Query 021906
Match_columns 305
No_of_seqs 312 out of 839
Neff 5.6
Searched_HMMs 46136
Date Fri Mar 29 06:33:39 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/021906.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/021906hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1946 RNA polymerase I trans 100.0 1.1E-31 2.4E-36 246.9 11.7 182 1-222 1-182 (240)
2 COG5531 SWIB-domain-containing 99.9 1.4E-26 3.1E-31 211.9 6.8 193 7-219 7-200 (237)
3 PF02201 SWIB: SWIB/MDM2 domai 99.9 1.5E-26 3.3E-31 178.5 0.7 75 140-214 1-75 (76)
4 smart00151 SWIB SWI complex, B 99.9 4.3E-25 9.3E-30 170.8 7.7 76 141-216 2-77 (77)
5 PRK14724 DNA topoisomerase III 99.8 2.5E-20 5.4E-25 200.5 8.0 77 139-215 911-987 (987)
6 KOG2570 SWI/SNF transcription 99.7 1.3E-18 2.8E-23 169.1 6.0 83 141-223 206-288 (420)
7 PF08766 DEK_C: DEK C terminal 99.6 2.6E-15 5.6E-20 108.7 6.1 54 3-56 1-54 (54)
8 KOG1946 RNA polymerase I trans 99.5 6.6E-14 1.4E-18 129.4 6.2 48 255-304 96-143 (240)
9 PRK06319 DNA topoisomerase I/S 99.4 1.9E-13 4.1E-18 146.1 5.5 74 142-215 786-859 (860)
10 PF02201 SWIB: SWIB/MDM2 domai 99.4 1.3E-13 2.8E-18 106.4 1.6 44 259-304 1-44 (76)
11 smart00151 SWIB SWI complex, B 99.4 8.2E-13 1.8E-17 102.2 5.1 44 259-304 1-44 (77)
12 COG5531 SWIB-domain-containing 99.2 1.1E-11 2.3E-16 114.3 4.9 47 256-304 118-164 (237)
13 PRK14724 DNA topoisomerase III 98.9 5.8E-10 1.2E-14 121.0 5.2 45 258-304 911-955 (987)
14 KOG2266 Chromatin-associated p 98.9 2.4E-09 5.2E-14 106.3 6.1 60 1-60 519-578 (594)
15 KOG2570 SWI/SNF transcription 97.9 8E-06 1.7E-10 80.5 3.8 41 262-304 208-248 (420)
16 PRK06319 DNA topoisomerase I/S 97.9 6.5E-06 1.4E-10 88.8 2.9 44 259-304 784-827 (860)
17 PF09312 SurA_N: SurA N-termin 75.3 4.6 0.0001 33.2 4.2 46 2-51 67-112 (118)
18 PRK05350 acyl carrier protein; 73.9 2.9 6.3E-05 32.1 2.5 54 159-215 2-55 (82)
19 KOG2522 Filamentous baseplate 72.0 6.9 0.00015 40.0 5.2 60 157-216 380-448 (560)
20 PRK05828 acyl carrier protein; 66.2 22 0.00048 27.8 6.0 52 3-54 2-75 (84)
21 PRK05828 acyl carrier protein; 64.3 9.4 0.0002 29.9 3.6 54 159-215 1-54 (84)
22 PF13565 HTH_32: Homeodomain-l 57.3 25 0.00054 25.9 4.7 35 4-40 32-66 (77)
23 PRK12449 acyl carrier protein; 56.2 17 0.00038 27.3 3.7 54 159-215 1-54 (80)
24 PF02881 SRP54_N: SRP54-type p 56.1 50 0.0011 24.4 6.2 42 5-46 24-67 (75)
25 CHL00124 acpP acyl carrier pro 55.1 11 0.00023 28.6 2.4 54 159-215 1-54 (82)
26 PF00538 Linker_histone: linke 47.4 62 0.0014 24.5 5.6 44 13-56 12-57 (77)
27 PTZ00171 acyl carrier protein; 45.9 23 0.0005 30.8 3.3 58 155-215 62-119 (148)
28 PRK05350 acyl carrier protein; 41.0 48 0.001 25.2 4.1 43 1-43 1-61 (82)
29 PF00550 PP-binding: Phosphopa 38.8 58 0.0013 23.0 4.1 39 5-43 1-52 (67)
30 PF03705 CheR_N: CheR methyltr 37.8 70 0.0015 22.3 4.3 31 26-56 6-37 (57)
31 smart00526 H15 Domain in histo 37.3 1.3E+02 0.0027 22.0 5.7 44 12-55 13-56 (66)
32 PF13699 DUF4157: Domain of un 35.7 28 0.0006 27.0 2.0 23 26-48 4-26 (79)
33 PRK07117 acyl carrier protein; 32.7 44 0.00096 25.8 2.7 53 159-215 1-54 (79)
34 PF09357 RteC: RteC protein; 32.4 1.9E+02 0.0041 26.7 7.2 56 3-58 143-214 (218)
35 cd04762 HTH_MerR-trunc Helix-T 29.5 73 0.0016 20.5 3.1 42 148-196 4-47 (49)
36 PF01047 MarR: MarR family; I 28.5 18 0.00038 25.4 -0.2 38 149-186 22-59 (59)
37 PF11693 DUF2990: Protein of u 28.3 46 0.001 25.1 2.0 24 259-295 15-38 (64)
38 PF13950 Epimerase_Csub: UDP-g 27.6 93 0.002 22.9 3.6 42 134-175 16-58 (62)
39 PF13276 HTH_21: HTH-like doma 26.7 1.1E+02 0.0024 21.7 3.8 41 4-45 3-43 (60)
40 cd00923 Cyt_c_Oxidase_Va Cytoc 26.5 1.5E+02 0.0032 24.5 4.8 45 3-50 4-48 (103)
41 PLN02945 nicotinamide-nucleoti 26.4 48 0.001 30.6 2.2 32 266-299 204-235 (236)
42 PRK00071 nadD nicotinic acid m 25.9 43 0.00093 29.8 1.8 32 147-178 170-201 (203)
43 PF13551 HTH_29: Winged helix- 25.6 1.2E+02 0.0026 23.4 4.1 40 4-43 59-102 (112)
44 PLN02945 nicotinamide-nucleoti 25.3 47 0.001 30.6 2.0 32 147-178 204-235 (236)
45 cd00073 H15 linker histone 1 a 24.8 2.3E+02 0.005 22.0 5.6 46 11-56 12-57 (88)
46 KOG2076 RNA polymerase III tra 24.6 1.2E+02 0.0025 33.7 5.0 80 134-220 123-208 (895)
47 PRK00071 nadD nicotinic acid m 24.4 54 0.0012 29.2 2.1 35 263-299 166-201 (203)
48 PRK06973 nicotinic acid mononu 24.2 48 0.001 30.9 1.9 32 147-178 202-241 (243)
49 PF13545 HTH_Crp_2: Crp-like h 24.1 50 0.0011 24.1 1.6 47 143-193 26-74 (76)
50 TIGR00482 nicotinate (nicotina 23.5 54 0.0012 29.0 2.0 32 147-178 162-193 (193)
51 PF11740 KfrA_N: Plasmid repli 23.1 2.4E+02 0.0053 22.5 5.7 42 2-48 1-42 (120)
52 TIGR00482 nicotinate (nicotina 22.3 63 0.0014 28.6 2.1 34 263-298 158-192 (193)
53 PF05402 PqqD: Coenzyme PQQ sy 21.9 2.2E+02 0.0048 20.3 4.7 42 12-54 20-61 (68)
54 PF13592 HTH_33: Winged helix- 21.9 81 0.0018 22.7 2.3 22 21-42 3-24 (60)
55 PRK09184 acyl carrier protein; 21.8 1.7E+02 0.0037 23.0 4.3 41 1-41 1-63 (89)
56 PF08938 HBS1_N: HBS1 N-termin 21.1 37 0.00081 26.1 0.4 29 143-171 28-56 (79)
57 KOG2522 Filamentous baseplate 20.9 71 0.0015 33.0 2.4 28 277-304 379-406 (560)
58 PRK07639 acyl carrier protein; 20.4 1.2E+02 0.0025 23.6 3.1 54 159-214 1-54 (86)
59 PF12824 MRP-L20: Mitochondria 20.3 1.2E+02 0.0026 26.9 3.4 31 3-39 87-117 (164)
60 PF12872 OST-HTH: OST-HTH/LOTU 20.1 2.4E+02 0.0052 20.4 4.6 40 3-43 2-43 (74)
61 PF03511 Fanconi_A: Fanconi an 20.0 60 0.0013 24.5 1.2 19 201-219 8-26 (64)
No 1
>KOG1946 consensus RNA polymerase I transcription factor UAF [Transcription]
Probab=99.97 E-value=1.1e-31 Score=246.88 Aligned_cols=182 Identities=35% Similarity=0.488 Sum_probs=137.4
Q ss_pred CCCHHHHHHHHHHHHhhCCCCCccHHHHHHHHHHHhCCCChhhhHHHHHHHHHHHhhhhhcccCCCCCCcccccccCchh
Q 021906 1 MVSDSELIARLQEFLKNSDLNTTTTGIVRRQLEKDFGVDLTDKKIFIREQVDLFLQSQFENDQNDGGNEEQQEEDDGEDD 80 (305)
Q Consensus 1 m~sd~ei~~~I~~IL~~aDl~~vT~K~VR~~Le~~fgvDLs~kK~~I~~~I~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 80 (305)
|.+...+...+..||...++.++|...||++++..||++++..+..++..|...+..-...... +.. .
T Consensus 1 ~~~~~~~~~~~~~~l~~~~~~~lt~~~vr~~~~~~~~v~~~~~k~~~~~~~~~~~~~~~~~~~k-----~~~-------~ 68 (240)
T KOG1946|consen 1 MDSLSWEYLFKDYILSLKDQETLTPDDVRRAMAPRSGVDGTAQKSLLAKAIDESSDEDSALPVK-----GSK-------K 68 (240)
T ss_pred CcchhhhhhhhHHHhcccccccCCHHHHHHHhccccCCCCcchhhhhhhhhhcccccccccccc-----ccc-------c
Confidence 5677889999999999999999999999999999999999999999998886655432110000 000 0
Q ss_pred hhhhccCCCCCCCCcccccCCCCCCCCCCCChhhhhhcCCcchhhccccccccccCCCCCCccccCCHHHHhhhCCCCcc
Q 021906 81 QMAKVKSDETDGSDDAAVEEGDDDNNDENDNDDEANEAKGPAKRRSRKLNNEVKKRGGGFSKLCALSPQLQEFIGVTELA 160 (305)
Q Consensus 81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~k~~~~~~~~~~g~~k~~~lS~~La~~lG~~~~s 160 (305)
. + .+ ... .. ..+.+.. .+.....+.+..++|+++.|.||+.|+.|+|.+++|
T Consensus 69 k--~-~~-----~~~------~~------------~~~~~~~--~~~~~~~~~~~~~~g~~kl~~ls~~L~~~~G~~~ls 120 (240)
T KOG1946|consen 69 K--K-RG-----SKT------RS------------RKPKSLE--SSGEKNKKKKKASWGSTKLIPLSPSLARFVGTSELS 120 (240)
T ss_pred c--c-cc-----ccc------cc------------ccCcccc--cccccchhccccCcCcccccccCHHHHhhccccccc
Confidence 0 0 00 000 00 0000000 000000111124689999999999999999999999
Q ss_pred HHHHHHHHHHHHhhhCCCCCCCCCccccchhHHhhhCCCccChhhHHHHHHccCCCCCCccc
Q 021906 161 RTEVVKQLWAYIREKDLQDPNNRRNIVCDERLRALFGVDTINMFQMNKALSKHIWPLDSDDV 222 (305)
Q Consensus 161 R~~vvk~lW~YIK~n~LqdP~nkr~I~cD~~Lk~lfg~~~i~~~~m~k~L~~Hl~pl~p~~~ 222 (305)
|++|++.||+|||+||||||.||+.|+||++|+.|||..+|+||+|+++|.+||++...+..
T Consensus 121 R~~vvk~iw~YIke~nLqDP~nkr~IlCDekL~~iF~~k~v~~fem~KLL~~H~~~~~d~~~ 182 (240)
T KOG1946|consen 121 RTDVVKKIWAYIKEHNLQDPKNKREILCDEKLKSIFGKKRVGMFEMLKLLTKHFLKNQDMVG 182 (240)
T ss_pred HHHHHHHHHHHHHHhccCCccccCeeeeHHHHHHHhccCccceeeHHHHHHHhccCcccccc
Confidence 99999999999999999999999999999999999999999999999999999998777643
No 2
>COG5531 SWIB-domain-containing proteins implicated in chromatin remodeling [Chromatin structure and dynamics]
Probab=99.93 E-value=1.4e-26 Score=211.87 Aligned_cols=193 Identities=24% Similarity=0.380 Sum_probs=129.6
Q ss_pred HHHHHHHHHhhCCCCCccHHHHHHHHHHHhCCCChhhhHHHHHHHHHHHhhhhhcccCCCCCCcccccccCchhhhhhcc
Q 021906 7 LIARLQEFLKNSDLNTTTTGIVRRQLEKDFGVDLTDKKIFIREQVDLFLQSQFENDQNDGGNEEQQEEDDGEDDQMAKVK 86 (305)
Q Consensus 7 i~~~I~~IL~~aDl~~vT~K~VR~~Le~~fgvDLs~kK~~I~~~I~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 86 (305)
+..++..+|...+..+++.+.|++.+...|+++|..+..++++++...+.+................+ .
T Consensus 7 ~~~~~~~~~~~~e~~~~~ek~v~~~~~~~~~~~l~~r~k~~~~~~~~~~~s~~~~~~~~~~~k~~~~r-------~---- 75 (237)
T COG5531 7 YGTMNDSWLQLDERDTNNEKDVGKLLFSEWTVRLEGRFKDNNDLIRDKFDSLAEEPRVLRKEKYNITR-------K---- 75 (237)
T ss_pred cccccceeeecccccccChhhcccccchhhheehhhhhhhccchhhhhhhhhcccchhhhhhhhccCc-------c----
Confidence 34467788999999999999999999999999999999999998877765542110000000000000 0
Q ss_pred CCCCCCCCcccccCCCCCCCCCCCChhhh-hhcCCcchhhccccccccccCCCCCCccccCCHHHHhhhCCCCccHHHHH
Q 021906 87 SDETDGSDDAAVEEGDDDNNDENDNDDEA-NEAKGPAKRRSRKLNNEVKKRGGGFSKLCALSPQLQEFIGVTELARTEVV 165 (305)
Q Consensus 87 ~~~~~~~~~~~~~~~~~~~~~~~~e~~~~-~~~~~~~~~~~~k~~~~~~~~~~g~~k~~~lS~~La~~lG~~~~sR~~vv 165 (305)
++...+ ..+.. ++......+ +.+..-.+...+++..+....++-+...|.||+.||.|||..++||++||
T Consensus 76 ---~~~~~~----~~~~~--~~~~~s~k~~~n~~te~k~~~~~k~~~~~~~~~~~~~~~~lS~~La~ilG~~~~tr~~~v 146 (237)
T COG5531 76 ---TTGKND----LPKEE--DSSLPSSKETENGDTEGKETDKKKKSSTISKNSPSGEKVKLSPKLAAILGLEPGTRPEAV 146 (237)
T ss_pred ---cccccc----ccccc--ccccCcchhhhcCccccccccccccccccccccCCCCceecCHHHHHHhCCCCCCccHHH
Confidence 000000 00000 000000000 00100000001111111113356678999999999999999999999999
Q ss_pred HHHHHHHhhhCCCCCCCCCccccchhHHhhhCCCccChhhHHHHHHccCCCCCC
Q 021906 166 KQLWAYIREKDLQDPNNRRNIVCDERLRALFGVDTINMFQMNKALSKHIWPLDS 219 (305)
Q Consensus 166 k~lW~YIK~n~LqdP~nkr~I~cD~~Lk~lfg~~~i~~~~m~k~L~~Hl~pl~p 219 (305)
+.||+||+.||||||+||+.|+||++|+.|||.+.+.||+|+++|.+|+.+++-
T Consensus 147 ~~lw~YIk~h~lq~~~nkr~I~~D~~L~~v~g~~p~~mf~~~k~l~~hl~~~~~ 200 (237)
T COG5531 147 KKLWKYIKKHNLQDPNNKRLILCDSKLKKVLGSDPIDMFELTKPLSPHLIKYTI 200 (237)
T ss_pred HHHHHHHHHhcCCCccccceecccHHHHHHhCCCchhhhhhhcccccceecCcc
Confidence 999999999999999999999999999999999999999999999999997544
No 3
>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=99.92 E-value=1.5e-26 Score=178.45 Aligned_cols=75 Identities=53% Similarity=1.027 Sum_probs=70.8
Q ss_pred CCccccCCHHHHhhhCCCCccHHHHHHHHHHHHhhhCCCCCCCCCccccchhHHhhhCCCccChhhHHHHHHccC
Q 021906 140 FSKLCALSPQLQEFIGVTELARTEVVKQLWAYIREKDLQDPNNRRNIVCDERLRALFGVDTINMFQMNKALSKHI 214 (305)
Q Consensus 140 ~~k~~~lS~~La~~lG~~~~sR~~vvk~lW~YIK~n~LqdP~nkr~I~cD~~Lk~lfg~~~i~~~~m~k~L~~Hl 214 (305)
|+++|+|||+|++|+|..++||++|+++||+||++||||||+|++.|+||+.|+.|||.++|+||+|+++|++||
T Consensus 1 ~~k~~~ls~~L~~~lg~~~~sr~~v~~~lw~YIk~~~L~dp~~k~~I~cD~~L~~lf~~~~v~~~~i~~~l~~hl 75 (76)
T PF02201_consen 1 FPKRFKLSPELAEFLGEDELSRSEVVKRLWQYIKENNLQDPKDKRIIICDEKLKKLFGKDSVNFFEIPKLLKPHL 75 (76)
T ss_dssp -EEEEHHHHHHHHHTT-SCEEHHHHHHHHHHHHHHTTSBESSSTTEEE-TTSHHHHHHTSECSEEETTHHHHHHH
T ss_pred CCCCccCCHHHHHHhCCCCCCHHHHHHHHHHHHHHhcCCCcccCceEecCHHHHHHhCCCeecHhhHHHHHHHhc
Confidence 578899999999999999999999999999999999999999999999999999999999999999999999997
No 4
>smart00151 SWIB SWI complex, BAF60b domains.
Probab=99.92 E-value=4.3e-25 Score=170.80 Aligned_cols=76 Identities=47% Similarity=0.966 Sum_probs=74.1
Q ss_pred CccccCCHHHHhhhCCCCccHHHHHHHHHHHHhhhCCCCCCCCCccccchhHHhhhCCCccChhhHHHHHHccCCC
Q 021906 141 SKLCALSPQLQEFIGVTELARTEVVKQLWAYIREKDLQDPNNRRNIVCDERLRALFGVDTINMFQMNKALSKHIWP 216 (305)
Q Consensus 141 ~k~~~lS~~La~~lG~~~~sR~~vvk~lW~YIK~n~LqdP~nkr~I~cD~~Lk~lfg~~~i~~~~m~k~L~~Hl~p 216 (305)
+++|.||++|++|+|..++||++|+++||+|||.||||||+|++.|+||+.|+.|||+++|.|++|+++|++||.|
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 TKKVTLSPELAKVLGAPEMTRTEIIKRLWEYIKEHNLQDPQNKREILCDSKLEQIFGKDRMDMFEMNKLLTPHLIK 77 (77)
T ss_pred CCcccCCHHHHHHhCCCcCcHHHHHHHHHHHHHHhcccCCccCCEEecCHHHHHHHCcCeecHHHHHHHHHHHcCC
Confidence 5789999999999999999999999999999999999999999999999999999999999999999999999975
No 5
>PRK14724 DNA topoisomerase III; Provisional
Probab=99.81 E-value=2.5e-20 Score=200.49 Aligned_cols=77 Identities=38% Similarity=0.673 Sum_probs=74.6
Q ss_pred CCCccccCCHHHHhhhCCCCccHHHHHHHHHHHHhhhCCCCCCCCCccccchhHHhhhCCCccChhhHHHHHHccCC
Q 021906 139 GFSKLCALSPQLQEFIGVTELARTEVVKQLWAYIREKDLQDPNNRRNIVCDERLRALFGVDTINMFQMNKALSKHIW 215 (305)
Q Consensus 139 g~~k~~~lS~~La~~lG~~~~sR~~vvk~lW~YIK~n~LqdP~nkr~I~cD~~Lk~lfg~~~i~~~~m~k~L~~Hl~ 215 (305)
.+...+.|||+|++|||..++||++||++||+|||.||||||.|+|.|+||++|+.|||+++|.||+|+++|++||.
T Consensus 911 ~~~~~~~ls~~La~~lg~~~~~r~~v~~~lW~YIK~~~Lqdp~~k~~i~cD~~L~~vfg~~~~~~~~~~~~l~~hl~ 987 (987)
T PRK14724 911 PPAAGLKPSAALAAVIGAEPVARPEVIKKLWDYIKANNLQDPADKRAINADAKLRPVFGKDQVTMFELAGIVGKHLS 987 (987)
T ss_pred ccccccCCCHHHHHHhCCCcCCHHHHHHHHHHHHHHccCCCcccCCeeccchHHHHHhCCCcccHHHHHHHHHHhcC
Confidence 37788999999999999999999999999999999999999999999999999999999999999999999999984
No 6
>KOG2570 consensus SWI/SNF transcription activation complex subunit [Chromatin structure and dynamics; Transcription]
Probab=99.74 E-value=1.3e-18 Score=169.07 Aligned_cols=83 Identities=31% Similarity=0.608 Sum_probs=79.9
Q ss_pred CccccCCHHHHhhhCCCCccHHHHHHHHHHHHhhhCCCCCCCCCccccchhHHhhhCCCccChhhHHHHHHccCCCCCCc
Q 021906 141 SKLCALSPQLQEFIGVTELARTEVVKQLWAYIREKDLQDPNNRRNIVCDERLRALFGVDTINMFQMNKALSKHIWPLDSD 220 (305)
Q Consensus 141 ~k~~~lS~~La~~lG~~~~sR~~vvk~lW~YIK~n~LqdP~nkr~I~cD~~Lk~lfg~~~i~~~~m~k~L~~Hl~pl~p~ 220 (305)
...|+|||.||.+||+...||+.||.+||+|||.|+||||.++.+|+||..|+.+||++++.|.+|+.+|++||.|++||
T Consensus 206 P~~fklsp~La~lLGi~t~Trp~iI~alWqYIk~n~Lqd~~e~~~incD~~l~qif~~~rl~F~elp~~l~~lL~P~dPI 285 (420)
T KOG2570|consen 206 PEEFKLSPRLANLLGIHTGTRPDIVTALWQYIKTNKLQDPEDSDFINCDKALEQIFGVDRLKFPELPQLLNPLLSPPDPI 285 (420)
T ss_pred CcccccCHHHHHHhhhccCcchHHHHHHHHHHHHhccCCcccchhhcchHHHHHhhcccccccccchhhhhhccCCCCCe
Confidence 34578999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccc
Q 021906 221 DVI 223 (305)
Q Consensus 221 ~~~ 223 (305)
.+.
T Consensus 286 vi~ 288 (420)
T KOG2570|consen 286 VID 288 (420)
T ss_pred eec
Confidence 865
No 7
>PF08766 DEK_C: DEK C terminal domain; InterPro: IPR014876 DEK is a chromatin associated protein that is linked with cancers and autoimmune disease. This domain is found at the C-terminal of DEK and is of clinical importance since it can reverse the characteristic abnormal DNA-mutagen sensitivity in fibroblasts from ataxia-telangiectasia (A-T) patients []. The structure of this domain shows it to be homologous to the E2F/DP transcription factor family []. This domain is also found in chitin synthase proteins like Q8TF96 from SWISSPROT, and in protein phosphatases such as Q6NN85 from SWISSPROT. ; PDB: 1Q1V_A.
Probab=99.58 E-value=2.6e-15 Score=108.73 Aligned_cols=54 Identities=46% Similarity=0.762 Sum_probs=45.7
Q ss_pred CHHHHHHHHHHHHhhCCCCCccHHHHHHHHHHHhCCCChhhhHHHHHHHHHHHh
Q 021906 3 SDSELIARLQEFLKNSDLNTTTTGIVRRQLEKDFGVDLTDKKIFIREQVDLFLQ 56 (305)
Q Consensus 3 sd~ei~~~I~~IL~~aDl~~vT~K~VR~~Le~~fgvDLs~kK~~I~~~I~~~l~ 56 (305)
||++|...|++||+++||+++|.|+||++||++||+||+++|+||+++|+.+|.
T Consensus 1 td~~i~~~i~~iL~~~dl~~vT~k~vr~~Le~~~~~dL~~~K~~I~~~I~~~l~ 54 (54)
T PF08766_consen 1 TDEEIREAIREILREADLDTVTKKQVREQLEERFGVDLSSRKKFIKELIDEFLS 54 (54)
T ss_dssp -HHHHHHHHHHHHTTS-GGG--HHHHHHHHHHH-SS--SHHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHhCCHhHhhHHHHHHHHHHHHCCCcHHHHHHHHHHHHHHhC
Confidence 799999999999999999999999999999999999999999999999999884
No 8
>KOG1946 consensus RNA polymerase I transcription factor UAF [Transcription]
Probab=99.46 E-value=6.6e-14 Score=129.42 Aligned_cols=48 Identities=42% Similarity=0.695 Sum_probs=45.8
Q ss_pred CCCCCCCCCCCcHHHHHhhCCCCCCCCHHHHHHHHHHHHHhcCCCcccCC
Q 021906 255 GKSGFLAPLQLSDALIKFLGTGESALPRSDVIKRMWDYIKEKNLQVSLRS 304 (305)
Q Consensus 255 ~~~g~~~~~~lS~~L~~~~g~~~~~~~r~~v~k~~W~YIk~~~Lqdp~nk 304 (305)
.++|+++++.||+.|+.|+|.+ +|||++|+++||+|||+||||||.||
T Consensus 96 ~~~g~~kl~~ls~~L~~~~G~~--~lsR~~vvk~iw~YIke~nLqDP~nk 143 (240)
T KOG1946|consen 96 ASWGSTKLIPLSPSLARFVGTS--ELSRTDVVKKIWAYIKEHNLQDPKNK 143 (240)
T ss_pred cCcCcccccccCHHHHhhcccc--cccHHHHHHHHHHHHHHhccCCcccc
Confidence 4579999999999999999977 99999999999999999999999997
No 9
>PRK06319 DNA topoisomerase I/SWI domain fusion protein; Validated
Probab=99.40 E-value=1.9e-13 Score=146.11 Aligned_cols=74 Identities=41% Similarity=0.759 Sum_probs=71.4
Q ss_pred ccccCCHHHHhhhCCCCccHHHHHHHHHHHHhhhCCCCCCCCCccccchhHHhhhCCCccChhhHHHHHHccCC
Q 021906 142 KLCALSPQLQEFIGVTELARTEVVKQLWAYIREKDLQDPNNRRNIVCDERLRALFGVDTINMFQMNKALSKHIW 215 (305)
Q Consensus 142 k~~~lS~~La~~lG~~~~sR~~vvk~lW~YIK~n~LqdP~nkr~I~cD~~Lk~lfg~~~i~~~~m~k~L~~Hl~ 215 (305)
..|.+|+.|+.|+|...++|+++++.||+||+.|+||||.|++.|+||++|+++||++.+.||.|+++|++||.
T Consensus 786 ~~~~~S~~La~~~g~~~~sr~~~~~~lw~yIk~~~lqdp~~Kr~i~~d~kl~kvf~~~~~~~~~~~k~l~~hl~ 859 (860)
T PRK06319 786 PLYTPSPALAAMIGAEPVGRGEATKKVWDYIKEHGLQSPENKKLIIPDSKLQGVIGPDPIDMFQLSKKLSQHLI 859 (860)
T ss_pred cccccccccccccCcCccCchHHHHHHHHHHHHhcccCccccccCCCchhhhhhhCcCccchhhhHHHHHhhhc
Confidence 45779999999999999999999999999999999999999999999999999999999999999999999985
No 10
>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=99.37 E-value=1.3e-13 Score=106.40 Aligned_cols=44 Identities=48% Similarity=0.801 Sum_probs=40.1
Q ss_pred CCCCCCCcHHHHHhhCCCCCCCCHHHHHHHHHHHHHhcCCCcccCC
Q 021906 259 FLAPLQLSDALIKFLGTGESALPRSDVIKRMWDYIKEKNLQVSLRS 304 (305)
Q Consensus 259 ~~~~~~lS~~L~~~~g~~~~~~~r~~v~k~~W~YIk~~~Lqdp~nk 304 (305)
|+++|.||++|++|+|.. ++||++|+++||+||++||||||+|+
T Consensus 1 ~~k~~~ls~~L~~~lg~~--~~sr~~v~~~lw~YIk~~~L~dp~~k 44 (76)
T PF02201_consen 1 FPKRFKLSPELAEFLGED--ELSRSEVVKRLWQYIKENNLQDPKDK 44 (76)
T ss_dssp -EEEEHHHHHHHHHTT-S--CEEHHHHHHHHHHHHHHTTSBESSST
T ss_pred CCCCccCCHHHHHHhCCC--CCCHHHHHHHHHHHHHHhcCCCcccC
Confidence 567899999999999987 89999999999999999999999997
No 11
>smart00151 SWIB SWI complex, BAF60b domains.
Probab=99.36 E-value=8.2e-13 Score=102.17 Aligned_cols=44 Identities=41% Similarity=0.717 Sum_probs=41.5
Q ss_pred CCCCCCCcHHHHHhhCCCCCCCCHHHHHHHHHHHHHhcCCCcccCC
Q 021906 259 FLAPLQLSDALIKFLGTGESALPRSDVIKRMWDYIKEKNLQVSLRS 304 (305)
Q Consensus 259 ~~~~~~lS~~L~~~~g~~~~~~~r~~v~k~~W~YIk~~~Lqdp~nk 304 (305)
++.+|.+|++|+.|+|.+ ++||++|+++||+|||.||||||.|+
T Consensus 1 ~~~~~~ls~~L~~~lg~~--~~tr~ev~~~lw~YIk~n~L~d~~~k 44 (77)
T smart00151 1 ITKKVTLSPELAKVLGAP--EMTRTEIIKRLWEYIKEHNLQDPQNK 44 (77)
T ss_pred CCCcccCCHHHHHHhCCC--cCcHHHHHHHHHHHHHHhcccCCccC
Confidence 367899999999999976 99999999999999999999999986
No 12
>COG5531 SWIB-domain-containing proteins implicated in chromatin remodeling [Chromatin structure and dynamics]
Probab=99.21 E-value=1.1e-11 Score=114.27 Aligned_cols=47 Identities=32% Similarity=0.475 Sum_probs=44.4
Q ss_pred CCCCCCCCCCcHHHHHhhCCCCCCCCHHHHHHHHHHHHHhcCCCcccCC
Q 021906 256 KSGFLAPLQLSDALIKFLGTGESALPRSDVIKRMWDYIKEKNLQVSLRS 304 (305)
Q Consensus 256 ~~g~~~~~~lS~~L~~~~g~~~~~~~r~~v~k~~W~YIk~~~Lqdp~nk 304 (305)
.+.+..+|.+|+.||.|||.+ ++||++||++||+|||.||||||+||
T Consensus 118 ~~~~~~~~~lS~~La~ilG~~--~~tr~~~v~~lw~YIk~h~lq~~~nk 164 (237)
T COG5531 118 NSPSGEKVKLSPKLAAILGLE--PGTRPEAVKKLWKYIKKHNLQDPNNK 164 (237)
T ss_pred ccCCCCceecCHHHHHHhCCC--CCCccHHHHHHHHHHHHhcCCCcccc
Confidence 456789999999999999988 99999999999999999999999997
No 13
>PRK14724 DNA topoisomerase III; Provisional
Probab=98.95 E-value=5.8e-10 Score=120.97 Aligned_cols=45 Identities=40% Similarity=0.603 Sum_probs=42.6
Q ss_pred CCCCCCCCcHHHHHhhCCCCCCCCHHHHHHHHHHHHHhcCCCcccCC
Q 021906 258 GFLAPLQLSDALIKFLGTGESALPRSDVIKRMWDYIKEKNLQVSLRS 304 (305)
Q Consensus 258 g~~~~~~lS~~L~~~~g~~~~~~~r~~v~k~~W~YIk~~~Lqdp~nk 304 (305)
.+..++.|||+|++|||.+ ++||++||++||+|||.||||||.|+
T Consensus 911 ~~~~~~~ls~~La~~lg~~--~~~r~~v~~~lW~YIK~~~Lqdp~~k 955 (987)
T PRK14724 911 PPAAGLKPSAALAAVIGAE--PVARPEVIKKLWDYIKANNLQDPADK 955 (987)
T ss_pred ccccccCCCHHHHHHhCCC--cCCHHHHHHHHHHHHHHccCCCcccC
Confidence 3678999999999999988 99999999999999999999999997
No 14
>KOG2266 consensus Chromatin-associated protein Dek and related proteins, contains SAP DNA binding domain [Chromatin structure and dynamics]
Probab=98.88 E-value=2.4e-09 Score=106.30 Aligned_cols=60 Identities=28% Similarity=0.447 Sum_probs=58.2
Q ss_pred CCCHHHHHHHHHHHHhhCCCCCccHHHHHHHHHHHhCCCChhhhHHHHHHHHHHHhhhhh
Q 021906 1 MVSDSELIARLQEFLKNSDLNTTTTGIVRRQLEKDFGVDLTDKKIFIREQVDLFLQSQFE 60 (305)
Q Consensus 1 m~sd~ei~~~I~~IL~~aDl~~vT~K~VR~~Le~~fgvDLs~kK~~I~~~I~~~l~~~~~ 60 (305)
.|||++|...|..||..+||+++|.+.|.++|..+|++||++||.||.++|..+|..+.+
T Consensus 519 ePTdeelk~~V~kILk~vdfntaTm~dIlKkl~~~f~~dLt~rK~~IK~~Ike~I~~~~d 578 (594)
T KOG2266|consen 519 EPTDEELKEVVKKILKEVDFNTATMKDILKKLYAKFPIDLTHRKDFIKDTIKELINKMAD 578 (594)
T ss_pred CCcHHHHHHHHHHHHHhcCcchhhHHHHHHHHHHhCCcccccchHHHHHHHHHHHHHhcc
Confidence 499999999999999999999999999999999999999999999999999999998866
No 15
>KOG2570 consensus SWI/SNF transcription activation complex subunit [Chromatin structure and dynamics; Transcription]
Probab=97.91 E-value=8e-06 Score=80.52 Aligned_cols=41 Identities=34% Similarity=0.586 Sum_probs=38.2
Q ss_pred CCCCcHHHHHhhCCCCCCCCHHHHHHHHHHHHHhcCCCcccCC
Q 021906 262 PLQLSDALIKFLGTGESALPRSDVIKRMWDYIKEKNLQVSLRS 304 (305)
Q Consensus 262 ~~~lS~~L~~~~g~~~~~~~r~~v~k~~W~YIk~~~Lqdp~nk 304 (305)
.|.+||.||.+||.. +-||+.||-.||.|||-|+||||.++
T Consensus 208 ~fklsp~La~lLGi~--t~Trp~iI~alWqYIk~n~Lqd~~e~ 248 (420)
T KOG2570|consen 208 EFKLSPRLANLLGIH--TGTRPDIVTALWQYIKTNKLQDPEDS 248 (420)
T ss_pred ccccCHHHHHHhhhc--cCcchHHHHHHHHHHHHhccCCcccc
Confidence 367999999999998 99999999999999999999999764
No 16
>PRK06319 DNA topoisomerase I/SWI domain fusion protein; Validated
Probab=97.88 E-value=6.5e-06 Score=88.78 Aligned_cols=44 Identities=32% Similarity=0.486 Sum_probs=40.9
Q ss_pred CCCCCCCcHHHHHhhCCCCCCCCHHHHHHHHHHHHHhcCCCcccCC
Q 021906 259 FLAPLQLSDALIKFLGTGESALPRSDVIKRMWDYIKEKNLQVSLRS 304 (305)
Q Consensus 259 ~~~~~~lS~~L~~~~g~~~~~~~r~~v~k~~W~YIk~~~Lqdp~nk 304 (305)
.+.+|.+|++|+.|+|+. +++|+++++.||+|||.|+||||.||
T Consensus 784 ~~~~~~~S~~La~~~g~~--~~sr~~~~~~lw~yIk~~~lqdp~~K 827 (860)
T PRK06319 784 AGPLYTPSPALAAMIGAE--PVGRGEATKKVWDYIKEHGLQSPENK 827 (860)
T ss_pred cccccccccccccccCcC--ccCchHHHHHHHHHHHHhcccCcccc
Confidence 356788999999999987 99999999999999999999999997
No 17
>PF09312 SurA_N: SurA N-terminal domain; InterPro: IPR015391 The correct folding of outer membrane proteins in Gram negative bacteria is facilitated by the survival protein SurA []. This entry represents the domain found at the N terminus of the chaperone SurA. It is a helical domain of unknown function. The C terminus of the SurA protein folds back and forms part of this domain also but is not included in the current alignment. ; PDB: 3RGC_B 2PV3_B 1M5Y_A.
Probab=75.28 E-value=4.6 Score=33.17 Aligned_cols=46 Identities=30% Similarity=0.476 Sum_probs=35.8
Q ss_pred CCHHHHHHHHHHHHhhCCCCCccHHHHHHHHHHHhCCCChhhhHHHHHHH
Q 021906 2 VSDSELIARLQEFLKNSDLNTTTTGIVRRQLEKDFGVDLTDKKIFIREQV 51 (305)
Q Consensus 2 ~sd~ei~~~I~~IL~~aDl~~vT~K~VR~~Le~~fgvDLs~kK~~I~~~I 51 (305)
+||++|-..|..|.+..++ |...++++|+. .|+++...+..|+..|
T Consensus 67 vsd~evd~~i~~ia~~n~l---s~~ql~~~L~~-~G~s~~~~r~~ir~~i 112 (118)
T PF09312_consen 67 VSDEEVDEAIANIAKQNNL---SVEQLRQQLEQ-QGISYEEYREQIRKQI 112 (118)
T ss_dssp --HHHHHHHHHHHHHHTT-----HHHHHHHCHH-CT--HHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHHcCC---CHHHHHHHHHH-cCCCHHHHHHHHHHHH
Confidence 7999999999999998877 67889999986 6999999999998775
No 18
>PRK05350 acyl carrier protein; Provisional
Probab=73.94 E-value=2.9 Score=32.06 Aligned_cols=54 Identities=20% Similarity=0.292 Sum_probs=46.5
Q ss_pred ccHHHHHHHHHHHHhhhCCCCCCCCCccccchhHHhhhCCCccChhhHHHHHHccCC
Q 021906 159 LARTEVVKQLWAYIREKDLQDPNNRRNIVCDERLRALFGVDTINMFQMNKALSKHIW 215 (305)
Q Consensus 159 ~sR~~vvk~lW~YIK~n~LqdP~nkr~I~cD~~Lk~lfg~~~i~~~~m~k~L~~Hl~ 215 (305)
|+|.+|...|+++|.+. +.- +...|.+|..|..-+|-+++.+.+|.-.|..+|-
T Consensus 2 m~~~~i~~~v~~ii~~~-~~~--~~~~i~~d~~l~~dlg~DSld~veli~~lE~~fg 55 (82)
T PRK05350 2 MTREEILERLRAILVEL-FEI--DPEDITPEANLYEDLDLDSIDAVDLVVHLQKLTG 55 (82)
T ss_pred CCHHHHHHHHHHHHHHH-hCC--CHHHCCCCccchhhcCCCHHHHHHHHHHHHHHHC
Confidence 78999999999999987 421 2257999999988889999999999999999984
No 19
>KOG2522 consensus Filamentous baseplate protein Ligatin, contains PUA domain [Translation, ribosomal structure and biogenesis]
Probab=72.01 E-value=6.9 Score=40.02 Aligned_cols=60 Identities=18% Similarity=0.236 Sum_probs=44.2
Q ss_pred CCccHHHHHHHHHHHHhhhCCCCCCCCCccccchhHHhhhCC---------CccChhhHHHHHHccCCC
Q 021906 157 TELARTEVVKQLWAYIREKDLQDPNNRRNIVCDERLRALFGV---------DTINMFQMNKALSKHIWP 216 (305)
Q Consensus 157 ~~~sR~~vvk~lW~YIK~n~LqdP~nkr~I~cD~~Lk~lfg~---------~~i~~~~m~k~L~~Hl~p 216 (305)
...+-.+|...+-+||..|||-|+.||..|+.|+-|-..... ..+..-.+...+...|.|
T Consensus 380 ~lyt~seir~~V~kYi~knnLad~~nKg~VrLDpILfd~~~k~~K~~~a~~~~~pw~~l~~~~~~rmtp 448 (560)
T KOG2522|consen 380 TLYTSSEIRSAVSKYISKNNLADTKNKGKVRLDPILFDMVNKKKKVLNASRIIAPWEILHPLLTNRMTP 448 (560)
T ss_pred ceeeHHHHHHHHHHHhhhhhccccccCCcEEeccHHHHHHHhhhhccccccccccHHHHHHHHHhcCCc
Confidence 467889999999999999999999999998888877655432 223333555666555544
No 20
>PRK05828 acyl carrier protein; Validated
Probab=66.21 E-value=22 Score=27.83 Aligned_cols=52 Identities=15% Similarity=0.307 Sum_probs=35.8
Q ss_pred CHHHHHHHHHHHHhh----CCCCCcc--------------HHHHHHHHHHHhCCCChhh----hHHHHHHHHHH
Q 021906 3 SDSELIARLQEFLKN----SDLNTTT--------------TGIVRRQLEKDFGVDLTDK----KIFIREQVDLF 54 (305)
Q Consensus 3 sd~ei~~~I~~IL~~----aDl~~vT--------------~K~VR~~Le~~fgvDLs~k----K~~I~~~I~~~ 54 (305)
|.++|...|.+||.. .+++.++ .-.+.-+||+.||+.+... -.-+.++++.+
T Consensus 2 ~~~eI~~~i~~ii~e~~~~~~~d~i~~~~~~~dLg~DSLd~velv~~lE~~f~I~i~~e~~~~i~Tv~d~~~~v 75 (84)
T PRK05828 2 QEMEILLKIKEIAKKKNFAVTLDESNINKPYRELKIDSLDMFSIIVSLESEFNIEFSDEKLMKLKNLADLILEV 75 (84)
T ss_pred CHHHHHHHHHHHHHHhccCCCcccccCCCCHHhcCCCHHHHHHHHHHHHHHHCCCcCHHHHHhCCCHHHHHHHH
Confidence 678999999999996 3333332 3368889999999999873 23345555443
No 21
>PRK05828 acyl carrier protein; Validated
Probab=64.28 E-value=9.4 Score=29.95 Aligned_cols=54 Identities=13% Similarity=0.285 Sum_probs=44.6
Q ss_pred ccHHHHHHHHHHHHhhhCCCCCCCCCccccchhHHhhhCCCccChhhHHHHHHccCC
Q 021906 159 LARTEVVKQLWAYIREKDLQDPNNRRNIVCDERLRALFGVDTINMFQMNKALSKHIW 215 (305)
Q Consensus 159 ~sR~~vvk~lW~YIK~n~LqdP~nkr~I~cD~~Lk~lfg~~~i~~~~m~k~L~~Hl~ 215 (305)
|+|.+|..+|-..|.+.++. -+-..|.+|..|.. +|-|++.+.+|.-.|..+|-
T Consensus 1 m~~~eI~~~i~~ii~e~~~~--~~~d~i~~~~~~~d-Lg~DSLd~velv~~lE~~f~ 54 (84)
T PRK05828 1 MQEMEILLKIKEIAKKKNFA--VTLDESNINKPYRE-LKIDSLDMFSIIVSLESEFN 54 (84)
T ss_pred CCHHHHHHHHHHHHHHhccC--CCcccccCCCCHHh-cCCCHHHHHHHHHHHHHHHC
Confidence 78999999999999886542 12245678888877 99999999999999999984
No 22
>PF13565 HTH_32: Homeodomain-like domain
Probab=57.32 E-value=25 Score=25.95 Aligned_cols=35 Identities=23% Similarity=0.413 Sum_probs=28.1
Q ss_pred HHHHHHHHHHHHhhCCCCCccHHHHHHHHHHHhCCCC
Q 021906 4 DSELIARLQEFLKNSDLNTTTTGIVRRQLEKDFGVDL 40 (305)
Q Consensus 4 d~ei~~~I~~IL~~aDl~~vT~K~VR~~Le~~fgvDL 40 (305)
++++...|.+++..-- ..|...|...|++.||+.+
T Consensus 32 ~~e~~~~i~~~~~~~p--~wt~~~i~~~L~~~~g~~~ 66 (77)
T PF13565_consen 32 DPEQRERIIALIEEHP--RWTPREIAEYLEEEFGISV 66 (77)
T ss_pred cHHHHHHHHHHHHhCC--CCCHHHHHHHHHHHhCCCC
Confidence 4677677777766433 7899999999999999987
No 23
>PRK12449 acyl carrier protein; Provisional
Probab=56.18 E-value=17 Score=27.31 Aligned_cols=54 Identities=17% Similarity=0.269 Sum_probs=44.7
Q ss_pred ccHHHHHHHHHHHHhhhCCCCCCCCCccccchhHHhhhCCCccChhhHHHHHHccCC
Q 021906 159 LARTEVVKQLWAYIREKDLQDPNNRRNIVCDERLRALFGVDTINMFQMNKALSKHIW 215 (305)
Q Consensus 159 ~sR~~vvk~lW~YIK~n~LqdP~nkr~I~cD~~Lk~lfg~~~i~~~~m~k~L~~Hl~ 215 (305)
|+|.+|..+|-+++.+.-=.++ ..|.+|..|..-+|.|++.+.+|.-.|...|-
T Consensus 1 m~~~~i~~~l~~il~~~~~~~~---~~i~~~~~l~~dlg~DSl~~~~li~~lE~~f~ 54 (80)
T PRK12449 1 MTREEIFERLINLIQKQRSYLS---LAITEQTHLKDDLAVDSIELVEFIINVEDEFH 54 (80)
T ss_pred CCHHHHHHHHHHHHHHHhCCCc---cccCCCCcHHHHcCCcHHHHHHHHHHHHHHhC
Confidence 5788999999999987543333 35999999999999999999999999888773
No 24
>PF02881 SRP54_N: SRP54-type protein, helical bundle domain; InterPro: IPR013822 The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes [, ]. SRP recognises the signal sequence of the nascent polypeptide on the ribosome, retards its elongation, and docks the SRP-ribosome-polypeptide complex to the RER membrane via the SR receptor. Eukaryotic SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor []. In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane. In archaea, the SRP complex contains 7S RNA like its eukaryotic counterpart, yet only includes two of the six protein subunits found in the eukarytic complex: SRP19 and SRP54 []. This entry represents the N-terminal helical bundle domain of the 54 kDa SRP54 component, a GTP-binding protein that interacts with the signal sequence when it emerges from the ribosome. SRP54 of the signal recognition particle has a three-domain structure: an N-terminal helical bundle domain, a GTPase domain, and the M-domain that binds the 7s RNA and also binds the signal sequence. The extreme C-terminal region is glycine-rich and lower in complexity and poorly conserved between species. These proteins include Escherichia coli and Bacillus subtilis ffh protein (P48), which seems to be the prokaryotic counterpart of SRP54; signal recognition particle receptor alpha subunit (docking protein), an integral membrane GTP-binding protein which ensures, in conjunction with SRP, the correct targeting of nascent secretory proteins to the endoplasmic reticulum membrane; bacterial FtsY protein, which is believed to play a similar role to that of the docking protein in eukaryotes; the pilA protein from Neisseria gonorrhoeae, the homologue of ftsY; and bacterial flagellar biosynthesis protein flhF.; GO: 0005525 GTP binding, 0006614 SRP-dependent cotranslational protein targeting to membrane; PDB: 1J8M_F 1J8Y_F 2J37_W 2OG2_A 3B9Q_A 2V3C_C 3NDB_B 1ZU5_B 1ZU4_A 1WGW_A ....
Probab=56.13 E-value=50 Score=24.44 Aligned_cols=42 Identities=14% Similarity=0.252 Sum_probs=33.6
Q ss_pred HHHHHHHHHHHhhCCCCCccHHHHHHHHHH-HhC-CCChhhhHH
Q 021906 5 SELIARLQEFLKNSDLNTTTTGIVRRQLEK-DFG-VDLTDKKIF 46 (305)
Q Consensus 5 ~ei~~~I~~IL~~aDl~~vT~K~VR~~Le~-~fg-vDLs~kK~~ 46 (305)
+++...|...|=.||...-++..|...|.. ..+ -.+..+..+
T Consensus 24 ~~~l~ele~~Li~aDVg~~~a~~i~~~ik~~~~~~~~~~~~~~v 67 (75)
T PF02881_consen 24 EEFLEELEEALIEADVGVEVAEKIIENIKKKLIKKKGINPREEV 67 (75)
T ss_dssp HHHHHHHHHHHHHTTTSHHHHHHHHHHHHHHHHCTTSSHHHHHH
T ss_pred HHHHHHHHHHHHHcCcCHHHHHHHHHHHHHHHhcccCCCcHHHH
Confidence 567889999999999999999999999999 776 334444433
No 25
>CHL00124 acpP acyl carrier protein; Validated
Probab=55.12 E-value=11 Score=28.64 Aligned_cols=54 Identities=9% Similarity=0.274 Sum_probs=45.7
Q ss_pred ccHHHHHHHHHHHHhhhCCCCCCCCCccccchhHHhhhCCCccChhhHHHHHHccCC
Q 021906 159 LARTEVVKQLWAYIREKDLQDPNNRRNIVCDERLRALFGVDTINMFQMNKALSKHIW 215 (305)
Q Consensus 159 ~sR~~vvk~lW~YIK~n~LqdP~nkr~I~cD~~Lk~lfg~~~i~~~~m~k~L~~Hl~ 215 (305)
|+|.+|...|-++|.+.-=.+| ..|.+|..|...+|-+++.+.+|.-.|..+|-
T Consensus 1 M~~~~i~~~l~~ii~~~~~~~~---~~i~~d~~l~~dlg~DSl~~~eli~~le~~f~ 54 (82)
T CHL00124 1 MTKNDIFEKVQSIVAEQLGIEK---SEVTLDANFTRDLGADSLDVVELVMAIEEKFD 54 (82)
T ss_pred CCHHHHHHHHHHHHHHHHCCCH---HHCCCCcchhhhcCCcHHHHHHHHHHHHHHHC
Confidence 6889999999999988743344 35999999999999999999999999988874
No 26
>PF00538 Linker_histone: linker histone H1 and H5 family; InterPro: IPR005818 Histone proteins have central roles in both chromatin organisation (as structural units of the nucleosome) and gene regulation (as dynamic components that have a direct impact on DNA transcription and replication). Eukaryotic DNA wraps around a histone octamer to form a nucleosome, the first order of compaction of eukaryotic chromatin. The core histone octamer is composed of a central H3-H4 tetramer and two flanking H2A-H2B dimers. Each of the core histone contains a common structural motif, called the histone fold, which facilitates the interactions between the individual core histones. In addition to the core histones, there is a "linker histone" called H1 (or H5 in avian species). The linker histones present in all multicellular eukaryotes are the most divergent group of histones, with numerous cell type- and stage-specific variant. Linker histone H1 is an essential component of chromatin structure. H1 links nucleosomes into higher order structures. Histone H5 performs the same function as histone H1, and replaces H1 in certain cells. The structure of GH5, the globular domain of the linker histone H5 is known [, ]. The fold is similar to the DNA-binding domain of the catabolite gene activator protein, CAP, thus providing a possible model for the binding of GH5 to DNA. The linker histones, which do not contain the histone fold motif, are critical to the higher-order compaction of chromatin, because they bind to internucleosomal DNA and facilitate interactions between individual nucleosomes. In addition, H1 variants have been shown to be involved in the regulation of developmental genes. A common feature of this protein family is a tripartite structure in which a globular (H15) domain of about 80 amino acids is flanked by two less structured N- and C-terminal tails. The H15 domain is also characterised by high sequence homology among the family of linker histones. The highly conserved H15 domain is essential for the binding of H1 or H5 to the nucleosome. It consists of a three helix bundle (I-III), with a beta-hairpin at the C terminus. There is also a short three-residue stretch between helices I and II that is in the beta-strand conformation. Together with the C-terminal beta-hairpin, this strand forms the third strand of an antiparallel beta-sheet [, , , ]. Proteins known to contain a H15 domain are: - Eukaryotic histone H1. The histones H1 constitute a family with many variants, differing in their affinity for chromatin. Several variants are simultaneously present in a single cell. For example, the nucleated erythrocytes of birds contain both H1 and H5, the latter being an extreme variant of H1. - Eukaryotic MHYST family of histone acetyltransferase. Histone acetyltransferases transfer an acetyl group from acetyl-CoA to the epsylon- amino group of lysine within the basic NH2-termini of histones, which bind the acidic phosphates of DNA []. This entry represents the H15 domain.; GO: 0003677 DNA binding, 0006334 nucleosome assembly, 0000786 nucleosome, 0005634 nucleus; PDB: 2LSO_A 2RQP_A 1UHM_A 1UST_A 1GHC_A 1HST_A 1YQA_A 1USS_A.
Probab=47.39 E-value=62 Score=24.45 Aligned_cols=44 Identities=9% Similarity=0.165 Sum_probs=34.4
Q ss_pred HHHhhCCCCCccHHHHHHHHHHHhCCCChh--hhHHHHHHHHHHHh
Q 021906 13 EFLKNSDLNTTTTGIVRRQLEKDFGVDLTD--KKIFIREQVDLFLQ 56 (305)
Q Consensus 13 ~IL~~aDl~~vT~K~VR~~Le~~fgvDLs~--kK~~I~~~I~~~l~ 56 (305)
+|-.-.|-.-.|...|.+-|++.|++++.. .+.+++..+...+.
T Consensus 12 AI~~l~er~GsS~~aI~kyI~~~y~~~~~~~~~~~~l~~aLk~~v~ 57 (77)
T PF00538_consen 12 AIKALKERKGSSLQAIKKYIKAKYKVDLNPANFKSRLKRALKRGVE 57 (77)
T ss_dssp HHHHCCSSSSEEHHHHHHHHHHHSSCCCCHTTHHHHHHHHHHHHHH
T ss_pred HHHHcCCCCCCCHHHHHHHHHHhcCcCCChHHHHHHHHHHHHHHHH
Confidence 344446788899999999999999999876 67777777666654
No 27
>PTZ00171 acyl carrier protein; Provisional
Probab=45.93 E-value=23 Score=30.76 Aligned_cols=58 Identities=12% Similarity=0.233 Sum_probs=49.6
Q ss_pred CCCCccHHHHHHHHHHHHhhhCCCCCCCCCccccchhHHhhhCCCccChhhHHHHHHccCC
Q 021906 155 GVTELARTEVVKQLWAYIREKDLQDPNNRRNIVCDERLRALFGVDTINMFQMNKALSKHIW 215 (305)
Q Consensus 155 G~~~~sR~~vvk~lW~YIK~n~LqdP~nkr~I~cD~~Lk~lfg~~~i~~~~m~k~L~~Hl~ 215 (305)
|...|++.+|...|+++|.+.--.+| ..|.+|..|..-+|-|++.+.+|.-.|..+|-
T Consensus 62 ~~~~~~~~~v~~~l~eiiae~l~vd~---~~I~~ds~~~~dLg~DSLd~veLv~~LEdeFg 119 (148)
T PTZ00171 62 KQYLLSKEDVLTRVKKVVKNFEKVDA---SKITPESNFVKDLGADSLDVVELLIAIEQEFN 119 (148)
T ss_pred cccccCHHHHHHHHHHHHHHHhCCCH---hhCCCCcchhhhcCCCHHHHHHHHHHHHHHHC
Confidence 45678899999999999998853344 45889999999999999999999999999884
No 28
>PRK05350 acyl carrier protein; Provisional
Probab=41.03 E-value=48 Score=25.20 Aligned_cols=43 Identities=21% Similarity=0.279 Sum_probs=30.2
Q ss_pred CCCHHHHHHHHHHHHhh---CCCCC---------------ccHHHHHHHHHHHhCCCChhh
Q 021906 1 MVSDSELIARLQEFLKN---SDLNT---------------TTTGIVRRQLEKDFGVDLTDK 43 (305)
Q Consensus 1 m~sd~ei~~~I~~IL~~---aDl~~---------------vT~K~VR~~Le~~fgvDLs~k 43 (305)
|.+.+++...|.+||.. .++.. +..-.+.-.||+.||+.+...
T Consensus 1 ~m~~~~i~~~v~~ii~~~~~~~~~~i~~d~~l~~dlg~DSld~veli~~lE~~fgI~i~~~ 61 (82)
T PRK05350 1 MMTREEILERLRAILVELFEIDPEDITPEANLYEDLDLDSIDAVDLVVHLQKLTGKKIKPE 61 (82)
T ss_pred CCCHHHHHHHHHHHHHHHhCCCHHHCCCCccchhhcCCCHHHHHHHHHHHHHHHCCccCHH
Confidence 56788888888888863 22222 223357888999999998863
No 29
>PF00550 PP-binding: Phosphopantetheine attachment site; InterPro: IPR006163 Phosphopantetheine (or pantetheine 4' phosphate) is the prosthetic group of acyl carrier proteins (ACP) in some multienzyme complexes where it serves as a 'swinging arm' for the attachment of activated fatty acid and amino-acid groups []. The amino-terminal region of the ACP proteins is well defined and consists of alpha four helices arranged in a right-handed bundle held together by interhelical hydrophobic interactions. The Asp-Ser-Leu (DSL)motif is conserved in all of the ACP sequences, and the 4'-PP prosthetic group is covalently linked via a phosphodiester bond to the serine residue. The DSL sequence is present at the amino terminus of helix II, a domain of the protein referred to as the recognition helix and which is responsible for the interaction of ACPs with the enzymes of type II fatty acid synthesis [].; GO: 0048037 cofactor binding; PDB: 3EJB_E 3EJE_G 1L0I_A 2FHS_C 3EJD_E 2FAE_B 2FAD_B 2FAC_B 2K94_A 1ACP_A ....
Probab=38.80 E-value=58 Score=22.98 Aligned_cols=39 Identities=21% Similarity=0.328 Sum_probs=28.7
Q ss_pred HHHHHHHHHHHhh-------------CCCCCccHHHHHHHHHHHhCCCChhh
Q 021906 5 SELIARLQEFLKN-------------SDLNTTTTGIVRRQLEKDFGVDLTDK 43 (305)
Q Consensus 5 ~ei~~~I~~IL~~-------------aDl~~vT~K~VR~~Le~~fgvDLs~k 43 (305)
++|+..+.++|.. ..++.+..-.++..|++.||+.++..
T Consensus 1 e~l~~~~~~~l~~~~~~i~~~~~~~~lG~DSl~~~~l~~~l~~~~g~~i~~~ 52 (67)
T PF00550_consen 1 EQLREIIAEVLGVDPEEIDPDTDFFDLGLDSLDAIELVSELEEEFGIKIPPS 52 (67)
T ss_dssp HHHHHHHHHHHTSSGGCTSTTSBTTTTTSSHHHHHHHHHHHHHHHTSSTTHH
T ss_pred CHHHHHHHHHHCcCHhhCCCCCCHHHhCCchHHHHHHHHHHHHHHcCCCCHH
Confidence 4677777777762 12455566689999999999998875
No 30
>PF03705 CheR_N: CheR methyltransferase, all-alpha domain; InterPro: IPR022641 CheR proteins are part of the chemotaxis signaling mechanism which methylates the chemotaxis receptor at specific glutamate residues. This entry refers to the N-terminal domain of the CherR-type MCP methyltransferases, which are found in bacteria, archaea and green plants. This entry is found in association with PF01739 from PFAM. Methyl transfer from the ubiquitous S-adenosyl-L-methionine (AdoMet) to either nitrogen, oxygen or carbon atoms is frequently employed in diverse organisms ranging from bacteria to plants and mammals. The reaction is catalysed by methyltransferases (Mtases) and modifies DNA, RNA, proteins and small molecules, such as catechol for regulatory purposes. The various aspects of the role of DNA methylation in prokaryotic restriction-modification systems and in a number of cellular processes in eukaryotes including gene regulation and differentiation is well documented. Three classes of DNA Mtases transfer the methyl group from AdoMet to the target base to form either N-6-methyladenine, or N-4-methylcytosine, or C-5- methylcytosine. In C-5-cytosine Mtases, ten conserved motifs are arranged in the same order []. Motif I (a glycine-rich or closely related consensus sequence; FAGxGG in M.HhaI []), shared by other AdoMet-Mtases [], is part of the cofactor binding site and motif IV (PCQ) is part of the catalytic site. In contrast, sequence comparison among N-6-adenine and N-4-cytosine Mtases indicated two of the conserved segments [], although more conserved segments may be present. One of them corresponds to motif I in C-5-cytosine Mtases, and the other is named (D/N/S)PP(Y/F). Crystal structures are known for a number of Mtases [, , , ]. The cofactor binding sites are almost identical and the essential catalytic amino acids coincide. The comparable protein folding and the existence of equivalent amino acids in similar secondary and tertiary positions indicate that many (if not all) AdoMet-Mtases have a common catalytic domain structure. This permits tertiary structure prediction of other DNA, RNA, protein, and small-molecule AdoMet-Mtases from their amino acid sequences []. Flagellated bacteria swim towards favourable chemicals and away from deleterious ones. Sensing of chemoeffector gradients involves chemotaxis receptors, transmembrane (TM) proteins that detect stimuli through their periplasmic domains and transduce the signals via their cytoplasmic domains []. Signalling outputs from these receptors are influenced both by the binding of the chemoeffector ligand to their periplasmic domains and by methylation of specific glutamate residues on their cytoplasmic domains. Methylation is catalysed by CheR, an S-adenosylmethionine-dependent methyltransferase [], which reversibly methylates specific glutamate residues within a coiled coil region, to form gamma-glutamyl methyl ester residues [, ]. The structure of the Salmonella typhimurium chemotaxis receptor methyltransferase CheR, bound to S-adenosylhomocysteine, has been determined to a resolution of 2.0 A []. The structure reveals CheR to be a two-domain protein, with a smaller N-terminal helical domain linked via a single polypeptide connection to a larger C-terminal alpha/beta domain. The C-terminal domain has the characteristics of a nucleotide-binding fold, with an insertion of a small anti-parallel beta-sheet subdomain. The S-adenosylhomocysteine-binding site is formed mainly by the large domain, with contributions from residues within the N-terminal domain and the linker region [].; PDB: 1AF7_A 1BC5_A.
Probab=37.83 E-value=70 Score=22.26 Aligned_cols=31 Identities=16% Similarity=0.325 Sum_probs=19.0
Q ss_pred HHHHHHHHHHhCCCChhhh-HHHHHHHHHHHh
Q 021906 26 GIVRRQLEKDFGVDLTDKK-IFIREQVDLFLQ 56 (305)
Q Consensus 26 K~VR~~Le~~fgvDLs~kK-~~I~~~I~~~l~ 56 (305)
..++..|.+.+|+||++.| ..|..-|...+.
T Consensus 6 ~~~~~~i~~~~Gi~l~~~K~~~l~rRl~~rm~ 37 (57)
T PF03705_consen 6 ERFRELIYRRTGIDLSEYKRSLLERRLARRMR 37 (57)
T ss_dssp HHHHHHHHHHH-----GGGHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHCCCCchhhHHHHHHHHHHHHH
Confidence 5688999999999999976 666666655554
No 31
>smart00526 H15 Domain in histone families 1 and 5.
Probab=37.33 E-value=1.3e+02 Score=21.95 Aligned_cols=44 Identities=5% Similarity=0.171 Sum_probs=31.4
Q ss_pred HHHHhhCCCCCccHHHHHHHHHHHhCCCChhhhHHHHHHHHHHH
Q 021906 12 QEFLKNSDLNTTTTGIVRRQLEKDFGVDLTDKKIFIREQVDLFL 55 (305)
Q Consensus 12 ~~IL~~aDl~~vT~K~VR~~Le~~fgvDLs~kK~~I~~~I~~~l 55 (305)
.+|..-.|....|...|++-+++.|+++-...+.+++..+...+
T Consensus 13 eAI~~l~er~GsS~~aI~kyi~~~~~~~~~~~~~~l~~~Lk~~v 56 (66)
T smart00526 13 EAISALKERKGSSLQAIKKYIEANYKVLPNNFRSLLKLALKKLV 56 (66)
T ss_pred HHHHHcCCCCCCCHHHHHHHHHHhCCCChHHHHHHHHHHHHHHH
Confidence 44445567788899999999999999875554566655554444
No 32
>PF13699 DUF4157: Domain of unknown function (DUF4157)
Probab=35.68 E-value=28 Score=26.97 Aligned_cols=23 Identities=35% Similarity=0.689 Sum_probs=18.2
Q ss_pred HHHHHHHHHHhCCCChhhhHHHH
Q 021906 26 GIVRRQLEKDFGVDLTDKKIFIR 48 (305)
Q Consensus 26 K~VR~~Le~~fgvDLs~kK~~I~ 48 (305)
..||..||..||+||+.=+-..+
T Consensus 4 ~~~r~~~e~~~G~dl~~Vrvh~~ 26 (79)
T PF13699_consen 4 ESIRSRLERAFGADLSDVRVHTG 26 (79)
T ss_pred HHHHHHHHHHhCCCccceEEEeC
Confidence 35899999999999998654433
No 33
>PRK07117 acyl carrier protein; Validated
Probab=32.74 E-value=44 Score=25.78 Aligned_cols=53 Identities=13% Similarity=0.221 Sum_probs=42.6
Q ss_pred ccHHHHHHHHHHHHhhhCCCCC-CCCCccccchhHHhhhCCCccChhhHHHHHHccCC
Q 021906 159 LARTEVVKQLWAYIREKDLQDP-NNRRNIVCDERLRALFGVDTINMFQMNKALSKHIW 215 (305)
Q Consensus 159 ~sR~~vvk~lW~YIK~n~LqdP-~nkr~I~cD~~Lk~lfg~~~i~~~~m~k~L~~Hl~ 215 (305)
|+|.+|..+|-+.|.+.- | -+...|..|..|+. ||.+++.+.+|--.|...|-
T Consensus 1 M~~~ei~~~v~~ii~e~~---p~i~~~~I~~~~~l~D-Lg~DSlD~veiv~~led~f~ 54 (79)
T PRK07117 1 MDKQRIFDILVRHIREVL---PDLDQHQFQPEDSLVD-LGANSMDRAEIVIMTLESLS 54 (79)
T ss_pred CCHHHHHHHHHHHHHHHc---CCCCHHHCCCCCChhh-cCCChHHHHHHHHHHHHHHC
Confidence 578888888888888865 2 23357899999988 99999999999888777663
No 34
>PF09357 RteC: RteC protein; InterPro: IPR018534 Human colonic Bacteroides species harbour a family of large conjugative transposons, called tetracycline resistance (Tcr) elements. Activities of these elements are enhanced by pregrowth of bacteria in medium containing tetracycline, indicating that at least some Tcr element genes are regulated by tetracycline. An insertional disruption in the rteC gene abolished self-transfer of the Tcr element to Bacteroides recipients, indicating that the gene was essential for self-transfer [].
Probab=32.40 E-value=1.9e+02 Score=26.68 Aligned_cols=56 Identities=20% Similarity=0.292 Sum_probs=40.5
Q ss_pred CHHHHHHHHHHHHhhCCC--CCccHHHHHHHHHHHhCCCChhh--------------hHHHHHHHHHHHhhh
Q 021906 3 SDSELIARLQEFLKNSDL--NTTTTGIVRRQLEKDFGVDLTDK--------------KIFIREQVDLFLQSQ 58 (305)
Q Consensus 3 sd~ei~~~I~~IL~~aDl--~~vT~K~VR~~Le~~fgvDLs~k--------------K~~I~~~I~~~l~~~ 58 (305)
|.-+|++-|=++-...-+ .+++-+.|-..+|..|||+|.+- -.|++.+.+.++..+
T Consensus 143 sk~~LiELiYaL~~~g~in~G~~~i~~i~~~fe~~F~i~l~~~y~~~~~ik~RK~~rT~FLd~L~~~L~~~m 214 (218)
T PF09357_consen 143 SKTDLIELIYALYASGCINNGNADIKEIARFFEKLFNIDLGDYYRTFHEIKNRKKSRTKFLDKLKESLNKRM 214 (218)
T ss_pred hHHHHHHHHHHHHHcCCcCCCccCHHHHHHHHHHHhCCCcchHHHHHHHHHhcCCChhHHHHHHHHHHHHHH
Confidence 445677777777766666 67788999999999999999761 155666666655544
No 35
>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=29.54 E-value=73 Score=20.52 Aligned_cols=42 Identities=21% Similarity=0.361 Sum_probs=25.6
Q ss_pred HHHHhhhCCCCccHHHHHHHHHHHHhhhCCCCCC--CCCccccchhHHhhh
Q 021906 148 PQLQEFIGVTELARTEVVKQLWAYIREKDLQDPN--NRRNIVCDERLRALF 196 (305)
Q Consensus 148 ~~La~~lG~~~~sR~~vvk~lW~YIK~n~LqdP~--nkr~I~cD~~Lk~lf 196 (305)
.++|.+||++.- .||.|++...+.-.. +++.....+.+..++
T Consensus 4 ~e~a~~lgvs~~-------tl~~~~~~g~~~~~~~~~~~~~~~~~ei~~~~ 47 (49)
T cd04762 4 KEAAELLGVSPS-------TLRRWVKEGKLKAIRTPGGHRRFPEEDLERLL 47 (49)
T ss_pred HHHHHHHCcCHH-------HHHHHHHcCCCCceeCCCCceecCHHHHHHHH
Confidence 478888888765 789999987764221 233344444444433
No 36
>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=28.51 E-value=18 Score=25.36 Aligned_cols=38 Identities=26% Similarity=0.420 Sum_probs=21.8
Q ss_pred HHHhhhCCCCccHHHHHHHHHHHHhhhCCCCCCCCCcc
Q 021906 149 QLQEFIGVTELARTEVVKQLWAYIREKDLQDPNNRRNI 186 (305)
Q Consensus 149 ~La~~lG~~~~sR~~vvk~lW~YIK~n~LqdP~nkr~I 186 (305)
+|+.++|....+-+.+++.|-+.==-..-++|.|+|.|
T Consensus 22 ~la~~~~~~~~~~t~~i~~L~~~g~I~r~~~~~D~R~v 59 (59)
T PF01047_consen 22 ELAEKLGISRSTVTRIIKRLEKKGLIERERDPDDRRQV 59 (59)
T ss_dssp HHHHHHTS-HHHHHHHHHHHHHTTSEEEEEETTETTSE
T ss_pred HHHHHHCCChhHHHHHHHHHHHCCCEEeccCCCCCCcC
Confidence 88999988666555555555442111223567777654
No 37
>PF11693 DUF2990: Protein of unknown function (DUF2990); InterPro: IPR021706 This family of proteins represents a fungal protein with unknown function.
Probab=28.28 E-value=46 Score=25.10 Aligned_cols=24 Identities=38% Similarity=0.599 Sum_probs=19.4
Q ss_pred CCCCCCCcHHHHHhhCCCCCCCCHHHHHHHHHHHHHh
Q 021906 259 FLAPLQLSDALIKFLGTGESALPRSDVIKRMWDYIKE 295 (305)
Q Consensus 259 ~~~~~~lS~~L~~~~g~~~~~~~r~~v~k~~W~YIk~ 295 (305)
|...|.-|++|++|+| +|-.||-.
T Consensus 15 fd~~Yd~S~dlaeFy~-------------rVSk~I~~ 38 (64)
T PF11693_consen 15 FDNVYDYSDDLAEFYG-------------RVSKYIES 38 (64)
T ss_pred hhccccCCHHHHHHHH-------------HHHHHHHH
Confidence 4556999999999998 67777754
No 38
>PF13950 Epimerase_Csub: UDP-glucose 4-epimerase C-term subunit; PDB: 1EK5_A 1I3K_B 1I3M_B 1HZJ_A 1EK6_A 1I3N_A 1I3L_A 2CNB_B 1GY8_D 1NAI_A ....
Probab=27.60 E-value=93 Score=22.87 Aligned_cols=42 Identities=17% Similarity=0.404 Sum_probs=24.6
Q ss_pred ccCCCCCCccccCCHHHHhhhC-CCCccHHHHHHHHHHHHhhh
Q 021906 134 KKRGGGFSKLCALSPQLQEFIG-VTELARTEVVKQLWAYIREK 175 (305)
Q Consensus 134 ~~~~~g~~k~~~lS~~La~~lG-~~~~sR~~vvk~lW~YIK~n 175 (305)
.++.|.....+-=..-....|| ....+-.+++...|++.+.|
T Consensus 16 ~rR~GD~~~~~Ad~~kA~~~LgW~p~~~L~~~i~~~w~W~~~n 58 (62)
T PF13950_consen 16 PRRPGDPAHLVADISKAREELGWKPKYSLEDMIRDAWNWQKKN 58 (62)
T ss_dssp ---TT--SEE-B--HHHHHHC----SSSHHHHHHHHHHHHHHS
T ss_pred CCCCCchhhhhCCHHHHHHHhCCCcCCCHHHHHHHHHHHHHHC
Confidence 3455666555554555558899 56779999999999999876
No 39
>PF13276 HTH_21: HTH-like domain
Probab=26.71 E-value=1.1e+02 Score=21.68 Aligned_cols=41 Identities=22% Similarity=0.347 Sum_probs=34.1
Q ss_pred HHHHHHHHHHHHhhCCCCCccHHHHHHHHHHHhCCCChhhhH
Q 021906 4 DSELIARLQEFLKNSDLNTTTTGIVRRQLEKDFGVDLTDKKI 45 (305)
Q Consensus 4 d~ei~~~I~~IL~~aDl~~vT~K~VR~~Le~~fgvDLs~kK~ 45 (305)
|++|...|.+|...... +.-...|...|...+|+.++.++-
T Consensus 3 ~~~l~~~I~~i~~~~~~-~yG~rri~~~L~~~~~~~v~~krV 43 (60)
T PF13276_consen 3 DEALRELIKEIFKESKP-TYGYRRIWAELRREGGIRVSRKRV 43 (60)
T ss_pred hHHHHHHHHHHHHHcCC-CeehhHHHHHHhccCcccccHHHH
Confidence 68899999999998866 556778999999998888887653
No 40
>cd00923 Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. Found only in eukaryotes, subunit Va is one of three mammalian subunits that lacks a transmembrane region. Subunit Va is located on the matrix side of the membrane and binds thyroid hormone T2, releasing allosteric inhibition caused by the binding of ATP to subunit IV and allowing high turnover at elevated intramitochondrial ATP/ADP ratios.
Probab=26.45 E-value=1.5e+02 Score=24.51 Aligned_cols=45 Identities=29% Similarity=0.488 Sum_probs=36.6
Q ss_pred CHHHHHHHHHHHHhhCCCCCccHHHHHHHHHHHhCCCChhhhHHHHHH
Q 021906 3 SDSELIARLQEFLKNSDLNTTTTGIVRRQLEKDFGVDLTDKKIFIREQ 50 (305)
Q Consensus 3 sd~ei~~~I~~IL~~aDl~~vT~K~VR~~Le~~fgvDLs~kK~~I~~~ 50 (305)
|++++-.+-.......|++.-. ||+.|...||.||-+-=+.|.+.
T Consensus 4 t~EeF~aRye~~F~~~~iD~we---~rr~mN~l~~~DlVP~P~ii~aa 48 (103)
T cd00923 4 TDEEFDARYETYFNRPDIDGWE---LRRGLNNLFGYDLVPEPKVIEAA 48 (103)
T ss_pred cHHHHHHHHHHHhCCcCccHHH---HHHHHHHHhccccCCCcHHHHHH
Confidence 7888888888888888877654 99999999999998876655433
No 41
>PLN02945 nicotinamide-nucleotide adenylyltransferase/nicotinate-nucleotide adenylyltransferase
Probab=26.36 E-value=48 Score=30.56 Aligned_cols=32 Identities=25% Similarity=0.272 Sum_probs=24.1
Q ss_pred cHHHHHhhCCCCCCCCHHHHHHHHHHHHHhcCCC
Q 021906 266 SDALIKFLGTGESALPRSDVIKRMWDYIKEKNLQ 299 (305)
Q Consensus 266 S~~L~~~~g~~~~~~~r~~v~k~~W~YIk~~~Lq 299 (305)
|.++...+..+ .--+.-|-..|++||++|+|-
T Consensus 204 ST~IR~~l~~g--~~i~~lvP~~V~~YI~~~~LY 235 (236)
T PLN02945 204 STRVRECISRG--LSVKYLTPDGVIDYIKEHGLY 235 (236)
T ss_pred HHHHHHHHHcC--CCchhhCCHHHHHHHHHcCCC
Confidence 44777777655 445567788999999999983
No 42
>PRK00071 nadD nicotinic acid mononucleotide adenylyltransferase; Provisional
Probab=25.95 E-value=43 Score=29.82 Aligned_cols=32 Identities=22% Similarity=0.233 Sum_probs=21.9
Q ss_pred CHHHHhhhCCCCccHHHHHHHHHHHHhhhCCC
Q 021906 147 SPQLQEFIGVTELARTEVVKQLWAYIREKDLQ 178 (305)
Q Consensus 147 S~~La~~lG~~~~sR~~vvk~lW~YIK~n~Lq 178 (305)
|..+.+.|.....-+.-|-..+++||++|+|+
T Consensus 170 ST~IR~~l~~g~~~~~lvp~~V~~YI~~~~LY 201 (203)
T PRK00071 170 STAIRERIKEGRPIRYLLPEAVLDYIEKHGLY 201 (203)
T ss_pred HHHHHHHHHcCCChhHhCCHHHHHHHHHhCcc
Confidence 34455555444444566777899999999996
No 43
>PF13551 HTH_29: Winged helix-turn helix
Probab=25.61 E-value=1.2e+02 Score=23.43 Aligned_cols=40 Identities=28% Similarity=0.391 Sum_probs=30.0
Q ss_pred HHHHHHHHHHHHhhCCC---CCccHHHHHHHH-HHHhCCCChhh
Q 021906 4 DSELIARLQEFLKNSDL---NTTTTGIVRRQL-EKDFGVDLTDK 43 (305)
Q Consensus 4 d~ei~~~I~~IL~~aDl---~~vT~K~VR~~L-e~~fgvDLs~k 43 (305)
+++....|.+++..-.. ...|...|+..| ++.||+++|..
T Consensus 59 ~~~~~~~l~~~~~~~p~~g~~~~t~~~l~~~l~~~~~~~~~s~~ 102 (112)
T PF13551_consen 59 SEEQRAQLIELLRENPPEGRSRWTLEELAEWLIEEEFGIDVSPS 102 (112)
T ss_pred CHHHHHHHHHHHHHCCCCCCCcccHHHHHHHHHHhccCccCCHH
Confidence 35566677777775443 357899999988 99999999873
No 44
>PLN02945 nicotinamide-nucleotide adenylyltransferase/nicotinate-nucleotide adenylyltransferase
Probab=25.29 E-value=47 Score=30.59 Aligned_cols=32 Identities=22% Similarity=0.240 Sum_probs=22.6
Q ss_pred CHHHHhhhCCCCccHHHHHHHHHHHHhhhCCC
Q 021906 147 SPQLQEFIGVTELARTEVVKQLWAYIREKDLQ 178 (305)
Q Consensus 147 S~~La~~lG~~~~sR~~vvk~lW~YIK~n~Lq 178 (305)
|..+...|.....-+.-|-..+++||++|+|.
T Consensus 204 ST~IR~~l~~g~~i~~lvP~~V~~YI~~~~LY 235 (236)
T PLN02945 204 STRVRECISRGLSVKYLTPDGVIDYIKEHGLY 235 (236)
T ss_pred HHHHHHHHHcCCCchhhCCHHHHHHHHHcCCC
Confidence 44555555544445566777899999999996
No 45
>cd00073 H15 linker histone 1 and histone 5 domains; the basic subunit of chromatin is the nucleosome, consisting of an octamer of core histones, two full turns of DNA, a linker histone (H1 or H5) and a variable length of linker DNA; H1/H5 are chromatin-associated proteins that bind to the exterior of nucleosomes and dramatically stabilize the highly condensed states of chromatin fibers; stabilization of higher order folding occurs through electrostatic neutralization of the linker DNA segments, through a highly positively charged carboxy- terminal domain known as the AKP helix (Ala, Lys, Pro); thought to be involved in specific protein-protein and protein-DNA interactions and play a role in suppressing core histone tail domain acetylation in the chromatin fiber
Probab=24.78 E-value=2.3e+02 Score=22.01 Aligned_cols=46 Identities=7% Similarity=0.119 Sum_probs=33.2
Q ss_pred HHHHHhhCCCCCccHHHHHHHHHHHhCCCChhhhHHHHHHHHHHHh
Q 021906 11 LQEFLKNSDLNTTTTGIVRRQLEKDFGVDLTDKKIFIREQVDLFLQ 56 (305)
Q Consensus 11 I~~IL~~aDl~~vT~K~VR~~Le~~fgvDLs~kK~~I~~~I~~~l~ 56 (305)
+++|..-.|....|...|++-+++.|.++....+.+++..+...+.
T Consensus 12 ~eAI~~l~er~GsS~~aI~kyI~~~y~~~~~~~~~~l~~aLkk~v~ 57 (88)
T cd00073 12 TEAIKALKERKGSSLQAIKKYIEAKYKVDDENFNKLLKLALKKGVA 57 (88)
T ss_pred HHHHHHcCCCCCcCHHHHHHHHHHHCCcchHHHHHHHHHHHHHHHH
Confidence 3445555678888999999999999998875556666655554443
No 46
>KOG2076 consensus RNA polymerase III transcription factor TFIIIC [Transcription]
Probab=24.63 E-value=1.2e+02 Score=33.75 Aligned_cols=80 Identities=28% Similarity=0.341 Sum_probs=53.5
Q ss_pred ccCCCCCCccccCCHHHHhhhCCC-----CccHHHHHHHHHHHHhhhCCCCCCCCCccccchhHHhhhCCC-ccChhhHH
Q 021906 134 KKRGGGFSKLCALSPQLQEFIGVT-----ELARTEVVKQLWAYIREKDLQDPNNRRNIVCDERLRALFGVD-TINMFQMN 207 (305)
Q Consensus 134 ~~~~~g~~k~~~lS~~La~~lG~~-----~~sR~~vvk~lW~YIK~n~LqdP~nkr~I~cD~~Lk~lfg~~-~i~~~~m~ 207 (305)
++++++--..-.|+++|+.+||.- ..-..+....+-.-|| ||| +.+++=..|-.|+..- .+.-+-.-
T Consensus 123 ~k~~~~~r~~~~l~~~l~~ll~eAN~lfarg~~eeA~~i~~EvIk----qdp---~~~~ay~tL~~IyEqrGd~eK~l~~ 195 (895)
T KOG2076|consen 123 KKRGRRSRGKSKLAPELRQLLGEANNLFARGDLEEAEEILMEVIK----QDP---RNPIAYYTLGEIYEQRGDIEKALNF 195 (895)
T ss_pred CccCCCCCcccccCHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHH----hCc---cchhhHHHHHHHHHHcccHHHHHHH
Confidence 334444446678999999999953 4566778888888888 455 4556666777777321 23333345
Q ss_pred HHHHccCCCCCCc
Q 021906 208 KALSKHIWPLDSD 220 (305)
Q Consensus 208 k~L~~Hl~pl~p~ 220 (305)
-+|..||-|-++.
T Consensus 196 ~llAAHL~p~d~e 208 (895)
T KOG2076|consen 196 WLLAAHLNPKDYE 208 (895)
T ss_pred HHHHHhcCCCChH
Confidence 5788999888773
No 47
>PRK00071 nadD nicotinic acid mononucleotide adenylyltransferase; Provisional
Probab=24.40 E-value=54 Score=29.21 Aligned_cols=35 Identities=26% Similarity=0.330 Sum_probs=24.6
Q ss_pred CCCcH-HHHHhhCCCCCCCCHHHHHHHHHHHHHhcCCC
Q 021906 263 LQLSD-ALIKFLGTGESALPRSDVIKRMWDYIKEKNLQ 299 (305)
Q Consensus 263 ~~lS~-~L~~~~g~~~~~~~r~~v~k~~W~YIk~~~Lq 299 (305)
+.||. ++...+..+ .--+.-|-..|++||++|+|-
T Consensus 166 ~~ISST~IR~~l~~g--~~~~~lvp~~V~~YI~~~~LY 201 (203)
T PRK00071 166 LAISSTAIRERIKEG--RPIRYLLPEAVLDYIEKHGLY 201 (203)
T ss_pred CccCHHHHHHHHHcC--CChhHhCCHHHHHHHHHhCcc
Confidence 44554 667766654 334566778899999999984
No 48
>PRK06973 nicotinic acid mononucleotide adenylyltransferase; Provisional
Probab=24.23 E-value=48 Score=30.95 Aligned_cols=32 Identities=19% Similarity=0.452 Sum_probs=23.6
Q ss_pred CHHHHhhhCCC--------CccHHHHHHHHHHHHhhhCCC
Q 021906 147 SPQLQEFIGVT--------ELARTEVVKQLWAYIREKDLQ 178 (305)
Q Consensus 147 S~~La~~lG~~--------~~sR~~vvk~lW~YIK~n~Lq 178 (305)
|.++.+.|+.. ..-+.-|=..+++||++|+|+
T Consensus 202 ST~IR~~l~~g~~~~~~~~~~i~~lvP~~V~~YI~~~~LY 241 (243)
T PRK06973 202 ATDIRAHLRACIARRAQVPDASAEHVPAAVWAYILQHRLY 241 (243)
T ss_pred HHHHHHHHHcCCCcccccCCChhHhCCHHHHHHHHHcCCC
Confidence 45666666654 445566777899999999997
No 49
>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=24.08 E-value=50 Score=24.10 Aligned_cols=47 Identities=19% Similarity=0.439 Sum_probs=31.2
Q ss_pred cccCC-HHHHhhhCCCCccHHHHHHHHHHHHhhhCCCCCCCCCccccc-hhHH
Q 021906 143 LCALS-PQLQEFIGVTELARTEVVKQLWAYIREKDLQDPNNRRNIVCD-ERLR 193 (305)
Q Consensus 143 ~~~lS-~~La~~lG~~~~sR~~vvk~lW~YIK~n~LqdP~nkr~I~cD-~~Lk 193 (305)
.+.++ .+||.++|++..+ |.++-...+..++-+-..+.++++| +.|+
T Consensus 26 ~~~lt~~~iA~~~g~sr~t----v~r~l~~l~~~g~I~~~~~~i~I~d~~~L~ 74 (76)
T PF13545_consen 26 PLPLTQEEIADMLGVSRET----VSRILKRLKDEGIIEVKRGKIIILDPERLE 74 (76)
T ss_dssp EEESSHHHHHHHHTSCHHH----HHHHHHHHHHTTSEEEETTEEEESSHHHHH
T ss_pred EecCCHHHHHHHHCCCHHH----HHHHHHHHHHCCCEEEcCCEEEECCHHHHh
Confidence 34444 5799999976543 3444455667777777778888888 4444
No 50
>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=23.54 E-value=54 Score=28.97 Aligned_cols=32 Identities=16% Similarity=0.213 Sum_probs=22.4
Q ss_pred CHHHHhhhCCCCccHHHHHHHHHHHHhhhCCC
Q 021906 147 SPQLQEFIGVTELARTEVVKQLWAYIREKDLQ 178 (305)
Q Consensus 147 S~~La~~lG~~~~sR~~vvk~lW~YIK~n~Lq 178 (305)
|.+..+.+.....-+.-|-..+++||++|+|.
T Consensus 162 ST~IR~~l~~g~~~~~lvP~~V~~YI~~~~LY 193 (193)
T TIGR00482 162 STEIRQRIRQGKSIEYLLPDPVIKYIKQHGLY 193 (193)
T ss_pred HHHHHHHHHcCCCchhhCCHHHHHHHHHhCCC
Confidence 44555555544445566778899999999984
No 51
>PF11740 KfrA_N: Plasmid replication region DNA-binding N-term; InterPro: IPR021104 The KfrA family of protiens are encoded on plasmids, generally in or near gene clusters invloved in stable inheritance functions. These proteins are thought to form an all-helical structure, consisting of an N-terminal helix-turn-helix DNA binding domain and an extended coiled-coil tail. The best-characterised KfrA protein, encoded on the broad host-range Plasmid RK2, is a site-specific DNA-binding protein whose operator overlaps its own promoter. The DNA-binding domain is essential for function, while the coiled-coil domain is probably responsible for formation of multimers, and may provide an example of a bridge to host structures required for plasmid partitioning []. This entry represents the N-terminal DNA-binding domain.
Probab=23.13 E-value=2.4e+02 Score=22.50 Aligned_cols=42 Identities=19% Similarity=0.342 Sum_probs=32.8
Q ss_pred CCHHHHHHHHHHHHhhCCCCCccHHHHHHHHHHHhCCCChhhhHHHH
Q 021906 2 VSDSELIARLQEFLKNSDLNTTTTGIVRRQLEKDFGVDLTDKKIFIR 48 (305)
Q Consensus 2 ~sd~ei~~~I~~IL~~aDl~~vT~K~VR~~Le~~fgvDLs~kK~~I~ 48 (305)
+|.++|......|+...- .+|...||..|. +..++.=.++|+
T Consensus 1 IT~e~V~~Aa~~L~~~G~--~pT~~~Vr~~lG---~GS~~ti~~~l~ 42 (120)
T PF11740_consen 1 ITYEDVIEAADELLAAGK--KPTVRAVRERLG---GGSMSTISKHLK 42 (120)
T ss_pred CcHHHHHHHHHHHHHcCC--CCCHHHHHHHHC---CCCHHHHHHHHH
Confidence 688999999999997766 889999999887 566665444443
No 52
>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=22.29 E-value=63 Score=28.56 Aligned_cols=34 Identities=18% Similarity=0.241 Sum_probs=24.8
Q ss_pred CCCcH-HHHHhhCCCCCCCCHHHHHHHHHHHHHhcCC
Q 021906 263 LQLSD-ALIKFLGTGESALPRSDVIKRMWDYIKEKNL 298 (305)
Q Consensus 263 ~~lS~-~L~~~~g~~~~~~~r~~v~k~~W~YIk~~~L 298 (305)
+.||. +..+.+..+ .--+.-|-..|++||++|+|
T Consensus 158 ~~iSST~IR~~l~~g--~~~~~lvP~~V~~YI~~~~L 192 (193)
T TIGR00482 158 VPISSTEIRQRIRQG--KSIEYLLPDPVIKYIKQHGL 192 (193)
T ss_pred cccCHHHHHHHHHcC--CCchhhCCHHHHHHHHHhCC
Confidence 44554 777777654 33456778899999999998
No 53
>PF05402 PqqD: Coenzyme PQQ synthesis protein D (PqqD); InterPro: IPR008792 This family contains several bacterial coenzyme PQQ synthesis protein D (PqqD) sequences. This protein is required for coenzyme pyrrolo-quinoline-quinone (PQQ) biosynthesis.; PDB: 3G2B_A.
Probab=21.92 E-value=2.2e+02 Score=20.30 Aligned_cols=42 Identities=14% Similarity=0.172 Sum_probs=25.8
Q ss_pred HHHHhhCCCCCccHHHHHHHHHHHhCCCChhhhHHHHHHHHHH
Q 021906 12 QEFLKNSDLNTTTTGIVRRQLEKDFGVDLTDKKIFIREQVDLF 54 (305)
Q Consensus 12 ~~IL~~aDl~~vT~K~VR~~Le~~fgvDLs~kK~~I~~~I~~~ 54 (305)
..|+.-.| ...|...|.+.|.+.|+++-..-+.-|...+..+
T Consensus 20 ~~Iw~~~~-g~~t~~ei~~~l~~~y~~~~~~~~~dv~~fl~~L 61 (68)
T PF05402_consen 20 AFIWELLD-GPRTVEEIVDALAEEYDVDPEEAEEDVEEFLEQL 61 (68)
T ss_dssp HHHHHH---SSS-HHHHHHHHHHHTT--HHHHHHHHHHHHHHH
T ss_pred HHHHHHcc-CCCCHHHHHHHHHHHcCCCHHHHHHHHHHHHHHH
Confidence 34555554 4688999999999999988776555554444443
No 54
>PF13592 HTH_33: Winged helix-turn helix
Probab=21.87 E-value=81 Score=22.70 Aligned_cols=22 Identities=23% Similarity=0.348 Sum_probs=18.9
Q ss_pred CCccHHHHHHHHHHHhCCCChh
Q 021906 21 NTTTTGIVRRQLEKDFGVDLTD 42 (305)
Q Consensus 21 ~~vT~K~VR~~Le~~fgvDLs~ 42 (305)
..-|.+.|+.-|++.|||.++.
T Consensus 3 ~~wt~~~i~~~I~~~fgv~ys~ 24 (60)
T PF13592_consen 3 GRWTLKEIAAYIEEEFGVKYSP 24 (60)
T ss_pred CcccHHHHHHHHHHHHCCEEcH
Confidence 3468899999999999999954
No 55
>PRK09184 acyl carrier protein; Provisional
Probab=21.81 E-value=1.7e+02 Score=23.01 Aligned_cols=41 Identities=22% Similarity=0.302 Sum_probs=27.1
Q ss_pred CCCHHHHHHHHHHHHhh------CC----------------CCCccHHHHHHHHHHHhCCCCh
Q 021906 1 MVSDSELIARLQEFLKN------SD----------------LNTTTTGIVRRQLEKDFGVDLT 41 (305)
Q Consensus 1 m~sd~ei~~~I~~IL~~------aD----------------l~~vT~K~VR~~Le~~fgvDLs 41 (305)
|-+-++|...|.+||.. .+ |+.+..-.+.-+||+.||+.+.
T Consensus 1 ~~~~~~l~~~l~~~I~e~l~~~~i~~~~I~~d~~l~~~dLglDSld~velv~~lE~~fgi~i~ 63 (89)
T PRK09184 1 MSSMTALERELAELIVEELNLEDVQPESIDADAPLYGEGLGLDSIDILEIALVISKRYGFQLR 63 (89)
T ss_pred CchHHHHHHHHHHHHHHHHCCCCCCHHHCCCCcccccccCCCcHHHHHHHHHHHHHHHCCcCC
Confidence 45667777777777755 13 2333334578899999999885
No 56
>PF08938 HBS1_N: HBS1 N-terminus; InterPro: IPR015033 This domain is found in various eukaryotic HBS1-like proteins. ; PDB: 1UFZ_A 3IZQ_1.
Probab=21.07 E-value=37 Score=26.09 Aligned_cols=29 Identities=28% Similarity=0.559 Sum_probs=22.7
Q ss_pred cccCCHHHHhhhCCCCccHHHHHHHHHHH
Q 021906 143 LCALSPQLQEFIGVTELARTEVVKQLWAY 171 (305)
Q Consensus 143 ~~~lS~~La~~lG~~~~sR~~vvk~lW~Y 171 (305)
.+.+-+.+..+||....|..+|+.+||.|
T Consensus 28 L~~~l~~vr~~Lg~~~~~e~~i~eal~~~ 56 (79)
T PF08938_consen 28 LYSCLPQVREVLGDYVPPEEQIKEALWHY 56 (79)
T ss_dssp HCHHCCCHHHHCCCCC--CCHHHHHHHHT
T ss_pred HHHHHHHHHHHHcccCCCHHHHHHHHHHH
Confidence 35667889999997665999999999987
No 57
>KOG2522 consensus Filamentous baseplate protein Ligatin, contains PUA domain [Translation, ribosomal structure and biogenesis]
Probab=20.94 E-value=71 Score=32.98 Aligned_cols=28 Identities=18% Similarity=0.260 Sum_probs=25.4
Q ss_pred CCCCCHHHHHHHHHHHHHhcCCCcccCC
Q 021906 277 ESALPRSDVIKRMWDYIKEKNLQVSLRS 304 (305)
Q Consensus 277 ~~~~~r~~v~k~~W~YIk~~~Lqdp~nk 304 (305)
++-.+-.||...|..||..|||-|+.||
T Consensus 379 g~lyt~seir~~V~kYi~knnLad~~nK 406 (560)
T KOG2522|consen 379 GTLYTSSEIRSAVSKYISKNNLADTKNK 406 (560)
T ss_pred cceeeHHHHHHHHHHHhhhhhccccccC
Confidence 3467889999999999999999999997
No 58
>PRK07639 acyl carrier protein; Provisional
Probab=20.42 E-value=1.2e+02 Score=23.65 Aligned_cols=54 Identities=17% Similarity=0.202 Sum_probs=43.5
Q ss_pred ccHHHHHHHHHHHHhhhCCCCCCCCCccccchhHHhhhCCCccChhhHHHHHHccC
Q 021906 159 LARTEVVKQLWAYIREKDLQDPNNRRNIVCDERLRALFGVDTINMFQMNKALSKHI 214 (305)
Q Consensus 159 ~sR~~vvk~lW~YIK~n~LqdP~nkr~I~cD~~Lk~lfg~~~i~~~~m~k~L~~Hl 214 (305)
|+|.+|..+|-..|.+.= ..+. -..|..|..|..=+|-+++.+.++.-.|..+|
T Consensus 1 M~~~ei~~~i~~il~e~l-~~~~-~~~i~~d~~l~edL~lDSld~velv~~lE~~f 54 (86)
T PRK07639 1 MRREALKNAVLKIMEEKL-ELKN-VTHLEETMRLNEDLYIDSVMMLQLIVYIEMDV 54 (86)
T ss_pred CCHHHHHHHHHHHHHHHh-CCCc-cccCCCCCCcccccCCChHHHHHHHHHHHHHH
Confidence 678899999999888763 2221 14678899998878999999999999999988
No 59
>PF12824 MRP-L20: Mitochondrial ribosomal protein subunit L20; InterPro: IPR024388 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This entry represents the essential mitochondrial ribosomal protein L20 family from fungi [].
Probab=20.29 E-value=1.2e+02 Score=26.87 Aligned_cols=31 Identities=23% Similarity=0.378 Sum_probs=22.7
Q ss_pred CHHHHHHHHHHHHhhCCCCCccHHHHHHHHHHHhCCC
Q 021906 3 SDSELIARLQEFLKNSDLNTTTTGIVRRQLEKDFGVD 39 (305)
Q Consensus 3 sd~ei~~~I~~IL~~aDl~~vT~K~VR~~Le~~fgvD 39 (305)
|.++|.+.-+ |+..|+.+-| |..|.++|||.
T Consensus 87 t~e~i~Eir~--LR~~DP~~wT----r~~LAkkF~~S 117 (164)
T PF12824_consen 87 TPEDIQEIRR--LRAEDPEKWT----RKKLAKKFNCS 117 (164)
T ss_pred CHHHHHHHHH--HHHcCchHhh----HHHHHHHhCCC
Confidence 4455444332 8999999999 56788999995
No 60
>PF12872 OST-HTH: OST-HTH/LOTUS domain; PDB: 2KPM_A 3S93_B 3RCO_A 2KZV_A.
Probab=20.06 E-value=2.4e+02 Score=20.38 Aligned_cols=40 Identities=20% Similarity=0.276 Sum_probs=28.9
Q ss_pred CHHHHHHHHHHHH-hhCCCC-CccHHHHHHHHHHHhCCCChhh
Q 021906 3 SDSELIARLQEFL-KNSDLN-TTTTGIVRRQLEKDFGVDLTDK 43 (305)
Q Consensus 3 sd~ei~~~I~~IL-~~aDl~-~vT~K~VR~~Le~~fgvDLs~k 43 (305)
+.+++...|.++| +..+-+ .++...|...+...| -++..+
T Consensus 2 ~~~~~~~~l~~ll~~~~~~~g~v~ls~l~~~~~~~~-~~f~~~ 43 (74)
T PF12872_consen 2 SLEELKKLLRELLESQKGEDGWVSLSQLGQEYKKKY-PDFDPR 43 (74)
T ss_dssp --HHHHHHHHHHHHHTCTTTSSEEHHHHHHHHHHHH-TT--TC
T ss_pred hHHHHHHHHHHHHHhCcCCCceEEHHHHHHHHHHHC-CCCCcc
Confidence 4678999999999 444433 699999999999999 666554
No 61
>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=20.01 E-value=60 Score=24.52 Aligned_cols=19 Identities=21% Similarity=0.329 Sum_probs=15.8
Q ss_pred cChhhHHHHHHccCCCCCC
Q 021906 201 INMFQMNKALSKHIWPLDS 219 (305)
Q Consensus 201 i~~~~m~k~L~~Hl~pl~p 219 (305)
+.||.++.+|+.|+.|-+-
T Consensus 8 LfFFSLM~LlSs~l~p~~~ 26 (64)
T PF03511_consen 8 LFFFSLMGLLSSYLAPKEG 26 (64)
T ss_pred HHHHHHHHHHHHhcCcccc
Confidence 5699999999999987543
Done!