Query psy7983
Match_columns 184
No_of_seqs 119 out of 335
Neff 5.4
Searched_HMMs 46136
Date Fri Aug 16 23:49:44 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy7983.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/7983hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1897|consensus 100.0 7.8E-38 1.7E-42 302.0 13.4 106 73-184 991-1096(1096)
2 KOG1898|consensus 99.6 2.9E-16 6.2E-21 154.0 7.6 94 73-182 1108-1202(1205)
3 PF03178 CPSF_A: CPSF A subuni 99.6 3.6E-16 7.7E-21 135.5 3.9 69 73-142 252-321 (321)
4 KOG1896|consensus 99.6 1.4E-15 2.9E-20 150.8 8.1 100 73-183 1262-1362(1366)
5 COG5161 SFT1 Pre-mRNA cleavage 98.9 4.9E-09 1.1E-13 102.7 7.3 156 18-183 1144-1319(1319)
6 PHA02945 interferon resistance 83.9 0.87 1.9E-05 33.9 2.2 35 12-48 2-36 (88)
7 PF09288 UBA_3: Fungal ubiquit 70.7 9.9 0.00021 26.0 4.2 44 132-180 8-53 (55)
8 PF02023 SCAN: SCAN domain; I 61.8 18 0.00038 26.8 4.4 45 129-184 43-88 (95)
9 TIGR02276 beta_rpt_yvtn 40-res 49.6 15 0.00033 21.6 2.0 28 21-50 13-40 (42)
10 PF02978 SRP_SPB: Signal pepti 46.7 18 0.0004 27.2 2.5 29 144-183 72-100 (104)
11 PRK09706 transcriptional repre 45.1 26 0.00056 26.8 3.1 38 133-181 89-126 (135)
12 PF00536 SAM_1: SAM domain (St 34.9 64 0.0014 21.1 3.5 38 129-183 26-63 (64)
13 KOG3824|consensus 34.9 26 0.00056 32.5 1.9 88 18-136 289-380 (472)
14 cd07936 SCAN SCAN oligomerizat 31.3 1.1E+02 0.0023 22.2 4.3 42 129-181 42-84 (85)
15 PF04361 DUF494: Protein of un 30.8 61 0.0013 26.1 3.3 61 108-175 60-123 (155)
16 PF13543 KSR1-SAM: SAM like do 30.8 1.1E+02 0.0024 24.2 4.7 40 133-183 89-128 (129)
17 smart00435 TOPEUc DNA Topoisom 30.2 71 0.0015 29.8 4.0 70 51-120 135-228 (391)
18 COG3877 Uncharacterized protei 26.0 1.5E+02 0.0033 23.1 4.5 41 137-178 63-107 (122)
19 PF09124 Endonuc-dimeris: T4 r 24.8 2E+02 0.0043 19.5 4.4 38 134-176 7-44 (54)
20 PF11239 DUF3040: Protein of u 23.1 84 0.0018 22.3 2.5 22 85-106 2-23 (82)
21 COG0541 Ffh Signal recognition 23.1 81 0.0018 30.0 3.0 30 143-183 392-421 (451)
22 cd01207 Ena-Vasp Enabled-VASP- 23.0 3.1E+02 0.0068 21.0 5.8 73 28-103 13-109 (111)
23 PHA02955 hypothetical protein; 22.8 63 0.0014 27.8 2.1 25 134-158 68-92 (213)
24 KOG1702|consensus 22.6 36 0.00078 29.5 0.6 39 105-146 202-241 (264)
25 PF00325 Crp: Bacterial regula 22.1 1.5E+02 0.0032 17.9 3.1 24 148-182 5-28 (32)
No 1
>KOG1897|consensus
Probab=100.00 E-value=7.8e-38 Score=302.04 Aligned_cols=106 Identities=42% Similarity=0.713 Sum_probs=98.0
Q ss_pred ccceeeeEEEEEecChHHHHHHHHHHHHHHhhcCCCcCCCCcccceeecCCCCCCCcceeehhHHHHHhcCCHHHHHHHH
Q psy7983 73 SLNSFVSTGLVTQISPELYSFLFDLQERLAQTIRSVGRIEHSFWRSFNTDVKSDACEGFIDGDLIESFLDLNIKDMKSIA 152 (184)
Q Consensus 73 ~~Ts~GsIG~V~pIs~~~y~~L~~LQ~~L~~~v~~vGGl~h~~yRs~~~~~r~~p~kgfIDGDLIE~FL~L~~~~q~eV~ 152 (184)
|+|..|+||+|+.++++.|.||..||++|++.++++||++|.+||+|+.+.+.+|++|||||||||+|++|+++++.+|+
T Consensus 991 fgTv~GsIG~i~sl~~d~~~fL~~Lq~~irk~i~s~gglsH~~yrsf~~e~~~~P~~gfIDGDLiEsfl~l~~~~~~~i~ 1070 (1096)
T KOG1897|consen 991 FGTVNGSIGIIVSLPQDWYDFLEELQRRIRKVIKSVGGLSHMDYRSFEFEKRTSPVKGFIDGDLIESFLDLSRSKMREIV 1070 (1096)
T ss_pred EEEccceEEEEEecCcchhHHHHHHHHHHHHhhcccCCcchhhHhhhhcccccCCCcCcccchHHHhhhccCHHHHHHHH
Confidence 34444999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhcCCCCCCCCCCCCCCHHHHHHHHHHHhccC
Q psy7983 153 TGLQITPPGSTTKRDATVDDIIKIVEDLTRIH 184 (184)
Q Consensus 153 ~~l~~~~~~~~~~~~~svedI~k~IEeL~rlH 184 (184)
+++. ..++. .+++|+.|+||||+|||
T Consensus 1071 ~~~~-----~~~~~-~s~~el~k~vEel~rlh 1096 (1096)
T KOG1897|consen 1071 RGLE-----HTESL-ASVQELLKIVEELTRLH 1096 (1096)
T ss_pred hhcc-----ccccc-CCHHHHHHHHHHHHhcC
Confidence 9997 22222 79999999999999999
No 2
>KOG1898|consensus
Probab=99.64 E-value=2.9e-16 Score=154.01 Aligned_cols=94 Identities=26% Similarity=0.386 Sum_probs=89.4
Q ss_pred ccceeeeEEEEEec-ChHHHHHHHHHHHHHHhhcCCCcCCCCcccceeecCCCCCCCcceeehhHHHHHhcCCHHHHHHH
Q psy7983 73 SLNSFVSTGLVTQI-SPELYSFLFDLQERLAQTIRSVGRIEHSFWRSFNTDVKSDACEGFIDGDLIESFLDLNIKDMKSI 151 (184)
Q Consensus 73 ~~Ts~GsIG~V~pI-s~~~y~~L~~LQ~~L~~~v~~vGGl~h~~yRs~~~~~r~~p~kgfIDGDLIE~FL~L~~~~q~eV 151 (184)
+.|..|+||+++|+ +.+.++|+..+|..|++.-++++|.+|.+||+|++ |.|.+|||||||+|+.|+..+|++|
T Consensus 1108 y~tl~GtiG~f~p~~s~~d~~Ff~~~e~~~r~e~ppl~GrDH~~yRsyy~-----Pvk~VIDGDlceqF~~L~~~~Qe~v 1182 (1205)
T KOG1898|consen 1108 YTTLLGTIGVFAPFLSREDVDFFQHLEMHMRKEYPPLLGRDHLEYRSYYA-----PVKKVIDGDLCEQFLRLEENQQEEV 1182 (1205)
T ss_pred eeeccccceEEeecccccchHHHHHHHHhccccCCcccCcchhhhhhhcc-----chhhcccHHHHHHHhhCCHHHHHHH
Confidence 78999999999999 55699999999999999999999999999999998 6899999999999999999999999
Q ss_pred HhhcCCCCCCCCCCCCCCHHHHHHHHHHHhc
Q psy7983 152 ATGLQITPPGSTTKRDATVDDIIKIVEDLTR 182 (184)
Q Consensus 152 ~~~l~~~~~~~~~~~~~svedI~k~IEeL~r 182 (184)
++.++ .+++||.|+||+++.
T Consensus 1183 a~el~-----------~ti~eI~kkledir~ 1202 (1205)
T KOG1898|consen 1183 AEELD-----------RTIEEISKKLEDIRT 1202 (1205)
T ss_pred Hhccc-----------CCHHHHHHHHHHHHh
Confidence 99997 799999999999873
No 3
>PF03178 CPSF_A: CPSF A subunit region; InterPro: IPR004871 This family includes a region that lies towards the C terminus of the cleavage and polyadenylation specificity factor (CPSF) A (160 kDa) subunit. CPSF is involved in mRNA polyadenylation and binds the AAUAAA conserved sequence in pre-mRNA. CPSF has also been found to be necessary for splicing of single-intron pre-mRNAs []. The function of the aligned region is unknown but may be involved in RNA/DNA binding.; GO: 0003676 nucleic acid binding, 0005634 nucleus; PDB: 2B5M_A 4A0K_C 4A0B_C 3I7L_A 3I8E_A 4A09_A 4A0A_A 3EI4_C 2B5L_A 3I7O_A ....
Probab=99.61 E-value=3.6e-16 Score=135.48 Aligned_cols=69 Identities=36% Similarity=0.574 Sum_probs=57.6
Q ss_pred ccceeeeEEEEEe-cChHHHHHHHHHHHHHHhhcCCCcCCCCcccceeecCCCCCCCcceeehhHHHHHhc
Q psy7983 73 SLNSFVSTGLVTQ-ISPELYSFLFDLQERLAQTIRSVGRIEHSFWRSFNTDVKSDACEGFIDGDLIESFLD 142 (184)
Q Consensus 73 ~~Ts~GsIG~V~p-Is~~~y~~L~~LQ~~L~~~v~~vGGl~h~~yRs~~~~~r~~p~kgfIDGDLIE~FL~ 142 (184)
++|.+|+||++.| ++++.|++|..||+.|.+.++++||++|++||+++++ +.++++|||||||||+||+
T Consensus 252 ~~T~~G~Ig~l~p~l~~~~~~~L~~lQ~~l~~~~~~~~gl~~~~~R~~~~~-~~~~~~~~iDgdll~~fl~ 321 (321)
T PF03178_consen 252 YGTVDGSIGVLIPFLSEEEYRFLQALQNNLRKHIPSLGGLNPRSFRSYKNP-RMKRSKGFIDGDLLEQFLE 321 (321)
T ss_dssp EEETTS-EEEEEE-E-HHHHHHHHHHHHHHHHHS--TTS--HHHHTSEEES-EEE--BSEEEHHHHHGGGG
T ss_pred EEecCCEEEEEEecCCHHHHHHHHHHHHHHHhhCCCCccCChHHhccccCc-cccCCCccCcHHHHHHhhC
Confidence 8899999999999 8999999999999999999999999999999999997 4334899999999999996
No 4
>KOG1896|consensus
Probab=99.60 E-value=1.4e-15 Score=150.75 Aligned_cols=100 Identities=20% Similarity=0.344 Sum_probs=93.9
Q ss_pred ccceeeeEEEEEecChHHHHHHHHHHHHHHhhcCCCcCCCCcccceeecCC-CCCCCcceeehhHHHHHhcCCHHHHHHH
Q psy7983 73 SLNSFVSTGLVTQISPELYSFLFDLQERLAQTIRSVGRIEHSFWRSFNTDV-KSDACEGFIDGDLIESFLDLNIKDMKSI 151 (184)
Q Consensus 73 ~~Ts~GsIG~V~pIs~~~y~~L~~LQ~~L~~~v~~vGGl~h~~yRs~~~~~-r~~p~kgfIDGDLIE~FL~L~~~~q~eV 151 (184)
++|+||++|.++||++++||+|..||+.|.+.++++|||||++||.+.... ...|+|++|||+||.+|..|+-++|+++
T Consensus 1262 ~gtlDG~l~~~~Pl~e~~YRRL~~lQn~L~~~~~hv~GLNPr~yR~~~s~~~~~n~~r~ilDg~ll~~f~yl~~~er~el 1341 (1366)
T KOG1896|consen 1262 FGTLDGGLGHLVPLDEKTYRRLLMLQNALMDRLPHVGGLNPRAYRLLDSSLQLSNSLRSILDGELLNRFSYLSMSEREEL 1341 (1366)
T ss_pred hcccCCceeEEecCCHHHHHHHHHHHHHHHHhhhhhcCCCHHHhhhccchhhhcCCCcccchHhHHHHhhccchhhHHHH
Confidence 789999999999999999999999999999999999999999999887766 3678999999999999999999999999
Q ss_pred HhhcCCCCCCCCCCCCCCHHHHHHHHHHHhcc
Q psy7983 152 ATGLQITPPGSTTKRDATVDDIIKIVEDLTRI 183 (184)
Q Consensus 152 ~~~l~~~~~~~~~~~~~svedI~k~IEeL~rl 183 (184)
|+++| .++++|+++|-+|.++
T Consensus 1342 A~kiG-----------t~~~eIl~DLvel~~~ 1362 (1366)
T KOG1896|consen 1342 AHKIG-----------TTRKEILDDLVELDRL 1362 (1366)
T ss_pred HHhcC-----------CCHHHHHHHHHHHHHH
Confidence 99999 6899999999888763
No 5
>COG5161 SFT1 Pre-mRNA cleavage and polyadenylation specificity factor [RNA processing and modification]
Probab=98.85 E-value=4.9e-09 Score=102.66 Aligned_cols=156 Identities=19% Similarity=0.184 Sum_probs=111.7
Q ss_pred ecCCCeeeeeehhhhhcccceee----cCCCCccccccccccceeEEEeeee-----------cccccCc----ccceee
Q psy7983 18 LATDSTFTFGTIDEIQKLHIRTV----PLGEAPRRIAYQESSQTFGVITTRI-----------DIQEADA----SLNSFV 78 (184)
Q Consensus 18 ~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~qs~tfa~~s~~~-----------~v~~~~~----~~Ts~G 78 (184)
|.+.++|..---|.=-.+|.-|- |..-+.-|+-|- ++|-+=++.. ...-.++ ...++|
T Consensus 1144 Lv~G~~lyf~~~Da~gnih~l~Y~P~np~S~sG~RLV~r---ssFtlhs~~~~m~llPrn~efG~~~~~~f~~v~~~sdG 1220 (1319)
T COG5161 1144 LVTGNELYFLCCDAKGNIHGLTYSPNNPISMSGARLVKR---SSFTLHSAEIKMNLLPRNSEFGAGFKKNFIMVYSRSDG 1220 (1319)
T ss_pred hccCCeeEEEEEcCCCCEEEEecCCCCccccCcceeEee---ccccccchhhhhhhccchhhhCCCCCCceeEEEEccCC
Confidence 45677777777777777777764 444455555542 1221111110 0011111 457999
Q ss_pred eEEEEEecChHHHHHHHHHHHHHHhhcCCCcCCCCcccceeecCCC-CCCCcceeehhHHHHHhcCCHHHHHHHHhhcCC
Q psy7983 79 STGLVTQISPELYSFLFDLQERLAQTIRSVGRIEHSFWRSFNTDVK-SDACEGFIDGDLIESFLDLNIKDMKSIATGLQI 157 (184)
Q Consensus 79 sIG~V~pIs~~~y~~L~~LQ~~L~~~v~~vGGl~h~~yRs~~~~~r-~~p~kgfIDGDLIE~FL~L~~~~q~eV~~~l~~ 157 (184)
++-.|+||++..|++|..+|+++.+.++.+|||||+.||-...++. ..+.|..+||.+|..|-.|+-+.|++|+++.|-
T Consensus 1221 ~l~~vvpisd~~YrrL~~IQ~~i~~r~~~vgGLNpr~yRL~~d~~~~~~s~r~~ld~~ii~~F~y~~~~~r~sva~kaGr 1300 (1319)
T COG5161 1221 MLIHVVPISDAHYRRLLGIQTAIMARLKSVGGLNPRDYRLNSDIHLHSLSLRSPLDLHIINLFSYFDMSTRESVASKAGR 1300 (1319)
T ss_pred cEEEEeccCHHHHHHHHHHHHHHHHHHHhhcCCChhhhhhccCHHHhcCCcccchhhhhhhhhhhcchhhhhHHHhhcCC
Confidence 9999999999999999999999999999999999999997655554 567899999999999999999999999999983
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHhcc
Q psy7983 158 TPPGSTTKRDATVDDIIKIVEDLTRI 183 (184)
Q Consensus 158 ~~~~~~~~~~~svedI~k~IEeL~rl 183 (184)
. . ..-..|+....+-|+.|
T Consensus 1301 ~-~------~~e~~D~i~~~~~lrsl 1319 (1319)
T COG5161 1301 I-D------RKEISDMIASLNLLRSL 1319 (1319)
T ss_pred c-h------HHHHHHHHHHHHHHhcC
Confidence 1 1 01233666666666644
No 6
>PHA02945 interferon resistance protein; Provisional
Probab=83.91 E-value=0.87 Score=33.89 Aligned_cols=35 Identities=23% Similarity=0.198 Sum_probs=31.8
Q ss_pred eeeeeeecCCCeeeeeehhhhhcccceeecCCCCccc
Q psy7983 12 LAFHLALATDSTFTFGTIDEIQKLHIRTVPLGEAPRR 48 (184)
Q Consensus 12 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 48 (184)
||||-.+-++|+|+||++.+ +=++-+|-|.|+|=.
T Consensus 2 lafcy~~P~~GelvigtV~~--~d~ga~v~L~EY~g~ 36 (88)
T PHA02945 2 LAFCYSLPNVGDVLKGKVYE--NGYALYIDLFDYPHS 36 (88)
T ss_pred eeeeecCCCCCcEEEEEEEe--cCceEEEEecccCCc
Confidence 78999999999999999999 999999999998643
No 7
>PF09288 UBA_3: Fungal ubiquitin-associated domain ; InterPro: IPR015368 This C-terminal domain is found in ubiquitin binding proteins, it adopts a structure consisting of a three alpha-helix bundle. This domain is predominantly found in fungi []. ; PDB: 1TTE_A.
Probab=70.69 E-value=9.9 Score=25.96 Aligned_cols=44 Identities=25% Similarity=0.394 Sum_probs=28.0
Q ss_pred eehhHHHHHhcC--CHHHHHHHHhhcCCCCCCCCCCCCCCHHHHHHHHHHH
Q psy7983 132 IDGDLIESFLDL--NIKDMKSIATGLQITPPGSTTKRDATVDDIIKIVEDL 180 (184)
Q Consensus 132 IDGDLIE~FL~L--~~~~q~eV~~~l~~~~~~~~~~~~~svedI~k~IEeL 180 (184)
||=|+|++|..| +.++-.++++++|+... . +.+-+.--++||+|
T Consensus 8 i~~~lVd~F~~mGF~~dkVvevlrrlgik~~--n---~~dn~t~~~ilEEL 53 (55)
T PF09288_consen 8 IDKDLVDQFENMGFERDKVVEVLRRLGIKSM--N---GVDNETENKILEEL 53 (55)
T ss_dssp -SHHHHHHHHHHT--HHHHHHHHHHS--SS-------SS--HHHHHHHHHH
T ss_pred CCHHHHHHHHHcCCcHHHHHHHHHHhCCCCC--C---CccchhHHHHHHHH
Confidence 688999999986 88888999999986110 0 12345567788877
No 8
>PF02023 SCAN: SCAN domain; InterPro: IPR003309 A number of C2H2-zinc finger proteins contain a highly conserved N-terminal motif termed the SCAN domain. The SCAN domain may play an important role in the assembly and function of this newly defined subclass of transcriptional regulators [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3LHR_B 4E6S_A 2FI2_A 1Y7Q_A.
Probab=61.77 E-value=18 Score=26.82 Aligned_cols=45 Identities=18% Similarity=0.299 Sum_probs=36.2
Q ss_pred cceeehhHHHHHhc-CCHHHHHHHHhhcCCCCCCCCCCCCCCHHHHHHHHHHHhccC
Q psy7983 129 EGFIDGDLIESFLD-LNIKDMKSIATGLQITPPGSTTKRDATVDDIIKIVEDLTRIH 184 (184)
Q Consensus 129 kgfIDGDLIE~FL~-L~~~~q~eV~~~l~~~~~~~~~~~~~svedI~k~IEeL~rlH 184 (184)
.-++|==++|+||. ||++.+..|-+.- +.|.++....+|++.+.|
T Consensus 43 eqi~ellvlEQFL~~lP~e~~~wV~e~~-----------p~s~~ea~~Lae~~~~~~ 88 (95)
T PF02023_consen 43 EQILELLVLEQFLNILPPEVQTWVRERK-----------PESAEEAVALAEDYQRAR 88 (95)
T ss_dssp HHHHHHHHHHHHHHHS-HHHHHHHHTCS------------SSHHHHHHHHHHHHCCC
T ss_pred HHHHHHHHHHHHHHHCCHHHHHHHHhcC-----------CCCHHHHHHHHHHHHHhh
Confidence 56888889999999 8988888887754 258999999999987654
No 9
>TIGR02276 beta_rpt_yvtn 40-residue YVTN family beta-propeller repeat. This repeat of about 40 amino acids is found in up to 14 copies per protein. Archaea Methanosarcina mazei and Methanosarcina acetivorans each have over 10 genes that encode tandem copies of this repeat, which is also found in other species. PSIPRED predicts with high confidence that each 40-residue repeats contains four beta strands. This model overlaps somewhat with the NHL repeat (Pfam pfam01436) and also shows sequence similarity to the WD domain, G-beta repeat (Pfam pfam00400).
Probab=49.63 E-value=15 Score=21.63 Aligned_cols=28 Identities=32% Similarity=0.489 Sum_probs=21.1
Q ss_pred CCeeeeeehhhhhcccceeecCCCCccccc
Q psy7983 21 DSTFTFGTIDEIQKLHIRTVPLGEAPRRIA 50 (184)
Q Consensus 21 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 50 (184)
.+++++ +|--...-++.++.|+.|+.|+
T Consensus 13 ~~~v~~--id~~~~~~~~~i~vg~~P~~i~ 40 (42)
T TIGR02276 13 SNTVSV--IDTATNKVIATIPVGGYPFGVA 40 (42)
T ss_pred CCEEEE--EECCCCeEEEEEECCCCCceEE
Confidence 345554 6666667778999999999987
No 10
>PF02978 SRP_SPB: Signal peptide binding domain; InterPro: IPR004125 The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes [, ]. SRP recognises the signal sequence of the nascent polypeptide on the ribosome, retards its elongation, and docks the SRP-ribosome-polypeptide complex to the RER membrane via the SR receptor. Eukaryotic SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor []. In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane. In archaea, the SRP complex contains 7S RNA like its eukaryotic counterpart, yet only includes two of the six protein subunits found in the eukarytic complex: SRP19 and SRP54 []. This entry represents the M domain of the 54 kDa SRP54 component, a GTP-binding protein that interacts with the signal sequence when it emerges from the ribosome. SRP54 of the signal recognition particle has a three-domain structure: an N-terminal helical bundle domain, a GTPase domain, and the M-domain that binds the 7s RNA and also binds the signal sequence. The extreme C-terminal region is glycine-rich and lower in complexity and poorly conserved between species. These proteins include Escherichia coli and Bacillus subtilis ffh protein (P48), which seems to be the prokaryotic counterpart of SRP54; signal recognition particle receptor alpha subunit (docking protein), an integral membrane GTP-binding protein which ensures, in conjunction with SRP, the correct targeting of nascent secretory proteins to the endoplasmic reticulum membrane; bacterial FtsY protein, which is believed to play a similar role to that of the docking protein in eukaryotes; the pilA protein from Neisseria gonorrhoeae, the homologue of ftsY; and bacterial flagellar biosynthesis protein flhF.; GO: 0008312 7S RNA binding, 0006614 SRP-dependent cotranslational protein targeting to membrane, 0048500 signal recognition particle; PDB: 2FFH_B 3NDB_B 2V3C_C 1QZW_G 1QZX_B 3KL4_A 2JQE_A 1HQ1_A 1RY1_W 1MFQ_C ....
Probab=46.74 E-value=18 Score=27.17 Aligned_cols=29 Identities=21% Similarity=0.413 Sum_probs=23.1
Q ss_pred CHHHHHHHHhhcCCCCCCCCCCCCCCHHHHHHHHHHHhcc
Q psy7983 144 NIKDMKSIATGLQITPPGSTTKRDATVDDIIKIVEDLTRI 183 (184)
Q Consensus 144 ~~~~q~eV~~~l~~~~~~~~~~~~~svedI~k~IEeL~rl 183 (184)
+.+++.+||.|.| ++++||.+.|.....+
T Consensus 72 ~~sR~~RIA~GSG-----------~~~~eV~~ll~~f~~~ 100 (104)
T PF02978_consen 72 NESRRRRIARGSG-----------TTVQEVNELLKQFKQM 100 (104)
T ss_dssp HHHHHHHHHHHTT-----------S-HHHHHHHHHHHHHH
T ss_pred chHHHHHHHHHcC-----------CCHHHHHHHHHHHHHH
Confidence 4499999999999 7999999888876543
No 11
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=45.06 E-value=26 Score=26.82 Aligned_cols=38 Identities=24% Similarity=0.378 Sum_probs=32.2
Q ss_pred ehhHHHHHhcCCHHHHHHHHhhcCCCCCCCCCCCCCCHHHHHHHHHHHh
Q psy7983 133 DGDLIESFLDLNIKDMKSIATGLQITPPGSTTKRDATVDDIIKIVEDLT 181 (184)
Q Consensus 133 DGDLIE~FL~L~~~~q~eV~~~l~~~~~~~~~~~~~svedI~k~IEeL~ 181 (184)
+-+|++.|-.||+++|..+++-+. ..++.+.+.++++.
T Consensus 89 ~~~ll~~~~~L~~~~~~~~l~~l~-----------~~~~~~~~~~~~~~ 126 (135)
T PRK09706 89 QKELLELFDALPESEQDAQLSEMR-----------ARVENFNKLFEELL 126 (135)
T ss_pred HHHHHHHHHHCCHHHHHHHHHHHH-----------HHHHHHHHHHHHHH
Confidence 358999999999999999999886 56778888888774
No 12
>PF00536 SAM_1: SAM domain (Sterile alpha motif); InterPro: IPR021129 The sterile alpha motif (SAM) domain is a putative protein interaction module present in a wide variety of proteins [] involved in many biological processes. The SAM domain that spreads over around 70 residues is found in diverse eukaryotic organisms []. SAM domains have been shown to homo- and hetero-oligomerise, forming multiple self-association architectures and also binding to various non-SAM domain-containing proteins [], nevertheless with a low affinity constant []. SAM domains also appear to possess the ability to bind RNA []. Smaug, a protein that helps to establish a morphogen gradient in Drosophila embryos by repressing the translation of nanos (nos) mRNA, binds to the 3' untranslated region (UTR) of nos mRNA via two similar hairpin structures. The 3D crystal structure of the Smaug RNA-binding region shows a cluster of positively charged residues on the Smaug-SAM domain, which could be the RNA-binding surface. This electropositive potential is unique among all previously determined SAM-domain structures and is conserved among Smaug-SAM homologs. These results suggest that the SAM domain might have a primary role in RNA binding. Structural analyses show that the SAM domain is arranged in a small five-helix bundle with two large interfaces []. In the case of the SAM domain of EphB2, each of these interfaces is able to form dimers. The presence of these two distinct intermonomers binding surface suggest that SAM could form extended polymeric structures []. This entry represents type 1 SAM domains. ; PDB: 2KIV_A 3HIL_B 3KKA_A 3K1R_B 3SEN_B 3SEI_B 1V85_A 2KE7_A 2EAM_A 1WWV_A ....
Probab=34.88 E-value=64 Score=21.06 Aligned_cols=38 Identities=26% Similarity=0.529 Sum_probs=24.9
Q ss_pred cceeehhHHHHHhcCCHHHHHHHHhhcCCCCCCCCCCCCCCHHHHHHHHHHHhcc
Q psy7983 129 EGFIDGDLIESFLDLNIKDMKSIATGLQITPPGSTTKRDATVDDIIKIVEDLTRI 183 (184)
Q Consensus 129 kgfIDGDLIE~FL~L~~~~q~eV~~~l~~~~~~~~~~~~~svedI~k~IEeL~rl 183 (184)
+|+|||+ .++.|+.+. +..+|+ ..+..-.+++..++.|
T Consensus 26 ~~~i~g~---~L~~lt~~d----L~~lgi----------~~~ghr~ki~~~i~~L 63 (64)
T PF00536_consen 26 KNYIDGE---DLLSLTEED----LEELGI----------TKLGHRKKILRAIQKL 63 (64)
T ss_dssp HTTSSHH---HHTTSCHHH----HHHTT-----------SSHHHHHHHHHHHHHH
T ss_pred cCCchHH---HHHhcCHHH----HHHcCC----------CCHHHHHHHHHHHHHh
Confidence 7889998 678898777 444875 3555666665555543
No 13
>KOG3824|consensus
Probab=34.88 E-value=26 Score=32.47 Aligned_cols=88 Identities=22% Similarity=0.226 Sum_probs=60.1
Q ss_pred ecCCCeeeeeehhhhhcccceeecCCCCccccccccccceeEEEeeeecccccCcccceeeeEEEEEecCh-HHHHHHHH
Q psy7983 18 LATDSTFTFGTIDEIQKLHIRTVPLGEAPRRIAYQESSQTFGVITTRIDIQEADASLNSFVSTGLVTQISP-ELYSFLFD 96 (184)
Q Consensus 18 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~qs~tfa~~s~~~~v~~~~~~~Ts~GsIG~V~pIs~-~~y~~L~~ 96 (184)
+++.+. .|||||-.+|-|-. + .-|.+++-.|-|...-+|--.|-++ +.-+.+..
T Consensus 289 vski~~---itI~DiLE~HRRVL---------G-------------~vDPvEaGrfRttQVyVG~hiPp~P~dv~~qmq~ 343 (472)
T KOG3824|consen 289 VSKIHD---ITIDDILEMHRRVL---------G-------------NVDPVEAGRFRTTQVYVGRHIPPSPEDVMEQMQD 343 (472)
T ss_pred hhhccc---eeHHHHHHHHHHHh---------c-------------CCCcccccceeeeeEEecCCCCCChHHHHHHHHH
Confidence 344444 47899999985531 1 1244555558899999999999865 67777888
Q ss_pred HHHHHHhhcCCCcCCCCcccce---eecCCCCCCCcceeehhH
Q psy7983 97 LQERLAQTIRSVGRIEHSFWRS---FNTDVKSDACEGFIDGDL 136 (184)
Q Consensus 97 LQ~~L~~~v~~vGGl~h~~yRs---~~~~~r~~p~kgfIDGDL 136 (184)
+.+.|.+. +-..+.|-+|-+ |+.- --..|+||+=
T Consensus 344 fv~WLNsE--~~~tlhPve~AAlAHYKLV----~iHPF~DGNG 380 (472)
T KOG3824|consen 344 FVDWLNSE--STLTLHPVERAALAHYKLV----LIHPFTDGNG 380 (472)
T ss_pred HHHHhccc--cccccChHHHHHHhhheeE----EEeccccCCc
Confidence 88888876 566677776654 2221 2478999973
No 14
>cd07936 SCAN SCAN oligomerization domain. The SCAN domain (named after SRE-ZBP, CTfin51, AW-1 and Number 18 cDNA) is found in several vertebrate proteins that contain C2H2 zinc finger motifs, many of which may be transcription factors playing roles in cell survival and differentiation. This protein-interaction domain is able to mediate homo- and hetero-oligomerization of SCAN-containing proteins. Some SCAN-containing proteins, including those of lower vertebrates, do not contain zinc finger motifs. It has been noted that the SCAN domain resembles a domain-swapped version of the C-terminal domain of the HIV capsid protein. This domain model features elements common to the three general groups of SCAN domains (SCAN-A1, SCAN-A2, and SCAN-B). The SCAND1 protein is truncated at the C-terminus with respect to this model, the SCAND2 protein appears to have a truncated central helix.
Probab=31.25 E-value=1.1e+02 Score=22.22 Aligned_cols=42 Identities=19% Similarity=0.200 Sum_probs=33.4
Q ss_pred cceeehhHHHHHhc-CCHHHHHHHHhhcCCCCCCCCCCCCCCHHHHHHHHHHHh
Q psy7983 129 EGFIDGDLIESFLD-LNIKDMKSIATGLQITPPGSTTKRDATVDDIIKIVEDLT 181 (184)
Q Consensus 129 kgfIDGDLIE~FL~-L~~~~q~eV~~~l~~~~~~~~~~~~~svedI~k~IEeL~ 181 (184)
..+++-=.+|+|+. |+.+.+.+|...- +-|.+++...+|++.
T Consensus 42 eqilelLVlEQfl~~lp~e~q~~v~~~~-----------p~s~eea~~l~e~~~ 84 (85)
T cd07936 42 EQILELLVLEQFLIILPPEVQAWVRERK-----------PESGEEAATLAEDLL 84 (85)
T ss_pred HHHHHHHHHHHHhhhCCHHHHHHHHhcC-----------CCCHHHHHHHHHHhc
Confidence 56788888999988 7888888876653 258899999999875
No 15
>PF04361 DUF494: Protein of unknown function (DUF494); InterPro: IPR007456 Members of this family of uncharacterised proteins are often named Smg.
Probab=30.84 E-value=61 Score=26.14 Aligned_cols=61 Identities=13% Similarity=0.216 Sum_probs=41.3
Q ss_pred CcCCCCcccceeecCCC---CCCCcceeehhHHHHHhcCCHHHHHHHHhhcCCCCCCCCCCCCCCHHHHHH
Q psy7983 108 VGRIEHSFWRSFNTDVK---SDACEGFIDGDLIESFLDLNIKDMKSIATGLQITPPGSTTKRDATVDDIIK 175 (184)
Q Consensus 108 vGGl~h~~yRs~~~~~r---~~p~kgfIDGDLIE~FL~L~~~~q~eV~~~l~~~~~~~~~~~~~svedI~k 175 (184)
..-.++..+|-|..++. ..+++||| -++|+.--|++.+++.|++++- .-.....+++++.-
T Consensus 60 ~~~~~~~s~Riyt~~E~~~L~~e~rgfL--~fLeq~gvL~~~~RE~VIdr~m-----al~~~~i~Ld~lKw 123 (155)
T PF04361_consen 60 AQFASPRSMRIYTPEEQEKLDTECRGFL--LFLEQAGVLDPEQREMVIDRAM-----ALDSDEISLDDLKW 123 (155)
T ss_pred cccCCCCceEecCHHHHHHCCHHHHHHH--HHHHHcCCCCHHHHHHHHHHHH-----hCCCCCCCHHHHHH
Confidence 34455667788776554 45678887 3566666689999999999984 12223577777643
No 16
>PF13543 KSR1-SAM: SAM like domain present in kinase suppressor RAS 1
Probab=30.81 E-value=1.1e+02 Score=24.17 Aligned_cols=40 Identities=15% Similarity=0.287 Sum_probs=32.4
Q ss_pred ehhHHHHHhcCCHHHHHHHHhhcCCCCCCCCCCCCCCHHHHHHHHHHHhcc
Q psy7983 133 DGDLIESFLDLNIKDMKSIATGLQITPPGSTTKRDATVDDIIKIVEDLTRI 183 (184)
Q Consensus 133 DGDLIE~FL~L~~~~q~eV~~~l~~~~~~~~~~~~~svedI~k~IEeL~rl 183 (184)
..--+|.-++|++.+.+++++..| .+-||..+..-.|+.|
T Consensus 89 ~~~tLe~Llemsd~el~~~l~~~g-----------~~~EE~rRL~~Al~~L 128 (129)
T PF13543_consen 89 KVLTLEALLEMSDEELKEILNRCG-----------AREEECRRLCRALSNL 128 (129)
T ss_pred hhcCHHHHHhCCHHHHHHHHHHhC-----------CCHHHHHHHHHHHHhc
Confidence 344578899999999999999988 6888888887776654
No 17
>smart00435 TOPEUc DNA Topoisomerase I (eukaryota). DNA Topoisomerase I (eukaryota), DNA topoisomerase V, Vaccina virus topoisomerase, Variola virus topoisomerase, Shope fibroma virus topoisomeras
Probab=30.15 E-value=71 Score=29.79 Aligned_cols=70 Identities=11% Similarity=0.170 Sum_probs=43.5
Q ss_pred cccccceeEEEeeeeccccc--Cc-----ccceeeeEE-EEEecChHHHHHHHHHHH------HHHhhcC---------C
Q psy7983 51 YQESSQTFGVITTRIDIQEA--DA-----SLNSFVSTG-LVTQISPELYSFLFDLQE------RLAQTIR---------S 107 (184)
Q Consensus 51 ~~~qs~tfa~~s~~~~v~~~--~~-----~~Ts~GsIG-~V~pIs~~~y~~L~~LQ~------~L~~~v~---------~ 107 (184)
|-++.+|||.||++..=+.. +. |.--+|--. .-+.+++..|+.|..+.. .|.+.+. .
T Consensus 135 Ya~en~T~Gl~TLR~eHV~l~~~~~v~fdF~GKdgir~~~~v~vd~~l~k~L~~~~~~k~pg~~LF~~l~s~~lN~yLke 214 (391)
T smart00435 135 GEDEADTVGCCSLRVEHVTLKPPNKVIFDFLGKDSIRYYNEVEVDKQVFKNLKIFMKPKKPGDDLFDRLNTSKLNKHLKE 214 (391)
T ss_pred hhhcCCCEeecccchhheEecCCCEEEEEEeCCCCcEEEEEEecCHHHHHHHHHHhcCCCChHHHHhhCCHHHHHHHHHH
Confidence 77889999999999773332 12 333333222 233557888888877743 2322222 2
Q ss_pred -CcCCCCcccceee
Q psy7983 108 -VGRIEHSFWRSFN 120 (184)
Q Consensus 108 -vGGl~h~~yRs~~ 120 (184)
.||++-+.||.|.
T Consensus 215 ~mgglTAKdFRTwn 228 (391)
T smart00435 215 LMPGLTAKVFRTYN 228 (391)
T ss_pred HcCCCeeeeeecCh
Confidence 4789999999873
No 18
>COG3877 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=25.95 E-value=1.5e+02 Score=23.07 Aligned_cols=41 Identities=15% Similarity=0.272 Sum_probs=24.2
Q ss_pred HHHHhcCC----HHHHHHHHhhcCCCCCCCCCCCCCCHHHHHHHHH
Q psy7983 137 IESFLDLN----IKDMKSIATGLQITPPGSTTKRDATVDDIIKIVE 178 (184)
Q Consensus 137 IE~FL~L~----~~~q~eV~~~l~~~~~~~~~~~~~svedI~k~IE 178 (184)
||++|.++ +.+-.+|+.+||-++.+ ..+.+.+-++|.+-+|
T Consensus 63 vEr~lg~sYptvR~kld~vlramgy~p~~-e~~~~i~~~~i~~qle 107 (122)
T COG3877 63 VERELGISYPTVRTKLDEVLRAMGYNPDS-ENSVNIGKKKIIDQLE 107 (122)
T ss_pred HHHHHCCccHHHHHHHHHHHHHcCCCCCC-CChhhhhHHHHHHHHH
Confidence 67777775 45667888888865553 2233444444555444
No 19
>PF09124 Endonuc-dimeris: T4 recombination endonuclease VII, dimerisation; InterPro: IPR015208 This entry represents a dimerisation domain predominantly found in Bacteriophage T4 recombination endonuclease VII. It adopts a helical secondary structure, with three alpha helices oriented parallel to each other. As well as mediating dimerisation of the protein, this domain is also involved in binding to the DNA major groove []. ; PDB: 1EN7_B 1E7L_B 2QNF_A 2QNC_A 1E7D_A.
Probab=24.82 E-value=2e+02 Score=19.51 Aligned_cols=38 Identities=18% Similarity=0.224 Sum_probs=25.8
Q ss_pred hhHHHHHhcCCHHHHHHHHhhcCCCCCCCCCCCCCCHHHHHHH
Q psy7983 134 GDLIESFLDLNIKDMKSIATGLQITPPGSTTKRDATVDDIIKI 176 (184)
Q Consensus 134 GDLIE~FL~L~~~~q~eV~~~l~~~~~~~~~~~~~svedI~k~ 176 (184)
+|++..|-.|+..++...++..|+ .-....+-+++++.
T Consensus 7 ~D~~K~FSRl~k~eMiaem~~~G~-----~y~~~~tK~~Lvk~ 44 (54)
T PF09124_consen 7 PDKVKWFSRLTKPEMIAEMDSYGF-----EYNEKDTKAQLVKI 44 (54)
T ss_dssp HHHHHHHHTS-HHHHHHHHHHTT---------TTS-HHHHHHH
T ss_pred hHHHHHHHhcCHHHHHHHHHHhCC-----cCCccccHHHHHHH
Confidence 689999999999999999999985 11123456666553
No 20
>PF11239 DUF3040: Protein of unknown function (DUF3040); InterPro: IPR021401 Some members in this family of proteins with unknown function are annotated as membrane proteins however this cannot be confirmed.
Probab=23.10 E-value=84 Score=22.29 Aligned_cols=22 Identities=14% Similarity=0.070 Sum_probs=19.3
Q ss_pred ecChHHHHHHHHHHHHHHhhcC
Q psy7983 85 QISPELYSFLFDLQERLAQTIR 106 (184)
Q Consensus 85 pIs~~~y~~L~~LQ~~L~~~v~ 106 (184)
|++++.-+.|..||++|...-+
T Consensus 2 ~LSe~E~r~L~eiEr~L~~~DP 23 (82)
T PF11239_consen 2 PLSEHEQRRLEEIERQLRADDP 23 (82)
T ss_pred CCCHHHHHHHHHHHHHHHhcCc
Confidence 7899999999999999988744
No 21
>COG0541 Ffh Signal recognition particle GTPase [Intracellular trafficking and secretion]
Probab=23.08 E-value=81 Score=29.97 Aligned_cols=30 Identities=23% Similarity=0.488 Sum_probs=24.8
Q ss_pred CCHHHHHHHHhhcCCCCCCCCCCCCCCHHHHHHHHHHHhcc
Q psy7983 143 LNIKDMKSIATGLQITPPGSTTKRDATVDDIIKIVEDLTRI 183 (184)
Q Consensus 143 L~~~~q~eV~~~l~~~~~~~~~~~~~svedI~k~IEeL~rl 183 (184)
++++++++|+.|.| .+++||.+.+...+.|
T Consensus 392 i~~SR~rRIA~GSG-----------~sv~dVn~Llkq~~~m 421 (451)
T COG0541 392 INASRKRRIARGSG-----------TSVQDVNKLLKQFKQM 421 (451)
T ss_pred cChHHHHHHHhcCC-----------CCHHHHHHHHHHHHHH
Confidence 46899999999998 7999998888776654
No 22
>cd01207 Ena-Vasp Enabled-VASP-type homology (EVH1) domain. Enabled-VASP-type homology (EVH1) domain. The EVH1 domain binds to other proteins at proline rich sequences. It is found in proteins involved in cytoskeletal reorganization such as Enabled and VASP. Ena-VASP type EVH1 domains specifically recognize FPPPP motifs in the focal adhesion proteins zyxin and vinculin, and the ActA surface protein of Listeria monocytogenes. It has a PH-like fold, despite having minimal sequence similarity to PH or PTB domains.
Probab=23.05 E-value=3.1e+02 Score=21.03 Aligned_cols=73 Identities=18% Similarity=0.208 Sum_probs=47.3
Q ss_pred ehhhhhcccceeecCCC-----CccccccccccceeEEEeeeec---c-cc------------cCc---ccceeeeEEEE
Q psy7983 28 TIDEIQKLHIRTVPLGE-----APRRIAYQESSQTFGVITTRID---I-QE------------ADA---SLNSFVSTGLV 83 (184)
Q Consensus 28 ~~~~~~~~~~~~~~~~~-----~~~~~~~~~qs~tfa~~s~~~~---v-~~------------~~~---~~Ts~GsIG~V 83 (184)
++||-.| .-+|+|. ++..|+|.+..++|.+++.+.. + .+ .+. |+......|+=
T Consensus 13 ~~d~~tk---~W~P~~~~~~~ls~V~~~~~~~~~~yrIvg~~~~~~~~v~e~~l~~~l~y~k~~p~Fh~w~~~~~v~GLn 89 (111)
T cd01207 13 VYDDSNK---KWVPAGGGSQGFSRVQIYHHPRNNTFRVVGRKLQDHQVVINCAIVKGLKYNQATPTFHQWRDARQVYGLN 89 (111)
T ss_pred EEcCCCC---cEEcCCCCCCCcceEEEEEcCCCCEEEEEEeecCCCcEEEEEEecCCceeeecCCcceeeecCCeEEeec
Confidence 5677666 3789988 4788999999999999987722 0 00 000 33444445533
Q ss_pred EecChHHHHHHHHHHHHHHh
Q psy7983 84 TQISPELYSFLFDLQERLAQ 103 (184)
Q Consensus 84 ~pIs~~~y~~L~~LQ~~L~~ 103 (184)
.+=.++.-.|...++..|..
T Consensus 90 F~Se~eA~~F~~~v~~Al~~ 109 (111)
T cd01207 90 FGSKEDATMFASAMLSALEV 109 (111)
T ss_pred cCCHHHHHHHHHHHHHHHHh
Confidence 33345777888888887764
No 23
>PHA02955 hypothetical protein; Provisional
Probab=22.77 E-value=63 Score=27.76 Aligned_cols=25 Identities=32% Similarity=0.434 Sum_probs=21.1
Q ss_pred hhHHHHHhcCCHHHHHHHHhhcCCC
Q psy7983 134 GDLIESFLDLNIKDMKSIATGLQIT 158 (184)
Q Consensus 134 GDLIE~FL~L~~~~q~eV~~~l~~~ 158 (184)
--+.|-+..||+++|.+|+..+|++
T Consensus 68 ~a~~Et~~~Lp~~qk~~ia~~lgI~ 92 (213)
T PHA02955 68 EALIETIENFPEKEQKEIAADIGIN 92 (213)
T ss_pred HHHHHHHHhCCHHHHHHHHHHhCCC
Confidence 3467778889999999999999973
No 24
>KOG1702|consensus
Probab=22.63 E-value=36 Score=29.49 Aligned_cols=39 Identities=21% Similarity=0.315 Sum_probs=25.3
Q ss_pred cCCCcCCCCcccceeecCCC-CCCCcceeehhHHHHHhcCCHH
Q psy7983 105 IRSVGRIEHSFWRSFNTDVK-SDACEGFIDGDLIESFLDLNIK 146 (184)
Q Consensus 105 v~~vGGl~h~~yRs~~~~~r-~~p~kgfIDGDLIE~FL~L~~~ 146 (184)
.++++| +.||+|++-.. .+.---|.|||.|--.-.++..
T Consensus 202 ~~~~~g---ktyra~ydysaqdedevsF~dgd~ivnvq~iddG 241 (264)
T KOG1702|consen 202 QKSCTG---KTYRAFYDYSAQDEDEVSFVDGDYIVNVQSIDDG 241 (264)
T ss_pred ccCCCC---ccchhhccCcccCcceeEEecCCeEEEEEeccCC
Confidence 457777 67888775432 3445789999987555445443
No 25
>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. This family groups together a range of proteins, including anr, crp, clp, cysR, fixK, flp, fnr, fnrN, hlyX and ntcA [, ]. Within this family, the HTH motif is situated towards the C terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2OZ6_A 1CGP_B 2GZW_C 1O3T_B 3ROU_A 2CGP_A 3RDI_A 1I5Z_A 3IYD_H 3FWE_B ....
Probab=22.13 E-value=1.5e+02 Score=17.85 Aligned_cols=24 Identities=29% Similarity=0.387 Sum_probs=17.7
Q ss_pred HHHHHhhcCCCCCCCCCCCCCCHHHHHHHHHHHhc
Q psy7983 148 MKSIATGLQITPPGSTTKRDATVDDIIKIVEDLTR 182 (184)
Q Consensus 148 q~eV~~~l~~~~~~~~~~~~~svedI~k~IEeL~r 182 (184)
+++|++-+| .++|-+-+.+..|++
T Consensus 5 r~diA~~lG-----------~t~ETVSR~l~~l~~ 28 (32)
T PF00325_consen 5 RQDIADYLG-----------LTRETVSRILKKLER 28 (32)
T ss_dssp HHHHHHHHT-----------S-HHHHHHHHHHHHH
T ss_pred HHHHHHHhC-----------CcHHHHHHHHHHHHH
Confidence 678899998 688888777776653
Done!