Query 026167
Match_columns 242
No_of_seqs 115 out of 209
Neff 6.5
Searched_HMMs 46136
Date Fri Mar 29 04:33:23 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/026167.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/026167hhsearch_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 1.1E-65 2.5E-70 442.8 15.6 217 11-239 7-231 (254)
2 PF02270 TFIIF_beta: Transcrip 100.0 1.2E-63 2.6E-68 447.9 10.6 217 12-239 1-261 (275)
3 COG5090 TFG2 Transcription ini 100.0 9.2E-56 2E-60 379.7 17.0 217 11-239 18-240 (297)
4 PF05132 RNA_pol_Rpc4: RNA pol 83.2 5.4 0.00012 31.9 6.8 60 47-121 67-130 (131)
5 PF09734 Tau95: RNA polymerase 82.2 1.6 3.4E-05 39.9 3.7 50 190-239 231-282 (310)
6 PF04801 Sin_N: Sin-like prote 79.0 2.7 5.8E-05 40.1 4.3 47 194-240 337-385 (421)
7 PF04004 Leo1: Leo1-like prote 78.3 24 0.00053 29.6 9.4 42 94-135 99-141 (171)
8 KOG2428 Uncharacterized conser 68.6 24 0.00052 34.1 7.7 47 96-143 243-289 (443)
9 KOG3122 DNA-directed RNA polym 68.1 11 0.00024 34.8 5.3 61 46-121 244-309 (310)
10 PRK10857 DNA-binding transcrip 64.8 12 0.00027 31.1 4.6 42 192-233 8-50 (164)
11 PF13817 DDE_Tnp_IS66_C: IS66 64.6 4.5 9.8E-05 25.8 1.5 15 220-234 12-26 (39)
12 PF02082 Rrf2: Transcriptional 60.0 22 0.00047 25.7 4.7 27 208-234 25-51 (83)
13 TIGR02010 IscR iron-sulfur clu 59.3 19 0.0004 28.7 4.6 40 194-233 10-50 (135)
14 PF13565 HTH_32: Homeodomain-l 51.8 14 0.00031 25.9 2.5 29 192-220 32-60 (77)
15 PF05595 DUF771: Domain of unk 50.6 24 0.00051 26.5 3.6 39 191-230 7-46 (91)
16 PF09339 HTH_IclR: IclR helix- 50.1 33 0.00072 22.5 3.9 37 198-234 7-44 (52)
17 PF08208 RNA_polI_A34: DNA-dir 37.5 11 0.00023 32.1 -0.1 15 20-34 3-17 (198)
18 PRK14741 spoVM stage V sporula 31.2 41 0.00089 19.4 1.7 14 24-37 3-16 (26)
19 KOG2473 RNA polymerase III tra 30.6 90 0.0019 30.6 4.9 49 191-239 229-278 (484)
20 PF12157 DUF3591: Protein of u 30.0 1E+02 0.0022 30.1 5.3 55 186-240 234-291 (457)
21 PHA02571 a-gt.4 hypothetical p 29.8 34 0.00073 26.9 1.6 37 193-231 51-87 (109)
22 PF14493 HTH_40: Helix-turn-he 28.2 65 0.0014 23.7 2.9 34 190-224 50-83 (91)
23 smart00550 Zalpha Z-DNA-bindin 26.3 2E+02 0.0044 20.0 5.0 41 191-231 3-45 (68)
24 PF13412 HTH_24: Winged helix- 25.5 1.8E+02 0.0039 18.3 5.0 37 197-233 6-42 (48)
25 smart00076 IFabd Interferon al 24.2 1E+02 0.0022 24.4 3.4 41 193-233 24-70 (117)
26 TIGR00738 rrf2_super rrf2 fami 23.1 1.5E+02 0.0032 22.9 4.2 29 206-234 23-51 (132)
27 PRK10219 DNA-binding transcrip 22.6 2.4E+02 0.0053 20.8 5.2 42 192-233 3-46 (107)
28 smart00342 HTH_ARAC helix_turn 22.2 1.1E+02 0.0024 20.6 3.1 25 209-233 2-26 (84)
29 TIGR03879 near_KaiC_dom probab 21.4 1.8E+02 0.004 21.1 4.0 38 193-230 17-54 (73)
30 PF14668 RICTOR_V: Rapamycin-i 21.2 72 0.0016 23.1 1.9 24 191-214 25-48 (73)
31 PF07587 PSD1: Protein of unkn 20.9 1E+02 0.0022 27.5 3.2 34 190-224 49-82 (266)
No 1
>KOG2905 consensus Transcription initiation factor IIF, small subunit (RAP30) [Transcription]
Probab=100.00 E-value=1.1e-65 Score=442.78 Aligned_cols=217 Identities=37% Similarity=0.575 Sum_probs=191.2
Q ss_pred CCcccccCCCCCcEEEEeccHHHHHHHhcccCCCCCcceeEEEEEcCCCCCCCceEEEEeccc-------CCCCCCCCce
Q 026167 11 GKGNLDTAKADRSVWLMKCPLVVAKSWQNQASSQDSQPVAKVILSLDPLQSDSMQFTMETTAV-------SNDSLNRPKS 83 (242)
Q Consensus 11 ~~~~Ld~~~a~~~vWLvKVPk~L~e~W~~~~~~~~~~~lG~iri~~~~~~~~~~~~~l~l~~~-------~~~~~~~Pke 83 (242)
+.++||.++++++|||||||+||+++|..++.+. ++|+++|.+.++. .+ +.|.|++. ..+.+.+|..
T Consensus 7 ~~~dl~l~~~~~~vWLvKvP~fLa~kw~~~~~~~---e~g~l~i~k~~~d-ak--i~l~L~e~~p~~~~~~a~~g~~p~~ 80 (254)
T KOG2905|consen 7 ESLDLDLENSGRGVWLVKVPKFLAEKWRKIPNSH---ESGKLRINKTPSD-AK--IVLLLNEAIPEKQEREADVGKFPQQ 80 (254)
T ss_pred hhhhhccccccceEEEEeccHHHHHHHHhccccc---ccccccccCCCCc-ce--EEEEeccccccchhhhhhcccCchh
Confidence 6789999999999999999999999999777533 7999999977542 34 44444421 1346789999
Q ss_pred eeeccccCCcceEEEEecC-CCceeEEEEEeeEeEEeecCCChHHHHHHHHHHhhHhhcCCCceEEeccCCCcccccCCC
Q 026167 84 YSLNMFKDFVPMSVFSESN-QGKVAMEGKVEHKFDMKPHEKNMEEYGRLCRERTNKSMIKNRQIQVIDNDHGVHMRPMPG 162 (242)
Q Consensus 84 y~l~~~~~~~~~~VFse~~-~~~~~l~G~V~~e~~~~P~~~~n~~Y~~l~r~R~~~a~~p~R~vq~ld~~~~~~~~p~~~ 162 (242)
|.+++...+.|+||||+++ +++++++|+|+|+|+|+|+ .|++|++++++|+.+++.|+|+||+||+++|++|+|++|
T Consensus 81 ~~~~~~~~~~~~~~~sd~~~~~k~a~eG~V~~e~~~~P~--~ne~Y~Rl~r~r~~k~~~k~r~vQ~iD~~~g~~~~p~~~ 158 (254)
T KOG2905|consen 81 YKLNMKRRFFNMFVESDSSGPKKTAVEGTVVHECDVRPS--ANEEYMRLKRERIVKASKKKRQVQVIDKVVGVHMKPVPG 158 (254)
T ss_pred hhhccCccccceeeeecCCCCccceeeeeeeeeeecccc--cCHHHHHHHHHHHHHhcCcccccccchhhcccccccCCC
Confidence 9999999999999999998 7899999999999999999 569999999999999999999999999999999999999
Q ss_pred cccccccCcccccccccccccccccccCChhHHHHHHHHhhhhCCCcchHHHHHhcCCcHHHHHHHHHHhhHhhcCC
Q 026167 163 MVGLISSNSKDKKKAQPVKQTEVKRTRRDRGELEDIMFKLFERQPNWALKQLVQETDQPAVWFLIFLIPLHHINLRC 239 (242)
Q Consensus 163 ~~~~~~~~~~~~k~~~~~kk~e~K~~Rm~k~eLld~LF~lFe~~~yWslK~L~~~t~QPe~yLKEiL~eIa~lnk~G 239 (242)
|...++..+++++| .++++|++|+||+||+|+||+|||+|+||+||+|+++|+||++||||||++||+||++|
T Consensus 159 ~~~~~~~~~~~rkK----~k~e~Kr~R~dk~evld~lFk~FEk~~ywtlK~Lv~~t~QP~~fLKEiL~~icv~NkKg 231 (254)
T KOG2905|consen 159 HLRSSSNIAYERKK----AKEEGKRTRRDKNEVLDMLFKAFEKYQYWTLKDLVEITKQPEAFLKEILKDICVLNKKG 231 (254)
T ss_pred cccccchhHHHHHh----hhhccccccccHHHHHHHHHHHhhcCccccHHHHHHHhcCHHHHHHHHHHHHHHHhccC
Confidence 97544444465431 47899999999999999999999999999999999999999999999999999999999
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=1.2e-63 Score=447.88 Aligned_cols=217 Identities=37% Similarity=0.557 Sum_probs=118.5
Q ss_pred CcccccCCCCCcEEEEeccHHHHHHHhcccCCCCCcceeEEEEEcCCCCCCCceEEEEecccCCCCCCCCceeeeccccC
Q 026167 12 KGNLDTAKADRSVWLMKCPLVVAKSWQNQASSQDSQPVAKVILSLDPLQSDSMQFTMETTAVSNDSLNRPKSYSLNMFKD 91 (242)
Q Consensus 12 ~~~Ld~~~a~~~vWLvKVPk~L~e~W~~~~~~~~~~~lG~iri~~~~~~~~~~~~~l~l~~~~~~~~~~Pkey~l~~~~~ 91 (242)
+++||+++|+++|||||||+|||++|++..+ +++++||+|+|+.+++++ .+++|.|+.....++.+|++|+|+|++.
T Consensus 1 ~~~LD~s~a~~~vWLvKVPk~l~e~W~~~~~-~~~~~iG~lri~~~~~~~--~~v~l~L~~~~~~~~~iPkey~L~~~~~ 77 (275)
T PF02270_consen 1 DGDLDTSKADRSVWLVKVPKFLSEKWSKAPD-DDEIEIGKLRISKDPNGK--PKVSLTLNDSLANHGNIPKEYDLDMSKD 77 (275)
T ss_dssp -TBEE-HHHHTEEEEEEEEHHHHHHHTTSBT-T--TEEEEEEEEEE-TTE--EEEEEEE-HHHHT-T-S--EEEEEEE--
T ss_pred Ccccccccccccccccccccccccccccccc-cccccccccccccccccc--cccccccccccccccccccccccccccc
Confidence 4799999999999999999999999996654 367899999999884433 3555555554345578999999999988
Q ss_pred C-cceEEEEecCC-------------------------------------------CceeEEEEEeeEeEEeecCCChHH
Q 026167 92 F-VPMSVFSESNQ-------------------------------------------GKVAMEGKVEHKFDMKPHEKNMEE 127 (242)
Q Consensus 92 ~-~~~~VFse~~~-------------------------------------------~~~~l~G~V~~e~~~~P~~~~n~~ 127 (242)
. +|+|||||.+. ++++|+|+|.|+|+|+|+ .+++
T Consensus 78 ~~~n~~VFse~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~l~G~I~~~~~~~P~--~~~~ 155 (275)
T PF02270_consen 78 NVQNMYVFSESDQPGFKAKNKERAGAPNAGIPASLLREKKKKDRKRKYQPYVKTIPKKTALEGRIVHECDCRPV--LNDE 155 (275)
T ss_dssp TTEEEEEEEEETT----------------------------------------ETT--EEEEEEEEEEEEE---------
T ss_pred cccccccccccccccccccccccccccccccccccccccccccccccccccccCCCCceEEEEEEEEEEEeEEC--CCHH
Confidence 7 69999999864 589999999999999999 4689
Q ss_pred HHHHHHHHhhHhhcCCCceEEeccCCCcccccCCCcccccccCcccccccccccccccccccCChhHHHHHHHHhhhhCC
Q 026167 128 YGRLCRERTNKSMIKNRQIQVIDNDHGVHMRPMPGMVGLISSNSKDKKKAQPVKQTEVKRTRRDRGELEDIMFKLFERQP 207 (242)
Q Consensus 128 Y~~l~r~R~~~a~~p~R~vq~ld~~~~~~~~p~~~~~~~~~~~~~~~k~~~~~kk~e~K~~Rm~k~eLld~LF~lFe~~~ 207 (242)
|++++++|+.++++|+|++++|++.+...+.|++.+...... |. .++|++++|++|||+++|+|+||+|||+|+
T Consensus 156 Y~~~~~~r~~~a~~~kr~~~~i~~~~~~~~~~~~~~~~~~~~--~~----~~~k~~~~K~~R~~~~eL~d~lF~~Fe~~~ 229 (275)
T PF02270_consen 156 YRRLKRERIEKANKPKRTVQQIDEDVSQSYKPVSFHSANSKF--FI----KKKKKQEEKRARMDKNELLDLLFKLFEKHQ 229 (275)
T ss_dssp ------------------------------------------------------------THHHHHHHHHHHHHHHHH-S
T ss_pred HHHHHHHHHHHhcCCCCeeEEeccccccCCCCcccccccchh--cc----cccccccccceeCCHHHHHHHHHHHHHhCC
Confidence 999999999999999999999998655567764433211110 22 123778999999999999999999999999
Q ss_pred CcchHHHHHhcCCcHHHHHHHHHHhhHhhcCC
Q 026167 208 NWALKQLVQETDQPAVWFLIFLIPLHHINLRC 239 (242)
Q Consensus 208 yWslK~L~~~t~QPe~yLKEiL~eIa~lnk~G 239 (242)
||+||+|+++|+||++||||||++||+||++|
T Consensus 230 ywslK~L~~~t~QP~~yLKeiL~eIa~~~k~g 261 (275)
T PF02270_consen 230 YWSLKDLRQRTQQPEAYLKEILEEIAVLNKRG 261 (275)
T ss_dssp -B-HHHHHHH--S-HHHHHHHHHHH--EE--T
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHhccC
Confidence 99999999999999999999999999999999
No 3
>COG5090 TFG2 Transcription initiation factor IIF, small subunit (RAP30) [Transcription]
Probab=100.00 E-value=9.2e-56 Score=379.69 Aligned_cols=217 Identities=28% Similarity=0.376 Sum_probs=182.6
Q ss_pred CCcccccCCCCCcEEEEeccHHHHHHHhcccCCCCCcceeEEEEEcCCCCCCCceEEEEecccCCCCCCCCceeeecccc
Q 026167 11 GKGNLDTAKADRSVWLMKCPLVVAKSWQNQASSQDSQPVAKVILSLDPLQSDSMQFTMETTAVSNDSLNRPKSYSLNMFK 90 (242)
Q Consensus 11 ~~~~Ld~~~a~~~vWLvKVPk~L~e~W~~~~~~~~~~~lG~iri~~~~~~~~~~~~~l~l~~~~~~~~~~Pkey~l~~~~ 90 (242)
++.|||+.+.+++|||||||.||+++|.+... +.|..+|++|+..+|. .++|.|.. ..+.+.+|++|+|.+.+
T Consensus 18 d~~dLdl~~~~~kVWLvkvP~FLaekw~sr~~-~~g~~lg~~r~~~d~a-----~isLlL~n-e~~n~~~P~~ydl~i~~ 90 (297)
T COG5090 18 DDADLDLNNRHTKVWLVKVPLFLAEKWLSREA-EIGELLGTKRTSTDPA-----VISLLLSN-EFCNGGFPSSYDLKIKP 90 (297)
T ss_pred ccccccccccCceEEEEeccHHHHHHHhcchh-hhhhhhceeeecCCcc-----eEEEEecc-CCccCCCCcceeeeecc
Confidence 45599999999999999999999999986654 4577899999987642 45555533 26788999999999988
Q ss_pred CCc-ceEEEEecC----CCceeEEEEEeeEeEEeecCCChHHHHHHHHHHhhHhhcCCCceEEeccCCCcccccCCCccc
Q 026167 91 DFV-PMSVFSESN----QGKVAMEGKVEHKFDMKPHEKNMEEYGRLCRERTNKSMIKNRQIQVIDNDHGVHMRPMPGMVG 165 (242)
Q Consensus 91 ~~~-~~~VFse~~----~~~~~l~G~V~~e~~~~P~~~~n~~Y~~l~r~R~~~a~~p~R~vq~ld~~~~~~~~p~~~~~~ 165 (242)
.++ |.|||.|+. .+.|+|+|+|.|+|.+.|. .|++|+++++.|..++..|++.||+||...|+.+.| +..+
T Consensus 91 k~v~n~yVfre~et~t~~k~tavvGtV~hEC~V~P~--vNd~Y~r~~q~r~~~~~~~K~~vq~iD~~~g~~~~~--~~~s 166 (297)
T COG5090 91 KDVNNYYVFRESETSTHEKNTAVVGTVNHECYVTPE--VNDEYLRYKQDRGFKSDSKKSDVQVIDYLKGGKRGE--KFGS 166 (297)
T ss_pred ccccceEEEecccccccccccceeeeeccceeeccc--ccHHHHHHHHHhhhhhcCccccceeeecccCceecc--Cccc
Confidence 877 689996643 5799999999999999999 568999999999999999999999999888877664 3223
Q ss_pred ccccCc-ccccccccccccccccccCChhHHHHHHHHhhhhCCCcchHHHHHhcCCcHHHHHHHHHHhhHhhcCC
Q 026167 166 LISSNS-KDKKKAQPVKQTEVKRTRRDRGELEDIMFKLFERQPNWALKQLVQETDQPAVWFLIFLIPLHHINLRC 239 (242)
Q Consensus 166 ~~~~~~-~~~k~~~~~kk~e~K~~Rm~k~eLld~LF~lFe~~~yWslK~L~~~t~QPe~yLKEiL~eIa~lnk~G 239 (242)
+.+++. |.++ ..++.+...|+.|||++||+|+||+|||+|+||+||+|+++++||++||||||++||+|||+|
T Consensus 167 ~Rs~~~~fl~~-~r~k~~~~~K~~RlpknEvlD~lFK~Fe~Y~yWtlKgL~e~~~QPea~lkEild~iavLnKkg 240 (297)
T COG5090 167 LRSSTLEFLAR-KRKKMLMDKKRERLPKNEVLDMLFKAFEKYPYWTLKGLAEFCGQPEAFLKEILDDIAVLNKKG 240 (297)
T ss_pred cccchHHHHHh-cchhhhcchhhcccchhHHHHHHHHHhhcCCchhhhhHHHHhcChHHHHHHHHHHHHhhhccC
Confidence 333333 6543 333346778999999999999999999999999999999999999999999999999999999
No 4
>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=83.22 E-value=5.4 Score=31.93 Aligned_cols=60 Identities=17% Similarity=0.289 Sum_probs=36.2
Q ss_pred cceeEEEEEcCCCCCCCceEEEEecccCCCCCCCCceeeeccccC--C-cceEEEE-ecCCCceeEEEEEeeEeEEeec
Q 026167 47 QPVAKVILSLDPLQSDSMQFTMETTAVSNDSLNRPKSYSLNMFKD--F-VPMSVFS-ESNQGKVAMEGKVEHKFDMKPH 121 (242)
Q Consensus 47 ~~lG~iri~~~~~~~~~~~~~l~l~~~~~~~~~~Pkey~l~~~~~--~-~~~~VFs-e~~~~~~~l~G~V~~e~~~~P~ 121 (242)
..||+|+|.++ | +++|.+-+ -.|++..... + +...+.. +...+.....|.|.+++.|.|.
T Consensus 67 G~iGkL~V~kS-G-----kv~l~iG~---------~~~dV~~G~~~~FlQevv~i~~~~~~~~~~~LG~v~~k~v~tPd 130 (131)
T PF05132_consen 67 GQIGKLRVHKS-G-----KVTLKIGG---------VVFDVSPGTQCSFLQEVVAIDEEEEEGECYFLGQVSGKFVVTPD 130 (131)
T ss_pred CeeEEEEEEeC-C-----cEEEEECC---------EEEEecCCCCCCchheEEEeeccCCCCeEEEeccccceEEEccC
Confidence 47999999964 2 34444332 2244433222 1 1222222 2356889999999999999995
No 5
>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=82.20 E-value=1.6 Score=39.89 Aligned_cols=50 Identities=20% Similarity=0.149 Sum_probs=44.0
Q ss_pred CChhHHHHHHHHhhhhCCCcchHHHHHhcCC--cHHHHHHHHHHhhHhhcCC
Q 026167 190 RDRGELEDIMFKLFERQPNWALKQLVQETDQ--PAVWFLIFLIPLHHINLRC 239 (242)
Q Consensus 190 m~k~eLld~LF~lFe~~~yWslK~L~~~t~Q--Pe~yLKEiL~eIa~lnk~G 239 (242)
-.-.+++..|=+|||+.+-|+-++|...+.. -..+||.+|--+|=+=+.|
T Consensus 231 ~~~~~~~~~l~~lFeeRPIW~r~~L~~~~~~~~~~~~~k~~l~~v~Y~f~~G 282 (310)
T PF09734_consen 231 PVLQELIQELKKLFEERPIWTRRALLNHLPKSGSQSKLKRALPYVAYYFKNG 282 (310)
T ss_pred hhHHHHHHHHHHHHhcCCccCHHHHHHhhhhcccHHHHHHHHHhhEEEEecC
Confidence 3447889999999999999999999999999 5889999999998776665
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=79.03 E-value=2.7 Score=40.10 Aligned_cols=47 Identities=19% Similarity=0.210 Sum_probs=41.9
Q ss_pred HHHHHHHHhhhhCCCcchHHHHHhcCCcHHHHHHHHHHhhHhh--cCCC
Q 026167 194 ELEDIMFKLFERQPNWALKQLVQETDQPAVWFLIFLIPLHHIN--LRCF 240 (242)
Q Consensus 194 eLld~LF~lFe~~~yWslK~L~~~t~QPe~yLKEiL~eIa~ln--k~G~ 240 (242)
-..|.|--+|.++.+=+-++|...|+-|..=+||||++||+++ .+|.
T Consensus 337 ~aRD~iL~~F~~~~~v~r~~l~~~~~l~~~~~~eiL~~~a~~~~~~~~W 385 (421)
T PF04801_consen 337 RARDYILLLFTKSRYVKRKELMSATKLPPEDVKEILKEIAVLRPSNRGW 385 (421)
T ss_pred hhHHHHHHHhcCCCceeHHHhhhhcCCCHHHHHHHHHHHhhccCCCCce
Confidence 3457888899999999999999999999999999999999999 5554
No 7
>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=78.28 E-value=24 Score=29.55 Aligned_cols=42 Identities=17% Similarity=0.325 Sum_probs=30.4
Q ss_pred ceEEEEecCC-CceeEEEEEeeEeEEeecCCChHHHHHHHHHH
Q 026167 94 PMSVFSESNQ-GKVAMEGKVEHKFDMKPHEKNMEEYGRLCRER 135 (242)
Q Consensus 94 ~~~VFse~~~-~~~~l~G~V~~e~~~~P~~~~n~~Y~~l~r~R 135 (242)
..|+|..... +-+...|.|.+++.++|...++...+++-...
T Consensus 99 ~~~L~~~~~~~~~l~~~~~i~~~l~~rP~s~~s~thr~l~~~~ 141 (171)
T PF04004_consen 99 HNYLFVRHGSSGVLQGQGHITKKLTFRPASTDSATHRRLTQAV 141 (171)
T ss_pred cceEEEEcCCcceEEEEEEecccEEEecCCccCHHHHHHHHHH
Confidence 4788887753 67889999999999999865444555554333
No 8
>KOG2428 consensus Uncharacterized conserved protein [Function unknown]
Probab=68.56 E-value=24 Score=34.09 Aligned_cols=47 Identities=15% Similarity=0.318 Sum_probs=33.7
Q ss_pred EEEEecCCCceeEEEEEeeEeEEeecCCChHHHHHHHHHHhhHhhcCC
Q 026167 96 SVFSESNQGKVAMEGKVEHKFDMKPHEKNMEEYGRLCRERTNKSMIKN 143 (242)
Q Consensus 96 ~VFse~~~~~~~l~G~V~~e~~~~P~~~~n~~Y~~l~r~R~~~a~~p~ 143 (242)
+.|-.. ..-+.-.|.|.+++..+|++.+..-+++|.+.++....++.
T Consensus 243 hl~vrq-~t~l~~Q~~ik~kltFrP~S~~S~tHrklt~~~a~r~~k~s 289 (443)
T KOG2428|consen 243 HLFVRQ-GTGLQGQAVIKKKLTFRPHSTDSATHRKLTLNRADRSQKTS 289 (443)
T ss_pred eeEEec-ccccchhheeeceeEeeccccchHHHHHHHHHHhhcccccc
Confidence 445544 23445567999999999998777778998888877554433
No 9
>KOG3122 consensus DNA-directed RNA polymerase III subunit [Transcription]
Probab=68.14 E-value=11 Score=34.76 Aligned_cols=61 Identities=20% Similarity=0.266 Sum_probs=40.2
Q ss_pred CcceeEEEEEcCCCCCCCceEEEEecccCCCCCCCCceeeeccccC---Cc-ceEEEEec-CCCceeEEEEEeeEeEEee
Q 026167 46 SQPVAKVILSLDPLQSDSMQFTMETTAVSNDSLNRPKSYSLNMFKD---FV-PMSVFSES-NQGKVAMEGKVEHKFDMKP 120 (242)
Q Consensus 46 ~~~lG~iri~~~~~~~~~~~~~l~l~~~~~~~~~~Pkey~l~~~~~---~~-~~~VFse~-~~~~~~l~G~V~~e~~~~P 120 (242)
+.+||+|+|.+. | +++|.|-+ --|++.|... .+ .++|=... .++...+.|.|.|++.|.|
T Consensus 244 eGqvGkllV~KS-G-----rVkLklG~---------V~fDV~~G~~~~FLQEl~sV~l~d~rs~nm~~LG~v~~klvvTP 308 (310)
T KOG3122|consen 244 EGQVGKLLVYKS-G-----RVKLKLGD---------VLFDVSMGLDCSFLQELMSVGLGDSRSGNMTLLGSVKKKLVVTP 308 (310)
T ss_pred cCcceeEEEEec-C-----ceEEEecC---------EEEEeccCchhHhhhhhheeecccccCCceEEeccccceeeeCC
Confidence 458999999964 2 34454432 2256665433 12 34443332 5789999999999999999
Q ss_pred c
Q 026167 121 H 121 (242)
Q Consensus 121 ~ 121 (242)
.
T Consensus 309 D 309 (310)
T KOG3122|consen 309 D 309 (310)
T ss_pred C
Confidence 6
No 10
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=64.78 E-value=12 Score=31.14 Aligned_cols=42 Identities=7% Similarity=0.080 Sum_probs=34.4
Q ss_pred hhHHHHHHHHhhhh-CCCcchHHHHHhcCCcHHHHHHHHHHhh
Q 026167 192 RGELEDIMFKLFER-QPNWALKQLVQETDQPAVWFLIFLIPLH 233 (242)
Q Consensus 192 k~eLld~LF~lFe~-~~yWslK~L~~~t~QPe~yLKEiL~eIa 233 (242)
+=.|.-+++=+|.. .+.|++++|.++++-|..||..||....
T Consensus 8 ~yAl~~l~~lA~~~~~~~vs~~eIA~~~~ip~~~l~kIl~~L~ 50 (164)
T PRK10857 8 RYAVTAMLDVALNSEAGPVPLADISERQGISLSYLEQLFSRLR 50 (164)
T ss_pred HHHHHHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHH
Confidence 34566777777764 4689999999999999999999998754
No 11
>PF13817 DDE_Tnp_IS66_C: IS66 C-terminal element
Probab=64.58 E-value=4.5 Score=25.85 Aligned_cols=15 Identities=13% Similarity=0.237 Sum_probs=13.9
Q ss_pred CcHHHHHHHHHHhhH
Q 026167 220 QPAVWFLIFLIPLHH 234 (242)
Q Consensus 220 QPe~yLKEiL~eIa~ 234 (242)
.|.+||+.||+.|+.
T Consensus 12 ~P~~yL~~vL~~i~~ 26 (39)
T PF13817_consen 12 NPYAYLTDVLERIPN 26 (39)
T ss_pred CHHHHHHHHHHHHcc
Confidence 499999999999987
No 12
>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=59.99 E-value=22 Score=25.75 Aligned_cols=27 Identities=11% Similarity=0.144 Sum_probs=22.9
Q ss_pred CcchHHHHHhcCCcHHHHHHHHHHhhH
Q 026167 208 NWALKQLVQETDQPAVWFLIFLIPLHH 234 (242)
Q Consensus 208 yWslK~L~~~t~QPe~yLKEiL~eIa~ 234 (242)
.+++++|.++++-|..||..+|.....
T Consensus 25 ~~s~~eiA~~~~i~~~~l~kil~~L~~ 51 (83)
T PF02082_consen 25 PVSSKEIAERLGISPSYLRKILQKLKK 51 (83)
T ss_dssp -BEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHhh
Confidence 499999999999999999999987653
No 13
>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=59.34 E-value=19 Score=28.68 Aligned_cols=40 Identities=5% Similarity=0.086 Sum_probs=32.5
Q ss_pred HHHHHHHHhhhh-CCCcchHHHHHhcCCcHHHHHHHHHHhh
Q 026167 194 ELEDIMFKLFER-QPNWALKQLVQETDQPAVWFLIFLIPLH 233 (242)
Q Consensus 194 eLld~LF~lFe~-~~yWslK~L~~~t~QPe~yLKEiL~eIa 233 (242)
.|.-+++=++.. .+.|+.++|.++++-|..||..||....
T Consensus 10 Al~~l~~La~~~~~~~~s~~~ia~~~~ip~~~l~kil~~L~ 50 (135)
T TIGR02010 10 AVTAMLDLALNAETGPVTLADISERQGISLSYLEQLFAKLR 50 (135)
T ss_pred HHHHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHH
Confidence 455666767643 4589999999999999999999998764
No 14
>PF13565 HTH_32: Homeodomain-like domain
Probab=51.82 E-value=14 Score=25.88 Aligned_cols=29 Identities=17% Similarity=0.505 Sum_probs=25.5
Q ss_pred hhHHHHHHHHhhhhCCCcchHHHHHhcCC
Q 026167 192 RGELEDIMFKLFERQPNWALKQLVQETDQ 220 (242)
Q Consensus 192 k~eLld~LF~lFe~~~yWslK~L~~~t~Q 220 (242)
-.++.+.|.+++.+++.|+.+.|.+.+.+
T Consensus 32 ~~e~~~~i~~~~~~~p~wt~~~i~~~L~~ 60 (77)
T PF13565_consen 32 DPEQRERIIALIEEHPRWTPREIAEYLEE 60 (77)
T ss_pred cHHHHHHHHHHHHhCCCCCHHHHHHHHHH
Confidence 57788999999999999999999987653
No 15
>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=50.65 E-value=24 Score=26.47 Aligned_cols=39 Identities=26% Similarity=0.408 Sum_probs=27.0
Q ss_pred ChhHHHHHHHHhhhhCCCcchHHHHHhcCCcHHHHHH-HHH
Q 026167 191 DRGELEDIMFKLFERQPNWALKQLVQETDQPAVWFLI-FLI 230 (242)
Q Consensus 191 ~k~eLld~LF~lFe~~~yWslK~L~~~t~QPe~yLKE-iL~ 230 (242)
++.++..++-.. ....+|+|++|+.+|.--..||++ ||.
T Consensus 7 ~k~ey~el~~~~-~~~~~W~~~dl~k~~~~s~~wi~~~il~ 46 (91)
T PF05595_consen 7 DKEEYEELKKKD-LEGKWWDMKDLRKRTGKSREWIKENILY 46 (91)
T ss_pred eHHHHHHHHHHh-hccceeeHHHHHHHHCCCHHHHHHHccc
Confidence 444555544333 455679999999999988899974 444
No 16
>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=50.08 E-value=33 Score=22.46 Aligned_cols=37 Identities=11% Similarity=0.145 Sum_probs=29.1
Q ss_pred HHHHhhhhCCC-cchHHHHHhcCCcHHHHHHHHHHhhH
Q 026167 198 IMFKLFERQPN-WALKQLVQETDQPAVWFLIFLIPLHH 234 (242)
Q Consensus 198 ~LF~lFe~~~y-WslK~L~~~t~QPe~yLKEiL~eIa~ 234 (242)
.|+.+|.+++- |++.+|.++++=|-+-+--+|...+.
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 99999999999999987777766543
No 17
>PF08208 RNA_polI_A34: DNA-directed RNA polymerase I subunit RPA34.5; InterPro: IPR013240 This is a family of proteins conserved from yeasts to human. Subunit A34.5 of RNA polymerase I is a non-essential subunit which is thought to help Pol I overcome topological constraints imposed on ribosomal DNA during the process of transcription [].; PDB: 3NFG_N.
Probab=37.54 E-value=11 Score=32.15 Aligned_cols=15 Identities=27% Similarity=0.771 Sum_probs=11.9
Q ss_pred CCCcEEEEeccHHHH
Q 026167 20 ADRSVWLMKCPLVVA 34 (242)
Q Consensus 20 a~~~vWLvKVPk~L~ 34 (242)
.+.+|||+++|..|-
T Consensus 3 ~~kelWlI~~P~~~~ 17 (198)
T PF08208_consen 3 DGKELWLIKAPASFP 17 (198)
T ss_dssp TTEEEEEEEEETTS-
T ss_pred CCCEEEEEeCCCCCC
Confidence 467899999998763
No 18
>PRK14741 spoVM stage V sporulation protein M; Provisional
Probab=31.21 E-value=41 Score=19.43 Aligned_cols=14 Identities=14% Similarity=0.228 Sum_probs=10.8
Q ss_pred EEEEeccHHHHHHH
Q 026167 24 VWLMKCPLVVAKSW 37 (242)
Q Consensus 24 vWLvKVPk~L~e~W 37 (242)
.|-+|+|+||.---
T Consensus 3 fytiklpkflgg~v 16 (26)
T PRK14741 3 FYTIKLPKFLGGIV 16 (26)
T ss_pred eEEEeccHHHHHHH
Confidence 57799999997543
No 19
>KOG2473 consensus RNA polymerase III transcription factor (TF)IIIC subunit [Transcription]
Probab=30.58 E-value=90 Score=30.64 Aligned_cols=49 Identities=20% Similarity=0.195 Sum_probs=41.4
Q ss_pred ChhHHHHHHHHhhhhCCCcchHHHHH-hcCCcHHHHHHHHHHhhHhhcCC
Q 026167 191 DRGELEDIMFKLFERQPNWALKQLVQ-ETDQPAVWFLIFLIPLHHINLRC 239 (242)
Q Consensus 191 ~k~eLld~LF~lFe~~~yWslK~L~~-~t~QPe~yLKEiL~eIa~lnk~G 239 (242)
.-+|++-.|=.||++.+-|+-+.|.. .++==.-+||-+|--||-|--+|
T Consensus 229 ~~~e~~~~l~eLF~~RPIWtR~al~~~~~~~~~h~LK~~Lp~~AYyfssG 278 (484)
T KOG2473|consen 229 SLEEVLRSLRELFEERPIWTRRALLYKELGCTHHKLKRFLPLIAYYFSSG 278 (484)
T ss_pred hhHHHHHHHHHHHHhCchhhHHhHhhcccCccHHHHHHHHHHHHHHhccC
Confidence 34567777778999999999999999 66666789999999999987776
No 20
>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=30.00 E-value=1e+02 Score=30.08 Aligned_cols=55 Identities=16% Similarity=0.178 Sum_probs=46.8
Q ss_pred ccccCChhHHHHHHHHhhh--hCCCcchHHHHHhc-CCcHHHHHHHHHHhhHhhcCCC
Q 026167 186 KRTRRDRGELEDIMFKLFE--RQPNWALKQLVQET-DQPAVWFLIFLIPLHHINLRCF 240 (242)
Q Consensus 186 K~~Rm~k~eLld~LF~lFe--~~~yWslK~L~~~t-~QPe~yLKEiL~eIa~lnk~G~ 240 (242)
|..=.-++-|.-.+|.+|. ...--.+.+|.... .|.+.=+|.-|++.|.|.|.|-
T Consensus 234 ~~t~~~knrL~~~iyRlf~~~~~~ri~~~di~~~Fp~~se~~iRkrLKe~~~~~R~g~ 291 (457)
T PF12157_consen 234 KVTNFSKNRLKMIIYRLFNKSQPRRIKVDDIKKHFPDQSESQIRKRLKEFADFQRTGD 291 (457)
T ss_pred hHHHHHHHHHHHHHHHHHhhccCCccCHHHHHHhCCCCcHHHHHHHHHHHHhccCCCC
Confidence 4455677889999999998 44469999999885 7899999999999999999984
No 21
>PHA02571 a-gt.4 hypothetical protein; Provisional
Probab=29.77 E-value=34 Score=26.86 Aligned_cols=37 Identities=22% Similarity=0.248 Sum_probs=25.8
Q ss_pred hHHHHHHHHhhhhCCCcchHHHHHhcCCcHHHHHHHHHH
Q 026167 193 GELEDIMFKLFERQPNWALKQLVQETDQPAVWFLIFLIP 231 (242)
Q Consensus 193 ~eLld~LF~lFe~~~yWslK~L~~~t~QPe~yLKEiL~e 231 (242)
..-...||.+=...=-|.|+-||.+++|| |-.|+|+-
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 44556677763332237999999999999 77776653
No 22
>PF14493 HTH_40: Helix-turn-helix domain
Probab=28.16 E-value=65 Score=23.70 Aligned_cols=34 Identities=9% Similarity=-0.034 Sum_probs=26.9
Q ss_pred CChhHHHHHHHHhhhhCCCcchHHHHHhcCCcHHH
Q 026167 190 RDRGELEDIMFKLFERQPNWALKQLVQETDQPAVW 224 (242)
Q Consensus 190 m~k~eLld~LF~lFe~~~yWslK~L~~~t~QPe~y 224 (242)
.+++ ..+.|-.+|+++.+|+||.|++..+-=..|
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 4444 588899999999999999999988753444
No 23
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=26.26 E-value=2e+02 Score=19.97 Aligned_cols=41 Identities=17% Similarity=0.201 Sum_probs=34.3
Q ss_pred ChhHHHHHHHHhhhhCCC--cchHHHHHhcCCcHHHHHHHHHH
Q 026167 191 DRGELEDIMFKLFERQPN--WALKQLVQETDQPAVWFLIFLIP 231 (242)
Q Consensus 191 ~k~eLld~LF~lFe~~~y--WslK~L~~~t~QPe~yLKEiL~e 231 (242)
+.+.+.+.|..++.++.- .+.++|...++.|-.=+..+|..
T Consensus 3 ~~~~~~~~IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~ 45 (68)
T smart00550 3 TQDSLEEKILEFLENSGDETSTALQLAKNLGLPKKEVNRVLYS 45 (68)
T ss_pred CchHHHHHHHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHH
Confidence 456788899999999987 99999999999999866666654
No 24
>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=25.46 E-value=1.8e+02 Score=18.27 Aligned_cols=37 Identities=14% Similarity=0.192 Sum_probs=29.0
Q ss_pred HHHHHhhhhCCCcchHHHHHhcCCcHHHHHHHHHHhh
Q 026167 197 DIMFKLFERQPNWALKQLVQETDQPAVWFLIFLIPLH 233 (242)
Q Consensus 197 d~LF~lFe~~~yWslK~L~~~t~QPe~yLKEiL~eIa 233 (242)
-.|+.+..+++.-|.++|.+.++=+...+...|++..
T Consensus 6 ~~Il~~l~~~~~~t~~ela~~~~is~~tv~~~l~~L~ 42 (48)
T PF13412_consen 6 RKILNYLRENPRITQKELAEKLGISRSTVNRYLKKLE 42 (48)
T ss_dssp HHHHHHHHHCTTS-HHHHHHHHTS-HHHHHHHHHHHH
T ss_pred HHHHHHHHHcCCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 3456666779999999999999999999988887754
No 25
>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=24.19 E-value=1e+02 Score=24.36 Aligned_cols=41 Identities=20% Similarity=0.289 Sum_probs=31.4
Q ss_pred hHHHHHHHHhhhhCC---CcchH---HHHHhcCCcHHHHHHHHHHhh
Q 026167 193 GELEDIMFKLFERQP---NWALK---QLVQETDQPAVWFLIFLIPLH 233 (242)
Q Consensus 193 ~eLld~LF~lFe~~~---yWslK---~L~~~t~QPe~yLKEiL~eIa 233 (242)
-+++..||.+|..+. .|+-. .|...+.|=..+|+.||.+..
T Consensus 24 ~emlqqif~lF~~~~ssa~W~~t~le~~l~~L~~Ql~~Le~Cl~~~~ 70 (117)
T smart00076 24 HEMLQQIFNIFSSPSSSAAWNETLLESLLNELHQQLNHLEACLKQEM 70 (117)
T ss_pred HHHHHHHHHHHcCCCCcccccHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 689999999999774 48754 455556777888999988755
No 26
>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=23.06 E-value=1.5e+02 Score=22.88 Aligned_cols=29 Identities=10% Similarity=0.180 Sum_probs=25.7
Q ss_pred CCCcchHHHHHhcCCcHHHHHHHHHHhhH
Q 026167 206 QPNWALKQLVQETDQPAVWFLIFLIPLHH 234 (242)
Q Consensus 206 ~~yWslK~L~~~t~QPe~yLKEiL~eIa~ 234 (242)
.+.++..+|.+.++-|..++..+|.....
T Consensus 23 ~~~~s~~eia~~~~i~~~~v~~il~~L~~ 51 (132)
T TIGR00738 23 EGPVSVKEIAERQGISRSYLEKILRTLRR 51 (132)
T ss_pred CCcCcHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 45899999999999999999999987653
No 27
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=22.58 E-value=2.4e+02 Score=20.81 Aligned_cols=42 Identities=0% Similarity=0.108 Sum_probs=29.7
Q ss_pred hhHHHHHHHHhhhhCC--CcchHHHHHhcCCcHHHHHHHHHHhh
Q 026167 192 RGELEDIMFKLFERQP--NWALKQLVQETDQPAVWFLIFLIPLH 233 (242)
Q Consensus 192 k~eLld~LF~lFe~~~--yWslK~L~~~t~QPe~yLKEiL~eIa 233 (242)
.++++..+...-+.+. .|++.+|.+.+.-...||..+..+..
T Consensus 3 ~~~~~~~~~~~i~~~~~~~~~~~~lA~~~~~S~~~l~r~f~~~~ 46 (107)
T PRK10219 3 HQKIIQTLIAWIDEHIDQPLNIDVVAKKSGYSKWYLQRMFRTVT 46 (107)
T ss_pred hHHHHHHHHHHHHHhcCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 3445555555555443 39999999999999988888877753
No 28
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=22.23 E-value=1.1e+02 Score=20.62 Aligned_cols=25 Identities=8% Similarity=0.052 Sum_probs=19.6
Q ss_pred cchHHHHHhcCCcHHHHHHHHHHhh
Q 026167 209 WALKQLVQETDQPAVWFLIFLIPLH 233 (242)
Q Consensus 209 WslK~L~~~t~QPe~yLKEiL~eIa 233 (242)
|++++|.+.+.-+..+|..++.+..
T Consensus 2 ~~~~~la~~~~~s~~~l~~~f~~~~ 26 (84)
T smart00342 2 LTLEDLAEALGMSPRHLQRLFKKET 26 (84)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHh
Confidence 7788888888888888888777654
No 29
>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=21.39 E-value=1.8e+02 Score=21.06 Aligned_cols=38 Identities=11% Similarity=0.054 Sum_probs=32.7
Q ss_pred hHHHHHHHHhhhhCCCcchHHHHHhcCCcHHHHHHHHH
Q 026167 193 GELEDIMFKLFERQPNWALKQLVQETDQPAVWFLIFLI 230 (242)
Q Consensus 193 ~eLld~LF~lFe~~~yWslK~L~~~t~QPe~yLKEiL~ 230 (242)
.+..-.+|.++...+-+|.+++.++++-|+.-++..+.
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 46677888888777889999999999999998888775
No 30
>PF14668 RICTOR_V: Rapamycin-insensitive companion of mTOR, domain 5
Probab=21.16 E-value=72 Score=23.09 Aligned_cols=24 Identities=17% Similarity=0.382 Sum_probs=21.2
Q ss_pred ChhHHHHHHHHhhhhCCCcchHHH
Q 026167 191 DRGELEDIMFKLFERQPNWALKQL 214 (242)
Q Consensus 191 ~k~eLld~LF~lFe~~~yWslK~L 214 (242)
+..++.+.|.++++..+.|++++-
T Consensus 25 ~~~~iv~~iv~~a~~s~v~siRGT 48 (73)
T PF14668_consen 25 DESDIVEDIVKIAENSPVLSIRGT 48 (73)
T ss_pred hhcCHHHHHHHHHHhCCccchHHH
Confidence 366899999999999999999963
No 31
>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=20.89 E-value=1e+02 Score=27.48 Aligned_cols=34 Identities=24% Similarity=0.366 Sum_probs=27.0
Q ss_pred CChhHHHHHHHHhhhhCCCcchHHHHHhcCCcHHH
Q 026167 190 RDRGELEDIMFKLFERQPNWALKQLVQETDQPAVW 224 (242)
Q Consensus 190 m~k~eLld~LF~lFe~~~yWslK~L~~~t~QPe~y 224 (242)
-...||||.|=.-|-+|. |+||.|...+=.-.+|
T Consensus 49 PshPeLLd~La~~F~~~g-~dlK~L~R~I~~S~tY 82 (266)
T PF07587_consen 49 PSHPELLDWLAAEFVEHG-WDLKHLIRLIVTSRTY 82 (266)
T ss_pred CCCHHHHHHHHHHHHHcC-CCHHHHHHHHHccHHH
Confidence 346899999999999965 9999998776544444
Done!