Query psy7385
Match_columns 208
No_of_seqs 170 out of 757
Neff 6.5
Searched_HMMs 46136
Date Fri Aug 16 16:52:00 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy7385.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/7385hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK08719 ribonuclease H; Revie 98.9 1.3E-09 2.8E-14 87.2 3.4 42 11-53 105-146 (147)
2 PF00075 RNase_H: RNase H; In 98.7 2.3E-09 5E-14 82.2 0.2 34 19-52 97-131 (132)
3 PRK06548 ribonuclease H; Provi 98.7 6.3E-09 1.4E-13 84.6 2.4 43 11-54 100-142 (161)
4 PRK00203 rnhA ribonuclease H; 98.7 5.6E-09 1.2E-13 83.4 1.9 41 13-54 102-142 (150)
5 COG0328 RnhA Ribonuclease HI [ 98.5 4.5E-08 9.8E-13 79.0 2.6 44 11-54 102-145 (154)
6 cd06222 RnaseH RNase H (RNase 98.3 6.7E-07 1.4E-11 65.7 4.6 45 8-52 86-130 (130)
7 KOG3752|consensus 97.7 2.3E-05 5.1E-10 70.9 3.7 30 23-52 334-363 (371)
8 PF13966 zf-RVT: zinc-binding 95.4 0.011 2.4E-07 42.6 2.2 43 124-178 38-83 (86)
9 PRK13907 rnhA ribonuclease H; 95.2 0.018 3.9E-07 44.1 2.9 40 10-53 87-126 (128)
10 PF13456 RVT_3: Reverse transc 93.5 0.045 9.8E-07 38.2 1.8 40 9-52 46-85 (87)
11 PRK07238 bifunctional RNase H/ 90.8 0.22 4.8E-06 45.1 3.2 41 10-54 92-132 (372)
12 PRK07708 hypothetical protein; 87.5 0.45 9.8E-06 40.5 2.6 40 11-54 168-208 (219)
13 COG0296 GlgB 1,4-alpha-glucan 66.2 8.2 0.00018 38.0 4.3 34 13-46 216-249 (628)
14 PF09345 DUF1987: Domain of un 60.4 14 0.00031 27.6 3.8 26 8-33 60-85 (99)
15 PRK00061 ribH 6,7-dimethyl-8-r 37.9 29 0.00064 27.9 2.5 33 16-50 34-69 (154)
16 TIGR01506 ribC_arch riboflavin 34.6 36 0.00079 27.5 2.6 33 15-49 17-51 (151)
17 PF00885 DMRL_synthase: 6,7-di 34.5 42 0.00091 26.6 2.9 33 16-50 25-60 (144)
18 PRK12419 riboflavin synthase s 34.5 35 0.00076 27.8 2.5 32 16-49 32-66 (158)
19 PF02156 Glyco_hydro_26: Glyco 34.0 55 0.0012 29.3 3.9 31 5-37 131-161 (311)
20 PLN02404 6,7-dimethyl-8-ribity 31.3 46 0.00099 26.5 2.6 33 16-50 29-64 (141)
21 PRK06455 riboflavin synthase; 30.1 48 0.001 26.9 2.6 32 16-49 20-53 (155)
22 TIGR00114 lumazine-synth 6,7-d 29.5 50 0.0011 26.1 2.6 33 16-50 22-57 (138)
23 PRK12568 glycogen branching en 27.8 75 0.0016 32.0 4.0 32 10-41 318-349 (730)
24 KOG1930|consensus 26.7 64 0.0014 30.4 3.0 60 104-176 211-282 (483)
25 PF08030 NAD_binding_6: Ferric 25.4 77 0.0017 24.2 3.0 32 6-37 16-47 (156)
26 PHA02734 coat protein; Provisi 21.9 81 0.0017 24.9 2.4 42 8-49 57-108 (149)
27 TIGR02402 trehalose_TreZ malto 21.1 1.4E+02 0.0029 28.8 4.2 33 10-42 159-191 (542)
No 1
>PRK08719 ribonuclease H; Reviewed
Probab=98.87 E-value=1.3e-09 Score=87.25 Aligned_cols=42 Identities=29% Similarity=0.378 Sum_probs=36.9
Q ss_pred HHHHHHHHHHHhCCCceEEEEeccCCCCCcchHHhHhhCCCCC
Q psy7385 11 KNLFCLERSLKSCGKEGTLMWCPSQCGISGNEAVDMAAKNPTT 53 (208)
Q Consensus 11 ~~I~~~~~~L~~~g~~I~l~WVPgH~gi~GNE~AD~~Ak~A~~ 53 (208)
+++++.+..|.+. ..|+|.|||||+|++|||.||++|++|+.
T Consensus 105 ~dl~~~i~~l~~~-~~i~~~~VkgH~g~~~Ne~aD~lA~~a~~ 146 (147)
T PRK08719 105 RDLWQQVDELRAR-KYVEVEKVTAHSGIEGNEAADMLAQAAAE 146 (147)
T ss_pred HHHHHHHHHHhCC-CcEEEEEecCCCCChhHHHHHHHHHHHhh
Confidence 5678888888774 56999999999999999999999999874
No 2
>PF00075 RNase_H: RNase H; InterPro: IPR002156 The RNase H domain is responsible for hydrolysis of the RNA portion of RNA x DNA hybrids, and this activity requires the presence of divalent cations (Mg2+ or Mn2+) that bind its active site. This domain is a part of a large family of homologous RNase H enzymes of which the RNase HI protein from Escherichia coli is the best characterised []. Secondary structure predictions for the enzymes from E. coli, yeast, human liver and diverse retroviruses (such as Rous sarcoma virus and the Foamy viruses) supported, in every case, the five beta-strands (1 to 5) and four or five alpha-helices (A, B/C, D, E) that have been identified by crystallography in the RNase H domain of Human immunodeficiency virus 1 (HIV-1) reverse transcriptase and in E. coli RNase H []. Reverse transcriptase (RT) is a modular enzyme carrying polymerase and ribonuclease H (RNase H) activities in separable domains. Reverse transcriptase (RT) converts the single-stranded RNA genome of a retrovirus into a double-stranded DNA copy for integration into the host genome. This process requires ribonuclease H as well as RNA- and DNA-directed DNA polymerase activities. Retroviral RNase H is synthesised as part of the POL polyprotein that contains; an aspartyl protease, a reverse transcriptase, RNase H and integrase. POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. Bacterial RNase H 3.1.26.4 from EC catalyses endonucleolytic cleavage to 5'-phosphomonoester acting on RNA-DNA hybrids. The 3D structure of the RNase H domain from diverse bacteria and retroviruses has been solved [, , ]. All have four beta strands and four to five alpha helices. The E. coli RNase H1 protein binds a single Mg2+ ion cofactor in the active site of the enzyme. The divalent cation is bound by the carboxyl groups of four acidic residues, Asp-10, Glu-48, Asp-70, and Asp-134 []. The first three acidic residues are highly conserved in all bacterial and retroviral RNase H sequences. ; GO: 0003676 nucleic acid binding, 0004523 ribonuclease H activity; PDB: 3LP3_B 2KW4_A 3P1G_A 1RIL_A 2RPI_A 4EQJ_G 4EP2_B 3OTY_P 3U3G_D 2ZQB_D ....
Probab=98.72 E-value=2.3e-09 Score=82.19 Aligned_cols=34 Identities=35% Similarity=0.596 Sum_probs=29.6
Q ss_pred HHHhCCCceEEEEeccCCCC-CcchHHhHhhCCCC
Q psy7385 19 SLKSCGKEGTLMWCPSQCGI-SGNEAVDMAAKNPT 52 (208)
Q Consensus 19 ~L~~~g~~I~l~WVPgH~gi-~GNE~AD~~Ak~A~ 52 (208)
++...+..|.|.|||||+|+ .|||.||++||+|+
T Consensus 97 ~~~~~~~~v~~~~V~~H~~~~~~N~~aD~lAk~a~ 131 (132)
T PF00075_consen 97 ELLSRGIKVRFRWVPGHSGVPQGNERADRLAKEAA 131 (132)
T ss_dssp HHHHHSSEEEEEESSSSSSSHHHHHHHHHHHHHHH
T ss_pred eccccceEEeeeeccCcCCCchhHHHHHHHHHHhc
Confidence 33366889999999999999 69999999999874
No 3
>PRK06548 ribonuclease H; Provisional
Probab=98.71 E-value=6.3e-09 Score=84.63 Aligned_cols=43 Identities=21% Similarity=0.247 Sum_probs=36.6
Q ss_pred HHHHHHHHHHHhCCCceEEEEeccCCCCCcchHHhHhhCCCCCC
Q psy7385 11 KNLFCLERSLKSCGKEGTLMWCPSQCGISGNEAVDMAAKNPTTP 54 (208)
Q Consensus 11 ~~I~~~~~~L~~~g~~I~l~WVPgH~gi~GNE~AD~~Ak~A~~~ 54 (208)
+++++.+..|.+.. .|+|.|||||+|++|||.||++|++|+..
T Consensus 100 ~dL~~~l~~l~~~~-~v~~~wVkgHsg~~gNe~aD~LA~~aa~~ 142 (161)
T PRK06548 100 QEIIQEIDSLMENR-NIRMSWVNAHTGHPLNEAADSLARQAANN 142 (161)
T ss_pred HHHHHHHHHHHhcC-ceEEEEEecCCCCHHHHHHHHHHHHHHHH
Confidence 46667777777664 69999999999999999999999998865
No 4
>PRK00203 rnhA ribonuclease H; Reviewed
Probab=98.70 E-value=5.6e-09 Score=83.37 Aligned_cols=41 Identities=17% Similarity=0.187 Sum_probs=33.4
Q ss_pred HHHHHHHHHhCCCceEEEEeccCCCCCcchHHhHhhCCCCCC
Q psy7385 13 LFCLERSLKSCGKEGTLMWCPSQCGISGNEAVDMAAKNPTTP 54 (208)
Q Consensus 13 I~~~~~~L~~~g~~I~l~WVPgH~gi~GNE~AD~~Ak~A~~~ 54 (208)
+++.+.++... ..|.|.|||||+|++|||.||++||+|+..
T Consensus 102 l~~~i~~l~~~-~~v~~~wV~~H~~~~~N~~AD~lA~~a~~~ 142 (150)
T PRK00203 102 LWQRLDAALKR-HQIKWHWVKGHAGHPENERCDELARAGAEE 142 (150)
T ss_pred HHHHHHHHhcc-CceEEEEecCCCCCHHHHHHHHHHHHHHHH
Confidence 44555555444 679999999999999999999999988765
No 5
>COG0328 RnhA Ribonuclease HI [DNA replication, recombination, and repair]
Probab=98.53 E-value=4.5e-08 Score=79.00 Aligned_cols=44 Identities=20% Similarity=0.222 Sum_probs=39.2
Q ss_pred HHHHHHHHHHHhCCCceEEEEeccCCCCCcchHHhHhhCCCCCC
Q psy7385 11 KNLFCLERSLKSCGKEGTLMWCPSQCGISGNEAVDMAAKNPTTP 54 (208)
Q Consensus 11 ~~I~~~~~~L~~~g~~I~l~WVPgH~gi~GNE~AD~~Ak~A~~~ 54 (208)
+++++.+.++.++--.|.+.|||||.|.++||+||++|+.|+..
T Consensus 102 ~dl~~~~~~~~~~~~~v~~~WVkgH~g~~~NeraD~LA~~~~~~ 145 (154)
T COG0328 102 KDLWEELDELLKRHELVFWEWVKGHAGHPENERADQLAREAARA 145 (154)
T ss_pred HHHHHHHHHHHhhCCeEEEEEeeCCCCChHHHHHHHHHHHHHHh
Confidence 36788888888888789999999999999999999999988754
No 6
>cd06222 RnaseH RNase H (RNase HI) is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a not sequence-specific manner. One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. RNase H knockout mice lack mitochondrial DNA replication and die as embryos. The retroviral reverse transcriptase contains an RNase H domain that plays an important role in converting a single stranded retroviral genomic RNA into a dsDNA for integration into host chromosomes. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription.
Probab=98.34 E-value=6.7e-07 Score=65.71 Aligned_cols=45 Identities=27% Similarity=0.350 Sum_probs=38.0
Q ss_pred HHHHHHHHHHHHHHhCCCceEEEEeccCCCCCcchHHhHhhCCCC
Q psy7385 8 SDLKNLFCLERSLKSCGKEGTLMWCPSQCGISGNEAVDMAAKNPT 52 (208)
Q Consensus 8 ~~i~~I~~~~~~L~~~g~~I~l~WVPgH~gi~GNE~AD~~Ak~A~ 52 (208)
+.+..++..+..+...+..+.|.|||+|+|+++|+.||.+||+|.
T Consensus 86 ~~~~~~~~~i~~~~~~~~~~~i~~v~~h~~~~~n~~ad~la~~~~ 130 (130)
T cd06222 86 VKNVDLWQRLLALLKRFHKVRFEWVPGHSGIEGNERADALAKEAA 130 (130)
T ss_pred hhhHHHHHHHHHHHhCCCeEEEEEcCCCCCCcchHHHHHHHHhhC
Confidence 355666667777777888999999999999999999999999873
No 7
>KOG3752|consensus
Probab=97.75 E-value=2.3e-05 Score=70.89 Aligned_cols=30 Identities=27% Similarity=0.365 Sum_probs=28.1
Q ss_pred CCCceEEEEeccCCCCCcchHHhHhhCCCC
Q psy7385 23 CGKEGTLMWCPSQCGISGNEAVDMAAKNPT 52 (208)
Q Consensus 23 ~g~~I~l~WVPgH~gi~GNE~AD~~Ak~A~ 52 (208)
++..|++.|||||.||.|||+||.+|++.+
T Consensus 334 ~~~~vq~~~V~Gh~gi~gne~Ad~lARkgs 363 (371)
T KOG3752|consen 334 SNKKVQQEYVGGHSGILGNEMADALARKGS 363 (371)
T ss_pred ccCceEEEEecCcCCcchHHHHHHHHhhhh
Confidence 578999999999999999999999999875
No 8
>PF13966 zf-RVT: zinc-binding in reverse transcriptase
Probab=95.36 E-value=0.011 Score=42.56 Aligned_cols=43 Identities=26% Similarity=0.232 Sum_probs=28.8
Q ss_pred cccCcccc-ccccc--cCCCCCCCCcccccCCCCCccccCCCcccCCCeeeecCCCCh
Q psy7385 124 MRIGHTRL-THSHL--FTRSPQPACRQDIRRGPAGKTCCNTSVKAPNRKKEQHCKPHV 178 (208)
Q Consensus 124 LRTGH~~L-t~~yl--~~~~d~p~C~~C~~~~p~~~~~Cg~~~t~~~~HiL~~Cp~~~ 178 (208)
-|.-|.+| +..-| .+...++.|..| ++..||+ .|++++||.-.
T Consensus 38 W~~~~~rL~t~~~l~~r~~~~~~~C~~C----------~~~~Et~--~Hlf~~C~~a~ 83 (86)
T PF13966_consen 38 WRALHNRLPTKDNLQRRGIQVDPICPLC----------GNEEETI--EHLFFHCPFAR 83 (86)
T ss_pred eeeccccchhhhhhhccCCccCCccccC----------CCccccc--cceeccCcCcc
Confidence 34556666 23333 344567889876 5568877 99999999654
No 9
>PRK13907 rnhA ribonuclease H; Provisional
Probab=95.16 E-value=0.018 Score=44.14 Aligned_cols=40 Identities=20% Similarity=0.157 Sum_probs=32.4
Q ss_pred HHHHHHHHHHHHhCCCceEEEEeccCCCCCcchHHhHhhCCCCC
Q psy7385 10 LKNLFCLERSLKSCGKEGTLMWCPSQCGISGNEAVDMAAKNPTT 53 (208)
Q Consensus 10 i~~I~~~~~~L~~~g~~I~l~WVPgH~gi~GNE~AD~~Ak~A~~ 53 (208)
++.+++.+..|..+-..+.|.|||. ++|+.||.+|+.|..
T Consensus 87 ~~~l~~~~~~l~~~f~~~~~~~v~r----~~N~~Ad~LA~~a~~ 126 (128)
T PRK13907 87 FAPLLEEALQYIKSFDLFFIKWIPS----SQNKVADELARKAIL 126 (128)
T ss_pred HHHHHHHHHHHHhcCCceEEEEcCc----hhchhHHHHHHHHHh
Confidence 5566777777777777788899998 599999999998753
No 10
>PF13456 RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EHG_A 3HST_B.
Probab=93.52 E-value=0.045 Score=38.15 Aligned_cols=40 Identities=25% Similarity=0.121 Sum_probs=32.4
Q ss_pred HHHHHHHHHHHHHhCCCceEEEEeccCCCCCcchHHhHhhCCCC
Q psy7385 9 DLKNLFCLERSLKSCGKEGTLMWCPSQCGISGNEAVDMAAKNPT 52 (208)
Q Consensus 9 ~i~~I~~~~~~L~~~g~~I~l~WVPgH~gi~GNE~AD~~Ak~A~ 52 (208)
.+..+++.+..+.+.-..+.|.||| =++|..||.+||.|.
T Consensus 46 ~~~~~~~~i~~~~~~~~~~~~~~i~----r~~N~~A~~LA~~a~ 85 (87)
T PF13456_consen 46 ELRPLIQDIRSLLDRFWNVSVSHIP----REQNKVADALAKFAL 85 (87)
T ss_dssp CCHHHHHHHHHHHCCCSCEEEEE------GGGSHHHHHHHHHHH
T ss_pred cccccchhhhhhhccccceEEEEEC----hHHhHHHHHHHHHHh
Confidence 4567788888888888889999999 799999999998763
No 11
>PRK07238 bifunctional RNase H/acid phosphatase; Provisional
Probab=90.78 E-value=0.22 Score=45.07 Aligned_cols=41 Identities=27% Similarity=0.297 Sum_probs=32.4
Q ss_pred HHHHHHHHHHHHhCCCceEEEEeccCCCCCcchHHhHhhCCCCCC
Q psy7385 10 LKNLFCLERSLKSCGKEGTLMWCPSQCGISGNEAVDMAAKNPTTP 54 (208)
Q Consensus 10 i~~I~~~~~~L~~~g~~I~l~WVPgH~gi~GNE~AD~~Ak~A~~~ 54 (208)
+...++.+..|.+.-..+++.|||. ++|+.||.+|+.|...
T Consensus 92 l~~~~~~i~~l~~~f~~~~i~~v~r----~~N~~AD~LA~~a~~~ 132 (372)
T PRK07238 92 MKPLAAQARELASQFGRVTYTWIPR----ARNAHADRLANEAMDA 132 (372)
T ss_pred HHHHHHHHHHHHhcCCceEEEECCc----hhhhHHHHHHHHHHHh
Confidence 4455566667777667799999997 7899999999988655
No 12
>PRK07708 hypothetical protein; Validated
Probab=87.50 E-value=0.45 Score=40.51 Aligned_cols=40 Identities=8% Similarity=-0.144 Sum_probs=28.2
Q ss_pred HHHHHHHHHHHh-CCCceEEEEeccCCCCCcchHHhHhhCCCCCC
Q psy7385 11 KNLFCLERSLKS-CGKEGTLMWCPSQCGISGNEAVDMAAKNPTTP 54 (208)
Q Consensus 11 ~~I~~~~~~L~~-~g~~I~l~WVPgH~gi~GNE~AD~~Ak~A~~~ 54 (208)
+..++.+..+.+ -...+.+.||| -+.|+.||++|+.|...
T Consensus 168 ~~y~~~i~~l~~~~~l~~~~~~Vp----R~~N~~AD~LAk~Al~~ 208 (219)
T PRK07708 168 NHWLDRIEQKLKQLKLTPVYEPIS----RKQNKEADQLATQALEG 208 (219)
T ss_pred HHHHHHHHHHHhhCCceEEEEECC----chhhhHHHHHHHHHHhc
Confidence 344444444433 34457889998 46799999999999976
No 13
>COG0296 GlgB 1,4-alpha-glucan branching enzyme [Carbohydrate transport and metabolism]
Probab=66.18 E-value=8.2 Score=37.97 Aligned_cols=34 Identities=21% Similarity=0.299 Sum_probs=28.8
Q ss_pred HHHHHHHHHhCCCceEEEEeccCCCCCcchHHhH
Q psy7385 13 LFCLERSLKSCGKEGTLMWCPSQCGISGNEAVDM 46 (208)
Q Consensus 13 I~~~~~~L~~~g~~I~l~WVPgH~gi~GNE~AD~ 46 (208)
.-..++...+.|..|-|-|||+|-+..||-++--
T Consensus 216 fk~fVD~aH~~GIgViLD~V~~HF~~d~~~L~~f 249 (628)
T COG0296 216 FKALVDAAHQAGIGVILDWVPNHFPPDGNYLARF 249 (628)
T ss_pred HHHHHHHHHHcCCEEEEEecCCcCCCCcchhhhc
Confidence 3455668899999999999999999999987753
No 14
>PF09345 DUF1987: Domain of unknown function (DUF1987); InterPro: IPR018530 This family of proteins are functionally uncharacterised.
Probab=60.44 E-value=14 Score=27.58 Aligned_cols=26 Identities=23% Similarity=0.325 Sum_probs=21.8
Q ss_pred HHHHHHHHHHHHHHhCCCceEEEEec
Q psy7385 8 SDLKNLFCLERSLKSCGKEGTLMWCP 33 (208)
Q Consensus 8 ~~i~~I~~~~~~L~~~g~~I~l~WVP 33 (208)
+.|-.|++.++++.+.|..|++.|.=
T Consensus 60 k~l~~i~~~Le~~~~~g~~V~v~Wyy 85 (99)
T PF09345_consen 60 KALMDIFDLLEDAAQKGGKVTVNWYY 85 (99)
T ss_pred HHHHHHHHHHHHHHhcCCcEEEEEEE
Confidence 45667888888889999999999974
No 15
>PRK00061 ribH 6,7-dimethyl-8-ribityllumazine synthase; Provisional
Probab=37.89 E-value=29 Score=27.93 Aligned_cols=33 Identities=21% Similarity=0.200 Sum_probs=24.5
Q ss_pred HHHHHHhCC---CceEEEEeccCCCCCcchHHhHhhCC
Q psy7385 16 LERSLKSCG---KEGTLMWCPSQCGISGNEAVDMAAKN 50 (208)
Q Consensus 16 ~~~~L~~~g---~~I~l~WVPgH~gi~GNE~AD~~Ak~ 50 (208)
+++.|.+.| ..|.+.||||=-.||. .|.++|+.
T Consensus 34 a~~~l~~~gv~~~~i~v~~VPGa~EiP~--a~~~l~~~ 69 (154)
T PRK00061 34 ALDALKRHGVSEENIDVVRVPGAFEIPL--AAKKLAES 69 (154)
T ss_pred HHHHHHHcCCCccceEEEECCCHHHHHH--HHHHHHHc
Confidence 456778888 6799999999887775 45556643
No 16
>TIGR01506 ribC_arch riboflavin synthase. This archaeal protein catalyzes the same reaction, the final step in riboflavin biosynthesis, as bacterial riboflavin biosynthesis alpha chain. However, it is more similar in sequence to 6,7-dimethyl-8-ribityllumazine synthase, which catalyzes the previous reaction and which (in bacteria) is called the riboflavin synthase beta chain.
Probab=34.65 E-value=36 Score=27.46 Aligned_cols=33 Identities=12% Similarity=0.010 Sum_probs=24.8
Q ss_pred HHHHHHHh--CCCceEEEEeccCCCCCcchHHhHhhC
Q psy7385 15 CLERSLKS--CGKEGTLMWCPSQCGISGNEAVDMAAK 49 (208)
Q Consensus 15 ~~~~~L~~--~g~~I~l~WVPgH~gi~GNE~AD~~Ak 49 (208)
-+++.|.+ .|..|.+.||||=-.||. .|+++++
T Consensus 17 gA~~~L~~~g~g~~i~v~~VPGa~EiP~--aak~l~~ 51 (151)
T TIGR01506 17 AAIDELRKHTAGIKIIRRTVPGIKDLPV--AAKKLLE 51 (151)
T ss_pred HHHHHHHhcCCCCeEEEEECCcHhHHHH--HHHHHHh
Confidence 35667777 788899999999887774 4556664
No 17
>PF00885 DMRL_synthase: 6,7-dimethyl-8-ribityllumazine synthase; InterPro: IPR002180 6,7-dimethyl-8-ribityllumazine synthase (riboflavin synthase) catalyses the biosynthesis of riboflavin according to the reaction: 2 6,7-dimethyl-8-(1-D-ribityl)lumazine = riboflavin + 4-(1-D-ribitylamino)-5-amino-2,6-dihydroxypyrimidine. The biosynthesis of one riboflavin molecule requires one molecule of GTP and two molecules of ribulose 5-phosphate as substrates. The final step in the biosynthesis of the vitamin involves the dismutation of 6,7-dimethyl-8-ribityllumazine catalyzed by riboflavin synthase. The second product, 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione, is recycled in the biosynthetic pathway by 6,7-dimethyl-8-ribityllumazine synthase []. N-[2,4-dioxo-6-d-ribitylamino-1,2,3,4-tetrahydropyrimidin-5-yl]oxalamic acid derivatives inhibit riboflavin synthase []. This family includes the beta chain of 6,7-dimethyl-8-ribityllumazine synthase 2.5.1.9 from EC. The family also includes a subfamily of distant archaebacterial proteins that may also have the same function for example O28856 from SWISSPROT.; GO: 0009231 riboflavin biosynthetic process, 0009349 riboflavin synthase complex; PDB: 2O6H_D 1C41_C 2OBX_H 1VSX_H 1VSW_3 3JV8_C 3MK3_r 3NQ4_G 2A58_A 2A57_D ....
Probab=34.54 E-value=42 Score=26.64 Aligned_cols=33 Identities=18% Similarity=0.162 Sum_probs=25.7
Q ss_pred HHHHHHhCCC---ceEEEEeccCCCCCcchHHhHhhCC
Q psy7385 16 LERSLKSCGK---EGTLMWCPSQCGISGNEAVDMAAKN 50 (208)
Q Consensus 16 ~~~~L~~~g~---~I~l~WVPgH~gi~GNE~AD~~Ak~ 50 (208)
+++.|.+.|. .|...||||=-.+|. .|+++++.
T Consensus 25 a~~~l~~~g~~~~~i~~~~VPGa~ElP~--a~~~l~~~ 60 (144)
T PF00885_consen 25 ALEELKRHGVAEENIEVIRVPGAFELPL--AAKRLAES 60 (144)
T ss_dssp HHHHHHHTTTTGGCEEEEEESSGGGHHH--HHHHHHHC
T ss_pred HHHHHHHcCCCccceEEEEcCCHHHHHH--HHHHHhcc
Confidence 5677888887 899999999877764 56777754
No 18
>PRK12419 riboflavin synthase subunit beta; Provisional
Probab=34.52 E-value=35 Score=27.76 Aligned_cols=32 Identities=16% Similarity=0.164 Sum_probs=22.9
Q ss_pred HHHHHHhCC---CceEEEEeccCCCCCcchHHhHhhC
Q psy7385 16 LERSLKSCG---KEGTLMWCPSQCGISGNEAVDMAAK 49 (208)
Q Consensus 16 ~~~~L~~~g---~~I~l~WVPgH~gi~GNE~AD~~Ak 49 (208)
+.+.|.+.| ..|.+.||||--.||. .|.++|+
T Consensus 32 A~~~l~~~G~~~~~i~v~~VPGA~EiP~--~a~~l~~ 66 (158)
T PRK12419 32 FVAEIAARGGAASQVDIFDVPGAFEIPL--HAQTLAK 66 (158)
T ss_pred HHHHHHHcCCCccceEEEECCcHHHHHH--HHHHHHh
Confidence 455677888 5699999999877764 4455554
No 19
>PF02156 Glyco_hydro_26: Glycosyl hydrolase family 26; InterPro: IPR022790 O-Glycosyl hydrolases 3.2.1. from EC are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families [, ]. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. Glycoside hydrolase family 26 GH26 from CAZY encompasses mainly mannan endo-1,4-beta-mannosidases (3.2.1.78 from EC). Mannan endo-1,4-beta-mannosidase hydrolyses mannan and galactomannan, but displays little activity towards other plant cell wall polysaccharides []. The enzyme randomly hydrolyses 1,4-beta-D-linkages in mannans, galacto-mannans, glucomannans and galactoglucomannans. This entry also incoporates the enzyme Endogluconase H 3.2.1.4 from EC catalyzes the endohydrolysis of 1,4-beta-glucosidic linkages in cellulose, lichenin and cereal beta-D-glucans. ; GO: 0008810 cellulase activity, 0016985 mannan endo-1,4-beta-mannosidase activity, 0006080 substituted mannan metabolic process; PDB: 2QHA_A 3CBW_A 2WHK_A 2VI0_A 2BVD_A 2BV9_A 2CIT_A 2V3G_A 2CIP_A 2X2Y_B ....
Probab=34.03 E-value=55 Score=29.29 Aligned_cols=31 Identities=19% Similarity=0.233 Sum_probs=25.7
Q ss_pred HHHHHHHHHHHHHHHHHhCCCceEEEEeccCCC
Q psy7385 5 QKLSDLKNLFCLERSLKSCGKEGTLMWCPSQCG 37 (208)
Q Consensus 5 ~~~~~i~~I~~~~~~L~~~g~~I~l~WVPgH~g 37 (208)
-+++.|..|.+.+++|+..| |-+.|=|+|.-
T Consensus 131 ~~~~~ld~iA~~l~~l~~~~--vPVl~Rp~HE~ 161 (311)
T PF02156_consen 131 AFKADLDRIADFLKQLKDAG--VPVLFRPFHEM 161 (311)
T ss_dssp HHHHHHHHHHHHHHHHHCTT--S-EEEEESTST
T ss_pred HHHHHHHHHHHHHHHhhcCC--CeEEEeehhhc
Confidence 35788899999999999888 88889999974
No 20
>PLN02404 6,7-dimethyl-8-ribityllumazine synthase
Probab=31.28 E-value=46 Score=26.53 Aligned_cols=33 Identities=18% Similarity=0.282 Sum_probs=24.2
Q ss_pred HHHHHHhCCCc---eEEEEeccCCCCCcchHHhHhhCC
Q psy7385 16 LERSLKSCGKE---GTLMWCPSQCGISGNEAVDMAAKN 50 (208)
Q Consensus 16 ~~~~L~~~g~~---I~l~WVPgH~gi~GNE~AD~~Ak~ 50 (208)
+.+.|...|.. |.+.||||=-.||. .|+++|+.
T Consensus 29 a~~~l~~~gv~~~~i~v~~VPGa~EiP~--a~~~l~~s 64 (141)
T PLN02404 29 ALETFKRYSVKEENIDVVWVPGSFEIPV--VAQRLAKS 64 (141)
T ss_pred HHHHHHHcCCCccceEEEEcCcHHHHHH--HHHHHHhc
Confidence 44577788864 89999999887774 56666653
No 21
>PRK06455 riboflavin synthase; Provisional
Probab=30.13 E-value=48 Score=26.90 Aligned_cols=32 Identities=9% Similarity=-0.060 Sum_probs=22.9
Q ss_pred HHHHHHh--CCCceEEEEeccCCCCCcchHHhHhhC
Q psy7385 16 LERSLKS--CGKEGTLMWCPSQCGISGNEAVDMAAK 49 (208)
Q Consensus 16 ~~~~L~~--~g~~I~l~WVPgH~gi~GNE~AD~~Ak 49 (208)
+++.|++ .|..|.+.||||=-.||. .|.++++
T Consensus 20 Ai~~L~~~g~~~~I~v~~VPGa~ELP~--aakkL~~ 53 (155)
T PRK06455 20 AIDELRKLDPSAKIIRYTVPGIKDLPV--AAKKLIE 53 (155)
T ss_pred HHHHHHhcCCCCceEEEECCCHHHHHH--HHHHHHh
Confidence 5566777 557899999999777764 4556664
No 22
>TIGR00114 lumazine-synth 6,7-dimethyl-8-ribityllumazine synthase. Archaeal members of this family are considered putative, although included in the seed and scoring above the trusted cutoff.
Probab=29.46 E-value=50 Score=26.11 Aligned_cols=33 Identities=27% Similarity=0.395 Sum_probs=24.1
Q ss_pred HHHHHHhCCCc---eEEEEeccCCCCCcchHHhHhhCC
Q psy7385 16 LERSLKSCGKE---GTLMWCPSQCGISGNEAVDMAAKN 50 (208)
Q Consensus 16 ~~~~L~~~g~~---I~l~WVPgH~gi~GNE~AD~~Ak~ 50 (208)
+.+.|.+.|.. |...||||=-.||. .|+++++.
T Consensus 22 a~~~l~~~g~~~~~i~v~~VPGa~EiP~--a~~~l~~~ 57 (138)
T TIGR00114 22 AIDALKRLGAEVDNIDVIWVPGAFELPL--AVKKLAET 57 (138)
T ss_pred HHHHHHHcCCCccceEEEECCcHHHHHH--HHHHHHhc
Confidence 45567777764 78999999888875 56666654
No 23
>PRK12568 glycogen branching enzyme; Provisional
Probab=27.78 E-value=75 Score=31.98 Aligned_cols=32 Identities=9% Similarity=0.105 Sum_probs=26.8
Q ss_pred HHHHHHHHHHHHhCCCceEEEEeccCCCCCcc
Q psy7385 10 LKNLFCLERSLKSCGKEGTLMWCPSQCGISGN 41 (208)
Q Consensus 10 i~~I~~~~~~L~~~g~~I~l~WVPgH~gi~GN 41 (208)
..+.-+.++++.+.|..|-+-|||.|++-.++
T Consensus 318 ~~dfk~lV~~~H~~Gi~VIlD~V~nH~~~d~~ 349 (730)
T PRK12568 318 PDGFAQFVDACHRAGIGVILDWVSAHFPDDAH 349 (730)
T ss_pred HHHHHHHHHHHHHCCCEEEEEeccccCCcccc
Confidence 34566778899999999999999999987654
No 24
>KOG1930|consensus
Probab=26.69 E-value=64 Score=30.44 Aligned_cols=60 Identities=23% Similarity=0.268 Sum_probs=36.3
Q ss_pred cccCCCCCCCchhhhhhhhh--------cccCccccccccc--cCCCCCCCCcccccCCCCCccccCC--CcccCCCeee
Q psy7385 104 VENWASRNRDTRYEEVALAR--------MRIGHTRLTHSHL--FTRSPQPACRQDIRRGPAGKTCCNT--SVKAPNRKKE 171 (208)
Q Consensus 104 ~~~w~~~~L~sR~~~~iL~q--------LRTGH~~Lt~~yl--~~~~d~p~C~~C~~~~p~~~~~Cg~--~~t~~~~HiL 171 (208)
.+.|..+++ +|.+++.|-+ +|-.|++- -.|- ++...+|--.. |-+ |. .|-| +|||
T Consensus 211 SKyWYKP~i-sREQAIalLrdkePGtFvvRDS~Sfr-GayGLAlKVstPPPs~~-----~~~----g~~~neLV--RHFL 277 (483)
T KOG1930|consen 211 SKYWYKPNI-SREQAIALLRDKEPGTFVVRDSHSFR-GAYGLALKVSTPPPSVQ-----PGD----GSDSNELV--RHFL 277 (483)
T ss_pred cccccCCCC-CHHHHHHHhhcCCCCeEEEecCCcCC-CccceEEEeccCCCccc-----CCC----CCchhhhh--hhhe
Confidence 578877899 9999987765 45555554 3343 45554443221 110 22 2545 9999
Q ss_pred ecCCC
Q psy7385 172 QHCKP 176 (208)
Q Consensus 172 ~~Cp~ 176 (208)
+||..
T Consensus 278 IE~sp 282 (483)
T KOG1930|consen 278 IEPSP 282 (483)
T ss_pred eccCC
Confidence 99864
No 25
>PF08030 NAD_binding_6: Ferric reductase NAD binding domain; InterPro: IPR013121 This entry contains ferric reductase NAD binding proteins.; GO: 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 3A1F_A.
Probab=25.45 E-value=77 Score=24.21 Aligned_cols=32 Identities=19% Similarity=0.243 Sum_probs=18.9
Q ss_pred HHHHHHHHHHHHHHHHhCCCceEEEEeccCCC
Q psy7385 6 KLSDLKNLFCLERSLKSCGKEGTLMWCPSQCG 37 (208)
Q Consensus 6 ~~~~i~~I~~~~~~L~~~g~~I~l~WVPgH~g 37 (208)
.|++|..+....+.-......|.|.|+==+.+
T Consensus 16 ~l~~l~~l~~~~~~~~~~~~~i~lvW~vR~~~ 47 (156)
T PF08030_consen 16 ILPILRDLLQRQNRGSSRTRRIKLVWVVRDAD 47 (156)
T ss_dssp HHHHHHHHHHHHHTT-----EEEEEEEES-TT
T ss_pred HHHHHHHHHHhhccccccccceEEEEeeCchh
Confidence 46777777776664445567799999864443
No 26
>PHA02734 coat protein; Provisional
Probab=21.91 E-value=81 Score=24.87 Aligned_cols=42 Identities=26% Similarity=0.342 Sum_probs=30.9
Q ss_pred HHHHHHHHHHHHHHhCCCceEEEEe----------ccCCCCCcchHHhHhhC
Q psy7385 8 SDLKNLFCLERSLKSCGKEGTLMWC----------PSQCGISGNEAVDMAAK 49 (208)
Q Consensus 8 ~~i~~I~~~~~~L~~~g~~I~l~WV----------PgH~gi~GNE~AD~~Ak 49 (208)
.+|+.|-++-+-|+++|+...=-|| |-...|+||-.|.--||
T Consensus 57 eiIK~IreA~kp~rn~g~gfkeawvyfsqvpenappns~~~p~~i~~qv~a~ 108 (149)
T PHA02734 57 AIIKMIKDAMKPLRNKGKGFKEAWVYFSQVPENAPPNSQAIPGEIAAQVKAK 108 (149)
T ss_pred HHHHHHHHHhhhhhhcCCchhHHHHhhhcCcccCCCcCCCCCHHHHHHHHhc
Confidence 4678888888889999998887776 34556777766665554
No 27
>TIGR02402 trehalose_TreZ malto-oligosyltrehalose trehalohydrolase. Members of this family are the trehalose biosynthetic enzyme malto-oligosyltrehalose trehalohydrolase, formally known as 4-alpha-D-{(1-4)-alpha-D-glucano}trehalose trehalohydrolase (EC 3.2.1.141). It is the TreZ protein of the TreYZ pathway for trehalose biosynthesis, and alternative to the OtsAB system.
Probab=21.05 E-value=1.4e+02 Score=28.83 Aligned_cols=33 Identities=21% Similarity=0.114 Sum_probs=27.9
Q ss_pred HHHHHHHHHHHHhCCCceEEEEeccCCCCCcch
Q psy7385 10 LKNLFCLERSLKSCGKEGTLMWCPSQCGISGNE 42 (208)
Q Consensus 10 i~~I~~~~~~L~~~g~~I~l~WVPgH~gi~GNE 42 (208)
+.+.-+.++.+.++|..|-+-+|+.|+|-.|+-
T Consensus 159 ~~e~k~lV~~aH~~Gi~VilD~V~NH~~~~~~~ 191 (542)
T TIGR02402 159 PDDLKALVDAAHGLGLGVILDVVYNHFGPEGNY 191 (542)
T ss_pred HHHHHHHHHHHHHCCCEEEEEEccCCCCCcccc
Confidence 356677788999999999999999999877664
Done!