Query 026390
Match_columns 239
No_of_seqs 217 out of 1079
Neff 4.3
Searched_HMMs 46136
Date Fri Mar 29 07:25:25 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/026390.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/026390hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd00083 HLH Helix-loop-helix d 99.4 2.3E-13 5E-18 95.0 5.3 54 155-208 5-60 (60)
2 PF00010 HLH: Helix-loop-helix 99.4 1E-12 2.2E-17 91.8 5.8 49 156-204 3-55 (55)
3 smart00353 HLH helix loop heli 99.3 4.1E-12 9E-17 87.3 6.8 50 159-208 1-52 (53)
4 KOG1318 Helix loop helix trans 99.2 2.8E-11 6E-16 115.9 6.7 59 150-208 229-290 (411)
5 KOG1319 bHLHZip transcription 99.2 1.6E-11 3.4E-16 107.8 4.5 66 156-221 64-135 (229)
6 KOG4304 Transcriptional repres 98.7 1E-08 2.3E-13 92.8 2.7 52 157-208 35-93 (250)
7 KOG3561 Aryl-hydrocarbon recep 98.5 3E-07 6.6E-12 94.5 7.6 52 155-206 21-75 (803)
8 KOG2483 Upstream transcription 98.4 6.1E-07 1.3E-11 80.8 7.1 55 154-208 59-115 (232)
9 KOG2588 Predicted DNA-binding 98.3 4.7E-07 1E-11 94.0 2.8 66 153-218 275-340 (953)
10 PLN03217 transcription factor 98.0 2.1E-05 4.6E-10 61.7 6.9 55 166-220 19-78 (93)
11 KOG0561 bHLH transcription fac 97.5 0.00011 2.3E-09 69.2 4.7 55 156-210 62-117 (373)
12 KOG3960 Myogenic helix-loop-he 97.3 0.00077 1.7E-08 62.0 7.0 61 158-218 122-183 (284)
13 KOG4029 Transcription factor H 97.1 0.00039 8.4E-09 61.5 3.6 58 157-214 112-172 (228)
14 KOG3910 Helix loop helix trans 96.2 0.0056 1.2E-07 61.0 4.6 67 140-210 516-585 (632)
15 KOG4447 Transcription factor T 91.4 0.11 2.4E-06 45.0 1.7 50 156-205 80-130 (173)
16 KOG3582 Mlx interactors and re 88.1 0.072 1.6E-06 55.1 -2.2 67 155-221 652-722 (856)
17 KOG3558 Hypoxia-inducible fact 81.8 1.1 2.4E-05 46.7 2.8 47 156-202 48-97 (768)
18 KOG3898 Transcription factor N 74.4 7.9 0.00017 35.4 5.8 49 157-205 75-125 (254)
19 KOG4395 Transcription factor A 71.3 7.6 0.00016 36.4 4.9 53 156-208 176-230 (285)
20 KOG3559 Transcriptional regula 68.4 5.7 0.00012 39.7 3.7 44 160-203 7-53 (598)
21 PF09849 DUF2076: Uncharacteri 60.8 38 0.00083 31.1 7.3 27 190-219 50-76 (247)
22 PF13334 DUF4094: Domain of un 59.6 21 0.00045 28.3 4.7 30 190-219 65-94 (95)
23 PF10393 Matrilin_ccoil: Trime 55.3 24 0.00051 24.9 3.9 32 190-221 15-46 (47)
24 COG3074 Uncharacterized protei 52.4 25 0.00053 27.2 3.9 27 193-219 13-39 (79)
25 KOG3560 Aryl-hydrocarbon recep 52.3 14 0.00029 38.2 3.2 38 164-202 35-76 (712)
26 PF03195 DUF260: Protein of un 51.4 60 0.0013 25.9 6.2 51 170-221 40-101 (101)
27 PF06005 DUF904: Protein of un 50.3 34 0.00073 25.8 4.3 26 193-218 13-38 (72)
28 PRK15422 septal ring assembly 49.5 27 0.00059 27.2 3.8 29 193-221 13-41 (79)
29 PHA03386 P10 fibrous body prot 47.9 34 0.00074 27.5 4.2 31 187-217 1-31 (94)
30 PF07544 Med9: RNA polymerase 47.3 1.1E+02 0.0025 23.2 6.9 48 168-221 32-82 (83)
31 KOG3582 Mlx interactors and re 47.2 6.3 0.00014 41.5 -0.0 60 155-217 788-851 (856)
32 smart00338 BRLZ basic region l 45.0 23 0.0005 25.2 2.7 21 199-219 27-47 (65)
33 PF09006 Surfac_D-trimer: Lung 43.4 33 0.00072 24.2 3.1 22 200-221 1-22 (46)
34 KOG0139 Short-chain acyl-CoA d 38.5 38 0.00083 33.2 3.8 28 192-219 288-328 (398)
35 KOG4447 Transcription factor T 37.2 18 0.0004 31.6 1.3 44 161-204 29-73 (173)
36 PF13870 DUF4201: Domain of un 36.4 2E+02 0.0043 24.3 7.5 58 160-221 115-175 (177)
37 PF00170 bZIP_1: bZIP transcri 36.1 37 0.00081 24.1 2.6 20 160-179 15-34 (64)
38 PRK14066 exodeoxyribonuclease 35.3 1.4E+02 0.003 22.7 5.7 53 169-221 6-62 (75)
39 PF14197 Cep57_CLD_2: Centroso 33.9 83 0.0018 23.5 4.2 30 189-218 38-67 (69)
40 PF08826 DMPK_coil: DMPK coile 33.0 96 0.0021 22.8 4.3 53 161-219 8-60 (61)
41 PRK14127 cell division protein 32.8 66 0.0014 26.2 3.8 31 191-221 30-60 (109)
42 PF09789 DUF2353: Uncharacteri 30.1 1.9E+02 0.004 27.8 6.9 62 159-221 30-102 (319)
43 PRK00977 exodeoxyribonuclease 28.3 1.9E+02 0.0041 22.0 5.5 53 169-221 12-68 (80)
44 PF05103 DivIVA: DivIVA protei 28.2 78 0.0017 24.8 3.5 33 190-222 24-56 (131)
45 PF05597 Phasin: Poly(hydroxya 26.2 1.5E+02 0.0033 24.7 5.0 20 200-219 111-130 (132)
46 PF07716 bZIP_2: Basic region 26.1 72 0.0016 22.1 2.6 19 200-218 34-52 (54)
47 PF06305 DUF1049: Protein of u 26.0 68 0.0015 22.6 2.5 18 200-217 50-67 (68)
48 PF11336 DUF3138: Protein of u 26.0 53 0.0011 33.1 2.5 24 198-221 25-48 (514)
49 PRK14069 exodeoxyribonuclease 25.9 1.8E+02 0.0038 23.3 5.0 53 169-221 10-66 (95)
50 PRK14126 cell division protein 25.9 3.1E+02 0.0066 21.0 6.4 42 167-211 34-75 (85)
51 TIGR01280 xseB exodeoxyribonuc 25.3 1.4E+02 0.0031 21.9 4.2 52 170-221 4-59 (67)
52 PRK14011 prefoldin subunit alp 24.6 1.2E+02 0.0027 25.6 4.2 29 193-221 5-33 (144)
53 PF10465 Inhibitor_I24: PinA p 24.5 62 0.0013 27.4 2.3 20 188-207 120-139 (140)
54 PF11853 DUF3373: Protein of u 23.7 1.3E+02 0.0028 30.6 4.7 23 199-221 32-54 (489)
55 PF02185 HR1: Hr1 repeat; Int 22.5 3E+02 0.0066 19.8 6.9 49 168-221 15-63 (70)
56 PF05531 NPV_P10: Nucleopolyhe 21.8 2.3E+02 0.0051 21.8 4.8 15 188-202 18-32 (75)
57 PF11336 DUF3138: Protein of u 21.4 2.1E+02 0.0046 29.0 5.7 49 173-221 6-55 (514)
58 PF09278 MerR-DNA-bind: MerR, 20.5 2.5E+02 0.0053 19.3 4.5 31 188-218 33-63 (65)
59 PF05928 Zea_mays_MuDR: Zea ma 20.5 4.4E+02 0.0095 23.6 6.8 77 158-236 77-156 (207)
60 PF10359 Fmp27_WPPW: RNA pol I 20.4 1.2E+02 0.0026 30.0 3.8 65 158-222 164-231 (475)
61 PF12097 DUF3573: Protein of u 20.1 1.2E+02 0.0027 29.7 3.6 23 198-220 42-64 (383)
No 1
>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=2.3e-13 Score=94.99 Aligned_cols=54 Identities=37% Similarity=0.654 Sum_probs=49.0
Q ss_pred CCcccHHHHhHHHHHHHHHHHHHhcCCCC--CCCCChHhHHHHHHHHHHHHHHHHH
Q 026390 155 TDSHSLAERARREKISERMKILQDLVPGC--NKVIGKALVLDEIINYIQSLQRQVE 208 (239)
Q Consensus 155 t~sHs~aERrRR~kIne~~~~LrsLVP~~--~k~~dKAsIL~eAIdYIk~LQ~qVe 208 (239)
+..|+..||+||++||+.|..|+.|||.+ ...++|+.||+.||+||++|+.+++
T Consensus 5 r~~~~~~Er~RR~~~n~~~~~L~~llp~~~~~~k~~k~~iL~~a~~yI~~L~~~~~ 60 (60)
T cd00083 5 REAHNLRERRRRERINDAFDELRSLLPTLPPSKKLSKAEILRKAVDYIKSLQELLQ 60 (60)
T ss_pred HHHHhHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHhC
Confidence 35799999999999999999999999999 3456999999999999999998863
No 2
>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=99.37 E-value=1e-12 Score=91.75 Aligned_cols=49 Identities=37% Similarity=0.739 Sum_probs=45.1
Q ss_pred CcccHHHHhHHHHHHHHHHHHHhcCCCC----CCCCChHhHHHHHHHHHHHHH
Q 026390 156 DSHSLAERARREKISERMKILQDLVPGC----NKVIGKALVLDEIINYIQSLQ 204 (239)
Q Consensus 156 ~sHs~aERrRR~kIne~~~~LrsLVP~~----~k~~dKAsIL~eAIdYIk~LQ 204 (239)
..|+..||+||..||+.|..|+.|||.+ ...++|++||+.||+||++||
T Consensus 3 ~~h~~~Er~RR~~i~~~~~~L~~llp~~~~~~~~k~~K~~iL~~ai~yI~~Lq 55 (55)
T PF00010_consen 3 QKHNERERRRRDRINDCFDELRELLPSCSAGSSRKLSKASILQKAIDYIKQLQ 55 (55)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHCCSSHHCCTTSSSSHHHHHHHHHHHHHHHH
T ss_pred chHHHHHHHHHHHHHHHHHHHHHhccchhccccccCCHHHHHHHHHHHHHHhC
Confidence 4699999999999999999999999997 233799999999999999997
No 3
>smart00353 HLH helix loop helix domain.
Probab=99.33 E-value=4.1e-12 Score=87.27 Aligned_cols=50 Identities=40% Similarity=0.577 Sum_probs=44.8
Q ss_pred cHHHHhHHHHHHHHHHHHHhcCCCCC--CCCChHhHHHHHHHHHHHHHHHHH
Q 026390 159 SLAERARREKISERMKILQDLVPGCN--KVIGKALVLDEIINYIQSLQRQVE 208 (239)
Q Consensus 159 s~aERrRR~kIne~~~~LrsLVP~~~--k~~dKAsIL~eAIdYIk~LQ~qVe 208 (239)
+..||+||++||++|..|+.|||.+. ..++|+.||..||+||++|+.+++
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 46899999999999999999999753 335999999999999999999886
No 4
>KOG1318 consensus Helix loop helix transcription factor EB [Transcription]
Probab=99.19 E-value=2.8e-11 Score=115.95 Aligned_cols=59 Identities=37% Similarity=0.650 Sum_probs=51.8
Q ss_pred cCCCCCCcccHHHHhHHHHHHHHHHHHHhcCCCCCCC---CChHhHHHHHHHHHHHHHHHHH
Q 026390 150 RRGQATDSHSLAERARREKISERMKILQDLVPGCNKV---IGKALVLDEIINYIQSLQRQVE 208 (239)
Q Consensus 150 rr~~at~sHs~aERrRR~kIne~~~~LrsLVP~~~k~---~dKAsIL~eAIdYIk~LQ~qVe 208 (239)
|.+++++.|+.+|||||++||++|++|..|||.|+.. +.|.+||..+++||++||+..+
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 3344558999999999999999999999999999543 6899999999999999998665
No 5
>KOG1319 consensus bHLHZip transcription factor BIGMAX [Transcription]
Probab=99.19 E-value=1.6e-11 Score=107.77 Aligned_cols=66 Identities=30% Similarity=0.537 Sum_probs=59.4
Q ss_pred CcccHHHHhHHHHHHHHHHHHHhcCCCCCCC------CChHhHHHHHHHHHHHHHHHHHHHHHHHHHHhccC
Q 026390 156 DSHSLAERARREKISERMKILQDLVPGCNKV------IGKALVLDEIINYIQSLQRQVEFLSMKLEAVNSRM 221 (239)
Q Consensus 156 ~sHs~aERrRR~kIne~~~~LrsLVP~~~k~------~dKAsIL~eAIdYIk~LQ~qVe~L~~~le~l~~~l 221 (239)
.+|..+||+||+.||.+++.|++|||.|... ++||.||.++|+||.+|+.++...+.++.+|+.++
T Consensus 64 ~aHtqaEqkRRdAIk~GYddLq~LvP~cq~~ds~g~KlskA~ILqksidyi~~L~~~k~kqe~e~s~L~k~v 135 (229)
T KOG1319|consen 64 RAHTQAEQKRRDAIKRGYDDLQTLVPTCQQQDSIGQKLSKAIILQKTIDYIQFLHKEKKKQEEEVSTLRKDV 135 (229)
T ss_pred HHHHHHHHHHHHHHHhchHHHHHhccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4799999999999999999999999988544 58999999999999999999888888888877665
No 6
>KOG4304 consensus Transcriptional repressors of the hairy/E(spl) family (contains HLH) [Transcription]
Probab=98.66 E-value=1e-08 Score=92.81 Aligned_cols=52 Identities=33% Similarity=0.510 Sum_probs=46.5
Q ss_pred cccHHHHhHHHHHHHHHHHHHhcCCCCCCC-------CChHhHHHHHHHHHHHHHHHHH
Q 026390 157 SHSLAERARREKISERMKILQDLVPGCNKV-------IGKALVLDEIINYIQSLQRQVE 208 (239)
Q Consensus 157 sHs~aERrRR~kIne~~~~LrsLVP~~~k~-------~dKAsIL~eAIdYIk~LQ~qVe 208 (239)
.|-+.||+||.+||++|.+|++|||.+-++ ++||.||+.||+|++.||....
T Consensus 35 ~Kpl~EKkRRaRIN~~L~eLK~Li~e~~~~~~~~~sklEKAdILEltV~hL~~l~~~~~ 93 (250)
T KOG4304|consen 35 RKPLLEKKRRARINRCLDELKDLIPEALKKDGQRHSKLEKADILELTVNHLRQLQRSQQ 93 (250)
T ss_pred cchhHHHHHHHHHHHHHHHHHHHHHHHHhhcchhhhhhHHHHHHHHHHHHHHHHhcccc
Confidence 588999999999999999999999976433 6999999999999999997654
No 7
>KOG3561 consensus Aryl-hydrocarbon receptor nuclear translocator [Transcription]
Probab=98.48 E-value=3e-07 Score=94.52 Aligned_cols=52 Identities=21% Similarity=0.382 Sum_probs=48.5
Q ss_pred CCcccHHHHhHHHHHHHHHHHHHhcCCCCC---CCCChHhHHHHHHHHHHHHHHH
Q 026390 155 TDSHSLAERARREKISERMKILQDLVPGCN---KVIGKALVLDEIINYIQSLQRQ 206 (239)
Q Consensus 155 t~sHs~aERrRR~kIne~~~~LrsLVP~~~---k~~dKAsIL~eAIdYIk~LQ~q 206 (239)
+++|+.+||+||+++|..|.+|.+|||+|. .++||.+||.+||++|+.++..
T Consensus 21 Re~~~~~EKrRRdq~N~yI~ELs~Mvp~~~~~~RK~DK~tVLr~aV~~lr~~k~~ 75 (803)
T KOG3561|consen 21 RENRSEIEKRRRDQMNKYIEELSEMVPTNASLSRKPDKLTVLRMAVDHLRLIKEQ 75 (803)
T ss_pred cccchhHHHHHHHHHHHHHHHHHHhhhcchhcccCchHHHHHHHHHHHHHHHhhh
Confidence 378999999999999999999999999997 5579999999999999999875
No 8
>KOG2483 consensus Upstream transcription factor 2/L-myc-2 protein [Transcription]
Probab=98.42 E-value=6.1e-07 Score=80.79 Aligned_cols=55 Identities=29% Similarity=0.420 Sum_probs=46.9
Q ss_pred CCCcccHHHHhHHHHHHHHHHHHHhcCCCCCCCC-C-hHhHHHHHHHHHHHHHHHHH
Q 026390 154 ATDSHSLAERARREKISERMKILQDLVPGCNKVI-G-KALVLDEIINYIQSLQRQVE 208 (239)
Q Consensus 154 at~sHs~aERrRR~kIne~~~~LrsLVP~~~k~~-d-KAsIL~eAIdYIk~LQ~qVe 208 (239)
++..|+..||+||..|+++|..|+.+||...... . .++||++|++||+.|+.+..
T Consensus 59 ~R~~HN~LEk~RRahlk~~~~~Lk~~vP~~~~~~~~t~lsiL~kA~~~i~~l~~~~~ 115 (232)
T KOG2483|consen 59 SRAHHNALEKRRRAHLKDCFESLKDSVPLLNGETRSTTLSILDKALEHIQSLERKSA 115 (232)
T ss_pred chhhhhhhhHHHHHHHHHHHHHHHHhCCCCCCcchhhhhHhhhhHHHHHHHHHhHHH
Confidence 3467999999999999999999999999775442 2 58999999999999987544
No 9
>KOG2588 consensus Predicted DNA-binding protein [Transcription]
Probab=98.25 E-value=4.7e-07 Score=93.98 Aligned_cols=66 Identities=29% Similarity=0.509 Sum_probs=60.7
Q ss_pred CCCCcccHHHHhHHHHHHHHHHHHHhcCCCCCCCCChHhHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 026390 153 QATDSHSLAERARREKISERMKILQDLVPGCNKVIGKALVLDEIINYIQSLQRQVEFLSMKLEAVN 218 (239)
Q Consensus 153 ~at~sHs~aERrRR~kIne~~~~LrsLVP~~~k~~dKAsIL~eAIdYIk~LQ~qVe~L~~~le~l~ 218 (239)
..+.+||++|++-|..||++|.+|+++||+..-++.|..+|..||+||++|+...+.|....+++.
T Consensus 275 ~kRtAHN~IEKRYRsSINDKI~eLk~lV~g~~aKl~kSavLr~ai~~i~dl~~~nq~lk~~~~~l~ 340 (953)
T KOG2588|consen 275 EKRTAHNIIEKRYRSSINDKIIELKDLVPGTEAKLNKSAVLRKAIDYIEDLQGYNQKLKLENASLR 340 (953)
T ss_pred cccchhhHHHHHhhcchhHHHHHHHHhcCccHhhhhhhhhHHHHHHHHHHhhccccccchhhhhhh
Confidence 557899999999999999999999999999876679999999999999999999998887777776
No 10
>PLN03217 transcription factor ATBS1; Provisional
Probab=98.00 E-value=2.1e-05 Score=61.67 Aligned_cols=55 Identities=31% Similarity=0.493 Sum_probs=47.4
Q ss_pred HHHHHHHHHHHHhcCCCCCC-----CCChHhHHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Q 026390 166 REKISERMKILQDLVPGCNK-----VIGKALVLDEIINYIQSLQRQVEFLSMKLEAVNSR 220 (239)
Q Consensus 166 R~kIne~~~~LrsLVP~~~k-----~~dKAsIL~eAIdYIk~LQ~qVe~L~~~le~l~~~ 220 (239)
-+.|++.+..||.|+|.... ..+-+-||++|+.||+.|+++|..|.+.|.+|-..
T Consensus 19 ddqi~dLvsKLq~llPe~r~~r~s~k~saskvLqEtC~YIrsLhrEvDdLSerLs~LL~t 78 (93)
T PLN03217 19 EDQINDLIIKLQQLLPELRDSRRSDKVSAARVLQDTCNYIRNLHREVDDLSERLSELLAN 78 (93)
T ss_pred HHHHHHHHHHHHHHChHHHhhhccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 35799999999999996532 14778899999999999999999999999988655
No 11
>KOG0561 consensus bHLH transcription factor [Transcription]
Probab=97.52 E-value=0.00011 Score=69.20 Aligned_cols=55 Identities=25% Similarity=0.404 Sum_probs=46.6
Q ss_pred CcccHHHHhHHHHHHHHHHHHHhcCCCC-CCCCChHhHHHHHHHHHHHHHHHHHHH
Q 026390 156 DSHSLAERARREKISERMKILQDLVPGC-NKVIGKALVLDEIINYIQSLQRQVEFL 210 (239)
Q Consensus 156 ~sHs~aERrRR~kIne~~~~LrsLVP~~-~k~~dKAsIL~eAIdYIk~LQ~qVe~L 210 (239)
+.-+..||+|=.-||-+|..|+.|+|.- ..+++||.||+.+.+||..|+.+.-+|
T Consensus 62 eIANsNERRRMQSINAGFqsLr~LlPr~eGEKLSKAAILQQTa~yI~~Le~~Kt~l 117 (373)
T KOG0561|consen 62 EIANSNERRRMQSINAGFQSLRALLPRKEGEKLSKAAILQQTADYIHQLEGHKTEL 117 (373)
T ss_pred HhhcchHHHHHHhhhHHHHHHHHhcCcccchhhHHHHHHHHHHHHHHHHHhccccc
Confidence 4567889999999999999999999965 333699999999999999998754433
No 12
>KOG3960 consensus Myogenic helix-loop-helix transcription factor [Transcription]
Probab=97.27 E-value=0.00077 Score=62.01 Aligned_cols=61 Identities=23% Similarity=0.319 Sum_probs=51.4
Q ss_pred ccHHHHhHHHHHHHHHHHHHh-cCCCCCCCCChHhHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 026390 158 HSLAERARREKISERMKILQD-LVPGCNKVIGKALVLDEIINYIQSLQRQVEFLSMKLEAVN 218 (239)
Q Consensus 158 Hs~aERrRR~kIne~~~~Lrs-LVP~~~k~~dKAsIL~eAIdYIk~LQ~qVe~L~~~le~l~ 218 (239)
-.+-||+|=.|||+.|.+|+. -+++-+.-+-|..||..||+||..||.-++++.+.-..++
T Consensus 122 ATMRERRRLkKVNEAFE~LKRrT~~NPNQRLPKVEILRsAI~YIE~Lq~LL~~~~~~~~~~~ 183 (284)
T KOG3960|consen 122 ATMRERRRLKKVNEAFETLKRRTSSNPNQRLPKVEILRSAIRYIERLQALLQEQDQAEKGLA 183 (284)
T ss_pred HHHHHHHHHHHHHHHHHHHHhhcCCCccccccHHHHHHHHHHHHHHHHHHHHHhhccchhhh
Confidence 468999999999999999975 4566666689999999999999999998888876655553
No 13
>KOG4029 consensus Transcription factor HAND2/Transcription factor TAL1/TAL2/LYL1 [Transcription]
Probab=97.13 E-value=0.00039 Score=61.47 Aligned_cols=58 Identities=22% Similarity=0.311 Sum_probs=49.5
Q ss_pred cccHHHHhHHHHHHHHHHHHHhcCCCC---CCCCChHhHHHHHHHHHHHHHHHHHHHHHHH
Q 026390 157 SHSLAERARREKISERMKILQDLVPGC---NKVIGKALVLDEIINYIQSLQRQVEFLSMKL 214 (239)
Q Consensus 157 sHs~aERrRR~kIne~~~~LrsLVP~~---~k~~dKAsIL~eAIdYIk~LQ~qVe~L~~~l 214 (239)
.++..||.|=..+|..|..|+.+||.. .++++|..+|.-||.||++|+.-++.-...+
T Consensus 112 ~~n~RER~Rv~~vN~~f~~Lr~~lP~~~~~~kklSKveTLr~A~~YI~~L~~lL~~~~~~~ 172 (228)
T KOG4029|consen 112 ARNARERQRVQSVNSAFAELRALLPTEPPQSKKLSKVETLRLATSYIRYLTKLLATQEAPL 172 (228)
T ss_pred hhhhhhhhcccchhhhhHHHHhcCCCCCCcccccCcccchHHHHHHHHHHHHHhcccccCC
Confidence 466779999999999999999999964 4558999999999999999998877665443
No 14
>KOG3910 consensus Helix loop helix transcription factor [Transcription]
Probab=96.22 E-value=0.0056 Score=61.02 Aligned_cols=67 Identities=27% Similarity=0.271 Sum_probs=52.2
Q ss_pred CCCccccccccCCCCCCcccHHHHhHHHHHHHHHHHHHhcCCCC---CCCCChHhHHHHHHHHHHHHHHHHHHH
Q 026390 140 PPKDYIHVRARRGQATDSHSLAERARREKISERMKILQDLVPGC---NKVIGKALVLDEIINYIQSLQRQVEFL 210 (239)
Q Consensus 140 p~~d~~~~R~rr~~at~sHs~aERrRR~kIne~~~~LrsLVP~~---~k~~dKAsIL~eAIdYIk~LQ~qVe~L 210 (239)
|.+...+.+.|| ...+.-||-|=.-||+.|++|-.|.-.- .|..-|..||..||.-|-.|++||++-
T Consensus 516 peqkaeREkERR----~aNNARERlRVRDINeAfKELGRMCqlHlkSeKpQTKLgILhqAVsVIlsLEQQVRER 585 (632)
T KOG3910|consen 516 PEQKAEREKERR----MANNARERLRVRDINEAFKELGRMCQLHLKSEKPQTKLGILHQAVSVILSLEQQVRER 585 (632)
T ss_pred hhhhhhHHHHHH----hhhhhhhheehhhHHHHHHHHHHHHHHhhcccCcchhhhHHHHHHHHHHHHHHHHHHc
Confidence 344444444455 6789999999889999999999987422 233589999999999999999999863
No 15
>KOG4447 consensus Transcription factor TWIST [Transcription]
Probab=91.38 E-value=0.11 Score=45.02 Aligned_cols=50 Identities=22% Similarity=0.356 Sum_probs=44.4
Q ss_pred CcccHHHHhHHHHHHHHHHHHHhcCCCC-CCCCChHhHHHHHHHHHHHHHH
Q 026390 156 DSHSLAERARREKISERMKILQDLVPGC-NKVIGKALVLDEIINYIQSLQR 205 (239)
Q Consensus 156 ~sHs~aERrRR~kIne~~~~LrsLVP~~-~k~~dKAsIL~eAIdYIk~LQ~ 205 (239)
.-|++-||+|-..+|+.|..||.++|.. ....+|...|+-|.-||-+|-+
T Consensus 80 v~anvrerqRtqsLn~AF~~lr~iiptlPsdklSkiqtLklA~ryidfl~~ 130 (173)
T KOG4447|consen 80 VMANVRERQRTQSLNEAFAALRKIIPTLPSDKLSKIQTLKLAARYIDFLYQ 130 (173)
T ss_pred HHHHHHHHHhhhhHHHHHHHHHhhcCCCCccccccccchhhcccCCchhhh
Confidence 4599999999999999999999999976 3335999999999999999864
No 16
>KOG3582 consensus Mlx interactors and related transcription factors [Transcription]
Probab=88.11 E-value=0.072 Score=55.14 Aligned_cols=67 Identities=18% Similarity=0.271 Sum_probs=53.7
Q ss_pred CCcccHHHHhHHHHHHHHHHHHHhcCCCCCCC----CChHhHHHHHHHHHHHHHHHHHHHHHHHHHHhccC
Q 026390 155 TDSHSLAERARREKISERMKILQDLVPGCNKV----IGKALVLDEIINYIQSLQRQVEFLSMKLEAVNSRM 221 (239)
Q Consensus 155 t~sHs~aERrRR~kIne~~~~LrsLVP~~~k~----~dKAsIL~eAIdYIk~LQ~qVe~L~~~le~l~~~l 221 (239)
...|+-+|++||+.|+-+|..|-.++...... +.+++-|+.+++||..++.+...++++--.+...+
T Consensus 652 ~it~~Sa~qkrr~n~kl~~~~~Ns~~Sn~~~l~s~k~t~~~~~q~~vhYi~~t~~e~~~v~~e~~~lr~~~ 722 (856)
T KOG3582|consen 652 PITHISAEQKRRFNIKLQFDVLNSLSSNSSSLSSIKTTNSNSLQKTVHYINVTQQERVPVQEEAHSLRKEI 722 (856)
T ss_pred cccCccHHHHHHhhHHhhhHhhhhhccCcccccchhhhccccccCceeeeeccchhccccchhhhhhhhhh
Confidence 36799999999999999999999999765443 56777799999999999887776665555555554
No 17
>KOG3558 consensus Hypoxia-inducible factor 1/Neuronal PAS domain protein NPAS1 [Signal transduction mechanisms; Transcription]
Probab=81.81 E-value=1.1 Score=46.70 Aligned_cols=47 Identities=28% Similarity=0.355 Sum_probs=38.8
Q ss_pred CcccHHHHhHHHHHHHHHHHHHhcCCCCC---CCCChHhHHHHHHHHHHH
Q 026390 156 DSHSLAERARREKISERMKILQDLVPGCN---KVIGKALVLDEIINYIQS 202 (239)
Q Consensus 156 ~sHs~aERrRR~kIne~~~~LrsLVP~~~---k~~dKAsIL~eAIdYIk~ 202 (239)
+.-.-+-|.||.|-|+-|.+|..+||--. -.+|||+|+.-||-|++-
T Consensus 48 EkSRdAARsRRsKEn~~FyeLa~~lPlp~aisshLDkaSimRLtISyLRl 97 (768)
T KOG3558|consen 48 EKSRDAARSRRSKENEEFYELAKLLPLPAAISSHLDKASIMRLTISYLRL 97 (768)
T ss_pred hhhhhhhhhhcccchHHHHHHHHhCCCcchhhhhhhhHHHHHHHHHHHHH
Confidence 33456789999999999999999999332 227999999999999973
No 18
>KOG3898 consensus Transcription factor NeuroD and related HTH proteins [Transcription]
Probab=74.43 E-value=7.9 Score=35.42 Aligned_cols=49 Identities=22% Similarity=0.388 Sum_probs=41.1
Q ss_pred cccHHHHhHHHHHHHHHHHHHhcCCCC--CCCCChHhHHHHHHHHHHHHHH
Q 026390 157 SHSLAERARREKISERMKILQDLVPGC--NKVIGKALVLDEIINYIQSLQR 205 (239)
Q Consensus 157 sHs~aERrRR~kIne~~~~LrsLVP~~--~k~~dKAsIL~eAIdYIk~LQ~ 205 (239)
.=+.-||.|=-.+|+.|+.|+.+||.. ...+.|+-.|.-|-+||-.|+.
T Consensus 75 kaNaRER~RMH~LNdAld~LReviP~~~~~~klskIetl~~a~~yi~als~ 125 (254)
T KOG3898|consen 75 KANARERTRMHDLNDALDALREVIPHGLHPPKLSKIETLRLAANYIAALSE 125 (254)
T ss_pred cccchhhccccchhHHHHHhHhhccCcCCCCCCCcchhHHhhhcchhhhcc
Confidence 356789999999999999999999943 2226999999999999998875
No 19
>KOG4395 consensus Transcription factor Atonal, contains HTH domain [Transcription]
Probab=71.30 E-value=7.6 Score=36.35 Aligned_cols=53 Identities=23% Similarity=0.266 Sum_probs=44.7
Q ss_pred CcccHHHHhHHHHHHHHHHHHHhcCCCCC--CCCChHhHHHHHHHHHHHHHHHHH
Q 026390 156 DSHSLAERARREKISERMKILQDLVPGCN--KVIGKALVLDEIINYIQSLQRQVE 208 (239)
Q Consensus 156 ~sHs~aERrRR~kIne~~~~LrsLVP~~~--k~~dKAsIL~eAIdYIk~LQ~qVe 208 (239)
.+-+..||+|=..+|..|+.|+..||... +.++|-..|++|-.||-.|-....
T Consensus 176 ~aanarErrrm~gLN~AfD~Lr~v~p~~~~d~~LSkyetLqmaq~yi~~l~~~l~ 230 (285)
T KOG4395|consen 176 LAANARERRRMNGLNSAFDRLRLVVPDGDSDKKLSKYETLQMAQGYILALGCLLD 230 (285)
T ss_pred cccchHHHHHhhhHHHHHHHHHHhcCCCCccchhhhhhHHHHHHHHHhhhHHhhc
Confidence 35678999999999999999999999663 337899999999999988876554
No 20
>KOG3559 consensus Transcriptional regulator SIM1 [Transcription]
Probab=68.39 E-value=5.7 Score=39.66 Aligned_cols=44 Identities=27% Similarity=0.334 Sum_probs=37.5
Q ss_pred HHHHhHHHHHHHHHHHHHhcCCCC---CCCCChHhHHHHHHHHHHHH
Q 026390 160 LAERARREKISERMKILQDLVPGC---NKVIGKALVLDEIINYIQSL 203 (239)
Q Consensus 160 ~aERrRR~kIne~~~~LrsLVP~~---~k~~dKAsIL~eAIdYIk~L 203 (239)
-+-|.||++-|--|.+|..|+|-. ..++||++|+.-|.-|||.-
T Consensus 7 naA~tRRekEN~EF~eLAklLPLa~AItsQlDKasiiRLtTsYlKmr 53 (598)
T KOG3559|consen 7 NAARTRREKENYEFYELAKLLPLASAITSQLDKASIIRLTTSYLKMR 53 (598)
T ss_pred hHHHHHHHhhcchHHHHHhhccchhhhhhccchhhhhhHHHHHHHHH
Confidence 456889999999999999999954 33479999999999999853
No 21
>PF09849 DUF2076: Uncharacterized protein conserved in bacteria (DUF2076); InterPro: IPR018648 This family of hypothetical prokaryotic proteins has no known function but includes putative perimplasmic ligand-binding sensor proteins.
Probab=60.84 E-value=38 Score=31.15 Aligned_cols=27 Identities=19% Similarity=0.368 Sum_probs=19.7
Q ss_pred HhHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 026390 190 ALVLDEIINYIQSLQRQVEFLSMKLEAVNS 219 (239)
Q Consensus 190 AsIL~eAIdYIk~LQ~qVe~L~~~le~l~~ 219 (239)
+.|++.| |+.|+.+|++|+.+|.+...
T Consensus 50 vlvQE~A---L~~a~~ri~eLe~ql~q~~~ 76 (247)
T PF09849_consen 50 VLVQEQA---LKQAQARIQELEAQLQQAQA 76 (247)
T ss_pred HHHHHHH---HHHHHHHHHHHHHHHHhhcc
Confidence 4444444 57899999999999977544
No 22
>PF13334 DUF4094: Domain of unknown function (DUF4094)
Probab=59.59 E-value=21 Score=28.27 Aligned_cols=30 Identities=27% Similarity=0.302 Sum_probs=24.7
Q ss_pred HhHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 026390 190 ALVLDEIINYIQSLQRQVEFLSMKLEAVNS 219 (239)
Q Consensus 190 AsIL~eAIdYIk~LQ~qVe~L~~~le~l~~ 219 (239)
..=+.++-+=|+.|.+.|..|+++|++.+.
T Consensus 65 ~~eV~kTh~aIq~LdKtIS~LEMELAaARa 94 (95)
T PF13334_consen 65 MGEVSKTHEAIQSLDKTISSLEMELAAARA 94 (95)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 333467777889999999999999999875
No 23
>PF10393 Matrilin_ccoil: Trimeric coiled-coil oligomerisation domain of matrilin; InterPro: IPR019466 This entry represents a short domain found the matrilin (cartilage matrix) proteins. It forms a coiled coil structure and contains a single cysteine residue at its start which is likely to form a di-sulphide bridge with a corresponding cysteine in an upstream EGF domain (IPR006209 from INTERPRO), thereby spanning the VWA domain of the protein (IPR002035 from INTERPRO).This domain is likely to be responsible for protein trimerisation []. ; PDB: 1AQ5_C.
Probab=55.32 E-value=24 Score=24.87 Aligned_cols=32 Identities=25% Similarity=0.473 Sum_probs=27.3
Q ss_pred HhHHHHHHHHHHHHHHHHHHHHHHHHHHhccC
Q 026390 190 ALVLDEIINYIQSLQRQVEFLSMKLEAVNSRM 221 (239)
Q Consensus 190 AsIL~eAIdYIk~LQ~qVe~L~~~le~l~~~l 221 (239)
...-..+-.||+.|.+++..+..+|++++.++
T Consensus 15 v~FQ~~v~~~lq~Lt~kL~~vs~RLe~LEn~~ 46 (47)
T PF10393_consen 15 VAFQNKVTSALQSLTQKLDAVSKRLEALENRL 46 (47)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence 45567888999999999999999999998654
No 24
>COG3074 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=52.39 E-value=25 Score=27.17 Aligned_cols=27 Identities=26% Similarity=0.329 Sum_probs=19.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 026390 193 LDEIINYIQSLQRQVEFLSMKLEAVNS 219 (239)
Q Consensus 193 L~eAIdYIk~LQ~qVe~L~~~le~l~~ 219 (239)
++.||+-|.-||.+|++|+++...+..
T Consensus 13 iqqAvdTI~LLQmEieELKEknn~l~~ 39 (79)
T COG3074 13 VQQAIDTITLLQMEIEELKEKNNSLSQ 39 (79)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhHhHH
Confidence 456888888888888888777665543
No 25
>KOG3560 consensus Aryl-hydrocarbon receptor [Transcription]
Probab=52.34 E-value=14 Score=38.21 Aligned_cols=38 Identities=24% Similarity=0.433 Sum_probs=32.5
Q ss_pred hHHHHHHHHHHHHHhcCCCC----CCCCChHhHHHHHHHHHHH
Q 026390 164 ARREKISERMKILQDLVPGC----NKVIGKALVLDEIINYIQS 202 (239)
Q Consensus 164 rRR~kIne~~~~LrsLVP~~----~k~~dKAsIL~eAIdYIk~ 202 (239)
+-|+++|--++.|.+|+|-- +| +||.+||.-+|-|++-
T Consensus 35 RHRdRLNaELD~lAsLLPfpqdiisK-LDkLSVLRLSVSyLr~ 76 (712)
T KOG3560|consen 35 RHRDRLNAELDHLASLLPFPQDIISK-LDKLSVLRLSVSYLRV 76 (712)
T ss_pred hHHHHhhhHHHHHHHhcCCCHHHHhh-hhhhhhhhhhHHHHHH
Confidence 45899999999999999954 44 5999999999999863
No 26
>PF03195 DUF260: Protein of unknown function DUF260; InterPro: IPR004883 The lateral organ boundaries (LOB) gene is expressed at the adaxial base of initiating lateral organs and encodes a plant-specific protein of unknown function. The N-terminal one half of the LOB protein contains a conserved approximately 100-amino acid domain (the LOB domain) that is present in 42 other Arabidopsis thaliana proteins and in proteins from a variety of other plant species. Genes encoding LOB domain (LBD) proteins are expressed in a variety of temporal- and tissue-specific patterns, suggesting that they may function in diverse processes [] The LOB domain contains conserved blocks of amino acids that identify the LBD gene family. In particular, a conserved C-x(2)-C-x(6)-C-x(3)-C motif, which is defining feature of the LOB domain, is present in all LBD proteins. It is possible that this motif forms a new zinc finger [].
Probab=51.39 E-value=60 Score=25.92 Aligned_cols=51 Identities=27% Similarity=0.362 Sum_probs=36.2
Q ss_pred HHHHHHHHhcCCCCCCCCChHhHHHHH-----------HHHHHHHHHHHHHHHHHHHHHhccC
Q 026390 170 SERMKILQDLVPGCNKVIGKALVLDEI-----------INYIQSLQRQVEFLSMKLEAVNSRM 221 (239)
Q Consensus 170 ne~~~~LrsLVP~~~k~~dKAsIL~eA-----------IdYIk~LQ~qVe~L~~~le~l~~~l 221 (239)
.+-++.|+.+-|..... --.+|+.+| +..|..||.++..+++++..+..+|
T Consensus 40 sni~k~L~~~~~~~R~~-a~~Sl~yEA~~R~~dPv~Gc~G~i~~L~~ql~~~~~el~~~~~~l 101 (101)
T PF03195_consen 40 SNISKMLQELPPEQRED-AMRSLVYEANARARDPVYGCVGIISQLQQQLQQLQAELALVRAQL 101 (101)
T ss_pred hHHHHHHHhCCccchhh-HHHHHHHHHHhhccCCCcchHHHHHHHHHHHHHHHHHHHHHHccC
Confidence 44567788875544333 234455444 6789999999999999999988764
No 27
>PF06005 DUF904: Protein of unknown function (DUF904); InterPro: IPR009252 Cell division protein ZapB is a non-essential, abundant cell division factor that is required for proper Z-ring formation. It is recruited early to the divisome by direct interaction with FtsZ, stimulating Z-ring assembly and thereby promoting cell division earlier in the cell cycle. Its recruitment to the Z-ring requires functional FtsA or ZipA.; GO: 0000917 barrier septum formation, 0043093 cytokinesis by binary fission, 0005737 cytoplasm; PDB: 2JEE_A.
Probab=50.26 E-value=34 Score=25.82 Aligned_cols=26 Identities=23% Similarity=0.238 Sum_probs=20.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHh
Q 026390 193 LDEIINYIQSLQRQVEFLSMKLEAVN 218 (239)
Q Consensus 193 L~eAIdYIk~LQ~qVe~L~~~le~l~ 218 (239)
+..||+-|..||.+|+.|+.+...+.
T Consensus 13 i~~aveti~~Lq~e~eeLke~n~~L~ 38 (72)
T PF06005_consen 13 IQQAVETIALLQMENEELKEKNNELK 38 (72)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhHH
Confidence 46789999999999999988755543
No 28
>PRK15422 septal ring assembly protein ZapB; Provisional
Probab=49.54 E-value=27 Score=27.19 Aligned_cols=29 Identities=24% Similarity=0.329 Sum_probs=23.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhccC
Q 026390 193 LDEIINYIQSLQRQVEFLSMKLEAVNSRM 221 (239)
Q Consensus 193 L~eAIdYIk~LQ~qVe~L~~~le~l~~~l 221 (239)
++.|||-|.-||.+|++|+++...+....
T Consensus 13 IqqAvdtI~LLqmEieELKekn~~L~~e~ 41 (79)
T PRK15422 13 VQQAIDTITLLQMEIEELKEKNNSLSQEV 41 (79)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 56789999999999999988877766654
No 29
>PHA03386 P10 fibrous body protein; Provisional
Probab=47.87 E-value=34 Score=27.46 Aligned_cols=31 Identities=26% Similarity=0.499 Sum_probs=17.7
Q ss_pred CChHhHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026390 187 IGKALVLDEIINYIQSLQRQVEFLSMKLEAV 217 (239)
Q Consensus 187 ~dKAsIL~eAIdYIk~LQ~qVe~L~~~le~l 217 (239)
|+|..||--+..-|+.+-.+|..|+.++..+
T Consensus 1 MSKpnILl~Ir~dIkavd~KVdaLQ~qV~dv 31 (94)
T PHA03386 1 MSKPSVLTQILDAVQEVDTKVDALQTQLNGL 31 (94)
T ss_pred CCcchHHHHHHHHHHHHhhHHHHHHHHHHHH
Confidence 4677777777777777444444444333333
No 30
>PF07544 Med9: RNA polymerase II transcription mediator complex subunit 9; InterPro: IPR011425 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. This entry represents subunit Med9 of the Mediator complex. Subunit Med9 is part of the middle module of the Mediator complex []; this associates with the core polymerase subunits to form the RNA polymerase II holoenzyme. Med9 alternatively known as the chromosome segregation protein, CSE2 (P33308 from SWISSPROT) is required, along with CSE1 (P33307 from SWISSPROT) for accurate mitotic chromosome segregation in Saccharomyces cerevisiae (Baker's yeast) [].; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006357 regulation of transcription from RNA polymerase II promoter, 0016592 mediator complex
Probab=47.33 E-value=1.1e+02 Score=23.15 Aligned_cols=48 Identities=17% Similarity=0.352 Sum_probs=32.5
Q ss_pred HHHHHHHHHHhcC---CCCCCCCChHhHHHHHHHHHHHHHHHHHHHHHHHHHHhccC
Q 026390 168 KISERMKILQDLV---PGCNKVIGKALVLDEIINYIQSLQRQVEFLSMKLEAVNSRM 221 (239)
Q Consensus 168 kIne~~~~LrsLV---P~~~k~~dKAsIL~eAIdYIk~LQ~qVe~L~~~le~l~~~l 221 (239)
.|+.+|...+.+| |+.... +++--++|+.|+++++....-|..+..++
T Consensus 32 ~lk~Klq~ar~~i~~lpgi~~s------~eeq~~~i~~Le~~i~~k~~~L~~~~~~~ 82 (83)
T PF07544_consen 32 SLKHKLQKARAAIRELPGIDRS------VEEQEEEIEELEEQIRKKREVLQKFKERV 82 (83)
T ss_pred HHHHHHHHHHHHHHhCCCccCC------HHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 3444455555544 554443 56777889999999999888888776654
No 31
>KOG3582 consensus Mlx interactors and related transcription factors [Transcription]
Probab=47.18 E-value=6.3 Score=41.48 Aligned_cols=60 Identities=17% Similarity=0.218 Sum_probs=50.4
Q ss_pred CCcccHHHHhHHHHHHHHHHHHHhcCCCC----CCCCChHhHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026390 155 TDSHSLAERARREKISERMKILQDLVPGC----NKVIGKALVLDEIINYIQSLQRQVEFLSMKLEAV 217 (239)
Q Consensus 155 t~sHs~aERrRR~kIne~~~~LrsLVP~~----~k~~dKAsIL~eAIdYIk~LQ~qVe~L~~~le~l 217 (239)
...|..++|++|-.+.++|..|-.|.|.. ++..++++||. +.|+.+++.-+.+.++.+..
T Consensus 788 ~a~sih~lrr~~~~~~dq~~sL~alrp~v~~~~~ql~S~tS~L~---dp~~~~eq~ska~~e~~~~k 851 (856)
T KOG3582|consen 788 SAGSIHALRRTRLNWLDQFCSLPALRPQVLLNLRQLLSSTSILT---DPIKQPEQASKAVTEKIEGK 851 (856)
T ss_pred ecchHHHHHHHHHHHhhccccHHHHHHHHHhhHHHhhhhhhccc---CcccchHHHHHHHHhhhhhh
Confidence 34589999999999999999999999954 33378999998 99999999988888776654
No 32
>smart00338 BRLZ basic region leucin zipper.
Probab=44.96 E-value=23 Score=25.23 Aligned_cols=21 Identities=33% Similarity=0.428 Sum_probs=9.3
Q ss_pred HHHHHHHHHHHHHHHHHHHhc
Q 026390 199 YIQSLQRQVEFLSMKLEAVNS 219 (239)
Q Consensus 199 YIk~LQ~qVe~L~~~le~l~~ 219 (239)
||..|+.+|+.|+.+...|..
T Consensus 27 ~~~~Le~~~~~L~~en~~L~~ 47 (65)
T smart00338 27 EIEELERKVEQLEAENERLKK 47 (65)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 444444444444444444433
No 33
>PF09006 Surfac_D-trimer: Lung surfactant protein D coiled-coil trimerisation; InterPro: IPR015097 This domain is found in the SFTPD family, which includes lung surfactant protein D (SFTPD), conglutinin, collectin-43 and collectin-46. It forms a triple-helical parallel coiled coil, and mediates trimerisation of the protein []. ; PDB: 4DN8_A 3G84_A 2RIE_C 3IKR_B 1B08_A 2GGX_B 2OS9_C 2ORK_B 1PWB_A 2RIA_C ....
Probab=43.41 E-value=33 Score=24.20 Aligned_cols=22 Identities=27% Similarity=0.454 Sum_probs=16.8
Q ss_pred HHHHHHHHHHHHHHHHHHhccC
Q 026390 200 IQSLQRQVEFLSMKLEAVNSRM 221 (239)
Q Consensus 200 Ik~LQ~qVe~L~~~le~l~~~l 221 (239)
|..|++||+.|+.++..|...+
T Consensus 1 i~aLrqQv~aL~~qv~~Lq~~f 22 (46)
T PF09006_consen 1 INALRQQVEALQGQVQRLQAAF 22 (46)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHH
T ss_pred ChHHHHHHHHHHHHHHHHHHHH
Confidence 4678888888888888777655
No 34
>KOG0139 consensus Short-chain acyl-CoA dehydrogenase [Lipid transport and metabolism]
Probab=38.51 E-value=38 Score=33.24 Aligned_cols=28 Identities=36% Similarity=0.511 Sum_probs=23.4
Q ss_pred HHHHHHHHHHH-------------HHHHHHHHHHHHHHHhc
Q 026390 192 VLDEIINYIQS-------------LQRQVEFLSMKLEAVNS 219 (239)
Q Consensus 192 IL~eAIdYIk~-------------LQ~qVe~L~~~le~l~~ 219 (239)
-++.||+|++. ||.|+.+++.++|+.+-
T Consensus 288 c~d~tI~Y~q~R~~FGk~l~d~Q~iQhqiA~~~teiEaaRl 328 (398)
T KOG0139|consen 288 CFDETIPYAQERLQFGKRLLDFQGLQHQIADMATEIEAARL 328 (398)
T ss_pred HHHhhhHHHHHHHHhcchhhhHHHHHHHHHHHHHHHHHHHH
Confidence 46889999865 99999999999998764
No 35
>KOG4447 consensus Transcription factor TWIST [Transcription]
Probab=37.15 E-value=18 Score=31.60 Aligned_cols=44 Identities=30% Similarity=0.354 Sum_probs=29.8
Q ss_pred HHHhHHHHHHHHHHHHHhcCCCCCCC-CChHhHHHHHHHHHHHHH
Q 026390 161 AERARREKISERMKILQDLVPGCNKV-IGKALVLDEIINYIQSLQ 204 (239)
Q Consensus 161 aERrRR~kIne~~~~LrsLVP~~~k~-~dKAsIL~eAIdYIk~LQ 204 (239)
.|+.|..++++.+.-|+.|+|+..-. +.+.-.|.-+-+||++|.
T Consensus 29 ~e~~R~~~ls~~s~l~g~l~pgspa~gk~~~ktlr~~~~~~~~~d 73 (173)
T KOG4447|consen 29 KERGRKRRLSDASTLLGKLEPGSPADGKRGKKTLRIGTDSIQSLD 73 (173)
T ss_pred HHHhHHhhhhhhhhhccccCCCCCCcccccccccccCCCchhhHH
Confidence 58888999999999999999986321 233333555555555543
No 36
>PF13870 DUF4201: Domain of unknown function (DUF4201)
Probab=36.41 E-value=2e+02 Score=24.25 Aligned_cols=58 Identities=19% Similarity=0.291 Sum_probs=40.4
Q ss_pred HHHHhHHHHHHHHHHHHHhcCCCCCCCCChHhH---HHHHHHHHHHHHHHHHHHHHHHHHHhccC
Q 026390 160 LAERARREKISERMKILQDLVPGCNKVIGKALV---LDEIINYIQSLQRQVEFLSMKLEAVNSRM 221 (239)
Q Consensus 160 ~aERrRR~kIne~~~~LrsLVP~~~k~~dKAsI---L~eAIdYIk~LQ~qVe~L~~~le~l~~~l 221 (239)
...+..|.++......|+.--... ....+ .+.+++++..|+..|+.|+.+++.+..++
T Consensus 115 ~~~k~~r~k~~~~~~~l~~~~~~~----~~P~ll~Dy~~~~~~~~~l~~~i~~l~rk~~~l~~~i 175 (177)
T PF13870_consen 115 YRVKKERDKLRKQNKKLRQQGGLL----GVPALLRDYDKTKEEVEELRKEIKELERKVEILEMRI 175 (177)
T ss_pred HHHHHHHHHHHHHHHHHHHhcCCC----CCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 344455667777777776543322 22333 56789999999999999999999887665
No 37
>PF00170 bZIP_1: bZIP transcription factor cAMP response element binding (CREB) protein signature fos transforming protein signature jun transcription factor signature; InterPro: IPR011616 The basic-leucine zipper (bZIP) transcription factors [, ] of eukaryotic are proteins that contain a basic region mediating sequence-specific DNA-binding followed by a leucine zipper region (see IPR002158 from INTERPRO) required for dimerization.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0046983 protein dimerization activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2H7H_B 2OQQ_B 1S9K_E 1JNM_A 1JUN_A 1FOS_H 1A02_J 1T2K_C 1CI6_A 1DH3_C ....
Probab=36.12 E-value=37 Score=24.11 Aligned_cols=20 Identities=20% Similarity=0.298 Sum_probs=11.4
Q ss_pred HHHHhHHHHHHHHHHHHHhc
Q 026390 160 LAERARREKISERMKILQDL 179 (239)
Q Consensus 160 ~aERrRR~kIne~~~~LrsL 179 (239)
.+-++-|.+-+..+..|..-
T Consensus 15 ~AAr~~R~RKk~~~~~Le~~ 34 (64)
T PF00170_consen 15 EAARRSRQRKKQYIEELEEK 34 (64)
T ss_dssp HHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHhhHHHHHHH
Confidence 44455566666666666653
No 38
>PRK14066 exodeoxyribonuclease VII small subunit; Provisional
Probab=35.34 E-value=1.4e+02 Score=22.67 Aligned_cols=53 Identities=9% Similarity=0.092 Sum_probs=39.2
Q ss_pred HHHHHHHHHhcCCCCCCC----CChHhHHHHHHHHHHHHHHHHHHHHHHHHHHhccC
Q 026390 169 ISERMKILQDLVPGCNKV----IGKALVLDEIINYIQSLQRQVEFLSMKLEAVNSRM 221 (239)
Q Consensus 169 Ine~~~~LrsLVP~~~k~----~dKAsIL~eAIdYIk~LQ~qVe~L~~~le~l~~~l 221 (239)
+-+.|..|..||-..... -+-....+++|.++++.+..+...+.++..+-..-
T Consensus 6 fEeal~~LE~IV~~LE~g~l~Leesl~lyeeG~~L~k~C~~~L~~ae~kv~~l~~~~ 62 (75)
T PRK14066 6 FETALKKLEEVVKKLEGGELSLDDSLKAFEEGVKHAAFCSKKLDEAERRVEVLLKQK 62 (75)
T ss_pred HHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence 456777788887544222 23456778999999999999999999998886544
No 39
>PF14197 Cep57_CLD_2: Centrosome localisation domain of PPC89
Probab=33.95 E-value=83 Score=23.48 Aligned_cols=30 Identities=20% Similarity=0.195 Sum_probs=25.0
Q ss_pred hHhHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 026390 189 KALVLDEIINYIQSLQRQVEFLSMKLEAVN 218 (239)
Q Consensus 189 KAsIL~eAIdYIk~LQ~qVe~L~~~le~l~ 218 (239)
-+.=|.+|+.-+..|+.+++.|..+++...
T Consensus 38 ~~~~l~~a~~e~~~Lk~E~e~L~~el~~~r 67 (69)
T PF14197_consen 38 AERQLGDAYEENNKLKEENEALRKELEELR 67 (69)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 355688899999999999999999987654
No 40
>PF08826 DMPK_coil: DMPK coiled coil domain like; InterPro: IPR014930 This domain is found in the myotonic dystrophy protein kinase (DMPK) and adopts a coiled coil structure. It plays a role in dimerisation []. ; GO: 0004674 protein serine/threonine kinase activity, 0005524 ATP binding, 0006468 protein phosphorylation; PDB: 1WT6_D.
Probab=33.04 E-value=96 Score=22.84 Aligned_cols=53 Identities=23% Similarity=0.303 Sum_probs=38.2
Q ss_pred HHHhHHHHHHHHHHHHHhcCCCCCCCCChHhHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 026390 161 AERARREKISERMKILQDLVPGCNKVIGKALVLDEIINYIQSLQRQVEFLSMKLEAVNS 219 (239)
Q Consensus 161 aERrRR~kIne~~~~LrsLVP~~~k~~dKAsIL~eAIdYIk~LQ~qVe~L~~~le~l~~ 219 (239)
+|-+-+..|.+-+...+.- + +.-..-|+++=...+.|+.+|+.|..+++.++.
T Consensus 8 ~EirakQ~~~eEL~kvk~~----n--~~~e~kLqeaE~rn~eL~~ei~~L~~e~ee~r~ 60 (61)
T PF08826_consen 8 AEIRAKQAIQEELTKVKSA----N--LAFESKLQEAEKRNRELEQEIERLKKEMEELRS 60 (61)
T ss_dssp HHHHHHHHHHHHHHHHHHH----H--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-
T ss_pred HHHHHHHHHHHHHHHHHHH----H--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 4555666677755544431 1 245677899999999999999999999988765
No 41
>PRK14127 cell division protein GpsB; Provisional
Probab=32.76 E-value=66 Score=26.22 Aligned_cols=31 Identities=19% Similarity=0.389 Sum_probs=16.1
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHhccC
Q 026390 191 LVLDEIINYIQSLQRQVEFLSMKLEAVNSRM 221 (239)
Q Consensus 191 sIL~eAIdYIk~LQ~qVe~L~~~le~l~~~l 221 (239)
..|+..|+-+..|..++..|+.++..++.++
T Consensus 30 ~FLd~V~~dye~l~~e~~~Lk~e~~~l~~~l 60 (109)
T PRK14127 30 KFLDDVIKDYEAFQKEIEELQQENARLKAQV 60 (109)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4566666555555555554444444444433
No 42
>PF09789 DUF2353: Uncharacterized coiled-coil protein (DUF2353); InterPro: IPR019179 Members of this family have been annotated as being coiled-coil domain-containing protein 149, however they currently have no known function.
Probab=30.14 E-value=1.9e+02 Score=27.80 Aligned_cols=62 Identities=23% Similarity=0.288 Sum_probs=42.9
Q ss_pred cHHHHh--HHHHHHHHHHHHHh---------cCCCCCCCCChHhHHHHHHHHHHHHHHHHHHHHHHHHHHhccC
Q 026390 159 SLAERA--RREKISERMKILQD---------LVPGCNKVIGKALVLDEIINYIQSLQRQVEFLSMKLEAVNSRM 221 (239)
Q Consensus 159 s~aERr--RR~kIne~~~~Lrs---------LVP~~~k~~dKAsIL~eAIdYIk~LQ~qVe~L~~~le~l~~~l 221 (239)
.++|+- |...++..+.+|-- +.|.-.. .+=+.+|.++-+-.+.|+.+|..|..++..+.+.+
T Consensus 30 lMAEqLqer~q~LKkk~~el~~~~~~~~d~~~~~~~~~-~~La~lL~~sre~Nk~L~~Ev~~Lrqkl~E~qGD~ 102 (319)
T PF09789_consen 30 LMAEQLQERYQALKKKYRELIQEAAGFGDPSIPPEKEN-KNLAQLLSESREQNKKLKEEVEELRQKLNEAQGDI 102 (319)
T ss_pred HHHHHHHHHHHHHHHHHHHhhhhhcccCCccCCcccch-hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhchH
Confidence 345543 34566666666552 2232222 25578899999999999999999999998888775
No 43
>PRK00977 exodeoxyribonuclease VII small subunit; Provisional
Probab=28.27 E-value=1.9e+02 Score=22.02 Aligned_cols=53 Identities=9% Similarity=0.169 Sum_probs=37.6
Q ss_pred HHHHHHHHHhcCCCCCCC---C-ChHhHHHHHHHHHHHHHHHHHHHHHHHHHHhccC
Q 026390 169 ISERMKILQDLVPGCNKV---I-GKALVLDEIINYIQSLQRQVEFLSMKLEAVNSRM 221 (239)
Q Consensus 169 Ine~~~~LrsLVP~~~k~---~-dKAsIL~eAIdYIk~LQ~qVe~L~~~le~l~~~l 221 (239)
+-+.|..|..||-..... + +=.....+++.++++.+..++..+.++..+...-
T Consensus 12 fEea~~~LEeIv~~LE~~~l~Lees~~lyeeg~~L~k~C~~~L~~ae~ki~~l~~~~ 68 (80)
T PRK00977 12 FEEALAELEEIVTRLESGDLPLEESLAAFERGVALARQCQKKLQQAEQRVEKLLDED 68 (80)
T ss_pred HHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence 445667777777543211 2 3345668899999999999999999999885543
No 44
>PF05103 DivIVA: DivIVA protein; InterPro: IPR007793 The Bacillus subtilis divIVA1 mutation causes misplacement of the septum during cell division, resulting in the formation of small, circular, anucleate minicells []. Inactivation of divIVA produces a minicell phenotype, whereas overproduction of DivIVA results in a filamentation phenotype []. These proteins appear to contain coiled-coils.; PDB: 2WUK_C 2WUJ_A.
Probab=28.22 E-value=78 Score=24.83 Aligned_cols=33 Identities=24% Similarity=0.386 Sum_probs=25.6
Q ss_pred HhHHHHHHHHHHHHHHHHHHHHHHHHHHhccCC
Q 026390 190 ALVLDEIINYIQSLQRQVEFLSMKLEAVNSRMN 222 (239)
Q Consensus 190 AsIL~eAIdYIk~LQ~qVe~L~~~le~l~~~l~ 222 (239)
-..|+..++.|..|+.++..|..+++.++..+.
T Consensus 24 D~fl~~l~~~~~~l~~e~~~L~~~~~~l~~~l~ 56 (131)
T PF05103_consen 24 DDFLDELAEELERLQRENAELKEEIEELQAQLE 56 (131)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHCCCCT--
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Confidence 356778888888888888888888888888874
No 45
>PF05597 Phasin: Poly(hydroxyalcanoate) granule associated protein (phasin); InterPro: IPR008769 Polyhydroxyalkanoates (PHAs) are storage polyesters synthesised by various bacteria as intracellular carbon and energy reserve material. PHAs are accumulated as water-insoluble inclusions within the cells. This family consists of the phasins PhaF and PhaI which act as a transcriptional regulator of PHA biosynthesis genes. PhaF has been proposed to repress expression of the phaC1 gene and the phaIF operon.
Probab=26.19 E-value=1.5e+02 Score=24.75 Aligned_cols=20 Identities=15% Similarity=0.463 Sum_probs=13.6
Q ss_pred HHHHHHHHHHHHHHHHHHhc
Q 026390 200 IQSLQRQVEFLSMKLEAVNS 219 (239)
Q Consensus 200 Ik~LQ~qVe~L~~~le~l~~ 219 (239)
|..|..+|..|..+|+.|..
T Consensus 111 v~~L~~rId~L~~~v~~l~~ 130 (132)
T PF05597_consen 111 VEALSARIDQLTAQVERLAN 130 (132)
T ss_pred HHHHHHHHHHHHHHHHHHhc
Confidence 56677777777777776653
No 46
>PF07716 bZIP_2: Basic region leucine zipper; InterPro: IPR011700 The basic-leucine zipper (bZIP) transcription factors [, ] of eukaryotes are proteins that contain a basic region mediating sequence-specific DNA-binding, followed by a leucine zipper region (see IPR002158 from INTERPRO), which is required for dimerization.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0046983 protein dimerization activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NWQ_A 1H89_B 1H88_A 1GTW_B 2E43_A 1IO4_A 1GU4_B 2E42_A 1H8A_B 1GU5_B ....
Probab=26.12 E-value=72 Score=22.06 Aligned_cols=19 Identities=21% Similarity=0.386 Sum_probs=10.2
Q ss_pred HHHHHHHHHHHHHHHHHHh
Q 026390 200 IQSLQRQVEFLSMKLEAVN 218 (239)
Q Consensus 200 Ik~LQ~qVe~L~~~le~l~ 218 (239)
|..|+.++..|..+++.|.
T Consensus 34 ~~~L~~en~~L~~~i~~L~ 52 (54)
T PF07716_consen 34 VQELEEENEQLRQEIAQLE 52 (54)
T ss_dssp HHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHh
Confidence 3455555555555555543
No 47
>PF06305 DUF1049: Protein of unknown function (DUF1049); InterPro: IPR010445 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=25.97 E-value=68 Score=22.55 Aligned_cols=18 Identities=28% Similarity=0.521 Sum_probs=9.1
Q ss_pred HHHHHHHHHHHHHHHHHH
Q 026390 200 IQSLQRQVEFLSMKLEAV 217 (239)
Q Consensus 200 Ik~LQ~qVe~L~~~le~l 217 (239)
++.++++++.++.+++++
T Consensus 50 ~~~~~k~l~~le~e~~~l 67 (68)
T PF06305_consen 50 IRRLRKELKKLEKELEQL 67 (68)
T ss_pred HHHHHHHHHHHHHHHHhc
Confidence 344555555555555543
No 48
>PF11336 DUF3138: Protein of unknown function (DUF3138); InterPro: IPR021485 This family of proteins with unknown function appear to be restricted to Proteobacteria.
Probab=25.96 E-value=53 Score=33.14 Aligned_cols=24 Identities=21% Similarity=0.434 Sum_probs=14.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHhccC
Q 026390 198 NYIQSLQRQVEFLSMKLEAVNSRM 221 (239)
Q Consensus 198 dYIk~LQ~qVe~L~~~le~l~~~l 221 (239)
+-|+.||.|++.|+.++.+|+.++
T Consensus 25 ~~i~~L~~ql~aLq~~v~eL~~~l 48 (514)
T PF11336_consen 25 DQIKALQAQLQALQDQVNELRAKL 48 (514)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345666666666666666666655
No 49
>PRK14069 exodeoxyribonuclease VII small subunit; Provisional
Probab=25.90 E-value=1.8e+02 Score=23.30 Aligned_cols=53 Identities=8% Similarity=0.071 Sum_probs=39.1
Q ss_pred HHHHHHHHHhcCCCCCCC----CChHhHHHHHHHHHHHHHHHHHHHHHHHHHHhccC
Q 026390 169 ISERMKILQDLVPGCNKV----IGKALVLDEIINYIQSLQRQVEFLSMKLEAVNSRM 221 (239)
Q Consensus 169 Ine~~~~LrsLVP~~~k~----~dKAsIL~eAIdYIk~LQ~qVe~L~~~le~l~~~l 221 (239)
+-+.|..|..||-..... -+-..+.++++.+|++.+..++..+.++..+...-
T Consensus 10 FEeal~~LEeIV~~LEsgdl~LEesl~lyeeGv~L~k~C~~~L~~AE~kV~~L~~~~ 66 (95)
T PRK14069 10 FEDALRELEQIAEKLERQDFSLEESLKAYERGMELKKICSGILDDAEGKIEALTKDE 66 (95)
T ss_pred HHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence 456677777777543221 23456778999999999999999999999887544
No 50
>PRK14126 cell division protein ZapA; Provisional
Probab=25.86 E-value=3.1e+02 Score=21.02 Aligned_cols=42 Identities=21% Similarity=0.317 Sum_probs=29.3
Q ss_pred HHHHHHHHHHHhcCCCCCCCCChHhHHHHHHHHHHHHHHHHHHHH
Q 026390 167 EKISERMKILQDLVPGCNKVIGKALVLDEIINYIQSLQRQVEFLS 211 (239)
Q Consensus 167 ~kIne~~~~LrsLVP~~~k~~dKAsIL~eAIdYIk~LQ~qVe~L~ 211 (239)
..++++|..++.--|..+. .++.|| -|++....|-+-.+++.
T Consensus 34 ~~vd~km~ei~~~~~~ls~--~~iAVL-aALNia~El~k~~~~~~ 75 (85)
T PRK14126 34 AIVDDKMRELNEKNPSLDT--SKLAVL-TAVNVIHDYIKLKEEYE 75 (85)
T ss_pred HHHHHHHHHHHHhCCCCCH--HHHHHH-HHHHHHHHHHHHHHHHH
Confidence 4789999999998776653 688888 47777776654443333
No 51
>TIGR01280 xseB exodeoxyribonuclease VII, small subunit. This protein is the small subunit for exodeoxyribonuclease VII. Exodeoxyribonuclease VII is made of a complex of four small subunits to one large subunit. The complex degrades single-stranded DNA into large acid-insoluble oligonucleotides. These nucleotides are then degraded further into acid-soluble oligonucleotides.
Probab=25.35 E-value=1.4e+02 Score=21.94 Aligned_cols=52 Identities=6% Similarity=0.105 Sum_probs=37.7
Q ss_pred HHHHHHHHhcCCCCCCC---C-ChHhHHHHHHHHHHHHHHHHHHHHHHHHHHhccC
Q 026390 170 SERMKILQDLVPGCNKV---I-GKALVLDEIINYIQSLQRQVEFLSMKLEAVNSRM 221 (239)
Q Consensus 170 ne~~~~LrsLVP~~~k~---~-dKAsIL~eAIdYIk~LQ~qVe~L~~~le~l~~~l 221 (239)
-+.|..|..||-..... + +-....++++.++++.+..++..+.++..+...-
T Consensus 4 Ee~l~~Le~Iv~~LE~~~l~Leesl~lyeeG~~L~k~c~~~L~~ae~kv~~l~~~~ 59 (67)
T TIGR01280 4 EEALSELEQIVQKLESGDLALEEALNLFERGMALARRCEKKLAQAEQRVRKLLKED 59 (67)
T ss_pred HHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence 35566677776543221 2 3345678999999999999999999999987655
No 52
>PRK14011 prefoldin subunit alpha; Provisional
Probab=24.59 E-value=1.2e+02 Score=25.56 Aligned_cols=29 Identities=17% Similarity=0.234 Sum_probs=21.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhccC
Q 026390 193 LDEIINYIQSLQRQVEFLSMKLEAVNSRM 221 (239)
Q Consensus 193 L~eAIdYIk~LQ~qVe~L~~~le~l~~~l 221 (239)
|+.-+.||+.|++|++.|+..+..++...
T Consensus 5 lq~~~~~l~~~~~qie~L~~si~~L~~a~ 33 (144)
T PRK14011 5 LQNQFMALEVYNQQVQKLQEELSSIDMMK 33 (144)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45567788888888888887777776543
No 53
>PF10465 Inhibitor_I24: PinA peptidase inhibitor ; InterPro: IPR019506 Peptide proteinase inhibitors can be found as single domain proteins or as single or multiple domains within proteins; these are referred to as either simple or compound inhibitors, respectively. In many cases they are synthesised as part of a larger precursor protein, either as a prepropeptide or as an N-terminal domain associated with an inactive peptidase or zymogen. This domain prevents access of the substrate to the active site. Removal of the N-terminal inhibitor domain either by interaction with a second peptidase or by autocatalytic cleavage activates the zymogen. Other inhibitors interact direct with proteinases using a simple noncovalent lock and key mechanism; while yet others use a conformational change-based trapping mechanism that depends on their structural and thermodynamic properties. PinA inhibits the endopeptidase La. It binds to the La homotetramer but does not interfere with the ATP binding site or the active site of La.
Probab=24.52 E-value=62 Score=27.44 Aligned_cols=20 Identities=20% Similarity=0.330 Sum_probs=17.3
Q ss_pred ChHhHHHHHHHHHHHHHHHH
Q 026390 188 GKALVLDEIINYIQSLQRQV 207 (239)
Q Consensus 188 dKAsIL~eAIdYIk~LQ~qV 207 (239)
--..+.+.|.+||++|+.|+
T Consensus 120 yEgnLMQAAAeYIewLE~ql 139 (140)
T PF10465_consen 120 YEGNLMQAAAEYIEWLETQL 139 (140)
T ss_pred chhhHHHHHHHHHHHHHhhc
Confidence 45778899999999999885
No 54
>PF11853 DUF3373: Protein of unknown function (DUF3373); InterPro: IPR021803 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 472 to 574 amino acids in length.
Probab=23.73 E-value=1.3e+02 Score=30.57 Aligned_cols=23 Identities=30% Similarity=0.511 Sum_probs=17.2
Q ss_pred HHHHHHHHHHHHHHHHHHHhccC
Q 026390 199 YIQSLQRQVEFLSMKLEAVNSRM 221 (239)
Q Consensus 199 YIk~LQ~qVe~L~~~le~l~~~l 221 (239)
=|+.|++|+++|+++++.++.++
T Consensus 32 kie~L~kql~~Lk~q~~~l~~~v 54 (489)
T PF11853_consen 32 KIEALKKQLEELKAQQDDLNDRV 54 (489)
T ss_pred HHHHHHHHHHHHHHhhccccccc
Confidence 46778888888888877666666
No 55
>PF02185 HR1: Hr1 repeat; InterPro: IPR000861 The HR1 repeat was first described as a three times repeated homology region of the N-terminal non-catalytic part of protein kinase PRK1(PKN) []. The first two of these repeats were later shown to bind the small G protein rho [, ] known to activate PKN in its GTP-bound form. Similar rho-binding domains also occur in a number of other protein kinases and in the rho-binding proteins rhophilin and rhotekin. Recently, the structure of the N-terminal HR1 repeat complexed with RhoA has been determined by X-ray crystallography []. It forms an antiparallel coiled-coil fold termed an ACC finger. This entry includes domains found within rho-associated protein kinases.; GO: 0007165 signal transduction, 0005622 intracellular; PDB: 1CXZ_B 3O0Z_C 2RMK_B 1URF_A.
Probab=22.48 E-value=3e+02 Score=19.77 Aligned_cols=49 Identities=24% Similarity=0.316 Sum_probs=34.3
Q ss_pred HHHHHHHHHHhcCCCCCCCCChHhHHHHHHHHHHHHHHHHHHHHHHHHHHhccC
Q 026390 168 KISERMKILQDLVPGCNKVIGKALVLDEIINYIQSLQRQVEFLSMKLEAVNSRM 221 (239)
Q Consensus 168 kIne~~~~LrsLVP~~~k~~dKAsIL~eAIdYIk~LQ~qVe~L~~~le~l~~~l 221 (239)
+|.+++..|..++ . .++..++..+-.=|......++.|+++|+.+....
T Consensus 15 ki~~Gae~m~~~~----~-t~~~~~~~~~~~~l~~s~~kI~~L~~~L~~l~~~~ 63 (70)
T PF02185_consen 15 KIKEGAENMLQAY----S-TDKKKVLSEAESQLRESNQKIELLREQLEKLQQRS 63 (70)
T ss_dssp HHHHHHHHHHHHH----C-CHHCH-HHHHHHHHHHHHHHHHHHHHHHHHHHCCH
T ss_pred HHHHHHHHHHHHH----c-cCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence 4555555555544 1 25555888888888889999999999998887665
No 56
>PF05531 NPV_P10: Nucleopolyhedrovirus P10 protein; InterPro: IPR008702 This family consists of several nucleopolyhedrovirus P10 proteins which are thought to be involved in the morphogenesis of the polyhedra [].; GO: 0019028 viral capsid
Probab=21.83 E-value=2.3e+02 Score=21.78 Aligned_cols=15 Identities=20% Similarity=0.260 Sum_probs=7.1
Q ss_pred ChHhHHHHHHHHHHH
Q 026390 188 GKALVLDEIINYIQS 202 (239)
Q Consensus 188 dKAsIL~eAIdYIk~ 202 (239)
+|..-|+..|+-++.
T Consensus 18 ~KVdaLq~~V~~l~~ 32 (75)
T PF05531_consen 18 DKVDALQTQVDDLES 32 (75)
T ss_pred HHHHHHHHHHHHHHh
Confidence 344445555544444
No 57
>PF11336 DUF3138: Protein of unknown function (DUF3138); InterPro: IPR021485 This family of proteins with unknown function appear to be restricted to Proteobacteria.
Probab=21.35 E-value=2.1e+02 Score=29.01 Aligned_cols=49 Identities=27% Similarity=0.291 Sum_probs=34.0
Q ss_pred HHHHHh-cCCCCCCCCChHhHHHHHHHHHHHHHHHHHHHHHHHHHHhccC
Q 026390 173 MKILQD-LVPGCNKVIGKALVLDEIINYIQSLQRQVEFLSMKLEAVNSRM 221 (239)
Q Consensus 173 ~~~Lrs-LVP~~~k~~dKAsIL~eAIdYIk~LQ~qVe~L~~~le~l~~~l 221 (239)
|..|.- -+|+......++.-++.-..-|+.||+||.+|+.+|++-....
T Consensus 6 ~~alv~~al~~~a~a~a~a~~i~~L~~ql~aLq~~v~eL~~~laa~~~aa 55 (514)
T PF11336_consen 6 ITALVAGALPGAAMAAATADQIKALQAQLQALQDQVNELRAKLAAKPAAA 55 (514)
T ss_pred HHHHHHhhccccccccCCHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCC
Confidence 344444 3566544445666666666778999999999999998776644
No 58
>PF09278 MerR-DNA-bind: MerR, DNA binding; InterPro: IPR015358 This entry represents a family of DNA-binding domains that are predominantly found in the prokaryotic transcriptional regulator MerR. They adopt a structure consisting of a core of three alpha helices, with an architecture that is similar to that of the 'winged helix' fold []. ; PDB: 3QAO_A 1R8D_B 1JBG_A 2VZ4_A 2ZHH_A 2ZHG_A 1Q09_A 1Q08_B 1Q0A_B 1Q07_A ....
Probab=20.51 E-value=2.5e+02 Score=19.34 Aligned_cols=31 Identities=10% Similarity=-0.010 Sum_probs=21.5
Q ss_pred ChHhHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 026390 188 GKALVLDEIINYIQSLQRQVEFLSMKLEAVN 218 (239)
Q Consensus 188 dKAsIL~eAIdYIk~LQ~qVe~L~~~le~l~ 218 (239)
....+++..-+.++.|.++++.|+.-...++
T Consensus 33 ~~~~~~~~l~~~~~~i~~~i~~L~~~~~~L~ 63 (65)
T PF09278_consen 33 PCADRRALLEEKLEEIEEQIAELQALRAQLE 63 (65)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 4566666777777888888887776665553
No 59
>PF05928 Zea_mays_MuDR: Zea mays MURB-like protein (MuDR); InterPro: IPR009227 This family consists of several Zea mays (Maize) specific MURB-like proteins. The transposition of Mu elements underlying Mutator activity in maize requires a transcriptionally active MuDR element. Despite variation in MuDR copy number and RNA levels in Mutator lines, transposition events are consistently late in plant development, and Mu excision frequencies are similar [].
Probab=20.46 E-value=4.4e+02 Score=23.57 Aligned_cols=77 Identities=18% Similarity=0.248 Sum_probs=48.0
Q ss_pred ccHHHHhHHHHHHHHHHHHHhcCCCCCCCCChHhHHHHHHHHHHHH-HHHHHHHHHHHHHHhccCC--CCCCccCCCCCC
Q 026390 158 HSLAERARREKISERMKILQDLVPGCNKVIGKALVLDEIINYIQSL-QRQVEFLSMKLEAVNSRMN--LTPTIEGFHPKD 234 (239)
Q Consensus 158 Hs~aERrRR~kIne~~~~LrsLVP~~~k~~dKAsIL~eAIdYIk~L-Q~qVe~L~~~le~l~~~l~--~~~~i~~~~~k~ 234 (239)
..+-|.+|-.+|-..+..|.+-||.... +|.+-+..-.++|..= ..--..-++.++.-++..+ .+|.++.+.|-+
T Consensus 77 yaIQEmRRQs~~l~s~~~Lc~~Ipev~G--gkIgk~~~~l~hVck~l~ktS~lCeEdle~k~p~wdl~~~psvdd~~p~~ 154 (207)
T PF05928_consen 77 YAIQEMRRQSQQLPSTTNLCQCIPEVAG--GKIGKYKEKLNHVCKDLNKTSALCEEDLENKCPTWDLYHNPSVDDCHPSD 154 (207)
T ss_pred HHHHHHHHHHHhhhHHHHHHHhcccccC--cchhhHHHHHHHHHhccchhhHHHHHHHhccCCCCcCCCCCCcCcCCCCc
Confidence 3467778888888888889998987654 4555555444444332 2222223455666666554 667788887777
Q ss_pred cc
Q 026390 235 VS 236 (239)
Q Consensus 235 ~~ 236 (239)
|.
T Consensus 155 ~~ 156 (207)
T PF05928_consen 155 FD 156 (207)
T ss_pred hh
Confidence 64
No 60
>PF10359 Fmp27_WPPW: RNA pol II promoter Fmp27 protein domain; InterPro: IPR019449 The function of the FMP27 protein is not known. FMP27 is the product of a nuclear encoded gene but it is detected in highly purified mitochondria in high-throughput studies []. This entry represents a domain within FMP27 that contains characteristic HQR and WPPW sequence motifs.
Probab=20.43 E-value=1.2e+02 Score=29.96 Aligned_cols=65 Identities=17% Similarity=0.198 Sum_probs=40.4
Q ss_pred ccHHHHhHHHHHHHHHHHHHhcCCCCCC--C-CChHhHHHHHHHHHHHHHHHHHHHHHHHHHHhccCC
Q 026390 158 HSLAERARREKISERMKILQDLVPGCNK--V-IGKALVLDEIINYIQSLQRQVEFLSMKLEAVNSRMN 222 (239)
Q Consensus 158 Hs~aERrRR~kIne~~~~LrsLVP~~~k--~-~dKAsIL~eAIdYIk~LQ~qVe~L~~~le~l~~~l~ 222 (239)
+...-+.|-..|.+.+..+...+-.... . .....-++.....|+.|+++++.|+..++.+.....
T Consensus 164 Q~~L~~~Rl~~L~~qi~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~~~l~~~l~~l~~~~~ 231 (475)
T PF10359_consen 164 QIELIQERLDELEEQIEKHEEKLGELELNPDDPELKSDIEELERHISSLKERIEFLENMLEDLEDSES 231 (475)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhhccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcc
Confidence 3344455555566666666655543221 0 112344556667789999999999999988887773
No 61
>PF12097 DUF3573: Protein of unknown function (DUF3573); InterPro: IPR021956 This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 372 to 530 amino acids in length.
Probab=20.06 E-value=1.2e+02 Score=29.71 Aligned_cols=23 Identities=22% Similarity=0.426 Sum_probs=18.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcc
Q 026390 198 NYIQSLQRQVEFLSMKLEAVNSR 220 (239)
Q Consensus 198 dYIk~LQ~qVe~L~~~le~l~~~ 220 (239)
+-|-.||+|++.|+.++..++..
T Consensus 42 ~~i~~Lq~QI~~Lq~ei~~l~~~ 64 (383)
T PF12097_consen 42 QEISELQKQIQQLQAEINQLEEQ 64 (383)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHh
Confidence 34567888999998888888877
Done!