Query 004499
Match_columns 748
No_of_seqs 148 out of 324
Neff 4.4
Searched_HMMs 46136
Date Fri Mar 29 00:26:21 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/004499.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/004499hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF14215 bHLH-MYC_N: bHLH-MYC 100.0 1.4E-42 3E-47 338.7 12.0 152 10-171 1-163 (163)
2 smart00353 HLH helix loop heli 97.9 2.2E-05 4.7E-10 62.8 5.7 43 578-620 6-51 (53)
3 cd00083 HLH Helix-loop-helix d 97.8 4.4E-05 9.6E-10 62.0 5.5 42 578-619 14-58 (60)
4 PF00010 HLH: Helix-loop-helix 97.7 6E-05 1.3E-09 61.2 4.7 40 578-617 11-55 (55)
5 KOG1318 Helix loop helix trans 96.8 0.0012 2.5E-08 73.9 4.9 45 576-621 242-290 (411)
6 KOG1319 bHLHZip transcription 96.7 0.00067 1.5E-08 68.6 1.7 73 553-625 47-126 (229)
7 KOG4304 Transcriptional repres 94.5 0.023 5E-07 60.3 2.6 45 578-622 42-94 (250)
8 cd04927 ACT_ACR-like_2 Second 92.3 0.24 5.2E-06 43.1 4.9 47 676-722 1-49 (76)
9 cd04900 ACT_UUR-like_1 ACT dom 92.2 0.35 7.7E-06 41.2 5.7 46 678-723 4-51 (73)
10 KOG2483 Upstream transcription 91.8 0.36 7.8E-06 51.0 6.4 42 578-619 69-113 (232)
11 cd04925 ACT_ACR_2 ACT domain-c 90.8 0.44 9.5E-06 41.0 4.9 46 677-722 2-48 (74)
12 TIGR01817 nifA Nif-specific re 89.3 1.3 2.9E-05 51.1 8.8 129 3-172 17-153 (534)
13 PF13185 GAF_2: GAF domain; PD 88.4 2.3 5E-05 38.6 8.0 131 6-170 4-139 (148)
14 PRK11061 fused phosphoenolpyru 88.2 2.5 5.4E-05 51.5 10.3 129 5-174 17-150 (748)
15 cd04926 ACT_ACR_4 C-terminal 87.5 1 2.2E-05 38.5 4.7 41 681-721 7-48 (72)
16 cd04899 ACT_ACR-UUR-like_2 C-t 87.3 1.5 3.3E-05 36.1 5.6 51 677-727 2-53 (70)
17 KOG2588 Predicted DNA-binding 84.7 0.69 1.5E-05 56.8 3.1 59 561-619 264-328 (953)
18 KOG4029 Transcription factor H 83.6 1.5 3.2E-05 45.7 4.6 56 567-623 109-169 (228)
19 KOG3561 Aryl-hydrocarbon recep 83.4 1.2 2.5E-05 54.5 4.2 58 562-619 14-75 (803)
20 cd04895 ACT_ACR_1 ACT domain-c 83.2 3.3 7.1E-05 36.4 5.9 53 676-728 2-55 (72)
21 PF01590 GAF: GAF domain; Int 82.9 1.7 3.7E-05 39.7 4.3 114 7-156 3-131 (154)
22 smart00065 GAF Domain present 79.4 20 0.00043 30.6 9.5 123 7-171 3-135 (149)
23 TIGR01693 UTase_glnD [Protein- 79.3 13 0.00029 45.8 11.4 65 664-728 656-723 (850)
24 PLN03217 transcription factor 77.7 8.6 0.00019 35.2 6.7 56 576-632 16-78 (93)
25 cd04873 ACT_UUR-ACR-like ACT d 74.7 7.1 0.00015 31.7 5.1 44 679-722 4-48 (70)
26 cd04928 ACT_TyrKc Uncharacteri 66.7 13 0.00029 32.3 5.2 39 684-722 11-50 (68)
27 KOG0561 bHLH transcription fac 65.7 7.6 0.00017 42.7 4.3 42 578-619 70-113 (373)
28 PRK01759 glnD PII uridylyl-tra 65.4 23 0.0005 44.0 8.9 60 669-728 671-732 (854)
29 PF13291 ACT_4: ACT domain; PD 65.1 6.9 0.00015 33.5 3.2 50 678-727 9-61 (80)
30 PRK05092 PII uridylyl-transfer 63.2 33 0.00072 43.0 9.8 52 671-722 728-781 (931)
31 PRK00275 glnD PII uridylyl-tra 63.1 44 0.00096 41.8 10.8 53 674-726 703-757 (895)
32 cd04887 ACT_MalLac-Enz ACT_Mal 62.0 12 0.00027 31.1 4.1 46 684-729 9-55 (74)
33 PRK05092 PII uridylyl-transfer 61.5 16 0.00035 45.6 6.7 74 669-742 837-915 (931)
34 PRK00275 glnD PII uridylyl-tra 59.8 20 0.00044 44.7 7.1 60 669-728 808-868 (895)
35 PRK05007 PII uridylyl-transfer 58.8 45 0.00097 41.7 9.8 61 669-729 695-757 (884)
36 cd02116 ACT ACT domains are co 58.6 23 0.00051 25.4 4.7 43 680-722 3-46 (60)
37 cd04896 ACT_ACR-like_3 ACT dom 57.7 22 0.00047 31.6 5.0 46 677-722 2-50 (75)
38 PF01842 ACT: ACT domain; Int 56.1 22 0.00048 28.4 4.5 45 678-722 3-48 (66)
39 KOG3560 Aryl-hydrocarbon recep 54.7 12 0.00026 44.1 3.6 64 558-621 5-85 (712)
40 cd04877 ACT_TyrR N-terminal AC 54.0 9.2 0.0002 32.5 2.0 45 676-723 1-46 (74)
41 PRK03381 PII uridylyl-transfer 50.5 31 0.00068 42.4 6.5 59 671-729 703-762 (774)
42 PRK03059 PII uridylyl-transfer 47.5 32 0.0007 42.8 6.0 53 669-721 780-833 (856)
43 PF13740 ACT_6: ACT domain; PD 47.1 42 0.0009 28.9 5.0 49 675-723 2-51 (76)
44 PRK04374 PII uridylyl-transfer 46.8 34 0.00074 42.7 6.1 52 671-722 792-844 (869)
45 PF13492 GAF_3: GAF domain; PD 46.0 39 0.00085 29.7 4.9 113 7-170 3-119 (129)
46 cd04897 ACT_ACR_3 ACT domain-c 45.6 47 0.001 29.5 5.2 52 677-728 3-55 (75)
47 PRK03381 PII uridylyl-transfer 43.1 41 0.00088 41.5 5.9 50 673-722 597-647 (774)
48 PF02845 CUE: CUE domain; Int 40.6 50 0.0011 25.6 4.1 34 584-617 2-42 (42)
49 COG3226 Uncharacterized protei 39.8 53 0.0011 34.3 5.2 41 577-617 12-72 (204)
50 PRK03059 PII uridylyl-transfer 36.4 1.4E+02 0.0031 37.3 9.2 43 680-722 683-727 (856)
51 PRK08577 hypothetical protein; 29.5 2E+02 0.0042 27.6 7.1 77 646-724 27-108 (136)
52 cd04870 ACT_PSP_1 CT domains f 29.3 70 0.0015 27.3 3.6 47 679-725 3-50 (75)
53 PF04281 Tom22: Mitochondrial 29.3 53 0.0011 32.5 3.2 40 580-619 50-89 (137)
54 PRK05022 anaerobic nitric oxid 28.7 63 0.0014 37.6 4.2 80 88-173 65-154 (509)
55 PRK05007 PII uridylyl-transfer 28.2 94 0.002 39.0 5.8 59 671-729 804-863 (884)
56 PRK04374 PII uridylyl-transfer 28.1 2.4E+02 0.0052 35.6 9.2 42 681-722 696-739 (869)
57 cd04869 ACT_GcvR_2 ACT domains 27.6 1.4E+02 0.003 25.3 5.1 44 679-722 3-53 (81)
58 cd04886 ACT_ThrD-II-like C-ter 27.3 1.8E+02 0.0039 23.1 5.6 40 683-722 7-51 (73)
59 PF09383 NIL: NIL domain; Int 26.1 1.7E+02 0.0036 25.1 5.4 33 691-723 19-53 (76)
60 cd04902 ACT_3PGDH-xct C-termin 23.7 1.3E+02 0.0028 24.6 4.1 40 683-722 8-49 (73)
61 TIGR01693 UTase_glnD [Protein- 23.2 1.5E+02 0.0032 37.0 6.2 60 669-728 773-833 (850)
62 PRK13753 dihydropteroate synth 23.0 3E+02 0.0065 30.3 7.8 42 570-614 46-93 (279)
63 TIGR00986 3a0801s05tom22 mitoc 22.7 78 0.0017 31.7 3.0 39 581-619 49-87 (145)
64 cd04893 ACT_GcvR_1 ACT domains 22.2 1.7E+02 0.0036 25.3 4.7 47 676-722 2-49 (77)
65 cd04894 ACT_ACR-like_1 ACT dom 21.7 1.9E+02 0.004 25.6 4.6 51 685-739 11-61 (69)
66 KOG4395 Transcription factor A 21.4 1.2E+02 0.0026 33.1 4.2 59 563-622 170-231 (285)
67 cd04876 ACT_RelA-SpoT ACT dom 20.7 1.2E+02 0.0026 23.0 3.2 41 682-722 5-47 (71)
68 COG3696 Putative silver efflux 20.2 1.1E+02 0.0025 38.6 4.3 43 568-613 290-336 (1027)
No 1
>PF14215 bHLH-MYC_N: bHLH-MYC and R2R3-MYB transcription factors N-terminal
Probab=100.00 E-value=1.4e-42 Score=338.72 Aligned_cols=152 Identities=38% Similarity=0.710 Sum_probs=124.9
Q ss_pred HHHHHHhhccCCCcEEEEEeeecCCCCeEEEecCCccCCCCCcchhh---hhcchhhhhcccCCC--CCCCc------cc
Q 004499 10 LHGILKSLCFNTAWKYAVFWKLKHRTRMVLTWEDGYYDNCGQQDSLE---NKCSSESLENFHGGR--YSHDP------LG 78 (748)
Q Consensus 10 Lqq~LrsLc~~~~WsYAIFWqls~~~~~vL~WgDGyc~g~~~~~~~e---~~~~~k~l~~L~gg~--~~~d~------~~ 78 (748)
|||+||+||++.+|+||||||++++++ +|+||||||++++++++.. ....+++++.++.+. ++..+ +.
T Consensus 1 Lq~~Lr~lv~~~~W~YaVFWk~~~~~~-~L~W~DG~~~g~~~~~~~~~~~~~~~~~~l~~l~~~~~~~~~~~~~v~~~e~ 79 (163)
T PF14215_consen 1 LQQRLRSLVENSQWTYAVFWKLSPDNS-VLVWGDGYCNGPKETRKNGEEEQEQRSKVLRELHSSFSSYALSPEEVTDTEW 79 (163)
T ss_pred ChHHHHHHhCCCCCcEEEEeEEcCCCC-eeeEcceeecCCcccccchhhccchhhhHHHHHhhhccccccccchhHHHHH
Confidence 799999999999999999999999996 9999999999988765432 122455666654321 22233 33
Q ss_pred ceeeeEEEEEecCCCCeeeeEeeCCCeEeeeCCCCccCcCCCCCcchhhhcccccCceeEEEEEecCCcEEEeccccccc
Q 004499 79 LAVAKMSYHVYSLGEGIVGQVAVTGKHQWIFSDQLVTNSCSSFEFSDGWQSQFSAGIRTIAVVAVVPHGVVQLGSLDEVT 158 (748)
Q Consensus 79 l~v~~MS~~sF~~GeGlpGrAaaSG~hvWI~~~~~~~~~~~~~e~~r~~~~QfSAGIQTIVcIPV~~~GVLELGSTe~V~ 158 (748)
+++.+|+| +| |+|+|||||++|+|+||++++.... ..|.|++++|+ +|||||||||| ++||||||||++|+
T Consensus 80 f~~~s~~~-sf--g~G~~G~a~~sg~~~Wi~~~~~~~~----~~~~r~~~aq~-~~~~Tiv~IPv-~~GVvELGSt~~I~ 150 (163)
T PF14215_consen 80 FYLVSMSY-SF--GEGIPGRAAASGQHIWISGANELDS----SYCERAWLAQF-AGIQTIVCIPV-PNGVVELGSTEKIP 150 (163)
T ss_pred HhhceeeE-Ee--cCCccEEEeecCccEEEeCCCcccc----ccchhhhhhcc-cccceEEEEEe-cCCEEEeeeeeeec
Confidence 45667743 44 9999999999999999999987543 44889998777 99999999998 99999999999999
Q ss_pred CCHHHHHHHHHHH
Q 004499 159 EDMKVVTHIRDVF 171 (748)
Q Consensus 159 Ed~~lV~~VKslF 171 (748)
||++||++||++|
T Consensus 151 Ed~~~v~~vk~~F 163 (163)
T PF14215_consen 151 EDSNLVQRVKSLF 163 (163)
T ss_pred cCHHHHHHHHhhC
Confidence 9999999999998
No 2
>smart00353 HLH helix loop helix domain.
Probab=97.91 E-value=2.2e-05 Score=62.76 Aligned_cols=43 Identities=35% Similarity=0.449 Sum_probs=40.1
Q ss_pred hhhHHHHHHHHHHHhhcC---CCcccchhhHHHHHHHHHHHHHHhh
Q 004499 578 RDRQLIQDRIKELRELVP---NGSKCSIDSLLERTIKHMLFLQSIT 620 (748)
Q Consensus 578 ~~r~~i~~r~~~lr~~vp---~~~k~~i~~~l~~~i~~~~~l~~~~ 620 (748)
+||+.|++++.+||.+|| .+.|.|..++|+.||+||.+|+...
T Consensus 6 ~RR~~~n~~~~~L~~lip~~~~~~k~~k~~iL~~ai~yi~~L~~~~ 51 (53)
T smart00353 6 RRRRKINEAFDELRSLLPTLPNNKKLSKAEILRLAIEYIKSLQEEL 51 (53)
T ss_pred HHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHH
Confidence 799999999999999999 5789999999999999999998763
No 3
>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=97.78 E-value=4.4e-05 Score=62.04 Aligned_cols=42 Identities=33% Similarity=0.492 Sum_probs=40.3
Q ss_pred hhhHHHHHHHHHHHhhcCCC---cccchhhHHHHHHHHHHHHHHh
Q 004499 578 RDRQLIQDRIKELRELVPNG---SKCSIDSLLERTIKHMLFLQSI 619 (748)
Q Consensus 578 ~~r~~i~~r~~~lr~~vp~~---~k~~i~~~l~~~i~~~~~l~~~ 619 (748)
+||+.|++++.+|+.+||.. .|.|..++|+.||+||.+|+..
T Consensus 14 ~RR~~~n~~~~~L~~llp~~~~~~k~~k~~iL~~a~~yI~~L~~~ 58 (60)
T cd00083 14 RRRERINDAFDELRSLLPTLPPSKKLSKAEILRKAVDYIKSLQEL 58 (60)
T ss_pred HHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHH
Confidence 79999999999999999999 8999999999999999999975
No 4
>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=97.67 E-value=6e-05 Score=61.16 Aligned_cols=40 Identities=43% Similarity=0.557 Sum_probs=37.9
Q ss_pred hhhHHHHHHHHHHHhhcCCC-----cccchhhHHHHHHHHHHHHH
Q 004499 578 RDRQLIQDRIKELRELVPNG-----SKCSIDSLLERTIKHMLFLQ 617 (748)
Q Consensus 578 ~~r~~i~~r~~~lr~~vp~~-----~k~~i~~~l~~~i~~~~~l~ 617 (748)
+||..|++.+.+|+++||.. .|.|..++|+.||.||.+||
T Consensus 11 ~RR~~i~~~~~~L~~llp~~~~~~~~k~~K~~iL~~ai~yI~~Lq 55 (55)
T PF00010_consen 11 RRRDRINDCFDELRELLPSCSAGSSRKLSKASILQKAIDYIKQLQ 55 (55)
T ss_dssp HHHHHHHHHHHHHHHCCSSHHCCTTSSSSHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHhccchhccccccCCHHHHHHHHHHHHHHhC
Confidence 78999999999999999986 67899999999999999998
No 5
>KOG1318 consensus Helix loop helix transcription factor EB [Transcription]
Probab=96.84 E-value=0.0012 Score=73.95 Aligned_cols=45 Identities=36% Similarity=0.496 Sum_probs=40.2
Q ss_pred CchhhHHHHHHHHHHHhhcCCC----cccchhhHHHHHHHHHHHHHHhhh
Q 004499 576 RPRDRQLIQDRIKELRELVPNG----SKCSIDSLLERTIKHMLFLQSITK 621 (748)
Q Consensus 576 rp~~r~~i~~r~~~lr~~vp~~----~k~~i~~~l~~~i~~~~~l~~~~~ 621 (748)
| |||..|+||||||-.|||.- .|-.+-++|.++..|+..||.-..
T Consensus 242 R-RRR~nIN~~IkeLg~liP~~~~~~~~~nKgtILk~s~dYIr~Lqq~~q 290 (411)
T KOG1318|consen 242 R-RRRENINDRIKELGQLIPKCNSEDMKSNKGTILKASCDYIRELQQTLQ 290 (411)
T ss_pred H-HHHHHHHHHHHHHHHhCCCCCcchhhcccchhhHHHHHHHHHHHHHHH
Confidence 5 89999999999999999987 366799999999999999987644
No 6
>KOG1319 consensus bHLHZip transcription factor BIGMAX [Transcription]
Probab=96.72 E-value=0.00067 Score=68.56 Aligned_cols=73 Identities=29% Similarity=0.413 Sum_probs=54.0
Q ss_pred ccCCCccccccccccCCCCCCCCCchhhHHHHHHHHHHHhhcCC-------CcccchhhHHHHHHHHHHHHHHhhhhHhh
Q 004499 553 LDRSSEPAKNNKKRARTGENGRPRPRDRQLIQDRIKELRELVPN-------GSKCSIDSLLERTIKHMLFLQSITKHADK 625 (748)
Q Consensus 553 ~k~~~~~~~~~k~r~~~~~~~~prp~~r~~i~~r~~~lr~~vp~-------~~k~~i~~~l~~~i~~~~~l~~~~~~~dk 625 (748)
..++.+..|..-|..|+..-++---|||+-|+..-..|++|||- |-|.+-..||-+||+||.||-...+.+||
T Consensus 47 s~~hS~a~k~syk~rrr~aHtqaEqkRRdAIk~GYddLq~LvP~cq~~ds~g~KlskA~ILqksidyi~~L~~~k~kqe~ 126 (229)
T KOG1319|consen 47 SDYHSEAYKESYKDRRRRAHTQAEQKRRDAIKRGYDDLQTLVPTCQQQDSIGQKLSKAIILQKTIDYIQFLHKEKKKQEE 126 (229)
T ss_pred ccchhHHHHhhHHHHHHHHHHHHHHHHHHHHHhchHHHHHhccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33555555544444444444555569999999999999999994 34789999999999999999988544443
No 7
>KOG4304 consensus Transcriptional repressors of the hairy/E(spl) family (contains HLH) [Transcription]
Probab=94.49 E-value=0.023 Score=60.28 Aligned_cols=45 Identities=31% Similarity=0.486 Sum_probs=39.9
Q ss_pred hhhHHHHHHHHHHHhhcCCC--------cccchhhHHHHHHHHHHHHHHhhhh
Q 004499 578 RDRQLIQDRIKELRELVPNG--------SKCSIDSLLERTIKHMLFLQSITKH 622 (748)
Q Consensus 578 ~~r~~i~~r~~~lr~~vp~~--------~k~~i~~~l~~~i~~~~~l~~~~~~ 622 (748)
|||-|||..|-|||.|||.- +|...+.|||-|++||+-||.....
T Consensus 42 kRRaRIN~~L~eLK~Li~e~~~~~~~~~sklEKAdILEltV~hL~~l~~~~~~ 94 (250)
T KOG4304|consen 42 KRRARINRCLDELKDLIPEALKKDGQRHSKLEKADILELTVNHLRQLQRSQQA 94 (250)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhcchhhhhhHHHHHHHHHHHHHHHHhccccc
Confidence 89999999999999999964 5678899999999999999987443
No 8
>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=92.34 E-value=0.24 Score=43.05 Aligned_cols=47 Identities=17% Similarity=0.358 Sum_probs=42.8
Q ss_pred hhhhhhhcc-cchHHHHHHHHHhcCceEEeeeeee-eCCeEEEEEEEEe
Q 004499 676 MLVEMLCEE-CSHFLEIAEAIRSLGLTILKGVTEA-HGDKTWICFVVEG 722 (748)
Q Consensus 676 ~liem~ce~-~~~flei~~~i~~l~l~il~g~~e~-~~~~~~~~f~ve~ 722 (748)
+++|..|.+ -|+|-.|+.++..+||.|+...+.+ .++.+...|.|.-
T Consensus 1 ~~~ei~~~Dr~gLfa~i~~~l~~~~l~I~~A~I~Tt~~~~v~D~F~V~d 49 (76)
T cd04927 1 FLLKLFCSDRKGLLHDVTEVLYELELTIERVKVSTTPDGRVLDLFFITD 49 (76)
T ss_pred CEEEEEECCCCCHHHHHHHHHHHCCCeEEEEEEEECCCCEEEEEEEEeC
Confidence 368888988 8999999999999999999998885 9999999999964
No 9
>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=92.17 E-value=0.35 Score=41.18 Aligned_cols=46 Identities=28% Similarity=0.281 Sum_probs=40.3
Q ss_pred hhhhhcc-cchHHHHHHHHHhcCceEEeeeeeee-CCeEEEEEEEEec
Q 004499 678 VEMLCEE-CSHFLEIAEAIRSLGLTILKGVTEAH-GDKTWICFVVEGQ 723 (748)
Q Consensus 678 iem~ce~-~~~flei~~~i~~l~l~il~g~~e~~-~~~~~~~f~ve~~ 723 (748)
|+..|.+ .|+|..|+-++..+||+|+...+.+. ++.++..|.|.-.
T Consensus 4 i~v~~~Dr~gLl~~i~~~l~~~~l~I~~A~i~T~~~~~v~D~F~v~~~ 51 (73)
T cd04900 4 VFIYTPDRPGLFARIAGALDQLGLNILDARIFTTRDGYALDTFVVLDP 51 (73)
T ss_pred EEEEecCCCCHHHHHHHHHHHCCCCeEEeEEEEeCCCeEEEEEEEECC
Confidence 5566777 89999999999999999999998777 7999999999643
No 10
>KOG2483 consensus Upstream transcription factor 2/L-myc-2 protein [Transcription]
Probab=91.80 E-value=0.36 Score=50.99 Aligned_cols=42 Identities=24% Similarity=0.377 Sum_probs=38.2
Q ss_pred hhhHHHHHHHHHHHhhcCCCcccc---hhhHHHHHHHHHHHHHHh
Q 004499 578 RDRQLIQDRIKELRELVPNGSKCS---IDSLLERTIKHMLFLQSI 619 (748)
Q Consensus 578 ~~r~~i~~r~~~lr~~vp~~~k~~---i~~~l~~~i~~~~~l~~~ 619 (748)
+||-.|.+++..|+.+||++.-+. -.+||++|+.||..|+..
T Consensus 69 ~RRahlk~~~~~Lk~~vP~~~~~~~~t~lsiL~kA~~~i~~l~~~ 113 (232)
T KOG2483|consen 69 RRRAHLKDCFESLKDSVPLLNGETRSTTLSILDKALEHIQSLERK 113 (232)
T ss_pred HHHHHHHHHHHHHHHhCCCCCCcchhhhhHhhhhHHHHHHHHHhH
Confidence 889999999999999999987763 568999999999999876
No 11
>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=90.77 E-value=0.44 Score=41.01 Aligned_cols=46 Identities=11% Similarity=0.148 Sum_probs=42.1
Q ss_pred hhhhhhcc-cchHHHHHHHHHhcCceEEeeeeeeeCCeEEEEEEEEe
Q 004499 677 LVEMLCEE-CSHFLEIAEAIRSLGLTILKGVTEAHGDKTWICFVVEG 722 (748)
Q Consensus 677 liem~ce~-~~~flei~~~i~~l~l~il~g~~e~~~~~~~~~f~ve~ 722 (748)
+||..+.+ -|+|..|+.++..+|++|+...+.+.++.+...|.|.-
T Consensus 2 ~~~v~~~Dr~gLl~~i~~~l~~~~lnI~~A~i~t~~~~~~d~f~V~d 48 (74)
T cd04925 2 AIELTGTDRPGLLSEVFAVLADLHCNVVEARAWTHNGRLACVIYVRD 48 (74)
T ss_pred EEEEEECCCCCHHHHHHHHHHHCCCcEEEEEEEEECCEEEEEEEEEc
Confidence 57777877 89999999999999999999999999999999999963
No 12
>TIGR01817 nifA Nif-specific regulatory protein. This model represents NifA, a DNA-binding regulatory protein for nitrogen fixation. The model produces scores between the trusted and noise cutoffs for a well-described NifA homolog in Aquifex aeolicus (which lacks nitrogenase), for transcriptional activators of alternative nitrogenases (VFe or FeFe instead of MoFe), and truncated forms.
Probab=89.33 E-value=1.3 Score=51.14 Aligned_cols=129 Identities=16% Similarity=0.194 Sum_probs=79.6
Q ss_pred CCCchHHHHHHHHhhccCCCcEEEEEeeecCCCCeEEEecCCccCCCCCcchhhhhcchhhhhcccCCCCCCCcccceee
Q 004499 3 ASSTTFDLHGILKSLCFNTAWKYAVFWKLKHRTRMVLTWEDGYYDNCGQQDSLENKCSSESLENFHGGRYSHDPLGLAVA 82 (748)
Q Consensus 3 ~~~~~~~Lqq~LrsLc~~~~WsYAIFWqls~~~~~vL~WgDGyc~g~~~~~~~e~~~~~k~l~~L~gg~~~~d~~~l~v~ 82 (748)
...+...|+..++.+++..+=.++.++-.+.++...+.= .+....+ ...
T Consensus 17 ~~dl~~lL~~il~~l~~~l~a~~~~I~L~d~~~~~l~~a---a~g~~~~----------------------------~~~ 65 (534)
T TIGR01817 17 PTRLEKTLANVLNVLSNDLGMRHGLITLSDSEGEPLLVA---AIGWSEE----------------------------GFA 65 (534)
T ss_pred cCCHHHHHHHHHHHHHHhcCCCEEEEEEECCCCCEEEEE---EeCCChh----------------------------hcc
Confidence 345566788888888886666666666666665432221 1111100 000
Q ss_pred eEEEEEecCCCCeeeeEeeCCCeEeeeCCCCccCcCCCCCcchhhhcccccCceeEEEEEecCC----cEEEeccccc--
Q 004499 83 KMSYHVYSLGEGIVGQVAVTGKHQWIFSDQLVTNSCSSFEFSDGWQSQFSAGIRTIAVVAVVPH----GVVQLGSLDE-- 156 (748)
Q Consensus 83 ~MS~~sF~~GeGlpGrAaaSG~hvWI~~~~~~~~~~~~~e~~r~~~~QfSAGIQTIVcIPV~~~----GVLELGSTe~-- 156 (748)
...|..|+|+.|+|+.+++++++.+...... |.... .....|+++++|||+..+ |||.+.+...
T Consensus 66 ---~~~~~~~~gi~g~v~~~~~pvii~Dv~~d~~------~~~~~-~~~~~~~~S~l~VPL~~~g~viGvL~v~s~~~~~ 135 (534)
T TIGR01817 66 ---PIRYRVGEGAIGQIVATGNSLVVPDVAAEPL------FLDRL-SLYDPGPVPFIGVPIKADSETIGVLAADRDFRSR 135 (534)
T ss_pred ---cccccCCccHHHHHHhcCCeEEecccccCch------hhhcc-ccccCCcceEEEEEEcCCCEEEEEEEEEeccccc
Confidence 1247889999999999999999987643211 21111 122367999999998544 8999998854
Q ss_pred --ccCCHHHHHHHHHHHh
Q 004499 157 --VTEDMKVVTHIRDVFA 172 (748)
Q Consensus 157 --V~Ed~~lV~~VKslF~ 172 (748)
-.+|.+++..+-....
T Consensus 136 ~ft~~d~~lL~~lA~~ia 153 (534)
T TIGR01817 136 ERLEEEVRFLEMVANLIG 153 (534)
T ss_pred cccHHHHHHHHHHHHHHH
Confidence 3456666666655544
No 13
>PF13185 GAF_2: GAF domain; PDB: 2QYB_A 3KSG_B 3KSF_C 3KSI_A 3KSH_A 3MMH_A 3RFB_B 1F5M_A 3KO6_B 3HCY_A ....
Probab=88.42 E-value=2.3 Score=38.59 Aligned_cols=131 Identities=19% Similarity=0.153 Sum_probs=67.0
Q ss_pred chHHHHHHHHhhccCCCcEEEEEeeecCCCC-eEEEecCCccCCCCCcchhhhhcchhhhhcccCCCCCCCcccceeeeE
Q 004499 6 TTFDLHGILKSLCFNTAWKYAVFWKLKHRTR-MVLTWEDGYYDNCGQQDSLENKCSSESLENFHGGRYSHDPLGLAVAKM 84 (748)
Q Consensus 6 ~~~~Lqq~LrsLc~~~~WsYAIFWqls~~~~-~vL~WgDGyc~g~~~~~~~e~~~~~k~l~~L~gg~~~~d~~~l~v~~M 84 (748)
+...|+..++.+++-.+|..+.+|-++.++. ..+.+..+- ....... .. ... ........+
T Consensus 4 ~~ell~~~~~~~~~~~~~~~~~i~l~d~~~~~~~~~~~~~~-~~~~~~~--------------~~--~~~-~~~~~~~~~ 65 (148)
T PF13185_consen 4 LEELLQQILDALLELTGADAGAIYLYDPDGQLLPVAASGDP-SEFLKEE--------------IP--LPP-PPDEPPAYA 65 (148)
T ss_dssp HHHHHHHHHHHHHHHHS-SEEEEEEEETTSEEEEEEEESSS-CTSTCCE--------------CC--CCC-CCESCHHHC
T ss_pred HHHHHHHHHHHHHHHhCCCEEEEEEEECCCcEEEEEEeCCc-hhhhhhh--------------cc--cCc-ccccccchh
Confidence 3556777777777778999999999977752 233332111 1110000 00 000 000000000
Q ss_pred EEEEecCCCCeeeeEeeCCCeEeeeCCCCccCcCCCCCcchhhhcccccCceeEEEEEecCC----cEEEecccccccCC
Q 004499 85 SYHVYSLGEGIVGQVAVTGKHQWIFSDQLVTNSCSSFEFSDGWQSQFSAGIRTIAVVAVVPH----GVVQLGSLDEVTED 160 (748)
Q Consensus 85 S~~sF~~GeGlpGrAaaSG~hvWI~~~~~~~~~~~~~e~~r~~~~QfSAGIQTIVcIPV~~~----GVLELGSTe~V~Ed 160 (748)
. .|+.+.++.+++++|+. ... .. ... +......|++.++|||+.-+ |||.|++.+.-.=+
T Consensus 66 --~-----~~~~~~~~~~~~~~~~~-~~~--~~-----~~~-~~~~~~~~~~s~l~vPl~~~~~~~Gvl~l~~~~~~~f~ 129 (148)
T PF13185_consen 66 --A-----VGLWEGVLRTGEPIIIN-DDD--SS-----FPP-WELARHPGIRSILCVPLRSGGEVIGVLSLYSKEPNAFS 129 (148)
T ss_dssp --C-----EETTSHHHHHTS-EEES-CCC--GG-----GST-THHHCCTT-SEEEEEEEEETTEEEEEEEEEESSTT---
T ss_pred --h-----hhHHHHHHhcCceEEEe-Ccc--cc-----ccc-hhhhccccCCEEEEEEEeECCEEEEEEEEeeCCCCCcC
Confidence 0 23333448899999998 111 10 111 22345589999999999665 99999997764444
Q ss_pred HHHHHHHHHH
Q 004499 161 MKVVTHIRDV 170 (748)
Q Consensus 161 ~~lV~~VKsl 170 (748)
..-+..++.+
T Consensus 130 ~~~~~~l~~l 139 (148)
T PF13185_consen 130 EEDLELLEAL 139 (148)
T ss_dssp HHHHHHHHHH
T ss_pred HHHHHHHHHH
Confidence 4444444443
No 14
>PRK11061 fused phosphoenolpyruvate-protein phosphotransferase PtsP/GAF domain; Provisional
Probab=88.17 E-value=2.5 Score=51.49 Aligned_cols=129 Identities=16% Similarity=0.155 Sum_probs=81.0
Q ss_pred CchHHHHHHHHhhccCCCcEEEEEeeecCCCCe-EEEecCCccCCCCCcchhhhhcchhhhhcccCCCCCCCcccceeee
Q 004499 5 STTFDLHGILKSLCFNTAWKYAVFWKLKHRTRM-VLTWEDGYYDNCGQQDSLENKCSSESLENFHGGRYSHDPLGLAVAK 83 (748)
Q Consensus 5 ~~~~~Lqq~LrsLc~~~~WsYAIFWqls~~~~~-vL~WgDGyc~g~~~~~~~e~~~~~k~l~~L~gg~~~~d~~~l~v~~ 83 (748)
.....|+..++.+++-.+..++..|-.+.+... .+.=.+|.-.. .+..
T Consensus 17 dL~e~L~~Iv~~~~~~l~~d~~sI~L~D~~~~~L~~~as~Gl~~~-------------------------------~~~~ 65 (748)
T PRK11061 17 RLNEALDILVTETCLAMDTEVCSVYLADHDRRCYYLMATRGLKKP-------------------------------RGRT 65 (748)
T ss_pred CHHHHHHHHHHHHHHHhCCCEEEEEEEECCCCEEEEEEeeCCChH-------------------------------hccc
Confidence 345667777777777889999999998877542 22222222000 0011
Q ss_pred EEEEEecCCCCeeeeEeeCCCeEeeeCCCCccCcCCCCCcchhhhcccccCceeEEEEEecCC----cEEEecccccccC
Q 004499 84 MSYHVYSLGEGIVGQVAVTGKHQWIFSDQLVTNSCSSFEFSDGWQSQFSAGIRTIAVVAVVPH----GVVQLGSLDEVTE 159 (748)
Q Consensus 84 MS~~sF~~GeGlpGrAaaSG~hvWI~~~~~~~~~~~~~e~~r~~~~QfSAGIQTIVcIPV~~~----GVLELGSTe~V~E 159 (748)
..|+.|+|+.|+++.+|++++|.+...... +.+... ....+++..+|||+.-. |||.+.....-.-
T Consensus 66 ---~~l~~geGi~G~Va~tg~pV~V~Dv~~dpr----f~~~~~---~~~~~~~S~L~VPL~~~geVIGVL~v~~~~~~~F 135 (748)
T PRK11061 66 ---VTLAFDEGIVGLVGRLAEPINLADAQKHPS----FKYIPS---VKEERFRAFLGVPIIYRRQLLGVLVVQQRELRQF 135 (748)
T ss_pred ---eeccCCcchHHHHhccCceEEECCcccCcc----cccCcc---ccCccceEEEEEEEeeCCEEEEEEEEeeCCCCCC
Confidence 147889999999999999999976643211 111111 12368999999998533 7887777665444
Q ss_pred CHHHHHHHHHHHhhc
Q 004499 160 DMKVVTHIRDVFAAL 174 (748)
Q Consensus 160 d~~lV~~VKslF~~l 174 (748)
+.+-+..+..+..+.
T Consensus 136 s~~d~~lL~~LA~~a 150 (748)
T PRK11061 136 DESEESFLVTLATQL 150 (748)
T ss_pred CHHHHHHHHHHHHHH
Confidence 454455555555444
No 15
>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=87.47 E-value=1 Score=38.46 Aligned_cols=41 Identities=22% Similarity=0.357 Sum_probs=36.3
Q ss_pred hhcc-cchHHHHHHHHHhcCceEEeeeeeeeCCeEEEEEEEE
Q 004499 681 LCEE-CSHFLEIAEAIRSLGLTILKGVTEAHGDKTWICFVVE 721 (748)
Q Consensus 681 ~ce~-~~~flei~~~i~~l~l~il~g~~e~~~~~~~~~f~ve 721 (748)
.+.+ -|.|.+|+.++..+|+.|+...+.+.++++...|.|.
T Consensus 7 ~~~D~~Gll~~i~~~l~~~~lnI~sa~i~t~~~~~~d~f~v~ 48 (72)
T cd04926 7 RTEDRVGLLSDVTRVFRENGLTVTRAEISTQGDMAVNVFYVT 48 (72)
T ss_pred EECCccCHHHHHHHHHHHCCcEEEEEEEecCCCeEEEEEEEE
Confidence 3444 8999999999999999999998888888999999995
No 16
>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=87.31 E-value=1.5 Score=36.15 Aligned_cols=51 Identities=18% Similarity=0.305 Sum_probs=42.7
Q ss_pred hhhhhhcc-cchHHHHHHHHHhcCceEEeeeeeeeCCeEEEEEEEEecCCCc
Q 004499 677 LVEMLCEE-CSHFLEIAEAIRSLGLTILKGVTEAHGDKTWICFVVEGQDNRI 727 (748)
Q Consensus 677 liem~ce~-~~~flei~~~i~~l~l~il~g~~e~~~~~~~~~f~ve~~~~~~ 727 (748)
+|+..|.+ .|.|.+|+.+|...|+.|.+..+.+.++.+-..|.|+..+...
T Consensus 2 ~l~v~~~d~~gll~~i~~~l~~~~~~I~~~~~~~~~~~~~~~f~i~~~~~~~ 53 (70)
T cd04899 2 VLELTALDRPGLLADVTRVLAELGLNIHSAKIATLGERAEDVFYVTDADGQP 53 (70)
T ss_pred EEEEEEcCCccHHHHHHHHHHHCCCeEEEEEEEecCCEEEEEEEEECCCCCc
Confidence 45566777 7889999999999999999999999888888999998644443
No 17
>KOG2588 consensus Predicted DNA-binding protein [Transcription]
Probab=84.70 E-value=0.69 Score=56.77 Aligned_cols=59 Identities=34% Similarity=0.446 Sum_probs=46.9
Q ss_pred cccccccCCCCCCCC-----CchhhHHHHHHHHHHHhhcC-CCcccchhhHHHHHHHHHHHHHHh
Q 004499 561 KNNKKRARTGENGRP-----RPRDRQLIQDRIKELRELVP-NGSKCSIDSLLERTIKHMLFLQSI 619 (748)
Q Consensus 561 ~~~k~r~~~~~~~~p-----rp~~r~~i~~r~~~lr~~vp-~~~k~~i~~~l~~~i~~~~~l~~~ 619 (748)
|...+|.+||+..|- --|=|--|+|||-|||.+|| --+|....+-|.+||+|+.|||..
T Consensus 264 k~Pi~rl~~G~~kRtAHN~IEKRYRsSINDKI~eLk~lV~g~~aKl~kSavLr~ai~~i~dl~~~ 328 (953)
T KOG2588|consen 264 KKPIKRLLPGGEKRTAHNIIEKRYRSSINDKIIELKDLVPGTEAKLNKSAVLRKAIDYIEDLQGY 328 (953)
T ss_pred cCchhhcCCCCcccchhhHHHHHhhcchhHHHHHHHHhcCccHhhhhhhhhHHHHHHHHHHhhcc
Confidence 567788888844443 11668889999999999999 445677778899999999999976
No 18
>KOG4029 consensus Transcription factor HAND2/Transcription factor TAL1/TAL2/LYL1 [Transcription]
Probab=83.60 E-value=1.5 Score=45.73 Aligned_cols=56 Identities=25% Similarity=0.360 Sum_probs=43.9
Q ss_pred cCCCCCCCCCchhhHHHHHHHHHHHhhcCCC----cccchhhHHHHHHHHHHHHHHh-hhhH
Q 004499 567 ARTGENGRPRPRDRQLIQDRIKELRELVPNG----SKCSIDSLLERTIKHMLFLQSI-TKHA 623 (748)
Q Consensus 567 ~~~~~~~~prp~~r~~i~~r~~~lr~~vp~~----~k~~i~~~l~~~i~~~~~l~~~-~~~~ 623 (748)
.|...+.|.| +|=+.++..--+||+++|.. .|.|....|--||+||.||+.+ ....
T Consensus 109 ~~~~~n~RER-~Rv~~vN~~f~~Lr~~lP~~~~~~kklSKveTLr~A~~YI~~L~~lL~~~~ 169 (228)
T KOG4029|consen 109 QRQARNARER-QRVQSVNSAFAELRALLPTEPPQSKKLSKVETLRLATSYIRYLTKLLATQE 169 (228)
T ss_pred hhhhhhhhhh-hcccchhhhhHHHHhcCCCCCCcccccCcccchHHHHHHHHHHHHHhcccc
Confidence 3444455555 55568999999999999974 4679999999999999999988 4443
No 19
>KOG3561 consensus Aryl-hydrocarbon receptor nuclear translocator [Transcription]
Probab=83.43 E-value=1.2 Score=54.48 Aligned_cols=58 Identities=22% Similarity=0.405 Sum_probs=46.5
Q ss_pred ccccccCCCCCCCCCchhhHHHHHHHHHHHhhcCCCc----ccchhhHHHHHHHHHHHHHHh
Q 004499 562 NNKKRARTGENGRPRPRDRQLIQDRIKELRELVPNGS----KCSIDSLLERTIKHMLFLQSI 619 (748)
Q Consensus 562 ~~k~r~~~~~~~~prp~~r~~i~~r~~~lr~~vp~~~----k~~i~~~l~~~i~~~~~l~~~ 619 (748)
..|+|+++.....--=|||++.+--|+||-+|||--+ |.|.-++|..||+||+=+...
T Consensus 14 d~k~r~~Re~~~~~EKrRRdq~N~yI~ELs~Mvp~~~~~~RK~DK~tVLr~aV~~lr~~k~~ 75 (803)
T KOG3561|consen 14 DSKDRKKRENRSEIEKRRRDQMNKYIEELSEMVPTNASLSRKPDKLTVLRMAVDHLRLIKEQ 75 (803)
T ss_pred cchhhhccccchhHHHHHHHHHHHHHHHHHHhhhcchhcccCchHHHHHHHHHHHHHHHhhh
Confidence 3444444433333334899999999999999999877 999999999999999988886
No 20
>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=83.16 E-value=3.3 Score=36.37 Aligned_cols=53 Identities=23% Similarity=0.214 Sum_probs=45.1
Q ss_pred hhhhhhhcc-cchHHHHHHHHHhcCceEEeeeeeeeCCeEEEEEEEEecCCCcc
Q 004499 676 MLVEMLCEE-CSHFLEIAEAIRSLGLTILKGVTEAHGDKTWICFVVEGQDNRIM 728 (748)
Q Consensus 676 ~liem~ce~-~~~flei~~~i~~l~l~il~g~~e~~~~~~~~~f~ve~~~~~~~ 728 (748)
.+||..+.+ -|+-.+|+.+++.+||.|-+..+.+.++.+-..|.|.-.....+
T Consensus 2 Tviev~a~DRpGLL~~i~~~l~~~gl~I~~AkIsT~Gerv~DvFyV~d~~g~kl 55 (72)
T cd04895 2 TLVKVDSARKPGILLEAVQVLTDLDLCITKAYISSDGGWFMDVFHVTDQLGNKL 55 (72)
T ss_pred EEEEEEECCcCCHHHHHHHHHHHCCcEEEEEEEeecCCeEEEEEEEECCCCCCC
Confidence 357777777 67888999999999999999999999999999999976544444
No 21
>PF01590 GAF: GAF domain; InterPro: IPR003018 This domain is present in phytochromes and cGMP-specific phosphodiesterases. cGMP-dependent 3',5'-cyclic phosphodiesterase (3.1.4.17 from EC) catalyses the conversion of guanosine 3',5'-cyclic phosphate to guanosine 5'-phosphate. A phytochrome is a regulatory photoreceptor which exists in 2 forms that are reversibly interconvertible by light, the PR form that absorbs maximally in the red region of the spectrum, and the PFR form that absorbs maximally in the far-red region. This domain is also found in NifA, a transcriptional activator which is required for activation of most Nif operons which are directly involved in nitrogen fixation. NifA interacts with sigma-54.; GO: 0005515 protein binding; PDB: 2Y8H_A 3DBA_B 3CI6_A 3E0Y_B 2W3G_B 2W3D_A 2W3E_A 2Y79_B 2W3H_A 2W3F_A ....
Probab=82.88 E-value=1.7 Score=39.69 Aligned_cols=114 Identities=18% Similarity=0.080 Sum_probs=74.1
Q ss_pred hHHHHHHHHhhccCCCcEEEEEeeecCCCC-eEEEecCCccCCCCCcchhhhhcchhhhhcccCCCCCCCcccceeeeEE
Q 004499 7 TFDLHGILKSLCFNTAWKYAVFWKLKHRTR-MVLTWEDGYYDNCGQQDSLENKCSSESLENFHGGRYSHDPLGLAVAKMS 85 (748)
Q Consensus 7 ~~~Lqq~LrsLc~~~~WsYAIFWqls~~~~-~vL~WgDGyc~g~~~~~~~e~~~~~k~l~~L~gg~~~~d~~~l~v~~MS 85 (748)
...|+..|+.+++..+..++.++....+.. ....++.+-..... .
T Consensus 3 ~~~l~~~~~~l~~~l~~~~~~i~~~d~~~~~~~~~~~~~~~~~~~-------------------------------~--- 48 (154)
T PF01590_consen 3 DELLQRILRELAELLGADRASIFLLDPDGNRLYSVAGVGLPDPPP-------------------------------G--- 48 (154)
T ss_dssp HHHHHHHHHHHHHHHTESEEEEEEEETTTTEEEEEEEEEGGGSEH-------------------------------H---
T ss_pred HHHHHHHHHHHHHHHCCCEEEEEEEecCCCeEEEEEeeccccccc-------------------------------c---
Confidence 457888889999888999999988888854 33455444322210 0
Q ss_pred EEEecCCCCeeeeEeeCCCeEeeeCCCCccCcC--------C--CCCcchhhhcccccCceeEEEEEecCC----cEEEe
Q 004499 86 YHVYSLGEGIVGQVAVTGKHQWIFSDQLVTNSC--------S--SFEFSDGWQSQFSAGIRTIAVVAVVPH----GVVQL 151 (748)
Q Consensus 86 ~~sF~~GeGlpGrAaaSG~hvWI~~~~~~~~~~--------~--~~e~~r~~~~QfSAGIQTIVcIPV~~~----GVLEL 151 (748)
-..+..+.++.|+++.+++++.|.+........ . ...+.+.. -...|+++++++|+..+ |||.|
T Consensus 49 ~~~~~~~~~~~~~~~~~~~~~~i~d~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~s~l~vPi~~~g~~~G~l~l 126 (154)
T PF01590_consen 49 GRRLSMDESICGQVLQSREPIVISDVAADPRFAPQIAAQSALRALSSAERPF--LAEYGVRSYLCVPIISGGRLIGVLSL 126 (154)
T ss_dssp HEEEETTSSHHHHHHHHTSCEEESSSGGSTTSSCHHHHHHTTBTTTHHHHHH--HHTTTESEEEEEEEEETTEEEEEEEE
T ss_pred cccccccccHHHHHHhCCCeEeeccccccccccccccccccccccccccccc--cccccCceeeEeeeecccCcEEEEEE
Confidence 014566788899999999999998664322100 0 00000011 11469999999998544 89999
Q ss_pred ccccc
Q 004499 152 GSLDE 156 (748)
Q Consensus 152 GSTe~ 156 (748)
..+..
T Consensus 127 ~~~~~ 131 (154)
T PF01590_consen 127 YRTRP 131 (154)
T ss_dssp EEESS
T ss_pred EECCC
Confidence 88887
No 22
>smart00065 GAF Domain present in phytochromes and cGMP-specific phosphodiesterases. Mutations within these domains in PDE6B result in autosomal recessive inheritance of retinitis pigmentosa.
Probab=79.35 E-value=20 Score=30.58 Aligned_cols=123 Identities=24% Similarity=0.273 Sum_probs=73.3
Q ss_pred hHHHHHHHHhhccCCCcEEEEEeeecCC-C-CeEEEecCCccCCCCCcchhhhhcchhhhhcccCCCCCCCcccceeeeE
Q 004499 7 TFDLHGILKSLCFNTAWKYAVFWKLKHR-T-RMVLTWEDGYYDNCGQQDSLENKCSSESLENFHGGRYSHDPLGLAVAKM 84 (748)
Q Consensus 7 ~~~Lqq~LrsLc~~~~WsYAIFWqls~~-~-~~vL~WgDGyc~g~~~~~~~e~~~~~k~l~~L~gg~~~~d~~~l~v~~M 84 (748)
...++..++.++...++.++.+|.++.+ . .....+..+.....
T Consensus 3 ~~~~~~~~~~l~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~----------------------------------- 47 (149)
T smart00065 3 EELLQTILEELRQLLGADRVLIYLVDEDDRGELVLVAADGLTLPL----------------------------------- 47 (149)
T ss_pred HHHHHHHHHHHHHHhCCceEEEEEEecCCCCcEEEEEecCCCccc-----------------------------------
Confidence 4567788888888889999999999984 2 22222222221110
Q ss_pred EEEEecCCCCeeeeEeeCCCeEeeeCCCCccCcCCCCCcchhhhcccccCceeEEEEEecCC----cEEEeccccc----
Q 004499 85 SYHVYSLGEGIVGQVAVTGKHQWIFSDQLVTNSCSSFEFSDGWQSQFSAGIRTIAVVAVVPH----GVVQLGSLDE---- 156 (748)
Q Consensus 85 S~~sF~~GeGlpGrAaaSG~hvWI~~~~~~~~~~~~~e~~r~~~~QfSAGIQTIVcIPV~~~----GVLELGSTe~---- 156 (748)
....|+.+.++.++++.+++++.+.+..... ....... ....|++.++++|+.-+ |+|.+.+.+.
T Consensus 48 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------~~~~~~~-~~~~~~~s~~~~Pl~~~~~~~G~l~~~~~~~~~~~ 120 (149)
T smart00065 48 LGLRYPLGEGLAGRVAETGRPLNIPDVEADP------VFALDLL-GRYQGVRSFLAVPLVADGELVGVLALHNKDSPRPF 120 (149)
T ss_pred ceEEecCCCChHHHHHHcCCeEEeechhhCC------ccccccc-cceeceeeEEEeeeeecCEEEEEEEEEecCCCCCC
Confidence 0124667778889999999998887543211 1111111 12245999999997443 7888887621
Q ss_pred ccCCHHHHHHHHHHH
Q 004499 157 VTEDMKVVTHIRDVF 171 (748)
Q Consensus 157 V~Ed~~lV~~VKslF 171 (748)
-.++..+++.+-..+
T Consensus 121 ~~~~~~~l~~~~~~i 135 (149)
T smart00065 121 TEEDEELLQALANQL 135 (149)
T ss_pred CHHHHHHHHHHHHHH
Confidence 123445555554443
No 23
>TIGR01693 UTase_glnD [Protein-PII] uridylyltransferase. This model describes GlnD, the uridylyltransferase/uridylyl-removing enzyme for the nitrogen regulatory protein PII. Not all homologs of PII share the property of uridylyltransferase modification on the characteristic Tyr residue (see Prosite pattern PS00496 and document PDOC00439), but the modification site is preserved in the PII homolog of all species with a member of this family.
Probab=79.31 E-value=13 Score=45.80 Aligned_cols=65 Identities=15% Similarity=0.153 Sum_probs=51.6
Q ss_pred eeEEeec-CCCcchhhhhhhcc-cchHHHHHHHHHhcCceEEeeeee-eeCCeEEEEEEEEecCCCcc
Q 004499 664 SIVVENL-NKNGQMLVEMLCEE-CSHFLEIAEAIRSLGLTILKGVTE-AHGDKTWICFVVEGQDNRIM 728 (748)
Q Consensus 664 ~i~ve~l-~~~~~~liem~ce~-~~~flei~~~i~~l~l~il~g~~e-~~~~~~~~~f~ve~~~~~~~ 728 (748)
|+++.+- ..++...|+..+.+ -|+|-.|+.++..+||+|+.+.+- +.++.+...|.|....+..+
T Consensus 656 ~~v~~~~~~~~~~t~i~V~~~DrpgLla~i~~~L~~~~l~I~~A~I~tt~~g~~lD~F~V~~~~g~~~ 723 (850)
T TIGR01693 656 PLALIDGTRPSGGTEVFIYAPDQPGLFAKVAGALAMLSLSVHDAQVNTTKDGVALDTFVVQDLFGSPP 723 (850)
T ss_pred CEEEEeccCCCCeEEEEEEeCCCCcHHHHHHHHHHHCCCeEEEEEEEEecCCEEEEEEEEECCCCCCC
Confidence 4444433 33566678888988 788999999999999999999776 88999999999976554444
No 24
>PLN03217 transcription factor ATBS1; Provisional
Probab=77.74 E-value=8.6 Score=35.25 Aligned_cols=56 Identities=25% Similarity=0.347 Sum_probs=47.0
Q ss_pred CchhhHHHHHHHHHHHhhcCC------CcccchhhHHHHHHHHHHHHHHh-hhhHhhhhhhccc
Q 004499 576 RPRDRQLIQDRIKELRELVPN------GSKCSIDSLLERTIKHMLFLQSI-TKHADKLSKCAES 632 (748)
Q Consensus 576 rp~~r~~i~~r~~~lr~~vp~------~~k~~i~~~l~~~i~~~~~l~~~-~~~~dkl~~~~~~ 632 (748)
|.-| .+|.|-+-.||+|+|. +.|++-.-+|.+|-.||.-|..+ -.+.|+|-+.-++
T Consensus 16 risd-dqi~dLvsKLq~llPe~r~~r~s~k~saskvLqEtC~YIrsLhrEvDdLSerLs~LL~t 78 (93)
T PLN03217 16 RISE-DQINDLIIKLQQLLPELRDSRRSDKVSAARVLQDTCNYIRNLHREVDDLSERLSELLAN 78 (93)
T ss_pred CCCH-HHHHHHHHHHHHHChHHHhhhccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 4444 5789999999999996 46799999999999999999887 7888888776544
No 25
>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=74.74 E-value=7.1 Score=31.71 Aligned_cols=44 Identities=20% Similarity=0.366 Sum_probs=38.4
Q ss_pred hhhhcc-cchHHHHHHHHHhcCceEEeeeeeeeCCeEEEEEEEEe
Q 004499 679 EMLCEE-CSHFLEIAEAIRSLGLTILKGVTEAHGDKTWICFVVEG 722 (748)
Q Consensus 679 em~ce~-~~~flei~~~i~~l~l~il~g~~e~~~~~~~~~f~ve~ 722 (748)
...|.+ .|.|-+|+.++...|++|+...+.+.+++....|.|..
T Consensus 4 ~i~~~d~~g~l~~i~~~l~~~~~~I~~~~~~~~~~~~~~~~~v~~ 48 (70)
T cd04873 4 EVYAPDRPGLLADITRVLADLGLNIHDARISTTGERALDVFYVTD 48 (70)
T ss_pred EEEeCCCCCHHHHHHHHHHHCCCeEEEEEEeecCCEEEEEEEEEC
Confidence 345666 78899999999999999999999998888888999875
No 26
>cd04928 ACT_TyrKc Uncharacterized, N-terminal ACT domain of an Arabidopsis/Oryza predicted tyrosine kinase and other related ACT domains. This CD includes a novel, yet uncharacterized, N-terminal ACT domain of an Arabidopsis/Oryza predicted tyrosine kinase and other related ACT domains. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=66.72 E-value=13 Score=32.32 Aligned_cols=39 Identities=21% Similarity=0.308 Sum_probs=34.0
Q ss_pred ccchHHHHHHHHHhcCceEEeeee-eeeCCeEEEEEEEEe
Q 004499 684 ECSHFLEIAEAIRSLGLTILKGVT-EAHGDKTWICFVVEG 722 (748)
Q Consensus 684 ~~~~flei~~~i~~l~l~il~g~~-e~~~~~~~~~f~ve~ 722 (748)
..|+|-.|+-++-.+||+|+...+ ++.++.++..|+|--
T Consensus 11 r~gLFa~iag~L~~~~LnI~~A~i~tt~dG~~LDtF~V~d 50 (68)
T cd04928 11 KPKLLSQLSSLLGDLGLNIAEAHAFSTDDGLALDIFVVTG 50 (68)
T ss_pred CcchHHHHHHHHHHCCCceEEEEEEEcCCCeEEEEEEEec
Confidence 389999999999999999999655 577899999999953
No 27
>KOG0561 consensus bHLH transcription factor [Transcription]
Probab=65.68 E-value=7.6 Score=42.72 Aligned_cols=42 Identities=31% Similarity=0.427 Sum_probs=39.6
Q ss_pred hhhHHHHHHHHHHHhhcC--CCcccchhhHHHHHHHHHHHHHHh
Q 004499 578 RDRQLIQDRIKELRELVP--NGSKCSIDSLLERTIKHMLFLQSI 619 (748)
Q Consensus 578 ~~r~~i~~r~~~lr~~vp--~~~k~~i~~~l~~~i~~~~~l~~~ 619 (748)
||-|-|+-...-||.|+| .|.|.+..+||..|..||..|..+
T Consensus 70 RRMQSINAGFqsLr~LlPr~eGEKLSKAAILQQTa~yI~~Le~~ 113 (373)
T KOG0561|consen 70 RRMQSINAGFQSLRALLPRKEGEKLSKAAILQQTADYIHQLEGH 113 (373)
T ss_pred HHHHhhhHHHHHHHHhcCcccchhhHHHHHHHHHHHHHHHHHhc
Confidence 678999999999999999 699999999999999999999877
No 28
>PRK01759 glnD PII uridylyl-transferase; Provisional
Probab=65.39 E-value=23 Score=43.99 Aligned_cols=60 Identities=17% Similarity=0.315 Sum_probs=48.6
Q ss_pred ecCCCcchhhhhhhcc-cchHHHHHHHHHhcCceEEeeeeee-eCCeEEEEEEEEecCCCcc
Q 004499 669 NLNKNGQMLVEMLCEE-CSHFLEIAEAIRSLGLTILKGVTEA-HGDKTWICFVVEGQDNRIM 728 (748)
Q Consensus 669 ~l~~~~~~liem~ce~-~~~flei~~~i~~l~l~il~g~~e~-~~~~~~~~f~ve~~~~~~~ 728 (748)
+-...+.-.|++.|.+ -|+|-.|+.++-.+||+|+.+.+-+ .++.+...|.|.-.....+
T Consensus 671 ~~~~~~~t~V~V~~~DrpGLfa~Ia~~L~~~~L~I~~A~I~T~~~g~alD~F~V~d~~g~~~ 732 (854)
T PRK01759 671 NRFSRGGTEIFIYCQDQANLFLKVVSTIGAKKLSIHDAQIITSQDGYVLDSFIVTELNGKLL 732 (854)
T ss_pred ecCCCCeEEEEEEecCCccHHHHHHHHHHHCCCeEEEEEEEEccCCEEEEEEEEeCCCCCCC
Confidence 3344466678888888 8999999999999999999999755 9999999999965444434
No 29
>PF13291 ACT_4: ACT domain; PDB: 2KO1_B 3IBW_A.
Probab=65.15 E-value=6.9 Score=33.55 Aligned_cols=50 Identities=18% Similarity=0.204 Sum_probs=39.7
Q ss_pred hhhhhcc-cchHHHHHHHHHhcCceEEeeeeeee--CCeEEEEEEEEecCCCc
Q 004499 678 VEMLCEE-CSHFLEIAEAIRSLGLTILKGVTEAH--GDKTWICFVVEGQDNRI 727 (748)
Q Consensus 678 iem~ce~-~~~flei~~~i~~l~l~il~g~~e~~--~~~~~~~f~ve~~~~~~ 727 (748)
|++.|.+ .|..-+|+.+|-..|..|..-.++.. ++-.-..|.||+.+..+
T Consensus 9 l~i~~~dr~GlL~dI~~~i~~~~~nI~~i~~~~~~~~~~~~~~l~v~V~d~~~ 61 (80)
T PF13291_consen 9 LRIEAEDRPGLLADITSVISENGVNIRSINARTNKDDGTARITLTVEVKDLEH 61 (80)
T ss_dssp EEEEEE--TTHHHHHHHHHHCSSSEEEEEEEEE--ETTEEEEEEEEEESSHHH
T ss_pred EEEEEEcCCCHHHHHHHHHHHCCCCeEEEEeEEeccCCEEEEEEEEEECCHHH
Confidence 3455655 68999999999999999999999995 67888899999854433
No 30
>PRK05092 PII uridylyl-transferase; Provisional
Probab=63.19 E-value=33 Score=42.98 Aligned_cols=52 Identities=19% Similarity=0.220 Sum_probs=43.8
Q ss_pred CCCcchhhhhhhcc-cchHHHHHHHHHhcCceEEeeeee-eeCCeEEEEEEEEe
Q 004499 671 NKNGQMLVEMLCEE-CSHFLEIAEAIRSLGLTILKGVTE-AHGDKTWICFVVEG 722 (748)
Q Consensus 671 ~~~~~~liem~ce~-~~~flei~~~i~~l~l~il~g~~e-~~~~~~~~~f~ve~ 722 (748)
..+|...|...|.+ -|+|-.|+.++..+||+|+...+- +.++.+...|.|.-
T Consensus 728 ~~~~~t~v~I~~~Dr~GLfa~i~~~L~~~glnI~~A~I~t~~dg~alD~F~V~~ 781 (931)
T PRK05092 728 PARGVTEVTVLAADHPGLFSRIAGACAAAGANIVDARIFTTTDGRALDTFWIQD 781 (931)
T ss_pred CCCCeEEEEEEeCCCCcHHHHHHHHHHHCCCcEEEEEEEEecCCeEEEEEEEEC
Confidence 34466677888888 788999999999999999999865 48999999999943
No 31
>PRK00275 glnD PII uridylyl-transferase; Provisional
Probab=63.08 E-value=44 Score=41.83 Aligned_cols=53 Identities=17% Similarity=0.241 Sum_probs=42.5
Q ss_pred cchhhhhhhcc-cchHHHHHHHHHhcCceEEeeee-eeeCCeEEEEEEEEecCCC
Q 004499 674 GQMLVEMLCEE-CSHFLEIAEAIRSLGLTILKGVT-EAHGDKTWICFVVEGQDNR 726 (748)
Q Consensus 674 ~~~liem~ce~-~~~flei~~~i~~l~l~il~g~~-e~~~~~~~~~f~ve~~~~~ 726 (748)
|-.-|-+.|.+ -|+|..|+-++-.+||+|+++.+ ++.++.++..|.|--....
T Consensus 703 ~~t~V~V~~~DrpgLFa~i~g~L~~~~lnI~~A~I~Tt~dg~alD~F~V~d~~g~ 757 (895)
T PRK00275 703 GGTQIFIYAPDQHDFFAATVAAMDQLNLNIHDARIITSSSQFTLDTYIVLDDDGE 757 (895)
T ss_pred CeEEEEEEeCCCCcHHHHHHHHHHHCCCeEEEEEEEEcCCCeEEEEEEEeCCCCC
Confidence 33345566766 89999999999999999999974 8889999999999543333
No 32
>cd04887 ACT_MalLac-Enz ACT_MalLac-Enz CD includes the N-terminal ACT domain of putative NAD-dependent malic enzyme 1, Bacillus subtilis YqkI and related domains. The ACT_MalLac-Enz CD includes the N-terminal ACT domain of putative NAD-dependent malic enzyme 1, Bacillus subtilis YqkI, a malolactic enzyme (MalLac-Enz) which converts malate to lactate, and other related ACT domains. The yqkJ product is predicted to convert malate directly to lactate, as opposed to related malic enzymes that convert malate to pyruvate. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=62.02 E-value=12 Score=31.13 Aligned_cols=46 Identities=17% Similarity=0.036 Sum_probs=35.6
Q ss_pred ccchHHHHHHHHHhcCceEEeeeeeeeC-CeEEEEEEEEecCCCcce
Q 004499 684 ECSHFLEIAEAIRSLGLTILKGVTEAHG-DKTWICFVVEGQDNRIMH 729 (748)
Q Consensus 684 ~~~~flei~~~i~~l~l~il~g~~e~~~-~~~~~~f~ve~~~~~~~~ 729 (748)
+.|.+.+|+.+|...|..|++-.+.... +..=..|.||+.+..++.
T Consensus 9 ~~g~L~~i~~~i~~~~~nI~~v~~~~~~~~~~~~~~~vev~~~~~l~ 55 (74)
T cd04887 9 RPGMLGRVTTAIGEAGGDIGAIDLVEQGRDYTVRDITVDAPSEEHAE 55 (74)
T ss_pred CCchHHHHHHHHHHcCCcEEEEEEEEecCCEEEEEEEEEcCCHHHHH
Confidence 3788999999999999999988887764 445567889985544433
No 33
>PRK05092 PII uridylyl-transferase; Provisional
Probab=61.46 E-value=16 Score=45.61 Aligned_cols=74 Identities=18% Similarity=0.208 Sum_probs=57.4
Q ss_pred ecCCCcchhhhhhhcc-cchHHHHHHHHHhcCceEEeeeeeeeCCeEEEEEEEEecCCCcce---Ee-ehhHHHHHHhc
Q 004499 669 NLNKNGQMLVEMLCEE-CSHFLEIAEAIRSLGLTILKGVTEAHGDKTWICFVVEGQDNRIMH---RM-DVLWSLVQLLQ 742 (748)
Q Consensus 669 ~l~~~~~~liem~ce~-~~~flei~~~i~~l~l~il~g~~e~~~~~~~~~f~ve~~~~~~~~---r~-~i~~~l~~~l~ 742 (748)
+-..++...||+.|.+ -|+|-+|+.++..+||+|....+.+.++.+...|.|.......++ +. +|--.|...|.
T Consensus 837 ~~~s~~~t~i~I~~~DrpGLl~~I~~~l~~~gl~I~~A~I~T~~~~~~D~F~v~d~~g~~i~~~~~~~~l~~~L~~~L~ 915 (931)
T PRK05092 837 NEASNRFTVIEVNGRDRPGLLYDLTRALSDLNLNIASAHIATYGERAVDVFYVTDLFGLKITNEARQAAIRRALLAALA 915 (931)
T ss_pred eCCCCCeEEEEEEECCcCcHHHHHHHHHHHCCceEEEEEEEEcCCEEEEEEEEeCCCCCcCCCHHHHHHHHHHHHHHhc
Confidence 3355667899999999 899999999999999999999999999999999999754333332 22 24445555553
No 34
>PRK00275 glnD PII uridylyl-transferase; Provisional
Probab=59.80 E-value=20 Score=44.72 Aligned_cols=60 Identities=13% Similarity=0.241 Sum_probs=50.8
Q ss_pred ecCCCcchhhhhhhcc-cchHHHHHHHHHhcCceEEeeeeeeeCCeEEEEEEEEecCCCcc
Q 004499 669 NLNKNGQMLVEMLCEE-CSHFLEIAEAIRSLGLTILKGVTEAHGDKTWICFVVEGQDNRIM 728 (748)
Q Consensus 669 ~l~~~~~~liem~ce~-~~~flei~~~i~~l~l~il~g~~e~~~~~~~~~f~ve~~~~~~~ 728 (748)
+-..++...||..+.+ -|+|-.|+.++..+||+|+...+.+.++.+...|.|--..+..+
T Consensus 808 ~~~~~~~T~i~V~a~DrpGLLa~I~~~L~~~~l~I~~AkI~T~g~~v~D~F~V~d~~g~~l 868 (895)
T PRK00275 808 NDAQRPVTVLEIIAPDRPGLLARIGRIFLEFDLSLQNAKIATLGERVEDVFFITDADNQPL 868 (895)
T ss_pred ECCCCCeEEEEEEECCCCCHHHHHHHHHHHCCCEEEEeEEEecCCEEEEEEEEECCCCCCC
Confidence 3345677788999988 89999999999999999999999999999999999965444433
No 35
>PRK05007 PII uridylyl-transferase; Provisional
Probab=58.82 E-value=45 Score=41.72 Aligned_cols=61 Identities=10% Similarity=0.111 Sum_probs=48.1
Q ss_pred ecCCCcchhhhhhhcc-cchHHHHHHHHHhcCceEEeeeee-eeCCeEEEEEEEEecCCCcce
Q 004499 669 NLNKNGQMLVEMLCEE-CSHFLEIAEAIRSLGLTILKGVTE-AHGDKTWICFVVEGQDNRIMH 729 (748)
Q Consensus 669 ~l~~~~~~liem~ce~-~~~flei~~~i~~l~l~il~g~~e-~~~~~~~~~f~ve~~~~~~~~ 729 (748)
+-...+...|+..|.+ -|+|..|+.++-.+||+|++..+- +.++.+...|.|--.+...++
T Consensus 695 ~~~~~~~t~V~V~a~DrpGLfa~Ia~~La~~~L~I~~A~I~T~~dg~alD~F~V~d~~g~~~~ 757 (884)
T PRK05007 695 KQATRGGTEIFIWSPDRPYLFAAVCAELDRRNLSVHDAQIFTSRDGMAMDTFIVLEPDGSPLS 757 (884)
T ss_pred ecCCCCeEEEEEEecCCcCHHHHHHHHHHHCCCEEEEEEEEEcCCCeEEEEEEEECCCCCCCC
Confidence 3344567778899998 788999999999999999999855 556699999999654444443
No 36
>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=58.58 E-value=23 Score=25.44 Aligned_cols=43 Identities=9% Similarity=0.060 Sum_probs=32.1
Q ss_pred hhhcc-cchHHHHHHHHHhcCceEEeeeeeeeCCeEEEEEEEEe
Q 004499 680 MLCEE-CSHFLEIAEAIRSLGLTILKGVTEAHGDKTWICFVVEG 722 (748)
Q Consensus 680 m~ce~-~~~flei~~~i~~l~l~il~g~~e~~~~~~~~~f~ve~ 722 (748)
..|.+ .|.|.+|.+++...|+.|.+-........-.++|.|..
T Consensus 3 i~~~~~~~~l~~i~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~ 46 (60)
T cd02116 3 VSGPDRPGLLAKVLSVLAEAGINITSIEQRTSGDGGEADIFIVV 46 (60)
T ss_pred EEecCCCchHHHHHHHHHHCCCcEEEEEeEEcCCCCeEEEEEEE
Confidence 34555 78899999999999999999987665444456655544
No 37
>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=57.69 E-value=22 Score=31.57 Aligned_cols=46 Identities=17% Similarity=0.325 Sum_probs=41.8
Q ss_pred hhhhhhcc-cchHHHHHHHHHhcCceEEeeeee--eeCCeEEEEEEEEe
Q 004499 677 LVEMLCEE-CSHFLEIAEAIRSLGLTILKGVTE--AHGDKTWICFVVEG 722 (748)
Q Consensus 677 liem~ce~-~~~flei~~~i~~l~l~il~g~~e--~~~~~~~~~f~ve~ 722 (748)
+||+.|.+ -|+--+|+.++..+||.|-.+.+. +.++.+-..|.|..
T Consensus 2 vlev~a~DRpGLL~~i~~~l~~~~l~i~~AkI~~~T~Gerv~D~Fyv~~ 50 (75)
T cd04896 2 LLQIRCVDQKGLLYDILRTSKDCNIQISYGRFSSKVKGYREVDLFIVQS 50 (75)
T ss_pred EEEEEeCCcccHHHHHHHHHHHCCeEEEEEEEecCcccCEEEEEEEEeC
Confidence 57888888 577779999999999999999999 99999999999954
No 38
>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=56.08 E-value=22 Score=28.44 Aligned_cols=45 Identities=18% Similarity=0.242 Sum_probs=37.6
Q ss_pred hhhhhcc-cchHHHHHHHHHhcCceEEeeeeeeeCCeEEEEEEEEe
Q 004499 678 VEMLCEE-CSHFLEIAEAIRSLGLTILKGVTEAHGDKTWICFVVEG 722 (748)
Q Consensus 678 iem~ce~-~~~flei~~~i~~l~l~il~g~~e~~~~~~~~~f~ve~ 722 (748)
|.+.|++ -|.+.+|+.++...|+.|..-.....++..|..|.+..
T Consensus 3 v~v~~~drpG~l~~v~~~la~~~inI~~~~~~~~~~~~~~~~~~~~ 48 (66)
T PF01842_consen 3 VRVIVPDRPGILADVTEILADHGINIDSISQSSDKDGVGIVFIVIV 48 (66)
T ss_dssp EEEEEETSTTHHHHHHHHHHHTTEEEEEEEEEEESSTTEEEEEEEE
T ss_pred EEEEcCCCCCHHHHHHHHHHHcCCCHHHeEEEecCCCceEEEEEEE
Confidence 4456777 89999999999999999999999988886677776654
No 39
>KOG3560 consensus Aryl-hydrocarbon receptor [Transcription]
Probab=54.70 E-value=12 Score=44.15 Aligned_cols=64 Identities=27% Similarity=0.385 Sum_probs=51.8
Q ss_pred ccccccccccCCCCCCCCCchh----------hHHHHHHHHHHHhhcCC----CcccchhhHHHHHHHHHH---HHHHhh
Q 004499 558 EPAKNNKKRARTGENGRPRPRD----------RQLIQDRIKELRELVPN----GSKCSIDSLLERTIKHML---FLQSIT 620 (748)
Q Consensus 558 ~~~~~~k~r~~~~~~~~prp~~----------r~~i~~r~~~lr~~vp~----~~k~~i~~~l~~~i~~~~---~l~~~~ 620 (748)
+..-++|||.||+.+.||-||+ |+|.+--|..|--|.|= ++|.|.-++|.-++-|+. |.|.+-
T Consensus 5 ~~tYAsrkRrrp~qk~rpp~~a~tkSNPSKRHRdRLNaELD~lAsLLPfpqdiisKLDkLSVLRLSVSyLr~KSfFqvvl 84 (712)
T KOG3560|consen 5 ECTYASRKRRRPLQKQRPPPKALTKSNPSKRHRDRLNAELDHLASLLPFPQDIISKLDKLSVLRLSVSYLRVKSFFQVVL 84 (712)
T ss_pred cceehhhhccCCccccCCCccccccCCcchhHHHHhhhHHHHHHHhcCCCHHHHhhhhhhhhhhhhHHHHHHHHHHHHHH
Confidence 4456788999999999987765 99999999999999995 678888889999998875 566554
Q ss_pred h
Q 004499 621 K 621 (748)
Q Consensus 621 ~ 621 (748)
+
T Consensus 85 ~ 85 (712)
T KOG3560|consen 85 H 85 (712)
T ss_pred h
Confidence 3
No 40
>cd04877 ACT_TyrR N-terminal ACT domain of the TyrR protein. ACT_TyrR: N-terminal ACT domain of the TyrR protein. The TyrR protein of Escherichia coli controls the expression of a group of transcription units (TyrR regulon) whose gene products are involved in the biosynthesis or transport of the aromatic amino acids. Binding to specific DNA sequences known as TyrR boxes, the TyrR protein can either activate or repress transcription at different sigma70 promoters. Its regulatory activity occurs in response to intracellular levels of tyrosine, phenylalanine and tryptophan. The TyrR protein consists of an N-terminal region important for transcription activation with an ATP-independent aromatic amino acid binding site (contained within the ACT domain) and is involved in dimerization; a central region with an ATP binding site, an ATP-dependent aromatic amino acid binding site and is involved in hexamerization; and a helix turn helix DNA binding C-terminal region. In solution, in the absence
Probab=53.95 E-value=9.2 Score=32.55 Aligned_cols=45 Identities=13% Similarity=0.175 Sum_probs=35.8
Q ss_pred hhhhhhhcc-cchHHHHHHHHHhcCceEEeeeeeeeCCeEEEEEEEEec
Q 004499 676 MLVEMLCEE-CSHFLEIAEAIRSLGLTILKGVTEAHGDKTWICFVVEGQ 723 (748)
Q Consensus 676 ~liem~ce~-~~~flei~~~i~~l~l~il~g~~e~~~~~~~~~f~ve~~ 723 (748)
|=|+..|++ .|.+-+|+++|...|..|......+. .. .+|.+|+.
T Consensus 1 ~~l~I~~~dr~Gll~dI~~~i~~~~~nI~~~~~~~~--~~-i~l~i~v~ 46 (74)
T cd04877 1 MRLEITCEDRLGITQEVLDLLVEHNIDLRGIEIDPK--GR-IYLNFPTI 46 (74)
T ss_pred CEEEEEEEccchHHHHHHHHHHHCCCceEEEEEecC--Ce-EEEEeEec
Confidence 345677777 77899999999999999988887664 33 77888874
No 41
>PRK03381 PII uridylyl-transferase; Provisional
Probab=50.53 E-value=31 Score=42.41 Aligned_cols=59 Identities=14% Similarity=0.182 Sum_probs=50.6
Q ss_pred CCCcchhhhhhhcc-cchHHHHHHHHHhcCceEEeeeeeeeCCeEEEEEEEEecCCCcce
Q 004499 671 NKNGQMLVEMLCEE-CSHFLEIAEAIRSLGLTILKGVTEAHGDKTWICFVVEGQDNRIMH 729 (748)
Q Consensus 671 ~~~~~~liem~ce~-~~~flei~~~i~~l~l~il~g~~e~~~~~~~~~f~ve~~~~~~~~ 729 (748)
..++..+||..|.+ -|+|-.|+.++..+||+|....+.+.++.+...|.|.-.....++
T Consensus 703 ~~~~~t~i~V~a~DrpGLla~Ia~~L~~~~lnI~~AkI~T~g~~a~D~F~V~d~~g~~~~ 762 (774)
T PRK03381 703 ASPDATVLEVRAADRPGLLARLARALERAGVDVRWARVATLGADVVDVFYVTGAAGGPLA 762 (774)
T ss_pred CCCCeEEEEEEeCCchhHHHHHHHHHHHCCCeEEEEEEeecCCeEEEEEEEECCCCCcCc
Confidence 34456889999998 899999999999999999999999999999999999754444443
No 42
>PRK03059 PII uridylyl-transferase; Provisional
Probab=47.48 E-value=32 Score=42.82 Aligned_cols=53 Identities=8% Similarity=0.183 Sum_probs=47.6
Q ss_pred ecCCCcchhhhhhhcc-cchHHHHHHHHHhcCceEEeeeeeeeCCeEEEEEEEE
Q 004499 669 NLNKNGQMLVEMLCEE-CSHFLEIAEAIRSLGLTILKGVTEAHGDKTWICFVVE 721 (748)
Q Consensus 669 ~l~~~~~~liem~ce~-~~~flei~~~i~~l~l~il~g~~e~~~~~~~~~f~ve 721 (748)
+-..++...||..|.+ -|+|-.|+.++..+||.|+...+.+.++.+...|.|.
T Consensus 780 ~~~~~~~T~i~V~a~DrpGLLa~Ia~~L~~~~l~I~~AkI~T~~~~v~DvF~V~ 833 (856)
T PRK03059 780 PDERGQYYILSVSANDRPGLLYAIARVLAEHRVSVHTAKINTLGERVEDTFLID 833 (856)
T ss_pred EcCCCCEEEEEEEeCCcchHHHHHHHHHHHCCCeEEEEEEeecCCEEEEEEEEc
Confidence 3345677889999998 8999999999999999999999999999999999994
No 43
>PF13740 ACT_6: ACT domain; PDB: 1ZPV_A 3P96_A 1U8S_A.
Probab=47.05 E-value=42 Score=28.92 Aligned_cols=49 Identities=10% Similarity=0.159 Sum_probs=42.7
Q ss_pred chhhhhhhcc-cchHHHHHHHHHhcCceEEeeeeeeeCCeEEEEEEEEec
Q 004499 675 QMLVEMLCEE-CSHFLEIAEAIRSLGLTILKGVTEAHGDKTWICFVVEGQ 723 (748)
Q Consensus 675 ~~liem~ce~-~~~flei~~~i~~l~l~il~g~~e~~~~~~~~~f~ve~~ 723 (748)
+++|-+++++ -|+.-+++.++...|.+|++-.+.+.++..=..+.|++.
T Consensus 2 ~~vItv~G~DrpGiv~~v~~~l~~~g~ni~d~~~~~~~~~f~~~~~v~~~ 51 (76)
T PF13740_consen 2 QLVITVVGPDRPGIVAAVTGVLAEHGCNIEDSRQAVLGGRFTLIMLVSIP 51 (76)
T ss_dssp EEEEEEEEE--TTHHHHHHHHHHCTT-EEEEEEEEEETTEEEEEEEEEES
T ss_pred EEEEEEEecCCCcHHHHHHHHHHHCCCcEEEEEEEEEcCeEEEEEEEEeC
Confidence 4667788888 799999999999999999999999999999999999983
No 44
>PRK04374 PII uridylyl-transferase; Provisional
Probab=46.75 E-value=34 Score=42.72 Aligned_cols=52 Identities=10% Similarity=0.194 Sum_probs=47.5
Q ss_pred CCCcchhhhhhhcc-cchHHHHHHHHHhcCceEEeeeeeeeCCeEEEEEEEEe
Q 004499 671 NKNGQMLVEMLCEE-CSHFLEIAEAIRSLGLTILKGVTEAHGDKTWICFVVEG 722 (748)
Q Consensus 671 ~~~~~~liem~ce~-~~~flei~~~i~~l~l~il~g~~e~~~~~~~~~f~ve~ 722 (748)
..++...||..+.+ -|+|-.|+.++..+||.|+...+.+.++.+...|.|.-
T Consensus 792 ~~~~~t~leI~a~DrpGLLa~Ia~~l~~~~l~I~~AkI~T~g~~a~D~F~V~d 844 (869)
T PRK04374 792 AGGRRTRISLVAPDRPGLLADVAHVLRMQHLRVHDARIATFGERAEDQFQITD 844 (869)
T ss_pred CCCCeEEEEEEeCCcCcHHHHHHHHHHHCCCeEEEeEEEecCCEEEEEEEEEC
Confidence 44567789999998 89999999999999999999999999999999999954
No 45
>PF13492 GAF_3: GAF domain; PDB: 3EEA_A 4DMZ_A 4DN0_A 1VHM_A.
Probab=46.01 E-value=39 Score=29.72 Aligned_cols=113 Identities=19% Similarity=0.173 Sum_probs=66.0
Q ss_pred hHHHHHHHHhhccCCCcEEEEEeeecCCCCeEEEecCCccCCCCCcchhhhhcchhhhhcccCCCCCCCcccceeeeEEE
Q 004499 7 TFDLHGILKSLCFNTAWKYAVFWKLKHRTRMVLTWEDGYYDNCGQQDSLENKCSSESLENFHGGRYSHDPLGLAVAKMSY 86 (748)
Q Consensus 7 ~~~Lqq~LrsLc~~~~WsYAIFWqls~~~~~vL~WgDGyc~g~~~~~~~e~~~~~k~l~~L~gg~~~~d~~~l~v~~MS~ 86 (748)
...+++.++.+++..+...+.+|....++. .+...-++ +.... ..
T Consensus 3 ~~l~~~i~~~l~~~~~~~~~~l~~~d~~~~-~~~~~~~~--~~~~~------------------------~~-------- 47 (129)
T PF13492_consen 3 DELLERILELLRELLGADRAALFLLDEDGN-RLRVVAGW--GGDPR------------------------LS-------- 47 (129)
T ss_dssp HHHHHHHHHHHHHHST-SEEEEEEEETTCE-CEEEEEEE--SS-GC------------------------GH--------
T ss_pred HHHHHHHHHHHHHHhCCCEEEEEEEECCCC-EEEEEEEe--CCCcc------------------------cc--------
Confidence 456778888888888999999999987743 22222222 11100 00
Q ss_pred EEecCCCCeeeeEeeCCCeEeeeCCCCccCcCCCCCcchhhhcccccCceeEEEEEecC----CcEEEecccccccCCHH
Q 004499 87 HVYSLGEGIVGQVAVTGKHQWIFSDQLVTNSCSSFEFSDGWQSQFSAGIRTIAVVAVVP----HGVVQLGSLDEVTEDMK 162 (748)
Q Consensus 87 ~sF~~GeGlpGrAaaSG~hvWI~~~~~~~~~~~~~e~~r~~~~QfSAGIQTIVcIPV~~----~GVLELGSTe~V~Ed~~ 162 (748)
..++.+.++.++++.++++ +...+.. . +. ..+++.+++||+.. -|||.+++.+.-.=+..
T Consensus 48 ~~l~~~~~~~~~~~~~~~~-~~~~~~~--~--------~~-----~~~~~s~~~vPl~~~~~~~Gvl~~~~~~~~~~~~~ 111 (129)
T PF13492_consen 48 ESLPEDDPLIGRALETGEP-VSVPDID--E--------RD-----FLGIRSLLVVPLRSRDRVIGVLCLDSREPEEFSDE 111 (129)
T ss_dssp HCEETTSHHHHHHHHHTS--EEESTCC--C---------T-----TTTTCEEEEEEEEETTEEEEEEEEEECTTCG-SHH
T ss_pred ccCCCCccHHHHHHhhCCe-EEecccc--c--------cc-----CCCCCEEEEEEEeECCEEEEEEEEEECCCCCCCHH
Confidence 0244777888888888876 4442211 0 00 15678999999855 39999988875544444
Q ss_pred HHHHHHHH
Q 004499 163 VVTHIRDV 170 (748)
Q Consensus 163 lV~~VKsl 170 (748)
-++.++.+
T Consensus 112 d~~~l~~~ 119 (129)
T PF13492_consen 112 DLQLLESL 119 (129)
T ss_dssp HHHHHHHH
T ss_pred HHHHHHHH
Confidence 44444443
No 46
>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=45.61 E-value=47 Score=29.48 Aligned_cols=52 Identities=12% Similarity=0.411 Sum_probs=45.0
Q ss_pred hhhhhhcc-cchHHHHHHHHHhcCceEEeeeeeeeCCeEEEEEEEEecCCCcc
Q 004499 677 LVEMLCEE-CSHFLEIAEAIRSLGLTILKGVTEAHGDKTWICFVVEGQDNRIM 728 (748)
Q Consensus 677 liem~ce~-~~~flei~~~i~~l~l~il~g~~e~~~~~~~~~f~ve~~~~~~~ 728 (748)
+||+.|.+ -|+--.|+.++..+||.|-.+.+.+.++..--.|-|.-.....+
T Consensus 3 vveV~~~DRpGLL~~i~~~l~~~~l~I~~A~I~T~gera~D~FyV~d~~g~kl 55 (75)
T cd04897 3 VVTVQCRDRPKLLFDVVCTLTDMDYVVFHATIDTDGDDAHQEYYIRHKDGRTL 55 (75)
T ss_pred EEEEEeCCcCcHHHHHHHHHHhCCeEEEEEEEeecCceEEEEEEEEcCCCCcc
Confidence 57888888 68888999999999999999999999999999999976444433
No 47
>PRK03381 PII uridylyl-transferase; Provisional
Probab=43.14 E-value=41 Score=41.47 Aligned_cols=50 Identities=14% Similarity=0.141 Sum_probs=45.2
Q ss_pred Ccchhhhhhhcc-cchHHHHHHHHHhcCceEEeeeeeeeCCeEEEEEEEEe
Q 004499 673 NGQMLVEMLCEE-CSHFLEIAEAIRSLGLTILKGVTEAHGDKTWICFVVEG 722 (748)
Q Consensus 673 ~~~~liem~ce~-~~~flei~~~i~~l~l~il~g~~e~~~~~~~~~f~ve~ 722 (748)
++-..|-..|.+ -|+|-.|+-++-.+|+.|+...+.+.++.+...|+|..
T Consensus 597 ~~~~~V~V~~~DrpGLfa~i~~vL~~~glnI~dA~i~t~dg~~ld~F~V~~ 647 (774)
T PRK03381 597 PHMVEVTVVAPDRRGLLSKAAGVLALHRLRVRSASVRSHDGVAVLEFVVSP 647 (774)
T ss_pred CCeEEEEEEecCCccHHHHHHHHHHHCCCeEEEeEEEecCCEEEEEEEEEC
Confidence 566668888888 89999999999999999999999999999999999975
No 48
>PF02845 CUE: CUE domain; InterPro: IPR003892 This domain may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two proteins of the IL-1 signal transduction pathway, tollip and TAB2.; GO: 0005515 protein binding; PDB: 2EKF_A 1OTR_A 1P3Q_Q 1MN3_A 1WGL_A 2EJS_A 2DAE_A 2DHY_A 2DI0_A.
Probab=40.62 E-value=50 Score=25.59 Aligned_cols=34 Identities=24% Similarity=0.514 Sum_probs=26.4
Q ss_pred HHHHHHHHhhcCCCcccchhhHH-------HHHHHHHHHHH
Q 004499 584 QDRIKELRELVPNGSKCSIDSLL-------ERTIKHMLFLQ 617 (748)
Q Consensus 584 ~~r~~~lr~~vp~~~k~~i~~~l-------~~~i~~~~~l~ 617 (748)
++-++.|+++.|+-..-.|...| |.||.+++.++
T Consensus 2 ~~~v~~L~~mFP~~~~~~I~~~L~~~~~~ve~ai~~LL~~~ 42 (42)
T PF02845_consen 2 EEMVQQLQEMFPDLDREVIEAVLQANNGDVEAAIDALLEMS 42 (42)
T ss_dssp HHHHHHHHHHSSSS-HHHHHHHHHHTTTTHHHHHHHHHHHH
T ss_pred HHHHHHHHHHCCCCCHHHHHHHHHHcCCCHHHHHHHHHcCC
Confidence 35688999999999998887776 67888887653
No 49
>COG3226 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=39.83 E-value=53 Score=34.31 Aligned_cols=41 Identities=34% Similarity=0.482 Sum_probs=32.6
Q ss_pred chhhHHHHHHHHHH----------------HhhcCCCccc----chhhHHHHHHHHHHHHH
Q 004499 577 PRDRQLIQDRIKEL----------------RELVPNGSKC----SIDSLLERTIKHMLFLQ 617 (748)
Q Consensus 577 p~~r~~i~~r~~~l----------------r~~vp~~~k~----~i~~~l~~~i~~~~~l~ 617 (748)
|+|||.|-+.--|| ++=||=|+-- |||.|+.+|..|.-..-
T Consensus 12 p~RRqaIv~Aa~eli~~~Gv~aV~HR~VAa~A~vPLgStTYYF~~lDdLi~~Afa~f~e~~ 72 (204)
T COG3226 12 PRRRQAIVQAALELIKRYGVHAVRHRAVAAEAGVPLGSTTYYFSDLDDLIAEAFAHFTEIM 72 (204)
T ss_pred hHHHHHHHHHHHHHHHhcchhhhhHHHHHHHhCCCccceeeecccHHHHHHHHHHHHHHHH
Confidence 67999998876655 2448988874 99999999999986643
No 50
>PRK03059 PII uridylyl-transferase; Provisional
Probab=36.40 E-value=1.4e+02 Score=37.33 Aligned_cols=43 Identities=16% Similarity=0.176 Sum_probs=37.4
Q ss_pred hhhcc-cchHHHHHHHHHhcCceEEeeee-eeeCCeEEEEEEEEe
Q 004499 680 MLCEE-CSHFLEIAEAIRSLGLTILKGVT-EAHGDKTWICFVVEG 722 (748)
Q Consensus 680 m~ce~-~~~flei~~~i~~l~l~il~g~~-e~~~~~~~~~f~ve~ 722 (748)
..|.+ -|+|-.||-++-..||+|++..+ +++++.++..|.|--
T Consensus 683 i~~~d~~gLFa~i~g~l~~~~l~I~~A~i~t~~~g~~ld~f~V~~ 727 (856)
T PRK03059 683 VYTPDQPDLFARICGYFDRAGFSILDARVHTTRHGYALDTFQVLD 727 (856)
T ss_pred EEecCCCcHHHHHHHHHHHCCCceeeeEEEEcCCCeEEEEEEEeC
Confidence 45555 89999999999999999999755 789999999999953
No 51
>PRK08577 hypothetical protein; Provisional
Probab=29.48 E-value=2e+02 Score=27.63 Aligned_cols=77 Identities=16% Similarity=0.177 Sum_probs=54.3
Q ss_pred CCCCCceeEecCCcceeeeeEEeecCCCc--chhhhhhhcc-cchHHHHHHHHHhcCceEEeeeeeeeC-Ce-EEEEEEE
Q 004499 646 YEQGSSWAVEMGSHLKVCSIVVENLNKNG--QMLVEMLCEE-CSHFLEIAEAIRSLGLTILKGVTEAHG-DK-TWICFVV 720 (748)
Q Consensus 646 ~~~g~~wa~e~~~~~~~~~i~ve~l~~~~--~~liem~ce~-~~~flei~~~i~~l~l~il~g~~e~~~-~~-~~~~f~v 720 (748)
...|..-.|.+.+.. --|+++-+..+. ..-|...+++ -|.+-+|+++|...|..|..-...... +. .-+.|+|
T Consensus 27 ~~~g~~~~~~~~~~~--~~~~~~~~~~~~k~~~~I~V~~~Dr~GvLa~I~~~l~~~~inI~~i~~~~~~~~~~~~i~l~v 104 (136)
T PRK08577 27 IREGMYVLLIADTDK--KEIHLEPIALPGKKLVEIELVVEDRPGVLAKITGLLAEHGVDILATECEELKRGELAECVIIV 104 (136)
T ss_pred cCCCCEEEEEEECCC--CEEEEEEcCCCCccEEEEEEEEcCCCCHHHHHHHHHHHCCCCEEEEEEEEecCCCEEEEEEEE
Confidence 346677776655432 246777664444 6678888888 788889999999999999987766643 33 3467888
Q ss_pred EecC
Q 004499 721 EGQD 724 (748)
Q Consensus 721 e~~~ 724 (748)
|..+
T Consensus 105 ev~~ 108 (136)
T PRK08577 105 DLSK 108 (136)
T ss_pred EeCC
Confidence 8743
No 52
>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=29.33 E-value=70 Score=27.28 Aligned_cols=47 Identities=13% Similarity=0.104 Sum_probs=39.2
Q ss_pred hhhhcc-cchHHHHHHHHHhcCceEEeeeeeeeCCeEEEEEEEEecCC
Q 004499 679 EMLCEE-CSHFLEIAEAIRSLGLTILKGVTEAHGDKTWICFVVEGQDN 725 (748)
Q Consensus 679 em~ce~-~~~flei~~~i~~l~l~il~g~~e~~~~~~~~~f~ve~~~~ 725 (748)
..++.+ -|+--++++++...|++|++=-+....+...+.|.|+..++
T Consensus 3 tv~G~DrpGiv~~vt~~la~~~~nI~dl~~~~~~~~f~~~~~v~~p~~ 50 (75)
T cd04870 3 TVTGPDRPGLTSALTEVLAAHGVRILDVGQAVIHGRLSLGILVQIPDS 50 (75)
T ss_pred EEEcCCCCCHHHHHHHHHHHCCCCEEecccEEEcCeeEEEEEEEcCCC
Confidence 344555 57888999999999999999989999999999999988433
No 53
>PF04281 Tom22: Mitochondrial import receptor subunit Tom22 ; InterPro: IPR005683 The mitochondrial protein translocase family, which is responsible for movement of nuclear encoded pre-proteins into mitochondria, is very complex with at least 19 components. These proteins include several chaperone proteins, four proteins of the outer membrane translocase (Tom) import receptor, five proteins of the Tom channel complex, five proteins of the inner membrane translocase (Tim) and three "motor" proteins. This family represents the Tom22 proteins []. The N-terminal region of Tom22 has been shown to have chaperone-like activity, and the C-terminal region faces the intermembrane face []. ; GO: 0006886 intracellular protein transport, 0005741 mitochondrial outer membrane
Probab=29.30 E-value=53 Score=32.53 Aligned_cols=40 Identities=20% Similarity=0.273 Sum_probs=33.1
Q ss_pred hHHHHHHHHHHHhhcCCCcccchhhHHHHHHHHHHHHHHh
Q 004499 580 RQLIQDRIKELRELVPNGSKCSIDSLLERTIKHMLFLQSI 619 (748)
Q Consensus 580 r~~i~~r~~~lr~~vp~~~k~~i~~~l~~~i~~~~~l~~~ 619 (748)
-+-|-|||..|+++||....-.|...+..+...++-+-+.
T Consensus 50 dETl~ERl~aLkdi~P~~~R~~i~~~~~~~~~~~k~~~~~ 89 (137)
T PF04281_consen 50 DETLLERLWALKDIFPPSVRNWISSTVSTTSSAVKSLFSF 89 (137)
T ss_pred cccHHHHHHHHhccCCHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 4669999999999999999999988888887776655443
No 54
>PRK05022 anaerobic nitric oxide reductase transcription regulator; Provisional
Probab=28.66 E-value=63 Score=37.59 Aligned_cols=80 Identities=15% Similarity=0.126 Sum_probs=51.6
Q ss_pred EecCCCC-eeeeEeeCCCeEeeeCCCCccCcCCCCC-cchhhh-cccccCceeEEEEEecCC----cEEEeccccc---c
Q 004499 88 VYSLGEG-IVGQVAVTGKHQWIFSDQLVTNSCSSFE-FSDGWQ-SQFSAGIRTIAVVAVVPH----GVVQLGSLDE---V 157 (748)
Q Consensus 88 sF~~GeG-lpGrAaaSG~hvWI~~~~~~~~~~~~~e-~~r~~~-~QfSAGIQTIVcIPV~~~----GVLELGSTe~---V 157 (748)
.|..|+| ..|.++.+|.++.+.++... +. +.+... .+...||+..+|||+..+ |||.+-+... -
T Consensus 65 ~~~~geGP~l~av~~~g~~v~v~~~~~~------p~~~~~~~~~~~~~~gi~S~l~vPL~~~~~~~GvL~l~~~~~~~f~ 138 (509)
T PRK05022 65 RFALEEHPRLEAILRAGDPVRFPADSEL------PDPYDGLIPGVQESLPVHDCMGLPLFVDGRLIGALTLDALDPGQFD 138 (509)
T ss_pred ccCCCcchHHHHHHhcCCeEEEecCCCC------CcccccccccccccCCcceEEEEEEEECCEEEEEEEEeeCCCCcCC
Confidence 5899999 77888888999988744221 12 211111 133368999999998443 8888877653 3
Q ss_pred cCCHHHHHHHHHHHhh
Q 004499 158 TEDMKVVTHIRDVFAA 173 (748)
Q Consensus 158 ~Ed~~lV~~VKslF~~ 173 (748)
.+|..++..+-.++..
T Consensus 139 ~~~~~~l~~~a~~~a~ 154 (509)
T PRK05022 139 AFSDEELRALAALAAA 154 (509)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 3456666666655544
No 55
>PRK05007 PII uridylyl-transferase; Provisional
Probab=28.24 E-value=94 Score=38.99 Aligned_cols=59 Identities=12% Similarity=0.296 Sum_probs=51.5
Q ss_pred CCCcchhhhhhhcc-cchHHHHHHHHHhcCceEEeeeeeeeCCeEEEEEEEEecCCCcce
Q 004499 671 NKNGQMLVEMLCEE-CSHFLEIAEAIRSLGLTILKGVTEAHGDKTWICFVVEGQDNRIMH 729 (748)
Q Consensus 671 ~~~~~~liem~ce~-~~~flei~~~i~~l~l~il~g~~e~~~~~~~~~f~ve~~~~~~~~ 729 (748)
..+..-+||..|.+ -|+--+|+.++..+||.|....+.|.++++=..|.|.-.++..++
T Consensus 804 ~s~~~TvlEV~a~DRpGLL~~I~~~l~~~~l~I~~AkI~T~gera~DvFyV~~~~g~~l~ 863 (884)
T PRK05007 804 HTDRRSYMELIALDQPGLLARVGKIFADLGISLHGARITTIGERVEDLFILATADRRALN 863 (884)
T ss_pred CCCCeEEEEEEeCCchHHHHHHHHHHHHCCcEEEEEEEeccCceEEEEEEEEcCCCCcCC
Confidence 55778899999999 788889999999999999999999999999999999754444443
No 56
>PRK04374 PII uridylyl-transferase; Provisional
Probab=28.08 E-value=2.4e+02 Score=35.57 Aligned_cols=42 Identities=19% Similarity=0.218 Sum_probs=36.1
Q ss_pred hhcc-cchHHHHHHHHHhcCceEEeeee-eeeCCeEEEEEEEEe
Q 004499 681 LCEE-CSHFLEIAEAIRSLGLTILKGVT-EAHGDKTWICFVVEG 722 (748)
Q Consensus 681 ~ce~-~~~flei~~~i~~l~l~il~g~~-e~~~~~~~~~f~ve~ 722 (748)
.|.+ .|+|-.||-++-..||+|+...+ ++.++-++..|.|.-
T Consensus 696 ~~~d~~gLFa~i~g~l~~~~lnI~~A~i~t~~~g~~ld~f~V~~ 739 (869)
T PRK04374 696 YSPDRDGLFAAIVATLDRKGYGIHRARVLDAPHDAIFDVFEVLP 739 (869)
T ss_pred EeCCCccHHHHHHHHHHHCCCeEEEEEEEEcCCCEEEEEEEEeC
Confidence 4444 89999999999999999999755 558999999999964
No 57
>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=27.55 E-value=1.4e+02 Score=25.29 Aligned_cols=44 Identities=11% Similarity=-0.019 Sum_probs=37.2
Q ss_pred hhhhcc-cchHHHHHHHHHhcCceEEeeeeeeeC------CeEEEEEEEEe
Q 004499 679 EMLCEE-CSHFLEIAEAIRSLGLTILKGVTEAHG------DKTWICFVVEG 722 (748)
Q Consensus 679 em~ce~-~~~flei~~~i~~l~l~il~g~~e~~~------~~~~~~f~ve~ 722 (748)
...|.+ -|+--+|++++...|+.|++-.+.+.+ +..-.++.|..
T Consensus 3 ~v~g~D~~Giv~~it~~l~~~~~nI~~~~~~~~~~~~~~~~~~~~~~~v~~ 53 (81)
T cd04869 3 EVVGNDRPGIVHEVTQFLAQRNINIEDLSTETYSAPMSGTPLFKAQATLAL 53 (81)
T ss_pred EEEeCCCCCHHHHHHHHHHHcCCCeEEeEeeeecCCCCCcceEEEEEEEec
Confidence 456777 788999999999999999999999988 56667788876
No 58
>cd04886 ACT_ThrD-II-like C-terminal ACT domain of biodegradative (catabolic) threonine dehydratase II (ThrD-II) and other related ACT domains. This CD includes the C-terminal ACT domain of biodegradative (catabolic) threonine dehydratase II (ThrD-II) and other related ACT domains. The Escherichia coli tdcB gene product, ThrD-II, anaerobically catalyzes the pyridoxal phosphate-dependent dehydration of L-threonine and L-serine to ammonia and to alpha-ketobutyrate and pyruvate, respectively. Tetrameric ThrD-II is subject to allosteric activation by AMP, inhibition by alpha-keto acids, and catabolite inactivation by several metabolites of glycolysis and the citric acid cycle. Also included in this CD are N-terminal ACT domains present in smaller (~170 a.a.) archaeal proteins of unknown function. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=27.35 E-value=1.8e+02 Score=23.10 Aligned_cols=40 Identities=10% Similarity=0.146 Sum_probs=30.3
Q ss_pred cccchHHHHHHHHHhcCceEEeeeeeee-----CCeEEEEEEEEe
Q 004499 683 EECSHFLEIAEAIRSLGLTILKGVTEAH-----GDKTWICFVVEG 722 (748)
Q Consensus 683 e~~~~flei~~~i~~l~l~il~g~~e~~-----~~~~~~~f~ve~ 722 (748)
++.|.+.+|+++|...|+.|..-..... .+..-..|.||+
T Consensus 7 d~~G~L~~i~~~i~~~~~nI~~i~~~~~~~~~~~~~~~~~i~v~~ 51 (73)
T cd04886 7 DRPGQLAKLLAVIAEAGANIIEVSHDRAFKTLPLGEVEVELTLET 51 (73)
T ss_pred CCCChHHHHHHHHHHcCCCEEEEEEEeccCCCCCceEEEEEEEEe
Confidence 4589999999999999999987665543 244556667776
No 59
>PF09383 NIL: NIL domain; InterPro: IPR018449 This domain is found at the C terminus of ABC transporter proteins involved in D-methionine transport as well as a number of ferredoxin-like proteins. This domain is likely to act as a substrate binding domain. The domain has been named after a conserved sequence in some members of the family. ; PDB: 2QRR_A 3CED_A 2QSW_A 3TUZ_D 3TUJ_D 3DHX_B 3TUI_H 3DHW_D.
Probab=26.13 E-value=1.7e+02 Score=25.06 Aligned_cols=33 Identities=24% Similarity=0.364 Sum_probs=28.1
Q ss_pred HHHHHHhc--CceEEeeeeeeeCCeEEEEEEEEec
Q 004499 691 IAEAIRSL--GLTILKGVTEAHGDKTWICFVVEGQ 723 (748)
Q Consensus 691 i~~~i~~l--~l~il~g~~e~~~~~~~~~f~ve~~ 723 (748)
|++++|.+ ..+||.|.++.-.++..-.|+||..
T Consensus 19 is~l~~~~~v~~nIl~g~i~~i~~~~~G~l~l~l~ 53 (76)
T PF09383_consen 19 ISQLIREFGVDVNILHGNIEEIQGTPFGILILELP 53 (76)
T ss_dssp HHHHHHHHT-EEEEEEEEEEEETTEEEEEEEEEEE
T ss_pred HHHHHHHhCCCEEEEEEEeEEcCCeeEEEEEEEEE
Confidence 56777665 5689999999999999999999983
No 60
>cd04902 ACT_3PGDH-xct C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH). The C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH), with an extended C-terminal (xct) region from bacteria, archaea, fungi, and plants. 3PGDH is an enzyme that belongs to the D-isomer specific, 2-hydroxyacid dehydrogenase family and catalyzes the oxidation of D-3-phosphoglycerate to 3- phosphohydroxypyruvate, which is the first step in the biosynthesis of L-serine, using NAD+ as the oxidizing agent. In bacteria, 3PGDH is feedback-controlled by the end product L-serine in an allosteric manner. Some 3PGDH enzymes have an additional domain formed by an extended C-terminal region. This additional domain introduces significant asymmetry to the homotetramer. Adjacent ACT (regulatory) domains interact, creating two serine-binding sites, however, this asymmetric arrangement results in the formation of two different and distinct domain interfaces between iden
Probab=23.67 E-value=1.3e+02 Score=24.57 Aligned_cols=40 Identities=10% Similarity=0.206 Sum_probs=29.5
Q ss_pred cccchHHHHHHHHHhcCceEEeeee--eeeCCeEEEEEEEEe
Q 004499 683 EECSHFLEIAEAIRSLGLTILKGVT--EAHGDKTWICFVVEG 722 (748)
Q Consensus 683 e~~~~flei~~~i~~l~l~il~g~~--e~~~~~~~~~f~ve~ 722 (748)
++-|.+.+|++++...|+.|..-.. +..+++.-..|.|+.
T Consensus 8 d~~G~l~~i~~~l~~~~inI~~~~~~~~~~~~~~~~~i~v~~ 49 (73)
T cd04902 8 DRPGVIGKVGTILGEAGINIAGMQVGRDEPGGEALMVLSVDE 49 (73)
T ss_pred CCCCHHHHHHHHHHHcCcChhheEeeccCCCCEEEEEEEeCC
Confidence 4478889999999999999965443 225567667777764
No 61
>TIGR01693 UTase_glnD [Protein-PII] uridylyltransferase. This model describes GlnD, the uridylyltransferase/uridylyl-removing enzyme for the nitrogen regulatory protein PII. Not all homologs of PII share the property of uridylyltransferase modification on the characteristic Tyr residue (see Prosite pattern PS00496 and document PDOC00439), but the modification site is preserved in the PII homolog of all species with a member of this family.
Probab=23.20 E-value=1.5e+02 Score=37.01 Aligned_cols=60 Identities=17% Similarity=0.210 Sum_probs=52.0
Q ss_pred ecCCCcchhhhhhhcc-cchHHHHHHHHHhcCceEEeeeeeeeCCeEEEEEEEEecCCCcc
Q 004499 669 NLNKNGQMLVEMLCEE-CSHFLEIAEAIRSLGLTILKGVTEAHGDKTWICFVVEGQDNRIM 728 (748)
Q Consensus 669 ~l~~~~~~liem~ce~-~~~flei~~~i~~l~l~il~g~~e~~~~~~~~~f~ve~~~~~~~ 728 (748)
+-..++.-+||..|.+ -|+.-+|+.++..+|+.|....+.+.++..=..|.|.......+
T Consensus 773 ~~~s~~~t~~~v~~~DrpGll~~i~~~l~~~~~~i~~a~i~t~~~~~~d~F~v~~~~g~~~ 833 (850)
T TIGR01693 773 NTASRKATIMEVRALDRPGLLARVGRTLEELGLSIQSAKITTFGEKAEDVFYVTDLFGLKL 833 (850)
T ss_pred cCCCCCeEEEEEEECCccHHHHHHHHHHHHCCCeEEEEEEEecCccceeEEEEECCCCCCC
Confidence 4466778999999999 78889999999999999999999999999999999976444333
No 62
>PRK13753 dihydropteroate synthase; Provisional
Probab=22.98 E-value=3e+02 Score=30.27 Aligned_cols=42 Identities=24% Similarity=0.294 Sum_probs=30.9
Q ss_pred CCCCCCCch------hhHHHHHHHHHHHhhcCCCcccchhhHHHHHHHHHH
Q 004499 570 GENGRPRPR------DRQLIQDRIKELRELVPNGSKCSIDSLLERTIKHML 614 (748)
Q Consensus 570 ~~~~~prp~------~r~~i~~r~~~lr~~vp~~~k~~i~~~l~~~i~~~~ 614 (748)
||++||-+. ..+|+..-|+.||+. +...|||+.=-+.++..+
T Consensus 46 geSTrPga~~vs~eeE~~Rv~pvI~~l~~~---~~~ISIDT~~~~va~~al 93 (279)
T PRK13753 46 PAASHPDARPVSPADEIRRIAPLLDALSDQ---MHRVSIDSFQPETQRYAL 93 (279)
T ss_pred CCCCCCCCCcCCHHHHHHHHHHHHHHHHhC---CCcEEEECCCHHHHHHHH
Confidence 677788665 677888999999875 567899987666555443
No 63
>TIGR00986 3a0801s05tom22 mitochondrial import receptor subunit Tom22. translocase (Tom) import receptor, five proteins of the Tom channel complex, five proteins of the inner membrane translocase (Tim) and three "motor" proteins. This family is specific for the Tom22 proteins.
Probab=22.66 E-value=78 Score=31.72 Aligned_cols=39 Identities=23% Similarity=0.269 Sum_probs=33.4
Q ss_pred HHHHHHHHHHHhhcCCCcccchhhHHHHHHHHHHHHHHh
Q 004499 581 QLIQDRIKELRELVPNGSKCSIDSLLERTIKHMLFLQSI 619 (748)
Q Consensus 581 ~~i~~r~~~lr~~vp~~~k~~i~~~l~~~i~~~~~l~~~ 619 (748)
+-|-|||..|+++||...+-.|.+...-+....+-+-+.
T Consensus 49 ETl~ERi~ALkDm~Pp~~R~~i~~~~s~t~s~~ks~~sf 87 (145)
T TIGR00986 49 ETFTDRIYALKDIVPPTTRGWIYHKYSTTTNFVKSTLSF 87 (145)
T ss_pred CcHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 569999999999999999999999988888877665543
No 64
>cd04893 ACT_GcvR_1 ACT domains that comprise the Glycine Cleavage System Transcriptional Repressor (GcvR) protein, and other related domains. This CD includes the first 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 int
Probab=22.19 E-value=1.7e+02 Score=25.32 Aligned_cols=47 Identities=21% Similarity=0.336 Sum_probs=42.0
Q ss_pred hhhhhhhcc-cchHHHHHHHHHhcCceEEeeeeeeeCCeEEEEEEEEe
Q 004499 676 MLVEMLCEE-CSHFLEIAEAIRSLGLTILKGVTEAHGDKTWICFVVEG 722 (748)
Q Consensus 676 ~liem~ce~-~~~flei~~~i~~l~l~il~g~~e~~~~~~~~~f~ve~ 722 (748)
++|-..|.+ .|+.-+|+.+|...|..|++-.+...++..-.+..|++
T Consensus 2 ~iltv~g~Dr~GiVa~vs~~la~~g~nI~d~~q~~~~~~F~m~~~~~~ 49 (77)
T cd04893 2 LVISALGTDRPGILNELTRAVSESGCNILDSRMAILGTEFALTMLVEG 49 (77)
T ss_pred EEEEEEeCCCChHHHHHHHHHHHcCCCEEEceeeEEcCEEEEEEEEEe
Confidence 345567887 89999999999999999999999999999999999987
No 65
>cd04894 ACT_ACR-like_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 (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=21.68 E-value=1.9e+02 Score=25.65 Aligned_cols=51 Identities=24% Similarity=0.374 Sum_probs=35.4
Q ss_pred cchHHHHHHHHHhcCceEEeeeeeeeCCeEEEEEEEEecCCCcceEeehhHHHHH
Q 004499 685 CSHFLEIAEAIRSLGLTILKGVTEAHGDKTWICFVVEGQDNRIMHRMDVLWSLVQ 739 (748)
Q Consensus 685 ~~~flei~~~i~~l~l~il~g~~e~~~~~~~~~f~ve~~~~~~~~r~~i~~~l~~ 739 (748)
-|.=-.|+.+|-.+||.|.||-+.+.+-=-...|-|-. .-..+.+-|.|++
T Consensus 11 tGLgcdlcr~il~fGl~i~rgd~sTDGkWCyiv~wVv~----~~~~~~~rW~lLK 61 (69)
T cd04894 11 TGLGCDLCRIILEFGLNITRGDDSTDGRWCYIVFWVVP----RPPSIKVRWDLLK 61 (69)
T ss_pred cCcccHHHHHHHHhceEEEecccccCCcEEEEEEEEec----CCCCCcccHHHHH
Confidence 56666789999999999999999987763333344432 2244667787764
No 66
>KOG4395 consensus Transcription factor Atonal, contains HTH domain [Transcription]
Probab=21.41 E-value=1.2e+02 Score=33.12 Aligned_cols=59 Identities=25% Similarity=0.300 Sum_probs=43.7
Q ss_pred cccccCCCCCCCCCchhhHHHHHHHHHHHhhcCCCc---ccchhhHHHHHHHHHHHHHHhhhh
Q 004499 563 NKKRARTGENGRPRPRDRQLIQDRIKELRELVPNGS---KCSIDSLLERTIKHMLFLQSITKH 622 (748)
Q Consensus 563 ~k~r~~~~~~~~prp~~r~~i~~r~~~lr~~vp~~~---k~~i~~~l~~~i~~~~~l~~~~~~ 622 (748)
.+++.|-..+-|-| ||-+-++..+..||+.||.+. |.+.-.-|.-|-.|++-|-..-+.
T Consensus 170 v~~~rr~aanarEr-rrm~gLN~AfD~Lr~v~p~~~~d~~LSkyetLqmaq~yi~~l~~~l~~ 231 (285)
T KOG4395|consen 170 VNSHRRLAANARER-RRMNGLNSAFDRLRLVVPDGDSDKKLSKYETLQMAQGYILALGCLLDL 231 (285)
T ss_pred HHHhhhcccchHHH-HHhhhHHHHHHHHHHhcCCCCccchhhhhhHHHHHHHHHhhhHHhhcC
Confidence 45555555666666 667889999999999999874 457777788888888877655444
No 67
>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=20.67 E-value=1.2e+02 Score=22.99 Aligned_cols=41 Identities=20% Similarity=0.166 Sum_probs=30.3
Q ss_pred hcc-cchHHHHHHHHHhcCceEEeeeeeeeCCe-EEEEEEEEe
Q 004499 682 CEE-CSHFLEIAEAIRSLGLTILKGVTEAHGDK-TWICFVVEG 722 (748)
Q Consensus 682 ce~-~~~flei~~~i~~l~l~il~g~~e~~~~~-~~~~f~ve~ 722 (748)
|.+ -|.+-+|.+++...++.|.+-..+..++. .-..|.++.
T Consensus 5 ~~~~~~~l~~i~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~ 47 (71)
T cd04876 5 AIDRPGLLADITTVIAEEKINILSVNTRTDDDGLATIRLTLEV 47 (71)
T ss_pred EeccCcHHHHHHHHHHhCCCCEEEEEeEECCCCEEEEEEEEEE
Confidence 444 57888999999999999998888776633 324566664
No 68
>COG3696 Putative silver efflux pump [Inorganic ion transport and metabolism]
Probab=20.19 E-value=1.1e+02 Score=38.58 Aligned_cols=43 Identities=26% Similarity=0.553 Sum_probs=35.6
Q ss_pred CCCCCCCCCchhhHHHHHHHHHHHhhcCCCccc----chhhHHHHHHHHH
Q 004499 568 RTGENGRPRPRDRQLIQDRIKELRELVPNGSKC----SIDSLLERTIKHM 613 (748)
Q Consensus 568 ~~~~~~~prp~~r~~i~~r~~~lr~~vp~~~k~----~i~~~l~~~i~~~ 613 (748)
++|+++| +==+.+++||+||+.-.|+|-|. |-..++|+||+.+
T Consensus 290 ~~~~nt~---~V~~aV~~kl~elk~~LP~gVki~~~ydRs~lid~AI~tv 336 (1027)
T COG3696 290 RKGANTR---EVIAAVKEKLEELKKSLPEGVKIVTTYDRSELIDKAIDTV 336 (1027)
T ss_pred ecCCChH---HHHHHHHHHHHHHHhhCCCCcEEEEEeeHHHHHHHHHHHH
Confidence 4455543 45678999999999999999996 9999999999875
Done!