Query psy3161
Match_columns 211
No_of_seqs 160 out of 580
Neff 7.2
Searched_HMMs 46136
Date Fri Aug 16 17:57:25 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy3161.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/3161hhsearch_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 99.4 5.3E-13 1.2E-17 101.9 8.0 97 26-126 2-116 (132)
2 COG0328 RnhA Ribonuclease HI [ 99.4 3.1E-12 6.8E-17 101.4 9.5 75 26-101 2-82 (154)
3 PRK00203 rnhA ribonuclease H; 99.4 5.7E-12 1.2E-16 99.6 9.8 99 27-127 3-127 (150)
4 PRK13907 rnhA ribonuclease H; 99.3 8.3E-12 1.8E-16 95.7 9.7 97 27-123 1-112 (128)
5 PRK06548 ribonuclease H; Provi 99.3 7.4E-12 1.6E-16 100.3 8.9 75 25-100 3-79 (161)
6 PRK08719 ribonuclease H; Revie 99.2 3E-11 6.6E-16 95.4 8.0 71 25-99 2-83 (147)
7 KOG3752|consensus 99.1 4.3E-10 9.3E-15 99.5 8.2 78 26-103 211-297 (371)
8 PRK07708 hypothetical protein; 98.9 8.2E-09 1.8E-13 86.7 10.6 91 11-103 59-161 (219)
9 cd06222 RnaseH RNase H (RNase 98.9 8.3E-09 1.8E-13 75.9 9.3 96 29-124 1-114 (130)
10 PRK07238 bifunctional RNase H/ 98.8 4.8E-08 1E-12 87.7 10.2 95 28-122 3-116 (372)
11 PF13456 RVT_3: Reverse transc 98.0 2.5E-05 5.5E-10 54.7 6.4 52 62-113 1-57 (87)
12 PF13966 zf-RVT: zinc-binding 96.7 0.001 2.2E-08 47.5 1.8 30 147-176 51-83 (86)
13 PF05380 Peptidase_A17: Pao re 92.4 0.66 1.4E-05 36.7 7.2 52 26-79 80-143 (159)
14 PF00336 DNA_pol_viral_C: DNA 80.8 3.8 8.2E-05 34.3 5.1 60 27-95 94-153 (245)
15 cd01285 nucleoside_deaminase N 62.8 37 0.0008 24.8 6.4 52 39-90 17-73 (109)
16 cd01286 deoxycytidylate_deamin 53.0 64 0.0014 24.6 6.4 27 61-89 67-93 (131)
17 PF05741 zf-nanos: Nanos RNA b 49.9 8 0.00017 25.4 0.8 19 156-174 34-54 (55)
18 cd01284 Riboflavin_deaminase-r 48.7 81 0.0017 23.6 6.3 37 40-76 20-57 (115)
19 PF00098 zf-CCHC: Zinc knuckle 48.2 14 0.0003 18.5 1.3 15 157-174 2-18 (18)
20 COG0295 Cdd Cytidine deaminase 47.8 50 0.0011 25.7 5.1 51 40-91 27-81 (134)
21 PRK10860 tRNA-specific adenosi 47.0 70 0.0015 25.8 6.0 51 39-89 33-87 (172)
22 PF13696 zf-CCHC_2: Zinc knuck 46.9 10 0.00022 22.1 0.9 18 154-174 7-26 (32)
23 PRK06848 hypothetical protein; 45.6 88 0.0019 24.3 6.2 57 31-91 22-82 (139)
24 PRK08298 cytidine deaminase; V 39.4 1.4E+02 0.003 23.1 6.4 56 31-91 19-78 (136)
25 TIGR01354 cyt_deam_tetra cytid 38.3 64 0.0014 24.4 4.4 51 40-91 22-76 (127)
26 PRK05578 cytidine deaminase; V 37.6 1.4E+02 0.0031 22.8 6.2 72 11-92 5-80 (131)
27 PRK12411 cytidine deaminase; P 37.3 1.3E+02 0.0028 23.1 5.9 71 11-91 5-79 (132)
28 COG0590 CumB Cytosine/adenosin 35.7 1.3E+02 0.0028 23.6 5.9 51 38-88 27-82 (152)
29 PF00383 dCMP_cyt_deam_1: Cyti 31.9 1.8E+02 0.0039 20.3 5.8 51 38-89 23-78 (102)
30 KOG0481|consensus 28.3 3E+02 0.0065 26.8 7.7 31 7-39 371-401 (729)
31 COG0117 RibD Pyrimidine deamin 25.6 1.5E+02 0.0033 23.3 4.6 37 37-73 25-62 (146)
32 TIGR02571 ComEB ComE operon pr 24.3 3.3E+02 0.0071 21.3 6.4 13 63-75 68-80 (151)
33 PF09862 DUF2089: Protein of u 22.1 72 0.0016 24.1 2.1 49 158-208 1-52 (113)
34 PF13917 zf-CCHC_3: Zinc knuck 21.8 61 0.0013 20.0 1.3 18 154-174 3-22 (42)
35 TIGR00326 eubact_ribD riboflav 21.3 1.7E+02 0.0038 25.9 4.8 37 40-76 20-56 (344)
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=99.42 E-value=5.3e-13 Score=101.91 Aligned_cols=97 Identities=28% Similarity=0.280 Sum_probs=69.8
Q ss_pred CceEEEecCCCCCC--ceeEEEE-eCCeeeeeecCCCCchhHHHHHHHHHHHHHHHcCCCCcEEEEeCcHHHHHHHhc--
Q psy3161 26 NHTICYTDGSKSPD--ATGCAFS-IGDMVRSTSLNPINSIFSAELIAIFLCLEAILESPSDQFLIVSDSRSAIAALAN-- 100 (211)
Q Consensus 26 ~~~~IyTDgS~~~~--~~G~ai~-~~~~~~~~~l~~~~si~~AEl~AI~~AL~~~~~~~~~~i~I~SDS~sal~al~~-- 100 (211)
+.+.||||||+..+ ..|+|++ ..+......++ ..|++.||+.||.+||+.+ . ..+++|+|||+++++.|..
T Consensus 2 ~~~~iytDgS~~~~~~~~~~g~v~~~~~~~~~~~~-~~s~~~aEl~Ai~~AL~~~-~--~~~v~I~tDS~~v~~~l~~~~ 77 (132)
T PF00075_consen 2 KAIIIYTDGSCRPNPGKGGAGYVVWGGRNFSFRLG-GQSNNRAELQAIIEALKAL-E--HRKVTIYTDSQYVLNALNKWL 77 (132)
T ss_dssp TSEEEEEEEEECTTTTEEEEEEEEETTEEEEEEEE-SECHHHHHHHHHHHHHHTH-S--TSEEEEEES-HHHHHHHHTHH
T ss_pred CcEEEEEeCCccCCCCceEEEEEEECCeEEEeccc-ccchhhhheehHHHHHHHh-h--cccccccccHHHHHHHHHHhc
Confidence 57899999997633 3566654 44444445556 9999999999999999954 3 4999999999999998877
Q ss_pred ---CCC----C-chhhhhhhcCC-----CCcccCCCccc
Q psy3161 101 ---WNN----V-PNTNKLKSIRP-----NIKHWNTSTQD 126 (211)
Q Consensus 101 ---~~~----~-~~~~~I~~i~p-----~~~W~~~~~~l 126 (211)
... . ++...|.+++. .|+|+|.|.+.
T Consensus 78 ~~~~~~~~~~~~~i~~~i~~~~~~~~~v~~~~V~~H~~~ 116 (132)
T PF00075_consen 78 HGNGWKKTSNGRPIKNEIWELLSRGIKVRFRWVPGHSGV 116 (132)
T ss_dssp HHTTSBSCTSSSBHTHHHHHHHHHSSEEEEEESSSSSSS
T ss_pred cccccccccccccchhheeeccccceEEeeeeccCcCCC
Confidence 222 1 45556655531 26999999776
No 2
>COG0328 RnhA Ribonuclease HI [DNA replication, recombination, and repair]
Probab=99.37 E-value=3.1e-12 Score=101.36 Aligned_cols=75 Identities=24% Similarity=0.301 Sum_probs=60.8
Q ss_pred CceEEEecCCCCCC--ceeEEEEe--CCee--eeeecCCCCchhHHHHHHHHHHHHHHHcCCCCcEEEEeCcHHHHHHHh
Q psy3161 26 NHTICYTDGSKSPD--ATGCAFSI--GDMV--RSTSLNPINSIFSAELIAIFLCLEAILESPSDQFLIVSDSRSAIAALA 99 (211)
Q Consensus 26 ~~~~IyTDgS~~~~--~~G~ai~~--~~~~--~~~~l~~~~si~~AEl~AI~~AL~~~~~~~~~~i~I~SDS~sal~al~ 99 (211)
..+.||||||+.++ ..|+|+|. ++.. .+..+. .+|++.||+.|++.||+++.+.+...+.|+|||+.++++|.
T Consensus 2 ~~v~if~DGa~~gNpG~gG~g~vl~~~~~~~~~s~~~~-~tTNNraEl~A~i~AL~~l~~~~~~~v~l~tDS~yv~~~i~ 80 (154)
T COG0328 2 KKVEIFTDGACLGNPGPGGWGAVLRYGDGEKELSGGEG-RTTNNRAELRALIEALEALKELGACEVTLYTDSKYVVEGIT 80 (154)
T ss_pred CceEEEecCccCCCCCCceEEEEEEcCCceEEEeeeee-cccChHHHHHHHHHHHHHHHhcCCceEEEEecHHHHHHHHH
Confidence 46899999999966 36777553 3322 333334 89999999999999999999888899999999999999998
Q ss_pred cC
Q psy3161 100 NW 101 (211)
Q Consensus 100 ~~ 101 (211)
.|
T Consensus 81 ~w 82 (154)
T COG0328 81 RW 82 (154)
T ss_pred HH
Confidence 55
No 3
>PRK00203 rnhA ribonuclease H; Reviewed
Probab=99.35 E-value=5.7e-12 Score=99.60 Aligned_cols=99 Identities=17% Similarity=0.222 Sum_probs=68.4
Q ss_pred ceEEEecCCCCCC--ceeEEEEe--CCeeee-eecCCCCchhHHHHHHHHHHHHHHHcCCCCcEEEEeCcHHHHHHHhcC
Q psy3161 27 HTICYTDGSKSPD--ATGCAFSI--GDMVRS-TSLNPINSIFSAELIAIFLCLEAILESPSDQFLIVSDSRSAIAALANW 101 (211)
Q Consensus 27 ~~~IyTDgS~~~~--~~G~ai~~--~~~~~~-~~l~~~~si~~AEl~AI~~AL~~~~~~~~~~i~I~SDS~sal~al~~~ 101 (211)
++.||||||+..+ ..|+|++. ++.... ....+..|+..||+.||+.||+.+.. ...+.|+|||++++++|..|
T Consensus 3 ~v~iytDGs~~~n~~~~g~g~v~~~~~~~~~~~~~~~~~TN~~aEL~Ai~~AL~~~~~--~~~v~I~tDS~yvi~~i~~w 80 (150)
T PRK00203 3 QVEIYTDGACLGNPGPGGWGAILRYKGHEKELSGGEALTTNNRMELMAAIEALEALKE--PCEVTLYTDSQYVRQGITEW 80 (150)
T ss_pred eEEEEEEecccCCCCceEEEEEEEECCeeEEEecCCCCCcHHHHHHHHHHHHHHHcCC--CCeEEEEECHHHHHHHHHHH
Confidence 5899999999854 46777553 333222 22235788999999999999998865 46799999999999999862
Q ss_pred ---------CC---Cch-----hhhhhhcCC----CCcccCCCcccc
Q psy3161 102 ---------NN---VPN-----TNKLKSIRP----NIKHWNTSTQDR 127 (211)
Q Consensus 102 ---------~~---~~~-----~~~I~~i~p----~~~W~~~~~~l~ 127 (211)
.. .++ .+.|.++.. .|.|+|.|.+..
T Consensus 81 ~~~Wk~~~~~~~~g~~v~n~dl~~~i~~l~~~~~v~~~wV~~H~~~~ 127 (150)
T PRK00203 81 IHGWKKNGWKTADKKPVKNVDLWQRLDAALKRHQIKWHWVKGHAGHP 127 (150)
T ss_pred HHHHHHcCCcccCCCccccHHHHHHHHHHhccCceEEEEecCCCCCH
Confidence 11 133 233444322 369999986543
No 4
>PRK13907 rnhA ribonuclease H; Provisional
Probab=99.34 E-value=8.3e-12 Score=95.72 Aligned_cols=97 Identities=20% Similarity=0.105 Sum_probs=71.7
Q ss_pred ceEEEecCCCCCC--ceeEEEEeC--Ceeeeee-cCCCCchhHHHHHHHHHHHHHHHcCCCCcEEEEeCcHHHHHHHhcC
Q psy3161 27 HTICYTDGSKSPD--ATGCAFSIG--DMVRSTS-LNPINSIFSAELIAIFLCLEAILESPSDQFLIVSDSRSAIAALANW 101 (211)
Q Consensus 27 ~~~IyTDgS~~~~--~~G~ai~~~--~~~~~~~-l~~~~si~~AEl~AI~~AL~~~~~~~~~~i~I~SDS~sal~al~~~ 101 (211)
|++||||||...+ ..|+|++.. +.....+ .....++..||+.|++.||+.+.......+.|+|||+.++..+++.
T Consensus 1 ~~~iy~DGa~~~~~g~~G~G~vi~~~~~~~~~~~~~~~~tn~~AE~~All~aL~~a~~~g~~~v~i~sDS~~vi~~~~~~ 80 (128)
T PRK13907 1 MIEVYIDGASKGNPGPSGAGVFIKGVQPAVQLSLPLGTMSNHEAEYHALLAALKYCTEHNYNIVSFRTDSQLVERAVEKE 80 (128)
T ss_pred CEEEEEeeCCCCCCCccEEEEEEEECCeeEEEEecccccCCcHHHHHHHHHHHHHHHhCCCCEEEEEechHHHHHHHhHH
Confidence 6899999999865 578886642 2221222 2356899999999999999999998888999999999999999885
Q ss_pred CC-C----chhhhhhhcCCC-----CcccCCC
Q psy3161 102 NN-V----PNTNKLKSIRPN-----IKHWNTS 123 (211)
Q Consensus 102 ~~-~----~~~~~I~~i~p~-----~~W~~~~ 123 (211)
.. + ++.+.++.+... ++|+|..
T Consensus 81 ~~~~~~~~~l~~~~~~l~~~f~~~~~~~v~r~ 112 (128)
T PRK13907 81 YAKNKMFAPLLEEALQYIKSFDLFFIKWIPSS 112 (128)
T ss_pred HhcChhHHHHHHHHHHHHhcCCceEEEEcCch
Confidence 54 2 345555555433 3788764
No 5
>PRK06548 ribonuclease H; Provisional
Probab=99.32 E-value=7.4e-12 Score=100.30 Aligned_cols=75 Identities=29% Similarity=0.298 Sum_probs=57.1
Q ss_pred CCceEEEecCCCCCC--ceeEEEEeCCeeeeeecCCCCchhHHHHHHHHHHHHHHHcCCCCcEEEEeCcHHHHHHHhc
Q psy3161 25 ANHTICYTDGSKSPD--ATGCAFSIGDMVRSTSLNPINSIFSAELIAIFLCLEAILESPSDQFLIVSDSRSAIAALAN 100 (211)
Q Consensus 25 ~~~~~IyTDgS~~~~--~~G~ai~~~~~~~~~~l~~~~si~~AEl~AI~~AL~~~~~~~~~~i~I~SDS~sal~al~~ 100 (211)
+..+.||||||+.++ ..|+|++..+...........|++.||+.||+.||+.+.. ...++.|+|||++++++|..
T Consensus 3 ~~~~~IytDGa~~gnpg~~G~g~~~~~~~~~~g~~~~~TNnraEl~Aii~aL~~~~~-~~~~v~I~TDS~yvi~~i~~ 79 (161)
T PRK06548 3 NNEIIAATDGSSLANPGPSGWAWYVDENTWDSGGWDIATNNIAELTAVRELLIATRH-TDRPILILSDSKYVINSLTK 79 (161)
T ss_pred CCEEEEEEeeccCCCCCceEEEEEEeCCcEEccCCCCCCHHHHHHHHHHHHHHhhhc-CCceEEEEeChHHHHHHHHH
Confidence 345899999999865 4788877543322222235689999999999999986653 34579999999999999993
No 6
>PRK08719 ribonuclease H; Reviewed
Probab=99.24 E-value=3e-11 Score=95.45 Aligned_cols=71 Identities=23% Similarity=0.303 Sum_probs=54.3
Q ss_pred CCceEEEecCCCCCCc-----eeEEEEe--CC--ee--eeeecCCCCchhHHHHHHHHHHHHHHHcCCCCcEEEEeCcHH
Q psy3161 25 ANHTICYTDGSKSPDA-----TGCAFSI--GD--MV--RSTSLNPINSIFSAELIAIFLCLEAILESPSDQFLIVSDSRS 93 (211)
Q Consensus 25 ~~~~~IyTDgS~~~~~-----~G~ai~~--~~--~~--~~~~l~~~~si~~AEl~AI~~AL~~~~~~~~~~i~I~SDS~s 93 (211)
.+.+.||||||+..++ .|+|++. ++ .. ....+....|+++||+.||+.||+.+... ..|+|||+.
T Consensus 2 ~~~~~iYtDGs~~~n~~~~~~~G~G~vv~~~~~~~~~~~~~~~~~~~Tnn~aEl~A~~~aL~~~~~~----~~i~tDS~y 77 (147)
T PRK08719 2 RASYSIYIDGAAPNNQHGCVRGGIGLVVYDEAGEIVDEQSITVNRYTDNAELELLALIEALEYARDG----DVIYSDSDY 77 (147)
T ss_pred CceEEEEEecccCCCCCCCCCcEEEEEEEeCCCCeeEEEEecCCCCccHHHHHHHHHHHHHHHcCCC----CEEEechHH
Confidence 4578999999997553 4777653 32 22 33335556899999999999999998753 379999999
Q ss_pred HHHHHh
Q psy3161 94 AIAALA 99 (211)
Q Consensus 94 al~al~ 99 (211)
++++|+
T Consensus 78 vi~~i~ 83 (147)
T PRK08719 78 CVRGFN 83 (147)
T ss_pred HHHHHH
Confidence 999984
No 7
>KOG3752|consensus
Probab=99.07 E-value=4.3e-10 Score=99.50 Aligned_cols=78 Identities=28% Similarity=0.336 Sum_probs=66.9
Q ss_pred CceEEEecCCCCCC-----ceeEEEEeCC---eeeeeecC-CCCchhHHHHHHHHHHHHHHHcCCCCcEEEEeCcHHHHH
Q psy3161 26 NHTICYTDGSKSPD-----ATGCAFSIGD---MVRSTSLN-PINSIFSAELIAIFLCLEAILESPSDQFLIVSDSRSAIA 96 (211)
Q Consensus 26 ~~~~IyTDgS~~~~-----~~G~ai~~~~---~~~~~~l~-~~~si~~AEl~AI~~AL~~~~~~~~~~i~I~SDS~sal~ 96 (211)
+...||||||+..+ .+|+||+.++ ...+..+. ...++|.||+.||..||+.+.+.+..+++|.|||+..++
T Consensus 211 ~~~vvytDGS~~~ng~~~~~AGyGvywg~~~e~N~s~pv~~g~qtNnrAEl~Av~~ALkka~~~~~~kv~I~TDS~~~i~ 290 (371)
T KOG3752|consen 211 EIQVVYTDGSSSGNGRKSSRAGYGVYWGPGHELNVSGPLAGGRQTNNRAELIAAIEALKKARSKNINKVVIRTDSEYFIN 290 (371)
T ss_pred cceEEEecCccccCCCCCCcceeEEeeCCCCcccccccCCCCcccccHHHHHHHHHHHHHHHhcCCCcEEEEechHHHHH
Confidence 34889999999975 4899999753 45666664 889999999999999999999888889999999999999
Q ss_pred HHhcCCC
Q psy3161 97 ALANWNN 103 (211)
Q Consensus 97 al~~~~~ 103 (211)
+|+.|..
T Consensus 291 ~l~~wv~ 297 (371)
T KOG3752|consen 291 SLTLWVQ 297 (371)
T ss_pred HHHHHHh
Confidence 9987654
No 8
>PRK07708 hypothetical protein; Validated
Probab=98.94 E-value=8.2e-09 Score=86.65 Aligned_cols=91 Identities=18% Similarity=0.182 Sum_probs=66.7
Q ss_pred HHHHHHHHHHHhhcCCceEEEecCCCCC--CceeEEEEe--CC--eeee----eecCCCCchhHHHHHHHHHHHHHHHcC
Q psy3161 11 VFQQKFSEVINTKYANHTICYTDGSKSP--DATGCAFSI--GD--MVRS----TSLNPINSIFSAELIAIFLCLEAILES 80 (211)
Q Consensus 11 ~~~~~~~~~~~~~~~~~~~IyTDgS~~~--~~~G~ai~~--~~--~~~~----~~l~~~~si~~AEl~AI~~AL~~~~~~ 80 (211)
+++++..++-.. ++.+.||+|||... +++|+|++. +. .... ..+....+++.||+.|++.||+.+...
T Consensus 59 ~~~~~~~~~~~e--p~~~~vY~DGs~~~n~g~aG~GvVI~~~~g~~~~~~~~~~~l~~~~TNN~AEy~Ali~aL~~A~e~ 136 (219)
T PRK07708 59 ELKKLSKEVEEE--PHEILVYFDGGFDKETKLAGLGIVIYYKQGNKRYRIRRNAYIEGIYDNNEAEYAALYYAMQELEEL 136 (219)
T ss_pred HHhhhhhhhccC--CCcEEEEEeeccCCCCCCcEEEEEEEECCCCEEEEEEeeccccccccCcHHHHHHHHHHHHHHHHc
Confidence 345555555454 67899999999863 457777553 22 2221 234556899999999999999999987
Q ss_pred CCC--cEEEEeCcHHHHHHHhcCCC
Q psy3161 81 PSD--QFLIVSDSRSAIAALANWNN 103 (211)
Q Consensus 81 ~~~--~i~I~SDS~sal~al~~~~~ 103 (211)
+.+ .+.|++||+.+++.+.+.+.
T Consensus 137 g~~~~~V~I~~DSqlVi~qi~g~wk 161 (219)
T PRK07708 137 GVKHEPVTFRGDSQVVLNQLAGEWP 161 (219)
T ss_pred CCCcceEEEEeccHHHHHHhCCCce
Confidence 654 38999999999999988654
No 9
>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=98.93 E-value=8.3e-09 Score=75.92 Aligned_cols=96 Identities=25% Similarity=0.270 Sum_probs=70.4
Q ss_pred EEEecCCCCCC--ceeEEEEe--CCeeeee---ecCCCCchhHHHHHHHHHHHHHHHcCCCCcEEEEeCcHHHHHHHhcC
Q psy3161 29 ICYTDGSKSPD--ATGCAFSI--GDMVRST---SLNPINSIFSAELIAIFLCLEAILESPSDQFLIVSDSRSAIAALANW 101 (211)
Q Consensus 29 ~IyTDgS~~~~--~~G~ai~~--~~~~~~~---~l~~~~si~~AEl~AI~~AL~~~~~~~~~~i~I~SDS~sal~al~~~ 101 (211)
.+|||||...+ ++|+|++. .+....+ ......+++.||+.|++.||+++......++.|++||+.++..+.++
T Consensus 1 ~~~~Dgs~~~~~~~~g~g~v~~~~~~~~~~~~~~~~~~~s~~~aEl~al~~al~~~~~~~~~~i~i~~Ds~~~~~~~~~~ 80 (130)
T cd06222 1 VIYTDGSCRGNPGPAGAGVVLRDPGGEVLLSGGLLGGNTTNNRAELLALIEALELALELGGKKVNIYTDSQYVINALTGW 80 (130)
T ss_pred CEEecccCCCCCCceEEEEEEEeCCCeEEEeccccCCCCcHHHHHHHHHHHHHHHHHhCCCceEEEEECHHHHHHHhhcc
Confidence 48999999866 57777664 2222121 12258899999999999999999887889999999999999999987
Q ss_pred CC------CchhhhhhhcC---C--CCcccCCCc
Q psy3161 102 NN------VPNTNKLKSIR---P--NIKHWNTST 124 (211)
Q Consensus 102 ~~------~~~~~~I~~i~---p--~~~W~~~~~ 124 (211)
.. .++...|++++ . .|.|+|.|.
T Consensus 81 ~~~~~~~~~~~~~~i~~~~~~~~~~~i~~v~~h~ 114 (130)
T cd06222 81 YEGKPVKNVDLWQRLLALLKRFHKVRFEWVPGHS 114 (130)
T ss_pred ccCCChhhHHHHHHHHHHHhCCCeEEEEEcCCCC
Confidence 53 12344454443 1 258888865
No 10
>PRK07238 bifunctional RNase H/acid phosphatase; Provisional
Probab=98.77 E-value=4.8e-08 Score=87.71 Aligned_cols=95 Identities=15% Similarity=0.135 Sum_probs=68.5
Q ss_pred eEEEecCCCCCC--ceeEEEEe--CC-e-e-eeee-cCCCCchhHHHHHHHHHHHHHHHcCCCCcEEEEeCcHHHHHHHh
Q psy3161 28 TICYTDGSKSPD--ATGCAFSI--GD-M-V-RSTS-LNPINSIFSAELIAIFLCLEAILESPSDQFLIVSDSRSAIAALA 99 (211)
Q Consensus 28 ~~IyTDgS~~~~--~~G~ai~~--~~-~-~-~~~~-l~~~~si~~AEl~AI~~AL~~~~~~~~~~i~I~SDS~sal~al~ 99 (211)
+.||||||..++ ..|+|++. .+ . . ..++ .....++..||+.|++.||+++.+.....+.|++||+.+++.+.
T Consensus 3 ~~i~~DGa~~~n~g~aG~G~vi~~~~~~~~~~~~~~~~~~~tnn~AE~~All~gL~~a~~~g~~~v~i~~DS~lvi~~i~ 82 (372)
T PRK07238 3 VVVEADGGSRGNPGPAGYGAVVWDADRGEVLAERAEAIGRATNNVAEYRGLIAGLEAAAELGATEVEVRMDSKLVVEQMS 82 (372)
T ss_pred EEEEecCCCCCCCCceEEEEEEEeCCCCcEEEEeecccCCCCchHHHHHHHHHHHHHHHhCCCCeEEEEeCcHHHHHHhC
Confidence 789999999976 47777653 32 1 1 1222 23477888999999999999999988889999999999999998
Q ss_pred cCCC--Cc----hhhhhhhcC---CC--CcccCC
Q psy3161 100 NWNN--VP----NTNKLKSIR---PN--IKHWNT 122 (211)
Q Consensus 100 ~~~~--~~----~~~~I~~i~---p~--~~W~~~ 122 (211)
+... ++ +...++++. +. ++|++.
T Consensus 83 ~~~~~~~~~l~~~~~~i~~l~~~f~~~~i~~v~r 116 (372)
T PRK07238 83 GRWKVKHPDMKPLAAQARELASQFGRVTYTWIPR 116 (372)
T ss_pred CCCccCChHHHHHHHHHHHHHhcCCceEEEECCc
Confidence 7554 32 344555553 32 366654
No 11
>PF13456 RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EHG_A 3HST_B.
Probab=97.97 E-value=2.5e-05 Score=54.68 Aligned_cols=52 Identities=19% Similarity=0.277 Sum_probs=41.5
Q ss_pred hhHHHHHHHHHHHHHHHcCCCCcEEEEeCcHHHHHHHhcCCC--Cc---hhhhhhhc
Q psy3161 62 IFSAELIAIFLCLEAILESPSDQFLIVSDSRSAIAALANWNN--VP---NTNKLKSI 113 (211)
Q Consensus 62 i~~AEl~AI~~AL~~~~~~~~~~i~I~SDS~sal~al~~~~~--~~---~~~~I~~i 113 (211)
+..||+.|+..||+++.+.+..+++|.|||+.+++.|++... +. +.+.|+.+
T Consensus 1 ~~~aE~~al~~al~~a~~~g~~~i~v~sDs~~vv~~i~~~~~~~~~~~~~~~~i~~~ 57 (87)
T PF13456_consen 1 PLEAEALALLEALQLAWELGIRKIIVESDSQLVVDAINGRSSSRSELRPLIQDIRSL 57 (87)
T ss_dssp HHHHHHHHHHHHHHHHHCCT-SCEEEEES-HHHHHHHTTSS---SCCHHHHHHHHHH
T ss_pred CcHHHHHHHHHHHHHHHHCCCCEEEEEecCccccccccccccccccccccchhhhhh
Confidence 468999999999999999999999999999999999988754 33 44555555
No 12
>PF13966 zf-RVT: zinc-binding in reverse transcriptase
Probab=96.66 E-value=0.001 Score=47.49 Aligned_cols=30 Identities=30% Similarity=0.609 Sum_probs=24.8
Q ss_pred ccccCCCCCCCcc-CC-Cccccceec-cccCch
Q psy3161 147 NHLFTKSDPPICQ-CG-APLSVRHLL-SCPRHG 176 (211)
Q Consensus 147 ~~~~~~~~~p~C~-Cg-~~~t~~Hil-~C~~~~ 176 (211)
+++.+...++.|. |+ ..||++|+| +||...
T Consensus 51 l~~r~~~~~~~C~~C~~~~Et~~Hlf~~C~~a~ 83 (86)
T PF13966_consen 51 LQRRGIQVDPICPLCGNEEETIEHLFFHCPFAR 83 (86)
T ss_pred hhccCCccCCccccCCCccccccceeccCcCcc
Confidence 4556667789999 99 599999999 999753
No 13
>PF05380 Peptidase_A17: Pao retrotransposon peptidase ; InterPro: IPR008042 This signature identifies members of the Pao retrotransposon family.
Probab=92.43 E-value=0.66 Score=36.73 Aligned_cols=52 Identities=19% Similarity=0.150 Sum_probs=34.1
Q ss_pred CceEEEecCCCCCCceeEEEEeC---Ceeeee-------ec--CCCCchhHHHHHHHHHHHHHHHc
Q psy3161 26 NHTICYTDGSKSPDATGCAFSIG---DMVRST-------SL--NPINSIFSAELIAIFLCLEAILE 79 (211)
Q Consensus 26 ~~~~IyTDgS~~~~~~G~ai~~~---~~~~~~-------~l--~~~~si~~AEl~AI~~AL~~~~~ 79 (211)
..+++|+|||. .+.|+.+|.. +..... ++ ....||-.-|++|+..|.+++..
T Consensus 80 ~~L~~F~DAS~--~aygavvYlr~~~~~~~~~~ll~aKsrv~P~k~~tIPRlEL~a~~l~~~l~~~ 143 (159)
T PF05380_consen 80 VELHVFCDASE--SAYGAVVYLRSYSDGSVQVRLLFAKSRVAPLKTVTIPRLELLAALLGVRLANT 143 (159)
T ss_pred eeeeEeecccc--cceeeEeEeeeccCCceeeeeeeecccccCCCCCcHHHHHHHHHHHHHHHHHH
Confidence 36889999994 4455555532 211111 12 23559999999999999999763
No 14
>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=80.77 E-value=3.8 Score=34.27 Aligned_cols=60 Identities=17% Similarity=0.121 Sum_probs=39.3
Q ss_pred ceEEEecCCCCCCceeEEEEeCCeeeeeecCCCCchhHHHHHHHHHHHHHHHcCCCCcEEEEeCcHHHH
Q psy3161 27 HTICYTDGSKSPDATGCAFSIGDMVRSTSLNPINSIFSAELIAIFLCLEAILESPSDQFLIVSDSRSAI 95 (211)
Q Consensus 27 ~~~IyTDgS~~~~~~G~ai~~~~~~~~~~l~~~~si~~AEl~AI~~AL~~~~~~~~~~i~I~SDS~sal 95 (211)
--.||+|+.-...+ +..+.....+.+..--.|++||++|...|.-+... + .|.|||-.++
T Consensus 94 lc~VfaDATpTgwg----i~i~~~~~~~Tfs~~l~IhtaELlaaClAr~~~~~----r-~l~tDnt~Vl 153 (245)
T PF00336_consen 94 LCQVFADATPTGWG----ISITGQRMRGTFSKPLPIHTAELLAACLARLMSGA----R-CLGTDNTVVL 153 (245)
T ss_pred CCceeccCCCCcce----eeecCceeeeeecccccchHHHHHHHHHHHhccCC----c-EEeecCcEEE
Confidence 45899998665443 22333333333344667999999999888766543 2 5999998766
No 15
>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=62.82 E-value=37 Score=24.81 Aligned_cols=52 Identities=13% Similarity=0.003 Sum_probs=33.4
Q ss_pred CceeEEEEeC-CeeeeeecC----CCCchhHHHHHHHHHHHHHHHcCCCCcEEEEeC
Q psy3161 39 DATGCAFSIG-DMVRSTSLN----PINSIFSAELIAIFLCLEAILESPSDQFLIVSD 90 (211)
Q Consensus 39 ~~~G~ai~~~-~~~~~~~l~----~~~si~~AEl~AI~~AL~~~~~~~~~~i~I~SD 90 (211)
..+|+.+++. +........ ......-||..||..|.+..........++|+.
T Consensus 17 ~~vgaviv~~~~~ii~~g~n~~~~~~~~~~HAE~~ai~~~~~~~~~~~~~~~~ly~t 73 (109)
T cd01285 17 VPFGAVIVDDDGKVIARGHNRVEQDGDPTAHAEIVAIRNAARRLGSYLLSGCTLYTT 73 (109)
T ss_pred CcEEEEEEeCCCEEEEEEeCCCCCCCCCcccHHHHHHHHHHHHhCCCccCCeEEEEe
Confidence 3688888876 444333332 234667799999999988754433455666664
No 16
>cd01286 deoxycytidylate_deaminase Deoxycytidylate deaminase domain. Deoxycytidylate deaminase catalyzes the deamination of dCMP to dUMP, providing the nucleotide substrate for thymidylate synthase. The enzyme binds Zn++, which is required for catalytic activity. The activity of the enzyme is allosterically regulated by the ratio of dCTP to dTTP not only in eukaryotic cells but also in T-even phage-infected Escherichia coli, with dCTP acting as an activator and dTTP as an inhibitor.
Probab=53.01 E-value=64 Score=24.58 Aligned_cols=27 Identities=15% Similarity=0.023 Sum_probs=16.7
Q ss_pred chhHHHHHHHHHHHHHHHcCCCCcEEEEe
Q psy3161 61 SIFSAELIAIFLCLEAILESPSDQFLIVS 89 (211)
Q Consensus 61 si~~AEl~AI~~AL~~~~~~~~~~i~I~S 89 (211)
...-||..||..|.+. .......++|+
T Consensus 67 ~~~HAE~~Ai~~a~~~--~~~~~~~tLyv 93 (131)
T cd01286 67 RTVHAEQNAILQAARH--GVSLEGATLYV 93 (131)
T ss_pred CCCCHHHHHHHHHhHc--CCCcCCeEEEE
Confidence 3445999999988764 22234455554
No 17
>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=49.92 E-value=8 Score=25.42 Aligned_cols=19 Identities=37% Similarity=0.922 Sum_probs=8.1
Q ss_pred CCcc-CCCccccceec-cccC
Q psy3161 156 PICQ-CGAPLSVRHLL-SCPR 174 (211)
Q Consensus 156 p~C~-Cg~~~t~~Hil-~C~~ 174 (211)
-.|+ ||+..+-.|-. .||.
T Consensus 34 y~Cp~CgAtGd~AHT~~yCP~ 54 (55)
T PF05741_consen 34 YVCPICGATGDNAHTIKYCPK 54 (55)
T ss_dssp ---TTT---GGG---GGG-TT
T ss_pred CcCCCCcCcCccccccccCcC
Confidence 4799 99999999999 9996
No 18
>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=48.68 E-value=81 Score=23.56 Aligned_cols=37 Identities=16% Similarity=0.089 Sum_probs=25.2
Q ss_pred ceeEEEEeC-CeeeeeecCCCCchhHHHHHHHHHHHHH
Q psy3161 40 ATGCAFSIG-DMVRSTSLNPINSIFSAELIAIFLCLEA 76 (211)
Q Consensus 40 ~~G~ai~~~-~~~~~~~l~~~~si~~AEl~AI~~AL~~ 76 (211)
.+|+.++.+ +..............-||..||.+|.+.
T Consensus 20 pvGaviv~~~g~iv~~g~n~~~~~~HAE~~ai~~a~~~ 57 (115)
T cd01284 20 PVGCVIVDDDGEIVGEGYHRKAGGPHAEVNALASAGEK 57 (115)
T ss_pred CEEEEEEeCCCeEEEEecCCCCCcccHHHHHHHHHhhc
Confidence 588888865 4444434333335667999999999874
No 19
>PF00098 zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the CysCysHisCys (CCHC) type zinc finger domains, and have the sequence: C-X2-C-X4-H-X4-C where X can be any amino acid, and number indicates the number of residues. These 18 residues CCHC zinc finger domains are mainly found in the nucleocapsid protein of retroviruses. It is required for viral genome packaging and for early infection process [, , ]. It is also found in eukaryotic proteins involved in RNA binding or single-stranded DNA binding []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding; PDB: 2L44_A 1A1T_A 1WWG_A 1U6P_A 1WWD_A 1WWE_A 1A6B_B 1F6U_A 1MFS_A 1NCP_C ....
Probab=48.19 E-value=14 Score=18.48 Aligned_cols=15 Identities=47% Similarity=1.362 Sum_probs=11.1
Q ss_pred Ccc-CCCccccceec-cccC
Q psy3161 157 ICQ-CGAPLSVRHLL-SCPR 174 (211)
Q Consensus 157 ~C~-Cg~~~t~~Hil-~C~~ 174 (211)
.|- ||.. .|+. +||.
T Consensus 2 ~C~~C~~~---GH~~~~Cp~ 18 (18)
T PF00098_consen 2 KCFNCGEP---GHIARDCPK 18 (18)
T ss_dssp BCTTTSCS---SSCGCTSSS
T ss_pred cCcCCCCc---CcccccCcc
Confidence 566 7754 7999 9984
No 20
>COG0295 Cdd Cytidine deaminase [Nucleotide transport and metabolism]
Probab=47.85 E-value=50 Score=25.66 Aligned_cols=51 Identities=24% Similarity=0.219 Sum_probs=32.4
Q ss_pred ceeEEEEeCCeeeeeec----CCCCchhHHHHHHHHHHHHHHHcCCCCcEEEEeCc
Q psy3161 40 ATGCAFSIGDMVRSTSL----NPINSIFSAELIAIFLCLEAILESPSDQFLIVSDS 91 (211)
Q Consensus 40 ~~G~ai~~~~~~~~~~l----~~~~si~~AEl~AI~~AL~~~~~~~~~~i~I~SDS 91 (211)
.+|+++...+...-++. ..+.---.||..||..|+.. -......+.+++|+
T Consensus 27 ~VGAa~~t~~G~i~tG~NiEnasy~~t~CAErsAI~~ais~-G~~~~~~v~v~~~~ 81 (134)
T COG0295 27 KVGAALRTKDGRIYTGANVENASYGLTVCAERSAIFKAISE-GKRKFDAVVVVADT 81 (134)
T ss_pred cEEEEEEeCCCCEEEEEeeecccccchhhHHHHHHHHHHHc-CCCcEEEEEEEcCC
Confidence 58888775432222221 12333346999999999987 33346788899997
No 21
>PRK10860 tRNA-specific adenosine deaminase; Provisional
Probab=47.02 E-value=70 Score=25.76 Aligned_cols=51 Identities=10% Similarity=-0.024 Sum_probs=29.1
Q ss_pred CceeEEEEeCCeeeeeec----CCCCchhHHHHHHHHHHHHHHHcCCCCcEEEEe
Q psy3161 39 DATGCAFSIGDMVRSTSL----NPINSIFSAELIAIFLCLEAILESPSDQFLIVS 89 (211)
Q Consensus 39 ~~~G~ai~~~~~~~~~~l----~~~~si~~AEl~AI~~AL~~~~~~~~~~i~I~S 89 (211)
..+|+.+|..+....... ......--||..||..|.+..........++|+
T Consensus 33 ~pvGAVIV~~g~IIa~g~N~~~~~~d~~~HAEi~Ai~~a~~~~~~~~l~g~tlY~ 87 (172)
T PRK10860 33 VPVGAVLVHNNRVIGEGWNRPIGRHDPTAHAEIMALRQGGLVLQNYRLLDATLYV 87 (172)
T ss_pred CCEEEEEEeCCEEEEEeeCCCCCCCCCccCHHHHHHHHHHHhcCCCCcCCcEEEe
Confidence 368888886554433322 111223459999999998765433333445553
No 22
>PF13696 zf-CCHC_2: Zinc knuckle
Probab=46.91 E-value=10 Score=22.11 Aligned_cols=18 Identities=33% Similarity=0.940 Sum_probs=13.5
Q ss_pred CCCCcc-CCCccccceec-cccC
Q psy3161 154 DPPICQ-CGAPLSVRHLL-SCPR 174 (211)
Q Consensus 154 ~~p~C~-Cg~~~t~~Hil-~C~~ 174 (211)
+.-.|- |+... |++ +||.
T Consensus 7 ~~Y~C~~C~~~G---H~i~dCP~ 26 (32)
T PF13696_consen 7 PGYVCHRCGQKG---HWIQDCPT 26 (32)
T ss_pred CCCEeecCCCCC---ccHhHCCC
Confidence 344687 88654 999 9998
No 23
>PRK06848 hypothetical protein; Validated
Probab=45.64 E-value=88 Score=24.29 Aligned_cols=57 Identities=18% Similarity=0.078 Sum_probs=32.9
Q ss_pred EecCCCCCCceeEEEEeCCeeeeeecC----CCCchhHHHHHHHHHHHHHHHcCCCCcEEEEeCc
Q psy3161 31 YTDGSKSPDATGCAFSIGDMVRSTSLN----PINSIFSAELIAIFLCLEAILESPSDQFLIVSDS 91 (211)
Q Consensus 31 yTDgS~~~~~~G~ai~~~~~~~~~~l~----~~~si~~AEl~AI~~AL~~~~~~~~~~i~I~SDS 91 (211)
|.. | ...+|+++...+-....+.. .+..--.||..||..|+..-.+ ....+.+.+++
T Consensus 22 y~p-s--~f~VgAa~l~~~G~i~~G~NvEnas~~~tiCAEr~Ai~~av~~g~~-~i~~i~~v~~~ 82 (139)
T PRK06848 22 YRN-D--WHHVGAALRTKTGRIYAAVHLEAYVGRITVCAEAIAIGKAISEGDH-EIDTIVAVRHP 82 (139)
T ss_pred cCC-C--CCcEEEEEEeCCCCEEEEEEeecCCCCcccCHHHHHHHHHHHcCCC-ceEEEEEEecC
Confidence 554 4 36799998864433222221 2333447999999999865221 23455556544
No 24
>PRK08298 cytidine deaminase; Validated
Probab=39.42 E-value=1.4e+02 Score=23.15 Aligned_cols=56 Identities=16% Similarity=0.146 Sum_probs=33.9
Q ss_pred EecCCCCCCceeEEEEeCCeeeeeecC----CCCchhHHHHHHHHHHHHHHHcCCCCcEEEEeCc
Q psy3161 31 YTDGSKSPDATGCAFSIGDMVRSTSLN----PINSIFSAELIAIFLCLEAILESPSDQFLIVSDS 91 (211)
Q Consensus 31 yTDgS~~~~~~G~ai~~~~~~~~~~l~----~~~si~~AEl~AI~~AL~~~~~~~~~~i~I~SDS 91 (211)
|...| ++|+|+...+-..-.+.. ....-..||..||..|+..-.+ ....+.|.+|.
T Consensus 19 Y~PYS----~VgAAllt~dG~i~tG~NvEnas~~~t~CAEr~Ai~~av~~G~~-~~~~i~v~~~~ 78 (136)
T PRK08298 19 YPNGW----GGAAAMRVEDGTILTSVAPEVINASTELCMETGAICEAHKLQKR-VTHSICVAREN 78 (136)
T ss_pred cCCCC----ceeEEEEeCCCCEEEEEeecCCCCCcchhHHHHHHHHHHHCCCc-eEEEEEEEcCC
Confidence 65555 899998864432222221 2334568999999999865221 24556677776
No 25
>TIGR01354 cyt_deam_tetra cytidine deaminase, homotetrameric. This small, homotetrameric zinc metalloprotein is found in humans and most bacteria. A related, homodimeric form with a much larger subunit is found in E. coli and in Arabidopsis. Both types may act on deoxycytidine as well as cytidine.
Probab=38.31 E-value=64 Score=24.44 Aligned_cols=51 Identities=16% Similarity=0.106 Sum_probs=30.3
Q ss_pred ceeEEEEeCC--eeeeeec--CCCCchhHHHHHHHHHHHHHHHcCCCCcEEEEeCc
Q psy3161 40 ATGCAFSIGD--MVRSTSL--NPINSIFSAELIAIFLCLEAILESPSDQFLIVSDS 91 (211)
Q Consensus 40 ~~G~ai~~~~--~~~~~~l--~~~~si~~AEl~AI~~AL~~~~~~~~~~i~I~SDS 91 (211)
.+|++++..+ .....-. ........||..||..|...-.+ ....+.+..++
T Consensus 22 ~vgAa~~~~~G~i~~G~n~e~~~~~~s~~AE~~Ai~~a~~~g~~-~i~~i~vv~~~ 76 (127)
T TIGR01354 22 KVGAALLTKDGRIFTGVNVENASYPLTICAERSAIGKAISAGYR-KFVAIAVADSA 76 (127)
T ss_pred eEEEEEEeCCCCEEEEEeecccCCCCCcCHHHHHHHHHHHcCCC-CeEEEEEEeCC
Confidence 5788877543 2222211 12333446999999999876332 35677777765
No 26
>PRK05578 cytidine deaminase; Validated
Probab=37.57 E-value=1.4e+02 Score=22.84 Aligned_cols=72 Identities=19% Similarity=0.136 Sum_probs=40.4
Q ss_pred HHHHHHHHHHHhhcCCceEEEecCCCCCCceeEEEEeCC--eeeeeecC--CCCchhHHHHHHHHHHHHHHHcCCCCcEE
Q psy3161 11 VFQQKFSEVINTKYANHTICYTDGSKSPDATGCAFSIGD--MVRSTSLN--PINSIFSAELIAIFLCLEAILESPSDQFL 86 (211)
Q Consensus 11 ~~~~~~~~~~~~~~~~~~~IyTDgS~~~~~~G~ai~~~~--~~~~~~l~--~~~si~~AEl~AI~~AL~~~~~~~~~~i~ 86 (211)
.+.+...+.+++.|.. .|+. .+|+++...+ .....-.. ...--..||..||..|+..-. .....+.
T Consensus 5 ~L~~~a~~~~~~ay~P-------yS~f--~Vgaa~~~~~G~i~~G~nvEna~~~~~~CAE~~Ai~~av~~G~-~~i~~i~ 74 (131)
T PRK05578 5 ELIEAAIEASEKAYAP-------YSKF--PVGAALLTDDGRIYTGCNIENASYGLTNCAERTAIFKAISEGG-GRLVAIA 74 (131)
T ss_pred HHHHHHHHHHHhcCCC-------cCCC--ceEEEEEeCCCCEEEEEEeeCccccCCcCHHHHHHHHHHHcCC-CceEEEE
Confidence 3445555555653433 3333 5888887643 22222221 222345699999999985432 1356778
Q ss_pred EEeCcH
Q psy3161 87 IVSDSR 92 (211)
Q Consensus 87 I~SDS~ 92 (211)
|.+|+.
T Consensus 75 vv~~~~ 80 (131)
T PRK05578 75 CVGETG 80 (131)
T ss_pred EEecCC
Confidence 887763
No 27
>PRK12411 cytidine deaminase; Provisional
Probab=37.33 E-value=1.3e+02 Score=23.13 Aligned_cols=71 Identities=21% Similarity=0.074 Sum_probs=37.9
Q ss_pred HHHHHHHHHHHhhcCCceEEEecCCCCCCceeEEEEeCCeeeeeecC----CCCchhHHHHHHHHHHHHHHHcCCCCcEE
Q psy3161 11 VFQQKFSEVINTKYANHTICYTDGSKSPDATGCAFSIGDMVRSTSLN----PINSIFSAELIAIFLCLEAILESPSDQFL 86 (211)
Q Consensus 11 ~~~~~~~~~~~~~~~~~~~IyTDgS~~~~~~G~ai~~~~~~~~~~l~----~~~si~~AEl~AI~~AL~~~~~~~~~~i~ 86 (211)
.+.....+.+++.|.. =| .-.+|+++...+-....+.. ...-.-.||..||..|+..-. .....+.
T Consensus 5 ~L~~~a~~~~~~ay~p-------yS--~~~VgAa~~t~~G~i~~G~nvEn~s~~~s~CAE~~Ai~~av~~g~-~~i~~i~ 74 (132)
T PRK12411 5 QLIQEAIEARKQAYVP-------YS--KFQVGAALLTQDGKVYRGCNVENASYGLCNCAERTALFKAVSEGD-KEFVAIA 74 (132)
T ss_pred HHHHHHHHHHHhcCCC-------cc--CCceEEEEEeCCCCEEEEEEeecCCCCcCcCHHHHHHHHHHHCCC-CceEEEE
Confidence 4455555666653322 22 23477777654322222221 122234799999999975422 1356677
Q ss_pred EEeCc
Q psy3161 87 IVSDS 91 (211)
Q Consensus 87 I~SDS 91 (211)
|.+|.
T Consensus 75 v~~~~ 79 (132)
T PRK12411 75 IVADT 79 (132)
T ss_pred EEeCC
Confidence 77765
No 28
>COG0590 CumB Cytosine/adenosine deaminases [Nucleotide transport and metabolism / Translation, ribosomal structure and biogenesis]
Probab=35.66 E-value=1.3e+02 Score=23.57 Aligned_cols=51 Identities=12% Similarity=0.049 Sum_probs=30.7
Q ss_pred CCceeEEEEe-CCeeeeee----cCCCCchhHHHHHHHHHHHHHHHcCCCCcEEEE
Q psy3161 38 PDATGCAFSI-GDMVRSTS----LNPINSIFSAELIAIFLCLEAILESPSDQFLIV 88 (211)
Q Consensus 38 ~~~~G~ai~~-~~~~~~~~----l~~~~si~~AEl~AI~~AL~~~~~~~~~~i~I~ 88 (211)
+.++|+.+|. .+...... .....-.--||..||..|-+.+....-...++|
T Consensus 27 e~PvGaviV~~~~~ii~~~~N~~~~~~dptaHAEi~air~a~~~~~~~~l~~~tly 82 (152)
T COG0590 27 EVPVGAVIVDADGEIIARGHNRREEDNDPTAHAEILAIRAAAETLGNYRLKDCTLY 82 (152)
T ss_pred CCCEEEEEEcCCCCEEEEecCccccCCCccccHHHHHHHHHHHhhCCCCcCCcEEE
Confidence 4468888887 33222221 122233336999999999998876444444444
No 29
>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=31.89 E-value=1.8e+02 Score=20.32 Aligned_cols=51 Identities=18% Similarity=0.043 Sum_probs=30.0
Q ss_pred CCceeEEEEe-CCeeeeeecC----CCCchhHHHHHHHHHHHHHHHcCCCCcEEEEe
Q psy3161 38 PDATGCAFSI-GDMVRSTSLN----PINSIFSAELIAIFLCLEAILESPSDQFLIVS 89 (211)
Q Consensus 38 ~~~~G~ai~~-~~~~~~~~l~----~~~si~~AEl~AI~~AL~~~~~~~~~~i~I~S 89 (211)
...+|+.++. .+........ .....--||..||..+-+. ........++|+
T Consensus 23 ~~~vgaviv~~~~~~i~~g~n~~~~~~~~~~HAE~~Ai~~~~~~-~~~~~~~~~lyv 78 (102)
T PF00383_consen 23 NFPVGAVIVDPDGKIIATGYNGEPPGKNPTIHAEMNAIRKAARN-GGSSLKGCTLYV 78 (102)
T ss_dssp SSSEEEEEEETTTEEEEEEESBHHSTTGGTB-HHHHHHHHHHHT-TSSGETTEEEEE
T ss_pred CCCEEEEEEeccCccEEEEeeeeeeeccccccchhhhhhhhhhh-ccccccCccccc
Confidence 4468999998 4444444332 2223346999999998887 222234466665
No 30
>KOG0481|consensus
Probab=28.27 E-value=3e+02 Score=26.76 Aligned_cols=31 Identities=16% Similarity=0.248 Sum_probs=26.1
Q ss_pred CChHHHHHHHHHHHHhhcCCceEEEecCCCCCC
Q psy3161 7 IAPVVFQQKFSEVINTKYANHTICYTDGSKSPD 39 (211)
Q Consensus 7 ~~~~~~~~~~~~~~~~~~~~~~~IyTDgS~~~~ 39 (211)
.+|.+.++.|+.+.+. -.-+.|||.|-++.-
T Consensus 371 GDPgtAKSQlLKFvEk--vsPIaVYTSGKGSSA 401 (729)
T KOG0481|consen 371 GDPGTAKSQLLKFVEK--VSPIAVYTSGKGSSA 401 (729)
T ss_pred cCCchhHHHHHHHHHh--cCceEEEecCCCccc
Confidence 4799999999999999 677999999866543
No 31
>COG0117 RibD Pyrimidine deaminase [Coenzyme metabolism]
Probab=25.58 E-value=1.5e+02 Score=23.34 Aligned_cols=37 Identities=19% Similarity=0.284 Sum_probs=24.4
Q ss_pred CCC-ceeEEEEeCCeeeeeecCCCCchhHHHHHHHHHH
Q psy3161 37 SPD-ATGCAFSIGDMVRSTSLNPINSIFSAELIAIFLC 73 (211)
Q Consensus 37 ~~~-~~G~ai~~~~~~~~~~l~~~~si~~AEl~AI~~A 73 (211)
.+| .+|+-|+.++...........-.--||..|+.+|
T Consensus 25 ~pNP~VG~VIV~~~~Ivg~G~h~~aG~pHAEv~Al~~a 62 (146)
T COG0117 25 SPNPSVGCVIVKDGEIVGEGYHEKAGGPHAEVCALRMA 62 (146)
T ss_pred CCCCceeEEEEECCEEEeeeecCCCCCCcHHHHHHHHc
Confidence 455 5999999887654444322233334999999888
No 32
>TIGR02571 ComEB ComE operon protein 2. This protein is found in the ComE operon for "late competence" as characterized in B. subtilis. Proteins in this family contain homology to a cytidine/deoxycytidine deaminase domain family (pfam00383), and may carry out this activity.
Probab=24.33 E-value=3.3e+02 Score=21.35 Aligned_cols=13 Identities=31% Similarity=0.613 Sum_probs=10.5
Q ss_pred hHHHHHHHHHHHH
Q psy3161 63 FSAELIAIFLCLE 75 (211)
Q Consensus 63 ~~AEl~AI~~AL~ 75 (211)
--||..||..|..
T Consensus 68 ~HAE~nAI~~a~~ 80 (151)
T TIGR02571 68 IHAEMNALLQCAK 80 (151)
T ss_pred cCHHHHHHHHHHh
Confidence 3599999998864
No 33
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=22.14 E-value=72 Score=24.05 Aligned_cols=49 Identities=20% Similarity=0.283 Sum_probs=30.9
Q ss_pred cc-CCCccccceec--cccCchHhhhhcCCCCCCCCChhhHHHHHHHHHHhccc
Q psy3161 158 CQ-CGAPLSVRHLL--SCPRHGHIRASLRPPPSLGDDEEGVNSLFSYLQKLNIY 208 (211)
Q Consensus 158 C~-Cg~~~t~~Hil--~C~~~~~~R~~~~~~~~l~l~~~~~~~i~~fl~~t~l~ 208 (211)
|+ ||....|..+- .|..--.-+ +..+.-..|+++...=+..|++..|=+
T Consensus 1 CPvCg~~l~vt~l~C~~C~t~i~G~--F~l~~~~~L~~E~~~Fi~~Fi~~rGnl 52 (113)
T PF09862_consen 1 CPVCGGELVVTRLKCPSCGTEIEGE--FELPWFARLSPEQLEFIKLFIKNRGNL 52 (113)
T ss_pred CCCCCCceEEEEEEcCCCCCEEEee--eccchhhcCCHHHHHHHHHHHHhcCCH
Confidence 88 99988888776 665543222 222222237777777777787776644
No 34
>PF13917 zf-CCHC_3: Zinc knuckle
Probab=21.78 E-value=61 Score=20.02 Aligned_cols=18 Identities=39% Similarity=0.901 Sum_probs=14.4
Q ss_pred CCCCcc-CCCccccceec-cccC
Q psy3161 154 DPPICQ-CGAPLSVRHLL-SCPR 174 (211)
Q Consensus 154 ~~p~C~-Cg~~~t~~Hil-~C~~ 174 (211)
....|. |+.. .|+- +||.
T Consensus 3 ~~~~CqkC~~~---GH~tyeC~~ 22 (42)
T PF13917_consen 3 ARVRCQKCGQK---GHWTYECPN 22 (42)
T ss_pred CCCcCcccCCC---CcchhhCCC
Confidence 356799 9855 6999 9997
No 35
>TIGR00326 eubact_ribD riboflavin biosynthesis protein RibD. This model describes the ribD protein as found in Escherichia coli. The N-terminal domain includes the conserved zinc-binding site region captured in the model dCMP_cyt_deam and shared by proteins such as cytosine deaminase, mammalian apolipoprotein B mRNA editing protein, blasticidin-S deaminase, and Bacillus subtilis competence protein comEB. The C-terminal domain is homologous to the full length of yeast HTP reductase, a protein required for riboflavin biosynthesis. A number of archaeal proteins believed related to riboflavin biosynthesis contain only this C-terminal domain and are not found as full-length matches to this model.
Probab=21.29 E-value=1.7e+02 Score=25.85 Aligned_cols=37 Identities=16% Similarity=0.108 Sum_probs=24.0
Q ss_pred ceeEEEEeCCeeeeeecCCCCchhHHHHHHHHHHHHH
Q psy3161 40 ATGCAFSIGDMVRSTSLNPINSIFSAELIAIFLCLEA 76 (211)
Q Consensus 40 ~~G~ai~~~~~~~~~~l~~~~si~~AEl~AI~~AL~~ 76 (211)
.+|+.++..+.............--||..||..|.+.
T Consensus 20 ~vGaviv~~~~ii~~g~n~~~~~~HAE~~ai~~a~~~ 56 (344)
T TIGR00326 20 LVGCVIVKNGEIVGEGAHQKAGEPHAEVHALRQAGEN 56 (344)
T ss_pred CEEEEEEeCCEEEEEeeCCCCCCCCHHHHHHHHhccc
Confidence 5888888755544443332233446999999998764
Done!