Query 035454
Match_columns 52
No_of_seqs 100 out of 106
Neff 4.0
Searched_HMMs 46136
Date Fri Mar 29 03:05:32 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/035454.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/035454hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF13456 RVT_3: Reverse transc 99.2 3.6E-11 7.9E-16 66.2 4.3 40 1-40 47-86 (87)
2 PRK13907 rnhA ribonuclease H; 99.0 2.7E-10 5.8E-15 68.6 4.0 41 1-41 87-127 (128)
3 PRK07238 bifunctional RNase H/ 98.9 1.7E-09 3.8E-14 75.1 3.8 47 1-47 92-138 (372)
4 PRK07708 hypothetical protein; 98.8 5.1E-09 1.1E-13 70.7 3.9 42 1-42 167-209 (219)
5 cd06222 RnaseH RNase H (RNase 98.6 1.1E-07 2.4E-12 52.5 4.2 38 2-39 89-130 (130)
6 COG0328 RnhA Ribonuclease HI [ 98.2 1.4E-06 3.1E-11 57.2 3.8 41 2-42 102-146 (154)
7 PRK00203 rnhA ribonuclease H; 97.9 1.5E-05 3.3E-10 49.8 3.5 41 2-43 100-144 (150)
8 PRK08719 ribonuclease H; Revie 97.8 3.7E-05 8.1E-10 48.9 4.1 39 2-41 105-147 (147)
9 PF00075 RNase_H: RNase H; In 97.7 3E-05 6.5E-10 45.5 2.5 37 3-39 90-131 (132)
10 PRK06548 ribonuclease H; Provi 96.2 0.01 2.2E-07 38.7 4.2 40 2-42 100-143 (161)
11 PF03993 DUF349: Domain of Unk 67.3 3.3 7.2E-05 22.6 1.1 24 3-28 54-77 (77)
12 COG0695 GrxC Glutaredoxin and 59.5 25 0.00053 19.9 3.8 35 3-37 12-47 (80)
13 PHA03044 IMV membrane protein; 42.8 13 0.00028 22.4 0.8 25 5-30 49-73 (74)
14 smart00843 Ftsk_gamma This dom 42.7 15 0.00032 21.1 1.1 27 2-28 4-30 (63)
15 PRK11200 grxA glutaredoxin 1; 42.2 54 0.0012 18.0 3.4 26 3-28 12-41 (85)
16 cd03029 GRX_hybridPRX5 Glutare 36.0 70 0.0015 16.8 3.3 29 3-32 12-40 (72)
17 KOG3752 Ribonuclease H [Replic 34.8 60 0.0013 24.4 3.5 38 4-41 322-365 (371)
18 TIGR00228 ruvC crossover junct 32.6 32 0.00069 22.6 1.6 27 6-36 117-143 (156)
19 TIGR02190 GlrX-dom Glutaredoxi 30.3 99 0.0021 16.8 3.3 30 3-33 19-48 (79)
20 TIGR02180 GRX_euk Glutaredoxin 30.0 91 0.002 16.3 4.1 27 3-29 10-39 (84)
21 TIGR02194 GlrX_NrdH Glutaredox 27.6 1E+02 0.0022 16.3 2.9 32 3-35 10-42 (72)
22 TIGR02189 GlrX-like_plant Glut 26.8 1.3E+02 0.0027 17.5 3.3 22 3-24 19-41 (99)
23 cd03027 GRX_DEP Glutaredoxin ( 25.6 1.2E+02 0.0025 16.0 3.3 27 3-30 12-38 (73)
24 TIGR02183 GRXA Glutaredoxin, G 23.9 1E+02 0.0022 17.2 2.5 13 3-15 11-23 (86)
25 PF13250 DUF4041: Domain of un 22.8 24 0.00053 19.5 -0.3 14 23-36 3-16 (56)
26 PF09397 Ftsk_gamma: Ftsk gamm 21.6 22 0.00048 20.3 -0.6 27 2-28 5-31 (65)
27 PF13641 Glyco_tranf_2_3: Glyc 21.2 1.2E+02 0.0026 18.5 2.6 39 6-45 46-88 (228)
No 1
>PF13456 RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EHG_A 3HST_B.
Probab=99.18 E-value=3.6e-11 Score=66.21 Aligned_cols=40 Identities=35% Similarity=0.516 Sum_probs=35.3
Q ss_pred ChHHHHHHHHHhhcccceeEeeecCCCChHHHHHHhHhhc
Q 035454 1 MAKLCGEARRLKDKFLSFQISHVLRNLNSEADAQATLAVG 40 (52)
Q Consensus 1 m~~L~~~a~~L~~~F~~f~i~HVpRE~N~~AD~LAN~A~d 40 (52)
+.++...++.++..|.+|++.||||+.|+.||.||+.|+.
T Consensus 47 ~~~~~~~i~~~~~~~~~~~~~~i~r~~N~~A~~LA~~a~~ 86 (87)
T PF13456_consen 47 LRPLIQDIRSLLDRFWNVSVSHIPREQNKVADALAKFALS 86 (87)
T ss_dssp CHHHHHHHHHHHCCCSCEEEEE--GGGSHHHHHHHHHHHH
T ss_pred ccccchhhhhhhccccceEEEEEChHHhHHHHHHHHHHhh
Confidence 4678899999999999999999999999999999999874
No 2
>PRK13907 rnhA ribonuclease H; Provisional
Probab=99.04 E-value=2.7e-10 Score=68.64 Aligned_cols=41 Identities=29% Similarity=0.201 Sum_probs=38.1
Q ss_pred ChHHHHHHHHHhhcccceeEeeecCCCChHHHHHHhHhhcc
Q 035454 1 MAKLCGEARRLKDKFLSFQISHVLRNLNSEADAQATLAVGL 41 (52)
Q Consensus 1 m~~L~~~a~~L~~~F~~f~i~HVpRE~N~~AD~LAN~A~dl 41 (52)
+.+|+++++.|+.+|+.+.+.||||+.|+.||+||+.|+..
T Consensus 87 ~~~l~~~~~~l~~~f~~~~~~~v~r~~N~~Ad~LA~~a~~~ 127 (128)
T PRK13907 87 FAPLLEEALQYIKSFDLFFIKWIPSSQNKVADELARKAILQ 127 (128)
T ss_pred HHHHHHHHHHHHhcCCceEEEEcCchhchhHHHHHHHHHhc
Confidence 46789999999999999999999999999999999999863
No 3
>PRK07238 bifunctional RNase H/acid phosphatase; Provisional
Probab=98.88 E-value=1.7e-09 Score=75.08 Aligned_cols=47 Identities=30% Similarity=0.343 Sum_probs=42.6
Q ss_pred ChHHHHHHHHHhhcccceeEeeecCCCChHHHHHHhHhhcccCcchh
Q 035454 1 MAKLCGEARRLKDKFLSFQISHVLRNLNSEADAQATLAVGLADGEVA 47 (52)
Q Consensus 1 m~~L~~~a~~L~~~F~~f~i~HVpRE~N~~AD~LAN~A~dl~~g~~~ 47 (52)
|..|+.++++|+.+|++++|.||||+.|..||.||+.|++...+.+.
T Consensus 92 l~~~~~~i~~l~~~f~~~~i~~v~r~~N~~AD~LA~~a~~~~~~~~~ 138 (372)
T PRK07238 92 MKPLAAQARELASQFGRVTYTWIPRARNAHADRLANEAMDAAAGGEP 138 (372)
T ss_pred HHHHHHHHHHHHhcCCceEEEECCchhhhHHHHHHHHHHHhhccCCC
Confidence 45788999999999999999999999999999999999998876554
No 4
>PRK07708 hypothetical protein; Validated
Probab=98.80 E-value=5.1e-09 Score=70.72 Aligned_cols=42 Identities=19% Similarity=0.124 Sum_probs=37.6
Q ss_pred ChHHHHHHHHHhhccc-ceeEeeecCCCChHHHHHHhHhhccc
Q 035454 1 MAKLCGEARRLKDKFL-SFQISHVLRNLNSEADAQATLAVGLA 42 (52)
Q Consensus 1 m~~L~~~a~~L~~~F~-~f~i~HVpRE~N~~AD~LAN~A~dl~ 42 (52)
|.+++.++.+++.+|. +|.+.||||+.|+.||+|||.|++..
T Consensus 167 l~~y~~~i~~l~~~~~l~~~~~~VpR~~N~~AD~LAk~Al~~~ 209 (219)
T PRK07708 167 LNHWLDRIEQKLKQLKLTPVYEPISRKQNKEADQLATQALEGT 209 (219)
T ss_pred HHHHHHHHHHHHhhCCceEEEEECCchhhhHHHHHHHHHHhcC
Confidence 4578899999999998 48999999999999999999999854
No 5
>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=98.58 E-value=1.1e-07 Score=52.52 Aligned_cols=38 Identities=26% Similarity=0.198 Sum_probs=34.4
Q ss_pred hHHHHHHHHHhhcccceeEeeecC----CCChHHHHHHhHhh
Q 035454 2 AKLCGEARRLKDKFLSFQISHVLR----NLNSEADAQATLAV 39 (52)
Q Consensus 2 ~~L~~~a~~L~~~F~~f~i~HVpR----E~N~~AD~LAN~A~ 39 (52)
.+++..+.+++.++..+.|.|||| ..|..||.||++|+
T Consensus 89 ~~~~~~i~~~~~~~~~~~i~~v~~h~~~~~n~~ad~la~~~~ 130 (130)
T cd06222 89 VDLWQRLLALLKRFHKVRFEWVPGHSGIEGNERADALAKEAA 130 (130)
T ss_pred HHHHHHHHHHHhCCCeEEEEEcCCCCCCcchHHHHHHHHhhC
Confidence 567788888888899999999999 99999999999875
No 6
>COG0328 RnhA Ribonuclease HI [DNA replication, recombination, and repair]
Probab=98.23 E-value=1.4e-06 Score=57.17 Aligned_cols=41 Identities=24% Similarity=0.084 Sum_probs=38.3
Q ss_pred hHHHHHHHHHhhcccceeEeeec----CCCChHHHHHHhHhhccc
Q 035454 2 AKLCGEARRLKDKFLSFQISHVL----RNLNSEADAQATLAVGLA 42 (52)
Q Consensus 2 ~~L~~~a~~L~~~F~~f~i~HVp----RE~N~~AD~LAN~A~dl~ 42 (52)
+.||.++.++..+|..|.++||| +..|.+||+||+.|++.+
T Consensus 102 ~dl~~~~~~~~~~~~~v~~~WVkgH~g~~~NeraD~LA~~~~~~~ 146 (154)
T COG0328 102 KDLWEELDELLKRHELVFWEWVKGHAGHPENERADQLAREAARAA 146 (154)
T ss_pred HHHHHHHHHHHhhCCeEEEEEeeCCCCChHHHHHHHHHHHHHHhh
Confidence 46899999999999999999999 999999999999998865
No 7
>PRK00203 rnhA ribonuclease H; Reviewed
Probab=97.89 E-value=1.5e-05 Score=49.80 Aligned_cols=41 Identities=15% Similarity=0.046 Sum_probs=34.9
Q ss_pred hHHHHHHHHHhhcccceeEeeec----CCCChHHHHHHhHhhcccC
Q 035454 2 AKLCGEARRLKDKFLSFQISHVL----RNLNSEADAQATLAVGLAD 43 (52)
Q Consensus 2 ~~L~~~a~~L~~~F~~f~i~HVp----RE~N~~AD~LAN~A~dl~~ 43 (52)
.+|+++..+++.+ ..++|.||| ++.|..||+||+.|++.+.
T Consensus 100 ~dl~~~i~~l~~~-~~v~~~wV~~H~~~~~N~~AD~lA~~a~~~~~ 144 (150)
T PRK00203 100 VDLWQRLDAALKR-HQIKWHWVKGHAGHPENERCDELARAGAEEAT 144 (150)
T ss_pred HHHHHHHHHHhcc-CceEEEEecCCCCCHHHHHHHHHHHHHHHHhh
Confidence 3578888888877 469999999 8889999999999998654
No 8
>PRK08719 ribonuclease H; Reviewed
Probab=97.79 E-value=3.7e-05 Score=48.88 Aligned_cols=39 Identities=23% Similarity=0.193 Sum_probs=33.1
Q ss_pred hHHHHHHHHHhhcccceeEeeecC----CCChHHHHHHhHhhcc
Q 035454 2 AKLCGEARRLKDKFLSFQISHVLR----NLNSEADAQATLAVGL 41 (52)
Q Consensus 2 ~~L~~~a~~L~~~F~~f~i~HVpR----E~N~~AD~LAN~A~dl 41 (52)
..|++++.+|.. +..++|.|||+ ..|..||+||+.|..+
T Consensus 105 ~dl~~~i~~l~~-~~~i~~~~VkgH~g~~~Ne~aD~lA~~a~~~ 147 (147)
T PRK08719 105 RDLWQQVDELRA-RKYVEVEKVTAHSGIEGNEAADMLAQAAAEL 147 (147)
T ss_pred HHHHHHHHHHhC-CCcEEEEEecCCCCChhHHHHHHHHHHHhhC
Confidence 357888888877 56799999999 6799999999999764
No 9
>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=97.70 E-value=3e-05 Score=45.51 Aligned_cols=37 Identities=22% Similarity=0.130 Sum_probs=31.7
Q ss_pred HHHHHHHHHhhcccceeEeeecCC-----CChHHHHHHhHhh
Q 035454 3 KLCGEARRLKDKFLSFQISHVLRN-----LNSEADAQATLAV 39 (52)
Q Consensus 3 ~L~~~a~~L~~~F~~f~i~HVpRE-----~N~~AD~LAN~A~ 39 (52)
++.++..+++.+...+.|.|||.. .|..||+||+.|+
T Consensus 90 ~i~~~i~~~~~~~~~v~~~~V~~H~~~~~~N~~aD~lAk~a~ 131 (132)
T PF00075_consen 90 PIKNEIWELLSRGIKVRFRWVPGHSGVPQGNERADRLAKEAA 131 (132)
T ss_dssp BHTHHHHHHHHHSSEEEEEESSSSSSSHHHHHHHHHHHHHHH
T ss_pred cchhheeeccccceEEeeeeccCcCCCchhHHHHHHHHHHhc
Confidence 566778888877788999999999 5679999999986
No 10
>PRK06548 ribonuclease H; Provisional
Probab=96.18 E-value=0.01 Score=38.74 Aligned_cols=40 Identities=25% Similarity=0.218 Sum_probs=32.5
Q ss_pred hHHHHHHHHHhhcccceeEeeecC----CCChHHHHHHhHhhccc
Q 035454 2 AKLCGEARRLKDKFLSFQISHVLR----NLNSEADAQATLAVGLA 42 (52)
Q Consensus 2 ~~L~~~a~~L~~~F~~f~i~HVpR----E~N~~AD~LAN~A~dl~ 42 (52)
..|+++..+|+.+. .++|.||+= ..|..||+||++|.+..
T Consensus 100 ~dL~~~l~~l~~~~-~v~~~wVkgHsg~~gNe~aD~LA~~aa~~~ 143 (161)
T PRK06548 100 QEIIQEIDSLMENR-NIRMSWVNAHTGHPLNEAADSLARQAANNF 143 (161)
T ss_pred HHHHHHHHHHHhcC-ceEEEEEecCCCCHHHHHHHHHHHHHHHHh
Confidence 46888888998875 699999875 45999999999987543
No 11
>PF03993 DUF349: Domain of Unknown Function (DUF349); InterPro: IPR007139 This motif is found singly or as up to five tandem repeats in a small set of bacterial proteins. There are two or three alpha-helices, and possibly a beta-strand.
Probab=67.32 E-value=3.3 Score=22.57 Aligned_cols=24 Identities=21% Similarity=0.368 Sum_probs=16.6
Q ss_pred HHHHHHHHHhhcccceeEeeecCCCC
Q 035454 3 KLCGEARRLKDKFLSFQISHVLRNLN 28 (52)
Q Consensus 3 ~L~~~a~~L~~~F~~f~i~HVpRE~N 28 (52)
....++++|...+. +|.+|||+.|
T Consensus 54 ~~~~~~k~l~~~Wk--~iG~vpr~~~ 77 (77)
T PF03993_consen 54 EAAEEIKELQQEWK--EIGPVPRKKD 77 (77)
T ss_pred HHHHHHHHHHHHHH--HcCCCCcCCC
Confidence 34566677777664 5669999876
No 12
>COG0695 GrxC Glutaredoxin and related proteins [Posttranslational modification, protein turnover, chaperones]
Probab=59.46 E-value=25 Score=19.90 Aligned_cols=35 Identities=23% Similarity=0.243 Sum_probs=22.5
Q ss_pred HHHHHHHHHhhccc-ceeEeeecCCCChHHHHHHhH
Q 035454 3 KLCGEARRLKDKFL-SFQISHVLRNLNSEADAQATL 37 (52)
Q Consensus 3 ~L~~~a~~L~~~F~-~f~i~HVpRE~N~~AD~LAN~ 37 (52)
|.|++|++++.+.. .|+...|.......+...+..
T Consensus 12 PyC~~ak~~L~~~g~~~~~i~~~~~~~~~~~~~~~~ 47 (80)
T COG0695 12 PYCKRAKRLLDRKGVDYEEIDVDDDEPEEAREMVKR 47 (80)
T ss_pred chHHHHHHHHHHcCCCcEEEEecCCcHHHHHHHHHH
Confidence 78999999998753 455555655554455444433
No 13
>PHA03044 IMV membrane protein; Provisional
Probab=42.81 E-value=13 Score=22.37 Aligned_cols=25 Identities=20% Similarity=0.098 Sum_probs=15.6
Q ss_pred HHHHHHHhhcccceeEeeecCCCChH
Q 035454 5 CGEARRLKDKFLSFQISHVLRNLNSE 30 (52)
Q Consensus 5 ~~~a~~L~~~F~~f~i~HVpRE~N~~ 30 (52)
-++.|+-...- .-+++||||-.|.+
T Consensus 49 NKKsKKn~r~~-e~~~~~v~~re~~r 73 (74)
T PHA03044 49 NKKSKKNFRSN-DQQLSYVSRRENNR 73 (74)
T ss_pred HHHHhhccCCc-cccccccCcccCCC
Confidence 34444444433 36788999988864
No 14
>smart00843 Ftsk_gamma This domain directs oriented DNA translocation and forms a winged helix structure. Mutated proteins with substitutions in the FtsK gamma DNA-recognition helix are impaired in DNA binding.
Probab=42.75 E-value=15 Score=21.05 Aligned_cols=27 Identities=26% Similarity=0.150 Sum_probs=23.8
Q ss_pred hHHHHHHHHHhhcccceeEeeecCCCC
Q 035454 2 AKLCGEARRLKDKFLSFQISHVLRNLN 28 (52)
Q Consensus 2 ~~L~~~a~~L~~~F~~f~i~HVpRE~N 28 (52)
.|||.+|.++.-.-...+++++-|.+.
T Consensus 4 D~ly~~a~~~V~~~~~~S~S~lQR~~~ 30 (63)
T smart00843 4 DELYDEAVELVIETQKASTSLLQRRLR 30 (63)
T ss_pred cHHHHHHHHHHHHhCCCChHHHHHHHh
Confidence 479999999988888999999999764
No 15
>PRK11200 grxA glutaredoxin 1; Provisional
Probab=42.19 E-value=54 Score=17.95 Aligned_cols=26 Identities=23% Similarity=0.312 Sum_probs=17.4
Q ss_pred HHHHHHHHHhhcc----cceeEeeecCCCC
Q 035454 3 KLCGEARRLKDKF----LSFQISHVLRNLN 28 (52)
Q Consensus 3 ~L~~~a~~L~~~F----~~f~i~HVpRE~N 28 (52)
|.|.+|+++++++ .++.+.-+.-..+
T Consensus 12 ~~C~~a~~~L~~l~~~~~~i~~~~idi~~~ 41 (85)
T PRK11200 12 PYCVRAKELAEKLSEERDDFDYRYVDIHAE 41 (85)
T ss_pred hhHHHHHHHHHhhcccccCCcEEEEECCCC
Confidence 6899999999885 3455555444444
No 16
>cd03029 GRX_hybridPRX5 Glutaredoxin (GRX) family, PRX5 hybrid subfamily; composed of hybrid proteins containing peroxiredoxin (PRX) and GRX domains, which is found in some pathogenic bacteria and cyanobacteria. PRXs are thiol-specific antioxidant (TSA) proteins that confer a protective antioxidant role in cells through their peroxidase activity in which hydrogen peroxide, peroxynitrate, and organic hydroperoxides are reduced and detoxified using reducing equivalents derived from either thioredoxin, glutathione, trypanothione and AhpF. GRX is a glutathione (GSH) dependent reductase, catalyzing the disulfide reduction of target proteins. PRX-GRX hybrid proteins from Haemophilus influenza and Neisseria meningitis exhibit GSH-dependent peroxidase activity. The flow of reducing equivalents in the catalytic cycle of the hybrid protein goes from NADPH - GSH reductase - GSH - GRX domain of hybrid - PRX domain of hybrid - peroxide substrate.
Probab=36.03 E-value=70 Score=16.82 Aligned_cols=29 Identities=7% Similarity=0.095 Sum_probs=17.9
Q ss_pred HHHHHHHHHhhcccceeEeeecCCCChHHH
Q 035454 3 KLCGEARRLKDKFLSFQISHVLRNLNSEAD 32 (52)
Q Consensus 3 ~L~~~a~~L~~~F~~f~i~HVpRE~N~~AD 32 (52)
|.|.+|++++.+.. +.+.-+.=..+..++
T Consensus 12 p~C~~ak~~L~~~~-i~~~~~~v~~~~~~~ 40 (72)
T cd03029 12 PFCARAKAALQENG-ISYEEIPLGKDITGR 40 (72)
T ss_pred HHHHHHHHHHHHcC-CCcEEEECCCChhHH
Confidence 68999999998753 444444333444333
No 17
>KOG3752 consensus Ribonuclease H [Replication, recombination and repair]
Probab=34.75 E-value=60 Score=24.43 Aligned_cols=38 Identities=26% Similarity=0.110 Sum_probs=27.6
Q ss_pred HHHHHHHHhhcc--cceeEeeecC----CCChHHHHHHhHhhcc
Q 035454 4 LCGEARRLKDKF--LSFQISHVLR----NLNSEADAQATLAVGL 41 (52)
Q Consensus 4 L~~~a~~L~~~F--~~f~i~HVpR----E~N~~AD~LAN~A~dl 41 (52)
...+.-+|.... .+|+++||+= ..|..||.||-..-.+
T Consensus 322 ~~~e~~~l~q~~~~~~vq~~~V~Gh~gi~gne~Ad~lARkgs~~ 365 (371)
T KOG3752|consen 322 FFNELDELEQEISNKKVQQEYVGGHSGILGNEMADALARKGSTL 365 (371)
T ss_pred HHHHHHHHHhhhccCceEEEEecCcCCcchHHHHHHHHhhhhhh
Confidence 345555666663 6799999984 5689999999876433
No 18
>TIGR00228 ruvC crossover junction endodeoxyribonuclease RuvC. Endonuclease that resolves Holliday junction intermediates in genetic recombination. The active form of the protein is a dimer. Structure studies reveals that the catalytic center, comprised of four acidic residues, lies at the bottom of a cleft that fits a DNA duplex. The model hits a single Synechocystis PCC6803 protein at a score of 30, below the trusted cutoff, that appears orthologous and may act as authentic RuvC.
Probab=32.58 E-value=32 Score=22.58 Aligned_cols=27 Identities=19% Similarity=0.305 Sum_probs=17.6
Q ss_pred HHHHHHhhcccceeEeeecCCCChHHHHHHh
Q 035454 6 GEARRLKDKFLSFQISHVLRNLNSEADAQAT 36 (52)
Q Consensus 6 ~~a~~L~~~F~~f~i~HVpRE~N~~AD~LAN 36 (52)
+++..+..++- .+.-.|| +..||+||=
T Consensus 117 eQV~~mV~~lL--~l~~~p~--~DaaDALAi 143 (156)
T TIGR00228 117 SQVQHMVRRLL--KLPANPQ--ADAADALAI 143 (156)
T ss_pred HHHHHHHHHHc--CCCCCCC--CCHHHHHHH
Confidence 34555555553 3445777 899999984
No 19
>TIGR02190 GlrX-dom Glutaredoxin-family domain. This C-terminal domain with homology to glutaredoxin is fused to an N-terminal peroxiredoxin-like domain.
Probab=30.29 E-value=99 Score=16.80 Aligned_cols=30 Identities=7% Similarity=0.205 Sum_probs=18.5
Q ss_pred HHHHHHHHHhhcccceeEeeecCCCChHHHH
Q 035454 3 KLCGEARRLKDKFLSFQISHVLRNLNSEADA 33 (52)
Q Consensus 3 ~L~~~a~~L~~~F~~f~i~HVpRE~N~~AD~ 33 (52)
|.|.+|++++.... +.+.-+.=+.+..+..
T Consensus 19 p~C~~ak~~L~~~g-i~y~~idi~~~~~~~~ 48 (79)
T TIGR02190 19 PFCAKAKATLKEKG-YDFEEIPLGNDARGRS 48 (79)
T ss_pred HhHHHHHHHHHHcC-CCcEEEECCCChHHHH
Confidence 68999999998764 4444444334444433
No 20
>TIGR02180 GRX_euk Glutaredoxin. This model represents eukaryotic glutaredoxins and includes sequences from fungi, plants and metazoans as well as viruses.
Probab=29.99 E-value=91 Score=16.27 Aligned_cols=27 Identities=15% Similarity=0.333 Sum_probs=19.6
Q ss_pred HHHHHHHHHhhccc-c--eeEeeecCCCCh
Q 035454 3 KLCGEARRLKDKFL-S--FQISHVLRNLNS 29 (52)
Q Consensus 3 ~L~~~a~~L~~~F~-~--f~i~HVpRE~N~ 29 (52)
|.|.+++.++.++. . |.+..|.++.+.
T Consensus 10 p~C~~~~~~L~~~~i~~~~~~~~v~~~~~~ 39 (84)
T TIGR02180 10 PYCKKAKEILAKLNVKPAYEVVELDQLSNG 39 (84)
T ss_pred hhHHHHHHHHHHcCCCCCCEEEEeeCCCCh
Confidence 67999999988876 2 567777766553
No 21
>TIGR02194 GlrX_NrdH Glutaredoxin-like protein NrdH. NrdH-redoxin is a representative of a class of small redox proteins that contain a conserved CXXC motif and are characterized by a glutaredoxin-like amino acid sequence and thioredoxin-like activity profile. Unlike other the glutaredoxins to which it is most closely related, NrdH aparrently does not interact with glutathione/glutathione reductase, but rather with thioredoxin reductase to catalyze the reduction of ribonucleotide reductase.
Probab=27.64 E-value=1e+02 Score=16.32 Aligned_cols=32 Identities=9% Similarity=0.123 Sum_probs=19.7
Q ss_pred HHHHHHHHHhhccc-ceeEeeecCCCChHHHHHH
Q 035454 3 KLCGEARRLKDKFL-SFQISHVLRNLNSEADAQA 35 (52)
Q Consensus 3 ~L~~~a~~L~~~F~-~f~i~HVpRE~N~~AD~LA 35 (52)
|.|.+|++++++.. .|+..+|..+. ..++.+.
T Consensus 10 p~C~~ak~~L~~~~i~~~~~di~~~~-~~~~~~~ 42 (72)
T TIGR02194 10 VQCKMTKKALEEHGIAFEEINIDEQP-EAIDYVK 42 (72)
T ss_pred HHHHHHHHHHHHCCCceEEEECCCCH-HHHHHHH
Confidence 67999999877643 56666665432 3344443
No 22
>TIGR02189 GlrX-like_plant Glutaredoxin-like family. This family of glutaredoxin-like proteins is aparrently limited to plants. Multiple isoforms are found in A. thaliana and O.sativa.
Probab=26.79 E-value=1.3e+02 Score=17.49 Aligned_cols=22 Identities=14% Similarity=0.163 Sum_probs=15.1
Q ss_pred HHHHHHHHHhhccc-ceeEeeec
Q 035454 3 KLCGEARRLKDKFL-SFQISHVL 24 (52)
Q Consensus 3 ~L~~~a~~L~~~F~-~f~i~HVp 24 (52)
|.|.+|++++++.. .|.+.-|.
T Consensus 19 p~C~~ak~~L~~~~i~~~~vdid 41 (99)
T TIGR02189 19 CMCHVVKRLLLTLGVNPAVHEID 41 (99)
T ss_pred HHHHHHHHHHHHcCCCCEEEEcC
Confidence 78999999988764 24444343
No 23
>cd03027 GRX_DEP Glutaredoxin (GRX) family, Dishevelled, Egl-10, and Pleckstrin (DEP) subfamily; composed of uncharacterized proteins containing a GRX domain and additional domains DEP and DUF547, both of which have unknown functions. GRX is a glutathione (GSH) dependent reductase containing a redox active CXXC motif in a TRX fold. It has preference for mixed GSH disulfide substrates, in which it uses a monothiol mechanism where only the N-terminal cysteine is required. By altering the redox state of target proteins, GRX is involved in many cellular functions.
Probab=25.62 E-value=1.2e+02 Score=16.04 Aligned_cols=27 Identities=11% Similarity=0.094 Sum_probs=18.2
Q ss_pred HHHHHHHHHhhcccceeEeeecCCCChH
Q 035454 3 KLCGEARRLKDKFLSFQISHVLRNLNSE 30 (52)
Q Consensus 3 ~L~~~a~~L~~~F~~f~i~HVpRE~N~~ 30 (52)
|.|.+|+++++... +.++.+.=..+..
T Consensus 12 ~~C~ka~~~L~~~g-i~~~~~di~~~~~ 38 (73)
T cd03027 12 EDCTAVRLFLREKG-LPYVEINIDIFPE 38 (73)
T ss_pred hhHHHHHHHHHHCC-CceEEEECCCCHH
Confidence 67999999998764 5555554444443
No 24
>TIGR02183 GRXA Glutaredoxin, GrxA family. This model includes the E. coli glyutaredoxin GrxA which appears to have primary responsibility for the reduction of ribonucleotide reductase.
Probab=23.93 E-value=1e+02 Score=17.16 Aligned_cols=13 Identities=31% Similarity=0.669 Sum_probs=11.6
Q ss_pred HHHHHHHHHhhcc
Q 035454 3 KLCGEARRLKDKF 15 (52)
Q Consensus 3 ~L~~~a~~L~~~F 15 (52)
|+|.+|++++.+.
T Consensus 11 p~C~~ak~~L~~~ 23 (86)
T TIGR02183 11 PYCVRAKQLAEKL 23 (86)
T ss_pred ccHHHHHHHHHHh
Confidence 6899999999886
No 25
>PF13250 DUF4041: Domain of unknown function (DUF4041)
Probab=22.76 E-value=24 Score=19.47 Aligned_cols=14 Identities=43% Similarity=0.665 Sum_probs=11.3
Q ss_pred ecCCCChHHHHHHh
Q 035454 23 VLRNLNSEADAQAT 36 (52)
Q Consensus 23 VpRE~N~~AD~LAN 36 (52)
+.|.+|.++|.+.+
T Consensus 3 ~lraFN~EcD~~i~ 16 (56)
T PF13250_consen 3 MLRAFNGECDAAIS 16 (56)
T ss_pred hHHHHHHHHHHHHH
Confidence 56889999998765
No 26
>PF09397 Ftsk_gamma: Ftsk gamma domain; InterPro: IPR018541 This domain directs oriented DNA translocation and forms a winged helix structure []. Mutated proteins with substitutions in the FtsK gamma DNA-recognition helix are impaired in DNA binding []. ; PDB: 2VE9_B 2VE8_E 2J5O_A 2J5P_A.
Probab=21.62 E-value=22 Score=20.28 Aligned_cols=27 Identities=22% Similarity=0.075 Sum_probs=22.4
Q ss_pred hHHHHHHHHHhhcccceeEeeecCCCC
Q 035454 2 AKLCGEARRLKDKFLSFQISHVLRNLN 28 (52)
Q Consensus 2 ~~L~~~a~~L~~~F~~f~i~HVpRE~N 28 (52)
.+||.+|.++.-.-...+++.+-|.+.
T Consensus 5 D~ly~~a~~~V~~~~~~S~S~lQR~~r 31 (65)
T PF09397_consen 5 DPLYEEAVEFVIEEGKASISLLQRKFR 31 (65)
T ss_dssp STTHHHHHHHHHHCTCECHHHHHHHHT
T ss_pred cHHHHHHHHHHHHcCCccHHHHHHHhC
Confidence 478999999988777888888888765
No 27
>PF13641 Glyco_tranf_2_3: Glycosyltransferase like family 2; PDB: 4FIY_B 4FIX_A.
Probab=21.22 E-value=1.2e+02 Score=18.53 Aligned_cols=39 Identities=23% Similarity=0.274 Sum_probs=20.6
Q ss_pred HHHHHHhhcccceeEeeecCCCChH----HHHHHhHhhcccCcc
Q 035454 6 GEARRLKDKFLSFQISHVLRNLNSE----ADAQATLAVGLADGE 45 (52)
Q Consensus 6 ~~a~~L~~~F~~f~i~HVpRE~N~~----AD~LAN~A~dl~~g~ 45 (52)
+.++++...++...+..+++..|.. +..+ |.|+....++
T Consensus 46 ~~~~~~~~~~~~~~v~vi~~~~~~g~~~k~~a~-n~~~~~~~~d 88 (228)
T PF13641_consen 46 EILRALAARYPRVRVRVIRRPRNPGPGGKARAL-NEALAAARGD 88 (228)
T ss_dssp TTHHHHHHTTGG-GEEEEE----HHHHHHHHHH-HHHHHH---S
T ss_pred HHHHHHHHHcCCCceEEeecCCCCCcchHHHHH-HHHHHhcCCC
Confidence 3456777778776777777766553 4444 8888776654
Done!