Query psy2212
Match_columns 267
No_of_seqs 198 out of 1574
Neff 8.1
Searched_HMMs 46136
Date Fri Aug 16 19:04:35 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy2212.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/2212hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0328 RnhA Ribonuclease HI [ 99.8 4E-21 8.6E-26 153.5 8.7 114 2-115 19-145 (154)
2 PRK06548 ribonuclease H; Provi 99.8 4.2E-20 9.2E-25 149.9 11.2 112 2-115 19-142 (161)
3 PRK08719 ribonuclease H; Revie 99.8 8.6E-20 1.9E-24 146.6 12.2 106 4-114 25-146 (147)
4 PF00075 RNase_H: RNase H; In 99.8 4.9E-20 1.1E-24 144.9 7.5 102 3-113 20-131 (132)
5 PRK00203 rnhA ribonuclease H; 99.8 1.1E-18 2.4E-23 140.9 10.7 109 4-115 21-142 (150)
6 cd06222 RnaseH RNase H (RNase 99.7 8E-16 1.7E-20 118.0 13.8 111 3-113 16-130 (130)
7 PRK13907 rnhA ribonuclease H; 99.6 2E-15 4.3E-20 118.5 10.6 108 3-114 18-126 (128)
8 KOG3752|consensus 99.6 3.3E-15 7.1E-20 133.2 9.3 113 3-115 230-365 (371)
9 PRK07708 hypothetical protein; 99.4 1E-12 2.2E-17 112.1 11.9 111 3-117 90-210 (219)
10 PF13456 RVT_3: Reverse transc 99.4 1.3E-12 2.9E-17 94.8 7.4 85 25-113 1-85 (87)
11 PRK07238 bifunctional RNase H/ 99.3 2E-11 4.4E-16 112.5 12.1 108 3-115 19-132 (372)
12 PF13966 zf-RVT: zinc-binding 96.1 0.0031 6.7E-08 45.7 1.6 42 177-218 36-83 (86)
13 cd01285 nucleoside_deaminase N 82.1 7 0.00015 29.3 6.7 54 2-55 17-75 (109)
14 PRK10860 tRNA-specific adenosi 80.4 6.5 0.00014 32.3 6.4 50 3-52 34-87 (172)
15 cd01284 Riboflavin_deaminase-r 78.2 9.4 0.0002 29.1 6.3 47 2-52 19-66 (115)
16 cd01286 deoxycytidylate_deamin 72.9 15 0.00033 28.6 6.4 49 2-52 20-93 (131)
17 COG0295 Cdd Cytidine deaminase 71.5 13 0.00027 29.4 5.5 51 3-54 27-81 (134)
18 COG0590 CumB Cytosine/adenosin 70.5 13 0.00029 29.8 5.7 50 3-52 29-83 (152)
19 TIGR01354 cyt_deam_tetra cytid 63.0 20 0.00044 27.7 5.2 52 2-54 21-76 (127)
20 PF00383 dCMP_cyt_deam_1: Cyti 62.4 29 0.00062 25.1 5.8 50 2-52 24-78 (102)
21 COG0117 RibD Pyrimidine deamin 58.7 20 0.00043 28.6 4.4 39 2-40 28-66 (146)
22 COG0296 GlgB 1,4-alpha-glucan 58.6 13 0.00028 36.8 4.2 35 72-106 214-248 (628)
23 PRK06848 hypothetical protein; 52.6 36 0.00079 26.9 5.1 52 2-54 27-82 (139)
24 TIGR02571 ComEB ComE operon pr 52.5 52 0.0011 26.3 6.1 37 2-38 25-80 (151)
25 PF08513 LisH: LisH; InterPro 51.3 12 0.00026 20.7 1.5 23 238-260 5-27 (27)
26 KOG1812|consensus 50.6 36 0.00077 31.7 5.5 43 23-65 47-89 (384)
27 PRK12411 cytidine deaminase; P 48.1 42 0.00091 26.3 4.8 52 2-54 24-79 (132)
28 PF13821 DUF4187: Domain of un 47.3 8 0.00017 25.5 0.5 21 197-217 27-50 (55)
29 TIGR00326 eubact_ribD riboflav 47.1 38 0.00082 30.9 5.1 38 3-40 20-57 (344)
30 KOG1994|consensus 45.3 7.8 0.00017 33.1 0.3 23 195-217 237-262 (268)
31 PRK08298 cytidine deaminase; V 44.5 63 0.0014 25.4 5.3 51 3-54 24-78 (136)
32 COG3341 Predicted double-stran 44.1 19 0.00041 30.6 2.4 89 22-115 105-201 (225)
33 PRK05578 cytidine deaminase; V 43.7 65 0.0014 25.1 5.3 52 2-54 24-79 (131)
34 PF13696 zf-CCHC_2: Zinc knuck 42.6 14 0.00031 21.5 1.0 18 196-216 7-26 (32)
35 PHA02588 cd deoxycytidylate de 42.4 89 0.0019 25.5 6.1 18 3-20 23-40 (168)
36 PF00336 DNA_pol_viral_C: DNA 39.3 36 0.00077 28.9 3.2 44 10-58 110-153 (245)
37 PF05741 zf-nanos: Nanos RNA b 37.0 15 0.00031 24.3 0.5 19 198-216 34-54 (55)
38 cd00786 cytidine_deaminase-lik 36.9 1E+02 0.0022 22.2 5.2 47 3-52 19-71 (96)
39 smart00667 LisH Lissencephaly 35.4 39 0.00086 18.6 2.2 28 236-263 6-33 (34)
40 PRK10786 ribD bifunctional dia 32.9 73 0.0016 29.4 4.6 38 3-40 26-63 (367)
41 smart00642 Aamy Alpha-amylase 32.7 1.5E+02 0.0033 23.9 6.0 72 28-99 16-97 (166)
42 PLN02807 diaminohydroxyphospho 31.9 85 0.0018 29.2 4.9 38 3-40 55-92 (380)
43 cd01283 cytidine_deaminase Cyt 27.9 1.7E+02 0.0036 21.7 5.2 40 2-41 18-61 (112)
44 PF06839 zf-GRF: GRF zinc fing 26.2 36 0.00078 21.1 1.0 14 206-219 19-33 (45)
45 PF04863 EGF_alliinase: Alliin 25.1 15 0.00033 24.1 -0.9 23 181-204 20-42 (56)
46 PRK10933 trehalose-6-phosphate 23.3 1.8E+02 0.0039 28.4 5.7 73 27-99 29-108 (551)
47 PRK03681 hypA hydrogenase nick 22.9 37 0.0008 25.8 0.7 26 196-221 69-97 (114)
48 COG3364 Zn-ribbon containing p 22.5 39 0.00085 25.2 0.7 24 198-221 3-30 (112)
49 COG2131 ComEB Deoxycytidylate 21.4 3.3E+02 0.0072 22.2 5.9 62 2-63 28-117 (164)
50 PF09345 DUF1987: Domain of un 21.3 1.2E+02 0.0025 22.6 3.0 26 69-94 60-85 (99)
51 PF14293 YWFCY: YWFCY protein 21.0 68 0.0015 21.6 1.5 26 231-256 3-28 (61)
52 TIGR02403 trehalose_treC alpha 20.4 2.3E+02 0.0049 27.7 5.7 74 27-100 23-103 (543)
No 1
>COG0328 RnhA Ribonuclease HI [DNA replication, recombination, and repair]
Probab=99.84 E-value=4e-21 Score=153.54 Aligned_cols=114 Identities=19% Similarity=0.171 Sum_probs=92.0
Q ss_pred CceEEEEEeCCceEEEecC-CCCChhHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHHHHhcCCCCC-----------Ch
Q psy2212 2 NTSCAYIIDKTSIYSFVLN-NVNSVFTSELIAVLLCLKHLKFLPKEKFVIISDSKSTLLALSNPSNI-----------NP 69 (267)
Q Consensus 2 ~~~g~ai~~~~~~~~~~l~-~~~t~~~AEl~Ai~~AL~~~~~~~~~~i~I~sDS~~ai~~l~~~~~~-----------~~ 69 (267)
+..|+++..++..+.++.+ ..+||++||+.|++.||+++...+...|.|+|||++|+++|+.|... .|
T Consensus 19 gG~g~vl~~~~~~~~~s~~~~~tTNNraEl~A~i~AL~~l~~~~~~~v~l~tDS~yv~~~i~~w~~~w~~~~w~~~~~~p 98 (154)
T COG0328 19 GGWGAVLRYGDGEKELSGGEGRTTNNRAELRALIEALEALKELGACEVTLYTDSKYVVEGITRWIVKWKKNGWKTADKKP 98 (154)
T ss_pred ceEEEEEEcCCceEEEeeeeecccChHHHHHHHHHHHHHHHhcCCceEEEEecHHHHHHHHHHHHhhccccCccccccCc
Confidence 3567777756554433332 38999999999999999999988889999999999999999944222 12
Q ss_pred H-HHHHHHhHHHHHhcCCeEEEEEecCCCCCchhhHHhHHhcCCCCC
Q psy2212 70 I-VSLIHSCWSDLLCCGKQLAFLWCPSHTGIQGNEAVDRAARNPSAS 115 (267)
Q Consensus 70 ~-~~~i~~~~~~l~~~~~~v~~~WvpgH~g~~gNe~AD~lAk~a~~~ 115 (267)
+ -.+++..+.++......|.+.|||||+|.++||.||+||+.|+..
T Consensus 99 vkn~dl~~~~~~~~~~~~~v~~~WVkgH~g~~~NeraD~LA~~~~~~ 145 (154)
T COG0328 99 VKNKDLWEELDELLKRHELVFWEWVKGHAGHPENERADQLAREAARA 145 (154)
T ss_pred cccHHHHHHHHHHHhhCCeEEEEEeeCCCCChHHHHHHHHHHHHHHh
Confidence 2 256777788787787899999999999999999999999999875
No 2
>PRK06548 ribonuclease H; Provisional
Probab=99.83 E-value=4.2e-20 Score=149.88 Aligned_cols=112 Identities=22% Similarity=0.226 Sum_probs=83.5
Q ss_pred CceEEEEEeCCceEEEecCCCCChhHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHHHHhcC---------CCCC--ChH
Q psy2212 2 NTSCAYIIDKTSIYSFVLNNVNSVFTSELIAVLLCLKHLKFLPKEKFVIISDSKSTLLALSN---------PSNI--NPI 70 (267)
Q Consensus 2 ~~~g~ai~~~~~~~~~~l~~~~t~~~AEl~Ai~~AL~~~~~~~~~~i~I~sDS~~ai~~l~~---------~~~~--~~~ 70 (267)
+.+|.+++..+..........+||+.|||.||+.||+.+.. +...+.|+|||++|+++|+. |... .|+
T Consensus 19 g~~G~g~~~~~~~~~~g~~~~~TNnraEl~Aii~aL~~~~~-~~~~v~I~TDS~yvi~~i~~W~~~Wk~~gWk~s~G~pV 97 (161)
T PRK06548 19 GPSGWAWYVDENTWDSGGWDIATNNIAELTAVRELLIATRH-TDRPILILSDSKYVINSLTKWVYSWKMRKWRKADGKPV 97 (161)
T ss_pred CceEEEEEEeCCcEEccCCCCCCHHHHHHHHHHHHHHhhhc-CCceEEEEeChHHHHHHHHHHHHHHHHCCCcccCCCcc
Confidence 35566655443222222224689999999999999986643 44579999999999999993 3222 355
Q ss_pred H-HHHHHhHHHHHhcCCeEEEEEecCCCCCchhhHHhHHhcCCCCC
Q psy2212 71 V-SLIHSCWSDLLCCGKQLAFLWCPSHTGIQGNEAVDRAARNPSAS 115 (267)
Q Consensus 71 ~-~~i~~~~~~l~~~~~~v~~~WvpgH~g~~gNe~AD~lAk~a~~~ 115 (267)
. +++++.+..+... ..|.|.|||||+|++|||.||+||++|+..
T Consensus 98 ~N~dL~~~l~~l~~~-~~v~~~wVkgHsg~~gNe~aD~LA~~aa~~ 142 (161)
T PRK06548 98 LNQEIIQEIDSLMEN-RNIRMSWVNAHTGHPLNEAADSLARQAANN 142 (161)
T ss_pred ccHHHHHHHHHHHhc-CceEEEEEecCCCCHHHHHHHHHHHHHHHH
Confidence 4 6677777777554 479999999999999999999999998865
No 3
>PRK08719 ribonuclease H; Reviewed
Probab=99.82 E-value=8.6e-20 Score=146.59 Aligned_cols=106 Identities=23% Similarity=0.211 Sum_probs=79.6
Q ss_pred eEEEEEeCCc----eEEEecCCCCChhHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHHHHhc--------CCCCC---C
Q psy2212 4 SCAYIIDKTS----IYSFVLNNVNSVFTSELIAVLLCLKHLKFLPKEKFVIISDSKSTLLALS--------NPSNI---N 68 (267)
Q Consensus 4 ~g~ai~~~~~----~~~~~l~~~~t~~~AEl~Ai~~AL~~~~~~~~~~i~I~sDS~~ai~~l~--------~~~~~---~ 68 (267)
.|++|.+++. .....+....||++|||.||+.||+.+... ..|+|||++|+++|+ +.+.. .
T Consensus 25 ~G~vv~~~~~~~~~~~~~~~~~~~Tnn~aEl~A~~~aL~~~~~~----~~i~tDS~yvi~~i~~~~~~W~~~~w~~s~g~ 100 (147)
T PRK08719 25 IGLVVYDEAGEIVDEQSITVNRYTDNAELELLALIEALEYARDG----DVIYSDSDYCVRGFNEWLDTWKQKGWRKSDKK 100 (147)
T ss_pred EEEEEEeCCCCeeEEEEecCCCCccHHHHHHHHHHHHHHHcCCC----CEEEechHHHHHHHHHHHHHHHhCCcccCCCc
Confidence 3555555432 234445566899999999999999998753 379999999999984 33322 1
Q ss_pred hH-HHHHHHhHHHHHhcCCeEEEEEecCCCCCchhhHHhHHhcCCCC
Q psy2212 69 PI-VSLIHSCWSDLLCCGKQLAFLWCPSHTGIQGNEAVDRAARNPSA 114 (267)
Q Consensus 69 ~~-~~~i~~~~~~l~~~~~~v~~~WvpgH~g~~gNe~AD~lAk~a~~ 114 (267)
++ -.++++.+..+.. ...|+|.|||||+|++|||.||+||++|+.
T Consensus 101 ~v~n~dl~~~i~~l~~-~~~i~~~~VkgH~g~~~Ne~aD~lA~~a~~ 146 (147)
T PRK08719 101 PVANRDLWQQVDELRA-RKYVEVEKVTAHSGIEGNEAADMLAQAAAE 146 (147)
T ss_pred ccccHHHHHHHHHHhC-CCcEEEEEecCCCCChhHHHHHHHHHHHhh
Confidence 33 2567777776654 567999999999999999999999999864
No 4
>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=99.81 E-value=4.9e-20 Score=144.90 Aligned_cols=102 Identities=31% Similarity=0.408 Sum_probs=78.3
Q ss_pred ceEEEEEeCCceEEEecCCCCChhHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHHHHhcC-----CCCC---C-hHHHH
Q psy2212 3 TSCAYIIDKTSIYSFVLNNVNSVFTSELIAVLLCLKHLKFLPKEKFVIISDSKSTLLALSN-----PSNI---N-PIVSL 73 (267)
Q Consensus 3 ~~g~ai~~~~~~~~~~l~~~~t~~~AEl~Ai~~AL~~~~~~~~~~i~I~sDS~~ai~~l~~-----~~~~---~-~~~~~ 73 (267)
.+|+ |+..+......++ ..|++.|||.||..||+ +.. ...+.|+|||+++++.+.. .... . ++...
T Consensus 20 ~~g~-v~~~~~~~~~~~~-~~s~~~aEl~Ai~~AL~-~~~--~~~v~I~tDS~~v~~~l~~~~~~~~~~~~~~~~~i~~~ 94 (132)
T PF00075_consen 20 GAGY-VVWGGRNFSFRLG-GQSNNRAELQAIIEALK-ALE--HRKVTIYTDSQYVLNALNKWLHGNGWKKTSNGRPIKNE 94 (132)
T ss_dssp EEEE-EEETTEEEEEEEE-SECHHHHHHHHHHHHHH-THS--TSEEEEEES-HHHHHHHHTHHHHTTSBSCTSSSBHTHH
T ss_pred EEEE-EEECCeEEEeccc-ccchhhhheehHHHHHH-Hhh--cccccccccHHHHHHHHHHhccccccccccccccchhh
Confidence 4555 3454555556666 89999999999999999 443 3899999999999998877 2222 2 45565
Q ss_pred HHHhHHHHHhcCCeEEEEEecCCCCC-chhhHHhHHhcCCC
Q psy2212 74 IHSCWSDLLCCGKQLAFLWCPSHTGI-QGNEAVDRAARNPS 113 (267)
Q Consensus 74 i~~~~~~l~~~~~~v~~~WvpgH~g~-~gNe~AD~lAk~a~ 113 (267)
|++.+ ..+..|.|.|||||+|+ .||+.||+|||+|+
T Consensus 95 i~~~~----~~~~~v~~~~V~~H~~~~~~N~~aD~lAk~a~ 131 (132)
T PF00075_consen 95 IWELL----SRGIKVRFRWVPGHSGVPQGNERADRLAKEAA 131 (132)
T ss_dssp HHHHH----HHSSEEEEEESSSSSSSHHHHHHHHHHHHHHH
T ss_pred eeecc----ccceEEeeeeccCcCCCchhHHHHHHHHHHhc
Confidence 65544 55889999999999999 69999999999874
No 5
>PRK00203 rnhA ribonuclease H; Reviewed
Probab=99.78 E-value=1.1e-18 Score=140.92 Aligned_cols=109 Identities=19% Similarity=0.193 Sum_probs=80.3
Q ss_pred eEEEEEeCCceEEEe-cCCCCChhHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHHHHhcCC---------CCC--ChHH
Q psy2212 4 SCAYIIDKTSIYSFV-LNNVNSVFTSELIAVLLCLKHLKFLPKEKFVIISDSKSTLLALSNP---------SNI--NPIV 71 (267)
Q Consensus 4 ~g~ai~~~~~~~~~~-l~~~~t~~~AEl~Ai~~AL~~~~~~~~~~i~I~sDS~~ai~~l~~~---------~~~--~~~~ 71 (267)
.|+++..++....+. .....||+.|||.|++.||+.+.. ...+.|+|||++++++|..| ... .|+.
T Consensus 21 ~g~v~~~~~~~~~~~~~~~~~TN~~aEL~Ai~~AL~~~~~--~~~v~I~tDS~yvi~~i~~w~~~Wk~~~~~~~~g~~v~ 98 (150)
T PRK00203 21 WGAILRYKGHEKELSGGEALTTNNRMELMAAIEALEALKE--PCEVTLYTDSQYVRQGITEWIHGWKKNGWKTADKKPVK 98 (150)
T ss_pred EEEEEEECCeeEEEecCCCCCcHHHHHHHHHHHHHHHcCC--CCeEEEEECHHHHHHHHHHHHHHHHHcCCcccCCCccc
Confidence 345555555443333 235789999999999999998864 46799999999999999962 111 2332
Q ss_pred -HHHHHhHHHHHhcCCeEEEEEecCCCCCchhhHHhHHhcCCCCC
Q psy2212 72 -SLIHSCWSDLLCCGKQLAFLWCPSHTGIQGNEAVDRAARNPSAS 115 (267)
Q Consensus 72 -~~i~~~~~~l~~~~~~v~~~WvpgH~g~~gNe~AD~lAk~a~~~ 115 (267)
.++++.+..+.. ...|.|.|||||+|++||+.||+||++|...
T Consensus 99 n~dl~~~i~~l~~-~~~v~~~wV~~H~~~~~N~~AD~lA~~a~~~ 142 (150)
T PRK00203 99 NVDLWQRLDAALK-RHQIKWHWVKGHAGHPENERCDELARAGAEE 142 (150)
T ss_pred cHHHHHHHHHHhc-cCceEEEEecCCCCCHHHHHHHHHHHHHHHH
Confidence 345555555533 3689999999999999999999999998875
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=99.69 E-value=8e-16 Score=117.99 Aligned_cols=111 Identities=23% Similarity=0.237 Sum_probs=85.3
Q ss_pred ceEEEEEeCCceEEEe---cCCCCChhHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHHHHhcCCCC-CChHHHHHHHhH
Q psy2212 3 TSCAYIIDKTSIYSFV---LNNVNSVFTSELIAVLLCLKHLKFLPKEKFVIISDSKSTLLALSNPSN-INPIVSLIHSCW 78 (267)
Q Consensus 3 ~~g~ai~~~~~~~~~~---l~~~~t~~~AEl~Ai~~AL~~~~~~~~~~i~I~sDS~~ai~~l~~~~~-~~~~~~~i~~~~ 78 (267)
++|+++.+.+....+. .....+++.+|+.|+..||+.+...+..++.|++||+.++..+++... ..+....+...+
T Consensus 16 g~g~v~~~~~~~~~~~~~~~~~~~s~~~aEl~al~~al~~~~~~~~~~i~i~~Ds~~~~~~~~~~~~~~~~~~~~~~~~i 95 (130)
T cd06222 16 GAGVVLRDPGGEVLLSGGLLGGNTTNNRAELLALIEALELALELGGKKVNIYTDSQYVINALTGWYEGKPVKNVDLWQRL 95 (130)
T ss_pred EEEEEEEeCCCeEEEeccccCCCCcHHHHHHHHHHHHHHHHHhCCCceEEEEECHHHHHHHhhccccCCChhhHHHHHHH
Confidence 3444555554433332 214789999999999999999988889999999999999999998764 223333444444
Q ss_pred HHHHhcCCeEEEEEecCCCCCchhhHHhHHhcCCC
Q psy2212 79 SDLLCCGKQLAFLWCPSHTGIQGNEAVDRAARNPS 113 (267)
Q Consensus 79 ~~l~~~~~~v~~~WvpgH~g~~gNe~AD~lAk~a~ 113 (267)
..+...+..+.|.|||+|+|+.+|+.||.||+.+.
T Consensus 96 ~~~~~~~~~~~i~~v~~h~~~~~n~~ad~la~~~~ 130 (130)
T cd06222 96 LALLKRFHKVRFEWVPGHSGIEGNERADALAKEAA 130 (130)
T ss_pred HHHHhCCCeEEEEEcCCCCCCcchHHHHHHHHhhC
Confidence 44546788999999999999999999999999873
No 7
>PRK13907 rnhA ribonuclease H; Provisional
Probab=99.63 E-value=2e-15 Score=118.54 Aligned_cols=108 Identities=18% Similarity=0.105 Sum_probs=85.7
Q ss_pred ceEEEEEeCCceEEEec-CCCCChhHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHHHHhcCCCCCChHHHHHHHhHHHH
Q psy2212 3 TSCAYIIDKTSIYSFVL-NNVNSVFTSELIAVLLCLKHLKFLPKEKFVIISDSKSTLLALSNPSNINPIVSLIHSCWSDL 81 (267)
Q Consensus 3 ~~g~ai~~~~~~~~~~l-~~~~t~~~AEl~Ai~~AL~~~~~~~~~~i~I~sDS~~ai~~l~~~~~~~~~~~~i~~~~~~l 81 (267)
.+|++|.+.+....... ....||+.||+.|++.||+.+...+..++.|+|||+++++.+++.+...+....++..+..+
T Consensus 18 G~G~vi~~~~~~~~~~~~~~~~tn~~AE~~All~aL~~a~~~g~~~v~i~sDS~~vi~~~~~~~~~~~~~~~l~~~~~~l 97 (128)
T PRK13907 18 GAGVFIKGVQPAVQLSLPLGTMSNHEAEYHALLAALKYCTEHNYNIVSFRTDSQLVERAVEKEYAKNKMFAPLLEEALQY 97 (128)
T ss_pred EEEEEEEECCeeEEEEecccccCCcHHHHHHHHHHHHHHHhCCCCEEEEEechHHHHHHHhHHHhcChhHHHHHHHHHHH
Confidence 34566656555444332 35689999999999999999999888899999999999999998765544456666666667
Q ss_pred HhcCCeEEEEEecCCCCCchhhHHhHHhcCCCC
Q psy2212 82 LCCGKQLAFLWCPSHTGIQGNEAVDRAARNPSA 114 (267)
Q Consensus 82 ~~~~~~v~~~WvpgH~g~~gNe~AD~lAk~a~~ 114 (267)
...+..+.|.|||. +.|+.||.||++|..
T Consensus 98 ~~~f~~~~~~~v~r----~~N~~Ad~LA~~a~~ 126 (128)
T PRK13907 98 IKSFDLFFIKWIPS----SQNKVADELARKAIL 126 (128)
T ss_pred HhcCCceEEEEcCc----hhchhHHHHHHHHHh
Confidence 67788889999997 599999999998864
No 8
>KOG3752|consensus
Probab=99.60 E-value=3.3e-15 Score=133.22 Aligned_cols=113 Identities=24% Similarity=0.136 Sum_probs=88.6
Q ss_pred ceEEEEEeC---CceEEEecC-CCCChhHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHHHHhcCCCCC-----------
Q psy2212 3 TSCAYIIDK---TSIYSFVLN-NVNSVFTSELIAVLLCLKHLKFLPKEKFVIISDSKSTLLALSNPSNI----------- 67 (267)
Q Consensus 3 ~~g~ai~~~---~~~~~~~l~-~~~t~~~AEl~Ai~~AL~~~~~~~~~~i~I~sDS~~ai~~l~~~~~~----------- 67 (267)
++|.+|+=+ +...+.++. +..|||.|||.||..||+.+.+....+++|.|||++++++|+.|...
T Consensus 230 ~AGyGvywg~~~e~N~s~pv~~g~qtNnrAEl~Av~~ALkka~~~~~~kv~I~TDS~~~i~~l~~wv~~~k~~~~k~~~~ 309 (371)
T KOG3752|consen 230 RAGYGVYWGPGHELNVSGPLAGGRQTNNRAELIAAIEALKKARSKNINKVVIRTDSEYFINSLTLWVQGWKKNGWKTSNG 309 (371)
T ss_pred cceeEEeeCCCCcccccccCCCCcccccHHHHHHHHHHHHHHHhcCCCcEEEEechHHHHHHHHHHHhhhccCccccccC
Confidence 578888844 346667766 78999999999999999999988888999999999999999964322
Q ss_pred Ch----HH--HHHHHhHHHHHh--cCCeEEEEEecCCCCCchhhHHhHHhcCCCCC
Q psy2212 68 NP----IV--SLIHSCWSDLLC--CGKQLAFLWCPSHTGIQGNEAVDRAARNPSAS 115 (267)
Q Consensus 68 ~~----~~--~~i~~~~~~l~~--~~~~v~~~WvpgH~g~~gNe~AD~lAk~a~~~ 115 (267)
++ ++ ......+..|.+ .+.+|.+.|||||.|+.||+.||.+|+++...
T Consensus 310 ~~~i~~~v~n~~~~~e~~~l~q~~~~~~vq~~~V~Gh~gi~gne~Ad~lARkgs~~ 365 (371)
T KOG3752|consen 310 SDRICAYVKNQDFFNELDELEQEISNKKVQQEYVGGHSGILGNEMADALARKGSTL 365 (371)
T ss_pred CCccceeeecchHHHHHHHHHhhhccCceEEEEecCcCCcchHHHHHHHHhhhhhh
Confidence 12 11 223333444433 36899999999999999999999999998543
No 9
>PRK07708 hypothetical protein; Validated
Probab=99.45 E-value=1e-12 Score=112.15 Aligned_cols=111 Identities=13% Similarity=0.008 Sum_probs=82.1
Q ss_pred ceEEEEEeCCceEE------EecCCCCChhHHHHHHHHHHHHHhhhCCCCe--EEEEeccHHHHHHhcCCC-CCChHHHH
Q psy2212 3 TSCAYIIDKTSIYS------FVLNNVNSVFTSELIAVLLCLKHLKFLPKEK--FVIISDSKSTLLALSNPS-NINPIVSL 73 (267)
Q Consensus 3 ~~g~ai~~~~~~~~------~~l~~~~t~~~AEl~Ai~~AL~~~~~~~~~~--i~I~sDS~~ai~~l~~~~-~~~~~~~~ 73 (267)
.+|++|++.+.... ..++...||+.||+.|++.||+.+...+.+. |.|++||+.+++.+++.+ ..++....
T Consensus 90 G~GvVI~~~~g~~~~~~~~~~~l~~~~TNN~AEy~Ali~aL~~A~e~g~~~~~V~I~~DSqlVi~qi~g~wk~~~~~l~~ 169 (219)
T PRK07708 90 GLGIVIYYKQGNKRYRIRRNAYIEGIYDNNEAEYAALYYAMQELEELGVKHEPVTFRGDSQVVLNQLAGEWPCYDEHLNH 169 (219)
T ss_pred EEEEEEEECCCCEEEEEEeeccccccccCcHHHHHHHHHHHHHHHHcCCCcceEEEEeccHHHHHHhCCCceeCChhHHH
Confidence 45677776433222 2455568999999999999999999877654 899999999999999865 33455555
Q ss_pred HHHhHHHHHhc-CCeEEEEEecCCCCCchhhHHhHHhcCCCCCCC
Q psy2212 74 IHSCWSDLLCC-GKQLAFLWCPSHTGIQGNEAVDRAARNPSASLP 117 (267)
Q Consensus 74 i~~~~~~l~~~-~~~v~~~WvpgH~g~~gNe~AD~lAk~a~~~~~ 117 (267)
+.+.+..+... ...+.|.||| ...|+.||+||++|....+
T Consensus 170 y~~~i~~l~~~~~l~~~~~~Vp----R~~N~~AD~LAk~Al~~~~ 210 (219)
T PRK07708 170 WLDRIEQKLKQLKLTPVYEPIS----RKQNKEADQLATQALEGTV 210 (219)
T ss_pred HHHHHHHHHhhCCceEEEEECC----chhhhHHHHHHHHHHhcCC
Confidence 55555444333 3457889998 5689999999999998643
No 10
>PF13456 RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EHG_A 3HST_B.
Probab=99.38 E-value=1.3e-12 Score=94.78 Aligned_cols=85 Identities=20% Similarity=0.120 Sum_probs=65.8
Q ss_pred hhHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHHHHhcCCCCCChHHHHHHHhHHHHHhcCCeEEEEEecCCCCCchhhH
Q psy2212 25 VFTSELIAVLLCLKHLKFLPKEKFVIISDSKSTLLALSNPSNINPIVSLIHSCWSDLLCCGKQLAFLWCPSHTGIQGNEA 104 (267)
Q Consensus 25 ~~~AEl~Ai~~AL~~~~~~~~~~i~I~sDS~~ai~~l~~~~~~~~~~~~i~~~~~~l~~~~~~v~~~WvpgH~g~~gNe~ 104 (267)
+..||+.|+..||+++.+.+..++.|.|||+.+++.|++..........+...+..+...+..+.|.||| .++|..
T Consensus 1 ~~~aE~~al~~al~~a~~~g~~~i~v~sDs~~vv~~i~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~i~----r~~N~~ 76 (87)
T PF13456_consen 1 PLEAEALALLEALQLAWELGIRKIIVESDSQLVVDAINGRSSSRSELRPLIQDIRSLLDRFWNVSVSHIP----REQNKV 76 (87)
T ss_dssp HHHHHHHHHHHHHHHHHCCT-SCEEEEES-HHHHHHHTTSS---SCCHHHHHHHHHHHCCCSCEEEEE------GGGSHH
T ss_pred CcHHHHHHHHHHHHHHHHCCCCEEEEEecCccccccccccccccccccccchhhhhhhccccceEEEEEC----hHHhHH
Confidence 4689999999999999999999999999999999999987544223344444455566778999999999 789999
Q ss_pred HhHHhcCCC
Q psy2212 105 VDRAARNPS 113 (267)
Q Consensus 105 AD~lAk~a~ 113 (267)
||.||+.|.
T Consensus 77 A~~LA~~a~ 85 (87)
T PF13456_consen 77 ADALAKFAL 85 (87)
T ss_dssp HHHHHHHHH
T ss_pred HHHHHHHHh
Confidence 999999764
No 11
>PRK07238 bifunctional RNase H/acid phosphatase; Provisional
Probab=99.30 E-value=2e-11 Score=112.50 Aligned_cols=108 Identities=16% Similarity=0.147 Sum_probs=84.7
Q ss_pred ceEEEEEeCC-c-e-EE--EecCCCCChhHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHHHHhcCCCC-CChHHHHHHH
Q psy2212 3 TSCAYIIDKT-S-I-YS--FVLNNVNSVFTSELIAVLLCLKHLKFLPKEKFVIISDSKSTLLALSNPSN-INPIVSLIHS 76 (267)
Q Consensus 3 ~~g~ai~~~~-~-~-~~--~~l~~~~t~~~AEl~Ai~~AL~~~~~~~~~~i~I~sDS~~ai~~l~~~~~-~~~~~~~i~~ 76 (267)
.+|++|.+.+ . . .. ..+ ...||+.||+.|++.||+.+.+.+..++.|++||+++++.+++.+. +++-...+++
T Consensus 19 G~G~vi~~~~~~~~~~~~~~~~-~~~tnn~AE~~All~gL~~a~~~g~~~v~i~~DS~lvi~~i~~~~~~~~~~l~~~~~ 97 (372)
T PRK07238 19 GYGAVVWDADRGEVLAERAEAI-GRATNNVAEYRGLIAGLEAAAELGATEVEVRMDSKLVVEQMSGRWKVKHPDMKPLAA 97 (372)
T ss_pred EEEEEEEeCCCCcEEEEeeccc-CCCCchHHHHHHHHHHHHHHHhCCCCeEEEEeCcHHHHHHhCCCCccCChHHHHHHH
Confidence 3455555653 2 1 22 233 3789999999999999999999888999999999999999998653 4454555555
Q ss_pred hHHHHHhcCCeEEEEEecCCCCCchhhHHhHHhcCCCCC
Q psy2212 77 CWSDLLCCGKQLAFLWCPSHTGIQGNEAVDRAARNPSAS 115 (267)
Q Consensus 77 ~~~~l~~~~~~v~~~WvpgH~g~~gNe~AD~lAk~a~~~ 115 (267)
.+..+...+..+.|.|||. .+|+.||.||+.|...
T Consensus 98 ~i~~l~~~f~~~~i~~v~r----~~N~~AD~LA~~a~~~ 132 (372)
T PRK07238 98 QARELASQFGRVTYTWIPR----ARNAHADRLANEAMDA 132 (372)
T ss_pred HHHHHHhcCCceEEEECCc----hhhhHHHHHHHHHHHh
Confidence 6666777888999999996 6999999999998765
No 12
>PF13966 zf-RVT: zinc-binding in reverse transcriptase
Probab=96.07 E-value=0.0031 Score=45.70 Aligned_cols=42 Identities=19% Similarity=0.313 Sum_probs=30.8
Q ss_pred eeeeeccccc--c-cccccCCCCCCCc-ccCC-CCCcchhhc-CcccH
Q psy2212 177 CRMRIGHTRA--T-HGHLFKRAPPSTC-GCGE-ILSVQHILT-CALHG 218 (267)
Q Consensus 177 ~qlrTGH~~~--~-~~~r~~~~~~p~C-~Cg~-~et~~H~l~-Cp~~~ 218 (267)
.--+.-|.++ . -+.+.+...++.| .|+. .||++|+|+ ||...
T Consensus 36 f~W~~~~~rL~t~~~l~~r~~~~~~~C~~C~~~~Et~~Hlf~~C~~a~ 83 (86)
T PF13966_consen 36 FLWRALHNRLPTKDNLQRRGIQVDPICPLCGNEEETIEHLFFHCPFAR 83 (86)
T ss_pred EeeeeccccchhhhhhhccCCccCCccccCCCccccccceeccCcCcc
Confidence 3344555555 2 3456677888999 9997 999999999 99753
No 13
>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=82.12 E-value=7 Score=29.29 Aligned_cols=54 Identities=13% Similarity=0.075 Sum_probs=37.3
Q ss_pred CceEEEEEeC-CceEEEecCC----CCChhHHHHHHHHHHHHHhhhCCCCeEEEEeccH
Q psy2212 2 NTSCAYIIDK-TSIYSFVLNN----VNSVFTSELIAVLLCLKHLKFLPKEKFVIISDSK 55 (267)
Q Consensus 2 ~~~g~ai~~~-~~~~~~~l~~----~~t~~~AEl~Ai~~AL~~~~~~~~~~i~I~sDS~ 55 (267)
..+|++|++. ++........ ......||..||..+.+...........+|+.-+
T Consensus 17 ~~vgaviv~~~~~ii~~g~n~~~~~~~~~~HAE~~ai~~~~~~~~~~~~~~~~ly~t~E 75 (109)
T cd01285 17 VPFGAVIVDDDGKVIARGHNRVEQDGDPTAHAEIVAIRNAARRLGSYLLSGCTLYTTLE 75 (109)
T ss_pred CcEEEEEEeCCCEEEEEEeCCCCCCCCCcccHHHHHHHHHHHHhCCCccCCeEEEEeCC
Confidence 4689999987 5555555442 2356789999999998875443456677777443
No 14
>PRK10860 tRNA-specific adenosine deaminase; Provisional
Probab=80.42 E-value=6.5 Score=32.32 Aligned_cols=50 Identities=10% Similarity=-0.005 Sum_probs=33.6
Q ss_pred ceEEEEEeCCceEEEecCCC----CChhHHHHHHHHHHHHHhhhCCCCeEEEEe
Q psy2212 3 TSCAYIIDKTSIYSFVLNNV----NSVFTSELIAVLLCLKHLKFLPKEKFVIIS 52 (267)
Q Consensus 3 ~~g~ai~~~~~~~~~~l~~~----~t~~~AEl~Ai~~AL~~~~~~~~~~i~I~s 52 (267)
.+|++|++.++.+....... .....||+.||..|.+.+........++|+
T Consensus 34 pvGAVIV~~g~IIa~g~N~~~~~~d~~~HAEi~Ai~~a~~~~~~~~l~g~tlY~ 87 (172)
T PRK10860 34 PVGAVLVHNNRVIGEGWNRPIGRHDPTAHAEIMALRQGGLVLQNYRLLDATLYV 87 (172)
T ss_pred CEEEEEEeCCEEEEEeeCCCCCCCCCccCHHHHHHHHHHHhcCCCCcCCcEEEe
Confidence 68999998777666554321 123579999999998766443344566665
No 15
>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=78.18 E-value=9.4 Score=29.13 Aligned_cols=47 Identities=11% Similarity=-0.043 Sum_probs=33.1
Q ss_pred CceEEEEEeC-CceEEEecCCCCChhHHHHHHHHHHHHHhhhCCCCeEEEEe
Q psy2212 2 NTSCAYIIDK-TSIYSFVLNNVNSVFTSELIAVLLCLKHLKFLPKEKFVIIS 52 (267)
Q Consensus 2 ~~~g~ai~~~-~~~~~~~l~~~~t~~~AEl~Ai~~AL~~~~~~~~~~i~I~s 52 (267)
-.+|++|++. ++..............||..||..|.+. .....++|+
T Consensus 19 ~pvGaviv~~~g~iv~~g~n~~~~~~HAE~~ai~~a~~~----~l~g~tly~ 66 (115)
T cd01284 19 PPVGCVIVDDDGEIVGEGYHRKAGGPHAEVNALASAGEK----LARGATLYV 66 (115)
T ss_pred CCEEEEEEeCCCeEEEEecCCCCCcccHHHHHHHHHhhc----CCCCeEEEE
Confidence 3689999987 5656655554446778999999998875 234556665
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=72.86 E-value=15 Score=28.61 Aligned_cols=49 Identities=20% Similarity=0.138 Sum_probs=32.0
Q ss_pred CceEEEEEeCCceEEEecCCC-------------------------CChhHHHHHHHHHHHHHhhhCCCCeEEEEe
Q psy2212 2 NTSCAYIIDKTSIYSFVLNNV-------------------------NSVFTSELIAVLLCLKHLKFLPKEKFVIIS 52 (267)
Q Consensus 2 ~~~g~ai~~~~~~~~~~l~~~-------------------------~t~~~AEl~Ai~~AL~~~~~~~~~~i~I~s 52 (267)
-.+|++|+++++.+....... .....||..||..|.+. .......++|+
T Consensus 20 ~~VGAViv~~~~iI~~G~N~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~HAE~~Ai~~a~~~--~~~~~~~tLyv 93 (131)
T cd01286 20 RQVGAVIVKDKRIISTGYNGSPSGLPHCAEVGCERDDLPSGEDQKCCRTVHAEQNAILQAARH--GVSLEGATLYV 93 (131)
T ss_pred CCEEEEEEECCEEEEEeeCCCCCCCCCcccccccccccccccccccCCCCCHHHHHHHHHhHc--CCCcCCeEEEE
Confidence 468999998877666543321 23457999999988764 22334566665
No 17
>COG0295 Cdd Cytidine deaminase [Nucleotide transport and metabolism]
Probab=71.47 E-value=13 Score=29.36 Aligned_cols=51 Identities=14% Similarity=0.066 Sum_probs=36.1
Q ss_pred ceEEEEEeCCceEEEecC----CCCChhHHHHHHHHHHHHHhhhCCCCeEEEEecc
Q psy2212 3 TSCAYIIDKTSIYSFVLN----NVNSVFTSELIAVLLCLKHLKFLPKEKFVIISDS 54 (267)
Q Consensus 3 ~~g~ai~~~~~~~~~~l~----~~~t~~~AEl~Ai~~AL~~~~~~~~~~i~I~sDS 54 (267)
++|+++...+..+.++.. ...--..||-.||..|+.. -......+.+++|+
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 689999977654444322 2334457999999999876 33456778999988
No 18
>COG0590 CumB Cytosine/adenosine deaminases [Nucleotide transport and metabolism / Translation, ribosomal structure and biogenesis]
Probab=70.53 E-value=13 Score=29.80 Aligned_cols=50 Identities=16% Similarity=0.129 Sum_probs=32.9
Q ss_pred ceEEEEEe-CCceEEEecCC----CCChhHHHHHHHHHHHHHhhhCCCCeEEEEe
Q psy2212 3 TSCAYIID-KTSIYSFVLNN----VNSVFTSELIAVLLCLKHLKFLPKEKFVIIS 52 (267)
Q Consensus 3 ~~g~ai~~-~~~~~~~~l~~----~~t~~~AEl~Ai~~AL~~~~~~~~~~i~I~s 52 (267)
.+|++|++ .+......-.. .--...||+.||..|.+.+........++|+
T Consensus 29 PvGaviV~~~~~ii~~~~N~~~~~~dptaHAEi~air~a~~~~~~~~l~~~tlyv 83 (152)
T COG0590 29 PVGAVIVDADGEIIARGHNRREEDNDPTAHAEILAIRAAAETLGNYRLKDCTLYV 83 (152)
T ss_pred CEEEEEEcCCCCEEEEecCccccCCCccccHHHHHHHHHHHhhCCCCcCCcEEEE
Confidence 48999999 44444433321 1122479999999999998664455566665
No 19
>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=62.98 E-value=20 Score=27.73 Aligned_cols=52 Identities=10% Similarity=-0.102 Sum_probs=34.1
Q ss_pred CceEEEEEeCCceEEEecCC----CCChhHHHHHHHHHHHHHhhhCCCCeEEEEecc
Q psy2212 2 NTSCAYIIDKTSIYSFVLNN----VNSVFTSELIAVLLCLKHLKFLPKEKFVIISDS 54 (267)
Q Consensus 2 ~~~g~ai~~~~~~~~~~l~~----~~t~~~AEl~Ai~~AL~~~~~~~~~~i~I~sDS 54 (267)
..+|+++...+..+.....- ..-...||..||..|...-.. ....+.|+.++
T Consensus 21 ~~vgAa~~~~~G~i~~G~n~e~~~~~~s~~AE~~Ai~~a~~~g~~-~i~~i~vv~~~ 76 (127)
T TIGR01354 21 FKVGAALLTKDGRIFTGVNVENASYPLTICAERSAIGKAISAGYR-KFVAIAVADSA 76 (127)
T ss_pred CeEEEEEEeCCCCEEEEEeecccCCCCCcCHHHHHHHHHHHcCCC-CeEEEEEEeCC
Confidence 46899999765433333332 223457999999998876332 56778888876
No 20
>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=62.44 E-value=29 Score=25.15 Aligned_cols=50 Identities=16% Similarity=0.083 Sum_probs=32.4
Q ss_pred CceEEEEEe-CCceEEEecCCC----CChhHHHHHHHHHHHHHhhhCCCCeEEEEe
Q psy2212 2 NTSCAYIID-KTSIYSFVLNNV----NSVFTSELIAVLLCLKHLKFLPKEKFVIIS 52 (267)
Q Consensus 2 ~~~g~ai~~-~~~~~~~~l~~~----~t~~~AEl~Ai~~AL~~~~~~~~~~i~I~s 52 (267)
..+|++|++ ++.......... ...-.||..||..+.+. .........+|+
T Consensus 24 ~~vgaviv~~~~~~i~~g~n~~~~~~~~~~HAE~~Ai~~~~~~-~~~~~~~~~lyv 78 (102)
T PF00383_consen 24 FPVGAVIVDPDGKIIATGYNGEPPGKNPTIHAEMNAIRKAARN-GGSSLKGCTLYV 78 (102)
T ss_dssp SSEEEEEEETTTEEEEEEESBHHSTTGGTB-HHHHHHHHHHHT-TSSGETTEEEEE
T ss_pred CCEEEEEEeccCccEEEEeeeeeeeccccccchhhhhhhhhhh-ccccccCccccc
Confidence 468999999 566666665422 22358999999998887 222234566666
No 21
>COG0117 RibD Pyrimidine deaminase [Coenzyme metabolism]
Probab=58.67 E-value=20 Score=28.62 Aligned_cols=39 Identities=10% Similarity=-0.007 Sum_probs=30.9
Q ss_pred CceEEEEEeCCceEEEecCCCCChhHHHHHHHHHHHHHh
Q psy2212 2 NTSCAYIIDKTSIYSFVLNNVNSVFTSELIAVLLCLKHL 40 (267)
Q Consensus 2 ~~~g~ai~~~~~~~~~~l~~~~t~~~AEl~Ai~~AL~~~ 40 (267)
--+|++|+++++..........-.-.||..|+..|=+.+
T Consensus 28 P~VG~VIV~~~~Ivg~G~h~~aG~pHAEv~Al~~ag~~a 66 (146)
T COG0117 28 PSVGCVIVKDGEIVGEGYHEKAGGPHAEVCALRMAGEAA 66 (146)
T ss_pred CceeEEEEECCEEEeeeecCCCCCCcHHHHHHHHcCccc
Confidence 458999999998888777666677789999999884433
No 22
>COG0296 GlgB 1,4-alpha-glucan branching enzyme [Carbohydrate transport and metabolism]
Probab=58.59 E-value=13 Score=36.81 Aligned_cols=35 Identities=17% Similarity=0.211 Sum_probs=28.2
Q ss_pred HHHHHhHHHHHhcCCeEEEEEecCCCCCchhhHHh
Q psy2212 72 SLIHSCWSDLLCCGKQLAFLWCPSHTGIQGNEAVD 106 (267)
Q Consensus 72 ~~i~~~~~~l~~~~~~v~~~WvpgH~g~~gNe~AD 106 (267)
..+...++..-+.|..|-+-|||+|.+..||-++-
T Consensus 214 edfk~fVD~aH~~GIgViLD~V~~HF~~d~~~L~~ 248 (628)
T COG0296 214 EDFKALVDAAHQAGIGVILDWVPNHFPPDGNYLAR 248 (628)
T ss_pred HHHHHHHHHHHHcCCEEEEEecCCcCCCCcchhhh
Confidence 45556666666899999999999999998887663
No 23
>PRK06848 hypothetical protein; Validated
Probab=52.61 E-value=36 Score=26.88 Aligned_cols=52 Identities=13% Similarity=0.034 Sum_probs=33.5
Q ss_pred CceEEEEEeCCceEEEecC----CCCChhHHHHHHHHHHHHHhhhCCCCeEEEEecc
Q psy2212 2 NTSCAYIIDKTSIYSFVLN----NVNSVFTSELIAVLLCLKHLKFLPKEKFVIISDS 54 (267)
Q Consensus 2 ~~~g~ai~~~~~~~~~~l~----~~~t~~~AEl~Ai~~AL~~~~~~~~~~i~I~sDS 54 (267)
.++|+|+...+..+..+.. .......||-.||..|+..-. .....+.+.+++
T Consensus 27 f~VgAa~l~~~G~i~~G~NvEnas~~~tiCAEr~Ai~~av~~g~-~~i~~i~~v~~~ 82 (139)
T PRK06848 27 HHVGAALRTKTGRIYAAVHLEAYVGRITVCAEAIAIGKAISEGD-HEIDTIVAVRHP 82 (139)
T ss_pred CcEEEEEEeCCCCEEEEEEeecCCCCcccCHHHHHHHHHHHcCC-CceEEEEEEecC
Confidence 4699999987665544433 233445899999999886522 234556666654
No 24
>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=52.48 E-value=52 Score=26.35 Aligned_cols=37 Identities=24% Similarity=0.231 Sum_probs=25.9
Q ss_pred CceEEEEEeCCceEEEecCCCC-------------------ChhHHHHHHHHHHHH
Q psy2212 2 NTSCAYIIDKTSIYSFVLNNVN-------------------SVFTSELIAVLLCLK 38 (267)
Q Consensus 2 ~~~g~ai~~~~~~~~~~l~~~~-------------------t~~~AEl~Ai~~AL~ 38 (267)
.++|++|+..++..+.+..... -...||..||..|.+
T Consensus 25 ~~VGAVIV~d~~IIs~GyN~~~~g~~~~~~~~~~~~~~~~~~~~HAE~nAI~~a~~ 80 (151)
T TIGR02571 25 LSVGATIVRDKRIIAGGYNGSVAGGVHCIDEGCYVVDGHCVRTIHAEMNALLQCAK 80 (151)
T ss_pred CCEEEEEEECCEEEEEEECCCCCCCCccccccccccccccCCccCHHHHHHHHHHh
Confidence 4789999987777665543211 235799999998865
No 25
>PF08513 LisH: LisH; InterPro: IPR013720 The LisH motif is found in a large number of eukaryotic proteins, from metazoa, fungi and plants that have a wide range of functions. The recently solved structure of the LisH domain in the N-terminal region of LIS1 depicted it as a novel dimerization motif, and that other structural elements are likely to play an important role in dimerisation [, , ]. The LisH (lis homology) domain mediates protein dimerisation and tetramerisation. The LisH domain is found in Sif2, a component of the Set3 complex which is responsible for repressing meiotic genes. It has been shown that the LisH domain helps mediate interaction with components of the Set3 complex []. ; PDB: 2XTE_L 2XTC_B 2XTD_A 1UUJ_B.
Probab=51.25 E-value=12 Score=20.70 Aligned_cols=23 Identities=22% Similarity=0.382 Sum_probs=19.7
Q ss_pred HHHHHHHHHhcchhhhhhhchhh
Q psy2212 238 DSLLSYLKKLNLRVVAVSFEKDE 260 (267)
Q Consensus 238 ~~i~~f~~~t~~~~~~~~~~~~~ 260 (267)
.-|.+|+...|......+|+||.
T Consensus 5 ~lI~~YL~~~Gy~~tA~~f~~Ea 27 (27)
T PF08513_consen 5 QLIYDYLVENGYKETAKAFAKEA 27 (27)
T ss_dssp HHHHHHHHHCT-HHHHHHHHHHT
T ss_pred HHHHHHHHHCCcHHHHHHHHhcC
Confidence 56899999999999999999974
No 26
>KOG1812|consensus
Probab=50.62 E-value=36 Score=31.74 Aligned_cols=43 Identities=19% Similarity=0.152 Sum_probs=36.1
Q ss_pred CChhHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHHHHhcCCC
Q psy2212 23 NSVFTSELIAVLLCLKHLKFLPKEKFVIISDSKSTLLALSNPS 65 (267)
Q Consensus 23 ~t~~~AEl~Ai~~AL~~~~~~~~~~i~I~sDS~~ai~~l~~~~ 65 (267)
.+...||++|+..+|..+.+.+...+.+++|+......+....
T Consensus 47 ~~~~~ae~~al~~~l~ea~~~~~~~~~~~~d~~~~~~~v~~~~ 89 (384)
T KOG1812|consen 47 ITPLEAELMALKRGLTEALELGLNHIVIYCDDELIYESVAGRE 89 (384)
T ss_pred cchhhHHHHHHhhccHHHHhhccccceEecccHHHHHHHhhhh
Confidence 7789999999999999999999999999999766666444433
No 27
>PRK12411 cytidine deaminase; Provisional
Probab=48.08 E-value=42 Score=26.26 Aligned_cols=52 Identities=12% Similarity=-0.056 Sum_probs=33.7
Q ss_pred CceEEEEEeCCceEEEecCC----CCChhHHHHHHHHHHHHHhhhCCCCeEEEEecc
Q psy2212 2 NTSCAYIIDKTSIYSFVLNN----VNSVFTSELIAVLLCLKHLKFLPKEKFVIISDS 54 (267)
Q Consensus 2 ~~~g~ai~~~~~~~~~~l~~----~~t~~~AEl~Ai~~AL~~~~~~~~~~i~I~sDS 54 (267)
.++|+|+...+..+..+..- ..-...||..||..|+..- ......|.|.+|.
T Consensus 24 ~~VgAa~~t~~G~i~~G~nvEn~s~~~s~CAE~~Ai~~av~~g-~~~i~~i~v~~~~ 79 (132)
T PRK12411 24 FQVGAALLTQDGKVYRGCNVENASYGLCNCAERTALFKAVSEG-DKEFVAIAIVADT 79 (132)
T ss_pred CceEEEEEeCCCCEEEEEEeecCCCCcCcCHHHHHHHHHHHCC-CCceEEEEEEeCC
Confidence 47899999776544444331 2224479999999987542 1245677888765
No 28
>PF13821 DUF4187: Domain of unknown function (DUF4187)
Probab=47.29 E-value=8 Score=25.50 Aligned_cols=21 Identities=19% Similarity=0.406 Sum_probs=16.9
Q ss_pred CCCc-ccCC-CCCcchhhc-Cccc
Q psy2212 197 PSTC-GCGE-ILSVQHILT-CALH 217 (267)
Q Consensus 197 ~p~C-~Cg~-~et~~H~l~-Cp~~ 217 (267)
.-.| +||. .++.+-+.. ||-.
T Consensus 27 ~~YC~~Cg~~Y~d~~dL~~~CPG~ 50 (55)
T PF13821_consen 27 HNYCFWCGTKYDDEEDLERNCPGP 50 (55)
T ss_pred CceeeeeCCccCCHHHHHhCCCCC
Confidence 3568 9998 788888888 9954
No 29
>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=47.07 E-value=38 Score=30.88 Aligned_cols=38 Identities=11% Similarity=-0.052 Sum_probs=28.9
Q ss_pred ceEEEEEeCCceEEEecCCCCChhHHHHHHHHHHHHHh
Q psy2212 3 TSCAYIIDKTSIYSFVLNNVNSVFTSELIAVLLCLKHL 40 (267)
Q Consensus 3 ~~g~ai~~~~~~~~~~l~~~~t~~~AEl~Ai~~AL~~~ 40 (267)
.+|++|++.++..............||..||..|.+.+
T Consensus 20 ~vGaviv~~~~ii~~g~n~~~~~~HAE~~ai~~a~~~~ 57 (344)
T TIGR00326 20 LVGCVIVKNGEIVGEGAHQKAGEPHAEVHALRQAGENA 57 (344)
T ss_pred CEEEEEEeCCEEEEEeeCCCCCCCCHHHHHHHHhcccc
Confidence 58999998777676665544456789999999987653
No 30
>KOG1994|consensus
Probab=45.29 E-value=7.8 Score=33.14 Aligned_cols=23 Identities=17% Similarity=0.340 Sum_probs=18.8
Q ss_pred CCCCCc-ccCC-CCCcchhhc-Cccc
Q psy2212 195 APPSTC-GCGE-ILSVQHILT-CALH 217 (267)
Q Consensus 195 ~~~p~C-~Cg~-~et~~H~l~-Cp~~ 217 (267)
++.-.| +||. ..|.+.++- ||--
T Consensus 237 ~eh~YC~fCG~~y~~~edl~ehCPGv 262 (268)
T KOG1994|consen 237 SEHYYCFFCGIKYKDEEDLYEHCPGV 262 (268)
T ss_pred ccceEEEEeccccCCHHHHHHhCCCC
Confidence 455668 9998 899999999 9954
No 31
>PRK08298 cytidine deaminase; Validated
Probab=44.49 E-value=63 Score=25.44 Aligned_cols=51 Identities=12% Similarity=0.016 Sum_probs=32.7
Q ss_pred ceEEEEEeCCceEEEecC----CCCChhHHHHHHHHHHHHHhhhCCCCeEEEEecc
Q psy2212 3 TSCAYIIDKTSIYSFVLN----NVNSVFTSELIAVLLCLKHLKFLPKEKFVIISDS 54 (267)
Q Consensus 3 ~~g~ai~~~~~~~~~~l~----~~~t~~~AEl~Ai~~AL~~~~~~~~~~i~I~sDS 54 (267)
++|+|+...+..+..+.. ....-.-||..||..|+..-. .....|.|.+|.
T Consensus 24 ~VgAAllt~dG~i~tG~NvEnas~~~t~CAEr~Ai~~av~~G~-~~~~~i~v~~~~ 78 (136)
T PRK08298 24 GGAAAMRVEDGTILTSVAPEVINASTELCMETGAICEAHKLQK-RVTHSICVAREN 78 (136)
T ss_pred ceeEEEEeCCCCEEEEEeecCCCCCcchhHHHHHHHHHHHCCC-ceEEEEEEEcCC
Confidence 689999976654444332 233456899999999875421 224556666665
No 32
>COG3341 Predicted double-stranded RNA/RNA-DNA hybrid binding protein [General function prediction only]
Probab=44.11 E-value=19 Score=30.64 Aligned_cols=89 Identities=17% Similarity=0.081 Sum_probs=60.6
Q ss_pred CCChhHHHHHHHHHHHHHhhhCCCCeEEE-E----eccHHHHHHhcCCCCCC-hHHHHHHHhHHHHHhc--CCeEEEEEe
Q psy2212 22 VNSVFTSELIAVLLCLKHLKFLPKEKFVI-I----SDSKSTLLALSNPSNIN-PIVSLIHSCWSDLLCC--GKQLAFLWC 93 (267)
Q Consensus 22 ~~t~~~AEl~Ai~~AL~~~~~~~~~~i~I-~----sDS~~ai~~l~~~~~~~-~~~~~i~~~~~~l~~~--~~~v~~~Wv 93 (267)
..++..+|.+|++.+|+.+...+....+| + .||++.++-+.+-.... .+... .+.... +....+.|+
T Consensus 105 ~~~n~s~d~la~ly~~~~~~~~~nrk~~i~y~~~~~ds~a~~k~~k~~~~~k~~~~~~-----~e~~~~~~~v~h~~k~i 179 (225)
T COG3341 105 IKSNDSGDVLAKLYGLRYEVPLDNRKSVINYLTPGNDSWAYFKYVKDKCETKVNLLKD-----REFFSIGKGVFHDEKDI 179 (225)
T ss_pred cccCchHHHHHHhccccccccccCccceeeccCCcchhHHHHHHHhhhhhhHHHHHHh-----HHhhhccchhhhhhhhc
Confidence 45788999999999999988766655555 7 79999888776544221 11111 111122 234556788
Q ss_pred cCCCCCchhhHHhHHhcCCCCC
Q psy2212 94 PSHTGIQGNEAVDRAARNPSAS 115 (267)
Q Consensus 94 pgH~g~~gNe~AD~lAk~a~~~ 115 (267)
--|.++..+..++.++......
T Consensus 180 ~~~~~~~~~~~~~s~~~~~~k~ 201 (225)
T COG3341 180 NIHIWIFESKKGNSHVYNTSKK 201 (225)
T ss_pred ccccccchhhhhhhhhhchhhh
Confidence 8999999998888888777654
No 33
>PRK05578 cytidine deaminase; Validated
Probab=43.68 E-value=65 Score=25.12 Aligned_cols=52 Identities=10% Similarity=-0.039 Sum_probs=34.3
Q ss_pred CceEEEEEeCCceEEEecC--C--CCChhHHHHHHHHHHHHHhhhCCCCeEEEEecc
Q psy2212 2 NTSCAYIIDKTSIYSFVLN--N--VNSVFTSELIAVLLCLKHLKFLPKEKFVIISDS 54 (267)
Q Consensus 2 ~~~g~ai~~~~~~~~~~l~--~--~~t~~~AEl~Ai~~AL~~~~~~~~~~i~I~sDS 54 (267)
-++|+|+...+..+..... . ..-...||-.||..|+..-. .....+.|.+|+
T Consensus 24 f~Vgaa~~~~~G~i~~G~nvEna~~~~~~CAE~~Ai~~av~~G~-~~i~~i~vv~~~ 79 (131)
T PRK05578 24 FPVGAALLTDDGRIYTGCNIENASYGLTNCAERTAIFKAISEGG-GRLVAIACVGET 79 (131)
T ss_pred CceEEEEEeCCCCEEEEEEeeCccccCCcCHHHHHHHHHHHcCC-CceEEEEEEecC
Confidence 4789999977654444332 1 22345799999999885422 245778888876
No 34
>PF13696 zf-CCHC_2: Zinc knuckle
Probab=42.62 E-value=14 Score=21.48 Aligned_cols=18 Identities=33% Similarity=0.840 Sum_probs=14.3
Q ss_pred CCCCc-ccCCCCCcchhhc-Ccc
Q psy2212 196 PPSTC-GCGEILSVQHILT-CAL 216 (267)
Q Consensus 196 ~~p~C-~Cg~~et~~H~l~-Cp~ 216 (267)
++-.| .|+... |++. ||.
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 45568 898765 9999 998
No 35
>PHA02588 cd deoxycytidylate deaminase; Provisional
Probab=42.40 E-value=89 Score=25.46 Aligned_cols=18 Identities=28% Similarity=0.067 Sum_probs=13.0
Q ss_pred ceEEEEEeCCceEEEecC
Q psy2212 3 TSCAYIIDKTSIYSFVLN 20 (267)
Q Consensus 3 ~~g~ai~~~~~~~~~~l~ 20 (267)
.+|++|+.+++..+....
T Consensus 23 ~VGAVIV~~~~Iis~GyN 40 (168)
T PHA02588 23 KVGAVIEKNGRIISTGYN 40 (168)
T ss_pred CEEEEEEECCEEEEEEeC
Confidence 689999977776665543
No 36
>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=39.33 E-value=36 Score=28.86 Aligned_cols=44 Identities=16% Similarity=0.084 Sum_probs=29.6
Q ss_pred eCCceEEEecCCCCChhHHHHHHHHHHHHHhhhCCCCeEEEEeccHHHH
Q psy2212 10 DKTSIYSFVLNNVNSVFTSELIAVLLCLKHLKFLPKEKFVIISDSKSTL 58 (267)
Q Consensus 10 ~~~~~~~~~l~~~~t~~~AEl~Ai~~AL~~~~~~~~~~i~I~sDS~~ai 58 (267)
.+.+...+....--.++.+||+|.-.|.-+. ..++ |.|||..|+
T Consensus 110 i~~~~~~~Tfs~~l~IhtaELlaaClAr~~~----~~r~-l~tDnt~Vl 153 (245)
T PF00336_consen 110 ITGQRMRGTFSKPLPIHTAELLAACLARLMS----GARC-LGTDNTVVL 153 (245)
T ss_pred ecCceeeeeecccccchHHHHHHHHHHHhcc----CCcE-EeecCcEEE
Confidence 4444444555455679999999987766543 2344 899998775
No 37
>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=37.04 E-value=15 Score=24.31 Aligned_cols=19 Identities=26% Similarity=0.602 Sum_probs=8.1
Q ss_pred CCc-ccCCCCCcchhhc-Ccc
Q psy2212 198 STC-GCGEILSVQHILT-CAL 216 (267)
Q Consensus 198 p~C-~Cg~~et~~H~l~-Cp~ 216 (267)
-.| .||...+..|.+. ||+
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 368 9999899999999 996
No 38
>cd00786 cytidine_deaminase-like Cytidine and deoxycytidylate deaminase zinc-binding region. The family contains cytidine deaminases, nucleoside deaminases, deoxycytidylate deaminases and riboflavin deaminases. Also included are the apoBec family of mRNA editing enzymes. All members 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.
Probab=36.93 E-value=1e+02 Score=22.25 Aligned_cols=47 Identities=11% Similarity=-0.039 Sum_probs=29.1
Q ss_pred ceEEEEEeC--CceEEEecC----CCCChhHHHHHHHHHHHHHhhhCCCCeEEEEe
Q psy2212 3 TSCAYIIDK--TSIYSFVLN----NVNSVFTSELIAVLLCLKHLKFLPKEKFVIIS 52 (267)
Q Consensus 3 ~~g~ai~~~--~~~~~~~l~----~~~t~~~AEl~Ai~~AL~~~~~~~~~~i~I~s 52 (267)
.+|++|++. +........ .......||..||..|.... ......+|+
T Consensus 19 pVGaviv~~~~g~ii~~g~n~~~~~~~~~~HAE~~ai~~a~~~~---~~~~~tly~ 71 (96)
T cd00786 19 QVGACLVNKKDGGKVGRGCNIENAAYSMCNHAERTALFNAGSEG---DTKGQMLYV 71 (96)
T ss_pred CEEEEEEEeCCCCeEeeeEeccCCCCCCeeCHHHHHHHHHHHcC---CCCceEEEE
Confidence 579999875 444443322 23355679999999887643 134555565
No 39
>smart00667 LisH Lissencephaly type-1-like homology motif. Alpha-helical motif present in Lis1, treacle, Nopp140, some katanin p60 subunits, muskelin, tonneau, LEUNIG and numerous WD40 repeat-containing proteins. It is suggested that LisH motifs contribute to the regulation of microtubule dynamics, either by mediating dimerisation, or else by binding cytoplasmic dynein heavy chain or microtubules directly.
Probab=35.45 E-value=39 Score=18.61 Aligned_cols=28 Identities=18% Similarity=0.262 Sum_probs=23.6
Q ss_pred hHHHHHHHHHHhcchhhhhhhchhhhhh
Q psy2212 236 SVDSLLSYLKKLNLRVVAVSFEKDEEVD 263 (267)
Q Consensus 236 ~~~~i~~f~~~t~~~~~~~~~~~~~~~~ 263 (267)
-...|++|+...|...+...|.+|..++
T Consensus 6 l~~lI~~yL~~~g~~~ta~~l~~e~~~~ 33 (34)
T smart00667 6 LNRLILEYLLRNGYEETAETLQKESGLS 33 (34)
T ss_pred HHHHHHHHHHHcCHHHHHHHHHHHhCCC
Confidence 3467999999999999999999887654
No 40
>PRK10786 ribD bifunctional diaminohydroxyphosphoribosylaminopyrimidine deaminase/5-amino-6-(5-phosphoribosylamino)uracil reductase; Provisional
Probab=32.88 E-value=73 Score=29.42 Aligned_cols=38 Identities=11% Similarity=0.003 Sum_probs=27.7
Q ss_pred ceEEEEEeCCceEEEecCCCCChhHHHHHHHHHHHHHh
Q psy2212 3 TSCAYIIDKTSIYSFVLNNVNSVFTSELIAVLLCLKHL 40 (267)
Q Consensus 3 ~~g~ai~~~~~~~~~~l~~~~t~~~AEl~Ai~~AL~~~ 40 (267)
.+|++|++.+.............-.||..||..|-+.+
T Consensus 26 ~vGaviv~~g~ii~~g~n~~~g~~HAE~~ai~~a~~~~ 63 (367)
T PRK10786 26 NVGCVIVKDGEIVGEGYHQRAGEPHAEVHALRMAGEKA 63 (367)
T ss_pred CEEEEEEeCCEEEEEEeCCCCCCCCHHHHHHHHHhhhc
Confidence 58999998777666655533334689999999987654
No 41
>smart00642 Aamy Alpha-amylase domain.
Probab=32.70 E-value=1.5e+02 Score=23.90 Aligned_cols=72 Identities=11% Similarity=-0.033 Sum_probs=43.0
Q ss_pred HHHHHHHHHHHHhhhCCCCeEEEEe----------ccHHHHHHhcCCCCCChHHHHHHHhHHHHHhcCCeEEEEEecCCC
Q psy2212 28 SELIAVLLCLKHLKFLPKEKFVIIS----------DSKSTLLALSNPSNINPIVSLIHSCWSDLLCCGKQLAFLWCPSHT 97 (267)
Q Consensus 28 AEl~Ai~~AL~~~~~~~~~~i~I~s----------DS~~ai~~l~~~~~~~~~~~~i~~~~~~l~~~~~~v~~~WvpgH~ 97 (267)
.-+.+|..-|..+.+.+...|.+-- ++-|...-.......-....++.+++..+..+|..|.+-.|+.|+
T Consensus 16 G~~~gi~~~l~yl~~lG~~~I~l~Pi~~~~~~~~~~~gY~~~d~~~i~~~~Gt~~d~~~lv~~~h~~Gi~vilD~V~NH~ 95 (166)
T smart00642 16 GDLQGIIEKLDYLKDLGVTAIWLSPIFESPQGYPSYHGYDISDYKQIDPRFGTMEDFKELVDAAHARGIKVILDVVINHT 95 (166)
T ss_pred cCHHHHHHHHHHHHHCCCCEEEECcceeCCCCCCCCCCcCccccCCCCcccCCHHHHHHHHHHHHHCCCEEEEEECCCCC
Confidence 3466677777777776665554421 111111111110000012467777788888999999999999999
Q ss_pred CC
Q psy2212 98 GI 99 (267)
Q Consensus 98 g~ 99 (267)
+.
T Consensus 96 ~~ 97 (166)
T smart00642 96 SD 97 (166)
T ss_pred CC
Confidence 87
No 42
>PLN02807 diaminohydroxyphosphoribosylaminopyrimidine deaminase
Probab=31.89 E-value=85 Score=29.23 Aligned_cols=38 Identities=11% Similarity=-0.060 Sum_probs=28.0
Q ss_pred ceEEEEEeCCceEEEecCCCCChhHHHHHHHHHHHHHh
Q psy2212 3 TSCAYIIDKTSIYSFVLNNVNSVFTSELIAVLLCLKHL 40 (267)
Q Consensus 3 ~~g~ai~~~~~~~~~~l~~~~t~~~AEl~Ai~~AL~~~ 40 (267)
.+|++|++.++..............||..||..|-+.+
T Consensus 55 ~VGaViV~~g~Ii~~g~n~~~g~~HAEi~Ai~~a~~~~ 92 (380)
T PLN02807 55 MVGCVIVKDGRIVGEGFHPKAGQPHAEVFALRDAGDLA 92 (380)
T ss_pred CEEEEEEECCEEEEEEeCCCCCCcCHHHHHHHHhhhhc
Confidence 38999997777666665533344689999999987653
No 43
>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=27.90 E-value=1.7e+02 Score=21.67 Aligned_cols=40 Identities=15% Similarity=-0.024 Sum_probs=24.8
Q ss_pred CceEEEEEeCCceEEEecC----CCCChhHHHHHHHHHHHHHhh
Q psy2212 2 NTSCAYIIDKTSIYSFVLN----NVNSVFTSELIAVLLCLKHLK 41 (267)
Q Consensus 2 ~~~g~ai~~~~~~~~~~l~----~~~t~~~AEl~Ai~~AL~~~~ 41 (267)
-.+|++++..+..+..... .......||..||..+.....
T Consensus 18 ~~vga~i~~~~g~i~~G~n~e~~~~~~~~hAE~~ai~~~~~~~~ 61 (112)
T cd01283 18 FTVGAALLTKDGRIFTGVNVENASYGLTLCAERTAIGKAVSEGL 61 (112)
T ss_pred CeEEEEEEECCCCEEEeEEeecCCCCCCcCHHHHHHHHHHHcCC
Confidence 3688999875332223322 223456799999999886543
No 44
>PF06839 zf-GRF: GRF zinc finger; InterPro: IPR010666 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 presumed zinc-binding domain is found in a variety of DNA-binding proteins. It seems likely that this domain is involved in nucleic acid binding. It is named GRF after three conserved residues in the centre of the alignment of the domain. This zinc finger may be related to IPR000380 from INTERPRO. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding
Probab=26.19 E-value=36 Score=21.10 Aligned_cols=14 Identities=7% Similarity=0.002 Sum_probs=9.5
Q ss_pred CCcchhhc-CcccHH
Q psy2212 206 LSVQHILT-CALHGH 219 (267)
Q Consensus 206 et~~H~l~-Cp~~~~ 219 (267)
++....++ ||.+..
T Consensus 19 ~N~GR~Fy~C~~~~~ 33 (45)
T PF06839_consen 19 PNPGRRFYKCPNYKD 33 (45)
T ss_pred CCCCCcceECCCCCC
Confidence 45567777 887754
No 45
>PF04863 EGF_alliinase: Alliinase EGF-like domain; InterPro: IPR006947 Allicin is a thiosulphinate that gives rise to dithiines, allyl sulphides and ajoenes, the three groups of active compounds in Allium species. Allicin is synthesised from sulphoxide cysteine derivatives by alliinase, whose C-S lyase activity cleaves C(beta)-S(gamma) bonds. It is thought that this enzyme forms part of a primitive plant defence system [].; GO: 0016846 carbon-sulfur lyase activity; PDB: 1LK9_B 2HOX_C 2HOR_A.
Probab=25.12 E-value=15 Score=24.10 Aligned_cols=23 Identities=26% Similarity=0.426 Sum_probs=10.8
Q ss_pred ecccccccccccCCCCCCCcccCC
Q psy2212 181 IGHTRATHGHLFKRAPPSTCGCGE 204 (267)
Q Consensus 181 TGH~~~~~~~r~~~~~~p~C~Cg~ 204 (267)
+|||+. |+=-+.....|.|.|+.
T Consensus 20 SGHGr~-flDg~~~dG~p~CECn~ 42 (56)
T PF04863_consen 20 SGHGRA-FLDGLIADGSPVCECNS 42 (56)
T ss_dssp TTSEE---TTS-EETTEE--EE-T
T ss_pred CCCCee-eeccccccCCccccccC
Confidence 789886 11122245669998875
No 46
>PRK10933 trehalose-6-phosphate hydrolase; Provisional
Probab=23.29 E-value=1.8e+02 Score=28.44 Aligned_cols=73 Identities=14% Similarity=0.067 Sum_probs=47.5
Q ss_pred HHHHHHHHHHHHHhhhCCCCeEEEEe-------ccHHHHHHhcCCCCCChHHHHHHHhHHHHHhcCCeEEEEEecCCCCC
Q psy2212 27 TSELIAVLLCLKHLKFLPKEKFVIIS-------DSKSTLLALSNPSNINPIVSLIHSCWSDLLCCGKQLAFLWCPSHTGI 99 (267)
Q Consensus 27 ~AEl~Ai~~AL~~~~~~~~~~i~I~s-------DS~~ai~~l~~~~~~~~~~~~i~~~~~~l~~~~~~v~~~WvpgH~g~ 99 (267)
.+.|.+|...|..+...+...|.+-- |+-|.+.-....-..=....++..++..+..+|..|.+-.|+.|++.
T Consensus 29 ~Gdl~gi~~~ldyl~~lGv~~i~l~P~~~~~~~~~gY~~~d~~~id~~~Gt~~d~~~lv~~~h~~gi~vilD~V~NH~s~ 108 (551)
T PRK10933 29 TGDLRGVTQRLDYLQKLGVDAIWLTPFYVSPQVDNGYDVANYTAIDPTYGTLDDFDELVAQAKSRGIRIILDMVFNHTST 108 (551)
T ss_pred CcCHHHHHHhhHHHHhCCCCEEEECCCCCCCCCCCCCCcccCCCcCcccCCHHHHHHHHHHHHHCCCEEEEEECCCCccC
Confidence 57899999999999998877776522 11111110000000001235677777778889999999999999886
No 47
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=22.95 E-value=37 Score=25.81 Aligned_cols=26 Identities=12% Similarity=0.277 Sum_probs=15.7
Q ss_pred CCCCc-ccCC-CCCcchhhc-CcccHHhh
Q psy2212 196 PPSTC-GCGE-ILSVQHILT-CALHGHIR 221 (267)
Q Consensus 196 ~~p~C-~Cg~-~et~~H~l~-Cp~~~~~R 221 (267)
..-.| .||. .....+.++ ||......
T Consensus 69 ~~~~C~~Cg~~~~~~~~~~~~CP~Cgs~~ 97 (114)
T PRK03681 69 AECWCETCQQYVTLLTQRVRRCPQCHGDM 97 (114)
T ss_pred cEEEcccCCCeeecCCccCCcCcCcCCCC
Confidence 33458 7887 444455556 88776443
No 48
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=22.49 E-value=39 Score=25.23 Aligned_cols=24 Identities=25% Similarity=0.545 Sum_probs=15.8
Q ss_pred CCc-ccCC-CCCcchhhc--CcccHHhh
Q psy2212 198 STC-GCGE-ILSVQHILT--CALHGHIR 221 (267)
Q Consensus 198 p~C-~Cg~-~et~~H~l~--Cp~~~~~R 221 (267)
-.| .||. .++.+-.++ ||...-..
T Consensus 3 H~CtrCG~vf~~g~~~il~GCp~CG~nk 30 (112)
T COG3364 3 HQCTRCGEVFDDGSEEILSGCPKCGCNK 30 (112)
T ss_pred ceecccccccccccHHHHccCccccchh
Confidence 469 9998 667555554 99765443
No 49
>COG2131 ComEB Deoxycytidylate deaminase [Nucleotide transport and metabolism]
Probab=21.38 E-value=3.3e+02 Score=22.22 Aligned_cols=62 Identities=18% Similarity=0.084 Sum_probs=36.8
Q ss_pred CceEEEEEeCCceEEEecCCCC--------------------------ChhHHHHHHHHHHHHHhhhCCC--CeEEEEec
Q psy2212 2 NTSCAYIIDKTSIYSFVLNNVN--------------------------SVFTSELIAVLLCLKHLKFLPK--EKFVIISD 53 (267)
Q Consensus 2 ~~~g~ai~~~~~~~~~~l~~~~--------------------------t~~~AEl~Ai~~AL~~~~~~~~--~~i~I~sD 53 (267)
.++|++|+.+++..+....+.. -.-.||.-||+.|.+....... --++.|-+
T Consensus 28 ~~VGAvIvkd~rIiatGYNG~p~g~~~c~~~g~~~~~~~~~~~~~~~~r~vHAE~NAil~aa~~g~~~~~atlYvt~~PC 107 (164)
T COG2131 28 RQVGAVIVKDGRIIATGYNGAPSGEDHCIDRGCLRDKVVFVTTCGHCCRTLHAEQNAILQAARHGVGLEGATLYVTHFPC 107 (164)
T ss_pred cceeEEEEeCCeEEEeecCCCCcccCCcCccCceecccccccchhHHHHHHHHHHHHHHHHHhcCCCCCCcEEEEEeccc
Confidence 4789999997776665432110 0134899999999887654221 23444555
Q ss_pred cHHHHHHhcC
Q psy2212 54 SKSTLLALSN 63 (267)
Q Consensus 54 S~~ai~~l~~ 63 (267)
+.=+-..++.
T Consensus 108 ~~Cak~Ii~a 117 (164)
T COG2131 108 SNCAKLIIQA 117 (164)
T ss_pred HHHHHHHHHh
Confidence 5544444444
No 50
>PF09345 DUF1987: Domain of unknown function (DUF1987); InterPro: IPR018530 This family of proteins are functionally uncharacterised.
Probab=21.31 E-value=1.2e+02 Score=22.56 Aligned_cols=26 Identities=15% Similarity=0.151 Sum_probs=20.8
Q ss_pred hHHHHHHHhHHHHHhcCCeEEEEEec
Q psy2212 69 PIVSLIHSCWSDLLCCGKQLAFLWCP 94 (267)
Q Consensus 69 ~~~~~i~~~~~~l~~~~~~v~~~Wvp 94 (267)
..+..|.+.++.+...|..|.+.|.-
T Consensus 60 k~l~~i~~~Le~~~~~g~~V~v~Wyy 85 (99)
T PF09345_consen 60 KALMDIFDLLEDAAQKGGKVTVNWYY 85 (99)
T ss_pred HHHHHHHHHHHHHHhcCCcEEEEEEE
Confidence 45567777777778899999999985
No 51
>PF14293 YWFCY: YWFCY protein
Probab=21.05 E-value=68 Score=21.60 Aligned_cols=26 Identities=12% Similarity=0.599 Sum_probs=20.4
Q ss_pred CCChhhHHHHHHHHHHhcchhhhhhh
Q psy2212 231 TDDVESVDSLLSYLKKLNLRVVAVSF 256 (267)
Q Consensus 231 ~~~~~~~~~i~~f~~~t~~~~~~~~~ 256 (267)
++|.++..+|++|.+.-.++.....|
T Consensus 3 eddlr~L~KImdf~R~iSI~~l~ih~ 28 (61)
T PF14293_consen 3 EDDLRALRKIMDFMRAISILFLVIHF 28 (61)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 35778899999999988887766554
No 52
>TIGR02403 trehalose_treC alpha,alpha-phosphotrehalase. Trehalose is a glucose disaccharide that serves in many biological systems as a compatible solute for protection against hyperosmotic and thermal stress. This family describes trehalose-6-phosphate hydrolase, product of the treC (or treA) gene, which is often found together with a trehalose uptake transporter and a trehalose operon repressor.
Probab=20.42 E-value=2.3e+02 Score=27.68 Aligned_cols=74 Identities=14% Similarity=0.038 Sum_probs=46.5
Q ss_pred HHHHHHHHHHHHHhhhCCCCeEEEEe-------ccHHHHHHhcCCCCCChHHHHHHHhHHHHHhcCCeEEEEEecCCCCC
Q psy2212 27 TSELIAVLLCLKHLKFLPKEKFVIIS-------DSKSTLLALSNPSNINPIVSLIHSCWSDLLCCGKQLAFLWCPSHTGI 99 (267)
Q Consensus 27 ~AEl~Ai~~AL~~~~~~~~~~i~I~s-------DS~~ai~~l~~~~~~~~~~~~i~~~~~~l~~~~~~v~~~WvpgH~g~ 99 (267)
.+-+.+|..-|..+.+.+...|.+-- |+.|.+.-....-+.=....++..++..+..+|..|.+-+|+.|++.
T Consensus 23 ~G~~~gi~~~l~yl~~lG~~~i~l~Pi~~~~~~~~gY~~~d~~~id~~~Gt~~~~~~lv~~ah~~gi~vilD~v~NH~~~ 102 (543)
T TIGR02403 23 TGDLRGIIEKLDYLKKLGVDYIWLNPFYVSPQKDNGYDVSDYYAINPLFGTMADFEELVSEAKKRNIKIMLDMVFNHTST 102 (543)
T ss_pred ccCHHHHHHhHHHHHHcCCCEEEECCcccCCCCCCCCCccccCccCcccCCHHHHHHHHHHHHHCCCEEEEEECcccccc
Confidence 46788999999999887776665422 11111111110000001235677777777789999999999999985
Q ss_pred c
Q psy2212 100 Q 100 (267)
Q Consensus 100 ~ 100 (267)
.
T Consensus 103 ~ 103 (543)
T TIGR02403 103 E 103 (543)
T ss_pred c
Confidence 3
Done!