Query 033520
Match_columns 117
No_of_seqs 149 out of 461
Neff 3.8
Searched_HMMs 46136
Date Fri Mar 29 03:14:14 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033520.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033520hhsearch_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 99.8 3.8E-19 8.2E-24 143.2 5.8 114 1-115 32-164 (240)
2 PF02201 SWIB: SWIB/MDM2 domai 99.7 3.9E-19 8.4E-24 119.4 0.3 53 63-115 1-65 (76)
3 smart00151 SWIB SWI complex, B 99.7 3.9E-18 8.4E-23 114.8 4.5 52 63-114 1-64 (77)
4 PRK14724 DNA topoisomerase III 99.6 2.7E-15 5.9E-20 138.4 4.9 54 62-115 911-976 (987)
5 COG5531 SWIB-domain-containing 99.6 2.8E-15 6.2E-20 121.0 4.2 55 60-114 118-184 (237)
6 KOG2570 SWI/SNF transcription 99.1 5.7E-11 1.2E-15 102.4 3.6 50 65-114 207-268 (420)
7 PRK06319 DNA topoisomerase I/S 98.8 2.7E-09 5.8E-14 97.6 3.8 53 62-114 783-847 (860)
8 PLN02945 nicotinamide-nucleoti 71.5 2.9 6.2E-05 33.0 2.0 32 70-101 204-235 (236)
9 PRK00071 nadD nicotinic acid m 71.2 2.7 5.8E-05 32.0 1.7 32 70-101 170-201 (203)
10 TIGR00482 nicotinate (nicotina 70.7 3 6.4E-05 31.6 1.8 31 70-100 162-192 (193)
11 PRK06973 nicotinic acid mononu 68.7 3.3 7.1E-05 33.3 1.8 32 70-101 202-241 (243)
12 TIGR01764 excise DNA binding d 58.0 10 0.00022 21.4 2.1 27 71-104 5-31 (49)
13 cd02165 NMNAT Nicotinamide/nic 54.6 9.1 0.0002 28.7 1.9 32 69-100 160-191 (192)
14 PRK08887 nicotinic acid mononu 54.5 9.7 0.00021 28.8 2.0 32 70-101 139-170 (174)
15 COG1654 BirA Biotin operon rep 53.6 9.8 0.00021 26.2 1.8 22 69-97 21-42 (79)
16 PF08031 BBE: Berberine and be 53.4 9.7 0.00021 23.2 1.5 28 71-108 14-41 (47)
17 TIGR02057 PAPS_reductase phosp 50.3 11 0.00023 29.8 1.7 13 90-102 172-184 (226)
18 cd09286 NMNAT_Eukarya Nicotina 50.0 11 0.00025 29.6 1.9 32 69-100 193-224 (225)
19 PF08513 LisH: LisH; InterPro 49.0 3.9 8.4E-05 22.6 -0.7 25 86-110 2-26 (27)
20 TIGR02055 APS_reductase thiore 47.9 12 0.00027 28.4 1.7 12 90-101 136-147 (191)
21 PF13950 Epimerase_Csub: UDP-g 45.6 37 0.00081 21.9 3.5 43 57-99 16-59 (62)
22 PRK12563 sulfate adenylyltrans 43.4 15 0.00033 31.1 1.7 15 90-104 203-217 (312)
23 PLN02309 5'-adenylylsulfate re 42.9 15 0.00033 32.5 1.7 13 89-101 261-273 (457)
24 PF06039 Mqo: Malate:quinone o 42.3 12 0.00026 33.8 1.0 23 83-105 82-105 (488)
25 TIGR00434 cysH phosophoadenyly 42.1 17 0.00037 27.6 1.7 12 90-101 157-168 (212)
26 PF01507 PAPS_reduct: Phosphoa 41.3 15 0.00033 25.8 1.3 13 89-101 142-154 (174)
27 smart00667 LisH Lissencephaly 41.3 22 0.00047 18.6 1.6 25 83-107 2-26 (34)
28 cd04762 HTH_MerR-trunc Helix-T 40.7 28 0.00061 19.2 2.1 24 71-101 4-27 (49)
29 PRK07152 nadD putative nicotin 39.0 16 0.00036 30.1 1.2 21 87-107 170-190 (342)
30 PF08938 HBS1_N: HBS1 N-termin 37.0 14 0.0003 24.8 0.4 26 69-94 31-56 (79)
31 PF12728 HTH_17: Helix-turn-he 36.5 33 0.00072 20.2 2.0 26 71-103 5-30 (51)
32 PF02926 THUMP: THUMP domain; 36.4 67 0.0015 22.0 3.8 36 81-116 98-142 (144)
33 PF13333 rve_2: Integrase core 36.3 39 0.00085 20.6 2.4 22 78-99 14-35 (52)
34 TIGR00424 APS_reduc 5'-adenyly 36.0 22 0.00049 31.5 1.7 12 90-101 267-278 (463)
35 PRK05253 sulfate adenylyltrans 34.6 32 0.0007 28.6 2.3 18 90-107 193-210 (301)
36 cd04761 HTH_MerR-SF Helix-Turn 33.7 42 0.00092 19.1 2.1 26 71-104 4-29 (49)
37 PF07898 DUF1676: Protein of u 33.6 24 0.00051 23.9 1.2 18 84-101 52-69 (106)
38 cd01713 PAPS_reductase This do 33.3 30 0.00066 23.7 1.7 13 89-101 148-160 (173)
39 TIGR02039 CysD sulfate adenyly 33.1 27 0.00059 29.1 1.7 15 90-104 185-199 (294)
40 PRK02090 phosphoadenosine phos 32.2 30 0.00065 27.1 1.7 13 89-101 181-193 (241)
41 PF14838 INTS5_C: Integrator c 32.1 38 0.00083 31.9 2.6 35 66-100 615-654 (696)
42 TIGR01510 coaD_prev_kdtB pante 30.6 34 0.00073 25.1 1.6 29 70-98 126-154 (155)
43 smart00581 PSP proline-rich do 30.1 42 0.00092 22.0 1.8 19 65-83 5-23 (54)
44 COG0175 CysH 3'-phosphoadenosi 28.9 31 0.00067 27.7 1.3 15 90-104 184-198 (261)
45 PHA01748 hypothetical protein 28.3 41 0.00088 21.7 1.5 49 67-115 7-60 (60)
46 smart00224 GGL G protein gamma 28.2 1.3E+02 0.0028 19.5 3.9 46 71-116 9-62 (63)
47 PF03656 Pam16: Pam16; InterP 27.7 88 0.0019 23.3 3.4 30 71-100 58-88 (127)
48 PF12368 DUF3650: Protein of u 27.4 30 0.00066 20.0 0.7 11 93-103 9-19 (28)
49 PF04046 PSP: PSP; InterPro: 26.1 54 0.0012 20.9 1.8 19 65-83 1-19 (48)
50 PF01381 HTH_3: Helix-turn-hel 25.9 36 0.00077 20.0 0.9 27 71-104 13-39 (55)
51 COG1057 NadD Nicotinic acid mo 25.3 51 0.0011 25.9 1.9 32 70-101 164-195 (197)
52 cd01104 HTH_MlrA-CarA Helix-Tu 24.1 87 0.0019 19.1 2.5 27 71-104 4-30 (68)
53 KOG2522 Filamentous baseplate 23.8 57 0.0012 30.0 2.1 26 80-105 380-405 (560)
54 PHA01399 membrane protein P6 22.2 44 0.00095 27.6 1.0 13 86-98 160-172 (242)
55 PF02614 UxaC: Glucuronate iso 21.0 71 0.0015 28.4 2.1 33 71-104 105-137 (462)
56 PRK12757 cell division protein 20.4 47 0.001 27.6 0.8 9 89-97 46-54 (256)
57 PF00010 HLH: Helix-loop-helix 20.4 1.5E+02 0.0033 17.7 3.0 18 80-97 36-53 (55)
No 1
>KOG1946 consensus RNA polymerase I transcription factor UAF [Transcription]
Probab=99.77 E-value=3.8e-19 Score=143.18 Aligned_cols=114 Identities=31% Similarity=0.326 Sum_probs=76.1
Q ss_pred CccccccccccccCccccccccCCCCCCCC--CCCCcch--hhHHHHHhhhcC---CCCCCCCCCCCCCCCCCCCCCHHH
Q 033520 1 MAVSSGVFTTTFLSPETASSFLKPSSSGKP--GQFSPVH--LRTVRTVTLATA---SPKPVTGKREPRGIMKPRRVSPEM 73 (117)
Q Consensus 1 m~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~p~~--~~~~r~~~s~~~---~~~~~~~~k~~~g~~kp~~LSpeL 73 (117)
|+..+|+.+|++.+..+- .+..+...-+. ..-.+.+ .+..|+...... .+...++++.++|+++++.||++|
T Consensus 32 ~~~~~~v~~~~~k~~~~~-~~~~~~~~~~~~~~k~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~kl~~ls~~L 110 (240)
T KOG1946|consen 32 MAPRSGVDGTAQKSLLAK-AIDESSDEDSALPVKGSKKKKRGSKTRSRKPKSLESSGEKNKKKKKASWGSTKLIPLSPSL 110 (240)
T ss_pred hccccCCCCcchhhhhhh-hhhcccccccccccccccccccccccccccCcccccccccchhccccCcCcccccccCHHH
Confidence 566788888887766554 44442222111 1111222 233332222111 112222333557999999999999
Q ss_pred HhhhCCCCcCHHHHHHHHHHHhhhcCCCCccc------------ccCcceeEEe
Q 033520 74 EAFVGAPEIPRTQALKLIWAHIKQHNLQWKTI------------VFGKWECWIW 115 (117)
Q Consensus 74 a~~lG~~e~sR~evvK~lW~YIK~nnLQDP~N------------vFG~d~v~~~ 115 (117)
++|+|.++++|.+|+++||+|||+||||||.| |||+++|.|.
T Consensus 111 ~~~~G~~~lsR~~vvk~iw~YIke~nLqDP~nkr~IlCDekL~~iF~~k~v~~f 164 (240)
T KOG1946|consen 111 ARFVGTSELSRTDVVKKIWAYIKEHNLQDPKNKREILCDEKLKSIFGKKRVGMF 164 (240)
T ss_pred HhhcccccccHHHHHHHHHHHHHHhccCCccccCeeeeHHHHHHHhccCcccee
Confidence 99999999999999999999999999999996 9998887663
No 2
>PF02201 SWIB: SWIB/MDM2 domain; InterPro: IPR003121 The SWI/SNF family of complexes, which are conserved from yeast to humans, are ATP-dependent chromatin-remodelling proteins that facilitate transcription activation []. The mammalian complexes are made up of 9-12 proteins called BAFs (BRG1-associated factors). The BAF60 family have at least three members: BAF60a, which is ubiquitous, BAF60b and BAF60c, which are expressed in muscle and pancreatic tissues, respectively. BAF60b is present in alternative forms of the SWI/SNF complex, including complex B (SWIB), which lacks BAF60a. The SWIB domain is a conserved region found within the BAF60b proteins [], and can be found fused to the C terminus of DNA topoisomerase in Chlamydia. MDM2 is an oncoprotein that acts as a cellular inhibitor of the p53 tumour suppressor by binding to the transactivation domain of p53 and suppressing its ability to activate transcription []. p53 acts in response to DNA damage, inducing cell cycle arrest and apoptosis. Inactivation of p53 is a common occurrence in neoplastic transformations. The core of MDM2 folds into an open bundle of four helices, which is capped by two small 3-stranded beta-sheets. It consists of a duplication of two structural repeats. MDM2 has a deep hydrophobic cleft on which the p53 alpha-helix binds; p53 residues involved in transactivation are buried deep within the cleft of MDM2, thereby concealing the p53 transactivation domain. The SWIB and MDM2 domains are homologous and share a common fold.; GO: 0005515 protein binding; PDB: 1V31_A 3FE7_A 3JZQ_B 3EQY_B 2VYR_A 3JZO_A 3DAB_E 3LBJ_E 3FEA_A 3FDO_A ....
Probab=99.73 E-value=3.9e-19 Score=119.45 Aligned_cols=53 Identities=34% Similarity=0.573 Sum_probs=47.6
Q ss_pred CCCCCCCCHHHHhhhCCCCcCHHHHHHHHHHHhhhcCCCCccc------------ccCcceeEEe
Q 033520 63 IMKPRRVSPEMEAFVGAPEIPRTQALKLIWAHIKQHNLQWKTI------------VFGKWECWIW 115 (117)
Q Consensus 63 ~~kp~~LSpeLa~~lG~~e~sR~evvK~lW~YIK~nnLQDP~N------------vFG~d~v~~~ 115 (117)
|.++|+||++|++++|..++||++|+++||+|||+||||||+| |||+|+|.+.
T Consensus 1 ~~k~~~ls~~L~~~lg~~~~sr~~v~~~lw~YIk~~~L~dp~~k~~I~cD~~L~~lf~~~~v~~~ 65 (76)
T PF02201_consen 1 FPKRFKLSPELAEFLGEDELSRSEVVKRLWQYIKENNLQDPKDKRIIICDEKLKKLFGKDSVNFF 65 (76)
T ss_dssp -EEEEHHHHHHHHHTT-SCEEHHHHHHHHHHHHHHTTSBESSSTTEEE-TTSHHHHHHTSECSEE
T ss_pred CCCCccCCHHHHHHhCCCCCCHHHHHHHHHHHHHHhcCCCcccCceEecCHHHHHHhCCCeecHh
Confidence 5688999999999999999999999999999999999999994 9999988763
No 3
>smart00151 SWIB SWI complex, BAF60b domains.
Probab=99.72 E-value=3.9e-18 Score=114.83 Aligned_cols=52 Identities=42% Similarity=0.648 Sum_probs=48.2
Q ss_pred CCCCCCCCHHHHhhhCCCCcCHHHHHHHHHHHhhhcCCCCccc------------ccCcceeEE
Q 033520 63 IMKPRRVSPEMEAFVGAPEIPRTQALKLIWAHIKQHNLQWKTI------------VFGKWECWI 114 (117)
Q Consensus 63 ~~kp~~LSpeLa~~lG~~e~sR~evvK~lW~YIK~nnLQDP~N------------vFG~d~v~~ 114 (117)
++++|.+|++|++|+|.++++|+||++.+|+|||+||||||+| +||+++|.|
T Consensus 1 ~~~~~~ls~~L~~~lg~~~~tr~ev~~~lw~YIk~n~L~d~~~k~~i~~D~~L~~l~~~~~v~~ 64 (77)
T smart00151 1 ITKKVTLSPELAKVLGAPEMTRTEIIKRLWEYIKEHNLQDPQNKREILCDSKLEQIFGKDRMDM 64 (77)
T ss_pred CCCcccCCHHHHHHhCCCcCcHHHHHHHHHHHHHHhcccCCccCCEEecCHHHHHHHCcCeecH
Confidence 4789999999999999999999999999999999999999984 899887764
No 4
>PRK14724 DNA topoisomerase III; Provisional
Probab=99.55 E-value=2.7e-15 Score=138.39 Aligned_cols=54 Identities=30% Similarity=0.422 Sum_probs=50.6
Q ss_pred CCCCCCCCCHHHHhhhCCCCcCHHHHHHHHHHHhhhcCCCCccc------------ccCcceeEEe
Q 033520 62 GIMKPRRVSPEMEAFVGAPEIPRTQALKLIWAHIKQHNLQWKTI------------VFGKWECWIW 115 (117)
Q Consensus 62 g~~kp~~LSpeLa~~lG~~e~sR~evvK~lW~YIK~nnLQDP~N------------vFG~d~v~~~ 115 (117)
.+..+++|||+|++|||.++++|++||++||+|||+||||||+| |||+|+|.|.
T Consensus 911 ~~~~~~~ls~~La~~lg~~~~~r~~v~~~lW~YIK~~~Lqdp~~k~~i~cD~~L~~vfg~~~~~~~ 976 (987)
T PRK14724 911 PPAAGLKPSAALAAVIGAEPVARPEVIKKLWDYIKANNLQDPADKRAINADAKLRPVFGKDQVTMF 976 (987)
T ss_pred ccccccCCCHHHHHHhCCCcCCHHHHHHHHHHHHHHccCCCcccCCeeccchHHHHHhCCCcccHH
Confidence 47779999999999999999999999999999999999999995 9999999873
No 5
>COG5531 SWIB-domain-containing proteins implicated in chromatin remodeling [Chromatin structure and dynamics]
Probab=99.55 E-value=2.8e-15 Score=120.98 Aligned_cols=55 Identities=29% Similarity=0.365 Sum_probs=49.6
Q ss_pred CCCCCCCCCCCHHHHhhhCCCCcCHHHHHHHHHHHhhhcCCCCccc------------ccCcceeEE
Q 033520 60 PRGIMKPRRVSPEMEAFVGAPEIPRTQALKLIWAHIKQHNLQWKTI------------VFGKWECWI 114 (117)
Q Consensus 60 ~~g~~kp~~LSpeLa~~lG~~e~sR~evvK~lW~YIK~nnLQDP~N------------vFG~d~v~~ 114 (117)
++....+|.+|+.||.+||.++++|+|||++||+|||+||||||+| |||.|.+.|
T Consensus 118 ~~~~~~~~~lS~~La~ilG~~~~tr~~~v~~lw~YIk~h~lq~~~nkr~I~~D~~L~~v~g~~p~~m 184 (237)
T COG5531 118 NSPSGEKVKLSPKLAAILGLEPGTRPEAVKKLWKYIKKHNLQDPNNKRLILCDSKLKKVLGSDPIDM 184 (237)
T ss_pred ccCCCCceecCHHHHHHhCCCCCCccHHHHHHHHHHHHhcCCCccccceecccHHHHHHhCCCchhh
Confidence 3457899999999999999999999999999999999999999995 898666554
No 6
>KOG2570 consensus SWI/SNF transcription activation complex subunit [Chromatin structure and dynamics; Transcription]
Probab=99.09 E-value=5.7e-11 Score=102.44 Aligned_cols=50 Identities=22% Similarity=0.356 Sum_probs=46.4
Q ss_pred CCCCCCHHHHhhhCCCCcCHHHHHHHHHHHhhhcCCCCcc------------cccCcceeEE
Q 033520 65 KPRRVSPEMEAFVGAPEIPRTQALKLIWAHIKQHNLQWKT------------IVFGKWECWI 114 (117)
Q Consensus 65 kp~~LSpeLa~~lG~~e~sR~evvK~lW~YIK~nnLQDP~------------NvFG~d~v~~ 114 (117)
..|++||.||.+||.++.+|++||..||.|||.|+||||+ .|||+|+..|
T Consensus 207 ~~fklsp~La~lLGi~t~Trp~iI~alWqYIk~n~Lqd~~e~~~incD~~l~qif~~~rl~F 268 (420)
T KOG2570|consen 207 EEFKLSPRLANLLGIHTGTRPDIVTALWQYIKTNKLQDPEDSDFINCDKALEQIFGVDRLKF 268 (420)
T ss_pred cccccCHHHHHHhhhccCcchHHHHHHHHHHHHhccCCcccchhhcchHHHHHhhccccccc
Confidence 3488999999999999999999999999999999999998 3999998876
No 7
>PRK06319 DNA topoisomerase I/SWI domain fusion protein; Validated
Probab=98.82 E-value=2.7e-09 Score=97.63 Aligned_cols=53 Identities=30% Similarity=0.351 Sum_probs=48.3
Q ss_pred CCCCCCCCCHHHHhhhCCCCcCHHHHHHHHHHHhhhcCCCCccc------------ccCcceeEE
Q 033520 62 GIMKPRRVSPEMEAFVGAPEIPRTQALKLIWAHIKQHNLQWKTI------------VFGKWECWI 114 (117)
Q Consensus 62 g~~kp~~LSpeLa~~lG~~e~sR~evvK~lW~YIK~nnLQDP~N------------vFG~d~v~~ 114 (117)
..+.+|.+|++|+.++|..+++|.++++.+|+|||+|+||||+| |||++++.|
T Consensus 783 ~~~~~~~~S~~La~~~g~~~~sr~~~~~~lw~yIk~~~lqdp~~Kr~i~~d~kl~kvf~~~~~~~ 847 (860)
T PRK06319 783 RAGPLYTPSPALAAMIGAEPVGRGEATKKVWDYIKEHGLQSPENKKLIIPDSKLQGVIGPDPIDM 847 (860)
T ss_pred ccccccccccccccccCcCccCchHHHHHHHHHHHHhcccCccccccCCCchhhhhhhCcCccch
Confidence 35667889999999999999999999999999999999999984 899888776
No 8
>PLN02945 nicotinamide-nucleotide adenylyltransferase/nicotinate-nucleotide adenylyltransferase
Probab=71.46 E-value=2.9 Score=33.03 Aligned_cols=32 Identities=16% Similarity=0.094 Sum_probs=24.1
Q ss_pred CHHHHhhhCCCCcCHHHHHHHHHHHhhhcCCC
Q 033520 70 SPEMEAFVGAPEIPRTQALKLIWAHIKQHNLQ 101 (117)
Q Consensus 70 SpeLa~~lG~~e~sR~evvK~lW~YIK~nnLQ 101 (117)
|.++++.+.....-+..+-..+++||++|+|-
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 56667766655556677778899999999983
No 9
>PRK00071 nadD nicotinic acid mononucleotide adenylyltransferase; Provisional
Probab=71.25 E-value=2.7 Score=31.97 Aligned_cols=32 Identities=16% Similarity=0.113 Sum_probs=21.8
Q ss_pred CHHHHhhhCCCCcCHHHHHHHHHHHhhhcCCC
Q 033520 70 SPEMEAFVGAPEIPRTQALKLIWAHIKQHNLQ 101 (117)
Q Consensus 70 SpeLa~~lG~~e~sR~evvK~lW~YIK~nnLQ 101 (117)
|.++.+.+.....-+.-+-..+++||++|+|-
T Consensus 170 ST~IR~~l~~g~~~~~lvp~~V~~YI~~~~LY 201 (203)
T PRK00071 170 STAIRERIKEGRPIRYLLPEAVLDYIEKHGLY 201 (203)
T ss_pred HHHHHHHHHcCCChhHhCCHHHHHHHHHhCcc
Confidence 34555555444444566677899999999984
No 10
>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=70.68 E-value=3 Score=31.57 Aligned_cols=31 Identities=23% Similarity=0.143 Sum_probs=22.8
Q ss_pred CHHHHhhhCCCCcCHHHHHHHHHHHhhhcCC
Q 033520 70 SPEMEAFVGAPEIPRTQALKLIWAHIKQHNL 100 (117)
Q Consensus 70 SpeLa~~lG~~e~sR~evvK~lW~YIK~nnL 100 (117)
|.+.++-+.....-+..+=..|++||++|+|
T Consensus 162 ST~IR~~l~~g~~~~~lvP~~V~~YI~~~~L 192 (193)
T TIGR00482 162 STEIRQRIRQGKSIEYLLPDPVIKYIKQHGL 192 (193)
T ss_pred HHHHHHHHHcCCCchhhCCHHHHHHHHHhCC
Confidence 4566666655445566777889999999998
No 11
>PRK06973 nicotinic acid mononucleotide adenylyltransferase; Provisional
Probab=68.71 E-value=3.3 Score=33.33 Aligned_cols=32 Identities=25% Similarity=0.406 Sum_probs=24.5
Q ss_pred CHHHHhhhCCC--------CcCHHHHHHHHHHHhhhcCCC
Q 033520 70 SPEMEAFVGAP--------EIPRTQALKLIWAHIKQHNLQ 101 (117)
Q Consensus 70 SpeLa~~lG~~--------e~sR~evvK~lW~YIK~nnLQ 101 (117)
|.++.+.++.. .--+.-|=..|++||++|+|-
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 56777777665 455666777899999999984
No 12
>TIGR01764 excise DNA binding domain, excisionase family. An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).
Probab=57.96 E-value=10 Score=21.38 Aligned_cols=27 Identities=15% Similarity=0.260 Sum_probs=21.6
Q ss_pred HHHHhhhCCCCcCHHHHHHHHHHHhhhcCCCCcc
Q 033520 71 PEMEAFVGAPEIPRTQALKLIWAHIKQHNLQWKT 104 (117)
Q Consensus 71 peLa~~lG~~e~sR~evvK~lW~YIK~nnLQDP~ 104 (117)
+|.|+++|...- .|+.+|++..+.-+.
T Consensus 5 ~e~a~~lgis~~-------ti~~~~~~g~i~~~~ 31 (49)
T TIGR01764 5 EEAAEYLGVSKD-------TVYRLIHEGELPAYR 31 (49)
T ss_pred HHHHHHHCCCHH-------HHHHHHHcCCCCeEE
Confidence 578899998766 799999998877543
No 13
>cd02165 NMNAT Nicotinamide/nicotinate mononucleotide adenylyltransferase. Nicotinamide/nicotinate mononucleotide (NMN/ NaMN)adenylyltransferase (NMNAT). NMNAT represents the primary bacterial and eukaryotic adenylyltransferases for nicotinamide-nucleotide and for the deamido form, nicotinate nucleotide. It is an indispensable enzyme in the biosynthesis of NAD(+) and NADP(+). Nicotinamide-nucleotide adenylyltransferase synthesizes NAD via the salvage pathway, while nicotinate-nucleotide adenylyltransferase synthesizes the immediate precursor of NAD via the de novo pathway. Human NMNAT displays unique dual substrate specificity toward both NMN and NaMN, and can participate in both de novo and salvage pathways of NAD synthesis.
Probab=54.58 E-value=9.1 Score=28.70 Aligned_cols=32 Identities=22% Similarity=0.131 Sum_probs=23.5
Q ss_pred CCHHHHhhhCCCCcCHHHHHHHHHHHhhhcCC
Q 033520 69 VSPEMEAFVGAPEIPRTQALKLIWAHIKQHNL 100 (117)
Q Consensus 69 LSpeLa~~lG~~e~sR~evvK~lW~YIK~nnL 100 (117)
=|.++++.+.....-+.-+-..+.+||++|+|
T Consensus 160 SST~IR~~~~~g~~~~~lvp~~V~~yI~~~~l 191 (192)
T cd02165 160 SSTEIRERLKNGKSIRYLLPPAVADYIKEHGL 191 (192)
T ss_pred CHHHHHHHHHcCCChhHhCCHHHHHHHHHccC
Confidence 35667777765444556677789999999998
No 14
>PRK08887 nicotinic acid mononucleotide adenylyltransferase; Provisional
Probab=54.54 E-value=9.7 Score=28.77 Aligned_cols=32 Identities=13% Similarity=0.053 Sum_probs=21.1
Q ss_pred CHHHHhhhCCCCcCHHHHHHHHHHHhhhcCCC
Q 033520 70 SPEMEAFVGAPEIPRTQALKLIWAHIKQHNLQ 101 (117)
Q Consensus 70 SpeLa~~lG~~e~sR~evvK~lW~YIK~nnLQ 101 (117)
|.++.+.+.....-+.-+-..+.+||++|+|-
T Consensus 139 ST~IR~~l~~g~~i~~lvp~~V~~yI~~~~LY 170 (174)
T PRK08887 139 STDIRNALQNGKDISHLTTPGVARLLKEHQLY 170 (174)
T ss_pred HHHHHHHHHcCCChhHhCCHHHHHHHHHcccc
Confidence 44555555443344455667789999999984
No 15
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=53.60 E-value=9.8 Score=26.21 Aligned_cols=22 Identities=23% Similarity=0.557 Sum_probs=17.9
Q ss_pred CCHHHHhhhCCCCcCHHHHHHHHHHHhhh
Q 033520 69 VSPEMEAFVGAPEIPRTQALKLIWAHIKQ 97 (117)
Q Consensus 69 LSpeLa~~lG~~e~sR~evvK~lW~YIK~ 97 (117)
--++|++-||..+. .||++|+.
T Consensus 21 SGe~La~~LgiSRt-------aVwK~Iq~ 42 (79)
T COG1654 21 SGEKLAEELGISRT-------AVWKHIQQ 42 (79)
T ss_pred cHHHHHHHHCccHH-------HHHHHHHH
Confidence 34789999998776 89999976
No 16
>PF08031 BBE: Berberine and berberine like ; InterPro: IPR012951 This domain is found in the berberine bridge and berberine bridge-like enzymes, which are involved in the biosynthesis of numerous isoquinoline alkaloids. They catalyse the transformation of the N-methyl group of (S)-reticuline into the C-8 berberine bridge carbon of (S)-scoulerine [].; GO: 0016491 oxidoreductase activity, 0050660 flavin adenine dinucleotide binding, 0055114 oxidation-reduction process; PDB: 2IPI_A 2Y3S_A 2Y3R_D 2Y08_B 2Y4G_A 3D2H_A 3FW9_A 3FW8_A 3FWA_A 3D2J_A ....
Probab=53.41 E-value=9.7 Score=23.22 Aligned_cols=28 Identities=29% Similarity=0.281 Sum_probs=20.0
Q ss_pred HHHHhhhCCCCcCHHHHHHHHHHHhhhcCCCCcccccC
Q 033520 71 PEMEAFVGAPEIPRTQALKLIWAHIKQHNLQWKTIVFG 108 (117)
Q Consensus 71 peLa~~lG~~e~sR~evvK~lW~YIK~nnLQDP~NvFG 108 (117)
.......| +...|...||+-| ||+|||.
T Consensus 14 ~~~~~yyg-~n~~rL~~iK~~y---------DP~n~F~ 41 (47)
T PF08031_consen 14 DWQEAYYG-ENYDRLRAIKRKY---------DPDNVFR 41 (47)
T ss_dssp HHHHHHHG-GGHHHHHHHHHHH----------TT-TS-
T ss_pred HHHHHHhc-hhHHHHHHHHHHh---------CccceeC
Confidence 44556667 6688999999998 8999995
No 17
>TIGR02057 PAPS_reductase phosphoadenosine phosphosulfate reductase, thioredoxin dependent. Requiring thioredoxin as an electron donor, phosphoadenosine phosphosulfate reductase catalyzes the reduction of 3'-phosphoadenylylsulfate (PAPS) to sulfite and phospho-adenosine-phosphate (PAP). Found in enterobacteria, cyanobacteria, and yeast, PAPS reductase is related to a group of plant (TIGR00424) and bacterial (TIGR02055) enzymes preferring 5'-adenylylsulfate (APS) over PAPS as a substrate for reduction to sulfite.
Probab=50.30 E-value=11 Score=29.78 Aligned_cols=13 Identities=15% Similarity=0.560 Sum_probs=11.2
Q ss_pred HHHHHhhhcCCCC
Q 033520 90 LIWAHIKQHNLQW 102 (117)
Q Consensus 90 ~lW~YIK~nnLQD 102 (117)
.||+||++|||--
T Consensus 172 dVw~Yi~~~~lP~ 184 (226)
T TIGR02057 172 QVYQYLDAHNVPY 184 (226)
T ss_pred HHHHHHHHcCCCC
Confidence 6899999999854
No 18
>cd09286 NMNAT_Eukarya Nicotinamide/nicotinate mononucleotide adenylyltransferase, Eukaryotic. Nicotinamide/nicotinate mononucleotide (NMN/ NaMN)adenylyltransferase (NMNAT). NMNAT represents the primary bacterial and eukaryotic adenylyltransferases for nicotinamide-nucleotide and for the deamido form, nicotinate nucleotide. It is an indispensable enzyme in the biosynthesis of NAD(+) and NADP(+). Nicotinamide-nucleotide adenylyltransferase synthesizes NAD via the salvage pathway, while nicotinate-nucleotide adenylyltransferase synthesizes the immediate precursor of NAD via the de novo pathway. Human NMNAT displays unique dual substrate specificity toward both NMN and NaMN, and can participate in both de novo and salvage pathways of NAD synthesis. This subfamily consists strictly of eukaryotic members and includes secondary structural elements not found in all NMNATs.
Probab=49.98 E-value=11 Score=29.61 Aligned_cols=32 Identities=16% Similarity=0.067 Sum_probs=23.7
Q ss_pred CCHHHHhhhCCCCcCHHHHHHHHHHHhhhcCC
Q 033520 69 VSPEMEAFVGAPEIPRTQALKLIWAHIKQHNL 100 (117)
Q Consensus 69 LSpeLa~~lG~~e~sR~evvK~lW~YIK~nnL 100 (117)
=|.++++-+...+.-+..+-..|.+||++|+|
T Consensus 193 SST~IR~~l~~g~~~~~llp~~V~~YI~~~~L 224 (225)
T cd09286 193 SSTKVRRALRRGMSVKYLLPDPVIEYIEQHQL 224 (225)
T ss_pred ChHHHHHHHHcCCCchhcCCHHHHHHHHHcCC
Confidence 35666666665555566677889999999998
No 19
>PF08513 LisH: LisH; InterPro: IPR013720 The LisH motif is found in a large number of eukaryotic proteins, from metazoa, fungi and plants that have a wide range of functions. The recently solved structure of the LisH domain in the N-terminal region of LIS1 depicted it as a novel dimerization motif, and that other structural elements are likely to play an important role in dimerisation [, , ]. The LisH (lis homology) domain mediates protein dimerisation and tetramerisation. The LisH domain is found in Sif2, a component of the Set3 complex which is responsible for repressing meiotic genes. It has been shown that the LisH domain helps mediate interaction with components of the Set3 complex []. ; PDB: 2XTE_L 2XTC_B 2XTD_A 1UUJ_B.
Probab=49.01 E-value=3.9 Score=22.61 Aligned_cols=25 Identities=16% Similarity=0.206 Sum_probs=18.9
Q ss_pred HHHHHHHHHhhhcCCCCcccccCcc
Q 033520 86 QALKLIWAHIKQHNLQWKTIVFGKW 110 (117)
Q Consensus 86 evvK~lW~YIK~nnLQDP~NvFG~d 110 (117)
++-..||+|..++|+++-...|.+|
T Consensus 2 ~Ln~lI~~YL~~~Gy~~tA~~f~~E 26 (27)
T PF08513_consen 2 ELNQLIYDYLVENGYKETAKAFAKE 26 (27)
T ss_dssp HHHHHHHHHHHHCT-HHHHHHHHHH
T ss_pred HHHHHHHHHHHHCCcHHHHHHHHhc
Confidence 4667899999999998877666543
No 20
>TIGR02055 APS_reductase thioredoxin-dependent adenylylsulfate APS reductase. This model describes recently identified adenosine 5'-phosphosulfate (APS) reductase activity found in sulfate-assimilatory prokaryotes, thus separating it from the traditionally described phosphoadenosine 5'-phosphosulfate (PAPS) reductases found in bacteria and fungi. Homologous to PAPS reductase in enterobacteria, cyanobacteria, and yeast, APS reductase here clusters with, and demonstrates greater homology to plant APS reductase. Additionally, the presence of two conserved C-terminal motifs (CCXXRKXXPL & SXGCXXCT) distinguishes APS substrate specificity and serves as a FeS cluster.
Probab=47.88 E-value=12 Score=28.43 Aligned_cols=12 Identities=25% Similarity=0.598 Sum_probs=10.9
Q ss_pred HHHHHhhhcCCC
Q 033520 90 LIWAHIKQHNLQ 101 (117)
Q Consensus 90 ~lW~YIK~nnLQ 101 (117)
.||+||++|||.
T Consensus 136 dVw~Yi~~~~lp 147 (191)
T TIGR02055 136 DVWEYIADNELP 147 (191)
T ss_pred HHHHHHHHcCCC
Confidence 799999999994
No 21
>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=45.57 E-value=37 Score=21.85 Aligned_cols=43 Identities=14% Similarity=0.216 Sum_probs=25.1
Q ss_pred CCCCCCCCCCCCCCHHHHhhhC-CCCcCHHHHHHHHHHHhhhcC
Q 033520 57 KREPRGIMKPRRVSPEMEAFVG-APEIPRTQALKLIWAHIKQHN 99 (117)
Q Consensus 57 ~k~~~g~~kp~~LSpeLa~~lG-~~e~sR~evvK~lW~YIK~nn 99 (117)
.+|.|.....+-=..-..+.|| ..+.+=.++++..|++.+.|-
T Consensus 16 ~rR~GD~~~~~Ad~~kA~~~LgW~p~~~L~~~i~~~w~W~~~np 59 (62)
T PF13950_consen 16 PRRPGDPAHLVADISKAREELGWKPKYSLEDMIRDAWNWQKKNP 59 (62)
T ss_dssp ---TT--SEE-B--HHHHHHC----SSSHHHHHHHHHHHHHHST
T ss_pred CCCCCchhhhhCCHHHHHHHhCCCcCCCHHHHHHHHHHHHHHCc
Confidence 3555555555544445557889 677799999999999999874
No 22
>PRK12563 sulfate adenylyltransferase subunit 2; Provisional
Probab=43.44 E-value=15 Score=31.07 Aligned_cols=15 Identities=13% Similarity=0.390 Sum_probs=12.7
Q ss_pred HHHHHhhhcCCCCcc
Q 033520 90 LIWAHIKQHNLQWKT 104 (117)
Q Consensus 90 ~lW~YIK~nnLQDP~ 104 (117)
.||+||+.|||--..
T Consensus 203 DVW~YI~~~~IP~~p 217 (312)
T PRK12563 203 DVWQYIAREKIPLVP 217 (312)
T ss_pred HHHHHHHHcCCCCCc
Confidence 799999999986544
No 23
>PLN02309 5'-adenylylsulfate reductase
Probab=42.88 E-value=15 Score=32.45 Aligned_cols=13 Identities=8% Similarity=0.588 Sum_probs=11.0
Q ss_pred HHHHHHhhhcCCC
Q 033520 89 KLIWAHIKQHNLQ 101 (117)
Q Consensus 89 K~lW~YIK~nnLQ 101 (117)
..||+||++|||-
T Consensus 261 ~dVw~Yi~~~~lP 273 (457)
T PLN02309 261 NEVWNFLRTMDVP 273 (457)
T ss_pred HHHHHHHHHcCCC
Confidence 4789999999983
No 24
>PF06039 Mqo: Malate:quinone oxidoreductase (Mqo); InterPro: IPR006231 The membrane-associated enzyme, malate:quinone-oxidoreductase, is an alternative to the better-known NAD-dependent malate dehydrogenase as part of the TCA cycle. The reduction of a quinone rather than NAD+ makes the reaction essentially irreversible in the direction of malate oxidation to oxaloacetate. Both forms of malate dehydrogenase are active in Escherichia coli; disruption of this form causes less phenotypic change. In some bacteria, this form is the only or the more important malate dehydrogenase []. ; GO: 0008924 malate dehydrogenase (quinone) activity, 0006099 tricarboxylic acid cycle, 0055114 oxidation-reduction process
Probab=42.27 E-value=12 Score=33.83 Aligned_cols=23 Identities=13% Similarity=0.273 Sum_probs=18.1
Q ss_pred CHHHHHHHHHHHhhhcC-CCCccc
Q 033520 83 PRTQALKLIWAHIKQHN-LQWKTI 105 (117)
Q Consensus 83 sR~evvK~lW~YIK~nn-LQDP~N 105 (117)
...|+.+++|+|.-+++ |+||++
T Consensus 82 eqFevsrqfWs~lv~~g~l~~p~~ 105 (488)
T PF06039_consen 82 EQFEVSRQFWSYLVENGILQNPES 105 (488)
T ss_pred HHHHHHHHHHHHHHHCCCCCChHH
Confidence 35688899999987665 688884
No 25
>TIGR00434 cysH phosophoadenylyl-sulfate reductase (thioredoxin). This enzyme, involved in the assimilation of inorganic sulfate, is designated cysH in Bacteria and MET16 in Saccharomyces cerevisiae. Synonyms include phosphoadenosine phosphosulfate reductase, PAPS reductase, and PAPS reductase, thioredoxin-dependent. In a reaction requiring reduced thioredoxin and NADPH, it converts 3(prime)-phosphoadenylylsulfate (PAPS) to sulfite and adenosine 3(prime),5(prime) diphosphate (PAP). A related family of plant enzymes, scoring below the trusted cutoff, differs in having a thioredoxin-like C-terminal domain, not requiring thioredoxin, and in having a preference for 5(prime)-adenylylsulfate (APS) over PAPS.
Probab=42.15 E-value=17 Score=27.56 Aligned_cols=12 Identities=33% Similarity=0.520 Sum_probs=11.0
Q ss_pred HHHHHhhhcCCC
Q 033520 90 LIWAHIKQHNLQ 101 (117)
Q Consensus 90 ~lW~YIK~nnLQ 101 (117)
.||+||++|||-
T Consensus 157 dVw~Yi~~~~lp 168 (212)
T TIGR00434 157 DVYQYIDAHNLP 168 (212)
T ss_pred HHHHHHHHcCCC
Confidence 679999999987
No 26
>PF01507 PAPS_reduct: Phosphoadenosine phosphosulfate reductase family; InterPro: IPR002500 This domain is found in phosphoadenosine phosphosulphate (PAPS) reductase enzymes or PAPS sulphotransferase. PAPS reductase is part of the adenine nucleotide alpha hydrolases superfamily also including N type ATP PPases and ATP sulphurylases []. The enzyme uses thioredoxin as an electron donor for the reduction of PAPS to phospho-adenosine-phosphate (PAP) [, ]. It is also found in NodP nodulation protein P from Rhizobium meliloti (Sinorhizobium meliloti) which has ATP sulphurylase activity (sulphate adenylate transferase) [].; GO: 0003824 catalytic activity, 0008152 metabolic process; PDB: 2GOY_C 3G5A_C 3G6K_D 3G59_A 3FWK_A 2WSI_A 2OQ2_B 1SUR_A 2O8V_A 1ZUN_A.
Probab=41.33 E-value=15 Score=25.80 Aligned_cols=13 Identities=31% Similarity=0.626 Sum_probs=9.9
Q ss_pred HHHHHHhhhcCCC
Q 033520 89 KLIWAHIKQHNLQ 101 (117)
Q Consensus 89 K~lW~YIK~nnLQ 101 (117)
..||+||+.++|.
T Consensus 142 ~dV~~yi~~~~l~ 154 (174)
T PF01507_consen 142 EDVWDYIKANGLP 154 (174)
T ss_dssp HHHHHHHHHHT--
T ss_pred HHHHHHHHHhcCC
Confidence 4789999999985
No 27
>smart00667 LisH Lissencephaly type-1-like homology motif. Alpha-helical motif present in Lis1, treacle, Nopp140, some katanin p60 subunits, muskelin, tonneau, LEUNIG and numerous WD40 repeat-containing proteins. It is suggested that LisH motifs contribute to the regulation of microtubule dynamics, either by mediating dimerisation, or else by binding cytoplasmic dynein heavy chain or microtubules directly.
Probab=41.26 E-value=22 Score=18.64 Aligned_cols=25 Identities=12% Similarity=0.177 Sum_probs=20.2
Q ss_pred CHHHHHHHHHHHhhhcCCCCccccc
Q 033520 83 PRTQALKLIWAHIKQHNLQWKTIVF 107 (117)
Q Consensus 83 sR~evvK~lW~YIK~nnLQDP~NvF 107 (117)
.+.++.+.|++|...+++.+-...|
T Consensus 2 ~~~~l~~lI~~yL~~~g~~~ta~~l 26 (34)
T smart00667 2 SRSELNRLILEYLLRNGYEETAETL 26 (34)
T ss_pred cHHHHHHHHHHHHHHcCHHHHHHHH
Confidence 4678899999999999987765444
No 28
>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=40.65 E-value=28 Score=19.24 Aligned_cols=24 Identities=17% Similarity=0.311 Sum_probs=19.4
Q ss_pred HHHHhhhCCCCcCHHHHHHHHHHHhhhcCCC
Q 033520 71 PEMEAFVGAPEIPRTQALKLIWAHIKQHNLQ 101 (117)
Q Consensus 71 peLa~~lG~~e~sR~evvK~lW~YIK~nnLQ 101 (117)
.|+|+.+|.++- .||.|+++..+.
T Consensus 4 ~e~a~~lgvs~~-------tl~~~~~~g~~~ 27 (49)
T cd04762 4 KEAAELLGVSPS-------TLRRWVKEGKLK 27 (49)
T ss_pred HHHHHHHCcCHH-------HHHHHHHcCCCC
Confidence 578888898766 799999988764
No 29
>PRK07152 nadD putative nicotinate-nucleotide adenylyltransferase; Validated
Probab=38.95 E-value=16 Score=30.08 Aligned_cols=21 Identities=14% Similarity=-0.013 Sum_probs=15.9
Q ss_pred HHHHHHHHhhhcCCCCccccc
Q 033520 87 ALKLIWAHIKQHNLQWKTIVF 107 (117)
Q Consensus 87 vvK~lW~YIK~nnLQDP~NvF 107 (117)
+=..+++||++|+|-.-+.+|
T Consensus 170 vP~~V~~YI~~~~LY~e~~l~ 190 (342)
T PRK07152 170 LDPKVNDYINENFLYLEDILK 190 (342)
T ss_pred CCHHHHHHHHHcCccccHHHH
Confidence 445699999999998655444
No 30
>PF08938 HBS1_N: HBS1 N-terminus; InterPro: IPR015033 This domain is found in various eukaryotic HBS1-like proteins. ; PDB: 1UFZ_A 3IZQ_1.
Probab=37.02 E-value=14 Score=24.77 Aligned_cols=26 Identities=19% Similarity=0.405 Sum_probs=19.5
Q ss_pred CCHHHHhhhCCCCcCHHHHHHHHHHH
Q 033520 69 VSPEMEAFVGAPEIPRTQALKLIWAH 94 (117)
Q Consensus 69 LSpeLa~~lG~~e~sR~evvK~lW~Y 94 (117)
+-+.+.++||....+..+|+.+||.|
T Consensus 31 ~l~~vr~~Lg~~~~~e~~i~eal~~~ 56 (79)
T PF08938_consen 31 CLPQVREVLGDYVPPEEQIKEALWHY 56 (79)
T ss_dssp HCCCHHHHCCCCC--CCHHHHHHHHT
T ss_pred HHHHHHHHHcccCCCHHHHHHHHHHH
Confidence 34568889997555999999999986
No 31
>PF12728 HTH_17: Helix-turn-helix domain
Probab=36.54 E-value=33 Score=20.23 Aligned_cols=26 Identities=15% Similarity=0.239 Sum_probs=20.5
Q ss_pred HHHHhhhCCCCcCHHHHHHHHHHHhhhcCCCCc
Q 033520 71 PEMEAFVGAPEIPRTQALKLIWAHIKQHNLQWK 103 (117)
Q Consensus 71 peLa~~lG~~e~sR~evvK~lW~YIK~nnLQDP 103 (117)
+|.|++||.+.- .++.+|+...+.-.
T Consensus 5 ~e~a~~l~is~~-------tv~~~~~~g~i~~~ 30 (51)
T PF12728_consen 5 KEAAELLGISRS-------TVYRWIRQGKIPPF 30 (51)
T ss_pred HHHHHHHCcCHH-------HHHHHHHcCCCCeE
Confidence 578999998655 68899998877654
No 32
>PF02926 THUMP: THUMP domain; InterPro: IPR004114 The THUMP domain is shared by 4-thiouridine, pseudouridine synthases and RNA methylases[] and is probably an RNA-binding domain that adopts an alpha/beta fold similar to that found in the C-terminal domain of translation initiation factor 3 and ribosomal protein S8. The THUMP domain probably functions by delivering a variety of RNA modification enzymes to their targets []. This domain is found in the thiamine biosynthesis proteins (ThiI) (see IPR003720 from INTERPRO).; PDB: 3TLJ_A 3TM5_B 3TM4_A 2DIR_A 3TMA_A 1VBK_B 3K0B_A 2C5S_A 3LDU_A 3V8V_B ....
Probab=36.37 E-value=67 Score=22.05 Aligned_cols=36 Identities=22% Similarity=0.300 Sum_probs=27.0
Q ss_pred CcCHHHHHHHHHHHhhh-----cCCCCccccc----CcceeEEee
Q 033520 81 EIPRTQALKLIWAHIKQ-----HNLQWKTIVF----GKWECWIWI 116 (117)
Q Consensus 81 e~sR~evvK~lW~YIK~-----nnLQDP~NvF----G~d~v~~~~ 116 (117)
..++.++.+.|.+||.+ =+|.||+-++ -++.+++-|
T Consensus 98 ~~~s~ei~~~vg~~i~~~~~~~Vdl~~Pd~~i~Vev~~~~~~i~i 142 (144)
T PF02926_consen 98 PFTSMEIEREVGDAIKEKGGPKVDLKNPDVVIHVEVRKDKCYISI 142 (144)
T ss_dssp SSCHHHHHHHHHHHHHHHHHTEE-SSSSSEEEEEEEETTEEEEEE
T ss_pred ccCHHHHHHHHHHHHHHHhCCCccCcCcCEEEEEEEECCEEEEEE
Confidence 88999999999999999 7899999422 244555544
No 33
>PF13333 rve_2: Integrase core domain
Probab=36.28 E-value=39 Score=20.59 Aligned_cols=22 Identities=18% Similarity=-0.049 Sum_probs=18.4
Q ss_pred CCCCcCHHHHHHHHHHHhhhcC
Q 033520 78 GAPEIPRTQALKLIWAHIKQHN 99 (117)
Q Consensus 78 G~~e~sR~evvK~lW~YIK~nn 99 (117)
|..-.++.++...|++||.-.|
T Consensus 14 ~~~~~t~eel~~~I~~YI~~yN 35 (52)
T PF13333_consen 14 RQKFKTREELKQAIDEYIDYYN 35 (52)
T ss_pred CcccchHHHHHHHHHHHHHHhc
Confidence 4566799999999999998754
No 34
>TIGR00424 APS_reduc 5'-adenylylsulfate reductase, thioredoxin-independent. This enzyme, involved in the assimilation of inorganic sulfate, is closely related to the thioredoxin-dependent PAPS reductase of Bacteria (CysH) and Saccharomyces cerevisiae. However, it has its own C-terminal thioredoxin-like domain and is not thioredoxin-dependent. Also, it has a substrate preference for 5'-adenylylsulfate (APS) over 3'-phosphoadenylylsulfate (PAPS) so the pathway does not require an APS kinase (CysC) to convert APS to PAPS. Arabidopsis thaliana appears to have three isozymes, all able to complement E. coli CysH mutants (even in backgrounds lacking thioredoxin or APS kinase) but likely localized to different compartments in Arabidopsis.
Probab=36.03 E-value=22 Score=31.48 Aligned_cols=12 Identities=8% Similarity=0.581 Sum_probs=10.4
Q ss_pred HHHHHhhhcCCC
Q 033520 90 LIWAHIKQHNLQ 101 (117)
Q Consensus 90 ~lW~YIK~nnLQ 101 (117)
.||+||++|||-
T Consensus 267 dVw~Yi~~~~LP 278 (463)
T TIGR00424 267 DVWNFLRTMDVP 278 (463)
T ss_pred HHHHHHHHcCCC
Confidence 599999999983
No 35
>PRK05253 sulfate adenylyltransferase subunit 2; Provisional
Probab=34.61 E-value=32 Score=28.58 Aligned_cols=18 Identities=28% Similarity=0.567 Sum_probs=14.9
Q ss_pred HHHHHhhhcCCCCccccc
Q 033520 90 LIWAHIKQHNLQWKTIVF 107 (117)
Q Consensus 90 ~lW~YIK~nnLQDP~NvF 107 (117)
.||+||+.|||.=+..-|
T Consensus 193 DIw~Yi~~~~IP~~pLY~ 210 (301)
T PRK05253 193 DIWQYIERENIPIVPLYF 210 (301)
T ss_pred HHHHHHHHcCCCCCcccc
Confidence 799999999998766544
No 36
>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily. Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=33.66 E-value=42 Score=19.11 Aligned_cols=26 Identities=12% Similarity=0.061 Sum_probs=20.6
Q ss_pred HHHHhhhCCCCcCHHHHHHHHHHHhhhcCCCCcc
Q 033520 71 PEMEAFVGAPEIPRTQALKLIWAHIKQHNLQWKT 104 (117)
Q Consensus 71 peLa~~lG~~e~sR~evvK~lW~YIK~nnLQDP~ 104 (117)
.|+|+.+|..+- .||.|+++..|. |.
T Consensus 4 ~e~a~~~gv~~~-------tlr~~~~~g~l~-~~ 29 (49)
T cd04761 4 GELAKLTGVSPS-------TLRYYERIGLLS-PA 29 (49)
T ss_pred HHHHHHHCcCHH-------HHHHHHHCCCCC-CC
Confidence 478888998876 799999888776 54
No 37
>PF07898 DUF1676: Protein of unknown function (DUF1676); InterPro: IPR012464 This family contains sequences derived from proteins of unknown function expressed by Drosophila melanogaster and Anopheles gambiae.
Probab=33.59 E-value=24 Score=23.91 Aligned_cols=18 Identities=17% Similarity=0.272 Sum_probs=15.5
Q ss_pred HHHHHHHHHHHhhhcCCC
Q 033520 84 RTQALKLIWAHIKQHNLQ 101 (117)
Q Consensus 84 R~evvK~lW~YIK~nnLQ 101 (117)
..-+..++|.|+..|.||
T Consensus 52 ~~~l~~k~~~fl~th~L~ 69 (106)
T PF07898_consen 52 DNLLLDKVERFLQTHSLR 69 (106)
T ss_pred HHHHHHHHHHHHHhceEE
Confidence 456889999999999987
No 38
>cd01713 PAPS_reductase This domain is found in phosphoadenosine phosphosulphate (PAPS) reductase enzymes or PAPS sulphotransferase. PAPS reductase is part of the adenine nucleotide alpha hydrolases superfamily also including N type ATP PPases and ATP sulphurylases. A highly modified version of the P loop, the fingerprint peptide of mononucleotide-binding proteins, is present in the active site of the protein, which appears to be a positively charged cleft containing a number of conserved arginine and lysine residues. Although PAPS reductase has no ATPase activity, it shows a striking similarity to the structure of the ATP pyrophosphatase (ATP PPase) domain of GMP synthetase, indicating that both enzyme families have evolved from a common ancestral nucleotide-binding fold. The enzyme uses thioredoxin as an electron donor for the reduction of PAPS to phospho-adenosine-phosphate (PAP) . It is also found in NodP nodulation protein P from Rhizobium meliloti which has ATP sulphurylase acti
Probab=33.28 E-value=30 Score=23.71 Aligned_cols=13 Identities=31% Similarity=0.739 Sum_probs=10.8
Q ss_pred HHHHHHhhhcCCC
Q 033520 89 KLIWAHIKQHNLQ 101 (117)
Q Consensus 89 K~lW~YIK~nnLQ 101 (117)
..||+||++++|.
T Consensus 148 ~di~~~~~~~~l~ 160 (173)
T cd01713 148 EDVWAYLARHGLP 160 (173)
T ss_pred HHHHHHHHHcCCC
Confidence 3679999999974
No 39
>TIGR02039 CysD sulfate adenylyltransferase, small subunit. In Escherichia coli, ATP sulfurylase is a heterodimer composed of two subunits encoded by cysD and cysN, with APS kinase encoded by cysC. These genes are located in a unidirectionally transcribed gene cluster, and have been shown to be required for the synthesis of sulfur-containing amino acids. Homologous to this E.coli activation pathway are nodPQH gene products found among members of the Rhizobiaceae family. These gene products have been shown to exhibit ATP sulfurase and APS kinase activity, yet are involved in Nod factor sulfation, and sulfation of other macromolecules.
Probab=33.11 E-value=27 Score=29.13 Aligned_cols=15 Identities=27% Similarity=0.406 Sum_probs=13.0
Q ss_pred HHHHHhhhcCCCCcc
Q 033520 90 LIWAHIKQHNLQWKT 104 (117)
Q Consensus 90 ~lW~YIK~nnLQDP~ 104 (117)
.||.||+.|||-=+.
T Consensus 185 DVW~YI~~~~IP~~p 199 (294)
T TIGR02039 185 DIWRYIAAENIPIVP 199 (294)
T ss_pred HHHHHHHHcCCCCCc
Confidence 799999999997655
No 40
>PRK02090 phosphoadenosine phosphosulfate reductase; Provisional
Probab=32.24 E-value=30 Score=27.14 Aligned_cols=13 Identities=38% Similarity=0.882 Sum_probs=11.3
Q ss_pred HHHHHHhhhcCCC
Q 033520 89 KLIWAHIKQHNLQ 101 (117)
Q Consensus 89 K~lW~YIK~nnLQ 101 (117)
+.||+||+.|||.
T Consensus 181 ~dV~~Yi~~~~lp 193 (241)
T PRK02090 181 EDVWAYLKEHDLP 193 (241)
T ss_pred HHHHHHHHHcCCC
Confidence 3689999999996
No 41
>PF14838 INTS5_C: Integrator complex subunit 5 C-terminus
Probab=32.09 E-value=38 Score=31.90 Aligned_cols=35 Identities=20% Similarity=0.339 Sum_probs=22.3
Q ss_pred CCCCCHHHHhhhCC-CCcCHHH---HHHH-HHHHhhhcCC
Q 033520 66 PRRVSPEMEAFVGA-PEIPRTQ---ALKL-IWAHIKQHNL 100 (117)
Q Consensus 66 p~~LSpeLa~~lG~-~e~sR~e---vvK~-lW~YIK~nnL 100 (117)
.--|.|+|..+... +..+=.| +.+. ||+|||+|.=
T Consensus 615 gqlLPppL~~~~el~~~ltp~Ei~~lL~~cIW~y~kdh~P 654 (696)
T PF14838_consen 615 GQLLPPPLSYIHELFPYLTPHEIYLLLLSCIWNYMKDHVP 654 (696)
T ss_pred cCcCCchHHHHHHHHHhcCHHHHHHHHHHHHHHHHhhCCC
Confidence 33566666666552 4444444 4566 9999999973
No 42
>TIGR01510 coaD_prev_kdtB pantetheine-phosphate adenylyltransferase, bacterial. This model describes pantetheine-phosphate adenylyltransferase, the penultimate enzyme of coenzyme A (CoA) biosynthesis in bacteria. It does not show any strong homology to eukaryotic enzymes of coenzyme A biosynthesis. This protein was previously designated KdtB and postulated (because of cytidyltransferase homology and proximity to kdtA) to be an enzyme of LPS biosynthesis, a cytidyltransferase for 3-deoxy-D-manno-2-octulosonic acid. However, no activity toward that compound was found with either CTP or ATP. The phylogenetic distribution of this enzyme is more consistent with coenzyme A biosynthesis than with LPS biosynthesis.
Probab=30.60 E-value=34 Score=25.11 Aligned_cols=29 Identities=7% Similarity=-0.062 Sum_probs=22.7
Q ss_pred CHHHHhhhCCCCcCHHHHHHHHHHHhhhc
Q 033520 70 SPEMEAFVGAPEIPRTQALKLIWAHIKQH 98 (117)
Q Consensus 70 SpeLa~~lG~~e~sR~evvK~lW~YIK~n 98 (117)
|.++.+.+.....-+.-+=..+++||++|
T Consensus 126 ST~IR~~i~~g~~~~~lvP~~V~~YI~~~ 154 (155)
T TIGR01510 126 SSLVKEIASFGGDVSNLVPPAVARRLKAK 154 (155)
T ss_pred HHHHHHHHHcCCChhHHCCHHHHHHHHHh
Confidence 56677777666666778888999999986
No 43
>smart00581 PSP proline-rich domain in spliceosome associated proteins.
Probab=30.07 E-value=42 Score=21.96 Aligned_cols=19 Identities=37% Similarity=0.583 Sum_probs=15.7
Q ss_pred CCCCCCHHHHhhhCCCCcC
Q 033520 65 KPRRVSPEMEAFVGAPEIP 83 (117)
Q Consensus 65 kp~~LSpeLa~~lG~~e~s 83 (117)
+|=.||++|.+.||..+..
T Consensus 5 kPG~lS~~LR~ALG~~~~~ 23 (54)
T smart00581 5 KPGRISDELREALGLPPGQ 23 (54)
T ss_pred cCCcCCHHHHHHcCCCCCC
Confidence 5568999999999987653
No 44
>COG0175 CysH 3'-phosphoadenosine 5'-phosphosulfate sulfotransferase (PAPS reductase)/FAD synthetase and related enzymes [Amino acid transport and metabolism / Coenzyme metabolism]
Probab=28.90 E-value=31 Score=27.74 Aligned_cols=15 Identities=27% Similarity=0.565 Sum_probs=12.2
Q ss_pred HHHHHhhhcCCCCcc
Q 033520 90 LIWAHIKQHNLQWKT 104 (117)
Q Consensus 90 ~lW~YIK~nnLQDP~ 104 (117)
.||+||..|||--..
T Consensus 184 dVw~Yi~~~~lp~np 198 (261)
T COG0175 184 DVWLYILANNLPYNP 198 (261)
T ss_pred HHHHHHHHhCCCCCc
Confidence 799999999985443
No 45
>PHA01748 hypothetical protein
Probab=28.33 E-value=41 Score=21.70 Aligned_cols=49 Identities=10% Similarity=0.141 Sum_probs=32.9
Q ss_pred CCCCHHHHhhhC----CCCcCHHHHHHHH-HHHhhhcCCCCcccccCcceeEEe
Q 033520 67 RRVSPEMEAFVG----APEIPRTQALKLI-WAHIKQHNLQWKTIVFGKWECWIW 115 (117)
Q Consensus 67 ~~LSpeLa~~lG----~~e~sR~evvK~l-W~YIK~nnLQDP~NvFG~d~v~~~ 115 (117)
+.|+++|.+-+. ...++|++++... =.|+++.-...--.+|...+|..|
T Consensus 7 vrLp~el~~eld~~a~~~g~~RSE~Ir~Ai~~~~~~~~~~~~~~~~~~~~~~~~ 60 (60)
T PHA01748 7 FKIEEDLLELLDRYAIKHGLNRSEAIRKAIEKMVKDELKKETVPVAKVEKISLW 60 (60)
T ss_pred EECCHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhcccchhhhhheecC
Confidence 456666555543 3457899998765 667776665655578877777766
No 46
>smart00224 GGL G protein gamma subunit-like motifs.
Probab=28.19 E-value=1.3e+02 Score=19.47 Aligned_cols=46 Identities=17% Similarity=0.123 Sum_probs=36.7
Q ss_pred HHHHhhhCCCCcCHHHHHHHHHHHhhhcCCCCcc--------cccCcceeEEee
Q 033520 71 PEMEAFVGAPEIPRTQALKLIWAHIKQHNLQWKT--------IVFGKWECWIWI 116 (117)
Q Consensus 71 peLa~~lG~~e~sR~evvK~lW~YIK~nnLQDP~--------NvFG~d~v~~~~ 116 (117)
..|..-++.+.+.=+++...|=+|+.+|.=.||- |=|..|+...|+
T Consensus 9 e~Lr~el~~~RikvS~a~~~li~y~e~~~~~DP~l~g~~~~~NP~~~dk~~c~~ 62 (63)
T smart00224 9 EQLRKELSRERIKVSKAAEELLAYCEQHAEEDPLLTGPPPSKNPFIEDKTSCWI 62 (63)
T ss_pred HHHHHHHCCceehHHHHHHHHHHHHHcCCCCCCCcCCCCCCCCCCCCCCCCcCc
Confidence 4566667888888899999999999998877875 677777777775
No 47
>PF03656 Pam16: Pam16; InterPro: IPR005341 The Pam16 protein is the fifth essential subunit of the pre-sequence translocase-associated protein import motor (PAM) []. In Saccharomyces cerevisiae (Baker's yeast), Pam16 is required for preprotein translocation into the matrix, but not for protein insertion into the inner membrane [].; PDB: 2GUZ_J.
Probab=27.70 E-value=88 Score=23.29 Aligned_cols=30 Identities=17% Similarity=0.169 Sum_probs=22.4
Q ss_pred HHHHhhhCCCC-cCHHHHHHHHHHHhhhcCC
Q 033520 71 PEMEAFVGAPE-IPRTQALKLIWAHIKQHNL 100 (117)
Q Consensus 71 peLa~~lG~~e-~sR~evvK~lW~YIK~nnL 100 (117)
+|-..+||.++ .++.+|.++.+.+.+.|+-
T Consensus 58 ~EA~~ILnv~~~~~~eeI~k~y~~Lf~~Nd~ 88 (127)
T PF03656_consen 58 DEARQILNVKEELSREEIQKRYKHLFKANDP 88 (127)
T ss_dssp HHHHHHHT--G--SHHHHHHHHHHHHHHT-C
T ss_pred HHHHHHcCCCCccCHHHHHHHHHHHHhccCC
Confidence 35568999876 9999999999999999863
No 48
>PF12368 DUF3650: Protein of unknown function (DUF3650) ; InterPro: IPR022111 This domain family is found in bacteria, and is approximately 30 amino acids in length. The family is found in association with PF00581 from PFAM. There is a single completely conserved residue N that may be functionally important.
Probab=27.44 E-value=30 Score=19.99 Aligned_cols=11 Identities=27% Similarity=0.386 Sum_probs=8.7
Q ss_pred HHhhhcCCCCc
Q 033520 93 AHIKQHNLQWK 103 (117)
Q Consensus 93 ~YIK~nnLQDP 103 (117)
-|+++|||-+-
T Consensus 9 rYV~eh~ls~e 19 (28)
T PF12368_consen 9 RYVKEHGLSEE 19 (28)
T ss_pred hhHHhcCCCHH
Confidence 49999998654
No 49
>PF04046 PSP: PSP; InterPro: IPR006568 PSP is a proline-rich domain of unknown function found in spliceosome associated proteins.
Probab=26.06 E-value=54 Score=20.92 Aligned_cols=19 Identities=32% Similarity=0.490 Sum_probs=15.0
Q ss_pred CCCCCCHHHHhhhCCCCcC
Q 033520 65 KPRRVSPEMEAFVGAPEIP 83 (117)
Q Consensus 65 kp~~LSpeLa~~lG~~e~s 83 (117)
||=.||++|.+.||..+..
T Consensus 1 kPG~lS~~LR~ALg~~~~~ 19 (48)
T PF04046_consen 1 KPGKLSDELREALGMQEND 19 (48)
T ss_pred CCcccCHHHHHHcCCCCCC
Confidence 3457999999999987654
No 50
>PF01381 HTH_3: Helix-turn-helix; InterPro: IPR001387 This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould).; GO: 0043565 sequence-specific DNA binding; PDB: 2AXU_A 2AWI_D 2AXV_D 2AXZ_C 2AW6_A 3KXA_C 3BS3_A 2CRO_A 1ZUG_A 3CRO_R ....
Probab=25.86 E-value=36 Score=20.00 Aligned_cols=27 Identities=11% Similarity=-0.058 Sum_probs=18.5
Q ss_pred HHHHhhhCCCCcCHHHHHHHHHHHhhhcCCCCcc
Q 033520 71 PEMEAFVGAPEIPRTQALKLIWAHIKQHNLQWKT 104 (117)
Q Consensus 71 peLa~~lG~~e~sR~evvK~lW~YIK~nnLQDP~ 104 (117)
.+||+.+|.... .++.|++.+..-+++
T Consensus 13 ~~la~~~gis~~-------~i~~~~~g~~~~~~~ 39 (55)
T PF01381_consen 13 KELAEKLGISRS-------TISRIENGKRNPSLD 39 (55)
T ss_dssp HHHHHHHTS-HH-------HHHHHHTTSSTSBHH
T ss_pred HHHHHHhCCCcc-------hhHHHhcCCCCCCHH
Confidence 678888886655 788888886544444
No 51
>COG1057 NadD Nicotinic acid mononucleotide adenylyltransferase [Coenzyme metabolism]
Probab=25.26 E-value=51 Score=25.92 Aligned_cols=32 Identities=13% Similarity=0.049 Sum_probs=23.3
Q ss_pred CHHHHhhhCCCCcCHHHHHHHHHHHhhhcCCC
Q 033520 70 SPEMEAFVGAPEIPRTQALKLIWAHIKQHNLQ 101 (117)
Q Consensus 70 SpeLa~~lG~~e~sR~evvK~lW~YIK~nnLQ 101 (117)
|.+..+.+....-....+-..+.+||++|+|.
T Consensus 164 St~IR~~~~~~~~~~~llP~~V~~YI~~~~LY 195 (197)
T COG1057 164 STEIRERIRRGASVDYLLPDSVLSYIEERGLY 195 (197)
T ss_pred hHHHHHHHhCCCCchhcCCHHHHHHHHHhccc
Confidence 44555666555555667778899999999985
No 52
>cd01104 HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA- and CarA-like proteins in this group appear to lack the long dimerization helix seen i
Probab=24.11 E-value=87 Score=19.10 Aligned_cols=27 Identities=11% Similarity=0.064 Sum_probs=20.6
Q ss_pred HHHHhhhCCCCcCHHHHHHHHHHHhhhcCCCCcc
Q 033520 71 PEMEAFVGAPEIPRTQALKLIWAHIKQHNLQWKT 104 (117)
Q Consensus 71 peLa~~lG~~e~sR~evvK~lW~YIK~nnLQDP~ 104 (117)
.|+|+.+|...- .|+.|+++.++..|.
T Consensus 4 ~eva~~~gvs~~-------tlr~w~~~~g~~~~~ 30 (68)
T cd01104 4 GAVARLTGVSPD-------TLRAWERRYGLPAPQ 30 (68)
T ss_pred HHHHHHHCcCHH-------HHHHHHHhCCCCCCC
Confidence 578888898766 788888887776653
No 53
>KOG2522 consensus Filamentous baseplate protein Ligatin, contains PUA domain [Translation, ribosomal structure and biogenesis]
Probab=23.78 E-value=57 Score=29.96 Aligned_cols=26 Identities=12% Similarity=-0.005 Sum_probs=23.3
Q ss_pred CCcCHHHHHHHHHHHhhhcCCCCccc
Q 033520 80 PEIPRTQALKLIWAHIKQHNLQWKTI 105 (117)
Q Consensus 80 ~e~sR~evvK~lW~YIK~nnLQDP~N 105 (117)
.-.+-+||-..+-.||+.|||-|+.|
T Consensus 380 ~lyt~seir~~V~kYi~knnLad~~n 405 (560)
T KOG2522|consen 380 TLYTSSEIRSAVSKYISKNNLADTKN 405 (560)
T ss_pred ceeeHHHHHHHHHHHhhhhhcccccc
Confidence 45778999999999999999999986
No 54
>PHA01399 membrane protein P6
Probab=22.17 E-value=44 Score=27.59 Aligned_cols=13 Identities=31% Similarity=0.603 Sum_probs=11.1
Q ss_pred HHHHHHHHHhhhc
Q 033520 86 QALKLIWAHIKQH 98 (117)
Q Consensus 86 evvK~lW~YIK~n 98 (117)
.++..+|+|||+|
T Consensus 160 gv~~g~wdfik~n 172 (242)
T PHA01399 160 GVIGGIWDFIKDN 172 (242)
T ss_pred chhhhHHHHhccC
Confidence 4778999999986
No 55
>PF02614 UxaC: Glucuronate isomerase; InterPro: IPR003766 Uronate isomerase (also known as glucuronate isomerase) catalyses the reaction D-glucuronate to D-fructuronate and also converts D-galacturonate to D-tagaturonate [].; GO: 0008880 glucuronate isomerase activity, 0006064 glucuronate catabolic process; PDB: 2QEE_B 3HKA_A 3HK8_A 2PNK_H 2Q6E_A 3HK7_A 3HK5_B 3HK9_A 2Q08_L 1J5S_B ....
Probab=20.97 E-value=71 Score=28.40 Aligned_cols=33 Identities=18% Similarity=0.305 Sum_probs=25.5
Q ss_pred HHHHhhhCCCCcCHHHHHHHHHHHhhhcCCCCcc
Q 033520 71 PEMEAFVGAPEIPRTQALKLIWAHIKQHNLQWKT 104 (117)
Q Consensus 71 peLa~~lG~~e~sR~evvK~lW~YIK~nnLQDP~ 104 (117)
-||.+++|..+.--.+-...||+++++. ||+|+
T Consensus 105 leL~r~FGid~~L~~~~a~~I~d~~n~~-l~~~~ 137 (462)
T PF02614_consen 105 LELKRYFGIDEPLSEENADEIWDACNEK-LATPE 137 (462)
T ss_dssp HHHHHCTT--C-GSHHHHHHHHHHHHHH-HTSGG
T ss_pred HHHHHHcCCCCCCCccCHHHHHHHHHHH-hcccC
Confidence 4788899998877788889999999987 67777
No 56
>PRK12757 cell division protein FtsN; Provisional
Probab=20.44 E-value=47 Score=27.63 Aligned_cols=9 Identities=33% Similarity=0.604 Sum_probs=7.6
Q ss_pred HHHHHHhhh
Q 033520 89 KLIWAHIKQ 97 (117)
Q Consensus 89 K~lW~YIK~ 97 (117)
+.-|.||||
T Consensus 46 eErWrYIke 54 (256)
T PRK12757 46 EERWRYIKE 54 (256)
T ss_pred chhHHHHHH
Confidence 467999998
No 57
>PF00010 HLH: Helix-loop-helix DNA-binding domain only nuclear translocator protein (Arnt).; InterPro: IPR011598 The helix-loop-helix (HLH) DNA-binding domain consists of a closed bundle of four helices in a left-handed twist with two crossover connections. The HLH domain directs dimerisation, and is juxtaposed to basic regions to create a DNA interaction interface surface that recognises specific DNA sequences. Basic region/HLH (bHLH) proteins regulate diverse biological pathways []. bHLH proteins include MyoD [], SREBPs (sterol regulatory element binding proteins) [], and yeast Pho4 (phosphatase system) []. In certain proteins the bHLH domain contains a leucine-zipper motif. The bHLH/leucine zipper (bHLHZip) domain specifies dimerisation within a network of proteins and determines sequence-specific DNA binding []. bHLHZip domains occur in the transcription factors Myc, Mad, Max and Usf [, ]. This entry is bHLHZip, which covers the bHLH domain and the leucine zipper motif, when present.; PDB: 1NLW_A 1NKP_D 1A93_A 2A93_A 1AM9_C 3U5V_A 1A0A_B 2QL2_C 1UKL_C 1AN4_B ....
Probab=20.35 E-value=1.5e+02 Score=17.69 Aligned_cols=18 Identities=22% Similarity=0.268 Sum_probs=16.3
Q ss_pred CCcCHHHHHHHHHHHhhh
Q 033520 80 PEIPRTQALKLIWAHIKQ 97 (117)
Q Consensus 80 ~e~sR~evvK~lW~YIK~ 97 (117)
..++..+|+....+||+.
T Consensus 36 ~k~~K~~iL~~ai~yI~~ 53 (55)
T PF00010_consen 36 RKLSKASILQKAIDYIKQ 53 (55)
T ss_dssp SSSSHHHHHHHHHHHHHH
T ss_pred ccCCHHHHHHHHHHHHHH
Confidence 569999999999999985
Done!