Query psy16958
Match_columns 257
No_of_seqs 160 out of 251
Neff 5.3
Searched_HMMs 46136
Date Fri Aug 16 18:03:57 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy16958.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/16958hhsearch_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 97.6 4.5E-05 9.7E-10 60.7 3.6 51 95-146 2-55 (132)
2 cd06222 RnaseH RNase H (RNase 96.9 0.0026 5.7E-08 47.9 6.2 51 98-148 1-58 (130)
3 PRK08719 ribonuclease H; Revie 96.7 0.0049 1.1E-07 51.9 6.2 57 94-150 2-69 (147)
4 PF13966 zf-RVT: zinc-binding 96.2 0.0026 5.6E-08 48.4 1.9 42 176-217 38-83 (86)
5 PRK00203 rnhA ribonuclease H; 96.2 0.011 2.4E-07 49.4 5.5 53 96-149 3-61 (150)
6 PRK13907 rnhA ribonuclease H; 96.0 0.012 2.5E-07 47.4 4.9 53 97-149 2-59 (128)
7 KOG3752|consensus 94.8 0.053 1.1E-06 52.3 5.5 58 93-150 209-275 (371)
8 PRK07708 hypothetical protein; 93.2 0.3 6.5E-06 43.9 6.9 56 94-149 71-136 (219)
9 PRK06548 ribonuclease H; Provi 93.1 0.24 5.2E-06 42.6 5.9 52 95-147 4-58 (161)
10 COG0328 RnhA Ribonuclease HI [ 92.9 0.33 7.2E-06 41.6 6.5 54 95-148 2-60 (154)
11 PRK07238 bifunctional RNase H/ 91.1 0.58 1.3E-05 44.4 6.5 51 97-148 3-62 (372)
12 PF05380 Peptidase_A17: Pao re 85.7 1.9 4.1E-05 36.3 5.4 53 94-148 79-143 (159)
13 PRK08298 cytidine deaminase; V 66.9 8.2 0.00018 32.3 3.9 40 100-143 19-62 (136)
14 PRK06848 hypothetical protein; 60.3 23 0.0005 29.7 5.4 41 100-143 22-66 (139)
15 COG0295 Cdd Cytidine deaminase 50.6 20 0.00044 30.1 3.5 36 109-144 27-66 (134)
16 KOG1930|consensus 49.6 14 0.00031 36.7 2.8 65 151-216 206-283 (483)
17 PRK05578 cytidine deaminase; V 43.7 65 0.0014 26.6 5.5 35 109-143 25-63 (131)
18 PF00325 Crp: Bacterial regula 35.0 53 0.0011 21.0 2.9 26 229-254 7-32 (32)
19 PF00098 zf-CCHC: Zinc knuckle 33.6 26 0.00056 19.4 1.1 17 196-215 2-18 (18)
20 PF09538 FYDLN_acid: Protein o 31.9 28 0.00062 28.1 1.5 22 185-207 18-39 (108)
21 PF13456 RVT_3: Reverse transc 30.3 44 0.00094 23.8 2.2 19 132-150 2-20 (87)
22 cd01286 deoxycytidylate_deamin 27.8 1.3E+02 0.0028 24.6 4.8 37 107-143 19-80 (131)
23 PRK12411 cytidine deaminase; P 27.4 85 0.0019 26.0 3.7 36 108-143 24-63 (132)
24 PF13917 zf-CCHC_3: Zinc knuck 27.3 49 0.0011 22.4 1.9 24 194-221 4-27 (42)
25 TIGR01354 cyt_deam_tetra cytid 26.2 1.1E+02 0.0025 24.8 4.2 37 108-144 21-61 (127)
26 PF00383 dCMP_cyt_deam_1: Cyti 24.8 1.4E+02 0.0031 22.3 4.3 41 105-145 21-66 (102)
27 COG1244 Predicted Fe-S oxidore 23.1 98 0.0021 30.1 3.7 33 75-107 77-114 (358)
28 cd01285 nucleoside_deaminase N 22.1 2.3E+02 0.005 22.0 5.1 39 107-145 16-59 (109)
29 smart00507 HNHc HNH nucleases. 21.1 54 0.0012 20.8 1.1 17 195-211 11-31 (52)
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=97.65 E-value=4.5e-05 Score=60.66 Aligned_cols=51 Identities=27% Similarity=0.485 Sum_probs=37.7
Q ss_pred CcceEEecCCCC--CCceeeEE-eeCCceEEeeCCCCccchHHHHHHHHHHHHHH
Q psy16958 95 RKETFYCDGSKS--PQHCGSAF-VHEGNTITFKLPNISSSYTAEIIALQKCIQFI 146 (257)
Q Consensus 95 ~~~~iyTDgSK~--~~~vG~ai-~~~~~~~~~kLp~~~SIftAE~~AIl~Al~~i 146 (257)
++..||||||-. .+..|+++ +..+....+.++ ..|.+.||..||..||+.+
T Consensus 2 ~~~~iytDgS~~~~~~~~~~g~v~~~~~~~~~~~~-~~s~~~aEl~Ai~~AL~~~ 55 (132)
T PF00075_consen 2 KAIIIYTDGSCRPNPGKGGAGYVVWGGRNFSFRLG-GQSNNRAELQAIIEALKAL 55 (132)
T ss_dssp TSEEEEEEEEECTTTTEEEEEEEEETTEEEEEEEE-SECHHHHHHHHHHHHHHTH
T ss_pred CcEEEEEeCCccCCCCceEEEEEEECCeEEEeccc-ccchhhhheehHHHHHHHh
Confidence 467899999943 33334444 455555667777 7899999999999999955
No 2
>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=96.95 E-value=0.0026 Score=47.87 Aligned_cols=51 Identities=24% Similarity=0.432 Sum_probs=35.6
Q ss_pred eEEecCCCCCC--ceeeEEe--eCCceEEee---CCCCccchHHHHHHHHHHHHHHhh
Q psy16958 98 TFYCDGSKSPQ--HCGSAFV--HEGNTITFK---LPNISSSYTAEIIALQKCIQFITQ 148 (257)
Q Consensus 98 ~iyTDgSK~~~--~vG~ai~--~~~~~~~~k---Lp~~~SIftAE~~AIl~Al~~i~q 148 (257)
.+|||||-..+ +.|++++ ..+....+. .....|++.||..|++.|++++.+
T Consensus 1 ~~~~Dgs~~~~~~~~g~g~v~~~~~~~~~~~~~~~~~~~s~~~aEl~al~~al~~~~~ 58 (130)
T cd06222 1 VIYTDGSCRGNPGPAGAGVVLRDPGGEVLLSGGLLGGNTTNNRAELLALIEALELALE 58 (130)
T ss_pred CEEecccCCCCCCceEEEEEEEeCCCeEEEeccccCCCCcHHHHHHHHHHHHHHHHHh
Confidence 48999998765 5666665 333222222 224679999999999999998764
No 3
>PRK08719 ribonuclease H; Reviewed
Probab=96.65 E-value=0.0049 Score=51.87 Aligned_cols=57 Identities=16% Similarity=0.332 Sum_probs=38.4
Q ss_pred CCcceEEecCCCCCCc-----eeeEEe--eCC--ce--EEeeCCCCccchHHHHHHHHHHHHHHhhhc
Q psy16958 94 NRKETFYCDGSKSPQH-----CGSAFV--HEG--NT--ITFKLPNISSSYTAEIIALQKCIQFITQNK 150 (257)
Q Consensus 94 ~~~~~iyTDgSK~~~~-----vG~ai~--~~~--~~--~~~kLp~~~SIftAE~~AIl~Al~~i~q~~ 150 (257)
+....||||||...+. .|++++ +.+ .. ....+....+-..||..|++.||+.+....
T Consensus 2 ~~~~~iYtDGs~~~n~~~~~~~G~G~vv~~~~~~~~~~~~~~~~~~~Tnn~aEl~A~~~aL~~~~~~~ 69 (147)
T PRK08719 2 RASYSIYIDGAAPNNQHGCVRGGIGLVVYDEAGEIVDEQSITVNRYTDNAELELLALIEALEYARDGD 69 (147)
T ss_pred CceEEEEEecccCCCCCCCCCcEEEEEEEeCCCCeeEEEEecCCCCccHHHHHHHHHHHHHHHcCCCC
Confidence 3567899999986543 366654 332 22 334454556778899999999999876543
No 4
>PF13966 zf-RVT: zinc-binding in reverse transcriptase
Probab=96.24 E-value=0.0026 Score=48.36 Aligned_cols=42 Identities=21% Similarity=0.447 Sum_probs=31.9
Q ss_pred hhcCcccc-c--cccccCCCCCCCCCCCCC-ccccceeeccccccH
Q psy16958 176 LRIGHTRV-S--HSYLIDKKPRPICDTCHT-PLSVAHILIECTKFQ 217 (257)
Q Consensus 176 LRtGHt~l-t--h~~~i~~~~~p~C~~Cg~-~~Tv~HIL~eCp~~~ 217 (257)
-|.-|.+| | -+++.+...++.|..||. .||+.|++++||.-.
T Consensus 38 W~~~~~rL~t~~~l~~r~~~~~~~C~~C~~~~Et~~Hlf~~C~~a~ 83 (86)
T PF13966_consen 38 WRALHNRLPTKDNLQRRGIQVDPICPLCGNEEETIEHLFFHCPFAR 83 (86)
T ss_pred eeeccccchhhhhhhccCCccCCccccCCCccccccceeccCcCcc
Confidence 34556666 3 355566678899999995 899999999999753
No 5
>PRK00203 rnhA ribonuclease H; Reviewed
Probab=96.16 E-value=0.011 Score=49.35 Aligned_cols=53 Identities=13% Similarity=0.201 Sum_probs=34.7
Q ss_pred cceEEecCCCCC--CceeeEEe--eCCceE--EeeCCCCccchHHHHHHHHHHHHHHhhh
Q psy16958 96 KETFYCDGSKSP--QHCGSAFV--HEGNTI--TFKLPNISSSYTAEIIALQKCIQFITQN 149 (257)
Q Consensus 96 ~~~iyTDgSK~~--~~vG~ai~--~~~~~~--~~kLp~~~SIftAE~~AIl~Al~~i~q~ 149 (257)
...||||||... +..|.+++ .++... ....+ ..+--.||+.|++.||+.+...
T Consensus 3 ~v~iytDGs~~~n~~~~g~g~v~~~~~~~~~~~~~~~-~~TN~~aEL~Ai~~AL~~~~~~ 61 (150)
T PRK00203 3 QVEIYTDGACLGNPGPGGWGAILRYKGHEKELSGGEA-LTTNNRMELMAAIEALEALKEP 61 (150)
T ss_pred eEEEEEEecccCCCCceEEEEEEEECCeeEEEecCCC-CCcHHHHHHHHHHHHHHHcCCC
Confidence 478999999764 33555544 444332 22233 3455679999999999987654
No 6
>PRK13907 rnhA ribonuclease H; Provisional
Probab=96.02 E-value=0.012 Score=47.36 Aligned_cols=53 Identities=23% Similarity=0.344 Sum_probs=34.4
Q ss_pred ceEEecCCCCC--CceeeEEe--eCCceEEeeCC-CCccchHHHHHHHHHHHHHHhhh
Q psy16958 97 ETFYCDGSKSP--QHCGSAFV--HEGNTITFKLP-NISSSYTAEIIALQKCIQFITQN 149 (257)
Q Consensus 97 ~~iyTDgSK~~--~~vG~ai~--~~~~~~~~kLp-~~~SIftAE~~AIl~Al~~i~q~ 149 (257)
.+||||||-.. +..|++++ +.+....+..+ ..++=..||..|++.||+++...
T Consensus 2 ~~iy~DGa~~~~~g~~G~G~vi~~~~~~~~~~~~~~~~tn~~AE~~All~aL~~a~~~ 59 (128)
T PRK13907 2 IEVYIDGASKGNPGPSGAGVFIKGVQPAVQLSLPLGTMSNHEAEYHALLAALKYCTEH 59 (128)
T ss_pred EEEEEeeCCCCCCCccEEEEEEEECCeeEEEEecccccCCcHHHHHHHHHHHHHHHhC
Confidence 57999998653 34666655 33222222222 23455679999999999988765
No 7
>KOG3752|consensus
Probab=94.76 E-value=0.053 Score=52.32 Aligned_cols=58 Identities=19% Similarity=0.204 Sum_probs=45.0
Q ss_pred cCCcceEEecCCCCC-----CceeeEEeeC---CceEEeeCC-CCccchHHHHHHHHHHHHHHhhhc
Q psy16958 93 VNRKETFYCDGSKSP-----QHCGSAFVHE---GNTITFKLP-NISSSYTAEIIALQKCIQFITQNK 150 (257)
Q Consensus 93 ~~~~~~iyTDgSK~~-----~~vG~ai~~~---~~~~~~kLp-~~~SIftAE~~AIl~Al~~i~q~~ 150 (257)
+.+...+|||||-.- -++|.+|+-+ .....++|. .--.-|.||.+|+.+||+-+.+..
T Consensus 209 ~~~~~vvytDGS~~~ng~~~~~AGyGvywg~~~e~N~s~pv~~g~qtNnrAEl~Av~~ALkka~~~~ 275 (371)
T KOG3752|consen 209 EIEIQVVYTDGSSSGNGRKSSRAGYGVYWGPGHELNVSGPLAGGRQTNNRAELIAAIEALKKARSKN 275 (371)
T ss_pred cccceEEEecCccccCCCCCCcceeEEeeCCCCcccccccCCCCcccccHHHHHHHHHHHHHHHhcC
Confidence 345589999999765 3589999843 356788887 555889999999999999887643
No 8
>PRK07708 hypothetical protein; Validated
Probab=93.18 E-value=0.3 Score=43.86 Aligned_cols=56 Identities=20% Similarity=0.179 Sum_probs=36.7
Q ss_pred CCcceEEecCCCC--CCceeeEEe--eCCceEE------eeCCCCccchHHHHHHHHHHHHHHhhh
Q psy16958 94 NRKETFYCDGSKS--PQHCGSAFV--HEGNTIT------FKLPNISSSYTAEIIALQKCIQFITQN 149 (257)
Q Consensus 94 ~~~~~iyTDgSK~--~~~vG~ai~--~~~~~~~------~kLp~~~SIftAE~~AIl~Al~~i~q~ 149 (257)
.+...+|+|||-. .++.|++++ ....... ..|...++=-.||..|++.||+.+...
T Consensus 71 p~~~~vY~DGs~~~n~g~aG~GvVI~~~~g~~~~~~~~~~~l~~~~TNN~AEy~Ali~aL~~A~e~ 136 (219)
T PRK07708 71 PHEILVYFDGGFDKETKLAGLGIVIYYKQGNKRYRIRRNAYIEGIYDNNEAEYAALYYAMQELEEL 136 (219)
T ss_pred CCcEEEEEeeccCCCCCCcEEEEEEEECCCCEEEEEEeeccccccccCcHHHHHHHHHHHHHHHHc
Confidence 4468999999853 344555544 4332222 245544566679999999999988764
No 9
>PRK06548 ribonuclease H; Provisional
Probab=93.08 E-value=0.24 Score=42.58 Aligned_cols=52 Identities=17% Similarity=0.064 Sum_probs=31.6
Q ss_pred CcceEEecCCCCC--CceeeEEeeCCc-eEEeeCCCCccchHHHHHHHHHHHHHHh
Q psy16958 95 RKETFYCDGSKSP--QHCGSAFVHEGN-TITFKLPNISSSYTAEIIALQKCIQFIT 147 (257)
Q Consensus 95 ~~~~iyTDgSK~~--~~vG~ai~~~~~-~~~~kLp~~~SIftAE~~AIl~Al~~i~ 147 (257)
+...||||||-.. +..|.+++..+. ......+.. +==.||..|++.||+.+.
T Consensus 4 ~~~~IytDGa~~gnpg~~G~g~~~~~~~~~~g~~~~~-TNnraEl~Aii~aL~~~~ 58 (161)
T PRK06548 4 NEIIAATDGSSLANPGPSGWAWYVDENTWDSGGWDIA-TNNIAELTAVRELLIATR 58 (161)
T ss_pred CEEEEEEeeccCCCCCceEEEEEEeCCcEEccCCCCC-CHHHHHHHHHHHHHHhhh
Confidence 4578999998664 346677663332 221112111 112499999999998665
No 10
>COG0328 RnhA Ribonuclease HI [DNA replication, recombination, and repair]
Probab=92.93 E-value=0.33 Score=41.62 Aligned_cols=54 Identities=15% Similarity=0.195 Sum_probs=35.3
Q ss_pred CcceEEecCCCCC----CceeeEEeeCCceEEeeCCC-CccchHHHHHHHHHHHHHHhh
Q psy16958 95 RKETFYCDGSKSP----QHCGSAFVHEGNTITFKLPN-ISSSYTAEIIALQKCIQFITQ 148 (257)
Q Consensus 95 ~~~~iyTDgSK~~----~~vG~ai~~~~~~~~~kLp~-~~SIftAE~~AIl~Al~~i~q 148 (257)
....||||||-.. ++.|+.+.+++....+..+- .++==.||..|+++||+++..
T Consensus 2 ~~v~if~DGa~~gNpG~gG~g~vl~~~~~~~~~s~~~~~tTNNraEl~A~i~AL~~l~~ 60 (154)
T COG0328 2 KKVEIFTDGACLGNPGPGGWGAVLRYGDGEKELSGGEGRTTNNRAELRALIEALEALKE 60 (154)
T ss_pred CceEEEecCccCCCCCCceEEEEEEcCCceEEEeeeeecccChHHHHHHHHHHHHHHHh
Confidence 3578999999653 34555554444433233322 344456999999999999984
No 11
>PRK07238 bifunctional RNase H/acid phosphatase; Provisional
Probab=91.06 E-value=0.58 Score=44.36 Aligned_cols=51 Identities=14% Similarity=0.099 Sum_probs=33.9
Q ss_pred ceEEecCCCCCC--ceeeEEe--eCC-c----eEEeeCCCCccchHHHHHHHHHHHHHHhh
Q psy16958 97 ETFYCDGSKSPQ--HCGSAFV--HEG-N----TITFKLPNISSSYTAEIIALQKCIQFITQ 148 (257)
Q Consensus 97 ~~iyTDgSK~~~--~vG~ai~--~~~-~----~~~~kLp~~~SIftAE~~AIl~Al~~i~q 148 (257)
+.||||||-..+ ..|++++ +.+ . .....+. .++--.||..|++.||+++..
T Consensus 3 ~~i~~DGa~~~n~g~aG~G~vi~~~~~~~~~~~~~~~~~-~~tnn~AE~~All~gL~~a~~ 62 (372)
T PRK07238 3 VVVEADGGSRGNPGPAGYGAVVWDADRGEVLAERAEAIG-RATNNVAEYRGLIAGLEAAAE 62 (372)
T ss_pred EEEEecCCCCCCCCceEEEEEEEeCCCCcEEEEeecccC-CCCchHHHHHHHHHHHHHHHh
Confidence 579999996643 3555544 432 1 1233344 456668999999999998775
No 12
>PF05380 Peptidase_A17: Pao retrotransposon peptidase ; InterPro: IPR008042 This signature identifies members of the Pao retrotransposon family.
Probab=85.67 E-value=1.9 Score=36.35 Aligned_cols=53 Identities=13% Similarity=0.260 Sum_probs=33.9
Q ss_pred CCcceEEecCCCCCCceeeEEe--e-CCceEE-------eeC--CCCccchHHHHHHHHHHHHHHhh
Q psy16958 94 NRKETFYCDGSKSPQHCGSAFV--H-EGNTIT-------FKL--PNISSSYTAEIIALQKCIQFITQ 148 (257)
Q Consensus 94 ~~~~~iyTDgSK~~~~vG~ai~--~-~~~~~~-------~kL--p~~~SIftAE~~AIl~Al~~i~q 148 (257)
....++|+|||+.. .|+.++ . .+.... -|+ -+..||-.-|..|++.|+.++..
T Consensus 79 ~~~L~~F~DAS~~a--ygavvYlr~~~~~~~~~~ll~aKsrv~P~k~~tIPRlEL~a~~l~~~l~~~ 143 (159)
T PF05380_consen 79 SVELHVFCDASESA--YGAVVYLRSYSDGSVQVRLLFAKSRVAPLKTVTIPRLELLAALLGVRLANT 143 (159)
T ss_pred ceeeeEeecccccc--eeeEeEeeeccCCceeeeeeeecccccCCCCCcHHHHHHHHHHHHHHHHHH
Confidence 34688999999554 455544 1 222111 122 13459999999999999887664
No 13
>PRK08298 cytidine deaminase; Validated
Probab=66.88 E-value=8.2 Score=32.34 Aligned_cols=40 Identities=23% Similarity=0.153 Sum_probs=24.8
Q ss_pred EecCCCCCCceeeEEeeCCce--EEeeCCCC--ccchHHHHHHHHHHH
Q psy16958 100 YCDGSKSPQHCGSAFVHEGNT--ITFKLPNI--SSSYTAEIIALQKCI 143 (257)
Q Consensus 100 yTDgSK~~~~vG~ai~~~~~~--~~~kLp~~--~SIftAE~~AIl~Al 143 (257)
|...| +||+|+...+-. .-..+-+. ..-.=||..||..|+
T Consensus 19 Y~PYS----~VgAAllt~dG~i~tG~NvEnas~~~t~CAEr~Ai~~av 62 (136)
T PRK08298 19 YPNGW----GGAAAMRVEDGTILTSVAPEVINASTELCMETGAICEAH 62 (136)
T ss_pred cCCCC----ceeEEEEeCCCCEEEEEeecCCCCCcchhHHHHHHHHHH
Confidence 66666 899999854433 33333222 111229999999886
No 14
>PRK06848 hypothetical protein; Validated
Probab=60.29 E-value=23 Score=29.68 Aligned_cols=41 Identities=29% Similarity=0.340 Sum_probs=24.9
Q ss_pred EecCCCCCCceeeEEeeCCceE--EeeCC--CCccchHHHHHHHHHHH
Q psy16958 100 YCDGSKSPQHCGSAFVHEGNTI--TFKLP--NISSSYTAEIIALQKCI 143 (257)
Q Consensus 100 yTDgSK~~~~vG~ai~~~~~~~--~~kLp--~~~SIftAE~~AIl~Al 143 (257)
|.. | ...||+|+...+-.+ ...+- .+..-.=||..||..|+
T Consensus 22 y~p-s--~f~VgAa~l~~~G~i~~G~NvEnas~~~tiCAEr~Ai~~av 66 (139)
T PRK06848 22 YRN-D--WHHVGAALRTKTGRIYAAVHLEAYVGRITVCAEAIAIGKAI 66 (139)
T ss_pred cCC-C--CCcEEEEEEeCCCCEEEEEEeecCCCCcccCHHHHHHHHHH
Confidence 554 4 478999998554322 22222 22222349999999985
No 15
>COG0295 Cdd Cytidine deaminase [Nucleotide transport and metabolism]
Probab=50.65 E-value=20 Score=30.15 Aligned_cols=36 Identities=31% Similarity=0.308 Sum_probs=21.7
Q ss_pred ceeeEEeeCCceE--EeeCCCCccchH--HHHHHHHHHHH
Q psy16958 109 HCGSAFVHEGNTI--TFKLPNISSSYT--AEIIALQKCIQ 144 (257)
Q Consensus 109 ~vG~ai~~~~~~~--~~kLp~~~SIft--AE~~AIl~Al~ 144 (257)
.||+++...+-.+ -..+-+.+--.| ||..||.+|+.
T Consensus 27 ~VGAa~~t~~G~i~tG~NiEnasy~~t~CAErsAI~~ais 66 (134)
T COG0295 27 KVGAALRTKDGRIYTGANVENASYGLTVCAERSAIFKAIS 66 (134)
T ss_pred cEEEEEEeCCCCEEEEEeeecccccchhhHHHHHHHHHHH
Confidence 6899988544322 333333322222 99999999953
No 16
>KOG1930|consensus
Probab=49.61 E-value=14 Score=36.68 Aligned_cols=65 Identities=20% Similarity=0.283 Sum_probs=48.1
Q ss_pred cccccccCCCCCCCCCchhHHHHHh--------hhcCcccc-ccccccCCCCCC-CCCCC-CC--ccccceeecccccc
Q psy16958 151 KIKPETQYWPTSSRQKRIEEVIIAR--------LRIGHTRV-SHSYLIDKKPRP-ICDTC-HT--PLSVAHILIECTKF 216 (257)
Q Consensus 151 ~IK~~i~~W~~~~~l~R~~~~iL~r--------LRtGHt~l-th~~~i~~~~~p-~C~~C-g~--~~Tv~HIL~eCp~~ 216 (257)
-++-.-+.|..| +++|-+++.|-| +|--|++- .++--|++..+| .-..- |. .+=|+|+|+||-.-
T Consensus 206 FV~DTSKyWYKP-~isREQAIalLrdkePGtFvvRDS~SfrGayGLAlKVstPPPs~~~~~g~~~neLVRHFLIE~spk 283 (483)
T KOG1930|consen 206 FVKDTSKYWYKP-NISREQAIALLRDKEPGTFVVRDSHSFRGAYGLALKVSTPPPSVQPGDGSDSNELVRHFLIEPSPK 283 (483)
T ss_pred eeecccccccCC-CCCHHHHHHHhhcCCCCeEEEecCCcCCCccceEEEeccCCCcccCCCCCchhhhhhhheeccCCC
Confidence 346667899998 899999998887 78888887 466667876654 33322 22 38999999998643
No 17
>PRK05578 cytidine deaminase; Validated
Probab=43.68 E-value=65 Score=26.65 Aligned_cols=35 Identities=23% Similarity=0.274 Sum_probs=20.9
Q ss_pred ceeeEEeeCCc--eEEeeCCCC--ccchHHHHHHHHHHH
Q psy16958 109 HCGSAFVHEGN--TITFKLPNI--SSSYTAEIIALQKCI 143 (257)
Q Consensus 109 ~vG~ai~~~~~--~~~~kLp~~--~SIftAE~~AIl~Al 143 (257)
.||+|+...+- -.-..+-+- .--.-||..||..|+
T Consensus 25 ~Vgaa~~~~~G~i~~G~nvEna~~~~~~CAE~~Ai~~av 63 (131)
T PRK05578 25 PVGAALLTDDGRIYTGCNIENASYGLTNCAERTAIFKAI 63 (131)
T ss_pred ceEEEEEeCCCCEEEEEEeeCccccCCcCHHHHHHHHHH
Confidence 69999985442 223333221 122349999999885
No 18
>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. This family groups together a range of proteins, including anr, crp, clp, cysR, fixK, flp, fnr, fnrN, hlyX and ntcA [, ]. Within this family, the HTH motif is situated towards the C terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2OZ6_A 1CGP_B 2GZW_C 1O3T_B 3ROU_A 2CGP_A 3RDI_A 1I5Z_A 3IYD_H 3FWE_B ....
Probab=35.03 E-value=53 Score=20.97 Aligned_cols=26 Identities=31% Similarity=0.484 Sum_probs=22.6
Q ss_pred cHHHhhCCChHhHHHHHHHHHHhccc
Q psy16958 229 TLENLLGNNKETIDSTLKYLYKTKLF 254 (257)
Q Consensus 229 ~l~~lLg~~~~~I~~ii~Fi~~T~l~ 254 (257)
++.+.||-..+.+..+++.+++.|++
T Consensus 7 diA~~lG~t~ETVSR~l~~l~~~glI 32 (32)
T PF00325_consen 7 DIADYLGLTRETVSRILKKLERQGLI 32 (32)
T ss_dssp HHHHHHTS-HHHHHHHHHHHHHTTSE
T ss_pred HHHHHhCCcHHHHHHHHHHHHHcCCC
Confidence 68899999999999999999999874
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=33.62 E-value=26 Score=19.38 Aligned_cols=17 Identities=41% Similarity=0.929 Sum_probs=13.6
Q ss_pred CCCCCCCccccceeeccccc
Q psy16958 196 ICDTCHTPLSVAHILIECTK 215 (257)
Q Consensus 196 ~C~~Cg~~~Tv~HIL~eCp~ 215 (257)
.|-.||+. .|+.-+||.
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 57788865 899999984
No 20
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=31.88 E-value=28 Score=28.08 Aligned_cols=22 Identities=23% Similarity=0.490 Sum_probs=16.7
Q ss_pred cccccCCCCCCCCCCCCCccccc
Q psy16958 185 HSYLIDKKPRPICDTCHTPLSVA 207 (257)
Q Consensus 185 h~~~i~~~~~p~C~~Cg~~~Tv~ 207 (257)
..|=+++ +|-.|+.||..+.+.
T Consensus 18 kFYDLnk-~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 18 KFYDLNK-DPIVCPKCGTEFPPE 39 (108)
T ss_pred hhccCCC-CCccCCCCCCccCcc
Confidence 4566788 667799999877666
No 21
>PF13456 RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EHG_A 3HST_B.
Probab=30.31 E-value=44 Score=23.78 Aligned_cols=19 Identities=26% Similarity=0.268 Sum_probs=16.2
Q ss_pred hHHHHHHHHHHHHHHhhhc
Q psy16958 132 YTAEIIALQKCIQFITQNK 150 (257)
Q Consensus 132 ftAE~~AIl~Al~~i~q~~ 150 (257)
..||+.|++.||+++....
T Consensus 2 ~~aE~~al~~al~~a~~~g 20 (87)
T PF13456_consen 2 LEAEALALLEALQLAWELG 20 (87)
T ss_dssp HHHHHHHHHHHHHHHHCCT
T ss_pred cHHHHHHHHHHHHHHHHCC
Confidence 3699999999999998654
No 22
>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=27.84 E-value=1.3e+02 Score=24.57 Aligned_cols=37 Identities=19% Similarity=0.267 Sum_probs=23.7
Q ss_pred CCceeeEEeeCCceEEee---CC----------------------CCccchHHHHHHHHHHH
Q psy16958 107 PQHCGSAFVHEGNTITFK---LP----------------------NISSSYTAEIIALQKCI 143 (257)
Q Consensus 107 ~~~vG~ai~~~~~~~~~k---Lp----------------------~~~SIftAE~~AIl~Al 143 (257)
+-.||+.++.++..+.-. .| .++...=||..||..|.
T Consensus 19 ~~~VGAViv~~~~iI~~G~N~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~HAE~~Ai~~a~ 80 (131)
T cd01286 19 RRQVGAVIVKDKRIISTGYNGSPSGLPHCAEVGCERDDLPSGEDQKCCRTVHAEQNAILQAA 80 (131)
T ss_pred CCCEEEEEEECCEEEEEeeCCCCCCCCCcccccccccccccccccccCCCCCHHHHHHHHHh
Confidence 346999988765543221 12 33455569999999884
No 23
>PRK12411 cytidine deaminase; Provisional
Probab=27.38 E-value=85 Score=25.98 Aligned_cols=36 Identities=25% Similarity=0.272 Sum_probs=21.0
Q ss_pred CceeeEEeeCCceEEeeCCCCccch----HHHHHHHHHHH
Q psy16958 108 QHCGSAFVHEGNTITFKLPNISSSY----TAEIIALQKCI 143 (257)
Q Consensus 108 ~~vG~ai~~~~~~~~~kLp~~~SIf----tAE~~AIl~Al 143 (257)
-.||+|+...+-.+....--+...| -||..||..|+
T Consensus 24 ~~VgAa~~t~~G~i~~G~nvEn~s~~~s~CAE~~Ai~~av 63 (132)
T PRK12411 24 FQVGAALLTQDGKVYRGCNVENASYGLCNCAERTALFKAV 63 (132)
T ss_pred CceEEEEEeCCCCEEEEEEeecCCCCcCcCHHHHHHHHHH
Confidence 3589998854432222222222233 49999999885
No 24
>PF13917 zf-CCHC_3: Zinc knuckle
Probab=27.31 E-value=49 Score=22.44 Aligned_cols=24 Identities=33% Similarity=0.699 Sum_probs=18.1
Q ss_pred CCCCCCCCCccccceeeccccccHHHhh
Q psy16958 194 RPICDTCHTPLSVAHILIECTKFQVERQ 221 (257)
Q Consensus 194 ~p~C~~Cg~~~Tv~HIL~eCp~~~~~R~ 221 (257)
...|.-||.. .|+-.||+. ..+|.
T Consensus 4 ~~~CqkC~~~---GH~tyeC~~-~~~r~ 27 (42)
T PF13917_consen 4 RVRCQKCGQK---GHWTYECPN-KNERK 27 (42)
T ss_pred CCcCcccCCC---CcchhhCCC-CCCcc
Confidence 4579999965 899999997 33343
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=26.20 E-value=1.1e+02 Score=24.80 Aligned_cols=37 Identities=19% Similarity=0.228 Sum_probs=21.6
Q ss_pred CceeeEEeeCCc--eEEeeC--CCCccchHHHHHHHHHHHH
Q psy16958 108 QHCGSAFVHEGN--TITFKL--PNISSSYTAEIIALQKCIQ 144 (257)
Q Consensus 108 ~~vG~ai~~~~~--~~~~kL--p~~~SIftAE~~AIl~Al~ 144 (257)
-.||+++...+- ...... ..+....-||..||..|+.
T Consensus 21 ~~vgAa~~~~~G~i~~G~n~e~~~~~~s~~AE~~Ai~~a~~ 61 (127)
T TIGR01354 21 FKVGAALLTKDGRIFTGVNVENASYPLTICAERSAIGKAIS 61 (127)
T ss_pred CeEEEEEEeCCCCEEEEEeecccCCCCCcCHHHHHHHHHHH
Confidence 358999885432 222222 2222334599999998853
No 26
>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=24.77 E-value=1.4e+02 Score=22.31 Aligned_cols=41 Identities=20% Similarity=0.240 Sum_probs=25.7
Q ss_pred CCCCceeeEEee-CCceEEeeCC----CCccchHHHHHHHHHHHHH
Q psy16958 105 KSPQHCGSAFVH-EGNTITFKLP----NISSSYTAEIIALQKCIQF 145 (257)
Q Consensus 105 K~~~~vG~ai~~-~~~~~~~kLp----~~~SIftAE~~AIl~Al~~ 145 (257)
.....||++|+. ++..+....- .....-=||..||..|...
T Consensus 21 ~~~~~vgaviv~~~~~~i~~g~n~~~~~~~~~~HAE~~Ai~~~~~~ 66 (102)
T PF00383_consen 21 CGNFPVGAVIVDPDGKIIATGYNGEPPGKNPTIHAEMNAIRKAARN 66 (102)
T ss_dssp TTSSSEEEEEEETTTEEEEEEESBHHSTTGGTB-HHHHHHHHHHHT
T ss_pred cCCCCEEEEEEeccCccEEEEeeeeeeeccccccchhhhhhhhhhh
Confidence 445679999998 4454433332 2223445999999988654
No 27
>COG1244 Predicted Fe-S oxidoreductase [General function prediction only]
Probab=23.11 E-value=98 Score=30.09 Aligned_cols=33 Identities=15% Similarity=0.307 Sum_probs=26.0
Q ss_pred cCCChHHHHHHHHHHHHhcC---Cc--ceEEecCCCCC
Q psy16958 75 TNISPNEIKSKFNQLLNKVN---RK--ETFYCDGSKSP 107 (257)
Q Consensus 75 ~~T~p~~~~~~f~~ii~~~~---~~--~~iyTDgSK~~ 107 (257)
...+.+.+-++|.+.+++|. +. ++|||-||=.+
T Consensus 77 ~~vs~E~l~~qfd~~~~k~~~~~~~~~vkIFTSGSFLD 114 (358)
T COG1244 77 EPVSEENLINQFDEAYSKYEGKFDEFVVKIFTSGSFLD 114 (358)
T ss_pred CCCCHHHHHHHHHHHHHHhcccCCCceEEEEcccccCC
Confidence 45667779999999999665 33 89999999654
No 28
>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=22.13 E-value=2.3e+02 Score=21.99 Aligned_cols=39 Identities=21% Similarity=0.273 Sum_probs=26.0
Q ss_pred CCceeeEEeeC-CceEEe----eCCCCccchHHHHHHHHHHHHH
Q psy16958 107 PQHCGSAFVHE-GNTITF----KLPNISSSYTAEIIALQKCIQF 145 (257)
Q Consensus 107 ~~~vG~ai~~~-~~~~~~----kLp~~~SIftAE~~AIl~Al~~ 145 (257)
+..||+.|++. +..... ..+...+..-||..||..|...
T Consensus 16 ~~~vgaviv~~~~~ii~~g~n~~~~~~~~~~HAE~~ai~~~~~~ 59 (109)
T cd01285 16 EVPFGAVIVDDDGKVIARGHNRVEQDGDPTAHAEIVAIRNAARR 59 (109)
T ss_pred CCcEEEEEEeCCCEEEEEEeCCCCCCCCCcccHHHHHHHHHHHH
Confidence 45689999866 443322 2233456777999999998654
No 29
>smart00507 HNHc HNH nucleases.
Probab=21.09 E-value=54 Score=20.82 Aligned_cols=17 Identities=41% Similarity=0.903 Sum_probs=12.5
Q ss_pred CCCCCCCCc----cccceeec
Q psy16958 195 PICDTCHTP----LSVAHILI 211 (257)
Q Consensus 195 p~C~~Cg~~----~Tv~HIL~ 211 (257)
..|..||.. .+|.||.-
T Consensus 11 ~~C~~C~~~~~~~~~v~Hi~p 31 (52)
T smart00507 11 GVCAYCGKPASEGLEVDHIIP 31 (52)
T ss_pred CCCcCCcCCCCCCeEEEecCC
Confidence 689999965 47777763
Done!