIEEGQIEEAIEKVNQLNPE 93 (228)
T ss_pred hhHHHHhccCcchhhHHHHHHHHHHhccHHHHHHHhccccCCCCccCchhhHhHHHHHHHHHHhccHHHHHHHHHHhChH
Confidence 35678999999999999999999999999999999999999998777899999999999999999999999999999999
Q ss_pred HHccCCcchhhhhHHHHHHHHhccchhhHHHHHHHhccccCC-chhHHHHHHHHHhHhccCCCCCCchhhhCCHHHHHHH
Q 027999 83 LLEKNKDLHFDLLSLHFVELVCSRKCTEALEFAQTKLTPFGK-VQKYVEKLEDFMALLAYEEPEKSPMFHLLSLEYRQHV 161 (215)
Q Consensus 83 l~~~~~~l~F~L~~q~fiEli~~~~~~~Al~~ar~~l~~~~~-~~~~~~~l~~~~~lla~~~~~~s~~~~ll~~~~r~~l 161 (215)
+++.|.+|.|.|++|+||||||.|...+||+|+|++++|++. ++.+..+++++|++|+|++|+.||++++++.++|.++
T Consensus 94 iLd~n~~l~F~Lq~q~lIEliR~~~~eeal~F~q~~LA~~a~e~~~~~~elE~~l~lLvf~~~~~sp~~~l~~~s~R~kv 173 (228)
T KOG2659|consen 94 ILDTNRELFFHLQQLHLIELIREGKTEEALEFAQTKLAPFAEENPKKMEELERTLALLVFELSQESPSAELLSQSLRQKV 173 (228)
T ss_pred HHccchhHHHHHHHHHHHHHHHhhhHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHcCCcccCcHHHHHHHHHHHHH
Confidence 999999999999999999999999999999999999999996 6789999999999999999999999999999999999
Q ss_pred HHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHHHHHhhc
Q 027999 162 ADNLNRAILAHAERPRYAAMERLIQQTTAVRQCLSQEL 199 (215)
Q Consensus 162 a~~vn~~il~~~~~~~~s~Le~l~~~~~~~~~~l~~~~ 199 (215)
|+.||++|+.+++.+..+.|..|++...+.+..+..+.
T Consensus 174 A~~vN~aiL~~~~~~~~~~l~~llk~~~~~~~~~~~~~ 211 (228)
T KOG2659|consen 174 ASEVNSAILASQEHESEPKLPFLLKLISWAQEELDREK 211 (228)
T ss_pred HHHHHHHHHHHhcccccchHHHHHHHHHHHHHHHhHhh
Confidence 99999999999999999999999998888887776643
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=1.9e-32 Score=211.75 Aligned_cols=140 Identities=35% Similarity=0.577 Sum_probs=132.7
Q ss_pred HHHHHHHHHHHHcCCHHHHHHHHHHhcHHHHccCCcchhhhhHHHHHHHHhccchhhHHHHHHHhccccCCchhHHHHHH
Q 027999 54 MEMRKRILHFALEGNALKAIELTEELAQDLLEKNKDLHFDLLSLHFVELVCSRKCTEALEFAQTKLTPFGKVQKYVEKLE 133 (215)
Q Consensus 54 ~~~r~~I~~~I~~G~i~~Ai~~~~~~~p~l~~~~~~l~F~L~~q~fiEli~~~~~~~Al~~ar~~l~~~~~~~~~~~~l~ 133 (215)
+.+|++|+++|++||+++|++|+++++|.+++.++.++|.|++|+|||||++|++.+||+|||+++.++. ..+.++++
T Consensus 2 ~~~r~~I~~~I~~g~i~~Ai~w~~~~~~~l~~~~~~L~f~L~~q~fiell~~~~~~~Ai~y~r~~l~~~~--~~~~~~l~ 79 (145)
T PF10607_consen 2 FKERKKIRQAILNGDIDPAIEWLNENFPELLKRNSSLEFELRCQQFIELLREGDIMEAIEYARKHLSPFN--DEFLEELK 79 (145)
T ss_pred HHHHHHHHHHHHcCCHHHHHHHHHHcCHHHHhcCCchhHHHHHHHHHHHHHHHhHHHHHHHHHHHhhhhH--HHHHHHHH
Confidence 6899999999999999999999999999999999999999999999999999999999999999997775 46889999
Q ss_pred HHHhHhccCCCCC---CchhhhCCHHHHHHHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHHHH
Q 027999 134 DFMALLAYEEPEK---SPMFHLLSLEYRQHVADNLNRAILAHAERPRYAAMERLIQQTTAVRQCL 195 (215)
Q Consensus 134 ~~~~lla~~~~~~---s~~~~ll~~~~r~~la~~vn~~il~~~~~~~~s~Le~l~~~~~~~~~~l 195 (215)
++|++|+|++|.. +|+++++++++|+.|++.||+++|..+|+|+.|+|+.++++..++...+
T Consensus 80 ~~~~lL~~~~~~~~~~s~~~~l~~~~~~~~la~~~~~~~l~~~~~~~~s~L~~~~~~g~~~l~~l 144 (145)
T PF10607_consen 80 KLMSLLAYPDPEEPLPSPYKELLSPERREELAEEFNSAILKSYGLPKESPLEVILKAGLSALKTL 144 (145)
T ss_pred HHHHHHHcCCcccccchHHHHHhChHHHHHHHHHHHHHHHHHhCcCCCCHHHHHHHHHHHHhhhc
Confidence 9999999999887 8999999999999999999999999999999999999999988876543
No 3
>KOG0396 consensus Uncharacterized conserved protein [Function unknown]
Probab=99.97 E-value=6.7e-30 Score=217.46 Aligned_cols=176 Identities=19% Similarity=0.225 Sum_probs=166.0
Q ss_pred hcCCCCHHHHHHHHHHHHHhhcHHHHHHHHHHhhCCCCCCCCHHhHHHHHHHHHHHHcCCHHHHHHHHHHhcHHHHccCC
Q 027999 9 EHIAINDNDIHNIVLSYLVHNCYKETVDSFISCTGMKQPANCLEDMEMRKRILHFALEGNALKAIELTEELAQDLLEKNK 88 (215)
Q Consensus 9 ~~~~~~~~~l~~lI~~yL~~~Gy~eta~~f~~e~~~~~~~~~~~~~~~r~~I~~~I~~G~i~~Ai~~~~~~~p~l~~~~~ 88 (215)
+..++++..++++|++||.|+||.+||..|.+++.+.... +.+.+...+.|+++|+.|++.+|+.||++|.-.|-+.++
T Consensus 109 ~~~~w~r~~l~r~vvdhmlr~gy~~~A~~L~K~s~ledlv-D~Dv~~~~~~I~~sll~~~l~~~Lswc~ehk~~LkK~~S 187 (389)
T KOG0396|consen 109 NSRKWPRNKLDRFVVDHMLRNGYFGAAVLLGKKSQLEDLV-DSDVYKRAYGIRDSLLAGELEPALSWCKEHKVELKKEES 187 (389)
T ss_pred HHHHhHHHHHHHHHHHHHHHcCchhHHHHHHHhhhhhhhH-hHHHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHHhccc
Confidence 3467889999999999999999999999999999998665 588999999999999999999999999999999999999
Q ss_pred cchhhhhHHHHHHHHhccchhhHHHHHHHhccccCCchhHHHHHHHHHhHhccC-CCCCCchhhhCCHHHHHHHHHHHHH
Q 027999 89 DLHFDLLSLHFVELVCSRKCTEALEFAQTKLTPFGKVQKYVEKLEDFMALLAYE-EPEKSPMFHLLSLEYRQHVADNLNR 167 (215)
Q Consensus 89 ~l~F~L~~q~fiEli~~~~~~~Al~~ar~~l~~~~~~~~~~~~l~~~~~lla~~-~~~~s~~~~ll~~~~r~~la~~vn~ 167 (215)
.++|.++.|+|||||+.++..+||+|++++|+|++ ..+..+++.+||++||+ .++.++|..+++..+|+.+++.|-+
T Consensus 188 ~lEf~lRlQefIELi~~~~~~~Ai~~akk~f~~~~--~~~~~~Lk~a~g~laF~~~t~~sky~~l~~~~rw~~l~~lF~s 265 (389)
T KOG0396|consen 188 SLEFQLRLQEFIELIKVDNYDKAIAFAKKHFAPWA--KSHKSDLKLAMGLLAFPKYTSSSKYLNLLTADRWSVLADLFLS 265 (389)
T ss_pred hhhhHHHHHHHHHHHHhccHHHHHHHHHHHHhhhh--hhhHHHHHHHHHhhcCccccCcccccCcccHHHHHHHHHHhhH
Confidence 99999999999999999999999999999999999 68899999999999996 5667779999999999999999999
Q ss_pred HHHHhcCCCCCcHHHHHHHH
Q 027999 168 AILAHAERPRYAAMERLIQQ 187 (215)
Q Consensus 168 ~il~~~~~~~~s~Le~l~~~ 187 (215)
..++.+|+|..|+|-+.++.
T Consensus 266 ~a~~l~~i~~~~~L~~~l~~ 285 (389)
T KOG0396|consen 266 EALKLFGIPINPALTIYLQA 285 (389)
T ss_pred HHHHHhCCCCCcHHHHHHHh
Confidence 99999999999999999985
No 4
>KOG2817 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.95 E-value=1.8e-26 Score=198.52 Aligned_cols=175 Identities=22% Similarity=0.357 Sum_probs=159.2
Q ss_pred cCCCCHHH-HHHHHHHHHHhhcHHHHHHHHHHhhCCCCC-CCCHHhHHHHHHHHHHHHcCCHHHHHHHHHHhcHHHHccC
Q 027999 10 HIAINDND-IHNIVLSYLVHNCYKETVDSFISCTGMKQP-ANCLEDMEMRKRILHFALEGNALKAIELTEELAQDLLEKN 87 (215)
Q Consensus 10 ~~~~~~~~-l~~lI~~yL~~~Gy~eta~~f~~e~~~~~~-~~~~~~~~~r~~I~~~I~~G~i~~Ai~~~~~~~p~l~~~~ 87 (215)
++..+... +|.+|+.|++++|..++|..|++|+|...+ ......+.+.++|.++|..||+.+|++|+..+...|.+.+
T Consensus 110 ~v~~~~~~~ln~ai~~h~~rqGm~dv~~~l~~Ea~~~~~~~~~~~~F~el~~Iv~~lke~Dl~~aLeWa~~~~~~L~~~~ 189 (394)
T KOG2817|consen 110 SVDFDTSQVLNEAIVYHFYRQGMDDVGECLIKEAGLSEDESKSRTEFVELNQIVEALKERDLEPALEWAESNRQKLKEKS 189 (394)
T ss_pred CcChhHHHHHHHHHHHHHHHcCchHHHHHHHHHhcCCCcchhhhhhHHHHHHHHHHHHhccchhHHHHHHHhhhhhcccc
Confidence 44455444 499999999999999999999999999765 3345678899999999999999999999999999999999
Q ss_pred CcchhhhhHHHHHHHHhccchh--hHHHHHHHhccccCCchhHHHHHHHHHhHhcc--CCCCCCchhhhCCHHHHHHHHH
Q 027999 88 KDLHFDLLSLHFVELVCSRKCT--EALEFAQTKLTPFGKVQKYVEKLEDFMALLAY--EEPEKSPMFHLLSLEYRQHVAD 163 (215)
Q Consensus 88 ~~l~F~L~~q~fiEli~~~~~~--~Al~~ar~~l~~~~~~~~~~~~l~~~~~lla~--~~~~~s~~~~ll~~~~r~~la~ 163 (215)
+.|+|.|+.++|+++++.|... +||.|||++++||+ ..+.++||.+|++|.| ...++|||.+++++..|..+..
T Consensus 190 s~LE~~Lh~l~fl~l~~~g~~~~~eAl~Yar~~~~~F~--~~~~~eIQklm~sl~~l~~gl~~spy~~~ls~~~w~~~~~ 267 (394)
T KOG2817|consen 190 SSLEFKLHSLHFLSLIRGGKSDQREALRYARTHFAPFV--ADHLREIQKLMGSLLYLRNGLEKSPYSEILSPKLWKELTE 267 (394)
T ss_pred ccHHHHHHHHHHHHHHhcCCcCcHHHHHHHHHhcCccc--cchHHHHHHHHHHHHHHHcCCCCCChHHHhCHHHHHHHHH
Confidence 9999999999999999998766 99999999999998 6668999999999999 3478999999999999999999
Q ss_pred HHHHHHHHhcCCCCCcHHHHHHH
Q 027999 164 NLNRAILAHAERPRYAAMERLIQ 186 (215)
Q Consensus 164 ~vn~~il~~~~~~~~s~Le~l~~ 186 (215)
+|-+..|..+|+|.+|||..++.
T Consensus 268 ~f~r~ycallg~s~eSPL~v~v~ 290 (394)
T KOG2817|consen 268 EFTREYCALLGISVESPLSVLVN 290 (394)
T ss_pred HHHHHHHHHcCCCccCcHHHHHH
Confidence 99999999999999999988776
No 5
>smart00757 CRA CT11-RanBPM. protein-protein interaction domain present in crown eukaryotes (plants, animals, fungi)
Probab=99.76 E-value=1.1e-17 Score=120.91 Aligned_cols=94 Identities=39% Similarity=0.560 Sum_probs=85.8
Q ss_pred chhhHHHHHHHhccccCC-chhHHHHHHHHHhHhccCCC-CCCchhhhCCHHHHHHHHHHHHHHHHHhc-CCCCCcHHHH
Q 027999 107 KCTEALEFAQTKLTPFGK-VQKYVEKLEDFMALLAYEEP-EKSPMFHLLSLEYRQHVADNLNRAILAHA-ERPRYAAMER 183 (215)
Q Consensus 107 ~~~~Al~~ar~~l~~~~~-~~~~~~~l~~~~~lla~~~~-~~s~~~~ll~~~~r~~la~~vn~~il~~~-~~~~~s~Le~ 183 (215)
++.+||+|||+++++|.. ++...++|+++|++|+|+++ +.+||++++++++|+.+++.||++||..+ |.+.+|+|+.
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 578999999999999995 44457899999999999998 89999999999999999999999999998 9999999999
Q ss_pred HHHHHHHHHHHHHhhcC
Q 027999 184 LIQQTTAVRQCLSQELG 200 (215)
Q Consensus 184 l~~~~~~~~~~l~~~~~ 200 (215)
++++..++...+....+
T Consensus 82 ~~~~~~~~~~~l~~~~~ 98 (99)
T smart00757 82 LLSAGLAALKTLLEKGG 98 (99)
T ss_pred HHHHHHHHHHHHHHhcC
Confidence 99999999888876554
No 6
>smart00668 CTLH C-terminal to LisH motif. Alpha-helical motif of unknown function.
Probab=99.46 E-value=1.8e-13 Score=89.22 Aligned_cols=56 Identities=38% Similarity=0.524 Sum_probs=52.6
Q ss_pred HHHHHHHHHHHHcCCHHHHHHHHHHhcHHHHccCCcchhhhhHHHHHHHHhccchh
Q 027999 54 MEMRKRILHFALEGNALKAIELTEELAQDLLEKNKDLHFDLLSLHFVELVCSRKCT 109 (215)
Q Consensus 54 ~~~r~~I~~~I~~G~i~~Ai~~~~~~~p~l~~~~~~l~F~L~~q~fiEli~~~~~~ 109 (215)
+..|..|+++|+.|+|++|++|++.++|.+.+.++.+.|.|++|+|||+++.|+..
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 46889999999999999999999999999999999999999999999999988653
No 7
>KOG0293 consensus WD40 repeat-containing protein [Function unknown]
Probab=99.42 E-value=1.4e-12 Score=113.45 Aligned_cols=170 Identities=16% Similarity=0.165 Sum_probs=139.3
Q ss_pred CCCHHHHHHHHHHHHHhhcHHHHHHHHHHhhCCCCCCCCHHhHHHHHHHHHHHHcCCHHHHHHHHHHh-cHHHHccCCcc
Q 027999 12 AINDNDIHNIVLSYLVHNCYKETVDSFISCTGMKQPANCLEDMEMRKRILHFALEGNALKAIELTEEL-AQDLLEKNKDL 90 (215)
Q Consensus 12 ~~~~~~l~~lI~~yL~~~Gy~eta~~f~~e~~~~~~~~~~~~~~~r~~I~~~I~~G~i~~Ai~~~~~~-~p~l~~~~~~l 90 (215)
-+.+.++.+++.+.|+..||.+++..++.|+|+..+. +.-+.+.+++++|+|+.++..+... +++ ..+....
T Consensus 14 likk~efi~il~q~l~slgy~~S~~~lE~es~ll~~t------at~klf~q~vlqg~w~q~v~~~~~i~~~d-e~~~~ea 86 (519)
T KOG0293|consen 14 LIKKGEFIRILWQILYSLGYDHSSPLLEWESGLLIPT------ATTKLFDQQVLQGQWDQQVMSLVRISFED-ERNRKEA 86 (519)
T ss_pred eeccchhhHhHHHHHHhcCccccchhhHHhhCccccc------chHHHHHHHHHcccHHHHHHHHhhccCcc-hhhhHHH
Confidence 3567789999999999999999999999999997665 4567888999999999999888776 555 5556789
Q ss_pred hhhhhHHHHHHHHhccchhhHHHHHHHhccccCCchhHHHHHHHHHhHhccCCCCCCch--hhhCCHHHHHHHHHHHHHH
Q 027999 91 HFDLLSLHFVELVCSRKCTEALEFAQTKLTPFGKVQKYVEKLEDFMALLAYEEPEKSPM--FHLLSLEYRQHVADNLNRA 168 (215)
Q Consensus 91 ~F~L~~q~fiEli~~~~~~~Al~~ar~~l~~~~~~~~~~~~l~~~~~lla~~~~~~s~~--~~ll~~~~r~~la~~vn~~ 168 (215)
.|.+.+|.|+|.++.|++..|+...|..+.+...+ .+.+.++.+.|.+++...+.. -.-.....|..|.+++...
T Consensus 87 ~fLv~kQ~fLEf~k~~~is~al~~l~~~~~~lr~~---~kk~~el~~sll~sn~~~~ne~~~~~~~~n~R~~ll~elsky 163 (519)
T KOG0293|consen 87 MFLVNKQIFLEFLKTGSISHALPVLRNPVLYLRKN---KKKFHELASSLLVSNDQFSNEENTTAQLNNERDKLLDELSKY 163 (519)
T ss_pred HHHHHHHHHHHHHhhccHhhhhHhhhcchhhhhhh---HHHHHHHHHHHhccccccccccchhhhhchhHHHHHHHHHhh
Confidence 99999999999999999999999999877776544 467788889999875332221 0111234588899999999
Q ss_pred HHHhcCCCCCcHHHHHHHHHHHHH
Q 027999 169 ILAHAERPRYAAMERLIQQTTAVR 192 (215)
Q Consensus 169 il~~~~~~~~s~Le~l~~~~~~~~ 192 (215)
|....-+| +.+||.|++|+...|
T Consensus 164 i~p~illP-~rRLehLl~qAv~~Q 186 (519)
T KOG0293|consen 164 IPPNILLP-KRRLEHLLEQAVKYQ 186 (519)
T ss_pred CCHhhcCC-hHHHHHHHHHHHHHH
Confidence 99999997 689999999999885
No 8
>KOG1477 consensus SPRY domain-containing proteins [General function prediction only]
Probab=98.90 E-value=4.9e-10 Score=101.41 Aligned_cols=195 Identities=18% Similarity=0.101 Sum_probs=154.2
Q ss_pred HHHHHHHHHhhcHHHHHHHHHHhhCCCCCC---CCH-HhHH-------HHHHHHHHHHcCCHHHHHHHHHHhcHHHHc--
Q 027999 19 HNIVLSYLVHNCYKETVDSFISCTGMKQPA---NCL-EDME-------MRKRILHFALEGNALKAIELTEELAQDLLE-- 85 (215)
Q Consensus 19 ~~lI~~yL~~~Gy~eta~~f~~e~~~~~~~---~~~-~~~~-------~r~~I~~~I~~G~i~~Ai~~~~~~~p~l~~-- 85 (215)
...+..|+++.||.+++..|+..+.-..++ ... .... .+...+.-+-.|.+..+++.+.+.-+....
T Consensus 253 t~~~~~~~l~~~~~~s~~~~s~~~~~~~~~~~~~e~~s~~~~~~~~~~~~~~~~~~~g~~~~~~~g~~~~~~~~~~~~~~ 332 (469)
T KOG1477|consen 253 TVPYPYFLLPGGYEESIAYFSTGARRFNDPFTGKEENSIDAVGSQTDKIGLDYHQRKGRGQFTRNGAYNAALIPTYRKVG 332 (469)
T ss_pred CCCccceecCcchhhhhhhhcchhhccCCcccchhhhhhhccccccchhhhhhhhhcCcceeechhhhcccccccccccc
Confidence 357889999999999999998876432111 001 1111 233334444445555566666555554444
Q ss_pred -----cCCcchhhhhHHHHHHHHhccchhhHHHHHHHhccccCC---chhHHHHHHHHHhHhccCCCCCCchhhhCCHHH
Q 027999 86 -----KNKDLHFDLLSLHFVELVCSRKCTEALEFAQTKLTPFGK---VQKYVEKLEDFMALLAYEEPEKSPMFHLLSLEY 157 (215)
Q Consensus 86 -----~~~~l~F~L~~q~fiEli~~~~~~~Al~~ar~~l~~~~~---~~~~~~~l~~~~~lla~~~~~~s~~~~ll~~~~ 157 (215)
..+...+.+.|+.+|.+.+-+.+...+++.+..+++... +......+...++|++|.+|..||...++++.+
T Consensus 333 ~~~~~~~~~~~~~~~~~~~v~~~~~g~v~~e~~~~k~~l~~~~g~~~~~~~~~~~~~s~~Llays~p~~s~~g~~~~~~~ 412 (469)
T KOG1477|consen 333 QVFEVDYPQRGAKDPCGLHVNLGRAGFVFIEANAKKWELAKDYGIKKNSAAVGMLSDSSSLLAYSDPEESPVGYLLDPIQ 412 (469)
T ss_pred eeecccccchhhccchhhhhhHHHHHHHHHHHHHHHHhhhhhhCcCccccccccccchHHHHHhcCcccCccccccCccc
Confidence 346788999999999999999999999999988888775 567788999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHHHHHhhcCCCCCCCCChhhhhc
Q 027999 158 RQHVADNLNRAILAHAERPRYAAMERLIQQTTAVRQCLSQELGKDVHPPFSLKDFMK 214 (215)
Q Consensus 158 r~~la~~vn~~il~~~~~~~~s~Le~l~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~ 214 (215)
|+-+++.+|.+|+...+.++.+.|+.++.|+.++...+....+++. .+++++++++
T Consensus 413 ~e~v~~~~n~~il~t~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~-~~~~~~~~~~ 468 (469)
T KOG1477|consen 413 REPVAEALNSAILETDNNSKDPDLERVLSQTPAELSLYARDNPPRN-DFVRDRDYFH 468 (469)
T ss_pred chhHHhhhcccccccCCCCccchhhhhhccchhhHhhhhhcCCCcc-ceecchhhhc
Confidence 9999999999999999999999999999999999999988887766 7778877654
No 9
>PF08513 LisH: LisH; InterPro: IPR013720 The LisH motif is found in a large number of eukaryotic proteins, from metazoa, fungi and plants that have a wide range of functions. The recently solved structure of the LisH domain in the N-terminal region of LIS1 depicted it as a novel dimerization motif, and that other structural elements are likely to play an important role in dimerisation [, , ]. The LisH (lis homology) domain mediates protein dimerisation and tetramerisation. The LisH domain is found in Sif2, a component of the Set3 complex which is responsible for repressing meiotic genes. It has been shown that the LisH domain helps mediate interaction with components of the Set3 complex []. ; PDB: 2XTE_L 2XTC_B 2XTD_A 1UUJ_B.
Probab=98.62 E-value=5.4e-08 Score=53.55 Aligned_cols=27 Identities=33% Similarity=0.677 Sum_probs=24.3
Q ss_pred HHHHHHHHHHHHhhcHHHHHHHHHHhh
Q 027999 16 NDIHNIVLSYLVHNCYKETVDSFISCT 42 (215)
Q Consensus 16 ~~l~~lI~~yL~~~Gy~eta~~f~~e~ 42 (215)
++||++|.+||.++||.+||.+|.+|+
T Consensus 1 ~~Ln~lI~~YL~~~Gy~~tA~~f~~Ea 27 (27)
T PF08513_consen 1 EELNQLIYDYLVENGYKETAKAFAKEA 27 (27)
T ss_dssp HHHHHHHHHHHHHCT-HHHHHHHHHHT
T ss_pred CHHHHHHHHHHHHCCcHHHHHHHHhcC
Confidence 479999999999999999999999985
No 10
>smart00667 LisH Lissencephaly type-1-like homology motif. Alpha-helical motif present in Lis1, treacle, Nopp140, some katanin p60 subunits, muskelin, tonneau, LEUNIG and numerous WD40 repeat-containing proteins. It is suggested that LisH motifs contribute to the regulation of microtubule dynamics, either by mediating dimerisation, or else by binding cytoplasmic dynein heavy chain or microtubules directly.
Probab=98.39 E-value=6.8e-07 Score=51.23 Aligned_cols=32 Identities=25% Similarity=0.648 Sum_probs=29.4
Q ss_pred CHHHHHHHHHHHHHhhcHHHHHHHHHHhhCCC
Q 027999 14 NDNDIHNIVLSYLVHNCYKETVDSFISCTGMK 45 (215)
Q Consensus 14 ~~~~l~~lI~~yL~~~Gy~eta~~f~~e~~~~ 45 (215)
.+.+++++|++||.++||.+||.+|++|+++.
T Consensus 2 ~~~~l~~lI~~yL~~~g~~~ta~~l~~e~~~~ 33 (34)
T smart00667 2 SRSELNRLILEYLLRNGYEETAETLQKESGLS 33 (34)
T ss_pred cHHHHHHHHHHHHHHcCHHHHHHHHHHHhCCC
Confidence 46789999999999999999999999999874
No 11
>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=98.27 E-value=1.4e-05 Score=68.00 Aligned_cols=185 Identities=14% Similarity=0.145 Sum_probs=139.9
Q ss_pred hhhhcCCCCHHHHHHHHHHHHHhhcHHHHHHHHHHhhCCCCCCCCHHhHHHHHHHHHHHHcCCHHHHHHHHHHhcHHHHc
Q 027999 6 RQYEHIAINDNDIHNIVLSYLVHNCYKETVDSFISCTGMKQPANCLEDMEMRKRILHFALEGNALKAIELTEELAQDLLE 85 (215)
Q Consensus 6 ~~~~~~~~~~~~l~~lI~~yL~~~Gy~eta~~f~~e~~~~~~~~~~~~~~~r~~I~~~I~~G~i~~Ai~~~~~~~p~l~~ 85 (215)
+.+..++++...++.+--.++.+.|-..-+..|+.+.|...+....+.+...+.|.+-|.+.+...-|+|+ +....+.+
T Consensus 91 n~~~~f~~~~v~~~~~~~l~~~n~~dv~~~hi~~~~~g~~e~~~~~~~f~~lK~v~~gI~~k~~~l~iE~~-Qi~gyl~k 169 (396)
T COG5109 91 NQIYPFSTQTVTYLVVYYLLENNCADVVERHISETKDGKDEIIKIRDGFVKLKKVISGISEKSTFLLIEFL-QIEGYLSK 169 (396)
T ss_pred hhcCCCccceeeehHHHHHHHhhHHHHHHHHHHHhhcCccchhhHHHHHHHHHHHHHhhccchhHhHHHHH-HhcCcccc
Confidence 44555666677777788888888899999999999999988777778899999999999999999999999 55556666
Q ss_pred cCCcchhhhhHHHHHHHH-hccchhhHHHHHHHhccccCCchhHHHHHHHHHhHhccCCC--CCC-------chhhhC--
Q 027999 86 KNKDLHFDLLSLHFVELV-CSRKCTEALEFAQTKLTPFGKVQKYVEKLEDFMALLAYEEP--EKS-------PMFHLL-- 153 (215)
Q Consensus 86 ~~~~l~F~L~~q~fiEli-~~~~~~~Al~~ar~~l~~~~~~~~~~~~l~~~~~lla~~~~--~~s-------~~~~ll-- 153 (215)
.++..++.|+......+. ...++++|+-+.++.++.|. +.|...++.++-.+.+-.. ..+ ...+++
T Consensus 170 gdtesel~l~~~~~esl~l~hk~~~~a~r~c~t~~a~f~--~kh~~dv~~~~~~l~nap~dcfrhrekelmqnI~~~l~k 247 (396)
T COG5109 170 GDTESELELYLVSHESLLLIHKRYDEALRLCFTKLASFV--PKHIQDVKPLLRFLVNAPTDCFRHREKELMQNIQEALKK 247 (396)
T ss_pred CCchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHhccchHHHHHHHHcCchHHhhhcchhHHHHHHHHHHH
Confidence 666666666555544433 22379999999999999999 8888888888877776211 000 011111
Q ss_pred ----------C--HHHHHHHHHHHHHHHHHhcCCCCCcHHHHHHHH-HHHHHH
Q 027999 154 ----------S--LEYRQHVADNLNRAILAHAERPRYAAMERLIQQ-TTAVRQ 193 (215)
Q Consensus 154 ----------~--~~~r~~la~~vn~~il~~~~~~~~s~Le~l~~~-~~~~~~ 193 (215)
+ ...|..+-..|-+..|+..|+|-+|+|..+|.. +.+...
T Consensus 248 sligqPiEdIDkvnk~~k~l~~lF~~eycaa~gm~~~spL~~~v~tG~iaf~~ 300 (396)
T COG5109 248 SLIGQPIEDIDKVNKSRKKLIELFKSEYCAANGMPNRSPLRELVETGTIAFLQ 300 (396)
T ss_pred hhcCCcHHHHHHhhhhHHHHHHHHHHHHHHhcCCCccChHHHHHHhhhHHHHH
Confidence 1 245899999999999999999999999998874 455443
No 12
>KOG0275 consensus Conserved WD40 repeat-containing protein [General function prediction only]
Probab=97.83 E-value=0.00025 Score=61.05 Aligned_cols=168 Identities=17% Similarity=0.174 Sum_probs=115.0
Q ss_pred CCCCHHHHHHHHHHHHHhhcHHHHHHHHHHhhCCCCCCCCHHhHHHHHHHHHHHHcCCHHHHHHHHHHhcHHHHccCCcc
Q 027999 11 IAINDNDIHNIVLSYLVHNCYKETVDSFISCTGMKQPANCLEDMEMRKRILHFALEGNALKAIELTEELAQDLLEKNKDL 90 (215)
Q Consensus 11 ~~~~~~~l~~lI~~yL~~~Gy~eta~~f~~e~~~~~~~~~~~~~~~r~~I~~~I~~G~i~~Ai~~~~~~~p~l~~~~~~l 90 (215)
+.+...++.++|.+||-.+....|...+..|+++.... ......+.+.|.+|+|+..+..+++.. --..-
T Consensus 3 ieiessdVIrli~QflKE~~L~rtl~tLQeEt~VSLNT-----VDSvd~Fv~dI~sG~WD~VL~~vqsLK-----LP~kk 72 (508)
T KOG0275|consen 3 IEIESSDVIRLIEQFLKENSLHRTLQTLQEETNVSLNT-----VDSVDGFVNDINSGHWDTVLKTVQSLK-----LPDKK 72 (508)
T ss_pred eeeecchHHHHHHHHHhhhhHHHHHHHHHHhhccceee-----chhHHHHHHhcccCchHHHHHHHHhcc-----CchhH
Confidence 44556689999999999999999999999999976433 344567889999999999999988763 11234
Q ss_pred hhhhhHHHHHHHHhccchhhHHHHHHHhccccCC----chhHHHHHHHHHhHhc--cCCCCCCchhhhCCHHHHHHHHHH
Q 027999 91 HFDLLSLHFVELVCSRKCTEALEFAQTKLTPFGK----VQKYVEKLEDFMALLA--YEEPEKSPMFHLLSLEYRQHVADN 164 (215)
Q Consensus 91 ~F~L~~q~fiEli~~~~~~~Al~~ar~~l~~~~~----~~~~~~~l~~~~~lla--~~~~~~s~~~~ll~~~~r~~la~~ 164 (215)
...|+-|-.+|||.-.....|-..+|+. .|... .|+..-.++ .+|. |-||. ..|.+--.+.+|..+|..
T Consensus 73 L~dLYEqivlEliELREL~tAR~~lRQT-dpM~~lKQ~~peRy~~lE---~ll~R~YFDp~-EaY~dssKEkrRa~IAQ~ 147 (508)
T KOG0275|consen 73 LIDLYEQIVLELIELRELGTARSLLRQT-DPMIMLKQIQPERYIRLE---NLLNRSYFDPR-EAYGDSSKEKRRAVIAQA 147 (508)
T ss_pred HHHHHHHHHHHHHHHHhhhHHHHHHhcc-CceehhhccChHHHHHHH---HHhcccccChh-hhcCcchHHHHHHHHHHH
Confidence 4678899999999877677776666642 22221 344444455 4553 44552 335553335677888876
Q ss_pred HHHHHHHhcCCCCCcHHHHHHHHHHHHHHHHHh
Q 027999 165 LNRAILAHAERPRYAAMERLIQQTTAVRQCLSQ 197 (215)
Q Consensus 165 vn~~il~~~~~~~~s~Le~l~~~~~~~~~~l~~ 197 (215)
+.... .-. +.|+|-.|+-|+..-++..+-
T Consensus 148 ls~EV---~VV-ppSRLlaLlGQaLKWQqHQGL 176 (508)
T KOG0275|consen 148 LSGEV---HVV-PPSRLLALLGQALKWQQHQGL 176 (508)
T ss_pred hcCce---EEc-ChHHHHHHHHHHhhhHhhcCC
Confidence 65432 223 468999999988666655443
No 13
>KOG1333 consensus Uncharacterized conserved protein [Function unknown]
Probab=94.05 E-value=0.28 Score=39.80 Aligned_cols=137 Identities=11% Similarity=0.128 Sum_probs=81.3
Q ss_pred HHHHHHHHHHHHhhcHHHHHHHHHHhhCCCCCCCCHHhHHHHHHHHHHHHcCCHHHHHHHH----HHhcHHHHccC----
Q 027999 16 NDIHNIVLSYLVHNCYKETVDSFISCTGMKQPANCLEDMEMRKRILHFALEGNALKAIELT----EELAQDLLEKN---- 87 (215)
Q Consensus 16 ~~l~~lI~~yL~~~Gy~eta~~f~~e~~~~~~~~~~~~~~~r~~I~~~I~~G~i~~Ai~~~----~~~~p~l~~~~---- 87 (215)
+..+.+|-+||+-.|+.-|.++|-.|....-..... .=....++.++|...|++.--+.- +..|..|....
T Consensus 6 ~~tDelvReYL~frgf~~tLkalD~E~~~~Ke~~fr-vdrivdq~~~a~q~~Dl~aLr~~W~~l~~r~Fs~Le~~y~~~~ 84 (241)
T KOG1333|consen 6 ERTDELVREYLLFRGFTHTLKALDAEIKADKEKGFR-VDRIVDQLQQAMQVYDLAALRDYWSYLERRLFSRLEDIYRPTI 84 (241)
T ss_pred HHHHHHHHHHHHHhhHHHHHHHHhHHHhhhhhcCCc-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHH
Confidence 457899999999999999999998776543221100 002334566777777776543332 23333333321
Q ss_pred CcchhhhhHHHHHHHHhccchhhHHHHHHHhccccCCchhHHHHHHHHHhHhccCCCC-CCchhhhCCHHH
Q 027999 88 KDLHFDLLSLHFVELVCSRKCTEALEFAQTKLTPFGKVQKYVEKLEDFMALLAYEEPE-KSPMFHLLSLEY 157 (215)
Q Consensus 88 ~~l~F~L~~q~fiEli~~~~~~~Al~~ar~~l~~~~~~~~~~~~l~~~~~lla~~~~~-~s~~~~ll~~~~ 157 (215)
..++=.|.+..++-.+.++..++|=+|-++.-+...++++..+++ .+=..++-. ..|++.+++...
T Consensus 85 ~kle~Sl~r~yLV~~~q~nr~~K~~EFF~K~a~~lqnq~eWkDWF----~fPf~~~a~~tppf~~~F~ktw 151 (241)
T KOG1333|consen 85 HKLETSLFRFYLVYTIQTNRNDKAQEFFAKQATELQNQAEWKDWF----VLPFLPSAKDTPPFRKYFDKTW 151 (241)
T ss_pred HHHHHHHHHHHHhhhhhcCChHHHHHHHHHHHHHHhcchhhhhhe----ecccCCCCCCCccHHHHHHhhh
Confidence 135566777778888888889998888876555554455444432 111112222 445666665443
No 14
>PF09398 FOP_dimer: FOP N terminal dimerisation domain; InterPro: IPR018993 Fibroblast growth factor receptor 1 (FGFR1) oncogene partner (FOP) is a centrosomal protein that is involved in anchoring microtubules to centrosomes. This domain includes a Lis-homology motif. It forms an alpha-helical bundle and is involved in dimerisation []. ; GO: 0034453 microtubule anchoring, 0005813 centrosome; PDB: 2D68_A.
Probab=93.17 E-value=0.19 Score=34.84 Aligned_cols=31 Identities=23% Similarity=0.320 Sum_probs=26.3
Q ss_pred HHHHHHHHHHHhhcHHHHHHHHHHhhCCCCC
Q 027999 17 DIHNIVLSYLVHNCYKETVDSFISCTGMKQP 47 (215)
Q Consensus 17 ~l~~lI~~yL~~~Gy~eta~~f~~e~~~~~~ 47 (215)
.++.||.+||-.+||.=|+..|..|+|.+..
T Consensus 20 Li~eLIrEyLef~~l~~TlsVf~~Es~~~~~ 50 (81)
T PF09398_consen 20 LINELIREYLEFNNLDYTLSVFQPESGQPEE 50 (81)
T ss_dssp HHHHHHHHHHHHTT-HHHHHHHHHHHT-TT-
T ss_pred HHHHHHHHHHHHcCCccHHHHHhhccCCCCC
Confidence 5799999999999999999999999998643
No 15
>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=86.58 E-value=4 Score=26.03 Aligned_cols=56 Identities=23% Similarity=0.129 Sum_probs=35.5
Q ss_pred HHHcCCHHHHHHHHHHhcHHHHccCCcchhhhhHHHHHHHHhccchhhHHHHHHHhccccC
Q 027999 63 FALEGNALKAIELTEELAQDLLEKNKDLHFDLLSLHFVELVCSRKCTEALEFAQTKLTPFG 123 (215)
Q Consensus 63 ~I~~G~i~~Ai~~~~~~~p~l~~~~~~l~F~L~~q~fiEli~~~~~~~Al~~ar~~l~~~~ 123 (215)
++..|++++|++.+++... ....+..+.+.| ..=+++.|+.++|.....+.+....
T Consensus 1 ll~~~~~~~A~~~~~~~l~-~~p~~~~~~~~l----a~~~~~~g~~~~A~~~l~~~~~~~~ 56 (68)
T PF14559_consen 1 LLKQGDYDEAIELLEKALQ-RNPDNPEARLLL----AQCYLKQGQYDEAEELLERLLKQDP 56 (68)
T ss_dssp HHHTTHHHHHHHHHHHHHH-HTTTSHHHHHHH----HHHHHHTT-HHHHHHHHHCCHGGGT
T ss_pred ChhccCHHHHHHHHHHHHH-HCCCCHHHHHHH----HHHHHHcCCHHHHHHHHHHHHHHCc
Confidence 4778999999999987531 122233444432 2224578999999998886555443
No 16
>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=82.89 E-value=9.4 Score=28.68 Aligned_cols=59 Identities=14% Similarity=0.117 Sum_probs=42.4
Q ss_pred HHHHHHHhhcHHHHHHHHHHhhC--CCCCCCCHHhHHHHHHHHHHHHcCCHHHHHHHHHHhc
Q 027999 21 IVLSYLVHNCYKETVDSFISCTG--MKQPANCLEDMEMRKRILHFALEGNALKAIELTEELA 80 (215)
Q Consensus 21 lI~~yL~~~Gy~eta~~f~~e~~--~~~~~~~~~~~~~r~~I~~~I~~G~i~~Ai~~~~~~~ 80 (215)
-|.+.+ ..|-.+.|-..+++.. +.........--.+.++.+.|.+|++.+||++++.+.
T Consensus 7 ~I~~~I-~~g~i~~Ai~w~~~~~~~l~~~~~~L~f~L~~q~fiell~~~~~~~Ai~y~r~~l 67 (145)
T PF10607_consen 7 KIRQAI-LNGDIDPAIEWLNENFPELLKRNSSLEFELRCQQFIELLREGDIMEAIEYARKHL 67 (145)
T ss_pred HHHHHH-HcCCHHHHHHHHHHcCHHHHhcCCchhHHHHHHHHHHHHHHHhHHHHHHHHHHHh
Confidence 355556 8888888888876632 1111123555567789999999999999999999865
No 17
>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=79.34 E-value=21 Score=30.86 Aligned_cols=98 Identities=16% Similarity=0.134 Sum_probs=63.7
Q ss_pred HHHHHHHHHHHhhcHHHHHHHHHHhhC-----------------CCCCC--------------------------CCHHh
Q 027999 17 DIHNIVLSYLVHNCYKETVDSFISCTG-----------------MKQPA--------------------------NCLED 53 (215)
Q Consensus 17 ~l~~lI~~yL~~~Gy~eta~~f~~e~~-----------------~~~~~--------------------------~~~~~ 53 (215)
++++++.+.|.+.||.+++.++..+.. .++-+ ...+.
T Consensus 134 Dgq~~~~qal~~lG~~~~a~aI~~el~~fL~RlP~L~~L~F~DGtPFad~~T~~WL~~~~~~~~~~~~~~~~~~~~~~~~ 213 (301)
T TIGR03362 134 DGQRLSAQALERLGYAAVAQAIRDELAAFLERLPGLLELKFSDGTPFADDETRAWLAQHATRSNAASVAPVAEVGEESDW 213 (301)
T ss_pred HHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHhCcChhhcccCCCCCCCCHHHHHHHHhcccccccccccccccCcccccH
Confidence 578999999999999999999888752 11100 00112
Q ss_pred HHHHHHHHHHHHcCCHHHHHHHHHHhcHHHHccCCcchhhhhHHHHHHHHhccchhhHHHHHH
Q 027999 54 MEMRKRILHFALEGNALKAIELTEELAQDLLEKNKDLHFDLLSLHFVELVCSRKCTEALEFAQ 116 (215)
Q Consensus 54 ~~~r~~I~~~I~~G~i~~Ai~~~~~~~p~l~~~~~~l~F~L~~q~fiEli~~~~~~~Al~~ar 116 (215)
.+...+.+..+.+|.+.+|+.|+++..|..-......+..|..-+..+- .|...-|....+
T Consensus 214 ~~~~~eA~~l~~~~gl~~Al~~L~~~~~~~~s~R~rf~~rL~~A~l~~~--~g~~~lA~~ll~ 274 (301)
T TIGR03362 214 EELREEARALAAEGGLEAALQRLQQRLAQAREPRERFHWRLLLARLLEQ--AGKAELAQQLYA 274 (301)
T ss_pred HHHHHHHHHHHHcCCHHHHHHHHHhhcccCCChHHHHHHHHHHHHHHHH--cCCHHHHHHHHH
Confidence 3455678888999999999999998655544443455555555555443 344444444444
No 18
>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=78.93 E-value=4.8 Score=30.71 Aligned_cols=48 Identities=19% Similarity=0.297 Sum_probs=38.4
Q ss_pred CcchhhhhHHHHHHHHhccchhhHHHHHHHhccccCCchhHHHHHHHHHh
Q 027999 88 KDLHFDLLSLHFVELVCSRKCTEALEFAQTKLTPFGKVQKYVEKLEDFMA 137 (215)
Q Consensus 88 ~~l~F~L~~q~fiEli~~~~~~~Al~~ar~~l~~~~~~~~~~~~l~~~~~ 137 (215)
..+.|=+-+.-|++|+.+|...+|..|..++-..+. ..+.++|+++..
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 358899999999999999999999999998776665 556677776643
No 19
>KOG0273 consensus Beta-transducin family (WD-40 repeat) protein [Chromatin structure and dynamics]
Probab=78.26 E-value=0.82 Score=41.52 Aligned_cols=105 Identities=17% Similarity=0.179 Sum_probs=60.3
Q ss_pred CCCCHHHHHHHHHHHHHhhcHHHHHHHHHHhhCCCCCCCCHHhHHHHHHHHHHHHcC-CHHHHHHHHHHhcH--------
Q 027999 11 IAINDNDIHNIVLSYLVHNCYKETVDSFISCTGMKQPANCLEDMEMRKRILHFALEG-NALKAIELTEELAQ-------- 81 (215)
Q Consensus 11 ~~~~~~~l~~lI~~yL~~~Gy~eta~~f~~e~~~~~~~~~~~~~~~r~~I~~~I~~G-~i~~Ai~~~~~~~p-------- 81 (215)
++++.+++|.||--||-..||.=+|=+|..|+++...+...+. -.--.+...+..| ...++..-+++.-.
T Consensus 1 msitsdEvN~LV~RYLqE~G~~hsaftf~~Et~is~~n~~~~~-vp~gaLi~ivQKGLqY~E~E~~~~~~~~v~d~~~e~ 79 (524)
T KOG0273|consen 1 MSITSDEVNFLVWRYLQESGFSHSAFTFGIETGISQSNINGSL-VPPGALISIVQKGLQYVEAEKHLNESGVVFDAPIES 79 (524)
T ss_pred CcccHHHHHHHHHHHHHHcCcceeeEEeeecccccccCCCccc-cChHHHHHHHHhhhhhhheeeeeccCCccccccccc
Confidence 4678999999999999999999999999999998754422211 1111222222222 11122111111100
Q ss_pred -HHHccCCcchhhhhHHHHHHHHhccchhhHHHHHH
Q 027999 82 -DLLEKNKDLHFDLLSLHFVELVCSRKCTEALEFAQ 116 (215)
Q Consensus 82 -~l~~~~~~l~F~L~~q~fiEli~~~~~~~Al~~ar 116 (215)
.+.+-...=.+.|.++.|=|....+......+.++
T Consensus 80 ~~~~d~v~~~~~ql~~~~~~e~~s~~~~~~~~~~~~ 115 (524)
T KOG0273|consen 80 LSLEDLVMEDVVQLRQQAFREKLSEEQFCAQLKIAQ 115 (524)
T ss_pred cchhhhccccccccchhhhhhhccccchhhhhhhhh
Confidence 01111223457888999998887776654443333
No 20
>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=78.12 E-value=1.3 Score=33.46 Aligned_cols=48 Identities=19% Similarity=0.328 Sum_probs=38.3
Q ss_pred cchhhhhHHHHHHHHhccchhhHHHHHHHhccccCCchhHHHHHHHHHhH
Q 027999 89 DLHFDLLSLHFVELVCSRKCTEALEFAQTKLTPFGKVQKYVEKLEDFMAL 138 (215)
Q Consensus 89 ~l~F~L~~q~fiEli~~~~~~~Al~~ar~~l~~~~~~~~~~~~l~~~~~l 138 (215)
.+.|=+.+.-|++|+.+|...+|..|-.+.-..+. +.+.+.|+.+.++
T Consensus 28 ~lLyPiFvh~yL~lv~~~~~~~A~~F~~~f~~~~~--~~~~~~i~~L~~i 75 (133)
T cd08044 28 QLLYPIFVHSYLDLVASGHLEEAKSFFERFSGDFE--DSHSEDIKKLSSI 75 (133)
T ss_pred HHHHHHHHHHHHHHHHCCCHHHHHHHHHHhhHhhH--HHHHHHHHHHHcc
Confidence 47888999999999999999999999987555553 6677778766443
No 21
>PF04053 Coatomer_WDAD: Coatomer WD associated region ; InterPro: IPR006692 Proteins synthesised on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment. This traffic is bidirectional, to ensure that proteins required to form vesicles are recycled. Vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transfer []. While clathrin mediates endocytic protein transport, and transport from ER to Golgi, coatomers primarily mediate intra-Golgi transport, as well as the reverse Golgi to ER transport of dilysine-tagged proteins []. For example, the coatomer COP1 (coat protein complex 1) is responsible for reverse transport of recycled proteins from Golgi and pre-Golgi compartments back to the ER, while COPII buds vesicles from the ER to the Golgi []. Coatomers reversibly associate with Golgi (non-clathrin-coated) vesicles to mediate protein transport and for budding from Golgi membranes []. Activated small guanine triphosphatases (GTPases) attract coat proteins to specific membrane export sites, thereby linking coatomers to export cargos. As coat proteins polymerise, vesicles are formed and budded from membrane-bound organelles. Coatomer complexes also influence Golgi structural integrity, as well as the processing, activity, and endocytic recycling of LDL receptors. In mammals, coatomer complexes can only be recruited by membranes associated to ADP-ribosylation factors (ARFs), which are small GTP-binding proteins. Coatomer complexes are hetero-oligomers composed of at least an alpha, beta, beta', gamma, delta, epsilon and zeta subunits. This entry represents the WD-associated region found in coatomer subunits alpha, beta and beta' subunits. The alpha-subunit (RET1P) of the coatomer complex in Saccharomyces cerevisiae (Baker's yeast), participates in membrane transport between the endoplasmic reticulum and Golgi apparatus. The protein contains six WD-40 repeat motifs in its N-terminal region []. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0005198 structural molecule activity, 0006886 intracellular protein transport, 0016192 vesicle-mediated transport, 0030117 membrane coat; PDB: 3MKQ_B.
Probab=77.05 E-value=11 Score=34.34 Aligned_cols=76 Identities=21% Similarity=0.105 Sum_probs=55.3
Q ss_pred HHHHHHHHHHHhhcHHHHHHHHHHhhCCCCCCCCHHhHHHHHHHHHHHHcCCHHHHHHHHHHhcHHHHccCCcchhhhhH
Q 027999 17 DIHNIVLSYLVHNCYKETVDSFISCTGMKQPANCLEDMEMRKRILHFALEGNALKAIELTEELAQDLLEKNKDLHFDLLS 96 (215)
Q Consensus 17 ~l~~lI~~yL~~~Gy~eta~~f~~e~~~~~~~~~~~~~~~r~~I~~~I~~G~i~~Ai~~~~~~~p~l~~~~~~l~F~L~~ 96 (215)
..-.-|+.||...||.|.|-.|+++ .++++--+|.-|+++.|.+.+.+.. .-..++
T Consensus 296 ~~~~~i~~fL~~~G~~e~AL~~~~D--------------~~~rFeLAl~lg~L~~A~~~a~~~~----------~~~~W~ 351 (443)
T PF04053_consen 296 DQGQSIARFLEKKGYPELALQFVTD--------------PDHRFELALQLGNLDIALEIAKELD----------DPEKWK 351 (443)
T ss_dssp HHHHHHHHHHHHTT-HHHHHHHSS---------------HHHHHHHHHHCT-HHHHHHHCCCCS----------THHHHH
T ss_pred hHHHHHHHHHHHCCCHHHHHhhcCC--------------hHHHhHHHHhcCCHHHHHHHHHhcC----------cHHHHH
Confidence 3577889999999999999999753 3478999999999999999987653 112455
Q ss_pred HHHHHHHhccchhhHHHHHH
Q 027999 97 LHFVELVCSRKCTEALEFAQ 116 (215)
Q Consensus 97 q~fiEli~~~~~~~Al~~ar 116 (215)
+=-=+-+++|++.-|-+..+
T Consensus 352 ~Lg~~AL~~g~~~lAe~c~~ 371 (443)
T PF04053_consen 352 QLGDEALRQGNIELAEECYQ 371 (443)
T ss_dssp HHHHHHHHTTBHHHHHHHHH
T ss_pred HHHHHHHHcCCHHHHHHHHH
Confidence 55555667788877766555
No 22
>PF13838 Clathrin_H_link: Clathrin-H-link; PDB: 2XZG_A 3GD1_I 1BPO_C 1C9I_B 1C9L_A.
Probab=60.61 E-value=28 Score=23.13 Aligned_cols=41 Identities=20% Similarity=0.271 Sum_probs=27.3
Q ss_pred hhhHHHHHHHHhccchhhHHHHHHHhccccCCchhHHHHHH
Q 027999 93 DLLSLHFVELVCSRKCTEALEFAQTKLTPFGKVQKYVEKLE 133 (215)
Q Consensus 93 ~L~~q~fiEli~~~~~~~Al~~ar~~l~~~~~~~~~~~~l~ 133 (215)
.|..++|=+++..|++.+|-..|-+.=.-.-.+++...+++
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 46789999999999999998888752222223555555555
No 23
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=60.27 E-value=25 Score=23.07 Aligned_cols=48 Identities=17% Similarity=0.416 Sum_probs=32.4
Q ss_pred CHHHHHHHHHHHHHhhcHHHHHHHHHHhhCCCCCCCCHHhHHHHHHHHHHHHcC
Q 027999 14 NDNDIHNIVLSYLVHNCYKETVDSFISCTGMKQPANCLEDMEMRKRILHFALEG 67 (215)
Q Consensus 14 ~~~~l~~lI~~yL~~~Gy~eta~~f~~e~~~~~~~~~~~~~~~r~~I~~~I~~G 67 (215)
.+.++-..|.+|...+||.=|...+++..|+..+. .....++.+...|
T Consensus 7 rQ~~vL~~I~~~~~~~G~~Pt~rEIa~~~g~~S~~------tv~~~L~~Le~kG 54 (65)
T PF01726_consen 7 RQKEVLEFIREYIEENGYPPTVREIAEALGLKSTS------TVQRHLKALERKG 54 (65)
T ss_dssp HHHHHHHHHHHHHHHHSS---HHHHHHHHTSSSHH------HHHHHHHHHHHTT
T ss_pred HHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChH------HHHHHHHHHHHCc
Confidence 35567789999999999999999999999986433 3344444444444
No 24
>PF09295 ChAPs: ChAPs (Chs5p-Arf1p-binding proteins); InterPro: IPR015374 ChAPs (Chs5p-Arf1p-binding proteins) are required for the export of specialised cargo from the Golgi. They physically interact with Chs3, Chs5 and the small GTPase Arf1, and they also form interactions with each other [].
Probab=58.80 E-value=1.4e+02 Score=26.94 Aligned_cols=97 Identities=22% Similarity=0.229 Sum_probs=66.3
Q ss_pred cCCCCHHHHHHHHHHHHHhhcHHHHHHHHHHhhCCCCCCCCHHhHHHHHHHHHHHHcCCHHHHHHHHHHhcHHHHccCCc
Q 027999 10 HIAINDNDIHNIVLSYLVHNCYKETVDSFISCTGMKQPANCLEDMEMRKRILHFALEGNALKAIELTEELAQDLLEKNKD 89 (215)
Q Consensus 10 ~~~~~~~~l~~lI~~yL~~~Gy~eta~~f~~e~~~~~~~~~~~~~~~r~~I~~~I~~G~i~~Ai~~~~~~~p~l~~~~~~ 89 (215)
..+.-.+-|..-++.|+...|-.+.|..+.++.....|. . ...-.+-.+..++-.+|+.++++.- +.++
T Consensus 163 ~~t~~~NyLv~~Ll~~l~~t~~~~~ai~lle~L~~~~pe--v----~~~LA~v~l~~~~E~~AI~ll~~aL----~~~p- 231 (395)
T PF09295_consen 163 VPTIVNNYLVDTLLKYLSLTQRYDEAIELLEKLRERDPE--V----AVLLARVYLLMNEEVEAIRLLNEAL----KENP- 231 (395)
T ss_pred CCCCcchHHHHHHHHHHhhcccHHHHHHHHHHHHhcCCc--H----HHHHHHHHHhcCcHHHHHHHHHHHH----HhCC-
Confidence 344556677777788888888888888887776655443 1 1223455567788899999998752 3222
Q ss_pred chhhhhHHHHHHHHhccchhhHHHHHHH
Q 027999 90 LHFDLLSLHFVELVCSRKCTEALEFAQT 117 (215)
Q Consensus 90 l~F~L~~q~fiEli~~~~~~~Al~~ar~ 117 (215)
-...|.+.+-==++.+++.+.|+..|++
T Consensus 232 ~d~~LL~~Qa~fLl~k~~~~lAL~iAk~ 259 (395)
T PF09295_consen 232 QDSELLNLQAEFLLSKKKYELALEIAKK 259 (395)
T ss_pred CCHHHHHHHHHHHHhcCCHHHHHHHHHH
Confidence 1255666665557788899999999985
No 25
>KOG2910 consensus Uncharacterized conserved protein predicted to be involved in protein sorting [General function prediction only]
Probab=56.64 E-value=74 Score=25.75 Aligned_cols=63 Identities=21% Similarity=0.260 Sum_probs=45.9
Q ss_pred HHHHHHHHHHHcCCHHHHHHHHHHhc--HHHHcc-----------CCcchhhhhHHHHHHHHhccchhhHHHHHHHhc
Q 027999 55 EMRKRILHFALEGNALKAIELTEELA--QDLLEK-----------NKDLHFDLLSLHFVELVCSRKCTEALEFAQTKL 119 (215)
Q Consensus 55 ~~r~~I~~~I~~G~i~~Ai~~~~~~~--p~l~~~-----------~~~l~F~L~~q~fiEli~~~~~~~Al~~ar~~l 119 (215)
.+|..-|++|++|+=+.|+-.+.... ..|+.. -++++|.....++++=++.| ++||.-.+..|
T Consensus 41 ~Er~~Ar~lird~rKdrAlllLKkKryQE~Ll~qt~~qL~nlEqmvsdiEft~vqk~V~~gLk~G--N~~lkkl~~~~ 116 (209)
T KOG2910|consen 41 AERQLARDLIRDGRKDRALLLLKKKRYQEELLTQTDNQLINLEQMVSDIEFTQVQKKVMEGLKQG--NEALKKLQQEF 116 (209)
T ss_pred HHHHHHHHHHHhChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHhc
Confidence 46777889999999998887665332 333332 36899999999999999988 56666666544
No 26
>PRK02289 4-oxalocrotonate tautomerase; Provisional
Probab=53.39 E-value=23 Score=22.54 Aligned_cols=26 Identities=19% Similarity=0.249 Sum_probs=23.4
Q ss_pred CCHHHHHHHHHHHHHHHHHhcCCCCC
Q 027999 153 LSLEYRQHVADNLNRAILAHAERPRY 178 (215)
Q Consensus 153 l~~~~r~~la~~vn~~il~~~~~~~~ 178 (215)
.+++++.+|++.+..++.+.+|.|.+
T Consensus 12 rs~EqK~~L~~~it~a~~~~~~~p~~ 37 (60)
T PRK02289 12 RSQEQKNALAREVTEVVSRIAKAPKE 37 (60)
T ss_pred CCHHHHHHHHHHHHHHHHHHhCcCcc
Confidence 47899999999999999999999864
No 27
>PRK10564 maltose regulon periplasmic protein; Provisional
Probab=53.28 E-value=16 Score=31.59 Aligned_cols=24 Identities=25% Similarity=0.350 Sum_probs=21.7
Q ss_pred HHHHHHHHHHcCCHHHHHHHHHHh
Q 027999 56 MRKRILHFALEGNALKAIELTEEL 79 (215)
Q Consensus 56 ~r~~I~~~I~~G~i~~Ai~~~~~~ 79 (215)
-...|++++..|||++|+.++++-
T Consensus 260 y~~aI~~AVk~gDi~KAL~LldEA 283 (303)
T PRK10564 260 FNQAIKQAVKKGDVDKALKLLDEA 283 (303)
T ss_pred HHHHHHHHHHcCCHHHHHHHHHHH
Confidence 457999999999999999999876
No 28
>PF10602 RPN7: 26S proteasome subunit RPN7; InterPro: IPR019585 This entry represents the regulatory subunit RPN7 (known as the non-ATPase regulatory subunit 6 in higher eukaryotes) of the 26S proteasome. This entry also matches the evolutionarily related subunit 1 of the COP9 signalosome complex (CSN) from Arabidopsis []. The 26S proteasome plays a major role in ATP-dependent degradation of ubiquitinated proteins. Substrate specificity is conferred by the regulatory particle (RP), which can dissociate into stable lid and base subcomplexes. The regulatory subunit RPN7 is one of the lid subunits of the 26S proteasome and has been shown in Saccharomyces cerevisiae (Baker's yeast) to be required for structural integrity []. The COP9 signalosome is a conserved protein complex composed of eight subunits, where Individual subunits of the complex have been linked to various signal transduction pathways leading to gene expression and cell cycle control []. The overall organisation and the amino acid sequences of the COP9 signalosome subunits resemble the lid subcomplex of the 19 S regulatory particle for the 26 S proteasome []. COP9 subunit 1 (CSN1 or GPS1) of the COP9 complex is an essential subunit of the complex with regard to both structural integrity and functionality. The N-terminal region of subunit 1 (CSN1-N) can inhibit c-fos expression from either a transfected template or a chromosomal transgene (fos-lacZ), and may contain the activity domain that confers most of the repression functions of CSN1. The C-terminal region of subunit 1 (CSN1-C) allows integration of the protein into the COP9 signalosome.
Probab=52.41 E-value=1.1e+02 Score=23.98 Aligned_cols=112 Identities=11% Similarity=-0.092 Sum_probs=74.4
Q ss_pred CCCCHHHHHHHHHHHHHhhcHHHHHHHHHHhhCCCCCCCCHHhHH-HHHHHHHHHHcCCHHHHHHHHHHhcHHHHc-cCC
Q 027999 11 IAINDNDIHNIVLSYLVHNCYKETVDSFISCTGMKQPANCLEDME-MRKRILHFALEGNALKAIELTEELAQDLLE-KNK 88 (215)
Q Consensus 11 ~~~~~~~l~~lI~~yL~~~Gy~eta~~f~~e~~~~~~~~~~~~~~-~r~~I~~~I~~G~i~~Ai~~~~~~~p~l~~-~~~ 88 (215)
++.+-.....-+++|+.+.|-.+.|-.-...+--.... ....+. ...-|+-+|..|||..+...+++...-+.+ .+.
T Consensus 31 ~kesir~~~~~l~~~~~~~Gd~~~A~k~y~~~~~~~~~-~~~~id~~l~~irv~i~~~d~~~v~~~i~ka~~~~~~~~d~ 109 (177)
T PF10602_consen 31 GKESIRMALEDLADHYCKIGDLEEALKAYSRARDYCTS-PGHKIDMCLNVIRVAIFFGDWSHVEKYIEKAESLIEKGGDW 109 (177)
T ss_pred chHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHhhhcCC-HHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhccchH
Confidence 33333445567889999999777666554433211111 122333 356789999999999999999887655544 234
Q ss_pred cchhhhhHHHHHHHHhccchhhHHHHHHHhccccC
Q 027999 89 DLHFDLLSLHFVELVCSRKCTEALEFAQTKLTPFG 123 (215)
Q Consensus 89 ~l~F~L~~q~fiEli~~~~~~~Al~~ar~~l~~~~ 123 (215)
...-.|.+.+-+-.+..++..+|-..--...+.|.
T Consensus 110 ~~~nrlk~~~gL~~l~~r~f~~AA~~fl~~~~t~~ 144 (177)
T PF10602_consen 110 ERRNRLKVYEGLANLAQRDFKEAAELFLDSLSTFT 144 (177)
T ss_pred HHHHHHHHHHHHHHHHhchHHHHHHHHHccCcCCC
Confidence 67778999999999998888887555544444453
No 29
>PF14276 DUF4363: Domain of unknown function (DUF4363)
Probab=52.25 E-value=31 Score=25.24 Aligned_cols=47 Identities=19% Similarity=0.078 Sum_probs=38.4
Q ss_pred HHHHHHHHHHHcCCHHHHHHHHHHhcHHHHccCCcchhhhhHHHHHH
Q 027999 55 EMRKRILHFALEGNALKAIELTEELAQDLLEKNKDLHFDLLSLHFVE 101 (215)
Q Consensus 55 ~~r~~I~~~I~~G~i~~Ai~~~~~~~p~l~~~~~~l~F~L~~q~fiE 101 (215)
.....+.+.|.++||+.|.+.+.+....--+..+.+.|.+..+++=+
T Consensus 30 ~~l~~i~~~i~~~dW~~A~~~~~~l~~~W~k~~~~~~~~~~h~eid~ 76 (121)
T PF14276_consen 30 EQLEQIEEAIENEDWEKAYKETEELEKEWDKNKKRWSILIEHQEIDN 76 (121)
T ss_pred HHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhhchheeeeecHHHHHH
Confidence 56778999999999999999998876655666677888888888644
No 30
>PTZ00196 60S ribosomal protein L36; Provisional
Probab=50.78 E-value=32 Score=24.67 Aligned_cols=44 Identities=18% Similarity=0.330 Sum_probs=31.5
Q ss_pred hhhhHHHHHHHHhccchhhHHHHHHHhccccCCchhHHHHHHHH
Q 027999 92 FDLLSLHFVELVCSRKCTEALEFAQTKLTPFGKVQKYVEKLEDF 135 (215)
Q Consensus 92 F~L~~q~fiEli~~~~~~~Al~~ar~~l~~~~~~~~~~~~l~~~ 135 (215)
|.=+-.+.+|||+.|.--.|+.|++..+..+..-....++++.+
T Consensus 48 faPYErr~mELLkv~kdKrAlKfaKkRlGth~RaK~Kreel~~v 91 (98)
T PTZ00196 48 FSPYERRMIELLKVGKDKRALKYAKKRLGTHKRAKAKRDEIQEA 91 (98)
T ss_pred ccHHHHHHHHHHHhcchHHHHHHHHHHhhhHHHHHHHHHHHHHH
Confidence 45567788999999988999999999887765322233444443
No 31
>PF07729 FCD: FCD domain; InterPro: IPR011711 Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities. The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon []. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector binding or oligomerisation domain at the C terminus. The winged-helix DNA-binding domain is well conserved in structure for the whole of the GntR family (IPR000524 from INTERPRO), and is similar in structure to other transcriptional regulator families. The C-terminal effector-binding and oligomerisation domains are more variable and are consequently used to define the subfamilies. Based on the sequence and structure of the C-terminal domains, the GtnR family can be divided into four major groups, as represented by FadR (IPR008920 from INTERPRO), HutC, MocR and YtrA, as well as some minor groups such as those represented by AraR and PlmA []. This entry represents the C-terminal ligand binding domain of many members of the GntR family. This domain probably binds to a range of effector molecules that regulate the transcription of genes through the action of the N-terminal DNA-binding domain. This domain is found in P45427 from SWISSPROT and P31460 from SWISSPROT that are regulators of sugar biosynthesis operons.; PDB: 3SXK_A 3SXY_A 3SXM_B 3SXZ_A 3FMS_A 2DI3_B 2HS5_A 3IHU_B 3C7J_A.
Probab=50.66 E-value=33 Score=23.95 Aligned_cols=29 Identities=17% Similarity=0.201 Sum_probs=22.0
Q ss_pred HhHHHHHHHHHHHHcCCHHHHHHHHHHhc
Q 027999 52 EDMEMRKRILHFALEGNALKAIELTEELA 80 (215)
Q Consensus 52 ~~~~~r~~I~~~I~~G~i~~Ai~~~~~~~ 80 (215)
........|.++|.+||.+.|.+++..+.
T Consensus 95 ~~~~~h~~i~~ai~~~d~~~a~~~~~~h~ 123 (125)
T PF07729_consen 95 RSLEEHREIIDAIRAGDPEAAREALRQHI 123 (125)
T ss_dssp HHHHHHHHHHHHHHTT-HHHHHHHHHHHH
T ss_pred hhHHHHHHHHHHHHcCCHHHHHHHHHHHh
Confidence 45667788888888888888888887764
No 32
>KOG2437 consensus Muskelin [Signal transduction mechanisms]
Probab=50.05 E-value=62 Score=30.32 Aligned_cols=62 Identities=11% Similarity=0.090 Sum_probs=46.7
Q ss_pred HHHHHHHHHHhhcHHHHHHHHHHhhCCCCCCCCHHhHHHHHHHHHHHHcCCHHHHHHHHHHhcHHHHc
Q 027999 18 IHNIVLSYLVHNCYKETVDSFISCTGMKQPANCLEDMEMRKRILHFALEGNALKAIELTEELAQDLLE 85 (215)
Q Consensus 18 l~~lI~~yL~~~Gy~eta~~f~~e~~~~~~~~~~~~~~~r~~I~~~I~~G~i~~Ai~~~~~~~p~l~~ 85 (215)
--+..+.||-..||.+....+.+.+.+..+. +...+|++++....-...........|.++.
T Consensus 168 a~r~cL~~fr~~G~~DI~e~l~k~~~~~Ieh------~~l~~i~d~l~~~gd~~~e~i~~~~~~~lf~ 229 (723)
T KOG2437|consen 168 AIRLCLKHFRQHGYTDIFESLQKKTKIAIEH------PMLTDIHDKLVLKGDACEELIEKAVNDGLFN 229 (723)
T ss_pred HHHHHHHHHHHcCchHHHHHHHHhhcccCCC------hHHHHHHHHHHHcccHHHHHHHhhhccHHHh
Confidence 4467889999999999999999998877655 5567888888666555555555566666654
No 33
>KOG0292 consensus Vesicle coat complex COPI, alpha subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=50.02 E-value=5.3 Score=39.41 Aligned_cols=48 Identities=23% Similarity=0.289 Sum_probs=37.4
Q ss_pred HHHHHHHHHHhhcHHHHHHHHHHhhCCCCCCCCHHhHHHHHHHHHHHHcCCHHHHHHHHHHh
Q 027999 18 IHNIVLSYLVHNCYKETVDSFISCTGMKQPANCLEDMEMRKRILHFALEGNALKAIELTEEL 79 (215)
Q Consensus 18 l~~lI~~yL~~~Gy~eta~~f~~e~~~~~~~~~~~~~~~r~~I~~~I~~G~i~~Ai~~~~~~ 79 (215)
+-+-|..||...||.|.|--|.++.. .++--++..|+++.|++.+...
T Consensus 622 vGqaiIaYLqKkgypeiAL~FVkD~~--------------tRF~LaLe~gnle~ale~akkl 669 (1202)
T KOG0292|consen 622 VGQAIIAYLQKKGYPEIALHFVKDER--------------TRFELALECGNLEVALEAAKKL 669 (1202)
T ss_pred ccHHHHHHHHhcCCcceeeeeecCcc--------------hheeeehhcCCHHHHHHHHHhc
Confidence 34568899999999999998887533 4566678888888888887655
No 34
>PRK00794 flbT flagellar biosynthesis repressor FlbT; Reviewed
Probab=49.48 E-value=92 Score=23.58 Aligned_cols=31 Identities=16% Similarity=0.062 Sum_probs=26.0
Q ss_pred HhHHHHHHHHHHHHcCCHHHHHHHHHHhcHH
Q 027999 52 EDMEMRKRILHFALEGNALKAIELTEELAQD 82 (215)
Q Consensus 52 ~~~~~r~~I~~~I~~G~i~~Ai~~~~~~~p~ 82 (215)
+.......|.++|..|++.+|++.+....|.
T Consensus 92 ~~~~~l~~i~~~V~~g~~y~ALk~lR~L~~~ 122 (132)
T PRK00794 92 DILAGLKAIDELVEAGRYYEALKALRGLYPI 122 (132)
T ss_pred HHHHHHHHHHHHHHCCcHHHHHHHHHHhhHH
Confidence 3446677899999999999999999988764
No 35
>PF12895 Apc3: Anaphase-promoting complex, cyclosome, subunit 3; PDB: 3KAE_D 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2XPI_A 3ULQ_A.
Probab=49.31 E-value=30 Score=23.10 Aligned_cols=52 Identities=25% Similarity=0.276 Sum_probs=29.9
Q ss_pred HHHHHHHcCCHHHHHHHHHHhcHHHHccCCcchhhhhHHHHHHHHhccchhhHHHHHH
Q 027999 59 RILHFALEGNALKAIELTEELAQDLLEKNKDLHFDLLSLHFVELVCSRKCTEALEFAQ 116 (215)
Q Consensus 59 ~I~~~I~~G~i~~Ai~~~~~~~p~l~~~~~~l~F~L~~q~fiEli~~~~~~~Al~~ar 116 (215)
.-.-....|+...|+++++. ...-..+....+.+ -+-+ ++.|+.++|++...
T Consensus 31 la~~~~~~~~y~~A~~~~~~--~~~~~~~~~~~~l~-a~~~---~~l~~y~eAi~~l~ 82 (84)
T PF12895_consen 31 LAQCYFQQGKYEEAIELLQK--LKLDPSNPDIHYLL-ARCL---LKLGKYEEAIKALE 82 (84)
T ss_dssp HHHHHHHTTHHHHHHHHHHC--HTHHHCHHHHHHHH-HHHH---HHTT-HHHHHHHHH
T ss_pred HHHHHHHCCCHHHHHHHHHH--hCCCCCCHHHHHHH-HHHH---HHhCCHHHHHHHHh
Confidence 44567788999999999876 22222332333322 3333 34577888877654
No 36
>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=48.01 E-value=1.1e+02 Score=24.20 Aligned_cols=88 Identities=15% Similarity=0.191 Sum_probs=46.5
Q ss_pred CCCCHHHHHHHHHHHHHhhcHHHHHHHHHHhhCCCCCCCCHHhHHHHHHHHHHHHcCCHHHHHHHHHHhcHHHHccCCcc
Q 027999 11 IAINDNDIHNIVLSYLVHNCYKETVDSFISCTGMKQPANCLEDMEMRKRILHFALEGNALKAIELTEELAQDLLEKNKDL 90 (215)
Q Consensus 11 ~~~~~~~l~~lI~~yL~~~Gy~eta~~f~~e~~~~~~~~~~~~~~~r~~I~~~I~~G~i~~Ai~~~~~~~p~l~~~~~~l 90 (215)
++++.. +..++.+=|++.|-......|.+-.=++++. +. . ...+--|. .+|...+-.-++
T Consensus 25 i~~~~~-L~~lli~lLi~~~~~~~L~qllq~~Vi~DSk---~l---A---~~LLs~~~----------~~~~~~Ql~lDM 84 (167)
T PF07035_consen 25 IPVQHE-LYELLIDLLIRNGQFSQLHQLLQYHVIPDSK---PL---A---CQLLSLGN----------QYPPAYQLGLDM 84 (167)
T ss_pred CCCCHH-HHHHHHHHHHHcCCHHHHHHHHhhcccCCcH---HH---H---HHHHHhHc----------cChHHHHHHHHH
Confidence 444433 6777777777777777666666543332211 10 0 11111111 233333333344
Q ss_pred hhhhh--HHHHHH-HHhccchhhHHHHHHHh
Q 027999 91 HFDLL--SLHFVE-LVCSRKCTEALEFAQTK 118 (215)
Q Consensus 91 ~F~L~--~q~fiE-li~~~~~~~Al~~ar~~ 118 (215)
...|. .-..+| |+..|++-+|+.|+|+.
T Consensus 85 LkRL~~~~~~iievLL~~g~vl~ALr~ar~~ 115 (167)
T PF07035_consen 85 LKRLGTAYEEIIEVLLSKGQVLEALRYARQY 115 (167)
T ss_pred HHHhhhhHHHHHHHHHhCCCHHHHHHHHHHc
Confidence 44444 233456 77899999999999973
No 37
>PF06794 UPF0270: Uncharacterised protein family (UPF0270); InterPro: IPR010648 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.; PDB: 1Y0N_A.
Probab=47.27 E-value=59 Score=21.82 Aligned_cols=44 Identities=11% Similarity=0.229 Sum_probs=24.5
Q ss_pred CCCHHHHHHHHHHHHHhhcHHHHHHHHHHhhCCCCCCCCHHhHHHHHHHHHHHHcCC
Q 027999 12 AINDNDIHNIVLSYLVHNCYKETVDSFISCTGMKQPANCLEDMEMRKRILHFALEGN 68 (215)
Q Consensus 12 ~~~~~~l~~lI~~yL~~~Gy~eta~~f~~e~~~~~~~~~~~~~~~r~~I~~~I~~G~ 68 (215)
..+++-|++||-+|..|+|..- |... ...-....+++..+.+|+
T Consensus 7 ~L~~eTL~nLIeefv~ReGTdy---------G~~E----~sL~~kv~qv~~qL~~G~ 50 (70)
T PF06794_consen 7 QLPPETLNNLIEEFVLREGTDY---------GEQE----LSLEEKVEQVKQQLKSGE 50 (70)
T ss_dssp GS-HHHHHHHHHHHHH-------------------------HHHHHHHHHHHHHTTS
T ss_pred HCCHHHHHHHHHHHHHccCccc---------Cccc----ccHHHHHHHHHHHHHcCC
Confidence 4678899999999999999532 2110 112245678888888886
No 38
>KOG0640 consensus mRNA cleavage stimulating factor complex; subunit 1 [RNA processing and modification]
Probab=46.82 E-value=35 Score=29.92 Aligned_cols=33 Identities=9% Similarity=0.125 Sum_probs=29.1
Q ss_pred CHHHHHHHHHHHHHhhcHHHHHHHHHHhhCCCC
Q 027999 14 NDNDIHNIVLSYLVHNCYKETVDSFISCTGMKQ 46 (215)
Q Consensus 14 ~~~~l~~lI~~yL~~~Gy~eta~~f~~e~~~~~ 46 (215)
|++.+-+||...|.+.||...|.++......+.
T Consensus 10 dre~lyrLiisqL~ydg~~qiA~~lan~~~~~~ 42 (430)
T KOG0640|consen 10 DREILYRLIISQLRYDGLSQIASALANATMTPA 42 (430)
T ss_pred hHHHHHHHHHHHHhhccHHHHHHHHHHhhcCcC
Confidence 688899999999999999999999998766543
No 39
>KOG2659 consensus LisH motif-containing protein [Cytoskeleton]
Probab=45.76 E-value=1.1e+02 Score=25.50 Aligned_cols=68 Identities=10% Similarity=0.072 Sum_probs=51.6
Q ss_pred CCHHHHH-HHHHHHHHhhcHHHHHHHHHHhhCCCC--CCCCHHhHHHHHHHHHHHHcCCHHHHHHHHHHhc
Q 027999 13 INDNDIH-NIVLSYLVHNCYKETVDSFISCTGMKQ--PANCLEDMEMRKRILHFALEGNALKAIELTEELA 80 (215)
Q Consensus 13 ~~~~~l~-~lI~~yL~~~Gy~eta~~f~~e~~~~~--~~~~~~~~~~r~~I~~~I~~G~i~~Ai~~~~~~~ 80 (215)
++.+.++ |+....++..|-.+.|-.+.....=.. ...++.+.-...+..+.|++|...+|++.++..-
T Consensus 60 ~d~~~~~eR~~Ir~~I~~G~Ie~Aie~in~l~PeiLd~n~~l~F~Lq~q~lIEliR~~~~eeal~F~q~~L 130 (228)
T KOG2659|consen 60 IDLDSMDERLQIRRAIEEGQIEEAIEKVNQLNPEILDTNRELFFHLQQLHLIELIREGKTEEALEFAQTKL 130 (228)
T ss_pred CchhhHhHHHHHHHHHHhccHHHHHHHHHHhChHHHccchhHHHHHHHHHHHHHHHhhhHHHHHHHHHHHc
Confidence 4445555 888899999999999999987755221 1112455667889999999999999999998653
No 40
>PF13432 TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL_A 3CVQ_A 3CV0_A 2GW1_B 3CVN_A 3QKY_A 2PL2_B.
Probab=45.12 E-value=74 Score=19.73 Aligned_cols=55 Identities=22% Similarity=0.174 Sum_probs=32.6
Q ss_pred HHHHHHcCCHHHHHHHHHHhcHHHHccCCcchhhhhHHHHHHHHhccchhhHHHHHHHhc
Q 027999 60 ILHFALEGNALKAIELTEELAQDLLEKNKDLHFDLLSLHFVELVCSRKCTEALEFAQTKL 119 (215)
Q Consensus 60 I~~~I~~G~i~~Ai~~~~~~~p~l~~~~~~l~F~L~~q~fiEli~~~~~~~Al~~ar~~l 119 (215)
-+.++..|+++.|++.+++ +++.++. .-..+...-.=+...|+..+|+.+.+.-+
T Consensus 4 a~~~~~~g~~~~A~~~~~~----~l~~~P~-~~~a~~~lg~~~~~~g~~~~A~~~~~~a~ 58 (65)
T PF13432_consen 4 ARALYQQGDYDEAIAAFEQ----ALKQDPD-NPEAWYLLGRILYQQGRYDEALAYYERAL 58 (65)
T ss_dssp HHHHHHCTHHHHHHHHHHH----HHCCSTT-HHHHHHHHHHHHHHTT-HHHHHHHHHHHH
T ss_pred HHHHHHcCCHHHHHHHHHH----HHHHCCC-CHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence 3567889999999988875 3555443 11111111112336788999988887644
No 41
>PF07079 DUF1347: Protein of unknown function (DUF1347); InterPro: IPR010764 This family consists of several hypothetical bacterial proteins of around 610 residues in length. Members of this family are highly conserved and seem to be specific to Chlamydia species. The function of this family is unknown.
Probab=45.06 E-value=97 Score=28.70 Aligned_cols=54 Identities=15% Similarity=0.083 Sum_probs=43.4
Q ss_pred HHHHHHHHHHHHcCCHHHHHHHHHHhcHHHHccCC--------cchhhhhHHHHHHHHhccc
Q 027999 54 MEMRKRILHFALEGNALKAIELTEELAQDLLEKNK--------DLHFDLLSLHFVELVCSRK 107 (215)
Q Consensus 54 ~~~r~~I~~~I~~G~i~~Ai~~~~~~~p~l~~~~~--------~l~F~L~~q~fiEli~~~~ 107 (215)
+-.-..+-..|..|.+.++-..+++..|.++++.. .+...|-+-.|+|+.....
T Consensus 129 ~l~~i~a~sLIe~g~f~EgR~iLn~i~~~llkrE~~w~~d~yd~~vlmlsrSYfLEl~e~~s 190 (549)
T PF07079_consen 129 FLDEIEAHSLIETGRFSEGRAILNRIIERLLKRECEWNSDMYDRAVLMLSRSYFLELKESMS 190 (549)
T ss_pred HHHHHHHHHHHhcCCcchHHHHHHHHHHHHhhhhhcccHHHHHHHHHHHhHHHHHHHHHhcc
Confidence 33445777899999999999999999999999522 3566888999999987543
No 42
>PF14689 SPOB_a: Sensor_kinase_SpoOB-type, alpha-helical domain; PDB: 1F51_C 2FTK_B 1IXM_B.
Probab=43.68 E-value=72 Score=20.54 Aligned_cols=34 Identities=24% Similarity=0.202 Sum_probs=26.6
Q ss_pred HHhHHHHHHHHHHHHcCCHHHHHHHHHHhcHHHH
Q 027999 51 LEDMEMRKRILHFALEGNALKAIELTEELAQDLL 84 (215)
Q Consensus 51 ~~~~~~r~~I~~~I~~G~i~~Ai~~~~~~~p~l~ 84 (215)
.+.....+-|...+.-|++++|.+.+++....+-
T Consensus 21 HD~~NhLqvI~gllqlg~~~~a~eYi~~~~~~~~ 54 (62)
T PF14689_consen 21 HDFLNHLQVIYGLLQLGKYEEAKEYIKELSKDLQ 54 (62)
T ss_dssp HHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 3566778889999999999999999988765443
No 43
>COG4105 ComL DNA uptake lipoprotein [General function prediction only]
Probab=42.25 E-value=2.1e+02 Score=24.19 Aligned_cols=65 Identities=17% Similarity=0.135 Sum_probs=47.7
Q ss_pred HHHHHHHHHHHHcCCHHHHHHHHHHhcHHHHccCCcchhhhhHHHHHHHH----hccchhhHHHHHHHhccccCC
Q 027999 54 MEMRKRILHFALEGNALKAIELTEELAQDLLEKNKDLHFDLLSLHFVELV----CSRKCTEALEFAQTKLTPFGK 124 (215)
Q Consensus 54 ~~~r~~I~~~I~~G~i~~Ai~~~~~~~p~l~~~~~~l~F~L~~q~fiEli----~~~~~~~Al~~ar~~l~~~~~ 124 (215)
-..-.+....+..|+++.|++..+.. ...++.-.+. .|--|+++ ++++..+|+.++-..+.-|..
T Consensus 35 ~~LY~~g~~~L~~gn~~~A~~~fe~l----~~~~p~s~~~--~qa~l~l~yA~Yk~~~y~~A~~~~drFi~lyP~ 103 (254)
T COG4105 35 SELYNEGLTELQKGNYEEAIKYFEAL----DSRHPFSPYS--EQAQLDLAYAYYKNGEYDLALAYIDRFIRLYPT 103 (254)
T ss_pred HHHHHHHHHHHhcCCHHHHHHHHHHH----HHcCCCCccc--HHHHHHHHHHHHhcccHHHHHHHHHHHHHhCCC
Confidence 35567899999999999999888754 4555544444 55556665 678899999888877766654
No 44
>PF04840 Vps16_C: Vps16, C-terminal region; InterPro: IPR006925 This protein forms part of the Class C vacuolar protein sorting (Vps) complex. Vps16 is essential for vacuolar protein sorting, which is essential for viability in plants, but not yeast []. The Class C Vps complex is required for SNARE-mediated membrane fusion at the lysosome-like yeast vacuole. It is thought to play essential roles in membrane docking and fusion at the Golgi-to-endosome and endosome-to-vacuole stages of transport []. The role of VPS16 in this complex is not known.; GO: 0006886 intracellular protein transport, 0005737 cytoplasm
Probab=41.55 E-value=1.3e+02 Score=26.22 Aligned_cols=77 Identities=12% Similarity=0.087 Sum_probs=47.9
Q ss_pred HHHHhhcHHHHHHHHHHhhCCCCCCCCHHhHHHHHHHHHHHHcCCHHHHHHHHHHhcHHHHccCCcchhhhhHHHHHHH-
Q 027999 24 SYLVHNCYKETVDSFISCTGMKQPANCLEDMEMRKRILHFALEGNALKAIELTEELAQDLLEKNKDLHFDLLSLHFVEL- 102 (215)
Q Consensus 24 ~yL~~~Gy~eta~~f~~e~~~~~~~~~~~~~~~r~~I~~~I~~G~i~~Ai~~~~~~~p~l~~~~~~l~F~L~~q~fiEl- 102 (215)
..|+..|....|..+.++.++++- . =-+-+|+.++..|+|++--.+..+ +.|.+=|.- |++.
T Consensus 185 ~~li~~~~~k~A~kl~k~Fkv~dk-----r-fw~lki~aLa~~~~w~eL~~fa~s-------kKsPIGyep----Fv~~~ 247 (319)
T PF04840_consen 185 RKLIEMGQEKQAEKLKKEFKVPDK-----R-FWWLKIKALAENKDWDELEKFAKS-------KKSPIGYEP----FVEAC 247 (319)
T ss_pred HHHHHCCCHHHHHHHHHHcCCcHH-----H-HHHHHHHHHHhcCCHHHHHHHHhC-------CCCCCChHH----HHHHH
Confidence 455667788888888888776421 1 234577778888888776666543 234444443 4443
Q ss_pred HhccchhhHHHHHHH
Q 027999 103 VCSRKCTEALEFAQT 117 (215)
Q Consensus 103 i~~~~~~~Al~~ar~ 117 (215)
++.|+..+|..|...
T Consensus 248 ~~~~~~~eA~~yI~k 262 (319)
T PF04840_consen 248 LKYGNKKEASKYIPK 262 (319)
T ss_pred HHCCCHHHHHHHHHh
Confidence 356667777777664
No 45
>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=40.69 E-value=50 Score=23.71 Aligned_cols=32 Identities=28% Similarity=0.293 Sum_probs=27.0
Q ss_pred hhhhHHHHHHHHhccchhhHHHHHHHhccccC
Q 027999 92 FDLLSLHFVELVCSRKCTEALEFAQTKLTPFG 123 (215)
Q Consensus 92 F~L~~q~fiEli~~~~~~~Al~~ar~~l~~~~ 123 (215)
|.=+-.+-+||++.+.--.|+.|++..+..+.
T Consensus 48 faPYEkr~mELlkv~kdKrAlKf~KKRlGth~ 79 (98)
T PF01158_consen 48 FAPYEKRAMELLKVSKDKRALKFAKKRLGTHI 79 (98)
T ss_dssp HCHHHHHHHHHHHHCCHHHHHHHHHHHHCHHH
T ss_pred CChHHHHHHHHHhcchhHHHHHHHHHHhhhhH
Confidence 45567788999999988999999999887664
No 46
>KOG1156 consensus N-terminal acetyltransferase [Chromatin structure and dynamics]
Probab=38.19 E-value=3.8e+02 Score=25.97 Aligned_cols=79 Identities=18% Similarity=0.146 Sum_probs=55.7
Q ss_pred HHHHHHHHHHHHcCCHHHHHHHHHHhcHHHHccCCcchhhhhHHHHHHHHhccchhhHHHHHHHhccccCCchhHHHHHH
Q 027999 54 MEMRKRILHFALEGNALKAIELTEELAQDLLEKNKDLHFDLLSLHFVELVCSRKCTEALEFAQTKLTPFGKVQKYVEKLE 133 (215)
Q Consensus 54 ~~~r~~I~~~I~~G~i~~Ai~~~~~~~p~l~~~~~~l~F~L~~q~fiEli~~~~~~~Al~~ar~~l~~~~~~~~~~~~l~ 133 (215)
.....++...+..|..+.|++.+..+-|.+.++ +-|...+-.+.. +-+..++|+...+..+.+...|-.+-..++
T Consensus 186 e~~Ly~n~i~~E~g~~q~ale~L~~~e~~i~Dk---la~~e~ka~l~~--kl~~lEeA~~~y~~Ll~rnPdn~~Yy~~l~ 260 (700)
T KOG1156|consen 186 ELLLYQNQILIEAGSLQKALEHLLDNEKQIVDK---LAFEETKADLLM--KLGQLEEAVKVYRRLLERNPDNLDYYEGLE 260 (700)
T ss_pred HHHHHHHHHHHHcccHHHHHHHHHhhhhHHHHH---HHHhhhHHHHHH--HHhhHHhHHHHHHHHHhhCchhHHHHHHHH
Confidence 345567788899999999999999998887754 445555544433 345689999999988887765444445555
Q ss_pred HHHh
Q 027999 134 DFMA 137 (215)
Q Consensus 134 ~~~~ 137 (215)
.+++
T Consensus 261 ~~lg 264 (700)
T KOG1156|consen 261 KALG 264 (700)
T ss_pred HHHH
Confidence 5554
No 47
>KOG3060 consensus Uncharacterized conserved protein [Function unknown]
Probab=37.74 E-value=2.6e+02 Score=23.95 Aligned_cols=106 Identities=21% Similarity=0.145 Sum_probs=70.7
Q ss_pred HHHHHHHHHHHhhcHHHHHHHHHHhhCCCCCCCCHHhHHHHHHHHHHH---HcCCHHHHHHHHHHhcHHHHccCCcchhh
Q 027999 17 DIHNIVLSYLVHNCYKETVDSFISCTGMKQPANCLEDMEMRKRILHFA---LEGNALKAIELTEELAQDLLEKNKDLHFD 93 (215)
Q Consensus 17 ~l~~lI~~yL~~~Gy~eta~~f~~e~~~~~~~~~~~~~~~r~~I~~~I---~~G~i~~Ai~~~~~~~p~l~~~~~~l~F~ 93 (215)
.+...|.=-.+..|-.+.|..-.+...-.+|. +.|-.+..+. ..|++++|++..+. +++++ ...+-
T Consensus 53 ~l~EqV~IAAld~~~~~lAq~C~~~L~~~fp~------S~RV~~lkam~lEa~~~~~~A~e~y~~----lL~dd-pt~~v 121 (289)
T KOG3060|consen 53 TLYEQVFIAALDTGRDDLAQKCINQLRDRFPG------SKRVGKLKAMLLEATGNYKEAIEYYES----LLEDD-PTDTV 121 (289)
T ss_pred HHHHHHHHHHHHhcchHHHHHHHHHHHHhCCC------ChhHHHHHHHHHHHhhchhhHHHHHHH----HhccC-cchhH
Confidence 34445555556666666666655554444444 3344443333 46999999988864 56654 67788
Q ss_pred hhHHHHHHHHhccchhhHHHHHHHhccccCCchhHHHHHH
Q 027999 94 LLSLHFVELVCSRKCTEALEFAQTKLTPFGKVQKYVEKLE 133 (215)
Q Consensus 94 L~~q~fiEli~~~~~~~Al~~ar~~l~~~~~~~~~~~~l~ 133 (215)
.++.+..=+-..|+..+||.-..+++..|-.|++.-.++.
T Consensus 122 ~~KRKlAilka~GK~l~aIk~ln~YL~~F~~D~EAW~eLa 161 (289)
T KOG3060|consen 122 IRKRKLAILKAQGKNLEAIKELNEYLDKFMNDQEAWHELA 161 (289)
T ss_pred HHHHHHHHHHHcCCcHHHHHHHHHHHHHhcCcHHHHHHHH
Confidence 8888877777789889999999999999987665433333
No 48
>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=37.67 E-value=42 Score=17.30 Aligned_cols=17 Identities=18% Similarity=0.155 Sum_probs=12.5
Q ss_pred HHHHHcCCHHHHHHHHH
Q 027999 61 LHFALEGNALKAIELTE 77 (215)
Q Consensus 61 ~~~I~~G~i~~Ai~~~~ 77 (215)
+-+...|++++|..++.
T Consensus 9 ~~~~~~G~~~eA~~~l~ 25 (26)
T PF07721_consen 9 RALLAQGDPDEAERLLR 25 (26)
T ss_pred HHHHHcCCHHHHHHHHh
Confidence 45667888888887764
No 49
>COG5443 FlbT Flagellar biosynthesis regulator FlbT [Cell motility and secretion]
Probab=37.15 E-value=58 Score=24.68 Aligned_cols=58 Identities=17% Similarity=0.122 Sum_probs=42.9
Q ss_pred HHHhhcHHHHHHHHHHhhCCCC-CCCCHHhHHHHHHHHHHHHcCCHHHHHHHHHHhcHH
Q 027999 25 YLVHNCYKETVDSFISCTGMKQ-PANCLEDMEMRKRILHFALEGNALKAIELTEELAQD 82 (215)
Q Consensus 25 yL~~~Gy~eta~~f~~e~~~~~-~~~~~~~~~~r~~I~~~I~~G~i~~Ai~~~~~~~p~ 82 (215)
|+--.|-.++...|.+..+.-. ...+-+.+...++|-.++.+|++-+|+..+...||-
T Consensus 65 linp~gaeq~~~~F~~~l~~l~~~f~~~eil~~lk~Id~lV~~~~~feALkaiR~lyp~ 123 (148)
T COG5443 65 LINPAGAEQATEMFRKSLNMLLACFKDAEILAALKRIDGLVMAGRAFEALKAIRGLYPI 123 (148)
T ss_pred hcCHhhHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHhccHHHHHHHHHhhhchh
Confidence 4445677777777776543211 112357788999999999999999999999999874
No 50
>COG5051 RPL36A Ribosomal protein L36E [Translation, ribosomal structure and biogenesis]
Probab=36.79 E-value=87 Score=21.98 Aligned_cols=43 Identities=16% Similarity=0.320 Sum_probs=33.2
Q ss_pred hHHHHHHHHhccchhhHHHHHHHhccccCCchhHHHHHHHHHhHhc
Q 027999 95 LSLHFVELVCSRKCTEALEFAQTKLTPFGKVQKYVEKLEDFMALLA 140 (215)
Q Consensus 95 ~~q~fiEli~~~~~~~Al~~ar~~l~~~~~~~~~~~~l~~~~~lla 140 (215)
+-.+.|+||++.+-..|-..+++.|..+. .-...++++...|.
T Consensus 53 yErr~i~Lirns~~krArKlakKRLGs~k---RAkaKvEel~~~i~ 95 (97)
T COG5051 53 YERRVIELIRNSQDKRARKLAKKRLGSLK---RAKAKVEELTSVIQ 95 (97)
T ss_pred HHHHHHHHHHhcccHHHHHHHHHHhhhHH---HHHHHHHHHHHHHh
Confidence 45678999999999999999999998874 55566666655543
No 51
>TIGR02531 yecD_yerC TrpR-related protein YerC/YecD. This model represents a protein subfamily found mostly in the Firmicutes (Bacillus and allies). This family is similar in sequence to the trp operon repressor TrpR described by TIGR01321, and represents a distinct clade within the broader family described by pfam01371. At least one species, Xylella fastidiosa, in the Proteobacteria, has a member of both this family and TIGR01321. Several genomes with a member of this family do not synthesize tryptophan, and members of this family should not be considered trp operon repressors without new evidence.
Probab=36.66 E-value=1.2e+02 Score=21.12 Aligned_cols=56 Identities=11% Similarity=0.175 Sum_probs=43.5
Q ss_pred HHHHHHHHHHhhcHHHHHHHHHHhhCCCCCCCCHHhHHHHHHHHHHHHcCCHHHHHHHH
Q 027999 18 IHNIVLSYLVHNCYKETVDSFISCTGMKQPANCLEDMEMRKRILHFALEGNALKAIELT 76 (215)
Q Consensus 18 l~~lI~~yL~~~Gy~eta~~f~~e~~~~~~~~~~~~~~~r~~I~~~I~~G~i~~Ai~~~ 76 (215)
..+.+.+.|+..+-.+.+..|..+.=. |. ..+.+..|..|...+.+|....+|+..
T Consensus 4 ~~~~~~~~~~~~~~~~~~~~~~~~l~t--~~-e~~~Ls~R~~I~~ll~~G~S~~eIA~~ 59 (88)
T TIGR02531 4 LLDELFDAILTLKNREECYRFFDDIAT--IN-EIQSLAQRLQVAKMLKQGKTYSDIEAE 59 (88)
T ss_pred HHHHHHHHHHhCCCHHHHHHHHHHhCC--HH-HHHhhhHHHHHHHHHHCCCCHHHHHHH
Confidence 456788899999999999999876442 22 356788999999999999877766544
No 52
>PF10827 DUF2552: Protein of unknown function (DUF2552) ; InterPro: IPR020157 This entry contains proteins with no known function.
Probab=36.33 E-value=24 Score=23.76 Aligned_cols=16 Identities=19% Similarity=0.034 Sum_probs=13.7
Q ss_pred CHHHHHHHHHHhcHHH
Q 027999 68 NALKAIELTEELAQDL 83 (215)
Q Consensus 68 ~i~~Ai~~~~~~~p~l 83 (215)
-++.||+|+.++.|.+
T Consensus 60 tld~Ai~Wi~e~M~~i 75 (79)
T PF10827_consen 60 TLDLAIAWIGEHMPHI 75 (79)
T ss_pred cHHHHHHHHHhcccch
Confidence 4789999999998865
No 53
>PF03477 ATP-cone: ATP cone domain; InterPro: IPR005144 The ATP-cone is an evolutionarily mobile, ATP-binding regulatory domain which is found in a variety of proteins including ribonucleotide reductases, phosphoglycerate kinases and transcriptional regulators []. In ribonucleotide reductase protein R1 (P28903 from SWISSPROT) from Escherichia coli this domain is located at the N terminus, and is composed mostly of helices []. It forms part of the allosteric effector region and contains the general allosteric activity site in a cleft located at the tip of the N-terminal region []. This site binds either ATP (activating) or dATP (inhibitory), with the base bound in a hydrophobic pocket and the phosphates bound to basic residues. Substrate binding to this site is thought to affect enzyme activity by altering the relative positions of the two subunits of ribonucleotide reductase.; PDB: 2XO4_A 1RLR_A 7R1R_B 5R1R_A 2XO5_B 2XAW_A 2R1R_C 2XAY_B 2X0X_C 2XAZ_A ....
Probab=36.10 E-value=35 Score=23.29 Aligned_cols=28 Identities=21% Similarity=0.475 Sum_probs=25.3
Q ss_pred CCCHHHHHHHHHHHHHhhcHHHHHHHHH
Q 027999 12 AINDNDIHNIVLSYLVHNCYKETVDSFI 39 (215)
Q Consensus 12 ~~~~~~l~~lI~~yL~~~Gy~eta~~f~ 39 (215)
.++..++..+|.+.|...|+.+.|+++.
T Consensus 55 ~is~~eI~~~v~~~L~~~~~~~~a~~yi 82 (90)
T PF03477_consen 55 EISTEEIQDIVENALMEEGFYDVARAYI 82 (90)
T ss_dssp TEEHHHHHHHHHHHHHTSTTHHHHHHHH
T ss_pred CeeHHHHHHHHHHHHHcCChHHHHHHHH
Confidence 5788999999999999999999998875
No 54
>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=35.82 E-value=56 Score=18.49 Aligned_cols=18 Identities=17% Similarity=0.213 Sum_probs=12.0
Q ss_pred HHHHHH--HcCCHHHHHHHH
Q 027999 59 RILHFA--LEGNALKAIELT 76 (215)
Q Consensus 59 ~I~~~I--~~G~i~~Ai~~~ 76 (215)
..+.++ ..|+++.|++|+
T Consensus 18 ~~~~AL~~~~~nve~A~~~L 37 (37)
T PF00627_consen 18 QAREALRACNGNVERAVDWL 37 (37)
T ss_dssp HHHHHHHHTTTSHHHHHHHH
T ss_pred HHHHHHHHcCCCHHHHHHhC
Confidence 344444 356899999886
No 55
>PRK01271 4-oxalocrotonate tautomerase; Provisional
Probab=35.24 E-value=65 Score=21.87 Aligned_cols=26 Identities=19% Similarity=0.301 Sum_probs=23.2
Q ss_pred CCHHHHHHHHHHHHHHHHHhcCCCCC
Q 027999 153 LSLEYRQHVADNLNRAILAHAERPRY 178 (215)
Q Consensus 153 l~~~~r~~la~~vn~~il~~~~~~~~ 178 (215)
.+.++..+++..|.+++.+.+|.|++
T Consensus 13 ~s~EqK~~La~~iT~a~~~~lg~~~e 38 (76)
T PRK01271 13 LDEEQKAALAADITDVIIRHLNSKDS 38 (76)
T ss_pred CCHHHHHHHHHHHHHHHHHHhCcCcc
Confidence 46789999999999999999999864
No 56
>PF13371 TPR_9: Tetratricopeptide repeat
Probab=34.50 E-value=1.2e+02 Score=19.09 Aligned_cols=53 Identities=25% Similarity=0.199 Sum_probs=35.9
Q ss_pred HHHcCCHHHHHHHHHHhcHHHHccCCcchhhhhHHHHHHHHhccchhhHHHHHHHhcc
Q 027999 63 FALEGNALKAIELTEELAQDLLEKNKDLHFDLLSLHFVELVCSRKCTEALEFAQTKLT 120 (215)
Q Consensus 63 ~I~~G~i~~Ai~~~~~~~p~l~~~~~~l~F~L~~q~fiEli~~~~~~~Al~~ar~~l~ 120 (215)
++..++++.|++.++.. +..+|. ...++...=.=+...|+..+|+....+.+.
T Consensus 5 ~~~~~~~~~A~~~~~~~----l~~~p~-~~~~~~~~a~~~~~~g~~~~A~~~l~~~l~ 57 (73)
T PF13371_consen 5 YLQQEDYEEALEVLERA----LELDPD-DPELWLQRARCLFQLGRYEEALEDLERALE 57 (73)
T ss_pred HHhCCCHHHHHHHHHHH----HHhCcc-cchhhHHHHHHHHHhccHHHHHHHHHHHHH
Confidence 57889999999998754 333333 333444444445677889999888887664
No 57
>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=34.08 E-value=2e+02 Score=21.53 Aligned_cols=30 Identities=17% Similarity=0.133 Sum_probs=26.1
Q ss_pred HhHHHHHHHHHHHHcCCHHHHHHHHHHhcH
Q 027999 52 EDMEMRKRILHFALEGNALKAIELTEELAQ 81 (215)
Q Consensus 52 ~~~~~r~~I~~~I~~G~i~~Ai~~~~~~~p 81 (215)
+.......+.++|.+|++-+|++.+...+|
T Consensus 90 ~~~~~l~~~~~~v~~g~~y~ALk~~R~L~~ 119 (126)
T PF07378_consen 90 DAREGLDEANELVEAGRYYKALKALRKLIP 119 (126)
T ss_pred HHHHHHHHHHHHHHCCcHHHHHHHHHHhHH
Confidence 455677899999999999999999998765
No 58
>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=33.20 E-value=76 Score=19.30 Aligned_cols=20 Identities=20% Similarity=0.351 Sum_probs=16.2
Q ss_pred CCHHHHHHHHHHHHHHHHHh
Q 027999 153 LSLEYRQHVADNLNRAILAH 172 (215)
Q Consensus 153 l~~~~r~~la~~vn~~il~~ 172 (215)
..+++|+.+|+.|..++..+
T Consensus 24 V~~~qR~~iAe~Fa~AL~~S 43 (44)
T PF07208_consen 24 VPPAQRQAIAEKFAQALKSS 43 (44)
T ss_dssp S-HHHHHHHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHHHHhc
Confidence 35789999999999988764
No 59
>PRK02220 4-oxalocrotonate tautomerase; Provisional
Probab=33.17 E-value=66 Score=20.09 Aligned_cols=26 Identities=12% Similarity=0.142 Sum_probs=23.0
Q ss_pred CCHHHHHHHHHHHHHHHHHhcCCCCC
Q 027999 153 LSLEYRQHVADNLNRAILAHAERPRY 178 (215)
Q Consensus 153 l~~~~r~~la~~vn~~il~~~~~~~~ 178 (215)
.+.+++.+++..+..++....|.|+.
T Consensus 12 rs~eqk~~l~~~it~~l~~~~~~p~~ 37 (61)
T PRK02220 12 RTEEQLKALVKDVTAAVSKNTGAPAE 37 (61)
T ss_pred CCHHHHHHHHHHHHHHHHHHhCcChh
Confidence 46889999999999999999999853
No 60
>smart00299 CLH Clathrin heavy chain repeat homology.
Probab=32.98 E-value=1.9e+02 Score=21.12 Aligned_cols=11 Identities=55% Similarity=0.440 Sum_probs=4.7
Q ss_pred CCHHHHHHHHH
Q 027999 67 GNALKAIELTE 77 (215)
Q Consensus 67 G~i~~Ai~~~~ 77 (215)
++.+.|++.+.
T Consensus 110 ~d~~~a~~~~~ 120 (140)
T smart00299 110 GNYEKAIEYFV 120 (140)
T ss_pred cCHHHHHHHHH
Confidence 34444444443
No 61
>KOG4594 consensus Sequence-specific single-stranded-DNA-binding protein [Replication, recombination and repair; Transcription; General function prediction only]
Probab=32.39 E-value=57 Score=28.13 Aligned_cols=28 Identities=21% Similarity=0.374 Sum_probs=24.8
Q ss_pred HHHHHHHHHHHHHhhcHHHHHHHHHHhh
Q 027999 15 DNDIHNIVLSYLVHNCYKETVDSFISCT 42 (215)
Q Consensus 15 ~~~l~~lI~~yL~~~Gy~eta~~f~~e~ 42 (215)
++.|.--|-+||+|-|-..+|+.|..|.
T Consensus 17 rekLa~YvYEYLlhvgaqksaqtflsei 44 (354)
T KOG4594|consen 17 REKLALYVYEYLLHVGAQKSAQTFLSEI 44 (354)
T ss_pred HHHHHHHHHHHHHHhhhhhhhhhhHHHH
Confidence 6678888999999999999999998764
No 62
>PF09312 SurA_N: SurA N-terminal domain; InterPro: IPR015391 The correct folding of outer membrane proteins in Gram negative bacteria is facilitated by the survival protein SurA []. This entry represents the domain found at the N terminus of the chaperone SurA. It is a helical domain of unknown function. The C terminus of the SurA protein folds back and forms part of this domain also but is not included in the current alignment. ; PDB: 3RGC_B 2PV3_B 1M5Y_A.
Probab=32.28 E-value=93 Score=22.62 Aligned_cols=48 Identities=21% Similarity=0.333 Sum_probs=26.7
Q ss_pred hcCCCCHHHHHHHHHHHHHhhcHHHHHHHHHHh---hCCCCCCCCHHhHHHHHHHHHHHH
Q 027999 9 EHIAINDNDIHNIVLSYLVHNCYKETVDSFISC---TGMKQPANCLEDMEMRKRILHFAL 65 (215)
Q Consensus 9 ~~~~~~~~~l~~lI~~yL~~~Gy~eta~~f~~e---~~~~~~~~~~~~~~~r~~I~~~I~ 65 (215)
.++.++..++++.|.+..-.+|. |...|.+. .|++. + .-|..|+..|.
T Consensus 63 ~gI~vsd~evd~~i~~ia~~n~l--s~~ql~~~L~~~G~s~-----~--~~r~~ir~~i~ 113 (118)
T PF09312_consen 63 LGIKVSDEEVDEAIANIAKQNNL--SVEQLRQQLEQQGISY-----E--EYREQIRKQIL 113 (118)
T ss_dssp CT----HHHHHHHHHHHHHHTT----HHHHHHHCHHCT--H-----H--HHHHHHHHHHH
T ss_pred cCCCCCHHHHHHHHHHHHHHcCC--CHHHHHHHHHHcCCCH-----H--HHHHHHHHHHH
Confidence 56788888888888888888887 45566554 45421 1 45667776654
No 63
>PRK09239 chorismate mutase; Provisional
Probab=32.14 E-value=1.9e+02 Score=20.79 Aligned_cols=50 Identities=10% Similarity=0.070 Sum_probs=33.3
Q ss_pred hhCCHHHHHHHHHHHHHHHHHhcCCCC---CcHHHHHHHHHHHHHHHHHhhcCC
Q 027999 151 HLLSLEYRQHVADNLNRAILAHAERPR---YAAMERLIQQTTAVRQCLSQELGK 201 (215)
Q Consensus 151 ~ll~~~~r~~la~~vn~~il~~~~~~~---~s~Le~l~~~~~~~~~~l~~~~~~ 201 (215)
..+++.++..+.+.+. ......|+++ .+.+..++......+.......|+
T Consensus 50 ~i~dp~RE~~vl~~~~-~~a~~~gl~p~~~~~i~~~ii~esir~q~~i~~~~~~ 102 (104)
T PRK09239 50 PPADPAREAYQIERLR-QLAKDANLDPDFAEKFLNFIIKEVIRHHERIAAEHGD 102 (104)
T ss_pred CCCCHHHHHHHHHHHH-HHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHhccCC
Confidence 3578999999999885 5667789875 234455555555556666555554
No 64
>cd00491 4Oxalocrotonate_Tautomerase 4-Oxalocrotonate Tautomerase: Catalyzes the isomerization of unsaturated ketones. The structure is a homohexamer that is arranged as a trimer of dimers. The hexamer contains six active sites, each formed by residues from three monomers, two from one dimer and the third from a neighboring monomer. Each monomer is a beta-alpha-beta fold with two small beta strands at the C-terminus that fold back on themselves. A pair of monomers form a dimer with two-fold symmetry, consisting of a 4-stranded beta sheet with two helices on one side and two additional small beta strands at each end. The dimers are assembled around a 3-fold axis of rotation to form a hexamer, with the short beta strands from each dimer contacting the neighboring dimers.
Probab=31.73 E-value=84 Score=19.22 Aligned_cols=25 Identities=12% Similarity=0.203 Sum_probs=22.3
Q ss_pred CHHHHHHHHHHHHHHHHHhcCCCCC
Q 027999 154 SLEYRQHVADNLNRAILAHAERPRY 178 (215)
Q Consensus 154 ~~~~r~~la~~vn~~il~~~~~~~~ 178 (215)
+++++.+++..+..++....|.|++
T Consensus 12 t~eqk~~l~~~i~~~l~~~~g~~~~ 36 (58)
T cd00491 12 TDEQKRELIERVTEAVSEILGAPEA 36 (58)
T ss_pred CHHHHHHHHHHHHHHHHHHhCcCcc
Confidence 5788999999999999999999864
No 65
>PF01361 Tautomerase: Tautomerase enzyme; InterPro: IPR004370 4-Oxalocrotonate tautomerase (4-OT) catalyzes the isomerisation of beta,gamma-unsaturated enones to their alpha,beta-isomers. The enzyme is part of a plasmid-encoded pathway, which enables bacteria harbouring the plasmid to use various aromatic hydrocarbons as their sole sources of carbon and energy. The enzyme is a barrel-shaped hexamer, which can be viewed as a trimer of dimers. The hexamer contains a hydrophobic core formed by three beta-sheets and surrounded by three pairs of alpha-helices. Each 4-OT monomer of 62 amino acids has a relatively simple beta-alpha-beta fold as described by the structure of the enzyme from Pseudomonas putida []. The monomer begins with a conserved proline at the start of a beta-strand, followed by an alpha-helix and a 310 helix preceding a second parallel beta-strand, and ends with a beta-hairpin near the C terminus. The dimer results from antiparallel interactions between the beta-sheets and alpha-helices of the two monomers, forming a four-stranded beta-sheet with antiparallel alpha-helices on one side, creating two active sites, one at each end of the beta-sheet. Three dimers further associate to form a hexamer by the interactions of the strands of the C-terminal beta-hairpin loops with the edges of the four-stranded beta-sheets of neighbouring dimers, creating a series of cross-links that stabilise the hexamer Pro-1 of the mature protein functions as the general base while Arg-39 and an ordered water molecule each provide a hydrogen bond to the C-2 oxygen of substrate. Arg-39 plays an additional role in the binding of the C-1 carboxylate group. Arg-11 participates both in substrate binding and in catalysis. It interacts with the C-6 carboxylate group, thereby holding the substrate in place and drawing electron density to the C-5 position. The hydrophobic nature of the active site, which lowers the pKa of Pro-1 and provides a favourable environment for catalysis, is largely maintained by Phe-50. Because several Arg residues located near the active site are not conserved among all members of this family and because of the presence of fairly distantly related paralogs in Campylobacter jejuni, the family is regarded as not necessarily uniform in function.; GO: 0016853 isomerase activity, 0006725 cellular aromatic compound metabolic process; PDB: 4OTA_H 4OTC_G 4OTB_J 2FM7_A 1BJP_B 1S0Y_K 3EJ9_E 3EJ7_K 3EJ3_I 3MB2_A ....
Probab=31.56 E-value=62 Score=20.23 Aligned_cols=25 Identities=16% Similarity=0.286 Sum_probs=20.9
Q ss_pred CHHHHHHHHHHHHHHHHHhcCCCCC
Q 027999 154 SLEYRQHVADNLNRAILAHAERPRY 178 (215)
Q Consensus 154 ~~~~r~~la~~vn~~il~~~~~~~~ 178 (215)
+.+++.+++..+..++.+.+|.|++
T Consensus 12 ~~e~K~~l~~~it~~~~~~lg~~~~ 36 (60)
T PF01361_consen 12 TAEQKRELAEAITDAVVEVLGIPPE 36 (60)
T ss_dssp -HHHHHHHHHHHHHHHHHHHTS-GG
T ss_pred CHHHHHHHHHHHHHHHHHHhCcCCC
Confidence 6788999999999999999999754
No 66
>PRK01964 4-oxalocrotonate tautomerase; Provisional
Probab=30.99 E-value=77 Score=20.13 Aligned_cols=26 Identities=19% Similarity=0.194 Sum_probs=23.0
Q ss_pred CCHHHHHHHHHHHHHHHHHhcCCCCC
Q 027999 153 LSLEYRQHVADNLNRAILAHAERPRY 178 (215)
Q Consensus 153 l~~~~r~~la~~vn~~il~~~~~~~~ 178 (215)
-+.+++.+++..+..++...+|.|++
T Consensus 12 rt~eqk~~l~~~it~~l~~~lg~p~~ 37 (64)
T PRK01964 12 RPEEKIKNLIREVTEAISATLDVPKE 37 (64)
T ss_pred CCHHHHHHHHHHHHHHHHHHhCcChh
Confidence 36789999999999999999999863
No 67
>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=30.86 E-value=1.5e+02 Score=23.97 Aligned_cols=64 Identities=16% Similarity=0.119 Sum_probs=41.7
Q ss_pred HHHHHHHHHHHcCCHHHHHHHHHHhcHHHHccCC------cchhhhhHHHHHHHHhccchhhHHHHHHHhc
Q 027999 55 EMRKRILHFALEGNALKAIELTEELAQDLLEKNK------DLHFDLLSLHFVELVCSRKCTEALEFAQTKL 119 (215)
Q Consensus 55 ~~r~~I~~~I~~G~i~~Ai~~~~~~~p~l~~~~~------~l~F~L~~q~fiEli~~~~~~~Al~~ar~~l 119 (215)
..|.+|.+.+- -.++.-++++......+.+..+ .+...+..-.|.++++.|+..+|...+.+.+
T Consensus 135 ~lr~~ie~~l~-~~~~~~~~~~~~~R~~~k~~~~~~~~r~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~ 204 (205)
T TIGR01470 135 LLRERIETLLP-PSLGDLATLAATWRDAVKKRLPNGAARRRFWEKFFDGAFAERVLAGREEQAERVLATRL 204 (205)
T ss_pred HHHHHHHHhcc-hhHHHHHHHHHHHHHHHHhhCCCHHHHHHHHHHHhccHHHHHHHcCCHHHHHHHHHHhh
Confidence 34566666553 3567777777777776665432 2333444456788889999988888877644
No 68
>PF15658 Latrotoxin_C: Latrotoxin C-terminal domain
Probab=30.74 E-value=2e+02 Score=21.63 Aligned_cols=52 Identities=10% Similarity=0.174 Sum_probs=34.8
Q ss_pred HhhcHHHHHHHHHHhhCCCCCCCCHHhHHHHHHHHHHHHcCCHHHHHHHHHH
Q 027999 27 VHNCYKETVDSFISCTGMKQPANCLEDMEMRKRILHFALEGNALKAIELTEE 78 (215)
Q Consensus 27 ~~~Gy~eta~~f~~e~~~~~~~~~~~~~~~r~~I~~~I~~G~i~~Ai~~~~~ 78 (215)
+..++.++....+-.+|+.-..-..+..+....|-..|.+|+..+--..+..
T Consensus 43 I~~kFE~VL~q~a~k~Gis~~~lniD~~evqs~I~~kI~sG~~neIs~~L~S 94 (127)
T PF15658_consen 43 ITEKFEEVLNQAALKSGISMHSLNIDFVEVQSKITKKIMSGKFNEISKILCS 94 (127)
T ss_pred HHHHHHHHHHHHHHhcCCCchhccCCHHHHHHHHHHHHHcCCchHHHHHHHH
Confidence 3455556666555566776544335677778889999999998876666544
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=30.62 E-value=82 Score=17.61 Aligned_cols=13 Identities=23% Similarity=0.210 Sum_probs=10.3
Q ss_pred HcCCHHHHHHHHH
Q 027999 65 LEGNALKAIELTE 77 (215)
Q Consensus 65 ~~G~i~~Ai~~~~ 77 (215)
..||++.|++|+-
T Consensus 25 ~~~d~~~A~~~L~ 37 (38)
T cd00194 25 TNNNVERAVEWLL 37 (38)
T ss_pred hCCCHHHHHHHHh
Confidence 4689999998873
No 70
>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=30.57 E-value=35 Score=29.30 Aligned_cols=51 Identities=12% Similarity=-0.217 Sum_probs=34.9
Q ss_pred hcHHHHHHHHHHhhCCCC----CCCCHHhHHHHHHHHHHHHcCCHHHHHHHHHHhc
Q 027999 29 NCYKETVDSFISCTGMKQ----PANCLEDMEMRKRILHFALEGNALKAIELTEELA 80 (215)
Q Consensus 29 ~Gy~eta~~f~~e~~~~~----~~~~~~~~~~r~~I~~~I~~G~i~~Ai~~~~~~~ 80 (215)
.|-.+..+.+.++.|+.. +...... -.-..||++|.+|+++.|-+++-..|
T Consensus 115 ~G~~~~L~~~~~~~g~~v~~~~~~~~~~~-ISST~IR~~l~~G~i~~A~~lLGr~y 169 (288)
T TIGR00083 115 QGDFLLLQLFGNTTIFCVIVKQLFCQDIR-ISSSAIRQALKNGDLELANKLLGRPY 169 (288)
T ss_pred CCCHHHHHHhccccCcEEEEeccccCCCe-ECHHHHHHHHHcCCHHHHHHhhhhhh
Confidence 467788888887777431 1110111 12368999999999999999998765
No 71
>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional
Probab=30.26 E-value=87 Score=25.21 Aligned_cols=28 Identities=14% Similarity=0.172 Sum_probs=20.2
Q ss_pred hHHHHHHHHHHHHcCCHHHHHHHHHHhc
Q 027999 53 DMEMRKRILHFALEGNALKAIELTEELA 80 (215)
Q Consensus 53 ~~~~r~~I~~~I~~G~i~~Ai~~~~~~~ 80 (215)
.+.+...|.++|.+||.+.|.+.+..|.
T Consensus 183 ~~~eH~~Il~Ai~~~D~~~A~~~~~~Hi 210 (224)
T PRK11534 183 KHDQHQTLTAAILARDTARASELMRQHL 210 (224)
T ss_pred HHHHHHHHHHHHHhCCHHHHHHHHHHHH
Confidence 4556677777777777777777777664
No 72
>TIGR00013 taut 4-oxalocrotonate tautomerase family enzyme. 4-oxalocrotonate tautomerase is a homohexamer in which each monomer is very small, at about 62 amino acids. Pro-1 of the mature protein serves as a general base. The enzyme functions in meta-cleavage pathways of aromatic hydrocarbon catabolism. Because several Arg residues located near the active site in the crystal structure of Pseudomonas putida are not conserved among all members of this family, because the literature describes a general role in the isomerization of beta,gamma-unsaturated enones to their alpha,beta-isomers, and because of the presence of fairly distantly related paralogs in Campylobacter jejuni, the family is regarded as not necessarily uniform in function.
Probab=29.56 E-value=96 Score=19.42 Aligned_cols=26 Identities=8% Similarity=0.059 Sum_probs=23.1
Q ss_pred CCHHHHHHHHHHHHHHHHHhcCCCCC
Q 027999 153 LSLEYRQHVADNLNRAILAHAERPRY 178 (215)
Q Consensus 153 l~~~~r~~la~~vn~~il~~~~~~~~ 178 (215)
.+.+++.+++..+..++...+|.|++
T Consensus 12 rt~eqK~~l~~~it~~l~~~lg~~~~ 37 (63)
T TIGR00013 12 RTDEQKRQLIEGVTEAMAETLGANLE 37 (63)
T ss_pred CCHHHHHHHHHHHHHHHHHHhCCCcc
Confidence 46889999999999999999999864
No 73
>PF09976 TPR_21: Tetratricopeptide repeat; InterPro: IPR018704 This domain, found in various hypothetical prokaryotic proteins, has no known function.
Probab=29.07 E-value=2.4e+02 Score=20.81 Aligned_cols=60 Identities=18% Similarity=0.125 Sum_probs=29.2
Q ss_pred HHHHHHHHHHHcCCHHHHHHHHHHhcHHHHccCCcchhhhhHHHHHH-HHhccchhhHHHHHHH
Q 027999 55 EMRKRILHFALEGNALKAIELTEELAQDLLEKNKDLHFDLLSLHFVE-LVCSRKCTEALEFAQT 117 (215)
Q Consensus 55 ~~r~~I~~~I~~G~i~~Ai~~~~~~~p~l~~~~~~l~F~L~~q~fiE-li~~~~~~~Al~~ar~ 117 (215)
.....-...+..|++++|++.++..--.- .++.+. .+-..+.-. ++..|+.++|+...+.
T Consensus 50 A~l~lA~~~~~~g~~~~A~~~l~~~~~~~--~d~~l~-~~a~l~LA~~~~~~~~~d~Al~~L~~ 110 (145)
T PF09976_consen 50 AALQLAKAAYEQGDYDEAKAALEKALANA--PDPELK-PLARLRLARILLQQGQYDEALATLQQ 110 (145)
T ss_pred HHHHHHHHHHHCCCHHHHHHHHHHHHhhC--CCHHHH-HHHHHHHHHHHHHcCCHHHHHHHHHh
Confidence 33334456667777877777776532110 111111 111111111 2356777777777765
No 74
>PF13424 TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15_A 3ASG_A 3ASD_A 3AS5_A 3AS4_A 3ASH_B 4A1S_B 3CEQ_B 3EDT_H ....
Probab=28.54 E-value=1.6e+02 Score=18.80 Aligned_cols=56 Identities=21% Similarity=0.112 Sum_probs=29.8
Q ss_pred HHHcCCHHHHHHHHHHhcHHHHccCC-cchhhhhHHHHHH--HHhccchhhHHHHHHHhc
Q 027999 63 FALEGNALKAIELTEELAQDLLEKNK-DLHFDLLSLHFVE--LVCSRKCTEALEFAQTKL 119 (215)
Q Consensus 63 ~I~~G~i~~Ai~~~~~~~p~l~~~~~-~l~F~L~~q~fiE--li~~~~~~~Al~~ar~~l 119 (215)
....|++++|+++.++--.- .+... .-........=+- ....|+.++|+++.++-+
T Consensus 15 ~~~~~~~~~A~~~~~~al~~-~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~al 73 (78)
T PF13424_consen 15 YRELGRYDEALDYYEKALDI-EEQLGDDHPDTANTLNNLGECYYRLGDYEEALEYYQKAL 73 (78)
T ss_dssp HHHTT-HHHHHHHHHHHHHH-HHHTTTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHH
T ss_pred HHHcCCHHHHHHHHHHHHHH-HHHHCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence 34778999999888876543 33211 1111122211111 124578888988887643
No 75
>COG0268 RpsT Ribosomal protein S20 [Translation, ribosomal structure and biogenesis]
Probab=28.47 E-value=1e+02 Score=21.67 Aligned_cols=29 Identities=14% Similarity=0.066 Sum_probs=24.8
Q ss_pred HHHHHHHHHcCCHHHHHHHHHHhcHHHHc
Q 027999 57 RKRILHFALEGNALKAIELTEELAQDLLE 85 (215)
Q Consensus 57 r~~I~~~I~~G~i~~Ai~~~~~~~p~l~~ 85 (215)
.+.+..+|..||.+.|.+.+...+|.+..
T Consensus 32 iKk~~~ai~~gd~~~A~~~l~~a~~~idk 60 (88)
T COG0268 32 IKKVEAAIEAGDKEAAKAALKEAQKKIDK 60 (88)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHHHHHHHH
Confidence 45778899999999999999998887665
No 76
>PF04840 Vps16_C: Vps16, C-terminal region; InterPro: IPR006925 This protein forms part of the Class C vacuolar protein sorting (Vps) complex. Vps16 is essential for vacuolar protein sorting, which is essential for viability in plants, but not yeast []. The Class C Vps complex is required for SNARE-mediated membrane fusion at the lysosome-like yeast vacuole. It is thought to play essential roles in membrane docking and fusion at the Golgi-to-endosome and endosome-to-vacuole stages of transport []. The role of VPS16 in this complex is not known.; GO: 0006886 intracellular protein transport, 0005737 cytoplasm
Probab=28.45 E-value=2.2e+02 Score=24.74 Aligned_cols=62 Identities=13% Similarity=0.124 Sum_probs=48.0
Q ss_pred hcCCCCHHHHHHHHHHHHHhhcHHHHHHHHHHhhCCCCCCCCHHhHHHHHHHHHHHHcCCHHHHHHHHHH
Q 027999 9 EHIAINDNDIHNIVLSYLVHNCYKETVDSFISCTGMKQPANCLEDMEMRKRILHFALEGNALKAIELTEE 78 (215)
Q Consensus 9 ~~~~~~~~~l~~lI~~yL~~~Gy~eta~~f~~e~~~~~~~~~~~~~~~r~~I~~~I~~G~i~~Ai~~~~~ 78 (215)
..++|+....-++...-|...|.++-...|.++-. .|.-..++ |...+..|+..+|..++..
T Consensus 201 k~Fkv~dkrfw~lki~aLa~~~~w~eL~~fa~skK--sPIGyepF------v~~~~~~~~~~eA~~yI~k 262 (319)
T PF04840_consen 201 KEFKVPDKRFWWLKIKALAENKDWDELEKFAKSKK--SPIGYEPF------VEACLKYGNKKEASKYIPK 262 (319)
T ss_pred HHcCCcHHHHHHHHHHHHHhcCCHHHHHHHHhCCC--CCCChHHH------HHHHHHCCCHHHHHHHHHh
Confidence 45899999999999999999999999999998633 23222222 3445678889999988876
No 77
>TIGR03338 phnR_burk phosphonate utilization associated transcriptional regulator. This family of proteins are members of the GntR family (pfam00392) containing an N-terminal helix-turn-helix (HTH) motif. This clade is found adjacent to or inside of operons for the degradation of 2-aminoethylphosphonate (AEP) in Polaromonas, Burkholderia, Ralstonia and Verminephrobacter.
Probab=28.32 E-value=1.1e+02 Score=24.23 Aligned_cols=29 Identities=17% Similarity=0.137 Sum_probs=20.5
Q ss_pred HhHHHHHHHHHHHHcCCHHHHHHHHHHhc
Q 027999 52 EDMEMRKRILHFALEGNALKAIELTEELA 80 (215)
Q Consensus 52 ~~~~~r~~I~~~I~~G~i~~Ai~~~~~~~ 80 (215)
..+.....|.++|..||.+.|.+.+..|.
T Consensus 178 ~~~~~H~~i~~ai~~~d~~~A~~~~~~Hl 206 (212)
T TIGR03338 178 VSAAEHRAIVDAIASGDAERAGALMRAHV 206 (212)
T ss_pred HHHHHHHHHHHHHHhCCHHHHHHHHHHHH
Confidence 34566677777777777777777777664
No 78
>PF14691 Fer4_20: Dihydroprymidine dehydrogenase domain II, 4Fe-4S cluster; PDB: 2VDC_G 1H7X_C 1H7W_A 1GT8_A 1GTE_B 1GTH_B.
Probab=28.26 E-value=80 Score=23.02 Aligned_cols=25 Identities=28% Similarity=0.243 Sum_probs=19.3
Q ss_pred HHHHHHHHHcCCHHHHHHHHHHhcH
Q 027999 57 RKRILHFALEGNALKAIELTEELAQ 81 (215)
Q Consensus 57 r~~I~~~I~~G~i~~Ai~~~~~~~p 81 (215)
-.++..+|..|++.+|++.+.+..|
T Consensus 42 ip~~i~~i~~g~~~~A~~~i~~~np 66 (111)
T PF14691_consen 42 IPEYIRLIREGNFKEAYELIREDNP 66 (111)
T ss_dssp HHHHHHHHHCT-HHHHHHHHHHH-T
T ss_pred HHHHHHHHHCCCHHHHHHHHHHhCC
Confidence 4678889999999999999987643
No 79
>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional
Probab=27.86 E-value=98 Score=25.54 Aligned_cols=24 Identities=8% Similarity=0.021 Sum_probs=12.2
Q ss_pred HHHHHHHhccchhhHHHHHHHhcc
Q 027999 97 LHFVELVCSRKCTEALEFAQTKLT 120 (215)
Q Consensus 97 q~fiEli~~~~~~~Al~~ar~~l~ 120 (215)
.+.++.|++||...|-...+.|+.
T Consensus 202 ~~I~~Ai~~~D~~~A~~~m~~Hi~ 225 (257)
T PRK10225 202 KQILAALIKKDARAAKLAMWQHLE 225 (257)
T ss_pred HHHHHHHHhCCHHHHHHHHHHHHH
Confidence 344455555555555555555553
No 80
>PF12931 Sec16_C: Sec23-binding domain of Sec16; PDB: 3MZK_C.
Probab=27.69 E-value=62 Score=27.54 Aligned_cols=21 Identities=33% Similarity=0.445 Sum_probs=14.6
Q ss_pred HHHHHHHcCCHHHHHHHHHHh
Q 027999 59 RILHFALEGNALKAIELTEEL 79 (215)
Q Consensus 59 ~I~~~I~~G~i~~Ai~~~~~~ 79 (215)
+|+++++.|+.++|+++|-+.
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 477788888888888777544
No 81
>PRK12791 flbT flagellar biosynthesis repressor FlbT; Reviewed
Probab=27.17 E-value=1.3e+02 Score=22.83 Aligned_cols=30 Identities=20% Similarity=0.252 Sum_probs=24.8
Q ss_pred hHHHHHHHHHHHHcCCHHHHHHHHHHhcHH
Q 027999 53 DMEMRKRILHFALEGNALKAIELTEELAQD 82 (215)
Q Consensus 53 ~~~~r~~I~~~I~~G~i~~Ai~~~~~~~p~ 82 (215)
.......|.++|.+|++-+|++.+....|.
T Consensus 90 ~~~~l~~~~~~v~~g~~Y~ALK~~R~Li~~ 119 (131)
T PRK12791 90 AWPIIEAINNHILNGDLYKALKELRKLIAR 119 (131)
T ss_pred HHHHHHHHHHHHhCCCHHHHHHHHHHhHHH
Confidence 345667788999999999999999987753
No 82
>COG3492 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=26.62 E-value=1.7e+02 Score=20.72 Aligned_cols=45 Identities=24% Similarity=0.308 Sum_probs=36.2
Q ss_pred CCHHHHHHHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHHHHHh
Q 027999 153 LSLEYRQHVADNLNRAILAHAERPRYAAMERLIQQTTAVRQCLSQ 197 (215)
Q Consensus 153 l~~~~r~~la~~vn~~il~~~~~~~~s~Le~l~~~~~~~~~~l~~ 197 (215)
+++++|.++.-..-+.++.++...+...--.|+.-+.-|++||+.
T Consensus 6 ls~~q~~~leAAaFRrLv~HL~~rsdvQNIDLMnLAgFCRNCLs~ 50 (104)
T COG3492 6 LSEEQRDRLEAAAFRRLVEHLQERSDVQNIDLMNLAGFCRNCLSN 50 (104)
T ss_pred cCHHHHHHHHHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHHH
Confidence 567888888888888888888776666667788888888888854
No 83
>KOG0396 consensus Uncharacterized conserved protein [Function unknown]
Probab=26.39 E-value=2.6e+02 Score=25.12 Aligned_cols=65 Identities=14% Similarity=0.015 Sum_probs=43.4
Q ss_pred HHHHHHHhhcHHHHHHHHHHhhCCCC--CCCCHHhHHHHHHHHHHHHcCCHHHHHHHHHHhcHHHHcc
Q 027999 21 IVLSYLVHNCYKETVDSFISCTGMKQ--PANCLEDMEMRKRILHFALEGNALKAIELTEELAQDLLEK 86 (215)
Q Consensus 21 lI~~yL~~~Gy~eta~~f~~e~~~~~--~~~~~~~~~~r~~I~~~I~~G~i~~Ai~~~~~~~p~l~~~ 86 (215)
.|.+-|.+.- .+.|-++|+|-.... .....+.--..++..++|..+++++||+.+++++...-+.
T Consensus 158 ~I~~sll~~~-l~~~Lswc~ehk~~LkK~~S~lEf~lRlQefIELi~~~~~~~Ai~~akk~f~~~~~~ 224 (389)
T KOG0396|consen 158 GIRDSLLAGE-LEPALSWCKEHKVELKKEESSLEFQLRLQEFIELIKVDNYDKAIAFAKKHFAPWAKS 224 (389)
T ss_pred HHHHHHHhcc-hHHHHHHHHHHHHHHHhccchhhhHHHHHHHHHHHHhccHHHHHHHHHHHHhhhhhh
Confidence 3555555554 666777777754321 1122444455678889999999999999999987655544
No 84
>PRK00745 4-oxalocrotonate tautomerase; Provisional
Probab=26.25 E-value=1.1e+02 Score=19.13 Aligned_cols=25 Identities=12% Similarity=0.332 Sum_probs=22.5
Q ss_pred CCHHHHHHHHHHHHHHHHHhcCCCC
Q 027999 153 LSLEYRQHVADNLNRAILAHAERPR 177 (215)
Q Consensus 153 l~~~~r~~la~~vn~~il~~~~~~~ 177 (215)
.+.+++.+|+..+..++...+|.|+
T Consensus 12 rs~eqk~~l~~~it~~l~~~~~~p~ 36 (62)
T PRK00745 12 RTVEQKRKLVEEITRVTVETLGCPP 36 (62)
T ss_pred CCHHHHHHHHHHHHHHHHHHcCCCh
Confidence 3688999999999999999999985
No 85
>PF09048 Cro: Cro; InterPro: IPR000655 Bacteriophage lambda encodes two repressors: the Cro repressor that acts to turn off early gene transcription during the lytic cycle, and the lambda or cI repressor that is required to maintain lysogenic growth. Together the Cro and cI repressors form a helix-turn-helix (HTH) superfamily. The lambda Cro repressor binds to DNA as a highly flexible dimer. The crystal structure of the lambda Cro repressor [] reveals a HTH DNA-binding protein with an alpha/beta fold that differs from other Cro family members, possibly by an evolutionary fold change []. Most Cro proteins, such as Enterobacteria phage P22 Cro and Bacteriophage 434 Cro, have an all-alpha structure that is thought to be ancestral to lambda Cro, where the fourth and fifth helices are replaced by a beta-sheet, possibly as a result of secondary structure switching rather than by nonhomologous replacement []. This entry represents the lambda-type Cro repressor with an alpha/beta topology.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 5CRO_A 2ECS_A 2OVG_A 6CRO_A 1D1L_A 2ORC_A 1D1M_B 3ORC_A 1ORC_A 2A63_A ....
Probab=26.13 E-value=1.4e+02 Score=19.39 Aligned_cols=17 Identities=6% Similarity=0.216 Sum_probs=15.1
Q ss_pred HHHHHHhhcHHHHHHHH
Q 027999 22 VLSYLVHNCYKETVDSF 38 (215)
Q Consensus 22 I~~yL~~~Gy~eta~~f 38 (215)
+.+|....|-.++|+.|
T Consensus 6 L~eyv~~~GQ~kaA~~l 22 (59)
T PF09048_consen 6 LAEYVKEHGQAKAARAL 22 (59)
T ss_dssp HHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHhChHHHHHHc
Confidence 57899999999999987
No 86
>KOG1920 consensus IkappaB kinase complex, IKAP component [Transcription]
Probab=25.76 E-value=7.9e+02 Score=25.76 Aligned_cols=85 Identities=18% Similarity=0.191 Sum_probs=51.4
Q ss_pred HHHHHHHHHHhhcHHHHHHHHHHhhCCCCCCCCHHhHHHHHHHHHHHHcCCHHHHHHHHHHhcHHHHccCCcchhhhhHH
Q 027999 18 IHNIVLSYLVHNCYKETVDSFISCTGMKQPANCLEDMEMRKRILHFALEGNALKAIELTEELAQDLLEKNKDLHFDLLSL 97 (215)
Q Consensus 18 l~~lI~~yL~~~Gy~eta~~f~~e~~~~~~~~~~~~~~~r~~I~~~I~~G~i~~Ai~~~~~~~p~l~~~~~~l~F~L~~q 97 (215)
+-.+=++||..++..+-|..+-.-+| ..-+.+..+...|+|.+|+..+.+..+. .-++..+-.
T Consensus 941 i~~~ya~hL~~~~~~~~Aal~Ye~~G-----------klekAl~a~~~~~dWr~~l~~a~ql~~~------~de~~~~a~ 1003 (1265)
T KOG1920|consen 941 IYEAYADHLREELMSDEAALMYERCG-----------KLEKALKAYKECGDWREALSLAAQLSEG------KDELVILAE 1003 (1265)
T ss_pred HHHHHHHHHHHhccccHHHHHHHHhc-----------cHHHHHHHHHHhccHHHHHHHHHhhcCC------HHHHHHHHH
Confidence 33455777777776666665555555 2235677788899999999999876542 222333334
Q ss_pred HHHHHH-hccchhhHHHHHHHhc
Q 027999 98 HFVELV-CSRKCTEALEFAQTKL 119 (215)
Q Consensus 98 ~fiEli-~~~~~~~Al~~ar~~l 119 (215)
..+..+ ..+...+|=....+++
T Consensus 1004 ~L~s~L~e~~kh~eAa~il~e~~ 1026 (1265)
T KOG1920|consen 1004 ELVSRLVEQRKHYEAAKILLEYL 1026 (1265)
T ss_pred HHHHHHHHcccchhHHHHHHHHh
Confidence 444433 4566666655555433
No 87
>PF10075 PCI_Csn8: COP9 signalosome, subunit CSN8; InterPro: IPR019280 The photomorphogenic 9 (COP9) signalosome or CSN complex is composed of eight subunits: Cops1/GPS1, Cops2, Cops3, Cops4, Cops5, Cop6, Cops7 (Cops7A or Cops7B) and Cops8. In the complex, Cops8, which is the smallest subunit, probably interacts directly with Cops3, Cops4 and Cops7 (Cops7A or Cops7B). This signalosome is homologous to the lid subcomplex of the 26S proteasome and regulates the ubiquitin-proteasome pathway. It functions as a structural scaffold for subunit-subunit interactions within the complex and is a key regulator of photomorphogenic development [].; PDB: 1RZ4_A.
Probab=25.60 E-value=2.1e+02 Score=21.37 Aligned_cols=55 Identities=5% Similarity=0.061 Sum_probs=30.7
Q ss_pred HHHHHHHcCCHHHHHHHHHHhcHHHHccCCcchhhhhHHHHHHHHhccchhhHHHHHH
Q 027999 59 RILHFALEGNALKAIELTEELAQDLLEKNKDLHFDLLSLHFVELVCSRKCTEALEFAQ 116 (215)
Q Consensus 59 ~I~~~I~~G~i~~Ai~~~~~~~p~l~~~~~~l~F~L~~q~fiEli~~~~~~~Al~~ar 116 (215)
-+..++..+++.+|--.....-+.+...++.+..-..-.++ +..++..+....++
T Consensus 10 ~Ll~~L~~~~~~df~~~~~rip~~~~~~~~~i~~i~~l~~~---L~~~~~~~~~~~~~ 64 (143)
T PF10075_consen 10 ILLKYLMQNDLSDFRLLWKRIPEELKQSDPEIKAIWSLGQA---LWEGDYSKFWQALR 64 (143)
T ss_dssp HHHHHHHTTTSTHHHHHHHTS-HHHHTS-TTHHHHHHHHHH---HHTT-HHHHHHHS-
T ss_pred HHHHHHHcCCchHHHHHHHcCCHHHHhhhHHHHHHHHHHHH---HHCCCHHHHHHHHH
Confidence 44577788888887777777666666655666554433333 33555555554444
No 88
>PRK04984 fatty acid metabolism regulator; Provisional
Probab=25.56 E-value=1.2e+02 Score=24.65 Aligned_cols=29 Identities=14% Similarity=0.169 Sum_probs=21.2
Q ss_pred HhHHHHHHHHHHHHcCCHHHHHHHHHHhc
Q 027999 52 EDMEMRKRILHFALEGNALKAIELTEELA 80 (215)
Q Consensus 52 ~~~~~r~~I~~~I~~G~i~~Ai~~~~~~~ 80 (215)
..+.....|.++|..||.+.|.+.+..|.
T Consensus 188 ~~~~~H~~I~~Ai~~~D~~~a~~~~~~H~ 216 (239)
T PRK04984 188 LALGFYHKLSALCEEGNHDQVPECVRQYG 216 (239)
T ss_pred HHHHHHHHHHHHHHhCCHHHHHHHHHHHH
Confidence 34566777888888888888887777664
No 89
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=25.37 E-value=1.4e+02 Score=19.49 Aligned_cols=50 Identities=12% Similarity=0.302 Sum_probs=36.6
Q ss_pred CCHHHHHHHHHHHHHhhcH-HHHHHHHHHhhCCCCCCCCHHhHHHHHHHHHHHHcCCH
Q 027999 13 INDNDIHNIVLSYLVHNCY-KETVDSFISCTGMKQPANCLEDMEMRKRILHFALEGNA 69 (215)
Q Consensus 13 ~~~~~l~~lI~~yL~~~Gy-~eta~~f~~e~~~~~~~~~~~~~~~r~~I~~~I~~G~i 69 (215)
++++...+-|+.+|...|- .=++..++++.|++.. ..++.+..+...|-+
T Consensus 2 ~~~~~~~~~IL~~L~~~g~~~~ta~eLa~~lgl~~~-------~v~r~L~~L~~~G~V 52 (68)
T smart00550 2 LTQDSLEEKILEFLENSGDETSTALQLAKNLGLPKK-------EVNRVLYSLEKKGKV 52 (68)
T ss_pred CCchHHHHHHHHHHHHCCCCCcCHHHHHHHHCCCHH-------HHHHHHHHHHHCCCE
Confidence 4667788999999999987 3689999999997532 345555566666654
No 90
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=25.34 E-value=1.1e+02 Score=16.92 Aligned_cols=12 Identities=33% Similarity=0.390 Sum_probs=9.6
Q ss_pred HcCCHHHHHHHH
Q 027999 65 LEGNALKAIELT 76 (215)
Q Consensus 65 ~~G~i~~Ai~~~ 76 (215)
..||++.|++|+
T Consensus 25 ~~~d~~~A~~~L 36 (37)
T smart00165 25 ANGNVERAAEYL 36 (37)
T ss_pred hCCCHHHHHHHH
Confidence 468899999886
No 91
>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=24.91 E-value=1.3e+02 Score=24.45 Aligned_cols=28 Identities=11% Similarity=0.191 Sum_probs=17.5
Q ss_pred hHHHHHHHHHHHHcCCHHHHHHHHHHhc
Q 027999 53 DMEMRKRILHFALEGNALKAIELTEELA 80 (215)
Q Consensus 53 ~~~~r~~I~~~I~~G~i~~Ai~~~~~~~ 80 (215)
.+.....|.++|..||.+.|..++..|.
T Consensus 188 ~~~~H~~I~~Ai~~~d~~~A~~~m~~H~ 215 (235)
T TIGR02812 188 ALQFYKELQALCKAGNHDEVPDCIRQYG 215 (235)
T ss_pred HHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence 3455566666666666666666666553
No 92
>PF13934 ELYS: Nuclear pore complex assembly
Probab=24.85 E-value=3.9e+02 Score=21.88 Aligned_cols=49 Identities=22% Similarity=0.213 Sum_probs=26.6
Q ss_pred HHHHHHHHhhcH---HHHHHHHHHhhCCCCCCCCHHhHHHHHHHH--HHHHcCCHHHHHHHH
Q 027999 20 NIVLSYLVHNCY---KETVDSFISCTGMKQPANCLEDMEMRKRIL--HFALEGNALKAIELT 76 (215)
Q Consensus 20 ~lI~~yL~~~Gy---~eta~~f~~e~~~~~~~~~~~~~~~r~~I~--~~I~~G~i~~Ai~~~ 76 (215)
.+|.=+|...+- .+.+..|....+++.. -++.|+ =++-.|+++.|++.+
T Consensus 48 ~l~~YlLlD~~~~~~~~~~~~Fa~~f~ip~~--------~~~~~~g~W~LD~~~~~~A~~~L 101 (226)
T PF13934_consen 48 SLFYYLLLDLDDTRPSELAESFARAFGIPPK--------YIKFIQGFWLLDHGDFEEALELL 101 (226)
T ss_pred HHHHHHHHhcCccccccHHHHHHHHhCCCHH--------HHHHHHHHHHhChHhHHHHHHHh
Confidence 344444444433 4588889988887521 122222 123346777777766
No 93
>PF14691 Fer4_20: Dihydroprymidine dehydrogenase domain II, 4Fe-4S cluster; PDB: 2VDC_G 1H7X_C 1H7W_A 1GT8_A 1GTE_B 1GTH_B.
Probab=24.84 E-value=88 Score=22.80 Aligned_cols=30 Identities=20% Similarity=0.327 Sum_probs=21.5
Q ss_pred hhhhHHHHHHHHhccchhhHHHHHHHhcccc
Q 027999 92 FDLLSLHFVELVCSRKCTEALEFAQTKLTPF 122 (215)
Q Consensus 92 F~L~~q~fiEli~~~~~~~Al~~ar~~l~~~ 122 (215)
..+....||.+++.|+..+|++..++ -.||
T Consensus 38 ~~~dip~~i~~i~~g~~~~A~~~i~~-~np~ 67 (111)
T PF14691_consen 38 AHIDIPEYIRLIREGNFKEAYELIRE-DNPF 67 (111)
T ss_dssp T---HHHHHHHHHCT-HHHHHHHHHH-H-TT
T ss_pred CCCcHHHHHHHHHCCCHHHHHHHHHH-hCCC
Confidence 46677999999999999999999985 3344
No 94
>COG3071 HemY Uncharacterized enzyme of heme biosynthesis [Coenzyme metabolism]
Probab=24.68 E-value=5.3e+02 Score=23.36 Aligned_cols=123 Identities=9% Similarity=0.040 Sum_probs=65.8
Q ss_pred hhcCCCCHHHHHHHHHHHHHhhcHHHHHHHHHHh---hCCCCCCC--------------------CH-------------
Q 027999 8 YEHIAINDNDIHNIVLSYLVHNCYKETVDSFISC---TGMKQPAN--------------------CL------------- 51 (215)
Q Consensus 8 ~~~~~~~~~~l~~lI~~yL~~~Gy~eta~~f~~e---~~~~~~~~--------------------~~------------- 51 (215)
+..+.....++-+|-.++.++.|-...+-++-.. +|.-.+++ ..
T Consensus 179 ll~~~pr~~~vlrLa~r~y~~~g~~~~ll~~l~~L~ka~~l~~~e~~~le~~a~~glL~q~~~~~~~~gL~~~W~~~pr~ 258 (400)
T COG3071 179 LLEMTPRHPEVLRLALRAYIRLGAWQALLAILPKLRKAGLLSDEEAARLEQQAWEGLLQQARDDNGSEGLKTWWKNQPRK 258 (400)
T ss_pred HHHhCcCChHHHHHHHHHHHHhccHHHHHHHHHHHHHccCCChHHHHHHHHHHHHHHHHHHhccccchHHHHHHHhccHH
Confidence 3345555667889999999999988877665432 22211110 00
Q ss_pred ---HhHHHHHHHHHHHHcCCHHHHHHHHHHhcHHHHccCCcchhhhhHHHHHHHHhccchhhHHHHHHHhccccCCchhH
Q 027999 52 ---EDMEMRKRILHFALEGNALKAIELTEELAQDLLEKNKDLHFDLLSLHFVELVCSRKCTEALEFAQTKLTPFGKVQKY 128 (215)
Q Consensus 52 ---~~~~~r~~I~~~I~~G~i~~Ai~~~~~~~p~l~~~~~~l~F~L~~q~fiEli~~~~~~~Al~~ar~~l~~~~~~~~~ 128 (215)
+.--...-+..+|..|+-++|.+|+.+..+.-.+.+ ...+|.-++-++...-++-+++-+.....+|
T Consensus 259 lr~~p~l~~~~a~~li~l~~~~~A~~~i~~~Lk~~~D~~--------L~~~~~~l~~~d~~~l~k~~e~~l~~h~~~p-- 328 (400)
T COG3071 259 LRNDPELVVAYAERLIRLGDHDEAQEIIEDALKRQWDPR--------LCRLIPRLRPGDPEPLIKAAEKWLKQHPEDP-- 328 (400)
T ss_pred hhcChhHHHHHHHHHHHcCChHHHHHHHHHHHHhccChh--------HHHHHhhcCCCCchHHHHHHHHHHHhCCCCh--
Confidence 000112244566677777777777766544333222 3445566666665555555555444444343
Q ss_pred HHHHHHHHhHhccC
Q 027999 129 VEKLEDFMALLAYE 142 (215)
Q Consensus 129 ~~~l~~~~~lla~~ 142 (215)
.+-.+.|-|++.
T Consensus 329 --~L~~tLG~L~~k 340 (400)
T COG3071 329 --LLLSTLGRLALK 340 (400)
T ss_pred --hHHHHHHHHHHH
Confidence 344445555553
No 95
>PF12854 PPR_1: PPR repeat
Probab=24.67 E-value=1.2e+02 Score=16.71 Aligned_cols=21 Identities=29% Similarity=0.308 Sum_probs=15.2
Q ss_pred HHHHHHHHcCCHHHHHHHHHH
Q 027999 58 KRILHFALEGNALKAIELTEE 78 (215)
Q Consensus 58 ~~I~~~I~~G~i~~Ai~~~~~ 78 (215)
.-|...-..|++++|++.+++
T Consensus 12 ~lI~~~Ck~G~~~~A~~l~~~ 32 (34)
T PF12854_consen 12 TLIDGYCKAGRVDEAFELFDE 32 (34)
T ss_pred HHHHHHHHCCCHHHHHHHHHh
Confidence 345566688888888887764
No 96
>PRK10421 DNA-binding transcriptional repressor LldR; Provisional
Probab=24.20 E-value=1.5e+02 Score=24.43 Aligned_cols=30 Identities=17% Similarity=0.115 Sum_probs=23.8
Q ss_pred HhHHHHHHHHHHHHcCCHHHHHHHHHHhcH
Q 027999 52 EDMEMRKRILHFALEGNALKAIELTEELAQ 81 (215)
Q Consensus 52 ~~~~~r~~I~~~I~~G~i~~Ai~~~~~~~p 81 (215)
..+.....|.++|..||.+.|..++.+|..
T Consensus 189 ~~~~~H~~I~~AI~~~D~~~A~~~~~~H~~ 218 (253)
T PRK10421 189 QLTEQHQAVMDAILAGDAEGARKAMMAHLS 218 (253)
T ss_pred HHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence 456677888888888888888888887753
No 97
>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=23.88 E-value=1.2e+02 Score=15.58 Aligned_cols=21 Identities=29% Similarity=0.325 Sum_probs=16.1
Q ss_pred HHHHHHHcCCHHHHHHHHHHh
Q 027999 59 RILHFALEGNALKAIELTEEL 79 (215)
Q Consensus 59 ~I~~~I~~G~i~~Ai~~~~~~ 79 (215)
-|......|++++|++..++.
T Consensus 6 li~~~~~~~~~~~a~~~~~~M 26 (35)
T TIGR00756 6 LIDGLCKAGRVEEALELFKEM 26 (35)
T ss_pred HHHHHHHCCCHHHHHHHHHHH
Confidence 355677888899988888765
No 98
>COG1802 GntR Transcriptional regulators [Transcription]
Probab=23.85 E-value=3.3e+02 Score=21.90 Aligned_cols=29 Identities=17% Similarity=0.140 Sum_probs=25.0
Q ss_pred hHHHHHHHHHHHHcCCHHHHHHHHHHhcH
Q 027999 53 DMEMRKRILHFALEGNALKAIELTEELAQ 81 (215)
Q Consensus 53 ~~~~r~~I~~~I~~G~i~~Ai~~~~~~~p 81 (215)
.+.+...|.++|.+||.+.|.+.+.+|.-
T Consensus 184 ~~~eH~~il~Ai~~~d~~~A~~~m~~Hl~ 212 (230)
T COG1802 184 AIDEHRAILEALEARDAEAAAEAMRQHLR 212 (230)
T ss_pred hHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence 46788899999999999999999988753
No 99
>PRK00239 rpsT 30S ribosomal protein S20; Reviewed
Probab=23.75 E-value=1.4e+02 Score=20.88 Aligned_cols=29 Identities=14% Similarity=0.062 Sum_probs=23.0
Q ss_pred HHHHHHHHHcCCHHHHHHHHHHhcHHHHc
Q 027999 57 RKRILHFALEGNALKAIELTEELAQDLLE 85 (215)
Q Consensus 57 r~~I~~~I~~G~i~~Ai~~~~~~~p~l~~ 85 (215)
.+.+..+|..||.++|.+.+...++.+-.
T Consensus 32 iKk~~~ai~~~~~~~a~~~~~~a~s~iDk 60 (88)
T PRK00239 32 IKKVEAAIAAGDKEAAEEALKAAQSKIDK 60 (88)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHHHHHHHH
Confidence 35677888999999999999887765544
No 100
>cd02064 FAD_synthetase_N FAD synthetase, N-terminal domain of the bifunctional enzyme. FAD synthetase_N. N-terminal domain of the bifunctional riboflavin biosynthesis protein riboflavin kinase/FAD synthetase. These enzymes have both ATP:riboflavin 5'-phosphotransferase and ATP:FMN-adenylyltransferase activities. The N-terminal domain is believed to play a role in the adenylylation reaction of FAD synthetases. The C-terminal domain is thought to have kinase activity. FAD synthetase is present among all kingdoms of life. However, the bifunctional enzyme is not found in mammals, which use separate enzymes for FMN and FAD formation.
Probab=23.60 E-value=55 Score=25.73 Aligned_cols=50 Identities=20% Similarity=0.033 Sum_probs=31.6
Q ss_pred hcHHHHHHHHHHhhCCCCCCC-----CHHhHHHHHHHHHHHHcCCHHHHHHHHHHh
Q 027999 29 NCYKETVDSFISCTGMKQPAN-----CLEDMEMRKRILHFALEGNALKAIELTEEL 79 (215)
Q Consensus 29 ~Gy~eta~~f~~e~~~~~~~~-----~~~~~~~r~~I~~~I~~G~i~~Ai~~~~~~ 79 (215)
.|..+..+.++++.|+..... .... -.-..||++|.+|+++.|-+++-..
T Consensus 116 ~g~~~~L~~~~~~~g~~v~~v~~~~~~~~~-iSST~IR~~i~~G~i~~an~lLg~~ 170 (180)
T cd02064 116 SGDAELLKELGKKYGFEVTVVPPVTLDGER-VSSTRIREALAEGDVELANELLGRP 170 (180)
T ss_pred CCCHHHHHHhhhhcCcEEEEeCcEecCCcE-EcHHHHHHHHHhCCHHHHHHHcCCC
Confidence 345667777777766532100 0011 1236899999999999998887544
No 101
>PRK07143 hypothetical protein; Provisional
Probab=23.52 E-value=55 Score=28.03 Aligned_cols=23 Identities=13% Similarity=-0.145 Sum_probs=20.3
Q ss_pred HHHHHHHHcCCHHHHHHHHHHhc
Q 027999 58 KRILHFALEGNALKAIELTEELA 80 (215)
Q Consensus 58 ~~I~~~I~~G~i~~Ai~~~~~~~ 80 (215)
.+||++|.+|+++.|-+++-..|
T Consensus 153 T~IR~~l~~G~i~~A~~lLGr~y 175 (279)
T PRK07143 153 SLLKEFIEFGDIELLNSLLLYNY 175 (279)
T ss_pred HHHHHHHHcCCHHHHHHHcCCCc
Confidence 68999999999999998887655
No 102
>KOG3452 consensus 60S ribosomal protein L36 [Translation, ribosomal structure and biogenesis]
Probab=23.22 E-value=2.2e+02 Score=20.39 Aligned_cols=45 Identities=22% Similarity=0.263 Sum_probs=31.7
Q ss_pred hhhhHHHHHHHHhccchhhHHHHHHHhccccCCchhHHHHHHHHHhHh
Q 027999 92 FDLLSLHFVELVCSRKCTEALEFAQTKLTPFGKVQKYVEKLEDFMALL 139 (215)
Q Consensus 92 F~L~~q~fiEli~~~~~~~Al~~ar~~l~~~~~~~~~~~~l~~~~~ll 139 (215)
|-=+--+-+||++.++-..|+.+++..+..+. .-....+++...|
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 33456678999999989999999999888775 3333444444444
No 103
>PRK11414 colanic acid/biofilm transcriptional regulator; Provisional
Probab=23.17 E-value=1.3e+02 Score=24.07 Aligned_cols=29 Identities=14% Similarity=0.062 Sum_probs=22.7
Q ss_pred HhHHHHHHHHHHHHcCCHHHHHHHHHHhc
Q 027999 52 EDMEMRKRILHFALEGNALKAIELTEELA 80 (215)
Q Consensus 52 ~~~~~r~~I~~~I~~G~i~~Ai~~~~~~~ 80 (215)
..+....+|.++|..||.+.|.+.+..+.
T Consensus 180 ~~~~~H~~I~~Ai~~~D~~~A~~~~~~hl 208 (221)
T PRK11414 180 EHIENYRLLLAALKAKDKEGCRHCLAEIM 208 (221)
T ss_pred hhHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence 34567778888888888888888887764
No 104
>KOG1538 consensus Uncharacterized conserved protein WDR10, contains WD40 repeats [General function prediction only]
Probab=22.88 E-value=2e+02 Score=28.13 Aligned_cols=56 Identities=13% Similarity=0.023 Sum_probs=39.5
Q ss_pred HHHHHcCCHHHHHHHHHHhcHHHHcc--CCcchhhhhHHHHHHH----HhccchhhHHHHHHH
Q 027999 61 LHFALEGNALKAIELTEELAQDLLEK--NKDLHFDLLSLHFVEL----VCSRKCTEALEFAQT 117 (215)
Q Consensus 61 ~~~I~~G~i~~Ai~~~~~~~p~l~~~--~~~l~F~L~~q~fiEl----i~~~~~~~Al~~ar~ 117 (215)
.-+|..|+|++|.+++.++ |++.+. -+...|.--.-+|+|- .+.|...||+....+
T Consensus 781 qlHve~~~W~eAFalAe~h-Pe~~~dVy~pyaqwLAE~DrFeEAqkAfhkAGr~~EA~~vLeQ 842 (1081)
T KOG1538|consen 781 QLHVETQRWDEAFALAEKH-PEFKDDVYMPYAQWLAENDRFEEAQKAFHKAGRQREAVQVLEQ 842 (1081)
T ss_pred hheeecccchHhHhhhhhC-ccccccccchHHHHhhhhhhHHHHHHHHHHhcchHHHHHHHHH
Confidence 4567889999999998766 777764 2345566667778774 356777777766654
No 105
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=22.87 E-value=4.8e+02 Score=22.27 Aligned_cols=20 Identities=30% Similarity=0.390 Sum_probs=12.5
Q ss_pred HHHHHHcCCHHHHHHHHHHh
Q 027999 60 ILHFALEGNALKAIELTEEL 79 (215)
Q Consensus 60 I~~~I~~G~i~~Ai~~~~~~ 79 (215)
+.-....|++++|++.....
T Consensus 148 a~~~~~~g~~~~A~~~~~~~ 167 (389)
T PRK11788 148 LEIYQQEKDWQKAIDVAERL 167 (389)
T ss_pred HHHHHHhchHHHHHHHHHHH
Confidence 33455677777777766543
No 106
>TIGR01159 DRP1 density-regulated protein DRP1. This protein family shows weak but suggestive similarity to translation initiation factor SUI1 and its prokaryotic homologs.
Probab=22.41 E-value=73 Score=25.31 Aligned_cols=21 Identities=29% Similarity=0.284 Sum_probs=18.5
Q ss_pred cCCHHHHHHHHHHhcHHHHcc
Q 027999 66 EGNALKAIELTEELAQDLLEK 86 (215)
Q Consensus 66 ~G~i~~Ai~~~~~~~p~l~~~ 86 (215)
.|.+..+-+|+.+|+|+++..
T Consensus 20 ~~~~~kCk~WL~~n~p~l~~~ 40 (173)
T TIGR01159 20 SGDLKRCKVWLSENAPDLYAK 40 (173)
T ss_pred CCCHHHHHHHHHHhChHHHHH
Confidence 578999999999999998853
No 107
>PF01671 ASFV_360: African swine fever virus multigene family 360 protein; InterPro: IPR002595 The multigene family 360 protein are found within the African swine fever virus (ASFV) genome which consist of dsDNA and has similar structural features to the poxviruses []. The biological function of this family is not known [], although Q65137 from SWISSPROT is a major structural protein [].; GO: 0042330 taxis
Probab=22.20 E-value=1.8e+02 Score=23.84 Aligned_cols=87 Identities=18% Similarity=0.184 Sum_probs=53.2
Q ss_pred HHHHHHhhCCCCCCCCHHhHHHHHHHHHHHHcCCHHHHHHHHHHhcHHHHccC-----CcchhhhhHHHHHHHHh-----
Q 027999 35 VDSFISCTGMKQPANCLEDMEMRKRILHFALEGNALKAIELTEELAQDLLEKN-----KDLHFDLLSLHFVELVC----- 104 (215)
Q Consensus 35 a~~f~~e~~~~~~~~~~~~~~~r~~I~~~I~~G~i~~Ai~~~~~~~p~l~~~~-----~~l~F~L~~q~fiEli~----- 104 (215)
-+.||++.|-+.+-...+.+..-.+++..-.++++--+.+....+ |-+..-+ ..+.+.|+.....+++.
T Consensus 3 tr~LC~~LGAk~~l~~~~il~iF~~~~~~kts~nIILcheif~nN-p~l~~v~~~~l~~~I~~~l~~l~~~~~l~~~s~~ 81 (215)
T PF01671_consen 3 TRDLCRELGAKEPLNEMEILQIFFKIKRNKTSSNIILCHEIFSNN-PLLENVNNHDLRMIIYWELRRLSINEILDEISFN 81 (215)
T ss_pred HHHHHHHhCCCccccHHHHHHHHHHHHhcCCccceeeehHhhcCC-hHHhhhhHHHHHHHHHHHHccchHHHHhccchHH
Confidence 356889988776654455555555566666777788888888776 6554332 13444554442222222
Q ss_pred ------------ccchhhHHHHHHHhcccc
Q 027999 105 ------------SRKCTEALEFAQTKLTPF 122 (215)
Q Consensus 105 ------------~~~~~~Al~~ar~~l~~~ 122 (215)
..+..+||.|--++...+
T Consensus 82 ~~LtkyWY~~Av~ynL~~AI~Yfyq~y~hl 111 (215)
T PF01671_consen 82 EMLTKYWYAIAVQYNLKEAIQYFYQKYPHL 111 (215)
T ss_pred HHHHHHHHHHHHHhhhHHHHHHHHHhccch
Confidence 126788999987766554
No 108
>PRK04966 hypothetical protein; Provisional
Probab=22.20 E-value=88 Score=21.14 Aligned_cols=45 Identities=11% Similarity=0.141 Sum_probs=30.2
Q ss_pred CCCHHHHHHHHHHHHHhhcHHHHHHHHHHhhCCCCCCCCHHhHHHHHHHHHHHHcCCH
Q 027999 12 AINDNDIHNIVLSYLVHNCYKETVDSFISCTGMKQPANCLEDMEMRKRILHFALEGNA 69 (215)
Q Consensus 12 ~~~~~~l~~lI~~yL~~~Gy~eta~~f~~e~~~~~~~~~~~~~~~r~~I~~~I~~G~i 69 (215)
..+++-|++||-+|+.|.|- +.|... ...-....+++..+.+|+.
T Consensus 7 ~L~~eTL~nLIeefv~ReGT---------dyG~~E----~sl~~kv~qv~~qL~~G~~ 51 (72)
T PRK04966 7 DLAPETLENLIESFVLREGT---------DYGEHE----RSLEQKVADVKRQLQSGEA 51 (72)
T ss_pred hCCHHHHHHHHHHHHhccCc---------cCCccc----ccHHHHHHHHHHHHHcCCE
Confidence 46788899999999999874 223211 1222456778888888863
No 109
>PRK03837 transcriptional regulator NanR; Provisional
Probab=22.20 E-value=1.7e+02 Score=23.67 Aligned_cols=30 Identities=7% Similarity=-0.067 Sum_probs=21.6
Q ss_pred HhHHHHHHHHHHHHcCCHHHHHHHHHHhcH
Q 027999 52 EDMEMRKRILHFALEGNALKAIELTEELAQ 81 (215)
Q Consensus 52 ~~~~~r~~I~~~I~~G~i~~Ai~~~~~~~p 81 (215)
..+.....|.++|..||.+.|.+.+..|.-
T Consensus 198 ~~~~~H~~i~~Ai~~~d~~~a~~~~~~H~~ 227 (241)
T PRK03837 198 VTLQEHIAIVDAIRAHDPDEADRALQSHLN 227 (241)
T ss_pred HHHHHHHHHHHHHHhCCHHHHHHHHHHHHH
Confidence 345666677888888888888877777653
No 110
>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=21.99 E-value=1.8e+02 Score=23.04 Aligned_cols=39 Identities=18% Similarity=0.065 Sum_probs=31.9
Q ss_pred chhHHHHHHHHHhHhccCCCCCCchhhhCCHHHHHHHHH
Q 027999 125 VQKYVEKLEDFMALLAYEEPEKSPMFHLLSLEYRQHVAD 163 (215)
Q Consensus 125 ~~~~~~~l~~~~~lla~~~~~~s~~~~ll~~~~r~~la~ 163 (215)
++.+.+.++++|+-+.-+.......+..++.++|+.+..
T Consensus 123 D~~~ve~Vk~~Ma~i~LP~~~vP~WA~~IseeqWk~~l~ 161 (174)
T PF06910_consen 123 DAEHVELVKRTMAGITLPSSAVPEWAKEISEEQWKDVLQ 161 (174)
T ss_pred CHHHHHHHHHHHhcccCCCCCCcHHHhhCCHHHHHHHHH
Confidence 678899999999999988766666788899999976443
No 111
>PRK09990 DNA-binding transcriptional regulator GlcC; Provisional
Probab=21.97 E-value=1.5e+02 Score=24.28 Aligned_cols=27 Identities=11% Similarity=0.058 Sum_probs=16.4
Q ss_pred HHHHHHHHHHHHcCCHHHHHHHHHHhc
Q 027999 54 MEMRKRILHFALEGNALKAIELTEELA 80 (215)
Q Consensus 54 ~~~r~~I~~~I~~G~i~~Ai~~~~~~~ 80 (215)
+.....|.++|..||.+.|.+.+..|.
T Consensus 199 ~~~H~~I~~Ai~~~D~~~A~~~~~~Hi 225 (251)
T PRK09990 199 DRQHARLYNAVLQRLPEQAQRAARDHI 225 (251)
T ss_pred HHHHHHHHHHHHhCCHHHHHHHHHHHH
Confidence 345556666666666666666666553
No 112
>KOG3239 consensus Density-regulated protein related to translation initiation factor 1 (eIF-1/SUI1) [General function prediction only]
Probab=21.97 E-value=70 Score=25.49 Aligned_cols=22 Identities=36% Similarity=0.395 Sum_probs=19.3
Q ss_pred HcCCHHHHHHHHHHhcHHHHcc
Q 027999 65 LEGNALKAIELTEELAQDLLEK 86 (215)
Q Consensus 65 ~~G~i~~Ai~~~~~~~p~l~~~ 86 (215)
-.|++..+-.|+.+|+|+++..
T Consensus 27 f~~~~~kCk~WL~~n~pdly~k 48 (193)
T KOG3239|consen 27 FSGDLKKCKEWLEENHPDLYAK 48 (193)
T ss_pred ccccHHHHHHHHHhcChhHHHh
Confidence 3689999999999999998864
No 113
>PF12862 Apc5: Anaphase-promoting complex subunit 5
Probab=21.72 E-value=2.8e+02 Score=19.02 Aligned_cols=29 Identities=17% Similarity=0.159 Sum_probs=22.1
Q ss_pred HHHHHHHcCCHHHHHHHHHHhcHHHHccC
Q 027999 59 RILHFALEGNALKAIELTEELAQDLLEKN 87 (215)
Q Consensus 59 ~I~~~I~~G~i~~Ai~~~~~~~p~l~~~~ 87 (215)
....++..||+..|++.+.+.+-.-...+
T Consensus 4 ~~~~~~~~~dy~~A~d~L~~~fD~~~~~~ 32 (94)
T PF12862_consen 4 RYLNALRSGDYSEALDALHRYFDYAKQSN 32 (94)
T ss_pred HHHHHHHcCCHHHHHHHHHHHHHHHhhcc
Confidence 34578999999999999998875444443
No 114
>PRK11523 DNA-binding transcriptional repressor ExuR; Provisional
Probab=21.49 E-value=1.7e+02 Score=24.01 Aligned_cols=28 Identities=11% Similarity=-0.073 Sum_probs=20.3
Q ss_pred hHHHHHHHHHHHHcCCHHHHHHHHHHhc
Q 027999 53 DMEMRKRILHFALEGNALKAIELTEELA 80 (215)
Q Consensus 53 ~~~~r~~I~~~I~~G~i~~Ai~~~~~~~ 80 (215)
.+.....|.++|..||.+.|.+.+.+|.
T Consensus 191 ~~~eH~~I~~Ai~~~D~~~A~~~~~~Hi 218 (253)
T PRK11523 191 WCDDHDQILKALIRKDPHAAKLAMWQHL 218 (253)
T ss_pred HHHHHHHHHHHHHhCCHHHHHHHHHHHH
Confidence 3456677778888888777777777664
No 115
>PF14498 Glyco_hyd_65N_2: Glycosyl hydrolase family 65, N-terminal domain; PDB: 2EAE_A 2EAB_B 2EAC_A 2EAD_B 2RDY_A.
Probab=21.26 E-value=77 Score=26.03 Aligned_cols=30 Identities=30% Similarity=0.266 Sum_probs=23.7
Q ss_pred HHhHHHHHHHHHHHHcCCHHHHHHHHHHhc
Q 027999 51 LEDMEMRKRILHFALEGNALKAIELTEELA 80 (215)
Q Consensus 51 ~~~~~~r~~I~~~I~~G~i~~Ai~~~~~~~ 80 (215)
........+||++|.+|+..+|-+++.+++
T Consensus 52 ~~~~~~L~~iR~l~~~g~~~~A~~l~~~~~ 81 (236)
T PF14498_consen 52 PDAAEYLPEIRELLFEGDYEEAEELAEENF 81 (236)
T ss_dssp HHHHHHHHHHHHHHHTT-CCHHHHHHCCS-
T ss_pred ccHHHHHHHHHHHHHcCChhHHHHHHHHhc
Confidence 345678889999999999999999887653
No 116
>PRK00304 hypothetical protein; Provisional
Probab=21.19 E-value=94 Score=21.18 Aligned_cols=43 Identities=9% Similarity=0.196 Sum_probs=30.0
Q ss_pred CCHHHHHHHHHHHHHhhcHHHHHHHHHHhhCCCCCCCCHHhHHHHHHHHHHHHcCCH
Q 027999 13 INDNDIHNIVLSYLVHNCYKETVDSFISCTGMKQPANCLEDMEMRKRILHFALEGNA 69 (215)
Q Consensus 13 ~~~~~l~~lI~~yL~~~Gy~eta~~f~~e~~~~~~~~~~~~~~~r~~I~~~I~~G~i 69 (215)
.+.+-|+.||-+|+.|.|- + .|-+ .+.-....+++.++.+|+.
T Consensus 8 L~~eTL~nLIeefv~ReGT-D--------yg~E-----~sL~~kv~qv~~qL~~G~~ 50 (75)
T PRK00304 8 LEADTLTRLIEDFVTRDGT-D--------NGDE-----TPLETRVLRVRQALTKGQA 50 (75)
T ss_pred CCHHHHHHHHHHHHhccCc-c--------Cccc-----ccHHHHHHHHHHHHHcCCE
Confidence 6788899999999999996 2 2211 1111445788888888864
No 117
>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=20.90 E-value=1.7e+02 Score=20.17 Aligned_cols=29 Identities=17% Similarity=0.098 Sum_probs=22.4
Q ss_pred HHHHHHHHHcCCHHHHHHHHHHhcHHHHc
Q 027999 57 RKRILHFALEGNALKAIELTEELAQDLLE 85 (215)
Q Consensus 57 r~~I~~~I~~G~i~~Ai~~~~~~~p~l~~ 85 (215)
.+.++.+|..|+-++|.+.+...++.|..
T Consensus 31 iKk~~~ai~~~~~~~a~~~l~~a~s~iDk 59 (84)
T PF01649_consen 31 IKKFREAIEAGDKEEAKELLRKAYSAIDK 59 (84)
T ss_dssp HHHHHHHHHTT-HHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHccChHHHHHHHHHHHHHHHH
Confidence 45788899999999999999887766543
No 118
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=20.77 E-value=2.1e+02 Score=21.12 Aligned_cols=54 Identities=19% Similarity=0.233 Sum_probs=30.1
Q ss_pred HHHHHHHHHhhcHHHHHHHHHHhhCCCCCC-----------------CCHHhHHHHHHHHHHHHcCCHHH--HHHH
Q 027999 19 HNIVLSYLVHNCYKETVDSFISCTGMKQPA-----------------NCLEDMEMRKRILHFALEGNALK--AIEL 75 (215)
Q Consensus 19 ~~lI~~yL~~~Gy~eta~~f~~e~~~~~~~-----------------~~~~~~~~r~~I~~~I~~G~i~~--Ai~~ 75 (215)
...|..|+...|-. +.++++.|+.-|. ...+.-..|.+|.+.+.+|.|+. |++.
T Consensus 39 ~~Fi~~Fi~~rGnl---Ke~e~~lgiSYPTvR~rLd~ii~~lg~~~~~~~~~~~~~~~IL~~L~~GeIs~eeA~~~ 111 (113)
T PF09862_consen 39 LEFIKLFIKNRGNL---KEMEKELGISYPTVRNRLDKIIEKLGYEEDEEEEEEDERKEILDKLEKGEISVEEALEI 111 (113)
T ss_pred HHHHHHHHHhcCCH---HHHHHHHCCCcHHHHHHHHHHHHHhCCCCCcccccchhHHHHHHHHHcCCCCHHHHHHH
Confidence 35667777777743 3445555554221 11222356777888888886643 5544
No 119
>PRK09464 pdhR transcriptional regulator PdhR; Reviewed
Probab=20.66 E-value=1.9e+02 Score=23.73 Aligned_cols=27 Identities=22% Similarity=0.288 Sum_probs=17.0
Q ss_pred HHHHH-HHHHHHHcCCHHHHHHHHHHhc
Q 027999 54 MEMRK-RILHFALEGNALKAIELTEELA 80 (215)
Q Consensus 54 ~~~r~-~I~~~I~~G~i~~Ai~~~~~~~ 80 (215)
+.... .|.++|..||.+.|...+.+|.
T Consensus 198 ~~~H~~~I~~Ai~~~D~~~A~~~~~~Hl 225 (254)
T PRK09464 198 VSSHRARIFEAIVAGKPEKAREASHRHL 225 (254)
T ss_pred HHHHHHHHHHHHHhCCHHHHHHHHHHHH
Confidence 33443 6777777777777777666664
No 120
>PF12793 SgrR_N: Sugar transport-related sRNA regulator N-term
Probab=20.21 E-value=1.6e+02 Score=21.50 Aligned_cols=23 Identities=13% Similarity=0.219 Sum_probs=19.9
Q ss_pred HHHHHHHHHHcCCHHHHHHHHHH
Q 027999 56 MRKRILHFALEGNALKAIELTEE 78 (215)
Q Consensus 56 ~r~~I~~~I~~G~i~~Ai~~~~~ 78 (215)
....+++.|.+|+++.|++++..
T Consensus 73 ~~~~~~~~l~~g~~~~a~~ll~~ 95 (115)
T PF12793_consen 73 LEQQAEELLEQGKYEQALQLLDF 95 (115)
T ss_pred HHHHHHHHHHcCCHHHHHHHHHh
Confidence 45678899999999999999983
Done!