Query 028628
Match_columns 206
No_of_seqs 124 out of 832
Neff 7.6
Searched_HMMs 46136
Date Fri Mar 29 14:29:41 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028628.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028628hhsearch_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 8.2E-40 1.8E-44 266.3 18.1 185 22-206 8-193 (228)
2 PF10607 CLTH: CTLH/CRA C-term 100.0 2.5E-30 5.3E-35 200.1 12.1 126 78-206 2-130 (145)
3 KOG0396 Uncharacterized conser 100.0 8.4E-30 1.8E-34 218.0 14.7 165 39-206 114-279 (389)
4 KOG2817 Predicted E3 ubiquitin 99.9 2E-24 4.3E-29 186.9 17.1 169 35-206 110-285 (394)
5 smart00757 CRA CT11-RanBPM. pr 99.7 2.6E-16 5.7E-21 113.8 7.9 76 131-206 2-79 (99)
6 smart00668 CTLH C-terminal to 99.4 6.2E-13 1.3E-17 86.9 5.9 55 78-132 2-56 (58)
7 KOG0293 WD40 repeat-containing 98.6 2.2E-07 4.7E-12 81.9 9.9 128 18-169 9-137 (519)
8 PF08513 LisH: LisH; InterPro 98.5 2E-07 4.4E-12 51.7 3.9 27 41-67 1-27 (27)
9 KOG1477 SPRY domain-containing 98.3 1.8E-07 3.9E-12 85.1 1.1 165 42-206 251-436 (469)
10 smart00667 LisH Lissencephaly 98.2 3.8E-06 8.1E-11 48.2 4.7 32 39-70 2-33 (34)
11 COG5109 Uncharacterized conser 97.8 0.00055 1.2E-08 58.8 12.1 186 15-206 76-287 (396)
12 KOG0275 Conserved WD40 repeat- 95.7 0.14 3.1E-06 44.7 10.6 144 37-191 4-149 (508)
13 KOG1333 Uncharacterized conser 94.3 0.35 7.6E-06 39.5 8.2 104 41-144 6-117 (241)
14 PF09398 FOP_dimer: FOP N term 89.4 0.85 1.8E-05 31.8 4.5 30 42-71 20-49 (81)
15 PF04494 TFIID_90kDa: WD40 ass 80.0 4.1 8.8E-05 31.2 4.8 48 112-162 38-85 (142)
16 TIGR03362 VI_chp_7 type VI sec 75.4 37 0.00081 29.4 10.0 98 42-141 134-275 (301)
17 PF07035 Mic1: Colon cancer-as 74.9 30 0.00064 27.4 8.5 81 42-142 30-115 (167)
18 cd08044 TAF5_NTD2 TAF5_NTD2 is 72.3 9.6 0.00021 28.7 5.0 50 112-164 27-76 (133)
19 PF04053 Coatomer_WDAD: Coatom 69.5 23 0.0005 32.4 7.6 77 42-141 296-372 (443)
20 PF01726 LexA_DNA_bind: LexA D 67.8 14 0.00029 24.5 4.4 48 39-91 7-54 (65)
21 PF10607 CLTH: CTLH/CRA C-term 66.8 20 0.00043 26.9 5.8 58 46-104 7-67 (145)
22 PF13934 ELYS: Nuclear pore co 63.9 82 0.0018 26.0 9.5 115 24-145 27-169 (226)
23 smart00668 CTLH C-terminal to 59.2 15 0.00032 22.8 3.2 30 119-148 4-33 (58)
24 PF14559 TPR_19: Tetratricopep 58.8 43 0.00093 21.0 5.8 56 87-147 1-56 (68)
25 PF05843 Suf: Suppressor of fo 58.2 75 0.0016 26.9 8.4 94 5-99 35-129 (280)
26 KOG0273 Beta-transducin family 56.9 3.3 7.1E-05 37.9 -0.2 34 37-70 2-35 (524)
27 PF12895 Apc3: Anaphase-promot 55.8 53 0.0011 21.9 5.8 53 83-141 31-83 (84)
28 PF06794 UPF0270: Uncharacteri 55.6 37 0.0008 23.0 4.8 44 37-92 7-50 (70)
29 PF04433 SWIRM: SWIRM domain; 55.1 30 0.00064 23.8 4.5 50 5-57 35-84 (86)
30 KOG4594 Sequence-specific sing 54.8 15 0.00033 31.7 3.4 29 40-68 17-45 (354)
31 PF13833 EF-hand_8: EF-hand do 53.7 20 0.00044 21.9 3.2 30 20-49 1-33 (54)
32 PF12550 GCR1_C: Transcription 52.3 40 0.00087 23.1 4.7 65 39-103 7-80 (81)
33 PF04840 Vps16_C: Vps16, C-ter 52.2 1.6E+02 0.0034 25.7 9.5 78 48-141 184-262 (319)
34 KOG1585 Protein required for f 48.7 1.1E+02 0.0023 26.3 7.4 69 34-102 184-252 (308)
35 PRK04966 hypothetical protein; 47.4 50 0.0011 22.5 4.4 45 37-93 7-51 (72)
36 PF07575 Nucleopor_Nup85: Nup8 47.1 61 0.0013 30.5 6.5 72 14-102 379-450 (566)
37 PF10602 RPN7: 26S proteasome 46.5 1.4E+02 0.0031 23.4 11.8 106 42-147 37-144 (177)
38 PF06588 Muskelin_N: Muskelin 46.0 36 0.00078 27.8 4.1 30 41-70 166-195 (199)
39 PF13838 Clathrin_H_link: Clat 45.1 34 0.00074 22.8 3.3 40 117-158 7-47 (66)
40 PRK02289 4-oxalocrotonate taut 44.9 32 0.00069 21.9 3.1 26 179-204 13-38 (60)
41 COG5443 FlbT Flagellar biosynt 44.9 40 0.00088 25.7 4.0 55 52-106 67-123 (148)
42 PRK10564 maltose regulon perip 44.8 25 0.00055 30.5 3.3 24 80-103 260-283 (303)
43 KOG2659 LisH motif-containing 44.5 1.3E+02 0.0028 25.1 7.3 67 39-105 61-131 (228)
44 PF12569 NARP1: NMDA receptor- 43.1 2.9E+02 0.0062 25.9 11.9 115 6-139 161-285 (517)
45 PF10827 DUF2552: Protein of u 42.4 18 0.00039 24.5 1.6 18 91-108 59-76 (79)
46 PF14276 DUF4363: Domain of un 42.0 51 0.0011 24.1 4.3 49 77-125 28-76 (121)
47 cd00052 EH Eps15 homology doma 41.8 48 0.0011 20.7 3.7 30 19-48 11-40 (67)
48 PF07729 FCD: FCD domain; Int 41.0 53 0.0011 22.8 4.1 29 76-104 95-123 (125)
49 PF07721 TPR_4: Tetratricopept 39.9 40 0.00086 17.5 2.5 17 85-101 9-25 (26)
50 PF13934 ELYS: Nuclear pore co 39.6 2.1E+02 0.0047 23.5 12.9 67 88-169 89-156 (226)
51 PF04121 Nup84_Nup100: Nuclear 39.4 1.2E+02 0.0025 29.5 7.3 28 77-104 133-160 (697)
52 smart00027 EH Eps15 homology d 38.9 43 0.00094 23.3 3.3 31 19-49 22-52 (96)
53 KOG0292 Vesicle coat complex C 38.7 15 0.00034 36.5 1.2 49 42-103 621-669 (1202)
54 PF04840 Vps16_C: Vps16, C-ter 37.8 2.7E+02 0.006 24.2 11.2 90 31-141 198-287 (319)
55 PF12174 RST: RCD1-SRO-TAF4 (R 37.5 35 0.00076 23.0 2.5 24 13-36 31-54 (70)
56 KOG0263 Transcription initiati 35.8 61 0.0013 31.4 4.6 35 36-70 17-51 (707)
57 KOG1961 Vacuolar sorting prote 34.8 3.2E+02 0.007 26.3 9.0 118 24-141 131-257 (683)
58 KOG1156 N-terminal acetyltrans 34.7 4.4E+02 0.0096 25.6 10.3 112 77-194 185-315 (700)
59 PF09052 SipA: Salmonella inva 34.3 66 0.0014 30.3 4.4 90 7-96 556-651 (674)
60 smart00550 Zalpha Z-DNA-bindin 32.3 1.1E+02 0.0024 20.0 4.3 50 38-93 2-52 (68)
61 cd05029 S-100A6 S-100A6: S-100 31.9 1.5E+02 0.0033 20.5 5.1 28 21-48 26-58 (88)
62 PF07208 DUF1414: Protein of u 31.4 70 0.0015 19.6 2.8 19 179-197 25-43 (44)
63 TIGR02531 yecD_yerC TrpR-relat 31.3 1.9E+02 0.004 20.3 5.7 54 44-99 5-58 (88)
64 PF09012 FeoC: FeoC like trans 31.2 47 0.001 21.8 2.3 43 12-58 3-45 (69)
65 PRK09263 anaerobic ribonucleos 31.1 1.8E+02 0.0039 28.5 7.1 28 37-64 55-82 (711)
66 PF03979 Sigma70_r1_1: Sigma-7 30.9 1.1E+02 0.0024 20.9 4.2 45 8-56 9-53 (82)
67 PF09862 DUF2089: Protein of u 30.6 2.1E+02 0.0045 21.2 5.8 53 45-100 40-112 (113)
68 PRK14574 hmsH outer membrane p 30.6 5.6E+02 0.012 25.6 11.4 17 86-102 111-127 (822)
69 PF00036 EF-hand_1: EF hand; 30.2 25 0.00054 19.2 0.7 17 18-34 11-27 (29)
70 TIGR01470 cysG_Nterm siroheme 28.9 1.8E+02 0.004 23.4 5.9 66 77-143 133-204 (205)
71 KOG1538 Uncharacterized conser 28.8 2.7E+02 0.0059 27.4 7.5 60 82-142 777-843 (1081)
72 PF09731 Mitofilin: Mitochondr 28.6 92 0.002 29.3 4.6 93 11-105 453-551 (582)
73 PLN03077 Protein ECB2; Provisi 28.2 5.8E+02 0.013 25.0 11.9 103 31-141 545-650 (857)
74 PRK01271 4-oxalocrotonate taut 28.1 82 0.0018 21.5 3.1 27 178-204 13-39 (76)
75 PF12854 PPR_1: PPR repeat 28.0 89 0.0019 17.3 2.8 20 83-102 13-32 (34)
76 PRK07111 anaerobic ribonucleos 28.0 2.2E+02 0.0049 27.9 7.1 28 37-64 58-85 (735)
77 PF14689 SPOB_a: Sensor_kinase 27.7 1.4E+02 0.0031 19.2 4.1 32 76-107 22-53 (62)
78 PF14691 Fer4_20: Dihydroprymi 27.5 93 0.002 22.8 3.5 27 116-142 38-64 (111)
79 PRK00794 flbT flagellar biosyn 27.2 2.2E+02 0.0048 21.6 5.6 30 76-105 92-121 (132)
80 PLN02839 nudix hydrolase 26.5 49 0.0011 29.7 2.2 35 23-57 318-352 (372)
81 PRK00304 hypothetical protein; 26.2 67 0.0014 22.0 2.3 43 38-93 8-50 (75)
82 KOG2910 Uncharacterized conser 25.8 3.7E+02 0.008 22.0 8.3 53 79-131 41-106 (209)
83 cd00491 4Oxalocrotonate_Tautom 25.5 1.1E+02 0.0024 18.7 3.2 25 179-203 12-36 (58)
84 KOG0097 GTPase Rab14, small G 25.5 1E+02 0.0022 24.0 3.5 39 56-94 135-182 (215)
85 PRK01964 4-oxalocrotonate taut 25.1 1E+02 0.0022 19.7 3.0 25 179-203 13-37 (64)
86 PF15391 DUF4614: Domain of un 24.9 96 0.0021 24.9 3.4 50 94-143 113-179 (181)
87 KOG3192 Mitochondrial J-type c 24.8 85 0.0018 24.7 3.0 80 21-103 69-154 (168)
88 TIGR00013 taut 4-oxalocrotonat 24.5 1.2E+02 0.0026 19.0 3.3 27 178-204 12-38 (63)
89 PF03477 ATP-cone: ATP cone do 24.2 82 0.0018 21.4 2.6 28 37-64 55-82 (90)
90 TIGR00756 PPR pentatricopeptid 23.6 1.2E+02 0.0026 15.6 2.8 20 84-103 7-26 (35)
91 COG5117 NOC3 Protein involved 23.5 4E+02 0.0087 25.0 7.4 168 11-192 240-477 (657)
92 PF12793 SgrR_N: Sugar transpo 22.9 1.2E+02 0.0025 22.4 3.3 24 80-103 73-96 (115)
93 PF00627 UBA: UBA/TS-N domain; 22.9 68 0.0015 18.2 1.7 17 84-100 19-37 (37)
94 PF03997 VPS28: VPS28 protein; 22.9 2.5E+02 0.0054 22.7 5.5 56 4-70 4-64 (188)
95 PF12931 Sec16_C: Sec23-bindin 22.7 91 0.002 26.6 3.1 22 83-104 1-22 (284)
96 KOG0640 mRNA cleavage stimulat 22.6 2.9E+02 0.0064 24.5 6.1 32 39-70 10-41 (430)
97 COG3071 HemY Uncharacterized e 22.0 5.1E+02 0.011 23.5 7.7 132 23-168 170-341 (400)
98 KOG3380 Actin-related protein 22.0 2.2E+02 0.0048 22.2 4.8 58 82-140 40-99 (152)
99 TIGR00083 ribF riboflavin kina 22.0 53 0.0011 28.3 1.5 51 54-104 115-169 (288)
100 PF10552 ORF6C: ORF6C domain; 21.6 1.5E+02 0.0032 21.6 3.7 23 85-107 87-109 (116)
101 PF12169 DNA_pol3_gamma3: DNA 21.4 2.6E+02 0.0056 20.6 5.1 24 81-104 18-41 (143)
102 PHA01351 putative minor struct 21.2 8.2E+02 0.018 24.3 12.8 46 19-64 492-537 (1070)
103 PRK02220 4-oxalocrotonate taut 21.2 1.3E+02 0.0029 18.7 3.0 25 179-203 13-37 (61)
104 COG5096 Vesicle coat complex, 21.1 6.6E+02 0.014 24.9 8.8 80 67-152 25-107 (757)
105 PRK00745 4-oxalocrotonate taut 21.0 1.4E+02 0.003 18.7 3.1 25 179-203 13-37 (62)
106 PHA02701 ORF020 dsRNA-binding 20.9 66 0.0014 25.9 1.7 27 44-70 6-32 (183)
107 COG5051 RPL36A Ribosomal prote 20.9 1.4E+02 0.0031 21.1 3.2 43 119-165 53-95 (97)
108 PF09312 SurA_N: SurA N-termin 20.7 2.8E+02 0.006 20.1 5.0 31 34-66 63-93 (118)
109 PF13812 PPR_3: Pentatricopept 20.5 1.5E+02 0.0032 15.5 2.8 21 83-103 7-27 (34)
110 PF01361 Tautomerase: Tautomer 20.3 89 0.0019 19.5 2.0 25 179-203 12-36 (60)
111 PF01535 PPR: PPR repeat; Int 20.3 1.2E+02 0.0026 15.4 2.3 20 84-103 7-26 (31)
112 cd00194 UBA Ubiquitin Associat 20.2 1.7E+02 0.0036 16.3 3.0 18 84-101 18-37 (38)
113 PF04699 P16-Arc: ARP2/3 compl 20.2 1.2E+02 0.0025 23.7 3.0 27 79-105 38-64 (152)
114 KOG0396 Uncharacterized conser 20.1 4.3E+02 0.0094 23.8 6.7 63 46-109 158-223 (389)
115 PRK03095 prsA peptidylprolyl i 20.1 4.8E+02 0.011 22.1 7.1 36 19-55 30-65 (287)
No 1
>KOG2659 consensus LisH motif-containing protein [Cytoskeleton]
Probab=100.00 E-value=8.2e-40 Score=266.31 Aligned_cols=185 Identities=60% Similarity=0.893 Sum_probs=180.3
Q ss_pred cCCCHHHHHHHHhcCCCCHHHHHHHHHHHHHhhCHHHHHHHHHHHhCCCC-CccHHHHHHHHHHHHHHHcCCHHHHHHHH
Q 028628 22 KVITREEWEKKLNDVKIRKEDMNKLVMNFLVTEGYVDAAEKFRMESGTEP-DIDLATITDRMAVKKAVQCGNVEDAIEKV 100 (206)
Q Consensus 22 ~~~~~~~~~~~~~~~~~~~~~l~~lI~~YL~~~Gy~~ta~~f~~e~~~~~-~~~~~~~~~r~~I~~~I~~g~i~~Ai~~~ 100 (206)
+.+++++|.+.+.++.+....+|+||++||+|+||.++|+.|++++|+++ ..+.+.+..|.+|+.+|..|+++.|++.+
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 88999999999999999999999999999
Q ss_pred HhhCchhhhcccchhhhhHHHHHHHHHHcCChHHHHHHHHHhcCccccCChhHHHHHHHHHhhhcccCCCCCchhhhcCh
Q 028628 101 NDLNPEILDTNPQLFFHLQQQRLIELIRNGKVEEALEFAQEELAPRGEENQSFLEELERTVALLAFEDVSNCPVGDLLDI 180 (206)
Q Consensus 101 ~~~~p~l~~~~s~L~F~L~~q~fieli~~~~~~~Al~y~r~~l~~~~~~~~~~~~~i~~l~~LLay~~~~~sp~~~ll~~ 180 (206)
+++.|.++..+..|.|.|++|+||||||.|...+||+|+|+.++|++..+++++.+++++|++|+|+++..||++.++..
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 hhHHHHHHHHHHHHHhhCCCCCCCCC
Q 028628 181 SQRLKTASEVNAAILTSQSHEKGDKL 206 (206)
Q Consensus 181 ~~r~~la~~vN~aiL~~~~~~~~~~l 206 (206)
++|.++|+.||++||++++.+..|+|
T Consensus 168 s~R~kvA~~vN~aiL~~~~~~~~~~l 193 (228)
T KOG2659|consen 168 SLRQKVASEVNSAILASQEHESEPKL 193 (228)
T ss_pred HHHHHHHHHHHHHHHHHhcccccchH
Confidence 99999999999999999999988864
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=99.97 E-value=2.5e-30 Score=200.05 Aligned_cols=126 Identities=38% Similarity=0.616 Sum_probs=120.2
Q ss_pred HHHHHHHHHHHHcCCHHHHHHHHHhhCchhhhcccchhhhhHHHHHHHHHHcCChHHHHHHHHHhcCccccCChhHHHHH
Q 028628 78 ITDRMAVKKAVQCGNVEDAIEKVNDLNPEILDTNPQLFFHLQQQRLIELIRNGKVEEALEFAQEELAPRGEENQSFLEEL 157 (206)
Q Consensus 78 ~~~r~~I~~~I~~g~i~~Ai~~~~~~~p~l~~~~s~L~F~L~~q~fieli~~~~~~~Al~y~r~~l~~~~~~~~~~~~~i 157 (206)
+.+|+.|+++|.+||+++|++|+++++|.+++.++.++|.|++|+||++|+.|++.+||+|||+++.|+.. .+.+++
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 67899999999999999999999999999999999999999999999999999999999999999976654 468999
Q ss_pred HHHHhhhcccCCCC---CchhhhcChhhHHHHHHHHHHHHHhhCCCCCCCCC
Q 028628 158 ERTVALLAFEDVSN---CPVGDLLDISQRLKTASEVNAAILTSQSHEKGDKL 206 (206)
Q Consensus 158 ~~l~~LLay~~~~~---sp~~~ll~~~~r~~la~~vN~aiL~~~~~~~~~~l 206 (206)
+++|++|+|+++.+ +||++++++++|++||+.||++++..+|.|++|+|
T Consensus 79 ~~~~~lL~~~~~~~~~~s~~~~l~~~~~~~~la~~~~~~~l~~~~~~~~s~L 130 (145)
T PF10607_consen 79 KKLMSLLAYPDPEEPLPSPYKELLSPERREELAEEFNSAILKSYGLPKESPL 130 (145)
T ss_pred HHHHHHHHcCCcccccchHHHHHhChHHHHHHHHHHHHHHHHHhCcCCCCHH
Confidence 99999999999987 79999999999999999999999999999999986
No 3
>KOG0396 consensus Uncharacterized conserved protein [Function unknown]
Probab=99.97 E-value=8.4e-30 Score=218.05 Aligned_cols=165 Identities=21% Similarity=0.328 Sum_probs=157.5
Q ss_pred CHHHHHHHHHHHHHhhCHHHHHHHHHHHhCCCCCccHHHHHHHHHHHHHHHcCCHHHHHHHHHhhCchhhhcccchhhhh
Q 028628 39 RKEDMNKLVMNFLVTEGYVDAAEKFRMESGTEPDIDLATITDRMAVKKAVQCGNVEDAIEKVNDLNPEILDTNPQLFFHL 118 (206)
Q Consensus 39 ~~~~l~~lI~~YL~~~Gy~~ta~~f~~e~~~~~~~~~~~~~~r~~I~~~I~~g~i~~Ai~~~~~~~p~l~~~~s~L~F~L 118 (206)
++..++++|.||+.|+||++||..|.+++.++...|.+.+...+.|+++|++|++.+|+.||++|...|.+.+|.|+|.+
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 56789999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHcCChHHHHHHHHHhcCccccCChhHHHHHHHHHhhhcccCCC-CCchhhhcChhhHHHHHHHHHHHHHhh
Q 028628 119 QQQRLIELIRNGKVEEALEFAQEELAPRGEENQSFLEELERTVALLAFEDVS-NCPVGDLLDISQRLKTASEVNAAILTS 197 (206)
Q Consensus 119 ~~q~fieli~~~~~~~Al~y~r~~l~~~~~~~~~~~~~i~~l~~LLay~~~~-~sp~~~ll~~~~r~~la~~vN~aiL~~ 197 (206)
+.|+|||||+.+++.+||+|+|++|+|++..+ .++++.+||+|+|+.-. .+||..+++..||+.+++.|-+.-+..
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 99999999999999999999999999999765 79999999999999854 467999999999999999999999999
Q ss_pred CCCCCCCCC
Q 028628 198 QSHEKGDKL 206 (206)
Q Consensus 198 ~~~~~~~~l 206 (206)
.|.|-.|+|
T Consensus 271 ~~i~~~~~L 279 (389)
T KOG0396|consen 271 FGIPINPAL 279 (389)
T ss_pred hCCCCCcHH
Confidence 999988875
No 4
>KOG2817 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.92 E-value=2e-24 Score=186.92 Aligned_cols=169 Identities=20% Similarity=0.305 Sum_probs=155.0
Q ss_pred cCCCCHHH-HHHHHHHHHHhhCHHHHHHHHHHHhCCCCC--ccHHHHHHHHHHHHHHHcCCHHHHHHHHHhhCchhhhcc
Q 028628 35 DVKIRKED-MNKLVMNFLVTEGYVDAAEKFRMESGTEPD--IDLATITDRMAVKKAVQCGNVEDAIEKVNDLNPEILDTN 111 (206)
Q Consensus 35 ~~~~~~~~-l~~lI~~YL~~~Gy~~ta~~f~~e~~~~~~--~~~~~~~~r~~I~~~I~~g~i~~Ai~~~~~~~p~l~~~~ 111 (206)
++..+... +|.+|..|++|+|..|++..|++|+|.... .....|.+.++|.++|.+||+++|++|+..++..|.+.+
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 44444444 599999999999999999999999998753 456799999999999999999999999999999999999
Q ss_pred cchhhhhHHHHHHHHHHcCChH--HHHHHHHHhcCccccCChhHHHHHHHHHhhhcccCC--CCCchhhhcChhhHHHHH
Q 028628 112 PQLFFHLQQQRLIELIRNGKVE--EALEFAQEELAPRGEENQSFLEELERTVALLAFEDV--SNCPVGDLLDISQRLKTA 187 (206)
Q Consensus 112 s~L~F~L~~q~fieli~~~~~~--~Al~y~r~~l~~~~~~~~~~~~~i~~l~~LLay~~~--~~sp~~~ll~~~~r~~la 187 (206)
+.|+|.|+.++|+++++.|.-. +||.|+|++++||+.++ ..+||.+|++|.|-.. +.+||.+++++..|..+.
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 9999999999999999998765 99999999999998766 6899999999999776 689999999999999999
Q ss_pred HHHHHHHHhhCCCCCCCCC
Q 028628 188 SEVNAAILTSQSHEKGDKL 206 (206)
Q Consensus 188 ~~vN~aiL~~~~~~~~~~l 206 (206)
..|-+--+..+|.+.++||
T Consensus 267 ~~f~r~ycallg~s~eSPL 285 (394)
T KOG2817|consen 267 EEFTREYCALLGISVESPL 285 (394)
T ss_pred HHHHHHHHHHcCCCccCcH
Confidence 9999999999999999986
No 5
>smart00757 CRA CT11-RanBPM. protein-protein interaction domain present in crown eukaryotes (plants, animals, fungi)
Probab=99.66 E-value=2.6e-16 Score=113.77 Aligned_cols=76 Identities=47% Similarity=0.638 Sum_probs=71.9
Q ss_pred ChHHHHHHHHHhcCccccCChhHHHHHHHHHhhhcccCC-CCCchhhhcChhhHHHHHHHHHHHHHhhC-CCCCCCCC
Q 028628 131 KVEEALEFAQEELAPRGEENQSFLEELERTVALLAFEDV-SNCPVGDLLDISQRLKTASEVNAAILTSQ-SHEKGDKL 206 (206)
Q Consensus 131 ~~~~Al~y~r~~l~~~~~~~~~~~~~i~~l~~LLay~~~-~~sp~~~ll~~~~r~~la~~vN~aiL~~~-~~~~~~~l 206 (206)
++.+||+|||+++++|..+++.+.++|+++|++|+|+++ +.+||++++++++|+.+++.||++||..+ |.+.+|+|
T Consensus 2 ~~~eAi~yar~~l~~~~~~~~~~~~el~~~m~llaf~~~~~~sp~~~ll~~~~~~~la~~~n~~~l~~~~~~~~~s~L 79 (99)
T smart00757 2 KIEEALAYARELLAPFAKEHEKFLKELEKTMALLAYPDPTEPSPYKELLSPSQREKLAEELNSAILELLHGKSSESPL 79 (99)
T ss_pred cHHHHHHHHHHHHhhhcccCHHHHHHHHHHHHHHhcCCCCCCccHHHHCCHHHHHHHHHHHHHHHHHHccCCCCCChH
Confidence 578999999999999998888888999999999999999 88999999999999999999999999998 99998875
No 6
>smart00668 CTLH C-terminal to LisH motif. Alpha-helical motif of unknown function.
Probab=99.40 E-value=6.2e-13 Score=86.88 Aligned_cols=55 Identities=31% Similarity=0.669 Sum_probs=52.2
Q ss_pred HHHHHHHHHHHHcCCHHHHHHHHHhhCchhhhcccchhhhhHHHHHHHHHHcCCh
Q 028628 78 ITDRMAVKKAVQCGNVEDAIEKVNDLNPEILDTNPQLFFHLQQQRLIELIRNGKV 132 (206)
Q Consensus 78 ~~~r~~I~~~I~~g~i~~Ai~~~~~~~p~l~~~~s~L~F~L~~q~fieli~~~~~ 132 (206)
+..++.|+++|++|+|++|++|+++++|.+.+.++.+.|.|++|+|+|+++.++.
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 5688999999999999999999999999999999999999999999999998764
No 7
>KOG0293 consensus WD40 repeat-containing protein [Function unknown]
Probab=98.64 E-value=2.2e-07 Score=81.90 Aligned_cols=128 Identities=15% Similarity=0.236 Sum_probs=107.2
Q ss_pred hhcccCCCHHHHHHHHhcCCCCHHHHHHHHHHHHHhhCHHHHHHHHHHHhCCCCCccHHHHHHHHHHHHHHHcCCHHHHH
Q 028628 18 AMSKKVITREEWEKKLNDVKIRKEDMNKLVMNFLVTEGYVDAAEKFRMESGTEPDIDLATITDRMAVKKAVQCGNVEDAI 97 (206)
Q Consensus 18 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~lI~~YL~~~Gy~~ta~~f~~e~~~~~~~~~~~~~~r~~I~~~I~~g~i~~Ai 97 (206)
.++++.|.+.|| .+++.+.|+.-||..++..++.|+|+.... +.-+...++++.|+|+.++
T Consensus 9 l~~k~likk~ef--------------i~il~q~l~slgy~~S~~~lE~es~ll~~t-----at~klf~q~vlqg~w~q~v 69 (519)
T KOG0293|consen 9 LGSKGLIKKGEF--------------IRILWQILYSLGYDHSSPLLEWESGLLIPT-----ATTKLFDQQVLQGQWDQQV 69 (519)
T ss_pred hhhhceeccchh--------------hHhHHHHHHhcCccccchhhHHhhCccccc-----chHHHHHHHHHcccHHHHH
Confidence 467888888898 899999999999999999999999986322 2346678999999999999
Q ss_pred HHHHhh-CchhhhcccchhhhhHHHHHHHHHHcCChHHHHHHHHHhcCccccCChhHHHHHHHHHhhhcccCC
Q 028628 98 EKVNDL-NPEILDTNPQLFFHLQQQRLIELIRNGKVEEALEFAQEELAPRGEENQSFLEELERTVALLAFEDV 169 (206)
Q Consensus 98 ~~~~~~-~p~l~~~~s~L~F~L~~q~fieli~~~~~~~Al~y~r~~l~~~~~~~~~~~~~i~~l~~LLay~~~ 169 (206)
.-+... ++. .+......|.+.+|.|+|+++.|.+..|+...|+.+.+.... .+.+.++.+.|++++.
T Consensus 70 ~~~~~i~~~d-e~~~~ea~fLv~kQ~fLEf~k~~~is~al~~l~~~~~~lr~~----~kk~~el~~sll~sn~ 137 (519)
T KOG0293|consen 70 MSLVRISFED-ERNRKEAMFLVNKQIFLEFLKTGSISHALPVLRNPVLYLRKN----KKKFHELASSLLVSND 137 (519)
T ss_pred HHHhhccCcc-hhhhHHHHHHHHHHHHHHHHhhccHhhhhHhhhcchhhhhhh----HHHHHHHHHHHhcccc
Confidence 887766 444 455578999999999999999999999999999877776542 4788899998888874
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=98.50 E-value=2e-07 Score=51.67 Aligned_cols=27 Identities=37% Similarity=0.811 Sum_probs=24.0
Q ss_pred HHHHHHHHHHHHhhCHHHHHHHHHHHh
Q 028628 41 EDMNKLVMNFLVTEGYVDAAEKFRMES 67 (206)
Q Consensus 41 ~~l~~lI~~YL~~~Gy~~ta~~f~~e~ 67 (206)
+.||.+|.+||.++||.+||.+|.+|+
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 368999999999999999999999985
No 9
>KOG1477 consensus SPRY domain-containing proteins [General function prediction only]
Probab=98.31 E-value=1.8e-07 Score=85.13 Aligned_cols=165 Identities=23% Similarity=0.188 Sum_probs=126.8
Q ss_pred HHHHHHHHHHHhhCHHHHHHHHHHHhCCCC--Cc-----cHHHH-----HHHHHHHHHHHcCCHHHHHHHHHhhCchhhh
Q 028628 42 DMNKLVMNFLVTEGYVDAAEKFRMESGTEP--DI-----DLATI-----TDRMAVKKAVQCGNVEDAIEKVNDLNPEILD 109 (206)
Q Consensus 42 ~l~~lI~~YL~~~Gy~~ta~~f~~e~~~~~--~~-----~~~~~-----~~r~~I~~~I~~g~i~~Ai~~~~~~~p~l~~ 109 (206)
.....+..|+++.|+.+++..|+..+.-.. .. ..+.. ..+.....-+-.+.+..+.+.+.+.-+....
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 445688999999999999999988765421 10 01100 1233334444445555556665555555444
Q ss_pred -------cccchhhhhHHHHHHHHHHcCChHHHHHHHHHhcCcccc--CChhHHHHHHHHHhhhcccCCCCCchhhhcCh
Q 028628 110 -------TNPQLFFHLQQQRLIELIRNGKVEEALEFAQEELAPRGE--ENQSFLEELERTVALLAFEDVSNCPVGDLLDI 180 (206)
Q Consensus 110 -------~~s~L~F~L~~q~fieli~~~~~~~Al~y~r~~l~~~~~--~~~~~~~~i~~l~~LLay~~~~~sp~~~ll~~ 180 (206)
..+...+.+.|+.+|.+.+.+.+...+++.+..+++... ........++..++||+|++|.+||...++++
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 347789999999999999999999999999998887765 34456789999999999999999999999999
Q ss_pred hhHHHHHHHHHHHHHhhCCCCCCCCC
Q 028628 181 SQRLKTASEVNAAILTSQSHEKGDKL 206 (206)
Q Consensus 181 ~~r~~la~~vN~aiL~~~~~~~~~~l 206 (206)
..|+-+++.+|.+||...+.+++|+|
T Consensus 411 ~~~e~v~~~~n~~il~t~~~~~~~~l 436 (469)
T KOG1477|consen 411 IQREPVAEALNSAILETDNNSKDPDL 436 (469)
T ss_pred ccchhHHhhhcccccccCCCCccchh
Confidence 99999999999999999999998863
No 10
>smart00667 LisH Lissencephaly type-1-like homology motif. Alpha-helical motif present in Lis1, treacle, Nopp140, some katanin p60 subunits, muskelin, tonneau, LEUNIG and numerous WD40 repeat-containing proteins. It is suggested that LisH motifs contribute to the regulation of microtubule dynamics, either by mediating dimerisation, or else by binding cytoplasmic dynein heavy chain or microtubules directly.
Probab=98.19 E-value=3.8e-06 Score=48.23 Aligned_cols=32 Identities=31% Similarity=0.754 Sum_probs=28.9
Q ss_pred CHHHHHHHHHHHHHhhCHHHHHHHHHHHhCCC
Q 028628 39 RKEDMNKLVMNFLVTEGYVDAAEKFRMESGTE 70 (206)
Q Consensus 39 ~~~~l~~lI~~YL~~~Gy~~ta~~f~~e~~~~ 70 (206)
.+..++++|.+||.++||.+||.+|.+|+|+.
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 11
>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=97.77 E-value=0.00055 Score=58.80 Aligned_cols=186 Identities=10% Similarity=0.015 Sum_probs=137.1
Q ss_pred HHhhhcccCCCHHHHHHHHhcCCCCHHHHHHHHHHHHHhhCHHHHHHHHHHHhCCCCC-ccHHHHHHHHHHHHHHHcCCH
Q 028628 15 EAMAMSKKVITREEWEKKLNDVKIRKEDMNKLVMNFLVTEGYVDAAEKFRMESGTEPD-IDLATITDRMAVKKAVQCGNV 93 (206)
Q Consensus 15 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~lI~~YL~~~Gy~~ta~~f~~e~~~~~~-~~~~~~~~r~~I~~~I~~g~i 93 (206)
+..+.....|+++.. +.+...+.....++.+-..++.++|-..-+..|+.+.|..+. ...+.|...+.|.+.|.+.+.
T Consensus 76 ~k~~~~~~nFd~~~~-n~~~~f~~~~v~~~~~~~l~~~n~~dv~~~hi~~~~~g~~e~~~~~~~f~~lK~v~~gI~~k~~ 154 (396)
T COG5109 76 LKEDCRPANFDVQVG-NQIYPFSTQTVTYLVVYYLLENNCADVVERHISETKDGKDEIIKIRDGFVKLKKVISGISEKST 154 (396)
T ss_pred HHHhhccccCCHHHH-hhcCCCccceeeehHHHHHHHhhHHHHHHHHHHHhhcCccchhhHHHHHHHHHHHHHhhccchh
Confidence 334455566777665 555566666677778888888888988889999999998654 446899999999999999999
Q ss_pred HHHHHHHHhhCchhhhcccchhhhhHHHHHHH--HHHcCChHHHHHHHHHhcCccccCChhHHHHHHHHHhhhcccCCC-
Q 028628 94 EDAIEKVNDLNPEILDTNPQLFFHLQQQRLIE--LIRNGKVEEALEFAQEELAPRGEENQSFLEELERTVALLAFEDVS- 170 (206)
Q Consensus 94 ~~Ai~~~~~~~p~l~~~~s~L~F~L~~q~fie--li~~~~~~~Al~y~r~~l~~~~~~~~~~~~~i~~l~~LLay~~~~- 170 (206)
..-|+|+ +-...+.+.++..++.+....... ++. .++.+|+.+.++.++.|..+| ...++.++-.+.+.+..
T Consensus 155 ~l~iE~~-Qi~gyl~kgdtesel~l~~~~~esl~l~h-k~~~~a~r~c~t~~a~f~~kh---~~dv~~~~~~l~nap~dc 229 (396)
T COG5109 155 FLLIEFL-QIEGYLSKGDTESELELYLVSHESLLLIH-KRYDEALRLCFTKLASFVPKH---IQDVKPLLRFLVNAPTDC 229 (396)
T ss_pred HhHHHHH-HhcCccccCCchhhhHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHh---ccchHHHHHHHHcCchHH
Confidence 9999999 555666666666666666554444 444 379999999999999998555 57777887777764421
Q ss_pred -----C-C--chhh-----hcC---------hhhHHHHHHHHHHHHHhhCCCCCCCCC
Q 028628 171 -----N-C--PVGD-----LLD---------ISQRLKTASEVNAAILTSQSHEKGDKL 206 (206)
Q Consensus 171 -----~-s--p~~~-----ll~---------~~~r~~la~~vN~aiL~~~~~~~~~~l 206 (206)
+ + ...+ +++ ..-|..+...|-+..++..|.+.++||
T Consensus 230 frhrekelmqnI~~~l~ksligqPiEdIDkvnk~~k~l~~lF~~eycaa~gm~~~spL 287 (396)
T COG5109 230 FRHREKELMQNIQEALKKSLIGQPIEDIDKVNKSRKKLIELFKSEYCAANGMPNRSPL 287 (396)
T ss_pred hhhcchhHHHHHHHHHHHhhcCCcHHHHHHhhhhHHHHHHHHHHHHHHhcCCCccChH
Confidence 1 0 0111 111 245889999999999999999999986
No 12
>KOG0275 consensus Conserved WD40 repeat-containing protein [General function prediction only]
Probab=95.75 E-value=0.14 Score=44.67 Aligned_cols=144 Identities=15% Similarity=0.204 Sum_probs=93.5
Q ss_pred CCCHHHHHHHHHHHHHhhCHHHHHHHHHHHhCCCCCccHHHHHHHHHHHHHHHcCCHHHHHHHHHhhCchhhhcccchhh
Q 028628 37 KIRKEDMNKLVMNFLVTEGYVDAAEKFRMESGTEPDIDLATITDRMAVKKAVQCGNVEDAIEKVNDLNPEILDTNPQLFF 116 (206)
Q Consensus 37 ~~~~~~l~~lI~~YL~~~Gy~~ta~~f~~e~~~~~~~~~~~~~~r~~I~~~I~~g~i~~Ai~~~~~~~p~l~~~~s~L~F 116 (206)
.+....+.++|.+||-.+.+..|...+.+|.++.-. -.+ ......+.|.+|.||..+.-++...- ...-.-
T Consensus 4 eiessdVIrli~QflKE~~L~rtl~tLQeEt~VSLN-TVD---Svd~Fv~dI~sG~WD~VL~~vqsLKL-----P~kkL~ 74 (508)
T KOG0275|consen 4 EIESSDVIRLIEQFLKENSLHRTLQTLQEETNVSLN-TVD---SVDGFVNDINSGHWDTVLKTVQSLKL-----PDKKLI 74 (508)
T ss_pred eeecchHHHHHHHHHhhhhHHHHHHHHHHhhcccee-ech---hHHHHHHhcccCchHHHHHHHHhccC-----chhHHH
Confidence 344457789999999999999999999999987421 111 12346778999999999999887652 123345
Q ss_pred hhHHHHHHHHHHcCChHHHHHHHHHhcC--ccccCChhHHHHHHHHHhhhcccCCCCCchhhhcChhhHHHHHHHHH
Q 028628 117 HLQQQRLIELIRNGKVEEALEFAQEELA--PRGEENQSFLEELERTVALLAFEDVSNCPVGDLLDISQRLKTASEVN 191 (206)
Q Consensus 117 ~L~~q~fieli~~~~~~~Al~y~r~~l~--~~~~~~~~~~~~i~~l~~LLay~~~~~sp~~~ll~~~~r~~la~~vN 191 (206)
.|+-|-.+|||.-+++..|-..+|+.-+ -..+..|+-.-.++.+..= .|-||.+ .|.+---..||..+|+.+.
T Consensus 75 dLYEqivlEliELREL~tAR~~lRQTdpM~~lKQ~~peRy~~lE~ll~R-~YFDp~E-aY~dssKEkrRa~IAQ~ls 149 (508)
T KOG0275|consen 75 DLYEQIVLELIELRELGTARSLLRQTDPMIMLKQIQPERYIRLENLLNR-SYFDPRE-AYGDSSKEKRRAVIAQALS 149 (508)
T ss_pred HHHHHHHHHHHHHHhhhHHHHHHhccCceehhhccChHHHHHHHHHhcc-cccChhh-hcCcchHHHHHHHHHHHhc
Confidence 7899999999998888888888885321 1122233322333332221 2444432 2445223566677777765
No 13
>KOG1333 consensus Uncharacterized conserved protein [Function unknown]
Probab=94.27 E-value=0.35 Score=39.46 Aligned_cols=104 Identities=15% Similarity=0.198 Sum_probs=69.7
Q ss_pred HHHHHHHHHHHHhhCHHHHHHHHHHHhCCCCCccHHHHHHHHHHHHHHHcCCHHHHHHHHHhhCchhhhc----c----c
Q 028628 41 EDMNKLVMNFLVTEGYVDAAEKFRMESGTEPDIDLATITDRMAVKKAVQCGNVEDAIEKVNDLNPEILDT----N----P 112 (206)
Q Consensus 41 ~~l~~lI~~YL~~~Gy~~ta~~f~~e~~~~~~~~~~~~~~r~~I~~~I~~g~i~~Ai~~~~~~~p~l~~~----~----s 112 (206)
..++.+|-+||+-.|+..|.++|-.|...........=+...+..++|...|++.--..=......++.+ . .
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 4578999999999999999999988877653332222233455667777777776543322222233321 1 3
Q ss_pred chhhhhHHHHHHHHHHcCChHHHHHHHHHhcC
Q 028628 113 QLFFHLQQQRLIELIRNGKVEEALEFAQEELA 144 (206)
Q Consensus 113 ~L~F~L~~q~fieli~~~~~~~Al~y~r~~l~ 144 (206)
.++--+.+...+--+.++.+++|=+|.++.-+
T Consensus 86 kle~Sl~r~yLV~~~q~nr~~K~~EFF~K~a~ 117 (241)
T KOG1333|consen 86 KLETSLFRFYLVYTIQTNRNDKAQEFFAKQAT 117 (241)
T ss_pred HHHHHHHHHHHhhhhhcCChHHHHHHHHHHHH
Confidence 35566777777888889999999999987443
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=89.40 E-value=0.85 Score=31.82 Aligned_cols=30 Identities=23% Similarity=0.288 Sum_probs=26.0
Q ss_pred HHHHHHHHHHHhhCHHHHHHHHHHHhCCCC
Q 028628 42 DMNKLVMNFLVTEGYVDAAEKFRMESGTEP 71 (206)
Q Consensus 42 ~l~~lI~~YL~~~Gy~~ta~~f~~e~~~~~ 71 (206)
.++.+|.+||--+||.=|+..|..|+|.+.
T Consensus 20 Li~eLIrEyLef~~l~~TlsVf~~Es~~~~ 49 (81)
T PF09398_consen 20 LINELIREYLEFNNLDYTLSVFQPESGQPE 49 (81)
T ss_dssp HHHHHHHHHHHHTT-HHHHHHHHHHHT-TT
T ss_pred HHHHHHHHHHHHcCCccHHHHHhhccCCCC
Confidence 579999999999999999999999999863
No 15
>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=79.95 E-value=4.1 Score=31.17 Aligned_cols=48 Identities=19% Similarity=0.362 Sum_probs=38.5
Q ss_pred cchhhhhHHHHHHHHHHcCChHHHHHHHHHhcCccccCChhHHHHHHHHHh
Q 028628 112 PQLFFHLQQQRLIELIRNGKVEEALEFAQEELAPRGEENQSFLEELERTVA 162 (206)
Q Consensus 112 s~L~F~L~~q~fieli~~~~~~~Al~y~r~~l~~~~~~~~~~~~~i~~l~~ 162 (206)
..+.|=+.++-|++||.+|...+|-.|..++-..+...+ ..+|+++.+
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 568999999999999999999999999998777776444 456766654
No 16
>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=75.43 E-value=37 Score=29.43 Aligned_cols=98 Identities=22% Similarity=0.263 Sum_probs=66.5
Q ss_pred HHHHHHHHHHHhhCHHHHHHHHHHHhC--------CC--------CCcc----------------------------HHH
Q 028628 42 DMNKLVMNFLVTEGYVDAAEKFRMESG--------TE--------PDID----------------------------LAT 77 (206)
Q Consensus 42 ~l~~lI~~YL~~~Gy~~ta~~f~~e~~--------~~--------~~~~----------------------------~~~ 77 (206)
++++++++.|.+.||.+.+.++..+.. +. |+.+ .+.
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 357999999999999999999888863 11 2211 112
Q ss_pred HHHHHHHHHHHHcCCHHHHHHHHHhhCchhhhcccchhhhhHHHHHHHHHHcCChHHHHHHHHH
Q 028628 78 ITDRMAVKKAVQCGNVEDAIEKVNDLNPEILDTNPQLFFHLQQQRLIELIRNGKVEEALEFAQE 141 (206)
Q Consensus 78 ~~~r~~I~~~I~~g~i~~Ai~~~~~~~p~l~~~~s~L~F~L~~q~fieli~~~~~~~Al~y~r~ 141 (206)
.....+.+.++.+|.+++|+.|+++..+...+....+...|..-+..+ ..|...-|....++
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 344566888899999999999999877766655555666665555554 34555555555543
No 17
>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=74.92 E-value=30 Score=27.45 Aligned_cols=81 Identities=19% Similarity=0.306 Sum_probs=48.3
Q ss_pred HHHHHHHHHHHhhCHHHHHHHHHHHhCCCCCccHHHHHHHHHHHHHHHcCCHHHHHHHHH--hhCchhhhcccchhhhhH
Q 028628 42 DMNKLVMNFLVTEGYVDAAEKFRMESGTEPDIDLATITDRMAVKKAVQCGNVEDAIEKVN--DLNPEILDTNPQLFFHLQ 119 (206)
Q Consensus 42 ~l~~lI~~YL~~~Gy~~ta~~f~~e~~~~~~~~~~~~~~r~~I~~~I~~g~i~~Ai~~~~--~~~p~l~~~~s~L~F~L~ 119 (206)
.+..++.+=|++.|.......|..-.=+. -...-|...+. ..+|...+-+-++...|.
T Consensus 30 ~L~~lli~lLi~~~~~~~L~qllq~~Vi~--------------------DSk~lA~~LLs~~~~~~~~~Ql~lDMLkRL~ 89 (167)
T PF07035_consen 30 ELYELLIDLLIRNGQFSQLHQLLQYHVIP--------------------DSKPLACQLLSLGNQYPPAYQLGLDMLKRLG 89 (167)
T ss_pred HHHHHHHHHHHHcCCHHHHHHHHhhcccC--------------------CcHHHHHHHHHhHccChHHHHHHHHHHHHhh
Confidence 47777777788877777776665433222 22222222221 233444444455555665
Q ss_pred -HHH-HHH-HHHcCChHHHHHHHHHh
Q 028628 120 -QQR-LIE-LIRNGKVEEALEFAQEE 142 (206)
Q Consensus 120 -~q~-fie-li~~~~~~~Al~y~r~~ 142 (206)
... .+| ++..|++-+|+.|+|+.
T Consensus 90 ~~~~~iievLL~~g~vl~ALr~ar~~ 115 (167)
T PF07035_consen 90 TAYEEIIEVLLSKGQVLEALRYARQY 115 (167)
T ss_pred hhHHHHHHHHHhCCCHHHHHHHHHHc
Confidence 443 445 78899999999999974
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=72.34 E-value=9.6 Score=28.71 Aligned_cols=50 Identities=20% Similarity=0.368 Sum_probs=38.6
Q ss_pred cchhhhhHHHHHHHHHHcCChHHHHHHHHHhcCccccCChhHHHHHHHHHhhh
Q 028628 112 PQLFFHLQQQRLIELIRNGKVEEALEFAQEELAPRGEENQSFLEELERTVALL 164 (206)
Q Consensus 112 s~L~F~L~~q~fieli~~~~~~~Al~y~r~~l~~~~~~~~~~~~~i~~l~~LL 164 (206)
..+.|=+.+.-|++||.+|...+|.+|.+++-..+.. .+.+.|+.+.++.
T Consensus 27 ~~lLyPiFvh~yL~lv~~~~~~~A~~F~~~f~~~~~~---~~~~~i~~L~~i~ 76 (133)
T cd08044 27 SQLLYPIFVHSYLDLVASGHLEEAKSFFERFSGDFED---SHSEDIKKLSSIT 76 (133)
T ss_pred HHHHHHHHHHHHHHHHHCCCHHHHHHHHHHhhHhhHH---HHHHHHHHHHccC
Confidence 4588999999999999999999999999976666542 3456666665544
No 19
>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=69.48 E-value=23 Score=32.45 Aligned_cols=77 Identities=29% Similarity=0.349 Sum_probs=54.9
Q ss_pred HHHHHHHHHHHhhCHHHHHHHHHHHhCCCCCccHHHHHHHHHHHHHHHcCCHHHHHHHHHhhCchhhhcccchhhhhHHH
Q 028628 42 DMNKLVMNFLVTEGYVDAAEKFRMESGTEPDIDLATITDRMAVKKAVQCGNVEDAIEKVNDLNPEILDTNPQLFFHLQQQ 121 (206)
Q Consensus 42 ~l~~lI~~YL~~~Gy~~ta~~f~~e~~~~~~~~~~~~~~r~~I~~~I~~g~i~~Ai~~~~~~~p~l~~~~s~L~F~L~~q 121 (206)
....-|+.||..+||.+.|-.|.++. +.+..=+|..|+++.|.+.+.+... -..+++
T Consensus 296 ~~~~~i~~fL~~~G~~e~AL~~~~D~-------------~~rFeLAl~lg~L~~A~~~a~~~~~----------~~~W~~ 352 (443)
T PF04053_consen 296 DQGQSIARFLEKKGYPELALQFVTDP-------------DHRFELALQLGNLDIALEIAKELDD----------PEKWKQ 352 (443)
T ss_dssp HHHHHHHHHHHHTT-HHHHHHHSS-H-------------HHHHHHHHHCT-HHHHHHHCCCCST----------HHHHHH
T ss_pred hHHHHHHHHHHHCCCHHHHHhhcCCh-------------HHHhHHHHhcCCHHHHHHHHHhcCc----------HHHHHH
Confidence 33677899999999999999996543 3567788999999999999876541 124455
Q ss_pred HHHHHHHcCChHHHHHHHHH
Q 028628 122 RLIELIRNGKVEEALEFAQE 141 (206)
Q Consensus 122 ~fieli~~~~~~~Al~y~r~ 141 (206)
=--..++.|++.-|-++.++
T Consensus 353 Lg~~AL~~g~~~lAe~c~~k 372 (443)
T PF04053_consen 353 LGDEALRQGNIELAEECYQK 372 (443)
T ss_dssp HHHHHHHTTBHHHHHHHHHH
T ss_pred HHHHHHHcCCHHHHHHHHHh
Confidence 55556788888777766663
No 20
>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=67.85 E-value=14 Score=24.48 Aligned_cols=48 Identities=17% Similarity=0.311 Sum_probs=31.8
Q ss_pred CHHHHHHHHHHHHHhhCHHHHHHHHHHHhCCCCCccHHHHHHHHHHHHHHHcC
Q 028628 39 RKEDMNKLVMNFLVTEGYVDAAEKFRMESGTEPDIDLATITDRMAVKKAVQCG 91 (206)
Q Consensus 39 ~~~~l~~lI~~YL~~~Gy~~ta~~f~~e~~~~~~~~~~~~~~r~~I~~~I~~g 91 (206)
.+..+-..|.+|...+||.-|...+++..|+.+ .-...+.+..+...|
T Consensus 7 rQ~~vL~~I~~~~~~~G~~Pt~rEIa~~~g~~S-----~~tv~~~L~~Le~kG 54 (65)
T PF01726_consen 7 RQKEVLEFIREYIEENGYPPTVREIAEALGLKS-----TSTVQRHLKALERKG 54 (65)
T ss_dssp HHHHHHHHHHHHHHHHSS---HHHHHHHHTSSS-----HHHHHHHHHHHHHTT
T ss_pred HHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCC-----hHHHHHHHHHHHHCc
Confidence 345667889999999999999999999999862 222334455554554
No 21
>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=66.76 E-value=20 Score=26.88 Aligned_cols=58 Identities=16% Similarity=0.118 Sum_probs=43.3
Q ss_pred HHHHHHHhhCHHHHHHHHHHHhC--C-CCCccHHHHHHHHHHHHHHHcCCHHHHHHHHHhhC
Q 028628 46 LVMNFLVTEGYVDAAEKFRMESG--T-EPDIDLATITDRMAVKKAVQCGNVEDAIEKVNDLN 104 (206)
Q Consensus 46 lI~~YL~~~Gy~~ta~~f~~e~~--~-~~~~~~~~~~~r~~I~~~I~~g~i~~Ai~~~~~~~ 104 (206)
-|.+.+ .+|-.+.|-..+.+.. + +...+....-.+++..+.|++|++.+|+++++++.
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 7888888877776653 1 22345666677888999999999999999999865
No 22
>PF13934 ELYS: Nuclear pore complex assembly
Probab=63.88 E-value=82 Score=25.95 Aligned_cols=115 Identities=15% Similarity=0.143 Sum_probs=68.1
Q ss_pred CCHHHHHHHHhcCCCCHHHHHHHHHHHHHhhCH---HHHHHHHHHHhCCCCCc----------cHH-------------H
Q 028628 24 ITREEWEKKLNDVKIRKEDMNKLVMNFLVTEGY---VDAAEKFRMESGTEPDI----------DLA-------------T 77 (206)
Q Consensus 24 ~~~~~~~~~~~~~~~~~~~l~~lI~~YL~~~Gy---~~ta~~f~~e~~~~~~~----------~~~-------------~ 77 (206)
.+.....+.+..-+++...=+-+|.=+|...+- .+.+..|+...++++.- |.. .
T Consensus 27 ~~L~~Ll~~i~~~~~~~~~K~~l~~YlLlD~~~~~~~~~~~~Fa~~f~ip~~~~~~~~g~W~LD~~~~~~A~~~L~~ps~ 106 (226)
T PF13934_consen 27 NDLRALLDLILSSNVSLLKKHSLFYYLLLDLDDTRPSELAESFARAFGIPPKYIKFIQGFWLLDHGDFEEALELLSHPSL 106 (226)
T ss_pred HHHHHHHHHHhcCCcCHHHhHHHHHHHHHhcCccccccHHHHHHHHhCCCHHHHHHHHHHHHhChHhHHHHHHHhCCCCC
Confidence 335566666666666654444555555555543 45789999999986310 000 0
Q ss_pred --HHHHHHHHHHHHcCCHHHHHHHHHhhCchhhhcccchhhhhHHHHHHHHHHcCChHHHHHHHHHhcCc
Q 028628 78 --ITDRMAVKKAVQCGNVEDAIEKVNDLNPEILDTNPQLFFHLQQQRLIELIRNGKVEEALEFAQEELAP 145 (206)
Q Consensus 78 --~~~r~~I~~~I~~g~i~~Ai~~~~~~~p~l~~~~s~L~F~L~~q~fieli~~~~~~~Al~y~r~~l~~ 145 (206)
--.-+-|+..+..|+.+.|+...+...|.+... --..-++.++..+.+.||..|.|++-.+
T Consensus 107 ~~~~~~~Il~~L~~~~~~~lAL~y~~~~~p~l~s~-------~~~~~~~~~La~~~v~EAf~~~R~~~~~ 169 (226)
T PF13934_consen 107 IPWFPDKILQALLRRGDPKLALRYLRAVGPPLSSP-------EALTLYFVALANGLVTEAFSFQRSYPDE 169 (226)
T ss_pred CcccHHHHHHHHHHCCChhHHHHHHHhcCCCCCCH-------HHHHHHHHHHHcCCHHHHHHHHHhCchh
Confidence 001123444456788888888888877766543 1122334446778899999999976553
No 23
>smart00668 CTLH C-terminal to LisH motif. Alpha-helical motif of unknown function.
Probab=59.17 E-value=15 Score=22.84 Aligned_cols=30 Identities=37% Similarity=0.485 Sum_probs=23.9
Q ss_pred HHHHHHHHHHcCChHHHHHHHHHhcCcccc
Q 028628 119 QQQRLIELIRNGKVEEALEFAQEELAPRGE 148 (206)
Q Consensus 119 ~~q~fieli~~~~~~~Al~y~r~~l~~~~~ 148 (206)
....+.+.|..|+..+|++++.+.-.+...
T Consensus 4 ~~~~i~~~i~~g~~~~a~~~~~~~~~~l~~ 33 (58)
T smart00668 4 ERKRIRELILKGDWDEALEWLSSLKPPLLE 33 (58)
T ss_pred HHHHHHHHHHcCCHHHHHHHHHHcCHHHhc
Confidence 356778899999999999999977655533
No 24
>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=58.82 E-value=43 Score=21.02 Aligned_cols=56 Identities=21% Similarity=0.266 Sum_probs=34.6
Q ss_pred HHHcCCHHHHHHHHHhhCchhhhcccchhhhhHHHHHHHHHHcCChHHHHHHHHHhcCccc
Q 028628 87 AVQCGNVEDAIEKVNDLNPEILDTNPQLFFHLQQQRLIELIRNGKVEEALEFAQEELAPRG 147 (206)
Q Consensus 87 ~I~~g~i~~Ai~~~~~~~p~l~~~~s~L~F~L~~q~fieli~~~~~~~Al~y~r~~l~~~~ 147 (206)
++..|++++|++.+++... ....+..+.+.+ -.-+++.|+..+|.+...+.+....
T Consensus 1 ll~~~~~~~A~~~~~~~l~-~~p~~~~~~~~l----a~~~~~~g~~~~A~~~l~~~~~~~~ 56 (68)
T PF14559_consen 1 LLKQGDYDEAIELLEKALQ-RNPDNPEARLLL----AQCYLKQGQYDEAEELLERLLKQDP 56 (68)
T ss_dssp HHHTTHHHHHHHHHHHHHH-HTTTSHHHHHHH----HHHHHHTT-HHHHHHHHHCCHGGGT
T ss_pred ChhccCHHHHHHHHHHHHH-HCCCCHHHHHHH----HHHHHHcCCHHHHHHHHHHHHHHCc
Confidence 4678999999999876431 111233333332 2225678999999999886554443
No 25
>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=58.18 E-value=75 Score=26.86 Aligned_cols=94 Identities=13% Similarity=0.134 Sum_probs=59.9
Q ss_pred HHHHHHHHHHHHhhhcccCCCHHHHHHHHhcCCCCHHHHHHHHHHHHHhhCHHHHHHHHHHHh-CCCCCccHHHHHHHHH
Q 028628 5 WIVIRQLAEIEAMAMSKKVITREEWEKKLNDVKIRKEDMNKLVMNFLVTEGYVDAAEKFRMES-GTEPDIDLATITDRMA 83 (206)
Q Consensus 5 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~lI~~YL~~~Gy~~ta~~f~~e~-~~~~~~~~~~~~~r~~ 83 (206)
|-|.-..|.+|+..+++....+..|+..+...+-+.+....-| +||++.|-.+-+.++-+.+ +..+.......--.+-
T Consensus 35 ~~vy~~~A~~E~~~~~d~~~A~~Ife~glk~f~~~~~~~~~Y~-~~l~~~~d~~~aR~lfer~i~~l~~~~~~~~iw~~~ 113 (280)
T PF05843_consen 35 YHVYVAYALMEYYCNKDPKRARKIFERGLKKFPSDPDFWLEYL-DFLIKLNDINNARALFERAISSLPKEKQSKKIWKKF 113 (280)
T ss_dssp THHHHHHHHHHHHTCS-HHHHHHHHHHHHHHHTT-HHHHHHHH-HHHHHTT-HHHHHHHHHHHCCTSSCHHHCHHHHHHH
T ss_pred HHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHCCCCHHHHHHHH-HHHHHhCcHHHHHHHHHHHHHhcCchhHHHHHHHHH
Confidence 5566678999999999999999999999999999888877766 9999999888887765543 3322111011111122
Q ss_pred HHHHHHcCCHHHHHHH
Q 028628 84 VKKAVQCGNVEDAIEK 99 (206)
Q Consensus 84 I~~~I~~g~i~~Ai~~ 99 (206)
|.---.-|+++.+.+.
T Consensus 114 i~fE~~~Gdl~~v~~v 129 (280)
T PF05843_consen 114 IEFESKYGDLESVRKV 129 (280)
T ss_dssp HHHHHHHS-HHHHHHH
T ss_pred HHHHHHcCCHHHHHHH
Confidence 3333455777766544
No 26
>KOG0273 consensus Beta-transducin family (WD-40 repeat) protein [Chromatin structure and dynamics]
Probab=56.86 E-value=3.3 Score=37.91 Aligned_cols=34 Identities=29% Similarity=0.555 Sum_probs=30.9
Q ss_pred CCCHHHHHHHHHHHHHhhCHHHHHHHHHHHhCCC
Q 028628 37 KIRKEDMNKLVMNFLVTEGYVDAAEKFRMESGTE 70 (206)
Q Consensus 37 ~~~~~~l~~lI~~YL~~~Gy~~ta~~f~~e~~~~ 70 (206)
.++.+++|.||..||-..||.-||=+|..|+++.
T Consensus 2 sitsdEvN~LV~RYLqE~G~~hsaftf~~Et~is 35 (524)
T KOG0273|consen 2 SITSDEVNFLVWRYLQESGFSHSAFTFGIETGIS 35 (524)
T ss_pred cccHHHHHHHHHHHHHHcCcceeeEEeeeccccc
Confidence 4667788999999999999999999999999875
No 27
>PF12895 Apc3: Anaphase-promoting complex, cyclosome, subunit 3; PDB: 3KAE_D 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2XPI_A 3ULQ_A.
Probab=55.83 E-value=53 Score=21.87 Aligned_cols=53 Identities=28% Similarity=0.424 Sum_probs=31.6
Q ss_pred HHHHHHHcCCHHHHHHHHHhhCchhhhcccchhhhhHHHHHHHHHHcCChHHHHHHHHH
Q 028628 83 AVKKAVQCGNVEDAIEKVNDLNPEILDTNPQLFFHLQQQRLIELIRNGKVEEALEFAQE 141 (206)
Q Consensus 83 ~I~~~I~~g~i~~Ai~~~~~~~p~l~~~~s~L~F~L~~q~fieli~~~~~~~Al~y~r~ 141 (206)
.-.-....|+.+.|+.+++. ......+....+.+ -+- ++..|+.++|++...+
T Consensus 31 la~~~~~~~~y~~A~~~~~~--~~~~~~~~~~~~l~-a~~---~~~l~~y~eAi~~l~~ 83 (84)
T PF12895_consen 31 LAQCYFQQGKYEEAIELLQK--LKLDPSNPDIHYLL-ARC---LLKLGKYEEAIKALEK 83 (84)
T ss_dssp HHHHHHHTTHHHHHHHHHHC--HTHHHCHHHHHHHH-HHH---HHHTT-HHHHHHHHHH
T ss_pred HHHHHHHCCCHHHHHHHHHH--hCCCCCCHHHHHHH-HHH---HHHhCCHHHHHHHHhc
Confidence 34555788999999999987 33333332333322 333 3345888888877653
No 28
>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=55.64 E-value=37 Score=22.97 Aligned_cols=44 Identities=25% Similarity=0.434 Sum_probs=24.4
Q ss_pred CCCHHHHHHHHHHHHHhhCHHHHHHHHHHHhCCCCCccHHHHHHHHHHHHHHHcCC
Q 028628 37 KIRKEDMNKLVMNFLVTEGYVDAAEKFRMESGTEPDIDLATITDRMAVKKAVQCGN 92 (206)
Q Consensus 37 ~~~~~~l~~lI~~YL~~~Gy~~ta~~f~~e~~~~~~~~~~~~~~r~~I~~~I~~g~ 92 (206)
.++++.|+.+|-+|..|.|.. .|. .....-....++++.+.+|+
T Consensus 7 ~L~~eTL~nLIeefv~ReGTd---------yG~---~E~sL~~kv~qv~~qL~~G~ 50 (70)
T PF06794_consen 7 QLPPETLNNLIEEFVLREGTD---------YGE---QELSLEEKVEQVKQQLKSGE 50 (70)
T ss_dssp GS-HHHHHHHHHHHHH------------------------HHHHHHHHHHHHHTTS
T ss_pred HCCHHHHHHHHHHHHHccCcc---------cCc---ccccHHHHHHHHHHHHHcCC
Confidence 367888999999999999862 221 12233445677888888885
No 29
>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=55.06 E-value=30 Score=23.81 Aligned_cols=50 Identities=20% Similarity=0.284 Sum_probs=31.5
Q ss_pred HHHHHHHHHHHHhhhcccCCCHHHHHHHHhcCCCCHHHHHHHHHHHHHhhCHH
Q 028628 5 WIVIRQLAEIEAMAMSKKVITREEWEKKLNDVKIRKEDMNKLVMNFLVTEGYV 57 (206)
Q Consensus 5 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~lI~~YL~~~Gy~ 57 (206)
.+.||..-=-.+..-+.+++++.+..+.+. ..+...+. -|-+||.+.||+
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 345665544445566889999999977765 24544444 458999999985
No 30
>KOG4594 consensus Sequence-specific single-stranded-DNA-binding protein [Replication, recombination and repair; Transcription; General function prediction only]
Probab=54.80 E-value=15 Score=31.68 Aligned_cols=29 Identities=24% Similarity=0.379 Sum_probs=25.3
Q ss_pred HHHHHHHHHHHHHhhCHHHHHHHHHHHhC
Q 028628 40 KEDMNKLVMNFLVTEGYVDAAEKFRMESG 68 (206)
Q Consensus 40 ~~~l~~lI~~YL~~~Gy~~ta~~f~~e~~ 68 (206)
++.|..-|.+||+|-|-..+|++|..|..
T Consensus 17 rekLa~YvYEYLlhvgaqksaqtflseir 45 (354)
T KOG4594|consen 17 REKLALYVYEYLLHVGAQKSAQTFLSEIR 45 (354)
T ss_pred HHHHHHHHHHHHHHhhhhhhhhhhHHHHH
Confidence 35678899999999999999999987754
No 31
>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=53.74 E-value=20 Score=21.89 Aligned_cols=30 Identities=30% Similarity=0.602 Sum_probs=22.5
Q ss_pred cccCCCHHHHHHHHhc--CC-CCHHHHHHHHHH
Q 028628 20 SKKVITREEWEKKLND--VK-IRKEDMNKLVMN 49 (206)
Q Consensus 20 ~~~~~~~~~~~~~~~~--~~-~~~~~l~~lI~~ 49 (206)
++|.|+++++...+.. ++ .++..++.++..
T Consensus 1 ~~G~i~~~~~~~~l~~~g~~~~s~~e~~~l~~~ 33 (54)
T PF13833_consen 1 KDGKITREEFRRALSKLGIKDLSEEEVDRLFRE 33 (54)
T ss_dssp SSSEEEHHHHHHHHHHTTSSSSCHHHHHHHHHH
T ss_pred CcCEECHHHHHHHHHHhCCCCCCHHHHHHHHHh
Confidence 4688999999998864 46 777777777643
No 32
>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=52.34 E-value=40 Score=23.06 Aligned_cols=65 Identities=14% Similarity=0.208 Sum_probs=45.9
Q ss_pred CHHHHHHHHHHHHHhhCHHHHHHHHHHHhCCC---CCccHHHHHHHHHHHHHHHc-----C-CHHHHHHHHHhh
Q 028628 39 RKEDMNKLVMNFLVTEGYVDAAEKFRMESGTE---PDIDLATITDRMAVKKAVQC-----G-NVEDAIEKVNDL 103 (206)
Q Consensus 39 ~~~~l~~lI~~YL~~~Gy~~ta~~f~~e~~~~---~~~~~~~~~~r~~I~~~I~~-----g-~i~~Ai~~~~~~ 103 (206)
+...+..+..+|..-.+-..+...|.+..|.. ...+...+..|+.|.+.|.. | +.++|++.++..
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 34456677777766544555778888887753 34455789999999999887 4 778888877653
No 33
>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=52.16 E-value=1.6e+02 Score=25.71 Aligned_cols=78 Identities=14% Similarity=0.191 Sum_probs=50.8
Q ss_pred HHHHHhhCHHHHHHHHHHHhCCCCCccHHHHHHHHHHHHHHHcCCHHHHHHHHHhhCchhhhcccchhhhhHHHHHHHH-
Q 028628 48 MNFLVTEGYVDAAEKFRMESGTEPDIDLATITDRMAVKKAVQCGNVEDAIEKVNDLNPEILDTNPQLFFHLQQQRLIEL- 126 (206)
Q Consensus 48 ~~YL~~~Gy~~ta~~f~~e~~~~~~~~~~~~~~r~~I~~~I~~g~i~~Ai~~~~~~~p~l~~~~s~L~F~L~~q~fiel- 126 (206)
...|+..|....|..+.++.+++ |.-=-.-.|+.++..|+|++-.++.... .|++=|. -|++.
T Consensus 184 i~~li~~~~~k~A~kl~k~Fkv~-----dkrfw~lki~aLa~~~~w~eL~~fa~sk-------KsPIGye----pFv~~~ 247 (319)
T PF04840_consen 184 IRKLIEMGQEKQAEKLKKEFKVP-----DKRFWWLKIKALAENKDWDELEKFAKSK-------KSPIGYE----PFVEAC 247 (319)
T ss_pred HHHHHHCCCHHHHHHHHHHcCCc-----HHHHHHHHHHHHHhcCCHHHHHHHHhCC-------CCCCChH----HHHHHH
Confidence 34566778888888888888875 2223456677888888888877776532 3444333 35553
Q ss_pred HHcCChHHHHHHHHH
Q 028628 127 IRNGKVEEALEFAQE 141 (206)
Q Consensus 127 i~~~~~~~Al~y~r~ 141 (206)
+..|+..+|..|..+
T Consensus 248 ~~~~~~~eA~~yI~k 262 (319)
T PF04840_consen 248 LKYGNKKEASKYIPK 262 (319)
T ss_pred HHCCCHHHHHHHHHh
Confidence 456667777777775
No 34
>KOG1585 consensus Protein required for fusion of vesicles in vesicular transport, gamma-SNAP [Intracellular trafficking, secretion, and vesicular transport]
Probab=48.69 E-value=1.1e+02 Score=26.34 Aligned_cols=69 Identities=13% Similarity=0.161 Sum_probs=55.9
Q ss_pred hcCCCCHHHHHHHHHHHHHhhCHHHHHHHHHHHhCCCCCccHHHHHHHHHHHHHHHcCCHHHHHHHHHh
Q 028628 34 NDVKIRKEDMNKLVMNFLVTEGYVDAAEKFRMESGTEPDIDLATITDRMAVKKAVQCGNVEDAIEKVND 102 (206)
Q Consensus 34 ~~~~~~~~~l~~lI~~YL~~~Gy~~ta~~f~~e~~~~~~~~~~~~~~r~~I~~~I~~g~i~~Ai~~~~~ 102 (206)
++.+.--......|+=||..+.|..+-+.+...+.++.+...+.-.....+...--+||++++-..++.
T Consensus 184 ~~y~~~~k~~va~ilv~L~~~Dyv~aekc~r~~~qip~f~~sed~r~lenLL~ayd~gD~E~~~kvl~s 252 (308)
T KOG1585|consen 184 DAYNSQCKAYVAAILVYLYAHDYVQAEKCYRDCSQIPAFLKSEDSRSLENLLTAYDEGDIEEIKKVLSS 252 (308)
T ss_pred hhcccHHHHHHHHHHHHhhHHHHHHHHHHhcchhcCccccChHHHHHHHHHHHHhccCCHHHHHHHHcC
Confidence 333433344677888999999999999999998999888888888888888888899999999887753
No 35
>PRK04966 hypothetical protein; Provisional
Probab=47.36 E-value=50 Score=22.47 Aligned_cols=45 Identities=22% Similarity=0.419 Sum_probs=31.2
Q ss_pred CCCHHHHHHHHHHHHHhhCHHHHHHHHHHHhCCCCCccHHHHHHHHHHHHHHHcCCH
Q 028628 37 KIRKEDMNKLVMNFLVTEGYVDAAEKFRMESGTEPDIDLATITDRMAVKKAVQCGNV 93 (206)
Q Consensus 37 ~~~~~~l~~lI~~YL~~~Gy~~ta~~f~~e~~~~~~~~~~~~~~r~~I~~~I~~g~i 93 (206)
.++++.|+.+|-+|..|.|- +.|. .....-....++++.+..|+.
T Consensus 7 ~L~~eTL~nLIeefv~ReGT---------dyG~---~E~sl~~kv~qv~~qL~~G~~ 51 (72)
T PRK04966 7 DLAPETLENLIESFVLREGT---------DYGE---HERSLEQKVADVKRQLQSGEA 51 (72)
T ss_pred hCCHHHHHHHHHHHHhccCc---------cCCc---ccccHHHHHHHHHHHHHcCCE
Confidence 36788999999999999885 2332 123344566778888888863
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=47.08 E-value=61 Score=30.46 Aligned_cols=72 Identities=19% Similarity=0.185 Sum_probs=47.0
Q ss_pred HHHhhhcccCCCHHHHHHHHhcCCCCHHHHHHHHHHHHHhhCHHHHHHHHHHHhCCCCCccHHHHHHHHHHHHHHHcCCH
Q 028628 14 IEAMAMSKKVITREEWEKKLNDVKIRKEDMNKLVMNFLVTEGYVDAAEKFRMESGTEPDIDLATITDRMAVKKAVQCGNV 93 (206)
Q Consensus 14 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~lI~~YL~~~Gy~~ta~~f~~e~~~~~~~~~~~~~~r~~I~~~I~~g~i 93 (206)
++|.. .++...+.-....+..+++..+.-..=+...+...|+.++++..++-.|. .++.+|++
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 35555689999999999988877666666888889999999998887773 24556777
Q ss_pred HHHHHHHHh
Q 028628 94 EDAIEKVND 102 (206)
Q Consensus 94 ~~Ai~~~~~ 102 (206)
.+|+.|...
T Consensus 442 g~AL~~~~r 450 (566)
T PF07575_consen 442 GEALSWFIR 450 (566)
T ss_dssp HHHHHHHH-
T ss_pred HHHHHHHHH
Confidence 777777644
No 37
>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=46.49 E-value=1.4e+02 Score=23.44 Aligned_cols=106 Identities=10% Similarity=-0.041 Sum_probs=72.1
Q ss_pred HHHHHHHHHHHhhCHHHHHHHHHHHhCCCCCccHH-HHHHHHHHHHHHHcCCHHHHHHHHHhhCchhhhc-ccchhhhhH
Q 028628 42 DMNKLVMNFLVTEGYVDAAEKFRMESGTEPDIDLA-TITDRMAVKKAVQCGNVEDAIEKVNDLNPEILDT-NPQLFFHLQ 119 (206)
Q Consensus 42 ~l~~lI~~YL~~~Gy~~ta~~f~~e~~~~~~~~~~-~~~~r~~I~~~I~~g~i~~Ai~~~~~~~p~l~~~-~s~L~F~L~ 119 (206)
....-+++|+.+.|-.+.|..-....--....... .--....|+-+|..|||..+...+++....+.+. +......|.
T Consensus 37 ~~~~~l~~~~~~~Gd~~~A~k~y~~~~~~~~~~~~~id~~l~~irv~i~~~d~~~v~~~i~ka~~~~~~~~d~~~~nrlk 116 (177)
T PF10602_consen 37 MALEDLADHYCKIGDLEEALKAYSRARDYCTSPGHKIDMCLNVIRVAIFFGDWSHVEKYIEKAESLIEKGGDWERRNRLK 116 (177)
T ss_pred HHHHHHHHHHHHhhhHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhccchHHHHHHHH
Confidence 34567899999999777764444333211111111 1123577899999999999999998876555442 356777899
Q ss_pred HHHHHHHHHcCChHHHHHHHHHhcCccc
Q 028628 120 QQRLIELIRNGKVEEALEFAQEELAPRG 147 (206)
Q Consensus 120 ~q~fieli~~~~~~~Al~y~r~~l~~~~ 147 (206)
+..-+-.+..++..+|-+..-+-.+-|.
T Consensus 117 ~~~gL~~l~~r~f~~AA~~fl~~~~t~~ 144 (177)
T PF10602_consen 117 VYEGLANLAQRDFKEAAELFLDSLSTFT 144 (177)
T ss_pred HHHHHHHHHhchHHHHHHHHHccCcCCC
Confidence 9999999999999888666665554443
No 38
>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=46.00 E-value=36 Score=27.76 Aligned_cols=30 Identities=23% Similarity=0.548 Sum_probs=27.2
Q ss_pred HHHHHHHHHHHHhhCHHHHHHHHHHHhCCC
Q 028628 41 EDMNKLVMNFLVTEGYVDAAEKFRMESGTE 70 (206)
Q Consensus 41 ~~l~~lI~~YL~~~Gy~~ta~~f~~e~~~~ 70 (206)
...-|+++-||-.+||.++.+++.+.+++.
T Consensus 166 ~eaiRlcLKHlRq~~y~~aFesLqk~t~v~ 195 (199)
T PF06588_consen 166 KEAIRLCLKHLRQRGYLEAFESLQKQTGVQ 195 (199)
T ss_pred HHHHHHHHHHhhhcCchhHHHHHHHHcCCC
Confidence 456699999999999999999999999975
No 39
>PF13838 Clathrin_H_link: Clathrin-H-link; PDB: 2XZG_A 3GD1_I 1BPO_C 1C9I_B 1C9L_A.
Probab=45.08 E-value=34 Score=22.84 Aligned_cols=40 Identities=30% Similarity=0.473 Sum_probs=27.1
Q ss_pred hhHHHHHHHHHHcCChHHHHHHHHHhcCccc-cCChhHHHHHH
Q 028628 117 HLQQQRLIELIRNGKVEEALEFAQEELAPRG-EENQSFLEELE 158 (206)
Q Consensus 117 ~L~~q~fieli~~~~~~~Al~y~r~~l~~~~-~~~~~~~~~i~ 158 (206)
.|..++|-+++..|+..+|-..|-+ +|-+ -..++.+.+++
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 5789999999999999999888874 3322 12344455554
No 40
>PRK02289 4-oxalocrotonate tautomerase; Provisional
Probab=44.90 E-value=32 Score=21.93 Aligned_cols=26 Identities=19% Similarity=0.118 Sum_probs=23.6
Q ss_pred ChhhHHHHHHHHHHHHHhhCCCCCCC
Q 028628 179 DISQRLKTASEVNAAILTSQSHEKGD 204 (206)
Q Consensus 179 ~~~~r~~la~~vN~aiL~~~~~~~~~ 204 (206)
+.+++.++++.|..++-+..|.|.++
T Consensus 13 s~EqK~~L~~~it~a~~~~~~~p~~~ 38 (60)
T PRK02289 13 SQEQKNALAREVTEVVSRIAKAPKEA 38 (60)
T ss_pred CHHHHHHHHHHHHHHHHHHhCcCcce
Confidence 68999999999999999999998753
No 41
>COG5443 FlbT Flagellar biosynthesis regulator FlbT [Cell motility and secretion]
Probab=44.89 E-value=40 Score=25.68 Aligned_cols=55 Identities=20% Similarity=0.207 Sum_probs=45.0
Q ss_pred HhhCHHHHHHHHHHHhCC--CCCccHHHHHHHHHHHHHHHcCCHHHHHHHHHhhCch
Q 028628 52 VTEGYVDAAEKFRMESGT--EPDIDLATITDRMAVKKAVQCGNVEDAIEKVNDLNPE 106 (206)
Q Consensus 52 ~~~Gy~~ta~~f~~e~~~--~~~~~~~~~~~r~~I~~~I~~g~i~~Ai~~~~~~~p~ 106 (206)
.-.|-.++...|.+..++ ..+.+.+.+...+.|-.++.+|..-+|++.+...+|-
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 335777777888877653 2456778999999999999999999999999999984
No 42
>PRK10564 maltose regulon periplasmic protein; Provisional
Probab=44.84 E-value=25 Score=30.55 Aligned_cols=24 Identities=29% Similarity=0.483 Sum_probs=21.5
Q ss_pred HHHHHHHHHHcCCHHHHHHHHHhh
Q 028628 80 DRMAVKKAVQCGNVEDAIEKVNDL 103 (206)
Q Consensus 80 ~r~~I~~~I~~g~i~~Ai~~~~~~ 103 (206)
-.+.|++++..||++.|+.+++|-
T Consensus 260 y~~aI~~AVk~gDi~KAL~LldEA 283 (303)
T PRK10564 260 FNQAIKQAVKKGDVDKALKLLDEA 283 (303)
T ss_pred HHHHHHHHHHcCCHHHHHHHHHHH
Confidence 357899999999999999999875
No 43
>KOG2659 consensus LisH motif-containing protein [Cytoskeleton]
Probab=44.50 E-value=1.3e+02 Score=25.15 Aligned_cols=67 Identities=15% Similarity=0.220 Sum_probs=51.8
Q ss_pred CHHHHH-HHHHHHHHhhCHHHHHHHHHHHhCC---CCCccHHHHHHHHHHHHHHHcCCHHHHHHHHHhhCc
Q 028628 39 RKEDMN-KLVMNFLVTEGYVDAAEKFRMESGT---EPDIDLATITDRMAVKKAVQCGNVEDAIEKVNDLNP 105 (206)
Q Consensus 39 ~~~~l~-~lI~~YL~~~Gy~~ta~~f~~e~~~---~~~~~~~~~~~r~~I~~~I~~g~i~~Ai~~~~~~~p 105 (206)
+.+.++ |+....++..|-++.|-.+.....= +...+....-..++....|++|.+++|++.++..-.
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 333444 7888889999999999988887762 122335677788899999999999999999987654
No 44
>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=43.06 E-value=2.9e+02 Score=25.93 Aligned_cols=115 Identities=17% Similarity=0.209 Sum_probs=0.0
Q ss_pred HHHHHHHHHHHhhhcccCCCHHHHHHHHhcCCCCHHH---HHHHHHHHHHhhCHHHHHHHHHHHhCCCCCccHHHHHHHH
Q 028628 6 IVIRQLAEIEAMAMSKKVITREEWEKKLNDVKIRKED---MNKLVMNFLVTEGYVDAAEKFRMESGTEPDIDLATITDRM 82 (206)
Q Consensus 6 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---l~~lI~~YL~~~Gy~~ta~~f~~e~~~~~~~~~~~~~~r~ 82 (206)
++..-+.+.....-.++.++-.. ....-++.. +.-.+++|.-+.|..+.|-.+..++=--.+...+.+-.+-
T Consensus 161 ~i~~l~~~~~~~l~~~~~~~~~~-----~~~~~~p~~~lw~~~~lAqhyd~~g~~~~Al~~Id~aI~htPt~~ely~~Ka 235 (517)
T PF12569_consen 161 IIESLVEEYVNSLESNGSFSNGD-----DEEKEPPSTLLWTLYFLAQHYDYLGDYEKALEYIDKAIEHTPTLVELYMTKA 235 (517)
T ss_pred HHHHHHHHHHHhhcccCCCCCcc-----ccccCCchHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHhcCCCcHHHHHHHH
Q ss_pred HHHHHHHcCCHHHHHHHHHhhCchhhhcccchhhhhHHH-HHHH------HHHcCChHHHHHHH
Q 028628 83 AVKKAVQCGNVEDAIEKVNDLNPEILDTNPQLFFHLQQQ-RLIE------LIRNGKVEEALEFA 139 (206)
Q Consensus 83 ~I~~~I~~g~i~~Ai~~~~~~~p~l~~~~s~L~F~L~~q-~fie------li~~~~~~~Al~y~ 139 (206)
+|..+ .|++.+|.++++.-+ .|..+ +||. ++|.|.+++|.+.+
T Consensus 236 rilKh--~G~~~~Aa~~~~~Ar------------~LD~~DRyiNsK~aKy~LRa~~~e~A~~~~ 285 (517)
T PF12569_consen 236 RILKH--AGDLKEAAEAMDEAR------------ELDLADRYINSKCAKYLLRAGRIEEAEKTA 285 (517)
T ss_pred HHHHH--CCCHHHHHHHHHHHH------------hCChhhHHHHHHHHHHHHHCCCHHHHHHHH
No 45
>PF10827 DUF2552: Protein of unknown function (DUF2552) ; InterPro: IPR020157 This entry contains proteins with no known function.
Probab=42.38 E-value=18 Score=24.52 Aligned_cols=18 Identities=22% Similarity=0.281 Sum_probs=15.1
Q ss_pred CCHHHHHHHHHhhCchhh
Q 028628 91 GNVEDAIEKVNDLNPEIL 108 (206)
Q Consensus 91 g~i~~Ai~~~~~~~p~l~ 108 (206)
-.++.|++|+.+|.|.+-
T Consensus 59 ~tld~Ai~Wi~e~M~~iT 76 (79)
T PF10827_consen 59 PTLDLAIAWIGEHMPHIT 76 (79)
T ss_pred ccHHHHHHHHHhcccchh
Confidence 368999999999998763
No 46
>PF14276 DUF4363: Domain of unknown function (DUF4363)
Probab=41.99 E-value=51 Score=24.09 Aligned_cols=49 Identities=12% Similarity=0.163 Sum_probs=38.1
Q ss_pred HHHHHHHHHHHHHcCCHHHHHHHHHhhCchhhhcccchhhhhHHHHHHH
Q 028628 77 TITDRMAVKKAVQCGNVEDAIEKVNDLNPEILDTNPQLFFHLQQQRLIE 125 (206)
Q Consensus 77 ~~~~r~~I~~~I~~g~i~~Ai~~~~~~~p~l~~~~s~L~F~L~~q~fie 125 (206)
.-.....+.+.|.++||+.|.+.+.+....-.+....+.|.+..+++=+
T Consensus 28 i~~~l~~i~~~i~~~dW~~A~~~~~~l~~~W~k~~~~~~~~~~h~eid~ 76 (121)
T PF14276_consen 28 IEEQLEQIEEAIENEDWEKAYKETEELEKEWDKNKKRWSILIEHQEIDN 76 (121)
T ss_pred HHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhhchheeeeecHHHHHH
Confidence 3345677999999999999999988877666666677788887777644
No 47
>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=41.82 E-value=48 Score=20.67 Aligned_cols=30 Identities=10% Similarity=0.093 Sum_probs=22.3
Q ss_pred hcccCCCHHHHHHHHhcCCCCHHHHHHHHH
Q 028628 19 MSKKVITREEWEKKLNDVKIRKEDMNKLVM 48 (206)
Q Consensus 19 ~~~~~~~~~~~~~~~~~~~~~~~~l~~lI~ 48 (206)
-++|.|+.+++.+.+.....+...+..++.
T Consensus 11 ~~~G~i~~~el~~~l~~~g~~~~~~~~i~~ 40 (67)
T cd00052 11 DGDGLISGDEARPFLGKSGLPRSVLAQIWD 40 (67)
T ss_pred CCCCcCcHHHHHHHHHHcCCCHHHHHHHHH
Confidence 357899999998888777666666666543
No 48
>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=40.95 E-value=53 Score=22.80 Aligned_cols=29 Identities=17% Similarity=0.300 Sum_probs=21.8
Q ss_pred HHHHHHHHHHHHHHcCCHHHHHHHHHhhC
Q 028628 76 ATITDRMAVKKAVQCGNVEDAIEKVNDLN 104 (206)
Q Consensus 76 ~~~~~r~~I~~~I~~g~i~~Ai~~~~~~~ 104 (206)
.....-..|.++|.+||.+.|.+.+.+|.
T Consensus 95 ~~~~~h~~i~~ai~~~d~~~a~~~~~~h~ 123 (125)
T PF07729_consen 95 RSLEEHREIIDAIRAGDPEAAREALRQHI 123 (125)
T ss_dssp HHHHHHHHHHHHHHTT-HHHHHHHHHHHH
T ss_pred hhHHHHHHHHHHHHcCCHHHHHHHHHHHh
Confidence 46667778888888888888888887663
No 49
>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=39.89 E-value=40 Score=17.53 Aligned_cols=17 Identities=12% Similarity=0.253 Sum_probs=12.3
Q ss_pred HHHHHcCCHHHHHHHHH
Q 028628 85 KKAVQCGNVEDAIEKVN 101 (206)
Q Consensus 85 ~~~I~~g~i~~Ai~~~~ 101 (206)
+.+...|++++|..++.
T Consensus 9 ~~~~~~G~~~eA~~~l~ 25 (26)
T PF07721_consen 9 RALLAQGDPDEAERLLR 25 (26)
T ss_pred HHHHHcCCHHHHHHHHh
Confidence 34567788888887765
No 50
>PF13934 ELYS: Nuclear pore complex assembly
Probab=39.55 E-value=2.1e+02 Score=23.46 Aligned_cols=67 Identities=24% Similarity=0.367 Sum_probs=42.5
Q ss_pred HHcCCHHHHHHHHHhhCchhhhcccchhhhhHHHHHHH-HHHcCChHHHHHHHHHhcCccccCChhHHHHHHHHHhhhcc
Q 028628 88 VQCGNVEDAIEKVNDLNPEILDTNPQLFFHLQQQRLIE-LIRNGKVEEALEFAQEELAPRGEENQSFLEELERTVALLAF 166 (206)
Q Consensus 88 I~~g~i~~Ai~~~~~~~p~l~~~~s~L~F~L~~q~fie-li~~~~~~~Al~y~r~~l~~~~~~~~~~~~~i~~l~~LLay 166 (206)
+=.|+++.|+..+.. |.+... +..+.+. +++.|+...|+.|.|.--++... .+.+.-.+.+|+.
T Consensus 89 LD~~~~~~A~~~L~~--ps~~~~--------~~~~Il~~L~~~~~~~lAL~y~~~~~p~l~s-----~~~~~~~~~~La~ 153 (226)
T PF13934_consen 89 LDHGDFEEALELLSH--PSLIPW--------FPDKILQALLRRGDPKLALRYLRAVGPPLSS-----PEALTLYFVALAN 153 (226)
T ss_pred hChHhHHHHHHHhCC--CCCCcc--------cHHHHHHHHHHCCChhHHHHHHHhcCCCCCC-----HHHHHHHHHHHHc
Confidence 346899999999843 433211 1122444 45578899999999976555543 2556666667776
Q ss_pred cCC
Q 028628 167 EDV 169 (206)
Q Consensus 167 ~~~ 169 (206)
...
T Consensus 154 ~~v 156 (226)
T PF13934_consen 154 GLV 156 (226)
T ss_pred CCH
Confidence 653
No 51
>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=39.35 E-value=1.2e+02 Score=29.45 Aligned_cols=28 Identities=14% Similarity=0.138 Sum_probs=22.2
Q ss_pred HHHHHHHHHHHHHcCCHHHHHHHHHhhC
Q 028628 77 TITDRMAVKKAVQCGNVEDAIEKVNDLN 104 (206)
Q Consensus 77 ~~~~r~~I~~~I~~g~i~~Ai~~~~~~~ 104 (206)
.-...+.|-.+|+.|++++|.+||.+.-
T Consensus 133 e~~~~~~i~~llR~G~~~eA~~lc~~~g 160 (697)
T PF04121_consen 133 ERALLKYIFELLRAGRIEEAQELCRERG 160 (697)
T ss_dssp HHHHHHHHHHHHHTT-HHHHHHHHHHTT
T ss_pred HHHHHHHHHHHHHCCCHHHHHHHHHHCC
Confidence 4455678889999999999999998753
No 52
>smart00027 EH Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
Probab=38.91 E-value=43 Score=23.28 Aligned_cols=31 Identities=10% Similarity=-0.019 Sum_probs=25.6
Q ss_pred hcccCCCHHHHHHHHhcCCCCHHHHHHHHHH
Q 028628 19 MSKKVITREEWEKKLNDVKIRKEDMNKLVMN 49 (206)
Q Consensus 19 ~~~~~~~~~~~~~~~~~~~~~~~~l~~lI~~ 49 (206)
.++|.|+.+++.+.+....++...+.+++..
T Consensus 22 d~~G~Is~~el~~~l~~~~~~~~ev~~i~~~ 52 (96)
T smart00027 22 NQDGTVTGAQAKPILLKSGLPQTLLAKIWNL 52 (96)
T ss_pred CCCCeEeHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 3678999999999998888888888877653
No 53
>KOG0292 consensus Vesicle coat complex COPI, alpha subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=38.66 E-value=15 Score=36.46 Aligned_cols=49 Identities=29% Similarity=0.537 Sum_probs=35.9
Q ss_pred HHHHHHHHHHHhhCHHHHHHHHHHHhCCCCCccHHHHHHHHHHHHHHHcCCHHHHHHHHHhh
Q 028628 42 DMNKLVMNFLVTEGYVDAAEKFRMESGTEPDIDLATITDRMAVKKAVQCGNVEDAIEKVNDL 103 (206)
Q Consensus 42 ~l~~lI~~YL~~~Gy~~ta~~f~~e~~~~~~~~~~~~~~r~~I~~~I~~g~i~~Ai~~~~~~ 103 (206)
.+-+.|..||...||-+.|--|.++.... ..-++..||++.|++.+.+.
T Consensus 621 LvGqaiIaYLqKkgypeiAL~FVkD~~tR-------------F~LaLe~gnle~ale~akkl 669 (1202)
T KOG0292|consen 621 LVGQAIIAYLQKKGYPEIALHFVKDERTR-------------FELALECGNLEVALEAAKKL 669 (1202)
T ss_pred cccHHHHHHHHhcCCcceeeeeecCcchh-------------eeeehhcCCHHHHHHHHHhc
Confidence 34678899999999999999998876542 33456666777666666544
No 54
>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=37.82 E-value=2.7e+02 Score=24.20 Aligned_cols=90 Identities=19% Similarity=0.233 Sum_probs=64.5
Q ss_pred HHHhcCCCCHHHHHHHHHHHHHhhCHHHHHHHHHHHhCCCCCccHHHHHHHHHHHHHHHcCCHHHHHHHHHhhCchhhhc
Q 028628 31 KKLNDVKIRKEDMNKLVMNFLVTEGYVDAAEKFRMESGTEPDIDLATITDRMAVKKAVQCGNVEDAIEKVNDLNPEILDT 110 (206)
Q Consensus 31 ~~~~~~~~~~~~l~~lI~~YL~~~Gy~~ta~~f~~e~~~~~~~~~~~~~~r~~I~~~I~~g~i~~Ai~~~~~~~p~l~~~ 110 (206)
+.-...+|+....-++.+.=|...|.++-...|.++-. ++...++| |..++..|+..+|..++....+
T Consensus 198 kl~k~Fkv~dkrfw~lki~aLa~~~~w~eL~~fa~skK--sPIGyepF-----v~~~~~~~~~~eA~~yI~k~~~----- 265 (319)
T PF04840_consen 198 KLKKEFKVPDKRFWWLKIKALAENKDWDELEKFAKSKK--SPIGYEPF-----VEACLKYGNKKEASKYIPKIPD----- 265 (319)
T ss_pred HHHHHcCCcHHHHHHHHHHHHHhcCCHHHHHHHHhCCC--CCCChHHH-----HHHHHHCCCHHHHHHHHHhCCh-----
Confidence 33445589999999999999999999999999998633 33444433 6678899999999999976221
Q ss_pred ccchhhhhHHHHHHHHHHcCChHHHHHHHHH
Q 028628 111 NPQLFFHLQQQRLIELIRNGKVEEALEFAQE 141 (206)
Q Consensus 111 ~s~L~F~L~~q~fieli~~~~~~~Al~y~r~ 141 (206)
...+..- ++.|+..+|++.|.+
T Consensus 266 ~~rv~~y---------~~~~~~~~A~~~A~~ 287 (319)
T PF04840_consen 266 EERVEMY---------LKCGDYKEAAQEAFK 287 (319)
T ss_pred HHHHHHH---------HHCCCHHHHHHHHHH
Confidence 1223332 456777777777664
No 55
>PF12174 RST: RCD1-SRO-TAF4 (RST) plant domain; InterPro: IPR022003 This domain is found in many plant proteins including SROs and RCD1s; it is required for interaction with multiple plant transcription factors.
Probab=37.52 E-value=35 Score=22.98 Aligned_cols=24 Identities=33% Similarity=0.494 Sum_probs=18.8
Q ss_pred HHHHhhhcccCCCHHHHHHHHhcC
Q 028628 13 EIEAMAMSKKVITREEWEKKLNDV 36 (206)
Q Consensus 13 ~~~~~~~~~~~~~~~~~~~~~~~~ 36 (206)
.--|..+.++.|+|++|.+.+..+
T Consensus 31 ~~~Y~~~k~~kIsR~~fvr~lR~I 54 (70)
T PF12174_consen 31 QKHYEEFKKKKISREEFVRKLRQI 54 (70)
T ss_pred HHHHHHHHHCCCCHHHHHHHHHHH
Confidence 345778899999999998877443
No 56
>KOG0263 consensus Transcription initiation factor TFIID, subunit TAF5 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=35.77 E-value=61 Score=31.42 Aligned_cols=35 Identities=23% Similarity=0.424 Sum_probs=30.2
Q ss_pred CCCCHHHHHHHHHHHHHhhCHHHHHHHHHHHhCCC
Q 028628 36 VKIRKEDMNKLVMNFLVTEGYVDAAEKFRMESGTE 70 (206)
Q Consensus 36 ~~~~~~~l~~lI~~YL~~~Gy~~ta~~f~~e~~~~ 70 (206)
-.++.+.+|+.+.+||...||..|-..+..|.++.
T Consensus 17 ~~~~~~~~n~~v~~yl~~~~y~~te~~l~~e~~l~ 51 (707)
T KOG0263|consen 17 GGSHTRDLNRIVLEYLRKKKYSRTEEMLRQEANLP 51 (707)
T ss_pred cCcchHHHHHHHHHHHhhhcccccchhhhhhhccc
Confidence 34566788999999999999999999999998753
No 57
>KOG1961 consensus Vacuolar sorting protein VPS52/suppressor of actin Sac2 [Intracellular trafficking, secretion, and vesicular transport; Cytoskeleton]
Probab=34.84 E-value=3.2e+02 Score=26.27 Aligned_cols=118 Identities=13% Similarity=0.125 Sum_probs=71.6
Q ss_pred CCHHHHHHHHhcCCCCHHHHHHHHHHHHHhhCHHHHHHHHHHHhCCCC----CccHHHHHHHHHHHHHHHcCCHHHHHHH
Q 028628 24 ITREEWEKKLNDVKIRKEDMNKLVMNFLVTEGYVDAAEKFRMESGTEP----DIDLATITDRMAVKKAVQCGNVEDAIEK 99 (206)
Q Consensus 24 ~~~~~~~~~~~~~~~~~~~l~~lI~~YL~~~Gy~~ta~~f~~e~~~~~----~~~~~~~~~r~~I~~~I~~g~i~~Ai~~ 99 (206)
..+....+.++++-|+++.++-++-.-..+.+|.++...+........ .-+......-..+.+-++..-++..-.|
T Consensus 131 ~v~s~Ls~fVdd~iVpp~lI~~I~~g~vne~~f~~~LeeL~~Kl~~v~~dq~~k~a~a~~Dv~~lLdkLR~KAi~kir~~ 210 (683)
T KOG1961|consen 131 AVESKLSQFVDDLIVPPELIKTIVDGDVNEPEFLEALEELSHKLKLVELDQSNKDAKALKDVEPLLDKLRLKAIEKIREF 210 (683)
T ss_pred HHHHHHHHHhccccCCHHHHHHHHcCCCCchHHHHHHHHHHHHHHhhhhhhhccchhhhhhHHHHHHHHHHHHHHHHHHH
Confidence 345667788899999999999998888888899999888877654321 1122233334444444444444444444
Q ss_pred HHhhCchhhhcccch-----hhhhHHHHHHHHHHcCChHHHHHHHHH
Q 028628 100 VNDLNPEILDTNPQL-----FFHLQQQRLIELIRNGKVEEALEFAQE 141 (206)
Q Consensus 100 ~~~~~p~l~~~~s~L-----~F~L~~q~fieli~~~~~~~Al~y~r~ 141 (206)
+-+.--.+.+..++. .=.|.++.|.+.+..++..-|++.-+.
T Consensus 211 IlqkI~~fRkp~tn~qi~~Q~~LLK~k~~y~FL~~n~r~~A~Elr~a 257 (683)
T KOG1961|consen 211 ILQKIKAFRKPMTNYQIPQQHALLKYKFFYEFLLENNRELALELRDA 257 (683)
T ss_pred HHHHHHHHhCCCCCcchHHHHHHHHHHHHHHHHHhccHHHHHHHHHH
Confidence 433222222222221 224666777888998888777765554
No 58
>KOG1156 consensus N-terminal acetyltransferase [Chromatin structure and dynamics]
Probab=34.65 E-value=4.4e+02 Score=25.63 Aligned_cols=112 Identities=19% Similarity=0.296 Sum_probs=69.5
Q ss_pred HHHHHHHHHHHHHcCCHHHHHHHHHhhCchhhhcccchhhhhHHHHHHHHHHcCChHHHHHHHHHhcCccccCChhHHHH
Q 028628 77 TITDRMAVKKAVQCGNVEDAIEKVNDLNPEILDTNPQLFFHLQQQRLIELIRNGKVEEALEFAQEELAPRGEENQSFLEE 156 (206)
Q Consensus 77 ~~~~r~~I~~~I~~g~i~~Ai~~~~~~~p~l~~~~s~L~F~L~~q~fieli~~~~~~~Al~y~r~~l~~~~~~~~~~~~~ 156 (206)
......++...+..|..+.|++-+..+.|.+.. .+.|...+-.+.. +.+..++|+...+..+.+..+.. ++...
T Consensus 185 se~~Ly~n~i~~E~g~~q~ale~L~~~e~~i~D---kla~~e~ka~l~~--kl~~lEeA~~~y~~Ll~rnPdn~-~Yy~~ 258 (700)
T KOG1156|consen 185 SELLLYQNQILIEAGSLQKALEHLLDNEKQIVD---KLAFEETKADLLM--KLGQLEEAVKVYRRLLERNPDNL-DYYEG 258 (700)
T ss_pred HHHHHHHHHHHHHcccHHHHHHHHHhhhhHHHH---HHHHhhhHHHHHH--HHhhHHhHHHHHHHHHhhCchhH-HHHHH
Confidence 445566777888999999999999999887764 4555555555443 34668899999998887765433 23344
Q ss_pred HHHHHh--------h-hcccC-----C-CCC----chhhhcChhhHHHHHHHHHHHH
Q 028628 157 LERTVA--------L-LAFED-----V-SNC----PVGDLLDISQRLKTASEVNAAI 194 (206)
Q Consensus 157 i~~l~~--------L-Lay~~-----~-~~s----p~~~ll~~~~r~~la~~vN~ai 194 (206)
++.+++ + .+|.. | ..+ |..-+-+.+-+..+...++..+
T Consensus 259 l~~~lgk~~d~~~~lk~ly~~ls~~y~r~e~p~Rlplsvl~~eel~~~vdkyL~~~l 315 (700)
T KOG1156|consen 259 LEKALGKIKDMLEALKALYAILSEKYPRHECPRRLPLSVLNGEELKEIVDKYLRPLL 315 (700)
T ss_pred HHHHHHHHhhhHHHHHHHHHHHhhcCcccccchhccHHHhCcchhHHHHHHHHHHHh
Confidence 444443 1 11211 1 223 3444445666666666666654
No 59
>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=34.29 E-value=66 Score=30.34 Aligned_cols=90 Identities=10% Similarity=0.124 Sum_probs=57.7
Q ss_pred HHHHHHHHHHhhhcccCCCHHHHHHHHhcCCC------CHHHHHHHHHHHHHhhCHHHHHHHHHHHhCCCCCccHHHHHH
Q 028628 7 VIRQLAEIEAMAMSKKVITREEWEKKLNDVKI------RKEDMNKLVMNFLVTEGYVDAAEKFRMESGTEPDIDLATITD 80 (206)
Q Consensus 7 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------~~~~l~~lI~~YL~~~Gy~~ta~~f~~e~~~~~~~~~~~~~~ 80 (206)
|-|.+.+...-+-++-++++...+.....++. +-+.|.+.|..|=...-..++|.+|.+|.|+.+..+...+-.
T Consensus 556 qrRefd~lr~eIl~sdt~~~~~~k~q~sd~~~~~~l~~~adtLke~i~~Hp~~EKl~evA~~~~Rea~Ltkl~~~t~~lL 635 (674)
T PF09052_consen 556 QRREFDGLRKEILPSDTEKSIALKAQCSDINIHPELKEKADTLKEVITNHPQYEKLAEVARQFAREAGLTKLKGETDYLL 635 (674)
T ss_dssp HHHHHHHHHHHHS-SSHHHHHHHHHHHGGGGG-HHHHHHHHHHHHHHHT-TCHHHHHHHHHHHHHHH-CCCCGGGS-HHH
T ss_pred HHHHHHHHHhhcCCcchhHHHHHHhhhcccccchHHHHHHHHHHHHHhcCchHHHHHHHHHHHHHhhCcccccCcchHHH
Confidence 45666777777777777888877777777765 346788889999888889999999999999876544322222
Q ss_pred HHHHHHHHHcCCHHHH
Q 028628 81 RMAVKKAVQCGNVEDA 96 (206)
Q Consensus 81 r~~I~~~I~~g~i~~A 96 (206)
-..|-..+-+++|..+
T Consensus 636 s~~Ldgl~~d~~~r~~ 651 (674)
T PF09052_consen 636 SDDLDGLIGDNDWRAG 651 (674)
T ss_dssp HHHHHHHSTT-GGG--
T ss_pred HhhHhhhccCcccccC
Confidence 2233344455555443
No 60
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=32.30 E-value=1.1e+02 Score=20.00 Aligned_cols=50 Identities=14% Similarity=0.238 Sum_probs=35.6
Q ss_pred CCHHHHHHHHHHHHHhhCH-HHHHHHHHHHhCCCCCccHHHHHHHHHHHHHHHcCCH
Q 028628 38 IRKEDMNKLVMNFLVTEGY-VDAAEKFRMESGTEPDIDLATITDRMAVKKAVQCGNV 93 (206)
Q Consensus 38 ~~~~~l~~lI~~YL~~~Gy-~~ta~~f~~e~~~~~~~~~~~~~~r~~I~~~I~~g~i 93 (206)
++++.+.+-|+++|..+|- --++..++++.|+.. -..++.+..+..+|-+
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 3456678899999999986 368999999999863 1344555555666654
No 61
>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=31.90 E-value=1.5e+02 Score=20.46 Aligned_cols=28 Identities=18% Similarity=0.450 Sum_probs=21.3
Q ss_pred ccCCCHHHHHHHHh-----cCCCCHHHHHHHHH
Q 028628 21 KKVITREEWEKKLN-----DVKIRKEDMNKLVM 48 (206)
Q Consensus 21 ~~~~~~~~~~~~~~-----~~~~~~~~l~~lI~ 48 (206)
+++|+.+|+.+.+. +.++++..+.+++.
T Consensus 26 ~g~Is~~EL~~~l~~~~~lg~k~t~~ev~~m~~ 58 (88)
T cd05029 26 KNTLSKKELKELIQKELTIGSKLQDAEIAKLME 58 (88)
T ss_pred CCEECHHHHHHHHHHHHhcCCCCCHHHHHHHHH
Confidence 67999999988884 55667777777653
No 62
>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=31.41 E-value=70 Score=19.59 Aligned_cols=19 Identities=26% Similarity=0.226 Sum_probs=16.3
Q ss_pred ChhhHHHHHHHHHHHHHhh
Q 028628 179 DISQRLKTASEVNAAILTS 197 (206)
Q Consensus 179 ~~~~r~~la~~vN~aiL~~ 197 (206)
.++.|+.+|+.|..|+..+
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 4799999999999999864
No 63
>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=31.28 E-value=1.9e+02 Score=20.30 Aligned_cols=54 Identities=17% Similarity=0.231 Sum_probs=41.3
Q ss_pred HHHHHHHHHhhCHHHHHHHHHHHhCCCCCccHHHHHHHHHHHHHHHcCCHHHHHHH
Q 028628 44 NKLVMNFLVTEGYVDAAEKFRMESGTEPDIDLATITDRMAVKKAVQCGNVEDAIEK 99 (206)
Q Consensus 44 ~~lI~~YL~~~Gy~~ta~~f~~e~~~~~~~~~~~~~~r~~I~~~I~~g~i~~Ai~~ 99 (206)
.+.+.+.|+..+-.+.+..|..+.=.+ ...+.++.|..|...+.+|....+|+-
T Consensus 5 ~~~~~~~~~~~~~~~~~~~~~~~l~t~--~e~~~Ls~R~~I~~ll~~G~S~~eIA~ 58 (88)
T TIGR02531 5 LDELFDAILTLKNREECYRFFDDIATI--NEIQSLAQRLQVAKMLKQGKTYSDIEA 58 (88)
T ss_pred HHHHHHHHHhCCCHHHHHHHHHHhCCH--HHHHhhhHHHHHHHHHHCCCCHHHHHH
Confidence 566778888888888999988876542 344568889999999999976666644
No 64
>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.
Probab=31.15 E-value=47 Score=21.76 Aligned_cols=43 Identities=19% Similarity=0.390 Sum_probs=27.0
Q ss_pred HHHHHhhhcccCCCHHHHHHHHhcCCCCHHHHHHHHHHHHHhhCHHH
Q 028628 12 AEIEAMAMSKKVITREEWEKKLNDVKIRKEDMNKLVMNFLVTEGYVD 58 (206)
Q Consensus 12 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~lI~~YL~~~Gy~~ 58 (206)
.+|...+-.++.+|..++.+. ++++++.+..+ +++|++.||+.
T Consensus 3 ~~i~~~l~~~~~~S~~eLa~~---~~~s~~~ve~m-L~~l~~kG~I~ 45 (69)
T PF09012_consen 3 QEIRDYLRERGRVSLAELARE---FGISPEAVEAM-LEQLIRKGYIR 45 (69)
T ss_dssp HHHHHHHHHS-SEEHHHHHHH---TT--HHHHHHH-HHHHHCCTSCE
T ss_pred HHHHHHHHHcCCcCHHHHHHH---HCcCHHHHHHH-HHHHHHCCcEE
Confidence 344445556777888888554 57777666554 58889998864
No 65
>PRK09263 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=31.09 E-value=1.8e+02 Score=28.45 Aligned_cols=28 Identities=21% Similarity=0.321 Sum_probs=24.9
Q ss_pred CCCHHHHHHHHHHHHHhhCHHHHHHHHH
Q 028628 37 KIRKEDMNKLVMNFLVTEGYVDAAEKFR 64 (206)
Q Consensus 37 ~~~~~~l~~lI~~YL~~~Gy~~ta~~f~ 64 (206)
.++...+..+|.+.|...|+.++|+++.
T Consensus 55 ~isve~Iqd~Ve~~L~~~g~~~vAkaYI 82 (711)
T PRK09263 55 EVDIEEIQDAVENQLMAGPYKALARAYI 82 (711)
T ss_pred CCCHHHHHHHHHHHHHhcChHHHHHHHH
Confidence 4777778999999999999999999985
No 66
>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=30.92 E-value=1.1e+02 Score=20.86 Aligned_cols=45 Identities=24% Similarity=0.377 Sum_probs=27.3
Q ss_pred HHHHHHHHHhhhcccCCCHHHHHHHHhcCCCCHHHHHHHHHHHHHhhCH
Q 028628 8 IRQLAEIEAMAMSKKVITREEWEKKLNDVKIRKEDMNKLVMNFLVTEGY 56 (206)
Q Consensus 8 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~lI~~YL~~~Gy 56 (206)
|++|-+.| -.+|++|.+++.+.+....++++.+..+ .++|...|.
T Consensus 9 i~~Li~~g---K~~G~lT~~eI~~~L~~~~~~~e~id~i-~~~L~~~gI 53 (82)
T PF03979_consen 9 IKKLIEKG---KKKGYLTYDEINDALPEDDLDPEQIDEI-YDTLEDEGI 53 (82)
T ss_dssp HHHHHHHH---HHHSS-BHHHHHHH-S-S---HHHHHHH-HHHHHTT--
T ss_pred HHHHHHHH---hhcCcCCHHHHHHHcCccCCCHHHHHHH-HHHHHHCCC
Confidence 45555554 3689999999999999888999887765 466666664
No 67
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=30.62 E-value=2.1e+02 Score=21.22 Aligned_cols=53 Identities=21% Similarity=0.383 Sum_probs=32.6
Q ss_pred HHHHHHHHhhCHHHHHHHHHHHhCCC------------------CCccHHHHHHHHHHHHHHHcCC--HHHHHHHH
Q 028628 45 KLVMNFLVTEGYVDAAEKFRMESGTE------------------PDIDLATITDRMAVKKAVQCGN--VEDAIEKV 100 (206)
Q Consensus 45 ~lI~~YL~~~Gy~~ta~~f~~e~~~~------------------~~~~~~~~~~r~~I~~~I~~g~--i~~Ai~~~ 100 (206)
..|..|+...|-. +.++++.|+. +....+.-..+..|.+.+.+|. .++|++.+
T Consensus 40 ~Fi~~Fi~~rGnl---Ke~e~~lgiSYPTvR~rLd~ii~~lg~~~~~~~~~~~~~~~IL~~L~~GeIs~eeA~~~L 112 (113)
T PF09862_consen 40 EFIKLFIKNRGNL---KEMEKELGISYPTVRNRLDKIIEKLGYEEDEEEEEEDERKEILDKLEKGEISVEEALEIL 112 (113)
T ss_pred HHHHHHHHhcCCH---HHHHHHHCCCcHHHHHHHHHHHHHhCCCCCcccccchhHHHHHHHHHcCCCCHHHHHHHh
Confidence 5677888888843 4445555542 2223345567788888888884 45555543
No 68
>PRK14574 hmsH outer membrane protein; Provisional
Probab=30.57 E-value=5.6e+02 Score=25.58 Aligned_cols=17 Identities=6% Similarity=-0.095 Sum_probs=9.5
Q ss_pred HHHHcCCHHHHHHHHHh
Q 028628 86 KAVQCGNVEDAIEKVND 102 (206)
Q Consensus 86 ~~I~~g~i~~Ai~~~~~ 102 (206)
-....|+++.|++..++
T Consensus 111 ly~~~gdyd~Aiely~k 127 (822)
T PRK14574 111 AYRNEKRWDQALALWQS 127 (822)
T ss_pred HHHHcCCHHHHHHHHHH
Confidence 34455666666666544
No 69
>PF00036 EF-hand_1: EF hand; InterPro: IPR018248 Many calcium-binding proteins belong to the same evolutionary family and share a type of calcium-binding domain known as the EF-hand. This type of domain consists of a twelve residue loop flanked on both sides by a twelve residue alpha-helical domain. In an EF-hand loop the calcium ion is coordinated in a pentagonal bipyramidal configuration. The six residues involved in the binding are in positions 1, 3, 5, 7, 9 and 12; these residues are denoted by X, Y, Z, -Y, -X and -Z. The invariant Glu or Asp at position 12 provides two oxygens for liganding Ca (bidentate ligand).; PDB: 1BJF_A 1XFW_R 1XFV_O 2K0J_A 2F3Z_A 3BYA_A 1XFU_Q 2R28_B 1ZOT_B 3G43_D ....
Probab=30.16 E-value=25 Score=19.19 Aligned_cols=17 Identities=18% Similarity=0.216 Sum_probs=13.6
Q ss_pred hhcccCCCHHHHHHHHh
Q 028628 18 AMSKKVITREEWEKKLN 34 (206)
Q Consensus 18 ~~~~~~~~~~~~~~~~~ 34 (206)
..++|+||.+||...+.
T Consensus 11 ~d~dG~I~~~Ef~~~~~ 27 (29)
T PF00036_consen 11 KDGDGKIDFEEFKEMMK 27 (29)
T ss_dssp TTSSSEEEHHHHHHHHH
T ss_pred CCCCCcCCHHHHHHHHH
Confidence 45789999999977664
No 70
>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=28.89 E-value=1.8e+02 Score=23.42 Aligned_cols=66 Identities=12% Similarity=0.136 Sum_probs=42.2
Q ss_pred HHHHHHHHHHHHHcCCHHHHHHHHHhhCchhhhccc------chhhhhHHHHHHHHHHcCChHHHHHHHHHhc
Q 028628 77 TITDRMAVKKAVQCGNVEDAIEKVNDLNPEILDTNP------QLFFHLQQQRLIELIRNGKVEEALEFAQEEL 143 (206)
Q Consensus 77 ~~~~r~~I~~~I~~g~i~~Ai~~~~~~~p~l~~~~s------~L~F~L~~q~fieli~~~~~~~Al~y~r~~l 143 (206)
.-..|.+|.+.+- -+++.-++++...+..+.+... .+...+..-.|.++++.|+..+|.+.+.+.+
T Consensus 133 a~~lr~~ie~~l~-~~~~~~~~~~~~~R~~~k~~~~~~~~r~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~ 204 (205)
T TIGR01470 133 ARLLRERIETLLP-PSLGDLATLAATWRDAVKKRLPNGAARRRFWEKFFDGAFAERVLAGREEQAERVLATRL 204 (205)
T ss_pred HHHHHHHHHHhcc-hhHHHHHHHHHHHHHHHHhhCCCHHHHHHHHHHHhccHHHHHHHcCCHHHHHHHHHHhh
Confidence 3344556665553 3567777888877777765322 2223333446788899999999888887654
No 71
>KOG1538 consensus Uncharacterized conserved protein WDR10, contains WD40 repeats [General function prediction only]
Probab=28.76 E-value=2.7e+02 Score=27.36 Aligned_cols=60 Identities=18% Similarity=0.299 Sum_probs=41.9
Q ss_pred HHHHH-HHHcCCHHHHHHHHHhhCchhhhcc--cchhhhhHHHHHHH----HHHcCChHHHHHHHHHh
Q 028628 82 MAVKK-AVQCGNVEDAIEKVNDLNPEILDTN--PQLFFHLQQQRLIE----LIRNGKVEEALEFAQEE 142 (206)
Q Consensus 82 ~~I~~-~I~~g~i~~Ai~~~~~~~p~l~~~~--s~L~F~L~~q~fie----li~~~~~~~Al~y~r~~ 142 (206)
+.|.+ +|..|+|++|...++.| |+++..- +.-.|.--.-+|+| .++.|...+|.+...+.
T Consensus 777 ksiVqlHve~~~W~eAFalAe~h-Pe~~~dVy~pyaqwLAE~DrFeEAqkAfhkAGr~~EA~~vLeQL 843 (1081)
T KOG1538|consen 777 KSLVQLHVETQRWDEAFALAEKH-PEFKDDVYMPYAQWLAENDRFEEAQKAFHKAGRQREAVQVLEQL 843 (1081)
T ss_pred HHHhhheeecccchHhHhhhhhC-ccccccccchHHHHhhhhhhHHHHHHHHHHhcchHHHHHHHHHh
Confidence 34444 48899999999998776 7776541 33455666667887 45678888888777653
No 72
>PF09731 Mitofilin: Mitochondrial inner membrane protein; InterPro: IPR019133 Mitofilin controls mitochondrial cristae morphology. Mitofilin is enriched in the narrow space between the inner boundary and the outer membranes, where it forms a homotypic interaction and assembles into a large multimeric protein complex []. The first 78 amino acids contain a typical amino-terminal-cleavable mitochondrial presequence (residues 1-43) rich in positive-charged and hydroxylated residues and a membrane anchor domain (residues 47-66). In addition, it has three centrally located coiled coil domains (residues 200-240,280-310 and 400-420) []. ; GO: 0031305 integral to mitochondrial inner membrane
Probab=28.56 E-value=92 Score=29.25 Aligned_cols=93 Identities=14% Similarity=0.198 Sum_probs=50.4
Q ss_pred HHHHHHhhhcccCCCHHHHHHHHhcCCCCHHHHHHH------HHHHHHhhCHHHHHHHHHHHhCCCCCccHHHHHHHHHH
Q 028628 11 LAEIEAMAMSKKVITREEWEKKLNDVKIRKEDMNKL------VMNFLVTEGYVDAAEKFRMESGTEPDIDLATITDRMAV 84 (206)
Q Consensus 11 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l------I~~YL~~~Gy~~ta~~f~~e~~~~~~~~~~~~~~r~~I 84 (206)
++.|...++..|..|..+..+.+..+.-.-.....+ +..|+.. |.-+.-.|....|..+....+..+...+.
T Consensus 453 l~~l~~~a~~~Gv~s~~~L~~rf~~v~~~~r~~~l~~~~~~g~~~~~~s--~~~S~l~~~~~~~~~~~~~~d~~~ilara 530 (582)
T PF09731_consen 453 LSSLPPEAAQRGVPSEAQLRNRFERVAPEVRRASLVPPEGAGLLGHLLS--YLFSLLLFRPKGGEVDPEGDDVESILARA 530 (582)
T ss_pred HHhcCHHHhhCCCCCHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHH--HHHheeeeecCCCCCCCCCCCHHHHHHHH
Confidence 445555666677777777766664443221111111 1222221 11111112211222112334566777889
Q ss_pred HHHHHcCCHHHHHHHHHhhCc
Q 028628 85 KKAVQCGNVEDAIEKVNDLNP 105 (206)
Q Consensus 85 ~~~I~~g~i~~Ai~~~~~~~p 105 (206)
..++..||++.|+..++....
T Consensus 531 e~~l~~gdL~~A~~~~~~L~g 551 (582)
T PF09731_consen 531 EYYLERGDLDKAARELNQLKG 551 (582)
T ss_pred HHHHHCCCHHHHHHHHHhCch
Confidence 999999999999999988654
No 73
>PLN03077 Protein ECB2; Provisional
Probab=28.23 E-value=5.8e+02 Score=25.03 Aligned_cols=103 Identities=22% Similarity=0.308 Sum_probs=57.9
Q ss_pred HHHhcCCCCHHHHHHHHHHHHHhhCHHHHHHHHHH--HhCCCCCccHHHHHHHHHHHHHHHcCCHHHHHHHHHhhCchhh
Q 028628 31 KKLNDVKIRKEDMNKLVMNFLVTEGYVDAAEKFRM--ESGTEPDIDLATITDRMAVKKAVQCGNVEDAIEKVNDLNPEIL 108 (206)
Q Consensus 31 ~~~~~~~~~~~~l~~lI~~YL~~~Gy~~ta~~f~~--e~~~~~~~~~~~~~~r~~I~~~I~~g~i~~Ai~~~~~~~p~l~ 108 (206)
+.++.++.+...-|.+|..|..+--..++...|.+ +.|+.|.... + ..-|..+-..|++++|.++.++.... .
T Consensus 545 ~~f~~~~~d~~s~n~lI~~~~~~G~~~~A~~lf~~M~~~g~~Pd~~T--~--~~ll~a~~~~g~v~ea~~~f~~M~~~-~ 619 (857)
T PLN03077 545 NQFNSHEKDVVSWNILLTGYVAHGKGSMAVELFNRMVESGVNPDEVT--F--ISLLCACSRSGMVTQGLEYFHSMEEK-Y 619 (857)
T ss_pred HHHHhcCCChhhHHHHHHHHHHcCCHHHHHHHHHHHHHcCCCCCccc--H--HHHHHHHhhcChHHHHHHHHHHHHHH-h
Confidence 34444455555567777766554444444555553 4566653321 1 12345566789999999888764311 1
Q ss_pred hcccchhhhhHHHHHHH-HHHcCChHHHHHHHHH
Q 028628 109 DTNPQLFFHLQQQRLIE-LIRNGKVEEALEFAQE 141 (206)
Q Consensus 109 ~~~s~L~F~L~~q~fie-li~~~~~~~Al~y~r~ 141 (206)
...+++ -+..-.+. +.+.|+.++|.++.++
T Consensus 620 gi~P~~---~~y~~lv~~l~r~G~~~eA~~~~~~ 650 (857)
T PLN03077 620 SITPNL---KHYACVVDLLGRAGKLTEAYNFINK 650 (857)
T ss_pred CCCCch---HHHHHHHHHHHhCCCHHHHHHHHHH
Confidence 112222 12223344 4578899999999886
No 74
>PRK01271 4-oxalocrotonate tautomerase; Provisional
Probab=28.06 E-value=82 Score=21.48 Aligned_cols=27 Identities=19% Similarity=0.327 Sum_probs=23.9
Q ss_pred cChhhHHHHHHHHHHHHHhhCCCCCCC
Q 028628 178 LDISQRLKTASEVNAAILTSQSHEKGD 204 (206)
Q Consensus 178 l~~~~r~~la~~vN~aiL~~~~~~~~~ 204 (206)
.+.++..++++.|.+++-+.+|.+.+.
T Consensus 13 ~s~EqK~~La~~iT~a~~~~lg~~~e~ 39 (76)
T PRK01271 13 LDEEQKAALAADITDVIIRHLNSKDSS 39 (76)
T ss_pred CCHHHHHHHHHHHHHHHHHHhCcCcce
Confidence 467889999999999999999998763
No 75
>PF12854 PPR_1: PPR repeat
Probab=28.00 E-value=89 Score=17.33 Aligned_cols=20 Identities=20% Similarity=0.446 Sum_probs=14.8
Q ss_pred HHHHHHHcCCHHHHHHHHHh
Q 028628 83 AVKKAVQCGNVEDAIEKVND 102 (206)
Q Consensus 83 ~I~~~I~~g~i~~Ai~~~~~ 102 (206)
-|.-.-..|++++|++.+++
T Consensus 13 lI~~~Ck~G~~~~A~~l~~~ 32 (34)
T PF12854_consen 13 LIDGYCKAGRVDEAFELFDE 32 (34)
T ss_pred HHHHHHHCCCHHHHHHHHHh
Confidence 35566778888888887765
No 76
>PRK07111 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=27.95 E-value=2.2e+02 Score=27.92 Aligned_cols=28 Identities=25% Similarity=0.504 Sum_probs=25.7
Q ss_pred CCCHHHHHHHHHHHHHhhCHHHHHHHHH
Q 028628 37 KIRKEDMNKLVMNFLVTEGYVDAAEKFR 64 (206)
Q Consensus 37 ~~~~~~l~~lI~~YL~~~Gy~~ta~~f~ 64 (206)
.++...+..+|..-|...|+.++|+++.
T Consensus 58 ~isve~IqDiVe~~L~~~g~~~vAkaYI 85 (735)
T PRK07111 58 EVTVEDIQDLVEKVLIENGHAETAKAYI 85 (735)
T ss_pred CCCHHHHHHHHHHHHHhcCcHHHHHHHH
Confidence 5788888999999999999999999985
No 77
>PF14689 SPOB_a: Sensor_kinase_SpoOB-type, alpha-helical domain; PDB: 1F51_C 2FTK_B 1IXM_B.
Probab=27.67 E-value=1.4e+02 Score=19.19 Aligned_cols=32 Identities=19% Similarity=0.320 Sum_probs=23.9
Q ss_pred HHHHHHHHHHHHHHcCCHHHHHHHHHhhCchh
Q 028628 76 ATITDRMAVKKAVQCGNVEDAIEKVNDLNPEI 107 (206)
Q Consensus 76 ~~~~~r~~I~~~I~~g~i~~Ai~~~~~~~p~l 107 (206)
|.....+-|...+.-|++++|.+.+++....+
T Consensus 22 D~~NhLqvI~gllqlg~~~~a~eYi~~~~~~~ 53 (62)
T PF14689_consen 22 DFLNHLQVIYGLLQLGKYEEAKEYIKELSKDL 53 (62)
T ss_dssp HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 45566777888899999999999988765444
No 78
>PF14691 Fer4_20: Dihydroprymidine dehydrogenase domain II, 4Fe-4S cluster; PDB: 2VDC_G 1H7X_C 1H7W_A 1GT8_A 1GTE_B 1GTH_B.
Probab=27.47 E-value=93 Score=22.77 Aligned_cols=27 Identities=37% Similarity=0.630 Sum_probs=20.5
Q ss_pred hhhHHHHHHHHHHcCChHHHHHHHHHh
Q 028628 116 FHLQQQRLIELIRNGKVEEALEFAQEE 142 (206)
Q Consensus 116 F~L~~q~fieli~~~~~~~Al~y~r~~ 142 (206)
..+....||.+++.|+..+|++..++.
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 356678999999999999999999964
No 79
>PRK00794 flbT flagellar biosynthesis repressor FlbT; Reviewed
Probab=27.22 E-value=2.2e+02 Score=21.58 Aligned_cols=30 Identities=20% Similarity=0.388 Sum_probs=25.9
Q ss_pred HHHHHHHHHHHHHHcCCHHHHHHHHHhhCc
Q 028628 76 ATITDRMAVKKAVQCGNVEDAIEKVNDLNP 105 (206)
Q Consensus 76 ~~~~~r~~I~~~I~~g~i~~Ai~~~~~~~p 105 (206)
+.......|.++|..|+.-+|++.+....|
T Consensus 92 ~~~~~l~~i~~~V~~g~~y~ALk~lR~L~~ 121 (132)
T PRK00794 92 DILAGLKAIDELVEAGRYYEALKALRGLYP 121 (132)
T ss_pred HHHHHHHHHHHHHHCCcHHHHHHHHHHhhH
Confidence 555677889999999999999999988776
No 80
>PLN02839 nudix hydrolase
Probab=26.48 E-value=49 Score=29.66 Aligned_cols=35 Identities=14% Similarity=0.407 Sum_probs=26.3
Q ss_pred CCCHHHHHHHHhcCCCCHHHHHHHHHHHHHhhCHH
Q 028628 23 VITREEWEKKLNDVKIRKEDMNKLVMNFLVTEGYV 57 (206)
Q Consensus 23 ~~~~~~~~~~~~~~~~~~~~l~~lI~~YL~~~Gy~ 57 (206)
..+.+|+.+.+..-+.-+....-+|+|+|+|+|++
T Consensus 318 Lm~v~EV~~~l~~~~~fKpn~aLViiDFLiRhG~I 352 (372)
T PLN02839 318 LIPVAQVANVIRKTSFFKANCSLVIIDFLFRHGFI 352 (372)
T ss_pred EecHHHHHHHHHcCCCCCcccHHHHHHHHHHcCCC
Confidence 35788888888765534444567899999999995
No 81
>PRK00304 hypothetical protein; Provisional
Probab=26.20 E-value=67 Score=22.04 Aligned_cols=43 Identities=21% Similarity=0.493 Sum_probs=30.1
Q ss_pred CCHHHHHHHHHHHHHhhCHHHHHHHHHHHhCCCCCccHHHHHHHHHHHHHHHcCCH
Q 028628 38 IRKEDMNKLVMNFLVTEGYVDAAEKFRMESGTEPDIDLATITDRMAVKKAVQCGNV 93 (206)
Q Consensus 38 ~~~~~l~~lI~~YL~~~Gy~~ta~~f~~e~~~~~~~~~~~~~~r~~I~~~I~~g~i 93 (206)
++++.|+.+|-+|+.|.|- | .|- ....-....++++++.+|+.
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 6788999999999999996 2 221 11233445778888888863
No 82
>KOG2910 consensus Uncharacterized conserved protein predicted to be involved in protein sorting [General function prediction only]
Probab=25.84 E-value=3.7e+02 Score=21.95 Aligned_cols=53 Identities=17% Similarity=0.341 Sum_probs=37.0
Q ss_pred HHHHHHHHHHHcCCHHHHHHHHHhhC--chhhhc-----------ccchhhhhHHHHHHHHHHcCC
Q 028628 79 TDRMAVKKAVQCGNVEDAIEKVNDLN--PEILDT-----------NPQLFFHLQQQRLIELIRNGK 131 (206)
Q Consensus 79 ~~r~~I~~~I~~g~i~~Ai~~~~~~~--p~l~~~-----------~s~L~F~L~~q~fieli~~~~ 131 (206)
.+|..-+++|++|+=+-|+-.+...+ -.|+.. -++++|.....+|++-++.|+
T Consensus 41 ~Er~~Ar~lird~rKdrAlllLKkKryQE~Ll~qt~~qL~nlEqmvsdiEft~vqk~V~~gLk~GN 106 (209)
T KOG2910|consen 41 AERQLARDLIRDGRKDRALLLLKKKRYQEELLTQTDNQLINLEQMVSDIEFTQVQKKVMEGLKQGN 106 (209)
T ss_pred HHHHHHHHHHHhChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34566777888887777766554332 133332 378999999999999998873
No 83
>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=25.49 E-value=1.1e+02 Score=18.73 Aligned_cols=25 Identities=12% Similarity=0.054 Sum_probs=22.4
Q ss_pred ChhhHHHHHHHHHHHHHhhCCCCCC
Q 028628 179 DISQRLKTASEVNAAILTSQSHEKG 203 (206)
Q Consensus 179 ~~~~r~~la~~vN~aiL~~~~~~~~ 203 (206)
+.+++.++++.+.+++-..+|.|++
T Consensus 12 t~eqk~~l~~~i~~~l~~~~g~~~~ 36 (58)
T cd00491 12 TDEQKRELIERVTEAVSEILGAPEA 36 (58)
T ss_pred CHHHHHHHHHHHHHHHHHHhCcCcc
Confidence 5789999999999999999998865
No 84
>KOG0097 consensus GTPase Rab14, small G protein superfamily [Intracellular trafficking, secretion, and vesicular transport]
Probab=25.49 E-value=1e+02 Score=24.02 Aligned_cols=39 Identities=18% Similarity=0.294 Sum_probs=29.7
Q ss_pred HHHHHHHHHHHhCCCC---------CccHHHHHHHHHHHHHHHcCCHH
Q 028628 56 YVDAAEKFRMESGTEP---------DIDLATITDRMAVKKAVQCGNVE 94 (206)
Q Consensus 56 y~~ta~~f~~e~~~~~---------~~~~~~~~~r~~I~~~I~~g~i~ 94 (206)
-++-|+.|++|.|+.. ......++..++|-+.|.+|.++
T Consensus 135 ~yeeak~faeengl~fle~saktg~nvedafle~akkiyqniqdgsld 182 (215)
T KOG0097|consen 135 TYEEAKEFAEENGLMFLEASAKTGQNVEDAFLETAKKIYQNIQDGSLD 182 (215)
T ss_pred cHHHHHHHHhhcCeEEEEecccccCcHHHHHHHHHHHHHHhhhcCccc
Confidence 3567899999998741 23345788899999999999665
No 85
>PRK01964 4-oxalocrotonate tautomerase; Provisional
Probab=25.14 E-value=1e+02 Score=19.66 Aligned_cols=25 Identities=20% Similarity=0.069 Sum_probs=22.8
Q ss_pred ChhhHHHHHHHHHHHHHhhCCCCCC
Q 028628 179 DISQRLKTASEVNAAILTSQSHEKG 203 (206)
Q Consensus 179 ~~~~r~~la~~vN~aiL~~~~~~~~ 203 (206)
+.+.+.++++.|..++-..+|.|++
T Consensus 13 t~eqk~~l~~~it~~l~~~lg~p~~ 37 (64)
T PRK01964 13 PEEKIKNLIREVTEAISATLDVPKE 37 (64)
T ss_pred CHHHHHHHHHHHHHHHHHHhCcChh
Confidence 6788999999999999999999875
No 86
>PF15391 DUF4614: Domain of unknown function (DUF4614)
Probab=24.94 E-value=96 Score=24.95 Aligned_cols=50 Identities=30% Similarity=0.408 Sum_probs=36.2
Q ss_pred HHHHHHHHhhCchhhhcccchhhhh-HHHHHHHHHHcC----------------ChHHHHHHHHHhc
Q 028628 94 EDAIEKVNDLNPEILDTNPQLFFHL-QQQRLIELIRNG----------------KVEEALEFAQEEL 143 (206)
Q Consensus 94 ~~Ai~~~~~~~p~l~~~~s~L~F~L-~~q~fieli~~~----------------~~~~Al~y~r~~l 143 (206)
.+||+.+..+.|.++.-|..|.-+| .-|+||+.-|.= .++++-+|+|.+=
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 3578888889999888777775555 457999976531 2678888888654
No 87
>KOG3192 consensus Mitochondrial J-type chaperone [Posttranslational modification, protein turnover, chaperones]
Probab=24.83 E-value=85 Score=24.75 Aligned_cols=80 Identities=15% Similarity=0.238 Sum_probs=39.1
Q ss_pred ccCCCHHHHHHHHhcCCCCHHHHHH---HHHHHHHhhCHHHHHHHHHHHhCCC---CCccHHHHHHHHHHHHHHHcCCHH
Q 028628 21 KKVITREEWEKKLNDVKIRKEDMNK---LVMNFLVTEGYVDAAEKFRMESGTE---PDIDLATITDRMAVKKAVQCGNVE 94 (206)
Q Consensus 21 ~~~~~~~~~~~~~~~~~~~~~~l~~---lI~~YL~~~Gy~~ta~~f~~e~~~~---~~~~~~~~~~r~~I~~~I~~g~i~ 94 (206)
+.+++|..++-.+.+++...+.++. ++++=|-.+ +.......+.++. .............+.++..+.+++
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 KDPLARARYLLKLKGQEQTSNELSTDPEFLMEVLEYH---EAISEMDDEEDLKQLKSQNQERIAQCKQQLGEAFESKKYD 145 (168)
T ss_pred HhHHHHHHHHHHHhCCCCchhhhccCHHHHHHHHHHH---HHHHhccCcHHHHHHHHHHHHHHHHHHHHHHHHHhhccHH
Confidence 4566777777777776655554432 333322222 1111111111110 011122334456667777777888
Q ss_pred HHHHHHHhh
Q 028628 95 DAIEKVNDL 103 (206)
Q Consensus 95 ~Ai~~~~~~ 103 (206)
+|+..+...
T Consensus 146 ~Al~~i~rl 154 (168)
T KOG3192|consen 146 EALKKILRL 154 (168)
T ss_pred HHHHHHHHH
Confidence 887776543
No 88
>TIGR00013 taut 4-oxalocrotonate tautomerase family enzyme. 4-oxalocrotonate tautomerase is a homohexamer in which each monomer is very small, at about 62 amino acids. Pro-1 of the mature protein serves as a general base. The enzyme functions in meta-cleavage pathways of aromatic hydrocarbon catabolism. Because several Arg residues located near the active site in the crystal structure of Pseudomonas putida are not conserved among all members of this family, because the literature describes a general role in the isomerization of beta,gamma-unsaturated enones to their alpha,beta-isomers, and because of the presence of fairly distantly related paralogs in Campylobacter jejuni, the family is regarded as not necessarily uniform in function.
Probab=24.46 E-value=1.2e+02 Score=18.98 Aligned_cols=27 Identities=11% Similarity=0.024 Sum_probs=23.6
Q ss_pred cChhhHHHHHHHHHHHHHhhCCCCCCC
Q 028628 178 LDISQRLKTASEVNAAILTSQSHEKGD 204 (206)
Q Consensus 178 l~~~~r~~la~~vN~aiL~~~~~~~~~ 204 (206)
.+.+++.+++..+..++-..+|.|.+.
T Consensus 12 rt~eqK~~l~~~it~~l~~~lg~~~~~ 38 (63)
T TIGR00013 12 RTDEQKRQLIEGVTEAMAETLGANLES 38 (63)
T ss_pred CCHHHHHHHHHHHHHHHHHHhCCCccc
Confidence 368899999999999999999998653
No 89
>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=24.23 E-value=82 Score=21.45 Aligned_cols=28 Identities=32% Similarity=0.601 Sum_probs=23.9
Q ss_pred CCCHHHHHHHHHHHHHhhCHHHHHHHHH
Q 028628 37 KIRKEDMNKLVMNFLVTEGYVDAAEKFR 64 (206)
Q Consensus 37 ~~~~~~l~~lI~~YL~~~Gy~~ta~~f~ 64 (206)
.++...+..+|.+.|..+|+.+.|+++.
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 4677788999999999999999988764
No 90
>TIGR00756 PPR pentatricopeptide repeat domain (PPR motif). This family has a similar consensus to the TPR domain (tetratricopeptide), pfam pfam00515, a 33-residue repeat. It is predicted to form a pair of antiparallel helices similar to that of TPR.
Probab=23.63 E-value=1.2e+02 Score=15.65 Aligned_cols=20 Identities=25% Similarity=0.551 Sum_probs=15.0
Q ss_pred HHHHHHcCCHHHHHHHHHhh
Q 028628 84 VKKAVQCGNVEDAIEKVNDL 103 (206)
Q Consensus 84 I~~~I~~g~i~~Ai~~~~~~ 103 (206)
|......|++++|.+..++.
T Consensus 7 i~~~~~~~~~~~a~~~~~~M 26 (35)
T TIGR00756 7 IDGLCKAGRVEEALELFKEM 26 (35)
T ss_pred HHHHHHCCCHHHHHHHHHHH
Confidence 55667888888888887654
No 91
>COG5117 NOC3 Protein involved in the nuclear export of pre-ribosomes [Translation, ribosomal structure and biogenesis / Intracellular trafficking and secretion]
Probab=23.52 E-value=4e+02 Score=24.96 Aligned_cols=168 Identities=18% Similarity=0.225 Sum_probs=97.0
Q ss_pred HHHHHHhhhcccCCCHHHHHHHHhcCCCCHHHHHHHHHHHHHh------hCHHHHHHHHHHH--hCCC------------
Q 028628 11 LAEIEAMAMSKKVITREEWEKKLNDVKIRKEDMNKLVMNFLVT------EGYVDAAEKFRME--SGTE------------ 70 (206)
Q Consensus 11 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~lI~~YL~~------~Gy~~ta~~f~~e--~~~~------------ 70 (206)
++++..+.|---+++..+..+--.+.+.+.+...-++-.-+-. .|..+|.+..-+| .|..
T Consensus 240 ~~~~Q~SL~~vA~~~~~eli~~asHFN~~~kvfsl~lR~i~~~t~rp~s~~ii~t~ks~leeD~~G~~sl~~~~i~~~l~ 319 (657)
T COG5117 240 LDETQSSLYQVAYISLCELIQHASHFNCTDKVFSLVLRGILGTTKRPVSMLIIDTIKSKLEEDCTGKTSLVATVIDQMLD 319 (657)
T ss_pred cchhhHHHHHHHHHHHHHHHHHhhhcCcHHHHHHHHHHHhhCCCCCchHHHHHHHHHHHhcccccCceeEEeehHHHHHH
Confidence 4566666666667777777777777777766665555554432 3556666654443 2210
Q ss_pred --------------CC-----c-----------------------------cHHHHHHHHHHHHHHHcC-CHHHHHHHHH
Q 028628 71 --------------PD-----I-----------------------------DLATITDRMAVKKAVQCG-NVEDAIEKVN 101 (206)
Q Consensus 71 --------------~~-----~-----------------------------~~~~~~~r~~I~~~I~~g-~i~~Ai~~~~ 101 (206)
+. . ..-...+|++|.+-.++. ++.+|++.-
T Consensus 320 k~rN~~vle~vld~~ls~n~L~D~~~~~k~w~~n~~~~k~~KKd~~hlsKK~RK~~KE~~~I~~Emr~ae~i~~a~e~e- 398 (657)
T COG5117 320 KERNPLVLEYVLDIPLSDNSLRDEEKARKYWEANKPVSKREKKDIFHLSKKLRKIEKERLRIQSEMRDAEDIEEAIEEE- 398 (657)
T ss_pred hhhCchhHHHHHhccchhhhhhhhhhhHHhhhcCCcchhhhhcchhhhhHHHHHHHHHHHHHHHHhhhHHHHHHHHHHH-
Confidence 00 0 023556777888777653 555555442
Q ss_pred hhCchhhhcccchhhhhHHHHHHHHHHcCChHHHHHHHHHhcCcccc-CChhHHHHHHHHHhhhcccCCCCCchhhhcCh
Q 028628 102 DLNPEILDTNPQLFFHLQQQRLIELIRNGKVEEALEFAQEELAPRGE-ENQSFLEELERTVALLAFEDVSNCPVGDLLDI 180 (206)
Q Consensus 102 ~~~p~l~~~~s~L~F~L~~q~fieli~~~~~~~Al~y~r~~l~~~~~-~~~~~~~~i~~l~~LLay~~~~~sp~~~ll~~ 180 (206)
.+..++++.--.++|.+ -+|+....|.|+-+-+..|+. -++++...+=+++.-|+-++ |...+-+.
T Consensus 399 knqseIlkiif~~Yf~v---------Lk~~~k~lig~vleGl~k~~~~~n~eflGD~Levl~eL~~d~----~~dk~ss~ 465 (657)
T COG5117 399 KNQSEILKIIFRLYFMV---------LKGDRKDLIGYVLEGLVKYRKIINPEFLGDLLEVLYELLNDN----PLDKISSD 465 (657)
T ss_pred hhHHHHHHHHHHHHHHH---------HhcchHHHHHHHHHHHHHHHhhcCHHHHhHHHHHHHHHHcCC----chhhhhHH
Confidence 23344554323333333 345555555555555555542 35778888888888887777 44455567
Q ss_pred hhHHHHHHHHHH
Q 028628 181 SQRLKTASEVNA 192 (206)
Q Consensus 181 ~~r~~la~~vN~ 192 (206)
++|+.+...+.+
T Consensus 466 a~r~alLcI~tA 477 (657)
T COG5117 466 ARRQALLCILTA 477 (657)
T ss_pred HHHHHHHHhhHH
Confidence 888888777655
No 92
>PF12793 SgrR_N: Sugar transport-related sRNA regulator N-term
Probab=22.90 E-value=1.2e+02 Score=22.39 Aligned_cols=24 Identities=13% Similarity=0.123 Sum_probs=20.3
Q ss_pred HHHHHHHHHHcCCHHHHHHHHHhh
Q 028628 80 DRMAVKKAVQCGNVEDAIEKVNDL 103 (206)
Q Consensus 80 ~r~~I~~~I~~g~i~~Ai~~~~~~ 103 (206)
....+.+.+.+|+++.|++++...
T Consensus 73 ~~~~~~~~l~~g~~~~a~~ll~~~ 96 (115)
T PF12793_consen 73 LEQQAEELLEQGKYEQALQLLDFD 96 (115)
T ss_pred HHHHHHHHHHcCCHHHHHHHHHhC
Confidence 356788899999999999999843
No 93
>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=22.89 E-value=68 Score=18.24 Aligned_cols=17 Identities=35% Similarity=0.542 Sum_probs=11.6
Q ss_pred HHHHH--HcCCHHHHHHHH
Q 028628 84 VKKAV--QCGNVEDAIEKV 100 (206)
Q Consensus 84 I~~~I--~~g~i~~Ai~~~ 100 (206)
.+.++ ..||++.|+.|+
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 44443 356999999886
No 94
>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=22.89 E-value=2.5e+02 Score=22.66 Aligned_cols=56 Identities=21% Similarity=0.380 Sum_probs=40.6
Q ss_pred HHHHHHHHHHHHHhhhcccCCCHHHHHHHHhcCCCCHHHHHHHHHHH-----HHhhCHHHHHHHHHHHhCCC
Q 028628 4 FWIVIRQLAEIEAMAMSKKVITREEWEKKLNDVKIRKEDMNKLVMNF-----LVTEGYVDAAEKFRMESGTE 70 (206)
Q Consensus 4 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~lI~~Y-----L~~~Gy~~ta~~f~~e~~~~ 70 (206)
.+.+|.-|-.+|-. |-+..|+-+++.. ..++||.+| ..+.+.+...+.|.++.++.
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 45567777777754 8899999999844 469999999 33333567789999999974
No 95
>PF12931 Sec16_C: Sec23-binding domain of Sec16; PDB: 3MZK_C.
Probab=22.74 E-value=91 Score=26.56 Aligned_cols=22 Identities=27% Similarity=0.389 Sum_probs=15.0
Q ss_pred HHHHHHHcCCHHHHHHHHHhhC
Q 028628 83 AVKKAVQCGNVEDAIEKVNDLN 104 (206)
Q Consensus 83 ~I~~~I~~g~i~~Ai~~~~~~~ 104 (206)
+|++++..||.++|+++|-+..
T Consensus 1 ~I~~~Ll~G~~~~Av~~al~~~ 22 (284)
T PF12931_consen 1 KIQQLLLVGNREEAVELALDNG 22 (284)
T ss_dssp HHHHHHHTT-HHHHHHHHHHTT
T ss_pred CHHHHHhCCCHHHHHHHHHHCC
Confidence 4777788888888887775543
No 96
>KOG0640 consensus mRNA cleavage stimulating factor complex; subunit 1 [RNA processing and modification]
Probab=22.58 E-value=2.9e+02 Score=24.51 Aligned_cols=32 Identities=19% Similarity=0.253 Sum_probs=27.1
Q ss_pred CHHHHHHHHHHHHHhhCHHHHHHHHHHHhCCC
Q 028628 39 RKEDMNKLVMNFLVTEGYVDAAEKFRMESGTE 70 (206)
Q Consensus 39 ~~~~l~~lI~~YL~~~Gy~~ta~~f~~e~~~~ 70 (206)
+++.+-+||..+|.+.|+...|..++.....+
T Consensus 10 dre~lyrLiisqL~ydg~~qiA~~lan~~~~~ 41 (430)
T KOG0640|consen 10 DREILYRLIISQLRYDGLSQIASALANATMTP 41 (430)
T ss_pred hHHHHHHHHHHHHhhccHHHHHHHHHHhhcCc
Confidence 34567899999999999999999999876654
No 97
>COG3071 HemY Uncharacterized enzyme of heme biosynthesis [Coenzyme metabolism]
Probab=22.05 E-value=5.1e+02 Score=23.53 Aligned_cols=132 Identities=20% Similarity=0.202 Sum_probs=71.9
Q ss_pred CCCHHHHHHHHhcCCCCHHHHHHHHHHHHHhhCHHHHHHHHHHHh---CCCCCc---------------------c----
Q 028628 23 VITREEWEKKLNDVKIRKEDMNKLVMNFLVTEGYVDAAEKFRMES---GTEPDI---------------------D---- 74 (206)
Q Consensus 23 ~~~~~~~~~~~~~~~~~~~~l~~lI~~YL~~~Gy~~ta~~f~~e~---~~~~~~---------------------~---- 74 (206)
+..++.+.+.++..+ ...++-++-.++.++.|-.+.+-++-... |+-..+ +
T Consensus 170 ~aA~~~v~~ll~~~p-r~~~vlrLa~r~y~~~g~~~~ll~~l~~L~ka~~l~~~e~~~le~~a~~glL~q~~~~~~~~gL 248 (400)
T COG3071 170 PAARENVDQLLEMTP-RHPEVLRLALRAYIRLGAWQALLAILPKLRKAGLLSDEEAARLEQQAWEGLLQQARDDNGSEGL 248 (400)
T ss_pred hhHHHHHHHHHHhCc-CChHHHHHHHHHHHHhccHHHHHHHHHHHHHccCCChHHHHHHHHHHHHHHHHHHhccccchHH
Confidence 455566655444444 44566677788888888777665543332 211100 0
Q ss_pred ------------HHHHHHHHHHHHHHHcCCHHHHHHHHHhhCchhhhcccchhhhhHHHHHHHHHHcCChHHHHHHHHHh
Q 028628 75 ------------LATITDRMAVKKAVQCGNVEDAIEKVNDLNPEILDTNPQLFFHLQQQRLIELIRNGKVEEALEFAQEE 142 (206)
Q Consensus 75 ------------~~~~~~r~~I~~~I~~g~i~~Ai~~~~~~~p~l~~~~s~L~F~L~~q~fieli~~~~~~~Al~y~r~~ 142 (206)
.+.--...-+.+.|..|+-++|.+|+.+..+.-... . ...++.-++-++...-++-+++-
T Consensus 249 ~~~W~~~pr~lr~~p~l~~~~a~~li~l~~~~~A~~~i~~~Lk~~~D~--~------L~~~~~~l~~~d~~~l~k~~e~~ 320 (400)
T COG3071 249 KTWWKNQPRKLRNDPELVVAYAERLIRLGDHDEAQEIIEDALKRQWDP--R------LCRLIPRLRPGDPEPLIKAAEKW 320 (400)
T ss_pred HHHHHhccHHhhcChhHHHHHHHHHHHcCChHHHHHHHHHHHHhccCh--h------HHHHHhhcCCCCchHHHHHHHHH
Confidence 011112334666777888888888887665433322 1 44556666666666666666665
Q ss_pred cCccccCChhHHHHHHHHHhhhcccC
Q 028628 143 LAPRGEENQSFLEELERTVALLAFED 168 (206)
Q Consensus 143 l~~~~~~~~~~~~~i~~l~~LLay~~ 168 (206)
+.....+ +.+-.+.|-|++..
T Consensus 321 l~~h~~~-----p~L~~tLG~L~~k~ 341 (400)
T COG3071 321 LKQHPED-----PLLLSTLGRLALKN 341 (400)
T ss_pred HHhCCCC-----hhHHHHHHHHHHHh
Confidence 5544432 24455566666654
No 98
>KOG3380 consensus Actin-related protein Arp2/3 complex, subunit ARPC5 [Cytoskeleton]
Probab=22.04 E-value=2.2e+02 Score=22.16 Aligned_cols=58 Identities=12% Similarity=0.115 Sum_probs=37.9
Q ss_pred HHHHHHHHcCCHHHHHHHHHhhCchhhhcccch--hhhhHHHHHHHHHHcCChHHHHHHHH
Q 028628 82 MAVKKAVQCGNVEDAIEKVNDLNPEILDTNPQL--FFHLQQQRLIELIRNGKVEEALEFAQ 140 (206)
Q Consensus 82 ~~I~~~I~~g~i~~Ai~~~~~~~p~l~~~~s~L--~F~L~~q~fieli~~~~~~~Al~y~r 140 (206)
.+|+.++..|+...|++.+-.+-| ...++..+ ....-..+.+.-+++.+++.+++-.-
T Consensus 40 ~ev~sll~qg~~~~AL~~aL~~~P-~~t~~q~vK~~a~~~v~~vL~~ik~adI~~~v~~Ls 99 (152)
T KOG3380|consen 40 REVRSLLTQGKSLEALQTALLNPP-YGTKDQEVKDRALNVVLKVLTSIKQADIEAAVKKLS 99 (152)
T ss_pred HHHHHHHHcccHHHHHHHHHhCCC-CCCccHHHHHHHHHHHHHHHHHHHHHhHHHHHHHhh
Confidence 569999999999999998877655 32222222 33344455566667777777765433
No 99
>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=22.00 E-value=53 Score=28.28 Aligned_cols=51 Identities=14% Similarity=0.016 Sum_probs=34.5
Q ss_pred hCHHHHHHHHHHHhCCC----CCccHHHHHHHHHHHHHHHcCCHHHHHHHHHhhC
Q 028628 54 EGYVDAAEKFRMESGTE----PDIDLATITDRMAVKKAVQCGNVEDAIEKVNDLN 104 (206)
Q Consensus 54 ~Gy~~ta~~f~~e~~~~----~~~~~~~~~~r~~I~~~I~~g~i~~Ai~~~~~~~ 104 (206)
.|-.+..+.+.++.|.. +....+..--=..||++|.+||++.|-+++...+
T Consensus 115 ~G~~~~L~~~~~~~g~~v~~~~~~~~~~~ISST~IR~~l~~G~i~~A~~lLGr~y 169 (288)
T TIGR00083 115 QGDFLLLQLFGNTTIFCVIVKQLFCQDIRISSSAIRQALKNGDLELANKLLGRPY 169 (288)
T ss_pred CCCHHHHHHhccccCcEEEEeccccCCCeECHHHHHHHHHcCCHHHHHHhhhhhh
Confidence 46788888888887742 1111001112256999999999999999998655
No 100
>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=21.61 E-value=1.5e+02 Score=21.65 Aligned_cols=23 Identities=22% Similarity=0.437 Sum_probs=19.6
Q ss_pred HHHHHcCCHHHHHHHHHhhCchh
Q 028628 85 KKAVQCGNVEDAIEKVNDLNPEI 107 (206)
Q Consensus 85 ~~~I~~g~i~~Ai~~~~~~~p~l 107 (206)
...|...++++|+.++..+.|..
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 101
>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=21.40 E-value=2.6e+02 Score=20.57 Aligned_cols=24 Identities=25% Similarity=0.389 Sum_probs=19.0
Q ss_pred HHHHHHHHHcCCHHHHHHHHHhhC
Q 028628 81 RMAVKKAVQCGNVEDAIEKVNDLN 104 (206)
Q Consensus 81 r~~I~~~I~~g~i~~Ai~~~~~~~ 104 (206)
...+.++|.+||...|+..+++..
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 356889999999999999997654
No 102
>PHA01351 putative minor structural protein
Probab=21.20 E-value=8.2e+02 Score=24.32 Aligned_cols=46 Identities=9% Similarity=0.163 Sum_probs=34.4
Q ss_pred hcccCCCHHHHHHHHhcCCCCHHHHHHHHHHHHHhhCHHHHHHHHH
Q 028628 19 MSKKVITREEWEKKLNDVKIRKEDMNKLVMNFLVTEGYVDAAEKFR 64 (206)
Q Consensus 19 ~~~~~~~~~~~~~~~~~~~~~~~~l~~lI~~YL~~~Gy~~ta~~f~ 64 (206)
-++|.+|..+.++.+.+.+.+......++..|..---...+.+.+.
T Consensus 492 ~skGi~DqkkIke~LKa~gfnks~~d~~L~~~~n~a~iesqIK~LQ 537 (1070)
T PHA01351 492 VSLGIFDQKKIKEELKANKFNEQVALQILESELQFAQLQNQLKEYQ 537 (1070)
T ss_pred HHcccccHHHHHHHHHhcCccHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3568899999999999999999888887776665544444444444
No 103
>PRK02220 4-oxalocrotonate tautomerase; Provisional
Probab=21.18 E-value=1.3e+02 Score=18.69 Aligned_cols=25 Identities=16% Similarity=0.078 Sum_probs=22.5
Q ss_pred ChhhHHHHHHHHHHHHHhhCCCCCC
Q 028628 179 DISQRLKTASEVNAAILTSQSHEKG 203 (206)
Q Consensus 179 ~~~~r~~la~~vN~aiL~~~~~~~~ 203 (206)
+.+++.+++..|..++....|.|++
T Consensus 13 s~eqk~~l~~~it~~l~~~~~~p~~ 37 (61)
T PRK02220 13 TEEQLKALVKDVTAAVSKNTGAPAE 37 (61)
T ss_pred CHHHHHHHHHHHHHHHHHHhCcChh
Confidence 6889999999999999999998865
No 104
>COG5096 Vesicle coat complex, various subunits [Intracellular trafficking and secretion]
Probab=21.13 E-value=6.6e+02 Score=24.94 Aligned_cols=80 Identities=18% Similarity=0.147 Sum_probs=58.3
Q ss_pred hC-CCCCccHHHHHHHHHHHHHHHcCCHHHHHHHHHhhCchhhhc--ccchhhhhHHHHHHHHHHcCChHHHHHHHHHhc
Q 028628 67 SG-TEPDIDLATITDRMAVKKAVQCGNVEDAIEKVNDLNPEILDT--NPQLFFHLQQQRLIELIRNGKVEEALEFAQEEL 143 (206)
Q Consensus 67 ~~-~~~~~~~~~~~~r~~I~~~I~~g~i~~Ai~~~~~~~p~l~~~--~s~L~F~L~~q~fieli~~~~~~~Al~y~r~~l 143 (206)
+| +....+...++..++|...+..|+- ....+|.+.+. -.+.++.=.+.-|++.+-+++.++++-...+..
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 35 5555677788999999999999975 44455665553 245666667778888888888888888777777
Q ss_pred CccccCChh
Q 028628 144 APRGEENQS 152 (206)
Q Consensus 144 ~~~~~~~~~ 152 (206)
..+.+.+|.
T Consensus 99 kDl~d~N~~ 107 (757)
T COG5096 99 KDLQDPNEE 107 (757)
T ss_pred hhccCCCHH
Confidence 777766654
No 105
>PRK00745 4-oxalocrotonate tautomerase; Provisional
Probab=21.00 E-value=1.4e+02 Score=18.65 Aligned_cols=25 Identities=12% Similarity=0.183 Sum_probs=22.6
Q ss_pred ChhhHHHHHHHHHHHHHhhCCCCCC
Q 028628 179 DISQRLKTASEVNAAILTSQSHEKG 203 (206)
Q Consensus 179 ~~~~r~~la~~vN~aiL~~~~~~~~ 203 (206)
+.+.+.++++.|-.++-+.+|.|++
T Consensus 13 s~eqk~~l~~~it~~l~~~~~~p~~ 37 (62)
T PRK00745 13 TVEQKRKLVEEITRVTVETLGCPPE 37 (62)
T ss_pred CHHHHHHHHHHHHHHHHHHcCCChh
Confidence 6889999999999999999998865
No 106
>PHA02701 ORF020 dsRNA-binding PKR inhibitor; Provisional
Probab=20.93 E-value=66 Score=25.93 Aligned_cols=27 Identities=22% Similarity=0.351 Sum_probs=24.7
Q ss_pred HHHHHHHHHhhCHHHHHHHHHHHhCCC
Q 028628 44 NKLVMNFLVTEGYVDAAEKFRMESGTE 70 (206)
Q Consensus 44 ~~lI~~YL~~~Gy~~ta~~f~~e~~~~ 70 (206)
...|++||-++|---||..++++.|+.
T Consensus 6 ~~~i~~~l~~~~~~~~a~~i~k~l~i~ 32 (183)
T PHA02701 6 ASLILTLLSSSGDKLPAKRIAKELGIS 32 (183)
T ss_pred HHHHHHHHHhcCCCCcHHHHHHHhCcc
Confidence 678999999999778999999999986
No 107
>COG5051 RPL36A Ribosomal protein L36E [Translation, ribosomal structure and biogenesis]
Probab=20.87 E-value=1.4e+02 Score=21.07 Aligned_cols=43 Identities=26% Similarity=0.392 Sum_probs=33.1
Q ss_pred HHHHHHHHHHcCChHHHHHHHHHhcCccccCChhHHHHHHHHHhhhc
Q 028628 119 QQQRLIELIRNGKVEEALEFAQEELAPRGEENQSFLEELERTVALLA 165 (206)
Q Consensus 119 ~~q~fieli~~~~~~~Al~y~r~~l~~~~~~~~~~~~~i~~l~~LLa 165 (206)
+-.+.|+||++.+-..|-..+++.|..+.. -...++++...|.
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 345789999999999999999999988753 2466777766554
No 108
>PF09312 SurA_N: SurA N-terminal domain; InterPro: IPR015391 The correct folding of outer membrane proteins in Gram negative bacteria is facilitated by the survival protein SurA []. This entry represents the domain found at the N terminus of the chaperone SurA. It is a helical domain of unknown function. The C terminus of the SurA protein folds back and forms part of this domain also but is not included in the current alignment. ; PDB: 3RGC_B 2PV3_B 1M5Y_A.
Probab=20.73 E-value=2.8e+02 Score=20.10 Aligned_cols=31 Identities=16% Similarity=0.390 Sum_probs=17.8
Q ss_pred hcCCCCHHHHHHHHHHHHHhhCHHHHHHHHHHH
Q 028628 34 NDVKIRKEDMNKLVMNFLVTEGYVDAAEKFRME 66 (206)
Q Consensus 34 ~~~~~~~~~l~~lI~~YL~~~Gy~~ta~~f~~e 66 (206)
.++.++...++..|.+..-++|. |...|.+.
T Consensus 63 ~gI~vsd~evd~~i~~ia~~n~l--s~~ql~~~ 93 (118)
T PF09312_consen 63 LGIKVSDEEVDEAIANIAKQNNL--SVEQLRQQ 93 (118)
T ss_dssp CT----HHHHHHHHHHHHHHTT----HHHHHHH
T ss_pred cCCCCCHHHHHHHHHHHHHHcCC--CHHHHHHH
Confidence 45677888888888888888877 44555554
No 109
>PF13812 PPR_3: Pentatricopeptide repeat domain
Probab=20.54 E-value=1.5e+02 Score=15.45 Aligned_cols=21 Identities=10% Similarity=0.438 Sum_probs=15.7
Q ss_pred HHHHHHHcCCHHHHHHHHHhh
Q 028628 83 AVKKAVQCGNVEDAIEKVNDL 103 (206)
Q Consensus 83 ~I~~~I~~g~i~~Ai~~~~~~ 103 (206)
-|..+...|+++.|....++.
T Consensus 7 ll~a~~~~g~~~~a~~~~~~M 27 (34)
T PF13812_consen 7 LLRACAKAGDPDAALQLFDEM 27 (34)
T ss_pred HHHHHHHCCCHHHHHHHHHHH
Confidence 366677889999988877653
No 110
>PF01361 Tautomerase: Tautomerase enzyme; InterPro: IPR004370 4-Oxalocrotonate tautomerase (4-OT) catalyzes the isomerisation of beta,gamma-unsaturated enones to their alpha,beta-isomers. The enzyme is part of a plasmid-encoded pathway, which enables bacteria harbouring the plasmid to use various aromatic hydrocarbons as their sole sources of carbon and energy. The enzyme is a barrel-shaped hexamer, which can be viewed as a trimer of dimers. The hexamer contains a hydrophobic core formed by three beta-sheets and surrounded by three pairs of alpha-helices. Each 4-OT monomer of 62 amino acids has a relatively simple beta-alpha-beta fold as described by the structure of the enzyme from Pseudomonas putida []. The monomer begins with a conserved proline at the start of a beta-strand, followed by an alpha-helix and a 310 helix preceding a second parallel beta-strand, and ends with a beta-hairpin near the C terminus. The dimer results from antiparallel interactions between the beta-sheets and alpha-helices of the two monomers, forming a four-stranded beta-sheet with antiparallel alpha-helices on one side, creating two active sites, one at each end of the beta-sheet. Three dimers further associate to form a hexamer by the interactions of the strands of the C-terminal beta-hairpin loops with the edges of the four-stranded beta-sheets of neighbouring dimers, creating a series of cross-links that stabilise the hexamer Pro-1 of the mature protein functions as the general base while Arg-39 and an ordered water molecule each provide a hydrogen bond to the C-2 oxygen of substrate. Arg-39 plays an additional role in the binding of the C-1 carboxylate group. Arg-11 participates both in substrate binding and in catalysis. It interacts with the C-6 carboxylate group, thereby holding the substrate in place and drawing electron density to the C-5 position. The hydrophobic nature of the active site, which lowers the pKa of Pro-1 and provides a favourable environment for catalysis, is largely maintained by Phe-50. Because several Arg residues located near the active site are not conserved among all members of this family and because of the presence of fairly distantly related paralogs in Campylobacter jejuni, the family is regarded as not necessarily uniform in function.; GO: 0016853 isomerase activity, 0006725 cellular aromatic compound metabolic process; PDB: 4OTA_H 4OTC_G 4OTB_J 2FM7_A 1BJP_B 1S0Y_K 3EJ9_E 3EJ7_K 3EJ3_I 3MB2_A ....
Probab=20.33 E-value=89 Score=19.52 Aligned_cols=25 Identities=12% Similarity=0.126 Sum_probs=20.7
Q ss_pred ChhhHHHHHHHHHHHHHhhCCCCCC
Q 028628 179 DISQRLKTASEVNAAILTSQSHEKG 203 (206)
Q Consensus 179 ~~~~r~~la~~vN~aiL~~~~~~~~ 203 (206)
+.+++.+++..+..++.+.+|.|.+
T Consensus 12 ~~e~K~~l~~~it~~~~~~lg~~~~ 36 (60)
T PF01361_consen 12 TAEQKRELAEAITDAVVEVLGIPPE 36 (60)
T ss_dssp -HHHHHHHHHHHHHHHHHHHTS-GG
T ss_pred CHHHHHHHHHHHHHHHHHHhCcCCC
Confidence 6788999999999999999998754
No 111
>PF01535 PPR: PPR repeat; InterPro: IPR002885 This entry represents the PPR repeat. Pentatricopeptide repeat (PPR) proteins are characterised by tandem repeats of a degenerate 35 amino acid motif []. Most of PPR proteins have roles in mitochondria or plastid []. PPR repeats were discovered while screening Arabidopsis proteins for those predicted to be targeted to mitochondria or chloroplast [, ]. Some of these proteins have been shown to play a role in post-transcriptional processes within organelles and they are thought to be sequence-specific RNA-binding proteins [, , ]. Plant genomes have between one hundred to five hundred PPR genes per genome whereas non-plant genomes encode two to six PPR proteins. Although no PPR structures are yet known, the motif is predicted to fold into a helix-turn-helix structure similar to those found in the tetratricopeptide repeat (TPR) family (see PDOC50005 from PROSITEDOC) []. The plant PPR protein family has been divided in two subfamilies on the basis of their motif content and organisation [, ]. Examples of PPR repeat-containing proteins include PET309 P32522 from SWISSPROT, which may be involved in RNA stabilisation [], and crp1, which is involved in RNA processing []. The repeat is associated with a predicted plant protein O49549 from SWISSPROT that has a domain organisation similar to the human BRCA1 protein.
Probab=20.32 E-value=1.2e+02 Score=15.37 Aligned_cols=20 Identities=20% Similarity=0.486 Sum_probs=14.5
Q ss_pred HHHHHHcCCHHHHHHHHHhh
Q 028628 84 VKKAVQCGNVEDAIEKVNDL 103 (206)
Q Consensus 84 I~~~I~~g~i~~Ai~~~~~~ 103 (206)
|......|++++|.++.++.
T Consensus 7 i~~~~~~~~~~~a~~~~~~M 26 (31)
T PF01535_consen 7 ISGYCKMGQFEEALEVFDEM 26 (31)
T ss_pred HHHHHccchHHHHHHHHHHH
Confidence 45556778888888887653
No 112
>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=20.20 E-value=1.7e+02 Score=16.32 Aligned_cols=18 Identities=39% Similarity=0.440 Sum_probs=12.5
Q ss_pred HHHHH--HcCCHHHHHHHHH
Q 028628 84 VKKAV--QCGNVEDAIEKVN 101 (206)
Q Consensus 84 I~~~I--~~g~i~~Ai~~~~ 101 (206)
++.++ ..||++.|+.|+-
T Consensus 18 ~~~AL~~~~~d~~~A~~~L~ 37 (38)
T cd00194 18 ARKALRATNNNVERAVEWLL 37 (38)
T ss_pred HHHHHHHhCCCHHHHHHHHh
Confidence 44443 4589999998873
No 113
>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=20.15 E-value=1.2e+02 Score=23.71 Aligned_cols=27 Identities=19% Similarity=0.380 Sum_probs=20.7
Q ss_pred HHHHHHHHHHHcCCHHHHHHHHHhhCc
Q 028628 79 TDRMAVKKAVQCGNVEDAIEKVNDLNP 105 (206)
Q Consensus 79 ~~r~~I~~~I~~g~i~~Ai~~~~~~~p 105 (206)
..-.++++++..|+..+|++.+=++-|
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 345779999999999999999887755
No 114
>KOG0396 consensus Uncharacterized conserved protein [Function unknown]
Probab=20.10 E-value=4.3e+02 Score=23.80 Aligned_cols=63 Identities=13% Similarity=0.071 Sum_probs=44.5
Q ss_pred HHHHHHHhhCHHHHHHHHHHHhCCC---CCccHHHHHHHHHHHHHHHcCCHHHHHHHHHhhCchhhh
Q 028628 46 LVMNFLVTEGYVDAAEKFRMESGTE---PDIDLATITDRMAVKKAVQCGNVEDAIEKVNDLNPEILD 109 (206)
Q Consensus 46 lI~~YL~~~Gy~~ta~~f~~e~~~~---~~~~~~~~~~r~~I~~~I~~g~i~~Ai~~~~~~~p~l~~ 109 (206)
.|.+-|.+.. ...+-++++|-..+ .....|.-...++...+|..++++.||+.++.++...-+
T Consensus 158 ~I~~sll~~~-l~~~Lswc~ehk~~LkK~~S~lEf~lRlQefIELi~~~~~~~Ai~~akk~f~~~~~ 223 (389)
T KOG0396|consen 158 GIRDSLLAGE-LEPALSWCKEHKVELKKEESSLEFQLRLQEFIELIKVDNYDKAIAFAKKHFAPWAK 223 (389)
T ss_pred HHHHHHHhcc-hHHHHHHHHHHHHHHHhccchhhhHHHHHHHHHHHHhccHHHHHHHHHHHHhhhhh
Confidence 3555555555 66777788776432 234456666678888999999999999999998865433
No 115
>PRK03095 prsA peptidylprolyl isomerase; Reviewed
Probab=20.10 E-value=4.8e+02 Score=22.08 Aligned_cols=36 Identities=19% Similarity=0.361 Sum_probs=21.3
Q ss_pred hcccCCCHHHHHHHHhcCCCCHHHHHHHHHHHHHhhC
Q 028628 19 MSKKVITREEWEKKLNDVKIRKEDMNKLVMNFLVTEG 55 (206)
Q Consensus 19 ~~~~~~~~~~~~~~~~~~~~~~~~l~~lI~~YL~~~G 55 (206)
+..++|++.+|.+.+.. ..-+..|+++|.+-+.-.|
T Consensus 30 ~~~~~IT~~e~~~~~k~-~~~~~~L~~~I~~~l~~~~ 65 (287)
T PRK03095 30 SKAGDITKDEFYEQMKT-QAGKQVLNNMVMEKVLIKN 65 (287)
T ss_pred ecCCcccHHHHHHHHHH-HHHHHHHHHHHHHHHHHcC
Confidence 45678888888877755 2233445555555554444
Done!