Query psy7535
Match_columns 199
No_of_seqs 164 out of 327
Neff 6.6
Searched_HMMs 46136
Date Fri Aug 16 20:50:57 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy7535.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/7535hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF00075 RNase_H: RNase H; In 99.7 1.2E-16 2.7E-21 121.8 9.7 100 13-121 2-116 (132)
2 PRK06548 ribonuclease H; Provi 99.7 8.1E-16 1.8E-20 123.8 12.7 103 12-120 3-125 (161)
3 PRK08719 ribonuclease H; Revie 99.6 3.3E-15 7.2E-20 118.5 11.6 100 12-120 2-130 (147)
4 PRK00203 rnhA ribonuclease H; 99.6 5E-15 1.1E-19 117.3 11.6 101 14-121 3-126 (150)
5 COG0328 RnhA Ribonuclease HI [ 99.6 3.6E-14 7.7E-19 113.3 12.0 104 13-121 2-129 (154)
6 PRK13907 rnhA ribonuclease H; 99.6 3.4E-14 7.3E-19 109.1 10.8 105 15-124 2-118 (128)
7 cd06222 RnaseH RNase H (RNase 99.5 1.9E-13 4.1E-18 100.3 11.5 100 16-120 1-115 (130)
8 KOG3752|consensus 99.3 6.2E-12 1.3E-16 111.9 10.5 118 3-125 201-354 (371)
9 PRK07708 hypothetical protein; 99.3 8.2E-11 1.8E-15 99.1 12.2 111 7-123 67-198 (219)
10 PRK07238 bifunctional RNase H/ 99.2 2.1E-10 4.6E-15 102.8 12.2 102 14-120 2-119 (372)
11 PF13456 RVT_3: Reverse transc 98.7 6.3E-08 1.4E-12 68.1 7.5 69 49-122 1-76 (87)
12 PF13966 zf-RVT: zinc-binding 96.2 0.0021 4.6E-08 46.0 1.4 29 143-171 54-83 (86)
13 PF00336 DNA_pol_viral_C: DNA 95.7 0.024 5.1E-07 47.6 5.5 92 12-120 92-185 (245)
14 PF05380 Peptidase_A17: Pao re 92.0 0.54 1.2E-05 37.4 6.2 53 13-67 80-144 (159)
15 COG0295 Cdd Cytidine deaminase 71.4 7.2 0.00016 30.6 4.2 68 26-107 26-98 (134)
16 cd01285 nucleoside_deaminase N 65.7 31 0.00068 25.3 6.5 54 24-82 15-73 (109)
17 PF00098 zf-CCHC: Zinc knuckle 54.4 8.4 0.00018 19.6 1.2 17 150-169 2-18 (18)
18 PF15322 PMSI1: Protein missin 51.8 9.5 0.00021 33.6 1.8 18 121-138 210-227 (311)
19 PF00383 dCMP_cyt_deam_1: Cyti 49.4 45 0.00099 23.6 4.9 52 24-81 22-78 (102)
20 COG0590 CumB Cytosine/adenosin 49.1 54 0.0012 25.9 5.7 43 25-67 27-74 (152)
21 PRK10860 tRNA-specific adenosi 48.6 66 0.0014 26.0 6.2 41 25-65 32-76 (172)
22 PRK06848 hypothetical protein; 48.1 35 0.00075 26.7 4.3 53 25-83 26-82 (139)
23 PRK05578 cytidine deaminase; V 45.0 17 0.00038 28.1 2.2 51 27-83 25-79 (131)
24 PF13005 zf-IS66: zinc-finger 43.9 12 0.00026 23.2 0.9 13 147-159 1-13 (47)
25 PRK08298 cytidine deaminase; V 43.0 36 0.00078 26.6 3.7 51 27-83 24-78 (136)
26 cd01284 Riboflavin_deaminase-r 41.1 86 0.0019 23.6 5.4 39 25-63 18-57 (115)
27 cd01286 deoxycytidylate_deamin 40.8 1.1E+02 0.0024 23.3 6.1 16 48-63 67-82 (131)
28 TIGR01354 cyt_deam_tetra cytid 39.3 63 0.0014 24.6 4.5 52 26-83 21-76 (127)
29 PRK12411 cytidine deaminase; P 36.4 61 0.0013 25.1 4.1 52 26-83 24-79 (132)
30 PF05741 zf-nanos: Nanos RNA b 32.6 23 0.0005 23.5 0.9 20 150-169 35-54 (55)
31 TIGR03628 arch_S11P archaeal r 31.8 2.3E+02 0.005 21.5 7.0 78 7-94 7-97 (114)
32 PF09538 FYDLN_acid: Protein o 31.0 29 0.00064 26.1 1.4 20 141-161 20-39 (108)
33 PF05191 ADK_lid: Adenylate ki 31.0 29 0.00063 20.8 1.1 17 142-158 15-31 (36)
34 KOG1812|consensus 29.6 47 0.001 30.4 2.7 38 46-88 46-83 (384)
35 PF13696 zf-CCHC_2: Zinc knuck 28.5 40 0.00087 19.9 1.4 17 150-169 10-26 (32)
36 KOG0341|consensus 28.1 25 0.00055 32.8 0.7 27 150-179 572-600 (610)
37 PF04423 Rad50_zn_hook: Rad50 27.3 18 0.00039 23.3 -0.3 14 150-163 22-35 (54)
38 KOG0466|consensus 27.1 33 0.00072 31.1 1.2 33 141-173 102-138 (466)
39 PF07057 TraI: DNA helicase Tr 26.6 22 0.00047 27.7 0.0 14 10-23 5-18 (126)
40 PF14169 YdjO: Cold-inducible 25.7 42 0.00092 22.6 1.3 20 144-163 35-56 (59)
41 KOG1994|consensus 24.1 31 0.00067 29.6 0.5 32 125-170 230-262 (268)
42 KOG3284|consensus 21.1 84 0.0018 26.3 2.4 17 51-67 27-43 (213)
43 COG2093 DNA-directed RNA polym 21.0 65 0.0014 22.1 1.5 18 142-159 12-29 (64)
44 TIGR00100 hypA hydrogenase nic 21.0 40 0.00087 25.4 0.5 6 151-156 89-94 (115)
45 COG1592 Rubrerythrin [Energy p 20.9 58 0.0013 26.4 1.5 17 141-157 142-158 (166)
46 PRK12380 hydrogenase nickel in 20.8 40 0.00086 25.3 0.5 8 110-117 62-69 (113)
47 PF03997 VPS28: VPS28 protein; 20.7 87 0.0019 25.9 2.5 16 52-67 2-17 (188)
48 cd00350 rubredoxin_like Rubred 20.6 55 0.0012 18.9 1.0 11 147-157 16-26 (33)
49 PF05605 zf-Di19: Drought indu 20.5 46 0.00099 21.3 0.7 24 149-172 3-26 (54)
50 PRK00398 rpoP DNA-directed RNA 20.2 41 0.0009 20.8 0.4 10 149-158 22-31 (46)
No 1
>PF00075 RNase_H: RNase H; InterPro: IPR002156 The RNase H domain is responsible for hydrolysis of the RNA portion of RNA x DNA hybrids, and this activity requires the presence of divalent cations (Mg2+ or Mn2+) that bind its active site. This domain is a part of a large family of homologous RNase H enzymes of which the RNase HI protein from Escherichia coli is the best characterised []. Secondary structure predictions for the enzymes from E. coli, yeast, human liver and diverse retroviruses (such as Rous sarcoma virus and the Foamy viruses) supported, in every case, the five beta-strands (1 to 5) and four or five alpha-helices (A, B/C, D, E) that have been identified by crystallography in the RNase H domain of Human immunodeficiency virus 1 (HIV-1) reverse transcriptase and in E. coli RNase H []. Reverse transcriptase (RT) is a modular enzyme carrying polymerase and ribonuclease H (RNase H) activities in separable domains. Reverse transcriptase (RT) converts the single-stranded RNA genome of a retrovirus into a double-stranded DNA copy for integration into the host genome. This process requires ribonuclease H as well as RNA- and DNA-directed DNA polymerase activities. Retroviral RNase H is synthesised as part of the POL polyprotein that contains; an aspartyl protease, a reverse transcriptase, RNase H and integrase. POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. Bacterial RNase H 3.1.26.4 from EC catalyses endonucleolytic cleavage to 5'-phosphomonoester acting on RNA-DNA hybrids. The 3D structure of the RNase H domain from diverse bacteria and retroviruses has been solved [, , ]. All have four beta strands and four to five alpha helices. The E. coli RNase H1 protein binds a single Mg2+ ion cofactor in the active site of the enzyme. The divalent cation is bound by the carboxyl groups of four acidic residues, Asp-10, Glu-48, Asp-70, and Asp-134 []. The first three acidic residues are highly conserved in all bacterial and retroviral RNase H sequences. ; GO: 0003676 nucleic acid binding, 0004523 ribonuclease H activity; PDB: 3LP3_B 2KW4_A 3P1G_A 1RIL_A 2RPI_A 4EQJ_G 4EP2_B 3OTY_P 3U3G_D 2ZQB_D ....
Probab=99.69 E-value=1.2e-16 Score=121.78 Aligned_cols=100 Identities=27% Similarity=0.328 Sum_probs=75.3
Q ss_pred CceEEEEcCCCC--CCceEEEEEEc-CeeeEEecCCCcchhHHHHHHHHHHHHHHHhhCCCCCCCCcEEEEcCcHHHHHH
Q psy7535 13 NYKQIFTDASKN--EHSVSSAFCCE-ETKFSVKLDPRISICNAELISIQYAISFIISTTPLQVPTPKFVLYSDSLSALQS 89 (199)
Q Consensus 13 ~~~~IyTDgSk~--~~~~G~ai~~~-~~~~~~~l~~~~Si~tAEl~AI~~AL~~i~~~~~~~~~~~~i~I~SDS~sal~a 89 (199)
+++.||||||.. .+..|+|++.. +......++ ..|++.||+.||..||+.+ . ...++|+|||++++++
T Consensus 2 ~~~~iytDgS~~~~~~~~~~g~v~~~~~~~~~~~~-~~s~~~aEl~Ai~~AL~~~--~------~~~v~I~tDS~~v~~~ 72 (132)
T PF00075_consen 2 KAIIIYTDGSCRPNPGKGGAGYVVWGGRNFSFRLG-GQSNNRAELQAIIEALKAL--E------HRKVTIYTDSQYVLNA 72 (132)
T ss_dssp TSEEEEEEEEECTTTTEEEEEEEEETTEEEEEEEE-SECHHHHHHHHHHHHHHTH--S------TSEEEEEES-HHHHHH
T ss_pred CcEEEEEeCCccCCCCceEEEEEEECCeEEEeccc-ccchhhhheehHHHHHHHh--h------cccccccccHHHHHHH
Confidence 678999999964 33346665443 434555566 9999999999999999944 4 2889999999999998
Q ss_pred hhc-----CCC-C--c-HHHHHHHHHHhc---ceEEecCCCCcc
Q psy7535 90 LQN-----IIS-S--S-PIALEIINLLHK---IQCQVRPSHFNM 121 (199)
Q Consensus 90 I~n-----~~~-~--s-~i~~~I~~ll~~---I~l~WiP~h~nR 121 (199)
|.. ... . . ++..+|.+++.+ |.|+|+|+|.+.
T Consensus 73 l~~~~~~~~~~~~~~~~~i~~~i~~~~~~~~~v~~~~V~~H~~~ 116 (132)
T PF00075_consen 73 LNKWLHGNGWKKTSNGRPIKNEIWELLSRGIKVRFRWVPGHSGV 116 (132)
T ss_dssp HHTHHHHTTSBSCTSSSBHTHHHHHHHHHSSEEEEEESSSSSSS
T ss_pred HHHhccccccccccccccchhheeeccccceEEeeeeccCcCCC
Confidence 887 222 1 2 577788887754 999999999876
No 2
>PRK06548 ribonuclease H; Provisional
Probab=99.67 E-value=8.1e-16 Score=123.80 Aligned_cols=103 Identities=19% Similarity=0.115 Sum_probs=75.8
Q ss_pred CCceEEEEcCCCCCC--ceEEEEEEcCeeeEEecCCCcchhHHHHHHHHHHHHHHHhhCCCCCCCCcEEEEcCcHHHHHH
Q psy7535 12 PNYKQIFTDASKNEH--SVSSAFCCEETKFSVKLDPRISICNAELISIQYAISFIISTTPLQVPTPKFVLYSDSLSALQS 89 (199)
Q Consensus 12 ~~~~~IyTDgSk~~~--~~G~ai~~~~~~~~~~l~~~~Si~tAEl~AI~~AL~~i~~~~~~~~~~~~i~I~SDS~sal~a 89 (199)
++.+.||||||...+ ..|.|++..+......-....|+..||+.||+.||+.+.. ....+.|+|||+.++++
T Consensus 3 ~~~~~IytDGa~~gnpg~~G~g~~~~~~~~~~g~~~~~TNnraEl~Aii~aL~~~~~------~~~~v~I~TDS~yvi~~ 76 (161)
T PRK06548 3 NNEIIAATDGSSLANPGPSGWAWYVDENTWDSGGWDIATNNIAELTAVRELLIATRH------TDRPILILSDSKYVINS 76 (161)
T ss_pred CCEEEEEEeeccCCCCCceEEEEEEeCCcEEccCCCCCCHHHHHHHHHHHHHHhhhc------CCceEEEEeChHHHHHH
Confidence 455899999998544 5678877655432223335689999999999999986643 34579999999999999
Q ss_pred hhc---------CCCC-------cHHHHHHHHHHhc--ceEEecCCCCc
Q psy7535 90 LQN---------IISS-------SPIALEIINLLHK--IQCQVRPSHFN 120 (199)
Q Consensus 90 I~n---------~~~~-------s~i~~~I~~ll~~--I~l~WiP~h~n 120 (199)
|.. ++.+ .++.++|.+++.+ |+|.|||+|.+
T Consensus 77 i~~W~~~Wk~~gWk~s~G~pV~N~dL~~~l~~l~~~~~v~~~wVkgHsg 125 (161)
T PRK06548 77 LTKWVYSWKMRKWRKADGKPVLNQEIIQEIDSLMENRNIRMSWVNAHTG 125 (161)
T ss_pred HHHHHHHHHHCCCcccCCCccccHHHHHHHHHHHhcCceEEEEEecCCC
Confidence 993 3221 1456666666655 99999999997
No 3
>PRK08719 ribonuclease H; Reviewed
Probab=99.63 E-value=3.3e-15 Score=118.51 Aligned_cols=100 Identities=16% Similarity=0.197 Sum_probs=72.1
Q ss_pred CCceEEEEcCCCCCCc-----eEEEEEE--cCee----eEEecCCCcchhHHHHHHHHHHHHHHHhhCCCCCCCCcEEEE
Q psy7535 12 PNYKQIFTDASKNEHS-----VSSAFCC--EETK----FSVKLDPRISICNAELISIQYAISFIISTTPLQVPTPKFVLY 80 (199)
Q Consensus 12 ~~~~~IyTDgSk~~~~-----~G~ai~~--~~~~----~~~~l~~~~Si~tAEl~AI~~AL~~i~~~~~~~~~~~~i~I~ 80 (199)
++.+.||||||..+++ .|+|++. ++.. ....+....|+++||+.||+.||+.+.+. ..|+
T Consensus 2 ~~~~~iYtDGs~~~n~~~~~~~G~G~vv~~~~~~~~~~~~~~~~~~~Tnn~aEl~A~~~aL~~~~~~---------~~i~ 72 (147)
T PRK08719 2 RASYSIYIDGAAPNNQHGCVRGGIGLVVYDEAGEIVDEQSITVNRYTDNAELELLALIEALEYARDG---------DVIY 72 (147)
T ss_pred CceEEEEEecccCCCCCCCCCcEEEEEEEeCCCCeeEEEEecCCCCccHHHHHHHHHHHHHHHcCCC---------CEEE
Confidence 4568999999996543 4777654 3221 33345556899999999999999998643 2799
Q ss_pred cCcHHHHHHh--------hcCCCCc--------HHHHHHHHHHhc--ceEEecCCCCc
Q psy7535 81 SDSLSALQSL--------QNIISSS--------PIALEIINLLHK--IQCQVRPSHFN 120 (199)
Q Consensus 81 SDS~sal~aI--------~n~~~~s--------~i~~~I~~ll~~--I~l~WiP~h~n 120 (199)
|||+.++++| +|.+..+ ++.+.|..+..+ |+|.|+|+|.+
T Consensus 73 tDS~yvi~~i~~~~~~W~~~~w~~s~g~~v~n~dl~~~i~~l~~~~~i~~~~VkgH~g 130 (147)
T PRK08719 73 SDSDYCVRGFNEWLDTWKQKGWRKSDKKPVANRDLWQQVDELRARKYVEVEKVTAHSG 130 (147)
T ss_pred echHHHHHHHHHHHHHHHhCCcccCCCcccccHHHHHHHHHHhCCCcEEEEEecCCCC
Confidence 9999999999 4443311 345555555554 99999999987
No 4
>PRK00203 rnhA ribonuclease H; Reviewed
Probab=99.62 E-value=5e-15 Score=117.26 Aligned_cols=101 Identities=14% Similarity=0.084 Sum_probs=73.2
Q ss_pred ceEEEEcCCCCCC--ceEEEEEE--cCeeeEE-ecCCCcchhHHHHHHHHHHHHHHHhhCCCCCCCCcEEEEcCcHHHHH
Q psy7535 14 YKQIFTDASKNEH--SVSSAFCC--EETKFSV-KLDPRISICNAELISIQYAISFIISTTPLQVPTPKFVLYSDSLSALQ 88 (199)
Q Consensus 14 ~~~IyTDgSk~~~--~~G~ai~~--~~~~~~~-~l~~~~Si~tAEl~AI~~AL~~i~~~~~~~~~~~~i~I~SDS~sal~ 88 (199)
++.||||||...+ ..|+|++. ++....+ +.....|+..||+.|++.||+.+.+ ...+.|+|||+.+++
T Consensus 3 ~v~iytDGs~~~n~~~~g~g~v~~~~~~~~~~~~~~~~~TN~~aEL~Ai~~AL~~~~~-------~~~v~I~tDS~yvi~ 75 (150)
T PRK00203 3 QVEIYTDGACLGNPGPGGWGAILRYKGHEKELSGGEALTTNNRMELMAAIEALEALKE-------PCEVTLYTDSQYVRQ 75 (150)
T ss_pred eEEEEEEecccCCCCceEEEEEEEECCeeEEEecCCCCCcHHHHHHHHHHHHHHHcCC-------CCeEEEEECHHHHHH
Confidence 4889999998643 45666554 3333222 2345789999999999999998743 356999999999999
Q ss_pred HhhcC---------CCC-------cHHHHHHHHHHhc--ceEEecCCCCcc
Q psy7535 89 SLQNI---------ISS-------SPIALEIINLLHK--IQCQVRPSHFNM 121 (199)
Q Consensus 89 aI~n~---------~~~-------s~i~~~I~~ll~~--I~l~WiP~h~nR 121 (199)
+|..+ ..+ .++.++|.+++.. |.|.|+|+|.++
T Consensus 76 ~i~~w~~~Wk~~~~~~~~g~~v~n~dl~~~i~~l~~~~~v~~~wV~~H~~~ 126 (150)
T PRK00203 76 GITEWIHGWKKNGWKTADKKPVKNVDLWQRLDAALKRHQIKWHWVKGHAGH 126 (150)
T ss_pred HHHHHHHHHHHcCCcccCCCccccHHHHHHHHHHhccCceEEEEecCCCCC
Confidence 99851 111 1356677766654 999999999973
No 5
>COG0328 RnhA Ribonuclease HI [DNA replication, recombination, and repair]
Probab=99.57 E-value=3.6e-14 Score=113.27 Aligned_cols=104 Identities=17% Similarity=0.137 Sum_probs=77.7
Q ss_pred CceEEEEcCCCCCC-c-eEEEEEE--cCeeeEEecC-CCcchhHHHHHHHHHHHHHHHhhCCCCCCCCcEEEEcCcHHHH
Q psy7535 13 NYKQIFTDASKNEH-S-VSSAFCC--EETKFSVKLD-PRISICNAELISIQYAISFIISTTPLQVPTPKFVLYSDSLSAL 87 (199)
Q Consensus 13 ~~~~IyTDgSk~~~-~-~G~ai~~--~~~~~~~~l~-~~~Si~tAEl~AI~~AL~~i~~~~~~~~~~~~i~I~SDS~sal 87 (199)
..+.||||||...+ | .|+|++. ++..+.+..+ ..+|+..||+.|++.||+.+.+. +...+.|+|||+.++
T Consensus 2 ~~v~if~DGa~~gNpG~gG~g~vl~~~~~~~~~s~~~~~tTNNraEl~A~i~AL~~l~~~-----~~~~v~l~tDS~yv~ 76 (154)
T COG0328 2 KKVEIFTDGACLGNPGPGGWGAVLRYGDGEKELSGGEGRTTNNRAELRALIEALEALKEL-----GACEVTLYTDSKYVV 76 (154)
T ss_pred CceEEEecCccCCCCCCceEEEEEEcCCceEEEeeeeecccChHHHHHHHHHHHHHHHhc-----CCceEEEEecHHHHH
Confidence 45789999998443 3 4555444 3333323322 38999999999999999999987 889999999999999
Q ss_pred HHhhcCCC---------------Cc-HHHHHHHHHHhc---ceEEecCCCCcc
Q psy7535 88 QSLQNIIS---------------SS-PIALEIINLLHK---IQCQVRPSHFNM 121 (199)
Q Consensus 88 ~aI~n~~~---------------~s-~i~~~I~~ll~~---I~l~WiP~h~nR 121 (199)
++|..+.. ++ ++.+++.++.++ |.+.|||+|.++
T Consensus 77 ~~i~~w~~~w~~~~w~~~~~~pvkn~dl~~~~~~~~~~~~~v~~~WVkgH~g~ 129 (154)
T COG0328 77 EGITRWIVKWKKNGWKTADKKPVKNKDLWEELDELLKRHELVFWEWVKGHAGH 129 (154)
T ss_pred HHHHHHHhhccccCccccccCccccHHHHHHHHHHHhhCCeEEEEEeeCCCCC
Confidence 99983311 01 356677777665 899999999984
No 6
>PRK13907 rnhA ribonuclease H; Provisional
Probab=99.56 E-value=3.4e-14 Score=109.06 Aligned_cols=105 Identities=12% Similarity=0.161 Sum_probs=81.4
Q ss_pred eEEEEcCCCCCC--ceEEEEEEcCee--eEEec-CCCcchhHHHHHHHHHHHHHHHhhCCCCCCCCcEEEEcCcHHHHHH
Q psy7535 15 KQIFTDASKNEH--SVSSAFCCEETK--FSVKL-DPRISICNAELISIQYAISFIISTTPLQVPTPKFVLYSDSLSALQS 89 (199)
Q Consensus 15 ~~IyTDgSk~~~--~~G~ai~~~~~~--~~~~l-~~~~Si~tAEl~AI~~AL~~i~~~~~~~~~~~~i~I~SDS~sal~a 89 (199)
++||||||...+ ..|+|++..+.. ...+. ...+|+..||+.|++.||+.+... ....+.|+|||+.+++.
T Consensus 2 ~~iy~DGa~~~~~g~~G~G~vi~~~~~~~~~~~~~~~~tn~~AE~~All~aL~~a~~~-----g~~~v~i~sDS~~vi~~ 76 (128)
T PRK13907 2 IEVYIDGASKGNPGPSGAGVFIKGVQPAVQLSLPLGTMSNHEAEYHALLAALKYCTEH-----NYNIVSFRTDSQLVERA 76 (128)
T ss_pred EEEEEeeCCCCCCCccEEEEEEEECCeeEEEEecccccCCcHHHHHHHHHHHHHHHhC-----CCCEEEEEechHHHHHH
Confidence 579999998543 577887665432 22222 356899999999999999999987 77789999999999999
Q ss_pred hhcCCCCc----HHHHHHHHHHhc---ceEEecCCCCccchh
Q psy7535 90 LQNIISSS----PIALEIINLLHK---IQCQVRPSHFNMREQ 124 (199)
Q Consensus 90 I~n~~~~s----~i~~~I~~ll~~---I~l~WiP~h~nR~~~ 124 (199)
+++.+.++ ++.+++..++.+ +.|.|+|.+.|+...
T Consensus 77 ~~~~~~~~~~~~~l~~~~~~l~~~f~~~~~~~v~r~~N~~Ad 118 (128)
T PRK13907 77 VEKEYAKNKMFAPLLEEALQYIKSFDLFFIKWIPSSQNKVAD 118 (128)
T ss_pred HhHHHhcChhHHHHHHHHHHHHhcCCceEEEEcCchhchhHH
Confidence 99865433 467777777765 778999999886543
No 7
>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=99.52 E-value=1.9e-13 Score=100.29 Aligned_cols=100 Identities=18% Similarity=0.292 Sum_probs=77.3
Q ss_pred EEEEcCCCCCC--ceEEEEEEcCe--eeEEe---cCCCcchhHHHHHHHHHHHHHHHhhCCCCCCCCcEEEEcCcHHHHH
Q psy7535 16 QIFTDASKNEH--SVSSAFCCEET--KFSVK---LDPRISICNAELISIQYAISFIISTTPLQVPTPKFVLYSDSLSALQ 88 (199)
Q Consensus 16 ~IyTDgSk~~~--~~G~ai~~~~~--~~~~~---l~~~~Si~tAEl~AI~~AL~~i~~~~~~~~~~~~i~I~SDS~sal~ 88 (199)
.+|||||...+ +.|+|++..+. ...+. .....|++.||+.|++.||+.+... ...++.|+|||+.+++
T Consensus 1 ~~~~Dgs~~~~~~~~g~g~v~~~~~~~~~~~~~~~~~~~s~~~aEl~al~~al~~~~~~-----~~~~i~i~~Ds~~~~~ 75 (130)
T cd06222 1 VIYTDGSCRGNPGPAGAGVVLRDPGGEVLLSGGLLGGNTTNNRAELLALIEALELALEL-----GGKKVNIYTDSQYVIN 75 (130)
T ss_pred CEEecccCCCCCCceEEEEEEEeCCCeEEEeccccCCCCcHHHHHHHHHHHHHHHHHhC-----CCceEEEEECHHHHHH
Confidence 48999999655 67777665443 22222 2257899999999999999999876 8899999999999999
Q ss_pred HhhcCCC-----CcHHHHHHHHHHhc---ceEEecCCCCc
Q psy7535 89 SLQNIIS-----SSPIALEIINLLHK---IQCQVRPSHFN 120 (199)
Q Consensus 89 aI~n~~~-----~s~i~~~I~~ll~~---I~l~WiP~h~n 120 (199)
.+++... ..++...+.+++.+ ++|.|+|+|.+
T Consensus 76 ~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~i~~v~~h~~ 115 (130)
T cd06222 76 ALTGWYEGKPVKNVDLWQRLLALLKRFHKVRFEWVPGHSG 115 (130)
T ss_pred HhhccccCCChhhHHHHHHHHHHHhCCCeEEEEEcCCCCC
Confidence 9998754 12466677777743 99999999764
No 8
>KOG3752|consensus
Probab=99.34 E-value=6.2e-12 Score=111.85 Aligned_cols=118 Identities=20% Similarity=0.122 Sum_probs=91.2
Q ss_pred hhhhhcccCCCceEEEEcCCCCCC-----ceEEEEEEcCe---eeEEecC-CCcchhHHHHHHHHHHHHHHHhhCCCCCC
Q psy7535 3 LKTSIPLLLPNYKQIFTDASKNEH-----SVSSAFCCEET---KFSVKLD-PRISICNAELISIQYAISFIISTTPLQVP 73 (199)
Q Consensus 3 ~~~~i~~~~~~~~~IyTDgSk~~~-----~~G~ai~~~~~---~~~~~l~-~~~Si~tAEl~AI~~AL~~i~~~~~~~~~ 73 (199)
|+.++..++.+.+.||||||...+ .+|.||+.++. +.+..+. +..+++.||+.||.+||+-+.+. +
T Consensus 201 ~k~~~d~e~~~~~vvytDGS~~~ng~~~~~AGyGvywg~~~e~N~s~pv~~g~qtNnrAEl~Av~~ALkka~~~-----~ 275 (371)
T KOG3752|consen 201 EKLENDREEIEIQVVYTDGSSSGNGRKSSRAGYGVYWGPGHELNVSGPLAGGRQTNNRAELIAAIEALKKARSK-----N 275 (371)
T ss_pred hhcccccccccceEEEecCccccCCCCCCcceeEEeeCCCCcccccccCCCCcccccHHHHHHHHHHHHHHHhc-----C
Confidence 667777788888999999998553 58999988764 4777776 88999999999999999999887 7
Q ss_pred CCcEEEEcCcHHHHHHhhcCCCC-----------cH----------HHHHHHHHHhc-----ceEEecCCCCc-cchhh
Q psy7535 74 TPKFVLYSDSLSALQSLQNIISS-----------SP----------IALEIINLLHK-----IQCQVRPSHFN-MREQV 125 (199)
Q Consensus 74 ~~~i~I~SDS~sal~aI~n~~~~-----------s~----------i~~~I~~ll~~-----I~l~WiP~h~n-R~~~~ 125 (199)
..++.|.|||+.++++|+.+... ++ ...++-++.++ |.+.|+|+|.+ +.++.
T Consensus 276 ~~kv~I~TDS~~~i~~l~~wv~~~k~~~~k~~~~~~~i~~~v~n~~~~~e~~~l~q~~~~~~vq~~~V~Gh~gi~gne~ 354 (371)
T KOG3752|consen 276 INKVVIRTDSEYFINSLTLWVQGWKKNGWKTSNGSDRICAYVKNQDFFNELDELEQEISNKKVQQEYVGGHSGILGNEM 354 (371)
T ss_pred CCcEEEEechHHHHHHHHHHHhhhccCccccccCCCccceeeecchHHHHHHHHHhhhccCceEEEEecCcCCcchHHH
Confidence 77999999999999999865320 12 12333343332 99999999987 44443
No 9
>PRK07708 hypothetical protein; Validated
Probab=99.26 E-value=8.2e-11 Score=99.11 Aligned_cols=111 Identities=12% Similarity=0.049 Sum_probs=79.9
Q ss_pred hcccCCCceEEEEcCCCCC--CceEEEEEE--cCeeeEE------ecCCCcchhHHHHHHHHHHHHHHHhhCCCCCCCC-
Q psy7535 7 IPLLLPNYKQIFTDASKNE--HSVSSAFCC--EETKFSV------KLDPRISICNAELISIQYAISFIISTTPLQVPTP- 75 (199)
Q Consensus 7 i~~~~~~~~~IyTDgSk~~--~~~G~ai~~--~~~~~~~------~l~~~~Si~tAEl~AI~~AL~~i~~~~~~~~~~~- 75 (199)
|..+ |+...+|+|||... ++.|+|++. ++....+ .+....|+..||+.|++.||+.+.+. +.+
T Consensus 67 ~~~e-p~~~~vY~DGs~~~n~g~aG~GvVI~~~~g~~~~~~~~~~~l~~~~TNN~AEy~Ali~aL~~A~e~-----g~~~ 140 (219)
T PRK07708 67 VEEE-PHEILVYFDGGFDKETKLAGLGIVIYYKQGNKRYRIRRNAYIEGIYDNNEAEYAALYYAMQELEEL-----GVKH 140 (219)
T ss_pred hccC-CCcEEEEEeeccCCCCCCcEEEEEEEECCCCEEEEEEeeccccccccCcHHHHHHHHHHHHHHHHc-----CCCc
Confidence 3343 45689999999743 356666544 3222222 34556899999999999999999987 443
Q ss_pred -cEEEEcCcHHHHHHhhcCCC-Cc----HHHHHHHHHHhc----ceEEecCCCCccch
Q psy7535 76 -KFVLYSDSLSALQSLQNIIS-SS----PIALEIINLLHK----IQCQVRPSHFNMRE 123 (199)
Q Consensus 76 -~i~I~SDS~sal~aI~n~~~-~s----~i~~~I~~ll~~----I~l~WiP~h~nR~~ 123 (199)
.+.|++||+.+++.+.+.+. .+ ++..++..++++ +.+.|+|...|+..
T Consensus 141 ~~V~I~~DSqlVi~qi~g~wk~~~~~l~~y~~~i~~l~~~~~l~~~~~~VpR~~N~~A 198 (219)
T PRK07708 141 EPVTFRGDSQVVLNQLAGEWPCYDEHLNHWLDRIEQKLKQLKLTPVYEPISRKQNKEA 198 (219)
T ss_pred ceEEEEeccHHHHHHhCCCceeCChhHHHHHHHHHHHHhhCCceEEEEECCchhhhHH
Confidence 48999999999999998754 23 356666666654 66789999888544
No 10
>PRK07238 bifunctional RNase H/acid phosphatase; Provisional
Probab=99.19 E-value=2.1e-10 Score=102.78 Aligned_cols=102 Identities=11% Similarity=0.027 Sum_probs=77.4
Q ss_pred ceEEEEcCCCCCC--ceEEEEEEcCe--e---eEEe-cCCCcchhHHHHHHHHHHHHHHHhhCCCCCCCCcEEEEcCcHH
Q psy7535 14 YKQIFTDASKNEH--SVSSAFCCEET--K---FSVK-LDPRISICNAELISIQYAISFIISTTPLQVPTPKFVLYSDSLS 85 (199)
Q Consensus 14 ~~~IyTDgSk~~~--~~G~ai~~~~~--~---~~~~-l~~~~Si~tAEl~AI~~AL~~i~~~~~~~~~~~~i~I~SDS~s 85 (199)
.+.||||||...+ ..|+|++..+. . ..++ ....+|+..||+.|++.||+++.+. ....+.|++||+.
T Consensus 2 ~~~i~~DGa~~~n~g~aG~G~vi~~~~~~~~~~~~~~~~~~~tnn~AE~~All~gL~~a~~~-----g~~~v~i~~DS~l 76 (372)
T PRK07238 2 KVVVEADGGSRGNPGPAGYGAVVWDADRGEVLAERAEAIGRATNNVAEYRGLIAGLEAAAEL-----GATEVEVRMDSKL 76 (372)
T ss_pred eEEEEecCCCCCCCCceEEEEEEEeCCCCcEEEEeecccCCCCchHHHHHHHHHHHHHHHhC-----CCCeEEEEeCcHH
Confidence 3689999998654 46777655432 1 1222 2347888999999999999999988 7789999999999
Q ss_pred HHHHhhcCCC-Cc----HHHHHHHHHHhc---ceEEecCCCCc
Q psy7535 86 ALQSLQNIIS-SS----PIALEIINLLHK---IQCQVRPSHFN 120 (199)
Q Consensus 86 al~aI~n~~~-~s----~i~~~I~~ll~~---I~l~WiP~h~n 120 (199)
+++.+.+.+. ++ .+..++.++.++ +++.|+|...|
T Consensus 77 vi~~i~~~~~~~~~~l~~~~~~i~~l~~~f~~~~i~~v~r~~N 119 (372)
T PRK07238 77 VVEQMSGRWKVKHPDMKPLAAQARELASQFGRVTYTWIPRARN 119 (372)
T ss_pred HHHHhCCCCccCChHHHHHHHHHHHHHhcCCceEEEECCchhh
Confidence 9999987653 33 345567776665 99999998777
No 11
>PF13456 RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EHG_A 3HST_B.
Probab=98.72 E-value=6.3e-08 Score=68.08 Aligned_cols=69 Identities=22% Similarity=0.259 Sum_probs=55.1
Q ss_pred hhHHHHHHHHHHHHHHHhhCCCCCCCCcEEEEcCcHHHHHHhhcCCCC----cHHHHHHHHHHhc---ceEEecCCCCcc
Q psy7535 49 ICNAELISIQYAISFIISTTPLQVPTPKFVLYSDSLSALQSLQNIISS----SPIALEIINLLHK---IQCQVRPSHFNM 121 (199)
Q Consensus 49 i~tAEl~AI~~AL~~i~~~~~~~~~~~~i~I~SDS~sal~aI~n~~~~----s~i~~~I~~ll~~---I~l~WiP~h~nR 121 (199)
+..||+.|++.||+++.+. +..++.|.|||+.+++.|++.... ..++.+|+.++++ +.+.|+|...|+
T Consensus 1 ~~~aE~~al~~al~~a~~~-----g~~~i~v~sDs~~vv~~i~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~i~r~~N~ 75 (87)
T PF13456_consen 1 PLEAEALALLEALQLAWEL-----GIRKIIVESDSQLVVDAINGRSSSRSELRPLIQDIRSLLDRFWNVSVSHIPREQNK 75 (87)
T ss_dssp HHHHHHHHHHHHHHHHHCC-----T-SCEEEEES-HHHHHHHTTSS---SCCHHHHHHHHHHHCCCSCEEEEE--GGGSH
T ss_pred CcHHHHHHHHHHHHHHHHC-----CCCEEEEEecCccccccccccccccccccccchhhhhhhccccceEEEEEChHHhH
Confidence 3689999999999999988 899999999999999999887432 2678889888886 999999987775
Q ss_pred c
Q psy7535 122 R 122 (199)
Q Consensus 122 ~ 122 (199)
.
T Consensus 76 ~ 76 (87)
T PF13456_consen 76 V 76 (87)
T ss_dssp H
T ss_pred H
Confidence 3
No 12
>PF13966 zf-RVT: zinc-binding in reverse transcriptase
Probab=96.23 E-value=0.0021 Score=45.96 Aligned_cols=29 Identities=21% Similarity=0.264 Sum_probs=24.0
Q ss_pred cCCCCCCCcccCC-ccccccchhhcccchh
Q psy7535 143 MKREPPPECDTYN-CRLTVKHLLKYCNKYQ 171 (199)
Q Consensus 143 ~~~~~~p~C~~Cg-~~~tv~Hil~~Cp~~~ 171 (199)
.+...++.|..|+ ..||+.|+|++||...
T Consensus 54 r~~~~~~~C~~C~~~~Et~~Hlf~~C~~a~ 83 (86)
T PF13966_consen 54 RGIQVDPICPLCGNEEETIEHLFFHCPFAR 83 (86)
T ss_pred cCCccCCccccCCCccccccceeccCcCcc
Confidence 3456678999999 4899999999999754
No 13
>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=95.71 E-value=0.024 Score=47.59 Aligned_cols=92 Identities=22% Similarity=0.245 Sum_probs=62.4
Q ss_pred CCceEEEEcCCCCCCceEEEEEEcCeeeEEecCCCcchhHHHHHHHHHHHHHHHhhCCCCCCCCcEEEEcCcHHHHHHhh
Q psy7535 12 PNYKQIFTDASKNEHSVSSAFCCEETKFSVKLDPRISICNAELISIQYAISFIISTTPLQVPTPKFVLYSDSLSALQSLQ 91 (199)
Q Consensus 12 ~~~~~IyTDgSk~~~~~G~ai~~~~~~~~~~l~~~~Si~tAEl~AI~~AL~~i~~~~~~~~~~~~i~I~SDS~sal~aI~ 91 (199)
+-.-+||+|+.- +|.|+.+......+....--.|++||+.|...|--++... .|.|||-.++..
T Consensus 92 ~~lc~VfaDATp----Tgwgi~i~~~~~~~Tfs~~l~IhtaELlaaClAr~~~~~r----------~l~tDnt~Vlsr-- 155 (245)
T PF00336_consen 92 PGLCQVFADATP----TGWGISITGQRMRGTFSKPLPIHTAELLAACLARLMSGAR----------CLGTDNTVVLSR-- 155 (245)
T ss_pred CCCCceeccCCC----CcceeeecCceeeeeecccccchHHHHHHHHHHHhccCCc----------EEeecCcEEEec--
Confidence 334589999876 5555556666656666667789999999998887666432 499999877642
Q ss_pred cCCCCcH--HHHHHHHHHhcceEEecCCCCc
Q psy7535 92 NIISSSP--IALEIINLLHKIQCQVRPSHFN 120 (199)
Q Consensus 92 n~~~~s~--i~~~I~~ll~~I~l~WiP~h~n 120 (199)
.+.+=| ++-....++..+.|..+|+..|
T Consensus 156 -kyts~PW~lac~A~wiLrgts~~yVPS~~N 185 (245)
T PF00336_consen 156 -KYTSFPWLLACAANWILRGTSFYYVPSKYN 185 (245)
T ss_pred -ccccCcHHHHHHHHHhhcCceEEEeccccC
Confidence 222223 2333334455599999999888
No 14
>PF05380 Peptidase_A17: Pao retrotransposon peptidase ; InterPro: IPR008042 This signature identifies members of the Pao retrotransposon family.
Probab=91.99 E-value=0.54 Score=37.35 Aligned_cols=53 Identities=15% Similarity=0.235 Sum_probs=36.1
Q ss_pred CceEEEEcCCCCCCceEEEEEEcC---eeeEE-------ec-C-CCcchhHHHHHHHHHHHHHHHhh
Q psy7535 13 NYKQIFTDASKNEHSVSSAFCCEE---TKFSV-------KL-D-PRISICNAELISIQYAISFIIST 67 (199)
Q Consensus 13 ~~~~IyTDgSk~~~~~G~ai~~~~---~~~~~-------~l-~-~~~Si~tAEl~AI~~AL~~i~~~ 67 (199)
-.+++|+|||+ .+.|+.++... ..... +. | ...||=.-|+.|+..|.+++...
T Consensus 80 ~~L~~F~DAS~--~aygavvYlr~~~~~~~~~~ll~aKsrv~P~k~~tIPRlEL~a~~l~~~l~~~~ 144 (159)
T PF05380_consen 80 VELHVFCDASE--SAYGAVVYLRSYSDGSVQVRLLFAKSRVAPLKTVTIPRLELLAALLGVRLANTV 144 (159)
T ss_pred eeeeEeecccc--cceeeEeEeeeccCCceeeeeeeecccccCCCCCcHHHHHHHHHHHHHHHHHHH
Confidence 35789999995 55666654432 22111 12 2 35699999999999999998653
No 15
>COG0295 Cdd Cytidine deaminase [Nucleotide transport and metabolism]
Probab=71.45 E-value=7.2 Score=30.59 Aligned_cols=68 Identities=16% Similarity=0.137 Sum_probs=45.8
Q ss_pred CceEEEEEEcCeeeEEecCC-----CcchhHHHHHHHHHHHHHHHhhCCCCCCCCcEEEEcCcHHHHHHhhcCCCCcHHH
Q psy7535 26 HSVSSAFCCEETKFSVKLDP-----RISICNAELISIQYAISFIISTTPLQVPTPKFVLYSDSLSALQSLQNIISSSPIA 100 (199)
Q Consensus 26 ~~~G~ai~~~~~~~~~~l~~-----~~Si~tAEl~AI~~AL~~i~~~~~~~~~~~~i~I~SDS~sal~aI~n~~~~s~i~ 100 (199)
=.||+++...+.+..++-.= ..++ =||-.||.+|+.. -. .....+++++|+ ..+..+-..=
T Consensus 26 F~VGAa~~t~~G~i~tG~NiEnasy~~t~-CAErsAI~~ais~-G~-----~~~~~v~v~~~~-------~~~~sPCG~C 91 (134)
T COG0295 26 FKVGAALRTKDGRIYTGANVENASYGLTV-CAERSAIFKAISE-GK-----RKFDAVVVVADT-------GKPVSPCGAC 91 (134)
T ss_pred CcEEEEEEeCCCCEEEEEeeecccccchh-hHHHHHHHHHHHc-CC-----CcEEEEEEEcCC-------CCCcCCcHHH
Confidence 37999998888776555421 2233 3999999999887 32 367889999998 3444455565
Q ss_pred HHHHHHH
Q psy7535 101 LEIINLL 107 (199)
Q Consensus 101 ~~I~~ll 107 (199)
|+...-+
T Consensus 92 RQ~i~Ef 98 (134)
T COG0295 92 RQVLAEF 98 (134)
T ss_pred HHHHHHh
Confidence 5555444
No 16
>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=65.74 E-value=31 Score=25.28 Aligned_cols=54 Identities=17% Similarity=0.167 Sum_probs=34.5
Q ss_pred CCCceEEEEEEcCee-eEEecC----CCcchhHHHHHHHHHHHHHHHhhCCCCCCCCcEEEEcC
Q psy7535 24 NEHSVSSAFCCEETK-FSVKLD----PRISICNAELISIQYAISFIISTTPLQVPTPKFVLYSD 82 (199)
Q Consensus 24 ~~~~~G~ai~~~~~~-~~~~l~----~~~Si~tAEl~AI~~AL~~i~~~~~~~~~~~~i~I~SD 82 (199)
.+..+|+.++.++.+ ...+.. +.....-||..||..|.+..... .....++|+.
T Consensus 15 ~~~~vgaviv~~~~~ii~~g~n~~~~~~~~~~HAE~~ai~~~~~~~~~~-----~~~~~~ly~t 73 (109)
T cd01285 15 GEVPFGAVIVDDDGKVIARGHNRVEQDGDPTAHAEIVAIRNAARRLGSY-----LLSGCTLYTT 73 (109)
T ss_pred CCCcEEEEEEeCCCEEEEEEeCCCCCCCCCcccHHHHHHHHHHHHhCCC-----ccCCeEEEEe
Confidence 345789988877433 333332 23467789999999998775432 3445666654
No 17
>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=54.45 E-value=8.4 Score=19.61 Aligned_cols=17 Identities=24% Similarity=0.489 Sum_probs=13.5
Q ss_pred CcccCCccccccchhhcccc
Q psy7535 150 ECDTYNCRLTVKHLLKYCNK 169 (199)
Q Consensus 150 ~C~~Cg~~~tv~Hil~~Cp~ 169 (199)
.|-.||.. .|+-.+||+
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 57778765 899999985
No 18
>PF15322 PMSI1: Protein missing in infertile sperm 1, putative
Probab=51.76 E-value=9.5 Score=33.57 Aligned_cols=18 Identities=28% Similarity=0.242 Sum_probs=14.1
Q ss_pred cchhhhhhhhhccCcccc
Q psy7535 121 MREQVSLTRLRIGHTNLT 138 (199)
Q Consensus 121 R~~~~~l~rlR~GHt~l~ 138 (199)
|-..-+|.|||+.|-.-|
T Consensus 210 rLRvGALsqLrTehrPCt 227 (311)
T PF15322_consen 210 RLRVGALSQLRTEHRPCT 227 (311)
T ss_pred ceecchhhhhhhccCCcc
Confidence 444568999999998887
No 19
>PF00383 dCMP_cyt_deam_1: Cytidine and deoxycytidylate deaminase zinc-binding region; InterPro: IPR002125 Cytidine deaminase (3.5.4.5 from EC) (cytidine aminohydrolase) catalyzes the hydrolysis of cytidine into uridine and ammonia while deoxycytidylate deaminase (3.5.4.12 from EC) (dCMP deaminase) hydrolyzes dCMP into dUMP. Both enzymes are known to bind zinc and to require it for their catalytic activity [, ]. These two enzymes do not share any sequence similarity with the exception of a region that contains three conserved histidine and cysteine residues which are thought to be involved in the binding of the catalytic zinc ion. Such a region is also found in other proteins [, ]: Yeast cytosine deaminase (3.5.4.1 from EC) (gene FCY1) which transforms cytosine into uracil. Mammalian apolipoprotein B mRNA editing protein, responsible for the postranscriptional editing of a CAA codon into a UAA (stop) codon in the APOB mRNA. Riboflavin biosynthesis protein ribG, which converts 2,5-diamino-6-(ribosylamino)-4(3H)-pyrimidinone 5'-phosphate into 5-amino-6-(ribosylamino)-2,4(1H,3H)-pyrimidinedione 5'-phosphate. Bacillus cereus blasticidin-S deaminase (3.5.4.23 from EC), which catalyzes the deamination of the cytosine moiety of the antibiotics blasticidin S, cytomycin and acetylblasticidin S. Bacillus subtilis protein comEB. This protein is required for the binding and uptake of transforming DNA. B. subtilis hypothetical protein yaaJ. Escherichia coli hypothetical protein yfhC. Yeast hypothetical protein YJL035c. ; GO: 0008270 zinc ion binding, 0016787 hydrolase activity; PDB: 3MPZ_C 3R2N_C 1WKQ_A 1TIY_B 2B3J_C 2O7P_B 2OBC_A 2G6V_B 2D30_B 2D5N_B ....
Probab=49.38 E-value=45 Score=23.58 Aligned_cols=52 Identities=13% Similarity=0.105 Sum_probs=31.5
Q ss_pred CCCceEEEEEEc-CeeeEEecCC----CcchhHHHHHHHHHHHHHHHhhCCCCCCCCcEEEEc
Q psy7535 24 NEHSVSSAFCCE-ETKFSVKLDP----RISICNAELISIQYAISFIISTTPLQVPTPKFVLYS 81 (199)
Q Consensus 24 ~~~~~G~ai~~~-~~~~~~~l~~----~~Si~tAEl~AI~~AL~~i~~~~~~~~~~~~i~I~S 81 (199)
.+..+|++++.+ +.....+... ....--||..||..|-+. ... .....++|+
T Consensus 22 ~~~~vgaviv~~~~~~i~~g~n~~~~~~~~~~HAE~~Ai~~~~~~-~~~-----~~~~~~lyv 78 (102)
T PF00383_consen 22 GNFPVGAVIVDPDGKIIATGYNGEPPGKNPTIHAEMNAIRKAARN-GGS-----SLKGCTLYV 78 (102)
T ss_dssp TSSSEEEEEEETTTEEEEEEESBHHSTTGGTB-HHHHHHHHHHHT-TSS-----GETTEEEEE
T ss_pred CCCCEEEEEEeccCccEEEEeeeeeeeccccccchhhhhhhhhhh-ccc-----cccCccccc
Confidence 455799999985 4555444432 223456999999888877 221 234456665
No 20
>COG0590 CumB Cytosine/adenosine deaminases [Nucleotide transport and metabolism / Translation, ribosomal structure and biogenesis]
Probab=49.05 E-value=54 Score=25.87 Aligned_cols=43 Identities=14% Similarity=0.155 Sum_probs=27.6
Q ss_pred CCceEEEEEEcCeeeEEe-----cCCCcchhHHHHHHHHHHHHHHHhh
Q psy7535 25 EHSVSSAFCCEETKFSVK-----LDPRISICNAELISIQYAISFIIST 67 (199)
Q Consensus 25 ~~~~G~ai~~~~~~~~~~-----l~~~~Si~tAEl~AI~~AL~~i~~~ 67 (199)
+..+|+.+|..+.....+ ....--.--||..||..|-+.+...
T Consensus 27 e~PvGaviV~~~~~ii~~~~N~~~~~~dptaHAEi~air~a~~~~~~~ 74 (152)
T COG0590 27 EVPVGAVIVDADGEIIARGHNRREEDNDPTAHAEILAIRAAAETLGNY 74 (152)
T ss_pred CCCEEEEEEcCCCCEEEEecCccccCCCccccHHHHHHHHHHHhhCCC
Confidence 346888888744432221 2233334479999999999998654
No 21
>PRK10860 tRNA-specific adenosine deaminase; Provisional
Probab=48.64 E-value=66 Score=26.02 Aligned_cols=41 Identities=10% Similarity=0.123 Sum_probs=24.9
Q ss_pred CCceEEEEEEcCeeeEEecC----CCcchhHHHHHHHHHHHHHHH
Q psy7535 25 EHSVSSAFCCEETKFSVKLD----PRISICNAELISIQYAISFII 65 (199)
Q Consensus 25 ~~~~G~ai~~~~~~~~~~l~----~~~Si~tAEl~AI~~AL~~i~ 65 (199)
+..+|+.++..+.-...+-. .....--||..||..|.+.+.
T Consensus 32 ~~pvGAVIV~~g~IIa~g~N~~~~~~d~~~HAEi~Ai~~a~~~~~ 76 (172)
T PRK10860 32 EVPVGAVLVHNNRVIGEGWNRPIGRHDPTAHAEIMALRQGGLVLQ 76 (172)
T ss_pred CCCEEEEEEeCCEEEEEeeCCCCCCCCCccCHHHHHHHHHHHhcC
Confidence 34789887765443332221 122345699999999977554
No 22
>PRK06848 hypothetical protein; Validated
Probab=48.12 E-value=35 Score=26.73 Aligned_cols=53 Identities=21% Similarity=0.072 Sum_probs=34.1
Q ss_pred CCceEEEEEEcCeeeEEecCCCc----chhHHHHHHHHHHHHHHHhhCCCCCCCCcEEEEcCc
Q psy7535 25 EHSVSSAFCCEETKFSVKLDPRI----SICNAELISIQYAISFIISTTPLQVPTPKFVLYSDS 83 (199)
Q Consensus 25 ~~~~G~ai~~~~~~~~~~l~~~~----Si~tAEl~AI~~AL~~i~~~~~~~~~~~~i~I~SDS 83 (199)
+.+||+|+...+.....+..-+. .--=||..||..|+..=. .....+.+.+++
T Consensus 26 ~f~VgAa~l~~~G~i~~G~NvEnas~~~tiCAEr~Ai~~av~~g~------~~i~~i~~v~~~ 82 (139)
T PRK06848 26 WHHVGAALRTKTGRIYAAVHLEAYVGRITVCAEAIAIGKAISEGD------HEIDTIVAVRHP 82 (139)
T ss_pred CCcEEEEEEeCCCCEEEEEEeecCCCCcccCHHHHHHHHHHHcCC------CceEEEEEEecC
Confidence 46899999998887666553222 223599999999885421 133445555554
No 23
>PRK05578 cytidine deaminase; Validated
Probab=44.95 E-value=17 Score=28.10 Aligned_cols=51 Identities=16% Similarity=-0.044 Sum_probs=33.9
Q ss_pred ceEEEEEEcCeeeEEecCC----CcchhHHHHHHHHHHHHHHHhhCCCCCCCCcEEEEcCc
Q psy7535 27 SVSSAFCCEETKFSVKLDP----RISICNAELISIQYAISFIISTTPLQVPTPKFVLYSDS 83 (199)
Q Consensus 27 ~~G~ai~~~~~~~~~~l~~----~~Si~tAEl~AI~~AL~~i~~~~~~~~~~~~i~I~SDS 83 (199)
.||+|+...+.+...+..- +.----||..||..|+..=. .....++|.+|+
T Consensus 25 ~Vgaa~~~~~G~i~~G~nvEna~~~~~~CAE~~Ai~~av~~G~------~~i~~i~vv~~~ 79 (131)
T PRK05578 25 PVGAALLTDDGRIYTGCNIENASYGLTNCAERTAIFKAISEGG------GRLVAIACVGET 79 (131)
T ss_pred ceEEEEEeCCCCEEEEEEeeCccccCCcCHHHHHHHHHHHcCC------CceEEEEEEecC
Confidence 6999999988775555431 21233579999999874321 245677888876
No 24
>PF13005 zf-IS66: zinc-finger binding domain of transposase IS66 ; InterPro: IPR024474 This entry represents a predicted helix-turn-helix domain from insertion element IS66 transposases [].
Probab=43.91 E-value=12 Score=23.21 Aligned_cols=13 Identities=23% Similarity=0.498 Sum_probs=10.1
Q ss_pred CCCCcccCCcccc
Q psy7535 147 PPPECDTYNCRLT 159 (199)
Q Consensus 147 ~~p~C~~Cg~~~t 159 (199)
|+..|+.||..+.
T Consensus 1 e~~~C~~Cg~~l~ 13 (47)
T PF13005_consen 1 EPRACPDCGGELK 13 (47)
T ss_pred CCCcCCCCCceee
Confidence 5678999998654
No 25
>PRK08298 cytidine deaminase; Validated
Probab=43.02 E-value=36 Score=26.61 Aligned_cols=51 Identities=14% Similarity=0.095 Sum_probs=33.8
Q ss_pred ceEEEEEEcCeeeEEecCCCc----chhHHHHHHHHHHHHHHHhhCCCCCCCCcEEEEcCc
Q psy7535 27 SVSSAFCCEETKFSVKLDPRI----SICNAELISIQYAISFIISTTPLQVPTPKFVLYSDS 83 (199)
Q Consensus 27 ~~G~ai~~~~~~~~~~l~~~~----Si~tAEl~AI~~AL~~i~~~~~~~~~~~~i~I~SDS 83 (199)
+||+|+...+.+...+..-+. .--=||..||..|+..= .+....+.|.+|.
T Consensus 24 ~VgAAllt~dG~i~tG~NvEnas~~~t~CAEr~Ai~~av~~G------~~~~~~i~v~~~~ 78 (136)
T PRK08298 24 GGAAAMRVEDGTILTSVAPEVINASTELCMETGAICEAHKLQ------KRVTHSICVAREN 78 (136)
T ss_pred ceeEEEEeCCCCEEEEEeecCCCCCcchhHHHHHHHHHHHCC------CceEEEEEEEcCC
Confidence 899999998887666554222 23358999999887431 1235566777776
No 26
>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=41.06 E-value=86 Score=23.56 Aligned_cols=39 Identities=10% Similarity=0.020 Sum_probs=26.0
Q ss_pred CCceEEEEEEcCee-eEEecCCCcchhHHHHHHHHHHHHH
Q psy7535 25 EHSVSSAFCCEETK-FSVKLDPRISICNAELISIQYAISF 63 (199)
Q Consensus 25 ~~~~G~ai~~~~~~-~~~~l~~~~Si~tAEl~AI~~AL~~ 63 (199)
+..+|+.++.++.+ ....-.......-||..||.+|.+.
T Consensus 18 ~~pvGaviv~~~g~iv~~g~n~~~~~~HAE~~ai~~a~~~ 57 (115)
T cd01284 18 NPPVGCVIVDDDGEIVGEGYHRKAGGPHAEVNALASAGEK 57 (115)
T ss_pred CCCEEEEEEeCCCeEEEEecCCCCCcccHHHHHHHHHhhc
Confidence 45789888876433 3333333335677999999998764
No 27
>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=40.80 E-value=1.1e+02 Score=23.30 Aligned_cols=16 Identities=25% Similarity=0.108 Sum_probs=12.3
Q ss_pred chhHHHHHHHHHHHHH
Q psy7535 48 SICNAELISIQYAISF 63 (199)
Q Consensus 48 Si~tAEl~AI~~AL~~ 63 (199)
...-||..||..|.+.
T Consensus 67 ~~~HAE~~Ai~~a~~~ 82 (131)
T cd01286 67 RTVHAEQNAILQAARH 82 (131)
T ss_pred CCCCHHHHHHHHHhHc
Confidence 4556999999988653
No 28
>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=39.29 E-value=63 Score=24.59 Aligned_cols=52 Identities=15% Similarity=0.034 Sum_probs=34.1
Q ss_pred CceEEEEEEcCeeeEEecCCCc----chhHHHHHHHHHHHHHHHhhCCCCCCCCcEEEEcCc
Q psy7535 26 HSVSSAFCCEETKFSVKLDPRI----SICNAELISIQYAISFIISTTPLQVPTPKFVLYSDS 83 (199)
Q Consensus 26 ~~~G~ai~~~~~~~~~~l~~~~----Si~tAEl~AI~~AL~~i~~~~~~~~~~~~i~I~SDS 83 (199)
-.+|++++..+.+...+..-+. .-.-||..||..|...-. .....+.+.+++
T Consensus 21 ~~vgAa~~~~~G~i~~G~n~e~~~~~~s~~AE~~Ai~~a~~~g~------~~i~~i~vv~~~ 76 (127)
T TIGR01354 21 FKVGAALLTKDGRIFTGVNVENASYPLTICAERSAIGKAISAGY------RKFVAIAVADSA 76 (127)
T ss_pred CeEEEEEEeCCCCEEEEEeecccCCCCCcCHHHHHHHHHHHcCC------CCeEEEEEEeCC
Confidence 4699999887766444443222 234689999998886521 146677888766
No 29
>PRK12411 cytidine deaminase; Provisional
Probab=36.43 E-value=61 Score=25.06 Aligned_cols=52 Identities=15% Similarity=0.027 Sum_probs=34.4
Q ss_pred CceEEEEEEcCeeeEEecCCCcchh----HHHHHHHHHHHHHHHhhCCCCCCCCcEEEEcCc
Q psy7535 26 HSVSSAFCCEETKFSVKLDPRISIC----NAELISIQYAISFIISTTPLQVPTPKFVLYSDS 83 (199)
Q Consensus 26 ~~~G~ai~~~~~~~~~~l~~~~Si~----tAEl~AI~~AL~~i~~~~~~~~~~~~i~I~SDS 83 (199)
-+||+|+...+.+...+.--+...| -||..||..|+..=. .....+.|.+|.
T Consensus 24 ~~VgAa~~t~~G~i~~G~nvEn~s~~~s~CAE~~Ai~~av~~g~------~~i~~i~v~~~~ 79 (132)
T PRK12411 24 FQVGAALLTQDGKVYRGCNVENASYGLCNCAERTALFKAVSEGD------KEFVAIAIVADT 79 (132)
T ss_pred CceEEEEEeCCCCEEEEEEeecCCCCcCcCHHHHHHHHHHHCCC------CceEEEEEEeCC
Confidence 4699999888877665553332223 699999998864321 245667777765
No 30
>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=32.65 E-value=23 Score=23.54 Aligned_cols=20 Identities=30% Similarity=0.564 Sum_probs=10.1
Q ss_pred CcccCCccccccchhhcccc
Q psy7535 150 ECDTYNCRLTVKHLLKYCNK 169 (199)
Q Consensus 150 ~C~~Cg~~~tv~Hil~~Cp~ 169 (199)
.|+.||+...-.|-...||+
T Consensus 35 ~Cp~CgAtGd~AHT~~yCP~ 54 (55)
T PF05741_consen 35 VCPICGATGDNAHTIKYCPK 54 (55)
T ss_dssp --TTT---GGG---GGG-TT
T ss_pred cCCCCcCcCccccccccCcC
Confidence 59999999999999999996
No 31
>TIGR03628 arch_S11P archaeal ribosomal protein S11P. This model describes exclusively the archaeal ribosomal protein S11P. It excludes homologous ribosomal proteins S14 from eukaryotes and S11 from bacteria.
Probab=31.82 E-value=2.3e+02 Score=21.51 Aligned_cols=78 Identities=13% Similarity=-0.061 Sum_probs=45.7
Q ss_pred hcccCCCceEEEEcCCCCCCceEEEEEEcCeeeEEecCCCcchhHHHHHHHHHHHHHHHhhCCCCCCCCcEEEEc-----
Q psy7535 7 IPLLLPNYKQIFTDASKNEHSVSSAFCCEETKFSVKLDPRISICNAELISIQYAISFIISTTPLQVPTPKFVLYS----- 81 (199)
Q Consensus 7 i~~~~~~~~~IyTDgSk~~~~~G~ai~~~~~~~~~~l~~~~Si~tAEl~AI~~AL~~i~~~~~~~~~~~~i~I~S----- 81 (199)
|..-+.|.+.--||-.+.+- + .+.......++-....|.|.|++.|-..| +.+.+. ..+.+.|.-
T Consensus 7 I~as~NNTiitvTD~~G~~~-~---~~~S~G~~g~kg~kk~TpyAAq~aa~~~~-~~~~~~-----Gi~~v~v~ikG~gg 76 (114)
T TIGR03628 7 IYSSFNNTIITITDITGAET-I---ARSSGGMVVKADRDESSPYAAMQAAGRAA-EKAKER-----GITGLHIKVRAPGG 76 (114)
T ss_pred EEccCCCeEEEEEcCCCCEE-E---EEecCcceEeCCCccCCHHHHHHHHHHHH-HHHHHc-----CCcEEEEEEEecCC
Confidence 34556677777788655331 0 11111223456667889999998877444 444444 455555543
Q ss_pred --------CcHHHHHHhhcCC
Q psy7535 82 --------DSLSALQSLQNII 94 (199)
Q Consensus 82 --------DS~sal~aI~n~~ 94 (199)
-.++||++|++..
T Consensus 77 ~~~~~~G~Gr~~air~l~~~g 97 (114)
T TIGR03628 77 NGQKSPGPGAQAAIRALARAG 97 (114)
T ss_pred CCCCCCCCcHHHHHHHHHHCC
Confidence 4477888887654
No 32
>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=30.98 E-value=29 Score=26.09 Aligned_cols=20 Identities=10% Similarity=0.247 Sum_probs=15.1
Q ss_pred cccCCCCCCCcccCCcccccc
Q psy7535 141 HLMKREPPPECDTYNCRLTVK 161 (199)
Q Consensus 141 ~l~~~~~~p~C~~Cg~~~tv~ 161 (199)
|=+|+ +|-.|+.||..+.+.
T Consensus 20 YDLnk-~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 20 YDLNK-DPIVCPKCGTEFPPE 39 (108)
T ss_pred ccCCC-CCccCCCCCCccCcc
Confidence 44677 667799999887666
No 33
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2.7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....
Probab=30.96 E-value=29 Score=20.85 Aligned_cols=17 Identities=18% Similarity=0.251 Sum_probs=10.8
Q ss_pred ccCCCCCCCcccCCccc
Q psy7535 142 LMKREPPPECDTYNCRL 158 (199)
Q Consensus 142 l~~~~~~p~C~~Cg~~~ 158 (199)
......+..|+.||+++
T Consensus 15 ~~pP~~~~~Cd~cg~~L 31 (36)
T PF05191_consen 15 FNPPKVEGVCDNCGGEL 31 (36)
T ss_dssp TB--SSTTBCTTTTEBE
T ss_pred cCCCCCCCccCCCCCee
Confidence 33455567899999865
No 34
>KOG1812|consensus
Probab=29.58 E-value=47 Score=30.38 Aligned_cols=38 Identities=18% Similarity=0.292 Sum_probs=32.1
Q ss_pred CcchhHHHHHHHHHHHHHHHhhCCCCCCCCcEEEEcCcHHHHH
Q psy7535 46 RISICNAELISIQYAISFIISTTPLQVPTPKFVLYSDSLSALQ 88 (199)
Q Consensus 46 ~~Si~tAEl~AI~~AL~~i~~~~~~~~~~~~i~I~SDS~sal~ 88 (199)
..+.-.||++|+..+|..+.+. ....+.+++|+.--.+
T Consensus 46 ~~~~~~ae~~al~~~l~ea~~~-----~~~~~~~~~d~~~~~~ 83 (384)
T KOG1812|consen 46 SITPLEAELMALKRGLTEALEL-----GLNHIVIYCDDELIYE 83 (384)
T ss_pred ccchhhHHHHHHhhccHHHHhh-----ccccceEecccHHHHH
Confidence 3788999999999999999988 8889999999654444
No 35
>PF13696 zf-CCHC_2: Zinc knuckle
Probab=28.54 E-value=40 Score=19.94 Aligned_cols=17 Identities=18% Similarity=0.518 Sum_probs=14.1
Q ss_pred CcccCCccccccchhhcccc
Q psy7535 150 ECDTYNCRLTVKHLLKYCNK 169 (199)
Q Consensus 150 ~C~~Cg~~~tv~Hil~~Cp~ 169 (199)
.|--|+.. .|++-+||.
T Consensus 10 ~C~~C~~~---GH~i~dCP~ 26 (32)
T PF13696_consen 10 VCHRCGQK---GHWIQDCPT 26 (32)
T ss_pred EeecCCCC---CccHhHCCC
Confidence 58888766 499999998
No 36
>KOG0341|consensus
Probab=28.12 E-value=25 Score=32.80 Aligned_cols=27 Identities=15% Similarity=0.347 Sum_probs=21.8
Q ss_pred CcccCCccccccchhhcccchhhhcCc--CcH
Q psy7535 150 ECDTYNCRLTVKHLLKYCNKYQNIRSP--NDL 179 (199)
Q Consensus 150 ~C~~Cg~~~tv~Hil~~Cp~~~~~R~~--~~l 179 (199)
-|.+||+- .|=+++||+++..... +|+
T Consensus 572 GCayCgGL---GHRItdCPKle~~~~k~~sn~ 600 (610)
T KOG0341|consen 572 GCAYCGGL---GHRITDCPKLEAQQNKQISNI 600 (610)
T ss_pred ccccccCC---CcccccCchhhhhcchhhhhh
Confidence 49999875 7899999999987766 444
No 37
>PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair; PDB: 1L8D_B.
Probab=27.27 E-value=18 Score=23.33 Aligned_cols=14 Identities=21% Similarity=0.249 Sum_probs=7.8
Q ss_pred CcccCCccccccch
Q psy7535 150 ECDTYNCRLTVKHL 163 (199)
Q Consensus 150 ~C~~Cg~~~tv~Hi 163 (199)
.||.||.+++-.|-
T Consensus 22 ~CPlC~r~l~~e~~ 35 (54)
T PF04423_consen 22 CCPLCGRPLDEEHR 35 (54)
T ss_dssp E-TTT--EE-HHHH
T ss_pred cCCCCCCCCCHHHH
Confidence 89999988776653
No 38
>KOG0466|consensus
Probab=27.10 E-value=33 Score=31.13 Aligned_cols=33 Identities=24% Similarity=0.529 Sum_probs=25.0
Q ss_pred cccCCCCCCCcccCCcc--c-cccch-hhcccchhhh
Q psy7535 141 HLMKREPPPECDTYNCR--L-TVKHL-LKYCNKYQNI 173 (199)
Q Consensus 141 ~l~~~~~~p~C~~Cg~~--~-tv~Hi-l~~Cp~~~~~ 173 (199)
|--+++|.|.|+.||.. . -|+|+ +++||-..-.
T Consensus 102 ~gS~k~d~~~c~~~g~~~~~klvRHVSfVDCPGHDiL 138 (466)
T KOG0466|consen 102 FGSSKEDRPPCDRPGCEGKMKLVRHVSFVDCPGHDIL 138 (466)
T ss_pred cCCCCCCCCCcccCCCCCceEEEEEEEeccCCchHHH
Confidence 44578999999988854 3 67887 7899977544
No 39
>PF07057 TraI: DNA helicase TraI; InterPro: IPR009767 This entry represents a conserved region approximately 130 residues long within the bacterial DNA helicase TraI. TraI is a bifunctional protein that catalyses the unwinding of duplex DNA as well as acts as a sequence-specific DNA trans-esterase, providing the site- and strand-specific nick required to initiate DNA transfer [].; GO: 0003677 DNA binding, 0003678 DNA helicase activity, 0005524 ATP binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0000746 conjugation; PDB: 3FLD_B.
Probab=26.63 E-value=22 Score=27.66 Aligned_cols=14 Identities=21% Similarity=0.237 Sum_probs=0.0
Q ss_pred cCCCceEEEEcCCC
Q psy7535 10 LLPNYKQIFTDASK 23 (199)
Q Consensus 10 ~~~~~~~IyTDgSk 23 (199)
.-++|.+||||+-.
T Consensus 5 RaKeHVQvYTDn~~ 18 (126)
T PF07057_consen 5 RAKEHVQVYTDNLE 18 (126)
T ss_dssp --------------
T ss_pred hhhheeeeEeCCHH
Confidence 45789999999654
No 40
>PF14169 YdjO: Cold-inducible protein YdjO
Probab=25.66 E-value=42 Score=22.63 Aligned_cols=20 Identities=20% Similarity=0.275 Sum_probs=14.3
Q ss_pred CCCCCCCcccCCcc--ccccch
Q psy7535 144 KREPPPECDTYNCR--LTVKHL 163 (199)
Q Consensus 144 ~~~~~p~C~~Cg~~--~tv~Hi 163 (199)
..++.|.|+.|+++ ..++++
T Consensus 35 s~~~~p~CPlC~s~M~~~~r~L 56 (59)
T PF14169_consen 35 SFEEEPVCPLCKSPMVSGTRML 56 (59)
T ss_pred ccCCCccCCCcCCccccceeec
Confidence 45778999999975 355544
No 41
>KOG1994|consensus
Probab=24.13 E-value=31 Score=29.64 Aligned_cols=32 Identities=19% Similarity=0.146 Sum_probs=24.6
Q ss_pred hhhhhhhccCcccccccccCCCCCCCcccCCcc-ccccchhhcccch
Q psy7535 125 VSLTRLRIGHTNLTHVHLMKREPPPECDTYNCR-LTVKHLLKYCNKY 170 (199)
Q Consensus 125 ~~l~rlR~GHt~l~h~~l~~~~~~p~C~~Cg~~-~tv~Hil~~Cp~~ 170 (199)
.+..-||.||-+ |-.||.. .|..-++-.||--
T Consensus 230 ~in~~LR~eh~Y--------------C~fCG~~y~~~edl~ehCPGv 262 (268)
T KOG1994|consen 230 KINIFLRSEHYY--------------CFFCGIKYKDEEDLYEHCPGV 262 (268)
T ss_pred HHHHHHhccceE--------------EEEeccccCCHHHHHHhCCCC
Confidence 467788888843 8889975 4888889999854
No 42
>KOG3284|consensus
Probab=21.09 E-value=84 Score=26.30 Aligned_cols=17 Identities=24% Similarity=0.192 Sum_probs=15.0
Q ss_pred HHHHHHHHHHHHHHHhh
Q psy7535 51 NAELISIQYAISFIIST 67 (199)
Q Consensus 51 tAEl~AI~~AL~~i~~~ 67 (199)
-||++||+.||+.+.+.
T Consensus 27 lseLyaIi~ale~LEKA 43 (213)
T KOG3284|consen 27 LSELYAIIKALEQLEKA 43 (213)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 48999999999999874
No 43
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=21.04 E-value=65 Score=22.06 Aligned_cols=18 Identities=11% Similarity=0.093 Sum_probs=12.2
Q ss_pred ccCCCCCCCcccCCcccc
Q psy7535 142 LMKREPPPECDTYNCRLT 159 (199)
Q Consensus 142 l~~~~~~p~C~~Cg~~~t 159 (199)
++-.+|...|+.||.+..
T Consensus 12 ~l~~~d~e~CP~Cgs~~~ 29 (64)
T COG2093 12 RLTPEDTEICPVCGSTDL 29 (64)
T ss_pred ccCCCCCccCCCCCCccc
Confidence 344555667999997643
No 44
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=20.95 E-value=40 Score=25.37 Aligned_cols=6 Identities=17% Similarity=0.534 Sum_probs=3.3
Q ss_pred cccCCc
Q psy7535 151 CDTYNC 156 (199)
Q Consensus 151 C~~Cg~ 156 (199)
||.||.
T Consensus 89 CP~Cgs 94 (115)
T TIGR00100 89 CPKCHG 94 (115)
T ss_pred CcCCcC
Confidence 555553
No 45
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=20.94 E-value=58 Score=26.44 Aligned_cols=17 Identities=18% Similarity=0.280 Sum_probs=12.0
Q ss_pred cccCCCCCCCcccCCcc
Q psy7535 141 HLMKREPPPECDTYNCR 157 (199)
Q Consensus 141 ~l~~~~~~p~C~~Cg~~ 157 (199)
|+..-+.|..||.||++
T Consensus 142 y~~~ge~P~~CPiCga~ 158 (166)
T COG1592 142 YTHEGEAPEVCPICGAP 158 (166)
T ss_pred CcccCCCCCcCCCCCCh
Confidence 34333777899999965
No 46
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=20.78 E-value=40 Score=25.34 Aligned_cols=8 Identities=13% Similarity=0.488 Sum_probs=4.4
Q ss_pred ceEEecCC
Q psy7535 110 IQCQVRPS 117 (199)
Q Consensus 110 I~l~WiP~ 117 (199)
+.+.|+|.
T Consensus 62 L~I~~vp~ 69 (113)
T PRK12380 62 LHIVYKPA 69 (113)
T ss_pred EEEEeeCc
Confidence 55556653
No 47
>PF03997 VPS28: VPS28 protein; InterPro: IPR007143 The Endosomal Sorting Complex Required for Transport (ESCRT) complexes form the machinery driving protein sorting from endosomes to lysosomes. ESCRT complexes are central to receptor down-regulation, lysosome biogenesis, and budding of HIV. Yeast ESCRT-I consists of three protein subunits, VPS23, VPS28, and VPS37. In humans, ESCRT-I comprises TSG101, VPS28, and one of four potential human VPS37 homologues. The main role of ESCRT-I is to recognise ubiquitinated cargo via the UEV domain of the VPS23/TSG101 subunit. The assembly of the ESCRT-I complex is directed by the C-terminal steadiness box (SB) of VPS23, the N-terminal half of VPS28, and the C-terminal half of VPS37. The structure is primarily composed of three long, parallel helical hairpins, each corresponding to a different subunit. The additional domains and motifs extending beyond the core serve as gripping tools for ESCRT-I critical functions [, ].; PDB: 2J9W_B 2J9U_C 2G3K_A 2F66_E 2F6M_D 2J9V_A 2CAZ_E 2P22_B.
Probab=20.75 E-value=87 Score=25.90 Aligned_cols=16 Identities=31% Similarity=0.331 Sum_probs=14.7
Q ss_pred HHHHHHHHHHHHHHhh
Q psy7535 52 AELISIQYAISFIIST 67 (199)
Q Consensus 52 AEl~AI~~AL~~i~~~ 67 (199)
||++||+.||+.+.+.
T Consensus 2 AeLysII~tle~LEka 17 (188)
T PF03997_consen 2 AELYSIIKTLEHLEKA 17 (188)
T ss_dssp HHHHHHHHHHHHHHHH
T ss_pred hHHHHHHHHHHHHHHH
Confidence 8999999999999874
No 48
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=20.65 E-value=55 Score=18.94 Aligned_cols=11 Identities=18% Similarity=0.344 Sum_probs=9.1
Q ss_pred CCCCcccCCcc
Q psy7535 147 PPPECDTYNCR 157 (199)
Q Consensus 147 ~~p~C~~Cg~~ 157 (199)
++..|+.||+.
T Consensus 16 ~~~~CP~Cg~~ 26 (33)
T cd00350 16 APWVCPVCGAP 26 (33)
T ss_pred CCCcCcCCCCc
Confidence 67799999974
No 49
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=20.54 E-value=46 Score=21.33 Aligned_cols=24 Identities=13% Similarity=0.267 Sum_probs=17.2
Q ss_pred CCcccCCccccccchhhcccchhh
Q psy7535 149 PECDTYNCRLTVKHLLKYCNKYQN 172 (199)
Q Consensus 149 p~C~~Cg~~~tv~Hil~~Cp~~~~ 172 (199)
-.|+.||...++..+...|.....
T Consensus 3 f~CP~C~~~~~~~~L~~H~~~~H~ 26 (54)
T PF05605_consen 3 FTCPYCGKGFSESSLVEHCEDEHR 26 (54)
T ss_pred cCCCCCCCccCHHHHHHHHHhHCc
Confidence 469999987787777766655443
No 50
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=20.17 E-value=41 Score=20.84 Aligned_cols=10 Identities=20% Similarity=0.481 Sum_probs=5.6
Q ss_pred CCcccCCccc
Q psy7535 149 PECDTYNCRL 158 (199)
Q Consensus 149 p~C~~Cg~~~ 158 (199)
..|+.||.+.
T Consensus 22 ~~Cp~CG~~~ 31 (46)
T PRK00398 22 VRCPYCGYRI 31 (46)
T ss_pred eECCCCCCeE
Confidence 4566666543
Done!