Query 018007
Match_columns 362
No_of_seqs 213 out of 794
Neff 4.0
Searched_HMMs 46136
Date Fri Mar 29 05:20:23 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/018007.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/018007hhsearch_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 99.3 2.7E-12 5.8E-17 94.6 5.7 54 286-339 5-60 (60)
2 smart00353 HLH helix loop heli 99.3 5.6E-12 1.2E-16 91.5 6.2 50 290-339 1-52 (53)
3 PF00010 HLH: Helix-loop-helix 99.3 9.6E-12 2.1E-16 91.7 5.5 48 288-335 4-55 (55)
4 KOG1318 Helix loop helix trans 99.1 5.8E-11 1.3E-15 120.1 4.0 58 285-342 233-293 (411)
5 KOG1319 bHLHZip transcription 98.8 2.2E-09 4.7E-14 99.5 1.6 74 287-360 64-147 (229)
6 KOG4304 Transcriptional repres 98.4 8.8E-08 1.9E-12 91.8 2.6 51 289-339 36-93 (250)
7 KOG3561 Aryl-hydrocarbon recep 98.2 6.1E-07 1.3E-11 97.5 3.6 52 286-337 21-75 (803)
8 KOG2588 Predicted DNA-binding 98.2 8.7E-07 1.9E-11 97.1 2.6 66 284-349 275-340 (953)
9 KOG2483 Upstream transcription 97.9 3.8E-05 8.3E-10 73.3 7.2 65 285-349 59-125 (232)
10 KOG3960 Myogenic helix-loop-he 97.7 7.5E-05 1.6E-09 72.3 6.9 56 291-346 124-180 (284)
11 PLN03217 transcription factor 97.4 0.00036 7.8E-09 58.0 6.1 56 295-350 17-77 (93)
12 KOG4029 Transcription factor H 97.1 0.00036 7.9E-09 65.3 3.1 57 289-345 113-172 (228)
13 KOG0561 bHLH transcription fac 96.8 0.001 2.2E-08 66.2 3.2 52 290-342 65-118 (373)
14 KOG3910 Helix loop helix trans 94.3 0.031 6.7E-07 59.0 2.8 63 290-353 531-596 (632)
15 KOG3558 Hypoxia-inducible fact 88.9 0.26 5.5E-06 54.0 2.3 44 291-334 52-98 (768)
16 KOG4447 Transcription factor T 87.9 0.25 5.5E-06 45.4 1.3 49 288-337 81-131 (173)
17 KOG3560 Aryl-hydrocarbon recep 87.8 0.47 1E-05 51.0 3.4 40 293-333 33-76 (712)
18 KOG3559 Transcriptional regula 85.5 0.83 1.8E-05 47.8 3.7 44 291-334 7-53 (598)
19 KOG3898 Transcription factor N 66.3 3.6 7.8E-05 39.9 1.9 45 292-337 79-126 (254)
20 KOG4395 Transcription factor A 66.3 6.8 0.00015 38.8 3.7 49 290-338 179-229 (285)
21 COG3074 Uncharacterized protei 42.1 35 0.00076 28.0 3.5 26 324-349 13-38 (79)
22 PRK13702 replication protein; 37.6 71 0.0015 26.9 4.7 44 286-329 21-76 (85)
23 PF09321 DUF1978: Domain of un 34.1 61 0.0013 31.9 4.4 19 298-316 116-134 (241)
24 PRK15422 septal ring assembly 30.9 66 0.0014 26.7 3.5 26 323-348 12-37 (79)
25 PF14689 SPOB_a: Sensor_kinase 28.5 1.1E+02 0.0025 23.3 4.3 41 294-342 17-57 (62)
26 PF13334 DUF4094: Domain of un 28.5 89 0.0019 26.3 4.0 26 324-349 68-93 (95)
27 KOG0709 CREB/ATF family transc 28.2 64 0.0014 34.5 3.7 25 291-317 263-287 (472)
28 PF06005 DUF904: Protein of un 27.2 89 0.0019 25.1 3.6 24 324-347 13-36 (72)
29 TIGR00986 3a0801s05tom22 mitoc 26.1 38 0.00081 31.0 1.4 37 297-334 48-84 (145)
30 KOG3582 Mlx interactors and re 23.6 29 0.00063 38.9 0.3 57 287-346 789-849 (856)
31 PF04508 Pox_A_type_inc: Viral 21.9 98 0.0021 20.2 2.3 19 331-349 3-21 (23)
32 KOG3584 cAMP response element 20.5 79 0.0017 32.2 2.6 25 292-316 302-326 (348)
33 KOG3582 Mlx interactors and re 20.4 29 0.00062 38.9 -0.5 55 287-341 653-711 (856)
34 PF07544 Med9: RNA polymerase 20.2 2.4E+02 0.0052 22.8 4.9 43 300-348 33-78 (83)
35 PF04281 Tom22: Mitochondrial 20.1 58 0.0013 29.3 1.4 21 296-316 49-69 (137)
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=99.32 E-value=2.7e-12 Score=94.64 Aligned_cols=54 Identities=37% Similarity=0.655 Sum_probs=48.7
Q ss_pred CCCCcHHHHHHHHHHHHHHHHhhcccCCC--CCCCCHHHHHHHHHHHHHHHHHHHH
Q 018007 286 THPRSIAERVRRTRISERMRKLQELVPNM--DKQTNTADMLDLAVDYIKDLQNQFK 339 (362)
Q Consensus 286 ~~~hsiaERrRRerIneri~~Lr~LVP~~--~Kq~dKAsIL~eAI~YIK~LQ~qVq 339 (362)
...|+..||+||++||+.|..|+.+||.. ..+++|+.||+.||+||+.|+.+++
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 34688999999999999999999999998 3459999999999999999998863
No 2
>smart00353 HLH helix loop helix domain.
Probab=99.30 E-value=5.6e-12 Score=91.54 Aligned_cols=50 Identities=38% Similarity=0.726 Sum_probs=44.8
Q ss_pred cHHHHHHHHHHHHHHHHhhcccCCC--CCCCCHHHHHHHHHHHHHHHHHHHH
Q 018007 290 SIAERVRRTRISERMRKLQELVPNM--DKQTNTADMLDLAVDYIKDLQNQFK 339 (362)
Q Consensus 290 siaERrRRerIneri~~Lr~LVP~~--~Kq~dKAsIL~eAI~YIK~LQ~qVq 339 (362)
+..||+||++||+.|..|+.+||.+ ..+++|++||++||+||+.|+.+++
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 3689999999999999999999963 2348999999999999999999886
No 3
>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=99.25 E-value=9.6e-12 Score=91.74 Aligned_cols=48 Identities=40% Similarity=0.652 Sum_probs=44.4
Q ss_pred CCcHHHHHHHHHHHHHHHHhhcccCCC----CCCCCHHHHHHHHHHHHHHHH
Q 018007 288 PRSIAERVRRTRISERMRKLQELVPNM----DKQTNTADMLDLAVDYIKDLQ 335 (362)
Q Consensus 288 ~hsiaERrRRerIneri~~Lr~LVP~~----~Kq~dKAsIL~eAI~YIK~LQ 335 (362)
.|+..||+||++||+.|..|+.+||.+ ..+++|++||+.||+||+.||
T Consensus 4 ~h~~~Er~RR~~i~~~~~~L~~llp~~~~~~~~k~~K~~iL~~ai~yI~~Lq 55 (55)
T PF00010_consen 4 KHNERERRRRDRINDCFDELRELLPSCSAGSSRKLSKASILQKAIDYIKQLQ 55 (55)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHCCSSHHCCTTSSSSHHHHHHHHHHHHHHHH
T ss_pred hHHHHHHHHHHHHHHHHHHHHHhccchhccccccCCHHHHHHHHHHHHHHhC
Confidence 488999999999999999999999987 345999999999999999997
No 4
>KOG1318 consensus Helix loop helix transcription factor EB [Transcription]
Probab=99.09 E-value=5.8e-11 Score=120.08 Aligned_cols=58 Identities=28% Similarity=0.572 Sum_probs=50.3
Q ss_pred CCCCCcHHHHHHHHHHHHHHHHhhcccCCCCC---CCCHHHHHHHHHHHHHHHHHHHHHHH
Q 018007 285 ATHPRSIAERVRRTRISERMRKLQELVPNMDK---QTNTADMLDLAVDYIKDLQNQFKTLS 342 (362)
Q Consensus 285 a~~~hsiaERrRRerIneri~~Lr~LVP~~~K---q~dKAsIL~eAI~YIK~LQ~qVq~L~ 342 (362)
++..|+.+|||||++||+||++|..|||.|.. +++|+.||..+++||+.||+..++..
T Consensus 233 Krd~HNeVERRRR~nIN~~IkeLg~liP~~~~~~~~~nKgtILk~s~dYIr~Lqq~~q~~~ 293 (411)
T KOG1318|consen 233 KRDNHNEVERRRRENINDRIKELGQLIPKCNSEDMKSNKGTILKASCDYIRELQQTLQRAR 293 (411)
T ss_pred HHhhhhHHHHHHHHHHHHHHHHHHHhCCCCCcchhhcccchhhHHHHHHHHHHHHHHHHHH
Confidence 34569999999999999999999999999842 37899999999999999988776433
No 5
>KOG1319 consensus bHLHZip transcription factor BIGMAX [Transcription]
Probab=98.77 E-value=2.2e-09 Score=99.54 Aligned_cols=74 Identities=30% Similarity=0.378 Sum_probs=59.4
Q ss_pred CCCcHHHHHHHHHHHHHHHHhhcccCCCCC------CCCHHHHHHHHHHHHHHHHHHHHHHHhh----hhhhcccccccc
Q 018007 287 HPRSIAERVRRTRISERMRKLQELVPNMDK------QTNTADMLDLAVDYIKDLQNQFKTLSDN----RAKCKCSKIQKP 356 (362)
Q Consensus 287 ~~hsiaERrRRerIneri~~Lr~LVP~~~K------q~dKAsIL~eAI~YIK~LQ~qVq~L~~~----~~~~tc~~~~k~ 356 (362)
..|..+||+||+.|+.....|++|||.|.. ++.||.||..+|+||.+|..++..-+++ ++.++++.+-+.
T Consensus 64 ~aHtqaEqkRRdAIk~GYddLq~LvP~cq~~ds~g~KlskA~ILqksidyi~~L~~~k~kqe~e~s~L~k~vtAL~iIk~ 143 (229)
T KOG1319|consen 64 RAHTQAEQKRRDAIKRGYDDLQTLVPTCQQQDSIGQKLSKAIILQKTIDYIQFLHKEKKKQEEEVSTLRKDVTALKIIKV 143 (229)
T ss_pred HHHHHHHHHHHHHHHhchHHHHHhccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 457889999999999999999999997654 2789999999999999998777655544 466777766665
Q ss_pred cccc
Q 018007 357 VENQ 360 (362)
Q Consensus 357 ~~~q 360 (362)
.++|
T Consensus 144 ~YEq 147 (229)
T KOG1319|consen 144 NYEQ 147 (229)
T ss_pred HHHH
Confidence 5544
No 6
>KOG4304 consensus Transcriptional repressors of the hairy/E(spl) family (contains HLH) [Transcription]
Probab=98.44 E-value=8.8e-08 Score=91.81 Aligned_cols=51 Identities=31% Similarity=0.596 Sum_probs=44.7
Q ss_pred CcHHHHHHHHHHHHHHHHhhcccCCCCC-------CCCHHHHHHHHHHHHHHHHHHHH
Q 018007 289 RSIAERVRRTRISERMRKLQELVPNMDK-------QTNTADMLDLAVDYIKDLQNQFK 339 (362)
Q Consensus 289 hsiaERrRRerIneri~~Lr~LVP~~~K-------q~dKAsIL~eAI~YIK~LQ~qVq 339 (362)
|-+.||+||.|||+-|.+|++|||.+.| +++||+||+.||+|+|.|+.+..
T Consensus 36 Kpl~EKkRRaRIN~~L~eLK~Li~e~~~~~~~~~sklEKAdILEltV~hL~~l~~~~~ 93 (250)
T KOG4304|consen 36 KPLLEKKRRARINRCLDELKDLIPEALKKDGQRHSKLEKADILELTVNHLRQLQRSQQ 93 (250)
T ss_pred chhHHHHHHHHHHHHHHHHHHHHHHHHhhcchhhhhhHHHHHHHHHHHHHHHHhcccc
Confidence 4589999999999999999999995544 28899999999999999987654
No 7
>KOG3561 consensus Aryl-hydrocarbon receptor nuclear translocator [Transcription]
Probab=98.24 E-value=6.1e-07 Score=97.47 Aligned_cols=52 Identities=27% Similarity=0.485 Sum_probs=48.6
Q ss_pred CCCCcHHHHHHHHHHHHHHHHhhcccCCCC---CCCCHHHHHHHHHHHHHHHHHH
Q 018007 286 THPRSIAERVRRTRISERMRKLQELVPNMD---KQTNTADMLDLAVDYIKDLQNQ 337 (362)
Q Consensus 286 ~~~hsiaERrRRerIneri~~Lr~LVP~~~---Kq~dKAsIL~eAI~YIK~LQ~q 337 (362)
+.+|+.+|||||+++|..|.+|.+|||.|. .|+||-+||.+||++||.++++
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 567899999999999999999999999988 5699999999999999999886
No 8
>KOG2588 consensus Predicted DNA-binding protein [Transcription]
Probab=98.16 E-value=8.7e-07 Score=97.07 Aligned_cols=66 Identities=29% Similarity=0.463 Sum_probs=59.8
Q ss_pred CCCCCCcHHHHHHHHHHHHHHHHhhcccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHhhhhhhc
Q 018007 284 CATHPRSIAERVRRTRISERMRKLQELVPNMDKQTNTADMLDLAVDYIKDLQNQFKTLSDNRAKCK 349 (362)
Q Consensus 284 ~a~~~hsiaERrRRerIneri~~Lr~LVP~~~Kq~dKAsIL~eAI~YIK~LQ~qVq~L~~~~~~~t 349 (362)
..+..|+++|||-|.-||+||.+|++|||+..-++.|..+|..||+||++|+...+.|+.+.+..+
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 447889999999999999999999999999887799999999999999999999888887765554
No 9
>KOG2483 consensus Upstream transcription factor 2/L-myc-2 protein [Transcription]
Probab=97.85 E-value=3.8e-05 Score=73.31 Aligned_cols=65 Identities=22% Similarity=0.352 Sum_probs=52.0
Q ss_pred CCCCCcHHHHHHHHHHHHHHHHhhcccCCCCCCC--CHHHHHHHHHHHHHHHHHHHHHHHhhhhhhc
Q 018007 285 ATHPRSIAERVRRTRISERMRKLQELVPNMDKQT--NTADMLDLAVDYIKDLQNQFKTLSDNRAKCK 349 (362)
Q Consensus 285 a~~~hsiaERrRRerIneri~~Lr~LVP~~~Kq~--dKAsIL~eAI~YIK~LQ~qVq~L~~~~~~~t 349 (362)
++..|+.-||+||..|.+.|..|+.+||.....+ +.+.||+.|++||+.|+.+..+.....+++.
T Consensus 59 ~R~~HN~LEk~RRahlk~~~~~Lk~~vP~~~~~~~~t~lsiL~kA~~~i~~l~~~~~~~~~~~e~l~ 125 (232)
T KOG2483|consen 59 SRAHHNALEKRRRAHLKDCFESLKDSVPLLNGETRSTTLSILDKALEHIQSLERKSATQQQDIEDLS 125 (232)
T ss_pred chhhhhhhhHHHHHHHHHHHHHHHHhCCCCCCcchhhhhHhhhhHHHHHHHHHhHHHHHHHHHHHHH
Confidence 3445889999999999999999999999655422 2699999999999999887776665554443
No 10
>KOG3960 consensus Myogenic helix-loop-helix transcription factor [Transcription]
Probab=97.72 E-value=7.5e-05 Score=72.29 Aligned_cols=56 Identities=21% Similarity=0.380 Sum_probs=48.5
Q ss_pred HHHHHHHHHHHHHHHHhhc-ccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 018007 291 IAERVRRTRISERMRKLQE-LVPNMDKQTNTADMLDLAVDYIKDLQNQFKTLSDNRA 346 (362)
Q Consensus 291 iaERrRRerIneri~~Lr~-LVP~~~Kq~dKAsIL~eAI~YIK~LQ~qVq~L~~~~~ 346 (362)
+-||||=.|+||.|.+|+. -+++-+..+-|..||.-||+||..||.-++++.+...
T Consensus 124 MRERRRLkKVNEAFE~LKRrT~~NPNQRLPKVEILRsAI~YIE~Lq~LL~~~~~~~~ 180 (284)
T KOG3960|consen 124 MRERRRLKKVNEAFETLKRRTSSNPNQRLPKVEILRSAIRYIERLQALLQEQDQAEK 180 (284)
T ss_pred HHHHHHHHHHHHHHHHHHhhcCCCccccccHHHHHHHHHHHHHHHHHHHHHhhccch
Confidence 4599999999999999964 5677777799999999999999999999988876543
No 11
>PLN03217 transcription factor ATBS1; Provisional
Probab=97.42 E-value=0.00036 Score=58.01 Aligned_cols=56 Identities=23% Similarity=0.479 Sum_probs=46.5
Q ss_pred HHHHHHHHHHHHhhcccCCCCC-----CCCHHHHHHHHHHHHHHHHHHHHHHHhhhhhhcc
Q 018007 295 VRRTRISERMRKLQELVPNMDK-----QTNTADMLDLAVDYIKDLQNQFKTLSDNRAKCKC 350 (362)
Q Consensus 295 rRRerIneri~~Lr~LVP~~~K-----q~dKAsIL~eAI~YIK~LQ~qVq~L~~~~~~~tc 350 (362)
---+.|+|-+.+||.|+|.... +...+-||+||+.||+.|..+|..|.+.+..+-.
T Consensus 17 isddqi~dLvsKLq~llPe~r~~r~s~k~saskvLqEtC~YIrsLhrEvDdLSerLs~LL~ 77 (93)
T PLN03217 17 ISEDQINDLIIKLQQLLPELRDSRRSDKVSAARVLQDTCNYIRNLHREVDDLSERLSELLA 77 (93)
T ss_pred CCHHHHHHHHHHHHHHChHHHhhhccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 3347899999999999994321 2678899999999999999999999998866543
No 12
>KOG4029 consensus Transcription factor HAND2/Transcription factor TAL1/TAL2/LYL1 [Transcription]
Probab=97.09 E-value=0.00036 Score=65.32 Aligned_cols=57 Identities=26% Similarity=0.400 Sum_probs=49.6
Q ss_pred CcHHHHHHHHHHHHHHHHhhcccCC--C-CCCCCHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 018007 289 RSIAERVRRTRISERMRKLQELVPN--M-DKQTNTADMLDLAVDYIKDLQNQFKTLSDNR 345 (362)
Q Consensus 289 hsiaERrRRerIneri~~Lr~LVP~--~-~Kq~dKAsIL~eAI~YIK~LQ~qVq~L~~~~ 345 (362)
++..||.|=+-+|..|..||.+||. . +|++.|..+|..||.||++|+.-++.-+...
T Consensus 113 ~n~RER~Rv~~vN~~f~~Lr~~lP~~~~~~kklSKveTLr~A~~YI~~L~~lL~~~~~~~ 172 (228)
T KOG4029|consen 113 RNARERQRVQSVNSAFAELRALLPTEPPQSKKLSKVETLRLATSYIRYLTKLLATQEAPL 172 (228)
T ss_pred hhhhhhhcccchhhhhHHHHhcCCCCCCcccccCcccchHHHHHHHHHHHHHhcccccCC
Confidence 4556999999999999999999994 3 6679999999999999999998887766554
No 13
>KOG0561 consensus bHLH transcription factor [Transcription]
Probab=96.76 E-value=0.001 Score=66.15 Aligned_cols=52 Identities=29% Similarity=0.442 Sum_probs=44.4
Q ss_pred cHHHHHHHHHHHHHHHHhhcccCC--CCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q 018007 290 SIAERVRRTRISERMRKLQELVPN--MDKQTNTADMLDLAVDYIKDLQNQFKTLS 342 (362)
Q Consensus 290 siaERrRRerIneri~~Lr~LVP~--~~Kq~dKAsIL~eAI~YIK~LQ~qVq~L~ 342 (362)
+..||||=.-||-.|..||.|+|. ..| +.||.||+.+.+||.+|+.+.-+|=
T Consensus 65 NsNERRRMQSINAGFqsLr~LlPr~eGEK-LSKAAILQQTa~yI~~Le~~Kt~ll 118 (373)
T KOG0561|consen 65 NSNERRRMQSINAGFQSLRALLPRKEGEK-LSKAAILQQTADYIHQLEGHKTELL 118 (373)
T ss_pred cchHHHHHHhhhHHHHHHHHhcCcccchh-hHHHHHHHHHHHHHHHHHhcccccc
Confidence 345999999999999999999995 445 9999999999999999986654443
No 14
>KOG3910 consensus Helix loop helix transcription factor [Transcription]
Probab=94.27 E-value=0.031 Score=58.99 Aligned_cols=63 Identities=25% Similarity=0.373 Sum_probs=48.4
Q ss_pred cHHHHHHHHHHHHHHHHhhcccC---CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHhhhhhhccccc
Q 018007 290 SIAERVRRTRISERMRKLQELVP---NMDKQTNTADMLDLAVDYIKDLQNQFKTLSDNRAKCKCSKI 353 (362)
Q Consensus 290 siaERrRRerIneri~~Lr~LVP---~~~Kq~dKAsIL~eAI~YIK~LQ~qVq~L~~~~~~~tc~~~ 353 (362)
++-||.|=..|||.|++|.++.= ..+|...|--||-.||.-|-.|++||++-. .+-|+.|+++
T Consensus 531 NARERlRVRDINeAfKELGRMCqlHlkSeKpQTKLgILhqAVsVIlsLEQQVRERN-LNPKaaclkR 596 (632)
T KOG3910|consen 531 NARERLRVRDINEAFKELGRMCQLHLKSEKPQTKLGILHQAVSVILSLEQQVRERN-LNPKAACLKR 596 (632)
T ss_pred hhhhheehhhHHHHHHHHHHHHHHhhcccCcchhhhHHHHHHHHHHHHHHHHHHcc-CChhhhhhhc
Confidence 45577777889999999998874 455545799999999999999999998632 3345555543
No 15
>KOG3558 consensus Hypoxia-inducible factor 1/Neuronal PAS domain protein NPAS1 [Signal transduction mechanisms; Transcription]
Probab=88.88 E-value=0.26 Score=54.01 Aligned_cols=44 Identities=25% Similarity=0.499 Sum_probs=38.6
Q ss_pred HHHHHHHHHHHHHHHHhhcccC---CCCCCCCHHHHHHHHHHHHHHH
Q 018007 291 IAERVRRTRISERMRKLQELVP---NMDKQTNTADMLDLAVDYIKDL 334 (362)
Q Consensus 291 iaERrRRerIneri~~Lr~LVP---~~~Kq~dKAsIL~eAI~YIK~L 334 (362)
-|.|.||.|=|+-|.+|..++| ...-++|||+|+..||-|+|-=
T Consensus 52 dAARsRRsKEn~~FyeLa~~lPlp~aisshLDkaSimRLtISyLRlr 98 (768)
T KOG3558|consen 52 DAARSRRSKENEEFYELAKLLPLPAAISSHLDKASIMRLTISYLRLR 98 (768)
T ss_pred hhhhhhcccchHHHHHHHHhCCCcchhhhhhhhHHHHHHHHHHHHHH
Confidence 3789999999999999999999 3344699999999999999853
No 16
>KOG4447 consensus Transcription factor TWIST [Transcription]
Probab=87.88 E-value=0.25 Score=45.36 Aligned_cols=49 Identities=29% Similarity=0.445 Sum_probs=43.2
Q ss_pred CCcHHHHHHHHHHHHHHHHhhcccCC--CCCCCCHHHHHHHHHHHHHHHHHH
Q 018007 288 PRSIAERVRRTRISERMRKLQELVPN--MDKQTNTADMLDLAVDYIKDLQNQ 337 (362)
Q Consensus 288 ~hsiaERrRRerIneri~~Lr~LVP~--~~Kq~dKAsIL~eAI~YIK~LQ~q 337 (362)
.|++-||+|=.-+|+.|..||.++|. .+| +.|.--|..|-.||-+|=.-
T Consensus 81 ~anvrerqRtqsLn~AF~~lr~iiptlPsdk-lSkiqtLklA~ryidfl~~v 131 (173)
T KOG4447|consen 81 MANVRERQRTQSLNEAFAALRKIIPTLPSDK-LSKIQTLKLAARYIDFLYQV 131 (173)
T ss_pred HHHHHHHHhhhhHHHHHHHHHhhcCCCCccc-cccccchhhcccCCchhhhc
Confidence 37888999999999999999999994 566 88999999999999998543
No 17
>KOG3560 consensus Aryl-hydrocarbon receptor [Transcription]
Probab=87.76 E-value=0.47 Score=51.00 Aligned_cols=40 Identities=25% Similarity=0.533 Sum_probs=35.9
Q ss_pred HHHHHHHHHHHHHHhhcccC----CCCCCCCHHHHHHHHHHHHHH
Q 018007 293 ERVRRTRISERMRKLQELVP----NMDKQTNTADMLDLAVDYIKD 333 (362)
Q Consensus 293 ERrRRerIneri~~Lr~LVP----~~~Kq~dKAsIL~eAI~YIK~ 333 (362)
-+|-|+|+|-.|..|..|+| .+.| +||-+||..+|-|++.
T Consensus 33 SKRHRdRLNaELD~lAsLLPfpqdiisK-LDkLSVLRLSVSyLr~ 76 (712)
T KOG3560|consen 33 SKRHRDRLNAELDHLASLLPFPQDIISK-LDKLSVLRLSVSYLRV 76 (712)
T ss_pred chhHHHHhhhHHHHHHHhcCCCHHHHhh-hhhhhhhhhhHHHHHH
Confidence 47889999999999999999 4566 9999999999999874
No 18
>KOG3559 consensus Transcriptional regulator SIM1 [Transcription]
Probab=85.55 E-value=0.83 Score=47.85 Aligned_cols=44 Identities=27% Similarity=0.429 Sum_probs=38.9
Q ss_pred HHHHHHHHHHHHHHHHhhcccCC---CCCCCCHHHHHHHHHHHHHHH
Q 018007 291 IAERVRRTRISERMRKLQELVPN---MDKQTNTADMLDLAVDYIKDL 334 (362)
Q Consensus 291 iaERrRRerIneri~~Lr~LVP~---~~Kq~dKAsIL~eAI~YIK~L 334 (362)
-+.|.||++=|-.|.+|..|+|- ++.|+||++|+..|.-|||.-
T Consensus 7 naA~tRRekEN~EF~eLAklLPLa~AItsQlDKasiiRLtTsYlKmr 53 (598)
T KOG3559|consen 7 NAARTRREKENYEFYELAKLLPLASAITSQLDKASIIRLTTSYLKMR 53 (598)
T ss_pred hHHHHHHHhhcchHHHHHhhccchhhhhhccchhhhhhHHHHHHHHH
Confidence 46899999999999999999993 455799999999999999864
No 19
>KOG3898 consensus Transcription factor NeuroD and related HTH proteins [Transcription]
Probab=66.33 E-value=3.6 Score=39.93 Aligned_cols=45 Identities=29% Similarity=0.512 Sum_probs=38.4
Q ss_pred HHHHHHHHHHHHHHHhhcccCC---CCCCCCHHHHHHHHHHHHHHHHHH
Q 018007 292 AERVRRTRISERMRKLQELVPN---MDKQTNTADMLDLAVDYIKDLQNQ 337 (362)
Q Consensus 292 aERrRRerIneri~~Lr~LVP~---~~Kq~dKAsIL~eAI~YIK~LQ~q 337 (362)
-||+|=-.+|+-|..||++||. ..| +.|...|.-|-.||..|++-
T Consensus 79 RER~RMH~LNdAld~LReviP~~~~~~k-lskIetl~~a~~yi~als~~ 126 (254)
T KOG3898|consen 79 RERTRMHDLNDALDALREVIPHGLHPPK-LSKIETLRLAANYIAALSEV 126 (254)
T ss_pred hhhccccchhHHHHHhHhhccCcCCCCC-CCcchhHHhhhcchhhhccc
Confidence 4888888999999999999993 333 88999999999999998753
No 20
>KOG4395 consensus Transcription factor Atonal, contains HTH domain [Transcription]
Probab=66.32 E-value=6.8 Score=38.85 Aligned_cols=49 Identities=27% Similarity=0.413 Sum_probs=41.7
Q ss_pred cHHHHHHHHHHHHHHHHhhcccCC--CCCCCCHHHHHHHHHHHHHHHHHHH
Q 018007 290 SIAERVRRTRISERMRKLQELVPN--MDKQTNTADMLDLAVDYIKDLQNQF 338 (362)
Q Consensus 290 siaERrRRerIneri~~Lr~LVP~--~~Kq~dKAsIL~eAI~YIK~LQ~qV 338 (362)
+.-||+|=..+|..|..|+.+||. .++++.|=.-|..|-.||-.|-...
T Consensus 179 narErrrm~gLN~AfD~Lr~v~p~~~~d~~LSkyetLqmaq~yi~~l~~~l 229 (285)
T KOG4395|consen 179 NARERRRMNGLNSAFDRLRLVVPDGDSDKKLSKYETLQMAQGYILALGCLL 229 (285)
T ss_pred chHHHHHhhhHHHHHHHHHHhcCCCCccchhhhhhHHHHHHHHHhhhHHhh
Confidence 356999999999999999999995 4456889999999999999886554
No 21
>COG3074 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=42.14 E-value=35 Score=28.02 Aligned_cols=26 Identities=23% Similarity=0.311 Sum_probs=21.4
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhhhhc
Q 018007 324 LDLAVDYIKDLQNQFKTLSDNRAKCK 349 (362)
Q Consensus 324 L~eAI~YIK~LQ~qVq~L~~~~~~~t 349 (362)
+..||+-|.-||..|++|+.++..++
T Consensus 13 iqqAvdTI~LLQmEieELKEknn~l~ 38 (79)
T COG3074 13 VQQAIDTITLLQMEIEELKEKNNSLS 38 (79)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhHhH
Confidence 56799999999999999998776443
No 22
>PRK13702 replication protein; Provisional
Probab=37.60 E-value=71 Score=26.89 Aligned_cols=44 Identities=23% Similarity=0.357 Sum_probs=31.5
Q ss_pred CCCCcHHHHHHH--HHHHHHHHHhhcccCCCCC----------CCCHHHHHHHHHH
Q 018007 286 THPRSIAERVRR--TRISERMRKLQELVPNMDK----------QTNTADMLDLAVD 329 (362)
Q Consensus 286 ~~~hsiaERrRR--erIneri~~Lr~LVP~~~K----------q~dKAsIL~eAI~ 329 (362)
-.|.+.+||.|. -|..+--++|+-+||+--| .+..|.||+..|+
T Consensus 21 G~Pls~aErQr~svaRKr~THkei~vfi~n~lK~~L~elc~~~glTQAe~IE~LIe 76 (85)
T PRK13702 21 GNPLSAAEKQRASVARKRATHKEIKVFIQNPLKDKLMELCEEEGLTQAEMIERLIE 76 (85)
T ss_pred CCCCCHHHHHHHHHHHHHHhhhhhheeecHHHHHHHHHHHHHcCCcHHHHHHHHHH
Confidence 378899999987 5666777889999986544 2456666666554
No 23
>PF09321 DUF1978: Domain of unknown function (DUF1978); InterPro: IPR015400 This domain is found in various hypothetical proteins produced by the bacterium Chlamydia pneumoniae. Their exact function has not, as yet, been identified. This entry includes the IncA proteins
Probab=34.07 E-value=61 Score=31.85 Aligned_cols=19 Identities=42% Similarity=0.693 Sum_probs=16.3
Q ss_pred HHHHHHHHHhhcccCCCCC
Q 018007 298 TRISERMRKLQELVPNMDK 316 (362)
Q Consensus 298 erIneri~~Lr~LVP~~~K 316 (362)
++..+||++||+|.|+...
T Consensus 116 ~ra~eRl~~LqalYp~v~v 134 (241)
T PF09321_consen 116 ERAQERLRELQALYPEVSV 134 (241)
T ss_pred HHHHHHHHHHHHhCCCCch
Confidence 5667999999999998765
No 24
>PRK15422 septal ring assembly protein ZapB; Provisional
Probab=30.87 E-value=66 Score=26.74 Aligned_cols=26 Identities=23% Similarity=0.291 Sum_probs=21.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhhhhh
Q 018007 323 MLDLAVDYIKDLQNQFKTLSDNRAKC 348 (362)
Q Consensus 323 IL~eAI~YIK~LQ~qVq~L~~~~~~~ 348 (362)
-+..|||-|.-||..|++|+.++...
T Consensus 12 KIqqAvdtI~LLqmEieELKekn~~L 37 (79)
T PRK15422 12 KVQQAIDTITLLQMEIEELKEKNNSL 37 (79)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 36789999999999999999876443
No 25
>PF14689 SPOB_a: Sensor_kinase_SpoOB-type, alpha-helical domain; PDB: 1F51_C 2FTK_B 1IXM_B.
Probab=28.54 E-value=1.1e+02 Score=23.29 Aligned_cols=41 Identities=22% Similarity=0.352 Sum_probs=32.2
Q ss_pred HHHHHHHHHHHHHhhcccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q 018007 294 RVRRTRISERMRKLQELVPNMDKQTNTADMLDLAVDYIKDLQNQFKTLS 342 (362)
Q Consensus 294 RrRRerIneri~~Lr~LVP~~~Kq~dKAsIL~eAI~YIK~LQ~qVq~L~ 342 (362)
|.-|=.....|.++..|+--.. .++|.+||+.+-.+++.+.
T Consensus 17 R~~RHD~~NhLqvI~gllqlg~--------~~~a~eYi~~~~~~~~~~s 57 (62)
T PF14689_consen 17 RAQRHDFLNHLQVIYGLLQLGK--------YEEAKEYIKELSKDLQQES 57 (62)
T ss_dssp HHHHHHHHHHHHHHHHHHHTT---------HHHHHHHHHHHHHHHHHHH
T ss_pred HHHhHHHHHHHHHHHHHHHCCC--------HHHHHHHHHHHHHHHHHHH
Confidence 6677778888888888875432 4789999999999988874
No 26
>PF13334 DUF4094: Domain of unknown function (DUF4094)
Probab=28.47 E-value=89 Score=26.33 Aligned_cols=26 Identities=15% Similarity=0.241 Sum_probs=21.4
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhhhhc
Q 018007 324 LDLAVDYIKDLQNQFKTLSDNRAKCK 349 (362)
Q Consensus 324 L~eAI~YIK~LQ~qVq~L~~~~~~~t 349 (362)
+.++-+=|+.|.++|..|+++++..+
T Consensus 68 V~kTh~aIq~LdKtIS~LEMELAaAR 93 (95)
T PF13334_consen 68 VSKTHEAIQSLDKTISSLEMELAAAR 93 (95)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 36777778899999999999997643
No 27
>KOG0709 consensus CREB/ATF family transcription factor [Transcription]
Probab=28.19 E-value=64 Score=34.47 Aligned_cols=25 Identities=20% Similarity=0.282 Sum_probs=18.2
Q ss_pred HHHHHHHHHHHHHHHHhhcccCCCCCC
Q 018007 291 IAERVRRTRISERMRKLQELVPNMDKQ 317 (362)
Q Consensus 291 iaERrRRerIneri~~Lr~LVP~~~Kq 317 (362)
.-|.|||. ++.|..|..=|-.+.++
T Consensus 263 AQESRrkK--keYid~LE~rv~~~tae 287 (472)
T KOG0709|consen 263 AQESRRKK--KEYIDGLESRVSAFTAE 287 (472)
T ss_pred hHHHHHhH--hhHHHHHhhhhhhcccC
Confidence 44655544 78999999988888873
No 28
>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=27.25 E-value=89 Score=25.13 Aligned_cols=24 Identities=25% Similarity=0.298 Sum_probs=20.1
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhhh
Q 018007 324 LDLAVDYIKDLQNQFKTLSDNRAK 347 (362)
Q Consensus 324 L~eAI~YIK~LQ~qVq~L~~~~~~ 347 (362)
+..||+-|..||.+|++|+.++..
T Consensus 13 i~~aveti~~Lq~e~eeLke~n~~ 36 (72)
T PF06005_consen 13 IQQAVETIALLQMENEELKEKNNE 36 (72)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHh
Confidence 567999999999999999987543
No 29
>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=26.11 E-value=38 Score=30.99 Aligned_cols=37 Identities=14% Similarity=0.340 Sum_probs=24.9
Q ss_pred HHHHHHHHHHhhcccCCCCCCCCHHHHHHHHHHHHHHH
Q 018007 297 RTRISERMRKLQELVPNMDKQTNTADMLDLAVDYIKDL 334 (362)
Q Consensus 297 RerIneri~~Lr~LVP~~~Kq~dKAsIL~eAI~YIK~L 334 (362)
-|-|-|||.+|+++||.... .--.....-++.++|.+
T Consensus 48 ~ETl~ERi~ALkDm~Pp~~R-~~i~~~~s~t~s~~ks~ 84 (145)
T TIGR00986 48 EETFTDRIYALKDIVPPTTR-GWIYHKYSTTTNFVKST 84 (145)
T ss_pred cCcHHHHHHHHHhhCCHHHH-HHHHHHHHHHHHHHHHH
Confidence 35688899999999997655 23444555555555544
No 30
>KOG3582 consensus Mlx interactors and related transcription factors [Transcription]
Probab=23.62 E-value=29 Score=38.86 Aligned_cols=57 Identities=19% Similarity=0.202 Sum_probs=46.1
Q ss_pred CCCcHHHHHHHHHHHHHHHHhhcccCCCC----CCCCHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 018007 287 HPRSIAERVRRTRISERMRKLQELVPNMD----KQTNTADMLDLAVDYIKDLQNQFKTLSDNRA 346 (362)
Q Consensus 287 ~~hsiaERrRRerIneri~~Lr~LVP~~~----Kq~dKAsIL~eAI~YIK~LQ~qVq~L~~~~~ 346 (362)
..|.-++|++|-.+-+++..|-+|.|..- +.+.+++||. +.||.+|+.-+.+.+..+
T Consensus 789 a~sih~lrr~~~~~~dq~~sL~alrp~v~~~~~ql~S~tS~L~---dp~~~~eq~ska~~e~~~ 849 (856)
T KOG3582|consen 789 AGSIHALRRTRLNWLDQFCSLPALRPQVLLNLRQLLSSTSILT---DPIKQPEQASKAVTEKIE 849 (856)
T ss_pred cchHHHHHHHHHHHhhccccHHHHHHHHHhhHHHhhhhhhccc---CcccchHHHHHHHHhhhh
Confidence 34566899999999999999999999543 3478999998 889999888888776543
No 31
>PF04508 Pox_A_type_inc: Viral A-type inclusion protein repeat ; InterPro: IPR007596 The repeat is found in the A-type inclusion protein of the Poxvirus family [].; GO: 0016032 viral reproduction
Probab=21.93 E-value=98 Score=20.24 Aligned_cols=19 Identities=21% Similarity=0.594 Sum_probs=15.5
Q ss_pred HHHHHHHHHHHHhhhhhhc
Q 018007 331 IKDLQNQFKTLSDNRAKCK 349 (362)
Q Consensus 331 IK~LQ~qVq~L~~~~~~~t 349 (362)
|..|+.+|..|+.++..|+
T Consensus 3 ~~rlr~rI~dLer~L~~C~ 21 (23)
T PF04508_consen 3 MNRLRNRISDLERQLSECR 21 (23)
T ss_pred HHHHHHHHHHHHHHHHHHh
Confidence 5678888888888888875
No 32
>KOG3584 consensus cAMP response element binding protein and related transcription factors [Transcription]
Probab=20.51 E-value=79 Score=32.25 Aligned_cols=25 Identities=24% Similarity=0.317 Sum_probs=11.8
Q ss_pred HHHHHHHHHHHHHHHhhcccCCCCC
Q 018007 292 AERVRRTRISERMRKLQELVPNMDK 316 (362)
Q Consensus 292 aERrRRerIneri~~Lr~LVP~~~K 316 (362)
|.|.=|.|=.|.+++|..=|-....
T Consensus 302 AARECRRKKKEYVKCLENRVAVLEN 326 (348)
T KOG3584|consen 302 AARECRRKKKEYVKCLENRVAVLEN 326 (348)
T ss_pred HHHHHHHhHhHHHHHHHhHHHHHhc
Confidence 4444444445555555544444433
No 33
>KOG3582 consensus Mlx interactors and related transcription factors [Transcription]
Probab=20.35 E-value=29 Score=38.91 Aligned_cols=55 Identities=25% Similarity=0.265 Sum_probs=43.2
Q ss_pred CCCcHHHHHHHHHHHHHHHHhhcccCCCCCC----CCHHHHHHHHHHHHHHHHHHHHHH
Q 018007 287 HPRSIAERVRRTRISERMRKLQELVPNMDKQ----TNTADMLDLAVDYIKDLQNQFKTL 341 (362)
Q Consensus 287 ~~hsiaERrRRerIneri~~Lr~LVP~~~Kq----~dKAsIL~eAI~YIK~LQ~qVq~L 341 (362)
-.|+.+|.+||..|.-.+..|-.++-+..++ +.++.-+..+++||-.++.+...+
T Consensus 653 it~~Sa~qkrr~n~kl~~~~~Ns~~Sn~~~l~s~k~t~~~~~q~~vhYi~~t~~e~~~v 711 (856)
T KOG3582|consen 653 ITHISAEQKRRFNIKLQFDVLNSLSSNSSSLSSIKTTNSNSLQKTVHYINVTQQERVPV 711 (856)
T ss_pred ccCccHHHHHHhhHHhhhHhhhhhccCcccccchhhhccccccCceeeeeccchhcccc
Confidence 3478899999999999999999999876553 556666999999998776554433
No 34
>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=20.20 E-value=2.4e+02 Score=22.83 Aligned_cols=43 Identities=16% Similarity=0.414 Sum_probs=28.1
Q ss_pred HHHHHHHhhccc---CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHhhhhhh
Q 018007 300 ISERMRKLQELV---PNMDKQTNTADMLDLAVDYIKDLQNQFKTLSDNRAKC 348 (362)
Q Consensus 300 Ineri~~Lr~LV---P~~~Kq~dKAsIL~eAI~YIK~LQ~qVq~L~~~~~~~ 348 (362)
|..||...+++| |+++. + +++--++|+.|+++++....-.++.
T Consensus 33 lk~Klq~ar~~i~~lpgi~~--s----~eeq~~~i~~Le~~i~~k~~~L~~~ 78 (83)
T PF07544_consen 33 LKHKLQKARAAIRELPGIDR--S----VEEQEEEIEELEEQIRKKREVLQKF 78 (83)
T ss_pred HHHHHHHHHHHHHhCCCccC--C----HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 444555555554 66665 2 4566678999999988877665543
No 35
>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=20.14 E-value=58 Score=29.32 Aligned_cols=21 Identities=19% Similarity=0.411 Sum_probs=16.3
Q ss_pred HHHHHHHHHHHhhcccCCCCC
Q 018007 296 RRTRISERMRKLQELVPNMDK 316 (362)
Q Consensus 296 RRerIneri~~Lr~LVP~~~K 316 (362)
.-|-|-|||-+|+++||....
T Consensus 49 ~dETl~ERl~aLkdi~P~~~R 69 (137)
T PF04281_consen 49 EDETLLERLWALKDIFPPSVR 69 (137)
T ss_pred ccccHHHHHHHHhccCCHHHH
Confidence 446678889999999996544
Done!