Query psy11389
Match_columns 73
No_of_seqs 114 out of 474
Neff 5.4
Searched_HMMs 46136
Date Fri Aug 16 17:09:57 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy11389.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/11389hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF00075 RNase_H: RNase H; In 98.9 4.9E-10 1.1E-14 70.4 1.2 30 6-36 100-130 (132)
2 PRK08719 ribonuclease H; Revie 98.9 7.6E-10 1.6E-14 74.0 1.9 30 7-37 116-145 (147)
3 PRK00203 rnhA ribonuclease H; 98.8 1.1E-09 2.3E-14 72.5 0.8 31 7-38 111-141 (150)
4 PRK06548 ribonuclease H; Provi 98.7 6.4E-09 1.4E-13 71.0 1.1 28 8-36 112-139 (161)
5 COG0328 RnhA Ribonuclease HI [ 98.4 1.6E-07 3.4E-12 64.2 1.7 28 10-38 117-144 (154)
6 cd06222 RnaseH RNase H (RNase 98.4 2.8E-07 6E-12 54.8 2.5 29 7-36 101-129 (130)
7 KOG3752|consensus 98.0 3E-06 6.6E-11 64.6 2.7 29 7-36 334-362 (371)
8 PRK13907 rnhA ribonuclease H; 93.9 0.026 5.5E-07 35.7 0.9 23 9-36 102-124 (128)
9 PF13456 RVT_3: Reverse transc 93.1 0.04 8.7E-07 31.6 0.8 25 7-36 60-84 (87)
10 PRK07708 hypothetical protein; 92.4 0.072 1.6E-06 37.8 1.5 24 10-38 184-207 (219)
11 PRK07238 bifunctional RNase H/ 87.5 0.26 5.7E-06 36.5 1.0 23 9-36 107-129 (372)
12 COG0296 GlgB 1,4-alpha-glucan 50.1 11 0.00025 30.9 1.9 26 4-30 223-248 (628)
13 COG0820 Predicted Fe-S-cluster 47.8 13 0.00027 28.6 1.7 37 3-40 248-284 (349)
14 COG2988 Succinylglutamate desu 32.1 14 0.00031 28.2 -0.2 23 48-70 92-114 (324)
15 KOG4095|consensus 28.3 73 0.0016 22.2 2.8 27 47-73 15-42 (165)
16 PF10580 Neuromodulin_N: Gap j 23.4 72 0.0016 16.5 1.6 21 15-36 4-24 (32)
17 PF04714 BCL_N: BCL7, N-termin 22.9 1.3E+02 0.0028 17.3 2.8 27 46-72 13-40 (52)
18 COG4744 Uncharacterized conser 22.6 51 0.0011 21.9 1.2 13 11-28 107-119 (121)
19 COG5575 ORC2 Origin recognitio 21.4 74 0.0016 25.6 2.0 26 2-32 503-528 (535)
No 1
>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=98.89 E-value=4.9e-10 Score=70.40 Aligned_cols=30 Identities=30% Similarity=0.512 Sum_probs=27.0
Q ss_pred ecCceeEEEEeeCCCCCC-ccchHHHHHhcCC
Q psy11389 6 DKNSYLRYLSNPICHCGI-KGNEIVDVAARNP 36 (73)
Q Consensus 6 ~~~~~v~~~Wip~~H~gi-~gNE~AD~~Ak~a 36 (73)
..+..|.|.||| ||+|+ .|||.||+|||.|
T Consensus 100 ~~~~~v~~~~V~-~H~~~~~~N~~aD~lAk~a 130 (132)
T PF00075_consen 100 SRGIKVRFRWVP-GHSGVPQGNERADRLAKEA 130 (132)
T ss_dssp HHSSEEEEEESS-SSSSSHHHHHHHHHHHHHH
T ss_pred ccceEEeeeecc-CcCCCchhHHHHHHHHHHh
Confidence 457889999999 99999 6999999999865
No 2
>PRK08719 ribonuclease H; Reviewed
Probab=98.88 E-value=7.6e-10 Score=73.97 Aligned_cols=30 Identities=30% Similarity=0.505 Sum_probs=27.2
Q ss_pred cCceeEEEEeeCCCCCCccchHHHHHhcCCC
Q psy11389 7 KNSYLRYLSNPICHCGIKGNEIVDVAARNPT 37 (73)
Q Consensus 7 ~~~~v~~~Wip~~H~gi~gNE~AD~~Ak~a~ 37 (73)
....|+|.||| ||+|++|||.||+||++|.
T Consensus 116 ~~~~i~~~~Vk-gH~g~~~Ne~aD~lA~~a~ 145 (147)
T PRK08719 116 ARKYVEVEKVT-AHSGIEGNEAADMLAQAAA 145 (147)
T ss_pred CCCcEEEEEec-CCCCChhHHHHHHHHHHHh
Confidence 35679999999 9999999999999999874
No 3
>PRK00203 rnhA ribonuclease H; Reviewed
Probab=98.81 E-value=1.1e-09 Score=72.46 Aligned_cols=31 Identities=26% Similarity=0.260 Sum_probs=27.7
Q ss_pred cCceeEEEEeeCCCCCCccchHHHHHhcCCCC
Q psy11389 7 KNSYLRYLSNPICHCGIKGNEIVDVAARNPTN 38 (73)
Q Consensus 7 ~~~~v~~~Wip~~H~gi~gNE~AD~~Ak~a~~ 38 (73)
....|.|.||| ||+|++|||.||+|||+|..
T Consensus 111 ~~~~v~~~wV~-~H~~~~~N~~AD~lA~~a~~ 141 (150)
T PRK00203 111 KRHQIKWHWVK-GHAGHPENERCDELARAGAE 141 (150)
T ss_pred ccCceEEEEec-CCCCCHHHHHHHHHHHHHHH
Confidence 34689999999 99999999999999998843
No 4
>PRK06548 ribonuclease H; Provisional
Probab=98.67 E-value=6.4e-09 Score=70.95 Aligned_cols=28 Identities=32% Similarity=0.284 Sum_probs=26.3
Q ss_pred CceeEEEEeeCCCCCCccchHHHHHhcCC
Q psy11389 8 NSYLRYLSNPICHCGIKGNEIVDVAARNP 36 (73)
Q Consensus 8 ~~~v~~~Wip~~H~gi~gNE~AD~~Ak~a 36 (73)
...|+|.||| ||+|++|||.||+||+++
T Consensus 112 ~~~v~~~wVk-gHsg~~gNe~aD~LA~~a 139 (161)
T PRK06548 112 NRNIRMSWVN-AHTGHPLNEAADSLARQA 139 (161)
T ss_pred cCceEEEEEe-cCCCCHHHHHHHHHHHHH
Confidence 4579999999 999999999999999998
No 5
>COG0328 RnhA Ribonuclease HI [DNA replication, recombination, and repair]
Probab=98.37 E-value=1.6e-07 Score=64.18 Aligned_cols=28 Identities=25% Similarity=0.211 Sum_probs=26.1
Q ss_pred eeEEEEeeCCCCCCccchHHHHHhcCCCC
Q psy11389 10 YLRYLSNPICHCGIKGNEIVDVAARNPTN 38 (73)
Q Consensus 10 ~v~~~Wip~~H~gi~gNE~AD~~Ak~a~~ 38 (73)
.|.+.||| ||+|.++||.||+||+.+..
T Consensus 117 ~v~~~WVk-gH~g~~~NeraD~LA~~~~~ 144 (154)
T COG0328 117 LVFWEWVK-GHAGHPENERADQLAREAAR 144 (154)
T ss_pred eEEEEEee-CCCCChHHHHHHHHHHHHHH
Confidence 89999999 99999999999999998843
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=98.37 E-value=2.8e-07 Score=54.83 Aligned_cols=29 Identities=34% Similarity=0.526 Sum_probs=26.6
Q ss_pred cCceeEEEEeeCCCCCCccchHHHHHhcCC
Q psy11389 7 KNSYLRYLSNPICHCGIKGNEIVDVAARNP 36 (73)
Q Consensus 7 ~~~~v~~~Wip~~H~gi~gNE~AD~~Ak~a 36 (73)
....+.|.||| +|+|+++|+.||.+||.+
T Consensus 101 ~~~~~~i~~v~-~h~~~~~n~~ad~la~~~ 129 (130)
T cd06222 101 RFHKVRFEWVP-GHSGIEGNERADALAKEA 129 (130)
T ss_pred CCCeEEEEEcC-CCCCCcchHHHHHHHHhh
Confidence 46789999999 999999999999999875
No 7
>KOG3752|consensus
Probab=98.04 E-value=3e-06 Score=64.65 Aligned_cols=29 Identities=34% Similarity=0.393 Sum_probs=27.2
Q ss_pred cCceeEEEEeeCCCCCCccchHHHHHhcCC
Q psy11389 7 KNSYLRYLSNPICHCGIKGNEIVDVAARNP 36 (73)
Q Consensus 7 ~~~~v~~~Wip~~H~gi~gNE~AD~~Ak~a 36 (73)
+++.|++.||| ||.||.|||+||.||++.
T Consensus 334 ~~~~vq~~~V~-Gh~gi~gne~Ad~lARkg 362 (371)
T KOG3752|consen 334 SNKKVQQEYVG-GHSGILGNEMADALARKG 362 (371)
T ss_pred ccCceEEEEec-CcCCcchHHHHHHHHhhh
Confidence 46899999999 999999999999999987
No 8
>PRK13907 rnhA ribonuclease H; Provisional
Probab=93.92 E-value=0.026 Score=35.71 Aligned_cols=23 Identities=22% Similarity=0.222 Sum_probs=19.2
Q ss_pred ceeEEEEeeCCCCCCccchHHHHHhcCC
Q psy11389 9 SYLRYLSNPICHCGIKGNEIVDVAARNP 36 (73)
Q Consensus 9 ~~v~~~Wip~~H~gi~gNE~AD~~Ak~a 36 (73)
..+.|.||| . ++|+.||.+|+.|
T Consensus 102 ~~~~~~~v~-r----~~N~~Ad~LA~~a 124 (128)
T PRK13907 102 DLFFIKWIP-S----SQNKVADELARKA 124 (128)
T ss_pred CceEEEEcC-c----hhchhHHHHHHHH
Confidence 356679999 5 6999999999876
No 9
>PF13456 RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EHG_A 3HST_B.
Probab=93.15 E-value=0.04 Score=31.62 Aligned_cols=25 Identities=16% Similarity=0.133 Sum_probs=19.4
Q ss_pred cCceeEEEEeeCCCCCCccchHHHHHhcCC
Q psy11389 7 KNSYLRYLSNPICHCGIKGNEIVDVAARNP 36 (73)
Q Consensus 7 ~~~~v~~~Wip~~H~gi~gNE~AD~~Ak~a 36 (73)
.-..+.|.||| =++|..||.+||.|
T Consensus 60 ~~~~~~~~~i~-----r~~N~~A~~LA~~a 84 (87)
T PF13456_consen 60 RFWNVSVSHIP-----REQNKVADALAKFA 84 (87)
T ss_dssp CCSCEEEEE-------GGGSHHHHHHHHHH
T ss_pred cccceEEEEEC-----hHHhHHHHHHHHHH
Confidence 34678999999 78999999999864
No 10
>PRK07708 hypothetical protein; Validated
Probab=92.41 E-value=0.072 Score=37.82 Aligned_cols=24 Identities=21% Similarity=0.055 Sum_probs=20.4
Q ss_pred eeEEEEeeCCCCCCccchHHHHHhcCCCC
Q psy11389 10 YLRYLSNPICHCGIKGNEIVDVAARNPTN 38 (73)
Q Consensus 10 ~v~~~Wip~~H~gi~gNE~AD~~Ak~a~~ 38 (73)
.+.|.||| -..|+.||+||+.|..
T Consensus 184 ~~~~~~Vp-----R~~N~~AD~LAk~Al~ 207 (219)
T PRK07708 184 TPVYEPIS-----RKQNKEADQLATQALE 207 (219)
T ss_pred eEEEEECC-----chhhhHHHHHHHHHHh
Confidence 47788999 5789999999999944
No 11
>PRK07238 bifunctional RNase H/acid phosphatase; Provisional
Probab=87.52 E-value=0.26 Score=36.49 Aligned_cols=23 Identities=22% Similarity=0.171 Sum_probs=20.5
Q ss_pred ceeEEEEeeCCCCCCccchHHHHHhcCC
Q psy11389 9 SYLRYLSNPICHCGIKGNEIVDVAARNP 36 (73)
Q Consensus 9 ~~v~~~Wip~~H~gi~gNE~AD~~Ak~a 36 (73)
..+.|.||| . .+|+.||.||+.|
T Consensus 107 ~~~~i~~v~-r----~~N~~AD~LA~~a 129 (372)
T PRK07238 107 GRVTYTWIP-R----ARNAHADRLANEA 129 (372)
T ss_pred CceEEEECC-c----hhhhHHHHHHHHH
Confidence 578999999 4 7899999999987
No 12
>COG0296 GlgB 1,4-alpha-glucan branching enzyme [Carbohydrate transport and metabolism]
Probab=50.14 E-value=11 Score=30.93 Aligned_cols=26 Identities=15% Similarity=0.001 Sum_probs=22.5
Q ss_pred EeecCceeEEEEeeCCCCCCccchHHH
Q psy11389 4 ILDKNSYLRYLSNPICHCGIKGNEIVD 30 (73)
Q Consensus 4 ~~~~~~~v~~~Wip~~H~gi~gNE~AD 30 (73)
.|+.|+.|-+=||| +|.+..||=.+-
T Consensus 223 aH~~GIgViLD~V~-~HF~~d~~~L~~ 248 (628)
T COG0296 223 AHQAGIGVILDWVP-NHFPPDGNYLAR 248 (628)
T ss_pred HHHcCCEEEEEecC-CcCCCCcchhhh
Confidence 36789999999999 999999987664
No 13
>COG0820 Predicted Fe-S-cluster redox enzyme [General function prediction only]
Probab=47.83 E-value=13 Score=28.65 Aligned_cols=37 Identities=8% Similarity=-0.094 Sum_probs=31.8
Q ss_pred eEeecCceeEEEEeeCCCCCCccchHHHHHhcCCCCCC
Q psy11389 3 YILDKNSYLRYLSNPICHCGIKGNEIVDVAARNPTNAT 40 (73)
Q Consensus 3 ~~~~~~~~v~~~Wip~~H~gi~gNE~AD~~Ak~a~~~~ 40 (73)
|..+++.+|+|.++=+.+.+.. -|.|++||+...+.+
T Consensus 248 Y~~~t~~rVt~EY~Ll~~VND~-~e~A~~L~~ll~~~~ 284 (349)
T COG0820 248 YPEKSGRRVTFEYVLLDGVNDS-LEHAKELAKLLKGIP 284 (349)
T ss_pred hhhccCceEEEEeeecccccCC-HHHHHHHHHHhcCCC
Confidence 7778899999999998888887 999999999885443
No 14
>COG2988 Succinylglutamate desuccinylase [Amino acid transport and metabolism]
Probab=32.07 E-value=14 Score=28.22 Aligned_cols=23 Identities=9% Similarity=0.109 Sum_probs=17.4
Q ss_pred HhHHHHHHHHHHHHHHhhcccCC
Q psy11389 48 EDFKPFVASLMNSEWQSQWDNVP 70 (73)
Q Consensus 48 ~d~k~~ik~~~~~~Wq~~W~~~~ 70 (73)
..=+|+|.+-++...--+|++.+
T Consensus 92 ~~gkRYieqDlNR~F~gr~q~~~ 114 (324)
T COG2988 92 AAGKRYIEQDLNRMFGGRPQSFS 114 (324)
T ss_pred HhchHHHhhhHHHHhCCCcccCC
Confidence 34578888888888877777666
No 15
>KOG4095|consensus
Probab=28.34 E-value=73 Score=22.20 Aligned_cols=27 Identities=26% Similarity=0.668 Sum_probs=19.6
Q ss_pred HHhHHHHHHHHHH-HHHHhhcccCCCCC
Q psy11389 47 PEDFKPFVASLMN-SEWQSQWDNVPNTN 73 (73)
Q Consensus 47 ~~d~k~~ik~~~~-~~Wq~~W~~~~~tn 73 (73)
-.|+|+.+..+-+ ..|++.|-.+.+|+
T Consensus 15 KDDIKkVMaaiEKVRrWEKKwVtvgDTs 42 (165)
T KOG4095|consen 15 KDDIKKVMAAIEKVRRWEKKWVTVGDTS 42 (165)
T ss_pred HHHHHHHHHHHHHHHHHhhheEeecccc
Confidence 3567776654433 58999999999885
No 16
>PF10580 Neuromodulin_N: Gap junction protein N-terminal region; InterPro: IPR018947 Neuromodulin is a component of the motile growth cones. It is membrane protein whose expression is widely correlated with successful axon elongation []. It is a crucial component of an effective regeneration response in the nervous system []. Although its function is uncertain, the N-terminal region is well conserved and contains both a calmodulin binding domain, and sites for acylation, membrane attachment and protein kinase C phosphorylation. Structure predictions suggest that the C-terminal region may exist as an extended, negatively-charged rod with some similarity to the side arms of neurofilaments, indicating that the biological role of neuromodulin may depend on its ability to form a dynamic membrane-cytoplasm-calmodulin complex []. This entry represents the neuromodulin N-terminal domain.
Probab=23.43 E-value=72 Score=16.53 Aligned_cols=21 Identities=14% Similarity=0.001 Sum_probs=15.2
Q ss_pred EeeCCCCCCccchHHHHHhcCC
Q psy11389 15 SNPICHCGIKGNEIVDVAARNP 36 (73)
Q Consensus 15 Wip~~H~gi~gNE~AD~~Ak~a 36 (73)
.+. .+..++-||.||+-..+-
T Consensus 4 c~r-~tk~VEKNeeadQkieqD 24 (32)
T PF10580_consen 4 CIR-RTKPVEKNEEADQKIEQD 24 (32)
T ss_pred eee-ccccccccchhhhhhhhc
Confidence 344 666789999999866544
No 17
>PF04714 BCL_N: BCL7, N-terminal conserver region; InterPro: IPR006804 The members of this group of sequences contain a conserved N-terminal domain which is found in the BCL7 family. The function of BCL7 proteins is unknown, though they may be involved in early development. Notably, BCL7B is commonly hemizygously deleted in patients with Williams syndrome [].
Probab=22.94 E-value=1.3e+02 Score=17.26 Aligned_cols=27 Identities=30% Similarity=0.684 Sum_probs=19.5
Q ss_pred CHHhHHHHHHHHHH-HHHHhhcccCCCC
Q psy11389 46 TPEDFKPFVASLMN-SEWQSQWDNVPNT 72 (73)
Q Consensus 46 t~~d~k~~ik~~~~-~~Wq~~W~~~~~t 72 (73)
+-.|+|+.+...-+ ..|+..|-.+.+|
T Consensus 13 ~KddiKrv~~~iekVr~wEKKWVtv~dt 40 (52)
T PF04714_consen 13 AKDDIKRVMASIEKVRKWEKKWVTVGDT 40 (52)
T ss_pred hhHHHHHHHHHHHHHHHHhhceEEeccc
Confidence 45678887665432 6899999988776
No 18
>COG4744 Uncharacterized conserved protein [Function unknown]
Probab=22.58 E-value=51 Score=21.93 Aligned_cols=13 Identities=38% Similarity=0.434 Sum_probs=9.6
Q ss_pred eEEEEeeCCCCCCccchH
Q psy11389 11 LRYLSNPICHCGIKGNEI 28 (73)
Q Consensus 11 v~~~Wip~~H~gi~gNE~ 28 (73)
=+++||| | +|||.
T Consensus 107 gr~I~Vp-~----~~~~~ 119 (121)
T COG4744 107 GRVIYVP-E----EGNEA 119 (121)
T ss_pred CeEEEec-C----CCCcC
Confidence 3689999 7 67763
No 19
>COG5575 ORC2 Origin recognition complex, subunit 2 [DNA replication, recombination, and repair]
Probab=21.37 E-value=74 Score=25.65 Aligned_cols=26 Identities=19% Similarity=0.176 Sum_probs=20.1
Q ss_pred eeEeecCceeEEEEeeCCCCCCccchHHHHH
Q psy11389 2 VYILDKNSYLRYLSNPICHCGIKGNEIVDVA 32 (73)
Q Consensus 2 ~~~~~~~~~v~~~Wip~~H~gi~gNE~AD~~ 32 (73)
+=|...+..+.++||| -+.||.+..|
T Consensus 503 ~~i~rn~S~~eI~wvp-----y~~nele~lL 528 (535)
T COG5575 503 LKIKRNGSEIEICWVP-----YERNELEGLL 528 (535)
T ss_pred hheeccCCccEEEEee-----ccHHHHHHHH
Confidence 3455678899999999 7888877655
Done!