Query psy5725
Match_columns 117
No_of_seqs 169 out of 998
Neff 5.3
Searched_HMMs 46136
Date Sat Aug 17 01:00:00 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy5725.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/5725hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF04992 RNA_pol_Rpb1_6: RNA p 100.0 1.3E-30 2.9E-35 199.1 5.8 88 5-92 95-187 (187)
2 KOG0260|consensus 99.9 6E-27 1.3E-31 213.1 4.8 98 14-116 974-1071(1605)
3 TIGR02389 RNA_pol_rpoA2 DNA-di 99.8 1.2E-19 2.6E-24 150.9 4.2 50 68-117 14-64 (367)
4 cd06528 RNAP_A'' A'' subunit o 99.8 3.4E-19 7.4E-24 147.9 3.9 53 65-117 8-60 (363)
5 PRK14897 unknown domain/DNA-di 99.7 1.7E-18 3.8E-23 148.6 4.6 52 66-117 151-202 (509)
6 PRK04309 DNA-directed RNA poly 99.7 5.4E-18 1.2E-22 141.6 3.8 50 68-117 30-79 (383)
7 cd02584 RNAP_II_Rpb1_C Largest 99.7 7.7E-18 1.7E-22 141.7 3.5 47 71-117 1-47 (410)
8 PRK14977 bifunctional DNA-dire 99.6 5.3E-16 1.2E-20 144.7 6.0 66 50-117 933-998 (1321)
9 PRK14898 DNA-directed RNA poly 99.6 7.1E-16 1.5E-20 139.1 3.6 49 67-115 27-75 (858)
10 KOG0261|consensus 99.4 1.8E-13 3.9E-18 124.4 6.0 55 62-116 992-1046(1386)
11 TIGR02386 rpoC_TIGR DNA-direct 99.4 3.7E-14 8.1E-19 130.8 -1.7 73 34-115 815-889 (1140)
12 CHL00117 rpoC2 RNA polymerase 99.4 1.3E-13 2.8E-18 129.1 1.5 74 32-115 258-333 (1364)
13 PRK00566 DNA-directed RNA poly 99.3 1E-13 2.2E-18 128.2 -0.4 73 34-115 823-897 (1156)
14 PRK02597 rpoC2 DNA-directed RN 99.3 2.3E-13 4.9E-18 127.0 1.5 75 31-115 253-329 (1331)
15 PF04998 RNA_pol_Rpb1_5: RNA p 99.3 1.4E-13 2.9E-18 106.0 -0.3 23 93-115 67-89 (277)
16 TIGR02388 rpoC2_cyan DNA-direc 99.3 3.5E-13 7.7E-18 124.9 0.7 74 32-115 252-327 (1227)
17 PRK09603 bifunctional DNA-dire 99.3 3.4E-13 7.4E-18 131.3 -0.2 75 32-115 2219-2295(2890)
18 PRK14844 bifunctional DNA-dire 99.3 3.7E-13 8.1E-18 130.8 -0.3 74 33-115 2276-2351(2836)
19 PRK14906 DNA-directed RNA poly 99.3 3.7E-13 8E-18 125.9 -0.8 73 34-115 917-992 (1460)
20 KOG0262|consensus 99.1 3.6E-11 7.8E-16 111.5 2.0 37 80-116 1136-1172(1640)
21 PF05491 RuvB_C: Holliday junc 59.7 2.9 6.2E-05 28.1 -0.1 31 82-112 6-39 (76)
22 COG0086 RpoC DNA-directed RNA 53.1 4.9 0.00011 37.3 0.2 27 89-115 406-432 (808)
23 cd00692 ligninase Ligninase an 33.7 26 0.00055 29.3 1.6 29 82-110 150-178 (328)
24 PF09290 AcetDehyd-dimer: Prok 31.9 5.5 0.00012 29.6 -2.4 22 91-113 16-37 (137)
25 PLN03097 FHY3 Protein FAR-RED 29.1 1.1E+02 0.0023 29.0 4.9 91 11-115 602-693 (846)
26 PF02439 Adeno_E3_CR2: Adenovi 26.0 20 0.00042 21.2 -0.3 14 96-109 2-15 (38)
27 COG1058 CinA Predicted nucleot 25.0 2E+02 0.0044 23.2 5.3 76 18-109 46-141 (255)
28 PF00141 peroxidase: Peroxidas 22.3 60 0.0013 25.3 1.8 30 82-111 123-152 (230)
29 PF14745 WASH-7_N: WASH comple 22.3 77 0.0017 28.0 2.6 29 1-33 191-219 (567)
30 KOG0189|consensus 20.5 47 0.001 26.9 0.8 14 104-117 211-225 (261)
31 PF12502 DUF3710: Protein of u 20.1 76 0.0016 24.5 1.9 22 21-42 139-160 (181)
No 1
>PF04992 RNA_pol_Rpb1_6: RNA polymerase Rpb1, domain 6; InterPro: IPR007075 RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial and chloroplast polymerases). This domain, domain 6, represents a mobile module of the RNA polymerase. Domain 6 forms part of the shelf module [, ]. This family appears to be specific to the largest subunit of RNA polymerase II.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_M 1Y77_A 3CQZ_A 3GTM_A 1TWA_A 4A3I_A 2NVY_A 2NVT_A 1I6H_A 1TWF_A ....
Probab=99.96 E-value=1.3e-30 Score=199.06 Aligned_cols=88 Identities=49% Similarity=0.758 Sum_probs=74.0
Q ss_pred cccCCcccc-----CCCCChhhHHHHHHHhhhcceeEcCCCcccHHHHHhhhhhhhcccccccchhhHHHhhcCCHHHHH
Q psy5725 5 VRNSPAQYS-----GSARRIIGLNIGVRELLEKCVIVAGEDQLSKQANENATLLFQCLVRSTLCTKLVAENYRLSSEAFE 79 (117)
Q Consensus 5 ~~~~~~~~~-----~~~l~p~~vi~~v~~L~~~l~vv~g~D~ls~Eaq~NAt~Lf~i~lRS~LasK~vl~~~~Lsk~af~ 79 (117)
+.||-.+|. +|||+|.+||++|++|+++|+||+|+|+||+|||+|||+||+|||||+||+|+|+++|+||++||+
T Consensus 95 I~nAq~~f~i~~~~~sdL~P~~Vi~~V~~L~~~L~vv~g~D~ls~Eaq~NAtlLf~i~lRs~LasKrvi~e~rL~~~AF~ 174 (187)
T PF04992_consen 95 IWNAQKIFHIDPRKPSDLSPIYVIEKVEELLDRLVVVRGDDPLSREAQENATLLFKILLRSTLASKRVIEEYRLNKEAFD 174 (187)
T ss_dssp CCCCCCCTT--TTS-BS--HHHHHHHHHHHHTT--SS--SSCCCCHHHHCCCHHHHHHHCCCSSHHHHHHTSB--HHHHH
T ss_pred HHHHHHHcCCCCCCcccCCHHHHHHHHHHHHHHHhhccCCCcchHHHHhhHHHHHHHHHHHhhhhHHHHHHhCcCHHHHH
Confidence 345655554 899999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHhhhc
Q psy5725 80 WLVGEIENRFQQA 92 (117)
Q Consensus 80 ~il~ei~~rf~~a 92 (117)
|++|||+.||.+|
T Consensus 175 wilgEIe~rF~~a 187 (187)
T PF04992_consen 175 WILGEIESRFKKA 187 (187)
T ss_dssp HHHHHHHHHHHCC
T ss_pred HHHHHHHHHHHcC
Confidence 9999999999986
No 2
>KOG0260|consensus
Probab=99.93 E-value=6e-27 Score=213.09 Aligned_cols=98 Identities=57% Similarity=0.779 Sum_probs=94.8
Q ss_pred CCCCChhhHHHHHHHhhhcceeEcCCCcccHHHHHhhhhhhhcccccccchhhHHHhhcCCHHHHHHHHHHHHHHhhhcc
Q psy5725 14 GSARRIIGLNIGVRELLEKCVIVAGEDQLSKQANENATLLFQCLVRSTLCTKLVAENYRLSSEAFEWLVGEIENRFQQAQ 93 (117)
Q Consensus 14 ~~~l~p~~vi~~v~~L~~~l~vv~g~D~ls~Eaq~NAt~Lf~i~lRS~LasK~vl~~~~Lsk~af~~il~ei~~rf~~a~ 93 (117)
+++|.|.+|+.+++++.+++++++|+|.+|+ ||+ ||+|+|||.|++|+++++||||.++|+|++++|+.||.++.
T Consensus 974 ~t~l~~~~v~~g~~~l~e~l~iv~g~~~~sr-aqr----l~~~lLrs~l~~krv~~e~rls~eaf~w~~~~Ie~~f~qa~ 1048 (1605)
T KOG0260|consen 974 PTDLIPFKVVKGVKELAEKLVIVRGEDYISR-AQR----LFNILLRSTLATKRVLEEYRLSSEAFEWVLGEIEARFLQAE 1048 (1605)
T ss_pred ccccchhhhhhhhhhhhheeEEeeCchhHHH-HHH----HHHHHHHhhHHHHHHHHHhcccHHHHHHHhhhhhhheeeee
Confidence 4789999999999999999999999999999 886 99999999999999999999999999999999999999999
Q ss_pred cCCCchhhhhhhcccCcccCCCC
Q psy5725 94 CAPGEMVGALAAQSLGTSTYFPF 116 (117)
Q Consensus 94 v~PGe~VG~iaAQSIGEP~TQ~~ 116 (117)
++||||||++||||||||+||--
T Consensus 1049 a~pgemvg~lAaqsvgePatqmT 1071 (1605)
T KOG0260|consen 1049 ASPGEMVGALAAQSVGEPATQMT 1071 (1605)
T ss_pred cCccchHhHHHHHHhCCchhhcc
Confidence 99999999999999999999953
No 3
>TIGR02389 RNA_pol_rpoA2 DNA-directed RNA polymerase, subunit A''. This family consists of the archaeal A'' subunit of the DNA-directed RNA polymerase. The example from Methanocaldococcus jannaschii contains an intein.
Probab=99.78 E-value=1.2e-19 Score=150.91 Aligned_cols=50 Identities=24% Similarity=0.429 Sum_probs=46.9
Q ss_pred HHhhcCCHH-HHHHHHHHHHHHhhhcccCCCchhhhhhhcccCcccCCCCC
Q psy5725 68 AENYRLSSE-AFEWLVGEIENRFQQAQCAPGEMVGALAAQSLGTSTYFPFL 117 (117)
Q Consensus 68 l~~~~Lsk~-af~~il~ei~~rf~~a~v~PGe~VG~iaAQSIGEP~TQ~~~ 117 (117)
+++|+++++ +|+||+++|+.+|.+++|+||||||+|||||||||+||--|
T Consensus 14 ~~~~~~~~~~~~~~~l~~i~~ky~~alv~PGeaVG~IAAQSIGEP~TQMTL 64 (367)
T TIGR02389 14 VKKREISDKEELDEIIKRVEEEYLRSLIDPGEAVGIVAAQSIGEPGTQMTM 64 (367)
T ss_pred HHHcCCCHHHHHHHHHHHHHHHHHHhcCCCccccchhhhhhcCCccccccc
Confidence 567889999 99999999999999999999999999999999999999643
No 4
>cd06528 RNAP_A'' A'' subunit of Archaeal RNA Polymerase (RNAP). Archaeal RNA polymerase (RNAP), like bacterial RNAP, is a large multi-subunit complex responsible for the synthesis of all RNAs in the cell. The relative positioning of the RNAP core is highly conserved between archaeal RNAP and the three classes of eukaryotic RNAPs. In archaea, the largest subunit is split into two polypeptides, A' and A'', which are encoded by separate genes in an operon. Sequence alignments reveal that the archaeal A'' subunit corresponds to the C-terminal one-third of the RNAPII largest subunit (Rpb1). In subunit A'', several loops in the jaw domain are shorter. The RNAPII Rpb1 interacts with the second-largest subunit (Rpb2) to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis.
Probab=99.76 E-value=3.4e-19 Score=147.94 Aligned_cols=53 Identities=28% Similarity=0.342 Sum_probs=50.6
Q ss_pred hhHHHhhcCCHHHHHHHHHHHHHHhhhcccCCCchhhhhhhcccCcccCCCCC
Q psy5725 65 KLVAENYRLSSEAFEWLVGEIENRFQQAQCAPGEMVGALAAQSLGTSTYFPFL 117 (117)
Q Consensus 65 K~vl~~~~Lsk~af~~il~ei~~rf~~a~v~PGe~VG~iaAQSIGEP~TQ~~~ 117 (117)
|+++++|++++.+|+|++++++.+|.+++++||||||++||||||||+||--|
T Consensus 8 ~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~Ge~vG~iaAQSiGEP~TQMTL 60 (363)
T cd06528 8 EEVLKEHGLTLSEAEEIIKEVLREYLRSLIEPGEAVGIVAAQSIGEPGTQMTL 60 (363)
T ss_pred HHHHHHcCCCHHHHHHHHHHHHHHHHHHhhccCccccceeeeecCccceeccc
Confidence 67899999999999999999999999999999999999999999999999654
No 5
>PRK14897 unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional
Probab=99.73 E-value=1.7e-18 Score=148.64 Aligned_cols=52 Identities=27% Similarity=0.402 Sum_probs=48.7
Q ss_pred hHHHhhcCCHHHHHHHHHHHHHHhhhcccCCCchhhhhhhcccCcccCCCCC
Q psy5725 66 LVAENYRLSSEAFEWLVGEIENRFQQAQCAPGEMVGALAAQSLGTSTYFPFL 117 (117)
Q Consensus 66 ~vl~~~~Lsk~af~~il~ei~~rf~~a~v~PGe~VG~iaAQSIGEP~TQ~~~ 117 (117)
.+++++++++.+|+|++++|+.+|.+++|+||||||+|||||||||+||--|
T Consensus 151 ~~~~~~~l~~~~~~~i~~ei~~~y~~~~v~pGE~VG~IAAQSIGEP~TQMTL 202 (509)
T PRK14897 151 KAMKKKELSDDEYEEILRRIREEYERARVDPYEAVGIVAAQSIGEPGTQMTM 202 (509)
T ss_pred HHHHHcCCCHHHHHHHHHHHHHHHHHhccCCCCCcchhhhhhhCCccccccc
Confidence 3578999999999999999999999999999999999999999999999643
No 6
>PRK04309 DNA-directed RNA polymerase subunit A''; Validated
Probab=99.70 E-value=5.4e-18 Score=141.63 Aligned_cols=50 Identities=30% Similarity=0.461 Sum_probs=47.0
Q ss_pred HHhhcCCHHHHHHHHHHHHHHhhhcccCCCchhhhhhhcccCcccCCCCC
Q psy5725 68 AENYRLSSEAFEWLVGEIENRFQQAQCAPGEMVGALAAQSLGTSTYFPFL 117 (117)
Q Consensus 68 l~~~~Lsk~af~~il~ei~~rf~~a~v~PGe~VG~iaAQSIGEP~TQ~~~ 117 (117)
+.++++++++|+||+++|+.+|.+++++||||||++||||||||+||--|
T Consensus 30 ~~~~~l~~~~~~~~~~~i~~~y~~~~v~pGe~VG~iaAQsIGEP~TQMTL 79 (383)
T PRK04309 30 LEERKLTEEEVEEIIEEVVREYLRSLVEPGEAVGVVAAQSIGEPGTQMTM 79 (383)
T ss_pred HHHcCCCHHHHHHHHHHHHHHHHHhhcCCCCccchhhhhhccchhhhccc
Confidence 56788999999999999999999999999999999999999999999643
No 7
>cd02584 RNAP_II_Rpb1_C Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain. RNA polymerase II (RNAP II) is a large multi-subunit complex responsible for the synthesis of mRNA. RNAP II consists of a 10-subunit core enzyme and a peripheral heterodimer of two subunits. The largest core subunit (Rpb1) of yeast RNAP II is the best characterized member of this family. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure. In yeast, Rpb1 and Rpb2, the largest and the second largest subunits, each makes up one clamp, one jaw, and part of the cleft. Rpb1 interacts with Rpb2 to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis. The C-terminal domain of Rpb1 makes up part of the foot and jaw structures.
Probab=99.70 E-value=7.7e-18 Score=141.74 Aligned_cols=47 Identities=53% Similarity=0.945 Sum_probs=44.5
Q ss_pred hcCCHHHHHHHHHHHHHHhhhcccCCCchhhhhhhcccCcccCCCCC
Q psy5725 71 YRLSSEAFEWLVGEIENRFQQAQCAPGEMVGALAAQSLGTSTYFPFL 117 (117)
Q Consensus 71 ~~Lsk~af~~il~ei~~rf~~a~v~PGe~VG~iaAQSIGEP~TQ~~~ 117 (117)
|++++++|+||+++|+.+|.+++++||||||++||||||||+||--|
T Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~~~~ge~vg~~aaQSiGEP~TQmTL 47 (410)
T cd02584 1 YRLNKEAFDWILGEIETRFNRSLVHPGEMVGTIAAQSIGEPATQMTL 47 (410)
T ss_pred CCCCHHHHHHHHHHHHHHHHHhhcCCCCCcchhhhhhcCCchhcccc
Confidence 57899999999999999999999999999999999999999999643
No 8
>PRK14977 bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
Probab=99.61 E-value=5.3e-16 Score=144.73 Aligned_cols=66 Identities=23% Similarity=0.304 Sum_probs=56.4
Q ss_pred hhhhhhcccccccchhhHHHhhcCCHHHHHHHHHHHHHHhhhcccCCCchhhhhhhcccCcccCCCCC
Q psy5725 50 ATLLFQCLVRSTLCTKLVAENYRLSSEAFEWLVGEIENRFQQAQCAPGEMVGALAAQSLGTSTYFPFL 117 (117)
Q Consensus 50 At~Lf~i~lRS~LasK~vl~~~~Lsk~af~~il~ei~~rf~~a~v~PGe~VG~iaAQSIGEP~TQ~~~ 117 (117)
.+..|+..++..++ ..++++++++.+|+|++++++.+|.+++|+||||||+|||||||||+||--|
T Consensus 933 ~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~pGe~VG~iaAQSiGEP~TQmTL 998 (1321)
T PRK14977 933 YTKTFNANLPKLLA--DAIHGAELKEDELEAICAEGKEGFEKAKVEPGQAIGIISAQSIAEPGTQMTL 998 (1321)
T ss_pred HHHhhhhhhHHHHH--HHHHHcCCCHHHHHHHHHHHHHHHHhcccCCcccchhhhhhhccCceeeecc
Confidence 34455666666554 5677889999999999999999999999999999999999999999999643
No 9
>PRK14898 DNA-directed RNA polymerase subunit A''; Provisional
Probab=99.58 E-value=7.1e-16 Score=139.14 Aligned_cols=49 Identities=27% Similarity=0.351 Sum_probs=46.4
Q ss_pred HHHhhcCCHHHHHHHHHHHHHHhhhcccCCCchhhhhhhcccCcccCCC
Q psy5725 67 VAENYRLSSEAFEWLVGEIENRFQQAQCAPGEMVGALAAQSLGTSTYFP 115 (117)
Q Consensus 67 vl~~~~Lsk~af~~il~ei~~rf~~a~v~PGe~VG~iaAQSIGEP~TQ~ 115 (117)
+.++++|++++|+|++++|+.+|.+++|+||||||++||||||||+||-
T Consensus 27 ~~~~~~lt~~~~d~Il~~I~~~y~~a~vepge~vG~~aaqsi~~~~~~~ 75 (858)
T PRK14898 27 LSKRDGVTEEMVEEIIDEVVSAYLNALVEPYEAVGIVAAQSIGEPGTQM 75 (858)
T ss_pred HHhhcCCCHHHHHHHHHHHHHHHhhCCCCCCceeeeeeehhcCCCCccc
Confidence 3567899999999999999999999999999999999999999999984
No 10
>KOG0261|consensus
Probab=99.42 E-value=1.8e-13 Score=124.36 Aligned_cols=55 Identities=31% Similarity=0.495 Sum_probs=49.3
Q ss_pred cchhhHHHhhcCCHHHHHHHHHHHHHHhhhcccCCCchhhhhhhcccCcccCCCC
Q psy5725 62 LCTKLVAENYRLSSEAFEWLVGEIENRFQQAQCAPGEMVGALAAQSLGTSTYFPF 116 (117)
Q Consensus 62 LasK~vl~~~~Lsk~af~~il~ei~~rf~~a~v~PGe~VG~iaAQSIGEP~TQ~~ 116 (117)
.....+.+.++++.++++.|+..+..+|+++++|||++||+|||||||||+||--
T Consensus 992 ~~~~~~~~~~~~t~kql~~f~~~~~~ky~~a~~EpGTavGAi~aQSIGEPGTQMT 1046 (1386)
T KOG0261|consen 992 FCPDLLYQISRLTEKQLEKFVERCLDKYMRAKVEPGTAVGAIAAQSIGEPGTQMT 1046 (1386)
T ss_pred cCccceeeeeeccHHHHHHHHHHHHHHHHhhhcCCcchhhhhhcccCCCCCceee
Confidence 3334456778999999999999999999999999999999999999999999953
No 11
>TIGR02386 rpoC_TIGR DNA-directed RNA polymerase, beta' subunit, predominant form. Bacteria have a single DNA-directed RNA polymerase, with required subunits that include alpha, beta, and beta-prime. This model describes the predominant architecture of the beta-prime subunit in most bacteria. This model excludes from among the bacterial mostly sequences from the cyanobacteria, where RpoC is replaced by two tandem genes homologous to it but also encoding an additional domain.
Probab=99.37 E-value=3.7e-14 Score=130.84 Aligned_cols=73 Identities=21% Similarity=0.251 Sum_probs=58.4
Q ss_pred eeEcCCCcccHHHHH--hhhhhhhcccccccchhhHHHhhcCCHHHHHHHHHHHHHHhhhcccCCCchhhhhhhcccCcc
Q psy5725 34 VIVAGEDQLSKQANE--NATLLFQCLVRSTLCTKLVAENYRLSSEAFEWLVGEIENRFQQAQCAPGEMVGALAAQSLGTS 111 (117)
Q Consensus 34 ~vv~g~D~ls~Eaq~--NAt~Lf~i~lRS~LasK~vl~~~~Lsk~af~~il~ei~~rf~~a~v~PGe~VG~iaAQSIGEP 111 (117)
+++..++.|+.+..+ ....+-.+.+||.|.|+. .+.++..|+.|-+. ...+|+.||+||+|||||||||
T Consensus 815 ~i~~~~~~i~~~~~~~i~~~~i~~v~iRS~ltC~s---~~gvC~~CYG~~La------~~~~V~~GeaVGiiAAQSIGEP 885 (1140)
T TIGR02386 815 LIAEANTLITEEIAEKIENSGIEKVKVRSVLTCES---EHGVCQKCYGRDLA------TGKLVEIGEAVGVIAAQSIGEP 885 (1140)
T ss_pred EEEeCCCCcCHHHHHHHHHcCCCEEEecCCeeeCC---CCCCccccCCCccc------CCcEecccccceeEeeeecCCC
Confidence 444555667766543 233456789999999985 67888899999886 6889999999999999999999
Q ss_pred cCCC
Q psy5725 112 TYFP 115 (117)
Q Consensus 112 ~TQ~ 115 (117)
+||-
T Consensus 886 GTQL 889 (1140)
T TIGR02386 886 GTQL 889 (1140)
T ss_pred cchh
Confidence 9994
No 12
>CHL00117 rpoC2 RNA polymerase beta'' subunit; Reviewed
Probab=99.37 E-value=1.3e-13 Score=129.09 Aligned_cols=74 Identities=18% Similarity=0.276 Sum_probs=55.9
Q ss_pred cceeEcCCCcccHHHHH-h-hhhhhhcccccccchhhHHHhhcCCHHHHHHHHHHHHHHhhhcccCCCchhhhhhhcccC
Q psy5725 32 KCVIVAGEDQLSKQANE-N-ATLLFQCLVRSTLCTKLVAENYRLSSEAFEWLVGEIENRFQQAQCAPGEMVGALAAQSLG 109 (117)
Q Consensus 32 ~l~vv~g~D~ls~Eaq~-N-At~Lf~i~lRS~LasK~vl~~~~Lsk~af~~il~ei~~rf~~a~v~PGe~VG~iaAQSIG 109 (117)
++++-++ ..|+.+..+ - +..+-.+++||+|.|+. .++++..|+.|-+. ...+|+.||+||+|||||||
T Consensus 258 ~~i~~~n-~~I~~~~~~~i~~~~~~~v~iRSpltC~~---~~~vC~~CYG~~la------~~~lV~~GeaVGiiAaQSIG 327 (1364)
T CHL00117 258 RCIATRN-QDIGIGLANRFITFRAQPISIRSPLTCRS---TSWICQLCYGWSLA------HGDLVELGEAVGIIAGQSIG 327 (1364)
T ss_pred EEEEeCC-CCcCHHHHHHHHHcCCCEEEEeCCccccc---HHHHHHHHhCcccc------cCcccChhhhhhhhhhhccC
Confidence 3334444 445554433 2 22466789999999974 55677789999987 58899999999999999999
Q ss_pred cccCCC
Q psy5725 110 TSTYFP 115 (117)
Q Consensus 110 EP~TQ~ 115 (117)
|||||=
T Consensus 328 EPGTQL 333 (1364)
T CHL00117 328 EPGTQL 333 (1364)
T ss_pred CCchhh
Confidence 999993
No 13
>PRK00566 DNA-directed RNA polymerase subunit beta'; Provisional
Probab=99.35 E-value=1e-13 Score=128.16 Aligned_cols=73 Identities=21% Similarity=0.259 Sum_probs=57.9
Q ss_pred eeEcCCCcccHHHHH--hhhhhhhcccccccchhhHHHhhcCCHHHHHHHHHHHHHHhhhcccCCCchhhhhhhcccCcc
Q psy5725 34 VIVAGEDQLSKQANE--NATLLFQCLVRSTLCTKLVAENYRLSSEAFEWLVGEIENRFQQAQCAPGEMVGALAAQSLGTS 111 (117)
Q Consensus 34 ~vv~g~D~ls~Eaq~--NAt~Lf~i~lRS~LasK~vl~~~~Lsk~af~~il~ei~~rf~~a~v~PGe~VG~iaAQSIGEP 111 (117)
+++..++.|+.+..+ ....+-++.+||.|.|+. .+.++..|+.|-+. ...+|+-||+||+|||||||||
T Consensus 823 ~i~~~~~~i~~~~~~~i~~~~i~~v~iRS~ltC~s---~~gvC~~CYG~~La------~~~~v~iGeaVGiIAAQSIGEP 893 (1156)
T PRK00566 823 VIVPAGTLIDEEIADKIEEAGIEEVKIRSVLTCET---RHGVCAKCYGRDLA------TGKLVNIGEAVGVIAAQSIGEP 893 (1156)
T ss_pred EEEcCCCccCHHHHHHHHHcCCCEEEEcCCeeecC---CCcccHhhhCcccc------CCCCcccCcceeEEeeeecCCC
Confidence 444455666666433 223455789999999986 67888999999886 5789999999999999999999
Q ss_pred cCCC
Q psy5725 112 TYFP 115 (117)
Q Consensus 112 ~TQ~ 115 (117)
+||-
T Consensus 894 GTQL 897 (1156)
T PRK00566 894 GTQL 897 (1156)
T ss_pred ccce
Confidence 9994
No 14
>PRK02597 rpoC2 DNA-directed RNA polymerase subunit beta'; Provisional
Probab=99.34 E-value=2.3e-13 Score=126.97 Aligned_cols=75 Identities=19% Similarity=0.294 Sum_probs=58.1
Q ss_pred hcceeEcCCCcccHHHHH--hhhhhhhcccccccchhhHHHhhcCCHHHHHHHHHHHHHHhhhcccCCCchhhhhhhccc
Q psy5725 31 EKCVIVAGEDQLSKQANE--NATLLFQCLVRSTLCTKLVAENYRLSSEAFEWLVGEIENRFQQAQCAPGEMVGALAAQSL 108 (117)
Q Consensus 31 ~~l~vv~g~D~ls~Eaq~--NAt~Lf~i~lRS~LasK~vl~~~~Lsk~af~~il~ei~~rf~~a~v~PGe~VG~iaAQSI 108 (117)
.++++-++ ..|+.+..+ .+..+-++.+||+|.|+. .++++..|+.|-+. ...+|+.||+||+||||||
T Consensus 253 ~~~i~~~n-~~i~~~~~~~i~~~~~~~v~iRspltC~s---~~gvC~~CYG~~la------~~~lv~lGeaVGiiAaQSI 322 (1331)
T PRK02597 253 GEVIAERN-TAIDPDLAKKIEKAGVEEVMVRSPLTCEA---ARSVCRKCYGWSLA------HNHLVDLGEAVGIIAAQSI 322 (1331)
T ss_pred CCEEEeCC-CCcCHHHHHHHHHcCCCEEEEECCEEecC---CCCchhhccCcchh------cCcccchhhhhhhhhhccc
Confidence 34444444 445554433 222467899999999985 66888889999987 6889999999999999999
Q ss_pred CcccCCC
Q psy5725 109 GTSTYFP 115 (117)
Q Consensus 109 GEP~TQ~ 115 (117)
|||+||-
T Consensus 323 GEPGTQL 329 (1331)
T PRK02597 323 GEPGTQL 329 (1331)
T ss_pred cCCcchh
Confidence 9999994
No 15
>PF04998 RNA_pol_Rpb1_5: RNA polymerase Rpb1, domain 5; InterPro: IPR007081 RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial and chloroplast polymerases). This domain, domain 5, represents the discontinuous cleft domain that is required to form the central cleft or channel where the DNA is bound [, ].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 1ZYR_D 1SMY_D 2A68_N 2O5J_D 3AOH_N 2O5I_D 2CW0_N 2A6H_N 2A69_D 3EQL_D ....
Probab=99.34 E-value=1.4e-13 Score=106.03 Aligned_cols=23 Identities=43% Similarity=0.564 Sum_probs=20.4
Q ss_pred ccCCCchhhhhhhcccCcccCCC
Q psy5725 93 QCAPGEMVGALAAQSLGTSTYFP 115 (117)
Q Consensus 93 ~v~PGe~VG~iaAQSIGEP~TQ~ 115 (117)
+|+|||+||+|||||||||+||-
T Consensus 67 ~v~~Ge~VGiiaAQSIGEP~TQ~ 89 (277)
T PF04998_consen 67 LVEPGEAVGIIAAQSIGEPGTQM 89 (277)
T ss_dssp B--TTSBHHHHHHHHHHCHGCCS
T ss_pred ccCccccchhhhhchhcchhHHh
Confidence 99999999999999999999994
No 16
>TIGR02388 rpoC2_cyan DNA-directed RNA polymerase, beta'' subunit. The family consists of the product of the rpoC2 gene, a subunit of DNA-directed RNA polymerase of cyanobacteria and chloroplasts. RpoC2 corresponds largely to the C-terminal region of the RpoC (the beta' subunit) of other bacteria. Members of this family are designated beta'' in chloroplasts/plastids, and beta' (confusingly) in Cyanobacteria, where RpoC1 is called beta' in chloroplasts/plastids and gamma in Cyanobacteria. We prefer to name this family beta'', after its organellar members, to emphasize that this RpoC1 and RpoC2 together replace RpoC in other bacteria.
Probab=99.31 E-value=3.5e-13 Score=124.93 Aligned_cols=74 Identities=19% Similarity=0.310 Sum_probs=55.0
Q ss_pred cceeEcCCCcccHHHHH-h-hhhhhhcccccccchhhHHHhhcCCHHHHHHHHHHHHHHhhhcccCCCchhhhhhhcccC
Q psy5725 32 KCVIVAGEDQLSKQANE-N-ATLLFQCLVRSTLCTKLVAENYRLSSEAFEWLVGEIENRFQQAQCAPGEMVGALAAQSLG 109 (117)
Q Consensus 32 ~l~vv~g~D~ls~Eaq~-N-At~Lf~i~lRS~LasK~vl~~~~Lsk~af~~il~ei~~rf~~a~v~PGe~VG~iaAQSIG 109 (117)
++++-++ ..|+.+... - ....-.+.+||+|.|+. .+++++.|+.|-+. ...+|+.||+||+|||||||
T Consensus 252 ~~i~~~n-~~I~~~~~~~i~~~~~~~v~iRspltC~s---~~~vC~~CYG~~la------~~~lV~lGeaVGiiAaQSIG 321 (1227)
T TIGR02388 252 EVIVPKN-TAIDPDLAKTIETAGISEVVVRSPLTCEA---ARSVCRKCYGWSLA------HAHLVDLGEAVGIIAAQSIG 321 (1227)
T ss_pred cEEEeCC-CccCHHHHHHHHHcCCCEEEEeCcceecc---hhhHhHhccCCccc------cCcEechhhhhhhhhhhccC
Confidence 3333444 445554432 1 22356789999999984 55677788999886 58899999999999999999
Q ss_pred cccCCC
Q psy5725 110 TSTYFP 115 (117)
Q Consensus 110 EP~TQ~ 115 (117)
||+||-
T Consensus 322 EPGTQL 327 (1227)
T TIGR02388 322 EPGTQL 327 (1227)
T ss_pred Ccchhh
Confidence 999994
No 17
>PRK09603 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed
Probab=99.30 E-value=3.4e-13 Score=131.32 Aligned_cols=75 Identities=17% Similarity=0.283 Sum_probs=60.5
Q ss_pred cceeEcCCCcccHHHHH--hhhhhhhcccccccchhhHHHhhcCCHHHHHHHHHHHHHHhhhcccCCCchhhhhhhcccC
Q psy5725 32 KCVIVAGEDQLSKQANE--NATLLFQCLVRSTLCTKLVAENYRLSSEAFEWLVGEIENRFQQAQCAPGEMVGALAAQSLG 109 (117)
Q Consensus 32 ~l~vv~g~D~ls~Eaq~--NAt~Lf~i~lRS~LasK~vl~~~~Lsk~af~~il~ei~~rf~~a~v~PGe~VG~iaAQSIG 109 (117)
+-++++.+..|+++..+ ....+-++.+||.|.|+. .+.++..|+.|-+. ...+|+.||+||+|||||||
T Consensus 2219 ~~~i~~~~~~I~~~~~~~i~~~gi~~v~iRS~LtC~s---~~gvC~~CYG~dLa------~g~~V~iGeaVGiIAAQSIG 2289 (2890)
T PRK09603 2219 NEILLYADTLIDEEGAKKVVEAGIKSITIRTPVTCKA---PKGVCAKCYGLNLG------EGKMSYPGEAVGVVAAQSIG 2289 (2890)
T ss_pred CcEEEcCCcCcCHHHHHHHHHcCCCEEEEcCcceecC---CCcChhhhcCCccc------CCCCccCCceeeEEeecccC
Confidence 44566666777776544 233556889999999974 66788899999997 58899999999999999999
Q ss_pred cccCCC
Q psy5725 110 TSTYFP 115 (117)
Q Consensus 110 EP~TQ~ 115 (117)
|||||=
T Consensus 2290 EPGTQL 2295 (2890)
T PRK09603 2290 EPGTQL 2295 (2890)
T ss_pred CCcccc
Confidence 999994
No 18
>PRK14844 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Provisional
Probab=99.29 E-value=3.7e-13 Score=130.81 Aligned_cols=74 Identities=22% Similarity=0.224 Sum_probs=60.4
Q ss_pred ceeEcCCCcccHHHHH--hhhhhhhcccccccchhhHHHhhcCCHHHHHHHHHHHHHHhhhcccCCCchhhhhhhcccCc
Q psy5725 33 CVIVAGEDQLSKQANE--NATLLFQCLVRSTLCTKLVAENYRLSSEAFEWLVGEIENRFQQAQCAPGEMVGALAAQSLGT 110 (117)
Q Consensus 33 l~vv~g~D~ls~Eaq~--NAt~Lf~i~lRS~LasK~vl~~~~Lsk~af~~il~ei~~rf~~a~v~PGe~VG~iaAQSIGE 110 (117)
-+++..+..|+++..+ ++..+-.+.+||.|.|+. .+.++..|+.|-+. ...+|+.||+||+||||||||
T Consensus 2276 ~~i~~~~~~I~~~~~~~i~~~gi~~v~IRS~ltC~s---~~gvC~~CYG~~La------~~~~V~iGeaVGiIAAQSIGE 2346 (2836)
T PRK14844 2276 ELLVKAGELIDEDKVKQINIAGLDVVKIRSPLTCEI---SPGVCSLCYGRDLA------TGKIVSIGEAVGVIAAQSVGE 2346 (2836)
T ss_pred CEEEeCCCccCHHHHHHHHHcCCCEEEEcCCeeECC---CCCChhhccCcccc------CCCcccccccceeeeecccCC
Confidence 3455556667766543 455677899999999985 66888889999987 688999999999999999999
Q ss_pred ccCCC
Q psy5725 111 STYFP 115 (117)
Q Consensus 111 P~TQ~ 115 (117)
||||=
T Consensus 2347 PGTQL 2351 (2836)
T PRK14844 2347 PGTQL 2351 (2836)
T ss_pred Cccee
Confidence 99993
No 19
>PRK14906 DNA-directed RNA polymerase subunit beta'/alpha domain fusion protein; Provisional
Probab=99.28 E-value=3.7e-13 Score=125.91 Aligned_cols=73 Identities=18% Similarity=0.330 Sum_probs=58.1
Q ss_pred eeEcCCCcccHH--HHH-hhhhhhhcccccccchhhHHHhhcCCHHHHHHHHHHHHHHhhhcccCCCchhhhhhhcccCc
Q psy5725 34 VIVAGEDQLSKQ--ANE-NATLLFQCLVRSTLCTKLVAENYRLSSEAFEWLVGEIENRFQQAQCAPGEMVGALAAQSLGT 110 (117)
Q Consensus 34 ~vv~g~D~ls~E--aq~-NAt~Lf~i~lRS~LasK~vl~~~~Lsk~af~~il~ei~~rf~~a~v~PGe~VG~iaAQSIGE 110 (117)
+++..++.|+.+ ++. .+..+-++.+||.|.|+. .+.++..|+.|-+. ...+|+-||+||+||||||||
T Consensus 917 ~i~~~~~~I~~~~~~~~i~~~gi~~v~iRS~ltC~s---~~gvC~kCYG~dLa------tg~~V~iGeaVGiIAAQSIGE 987 (1460)
T PRK14906 917 VLLSAGDYIESMDDLKRLVEAGVTKVQIRTLMTCHA---EYGVCQKCYGWDLA------TRRPVNIGTAVGIIAAQSIGE 987 (1460)
T ss_pred EEEeCCCeeCcHHHHHHHHHCCCCEEEEeCCeeECC---CCCChhhCcCCccc------CCcEeccccceeeeeeeecCC
Confidence 445555666653 333 344567899999999985 66888889999987 578999999999999999999
Q ss_pred ccCCC
Q psy5725 111 STYFP 115 (117)
Q Consensus 111 P~TQ~ 115 (117)
|+||=
T Consensus 988 PGTQL 992 (1460)
T PRK14906 988 PGTQL 992 (1460)
T ss_pred Cccee
Confidence 99994
No 20
>KOG0262|consensus
Probab=99.08 E-value=3.6e-11 Score=111.54 Aligned_cols=37 Identities=32% Similarity=0.403 Sum_probs=32.5
Q ss_pred HHHHHHHHHhhhcccCCCchhhhhhhcccCcccCCCC
Q psy5725 80 WLVGEIENRFQQAQCAPGEMVGALAAQSLGTSTYFPF 116 (117)
Q Consensus 80 ~il~ei~~rf~~a~v~PGe~VG~iaAQSIGEP~TQ~~ 116 (117)
.+...+.-||.+|+++|||+||+|||||||||+||=-
T Consensus 1136 ~lr~ll~~K~~~SLa~PGE~VGvlAAQSIGEPSTQMT 1172 (1640)
T KOG0262|consen 1136 KLRRLLQLKYIRSLADPGEPVGVLAAQSIGEPSTQMT 1172 (1640)
T ss_pred HHHHHHHHHHHHHhcCCCCcceeeeecccCCCcceee
Confidence 3555567899999999999999999999999999953
No 21
>PF05491 RuvB_C: Holliday junction DNA helicase ruvB C-terminus; InterPro: IPR008823 The RuvB protein makes up part of the RuvABC revolvasome which catalyses the resolution of Holliday junctions that arise during genetic recombination and DNA repair. Branch migration is catalysed by the RuvB protein that is targeted to the Holliday junction by the structure specific RuvA protein []. This group of sequences contain this signature which is located in the C-terminal region of the proteins; it is thought to be a helicase DNA-binding domain.; GO: 0003677 DNA binding, 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination; PDB: 3PFI_B 1IXR_C 1HQC_B 1IXS_B 1IN8_A 1IN4_A 1IN5_A 1J7K_A 1IN6_A 1IN7_A.
Probab=59.69 E-value=2.9 Score=28.14 Aligned_cols=31 Identities=26% Similarity=0.447 Sum_probs=20.3
Q ss_pred HHHHHHHhhhcccC--CCchhhhhh-hcccCccc
Q psy5725 82 VGEIENRFQQAQCA--PGEMVGALA-AQSLGTST 112 (117)
Q Consensus 82 l~ei~~rf~~a~v~--PGe~VG~ia-AQSIGEP~ 112 (117)
+++...+|.+.+++ -|-+||+-+ |.++||+.
T Consensus 6 Ld~~D~~yL~~l~~~f~ggPvGl~tlA~~l~ed~ 39 (76)
T PF05491_consen 6 LDELDRRYLKTLIENFKGGPVGLDTLAAALGEDK 39 (76)
T ss_dssp -BHHHHHHHHHHHHCSTTS-B-HHHHHHHTTS-H
T ss_pred CCHHHHHHHHHHHHHcCCCCeeHHHHHHHHCCCH
Confidence 34456677777777 488999888 89999963
No 22
>COG0086 RpoC DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]
Probab=53.05 E-value=4.9 Score=37.32 Aligned_cols=27 Identities=15% Similarity=-0.058 Sum_probs=23.9
Q ss_pred hhhcccCCCchhhhhhhcccCcccCCC
Q psy5725 89 FQQAQCAPGEMVGALAAQSLGTSTYFP 115 (117)
Q Consensus 89 f~~a~v~PGe~VG~iaAQSIGEP~TQ~ 115 (117)
|-..++.+++.+|..+|||+|+|.||-
T Consensus 406 DGDeM~~Hvp~s~ea~AEa~~lm~tq~ 432 (808)
T COG0086 406 DGDEMAVHVPASGEAAAEARGLMGTQM 432 (808)
T ss_pred CchhhhccccchHHHHHHHHHhhcccc
Confidence 346788899999999999999999985
No 23
>cd00692 ligninase Ligninase and other manganese-dependent fungal peroxidases. Ligninases and related extracellular fungal peroxidases belong to class II of the plant heme-dependent peroxidase superfamily. All members of the superfamily share a heme prosthetic group and catalyze a multistep oxidative reaction involving hydrogen peroxide as the electron acceptor. Class II peroxidases are fungal glycoproteins that have been implicated in the oxidative breakdown of lignin, the main cell wall component of woody plants. They contain four conserved disulphide bridges and two conserved calcium binding sites.
Probab=33.69 E-value=26 Score=29.34 Aligned_cols=29 Identities=41% Similarity=0.594 Sum_probs=24.9
Q ss_pred HHHHHHHhhhcccCCCchhhhhhhcccCc
Q psy5725 82 VGEIENRFQQAQCAPGEMVGALAAQSLGT 110 (117)
Q Consensus 82 l~ei~~rf~~a~v~PGe~VG~iaAQSIGE 110 (117)
++.+..+|.+.=..+-|||-.++|+|||-
T Consensus 150 v~~l~~~F~~~Gf~~~E~VaLsGAHTiG~ 178 (328)
T cd00692 150 VDKILARFADAGFSPDELVALLAAHSVAA 178 (328)
T ss_pred HHHHHHHHHHcCCCHHHHhhhcccccccc
Confidence 45566788888899999999999999994
No 24
>PF09290 AcetDehyd-dimer: Prokaryotic acetaldehyde dehydrogenase, dimerisation; InterPro: IPR015426 This C-terminal domain is found in prokaryotic acetaldehyde dehydrogenases, it adopts a structure consisting of an alpha-beta-alpha-beta(3) core, which mediates dimerisation of the protein []. The acetaldehyde dehydrogenase family of bacterial enzymes catalyses the formation of acetyl-CoA from acetaldehyde in the 3-hydroxyphenylpropinoate degradation pathway. It occurs as a late step in the meta-cleavage pathways of a variety of compounds, including catechol, biphenyl, toluene, salicylate [].; GO: 0008774 acetaldehyde dehydrogenase (acetylating) activity, 0019439 aromatic compound catabolic process, 0055114 oxidation-reduction process; PDB: 1NVM_F.
Probab=31.94 E-value=5.5 Score=29.65 Aligned_cols=22 Identities=27% Similarity=0.327 Sum_probs=17.5
Q ss_pred hcccCCCchhhhhhhcccCcccC
Q psy5725 91 QAQCAPGEMVGALAAQSLGTSTY 113 (117)
Q Consensus 91 ~a~v~PGe~VG~iaAQSIGEP~T 113 (117)
..-|+-+|.|-.+|+-|.| |+|
T Consensus 16 v~~V~YaEIVatiaS~SaG-PgT 37 (137)
T PF09290_consen 16 VAPVEYAEIVATIASKSAG-PGT 37 (137)
T ss_dssp TS-EEEEEEEEEEEGGGS--HHH
T ss_pred ccccceeEEEeeeccccCC-chh
Confidence 3478889999999999999 887
No 25
>PLN03097 FHY3 Protein FAR-RED ELONGATED HYPOCOTYL 3; Provisional
Probab=29.13 E-value=1.1e+02 Score=29.00 Aligned_cols=91 Identities=16% Similarity=0.125 Sum_probs=54.1
Q ss_pred cccCCCCChhhHHHHHHHhhhcceeEcCCCcccHHHHHhhhhhhhcccccccchhhHHHhhcCCHHHHHHHHHHHHHHhh
Q psy5725 11 QYSGSARRIIGLNIGVRELLEKCVIVAGEDQLSKQANENATLLFQCLVRSTLCTKLVAENYRLSSEAFEWLVGEIENRFQ 90 (117)
Q Consensus 11 ~~~~~~l~p~~vi~~v~~L~~~l~vv~g~D~ls~Eaq~NAt~Lf~i~lRS~LasK~vl~~~~Lsk~af~~il~ei~~rf~ 90 (117)
.++...+.+.||++++++-.++..+. +.+.- .. .+.+.=|+.+.|.. -++.++-..+.++|+..++.++..+.
T Consensus 602 ~~~v~~IP~~YILkRWTKdAK~~~~~-~~~~~--~~-~~~~~Ryn~L~r~a---~kla~~as~S~E~y~~a~~~L~e~~~ 674 (846)
T PLN03097 602 MCQLSAIPSQYILKRWTKDAKSRHLL-GEESE--QV-QSRVQRYNDLCQRA---LKLSEEASLSQESYNIAFRALEEAFG 674 (846)
T ss_pred hcCcccCchhhhhhhchhhhhhcccC-ccccc--cc-cchhhHHHHHHHHH---HHHHHHHhCCHHHHHHHHHHHHHHHH
Confidence 45778899999999999998765432 22210 01 11223333333322 12345666888888888887777665
Q ss_pred hcccCCCchhhhhh-hcccCcccCCC
Q psy5725 91 QAQCAPGEMVGALA-AQSLGTSTYFP 115 (117)
Q Consensus 91 ~a~v~PGe~VG~ia-AQSIGEP~TQ~ 115 (117)
+. +++.. +.|++||.|.+
T Consensus 675 ~~-------~~~~n~~~~~~~~~~~~ 693 (846)
T PLN03097 675 NC-------ISMNNSNKSLVEAGTSP 693 (846)
T ss_pred HH-------HHhhccCCCcccccccc
Confidence 43 44443 56777777643
No 26
>PF02439 Adeno_E3_CR2: Adenovirus E3 region protein CR2; InterPro: IPR003470 Early region 3 (E3) of human adenoviruses (Ads) codes for proteins that appear to control viral interactions with the host []. This region called CR1 (conserved region 1) [] is found three times in Human adenovirus 19 (a subgroup D adenovirus) 49 kDa protein in the E3 region. CR1 is also found in the 20.1 Kd protein of subgroup B adenoviruses. The function of this 80 amino acid region is unknown. This region is probably a divergent immunoglobulin domain.
Probab=25.96 E-value=20 Score=21.21 Aligned_cols=14 Identities=21% Similarity=0.515 Sum_probs=11.0
Q ss_pred CCchhhhhhhcccC
Q psy5725 96 PGEMVGALAAQSLG 109 (117)
Q Consensus 96 PGe~VG~iaAQSIG 109 (117)
|+.+||+|+|.-.|
T Consensus 2 p~s~IaIIv~V~vg 15 (38)
T PF02439_consen 2 PSSTIAIIVAVVVG 15 (38)
T ss_pred CcchhhHHHHHHHH
Confidence 88899999986443
No 27
>COG1058 CinA Predicted nucleotide-utilizing enzyme related to molybdopterin-biosynthesis enzyme MoeA [General function prediction only]
Probab=24.98 E-value=2e+02 Score=23.22 Aligned_cols=76 Identities=24% Similarity=0.244 Sum_probs=49.0
Q ss_pred ChhhHHHHHHHhhhc--ceeEcC-----CCcccHHHHHhhhhhhhcccccccchhhHHHhhcCCHHHHHHHHHHHH----
Q psy5725 18 RIIGLNIGVRELLEK--CVIVAG-----EDQLSKQANENATLLFQCLVRSTLCTKLVAENYRLSSEAFEWLVGEIE---- 86 (117)
Q Consensus 18 ~p~~vi~~v~~L~~~--l~vv~g-----~D~ls~Eaq~NAt~Lf~i~lRS~LasK~vl~~~~Lsk~af~~il~ei~---- 86 (117)
+|.+|++.++.+.+| ++++.| .|.++.|+-..|- . ....+++++++|+.+..+
T Consensus 46 ~~~~I~~~l~~a~~r~D~vI~tGGLGPT~DDiT~e~vAka~-------g---------~~lv~~~~al~~i~~~~~~r~~ 109 (255)
T COG1058 46 NPDRIVEALREASERADVVITTGGLGPTHDDLTAEAVAKAL-------G---------RPLVLDEEALAMIEEKYAKRGR 109 (255)
T ss_pred CHHHHHHHHHHHHhCCCEEEECCCcCCCccHhHHHHHHHHh-------C---------CCcccCHHHHHHHHHHHHhcCC
Confidence 578899999999985 455665 5899999753221 1 122355677777776543
Q ss_pred ----HHhhhcccCCCc-----hhhhhhhcccC
Q psy5725 87 ----NRFQQAQCAPGE-----MVGALAAQSLG 109 (117)
Q Consensus 87 ----~rf~~a~v~PGe-----~VG~iaAQSIG 109 (117)
+++.++.+-+|- .||+..+..++
T Consensus 110 ~~~~~~~K~A~~P~Ga~~l~NpvG~APG~~v~ 141 (255)
T COG1058 110 EMTEANRKQAMLPEGAEVLDNPVGTAPGFVVE 141 (255)
T ss_pred CCChhhhhhccCCCCCEeCCCCCCCCCeeEEe
Confidence 567777777775 56665555443
No 28
>PF00141 peroxidase: Peroxidase; InterPro: IPR002016 Peroxidases are haem-containing enzymes that use hydrogen peroxide as the electron acceptor to catalyse a number of oxidative reactions. Most haem peroxidases follow the reaction scheme: Fe3+ + H2O2 --> [Fe4+=O]R' (Compound I) + H2O [Fe4+=O]R' + substrate --> [Fe4+=O]R (Compound II) + oxidised substrate [Fe4+=O]R + substrate --> Fe3+ + H2O + oxidised substrate In this mechanism, the enzyme reacts with one equivalent of H2O2 to give [Fe4+=O]R' (compound I). This is a two-electron oxidation/reduction reaction where H2O2 is reduced to water and the enzyme is oxidised. One oxidising equivalent resides on iron, giving the oxyferryl [] intermediate, while in many peroxidases the porphyrin (R) is oxidised to the porphyrin pi-cation radical (R'). Compound I then oxidises an organic substrate to give a substrate radical []. Haem peroxidases include two superfamilies: one found in bacteria, fungi, plants and the second found in animals. The first one can be viewed as consisting of 3 major classes []. Class I, the intracellular peroxidases, includes: yeast cytochrome c peroxidase (CCP), a soluble protein found in the mitochondrial electron transport chain, where it probably protects against toxic peroxides; ascorbate peroxidase (AP), the main enzyme responsible for hydrogen peroxide removal in chloroplasts and cytosol of higher plants; and bacterial catalase- peroxidases, exhibiting both peroxidase and catalase activities. It is thought that catalase-peroxidase provides protection to cells under oxidative stress []. Class II consists of secretory fungal peroxidases: ligninases, or lignin peroxidases (LiPs), and manganese-dependent peroxidases (MnPs). These are monomeric glycoproteins involved in the degradation of lignin. In MnP, Mn2+ serves as the reducing substrate []. Class II proteins contain four conserved disulphide bridges and two conserved calcium-binding sites. Class III consists of the secretory plant peroxidases, which have multiple tissue-specific functions: e.g., removal of hydrogen peroxide from chloroplasts and cytosol; oxidation of toxic compounds; biosynthesis of the cell wall; defence responses towards wounding; indole-3-acetic acid (IAA) catabolism; ethylene biosynthesis; and so on. Class III proteins are also monomeric glycoproteins, containing four conserved disulphide bridges and two calcium ions, although the placement of the disulphides differs from class II enzymes. The crystal structures of a number of these proteins show that they share the same architecture - two all-alpha domains between which the haem group is embedded. ; GO: 0004601 peroxidase activity, 0020037 heme binding, 0006979 response to oxidative stress, 0055114 oxidation-reduction process; PDB: 1QPA_B 2DV2_A 2B2R_B 1MWV_B 2FXJ_A 2FXG_A 2B2O_B 1X7U_B 2B2Q_A 2FXH_A ....
Probab=22.30 E-value=60 Score=25.32 Aligned_cols=30 Identities=23% Similarity=0.358 Sum_probs=22.7
Q ss_pred HHHHHHHhhhcccCCCchhhhhhhcccCcc
Q psy5725 82 VGEIENRFQQAQCAPGEMVGALAAQSLGTS 111 (117)
Q Consensus 82 l~ei~~rf~~a~v~PGe~VG~iaAQSIGEP 111 (117)
+.++...|.+.=..+-|||-..+|+|||.=
T Consensus 123 ~~~l~~~F~~~Gls~~e~VaLsGaHTiG~~ 152 (230)
T PF00141_consen 123 VDQLLAFFARKGLSAEEMVALSGAHTIGRA 152 (230)
T ss_dssp HHHHHHHHHHTT--HHHHHHHHGGGGSTEE
T ss_pred cchhhhhhhccccchhhhcceecccccccc
Confidence 444566788888899999999999999963
No 29
>PF14745 WASH-7_N: WASH complex subunit 7, N-terminal
Probab=22.29 E-value=77 Score=28.03 Aligned_cols=29 Identities=31% Similarity=0.462 Sum_probs=19.7
Q ss_pred CccccccCCccccCCCCChhhHHHHHHHhhhcc
Q psy5725 1 MVKSVRNSPAQYSGSARRIIGLNIGVRELLEKC 33 (117)
Q Consensus 1 ~~~~~~~~~~~~~~~~l~p~~vi~~v~~L~~~l 33 (117)
|+|++++.|.+|+.+ +.++ +..+.++.++
T Consensus 191 ~l~~v~~np~~f~~~---~~~l-~~le~ll~~l 219 (567)
T PF14745_consen 191 MLKSVRHNPSKFGVT---EEKL-RQLEKLLADL 219 (567)
T ss_pred HHHHHhcChhhcCCC---HHHH-HHHHHHHHHH
Confidence 678999999999854 3333 5555555555
No 30
>KOG0189|consensus
Probab=20.55 E-value=47 Score=26.88 Aligned_cols=14 Identities=29% Similarity=0.475 Sum_probs=9.5
Q ss_pred hhcccCc-ccCCCCC
Q psy5725 104 AAQSLGT-STYFPFL 117 (117)
Q Consensus 104 aAQSIGE-P~TQ~~~ 117 (117)
+=-|||. |+|||-|
T Consensus 211 GY~SIG~~~~TqpV~ 225 (261)
T KOG0189|consen 211 GYRSIGDEHSTQPVL 225 (261)
T ss_pred CCeeccCccccCcCC
Confidence 3457875 8888754
No 31
>PF12502 DUF3710: Protein of unknown function (DUF3710) ; InterPro: IPR022183 This family of proteins is found in bacteria. Proteins in this family are typically between 237 and 284 amino acids in length. There are two conserved sequence motifs: DLG and DGPRW.
Probab=20.14 E-value=76 Score=24.48 Aligned_cols=22 Identities=18% Similarity=0.434 Sum_probs=18.1
Q ss_pred hHHHHHHHhhhcceeEcCCCcc
Q psy5725 21 GLNIGVRELLEKCVIVAGEDQL 42 (117)
Q Consensus 21 ~vi~~v~~L~~~l~vv~g~D~l 42 (117)
+...-+++++.+++|+||++++
T Consensus 139 ~~a~~l~ev~~~~VV~RG~~P~ 160 (181)
T PF12502_consen 139 EAAALLEEVFRRTVVVRGDEPM 160 (181)
T ss_pred HHHHHHHHHhcceEEeCCCCCC
Confidence 3667788999999999998753
Done!