Query 030009
Match_columns 184
No_of_seqs 197 out of 804
Neff 6.4
Searched_HMMs 46136
Date Fri Mar 29 07:06:08 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030009.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030009hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2606 OTU (ovarian tumor)-li 99.8 5.3E-22 1.1E-26 169.3 4.5 91 1-93 195-299 (302)
2 KOG3288 OTU-like cysteine prot 99.5 7.4E-15 1.6E-19 123.7 3.4 104 1-108 144-250 (307)
3 PF02338 OTU: OTU-like cystein 99.5 1.3E-14 2.8E-19 108.6 4.1 77 2-86 33-121 (121)
4 KOG3991 Uncharacterized conser 99.4 8.9E-13 1.9E-17 109.6 5.8 91 1-92 162-256 (256)
5 PF10275 Peptidase_C65: Peptid 99.3 2.4E-12 5.2E-17 108.2 7.7 90 1-91 145-244 (244)
6 KOG2605 OTU (ovarian tumor)-li 98.4 8.9E-08 1.9E-12 85.5 2.6 90 1-92 251-344 (371)
7 COG5539 Predicted cysteine pro 98.4 1.9E-07 4.2E-12 80.3 3.9 84 4-90 212-305 (306)
8 COG5539 Predicted cysteine pro 98.2 1.6E-07 3.4E-12 80.8 -0.7 87 1-91 143-231 (306)
9 PF02845 CUE: CUE domain; Int 97.5 0.00027 5.8E-09 44.0 5.4 39 136-174 4-42 (42)
10 PF00627 UBA: UBA/TS-N domain; 97.4 0.00033 7.1E-09 42.4 4.5 35 134-170 3-37 (37)
11 PF14555 UBA_4: UBA-like domai 97.3 0.00052 1.1E-08 42.9 4.4 40 135-175 2-41 (43)
12 smart00546 CUE Domain that may 97.0 0.0018 3.9E-08 40.3 4.8 38 136-173 5-42 (43)
13 cd00194 UBA Ubiquitin Associat 97.0 0.0022 4.8E-08 38.5 4.8 36 135-172 3-38 (38)
14 TIGR00264 alpha-NAC-related pr 96.9 0.0014 3.1E-08 49.7 4.6 39 132-171 77-115 (116)
15 PRK06369 nac nascent polypepti 96.9 0.0018 4E-08 49.1 4.7 41 131-172 74-114 (115)
16 smart00165 UBA Ubiquitin assoc 96.4 0.0081 1.8E-07 35.8 4.5 34 136-171 4-37 (37)
17 COG1308 EGD2 Transcription fac 95.3 0.036 7.9E-07 42.4 4.9 40 131-171 82-121 (122)
18 PF06972 DUF1296: Protein of u 95.2 0.05 1.1E-06 36.6 4.6 39 136-174 8-46 (60)
19 PF03474 DMA: DMRTA motif; In 93.9 0.12 2.7E-06 31.9 4.0 28 144-171 12-39 (39)
20 TIGR00601 rad23 UV excision re 88.8 0.7 1.5E-05 41.8 4.8 38 134-173 157-194 (378)
21 PF08938 HBS1_N: HBS1 N-termin 84.1 0.68 1.5E-05 32.5 1.7 41 136-177 34-74 (79)
22 PF02954 HTH_8: Bacterial regu 81.6 2.3 5E-05 26.0 3.2 22 149-170 7-28 (42)
23 KOG0011 Nucleotide excision re 76.3 4.1 9E-05 36.3 4.3 41 134-176 136-176 (340)
24 PF05861 PhnI: Bacterial phosp 76.2 4.8 0.0001 36.1 4.7 44 136-179 44-87 (358)
25 KOG1071 Mitochondrial translat 75.0 4.4 9.6E-05 36.0 4.1 43 134-177 47-89 (340)
26 PF03943 TAP_C: TAP C-terminal 74.5 3.4 7.4E-05 26.7 2.6 40 136-176 3-42 (51)
27 smart00804 TAP_C C-terminal do 72.8 11 0.00024 25.4 4.9 40 134-174 13-52 (63)
28 KOG2605 OTU (ovarian tumor)-li 71.1 1.5 3.2E-05 39.7 0.3 90 2-94 89-179 (371)
29 PF11626 Rap1_C: TRF2-interact 69.9 7.1 0.00015 27.7 3.6 32 141-173 4-35 (87)
30 KOG2561 Adaptor protein NUB1, 69.8 2.4 5.3E-05 39.4 1.4 42 138-181 308-349 (568)
31 KOG2239 Transcription factor c 69.4 6.7 0.00015 32.6 3.8 36 134-170 172-207 (209)
32 PF11547 E3_UbLigase_EDD: E3 u 68.2 18 0.00039 23.5 4.7 37 137-176 16-52 (53)
33 COG2103 Predicted sugar phosph 66.2 9.2 0.0002 33.4 4.1 37 135-172 235-271 (298)
34 PRK05441 murQ N-acetylmuramic 65.0 10 0.00022 33.0 4.2 37 135-172 237-273 (299)
35 TIGR02934 nifT_nitrog probable 63.7 0.61 1.3E-05 32.1 -2.8 35 6-41 5-40 (67)
36 PF05415 Peptidase_C36: Beet n 63.1 13 0.00029 27.2 3.8 47 22-71 35-83 (104)
37 TIGR00274 N-acetylmuramic acid 60.2 14 0.00031 32.1 4.3 37 135-172 232-268 (291)
38 KOG0010 Ubiquitin-like protein 56.6 14 0.00031 34.5 3.8 34 139-172 459-492 (493)
39 PRK12570 N-acetylmuramic acid- 50.6 24 0.00052 30.7 4.1 37 135-172 233-269 (296)
40 KOG3450 Huntingtin interacting 48.1 22 0.00047 26.8 3.0 40 132-172 79-118 (119)
41 PF06988 NifT: NifT/FixU prote 47.8 0.26 5.6E-06 33.7 -6.7 34 7-41 6-40 (64)
42 KOG4167 Predicted DNA-binding 42.5 28 0.0006 34.5 3.5 31 145-175 573-603 (907)
43 PRK10963 hypothetical protein; 41.7 18 0.00039 30.0 1.9 35 2-43 8-42 (223)
44 COG3626 PhnI Uncharacterized e 41.7 41 0.0009 29.6 4.1 43 136-178 44-86 (367)
45 PF05381 Peptidase_C21: Tymovi 41.0 1E+02 0.0022 23.0 5.6 46 40-88 47-94 (104)
46 smart00668 CTLH C-terminal to 40.6 37 0.0008 21.2 2.9 24 148-173 4-27 (58)
47 PF03765 CRAL_TRIO_N: CRAL/TRI 39.9 51 0.0011 20.8 3.5 26 145-171 28-53 (55)
48 cd05007 SIS_Etherase N-acetylm 37.4 21 0.00046 30.2 1.7 33 134-167 223-255 (257)
49 PF10905 DUF2695: Protein of u 34.8 1E+02 0.0022 20.2 4.2 33 139-171 7-40 (53)
50 KOG2934 Uncharacterized conser 33.4 32 0.00069 28.2 2.0 24 139-162 73-96 (204)
51 COG3159 Uncharacterized protei 32.8 20 0.00042 30.2 0.8 15 2-16 9-23 (218)
52 PRK01905 DNA-binding protein F 29.6 77 0.0017 21.7 3.3 23 148-170 38-60 (77)
53 KOG4015 Fatty acid-binding pro 29.2 1.9E+02 0.0041 22.5 5.7 61 21-90 15-75 (133)
54 PF04340 DUF484: Protein of un 28.4 19 0.00042 29.7 0.0 16 2-17 11-26 (225)
55 PF07802 GCK: GCK domain; Int 27.6 11 0.00024 26.5 -1.3 16 4-19 49-64 (76)
56 TIGR00601 rad23 UV excision re 26.8 1.2E+02 0.0026 27.5 4.8 39 134-174 338-376 (378)
57 PRK00430 fis global DNA-bindin 26.3 89 0.0019 22.6 3.2 23 148-170 56-78 (95)
58 PRK05441 murQ N-acetylmuramic 26.0 98 0.0021 26.9 4.0 32 138-170 267-298 (299)
59 TIGR00149 TIGR00149_YbjQ secon 23.5 3.3E+02 0.0071 20.9 6.1 67 12-80 50-129 (132)
60 PF12244 DUF3606: Protein of u 23.2 2.2E+02 0.0047 18.5 4.4 36 134-170 20-55 (57)
61 COG0773 MurC UDP-N-acetylmuram 22.8 1E+02 0.0022 28.8 3.6 82 9-90 187-273 (459)
62 COG5481 Uncharacterized conser 22.5 99 0.0022 20.9 2.6 25 149-173 9-33 (67)
63 PF05952 ComX: Bacillus compet 22.2 25 0.00054 23.5 -0.4 19 2-20 5-23 (57)
64 PF04877 Hairpins: HrpZ; Inte 22.0 34 0.00074 30.2 0.3 43 1-49 169-211 (308)
65 PF01381 HTH_3: Helix-turn-hel 21.8 1E+02 0.0022 18.8 2.5 30 24-53 23-52 (55)
No 1
>KOG2606 consensus OTU (ovarian tumor)-like cysteine protease [Signal transduction mechanisms; Posttranslational modification, protein turnover, chaperones]
Probab=99.85 E-value=5.3e-22 Score=169.30 Aligned_cols=91 Identities=31% Similarity=0.582 Sum_probs=79.8
Q ss_pred ChHHHHHhCccccccccCCC--------CCHHHHHHhhhcCCccCCHHHHHHHHhhcCccEEEEEccCCceEEee-cccC
Q 030009 1 MVVQYIVKNRETFEPFIEDD--------VPFDEYCQSMETDGTWAGHMELQAASLVTHSNICIHRHMSPRWYIRN-FDYH 71 (184)
Q Consensus 1 lvv~yi~~n~d~F~pFv~~~--------~~f~~Y~~~m~k~g~WGg~iEL~Ala~~~~v~I~V~~~~~~~~~i~~-~~~~ 71 (184)
++|+||++|.++|.||+.++ .+|+.||+.|+.++.|||++||.|||.+|++||.||+.++|...++. |.
T Consensus 195 ~~a~Ymr~H~~df~pf~~~eet~d~~~~~~f~~Yc~eI~~t~~WGgelEL~AlShvL~~PI~Vy~~~~p~~~~geey~-- 272 (302)
T KOG2606|consen 195 ETADYMREHVEDFLPFLLDEETGDSLGPEDFDKYCREIRNTAAWGGELELKALSHVLQVPIEVYQADGPILEYGEEYG-- 272 (302)
T ss_pred HHHHHHHHHHHHhhhHhcCccccccCCHHHHHHHHHHhhhhccccchHHHHHHHHhhccCeEEeecCCCceeechhhC--
Confidence 47999999999999999864 25999999999999999999999999999999999999998776653 32
Q ss_pred CCcEEEEEEc-----cCCcccceeccC
Q 030009 72 EARMIHLSYH-----DGEHYNGVRLKE 93 (184)
Q Consensus 72 ~~~~i~L~Y~-----~g~HYdSV~~~~ 93 (184)
+.++|.|+|| .|+||||+.+..
T Consensus 273 kd~pL~lvY~rH~y~LGeHYNS~~~~~ 299 (302)
T KOG2606|consen 273 KDKPLILVYHRHAYGLGEHYNSVTPLK 299 (302)
T ss_pred CCCCeeeehHHhHHHHHhhhccccccc
Confidence 2579999998 499999998754
No 2
>KOG3288 consensus OTU-like cysteine protease [Signal transduction mechanisms; Posttranslational modification, protein turnover, chaperones]
Probab=99.51 E-value=7.4e-15 Score=123.65 Aligned_cols=104 Identities=23% Similarity=0.372 Sum_probs=84.2
Q ss_pred ChHHHHHhCccccccccCCCCCHHHHHHhhhcCCccCCHHHHHHHHhhcCccEEEEEccCCceEEeeccc--CCCcEEEE
Q 030009 1 MVVQYIVKNRETFEPFIEDDVPFDEYCQSMETDGTWAGHMELQAASLVTHSNICIHRHMSPRWYIRNFDY--HEARMIHL 78 (184)
Q Consensus 1 lvv~yi~~n~d~F~pFv~~~~~f~~Y~~~m~k~g~WGg~iEL~Ala~~~~v~I~V~~~~~~~~~i~~~~~--~~~~~i~L 78 (184)
|+++-...|++.|..-|.+ ++-.+||.||+++.+|||.|||..||..|++.|+|++.+. ..|..|++ .....+.|
T Consensus 144 iiA~~Vasnp~~yn~AiLg-K~n~eYc~WI~k~dsWGGaIElsILS~~ygveI~vvDiqt--~rid~fged~~~~~rv~l 220 (307)
T KOG3288|consen 144 IIAQEVASNPDKYNDAILG-KPNKEYCAWILKMDSWGGAIELSILSDYYGVEICVVDIQT--VRIDRFGEDKNFDNRVLL 220 (307)
T ss_pred HHHHHHhcChhhhhHHHhC-CCcHHHHHHHccccccCceEEeeeehhhhceeEEEEecce--eeehhcCCCCCCCceEEE
Confidence 4678889999999877776 7999999999999999999999999999999999999977 44444543 24566778
Q ss_pred EEccCCcccceeccC-CCCCCCCceeeeccc
Q 030009 79 SYHDGEHYNGVRLKE-DSCIGSARPIIIKAD 108 (184)
Q Consensus 79 ~Y~~g~HYdSV~~~~-~~~~gp~~p~~~~~~ 108 (184)
.| +|.|||++.... .|..-|..+.+...+
T Consensus 221 ly-dGIHYD~l~m~~~~~~~~~~tifp~~dd 250 (307)
T KOG3288|consen 221 LY-DGIHYDPLAMNEFKPTDVDNTIFPVSDD 250 (307)
T ss_pred Ee-cccccChhhhccCCccCCcccccccccc
Confidence 77 899999998765 666666665554444
No 3
>PF02338 OTU: OTU-like cysteine protease; InterPro: IPR003323 This is a group of proteins found primarily in viruses, eukaryotes and in the pathogenic bacterium Chlamydia pneumoniae. In viruses they are annotated as replicase or RNA-dependent RNA polymerase. The eukaryotic sequences are related to the Ovarian Tumour (OTU) gene in Drosophila, cezanne deubiquitinating peptidase and tumor necrosis factor, alpha-induced protein 3 (MEROPS peptidase family C64) and otubain 1 and otubain 2 (MEROPS peptidase family C65). None of these proteins has a known biochemical function but low sequence similarity with the polyprotein regions of arteriviruses, and conserved cysteine and histidine, and possibly the aspartate, residues suggests that those not yet recognised as peptidases could possess cysteine protease activity [].; PDB: 2VFJ_C 3DKB_F 3PHW_A 3PHU_B 3PHX_A 3BY4_A 3C0R_C 3PRM_C 3PRP_C 3ZRH_A ....
Probab=99.50 E-value=1.3e-14 Score=108.63 Aligned_cols=77 Identities=39% Similarity=0.626 Sum_probs=64.8
Q ss_pred hHHHHH-hCccccccccCCCCCHHHHHHhhhcCCccCCHHHHHHHHhhcCccEEEEEccCCceE--Eeec----ccCCCc
Q 030009 2 VVQYIV-KNRETFEPFIEDDVPFDEYCQSMETDGTWAGHMELQAASLVTHSNICIHRHMSPRWY--IRNF----DYHEAR 74 (184)
Q Consensus 2 vv~yi~-~n~d~F~pFv~~~~~f~~Y~~~m~k~g~WGg~iEL~Ala~~~~v~I~V~~~~~~~~~--i~~~----~~~~~~ 74 (184)
+++||+ .|++.|++|+.++ +|+++|+|||++||+|+|.+|+++|.|++...+... +... +....+
T Consensus 33 ~~~~l~~~~~~~~~~~~~~~--------~~~~~~~Wg~~~el~a~a~~~~~~I~v~~~~~~~~~~~~~~~~~~~~~~~~~ 104 (121)
T PF02338_consen 33 VVDYLRDKNRDKFEEFLEGD--------KMSKPGTWGGEIELQALANVLNRPIIVYSSSDGDNVVFIKFTGKYPPLESPP 104 (121)
T ss_dssp HHHHHHTHTTTHHHHHHHHH--------HHTSTTSHEEHHHHHHHHHHHTSEEEEECETTTBEEEEEEESCEESTTTTTT
T ss_pred HHHHHHHhccchhhhhhhhh--------hhccccccCcHHHHHHHHHHhCCeEEEEEcCCCCccceeeecCccccCCCCC
Confidence 789999 9999999999973 999999999999999999999999999988655432 2211 234578
Q ss_pred EEEEEEcc-----CCcc
Q 030009 75 MIHLSYHD-----GEHY 86 (184)
Q Consensus 75 ~i~L~Y~~-----g~HY 86 (184)
+|+|+|+. +.||
T Consensus 105 ~i~l~~~~~l~~~~~Hy 121 (121)
T PF02338_consen 105 PICLCYHGHLYYTGNHY 121 (121)
T ss_dssp SEEEEEETEEEEETTEE
T ss_pred eEEEEEcCCccCCCCCC
Confidence 89999998 9998
No 4
>KOG3991 consensus Uncharacterized conserved protein [Function unknown]
Probab=99.36 E-value=8.9e-13 Score=109.57 Aligned_cols=91 Identities=22% Similarity=0.350 Sum_probs=79.1
Q ss_pred ChHHHHHhCccccccccCCCCCHHHHHHh-hhcCCccCCHHHHHHHHhhcCccEEEEEccCCce-EE--eecccCCCcEE
Q 030009 1 MVVQYIVKNRETFEPFIEDDVPFDEYCQS-METDGTWAGHMELQAASLVTHSNICIHRHMSPRW-YI--RNFDYHEARMI 76 (184)
Q Consensus 1 lvv~yi~~n~d~F~pFv~~~~~f~~Y~~~-m~k~g~WGg~iEL~Ala~~~~v~I~V~~~~~~~~-~i--~~~~~~~~~~i 76 (184)
+++.+|+.|+|+|+|||+++++..+||.. +....+-.|||+|.|||+++++.|+|..++.... .. ..|++...+.|
T Consensus 162 vtS~~ik~~adfy~pFI~e~~tV~~fC~~eVEPm~kesdhi~I~ALs~Al~i~irVey~dr~~~~~~~hH~fpe~s~P~I 241 (256)
T KOG3991|consen 162 VTSGFIKSNADFYQPFIDEGMTVKAFCTQEVEPMYKESDHIHITALSQALGIRIRVEYVDRGSGDTVNHHDFPEASAPEI 241 (256)
T ss_pred HHHHHHhhChhhhhccCCCCCcHHHHHHhhcchhhhccCceeHHHHHhhhCceEEEEEecCCCCCCCCCCcCccccCceE
Confidence 36789999999999999999999999996 8999999999999999999999999999976433 22 23667788999
Q ss_pred EEEEccCCcccceecc
Q 030009 77 HLSYHDGEHYNGVRLK 92 (184)
Q Consensus 77 ~L~Y~~g~HYdSV~~~ 92 (184)
.|.|..| |||.++++
T Consensus 242 ~LLYrpG-HYdilY~~ 256 (256)
T KOG3991|consen 242 YLLYRPG-HYDILYKK 256 (256)
T ss_pred EEEecCC-ccccccCC
Confidence 9999887 99999873
No 5
>PF10275 Peptidase_C65: Peptidase C65 Otubain; InterPro: IPR019400 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This family of proteins is a highly specific ubiquitin iso-peptidase that removes ubiquitin from proteins. The modification of cellular proteins by ubiquitin (Ub) is an important event that underlies protein stability and function in eukaryotes, as it is a dynamic and reversible process. Otubain carries several key conserved domains: (i) the OTU (ovarian tumour domain) in which there is an active cysteine protease triad (ii) a nuclear localisation signal, (iii) a Ub interaction motif (UIM)-like motif phi-xx-A-xxxs-xx-Ac (where phi indicates an aromatic amino acid, x indicates any amino acid and Ac indicates an acidic amino acid), (iv) a Ub-associated (UBA)-like domain and (v) the LxxLL motif. ; PDB: 4DDG_C 3VON_O 2ZFY_A 4DHZ_A 4DDI_C 1TFF_A 4DHJ_I 4DHI_B.
Probab=99.34 E-value=2.4e-12 Score=108.24 Aligned_cols=90 Identities=23% Similarity=0.403 Sum_probs=69.4
Q ss_pred ChHHHHHhCccccccccCCC--CCHHHHHHh-hhcCCccCCHHHHHHHHhhcCccEEEEEccCC----ceEEeecc---c
Q 030009 1 MVVQYIVKNRETFEPFIEDD--VPFDEYCQS-METDGTWAGHMELQAASLVTHSNICIHRHMSP----RWYIRNFD---Y 70 (184)
Q Consensus 1 lvv~yi~~n~d~F~pFv~~~--~~f~~Y~~~-m~k~g~WGg~iEL~Ala~~~~v~I~V~~~~~~----~~~i~~~~---~ 70 (184)
+++.||+.|++.|+||+++. .++++||++ +...+.-++|+.|.|||++++++|.|+.++.. ......++ .
T Consensus 145 lts~~l~~~~d~y~~fi~~~~~~tve~~C~~~Vep~~~Ead~v~i~ALa~aL~v~i~v~yld~~~~~~~~~~~~~~~~~~ 224 (244)
T PF10275_consen 145 LTSAYLKSNSDEYEPFIDGLEYLTVEEFCSQEVEPMGKEADHVQIIALAQALGVPIRVEYLDRSVEGDEVNRHEFPPDNE 224 (244)
T ss_dssp HHHHHHHHTHHHHGGGSSTT--S-HHHHHHHHTSSTT--B-HHHHHHHHHHHT--EEEEESSSSGCSTTSEEEEES-SST
T ss_pred HHHHHHHhhHHHHhhhhcccccCCHHHHHHhhcccccccchhHHHHHHHHHhCCeEEEEEecCCCCCCccccccCCCccC
Confidence 47899999999999999976 799999975 99999999999999999999999999999854 11222342 3
Q ss_pred CCCcEEEEEEccCCcccceec
Q 030009 71 HEARMIHLSYHDGEHYNGVRL 91 (184)
Q Consensus 71 ~~~~~i~L~Y~~g~HYdSV~~ 91 (184)
...+.|+|.|..| |||.+++
T Consensus 225 ~~~~~i~LLyrpg-HYdIly~ 244 (244)
T PF10275_consen 225 SQEPQITLLYRPG-HYDILYP 244 (244)
T ss_dssp TSS-SEEEEEETB-EEEEEEE
T ss_pred CCCCEEEEEEcCC-ccccccC
Confidence 4678999999988 9999875
No 6
>KOG2605 consensus OTU (ovarian tumor)-like cysteine protease [Signal transduction mechanisms; Posttranslational modification, protein turnover, chaperones]
Probab=98.45 E-value=8.9e-08 Score=85.49 Aligned_cols=90 Identities=21% Similarity=0.306 Sum_probs=71.9
Q ss_pred ChHHHHHhCccccccccCCCCCHHHHHHhhhcCCccCCHHHHHHHH---hhcCccEEEEEccCCceEEee-cccCCCcEE
Q 030009 1 MVVQYIVKNRETFEPFIEDDVPFDEYCQSMETDGTWAGHMELQAAS---LVTHSNICIHRHMSPRWYIRN-FDYHEARMI 76 (184)
Q Consensus 1 lvv~yi~~n~d~F~pFv~~~~~f~~Y~~~m~k~g~WGg~iEL~Ala---~~~~v~I~V~~~~~~~~~i~~-~~~~~~~~i 76 (184)
++++++..++++|+.|+.. +|.+|+.+|++++.||.|+|+||+| .....++.|.+...+.|.-.. -.+.....+
T Consensus 251 ~~~dq~~~e~~~~~~~vt~--~~~~y~k~kr~~~~~gnhie~Qa~a~~~~~~~~~~~~~~~~~t~~~~~~~~~~~~~~~~ 328 (371)
T KOG2605|consen 251 ECVDQLKKERDFYEDYVTE--DFTSYIKRKRADGEPGNHIEQQAAADIYEEIEKPLNITSFKDTCYIQTPPAIEESVKME 328 (371)
T ss_pred HHHHHHhhccccccccccc--chhhcccccccCCCCcchHHHhhhhhhhhhccccceeecccccceeccCcccccchhhh
Confidence 4789999999999999995 8999999999999999999999999 555777778777776554321 112234457
Q ss_pred EEEEccCCcccceecc
Q 030009 77 HLSYHDGEHYNGVRLK 92 (184)
Q Consensus 77 ~L~Y~~g~HYdSV~~~ 92 (184)
++.|..-.||+.++.-
T Consensus 329 ~~n~~~~~h~~~~~~~ 344 (371)
T KOG2605|consen 329 KYNFWVEVHYNTARHS 344 (371)
T ss_pred hhcccchhhhhhcccc
Confidence 7777788999999884
No 7
>COG5539 Predicted cysteine protease (OTU family) [Posttranslational modification, protein turnover, chaperones]
Probab=98.42 E-value=1.9e-07 Score=80.29 Aligned_cols=84 Identities=19% Similarity=0.184 Sum_probs=64.1
Q ss_pred HHHHhCccccccccCCC-----CCHHHHHHhhhcCCccCCHHHHHHHHhhcCccEEEEEccCCceEEeecccCCCcEEEE
Q 030009 4 QYIVKNRETFEPFIEDD-----VPFDEYCQSMETDGTWAGHMELQAASLVTHSNICIHRHMSPRWYIRNFDYHEARMIHL 78 (184)
Q Consensus 4 ~yi~~n~d~F~pFv~~~-----~~f~~Y~~~m~k~g~WGg~iEL~Ala~~~~v~I~V~~~~~~~~~i~~~~~~~~~~i~L 78 (184)
.|..++.+.|.+|..|. .+|++||..|+-+..||+.+|++|||.+|++++.++...+|...-...+. ....-+
T Consensus 212 ~~~q~~~i~f~g~hfD~~t~~m~~~dt~~ne~~~~a~~g~~~ei~qLas~lk~~~~~~nT~~~~ik~n~c~~--~~~~e~ 289 (306)
T COG5539 212 PYVQRISILFTGIHFDEETLAMVLWDTYVNEVLFDASDGITIEIQQLASLLKNPHYYTNTASPSIKCNICGT--GFVGEK 289 (306)
T ss_pred hhhhhhhhhhcccccchhhhhcchHHHHHhhhcccccccchHHHHHHHHHhcCceEEeecCCceEEeecccc--ccchhh
Confidence 56778999999999875 37999999999999999999999999999999999988776443322111 111223
Q ss_pred EE-----ccCCccccee
Q 030009 79 SY-----HDGEHYNGVR 90 (184)
Q Consensus 79 ~Y-----~~g~HYdSV~ 90 (184)
.| -.| |||+..
T Consensus 290 ~~~~Ha~a~G-H~n~~~ 305 (306)
T COG5539 290 DYYAHALATG-HYNFGE 305 (306)
T ss_pred HHHHHHHhhc-CccccC
Confidence 33 358 999874
No 8
>COG5539 Predicted cysteine protease (OTU family) [Posttranslational modification, protein turnover, chaperones]
Probab=98.24 E-value=1.6e-07 Score=80.84 Aligned_cols=87 Identities=15% Similarity=0.206 Sum_probs=69.7
Q ss_pred ChHHHHHhCccccccccCCCCCHHHHHHhhhcCCccC-CHHHHHHHHhhcCccEEEEEccCCceEEeecc-cCCCcEEEE
Q 030009 1 MVVQYIVKNRETFEPFIEDDVPFDEYCQSMETDGTWA-GHMELQAASLVTHSNICIHRHMSPRWYIRNFD-YHEARMIHL 78 (184)
Q Consensus 1 lvv~yi~~n~d~F~pFv~~~~~f~~Y~~~m~k~g~WG-g~iEL~Ala~~~~v~I~V~~~~~~~~~i~~~~-~~~~~~i~L 78 (184)
+|+.-+.+|||.|.+.+.+ .+--.||.|+.++..|| |++||.++|..+++.|+++.++..... .|. ......+.+
T Consensus 143 ~vs~Ev~snPDl~n~~i~~-~~~i~y~~~i~k~d~~~dG~ieia~iS~~l~v~i~~Vdv~~~~~d--r~~~~~~~q~~~i 219 (306)
T COG5539 143 VVSLEVLSNPDLYNPAILE-IDVIAYATWIVKPDSQGDGCIEIAIISDQLPVRIHVVDVDKDSED--RYNSHPYVQRISI 219 (306)
T ss_pred HHHHHHhhCccccchhhcC-cchHHHHHhhhccccCCCceEEEeEeccccceeeeeeecchhHHh--hccCChhhhhhhh
Confidence 3567788999999999997 89999999999999999 999999999999999999999864221 122 122334666
Q ss_pred EEccCCcccceec
Q 030009 79 SYHDGEHYNGVRL 91 (184)
Q Consensus 79 ~Y~~g~HYdSV~~ 91 (184)
.| .|.|||....
T Consensus 220 ~f-~g~hfD~~t~ 231 (306)
T COG5539 220 LF-TGIHFDEETL 231 (306)
T ss_pred hh-cccccchhhh
Confidence 66 6889999873
No 9
>PF02845 CUE: CUE domain; InterPro: IPR003892 This domain may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two proteins of the IL-1 signal transduction pathway, tollip and TAB2.; GO: 0005515 protein binding; PDB: 2EKF_A 1OTR_A 1P3Q_Q 1MN3_A 1WGL_A 2EJS_A 2DAE_A 2DHY_A 2DI0_A.
Probab=97.55 E-value=0.00027 Score=43.96 Aligned_cols=39 Identities=28% Similarity=0.296 Sum_probs=32.6
Q ss_pred HHHHHHhcCCCCChHHHHHHHHHhCCCHHHHHHHHHHhc
Q 030009 136 SIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAEQ 174 (184)
Q Consensus 136 ~v~~v~~~tG~~d~~~i~~~L~~~~gdid~Ai~~Ll~~~ 174 (184)
.|+.+..-.+-.+.+.|+.+|++++||+|.||+.||+.+
T Consensus 4 ~v~~L~~mFP~~~~~~I~~~L~~~~~~ve~ai~~LL~~~ 42 (42)
T PF02845_consen 4 MVQQLQEMFPDLDREVIEAVLQANNGDVEAAIDALLEMS 42 (42)
T ss_dssp HHHHHHHHSSSS-HHHHHHHHHHTTTTHHHHHHHHHHHH
T ss_pred HHHHHHHHCCCCCHHHHHHHHHHcCCCHHHHHHHHHcCC
Confidence 466666666777899999999999999999999999863
No 10
>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=97.42 E-value=0.00033 Score=42.38 Aligned_cols=35 Identities=26% Similarity=0.504 Sum_probs=29.9
Q ss_pred hhHHHHHHhcCCCCChHHHHHHHHHhCCCHHHHHHHH
Q 030009 134 AGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFL 170 (184)
Q Consensus 134 ~~~v~~v~~~tG~~d~~~i~~~L~~~~gdid~Ai~~L 170 (184)
++.|++++.- |. +.+.++++|+.++||++.|+++|
T Consensus 3 ~~~v~~L~~m-Gf-~~~~~~~AL~~~~~nve~A~~~L 37 (37)
T PF00627_consen 3 EEKVQQLMEM-GF-SREQAREALRACNGNVERAVDWL 37 (37)
T ss_dssp HHHHHHHHHH-TS--HHHHHHHHHHTTTSHHHHHHHH
T ss_pred HHHHHHHHHc-CC-CHHHHHHHHHHcCCCHHHHHHhC
Confidence 4568888886 75 58899999999999999999987
No 11
>PF14555 UBA_4: UBA-like domain; PDB: 2DAL_A 3BQ3_A 2L4E_A 2L4F_A 2DZL_A 2L2D_A 2DAM_A 1V92_A 3E21_A.
Probab=97.29 E-value=0.00052 Score=42.94 Aligned_cols=40 Identities=18% Similarity=0.209 Sum_probs=33.2
Q ss_pred hHHHHHHhcCCCCChHHHHHHHHHhCCCHHHHHHHHHHhcC
Q 030009 135 GSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAEQG 175 (184)
Q Consensus 135 ~~v~~v~~~tG~~d~~~i~~~L~~~~gdid~Ai~~Ll~~~~ 175 (184)
..|++.|.-||| +.+..++.|+.+++|++.||..-++...
T Consensus 2 e~i~~F~~iTg~-~~~~A~~~L~~~~wdle~Av~~y~~~~~ 41 (43)
T PF14555_consen 2 EKIAQFMSITGA-DEDVAIQYLEANNWDLEAAVNAYFDDGE 41 (43)
T ss_dssp HHHHHHHHHH-S-SHHHHHHHHHHTTT-HHHHHHHHHHSS-
T ss_pred HHHHHHHHHHCc-CHHHHHHHHHHcCCCHHHHHHHHHhCCC
Confidence 358899999999 7899999999999999999999887654
No 12
>smart00546 CUE Domain that may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two protein of the IL-1 signal transduction pathway, tollip and TAB2. Ponting (Biochem. J.) "Proteins of the Endoplasmic reticulum" (in press)
Probab=97.01 E-value=0.0018 Score=40.32 Aligned_cols=38 Identities=21% Similarity=0.221 Sum_probs=31.9
Q ss_pred HHHHHHhcCCCCChHHHHHHHHHhCCCHHHHHHHHHHh
Q 030009 136 SIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAE 173 (184)
Q Consensus 136 ~v~~v~~~tG~~d~~~i~~~L~~~~gdid~Ai~~Ll~~ 173 (184)
.++.+..-.+--+...|+.+|++++||+|.||..||..
T Consensus 5 ~v~~L~~mFP~l~~~~I~~~L~~~~g~ve~~i~~LL~~ 42 (43)
T smart00546 5 ALHDLKDMFPNLDEEVIKAVLEANNGNVEATINNLLEG 42 (43)
T ss_pred HHHHHHHHCCCCCHHHHHHHHHHcCCCHHHHHHHHHcC
Confidence 45556665666789999999999999999999999964
No 13
>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=96.97 E-value=0.0022 Score=38.51 Aligned_cols=36 Identities=19% Similarity=0.442 Sum_probs=29.7
Q ss_pred hHHHHHHhcCCCCChHHHHHHHHHhCCCHHHHHHHHHH
Q 030009 135 GSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIA 172 (184)
Q Consensus 135 ~~v~~v~~~tG~~d~~~i~~~L~~~~gdid~Ai~~Ll~ 172 (184)
..|++++. .|. +.+.++++|+.++||++.|+++|+.
T Consensus 3 ~~v~~L~~-mGf-~~~~~~~AL~~~~~d~~~A~~~L~~ 38 (38)
T cd00194 3 EKLEQLLE-MGF-SREEARKALRATNNNVERAVEWLLE 38 (38)
T ss_pred HHHHHHHH-cCC-CHHHHHHHHHHhCCCHHHHHHHHhC
Confidence 34566665 575 5999999999999999999999973
No 14
>TIGR00264 alpha-NAC-related protein. This hypothetical protein is found so far only in the Archaea. Its C-terminal domain of about 40 amino acids is homologous to the C-termini of the nascent polypeptide-associated complex alpha chain (alpha-NAC) and its yeast ortholog Egd2p and to the huntingtin-interacting protein HYPK. It shows weaker similarity, possibly through shared structural constraints rather than through homology, with the amino-terminal domain of elongation factor Ts. Alpha-NAC plays a role in preventing nascent polypeptides from binding inappropriately to membrane-targeting apparatus during translation, but is also active as a transcription regulator.
Probab=96.94 E-value=0.0014 Score=49.68 Aligned_cols=39 Identities=33% Similarity=0.445 Sum_probs=34.8
Q ss_pred CChhHHHHHHhcCCCCChHHHHHHHHHhCCCHHHHHHHHH
Q 030009 132 INAGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLI 171 (184)
Q Consensus 132 ~~~~~v~~v~~~tG~~d~~~i~~~L~~~~gdid~Ai~~Ll 171 (184)
++++.|+.||..|||+ .+..+++|++|+||+-.||.+|-
T Consensus 77 i~~eDI~lV~eq~gvs-~e~A~~AL~~~~gDl~~AI~~L~ 115 (116)
T TIGR00264 77 ITEDDIELVMKQCNVS-KEEARRALEECGGDLAEAIMKLE 115 (116)
T ss_pred CCHHHHHHHHHHhCcC-HHHHHHHHHHcCCCHHHHHHHhh
Confidence 4566799999999995 89999999999999999999873
No 15
>PRK06369 nac nascent polypeptide-associated complex protein; Reviewed
Probab=96.88 E-value=0.0018 Score=49.10 Aligned_cols=41 Identities=29% Similarity=0.375 Sum_probs=35.9
Q ss_pred cCChhHHHHHHhcCCCCChHHHHHHHHHhCCCHHHHHHHHHH
Q 030009 131 IINAGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIA 172 (184)
Q Consensus 131 ~~~~~~v~~v~~~tG~~d~~~i~~~L~~~~gdid~Ai~~Ll~ 172 (184)
.++++.|+.||..|||+ .+..+++|++|+||+-.||.+|-.
T Consensus 74 ~i~~edI~lv~~q~gvs-~~~A~~AL~~~~gDl~~AI~~L~~ 114 (115)
T PRK06369 74 EIPEEDIELVAEQTGVS-EEEARKALEEANGDLAEAILKLSS 114 (115)
T ss_pred CCCHHHHHHHHHHHCcC-HHHHHHHHHHcCCcHHHHHHHHhc
Confidence 35566799999999996 899999999999999999998853
No 16
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=96.42 E-value=0.0081 Score=35.83 Aligned_cols=34 Identities=26% Similarity=0.457 Sum_probs=28.0
Q ss_pred HHHHHHhcCCCCChHHHHHHHHHhCCCHHHHHHHHH
Q 030009 136 SIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLI 171 (184)
Q Consensus 136 ~v~~v~~~tG~~d~~~i~~~L~~~~gdid~Ai~~Ll 171 (184)
.+++++. .| .+.+.++++|..++||++.|+++|+
T Consensus 4 ~v~~L~~-mG-f~~~~a~~aL~~~~~d~~~A~~~L~ 37 (37)
T smart00165 4 KIDQLLE-MG-FSREEALKALRAANGNVERAAEYLL 37 (37)
T ss_pred HHHHHHH-cC-CCHHHHHHHHHHhCCCHHHHHHHHC
Confidence 4555555 46 5688999999999999999999985
No 17
>COG1308 EGD2 Transcription factor homologous to NACalpha-BTF3 [Transcription]
Probab=95.31 E-value=0.036 Score=42.41 Aligned_cols=40 Identities=38% Similarity=0.474 Sum_probs=35.6
Q ss_pred cCChhHHHHHHhcCCCCChHHHHHHHHHhCCCHHHHHHHHH
Q 030009 131 IINAGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLI 171 (184)
Q Consensus 131 ~~~~~~v~~v~~~tG~~d~~~i~~~L~~~~gdid~Ai~~Ll 171 (184)
.+.++-|+.||..||.+ .+.++.+|++++||+-.||..|.
T Consensus 82 ~i~eeDIkLV~eQa~Vs-reeA~kAL~e~~GDlaeAIm~L~ 121 (122)
T COG1308 82 DISEEDIKLVMEQAGVS-REEAIKALEEAGGDLAEAIMKLT 121 (122)
T ss_pred CCCHHHHHHHHHHhCCC-HHHHHHHHHHcCCcHHHHHHHhc
Confidence 46677899999999985 99999999999999999998874
No 18
>PF06972 DUF1296: Protein of unknown function (DUF1296); InterPro: IPR009719 This family represents a conserved region approximately 60 residues long within a number of plant proteins of unknown function.
Probab=95.17 E-value=0.05 Score=36.61 Aligned_cols=39 Identities=18% Similarity=0.400 Sum_probs=33.4
Q ss_pred HHHHHHhcCCCCChHHHHHHHHHhCCCHHHHHHHHHHhc
Q 030009 136 SIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAEQ 174 (184)
Q Consensus 136 ~v~~v~~~tG~~d~~~i~~~L~~~~gdid~Ai~~Ll~~~ 174 (184)
.||.+=..+||+.-+-|..+|.+|+.|.+.|+..||..+
T Consensus 8 ~VQ~iKEiv~~hse~eIya~L~ecnMDpnea~qrLL~qD 46 (60)
T PF06972_consen 8 TVQSIKEIVGCHSEEEIYAMLKECNMDPNEAVQRLLSQD 46 (60)
T ss_pred HHHHHHHHhcCCCHHHHHHHHHHhCCCHHHHHHHHHhcC
Confidence 356666678998888999999999999999999999854
No 19
>PF03474 DMA: DMRTA motif; InterPro: IPR005173 This region is found to the C terminus of the DM DNA-binding domain IPR001275 from INTERPRO []. DM-domain proteins with this motif are known as DMRTA proteins. The function of this region is unknown.
Probab=93.94 E-value=0.12 Score=31.90 Aligned_cols=28 Identities=29% Similarity=0.345 Sum_probs=23.5
Q ss_pred CCCCChHHHHHHHHHhCCCHHHHHHHHH
Q 030009 144 SGCENSEKVEEVLLQVGGDVDAAIEFLI 171 (184)
Q Consensus 144 tG~~d~~~i~~~L~~~~gdid~Ai~~Ll 171 (184)
..-.....+..+|+.|+||+-.|||.+|
T Consensus 12 FP~~kr~~Le~iL~~C~GDvv~AIE~~l 39 (39)
T PF03474_consen 12 FPHQKRSVLELILQRCNGDVVQAIEQFL 39 (39)
T ss_pred CCCCChHHHHHHHHHcCCcHHHHHHHhC
Confidence 3445678888899999999999999875
No 20
>TIGR00601 rad23 UV excision repair protein Rad23. All proteins in this family for which functions are known are components of a multiprotein complex used for targeting nucleotide excision repair to specific parts of the genome. In humans, Rad23 complexes with the XPC protein. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=88.80 E-value=0.7 Score=41.78 Aligned_cols=38 Identities=29% Similarity=0.403 Sum_probs=33.4
Q ss_pred hhHHHHHHhcCCCCChHHHHHHHHHhCCCHHHHHHHHHHh
Q 030009 134 AGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAE 173 (184)
Q Consensus 134 ~~~v~~v~~~tG~~d~~~i~~~L~~~~gdid~Ai~~Ll~~ 173 (184)
+.+|+.+|.= | ++.+.|+.+|++.=+|-|.||||||.-
T Consensus 157 e~~I~~i~eM-G-f~R~qV~~ALRAafNNPdRAVEYL~tG 194 (378)
T TIGR00601 157 ETTIEEIMEM-G-YEREEVERALRAAFNNPDRAVEYLLTG 194 (378)
T ss_pred HHHHHHHHHh-C-CCHHHHHHHHHHHhCCHHHHHHHHHhC
Confidence 4578888883 4 799999999999999999999999964
No 21
>PF08938 HBS1_N: HBS1 N-terminus; InterPro: IPR015033 This domain is found in various eukaryotic HBS1-like proteins. ; PDB: 1UFZ_A 3IZQ_1.
Probab=84.08 E-value=0.68 Score=32.50 Aligned_cols=41 Identities=20% Similarity=0.314 Sum_probs=29.8
Q ss_pred HHHHHHhcCCCCChHHHHHHHHHhCCCHHHHHHHHHHhcCCC
Q 030009 136 SIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAEQGTE 177 (184)
Q Consensus 136 ~v~~v~~~tG~~d~~~i~~~L~~~~gdid~Ai~~Ll~~~~~~ 177 (184)
.|+.+|..+-- .-..|+++|-.+.+|++.||.+||......
T Consensus 34 ~vr~~Lg~~~~-~e~~i~eal~~~~fDvekAl~~Ll~~~~~~ 74 (79)
T PF08938_consen 34 QVREVLGDYVP-PEEQIKEALWHYYFDVEKALDYLLSKFKKK 74 (79)
T ss_dssp CHHHHCCCCC---CCHHHHHHHHTTT-CCHHHHHHHHCCHSS
T ss_pred HHHHHHcccCC-CHHHHHHHHHHHcCCHHHHHHHHHHhccCC
Confidence 36677764221 567788999999999999999999876544
No 22
>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences [,]. It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli []. Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion. In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor []. The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution [,]. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as `feelers' suitable for DNA or protein (invertase) recognition []. Other proteins belonging to this subfamily include: E. coli: atoC, hydG, ntrC, fhlA, tyrR, Rhizobium spp.: ntrC, nifA, dctD ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NTC_A 3JRH_A 3JRB_A 3IV5_A 3JRI_A 1ETQ_A 1ETW_B 1ETY_A 3JRF_A 3JRA_A ....
Probab=81.56 E-value=2.3 Score=26.02 Aligned_cols=22 Identities=27% Similarity=0.525 Sum_probs=18.3
Q ss_pred hHHHHHHHHHhCCCHHHHHHHH
Q 030009 149 SEKVEEVLLQVGGDVDAAIEFL 170 (184)
Q Consensus 149 ~~~i~~~L~~~~gdid~Ai~~L 170 (184)
.+.|+++|+.++||+..|-..|
T Consensus 7 ~~~i~~aL~~~~gn~~~aA~~L 28 (42)
T PF02954_consen 7 KQLIRQALERCGGNVSKAARLL 28 (42)
T ss_dssp HHHHHHHHHHTTT-HHHHHHHH
T ss_pred HHHHHHHHHHhCCCHHHHHHHH
Confidence 5789999999999999887765
No 23
>KOG0011 consensus Nucleotide excision repair factor NEF2, RAD23 component [Replication, recombination and repair]
Probab=76.26 E-value=4.1 Score=36.25 Aligned_cols=41 Identities=22% Similarity=0.337 Sum_probs=34.0
Q ss_pred hhHHHHHHhcCCCCChHHHHHHHHHhCCCHHHHHHHHHHhcCC
Q 030009 134 AGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAEQGT 176 (184)
Q Consensus 134 ~~~v~~v~~~tG~~d~~~i~~~L~~~~gdid~Ai~~Ll~~~~~ 176 (184)
..+|+++|.- | +|.+.|+.+|++.=+|-|+||+|||-=...
T Consensus 136 e~~V~~Im~M-G-y~re~V~~AlRAafNNPeRAVEYLl~GIP~ 176 (340)
T KOG0011|consen 136 EQTVQQIMEM-G-YDREEVERALRAAFNNPERAVEYLLNGIPE 176 (340)
T ss_pred HHHHHHHHHh-C-ccHHHHHHHHHHhhCChhhhHHHHhcCCcc
Confidence 3467788873 4 899999999999999999999999964444
No 24
>PF05861 PhnI: Bacterial phosphonate metabolism protein (PhnI); InterPro: IPR008773 This family consists of several proteobacterial phosphonate metabolism protein (PhnI) sequences. Bacteria that use phosphonates as a phosphorus source must be able to break the stable carbon-phosphorus bond. In Escherichia coli phosphonates are broken down by a C-P lyase that has a broad substrate specificity. The genes for phosphonate uptake and degradation in E. coli are organised in an operon of 14 genes, named phnC to phnP. Three gene products (PhnC, PhnD and PhnE) comprise a binding protein-dependent phosphonate transporter, which also transports phosphate, phosphite, and certain phosphate esters such as phosphoserine; two gene products (PhnF and PhnO) may have a role in gene regulation; and nine gene products (PhnG, PhnH, PhnI, PhnJ, PhnK, PhnL, PhnM, PhnN, and PhnP) probably comprise a membrane-associated C-P lyase enzyme complex [].; GO: 0015716 phosphonate transport
Probab=76.18 E-value=4.8 Score=36.11 Aligned_cols=44 Identities=25% Similarity=0.184 Sum_probs=39.0
Q ss_pred HHHHHHhcCCCCChHHHHHHHHHhCCCHHHHHHHHHHhcCCCcc
Q 030009 136 SIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAEQGTEEY 179 (184)
Q Consensus 136 ~v~~v~~~tG~~d~~~i~~~L~~~~gdid~Ai~~Ll~~~~~~~~ 179 (184)
+|..||...|.+|.++..-+|++..||.-.||..|.+=+++-..
T Consensus 44 avdrVMsEgsLYdp~LAAlAiKQa~GD~~EAiFLLRAyRtTlPR 87 (358)
T PF05861_consen 44 AVDRVMSEGSLYDPELAALAIKQARGDLIEAIFLLRAYRTTLPR 87 (358)
T ss_pred HHHHHhccccccCHHHHHHHHHHhcCCHHHHHHHHHHHHhhccc
Confidence 45689999999999999999999999999999999987766543
No 25
>KOG1071 consensus Mitochondrial translation elongation factor EF-Tsmt, catalyzes nucleotide exchange on EF-Tumt [Translation, ribosomal structure and biogenesis]
Probab=75.01 E-value=4.4 Score=35.98 Aligned_cols=43 Identities=23% Similarity=0.319 Sum_probs=36.5
Q ss_pred hhHHHHHHhcCCCCChHHHHHHHHHhCCCHHHHHHHHHHhcCCC
Q 030009 134 AGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAEQGTE 177 (184)
Q Consensus 134 ~~~v~~v~~~tG~~d~~~i~~~L~~~~gdid~Ai~~Ll~~~~~~ 177 (184)
...+++.-..||- .+..++++|++|+||++.|.++|-...+.+
T Consensus 47 ~allk~LR~kTga-s~~ncKkALee~~gDl~~A~~~L~k~aqk~ 89 (340)
T KOG1071|consen 47 KALLKKLREKTGA-SMVNCKKALEECGGDLVLAEEWLHKKAQKE 89 (340)
T ss_pred HHHHHHHHHHcCC-cHHHHHHHHHHhCCcHHHHHHHHHHHHHHh
Confidence 4467788889995 699999999999999999999998766555
No 26
>PF03943 TAP_C: TAP C-terminal domain; InterPro: IPR005637 This entry contains the NXF family of shuttling transport receptors for nuclear export of mRNA, which include: vertebrate mRNA export factor TAP or nuclear RNA export factor 1 (NXF1). Caenorhabditis elegans nuclear RNA export factor 1 (nxf-1). yeast mRNA export factor MEX67. Members of the NXF family have a modular structure. A nuclear localization sequence and a noncanonical RNA recognition motif (RRM) (see PDOC00030 from PROSITEDOC) followed by four LRR repeats are located in its N-terminal half. The C-terminal half contains a NTF2 domain (see PDOC50177 from PROSITEDOC) followed by a second domain, TAP-C. The TAP-C domain is important for binding to FG repeat-containing nuclear pore proteins (FG-nucleoporins) and is sufficient to mediate nuclear shuttling [,]. The Tap-C domain is made of four alpha helices packed against each other. The arrangement of helices 1, 2 and 3 is similar to that seen in a UBA fold. and is joined to the next module by flexible 12-residue Pro-rich linker [, ].; GO: 0051028 mRNA transport, 0005634 nucleus; PDB: 1OAI_A 1GO5_A 2KHH_A 2JP7_A.
Probab=74.53 E-value=3.4 Score=26.65 Aligned_cols=40 Identities=15% Similarity=0.128 Sum_probs=33.0
Q ss_pred HHHHHHhcCCCCChHHHHHHHHHhCCCHHHHHHHHHHhcCC
Q 030009 136 SIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAEQGT 176 (184)
Q Consensus 136 ~v~~v~~~tG~~d~~~i~~~L~~~~gdid~Ai~~Ll~~~~~ 176 (184)
.|.+++..||- +.+--+..|++++-|.++|+.........
T Consensus 3 mv~~~s~~Tgm-n~~~s~~CL~~n~Wd~~~A~~~F~~l~~~ 42 (51)
T PF03943_consen 3 MVQQFSQQTGM-NLEWSQKCLEENNWDYERALQNFEELKAQ 42 (51)
T ss_dssp HHHHHHHHCSS--CCHHHHHHHHTTT-CCHHHHHHHHCCCT
T ss_pred HHHHHHHHHCC-CHHHHHHHHHHcCCCHHHHHHHHHHHHHc
Confidence 46788889997 68889999999999999999998877655
No 27
>smart00804 TAP_C C-terminal domain of vertebrate Tap protein. The vertebrate Tap protein is a member of the NXF family of shuttling transport receptors for the nuclear export of mRNA. Its most C-terminal domain is important for binding to FG repeat-containing nuclear pore proteins (FG-nucleoporins) and is sufficient to mediate shuttling. This domain forms a compact four-helix fold related to that of a UBA domain.
Probab=72.78 E-value=11 Score=25.44 Aligned_cols=40 Identities=18% Similarity=0.159 Sum_probs=34.2
Q ss_pred hhHHHHHHhcCCCCChHHHHHHHHHhCCCHHHHHHHHHHhc
Q 030009 134 AGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAEQ 174 (184)
Q Consensus 134 ~~~v~~v~~~tG~~d~~~i~~~L~~~~gdid~Ai~~Ll~~~ 174 (184)
...|.+++..||. +.+--+..|++++.|.+.|+....+..
T Consensus 13 ~~~v~~~~~~Tgm-n~~~s~~cLe~~~Wd~~~Al~~F~~lk 52 (63)
T smart00804 13 QEMVQAFSAQTGM-NAEYSQMCLEDNNWDYERALKNFTELK 52 (63)
T ss_pred HHHHHHHHHHHCC-CHHHHHHHHHHcCCCHHHHHHHHHHHH
Confidence 3457788889997 599999999999999999999888744
No 28
>KOG2605 consensus OTU (ovarian tumor)-like cysteine protease [Signal transduction mechanisms; Posttranslational modification, protein turnover, chaperones]
Probab=71.08 E-value=1.5 Score=39.67 Aligned_cols=90 Identities=19% Similarity=0.121 Sum_probs=68.4
Q ss_pred hHHHHHhCccccccccCCCCCHHHHHHhhhcCCccCCHHHHHHHHhhcCccEEEEEccCCceEEeecccC-CCcEEEEEE
Q 030009 2 VVQYIVKNRETFEPFIEDDVPFDEYCQSMETDGTWAGHMELQAASLVTHSNICIHRHMSPRWYIRNFDYH-EARMIHLSY 80 (184)
Q Consensus 2 vv~yi~~n~d~F~pFv~~~~~f~~Y~~~m~k~g~WGg~iEL~Ala~~~~v~I~V~~~~~~~~~i~~~~~~-~~~~i~L~Y 80 (184)
++-|...+.+.|.+ .+|.++..|+..|-.+++|-|+..++|.+.-.-..+..+...++.|.+.++.+. ...+.+.+|
T Consensus 89 ~v~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~g~~~~~a~s~~~~~~~~~~~~~~~~~~~~~~sd~~~~~~~~~~~ 166 (371)
T KOG2605|consen 89 SVLFKVLYQERFKL--PSDTPCNGENSPMCSFHSRRGNESFQAASFGGLEIDLEVERNSPEWLGQSPSDPLRSVPSMEAI 166 (371)
T ss_pred hhhhhhhhhhcccC--CCCCcccccCCCCCcccccccccccccccccccccchhhhccCchhccccccccccccccccch
Confidence 45667777777877 555789999999999999999999999999888888888888888887765433 245666777
Q ss_pred ccCCcccceeccCC
Q 030009 81 HDGEHYNGVRLKED 94 (184)
Q Consensus 81 ~~g~HYdSV~~~~~ 94 (184)
+.+ |+++..-...
T Consensus 167 ~~~-~~~~~~~g~~ 179 (371)
T KOG2605|consen 167 HAR-HPEAKEVGVR 179 (371)
T ss_pred hhc-cccchhhccc
Confidence 765 6666544333
No 29
>PF11626 Rap1_C: TRF2-interacting telomeric protein/Rap1 - C terminal domain; InterPro: IPR021661 This family of proteins represents the C-terminal domain of the protein Rap-1, which plays a distinct role in silencing at the silent mating-type loci and telomeres []. The Rap-1 C terminus adopts an all-helical fold. Rap1 carries out its function by recruiting the Sir3 and Sir4 proteins to chromatin via its C-terminal domain []. ; PDB: 3K6G_C 3CZ6_A 3OWT_A.
Probab=69.85 E-value=7.1 Score=27.69 Aligned_cols=32 Identities=25% Similarity=0.322 Sum_probs=27.1
Q ss_pred HhcCCCCChHHHHHHHHHhCCCHHHHHHHHHHh
Q 030009 141 MAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAE 173 (184)
Q Consensus 141 ~~~tG~~d~~~i~~~L~~~~gdid~Ai~~Ll~~ 173 (184)
|..+|. +...|.++|..+.||+..|..++|..
T Consensus 4 ~~~~g~-~~~~v~~aL~~tSgd~~~a~~~vl~~ 35 (87)
T PF11626_consen 4 YEELGY-SREFVTHALYATSGDPELARRFVLNF 35 (87)
T ss_dssp HHHHTB--HHHHHHHHHHTTTBHHHHHHHHHHC
T ss_pred HHHhCC-CHHHHHHHHHHhCCCHHHHHHHHHHH
Confidence 566675 78999999999999999999988876
No 30
>KOG2561 consensus Adaptor protein NUB1, contains UBA domain [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=69.81 E-value=2.4 Score=39.37 Aligned_cols=42 Identities=24% Similarity=0.404 Sum_probs=31.6
Q ss_pred HHHHhcCCCCChHHHHHHHHHhCCCHHHHHHHHHHhcCCCcccc
Q 030009 138 KLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAEQGTEEYSV 181 (184)
Q Consensus 138 ~~v~~~tG~~d~~~i~~~L~~~~gdid~Ai~~Ll~~~~~~~~~~ 181 (184)
..+|. -|. -....|-+|+.|+||||+||.++...++-...-+
T Consensus 308 sllv~-mGf-eesdaRlaLRsc~g~Vd~AvqfI~erre~laq~R 349 (568)
T KOG2561|consen 308 SLLVG-MGF-EESDARLALRSCNGDVDSAVQFIIERREKLAQKR 349 (568)
T ss_pred HHHHH-cCC-CchHHHHHHHhccccHHHHHHHHHHHHHHHHHHH
Confidence 34443 454 4677888999999999999999998877654444
No 31
>KOG2239 consensus Transcription factor containing NAC and TS-N domains [Transcription]
Probab=69.43 E-value=6.7 Score=32.58 Aligned_cols=36 Identities=31% Similarity=0.310 Sum_probs=30.9
Q ss_pred hhHHHHHHhcCCCCChHHHHHHHHHhCCCHHHHHHHH
Q 030009 134 AGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFL 170 (184)
Q Consensus 134 ~~~v~~v~~~tG~~d~~~i~~~L~~~~gdid~Ai~~L 170 (184)
..-|+.||.-.+|+ ...+.++|..++|||-.||-.|
T Consensus 172 ~kDIeLVmsQanvS-R~kAVkALk~~~~DiVnAIM~L 207 (209)
T KOG2239|consen 172 AKDIELVMSQANVS-RAKAVKALKNNNNDIVNAIMEL 207 (209)
T ss_pred hhhHHHHHHHhhhh-HHHHHHHHHhccchHHHHHHHh
Confidence 44588999999997 7777779999999999999876
No 32
>PF11547 E3_UbLigase_EDD: E3 ubiquitin ligase EDD; InterPro: IPR024725 EDD, the ER ubiquitin ligase from the HECT ligases, contains an N-terminal ubiquitin-associated (UBA) domain which binds ubiquitin. Ubiquitin is recognised by helices alpha-1 and -3 in in the UBA domain. EDD is involved in DNA damage repair pathways and binds to mono-ubiquitinated proteins [].; GO: 0043130 ubiquitin binding; PDB: 2QHO_H.
Probab=68.23 E-value=18 Score=23.47 Aligned_cols=37 Identities=19% Similarity=0.295 Sum_probs=28.5
Q ss_pred HHHHHhcCCCCChHHHHHHHHHhCCCHHHHHHHHHHhcCC
Q 030009 137 IKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAEQGT 176 (184)
Q Consensus 137 v~~v~~~tG~~d~~~i~~~L~~~~gdid~Ai~~Ll~~~~~ 176 (184)
+|.|++ |. ..+.|.+-|+.-+=|+.-||-.||..+..
T Consensus 16 ~q~VLq--gk-sR~vIirELqrTnLdVN~AvNNlLsRDde 52 (53)
T PF11547_consen 16 AQVVLQ--GK-SRNVIIRELQRTNLDVNLAVNNLLSRDDE 52 (53)
T ss_dssp HHHHST--TS--HHHHHHHHHHTTT-HHHHHHHHHHHH--
T ss_pred HHHHHc--CC-cHHHHHHHHHHhcccHHHHHHHHhccccC
Confidence 466777 54 48899999999999999999999987643
No 33
>COG2103 Predicted sugar phosphate isomerase [General function prediction only]
Probab=66.16 E-value=9.2 Score=33.39 Aligned_cols=37 Identities=35% Similarity=0.751 Sum_probs=32.2
Q ss_pred hHHHHHHhcCCCCChHHHHHHHHHhCCCHHHHHHHHHH
Q 030009 135 GSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIA 172 (184)
Q Consensus 135 ~~v~~v~~~tG~~d~~~i~~~L~~~~gdid~Ai~~Ll~ 172 (184)
.++..||..||| +.+...+.|+++++++.-||-.++-
T Consensus 235 Ra~RIv~~aT~~-~~~~A~~~L~~~~~~vK~AIvm~~~ 271 (298)
T COG2103 235 RAVRIVMEATGC-SAEEAEALLEEAGGNVKLAIVMLLT 271 (298)
T ss_pred HHHHHHHHHhCC-CHHHHHHHHHHcCCccHhHHHHHHh
Confidence 467899999999 5999999999999999999977653
No 34
>PRK05441 murQ N-acetylmuramic acid-6-phosphate etherase; Reviewed
Probab=64.97 E-value=10 Score=33.03 Aligned_cols=37 Identities=27% Similarity=0.520 Sum_probs=31.6
Q ss_pred hHHHHHHhcCCCCChHHHHHHHHHhCCCHHHHHHHHHH
Q 030009 135 GSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIA 172 (184)
Q Consensus 135 ~~v~~v~~~tG~~d~~~i~~~L~~~~gdid~Ai~~Ll~ 172 (184)
-++..|+..||| +.+..+++|++++|++--||-.++.
T Consensus 237 ra~~i~~~~~~~-~~~~a~~~l~~~~~~vk~a~~~~~~ 273 (299)
T PRK05441 237 RAVRIVMEATGV-SREEAEAALEAADGSVKLAIVMILT 273 (299)
T ss_pred HHHHHHHHHHCc-CHHHHHHHHHHhCCCcHHHHHHHHh
Confidence 456788999999 5888999999999999999987765
No 35
>TIGR02934 nifT_nitrog probable nitrogen fixation protein FixT. This largely uncharacterized protein family is assigned a role in nitrogen fixation by two criteria. First, its gene occurs, generally, among genes essential for expression of active nitrogenase. Second, its phylogenetic profile closely matches that of nitrogen-fixing bacteria. However, mutational studies in Klebsiella pneumoniae failed to demonstrate any phenotype for deletion or overexpression of the protein.
Probab=63.73 E-value=0.61 Score=32.15 Aligned_cols=35 Identities=23% Similarity=0.526 Sum_probs=27.8
Q ss_pred HHhCccc-cccccCCCCCHHHHHHhhhcCCccCCHHH
Q 030009 6 IVKNRET-FEPFIEDDVPFDEYCQSMETDGTWAGHME 41 (184)
Q Consensus 6 i~~n~d~-F~pFv~~~~~f~~Y~~~m~k~g~WGg~iE 41 (184)
||+|.+- +..||.- .+.++=+-.|++++.|||.+.
T Consensus 5 iR~~~~g~l~~YvpK-KDLEE~Vv~~e~~~~WGG~v~ 40 (67)
T TIGR02934 5 IRRNRAGELSAYVPK-KDLEEVIVSVEKEELWGGWVT 40 (67)
T ss_pred EEeCCCCCEEEEEEC-CcchhheeeeecCccccCEEE
Confidence 3555665 7788885 789999999999999999753
No 36
>PF05415 Peptidase_C36: Beet necrotic yellow vein furovirus-type papain-like endopeptidase; InterPro: IPR008746 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of cysteine peptidases correspond to MEROPS peptidase family C36 (clan CA). The type example is beet necrotic yellow vein furovirus-type papain-like endopeptidase (beet necrotic yellow vein virus), which is involved in processing the viral polyprotein.
Probab=63.11 E-value=13 Score=27.19 Aligned_cols=47 Identities=9% Similarity=0.098 Sum_probs=33.7
Q ss_pred CHHHHHHhhh--cCCccCCHHHHHHHHhhcCccEEEEEccCCceEEeecccC
Q 030009 22 PFDEYCQSME--TDGTWAGHMELQAASLVTHSNICIHRHMSPRWYIRNFDYH 71 (184)
Q Consensus 22 ~f~~Y~~~m~--k~g~WGg~iEL~Ala~~~~v~I~V~~~~~~~~~i~~~~~~ 71 (184)
..+.||.|.+ ++.||-|-+ -||..+++.|.+-........+..+.++
T Consensus 35 ~i~~y~~W~r~~~~STW~DC~---mFA~~LkVsm~vkV~~~~~~~l~~~~d~ 83 (104)
T PF05415_consen 35 TIKKYHTWLRKKRPSTWDDCR---MFADALKVSMQVKVLSDKPYDLLYFVDG 83 (104)
T ss_pred HHHHHHHHHhcCCCCcHHHHH---HHHHhheeEEEEEEcCCCCceeeEeecC
Confidence 5789999975 588997654 8999999999886665444444444443
No 37
>TIGR00274 N-acetylmuramic acid 6-phosphate etherase. This protein, MurQ, is involved in recycling components of the bacterial murein sacculus turned over during cell growth. The cell wall metabolite anhydro-N-acetylmuramic acid (anhMurNAc) is converted by a kinase, AnmK, to MurNAc-phosphate, then converted to N-acetylglucosamine-phosphate by this etherase, called MurQ. This family of proteins is similar to the C-terminal half of a number of vertebrate glucokinase regulator proteins and contains a Prosite pattern which is shared by this group of proteins in a region of local similarity.
Probab=60.22 E-value=14 Score=32.07 Aligned_cols=37 Identities=24% Similarity=0.509 Sum_probs=31.6
Q ss_pred hHHHHHHhcCCCCChHHHHHHHHHhCCCHHHHHHHHHH
Q 030009 135 GSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIA 172 (184)
Q Consensus 135 ~~v~~v~~~tG~~d~~~i~~~L~~~~gdid~Ai~~Ll~ 172 (184)
-++..|+..|||. .+..+++|++++|++--||-.++.
T Consensus 232 Ra~~i~~~~~~~~-~~~a~~~l~~~~~~vk~Ai~~~~~ 268 (291)
T TIGR00274 232 RAVRIVRQATDCN-KELAEQTLLAADQNVKLAIVMILS 268 (291)
T ss_pred HHHHHHHHHhCcC-HHHHHHHHHHhCCCcHHHHHHHHh
Confidence 4567888899995 788999999999999999987654
No 38
>KOG0010 consensus Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones; General function prediction only]
Probab=56.56 E-value=14 Score=34.53 Aligned_cols=34 Identities=29% Similarity=0.416 Sum_probs=30.0
Q ss_pred HHHhcCCCCChHHHHHHHHHhCCCHHHHHHHHHH
Q 030009 139 LVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIA 172 (184)
Q Consensus 139 ~v~~~tG~~d~~~i~~~L~~~~gdid~Ai~~Ll~ 172 (184)
+-++.-|..|.+.-.|+|.+-+|||.+||+.||.
T Consensus 459 eQL~~MGF~nre~nlqAL~atgGdi~aAverll~ 492 (493)
T KOG0010|consen 459 EQLNDMGFLDREANLQALRATGGDINAAVERLLG 492 (493)
T ss_pred HHHHhcCCccHHHHHHHHHHhcCcHHHHHHHHhc
Confidence 4445669999999999999999999999999984
No 39
>PRK12570 N-acetylmuramic acid-6-phosphate etherase; Reviewed
Probab=50.60 E-value=24 Score=30.70 Aligned_cols=37 Identities=27% Similarity=0.630 Sum_probs=30.6
Q ss_pred hHHHHHHhcCCCCChHHHHHHHHHhCCCHHHHHHHHHH
Q 030009 135 GSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIA 172 (184)
Q Consensus 135 ~~v~~v~~~tG~~d~~~i~~~L~~~~gdid~Ai~~Ll~ 172 (184)
-++..|+..||| +.+..+++|++++|++--||-.++.
T Consensus 233 Ra~~i~~~~~~~-~~~~a~~~l~~~~~~vk~ai~~~~~ 269 (296)
T PRK12570 233 RAVRIVMQATGC-SEDEAKELLKESDNDVKLAILMILT 269 (296)
T ss_pred HHHHHHHHHHCc-CHHHHHHHHHHhCCccHHHHHHHHh
Confidence 356678888999 5778899999999999999986654
No 40
>KOG3450 consensus Huntingtin interacting protein HYPK [General function prediction only]
Probab=48.06 E-value=22 Score=26.82 Aligned_cols=40 Identities=25% Similarity=0.293 Sum_probs=31.5
Q ss_pred CChhHHHHHHhcCCCCChHHHHHHHHHhCCCHHHHHHHHHH
Q 030009 132 INAGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIA 172 (184)
Q Consensus 132 ~~~~~v~~v~~~tG~~d~~~i~~~L~~~~gdid~Ai~~Ll~ 172 (184)
+...-++.||+..-.+ ...++..|+.+.||+-+|...|+.
T Consensus 79 IkkeDlelImnELei~-k~~aer~LrE~~Gdvv~Alral~s 118 (119)
T KOG3450|consen 79 IKKEDLELIMNELEIS-KAAAERSLREHMGDVVEALRALTS 118 (119)
T ss_pred cCHHHHHHHHHHHHHH-HHHHHHHHHHhcccHHHHHHHHhc
Confidence 3344588999955443 678899999999999999998874
No 41
>PF06988 NifT: NifT/FixU protein; InterPro: IPR009727 This family consists of several NifT and FixU bacterial proteins. The function of NifT is unknown although it is thought that the protein may be involved in biosynthesis of the FeMo cofactor of nitrogenase although perturbation of nifT expression in Klebsiella pneumoniae has only a limited effect on nitrogen fixation [].; GO: 0009399 nitrogen fixation; PDB: 2JN4_A.
Probab=47.76 E-value=0.26 Score=33.69 Aligned_cols=34 Identities=24% Similarity=0.447 Sum_probs=22.7
Q ss_pred HhCcc-ccccccCCCCCHHHHHHhhhcCCccCCHHH
Q 030009 7 VKNRE-TFEPFIEDDVPFDEYCQSMETDGTWAGHME 41 (184)
Q Consensus 7 ~~n~d-~F~pFv~~~~~f~~Y~~~m~k~g~WGg~iE 41 (184)
|++.+ .+.-||.- .+.++=+-.|++++.|||.+.
T Consensus 6 R~~~~G~ls~YVpK-KDLEE~Vv~~E~~~~wGG~v~ 40 (64)
T PF06988_consen 6 RKNGAGGLSAYVPK-KDLEEPVVSMEKPELWGGEVT 40 (64)
T ss_dssp EE-SS--EEEEETT-TTEEEEEEEESSSSS-SSEEE
T ss_pred EeCCCcCEEEEEeC-CccccceeeeeccCccCCEEE
Confidence 45555 66777775 677777777889999999653
No 42
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=42.53 E-value=28 Score=34.46 Aligned_cols=31 Identities=32% Similarity=0.442 Sum_probs=27.6
Q ss_pred CCCChHHHHHHHHHhCCCHHHHHHHHHHhcC
Q 030009 145 GCENSEKVEEVLLQVGGDVDAAIEFLIAEQG 175 (184)
Q Consensus 145 G~~d~~~i~~~L~~~~gdid~Ai~~Ll~~~~ 175 (184)
|.++.++.-..|-+++|||..|+|-||-...
T Consensus 573 gGtN~ElALH~L~EakGnv~vAlE~LLlr~p 603 (907)
T KOG4167|consen 573 GGTNSELALHSLFEAKGNVMVALEMLLLRKP 603 (907)
T ss_pred CCccHHHHHHHHHHhcccHHHHHHHHHhcCC
Confidence 4579999999999999999999999997654
No 43
>PRK10963 hypothetical protein; Provisional
Probab=41.74 E-value=18 Score=30.05 Aligned_cols=35 Identities=23% Similarity=0.358 Sum_probs=26.2
Q ss_pred hHHHHHhCccccccccCCCCCHHHHHHhhhcCCccCCHHHHH
Q 030009 2 VVQYIVKNRETFEPFIEDDVPFDEYCQSMETDGTWAGHMELQ 43 (184)
Q Consensus 2 vv~yi~~n~d~F~pFv~~~~~f~~Y~~~m~k~g~WGg~iEL~ 43 (184)
|++|+++|||+|... .+-++.|.-|...||.+-|+
T Consensus 8 V~~yL~~~PdFf~~h-------~~Ll~~L~lph~~~gaVSL~ 42 (223)
T PRK10963 8 VVDYLLQNPDFFIRN-------ARLVEQMRVPHPVRGTVSLV 42 (223)
T ss_pred HHHHHHHCchHHhhC-------HHHHHhccCCCCCCCeecHH
Confidence 789999999999754 35667777777777755443
No 44
>COG3626 PhnI Uncharacterized enzyme of phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=41.70 E-value=41 Score=29.61 Aligned_cols=43 Identities=28% Similarity=0.220 Sum_probs=38.3
Q ss_pred HHHHHHhcCCCCChHHHHHHHHHhCCCHHHHHHHHHHhcCCCc
Q 030009 136 SIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAEQGTEE 178 (184)
Q Consensus 136 ~v~~v~~~tG~~d~~~i~~~L~~~~gdid~Ai~~Ll~~~~~~~ 178 (184)
+|..||..-+.+|.++.-=+|.+..||+-.||..|.+-+++-.
T Consensus 44 aVdRVM~EgslyDreLAALAikQa~GD~~EAIFLlRAYRTTLp 86 (367)
T COG3626 44 AVDRVMTEGSLYDRELAALALKQASGDLVEAIFLLRAYRTTLP 86 (367)
T ss_pred HHHHHhhccchhHHHHHHHHHHHhcchHHHHHHHHHHHHhccc
Confidence 5778999989999999999999999999999999988776643
No 45
>PF05381 Peptidase_C21: Tymovirus endopeptidase; InterPro: IPR008043 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This entry is found in cysteine peptidases belong to the MEROPS peptidase family C21 (tymovirus endopeptidase family, clan CA). The type example is tymovirus endopeptidase (turnip yellow mosaic virus). The noncapsid protein expressed from ORF-206 of turnip yellow mosaic virus (TYMV) is autocatalytically processed by a papain-like protease, producing N-terminal 150kDa and C-terminal 70kDa proteins.; GO: 0003968 RNA-directed RNA polymerase activity, 0016032 viral reproduction
Probab=41.01 E-value=1e+02 Score=23.04 Aligned_cols=46 Identities=13% Similarity=0.141 Sum_probs=32.5
Q ss_pred HHHHHHHhhcCccEEEEEccCCceEEeecccCCCcEEEEEEccC--Ccccc
Q 030009 40 MELQAASLVTHSNICIHRHMSPRWYIRNFDYHEARMIHLSYHDG--EHYNG 88 (184)
Q Consensus 40 iEL~Ala~~~~v~I~V~~~~~~~~~i~~~~~~~~~~i~L~Y~~g--~HYdS 88 (184)
..|.|||..|+..+.|+...+ +...+. ......++|.|..| .||..
T Consensus 47 DhltaLa~~~~~~~~~hs~~~--~~~~Gi-~~as~~~~I~ht~G~p~HFs~ 94 (104)
T PF05381_consen 47 DHLTALAYRYHFQCTFHSDHG--VLHYGI-KDASTVFTITHTPGPPGHFSL 94 (104)
T ss_pred HHHHHHHHHHheEEEEEcCCc--eEEeec-CCCceEEEEEeCCCCCCcccc
Confidence 457899999999999998766 222222 22456788877765 69987
No 46
>smart00668 CTLH C-terminal to LisH motif. Alpha-helical motif of unknown function.
Probab=40.55 E-value=37 Score=21.16 Aligned_cols=24 Identities=33% Similarity=0.632 Sum_probs=17.9
Q ss_pred ChHHHHHHHHHhCCCHHHHHHHHHHh
Q 030009 148 NSEKVEEVLLQVGGDVDAAIEFLIAE 173 (184)
Q Consensus 148 d~~~i~~~L~~~~gdid~Ai~~Ll~~ 173 (184)
+...|++.+. .||++.|++.+-..
T Consensus 4 ~~~~i~~~i~--~g~~~~a~~~~~~~ 27 (58)
T smart00668 4 ERKRIRELIL--KGDWDEALEWLSSL 27 (58)
T ss_pred HHHHHHHHHH--cCCHHHHHHHHHHc
Confidence 4567777776 89999999887443
No 47
>PF03765 CRAL_TRIO_N: CRAL/TRIO, N-terminal domain; InterPro: IPR008273 This entry defines the N-terminal of various retinaldehyde/retinal-binding proteins that may be functional components of the visual cycle. Cellular retinaldehyde-binding protein (CRALBP) carries 11-cis-retinol or 11-cis-retinaldehyde as endogenous ligands and may function as a substrate carrier protein that modulates interaction of these retinoids with visual cycle enzymes []. The multidomain protein Trio binds the LAR transmembrane tyrosine phosphatase, contains a protein kinase domain, and has separate rac-specific and rho-specific guanine nucleotide exchange factor domains []. Trio is a multifunctional protein that integrates and amplifies signals involved in coordinating actin remodeling, which is necessary for cell migration and growth. Other members of the family are transfer proteins that include, guanine nucleotide exchange factor that may function as an effector of RAC1, phosphatidylinositol/phosphatidylcholine transfer protein that is required for the transport of secretory proteins from the golgi complex and alpha-tocopherol transfer protein that enhances the transfer of the ligand between separate membranes.; PDB: 1OIZ_A 1R5L_A 1OIP_A 3HX3_A 3HY5_A 1AUA_A 3Q8G_A 3B7Q_B 3B7Z_A 3B7N_A ....
Probab=39.91 E-value=51 Score=20.76 Aligned_cols=26 Identities=19% Similarity=0.164 Sum_probs=20.0
Q ss_pred CCCChHHHHHHHHHhCCCHHHHHHHHH
Q 030009 145 GCENSEKVEEVLLQVGGDVDAAIEFLI 171 (184)
Q Consensus 145 G~~d~~~i~~~L~~~~gdid~Ai~~Ll 171 (184)
.+.| ..+.+-|++.++|++.|+..|.
T Consensus 28 ~~~d-~~llRFLRARkf~v~~A~~mL~ 53 (55)
T PF03765_consen 28 DHDD-NFLLRFLRARKFDVEKAFKMLK 53 (55)
T ss_dssp S-SH-HHHHHHHHHTTT-HHHHHHHHH
T ss_pred CCCH-HHHHHHHHHccCCHHHHHHHHH
Confidence 4444 6777799999999999998875
No 48
>cd05007 SIS_Etherase N-acetylmuramic acid 6-phosphate etherase. Members of this family contain the SIS (Sugar ISomerase) domain. The SIS domain is found in many phosphosugar isomerases and phosphosugar binding proteins. The bacterial cell wall sugar N-acetylmuramic acid carries a unique D-lactyl ether substituent at the C3 position. The etherase catalyzes the cleavage of the lactyl ether bond of N-acetylmuramic acid 6-phosphate.
Probab=37.37 E-value=21 Score=30.23 Aligned_cols=33 Identities=39% Similarity=0.671 Sum_probs=27.6
Q ss_pred hhHHHHHHhcCCCCChHHHHHHHHHhCCCHHHHH
Q 030009 134 AGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAI 167 (184)
Q Consensus 134 ~~~v~~v~~~tG~~d~~~i~~~L~~~~gdid~Ai 167 (184)
.-++..|+..|||. .+..+++|++++|++--||
T Consensus 223 ~ra~~i~~~~~~~~-~~~a~~~l~~~~~~~k~a~ 255 (257)
T cd05007 223 ERAIRIVMEATGVS-RDEAEAALEQAGGDVKTAI 255 (257)
T ss_pred HHHHHHHHHHHCcC-HHHHHHHHHHhCCCceeee
Confidence 34567899999995 8889999999999998776
No 49
>PF10905 DUF2695: Protein of unknown function (DUF2695); InterPro: IPR024248 This bacterial family of proteins has no known function.
Probab=34.83 E-value=1e+02 Score=20.20 Aligned_cols=33 Identities=21% Similarity=0.306 Sum_probs=25.7
Q ss_pred HHHhcCCCC-ChHHHHHHHHHhCCCHHHHHHHHH
Q 030009 139 LVMAGSGCE-NSEKVEEVLLQVGGDVDAAIEFLI 171 (184)
Q Consensus 139 ~v~~~tG~~-d~~~i~~~L~~~~gdid~Ai~~Ll 171 (184)
+-+.++||- ++.+.++.|.+.+=++++.++.|-
T Consensus 7 ~~l~~~~CdHtlr~t~~fl~~~~~~~~~vl~~l~ 40 (53)
T PF10905_consen 7 EKLSAFGCDHTLRLTRQFLRQRQLDWEDVLEWLR 40 (53)
T ss_pred hHcCcCCCCCcHHHHHHHHHHcCCCHHHHHHHHH
Confidence 445567886 899999999999999966666553
No 50
>KOG2934 consensus Uncharacterized conserved protein, contains Josephin domain [General function prediction only]
Probab=33.38 E-value=32 Score=28.23 Aligned_cols=24 Identities=21% Similarity=0.226 Sum_probs=21.0
Q ss_pred HHHhcCCCCChHHHHHHHHHhCCC
Q 030009 139 LVMAGSGCENSEKVEEVLLQVGGD 162 (184)
Q Consensus 139 ~v~~~tG~~d~~~i~~~L~~~~gd 162 (184)
..+-++||+|++.|-.+|++|+.-
T Consensus 73 rs~~g~Gnydvnvimaalq~~gl~ 96 (204)
T KOG2934|consen 73 RSWKGPGNYDVNVIMAALQQCGLE 96 (204)
T ss_pred ccccCCCcccHHHHHHHHHhcCce
Confidence 336789999999999999999876
No 51
>COG3159 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=32.81 E-value=20 Score=30.20 Aligned_cols=15 Identities=27% Similarity=0.450 Sum_probs=13.4
Q ss_pred hHHHHHhCccccccc
Q 030009 2 VVQYIVKNRETFEPF 16 (184)
Q Consensus 2 vv~yi~~n~d~F~pF 16 (184)
|++|+++||++|..+
T Consensus 9 VadyL~~hPeFf~~h 23 (218)
T COG3159 9 VADYLRQHPEFFIQH 23 (218)
T ss_pred HHHHHHhCcHHHHhC
Confidence 789999999999865
No 52
>PRK01905 DNA-binding protein Fis; Provisional
Probab=29.60 E-value=77 Score=21.74 Aligned_cols=23 Identities=35% Similarity=0.517 Sum_probs=19.1
Q ss_pred ChHHHHHHHHHhCCCHHHHHHHH
Q 030009 148 NSEKVEEVLLQVGGDVDAAIEFL 170 (184)
Q Consensus 148 d~~~i~~~L~~~~gdid~Ai~~L 170 (184)
....|+++|+.++||+..|...|
T Consensus 38 E~~~i~~aL~~~~gn~s~aAr~L 60 (77)
T PRK01905 38 EKPLLEVVMEQAGGNQSLAAEYL 60 (77)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHH
Confidence 46789999999999998886544
No 53
>KOG4015 consensus Fatty acid-binding protein FABP [Lipid transport and metabolism]
Probab=29.19 E-value=1.9e+02 Score=22.47 Aligned_cols=61 Identities=13% Similarity=0.252 Sum_probs=40.5
Q ss_pred CCHHHHHHhhhcCCccCCHHHHHHHHhhcCccEEEEEccCCceEEeecccCCCcEEEEEEccCCccccee
Q 030009 21 VPFDEYCQSMETDGTWAGHMELQAASLVTHSNICIHRHMSPRWYIRNFDYHEARMIHLSYHDGEHYNGVR 90 (184)
Q Consensus 21 ~~f~~Y~~~m~k~g~WGg~iEL~Ala~~~~v~I~V~~~~~~~~~i~~~~~~~~~~i~L~Y~~g~HYdSV~ 90 (184)
+.||+|+..+ |=.+.++=+|.+.+ |+..+..++..|.+.... .-+...+.|-.|+-++-..
T Consensus 15 ENFdeymk~l------GV~~~~Rk~a~~~k-p~~~i~~~G~~~~~~t~S--tfknt~~~f~lGeeFee~t 75 (133)
T KOG4015|consen 15 ENFDEYLKAL------GVGWATRKIAKLAK-PVLEITQDGDKFTIKTLS--TFKNTEISFKLGEEFEEET 75 (133)
T ss_pred cCHHHHHHhc------CCcHhHHHHHhhcC-CeEEEEEcCCEEEEEEee--cccceEEEEEEeeeecccc
Confidence 6899999886 33456777777777 777778788788876542 2344555666555554443
No 54
>PF04340 DUF484: Protein of unknown function, DUF484; InterPro: IPR007435 This family consists of several proteins of uncharacterised function.; PDB: 3E98_B.
Probab=28.39 E-value=19 Score=29.66 Aligned_cols=16 Identities=25% Similarity=0.443 Sum_probs=0.0
Q ss_pred hHHHHHhCcccccccc
Q 030009 2 VVQYIVKNRETFEPFI 17 (184)
Q Consensus 2 vv~yi~~n~d~F~pFv 17 (184)
|++|+++|||+|..+-
T Consensus 11 V~~yL~~~PdFf~~~~ 26 (225)
T PF04340_consen 11 VAAYLRQHPDFFERHP 26 (225)
T ss_dssp ----------------
T ss_pred HHHHHHhCcHHHHhCH
Confidence 7899999999998654
No 55
>PF07802 GCK: GCK domain; InterPro: IPR012891 This domain is found in proteins carrying other domains known to be involved in intracellular signalling pathways (such as IPR001806 from INTERPRO) indicating that it might also be involved in these pathways. It has 4 highly conserved cysteine residues, suggesting that it can bind zinc ions. Moreover, it is found repeated in some members of this family (such as Q9LMF3 from SWISSPROT); this may indicate that these domains are able to interact with one another, raising the possibility that this domain mediates heterodimerisation.
Probab=27.62 E-value=11 Score=26.52 Aligned_cols=16 Identities=13% Similarity=0.476 Sum_probs=13.9
Q ss_pred HHHHhCccccccccCC
Q 030009 4 QYIVKNRETFEPFIED 19 (184)
Q Consensus 4 ~yi~~n~d~F~pFv~~ 19 (184)
.-|.+|+|+|+||+..
T Consensus 49 kCM~ahsdYY~P~La~ 64 (76)
T PF07802_consen 49 KCMEAHSDYYEPILAA 64 (76)
T ss_pred HHHHhchhHHHHHHHH
Confidence 4588999999999984
No 56
>TIGR00601 rad23 UV excision repair protein Rad23. All proteins in this family for which functions are known are components of a multiprotein complex used for targeting nucleotide excision repair to specific parts of the genome. In humans, Rad23 complexes with the XPC protein. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=26.76 E-value=1.2e+02 Score=27.53 Aligned_cols=39 Identities=15% Similarity=0.249 Sum_probs=33.1
Q ss_pred hhHHHHHHhcCCCCChHHHHHHHHHhCCCHHHHHHHHHHhc
Q 030009 134 AGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFLIAEQ 174 (184)
Q Consensus 134 ~~~v~~v~~~tG~~d~~~i~~~L~~~~gdid~Ai~~Ll~~~ 174 (184)
.++|+..|. .| .+..+|.|+-.+|+-|-+-|..|||+..
T Consensus 338 ~~AIeRL~~-LG-F~r~~viqaY~ACdKNEelAAn~Lf~~~ 376 (378)
T TIGR00601 338 KEAIERLCA-LG-FDRGLVIQAYFACDKNEELAANYLLSQN 376 (378)
T ss_pred HHHHHHHHH-cC-CCHHHHHHHHHhcCCcHHHHHHHHHhhc
Confidence 456777776 36 5899999999999999999999999754
No 57
>PRK00430 fis global DNA-binding transcriptional dual regulator Fis; Provisional
Probab=26.30 E-value=89 Score=22.56 Aligned_cols=23 Identities=17% Similarity=0.218 Sum_probs=19.1
Q ss_pred ChHHHHHHHHHhCCCHHHHHHHH
Q 030009 148 NSEKVEEVLLQVGGDVDAAIEFL 170 (184)
Q Consensus 148 d~~~i~~~L~~~~gdid~Ai~~L 170 (184)
....|+++|+.++||+..|-..|
T Consensus 56 Er~~i~~aL~~~~gn~s~AAr~L 78 (95)
T PRK00430 56 EAPLLDMVMQYTRGNQTRAALML 78 (95)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHh
Confidence 46789999999999999886554
No 58
>PRK05441 murQ N-acetylmuramic acid-6-phosphate etherase; Reviewed
Probab=26.02 E-value=98 Score=26.85 Aligned_cols=32 Identities=25% Similarity=0.381 Sum_probs=26.7
Q ss_pred HHHHhcCCCCChHHHHHHHHHhCCCHHHHHHHH
Q 030009 138 KLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFL 170 (184)
Q Consensus 138 ~~v~~~tG~~d~~~i~~~L~~~~gdid~Ai~~L 170 (184)
-.+|..+|| |....++.|.+++|++-.|+..+
T Consensus 267 a~~~~~~~~-~~~~a~~~l~~~~g~~~~~~~~~ 298 (299)
T PRK05441 267 AIVMILTGL-DAAEAKALLARHGGFLRKALAEL 298 (299)
T ss_pred HHHHHHhCC-CHHHHHHHHHHcCCCHHHHHhhc
Confidence 356677787 69999999999999999998653
No 59
>TIGR00149 TIGR00149_YbjQ secondary thiamine-phosphate synthase enzyme. Members of this protein family have been studied extensively by crystallography. Members from several different species have been shown to have sufficient thiamin phosphate synthase activity (EC 2.5.1.3) to complement thiE mutants. However, it is presumed that this is a secondary activity, and the primary function of this enzyme remains unknown.
Probab=23.50 E-value=3.3e+02 Score=20.92 Aligned_cols=67 Identities=13% Similarity=0.219 Sum_probs=44.4
Q ss_pred ccccccCCCCCHHHHHHhhhcCCc------cCCHHHHHHHHhhcCccEEEEEccC----CceE---EeecccCCCcEEEE
Q 030009 12 TFEPFIEDDVPFDEYCQSMETDGT------WAGHMELQAASLVTHSNICIHRHMS----PRWY---IRNFDYHEARMIHL 78 (184)
Q Consensus 12 ~F~pFv~~~~~f~~Y~~~m~k~g~------WGg~iEL~Ala~~~~v~I~V~~~~~----~~~~---i~~~~~~~~~~i~L 78 (184)
.++|.+.. ++..+++++...+. |.|+.---.-|.+++..+.|--.++ +.|+ +.+|+....+.|.+
T Consensus 50 ~~dp~l~~--Dl~~~l~~lvP~~~~y~H~~~~~n~~aHlka~L~G~s~tipi~dG~L~LGtwQ~I~l~E~Dg~r~R~v~v 127 (132)
T TIGR00149 50 NADPDVLH--DIERFFERLVPDDGNYEHDEGDDNMDAHIKSSLLGTSQHVPVENGRLQLGTWQGIFFAEFDGPRTRRIIV 127 (132)
T ss_pred CCCccHHH--HHHHHHHHHCCCCCCccccCCCCCHHHHHHHHhcCccEEEEEeCCEEcccCccEEEEEECCCCCCcEEEE
Confidence 34566664 78899999877542 6677767777888888888776665 3443 34566555566666
Q ss_pred EE
Q 030009 79 SY 80 (184)
Q Consensus 79 ~Y 80 (184)
..
T Consensus 128 ~i 129 (132)
T TIGR00149 128 KV 129 (132)
T ss_pred EE
Confidence 53
No 60
>PF12244 DUF3606: Protein of unknown function (DUF3606); InterPro: IPR022037 This family of proteins is found in bacteria. Proteins in this family are typically between 58 and 85 amino acids in length. There is a single completely conserved residue G that may be functionally important.
Probab=23.18 E-value=2.2e+02 Score=18.54 Aligned_cols=36 Identities=19% Similarity=0.277 Sum_probs=28.5
Q ss_pred hhHHHHHHhcCCCCChHHHHHHHHHhCCCHHHHHHHH
Q 030009 134 AGSIKLVMAGSGCENSEKVEEVLLQVGGDVDAAIEFL 170 (184)
Q Consensus 134 ~~~v~~v~~~tG~~d~~~i~~~L~~~~gdid~Ai~~L 170 (184)
+..|+-.+...||+ .+.++++.++.+.++.+.-.+|
T Consensus 20 ~~ev~ywa~~~gvt-~~~L~~AV~~vG~~~~~V~~~L 55 (57)
T PF12244_consen 20 PYEVRYWAKRFGVT-EEQLREAVRAVGNSRAAVRAYL 55 (57)
T ss_pred HHHHHHHHHHHCcC-HHHHHHHHHHHCcCHHHHHHHH
Confidence 44688888899997 7888889999988877665554
No 61
>COG0773 MurC UDP-N-acetylmuramate-alanine ligase [Cell envelope biogenesis, outer membrane]
Probab=22.85 E-value=1e+02 Score=28.83 Aligned_cols=82 Identities=12% Similarity=0.150 Sum_probs=48.3
Q ss_pred CccccccccCCCCCHHHHHHhhhcCC---ccCCHHHHHH-HHhhcCccEEEEEccC-CceEEeecccCCCcEEEEEEccC
Q 030009 9 NRETFEPFIEDDVPFDEYCQSMETDG---TWAGHMELQA-ASLVTHSNICIHRHMS-PRWYIRNFDYHEARMIHLSYHDG 83 (184)
Q Consensus 9 n~d~F~pFv~~~~~f~~Y~~~m~k~g---~WGg~iEL~A-la~~~~v~I~V~~~~~-~~~~i~~~~~~~~~~i~L~Y~~g 83 (184)
|.|.|..|-.--..|.+|++++.+-| .+++..+|+. +++..++++.-|-.+. -.|++.+.........+=.+..|
T Consensus 187 H~D~y~~~~~i~~~F~~f~~~vp~~G~~v~~~dd~~l~~l~~~~~~~~v~tyG~~~~ad~~a~ni~~~~~~~~F~V~~~g 266 (459)
T COG0773 187 HLDYYGDLEAIKQAFHHFVRNVPFYGRAVVCGDDPNLRELLSRGCWSPVVTYGFDDEADWRAENIRQDGSGTTFDVLFRG 266 (459)
T ss_pred hhhhhCCHHHHHHHHHHHHHhCCccceEEEECCCHHHHHHHhcccCCcEEeecCCCcCcEEEEEeEEeccccEEEEEEcC
Confidence 55566544322247999999998873 5799999999 5556667666665542 35776654332222222223344
Q ss_pred Cccccee
Q 030009 84 EHYNGVR 90 (184)
Q Consensus 84 ~HYdSV~ 90 (184)
+.|-.++
T Consensus 267 ~~~~~~~ 273 (459)
T COG0773 267 EELGEVK 273 (459)
T ss_pred ceeEEEE
Confidence 4444443
No 62
>COG5481 Uncharacterized conserved small protein containing a coiled-coil domain [Function unknown]
Probab=22.55 E-value=99 Score=20.92 Aligned_cols=25 Identities=36% Similarity=0.260 Sum_probs=19.8
Q ss_pred hHHHHHHHHHhCCCHHHHHHHHHHh
Q 030009 149 SEKVEEVLLQVGGDVDAAIEFLIAE 173 (184)
Q Consensus 149 ~~~i~~~L~~~~gdid~Ai~~Ll~~ 173 (184)
..+-..-|++.+-|.|+||-+|++-
T Consensus 9 irl~~arLrqeH~D~DaaInAmi~~ 33 (67)
T COG5481 9 IRLTLARLRQEHADFDAAINAMIAT 33 (67)
T ss_pred HHHHHHHHHHHHhhHHHHHHHHHHh
Confidence 3444456889999999999999883
No 63
>PF05952 ComX: Bacillus competence pheromone ComX; InterPro: IPR009233 Competence is the ability of a cell to take up exogenous DNA from its environment, resulting in transformation. It is widespread among bacteria and is probably an important mechanism for the horizontal transfer of genes. Cells that take up DNA inevitably acquire the nucleotides the DNA consists of, and, because nucleotides are needed for DNA and RNA synthesis and are expensive to synthesise, these may make a significant contribution to the cell's energy budget []. The lateral gene transfer caused by competence also contributes to the genetic diversity that makes evolution possible. DNA usually becomes available by the death and lysis of other cells. Competent bacteria use components of extracellular filaments called type 4 pili to create pores in their membranes and pull DNA through the pores into the cytoplasm. This process, including the development of competence and the expression of the uptake machinery, is regulated in response to cell-cell signalling and/or nutritional conditions []. Natural genetic competence in Bacillus subtilis is controlled by quorum-sensing (QS). The ComP- ComA two-component system detects the signalling molecule ComX, and this signal is transduced by a conserved phosphotransfer mechanism. ComX is synthesised as an inactive precursor and is then cleaved and modified by ComQ before export to the extracellular environment [].
Probab=22.19 E-value=25 Score=23.46 Aligned_cols=19 Identities=37% Similarity=0.711 Sum_probs=16.5
Q ss_pred hHHHHHhCccccccccCCC
Q 030009 2 VVQYIVKNRETFEPFIEDD 20 (184)
Q Consensus 2 vv~yi~~n~d~F~pFv~~~ 20 (184)
+++|+.+||+-.....+++
T Consensus 5 iV~YLv~nPevl~kl~~g~ 23 (57)
T PF05952_consen 5 IVNYLVQNPEVLEKLKEGE 23 (57)
T ss_pred HHHHHHHChHHHHHHHcCC
Confidence 6899999999999888874
No 64
>PF04877 Hairpins: HrpZ; InterPro: IPR006961 HrpZ (harpin elicitor) from the plant pathogen Pseudomonas syringae binds to lipid bilayers and forms a cation-conducting pore in vivo. This pore-forming activity may allow nutrient release or delivery of virulence factors during bacterial colonisation of host plants []. The entry also represents hairpinN which is a virulence determinant which elicits lesion formation in Arabidopsis and tobacco and triggers systemic resistance in Arabidopsis [].
Probab=22.02 E-value=34 Score=30.16 Aligned_cols=43 Identities=14% Similarity=0.212 Sum_probs=27.0
Q ss_pred ChHHHHHhCccccccccCCCCCHHHHHHhhhcCCccCCHHHHHHHHhhc
Q 030009 1 MVVQYIVKNRETFEPFIEDDVPFDEYCQSMETDGTWAGHMELQAASLVT 49 (184)
Q Consensus 1 lvv~yi~~n~d~F~pFv~~~~~f~~Y~~~m~k~g~WGg~iEL~Ala~~~ 49 (184)
+|++||-.||+.|-+= ++.+|.+ ++ +.+.+=+--|..+|-.++
T Consensus 169 eIaqFMD~nPe~FgkP--d~~sW~~---eL-keD~~L~~~E~~~F~~Al 211 (308)
T PF04877_consen 169 EIAQFMDQNPEQFGKP--DRKSWAD---EL-KEDNGLDKAETEQFQKAL 211 (308)
T ss_pred HHHHHHhcCHhhcCCC--CCchHHH---Hh-hcCCCCCHHHHHHHHHHH
Confidence 4789999999999533 3345444 34 245555555666666654
No 65
>PF01381 HTH_3: Helix-turn-helix; InterPro: IPR001387 This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould).; GO: 0043565 sequence-specific DNA binding; PDB: 2AXU_A 2AWI_D 2AXV_D 2AXZ_C 2AW6_A 3KXA_C 3BS3_A 2CRO_A 1ZUG_A 3CRO_R ....
Probab=21.77 E-value=1e+02 Score=18.84 Aligned_cols=30 Identities=7% Similarity=-0.082 Sum_probs=24.3
Q ss_pred HHHHHhhhcCCccCCHHHHHHHHhhcCccE
Q 030009 24 DEYCQSMETDGTWAGHMELQAASLVTHSNI 53 (184)
Q Consensus 24 ~~Y~~~m~k~g~WGg~iEL~Ala~~~~v~I 53 (184)
..++.++.+....=.--.+.++|++|++++
T Consensus 23 ~~~i~~~~~g~~~~~~~~~~~ia~~l~~~~ 52 (55)
T PF01381_consen 23 RSTISRIENGKRNPSLDTLKKIAKALGVSP 52 (55)
T ss_dssp HHHHHHHHTTSSTSBHHHHHHHHHHHTSEH
T ss_pred cchhHHHhcCCCCCCHHHHHHHHHHHCCCH
Confidence 366777777777888889999999999875
Done!