Query psy14646
Match_columns 366
No_of_seqs 203 out of 1236
Neff 6.4
Searched_HMMs 46136
Date Fri Aug 16 17:00:31 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy14646.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/14646hhsearch_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 99.8 3.1E-18 6.8E-23 145.2 11.4 117 38-203 3-131 (132)
2 PRK08719 ribonuclease H; Revie 99.7 7.1E-17 1.5E-21 141.9 13.3 103 54-204 24-146 (147)
3 PRK00203 rnhA ribonuclease H; 99.7 2.5E-16 5.3E-21 138.5 13.2 108 53-206 19-143 (150)
4 COG0328 RnhA Ribonuclease HI [ 99.7 2.1E-16 4.6E-21 139.1 12.4 123 40-206 5-146 (154)
5 PRK06548 ribonuclease H; Provi 99.7 2.9E-16 6.3E-21 139.8 12.9 123 37-206 4-143 (161)
6 cd06222 RnaseH RNase H (RNase 99.6 2E-14 4.3E-19 117.5 14.3 110 51-203 13-130 (130)
7 KOG3752|consensus 99.4 1.6E-12 3.5E-17 127.5 11.2 126 38-205 212-365 (371)
8 PRK13907 rnhA ribonuclease H; 99.3 2.1E-11 4.6E-16 103.8 13.4 108 51-205 15-127 (128)
9 PRK07708 hypothetical protein; 99.2 5.4E-10 1.2E-14 104.5 14.3 130 30-206 65-209 (219)
10 PF13456 RVT_3: Reverse transc 98.9 6.2E-09 1.3E-13 81.4 9.8 68 132-204 15-86 (87)
11 PRK07238 bifunctional RNase H/ 98.9 1.6E-08 3.4E-13 101.2 13.6 118 41-206 5-133 (372)
12 PF13966 zf-RVT: zinc-binding 96.2 0.0031 6.8E-08 50.1 2.2 31 297-327 51-82 (86)
13 PRK08298 cytidine deaminase; V 62.1 28 0.00061 30.3 6.5 61 21-89 1-63 (136)
14 cd01285 nucleoside_deaminase N 44.1 90 0.0019 25.5 6.5 41 48-89 14-58 (109)
15 PF09862 DUF2089: Protein of u 33.2 27 0.00059 29.5 1.7 53 308-366 1-55 (113)
16 cd01284 Riboflavin_deaminase-r 32.9 1.1E+02 0.0024 25.6 5.4 41 48-89 16-56 (115)
17 PF05380 Peptidase_A17: Pao re 32.9 2E+02 0.0042 25.2 7.3 47 43-91 85-141 (159)
18 PF00336 DNA_pol_viral_C: DNA 30.1 65 0.0014 30.2 3.7 39 50-90 101-139 (245)
19 PF00383 dCMP_cyt_deam_1: Cyti 28.9 87 0.0019 24.7 4.0 43 47-90 20-66 (102)
20 PF05741 zf-nanos: Nanos RNA b 24.5 38 0.00082 25.0 1.0 20 307-326 35-54 (55)
21 COG0590 CumB Cytosine/adenosin 23.5 2.3E+02 0.005 24.9 5.9 43 48-90 25-70 (152)
22 PRK10860 tRNA-specific adenosi 22.8 2.6E+02 0.0056 25.2 6.2 39 49-89 31-73 (172)
23 COG2093 DNA-directed RNA polym 22.2 60 0.0013 24.6 1.6 21 299-319 12-32 (64)
24 cd01283 cytidine_deaminase Cyt 21.8 1.9E+02 0.0042 23.5 4.9 43 48-90 15-59 (112)
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=99.77 E-value=3.1e-18 Score=145.23 Aligned_cols=117 Identities=25% Similarity=0.298 Sum_probs=88.3
Q ss_pred cceeeCCCcc--CCCCceeEEEEEecCCeeEEEEcCCCCChhHHHHHHHHHHhhcccccccCCCchhhhhccchhhhHHH
Q psy14646 38 FPICSSSPID--LDETGVGCALTIPQLNETKRFALNKHSSIFHAELFSIPLHLSLTNCTIDRDSSIDIFFNNKHELKDKL 115 (366)
Q Consensus 38 ~~~~~~~~~~--~~~~~~g~a~~~~~~~~~~~~~l~~~~~~~~ae~~ai~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~ 115 (366)
..++|+ |+| ...+..|+|+++... ....+.++ ..|++.||+.||..||+.
T Consensus 3 ~~~iyt-DgS~~~~~~~~~~g~v~~~~-~~~~~~~~-~~s~~~aEl~Ai~~AL~~------------------------- 54 (132)
T PF00075_consen 3 AIIIYT-DGSCRPNPGKGGAGYVVWGG-RNFSFRLG-GQSNNRAELQAIIEALKA------------------------- 54 (132)
T ss_dssp SEEEEE-EEEECTTTTEEEEEEEEETT-EEEEEEEE-SECHHHHHHHHHHHHHHT-------------------------
T ss_pred cEEEEE-eCCccCCCCceEEEEEEECC-eEEEeccc-ccchhhhheehHHHHHHH-------------------------
Confidence 345666 555 334444667665444 45556676 899999999999999992
Q ss_pred HHHHHHHhHhHHHHHHhhhhcCCceEEEEeccHHHHHHHhc-----cCC---Cc-hHHHHHHHHHhcCCCcEEEEEeccc
Q psy14646 116 LQQIAYVDINSLQSLNHVKELDTRKILIISDSLSSFQAISN-----LYH---PN-PLVKKIQEEYSNSQANIKFLWCPSH 186 (366)
Q Consensus 116 ~~~~~~~~~~~l~al~~~~~~~~~~i~I~sDS~sal~ai~~-----~~~---~~-~i~~~I~~~l~~~~~~V~~~WVPgH 186 (366)
+ ....++|+|||++++..+.. ... .. ++..+|.+++. .+..|.|.|||||
T Consensus 55 -----------------~---~~~~v~I~tDS~~v~~~l~~~~~~~~~~~~~~~~~i~~~i~~~~~-~~~~v~~~~V~~H 113 (132)
T PF00075_consen 55 -----------------L---EHRKVTIYTDSQYVLNALNKWLHGNGWKKTSNGRPIKNEIWELLS-RGIKVRFRWVPGH 113 (132)
T ss_dssp -----------------H---STSEEEEEES-HHHHHHHHTHHHHTTSBSCTSSSBHTHHHHHHHH-HSSEEEEEESSSS
T ss_pred -----------------h---hcccccccccHHHHHHHHHHhccccccccccccccchhheeeccc-cceEEeeeeccCc
Confidence 2 13899999999999998887 221 12 57778888774 4789999999999
Q ss_pred ccc-ccchhhHHHHHHHh
Q psy14646 187 VSI-SGNERAEECYSNYL 203 (366)
Q Consensus 187 ~Gi-~GNE~AD~lAk~A~ 203 (366)
+|+ .|||.||+|||+|+
T Consensus 114 ~~~~~~N~~aD~lAk~a~ 131 (132)
T PF00075_consen 114 SGVPQGNERADRLAKEAA 131 (132)
T ss_dssp SSSHHHHHHHHHHHHHHH
T ss_pred CCCchhHHHHHHHHHHhc
Confidence 999 69999999999987
No 2
>PRK08719 ribonuclease H; Reviewed
Probab=99.72 E-value=7.1e-17 Score=141.88 Aligned_cols=103 Identities=17% Similarity=0.209 Sum_probs=73.3
Q ss_pred eEEEEEecC--Ce--eEEEEcCCCCChhHHHHHHHHHHhhcccccccCCCchhhhhccchhhhHHHHHHHHHHhHhHHHH
Q psy14646 54 GCALTIPQL--NE--TKRFALNKHSSIFHAELFSIPLHLSLTNCTIDRDSSIDIFFNNKHELKDKLLQQIAYVDINSLQS 129 (366)
Q Consensus 54 g~a~~~~~~--~~--~~~~~l~~~~~~~~ae~~ai~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~a 129 (366)
|+|+++... .. .....++...|++.||+.|+..||+.+
T Consensus 24 G~G~vv~~~~~~~~~~~~~~~~~~~Tnn~aEl~A~~~aL~~~-------------------------------------- 65 (147)
T PRK08719 24 GIGLVVYDEAGEIVDEQSITVNRYTDNAELELLALIEALEYA-------------------------------------- 65 (147)
T ss_pred EEEEEEEeCCCCeeEEEEecCCCCccHHHHHHHHHHHHHHHc--------------------------------------
Confidence 556554432 32 234445557899999999999999932
Q ss_pred HHhhhhcCCceEEEEeccHHHHHHHhc--------cCC-C-------chHHHHHHHHHhcCCCcEEEEEeccccccccch
Q psy14646 130 LNHVKELDTRKILIISDSLSSFQAISN--------LYH-P-------NPLVKKIQEEYSNSQANIKFLWCPSHVSISGNE 193 (366)
Q Consensus 130 l~~~~~~~~~~i~I~sDS~sal~ai~~--------~~~-~-------~~i~~~I~~~l~~~~~~V~~~WVPgH~Gi~GNE 193 (366)
.+ ...|+|||++++++|.. ... . .++.+.|.++.+ ...|.|.|||||+|++|||
T Consensus 66 ----~~----~~~i~tDS~yvi~~i~~~~~~W~~~~w~~s~g~~v~n~dl~~~i~~l~~--~~~i~~~~VkgH~g~~~Ne 135 (147)
T PRK08719 66 ----RD----GDVIYSDSDYCVRGFNEWLDTWKQKGWRKSDKKPVANRDLWQQVDELRA--RKYVEVEKVTAHSGIEGNE 135 (147)
T ss_pred ----CC----CCEEEechHHHHHHHHHHHHHHHhCCcccCCCcccccHHHHHHHHHHhC--CCcEEEEEecCCCCChhHH
Confidence 22 13799999999999943 221 1 123444444433 4679999999999999999
Q ss_pred hhHHHHHHHhc
Q psy14646 194 RAEECYSNYLA 204 (366)
Q Consensus 194 ~AD~lAk~A~~ 204 (366)
.||+||++|++
T Consensus 136 ~aD~lA~~a~~ 146 (147)
T PRK08719 136 AADMLAQAAAE 146 (147)
T ss_pred HHHHHHHHHhh
Confidence 99999999875
No 3
>PRK00203 rnhA ribonuclease H; Reviewed
Probab=99.69 E-value=2.5e-16 Score=138.51 Aligned_cols=108 Identities=18% Similarity=0.195 Sum_probs=78.5
Q ss_pred eeEEEEEecCCeeEEEEc-CCCCChhHHHHHHHHHHhhcccccccCCCchhhhhccchhhhHHHHHHHHHHhHhHHHHHH
Q psy14646 53 VGCALTIPQLNETKRFAL-NKHSSIFHAELFSIPLHLSLTNCTIDRDSSIDIFFNNKHELKDKLLQQIAYVDINSLQSLN 131 (366)
Q Consensus 53 ~g~a~~~~~~~~~~~~~l-~~~~~~~~ae~~ai~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~al~ 131 (366)
.|+|+++...+....+.- ....|+..|||.|+..||+.+
T Consensus 19 ~g~g~v~~~~~~~~~~~~~~~~~TN~~aEL~Ai~~AL~~~---------------------------------------- 58 (150)
T PRK00203 19 GGWGAILRYKGHEKELSGGEALTTNNRMELMAAIEALEAL---------------------------------------- 58 (150)
T ss_pred eEEEEEEEECCeeEEEecCCCCCcHHHHHHHHHHHHHHHc----------------------------------------
Confidence 455555544443333321 237889999999999999932
Q ss_pred hhhhcCCceEEEEeccHHHHHHHhcc---------CCC-------chHHHHHHHHHhcCCCcEEEEEeccccccccchhh
Q psy14646 132 HVKELDTRKILIISDSLSSFQAISNL---------YHP-------NPLVKKIQEEYSNSQANIKFLWCPSHVSISGNERA 195 (366)
Q Consensus 132 ~~~~~~~~~i~I~sDS~sal~ai~~~---------~~~-------~~i~~~I~~~l~~~~~~V~~~WVPgH~Gi~GNE~A 195 (366)
. ....+.|+|||++++++|..+ ... .++.+.|.+++.. ..|.|.|||||+|++|||.|
T Consensus 59 --~--~~~~v~I~tDS~yvi~~i~~w~~~Wk~~~~~~~~g~~v~n~dl~~~i~~l~~~--~~v~~~wV~~H~~~~~N~~A 132 (150)
T PRK00203 59 --K--EPCEVTLYTDSQYVRQGITEWIHGWKKNGWKTADKKPVKNVDLWQRLDAALKR--HQIKWHWVKGHAGHPENERC 132 (150)
T ss_pred --C--CCCeEEEEECHHHHHHHHHHHHHHHHHcCCcccCCCccccHHHHHHHHHHhcc--CceEEEEecCCCCCHHHHHH
Confidence 2 235799999999999999963 111 1345555555433 68999999999999999999
Q ss_pred HHHHHHHhccc
Q psy14646 196 EECYSNYLASV 206 (366)
Q Consensus 196 D~lAk~A~~~~ 206 (366)
|+|||+|+..+
T Consensus 133 D~lA~~a~~~~ 143 (150)
T PRK00203 133 DELARAGAEEA 143 (150)
T ss_pred HHHHHHHHHHh
Confidence 99999999874
No 4
>COG0328 RnhA Ribonuclease HI [DNA replication, recombination, and repair]
Probab=99.69 E-value=2.1e-16 Score=139.12 Aligned_cols=123 Identities=17% Similarity=0.162 Sum_probs=86.9
Q ss_pred eeeCCCccCCCCcee-EEEEEecCCee--EEEEcCCCCChhHHHHHHHHHHhhcccccccCCCchhhhhccchhhhHHHH
Q psy14646 40 ICSSSPIDLDETGVG-CALTIPQLNET--KRFALNKHSSIFHAELFSIPLHLSLTNCTIDRDSSIDIFFNNKHELKDKLL 116 (366)
Q Consensus 40 ~~~~~~~~~~~~~~g-~a~~~~~~~~~--~~~~l~~~~~~~~ae~~ai~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 116 (366)
..|+..++.++.|.| +|++....... ....+. .+|+..||+.|+..||+
T Consensus 5 ~if~DGa~~gNpG~gG~g~vl~~~~~~~~~s~~~~-~tTNNraEl~A~i~AL~--------------------------- 56 (154)
T COG0328 5 EIFTDGACLGNPGPGGWGAVLRYGDGEKELSGGEG-RTTNNRAELRALIEALE--------------------------- 56 (154)
T ss_pred EEEecCccCCCCCCceEEEEEEcCCceEEEeeeee-cccChHHHHHHHHHHHH---------------------------
Confidence 345544444443433 34444333322 333444 89999999999999999
Q ss_pred HHHHHHhHhHHHHHHhhhhcCCceEEEEeccHHHHHHHhccCC----C------------chHHHHHHHHHhcCCCcEEE
Q psy14646 117 QQIAYVDINSLQSLNHVKELDTRKILIISDSLSSFQAISNLYH----P------------NPLVKKIQEEYSNSQANIKF 180 (366)
Q Consensus 117 ~~~~~~~~~~l~al~~~~~~~~~~i~I~sDS~sal~ai~~~~~----~------------~~i~~~I~~~l~~~~~~V~~ 180 (366)
.+.+.+...|.|+|||++++++|..|.. . .++.+++.+++++. ..|.+
T Consensus 57 ---------------~l~~~~~~~v~l~tDS~yv~~~i~~w~~~w~~~~w~~~~~~pvkn~dl~~~~~~~~~~~-~~v~~ 120 (154)
T COG0328 57 ---------------ALKELGACEVTLYTDSKYVVEGITRWIVKWKKNGWKTADKKPVKNKDLWEELDELLKRH-ELVFW 120 (154)
T ss_pred ---------------HHHhcCCceEEEEecHHHHHHHHHHHHhhccccCccccccCccccHHHHHHHHHHHhhC-CeEEE
Confidence 4445678999999999999999995411 1 12344454444432 48999
Q ss_pred EEeccccccccchhhHHHHHHHhccc
Q psy14646 181 LWCPSHVSISGNERAEECYSNYLASV 206 (366)
Q Consensus 181 ~WVPgH~Gi~GNE~AD~lAk~A~~~~ 206 (366)
.|||||+|.++||.||+||+.|++..
T Consensus 121 ~WVkgH~g~~~NeraD~LA~~~~~~~ 146 (154)
T COG0328 121 EWVKGHAGHPENERADQLAREAARAA 146 (154)
T ss_pred EEeeCCCCChHHHHHHHHHHHHHHhh
Confidence 99999999999999999999999875
No 5
>PRK06548 ribonuclease H; Provisional
Probab=99.69 E-value=2.9e-16 Score=139.83 Aligned_cols=123 Identities=20% Similarity=0.187 Sum_probs=85.3
Q ss_pred CcceeeCCCccCCC-CceeEEEEEecCCeeEEEEcCCCCChhHHHHHHHHHHhhcccccccCCCchhhhhccchhhhHHH
Q psy14646 37 EFPICSSSPIDLDE-TGVGCALTIPQLNETKRFALNKHSSIFHAELFSIPLHLSLTNCTIDRDSSIDIFFNNKHELKDKL 115 (366)
Q Consensus 37 ~~~~~~~~~~~~~~-~~~g~a~~~~~~~~~~~~~l~~~~~~~~ae~~ai~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~ 115 (366)
+...+|+...+..+ +..|.|+++.... . ...-....|+..||+.|+..||+.
T Consensus 4 ~~~~IytDGa~~gnpg~~G~g~~~~~~~-~-~~g~~~~~TNnraEl~Aii~aL~~------------------------- 56 (161)
T PRK06548 4 NEIIAATDGSSLANPGPSGWAWYVDENT-W-DSGGWDIATNNIAELTAVRELLIA------------------------- 56 (161)
T ss_pred CEEEEEEeeccCCCCCceEEEEEEeCCc-E-EccCCCCCCHHHHHHHHHHHHHHh-------------------------
Confidence 34556664444433 4455677664322 1 111123689999999999999872
Q ss_pred HHHHHHHhHhHHHHHHhhhhcCCceEEEEeccHHHHHHHhc---------cCCC-------chHHHHHHHHHhcCCCcEE
Q psy14646 116 LQQIAYVDINSLQSLNHVKELDTRKILIISDSLSSFQAISN---------LYHP-------NPLVKKIQEEYSNSQANIK 179 (366)
Q Consensus 116 ~~~~~~~~~~~l~al~~~~~~~~~~i~I~sDS~sal~ai~~---------~~~~-------~~i~~~I~~~l~~~~~~V~ 179 (366)
+. .....|.|+|||++|+++|.. |... .+++++|.++++. ..|.
T Consensus 57 -----------------~~-~~~~~v~I~TDS~yvi~~i~~W~~~Wk~~gWk~s~G~pV~N~dL~~~l~~l~~~--~~v~ 116 (161)
T PRK06548 57 -----------------TR-HTDRPILILSDSKYVINSLTKWVYSWKMRKWRKADGKPVLNQEIIQEIDSLMEN--RNIR 116 (161)
T ss_pred -----------------hh-cCCceEEEEeChHHHHHHHHHHHHHHHHCCCcccCCCccccHHHHHHHHHHHhc--CceE
Confidence 11 234579999999999999995 2211 1345555555543 4799
Q ss_pred EEEeccccccccchhhHHHHHHHhccc
Q psy14646 180 FLWCPSHVSISGNERAEECYSNYLASV 206 (366)
Q Consensus 180 ~~WVPgH~Gi~GNE~AD~lAk~A~~~~ 206 (366)
|.|||||+|++|||.||+||++|+...
T Consensus 117 ~~wVkgHsg~~gNe~aD~LA~~aa~~~ 143 (161)
T PRK06548 117 MSWVNAHTGHPLNEAADSLARQAANNF 143 (161)
T ss_pred EEEEecCCCCHHHHHHHHHHHHHHHHh
Confidence 999999999999999999999999764
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=99.61 E-value=2e-14 Score=117.52 Aligned_cols=110 Identities=24% Similarity=0.359 Sum_probs=84.0
Q ss_pred CceeEEEEEecCCeeEEEEc---CCCCChhHHHHHHHHHHhhcccccccCCCchhhhhccchhhhHHHHHHHHHHhHhHH
Q psy14646 51 TGVGCALTIPQLNETKRFAL---NKHSSIFHAELFSIPLHLSLTNCTIDRDSSIDIFFNNKHELKDKLLQQIAYVDINSL 127 (366)
Q Consensus 51 ~~~g~a~~~~~~~~~~~~~l---~~~~~~~~ae~~ai~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l 127 (366)
++.|+|+++.+.+....+.. ....++++||+.|+..||++
T Consensus 13 ~~~g~g~v~~~~~~~~~~~~~~~~~~~s~~~aEl~al~~al~~------------------------------------- 55 (130)
T cd06222 13 GPAGAGVVLRDPGGEVLLSGGLLGGNTTNNRAELLALIEALEL------------------------------------- 55 (130)
T ss_pred CceEEEEEEEeCCCeEEEeccccCCCCcHHHHHHHHHHHHHHH-------------------------------------
Confidence 57777777766554433322 24789999999999999993
Q ss_pred HHHHhhhhcCCceEEEEeccHHHHHHHhccCC--Cc---hHHHHHHHHHhcCCCcEEEEEeccccccccchhhHHHHHHH
Q psy14646 128 QSLNHVKELDTRKILIISDSLSSFQAISNLYH--PN---PLVKKIQEEYSNSQANIKFLWCPSHVSISGNERAEECYSNY 202 (366)
Q Consensus 128 ~al~~~~~~~~~~i~I~sDS~sal~ai~~~~~--~~---~i~~~I~~~l~~~~~~V~~~WVPgH~Gi~GNE~AD~lAk~A 202 (366)
+...+..++.|++||+.++..+.+... .. .+...+.+++ .....+.|.|||+|+|+.+|+.||.|||+|
T Consensus 56 -----~~~~~~~~i~i~~Ds~~~~~~~~~~~~~~~~~~~~~~~~i~~~~-~~~~~~~i~~v~~h~~~~~n~~ad~la~~~ 129 (130)
T cd06222 56 -----ALELGGKKVNIYTDSQYVINALTGWYEGKPVKNVDLWQRLLALL-KRFHKVRFEWVPGHSGIEGNERADALAKEA 129 (130)
T ss_pred -----HHhCCCceEEEEECHHHHHHHhhccccCCChhhHHHHHHHHHHH-hCCCeEEEEEcCCCCCCcchHHHHHHHHhh
Confidence 224578899999999999999998653 12 3445555554 345789999999999999999999999987
Q ss_pred h
Q psy14646 203 L 203 (366)
Q Consensus 203 ~ 203 (366)
.
T Consensus 130 ~ 130 (130)
T cd06222 130 A 130 (130)
T ss_pred C
Confidence 4
No 7
>KOG3752|consensus
Probab=99.39 E-value=1.6e-12 Score=127.55 Aligned_cols=126 Identities=14% Similarity=0.113 Sum_probs=94.7
Q ss_pred cceeeCCCccCC----CCceeEEEEEecCC-eeEEEEcC-CCCChhHHHHHHHHHHhhcccccccCCCchhhhhccchhh
Q psy14646 38 FPICSSSPIDLD----ETGVGCALTIPQLN-ETKRFALN-KHSSIFHAELFSIPLHLSLTNCTIDRDSSIDIFFNNKHEL 111 (366)
Q Consensus 38 ~~~~~~~~~~~~----~~~~g~a~~~~~~~-~~~~~~l~-~~~~~~~ae~~ai~~~l~~~~~~~~~~~~~~~~~~~~~~~ 111 (366)
..+.|+...+.. ...+|+|++.+.+. ...++.+. ...++|.||+.||..||+
T Consensus 212 ~~vvytDGS~~~ng~~~~~AGyGvywg~~~e~N~s~pv~~g~qtNnrAEl~Av~~ALk---------------------- 269 (371)
T KOG3752|consen 212 IQVVYTDGSSSGNGRKSSRAGYGVYWGPGHELNVSGPLAGGRQTNNRAELIAAIEALK---------------------- 269 (371)
T ss_pred ceEEEecCccccCCCCCCcceeEEeeCCCCcccccccCCCCcccccHHHHHHHHHHHH----------------------
Confidence 356676332222 37789999987654 45677776 689999999999999999
Q ss_pred hHHHHHHHHHHhHhHHHHHHhhhhcCCceEEEEeccHHHHHHHhccCC-----------Cch----------HHHHHHHH
Q psy14646 112 KDKLLQQIAYVDINSLQSLNHVKELDTRKILIISDSLSSFQAISNLYH-----------PNP----------LVKKIQEE 170 (366)
Q Consensus 112 ~~~~~~~~~~~~~~~l~al~~~~~~~~~~i~I~sDS~sal~ai~~~~~-----------~~~----------i~~~I~~~ 170 (366)
-+.+....++.|.|||++++++|+.|.. .++ .+..+.++
T Consensus 270 --------------------ka~~~~~~kv~I~TDS~~~i~~l~~wv~~~k~~~~k~~~~~~~i~~~v~n~~~~~e~~~l 329 (371)
T KOG3752|consen 270 --------------------KARSKNINKVVIRTDSEYFINSLTLWVQGWKKNGWKTSNGSDRICAYVKNQDFFNELDEL 329 (371)
T ss_pred --------------------HHHhcCCCcEEEEechHHHHHHHHHHHhhhccCccccccCCCccceeeecchHHHHHHHH
Confidence 2334456699999999999999998632 112 23344455
Q ss_pred Hhc-CCCcEEEEEeccccccccchhhHHHHHHHhcc
Q psy14646 171 YSN-SQANIKFLWCPSHVSISGNERAEECYSNYLAS 205 (366)
Q Consensus 171 l~~-~~~~V~~~WVPgH~Gi~GNE~AD~lAk~A~~~ 205 (366)
.+. .+..|.+.|||||.|+.|||+||.||+++...
T Consensus 330 ~q~~~~~~vq~~~V~Gh~gi~gne~Ad~lARkgs~~ 365 (371)
T KOG3752|consen 330 EQEISNKKVQQEYVGGHSGILGNEMADALARKGSTL 365 (371)
T ss_pred HhhhccCceEEEEecCcCCcchHHHHHHHHhhhhhh
Confidence 554 56899999999999999999999999998654
No 8
>PRK13907 rnhA ribonuclease H; Provisional
Probab=99.34 E-value=2.1e-11 Score=103.85 Aligned_cols=108 Identities=19% Similarity=0.210 Sum_probs=79.0
Q ss_pred CceeEEEEEecCCeeEEEEc-CCCCChhHHHHHHHHHHhhcccccccCCCchhhhhccchhhhHHHHHHHHHHhHhHHHH
Q psy14646 51 TGVGCALTIPQLNETKRFAL-NKHSSIFHAELFSIPLHLSLTNCTIDRDSSIDIFFNNKHELKDKLLQQIAYVDINSLQS 129 (366)
Q Consensus 51 ~~~g~a~~~~~~~~~~~~~l-~~~~~~~~ae~~ai~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~a 129 (366)
+..|+|+++.+.......+. ....++..||+.|+..||++
T Consensus 15 g~~G~G~vi~~~~~~~~~~~~~~~~tn~~AE~~All~aL~~--------------------------------------- 55 (128)
T PRK13907 15 GPSGAGVFIKGVQPAVQLSLPLGTMSNHEAEYHALLAALKY--------------------------------------- 55 (128)
T ss_pred CccEEEEEEEECCeeEEEEecccccCCcHHHHHHHHHHHHH---------------------------------------
Confidence 45566777655444333332 23679999999999999993
Q ss_pred HHhhhhcCCceEEEEeccHHHHHHHhccCCCc----hHHHHHHHHHhcCCCcEEEEEeccccccccchhhHHHHHHHhcc
Q psy14646 130 LNHVKELDTRKILIISDSLSSFQAISNLYHPN----PLVKKIQEEYSNSQANIKFLWCPSHVSISGNERAEECYSNYLAS 205 (366)
Q Consensus 130 l~~~~~~~~~~i~I~sDS~sal~ai~~~~~~~----~i~~~I~~~l~~~~~~V~~~WVPgH~Gi~GNE~AD~lAk~A~~~ 205 (366)
+.+.+..++.|+|||+.+++.+++....+ ++.+++..+++. ...+.|.|||.+ +|+.||.||++|...
T Consensus 56 ---a~~~g~~~v~i~sDS~~vi~~~~~~~~~~~~~~~l~~~~~~l~~~-f~~~~~~~v~r~----~N~~Ad~LA~~a~~~ 127 (128)
T PRK13907 56 ---CTEHNYNIVSFRTDSQLVERAVEKEYAKNKMFAPLLEEALQYIKS-FDLFFIKWIPSS----QNKVADELARKAILQ 127 (128)
T ss_pred ---HHhCCCCEEEEEechHHHHHHHhHHHhcChhHHHHHHHHHHHHhc-CCceEEEEcCch----hchhHHHHHHHHHhc
Confidence 34446678999999999999999854332 355566555544 357888999986 999999999999753
No 9
>PRK07708 hypothetical protein; Validated
Probab=99.17 E-value=5.4e-10 Score=104.47 Aligned_cols=130 Identities=12% Similarity=0.125 Sum_probs=87.5
Q ss_pred HHhhhcCCcceeeCCCccC--CCCceeEEEEE--ecCCeeEEE----EcCCCCChhHHHHHHHHHHhhcccccccCCCch
Q psy14646 30 AQITDQNEFPICSSSPIDL--DETGVGCALTI--PQLNETKRF----ALNKHSSIFHAELFSIPLHLSLTNCTIDRDSSI 101 (366)
Q Consensus 30 ~~i~~~~~~~~~~~~~~~~--~~~~~g~a~~~--~~~~~~~~~----~l~~~~~~~~ae~~ai~~~l~~~~~~~~~~~~~ 101 (366)
..+....+..++|. |++- ..++.|+|+++ ++.+..... .++...++..||..|+..||++
T Consensus 65 ~~~~~ep~~~~vY~-DGs~~~n~g~aG~GvVI~~~~g~~~~~~~~~~~l~~~~TNN~AEy~Ali~aL~~----------- 132 (219)
T PRK07708 65 KEVEEEPHEILVYF-DGGFDKETKLAGLGIVIYYKQGNKRYRIRRNAYIEGIYDNNEAEYAALYYAMQE----------- 132 (219)
T ss_pred hhhccCCCcEEEEE-eeccCCCCCCcEEEEEEEECCCCEEEEEEeeccccccccCcHHHHHHHHHHHHH-----------
Confidence 34555555566666 4332 23445555554 344433322 3455689999999999999993
Q ss_pred hhhhccchhhhHHHHHHHHHHhHhHHHHHHhhhhcCCc--eEEEEeccHHHHHHHhccC-CCch----HHHHHHHHHhcC
Q psy14646 102 DIFFNNKHELKDKLLQQIAYVDINSLQSLNHVKELDTR--KILIISDSLSSFQAISNLY-HPNP----LVKKIQEEYSNS 174 (366)
Q Consensus 102 ~~~~~~~~~~~~~~~~~~~~~~~~~l~al~~~~~~~~~--~i~I~sDS~sal~ai~~~~-~~~~----i~~~I~~~l~~~ 174 (366)
+.+.+.+ .|.|++||+.+++.+...+ ..++ +...+.+++++.
T Consensus 133 -------------------------------A~e~g~~~~~V~I~~DSqlVi~qi~g~wk~~~~~l~~y~~~i~~l~~~~ 181 (219)
T PRK07708 133 -------------------------------LEELGVKHEPVTFRGDSQVVLNQLAGEWPCYDEHLNHWLDRIEQKLKQL 181 (219)
T ss_pred -------------------------------HHHcCCCcceEEEEeccHHHHHHhCCCceeCChhHHHHHHHHHHHHhhC
Confidence 2333333 4899999999999999854 3333 445555566666
Q ss_pred CCcEEEEEeccccccccchhhHHHHHHHhccc
Q psy14646 175 QANIKFLWCPSHVSISGNERAEECYSNYLASV 206 (366)
Q Consensus 175 ~~~V~~~WVPgH~Gi~GNE~AD~lAk~A~~~~ 206 (366)
...+.+.|||-. .|+.||+||++|+...
T Consensus 182 ~l~~~~~~VpR~----~N~~AD~LAk~Al~~~ 209 (219)
T PRK07708 182 KLTPVYEPISRK----QNKEADQLATQALEGT 209 (219)
T ss_pred CceEEEEECCch----hhhHHHHHHHHHHhcC
Confidence 566888898765 8999999999999864
No 10
>PF13456 RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EHG_A 3HST_B.
Probab=98.95 E-value=6.2e-09 Score=81.43 Aligned_cols=68 Identities=26% Similarity=0.267 Sum_probs=49.7
Q ss_pred hhhhcCCceEEEEeccHHHHHHHhccCC-Cc---hHHHHHHHHHhcCCCcEEEEEeccccccccchhhHHHHHHHhc
Q psy14646 132 HVKELDTRKILIISDSLSSFQAISNLYH-PN---PLVKKIQEEYSNSQANIKFLWCPSHVSISGNERAEECYSNYLA 204 (366)
Q Consensus 132 ~~~~~~~~~i~I~sDS~sal~ai~~~~~-~~---~i~~~I~~~l~~~~~~V~~~WVPgH~Gi~GNE~AD~lAk~A~~ 204 (366)
.+.+.+..+|.|.|||+.+++.|++... .+ .++..|+.+++. ...+.|.|||-- +|..||.|||.|.+
T Consensus 15 ~a~~~g~~~i~v~sDs~~vv~~i~~~~~~~~~~~~~~~~i~~~~~~-~~~~~~~~i~r~----~N~~A~~LA~~a~~ 86 (87)
T PF13456_consen 15 LAWELGIRKIIVESDSQLVVDAINGRSSSRSELRPLIQDIRSLLDR-FWNVSVSHIPRE----QNKVADALAKFALS 86 (87)
T ss_dssp HHHCCT-SCEEEEES-HHHHHHHTTSS---SCCHHHHHHHHHHHCC-CSCEEEEE--GG----GSHHHHHHHHHHHH
T ss_pred HHHHCCCCEEEEEecCccccccccccccccccccccchhhhhhhcc-ccceEEEEEChH----HhHHHHHHHHHHhh
Confidence 4455678999999999999999998642 22 456667666655 578999999855 99999999999864
No 11
>PRK07238 bifunctional RNase H/acid phosphatase; Provisional
Probab=98.91 E-value=1.6e-08 Score=101.25 Aligned_cols=118 Identities=16% Similarity=0.195 Sum_probs=81.0
Q ss_pred eeCCCccCCC-CceeEEEEEecC--Cee---EEEEcCCCCChhHHHHHHHHHHhhcccccccCCCchhhhhccchhhhHH
Q psy14646 41 CSSSPIDLDE-TGVGCALTIPQL--NET---KRFALNKHSSIFHAELFSIPLHLSLTNCTIDRDSSIDIFFNNKHELKDK 114 (366)
Q Consensus 41 ~~~~~~~~~~-~~~g~a~~~~~~--~~~---~~~~l~~~~~~~~ae~~ai~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~ 114 (366)
+|+..++..+ +..|+|+++.+. +.. ....++ .+++..||+.|+..||++
T Consensus 5 i~~DGa~~~n~g~aG~G~vi~~~~~~~~~~~~~~~~~-~~tnn~AE~~All~gL~~------------------------ 59 (372)
T PRK07238 5 VEADGGSRGNPGPAGYGAVVWDADRGEVLAERAEAIG-RATNNVAEYRGLIAGLEA------------------------ 59 (372)
T ss_pred EEecCCCCCCCCceEEEEEEEeCCCCcEEEEeecccC-CCCchHHHHHHHHHHHHH------------------------
Confidence 4443333332 345666665543 321 223344 788899999999999993
Q ss_pred HHHHHHHHhHhHHHHHHhhhhcCCceEEEEeccHHHHHHHhccC-CCch----HHHHHHHHHhcCCCcEEEEEecccccc
Q psy14646 115 LLQQIAYVDINSLQSLNHVKELDTRKILIISDSLSSFQAISNLY-HPNP----LVKKIQEEYSNSQANIKFLWCPSHVSI 189 (366)
Q Consensus 115 ~~~~~~~~~~~~l~al~~~~~~~~~~i~I~sDS~sal~ai~~~~-~~~~----i~~~I~~~l~~~~~~V~~~WVPgH~Gi 189 (366)
+.+.+..++.|++||+.+++.+.+.. .+++ +..++.+++++. ..+.|.|||..
T Consensus 60 ------------------a~~~g~~~v~i~~DS~lvi~~i~~~~~~~~~~l~~~~~~i~~l~~~f-~~~~i~~v~r~--- 117 (372)
T PRK07238 60 ------------------AAELGATEVEVRMDSKLVVEQMSGRWKVKHPDMKPLAAQARELASQF-GRVTYTWIPRA--- 117 (372)
T ss_pred ------------------HHhCCCCeEEEEeCcHHHHHHhCCCCccCChHHHHHHHHHHHHHhcC-CceEEEECCch---
Confidence 34456779999999999999998744 2332 344555555433 67999999974
Q ss_pred ccchhhHHHHHHHhccc
Q psy14646 190 SGNERAEECYSNYLASV 206 (366)
Q Consensus 190 ~GNE~AD~lAk~A~~~~ 206 (366)
+|+.||.||++|....
T Consensus 118 -~N~~AD~LA~~a~~~~ 133 (372)
T PRK07238 118 -RNAHADRLANEAMDAA 133 (372)
T ss_pred -hhhHHHHHHHHHHHhh
Confidence 9999999999997654
No 12
>PF13966 zf-RVT: zinc-binding in reverse transcriptase
Probab=96.17 E-value=0.0031 Score=50.07 Aligned_cols=31 Identities=29% Similarity=0.517 Sum_probs=26.3
Q ss_pred cccCCCCCCCCCCCCCC-ccCcceecccccCc
Q psy14646 297 SHLFKREERPECDTCHE-PVTVEHLLLHCNKL 327 (366)
Q Consensus 297 l~r~~~~dsp~C~~CG~-~eTv~HiLl~Cp~~ 327 (366)
+++.+...++.|..|+. .||++|+|++||..
T Consensus 51 l~~r~~~~~~~C~~C~~~~Et~~Hlf~~C~~a 82 (86)
T PF13966_consen 51 LQRRGIQVDPICPLCGNEEETIEHLFFHCPFA 82 (86)
T ss_pred hhccCCccCCccccCCCccccccceeccCcCc
Confidence 55667778899999985 79999999999974
No 13
>PRK08298 cytidine deaminase; Validated
Probab=62.06 E-value=28 Score=30.29 Aligned_cols=61 Identities=15% Similarity=-0.056 Sum_probs=42.4
Q ss_pred CchhHHHHHHHhhhcCCcceeeCCCccCCCCceeEEEEEecCCeeEEEEcCC--CCChhHHHHHHHHHHhh
Q psy14646 21 MNHYWDLFEAQITDQNEFPICSSSPIDLDETGVGCALTIPQLNETKRFALNK--HSSIFHAELFSIPLHLS 89 (366)
Q Consensus 21 ~~~~~~~f~~~i~~~~~~~~~~~~~~~~~~~~~g~a~~~~~~~~~~~~~l~~--~~~~~~ae~~ai~~~l~ 89 (366)
|+.|.++++....-.... |. |.| .||+|+...+++.....-+.. ...-.-||..||..|+.
T Consensus 1 ~~~~~~L~~~A~~a~~~a---Y~-PYS----~VgAAllt~dG~i~tG~NvEnas~~~t~CAEr~Ai~~av~ 63 (136)
T PRK08298 1 MNIEQALYDVAKQLIEQR---YP-NGW----GGAAAMRVEDGTILTSVAPEVINASTELCMETGAICEAHK 63 (136)
T ss_pred CcHHHHHHHHHHHHHHhc---cC-CCC----ceeEEEEeCCCCEEEEEeecCCCCCcchhHHHHHHHHHHH
Confidence 567888888876655443 33 665 899999876655554444422 44567899999999987
No 14
>cd01285 nucleoside_deaminase Nucleoside deaminases include adenosine, guanine and cytosine deaminases. These enzymes are Zn dependent and catalyze the deamination of nucleosides. The zinc ion in the active site plays a central role in the proposed catalytic mechanism, activating a water molecule to form a hydroxide ion that performs a nucleophilic attack on the substrate. The functional enzyme is a homodimer. Cytosine deaminase catalyzes the deamination of cytosine to uracil and ammonia and is a member of the pyrimidine salvage pathway. Cytosine deaminase is found in bacteria and fungi but is not present in mammals; for this reason, the enzyme is currently of interest for antimicrobial drug design and gene therapy applications against tumors. Some members of this family are tRNA-specific adenosine deaminases that generate inosine at the first position of their anticodon (position 34) of specific tRNAs; this modification is thought to enlarge the codon recognition capacity during protei
Probab=44.13 E-value=90 Score=25.48 Aligned_cols=41 Identities=17% Similarity=0.141 Sum_probs=28.5
Q ss_pred CCCCceeEEEEEecCCeeEEEEcCC----CCChhHHHHHHHHHHhh
Q psy14646 48 LDETGVGCALTIPQLNETKRFALNK----HSSIFHAELFSIPLHLS 89 (366)
Q Consensus 48 ~~~~~~g~a~~~~~~~~~~~~~l~~----~~~~~~ae~~ai~~~l~ 89 (366)
.++..+|+.++.++ ++......+. .....|||..||..+.+
T Consensus 14 ~~~~~vgaviv~~~-~~ii~~g~n~~~~~~~~~~HAE~~ai~~~~~ 58 (109)
T cd01285 14 EGEVPFGAVIVDDD-GKVIARGHNRVEQDGDPTAHAEIVAIRNAAR 58 (109)
T ss_pred cCCCcEEEEEEeCC-CEEEEEEeCCCCCCCCCcccHHHHHHHHHHH
Confidence 45778898887644 4333333333 35789999999999877
No 15
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=33.22 E-value=27 Score=29.50 Aligned_cols=53 Identities=23% Similarity=0.374 Sum_probs=32.6
Q ss_pred CCCCCCccCcceecccccCcC--CCCCCCCCCChHhhcCCCcccHHHHHHHHHHccccccC
Q psy14646 308 CDTCHEPVTVEHLLLHCNKLR--FRPPSFLGNSLSNILSDNPDSISTLMRFLKRNNFLKHM 366 (366)
Q Consensus 308 C~~CG~~eTv~HiLl~Cp~~~--~R~~l~~p~~L~~lLg~~~~~~~~l~~Fl~~T~l~~~~ 366 (366)
||.||.+..|..+ .|+.-. .+.++..+ .+...+++-..=+..|++..|=+++|
T Consensus 1 CPvCg~~l~vt~l--~C~~C~t~i~G~F~l~----~~~~L~~E~~~Fi~~Fi~~rGnlKe~ 55 (113)
T PF09862_consen 1 CPVCGGELVVTRL--KCPSCGTEIEGEFELP----WFARLSPEQLEFIKLFIKNRGNLKEM 55 (113)
T ss_pred CCCCCCceEEEEE--EcCCCCCEEEeeeccc----hhhcCCHHHHHHHHHHHHhcCCHHHH
Confidence 8999999888885 788765 44333222 22222355555666777776666554
No 16
>cd01284 Riboflavin_deaminase-reductase Riboflavin-specific deaminase. Riboflavin biosynthesis protein RibD (Diaminohydroxyphosphoribosylaminopyrimidine deaminase) catalyzes the deamination of 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate, which is an intermediate step in the biosynthesis of riboflavin.The ribG gene of Bacillus subtilis and the ribD gene of E. coli are bifunctional and contain this deaminase domain and a reductase domain which catalyzes the subsequent reduction of the ribosyl side chain.
Probab=32.91 E-value=1.1e+02 Score=25.56 Aligned_cols=41 Identities=17% Similarity=0.166 Sum_probs=28.7
Q ss_pred CCCCceeEEEEEecCCeeEEEEcCCCCChhHHHHHHHHHHhh
Q psy14646 48 LDETGVGCALTIPQLNETKRFALNKHSSIFHAELFSIPLHLS 89 (366)
Q Consensus 48 ~~~~~~g~a~~~~~~~~~~~~~l~~~~~~~~ae~~ai~~~l~ 89 (366)
.++..|||.++..+ ++......+......|||..||..+.+
T Consensus 16 ~~~~pvGaviv~~~-g~iv~~g~n~~~~~~HAE~~ai~~a~~ 56 (115)
T cd01284 16 SPNPPVGCVIVDDD-GEIVGEGYHRKAGGPHAEVNALASAGE 56 (115)
T ss_pred CCCCCEEEEEEeCC-CeEEEEecCCCCCcccHHHHHHHHHhh
Confidence 45678898887533 444444444444789999999999987
No 17
>PF05380 Peptidase_A17: Pao retrotransposon peptidase ; InterPro: IPR008042 This signature identifies members of the Pao retrotransposon family.
Probab=32.89 E-value=2e+02 Score=25.20 Aligned_cols=47 Identities=19% Similarity=0.258 Sum_probs=29.7
Q ss_pred CCCccCCCCceeEEEEEec-CCee--EEE-----EcC--CCCChhHHHHHHHHHHhhcc
Q psy14646 43 SSPIDLDETGVGCALTIPQ-LNET--KRF-----ALN--KHSSIFHAELFSIPLHLSLT 91 (366)
Q Consensus 43 ~~~~~~~~~~~g~a~~~~~-~~~~--~~~-----~l~--~~~~~~~ae~~ai~~~l~~~ 91 (366)
.+|+| +.+.|+++|... .+.. -++ ++. +..||=.-||.|+..|.+++
T Consensus 85 F~DAS--~~aygavvYlr~~~~~~~~~~ll~aKsrv~P~k~~tIPRlEL~a~~l~~~l~ 141 (159)
T PF05380_consen 85 FCDAS--ESAYGAVVYLRSYSDGSVQVRLLFAKSRVAPLKTVTIPRLELLAALLGVRLA 141 (159)
T ss_pred eeccc--ccceeeEeEeeeccCCceeeeeeeecccccCCCCCcHHHHHHHHHHHHHHHH
Confidence 33554 667777777654 1111 111 111 35699999999999999975
No 18
>PF00336 DNA_pol_viral_C: DNA polymerase (viral) C-terminal domain; InterPro: IPR001462 This domain is at the C terminus of hepatitis B-type viruses P proteins and represents a functional domain that controls the RNase H activities of the protein. The domain is always associated with IPR000201 from INTERPRO and .; GO: 0004523 ribonuclease H activity
Probab=30.07 E-value=65 Score=30.23 Aligned_cols=39 Identities=26% Similarity=0.278 Sum_probs=24.5
Q ss_pred CCceeEEEEEecCCeeEEEEcCCCCChhHHHHHHHHHHhhc
Q psy14646 50 ETGVGCALTIPQLNETKRFALNKHSSIFHAELFSIPLHLSL 90 (366)
Q Consensus 50 ~~~~g~a~~~~~~~~~~~~~l~~~~~~~~ae~~ai~~~l~~ 90 (366)
.+-.|.|+.+ ....-.+....--.|++||++|.-.|..+
T Consensus 101 ATpTgwgi~i--~~~~~~~Tfs~~l~IhtaELlaaClAr~~ 139 (245)
T PF00336_consen 101 ATPTGWGISI--TGQRMRGTFSKPLPIHTAELLAACLARLM 139 (245)
T ss_pred CCCCcceeee--cCceeeeeecccccchHHHHHHHHHHHhc
Confidence 3334444434 33444444455668999999999888774
No 19
>PF00383 dCMP_cyt_deam_1: Cytidine and deoxycytidylate deaminase zinc-binding region; InterPro: IPR002125 Cytidine deaminase (3.5.4.5 from EC) (cytidine aminohydrolase) catalyzes the hydrolysis of cytidine into uridine and ammonia while deoxycytidylate deaminase (3.5.4.12 from EC) (dCMP deaminase) hydrolyzes dCMP into dUMP. Both enzymes are known to bind zinc and to require it for their catalytic activity [, ]. These two enzymes do not share any sequence similarity with the exception of a region that contains three conserved histidine and cysteine residues which are thought to be involved in the binding of the catalytic zinc ion. Such a region is also found in other proteins [, ]: Yeast cytosine deaminase (3.5.4.1 from EC) (gene FCY1) which transforms cytosine into uracil. Mammalian apolipoprotein B mRNA editing protein, responsible for the postranscriptional editing of a CAA codon into a UAA (stop) codon in the APOB mRNA. Riboflavin biosynthesis protein ribG, which converts 2,5-diamino-6-(ribosylamino)-4(3H)-pyrimidinone 5'-phosphate into 5-amino-6-(ribosylamino)-2,4(1H,3H)-pyrimidinedione 5'-phosphate. Bacillus cereus blasticidin-S deaminase (3.5.4.23 from EC), which catalyzes the deamination of the cytosine moiety of the antibiotics blasticidin S, cytomycin and acetylblasticidin S. Bacillus subtilis protein comEB. This protein is required for the binding and uptake of transforming DNA. B. subtilis hypothetical protein yaaJ. Escherichia coli hypothetical protein yfhC. Yeast hypothetical protein YJL035c. ; GO: 0008270 zinc ion binding, 0016787 hydrolase activity; PDB: 3MPZ_C 3R2N_C 1WKQ_A 1TIY_B 2B3J_C 2O7P_B 2OBC_A 2G6V_B 2D30_B 2D5N_B ....
Probab=28.95 E-value=87 Score=24.74 Aligned_cols=43 Identities=19% Similarity=0.145 Sum_probs=28.7
Q ss_pred cCCCCceeEEEEEecCCeeEEEEcCC----CCChhHHHHHHHHHHhhc
Q psy14646 47 DLDETGVGCALTIPQLNETKRFALNK----HSSIFHAELFSIPLHLSL 90 (366)
Q Consensus 47 ~~~~~~~g~a~~~~~~~~~~~~~l~~----~~~~~~ae~~ai~~~l~~ 90 (366)
..+...+||+++.+ ++.......+. ....-|||..||..+-+.
T Consensus 20 ~~~~~~vgaviv~~-~~~~i~~g~n~~~~~~~~~~HAE~~Ai~~~~~~ 66 (102)
T PF00383_consen 20 PCGNFPVGAVIVDP-DGKIIATGYNGEPPGKNPTIHAEMNAIRKAARN 66 (102)
T ss_dssp TTTSSSEEEEEEET-TTEEEEEEESBHHSTTGGTB-HHHHHHHHHHHT
T ss_pred ccCCCCEEEEEEec-cCccEEEEeeeeeeeccccccchhhhhhhhhhh
Confidence 46788999999775 34444444443 234569999999999883
No 20
>PF05741 zf-nanos: Nanos RNA binding domain; InterPro: IPR024161 Nanos is a highly conserved RNA-binding protein in higher eukaryotes and functions as a key regulatory protein in translational control using a 3' untranslated region during the development and maintenance of germ cells. Nanos comprises a non-conserved amino-terminus and highly conserved carboxy- terminal regions. The C-terminal region has two conserved Cys-Cys-His-Cys (CCHC)-type zinc-finger motifs that are indispensable for nanos function [, , ]. The structure of the nanos-type zinc finger is composed of two independent zinc-finger (ZF) lobes, the N-terminal ZF1 and the C-terminal ZF2, which are connected by a linker helix []. These lobes create a large cleft. Zinc ions in ZF1 and ZF2 are bound to the CCHC motif by tetrahedral coordination.; PDB: 3ALR_B.
Probab=24.47 E-value=38 Score=24.99 Aligned_cols=20 Identities=25% Similarity=0.501 Sum_probs=10.1
Q ss_pred CCCCCCCccCcceecccccC
Q psy14646 307 ECDTCHEPVTVEHLLLHCNK 326 (366)
Q Consensus 307 ~C~~CG~~eTv~HiLl~Cp~ 326 (366)
.|+.||...+-.|....||+
T Consensus 35 ~Cp~CgAtGd~AHT~~yCP~ 54 (55)
T PF05741_consen 35 VCPICGATGDNAHTIKYCPK 54 (55)
T ss_dssp --TTT---GGG---GGG-TT
T ss_pred cCCCCcCcCccccccccCcC
Confidence 79999999999999999996
No 21
>COG0590 CumB Cytosine/adenosine deaminases [Nucleotide transport and metabolism / Translation, ribosomal structure and biogenesis]
Probab=23.47 E-value=2.3e+02 Score=24.87 Aligned_cols=43 Identities=19% Similarity=0.129 Sum_probs=26.6
Q ss_pred CCCCceeEEEEEecCCeeEEE---EcCCCCChhHHHHHHHHHHhhc
Q psy14646 48 LDETGVGCALTIPQLNETKRF---ALNKHSSIFHAELFSIPLHLSL 90 (366)
Q Consensus 48 ~~~~~~g~a~~~~~~~~~~~~---~l~~~~~~~~ae~~ai~~~l~~ 90 (366)
.++..+|+.++-++....... ....+--.-|||..||..|-+.
T Consensus 25 ~ge~PvGaviV~~~~~ii~~~~N~~~~~~dptaHAEi~air~a~~~ 70 (152)
T COG0590 25 EGEVPVGAVIVDADGEIIARGHNRREEDNDPTAHAEILAIRAAAET 70 (152)
T ss_pred cCCCCEEEEEEcCCCCEEEEecCccccCCCccccHHHHHHHHHHHh
Confidence 447778888876333222211 1122445569999999999884
No 22
>PRK10860 tRNA-specific adenosine deaminase; Provisional
Probab=22.79 E-value=2.6e+02 Score=25.19 Aligned_cols=39 Identities=26% Similarity=0.245 Sum_probs=25.2
Q ss_pred CCCceeEEEEEecCCeeEEEEcC----CCCChhHHHHHHHHHHhh
Q psy14646 49 DETGVGCALTIPQLNETKRFALN----KHSSIFHAELFSIPLHLS 89 (366)
Q Consensus 49 ~~~~~g~a~~~~~~~~~~~~~l~----~~~~~~~ae~~ai~~~l~ 89 (366)
++..|||.++. .++.....-+ .....-|||..||..|.+
T Consensus 31 g~~pvGAVIV~--~g~IIa~g~N~~~~~~d~~~HAEi~Ai~~a~~ 73 (172)
T PRK10860 31 REVPVGAVLVH--NNRVIGEGWNRPIGRHDPTAHAEIMALRQGGL 73 (172)
T ss_pred CCCCEEEEEEe--CCEEEEEeeCCCCCCCCCccCHHHHHHHHHHH
Confidence 45789987763 3443333322 234467999999998876
No 23
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=22.22 E-value=60 Score=24.62 Aligned_cols=21 Identities=19% Similarity=0.365 Sum_probs=15.2
Q ss_pred cCCCCCCCCCCCCCCccCcce
Q psy14646 299 LFKREERPECDTCHEPVTVEH 319 (366)
Q Consensus 299 r~~~~dsp~C~~CG~~eTv~H 319 (366)
|+-..|...|+.||.++..+-
T Consensus 12 ~l~~~d~e~CP~Cgs~~~te~ 32 (64)
T COG2093 12 RLTPEDTEICPVCGSTDLTEE 32 (64)
T ss_pred ccCCCCCccCCCCCCcccchh
Confidence 566667778999998865443
No 24
>cd01283 cytidine_deaminase Cytidine deaminase zinc-binding domain. These enzymes are Zn dependent. The zinc ion in the active site plays a central role in the proposed catalytic mechanism, activating a water molecule to form a hydroxide ion that performs a nucleophilic attack on the substrate. Cytidine deaminases catalyze the deamination of cytidine to uridine and are important in the pyrimadine salvage pathway in many cell types, from bacteria to humans. This family also includes the apoBec proteins, which are a mammal specific expansion of RNA editing enzymes, and the closely related phorbolins, and the AID (activation-induced) enzymes.
Probab=21.76 E-value=1.9e+02 Score=23.47 Aligned_cols=43 Identities=19% Similarity=0.047 Sum_probs=28.9
Q ss_pred CCCCceeEEEEEecCCeeEEEEcC--CCCChhHHHHHHHHHHhhc
Q psy14646 48 LDETGVGCALTIPQLNETKRFALN--KHSSIFHAELFSIPLHLSL 90 (366)
Q Consensus 48 ~~~~~~g~a~~~~~~~~~~~~~l~--~~~~~~~ae~~ai~~~l~~ 90 (366)
.++..|||+++..++.....+-.. ......+||..||..+...
T Consensus 15 ~~~~~vga~i~~~~g~i~~G~n~e~~~~~~~~hAE~~ai~~~~~~ 59 (112)
T cd01283 15 YSNFTVGAALLTKDGRIFTGVNVENASYGLTLCAERTAIGKAVSE 59 (112)
T ss_pred CCCCeEEEEEEECCCCEEEeEEeecCCCCCCcCHHHHHHHHHHHc
Confidence 457889998876544443322222 2446789999999999883
Done!