Query psy1195
Match_columns 223
No_of_seqs 202 out of 1263
Neff 4.7
Searched_HMMs 46136
Date Fri Aug 16 23:05:23 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy1195.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/1195hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK06548 ribonuclease H; Provi 99.9 1.1E-21 2.4E-26 164.5 10.9 125 18-173 13-143 (161)
2 COG0328 RnhA Ribonuclease HI [ 99.8 2.4E-19 5.3E-24 149.8 10.8 130 18-173 11-146 (154)
3 PRK00203 rnhA ribonuclease H; 99.8 6.8E-19 1.5E-23 143.7 10.5 125 19-172 12-142 (150)
4 PRK08719 ribonuclease H; Revie 99.7 1.2E-17 2.5E-22 137.6 11.0 122 19-171 13-146 (147)
5 PF00075 RNase_H: RNase H; In 99.6 2.5E-15 5.4E-20 116.7 6.3 115 20-171 13-132 (132)
6 PRK13907 rnhA ribonuclease H; 99.2 1.9E-10 4.1E-15 90.7 10.7 117 19-172 10-127 (128)
7 cd06222 RnaseH RNase H (RNase 99.1 2.7E-10 5.9E-15 83.8 7.4 73 91-170 58-130 (130)
8 PRK07238 bifunctional RNase H/ 98.9 2.1E-08 4.5E-13 92.4 12.1 118 19-172 11-132 (372)
9 KOG3752|consensus 98.8 4.8E-09 1E-13 98.3 6.4 85 86-172 267-365 (371)
10 PRK07708 hypothetical protein; 98.7 2.1E-07 4.6E-12 81.7 11.9 121 20-173 83-209 (219)
11 PF13456 RVT_3: Reverse transc 98.1 1.3E-05 2.9E-10 57.4 7.5 68 92-171 19-86 (87)
12 PF03066 Nucleoplasmin: Nucleo 91.7 0.053 1.2E-06 45.3 0.1 9 44-52 100-108 (149)
13 PF03066 Nucleoplasmin: Nucleo 75.8 0.87 1.9E-05 38.1 -0.0 8 39-46 99-106 (149)
14 TIGR00927 2A1904 K+-dependent 67.7 1.3 2.9E-05 47.1 -0.8 11 158-168 978-988 (1096)
15 TIGR00927 2A1904 K+-dependent 65.1 1.9 4.2E-05 46.0 -0.2 18 152-169 977-994 (1096)
16 KOG1832|consensus 59.4 2.4 5.2E-05 45.3 -0.7 9 25-33 1371-1379(1516)
17 PTZ00415 transmission-blocking 55.8 2.3 5.1E-05 47.9 -1.5 17 21-37 120-136 (2849)
18 KOG1834|consensus 46.9 4 8.6E-05 42.2 -1.4 6 8-13 851-856 (952)
19 PF03896 TRAP_alpha: Transloco 43.3 3 6.6E-05 38.4 -2.7 9 95-103 83-91 (285)
20 PF02724 CDC45: CDC45-like pro 43.3 5.5 0.00012 40.2 -1.1 16 26-41 74-89 (622)
21 KOG1189|consensus 40.1 12 0.00026 39.3 0.7 9 40-48 888-896 (960)
22 KOG1307|consensus 32.1 15 0.00032 36.9 -0.1 6 164-169 480-485 (588)
23 PF07423 DUF1510: Protein of u 31.5 34 0.00073 30.5 2.1 61 96-157 111-181 (217)
24 PF03986 Autophagy_N: Autophag 30.2 31 0.00068 28.9 1.6 12 5-16 67-78 (145)
25 PF11705 RNA_pol_3_Rpc31: DNA- 30.2 11 0.00023 33.2 -1.3 11 93-103 206-216 (233)
26 KOG2652|consensus 29.4 11 0.00024 35.8 -1.4 9 141-149 333-341 (348)
27 PF02724 CDC45: CDC45-like pro 26.9 17 0.00036 36.9 -0.7 11 29-39 98-108 (622)
28 KOG1909|consensus 21.4 31 0.00068 33.3 -0.0 58 20-87 322-379 (382)
No 1
>PRK06548 ribonuclease H; Provisional
Probab=99.86 E-value=1.1e-21 Score=164.52 Aligned_cols=125 Identities=18% Similarity=0.154 Sum_probs=96.3
Q ss_pred cccCCCCccceeEEEecCccccccCCCCCCcccchhhhhhhhhhhhHHHHHHHhhhhhhhhchHHHHHHHHHHhhcCceE
Q psy1195 18 YLSGLPDSEWLALVLIDSPRYLDNSGYDSGIFTYLEEEEEEEEEDDKEEERVEREEEEEEEDDEEEERFEREEEEERRKV 97 (223)
Q Consensus 18 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~I 97 (223)
-|.|||||.|.|+|+.+.. ..+|...+.+++..|- ... -+..+......++|
T Consensus 13 a~~gnpg~~G~g~~~~~~~---~~~g~~~~~TNnraEl-----------~Ai--------------i~aL~~~~~~~~~v 64 (161)
T PRK06548 13 SSLANPGPSGWAWYVDENT---WDSGGWDIATNNIAEL-----------TAV--------------RELLIATRHTDRPI 64 (161)
T ss_pred ccCCCCCceEEEEEEeCCc---EEccCCCCCCHHHHHH-----------HHH--------------HHHHHhhhcCCceE
Confidence 3789999999999987643 3467777777777655 222 22333333334579
Q ss_pred EEEecChhhHhhhccC------CCCCCCCchhhcccChhHHHHHHHHHhcCCceEEEEeccCCCCccChHHHHHHHHHHh
Q psy1195 98 TTYSENRQKTVEICPE------AVKIPPSAATILTKWPDDIQNFLILFLSKLDVQFVWVPSHVGIAGNEEADRLAKEALT 171 (223)
Q Consensus 98 ~IfTDSqyaI~aI~~~------~~~~~~Sgq~il~~~~~i~q~i~~ll~~~~~V~~~WVPGHsGi~GNE~AD~LAk~Aa~ 171 (223)
.|||||+||+++|++| .-|++++|++|.++ ++++.|.+++.. +.|+|.|||||+|++||+.||+||++|+.
T Consensus 65 ~I~TDS~yvi~~i~~W~~~Wk~~gWk~s~G~pV~N~--dL~~~l~~l~~~-~~v~~~wVkgHsg~~gNe~aD~LA~~aa~ 141 (161)
T PRK06548 65 LILSDSKYVINSLTKWVYSWKMRKWRKADGKPVLNQ--EIIQEIDSLMEN-RNIRMSWVNAHTGHPLNEAADSLARQAAN 141 (161)
T ss_pred EEEeChHHHHHHHHHHHHHHHHCCCcccCCCccccH--HHHHHHHHHHhc-CceEEEEEecCCCCHHHHHHHHHHHHHHH
Confidence 9999999999999963 11467789999874 899999998754 58999999999999999999999999987
Q ss_pred cC
Q psy1195 172 SA 173 (223)
Q Consensus 172 ~~ 173 (223)
..
T Consensus 142 ~~ 143 (161)
T PRK06548 142 NF 143 (161)
T ss_pred Hh
Confidence 63
No 2
>COG0328 RnhA Ribonuclease HI [DNA replication, recombination, and repair]
Probab=99.80 E-value=2.4e-19 Score=149.84 Aligned_cols=130 Identities=23% Similarity=0.160 Sum_probs=97.6
Q ss_pred cccCCCCccceeEEEecCccccccCCCCCCcccchhhhhhhhhhhhHHHHHHHhhhhhhhhchHHHHHHHHHHhhcCceE
Q psy1195 18 YLSGLPDSEWLALVLIDSPRYLDNSGYDSGIFTYLEEEEEEEEEDDKEEERVEREEEEEEEDDEEEERFEREEEEERRKV 97 (223)
Q Consensus 18 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~I 97 (223)
-|.|||||.|.|+||..+..-.+.||...-.+++-.|- ... =+-.+.+++ ..++.|
T Consensus 11 a~~gNpG~gG~g~vl~~~~~~~~~s~~~~~tTNNraEl-----------~A~-----------i~AL~~l~~--~~~~~v 66 (154)
T COG0328 11 ACLGNPGPGGWGAVLRYGDGEKELSGGEGRTTNNRAEL-----------RAL-----------IEALEALKE--LGACEV 66 (154)
T ss_pred ccCCCCCCceEEEEEEcCCceEEEeeeeecccChHHHH-----------HHH-----------HHHHHHHHh--cCCceE
Confidence 38999999999999995555556777776555554443 111 001222222 578999
Q ss_pred EEEecChhhHhhhccCCC------CCCCCchhhcccChhHHHHHHHHHhcCCceEEEEeccCCCCccChHHHHHHHHHHh
Q psy1195 98 TTYSENRQKTVEICPEAV------KIPPSAATILTKWPDDIQNFLILFLSKLDVQFVWVPSHVGIAGNEEADRLAKEALT 171 (223)
Q Consensus 98 ~IfTDSqyaI~aI~~~~~------~~~~Sgq~il~~~~~i~q~i~~ll~~~~~V~~~WVPGHsGi~GNE~AD~LAk~Aa~ 171 (223)
.|||||+||+++|..|.. |.+...+++.+ .++++++..++.....|.+.|||||+|+++|++||+||+.++.
T Consensus 67 ~l~tDS~yv~~~i~~w~~~w~~~~w~~~~~~pvkn--~dl~~~~~~~~~~~~~v~~~WVkgH~g~~~NeraD~LA~~~~~ 144 (154)
T COG0328 67 TLYTDSKYVVEGITRWIVKWKKNGWKTADKKPVKN--KDLWEELDELLKRHELVFWEWVKGHAGHPENERADQLAREAAR 144 (154)
T ss_pred EEEecHHHHHHHHHHHHhhccccCccccccCcccc--HHHHHHHHHHHhhCCeEEEEEeeCCCCChHHHHHHHHHHHHHH
Confidence 999999999999995411 45555667776 4899999999876669999999999999999999999999987
Q ss_pred cC
Q psy1195 172 SA 173 (223)
Q Consensus 172 ~~ 173 (223)
..
T Consensus 145 ~~ 146 (154)
T COG0328 145 AA 146 (154)
T ss_pred hh
Confidence 73
No 3
>PRK00203 rnhA ribonuclease H; Reviewed
Probab=99.79 E-value=6.8e-19 Score=143.73 Aligned_cols=125 Identities=18% Similarity=0.121 Sum_probs=92.7
Q ss_pred ccCCCCccceeEEEecCccccccCCCCCCcccchhhhhhhhhhhhHHHHHHHhhhhhhhhchHHHHHHHHHHhhcCceEE
Q psy1195 19 LSGLPDSEWLALVLIDSPRYLDNSGYDSGIFTYLEEEEEEEEEDDKEEERVEREEEEEEEDDEEEERFEREEEEERRKVT 98 (223)
Q Consensus 19 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~I~ 98 (223)
|.|+|++.+.|+|+.+.......+|..++.+++..|- ... .+..+.. ..+..|.
T Consensus 12 ~~~n~~~~g~g~v~~~~~~~~~~~~~~~~~TN~~aEL-----------~Ai--------------~~AL~~~-~~~~~v~ 65 (150)
T PRK00203 12 CLGNPGPGGWGAILRYKGHEKELSGGEALTTNNRMEL-----------MAA--------------IEALEAL-KEPCEVT 65 (150)
T ss_pred ccCCCCceEEEEEEEECCeeEEEecCCCCCcHHHHHH-----------HHH--------------HHHHHHc-CCCCeEE
Confidence 7889999999999987766666666655555544332 111 1222222 2356899
Q ss_pred EEecChhhHhhhccCC------CCCCCCchhhcccChhHHHHHHHHHhcCCceEEEEeccCCCCccChHHHHHHHHHHhc
Q psy1195 99 TYSENRQKTVEICPEA------VKIPPSAATILTKWPDDIQNFLILFLSKLDVQFVWVPSHVGIAGNEEADRLAKEALTS 172 (223)
Q Consensus 99 IfTDSqyaI~aI~~~~------~~~~~Sgq~il~~~~~i~q~i~~ll~~~~~V~~~WVPGHsGi~GNE~AD~LAk~Aa~~ 172 (223)
|||||+|++++|..|. -|.+++|+++.+ .++++.+.+++ ....|.|.|||||+|++||+.||+||+.|+..
T Consensus 66 I~tDS~yvi~~i~~w~~~Wk~~~~~~~~g~~v~n--~dl~~~i~~l~-~~~~v~~~wV~~H~~~~~N~~AD~lA~~a~~~ 142 (150)
T PRK00203 66 LYTDSQYVRQGITEWIHGWKKNGWKTADKKPVKN--VDLWQRLDAAL-KRHQIKWHWVKGHAGHPENERCDELARAGAEE 142 (150)
T ss_pred EEECHHHHHHHHHHHHHHHHHcCCcccCCCcccc--HHHHHHHHHHh-ccCceEEEEecCCCCCHHHHHHHHHHHHHHHH
Confidence 9999999999999631 134567788776 37889888876 45889999999999999999999999999876
No 4
>PRK08719 ribonuclease H; Reviewed
Probab=99.74 E-value=1.2e-17 Score=137.62 Aligned_cols=122 Identities=20% Similarity=0.046 Sum_probs=82.8
Q ss_pred ccCCCC---ccceeEEEecCccc-c-ccCCCCC-CcccchhhhhhhhhhhhHHHHHHHhhhhhhhhchHHHHHHHHHHhh
Q psy1195 19 LSGLPD---SEWLALVLIDSPRY-L-DNSGYDS-GIFTYLEEEEEEEEEDDKEEERVEREEEEEEEDDEEEERFEREEEE 92 (223)
Q Consensus 19 ~~~~~~---~~~~~~~~~~~~~~-~-~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 92 (223)
|.|||+ ++|.|+|+.+.... . ..+.... ..+++..|- .. ...+...
T Consensus 13 ~~~n~~~~~~~G~G~vv~~~~~~~~~~~~~~~~~~~Tnn~aEl-----------~A-----------------~~~aL~~ 64 (147)
T PRK08719 13 APNNQHGCVRGGIGLVVYDEAGEIVDEQSITVNRYTDNAELEL-----------LA-----------------LIEALEY 64 (147)
T ss_pred cCCCCCCCCCcEEEEEEEeCCCCeeEEEEecCCCCccHHHHHH-----------HH-----------------HHHHHHH
Confidence 667887 67999999875422 1 2232222 244555443 11 1222222
Q ss_pred cCceEEEEecChhhHhhhccC------CCCCCCCchhhcccChhHHHHHHHHHhcCCceEEEEeccCCCCccChHHHHHH
Q psy1195 93 ERRKVTTYSENRQKTVEICPE------AVKIPPSAATILTKWPDDIQNFLILFLSKLDVQFVWVPSHVGIAGNEEADRLA 166 (223)
Q Consensus 93 ~~~~I~IfTDSqyaI~aI~~~------~~~~~~Sgq~il~~~~~i~q~i~~ll~~~~~V~~~WVPGHsGi~GNE~AD~LA 166 (223)
-.....|||||+||+++|+.| .-|.++.|+++.+ .++++.+..+.. .+.|+|.|||||+|++||+.||+||
T Consensus 65 ~~~~~~i~tDS~yvi~~i~~~~~~W~~~~w~~s~g~~v~n--~dl~~~i~~l~~-~~~i~~~~VkgH~g~~~Ne~aD~lA 141 (147)
T PRK08719 65 ARDGDVIYSDSDYCVRGFNEWLDTWKQKGWRKSDKKPVAN--RDLWQQVDELRA-RKYVEVEKVTAHSGIEGNEAADMLA 141 (147)
T ss_pred cCCCCEEEechHHHHHHHHHHHHHHHhCCcccCCCccccc--HHHHHHHHHHhC-CCcEEEEEecCCCCChhHHHHHHHH
Confidence 223358999999999999641 1134555677766 388998888765 6779999999999999999999999
Q ss_pred HHHHh
Q psy1195 167 KEALT 171 (223)
Q Consensus 167 k~Aa~ 171 (223)
+.|++
T Consensus 142 ~~a~~ 146 (147)
T PRK08719 142 QAAAE 146 (147)
T ss_pred HHHhh
Confidence 99875
No 5
>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=99.58 E-value=2.5e-15 Score=116.71 Aligned_cols=115 Identities=28% Similarity=0.287 Sum_probs=75.1
Q ss_pred cCCCCccceeEEEecCccccccCCCCCCcccchhhhhhhhhhhhHHHHHHHhhhhhhhhchHHHHHHHHHHhhcCceEEE
Q psy1195 20 SGLPDSEWLALVLIDSPRYLDNSGYDSGIFTYLEEEEEEEEEDDKEEERVEREEEEEEEDDEEEERFEREEEEERRKVTT 99 (223)
Q Consensus 20 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~I~I 99 (223)
.++|+..+.|+|+ .+++ ..++...+.+++..|- ... ....+ .. .+..|+|
T Consensus 13 ~~~~~~~~~g~v~-~~~~--~~~~~~~~~s~~~aEl-----------~Ai--------------~~AL~-~~-~~~~v~I 62 (132)
T PF00075_consen 13 RPNPGKGGAGYVV-WGGR--NFSFRLGGQSNNRAEL-----------QAI--------------IEALK-AL-EHRKVTI 62 (132)
T ss_dssp CTTTTEEEEEEEE-ETTE--EEEEEEESECHHHHHH-----------HHH--------------HHHHH-TH-STSEEEE
T ss_pred cCCCCceEEEEEE-ECCe--EEEecccccchhhhhe-----------ehH--------------HHHHH-Hh-hcccccc
Confidence 3457888888865 6553 3333223555555544 222 23334 22 4589999
Q ss_pred EecChhhHhhhccC----CCCCCCCchhhcccChhHHHHHHHHHhcCCceEEEEeccCCCC-ccChHHHHHHHHHHh
Q psy1195 100 YSENRQKTVEICPE----AVKIPPSAATILTKWPDDIQNFLILFLSKLDVQFVWVPSHVGI-AGNEEADRLAKEALT 171 (223)
Q Consensus 100 fTDSqyaI~aI~~~----~~~~~~Sgq~il~~~~~i~q~i~~ll~~~~~V~~~WVPGHsGi-~GNE~AD~LAk~Aa~ 171 (223)
||||+++++.|..+ .+..+..+. .+...+.+++..+..|.|+|||||+|+ .||+.||+|||.|+.
T Consensus 63 ~tDS~~v~~~l~~~~~~~~~~~~~~~~-------~i~~~i~~~~~~~~~v~~~~V~~H~~~~~~N~~aD~lAk~a~~ 132 (132)
T PF00075_consen 63 YTDSQYVLNALNKWLHGNGWKKTSNGR-------PIKNEIWELLSRGIKVRFRWVPGHSGVPQGNERADRLAKEAAQ 132 (132)
T ss_dssp EES-HHHHHHHHTHHHHTTSBSCTSSS-------BHTHHHHHHHHHSSEEEEEESSSSSSSHHHHHHHHHHHHHHHH
T ss_pred cccHHHHHHHHHHhccccccccccccc-------cchhheeeccccceEEeeeeccCcCCCchhHHHHHHHHHHhcC
Confidence 99999999988872 110111111 244456666667889999999999999 699999999999974
No 6
>PRK13907 rnhA ribonuclease H; Provisional
Probab=99.20 E-value=1.9e-10 Score=90.66 Aligned_cols=117 Identities=15% Similarity=0.074 Sum_probs=81.6
Q ss_pred ccCCCCccceeEEEecCccccccCCCCCCcccchhhhhhhhhhhhHHHHHHHhhhhhhhhchHHHHHHHHHHh-hcCceE
Q psy1195 19 LSGLPDSEWLALVLIDSPRYLDNSGYDSGIFTYLEEEEEEEEEDDKEEERVEREEEEEEEDDEEEERFEREEE-EERRKV 97 (223)
Q Consensus 19 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~I 97 (223)
|.|+|++.|.|+||.|.......++..+..+++..|- ... -...+... ....+|
T Consensus 10 ~~~~~g~~G~G~vi~~~~~~~~~~~~~~~~tn~~AE~-----------~Al--------------l~aL~~a~~~g~~~v 64 (128)
T PRK13907 10 SKGNPGPSGAGVFIKGVQPAVQLSLPLGTMSNHEAEY-----------HAL--------------LAALKYCTEHNYNIV 64 (128)
T ss_pred CCCCCCccEEEEEEEECCeeEEEEecccccCCcHHHH-----------HHH--------------HHHHHHHHhCCCCEE
Confidence 6789999999999998876656666555555544433 111 22223222 334689
Q ss_pred EEEecChhhHhhhccCCCCCCCCchhhcccChhHHHHHHHHHhcCCceEEEEeccCCCCccChHHHHHHHHHHhc
Q psy1195 98 TTYSENRQKTVEICPEAVKIPPSAATILTKWPDDIQNFLILFLSKLDVQFVWVPSHVGIAGNEEADRLAKEALTS 172 (223)
Q Consensus 98 ~IfTDSqyaI~aI~~~~~~~~~Sgq~il~~~~~i~q~i~~ll~~~~~V~~~WVPGHsGi~GNE~AD~LAk~Aa~~ 172 (223)
.|||||+++++.+++.+. + ... ...+++.+..++.....+.|.|||. ++|..||.||+.|...
T Consensus 65 ~i~sDS~~vi~~~~~~~~---~--~~~---~~~l~~~~~~l~~~f~~~~~~~v~r----~~N~~Ad~LA~~a~~~ 127 (128)
T PRK13907 65 SFRTDSQLVERAVEKEYA---K--NKM---FAPLLEEALQYIKSFDLFFIKWIPS----SQNKVADELARKAILQ 127 (128)
T ss_pred EEEechHHHHHHHhHHHh---c--Chh---HHHHHHHHHHHHhcCCceEEEEcCc----hhchhHHHHHHHHHhc
Confidence 999999999999998441 1 111 1267778888776666778899998 4999999999998753
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=99.11 E-value=2.7e-10 Score=83.84 Aligned_cols=73 Identities=36% Similarity=0.427 Sum_probs=57.0
Q ss_pred hhcCceEEEEecChhhHhhhccCCCCCCCCchhhcccChhHHHHHHHHHhcCCceEEEEeccCCCCccChHHHHHHHHHH
Q psy1195 91 EEERRKVTTYSENRQKTVEICPEAVKIPPSAATILTKWPDDIQNFLILFLSKLDVQFVWVPSHVGIAGNEEADRLAKEAL 170 (223)
Q Consensus 91 ~~~~~~I~IfTDSqyaI~aI~~~~~~~~~Sgq~il~~~~~i~q~i~~ll~~~~~V~~~WVPGHsGi~GNE~AD~LAk~Aa 170 (223)
....+++.|+|||++++..+.++.. .. .... ..+++.+..++.....+.|.|||+|+|+.+|..||.||+.+.
T Consensus 58 ~~~~~~i~i~~Ds~~~~~~~~~~~~---~~-~~~~---~~~~~~i~~~~~~~~~~~i~~v~~h~~~~~n~~ad~la~~~~ 130 (130)
T cd06222 58 ELGGKKVNIYTDSQYVINALTGWYE---GK-PVKN---VDLWQRLLALLKRFHKVRFEWVPGHSGIEGNERADALAKEAA 130 (130)
T ss_pred hCCCceEEEEECHHHHHHHhhcccc---CC-Chhh---HHHHHHHHHHHhCCCeEEEEEcCCCCCCcchHHHHHHHHhhC
Confidence 3567899999999999999987541 01 1111 246666777666788999999999999999999999999873
No 8
>PRK07238 bifunctional RNase H/acid phosphatase; Provisional
Probab=98.88 E-value=2.1e-08 Score=92.36 Aligned_cols=118 Identities=16% Similarity=0.106 Sum_probs=81.6
Q ss_pred ccCCCCccceeEEEecCc-c-c-cccCCCCCCcccchhhhhhhhhhhhHHHHHHHhhhhhhhhchHHHHHHHHHHh-hcC
Q psy1195 19 LSGLPDSEWLALVLIDSP-R-Y-LDNSGYDSGIFTYLEEEEEEEEEDDKEEERVEREEEEEEEDDEEEERFEREEE-EER 94 (223)
Q Consensus 19 ~~~~~~~~~~~~~~~~~~-~-~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~ 94 (223)
|.||||++|+|+||.|.. . . ...++..+..+++..|- +.- ....+... ...
T Consensus 11 ~~~n~g~aG~G~vi~~~~~~~~~~~~~~~~~~~tnn~AE~-----------~Al--------------l~gL~~a~~~g~ 65 (372)
T PRK07238 11 SRGNPGPAGYGAVVWDADRGEVLAERAEAIGRATNNVAEY-----------RGL--------------IAGLEAAAELGA 65 (372)
T ss_pred CCCCCCceEEEEEEEeCCCCcEEEEeecccCCCCchHHHH-----------HHH--------------HHHHHHHHhCCC
Confidence 789999999999999964 2 2 35677777666765544 111 22223222 345
Q ss_pred ceEEEEecChhhHhhhccCCCCCCCCchhhcccChhHHHHHHHHHhcCCceEEEEeccCCCCccChHHHHHHHHHHhc
Q psy1195 95 RKVTTYSENRQKTVEICPEAVKIPPSAATILTKWPDDIQNFLILFLSKLDVQFVWVPSHVGIAGNEEADRLAKEALTS 172 (223)
Q Consensus 95 ~~I~IfTDSqyaI~aI~~~~~~~~~Sgq~il~~~~~i~q~i~~ll~~~~~V~~~WVPGHsGi~GNE~AD~LAk~Aa~~ 172 (223)
++|.||+||+++++.+.+.+ +.+.. -+. .++..+..++.....+.|.|||. .+|..||.||+.|...
T Consensus 66 ~~v~i~~DS~lvi~~i~~~~---~~~~~-~l~---~~~~~i~~l~~~f~~~~i~~v~r----~~N~~AD~LA~~a~~~ 132 (372)
T PRK07238 66 TEVEVRMDSKLVVEQMSGRW---KVKHP-DMK---PLAAQARELASQFGRVTYTWIPR----ARNAHADRLANEAMDA 132 (372)
T ss_pred CeEEEEeCcHHHHHHhCCCC---ccCCh-HHH---HHHHHHHHHHhcCCceEEEECCc----hhhhHHHHHHHHHHHh
Confidence 78999999999999998743 11111 111 34455666666667899999997 6899999999999755
No 9
>KOG3752|consensus
Probab=98.84 E-value=4.8e-09 Score=98.28 Aligned_cols=85 Identities=22% Similarity=0.167 Sum_probs=62.1
Q ss_pred HHHHH-hhcCceEEEEecChhhHhhhccCCC------CCCCCchh-----hcccChhHHHHHHHHHh--cCCceEEEEec
Q psy1195 86 FEREE-EEERRKVTTYSENRQKTVEICPEAV------KIPPSAAT-----ILTKWPDDIQNFLILFL--SKLDVQFVWVP 151 (223)
Q Consensus 86 ~~~~~-~~~~~~I~IfTDSqyaI~aI~~~~~------~~~~Sgq~-----il~~~~~i~q~i~~ll~--~~~~V~~~WVP 151 (223)
+.+.. ..+..+|+|.|||+|+|++|+.|-. |..+.++. +.+ .+....+..|.+ ....|++.||+
T Consensus 267 ALkka~~~~~~kv~I~TDS~~~i~~l~~wv~~~k~~~~k~~~~~~~i~~~v~n--~~~~~e~~~l~q~~~~~~vq~~~V~ 344 (371)
T KOG3752|consen 267 ALKKARSKNINKVVIRTDSEYFINSLTLWVQGWKKNGWKTSNGSDRICAYVKN--QDFFNELDELEQEISNKKVQQEYVG 344 (371)
T ss_pred HHHHHHhcCCCcEEEEechHHHHHHHHHHHhhhccCccccccCCCccceeeec--chHHHHHHHHHhhhccCceEEEEec
Confidence 44444 3445699999999999999997522 23444454 433 244455666654 35899999999
Q ss_pred cCCCCccChHHHHHHHHHHhc
Q psy1195 152 SHVGIAGNEEADRLAKEALTS 172 (223)
Q Consensus 152 GHsGi~GNE~AD~LAk~Aa~~ 172 (223)
||.||.||++||.||++++..
T Consensus 345 Gh~gi~gne~Ad~lARkgs~~ 365 (371)
T KOG3752|consen 345 GHSGILGNEMADALARKGSTL 365 (371)
T ss_pred CcCCcchHHHHHHHHhhhhhh
Confidence 999999999999999998654
No 10
>PRK07708 hypothetical protein; Validated
Probab=98.70 E-value=2.1e-07 Score=81.66 Aligned_cols=121 Identities=18% Similarity=0.113 Sum_probs=72.3
Q ss_pred cCCCCccceeEEEecCcc---c-cccCCCCCC-cccchhhhhhhhhhhhHHHHHHHhhhhhhhhchHHHHHHHHHHhhcC
Q psy1195 20 SGLPDSEWLALVLIDSPR---Y-LDNSGYDSG-IFTYLEEEEEEEEEDDKEEERVEREEEEEEEDDEEEERFEREEEEER 94 (223)
Q Consensus 20 ~~~~~~~~~~~~~~~~~~---~-~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 94 (223)
.|+|+++|.|+||++.+. + +..+.+.++ .+++..|-. .- -.-.+.+.+...++
T Consensus 83 ~~n~g~aG~GvVI~~~~g~~~~~~~~~~~l~~~~TNN~AEy~-----------Al-----------i~aL~~A~e~g~~~ 140 (219)
T PRK07708 83 DKETKLAGLGIVIYYKQGNKRYRIRRNAYIEGIYDNNEAEYA-----------AL-----------YYAMQELEELGVKH 140 (219)
T ss_pred CCCCCCcEEEEEEEECCCCEEEEEEeeccccccccCcHHHHH-----------HH-----------HHHHHHHHHcCCCc
Confidence 458999999999997543 1 233444543 444444331 11 01122233333334
Q ss_pred ceEEEEecChhhHhhhccCCCCCCCCchhhcccChhHHHHHHHHHhc-CCceEEEEeccCCCCccChHHHHHHHHHHhcC
Q psy1195 95 RKVTTYSENRQKTVEICPEAVKIPPSAATILTKWPDDIQNFLILFLS-KLDVQFVWVPSHVGIAGNEEADRLAKEALTSA 173 (223)
Q Consensus 95 ~~I~IfTDSqyaI~aI~~~~~~~~~Sgq~il~~~~~i~q~i~~ll~~-~~~V~~~WVPGHsGi~GNE~AD~LAk~Aa~~~ 173 (223)
..|.|++||+++++.+...+ +.. .+.+. ...+.+..++.+ ...+.|.||| -..|+.||+||+.|+...
T Consensus 141 ~~V~I~~DSqlVi~qi~g~w---k~~-~~~l~---~y~~~i~~l~~~~~l~~~~~~Vp----R~~N~~AD~LAk~Al~~~ 209 (219)
T PRK07708 141 EPVTFRGDSQVVLNQLAGEW---PCY-DEHLN---HWLDRIEQKLKQLKLTPVYEPIS----RKQNKEADQLATQALEGT 209 (219)
T ss_pred ceEEEEeccHHHHHHhCCCc---eeC-ChhHH---HHHHHHHHHHhhCCceEEEEECC----chhhhHHHHHHHHHHhcC
Confidence 45999999999999998743 111 11222 234445544432 2347778887 467999999999999863
No 11
>PF13456 RVT_3: Reverse transcriptase-like; PDB: 3ALY_A 2EHG_A 3HST_B.
Probab=98.13 E-value=1.3e-05 Score=57.45 Aligned_cols=68 Identities=26% Similarity=0.201 Sum_probs=50.6
Q ss_pred hcCceEEEEecChhhHhhhccCCCCCCCCchhhcccChhHHHHHHHHHhcCCceEEEEeccCCCCccChHHHHHHHHHHh
Q psy1195 92 EERRKVTTYSENRQKTVEICPEAVKIPPSAATILTKWPDDIQNFLILFLSKLDVQFVWVPSHVGIAGNEEADRLAKEALT 171 (223)
Q Consensus 92 ~~~~~I~IfTDSqyaI~aI~~~~~~~~~Sgq~il~~~~~i~q~i~~ll~~~~~V~~~WVPGHsGi~GNE~AD~LAk~Aa~ 171 (223)
.+.++|.|+|||+.+++.|++... ....+. .+++.+..++.....+.|.||| -.+|..||.|||.|.+
T Consensus 19 ~g~~~i~v~sDs~~vv~~i~~~~~-----~~~~~~---~~~~~i~~~~~~~~~~~~~~i~----r~~N~~A~~LA~~a~~ 86 (87)
T PF13456_consen 19 LGIRKIIVESDSQLVVDAINGRSS-----SRSELR---PLIQDIRSLLDRFWNVSVSHIP----REQNKVADALAKFALS 86 (87)
T ss_dssp CT-SCEEEEES-HHHHHHHTTSS--------SCCH---HHHHHHHHHHCCCSCEEEEE------GGGSHHHHHHHHHHHH
T ss_pred CCCCEEEEEecCcccccccccccc-----cccccc---ccchhhhhhhccccceEEEEEC----hHHhHHHHHHHHHHhh
Confidence 445789999999999999987531 111122 5788888888888899999999 6899999999999875
No 12
>PF03066 Nucleoplasmin: Nucleoplasmin; InterPro: IPR004301 The nucleophosmin/nucleoplasmin family of chaperones includes nucleophosmin, nucleoplasmin and nucleoplasmin-like proteins. They function as nuclear chaperones which are needed for the proper assembly of nucleosomes and the attainment of proper higher order chromatin structures [].; GO: 0003676 nucleic acid binding; PDB: 2P1B_E 1XB9_I 1XE0_C 1NLQ_A 2VTX_E 1K5J_D 1EJY_N 1EE5_B 3T30_J.
Probab=91.71 E-value=0.053 Score=45.29 Aligned_cols=9 Identities=22% Similarity=-0.101 Sum_probs=4.4
Q ss_pred CCCCcccch
Q psy1195 44 YDSGIFTYL 52 (223)
Q Consensus 44 ~~~~~~~~~ 52 (223)
+.+|...+.
T Consensus 100 hisG~~~~~ 108 (149)
T PF03066_consen 100 HISGQHLVA 108 (149)
T ss_dssp EEEEEEEEE
T ss_pred EeeCccccc
Confidence 355655433
No 13
>PF03066 Nucleoplasmin: Nucleoplasmin; InterPro: IPR004301 The nucleophosmin/nucleoplasmin family of chaperones includes nucleophosmin, nucleoplasmin and nucleoplasmin-like proteins. They function as nuclear chaperones which are needed for the proper assembly of nucleosomes and the attainment of proper higher order chromatin structures [].; GO: 0003676 nucleic acid binding; PDB: 2P1B_E 1XB9_I 1XE0_C 1NLQ_A 2VTX_E 1K5J_D 1EJY_N 1EE5_B 3T30_J.
Probab=75.82 E-value=0.87 Score=38.07 Aligned_cols=8 Identities=25% Similarity=0.202 Sum_probs=4.5
Q ss_pred cccCCCCC
Q psy1195 39 LDNSGYDS 46 (223)
Q Consensus 39 ~~~~~~~~ 46 (223)
.-.|||..
T Consensus 99 VhisG~~~ 106 (149)
T PF03066_consen 99 VHISGQHL 106 (149)
T ss_dssp EEEEEEEE
T ss_pred EEeeCccc
Confidence 34567763
No 14
>TIGR00927 2A1904 K+-dependent Na+/Ca+ exchanger.
Probab=67.68 E-value=1.3 Score=47.09 Aligned_cols=11 Identities=18% Similarity=0.274 Sum_probs=5.8
Q ss_pred cChHHHHHHHH
Q psy1195 158 GNEEADRLAKE 168 (223)
Q Consensus 158 GNE~AD~LAk~ 168 (223)
|+-..|-++..
T Consensus 978 GTSIPDlisSv 988 (1096)
T TIGR00927 978 GTSIPDLITSV 988 (1096)
T ss_pred hcccHHHHHHH
Confidence 55555555443
No 15
>TIGR00927 2A1904 K+-dependent Na+/Ca+ exchanger.
Probab=65.12 E-value=1.9 Score=45.95 Aligned_cols=18 Identities=11% Similarity=0.060 Sum_probs=10.5
Q ss_pred cCCCCccChHHHHHHHHH
Q psy1195 152 SHVGIAGNEEADRLAKEA 169 (223)
Q Consensus 152 GHsGi~GNE~AD~LAk~A 169 (223)
.=+.++..-.+--+|+++
T Consensus 977 ~GTSIPDlisSvivArkG 994 (1096)
T TIGR00927 977 AGTSIPDLITSVIVARKG 994 (1096)
T ss_pred hhcccHHHHHHHHHHHcc
Confidence 344566666666666665
No 16
>KOG1832|consensus
Probab=59.38 E-value=2.4 Score=45.27 Aligned_cols=9 Identities=11% Similarity=0.497 Sum_probs=4.3
Q ss_pred ccceeEEEe
Q psy1195 25 SEWLALVLI 33 (223)
Q Consensus 25 ~~~~~~~~~ 33 (223)
--.|||+--
T Consensus 1371 D~~l~vIe~ 1379 (1516)
T KOG1832|consen 1371 DSFLGVIEM 1379 (1516)
T ss_pred cceEEEEec
Confidence 345555543
No 17
>PTZ00415 transmission-blocking target antigen s230; Provisional
Probab=55.82 E-value=2.3 Score=47.94 Aligned_cols=17 Identities=24% Similarity=0.397 Sum_probs=9.0
Q ss_pred CCCCccceeEEEecCcc
Q psy1195 21 GLPDSEWLALVLIDSPR 37 (223)
Q Consensus 21 ~~~~~~~~~~~~~~~~~ 37 (223)
|--.-.-|-+|||--.|
T Consensus 120 g~~~~~~~d~~i~~~~~ 136 (2849)
T PTZ00415 120 GKAEIGDLDMIIIKRRR 136 (2849)
T ss_pred chhhcCCcceEEeehHH
Confidence 33334456677775433
No 18
>KOG1834|consensus
Probab=46.95 E-value=4 Score=42.24 Aligned_cols=6 Identities=33% Similarity=0.534 Sum_probs=2.3
Q ss_pred eecCCC
Q psy1195 8 IRSSPE 13 (223)
Q Consensus 8 ~~~~~~ 13 (223)
||+.+.
T Consensus 851 ir~~h~ 856 (952)
T KOG1834|consen 851 IRDAHR 856 (952)
T ss_pred eecccc
Confidence 333333
No 19
>PF03896 TRAP_alpha: Translocon-associated protein (TRAP), alpha subunit; InterPro: IPR005595 The alpha-subunit of the TRAP complex (TRAP alpha) is a single-spanning membrane protein of the endoplasmic reticulum (ER) which is found in proximity of nascent polypeptide chains translocating across the membrane [].; GO: 0005783 endoplasmic reticulum
Probab=43.33 E-value=3 Score=38.45 Aligned_cols=9 Identities=0% Similarity=0.139 Sum_probs=7.0
Q ss_pred ceEEEEecC
Q psy1195 95 RKVTTYSEN 103 (223)
Q Consensus 95 ~~I~IfTDS 103 (223)
....+|+++
T Consensus 83 dt~~~F~~~ 91 (285)
T PF03896_consen 83 DTTILFPKP 91 (285)
T ss_pred eEEEEeccc
Confidence 456889998
No 20
>PF02724 CDC45: CDC45-like protein; InterPro: IPR003874 CDC45 is an essential gene required for initiation of DNA replication in Saccharomyces cerevisiae (cell division control protein 45), forming a complex with MCM5/CDC46. Homologs of CDC45 have been identified in human [], mouse and the smut fungus, Melampsora spp., (tsd2 protein) among others.; GO: 0006270 DNA-dependent DNA replication initiation
Probab=43.25 E-value=5.5 Score=40.24 Aligned_cols=16 Identities=31% Similarity=0.297 Sum_probs=11.6
Q ss_pred cceeEEEecCcccccc
Q psy1195 26 EWLALVLIDSPRYLDN 41 (223)
Q Consensus 26 ~~~~~~~~~~~~~~~~ 41 (223)
...-+.||||-|-+.-
T Consensus 74 ~~~~iyViDshRP~~L 89 (622)
T PF02724_consen 74 EDVTIYVIDSHRPWNL 89 (622)
T ss_pred CceEEEEEeCCCCccH
Confidence 5667788888887653
No 21
>KOG1189|consensus
Probab=40.12 E-value=12 Score=39.35 Aligned_cols=9 Identities=22% Similarity=0.560 Sum_probs=4.4
Q ss_pred ccCCCCCCc
Q psy1195 40 DNSGYDSGI 48 (223)
Q Consensus 40 ~~~~~~~~~ 48 (223)
+-|+|....
T Consensus 888 e~~~y~psd 896 (960)
T KOG1189|consen 888 EDSAYEPSD 896 (960)
T ss_pred ccccCCccc
Confidence 345555543
No 22
>KOG1307|consensus
Probab=32.14 E-value=15 Score=36.87 Aligned_cols=6 Identities=17% Similarity=0.346 Sum_probs=2.6
Q ss_pred HHHHHH
Q psy1195 164 RLAKEA 169 (223)
Q Consensus 164 ~LAk~A 169 (223)
-.||++
T Consensus 480 IVARKG 485 (588)
T KOG1307|consen 480 IVARKG 485 (588)
T ss_pred hhcccc
Confidence 344444
No 23
>PF07423 DUF1510: Protein of unknown function (DUF1510); InterPro: IPR009988 This family consists of several hypothetical bacterial proteins of around 200 residues in length. The function of this family is unknown.
Probab=31.47 E-value=34 Score=30.52 Aligned_cols=61 Identities=13% Similarity=0.175 Sum_probs=28.2
Q ss_pred eEEEEecChhhHhhhccCCCC---CCCCchhhcc------cChhHHHHHHHHHh-cCCceEEEEeccCCCCc
Q psy1195 96 KVTTYSENRQKTVEICPEAVK---IPPSAATILT------KWPDDIQNFLILFL-SKLDVQFVWVPSHVGIA 157 (223)
Q Consensus 96 ~I~IfTDSqyaI~aI~~~~~~---~~~Sgq~il~------~~~~i~q~i~~ll~-~~~~V~~~WVPGHsGi~ 157 (223)
.++-=.|...+-..+.++.|. ..++|..+.. .|.++.++|.-... ..-...+.|| |+.|.|
T Consensus 111 ~~~~~~~~~~v~~~~t~~~W~pvgT~Q~g~h~~~y~~~S~DW~Em~~Ais~atgi~~~~mi~w~i-gn~G~~ 181 (217)
T PF07423_consen 111 TETEESDDPNVEKTITNPSWKPVGTEQTGEHVMTYDSGSVDWNEMLKAISYATGISEDNMIVWFI-GNNGSP 181 (217)
T ss_pred cccCCCCccccccceeccCccccccccCCCccccccCCCcCHHHHHHHHHHhhCCChhheEEEhh-hcCCcc
Confidence 344445555666777776652 3344443222 12223333322211 2234666665 777754
No 24
>PF03986 Autophagy_N: Autophagocytosis associated protein (Atg3), N-terminal domain ; InterPro: IPR007134 Proteins in this entry belong to the Atg3 group of proteins and the Atg3 conjugation enzymes. Autophagy is a degradative transport pathway that delivers cytosolic proteins to the lysosome (vacuole) [] and is induced by starvation []. Cytosolic proteins appear inside the vacuole enclosed in autophagic vesicles. Autophagy significantly differs from other transport pathways by using double membrane layered transport intermediates, called autophagosomes [, ]. The breakdown of vesicular transport intermediates is a unique feature of autophagy []. Autophagy can also function in the elimination of invading bacteria and antigens []. Atg3 is the E2 enzyme for the LC3 lipidation process []. It is essential for autophagocytosis. The super protein complex, the Atg16L complex, consists of multiple Atg12-Atg5 conjugates. Atg16L has an E3-like role in the LC3 lipidation reaction. The activated intermediate, LC3-Atg3 (E2), is recruited to the site where the lipidation takes place []. Atg3 catalyses the conjugation of Atg8 and phosphatidylethanolamine (PE). Atg3 has an alpha/beta-fold, and its core region is topologically similar to canonical E2 enzymes. Atg3 has two regions inserted in the core region and another with a long alpha-helical structure that protrudes from the core region as far as 30 A []. It interacts with atg8 through an intermediate thioester bond between Cys-288 and the C-terminal Gly of atg8. It also interacts with the C-terminal region of the E1-like atg7 enzyme. Autophagocytosis is a starvation-induced process responsible for transport of cytoplasmic proteins to the lysosome/vacuole. Atg3 is a ubiquitin like modifier that is topologically similar to the canonical E2 enzyme []. It catalyses the conjugation of Atg8 and phosphatidylethanolamine []. This domain is the N-terminal of Atg3 while the C-terminal is represented by IPR007135 from INTERPRO.; PDB: 3T7G_C 2DYT_A.
Probab=30.25 E-value=31 Score=28.86 Aligned_cols=12 Identities=42% Similarity=0.686 Sum_probs=6.3
Q ss_pred eEEeecCCCccc
Q psy1195 5 FLIIRSSPEPER 16 (223)
Q Consensus 5 ~~~~~~~~~~~~ 16 (223)
|||.|.-|--.|
T Consensus 67 fLvtRnVPC~~R 78 (145)
T PF03986_consen 67 FLVTRNVPCYRR 78 (145)
T ss_dssp -EEEEEEEE-S-
T ss_pred EEEecCcccHHh
Confidence 777777665555
No 25
>PF11705 RNA_pol_3_Rpc31: DNA-directed RNA polymerase III subunit Rpc31; InterPro: IPR024661 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. RNA polymerase III contains seventeen subunits in yeasts and in human cells. Twelve of these are akin to RNA polymerase I or II and the other five are RNA polymerase III-specific, and form the functionally distinct groups: (i) Rpc31-Rpc34-Rpc82, and (ii) Rpc37-Rpc53. Rpc31, Rpc34 and Rpc82 form a cluster of enzyme-specific subunits that contribute to transcription initiation in Saccharomyces cerevisiae and Homo sapiens. There is evidence that these subunits are anchored at or near the N-terminal Zn-fold of Rpc1, itself prolonged by a highly conserved but RNA polymerase III-specific domain []. This entry represents the Rpc31 subunit.
Probab=30.23 E-value=11 Score=33.24 Aligned_cols=11 Identities=18% Similarity=0.407 Sum_probs=5.7
Q ss_pred cCceEEEEecC
Q psy1195 93 ERRKVTTYSEN 103 (223)
Q Consensus 93 ~~~~I~IfTDS 103 (223)
.-.++.-|-|+
T Consensus 206 ~DYna~~YFDn 216 (233)
T PF11705_consen 206 DDYNAENYFDN 216 (233)
T ss_pred CCcchhccCCC
Confidence 34445555554
No 26
>KOG2652|consensus
Probab=29.38 E-value=11 Score=35.85 Aligned_cols=9 Identities=22% Similarity=0.069 Sum_probs=4.0
Q ss_pred cCCceEEEE
Q psy1195 141 SKLDVQFVW 149 (223)
Q Consensus 141 ~~~~V~~~W 149 (223)
.++...|.-
T Consensus 333 ngkDY~F~K 341 (348)
T KOG2652|consen 333 NGKDYVFQK 341 (348)
T ss_pred CCceeEeee
Confidence 344444443
No 27
>PF02724 CDC45: CDC45-like protein; InterPro: IPR003874 CDC45 is an essential gene required for initiation of DNA replication in Saccharomyces cerevisiae (cell division control protein 45), forming a complex with MCM5/CDC46. Homologs of CDC45 have been identified in human [], mouse and the smut fungus, Melampsora spp., (tsd2 protein) among others.; GO: 0006270 DNA-dependent DNA replication initiation
Probab=26.90 E-value=17 Score=36.86 Aligned_cols=11 Identities=9% Similarity=0.223 Sum_probs=6.1
Q ss_pred eEEEecCcccc
Q psy1195 29 ALVLIDSPRYL 39 (223)
Q Consensus 29 ~~~~~~~~~~~ 39 (223)
.+|++|-+..-
T Consensus 98 ~v~v~ddg~~~ 108 (622)
T PF02724_consen 98 QVIVFDDGDIE 108 (622)
T ss_pred cEEEEECCChh
Confidence 46666655543
No 28
>KOG1909|consensus
Probab=21.40 E-value=31 Score=33.29 Aligned_cols=58 Identities=33% Similarity=0.288 Sum_probs=0.0
Q ss_pred cCCCCccceeEEEecCccccccCCCCCCcccchhhhhhhhhhhhHHHHHHHhhhhhhhhchHHHHHHH
Q psy1195 20 SGLPDSEWLALVLIDSPRYLDNSGYDSGIFTYLEEEEEEEEEDDKEEERVEREEEEEEEDDEEEERFE 87 (223)
Q Consensus 20 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 87 (223)
++.|.-.++..-+-|+..++..- .+++++++..+++.+.+.+++++..+++.++|..+
T Consensus 322 ~~~~~~~~~~~~~~~s~e~l~~e----------g~e~e~~~~~~~~t~~e~~ed~e~ie~e~~ee~~e 379 (382)
T KOG1909|consen 322 SKFDTAHVLLEDIDDSEEELERE----------GEEDEEEEVEKKETFKELNEDGEVIEEEGIEELKE 379 (382)
T ss_pred HhcccccccchhhchhHHHHHhh----------hhhHHHHHHHhcCcchhhcccccccchhHHHHhhh
Done!