Query 028796
Match_columns 203
No_of_seqs 117 out of 828
Neff 7.6
Searched_HMMs 46136
Date Fri Mar 29 02:40:43 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028796.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028796hhsearch_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 5.3E-39 1.2E-43 261.2 18.5 181 22-202 8-189 (228)
2 PF10607 CLTH: CTLH/CRA C-term 100.0 1.4E-28 3E-33 189.9 12.4 122 78-202 2-126 (145)
3 KOG0396 Uncharacterized conser 100.0 5.8E-28 1.3E-32 206.5 15.1 159 39-200 114-273 (389)
4 KOG2817 Predicted E3 ubiquitin 99.9 5.4E-21 1.2E-25 165.4 17.4 165 35-202 110-281 (394)
5 smart00757 CRA CT11-RanBPM. pr 99.6 7.9E-15 1.7E-19 105.8 8.3 72 131-202 2-75 (99)
6 smart00668 CTLH C-terminal to 99.4 9.9E-13 2.2E-17 85.8 6.0 55 78-132 2-56 (58)
7 KOG0293 WD40 repeat-containing 98.9 1.1E-08 2.3E-13 89.9 10.2 130 17-169 8-137 (519)
8 PF08513 LisH: LisH; InterPro 98.5 2.4E-07 5.3E-12 51.3 3.9 27 41-67 1-27 (27)
9 smart00667 LisH Lissencephaly 98.2 4.9E-06 1.1E-10 47.7 4.7 32 39-70 2-33 (34)
10 KOG1477 SPRY domain-containing 98.2 1.9E-07 4.2E-12 84.8 -2.1 161 42-202 251-432 (469)
11 COG5109 Uncharacterized conser 97.1 0.0097 2.1E-07 51.2 11.3 145 17-166 78-224 (396)
12 KOG0275 Conserved WD40 repeat- 96.4 0.047 1E-06 47.6 10.8 144 37-191 4-149 (508)
13 KOG1333 Uncharacterized conser 93.3 0.61 1.3E-05 38.0 8.0 106 41-146 6-119 (241)
14 PF09398 FOP_dimer: FOP N term 89.4 0.89 1.9E-05 31.7 4.6 29 42-70 20-48 (81)
15 TIGR03362 VI_chp_7 type VI sec 79.1 29 0.00062 30.1 10.3 98 42-141 134-275 (301)
16 PF04494 TFIID_90kDa: WD40 ass 75.5 5.9 0.00013 30.2 4.6 48 112-162 38-85 (142)
17 PF14559 TPR_19: Tetratricopep 74.6 15 0.00032 23.3 5.8 56 87-147 1-56 (68)
18 cd08044 TAF5_NTD2 TAF5_NTD2 is 73.3 8.7 0.00019 28.9 5.0 51 112-165 27-77 (133)
19 PF07035 Mic1: Colon cancer-as 73.1 34 0.00073 27.1 8.4 83 42-142 30-115 (167)
20 PF10607 CLTH: CTLH/CRA C-term 70.2 16 0.00036 27.3 5.9 58 46-104 7-67 (145)
21 PF04053 Coatomer_WDAD: Coatom 67.6 26 0.00057 32.0 7.6 76 43-141 297-372 (443)
22 PF12895 Apc3: Anaphase-promot 64.6 30 0.00065 23.1 5.8 52 84-141 32-83 (84)
23 PF12550 GCR1_C: Transcription 63.1 20 0.00044 24.5 4.7 65 39-103 7-80 (81)
24 KOG0273 Beta-transducin family 62.9 2.3 5E-05 38.8 -0.1 34 37-70 2-35 (524)
25 KOG1585 Protein required for f 60.3 53 0.0012 28.1 7.4 74 29-102 179-252 (308)
26 KOG2659 LisH motif-containing 59.6 1E+02 0.0022 25.7 9.5 67 39-105 61-131 (228)
27 PF13934 ELYS: Nuclear pore co 59.4 99 0.0021 25.4 9.6 113 25-144 28-168 (226)
28 PF01726 LexA_DNA_bind: LexA D 55.8 56 0.0012 21.4 5.8 30 41-70 9-38 (65)
29 PF10602 RPN7: 26S proteasome 54.4 1.1E+02 0.0023 24.2 14.4 104 44-147 39-144 (177)
30 smart00668 CTLH C-terminal to 53.7 20 0.00044 22.1 3.2 28 120-147 5-32 (58)
31 KOG4594 Sequence-specific sing 52.8 17 0.00036 31.4 3.3 29 40-68 17-45 (354)
32 PF06588 Muskelin_N: Muskelin 52.3 22 0.00048 28.9 3.8 30 41-70 166-195 (199)
33 PF05843 Suf: Suppressor of fo 52.0 1.1E+02 0.0024 25.8 8.4 62 5-67 35-96 (280)
34 PF04840 Vps16_C: Vps16, C-ter 51.1 1.6E+02 0.0035 25.6 9.4 78 48-141 184-262 (319)
35 COG5443 FlbT Flagellar biosynt 49.9 30 0.00065 26.3 4.0 55 52-106 67-123 (148)
36 PF07575 Nucleopor_Nup85: Nup8 47.6 61 0.0013 30.4 6.6 72 14-102 379-450 (566)
37 PF04433 SWIRM: SWIRM domain; 46.9 54 0.0012 22.4 4.8 50 5-57 35-84 (86)
38 PRK10564 maltose regulon perip 46.6 23 0.0005 30.8 3.3 23 81-103 261-283 (303)
39 PHA01351 putative minor struct 45.0 3.2E+02 0.0069 27.0 13.2 47 18-64 491-537 (1070)
40 PF13838 Clathrin_H_link: Clat 42.8 40 0.00088 22.5 3.4 40 117-158 7-47 (66)
41 PF04121 Nup84_Nup100: Nuclear 42.8 83 0.0018 30.4 6.9 27 77-103 133-159 (697)
42 PF14276 DUF4363: Domain of un 41.5 38 0.00082 24.8 3.5 46 79-124 30-75 (121)
43 PF13934 ELYS: Nuclear pore co 41.2 2E+02 0.0043 23.6 12.9 66 88-168 89-155 (226)
44 KOG0640 mRNA cleavage stimulat 40.6 95 0.0021 27.4 6.1 32 39-70 10-41 (430)
45 PF07721 TPR_4: Tetratricopept 40.4 39 0.00084 17.6 2.5 17 85-101 9-25 (26)
46 KOG1961 Vacuolar sorting prote 40.3 2.4E+02 0.0051 27.1 9.0 118 26-143 133-259 (683)
47 PF12569 NARP1: NMDA receptor- 39.5 3.3E+02 0.007 25.5 10.4 25 38-62 259-283 (517)
48 KOG0396 Uncharacterized conser 39.2 1.2E+02 0.0025 27.3 6.5 64 45-109 157-223 (389)
49 KOG1156 N-terminal acetyltrans 38.1 3.9E+02 0.0084 26.0 10.3 115 42-162 146-264 (700)
50 KOG0292 Vesicle coat complex C 37.3 19 0.0004 35.9 1.5 27 43-69 622-648 (1202)
51 PF13833 EF-hand_8: EF-hand do 37.3 52 0.0011 19.9 3.2 29 21-49 2-33 (54)
52 PF13424 TPR_12: Tetratricopep 37.2 1.1E+02 0.0023 19.7 5.0 56 88-143 16-73 (78)
53 PF07729 FCD: FCD domain; Int 36.9 67 0.0015 22.2 4.2 28 76-103 95-122 (125)
54 PRK14574 hmsH outer membrane p 35.0 4.7E+02 0.01 26.0 11.8 21 174-194 229-254 (822)
55 KOG3380 Actin-related protein 34.0 1.1E+02 0.0024 23.8 5.0 59 82-141 40-100 (152)
56 KOG0263 Transcription initiati 33.1 65 0.0014 31.2 4.3 33 37-69 18-50 (707)
57 PF07208 DUF1414: Protein of u 33.1 63 0.0014 19.8 2.8 19 179-197 25-43 (44)
58 smart00550 Zalpha Z-DNA-bindin 33.1 1.1E+02 0.0025 19.9 4.4 50 38-93 2-52 (68)
59 PF00627 UBA: UBA/TS-N domain; 32.7 70 0.0015 18.1 3.0 17 84-100 19-37 (37)
60 PF10827 DUF2552: Protein of u 32.0 33 0.00072 23.2 1.6 18 91-108 59-76 (79)
61 PF12169 DNA_pol3_gamma3: DNA 31.4 1.2E+02 0.0027 22.3 5.0 24 81-104 18-41 (143)
62 PF12569 NARP1: NMDA receptor- 31.1 4.5E+02 0.0097 24.6 12.2 91 43-141 196-287 (517)
63 PRK02289 4-oxalocrotonate taut 30.0 77 0.0017 20.0 3.1 24 179-202 13-36 (60)
64 KOG1538 Uncharacterized conser 29.5 3.5E+02 0.0075 26.7 8.3 62 81-143 776-844 (1081)
65 PF04840 Vps16_C: Vps16, C-ter 28.7 3.9E+02 0.0085 23.2 12.7 89 32-141 199-287 (319)
66 PF13171 DUF4004: Protein of u 28.5 3.3E+02 0.0071 22.2 7.5 102 11-116 53-161 (199)
67 cd00052 EH Eps15 homology doma 28.4 1.1E+02 0.0024 18.9 3.7 30 19-48 11-40 (67)
68 cd02064 FAD_synthetase_N FAD s 28.2 82 0.0018 24.7 3.6 49 55-104 117-171 (180)
69 PF04699 P16-Arc: ARP2/3 compl 28.1 71 0.0015 24.9 3.1 27 79-105 38-64 (152)
70 PF13371 TPR_9: Tetratricopept 28.0 1.6E+02 0.0035 18.5 5.7 54 87-145 5-58 (73)
71 smart00027 EH Eps15 homology d 27.6 87 0.0019 21.7 3.3 30 20-49 23-52 (96)
72 TIGR01470 cysG_Nterm siroheme 27.5 1.8E+02 0.004 23.4 5.6 65 78-143 134-204 (205)
73 PF03997 VPS28: VPS28 protein; 27.3 1.8E+02 0.004 23.4 5.5 56 4-70 4-64 (188)
74 COG5096 Vesicle coat complex, 27.1 4.4E+02 0.0095 26.1 8.8 92 67-164 25-119 (757)
75 COG5051 RPL36A Ribosomal prote 27.0 95 0.002 21.9 3.2 43 119-165 53-95 (97)
76 PF09052 SipA: Salmonella inva 26.7 1.4E+02 0.003 28.2 5.2 68 7-74 556-629 (674)
77 PF09862 DUF2089: Protein of u 26.2 2.7E+02 0.0059 20.5 5.9 54 44-100 39-112 (113)
78 PF01158 Ribosomal_L36e: Ribos 25.8 86 0.0019 22.6 3.0 45 116-164 48-92 (98)
79 PF06794 UPF0270: Uncharacteri 25.6 68 0.0015 21.7 2.3 43 38-92 8-50 (70)
80 PF12931 Sec16_C: Sec23-bindin 25.4 75 0.0016 27.0 3.1 21 83-103 1-21 (284)
81 PF09295 ChAPs: ChAPs (Chs5p-A 24.4 5.3E+02 0.011 23.3 12.7 101 36-146 164-266 (395)
82 KOG2437 Muskelin [Signal trans 24.4 3.4E+02 0.0075 25.7 7.2 62 43-109 168-229 (723)
83 PRK07111 anaerobic ribonucleos 24.3 2.9E+02 0.0063 27.1 7.2 28 37-64 58-85 (735)
84 PTZ00196 60S ribosomal protein 23.9 1.1E+02 0.0024 22.1 3.2 31 117-147 49-79 (98)
85 PRK00794 flbT flagellar biosyn 23.7 2.8E+02 0.0061 21.0 5.6 30 76-105 92-121 (132)
86 PF14691 Fer4_20: Dihydroprymi 23.7 1.2E+02 0.0026 22.2 3.5 27 116-142 38-64 (111)
87 PF14689 SPOB_a: Sensor_kinase 23.6 1.9E+02 0.0042 18.5 4.2 31 76-106 22-52 (62)
88 PRK04966 hypothetical protein; 23.5 82 0.0018 21.4 2.4 43 38-92 8-50 (72)
89 cd05029 S-100A6 S-100A6: S-100 23.2 2.2E+02 0.0047 19.6 4.6 29 20-48 25-58 (88)
90 TIGR02531 yecD_yerC TrpR-relat 23.0 2.7E+02 0.0059 19.4 6.0 54 44-99 5-58 (88)
91 cd00194 UBA Ubiquitin Associat 23.0 1.4E+02 0.0029 16.7 3.0 18 84-101 18-37 (38)
92 TIGR00083 ribF riboflavin kina 23.0 52 0.0011 28.3 1.7 51 54-105 115-170 (288)
93 KOG3192 Mitochondrial J-type c 22.8 1.2E+02 0.0025 24.0 3.4 80 21-103 69-154 (168)
94 PF15391 DUF4614: Domain of un 22.5 1.5E+02 0.0033 23.8 4.1 50 94-143 113-179 (181)
95 PF10552 ORF6C: ORF6C domain; 22.3 1.4E+02 0.003 21.8 3.6 23 85-107 87-109 (116)
96 KOG3452 60S ribosomal protein 22.3 1.2E+02 0.0026 21.8 3.1 43 119-165 53-95 (102)
97 PLN03077 Protein ECB2; Provisi 22.1 7.5E+02 0.016 24.2 12.7 102 32-141 546-650 (857)
98 PF03477 ATP-cone: ATP cone do 22.0 97 0.0021 21.0 2.7 28 37-64 55-82 (90)
99 cd05804 StaR_like StaR_like; a 21.9 4.8E+02 0.01 21.9 10.5 94 46-143 119-213 (355)
100 PF03979 Sigma70_r1_1: Sigma-7 21.8 2E+02 0.0044 19.4 4.2 45 8-56 9-53 (82)
101 cd00491 4Oxalocrotonate_Tautom 21.8 1.4E+02 0.0031 18.2 3.2 25 179-203 12-36 (58)
102 PF09626 DHC: Dihaem cytochrom 21.7 1.6E+02 0.0034 22.0 3.8 40 17-56 10-56 (120)
103 PRK09263 anaerobic ribonucleos 21.7 3.5E+02 0.0077 26.4 7.2 28 37-64 55-82 (711)
104 PLN03081 pentatricopeptide (PP 21.3 7.2E+02 0.016 23.7 9.7 91 43-141 394-487 (697)
105 PRK00304 hypothetical protein; 21.0 98 0.0021 21.2 2.4 43 38-93 8-50 (75)
106 PF12793 SgrR_N: Sugar transpo 21.0 1.3E+02 0.0027 22.2 3.2 24 80-103 73-96 (115)
107 KOG0097 GTPase Rab14, small G 20.9 1.4E+02 0.0031 23.2 3.5 38 57-94 136-182 (215)
108 TIGR02795 tol_pal_ybgF tol-pal 20.8 2.8E+02 0.006 18.7 10.9 102 44-147 6-107 (119)
109 PF12854 PPR_1: PPR repeat 20.3 1.5E+02 0.0033 16.3 2.8 19 84-102 14-32 (34)
110 smart00165 UBA Ubiquitin assoc 20.2 1.6E+02 0.0036 16.3 3.0 12 89-100 25-36 (37)
111 PRK01271 4-oxalocrotonate taut 20.1 1.5E+02 0.0032 20.2 3.1 26 178-203 13-38 (76)
No 1
>KOG2659 consensus LisH motif-containing protein [Cytoskeleton]
Probab=100.00 E-value=5.3e-39 Score=261.23 Aligned_cols=181 Identities=60% Similarity=0.903 Sum_probs=176.5
Q ss_pred cCCCHHHHHHHhhcCCCCHHHHHHHHHHHHHhhCHHHHHHHHHHhhCCCC-CccHHHHHHHHHHHHHHHcCCHHHHHHHH
Q 028796 22 KVITREEWEKKLNDVKIRKEDMNKLVMNFLVTEGYVDAAEKFRMESGTEP-DIDLATITDRMAVKKAVQCGNVEDAIEKV 100 (203)
Q Consensus 22 ~~~~~~~~~~~~~~~~~~~~~l~~lI~~yL~~~Gy~eta~~f~ke~~~~~-~~~~e~~~~r~~I~~~I~~g~i~~Ai~~l 100 (203)
+.+++++|.+.+.++.+..+.+|+||++||+|+||.|+|..|++++|+++ ..+.+.+..|.+|+.+|..|++++|++.+
T Consensus 8 ~~~~~~~w~~~~~~~~~~~~d~n~LVmnylv~eg~~EaA~~Fa~e~~i~~~~~d~~~~~eR~~Ir~~I~~G~Ie~Aie~i 87 (228)
T KOG2659|consen 8 SFSTKEEWEEQLMKVSVMREDLNRLVMNYLVHEGYVEAAEKFAKESGIKPPSIDLDSMDERLQIRRAIEEGQIEEAIEKV 87 (228)
T ss_pred ccCchhhhHHHHhccCcchhhHHHHHHHHHHhccHHHHHHHhccccCCCCccCchhhHhHHHHHHHHHHhccHHHHHHHH
Confidence 67899999999999999999999999999999999999999999999987 89999999999999999999999999999
Q ss_pred HhhCchhhccCcchhhhhHHHHHHHHHHcCChHHHHHHHHHhcCccccCChhHHHHHHHHHhhhcccCCCCCchhhhcCH
Q 028796 101 NDLNPEILDTNPQLFFHLQQQRLIELIRNGKVEEALEFAQEELAPRGEENQSFLEELERTVALLAFEDVSNCPVGDLLDI 180 (203)
Q Consensus 101 ~~~~p~l~~~~~~l~F~L~~q~fIeli~~~~~~~Al~y~r~~l~~~~~~~~~~~~~l~~~~~LL~~~~~~~sp~~~l~~~ 180 (203)
+++.|.++..+.+|.|.|++|+||||||.|...+||+|+|..++|++..+++++.+++++|++|+|++++.||++.+++.
T Consensus 88 n~l~PeiLd~n~~l~F~Lq~q~lIEliR~~~~eeal~F~q~~LA~~a~e~~~~~~elE~~l~lLvf~~~~~sp~~~l~~~ 167 (228)
T KOG2659|consen 88 NQLNPEILDTNRELFFHLQQLHLIELIREGKTEEALEFAQTKLAPFAEENPKKMEELERTLALLVFELSQESPSAELLSQ 167 (228)
T ss_pred HHhChHHHccchhHHHHHHHHHHHHHHHhhhHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHcCCcccCcHHHHHHH
Confidence 99999999999999999999999999999999999999999999999988899999999999999999999999999999
Q ss_pred hhHHHHHHHHHHHHHhhcCCCC
Q 028796 181 SQRLKTASEVNAAILTSQSHEK 202 (203)
Q Consensus 181 ~~r~~la~~vN~aiL~~~~~~~ 202 (203)
++|.++|+.||++||++++.++
T Consensus 168 s~R~kvA~~vN~aiL~~~~~~~ 189 (228)
T KOG2659|consen 168 SLRQKVASEVNSAILASQEHES 189 (228)
T ss_pred HHHHHHHHHHHHHHHHHhcccc
Confidence 9999999999999999998764
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=99.96 E-value=1.4e-28 Score=189.89 Aligned_cols=122 Identities=39% Similarity=0.628 Sum_probs=116.2
Q ss_pred HHHHHHHHHHHHcCCHHHHHHHHHhhCchhhccCcchhhhhHHHHHHHHHHcCChHHHHHHHHHhcCccccCChhHHHHH
Q 028796 78 ITDRMAVKKAVQCGNVEDAIEKVNDLNPEILDTNPQLFFHLQQQRLIELIRNGKVEEALEFAQEELAPRGEENQSFLEEL 157 (203)
Q Consensus 78 ~~~r~~I~~~I~~g~i~~Ai~~l~~~~p~l~~~~~~l~F~L~~q~fIeli~~~~~~~Al~y~r~~l~~~~~~~~~~~~~l 157 (203)
+.+|+.|+++|.+||+++|++||++++|.+++.++++.|.|++|+||++|+.+++.+||+|+|+++.|+.. ...+++
T Consensus 2 ~~~r~~I~~~I~~g~i~~Ai~w~~~~~~~l~~~~~~L~f~L~~q~fiell~~~~~~~Ai~y~r~~l~~~~~---~~~~~l 78 (145)
T PF10607_consen 2 FKERKKIRQAILNGDIDPAIEWLNENFPELLKRNSSLEFELRCQQFIELLREGDIMEAIEYARKHLSPFND---EFLEEL 78 (145)
T ss_pred HHHHHHHHHHHHcCCHHHHHHHHHHcCHHHHhcCCchhHHHHHHHHHHHHHHHhHHHHHHHHHHHhhhhHH---HHHHHH
Confidence 67899999999999999999999999999999999999999999999999999999999999999976664 468999
Q ss_pred HHHHhhhcccCCCC---CchhhhcCHhhHHHHHHHHHHHHHhhcCCCC
Q 028796 158 ERTVALLAFEDVSN---CPVGDLLDISQRLKTASEVNAAILTSQSHEK 202 (203)
Q Consensus 158 ~~~~~LL~~~~~~~---sp~~~l~~~~~r~~la~~vN~aiL~~~~~~~ 202 (203)
+++|++|+|++|++ +||++++++++|+++|+.||++++...|.++
T Consensus 79 ~~~~~lL~~~~~~~~~~s~~~~l~~~~~~~~la~~~~~~~l~~~~~~~ 126 (145)
T PF10607_consen 79 KKLMSLLAYPDPEEPLPSPYKELLSPERREELAEEFNSAILKSYGLPK 126 (145)
T ss_pred HHHHHHHHcCCcccccchHHHHHhChHHHHHHHHHHHHHHHHHhCcCC
Confidence 99999999999998 7999999999999999999999999999875
No 3
>KOG0396 consensus Uncharacterized conserved protein [Function unknown]
Probab=99.96 E-value=5.8e-28 Score=206.53 Aligned_cols=159 Identities=21% Similarity=0.339 Sum_probs=148.5
Q ss_pred CHHHHHHHHHHHHHhhCHHHHHHHHHHhhCCCCCccHHHHHHHHHHHHHHHcCCHHHHHHHHHhhCchhhccCcchhhhh
Q 028796 39 RKEDMNKLVMNFLVTEGYVDAAEKFRMESGTEPDIDLATITDRMAVKKAVQCGNVEDAIEKVNDLNPEILDTNPQLFFHL 118 (203)
Q Consensus 39 ~~~~l~~lI~~yL~~~Gy~eta~~f~ke~~~~~~~~~e~~~~r~~I~~~I~~g~i~~Ai~~l~~~~p~l~~~~~~l~F~L 118 (203)
++..++++|.+||.|+||.+||..|.|++.++..+|.+.+.+.+.|+++|++|++.+|+.||++|...|.+.+|.++|.+
T Consensus 114 ~r~~l~r~vvdhmlr~gy~~~A~~L~K~s~ledlvD~Dv~~~~~~I~~sll~~~l~~~Lswc~ehk~~LkK~~S~lEf~l 193 (389)
T KOG0396|consen 114 PRNKLDRFVVDHMLRNGYFGAAVLLGKKSQLEDLVDSDVYKRAYGIRDSLLAGELEPALSWCKEHKVELKKEESSLEFQL 193 (389)
T ss_pred HHHHHHHHHHHHHHHcCchhHHHHHHHhhhhhhhHhHHHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHHhccchhhhHH
Confidence 45789999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHcCChHHHHHHHHHhcCccccCChhHHHHHHHHHhhhcccCCCC-CchhhhcCHhhHHHHHHHHHHHHHhh
Q 028796 119 QQQRLIELIRNGKVEEALEFAQEELAPRGEENQSFLEELERTVALLAFEDVSN-CPVGDLLDISQRLKTASEVNAAILTS 197 (203)
Q Consensus 119 ~~q~fIeli~~~~~~~Al~y~r~~l~~~~~~~~~~~~~l~~~~~LL~~~~~~~-sp~~~l~~~~~r~~la~~vN~aiL~~ 197 (203)
+.|+|||||+.++..+||+|+|++++|++..+ ..+++.+||+|+|+...+ ++|..+++..||+.+++.+-+-.++-
T Consensus 194 RlQefIELi~~~~~~~Ai~~akk~f~~~~~~~---~~~Lk~a~g~laF~~~t~~sky~~l~~~~rw~~l~~lF~s~a~~l 270 (389)
T KOG0396|consen 194 RLQEFIELIKVDNYDKAIAFAKKHFAPWAKSH---KSDLKLAMGLLAFPKYTSSSKYLNLLTADRWSVLADLFLSEALKL 270 (389)
T ss_pred HHHHHHHHHHhccHHHHHHHHHHHHhhhhhhh---HHHHHHHHHhhcCccccCcccccCcccHHHHHHHHHHhhHHHHHH
Confidence 99999999999999999999999999999755 799999999999998554 67999999999999999887776665
Q ss_pred cCC
Q 028796 198 QSH 200 (203)
Q Consensus 198 ~~~ 200 (203)
-|.
T Consensus 271 ~~i 273 (389)
T KOG0396|consen 271 FGI 273 (389)
T ss_pred hCC
Confidence 544
No 4
>KOG2817 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.87 E-value=5.4e-21 Score=165.43 Aligned_cols=165 Identities=19% Similarity=0.307 Sum_probs=146.7
Q ss_pred cCCCCHHH-HHHHHHHHHHhhCHHHHHHHHHHhhCCCCC--ccHHHHHHHHHHHHHHHcCCHHHHHHHHHhhCchhhccC
Q 028796 35 DVKIRKED-MNKLVMNFLVTEGYVDAAEKFRMESGTEPD--IDLATITDRMAVKKAVQCGNVEDAIEKVNDLNPEILDTN 111 (203)
Q Consensus 35 ~~~~~~~~-l~~lI~~yL~~~Gy~eta~~f~ke~~~~~~--~~~e~~~~r~~I~~~I~~g~i~~Ai~~l~~~~p~l~~~~ 111 (203)
++..+... +|.+|..||+++|..|++..|++|+|.... .....+.+.++|.++|..||+++|++|+..++..|.+.+
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 45555544 599999999999999999999999998754 445789999999999999999999999999999999999
Q ss_pred cchhhhhHHHHHHHHHHcCChH--HHHHHHHHhcCccccCChhHHHHHHHHHhhhcccCC--CCCchhhhcCHhhHHHHH
Q 028796 112 PQLFFHLQQQRLIELIRNGKVE--EALEFAQEELAPRGEENQSFLEELERTVALLAFEDV--SNCPVGDLLDISQRLKTA 187 (203)
Q Consensus 112 ~~l~F~L~~q~fIeli~~~~~~--~Al~y~r~~l~~~~~~~~~~~~~l~~~~~LL~~~~~--~~sp~~~l~~~~~r~~la 187 (203)
+.|+|.|+.++|+++++.|.-. +||.|+|++++||+.++ .++||++|++|.|-.. +++||.+++++..|..+.
T Consensus 190 s~LE~~Lh~l~fl~l~~~g~~~~~eAl~Yar~~~~~F~~~~---~~eIQklm~sl~~l~~gl~~spy~~~ls~~~w~~~~ 266 (394)
T KOG2817|consen 190 SSLEFKLHSLHFLSLIRGGKSDQREALRYARTHFAPFVADH---LREIQKLMGSLLYLRNGLEKSPYSEILSPKLWKELT 266 (394)
T ss_pred ccHHHHHHHHHHHHHHhcCCcCcHHHHHHHHHhcCccccch---HHHHHHHHHHHHHHHcCCCCCChHHHhCHHHHHHHH
Confidence 9999999999999999988766 99999999999998765 7999999999999765 689999999999999999
Q ss_pred HHHHHHHHhhcCCCC
Q 028796 188 SEVNAAILTSQSHEK 202 (203)
Q Consensus 188 ~~vN~aiL~~~~~~~ 202 (203)
+.+-+---..+|.+.
T Consensus 267 ~~f~r~ycallg~s~ 281 (394)
T KOG2817|consen 267 EEFTREYCALLGISV 281 (394)
T ss_pred HHHHHHHHHHcCCCc
Confidence 999887666666554
No 5
>smart00757 CRA CT11-RanBPM. protein-protein interaction domain present in crown eukaryotes (plants, animals, fungi)
Probab=99.58 E-value=7.9e-15 Score=105.80 Aligned_cols=72 Identities=49% Similarity=0.659 Sum_probs=67.5
Q ss_pred ChHHHHHHHHHhcCccccCChhHHHHHHHHHhhhcccCC-CCCchhhhcCHhhHHHHHHHHHHHHHhhc-CCCC
Q 028796 131 KVEEALEFAQEELAPRGEENQSFLEELERTVALLAFEDV-SNCPVGDLLDISQRLKTASEVNAAILTSQ-SHEK 202 (203)
Q Consensus 131 ~~~~Al~y~r~~l~~~~~~~~~~~~~l~~~~~LL~~~~~-~~sp~~~l~~~~~r~~la~~vN~aiL~~~-~~~~ 202 (203)
++.+||+|||++++++..+++.+.++++++|++|+|+++ +.+||++++++++|+++|+.||++||... |.++
T Consensus 2 ~~~eAi~yar~~l~~~~~~~~~~~~el~~~m~llaf~~~~~~sp~~~ll~~~~~~~la~~~n~~~l~~~~~~~~ 75 (99)
T smart00757 2 KIEEALAYARELLAPFAKEHEKFLKELEKTMALLAYPDPTEPSPYKELLSPSQREKLAEELNSAILELLHGKSS 75 (99)
T ss_pred cHHHHHHHHHHHHhhhcccCHHHHHHHHHHHHHHhcCCCCCCccHHHHCCHHHHHHHHHHHHHHHHHHccCCCC
Confidence 578999999999999998888888999999999999999 88999999999999999999999999998 8764
No 6
>smart00668 CTLH C-terminal to LisH motif. Alpha-helical motif of unknown function.
Probab=99.38 E-value=9.9e-13 Score=85.77 Aligned_cols=55 Identities=31% Similarity=0.669 Sum_probs=52.0
Q ss_pred HHHHHHHHHHHHcCCHHHHHHHHHhhCchhhccCcchhhhhHHHHHHHHHHcCCh
Q 028796 78 ITDRMAVKKAVQCGNVEDAIEKVNDLNPEILDTNPQLFFHLQQQRLIELIRNGKV 132 (203)
Q Consensus 78 ~~~r~~I~~~I~~g~i~~Ai~~l~~~~p~l~~~~~~l~F~L~~q~fIeli~~~~~ 132 (203)
+..+..|+++|+.|+|++|++||++++|.+.+.++.+.|.|++|+|+|+++.++.
T Consensus 2 ~~~~~~i~~~i~~g~~~~a~~~~~~~~~~l~~~~~~l~f~L~~q~~lell~~~~~ 56 (58)
T smart00668 2 FDERKRIRELILKGDWDEALEWLSSLKPPLLERNSKLEFELRKQKFLELVRQGKL 56 (58)
T ss_pred hHHHHHHHHHHHcCCHHHHHHHHHHcCHHHhccCCCchhHHHHHHHHHHHHcCCc
Confidence 5678999999999999999999999999999999999999999999999998764
No 7
>KOG0293 consensus WD40 repeat-containing protein [Function unknown]
Probab=98.90 E-value=1.1e-08 Score=89.90 Aligned_cols=130 Identities=15% Similarity=0.234 Sum_probs=109.2
Q ss_pred hhhcccCCCHHHHHHHhhcCCCCHHHHHHHHHHHHHhhCHHHHHHHHHHhhCCCCCccHHHHHHHHHHHHHHHcCCHHHH
Q 028796 17 MAMSKKVITREEWEKKLNDVKIRKEDMNKLVMNFLVTEGYVDAAEKFRMESGTEPDIDLATITDRMAVKKAVQCGNVEDA 96 (203)
Q Consensus 17 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~lI~~yL~~~Gy~eta~~f~ke~~~~~~~~~e~~~~r~~I~~~I~~g~i~~A 96 (203)
..++|+.|++.|| .+++.+.|+.-||-+++..++.|+|+.... ..-+.+.+++++|+|+.+
T Consensus 8 ~l~~k~likk~ef--------------i~il~q~l~slgy~~S~~~lE~es~ll~~t-----at~klf~q~vlqg~w~q~ 68 (519)
T KOG0293|consen 8 ILGSKGLIKKGEF--------------IRILWQILYSLGYDHSSPLLEWESGLLIPT-----ATTKLFDQQVLQGQWDQQ 68 (519)
T ss_pred hhhhhceeccchh--------------hHhHHHHHHhcCccccchhhHHhhCccccc-----chHHHHHHHHHcccHHHH
Confidence 3678999999999 899999999999999999999999986322 223668899999999999
Q ss_pred HHHHHhhCchhhccCcchhhhhHHHHHHHHHHcCChHHHHHHHHHhcCccccCChhHHHHHHHHHhhhcccCC
Q 028796 97 IEKVNDLNPEILDTNPQLFFHLQQQRLIELIRNGKVEEALEFAQEELAPRGEENQSFLEELERTVALLAFEDV 169 (203)
Q Consensus 97 i~~l~~~~p~l~~~~~~l~F~L~~q~fIeli~~~~~~~Al~y~r~~l~~~~~~~~~~~~~l~~~~~LL~~~~~ 169 (203)
+.-+....-...++.....|.+.+|.|+|+++.|++..|+...|+.+.+.... .+++.++.+.|+++..
T Consensus 69 v~~~~~i~~~de~~~~ea~fLv~kQ~fLEf~k~~~is~al~~l~~~~~~lr~~----~kk~~el~~sll~sn~ 137 (519)
T KOG0293|consen 69 VMSLVRISFEDERNRKEAMFLVNKQIFLEFLKTGSISHALPVLRNPVLYLRKN----KKKFHELASSLLVSND 137 (519)
T ss_pred HHHHhhccCcchhhhHHHHHHHHHHHHHHHHhhccHhhhhHhhhcchhhhhhh----HHHHHHHHHHHhcccc
Confidence 98887763333556688999999999999999999999999999877777653 4778889998888773
No 8
>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=98.48 E-value=2.4e-07 Score=51.32 Aligned_cols=27 Identities=37% Similarity=0.811 Sum_probs=24.1
Q ss_pred HHHHHHHHHHHHhhCHHHHHHHHHHhh
Q 028796 41 EDMNKLVMNFLVTEGYVDAAEKFRMES 67 (203)
Q Consensus 41 ~~l~~lI~~yL~~~Gy~eta~~f~ke~ 67 (203)
+.||.+|.+||.++||.+||.+|.+|+
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 468999999999999999999999985
No 9
>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=98.16 E-value=4.9e-06 Score=47.69 Aligned_cols=32 Identities=31% Similarity=0.754 Sum_probs=28.9
Q ss_pred CHHHHHHHHHHHHHhhCHHHHHHHHHHhhCCC
Q 028796 39 RKEDMNKLVMNFLVTEGYVDAAEKFRMESGTE 70 (203)
Q Consensus 39 ~~~~l~~lI~~yL~~~Gy~eta~~f~ke~~~~ 70 (203)
.+..++++|++||.++||.+|+.+|.+|+|+.
T Consensus 2 ~~~~l~~lI~~yL~~~g~~~ta~~l~~e~~~~ 33 (34)
T smart00667 2 SRSELNRLILEYLLRNGYEETAETLQKESGLS 33 (34)
T ss_pred cHHHHHHHHHHHHHHcCHHHHHHHHHHHhCCC
Confidence 35678999999999999999999999999874
No 10
>KOG1477 consensus SPRY domain-containing proteins [General function prediction only]
Probab=98.15 E-value=1.9e-07 Score=84.78 Aligned_cols=161 Identities=23% Similarity=0.185 Sum_probs=123.4
Q ss_pred HHHHHHHHHHHhhCHHHHHHHHHHhhCCCC--Cc-----cHHHH-----HHHHHHHHHHHcCCHHHHHHHHHhhCchhhc
Q 028796 42 DMNKLVMNFLVTEGYVDAAEKFRMESGTEP--DI-----DLATI-----TDRMAVKKAVQCGNVEDAIEKVNDLNPEILD 109 (203)
Q Consensus 42 ~l~~lI~~yL~~~Gy~eta~~f~ke~~~~~--~~-----~~e~~-----~~r~~I~~~I~~g~i~~Ai~~l~~~~p~l~~ 109 (203)
.....+-.|+++.|+.+++..|+..+.-.. .. ..+.. ..+......+-.+.+..+.+.+.+..+....
T Consensus 251 l~t~~~~~~~l~~~~~~s~~~~s~~~~~~~~~~~~~e~~s~~~~~~~~~~~~~~~~~~~g~~~~~~~g~~~~~~~~~~~~ 330 (469)
T KOG1477|consen 251 LSTVPYPYFLLPGGYEESIAYFSTGARRFNDPFTGKEENSIDAVGSQTDKIGLDYHQRKGRGQFTRNGAYNAALIPTYRK 330 (469)
T ss_pred ccCCCccceecCcchhhhhhhhcchhhccCCcccchhhhhhhccccccchhhhhhhhhcCcceeechhhhcccccccccc
Confidence 344688899999999999999998865421 10 00100 1233344444445566666666655555444
Q ss_pred -------cCcchhhhhHHHHHHHHHHcCChHHHHHHHHHhcCcccc--CChhHHHHHHHHHhhhcccCCCCCchhhhcCH
Q 028796 110 -------TNPQLFFHLQQQRLIELIRNGKVEEALEFAQEELAPRGE--ENQSFLEELERTVALLAFEDVSNCPVGDLLDI 180 (203)
Q Consensus 110 -------~~~~l~F~L~~q~fIeli~~~~~~~Al~y~r~~l~~~~~--~~~~~~~~l~~~~~LL~~~~~~~sp~~~l~~~ 180 (203)
..+...+.+.|+.++.+.+.+.+...+++.+..+++... ........++..++||+|++|..||...++++
T Consensus 331 ~~~~~~~~~~~~~~~~~~~~~v~~~~~g~v~~e~~~~k~~l~~~~g~~~~~~~~~~~~~s~~Llays~p~~s~~g~~~~~ 410 (469)
T KOG1477|consen 331 VGQVFEVDYPQRGAKDPCGLHVNLGRAGFVFIEANAKKWELAKDYGIKKNSAAVGMLSDSSSLLAYSDPEESPVGYLLDP 410 (469)
T ss_pred cceeecccccchhhccchhhhhhHHHHHHHHHHHHHHHHhhhhhhCcCccccccccccchHHHHHhcCcccCccccccCc
Confidence 347789999999999999999999999999999887765 33456789999999999999999999999999
Q ss_pred hhHHHHHHHHHHHHHhhcCCCC
Q 028796 181 SQRLKTASEVNAAILTSQSHEK 202 (203)
Q Consensus 181 ~~r~~la~~vN~aiL~~~~~~~ 202 (203)
..|+-+++.+|.+||...+..+
T Consensus 411 ~~~e~v~~~~n~~il~t~~~~~ 432 (469)
T KOG1477|consen 411 IQREPVAEALNSAILETDNNSK 432 (469)
T ss_pred ccchhHHhhhcccccccCCCCc
Confidence 9999999999999999888765
No 11
>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=97.09 E-value=0.0097 Score=51.25 Aligned_cols=145 Identities=9% Similarity=-0.011 Sum_probs=108.7
Q ss_pred hhhcccCCCHHHHHHHhhcCCCCHHHHHHHHHHHHHhhCHHHHHHHHHHhhCCCCC-ccHHHHHHHHHHHHHHHcCCHHH
Q 028796 17 MAMSKKVITREEWEKKLNDVKIRKEDMNKLVMNFLVTEGYVDAAEKFRMESGTEPD-IDLATITDRMAVKKAVQCGNVED 95 (203)
Q Consensus 17 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~lI~~yL~~~Gy~eta~~f~ke~~~~~~-~~~e~~~~r~~I~~~I~~g~i~~ 95 (203)
.+..+..|++... +.+-........++.+...++.++|-..-+..|+.+.|..+. ...+.+...+.|.+.|.+.+...
T Consensus 78 ~~~~~~nFd~~~~-n~~~~f~~~~v~~~~~~~l~~~n~~dv~~~hi~~~~~g~~e~~~~~~~f~~lK~v~~gI~~k~~~l 156 (396)
T COG5109 78 EDCRPANFDVQVG-NQIYPFSTQTVTYLVVYYLLENNCADVVERHISETKDGKDEIIKIRDGFVKLKKVISGISEKSTFL 156 (396)
T ss_pred HhhccccCCHHHH-hhcCCCccceeeehHHHHHHHhhHHHHHHHHHHHhhcCccchhhHHHHHHHHHHHHHhhccchhHh
Confidence 3444455666554 334444555566777777778888889999999999998754 44689999999999999999999
Q ss_pred HHHHHHhhCchhhccCcchhhhhHHHHHHHHH-HcCChHHHHHHHHHhcCccccCChhHHHHHHHHHhhhcc
Q 028796 96 AIEKVNDLNPEILDTNPQLFFHLQQQRLIELI-RNGKVEEALEFAQEELAPRGEENQSFLEELERTVALLAF 166 (203)
Q Consensus 96 Ai~~l~~~~p~l~~~~~~l~F~L~~q~fIeli-~~~~~~~Al~y~r~~l~~~~~~~~~~~~~l~~~~~LL~~ 166 (203)
-++|. +....+.+.++...+.+.......+. ...++++|+.++++.++.|...| ...++.++-.+.+
T Consensus 157 ~iE~~-Qi~gyl~kgdtesel~l~~~~~esl~l~hk~~~~a~r~c~t~~a~f~~kh---~~dv~~~~~~l~n 224 (396)
T COG5109 157 LIEFL-QIEGYLSKGDTESELELYLVSHESLLLIHKRYDEALRLCFTKLASFVPKH---IQDVKPLLRFLVN 224 (396)
T ss_pred HHHHH-HhcCccccCCchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh---ccchHHHHHHHHc
Confidence 99999 55566777677777777766655532 33489999999999999998544 6777777777665
No 12
>KOG0275 consensus Conserved WD40 repeat-containing protein [General function prediction only]
Probab=96.44 E-value=0.047 Score=47.59 Aligned_cols=144 Identities=16% Similarity=0.207 Sum_probs=94.7
Q ss_pred CCCHHHHHHHHHHHHHhhCHHHHHHHHHHhhCCCCCccHHHHHHHHHHHHHHHcCCHHHHHHHHHhhCchhhccCcchhh
Q 028796 37 KIRKEDMNKLVMNFLVTEGYVDAAEKFRMESGTEPDIDLATITDRMAVKKAVQCGNVEDAIEKVNDLNPEILDTNPQLFF 116 (203)
Q Consensus 37 ~~~~~~l~~lI~~yL~~~Gy~eta~~f~ke~~~~~~~~~e~~~~r~~I~~~I~~g~i~~Ai~~l~~~~p~l~~~~~~l~F 116 (203)
.+....+.++|.+||-.+....|...|.+|.++.. ..+..-..+.+.|-+|+||..+.-++...- ...-..
T Consensus 4 eiessdVIrli~QflKE~~L~rtl~tLQeEt~VSL----NTVDSvd~Fv~dI~sG~WD~VL~~vqsLKL-----P~kkL~ 74 (508)
T KOG0275|consen 4 EIESSDVIRLIEQFLKENSLHRTLQTLQEETNVSL----NTVDSVDGFVNDINSGHWDTVLKTVQSLKL-----PDKKLI 74 (508)
T ss_pred eeecchHHHHHHHHHhhhhHHHHHHHHHHhhccce----eechhHHHHHHhcccCchHHHHHHHHhccC-----chhHHH
Confidence 34445778999999999999999999999998742 111122347888999999999998876542 223455
Q ss_pred hhHHHHHHHHHHcCChHHHHHHHHHhcCc--cccCChhHHHHHHHHHhhhcccCCCCCchhhhcCHhhHHHHHHHHH
Q 028796 117 HLQQQRLIELIRNGKVEEALEFAQEELAP--RGEENQSFLEELERTVALLAFEDVSNCPVGDLLDISQRLKTASEVN 191 (203)
Q Consensus 117 ~L~~q~fIeli~~~~~~~Al~y~r~~l~~--~~~~~~~~~~~l~~~~~LL~~~~~~~sp~~~l~~~~~r~~la~~vN 191 (203)
.|+-|-.+|+|+-..+..|-..+|+.-.. .....|+..-.++.+.. -.|.||.. .|.+---..||..+|+.+.
T Consensus 75 dLYEqivlEliELREL~tAR~~lRQTdpM~~lKQ~~peRy~~lE~ll~-R~YFDp~E-aY~dssKEkrRa~IAQ~ls 149 (508)
T KOG0275|consen 75 DLYEQIVLELIELRELGTARSLLRQTDPMIMLKQIQPERYIRLENLLN-RSYFDPRE-AYGDSSKEKRRAVIAQALS 149 (508)
T ss_pred HHHHHHHHHHHHHHhhhHHHHHHhccCceehhhccChHHHHHHHHHhc-ccccChhh-hcCcchHHHHHHHHHHHhc
Confidence 78999999999988888888888864221 22223333333333222 12444432 2444223567778887765
No 13
>KOG1333 consensus Uncharacterized conserved protein [Function unknown]
Probab=93.30 E-value=0.61 Score=38.03 Aligned_cols=106 Identities=16% Similarity=0.180 Sum_probs=69.6
Q ss_pred HHHHHHHHHHHHhhCHHHHHHHHHHhhCCCCCccHHHHHHHHHHHHHHHcCCHHHHHHHH----HhhCchhhccC----c
Q 028796 41 EDMNKLVMNFLVTEGYVDAAEKFRMESGTEPDIDLATITDRMAVKKAVQCGNVEDAIEKV----NDLNPEILDTN----P 112 (203)
Q Consensus 41 ~~l~~lI~~yL~~~Gy~eta~~f~ke~~~~~~~~~e~~~~r~~I~~~I~~g~i~~Ai~~l----~~~~p~l~~~~----~ 112 (203)
+.++.+|-+||+-.|+.-|.++|-.|.........-.=+...+..++|...|++.--+.= +..++.|.... .
T Consensus 6 ~~tDelvReYL~frgf~~tLkalD~E~~~~Ke~~frvdrivdq~~~a~q~~Dl~aLr~~W~~l~~r~Fs~Le~~y~~~~~ 85 (241)
T KOG1333|consen 6 ERTDELVREYLLFRGFTHTLKALDAEIKADKEKGFRVDRIVDQLQQAMQVYDLAALRDYWSYLERRLFSRLEDIYRPTIH 85 (241)
T ss_pred HHHHHHHHHHHHHhhHHHHHHHHhHHHhhhhhcCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHH
Confidence 457899999999999999999998887654333222223345566777777777654322 22233332221 2
Q ss_pred chhhhhHHHHHHHHHHcCChHHHHHHHHHhcCcc
Q 028796 113 QLFFHLQQQRLIELIRNGKVEEALEFAQEELAPR 146 (203)
Q Consensus 113 ~l~F~L~~q~fIeli~~~~~~~Al~y~r~~l~~~ 146 (203)
.++--+.+..++--+.++.+++|=+|.++.-+..
T Consensus 86 kle~Sl~r~yLV~~~q~nr~~K~~EFF~K~a~~l 119 (241)
T KOG1333|consen 86 KLETSLFRFYLVYTIQTNRNDKAQEFFAKQATEL 119 (241)
T ss_pred HHHHHHHHHHHhhhhhcCChHHHHHHHHHHHHHH
Confidence 3455566666777788899999999999754433
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=89.41 E-value=0.89 Score=31.69 Aligned_cols=29 Identities=24% Similarity=0.304 Sum_probs=25.6
Q ss_pred HHHHHHHHHHHhhCHHHHHHHHHHhhCCC
Q 028796 42 DMNKLVMNFLVTEGYVDAAEKFRMESGTE 70 (203)
Q Consensus 42 ~l~~lI~~yL~~~Gy~eta~~f~ke~~~~ 70 (203)
.++.||.+||.-+||.=|+..|..|+|..
T Consensus 20 Li~eLIrEyLef~~l~~TlsVf~~Es~~~ 48 (81)
T PF09398_consen 20 LINELIREYLEFNNLDYTLSVFQPESGQP 48 (81)
T ss_dssp HHHHHHHHHHHHTT-HHHHHHHHHHHT-T
T ss_pred HHHHHHHHHHHHcCCccHHHHHhhccCCC
Confidence 57999999999999999999999999986
No 15
>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=79.05 E-value=29 Score=30.09 Aligned_cols=98 Identities=22% Similarity=0.272 Sum_probs=66.5
Q ss_pred HHHHHHHHHHHhhCHHHHHHHHHHhhCC----------------CCCccH----------------------------HH
Q 028796 42 DMNKLVMNFLVTEGYVDAAEKFRMESGT----------------EPDIDL----------------------------AT 77 (203)
Q Consensus 42 ~l~~lI~~yL~~~Gy~eta~~f~ke~~~----------------~~~~~~----------------------------e~ 77 (203)
+.++++++.|.+.||.+.+.++..+... .|+.+. +.
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 3579999999999999999998888531 123221 12
Q ss_pred HHHHHHHHHHHHcCCHHHHHHHHHhhCchhhccCcchhhhhHHHHHHHHHHcCChHHHHHHHHH
Q 028796 78 ITDRMAVKKAVQCGNVEDAIEKVNDLNPEILDTNPQLFFHLQQQRLIELIRNGKVEEALEFAQE 141 (203)
Q Consensus 78 ~~~r~~I~~~I~~g~i~~Ai~~l~~~~p~l~~~~~~l~F~L~~q~fIeli~~~~~~~Al~y~r~ 141 (203)
.....+.+.++.+|.+++|+.|+++..+...+....+...|..-++.+ ..|...-|....++
T Consensus 214 ~~~~~eA~~l~~~~gl~~Al~~L~~~~~~~~s~R~rf~~rL~~A~l~~--~~g~~~lA~~ll~~ 275 (301)
T TIGR03362 214 EELREEARALAAEGGLEAALQRLQQRLAQAREPRERFHWRLLLARLLE--QAGKAELAQQLYAA 275 (301)
T ss_pred HHHHHHHHHHHHcCCHHHHHHHHHhhcccCCChHHHHHHHHHHHHHHH--HcCCHHHHHHHHHH
Confidence 334466788889999999999999876666555555555555555544 35555556655554
No 16
>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=75.53 E-value=5.9 Score=30.22 Aligned_cols=48 Identities=19% Similarity=0.362 Sum_probs=38.1
Q ss_pred cchhhhhHHHHHHHHHHcCChHHHHHHHHHhcCccccCChhHHHHHHHHHh
Q 028796 112 PQLFFHLQQQRLIELIRNGKVEEALEFAQEELAPRGEENQSFLEELERTVA 162 (203)
Q Consensus 112 ~~l~F~L~~q~fIeli~~~~~~~Al~y~r~~l~~~~~~~~~~~~~l~~~~~ 162 (203)
..+.|=+.++-|++||.+|...+|-.|..++-.-+...+ ..+|+++.+
T Consensus 38 ~~lLyPvFvh~YL~Lv~~~~~~~A~~F~~kf~~~~~~~~---~~~i~~L~~ 85 (142)
T PF04494_consen 38 SRLLYPVFVHSYLDLVSKGHPEEAKSFLEKFSPDFEDSH---QEDIEKLSS 85 (142)
T ss_dssp GGGHHHHHHHHHHHHHHTT-HHHHHHHHHHHGGGGHGHG---HHHHHHHTT
T ss_pred HHHHHHHHHHHHHHHHHCCChHHHHHHHHHHHHHHhHHH---HHHHHHHHh
Confidence 568999999999999999999999999998777766433 455666654
No 17
>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=74.55 E-value=15 Score=23.26 Aligned_cols=56 Identities=21% Similarity=0.277 Sum_probs=35.4
Q ss_pred HHHcCCHHHHHHHHHhhCchhhccCcchhhhhHHHHHHHHHHcCChHHHHHHHHHhcCccc
Q 028796 87 AVQCGNVEDAIEKVNDLNPEILDTNPQLFFHLQQQRLIELIRNGKVEEALEFAQEELAPRG 147 (203)
Q Consensus 87 ~I~~g~i~~Ai~~l~~~~p~l~~~~~~l~F~L~~q~fIeli~~~~~~~Al~y~r~~l~~~~ 147 (203)
++..|++++|++.+++.. .....+..+.+.+ -.-+++.|+..+|.++..+.+....
T Consensus 1 ll~~~~~~~A~~~~~~~l-~~~p~~~~~~~~l----a~~~~~~g~~~~A~~~l~~~~~~~~ 56 (68)
T PF14559_consen 1 LLKQGDYDEAIELLEKAL-QRNPDNPEARLLL----AQCYLKQGQYDEAEELLERLLKQDP 56 (68)
T ss_dssp HHHTTHHHHHHHHHHHHH-HHTTTSHHHHHHH----HHHHHHTT-HHHHHHHHHCCHGGGT
T ss_pred ChhccCHHHHHHHHHHHH-HHCCCCHHHHHHH----HHHHHHcCCHHHHHHHHHHHHHHCc
Confidence 467899999999987652 1112233344332 2235678999999999997655444
No 18
>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=73.32 E-value=8.7 Score=28.91 Aligned_cols=51 Identities=20% Similarity=0.353 Sum_probs=39.2
Q ss_pred cchhhhhHHHHHHHHHHcCChHHHHHHHHHhcCccccCChhHHHHHHHHHhhhc
Q 028796 112 PQLFFHLQQQRLIELIRNGKVEEALEFAQEELAPRGEENQSFLEELERTVALLA 165 (203)
Q Consensus 112 ~~l~F~L~~q~fIeli~~~~~~~Al~y~r~~l~~~~~~~~~~~~~l~~~~~LL~ 165 (203)
..+.|=+.+.-|++||.+|...+|..|.+++-.-+. +.+..+++.+.++..
T Consensus 27 ~~lLyPiFvh~yL~lv~~~~~~~A~~F~~~f~~~~~---~~~~~~i~~L~~i~~ 77 (133)
T cd08044 27 SQLLYPIFVHSYLDLVASGHLEEAKSFFERFSGDFE---DSHSEDIKKLSSITT 77 (133)
T ss_pred HHHHHHHHHHHHHHHHHCCCHHHHHHHHHHhhHhhH---HHHHHHHHHHHccCC
Confidence 458899999999999999999999999998666554 334566666655443
No 19
>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=73.06 E-value=34 Score=27.08 Aligned_cols=83 Identities=20% Similarity=0.337 Sum_probs=47.4
Q ss_pred HHHHHHHHHHHhhCHHHHHHHHHHhhCCCCCccHHHHHHHHHHHHHHHcCCHHHHHHHHHhhCchhhccCcchhhhhH-H
Q 028796 42 DMNKLVMNFLVTEGYVDAAEKFRMESGTEPDIDLATITDRMAVKKAVQCGNVEDAIEKVNDLNPEILDTNPQLFFHLQ-Q 120 (203)
Q Consensus 42 ~l~~lI~~yL~~~Gy~eta~~f~ke~~~~~~~~~e~~~~r~~I~~~I~~g~i~~Ai~~l~~~~p~l~~~~~~l~F~L~-~ 120 (203)
.+..++.+=|++.|-......|-.-.=+.+.... . ...+.-|. .+|...+-+-++.-.|. .
T Consensus 30 ~L~~lli~lLi~~~~~~~L~qllq~~Vi~DSk~l---A-----~~LLs~~~----------~~~~~~Ql~lDMLkRL~~~ 91 (167)
T PF07035_consen 30 ELYELLIDLLIRNGQFSQLHQLLQYHVIPDSKPL---A-----CQLLSLGN----------QYPPAYQLGLDMLKRLGTA 91 (167)
T ss_pred HHHHHHHHHHHHcCCHHHHHHHHhhcccCCcHHH---H-----HHHHHhHc----------cChHHHHHHHHHHHHhhhh
Confidence 4778888888888877777777543333221111 0 11111111 23434343445555555 4
Q ss_pred HH-HHH-HHHcCChHHHHHHHHHh
Q 028796 121 QR-LIE-LIRNGKVEEALEFAQEE 142 (203)
Q Consensus 121 q~-fIe-li~~~~~~~Al~y~r~~ 142 (203)
.. .+| ++..|++.+|+.|+|+.
T Consensus 92 ~~~iievLL~~g~vl~ALr~ar~~ 115 (167)
T PF07035_consen 92 YEEIIEVLLSKGQVLEALRYARQY 115 (167)
T ss_pred HHHHHHHHHhCCCHHHHHHHHHHc
Confidence 43 445 78899999999999974
No 20
>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=70.17 E-value=16 Score=27.29 Aligned_cols=58 Identities=16% Similarity=0.118 Sum_probs=44.4
Q ss_pred HHHHHHHhhCHHHHHHHHHHhhC--C-CCCccHHHHHHHHHHHHHHHcCCHHHHHHHHHhhC
Q 028796 46 LVMNFLVTEGYVDAAEKFRMESG--T-EPDIDLATITDRMAVKKAVQCGNVEDAIEKVNDLN 104 (203)
Q Consensus 46 lI~~yL~~~Gy~eta~~f~ke~~--~-~~~~~~e~~~~r~~I~~~I~~g~i~~Ai~~l~~~~ 104 (203)
-|.+.+ .+|-.+.|-..+++.. + +...+.+..-.++++.+.|..|++.+|+++++++.
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 345555 7888888888777653 1 22356677778899999999999999999999865
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=67.63 E-value=26 Score=31.99 Aligned_cols=76 Identities=28% Similarity=0.333 Sum_probs=54.5
Q ss_pred HHHHHHHHHHhhCHHHHHHHHHHhhCCCCCccHHHHHHHHHHHHHHHcCCHHHHHHHHHhhCchhhccCcchhhhhHHHH
Q 028796 43 MNKLVMNFLVTEGYVDAAEKFRMESGTEPDIDLATITDRMAVKKAVQCGNVEDAIEKVNDLNPEILDTNPQLFFHLQQQR 122 (203)
Q Consensus 43 l~~lI~~yL~~~Gy~eta~~f~ke~~~~~~~~~e~~~~r~~I~~~I~~g~i~~Ai~~l~~~~p~l~~~~~~l~F~L~~q~ 122 (203)
...-|+.||...||.|.|-.|.++. +.+..=+|.-|+++.|.+.+.+... -..++|=
T Consensus 297 ~~~~i~~fL~~~G~~e~AL~~~~D~-------------~~rFeLAl~lg~L~~A~~~a~~~~~----------~~~W~~L 353 (443)
T PF04053_consen 297 QGQSIARFLEKKGYPELALQFVTDP-------------DHRFELALQLGNLDIALEIAKELDD----------PEKWKQL 353 (443)
T ss_dssp HHHHHHHHHHHTT-HHHHHHHSS-H-------------HHHHHHHHHCT-HHHHHHHCCCCST----------HHHHHHH
T ss_pred HHHHHHHHHHHCCCHHHHHhhcCCh-------------HHHhHHHHhcCCHHHHHHHHHhcCc----------HHHHHHH
Confidence 3677899999999999999996543 3567778999999999999876531 1245555
Q ss_pred HHHHHHcCChHHHHHHHHH
Q 028796 123 LIELIRNGKVEEALEFAQE 141 (203)
Q Consensus 123 fIeli~~~~~~~Al~y~r~ 141 (203)
--..++.|++.-|-+..++
T Consensus 354 g~~AL~~g~~~lAe~c~~k 372 (443)
T PF04053_consen 354 GDEALRQGNIELAEECYQK 372 (443)
T ss_dssp HHHHHHTTBHHHHHHHHHH
T ss_pred HHHHHHcCCHHHHHHHHHh
Confidence 5556788888877776664
No 22
>PF12895 Apc3: Anaphase-promoting complex, cyclosome, subunit 3; PDB: 3KAE_D 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2XPI_A 3ULQ_A.
Probab=64.59 E-value=30 Score=23.10 Aligned_cols=52 Identities=29% Similarity=0.440 Sum_probs=31.2
Q ss_pred HHHHHHcCCHHHHHHHHHhhCchhhccCcchhhhhHHHHHHHHHHcCChHHHHHHHHH
Q 028796 84 VKKAVQCGNVEDAIEKVNDLNPEILDTNPQLFFHLQQQRLIELIRNGKVEEALEFAQE 141 (203)
Q Consensus 84 I~~~I~~g~i~~Ai~~l~~~~p~l~~~~~~l~F~L~~q~fIeli~~~~~~~Al~y~r~ 141 (203)
-.-....|+.+.|+.+++. ......+....+.+ -+.++ +.|+.++|++...+
T Consensus 32 a~~~~~~~~y~~A~~~~~~--~~~~~~~~~~~~l~-a~~~~---~l~~y~eAi~~l~~ 83 (84)
T PF12895_consen 32 AQCYFQQGKYEEAIELLQK--LKLDPSNPDIHYLL-ARCLL---KLGKYEEAIKALEK 83 (84)
T ss_dssp HHHHHHTTHHHHHHHHHHC--HTHHHCHHHHHHHH-HHHHH---HTT-HHHHHHHHHH
T ss_pred HHHHHHCCCHHHHHHHHHH--hCCCCCCHHHHHHH-HHHHH---HhCCHHHHHHHHhc
Confidence 4445688999999999987 33333333344433 33333 45888888877653
No 23
>PF12550 GCR1_C: Transcriptional activator of glycolytic enzymes; InterPro: IPR022210 This domain family is found in eukaryotes, and is approximately 80 amino acids in length. This family is activates the transcription of glycolytic enzymes.
Probab=63.13 E-value=20 Score=24.52 Aligned_cols=65 Identities=14% Similarity=0.208 Sum_probs=47.9
Q ss_pred CHHHHHHHHHHHHHhhCHHHHHHHHHHhhCCC---CCccHHHHHHHHHHHHHHHc-----C-CHHHHHHHHHhh
Q 028796 39 RKEDMNKLVMNFLVTEGYVDAAEKFRMESGTE---PDIDLATITDRMAVKKAVQC-----G-NVEDAIEKVNDL 103 (203)
Q Consensus 39 ~~~~l~~lI~~yL~~~Gy~eta~~f~ke~~~~---~~~~~e~~~~r~~I~~~I~~-----g-~i~~Ai~~l~~~ 103 (203)
+...+..+..+|..-.+-..+...|.+..|.. ...+...+..|+.|.+.|.. | +.++|++.|+..
T Consensus 7 ~~~TV~dlw~Ew~~g~~g~psI~~le~~yG~~WR~~~~~~~~y~rRK~Ii~~I~~l~~~~g~~~~~ai~~le~~ 80 (81)
T PF12550_consen 7 SIKTVYDLWREWFTGLNGQPSIRSLEKKYGSKWRRDSKERRTYSRRKVIIDFIERLANERGISEEEAIEILEEI 80 (81)
T ss_pred CCCcHHHHHHHHhcCCCCCCCHHHHHHHhChhhccCcccchhHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHhc
Confidence 44556778888877655567888888888743 34556799999999999876 3 778888877653
No 24
>KOG0273 consensus Beta-transducin family (WD-40 repeat) protein [Chromatin structure and dynamics]
Probab=62.95 E-value=2.3 Score=38.82 Aligned_cols=34 Identities=29% Similarity=0.555 Sum_probs=31.3
Q ss_pred CCCHHHHHHHHHHHHHhhCHHHHHHHHHHhhCCC
Q 028796 37 KIRKEDMNKLVMNFLVTEGYVDAAEKFRMESGTE 70 (203)
Q Consensus 37 ~~~~~~l~~lI~~yL~~~Gy~eta~~f~ke~~~~ 70 (203)
.++++++|.||-.||-..||.=||=+|..|+++.
T Consensus 2 sitsdEvN~LV~RYLqE~G~~hsaftf~~Et~is 35 (524)
T KOG0273|consen 2 SITSDEVNFLVWRYLQESGFSHSAFTFGIETGIS 35 (524)
T ss_pred cccHHHHHHHHHHHHHHcCcceeeEEeeeccccc
Confidence 5678889999999999999999999999999875
No 25
>KOG1585 consensus Protein required for fusion of vesicles in vesicular transport, gamma-SNAP [Intracellular trafficking, secretion, and vesicular transport]
Probab=60.26 E-value=53 Score=28.09 Aligned_cols=74 Identities=14% Similarity=0.144 Sum_probs=61.1
Q ss_pred HHHHhhcCCCCHHHHHHHHHHHHHhhCHHHHHHHHHHhhCCCCCccHHHHHHHHHHHHHHHcCCHHHHHHHHHh
Q 028796 29 WEKKLNDVKIRKEDMNKLVMNFLVTEGYVDAAEKFRMESGTEPDIDLATITDRMAVKKAVQCGNVEDAIEKVND 102 (203)
Q Consensus 29 ~~~~~~~~~~~~~~l~~lI~~yL~~~Gy~eta~~f~ke~~~~~~~~~e~~~~r~~I~~~I~~g~i~~Ai~~l~~ 102 (203)
|-....+.+..-....-.|+=||..+.|..+-+.+...+.++.+...+..+....+...--+||++++-+.++.
T Consensus 179 ~~~~~~~y~~~~k~~va~ilv~L~~~Dyv~aekc~r~~~qip~f~~sed~r~lenLL~ayd~gD~E~~~kvl~s 252 (308)
T KOG1585|consen 179 AADKCDAYNSQCKAYVAAILVYLYAHDYVQAEKCYRDCSQIPAFLKSEDSRSLENLLTAYDEGDIEEIKKVLSS 252 (308)
T ss_pred HHHHHhhcccHHHHHHHHHHHHhhHHHHHHHHHHhcchhcCccccChHHHHHHHHHHHHhccCCHHHHHHHHcC
Confidence 44445555555555778899999999999999999999999888888888888888888999999999888764
No 26
>KOG2659 consensus LisH motif-containing protein [Cytoskeleton]
Probab=59.58 E-value=1e+02 Score=25.67 Aligned_cols=67 Identities=15% Similarity=0.220 Sum_probs=52.8
Q ss_pred CHHHHH-HHHHHHHHhhCHHHHHHHHHHhhCC---CCCccHHHHHHHHHHHHHHHcCCHHHHHHHHHhhCc
Q 028796 39 RKEDMN-KLVMNFLVTEGYVDAAEKFRMESGT---EPDIDLATITDRMAVKKAVQCGNVEDAIEKVNDLNP 105 (203)
Q Consensus 39 ~~~~l~-~lI~~yL~~~Gy~eta~~f~ke~~~---~~~~~~e~~~~r~~I~~~I~~g~i~~Ai~~l~~~~p 105 (203)
+.+.++ |+....++..|-.+.|-.+.....= +...+....-..++..++|++|..++|++..+..-.
T Consensus 61 d~~~~~eR~~Ir~~I~~G~Ie~Aie~in~l~PeiLd~n~~l~F~Lq~q~lIEliR~~~~eeal~F~q~~LA 131 (228)
T KOG2659|consen 61 DLDSMDERLQIRRAIEEGQIEEAIEKVNQLNPEILDTNRELFFHLQQLHLIELIREGKTEEALEFAQTKLA 131 (228)
T ss_pred chhhHhHHHHHHHHHHhccHHHHHHHHHHhChHHHccchhHHHHHHHHHHHHHHHhhhHHHHHHHHHHHcc
Confidence 444444 8888899999999999998887762 223345677888999999999999999999987643
No 27
>PF13934 ELYS: Nuclear pore complex assembly
Probab=59.45 E-value=99 Score=25.42 Aligned_cols=113 Identities=15% Similarity=0.149 Sum_probs=64.6
Q ss_pred CHHHHHHHhhcCCCCHHHHHHHHHHHHHhhCH---HHHHHHHHHhhCCCCCc----------cHH-------------H-
Q 028796 25 TREEWEKKLNDVKIRKEDMNKLVMNFLVTEGY---VDAAEKFRMESGTEPDI----------DLA-------------T- 77 (203)
Q Consensus 25 ~~~~~~~~~~~~~~~~~~l~~lI~~yL~~~Gy---~eta~~f~ke~~~~~~~----------~~e-------------~- 77 (203)
+.....+.+..-+++...=.-++.=+|...+- .+.+..|+...++++.. |.. .
T Consensus 28 ~L~~Ll~~i~~~~~~~~~K~~l~~YlLlD~~~~~~~~~~~~Fa~~f~ip~~~~~~~~g~W~LD~~~~~~A~~~L~~ps~~ 107 (226)
T PF13934_consen 28 DLRALLDLILSSNVSLLKKHSLFYYLLLDLDDTRPSELAESFARAFGIPPKYIKFIQGFWLLDHGDFEEALELLSHPSLI 107 (226)
T ss_pred HHHHHHHHHhcCCcCHHHhHHHHHHHHHhcCccccccHHHHHHHHhCCCHHHHHHHHHHHHhChHhHHHHHHHhCCCCCC
Confidence 35556666666566554334445444444443 36888899998885310 000 0
Q ss_pred HH-HHHHHHHHHHcCCHHHHHHHHHhhCchhhccCcchhhhhHHHHHHHHHHcCChHHHHHHHHHhcC
Q 028796 78 IT-DRMAVKKAVQCGNVEDAIEKVNDLNPEILDTNPQLFFHLQQQRLIELIRNGKVEEALEFAQEELA 144 (203)
Q Consensus 78 ~~-~r~~I~~~I~~g~i~~Ai~~l~~~~p~l~~~~~~l~F~L~~q~fIeli~~~~~~~Al~y~r~~l~ 144 (203)
-. --+-++-.+..|+.+.|+..+....|.+... --..-++..+.++.+.+|..|.|++-.
T Consensus 108 ~~~~~~Il~~L~~~~~~~lAL~y~~~~~p~l~s~-------~~~~~~~~~La~~~v~EAf~~~R~~~~ 168 (226)
T PF13934_consen 108 PWFPDKILQALLRRGDPKLALRYLRAVGPPLSSP-------EALTLYFVALANGLVTEAFSFQRSYPD 168 (226)
T ss_pred cccHHHHHHHHHHCCChhHHHHHHHhcCCCCCCH-------HHHHHHHHHHHcCCHHHHHHHHHhCch
Confidence 00 0122333445788888888888777766543 112223444677888899999987554
No 28
>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=55.83 E-value=56 Score=21.45 Aligned_cols=30 Identities=10% Similarity=0.355 Sum_probs=24.2
Q ss_pred HHHHHHHHHHHHhhCHHHHHHHHHHhhCCC
Q 028796 41 EDMNKLVMNFLVTEGYVDAAEKFRMESGTE 70 (203)
Q Consensus 41 ~~l~~lI~~yL~~~Gy~eta~~f~ke~~~~ 70 (203)
..+-..|.+|...+||.-|...+++..|+.
T Consensus 9 ~~vL~~I~~~~~~~G~~Pt~rEIa~~~g~~ 38 (65)
T PF01726_consen 9 KEVLEFIREYIEENGYPPTVREIAEALGLK 38 (65)
T ss_dssp HHHHHHHHHHHHHHSS---HHHHHHHHTSS
T ss_pred HHHHHHHHHHHHHcCCCCCHHHHHHHhCCC
Confidence 456788999999999999999999999986
No 29
>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=54.37 E-value=1.1e+02 Score=24.18 Aligned_cols=104 Identities=10% Similarity=0.012 Sum_probs=71.0
Q ss_pred HHHHHHHHHhhCHHHHH-HHHHHhhCCCCCccHHHHHHHHHHHHHHHcCCHHHHHHHHHhhCchhhcc-CcchhhhhHHH
Q 028796 44 NKLVMNFLVTEGYVDAA-EKFRMESGTEPDIDLATITDRMAVKKAVQCGNVEDAIEKVNDLNPEILDT-NPQLFFHLQQQ 121 (203)
Q Consensus 44 ~~lI~~yL~~~Gy~eta-~~f~ke~~~~~~~~~e~~~~r~~I~~~I~~g~i~~Ai~~l~~~~p~l~~~-~~~l~F~L~~q 121 (203)
..-+++|+.+.|-.+.| +++.+...-......-.--...-|+-.|..|||..+...++....-+.+. +......|.+.
T Consensus 39 ~~~l~~~~~~~Gd~~~A~k~y~~~~~~~~~~~~~id~~l~~irv~i~~~d~~~v~~~i~ka~~~~~~~~d~~~~nrlk~~ 118 (177)
T PF10602_consen 39 LEDLADHYCKIGDLEEALKAYSRARDYCTSPGHKIDMCLNVIRVAIFFGDWSHVEKYIEKAESLIEKGGDWERRNRLKVY 118 (177)
T ss_pred HHHHHHHHHHhhhHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhccchHHHHHHHHHH
Confidence 45789999999986544 44544332211111111123566888899999999999998876555442 35678889999
Q ss_pred HHHHHHHcCChHHHHHHHHHhcCccc
Q 028796 122 RLIELIRNGKVEEALEFAQEELAPRG 147 (203)
Q Consensus 122 ~fIeli~~~~~~~Al~y~r~~l~~~~ 147 (203)
.-+..+..++..+|-+..-+-.+.+.
T Consensus 119 ~gL~~l~~r~f~~AA~~fl~~~~t~~ 144 (177)
T PF10602_consen 119 EGLANLAQRDFKEAAELFLDSLSTFT 144 (177)
T ss_pred HHHHHHHhchHHHHHHHHHccCcCCC
Confidence 99999999999988766666555554
No 30
>smart00668 CTLH C-terminal to LisH motif. Alpha-helical motif of unknown function.
Probab=53.74 E-value=20 Score=22.13 Aligned_cols=28 Identities=36% Similarity=0.457 Sum_probs=22.8
Q ss_pred HHHHHHHHHcCChHHHHHHHHHhcCccc
Q 028796 120 QQRLIELIRNGKVEEALEFAQEELAPRG 147 (203)
Q Consensus 120 ~q~fIeli~~~~~~~Al~y~r~~l~~~~ 147 (203)
...+.+.|..|+..+|++++++.-.+..
T Consensus 5 ~~~i~~~i~~g~~~~a~~~~~~~~~~l~ 32 (58)
T smart00668 5 RKRIRELILKGDWDEALEWLSSLKPPLL 32 (58)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHcCHHHh
Confidence 4567889999999999999998665443
No 31
>KOG4594 consensus Sequence-specific single-stranded-DNA-binding protein [Replication, recombination and repair; Transcription; General function prediction only]
Probab=52.81 E-value=17 Score=31.40 Aligned_cols=29 Identities=24% Similarity=0.379 Sum_probs=25.3
Q ss_pred HHHHHHHHHHHHHhhCHHHHHHHHHHhhC
Q 028796 40 KEDMNKLVMNFLVTEGYVDAAEKFRMESG 68 (203)
Q Consensus 40 ~~~l~~lI~~yL~~~Gy~eta~~f~ke~~ 68 (203)
++.|.--|.+||+|-|-..+|++|..|..
T Consensus 17 rekLa~YvYEYLlhvgaqksaqtflseir 45 (354)
T KOG4594|consen 17 REKLALYVYEYLLHVGAQKSAQTFLSEIR 45 (354)
T ss_pred HHHHHHHHHHHHHHhhhhhhhhhhHHHHH
Confidence 36678899999999999999999987754
No 32
>PF06588 Muskelin_N: Muskelin N-terminus; InterPro: IPR010565 This entry represents the N-terminal region of muskelin and is found in conjunction with several IPR006652 from INTERPRO repeats. Muskelin is an intracellular, kelch repeat protein that is needed in cell-spreading responses to the matrix adhesion molecule, thrombospondin-1 [].
Probab=52.26 E-value=22 Score=28.92 Aligned_cols=30 Identities=23% Similarity=0.548 Sum_probs=27.4
Q ss_pred HHHHHHHHHHHHhhCHHHHHHHHHHhhCCC
Q 028796 41 EDMNKLVMNFLVTEGYVDAAEKFRMESGTE 70 (203)
Q Consensus 41 ~~l~~lI~~yL~~~Gy~eta~~f~ke~~~~ 70 (203)
.+..|+++-||-.+||.++..++.+.+++.
T Consensus 166 ~eaiRlcLKHlRq~~y~~aFesLqk~t~v~ 195 (199)
T PF06588_consen 166 KEAIRLCLKHLRQRGYLEAFESLQKQTGVQ 195 (199)
T ss_pred HHHHHHHHHHhhhcCchhHHHHHHHHcCCC
Confidence 456799999999999999999999999985
No 33
>PF05843 Suf: Suppressor of forked protein (Suf); InterPro: IPR008847 This domain consists of several eukaryotic suppressor of forked (Suf) like proteins. The Drosophila melanogaster suppressor of forked [Su(f)] protein shares homology with the Saccharomyces cerevisiae RNA14 protein and the 77 kDa subunit of Homo sapiens cleavage stimulation factor, which are proteins involved in mRNA 3' end formation. This suggests a role for Su(f) in mRNA 3' end formation in Drosophila. The su(f) gene produces three transcripts; two of them are polyadenylated at the end of the transcription unit, and one is a truncated transcript, polyadenylated in intron 4. It is thought that su(f) plays a role in the regulation of poly(A) site utilisation and the GU-rich sequence is important for this regulation to occur [].; GO: 0006397 mRNA processing, 0005634 nucleus; PDB: 2L9B_B 2OND_B 2OOE_A 4E85_B 4EBA_C 4E6H_A 2UY1_B.
Probab=52.02 E-value=1.1e+02 Score=25.77 Aligned_cols=62 Identities=15% Similarity=0.156 Sum_probs=46.9
Q ss_pred HHHHHHHHHHHHhhhcccCCCHHHHHHHhhcCCCCHHHHHHHHHHHHHhhCHHHHHHHHHHhh
Q 028796 5 WIVIRQLAEIEAMAMSKKVITREEWEKKLNDVKIRKEDMNKLVMNFLVTEGYVDAAEKFRMES 67 (203)
Q Consensus 5 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~lI~~yL~~~Gy~eta~~f~ke~ 67 (203)
|-|.-..|.+|+..+.+......-|+..+...+-+.+....-| +||++.|..+-+.++-+.+
T Consensus 35 ~~vy~~~A~~E~~~~~d~~~A~~Ife~glk~f~~~~~~~~~Y~-~~l~~~~d~~~aR~lfer~ 96 (280)
T PF05843_consen 35 YHVYVAYALMEYYCNKDPKRARKIFERGLKKFPSDPDFWLEYL-DFLIKLNDINNARALFERA 96 (280)
T ss_dssp THHHHHHHHHHHHTCS-HHHHHHHHHHHHHHHTT-HHHHHHHH-HHHHHTT-HHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHCCCCHHHHHHHH-HHHHHhCcHHHHHHHHHHH
Confidence 5556678999999988888889999999988888877777666 8999988877777765543
No 34
>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=51.09 E-value=1.6e+02 Score=25.56 Aligned_cols=78 Identities=14% Similarity=0.193 Sum_probs=50.6
Q ss_pred HHHHHhhCHHHHHHHHHHhhCCCCCccHHHHHHHHHHHHHHHcCCHHHHHHHHHhhCchhhccCcchhhhhHHHHHHH-H
Q 028796 48 MNFLVTEGYVDAAEKFRMESGTEPDIDLATITDRMAVKKAVQCGNVEDAIEKVNDLNPEILDTNPQLFFHLQQQRLIE-L 126 (203)
Q Consensus 48 ~~yL~~~Gy~eta~~f~ke~~~~~~~~~e~~~~r~~I~~~I~~g~i~~Ai~~l~~~~p~l~~~~~~l~F~L~~q~fIe-l 126 (203)
...|+..|....|..+.++.+++ |.---.-.|+-++..|+|++-.++... +.|.+-|+- |++ .
T Consensus 184 i~~li~~~~~k~A~kl~k~Fkv~-----dkrfw~lki~aLa~~~~w~eL~~fa~s-------kKsPIGyep----Fv~~~ 247 (319)
T PF04840_consen 184 IRKLIEMGQEKQAEKLKKEFKVP-----DKRFWWLKIKALAENKDWDELEKFAKS-------KKSPIGYEP----FVEAC 247 (319)
T ss_pred HHHHHHCCCHHHHHHHHHHcCCc-----HHHHHHHHHHHHHhcCCHHHHHHHHhC-------CCCCCChHH----HHHHH
Confidence 34556678888888888888875 333345667778888888887777653 234444443 444 2
Q ss_pred HHcCChHHHHHHHHH
Q 028796 127 IRNGKVEEALEFAQE 141 (203)
Q Consensus 127 i~~~~~~~Al~y~r~ 141 (203)
++.|...+|..|...
T Consensus 248 ~~~~~~~eA~~yI~k 262 (319)
T PF04840_consen 248 LKYGNKKEASKYIPK 262 (319)
T ss_pred HHCCCHHHHHHHHHh
Confidence 345667777777765
No 35
>COG5443 FlbT Flagellar biosynthesis regulator FlbT [Cell motility and secretion]
Probab=49.90 E-value=30 Score=26.34 Aligned_cols=55 Identities=20% Similarity=0.207 Sum_probs=45.6
Q ss_pred HhhCHHHHHHHHHHhhCC--CCCccHHHHHHHHHHHHHHHcCCHHHHHHHHHhhCch
Q 028796 52 VTEGYVDAAEKFRMESGT--EPDIDLATITDRMAVKKAVQCGNVEDAIEKVNDLNPE 106 (203)
Q Consensus 52 ~~~Gy~eta~~f~ke~~~--~~~~~~e~~~~r~~I~~~I~~g~i~~Ai~~l~~~~p~ 106 (203)
--.|-.++...|.+..+. -.+.+.+.....+.|-.++.+|..-+|++.+...+|-
T Consensus 67 np~gaeq~~~~F~~~l~~l~~~f~~~eil~~lk~Id~lV~~~~~feALkaiR~lyp~ 123 (148)
T COG5443 67 NPAGAEQATEMFRKSLNMLLACFKDAEILAALKRIDGLVMAGRAFEALKAIRGLYPI 123 (148)
T ss_pred CHhhHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHhccHHHHHHHHHhhhchh
Confidence 345777888888887653 2466788999999999999999999999999999884
No 36
>PF07575 Nucleopor_Nup85: Nup85 Nucleoporin; InterPro: IPR011502 This is a family of nucleoporins conserved from yeast to human. Nup85 Nucleoporin is an essential component of the nuclear pore complex (NPC) that seems to be required for NPC assembly and maintenance. As part of the NPC Nup107-160 subcomplex plays a role in RNA export and in tethering NUP98/Nup98 and NUP153 to the nucleus. The Nup107-160 complex seems to be required for spindle assembly during mitosis. NUP85 is required for membrane clustering of CCL2-activated CCR2. Seems to be involved in CCR2-mediated chemotaxis of monocytes and may link activated CCR2 to the phosphatidyl-inositol-3-kinase-Rac-lammellipodium protrusion cascade [, , ]. ; PDB: 3F3F_D 3F3P_G 3F3G_G 3EWE_B.
Probab=47.62 E-value=61 Score=30.38 Aligned_cols=72 Identities=19% Similarity=0.185 Sum_probs=47.3
Q ss_pred HHHhhhcccCCCHHHHHHHhhcCCCCHHHHHHHHHHHHHhhCHHHHHHHHHHhhCCCCCccHHHHHHHHHHHHHHHcCCH
Q 028796 14 IEAMAMSKKVITREEWEKKLNDVKIRKEDMNKLVMNFLVTEGYVDAAEKFRMESGTEPDIDLATITDRMAVKKAVQCGNV 93 (203)
Q Consensus 14 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~lI~~yL~~~Gy~eta~~f~ke~~~~~~~~~e~~~~r~~I~~~I~~g~i 93 (203)
++|.. .++...+......+.++++..+.-..=+.......|..+++...++-.|. .++.+|++
T Consensus 379 i~yL~-~c~~~g~~~i~~lL~~~p~~t~~~~~k~l~iC~~~~L~~~a~~I~~~~~~----------------~~~~~~~~ 441 (566)
T PF07575_consen 379 IGYLS-SCPDEGRERIEELLPRVPLDTNDDAEKLLEICAELGLEDVAREICKILGQ----------------RLLKEGRY 441 (566)
T ss_dssp HHHHH-S-SSS-HHHHHHHGGG----SHHHHHHHHHHHHHHT-HHHHHHHHHHHHH----------------HHHHHHHH
T ss_pred HHHHH-HCChhhHHHHHHHHhhCCCCchHHHHHHHHHHHHCCCHHHHHHHHHHHHH----------------HHHHCCCH
Confidence 45553 45666699999999999998887666667888889999999999888773 23455666
Q ss_pred HHHHHHHHh
Q 028796 94 EDAIEKVND 102 (203)
Q Consensus 94 ~~Ai~~l~~ 102 (203)
.+|+.|+..
T Consensus 442 g~AL~~~~r 450 (566)
T PF07575_consen 442 GEALSWFIR 450 (566)
T ss_dssp HHHHHHHH-
T ss_pred HHHHHHHHH
Confidence 666666644
No 37
>PF04433 SWIRM: SWIRM domain; InterPro: IPR007526 The SWIRM domain is a small alpha-helical domain of about 85 amino acid residues found in eukaryotic chromosomal proteins. It is named after the proteins SWI3, RSC8 and MOIRA in which it was first recognised. This domain is predicted to mediate protein-protein interactions in the assembly of chromatin-protein complexes. The SWIRM domain can be linked to different domains, such as the ZZ-type zinc finger (IPR000433 from INTERPRO), the Myb DNA-binding domain (IPR001005 from INTERPRO), the HORMA domain (IPR003511 from INTERPRO), the amino-oxidase domain, the chromo domain (IPR000953 from INTERPRO), and the JAB1/PAD1 domain.; GO: 0005515 protein binding; PDB: 2Z3Y_A 2UXN_A 2Y48_A 2HKO_A 2XAF_A 2X0L_A 2XAJ_A 2UXX_A 2V1D_A 2L3D_A ....
Probab=46.95 E-value=54 Score=22.44 Aligned_cols=50 Identities=20% Similarity=0.284 Sum_probs=31.4
Q ss_pred HHHHHHHHHHHHhhhcccCCCHHHHHHHhhcCCCCHHHHHHHHHHHHHhhCHH
Q 028796 5 WIVIRQLAEIEAMAMSKKVITREEWEKKLNDVKIRKEDMNKLVMNFLVTEGYV 57 (203)
Q Consensus 5 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~lI~~yL~~~Gy~ 57 (203)
.+.||..-=-.+..-+.+++++.+..+.+. .++...+. -|-+||.+.||.
T Consensus 35 Yl~iRn~il~~w~~n~~~~lt~~~~~~~i~--~~d~~~~~-ri~~FL~~~G~I 84 (86)
T PF04433_consen 35 YLKIRNTILAEWRKNPNKYLTKTDARKLIK--GIDVNKIR-RIYDFLERWGLI 84 (86)
T ss_dssp HHHHHHHHHHHHHHHTTS---HHHHHHHTT--SSSHHHHH-HHHHHHHHTTSS
T ss_pred HHHHHHHHHHHHHHCCCCcccHHHHHHHcc--ccCHHHHH-HHHHHHHHcCcc
Confidence 345565544445566788899999977765 34554544 458999999985
No 38
>PRK10564 maltose regulon periplasmic protein; Provisional
Probab=46.62 E-value=23 Score=30.76 Aligned_cols=23 Identities=30% Similarity=0.569 Sum_probs=21.1
Q ss_pred HHHHHHHHHcCCHHHHHHHHHhh
Q 028796 81 RMAVKKAVQCGNVEDAIEKVNDL 103 (203)
Q Consensus 81 r~~I~~~I~~g~i~~Ai~~l~~~ 103 (203)
...|++++..||++.|+.+++|-
T Consensus 261 ~~aI~~AVk~gDi~KAL~LldEA 283 (303)
T PRK10564 261 NQAIKQAVKKGDVDKALKLLDEA 283 (303)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHH
Confidence 57899999999999999999985
No 39
>PHA01351 putative minor structural protein
Probab=44.96 E-value=3.2e+02 Score=26.97 Aligned_cols=47 Identities=9% Similarity=0.154 Sum_probs=36.3
Q ss_pred hhcccCCCHHHHHHHhhcCCCCHHHHHHHHHHHHHhhCHHHHHHHHH
Q 028796 18 AMSKKVITREEWEKKLNDVKIRKEDMNKLVMNFLVTEGYVDAAEKFR 64 (203)
Q Consensus 18 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~lI~~yL~~~Gy~eta~~f~ 64 (203)
.-++|.+|..+.++.+...+++.+....++..|.-.--...+.+.+.
T Consensus 491 l~skGi~DqkkIke~LKa~gfnks~~d~~L~~~~n~a~iesqIK~LQ 537 (1070)
T PHA01351 491 IVSLGIFDQKKIKEELKANKFNEQVALQILESELQFAQLQNQLKEYQ 537 (1070)
T ss_pred HHHcccccHHHHHHHHHhcCccHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34678899999999999999999888888877766555555555554
No 40
>PF13838 Clathrin_H_link: Clathrin-H-link; PDB: 2XZG_A 3GD1_I 1BPO_C 1C9I_B 1C9L_A.
Probab=42.80 E-value=40 Score=22.46 Aligned_cols=40 Identities=30% Similarity=0.473 Sum_probs=28.4
Q ss_pred hhHHHHHHHHHHcCChHHHHHHHHHhcCccc-cCChhHHHHHH
Q 028796 117 HLQQQRLIELIRNGKVEEALEFAQEELAPRG-EENQSFLEELE 158 (203)
Q Consensus 117 ~L~~q~fIeli~~~~~~~Al~y~r~~l~~~~-~~~~~~~~~l~ 158 (203)
.+..++|-+++..|+..+|-..|-+ +|-+ -..++.+.+++
T Consensus 7 ~l~~~~F~~l~~~g~y~eAA~~AA~--sP~giLRt~~Ti~rFk 47 (66)
T PF13838_consen 7 DLYVQQFNELFSQGQYEEAAKVAAN--SPRGILRTPETINRFK 47 (66)
T ss_dssp HHHHHHHHHHHHTT-HHHHHHHHHH--SGGGTT-SHHHHHHHH
T ss_pred HHHHHHHHHHHHcCCHHHHHHHHHh--CccchhcCHHHHHHHH
Confidence 5788999999999999999988874 3432 12356666665
No 41
>PF04121 Nup84_Nup100: Nuclear pore protein 84 / 107 ; InterPro: IPR007252 Nup84p forms a complex with five proteins, including Nup120p, Nup85p, Sec13p, and a Sec13p homolog. This Nup84p complex in conjunction with Sec13-type proteins is required for correct nuclear pore biogenesis [].; GO: 0006810 transport, 0005643 nuclear pore; PDB: 3CQC_A 3CQG_A 3I4R_A 3IKO_I 3JRO_C.
Probab=42.78 E-value=83 Score=30.39 Aligned_cols=27 Identities=15% Similarity=0.138 Sum_probs=21.7
Q ss_pred HHHHHHHHHHHHHcCCHHHHHHHHHhh
Q 028796 77 TITDRMAVKKAVQCGNVEDAIEKVNDL 103 (203)
Q Consensus 77 ~~~~r~~I~~~I~~g~i~~Ai~~l~~~ 103 (203)
.-...+.|-.+|+.|++++|.+||.+.
T Consensus 133 e~~~~~~i~~llR~G~~~eA~~lc~~~ 159 (697)
T PF04121_consen 133 ERALLKYIFELLRAGRIEEAQELCRER 159 (697)
T ss_dssp HHHHHHHHHHHHHTT-HHHHHHHHHHT
T ss_pred HHHHHHHHHHHHHCCCHHHHHHHHHHC
Confidence 444567888999999999999999875
No 42
>PF14276 DUF4363: Domain of unknown function (DUF4363)
Probab=41.47 E-value=38 Score=24.79 Aligned_cols=46 Identities=13% Similarity=0.191 Sum_probs=34.4
Q ss_pred HHHHHHHHHHHcCCHHHHHHHHHhhCchhhccCcchhhhhHHHHHH
Q 028796 79 TDRMAVKKAVQCGNVEDAIEKVNDLNPEILDTNPQLFFHLQQQRLI 124 (203)
Q Consensus 79 ~~r~~I~~~I~~g~i~~Ai~~l~~~~p~l~~~~~~l~F~L~~q~fI 124 (203)
.....+.+.|.++||+.|.+.+.+....-.+....+.|.+..+.+-
T Consensus 30 ~~l~~i~~~i~~~dW~~A~~~~~~l~~~W~k~~~~~~~~~~h~eid 75 (121)
T PF14276_consen 30 EQLEQIEEAIENEDWEKAYKETEELEKEWDKNKKRWSILIEHQEID 75 (121)
T ss_pred HHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhhchheeeeecHHHHH
Confidence 3456799999999999999998887655555556667766666653
No 43
>PF13934 ELYS: Nuclear pore complex assembly
Probab=41.23 E-value=2e+02 Score=23.60 Aligned_cols=66 Identities=23% Similarity=0.382 Sum_probs=41.4
Q ss_pred HHcCCHHHHHHHHHhhCchhhccCcchhhhhHHHHHHH-HHHcCChHHHHHHHHHhcCccccCChhHHHHHHHHHhhhcc
Q 028796 88 VQCGNVEDAIEKVNDLNPEILDTNPQLFFHLQQQRLIE-LIRNGKVEEALEFAQEELAPRGEENQSFLEELERTVALLAF 166 (203)
Q Consensus 88 I~~g~i~~Ai~~l~~~~p~l~~~~~~l~F~L~~q~fIe-li~~~~~~~Al~y~r~~l~~~~~~~~~~~~~l~~~~~LL~~ 166 (203)
+=.|+++.|++.+.. |.+.. .. ..+.+. +++.++...|+.|.|.--.|... .+.+.-.+..|+-
T Consensus 89 LD~~~~~~A~~~L~~--ps~~~---~~-----~~~Il~~L~~~~~~~lAL~y~~~~~p~l~s-----~~~~~~~~~~La~ 153 (226)
T PF13934_consen 89 LDHGDFEEALELLSH--PSLIP---WF-----PDKILQALLRRGDPKLALRYLRAVGPPLSS-----PEALTLYFVALAN 153 (226)
T ss_pred hChHhHHHHHHHhCC--CCCCc---cc-----HHHHHHHHHHCCChhHHHHHHHhcCCCCCC-----HHHHHHHHHHHHc
Confidence 345899999999854 43322 11 112344 45578999999999975555543 2555666666666
Q ss_pred cC
Q 028796 167 ED 168 (203)
Q Consensus 167 ~~ 168 (203)
+.
T Consensus 154 ~~ 155 (226)
T PF13934_consen 154 GL 155 (226)
T ss_pred CC
Confidence 54
No 44
>KOG0640 consensus mRNA cleavage stimulating factor complex; subunit 1 [RNA processing and modification]
Probab=40.57 E-value=95 Score=27.45 Aligned_cols=32 Identities=19% Similarity=0.253 Sum_probs=27.9
Q ss_pred CHHHHHHHHHHHHHhhCHHHHHHHHHHhhCCC
Q 028796 39 RKEDMNKLVMNFLVTEGYVDAAEKFRMESGTE 70 (203)
Q Consensus 39 ~~~~l~~lI~~yL~~~Gy~eta~~f~ke~~~~ 70 (203)
+++.+-+||..+|.+.|+.+.|..++.....+
T Consensus 10 dre~lyrLiisqL~ydg~~qiA~~lan~~~~~ 41 (430)
T KOG0640|consen 10 DREILYRLIISQLRYDGLSQIASALANATMTP 41 (430)
T ss_pred hHHHHHHHHHHHHhhccHHHHHHHHHHhhcCc
Confidence 46678999999999999999999999876654
No 45
>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=40.38 E-value=39 Score=17.56 Aligned_cols=17 Identities=12% Similarity=0.253 Sum_probs=12.1
Q ss_pred HHHHHcCCHHHHHHHHH
Q 028796 85 KKAVQCGNVEDAIEKVN 101 (203)
Q Consensus 85 ~~~I~~g~i~~Ai~~l~ 101 (203)
+-+...|++++|..++.
T Consensus 9 ~~~~~~G~~~eA~~~l~ 25 (26)
T PF07721_consen 9 RALLAQGDPDEAERLLR 25 (26)
T ss_pred HHHHHcCCHHHHHHHHh
Confidence 34567788888887765
No 46
>KOG1961 consensus Vacuolar sorting protein VPS52/suppressor of actin Sac2 [Intracellular trafficking, secretion, and vesicular transport; Cytoskeleton]
Probab=40.29 E-value=2.4e+02 Score=27.11 Aligned_cols=118 Identities=13% Similarity=0.128 Sum_probs=72.4
Q ss_pred HHHHHHHhhcCCCCHHHHHHHHHHHHHhhCHHHHHHHHHHhhCCCC----CccHHHHHHHHHHHHHHHcCCHHHHHHHHH
Q 028796 26 REEWEKKLNDVKIRKEDMNKLVMNFLVTEGYVDAAEKFRMESGTEP----DIDLATITDRMAVKKAVQCGNVEDAIEKVN 101 (203)
Q Consensus 26 ~~~~~~~~~~~~~~~~~l~~lI~~yL~~~Gy~eta~~f~ke~~~~~----~~~~e~~~~r~~I~~~I~~g~i~~Ai~~l~ 101 (203)
+......++.+-|+++.++-++-.=.-+.+|.++...+........ .-+......-..+.+-++..-++..-+|+-
T Consensus 133 ~s~Ls~fVdd~iVpp~lI~~I~~g~vne~~f~~~LeeL~~Kl~~v~~dq~~k~a~a~~Dv~~lLdkLR~KAi~kir~~Il 212 (683)
T KOG1961|consen 133 ESKLSQFVDDLIVPPELIKTIVDGDVNEPEFLEALEELSHKLKLVELDQSNKDAKALKDVEPLLDKLRLKAIEKIREFIL 212 (683)
T ss_pred HHHHHHHhccccCCHHHHHHHHcCCCCchHHHHHHHHHHHHHHhhhhhhhccchhhhhhHHHHHHHHHHHHHHHHHHHHH
Confidence 4455667778889988888888877777899999988887654321 112233344444444455444444445544
Q ss_pred hhCchhhccCcch-----hhhhHHHHHHHHHHcCChHHHHHHHHHhc
Q 028796 102 DLNPEILDTNPQL-----FFHLQQQRLIELIRNGKVEEALEFAQEEL 143 (203)
Q Consensus 102 ~~~p~l~~~~~~l-----~F~L~~q~fIeli~~~~~~~Al~y~r~~l 143 (203)
+---.+.+..++. .=.|.++.|.+.+..++..-|++..+.+.
T Consensus 213 qkI~~fRkp~tn~qi~~Q~~LLK~k~~y~FL~~n~r~~A~Elr~aYI 259 (683)
T KOG1961|consen 213 QKIKAFRKPMTNYQIPQQHALLKYKFFYEFLLENNRELALELRDAYI 259 (683)
T ss_pred HHHHHHhCCCCCcchHHHHHHHHHHHHHHHHHhccHHHHHHHHHHHH
Confidence 3322222322221 23466677888999999888888777643
No 47
>PF12569 NARP1: NMDA receptor-regulated protein 1 ; InterPro: IPR021183 This group represents N-terminal acetyltransferase A (NatA) auxiliary subunit and represents a non-catalytic component of the NatA N-terminal acetyltransferase, which catalyzes acetylation of proteins beginning with Met-Ser, Met-Gly and Met-Ala. N-terminal acetylation plays a role in normal eukaryotic translation and processing, protect against proteolytic degradation and protein turnover. NAT1 anchors ARD1 and NAT5 to the ribosome and may present the N- terminal of nascent polypeptides for acetylation [], [].
Probab=39.52 E-value=3.3e+02 Score=25.53 Aligned_cols=25 Identities=24% Similarity=0.470 Sum_probs=11.6
Q ss_pred CCHHHHHHHHHHHHHhhCHHHHHHH
Q 028796 38 IRKEDMNKLVMNFLVTEGYVDAAEK 62 (203)
Q Consensus 38 ~~~~~l~~lI~~yL~~~Gy~eta~~ 62 (203)
....-||--.+-|++|.|-.+.|..
T Consensus 259 ~~DRyiNsK~aKy~LRa~~~e~A~~ 283 (517)
T PF12569_consen 259 LADRYINSKCAKYLLRAGRIEEAEK 283 (517)
T ss_pred hhhHHHHHHHHHHHHHCCCHHHHHH
Confidence 3333444445555555555444433
No 48
>KOG0396 consensus Uncharacterized conserved protein [Function unknown]
Probab=39.19 E-value=1.2e+02 Score=27.29 Aligned_cols=64 Identities=13% Similarity=0.059 Sum_probs=47.5
Q ss_pred HHHHHHHHhhCHHHHHHHHHHhhCCC---CCccHHHHHHHHHHHHHHHcCCHHHHHHHHHhhCchhhc
Q 028796 45 KLVMNFLVTEGYVDAAEKFRMESGTE---PDIDLATITDRMAVKKAVQCGNVEDAIEKVNDLNPEILD 109 (203)
Q Consensus 45 ~lI~~yL~~~Gy~eta~~f~ke~~~~---~~~~~e~~~~r~~I~~~I~~g~i~~Ai~~l~~~~p~l~~ 109 (203)
..|.+-|.+.. .+.+-++++|-..+ .....|.-...++..++|..++++.|++.++.++...-+
T Consensus 157 ~~I~~sll~~~-l~~~Lswc~ehk~~LkK~~S~lEf~lRlQefIELi~~~~~~~Ai~~akk~f~~~~~ 223 (389)
T KOG0396|consen 157 YGIRDSLLAGE-LEPALSWCKEHKVELKKEESSLEFQLRLQEFIELIKVDNYDKAIAFAKKHFAPWAK 223 (389)
T ss_pred HHHHHHHHhcc-hHHHHHHHHHHHHHHHhccchhhhHHHHHHHHHHHHhccHHHHHHHHHHHHhhhhh
Confidence 34555555555 77788888886542 345567778889999999999999999999988765433
No 49
>KOG1156 consensus N-terminal acetyltransferase [Chromatin structure and dynamics]
Probab=38.09 E-value=3.9e+02 Score=25.97 Aligned_cols=115 Identities=22% Similarity=0.314 Sum_probs=67.2
Q ss_pred HHHHHHHHHHHhhC--HHHHHHHHHHhhCCCCC-ccH-HHHHHHHHHHHHHHcCCHHHHHHHHHhhCchhhccCcchhhh
Q 028796 42 DMNKLVMNFLVTEG--YVDAAEKFRMESGTEPD-IDL-ATITDRMAVKKAVQCGNVEDAIEKVNDLNPEILDTNPQLFFH 117 (203)
Q Consensus 42 ~l~~lI~~yL~~~G--y~eta~~f~ke~~~~~~-~~~-e~~~~r~~I~~~I~~g~i~~Ai~~l~~~~p~l~~~~~~l~F~ 117 (203)
.+--.|+.||.-+- -.++...|.+..+..++ .+. .......++...+..|..+.|++.+..+.+.+.. .+.|.
T Consensus 146 w~~~Avs~~L~g~y~~A~~il~ef~~t~~~~~s~~~~e~se~~Ly~n~i~~E~g~~q~ale~L~~~e~~i~D---kla~~ 222 (700)
T KOG1156|consen 146 WIGFAVAQHLLGEYKMALEILEEFEKTQNTSPSKEDYEHSELLLYQNQILIEAGSLQKALEHLLDNEKQIVD---KLAFE 222 (700)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHhhhhHHHH---HHHHh
Confidence 34444555544321 13455555554431121 222 2344455667778999999999999998886655 34555
Q ss_pred hHHHHHHHHHHcCChHHHHHHHHHhcCccccCChhHHHHHHHHHh
Q 028796 118 LQQQRLIELIRNGKVEEALEFAQEELAPRGEENQSFLEELERTVA 162 (203)
Q Consensus 118 L~~q~fIeli~~~~~~~Al~y~r~~l~~~~~~~~~~~~~l~~~~~ 162 (203)
...-.+.. +-+.+++|+...+..+.+..++.. +...++.+++
T Consensus 223 e~ka~l~~--kl~~lEeA~~~y~~Ll~rnPdn~~-Yy~~l~~~lg 264 (700)
T KOG1156|consen 223 ETKADLLM--KLGQLEEAVKVYRRLLERNPDNLD-YYEGLEKALG 264 (700)
T ss_pred hhHHHHHH--HHhhHHhHHHHHHHHHhhCchhHH-HHHHHHHHHH
Confidence 44444433 446788999999988887765442 2344444443
No 50
>KOG0292 consensus Vesicle coat complex COPI, alpha subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=37.30 E-value=19 Score=35.88 Aligned_cols=27 Identities=22% Similarity=0.485 Sum_probs=23.3
Q ss_pred HHHHHHHHHHhhCHHHHHHHHHHhhCC
Q 028796 43 MNKLVMNFLVTEGYVDAAEKFRMESGT 69 (203)
Q Consensus 43 l~~lI~~yL~~~Gy~eta~~f~ke~~~ 69 (203)
.-+-|..||...||-+.|--|.++..+
T Consensus 622 vGqaiIaYLqKkgypeiAL~FVkD~~t 648 (1202)
T KOG0292|consen 622 VGQAIIAYLQKKGYPEIALHFVKDERT 648 (1202)
T ss_pred ccHHHHHHHHhcCCcceeeeeecCcch
Confidence 457789999999999999999887664
No 51
>PF13833 EF-hand_8: EF-hand domain pair; PDB: 3KF9_A 1TTX_A 1WLZ_A 1ALV_A 1NX3_A 1ALW_A 1NX2_A 1NX1_A 1NX0_A 1DF0_A ....
Probab=37.30 E-value=52 Score=19.90 Aligned_cols=29 Identities=31% Similarity=0.621 Sum_probs=21.2
Q ss_pred ccCCCHHHHHHHhhc--CC-CCHHHHHHHHHH
Q 028796 21 KKVITREEWEKKLND--VK-IRKEDMNKLVMN 49 (203)
Q Consensus 21 ~~~~~~~~~~~~~~~--~~-~~~~~l~~lI~~ 49 (203)
++.|+++++...+.. ++ .++..++.++..
T Consensus 2 ~G~i~~~~~~~~l~~~g~~~~s~~e~~~l~~~ 33 (54)
T PF13833_consen 2 DGKITREEFRRALSKLGIKDLSEEEVDRLFRE 33 (54)
T ss_dssp SSEEEHHHHHHHHHHTTSSSSCHHHHHHHHHH
T ss_pred cCEECHHHHHHHHHHhCCCCCCHHHHHHHHHh
Confidence 577889999888863 46 777777776643
No 52
>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=37.20 E-value=1.1e+02 Score=19.72 Aligned_cols=56 Identities=20% Similarity=0.147 Sum_probs=29.8
Q ss_pred HHcCCHHHHHHHHHhhCchhhccCcchhhhhHHHHHHH--HHHcCChHHHHHHHHHhc
Q 028796 88 VQCGNVEDAIEKVNDLNPEILDTNPQLFFHLQQQRLIE--LIRNGKVEEALEFAQEEL 143 (203)
Q Consensus 88 I~~g~i~~Ai~~l~~~~p~l~~~~~~l~F~L~~q~fIe--li~~~~~~~Al~y~r~~l 143 (203)
...|++++|+++.++--......+++-.....+..=+- ....|+..+|+++.++-+
T Consensus 16 ~~~~~~~~A~~~~~~al~~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~al 73 (78)
T PF13424_consen 16 RELGRYDEALDYYEKALDIEEQLGDDHPDTANTLNNLGECYYRLGDYEEALEYYQKAL 73 (78)
T ss_dssp HHTT-HHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHH
T ss_pred HHcCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence 36789999988887754431122222111122222222 235678888988888643
No 53
>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=36.92 E-value=67 Score=22.18 Aligned_cols=28 Identities=18% Similarity=0.344 Sum_probs=20.4
Q ss_pred HHHHHHHHHHHHHHcCCHHHHHHHHHhh
Q 028796 76 ATITDRMAVKKAVQCGNVEDAIEKVNDL 103 (203)
Q Consensus 76 e~~~~r~~I~~~I~~g~i~~Ai~~l~~~ 103 (203)
.....-..|.++|.+||.+.|.+.+.++
T Consensus 95 ~~~~~h~~i~~ai~~~d~~~a~~~~~~h 122 (125)
T PF07729_consen 95 RSLEEHREIIDAIRAGDPEAAREALRQH 122 (125)
T ss_dssp HHHHHHHHHHHHHHTT-HHHHHHHHHHH
T ss_pred hhHHHHHHHHHHHHcCCHHHHHHHHHHH
Confidence 4566677788888888888888877665
No 54
>PRK14574 hmsH outer membrane protein; Provisional
Probab=34.96 E-value=4.7e+02 Score=26.05 Aligned_cols=21 Identities=19% Similarity=0.229 Sum_probs=11.1
Q ss_pred hhhhcCHhhHH-----HHHHHHHHHH
Q 028796 174 VGDLLDISQRL-----KTASEVNAAI 194 (203)
Q Consensus 174 ~~~l~~~~~r~-----~la~~vN~ai 194 (203)
+..+|++..+. ..|+.|+-+.
T Consensus 229 ~p~~f~~~~~~~l~~~~~a~~vr~a~ 254 (822)
T PRK14574 229 NPNLVSAEHYRQLERDAAAEQVRMAV 254 (822)
T ss_pred CccccCHHHHHHHHHHHHHHHHhhcc
Confidence 44667654432 4566665543
No 55
>KOG3380 consensus Actin-related protein Arp2/3 complex, subunit ARPC5 [Cytoskeleton]
Probab=33.98 E-value=1.1e+02 Score=23.75 Aligned_cols=59 Identities=12% Similarity=0.079 Sum_probs=40.0
Q ss_pred HHHHHHHHcCCHHHHHHHHHhhCchhhccCc--chhhhhHHHHHHHHHHcCChHHHHHHHHH
Q 028796 82 MAVKKAVQCGNVEDAIEKVNDLNPEILDTNP--QLFFHLQQQRLIELIRNGKVEEALEFAQE 141 (203)
Q Consensus 82 ~~I~~~I~~g~i~~Ai~~l~~~~p~l~~~~~--~l~F~L~~q~fIeli~~~~~~~Al~y~r~ 141 (203)
.+++.++..|+..+|++.+-.+-| ...++. .=.......+.+.-+|..|++.+++-.-.
T Consensus 40 ~ev~sll~qg~~~~AL~~aL~~~P-~~t~~q~vK~~a~~~v~~vL~~ik~adI~~~v~~Ls~ 100 (152)
T KOG3380|consen 40 REVRSLLTQGKSLEALQTALLNPP-YGTKDQEVKDRALNVVLKVLTSIKQADIEAAVKKLST 100 (152)
T ss_pred HHHHHHHHcccHHHHHHHHHhCCC-CCCccHHHHHHHHHHHHHHHHHHHHHhHHHHHHHhhH
Confidence 569999999999999999887755 222222 22344445566666777788777765543
No 56
>KOG0263 consensus Transcription initiation factor TFIID, subunit TAF5 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=33.10 E-value=65 Score=31.23 Aligned_cols=33 Identities=24% Similarity=0.488 Sum_probs=29.5
Q ss_pred CCCHHHHHHHHHHHHHhhCHHHHHHHHHHhhCC
Q 028796 37 KIRKEDMNKLVMNFLVTEGYVDAAEKFRMESGT 69 (203)
Q Consensus 37 ~~~~~~l~~lI~~yL~~~Gy~eta~~f~ke~~~ 69 (203)
.++.+.+++.+.+||...||..|-..+..|.++
T Consensus 18 ~~~~~~~n~~v~~yl~~~~y~~te~~l~~e~~l 50 (707)
T KOG0263|consen 18 GSHTRDLNRIVLEYLRKKKYSRTEEMLRQEANL 50 (707)
T ss_pred CcchHHHHHHHHHHHhhhcccccchhhhhhhcc
Confidence 456678999999999999999999999999875
No 57
>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=33.09 E-value=63 Score=19.78 Aligned_cols=19 Identities=26% Similarity=0.226 Sum_probs=16.4
Q ss_pred CHhhHHHHHHHHHHHHHhh
Q 028796 179 DISQRLKTASEVNAAILTS 197 (203)
Q Consensus 179 ~~~~r~~la~~vN~aiL~~ 197 (203)
.+.+|+.+|+.|..|+..+
T Consensus 25 ~~~qR~~iAe~Fa~AL~~S 43 (44)
T PF07208_consen 25 PPAQRQAIAEKFAQALKSS 43 (44)
T ss_dssp -HHHHHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHHHHhc
Confidence 4899999999999999875
No 58
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=33.08 E-value=1.1e+02 Score=19.92 Aligned_cols=50 Identities=14% Similarity=0.238 Sum_probs=36.3
Q ss_pred CCHHHHHHHHHHHHHhhCH-HHHHHHHHHhhCCCCCccHHHHHHHHHHHHHHHcCCH
Q 028796 38 IRKEDMNKLVMNFLVTEGY-VDAAEKFRMESGTEPDIDLATITDRMAVKKAVQCGNV 93 (203)
Q Consensus 38 ~~~~~l~~lI~~yL~~~Gy-~eta~~f~ke~~~~~~~~~e~~~~r~~I~~~I~~g~i 93 (203)
++++...+-|+.+|..+|- -=++..++++.|+.. -.-++.+..+...|-+
T Consensus 2 ~~~~~~~~~IL~~L~~~g~~~~ta~eLa~~lgl~~------~~v~r~L~~L~~~G~V 52 (68)
T smart00550 2 LTQDSLEEKILEFLENSGDETSTALQLAKNLGLPK------KEVNRVLYSLEKKGKV 52 (68)
T ss_pred CCchHHHHHHHHHHHHCCCCCcCHHHHHHHHCCCH------HHHHHHHHHHHHCCCE
Confidence 4566678899999999987 378999999999863 1334556666666654
No 59
>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=32.66 E-value=70 Score=18.14 Aligned_cols=17 Identities=35% Similarity=0.542 Sum_probs=11.7
Q ss_pred HHHHH--HcCCHHHHHHHH
Q 028796 84 VKKAV--QCGNVEDAIEKV 100 (203)
Q Consensus 84 I~~~I--~~g~i~~Ai~~l 100 (203)
.+.++ .+||++.|+.|+
T Consensus 19 ~~~AL~~~~~nve~A~~~L 37 (37)
T PF00627_consen 19 AREALRACNGNVERAVDWL 37 (37)
T ss_dssp HHHHHHHTTTSHHHHHHHH
T ss_pred HHHHHHHcCCCHHHHHHhC
Confidence 44444 346899999886
No 60
>PF10827 DUF2552: Protein of unknown function (DUF2552) ; InterPro: IPR020157 This entry contains proteins with no known function.
Probab=31.96 E-value=33 Score=23.24 Aligned_cols=18 Identities=22% Similarity=0.281 Sum_probs=14.9
Q ss_pred CCHHHHHHHHHhhCchhh
Q 028796 91 GNVEDAIEKVNDLNPEIL 108 (203)
Q Consensus 91 g~i~~Ai~~l~~~~p~l~ 108 (203)
-.+|.|++|+.++.|.+-
T Consensus 59 ~tld~Ai~Wi~e~M~~iT 76 (79)
T PF10827_consen 59 PTLDLAIAWIGEHMPHIT 76 (79)
T ss_pred ccHHHHHHHHHhcccchh
Confidence 368999999999988653
No 61
>PF12169 DNA_pol3_gamma3: DNA polymerase III subunits gamma and tau domain III; InterPro: IPR022754 This domain is found in bacteria and eukaryotes, and is approximately 110 amino acids in length. It is found in association with PF00004 from PFAM. This domain is also present in the tau subunit before it undergoes cleavage. Domains I-III are shared between the tau and the gamma subunits, while most of the DnaB-binding Domain IV and all of the alpha-interacting Domain V are unique to tau. ; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 1NJF_B 3GLG_G 1XXH_I 1NJG_A 3GLF_B 3GLI_G.
Probab=31.45 E-value=1.2e+02 Score=22.30 Aligned_cols=24 Identities=25% Similarity=0.389 Sum_probs=19.2
Q ss_pred HHHHHHHHHcCCHHHHHHHHHhhC
Q 028796 81 RMAVKKAVQCGNVEDAIEKVNDLN 104 (203)
Q Consensus 81 r~~I~~~I~~g~i~~Ai~~l~~~~ 104 (203)
...+.++|.+||..+|+..+++..
T Consensus 18 i~~l~~ai~~~d~~~~l~~~~~l~ 41 (143)
T PF12169_consen 18 IFELLDAILEGDAAEALELLNELL 41 (143)
T ss_dssp HHHHHHHHHTT-HHHHHHHHHHHH
T ss_pred HHHHHHHHHcCCHHHHHHHHHHHH
Confidence 356889999999999999998753
No 62
>PF12569 NARP1: NMDA receptor-regulated protein 1 ; InterPro: IPR021183 This group represents N-terminal acetyltransferase A (NatA) auxiliary subunit and represents a non-catalytic component of the NatA N-terminal acetyltransferase, which catalyzes acetylation of proteins beginning with Met-Ser, Met-Gly and Met-Ala. N-terminal acetylation plays a role in normal eukaryotic translation and processing, protect against proteolytic degradation and protein turnover. NAT1 anchors ARD1 and NAT5 to the ribosome and may present the N- terminal of nascent polypeptides for acetylation [], [].
Probab=31.08 E-value=4.5e+02 Score=24.62 Aligned_cols=91 Identities=15% Similarity=0.205 Sum_probs=50.2
Q ss_pred HHHHHHHHHHhhCHHHHHHHHHHhh-CCCCCccHHHHHHHHHHHHHHHcCCHHHHHHHHHhhCchhhccCcchhhhhHHH
Q 028796 43 MNKLVMNFLVTEGYVDAAEKFRMES-GTEPDIDLATITDRMAVKKAVQCGNVEDAIEKVNDLNPEILDTNPQLFFHLQQQ 121 (203)
Q Consensus 43 l~~lI~~yL~~~Gy~eta~~f~ke~-~~~~~~~~e~~~~r~~I~~~I~~g~i~~Ai~~l~~~~p~l~~~~~~l~F~L~~q 121 (203)
+.-++++|.-+.|..+.|-.+..+. ..+| ...+.+-.+-+|- -..|++.+|.+++++-+.-.... . ...-.|-
T Consensus 196 ~~~~lAqhyd~~g~~~~Al~~Id~aI~htP-t~~ely~~Karil--Kh~G~~~~Aa~~~~~Ar~LD~~D-R--yiNsK~a 269 (517)
T PF12569_consen 196 TLYFLAQHYDYLGDYEKALEYIDKAIEHTP-TLVELYMTKARIL--KHAGDLKEAAEAMDEARELDLAD-R--YINSKCA 269 (517)
T ss_pred HHHHHHHHHHHhCCHHHHHHHHHHHHhcCC-CcHHHHHHHHHHH--HHCCCHHHHHHHHHHHHhCChhh-H--HHHHHHH
Confidence 5578889999999888777776643 3333 2234444333332 25688888888877654211111 1 1111111
Q ss_pred HHHHHHHcCChHHHHHHHHH
Q 028796 122 RLIELIRNGKVEEALEFAQE 141 (203)
Q Consensus 122 ~fIeli~~~~~~~Al~y~r~ 141 (203)
+ -++|.|.+++|.+.+..
T Consensus 270 K--y~LRa~~~e~A~~~~~~ 287 (517)
T PF12569_consen 270 K--YLLRAGRIEEAEKTASL 287 (517)
T ss_pred H--HHHHCCCHHHHHHHHHh
Confidence 1 14567777777666654
No 63
>PRK02289 4-oxalocrotonate tautomerase; Provisional
Probab=30.03 E-value=77 Score=20.05 Aligned_cols=24 Identities=21% Similarity=0.142 Sum_probs=21.8
Q ss_pred CHhhHHHHHHHHHHHHHhhcCCCC
Q 028796 179 DISQRLKTASEVNAAILTSQSHEK 202 (203)
Q Consensus 179 ~~~~r~~la~~vN~aiL~~~~~~~ 202 (203)
+.+++.++++.|..++-+..|.+.
T Consensus 13 s~EqK~~L~~~it~a~~~~~~~p~ 36 (60)
T PRK02289 13 SQEQKNALAREVTEVVSRIAKAPK 36 (60)
T ss_pred CHHHHHHHHHHHHHHHHHHhCcCc
Confidence 789999999999999999998865
No 64
>KOG1538 consensus Uncharacterized conserved protein WDR10, contains WD40 repeats [General function prediction only]
Probab=29.53 E-value=3.5e+02 Score=26.65 Aligned_cols=62 Identities=18% Similarity=0.269 Sum_probs=44.8
Q ss_pred HHHHHHH-HHcCCHHHHHHHHHhhCchhhccC--cchhhhhHHHHHHH----HHHcCChHHHHHHHHHhc
Q 028796 81 RMAVKKA-VQCGNVEDAIEKVNDLNPEILDTN--PQLFFHLQQQRLIE----LIRNGKVEEALEFAQEEL 143 (203)
Q Consensus 81 r~~I~~~-I~~g~i~~Ai~~l~~~~p~l~~~~--~~l~F~L~~q~fIe----li~~~~~~~Al~y~r~~l 143 (203)
.+.|.++ |..|+|++|....+.+ |++...- +.-+|.--.-+|+| +++.|...+|++...+.-
T Consensus 776 ~ksiVqlHve~~~W~eAFalAe~h-Pe~~~dVy~pyaqwLAE~DrFeEAqkAfhkAGr~~EA~~vLeQLt 844 (1081)
T KOG1538|consen 776 LKSLVQLHVETQRWDEAFALAEKH-PEFKDDVYMPYAQWLAENDRFEEAQKAFHKAGRQREAVQVLEQLT 844 (1081)
T ss_pred HHHHhhheeecccchHhHhhhhhC-ccccccccchHHHHhhhhhhHHHHHHHHHHhcchHHHHHHHHHhh
Confidence 4555555 7889999999998775 7776641 34566666667887 467788889988887643
No 65
>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=28.66 E-value=3.9e+02 Score=23.19 Aligned_cols=89 Identities=18% Similarity=0.232 Sum_probs=64.7
Q ss_pred HhhcCCCCHHHHHHHHHHHHHhhCHHHHHHHHHHhhCCCCCccHHHHHHHHHHHHHHHcCCHHHHHHHHHhhCchhhccC
Q 028796 32 KLNDVKIRKEDMNKLVMNFLVTEGYVDAAEKFRMESGTEPDIDLATITDRMAVKKAVQCGNVEDAIEKVNDLNPEILDTN 111 (203)
Q Consensus 32 ~~~~~~~~~~~l~~lI~~yL~~~Gy~eta~~f~ke~~~~~~~~~e~~~~r~~I~~~I~~g~i~~Ai~~l~~~~p~l~~~~ 111 (203)
.-...+|+..+.-++.+.-|...|..+-...|+++-. +++..++| |..++..|+..+|..++....+ .
T Consensus 199 l~k~Fkv~dkrfw~lki~aLa~~~~w~eL~~fa~skK--sPIGyepF-----v~~~~~~~~~~eA~~yI~k~~~-----~ 266 (319)
T PF04840_consen 199 LKKEFKVPDKRFWWLKIKALAENKDWDELEKFAKSKK--SPIGYEPF-----VEACLKYGNKKEASKYIPKIPD-----E 266 (319)
T ss_pred HHHHcCCcHHHHHHHHHHHHHhcCCHHHHHHHHhCCC--CCCChHHH-----HHHHHHCCCHHHHHHHHHhCCh-----H
Confidence 3344589999999999999999999999999998633 44555433 5667889999999999976321 1
Q ss_pred cchhhhhHHHHHHHHHHcCChHHHHHHHHH
Q 028796 112 PQLFFHLQQQRLIELIRNGKVEEALEFAQE 141 (203)
Q Consensus 112 ~~l~F~L~~q~fIeli~~~~~~~Al~y~r~ 141 (203)
..+.. +++.|+..+|++.|.+
T Consensus 267 ~rv~~---------y~~~~~~~~A~~~A~~ 287 (319)
T PF04840_consen 267 ERVEM---------YLKCGDYKEAAQEAFK 287 (319)
T ss_pred HHHHH---------HHHCCCHHHHHHHHHH
Confidence 22222 2566777777777764
No 66
>PF13171 DUF4004: Protein of unknown function (DUF4004)
Probab=28.52 E-value=3.3e+02 Score=22.25 Aligned_cols=102 Identities=17% Similarity=0.217 Sum_probs=57.5
Q ss_pred HHHHHHhhhcccCCCHHHHHHHhhcCCCCHHHHHHHHHHHHHhhCHH--HHHHHHHHhhCCCCCccHHHHHHHHHHHHHH
Q 028796 11 LAEIEAMAMSKKVITREEWEKKLNDVKIRKEDMNKLVMNFLVTEGYV--DAAEKFRMESGTEPDIDLATITDRMAVKKAV 88 (203)
Q Consensus 11 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~lI~~yL~~~Gy~--eta~~f~ke~~~~~~~~~e~~~~r~~I~~~I 88 (203)
|+.|+.-.-=|...|.+|..+.+..-..+ ..+-.+++.+.|-. .++..|....|-........+-...-+.+.+
T Consensus 53 L~RIekI~~mKd~~SLDELA~mfSp~~~~----~~~~~~~l~~~~ivs~~~~~~f~~~~~~~~~f~f~e~l~lyvl~~ll 128 (199)
T PF13171_consen 53 LERIEKIQKMKDDLSLDELAEMFSPNVSD----VVFTEEELLKRNIVSQAVLELFMEQIGEEEEFSFEELLFLYVLEKLL 128 (199)
T ss_pred HHHHHHHHHhcccCCHHHHHHHcCCCccc----ceecHHHHHHcCcccHHHHHHHHHHhCccccccHHHHHHHHHHHHHH
Confidence 45555555557788888887765322111 34556677777764 3444455555533233333334444466777
Q ss_pred HcCCHHH-----HHHHHHhhCchhhccCcchhh
Q 028796 89 QCGNVED-----AIEKVNDLNPEILDTNPQLFF 116 (203)
Q Consensus 89 ~~g~i~~-----Ai~~l~~~~p~l~~~~~~l~F 116 (203)
.+|++.. ++..+.+++|.+...+..+.+
T Consensus 129 ~sg~is~eE~k~l~~~l~~~~~~~~~~~~~l~l 161 (199)
T PF13171_consen 129 QSGEISLEEGKMLLQFLEENYPKFEGKNCELIL 161 (199)
T ss_pred HhCCCCHHHHHHHHHHHHHHHHHHhCCCcEEEE
Confidence 7786543 356667777777665555443
No 67
>cd00052 EH Eps15 homology domain; found in proteins implicated in endocytosis, vesicle transport, and signal transduction. The alignment contains a pair of EF-hand motifs, typically one of them is canonical and binds to Ca2+, while the other may not bind to Ca2+. A hydrophobic binding pocket is formed by residues from both EF-hand motifs. The EH domain binds to proteins containing NPF (class I), [WF]W or SWG (class II), or H[TS]F (class III) sequence motifs.
Probab=28.44 E-value=1.1e+02 Score=18.92 Aligned_cols=30 Identities=10% Similarity=0.093 Sum_probs=21.5
Q ss_pred hcccCCCHHHHHHHhhcCCCCHHHHHHHHH
Q 028796 19 MSKKVITREEWEKKLNDVKIRKEDMNKLVM 48 (203)
Q Consensus 19 ~~~~~~~~~~~~~~~~~~~~~~~~l~~lI~ 48 (203)
-.++.|+.+++.+.+.....+...+.+++.
T Consensus 11 ~~~G~i~~~el~~~l~~~g~~~~~~~~i~~ 40 (67)
T cd00052 11 DGDGLISGDEARPFLGKSGLPRSVLAQIWD 40 (67)
T ss_pred CCCCcCcHHHHHHHHHHcCCCHHHHHHHHH
Confidence 356789999998888776666666666543
No 68
>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=28.20 E-value=82 Score=24.71 Aligned_cols=49 Identities=22% Similarity=0.307 Sum_probs=32.2
Q ss_pred CHHHHHHHHHHhhCCC----CCc--cHHHHHHHHHHHHHHHcCCHHHHHHHHHhhC
Q 028796 55 GYVDAAEKFRMESGTE----PDI--DLATITDRMAVKKAVQCGNVEDAIEKVNDLN 104 (203)
Q Consensus 55 Gy~eta~~f~ke~~~~----~~~--~~e~~~~r~~I~~~I~~g~i~~Ai~~l~~~~ 104 (203)
|..+..+.++++.|.+ +.. +...+ .-..||++|.+|+++.|-+++-..+
T Consensus 117 g~~~~L~~~~~~~g~~v~~v~~~~~~~~~i-SST~IR~~i~~G~i~~an~lLg~~y 171 (180)
T cd02064 117 GDAELLKELGKKYGFEVTVVPPVTLDGERV-SSTRIREALAEGDVELANELLGRPY 171 (180)
T ss_pred CCHHHHHHhhhhcCcEEEEeCcEecCCcEE-cHHHHHHHHHhCCHHHHHHHcCCCc
Confidence 4567788888887753 111 00111 1245999999999999998876543
No 69
>PF04699 P16-Arc: ARP2/3 complex 16 kDa subunit (p16-Arc); InterPro: IPR006789 The Arp2/3 protein complex has been implicated in the control of actin polymerisation. The human complex consists of seven subunits which include the actin related proteins Arp2 and Arp3, and five others referred to as p41-Arc, p34-Arc, p21-Arc, p20-Arc, and p16-Arc. The precise function of p16-Arc is currently unknown. Its structure consists of a single domain containing a bundle of seven alpha helices [, ].; GO: 0030833 regulation of actin filament polymerization, 0005856 cytoskeleton; PDB: 3DWL_G 1TYQ_G 1U2V_G 2P9U_G 2P9L_G 1K8K_G 3DXM_G 2P9N_G 3DXK_G 2P9I_G ....
Probab=28.09 E-value=71 Score=24.87 Aligned_cols=27 Identities=19% Similarity=0.380 Sum_probs=20.9
Q ss_pred HHHHHHHHHHHcCCHHHHHHHHHhhCc
Q 028796 79 TDRMAVKKAVQCGNVEDAIEKVNDLNP 105 (203)
Q Consensus 79 ~~r~~I~~~I~~g~i~~Ai~~l~~~~p 105 (203)
..-.++++++..|+..+|++.+-++-|
T Consensus 38 ~~~~qvr~ll~~g~~~~ALk~aL~npP 64 (152)
T PF04699_consen 38 PKEQQVRQLLSSGDNEEALKAALENPP 64 (152)
T ss_dssp GTHHHHHHHHHCT-HHHHHHHHTSS--
T ss_pred hhHHHHHHHHhCCCHHHHHHHhccCCC
Confidence 345779999999999999999988755
No 70
>PF13371 TPR_9: Tetratricopeptide repeat
Probab=28.01 E-value=1.6e+02 Score=18.48 Aligned_cols=54 Identities=30% Similarity=0.270 Sum_probs=35.3
Q ss_pred HHHcCCHHHHHHHHHhhCchhhccCcchhhhhHHHHHHHHHHcCChHHHHHHHHHhcCc
Q 028796 87 AVQCGNVEDAIEKVNDLNPEILDTNPQLFFHLQQQRLIELIRNGKVEEALEFAQEELAP 145 (203)
Q Consensus 87 ~I~~g~i~~Ai~~l~~~~p~l~~~~~~l~F~L~~q~fIeli~~~~~~~Al~y~r~~l~~ 145 (203)
.+..++++.|++.++..- ..+++ ...++...=.-+...|+..+|++...+.+.-
T Consensus 5 ~~~~~~~~~A~~~~~~~l----~~~p~-~~~~~~~~a~~~~~~g~~~~A~~~l~~~l~~ 58 (73)
T PF13371_consen 5 YLQQEDYEEALEVLERAL----ELDPD-DPELWLQRARCLFQLGRYEEALEDLERALEL 58 (73)
T ss_pred HHhCCCHHHHHHHHHHHH----HhCcc-cchhhHHHHHHHHHhccHHHHHHHHHHHHHH
Confidence 467899999999887642 22232 2333333334455678999999999986643
No 71
>smart00027 EH Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
Probab=27.62 E-value=87 Score=21.66 Aligned_cols=30 Identities=10% Similarity=0.005 Sum_probs=24.9
Q ss_pred cccCCCHHHHHHHhhcCCCCHHHHHHHHHH
Q 028796 20 SKKVITREEWEKKLNDVKIRKEDMNKLVMN 49 (203)
Q Consensus 20 ~~~~~~~~~~~~~~~~~~~~~~~l~~lI~~ 49 (203)
.++.|+.+++.+.+.+..++...+.+++..
T Consensus 23 ~~G~Is~~el~~~l~~~~~~~~ev~~i~~~ 52 (96)
T smart00027 23 QDGTVTGAQAKPILLKSGLPQTLLAKIWNL 52 (96)
T ss_pred CCCeEeHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 568899999999998888888888877654
No 72
>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=27.52 E-value=1.8e+02 Score=23.39 Aligned_cols=65 Identities=12% Similarity=0.135 Sum_probs=41.4
Q ss_pred HHHHHHHHHHHHcCCHHHHHHHHHhhCchhhccCc------chhhhhHHHHHHHHHHcCChHHHHHHHHHhc
Q 028796 78 ITDRMAVKKAVQCGNVEDAIEKVNDLNPEILDTNP------QLFFHLQQQRLIELIRNGKVEEALEFAQEEL 143 (203)
Q Consensus 78 ~~~r~~I~~~I~~g~i~~Ai~~l~~~~p~l~~~~~------~l~F~L~~q~fIeli~~~~~~~Al~y~r~~l 143 (203)
-..|..|.+.+- -+++.-++++...+..+.+..+ .+...+..-.|.++++.|+..+|.+.+.+.+
T Consensus 134 ~~lr~~ie~~l~-~~~~~~~~~~~~~R~~~k~~~~~~~~r~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~ 204 (205)
T TIGR01470 134 RLLRERIETLLP-PSLGDLATLAATWRDAVKKRLPNGAARRRFWEKFFDGAFAERVLAGREEQAERVLATRL 204 (205)
T ss_pred HHHHHHHHHhcc-hhHHHHHHHHHHHHHHHHhhCCCHHHHHHHHHHHhccHHHHHHHcCCHHHHHHHHHHhh
Confidence 334555555543 3667777888888777765322 2223333346788899999999988887654
No 73
>PF03997 VPS28: VPS28 protein; InterPro: IPR007143 The Endosomal Sorting Complex Required for Transport (ESCRT) complexes form the machinery driving protein sorting from endosomes to lysosomes. ESCRT complexes are central to receptor down-regulation, lysosome biogenesis, and budding of HIV. Yeast ESCRT-I consists of three protein subunits, VPS23, VPS28, and VPS37. In humans, ESCRT-I comprises TSG101, VPS28, and one of four potential human VPS37 homologues. The main role of ESCRT-I is to recognise ubiquitinated cargo via the UEV domain of the VPS23/TSG101 subunit. The assembly of the ESCRT-I complex is directed by the C-terminal steadiness box (SB) of VPS23, the N-terminal half of VPS28, and the C-terminal half of VPS37. The structure is primarily composed of three long, parallel helical hairpins, each corresponding to a different subunit. The additional domains and motifs extending beyond the core serve as gripping tools for ESCRT-I critical functions [, ].; PDB: 2J9W_B 2J9U_C 2G3K_A 2F66_E 2F6M_D 2J9V_A 2CAZ_E 2P22_B.
Probab=27.28 E-value=1.8e+02 Score=23.42 Aligned_cols=56 Identities=23% Similarity=0.413 Sum_probs=41.2
Q ss_pred HHHHHHHHHHHHHhhhcccCCCHHHHHHHhhcCCCCHHHHHHHHHHH---H--HhhCHHHHHHHHHHhhCCC
Q 028796 4 FWIVIRQLAEIEAMAMSKKVITREEWEKKLNDVKIRKEDMNKLVMNF---L--VTEGYVDAAEKFRMESGTE 70 (203)
Q Consensus 4 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~lI~~y---L--~~~Gy~eta~~f~ke~~~~ 70 (203)
.+.+|.-|..+|-. |-|+.|+.+++.. ..++||.+| + .+.+.+.....|+++.++.
T Consensus 4 LysII~tle~LEka-yikD~It~~eYt~----------~c~kLl~Qyk~~~~~~~~~~~~~le~F~~~y~l~ 64 (188)
T PF03997_consen 4 LYSIIKTLEHLEKA-YIKDSITEKEYTT----------ACNKLLNQYKTILKQLKDDEFPDLEEFMKKYNLD 64 (188)
T ss_dssp HHHHHHHHHHHHHH-HHTTSS-HHHHHH----------HHHHHHHHHHHHHTSTTHHHHHHHHHHHHHTTS-
T ss_pred HHHHHHHHHHHHHH-HhhccCCHHHHHH----------HHHHHHHHHHHHHHHcccccCCCHHHHHHHhccc
Confidence 45667777777754 9999999999855 469999999 2 2333567799999999975
No 74
>COG5096 Vesicle coat complex, various subunits [Intracellular trafficking and secretion]
Probab=27.13 E-value=4.4e+02 Score=26.06 Aligned_cols=92 Identities=20% Similarity=0.157 Sum_probs=64.0
Q ss_pred hC-CCCCccHHHHHHHHHHHHHHHcCCHHHHHHHHHhhCchhhcc--CcchhhhhHHHHHHHHHHcCChHHHHHHHHHhc
Q 028796 67 SG-TEPDIDLATITDRMAVKKAVQCGNVEDAIEKVNDLNPEILDT--NPQLFFHLQQQRLIELIRNGKVEEALEFAQEEL 143 (203)
Q Consensus 67 ~~-~~~~~~~e~~~~r~~I~~~I~~g~i~~Ai~~l~~~~p~l~~~--~~~l~F~L~~q~fIeli~~~~~~~Al~y~r~~l 143 (203)
+| +....+...+...+.|...+..|+- +...+|.+.+. -.+.+++=.+.-|++.+-+.++.+++--....+
T Consensus 25 sg~l~s~n~~~kidAmK~iIa~M~~G~d------mssLf~dViK~~~trd~ElKrL~ylYl~~yak~~P~~~lLavNti~ 98 (757)
T COG5096 25 SGRLESSNDYKKIDAMKKIIAQMSLGED------MSSLFPDVIKNVATRDVELKRLLYLYLERYAKLKPELALLAVNTIQ 98 (757)
T ss_pred cccccccChHHHHHHHHHHHHHHhcCCC------hHHHHHHHHHHHHhcCHHHHHHHHHHHHHHhccCHHHHHHHHHHHH
Confidence 45 5555677788889999999999976 45556665543 356777777788888888889999888888777
Q ss_pred CccccCChhHHHHHHHHHhhh
Q 028796 144 APRGEENQSFLEELERTVALL 164 (203)
Q Consensus 144 ~~~~~~~~~~~~~l~~~~~LL 164 (203)
..+.+.+|..+.--=+.+++|
T Consensus 99 kDl~d~N~~iR~~AlR~ls~l 119 (757)
T COG5096 99 KDLQDPNEEIRGFALRTLSLL 119 (757)
T ss_pred hhccCCCHHHHHHHHHHHHhc
Confidence 777776654333322444444
No 75
>COG5051 RPL36A Ribosomal protein L36E [Translation, ribosomal structure and biogenesis]
Probab=26.96 E-value=95 Score=21.94 Aligned_cols=43 Identities=26% Similarity=0.392 Sum_probs=33.5
Q ss_pred HHHHHHHHHHcCChHHHHHHHHHhcCccccCChhHHHHHHHHHhhhc
Q 028796 119 QQQRLIELIRNGKVEEALEFAQEELAPRGEENQSFLEELERTVALLA 165 (203)
Q Consensus 119 ~~q~fIeli~~~~~~~Al~y~r~~l~~~~~~~~~~~~~l~~~~~LL~ 165 (203)
+-.+.|++|++.+-..|-..+++.|+.+.. ...+++++...|.
T Consensus 53 yErr~i~Lirns~~krArKlakKRLGs~kR----AkaKvEel~~~i~ 95 (97)
T COG5051 53 YERRVIELIRNSQDKRARKLAKKRLGSLKR----AKAKVEELTSVIQ 95 (97)
T ss_pred HHHHHHHHHHhcccHHHHHHHHHHhhhHHH----HHHHHHHHHHHHh
Confidence 446789999999999999999999988763 3466777776654
No 76
>PF09052 SipA: Salmonella invasion protein A; InterPro: IPR015138 Salmonella invasion protein A (SipA) is a virulence factor that is translocated into host cells by a type III secretion system. In the host cell it binds to actin, stimulates actin polymerisation and counteracts F-actin destabilising proteins. This contributes towards cytoskeletal rearrangements that allow the entry of the pathogen into the host cell []. ; PDB: 2HSQ_B 2IBF_B 3RF3_D 2GWW_B 2GDC_B 1Q5Z_A 2FM8_C 2FM9_A.
Probab=26.69 E-value=1.4e+02 Score=28.20 Aligned_cols=68 Identities=13% Similarity=0.213 Sum_probs=49.2
Q ss_pred HHHHHHHHHHhhhcccCCCHHHHHHHhhcCCCC------HHHHHHHHHHHHHhhCHHHHHHHHHHhhCCCCCcc
Q 028796 7 VIRQLAEIEAMAMSKKVITREEWEKKLNDVKIR------KEDMNKLVMNFLVTEGYVDAAEKFRMESGTEPDID 74 (203)
Q Consensus 7 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------~~~l~~lI~~yL~~~Gy~eta~~f~ke~~~~~~~~ 74 (203)
|-|.+.+.-.-+-+...+++...+.....++.. -+.|.+.|..|=..+..-+.|.+|.+|.|+.+..+
T Consensus 556 qrRefd~lr~eIl~sdt~~~~~~k~q~sd~~~~~~l~~~adtLke~i~~Hp~~EKl~evA~~~~Rea~Ltkl~~ 629 (674)
T PF09052_consen 556 QRREFDGLRKEILPSDTEKSIALKAQCSDINIHPELKEKADTLKEVITNHPQYEKLAEVARQFAREAGLTKLKG 629 (674)
T ss_dssp HHHHHHHHHHHHS-SSHHHHHHHHHHHGGGGG-HHHHHHHHHHHHHHHT-TCHHHHHHHHHHHHHHH-CCCCGG
T ss_pred HHHHHHHHHhhcCCcchhHHHHHHhhhcccccchHHHHHHHHHHHHHhcCchHHHHHHHHHHHHHhhCcccccC
Confidence 456666677777777777777777777776653 36788888888888888999999999999876443
No 77
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=26.16 E-value=2.7e+02 Score=20.55 Aligned_cols=54 Identities=20% Similarity=0.358 Sum_probs=31.8
Q ss_pred HHHHHHHHHhhCHHHHHHHHHHhhCCC------------------CCccHHHHHHHHHHHHHHHcCC--HHHHHHHH
Q 028796 44 NKLVMNFLVTEGYVDAAEKFRMESGTE------------------PDIDLATITDRMAVKKAVQCGN--VEDAIEKV 100 (203)
Q Consensus 44 ~~lI~~yL~~~Gy~eta~~f~ke~~~~------------------~~~~~e~~~~r~~I~~~I~~g~--i~~Ai~~l 100 (203)
...|..|+...|-. +.++++.|+. +....+.-..+..|.+.+.+|. .++|++.+
T Consensus 39 ~~Fi~~Fi~~rGnl---Ke~e~~lgiSYPTvR~rLd~ii~~lg~~~~~~~~~~~~~~~IL~~L~~GeIs~eeA~~~L 112 (113)
T PF09862_consen 39 LEFIKLFIKNRGNL---KEMEKELGISYPTVRNRLDKIIEKLGYEEDEEEEEEDERKEILDKLEKGEISVEEALEIL 112 (113)
T ss_pred HHHHHHHHHhcCCH---HHHHHHHCCCcHHHHHHHHHHHHHhCCCCCcccccchhHHHHHHHHHcCCCCHHHHHHHh
Confidence 35677888888853 3445555542 2222344456777778887774 45555543
No 78
>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=25.77 E-value=86 Score=22.62 Aligned_cols=45 Identities=27% Similarity=0.357 Sum_probs=32.6
Q ss_pred hhhHHHHHHHHHHcCChHHHHHHHHHhcCccccCChhHHHHHHHHHhhh
Q 028796 116 FHLQQQRLIELIRNGKVEEALEFAQEELAPRGEENQSFLEELERTVALL 164 (203)
Q Consensus 116 F~L~~q~fIeli~~~~~~~Al~y~r~~l~~~~~~~~~~~~~l~~~~~LL 164 (203)
|-=+-.+-+||++.+.-..|+.|+++-|+.+.. .....+++...|
T Consensus 48 faPYEkr~mELlkv~kdKrAlKf~KKRlGth~R----AKrKrEel~~vl 92 (98)
T PF01158_consen 48 FAPYEKRAMELLKVSKDKRALKFAKKRLGTHIR----AKRKREELSNVL 92 (98)
T ss_dssp HCHHHHHHHHHHHHCCHHHHHHHHHHHHCHHHH----HHHHHHHHHHHH
T ss_pred CChHHHHHHHHHhcchhHHHHHHHHHHhhhhHH----HHHHHHHHHHHH
Confidence 444667889999999999999999999987653 234444554444
No 79
>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=25.64 E-value=68 Score=21.66 Aligned_cols=43 Identities=23% Similarity=0.407 Sum_probs=22.7
Q ss_pred CCHHHHHHHHHHHHHhhCHHHHHHHHHHhhCCCCCccHHHHHHHHHHHHHHHcCC
Q 028796 38 IRKEDMNKLVMNFLVTEGYVDAAEKFRMESGTEPDIDLATITDRMAVKKAVQCGN 92 (203)
Q Consensus 38 ~~~~~l~~lI~~yL~~~Gy~eta~~f~ke~~~~~~~~~e~~~~r~~I~~~I~~g~ 92 (203)
++++.++.||-+|..|.|..--.. ....-....++++++.+|+
T Consensus 8 L~~eTL~nLIeefv~ReGTdyG~~------------E~sL~~kv~qv~~qL~~G~ 50 (70)
T PF06794_consen 8 LPPETLNNLIEEFVLREGTDYGEQ------------ELSLEEKVEQVKQQLKSGE 50 (70)
T ss_dssp S-HHHHHHHHHHHHH------------------------HHHHHHHHHHHHHTTS
T ss_pred CCHHHHHHHHHHHHHccCcccCcc------------cccHHHHHHHHHHHHHcCC
Confidence 577888999999999998531111 1122334566777777775
No 80
>PF12931 Sec16_C: Sec23-binding domain of Sec16; PDB: 3MZK_C.
Probab=25.44 E-value=75 Score=27.02 Aligned_cols=21 Identities=29% Similarity=0.401 Sum_probs=16.5
Q ss_pred HHHHHHHcCCHHHHHHHHHhh
Q 028796 83 AVKKAVQCGNVEDAIEKVNDL 103 (203)
Q Consensus 83 ~I~~~I~~g~i~~Ai~~l~~~ 103 (203)
+|+++++.|+.++|+++|-+.
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 478888999999999888665
No 81
>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=24.39 E-value=5.3e+02 Score=23.25 Aligned_cols=101 Identities=18% Similarity=0.203 Sum_probs=64.7
Q ss_pred CCCCHHHHHHHHHHHHHhhCHHHHHHHHHHhhCCCCCccHHHHHHHHHHHHHHHcCCHHHHHHHHHhhCchhhccCcchh
Q 028796 36 VKIRKEDMNKLVMNFLVTEGYVDAAEKFRMESGTEPDIDLATITDRMAVKKAVQCGNVEDAIEKVNDLNPEILDTNPQLF 115 (203)
Q Consensus 36 ~~~~~~~l~~lI~~yL~~~Gy~eta~~f~ke~~~~~~~~~e~~~~r~~I~~~I~~g~i~~Ai~~l~~~~p~l~~~~~~l~ 115 (203)
.+...+.|..-++.|+...|-.+.|..+.++..-..+ +. .. .-.+-.+..++-.+|++.+++. +.+...+
T Consensus 164 ~t~~~NyLv~~Ll~~l~~t~~~~~ai~lle~L~~~~p-ev--~~--~LA~v~l~~~~E~~AI~ll~~a---L~~~p~d-- 233 (395)
T PF09295_consen 164 PTIVNNYLVDTLLKYLSLTQRYDEAIELLEKLRERDP-EV--AV--LLARVYLLMNEEVEAIRLLNEA---LKENPQD-- 233 (395)
T ss_pred CCCcchHHHHHHHHHHhhcccHHHHHHHHHHHHhcCC-cH--HH--HHHHHHHhcCcHHHHHHHHHHH---HHhCCCC--
Confidence 4455677888888999888888777777777654321 11 11 1234445677888888888764 2222222
Q ss_pred hhhHHHHHHHHHHcCChHHHHHHHHH--hcCcc
Q 028796 116 FHLQQQRLIELIRNGKVEEALEFAQE--ELAPR 146 (203)
Q Consensus 116 F~L~~q~fIeli~~~~~~~Al~y~r~--~l~~~ 146 (203)
..|...+---++.+++.+.|++.+++ .++|.
T Consensus 234 ~~LL~~Qa~fLl~k~~~~lAL~iAk~av~lsP~ 266 (395)
T PF09295_consen 234 SELLNLQAEFLLSKKKYELALEIAKKAVELSPS 266 (395)
T ss_pred HHHHHHHHHHHHhcCCHHHHHHHHHHHHHhCch
Confidence 55555555556778888899999987 34444
No 82
>KOG2437 consensus Muskelin [Signal transduction mechanisms]
Probab=24.39 E-value=3.4e+02 Score=25.72 Aligned_cols=62 Identities=10% Similarity=0.104 Sum_probs=42.4
Q ss_pred HHHHHHHHHHhhCHHHHHHHHHHhhCCCCCccHHHHHHHHHHHHHHHcCCHHHHHHHHHhhCchhhc
Q 028796 43 MNKLVMNFLVTEGYVDAAEKFRMESGTEPDIDLATITDRMAVKKAVQCGNVEDAIEKVNDLNPEILD 109 (203)
Q Consensus 43 l~~lI~~yL~~~Gy~eta~~f~ke~~~~~~~~~e~~~~r~~I~~~I~~g~i~~Ai~~l~~~~p~l~~ 109 (203)
--+..+.||-.+||.|....+.+.+.+..... -..+|++++....-+..........|.++.
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 AIRLCLKHFRQHGYTDIFESLQKKTKIAIEHP-----MLTDIHDKLVLKGDACEELIEKAVNDGLFN 229 (723)
T ss_pred HHHHHHHHHHHcCchHHHHHHHHhhcccCCCh-----HHHHHHHHHHHcccHHHHHHHhhhccHHHh
Confidence 45788999999999999999999988653222 235688887655444444444555555543
No 83
>PRK07111 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=24.33 E-value=2.9e+02 Score=27.09 Aligned_cols=28 Identities=25% Similarity=0.504 Sum_probs=25.8
Q ss_pred CCCHHHHHHHHHHHHHhhCHHHHHHHHH
Q 028796 37 KIRKEDMNKLVMNFLVTEGYVDAAEKFR 64 (203)
Q Consensus 37 ~~~~~~l~~lI~~yL~~~Gy~eta~~f~ 64 (203)
.++-..|..+|..-|...|+.++|+++.
T Consensus 58 ~isve~IqDiVe~~L~~~g~~~vAkaYI 85 (735)
T PRK07111 58 EVTVEDIQDLVEKVLIENGHAETAKAYI 85 (735)
T ss_pred CCCHHHHHHHHHHHHHhcCcHHHHHHHH
Confidence 5788889999999999999999999985
No 84
>PTZ00196 60S ribosomal protein L36; Provisional
Probab=23.91 E-value=1.1e+02 Score=22.10 Aligned_cols=31 Identities=32% Similarity=0.562 Sum_probs=25.9
Q ss_pred hhHHHHHHHHHHcCChHHHHHHHHHhcCccc
Q 028796 117 HLQQQRLIELIRNGKVEEALEFAQEELAPRG 147 (203)
Q Consensus 117 ~L~~q~fIeli~~~~~~~Al~y~r~~l~~~~ 147 (203)
-=+-...+|||+.+.-..|+.|+++.|+.+.
T Consensus 49 aPYErr~mELLkv~kdKrAlKfaKkRlGth~ 79 (98)
T PTZ00196 49 SPYERRMIELLKVGKDKRALKYAKKRLGTHK 79 (98)
T ss_pred cHHHHHHHHHHHhcchHHHHHHHHHHhhhHH
Confidence 3456678999999988999999999997765
No 85
>PRK00794 flbT flagellar biosynthesis repressor FlbT; Reviewed
Probab=23.75 E-value=2.8e+02 Score=21.00 Aligned_cols=30 Identities=20% Similarity=0.388 Sum_probs=25.6
Q ss_pred HHHHHHHHHHHHHHcCCHHHHHHHHHhhCc
Q 028796 76 ATITDRMAVKKAVQCGNVEDAIEKVNDLNP 105 (203)
Q Consensus 76 e~~~~r~~I~~~I~~g~i~~Ai~~l~~~~p 105 (203)
+.......|.++|.+|++-+|++.+....|
T Consensus 92 ~~~~~l~~i~~~V~~g~~y~ALk~lR~L~~ 121 (132)
T PRK00794 92 DILAGLKAIDELVEAGRYYEALKALRGLYP 121 (132)
T ss_pred HHHHHHHHHHHHHHCCcHHHHHHHHHHhhH
Confidence 555677789999999999999999988766
No 86
>PF14691 Fer4_20: Dihydroprymidine dehydrogenase domain II, 4Fe-4S cluster; PDB: 2VDC_G 1H7X_C 1H7W_A 1GT8_A 1GTE_B 1GTH_B.
Probab=23.71 E-value=1.2e+02 Score=22.16 Aligned_cols=27 Identities=37% Similarity=0.630 Sum_probs=20.6
Q ss_pred hhhHHHHHHHHHHcCChHHHHHHHHHh
Q 028796 116 FHLQQQRLIELIRNGKVEEALEFAQEE 142 (203)
Q Consensus 116 F~L~~q~fIeli~~~~~~~Al~y~r~~ 142 (203)
..+....||.+++.|+..+|++..++.
T Consensus 38 ~~~dip~~i~~i~~g~~~~A~~~i~~~ 64 (111)
T PF14691_consen 38 AHIDIPEYIRLIREGNFKEAYELIRED 64 (111)
T ss_dssp T---HHHHHHHHHCT-HHHHHHHHHHH
T ss_pred CCCcHHHHHHHHHCCCHHHHHHHHHHh
Confidence 466778999999999999999999964
No 87
>PF14689 SPOB_a: Sensor_kinase_SpoOB-type, alpha-helical domain; PDB: 1F51_C 2FTK_B 1IXM_B.
Probab=23.63 E-value=1.9e+02 Score=18.54 Aligned_cols=31 Identities=19% Similarity=0.300 Sum_probs=22.8
Q ss_pred HHHHHHHHHHHHHHcCCHHHHHHHHHhhCch
Q 028796 76 ATITDRMAVKKAVQCGNVEDAIEKVNDLNPE 106 (203)
Q Consensus 76 e~~~~r~~I~~~I~~g~i~~Ai~~l~~~~p~ 106 (203)
|.....+-|...+..|++++|.+.+++....
T Consensus 22 D~~NhLqvI~gllqlg~~~~a~eYi~~~~~~ 52 (62)
T PF14689_consen 22 DFLNHLQVIYGLLQLGKYEEAKEYIKELSKD 52 (62)
T ss_dssp HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 5556667788888999999999988876443
No 88
>PRK04966 hypothetical protein; Provisional
Probab=23.51 E-value=82 Score=21.39 Aligned_cols=43 Identities=23% Similarity=0.410 Sum_probs=28.2
Q ss_pred CCHHHHHHHHHHHHHhhCHHHHHHHHHHhhCCCCCccHHHHHHHHHHHHHHHcCC
Q 028796 38 IRKEDMNKLVMNFLVTEGYVDAAEKFRMESGTEPDIDLATITDRMAVKKAVQCGN 92 (203)
Q Consensus 38 ~~~~~l~~lI~~yL~~~Gy~eta~~f~ke~~~~~~~~~e~~~~r~~I~~~I~~g~ 92 (203)
++++.++.||-+|..|.|-. .|.. ....-....++++.+.+|+
T Consensus 8 L~~eTL~nLIeefv~ReGTd---------yG~~---E~sl~~kv~qv~~qL~~G~ 50 (72)
T PRK04966 8 LAPETLENLIESFVLREGTD---------YGEH---ERSLEQKVADVKRQLQSGE 50 (72)
T ss_pred CCHHHHHHHHHHHHhccCcc---------CCcc---cccHHHHHHHHHHHHHcCC
Confidence 67888999999999998842 2211 1123344566777777775
No 89
>cd05029 S-100A6 S-100A6: S-100A6 domain found in proteins similar to S100A6. S100A6 is a member of the S100 domain family within EF-hand Ca2+-binding proteins superfamily. Note that the S-100 hierarchy, to which this S-100A6 group belongs, contains only S-100 EF-hand domains, other EF-hands have been modeled separately. S100 proteins exhibit unique patterns of tissue- and cell type-specific expression and have been implicated in the Ca2+-dependent regulation of diverse physiological processes, including cell cycle regulation, differentiation, growth, and metabolic control . S100A6 is normally expressed in the G1 phase of the cell cycle in neuronal cells. The function of S100A6 remains unclear, but evidence suggests that it is involved in cell cycle regulation and exocytosis. S100A6 may also be involved in tumorigenesis; the protein is overexpressed in several tumors. Ca2+ binding to S100A6 leads to a conformational change in the protein, which exposes a hydrophobic surface for interact
Probab=23.18 E-value=2.2e+02 Score=19.62 Aligned_cols=29 Identities=17% Similarity=0.440 Sum_probs=20.9
Q ss_pred cccCCCHHHHHHHhh-----cCCCCHHHHHHHHH
Q 028796 20 SKKVITREEWEKKLN-----DVKIRKEDMNKLVM 48 (203)
Q Consensus 20 ~~~~~~~~~~~~~~~-----~~~~~~~~l~~lI~ 48 (203)
.+++|+.+++.+.+. +.++++..+.+++.
T Consensus 25 ~~g~Is~~EL~~~l~~~~~lg~k~t~~ev~~m~~ 58 (88)
T cd05029 25 DKNTLSKKELKELIQKELTIGSKLQDAEIAKLME 58 (88)
T ss_pred CCCEECHHHHHHHHHHHHhcCCCCCHHHHHHHHH
Confidence 367999999988884 45567777776653
No 90
>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=23.04 E-value=2.7e+02 Score=19.44 Aligned_cols=54 Identities=17% Similarity=0.224 Sum_probs=41.4
Q ss_pred HHHHHHHHHhhCHHHHHHHHHHhhCCCCCccHHHHHHHHHHHHHHHcCCHHHHHHH
Q 028796 44 NKLVMNFLVTEGYVDAAEKFRMESGTEPDIDLATITDRMAVKKAVQCGNVEDAIEK 99 (203)
Q Consensus 44 ~~lI~~yL~~~Gy~eta~~f~ke~~~~~~~~~e~~~~r~~I~~~I~~g~i~~Ai~~ 99 (203)
.+.+.+.|+..+--|.+..|..+.=. +...+..+.|..|...+.+|....+|+-
T Consensus 5 ~~~~~~~~~~~~~~~~~~~~~~~l~t--~~e~~~Ls~R~~I~~ll~~G~S~~eIA~ 58 (88)
T TIGR02531 5 LDELFDAILTLKNREECYRFFDDIAT--INEIQSLAQRLQVAKMLKQGKTYSDIEA 58 (88)
T ss_pred HHHHHHHHHhCCCHHHHHHHHHHhCC--HHHHHhhhHHHHHHHHHHCCCCHHHHHH
Confidence 56678888888888999999877653 3344568888999999999986666644
No 91
>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=23.04 E-value=1.4e+02 Score=16.71 Aligned_cols=18 Identities=39% Similarity=0.440 Sum_probs=12.2
Q ss_pred HHHHH--HcCCHHHHHHHHH
Q 028796 84 VKKAV--QCGNVEDAIEKVN 101 (203)
Q Consensus 84 I~~~I--~~g~i~~Ai~~l~ 101 (203)
++.++ ..||++.|+.|+-
T Consensus 18 ~~~AL~~~~~d~~~A~~~L~ 37 (38)
T cd00194 18 ARKALRATNNNVERAVEWLL 37 (38)
T ss_pred HHHHHHHhCCCHHHHHHHHh
Confidence 44443 4578999988863
No 92
>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=22.98 E-value=52 Score=28.25 Aligned_cols=51 Identities=16% Similarity=0.020 Sum_probs=35.0
Q ss_pred hCHHHHHHHHHHhhCCC----CCcc-HHHHHHHHHHHHHHHcCCHHHHHHHHHhhCc
Q 028796 54 EGYVDAAEKFRMESGTE----PDID-LATITDRMAVKKAVQCGNVEDAIEKVNDLNP 105 (203)
Q Consensus 54 ~Gy~eta~~f~ke~~~~----~~~~-~e~~~~r~~I~~~I~~g~i~~Ai~~l~~~~p 105 (203)
.|-.+..+.++++.|.. +... .+.+ .=..||++|.+||++.|-+++-..+.
T Consensus 115 ~G~~~~L~~~~~~~g~~v~~~~~~~~~~~I-SST~IR~~l~~G~i~~A~~lLGr~y~ 170 (288)
T TIGR00083 115 QGDFLLLQLFGNTTIFCVIVKQLFCQDIRI-SSSAIRQALKNGDLELANKLLGRPYF 170 (288)
T ss_pred CCCHHHHHHhccccCcEEEEeccccCCCeE-CHHHHHHHHHcCCHHHHHHhhhhhhc
Confidence 36778888888887742 1111 0111 22569999999999999999986553
No 93
>KOG3192 consensus Mitochondrial J-type chaperone [Posttranslational modification, protein turnover, chaperones]
Probab=22.83 E-value=1.2e+02 Score=23.96 Aligned_cols=80 Identities=15% Similarity=0.228 Sum_probs=39.8
Q ss_pred ccCCCHHHHHHHhhcCCCCHHHHH---HHHHHHHHhhCHHHHHHHHHHhhCCC---CCccHHHHHHHHHHHHHHHcCCHH
Q 028796 21 KKVITREEWEKKLNDVKIRKEDMN---KLVMNFLVTEGYVDAAEKFRMESGTE---PDIDLATITDRMAVKKAVQCGNVE 94 (203)
Q Consensus 21 ~~~~~~~~~~~~~~~~~~~~~~l~---~lI~~yL~~~Gy~eta~~f~ke~~~~---~~~~~e~~~~r~~I~~~I~~g~i~ 94 (203)
+.+++|.++.-.+.+++...+++. .++++=|-.+- .......+.++. ..........-.++.++..+.+|+
T Consensus 69 k~pL~RA~Yilkl~g~e~~sne~stDpe~Lmevle~~E---~IS~~~De~~l~~lk~q~q~ri~q~~~qlge~~esk~~~ 145 (168)
T KOG3192|consen 69 KDPLARARYLLKLKGQEQTSNELSTDPEFLMEVLEYHE---AISEMDDEEDLKQLKSQNQERIAQCKQQLGEAFESKKYD 145 (168)
T ss_pred HhHHHHHHHHHHHhCCCCchhhhccCHHHHHHHHHHHH---HHHhccCcHHHHHHHHHHHHHHHHHHHHHHHHHhhccHH
Confidence 566777777777777666655544 23333332221 111111111100 001112334456677777778888
Q ss_pred HHHHHHHhh
Q 028796 95 DAIEKVNDL 103 (203)
Q Consensus 95 ~Ai~~l~~~ 103 (203)
+|+..+...
T Consensus 146 ~Al~~i~rl 154 (168)
T KOG3192|consen 146 EALKKILRL 154 (168)
T ss_pred HHHHHHHHH
Confidence 888777653
No 94
>PF15391 DUF4614: Domain of unknown function (DUF4614)
Probab=22.49 E-value=1.5e+02 Score=23.76 Aligned_cols=50 Identities=30% Similarity=0.408 Sum_probs=35.1
Q ss_pred HHHHHHHHhhCchhhccCcchhhhh-HHHHHHHHHHcC----------------ChHHHHHHHHHhc
Q 028796 94 EDAIEKVNDLNPEILDTNPQLFFHL-QQQRLIELIRNG----------------KVEEALEFAQEEL 143 (203)
Q Consensus 94 ~~Ai~~l~~~~p~l~~~~~~l~F~L-~~q~fIeli~~~----------------~~~~Al~y~r~~l 143 (203)
.+||+-+..+.|.++.-+..|.-+| ..|+||+.-|.= .++++-+|.|.+=
T Consensus 113 ~dAiEALTaYSPA~lALnDMLkQQL~LTqqFve~sr~LH~Sll~SL~~~~~hY~TLEetKeyIr~hr 179 (181)
T PF15391_consen 113 ADAIEALTAYSPAVLALNDMLKQQLSLTQQFVEASRHLHQSLLQSLDADSFHYHTLEETKEYIRRHR 179 (181)
T ss_pred HHHHHHHhccChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcceeeHHHHHHHHHHcC
Confidence 3577888888898888776664444 567999976531 3777888887653
No 95
>PF10552 ORF6C: ORF6C domain; InterPro: IPR018878 This entry represents the carboxy-terminal domain from ORF6 (Q9B012 from SWISSPROT), an antirepressor protein from Lactococcus phage bIL285 [].
Probab=22.34 E-value=1.4e+02 Score=21.81 Aligned_cols=23 Identities=22% Similarity=0.437 Sum_probs=19.6
Q ss_pred HHHHHcCCHHHHHHHHHhhCchh
Q 028796 85 KKAVQCGNVEDAIEKVNDLNPEI 107 (203)
Q Consensus 85 ~~~I~~g~i~~Ai~~l~~~~p~l 107 (203)
...|...++++|+++++.+.|..
T Consensus 87 Y~~I~~kdfd~A~~~I~~W~p~~ 109 (116)
T PF10552_consen 87 YKDIPRKDFDEALEFINNWEPST 109 (116)
T ss_pred HHhhhHHHHHHHHHHHHHcCCCH
Confidence 45688899999999999999853
No 96
>KOG3452 consensus 60S ribosomal protein L36 [Translation, ribosomal structure and biogenesis]
Probab=22.32 E-value=1.2e+02 Score=21.84 Aligned_cols=43 Identities=23% Similarity=0.339 Sum_probs=31.8
Q ss_pred HHHHHHHHHHcCChHHHHHHHHHhcCccccCChhHHHHHHHHHhhhc
Q 028796 119 QQQRLIELIRNGKVEEALEFAQEELAPRGEENQSFLEELERTVALLA 165 (203)
Q Consensus 119 ~~q~fIeli~~~~~~~Al~y~r~~l~~~~~~~~~~~~~l~~~~~LL~ 165 (203)
+-.+-+||++..+-..|+.++++.++.+... ..+.+++...|+
T Consensus 53 yErr~meLlkvskdkrA~K~lKkRlGth~RA----k~KrEELsnvl~ 95 (102)
T KOG3452|consen 53 YERRAMELLKVSKDKRALKLLKKRLGTHKRA----KRKREELSNVLA 95 (102)
T ss_pred HHHHHHHHHHHcccHHHHHHHHHHhhHHHHH----HHHHHHHHHHHH
Confidence 4567889999999999999999999877532 355556555543
No 97
>PLN03077 Protein ECB2; Provisional
Probab=22.15 E-value=7.5e+02 Score=24.21 Aligned_cols=102 Identities=23% Similarity=0.290 Sum_probs=57.5
Q ss_pred HhhcCCCCHHHHHHHHHHHHHhhCHHHHHHHHHH--hhCCCCCccHHHHHHHHHHHHHHHcCCHHHHHHHHHhhCchhhc
Q 028796 32 KLNDVKIRKEDMNKLVMNFLVTEGYVDAAEKFRM--ESGTEPDIDLATITDRMAVKKAVQCGNVEDAIEKVNDLNPEILD 109 (203)
Q Consensus 32 ~~~~~~~~~~~l~~lI~~yL~~~Gy~eta~~f~k--e~~~~~~~~~e~~~~r~~I~~~I~~g~i~~Ai~~l~~~~p~l~~ 109 (203)
.+..++-+...-+-+|..|..+--..++...|.+ +.|+.|.... -..-|.-.-..|++++|.++.++.... ..
T Consensus 546 ~f~~~~~d~~s~n~lI~~~~~~G~~~~A~~lf~~M~~~g~~Pd~~T----~~~ll~a~~~~g~v~ea~~~f~~M~~~-~g 620 (857)
T PLN03077 546 QFNSHEKDVVSWNILLTGYVAHGKGSMAVELFNRMVESGVNPDEVT----FISLLCACSRSGMVTQGLEYFHSMEEK-YS 620 (857)
T ss_pred HHHhcCCChhhHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCccc----HHHHHHHHhhcChHHHHHHHHHHHHHH-hC
Confidence 3344444445556777666555444566666663 4566653221 122244556789999999888764311 11
Q ss_pred cCcchhhhhHHHHHHH-HHHcCChHHHHHHHHH
Q 028796 110 TNPQLFFHLQQQRLIE-LIRNGKVEEALEFAQE 141 (203)
Q Consensus 110 ~~~~l~F~L~~q~fIe-li~~~~~~~Al~y~r~ 141 (203)
..+++ -+.-..+. +.+.|++.+|.++.++
T Consensus 621 i~P~~---~~y~~lv~~l~r~G~~~eA~~~~~~ 650 (857)
T PLN03077 621 ITPNL---KHYACVVDLLGRAGKLTEAYNFINK 650 (857)
T ss_pred CCCch---HHHHHHHHHHHhCCCHHHHHHHHHH
Confidence 12332 12233444 4577899999999886
No 98
>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=22.05 E-value=97 Score=21.03 Aligned_cols=28 Identities=32% Similarity=0.601 Sum_probs=23.9
Q ss_pred CCCHHHHHHHHHHHHHhhCHHHHHHHHH
Q 028796 37 KIRKEDMNKLVMNFLVTEGYVDAAEKFR 64 (203)
Q Consensus 37 ~~~~~~l~~lI~~yL~~~Gy~eta~~f~ 64 (203)
.++...|..+|.+.|...|+.+.|.++.
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 4677888999999999999999888764
No 99
>cd05804 StaR_like StaR_like; a well-conserved protein found in bacteria, plants, and animals. A family member from Streptomyces toyocaensis, StaR is part of a gene cluster involved in the biosynthesis of glycopeptide antibiotics (GPAs), specifically A47934. It has been speculated that StaR could be a flavoprotein hydroxylating a tyrosine sidechain. Some family members have been annotated as proteins containing tetratricopeptide (TPR) repeats, which may at least indicate mostly alpha-helical secondary structure.
Probab=21.86 E-value=4.8e+02 Score=21.88 Aligned_cols=94 Identities=18% Similarity=0.123 Sum_probs=51.3
Q ss_pred HHHHHHHhhCHH-HHHHHHHHhhCCCCCccHHHHHHHHHHHHHHHcCCHHHHHHHHHhhCchhhccCcchhhhhHHHHHH
Q 028796 46 LVMNFLVTEGYV-DAAEKFRMESGTEPDIDLATITDRMAVKKAVQCGNVEDAIEKVNDLNPEILDTNPQLFFHLQQQRLI 124 (203)
Q Consensus 46 lI~~yL~~~Gy~-eta~~f~ke~~~~~~~~~e~~~~r~~I~~~I~~g~i~~Ai~~l~~~~p~l~~~~~~l~F~L~~q~fI 124 (203)
+....+..+|.. ++...+.+-..+.|... ......-+| ....|++++|++++...-+.. ..++......+...-.
T Consensus 119 ~~a~~~~~~G~~~~A~~~~~~al~~~p~~~-~~~~~la~i--~~~~g~~~eA~~~l~~~l~~~-~~~~~~~~~~~~~la~ 194 (355)
T cd05804 119 MLAFGLEEAGQYDRAEEAARRALELNPDDA-WAVHAVAHV--LEMQGRFKEGIAFMESWRDTW-DCSSMLRGHNWWHLAL 194 (355)
T ss_pred HHHHHHHHcCCHHHHHHHHHHHHhhCCCCc-HHHHHHHHH--HHHcCCHHHHHHHHHhhhhcc-CCCcchhHHHHHHHHH
Confidence 444455566654 44455555555544322 222222222 246899999999988754322 1123333333222223
Q ss_pred HHHHcCChHHHHHHHHHhc
Q 028796 125 ELIRNGKVEEALEFAQEEL 143 (203)
Q Consensus 125 eli~~~~~~~Al~y~r~~l 143 (203)
-++..|+..+|+.+.++.+
T Consensus 195 ~~~~~G~~~~A~~~~~~~~ 213 (355)
T cd05804 195 FYLERGDYEAALAIYDTHI 213 (355)
T ss_pred HHHHCCCHHHHHHHHHHHh
Confidence 3567899999999998865
No 100
>PF03979 Sigma70_r1_1: Sigma-70 factor, region 1.1; InterPro: IPR007127 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. This entry represents Region 1.1 which modulates DNA binding by region 2 and 4 when sigma is unbound by the core RNA polymerase [, ]. Region 1.1 is also involved in promoter binding.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2K6X_A.
Probab=21.77 E-value=2e+02 Score=19.44 Aligned_cols=45 Identities=24% Similarity=0.384 Sum_probs=27.8
Q ss_pred HHHHHHHHHhhhcccCCCHHHHHHHhhcCCCCHHHHHHHHHHHHHhhCH
Q 028796 8 IRQLAEIEAMAMSKKVITREEWEKKLNDVKIRKEDMNKLVMNFLVTEGY 56 (203)
Q Consensus 8 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~lI~~yL~~~Gy 56 (203)
|++|-+.|- .+|+++..++.+++....++++.+..+ .++|...|.
T Consensus 9 i~~Li~~gK---~~G~lT~~eI~~~L~~~~~~~e~id~i-~~~L~~~gI 53 (82)
T PF03979_consen 9 IKKLIEKGK---KKGYLTYDEINDALPEDDLDPEQIDEI-YDTLEDEGI 53 (82)
T ss_dssp HHHHHHHHH---HHSS-BHHHHHHH-S-S---HHHHHHH-HHHHHTT--
T ss_pred HHHHHHHHh---hcCcCCHHHHHHHcCccCCCHHHHHHH-HHHHHHCCC
Confidence 466666665 488999999999999888998887765 456666664
No 101
>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=21.75 E-value=1.4e+02 Score=18.15 Aligned_cols=25 Identities=12% Similarity=0.054 Sum_probs=21.4
Q ss_pred CHhhHHHHHHHHHHHHHhhcCCCCC
Q 028796 179 DISQRLKTASEVNAAILTSQSHEKG 203 (203)
Q Consensus 179 ~~~~r~~la~~vN~aiL~~~~~~~~ 203 (203)
+.+++.++++.+.+++-+..|.+++
T Consensus 12 t~eqk~~l~~~i~~~l~~~~g~~~~ 36 (58)
T cd00491 12 TDEQKRELIERVTEAVSEILGAPEA 36 (58)
T ss_pred CHHHHHHHHHHHHHHHHHHhCcCcc
Confidence 5788999999999999998887753
No 102
>PF09626 DHC: Dihaem cytochrome c; InterPro: IPR018588 Dihaem cytochrome c (DHC) is a soluble c-type cytochrome that folds into two distinct domains, each binding a single haem group and connected by a small linker region. Despite little sequence similarity, the N-terminal domain (residues 12-75) is a class I type cytochrome c, that binds one of the haems, but the domain surrounding the other haem is structurally unique. DHC binds electrostatically to an oxygen-binding protein, sphaeroides haem protein (SHP), as a component of a conserved electron transfer pathway. DHC acts as the physiological electron donor for SHP during phototrophic growth []. In certain species DHC is found upstream of IPR011577 from INTERPRO. ; PDB: 2FWT_A 2FW5_A.
Probab=21.75 E-value=1.6e+02 Score=21.96 Aligned_cols=40 Identities=18% Similarity=0.355 Sum_probs=26.2
Q ss_pred hhhcccCCCHHHHHHHhhcCC-------CCHHHHHHHHHHHHHhhCH
Q 028796 17 MAMSKKVITREEWEKKLNDVK-------IRKEDMNKLVMNFLVTEGY 56 (203)
Q Consensus 17 ~~~~~~~~~~~~~~~~~~~~~-------~~~~~l~~lI~~yL~~~Gy 56 (203)
+.|+-+.++...|...|.+.. .=...-...|.+||..+.-
T Consensus 10 ~aypP~~Lpa~sW~~im~~l~~HFG~~a~Ld~~~~~~I~~YL~~nAa 56 (120)
T PF09626_consen 10 MAYPPGLLPAESWQKIMQDLDDHFGEDASLDPATQAEIWAYLQANAA 56 (120)
T ss_dssp ----GGGS-HHHHHHHHCGGGGBTTB-----HHHHHHHHHHHHHTST
T ss_pred CcCCcccCCHHHHHHHHHhHHHhcCCCCCCCHHHHHHHHHHHHHccc
Confidence 467778899999999998876 2224456889999988753
No 103
>PRK09263 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=21.65 E-value=3.5e+02 Score=26.41 Aligned_cols=28 Identities=21% Similarity=0.321 Sum_probs=25.1
Q ss_pred CCCHHHHHHHHHHHHHhhCHHHHHHHHH
Q 028796 37 KIRKEDMNKLVMNFLVTEGYVDAAEKFR 64 (203)
Q Consensus 37 ~~~~~~l~~lI~~yL~~~Gy~eta~~f~ 64 (203)
.++-+.|..+|...|...|+.++|+++.
T Consensus 55 ~isve~Iqd~Ve~~L~~~g~~~vAkaYI 82 (711)
T PRK09263 55 EVDIEEIQDAVENQLMAGPYKALARAYI 82 (711)
T ss_pred CCCHHHHHHHHHHHHHhcChHHHHHHHH
Confidence 4777788999999999999999999985
No 104
>PLN03081 pentatricopeptide (PPR) repeat-containing protein; Provisional
Probab=21.25 E-value=7.2e+02 Score=23.66 Aligned_cols=91 Identities=21% Similarity=0.284 Sum_probs=46.0
Q ss_pred HHHHHHHHHHhhCHHHHHHHHHH--hhCCCCCccHHHHHHHHHHHHHHHcCCHHHHHHHHHhhCchhhccCcchhhhhHH
Q 028796 43 MNKLVMNFLVTEGYVDAAEKFRM--ESGTEPDIDLATITDRMAVKKAVQCGNVEDAIEKVNDLNPEILDTNPQLFFHLQQ 120 (203)
Q Consensus 43 l~~lI~~yL~~~Gy~eta~~f~k--e~~~~~~~~~e~~~~r~~I~~~I~~g~i~~Ai~~l~~~~p~l~~~~~~l~F~L~~ 120 (203)
-+-||..|..+.-..++.+.|.+ +.|+.|. ...-..-|.-....|++++|.+..+..... ....++. .+.
T Consensus 394 ~n~lI~~y~~~G~~~~A~~lf~~M~~~g~~Pd----~~T~~~ll~a~~~~g~~~~a~~~f~~m~~~-~g~~p~~---~~y 465 (697)
T PLN03081 394 WNALIAGYGNHGRGTKAVEMFERMIAEGVAPN----HVTFLAVLSACRYSGLSEQGWEIFQSMSEN-HRIKPRA---MHY 465 (697)
T ss_pred HHHHHHHHHHcCCHHHHHHHHHHHHHhCCCCC----HHHHHHHHHHHhcCCcHHHHHHHHHHHHHh-cCCCCCc---cch
Confidence 45666655554444555555554 3566552 222223344455778888887776654210 0111111 111
Q ss_pred HHHHH-HHHcCChHHHHHHHHH
Q 028796 121 QRLIE-LIRNGKVEEALEFAQE 141 (203)
Q Consensus 121 q~fIe-li~~~~~~~Al~y~r~ 141 (203)
-..|+ +.+.|++++|.++.++
T Consensus 466 ~~li~~l~r~G~~~eA~~~~~~ 487 (697)
T PLN03081 466 ACMIELLGREGLLDEAYAMIRR 487 (697)
T ss_pred HhHHHHHHhcCCHHHHHHHHHH
Confidence 22334 3456778888877765
No 105
>PRK00304 hypothetical protein; Provisional
Probab=21.01 E-value=98 Score=21.21 Aligned_cols=43 Identities=21% Similarity=0.493 Sum_probs=29.0
Q ss_pred CCHHHHHHHHHHHHHhhCHHHHHHHHHHhhCCCCCccHHHHHHHHHHHHHHHcCCH
Q 028796 38 IRKEDMNKLVMNFLVTEGYVDAAEKFRMESGTEPDIDLATITDRMAVKKAVQCGNV 93 (203)
Q Consensus 38 ~~~~~l~~lI~~yL~~~Gy~eta~~f~ke~~~~~~~~~e~~~~r~~I~~~I~~g~i 93 (203)
++++.++.||-+|..|.|- + .|- ....-....++++++.+|+.
T Consensus 8 L~~eTL~nLIeefv~ReGT-D--------yg~----E~sL~~kv~qv~~qL~~G~~ 50 (75)
T PRK00304 8 LEADTLTRLIEDFVTRDGT-D--------NGD----ETPLETRVLRVRQALTKGQA 50 (75)
T ss_pred CCHHHHHHHHHHHHhccCc-c--------Ccc----cccHHHHHHHHHHHHHcCCE
Confidence 6778899999999999986 2 121 11122344678888888863
No 106
>PF12793 SgrR_N: Sugar transport-related sRNA regulator N-term
Probab=20.97 E-value=1.3e+02 Score=22.17 Aligned_cols=24 Identities=13% Similarity=0.123 Sum_probs=20.3
Q ss_pred HHHHHHHHHHcCCHHHHHHHHHhh
Q 028796 80 DRMAVKKAVQCGNVEDAIEKVNDL 103 (203)
Q Consensus 80 ~r~~I~~~I~~g~i~~Ai~~l~~~ 103 (203)
....+.+.+.+|+++.|++++...
T Consensus 73 ~~~~~~~~l~~g~~~~a~~ll~~~ 96 (115)
T PF12793_consen 73 LEQQAEELLEQGKYEQALQLLDFD 96 (115)
T ss_pred HHHHHHHHHHcCCHHHHHHHHHhC
Confidence 356788899999999999999843
No 107
>KOG0097 consensus GTPase Rab14, small G protein superfamily [Intracellular trafficking, secretion, and vesicular transport]
Probab=20.93 E-value=1.4e+02 Score=23.22 Aligned_cols=38 Identities=18% Similarity=0.318 Sum_probs=29.1
Q ss_pred HHHHHHHHHhhCCCC---------CccHHHHHHHHHHHHHHHcCCHH
Q 028796 57 VDAAEKFRMESGTEP---------DIDLATITDRMAVKKAVQCGNVE 94 (203)
Q Consensus 57 ~eta~~f~ke~~~~~---------~~~~e~~~~r~~I~~~I~~g~i~ 94 (203)
.+-|+.|++|.|+.. .+........++|.+.|.+|.+|
T Consensus 136 yeeak~faeengl~fle~saktg~nvedafle~akkiyqniqdgsld 182 (215)
T KOG0097|consen 136 YEEAKEFAEENGLMFLEASAKTGQNVEDAFLETAKKIYQNIQDGSLD 182 (215)
T ss_pred HHHHHHHHhhcCeEEEEecccccCcHHHHHHHHHHHHHHhhhcCccc
Confidence 578999999998742 22335778889999999999665
No 108
>TIGR02795 tol_pal_ybgF tol-pal system protein YbgF. Members of this protein family are the product of one of seven genes regularly clustered in operons to encode the proteins of the tol-pal system, which is critical for maintaining the integrity of the bacterial outer membrane. The gene for this periplasmic protein has been designated orf2 and ybgF. All members of the seed alignment were from unique tol-pal gene regions from completed bacterial genomes. The architecture of this protein is a signal sequence, a low-complexity region usually rich in Asn and Gln, a well-conserved region with tandem repeats that resemble the tetratricopeptide (TPR) repeat, involved in protein-protein interaction.
Probab=20.83 E-value=2.8e+02 Score=18.72 Aligned_cols=102 Identities=16% Similarity=0.070 Sum_probs=54.3
Q ss_pred HHHHHHHHHhhCHHHHHHHHHHhhCCCCCccHHHHHHHHHHHHHHHcCCHHHHHHHHHhhCchhhccCcchhhhhHHHHH
Q 028796 44 NKLVMNFLVTEGYVDAAEKFRMESGTEPDIDLATITDRMAVKKAVQCGNVEDAIEKVNDLNPEILDTNPQLFFHLQQQRL 123 (203)
Q Consensus 44 ~~lI~~yL~~~Gy~eta~~f~ke~~~~~~~~~e~~~~r~~I~~~I~~g~i~~Ai~~l~~~~p~l~~~~~~l~F~L~~q~f 123 (203)
-.+...++....|.++.+.|.+-....|......-.....-.-....|+++.|+..++.... ....++.. ...+...-
T Consensus 6 ~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~-~~p~~~~~-~~~~~~~~ 83 (119)
T TIGR02795 6 YDAALLVLKAGDYADAIQAFQAFLKKYPKSTYAPNAHYWLGEAYYAQGKYADAAKAFLAVVK-KYPKSPKA-PDALLKLG 83 (119)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHHHHHCCCccccHHHHHHHHHHHHhhccHHHHHHHHHHHHH-HCCCCCcc-cHHHHHHH
Confidence 44555556666677777777665544332221111223344556788999999988875421 11111111 11111111
Q ss_pred HHHHHcCChHHHHHHHHHhcCccc
Q 028796 124 IELIRNGKVEEALEFAQEELAPRG 147 (203)
Q Consensus 124 Ieli~~~~~~~Al~y~r~~l~~~~ 147 (203)
.-+...++..+|+.+.++.+..+.
T Consensus 84 ~~~~~~~~~~~A~~~~~~~~~~~p 107 (119)
T TIGR02795 84 MSLQELGDKEKAKATLQQVIKRYP 107 (119)
T ss_pred HHHHHhCChHHHHHHHHHHHHHCc
Confidence 113457888999988887666544
No 109
>PF12854 PPR_1: PPR repeat
Probab=20.31 E-value=1.5e+02 Score=16.29 Aligned_cols=19 Identities=21% Similarity=0.490 Sum_probs=13.8
Q ss_pred HHHHHHcCCHHHHHHHHHh
Q 028796 84 VKKAVQCGNVEDAIEKVND 102 (203)
Q Consensus 84 I~~~I~~g~i~~Ai~~l~~ 102 (203)
|.-.-..|++++|++.+++
T Consensus 14 I~~~Ck~G~~~~A~~l~~~ 32 (34)
T PF12854_consen 14 IDGYCKAGRVDEAFELFDE 32 (34)
T ss_pred HHHHHHCCCHHHHHHHHHh
Confidence 4455578888888887764
No 110
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=20.17 E-value=1.6e+02 Score=16.26 Aligned_cols=12 Identities=50% Similarity=0.556 Sum_probs=9.2
Q ss_pred HcCCHHHHHHHH
Q 028796 89 QCGNVEDAIEKV 100 (203)
Q Consensus 89 ~~g~i~~Ai~~l 100 (203)
..||++.|+.|+
T Consensus 25 ~~~d~~~A~~~L 36 (37)
T smart00165 25 ANGNVERAAEYL 36 (37)
T ss_pred hCCCHHHHHHHH
Confidence 357888888885
No 111
>PRK01271 4-oxalocrotonate tautomerase; Provisional
Probab=20.10 E-value=1.5e+02 Score=20.18 Aligned_cols=26 Identities=19% Similarity=0.334 Sum_probs=22.6
Q ss_pred cCHhhHHHHHHHHHHHHHhhcCCCCC
Q 028796 178 LDISQRLKTASEVNAAILTSQSHEKG 203 (203)
Q Consensus 178 ~~~~~r~~la~~vN~aiL~~~~~~~~ 203 (203)
.+.++..++|+.|.+++-+.+|.+.+
T Consensus 13 ~s~EqK~~La~~iT~a~~~~lg~~~e 38 (76)
T PRK01271 13 LDEEQKAALAADITDVIIRHLNSKDS 38 (76)
T ss_pred CCHHHHHHHHHHHHHHHHHHhCcCcc
Confidence 46788999999999999999998753
Done!