Query 015940
Match_columns 398
No_of_seqs 156 out of 531
Neff 3.8
Searched_HMMs 46136
Date Fri Mar 29 02:19:41 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/015940.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/015940hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4282 Transcription factor G 99.9 8.5E-25 1.8E-29 213.9 14.5 273 78-385 54-336 (345)
2 PF13837 Myb_DNA-bind_4: Myb/S 99.9 5.5E-22 1.2E-26 157.8 7.7 85 79-164 2-90 (90)
3 PF13873 Myb_DNA-bind_5: Myb/S 98.5 6.4E-07 1.4E-11 70.6 8.0 67 77-143 1-75 (78)
4 smart00595 MADF subfamily of S 98.3 4.3E-07 9.4E-12 72.6 3.9 71 89-164 2-84 (89)
5 PF12776 Myb_DNA-bind_3: Myb/S 98.2 7.4E-06 1.6E-10 66.1 8.5 71 80-150 1-75 (96)
6 PF10545 MADF_DNA_bdg: Alcohol 98.0 3.8E-06 8.2E-11 65.3 3.2 71 89-162 1-83 (85)
7 PF00249 Myb_DNA-binding: Myb- 97.6 0.0001 2.2E-09 53.7 5.0 47 79-137 2-48 (48)
8 PF13921 Myb_DNA-bind_6: Myb-l 97.5 0.00016 3.5E-09 54.3 4.2 43 81-137 1-44 (60)
9 smart00717 SANT SANT SWI3, AD 97.4 0.00031 6.7E-09 48.6 4.3 47 79-138 2-48 (49)
10 cd00167 SANT 'SWI3, ADA2, N-Co 97.2 0.0005 1.1E-08 46.9 3.8 45 80-137 1-45 (45)
11 PLN03212 Transcription repress 95.1 0.036 7.8E-07 54.5 5.3 48 78-137 25-72 (249)
12 PLN03091 hypothetical protein; 93.9 0.084 1.8E-06 55.7 5.3 48 76-135 12-59 (459)
13 PLN03091 hypothetical protein; 93.0 0.25 5.5E-06 52.2 6.9 56 73-142 62-117 (459)
14 PLN03212 Transcription repress 92.5 0.32 6.9E-06 48.0 6.4 54 73-140 73-126 (249)
15 PF04504 DUF573: Protein of un 84.2 7.4 0.00016 33.0 8.3 66 78-146 4-71 (98)
16 KOG1279 Chromatin remodeling f 84.0 1.1 2.5E-05 48.1 4.0 48 77-138 252-299 (506)
17 KOG0051 RNA polymerase I termi 78.9 2.8 6.2E-05 46.0 4.9 68 76-147 434-517 (607)
18 COG5259 RSC8 RSC chromatin rem 77.8 3.4 7.4E-05 44.4 4.9 49 77-139 278-326 (531)
19 TIGR02894 DNA_bind_RsfA transc 77.3 6.8 0.00015 36.7 6.2 60 76-143 2-62 (161)
20 KOG0048 Transcription factor, 73.9 3.2 7E-05 39.8 3.3 48 78-137 9-56 (238)
21 KOG0049 Transcription factor, 73.3 7.8 0.00017 43.5 6.3 58 72-141 247-304 (939)
22 PRK13923 putative spore coat p 71.4 13 0.00027 35.2 6.4 61 75-143 2-63 (170)
23 PRK09767 hypothetical protein; 68.3 4.8 0.0001 35.4 2.9 51 316-374 37-89 (117)
24 cd01812 BAG1_N Ubiquitin-like 63.9 16 0.00034 27.7 4.6 64 268-337 3-68 (71)
25 cd06398 PB1_Joka2 The PB1 doma 53.4 23 0.00049 29.9 4.2 34 267-300 2-42 (91)
26 KOG0860 Synaptobrevin/VAMP-lik 47.0 24 0.00052 31.5 3.6 62 78-139 30-95 (116)
27 cd01809 Scythe_N Ubiquitin-lik 40.1 74 0.0016 23.9 4.9 57 275-337 13-69 (72)
28 TIGR01557 myb_SHAQKYF myb-like 38.2 58 0.0013 25.3 4.1 44 77-132 2-49 (57)
29 KOG0048 Transcription factor, 37.0 90 0.002 30.0 6.1 57 74-144 58-115 (238)
30 cd02549 Peptidase_C39A A sub-f 36.6 1.5E+02 0.0032 24.7 6.6 80 284-369 45-134 (141)
31 cd01806 Nedd8 Nebb8-like ubiq 35.5 1E+02 0.0022 23.3 5.1 56 278-339 16-71 (76)
32 KOG4468 Polycomb-group transcr 34.7 64 0.0014 36.2 5.1 82 57-148 61-148 (782)
33 PF09608 Alph_Pro_TM: Putative 34.7 29 0.00063 33.9 2.4 52 283-334 120-184 (236)
34 PF00435 Spectrin: Spectrin re 34.1 1.5E+02 0.0032 22.6 5.9 62 83-145 33-94 (105)
35 PRK12354 carbamate kinase; Rev 33.0 52 0.0011 33.6 3.9 46 338-383 107-154 (307)
36 PF08994 T4_Gp59_C: T4 gene Gp 31.3 93 0.002 27.4 4.6 56 84-140 45-102 (103)
37 cd01789 Alp11_N Ubiquitin-like 29.8 94 0.002 25.2 4.3 60 275-337 15-78 (84)
38 COG3835 CdaR Sugar diacid util 26.7 75 0.0016 33.5 3.9 42 227-290 57-100 (376)
39 cd01236 PH_outspread Outspread 26.7 1.1E+02 0.0024 26.3 4.4 45 319-366 47-98 (104)
40 PF03353 Lin-8: Ras-mediated v 25.3 1.6E+02 0.0035 29.2 5.9 64 79-142 18-83 (313)
41 cd05992 PB1 The PB1 domain is 25.0 1.4E+02 0.0031 23.0 4.4 32 267-298 2-36 (81)
42 PF07750 GcrA: GcrA cell cycle 24.9 71 0.0015 29.5 3.0 37 79-128 1-37 (162)
43 smart00666 PB1 PB1 domain. Pho 24.1 1.6E+02 0.0034 22.9 4.5 32 267-298 3-36 (81)
44 cd01803 Ubiquitin Ubiquitin. U 24.0 2.2E+02 0.0048 21.5 5.2 62 264-339 9-71 (76)
45 PF07495 Y_Y_Y: Y_Y_Y domain; 23.9 42 0.00092 24.9 1.2 11 319-329 35-45 (66)
46 cd01038 Endonuclease_DUF559 Do 23.8 1.1E+02 0.0023 25.9 3.7 47 319-374 37-86 (108)
47 PTZ00044 ubiquitin; Provisiona 23.5 2.2E+02 0.0048 21.8 5.2 63 264-339 9-71 (76)
48 cd04041 C2A_fungal C2 domain f 23.4 76 0.0016 26.2 2.7 18 360-377 93-110 (111)
49 PRK12454 carbamate kinase-like 23.1 51 0.0011 33.7 1.9 29 354-382 134-163 (313)
50 cd01244 PH_RasGAP_CG9209 RAS_G 22.6 1.3E+02 0.0027 25.6 3.9 46 319-366 41-93 (98)
51 PRK12686 carbamate kinase; Rev 22.5 53 0.0011 33.5 1.8 31 352-382 130-161 (312)
52 KOG2916 Translation initiation 22.1 1E+02 0.0022 31.5 3.7 27 267-300 186-212 (304)
53 COG2852 Very-short-patch-repai 21.9 92 0.002 28.5 3.0 50 317-375 48-100 (129)
54 TIGR02870 spore_II_D stage II 21.5 60 0.0013 33.4 2.0 35 262-307 254-288 (338)
55 PF00046 Homeobox: Homeobox do 21.4 3.2E+02 0.007 19.7 8.4 54 78-142 4-57 (57)
56 cd01794 DC_UbP_C dendritic cel 20.9 2E+02 0.0044 22.6 4.5 64 263-339 6-69 (70)
57 PRK09411 carbamate kinase; Rev 20.8 60 0.0013 33.1 1.8 29 354-382 126-154 (297)
58 cd01792 ISG15_repeat1 ISG15 ub 20.7 2.4E+02 0.0052 22.3 5.0 52 282-339 22-75 (80)
59 cd04235 AAK_CK AAK_CK: Carbama 20.4 67 0.0015 32.7 2.1 27 354-380 130-157 (308)
No 1
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=99.92 E-value=8.5e-25 Score=213.90 Aligned_cols=273 Identities=22% Similarity=0.319 Sum_probs=204.9
Q ss_pred CCCCCHHHHHHHHHHHHHHHHhhccCCCchHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHhcccCCCC-CCCCCc
Q 015940 78 AETWVQDETRILIAFRREMDGLFNTSKSNKHLWEQISAKMREKGFDRSPTMCTDKWRNLLKEFKKTKHQDRGS-GSAKMS 156 (398)
Q Consensus 78 g~~WT~eET~lLIeL~~E~e~rF~~sKrnkkLWEeIAekMaEkGY~RSaeQCr~KWKNLKK~YKKIKd~nkGs-GskkWp 156 (398)
...|+.+||++||++|++++..|...++|.++|++||++|++.||.||+.||+.||+||+++||+.|....+. +...|+
T Consensus 54 ~~~Ws~~et~~Li~~~~~~~~~~~~~~~k~~~We~va~k~~~~g~~rs~~qck~K~~nl~k~Yk~~k~~~~~~~~~s~~~ 133 (345)
T KOG4282|consen 54 EPRWSEEETLTLIEIRGEMDVALRRGKLKGPLWEEVARKMAELGYPRSPKQCKAKIENLKKKYKKEKAKKEGSGEGSSWK 133 (345)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHhhhhcccHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHhcccCCCCCCccch
Confidence 6899999999999999999999999999999999999999999999999999999999999999999887644 467899
Q ss_pred ChHHHHHHHc-ccccccc-------cccccccCCcccccccccccCCCCCCCCCCCCcccCCCCC-CCccccccCCCCCc
Q 015940 157 YYKEIDEILK-ERSKNAQ-------YKATSVANSANKVDTFMQFSDKGFDDTSISFGPVEATGRP-TLNLERRLDHDGHP 227 (398)
Q Consensus 157 YFDEMDeILG-~rps~~~-------~~sP~~s~Ss~k~D~~~q~sD~~~~~tsi~f~pvea~gr~-~ln~E~~lD~d~h~ 227 (398)
||.+||.++. .++.... ...|....+++. .+|+..+.... .++.-.+.+..+ .+|.+.....+..+
T Consensus 134 ff~~le~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~-~~~~~~~~~~~p~~~~~~~~~~~~~~~ 208 (345)
T KOG4282|consen 134 FFSELEALLITFKARPRSDEVGPGNASAPLTLSVSSE----PQFSSNPTELQ-FDGSSLEDSSQPSGLNEDNSNSSSPEP 208 (345)
T ss_pred HHHHHHHHHhccCCCCCCCCCCcccccCccccCCCCC----CCCCCCccccc-cCCCcCCCCCcccccCccccccCCCCC
Confidence 9999999997 2221010 111111111111 33332222222 222333455555 44444444444566
Q ss_pred cccchhhHHHhcCCCCCCCCCCCCCCCCccCCCccccceEEEEeecccceeecccCChHHHHHHHHHhhcccccceeecc
Q 015940 228 LAITTADAVAAAGVPPWNWRDPPPGNGNLCGEGQSFGGKVISVKCGDYTRRIGIDGTPDAIKEAIKSAFGIRTKRAFWLE 307 (398)
Q Consensus 228 l~i~~ad~vaa~g~~p~~~~~~~~~~g~~~~~~~~~~g~~~~~~~~~~t~r~g~~g~~~~~~~~~~~~~~~~~~~~~~~~ 307 (398)
.+...++.++ .+++++++ ++.+ +. +.+.+.++.+++|..+.+++.++..++...+...|++
T Consensus 209 ~~~~~~~~~~----~s~~~~~s-~~~~---~~-----------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~ 269 (345)
T KOG4282|consen 209 VAGSLSNDTS----SSSSPDDS-ADSE---GG-----------KSSSRKRRVRKDGSKEGIEELMREVARSQERLDEVLE 269 (345)
T ss_pred CCcchhhccc----cccchhcc-cccc---cC-----------CCCCCCccccccccchhHHHHhhhhhhhHHHHHHHHH
Confidence 5543333333 78999999 5555 11 6788899999999999999999999999999999999
Q ss_pred ccchhhhhcccCCCCcceEEecCCCceeEEeecCCCCCcccccccceecchhhHHHHHHhhccccceeccCcccccCc
Q 015940 308 DEDQIVRCIDRDMPVGNYTLHLDEGLTIKVCLYDESDHISVHTEDKTFYTEEDYREFLARHGWTCLREFDGYRNVDNM 385 (398)
Q Consensus 308 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 385 (398)
.-.+ .+.+.|-++...+.....+. ..++.++.+++.+.++.+++..++.+++++-.-..--.+..+.
T Consensus 270 ~~~~-~~~~~~~~~~e~~r~~~~~r----------~ke~e~~~~~~~~~~~~~i~~i~~~~~~~~~~~~~~~~~~~~~ 336 (345)
T KOG4282|consen 270 RVEE-KKEQERMSEEEKWRMEEIER----------NKELELARQERIQETQLEIRSIKAIQASRRGSLIDPAQNTLTR 336 (345)
T ss_pred HHhc-cchHhhhhHHHHHHHHHHHh----------cchHHHHHHHHHHHHHHHHHHHHHHHhccccCCcCcccccCCC
Confidence 9988 89999999988887765554 4668999999999999999999999999987665544444443
No 2
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=99.86 E-value=5.5e-22 Score=157.78 Aligned_cols=85 Identities=39% Similarity=0.896 Sum_probs=60.1
Q ss_pred CCCCHHHHHHHHHHHHH--HHHhhcc--CCCchHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHhcccCCCCCCCC
Q 015940 79 ETWVQDETRILIAFRRE--MDGLFNT--SKSNKHLWEQISAKMREKGFDRSPTMCTDKWRNLLKEFKKTKHQDRGSGSAK 154 (398)
Q Consensus 79 ~~WT~eET~lLIeL~~E--~e~rF~~--sKrnkkLWEeIAekMaEkGY~RSaeQCr~KWKNLKK~YKKIKd~nkGsGskk 154 (398)
.+||++||.+||++|.+ ++..|.. ..++..+|+.||..|+++||.||+.||+.||+||++.|+++++...++| ..
T Consensus 2 ~~Wt~~et~~Li~~~~~~~~~~~~~~~~~~~~~~~w~~Ia~~l~~~G~~rt~~qc~~Kw~~L~~~Yk~~k~~~~~~~-~~ 80 (90)
T PF13837_consen 2 RNWTDEETKLLIELWKENLMELRFDNGGKKRNKKVWKEIAEELAEHGYNRTPEQCRNKWKNLKKKYKKIKDRNKKSG-SS 80 (90)
T ss_dssp -SS-HHHHHHHHHHHHH--HHHHHHH--SS--HHHHHHHHHHHHHHC----HHHHHHHHHHHHHHHHCSSSSSS-----S
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHhhhccccchHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHhcCCCCC-Cc
Confidence 48999999999999999 5667864 4577789999999999999999999999999999999999999987666 49
Q ss_pred CcChHHHHHH
Q 015940 155 MSYYKEIDEI 164 (398)
Q Consensus 155 WpYFDEMDeI 164 (398)
|+||++||+|
T Consensus 81 w~~f~~md~i 90 (90)
T PF13837_consen 81 WPYFDEMDEI 90 (90)
T ss_dssp ---TT-----
T ss_pred CcCHHHHhcC
Confidence 9999999986
No 3
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=98.48 E-value=6.4e-07 Score=70.59 Aligned_cols=67 Identities=25% Similarity=0.510 Sum_probs=56.1
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHhhcc-------CCCchHHHHHHHHHHHHcCC-CCCHHHHHHHHHHHHHHHHHh
Q 015940 77 RAETWVQDETRILIAFRREMDGLFNT-------SKSNKHLWEQISAKMREKGF-DRSPTMCTDKWRNLLKEFKKT 143 (398)
Q Consensus 77 Rg~~WT~eET~lLIeL~~E~e~rF~~-------sKrnkkLWEeIAekMaEkGY-~RSaeQCr~KWKNLKK~YKKI 143 (398)
|..+||.+|...||++..++...+.+ ...+...|++|+..|...|. .||+.|++.||+||+..=|+.
T Consensus 1 R~~~fs~~E~~~Lv~~v~~~~~il~~k~~~~~~~~~k~~~W~~I~~~lN~~~~~~Rs~~~lkkkW~nlk~~~Kk~ 75 (78)
T PF13873_consen 1 RKPNFSEEEKEILVELVEKHKDILENKFSDSVSNKEKRKAWEEIAEELNALGPGKRSWKQLKKKWKNLKSKAKKK 75 (78)
T ss_pred CCCCCCHHHHHHHHHHHHHhHHHHhcccccHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHH
Confidence 67899999999999998886554433 12578999999999999877 799999999999999876654
No 4
>smart00595 MADF subfamily of SANT domain.
Probab=98.34 E-value=4.3e-07 Score=72.62 Aligned_cols=71 Identities=21% Similarity=0.528 Sum_probs=52.6
Q ss_pred HHHHHHHHH-------HhhccCCCchHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHhcccC--C-CCC--CCCCc
Q 015940 89 LIAFRREMD-------GLFNTSKSNKHLWEQISAKMREKGFDRSPTMCTDKWRNLLKEFKKTKHQD--R-GSG--SAKMS 156 (398)
Q Consensus 89 LIeL~~E~e-------~rF~~sKrnkkLWEeIAekMaEkGY~RSaeQCr~KWKNLKK~YKKIKd~n--k-GsG--skkWp 156 (398)
||++++..- ..+.....+...|++||..|.. ++.+|+.||++|+..|++..... . ..| ..+|.
T Consensus 2 LI~~v~~~p~Lwd~~~~~y~~~~~r~~aW~~Ia~~l~~-----~~~~~~~kw~~LR~~y~~e~~r~~~~~~~~~~~~~w~ 76 (89)
T smart00595 2 LIELVRERPCLWDRRHPDYRNKEEKRKAWEEIAEELGL-----SVEECKKRWKNLRDRYRRELKRLQNGKSGGGKKSKWE 76 (89)
T ss_pred hHHHHHhCccccCCCChhhcChHHHHHHHHHHHHHHCc-----CHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCCch
Confidence 677777642 2333344567899999999965 99999999999999999885432 1 122 47899
Q ss_pred ChHHHHHH
Q 015940 157 YYKEIDEI 164 (398)
Q Consensus 157 YFDEMDeI 164 (398)
||++|.=|
T Consensus 77 ~~~~m~FL 84 (89)
T smart00595 77 YFDRLSFL 84 (89)
T ss_pred hhHhhhhH
Confidence 99999644
No 5
>PF12776 Myb_DNA-bind_3: Myb/SANT-like DNA-binding domain; InterPro: IPR024752 This domain, found in a range of uncharacterised proteins, may be related to Myb/SANT-like DNA binding domains.
Probab=98.22 E-value=7.4e-06 Score=66.09 Aligned_cols=71 Identities=23% Similarity=0.426 Sum_probs=59.1
Q ss_pred CCCHHHHHHHHHHHHHHHHh--h-ccCCCchHHHHHHHHHHHH-cCCCCCHHHHHHHHHHHHHHHHHhcccCCCC
Q 015940 80 TWVQDETRILIAFRREMDGL--F-NTSKSNKHLWEQISAKMRE-KGFDRSPTMCTDKWRNLLKEFKKTKHQDRGS 150 (398)
Q Consensus 80 ~WT~eET~lLIeL~~E~e~r--F-~~sKrnkkLWEeIAekMaE-kGY~RSaeQCr~KWKNLKK~YKKIKd~nkGs 150 (398)
+||.+++..||++..+.... . .++.-++..|+.|++.|.+ .|...+..||++||+.||+.|+.++.-...+
T Consensus 1 ~Wt~~~~~~ll~~~~e~~~~g~~~~~~~fk~~~w~~i~~~~~~~~~~~~t~~qlknk~~~lk~~y~~~~~l~~~s 75 (96)
T PF12776_consen 1 SWTPEMTRFLLDLLIEQINKGNRPTNGGFKKEGWNNIAEEFNEKTGLNYTKKQLKNKWKTLKKDYRIWKELRNHS 75 (96)
T ss_pred CCChHHHHHHHHHHHHHHHhCCCCCCCCcCHHHHHHHHHHHHHHhCCcccHHHHHHHHHHHHHHHHHHHHHHcCC
Confidence 69999999999999885332 2 2345788999999999988 4788999999999999999999998765433
No 6
>PF10545 MADF_DNA_bdg: Alcohol dehydrogenase transcription factor Myb/SANT-like; InterPro: IPR006578 The MADF (myb/SANT-like domain in Adf-1) domain is an approximately 80-amino-acid module that directs sequence specific DNA binding to a site consisting of multiple tri-nucleotide repeats. The MADF domain is found in one or more copies in eukaryotic and viral proteins and is often associated with the BESS domain []. MADF is related to the Myb DNA-binding domain (IPR001005 from INTERPRO). The retroviral oncogene v-myb, and its cellular counterpart c-myb, are nuclear DNA-binding proteins that specifically recognise the sequence YAAC(G/T)G. It is likely that the MADF domain is more closely related to the myb/SANT domain than it is to other HTH domains. Some proteins known to contain a MADF domain are listed below: Drosophila Adf-1, a transcription factor first identified on the basis of its interaction with the alcohol dehydrogenase promoter but that binds the promoters of a diverse group of genes []. Drosophila Dorsal-interacting protein 3 (Dip3), which functions both as an activator to bind DNA in a sequence specific manner and a coactivator to stimulate synergistic activation by Dorsal and Twist []. Drosophila Stonewall (Stwl), a putative transcription factor required for maintenance of female germline stem cells as well as oocyte differentiation.
Probab=98.03 E-value=3.8e-06 Score=65.26 Aligned_cols=71 Identities=23% Similarity=0.534 Sum_probs=51.7
Q ss_pred HHHHHHHHH-------HhhccCCCchHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHhcccCC---CC--CCCCCc
Q 015940 89 LIAFRREMD-------GLFNTSKSNKHLWEQISAKMREKGFDRSPTMCTDKWRNLLKEFKKTKHQDR---GS--GSAKMS 156 (398)
Q Consensus 89 LIeL~~E~e-------~rF~~sKrnkkLWEeIAekMaEkGY~RSaeQCr~KWKNLKK~YKKIKd~nk---Gs--GskkWp 156 (398)
||++++... ..|.....+...|++|+..| |...++.+|+.+|++|+..|++.+.... +. -...|.
T Consensus 1 LI~~v~~~p~Lwd~~~~~y~~~~~r~~aw~~Ia~~l---~~~~~~~~~~~~w~~Lr~~y~~~~~~~~~~~~~~~~~~~~~ 77 (85)
T PF10545_consen 1 LIELVKKHPCLWDPSHPDYKNRQLREEAWQEIAREL---GKEFSVDDCKKRWKNLRDRYRRELKKIKSSGGSEEYVPTWS 77 (85)
T ss_pred CHHHHhhCHHhhCCCCcccCCHHHHHHHHHHHHHHH---ccchhHHHHHHHHHHHHHHHHHHHHHHhccccCCCCCCccH
Confidence 566666532 23333346789999999999 5457799999999999999999876543 11 135799
Q ss_pred ChHHHH
Q 015940 157 YYKEID 162 (398)
Q Consensus 157 YFDEMD 162 (398)
||+.|.
T Consensus 78 ~~~~l~ 83 (85)
T PF10545_consen 78 YYEELS 83 (85)
T ss_pred HHHHCc
Confidence 999874
No 7
>PF00249 Myb_DNA-binding: Myb-like DNA-binding domain; InterPro: IPR014778 The retroviral oncogene v-myb, and its cellular counterpart c-myb, encode nuclear DNA-binding proteins. These belong to the SANT domain family that specifically recognise the sequence YAAC(G/T)G [, ]. In myb, one of the most conserved regions consisting of three tandem repeats has been shown to be involved in DNA-binding [].; PDB: 1X41_A 2XAF_B 2XAG_B 2XAH_B 2UXN_B 2Y48_B 2XAQ_B 2X0L_B 2IW5_B 2XAJ_B ....
Probab=97.63 E-value=0.0001 Score=53.66 Aligned_cols=47 Identities=23% Similarity=0.555 Sum_probs=38.5
Q ss_pred CCCCHHHHHHHHHHHHHHHHhhccCCCchHHHHHHHHHHHHcCCCCCHHHHHHHHHHHH
Q 015940 79 ETWVQDETRILIAFRREMDGLFNTSKSNKHLWEQISAKMREKGFDRSPTMCTDKWRNLL 137 (398)
Q Consensus 79 ~~WT~eET~lLIeL~~E~e~rF~~sKrnkkLWEeIAekMaEkGY~RSaeQCr~KWKNLK 137 (398)
..||.+|...|+++...+-.. -|..||..|. -.||+.||+.+|.+++
T Consensus 2 ~~Wt~eE~~~l~~~v~~~g~~---------~W~~Ia~~~~---~~Rt~~qc~~~~~~~~ 48 (48)
T PF00249_consen 2 GPWTEEEDEKLLEAVKKYGKD---------NWKKIAKRMP---GGRTAKQCRSRYQNLL 48 (48)
T ss_dssp -SS-HHHHHHHHHHHHHSTTT---------HHHHHHHHHS---SSSTHHHHHHHHHHHT
T ss_pred CCCCHHHHHHHHHHHHHhCCc---------HHHHHHHHcC---CCCCHHHHHHHHHhhC
Confidence 479999999999998864222 7999999997 4699999999999874
No 8
>PF13921 Myb_DNA-bind_6: Myb-like DNA-binding domain; PDB: 1A5J_A 1MBH_A 1GV5_A 1H89_C 1IDY_A 1MBK_A 1IDZ_A 1H88_C 1GVD_A 1MBG_A ....
Probab=97.46 E-value=0.00016 Score=54.28 Aligned_cols=43 Identities=28% Similarity=0.871 Sum_probs=34.8
Q ss_pred CCHHHHHHHHHHHHHHHHhhccCCCchHHHHHHHHHHHHcCCCCCHHHHHHHHHH-HH
Q 015940 81 WVQDETRILIAFRREMDGLFNTSKSNKHLWEQISAKMREKGFDRSPTMCTDKWRN-LL 137 (398)
Q Consensus 81 WT~eET~lLIeL~~E~e~rF~~sKrnkkLWEeIAekMaEkGY~RSaeQCr~KWKN-LK 137 (398)
||.+|...|+.++..+.. -|..||+.|. +||+.||+.||.+ |.
T Consensus 1 WT~eEd~~L~~~~~~~g~----------~W~~Ia~~l~----~Rt~~~~~~r~~~~l~ 44 (60)
T PF13921_consen 1 WTKEEDELLLELVKKYGN----------DWKKIAEHLG----NRTPKQCRNRWRNHLR 44 (60)
T ss_dssp S-HHHHHHHHHHHHHHTS-----------HHHHHHHST----TS-HHHHHHHHHHTTS
T ss_pred CCHHHHHHHHHHHHHHCc----------CHHHHHHHHC----cCCHHHHHHHHHHHCc
Confidence 999999999999987521 4999999973 7999999999999 63
No 9
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=97.36 E-value=0.00031 Score=48.55 Aligned_cols=47 Identities=30% Similarity=0.796 Sum_probs=40.0
Q ss_pred CCCCHHHHHHHHHHHHHHHHhhccCCCchHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHH
Q 015940 79 ETWVQDETRILIAFRREMDGLFNTSKSNKHLWEQISAKMREKGFDRSPTMCTDKWRNLLK 138 (398)
Q Consensus 79 ~~WT~eET~lLIeL~~E~e~rF~~sKrnkkLWEeIAekMaEkGY~RSaeQCr~KWKNLKK 138 (398)
..||.+|...|+.+...+-. ..|..||..|. .||+.+|+.+|.++.+
T Consensus 2 ~~Wt~~E~~~l~~~~~~~g~---------~~w~~Ia~~~~----~rt~~~~~~~~~~~~~ 48 (49)
T smart00717 2 GEWTEEEDELLIELVKKYGK---------NNWEKIAKELP----GRTAEQCRERWNNLLK 48 (49)
T ss_pred CCCCHHHHHHHHHHHHHHCc---------CCHHHHHHHcC----CCCHHHHHHHHHHHcC
Confidence 47999999999999886432 45999999986 7999999999998864
No 10
>cd00167 SANT 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA.
Probab=97.18 E-value=0.0005 Score=46.93 Aligned_cols=45 Identities=31% Similarity=0.855 Sum_probs=37.9
Q ss_pred CCCHHHHHHHHHHHHHHHHhhccCCCchHHHHHHHHHHHHcCCCCCHHHHHHHHHHHH
Q 015940 80 TWVQDETRILIAFRREMDGLFNTSKSNKHLWEQISAKMREKGFDRSPTMCTDKWRNLL 137 (398)
Q Consensus 80 ~WT~eET~lLIeL~~E~e~rF~~sKrnkkLWEeIAekMaEkGY~RSaeQCr~KWKNLK 137 (398)
.||.+|...|+.+...+-. ..|..||..|.. ||+.||+.+|.+++
T Consensus 1 ~Wt~eE~~~l~~~~~~~g~---------~~w~~Ia~~~~~----rs~~~~~~~~~~~~ 45 (45)
T cd00167 1 PWTEEEDELLLEAVKKYGK---------NNWEKIAKELPG----RTPKQCRERWRNLL 45 (45)
T ss_pred CCCHHHHHHHHHHHHHHCc---------CCHHHHHhHcCC----CCHHHHHHHHHHhC
Confidence 5999999999999886532 459999999853 99999999998863
No 11
>PLN03212 Transcription repressor MYB5; Provisional
Probab=95.05 E-value=0.036 Score=54.46 Aligned_cols=48 Identities=25% Similarity=0.632 Sum_probs=38.4
Q ss_pred CCCCCHHHHHHHHHHHHHHHHhhccCCCchHHHHHHHHHHHHcCCCCCHHHHHHHHHHHH
Q 015940 78 AETWVQDETRILIAFRREMDGLFNTSKSNKHLWEQISAKMREKGFDRSPTMCTDKWRNLL 137 (398)
Q Consensus 78 g~~WT~eET~lLIeL~~E~e~rF~~sKrnkkLWEeIAekMaEkGY~RSaeQCr~KWKNLK 137 (398)
...||.+|-..|+++...+- ..-|..||.+| |..|+++||+.+|.|..
T Consensus 25 Rg~WT~EEDe~L~~lV~kyG---------~~nW~~IAk~~---g~gRT~KQCReRW~N~L 72 (249)
T PLN03212 25 RGPWTVEEDEILVSFIKKEG---------EGRWRSLPKRA---GLLRCGKSCRLRWMNYL 72 (249)
T ss_pred CCCCCHHHHHHHHHHHHHhC---------cccHHHHHHhh---hcCCCcchHHHHHHHhh
Confidence 45899999999998876531 12499999875 46799999999999765
No 12
>PLN03091 hypothetical protein; Provisional
Probab=93.94 E-value=0.084 Score=55.67 Aligned_cols=48 Identities=21% Similarity=0.525 Sum_probs=38.1
Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHhhccCCCchHHHHHHHHHHHHcCCCCCHHHHHHHHHH
Q 015940 76 KRAETWVQDETRILIAFRREMDGLFNTSKSNKHLWEQISAKMREKGFDRSPTMCTDKWRN 135 (398)
Q Consensus 76 kRg~~WT~eET~lLIeL~~E~e~rF~~sKrnkkLWEeIAekMaEkGY~RSaeQCr~KWKN 135 (398)
-|...||.+|-..|+++...+- ..-|..||..| |..|+++||+.+|.|
T Consensus 12 lrKg~WTpEEDe~L~~~V~kyG---------~~nWs~IAk~~---g~gRT~KQCRERW~N 59 (459)
T PLN03091 12 LRKGLWSPEEDEKLLRHITKYG---------HGCWSSVPKQA---GLQRCGKSCRLRWIN 59 (459)
T ss_pred CcCCCCCHHHHHHHHHHHHHhC---------cCCHHHHhhhh---ccCcCcchHhHHHHh
Confidence 4456899999999998876531 13699999765 567999999999986
No 13
>PLN03091 hypothetical protein; Provisional
Probab=93.02 E-value=0.25 Score=52.23 Aligned_cols=56 Identities=23% Similarity=0.480 Sum_probs=45.1
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHHHHHhhccCCCchHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHH
Q 015940 73 APKKRAETWVQDETRILIAFRREMDGLFNTSKSNKHLWEQISAKMREKGFDRSPTMCTDKWRNLLKEFKK 142 (398)
Q Consensus 73 ~pskRg~~WT~eET~lLIeL~~E~e~rF~~sKrnkkLWEeIAekMaEkGY~RSaeQCr~KWKNLKK~YKK 142 (398)
.|.-+...||.+|-..||+++..+ ..-|..||..|. .||..||+++|..+.+++.+
T Consensus 62 dP~IkKgpWT~EED~lLLeL~k~~----------GnKWskIAk~LP----GRTDnqIKNRWnslLKKklr 117 (459)
T PLN03091 62 RPDLKRGTFSQQEENLIIELHAVL----------GNRWSQIAAQLP----GRTDNEIKNLWNSCLKKKLR 117 (459)
T ss_pred CCcccCCCCCHHHHHHHHHHHHHh----------CcchHHHHHhcC----CCCHHHHHHHHHHHHHHHHH
Confidence 344446799999999999998752 136999999883 59999999999998887655
No 14
>PLN03212 Transcription repressor MYB5; Provisional
Probab=92.49 E-value=0.32 Score=48.04 Aligned_cols=54 Identities=17% Similarity=0.428 Sum_probs=42.9
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHHHHHhhccCCCchHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHH
Q 015940 73 APKKRAETWVQDETRILIAFRREMDGLFNTSKSNKHLWEQISAKMREKGFDRSPTMCTDKWRNLLKEF 140 (398)
Q Consensus 73 ~pskRg~~WT~eET~lLIeL~~E~e~rF~~sKrnkkLWEeIAekMaEkGY~RSaeQCr~KWKNLKK~Y 140 (398)
.|.-....||.+|-.+||+++.. +. .-|..||..|. .||..||+++|.++.+..
T Consensus 73 ~P~I~kgpWT~EED~lLlel~~~----~G------nKWs~IAk~Lp----GRTDnqIKNRWns~LrK~ 126 (249)
T PLN03212 73 RPSVKRGGITSDEEDLILRLHRL----LG------NRWSLIAGRIP----GRTDNEIKNYWNTHLRKK 126 (249)
T ss_pred chhcccCCCChHHHHHHHHHHHh----cc------ccHHHHHhhcC----CCCHHHHHHHHHHHHhHH
Confidence 45555679999999999988654 21 35999999884 499999999999988654
No 15
>PF04504 DUF573: Protein of unknown function, DUF573; InterPro: IPR007592 This is a family of uncharacterised proteins.
Probab=84.21 E-value=7.4 Score=33.02 Aligned_cols=66 Identities=15% Similarity=0.323 Sum_probs=46.8
Q ss_pred CCCCCHHHHHHHHHHHHHHHHhhccCC--CchHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHhccc
Q 015940 78 AETWVQDETRILIAFRREMDGLFNTSK--SNKHLWEQISAKMREKGFDRSPTMCTDKWRNLLKEFKKTKHQ 146 (398)
Q Consensus 78 g~~WT~eET~lLIeL~~E~e~rF~~sK--rnkkLWEeIAekMaEkGY~RSaeQCr~KWKNLKK~YKKIKd~ 146 (398)
...||++.=..||+..-++...-.... --..+++.|...| .++.|..|..+|++.||+.|......
T Consensus 4 qR~WS~eDEi~iL~gl~~~~~~~G~~p~~d~~~f~~~vk~~l---~~~~s~~Ql~~KirrLK~Ky~~~~~k 71 (98)
T PF04504_consen 4 QRLWSEEDEIVILQGLIDFRAKTGKSPQPDMNAFYDFVKGSL---SFDVSKNQLYDKIRRLKKKYRNAVKK 71 (98)
T ss_pred cCCCCchHHHHHHHHHHHHHHhcCCCCCccHHHHHHHHHHHc---cCCCCHHHHHHHHHHHHHHHHHHhhh
Confidence 347999988888887776543322211 2245566665554 46789999999999999999998665
No 16
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=83.98 E-value=1.1 Score=48.08 Aligned_cols=48 Identities=19% Similarity=0.380 Sum_probs=39.6
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHhhccCCCchHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHH
Q 015940 77 RAETWVQDETRILIAFRREMDGLFNTSKSNKHLWEQISAKMREKGFDRSPTMCTDKWRNLLK 138 (398)
Q Consensus 77 Rg~~WT~eET~lLIeL~~E~e~rF~~sKrnkkLWEeIAekMaEkGY~RSaeQCr~KWKNLKK 138 (398)
-...||++||.+||+.-..+ +..|..||.+.. .+|..||-.||-.|-.
T Consensus 252 ~~~~WT~qE~lLLLE~ie~y----------~ddW~kVa~hVg----~ks~eqCI~kFL~LPi 299 (506)
T KOG1279|consen 252 ARPNWTEQETLLLLEAIEMY----------GDDWNKVADHVG----TKSQEQCILKFLRLPI 299 (506)
T ss_pred CCCCccHHHHHHHHHHHHHh----------cccHHHHHhccC----CCCHHHHHHHHHhcCc
Confidence 35799999999999866532 257999999886 7999999999988763
No 17
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=78.90 E-value=2.8 Score=46.04 Aligned_cols=68 Identities=24% Similarity=0.350 Sum_probs=49.4
Q ss_pred CCCCCCCHHHHHHHHHHHHHHHH---hhc---------cCC----CchHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHH
Q 015940 76 KRAETWVQDETRILIAFRREMDG---LFN---------TSK----SNKHLWEQISAKMREKGFDRSPTMCTDKWRNLLKE 139 (398)
Q Consensus 76 kRg~~WT~eET~lLIeL~~E~e~---rF~---------~sK----rnkkLWEeIAekMaEkGY~RSaeQCr~KWKNLKK~ 139 (398)
.+...||.+|...||.+..++.. +++ ... ...--|-.|++.|. .|+..||+-||..|...
T Consensus 434 ~~r~~Ws~eEe~~Llk~V~~~~~~~~q~q~~n~~~~~q~sp~s~~~d~I~Wt~vse~~~----TR~~~qCr~Kw~kl~~~ 509 (607)
T KOG0051|consen 434 RNRGAWSIEEEEKLLKTVNEMIREALQPQASNTDTGLQESPESTLKDDINWTLVSEMLG----TRSRIQCRYKWYKLTTS 509 (607)
T ss_pred cccCcchHHHHHHHHHHHHHHHHHhhcccccccchhhhcCccccccCCcchhhhhHhhc----CCCcchHHHHHHHHHhh
Confidence 34679999999999999987643 221 011 12345999999554 59999999999999987
Q ss_pred HHHhcccC
Q 015940 140 FKKTKHQD 147 (398)
Q Consensus 140 YKKIKd~n 147 (398)
+-..+.+-
T Consensus 510 ~s~n~~~~ 517 (607)
T KOG0051|consen 510 PSFNKRQE 517 (607)
T ss_pred HHhhcccc
Confidence 76655443
No 18
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=77.76 E-value=3.4 Score=44.38 Aligned_cols=49 Identities=16% Similarity=0.381 Sum_probs=40.6
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHhhccCCCchHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHH
Q 015940 77 RAETWVQDETRILIAFRREMDGLFNTSKSNKHLWEQISAKMREKGFDRSPTMCTDKWRNLLKE 139 (398)
Q Consensus 77 Rg~~WT~eET~lLIeL~~E~e~rF~~sKrnkkLWEeIAekMaEkGY~RSaeQCr~KWKNLKK~ 139 (398)
+..+|+.+|+.+||+-...+ ..-|.+||.+.. .+|.+||-.||=+|-..
T Consensus 278 ~dk~WS~qE~~LLLEGIe~y----------gDdW~kVA~HVg----tKt~EqCIl~FL~LPie 326 (531)
T COG5259 278 RDKNWSRQELLLLLEGIEMY----------GDDWDKVARHVG----TKTKEQCILHFLQLPIE 326 (531)
T ss_pred ccccccHHHHHHHHHHHHHh----------hhhHHHHHHHhC----CCCHHHHHHHHHcCCcc
Confidence 56799999999999866542 247999999886 79999999999988654
No 19
>TIGR02894 DNA_bind_RsfA transcription factor, RsfA family. In a subset of endospore-forming members of the Firmcutes, members of this protein family are found, several to a genome. Two very strongly conserved sequences regions are separated by a highly variable linker region. Much of the linker region was excised from the seed alignment for this model. A characterized member is the prespore-specific transcription RsfA from Bacillus subtilis, previously called YwfN, which is controlled by sigma factor F and seems to fine-tune expression of some genes in the sigma-F regulon. A paralog in Bacillus subtilis is designated YlbO.
Probab=77.33 E-value=6.8 Score=36.70 Aligned_cols=60 Identities=15% Similarity=0.480 Sum_probs=47.2
Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHhhccCCCchHHHHHHHHHHHHcCCCCCHHHHHHHHHHHH-HHHHHh
Q 015940 76 KRAETWVQDETRILIAFRREMDGLFNTSKSNKHLWEQISAKMREKGFDRSPTMCTDKWRNLL-KEFKKT 143 (398)
Q Consensus 76 kRg~~WT~eET~lLIeL~~E~e~rF~~sKrnkkLWEeIAekMaEkGY~RSaeQCr~KWKNLK-K~YKKI 143 (398)
.|-..||.+|-++|-++--. -.+.+...-..+++|+.+| +||+.-|.-+|.... +.|...
T Consensus 2 ~RQDAWT~eeDlLLAEtVLr---hIReG~TQL~AFeEvg~~L-----~RTsAACGFRWNs~VRkqY~~~ 62 (161)
T TIGR02894 2 TRQDAWTHEEDLLLAETVLR---HIREGSTQLSAFEEVGRAL-----NRTAAACGFRWNAYVRKQYEEA 62 (161)
T ss_pred ccccccccHHHHHHHHHHHH---HHhcchHHHHHHHHHHHHH-----cccHHHhcchHHHHHHHHHHHH
Confidence 46778999999998876654 3344455567899999998 599999999999876 468875
No 20
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=73.92 E-value=3.2 Score=39.76 Aligned_cols=48 Identities=21% Similarity=0.364 Sum_probs=37.8
Q ss_pred CCCCCHHHHHHHHHHHHHHHHhhccCCCchHHHHHHHHHHHHcCCCCCHHHHHHHHHHHH
Q 015940 78 AETWVQDETRILIAFRREMDGLFNTSKSNKHLWEQISAKMREKGFDRSPTMCTDKWRNLL 137 (398)
Q Consensus 78 g~~WT~eET~lLIeL~~E~e~rF~~sKrnkkLWEeIAekMaEkGY~RSaeQCr~KWKNLK 137 (398)
...||.+|-..|+++...+-.. -|..|++.+ |-.|++++|+.+|-|=.
T Consensus 9 kGpWt~EED~~L~~~V~~~G~~---------~W~~i~k~~---gl~R~GKSCRlRW~NyL 56 (238)
T KOG0048|consen 9 KGPWTQEEDLTQIRSIKSFGKH---------NGTALPKLA---GLRRCGKSCRLRWTNYL 56 (238)
T ss_pred CCCCChHHHHHHHHHHHHhCCC---------Ccchhhhhc---CCCccchHHHHHhhccc
Confidence 4699999999999887753221 688888765 45899999999998744
No 21
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=73.29 E-value=7.8 Score=43.47 Aligned_cols=58 Identities=24% Similarity=0.484 Sum_probs=44.8
Q ss_pred cCCCCCCCCCCHHHHHHHHHHHHHHHHhhccCCCchHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHH
Q 015940 72 RAPKKRAETWVQDETRILIAFRREMDGLFNTSKSNKHLWEQISAKMREKGFDRSPTMCTDKWRNLLKEFK 141 (398)
Q Consensus 72 s~pskRg~~WT~eET~lLIeL~~E~e~rF~~sKrnkkLWEeIAekMaEkGY~RSaeQCr~KWKNLKK~YK 141 (398)
..|+=+...|+.+|...|+++=.- .+..-|+.||..| |-+||.-||-.||+.-.+.-+
T Consensus 247 l~P~~nk~~WS~EE~E~L~AiA~A---------~~~~~W~~IA~~L---gt~RS~yQC~~kF~t~~~~L~ 304 (939)
T KOG0049|consen 247 LNPKWNKEHWSNEEVEKLKALAEA---------PKFVSWPMIALNL---GTNRSSYQCMEKFKTEVSQLS 304 (939)
T ss_pred cCCccchhccChHHHHHHHHHHhc---------cccccHHHHHHHh---CCCcchHHHHHHHHHHHHHHH
Confidence 457777889999999888887542 3345699999764 779999999999987665443
No 22
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=71.42 E-value=13 Score=35.18 Aligned_cols=61 Identities=16% Similarity=0.517 Sum_probs=45.9
Q ss_pred CCCCCCCCHHHHHHHHHHHHHHHHhhccCCCchHHHHHHHHHHHHcCCCCCHHHHHHHHHHHH-HHHHHh
Q 015940 75 KKRAETWVQDETRILIAFRREMDGLFNTSKSNKHLWEQISAKMREKGFDRSPTMCTDKWRNLL-KEFKKT 143 (398)
Q Consensus 75 skRg~~WT~eET~lLIeL~~E~e~rF~~sKrnkkLWEeIAekMaEkGY~RSaeQCr~KWKNLK-K~YKKI 143 (398)
+.|...||.++-++|-++.-+ ..+.+...-..+++++..|. ||+.+|..+|.... +.|...
T Consensus 2 k~rqdawt~e~d~llae~vl~---~i~eg~tql~afe~~g~~L~-----rt~aac~fRwNs~vrk~Yee~ 63 (170)
T PRK13923 2 KTRQDAWTQERDGLLAEVVLR---HIREGGTQLKAFEEVGDALK-----RTAAACGFRWNSVVRKQYQEQ 63 (170)
T ss_pred cchhhhhhhHHHHHHHHHHHH---HHhccchHHHHHHHHHHHHh-----hhHHHHHhHHHHHHHHHHHHH
Confidence 356789999999998666655 33445567788999999885 79999999996544 557754
No 23
>PRK09767 hypothetical protein; Provisional
Probab=68.31 E-value=4.8 Score=35.37 Aligned_cols=51 Identities=31% Similarity=0.603 Sum_probs=32.6
Q ss_pred cccCCCCcceEEecCCCceeEEee-cCCCCCcccccccceecchhhHH-HHHHhhccccce
Q 015940 316 IDRDMPVGNYTLHLDEGLTIKVCL-YDESDHISVHTEDKTFYTEEDYR-EFLARHGWTCLR 374 (398)
Q Consensus 316 ~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~ 374 (398)
.-|-.|+|.|++.+== ..-|||. ||...| .+. +..|--| .+|...||+.||
T Consensus 37 FrRQ~pig~yi~DF~c-~~~rLaIE~DG~~H----~~~---~~~D~~R~~~L~~~G~~VlR 89 (117)
T PRK09767 37 FRRQHPVGSYILDFAC-CSARVVVELDGGQH----DLA---VAYDTRRTSWLESQGWTVLR 89 (117)
T ss_pred eEecccccCeeeceec-cccCEEEEEeCccc----chh---HHHHHHHHHHHHHCCCEEEE
Confidence 4577999999975532 3344443 688655 222 2223333 599999999997
No 24
>cd01812 BAG1_N Ubiquitin-like domain of BAG1. BAG1_N N-terminal ubiquitin-like (Ubl) domain of the BAG1 protein. This domain occurs together with the BAG domain and is closely related to the Ubl domain of a family of deubiquitinases that includes Rpn11, UBP6 (USP14), USP7 (HAUSP).
Probab=63.91 E-value=16 Score=27.69 Aligned_cols=64 Identities=14% Similarity=0.215 Sum_probs=43.3
Q ss_pred EEEeeccccee--ecccCChHHHHHHHHHhhcccccceeeccccchhhhhcccCCCCcceEEecCCCceeEE
Q 015940 268 ISVKCGDYTRR--IGIDGTPDAIKEAIKSAFGIRTKRAFWLEDEDQIVRCIDRDMPVGNYTLHLDEGLTIKV 337 (398)
Q Consensus 268 ~~~~~~~~t~r--~g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 337 (398)
|.||++.-+.- +.-+-|-..+|+.|...+++-..|--++-. . +.|+.+.+|+.|- +.+|-+|-|
T Consensus 3 i~vk~~g~~~~i~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~-g---~~l~d~~~L~~~~--i~~g~~l~v 68 (71)
T cd01812 3 VRVKHGGESHDLSISSQATFGDLKKMLAPVTGVEPRDQKLIFK-G---KERDDAETLDMSG--VKDGSKVML 68 (71)
T ss_pred EEEEECCEEEEEEECCCCcHHHHHHHHHHhhCCChHHeEEeeC-C---cccCccCcHHHcC--CCCCCEEEE
Confidence 67788765443 344568899999999999987766433332 3 3356678888885 456766654
No 25
>cd06398 PB1_Joka2 The PB1 domain is present in the Nicotiana plumbaginifolia Joka2 protein which interacts with sulfur stress inducible UP9 protein. The PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes, such as osteoclastogenesis, angiogenesis, early cardiovascular development and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module
Probab=53.42 E-value=23 Score=29.91 Aligned_cols=34 Identities=26% Similarity=0.460 Sum_probs=30.1
Q ss_pred EEEEeecccceeeccc-------CChHHHHHHHHHhhcccc
Q 015940 267 VISVKCGDYTRRIGID-------GTPDAIKEAIKSAFGIRT 300 (398)
Q Consensus 267 ~~~~~~~~~t~r~g~~-------g~~~~~~~~~~~~~~~~~ 300 (398)
||-|+||+-+||+.+. .+.+..++=|+..|.|-.
T Consensus 2 ~vKv~y~~~~rRf~l~~~~~~~d~~~~~L~~kI~~~f~l~~ 42 (91)
T cd06398 2 VVKVKYGGTLRRFTFPVAENQLDLNMDGLREKVEELFSLSP 42 (91)
T ss_pred EEEEEeCCEEEEEEeccccccCCCCHHHHHHHHHHHhCCCC
Confidence 7899999999999998 588999999999998743
No 26
>KOG0860 consensus Synaptobrevin/VAMP-like protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=47.02 E-value=24 Score=31.54 Aligned_cols=62 Identities=11% Similarity=0.154 Sum_probs=41.3
Q ss_pred CCCCCHHHHHHHHHHHHHHHHhhccCCCchHHHHHHHHHHHH--cCCCCCHHHHHHH--HHHHHHH
Q 015940 78 AETWVQDETRILIAFRREMDGLFNTSKSNKHLWEQISAKMRE--KGFDRSPTMCTDK--WRNLLKE 139 (398)
Q Consensus 78 g~~WT~eET~lLIeL~~E~e~rF~~sKrnkkLWEeIAekMaE--kGY~RSaeQCr~K--WKNLKK~ 139 (398)
...=+.+++..-+.+.++.-+++....-+-..-++=|+.|.+ .+|.+++.+.+.| |+|+|-.
T Consensus 30 k~~~tq~QvdeVv~IMr~NV~KVlER~ekL~~L~drad~L~~~as~F~~~A~klkrk~wWkn~Km~ 95 (116)
T KOG0860|consen 30 KLQQTQAQVDEVVDIMRENVEKVLERGEKLDELDDRADQLQAGASQFEKTAVKLKRKMWWKNCKMR 95 (116)
T ss_pred HHHHHHHHHHHHHHHHHHhHHHHHHhcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344567788888888888766665544333344455666654 4788888888776 7777743
No 27
>cd01809 Scythe_N Ubiquitin-like domain of Scythe protein. Scythe protein (also known as Bat3) is an apoptotic regulator that is highly conserved in eukaryotes and contains a ubiquitin-like domain near its N-terminus. Scythe binds reaper, a potent apoptotic inducer, and Scythe/Reaper are thought to signal apoptosis, in part through regulating the folding and activity of apoptotic signaling molecules.
Probab=40.11 E-value=74 Score=23.89 Aligned_cols=57 Identities=23% Similarity=0.329 Sum_probs=38.5
Q ss_pred cceeecccCChHHHHHHHHHhhcccccceeeccccchhhhhcccCCCCcceEEecCCCceeEE
Q 015940 275 YTRRIGIDGTPDAIKEAIKSAFGIRTKRAFWLEDEDQIVRCIDRDMPVGNYTLHLDEGLTIKV 337 (398)
Q Consensus 275 ~t~r~g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 337 (398)
++-++.-+-|...+|+.|...+++-..+-=++-+ . +.|+-+.+|..| ++.+|-+|.+
T Consensus 13 ~~~~v~~~~tv~~lK~~i~~~~gi~~~~q~L~~~-g---~~L~d~~~L~~~--~i~~~~~l~l 69 (72)
T cd01809 13 HTFTVEEEITVLDLKEKIAEEVGIPVEQQRLIYS-G---RVLKDDETLSEY--KVEDGHTIHL 69 (72)
T ss_pred EEEEECCCCcHHHHHHHHHHHHCcCHHHeEEEEC-C---EECCCcCcHHHC--CCCCCCEEEE
Confidence 3455566678999999999998875554322222 2 346778899988 4567766654
No 28
>TIGR01557 myb_SHAQKYF myb-like DNA-binding domain, SHAQKYF class. This model describes a DNA-binding domain restricted to (but common in) plant proteins, many of which also contain a response regulator domain. The domain appears related to the Myb-like DNA-binding domain described by Pfam model pfam00249. It is distinguished in part by a well-conserved motif SH[AL]QKY[RF] at the C-terminal end of the motif.
Probab=38.23 E-value=58 Score=25.28 Aligned_cols=44 Identities=14% Similarity=0.256 Sum_probs=31.7
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHhhccCCCchHHH---HHHHHHHHHcCCCC-CHHHHHHH
Q 015940 77 RAETWVQDETRILIAFRREMDGLFNTSKSNKHLW---EQISAKMREKGFDR-SPTMCTDK 132 (398)
Q Consensus 77 Rg~~WT~eET~lLIeL~~E~e~rF~~sKrnkkLW---EeIAekMaEkGY~R-SaeQCr~K 132 (398)
....||.+|-..+|+..... .. .-| +.|++.|.. .+ |..||+.-
T Consensus 2 ~r~~WT~eeh~~Fl~ai~~~----G~-----g~~a~pk~I~~~~~~---~~lT~~qV~SH 49 (57)
T TIGR01557 2 PRVVWTEDLHDRFLQAVQKL----GG-----PDWATPKRILELMVV---DGLTRDQVASH 49 (57)
T ss_pred CCCCCCHHHHHHHHHHHHHh----CC-----CcccchHHHHHHcCC---CCCCHHHHHHH
Confidence 45689999999999988753 11 137 778877653 44 89998864
No 29
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=36.96 E-value=90 Score=30.00 Aligned_cols=57 Identities=16% Similarity=0.431 Sum_probs=41.9
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHHHHhhccCCCchHHHHHHHHHHHHcCCCCCHHHHHHHHHHH-HHHHHHhc
Q 015940 74 PKKRAETWVQDETRILIAFRREMDGLFNTSKSNKHLWEQISAKMREKGFDRSPTMCTDKWRNL-LKEFKKTK 144 (398)
Q Consensus 74 pskRg~~WT~eET~lLIeL~~E~e~rF~~sKrnkkLWEeIAekMaEkGY~RSaeQCr~KWKNL-KK~YKKIK 144 (398)
|.=+...||.+|..++|++...+-++ |..||..|- -||....++=|..- |+++++..
T Consensus 58 P~ikrg~fT~eEe~~Ii~lH~~~GNr----------Ws~IA~~LP----GRTDNeIKN~Wnt~lkkkl~~~~ 115 (238)
T KOG0048|consen 58 PDLKRGNFSDEEEDLIIKLHALLGNR----------WSLIAGRLP----GRTDNEVKNHWNTHLKKKLLKMG 115 (238)
T ss_pred CCccCCCCCHHHHHHHHHHHHHHCcH----------HHHHHhhCC----CcCHHHHHHHHHHHHHHHHHHcC
Confidence 44346799999999999998763222 999999986 38888888878643 55555544
No 30
>cd02549 Peptidase_C39A A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is conserved in this sub-family of proteins with a single peptidase domain, which are
Probab=36.57 E-value=1.5e+02 Score=24.71 Aligned_cols=80 Identities=19% Similarity=0.353 Sum_probs=54.4
Q ss_pred ChHHHHHHHHHhhcccccceeeccccchhhhhcccCCCCcceEEecC-------CCceeEEeecCCCCCccccc---ccc
Q 015940 284 TPDAIKEAIKSAFGIRTKRAFWLEDEDQIVRCIDRDMPVGNYTLHLD-------EGLTIKVCLYDESDHISVHT---EDK 353 (398)
Q Consensus 284 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~~~~~~~~~~~~~~~---~~~ 353 (398)
++..|.+++-..+|++.+. +.....|.+.|+...|+ .++++ .|=.+-|.-||+.+.+.++- ++.
T Consensus 45 ~~~~l~~~~a~~~G~~~~~---~~~~~~~~~~l~~~~Pv---i~~~~~~~~~~~~gH~vVv~g~~~~~~~~i~DP~~~~~ 118 (141)
T cd02549 45 YPKPIVSAAARKYGLVVRP---LTGLLALLRQLAAGHPV---IVSVNLGVSITPSGHAMVVIGYDRKGNVYVNDPGGGRR 118 (141)
T ss_pred CHHHHHHHHHhhCCCcEEE---CCCHHHHHHHHHCCCeE---EEEEecCcccCCCCeEEEEEEEcCCCCEEEECCCCCcC
Confidence 3677888834489998763 33333377889999997 44444 45566666688545555554 445
Q ss_pred eecchhhHHHHHHhhc
Q 015940 354 TFYTEEDYREFLARHG 369 (398)
Q Consensus 354 ~~~~~~~~~~~~~~~~ 369 (398)
..++.++|...-+.+|
T Consensus 119 ~~~~~~~f~~~w~~~~ 134 (141)
T cd02549 119 LVVSFDEFEKAWKRMG 134 (141)
T ss_pred EEEeHHHHHHHHHHcC
Confidence 5899999999988888
No 31
>cd01806 Nedd8 Nebb8-like ubiquitin protein. Nedd8 (also known as Rub1) has a single conserved ubiquitin-like domain that is part of a protein modification pathway similar to that of ubiquitin. Nedd8 modifies a family of molecular scaffold proteins called cullins that are responsible for assembling the ROC1/Rbx1 RING-based E3 ubiquitin ligases, of which several play a direct role in tumorigenesis.
Probab=35.51 E-value=1e+02 Score=23.34 Aligned_cols=56 Identities=20% Similarity=0.356 Sum_probs=39.5
Q ss_pred eecccCChHHHHHHHHHhhcccccceeeccccchhhhhcccCCCCcceEEecCCCceeEEee
Q 015940 278 RIGIDGTPDAIKEAIKSAFGIRTKRAFWLEDEDQIVRCIDRDMPVGNYTLHLDEGLTIKVCL 339 (398)
Q Consensus 278 r~g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 339 (398)
++.-+-|-..+|+.|.+.+++=..+-=++-+ . +.|+-|.+|..| ++.+|-+|.+.+
T Consensus 16 ~v~~~~tv~~lK~~i~~~~g~~~~~qrL~~~-g---~~L~d~~tl~~~--~i~~g~~i~l~~ 71 (76)
T cd01806 16 DIEPTDKVERIKERVEEKEGIPPQQQRLIYS-G---KQMNDDKTAADY--KLEGGSVLHLVL 71 (76)
T ss_pred EECCCCCHHHHHHHHhHhhCCChhhEEEEEC-C---eEccCCCCHHHc--CCCCCCEEEEEE
Confidence 4555678999999999998876665333322 1 346778899998 577787877654
No 32
>KOG4468 consensus Polycomb-group transcriptional regulator [Transcription]
Probab=34.74 E-value=64 Score=36.23 Aligned_cols=82 Identities=13% Similarity=0.192 Sum_probs=54.9
Q ss_pred hhhcccCCCCCCC-CccCCCCC-----CCCCCHHHHHHHHHHHHHHHHhhccCCCchHHHHHHHHHHHHcCCCCCHHHHH
Q 015940 57 QMILADSSGGEDH-EVRAPKKR-----AETWVQDETRILIAFRREMDGLFNTSKSNKHLWEQISAKMREKGFDRSPTMCT 130 (398)
Q Consensus 57 ~~~~~~~sgeD~~-~~s~pskR-----g~~WT~eET~lLIeL~~E~e~rF~~sKrnkkLWEeIAekMaEkGY~RSaeQCr 130 (398)
+++++-+|-|-.. +.+.+.+. ...||++|..++.+...++-. -++.|-+.|.++-...|-.|.+
T Consensus 61 p~~l~pss~ept~~~~k~~qk~Lkt~~ktaWt~~E~~~Ffdal~~~GK----------dFe~VinaklKRrna~s~~~~K 130 (782)
T KOG4468|consen 61 PNLLSPSSIEPTQFPAKKPQKQLKTWAKTAWTHQEEESFFDALRQVGK----------DFEKVINAKLKRRNATSRVQSK 130 (782)
T ss_pred CCcCCccccCCcccccccchhhcccccccccchhhHHHHHHHHHHhcc----------cHHHHHHHHHHhcccccchhhh
Confidence 6788777766554 22333322 348999999998887766433 3455556666655567788888
Q ss_pred HHHHHHHHHHHHhcccCC
Q 015940 131 DKWRNLLKEFKKTKHQDR 148 (398)
Q Consensus 131 ~KWKNLKK~YKKIKd~nk 148 (398)
+|.-+=...|+-++..++
T Consensus 131 tkdqvr~~yY~~~~~m~k 148 (782)
T KOG4468|consen 131 TKDQVRHYYYRLVRRMNK 148 (782)
T ss_pred hhHHHHHHHHHHHHHHHh
Confidence 888888888887765543
No 33
>PF09608 Alph_Pro_TM: Putative transmembrane protein (Alph_Pro_TM); InterPro: IPR019088 This entry consists of predicted transmembrane proteins of about 270 amino acids. They are found predominantly, though not exclusively, in alphaproteobacteria, generally only once in each genome.
Probab=34.68 E-value=29 Score=33.94 Aligned_cols=52 Identities=17% Similarity=0.441 Sum_probs=40.2
Q ss_pred CChHHHHHHHHHhhcccccceeeccccchhhh----------hcccCCCCcceEEe---cCCCce
Q 015940 283 GTPDAIKEAIKSAFGIRTKRAFWLEDEDQIVR----------CIDRDMPVGNYTLH---LDEGLT 334 (398)
Q Consensus 283 g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----------~~~~~~~~~~~~~~---~~~~~~ 334 (398)
..++...+-..+..+||.+...|.+++.+|-- .|--+||.|+|+++ +.+|--
T Consensus 120 ~~~~~~~~f~~alirlk~~~gLY~~~~~~V~~~~~~lFra~i~LPanvp~G~Y~v~v~l~rdG~v 184 (236)
T PF09608_consen 120 SDPDEQDDFREALIRLKERAGLYQENEGGVQFLEGTLFRARIPLPANVPPGDYTVRVYLFRDGQV 184 (236)
T ss_pred CChhhHHHHHHHHHHHHHhCCCceecCCeEEEcCCCeEEEEeEcCCCCCcceEEEEEEEEECCEE
Confidence 45666667778889999999999999987752 35578999999875 466643
No 34
>PF00435 Spectrin: Spectrin repeat; InterPro: IPR002017 Spectrin repeats [] are found in several proteins involved in cytoskeletal structure. These include spectrin alpha and beta subunits [, ], alpha-actinin [] and dystrophin. The spectrin repeat forms a three-helix bundle. The second helix is interrupted by proline in some sequences. The repeats are defined by a characteristic tryptophan (W) residue at position 17 in helix A and a leucine (L) at 2 residues from the carboxyl end of helix C.; GO: 0005515 protein binding; PDB: 1HCI_A 1QUU_A 3FB2_B 1S35_A 1U5P_A 1U4Q_A 1CUN_B 1YDI_B 3EDV_A 1AJ3_A ....
Probab=34.12 E-value=1.5e+02 Score=22.62 Aligned_cols=62 Identities=8% Similarity=0.146 Sum_probs=45.5
Q ss_pred HHHHHHHHHHHHHHHHhhccCCCchHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHhcc
Q 015940 83 QDETRILIAFRREMDGLFNTSKSNKHLWEQISAKMREKGFDRSPTMCTDKWRNLLKEFKKTKH 145 (398)
Q Consensus 83 ~eET~lLIeL~~E~e~rF~~sKrnkkLWEeIAekMaEkGY~RSaeQCr~KWKNLKK~YKKIKd 145 (398)
.+++..++.-...+...+......-..=...+..|...+ .-....++.+..+|...|..+..
T Consensus 33 ~~~~~~~~~~~~~~~~ei~~~~~~l~~l~~~~~~L~~~~-~~~~~~i~~~~~~l~~~w~~l~~ 94 (105)
T PF00435_consen 33 LEELEEQLKKHKELQEEIESRQERLESLNEQAQQLIDSG-PEDSDEIQEKLEELNQRWEALCE 94 (105)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-HTTHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHcC-CCcHHHHHHHHHHHHHHHHHHHH
Confidence 567788888777777777665444455557777885555 56779999999999999888754
No 35
>PRK12354 carbamate kinase; Reviewed
Probab=32.95 E-value=52 Score=33.57 Aligned_cols=46 Identities=26% Similarity=0.349 Sum_probs=36.0
Q ss_pred eecCCCCC-cccccc-cceecchhhHHHHHHhhccccceeccCccccc
Q 015940 338 CLYDESDH-ISVHTE-DKTFYTEEDYREFLARHGWTCLREFDGYRNVD 383 (398)
Q Consensus 338 ~~~~~~~~-~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 383 (398)
.+.|..|. .+..|- =-.|||||.-+.....+||+....=+|||-|-
T Consensus 107 ~~Vd~~dpAf~~ptKpiG~~y~~~~a~~~~~e~g~~~~~dg~g~rrVv 154 (307)
T PRK12354 107 VEVDANDPAFANPTKPIGPVYDEAEAERLAAEKGWTIKPDGDYFRRVV 154 (307)
T ss_pred EEEcCCCCccCCCCCCcCcccCHHHHHHHHHhcCCEEeecCCceEEEe
Confidence 45677776 555553 34699999999999999999988866888764
No 36
>PF08994 T4_Gp59_C: T4 gene Gp59 loader of gp41 DNA helicase C-term; InterPro: IPR015086 The Bacteriophage T4 gene 59 helicase assembly protein is required for recombination-dependent DNA replication, which is the predominant mode of DNA replication in the late stage of T4 infection. T4 gene 59 helicase assembly protein accelerates the loading of the T4 gene 41 helicase during DNA synthesis by the T4 replication system in vitro. T4 gene 59 helicase assembly protein binds to both T4 gene 41 helicase and T4 gene 32 single-stranded DNA binding protein, and to single and double-stranded DNA. The C-terminal domain of the T4 gene 59 helicase assembly protein consists of seven alpha-helices with short intervening loops and turns; the surface of the domain contains large regions of exposed hydrophobic residues and clusters of acidic and basic residues. The hydrophobic region on the 'bottom' surface of the domain near the C-terminal helix binds the leading strand DNA, whilst the hydrophobic region on the, top, surface of the domain lies between the two arms of the fork DNA, allowing for T4 gene 41 helicase binding and assembly into a hexameric complex around the lagging strand []. ; PDB: 1C1K_A.
Probab=31.28 E-value=93 Score=27.37 Aligned_cols=56 Identities=13% Similarity=0.196 Sum_probs=36.5
Q ss_pred HHHHHHHHHHHHHHHhhccCCCchHHHHHHHHHHHH-cC-CCCCHHHHHHHHHHHHHHH
Q 015940 84 DETRILIAFRREMDGLFNTSKSNKHLWEQISAKMRE-KG-FDRSPTMCTDKWRNLLKEF 140 (398)
Q Consensus 84 eET~lLIeL~~E~e~rF~~sKrnkkLWEeIAekMaE-kG-Y~RSaeQCr~KWKNLKK~Y 140 (398)
=||..+++-.-..-..|.. .....+|+.++.+|.+ +- ...+.++++..+....+.+
T Consensus 45 ~ET~vilds~Lg~v~~~Dk-~~~D~iW~~~s~kl~kYr~fl~Id~~kyk~~~~eti~~~ 102 (103)
T PF08994_consen 45 LETFVILDSFLGFVDKFDK-VLTDPIWKNYSTKLKKYRPFLKIDCEKYKKLFIETIKSC 102 (103)
T ss_dssp HHHHHHHHHHH-HHHHHHH-H---HHHHHHHHHHHHHHHHEEE-HHHHHHHHHHHHHHH
T ss_pred HhHHHHHHHHHhhHHhhhh-hccchhHHHHHHHHHHhcchhhcCHHHHHHHHHHHHHhc
Confidence 4899999877777667765 5678999999988875 11 2357777777776665544
No 37
>cd01789 Alp11_N Ubiquitin-like domain of Alp11 tubulin-folding cofactor B. Alp11, also known as tubulin-folding cofactor B, is one of at least three proteins required for the proper folding of tubulins prior to their incorporation into microtubules. These cofactors are necessary for the biogenesis of microtubules and for cell viability. Alp11 has three domains including an N-terminal ubiquitin-like domain (represented by this CD) which executes the essential function, a central coiled-coil domain necessary for maintenance of cellular alpha-tubulin levels, and a C-terminal CLIP-170 domain is required for efficient binding to alpha-tubulin.
Probab=29.83 E-value=94 Score=25.25 Aligned_cols=60 Identities=27% Similarity=0.443 Sum_probs=43.7
Q ss_pred cceeecccCChHHHHHHHHHhhcc--cccceeeccccch-hhhhc-ccCCCCcceEEecCCCceeEE
Q 015940 275 YTRRIGIDGTPDAIKEAIKSAFGI--RTKRAFWLEDEDQ-IVRCI-DRDMPVGNYTLHLDEGLTIKV 337 (398)
Q Consensus 275 ~t~r~g~~g~~~~~~~~~~~~~~~--~~~~~~~~~~~~~-~~~~~-~~~~~~~~~~~~~~~~~~~~~ 337 (398)
.+||+.-+-|-..+|+-|-..||+ .+-|= .|.|.++ .|-.| |-+.+||.|- +.+|.+|.|
T Consensus 15 ~ekr~~~~~Tv~~lK~kl~~~~G~~~~~mrL-~l~~~~~~~~~~l~~d~~~L~~y~--~~dg~~IhV 78 (84)
T cd01789 15 FEKKYSRGLTIAELKKKLELVVGTPASSMRL-QLFDGDDKLVSKLDDDDALLGSYP--VDDGCRIHV 78 (84)
T ss_pred eeEecCCCCcHHHHHHHHHHHHCCCccceEE-EEEcCCCCeEeecCCCccEeeecc--CCCCCEEEE
Confidence 568888899999999999999997 23332 3344443 33334 6678899995 789999987
No 38
>COG3835 CdaR Sugar diacid utilization regulator [Transcription / Signal transduction mechanisms]
Probab=26.74 E-value=75 Score=33.48 Aligned_cols=42 Identities=40% Similarity=0.695 Sum_probs=33.1
Q ss_pred ccccchhhHHHhcCCCCCCCCCCCCCCCCccCCCcc--ccceEEEEeecccceeecccCChHHHHH
Q 015940 227 PLAITTADAVAAAGVPPWNWRDPPPGNGNLCGEGQS--FGGKVISVKCGDYTRRIGIDGTPDAIKE 290 (398)
Q Consensus 227 ~l~i~~ad~vaa~g~~p~~~~~~~~~~g~~~~~~~~--~~g~~~~~~~~~~t~r~g~~g~~~~~~~ 290 (398)
-+-|+.+++..-+||-| |=|-. |.|+||.| |||.|.|+.|+.
T Consensus 57 ~V~Id~~~a~~l~gVkp--------------GINLPi~~~~~vVGV--------iGITGeP~~Vr~ 100 (376)
T COG3835 57 VVEIDQAVARKLKGVKP--------------GINLPIRFDGKVVGV--------IGITGEPEEVRK 100 (376)
T ss_pred EEEeeHHHHHHhcCCCC--------------CCCcceEecCceEEE--------EeccCChHHHHH
Confidence 45588888988888755 33444 77999998 999999999874
No 39
>cd01236 PH_outspread Outspread Pleckstrin homology (PH) domain. Outspread Pleckstrin homology (PH) domain. Outspread contains two PH domains and a C-terminal coiled-coil region. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinsases, regulators of G-proteins, endocytotic GTPAses, adaptors, a well as cytoskeletal associated molecules and in lipid associated enzymes.
Probab=26.72 E-value=1.1e+02 Score=26.26 Aligned_cols=45 Identities=20% Similarity=0.356 Sum_probs=33.8
Q ss_pred CCCCcceEEecCCCceeEEeecCCC---CCcccccccceec----chhhHHHHHH
Q 015940 319 DMPVGNYTLHLDEGLTIKVCLYDES---DHISVHTEDKTFY----TEEDYREFLA 366 (398)
Q Consensus 319 ~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~----~~~~~~~~~~ 366 (398)
.-|.|. +.|..+..|+-+. |.. .-+.+.|.++||| ||++..+++.
T Consensus 47 ~~p~G~--IdL~~~~~V~~~~-~~~~~~~~f~I~tp~R~f~l~Aete~E~~~Wi~ 98 (104)
T cd01236 47 TLPQGT--IDMNQCTDVVDAE-ARTGQKFSICILTPDKEHFIKAETKEEISWWLN 98 (104)
T ss_pred cccceE--EEccceEEEeecc-cccCCccEEEEECCCceEEEEeCCHHHHHHHHH
Confidence 368885 7788888887654 222 2488999999999 8888888764
No 40
>PF03353 Lin-8: Ras-mediated vulval-induction antagonist; InterPro: IPR005020 This is a family of Caenorhabditis elegans proteins of unknown function.
Probab=25.33 E-value=1.6e+02 Score=29.21 Aligned_cols=64 Identities=11% Similarity=0.234 Sum_probs=46.4
Q ss_pred CCCCHHHHHHHHHHHHHHHHhh-ccCCCchHHHHHHHHHHHH-cCCCCCHHHHHHHHHHHHHHHHH
Q 015940 79 ETWVQDETRILIAFRREMDGLF-NTSKSNKHLWEQISAKMRE-KGFDRSPTMCTDKWRNLLKEFKK 142 (398)
Q Consensus 79 ~~WT~eET~lLIeL~~E~e~rF-~~sKrnkkLWEeIAekMaE-kGY~RSaeQCr~KWKNLKK~YKK 142 (398)
..|...-.+++|.+.++.-... ..+......|+.|+..+-. .|.-.+..+++.=|++.|...++
T Consensus 18 ~~~~~~~kk~il~~i~~~p~lw~~~~~~~~~~~~~v~v~vy~Rtg~~~~~~~i~~~~~~aK~~Lr~ 83 (313)
T PF03353_consen 18 AKKDVELKKVILSEIEKFPELWKKKSRVPNEEWEEVAVEVYKRTGKLVSVKHIRSIFKNAKDSLRR 83 (313)
T ss_pred chhhHHHHHHHHHHHhcChHhhhccCCccHHHHHHHHHHHHHHHhhhcCHHHHHHHHHHHHHHHHH
Confidence 3455555556666666543322 4445678899999998865 69999999999999999987664
No 41
>cd05992 PB1 The PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes, such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as a noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants.
Probab=25.04 E-value=1.4e+02 Score=22.98 Aligned_cols=32 Identities=25% Similarity=0.404 Sum_probs=26.8
Q ss_pred EEEEeecccceeeccc---CChHHHHHHHHHhhcc
Q 015940 267 VISVKCGDYTRRIGID---GTPDAIKEAIKSAFGI 298 (398)
Q Consensus 267 ~~~~~~~~~t~r~g~~---g~~~~~~~~~~~~~~~ 298 (398)
++-|+|++-++|+=+. -|-+.+++.|...|++
T Consensus 2 ~vK~~~~~~~~~~~~~~~~~s~~~L~~~i~~~~~~ 36 (81)
T cd05992 2 RVKVKYGGEIRRFVVVSRSISFEDLRSKIAEKFGL 36 (81)
T ss_pred cEEEEecCCCEEEEEecCCCCHHHHHHHHHHHhCC
Confidence 4678898888888876 5778999999999986
No 42
>PF07750 GcrA: GcrA cell cycle regulator; InterPro: IPR011681 GcrA, together with CtrA (see IPR001789 from INTERPRO and IPR001867 from INTERPRO), form a master cell cycle regulator. These bacterial regulators are involved in controlling the progression and asymmetric polar morphogenesis []. During this process, there are temporal and spatial variations in the concentrations of GcrA and CtrA. The variation in concentration produces time and space dependent transcriptional regulation of modular functions that implement cell-cycle processes []. More specifically, GcrA acts as an activator of components of the replisome and the segregation machinery [].
Probab=24.91 E-value=71 Score=29.51 Aligned_cols=37 Identities=19% Similarity=0.321 Sum_probs=26.9
Q ss_pred CCCCHHHHHHHHHHHHHHHHhhccCCCchHHHHHHHHHHHHcCCCCCHHH
Q 015940 79 ETWVQDETRILIAFRREMDGLFNTSKSNKHLWEQISAKMREKGFDRSPTM 128 (398)
Q Consensus 79 ~~WT~eET~lLIeL~~E~e~rF~~sKrnkkLWEeIAekMaEkGY~RSaeQ 128 (398)
+.||++.+..|-++|.+- .--.+|++.|. |+.|++..
T Consensus 1 M~Wtde~~~~L~~lw~~G-----------~SasqIA~~lg--~vsRnAVi 37 (162)
T PF07750_consen 1 MSWTDERVERLRKLWAEG-----------LSASQIARQLG--GVSRNAVI 37 (162)
T ss_pred CCCCHHHHHHHHHHHHcC-----------CCHHHHHHHhC--Ccchhhhh
Confidence 579999999999999871 22346777665 57776665
No 43
>smart00666 PB1 PB1 domain. Phox and Bem1p domain, present in many eukaryotic cytoplasmic signalling proteins. The domain adopts a beta-grasp fold, similar to that found in ubiquitin and Ras-binding domains. A motif, variously termed OPR, PC and AID, represents the most conserved region of the majority of PB1 domains, and is necessary for PB1 domain function. This function is the formation of PB1 domain heterodimers, although not all PB1 domain pairs associate.
Probab=24.12 E-value=1.6e+02 Score=22.93 Aligned_cols=32 Identities=19% Similarity=0.509 Sum_probs=26.1
Q ss_pred EEEEeecccceeecccC--ChHHHHHHHHHhhcc
Q 015940 267 VISVKCGDYTRRIGIDG--TPDAIKEAIKSAFGI 298 (398)
Q Consensus 267 ~~~~~~~~~t~r~g~~g--~~~~~~~~~~~~~~~ 298 (398)
.+.|.||+-++|+=+.. |-+.+...|...|++
T Consensus 3 ~vK~~~~~~~~~~~~~~~~s~~dL~~~i~~~~~~ 36 (81)
T smart00666 3 DVKLRYGGETRRLSVPRDISFEDLRSKVAKRFGL 36 (81)
T ss_pred cEEEEECCEEEEEEECCCCCHHHHHHHHHHHhCC
Confidence 35678898999988865 668999999999984
No 44
>cd01803 Ubiquitin Ubiquitin. Ubiquitin (includes Ubq/RPL40e and Ubq/RPS27a fusions as well as homopolymeric multiubiquitin protein chains)
Probab=23.98 E-value=2.2e+02 Score=21.46 Aligned_cols=62 Identities=18% Similarity=0.388 Sum_probs=40.1
Q ss_pred cceEEEEeecccceeecccCChHHHHHHHHHhhcccccc-eeeccccchhhhhcccCCCCcceEEecCCCceeEEee
Q 015940 264 GGKVISVKCGDYTRRIGIDGTPDAIKEAIKSAFGIRTKR-AFWLEDEDQIVRCIDRDMPVGNYTLHLDEGLTIKVCL 339 (398)
Q Consensus 264 ~g~~~~~~~~~~t~r~g~~g~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 339 (398)
.|+.+.+. +.-+-|...||+.|...+++-..+ .+|.. . +.|+-+.+|+.| ++.+|-+|.+.+
T Consensus 9 ~g~~~~~~-------v~~~~tV~~lK~~i~~~~g~~~~~q~L~~~--g---~~L~d~~~L~~~--~i~~~~~i~l~~ 71 (76)
T cd01803 9 TGKTITLE-------VEPSDTIENVKAKIQDKEGIPPDQQRLIFA--G---KQLEDGRTLSDY--NIQKESTLHLVL 71 (76)
T ss_pred CCCEEEEE-------ECCcCcHHHHHHHHHHHhCCCHHHeEEEEC--C---EECCCCCcHHHc--CCCCCCEEEEEE
Confidence 35555553 334568999999999998875433 22322 1 236677888887 467777777654
No 45
>PF07495 Y_Y_Y: Y_Y_Y domain; InterPro: IPR011123 This region is mostly found at the end of the beta propellers (IPR011110 from INTERPRO) in a family of two component regulators. However they are also found tandemly repeated in Q891H4 from SWISSPROT without other signal conduction domains being present. It is named after the conserved tyrosines found in the alignment. The exact function is not known.; PDB: 3V9F_D 3VA6_B 3OTT_B 4A2M_D 4A2L_B.
Probab=23.91 E-value=42 Score=24.93 Aligned_cols=11 Identities=45% Similarity=1.050 Sum_probs=7.6
Q ss_pred CCCCcceEEec
Q 015940 319 DMPVGNYTLHL 329 (398)
Q Consensus 319 ~~~~~~~~~~~ 329 (398)
.+|.|+|+|++
T Consensus 35 ~L~~G~Y~l~V 45 (66)
T PF07495_consen 35 NLPPGKYTLEV 45 (66)
T ss_dssp S--SEEEEEEE
T ss_pred eCCCEEEEEEE
Confidence 47999999976
No 46
>cd01038 Endonuclease_DUF559 Domain of unknown function, appears to be related to a diverse group of endonucleases.
Probab=23.85 E-value=1.1e+02 Score=25.87 Aligned_cols=47 Identities=26% Similarity=0.542 Sum_probs=27.0
Q ss_pred CCCCcceEEecCCCc-eeEEee-cCCCCCcccccccceecchhhHH-HHHHhhccccce
Q 015940 319 DMPVGNYTLHLDEGL-TIKVCL-YDESDHISVHTEDKTFYTEEDYR-EFLARHGWTCLR 374 (398)
Q Consensus 319 ~~~~~~~~~~~~~~~-~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~ 374 (398)
..|+|.|.+.+ ++ .-||+. ||... |.... ..|-.| .+|..+||+.||
T Consensus 37 q~~i~~~~vD~--~~~~~kl~IE~DG~~----H~~~~---~~D~~R~~~L~~~Gw~vlR 86 (108)
T cd01038 37 QAPIGRYIVDF--ACPEAKLVVELDGGQ----HDEQI---AYDAERDAWLEARGFRVLR 86 (108)
T ss_pred ccCCCCcEeee--EccccCEEEEEeCcc----cCchH---HHHHHHHHHHHHCCCEEEE
Confidence 34567776544 21 234444 78763 44332 223332 588999999997
No 47
>PTZ00044 ubiquitin; Provisional
Probab=23.54 E-value=2.2e+02 Score=21.80 Aligned_cols=63 Identities=27% Similarity=0.357 Sum_probs=40.6
Q ss_pred cceEEEEeecccceeecccCChHHHHHHHHHhhcccccceeeccccchhhhhcccCCCCcceEEecCCCceeEEee
Q 015940 264 GGKVISVKCGDYTRRIGIDGTPDAIKEAIKSAFGIRTKRAFWLEDEDQIVRCIDRDMPVGNYTLHLDEGLTIKVCL 339 (398)
Q Consensus 264 ~g~~~~~~~~~~t~r~g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 339 (398)
.|+.+.+... -+-|-..||+-|.+..++=.. ...|.=.. +.|+-+.+|..| ++.+|.+|.+.+
T Consensus 9 ~G~~~~l~v~-------~~~tv~~lK~~i~~~~gi~~~-~q~L~~~g---~~L~d~~~l~~~--~i~~~~~i~l~~ 71 (76)
T PTZ00044 9 TGKKQSFNFE-------PDNTVQQVKMALQEKEGIDVK-QIRLIYSG---KQMSDDLKLSDY--KVVPGSTIHMVL 71 (76)
T ss_pred CCCEEEEEEC-------CCCcHHHHHHHHHHHHCCCHH-HeEEEECC---EEccCCCcHHHc--CCCCCCEEEEEE
Confidence 3555555444 456889999999998886332 22222222 236777889988 567888887764
No 48
>cd04041 C2A_fungal C2 domain first repeat; fungal group. C2 domains were first identified in Protein Kinase C (PKC). C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligan
Probab=23.38 E-value=76 Score=26.19 Aligned_cols=18 Identities=28% Similarity=0.553 Sum_probs=15.5
Q ss_pred hHHHHHHhhccccceecc
Q 015940 360 DYREFLARHGWTCLREFD 377 (398)
Q Consensus 360 ~~~~~~~~~~~~~~~~~~ 377 (398)
.+.+++..++|+.|||+|
T Consensus 93 ~l~~l~~~~~~~~~~~~~ 110 (111)
T cd04041 93 DLKELIEDRNWMGRREDG 110 (111)
T ss_pred EHHHHhcCCCCCcccccC
Confidence 457889999999999875
No 49
>PRK12454 carbamate kinase-like carbamoyl phosphate synthetase; Reviewed
Probab=23.11 E-value=51 Score=33.69 Aligned_cols=29 Identities=31% Similarity=0.721 Sum_probs=23.9
Q ss_pred eecchhhHHHHHHhhcccccee-ccCcccc
Q 015940 354 TFYTEEDYREFLARHGWTCLRE-FDGYRNV 382 (398)
Q Consensus 354 ~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~ 382 (398)
.||+||+-+....++||+.... =.|||-|
T Consensus 134 ~~y~~~~a~~~~~~~g~~~~~d~g~g~Rrv 163 (313)
T PRK12454 134 PFYDEEEAKKLAKEKGWIVKEDAGRGWRRV 163 (313)
T ss_pred CCcCHHHHHHHHHHcCCEEEEcCCCceEEE
Confidence 4999999999999999987755 3588754
No 50
>cd01244 PH_RasGAP_CG9209 RAS_GTPase activating protein (GAP)_CG9209 pleckstrin homology (PH) domain. RAS_GTPase activating protein (GAP)_CG9209 pleckstrin homology (PH) domain. This protein consists of two C2 domains, followed by a RasGAP domain, a PH domain and a BTK domain. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinsases, regulators of G-proteins, endocytotic GTPAses, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes.
Probab=22.58 E-value=1.3e+02 Score=25.56 Aligned_cols=46 Identities=15% Similarity=0.063 Sum_probs=29.1
Q ss_pred CCCCcceEEecCCCceeEEeec---CCCCCcccccccceec----chhhHHHHHH
Q 015940 319 DMPVGNYTLHLDEGLTIKVCLY---DESDHISVHTEDKTFY----TEEDYREFLA 366 (398)
Q Consensus 319 ~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~----~~~~~~~~~~ 366 (398)
+-|.|+ +.|..-..+..|-- +...-+.|-|.++||| +|++-.+++.
T Consensus 41 ~~~~g~--I~L~~i~~ve~v~~~~~~~~~~fqivt~~r~~yi~a~s~~E~~~Wi~ 93 (98)
T cd01244 41 CKKSAL--IKLAAIKGTEPLSDKSFVNVDIITIVCEDDTMQLQFEAPVEATDWLN 93 (98)
T ss_pred Cceeee--EEccceEEEEEcCCcccCCCceEEEEeCCCeEEEECCCHHHHHHHHH
Confidence 466664 45555555544432 2223478888999999 6788777764
No 51
>PRK12686 carbamate kinase; Reviewed
Probab=22.45 E-value=53 Score=33.54 Aligned_cols=31 Identities=35% Similarity=0.510 Sum_probs=23.6
Q ss_pred cceecchhhHHHHHHhhccccceec-cCcccc
Q 015940 352 DKTFYTEEDYREFLARHGWTCLREF-DGYRNV 382 (398)
Q Consensus 352 ~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~ 382 (398)
--.|||+++-+..-.++||+..... .|||-|
T Consensus 130 ig~~~~~~~a~~~~~~~g~~~~~d~~~G~rrv 161 (312)
T PRK12686 130 IGPFYTEEEAKQQAEQPGSTFKEDAGRGYRRV 161 (312)
T ss_pred ccCccCHHHHHHHHHHcCCcccccCCCCeEEe
Confidence 3469999999996667799877664 389753
No 52
>KOG2916 consensus Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=22.07 E-value=1e+02 Score=31.51 Aligned_cols=27 Identities=52% Similarity=0.780 Sum_probs=21.1
Q ss_pred EEEEeecccceeecccCChHHHHHHHHHhhcccc
Q 015940 267 VISVKCGDYTRRIGIDGTPDAIKEAIKSAFGIRT 300 (398)
Q Consensus 267 ~~~~~~~~~t~r~g~~g~~~~~~~~~~~~~~~~~ 300 (398)
=|-|++-.|- || +|||+|+++|.++=|
T Consensus 186 DIEv~Cf~ye---GI----~aIK~alk~a~~~~t 212 (304)
T KOG2916|consen 186 DIEVSCFGYE---GI----DAIKAALKAALNLST 212 (304)
T ss_pred eeEEEecccc---CH----HHHHHHHHHHHhCCc
Confidence 3778777665 55 699999999988766
No 53
>COG2852 Very-short-patch-repair endonuclease [Replication, recombination, and repair]
Probab=21.90 E-value=92 Score=28.45 Aligned_cols=50 Identities=34% Similarity=0.637 Sum_probs=32.4
Q ss_pred ccCCCCcceEE---ecCCCceeEEeecCCCCCcccccccceecchhhHHHHHHhhcccccee
Q 015940 317 DRDMPVGNYTL---HLDEGLTIKVCLYDESDHISVHTEDKTFYTEEDYREFLARHGWTCLRE 375 (398)
Q Consensus 317 ~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 375 (398)
-|--|+|.|++ |.+.-|-|.+ |.+-| ++..=|..+ =-.||..+||+-||=
T Consensus 48 rRQ~~ig~yivDF~c~~~klIvEl---DG~qH-----~~~~~~Da~-Rd~~L~~~G~~VLRf 100 (129)
T COG2852 48 RRQQPIGRYIVDFACRDAKLIVEL---DGGQH-----EEREEYDAE-RDAFLESQGFTVLRF 100 (129)
T ss_pred EEeeeccCEEEEEEcCCccEEEEe---cCccc-----hhhhhhhHH-HHHHHHhCCceEEEe
Confidence 47789999986 5566666654 77754 222222211 125999999999983
No 54
>TIGR02870 spore_II_D stage II sporulation protein D. Stage II sporulation protein D (SpoIID) is a protein of the endospore formation program in a number of lineages in the Firmicutes (low-GC Gram-positive bacteria). It is expressed in the mother cell compartment, under control of Sigma-E. SpoIID, along with SpoIIM and SpoIIP, is one of three major proteins involved in engulfment of the forespore by the mother cell.
Probab=21.46 E-value=60 Score=33.41 Aligned_cols=35 Identities=29% Similarity=0.618 Sum_probs=26.2
Q ss_pred cccceEEEEeecccceeecccCChHHHHHHHHHhhcccccceeecc
Q 015940 262 SFGGKVISVKCGDYTRRIGIDGTPDAIKEAIKSAFGIRTKRAFWLE 307 (398)
Q Consensus 262 ~~~g~~~~~~~~~~t~r~g~~g~~~~~~~~~~~~~~~~~~~~~~~~ 307 (398)
.-+|||..|+.|+.| +.| +.||.+|+||+-+ |-++
T Consensus 254 ~~sGrV~~l~vg~~~----~~g------~~~R~~lgL~St~-F~i~ 288 (338)
T TIGR02870 254 TAGGRVKTIKIGGVT----LKG------REIRERLGLNSTD-FTWK 288 (338)
T ss_pred CCCCCEEEEEEeeEE----EEH------HHHHHHhCCCCcc-eEEE
Confidence 356999999999855 444 3688889999987 5543
No 55
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=21.44 E-value=3.2e+02 Score=19.73 Aligned_cols=54 Identities=13% Similarity=0.254 Sum_probs=43.0
Q ss_pred CCCCCHHHHHHHHHHHHHHHHhhccCCCchHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHH
Q 015940 78 AETWVQDETRILIAFRREMDGLFNTSKSNKHLWEQISAKMREKGFDRSPTMCTDKWRNLLKEFKK 142 (398)
Q Consensus 78 g~~WT~eET~lLIeL~~E~e~rF~~sKrnkkLWEeIAekMaEkGY~RSaeQCr~KWKNLKK~YKK 142 (398)
...+|.+.+..|-+.|.. +.......-+.||..| ..+..|...-|.|=+..+|+
T Consensus 4 r~~~t~~q~~~L~~~f~~------~~~p~~~~~~~la~~l-----~l~~~~V~~WF~nrR~k~kk 57 (57)
T PF00046_consen 4 RTRFTKEQLKVLEEYFQE------NPYPSKEEREELAKEL-----GLTERQVKNWFQNRRRKEKK 57 (57)
T ss_dssp SSSSSHHHHHHHHHHHHH------SSSCHHHHHHHHHHHH-----TSSHHHHHHHHHHHHHHHHH
T ss_pred CCCCCHHHHHHHHHHHHH------hccccccccccccccc-----cccccccccCHHHhHHHhCc
Confidence 457888888888888774 3346667788898887 68999999999998888775
No 56
>cd01794 DC_UbP_C dendritic cell derived ubiquitin-like protein. DC_UbP (dendritic cell derived ubiquitin-like protein) is a ubiquitin-like protein from human dendritic cells that is expressed in the mitochondrion. The ubiquitin-like domain of this protein is found at the C-terminus and lacks the canonical gly-gly motif of ubiquitin required for ubiquitinization. DC_UbP is expressed in tumor cells but not in normal human adult tissue suggesting a role for DC_UbP in tumorogenesis.
Probab=20.86 E-value=2e+02 Score=22.56 Aligned_cols=64 Identities=11% Similarity=0.134 Sum_probs=44.1
Q ss_pred ccceEEEEeecccceeecccCChHHHHHHHHHhhcccccceeeccccchhhhhcccCCCCcceEEecCCCceeEEee
Q 015940 263 FGGKVISVKCGDYTRRIGIDGTPDAIKEAIKSAFGIRTKRAFWLEDEDQIVRCIDRDMPVGNYTLHLDEGLTIKVCL 339 (398)
Q Consensus 263 ~~g~~~~~~~~~~t~r~g~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 339 (398)
.+|+.+.+...+. -|-..||+.|.+.+++-...- .|--. =+.|+-|..|+.|-+ .+|.+|-||.
T Consensus 6 ~~G~~~~l~v~~~-------~TV~~lK~~I~~~~gi~~~~q-~Li~~---G~~L~D~~~l~~~~i--~~~~tv~~~~ 69 (70)
T cd01794 6 STGKDVKLSVSSK-------DTVGQLKKQLQAAEGVDPCCQ-RWFFS---GKLLTDKTRLQETKI--QKDYVVQVIV 69 (70)
T ss_pred CCCCEEEEEECCc-------ChHHHHHHHHHHHhCCCHHHe-EEEEC---CeECCCCCCHHHcCC--CCCCEEEEEe
Confidence 4677777766553 478899999999988754432 22111 134888889998754 4899998875
No 57
>PRK09411 carbamate kinase; Reviewed
Probab=20.77 E-value=60 Score=33.09 Aligned_cols=29 Identities=28% Similarity=0.417 Sum_probs=25.9
Q ss_pred eecchhhHHHHHHhhccccceeccCcccc
Q 015940 354 TFYTEEDYREFLARHGWTCLREFDGYRNV 382 (398)
Q Consensus 354 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 382 (398)
.||+++.-......+||+....=+|||-|
T Consensus 126 ~~y~~e~a~~l~~e~g~~~~~dg~g~rrV 154 (297)
T PRK09411 126 PVYQPEEQEALEAAYGWQMKRDGKYLRRV 154 (297)
T ss_pred CccCHHHHHHHHHhcCCEEEecCCceEEE
Confidence 59999999999999999988886689987
No 58
>cd01792 ISG15_repeat1 ISG15 ubiquitin-like protein, first repeat of 2. ISG15 is a ubiquitin-like protein containing two ubiquitin homology domains that becomes conjugated to a variety of proteins when cells are treated with type I interferon or lipopolysaccharide. Although ISG15 has properties similar to those of other ubiquitin-like molecules, it is a unique member of the ubiquitin-like superfamily, whose expression and conjugation to target proteins are tightly regulated by specific signaling pathways, indicating it may have specialized functions in the immune system.
Probab=20.73 E-value=2.4e+02 Score=22.32 Aligned_cols=52 Identities=19% Similarity=0.272 Sum_probs=37.2
Q ss_pred cCChHHHHHHHHHhhcccccceeec--cccchhhhhcccCCCCcceEEecCCCceeEEee
Q 015940 282 DGTPDAIKEAIKSAFGIRTKRAFWL--EDEDQIVRCIDRDMPVGNYTLHLDEGLTIKVCL 339 (398)
Q Consensus 282 ~g~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 339 (398)
+-|-..+|+.|...+++-.. .+|| ...- +.|+-+-+|..| .+.+|-+|.|.+
T Consensus 22 ~~TV~~lK~~I~~~~~i~~~-~qrL~~~~~G---~~L~D~~tL~~~--gi~~gs~l~l~~ 75 (80)
T cd01792 22 SMTVSELKQQIAQKIGVPAF-QQRLAHLDSR---EVLQDGVPLVSQ--GLGPGSTVLLVV 75 (80)
T ss_pred CCcHHHHHHHHHHHhCCCHH-HEEEEeccCC---CCCCCCCCHHHc--CCCCCCEEEEEE
Confidence 35788999999999998443 3566 4332 246667788887 678888887765
No 59
>cd04235 AAK_CK AAK_CK: Carbamate kinase (CK) catalyzes both the ATP-phosphorylation of carbamate and carbamoyl phosphate (CP) utilization with the production of ATP from ADP and CP. Both CK (this CD) and nonhomologous CP synthetase synthesize carbamoyl phosphate, an essential precursor of arginine and pyrimidine bases, in the presence of ATP, bicarbonate, and ammonia. CK is a homodimer of 33 kDa subunits and is a member of the Amino Acid Kinase Superfamily (AAK).
Probab=20.37 E-value=67 Score=32.70 Aligned_cols=27 Identities=44% Similarity=0.892 Sum_probs=22.6
Q ss_pred eecchhhHHHHHHhhccccceec-cCcc
Q 015940 354 TFYTEEDYREFLARHGWTCLREF-DGYR 380 (398)
Q Consensus 354 ~~~~~~~~~~~~~~~~~~~~~~~-~~~~ 380 (398)
-||+|+.-++.-.++||+....- .|||
T Consensus 130 ~~y~~~~a~~~~~~~g~~~~~d~~~g~r 157 (308)
T cd04235 130 PFYSEEEAEELAAEKGWTFKEDAGRGYR 157 (308)
T ss_pred CCcCHHHHHHHHHHcCCEEEEeCCCCce
Confidence 59999999999999999765444 5788
Done!