Query 025926
Match_columns 246
No_of_seqs 149 out of 198
Neff 6.0
Searched_HMMs 46136
Date Fri Mar 29 11:07:52 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025926.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025926hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2905 Transcription initiati 100.0 3E-68 6.5E-73 464.9 13.6 219 1-244 20-250 (254)
2 PF02270 TFIIF_beta: Transcrip 100.0 3.2E-66 6.9E-71 468.3 10.5 217 1-239 13-275 (275)
3 COG5090 TFG2 Transcription ini 100.0 6.2E-57 1.3E-61 392.4 14.1 219 1-242 31-257 (297)
4 PF09734 Tau95: RNA polymerase 95.4 0.017 3.6E-07 53.2 4.0 57 176-232 231-289 (310)
5 PF12157 DUF3591: Protein of u 95.0 0.043 9.3E-07 53.6 5.5 69 172-240 234-305 (457)
6 PF04801 Sin_N: Sin-like prote 91.2 0.29 6.3E-06 47.0 4.6 55 180-237 337-391 (421)
7 KOG0008 Transcription initiati 91.1 0.33 7.1E-06 52.7 5.2 73 171-243 688-765 (1563)
8 KOG2473 RNA polymerase III tra 88.2 0.79 1.7E-05 44.9 5.0 55 178-232 230-285 (484)
9 COG5179 TAF1 Transcription ini 86.8 0.76 1.7E-05 46.6 4.0 69 171-240 592-663 (968)
10 PF04004 Leo1: Leo1-like prote 66.2 68 0.0015 27.2 9.5 41 83-123 99-140 (171)
11 PF05132 RNA_pol_Rpc4: RNA pol 59.2 35 0.00076 27.5 6.2 20 91-110 111-130 (131)
12 PF13817 DDE_Tnp_IS66_C: IS66 59.1 6.9 0.00015 25.4 1.6 15 206-220 12-26 (39)
13 PRK10857 DNA-binding transcrip 58.0 18 0.0004 30.4 4.5 56 178-234 8-68 (164)
14 PF02082 Rrf2: Transcriptional 54.8 28 0.00062 25.4 4.6 41 194-235 25-69 (83)
15 TIGR02010 IscR iron-sulfur clu 54.4 25 0.00054 28.2 4.6 55 180-235 10-69 (135)
16 PF13565 HTH_32: Homeodomain-l 50.1 17 0.00037 25.8 2.7 29 178-206 32-60 (77)
17 KOG3122 DNA-directed RNA polym 48.4 34 0.00073 32.1 4.9 61 27-110 244-309 (310)
18 PF09339 HTH_IclR: IclR helix- 46.5 37 0.00081 22.5 3.8 37 184-220 7-44 (52)
19 PF05595 DUF771: Domain of unk 46.2 28 0.0006 26.4 3.4 40 176-216 6-46 (91)
20 smart00550 Zalpha Z-DNA-bindin 44.8 71 0.0015 22.7 5.2 59 177-235 3-66 (68)
21 cd00092 HTH_CRP helix_turn_hel 39.9 96 0.0021 20.8 5.2 43 192-235 23-67 (67)
22 PF10826 DUF2551: Protein of u 39.2 67 0.0015 24.4 4.5 65 176-240 7-82 (83)
23 PF10390 ELL: RNA polymerase I 38.5 12 0.00025 34.5 0.3 136 92-238 97-257 (284)
24 PHA02571 a-gt.4 hypothetical p 34.3 27 0.00058 27.8 1.7 37 179-217 51-87 (109)
25 smart00346 HTH_ICLR helix_turn 34.0 1.2E+02 0.0025 21.8 5.1 54 185-238 10-66 (91)
26 KOG2934 Uncharacterized conser 30.2 27 0.00058 30.3 1.2 34 196-229 37-74 (204)
27 smart00076 IFabd Interferon al 28.4 80 0.0017 25.3 3.6 44 179-222 24-73 (117)
28 PF13412 HTH_24: Winged helix- 26.2 1.8E+02 0.0039 18.5 5.1 38 182-219 5-42 (48)
29 TIGR00281 segregation and cond 25.7 2E+02 0.0042 24.9 5.8 60 179-240 4-73 (186)
30 PF14493 HTH_40: Helix-turn-he 25.5 71 0.0015 23.8 2.7 34 176-210 50-83 (91)
31 PRK10219 DNA-binding transcrip 24.8 2.2E+02 0.0048 21.3 5.4 41 178-218 3-45 (107)
32 TIGR03879 near_KaiC_dom probab 23.5 1.8E+02 0.0038 21.5 4.4 38 179-216 17-54 (73)
33 PF07587 PSD1: Protein of unkn 22.7 91 0.002 28.1 3.3 33 177-210 50-82 (266)
34 TIGR00738 rrf2_super rrf2 fami 22.2 1.6E+02 0.0034 22.9 4.3 42 192-234 23-68 (132)
35 smart00342 HTH_ARAC helix_turn 21.5 1.2E+02 0.0027 20.6 3.2 25 195-219 2-26 (84)
36 cd00095 IFab Interferon alpha, 20.6 1.3E+02 0.0028 25.0 3.6 43 179-221 56-104 (152)
37 smart00345 HTH_GNTR helix_turn 20.1 2.1E+02 0.0046 18.3 4.0 42 179-220 3-46 (60)
No 1
>KOG2905 consensus Transcription initiation factor IIF, small subunit (RAP30) [Transcription]
Probab=100.00 E-value=3e-68 Score=464.91 Aligned_cols=219 Identities=40% Similarity=0.684 Sum_probs=190.1
Q ss_pred CeeeeccHHHHHhhCCCCCCCCCCCCCCceeEEEEEeCCCCCCCCCCCCCCCCCcceeEEec---------ccCCCCCCc
Q 025926 1 MWLMKCPALVSRSLKIPSSDNDDDDSARPVAKVILSIDPLQSNEDSSSSSSSSSTRFTMELI---------STESGNAPK 71 (246)
Q Consensus 1 vWLvKvPk~l~e~W~~~~~~~~~~~~~~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~m~l~---------~~~~~~iPk 71 (246)
|||||||+||+++|.+++. ..++|++++...+.+ .++++.|+ ..+.+.+|.
T Consensus 20 vWLvKvP~fLa~kw~~~~~-------~~e~g~l~i~k~~~d-------------aki~l~L~e~~p~~~~~~a~~g~~p~ 79 (254)
T KOG2905|consen 20 VWLVKVPKFLAEKWRKIPN-------SHESGKLRINKTPSD-------------AKIVLLLNEAIPEKQEREADVGKFPQ 79 (254)
T ss_pred EEEEeccHHHHHHHHhccc-------ccccccccccCCCCc-------------ceEEEEeccccccchhhhhhcccCch
Confidence 7999999999999997555 224677766554311 24444444 345889999
Q ss_pred eeeeccccCCcceeeeeeec-CCceeEEEEEeeeeeEeecCCChHHHHHHHHHHHHHHhcCCcceEEecCCCCCcccCCC
Q 025926 72 RYSMDMSKDLIPMSVFAESS-NGKISVEGKIKNKFDMRPHHENMENYGKLCRERTNKYMTKSRQIQVIDNDNGSHMRPMP 150 (246)
Q Consensus 72 eY~L~~~~~~~~~~VFse~~-~~~~~i~G~V~~~~~~~P~~~~~~~Y~~l~~~R~~~a~~~~r~vq~ld~~~~~~~~p~~ 150 (246)
.|.+++..++.||||||+++ .|+++++|+|+|+|+|+|+. |++|++++++|+.+++.|+|+||+||++.|++|+|++
T Consensus 80 ~~~~~~~~~~~~~~~~sd~~~~~k~a~eG~V~~e~~~~P~~--ne~Y~Rl~r~r~~k~~~k~r~vQ~iD~~~g~~~~p~~ 157 (254)
T KOG2905|consen 80 QYKLNMKRRFFNMFVESDSSGPKKTAVEGTVVHECDVRPSA--NEEYMRLKRERIVKASKKKRQVQVIDKVVGVHMKPVP 157 (254)
T ss_pred hhhhccCccccceeeeecCCCCccceeeeeeeeeeeccccc--CHHHHHHHHHHHHHhcCcccccccchhhcccccccCC
Confidence 99999999999999999988 78999999999999999996 5999999999999999999999999999999999999
Q ss_pred CccccCCc--ccccCCCCCCcccccccCChhhHHHHHHHHhhhccCcchHHHHHhhCCcHHHHHHHHHHHhhHhccCCCC
Q 025926 151 GMMISTGF--TEKKKPQPKGSEVKRTRRDRGEMEDIMFKLFERQSNWTLRQLIQETDQPEQFLKDMLKDLCVYNNKGSNQ 228 (246)
Q Consensus 151 ~~~~~~~~--~~k~k~~~K~~~~K~~R~~~~eLld~LF~~Fek~~yWslK~L~~~t~QPe~yLKeiL~eIa~lnk~Gp~~ 228 (246)
||.....+ ++++| +++++|++|+|++||+|+||+|||+|+||+||+|+++|+||++||||||++||+||++|||+
T Consensus 158 ~~~~~~~~~~~~rkK---~k~e~Kr~R~dk~evld~lFk~FEk~~ywtlK~Lv~~t~QP~~fLKEiL~~icv~NkKg~~k 234 (254)
T KOG2905|consen 158 GHLRSSSNIAYERKK---AKEEGKRTRRDKNEVLDMLFKAFEKYQYWTLKDLVEITKQPEAFLKEILKDICVLNKKGPYK 234 (254)
T ss_pred CcccccchhHHHHHh---hhhccccccccHHHHHHHHHHHhhcCccccHHHHHHHhcCHHHHHHHHHHHHHHHhccCccc
Confidence 98732221 33331 37899999999999999999999999999999999999999999999999999999999999
Q ss_pred cccccchhhhhccCCC
Q 025926 229 GSYELKPEYKKAADGP 244 (246)
Q Consensus 229 ~~weLKpEYk~~~~~~ 244 (246)
|+||||||||++.++.
T Consensus 235 ~tyeLKPEYK~~~~ee 250 (254)
T KOG2905|consen 235 NTYELKPEYKKYKEEE 250 (254)
T ss_pred CceecCHHHhhhhhhh
Confidence 9999999999998875
No 2
>PF02270 TFIIF_beta: Transcription initiation factor IIF, beta subunit; InterPro: IPR003196 Accurate transcription in vivo requires at least six general transcription initiation factors, in addition to RNA polymerase II. Transcription initiation factor IIF (TFIIF) is a tetramer of two beta subunits associate with two alpha subunits which interacts directly with RNA polymerase II. The beta subunit of TFIIF is required for recruitment of RNA polymerase II onto the promoter. ; GO: 0005524 ATP binding, 0006367 transcription initiation from RNA polymerase II promoter, 0005674 transcription factor TFIIF complex; PDB: 1F3U_C 2BBY_A 1BBY_A.
Probab=100.00 E-value=3.2e-66 Score=468.30 Aligned_cols=217 Identities=37% Similarity=0.640 Sum_probs=112.3
Q ss_pred CeeeeccHHHHHhhCCCCCCCCCCCCCCceeEEEEEeCCCCCCCCCCCCCCCCCcceeEEeccc--CCCCCCceeeeccc
Q 025926 1 MWLMKCPALVSRSLKIPSSDNDDDDSARPVAKVILSIDPLQSNEDSSSSSSSSSTRFTMELIST--ESGNAPKRYSMDMS 78 (246)
Q Consensus 1 vWLvKvPk~l~e~W~~~~~~~~~~~~~~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~m~l~~~--~~~~iPkeY~L~~~ 78 (246)
|||||||+|||++|++++. +++++||+|+++.++. + ..++.|.|+.. .+++||++|+|+|+
T Consensus 13 vWLvKVPk~l~e~W~~~~~-----~~~~~iG~lri~~~~~----------~--~~~v~l~L~~~~~~~~~iPkey~L~~~ 75 (275)
T PF02270_consen 13 VWLVKVPKFLSEKWSKAPD-----DDEIEIGKLRISKDPN----------G--KPKVSLTLNDSLANHGNIPKEYDLDMS 75 (275)
T ss_dssp EEEEEEEHHHHHHHTTSBT-----T--TEEEEEEEEEE-T----------T--EEEEEEEE-HHHHT-T-S--EEEEEEE
T ss_pred ccccccccccccccccccc-----cccccccccccccccc----------c--ccccccccccccccccccccccccccc
Confidence 7999999999999986433 2367899999998731 1 23677777754 35699999999999
Q ss_pred cCC-cceeeeeeecC-------------------------------------------CceeEEEEEeeeeeEeecCCCh
Q 025926 79 KDL-IPMSVFAESSN-------------------------------------------GKISVEGKIKNKFDMRPHHENM 114 (246)
Q Consensus 79 ~~~-~~~~VFse~~~-------------------------------------------~~~~i~G~V~~~~~~~P~~~~~ 114 (246)
+.. +|||||||.++ ++++|+|+|.|+|+|+|+. +
T Consensus 76 ~~~~~n~~VFse~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~l~G~I~~~~~~~P~~--~ 153 (275)
T PF02270_consen 76 KDNVQNMYVFSESDQPGFKAKNKERAGAPNAGIPASLLREKKKKDRKRKYQPYVKTIPKKTALEGRIVHECDCRPVL--N 153 (275)
T ss_dssp --TTEEEEEEEEETT----------------------------------------ETT--EEEEEEEEEEEEE-------
T ss_pred cccccccccccccccccccccccccccccccccccccccccccccccccccccccCCCCceEEEEEEEEEEEeEECC--C
Confidence 997 59999999865 5889999999999999996 4
Q ss_pred HHHHHHHHHHHHHHhcCCcceEEecCCCCCcccCCCCccccCCcccccCCCCCCcccccccCChhhHHHHHHHHhhhccC
Q 025926 115 ENYGKLCRERTNKYMTKSRQIQVIDNDNGSHMRPMPGMMISTGFTEKKKPQPKGSEVKRTRRDRGEMEDIMFKLFERQSN 194 (246)
Q Consensus 115 ~~Y~~l~~~R~~~a~~~~r~vq~ld~~~~~~~~p~~~~~~~~~~~~k~k~~~K~~~~K~~R~~~~eLld~LF~~Fek~~y 194 (246)
++|++++++|+.++++|+|++++|+......+.|++.+..+...+. .+.|+.++|++|||+++|+|+||+|||+|+|
T Consensus 154 ~~Y~~~~~~r~~~a~~~kr~~~~i~~~~~~~~~~~~~~~~~~~~~~---~~~k~~~~K~~R~~~~eL~d~lF~~Fe~~~y 230 (275)
T PF02270_consen 154 DEYRRLKRERIEKANKPKRTVQQIDEDVSQSYKPVSFHSANSKFFI---KKKKKQEEKRARMDKNELLDLLFKLFEKHQY 230 (275)
T ss_dssp -----------------------------------------------------------THHHHHHHHHHHHHHHHH-S-
T ss_pred HHHHHHHHHHHHHhcCCCCeeEEeccccccCCCCcccccccchhcc---cccccccccceeCCHHHHHHHHHHHHHhCCC
Confidence 7999999999999999999999999865567777554443322111 1226788999999999999999999999999
Q ss_pred cchHHHHHhhCCcHHHHHHHHHHHhhHhccCCCCcccccchhhhh
Q 025926 195 WTLRQLIQETDQPEQFLKDMLKDLCVYNNKGSNQGSYELKPEYKK 239 (246)
Q Consensus 195 WslK~L~~~t~QPe~yLKeiL~eIa~lnk~Gp~~~~weLKpEYk~ 239 (246)
|+||+|+++|+||++||||||+|||+||++|||+|+|+||||||+
T Consensus 231 wslK~L~~~t~QP~~yLKeiL~eIa~~~k~g~~~~~w~LKpeyk~ 275 (275)
T PF02270_consen 231 WSLKDLRQRTQQPEAYLKEILEEIAVLNKRGPHKNMWELKPEYKH 275 (275)
T ss_dssp B-HHHHHHH--S-HHHHHHHHHHH--EE--TT---EE----SS--
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHhccCCcCCcEecchHHcC
Confidence 999999999999999999999999999999999999999999996
No 3
>COG5090 TFG2 Transcription initiation factor IIF, small subunit (RAP30) [Transcription]
Probab=100.00 E-value=6.2e-57 Score=392.44 Aligned_cols=219 Identities=28% Similarity=0.433 Sum_probs=183.7
Q ss_pred CeeeeccHHHHHhhCCCCCCCCCCCCCCceeEEEEEeCCCCCCCCCCCCCCCCCcceeEEe-cccCCCCCCceeeecccc
Q 025926 1 MWLMKCPALVSRSLKIPSSDNDDDDSARPVAKVILSIDPLQSNEDSSSSSSSSSTRFTMEL-ISTESGNAPKRYSMDMSK 79 (246)
Q Consensus 1 vWLvKvPk~l~e~W~~~~~~~~~~~~~~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~m~l-~~~~~~~iPkeY~L~~~~ 79 (246)
|||||||.||+++|...+. ++ +..+|++|+..+| ..+++.| +..+++++|++|+|.+.+
T Consensus 31 VWLvkvP~FLaekw~sr~~---~~--g~~lg~~r~~~d~---------------a~isLlL~ne~~n~~~P~~ydl~i~~ 90 (297)
T COG5090 31 VWLVKVPLFLAEKWLSREA---EI--GELLGTKRTSTDP---------------AVISLLLSNEFCNGGFPSSYDLKIKP 90 (297)
T ss_pred EEEEeccHHHHHHHhcchh---hh--hhhhceeeecCCc---------------ceEEEEeccCCccCCCCcceeeeecc
Confidence 7999999999999984222 23 3459999998765 2677777 456899999999999999
Q ss_pred CCc-ceeeeeeec----CCceeEEEEEeeeeeEeecCCChHHHHHHHHHHHHHHhcCCcceEEecCCCCCcccCCCCccc
Q 025926 80 DLI-PMSVFAESS----NGKISVEGKIKNKFDMRPHHENMENYGKLCRERTNKYMTKSRQIQVIDNDNGSHMRPMPGMMI 154 (246)
Q Consensus 80 ~~~-~~~VFse~~----~~~~~i~G~V~~~~~~~P~~~~~~~Y~~l~~~R~~~a~~~~r~vq~ld~~~~~~~~p~~~~~~ 154 (246)
..+ +-|||.|+. .+.|+|+|+|.|+|.+.|.. |++|+++++.|..++..+++.||+||...|+.+.+ .++++
T Consensus 91 k~v~n~yVfre~et~t~~k~tavvGtV~hEC~V~P~v--Nd~Y~r~~q~r~~~~~~~K~~vq~iD~~~g~~~~~-~~~s~ 167 (297)
T COG5090 91 KDVNNYYVFRESETSTHEKNTAVVGTVNHECYVTPEV--NDEYLRYKQDRGFKSDSKKSDVQVIDYLKGGKRGE-KFGSL 167 (297)
T ss_pred ccccceEEEecccccccccccceeeeeccceeecccc--cHHHHHHHHHhhhhhcCccccceeeecccCceecc-Ccccc
Confidence 988 689996653 37999999999999999997 58999999999999999999999999988877766 22222
Q ss_pred cC--CcccccCCCCCCcccccccCChhhHHHHHHHHhhhccCcchHHHHHhhCCcHHHHHHHHHHHhhHhccCCCCcccc
Q 025926 155 ST--GFTEKKKPQPKGSEVKRTRRDRGEMEDIMFKLFERQSNWTLRQLIQETDQPEQFLKDMLKDLCVYNNKGSNQGSYE 232 (246)
Q Consensus 155 ~~--~~~~k~k~~~K~~~~K~~R~~~~eLld~LF~~Fek~~yWslK~L~~~t~QPe~yLKeiL~eIa~lnk~Gp~~~~we 232 (246)
.+ ..|.+++.+.-+++.|+.|||++||+|+||+|||+|+||+||+|+++++||++||||||++||+|||+|||+++|+
T Consensus 168 Rs~~~~fl~~~r~k~~~~~K~~RlpknEvlD~lFK~Fe~Y~yWtlKgL~e~~~QPea~lkEild~iavLnKkgpya~kY~ 247 (297)
T COG5090 168 RSSTLEFLARKRKKMLMDKKRERLPKNEVLDMLFKAFEKYPYWTLKGLAEFCGQPEAFLKEILDDIAVLNKKGPYANKYE 247 (297)
T ss_pred ccchHHHHHhcchhhhcchhhcccchhHHHHHHHHHhhcCCchhhhhHHHHhcChHHHHHHHHHHHHhhhccCcccceee
Confidence 11 1133322211267789999999999999999999999999999999999999999999999999999999999999
Q ss_pred cchhhhhccC
Q 025926 233 LKPEYKKAAD 242 (246)
Q Consensus 233 LKpEYk~~~~ 242 (246)
|+||||...+
T Consensus 248 LrPEYK~~~d 257 (297)
T COG5090 248 LRPEYKQTMD 257 (297)
T ss_pred cCHHHHhHHH
Confidence 9999998653
No 4
>PF09734 Tau95: RNA polymerase III transcription factor (TF)IIIC subunit; InterPro: IPR019136 Transcription factor IIIC (TFIIIC) is a multisubunit DNA binding factor that serves as a dynamic platform for assembly of pre-initiation complexes on class III genes. This entry represents subunit 5 (also known as the tau 95 subunit) which holds a key position in TFIIIC, exerting both upstream and downstream influence on the TFIIIC-DNA complex by rendering the complex more stable []. Once bound to tDNA-intragenic promoter elements, TFIIIC directs the assembly of TFIIIB on the DNA, which in turn recruits the RNA polymerase III (pol III) and activates multiple rounds of transcription.
Probab=95.41 E-value=0.017 Score=53.23 Aligned_cols=57 Identities=25% Similarity=0.345 Sum_probs=52.8
Q ss_pred CChhhHHHHHHHHhhhccCcchHHHHHhhCC--cHHHHHHHHHHHhhHhccCCCCcccc
Q 025926 176 RDRGEMEDIMFKLFERQSNWTLRQLIQETDQ--PEQFLKDMLKDLCVYNNKGSNQGSYE 232 (246)
Q Consensus 176 ~~~~eLld~LF~~Fek~~yWslK~L~~~t~Q--Pe~yLKeiL~eIa~lnk~Gp~~~~we 232 (246)
....+++..|=+|||+.+-|+-++|...+.. -...||.+|--+|=|=+.||+++.|-
T Consensus 231 ~~~~~~~~~l~~lFeeRPIW~r~~L~~~~~~~~~~~~~k~~l~~v~Y~f~~GPwr~~~v 289 (310)
T PF09734_consen 231 PVLQELIQELKKLFEERPIWTRRALLNHLPKSGSQSKLKRALPYVAYYFKNGPWRDCWV 289 (310)
T ss_pred hhHHHHHHHHHHHHhcCCccCHHHHHHhhhhcccHHHHHHHHHhhEEEEecCcccceeE
Confidence 3447889999999999999999999999999 68899999999999999999999995
No 5
>PF12157 DUF3591: Protein of unknown function (DUF3591); InterPro: IPR022591 This functionally uncharacterised domain is found centrally in the eukaryotic transcription initiation factor TFIID subunit 1.
Probab=94.96 E-value=0.043 Score=53.64 Aligned_cols=69 Identities=22% Similarity=0.477 Sum_probs=60.1
Q ss_pred ccccCChhhHHHHHHHHhh--hccCcchHHHHHhh-CCcHHHHHHHHHHHhhHhccCCCCcccccchhhhhc
Q 025926 172 KRTRRDRGEMEDIMFKLFE--RQSNWTLRQLIQET-DQPEQFLKDMLKDLCVYNNKGSNQGSYELKPEYKKA 240 (246)
Q Consensus 172 K~~R~~~~eLld~LF~~Fe--k~~yWslK~L~~~t-~QPe~yLKeiL~eIa~lnk~Gp~~~~weLKpEYk~~ 240 (246)
|..-.-++-|.-.+|.+|. ...--.+.+|.... .|.+.=+++-|++.|.|.|.|...|.|.|||.|+--
T Consensus 234 ~~t~~~knrL~~~iyRlf~~~~~~ri~~~di~~~Fp~~se~~iRkrLKe~~~~~R~g~~~~~W~lk~~~~lp 305 (457)
T PF12157_consen 234 KVTNFSKNRLKMIIYRLFNKSQPRRIKVDDIKKHFPDQSESQIRKRLKEFADFQRTGDDSGWWVLKPGFRLP 305 (457)
T ss_pred hHHHHHHHHHHHHHHHHHhhccCCccCHHHHHHhCCCCcHHHHHHHHHHHHhccCCCCCCCeEEECCCCCCC
Confidence 4555778889999999998 44469999999885 789999999999999999999999999999987743
No 6
>PF04801 Sin_N: Sin-like protein conserved region; InterPro: IPR006886 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. RNA polymerase III (Pol III) is a complex consisting of 17 subunits, which synthesizes small RNAs, such as 5S rRNA and tRNAs. Pol III is essential for efficient transcription from both the type 2 VAI and type 3 U6 RNA polymerase III promoters and plays a key role in sensing and limiting infection by intracellular bacteria and DNA viruses. Subunit c5 is a specific peripheric component of RNA polymerase III complex. ; GO: 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent, 0005634 nucleus
Probab=91.24 E-value=0.29 Score=47.02 Aligned_cols=55 Identities=22% Similarity=0.401 Sum_probs=48.6
Q ss_pred hHHHHHHHHhhhccCcchHHHHHhhCCcHHHHHHHHHHHhhHhccCCCCcccccchhh
Q 025926 180 EMEDIMFKLFERQSNWTLRQLIQETDQPEQFLKDMLKDLCVYNNKGSNQGSYELKPEY 237 (246)
Q Consensus 180 eLld~LF~~Fek~~yWslK~L~~~t~QPe~yLKeiL~eIa~lnk~Gp~~~~weLKpEY 237 (246)
-..|.|--+|.++.+=+-++|...|+-|..=++|||++||+++ +....|+||=.+
T Consensus 337 ~aRD~iL~~F~~~~~v~r~~l~~~~~l~~~~~~eiL~~~a~~~---~~~~~W~lk~~~ 391 (421)
T PF04801_consen 337 RARDYILLLFTKSRYVKRKELMSATKLPPEDVKEILKEIAVLR---PSNRGWKLKLPP 391 (421)
T ss_pred hhHHHHHHHhcCCCceeHHHhhhhcCCCHHHHHHHHHHHhhcc---CCCCceEEccCc
Confidence 3568888999999999999999999999999999999999998 566889997543
No 7
>KOG0008 consensus Transcription initiation factor TFIID, subunit TAF1 [Transcription]
Probab=91.14 E-value=0.33 Score=52.72 Aligned_cols=73 Identities=21% Similarity=0.389 Sum_probs=64.9
Q ss_pred cccccCChhhHHHHHHHHhhhccC----cchHHHHHhh-CCcHHHHHHHHHHHhhHhccCCCCcccccchhhhhccCC
Q 025926 171 VKRTRRDRGEMEDIMFKLFERQSN----WTLRQLIQET-DQPEQFLKDMLKDLCVYNNKGSNQGSYELKPEYKKAADG 243 (246)
Q Consensus 171 ~K~~R~~~~eLld~LF~~Fek~~y----WslK~L~~~t-~QPe~yLKeiL~eIa~lnk~Gp~~~~weLKpEYk~~~~~ 243 (246)
.|..-+-+|=|.-.||.+|-+..- -.|.+|.... .|-++=+|.=|++.|.|.|.|+-.|.|.|||.|+--.++
T Consensus 688 Kk~tt~~~nrLkv~IYRlF~~s~~g~r~I~id~lsk~Fp~~se~siRKrLKecad~kR~G~~~~~W~LK~df~lp~ee 765 (1563)
T KOG0008|consen 688 KKLTTFLRNRLKVFIYRLFWKSDSGPRRIRIDDLSKAFPDQSESSIRKRLKECADFKRDGMGKNYWVLKPDFRLPDEE 765 (1563)
T ss_pred hhHHHHHHHHHHHHHHHHHHhcCCCCcceehhHHHhhCcccchHHHHHHHHHHHHHhhcCCCCCeeEecccccCCCHH
Confidence 356667889999999999998887 8899998876 889999999999999999999999999999999876543
No 8
>KOG2473 consensus RNA polymerase III transcription factor (TF)IIIC subunit [Transcription]
Probab=88.22 E-value=0.79 Score=44.94 Aligned_cols=55 Identities=25% Similarity=0.327 Sum_probs=48.7
Q ss_pred hhhHHHHHHHHhhhccCcchHHHHH-hhCCcHHHHHHHHHHHhhHhccCCCCcccc
Q 025926 178 RGEMEDIMFKLFERQSNWTLRQLIQ-ETDQPEQFLKDMLKDLCVYNNKGSNQGSYE 232 (246)
Q Consensus 178 ~~eLld~LF~~Fek~~yWslK~L~~-~t~QPe~yLKeiL~eIa~lnk~Gp~~~~we 232 (246)
-+|++-.|=.+|++.+-|+-+.|.. .++==.-+||-+|--||-|-.+||++++|-
T Consensus 230 ~~e~~~~l~eLF~~RPIWtR~al~~~~~~~~~h~LK~~Lp~~AYyfssGPwr~~wi 285 (484)
T KOG2473|consen 230 LEEVLRSLRELFEERPIWTRRALLYKELGCTHHKLKRFLPLIAYYFSSGPWRRLWI 285 (484)
T ss_pred hHHHHHHHHHHHHhCchhhHHhHhhcccCccHHHHHHHHHHHHHHhccCchhceee
Confidence 3567777777999999999999999 666677899999999999999999999994
No 9
>COG5179 TAF1 Transcription initiation factor TFIID, subunit TAF1 [Transcription]
Probab=86.75 E-value=0.76 Score=46.63 Aligned_cols=69 Identities=26% Similarity=0.354 Sum_probs=57.5
Q ss_pred cccccCChhhHHHHHHHHhhhccC--cchHHHHHhh-CCcHHHHHHHHHHHhhHhccCCCCcccccchhhhhc
Q 025926 171 VKRTRRDRGEMEDIMFKLFERQSN--WTLRQLIQET-DQPEQFLKDMLKDLCVYNNKGSNQGSYELKPEYKKA 240 (246)
Q Consensus 171 ~K~~R~~~~eLld~LF~~Fek~~y--WslK~L~~~t-~QPe~yLKeiL~eIa~lnk~Gp~~~~weLKpEYk~~ 240 (246)
.|-+-+-++-|..++|.+|...+. -.|.+|.... .|-+.-.++-|+|-+.|.|.||- |.|.|||.=.-.
T Consensus 592 RKvt~~~knRLKm~~fRl~n~~~~g~l~I~ql~khFpdq~egq~Rq~lKEfm~y~kdGp~-g~W~Lk~~e~ll 663 (968)
T COG5179 592 RKVTVFCKNRLKMAAFRLFNSKEGGSLRISQLDKHFPDQSEGQKRQWLKEFMDYVKDGPD-GVWVLKPSEALL 663 (968)
T ss_pred hhhHHHHhhhHHHHHHHHhhcCCCCceeeehhhhhCCCcchhHHHHHHHHHHHHhhcCCC-ceEEeccccccC
Confidence 366678888999999999988775 7778887765 78888888888899999999998 999999965433
No 10
>PF04004 Leo1: Leo1-like protein; InterPro: IPR007149 Members of this family are part of the Paf1/RNA polymerase II complex [, ]. The Paf1 complex probably functions during the elongation phase of transcription [].
Probab=66.16 E-value=68 Score=27.16 Aligned_cols=41 Identities=20% Similarity=0.387 Sum_probs=29.6
Q ss_pred ceeeeeeec-CCceeEEEEEeeeeeEeecCCChHHHHHHHHH
Q 025926 83 PMSVFAESS-NGKISVEGKIKNKFDMRPHHENMENYGKLCRE 123 (246)
Q Consensus 83 ~~~VFse~~-~~~~~i~G~V~~~~~~~P~~~~~~~Y~~l~~~ 123 (246)
..|+|.... .+-+...|.|..++.++|...++...+++-..
T Consensus 99 ~~~L~~~~~~~~~l~~~~~i~~~l~~rP~s~~s~thr~l~~~ 140 (171)
T PF04004_consen 99 HNYLFVRHGSSGVLQGQGHITKKLTFRPASTDSATHRRLTQA 140 (171)
T ss_pred cceEEEEcCCcceEEEEEEecccEEEecCCccCHHHHHHHHH
Confidence 378887765 36688999999999999986544445544433
No 11
>PF05132 RNA_pol_Rpc4: RNA polymerase III RPC4; InterPro: IPR007811 This family comprises a specific subunit for Pol III, the tRNA specific polymerase.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006383 transcription from RNA polymerase III promoter, 0005666 DNA-directed RNA polymerase III complex
Probab=59.20 E-value=35 Score=27.48 Aligned_cols=20 Identities=25% Similarity=0.527 Sum_probs=17.9
Q ss_pred cCCceeEEEEEeeeeeEeec
Q 025926 91 SNGKISVEGKIKNKFDMRPH 110 (246)
Q Consensus 91 ~~~~~~i~G~V~~~~~~~P~ 110 (246)
..+.....|.|.+++.|.|.
T Consensus 111 ~~~~~~~LG~v~~k~v~tPd 130 (131)
T PF05132_consen 111 EEGECYFLGQVSGKFVVTPD 130 (131)
T ss_pred CCCeEEEeccccceEEEccC
Confidence 55789999999999999995
No 12
>PF13817 DDE_Tnp_IS66_C: IS66 C-terminal element
Probab=59.14 E-value=6.9 Score=25.42 Aligned_cols=15 Identities=27% Similarity=0.518 Sum_probs=14.1
Q ss_pred CcHHHHHHHHHHHhh
Q 025926 206 QPEQFLKDMLKDLCV 220 (246)
Q Consensus 206 QPe~yLKeiL~eIa~ 220 (246)
.|.+||+.||..|+.
T Consensus 12 ~P~~yL~~vL~~i~~ 26 (39)
T PF13817_consen 12 NPYAYLTDVLERIPN 26 (39)
T ss_pred CHHHHHHHHHHHHcc
Confidence 499999999999998
No 13
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=58.02 E-value=18 Score=30.41 Aligned_cols=56 Identities=14% Similarity=0.245 Sum_probs=41.3
Q ss_pred hhhHHHHHHHHhhh-ccCcchHHHHHhhCCcHHHHHHHHHHHhh--H-h-ccCCCCcccccc
Q 025926 178 RGEMEDIMFKLFER-QSNWTLRQLIQETDQPEQFLKDMLKDLCV--Y-N-NKGSNQGSYELK 234 (246)
Q Consensus 178 ~~eLld~LF~~Fek-~~yWslK~L~~~t~QPe~yLKeiL~eIa~--l-n-k~Gp~~~~weLK 234 (246)
+=.|.-+++=+|.. .+.|++++|.+.++-|..||.+||..... | + .+|+ .|-|.|.
T Consensus 8 ~yAl~~l~~lA~~~~~~~vs~~eIA~~~~ip~~~l~kIl~~L~~aGLv~s~rG~-~GGy~La 68 (164)
T PRK10857 8 RYAVTAMLDVALNSEAGPVPLADISERQGISLSYLEQLFSRLRKNGLVSSVRGP-GGGYLLG 68 (164)
T ss_pred HHHHHHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeCCCC-CCCeecc
Confidence 34566677777754 46899999999999999999999988753 2 2 2454 3457774
No 14
>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulfovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis sp. (strain PCC 6803) hypothetical protein slr0846. These are small proteins of 12 to 18kDa which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.; PDB: 3T8T_A 3T8R_A 3K69_A 3LWF_C 1XD7_A 2Y75_E 1YLF_C.
Probab=54.76 E-value=28 Score=25.42 Aligned_cols=41 Identities=17% Similarity=0.386 Sum_probs=29.7
Q ss_pred CcchHHHHHhhCCcHHHHHHHHHHHhhH----hccCCCCcccccch
Q 025926 194 NWTLRQLIQETDQPEQFLKDMLKDLCVY----NNKGSNQGSYELKP 235 (246)
Q Consensus 194 yWslK~L~~~t~QPe~yLKeiL~eIa~l----nk~Gp~~~~weLKp 235 (246)
.+++++|.++++-|..||..+|.....- ..+|+ .|-|.|..
T Consensus 25 ~~s~~eiA~~~~i~~~~l~kil~~L~~~Gli~s~~G~-~GGy~L~~ 69 (83)
T PF02082_consen 25 PVSSKEIAERLGISPSYLRKILQKLKKAGLIESSRGR-GGGYRLAR 69 (83)
T ss_dssp -BEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETST-TSEEEESS
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHhhCCeeEecCCC-CCceeecC
Confidence 4999999999999999999999887642 23554 35555543
No 15
>TIGR02010 IscR iron-sulfur cluster assembly transcription factor IscR. This model describes IscR, an iron-sulfur binding transcription factor of the ISC iron-sulfur cluster assembly system.
Probab=54.38 E-value=25 Score=28.21 Aligned_cols=55 Identities=15% Similarity=0.291 Sum_probs=39.8
Q ss_pred hHHHHHHHHhhh-ccCcchHHHHHhhCCcHHHHHHHHHHHhh---Hhc-cCCCCcccccch
Q 025926 180 EMEDIMFKLFER-QSNWTLRQLIQETDQPEQFLKDMLKDLCV---YNN-KGSNQGSYELKP 235 (246)
Q Consensus 180 eLld~LF~~Fek-~~yWslK~L~~~t~QPe~yLKeiL~eIa~---lnk-~Gp~~~~weLKp 235 (246)
.|.-+++=++.. .+.|+.++|.+.++-|..||..||..... .+. +|+ .|-|.|..
T Consensus 10 Al~~l~~La~~~~~~~~s~~~ia~~~~ip~~~l~kil~~L~~~glv~s~~G~-~Ggy~l~~ 69 (135)
T TIGR02010 10 AVTAMLDLALNAETGPVTLADISERQGISLSYLEQLFAKLRKAGLVKSVRGP-GGGYQLGR 69 (135)
T ss_pred HHHHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCceEEEeCC-CCCEeccC
Confidence 455666666643 35899999999999999999999988743 222 353 45577653
No 16
>PF13565 HTH_32: Homeodomain-like domain
Probab=50.11 E-value=17 Score=25.77 Aligned_cols=29 Identities=21% Similarity=0.464 Sum_probs=25.2
Q ss_pred hhhHHHHHHHHhhhccCcchHHHHHhhCC
Q 025926 178 RGEMEDIMFKLFERQSNWTLRQLIQETDQ 206 (246)
Q Consensus 178 ~~eLld~LF~~Fek~~yWslK~L~~~t~Q 206 (246)
-.++.+.|..++.+++.|+.+.|.+.+.+
T Consensus 32 ~~e~~~~i~~~~~~~p~wt~~~i~~~L~~ 60 (77)
T PF13565_consen 32 DPEQRERIIALIEEHPRWTPREIAEYLEE 60 (77)
T ss_pred cHHHHHHHHHHHHhCCCCCHHHHHHHHHH
Confidence 57788999999999999999999887643
No 17
>KOG3122 consensus DNA-directed RNA polymerase III subunit [Transcription]
Probab=48.40 E-value=34 Score=32.07 Aligned_cols=61 Identities=25% Similarity=0.376 Sum_probs=40.3
Q ss_pred CCceeEEEEEeCCCCCCCCCCCCCCCCCcceeEEecccCCCCCCceeeeccccC---Ccc-eeeeeee-cCCceeEEEEE
Q 025926 27 ARPVAKVILSIDPLQSNEDSSSSSSSSSTRFTMELISTESGNAPKRYSMDMSKD---LIP-MSVFAES-SNGKISVEGKI 101 (246)
Q Consensus 27 ~~~~g~v~~~~~~~~~~~~~~~~~~~~~~~~~m~l~~~~~~~iPkeY~L~~~~~---~~~-~~VFse~-~~~~~~i~G~V 101 (246)
++++|+|++..+. +++|.|-. --|++.|..+ .+. ++|=... ..+...+.|.|
T Consensus 244 eGqvGkllV~KSG----------------rVkLklG~-------V~fDV~~G~~~~FLQEl~sV~l~d~rs~nm~~LG~v 300 (310)
T KOG3122|consen 244 EGQVGKLLVYKSG----------------RVKLKLGD-------VLFDVSMGLDCSFLQELMSVGLGDSRSGNMTLLGSV 300 (310)
T ss_pred cCcceeEEEEecC----------------ceEEEecC-------EEEEeccCchhHhhhhhheeecccccCCceEEeccc
Confidence 5679999998753 56666632 2355555443 122 4442222 47899999999
Q ss_pred eeeeeEeec
Q 025926 102 KNKFDMRPH 110 (246)
Q Consensus 102 ~~~~~~~P~ 110 (246)
.|++.|.|.
T Consensus 301 ~~klvvTPD 309 (310)
T KOG3122|consen 301 KKKLVVTPD 309 (310)
T ss_pred cceeeeCCC
Confidence 999999995
No 18
>PF09339 HTH_IclR: IclR helix-turn-helix domain; InterPro: IPR005471 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these subfamilies, called 'iclR', groups several proteins including: gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces. iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium. These proteins have a Helix-Turn-Helix motif at the N terminus that is similar to that of other DNA-binding proteins [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1MKM_A 3MQ0_A 3R4K_A 2G7U_C 2O0Y_C 2XRO_F 2XRN_B 2IA2_D.
Probab=46.52 E-value=37 Score=22.51 Aligned_cols=37 Identities=14% Similarity=0.297 Sum_probs=29.6
Q ss_pred HHHHHhhhccC-cchHHHHHhhCCcHHHHHHHHHHHhh
Q 025926 184 IMFKLFERQSN-WTLRQLIQETDQPEQFLKDMLKDLCV 220 (246)
Q Consensus 184 ~LF~~Fek~~y-WslK~L~~~t~QPe~yLKeiL~eIa~ 220 (246)
.|+.+|.+++- |++.+|.+.++=|-+-+--+|...+.
T Consensus 7 ~iL~~l~~~~~~~t~~eia~~~gl~~stv~r~L~tL~~ 44 (52)
T PF09339_consen 7 RILEALAESGGPLTLSEIARALGLPKSTVHRLLQTLVE 44 (52)
T ss_dssp HHHHCHHCTBSCEEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred HHHHHHHcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 46778877776 89999999999999988888776654
No 19
>PF05595 DUF771: Domain of unknown function (DUF771) ; InterPro: IPR008489 This entry is represented by Bacteriophage bIL285, Orf7. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry consists of uncharacterised ORFs found in Bacteriophage and Lactococcus lactis.
Probab=46.21 E-value=28 Score=26.44 Aligned_cols=40 Identities=23% Similarity=0.428 Sum_probs=27.9
Q ss_pred CChhhHHHHHHHHhhhccCcchHHHHHhhCCcHHHHH-HHHH
Q 025926 176 RDRGEMEDIMFKLFERQSNWTLRQLIQETDQPEQFLK-DMLK 216 (246)
Q Consensus 176 ~~~~eLld~LF~~Fek~~yWslK~L~~~t~QPe~yLK-eiL~ 216 (246)
.++.++.+++-.. ....+|+|++|+.+|.--..+|+ -||.
T Consensus 6 i~k~ey~el~~~~-~~~~~W~~~dl~k~~~~s~~wi~~~il~ 46 (91)
T PF05595_consen 6 IDKEEYEELKKKD-LEGKWWDMKDLRKRTGKSREWIKENILY 46 (91)
T ss_pred eeHHHHHHHHHHh-hccceeeHHHHHHHHCCCHHHHHHHccc
Confidence 3455555554433 45567999999999998889996 4444
No 20
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=44.78 E-value=71 Score=22.67 Aligned_cols=59 Identities=17% Similarity=0.285 Sum_probs=44.3
Q ss_pred ChhhHHHHHHHHhhhccC--cchHHHHHhhCCcHHHHHHHHHHHh---hHhccCCCCcccccch
Q 025926 177 DRGEMEDIMFKLFERQSN--WTLRQLIQETDQPEQFLKDMLKDLC---VYNNKGSNQGSYELKP 235 (246)
Q Consensus 177 ~~~eLld~LF~~Fek~~y--WslK~L~~~t~QPe~yLKeiL~eIa---~lnk~Gp~~~~weLKp 235 (246)
+.+++.+.|..++.++.- .+.++|...++.+..=+..+|..+- ...+.+..-..|.|..
T Consensus 3 ~~~~~~~~IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L~~~G~V~~~~~~~~~W~i~~ 66 (68)
T smart00550 3 TQDSLEEKILEFLENSGDETSTALQLAKNLGLPKKEVNRVLYSLEKKGKVCKQGGTPPLWKLTD 66 (68)
T ss_pred CchHHHHHHHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecCCCCCceEeec
Confidence 467788999999999987 9999999999999987777765432 2233333337888754
No 21
>cd00092 HTH_CRP helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family.
Probab=39.92 E-value=96 Score=20.83 Aligned_cols=43 Identities=19% Similarity=0.286 Sum_probs=31.1
Q ss_pred ccCcchHHHHHhhCCcHHHHHHHHHHHhh--HhccCCCCcccccch
Q 025926 192 QSNWTLRQLIQETDQPEQFLKDMLKDLCV--YNNKGSNQGSYELKP 235 (246)
Q Consensus 192 ~~yWslK~L~~~t~QPe~yLKeiL~eIa~--lnk~Gp~~~~weLKp 235 (246)
...++..+|.+.++=+...+..+|+.... +-...+ .+.|.|.|
T Consensus 23 ~~~~s~~ela~~~g~s~~tv~r~l~~L~~~g~i~~~~-~~~~~l~~ 67 (67)
T cd00092 23 QLPLTRQEIADYLGLTRETVSRTLKELEEEGLISRRG-RGKYRVNP 67 (67)
T ss_pred cCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecC-CCeEEeCC
Confidence 34699999999999999999888877665 222222 46677654
No 22
>PF10826 DUF2551: Protein of unknown function (DUF2551) ; InterPro: IPR020501 This entry contains proteins with no known function.
Probab=39.24 E-value=67 Score=24.42 Aligned_cols=65 Identities=17% Similarity=0.333 Sum_probs=42.9
Q ss_pred CChhhHHHHHHHHhhhccCcchHHHHHhhCCc--------HHHHHHHHHHHhhHhc---cCCCCcccccchhhhhc
Q 025926 176 RDRGEMEDIMFKLFERQSNWTLRQLIQETDQP--------EQFLKDMLKDLCVYNN---KGSNQGSYELKPEYKKA 240 (246)
Q Consensus 176 ~~~~eLld~LF~~Fek~~yWslK~L~~~t~QP--------e~yLKeiL~eIa~lnk---~Gp~~~~weLKpEYk~~ 240 (246)
.|++-+.-.+.++|=+..-.+..+|-+.+..- .+-+==|=..+++|+- +---.+.|+||++|+..
T Consensus 7 rD~~GiRr~vL~~fl~~~~~T~~di~e~L~~~f~vs~~~VasMVG~i~SrlGIL~~~k~~~g~~~~Y~LKe~Y~~l 82 (83)
T PF10826_consen 7 RDKDGIRRAVLKLFLKGKKFTTDDIYERLKEKFDVSYRGVASMVGLIHSRLGILSIHKDSYGDHNVYSLKEKYADL 82 (83)
T ss_pred cCCccHHHHHHHHHHhCCCeeHHHHHHHHHHHcCchHHHHHHHHHHHHHhhhheeecccccCCccEEEecHHhhcc
Confidence 35666777888888888888888887776432 1223333445555554 21246899999999864
No 23
>PF10390 ELL: RNA polymerase II elongation factor ELL ; InterPro: IPR019464 ELL is a family of RNA polymerase II elongation factors. It is bound stably to elongation-associated factors 1 and 2, EAFs, and together these act as a strong regulator of transcription activity. by direct interaction with Pol II. ELL binds to pol II on its own but the affinity is greatly increased by the cooperation of EAF []. Some members carry an occludin domain (IPR010844 from INTERPRO) just downstream. There is no Saccharomyces cerevisiae (Baker's yeast) member. ; GO: 0006368 transcription elongation from RNA polymerase II promoter, 0008023 transcription elongation factor complex; PDB: 2E5N_A 2DOA_A.
Probab=38.55 E-value=12 Score=34.48 Aligned_cols=136 Identities=20% Similarity=0.367 Sum_probs=39.3
Q ss_pred CCceeEEEEEeeeeeEeecCCChHHHHHHHHHHHHHHhcC--CcceEEecCC---CC--Ccc-cCCCCcc---ccCCccc
Q 025926 92 NGKISVEGKIKNKFDMRPHHENMENYGKLCRERTNKYMTK--SRQIQVIDND---NG--SHM-RPMPGMM---ISTGFTE 160 (246)
Q Consensus 92 ~~~~~i~G~V~~~~~~~P~~~~~~~Y~~l~~~R~~~a~~~--~r~vq~ld~~---~~--~~~-~p~~~~~---~~~~~~~ 160 (246)
.+.+...|.|.++..+... ++.|.. -++|...+..- .|.+.+|... .+ +.+ ++ +... .+.. ..
T Consensus 97 ~~~L~~lG~iq~KitV~At---dDSy~~-Tr~rmaq~Eee~k~~~t~~ik~~~~~~~~~~~~~~~-~~~~~~~~p~a-~~ 170 (284)
T PF10390_consen 97 PSQLSCLGSIQDKITVCAT---DDSYQA-TRERMAQAEEETKSRCTKVIKPGSSYVGKKVQIRKP-PSSISDSDPLA-SS 170 (284)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred CCccceeeeccceeEEecc---cchhHh-HHHHHHHHhhhccccccccccCCCcCcCcccccccC-CccCCCCCccc-cc
Confidence 4689999999999998776 477877 66666666543 3445555421 11 111 11 1110 0000 00
Q ss_pred ccCCCC-------CCccc-ccccCChhhHHHHHHHHhhhccCcchHHHHHhhCC------cHHHHHHHHHHHhhHhccCC
Q 025926 161 KKKPQP-------KGSEV-KRTRRDRGEMEDIMFKLFERQSNWTLRQLIQETDQ------PEQFLKDMLKDLCVYNNKGS 226 (246)
Q Consensus 161 k~k~~~-------K~~~~-K~~R~~~~eLld~LF~~Fek~~yWslK~L~~~t~Q------Pe~yLKeiL~eIa~lnk~Gp 226 (246)
.+...| ++... ...-..+..|.+.|-+|-.=.+| .=-+|..+++. --.=|..||.+||.+| ++
T Consensus 171 ~~~s~P~~~~~~~r~~~~~~~~~v~~rplReRvIHLLALkpy-kK~ELl~rL~~dg~~~~dk~~l~~iL~~Va~l~-~~- 247 (284)
T PF10390_consen 171 RKQSSPSNSASSSRKQNHRSNSAVSKRPLRERVIHLLALKPY-KKPELLLRLQKDGLSPKDKDELDSILQEVANLN-KD- 247 (284)
T ss_dssp -----------------------STTS-HHHHHHHHHHHS-E-EHHHHHHHHHHH---HHHHHHHHHHHHHCCEEE-TT-
T ss_pred cCCCCCCcccccccccccCCccccccccccccchhhhhcCcc-ccHHHHHHHHhcCCChHHHHHHHHHHHHHhccC-cC-
Confidence 000001 00000 13445666788888888777777 22245444433 2367999999999999 54
Q ss_pred CCcccccchhhh
Q 025926 227 NQGSYELKPEYK 238 (246)
Q Consensus 227 ~~~~weLKpEYk 238 (246)
|.|.||+.+=
T Consensus 248 --~~y~Lk~~~y 257 (284)
T PF10390_consen 248 --NSYTLKDHFY 257 (284)
T ss_dssp --TEEEE-STHH
T ss_pred --CeEEehHHHH
Confidence 8999999753
No 24
>PHA02571 a-gt.4 hypothetical protein; Provisional
Probab=34.27 E-value=27 Score=27.84 Aligned_cols=37 Identities=16% Similarity=0.386 Sum_probs=26.7
Q ss_pred hhHHHHHHHHhhhccCcchHHHHHhhCCcHHHHHHHHHH
Q 025926 179 GEMEDIMFKLFERQSNWTLRQLIQETDQPEQFLKDMLKD 217 (246)
Q Consensus 179 ~eLld~LF~~Fek~~yWslK~L~~~t~QPe~yLKeiL~e 217 (246)
..-...||.+=...--|.|+-|+.+++|| |-.|+|+-
T Consensus 51 ~HAe~al~~~Nk~~Y~YAI~KLR~i~kQp--~~de~i~t 87 (109)
T PHA02571 51 KHAEEALFDNNKEQYVYAIKKLRDIYKQP--YTDELIET 87 (109)
T ss_pred HHHHHHHHhcCHHHHHHHHHHHHHHHcCC--CcHHHHHH
Confidence 34456777773333338999999999999 77777754
No 25
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=34.03 E-value=1.2e+02 Score=21.84 Aligned_cols=54 Identities=19% Similarity=0.362 Sum_probs=39.1
Q ss_pred HHHHhhhc-cCcchHHHHHhhCCcHHHHHHHHHHHhh--HhccCCCCcccccchhhh
Q 025926 185 MFKLFERQ-SNWTLRQLIQETDQPEQFLKDMLKDLCV--YNNKGSNQGSYELKPEYK 238 (246)
Q Consensus 185 LF~~Fek~-~yWslK~L~~~t~QPe~yLKeiL~eIa~--lnk~Gp~~~~weLKpEYk 238 (246)
|+.+|.++ ...++.+|.+.++=|.+-+...|...+. |-.+.+..+.|.|-+..-
T Consensus 10 Il~~l~~~~~~~t~~~ia~~l~i~~~tv~r~l~~L~~~g~l~~~~~~~~y~l~~~~~ 66 (91)
T smart00346 10 VLRALAEEPGGLTLAELAERLGLSKSTAHRLLNTLQELGYVEQDGQNGRYRLGPKVL 66 (91)
T ss_pred HHHHHHhCCCCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCeeecCCCCceeecHHHH
Confidence 55566666 6899999999999999988888877653 222333456788877543
No 26
>KOG2934 consensus Uncharacterized conserved protein, contains Josephin domain [General function prediction only]
Probab=30.19 E-value=27 Score=30.35 Aligned_cols=34 Identities=18% Similarity=0.358 Sum_probs=27.6
Q ss_pred chHHHHHhhCCcHHHHHHHHHHHhhH----hccCCCCc
Q 025926 196 TLRQLIQETDQPEQFLKDMLKDLCVY----NNKGSNQG 229 (246)
Q Consensus 196 slK~L~~~t~QPe~yLKeiL~eIa~l----nk~Gp~~~ 229 (246)
-+.+|-..+|+|-+|-|++|.|||.- +..|||+.
T Consensus 37 ~lhAlnnv~q~~n~ftr~~~~d~c~~l~p~s~~~Phrs 74 (204)
T KOG2934|consen 37 ALHALNNVFQRSNAFTRPVLDDICTRLKPRSWLNPHRS 74 (204)
T ss_pred HHHHhhhhhhccccccchhhHHHHhhcCcccccCcccc
Confidence 36788888999999999999999874 44567764
No 27
>smart00076 IFabd Interferon alpha, beta and delta. Interferons produce antiviral and antiproliferative responses in cells. They are classified into five groups, all of them related but gamma-interferon.
Probab=28.40 E-value=80 Score=25.25 Aligned_cols=44 Identities=27% Similarity=0.392 Sum_probs=33.6
Q ss_pred hhHHHHHHHHhhhcc---CcchH---HHHHhhCCcHHHHHHHHHHHhhHh
Q 025926 179 GEMEDIMFKLFERQS---NWTLR---QLIQETDQPEQFLKDMLKDLCVYN 222 (246)
Q Consensus 179 ~eLld~LF~~Fek~~---yWslK---~L~~~t~QPe~yLKeiL~eIa~ln 222 (246)
-++++.||.+|..+. .|+-. .|...+.|=..+|+++|.+...-+
T Consensus 24 ~emlqqif~lF~~~~ssa~W~~t~le~~l~~L~~Ql~~Le~Cl~~~~~~~ 73 (117)
T smart00076 24 HEMLQQIFNIFSSPSSSAAWNETLLESLLNELHQQLNHLEACLKQEMEEE 73 (117)
T ss_pred HHHHHHHHHHHcCCCCcccccHHHHHHHHHHHHHHHHHHHHHHHHhcccc
Confidence 689999999999774 49754 555566777889999998766443
No 28
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=26.24 E-value=1.8e+02 Score=18.54 Aligned_cols=38 Identities=13% Similarity=0.220 Sum_probs=29.8
Q ss_pred HHHHHHHhhhccCcchHHHHHhhCCcHHHHHHHHHHHh
Q 025926 182 EDIMFKLFERQSNWTLRQLIQETDQPEQFLKDMLKDLC 219 (246)
Q Consensus 182 ld~LF~~Fek~~yWslK~L~~~t~QPe~yLKeiL~eIa 219 (246)
.-.|+.+..+++.-+.++|.+.++=+.+.+...|++..
T Consensus 5 ~~~Il~~l~~~~~~t~~ela~~~~is~~tv~~~l~~L~ 42 (48)
T PF13412_consen 5 QRKILNYLRENPRITQKELAEKLGISRSTVNRYLKKLE 42 (48)
T ss_dssp HHHHHHHHHHCTTS-HHHHHHHHTS-HHHHHHHHHHHH
T ss_pred HHHHHHHHHHcCCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 34566677779999999999999999999999888764
No 29
>TIGR00281 segregation and condensation protein B. Shown to be required for chromosome segregation and condensation in B. subtilis.
Probab=25.74 E-value=2e+02 Score=24.90 Aligned_cols=60 Identities=20% Similarity=0.297 Sum_probs=43.3
Q ss_pred hhHHHHHHHHhhhccCcchHHHHHhhCCc-HHHHHHHHHHHhhHhcc-C------CCCcccc--cchhhhhc
Q 025926 179 GEMEDIMFKLFERQSNWTLRQLIQETDQP-EQFLKDMLKDLCVYNNK-G------SNQGSYE--LKPEYKKA 240 (246)
Q Consensus 179 ~eLld~LF~~Fek~~yWslK~L~~~t~QP-e~yLKeiL~eIa~lnk~-G------p~~~~we--LKpEYk~~ 240 (246)
..|..+||.+ ..+--++++|++.++.+ ..-++++|+++..+..+ + ...|.|. +||||..+
T Consensus 4 ~~iEAlLF~s--g~pgls~~~La~il~~~~~~~~~~~l~~l~~~~~~~~~gl~l~~~~~~y~l~tk~e~~~~ 73 (186)
T TIGR00281 4 AIIEALLFVS--GEPGVTLAELVRILGKEKAEKLNAIMELLEDYLSRDTAGIEIIKFGQSYSLVTKPAFADY 73 (186)
T ss_pred HHHHHHHHHc--CCCCCCHHHHHHHhCCCchHHHHHHHHHHHHHHhcCCCCEEEEEECCEEEEEEhHHHHHH
Confidence 3467777776 23348999999999887 56899999999887443 2 1356674 58888765
No 30
>PF14493 HTH_40: Helix-turn-helix domain
Probab=25.55 E-value=71 Score=23.78 Aligned_cols=34 Identities=6% Similarity=0.006 Sum_probs=24.6
Q ss_pred CChhhHHHHHHHHhhhccCcchHHHHHhhCCcHHH
Q 025926 176 RDRGEMEDIMFKLFERQSNWTLRQLIQETDQPEQF 210 (246)
Q Consensus 176 ~~~~eLld~LF~~Fek~~yWslK~L~~~t~QPe~y 210 (246)
.+++ ..+.|-.+|++..+|+||.|++..+.=..|
T Consensus 50 l~~e-~~~~I~~~~~~~~~~~lk~i~e~l~~~~sy 83 (91)
T PF14493_consen 50 LSEE-EIKQIEDAIEKLGSEKLKPIKEALPGDYSY 83 (91)
T ss_pred CCHH-HHHHHHHHHHHcCcccHHHHHHHCCCCCCH
Confidence 3443 578888888888889999888877643333
No 31
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=24.80 E-value=2.2e+02 Score=21.26 Aligned_cols=41 Identities=5% Similarity=0.250 Sum_probs=29.2
Q ss_pred hhhHHHHHHHHhhhcc--CcchHHHHHhhCCcHHHHHHHHHHH
Q 025926 178 RGEMEDIMFKLFERQS--NWTLRQLIQETDQPEQFLKDMLKDL 218 (246)
Q Consensus 178 ~~eLld~LF~~Fek~~--yWslK~L~~~t~QPe~yLKeiL~eI 218 (246)
.+++++.+...-+.+. .|++.+|.+.+.-...+|..+..+.
T Consensus 3 ~~~~~~~~~~~i~~~~~~~~~~~~lA~~~~~S~~~l~r~f~~~ 45 (107)
T PRK10219 3 HQKIIQTLIAWIDEHIDQPLNIDVVAKKSGYSKWYLQRMFRTV 45 (107)
T ss_pred hHHHHHHHHHHHHHhcCCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 3455555555555543 3999999999888888888777765
No 32
>TIGR03879 near_KaiC_dom probable regulatory domain. This model describes a common domain shared by two different families of proteins, each of which occurs regularly next to its corresponding partner family, a probable regulatory with homology to KaiC. By implication, this protein family likely is also involved in sensory transduction and/or regulation.
Probab=23.53 E-value=1.8e+02 Score=21.50 Aligned_cols=38 Identities=18% Similarity=0.274 Sum_probs=33.2
Q ss_pred hhHHHHHHHHhhhccCcchHHHHHhhCCcHHHHHHHHH
Q 025926 179 GEMEDIMFKLFERQSNWTLRQLIQETDQPEQFLKDMLK 216 (246)
Q Consensus 179 ~eLld~LF~~Fek~~yWslK~L~~~t~QPe~yLKeiL~ 216 (246)
.+..-.+|.++...+-+|.+++.++++-++.-++..+.
T Consensus 17 ~~~~r~af~L~R~~eGlS~kEIAe~LGIS~~TVk~~l~ 54 (73)
T TIGR03879 17 DSLAEAAAALAREEAGKTASEIAEELGRTEQTVRNHLK 54 (73)
T ss_pred CHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHh
Confidence 56777889998777889999999999999999988875
No 33
>PF07587 PSD1: Protein of unknown function (DUF1553); InterPro: IPR022655 The function is not known. It is found associated with IPR011444 from INTERPRO It is also found associated with the Planctomycete cytochrome C domain IPR011429 from INTERPRO.
Probab=22.66 E-value=91 Score=28.13 Aligned_cols=33 Identities=21% Similarity=0.421 Sum_probs=25.7
Q ss_pred ChhhHHHHHHHHhhhccCcchHHHHHhhCCcHHH
Q 025926 177 DRGEMEDIMFKLFERQSNWTLRQLIQETDQPEQF 210 (246)
Q Consensus 177 ~~~eLld~LF~~Fek~~yWslK~L~~~t~QPe~y 210 (246)
...||||.|-.-|-+|. |+||.|...+=.-.+|
T Consensus 50 shPeLLd~La~~F~~~g-~dlK~L~R~I~~S~tY 82 (266)
T PF07587_consen 50 SHPELLDWLAAEFVEHG-WDLKHLIRLIVTSRTY 82 (266)
T ss_pred CCHHHHHHHHHHHHHcC-CCHHHHHHHHHccHHH
Confidence 45799999999999965 9999998775444433
No 34
>TIGR00738 rrf2_super rrf2 family protein (putative transcriptional regulator). This model represents a superfamily of probable transcriptional regulators. One member, RRF2 of Desulfovibrio vulgaris is an apparent regulatory protein experimentally (MEDLINE:97293189). The N-terminal region appears related to the DNA-binding biotin repressor region of the BirA bifunctional according to results after three rounds of PSI-BLAST with a fairly high stringency.
Probab=22.17 E-value=1.6e+02 Score=22.92 Aligned_cols=42 Identities=17% Similarity=0.458 Sum_probs=31.6
Q ss_pred ccCcchHHHHHhhCCcHHHHHHHHHHHhh---Hhc-cCCCCcccccc
Q 025926 192 QSNWTLRQLIQETDQPEQFLKDMLKDLCV---YNN-KGSNQGSYELK 234 (246)
Q Consensus 192 ~~yWslK~L~~~t~QPe~yLKeiL~eIa~---lnk-~Gp~~~~weLK 234 (246)
...++..+|.+.++-|..++..+|..... +.. +|. .+-|.|.
T Consensus 23 ~~~~s~~eia~~~~i~~~~v~~il~~L~~~gli~~~~g~-~ggy~l~ 68 (132)
T TIGR00738 23 EGPVSVKEIAERQGISRSYLEKILRTLRRAGLVESVRGP-GGGYRLA 68 (132)
T ss_pred CCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCcEEeccCC-CCCccCC
Confidence 45899999999999999999999987654 222 243 3457774
No 35
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=21.47 E-value=1.2e+02 Score=20.56 Aligned_cols=25 Identities=20% Similarity=0.288 Sum_probs=18.0
Q ss_pred cchHHHHHhhCCcHHHHHHHHHHHh
Q 025926 195 WTLRQLIQETDQPEQFLKDMLKDLC 219 (246)
Q Consensus 195 WslK~L~~~t~QPe~yLKeiL~eIa 219 (246)
|++++|.+.+.-+..+|..++.+..
T Consensus 2 ~~~~~la~~~~~s~~~l~~~f~~~~ 26 (84)
T smart00342 2 LTLEDLAEALGMSPRHLQRLFKKET 26 (84)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHh
Confidence 6777777777777777777776553
No 36
>cd00095 IFab Interferon alpha, beta. Includes also interferon omega and tau. Different from interferon gamma family. Type I interferons(alpha, beta) belong to the larger helical cytokine superfamily, which includes growth hormones, interleukins, several colony-stimulating factors and several other regulatory molecules. All function as regulators of cellular activty by interacting with cell-surface receptors and activating various signalling pathways. Interferons produce antiviral and antiproliferative responses in cells. Receptor specificity determines function of the various members of the family.
Probab=20.56 E-value=1.3e+02 Score=25.05 Aligned_cols=43 Identities=26% Similarity=0.375 Sum_probs=33.5
Q ss_pred hhHHHHHHHHhhhcc---Ccch---HHHHHhhCCcHHHHHHHHHHHhhH
Q 025926 179 GEMEDIMFKLFERQS---NWTL---RQLIQETDQPEQFLKDMLKDLCVY 221 (246)
Q Consensus 179 ~eLld~LF~~Fek~~---yWsl---K~L~~~t~QPe~yLKeiL~eIa~l 221 (246)
-++++.||.+|..+. .|+- .+|...+.|=..+|++++.+.+.-
T Consensus 56 ~emlqqif~LF~~~~ssa~Wnet~le~fl~~L~~Ql~~Le~C~~~~~~~ 104 (152)
T cd00095 56 HEMLQQIFNIFSTPSSSAAWNETLLESLLNELHQQLNHLETCLEQEMGE 104 (152)
T ss_pred HHHHHHHHHHHcCCCCcccccHHHHHHHHHHHHHHHHHHHHHHHHhccc
Confidence 689999999998774 4875 455556677788999999886644
No 37
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=20.05 E-value=2.1e+02 Score=18.32 Aligned_cols=42 Identities=10% Similarity=0.147 Sum_probs=31.3
Q ss_pred hhHHHHHHHH-hhhccCc-chHHHHHhhCCcHHHHHHHHHHHhh
Q 025926 179 GEMEDIMFKL-FERQSNW-TLRQLIQETDQPEQFLKDMLKDLCV 220 (246)
Q Consensus 179 ~eLld~LF~~-Fek~~yW-slK~L~~~t~QPe~yLKeiL~eIa~ 220 (246)
+.|...|... +...+.. +.++|.++++=+...+...|.....
T Consensus 3 ~~l~~~i~~~~~~~~~~l~s~~~la~~~~vs~~tv~~~l~~L~~ 46 (60)
T smart00345 3 ERLREDIVSGELRPGDKLPSERELAAQLGVSRTTVREALSRLEA 46 (60)
T ss_pred HHHHHHHHcCCCCCCCcCcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4566666665 3444445 8999999999999999998887764
Done!