Query 019960
Match_columns 333
No_of_seqs 202 out of 1115
Neff 4.6
Searched_HMMs 46136
Date Fri Mar 29 05:54:52 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/019960.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/019960hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF00010 HLH: Helix-loop-helix 99.4 7.5E-14 1.6E-18 102.2 4.5 51 45-95 1-55 (55)
2 cd00083 HLH Helix-loop-helix d 99.4 2.1E-13 4.6E-18 100.0 5.4 55 44-98 3-59 (60)
3 smart00353 HLH helix loop heli 99.3 3.6E-12 7.9E-17 91.9 6.6 50 50-99 1-52 (53)
4 KOG1318 Helix loop helix trans 99.2 1.5E-11 3.2E-16 123.2 5.7 59 41-99 229-290 (411)
5 KOG1319 bHLHZip transcription 99.1 2E-11 4.4E-16 111.2 2.2 89 42-130 59-154 (229)
6 KOG4304 Transcriptional repres 98.7 6.8E-09 1.5E-13 98.5 3.0 61 38-98 25-92 (250)
7 KOG2483 Upstream transcription 98.5 1.2E-07 2.6E-12 89.3 6.0 76 41-116 55-132 (232)
8 KOG3960 Myogenic helix-loop-he 98.5 1.6E-07 3.5E-12 89.1 6.7 74 36-109 109-183 (284)
9 KOG3561 Aryl-hydrocarbon recep 98.5 1.6E-07 3.4E-12 101.1 5.5 57 41-97 16-75 (803)
10 KOG2588 Predicted DNA-binding 98.3 3.1E-07 6.6E-12 99.5 1.8 67 43-109 274-340 (953)
11 KOG4029 Transcription factor H 98.0 7.1E-06 1.5E-10 76.3 4.2 65 41-105 105-172 (228)
12 KOG0561 bHLH transcription fac 97.7 2.8E-05 6.2E-10 75.8 3.7 59 41-99 56-115 (373)
13 KOG3910 Helix loop helix trans 97.4 0.00011 2.4E-09 75.7 4.1 61 41-101 522-585 (632)
14 PLN03217 transcription factor 96.5 0.0047 1E-07 50.5 4.8 52 57-108 19-75 (93)
15 KOG4447 Transcription factor T 95.4 0.007 1.5E-07 54.4 1.3 54 44-97 77-131 (173)
16 KOG3898 Transcription factor N 93.7 0.068 1.5E-06 51.2 3.8 56 41-96 68-125 (254)
17 KOG3558 Hypoxia-inducible fact 91.8 0.12 2.6E-06 55.8 2.8 50 44-93 45-97 (768)
18 KOG4395 Transcription factor A 89.4 0.52 1.1E-05 45.7 4.6 56 43-98 172-229 (285)
19 KOG3582 Mlx interactors and re 87.5 0.16 3.5E-06 54.8 -0.2 76 42-117 648-727 (856)
20 KOG3560 Aryl-hydrocarbon recep 85.6 0.69 1.5E-05 49.1 3.2 39 54-92 34-75 (712)
21 KOG3559 Transcriptional regula 84.3 0.99 2.1E-05 46.6 3.6 44 51-94 7-53 (598)
22 cd04895 ACT_ACR_1 ACT domain-c 67.4 3.7 8.1E-05 32.3 1.8 38 248-288 4-41 (72)
23 KOG4447 Transcription factor T 65.4 5.3 0.00011 36.3 2.6 45 52-96 29-74 (173)
24 PF01316 Arg_repressor: Argini 59.5 2.5 5.5E-05 33.2 -0.4 20 261-280 24-43 (70)
25 KOG3582 Mlx interactors and re 53.6 4 8.6E-05 44.7 -0.3 64 41-107 783-850 (856)
26 PRK04280 arginine repressor; P 50.8 5.4 0.00012 35.4 0.1 23 261-283 23-45 (148)
27 cd04897 ACT_ACR_3 ACT domain-c 48.5 11 0.00025 29.8 1.6 38 248-288 4-41 (75)
28 cd04896 ACT_ACR-like_3 ACT dom 47.1 13 0.00029 29.4 1.8 32 248-279 3-34 (75)
29 cd04900 ACT_UUR-like_1 ACT dom 45.6 20 0.00043 27.1 2.5 33 248-280 4-36 (73)
30 cd04919 ACT_AK-Hom3_2 ACT doma 45.2 31 0.00067 24.8 3.5 28 256-283 15-49 (66)
31 cd04922 ACT_AKi-HSDH-ThrA_2 AC 43.6 35 0.00075 24.4 3.5 29 255-283 14-49 (66)
32 cd04915 ACT_AK-Ectoine_2 ACT d 43.3 35 0.00076 25.6 3.6 28 256-283 15-49 (66)
33 PRK05066 arginine repressor; P 39.1 9.8 0.00021 34.1 -0.1 23 261-283 28-51 (156)
34 cd04937 ACT_AKi-DapG-BS_2 ACT 38.2 46 0.00099 24.4 3.4 29 255-283 14-47 (64)
35 cd04927 ACT_ACR-like_2 Second 36.6 26 0.00056 27.1 2.0 33 248-280 3-35 (76)
36 PRK03341 arginine repressor; P 33.6 14 0.00029 33.7 -0.1 23 261-283 34-56 (168)
37 cd04899 ACT_ACR-UUR-like_2 C-t 31.6 40 0.00087 24.5 2.2 32 248-279 3-34 (70)
38 cd04869 ACT_GcvR_2 ACT domains 28.9 46 0.001 25.0 2.2 31 248-278 2-32 (81)
39 cd02116 ACT ACT domains are co 28.2 54 0.0012 20.6 2.2 30 250-279 3-32 (60)
40 cd04916 ACT_AKiii-YclM-BS_2 AC 27.4 89 0.0019 22.2 3.4 30 255-284 14-50 (66)
41 PF01842 ACT: ACT domain; Int 26.2 43 0.00093 23.6 1.5 28 254-281 9-36 (66)
42 COG4710 Predicted DNA-binding 26.1 1.3E+02 0.0029 24.3 4.3 33 59-96 15-48 (80)
43 cd04925 ACT_ACR_2 ACT domain-c 25.9 58 0.0013 24.8 2.3 37 249-288 4-40 (74)
44 COG3074 Uncharacterized protei 25.9 70 0.0015 25.7 2.7 29 84-112 13-41 (79)
45 PRK00441 argR arginine repress 25.7 28 0.00061 30.8 0.6 23 260-282 22-44 (149)
46 COG1438 ArgR Arginine represso 25.4 24 0.00052 31.7 0.1 22 261-282 25-46 (150)
47 cd04876 ACT_RelA-SpoT ACT dom 24.6 60 0.0013 21.8 2.0 28 249-276 2-29 (71)
48 TIGR01529 argR_whole arginine 24.5 24 0.00052 31.1 -0.1 21 260-280 20-40 (146)
49 cd04918 ACT_AK1-AT_2 ACT domai 24.2 1.1E+02 0.0025 22.4 3.6 28 256-283 14-48 (65)
50 cd04924 ACT_AK-Arch_2 ACT doma 24.0 1.2E+02 0.0025 21.5 3.5 29 256-284 15-50 (66)
51 cd04870 ACT_PSP_1 CT domains f 23.5 86 0.0019 23.7 2.8 30 248-277 2-31 (75)
52 PF14794 DUF4479: Domain of un 23.2 70 0.0015 25.3 2.3 25 245-273 43-67 (73)
53 cd04873 ACT_UUR-ACR-like ACT d 22.4 72 0.0016 22.7 2.1 32 248-279 3-34 (70)
54 cd04872 ACT_1ZPV ACT domain pr 21.9 73 0.0016 24.8 2.2 35 246-280 2-36 (88)
55 cd04878 ACT_AHAS N-terminal AC 21.9 79 0.0017 22.2 2.2 29 247-275 2-30 (72)
56 PF06345 Drf_DAD: DRF Autoregu 21.9 90 0.002 17.8 1.9 12 257-268 1-12 (15)
57 cd04926 ACT_ACR_4 C-terminal 21.0 72 0.0016 24.1 2.0 32 247-278 3-34 (72)
No 1
>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=99.45 E-value=7.5e-14 Score=102.19 Aligned_cols=51 Identities=43% Similarity=0.711 Sum_probs=48.0
Q ss_pred ccccCchHHHHHHHHHHHHHHHHhccCCCC----CCCCChhhhhHHHHHHHHHHH
Q 019960 45 IRSKHSVTEQRRRSKINERFQILREIIPHS----DQKRDTASFLLEVIEYVQYLQ 95 (333)
Q Consensus 45 rr~~H~~~ERrRR~rINe~f~~LrsLVP~~----~~K~DKasIL~~AIeYIk~Lq 95 (333)
+|..|+..||+||++||+.|.+|+.+||.+ ..|++|++||..||+||++||
T Consensus 1 rR~~h~~~Er~RR~~i~~~~~~L~~llp~~~~~~~~k~~K~~iL~~ai~yI~~Lq 55 (55)
T PF00010_consen 1 RRQKHNERERRRRDRINDCFDELRELLPSCSAGSSRKLSKASILQKAIDYIKQLQ 55 (55)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHCCSSHHCCTTSSSSHHHHHHHHHHHHHHHH
T ss_pred CCchHHHHHHHHHHHHHHHHHHHHHhccchhccccccCCHHHHHHHHHHHHHHhC
Confidence 467899999999999999999999999986 479999999999999999997
No 2
>cd00083 HLH Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and
Probab=99.42 E-value=2.1e-13 Score=100.00 Aligned_cols=55 Identities=35% Similarity=0.625 Sum_probs=51.6
Q ss_pred cccccCchHHHHHHHHHHHHHHHHhccCCCC--CCCCChhhhhHHHHHHHHHHHHHH
Q 019960 44 VIRSKHSVTEQRRRSKINERFQILREIIPHS--DQKRDTASFLLEVIEYVQYLQEKV 98 (333)
Q Consensus 44 ~rr~~H~~~ERrRR~rINe~f~~LrsLVP~~--~~K~DKasIL~~AIeYIk~Lq~~v 98 (333)
.++..|+..||+||++||+.|..|+.+||.. ..|+||++||..||+||++|+.++
T Consensus 3 ~~r~~~~~~Er~RR~~~n~~~~~L~~llp~~~~~~k~~k~~iL~~a~~yI~~L~~~~ 59 (60)
T cd00083 3 SRREAHNLRERRRRERINDAFDELRSLLPTLPPSKKLSKAEILRKAVDYIKSLQELL 59 (60)
T ss_pred HHHHHHhHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHh
Confidence 4678899999999999999999999999998 589999999999999999999875
No 3
>smart00353 HLH helix loop helix domain.
Probab=99.32 E-value=3.6e-12 Score=91.89 Aligned_cols=50 Identities=44% Similarity=0.672 Sum_probs=46.1
Q ss_pred chHHHHHHHHHHHHHHHHhccCCCC--CCCCChhhhhHHHHHHHHHHHHHHH
Q 019960 50 SVTEQRRRSKINERFQILREIIPHS--DQKRDTASFLLEVIEYVQYLQEKVQ 99 (333)
Q Consensus 50 ~~~ERrRR~rINe~f~~LrsLVP~~--~~K~DKasIL~~AIeYIk~Lq~~v~ 99 (333)
+..||+||.+||++|..|+.+||.+ ..|++|++||..||+||++|+.+++
T Consensus 1 n~~Er~RR~~~n~~~~~L~~lip~~~~~~k~~k~~iL~~ai~yi~~L~~~~~ 52 (53)
T smart00353 1 NARERRRRRKINEAFDELRSLLPTLPNNKKLSKAEILRLAIEYIKSLQEELQ 52 (53)
T ss_pred CHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHh
Confidence 4689999999999999999999964 4799999999999999999998875
No 4
>KOG1318 consensus Helix loop helix transcription factor EB [Transcription]
Probab=99.20 E-value=1.5e-11 Score=123.15 Aligned_cols=59 Identities=32% Similarity=0.573 Sum_probs=55.4
Q ss_pred ccccccccCchHHHHHHHHHHHHHHHHhccCCCC---CCCCChhhhhHHHHHHHHHHHHHHH
Q 019960 41 KASVIRSKHSVTEQRRRSKINERFQILREIIPHS---DQKRDTASFLLEVIEYVQYLQEKVQ 99 (333)
Q Consensus 41 k~~~rr~~H~~~ERrRR~rINe~f~~LrsLVP~~---~~K~DKasIL~~AIeYIk~Lq~~v~ 99 (333)
|.+.+|..|+++|||||++||++|++|..|||.| +.|+.|..||..+++||++||+..+
T Consensus 229 rdr~Krd~HNeVERRRR~nIN~~IkeLg~liP~~~~~~~~~nKgtILk~s~dYIr~Lqq~~q 290 (411)
T KOG1318|consen 229 RDRRKRDNHNEVERRRRENINDRIKELGQLIPKCNSEDMKSNKGTILKASCDYIRELQQTLQ 290 (411)
T ss_pred HHHHHHhhhhHHHHHHHHHHHHHHHHHHHhCCCCCcchhhcccchhhHHHHHHHHHHHHHHH
Confidence 7888999999999999999999999999999998 5689999999999999999988666
No 5
>KOG1319 consensus bHLHZip transcription factor BIGMAX [Transcription]
Probab=99.12 E-value=2e-11 Score=111.17 Aligned_cols=89 Identities=26% Similarity=0.351 Sum_probs=68.9
Q ss_pred cccccccCchHHHHHHHHHHHHHHHHhccCCCC------CCCCChhhhhHHHHHHHHHHHHHHHHHHhhhcccccCcccc
Q 019960 42 ASVIRSKHSVTEQRRRSKINERFQILREIIPHS------DQKRDTASFLLEVIEYVQYLQEKVQKYEVSYQDWSAEPTKL 115 (333)
Q Consensus 42 ~~~rr~~H~~~ERrRR~rINe~f~~LrsLVP~~------~~K~DKasIL~~AIeYIk~Lq~~v~~Le~~~~~l~~e~~~l 115 (333)
+.+||..|.-+||+||+.||..+..|+.|||.| ..|+.||.||.++|+||.+|..+..+-+.+...|+.+...|
T Consensus 59 k~rrr~aHtqaEqkRRdAIk~GYddLq~LvP~cq~~ds~g~KlskA~ILqksidyi~~L~~~k~kqe~e~s~L~k~vtAL 138 (229)
T KOG1319|consen 59 KDRRRRAHTQAEQKRRDAIKRGYDDLQTLVPTCQQQDSIGQKLSKAIILQKTIDYIQFLHKEKKKQEEEVSTLRKDVTAL 138 (229)
T ss_pred HHHHHHHHHHHHHHHHHHHHhchHHHHHhccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 567899999999999999999999999999987 23889999999999999999988887777766666555433
Q ss_pred cc-CCCCcccccccCC
Q 019960 116 MP-WRNSHWRVQNFAT 130 (333)
Q Consensus 116 ~p-~~n~~~~~~s~~d 130 (333)
.- ..+++..+....+
T Consensus 139 ~iIk~~YEqM~~~~qd 154 (229)
T KOG1319|consen 139 KIIKVNYEQMVKAHQD 154 (229)
T ss_pred HHHHHHHHHHHHhccc
Confidence 22 2333334444333
No 6
>KOG4304 consensus Transcriptional repressors of the hairy/E(spl) family (contains HLH) [Transcription]
Probab=98.71 E-value=6.8e-09 Score=98.52 Aligned_cols=61 Identities=25% Similarity=0.429 Sum_probs=53.3
Q ss_pred CCcccccccccCchHHHHHHHHHHHHHHHHhccCCCC---C----CCCChhhhhHHHHHHHHHHHHHH
Q 019960 38 NSDKASVIRSKHSVTEQRRRSKINERFQILREIIPHS---D----QKRDTASFLLEVIEYVQYLQEKV 98 (333)
Q Consensus 38 ~~~k~~~rr~~H~~~ERrRR~rINe~f~~LrsLVP~~---~----~K~DKasIL~~AIeYIk~Lq~~v 98 (333)
.......|+..|-+.|||||+|||+.+.+|++|||.+ + .|++||.||+-|++|++.|+...
T Consensus 25 ~~~~~~~rk~~Kpl~EKkRRaRIN~~L~eLK~Li~e~~~~~~~~~sklEKAdILEltV~hL~~l~~~~ 92 (250)
T KOG4304|consen 25 SSKTRQYRKVRKPLLEKKRRARINRCLDELKDLIPEALKKDGQRHSKLEKADILELTVNHLRQLQRSQ 92 (250)
T ss_pred chhhHHHhhhcchhHHHHHHHHHHHHHHHHHHHHHHHHhhcchhhhhhHHHHHHHHHHHHHHHHhccc
Confidence 3336677889999999999999999999999999965 1 58999999999999999998643
No 7
>KOG2483 consensus Upstream transcription factor 2/L-myc-2 protein [Transcription]
Probab=98.53 E-value=1.2e-07 Score=89.26 Aligned_cols=76 Identities=30% Similarity=0.451 Sum_probs=62.8
Q ss_pred ccccccccCchHHHHHHHHHHHHHHHHhccCCCCCCC-CC-hhhhhHHHHHHHHHHHHHHHHHHhhhcccccCccccc
Q 019960 41 KASVIRSKHSVTEQRRRSKINERFQILREIIPHSDQK-RD-TASFLLEVIEYVQYLQEKVQKYEVSYQDWSAEPTKLM 116 (333)
Q Consensus 41 k~~~rr~~H~~~ERrRR~rINe~f~~LrsLVP~~~~K-~D-KasIL~~AIeYIk~Lq~~v~~Le~~~~~l~~e~~~l~ 116 (333)
.....|..|+..||+||..|+++|..|+.+||..+.. .. .++||++|++||+.|+.+....+..++.+..+..+|.
T Consensus 55 ~~~~~R~~HN~LEk~RRahlk~~~~~Lk~~vP~~~~~~~~t~lsiL~kA~~~i~~l~~~~~~~~~~~e~l~~e~~~l~ 132 (232)
T KOG2483|consen 55 SAASSRAHHNALEKRRRAHLKDCFESLKDSVPLLNGETRSTTLSILDKALEHIQSLERKSATQQQDIEDLSRENRKLK 132 (232)
T ss_pred CCCcchhhhhhhhHHHHHHHHHHHHHHHHhCCCCCCcchhhhhHhhhhHHHHHHHHHhHHHHHHHHHHHHHHHHHHHH
Confidence 5566789999999999999999999999999987433 33 5999999999999999988877777666666555444
No 8
>KOG3960 consensus Myogenic helix-loop-helix transcription factor [Transcription]
Probab=98.53 E-value=1.6e-07 Score=89.11 Aligned_cols=74 Identities=24% Similarity=0.359 Sum_probs=63.0
Q ss_pred CCCCcccccccccCchHHHHHHHHHHHHHHHH-hccCCCCCCCCChhhhhHHHHHHHHHHHHHHHHHHhhhcccc
Q 019960 36 GKNSDKASVIRSKHSVTEQRRRSKINERFQIL-REIIPHSDQKRDTASFLLEVIEYVQYLQEKVQKYEVSYQDWS 109 (333)
Q Consensus 36 g~~~~k~~~rr~~H~~~ERrRR~rINe~f~~L-rsLVP~~~~K~DKasIL~~AIeYIk~Lq~~v~~Le~~~~~l~ 109 (333)
.|.+.-...||++-.+.||||-.|+||.|.+| |.-.++.++++.|+.||..||+||..||.-++++......+.
T Consensus 109 ckrks~svDRRKAATMRERRRLkKVNEAFE~LKRrT~~NPNQRLPKVEILRsAI~YIE~Lq~LL~~~~~~~~~~~ 183 (284)
T KOG3960|consen 109 CKRKSTSVDRRKAATMRERRRLKKVNEAFETLKRRTSSNPNQRLPKVEILRSAIRYIERLQALLQEQDQAEKGLA 183 (284)
T ss_pred ccccccchhHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccccccHHHHHHHHHHHHHHHHHHHHHhhccchhhh
Confidence 34444556688888999999999999999999 667888889999999999999999999999998887665544
No 9
>KOG3561 consensus Aryl-hydrocarbon receptor nuclear translocator [Transcription]
Probab=98.47 E-value=1.6e-07 Score=101.10 Aligned_cols=57 Identities=26% Similarity=0.457 Sum_probs=51.9
Q ss_pred ccccccccCchHHHHHHHHHHHHHHHHhccCCCCC---CCCChhhhhHHHHHHHHHHHHH
Q 019960 41 KASVIRSKHSVTEQRRRSKINERFQILREIIPHSD---QKRDTASFLLEVIEYVQYLQEK 97 (333)
Q Consensus 41 k~~~rr~~H~~~ERrRR~rINe~f~~LrsLVP~~~---~K~DKasIL~~AIeYIk~Lq~~ 97 (333)
+....|.+|+.+|||||+++|..|.+|.+|||.|. .|+||..||..||.+||.+++.
T Consensus 16 k~r~~Re~~~~~EKrRRdq~N~yI~ELs~Mvp~~~~~~RK~DK~tVLr~aV~~lr~~k~~ 75 (803)
T KOG3561|consen 16 KDRKKRENRSEIEKRRRDQMNKYIEELSEMVPTNASLSRKPDKLTVLRMAVDHLRLIKEQ 75 (803)
T ss_pred hhhhccccchhHHHHHHHHHHHHHHHHHHhhhcchhcccCchHHHHHHHHHHHHHHHhhh
Confidence 33345999999999999999999999999999985 8999999999999999999874
No 10
>KOG2588 consensus Predicted DNA-binding protein [Transcription]
Probab=98.26 E-value=3.1e-07 Score=99.52 Aligned_cols=67 Identities=27% Similarity=0.477 Sum_probs=60.5
Q ss_pred ccccccCchHHHHHHHHHHHHHHHHhccCCCCCCCCChhhhhHHHHHHHHHHHHHHHHHHhhhcccc
Q 019960 43 SVIRSKHSVTEQRRRSKINERFQILREIIPHSDQKRDTASFLLEVIEYVQYLQEKVQKYEVSYQDWS 109 (333)
Q Consensus 43 ~~rr~~H~~~ERrRR~rINe~f~~LrsLVP~~~~K~DKasIL~~AIeYIk~Lq~~v~~Le~~~~~l~ 109 (333)
..+|.+||++|||.|..||+++.+|+++||+...|+.|..+|..||+||++|+...+.+......+.
T Consensus 274 ~~kRtAHN~IEKRYRsSINDKI~eLk~lV~g~~aKl~kSavLr~ai~~i~dl~~~nq~lk~~~~~l~ 340 (953)
T KOG2588|consen 274 GEKRTAHNIIEKRYRSSINDKIIELKDLVPGTEAKLNKSAVLRKAIDYIEDLQGYNQKLKLENASLR 340 (953)
T ss_pred CcccchhhHHHHHhhcchhHHHHHHHHhcCccHhhhhhhhhHHHHHHHHHHhhccccccchhhhhhh
Confidence 3679999999999999999999999999999888999999999999999999998887776655444
No 11
>KOG4029 consensus Transcription factor HAND2/Transcription factor TAL1/TAL2/LYL1 [Transcription]
Probab=97.96 E-value=7.1e-06 Score=76.26 Aligned_cols=65 Identities=23% Similarity=0.402 Sum_probs=56.2
Q ss_pred ccccccccCchHHHHHHHHHHHHHHHHhccCCCC---CCCCChhhhhHHHHHHHHHHHHHHHHHHhhh
Q 019960 41 KASVIRSKHSVTEQRRRSKINERFQILREIIPHS---DQKRDTASFLLEVIEYVQYLQEKVQKYEVSY 105 (333)
Q Consensus 41 k~~~rr~~H~~~ERrRR~rINe~f~~LrsLVP~~---~~K~DKasIL~~AIeYIk~Lq~~v~~Le~~~ 105 (333)
....++..++..||.|=..+|..|.+||.+||.. ++|+.|+.+|..||.||++|+.-++.-+...
T Consensus 105 ~~~~~~~~~n~RER~Rv~~vN~~f~~Lr~~lP~~~~~~kklSKveTLr~A~~YI~~L~~lL~~~~~~~ 172 (228)
T KOG4029|consen 105 QTSAQRQARNARERQRVQSVNSAFAELRALLPTEPPQSKKLSKVETLRLATSYIRYLTKLLATQEAPL 172 (228)
T ss_pred chhhhhhhhhhhhhhcccchhhhhHHHHhcCCCCCCcccccCcccchHHHHHHHHHHHHHhcccccCC
Confidence 4556777888999999999999999999999964 5799999999999999999998877666443
No 12
>KOG0561 consensus bHLH transcription factor [Transcription]
Probab=97.70 E-value=2.8e-05 Score=75.82 Aligned_cols=59 Identities=27% Similarity=0.456 Sum_probs=51.2
Q ss_pred ccccccccCchHHHHHHHHHHHHHHHHhccCCCC-CCCCChhhhhHHHHHHHHHHHHHHH
Q 019960 41 KASVIRSKHSVTEQRRRSKINERFQILREIIPHS-DQKRDTASFLLEVIEYVQYLQEKVQ 99 (333)
Q Consensus 41 k~~~rr~~H~~~ERrRR~rINe~f~~LrsLVP~~-~~K~DKasIL~~AIeYIk~Lq~~v~ 99 (333)
.++-||.--|-.||||=.-||..|..||.|||.. ..|++||.||..+.+||..|+.+..
T Consensus 56 erRmRReIANsNERRRMQSINAGFqsLr~LlPr~eGEKLSKAAILQQTa~yI~~Le~~Kt 115 (373)
T KOG0561|consen 56 ERRMRREIANSNERRRMQSINAGFQSLRALLPRKEGEKLSKAAILQQTADYIHQLEGHKT 115 (373)
T ss_pred HHHHHHHhhcchHHHHHHhhhHHHHHHHHhcCcccchhhHHHHHHHHHHHHHHHHHhccc
Confidence 3445677778889999999999999999999976 4699999999999999999976443
No 13
>KOG3910 consensus Helix loop helix transcription factor [Transcription]
Probab=97.44 E-value=0.00011 Score=75.69 Aligned_cols=61 Identities=18% Similarity=0.290 Sum_probs=52.0
Q ss_pred ccccccccCchHHHHHHHHHHHHHHHHhccCCCC---CCCCChhhhhHHHHHHHHHHHHHHHHH
Q 019960 41 KASVIRSKHSVTEQRRRSKINERFQILREIIPHS---DQKRDTASFLLEVIEYVQYLQEKVQKY 101 (333)
Q Consensus 41 k~~~rr~~H~~~ERrRR~rINe~f~~LrsLVP~~---~~K~DKasIL~~AIeYIk~Lq~~v~~L 101 (333)
|...||...++.||-|-..||+.|++|..+.--. ++.-.|.-||..||.-|-.|++||++-
T Consensus 522 REkERR~aNNARERlRVRDINeAfKELGRMCqlHlkSeKpQTKLgILhqAVsVIlsLEQQVRER 585 (632)
T KOG3910|consen 522 REKERRMANNARERLRVRDINEAFKELGRMCQLHLKSEKPQTKLGILHQAVSVILSLEQQVRER 585 (632)
T ss_pred HHHHHHhhhhhhhheehhhHHHHHHHHHHHHHHhhcccCcchhhhHHHHHHHHHHHHHHHHHHc
Confidence 5667899999999999999999999998876432 345569999999999999999999853
No 14
>PLN03217 transcription factor ATBS1; Provisional
Probab=96.49 E-value=0.0047 Score=50.55 Aligned_cols=52 Identities=19% Similarity=0.387 Sum_probs=44.1
Q ss_pred HHHHHHHHHHHhccCCCC-----CCCCChhhhhHHHHHHHHHHHHHHHHHHhhhccc
Q 019960 57 RSKINERFQILREIIPHS-----DQKRDTASFLLEVIEYVQYLQEKVQKYEVSYQDW 108 (333)
Q Consensus 57 R~rINe~f~~LrsLVP~~-----~~K~DKasIL~~AIeYIk~Lq~~v~~Le~~~~~l 108 (333)
-+.|++.+..|+.|+|.. ..|..-+-+|.++..||+.|+.+|..|....-++
T Consensus 19 ddqi~dLvsKLq~llPe~r~~r~s~k~saskvLqEtC~YIrsLhrEvDdLSerLs~L 75 (93)
T PLN03217 19 EDQINDLIIKLQQLLPELRDSRRSDKVSAARVLQDTCNYIRNLHREVDDLSERLSEL 75 (93)
T ss_pred HHHHHHHHHHHHHHChHHHhhhccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 478999999999999964 2366777899999999999999999999876443
No 15
>KOG4447 consensus Transcription factor TWIST [Transcription]
Probab=95.35 E-value=0.007 Score=54.36 Aligned_cols=54 Identities=30% Similarity=0.435 Sum_probs=48.3
Q ss_pred cccccCchHHHHHHHHHHHHHHHHhccCCCC-CCCCChhhhhHHHHHHHHHHHHH
Q 019960 44 VIRSKHSVTEQRRRSKINERFQILREIIPHS-DQKRDTASFLLEVIEYVQYLQEK 97 (333)
Q Consensus 44 ~rr~~H~~~ERrRR~rINe~f~~LrsLVP~~-~~K~DKasIL~~AIeYIk~Lq~~ 97 (333)
..|..|++.||+|-..+|+.|..||.+||.. ..|.+|+-.|.-|-.||-+|=.-
T Consensus 77 ~qrv~anvrerqRtqsLn~AF~~lr~iiptlPsdklSkiqtLklA~ryidfl~~v 131 (173)
T KOG4447|consen 77 KQRVMANVRERQRTQSLNEAFAALRKIIPTLPSDKLSKIQTLKLAARYIDFLYQV 131 (173)
T ss_pred HHHHHHHHHHHHhhhhHHHHHHHHHhhcCCCCccccccccchhhcccCCchhhhc
Confidence 4677899999999999999999999999976 46999999999999999998543
No 16
>KOG3898 consensus Transcription factor NeuroD and related HTH proteins [Transcription]
Probab=93.68 E-value=0.068 Score=51.17 Aligned_cols=56 Identities=29% Similarity=0.423 Sum_probs=49.7
Q ss_pred ccccccccCchHHHHHHHHHHHHHHHHhccCCCC--CCCCChhhhhHHHHHHHHHHHH
Q 019960 41 KASVIRSKHSVTEQRRRSKINERFQILREIIPHS--DQKRDTASFLLEVIEYVQYLQE 96 (333)
Q Consensus 41 k~~~rr~~H~~~ERrRR~rINe~f~~LrsLVP~~--~~K~DKasIL~~AIeYIk~Lq~ 96 (333)
....+|.+-|..||+|=-.+|+.|..||.+||.. +.|+.|+..|.-|-.||..|++
T Consensus 68 ~~~~rR~kaNaRER~RMH~LNdAld~LReviP~~~~~~klskIetl~~a~~yi~als~ 125 (254)
T KOG3898|consen 68 ALTLRRLKANARERTRMHDLNDALDALREVIPHGLHPPKLSKIETLRLAANYIAALSE 125 (254)
T ss_pred hhhhhcccccchhhccccchhHHHHHhHhhccCcCCCCCCCcchhHHhhhcchhhhcc
Confidence 4566788889999999999999999999999943 6899999999999999998874
No 17
>KOG3558 consensus Hypoxia-inducible factor 1/Neuronal PAS domain protein NPAS1 [Signal transduction mechanisms; Transcription]
Probab=91.78 E-value=0.12 Score=55.80 Aligned_cols=50 Identities=30% Similarity=0.438 Sum_probs=42.6
Q ss_pred cccccCchHHHHHHHHHHHHHHHHhccCCCC---CCCCChhhhhHHHHHHHHH
Q 019960 44 VIRSKHSVTEQRRRSKINERFQILREIIPHS---DQKRDTASFLLEVIEYVQY 93 (333)
Q Consensus 44 ~rr~~H~~~ERrRR~rINe~f~~LrsLVP~~---~~K~DKasIL~~AIeYIk~ 93 (333)
.||++-.-+-|.||.|-|+-|.+|..+||-. ...+|||+|+.-||-|++-
T Consensus 45 ~rkEkSRdAARsRRsKEn~~FyeLa~~lPlp~aisshLDkaSimRLtISyLRl 97 (768)
T KOG3558|consen 45 LRKEKSRDAARSRRSKENEEFYELAKLLPLPAAISSHLDKASIMRLTISYLRL 97 (768)
T ss_pred HHhhhhhhhhhhhcccchHHHHHHHHhCCCcchhhhhhhhHHHHHHHHHHHHH
Confidence 3466666778999999999999999999942 4689999999999999974
No 18
>KOG4395 consensus Transcription factor Atonal, contains HTH domain [Transcription]
Probab=89.40 E-value=0.52 Score=45.66 Aligned_cols=56 Identities=27% Similarity=0.317 Sum_probs=49.6
Q ss_pred ccccccCchHHHHHHHHHHHHHHHHhccCCCC--CCCCChhhhhHHHHHHHHHHHHHH
Q 019960 43 SVIRSKHSVTEQRRRSKINERFQILREIIPHS--DQKRDTASFLLEVIEYVQYLQEKV 98 (333)
Q Consensus 43 ~~rr~~H~~~ERrRR~rINe~f~~LrsLVP~~--~~K~DKasIL~~AIeYIk~Lq~~v 98 (333)
..+|..-+..||+|=..+|..|..||..||.. +.|++|-..|.-|-.||--|-..+
T Consensus 172 ~~rr~aanarErrrm~gLN~AfD~Lr~v~p~~~~d~~LSkyetLqmaq~yi~~l~~~l 229 (285)
T KOG4395|consen 172 SHRRLAANARERRRMNGLNSAFDRLRLVVPDGDSDKKLSKYETLQMAQGYILALGCLL 229 (285)
T ss_pred HhhhcccchHHHHHhhhHHHHHHHHHHhcCCCCccchhhhhhHHHHHHHHHhhhHHhh
Confidence 35677888999999999999999999999975 689999999999999998886554
No 19
>KOG3582 consensus Mlx interactors and related transcription factors [Transcription]
Probab=87.47 E-value=0.16 Score=54.84 Aligned_cols=76 Identities=21% Similarity=0.271 Sum_probs=60.1
Q ss_pred cccccccCchHHHHHHHHHHHHHHHHhccCCCC----CCCCChhhhhHHHHHHHHHHHHHHHHHHhhhcccccCcccccc
Q 019960 42 ASVIRSKHSVTEQRRRSKINERFQILREIIPHS----DQKRDTASFLLEVIEYVQYLQEKVQKYEVSYQDWSAEPTKLMP 117 (333)
Q Consensus 42 ~~~rr~~H~~~ERrRR~rINe~f~~LrsLVP~~----~~K~DKasIL~~AIeYIk~Lq~~v~~Le~~~~~l~~e~~~l~p 117 (333)
...+...|+-+|++||.+|+-+|..|-.++-+. ..|+.+..-+...++||-.++.+...+..+...+..+...++.
T Consensus 648 ~k~r~it~~Sa~qkrr~n~kl~~~~~Ns~~Sn~~~l~s~k~t~~~~~q~~vhYi~~t~~e~~~v~~e~~~lr~~~s~~~A 727 (856)
T KOG3582|consen 648 AKNRPITHISAEQKRRFNIKLQFDVLNSLSSNSSSLSSIKTTNSNSLQKTVHYINVTQQERVPVQEEAHSLRKEISELNA 727 (856)
T ss_pred ccCCcccCccHHHHHHhhHHhhhHhhhhhccCcccccchhhhccccccCceeeeeccchhccccchhhhhhhhhhHHHHH
Confidence 446788999999999999999999999988754 3588888889999999999987776666555555555544443
No 20
>KOG3560 consensus Aryl-hydrocarbon receptor [Transcription]
Probab=85.59 E-value=0.69 Score=49.13 Aligned_cols=39 Identities=26% Similarity=0.473 Sum_probs=35.3
Q ss_pred HHHHHHHHHHHHHHhccCCCC---CCCCChhhhhHHHHHHHH
Q 019960 54 QRRRSKINERFQILREIIPHS---DQKRDTASFLLEVIEYVQ 92 (333)
Q Consensus 54 RrRR~rINe~f~~LrsLVP~~---~~K~DKasIL~~AIeYIk 92 (333)
+|-|+|+|.-+..|.+|+|-. ..|+||.+||.-++.|++
T Consensus 34 KRHRdRLNaELD~lAsLLPfpqdiisKLDkLSVLRLSVSyLr 75 (712)
T KOG3560|consen 34 KRHRDRLNAELDHLASLLPFPQDIISKLDKLSVLRLSVSYLR 75 (712)
T ss_pred hhHHHHhhhHHHHHHHhcCCCHHHHhhhhhhhhhhhhHHHHH
Confidence 566899999999999999964 479999999999999987
No 21
>KOG3559 consensus Transcriptional regulator SIM1 [Transcription]
Probab=84.34 E-value=0.99 Score=46.60 Aligned_cols=44 Identities=25% Similarity=0.357 Sum_probs=38.3
Q ss_pred hHHHHHHHHHHHHHHHHhccCCCC---CCCCChhhhhHHHHHHHHHH
Q 019960 51 VTEQRRRSKINERFQILREIIPHS---DQKRDTASFLLEVIEYVQYL 94 (333)
Q Consensus 51 ~~ERrRR~rINe~f~~LrsLVP~~---~~K~DKasIL~~AIeYIk~L 94 (333)
-+-|.||++-|..|.+|..++|-. ...+||++|+.-+..|||.-
T Consensus 7 naA~tRRekEN~EF~eLAklLPLa~AItsQlDKasiiRLtTsYlKmr 53 (598)
T KOG3559|consen 7 NAARTRREKENYEFYELAKLLPLASAITSQLDKASIIRLTTSYLKMR 53 (598)
T ss_pred hHHHHHHHhhcchHHHHHhhccchhhhhhccchhhhhhHHHHHHHHH
Confidence 456889999999999999999954 45799999999999999854
No 22
>cd04895 ACT_ACR_1 ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). This CD includes the N-terminal ACT domain, of a novel type of ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). ACR proteins, found only in Arabidopsis and Oryza, as yet, are proposed to function as novel regulatory or sensor proteins in plants. Nine ACR gene products have been described (ACR1-8 in Arabidopsis and OsARC1-9 in Oryza) and are represented in this CD. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=67.39 E-value=3.7 Score=32.27 Aligned_cols=38 Identities=24% Similarity=0.286 Sum_probs=32.7
Q ss_pred eeeehhhhhhHHHHHHHHHHHcCCCCCCCeeEEEEecCccc
Q 019960 248 INISSIYSQGLLNNLTQALESAGIDLSQANISVQIDLGKRA 288 (333)
Q Consensus 248 isiss~ysqgll~~lt~al~~sgvdlsqa~isvqi~lgkr~ 288 (333)
|.|+..=-.|||..++++|...|+++..|.|+= +|-|+
T Consensus 4 iev~a~DRpGLL~~i~~~l~~~gl~I~~AkIsT---~Gerv 41 (72)
T cd04895 4 VKVDSARKPGILLEAVQVLTDLDLCITKAYISS---DGGWF 41 (72)
T ss_pred EEEEECCcCCHHHHHHHHHHHCCcEEEEEEEee---cCCeE
Confidence 567777788999999999999999999999984 45555
No 23
>KOG4447 consensus Transcription factor TWIST [Transcription]
Probab=65.44 E-value=5.3 Score=36.32 Aligned_cols=45 Identities=20% Similarity=0.293 Sum_probs=35.0
Q ss_pred HHHHHHHHHHHHHHHHhccCCCC-CCCCChhhhhHHHHHHHHHHHH
Q 019960 52 TEQRRRSKINERFQILREIIPHS-DQKRDTASFLLEVIEYVQYLQE 96 (333)
Q Consensus 52 ~ERrRR~rINe~f~~LrsLVP~~-~~K~DKasIL~~AIeYIk~Lq~ 96 (333)
.|+.|..++++.|.-|+.|+|+. ..++.+.--|..+-+||++|.+
T Consensus 29 ~e~~R~~~ls~~s~l~g~l~pgspa~gk~~~ktlr~~~~~~~~~dE 74 (173)
T KOG4447|consen 29 KERGRKRRLSDASTLLGKLEPGSPADGKRGKKTLRIGTDSIQSLDE 74 (173)
T ss_pred HHHhHHhhhhhhhhhccccCCCCCCcccccccccccCCCchhhHHH
Confidence 68899999999999999999987 3344444447777777777754
No 24
>PF01316 Arg_repressor: Arginine repressor, DNA binding domain; InterPro: IPR020900 The arginine dihydrolase (AD) pathway is found in many prokaryotes and some primitive eukaryotes, an example of the latter being Giardia lamblia (Giardia intestinalis) []. The three-enzyme anaerobic pathway breaks down L-arginine to form 1 mol of ATP, carbon dioxide and ammonia. In simpler bacteria, the first enzyme, arginine deiminase, can account for up to 10% of total cell protein []. Most prokaryotic arginine deiminase pathways are under the control of a repressor gene, termed ArgR []. This is a negative regulator, and will only release the arginine deiminase operon for expression in the presence of arginine []. The crystal structure of apo-ArgR from Bacillus stearothermophilus has been determined to 2.5A by means of X-ray crystallography []. The protein exists as a hexamer of identical subunits, and is shown to have six DNA-binding domains, clustered around a central oligomeric core when bound to arginine. It predominantly interacts with A.T residues in ARG boxes. This hexameric protein binds DNA at its N terminus to repress arginine biosyntheis or activate arginine catabolism. Some species have several ArgR paralogs. In a neighbour-joining tree, some of these paralogous sequences show long branches and differ significantly from the well-conserved C-terminal region. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0006525 arginine metabolic process; PDB: 1AOY_A 3V4G_A 3LAJ_D 3FHZ_A 3LAP_B 3ERE_D 2P5L_C 1F9N_D 2P5K_A 1B4A_A ....
Probab=59.54 E-value=2.5 Score=33.18 Aligned_cols=20 Identities=45% Similarity=0.660 Sum_probs=14.2
Q ss_pred HHHHHHHHcCCCCCCCeeEE
Q 019960 261 NLTQALESAGIDLSQANISV 280 (333)
Q Consensus 261 ~lt~al~~sgvdlsqa~isv 280 (333)
-|-++|+..|++.+||+||=
T Consensus 24 eL~~~L~~~Gi~vTQaTiSR 43 (70)
T PF01316_consen 24 ELVELLEEEGIEVTQATISR 43 (70)
T ss_dssp HHHHHHHHTT-T--HHHHHH
T ss_pred HHHHHHHHcCCCcchhHHHH
Confidence 46678899999999999983
No 25
>KOG3582 consensus Mlx interactors and related transcription factors [Transcription]
Probab=53.60 E-value=4 Score=44.67 Aligned_cols=64 Identities=13% Similarity=0.137 Sum_probs=52.0
Q ss_pred ccccccccCchHHHHHHHHHHHHHHHHhccCCCC----CCCCChhhhhHHHHHHHHHHHHHHHHHHhhhcc
Q 019960 41 KASVIRSKHSVTEQRRRSKINERFQILREIIPHS----DQKRDTASFLLEVIEYVQYLQEKVQKYEVSYQD 107 (333)
Q Consensus 41 k~~~rr~~H~~~ERrRR~rINe~f~~LrsLVP~~----~~K~DKasIL~~AIeYIk~Lq~~v~~Le~~~~~ 107 (333)
...-.+..|.-++||||..+.++|..|..|+|.. .++..+++||. +-|+.++..-+.+....++
T Consensus 783 ~n~~v~a~sih~lrr~~~~~~dq~~sL~alrp~v~~~~~ql~S~tS~L~---dp~~~~eq~ska~~e~~~~ 850 (856)
T KOG3582|consen 783 FNGMVSAGSIHALRRTRLNWLDQFCSLPALRPQVLLNLRQLLSSTSILT---DPIKQPEQASKAVTEKIEG 850 (856)
T ss_pred ccceeecchHHHHHHHHHHHhhccccHHHHHHHHHhhHHHhhhhhhccc---CcccchHHHHHHHHhhhhh
Confidence 3445678899999999999999999999999964 56889999998 8888888776666654443
No 26
>PRK04280 arginine repressor; Provisional
Probab=50.83 E-value=5.4 Score=35.39 Aligned_cols=23 Identities=30% Similarity=0.540 Sum_probs=20.0
Q ss_pred HHHHHHHHcCCCCCCCeeEEEEe
Q 019960 261 NLTQALESAGIDLSQANISVQID 283 (333)
Q Consensus 261 ~lt~al~~sgvdlsqa~isvqi~ 283 (333)
-|-++|+..|++.+||+||=.|.
T Consensus 23 eL~~~L~~~Gi~vTQATiSRDik 45 (148)
T PRK04280 23 ELVDRLREEGFNVTQATVSRDIK 45 (148)
T ss_pred HHHHHHHHcCCCeehHHHHHHHH
Confidence 46788999999999999997665
No 27
>cd04897 ACT_ACR_3 ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). This CD includes the third ACT domain, of a novel type of ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). ACR proteins, found only in Arabidopsis and Oryza, as yet, are proposed to function as novel regulatory or sensor proteins in plants. Nine ACR gene products have been described (ACR1-8 in Arabidopsis and OsARC1-9 in Oryza) and are represented in this CD. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=48.46 E-value=11 Score=29.82 Aligned_cols=38 Identities=18% Similarity=0.181 Sum_probs=33.0
Q ss_pred eeeehhhhhhHHHHHHHHHHHcCCCCCCCeeEEEEecCccc
Q 019960 248 INISSIYSQGLLNNLTQALESAGIDLSQANISVQIDLGKRA 288 (333)
Q Consensus 248 isiss~ysqgll~~lt~al~~sgvdlsqa~isvqi~lgkr~ 288 (333)
|.|+.-.-.|||..++.+|-.-|+++..|.|+= .|-|+
T Consensus 4 veV~~~DRpGLL~~i~~~l~~~~l~I~~A~I~T---~gera 41 (75)
T cd04897 4 VTVQCRDRPKLLFDVVCTLTDMDYVVFHATIDT---DGDDA 41 (75)
T ss_pred EEEEeCCcCcHHHHHHHHHHhCCeEEEEEEEee---cCceE
Confidence 567777789999999999999999999999986 56565
No 28
>cd04896 ACT_ACR-like_3 ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). This CD includes the third ACT domain, of a novel type of ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). ACR proteins, found only in Arabidopsis and Oryza, as yet, are proposed to function as novel regulatory or sensor proteins in plants. Nine ACR gene products (ACR1-8 in Arabidopsis and OsARC1-9 in Oryza) have been described, however, the ACR-like sequences in this CD are distinct from those characterized. This CD includes the Oryza sativa ACR-like protein (Os05g0113000) encoded on chromosome 5 and the Arabidopsis thaliana predicted gene product, At2g39570. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=47.07 E-value=13 Score=29.40 Aligned_cols=32 Identities=22% Similarity=0.429 Sum_probs=27.8
Q ss_pred eeeehhhhhhHHHHHHHHHHHcCCCCCCCeeE
Q 019960 248 INISSIYSQGLLNNLTQALESAGIDLSQANIS 279 (333)
Q Consensus 248 isiss~ysqgll~~lt~al~~sgvdlsqa~is 279 (333)
|.|...=-+|||..+.++|...||++.-|.|+
T Consensus 3 lev~a~DRpGLL~~i~~~l~~~~l~i~~AkI~ 34 (75)
T cd04896 3 LQIRCVDQKGLLYDILRTSKDCNIQISYGRFS 34 (75)
T ss_pred EEEEeCCcccHHHHHHHHHHHCCeEEEEEEEe
Confidence 44555556899999999999999999999998
No 29
>cd04900 ACT_UUR-like_1 ACT domain family, ACT_UUR-like_1, includes the first of two C-terminal ACT domains of the bacterial signal-transducing uridylyltransferase /uridylyl-removing (UUR) enzyme, GlnD and related domains. This ACT domain family, ACT_UUR-like_1, includes the first of two C-terminal ACT domains of the bacterial signal-transducing uridylyltransferase /uridylyl-removing (UUR) enzyme, GlnD; including those enzymes similar to the GlnD found in enteric Escherichia coli and those found in photosynthetic, nitrogen-fixing bacterium Rhodospirillum rubrum. Also included in this CD is the N-terminal ACT domain of a yet characterized Arabidopsis/Oryza predicted tyrosine kinase. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=45.56 E-value=20 Score=27.12 Aligned_cols=33 Identities=24% Similarity=0.385 Sum_probs=27.8
Q ss_pred eeeehhhhhhHHHHHHHHHHHcCCCCCCCeeEE
Q 019960 248 INISSIYSQGLLNNLTQALESAGIDLSQANISV 280 (333)
Q Consensus 248 isiss~ysqgll~~lt~al~~sgvdlsqa~isv 280 (333)
|.|...=-.|||..++.+|...|+++-.|.|.-
T Consensus 4 i~v~~~Dr~gLl~~i~~~l~~~~l~I~~A~i~T 36 (73)
T cd04900 4 VFIYTPDRPGLFARIAGALDQLGLNILDARIFT 36 (73)
T ss_pred EEEEecCCCCHHHHHHHHHHHCCCCeEEeEEEE
Confidence 455555578999999999999999999999853
No 30
>cd04919 ACT_AK-Hom3_2 ACT domains located C-terminal to the catalytic domain of the aspartokinase (AK) HOM3. This CD includes the second of two ACT domains located C-terminal to the catalytic domain of the aspartokinase (AK) HOM3, a monofunctional class enzyme found in Saccharomyces cerevisiae, and other related ACT domains. AK is the first enzyme in the aspartate metabolic pathway, catalyzes the conversion of aspartate and ATP to aspartylphosphate and ADP, and in fungi, is responsible for the production of threonine, isoleucine and methionine. S. cerevisiae has a single AK, which is regulated by feedback, allosteric inhibition by L-threonine. Recent studies shown that the allosteric transition triggered by binding of threonine to AK involves a large change in the conformation of the native hexameric enzyme that is converted to an inactive one of different shape and substantially smaller hydrodynamic size. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=45.21 E-value=31 Score=24.82 Aligned_cols=28 Identities=32% Similarity=0.480 Sum_probs=23.3
Q ss_pred hhHHHHHHHHHHHcCCCC-------CCCeeEEEEe
Q 019960 256 QGLLNNLTQALESAGIDL-------SQANISVQID 283 (333)
Q Consensus 256 qgll~~lt~al~~sgvdl-------sqa~isvqi~ 283 (333)
.|++..+.++|...||++ |..+||+-|+
T Consensus 15 ~~~~~~if~~L~~~~I~v~~i~q~~s~~~isf~v~ 49 (66)
T cd04919 15 IGIAGRMFTTLADHRINIEMISQGASEINISCVID 49 (66)
T ss_pred cCHHHHHHHHHHHCCCCEEEEEecCccceEEEEEe
Confidence 689999999999999998 6666776664
No 31
>cd04922 ACT_AKi-HSDH-ThrA_2 ACT domains of the bifunctional enzyme aspartokinase (AK) - homoserine dehydrogenase (HSDH). This CD includes the second of two ACT domains of the bifunctional enzyme aspartokinase (AK) - homoserine dehydrogenase (HSDH). The ACT domains are positioned between the N-terminal catalytic domain of AK and the C-terminal HSDH domain found in bacteria (Escherichia coli (EC) ThrA) and higher plants (Zea mays AK-HSDH). AK and HSDH are the first and third enzymes in the biosynthetic pathway of the aspartate family of amino acids. AK catalyzes the phosphorylation of Asp to P-aspartyl phosphate. HSDH catalyzes the NADPH-dependent conversion of Asp 3-semialdehyde to homoserine. HSDH is the first committed reaction in the branch of the pathway that leads to Thr and Met. In E. coli, ThrA is subject to allosteric regulation by the end product L-threonine and the native enzyme is reported to be tetrameric. As with bacteria, plant AK and HSDH are feedback inhibited by pathwa
Probab=43.56 E-value=35 Score=24.35 Aligned_cols=29 Identities=34% Similarity=0.538 Sum_probs=23.4
Q ss_pred hhhHHHHHHHHHHHcCCCC-------CCCeeEEEEe
Q 019960 255 SQGLLNNLTQALESAGIDL-------SQANISVQID 283 (333)
Q Consensus 255 sqgll~~lt~al~~sgvdl-------sqa~isvqi~ 283 (333)
.+|++.++.++|.+.||.+ |+-+||+-|+
T Consensus 14 ~~~~~~~i~~~l~~~~I~v~~i~~~~s~~~is~~v~ 49 (66)
T cd04922 14 TPGVAATFFSALAKANVNIRAIAQGSSERNISAVID 49 (66)
T ss_pred CccHHHHHHHHHHHCCCCEEEEEecCcccEEEEEEe
Confidence 4799999999999999988 5556666654
No 32
>cd04915 ACT_AK-Ectoine_2 ACT domains located C-terminal to the catalytic domain of the aspartokinase of the ectoine (1,4,5,6-tetrahydro-2-methyl pyrimidine-4-carboxylate) biosynthetic pathway. This CD includes the second of two ACT domains located C-terminal to the catalytic domain of the aspartokinase of the ectoine (1,4,5,6-tetrahydro-2-methyl pyrimidine-4-carboxylate) biosynthetic pathway found in Methylomicrobium alcaliphilum, Vibrio cholerae, and various other halotolerant or halophilic bacteria. Bacteria exposed to hyperosmotic stress accumulate organic solutes called 'compatible solutes' of which ectoine, a heterocyclic amino acid, is one. Apart from its osmotic function, ectoine also exhibits a protective effect on proteins, nucleic acids and membranes against a variety of stress factors. de novo synthesis of ectoine starts with the phosphorylation of L-aspartate and shares its first two enzymatic steps with the biosynthesis of amino acids of the aspartate family: aspartokinas
Probab=43.31 E-value=35 Score=25.56 Aligned_cols=28 Identities=29% Similarity=0.463 Sum_probs=23.5
Q ss_pred hhHHHHHHHHHHHcCCCC-------CCCeeEEEEe
Q 019960 256 QGLLNNLTQALESAGIDL-------SQANISVQID 283 (333)
Q Consensus 256 qgll~~lt~al~~sgvdl-------sqa~isvqi~ 283 (333)
.|++.++.+||...||++ |.-+||+=|+
T Consensus 15 ~gv~~ki~~~L~~~~I~v~~i~~~~s~~~is~~V~ 49 (66)
T cd04915 15 PGVLARGLAALAEAGIEPIAAHQSMRNVDVQFVVD 49 (66)
T ss_pred chHHHHHHHHHHHCCCCEEEEEecCCeeEEEEEEE
Confidence 589999999999999999 6567777664
No 33
>PRK05066 arginine repressor; Provisional
Probab=39.11 E-value=9.8 Score=34.11 Aligned_cols=23 Identities=26% Similarity=0.544 Sum_probs=19.4
Q ss_pred HHHHHHHHcCCC-CCCCeeEEEEe
Q 019960 261 NLTQALESAGID-LSQANISVQID 283 (333)
Q Consensus 261 ~lt~al~~sgvd-lsqa~isvqi~ 283 (333)
-|-+.|+..|++ .+||+||=-|.
T Consensus 28 eL~~~L~~~Gi~~vTQATiSRDik 51 (156)
T PRK05066 28 EIVTALQEQGFDNINQSKVSRMLT 51 (156)
T ss_pred HHHHHHHHCCCCeecHHHHHHHHH
Confidence 467789999999 99999997554
No 34
>cd04937 ACT_AKi-DapG-BS_2 ACT domains of the diaminopimelate-sensitive aspartokinase (AK) isoenzyme AKI. This CD includes the C-terminal of the two ACT domains of the diaminopimelate-sensitive aspartokinase (AK) isoenzyme AKI, a monofunctional class enzyme found in Bacilli (Bacillus subtilis (BS) strain 168), Clostridia, and Actinobacteria bacterial species. In B. subtilis, the regulation of the diaminopimelate-lysine biosynthetic pathway involves dual control by diaminopimelate and lysine, effected through separate diaminopimelate- and lysine-sensitive AK isoenzymes. AKI activity is invariant during the exponential and stationary phases of growth and is not altered by addition of amino acids to the growth medium. The role of this isoenzyme is most likely to provide a constant level of aspartyl-beta-phosphate for the biosynthesis of diaminopimelate for peptidoglycan synthesis and dipicolinate during sporulation. The BS AKI is tetrameric consisting of two alpha and two beta subunits; th
Probab=38.17 E-value=46 Score=24.43 Aligned_cols=29 Identities=28% Similarity=0.550 Sum_probs=22.4
Q ss_pred hhhHHHHHHHHHHHcCCCC-----CCCeeEEEEe
Q 019960 255 SQGLLNNLTQALESAGIDL-----SQANISVQID 283 (333)
Q Consensus 255 sqgll~~lt~al~~sgvdl-----sqa~isvqi~ 283 (333)
..|++.++++||...||.+ |+-+||+=|+
T Consensus 14 ~~gi~~~if~aL~~~~I~v~~~~~Se~~is~~v~ 47 (64)
T cd04937 14 VPGVMAKIVGALSKEGIEILQTADSHTTISCLVS 47 (64)
T ss_pred CcCHHHHHHHHHHHCCCCEEEEEcCccEEEEEEc
Confidence 5789999999999999998 4444555443
No 35
>cd04927 ACT_ACR-like_2 Second ACT domain, of a novel type of ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). This CD includes the second ACT domain, of a novel type of ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). ACR proteins, found only in Arabidopsis and Oryza, as yet, are proposed to function as novel regulatory or sensor proteins in plants. Nine ACR gene products (ACR1-8 in Arabidopsis and OsARC1-9 in Oryza) have been described, however, the ACR-like sequences in this CD are distinct from those characterized. This CD includes the Oryza sativa ACR-like protein (Os05g0113000) encoded on chromosome 5 and the Arabidopsis thaliana predicted gene product, At2g39570. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=36.58 E-value=26 Score=27.07 Aligned_cols=33 Identities=18% Similarity=0.380 Sum_probs=27.7
Q ss_pred eeeehhhhhhHHHHHHHHHHHcCCCCCCCeeEE
Q 019960 248 INISSIYSQGLLNNLTQALESAGIDLSQANISV 280 (333)
Q Consensus 248 isiss~ysqgll~~lt~al~~sgvdlsqa~isv 280 (333)
+.|...=..|||..++.+|...|+++-.|.|+-
T Consensus 3 ~ei~~~Dr~gLfa~i~~~l~~~~l~I~~A~I~T 35 (76)
T cd04927 3 LKLFCSDRKGLLHDVTEVLYELELTIERVKVST 35 (76)
T ss_pred EEEEECCCCCHHHHHHHHHHHCCCeEEEEEEEE
Confidence 445555578999999999999999999998863
No 36
>PRK03341 arginine repressor; Provisional
Probab=33.61 E-value=14 Score=33.67 Aligned_cols=23 Identities=35% Similarity=0.612 Sum_probs=19.6
Q ss_pred HHHHHHHHcCCCCCCCeeEEEEe
Q 019960 261 NLTQALESAGIDLSQANISVQID 283 (333)
Q Consensus 261 ~lt~al~~sgvdlsqa~isvqi~ 283 (333)
-|-+.|+..|++.+||+||=.|.
T Consensus 34 eL~~~L~~~Gi~vTQaTiSRDl~ 56 (168)
T PRK03341 34 ELAALLADEGIEVTQATLSRDLD 56 (168)
T ss_pred HHHHHHHHcCCcccHHHHHHHHH
Confidence 56788999999999999996554
No 37
>cd04899 ACT_ACR-UUR-like_2 C-terminal ACT domains of the bacterial signal-transducing uridylyltransferase /uridylyl-removing (UUR) enzyme, GlnD and related domains. This ACT domain family, ACT_ACR-UUR-like_2, includes the second of two C-terminal ACT domains of the bacterial signal-transducing uridylyltransferase /uridylyl-removing (UUR) enzyme, GlnD; including those enzymes similar to the GlnD found in enteric Escherichia coli and those found in photosynthetic, nitrogen-fixing bacterium Rhodospirillum rubrum. Also included in this CD are the second and fourth ACT domains of a novel protein composed almost entirely of ACT domain repeats, the ACR protein. These ACR proteins, found in Arabidopsis and Oryza, are proposed to function as novel regulatory or sensor proteins in plants. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=31.57 E-value=40 Score=24.47 Aligned_cols=32 Identities=25% Similarity=0.592 Sum_probs=26.1
Q ss_pred eeeehhhhhhHHHHHHHHHHHcCCCCCCCeeE
Q 019960 248 INISSIYSQGLLNNLTQALESAGIDLSQANIS 279 (333)
Q Consensus 248 isiss~ysqgll~~lt~al~~sgvdlsqa~is 279 (333)
|.|-..-..|||..|+.+|.+.|+++-.+.+.
T Consensus 3 l~v~~~d~~gll~~i~~~l~~~~~~I~~~~~~ 34 (70)
T cd04899 3 LELTALDRPGLLADVTRVLAELGLNIHSAKIA 34 (70)
T ss_pred EEEEEcCCccHHHHHHHHHHHCCCeEEEEEEE
Confidence 44555667899999999999999999777654
No 38
>cd04869 ACT_GcvR_2 ACT domains that comprise the Glycine Cleavage System Transcriptional Repressor (GcvR) protein, and other related domains. This CD includes the second of the two ACT domains that comprise the Glycine Cleavage System Transcriptional Repressor (GcvR) protein, and other related domains. The glycine cleavage enzyme system in Escherichia coli provides one-carbon units for cellular methylation reactions. This enzyme system, encoded by the gcvTHP operon and lpd gene, catalyzes the cleavage of glycine into CO2 + NH3 and transfers a one-carbon unit to tetrahydrofolate, producing 5,10-methylenetetrahydrofolate. The gcvTHP operon is activated by the GcvA protein in response to glycine and repressed by a GcvA/GcvR interaction in the absence of glycine. It has been proposed that the co-activator glycine acts through a mechanism of de-repression by binding to GcvR and preventing GcvR from interacting with GcvA to block GcvA's activator function. Evidence also suggests that GcvR in
Probab=28.90 E-value=46 Score=24.99 Aligned_cols=31 Identities=16% Similarity=0.342 Sum_probs=25.2
Q ss_pred eeeehhhhhhHHHHHHHHHHHcCCCCCCCee
Q 019960 248 INISSIYSQGLLNNLTQALESAGIDLSQANI 278 (333)
Q Consensus 248 isiss~ysqgll~~lt~al~~sgvdlsqa~i 278 (333)
|+|......||+..+++.|...|+++-..+.
T Consensus 2 l~v~g~D~~Giv~~it~~l~~~~~nI~~~~~ 32 (81)
T cd04869 2 VEVVGNDRPGIVHEVTQFLAQRNINIEDLST 32 (81)
T ss_pred EEEEeCCCCCHHHHHHHHHHHcCCCeEEeEe
Confidence 4566667889999999999999999865443
No 39
>cd02116 ACT ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme. Members of this CD belong to the superfamily of ACT regulatory domains. Pairs of ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme. The ACT domain has been detected in a number of diverse proteins; some of these proteins are involved in amino acid and purine biosynthesis, phenylalanine hydroxylation, regulation of bacterial metabolism and transcription, and many remain to be characterized. ACT domain-containing enzymes involved in amino acid and purine synthesis are in many cases allosteric enzymes with complex regulation enforced by the binding of ligands. The ACT domain is commonly involved in the binding of a small regulatory molecule, such as the amino acids L-Ser and L-Phe in the case of D-3-phosphoglycerate dehydrogenase and the bifunctional chorismate mutase-p
Probab=28.22 E-value=54 Score=20.62 Aligned_cols=30 Identities=27% Similarity=0.420 Sum_probs=23.2
Q ss_pred eehhhhhhHHHHHHHHHHHcCCCCCCCeeE
Q 019960 250 ISSIYSQGLLNNLTQALESAGIDLSQANIS 279 (333)
Q Consensus 250 iss~ysqgll~~lt~al~~sgvdlsqa~is 279 (333)
|......|+|..+.++|...|+++...+.+
T Consensus 3 i~~~~~~~~l~~i~~~l~~~~~~i~~~~~~ 32 (60)
T cd02116 3 VSGPDRPGLLAKVLSVLAEAGINITSIEQR 32 (60)
T ss_pred EEecCCCchHHHHHHHHHHCCCcEEEEEeE
Confidence 344446789999999999999998765543
No 40
>cd04916 ACT_AKiii-YclM-BS_2 ACT domains located C-terminal to the catalytic domain of the lysine plus threonine-sensitive aspartokinase isoenzyme AKIII. This CD includes the second of two ACT domains located C-terminal to the catalytic domain of the lysine plus threonine-sensitive aspartokinase isoenzyme AKIII, a monofunctional class enzyme found in Bacilli (Bacillus subtilis (BS) YclM) and Clostridia species. Aspartokinase is the first enzyme in the aspartate metabolic pathway and catalyzes the conversion of aspartate and ATP to aspartylphosphate and ADP. B. subtilis YclM is reported to be a single polypeptide of 50 kD. AKIII from B. subtilis strain 168 is induced by lysine and repressed by threonine and it is synergistically inhibited by lysine and threonine. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=27.41 E-value=89 Score=22.15 Aligned_cols=30 Identities=30% Similarity=0.458 Sum_probs=23.5
Q ss_pred hhhHHHHHHHHHHHcCCCC-------CCCeeEEEEec
Q 019960 255 SQGLLNNLTQALESAGIDL-------SQANISVQIDL 284 (333)
Q Consensus 255 sqgll~~lt~al~~sgvdl-------sqa~isvqi~l 284 (333)
.+|++..+..+|...||++ +..+||+-|+-
T Consensus 14 ~~~~~~~i~~~L~~~~i~v~~i~~~~s~~~isf~v~~ 50 (66)
T cd04916 14 TVGVSARATAALAKAGINIRMINQGSSEISIMIGVHN 50 (66)
T ss_pred CccHHHHHHHHHHHCCCCEEEEEecCcccEEEEEEeH
Confidence 3688999999999999998 55566666654
No 41
>PF01842 ACT: ACT domain; InterPro: IPR002912 The ACT domain is found in a variety of contexts and is proposed to be a conserved regulatory binding fold. ACT domains are linked to a wide range of metabolic enzymes that are regulated by amino acid concentration. The archetypical ACT domain is the C-terminal regulatory domain of 3-phosphoglycerate dehydrogenase (3PGDH), which folds with a ferredoxin-like topology. A pair of ACT domains form an eight-stranded antiparallel sheet with two molecules of allosteric inhibitor serine bound in the interface. Biochemical exploration of a few other proteins containing ACT domains supports the suggestions that these domains contain the archetypical ACT structure [].; GO: 0016597 amino acid binding, 0008152 metabolic process; PDB: 3L76_B 2F06_B 3NRB_C 1Y7P_C 2QMX_A 2DT9_A 2ZHO_D 3K5P_A 3TVI_K 3C1M_C ....
Probab=26.22 E-value=43 Score=23.64 Aligned_cols=28 Identities=25% Similarity=0.449 Sum_probs=23.2
Q ss_pred hhhhHHHHHHHHHHHcCCCCCCCeeEEE
Q 019960 254 YSQGLLNNLTQALESAGIDLSQANISVQ 281 (333)
Q Consensus 254 ysqgll~~lt~al~~sgvdlsqa~isvq 281 (333)
=..|+|..++++|-..||++..+.+...
T Consensus 9 drpG~l~~v~~~la~~~inI~~~~~~~~ 36 (66)
T PF01842_consen 9 DRPGILADVTEILADHGINIDSISQSSD 36 (66)
T ss_dssp TSTTHHHHHHHHHHHTTEEEEEEEEEEE
T ss_pred CCCCHHHHHHHHHHHcCCCHHHeEEEec
Confidence 3579999999999999999987766543
No 42
>COG4710 Predicted DNA-binding protein with an HTH domain [General function prediction only]
Probab=26.12 E-value=1.3e+02 Score=24.33 Aligned_cols=33 Identities=27% Similarity=0.533 Sum_probs=22.6
Q ss_pred HHHHHHHHHhccCCCCCCCCChhhhhHHHHH-HHHHHHH
Q 019960 59 KINERFQILREIIPHSDQKRDTASFLLEVIE-YVQYLQE 96 (333)
Q Consensus 59 rINe~f~~LrsLVP~~~~K~DKasIL~~AIe-YIk~Lq~ 96 (333)
.+.+++..|..- .-..|+.++.+||+ ||.+++.
T Consensus 15 E~~eRL~~Ls~~-----tgrtkayyvrEaIE~~ieemED 48 (80)
T COG4710 15 ELKERLDNLSKN-----TGRTKAYYVREAIEAYIEEMED 48 (80)
T ss_pred HHHHHHHHHHHh-----cCCchhHHHHHHHHHHHHHHHH
Confidence 355666666653 34459999999997 6766654
No 43
>cd04925 ACT_ACR_2 ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). This CD includes the second ACT domain, of a novel type of ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). ACR proteins, found only in Arabidopsis and Oryza, as yet, are proposed to function as novel regulatory or sensor proteins in plants. Nine ACR gene products have been described (ACR1-8 in Arabidopsis and OsARC1-9 in Oryza) and are represented in this CD. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=25.90 E-value=58 Score=24.81 Aligned_cols=37 Identities=16% Similarity=0.206 Sum_probs=29.6
Q ss_pred eeehhhhhhHHHHHHHHHHHcCCCCCCCeeEEEEecCccc
Q 019960 249 NISSIYSQGLLNNLTQALESAGIDLSQANISVQIDLGKRA 288 (333)
Q Consensus 249 siss~ysqgll~~lt~al~~sgvdlsqa~isvqi~lgkr~ 288 (333)
.|-..=-.|||..++.+|...|+++-.|.|+. +|.++
T Consensus 4 ~v~~~Dr~gLl~~i~~~l~~~~lnI~~A~i~t---~~~~~ 40 (74)
T cd04925 4 ELTGTDRPGLLSEVFAVLADLHCNVVEARAWT---HNGRL 40 (74)
T ss_pred EEEECCCCCHHHHHHHHHHHCCCcEEEEEEEE---ECCEE
Confidence 34444457999999999999999999999984 36655
No 44
>COG3074 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=25.88 E-value=70 Score=25.73 Aligned_cols=29 Identities=17% Similarity=0.279 Sum_probs=22.2
Q ss_pred hHHHHHHHHHHHHHHHHHHhhhcccccCc
Q 019960 84 LLEVIEYVQYLQEKVQKYEVSYQDWSAEP 112 (333)
Q Consensus 84 L~~AIeYIk~Lq~~v~~Le~~~~~l~~e~ 112 (333)
+..||+-|.-||..+.+|+..+..+.+|.
T Consensus 13 iqqAvdTI~LLQmEieELKEknn~l~~e~ 41 (79)
T COG3074 13 VQQAIDTITLLQMEIEELKEKNNSLSQEV 41 (79)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhHhHHHH
Confidence 56789999999999888887766555544
No 45
>PRK00441 argR arginine repressor; Provisional
Probab=25.71 E-value=28 Score=30.83 Aligned_cols=23 Identities=35% Similarity=0.611 Sum_probs=19.6
Q ss_pred HHHHHHHHHcCCCCCCCeeEEEE
Q 019960 260 NNLTQALESAGIDLSQANISVQI 282 (333)
Q Consensus 260 ~~lt~al~~sgvdlsqa~isvqi 282 (333)
..|-++|+..|++.|||+||=.|
T Consensus 22 ~eL~~~L~~~G~~vSqaTisRDl 44 (149)
T PRK00441 22 EELAEELKKMGFDVTQATVSRDI 44 (149)
T ss_pred HHHHHHHHhcCCCcCHHHHHHHH
Confidence 56788999999999999999543
No 46
>COG1438 ArgR Arginine repressor [Transcription]
Probab=25.37 E-value=24 Score=31.73 Aligned_cols=22 Identities=32% Similarity=0.614 Sum_probs=18.7
Q ss_pred HHHHHHHHcCCCCCCCeeEEEE
Q 019960 261 NLTQALESAGIDLSQANISVQI 282 (333)
Q Consensus 261 ~lt~al~~sgvdlsqa~isvqi 282 (333)
-|-..|+..|++++||++|=-|
T Consensus 25 Elv~~L~~~Gi~vTQaTvSRDl 46 (150)
T COG1438 25 ELVELLQEEGIEVTQATVSRDL 46 (150)
T ss_pred HHHHHHHHcCCeEehHHHHHHH
Confidence 4667899999999999999544
No 47
>cd04876 ACT_RelA-SpoT ACT domain found C-terminal of the RelA/SpoT domains. ACT_RelA-SpoT: the ACT domain found C-terminal of the RelA/SpoT domains. Enzymes of the Rel/Spo family enable bacteria to survive prolonged periods of nutrient limitation by controlling guanosine-3'-diphosphate-5'-(tri)diphosphate ((p)ppGpp) production and subsequent rRNA repression (stringent response). Both the synthesis of (p)ppGpp from ATP and GDP(GTP), and its hydrolysis to GDP(GTP) and pyrophosphate, are catalyzed by Rel/Spo proteins. In Escherichia coli and its close relatives, the metabolism of (p)ppGpp is governed by two homologous proteins, RelA and SpoT. The RelA protein catalyzes (p)ppGpp synthesis in a reaction requiring its binding to ribosomes bearing codon-specified uncharged tRNA. The major role of the SpoT protein is the breakdown of (p)ppGpp by a manganese-dependent (p)ppGpp pyrophosphohydrolase activity. Although the stringent response appears to be tightly regulated by these two enzymes i
Probab=24.59 E-value=60 Score=21.77 Aligned_cols=28 Identities=21% Similarity=0.436 Sum_probs=22.7
Q ss_pred eeehhhhhhHHHHHHHHHHHcCCCCCCC
Q 019960 249 NISSIYSQGLLNNLTQALESAGIDLSQA 276 (333)
Q Consensus 249 siss~ysqgll~~lt~al~~sgvdlsqa 276 (333)
.|......|+|..|++.|...|+++...
T Consensus 2 ~v~~~~~~~~l~~i~~~l~~~~~~i~~~ 29 (71)
T cd04876 2 RVEAIDRPGLLADITTVIAEEKINILSV 29 (71)
T ss_pred EEEEeccCcHHHHHHHHHHhCCCCEEEE
Confidence 4555567899999999999999998543
No 48
>TIGR01529 argR_whole arginine repressor. This model includes most members of the arginine-responsive transcriptional regulator family ArgR. This hexameric protein binds DNA at its amino end to repress arginine biosyntheis or activate arginine catabolism. Some species have several ArgR paralogs. In a neighbor-joining tree, some of these paralogous sequences show long branches and differ significantly in an otherwise well-conserved C-terminal region motif GT[VIL][AC]GDDT. These paralogs are excluded from the seed and score in the gray zone of this model, between trusted and noise cutoffs.
Probab=24.51 E-value=24 Score=31.06 Aligned_cols=21 Identities=33% Similarity=0.575 Sum_probs=17.9
Q ss_pred HHHHHHHHHcCCCCCCCeeEE
Q 019960 260 NNLTQALESAGIDLSQANISV 280 (333)
Q Consensus 260 ~~lt~al~~sgvdlsqa~isv 280 (333)
.-|-+.|+..|+++|||+||=
T Consensus 20 eeL~~~L~~~G~~vsqaTIsR 40 (146)
T TIGR01529 20 EELVALLKAEGIEVTQATVSR 40 (146)
T ss_pred HHHHHHHHHhCCCcCHHHHHH
Confidence 356778899999999999985
No 49
>cd04918 ACT_AK1-AT_2 ACT domains located C-terminal to the catalytic domain of a monofunctional, lysine-sensitive, plant aspartate kinase 1 (AK1). This CD includes the second of two ACT domains located C-terminal to the catalytic domain of a monofunctional, lysine-sensitive, plant aspartate kinase 1 (AK1), which can be synergistically inhibited by S-adenosylmethionine (SAM). This isoenzyme is found in higher plants, Arabidopsis thaliana (AT) and Zea mays, and also in Chlorophyta. In its inactive state, Arabidopsis AK1 binds the effectors lysine and SAM (two molecules each) at the interface of two ACT1 domain subunits. The second ACT domain (ACT2), this CD, does not interact with an effector. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=24.16 E-value=1.1e+02 Score=22.44 Aligned_cols=28 Identities=25% Similarity=0.439 Sum_probs=21.6
Q ss_pred hhHHHHHHHHHHHcCCCC-------CCCeeEEEEe
Q 019960 256 QGLLNNLTQALESAGIDL-------SQANISVQID 283 (333)
Q Consensus 256 qgll~~lt~al~~sgvdl-------sqa~isvqi~ 283 (333)
.|++..+.+||...||.+ |.-+||+=|+
T Consensus 14 ~~~~~~i~~aL~~~~I~v~~i~~g~s~~sis~~v~ 48 (65)
T cd04918 14 SLILERAFHVLYTKGVNVQMISQGASKVNISLIVN 48 (65)
T ss_pred ccHHHHHHHHHHHCCCCEEEEEecCccceEEEEEe
Confidence 589999999999999988 4445555443
No 50
>cd04924 ACT_AK-Arch_2 ACT domains of a monofunctional aspartokinase found mostly in Archaea species (ACT_AK-Arch_2). Included in this CD is the second of two ACT domains of a monofunctional aspartokinase found mostly in Archaea species (ACT_AK-Arch_2). The first or N-terminal ACT domain of these proteins cluster with the ThrA-like ACT 1 domains (ACT_AKi-HSDH-ThrA-like_1) which includes the threonine-sensitive archaeal Methanococcus jannaschii aspartokinase ACT 1 domain. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=23.96 E-value=1.2e+02 Score=21.45 Aligned_cols=29 Identities=34% Similarity=0.453 Sum_probs=22.4
Q ss_pred hhHHHHHHHHHHHcCCCC-------CCCeeEEEEec
Q 019960 256 QGLLNNLTQALESAGIDL-------SQANISVQIDL 284 (333)
Q Consensus 256 qgll~~lt~al~~sgvdl-------sqa~isvqi~l 284 (333)
.|++..+..+|...|+.+ ++.+||+-|+-
T Consensus 15 ~~~~~~i~~~L~~~~I~v~~i~q~~s~~~isf~i~~ 50 (66)
T cd04924 15 PGVAGRVFGALGKAGINVIMISQGSSEYNISFVVAE 50 (66)
T ss_pred ccHHHHHHHHHHHCCCCEEEEEecCccceEEEEEeH
Confidence 588999999999999887 45556666553
No 51
>cd04870 ACT_PSP_1 CT domains found N-terminal of phosphoserine phosphatase (PSP, SerB). The ACT_PSP_1 CD includes the first of the two ACT domains found N-terminal of phosphoserine phosphatase (PSP, SerB). PSPs belong to the L-2-haloacid dehalogenase-like protein superfamily. PSP is involved in serine metabolism; serine is synthesized from phosphoglycerate through sequential reactions catalyzed by 3-phosphoglycerate dehydrogenase (SerA), 3-phosphoserine aminotransferase (SerC), and SerB. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=23.48 E-value=86 Score=23.68 Aligned_cols=30 Identities=23% Similarity=0.420 Sum_probs=24.6
Q ss_pred eeeehhhhhhHHHHHHHHHHHcCCCCCCCe
Q 019960 248 INISSIYSQGLLNNLTQALESAGIDLSQAN 277 (333)
Q Consensus 248 isiss~ysqgll~~lt~al~~sgvdlsqa~ 277 (333)
|+|...-..||++.+|++|...|+++...+
T Consensus 2 vtv~G~DrpGiv~~vt~~la~~~~nI~dl~ 31 (75)
T cd04870 2 ITVTGPDRPGLTSALTEVLAAHGVRILDVG 31 (75)
T ss_pred EEEEcCCCCCHHHHHHHHHHHCCCCEEecc
Confidence 456666778999999999999999876554
No 52
>PF14794 DUF4479: Domain of unknown function (DUF4479); PDB: 3BU2_C.
Probab=23.19 E-value=70 Score=25.27 Aligned_cols=25 Identities=32% Similarity=0.537 Sum_probs=14.4
Q ss_pred CCceeeehhhhhhHHHHHHHHHHHcCCCC
Q 019960 245 GGTINISSIYSQGLLNNLTQALESAGIDL 273 (333)
Q Consensus 245 ~g~isiss~ysqgll~~lt~al~~sgvdl 273 (333)
.|.|-+ +..++..|.++|+.+|+|-
T Consensus 43 ~G~V~L----t~eqv~~LN~~l~~~Gf~~ 67 (73)
T PF14794_consen 43 NGQVFL----TEEQVAKLNQALQKAGFDE 67 (73)
T ss_dssp -----------HHHHHHHHHHHHHTT---
T ss_pred CcCEEc----CHHHHHHHHHHHHHcCCCc
Confidence 355655 4789999999999999874
No 53
>cd04873 ACT_UUR-ACR-like ACT domains of the bacterial signal-transducing uridylyltransferase /uridylyl-removing (UUR) enzyme, GlnD. This ACT domain family, ACT_UUR_ACR-like, includes the two C-terminal ACT domains of the bacterial signal-transducing uridylyltransferase /uridylyl-removing (UUR) enzyme, GlnD; including those enzymes similar to the GlnD found in enteric Escherichia coli and those found in photosynthetic, nitrogen-fixing bacterium Rhodospirillum rubrum. Also included in this CD are the four ACT domains of a novel protein composed almost entirely of ACT domain repeats (the ACR protein) and like proteins. These ACR proteins, found in Arabidopsis and Oryza, are proposed to function as novel regulatory or sensor proteins in plants. This CD also includes the first of the two ACT domains that comprise the Glycine Cleavage System Transcriptional Repressor (GcvR) protein and related domains, as well as, the N-terminal ACT domain of a yet characterized Arabidopsis/Oryza predicted t
Probab=22.42 E-value=72 Score=22.71 Aligned_cols=32 Identities=28% Similarity=0.534 Sum_probs=26.0
Q ss_pred eeeehhhhhhHHHHHHHHHHHcCCCCCCCeeE
Q 019960 248 INISSIYSQGLLNNLTQALESAGIDLSQANIS 279 (333)
Q Consensus 248 isiss~ysqgll~~lt~al~~sgvdlsqa~is 279 (333)
+.|...-..|+|..|+.+|...|+++-.+.+.
T Consensus 3 l~i~~~d~~g~l~~i~~~l~~~~~~I~~~~~~ 34 (70)
T cd04873 3 VEVYAPDRPGLLADITRVLADLGLNIHDARIS 34 (70)
T ss_pred EEEEeCCCCCHHHHHHHHHHHCCCeEEEEEEe
Confidence 45666678899999999999999998766543
No 54
>cd04872 ACT_1ZPV ACT domain proteins similar to the yet uncharacterized Streptococcus pneumoniae ACT domain protein. This CD, ACT_1ZPV, includes those single ACT domain proteins similar to the yet uncharacterized Streptococcus pneumoniae ACT domain protein (pdb structure 1ZPV). Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=21.95 E-value=73 Score=24.80 Aligned_cols=35 Identities=9% Similarity=0.270 Sum_probs=28.2
Q ss_pred CceeeehhhhhhHHHHHHHHHHHcCCCCCCCeeEE
Q 019960 246 GTINISSIYSQGLLNNLTQALESAGIDLSQANISV 280 (333)
Q Consensus 246 g~isiss~ysqgll~~lt~al~~sgvdlsqa~isv 280 (333)
..|+|...-..||+..+|+.|-..|+++-..+-.|
T Consensus 2 ~vl~i~g~D~pGiva~vt~~la~~g~nI~~~~~~~ 36 (88)
T cd04872 2 AVITVVGKDRVGIVAGVSTKLAELNVNILDISQTI 36 (88)
T ss_pred EEEEEEcCCCCCHHHHHHHHHHHcCCCEEechhHh
Confidence 35778888899999999999999999876554333
No 55
>cd04878 ACT_AHAS N-terminal ACT domain of the Escherichia coli IlvH-like regulatory subunit of acetohydroxyacid synthase (AHAS). ACT_AHAS: N-terminal ACT domain of the Escherichia coli IlvH-like regulatory subunit of acetohydroxyacid synthase (AHAS). AHAS catalyses the first common step in the biosynthesis of the three branched-chain amino acids. The first step involves the condensation of either pyruvate or 2-ketobutyrate with the two-carbon hydroxyethyl fragment derived from another pyruvate molecule, covalently bound to the coenzyme thiamine diphosphate. Bacterial AHASs generally consist of regulatory and catalytic subunits. The effector (valine) binding sites are proposed to be located in two symmetrically related positions in the interface between a pair of N-terminal ACT domains with the C-terminal domain of IlvH contacting the catalytic dimer. Plants Arabidopsis and Oryza have tandem IlvH subunits; both the first and second ACT domain sequences are present in this CD. Members of
Probab=21.93 E-value=79 Score=22.20 Aligned_cols=29 Identities=17% Similarity=0.402 Sum_probs=24.8
Q ss_pred ceeeehhhhhhHHHHHHHHHHHcCCCCCC
Q 019960 247 TINISSIYSQGLLNNLTQALESAGIDLSQ 275 (333)
Q Consensus 247 ~isiss~ysqgll~~lt~al~~sgvdlsq 275 (333)
++.|...-..|+|..|+..|...|+++..
T Consensus 2 ~l~i~~~d~~g~l~~i~~~l~~~~~~i~~ 30 (72)
T cd04878 2 TLSVLVENEPGVLNRISGLFARRGFNIES 30 (72)
T ss_pred EEEEEEcCCCcHHHHHHHHHHhCCCCEEE
Confidence 56677777889999999999999999853
No 56
>PF06345 Drf_DAD: DRF Autoregulatory Domain; InterPro: IPR010465 This domain is found in Diaphanous-related formins (Drfs). It binds the N-terminal GTPase-binding domain; this link is broken when GTP-bound Rho binds to the GBD and activates the protein. The addition of diaphanous activating domains (DAD) to mammalian cells induces actin filament formation, stabilises microtubules, and activates serum-response mediated transcription [].; PDB: 3O4X_H 3OBV_E 2BAP_C 2F31_B.
Probab=21.86 E-value=90 Score=17.82 Aligned_cols=12 Identities=33% Similarity=0.786 Sum_probs=9.7
Q ss_pred hHHHHHHHHHHH
Q 019960 257 GLLNNLTQALES 268 (333)
Q Consensus 257 gll~~lt~al~~ 268 (333)
|+.++|-+|||+
T Consensus 1 gvmdsllealqt 12 (15)
T PF06345_consen 1 GVMDSLLEALQT 12 (15)
T ss_dssp -HHHHHHHHHHH
T ss_pred CcHHHHHHHHHc
Confidence 678899999986
No 57
>cd04926 ACT_ACR_4 C-terminal ACT domain, of a novel type of ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). This CD includes the C-terminal ACT domain, of a novel type of ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). ACR proteins, found only in Arabidopsis and Oryza, as yet, are proposed to function as novel regulatory or sensor proteins in plants. Nine ACR gene products have been described (ACR1-8 in Arabidopsis and OsARC1-9 in Oryza) and are represented in this CD. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=21.05 E-value=72 Score=24.08 Aligned_cols=32 Identities=22% Similarity=0.499 Sum_probs=26.6
Q ss_pred ceeeehhhhhhHHHHHHHHHHHcCCCCCCCee
Q 019960 247 TINISSIYSQGLLNNLTQALESAGIDLSQANI 278 (333)
Q Consensus 247 ~isiss~ysqgll~~lt~al~~sgvdlsqa~i 278 (333)
.|.|...--.|||..|+.+|.+.|+++-.|.|
T Consensus 3 ri~V~~~D~~Gll~~i~~~l~~~~lnI~sa~i 34 (72)
T cd04926 3 RLELRTEDRVGLLSDVTRVFRENGLTVTRAEI 34 (72)
T ss_pred EEEEEECCccCHHHHHHHHHHHCCcEEEEEEE
Confidence 35566667789999999999999999877765
Done!