Query 044317
Match_columns 123
No_of_seqs 105 out of 548
Neff 5.0
Searched_HMMs 46136
Date Fri Mar 29 13:28:26 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/044317.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/044317hhsearch_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 3.6E-29 7.8E-34 168.8 7.9 76 41-119 2-77 (77)
2 PF02201 SWIB: SWIB/MDM2 domai 100.0 1.3E-30 2.9E-35 175.5 -0.5 76 40-118 1-76 (76)
3 KOG1946 RNA polymerase I trans 100.0 5.1E-29 1.1E-33 199.7 7.0 83 37-122 97-179 (240)
4 PRK14724 DNA topoisomerase III 99.9 2.3E-24 5E-29 198.5 8.0 76 40-118 912-987 (987)
5 COG5531 SWIB-domain-containing 99.9 2.7E-24 5.8E-29 172.2 5.7 74 46-120 125-198 (237)
6 KOG2570 SWI/SNF transcription 99.8 4.2E-21 9.1E-26 163.2 5.8 95 26-121 179-283 (420)
7 PRK06319 DNA topoisomerase I/S 99.6 4.9E-16 1.1E-20 141.9 6.8 73 46-119 788-860 (860)
8 KOG2522 Filamentous baseplate 90.2 0.35 7.6E-06 43.1 3.7 40 59-98 380-419 (560)
9 PRK05350 acyl carrier protein; 87.3 0.69 1.5E-05 30.7 2.9 54 61-118 2-55 (82)
10 PRK05828 acyl carrier protein; 84.7 1.9 4.1E-05 29.4 4.1 54 61-118 1-54 (84)
11 CHL00124 acpP acyl carrier pro 81.6 1.7 3.7E-05 28.5 2.8 54 61-118 1-54 (82)
12 PRK12449 acyl carrier protein; 79.8 3.9 8.5E-05 26.5 4.1 53 61-117 1-53 (80)
13 PTZ00171 acyl carrier protein; 70.0 6.9 0.00015 29.5 3.7 61 54-118 59-119 (148)
14 PF13545 HTH_Crp_2: Crp-like h 69.3 2.1 4.6E-05 27.1 0.7 44 49-96 31-75 (76)
15 cd04762 HTH_MerR-trunc Helix-T 67.6 8.1 0.00017 21.6 2.9 24 50-80 4-27 (49)
16 PF03656 Pam16: Pam16; InterP 66.7 5.7 0.00012 29.4 2.6 29 50-78 58-87 (127)
17 TIGR03697 NtcA_cyano global ni 62.5 11 0.00023 27.4 3.4 46 49-98 146-192 (193)
18 PRK00071 nadD nicotinic acid m 62.1 5.4 0.00012 30.5 1.8 33 48-80 169-201 (203)
19 PLN02945 nicotinamide-nucleoti 60.7 6.5 0.00014 31.1 2.1 34 47-80 202-235 (236)
20 TIGR00482 nicotinate (nicotina 59.7 6.8 0.00015 29.7 2.0 34 47-80 160-193 (193)
21 PRK06973 nicotinic acid mononu 58.5 6.8 0.00015 31.5 1.8 34 47-80 200-241 (243)
22 PRK07117 acyl carrier protein; 55.4 17 0.00038 24.3 3.2 52 61-117 1-53 (79)
23 cd01104 HTH_MlrA-CarA Helix-Tu 54.4 39 0.00085 20.7 4.6 27 49-82 3-29 (68)
24 TIGR01764 excise DNA binding d 53.8 14 0.0003 20.8 2.2 25 50-81 5-29 (49)
25 PF01047 MarR: MarR family; I 53.7 2.5 5.5E-05 25.6 -1.1 36 50-88 21-59 (59)
26 PRK09392 ftrB transcriptional 52.6 20 0.00043 27.2 3.5 48 46-98 172-221 (236)
27 PRK13918 CRP/FNR family transc 51.6 19 0.0004 26.5 3.1 46 49-98 152-198 (202)
28 COG1654 BirA Biotin operon rep 51.5 9.9 0.00022 25.9 1.5 21 49-76 22-42 (79)
29 PF08349 DUF1722: Protein of u 48.0 13 0.00028 26.3 1.7 64 52-121 38-103 (117)
30 KOG0542 Predicted exonuclease 47.8 24 0.00051 29.5 3.4 55 39-93 98-162 (280)
31 PRK07639 acyl carrier protein; 46.7 32 0.00069 23.2 3.4 54 61-117 1-54 (86)
32 cd02165 NMNAT Nicotinamide/nic 46.5 15 0.00033 27.6 2.0 35 46-80 158-192 (192)
33 PF12728 HTH_17: Helix-turn-he 45.6 16 0.00034 21.6 1.6 27 49-82 4-30 (51)
34 COG1846 MarR Transcriptional r 44.1 22 0.00048 23.3 2.3 42 46-87 35-77 (126)
35 smart00667 LisH Lissencephaly 42.8 19 0.00041 18.8 1.5 20 62-81 2-21 (34)
36 cd09286 NMNAT_Eukarya Nicotina 42.1 19 0.0004 28.4 2.0 34 47-80 192-225 (225)
37 PRK08887 nicotinic acid mononu 42.0 22 0.00049 26.8 2.3 35 48-82 138-172 (174)
38 TIGR00517 acyl_carrier acyl ca 39.8 33 0.00072 21.9 2.6 51 64-118 2-52 (77)
39 PF07037 DUF1323: Putative tra 39.3 31 0.00068 25.6 2.6 44 49-99 3-53 (122)
40 PRK05883 acyl carrier protein; 37.6 56 0.0012 22.2 3.6 56 59-118 8-63 (91)
41 PF08463 EcoEI_R_C: EcoEI R pr 37.2 24 0.00051 25.8 1.8 68 48-117 89-163 (164)
42 PRK08558 adenine phosphoribosy 36.9 9.1 0.0002 30.6 -0.6 32 50-88 27-58 (238)
43 TIGR02057 PAPS_reductase phosp 36.9 20 0.00042 28.3 1.3 11 69-79 172-182 (226)
44 KOG0747 Putative NAD+-dependen 36.1 41 0.0009 28.8 3.2 48 59-107 252-312 (331)
45 PF04492 Phage_rep_O: Bacterio 34.5 53 0.0012 23.1 3.1 42 35-79 43-84 (100)
46 PF14838 INTS5_C: Integrator c 34.2 24 0.00052 33.0 1.6 44 47-93 617-665 (696)
47 PRK09391 fixK transcriptional 34.0 43 0.00093 25.6 2.8 46 48-97 180-228 (230)
48 smart00581 PSP proline-rich do 33.1 61 0.0013 20.8 2.9 19 42-62 5-23 (54)
49 TIGR02055 APS_reductase thiore 32.4 26 0.00056 26.7 1.3 12 68-79 135-146 (191)
50 PF04046 PSP: PSP; InterPro: 32.4 52 0.0011 20.6 2.4 17 46-62 3-19 (48)
51 PRK12563 sulfate adenylyltrans 32.2 25 0.00055 29.6 1.3 24 69-92 203-238 (312)
52 PF08938 HBS1_N: HBS1 N-termin 31.5 19 0.00042 23.9 0.5 25 49-73 32-56 (79)
53 KOG3347 Predicted nucleotide k 31.4 47 0.001 26.1 2.6 45 47-98 22-69 (176)
54 cd04761 HTH_MerR-SF Helix-Turn 31.0 44 0.00096 19.0 1.9 25 49-80 3-27 (49)
55 PF13333 rve_2: Integrase core 30.8 54 0.0012 19.8 2.3 22 57-78 14-35 (52)
56 PF08513 LisH: LisH; InterPro 30.7 28 0.00061 18.7 0.9 17 65-81 2-18 (27)
57 PRK07152 nadD putative nicotin 30.2 28 0.00061 28.8 1.3 29 48-81 157-185 (342)
58 COG1057 NadD Nicotinic acid mo 29.3 39 0.00084 26.4 1.9 33 48-80 163-195 (197)
59 PF13867 SAP30_Sin3_bdg: Sin3 29.0 98 0.0021 19.2 3.3 33 68-119 4-36 (53)
60 PRK10402 DNA-binding transcrip 28.8 44 0.00096 25.4 2.1 46 49-98 172-218 (226)
61 PF13401 AAA_22: AAA domain; P 28.4 76 0.0016 21.2 3.0 41 48-94 54-97 (131)
62 PRK11161 fumarate/nitrate redu 28.1 47 0.001 25.0 2.1 45 50-98 188-233 (235)
63 PRK00982 acpP acyl carrier pro 27.4 62 0.0013 20.5 2.3 49 65-117 3-51 (78)
64 PF05643 DUF799: Putative bact 27.3 16 0.00035 29.4 -0.6 38 70-109 77-114 (215)
65 PF01726 LexA_DNA_bind: LexA D 26.7 62 0.0013 20.8 2.2 21 63-84 8-28 (65)
66 PRK05253 sulfate adenylyltrans 26.6 36 0.00078 28.2 1.3 11 69-79 193-203 (301)
67 smart00153 VHP Villin headpiec 26.5 26 0.00056 20.5 0.3 26 89-115 2-27 (36)
68 PLN02309 5'-adenylylsulfate re 26.3 41 0.00088 29.7 1.6 12 68-79 261-272 (457)
69 PF07308 DUF1456: Protein of u 24.9 1.3E+02 0.0028 19.7 3.5 41 49-98 16-58 (68)
70 TIGR00434 cysH phosophoadenyly 24.7 49 0.0011 25.2 1.7 13 68-80 156-168 (212)
71 COG5577 Spore coat protein [Ce 24.6 47 0.001 25.1 1.5 36 49-84 86-121 (145)
72 PF13758 Prefoldin_3: Prefoldi 24.0 1.3E+02 0.0028 21.5 3.6 29 49-77 49-83 (99)
73 PF06039 Mqo: Malate:quinone o 23.6 31 0.00067 31.0 0.4 53 61-116 81-135 (488)
74 smart00422 HTH_MERR helix_turn 23.2 1.3E+02 0.0029 18.2 3.2 24 50-80 4-27 (70)
75 TIGR02039 CysD sulfate adenyly 23.1 46 0.001 27.7 1.3 11 69-79 185-195 (294)
76 KOG4144 Arylalkylamine N-acety 22.7 46 0.001 26.2 1.2 33 66-98 119-151 (190)
77 cd04763 HTH_MlrA-like Helix-Tu 22.7 1.6E+02 0.0035 18.1 3.6 27 49-82 3-29 (68)
78 PF01507 PAPS_reduct: Phosphoa 22.3 58 0.0012 23.1 1.6 14 67-80 141-154 (174)
79 TIGR01510 coaD_prev_kdtB pante 22.2 59 0.0013 23.8 1.6 31 47-77 124-154 (155)
80 PF00010 HLH: Helix-loop-helix 22.1 1E+02 0.0022 18.4 2.4 18 59-76 36-53 (55)
81 PF03511 Fanconi_A: Fanconi an 22.0 89 0.0019 20.8 2.2 16 106-121 10-25 (64)
82 TIGR00424 APS_reduc 5'-adenyly 21.8 56 0.0012 28.9 1.6 11 69-79 267-277 (463)
83 PF12368 DUF3650: Protein of u 21.1 48 0.001 18.6 0.7 10 72-81 9-18 (28)
84 COG0175 CysH 3'-phosphoadenosi 20.9 54 0.0012 26.4 1.3 12 68-79 183-194 (261)
85 TIGR01889 Staph_reg_Sar staphy 20.8 79 0.0017 21.6 1.9 37 50-89 47-86 (109)
No 1
>smart00151 SWIB SWI complex, BAF60b domains.
Probab=99.96 E-value=3.6e-29 Score=168.84 Aligned_cols=76 Identities=36% Similarity=0.596 Sum_probs=73.1
Q ss_pred ccccCCCCCHHHHhhhCCCCCCHHHHHHHHHHHhhhcCCCCCCCCCccccchhHHhhhcCCCccCHHHHHHHHHhccCC
Q 044317 41 TKSVAPSSTSELGRFLNIPEPPRSETAKLITKFIKLNNRENPGMKKDLLGEEKLKSLLSGKDRIGIPEIAKLLSGQFVK 119 (123)
Q Consensus 41 ~kp~~~~LS~eLa~fLG~~e~sR~evvk~lW~YIK~n~LQDp~nKr~I~cDekLk~LF~g~d~i~~~~i~klL~~Hl~k 119 (123)
+++ |.+|++|++|+|.+++||++|++.||+|||+||||||+||+.|+||+.|+++| |+++|.|++|+++|++||.+
T Consensus 2 ~~~--~~ls~~L~~~lg~~~~tr~ev~~~lw~YIk~n~L~d~~~k~~i~~D~~L~~l~-~~~~v~~~~~~~ll~~Hl~~ 77 (77)
T smart00151 2 TKK--VTLSPELAKVLGAPEMTRTEIIKRLWEYIKEHNLQDPQNKREILCDSKLEQIF-GKDRMDMFEMNKLLTPHLIK 77 (77)
T ss_pred CCc--ccCCHHHHHHhCCCcCcHHHHHHHHHHHHHHhcccCCccCCEEecCHHHHHHH-CcCeecHHHHHHHHHHHcCC
Confidence 455 99999999999999999999999999999999999999999999999999999 89999999999999999974
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=99.96 E-value=1.3e-30 Score=175.47 Aligned_cols=76 Identities=38% Similarity=0.510 Sum_probs=69.9
Q ss_pred CccccCCCCCHHHHhhhCCCCCCHHHHHHHHHHHhhhcCCCCCCCCCccccchhHHhhhcCCCccCHHHHHHHHHhccC
Q 044317 40 KTKSVAPSSTSELGRFLNIPEPPRSETAKLITKFIKLNNRENPGMKKDLLGEEKLKSLLSGKDRIGIPEIAKLLSGQFV 118 (123)
Q Consensus 40 ~~kp~~~~LS~eLa~fLG~~e~sR~evvk~lW~YIK~n~LQDp~nKr~I~cDekLk~LF~g~d~i~~~~i~klL~~Hl~ 118 (123)
|+++ |.||++|++|+|..++||++|++.||+||++||||||+|++.|+||++|+.|| +.++|++++|+++|++||.
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 FPKR--FKLSPELAEFLGEDELSRSEVVKRLWQYIKENNLQDPKDKRIIICDEKLKKLF-GKDSVNFFEIPKLLKPHLI 76 (76)
T ss_dssp -EEE--EHHHHHHHHHTT-SCEEHHHHHHHHHHHHHHTTSBESSSTTEEE-TTSHHHHH-HTSECSEEETTHHHHHHHE
T ss_pred CCCC--ccCCHHHHHHhCCCCCCHHHHHHHHHHHHHHhcCCCcccCceEecCHHHHHHh-CCCeecHhhHHHHHHHhcC
Confidence 3455 88999999999999999999999999999999999999999999999999999 7899999999999999984
No 3
>KOG1946 consensus RNA polymerase I transcription factor UAF [Transcription]
Probab=99.95 E-value=5.1e-29 Score=199.70 Aligned_cols=83 Identities=37% Similarity=0.589 Sum_probs=79.3
Q ss_pred CCCCccccCCCCCHHHHhhhCCCCCCHHHHHHHHHHHhhhcCCCCCCCCCccccchhHHhhhcCCCccCHHHHHHHHHhc
Q 044317 37 AKGKTKSVAPSSTSELGRFLNIPEPPRSETAKLITKFIKLNNRENPGMKKDLLGEEKLKSLLSGKDRIGIPEIAKLLSGQ 116 (123)
Q Consensus 37 ~~g~~kp~~~~LS~eLa~fLG~~e~sR~evvk~lW~YIK~n~LQDp~nKr~I~cDekLk~LF~g~d~i~~~~i~klL~~H 116 (123)
+.|++++ +.||++|++|+|.+++||.+|++.||+|||+||||||.||+.|+||++|+.|| +.++|++|+|++||.+|
T Consensus 97 ~~g~~kl--~~ls~~L~~~~G~~~lsR~~vvk~iw~YIke~nLqDP~nkr~IlCDekL~~iF-~~k~v~~fem~KLL~~H 173 (240)
T KOG1946|consen 97 SWGSTKL--IPLSPSLARFVGTSELSRTDVVKKIWAYIKEHNLQDPKNKREILCDEKLKSIF-GKKRVGMFEMLKLLTKH 173 (240)
T ss_pred CcCcccc--cccCHHHHhhcccccccHHHHHHHHHHHHHHhccCCccccCeeeeHHHHHHHh-ccCccceeeHHHHHHHh
Confidence 4699999 88999999999999999999999999999999999999999999999999999 88889999999999999
Q ss_pred cCCCCC
Q 044317 117 FVKTGS 122 (123)
Q Consensus 117 l~k~~s 122 (123)
|++...
T Consensus 174 ~~~~~d 179 (240)
T KOG1946|consen 174 FLKNQD 179 (240)
T ss_pred ccCccc
Confidence 998754
No 4
>PRK14724 DNA topoisomerase III; Provisional
Probab=99.90 E-value=2.3e-24 Score=198.47 Aligned_cols=76 Identities=22% Similarity=0.406 Sum_probs=73.0
Q ss_pred CccccCCCCCHHHHhhhCCCCCCHHHHHHHHHHHhhhcCCCCCCCCCccccchhHHhhhcCCCccCHHHHHHHHHhccC
Q 044317 40 KTKSVAPSSTSELGRFLNIPEPPRSETAKLITKFIKLNNRENPGMKKDLLGEEKLKSLLSGKDRIGIPEIAKLLSGQFV 118 (123)
Q Consensus 40 ~~kp~~~~LS~eLa~fLG~~e~sR~evvk~lW~YIK~n~LQDp~nKr~I~cDekLk~LF~g~d~i~~~~i~klL~~Hl~ 118 (123)
+..+ +.|||+|++|||..++||++|++.||+|||+||||||+|||.|+||++|+.|| |+++|.||+|+++|++||.
T Consensus 912 ~~~~--~~ls~~La~~lg~~~~~r~~v~~~lW~YIK~~~Lqdp~~k~~i~cD~~L~~vf-g~~~~~~~~~~~~l~~hl~ 987 (987)
T PRK14724 912 PAAG--LKPSAALAAVIGAEPVARPEVIKKLWDYIKANNLQDPADKRAINADAKLRPVF-GKDQVTMFELAGIVGKHLS 987 (987)
T ss_pred cccc--cCCCHHHHHHhCCCcCCHHHHHHHHHHHHHHccCCCcccCCeeccchHHHHHh-CCCcccHHHHHHHHHHhcC
Confidence 5556 88999999999999999999999999999999999999999999999999999 9999999999999999984
No 5
>COG5531 SWIB-domain-containing proteins implicated in chromatin remodeling [Chromatin structure and dynamics]
Probab=99.90 E-value=2.7e-24 Score=172.19 Aligned_cols=74 Identities=32% Similarity=0.469 Sum_probs=72.1
Q ss_pred CCCCHHHHhhhCCCCCCHHHHHHHHHHHhhhcCCCCCCCCCccccchhHHhhhcCCCccCHHHHHHHHHhccCCC
Q 044317 46 PSSTSELGRFLNIPEPPRSETAKLITKFIKLNNRENPGMKKDLLGEEKLKSLLSGKDRIGIPEIAKLLSGQFVKT 120 (123)
Q Consensus 46 ~~LS~eLa~fLG~~e~sR~evvk~lW~YIK~n~LQDp~nKr~I~cDekLk~LF~g~d~i~~~~i~klL~~Hl~k~ 120 (123)
+.+|+.||.|||..++||++||+.||+|||.||||||+||+.|+||++|+.|| |.+.+.||+|.++|.+|+++-
T Consensus 125 ~~lS~~La~ilG~~~~tr~~~v~~lw~YIk~h~lq~~~nkr~I~~D~~L~~v~-g~~p~~mf~~~k~l~~hl~~~ 198 (237)
T COG5531 125 VKLSPKLAAILGLEPGTRPEAVKKLWKYIKKHNLQDPNNKRLILCDSKLKKVL-GSDPIDMFELTKPLSPHLIKY 198 (237)
T ss_pred eecCHHHHHHhCCCCCCccHHHHHHHHHHHHhcCCCccccceecccHHHHHHh-CCCchhhhhhhcccccceecC
Confidence 88899999999999999999999999999999999999999999999999999 699999999999999999983
No 6
>KOG2570 consensus SWI/SNF transcription activation complex subunit [Chromatin structure and dynamics; Transcription]
Probab=99.83 E-value=4.2e-21 Score=163.17 Aligned_cols=95 Identities=19% Similarity=0.302 Sum_probs=88.8
Q ss_pred hcchhhhhccCCCC----------CccccCCCCCHHHHhhhCCCCCCHHHHHHHHHHHhhhcCCCCCCCCCccccchhHH
Q 044317 26 ASSSKAQAKAKAKG----------KTKSVAPSSTSELGRFLNIPEPPRSETAKLITKFIKLNNRENPGMKKDLLGEEKLK 95 (123)
Q Consensus 26 a~~~~~~~kr~~~g----------~~kp~~~~LS~eLa~fLG~~e~sR~evvk~lW~YIK~n~LQDp~nKr~I~cDekLk 95 (123)
++..+++.||++.- -..|+.|++||.|+++||+.+.||++||.+||+|||.|+||||+++.+|+||..|+
T Consensus 179 ~etdGf~VKR~Gd~~v~ctIll~l~~~P~~fklsp~La~lLGi~t~Trp~iI~alWqYIk~n~Lqd~~e~~~incD~~l~ 258 (420)
T KOG2570|consen 179 NETDGFQVKRPGDRNVRCTILLLLDYQPEEFKLSPRLANLLGIHTGTRPDIVTALWQYIKTNKLQDPEDSDFINCDKALE 258 (420)
T ss_pred CCcCceeeeccCCCccceEEEEeeccCCcccccCHHHHHHhhhccCcchHHHHHHHHHHHHhccCCcccchhhcchHHHH
Confidence 56778899998877 34888899999999999999999999999999999999999999999999999999
Q ss_pred hhhcCCCccCHHHHHHHHHhccCCCC
Q 044317 96 SLLSGKDRIGIPEIAKLLSGQFVKTG 121 (123)
Q Consensus 96 ~LF~g~d~i~~~~i~klL~~Hl~k~~ 121 (123)
++| |++++.|.+|+.+|++||...+
T Consensus 259 qif-~~~rl~F~elp~~l~~lL~P~d 283 (420)
T KOG2570|consen 259 QIF-GVDRLKFPELPQLLNPLLSPPD 283 (420)
T ss_pred Hhh-cccccccccchhhhhhccCCCC
Confidence 999 9999999999999999998754
No 7
>PRK06319 DNA topoisomerase I/SWI domain fusion protein; Validated
Probab=99.62 E-value=4.9e-16 Score=141.87 Aligned_cols=73 Identities=25% Similarity=0.405 Sum_probs=71.1
Q ss_pred CCCCHHHHhhhCCCCCCHHHHHHHHHHHhhhcCCCCCCCCCccccchhHHhhhcCCCccCHHHHHHHHHhccCC
Q 044317 46 PSSTSELGRFLNIPEPPRSETAKLITKFIKLNNRENPGMKKDLLGEEKLKSLLSGKDRIGIPEIAKLLSGQFVK 119 (123)
Q Consensus 46 ~~LS~eLa~fLG~~e~sR~evvk~lW~YIK~n~LQDp~nKr~I~cDekLk~LF~g~d~i~~~~i~klL~~Hl~k 119 (123)
|.+|++|+.++|..+++|.++++.||+||+.|+||||+||+.|+||++|+.+| +++++.||+|+++|++||.+
T Consensus 788 ~~~S~~La~~~g~~~~sr~~~~~~lw~yIk~~~lqdp~~Kr~i~~d~kl~kvf-~~~~~~~~~~~k~l~~hl~~ 860 (860)
T PRK06319 788 YTPSPALAAMIGAEPVGRGEATKKVWDYIKEHGLQSPENKKLIIPDSKLQGVI-GPDPIDMFQLSKKLSQHLIK 860 (860)
T ss_pred cccccccccccCcCccCchHHHHHHHHHHHHhcccCccccccCCCchhhhhhh-CcCccchhhhHHHHHhhhcC
Confidence 77899999999999999999999999999999999999999999999999999 89999999999999999875
No 8
>KOG2522 consensus Filamentous baseplate protein Ligatin, contains PUA domain [Translation, ribosomal structure and biogenesis]
Probab=90.17 E-value=0.35 Score=43.13 Aligned_cols=40 Identities=20% Similarity=0.174 Sum_probs=35.7
Q ss_pred CCCCHHHHHHHHHHHhhhcCCCCCCCCCccccchhHHhhh
Q 044317 59 PEPPRSETAKLITKFIKLNNRENPGMKKDLLGEEKLKSLL 98 (123)
Q Consensus 59 ~e~sR~evvk~lW~YIK~n~LQDp~nKr~I~cDekLk~LF 98 (123)
.-.+-+||...+.+||+.|||-|+.||..|+.|+-|-+..
T Consensus 380 ~lyt~seir~~V~kYi~knnLad~~nKg~VrLDpILfd~~ 419 (560)
T KOG2522|consen 380 TLYTSSEIRSAVSKYISKNNLADTKNKGKVRLDPILFDMV 419 (560)
T ss_pred ceeeHHHHHHHHHHHhhhhhccccccCCcEEeccHHHHHH
Confidence 3478899999999999999999999999999888877766
No 9
>PRK05350 acyl carrier protein; Provisional
Probab=87.35 E-value=0.69 Score=30.67 Aligned_cols=54 Identities=19% Similarity=0.073 Sum_probs=45.7
Q ss_pred CCHHHHHHHHHHHhhhcCCCCCCCCCccccchhHHhhhcCCCccCHHHHHHHHHhccC
Q 044317 61 PPRSETAKLITKFIKLNNRENPGMKKDLLGEEKLKSLLSGKDRIGIPEIAKLLSGQFV 118 (123)
Q Consensus 61 ~sR~evvk~lW~YIK~n~LQDp~nKr~I~cDekLk~LF~g~d~i~~~~i~klL~~Hl~ 118 (123)
|+|.++...|+++|.+. +.-+. ..|.+|..|..-+ |-|++.+-+|--.|..+|-
T Consensus 2 m~~~~i~~~v~~ii~~~-~~~~~--~~i~~d~~l~~dl-g~DSld~veli~~lE~~fg 55 (82)
T PRK05350 2 MTREEILERLRAILVEL-FEIDP--EDITPEANLYEDL-DLDSIDAVDLVVHLQKLTG 55 (82)
T ss_pred CCHHHHHHHHHHHHHHH-hCCCH--HHCCCCccchhhc-CCCHHHHHHHHHHHHHHHC
Confidence 68999999999999987 53222 4799999998889 9999999999988888874
No 10
>PRK05828 acyl carrier protein; Validated
Probab=84.73 E-value=1.9 Score=29.37 Aligned_cols=54 Identities=17% Similarity=0.085 Sum_probs=43.5
Q ss_pred CCHHHHHHHHHHHhhhcCCCCCCCCCccccchhHHhhhcCCCccCHHHHHHHHHhccC
Q 044317 61 PPRSETAKLITKFIKLNNRENPGMKKDLLGEEKLKSLLSGKDRIGIPEIAKLLSGQFV 118 (123)
Q Consensus 61 ~sR~evvk~lW~YIK~n~LQDp~nKr~I~cDekLk~LF~g~d~i~~~~i~klL~~Hl~ 118 (123)
|+|.+|...|-+.|.+.++.-+ -..|.+|..|.+ + |-|++.+.+|--.|...|-
T Consensus 1 m~~~eI~~~i~~ii~e~~~~~~--~d~i~~~~~~~d-L-g~DSLd~velv~~lE~~f~ 54 (84)
T PRK05828 1 MQEMEILLKIKEIAKKKNFAVT--LDESNINKPYRE-L-KIDSLDMFSIIVSLESEFN 54 (84)
T ss_pred CCHHHHHHHHHHHHHHhccCCC--cccccCCCCHHh-c-CCCHHHHHHHHHHHHHHHC
Confidence 7899999999999988655322 245678889987 8 9999999999888887763
No 11
>CHL00124 acpP acyl carrier protein; Validated
Probab=81.59 E-value=1.7 Score=28.46 Aligned_cols=54 Identities=9% Similarity=0.184 Sum_probs=44.3
Q ss_pred CCHHHHHHHHHHHhhhcCCCCCCCCCccccchhHHhhhcCCCccCHHHHHHHHHhccC
Q 044317 61 PPRSETAKLITKFIKLNNRENPGMKKDLLGEEKLKSLLSGKDRIGIPEIAKLLSGQFV 118 (123)
Q Consensus 61 ~sR~evvk~lW~YIK~n~LQDp~nKr~I~cDekLk~LF~g~d~i~~~~i~klL~~Hl~ 118 (123)
|+|.+|...|-++|.+.-=.+| ..|.+|..|..-+ |-|++.+.+|--.|...|-
T Consensus 1 M~~~~i~~~l~~ii~~~~~~~~---~~i~~d~~l~~dl-g~DSl~~~eli~~le~~f~ 54 (82)
T CHL00124 1 MTKNDIFEKVQSIVAEQLGIEK---SEVTLDANFTRDL-GADSLDVVELVMAIEEKFD 54 (82)
T ss_pred CCHHHHHHHHHHHHHHHHCCCH---HHCCCCcchhhhc-CCcHHHHHHHHHHHHHHHC
Confidence 6899999999999988742333 3599999999989 9999999999888877663
No 12
>PRK12449 acyl carrier protein; Provisional
Probab=79.82 E-value=3.9 Score=26.54 Aligned_cols=53 Identities=19% Similarity=0.199 Sum_probs=42.8
Q ss_pred CCHHHHHHHHHHHhhhcCCCCCCCCCccccchhHHhhhcCCCccCHHHHHHHHHhcc
Q 044317 61 PPRSETAKLITKFIKLNNRENPGMKKDLLGEEKLKSLLSGKDRIGIPEIAKLLSGQF 117 (123)
Q Consensus 61 ~sR~evvk~lW~YIK~n~LQDp~nKr~I~cDekLk~LF~g~d~i~~~~i~klL~~Hl 117 (123)
|+|.+|...|-+++.+.-=.++ ..|.+|..|..-+ |-|++.+.+|--.|...|
T Consensus 1 m~~~~i~~~l~~il~~~~~~~~---~~i~~~~~l~~dl-g~DSl~~~~li~~lE~~f 53 (80)
T PRK12449 1 MTREEIFERLINLIQKQRSYLS---LAITEQTHLKDDL-AVDSIELVEFIINVEDEF 53 (80)
T ss_pred CCHHHHHHHHHHHHHHHhCCCc---cccCCCCcHHHHc-CCcHHHHHHHHHHHHHHh
Confidence 5788999999999987542233 3589999999999 999999999888887665
No 13
>PTZ00171 acyl carrier protein; Provisional
Probab=70.02 E-value=6.9 Score=29.46 Aligned_cols=61 Identities=13% Similarity=0.163 Sum_probs=48.9
Q ss_pred hhhCCCCCCHHHHHHHHHHHhhhcCCCCCCCCCccccchhHHhhhcCCCccCHHHHHHHHHhccC
Q 044317 54 RFLNIPEPPRSETAKLITKFIKLNNRENPGMKKDLLGEEKLKSLLSGKDRIGIPEIAKLLSGQFV 118 (123)
Q Consensus 54 ~fLG~~e~sR~evvk~lW~YIK~n~LQDp~nKr~I~cDekLk~LF~g~d~i~~~~i~klL~~Hl~ 118 (123)
..-+..-+++.+|...|+++|.+.-=.|| ..|.+|..+..-+ |-|++.+-+|--.|..+|-
T Consensus 59 ~~~~~~~~~~~~v~~~l~eiiae~l~vd~---~~I~~ds~~~~dL-g~DSLd~veLv~~LEdeFg 119 (148)
T PTZ00171 59 SKSKQYLLSKEDVLTRVKKVVKNFEKVDA---SKITPESNFVKDL-GADSLDVVELLIAIEQEFN 119 (148)
T ss_pred hcccccccCHHHHHHHHHHHHHHHhCCCH---hhCCCCcchhhhc-CCCHHHHHHHHHHHHHHHC
Confidence 33455678999999999999998852333 3588999999999 9999999999888887763
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=69.25 E-value=2.1 Score=27.07 Aligned_cols=44 Identities=20% Similarity=0.231 Sum_probs=30.7
Q ss_pred CHHHHhhhCCCCCCHHHHHHHHHHHhhhcCCCCCCCCCccccc-hhHHh
Q 044317 49 TSELGRFLNIPEPPRSETAKLITKFIKLNNRENPGMKKDLLGE-EKLKS 96 (123)
Q Consensus 49 S~eLa~fLG~~e~sR~evvk~lW~YIK~n~LQDp~nKr~I~cD-ekLk~ 96 (123)
-.+||+++|++ |.. +..+-...++.++-+-+.+++++.| ++|++
T Consensus 31 ~~~iA~~~g~s---r~t-v~r~l~~l~~~g~I~~~~~~i~I~d~~~L~~ 75 (76)
T PF13545_consen 31 QEEIADMLGVS---RET-VSRILKRLKDEGIIEVKRGKIIILDPERLEE 75 (76)
T ss_dssp HHHHHHHHTSC---HHH-HHHHHHHHHHTTSEEEETTEEEESSHHHHHH
T ss_pred HHHHHHHHCCC---HHH-HHHHHHHHHHCCCEEEcCCEEEECCHHHHhc
Confidence 36899999975 444 4445555666777777888888888 55554
No 15
>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=67.60 E-value=8.1 Score=21.64 Aligned_cols=24 Identities=13% Similarity=0.342 Sum_probs=19.7
Q ss_pred HHHHhhhCCCCCCHHHHHHHHHHHhhhcCCC
Q 044317 50 SELGRFLNIPEPPRSETAKLITKFIKLNNRE 80 (123)
Q Consensus 50 ~eLa~fLG~~e~sR~evvk~lW~YIK~n~LQ 80 (123)
.|++++||+++- .||.|+++..+.
T Consensus 4 ~e~a~~lgvs~~-------tl~~~~~~g~~~ 27 (49)
T cd04762 4 KEAAELLGVSPS-------TLRRWVKEGKLK 27 (49)
T ss_pred HHHHHHHCcCHH-------HHHHHHHcCCCC
Confidence 578899998766 799999987764
No 16
>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=66.69 E-value=5.7 Score=29.36 Aligned_cols=29 Identities=31% Similarity=0.416 Sum_probs=22.7
Q ss_pred HHHHhhhCCCC-CCHHHHHHHHHHHhhhcC
Q 044317 50 SELGRFLNIPE-PPRSETAKLITKFIKLNN 78 (123)
Q Consensus 50 ~eLa~fLG~~e-~sR~evvk~lW~YIK~n~ 78 (123)
+|-..+|++++ .++.+|.+..+.+++.|+
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 57778999876 999999999999999996
No 17
>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=62.49 E-value=11 Score=27.39 Aligned_cols=46 Identities=11% Similarity=0.015 Sum_probs=32.7
Q ss_pred CHHHHhhhCCCCCCHHHHHHHHHHHhhhcCCCCCCCCCccccc-hhHHhhh
Q 044317 49 TSELGRFLNIPEPPRSETAKLITKFIKLNNRENPGMKKDLLGE-EKLKSLL 98 (123)
Q Consensus 49 S~eLa~fLG~~e~sR~evvk~lW~YIK~n~LQDp~nKr~I~cD-ekLk~LF 98 (123)
-.+||+++|++ |. .+..+-.-.++.++-.-..++++++| ++|++.+
T Consensus 146 ~~~iA~~lG~t---re-tvsR~l~~l~~~g~I~~~~~~i~I~d~~~L~~~~ 192 (193)
T TIGR03697 146 HQAIAEAIGST---RV-TITRLLGDLRKKKLISIHKKKITVHDPIALGQRF 192 (193)
T ss_pred HHHHHHHhCCc---HH-HHHHHHHHHHHCCCEEecCCEEEEeCHHHHHHhc
Confidence 47999999954 33 34445556677888777788899998 6666654
No 18
>PRK00071 nadD nicotinic acid mononucleotide adenylyltransferase; Provisional
Probab=62.09 E-value=5.4 Score=30.48 Aligned_cols=33 Identities=12% Similarity=0.155 Sum_probs=24.8
Q ss_pred CCHHHHhhhCCCCCCHHHHHHHHHHHhhhcCCC
Q 044317 48 STSELGRFLNIPEPPRSETAKLITKFIKLNNRE 80 (123)
Q Consensus 48 LS~eLa~fLG~~e~sR~evvk~lW~YIK~n~LQ 80 (123)
-|+++.+.+.....-+.-|-..+++||++|+|.
T Consensus 169 SST~IR~~l~~g~~~~~lvp~~V~~YI~~~~LY 201 (203)
T PRK00071 169 SSTAIRERIKEGRPIRYLLPEAVLDYIEKHGLY 201 (203)
T ss_pred CHHHHHHHHHcCCChhHhCCHHHHHHHHHhCcc
Confidence 466777766554445566778999999999996
No 19
>PLN02945 nicotinamide-nucleotide adenylyltransferase/nicotinate-nucleotide adenylyltransferase
Probab=60.67 E-value=6.5 Score=31.12 Aligned_cols=34 Identities=12% Similarity=0.059 Sum_probs=25.6
Q ss_pred CCCHHHHhhhCCCCCCHHHHHHHHHHHhhhcCCC
Q 044317 47 SSTSELGRFLNIPEPPRSETAKLITKFIKLNNRE 80 (123)
Q Consensus 47 ~LS~eLa~fLG~~e~sR~evvk~lW~YIK~n~LQ 80 (123)
--|+++.+.+.....-+.-|-..+++||++|+|.
T Consensus 202 ISST~IR~~l~~g~~i~~lvP~~V~~YI~~~~LY 235 (236)
T PLN02945 202 ISSTRVRECISRGLSVKYLTPDGVIDYIKEHGLY 235 (236)
T ss_pred ccHHHHHHHHHcCCCchhhCCHHHHHHHHHcCCC
Confidence 3467777777654445666788999999999996
No 20
>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=59.71 E-value=6.8 Score=29.74 Aligned_cols=34 Identities=15% Similarity=0.117 Sum_probs=25.8
Q ss_pred CCCHHHHhhhCCCCCCHHHHHHHHHHHhhhcCCC
Q 044317 47 SSTSELGRFLNIPEPPRSETAKLITKFIKLNNRE 80 (123)
Q Consensus 47 ~LS~eLa~fLG~~e~sR~evvk~lW~YIK~n~LQ 80 (123)
.-|++..+-+.....-+.-|-..+++||++|+|.
T Consensus 160 iSST~IR~~l~~g~~~~~lvP~~V~~YI~~~~LY 193 (193)
T TIGR00482 160 ISSTEIRQRIRQGKSIEYLLPDPVIKYIKQHGLY 193 (193)
T ss_pred cCHHHHHHHHHcCCCchhhCCHHHHHHHHHhCCC
Confidence 3467777777655555667888999999999984
No 21
>PRK06973 nicotinic acid mononucleotide adenylyltransferase; Provisional
Probab=58.45 E-value=6.8 Score=31.51 Aligned_cols=34 Identities=9% Similarity=0.097 Sum_probs=26.3
Q ss_pred CCCHHHHhhhCCC--------CCCHHHHHHHHHHHhhhcCCC
Q 044317 47 SSTSELGRFLNIP--------EPPRSETAKLITKFIKLNNRE 80 (123)
Q Consensus 47 ~LS~eLa~fLG~~--------e~sR~evvk~lW~YIK~n~LQ 80 (123)
.-|+++.+.|... ..-+.-|=..+++||++|+|.
T Consensus 200 ISST~IR~~l~~g~~~~~~~~~~i~~lvP~~V~~YI~~~~LY 241 (243)
T PRK06973 200 LSATDIRAHLRACIARRAQVPDASAEHVPAAVWAYILQHRLY 241 (243)
T ss_pred ccHHHHHHHHHcCCCcccccCCChhHhCCHHHHHHHHHcCCC
Confidence 3477888888655 455666778899999999997
No 22
>PRK07117 acyl carrier protein; Validated
Probab=55.38 E-value=17 Score=24.28 Aligned_cols=52 Identities=15% Similarity=0.226 Sum_probs=40.4
Q ss_pred CCHHHHHHHHHHHhhhcCCCCC-CCCCccccchhHHhhhcCCCccCHHHHHHHHHhcc
Q 044317 61 PPRSETAKLITKFIKLNNRENP-GMKKDLLGEEKLKSLLSGKDRIGIPEIAKLLSGQF 117 (123)
Q Consensus 61 ~sR~evvk~lW~YIK~n~LQDp-~nKr~I~cDekLk~LF~g~d~i~~~~i~klL~~Hl 117 (123)
|+|.+|...|-+-|.+.- | -+...|..|..|+. | |-|++.+.+|--.|..-|
T Consensus 1 M~~~ei~~~v~~ii~e~~---p~i~~~~I~~~~~l~D-L-g~DSlD~veiv~~led~f 53 (79)
T PRK07117 1 MDKQRIFDILVRHIREVL---PDLDQHQFQPEDSLVD-L-GANSMDRAEIVIMTLESL 53 (79)
T ss_pred CCHHHHHHHHHHHHHHHc---CCCCHHHCCCCCChhh-c-CCChHHHHHHHHHHHHHH
Confidence 578888888888888864 2 23357899999998 8 999999999876665544
No 23
>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=54.44 E-value=39 Score=20.72 Aligned_cols=27 Identities=7% Similarity=0.201 Sum_probs=21.2
Q ss_pred CHHHHhhhCCCCCCHHHHHHHHHHHhhhcCCCCC
Q 044317 49 TSELGRFLNIPEPPRSETAKLITKFIKLNNRENP 82 (123)
Q Consensus 49 S~eLa~fLG~~e~sR~evvk~lW~YIK~n~LQDp 82 (123)
..++|+.+|+++. .|+.|+++.++..|
T Consensus 3 ~~eva~~~gvs~~-------tlr~w~~~~g~~~~ 29 (68)
T cd01104 3 IGAVARLTGVSPD-------TLRAWERRYGLPAP 29 (68)
T ss_pred HHHHHHHHCcCHH-------HHHHHHHhCCCCCC
Confidence 3688899998776 78889988777665
No 24
>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=53.81 E-value=14 Score=20.85 Aligned_cols=25 Identities=12% Similarity=0.291 Sum_probs=20.4
Q ss_pred HHHHhhhCCCCCCHHHHHHHHHHHhhhcCCCC
Q 044317 50 SELGRFLNIPEPPRSETAKLITKFIKLNNREN 81 (123)
Q Consensus 50 ~eLa~fLG~~e~sR~evvk~lW~YIK~n~LQD 81 (123)
+|.+++||++.. .|+.+|++..+.-
T Consensus 5 ~e~a~~lgis~~-------ti~~~~~~g~i~~ 29 (49)
T TIGR01764 5 EEAAEYLGVSKD-------TVYRLIHEGELPA 29 (49)
T ss_pred HHHHHHHCCCHH-------HHHHHHHcCCCCe
Confidence 688999998765 7899999887754
No 25
>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=53.66 E-value=2.5 Score=25.61 Aligned_cols=36 Identities=28% Similarity=0.494 Sum_probs=21.9
Q ss_pred HHHHhhhCCCCCCHHHHHHHHHHHhhh---cCCCCCCCCCcc
Q 044317 50 SELGRFLNIPEPPRSETAKLITKFIKL---NNRENPGMKKDL 88 (123)
Q Consensus 50 ~eLa~fLG~~e~sR~evvk~lW~YIK~---n~LQDp~nKr~I 88 (123)
.+|++++++ +++.++..+..=++. ..-+||+|+|.|
T Consensus 21 ~~la~~~~~---~~~~~t~~i~~L~~~g~I~r~~~~~D~R~v 59 (59)
T PF01047_consen 21 SELAEKLGI---SRSTVTRIIKRLEKKGLIERERDPDDRRQV 59 (59)
T ss_dssp HHHHHHHTS----HHHHHHHHHHHHHTTSEEEEEETTETTSE
T ss_pred HHHHHHHCC---ChhHHHHHHHHHHHCCCEEeccCCCCCCcC
Confidence 488888887 455555555554443 223778888764
No 26
>PRK09392 ftrB transcriptional activator FtrB; Provisional
Probab=52.62 E-value=20 Score=27.16 Aligned_cols=48 Identities=6% Similarity=0.063 Sum_probs=32.5
Q ss_pred CCCC-HHHHhhhCCCCCCHHHHHHHHHHHhhhcCCCCCCCCCccccc-hhHHhhh
Q 044317 46 PSST-SELGRFLNIPEPPRSETAKLITKFIKLNNRENPGMKKDLLGE-EKLKSLL 98 (123)
Q Consensus 46 ~~LS-~eLa~fLG~~e~sR~evvk~lW~YIK~n~LQDp~nKr~I~cD-ekLk~LF 98 (123)
..++ .++|++||++.. .|...+ .-.++.++ .-..++++++| ++|+.+.
T Consensus 172 i~~t~~~iA~~lG~tre---tvsR~l-~~L~~~gl-~~~~~~i~I~d~~~L~~~~ 221 (236)
T PRK09392 172 LPYEKRVLASYLGMTPE---NLSRAF-AALASHGV-HVDGSAVTITDPAGLARFA 221 (236)
T ss_pred eeCCHHHHHHHhCCChh---HHHHHH-HHHHhCCe-EeeCCEEEEcCHHHHHHhh
Confidence 3445 799999998443 333333 33566668 55667888998 7888877
No 27
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=51.61 E-value=19 Score=26.45 Aligned_cols=46 Identities=15% Similarity=0.086 Sum_probs=32.8
Q ss_pred CHHHHhhhCCCCCCHHHHHHHHHHHhhhcCCCCCCCCCccccc-hhHHhhh
Q 044317 49 TSELGRFLNIPEPPRSETAKLITKFIKLNNRENPGMKKDLLGE-EKLKSLL 98 (123)
Q Consensus 49 S~eLa~fLG~~e~sR~evvk~lW~YIK~n~LQDp~nKr~I~cD-ekLk~LF 98 (123)
-.+||++||++..+ +..+-.-.++.++-+-+.++++++| ++|+++.
T Consensus 152 ~~~iA~~lG~tret----vsR~l~~l~~~g~I~~~~~~i~I~d~~~L~~~~ 198 (202)
T PRK13918 152 HDELAAAVGSVRET----VTKVIGELSREGYIRSGYGKIQLLDLKGLEELA 198 (202)
T ss_pred HHHHHHHhCccHHH----HHHHHHHHHHCCCEEcCCCEEEEECHHHHHHHH
Confidence 46899999975433 3334444567788777778899998 6787776
No 28
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=51.49 E-value=9.9 Score=25.88 Aligned_cols=21 Identities=24% Similarity=0.256 Sum_probs=17.1
Q ss_pred CHHHHhhhCCCCCCHHHHHHHHHHHhhh
Q 044317 49 TSELGRFLNIPEPPRSETAKLITKFIKL 76 (123)
Q Consensus 49 S~eLa~fLG~~e~sR~evvk~lW~YIK~ 76 (123)
-++|++-||+++. .||++|+.
T Consensus 22 Ge~La~~LgiSRt-------aVwK~Iq~ 42 (79)
T COG1654 22 GEKLAEELGISRT-------AVWKHIQQ 42 (79)
T ss_pred HHHHHHHHCccHH-------HHHHHHHH
Confidence 5789999998776 78888865
No 29
>PF08349 DUF1722: Protein of unknown function (DUF1722); InterPro: IPR013560 This domain of unknown function is found in bacteria and archaea and is homologous to the hypothetical protein ybgA from Escherichia coli.
Probab=48.01 E-value=13 Score=26.33 Aligned_cols=64 Identities=16% Similarity=0.084 Sum_probs=40.6
Q ss_pred HHhhhCC--CCCCHHHHHHHHHHHhhhcCCCCCCCCCccccchhHHhhhcCCCccCHHHHHHHHHhccCCCC
Q 044317 52 LGRFLNI--PEPPRSETAKLITKFIKLNNRENPGMKKDLLGEEKLKSLLSGKDRIGIPEIAKLLSGQFVKTG 121 (123)
Q Consensus 52 La~fLG~--~e~sR~evvk~lW~YIK~n~LQDp~nKr~I~cDekLk~LF~g~d~i~~~~i~klL~~Hl~k~~ 121 (123)
|.+.+-. +.-+...|...||.|+|.+= ++++|+.+. .+-+-+ ....|.+..+-.+|..|..+-+
T Consensus 38 l~~al~~~~~~~~~~Nvl~Hi~Gyfk~~l--s~~EK~~~~---~~i~~y-r~g~i~l~~~l~~L~~~~~ry~ 103 (117)
T PF08349_consen 38 LMEALSKPPTRGSHINVLQHIFGYFKKKL--SSEEKQHFL---DLIEDY-REGKIPLSVPLTLLKHLARRYP 103 (117)
T ss_pred HHHHHhcCCCchhHHHHHHHHHHHHHHhC--CHHHHHHHH---HHHHHH-HcCCccHHHHHHHHHHHHHHCC
Confidence 4444443 45788899999999999753 333333221 122333 4678888888888887776544
No 30
>KOG0542 consensus Predicted exonuclease [Replication, recombination and repair]
Probab=47.80 E-value=24 Score=29.55 Aligned_cols=55 Identities=13% Similarity=0.208 Sum_probs=43.4
Q ss_pred CCccccCCCCCHHHHhhh----CCC------CCCHHHHHHHHHHHhhhcCCCCCCCCCccccchh
Q 044317 39 GKTKSVAPSSTSELGRFL----NIP------EPPRSETAKLITKFIKLNNRENPGMKKDLLGEEK 93 (123)
Q Consensus 39 g~~kp~~~~LS~eLa~fL----G~~------e~sR~evvk~lW~YIK~n~LQDp~nKr~I~cDek 93 (123)
.|++.++...+|.|++|+ |+. -.+-++|++.+.++++.++|++.+-+--.+||..
T Consensus 98 eF~qYVrP~~np~LS~fC~~lTgI~Q~tVD~a~~f~~vl~~f~~Wlr~~~~~~k~~~~Afvtdg~ 162 (280)
T KOG0542|consen 98 EFHQYVRPVENPRLSDFCTSLTGIQQETVDEAPTFPQVLSEFDSWLRKDSLGDKNGKFAFVTDGD 162 (280)
T ss_pred HHHhhcCcccCchHHHHHHHhhCchHhhhccCCCHHHHHHHHHHHHHHhhcccccCceEEEeCch
Confidence 577777778889999885 653 3788999999999999999997644455778753
No 31
>PRK07639 acyl carrier protein; Provisional
Probab=46.71 E-value=32 Score=23.17 Aligned_cols=54 Identities=13% Similarity=0.065 Sum_probs=41.8
Q ss_pred CCHHHHHHHHHHHhhhcCCCCCCCCCccccchhHHhhhcCCCccCHHHHHHHHHhcc
Q 044317 61 PPRSETAKLITKFIKLNNRENPGMKKDLLGEEKLKSLLSGKDRIGIPEIAKLLSGQF 117 (123)
Q Consensus 61 ~sR~evvk~lW~YIK~n~LQDp~nKr~I~cDekLk~LF~g~d~i~~~~i~klL~~Hl 117 (123)
|+|.++...|-+.|.+.= ..+. -..|..|..|..=+ |-|++.+.++--.|..+|
T Consensus 1 M~~~ei~~~i~~il~e~l-~~~~-~~~i~~d~~l~edL-~lDSld~velv~~lE~~f 54 (86)
T PRK07639 1 MRREALKNAVLKIMEEKL-ELKN-VTHLEETMRLNEDL-YIDSVMMLQLIVYIEMDV 54 (86)
T ss_pred CCHHHHHHHHHHHHHHHh-CCCc-cccCCCCCCccccc-CCChHHHHHHHHHHHHHH
Confidence 678899999999888753 2221 13678999998878 899999999988887766
No 32
>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=46.46 E-value=15 Score=27.63 Aligned_cols=35 Identities=17% Similarity=0.117 Sum_probs=25.7
Q ss_pred CCCCHHHHhhhCCCCCCHHHHHHHHHHHhhhcCCC
Q 044317 46 PSSTSELGRFLNIPEPPRSETAKLITKFIKLNNRE 80 (123)
Q Consensus 46 ~~LS~eLa~fLG~~e~sR~evvk~lW~YIK~n~LQ 80 (123)
..-|+++.+.+.....-..-|-..+.+||++|+|.
T Consensus 158 ~iSST~IR~~~~~g~~~~~lvp~~V~~yI~~~~lY 192 (192)
T cd02165 158 NISSTEIRERLKNGKSIRYLLPPAVADYIKEHGLY 192 (192)
T ss_pred ccCHHHHHHHHHcCCChhHhCCHHHHHHHHHccCC
Confidence 34577777777654444566778899999999984
No 33
>PF12728 HTH_17: Helix-turn-helix domain
Probab=45.62 E-value=16 Score=21.57 Aligned_cols=27 Identities=15% Similarity=0.247 Sum_probs=21.0
Q ss_pred CHHHHhhhCCCCCCHHHHHHHHHHHhhhcCCCCC
Q 044317 49 TSELGRFLNIPEPPRSETAKLITKFIKLNNRENP 82 (123)
Q Consensus 49 S~eLa~fLG~~e~sR~evvk~lW~YIK~n~LQDp 82 (123)
.+|.+++||++.. .|+.+|+...+.-.
T Consensus 4 ~~e~a~~l~is~~-------tv~~~~~~g~i~~~ 30 (51)
T PF12728_consen 4 VKEAAELLGISRS-------TVYRWIRQGKIPPF 30 (51)
T ss_pred HHHHHHHHCcCHH-------HHHHHHHcCCCCeE
Confidence 3689999998655 68899998887554
No 34
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=44.05 E-value=22 Score=23.33 Aligned_cols=42 Identities=14% Similarity=0.139 Sum_probs=29.9
Q ss_pred CCCC-HHHHhhhCCCCCCHHHHHHHHHHHhhhcCCCCCCCCCc
Q 044317 46 PSST-SELGRFLNIPEPPRSETAKLITKFIKLNNRENPGMKKD 87 (123)
Q Consensus 46 ~~LS-~eLa~fLG~~e~sR~evvk~lW~YIK~n~LQDp~nKr~ 87 (123)
...+ .+|++.++++..+=+.+++.|++-==-....||+|+|.
T Consensus 35 ~~~~~~~la~~l~i~~~~vt~~l~~Le~~glv~r~~~~~DrR~ 77 (126)
T COG1846 35 GGITVKELAERLGLDRSTVTRLLKRLEDKGLIERLRDPEDRRA 77 (126)
T ss_pred CCCcHHHHHHHHCCCHHHHHHHHHHHHHCCCeeecCCccccce
Confidence 3346 89999999988888888888876322234467888764
No 35
>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=42.79 E-value=19 Score=18.81 Aligned_cols=20 Identities=35% Similarity=0.507 Sum_probs=16.8
Q ss_pred CHHHHHHHHHHHhhhcCCCC
Q 044317 62 PRSETAKLITKFIKLNNREN 81 (123)
Q Consensus 62 sR~evvk~lW~YIK~n~LQD 81 (123)
.+.++...|++|...+++.+
T Consensus 2 ~~~~l~~lI~~yL~~~g~~~ 21 (34)
T smart00667 2 SRSELNRLILEYLLRNGYEE 21 (34)
T ss_pred cHHHHHHHHHHHHHHcCHHH
Confidence 46788999999999998754
No 36
>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=42.13 E-value=19 Score=28.44 Aligned_cols=34 Identities=12% Similarity=0.093 Sum_probs=25.3
Q ss_pred CCCHHHHhhhCCCCCCHHHHHHHHHHHhhhcCCC
Q 044317 47 SSTSELGRFLNIPEPPRSETAKLITKFIKLNNRE 80 (123)
Q Consensus 47 ~LS~eLa~fLG~~e~sR~evvk~lW~YIK~n~LQ 80 (123)
--|+++.+-+.....-+..|-..+.+||++|+|.
T Consensus 192 ISST~IR~~l~~g~~~~~llp~~V~~YI~~~~LY 225 (225)
T cd09286 192 ISSTKVRRALRRGMSVKYLLPDPVIEYIEQHQLY 225 (225)
T ss_pred cChHHHHHHHHcCCCchhcCCHHHHHHHHHcCCC
Confidence 3467777777654455566888899999999984
No 37
>PRK08887 nicotinic acid mononucleotide adenylyltransferase; Provisional
Probab=41.97 E-value=22 Score=26.78 Aligned_cols=35 Identities=9% Similarity=0.069 Sum_probs=23.9
Q ss_pred CCHHHHhhhCCCCCCHHHHHHHHHHHhhhcCCCCC
Q 044317 48 STSELGRFLNIPEPPRSETAKLITKFIKLNNRENP 82 (123)
Q Consensus 48 LS~eLa~fLG~~e~sR~evvk~lW~YIK~n~LQDp 82 (123)
-|+++.+.+.....-+.-|-..+.+||++|+|.-+
T Consensus 138 SST~IR~~l~~g~~i~~lvp~~V~~yI~~~~LY~~ 172 (174)
T PRK08887 138 RSTDIRNALQNGKDISHLTTPGVARLLKEHQLYTE 172 (174)
T ss_pred CHHHHHHHHHcCCChhHhCCHHHHHHHHHccccCC
Confidence 35666666654333446677789999999999743
No 38
>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=39.78 E-value=33 Score=21.89 Aligned_cols=51 Identities=18% Similarity=0.223 Sum_probs=38.7
Q ss_pred HHHHHHHHHHhhhcCCCCCCCCCccccchhHHhhhcCCCccCHHHHHHHHHhccC
Q 044317 64 SETAKLITKFIKLNNRENPGMKKDLLGEEKLKSLLSGKDRIGIPEIAKLLSGQFV 118 (123)
Q Consensus 64 ~evvk~lW~YIK~n~LQDp~nKr~I~cDekLk~LF~g~d~i~~~~i~klL~~Hl~ 118 (123)
.++...|.++|.+.-=.+| ..|.+|..|..-+ |-|++.+-+|--.|..+|-
T Consensus 2 ~~i~~~l~~il~~~~~~~~---~~i~~~~~l~~dl-glDSl~~veli~~lE~~f~ 52 (77)
T TIGR00517 2 QEIFEKVKAIIKEQLNVDE---DQVTPDASFVEDL-GADSLDTVELVMALEEEFD 52 (77)
T ss_pred hHHHHHHHHHHHHHHCCCH---HHCCCCcchhhhc-CCcHHHHHHHHHHHHHHHC
Confidence 3567788888888522333 3588999998888 8999999999888887763
No 39
>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=39.29 E-value=31 Score=25.60 Aligned_cols=44 Identities=9% Similarity=0.249 Sum_probs=33.1
Q ss_pred CHHHHhhhCCCCCCHHHHHHHHHHHhhhcCCCCCCC-------CCccccchhHHhhhc
Q 044317 49 TSELGRFLNIPEPPRSETAKLITKFIKLNNRENPGM-------KKDLLGEEKLKSLLS 99 (123)
Q Consensus 49 S~eLa~fLG~~e~sR~evvk~lW~YIK~n~LQDp~n-------Kr~I~cDekLk~LF~ 99 (123)
.+|||+.+|.... -|-.+|++.+-....- -|.|+-|+..+..+.
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 4799999997654 4667888877654322 389999999999883
No 40
>PRK05883 acyl carrier protein; Validated
Probab=37.63 E-value=56 Score=22.24 Aligned_cols=56 Identities=7% Similarity=0.071 Sum_probs=44.6
Q ss_pred CCCCHHHHHHHHHHHhhhcCCCCCCCCCccccchhHHhhhcCCCccCHHHHHHHHHhccC
Q 044317 59 PEPPRSETAKLITKFIKLNNRENPGMKKDLLGEEKLKSLLSGKDRIGIPEIAKLLSGQFV 118 (123)
Q Consensus 59 ~e~sR~evvk~lW~YIK~n~LQDp~nKr~I~cDekLk~LF~g~d~i~~~~i~klL~~Hl~ 118 (123)
..++..+|...|-++|.+.==.|| ..|..|..|...+ |-|++.+.+|--.|..+|-
T Consensus 8 ~~~~~~~I~~~l~~iia~~l~v~~---~~I~~d~~l~~dl-g~DSL~~v~lv~~lE~~fg 63 (91)
T PRK05883 8 MTSSPSTVSATLLSILRDDLNVDL---TRVTPDARLVDDV-GLDSVAFAVGMVAIEERLG 63 (91)
T ss_pred CCCCHHHHHHHHHHHHHHHhCCCh---hhCCCCCchhhcc-CCChHHHHHHHHHHHHHHC
Confidence 357889999999999987632233 3689999999999 9999998888777877764
No 41
>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=37.25 E-value=24 Score=25.81 Aligned_cols=68 Identities=18% Similarity=0.210 Sum_probs=45.5
Q ss_pred CCHHHHhhhCCCC--CCHHHHHHHHHHHhhhcCCCCCCCCCccccc-----hhHHhhhcCCCccCHHHHHHHHHhcc
Q 044317 48 STSELGRFLNIPE--PPRSETAKLITKFIKLNNRENPGMKKDLLGE-----EKLKSLLSGKDRIGIPEIAKLLSGQF 117 (123)
Q Consensus 48 LS~eLa~fLG~~e--~sR~evvk~lW~YIK~n~LQDp~nKr~I~cD-----ekLk~LF~g~d~i~~~~i~klL~~Hl 117 (123)
+....++|+.... ..+.+++..|-+||..++..++++=...-.. ..+..+| |... .+.++-.-|+.++
T Consensus 89 v~~~~~~~l~~~~~~~~Q~~~L~~i~~~~~~~G~~~~~~l~~~pF~~~G~~~~~~~~F-g~~~-~l~~~~~~l~~~L 163 (164)
T PF08463_consen 89 VEEAFSKFLNQHQFNAEQREFLERILDYYAQNGIIEPEDLKEPPFSDLGGPGGIIRVF-GGKE-QLDEILNELNKNL 163 (164)
T ss_pred HHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHhCcccHHHhCCCchhhcCCHHHHHHHc-CCHH-HHHHHHHHHHhhc
Confidence 4556677786555 7788999999999999998886654444333 3477778 4433 5555555555554
No 42
>PRK08558 adenine phosphoribosyltransferase; Provisional
Probab=36.91 E-value=9.1 Score=30.59 Aligned_cols=32 Identities=13% Similarity=0.372 Sum_probs=24.0
Q ss_pred HHHHhhhCCCCCCHHHHHHHHHHHhhhcCCCCCCCCCcc
Q 044317 50 SELGRFLNIPEPPRSETAKLITKFIKLNNRENPGMKKDL 88 (123)
Q Consensus 50 ~eLa~fLG~~e~sR~evvk~lW~YIK~n~LQDp~nKr~I 88 (123)
.||++++|+++. .||.|++-+-|-..+.-+.|
T Consensus 27 ~el~~~~g~p~~-------~l~RYv~g~~~P~~~~a~~~ 58 (238)
T PRK08558 27 EELSSITGLPES-------VLNRYVNGHVLPSVERAREI 58 (238)
T ss_pred HHHHHHHCCCHH-------HHHHHHcCCcCCCHHHHHHH
Confidence 799999999876 78888887777555544443
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=36.87 E-value=20 Score=28.29 Aligned_cols=11 Identities=9% Similarity=0.344 Sum_probs=10.2
Q ss_pred HHHHHhhhcCC
Q 044317 69 LITKFIKLNNR 79 (123)
Q Consensus 69 ~lW~YIK~n~L 79 (123)
-||.||++|+|
T Consensus 172 dVw~Yi~~~~l 182 (226)
T TIGR02057 172 QVYQYLDAHNV 182 (226)
T ss_pred HHHHHHHHcCC
Confidence 58999999998
No 44
>KOG0747 consensus Putative NAD+-dependent epimerases [Carbohydrate transport and metabolism]
Probab=36.15 E-value=41 Score=28.76 Aligned_cols=48 Identities=21% Similarity=0.121 Sum_probs=36.0
Q ss_pred CCCCHHHHHHHHHHHhhhcCC-----------CC--CCCCCccccchhHHhhhcCCCccCHH
Q 044317 59 PEPPRSETAKLITKFIKLNNR-----------EN--PGMKKDLLGEEKLKSLLSGKDRIGIP 107 (123)
Q Consensus 59 ~e~sR~evvk~lW~YIK~n~L-----------QD--p~nKr~I~cDekLk~LF~g~d~i~~~ 107 (123)
.|+++.++++.+.++|..... +| -+|.|.-+|+|++| =++=+.++.+.
T Consensus 252 ~e~~~~~l~k~i~eli~~~~~~~~~~p~~~~v~dRp~nd~Ry~~~~eKik-~LGw~~~~p~~ 312 (331)
T KOG0747|consen 252 DEMRVIDLAKDICELFEKRLPNIDTEPFIFFVEDRPYNDLRYFLDDEKIK-KLGWRPTTPWE 312 (331)
T ss_pred chhhHHHHHHHHHHHHHHhccCCCCCCcceecCCCCcccccccccHHHHH-hcCCcccCcHH
Confidence 689999999999999998544 11 23558999999999 55235666654
No 45
>PF04492 Phage_rep_O: Bacteriophage replication protein O ; InterPro: IPR006497 This entry is represented by the N-terminal domain of Bacteriophage lambda, GpO. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.; GO: 0006260 DNA replication
Probab=34.54 E-value=53 Score=23.08 Aligned_cols=42 Identities=19% Similarity=0.249 Sum_probs=35.0
Q ss_pred cCCCCCccccCCCCCHHHHhhhCCCCCCHHHHHHHHHHHhhhcCC
Q 044317 35 AKAKGKTKSVAPSSTSELGRFLNIPEPPRSETAKLITKFIKLNNR 79 (123)
Q Consensus 35 r~~~g~~kp~~~~LS~eLa~fLG~~e~sR~evvk~lW~YIK~n~L 79 (123)
|+.-|++|+....-.+.+++..| .+|..|.+.+-..|+.+=|
T Consensus 43 RkTyG~nKk~d~Is~sq~~e~tg---~~~~~V~~al~~Li~~~vI 84 (100)
T PF04492_consen 43 RKTYGWNKKMDRISNSQIAEMTG---LSRDHVSKALNELIRRGVI 84 (100)
T ss_pred HHccCCCCccceeeHHHHHHHHC---cCHHHHHHHHHHHHHCCCE
Confidence 77889999987767778888888 7788999999998887655
No 46
>PF14838 INTS5_C: Integrator complex subunit 5 C-terminus
Probab=34.22 E-value=24 Score=32.97 Aligned_cols=44 Identities=16% Similarity=0.133 Sum_probs=28.6
Q ss_pred CCCHHHHhhhCC-CCCCHHHH---HH-HHHHHhhhcCCCCCCCCCccccchh
Q 044317 47 SSTSELGRFLNI-PEPPRSET---AK-LITKFIKLNNRENPGMKKDLLGEEK 93 (123)
Q Consensus 47 ~LS~eLa~fLG~-~e~sR~ev---vk-~lW~YIK~n~LQDp~nKr~I~cDek 93 (123)
.|.|+|+.+..+ +..+=.|| .. +||.|||+|. |..-.++.||+.
T Consensus 617 lLPppL~~~~el~~~ltp~Ei~~lL~~cIW~y~kdh~---Psp~~f~~~~~~ 665 (696)
T PF14838_consen 617 LLPPPLSYIHELFPYLTPHEIYLLLLSCIWNYMKDHV---PSPALFVFNDET 665 (696)
T ss_pred cCCchHHHHHHHHHhcCHHHHHHHHHHHHHHHHhhCC---CCHHHHhcCccc
Confidence 345666666553 34555554 33 4999999998 555567778876
No 47
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=33.95 E-value=43 Score=25.64 Aligned_cols=46 Identities=9% Similarity=0.093 Sum_probs=30.8
Q ss_pred CC-HHHHhhhCCCCCCHHHHHHHHHHHhhhcCCCCCCC-CCccccch-hHHhh
Q 044317 48 ST-SELGRFLNIPEPPRSETAKLITKFIKLNNRENPGM-KKDLLGEE-KLKSL 97 (123)
Q Consensus 48 LS-~eLa~fLG~~e~sR~evvk~lW~YIK~n~LQDp~n-Kr~I~cDe-kLk~L 97 (123)
++ .+||++||++..| +..+-.-.++.++-+-.. ++++++|. +|..+
T Consensus 180 lt~~~IA~~lGisret----lsR~L~~L~~~GlI~~~~~~~i~I~D~~~L~~l 228 (230)
T PRK09391 180 MSRRDIADYLGLTIET----VSRALSQLQDRGLIGLSGARQIELRNRQALRNL 228 (230)
T ss_pred CCHHHHHHHHCCCHHH----HHHHHHHHHHCCcEEecCCceEEEcCHHHHHHh
Confidence 44 7999999986543 333444567778777654 68888984 55544
No 48
>smart00581 PSP proline-rich domain in spliceosome associated proteins.
Probab=33.13 E-value=61 Score=20.79 Aligned_cols=19 Identities=26% Similarity=0.338 Sum_probs=16.1
Q ss_pred cccCCCCCHHHHhhhCCCCCC
Q 044317 42 KSVAPSSTSELGRFLNIPEPP 62 (123)
Q Consensus 42 kp~~~~LS~eLa~fLG~~e~s 62 (123)
+| ..||++|.+.||+.+-.
T Consensus 5 kP--G~lS~~LR~ALG~~~~~ 23 (54)
T smart00581 5 KP--GRISDELREALGLPPGQ 23 (54)
T ss_pred cC--CcCCHHHHHHcCCCCCC
Confidence 45 78999999999998754
No 49
>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=32.40 E-value=26 Score=26.70 Aligned_cols=12 Identities=17% Similarity=0.147 Sum_probs=10.7
Q ss_pred HHHHHHhhhcCC
Q 044317 68 KLITKFIKLNNR 79 (123)
Q Consensus 68 k~lW~YIK~n~L 79 (123)
..||.||++|||
T Consensus 135 ~dVw~Yi~~~~l 146 (191)
T TIGR02055 135 EDVWEYIADNEL 146 (191)
T ss_pred HHHHHHHHHcCC
Confidence 368999999998
No 50
>PF04046 PSP: PSP; InterPro: IPR006568 PSP is a proline-rich domain of unknown function found in spliceosome associated proteins.
Probab=32.37 E-value=52 Score=20.60 Aligned_cols=17 Identities=24% Similarity=0.233 Sum_probs=14.7
Q ss_pred CCCCHHHHhhhCCCCCC
Q 044317 46 PSSTSELGRFLNIPEPP 62 (123)
Q Consensus 46 ~~LS~eLa~fLG~~e~s 62 (123)
..||++|.+.||+.+-.
T Consensus 3 G~lS~~LR~ALg~~~~~ 19 (48)
T PF04046_consen 3 GKLSDELREALGMQEND 19 (48)
T ss_pred cccCHHHHHHcCCCCCC
Confidence 67999999999987754
No 51
>PRK12563 sulfate adenylyltransferase subunit 2; Provisional
Probab=32.17 E-value=25 Score=29.59 Aligned_cols=24 Identities=4% Similarity=-0.053 Sum_probs=17.1
Q ss_pred HHHHHhhhcCCC-----CCC-------CCCccccch
Q 044317 69 LITKFIKLNNRE-----NPG-------MKKDLLGEE 92 (123)
Q Consensus 69 ~lW~YIK~n~LQ-----Dp~-------nKr~I~cDe 92 (123)
-||.||+.|||- ... |...|.||+
T Consensus 203 DVW~YI~~~~IP~~pLY~~~~r~~~~~~g~~~~~~~ 238 (312)
T PRK12563 203 DVWQYIAREKIPLVPLYFAKRRPVVERDGLLIMVDD 238 (312)
T ss_pred HHHHHHHHcCCCCCcchhcCCCceEEECCeEEeccc
Confidence 689999999982 222 455677776
No 52
>PF08938 HBS1_N: HBS1 N-terminus; InterPro: IPR015033 This domain is found in various eukaryotic HBS1-like proteins. ; PDB: 1UFZ_A 3IZQ_1.
Probab=31.50 E-value=19 Score=23.90 Aligned_cols=25 Identities=12% Similarity=0.258 Sum_probs=18.7
Q ss_pred CHHHHhhhCCCCCCHHHHHHHHHHH
Q 044317 49 TSELGRFLNIPEPPRSETAKLITKF 73 (123)
Q Consensus 49 S~eLa~fLG~~e~sR~evvk~lW~Y 73 (123)
-+.+.+.||-...+..+|+.+||.|
T Consensus 32 l~~vr~~Lg~~~~~e~~i~eal~~~ 56 (79)
T PF08938_consen 32 LPQVREVLGDYVPPEEQIKEALWHY 56 (79)
T ss_dssp CCCHHHHCCCCC--CCHHHHHHHHT
T ss_pred HHHHHHHHcccCCCHHHHHHHHHHH
Confidence 4567788887555999999999987
No 53
>KOG3347 consensus Predicted nucleotide kinase/nuclear protein involved oxidative stress response [Nucleotide transport and metabolism]
Probab=31.44 E-value=47 Score=26.07 Aligned_cols=45 Identities=22% Similarity=0.207 Sum_probs=32.4
Q ss_pred CCCHHHHhhhCCCCCCHHHHHHHHHHHhhhcCCCC---CCCCCccccchhHHhhh
Q 044317 47 SSTSELGRFLNIPEPPRSETAKLITKFIKLNNREN---PGMKKDLLGEEKLKSLL 98 (123)
Q Consensus 47 ~LS~eLa~fLG~~e~sR~evvk~lW~YIK~n~LQD---p~nKr~I~cDekLk~LF 98 (123)
.++..||+.+|...+ .+=+|+|+|||++ .+=+..|+-++++.+-+
T Consensus 22 tl~~~lae~~~~~~i-------~isd~vkEn~l~~gyDE~y~c~i~DEdkv~D~L 69 (176)
T KOG3347|consen 22 TLAERLAEKTGLEYI-------EISDLVKENNLYEGYDEEYKCHILDEDKVLDEL 69 (176)
T ss_pred hHHHHHHHHhCCceE-------ehhhHHhhhcchhcccccccCccccHHHHHHHH
Confidence 358899999999887 6778999999975 34445566556655544
No 54
>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily. Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=30.99 E-value=44 Score=19.00 Aligned_cols=25 Identities=8% Similarity=0.236 Sum_probs=20.2
Q ss_pred CHHHHhhhCCCCCCHHHHHHHHHHHhhhcCCC
Q 044317 49 TSELGRFLNIPEPPRSETAKLITKFIKLNNRE 80 (123)
Q Consensus 49 S~eLa~fLG~~e~sR~evvk~lW~YIK~n~LQ 80 (123)
..++|+++|+++. .||.|+++-.|.
T Consensus 3 ~~e~a~~~gv~~~-------tlr~~~~~g~l~ 27 (49)
T cd04761 3 IGELAKLTGVSPS-------TLRYYERIGLLS 27 (49)
T ss_pred HHHHHHHHCcCHH-------HHHHHHHCCCCC
Confidence 3578899998876 789999888775
No 55
>PF13333 rve_2: Integrase core domain
Probab=30.77 E-value=54 Score=19.79 Aligned_cols=22 Identities=23% Similarity=0.270 Sum_probs=18.1
Q ss_pred CCCCCCHHHHHHHHHHHhhhcC
Q 044317 57 NIPEPPRSETAKLITKFIKLNN 78 (123)
Q Consensus 57 G~~e~sR~evvk~lW~YIK~n~ 78 (123)
+..-.|+.++...|++||.--|
T Consensus 14 ~~~~~t~eel~~~I~~YI~~yN 35 (52)
T PF13333_consen 14 RQKFKTREELKQAIDEYIDYYN 35 (52)
T ss_pred CcccchHHHHHHHHHHHHHHhc
Confidence 3355799999999999998864
No 56
>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=30.69 E-value=28 Score=18.71 Aligned_cols=17 Identities=24% Similarity=0.354 Sum_probs=13.1
Q ss_pred HHHHHHHHHhhhcCCCC
Q 044317 65 ETAKLITKFIKLNNREN 81 (123)
Q Consensus 65 evvk~lW~YIK~n~LQD 81 (123)
++-..||+|..++++.+
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 56778999999998753
No 57
>PRK07152 nadD putative nicotinate-nucleotide adenylyltransferase; Validated
Probab=30.23 E-value=28 Score=28.81 Aligned_cols=29 Identities=10% Similarity=0.023 Sum_probs=19.8
Q ss_pred CCHHHHhhhCCCCCCHHHHHHHHHHHhhhcCCCC
Q 044317 48 STSELGRFLNIPEPPRSETAKLITKFIKLNNREN 81 (123)
Q Consensus 48 LS~eLa~fLG~~e~sR~evvk~lW~YIK~n~LQD 81 (123)
-|+++.+.+.... |-..+++||++|+|..
T Consensus 157 SST~IR~~~~~~~-----vP~~V~~YI~~~~LY~ 185 (342)
T PRK07152 157 SSTKIRKGNLLGK-----LDPKVNDYINENFLYL 185 (342)
T ss_pred CHHHHHHHHHcCC-----CCHHHHHHHHHcCccc
Confidence 3555555554322 5667999999999983
No 58
>COG1057 NadD Nicotinic acid mononucleotide adenylyltransferase [Coenzyme metabolism]
Probab=29.30 E-value=39 Score=26.44 Aligned_cols=33 Identities=9% Similarity=0.034 Sum_probs=26.6
Q ss_pred CCHHHHhhhCCCCCCHHHHHHHHHHHhhhcCCC
Q 044317 48 STSELGRFLNIPEPPRSETAKLITKFIKLNNRE 80 (123)
Q Consensus 48 LS~eLa~fLG~~e~sR~evvk~lW~YIK~n~LQ 80 (123)
-|++..+.+....-....+-..+.+||.+++|+
T Consensus 163 SSt~IR~~~~~~~~~~~llP~~V~~YI~~~~LY 195 (197)
T COG1057 163 SSTEIRERIRRGASVDYLLPDSVLSYIEERGLY 195 (197)
T ss_pred chHHHHHHHhCCCCchhcCCHHHHHHHHHhccc
Confidence 466777777766667777888999999999996
No 59
>PF13867 SAP30_Sin3_bdg: Sin3 binding region of histone deacetylase complex subunit SAP30; PDB: 2LD7_A.
Probab=28.96 E-value=98 Score=19.16 Aligned_cols=33 Identities=12% Similarity=0.179 Sum_probs=19.8
Q ss_pred HHHHHHhhhcCCCCCCCCCccccchhHHhhhcCCCccCHHHHHHHHHhccCC
Q 044317 68 KLITKFIKLNNRENPGMKKDLLGEEKLKSLLSGKDRIGIPEIAKLLSGQFVK 119 (123)
Q Consensus 68 k~lW~YIK~n~LQDp~nKr~I~cDekLk~LF~g~d~i~~~~i~klL~~Hl~k 119 (123)
..||.|-+.++|+.- ++++-.+|...+..||..
T Consensus 4 ~tLrrY~~~~~l~~~-------------------~~~sK~qLa~~V~kHF~s 36 (53)
T PF13867_consen 4 PTLRRYKKHYKLPER-------------------PRSSKEQLANAVRKHFNS 36 (53)
T ss_dssp HHHHHHHHHTT-----------------------SS--HHHHHHHHHHHHTT
T ss_pred HHHHHHHHHhCCCCC-------------------CCCCHHHHHHHHHHHHhc
Confidence 467999998888642 245556777777777754
No 60
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=28.77 E-value=44 Score=25.38 Aligned_cols=46 Identities=9% Similarity=0.079 Sum_probs=30.1
Q ss_pred CHHHHhhhCCCCCCHHHHHHHHHHHhhhcCCCCCCCCCccccc-hhHHhhh
Q 044317 49 TSELGRFLNIPEPPRSETAKLITKFIKLNNRENPGMKKDLLGE-EKLKSLL 98 (123)
Q Consensus 49 S~eLa~fLG~~e~sR~evvk~lW~YIK~n~LQDp~nKr~I~cD-ekLk~LF 98 (123)
-.+||++||++..+=+.+++. .+++++-....+++.++| +.|..+.
T Consensus 172 ~~~lA~~lG~sretvsR~L~~----L~~~G~I~~~~~~i~I~d~~~L~~~~ 218 (226)
T PRK10402 172 HTQAAEYLGVSYRHLLYVLAQ----FIQDGYLKKSKRGYLIKNRKQLSGLA 218 (226)
T ss_pred HHHHHHHHCCcHHHHHHHHHH----HHHCCCEEeeCCEEEEeCHHHHHHHH
Confidence 378999999754433333333 356677677778899998 4566554
No 61
>PF13401 AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S_B.
Probab=28.37 E-value=76 Score=21.22 Aligned_cols=41 Identities=17% Similarity=0.114 Sum_probs=30.7
Q ss_pred CCHHHHhhhCCCC---CCHHHHHHHHHHHhhhcCCCCCCCCCccccchhH
Q 044317 48 STSELGRFLNIPE---PPRSETAKLITKFIKLNNRENPGMKKDLLGEEKL 94 (123)
Q Consensus 48 LS~eLa~fLG~~e---~sR~evvk~lW~YIK~n~LQDp~nKr~I~cDekL 94 (123)
+-.++++.++... .+..++...+|++++.++- ..|+.||-=
T Consensus 54 ~~~~i~~~l~~~~~~~~~~~~l~~~~~~~l~~~~~------~~lviDe~~ 97 (131)
T PF13401_consen 54 FAQEILEALGLPLKSRQTSDELRSLLIDALDRRRV------VLLVIDEAD 97 (131)
T ss_dssp HHHHHHHHHT-SSSSTS-HHHHHHHHHHHHHHCTE------EEEEEETTH
T ss_pred HHHHHHHHhCccccccCCHHHHHHHHHHHHHhcCC------eEEEEeChH
Confidence 3566777777543 5689999999999999985 688888763
No 62
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=28.13 E-value=47 Score=25.02 Aligned_cols=45 Identities=13% Similarity=0.205 Sum_probs=30.8
Q ss_pred HHHHhhhCCCCCCHHHHHHHHHHHhhhcCCCCCCCCCccccc-hhHHhhh
Q 044317 50 SELGRFLNIPEPPRSETAKLITKFIKLNNRENPGMKKDLLGE-EKLKSLL 98 (123)
Q Consensus 50 ~eLa~fLG~~e~sR~evvk~lW~YIK~n~LQDp~nKr~I~cD-ekLk~LF 98 (123)
.+||++||++. ..|.+.+ .=.++.++-.-..+++++.| +.|..+.
T Consensus 188 ~~iA~~lG~sr---~tvsR~l-~~l~~~g~I~~~~~~i~i~d~~~L~~~~ 233 (235)
T PRK11161 188 GDIGNYLGLTV---ETISRLL-GRFQKSGMLAVKGKYITIENNDALAQLA 233 (235)
T ss_pred HHHHHHhCCcH---HHHHHHH-HHHHHCCCEEecCCEEEEcCHHHHHHHh
Confidence 79999999754 3444433 34567777777777888887 5666654
No 63
>PRK00982 acpP acyl carrier protein; Provisional
Probab=27.36 E-value=62 Score=20.52 Aligned_cols=49 Identities=20% Similarity=0.249 Sum_probs=37.6
Q ss_pred HHHHHHHHHhhhcCCCCCCCCCccccchhHHhhhcCCCccCHHHHHHHHHhcc
Q 044317 65 ETAKLITKFIKLNNRENPGMKKDLLGEEKLKSLLSGKDRIGIPEIAKLLSGQF 117 (123)
Q Consensus 65 evvk~lW~YIK~n~LQDp~nKr~I~cDekLk~LF~g~d~i~~~~i~klL~~Hl 117 (123)
++...|+++|.+.= .-+ ...|..|..|..-+ |-|++.+-+|-..|...|
T Consensus 3 ~i~~~l~~~l~~~l-~~~--~~~i~~d~~l~~dl-glDSl~~~~li~~le~~f 51 (78)
T PRK00982 3 EIFEKVKKIIVEQL-GVD--EEEVTPEASFVDDL-GADSLDTVELVMALEEEF 51 (78)
T ss_pred HHHHHHHHHHHHHH-CCC--HHHCCCCcchHhhc-CCCHHHHHHHHHHHHHHH
Confidence 56778888887643 332 34688999997778 899999999988887776
No 64
>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=27.33 E-value=16 Score=29.37 Aligned_cols=38 Identities=18% Similarity=0.239 Sum_probs=28.8
Q ss_pred HHHHhhhcCCCCCCCCCccccchhHHhhhcCCCccCHHHH
Q 044317 70 ITKFIKLNNRENPGMKKDLLGEEKLKSLLSGKDRIGIPEI 109 (123)
Q Consensus 70 lW~YIK~n~LQDp~nKr~I~cDekLk~LF~g~d~i~~~~i 109 (123)
+-+-+|+|+|.||++=..+- -.+|+++| |-|-+=|-.|
T Consensus 77 vde~fkqnGlt~~~~i~~v~-~~kL~eiF-GADAvLY~~I 114 (215)
T PF05643_consen 77 VDETFKQNGLTDAEDIHAVP-PAKLREIF-GADAVLYITI 114 (215)
T ss_pred HHHHHHHcCCCCHHHhccCC-HHHHHHHh-CCCEEEEEEE
Confidence 34456899999999875554 68999999 8887655444
No 65
>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=26.66 E-value=62 Score=20.84 Aligned_cols=21 Identities=24% Similarity=0.466 Sum_probs=15.6
Q ss_pred HHHHHHHHHHHhhhcCCCCCCC
Q 044317 63 RSETAKLITKFIKLNNRENPGM 84 (123)
Q Consensus 63 R~evvk~lW~YIK~n~LQDp~n 84 (123)
+.+|...|.+||.+|+. -|.-
T Consensus 8 Q~~vL~~I~~~~~~~G~-~Pt~ 28 (65)
T PF01726_consen 8 QKEVLEFIREYIEENGY-PPTV 28 (65)
T ss_dssp HHHHHHHHHHHHHHHSS----H
T ss_pred HHHHHHHHHHHHHHcCC-CCCH
Confidence 67899999999999994 3543
No 66
>PRK05253 sulfate adenylyltransferase subunit 2; Provisional
Probab=26.56 E-value=36 Score=28.23 Aligned_cols=11 Identities=27% Similarity=0.256 Sum_probs=10.2
Q ss_pred HHHHHhhhcCC
Q 044317 69 LITKFIKLNNR 79 (123)
Q Consensus 69 ~lW~YIK~n~L 79 (123)
-||.||+.++|
T Consensus 193 DIw~Yi~~~~I 203 (301)
T PRK05253 193 DIWQYIERENI 203 (301)
T ss_pred HHHHHHHHcCC
Confidence 68999999998
No 67
>smart00153 VHP Villin headpiece domain.
Probab=26.50 E-value=26 Score=20.49 Aligned_cols=26 Identities=15% Similarity=0.293 Sum_probs=21.0
Q ss_pred ccchhHHhhhcCCCccCHHHHHHHHHh
Q 044317 89 LGEEKLKSLLSGKDRIGIPEIAKLLSG 115 (123)
Q Consensus 89 ~cDekLk~LF~g~d~i~~~~i~klL~~ 115 (123)
+.|+....+| |..+-.|..||++=..
T Consensus 2 LsdeeF~~vf-gmsr~eF~~LP~WKq~ 27 (36)
T smart00153 2 LSDEDFEEVF-GMTREEFYKLPLWKQN 27 (36)
T ss_pred CCHHHHHHHH-CCCHHHHHhCcHhhHH
Confidence 4689999999 8888888888876443
No 68
>PLN02309 5'-adenylylsulfate reductase
Probab=26.27 E-value=41 Score=29.71 Aligned_cols=12 Identities=8% Similarity=0.213 Sum_probs=11.0
Q ss_pred HHHHHHhhhcCC
Q 044317 68 KLITKFIKLNNR 79 (123)
Q Consensus 68 k~lW~YIK~n~L 79 (123)
..||.||++|+|
T Consensus 261 ~dVw~Yi~~~~l 272 (457)
T PLN02309 261 NEVWNFLRTMDV 272 (457)
T ss_pred HHHHHHHHHcCC
Confidence 479999999999
No 69
>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=24.87 E-value=1.3e+02 Score=19.74 Aligned_cols=41 Identities=12% Similarity=0.047 Sum_probs=29.9
Q ss_pred CHHHHhhh--CCCCCCHHHHHHHHHHHhhhcCCCCCCCCCccccchhHHhhh
Q 044317 49 TSELGRFL--NIPEPPRSETAKLITKFIKLNNRENPGMKKDLLGEEKLKSLL 98 (123)
Q Consensus 49 S~eLa~fL--G~~e~sR~evvk~lW~YIK~n~LQDp~nKr~I~cDekLk~LF 98 (123)
++++.+++ +--++|+.++...+-. |+++.+..|++.+-.-|
T Consensus 16 d~~m~~if~l~~~~vs~~el~a~lrk---------e~~~~y~~c~D~~L~~F 58 (68)
T PF07308_consen 16 DDDMIEIFALAGFEVSKAELSAWLRK---------EDEKGYKECSDQLLRNF 58 (68)
T ss_pred hHHHHHHHHHcCCccCHHHHHHHHCC---------CCCccccccChHHHHHH
Confidence 45677775 4578999988876644 77788999987766665
No 70
>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=24.73 E-value=49 Score=25.17 Aligned_cols=13 Identities=23% Similarity=0.324 Sum_probs=10.9
Q ss_pred HHHHHHhhhcCCC
Q 044317 68 KLITKFIKLNNRE 80 (123)
Q Consensus 68 k~lW~YIK~n~LQ 80 (123)
..||+||.+++|-
T Consensus 156 ~dVw~Yi~~~~lp 168 (212)
T TIGR00434 156 KDVYQYIDAHNLP 168 (212)
T ss_pred HHHHHHHHHcCCC
Confidence 3579999999984
No 71
>COG5577 Spore coat protein [Cell envelope biogenesis, outer membrane]
Probab=24.57 E-value=47 Score=25.10 Aligned_cols=36 Identities=19% Similarity=0.126 Sum_probs=27.5
Q ss_pred CHHHHhhhCCCCCCHHHHHHHHHHHhhhcCCCCCCC
Q 044317 49 TSELGRFLNIPEPPRSETAKLITKFIKLNNRENPGM 84 (123)
Q Consensus 49 S~eLa~fLG~~e~sR~evvk~lW~YIK~n~LQDp~n 84 (123)
||+|..+|-..-..=.+--+.||+|...|+-.-|.+
T Consensus 86 tP~lR~vL~~~l~~~i~~~~~v~~ym~~~g~Y~py~ 121 (145)
T COG5577 86 TPELRAVLKDQLNQAIEMHKEVSEYMVQKGYYPPYN 121 (145)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCcCCCC
Confidence 677777776544444456789999999999988876
No 72
>PF13758 Prefoldin_3: Prefoldin subunit
Probab=24.00 E-value=1.3e+02 Score=21.52 Aligned_cols=29 Identities=14% Similarity=0.361 Sum_probs=22.3
Q ss_pred CHHHHhhhCCCC---CCHHHHHHHH---HHHhhhc
Q 044317 49 TSELGRFLNIPE---PPRSETAKLI---TKFIKLN 77 (123)
Q Consensus 49 S~eLa~fLG~~e---~sR~evvk~l---W~YIK~n 77 (123)
-.|+..+||... -|+.+|+..| .+||++|
T Consensus 49 ~kEi~~ilG~~~~i~Rt~~Qvv~~l~RRiDYV~~N 83 (99)
T PF13758_consen 49 EKEIKEILGEGQGITRTREQVVDVLSRRIDYVQQN 83 (99)
T ss_pred HHHHHHHhCCCCCCCcCHHHHHHHHHHHHHHHHHH
Confidence 578999999754 4788877766 6788876
No 73
>PF06039 Mqo: Malate:quinone oxidoreductase (Mqo); InterPro: IPR006231 The membrane-associated enzyme, malate:quinone-oxidoreductase, is an alternative to the better-known NAD-dependent malate dehydrogenase as part of the TCA cycle. The reduction of a quinone rather than NAD+ makes the reaction essentially irreversible in the direction of malate oxidation to oxaloacetate. Both forms of malate dehydrogenase are active in Escherichia coli; disruption of this form causes less phenotypic change. In some bacteria, this form is the only or the more important malate dehydrogenase []. ; GO: 0008924 malate dehydrogenase (quinone) activity, 0006099 tricarboxylic acid cycle, 0055114 oxidation-reduction process
Probab=23.62 E-value=31 Score=31.02 Aligned_cols=53 Identities=11% Similarity=0.162 Sum_probs=35.8
Q ss_pred CCHHHHHHHHHHHhhhcC-CCCCCCCCccccchhHHhhhcCCCccCHH-HHHHHHHhc
Q 044317 61 PPRSETAKLITKFIKLNN-RENPGMKKDLLGEEKLKSLLSGKDRIGIP-EIAKLLSGQ 116 (123)
Q Consensus 61 ~sR~evvk~lW~YIK~n~-LQDp~nKr~I~cDekLk~LF~g~d~i~~~-~i~klL~~H 116 (123)
..+.+|.+.+|.|.-+++ |+||+ .+|+.-+.+-=++ |.+.|.|- .=.+.|+.|
T Consensus 81 neqFevsrqfWs~lv~~g~l~~p~--~FI~~~PHmsfv~-Ge~~v~fLkkR~~~l~~~ 135 (488)
T PF06039_consen 81 NEQFEVSRQFWSYLVENGILQNPE--SFINPVPHMSFVW-GEENVDFLKKRYEALKEH 135 (488)
T ss_pred HHHHHHHHHHHHHHHHCCCCCChH--HhccCCCceEEEE-ChHhHHHHHHHHHHHhcC
Confidence 457899999999998776 56674 5777777776666 66666654 233444443
No 74
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=23.22 E-value=1.3e+02 Score=18.25 Aligned_cols=24 Identities=4% Similarity=0.178 Sum_probs=18.4
Q ss_pred HHHHhhhCCCCCCHHHHHHHHHHHhhhcCCC
Q 044317 50 SELGRFLNIPEPPRSETAKLITKFIKLNNRE 80 (123)
Q Consensus 50 ~eLa~fLG~~e~sR~evvk~lW~YIK~n~LQ 80 (123)
.++++.+|+++. .|+.|+++.-+.
T Consensus 4 ~eva~~~gvs~~-------tlr~~~~~gli~ 27 (70)
T smart00422 4 GEVAKLAGVSVR-------TLRYYERIGLLP 27 (70)
T ss_pred HHHHHHHCcCHH-------HHHHHHHCCCCC
Confidence 578889998876 788888865553
No 75
>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=23.06 E-value=46 Score=27.68 Aligned_cols=11 Identities=27% Similarity=0.274 Sum_probs=10.3
Q ss_pred HHHHHhhhcCC
Q 044317 69 LITKFIKLNNR 79 (123)
Q Consensus 69 ~lW~YIK~n~L 79 (123)
-||.||..+||
T Consensus 185 DVW~YI~~~~I 195 (294)
T TIGR02039 185 DIWRYIAAENI 195 (294)
T ss_pred HHHHHHHHcCC
Confidence 68999999998
No 76
>KOG4144 consensus Arylalkylamine N-acetyltransferase [General function prediction only]
Probab=22.74 E-value=46 Score=26.22 Aligned_cols=33 Identities=9% Similarity=0.171 Sum_probs=27.4
Q ss_pred HHHHHHHHhhhcCCCCCCCCCccccchhHHhhh
Q 044317 66 TAKLITKFIKLNNRENPGMKKDLLGEEKLKSLL 98 (123)
Q Consensus 66 vvk~lW~YIK~n~LQDp~nKr~I~cDekLk~LF 98 (123)
....||+|+.--.=|.-.+|-..+|.+.|-...
T Consensus 119 a~~Ll~~ylq~l~~q~i~~r~~Li~h~pLvPFY 151 (190)
T KOG4144|consen 119 APILLWRYLQHLGSQPIVRRAALICHDPLVPFY 151 (190)
T ss_pred chhHHHHHHHHhhcCccccceeeeecCCccchh
Confidence 356899999998888888888899999987654
No 77
>cd04763 HTH_MlrA-like Helix-Turn-Helix DNA binding domain of MlrA-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A) and related proteins, 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-like proteins in this group appear to lack the long dimerization helix seen
Probab=22.68 E-value=1.6e+02 Score=18.13 Aligned_cols=27 Identities=11% Similarity=0.149 Sum_probs=20.4
Q ss_pred CHHHHhhhCCCCCCHHHHHHHHHHHhhhcCCCCC
Q 044317 49 TSELGRFLNIPEPPRSETAKLITKFIKLNNRENP 82 (123)
Q Consensus 49 S~eLa~fLG~~e~sR~evvk~lW~YIK~n~LQDp 82 (123)
..++|+.+|+++- .|+.|.++-+|..|
T Consensus 3 i~e~A~~~gVs~~-------tlr~ye~~~gl~~~ 29 (68)
T cd04763 3 IGEVALLTGIKPH-------VLRAWEREFGLLKP 29 (68)
T ss_pred HHHHHHHHCcCHH-------HHHHHHHhcCCCCC
Confidence 4688999999876 78888777567654
No 78
>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=22.32 E-value=58 Score=23.07 Aligned_cols=14 Identities=21% Similarity=0.238 Sum_probs=10.2
Q ss_pred HHHHHHHhhhcCCC
Q 044317 67 AKLITKFIKLNNRE 80 (123)
Q Consensus 67 vk~lW~YIK~n~LQ 80 (123)
..-||+||+.++|.
T Consensus 141 ~~dV~~yi~~~~l~ 154 (174)
T PF01507_consen 141 EEDVWDYIKANGLP 154 (174)
T ss_dssp HHHHHHHHHHHT--
T ss_pred HHHHHHHHHHhcCC
Confidence 34689999999983
No 79
>TIGR01510 coaD_prev_kdtB pantetheine-phosphate adenylyltransferase, bacterial. This model describes pantetheine-phosphate adenylyltransferase, the penultimate enzyme of coenzyme A (CoA) biosynthesis in bacteria. It does not show any strong homology to eukaryotic enzymes of coenzyme A biosynthesis. This protein was previously designated KdtB and postulated (because of cytidyltransferase homology and proximity to kdtA) to be an enzyme of LPS biosynthesis, a cytidyltransferase for 3-deoxy-D-manno-2-octulosonic acid. However, no activity toward that compound was found with either CTP or ATP. The phylogenetic distribution of this enzyme is more consistent with coenzyme A biosynthesis than with LPS biosynthesis.
Probab=22.22 E-value=59 Score=23.81 Aligned_cols=31 Identities=10% Similarity=0.058 Sum_probs=24.5
Q ss_pred CCCHHHHhhhCCCCCCHHHHHHHHHHHhhhc
Q 044317 47 SSTSELGRFLNIPEPPRSETAKLITKFIKLN 77 (123)
Q Consensus 47 ~LS~eLa~fLG~~e~sR~evvk~lW~YIK~n 77 (123)
.-|+++.+.+.....-+.-|=..+++||++|
T Consensus 124 iSST~IR~~i~~g~~~~~lvP~~V~~YI~~~ 154 (155)
T TIGR01510 124 VSSSLVKEIASFGGDVSNLVPPAVARRLKAK 154 (155)
T ss_pred ccHHHHHHHHHcCCChhHHCCHHHHHHHHHh
Confidence 4577788888766666778888999999986
No 80
>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=22.13 E-value=1e+02 Score=18.43 Aligned_cols=18 Identities=11% Similarity=0.183 Sum_probs=16.1
Q ss_pred CCCCHHHHHHHHHHHhhh
Q 044317 59 PEPPRSETAKLITKFIKL 76 (123)
Q Consensus 59 ~e~sR~evvk~lW~YIK~ 76 (123)
...++.+|+....+||+.
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 459999999999999985
No 81
>PF03511 Fanconi_A: Fanconi anaemia group A protein; InterPro: IPR003516 Fanconi anaemia (FA) [, , ] is a recessive inherited disease characterised by defective DNA repair. FA cells are sensitive to DNA cross-linking agents that cause chromosomal instability and cell death. The disease is manifested clinically by progressive pancytopenia, variable physical anomalies, and predisposition to malignancy []. Four complementation groups have been identified, designated A to D. The FA group A gene (FAA) has been cloned [], but its function remains to be elucidated.
Probab=21.97 E-value=89 Score=20.76 Aligned_cols=16 Identities=19% Similarity=0.171 Sum_probs=14.2
Q ss_pred HHHHHHHHHhccCCCC
Q 044317 106 IPEIAKLLSGQFVKTG 121 (123)
Q Consensus 106 ~~~i~klL~~Hl~k~~ 121 (123)
||.++.+|+.|+...+
T Consensus 10 FFSLM~LlSs~l~p~~ 25 (64)
T PF03511_consen 10 FFSLMGLLSSYLAPKE 25 (64)
T ss_pred HHHHHHHHHHhcCccc
Confidence 8999999999998764
No 82
>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=21.84 E-value=56 Score=28.94 Aligned_cols=11 Identities=9% Similarity=0.172 Sum_probs=10.2
Q ss_pred HHHHHhhhcCC
Q 044317 69 LITKFIKLNNR 79 (123)
Q Consensus 69 ~lW~YIK~n~L 79 (123)
.||.||++|+|
T Consensus 267 dVw~Yi~~~~L 277 (463)
T TIGR00424 267 DVWNFLRTMDV 277 (463)
T ss_pred HHHHHHHHcCC
Confidence 39999999999
No 83
>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=21.08 E-value=48 Score=18.64 Aligned_cols=10 Identities=10% Similarity=0.395 Sum_probs=8.1
Q ss_pred HHhhhcCCCC
Q 044317 72 KFIKLNNREN 81 (123)
Q Consensus 72 ~YIK~n~LQD 81 (123)
.||++|+|-+
T Consensus 9 rYV~eh~ls~ 18 (28)
T PF12368_consen 9 RYVKEHGLSE 18 (28)
T ss_pred hhHHhcCCCH
Confidence 5999999854
No 84
>COG0175 CysH 3'-phosphoadenosine 5'-phosphosulfate sulfotransferase (PAPS reductase)/FAD synthetase and related enzymes [Amino acid transport and metabolism / Coenzyme metabolism]
Probab=20.91 E-value=54 Score=26.37 Aligned_cols=12 Identities=25% Similarity=0.075 Sum_probs=10.6
Q ss_pred HHHHHHhhhcCC
Q 044317 68 KLITKFIKLNNR 79 (123)
Q Consensus 68 k~lW~YIK~n~L 79 (123)
..||.||..|||
T Consensus 183 ~dVw~Yi~~~~l 194 (261)
T COG0175 183 LDVWLYILANNL 194 (261)
T ss_pred HHHHHHHHHhCC
Confidence 368999999998
No 85
>TIGR01889 Staph_reg_Sar staphylococcal accessory regulator family. This model represents a family of transcriptional regulatory proteins in Staphylococcus aureus and Staphylococcus epidermidis. Some members contain two tandem copies of this region. This family is related to the MarR transcriptional regulator family described by pfam model pfam01047.
Probab=20.82 E-value=79 Score=21.64 Aligned_cols=37 Identities=11% Similarity=0.139 Sum_probs=21.1
Q ss_pred HHHHhhhCCCCCCHHHHHHHHHHHhhh---cCCCCCCCCCccc
Q 044317 50 SELGRFLNIPEPPRSETAKLITKFIKL---NNRENPGMKKDLL 89 (123)
Q Consensus 50 ~eLa~fLG~~e~sR~evvk~lW~YIK~---n~LQDp~nKr~I~ 89 (123)
.+|++.++.+..+=+.+++.| ++. ....||+|+|.+.
T Consensus 47 ~eL~~~l~~~~stvs~~i~~L---e~kg~I~r~~~~~D~R~~~ 86 (109)
T TIGR01889 47 KEIIKEILIKQSALVKIIKKL---SKKGYLSKERSEDDERKVI 86 (109)
T ss_pred HHHHHHHCCCHHHHHHHHHHH---HHCCCEeccCCcccCCeEE
Confidence 467777766544444444443 333 2336899988753
Done!