Query 048564
Match_columns 114
No_of_seqs 110 out of 585
Neff 5.4
Searched_HMMs 46136
Date Fri Mar 29 10:41:25 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/048564.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/048564hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 smart00151 SWIB SWI complex, B 100.0 1.7E-28 3.8E-33 162.4 8.1 77 35-112 1-77 (77)
2 PF02201 SWIB: SWIB/MDM2 domai 100.0 6.1E-30 1.3E-34 169.0 -0.6 76 35-111 1-76 (76)
3 KOG1946 RNA polymerase I trans 99.9 4.1E-27 8.9E-32 184.9 6.3 80 33-113 98-177 (240)
4 PRK14724 DNA topoisomerase III 99.9 8E-24 1.7E-28 191.0 7.5 78 33-111 910-987 (987)
5 COG5531 SWIB-domain-containing 99.9 2.5E-23 5.4E-28 163.2 6.1 80 32-112 118-197 (237)
6 KOG2570 SWI/SNF transcription 99.7 6.6E-18 1.4E-22 140.7 5.1 77 35-112 205-281 (420)
7 PRK06319 DNA topoisomerase I/S 99.6 1.5E-15 3.3E-20 135.9 5.6 77 35-112 784-860 (860)
8 KOG2522 Filamentous baseplate 95.7 0.014 2.9E-07 50.6 4.3 58 35-92 357-420 (560)
9 PRK05350 acyl carrier protein; 89.4 0.57 1.2E-05 30.5 3.5 53 54-110 2-54 (82)
10 PRK05828 acyl carrier protein; 86.7 1.6 3.5E-05 29.1 4.4 53 54-110 1-53 (84)
11 CHL00124 acpP acyl carrier pro 83.8 1.6 3.4E-05 28.0 3.2 53 54-110 1-53 (82)
12 PRK12449 acyl carrier protein; 82.4 3.6 7.9E-05 26.2 4.5 53 54-110 1-53 (80)
13 PTZ00171 acyl carrier protein; 74.6 5.8 0.00013 29.2 4.1 57 50-110 62-118 (148)
14 PF13545 HTH_Crp_2: Crp-like h 68.4 4 8.7E-05 25.3 1.8 48 38-89 26-75 (76)
15 PF07587 PSD1: Protein of unkn 60.7 13 0.00027 29.4 3.7 58 44-113 5-65 (266)
16 PRK07117 acyl carrier protein; 60.0 15 0.00033 24.0 3.4 52 54-110 1-53 (79)
17 PF08463 EcoEI_R_C: EcoEI R pr 58.7 7.3 0.00016 28.0 1.9 69 40-110 88-163 (164)
18 PRK00071 nadD nicotinic acid m 54.4 9.2 0.0002 28.6 1.9 18 56-73 184-201 (203)
19 TIGR03697 NtcA_cyano global ni 53.4 20 0.00044 25.4 3.5 49 39-91 142-192 (193)
20 PF08225 Antimicrobial19: Pseu 52.7 11 0.00023 19.6 1.4 20 86-110 4-23 (23)
21 PRK07639 acyl carrier protein; 52.0 30 0.00065 22.8 3.9 54 54-110 1-54 (86)
22 PLN02945 nicotinamide-nucleoti 52.0 11 0.00025 29.1 2.1 30 44-73 206-235 (236)
23 TIGR00482 nicotinate (nicotina 50.7 13 0.00027 27.7 2.1 30 44-73 164-193 (193)
24 cd04762 HTH_MerR-trunc Helix-T 50.7 27 0.00059 18.9 3.1 24 43-73 4-27 (49)
25 smart00667 LisH Lissencephaly 50.3 12 0.00026 19.2 1.4 20 55-74 2-21 (34)
26 PRK13918 CRP/FNR family transc 48.6 21 0.00045 25.7 3.0 46 43-92 153-199 (202)
27 PRK05883 acyl carrier protein; 48.6 40 0.00086 22.5 4.1 55 52-110 8-62 (91)
28 PRK06973 nicotinic acid mononu 48.4 13 0.00028 29.3 1.9 31 43-73 203-241 (243)
29 cd01104 HTH_MlrA-CarA Helix-Tu 45.2 67 0.0014 19.2 5.0 57 43-106 4-67 (68)
30 PRK09392 ftrB transcriptional 44.6 33 0.00071 25.5 3.6 48 40-92 173-222 (236)
31 PF01047 MarR: MarR family; I 41.9 6 0.00013 23.4 -0.7 35 44-81 22-59 (59)
32 TIGR00517 acyl_carrier acyl ca 40.2 42 0.00091 20.9 3.1 50 57-110 2-51 (77)
33 PF08938 HBS1_N: HBS1 N-termin 39.4 7 0.00015 25.5 -0.7 28 39-66 29-56 (79)
34 PF01726 LexA_DNA_bind: LexA D 38.8 35 0.00077 21.5 2.5 21 55-76 7-27 (65)
35 TIGR01764 excise DNA binding d 37.1 35 0.00077 18.7 2.1 25 43-74 5-29 (49)
36 COG1654 BirA Biotin operon rep 36.6 31 0.00067 22.9 2.1 22 41-69 21-42 (79)
37 KOG0747 Putative NAD+-dependen 36.6 93 0.002 26.1 5.2 56 51-107 251-320 (331)
38 cd09286 NMNAT_Eukarya Nicotina 35.5 28 0.00061 26.9 2.0 31 43-73 195-225 (225)
39 PF08513 LisH: LisH; InterPro 35.4 24 0.00051 18.6 1.1 17 58-74 2-18 (27)
40 cd02165 NMNAT Nicotinamide/nic 35.4 30 0.00065 25.5 2.1 31 43-73 162-192 (192)
41 PF12728 HTH_17: Helix-turn-he 35.1 36 0.00079 19.5 2.0 26 43-75 5-30 (51)
42 PF03656 Pam16: Pam16; InterP 35.0 49 0.0011 23.9 3.1 29 43-71 58-87 (127)
43 TIGR02057 PAPS_reductase phosp 34.8 23 0.00049 27.4 1.4 12 62-73 172-183 (226)
44 PF13867 SAP30_Sin3_bdg: Sin3 34.7 65 0.0014 19.5 3.2 14 61-74 4-17 (53)
45 PF13333 rve_2: Integrase core 34.6 42 0.00092 19.8 2.3 21 51-71 15-35 (52)
46 PF07308 DUF1456: Protein of u 34.2 73 0.0016 20.5 3.5 40 43-91 17-58 (68)
47 PRK08887 nicotinic acid mononu 34.1 37 0.00081 25.1 2.4 18 57-74 154-171 (174)
48 PF13758 Prefoldin_3: Prefoldi 32.5 96 0.0021 21.6 4.1 37 34-70 41-83 (99)
49 COG5577 Spore coat protein [Ce 32.4 40 0.00087 24.9 2.3 38 40-77 84-121 (145)
50 PF12487 DUF3703: Protein of u 31.5 96 0.0021 22.0 4.0 40 10-49 72-111 (112)
51 PRK11161 fumarate/nitrate redu 31.1 51 0.0011 24.3 2.7 50 39-92 183-234 (235)
52 PF14838 INTS5_C: Integrator c 30.8 27 0.00058 32.0 1.3 43 41-86 618-665 (696)
53 COG1846 MarR Transcriptional r 30.7 44 0.00096 21.4 2.1 37 43-79 40-76 (126)
54 TIGR02055 APS_reductase thiore 30.5 30 0.00064 25.8 1.4 12 62-73 136-147 (191)
55 PRK12563 sulfate adenylyltrans 30.2 29 0.00063 28.6 1.4 24 62-85 203-238 (312)
56 PF07037 DUF1323: Putative tra 30.0 62 0.0013 23.5 2.9 44 42-92 3-53 (122)
57 PRK09391 fixK transcriptional 29.6 59 0.0013 24.4 2.9 48 39-90 178-228 (230)
58 PRK13727 conjugal transfer pil 28.2 52 0.0011 22.1 2.0 19 5-23 52-70 (80)
59 PF12368 DUF3650: Protein of u 27.2 32 0.00069 18.8 0.7 10 65-74 9-18 (28)
60 PRK00982 acpP acyl carrier pro 26.3 78 0.0017 19.6 2.6 50 57-110 2-51 (78)
61 PF05643 DUF799: Putative bact 25.4 66 0.0014 25.3 2.5 35 63-99 77-111 (215)
62 KOG4068 Uncharacterized conser 25.4 80 0.0017 24.1 2.9 23 57-79 68-90 (174)
63 smart00413 ETS erythroblast tr 25.3 1.3E+02 0.0028 20.5 3.7 48 62-110 3-65 (87)
64 PF00010 HLH: Helix-loop-helix 25.3 1E+02 0.0022 18.0 2.8 18 52-69 36-53 (55)
65 PRK05253 sulfate adenylyltrans 25.1 41 0.00089 27.3 1.4 12 62-73 193-204 (301)
66 PF07319 DnaI_N: Primosomal pr 24.6 99 0.0021 20.6 3.0 34 42-75 31-69 (94)
67 TIGR00434 cysH phosophoadenyly 24.5 44 0.00096 24.9 1.4 12 62-73 157-168 (212)
68 PF01507 PAPS_reduct: Phosphoa 23.8 47 0.001 23.1 1.3 12 62-73 143-154 (174)
69 PRK07152 nadD putative nicotin 23.8 46 0.00099 27.0 1.4 16 59-74 170-185 (342)
70 PLN02309 5'-adenylylsulfate re 23.5 45 0.00097 28.9 1.3 13 61-73 261-273 (457)
71 COG4389 Site-specific recombin 23.4 61 0.0013 29.1 2.1 24 50-73 637-660 (677)
72 TIGR02741 TraQ type-F conjugat 22.3 79 0.0017 21.2 2.1 19 5-23 52-70 (80)
73 PRK10402 DNA-binding transcrip 22.3 88 0.0019 23.3 2.6 46 43-92 173-219 (226)
74 TIGR02039 CysD sulfate adenyly 21.9 52 0.0011 26.8 1.4 13 62-74 185-197 (294)
75 COG1057 NadD Nicotinic acid mo 21.1 75 0.0016 24.3 2.0 31 43-73 165-195 (197)
76 cd04382 RhoGAP_MgcRacGAP RhoGA 21.0 95 0.0021 23.3 2.6 68 42-110 3-80 (193)
77 TIGR00424 APS_reduc 5'-adenyly 20.3 57 0.0012 28.3 1.3 12 62-73 267-278 (463)
No 1
>smart00151 SWIB SWI complex, BAF60b domains.
Probab=99.95 E-value=1.7e-28 Score=162.40 Aligned_cols=77 Identities=49% Similarity=0.933 Sum_probs=74.0
Q ss_pred CCCCccCCHHHHhhhCCCccCHHHHHHHHHHHHHHhCCCCCCCCCccccchhHHhhhCCCCcccHHHHHHHHhccccC
Q 048564 35 IGKPVPVSAQLSKFLGANEASRSDAVKKIWQYIRQHDLQNPANKREIRCDDKLKTIFNGKDSVGFLEIAKLLSQHFVK 112 (114)
Q Consensus 35 ~~~~~~lSp~La~flG~~~~sR~eV~~~lW~YIK~nnLqDp~dKr~I~cDekLk~Lfg~~~~v~~~el~~lL~~Hl~k 112 (114)
++++|.+||+|++|+|.+++||+||++.||+|||+||||||+|++.|+||+.|+++|| ++++.+++|+++|++||.+
T Consensus 1 ~~~~~~ls~~L~~~lg~~~~tr~ev~~~lw~YIk~n~L~d~~~k~~i~~D~~L~~l~~-~~~v~~~~~~~ll~~Hl~~ 77 (77)
T smart00151 1 ITKKVTLSPELAKVLGAPEMTRTEIIKRLWEYIKEHNLQDPQNKREILCDSKLEQIFG-KDRMDMFEMNKLLTPHLIK 77 (77)
T ss_pred CCCcccCCHHHHHHhCCCcCcHHHHHHHHHHHHHHhcccCCccCCEEecCHHHHHHHC-cCeecHHHHHHHHHHHcCC
Confidence 4689999999999999999999999999999999999999999999999999999998 7899999999999999975
No 2
>PF02201 SWIB: SWIB/MDM2 domain; InterPro: IPR003121 The SWI/SNF family of complexes, which are conserved from yeast to humans, are ATP-dependent chromatin-remodelling proteins that facilitate transcription activation []. The mammalian complexes are made up of 9-12 proteins called BAFs (BRG1-associated factors). The BAF60 family have at least three members: BAF60a, which is ubiquitous, BAF60b and BAF60c, which are expressed in muscle and pancreatic tissues, respectively. BAF60b is present in alternative forms of the SWI/SNF complex, including complex B (SWIB), which lacks BAF60a. The SWIB domain is a conserved region found within the BAF60b proteins [], and can be found fused to the C terminus of DNA topoisomerase in Chlamydia. MDM2 is an oncoprotein that acts as a cellular inhibitor of the p53 tumour suppressor by binding to the transactivation domain of p53 and suppressing its ability to activate transcription []. p53 acts in response to DNA damage, inducing cell cycle arrest and apoptosis. Inactivation of p53 is a common occurrence in neoplastic transformations. The core of MDM2 folds into an open bundle of four helices, which is capped by two small 3-stranded beta-sheets. It consists of a duplication of two structural repeats. MDM2 has a deep hydrophobic cleft on which the p53 alpha-helix binds; p53 residues involved in transactivation are buried deep within the cleft of MDM2, thereby concealing the p53 transactivation domain. The SWIB and MDM2 domains are homologous and share a common fold.; GO: 0005515 protein binding; PDB: 1V31_A 3FE7_A 3JZQ_B 3EQY_B 2VYR_A 3JZO_A 3DAB_E 3LBJ_E 3FEA_A 3FDO_A ....
Probab=99.95 E-value=6.1e-30 Score=169.02 Aligned_cols=76 Identities=51% Similarity=0.937 Sum_probs=70.5
Q ss_pred CCCCccCCHHHHhhhCCCccCHHHHHHHHHHHHHHhCCCCCCCCCccccchhHHhhhCCCCcccHHHHHHHHhcccc
Q 048564 35 IGKPVPVSAQLSKFLGANEASRSDAVKKIWQYIRQHDLQNPANKREIRCDDKLKTIFNGKDSVGFLEIAKLLSQHFV 111 (114)
Q Consensus 35 ~~~~~~lSp~La~flG~~~~sR~eV~~~lW~YIK~nnLqDp~dKr~I~cDekLk~Lfg~~~~v~~~el~~lL~~Hl~ 111 (114)
|+++|++||+|++++|.+++||+||++.||+||++||||||+|++.|.||+.|++||+ .++|++++|+++|++||.
T Consensus 1 ~~k~~~ls~~L~~~lg~~~~sr~~v~~~lw~YIk~~~L~dp~~k~~I~cD~~L~~lf~-~~~v~~~~i~~~l~~hl~ 76 (76)
T PF02201_consen 1 FPKRFKLSPELAEFLGEDELSRSEVVKRLWQYIKENNLQDPKDKRIIICDEKLKKLFG-KDSVNFFEIPKLLKPHLI 76 (76)
T ss_dssp -EEEEHHHHHHHHHTT-SCEEHHHHHHHHHHHHHHTTSBESSSTTEEE-TTSHHHHHH-TSECSEEETTHHHHHHHE
T ss_pred CCCCccCCHHHHHHhCCCCCCHHHHHHHHHHHHHHhcCCCcccCceEecCHHHHHHhC-CCeecHhhHHHHHHHhcC
Confidence 5678999999999999999999999999999999999999999999999999999999 599999999999999984
No 3
>KOG1946 consensus RNA polymerase I transcription factor UAF [Transcription]
Probab=99.94 E-value=4.1e-27 Score=184.88 Aligned_cols=80 Identities=54% Similarity=0.976 Sum_probs=77.0
Q ss_pred CCCCCCccCCHHHHhhhCCCccCHHHHHHHHHHHHHHhCCCCCCCCCccccchhHHhhhCCCCcccHHHHHHHHhccccC
Q 048564 33 GGIGKPVPVSAQLSKFLGANEASRSDAVKKIWQYIRQHDLQNPANKREIRCDDKLKTIFNGKDSVGFLEIAKLLSQHFVK 112 (114)
Q Consensus 33 ~g~~~~~~lSp~La~flG~~~~sR~eV~~~lW~YIK~nnLqDp~dKr~I~cDekLk~Lfg~~~~v~~~el~~lL~~Hl~k 112 (114)
+|+++.+.+|+.|+.|+|.+++||.+|++.||+|||+||||||.||+.|+||++|+.||++ ..|++|+|+++|.+||++
T Consensus 98 ~g~~kl~~ls~~L~~~~G~~~lsR~~vvk~iw~YIke~nLqDP~nkr~IlCDekL~~iF~~-k~v~~fem~KLL~~H~~~ 176 (240)
T KOG1946|consen 98 WGSTKLIPLSPSLARFVGTSELSRTDVVKKIWAYIKEHNLQDPKNKREILCDEKLKSIFGK-KRVGMFEMLKLLTKHFLK 176 (240)
T ss_pred cCcccccccCHHHHhhcccccccHHHHHHHHHHHHHHhccCCccccCeeeeHHHHHHHhcc-CccceeeHHHHHHHhccC
Confidence 6999999999999999999999999999999999999999999999999999999999995 569999999999999987
Q ss_pred C
Q 048564 113 S 113 (114)
Q Consensus 113 ~ 113 (114)
.
T Consensus 177 ~ 177 (240)
T KOG1946|consen 177 N 177 (240)
T ss_pred c
Confidence 4
No 4
>PRK14724 DNA topoisomerase III; Provisional
Probab=99.89 E-value=8e-24 Score=190.99 Aligned_cols=78 Identities=36% Similarity=0.700 Sum_probs=74.6
Q ss_pred CCCCCCccCCHHHHhhhCCCccCHHHHHHHHHHHHHHhCCCCCCCCCccccchhHHhhhCCCCcccHHHHHHHHhcccc
Q 048564 33 GGIGKPVPVSAQLSKFLGANEASRSDAVKKIWQYIRQHDLQNPANKREIRCDDKLKTIFNGKDSVGFLEIAKLLSQHFV 111 (114)
Q Consensus 33 ~g~~~~~~lSp~La~flG~~~~sR~eV~~~lW~YIK~nnLqDp~dKr~I~cDekLk~Lfg~~~~v~~~el~~lL~~Hl~ 111 (114)
-.+...|.+||+|++|||..++||++|++.||+|||+||||||.|++.|+||++|+.||| ++++.|++|+++|++||.
T Consensus 910 ~~~~~~~~ls~~La~~lg~~~~~r~~v~~~lW~YIK~~~Lqdp~~k~~i~cD~~L~~vfg-~~~~~~~~~~~~l~~hl~ 987 (987)
T PRK14724 910 APPAAGLKPSAALAAVIGAEPVARPEVIKKLWDYIKANNLQDPADKRAINADAKLRPVFG-KDQVTMFELAGIVGKHLS 987 (987)
T ss_pred cccccccCCCHHHHHHhCCCcCCHHHHHHHHHHHHHHccCCCcccCCeeccchHHHHHhC-CCcccHHHHHHHHHHhcC
Confidence 347779999999999999999999999999999999999999999999999999999998 899999999999999984
No 5
>COG5531 SWIB-domain-containing proteins implicated in chromatin remodeling [Chromatin structure and dynamics]
Probab=99.88 E-value=2.5e-23 Score=163.16 Aligned_cols=80 Identities=43% Similarity=0.806 Sum_probs=76.4
Q ss_pred CCCCCCCccCCHHHHhhhCCCccCHHHHHHHHHHHHHHhCCCCCCCCCccccchhHHhhhCCCCcccHHHHHHHHhcccc
Q 048564 32 KGGIGKPVPVSAQLSKFLGANEASRSDAVKKIWQYIRQHDLQNPANKREIRCDDKLKTIFNGKDSVGFLEIAKLLSQHFV 111 (114)
Q Consensus 32 ~~g~~~~~~lSp~La~flG~~~~sR~eV~~~lW~YIK~nnLqDp~dKr~I~cDekLk~Lfg~~~~v~~~el~~lL~~Hl~ 111 (114)
++...+.|.+||.|+.|||..++||+|||+.||+|||.||||||+||+.|.||++|+.||| .+.+.||+|.+.|.+|++
T Consensus 118 ~~~~~~~~~lS~~La~ilG~~~~tr~~~v~~lw~YIk~h~lq~~~nkr~I~~D~~L~~v~g-~~p~~mf~~~k~l~~hl~ 196 (237)
T COG5531 118 NSPSGEKVKLSPKLAAILGLEPGTRPEAVKKLWKYIKKHNLQDPNNKRLILCDSKLKKVLG-SDPIDMFELTKPLSPHLI 196 (237)
T ss_pred ccCCCCceecCHHHHHHhCCCCCCccHHHHHHHHHHHHhcCCCccccceecccHHHHHHhC-CCchhhhhhhccccccee
Confidence 3457789999999999999999999999999999999999999999999999999999999 789999999999999998
Q ss_pred C
Q 048564 112 K 112 (114)
Q Consensus 112 k 112 (114)
+
T Consensus 197 ~ 197 (237)
T COG5531 197 K 197 (237)
T ss_pred c
Confidence 7
No 6
>KOG2570 consensus SWI/SNF transcription activation complex subunit [Chromatin structure and dynamics; Transcription]
Probab=99.71 E-value=6.6e-18 Score=140.69 Aligned_cols=77 Identities=32% Similarity=0.635 Sum_probs=73.3
Q ss_pred CCCCccCCHHHHhhhCCCccCHHHHHHHHHHHHHHhCCCCCCCCCccccchhHHhhhCCCCcccHHHHHHHHhccccC
Q 048564 35 IGKPVPVSAQLSKFLGANEASRSDAVKKIWQYIRQHDLQNPANKREIRCDDKLKTIFNGKDSVGFLEIAKLLSQHFVK 112 (114)
Q Consensus 35 ~~~~~~lSp~La~flG~~~~sR~eV~~~lW~YIK~nnLqDp~dKr~I~cDekLk~Lfg~~~~v~~~el~~lL~~Hl~k 112 (114)
-...|++||.|+.+||....||++|+..||.|||.|+||||.++.+|.||..|+++|| ++++.|.+|+.+|++||..
T Consensus 205 ~P~~fklsp~La~lLGi~t~Trp~iI~alWqYIk~n~Lqd~~e~~~incD~~l~qif~-~~rl~F~elp~~l~~lL~P 281 (420)
T KOG2570|consen 205 QPEEFKLSPRLANLLGIHTGTRPDIVTALWQYIKTNKLQDPEDSDFINCDKALEQIFG-VDRLKFPELPQLLNPLLSP 281 (420)
T ss_pred CCcccccCHHHHHHhhhccCcchHHHHHHHHHHHHhccCCcccchhhcchHHHHHhhc-ccccccccchhhhhhccCC
Confidence 3455899999999999999999999999999999999999999999999999999998 8999999999999999975
No 7
>PRK06319 DNA topoisomerase I/SWI domain fusion protein; Validated
Probab=99.58 E-value=1.5e-15 Score=135.92 Aligned_cols=77 Identities=38% Similarity=0.682 Sum_probs=72.7
Q ss_pred CCCCccCCHHHHhhhCCCccCHHHHHHHHHHHHHHhCCCCCCCCCccccchhHHhhhCCCCcccHHHHHHHHhccccC
Q 048564 35 IGKPVPVSAQLSKFLGANEASRSDAVKKIWQYIRQHDLQNPANKREIRCDDKLKTIFNGKDSVGFLEIAKLLSQHFVK 112 (114)
Q Consensus 35 ~~~~~~lSp~La~flG~~~~sR~eV~~~lW~YIK~nnLqDp~dKr~I~cDekLk~Lfg~~~~v~~~el~~lL~~Hl~k 112 (114)
...+|.+|++|+.++|..+++|+++++.+|+||++|+||||+||+.|.||++|+++|+ ++.+.+++|+++++.|+.|
T Consensus 784 ~~~~~~~S~~La~~~g~~~~sr~~~~~~lw~yIk~~~lqdp~~Kr~i~~d~kl~kvf~-~~~~~~~~~~k~l~~hl~~ 860 (860)
T PRK06319 784 AGPLYTPSPALAAMIGAEPVGRGEATKKVWDYIKEHGLQSPENKKLIIPDSKLQGVIG-PDPIDMFQLSKKLSQHLIK 860 (860)
T ss_pred cccccccccccccccCcCccCchHHHHHHHHHHHHhcccCccccccCCCchhhhhhhC-cCccchhhhHHHHHhhhcC
Confidence 3455889999999999999999999999999999999999999999999999999998 7899999999999999875
No 8
>KOG2522 consensus Filamentous baseplate protein Ligatin, contains PUA domain [Translation, ribosomal structure and biogenesis]
Probab=95.74 E-value=0.014 Score=50.62 Aligned_cols=58 Identities=21% Similarity=0.246 Sum_probs=47.3
Q ss_pred CCCCccCCHHHHhhh---CC---CccCHHHHHHHHHHHHHHhCCCCCCCCCccccchhHHhhhC
Q 048564 35 IGKPVPVSAQLSKFL---GA---NEASRSDAVKKIWQYIRQHDLQNPANKREIRCDDKLKTIFN 92 (114)
Q Consensus 35 ~~~~~~lSp~La~fl---G~---~~~sR~eV~~~lW~YIK~nnLqDp~dKr~I~cDekLk~Lfg 92 (114)
+...|+.+.-...+| |. +-.|-+||...+.+||+.|||-|+.||..|+.|+-|-+...
T Consensus 357 i~~lYk~~~~~~~Lf~evg~~kg~lyt~seir~~V~kYi~knnLad~~nKg~VrLDpILfd~~~ 420 (560)
T KOG2522|consen 357 ILTLYKPFNLAKDLFKEVGLAKGTLYTSSEIRSAVSKYISKNNLADTKNKGKVRLDPILFDMVN 420 (560)
T ss_pred eeeeeccchHHHHHHHhcCccccceeeHHHHHHHHHHHhhhhhccccccCCcEEeccHHHHHHH
Confidence 445677766555554 43 56889999999999999999999999999999999888654
No 9
>PRK05350 acyl carrier protein; Provisional
Probab=89.38 E-value=0.57 Score=30.45 Aligned_cols=53 Identities=11% Similarity=0.234 Sum_probs=43.6
Q ss_pred cCHHHHHHHHHHHHHHhCCCCCCCCCccccchhHHhhhCCCCcccHHHHHHHHhccc
Q 048564 54 ASRSDAVKKIWQYIRQHDLQNPANKREIRCDDKLKTIFNGKDSVGFLEIAKLLSQHF 110 (114)
Q Consensus 54 ~sR~eV~~~lW~YIK~nnLqDp~dKr~I~cDekLk~Lfg~~~~v~~~el~~lL~~Hl 110 (114)
|+|.+|...|.++|.+. +.- +...|.+|..|..-+| -+++.+-+|.-.|..+|
T Consensus 2 m~~~~i~~~v~~ii~~~-~~~--~~~~i~~d~~l~~dlg-~DSld~veli~~lE~~f 54 (82)
T PRK05350 2 MTREEILERLRAILVEL-FEI--DPEDITPEANLYEDLD-LDSIDAVDLVVHLQKLT 54 (82)
T ss_pred CCHHHHHHHHHHHHHHH-hCC--CHHHCCCCccchhhcC-CCHHHHHHHHHHHHHHH
Confidence 78999999999999987 432 2246999999988787 79999999988888876
No 10
>PRK05828 acyl carrier protein; Validated
Probab=86.68 E-value=1.6 Score=29.08 Aligned_cols=53 Identities=15% Similarity=0.250 Sum_probs=41.7
Q ss_pred cCHHHHHHHHHHHHHHhCCCCCCCCCccccchhHHhhhCCCCcccHHHHHHHHhccc
Q 048564 54 ASRSDAVKKIWQYIRQHDLQNPANKREIRCDDKLKTIFNGKDSVGFLEIAKLLSQHF 110 (114)
Q Consensus 54 ~sR~eV~~~lW~YIK~nnLqDp~dKr~I~cDekLk~Lfg~~~~v~~~el~~lL~~Hl 110 (114)
|||.+|..+|-+.|.+.++.-+. .-|.+|..|.+ +| -+++.+.++.-.|..+|
T Consensus 1 m~~~eI~~~i~~ii~e~~~~~~~--d~i~~~~~~~d-Lg-~DSLd~velv~~lE~~f 53 (84)
T PRK05828 1 MQEMEILLKIKEIAKKKNFAVTL--DESNINKPYRE-LK-IDSLDMFSIIVSLESEF 53 (84)
T ss_pred CCHHHHHHHHHHHHHHhccCCCc--ccccCCCCHHh-cC-CCHHHHHHHHHHHHHHH
Confidence 78999999999999886554322 24678888877 76 68899888888887766
No 11
>CHL00124 acpP acyl carrier protein; Validated
Probab=83.84 E-value=1.6 Score=28.04 Aligned_cols=53 Identities=15% Similarity=0.293 Sum_probs=42.0
Q ss_pred cCHHHHHHHHHHHHHHhCCCCCCCCCccccchhHHhhhCCCCcccHHHHHHHHhccc
Q 048564 54 ASRSDAVKKIWQYIRQHDLQNPANKREIRCDDKLKTIFNGKDSVGFLEIAKLLSQHF 110 (114)
Q Consensus 54 ~sR~eV~~~lW~YIK~nnLqDp~dKr~I~cDekLk~Lfg~~~~v~~~el~~lL~~Hl 110 (114)
|+|.+|...|-++|.+.-=.+|. .|.+|..|..-+| -+++.+-+|...|...|
T Consensus 1 M~~~~i~~~l~~ii~~~~~~~~~---~i~~d~~l~~dlg-~DSl~~~eli~~le~~f 53 (82)
T CHL00124 1 MTKNDIFEKVQSIVAEQLGIEKS---EVTLDANFTRDLG-ADSLDVVELVMAIEEKF 53 (82)
T ss_pred CCHHHHHHHHHHHHHHHHCCCHH---HCCCCcchhhhcC-CcHHHHHHHHHHHHHHH
Confidence 68999999999999887423333 5999999999887 68888888887777655
No 12
>PRK12449 acyl carrier protein; Provisional
Probab=82.38 E-value=3.6 Score=26.17 Aligned_cols=53 Identities=17% Similarity=0.261 Sum_probs=41.3
Q ss_pred cCHHHHHHHHHHHHHHhCCCCCCCCCccccchhHHhhhCCCCcccHHHHHHHHhccc
Q 048564 54 ASRSDAVKKIWQYIRQHDLQNPANKREIRCDDKLKTIFNGKDSVGFLEIAKLLSQHF 110 (114)
Q Consensus 54 ~sR~eV~~~lW~YIK~nnLqDp~dKr~I~cDekLk~Lfg~~~~v~~~el~~lL~~Hl 110 (114)
|+|.+|...|-+++.+.-=.++. .|.+|..|..-+| -+++.+.+|.-.|...|
T Consensus 1 m~~~~i~~~l~~il~~~~~~~~~---~i~~~~~l~~dlg-~DSl~~~~li~~lE~~f 53 (80)
T PRK12449 1 MTREEIFERLINLIQKQRSYLSL---AITEQTHLKDDLA-VDSIELVEFIINVEDEF 53 (80)
T ss_pred CCHHHHHHHHHHHHHHHhCCCcc---ccCCCCcHHHHcC-CcHHHHHHHHHHHHHHh
Confidence 57899999999999875433333 4899999999997 78888888877776654
No 13
>PTZ00171 acyl carrier protein; Provisional
Probab=74.65 E-value=5.8 Score=29.21 Aligned_cols=57 Identities=14% Similarity=0.277 Sum_probs=45.4
Q ss_pred CCCccCHHHHHHHHHHHHHHhCCCCCCCCCccccchhHHhhhCCCCcccHHHHHHHHhccc
Q 048564 50 GANEASRSDAVKKIWQYIRQHDLQNPANKREIRCDDKLKTIFNGKDSVGFLEIAKLLSQHF 110 (114)
Q Consensus 50 G~~~~sR~eV~~~lW~YIK~nnLqDp~dKr~I~cDekLk~Lfg~~~~v~~~el~~lL~~Hl 110 (114)
+...+++.+|...|+++|.+.-=.|++ .|.+|..+.+-+| -|++.+-+|.-.|+.+|
T Consensus 62 ~~~~~~~~~v~~~l~eiiae~l~vd~~---~I~~ds~~~~dLg-~DSLd~veLv~~LEdeF 118 (148)
T PTZ00171 62 KQYLLSKEDVLTRVKKVVKNFEKVDAS---KITPESNFVKDLG-ADSLDVVELLIAIEQEF 118 (148)
T ss_pred cccccCHHHHHHHHHHHHHHHhCCCHh---hCCCCcchhhhcC-CCHHHHHHHHHHHHHHH
Confidence 456789999999999999988533433 5888999988887 68888888887777765
No 14
>PF13545 HTH_Crp_2: Crp-like helix-turn-helix domain; PDB: 3LA2_A 3LA3_B 3LA7_A 3B02_A 3E97_A 2H6C_B 1OMI_A 2BGC_H 2BEO_A 2GAU_A ....
Probab=68.42 E-value=4 Score=25.27 Aligned_cols=48 Identities=19% Similarity=0.499 Sum_probs=32.5
Q ss_pred CccCC-HHHHhhhCCCccCHHHHHHHHHHHHHHhCCCCCCCCCccccc-hhHHh
Q 048564 38 PVPVS-AQLSKFLGANEASRSDAVKKIWQYIRQHDLQNPANKREIRCD-DKLKT 89 (114)
Q Consensus 38 ~~~lS-p~La~flG~~~~sR~eV~~~lW~YIK~nnLqDp~dKr~I~cD-ekLk~ 89 (114)
.+.+| .+||+++|++..| +..+....++.|+.+-..+++++.| ++|++
T Consensus 26 ~~~lt~~~iA~~~g~sr~t----v~r~l~~l~~~g~I~~~~~~i~I~d~~~L~~ 75 (76)
T PF13545_consen 26 PLPLTQEEIADMLGVSRET----VSRILKRLKDEGIIEVKRGKIIILDPERLEE 75 (76)
T ss_dssp EEESSHHHHHHHHTSCHHH----HHHHHHHHHHTTSEEEETTEEEESSHHHHHH
T ss_pred EecCCHHHHHHHHCCCHHH----HHHHHHHHHHCCCEEEcCCEEEECCHHHHhc
Confidence 34444 4899999976544 3344455677888888888888888 55554
No 15
>PF07587 PSD1: Protein of unknown function (DUF1553); InterPro: IPR022655 The function is not known. It is found associated with IPR011444 from INTERPRO It is also found associated with the Planctomycete cytochrome C domain IPR011429 from INTERPRO.
Probab=60.68 E-value=13 Score=29.45 Aligned_cols=58 Identities=22% Similarity=0.400 Sum_probs=45.3
Q ss_pred HHHhhhC--CCccCHHHHHHHHHHHHHHhCCCCCCCCCccccchhHHhhhCC-CCcccHHHHHHHHhccccCC
Q 048564 44 QLSKFLG--ANEASRSDAVKKIWQYIRQHDLQNPANKREIRCDDKLKTIFNG-KDSVGFLEIAKLLSQHFVKS 113 (114)
Q Consensus 44 ~La~flG--~~~~sR~eV~~~lW~YIK~nnLqDp~dKr~I~cDekLk~Lfg~-~~~v~~~el~~lL~~Hl~k~ 113 (114)
+||+.|- .++.+---+|.+||.|.--.||-+|-|- ||. ...-+.+||-++|..+|...
T Consensus 5 ~LA~wlt~~~Np~faRv~VNRvW~~~fGrGlV~p~dD------------~g~~~~~PshPeLLd~La~~F~~~ 65 (266)
T PF07587_consen 5 ALADWLTSPDNPLFARVIVNRVWQHLFGRGLVEPVDD------------FGPQGNPPSHPELLDWLAAEFVEH 65 (266)
T ss_pred HHHHHhcCCCCcchHHHHHHHHHHHHcCCcCcCCHhh------------ccCCCCCCCCHHHHHHHHHHHHHc
Confidence 6788875 4788888999999999999999999763 442 13456789999998888653
No 16
>PRK07117 acyl carrier protein; Validated
Probab=60.02 E-value=15 Score=24.05 Aligned_cols=52 Identities=13% Similarity=0.156 Sum_probs=39.2
Q ss_pred cCHHHHHHHHHHHHHHhC-CCCCCCCCccccchhHHhhhCCCCcccHHHHHHHHhccc
Q 048564 54 ASRSDAVKKIWQYIRQHD-LQNPANKREIRCDDKLKTIFNGKDSVGFLEIAKLLSQHF 110 (114)
Q Consensus 54 ~sR~eV~~~lW~YIK~nn-LqDp~dKr~I~cDekLk~Lfg~~~~v~~~el~~lL~~Hl 110 (114)
||+.+|...|-+-|.+.- =-|| ..|..|..|++ +| .+++.+.++--.+...|
T Consensus 1 M~~~ei~~~v~~ii~e~~p~i~~---~~I~~~~~l~D-Lg-~DSlD~veiv~~led~f 53 (79)
T PRK07117 1 MDKQRIFDILVRHIREVLPDLDQ---HQFQPEDSLVD-LG-ANSMDRAEIVIMTLESL 53 (79)
T ss_pred CCHHHHHHHHHHHHHHHcCCCCH---HHCCCCCChhh-cC-CChHHHHHHHHHHHHHH
Confidence 578889899988888864 1333 46899999988 87 78888888776665443
No 17
>PF08463 EcoEI_R_C: EcoEI R protein C-terminal; InterPro: IPR013670 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type I restriction endonucleases are components of prokaryotic DNA restriction-modification mechanisms that protects the organism against invading foreign DNA. Type I enzymes have three different subunits subunits - M (modification), S (specificity) and R (restriction) - that form multifunctional enzymes with restriction (3.1.21.3 from EC), methylase (2.1.1.72 from EC) and ATPase activities [, ]. The S subunit is required for both restriction and modification and is responsible for recognition of the DNA sequence specific for the system. The M subunit is necessary for modification, and the R subunit is required for restriction. These enzymes use S-Adenosyl-L-methionine (AdoMet) as the methyl group donor in the methylation reaction, and have a requirement for ATP. They recognise asymmetric DNA sequences split into two domains of specific sequence, one 3-4 bp long and another 4-5 bp long, separated by a nonspecific spacer 6-8 bp in length. Cleavage occurs a considerable distance from the recognition sites, rarely less than 400 bp away and up to 7000 bp away. Adenosyl residues are methylated, one on each strand of the recognition sequence. These enzymes are widespread in eubacteria and archaea. In enteric bacteria they have been subdivide into four families: types IA, IB, IC and ID. Type III restriction endonucleases (3.1.21.5 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. Type III enzymes are hetero-oligomeric, multifunctional proteins composed of two subunits, Res and Mod. The Mod subunit recognises the DNA sequence specific for the system and is a modification methyltransferase; as such it is functionally equivalent to the M and S subunits of type I restriction endonuclease. Res is required for restriction, although it has no enzymatic activity on its own. Type III enzymes recognise short 5-6 bp long asymmetric DNA sequences and cleave 25-27 bp downstream to leave short, single-stranded 5' protrusions. They require the presence of two inversely oriented unmethylated recognition sites for restriction to occur. These enzymes methylate only one strand of the DNA, at the N-6 position of adenosyl residues, so newly replicated DNA will have only one strand methylated, which is sufficient to protect against restriction. Type III enzymes belong to the beta-subfamily of N6 adenine methyltransferases, containing the nine motifs that characterise this family, including motif I, the AdoMet binding pocket (FXGXG), and motif IV, the catalytic region (S/D/N (PP) Y/F) [, ]. This entry represents the C-terminal domain found in both the R subunit of type I enzymes and the Res subunit of type III enzymes. The type I enzyme represented is EcoEI, which recognises 5'-GAGN(7)ATGC-3; the R protein (HsdR) is required for both nuclease and ATPase activity [, ]. ; GO: 0003677 DNA binding, 0003824 catalytic activity, 0006304 DNA modification
Probab=58.75 E-value=7.3 Score=27.99 Aligned_cols=69 Identities=25% Similarity=0.456 Sum_probs=46.0
Q ss_pred cCCHHHHhhhCCCc--cCHHHHHHHHHHHHHHhCCCCCCCCCccccc-----hhHHhhhCCCCcccHHHHHHHHhccc
Q 048564 40 PVSAQLSKFLGANE--ASRSDAVKKIWQYIRQHDLQNPANKREIRCD-----DKLKTIFNGKDSVGFLEIAKLLSQHF 110 (114)
Q Consensus 40 ~lSp~La~flG~~~--~sR~eV~~~lW~YIK~nnLqDp~dKr~I~cD-----ekLk~Lfg~~~~v~~~el~~lL~~Hl 110 (114)
++....+.|++... ..+-+++..|-+|+..++..++++=...-.. ..+..+||+.+ .+.++-.-|+.+|
T Consensus 88 rv~~~~~~~l~~~~~~~~Q~~~L~~i~~~~~~~G~~~~~~l~~~pF~~~G~~~~~~~~Fg~~~--~l~~~~~~l~~~L 163 (164)
T PF08463_consen 88 RVEEAFSKFLNQHQFNAEQREFLERILDYYAQNGIIEPEDLKEPPFSDLGGPGGIIRVFGGKE--QLDEILNELNKNL 163 (164)
T ss_pred HHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHhCcccHHHhCCCchhhcCCHHHHHHHcCCHH--HHHHHHHHHHhhc
Confidence 33445566675544 6678899999999999999987653333222 45778888422 5666666666665
No 18
>PRK00071 nadD nicotinic acid mononucleotide adenylyltransferase; Provisional
Probab=54.45 E-value=9.2 Score=28.60 Aligned_cols=18 Identities=28% Similarity=0.409 Sum_probs=14.2
Q ss_pred HHHHHHHHHHHHHHhCCC
Q 048564 56 RSDAVKKIWQYIRQHDLQ 73 (114)
Q Consensus 56 R~eV~~~lW~YIK~nnLq 73 (114)
+.-|-..|++||++|||.
T Consensus 184 ~~lvp~~V~~YI~~~~LY 201 (203)
T PRK00071 184 RYLLPEAVLDYIEKHGLY 201 (203)
T ss_pred hHhCCHHHHHHHHHhCcc
Confidence 344556799999999996
No 19
>TIGR03697 NtcA_cyano global nitrogen regulator NtcA, cyanobacterial. Members of this protein family, found in the cyanobacteria, are the global nitrogen regulator NtcA. This DNA-binding transcriptional regulator is required for expressing many different ammonia-repressible genes. The consensus NtcA-binding site is G T A N(8)T A C.
Probab=53.38 E-value=20 Score=25.43 Aligned_cols=49 Identities=16% Similarity=0.283 Sum_probs=33.3
Q ss_pred ccCC-HHHHhhhCCCccCHHHHHHHHHHHHHHhCCCCCCCCCccccc-hhHHhhh
Q 048564 39 VPVS-AQLSKFLGANEASRSDAVKKIWQYIRQHDLQNPANKREIRCD-DKLKTIF 91 (114)
Q Consensus 39 ~~lS-p~La~flG~~~~sR~eV~~~lW~YIK~nnLqDp~dKr~I~cD-ekLk~Lf 91 (114)
+.+| .++|+++|++.. .+.++..-.++.|+..-..++++++| ++|++.+
T Consensus 142 ~~~t~~~iA~~lG~tre----tvsR~l~~l~~~g~I~~~~~~i~I~d~~~L~~~~ 192 (193)
T TIGR03697 142 LRLSHQAIAEAIGSTRV----TITRLLGDLRKKKLISIHKKKITVHDPIALGQRF 192 (193)
T ss_pred CCCCHHHHHHHhCCcHH----HHHHHHHHHHHCCCEEecCCEEEEeCHHHHHHhc
Confidence 4444 589999995433 33344455678888888888899998 5666543
No 20
>PF08225 Antimicrobial19: Pseudin antimicrobial peptide; InterPro: IPR013156 Pseudins are a subfamily of the FSAP family (Frog Secreted Active Peptides) extracted from the skin of the paradoxical frog Pseudis paradoxa (Paradoxical frog). The pseudins belong to the class of cationic, amphipathic-helical antimicrobial peptides [].; GO: 0006952 defense response
Probab=52.66 E-value=11 Score=19.58 Aligned_cols=20 Identities=40% Similarity=0.808 Sum_probs=15.2
Q ss_pred hHHhhhCCCCcccHHHHHHHHhccc
Q 048564 86 KLKTIFNGKDSVGFLEIAKLLSQHF 110 (114)
Q Consensus 86 kLk~Lfg~~~~v~~~el~~lL~~Hl 110 (114)
.|+++|+| +.|..++++.|.
T Consensus 4 tlkkv~qg-----lhe~ikli~nh~ 23 (23)
T PF08225_consen 4 TLKKVFQG-----LHEVIKLINNHV 23 (23)
T ss_pred HHHHHHHH-----HHHHHHHHhcCC
Confidence 47778863 778888888883
No 21
>PRK07639 acyl carrier protein; Provisional
Probab=51.99 E-value=30 Score=22.78 Aligned_cols=54 Identities=11% Similarity=0.111 Sum_probs=39.6
Q ss_pred cCHHHHHHHHHHHHHHhCCCCCCCCCccccchhHHhhhCCCCcccHHHHHHHHhccc
Q 048564 54 ASRSDAVKKIWQYIRQHDLQNPANKREIRCDDKLKTIFNGKDSVGFLEIAKLLSQHF 110 (114)
Q Consensus 54 ~sR~eV~~~lW~YIK~nnLqDp~dKr~I~cDekLk~Lfg~~~~v~~~el~~lL~~Hl 110 (114)
|||.+|...|-+.|.+.==.++. ..|..|..|..=+| -+++.+.++.-.|+.+|
T Consensus 1 M~~~ei~~~i~~il~e~l~~~~~--~~i~~d~~l~edL~-lDSld~velv~~lE~~f 54 (86)
T PRK07639 1 MRREALKNAVLKIMEEKLELKNV--THLEETMRLNEDLY-IDSVMMLQLIVYIEMDV 54 (86)
T ss_pred CCHHHHHHHHHHHHHHHhCCCcc--ccCCCCCCcccccC-CChHHHHHHHHHHHHHH
Confidence 68889999999988876311121 25788888877666 68888888888877765
No 22
>PLN02945 nicotinamide-nucleotide adenylyltransferase/nicotinate-nucleotide adenylyltransferase
Probab=51.98 E-value=11 Score=29.14 Aligned_cols=30 Identities=13% Similarity=0.286 Sum_probs=19.1
Q ss_pred HHHhhhCCCccCHHHHHHHHHHHHHHhCCC
Q 048564 44 QLSKFLGANEASRSDAVKKIWQYIRQHDLQ 73 (114)
Q Consensus 44 ~La~flG~~~~sR~eV~~~lW~YIK~nnLq 73 (114)
++.+.+.....-+..|-..|++||++|||.
T Consensus 206 ~IR~~l~~g~~i~~lvP~~V~~YI~~~~LY 235 (236)
T PLN02945 206 RVRECISRGLSVKYLTPDGVIDYIKEHGLY 235 (236)
T ss_pred HHHHHHHcCCCchhhCCHHHHHHHHHcCCC
Confidence 444444332233455666799999999986
No 23
>TIGR00482 nicotinate (nicotinamide) nucleotide adenylyltransferase. This model represents the predominant bacterial/eukaryotic adenylyltransferase for nicotinamide-nucleotide, its deamido form nicotinate nucleotide, or both. The first activity, nicotinamide-nucleotide adenylyltransferase (EC 2.7.7.1), synthesizes NAD by the salvage pathway, while the second, nicotinate-nucleotide adenylyltransferase (EC 2.7.7.18) synthesizes the immediate precursor of NAD by the de novo pathway. In E. coli, NadD activity is biased toward the de novo pathway while salvage activity is channeled through the multifunctional NadR protein, but this division of labor may be exceptional. The given name of this model, nicotinate (nicotinamide) nucleotide adenylyltransferase, reflects the lack of absolute specificity with respect to substrate amidation state in most species.
Probab=50.67 E-value=13 Score=27.71 Aligned_cols=30 Identities=17% Similarity=0.278 Sum_probs=18.1
Q ss_pred HHHhhhCCCccCHHHHHHHHHHHHHHhCCC
Q 048564 44 QLSKFLGANEASRSDAVKKIWQYIRQHDLQ 73 (114)
Q Consensus 44 ~La~flG~~~~sR~eV~~~lW~YIK~nnLq 73 (114)
+..+-+....--+.-|-..|++||++|+|.
T Consensus 164 ~IR~~l~~g~~~~~lvP~~V~~YI~~~~LY 193 (193)
T TIGR00482 164 EIRQRIRQGKSIEYLLPDPVIKYIKQHGLY 193 (193)
T ss_pred HHHHHHHcCCCchhhCCHHHHHHHHHhCCC
Confidence 344444332233445556789999999984
No 24
>cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins. Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.
Probab=50.66 E-value=27 Score=18.94 Aligned_cols=24 Identities=13% Similarity=0.495 Sum_probs=18.4
Q ss_pred HHHHhhhCCCccCHHHHHHHHHHHHHHhCCC
Q 048564 43 AQLSKFLGANEASRSDAVKKIWQYIRQHDLQ 73 (114)
Q Consensus 43 p~La~flG~~~~sR~eV~~~lW~YIK~nnLq 73 (114)
.++++.+|++.- .||.|++...+.
T Consensus 4 ~e~a~~lgvs~~-------tl~~~~~~g~~~ 27 (49)
T cd04762 4 KEAAELLGVSPS-------TLRRWVKEGKLK 27 (49)
T ss_pred HHHHHHHCcCHH-------HHHHHHHcCCCC
Confidence 477888887765 789999987654
No 25
>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=50.29 E-value=12 Score=19.23 Aligned_cols=20 Identities=25% Similarity=0.464 Sum_probs=17.0
Q ss_pred CHHHHHHHHHHHHHHhCCCC
Q 048564 55 SRSDAVKKIWQYIRQHDLQN 74 (114)
Q Consensus 55 sR~eV~~~lW~YIK~nnLqD 74 (114)
.+.++...|++|...+|+.+
T Consensus 2 ~~~~l~~lI~~yL~~~g~~~ 21 (34)
T smart00667 2 SRSELNRLILEYLLRNGYEE 21 (34)
T ss_pred cHHHHHHHHHHHHHHcCHHH
Confidence 46788999999999999765
No 26
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=48.65 E-value=21 Score=25.70 Aligned_cols=46 Identities=9% Similarity=0.139 Sum_probs=33.0
Q ss_pred HHHHhhhCCCccCHHHHHHHHHHHHHHhCCCCCCCCCccccc-hhHHhhhC
Q 048564 43 AQLSKFLGANEASRSDAVKKIWQYIRQHDLQNPANKREIRCD-DKLKTIFN 92 (114)
Q Consensus 43 p~La~flG~~~~sR~eV~~~lW~YIK~nnLqDp~dKr~I~cD-ekLk~Lfg 92 (114)
.+||+++|....|=+.++ .-.++.|+.+-+.++++++| ++|+++.+
T Consensus 153 ~~iA~~lG~tretvsR~l----~~l~~~g~I~~~~~~i~I~d~~~L~~~~~ 199 (202)
T PRK13918 153 DELAAAVGSVRETVTKVI----GELSREGYIRSGYGKIQLLDLKGLEELAE 199 (202)
T ss_pred HHHHHHhCccHHHHHHHH----HHHHHCCCEEcCCCEEEEECHHHHHHHHh
Confidence 489999997654433333 34568888887778888888 67887765
No 27
>PRK05883 acyl carrier protein; Validated
Probab=48.62 E-value=40 Score=22.48 Aligned_cols=55 Identities=16% Similarity=0.133 Sum_probs=43.2
Q ss_pred CccCHHHHHHHHHHHHHHhCCCCCCCCCccccchhHHhhhCCCCcccHHHHHHHHhccc
Q 048564 52 NEASRSDAVKKIWQYIRQHDLQNPANKREIRCDDKLKTIFNGKDSVGFLEIAKLLSQHF 110 (114)
Q Consensus 52 ~~~sR~eV~~~lW~YIK~nnLqDp~dKr~I~cDekLk~Lfg~~~~v~~~el~~lL~~Hl 110 (114)
...+..+|...|-++|.+.==.||+ .|..|..|...+| -+++.+.++.-.|..+|
T Consensus 8 ~~~~~~~I~~~l~~iia~~l~v~~~---~I~~d~~l~~dlg-~DSL~~v~lv~~lE~~f 62 (91)
T PRK05883 8 MTSSPSTVSATLLSILRDDLNVDLT---RVTPDARLVDDVG-LDSVAFAVGMVAIEERL 62 (91)
T ss_pred CCCCHHHHHHHHHHHHHHHhCCChh---hCCCCCchhhccC-CChHHHHHHHHHHHHHH
Confidence 4678899999999999876323333 5999999999998 78888877777777766
No 28
>PRK06973 nicotinic acid mononucleotide adenylyltransferase; Provisional
Probab=48.36 E-value=13 Score=29.28 Aligned_cols=31 Identities=32% Similarity=0.532 Sum_probs=21.8
Q ss_pred HHHHhhhCCC--------ccCHHHHHHHHHHHHHHhCCC
Q 048564 43 AQLSKFLGAN--------EASRSDAVKKIWQYIRQHDLQ 73 (114)
Q Consensus 43 p~La~flG~~--------~~sR~eV~~~lW~YIK~nnLq 73 (114)
.++.+-+... .--+.-|=..|++||++|+|.
T Consensus 203 T~IR~~l~~g~~~~~~~~~~i~~lvP~~V~~YI~~~~LY 241 (243)
T PRK06973 203 TDIRAHLRACIARRAQVPDASAEHVPAAVWAYILQHRLY 241 (243)
T ss_pred HHHHHHHHcCCCcccccCCChhHhCCHHHHHHHHHcCCC
Confidence 4566666543 344556667899999999997
No 29
>cd01104 HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA- and CarA-like proteins in this group appear to lack the long dimerization helix seen i
Probab=45.22 E-value=67 Score=19.22 Aligned_cols=57 Identities=12% Similarity=0.247 Sum_probs=32.5
Q ss_pred HHHHhhhCCCccCHHHHHHHHHHHHHHhCCCCCCC---CCccccchhHHhhhC----CCCcccHHHHHHHH
Q 048564 43 AQLSKFLGANEASRSDAVKKIWQYIRQHDLQNPAN---KREIRCDDKLKTIFN----GKDSVGFLEIAKLL 106 (114)
Q Consensus 43 p~La~flG~~~~sR~eV~~~lW~YIK~nnLqDp~d---Kr~I~cDekLk~Lfg----~~~~v~~~el~~lL 106 (114)
.++++.+|++.- .|+.|++..++..|.. ....-.++.+..+-. ....++..+|.++|
T Consensus 4 ~eva~~~gvs~~-------tlr~w~~~~g~~~~~r~~~~~r~yt~~~v~~l~~i~~l~~~g~~l~~i~~~~ 67 (68)
T cd01104 4 GAVARLTGVSPD-------TLRAWERRYGLPAPQRTDGGHRLYSEADVARLRLIRRLTSEGVRISQAAALA 67 (68)
T ss_pred HHHHHHHCcCHH-------HHHHHHHhCCCCCCCcCCCCCeecCHHHHHHHHHHHHHHHCCCCHHHHHHHh
Confidence 577888887765 7888898878876522 223334444322211 01345666666654
No 30
>PRK09392 ftrB transcriptional activator FtrB; Provisional
Probab=44.65 E-value=33 Score=25.50 Aligned_cols=48 Identities=15% Similarity=0.232 Sum_probs=32.5
Q ss_pred cCC-HHHHhhhCCCccCHHHHHHHHHHHHHHhCCCCCCCCCccccc-hhHHhhhC
Q 048564 40 PVS-AQLSKFLGANEASRSDAVKKIWQYIRQHDLQNPANKREIRCD-DKLKTIFN 92 (114)
Q Consensus 40 ~lS-p~La~flG~~~~sR~eV~~~lW~YIK~nnLqDp~dKr~I~cD-ekLk~Lfg 92 (114)
.++ .++|+++|....| |...+-+ .++.|+ .-..++++++| ++|+++.+
T Consensus 173 ~~t~~~iA~~lG~tret---vsR~l~~-L~~~gl-~~~~~~i~I~d~~~L~~~~~ 222 (236)
T PRK09392 173 PYEKRVLASYLGMTPEN---LSRAFAA-LASHGV-HVDGSAVTITDPAGLARFAK 222 (236)
T ss_pred eCCHHHHHHHhCCChhH---HHHHHHH-HHhCCe-EeeCCEEEEcCHHHHHHhhc
Confidence 344 6899999985444 4333333 566668 55567788888 88888776
No 31
>PF01047 MarR: MarR family; InterPro: IPR000835 The MarR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 135 amino acids present in transcription regulators of the MarR/SlyA family, involved in the development of antibiotic resistance. This family of transcription regulators is named after Escherichia coli MarR, a repressor of genes which activate the multiple antibiotic resistance and oxidative stress regulons, and after slyA from Salmonella typhimurium and E. coli, a transcription regulator that is required for virulence and survival in the macrophage environment. Regulators with the MarR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the MarR-like regulators respond to aromatic compounds [, , ]. The crystal structures of MarR, MexR and SlyA have been determined and show a winged HTH DNA-binding core flanked by helices involved in dimerisation. The DNA-binding domains are ascribed to the superfamily of winged helix proteins, containing a three (four)-helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-(H1')-H2-B1-H3-H4-B2-B3-H5-H6. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. The helices 1, 5 and 6 are involved in dimerisation, as most MarR-like transcription regulators form dimers [, ]. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1JGS_A 2NYX_D 2PEX_B 2PFB_A 3BPX_A 3BPV_A 2BV6_A 3BJA_A 3E6M_B 2ETH_A ....
Probab=41.87 E-value=6 Score=23.41 Aligned_cols=35 Identities=23% Similarity=0.470 Sum_probs=19.2
Q ss_pred HHHhhhCCCccCHHHHHHHHHHHHHH---hCCCCCCCCCcc
Q 048564 44 QLSKFLGANEASRSDAVKKIWQYIRQ---HDLQNPANKREI 81 (114)
Q Consensus 44 ~La~flG~~~~sR~eV~~~lW~YIK~---nnLqDp~dKr~I 81 (114)
+|++.+|.+ ++.++..+..-++. ..-+||+|+|.|
T Consensus 22 ~la~~~~~~---~~~~t~~i~~L~~~g~I~r~~~~~D~R~v 59 (59)
T PF01047_consen 22 ELAEKLGIS---RSTVTRIIKRLEKKGLIERERDPDDRRQV 59 (59)
T ss_dssp HHHHHHTS----HHHHHHHHHHHHHTTSEEEEEETTETTSE
T ss_pred HHHHHHCCC---hhHHHHHHHHHHHCCCEEeccCCCCCCcC
Confidence 777777764 44555555444443 233567776653
No 32
>TIGR00517 acyl_carrier acyl carrier protein. S (Ser) at position 37 in the seed alignment, in the motif DSLD, is the phosphopantetheine attachment site.
Probab=40.15 E-value=42 Score=20.94 Aligned_cols=50 Identities=16% Similarity=0.254 Sum_probs=36.7
Q ss_pred HHHHHHHHHHHHHhCCCCCCCCCccccchhHHhhhCCCCcccHHHHHHHHhccc
Q 048564 57 SDAVKKIWQYIRQHDLQNPANKREIRCDDKLKTIFNGKDSVGFLEIAKLLSQHF 110 (114)
Q Consensus 57 ~eV~~~lW~YIK~nnLqDp~dKr~I~cDekLk~Lfg~~~~v~~~el~~lL~~Hl 110 (114)
.++...|.++|.+.-=.+| ..|.+|..|..-+| -+++.+-+|.-.|..+|
T Consensus 2 ~~i~~~l~~il~~~~~~~~---~~i~~~~~l~~dlg-lDSl~~veli~~lE~~f 51 (77)
T TIGR00517 2 QEIFEKVKAIIKEQLNVDE---DQVTPDASFVEDLG-ADSLDTVELVMALEEEF 51 (77)
T ss_pred hHHHHHHHHHHHHHHCCCH---HHCCCCcchhhhcC-CcHHHHHHHHHHHHHHH
Confidence 4677788888888632343 35888988877777 68888888888777765
No 33
>PF08938 HBS1_N: HBS1 N-terminus; InterPro: IPR015033 This domain is found in various eukaryotic HBS1-like proteins. ; PDB: 1UFZ_A 3IZQ_1.
Probab=39.42 E-value=7 Score=25.51 Aligned_cols=28 Identities=18% Similarity=0.437 Sum_probs=20.8
Q ss_pred ccCCHHHHhhhCCCccCHHHHHHHHHHH
Q 048564 39 VPVSAQLSKFLGANEASRSDAVKKIWQY 66 (114)
Q Consensus 39 ~~lSp~La~flG~~~~sR~eV~~~lW~Y 66 (114)
+.+.+.+.+.||....|..+|..+||.|
T Consensus 29 ~~~l~~vr~~Lg~~~~~e~~i~eal~~~ 56 (79)
T PF08938_consen 29 YSCLPQVREVLGDYVPPEEQIKEALWHY 56 (79)
T ss_dssp CHHCCCHHHHCCCCC--CCHHHHHHHHT
T ss_pred HHHHHHHHHHHcccCCCHHHHHHHHHHH
Confidence 4455678888887655999999999987
No 34
>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=38.76 E-value=35 Score=21.49 Aligned_cols=21 Identities=19% Similarity=0.496 Sum_probs=15.8
Q ss_pred CHHHHHHHHHHHHHHhCCCCCC
Q 048564 55 SRSDAVKKIWQYIRQHDLQNPA 76 (114)
Q Consensus 55 sR~eV~~~lW~YIK~nnLqDp~ 76 (114)
.+.+|...|.+||.+|+.- |.
T Consensus 7 rQ~~vL~~I~~~~~~~G~~-Pt 27 (65)
T PF01726_consen 7 RQKEVLEFIREYIEENGYP-PT 27 (65)
T ss_dssp HHHHHHHHHHHHHHHHSS----
T ss_pred HHHHHHHHHHHHHHHcCCC-CC
Confidence 3678999999999999944 54
No 35
>TIGR01764 excise DNA binding domain, excisionase family. An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).
Probab=37.07 E-value=35 Score=18.65 Aligned_cols=25 Identities=16% Similarity=0.538 Sum_probs=19.4
Q ss_pred HHHHhhhCCCccCHHHHHHHHHHHHHHhCCCC
Q 048564 43 AQLSKFLGANEASRSDAVKKIWQYIRQHDLQN 74 (114)
Q Consensus 43 p~La~flG~~~~sR~eV~~~lW~YIK~nnLqD 74 (114)
++.++++|.+.- .|+.+|++..+.-
T Consensus 5 ~e~a~~lgis~~-------ti~~~~~~g~i~~ 29 (49)
T TIGR01764 5 EEAAEYLGVSKD-------TVYRLIHEGELPA 29 (49)
T ss_pred HHHHHHHCCCHH-------HHHHHHHcCCCCe
Confidence 578888988665 7899998877663
No 36
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=36.63 E-value=31 Score=22.92 Aligned_cols=22 Identities=27% Similarity=0.597 Sum_probs=16.3
Q ss_pred CCHHHHhhhCCCccCHHHHHHHHHHHHHH
Q 048564 41 VSAQLSKFLGANEASRSDAVKKIWQYIRQ 69 (114)
Q Consensus 41 lSp~La~flG~~~~sR~eV~~~lW~YIK~ 69 (114)
--++|++-||.+.. .||++|+.
T Consensus 21 SGe~La~~LgiSRt-------aVwK~Iq~ 42 (79)
T COG1654 21 SGEKLAEELGISRT-------AVWKHIQQ 42 (79)
T ss_pred cHHHHHHHHCccHH-------HHHHHHHH
Confidence 34678888887655 78999875
No 37
>KOG0747 consensus Putative NAD+-dependent epimerases [Carbohydrate transport and metabolism]
Probab=36.56 E-value=93 Score=26.09 Aligned_cols=56 Identities=16% Similarity=0.188 Sum_probs=41.0
Q ss_pred CCccCHHHHHHHHHHHHHHhCCC-----------CC--CCCCccccchhHHhhhCCCCcccHH-HHHHHHh
Q 048564 51 ANEASRSDAVKKIWQYIRQHDLQ-----------NP--ANKREIRCDDKLKTIFNGKDSVGFL-EIAKLLS 107 (114)
Q Consensus 51 ~~~~sR~eV~~~lW~YIK~nnLq-----------Dp--~dKr~I~cDekLk~Lfg~~~~v~~~-el~~lL~ 107 (114)
..++++-|+.+.+.++|...... |. +|-|.-+|+|+++ =+|-+....+. .|.+.+.
T Consensus 251 d~e~~~~~l~k~i~eli~~~~~~~~~~p~~~~v~dRp~nd~Ry~~~~eKik-~LGw~~~~p~~eGLrktie 320 (331)
T KOG0747|consen 251 DDEMRVIDLAKDICELFEKRLPNIDTEPFIFFVEDRPYNDLRYFLDDEKIK-KLGWRPTTPWEEGLRKTIE 320 (331)
T ss_pred cchhhHHHHHHHHHHHHHHhccCCCCCCcceecCCCCcccccccccHHHHH-hcCCcccCcHHHHHHHHHH
Confidence 37999999999999999985442 11 3567899999999 66656666663 4555443
No 38
>cd09286 NMNAT_Eukarya Nicotinamide/nicotinate mononucleotide adenylyltransferase, Eukaryotic. Nicotinamide/nicotinate mononucleotide (NMN/ NaMN)adenylyltransferase (NMNAT). NMNAT represents the primary bacterial and eukaryotic adenylyltransferases for nicotinamide-nucleotide and for the deamido form, nicotinate nucleotide. It is an indispensable enzyme in the biosynthesis of NAD(+) and NADP(+). Nicotinamide-nucleotide adenylyltransferase synthesizes NAD via the salvage pathway, while nicotinate-nucleotide adenylyltransferase synthesizes the immediate precursor of NAD via the de novo pathway. Human NMNAT displays unique dual substrate specificity toward both NMN and NaMN, and can participate in both de novo and salvage pathways of NAD synthesis. This subfamily consists strictly of eukaryotic members and includes secondary structural elements not found in all NMNATs.
Probab=35.53 E-value=28 Score=26.86 Aligned_cols=31 Identities=19% Similarity=0.279 Sum_probs=19.2
Q ss_pred HHHHhhhCCCccCHHHHHHHHHHHHHHhCCC
Q 048564 43 AQLSKFLGANEASRSDAVKKIWQYIRQHDLQ 73 (114)
Q Consensus 43 p~La~flG~~~~sR~eV~~~lW~YIK~nnLq 73 (114)
+++.+-+.....-+..|-..|.+||++|+|.
T Consensus 195 T~IR~~l~~g~~~~~llp~~V~~YI~~~~LY 225 (225)
T cd09286 195 TKVRRALRRGMSVKYLLPDPVIEYIEQHQLY 225 (225)
T ss_pred HHHHHHHHcCCCchhcCCHHHHHHHHHcCCC
Confidence 3444444433333455666789999999984
No 39
>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=35.42 E-value=24 Score=18.56 Aligned_cols=17 Identities=12% Similarity=0.427 Sum_probs=13.3
Q ss_pred HHHHHHHHHHHHhCCCC
Q 048564 58 DAVKKIWQYIRQHDLQN 74 (114)
Q Consensus 58 eV~~~lW~YIK~nnLqD 74 (114)
++-..||+|..++|..+
T Consensus 2 ~Ln~lI~~YL~~~Gy~~ 18 (27)
T PF08513_consen 2 ELNQLIYDYLVENGYKE 18 (27)
T ss_dssp HHHHHHHHHHHHCT-HH
T ss_pred HHHHHHHHHHHHCCcHH
Confidence 56788999999999754
No 40
>cd02165 NMNAT Nicotinamide/nicotinate mononucleotide adenylyltransferase. Nicotinamide/nicotinate mononucleotide (NMN/ NaMN)adenylyltransferase (NMNAT). NMNAT represents the primary bacterial and eukaryotic adenylyltransferases for nicotinamide-nucleotide and for the deamido form, nicotinate nucleotide. It is an indispensable enzyme in the biosynthesis of NAD(+) and NADP(+). Nicotinamide-nucleotide adenylyltransferase synthesizes NAD via the salvage pathway, while nicotinate-nucleotide adenylyltransferase synthesizes the immediate precursor of NAD via the de novo pathway. Human NMNAT displays unique dual substrate specificity toward both NMN and NaMN, and can participate in both de novo and salvage pathways of NAD synthesis.
Probab=35.41 E-value=30 Score=25.48 Aligned_cols=31 Identities=19% Similarity=0.283 Sum_probs=18.5
Q ss_pred HHHHhhhCCCccCHHHHHHHHHHHHHHhCCC
Q 048564 43 AQLSKFLGANEASRSDAVKKIWQYIRQHDLQ 73 (114)
Q Consensus 43 p~La~flG~~~~sR~eV~~~lW~YIK~nnLq 73 (114)
.++.+.+....--..-|-..+.+||++|+|.
T Consensus 162 T~IR~~~~~g~~~~~lvp~~V~~yI~~~~lY 192 (192)
T cd02165 162 TEIRERLKNGKSIRYLLPPAVADYIKEHGLY 192 (192)
T ss_pred HHHHHHHHcCCChhHhCCHHHHHHHHHccCC
Confidence 3444444332223344556789999999984
No 41
>PF12728 HTH_17: Helix-turn-helix domain
Probab=35.09 E-value=36 Score=19.53 Aligned_cols=26 Identities=19% Similarity=0.487 Sum_probs=19.7
Q ss_pred HHHHhhhCCCccCHHHHHHHHHHHHHHhCCCCC
Q 048564 43 AQLSKFLGANEASRSDAVKKIWQYIRQHDLQNP 75 (114)
Q Consensus 43 p~La~flG~~~~sR~eV~~~lW~YIK~nnLqDp 75 (114)
++.+++||++.- .|+.+|+...+.-.
T Consensus 5 ~e~a~~l~is~~-------tv~~~~~~g~i~~~ 30 (51)
T PF12728_consen 5 KEAAELLGISRS-------TVYRWIRQGKIPPF 30 (51)
T ss_pred HHHHHHHCcCHH-------HHHHHHHcCCCCeE
Confidence 588899997654 68888988876544
No 42
>PF03656 Pam16: Pam16; InterPro: IPR005341 The Pam16 protein is the fifth essential subunit of the pre-sequence translocase-associated protein import motor (PAM) []. In Saccharomyces cerevisiae (Baker's yeast), Pam16 is required for preprotein translocation into the matrix, but not for protein insertion into the inner membrane [].; PDB: 2GUZ_J.
Probab=34.96 E-value=49 Score=23.85 Aligned_cols=29 Identities=21% Similarity=0.346 Sum_probs=21.6
Q ss_pred HHHHhhhCCCc-cCHHHHHHHHHHHHHHhC
Q 048564 43 AQLSKFLGANE-ASRSDAVKKIWQYIRQHD 71 (114)
Q Consensus 43 p~La~flG~~~-~sR~eV~~~lW~YIK~nn 71 (114)
.|-..+|+.+. .++.+|.+..+.+.+.|.
T Consensus 58 ~EA~~ILnv~~~~~~eeI~k~y~~Lf~~Nd 87 (127)
T PF03656_consen 58 DEARQILNVKEELSREEIQKRYKHLFKAND 87 (127)
T ss_dssp HHHHHHHT--G--SHHHHHHHHHHHHHHT-
T ss_pred HHHHHHcCCCCccCHHHHHHHHHHHHhccC
Confidence 36667899866 999999999999999885
No 43
>TIGR02057 PAPS_reductase phosphoadenosine phosphosulfate reductase, thioredoxin dependent. Requiring thioredoxin as an electron donor, phosphoadenosine phosphosulfate reductase catalyzes the reduction of 3'-phosphoadenylylsulfate (PAPS) to sulfite and phospho-adenosine-phosphate (PAP). Found in enterobacteria, cyanobacteria, and yeast, PAPS reductase is related to a group of plant (TIGR00424) and bacterial (TIGR02055) enzymes preferring 5'-adenylylsulfate (APS) over PAPS as a substrate for reduction to sulfite.
Probab=34.81 E-value=23 Score=27.37 Aligned_cols=12 Identities=25% Similarity=0.869 Sum_probs=10.5
Q ss_pred HHHHHHHHhCCC
Q 048564 62 KIWQYIRQHDLQ 73 (114)
Q Consensus 62 ~lW~YIK~nnLq 73 (114)
-||.||++|||-
T Consensus 172 dVw~Yi~~~~lP 183 (226)
T TIGR02057 172 QVYQYLDAHNVP 183 (226)
T ss_pred HHHHHHHHcCCC
Confidence 579999999975
No 44
>PF13867 SAP30_Sin3_bdg: Sin3 binding region of histone deacetylase complex subunit SAP30; PDB: 2LD7_A.
Probab=34.73 E-value=65 Score=19.50 Aligned_cols=14 Identities=14% Similarity=0.354 Sum_probs=9.3
Q ss_pred HHHHHHHHHhCCCC
Q 048564 61 KKIWQYIRQHDLQN 74 (114)
Q Consensus 61 ~~lW~YIK~nnLqD 74 (114)
..||.|-+.+||..
T Consensus 4 ~tLrrY~~~~~l~~ 17 (53)
T PF13867_consen 4 PTLRRYKKHYKLPE 17 (53)
T ss_dssp HHHHHHHHHTT---
T ss_pred HHHHHHHHHhCCCC
Confidence 46899999998874
No 45
>PF13333 rve_2: Integrase core domain
Probab=34.65 E-value=42 Score=19.81 Aligned_cols=21 Identities=19% Similarity=0.222 Sum_probs=17.9
Q ss_pred CCccCHHHHHHHHHHHHHHhC
Q 048564 51 ANEASRSDAVKKIWQYIRQHD 71 (114)
Q Consensus 51 ~~~~sR~eV~~~lW~YIK~nn 71 (114)
..-.|+.++...|++||.-.|
T Consensus 15 ~~~~t~eel~~~I~~YI~~yN 35 (52)
T PF13333_consen 15 QKFKTREELKQAIDEYIDYYN 35 (52)
T ss_pred cccchHHHHHHHHHHHHHHhc
Confidence 356799999999999999864
No 46
>PF07308 DUF1456: Protein of unknown function (DUF1456); InterPro: IPR009921 This domain occurs in several hypothetical bacterial proteins of around 150 residues in length. The function of this domain is unknown.
Probab=34.19 E-value=73 Score=20.46 Aligned_cols=40 Identities=18% Similarity=0.291 Sum_probs=28.7
Q ss_pred HHHHhhh--CCCccCHHHHHHHHHHHHHHhCCCCCCCCCccccchhHHhhh
Q 048564 43 AQLSKFL--GANEASRSDAVKKIWQYIRQHDLQNPANKREIRCDDKLKTIF 91 (114)
Q Consensus 43 p~La~fl--G~~~~sR~eV~~~lW~YIK~nnLqDp~dKr~I~cDekLk~Lf 91 (114)
+++.+++ |.-++|.+||...+-. |+++.+..|++.+-.-|
T Consensus 17 ~~m~~if~l~~~~vs~~el~a~lrk---------e~~~~y~~c~D~~L~~F 58 (68)
T PF07308_consen 17 DDMIEIFALAGFEVSKAELSAWLRK---------EDEKGYKECSDQLLRNF 58 (68)
T ss_pred HHHHHHHHHcCCccCHHHHHHHHCC---------CCCccccccChHHHHHH
Confidence 3566665 5688999998876653 67788889987755544
No 47
>PRK08887 nicotinic acid mononucleotide adenylyltransferase; Provisional
Probab=34.13 E-value=37 Score=25.06 Aligned_cols=18 Identities=11% Similarity=0.235 Sum_probs=13.7
Q ss_pred HHHHHHHHHHHHHhCCCC
Q 048564 57 SDAVKKIWQYIRQHDLQN 74 (114)
Q Consensus 57 ~eV~~~lW~YIK~nnLqD 74 (114)
.-|-..|.+||++|||.-
T Consensus 154 ~lvp~~V~~yI~~~~LY~ 171 (174)
T PRK08887 154 HLTTPGVARLLKEHQLYT 171 (174)
T ss_pred HhCCHHHHHHHHHccccC
Confidence 445556899999999974
No 48
>PF13758 Prefoldin_3: Prefoldin subunit
Probab=32.54 E-value=96 Score=21.65 Aligned_cols=37 Identities=19% Similarity=0.483 Sum_probs=26.7
Q ss_pred CCCCCccCCHHHHhhhCCCc---cCHHHHHHHH---HHHHHHh
Q 048564 34 GIGKPVPVSAQLSKFLGANE---ASRSDAVKKI---WQYIRQH 70 (114)
Q Consensus 34 g~~~~~~lSp~La~flG~~~---~sR~eV~~~l---W~YIK~n 70 (114)
+|.....--.++.++||... -|+.+|+..| .+||++|
T Consensus 41 ~f~g~lv~~kEi~~ilG~~~~i~Rt~~Qvv~~l~RRiDYV~~N 83 (99)
T PF13758_consen 41 DFGGSLVTEKEIKEILGEGQGITRTREQVVDVLSRRIDYVQQN 83 (99)
T ss_pred hcCcccccHHHHHHHhCCCCCCCcCHHHHHHHHHHHHHHHHHH
Confidence 45555555678999999754 4788887766 6888876
No 49
>COG5577 Spore coat protein [Cell envelope biogenesis, outer membrane]
Probab=32.39 E-value=40 Score=24.88 Aligned_cols=38 Identities=18% Similarity=0.259 Sum_probs=29.5
Q ss_pred cCCHHHHhhhCCCccCHHHHHHHHHHHHHHhCCCCCCC
Q 048564 40 PVSAQLSKFLGANEASRSDAVKKIWQYIRQHDLQNPAN 77 (114)
Q Consensus 40 ~lSp~La~flG~~~~sR~eV~~~lW~YIK~nnLqDp~d 77 (114)
.-||+|..+|...-..--+--..||+|...|+-.-|.+
T Consensus 84 ~~tP~lR~vL~~~l~~~i~~~~~v~~ym~~~g~Y~py~ 121 (145)
T COG5577 84 TATPELRAVLKDQLNQAIEMHKEVSEYMVQKGYYPPYN 121 (145)
T ss_pred cCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCcCCCC
Confidence 44688888887655445556789999999999998876
No 50
>PF12487 DUF3703: Protein of unknown function (DUF3703) ; InterPro: IPR022172 This family of proteins is found in bacteria. Proteins in this family are typically between 113 and 135 amino acids in length.
Probab=31.54 E-value=96 Score=22.02 Aligned_cols=40 Identities=23% Similarity=0.273 Sum_probs=24.9
Q ss_pred HHHHHHHHhhhhhhhhccccCCCCCCCCCccCCHHHHhhh
Q 048564 10 RTMMAAAAKSGAEATAAAGKKAKGGIGKPVPVSAQLSKFL 49 (114)
Q Consensus 10 ~~~~~~~~~~~~~~~~~~~~k~~~g~~~~~~lSp~La~fl 49 (114)
|++++-..+..++-..---...|.+..+++.++++|+++|
T Consensus 72 Rl~~a~~gs~~G~~P~GNtG~anV~~f~pmpip~dl~~~l 111 (112)
T PF12487_consen 72 RLIVAAPGSLVGRVPVGNTGGANVSPFKPMPIPEDLQALL 111 (112)
T ss_pred HHHHHHHHHHhccCCCCCCCCCCCCCCCCCCCCHHHHHHh
Confidence 4444444444444333334455667889999999999876
No 51
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=31.07 E-value=51 Score=24.35 Aligned_cols=50 Identities=12% Similarity=0.195 Sum_probs=34.0
Q ss_pred ccCC-HHHHhhhCCCccCHHHHHHHHHHHHHHhCCCCCCCCCccccc-hhHHhhhC
Q 048564 39 VPVS-AQLSKFLGANEASRSDAVKKIWQYIRQHDLQNPANKREIRCD-DKLKTIFN 92 (114)
Q Consensus 39 ~~lS-p~La~flG~~~~sR~eV~~~lW~YIK~nnLqDp~dKr~I~cD-ekLk~Lfg 92 (114)
..+| .+||+.+|++..|=+.++ .=.++.|+..-.++++++.| +.|+++.+
T Consensus 183 ~~lt~~~iA~~lG~sr~tvsR~l----~~l~~~g~I~~~~~~i~i~d~~~L~~~~~ 234 (235)
T PRK11161 183 LTMTRGDIGNYLGLTVETISRLL----GRFQKSGMLAVKGKYITIENNDALAQLAG 234 (235)
T ss_pred ccccHHHHHHHhCCcHHHHHHHH----HHHHHCCCEEecCCEEEEcCHHHHHHHhc
Confidence 3454 699999997654433333 34577888888888888887 66666654
No 52
>PF14838 INTS5_C: Integrator complex subunit 5 C-terminus
Probab=30.85 E-value=27 Score=31.97 Aligned_cols=43 Identities=19% Similarity=0.312 Sum_probs=25.6
Q ss_pred CCHHHHhhhCC-CccCHHHHH----HHHHHHHHHhCCCCCCCCCccccchh
Q 048564 41 VSAQLSKFLGA-NEASRSDAV----KKIWQYIRQHDLQNPANKREIRCDDK 86 (114)
Q Consensus 41 lSp~La~flG~-~~~sR~eV~----~~lW~YIK~nnLqDp~dKr~I~cDek 86 (114)
|+|.|..+... +.+|-.||. .+||+|+|+|. |..-.++.||+.
T Consensus 618 LPppL~~~~el~~~ltp~Ei~~lL~~cIW~y~kdh~---Psp~~f~~~~~~ 665 (696)
T PF14838_consen 618 LPPPLSYIHELFPYLTPHEIYLLLLSCIWNYMKDHV---PSPALFVFNDET 665 (696)
T ss_pred CCchHHHHHHHHHhcCHHHHHHHHHHHHHHHHhhCC---CCHHHHhcCccc
Confidence 34444444432 556666653 34999999887 333346667765
No 53
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=30.75 E-value=44 Score=21.44 Aligned_cols=37 Identities=19% Similarity=0.347 Sum_probs=26.1
Q ss_pred HHHHhhhCCCccCHHHHHHHHHHHHHHhCCCCCCCCC
Q 048564 43 AQLSKFLGANEASRSDAVKKIWQYIRQHDLQNPANKR 79 (114)
Q Consensus 43 p~La~flG~~~~sR~eV~~~lW~YIK~nnLqDp~dKr 79 (114)
.+|++.++.+..+-+.+++.|++-==-....||.|+|
T Consensus 40 ~~la~~l~i~~~~vt~~l~~Le~~glv~r~~~~~DrR 76 (126)
T COG1846 40 KELAERLGLDRSTVTRLLKRLEDKGLIERLRDPEDRR 76 (126)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHCCCeeecCCccccc
Confidence 8899999988888888888887522223345777765
No 54
>TIGR02055 APS_reductase thioredoxin-dependent adenylylsulfate APS reductase. This model describes recently identified adenosine 5'-phosphosulfate (APS) reductase activity found in sulfate-assimilatory prokaryotes, thus separating it from the traditionally described phosphoadenosine 5'-phosphosulfate (PAPS) reductases found in bacteria and fungi. Homologous to PAPS reductase in enterobacteria, cyanobacteria, and yeast, APS reductase here clusters with, and demonstrates greater homology to plant APS reductase. Additionally, the presence of two conserved C-terminal motifs (CCXXRKXXPL & SXGCXXCT) distinguishes APS substrate specificity and serves as a FeS cluster.
Probab=30.52 E-value=30 Score=25.83 Aligned_cols=12 Identities=33% Similarity=1.091 Sum_probs=10.7
Q ss_pred HHHHHHHHhCCC
Q 048564 62 KIWQYIRQHDLQ 73 (114)
Q Consensus 62 ~lW~YIK~nnLq 73 (114)
-||.||++|||.
T Consensus 136 dVw~Yi~~~~lp 147 (191)
T TIGR02055 136 DVWEYIADNELP 147 (191)
T ss_pred HHHHHHHHcCCC
Confidence 689999999984
No 55
>PRK12563 sulfate adenylyltransferase subunit 2; Provisional
Probab=30.21 E-value=29 Score=28.59 Aligned_cols=24 Identities=29% Similarity=0.544 Sum_probs=17.5
Q ss_pred HHHHHHHHhCCCCC------------CCCCccccch
Q 048564 62 KIWQYIRQHDLQNP------------ANKREIRCDD 85 (114)
Q Consensus 62 ~lW~YIK~nnLqDp------------~dKr~I~cDe 85 (114)
-||.||+.|||--. .|+..|.||+
T Consensus 203 DVW~YI~~~~IP~~pLY~~~~r~~~~~~g~~~~~~~ 238 (312)
T PRK12563 203 DVWQYIAREKIPLVPLYFAKRRPVVERDGLLIMVDD 238 (312)
T ss_pred HHHHHHHHcCCCCCcchhcCCCceEEECCeEEeccc
Confidence 68999999998632 1555677776
No 56
>PF07037 DUF1323: Putative transcription regulator (DUF1323); InterPro: IPR010749 This family consists of several hypothetical Enterobacterial proteins of around 120 residues in length. The function of this family is unknown.
Probab=30.03 E-value=62 Score=23.47 Aligned_cols=44 Identities=16% Similarity=0.399 Sum_probs=32.8
Q ss_pred CHHHHhhhCCCccCHHHHHHHHHHHHHHhCCCCCC-------CCCccccchhHHhhhC
Q 048564 42 SAQLSKFLGANEASRSDAVKKIWQYIRQHDLQNPA-------NKREIRCDDKLKTIFN 92 (114)
Q Consensus 42 Sp~La~flG~~~~sR~eV~~~lW~YIK~nnLqDp~-------dKr~I~cDekLk~Lfg 92 (114)
+.|||+.+|.... .|-.+|++.|-.... .-|+|+-|+..++.+.
T Consensus 3 ~eELA~~tG~srQ-------TINrWvRkegW~T~p~pGVkGGrARLIhId~~V~efi~ 53 (122)
T PF07037_consen 3 PEELAELTGYSRQ-------TINRWVRKEGWKTEPKPGVKGGRARLIHIDEQVREFIR 53 (122)
T ss_pred HHHHHHHhCccHH-------HHHHHHHhcCceeccCCccccccceeeeecHHHHHHHH
Confidence 3689999997654 566778887766432 2468999999998776
No 57
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=29.61 E-value=59 Score=24.40 Aligned_cols=48 Identities=17% Similarity=0.324 Sum_probs=32.1
Q ss_pred ccCC-HHHHhhhCCCccCHHHHHHHHHHHHHHhCCCCCCC-CCccccc-hhHHhh
Q 048564 39 VPVS-AQLSKFLGANEASRSDAVKKIWQYIRQHDLQNPAN-KREIRCD-DKLKTI 90 (114)
Q Consensus 39 ~~lS-p~La~flG~~~~sR~eV~~~lW~YIK~nnLqDp~d-Kr~I~cD-ekLk~L 90 (114)
..++ .+||+.+|++..|=+.+ ..-.++.|+.+-.. ++++++| ++|.++
T Consensus 178 i~lt~~~IA~~lGisretlsR~----L~~L~~~GlI~~~~~~~i~I~D~~~L~~l 228 (230)
T PRK09391 178 LPMSRRDIADYLGLTIETVSRA----LSQLQDRGLIGLSGARQIELRNRQALRNL 228 (230)
T ss_pred ecCCHHHHHHHHCCCHHHHHHH----HHHHHHCCcEEecCCceEEEcCHHHHHHh
Confidence 3344 69999999865544433 44567888887654 6788888 466554
No 58
>PRK13727 conjugal transfer pilin chaperone TraQ; Provisional
Probab=28.17 E-value=52 Score=22.08 Aligned_cols=19 Identities=42% Similarity=0.630 Sum_probs=14.6
Q ss_pred hhhhHHHHHHHHHhhhhhh
Q 048564 5 LFGGYRTMMAAAAKSGAEA 23 (114)
Q Consensus 5 ~~~~~~~~~~~~~~~~~~~ 23 (114)
+++|||+|++-.+-.+-+.
T Consensus 52 l~GgYRilda~iarv~~ee 70 (80)
T PRK13727 52 LFGAYRVLDAWIARVSREE 70 (80)
T ss_pred hhhHHHHHHHHHHHHHHHH
Confidence 5799999999886655444
No 59
>PF12368 DUF3650: Protein of unknown function (DUF3650) ; InterPro: IPR022111 This domain family is found in bacteria, and is approximately 30 amino acids in length. The family is found in association with PF00581 from PFAM. There is a single completely conserved residue N that may be functionally important.
Probab=27.16 E-value=32 Score=18.83 Aligned_cols=10 Identities=30% Similarity=0.933 Sum_probs=8.1
Q ss_pred HHHHHhCCCC
Q 048564 65 QYIRQHDLQN 74 (114)
Q Consensus 65 ~YIK~nnLqD 74 (114)
-||++|||-+
T Consensus 9 rYV~eh~ls~ 18 (28)
T PF12368_consen 9 RYVKEHGLSE 18 (28)
T ss_pred hhHHhcCCCH
Confidence 4999999865
No 60
>PRK00982 acpP acyl carrier protein; Provisional
Probab=26.31 E-value=78 Score=19.63 Aligned_cols=50 Identities=18% Similarity=0.252 Sum_probs=35.8
Q ss_pred HHHHHHHHHHHHHhCCCCCCCCCccccchhHHhhhCCCCcccHHHHHHHHhccc
Q 048564 57 SDAVKKIWQYIRQHDLQNPANKREIRCDDKLKTIFNGKDSVGFLEIAKLLSQHF 110 (114)
Q Consensus 57 ~eV~~~lW~YIK~nnLqDp~dKr~I~cDekLk~Lfg~~~~v~~~el~~lL~~Hl 110 (114)
.++...|+++|.+.= .-+ ...|..|..|..-+| -|++.+-+|...|...|
T Consensus 2 ~~i~~~l~~~l~~~l-~~~--~~~i~~d~~l~~dlg-lDSl~~~~li~~le~~f 51 (78)
T PRK00982 2 SEIFEKVKKIIVEQL-GVD--EEEVTPEASFVDDLG-ADSLDTVELVMALEEEF 51 (78)
T ss_pred hHHHHHHHHHHHHHH-CCC--HHHCCCCcchHhhcC-CCHHHHHHHHHHHHHHH
Confidence 457788888887643 222 335888999977776 68888888887777665
No 61
>PF05643 DUF799: Putative bacterial lipoprotein (DUF799); InterPro: IPR008517 This family consists of several bacterial proteins of unknown function. Some of the family members are described as putative lipoproteins.
Probab=25.42 E-value=66 Score=25.32 Aligned_cols=35 Identities=23% Similarity=0.425 Sum_probs=25.9
Q ss_pred HHHHHHHhCCCCCCCCCccccchhHHhhhCCCCcccH
Q 048564 63 IWQYIRQHDLQNPANKREIRCDDKLKTIFNGKDSVGF 99 (114)
Q Consensus 63 lW~YIK~nnLqDp~dKr~I~cDekLk~Lfg~~~~v~~ 99 (114)
+-+-+|+|||.|+++=..+- -.+|+++|| .|-+-+
T Consensus 77 vde~fkqnGlt~~~~i~~v~-~~kL~eiFG-ADAvLY 111 (215)
T PF05643_consen 77 VDETFKQNGLTDAEDIHAVP-PAKLREIFG-ADAVLY 111 (215)
T ss_pred HHHHHHHcCCCCHHHhccCC-HHHHHHHhC-CCEEEE
Confidence 34457899999999864444 689999998 665543
No 62
>KOG4068 consensus Uncharacterized conserved protein [Function unknown]
Probab=25.37 E-value=80 Score=24.14 Aligned_cols=23 Identities=22% Similarity=0.524 Sum_probs=21.1
Q ss_pred HHHHHHHHHHHHHhCCCCCCCCC
Q 048564 57 SDAVKKIWQYIRQHDLQNPANKR 79 (114)
Q Consensus 57 ~eV~~~lW~YIK~nnLqDp~dKr 79 (114)
.+++..||+|....|+..|.||+
T Consensus 68 ~~~i~~Il~~l~k~g~~e~~Dk~ 90 (174)
T KOG4068|consen 68 QEFIDEILEELEKKGLAEPTDKR 90 (174)
T ss_pred HHHHHHHHHHHHHccCCcccccC
Confidence 57888999999999999999987
No 63
>smart00413 ETS erythroblast transformation specific domain. variation of the helix-turn-helix motif
Probab=25.35 E-value=1.3e+02 Score=20.46 Aligned_cols=48 Identities=21% Similarity=0.540 Sum_probs=30.1
Q ss_pred HHHHHHHHhCCCCCCCCCccccch------------hHHhhhCC---CCcccHHHHHHHHhccc
Q 048564 62 KIWQYIRQHDLQNPANKREIRCDD------------KLKTIFNG---KDSVGFLEIAKLLSQHF 110 (114)
Q Consensus 62 ~lW~YIK~nnLqDp~dKr~I~cDe------------kLk~Lfg~---~~~v~~~el~~lL~~Hl 110 (114)
.||+|+.+- |.||+++..|..-+ ++..+.|. ++.+++..|+..|..+.
T Consensus 3 ~Lw~FL~~L-L~d~~~~~~I~W~~k~~g~Fkl~~~~~vA~lWG~~Knk~~M~YeklSRaLRyyy 65 (87)
T smart00413 3 QLWQFLLDL-LLDPENGDIIRWTDRDGGEFKLVDPEEVARLWGQRKNKPNMNYEKLSRALRYYY 65 (87)
T ss_pred cHHHHHHHH-HcCccCCCeEEeeCCCCCEEEecCHHHHHHHHhhhcCCCCCCHHHHHHHHHHHH
Confidence 578888763 56777766555433 45566652 25577777777776554
No 64
>PF00010 HLH: Helix-loop-helix DNA-binding domain only nuclear translocator protein (Arnt).; InterPro: IPR011598 The helix-loop-helix (HLH) DNA-binding domain consists of a closed bundle of four helices in a left-handed twist with two crossover connections. The HLH domain directs dimerisation, and is juxtaposed to basic regions to create a DNA interaction interface surface that recognises specific DNA sequences. Basic region/HLH (bHLH) proteins regulate diverse biological pathways []. bHLH proteins include MyoD [], SREBPs (sterol regulatory element binding proteins) [], and yeast Pho4 (phosphatase system) []. In certain proteins the bHLH domain contains a leucine-zipper motif. The bHLH/leucine zipper (bHLHZip) domain specifies dimerisation within a network of proteins and determines sequence-specific DNA binding []. bHLHZip domains occur in the transcription factors Myc, Mad, Max and Usf [, ]. This entry is bHLHZip, which covers the bHLH domain and the leucine zipper motif, when present.; PDB: 1NLW_A 1NKP_D 1A93_A 2A93_A 1AM9_C 3U5V_A 1A0A_B 2QL2_C 1UKL_C 1AN4_B ....
Probab=25.25 E-value=1e+02 Score=18.04 Aligned_cols=18 Identities=28% Similarity=0.519 Sum_probs=16.3
Q ss_pred CccCHHHHHHHHHHHHHH
Q 048564 52 NEASRSDAVKKIWQYIRQ 69 (114)
Q Consensus 52 ~~~sR~eV~~~lW~YIK~ 69 (114)
...|+.+|+....+||+.
T Consensus 36 ~k~~K~~iL~~ai~yI~~ 53 (55)
T PF00010_consen 36 RKLSKASILQKAIDYIKQ 53 (55)
T ss_dssp SSSSHHHHHHHHHHHHHH
T ss_pred ccCCHHHHHHHHHHHHHH
Confidence 569999999999999985
No 65
>PRK05253 sulfate adenylyltransferase subunit 2; Provisional
Probab=25.12 E-value=41 Score=27.33 Aligned_cols=12 Identities=42% Similarity=1.118 Sum_probs=10.7
Q ss_pred HHHHHHHHhCCC
Q 048564 62 KIWQYIRQHDLQ 73 (114)
Q Consensus 62 ~lW~YIK~nnLq 73 (114)
-||+||+.+||.
T Consensus 193 DIw~Yi~~~~IP 204 (301)
T PRK05253 193 DIWQYIERENIP 204 (301)
T ss_pred HHHHHHHHcCCC
Confidence 689999999876
No 66
>PF07319 DnaI_N: Primosomal protein DnaI N-terminus; InterPro: IPR009928 This entry represents the N terminus (approximately 120 residues) of bacterial primosomal DnaI proteins, although one family member appears to be of viral origin. DnaI is one of the components of the Bacillus subtilis replication restart primosome, and is required for the DnaB75-dependent loading of the DnaC helicase [].; PDB: 2K7R_A.
Probab=24.57 E-value=99 Score=20.61 Aligned_cols=34 Identities=15% Similarity=0.353 Sum_probs=23.0
Q ss_pred CHHHHhhhCCC--ccCHHHHH---HHHHHHHHHhCCCCC
Q 048564 42 SAQLSKFLGAN--EASRSDAV---KKIWQYIRQHDLQNP 75 (114)
Q Consensus 42 Sp~La~flG~~--~~sR~eV~---~~lW~YIK~nnLqDp 75 (114)
.|+..+|+... ++|+..|- ..|.+|+.+++-.+-
T Consensus 31 dp~V~~Fl~~h~~eLt~~~i~rsl~kLyEy~~e~~~~~~ 69 (94)
T PF07319_consen 31 DPEVQAFLQEHQPELTQEMIERSLSKLYEYVSERKKCQN 69 (94)
T ss_dssp -HHHHHHHHHSTTT--HHHHHHTHHHHHHHHHS-SS-TT
T ss_pred CHHHHHHHHHhHHhcCHHHHHHHHHHHHHHHHHHHHHhh
Confidence 57888898765 88988885 578999999875543
No 67
>TIGR00434 cysH phosophoadenylyl-sulfate reductase (thioredoxin). This enzyme, involved in the assimilation of inorganic sulfate, is designated cysH in Bacteria and MET16 in Saccharomyces cerevisiae. Synonyms include phosphoadenosine phosphosulfate reductase, PAPS reductase, and PAPS reductase, thioredoxin-dependent. In a reaction requiring reduced thioredoxin and NADPH, it converts 3(prime)-phosphoadenylylsulfate (PAPS) to sulfite and adenosine 3(prime),5(prime) diphosphate (PAP). A related family of plant enzymes, scoring below the trusted cutoff, differs in having a thioredoxin-like C-terminal domain, not requiring thioredoxin, and in having a preference for 5(prime)-adenylylsulfate (APS) over PAPS.
Probab=24.47 E-value=44 Score=24.92 Aligned_cols=12 Identities=42% Similarity=0.935 Sum_probs=10.5
Q ss_pred HHHHHHHHhCCC
Q 048564 62 KIWQYIRQHDLQ 73 (114)
Q Consensus 62 ~lW~YIK~nnLq 73 (114)
-||+||.++||.
T Consensus 157 dVw~Yi~~~~lp 168 (212)
T TIGR00434 157 DVYQYIDAHNLP 168 (212)
T ss_pred HHHHHHHHcCCC
Confidence 469999999986
No 68
>PF01507 PAPS_reduct: Phosphoadenosine phosphosulfate reductase family; InterPro: IPR002500 This domain is found in phosphoadenosine phosphosulphate (PAPS) reductase enzymes or PAPS sulphotransferase. PAPS reductase is part of the adenine nucleotide alpha hydrolases superfamily also including N type ATP PPases and ATP sulphurylases []. The enzyme uses thioredoxin as an electron donor for the reduction of PAPS to phospho-adenosine-phosphate (PAP) [, ]. It is also found in NodP nodulation protein P from Rhizobium meliloti (Sinorhizobium meliloti) which has ATP sulphurylase activity (sulphate adenylate transferase) [].; GO: 0003824 catalytic activity, 0008152 metabolic process; PDB: 2GOY_C 3G5A_C 3G6K_D 3G59_A 3FWK_A 2WSI_A 2OQ2_B 1SUR_A 2O8V_A 1ZUN_A.
Probab=23.81 E-value=47 Score=23.11 Aligned_cols=12 Identities=33% Similarity=1.057 Sum_probs=9.1
Q ss_pred HHHHHHHHhCCC
Q 048564 62 KIWQYIRQHDLQ 73 (114)
Q Consensus 62 ~lW~YIK~nnLq 73 (114)
-||+||+.+||.
T Consensus 143 dV~~yi~~~~l~ 154 (174)
T PF01507_consen 143 DVWDYIKANGLP 154 (174)
T ss_dssp HHHHHHHHHT--
T ss_pred HHHHHHHHhcCC
Confidence 579999999984
No 69
>PRK07152 nadD putative nicotinate-nucleotide adenylyltransferase; Validated
Probab=23.76 E-value=46 Score=27.02 Aligned_cols=16 Identities=25% Similarity=0.183 Sum_probs=12.9
Q ss_pred HHHHHHHHHHHhCCCC
Q 048564 59 AVKKIWQYIRQHDLQN 74 (114)
Q Consensus 59 V~~~lW~YIK~nnLqD 74 (114)
|-..|++||++|||..
T Consensus 170 vP~~V~~YI~~~~LY~ 185 (342)
T PRK07152 170 LDPKVNDYINENFLYL 185 (342)
T ss_pred CCHHHHHHHHHcCccc
Confidence 4445899999999983
No 70
>PLN02309 5'-adenylylsulfate reductase
Probab=23.49 E-value=45 Score=28.85 Aligned_cols=13 Identities=23% Similarity=0.963 Sum_probs=11.0
Q ss_pred HHHHHHHHHhCCC
Q 048564 61 KKIWQYIRQHDLQ 73 (114)
Q Consensus 61 ~~lW~YIK~nnLq 73 (114)
.-||.||++|||-
T Consensus 261 ~dVw~Yi~~~~lP 273 (457)
T PLN02309 261 NEVWNFLRTMDVP 273 (457)
T ss_pred HHHHHHHHHcCCC
Confidence 3689999999885
No 71
>COG4389 Site-specific recombinase [DNA replication, recombination, and repair]
Probab=23.37 E-value=61 Score=29.08 Aligned_cols=24 Identities=25% Similarity=0.542 Sum_probs=20.9
Q ss_pred CCCccCHHHHHHHHHHHHHHhCCC
Q 048564 50 GANEASRSDAVKKIWQYIRQHDLQ 73 (114)
Q Consensus 50 G~~~~sR~eV~~~lW~YIK~nnLq 73 (114)
+++-.|+.+|++++|.-||.+-|.
T Consensus 637 ~t~i~s~r~I~~~VW~~Ik~~PL~ 660 (677)
T COG4389 637 GTKIGSIRNIIKSVWNQIKSNPLI 660 (677)
T ss_pred cccchhHHHHHHHHHHHHhcCCcE
Confidence 568899999999999999987653
No 72
>TIGR02741 TraQ type-F conjugative transfer system pilin chaperone TraQ. This protein makes a specific interaction with the pilin (TraA) protein to aid its transfer through the inner membrane during the process of F-type conjugative pilus assembly.
Probab=22.35 E-value=79 Score=21.20 Aligned_cols=19 Identities=37% Similarity=0.571 Sum_probs=14.5
Q ss_pred hhhhHHHHHHHHHhhhhhh
Q 048564 5 LFGGYRTMMAAAAKSGAEA 23 (114)
Q Consensus 5 ~~~~~~~~~~~~~~~~~~~ 23 (114)
+++|||+|++-.+-.+-+.
T Consensus 52 l~G~YRiLdawiarv~~ee 70 (80)
T TIGR02741 52 LWGAYRVLDAWIARVSREE 70 (80)
T ss_pred HhhHHHHHHHHHHHHHHHH
Confidence 5799999999886655443
No 73
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=22.29 E-value=88 Score=23.27 Aligned_cols=46 Identities=11% Similarity=0.126 Sum_probs=32.0
Q ss_pred HHHHhhhCCCccCHHHHHHHHHHHHHHhCCCCCCCCCccccc-hhHHhhhC
Q 048564 43 AQLSKFLGANEASRSDAVKKIWQYIRQHDLQNPANKREIRCD-DKLKTIFN 92 (114)
Q Consensus 43 p~La~flG~~~~sR~eV~~~lW~YIK~nnLqDp~dKr~I~cD-ekLk~Lfg 92 (114)
.+||+.+|.+..|=+.+++. .+++|+.+...+++.++| +.|..+..
T Consensus 173 ~~lA~~lG~sretvsR~L~~----L~~~G~I~~~~~~i~I~d~~~L~~~~~ 219 (226)
T PRK10402 173 TQAAEYLGVSYRHLLYVLAQ----FIQDGYLKKSKRGYLIKNRKQLSGLAL 219 (226)
T ss_pred HHHHHHHCCcHHHHHHHHHH----HHHCCCEEeeCCEEEEeCHHHHHHHHH
Confidence 68999999765544444444 457788887778888888 56666553
No 74
>TIGR02039 CysD sulfate adenylyltransferase, small subunit. In Escherichia coli, ATP sulfurylase is a heterodimer composed of two subunits encoded by cysD and cysN, with APS kinase encoded by cysC. These genes are located in a unidirectionally transcribed gene cluster, and have been shown to be required for the synthesis of sulfur-containing amino acids. Homologous to this E.coli activation pathway are nodPQH gene products found among members of the Rhizobiaceae family. These gene products have been shown to exhibit ATP sulfurase and APS kinase activity, yet are involved in Nod factor sulfation, and sulfation of other macromolecules.
Probab=21.85 E-value=52 Score=26.81 Aligned_cols=13 Identities=31% Similarity=0.861 Sum_probs=11.1
Q ss_pred HHHHHHHHhCCCC
Q 048564 62 KIWQYIRQHDLQN 74 (114)
Q Consensus 62 ~lW~YIK~nnLqD 74 (114)
-||.||..+|+-=
T Consensus 185 DVW~YI~~~~IP~ 197 (294)
T TIGR02039 185 DIWRYIAAENIPI 197 (294)
T ss_pred HHHHHHHHcCCCC
Confidence 6899999999863
No 75
>COG1057 NadD Nicotinic acid mononucleotide adenylyltransferase [Coenzyme metabolism]
Probab=21.08 E-value=75 Score=24.32 Aligned_cols=31 Identities=10% Similarity=0.169 Sum_probs=21.6
Q ss_pred HHHHhhhCCCccCHHHHHHHHHHHHHHhCCC
Q 048564 43 AQLSKFLGANEASRSDAVKKIWQYIRQHDLQ 73 (114)
Q Consensus 43 p~La~flG~~~~sR~eV~~~lW~YIK~nnLq 73 (114)
++..+.+....-....+-..|.+||.+++|+
T Consensus 165 t~IR~~~~~~~~~~~llP~~V~~YI~~~~LY 195 (197)
T COG1057 165 TEIRERIRRGASVDYLLPDSVLSYIEERGLY 195 (197)
T ss_pred HHHHHHHhCCCCchhcCCHHHHHHHHHhccc
Confidence 3445555554555566677899999999986
No 76
>cd04382 RhoGAP_MgcRacGAP RhoGAP_MgcRacGAP: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain present in MgcRacGAP proteins. MgcRacGAP plays an important dual role in cytokinesis: i) it is part of centralspindlin-complex, together with the mitotic kinesin MKLP1, which is critical for the structure of the central spindle by promoting microtuble bundling. ii) after phosphorylation by aurora B MgcRacGAP becomes an effective regulator of RhoA and plays an important role in the assembly of the contractile ring and the initiation of cytokinesis. MgcRacGAP-like proteins contain a N-terminal C1-like domain, and a C-terminal RhoGAP domain. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway
Probab=20.96 E-value=95 Score=23.29 Aligned_cols=68 Identities=19% Similarity=0.185 Sum_probs=43.2
Q ss_pred CHHHHhhhCCCccCHHHHHHHHHHHHHHhCCCCCCC----CCccccchhHHhhhC-CC-----CcccHHHHHHHHhccc
Q 048564 42 SAQLSKFLGANEASRSDAVKKIWQYIRQHDLQNPAN----KREIRCDDKLKTIFN-GK-----DSVGFLEIAKLLSQHF 110 (114)
Q Consensus 42 Sp~La~flG~~~~sR~eV~~~lW~YIK~nnLqDp~d----Kr~I~cDekLk~Lfg-~~-----~~v~~~el~~lL~~Hl 110 (114)
+-+|++|-+.....=+.++....+||.++||..++= +..-. =+.|++.|. +. +....+.+..+|+..|
T Consensus 3 ~~~~~~~~~~~~~~IP~~l~~ci~~ie~~gl~~EGIFRv~G~~~~-i~~l~~~~~~~~~~~~~~~~d~h~vaslLK~fL 80 (193)
T cd04382 3 TGELADFDPSTSPMIPALIVHCVNEIEARGLTEEGLYRVSGSERE-VKALKEKFLRGKTVPNLSKVDIHVICGCLKDFL 80 (193)
T ss_pred cccccccCCCCCCCccHHHHHHHHHHHHcCCCCCCeeecCCcHHH-HHHHHHHHHcCCCCcccccCCHHHHHHHHHHHH
Confidence 347888888888888999999999999999886531 11111 124444443 11 1235566777776655
No 77
>TIGR00424 APS_reduc 5'-adenylylsulfate reductase, thioredoxin-independent. This enzyme, involved in the assimilation of inorganic sulfate, is closely related to the thioredoxin-dependent PAPS reductase of Bacteria (CysH) and Saccharomyces cerevisiae. However, it has its own C-terminal thioredoxin-like domain and is not thioredoxin-dependent. Also, it has a substrate preference for 5'-adenylylsulfate (APS) over 3'-phosphoadenylylsulfate (PAPS) so the pathway does not require an APS kinase (CysC) to convert APS to PAPS. Arabidopsis thaliana appears to have three isozymes, all able to complement E. coli CysH mutants (even in backgrounds lacking thioredoxin or APS kinase) but likely localized to different compartments in Arabidopsis.
Probab=20.26 E-value=57 Score=28.29 Aligned_cols=12 Identities=25% Similarity=1.002 Sum_probs=10.4
Q ss_pred HHHHHHHHhCCC
Q 048564 62 KIWQYIRQHDLQ 73 (114)
Q Consensus 62 ~lW~YIK~nnLq 73 (114)
-||.||++|+|-
T Consensus 267 dVw~Yi~~~~LP 278 (463)
T TIGR00424 267 DVWNFLRTMDVP 278 (463)
T ss_pred HHHHHHHHcCCC
Confidence 389999999885
Done!