Query 000387
Match_columns 1588
No_of_seqs 185 out of 1030
Neff 3.4
Searched_HMMs 46136
Date Fri Mar 29 06:47:35 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/000387.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/000387hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG5260 TRF4 DNA polymerase si 100.0 8E-42 1.7E-46 394.3 26.1 278 1210-1563 54-349 (482)
2 KOG1906 DNA polymerase sigma [ 100.0 2.1E-41 4.6E-46 397.2 24.9 279 1210-1563 60-348 (514)
3 PTZ00418 Poly(A) polymerase; P 99.9 3.6E-21 7.7E-26 230.1 28.4 289 1210-1558 67-390 (593)
4 KOG2277 S-M checkpoint control 99.9 1.5E-21 3.3E-26 232.7 21.9 254 1236-1557 136-431 (596)
5 cd05402 NT_PAP_TUTase Nucleoti 99.8 5.4E-19 1.2E-23 170.2 13.5 112 1236-1422 3-114 (114)
6 KOG2245 Poly(A) polymerase and 99.8 1.7E-17 3.8E-22 193.5 20.5 300 1211-1580 31-361 (562)
7 COG5186 PAP1 Poly(A) polymeras 99.5 1.1E-12 2.4E-17 149.1 20.2 248 1253-1559 82-340 (552)
8 TIGR03671 cca_archaeal CCA-add 99.3 4.5E-10 9.6E-15 131.8 23.1 224 1222-1538 7-237 (408)
9 PRK13300 tRNA CCA-pyrophosphor 99.3 3.8E-10 8.2E-15 133.8 22.2 225 1221-1538 7-240 (447)
10 PF04928 PAP_central: Poly(A) 99.2 5.6E-11 1.2E-15 132.2 11.1 143 1409-1559 90-242 (254)
11 PF03828 PAP_assoc: Cid1 famil 99.1 3.7E-11 8.1E-16 105.3 2.3 54 1478-1531 1-60 (60)
12 COG1746 CCA1 tRNA nucleotidylt 98.7 9.5E-07 2.1E-11 104.1 21.0 236 1214-1553 4-255 (443)
13 KOG1906 DNA polymerase sigma [ 98.5 2.1E-07 4.6E-12 112.2 7.2 76 98-184 2-77 (514)
14 PF01909 NTP_transf_2: Nucleot 97.7 1.8E-05 3.9E-10 73.5 3.1 42 1239-1280 1-42 (93)
15 cd05397 NT_Pol-beta-like Nucle 97.4 0.00023 4.9E-09 61.9 5.2 40 1238-1277 3-42 (49)
16 PF09249 tRNA_NucTransf2: tRNA 97.0 0.0016 3.5E-08 66.2 7.0 85 1432-1538 3-89 (114)
17 cd05403 NT_KNTase_like Nucleot 96.9 0.0014 3E-08 60.3 4.8 42 1239-1280 4-46 (93)
18 PF10421 OAS1_C: 2'-5'-oligoad 96.8 0.0025 5.4E-08 69.7 6.9 117 1413-1537 28-154 (190)
19 PF03813 Nrap: Nrap protein; 96.3 0.031 6.8E-07 73.4 13.1 142 1413-1556 151-299 (972)
20 cd05400 NT_2-5OAS_ClassI-CCAas 95.9 0.022 4.8E-07 57.7 7.5 64 1240-1314 10-79 (143)
21 smart00572 DZF domain in DSRM 95.9 0.15 3.3E-06 58.2 14.4 98 1409-1536 111-209 (246)
22 COG1708 Predicted nucleotidylt 95.5 0.024 5.3E-07 54.8 5.6 37 1242-1278 16-52 (128)
23 COG1669 Predicted nucleotidylt 94.8 0.045 9.7E-07 54.8 5.3 44 1237-1280 9-52 (97)
24 PRK13746 aminoglycoside resist 93.7 0.099 2.1E-06 59.9 5.7 42 1239-1280 13-56 (262)
25 PF07528 DZF: DZF domain; Int 90.0 4.3 9.3E-05 46.7 13.1 82 1402-1492 106-187 (248)
26 KOG2054 Nucleolar RNA-associat 87.1 4 8.6E-05 54.2 11.4 132 1416-1556 298-435 (1121)
27 PF14792 DNA_pol_B_palm: DNA p 86.7 1.9 4.1E-05 43.7 6.9 69 1237-1318 9-77 (112)
28 KOG3793 Transcription factor N 86.5 9.2 0.0002 44.8 12.7 70 1211-1281 39-116 (362)
29 PF03813 Nrap: Nrap protein; 79.7 16 0.00034 49.2 12.8 114 1411-1532 668-797 (972)
30 PRK02098 phosphoribosyl-dephos 77.5 3.2 6.9E-05 47.0 4.9 38 1240-1279 110-153 (221)
31 TIGR03135 malonate_mdcG holo-A 76.9 3.4 7.5E-05 46.1 4.9 39 1239-1279 97-141 (202)
32 KOG2534 DNA polymerase IV (fam 68.6 18 0.00039 43.4 8.3 66 1237-1318 156-221 (353)
33 KOG2054 Nucleolar RNA-associat 53.1 1.4E+02 0.003 40.9 12.8 112 1413-1531 806-927 (1121)
34 cd05401 NT_GlnE_GlnD_like Nucl 46.8 30 0.00065 36.7 4.9 29 1252-1280 55-83 (172)
35 PRK05007 PII uridylyl-transfer 36.9 1.1E+02 0.0024 41.2 8.7 29 1252-1280 80-108 (884)
36 PF03281 Mab-21: Mab-21 protei 35.2 1.3E+02 0.0028 34.6 8.0 65 1425-1492 190-254 (292)
37 PF03445 DUF294: Putative nucl 30.8 1.6E+02 0.0035 31.0 7.2 29 1252-1280 49-77 (138)
38 PF10127 Nuc-transf: Predicted 30.8 41 0.00089 38.0 3.1 24 1255-1278 23-46 (247)
39 PF14091 DUF4269: Domain of un 30.0 5.1E+02 0.011 28.8 10.8 28 1409-1436 97-125 (152)
40 smart00483 POLXc DNA polymeras 28.6 1.4E+02 0.0031 35.7 7.1 44 1236-1280 148-191 (334)
41 PHA02603 nrdC.11 hypothetical 28.3 30 0.00065 41.8 1.5 24 1255-1278 6-29 (330)
42 PF10620 MdcG: Phosphoribosyl- 26.5 48 0.001 37.5 2.7 40 1238-1279 104-149 (213)
43 PF08310 LGFP: LGFP repeat; I 26.1 37 0.00081 30.5 1.4 20 898-917 13-32 (54)
44 COG1665 Predicted nucleotidylt 23.8 84 0.0018 37.5 3.9 37 1242-1278 110-147 (315)
45 cd00141 NT_POLXc Nucleotidyltr 22.8 1.3E+02 0.0029 35.6 5.4 43 1237-1280 145-187 (307)
46 PRK00227 glnD PII uridylyl-tra 22.2 1.3E+02 0.0029 39.6 5.7 44 1237-1280 10-55 (693)
No 1
>COG5260 TRF4 DNA polymerase sigma [DNA replication, recombination, and repair]
Probab=100.00 E-value=8e-42 Score=394.35 Aligned_cols=278 Identities=28% Similarity=0.462 Sum_probs=233.3
Q ss_pred HHHHHHHHHHHHHHhhhhHHhhhHHHHHHHHHHHHHHhccCCCCceEEecccccCCCCCCCCceEEEEcCCCCCCccccc
Q 000387 1210 HSLLHEEIDSFCKQVAAENTARKPYINWAVKRVTRSLQVLWPRSRTNIFGSNATGLSLPSSDVDLVVCLPPVRNLEPIKE 1289 (1588)
Q Consensus 1210 ~s~LheEIldF~k~I~PEeeeRK~~I~~AVkrVe~vIQsLwPdArVepFGS~ATGLaLPsSDIDLVVi~PpvrnlEPike 1289 (1588)
...|+.||.+|+.+++|+.++-+ .+..++++|+.++.+.||++.+.+|||+.|||++|.|||||||..++....+
T Consensus 54 ~~~lt~el~~~y~~I~ps~eEl~-~R~~~leklr~~lk~~~pda~l~vFGS~~t~L~l~~SDiDl~I~s~~~~~~e---- 128 (482)
T COG5260 54 SDELTSELLEFYDYIAPSDEELK-RRKALLEKLRTLLKKEFPDADLKVFGSTETGLALPKSDIDLCIISDPRGYKE---- 128 (482)
T ss_pred HHHHHHHHHHHHHhhCCCHHHHH-HHHHHHHHHHHHHHHhCCccceeEecccccccccCcccccEEEecCCccccc----
Confidence 34799999999999999643222 1356899999999999999999999999999999999999999987543322
Q ss_pred ccccccccchhHHHHHHHHHHHhhcCCcccCCeEEecCCCccEEEEEEccCchhhhhhccccCCCcccccccccccCCcc
Q 000387 1290 AGILEGRNGIKETCLQHAARYLANQEWVKSDSLKTVENTAIPIIMLVVEVPHDLIASAASSVQSPKEDAAHTTLKHDNHV 1369 (1588)
Q Consensus 1290 AGiLE~RN~IKet~Lq~LAR~Lr~~~~Vks~sVqvIenARVPIIKfv~dVP~DLs~~y~~~i~Sske~pv~i~~~~~spv 1369 (1588)
.++. +..+.-++++..|. .+++|.+||||||||++
T Consensus 129 -----t~~~-----~~l~~~l~~~~~~~---~~~~v~tarVPIIKl~d-------------------------------- 163 (482)
T COG5260 129 -----TRNA-----GSLASHLFKKNLAK---EVVVVSTARVPIIKLVD-------------------------------- 163 (482)
T ss_pred -----cccH-----HHHHHHHHHhccCe---eeEEEEecccceEEEec--------------------------------
Confidence 2221 11222334444554 68999999999999984
Q ss_pred ccccccccCCCCCCCCCCCCCcccCCCccEEEEEeeCCCCcHHHHHHHHHHHHhhCCChHHHHHHHHHHHHhCCCCCCCC
Q 000387 1370 HSDMVALDDSASPKCSHTSSDNIKAATSVRLDISFKSPSHTGLQTTDLVKELTEQFPASTPLALVLKQFLADRSLDQSYS 1449 (1588)
Q Consensus 1370 ~sDi~~sedS~sp~C~~~~~ds~D~~tGIsVDISFnnpSh~GLrnSeLIreyieqyPrLRPLVLVLK~WLKqRGLNDpyt 1449 (1588)
...+++|||+|++ ..|+.++++++.|...+|++|||+++||+||++|.||+++.
T Consensus 164 ------------------------~~s~l~~Disfn~--~~~~~~akl~~~~~~~~P~lrpLvliIKhwl~~R~ln~~~~ 217 (482)
T COG5260 164 ------------------------PQSGLHCDISFNN--TNGIVNAKLIRSYLKEDPRLRPLVLIIKHWLKRRALNDVAT 217 (482)
T ss_pred ------------------------CccceEEEeecCc--hhHHHHHHHHHHHHhcCcccchHHHHHHHHHHHHhhccccc
Confidence 2478999999999 89999999999999999999999999999999999999999
Q ss_pred CCcchHHHHHHHHHHHhccCc---C----CCC-----CCCcHHHHHHHHHHHhccCCCCCCceEEeeCCccccc-ccCCC
Q 000387 1450 GGLSSYCLMLLITRFLQHEHH---L----GRP-----INQNYGRLLMDFLYFFGNVFDPRQMRISVQGSGVYIK-RERGY 1516 (1588)
Q Consensus 1450 GGLSSYALVLMVIaFLQ~~p~---L----GRP-----iNqnLGeLLLdFF~FYG~eFDy~ttgISIr~gGiy~k-KErG~ 1516 (1588)
|||+||++++||+.|||+++. . ..+ .-.+||.||++||+|||..|+|...+|+++.++.|.+ .+.||
T Consensus 218 GtL~sy~i~cmV~sfLq~~~~~~~~~~~~~~~l~~~~~~~~lgvLf~dFf~~yG~~f~Y~~~~~si~~g~~~~~K~e~g~ 297 (482)
T COG5260 218 GTLSSYTISCMVLSFLQMHPPFLFFDNGLLSPLKYNKNIDNLGVLFDDFFELYGKSFNYSLVVLSINSGDFYLPKYEKGW 297 (482)
T ss_pred CcchhhhhHHHHHHHHHhCCccccccccccchhhccccccccchHHHHHHHHhccccChhheEEEecCCceeeehhhccc
Confidence 999999999999999999862 1 111 2368999999999999999999999999998866654 45555
Q ss_pred C---C-CCeEEeCCC-CCCCccccCcccHHHHHHHHHHHHHHHHHHhhhcCC
Q 000387 1517 S---I-DPIHIDDPR-FPTNNVGRNCFRIHQCIKAFSDAYSILESELTSLTP 1563 (1588)
Q Consensus 1517 s---~-spL~IEDPf-dpsNNVGRnsfrI~qIqkaFarAyeiLs~~L~~l~s 1563 (1588)
- . ..|+||||. +.++++++.++++..|+.+|++|+++|.+.+..+.+
T Consensus 298 ~~~~~p~~LsiqdP~td~n~~~~a~s~~ik~i~~~F~~aF~lls~~~~tl~~ 349 (482)
T COG5260 298 LKPSKPNSLSIQDPGTDRNNDISAVSFNIKDIKAAFIRAFELLSNKLFTLTS 349 (482)
T ss_pred ccccCCCcEeecCCCCCcccccccccchHHHHHHHHHHHHHHHhhhcchhhh
Confidence 3 2 679999999 999999999999999999999999999998876655
No 2
>KOG1906 consensus DNA polymerase sigma [Replication, recombination and repair]
Probab=100.00 E-value=2.1e-41 Score=397.19 Aligned_cols=279 Identities=32% Similarity=0.524 Sum_probs=232.7
Q ss_pred HHHHHHHHHHHHHHhhhhHHhhhHHHHHHHHHHHHHHhccCCCCceEEecccccCCCCCCCCceEEEEcCCCCCCccccc
Q 000387 1210 HSLLHEEIDSFCKQVAAENTARKPYINWAVKRVTRSLQVLWPRSRTNIFGSNATGLSLPSSDVDLVVCLPPVRNLEPIKE 1289 (1588)
Q Consensus 1210 ~s~LheEIldF~k~I~PEeeeRK~~I~~AVkrVe~vIQsLwPdArVepFGS~ATGLaLPsSDIDLVVi~PpvrnlEPike 1289 (1588)
...||+||.+|++|+.|+.++- .++..++++|++.|...||+|.|++|||+.|||+||+|||||+|........+
T Consensus 60 s~~l~~eI~~fv~~l~pt~~e~-~~R~~~~~~i~~~v~~~~~~a~v~~FGS~~tglyLP~sDIDl~v~~~~~~~~e---- 134 (514)
T KOG1906|consen 60 SERLRNEILDFVQYLIPTPEEI-EVRSELVEKIRDVVKQKWPDASVYVFGSVPTGLYLPDSDIDLVVLSKFLNDKE---- 134 (514)
T ss_pred HHHHHHHHHHHHHHhcCCchHH-HHHHHHHHHHHHHHHHhcccceeEEeeeeeccccccccceEEEEecccccCch----
Confidence 4469999999999999874332 24567899999999999999999999999999999999999999986432211
Q ss_pred ccccccccchhHHHHHHHHHHHhhcCCcccCCeEEecCCCccEEEEEEccCchhhhhhccccCCCcccccccccccCCcc
Q 000387 1290 AGILEGRNGIKETCLQHAARYLANQEWVKSDSLKTVENTAIPIIMLVVEVPHDLIASAASSVQSPKEDAAHTTLKHDNHV 1369 (1588)
Q Consensus 1290 AGiLE~RN~IKet~Lq~LAR~Lr~~~~Vks~sVqvIenARVPIIKfv~dVP~DLs~~y~~~i~Sske~pv~i~~~~~spv 1369 (1588)
.+ .....++..++... ....+++|.+|+||||||++
T Consensus 135 -----~~-----~~~~~l~~~~e~~~--~~~~v~~v~karvpiik~~d-------------------------------- 170 (514)
T KOG1906|consen 135 -----DR-----AVKLELALELEEDN--SAFHVKVVQKARVPIIKFKD-------------------------------- 170 (514)
T ss_pred -----hh-----HHHHHHHHhhhhcc--ccceEEEeeeeeeeeEEeec--------------------------------
Confidence 01 11122333332211 22368999999999999984
Q ss_pred ccccccccCCCCCCCCCCCCCcccCCCccEEEEEeeCCCCcHHHHHHHHHHHHhhCCChHHHHHHHHHHHHhCCCCCCCC
Q 000387 1370 HSDMVALDDSASPKCSHTSSDNIKAATSVRLDISFKSPSHTGLQTTDLVKELTEQFPASTPLALVLKQFLADRSLDQSYS 1449 (1588)
Q Consensus 1370 ~sDi~~sedS~sp~C~~~~~ds~D~~tGIsVDISFnnpSh~GLrnSeLIreyieqyPrLRPLVLVLK~WLKqRGLNDpyt 1449 (1588)
..++|.+||||++ .+|++++++++.+.+.+|.+++|++++|+||..|+||++++
T Consensus 171 ------------------------~~s~i~vDISFn~--~~G~~aa~~i~~~~~~~p~~~~lvlvlk~fl~~r~ln~v~t 224 (514)
T KOG1906|consen 171 ------------------------PVSNIHVDISFNQ--TNGVKAAKFIKDFLRDHPFLRSLVLVLKQFLYERRLNGVHT 224 (514)
T ss_pred ------------------------CccceEEEeeecc--cCchhHHHHHHHHHhcCccchhHHHHHHHHHHhhccccccc
Confidence 2478999999999 89999999999999999999999999999999999999999
Q ss_pred CCcchHHHHHHHHHHHhccCcC--CC-CCCCcHHHHHHHHHHHhccCCCCCCceEEeeCCcccccccC-CC------CCC
Q 000387 1450 GGLSSYCLMLLITRFLQHEHHL--GR-PINQNYGRLLMDFLYFFGNVFDPRQMRISVQGSGVYIKRER-GY------SID 1519 (1588)
Q Consensus 1450 GGLSSYALVLMVIaFLQ~~p~L--GR-PiNqnLGeLLLdFF~FYG~eFDy~ttgISIr~gGiy~kKEr-G~------s~s 1519 (1588)
|||+||+|++|+++|||+++.. ++ ....++|.||++||+|||..|+|.+.+|++..+|.+..++. ++ ...
T Consensus 225 GgisSyal~~Lv~~fl~l~~~~~s~~~~~~~~~~vll~~f~e~yG~~f~~~k~~i~~~~~g~~~~~~~~~~~~~~~~~~~ 304 (514)
T KOG1906|consen 225 GGISSYALELLVLSFLQLHPRSKSGRLAVLKNLGVLLIKFFELYGRNFGYDKLGISLSLGGEYVSKELTGFFNNSLERPG 304 (514)
T ss_pred ccchHHHHHHHHHHHHhhcccccCCccchhcccchHHHHHHHHhccccCchhhceeccCCcccccHHhhhhhcccccCCC
Confidence 9999999999999999999864 22 12468999999999999999999999999998887664432 22 235
Q ss_pred CeEEeCCCCCCCccccCcccHHHHHHHHHHHHHHHHHHhhhcCC
Q 000387 1520 PIHIDDPRFPTNNVGRNCFRIHQCIKAFSDAYSILESELTSLTP 1563 (1588)
Q Consensus 1520 pL~IEDPfdpsNNVGRnsfrI~qIqkaFarAyeiLs~~L~~l~s 1563 (1588)
.++|+||.+++||+||++|++.+|..+|.+|+..|.........
T Consensus 305 ~LsieDP~~P~ndigr~s~~~~~v~~~F~~af~~l~~~~~~~~s 348 (514)
T KOG1906|consen 305 SLSIEDPVDPTNDIGRSSFNFSQVKGAFAYAFKVLTNAVFSHGS 348 (514)
T ss_pred ccccCCCCCcccccccccccHHHHHHHHHHHHHHHhhhhcccch
Confidence 69999999999999999999999999999999999998886663
No 3
>PTZ00418 Poly(A) polymerase; Provisional
Probab=99.88 E-value=3.6e-21 Score=230.08 Aligned_cols=289 Identities=17% Similarity=0.219 Sum_probs=204.9
Q ss_pred HHHHHHHHHHHHHHhh--hh-HHhhhHHHHHHHHHHHHHHhcc---------C-------CCCceEEecccccCCCCCCC
Q 000387 1210 HSLLHEEIDSFCKQVA--AE-NTARKPYINWAVKRVTRSLQVL---------W-------PRSRTNIFGSNATGLSLPSS 1270 (1588)
Q Consensus 1210 ~s~LheEIldF~k~I~--PE-eeeRK~~I~~AVkrVe~vIQsL---------w-------PdArVepFGS~ATGLaLPsS 1270 (1588)
...+..||..|.+... ++ ++.++ ++.|+..|+++|+.. . ..++|++||||..|.+.|+|
T Consensus 67 d~~~s~~L~~~L~~~~~fes~ee~~k--R~~vL~~L~~iv~~wv~~vs~~k~~~~~~~~~~~g~I~tfGSYrLGV~~pgS 144 (593)
T PTZ00418 67 DLKLSNELINLLKSYNLYETEEGKKK--RERVLGSLNKLVREFVVEASIEQGINEEEASQISGKLFTFGSYRLGVVAPGS 144 (593)
T ss_pred HHhhhHHHHHHHHHcCCCCCHHHHHH--HHHHHHHHHHHHHHHHHHHHHhcCCChhHHhcCCeEEEEeccccccCCCCCC
Confidence 3456888888887532 22 22222 356777777777541 1 24799999999999999999
Q ss_pred CceEEEEcCCCCCCcccccccccccccchhHHHHHHHHHHHhhcCCcccCCeEEecCCCccEEEEEE-ccCchhhhhhcc
Q 000387 1271 DVDLVVCLPPVRNLEPIKEAGILEGRNGIKETCLQHAARYLANQEWVKSDSLKTVENTAIPIIMLVV-EVPHDLIASAAS 1349 (1588)
Q Consensus 1271 DIDLVVi~PpvrnlEPikeAGiLE~RN~IKet~Lq~LAR~Lr~~~~Vks~sVqvIenARVPIIKfv~-dVP~DLs~~y~~ 1349 (1588)
|||.++++|..-+ ++.....+...|++..-++ ++..|+.|+||||||+. +|.+||....
T Consensus 145 DID~L~V~P~~vt----------------redFF~~f~~~L~~~~~V~--eL~~V~~A~VPiIk~~~~GI~iDL~fa~-- 204 (593)
T PTZ00418 145 DIDTLCLAPRHIT----------------RESFFSDFYAKLQQDPNIT--KLQPVPDAYTPVIKFVYDGIDIDLLFAN-- 204 (593)
T ss_pred cccEEEECCCCCC----------------HHHHHHHHHHHHhcCCCcc--eeeccCccccCeEEEEECCEEEeeeecc--
Confidence 9999999984321 2355667777888876664 78999999999999986 4677765211
Q ss_pred ccCCCcccccccccccCCccccccccccCCCCCCCCCCCCCcccCCCccEEEEEeeCCCCcHHHHHHHHHHHHhhCCChH
Q 000387 1350 SVQSPKEDAAHTTLKHDNHVHSDMVALDDSASPKCSHTSSDNIKAATSVRLDISFKSPSHTGLQTTDLVKELTEQFPAST 1429 (1588)
Q Consensus 1350 ~i~Sske~pv~i~~~~~spv~sDi~~sedS~sp~C~~~~~ds~D~~tGIsVDISFnnpSh~GLrnSeLIreyieqyPrLR 1429 (1588)
+.. ..++ ...| ..++.. ...++. +-++. +.+|++.++.|.+++.....||
T Consensus 205 -l~~---~~vp--------~~~~--~l~d~~-------------lL~nld-e~s~r--SLNG~Rvtd~Il~lVPn~~~Fr 254 (593)
T PTZ00418 205 -LPL---PTIP--------DCLN--SLDDDY-------------ILRNVD-EKTVR--SLNGCRVADLILASVPNKDYFR 254 (593)
T ss_pred -cCC---CCCC--------cccc--ccCchh-------------hhhcCC-HHHhh--hhccHHHHHHHHHHCCChHHHH
Confidence 000 0000 0111 000000 011110 01233 3789999999999999999999
Q ss_pred HHHHHHHHHHHhCCCCCCCCCCcchHHHHHHHHHHHhccCcCCCCCCCcHHHHHHHHHHHhccCCCCCCceEEeeC----
Q 000387 1430 PLALVLKQFLADRSLDQSYSGGLSSYCLMLLITRFLQHEHHLGRPINQNYGRLLMDFLYFFGNVFDPRQMRISVQG---- 1505 (1588)
Q Consensus 1430 PLVLVLK~WLKqRGLNDpytGGLSSYALVLMVIaFLQ~~p~LGRPiNqnLGeLLLdFF~FYG~eFDy~ttgISIr~---- 1505 (1588)
.++++||.|+|+|||+....|+|++-+|.+||.+.+|.+|. .+.+.||..||++|+ .|+|.+- |.+..
T Consensus 255 ~aLR~IKlWAkrRGIYsNv~GflGGV~wAILvARVCQLyPn------a~~s~Lv~~FF~iys-~W~Wp~P-V~L~~i~~~ 326 (593)
T PTZ00418 255 TTLRFIKLWAKRRGIYSNVLGYLGGVSWAILTARICQLYPN------FAPSQLIHKFFRVYS-IWNWKNP-VLLCKIKEV 326 (593)
T ss_pred HHHHHHHHHHHHhccccccccccchHHHHHHHHHHHHhCCC------CCHHHHHHHHHHHhh-cCCCCCC-eEccccccc
Confidence 99999999999999999999999999999999999999874 567999999999998 5999885 33321
Q ss_pred ---Ccc-----cccc-cCCCCCCCeEEeCCCCCCCccccCcc--cHHHHHHHHHHHHHHHHHHh
Q 000387 1506 ---SGV-----YIKR-ERGYSIDPIHIDDPRFPTNNVGRNCF--RIHQCIKAFSDAYSILESEL 1558 (1588)
Q Consensus 1506 ---gGi-----y~kK-ErG~s~spL~IEDPfdpsNNVGRnsf--rI~qIqkaFarAyeiLs~~L 1558 (1588)
+|. +.++ ........|.|.-|..|..|.+++.. ..+.|.++|++|.+++...+
T Consensus 327 ~~~~g~~~~~VWdPr~~~~dr~h~MPIITPayP~mNst~nVt~sT~~vI~~Ef~Ra~~i~~~i~ 390 (593)
T PTZ00418 327 PNIPGLMNFKVWDPRVNPQDRAHLMPIITPAFPSMNSTHNVTYTTKRVITEEFKRAHEIIKYIE 390 (593)
T ss_pred ccCCcccCCcccCCCCCcccccccCCeecCCCCCccccccccHHHHHHHHHHHHHHHHHHHHHH
Confidence 222 2221 11122368999999999999888853 46779999999999999643
No 4
>KOG2277 consensus S-M checkpoint control protein CID1 and related nucleotidyltransferases [Cell cycle control, cell division, chromosome partitioning]
Probab=99.88 E-value=1.5e-21 Score=232.73 Aligned_cols=254 Identities=23% Similarity=0.366 Sum_probs=198.8
Q ss_pred HHHHHHHHHHHhccCCCCceE--EecccccCCCCCCCCceEEEEcCCCCCCcccccccccccccchhHHHHHHHHHHHhh
Q 000387 1236 NWAVKRVTRSLQVLWPRSRTN--IFGSNATGLSLPSSDVDLVVCLPPVRNLEPIKEAGILEGRNGIKETCLQHAARYLAN 1313 (1588)
Q Consensus 1236 ~~AVkrVe~vIQsLwPdArVe--pFGS~ATGLaLPsSDIDLVVi~PpvrnlEPikeAGiLE~RN~IKet~Lq~LAR~Lr~ 1313 (1588)
..+...+..++...+|.+... +|||...|+....+|+|+++..... ..+.. ... ....+..++++|..
T Consensus 136 ~~~~~~l~~~~~~~~p~~~~~~~~~gs~~~~~~~~~~d~d~~~~~~~~-~~~~~-------~~~--~~~~~~l~~~~~~~ 205 (596)
T KOG2277|consen 136 KLILDKLRALASLLFPDSILSLYLFGSSDLGLGERSSDLDLCVDFTSS-FLSFE-------KIK--GLEILKLLAKCLAS 205 (596)
T ss_pred HHHHHHHHHHHHHhcCCCcceeeccCcccccccccccCcceeeccccc-ccccc-------hhh--hHHHHHHHHHHHHh
Confidence 356788899999999987666 9999999999999999977765421 11110 000 12345566677765
Q ss_pred cCCcccCCeEEecCCCccEEEEEEccCchhhhhhccccCCCcccccccccccCCccccccccccCCCCCCCCCCCCCccc
Q 000387 1314 QEWVKSDSLKTVENTAIPIIMLVVEVPHDLIASAASSVQSPKEDAAHTTLKHDNHVHSDMVALDDSASPKCSHTSSDNIK 1393 (1588)
Q Consensus 1314 ~~~Vks~sVqvIenARVPIIKfv~dVP~DLs~~y~~~i~Sske~pv~i~~~~~spv~sDi~~sedS~sp~C~~~~~ds~D 1393 (1588)
..--....++.|..|+|||||+.+
T Consensus 206 ~~~~~~~~~~~i~~A~vPiik~~~-------------------------------------------------------- 229 (596)
T KOG2277|consen 206 LLEEGVREVQQILSARVPIIKFND-------------------------------------------------------- 229 (596)
T ss_pred ccccccceeeeeeecCCCEEEecC--------------------------------------------------------
Confidence 431002368899999999999852
Q ss_pred CCCccEEEEEeeCCCCcHHHHHHHHHHHHhhCCChHHHHHHHHHHHHhCCCCCCCCCCcc-hHHHHHHHHHHHhccCc--
Q 000387 1394 AATSVRLDISFKSPSHTGLQTTDLVKELTEQFPASTPLALVLKQFLADRSLDQSYSGGLS-SYCLMLLITRFLQHEHH-- 1470 (1588)
Q Consensus 1394 ~~tGIsVDISFnnpSh~GLrnSeLIreyieqyPrLRPLVLVLK~WLKqRGLNDpytGGLS-SYALVLMVIaFLQ~~p~-- 1470 (1588)
...++.+|+++++ ..|+.|+.+++.|.+.++++++|++++|+|++.++++++..|+++ ||+|++||++|||....
T Consensus 230 ~~~~~~~d~s~~n--~~~~~nS~ll~~~~~~d~r~~~L~~~vk~wa~~~~~~d~~~g~~~s~ysl~lmvi~fLq~~~~~i 307 (596)
T KOG2277|consen 230 SGSGLECDLSVNN--SDAILNSQLLRNYSEIDPRVRPLVLLVKHWAKEKGLNDAKPGGLNSSYSLTLMVIHFLQTLSPPI 307 (596)
T ss_pred CCCCCceeeeecc--chhhhhhHHHHHhHhcCCCcchHhHHHHHHHHhccCCCCCCCceeccccHHHHHHHHHHhcCCcC
Confidence 2467789999999 799999999999999999999999999999999999999999999 69999999999998631
Q ss_pred ---CC---------------------------C-----CCCCcHHHHHHHHHHHhccCCCCCCceEEeeCCcccccccCC
Q 000387 1471 ---LG---------------------------R-----PINQNYGRLLMDFLYFFGNVFDPRQMRISVQGSGVYIKRERG 1515 (1588)
Q Consensus 1471 ---LG---------------------------R-----PiNqnLGeLLLdFF~FYG~eFDy~ttgISIr~gGiy~kKErG 1515 (1588)
+. + +...+++.|+++||+||+..|||.+..|+++.+-.+......
T Consensus 308 lp~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~f~~yy~~~Fdf~~~~I~~r~~~~l~~~~~~ 387 (596)
T KOG2277|consen 308 LPPLSKLLPESDSNDKPVVKKKVLCSFLRVFQRNPSNSQNTGSLGELLLGFFSYYASLFDFRKNAISIRRGRALKRAKKI 387 (596)
T ss_pred CCchhhhchhcccccccchhhhhhhccccccccccccccccchHHHHHHHHHHHHhhhcccccceeeeeecccccccchh
Confidence 00 0 112467899999999999889999999999987555432234
Q ss_pred CCCCCeEEeCCCCCCCccccCc--ccHHHHHHHHHHHHHHHHHH
Q 000387 1516 YSIDPIHIDDPRFPTNNVGRNC--FRIHQCIKAFSDAYSILESE 1557 (1588)
Q Consensus 1516 ~s~spL~IEDPfdpsNNVGRns--frI~qIqkaFarAyeiLs~~ 1557 (1588)
+....++|+||++..+|++.+. -....|+.+|..+...+...
T Consensus 388 ~~~~~l~i~dp~~~~~n~~~~~~~~~~~~i~~~~~~~~~~~~~~ 431 (596)
T KOG2277|consen 388 KSKKFLCIEDPFEVSHNADAGVTLKVLLLIQDEFQESRRVFKDV 431 (596)
T ss_pred hhccceeeccccccccCccccchHHHHHHHHHHHHHHHHHhhhh
Confidence 4457899999999999988764 35677889999888888865
No 5
>cd05402 NT_PAP_TUTase Nucleotidyltransferase (NT) domain of poly(A) polymerases and terminal uridylyl transferases. Poly(A) polymerases (PAPs) catalyze mRNA poly(A) tail synthesis, and terminal uridylyl transferases (TUTases) uridylate RNA. PAPs in this subgroup include human PAP alpha, mouse testis-specific cytoplasmic PAP beta, human nuclear PAP gamma, Saccharomyces cerevisiae PAP1, TRF4 and-5, Schizosaccharomyces pombe caffeine-induced death proteins -1, and -14, Caenorhabditis elegans Germ Line Development-2, and Chlamydomonas reinhardtii MUT68. This family also includes human U6 snRNA-specific TUTase1, and Trypanosoma brucei 3'-TUTase-1,-2, and 4. This family belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. For the majority of proteins in this family, these carboxyla
Probab=99.80 E-value=5.4e-19 Score=170.20 Aligned_cols=112 Identities=30% Similarity=0.490 Sum_probs=96.8
Q ss_pred HHHHHHHHHHHhccCCCCceEEecccccCCCCCCCCceEEEEcCCCCCCcccccccccccccchhHHHHHHHHHHHhhcC
Q 000387 1236 NWAVKRVTRSLQVLWPRSRTNIFGSNATGLSLPSSDVDLVVCLPPVRNLEPIKEAGILEGRNGIKETCLQHAARYLANQE 1315 (1588)
Q Consensus 1236 ~~AVkrVe~vIQsLwPdArVepFGS~ATGLaLPsSDIDLVVi~PpvrnlEPikeAGiLE~RN~IKet~Lq~LAR~Lr~~~ 1315 (1588)
+.++++|+++++..||++++++|||++||+++|+||||++|..++... .....++.+++.|++.+
T Consensus 3 ~~i~~~l~~~i~~~~~~~~v~~fGS~~~g~~~~~SDiDl~i~~~~~~~---------------~~~~~l~~l~~~l~~~~ 67 (114)
T cd05402 3 EEVLDRLQELIKEWFPGAKLYPFGSYVTGLGLPGSDIDLCLLGPNHRV---------------DREDFLRKLAKLLKKSG 67 (114)
T ss_pred HHHHHHHHHHHHHHCCCCEEEEecccccCCCCCCCCeeEEEEeCCCCc---------------cHHHHHHHHHHHHHhCC
Confidence 457899999999999999999999999999999999999999874200 12367889999999988
Q ss_pred CcccCCeEEecCCCccEEEEEEccCchhhhhhccccCCCcccccccccccCCccccccccccCCCCCCCCCCCCCcccCC
Q 000387 1316 WVKSDSLKTVENTAIPIIMLVVEVPHDLIASAASSVQSPKEDAAHTTLKHDNHVHSDMVALDDSASPKCSHTSSDNIKAA 1395 (1588)
Q Consensus 1316 ~Vks~sVqvIenARVPIIKfv~dVP~DLs~~y~~~i~Sske~pv~i~~~~~spv~sDi~~sedS~sp~C~~~~~ds~D~~ 1395 (1588)
++ .+++.|.+|||||||+++ ..
T Consensus 68 ~~--~~~~~i~~ArVPiik~~~--------------------------------------------------------~~ 89 (114)
T cd05402 68 EV--VEVEPIINARVPIIKFVD--------------------------------------------------------KP 89 (114)
T ss_pred Cc--eeeEEeccCCCCEEEEEE--------------------------------------------------------cC
Confidence 64 378999999999999985 24
Q ss_pred CccEEEEEeeCCCCcHHHHHHHHHHHH
Q 000387 1396 TSVRLDISFKSPSHTGLQTTDLVKELT 1422 (1588)
Q Consensus 1396 tGIsVDISFnnpSh~GLrnSeLIreyi 1422 (1588)
+|+.|||||++ .+|++|+++|+.|+
T Consensus 90 ~~i~~Dis~~~--~~g~~~s~li~~y~ 114 (114)
T cd05402 90 TGIEVDISFNN--LNGIRNTKLLRAYV 114 (114)
T ss_pred CCeEEEEEccc--chHHHHHHHHHHhC
Confidence 78999999999 89999999999884
No 6
>KOG2245 consensus Poly(A) polymerase and related nucleotidyltransferases [RNA processing and modification]
Probab=99.76 E-value=1.7e-17 Score=193.48 Aligned_cols=300 Identities=19% Similarity=0.213 Sum_probs=207.3
Q ss_pred HHHHHHHHHHHHHh----hhhHHhhhHHHHHHHHHHHHHHhcc---------CC-------CCceEEecccccCCCCCCC
Q 000387 1211 SLLHEEIDSFCKQV----AAENTARKPYINWAVKRVTRSLQVL---------WP-------RSRTNIFGSNATGLSLPSS 1270 (1588)
Q Consensus 1211 s~LheEIldF~k~I----~PEeeeRK~~I~~AVkrVe~vIQsL---------wP-------dArVepFGS~ATGLaLPsS 1270 (1588)
..|+.|+....+.. ..++..|+ ..++.++..+++.. .| ++++..||||..|.+.|++
T Consensus 31 ~~lt~~L~~~L~~~g~fEs~eEt~~R---~~VL~~L~~iVk~wVk~vs~~k~~p~~~~~~aggkIftfGSYRLGVhg~GA 107 (562)
T KOG2245|consen 31 IALTQELIKTLKNEGLFESKEETQRR---EEVLGKLNQIVKEWVKKVSEQKGLPDGMIENAGGKIFTFGSYRLGVHGPGA 107 (562)
T ss_pred HHHHHHHHHHHHhcCCCCCHHHHHHH---HHHHHHHHHHHHHHHHHHHHhcCCChhhhhhcCceEEeccceeecccCCCC
Confidence 34666666655432 23333332 35667777666532 33 4699999999999999999
Q ss_pred CceEEEEcCCCCCCcccccccccccccchhHHHHHHHHHHHhhcCCcccCCeEEecCCCccEEEEEE-ccCchhhhhhcc
Q 000387 1271 DVDLVVCLPPVRNLEPIKEAGILEGRNGIKETCLQHAARYLANQEWVKSDSLKTVENTAIPIIMLVV-EVPHDLIASAAS 1349 (1588)
Q Consensus 1271 DIDLVVi~PpvrnlEPikeAGiLE~RN~IKet~Lq~LAR~Lr~~~~Vks~sVqvIenARVPIIKfv~-dVP~DLs~~y~~ 1349 (1588)
|||-.++.|...+ +......+.+.|+...-|. ++..|+.|.||||||+. ++++||..+.-
T Consensus 108 DIDtLcV~Prhv~----------------R~DFF~sf~~mL~~~~eVt--eL~~V~dAfVPiikfKf~GI~IDllfArL- 168 (562)
T KOG2245|consen 108 DIDTLCVGPRHVS----------------RSDFFTSFYDMLKERPEVT--ELHAVEDAFVPIIKFKFDGIEIDLLFARL- 168 (562)
T ss_pred Ccceeeecccccc----------------HHHHHHHHHHHHhcCcccc--ccccccccccceEEEEecCeeeeeeehhc-
Confidence 9999998874322 2356777888999888775 89999999999999985 57888753211
Q ss_pred ccCCCcccccccccccCCccccccccccCCCCCCCCCCCCCcccCCCccEEEE-EeeCCCCcHHHHHHHHHHHHhhCCCh
Q 000387 1350 SVQSPKEDAAHTTLKHDNHVHSDMVALDDSASPKCSHTSSDNIKAATSVRLDI-SFKSPSHTGLQTTDLVKELTEQFPAS 1428 (1588)
Q Consensus 1350 ~i~Sske~pv~i~~~~~spv~sDi~~sedS~sp~C~~~~~ds~D~~tGIsVDI-SFnnpSh~GLrnSeLIreyieqyPrL 1428 (1588)
. +.. +.-|+..++++.. -.+|. |+. +.+|.+.++-|-.++-....|
T Consensus 169 ~--------l~~-------VP~dldl~ddslL----------------knlDe~~vr--SLNGcRVtdqiL~LVPn~~~F 215 (562)
T KOG2245|consen 169 A--------LPV-------VPEDLDLSDDSLL----------------KNLDERCVR--SLNGCRVTDQILKLVPNQENF 215 (562)
T ss_pred c--------ccc-------CCCcccccchHhh----------------hcccHHHHH--HhcCcCHHHHHHHhCCCHHHH
Confidence 0 111 1122222222210 01222 222 378999999888888888889
Q ss_pred HHHHHHHHHHHHhCCCCCCCCCCcchHHHHHHHHHHHhccCcCCCCCCCcHHHHHHHHHHHhccCCCCCCceEEee-CCc
Q 000387 1429 TPLALVLKQFLADRSLDQSYSGGLSSYCLMLLITRFLQHEHHLGRPINQNYGRLLMDFLYFFGNVFDPRQMRISVQ-GSG 1507 (1588)
Q Consensus 1429 RPLVLVLK~WLKqRGLNDpytGGLSSYALVLMVIaFLQ~~p~LGRPiNqnLGeLLLdFF~FYG~eFDy~ttgISIr-~gG 1507 (1588)
+-..+.||.|+|.||++....|.+|+-++.|||.+.+|.+| |.....|+..||..|. .++|-+-++=-. ..+
T Consensus 216 ~~tLRaiKlWAKrrgVYsN~~GF~GGV~wA~LVARiCQLYP------NA~~s~Lv~kfF~ifs-~W~WP~PVlL~~ie~~ 288 (562)
T KOG2245|consen 216 RITLRAIKLWAKRRGVYSNVMGFLGGVAWAMLVARICQLYP------NASPSTLVAKFFRVFS-QWNWPNPVLLKPIEEG 288 (562)
T ss_pred HHHHHHHHHHHHhcccccccccccchHHHHHHHHHHHccCC------CcchHHHHHHHHHHHh-hccCCCceEecccccc
Confidence 99999999999999999999999999999999999999987 4667899999999998 699987654221 112
Q ss_pred c-----cccccC-CCCCCCeEEeCCCCCCCccccCcc--cHHHHHHHHHHHHHHHHHHhhhcCCCCCCCCCCCCCCcccc
Q 000387 1508 V-----YIKRER-GYSIDPIHIDDPRFPTNNVGRNCF--RIHQCIKAFSDAYSILESELTSLTPADDQCSRPPYRLLPKI 1579 (1588)
Q Consensus 1508 i-----y~kKEr-G~s~spL~IEDPfdpsNNVGRnsf--rI~qIqkaFarAyeiLs~~L~~l~s~~~~c~~p~~~LL~~I 1579 (1588)
. +.++-. ......|.|+-|..|..|.+.|.. ....|+.+|.+|..+..+.+..- .+|-.||+++
T Consensus 289 ~L~~~VWdPr~n~~DryHlMPIITPAyP~~nsthNVS~ST~~Vi~~Ef~~g~~I~~~i~~~k--------~~W~~LFE~~ 360 (562)
T KOG2245|consen 289 NLNLPVWDPRVNPSDRYHLMPIITPAYPQMNSTHNVSRSTLKVITEEFKRGLEICDDIELNK--------LDWSDLFELY 360 (562)
T ss_pred ccCccccCCCCCCCCcceecccccCCcccccccccccHHHHHHHHHHHHHHHHHHHHHHhcc--------ccHHHHhhhh
Confidence 1 112111 112357899999999776655532 34568999999999998765511 2244577765
Q ss_pred c
Q 000387 1580 I 1580 (1588)
Q Consensus 1580 i 1580 (1588)
.
T Consensus 361 ~ 361 (562)
T KOG2245|consen 361 N 361 (562)
T ss_pred H
Confidence 3
No 7
>COG5186 PAP1 Poly(A) polymerase [RNA processing and modification]
Probab=99.49 E-value=1.1e-12 Score=149.11 Aligned_cols=248 Identities=19% Similarity=0.211 Sum_probs=170.7
Q ss_pred CceEEecccccCCCCCCCCceEEEEcCCCCCCcccccccccccccchhHHHHHHHHHHHhhcCCcccCCeEEecCCCccE
Q 000387 1253 SRTNIFGSNATGLSLPSSDVDLVVCLPPVRNLEPIKEAGILEGRNGIKETCLQHAARYLANQEWVKSDSLKTVENTAIPI 1332 (1588)
Q Consensus 1253 ArVepFGS~ATGLaLPsSDIDLVVi~PpvrnlEPikeAGiLE~RN~IKet~Lq~LAR~Lr~~~~Vks~sVqvIenARVPI 1332 (1588)
.++..||||..|.+-|+||||-.++.|..- .+...++++-..|+...-+ +++..|+.|-|||
T Consensus 82 GKIFTyGSYRLGVhgpGsDIDtLvvVPkHV----------------sR~dFFt~f~~~Lrer~ei--~eva~vpDAfVPI 143 (552)
T COG5186 82 GKIFTYGSYRLGVHGPGSDIDTLVVVPKHV----------------SRSDFFTHFYEELRERPEI--EEVAKVPDAFVPI 143 (552)
T ss_pred ceeeeecceeeeccCCCCCcceEEEecccc----------------cHHHHHHHHHHHhccCcch--hhhccCCccccee
Confidence 589999999999999999999988876321 1235677888888887655 3788999999999
Q ss_pred EEEEE-ccCchhhhhhccccCCCcccccccccccCCccccccccccCCCCCCCCCCCCCcccCCCccEEEE-EeeCCCCc
Q 000387 1333 IMLVV-EVPHDLIASAASSVQSPKEDAAHTTLKHDNHVHSDMVALDDSASPKCSHTSSDNIKAATSVRLDI-SFKSPSHT 1410 (1588)
Q Consensus 1333 IKfv~-dVP~DLs~~y~~~i~Sske~pv~i~~~~~spv~sDi~~sedS~sp~C~~~~~ds~D~~tGIsVDI-SFnnpSh~ 1410 (1588)
||++. .+++||+..- + .++. +..+++.+++. ...+ +|- ++- +.+
T Consensus 144 IK~KF~GIsIDLifAR---L------s~P~-------Vp~~l~Lsd~n--------------LLk~--~dEkcil--sLN 189 (552)
T COG5186 144 IKLKFQGISIDLIFAR---L------SIPV-------VPDGLNLSDDN--------------LLKS--MDEKCIL--SLN 189 (552)
T ss_pred EEEEecCccceeeeee---c------cCCc-------CCCcccccchh--------------hhhc--chHHHHH--hhc
Confidence 99985 5788776321 1 0111 11222222221 0011 110 111 256
Q ss_pred HHHHHHHHHHHHhhCCChHHHHHHHHHHHHhCCCCCCCCCCcchHHHHHHHHHHHhccCcCCCCCCCcHHHHHHHHHHHh
Q 000387 1411 GLQTTDLVKELTEQFPASTPLALVLKQFLADRSLDQSYSGGLSSYCLMLLITRFLQHEHHLGRPINQNYGRLLMDFLYFF 1490 (1588)
Q Consensus 1411 GLrnSeLIreyieqyPrLRPLVLVLK~WLKqRGLNDpytGGLSSYALVLMVIaFLQ~~p~LGRPiNqnLGeLLLdFF~FY 1490 (1588)
|-+.++-|-++...-.-++...+.+|+|++.|.+.....|..++-++.|||...+|.+|. ..-..++-.||..+
T Consensus 190 GtRVTDeiL~LVP~~~vF~~ALRaIK~WAqRRavYaN~~GfpGGVAwam~VARiCQLYPN------A~S~vIv~kFF~il 263 (552)
T COG5186 190 GTRVTDEILNLVPSVKVFHSALRAIKYWAQRRAVYANPYGFPGGVAWAMCVARICQLYPN------ASSFVIVCKFFEIL 263 (552)
T ss_pred CceehHHHHHhCCchHHHHHHHHHHHHHHHhhhhhccccCCcchHHHHHHHHHHHhhccC------cchHhHHHHHHHHH
Confidence 777777777777666678889999999999999999999999999999999999999874 34567889999999
Q ss_pred ccCCCCCCceEE-eeCCcccc-----ccc-CCCCCCCeEEeCCCCCCCccccCcc--cHHHHHHHHHHHHHHHHHHhh
Q 000387 1491 GNVFDPRQMRIS-VQGSGVYI-----KRE-RGYSIDPIHIDDPRFPTNNVGRNCF--RIHQCIKAFSDAYSILESELT 1559 (1588)
Q Consensus 1491 G~eFDy~ttgIS-Ir~gGiy~-----kKE-rG~s~spL~IEDPfdpsNNVGRnsf--rI~qIqkaFarAyeiLs~~L~ 1559 (1588)
. .++|-+-+|- .-..|.+. ++- ......+|.|+.|..|+...+.|.. .-+.|..+|-+|.+++...+.
T Consensus 264 s-~WnWPqPviLkPieDgplqvrvWnPKvYpsDk~HRMPvITPAYPSMCATHNit~STq~vIl~EfvRa~~I~~di~~ 340 (552)
T COG5186 264 S-SWNWPQPVILKPIEDGPLQVRVWNPKVYPSDKYHRMPVITPAYPSMCATHNITNSTQHVILMEFVRAHKILSDIER 340 (552)
T ss_pred H-hcCCCCCeEeeeccCCCeeEEeeCCccCcccccccCccccCCchhhhhhccccchhhhhHHHHHHHHHHhhhhHhh
Confidence 8 6999887653 11112221 110 1112367999999998644433321 234578999999999987554
No 8
>TIGR03671 cca_archaeal CCA-adding enzyme.
Probab=99.26 E-value=4.5e-10 Score=131.81 Aligned_cols=224 Identities=19% Similarity=0.242 Sum_probs=126.5
Q ss_pred HHhhhhHHhhhH---HHHHHHHHHHHHHhccCCCCceEEecccccCCCCC-CCCceEEEEcCCCCCCccccccccccccc
Q 000387 1222 KQVAAENTARKP---YINWAVKRVTRSLQVLWPRSRTNIFGSNATGLSLP-SSDVDLVVCLPPVRNLEPIKEAGILEGRN 1297 (1588)
Q Consensus 1222 k~I~PEeeeRK~---~I~~AVkrVe~vIQsLwPdArVepFGS~ATGLaLP-sSDIDLVVi~PpvrnlEPikeAGiLE~RN 1297 (1588)
+.+.|+.++|+. ..+.++.+|+..+.+..++++|.+|||++-|.+|+ .|||||.|..+.... ++
T Consensus 7 ~~i~Ps~eE~~~~~~~~~~l~~~l~~~~~e~~~~~~v~~~GS~ArgT~L~G~sDIDIfi~f~~~~~------------~e 74 (408)
T TIGR03671 7 ERIKPTEEEREKLKKVADELIARLEEIIEELGVDAEVVLVGSYARGTWLKGDRDIDIFILFPKDTS------------RE 74 (408)
T ss_pred hhcCCCHHHHHHHHHHHHHHHHHHHHHHHhcCCcceEEEEeeEecCCccCCCCceeEEEEeCCCCC------------HH
Confidence 456776544443 34556667777777788889999999999999999 999999999863211 11
Q ss_pred chhHHHHHHHHHHHhhcCCcccCCeEEecCCCccEEEEEEc-cCchhhhhhccccCCCcccccccccccCCccccccccc
Q 000387 1298 GIKETCLQHAARYLANQEWVKSDSLKTVENTAIPIIMLVVE-VPHDLIASAASSVQSPKEDAAHTTLKHDNHVHSDMVAL 1376 (1588)
Q Consensus 1298 ~IKet~Lq~LAR~Lr~~~~Vks~sVqvIenARVPIIKfv~d-VP~DLs~~y~~~i~Sske~pv~i~~~~~spv~sDi~~s 1376 (1588)
.+++ ....+++.+.+.+. . .. +..|.=|=++...+ +.+|+ ||
T Consensus 75 ~l~~-~gl~i~~~~~~~~~-~-~~---~~yaeHpYv~~~~~G~~VDi---------------VP---------------- 117 (408)
T TIGR03671 75 ELEE-YGLEIGHEVLKRGG-N-YE---ERYAEHPYVSGEIEGFEVDV---------------VP---------------- 117 (408)
T ss_pred HHHH-HHHHHHHHHHhhCC-C-Hh---heeccCceEEEEEccEEEEE---------------Ee----------------
Confidence 2222 22333443332110 0 01 12233444443321 11111 00
Q ss_pred cCCCCCCCCCCCCCcccCCCccEEEEEeeCCCCcHHHHHHHHHHHHhhCCChHHHHHHHHHHHHhCCCC--CCCCCCcch
Q 000387 1377 DDSASPKCSHTSSDNIKAATSVRLDISFKSPSHTGLQTTDLVKELTEQFPASTPLALVLKQFLADRSLD--QSYSGGLSS 1454 (1588)
Q Consensus 1377 edS~sp~C~~~~~ds~D~~tGIsVDISFnnpSh~GLrnSeLIreyieqyPrLRPLVLVLK~WLKqRGLN--DpytGGLSS 1454 (1588)
|..+..+. .-.-.+|-+ ...++|++.-+... ++..++++|+|+|.-|+. +.+++|+||
T Consensus 118 -------cy~v~~g~---~~~taVDRt--------p~H~~fv~~rl~~~--~~d~VRLlK~f~k~igvYGsE~~~~GFSG 177 (408)
T TIGR03671 118 -------CYKVESGE---EIISAVDRT--------PFHTRYVLERLDGK--LRDDVRLLKQFLKGIGVYGSELKTRGFSG 177 (408)
T ss_pred -------eEEccCcC---eeeccccCc--------hHHHHHHHHhhhhh--HHHHHHHHHHHHHhCCccchhhccCCccH
Confidence 00000000 000012221 23355665544443 788999999999999997 677999999
Q ss_pred HHHHHHHHHHHhccCcCCCCCCCcHHHHHHHHHHHhccCCCCCCceEEeeCCcccccccCCCCCCCeEEeCCCCCCCccc
Q 000387 1455 YCLMLLITRFLQHEHHLGRPINQNYGRLLMDFLYFFGNVFDPRQMRISVQGSGVYIKRERGYSIDPIHIDDPRFPTNNVG 1534 (1588)
Q Consensus 1455 YALVLMVIaFLQ~~p~LGRPiNqnLGeLLLdFF~FYG~eFDy~ttgISIr~gGiy~kKErG~s~spL~IEDPfdpsNNVG 1534 (1588)
|..=|||++| | +...+|-.+-. |.. .+.+...+.-.+ .+ ..||.|.||.|+.+||+
T Consensus 178 Yl~ELLv~~y-------G-----~F~~~l~~a~~-----wk~---~~~id~~~~~~~---~f-~~PlvViDPvDp~RNVA 233 (408)
T TIGR03671 178 YLCELLVIHY-------G-----SFENVLKAASK-----WKP---GVVIDIEEHGTK---KF-DDPLVVIDPVDPKRNVA 233 (408)
T ss_pred HHHHHHHHHh-------C-----CHHHHHHHHHh-----cCC---CeEEecCccccc---cC-CCCEEEeCCCCCcchHH
Confidence 9999999996 1 22333333332 222 222322111101 11 47999999999999999
Q ss_pred cCcc
Q 000387 1535 RNCF 1538 (1588)
Q Consensus 1535 Rnsf 1538 (1588)
+.+.
T Consensus 234 aalS 237 (408)
T TIGR03671 234 AALS 237 (408)
T ss_pred HHcC
Confidence 8864
No 9
>PRK13300 tRNA CCA-pyrophosphorylase; Provisional
Probab=99.26 E-value=3.8e-10 Score=133.78 Aligned_cols=225 Identities=21% Similarity=0.283 Sum_probs=127.1
Q ss_pred HHHhhhhHHhhhH---HHHHHHHHHHHHHhccCCCCceEEecccccCCCCC-CCCceEEEEcCCCCCCcccccccccccc
Q 000387 1221 CKQVAAENTARKP---YINWAVKRVTRSLQVLWPRSRTNIFGSNATGLSLP-SSDVDLVVCLPPVRNLEPIKEAGILEGR 1296 (1588)
Q Consensus 1221 ~k~I~PEeeeRK~---~I~~AVkrVe~vIQsLwPdArVepFGS~ATGLaLP-sSDIDLVVi~PpvrnlEPikeAGiLE~R 1296 (1588)
.+.+.|+.++|+. ..+.++.+|+..+.+.-.+++|.++||++.|.+|+ +|||||.|..+.....+
T Consensus 7 l~~i~Ps~eE~~~l~~~~~~l~~~L~~~~~~~~~~~~V~l~GS~ArgT~L~GdsDIDIFv~fp~~~~~e----------- 75 (447)
T PRK13300 7 LERIKPTEEEREKLKKVAEELIERLEEAIKELGLDAEVELVGSTARGTWLSGDRDIDIFVLFPKDTSRE----------- 75 (447)
T ss_pred HHhcCCCHHHHHHHHHHHHHHHHHHHHHHHhcCCceEEEEEeeecCCcccCCCCceeEEEEeCCCCCHH-----------
Confidence 3456776544433 23445555666665554469999999999999999 88999999996422211
Q ss_pred cchhHHHHHHHHHHH-hh-cCCcccCCeEEecCCCccEEEEEEc-cCchhhhhhccccCCCcccccccccccCCcccccc
Q 000387 1297 NGIKETCLQHAARYL-AN-QEWVKSDSLKTVENTAIPIIMLVVE-VPHDLIASAASSVQSPKEDAAHTTLKHDNHVHSDM 1373 (1588)
Q Consensus 1297 N~IKet~Lq~LAR~L-r~-~~~Vks~sVqvIenARVPIIKfv~d-VP~DLs~~y~~~i~Sske~pv~i~~~~~spv~sDi 1373 (1588)
.+++.-+ .++..+ +. .+. ..++ -|.=|=++...+ +.+|+ ||
T Consensus 76 -~L~~~gl-~i~~~~~~~~~~~---~~~~---yaeHpyv~~~~~G~~VDi---------------VP------------- 119 (447)
T PRK13300 76 -ELEEKGL-EIGKEVAKELLGD---YEER---YAEHPYVTGEIDGFEVDI---------------VP------------- 119 (447)
T ss_pred -HHHHHHH-HHHHHHHHhhCCc---ceee---eccCceEEEEECCEEEEE---------------Ee-------------
Confidence 2222222 222222 22 111 1222 244555554421 11111 00
Q ss_pred ccccCCCCCCCCCCCCCcccCCCccEEEEEeeCCCCcHHHHHHHHHHHHhhCCChHHHHHHHHHHHHhCCCC--CCCCCC
Q 000387 1374 VALDDSASPKCSHTSSDNIKAATSVRLDISFKSPSHTGLQTTDLVKELTEQFPASTPLALVLKQFLADRSLD--QSYSGG 1451 (1588)
Q Consensus 1374 ~~sedS~sp~C~~~~~ds~D~~tGIsVDISFnnpSh~GLrnSeLIreyieqyPrLRPLVLVLK~WLKqRGLN--DpytGG 1451 (1588)
|..+..+. .-.-.||-+ ...++||+.-+.. .++..++++|+|+|..|+. +.+++|
T Consensus 120 ----------cy~v~~~~---~~~saVDRt--------p~H~~fv~~rl~~--~~~d~VRLlK~f~k~~gvYGsE~k~~G 176 (447)
T PRK13300 120 ----------CYKVESGE---EIISAVDRT--------PFHTKYVKERLKG--KLEDEVRLLKQFLKGIGVYGSELKTRG 176 (447)
T ss_pred ----------eEEccCcC---cccccccCc--------hHHHHHHHHhhhh--hHHHHHHHHHHHHHhCCccchhhccCC
Confidence 00000000 000011211 2335566554433 3888999999999999997 677999
Q ss_pred cchHHHHHHHHHHHhccCcCCCCCCCcHHHHHHHHHHHhccCCCCCCceEEeeCCcccccccCCCCCCCeEEeCCCCCCC
Q 000387 1452 LSSYCLMLLITRFLQHEHHLGRPINQNYGRLLMDFLYFFGNVFDPRQMRISVQGSGVYIKRERGYSIDPIHIDDPRFPTN 1531 (1588)
Q Consensus 1452 LSSYALVLMVIaFLQ~~p~LGRPiNqnLGeLLLdFF~FYG~eFDy~ttgISIr~gGiy~kKErG~s~spL~IEDPfdpsN 1531 (1588)
+|||..=|||++| | +...+|-.+-. |.+ ...|.+...+... ....||.|.||.|+.+
T Consensus 177 FSGYl~ELLv~~y-------G-----~F~~~l~~a~~-----w~~-~~~I~~~~~~~~~-----~f~~PlvViDPvDp~R 233 (447)
T PRK13300 177 FSGYLCELLIIHY-------G-----SFENVLKAASK-----WKP-PVKIDLEKHGKEY-----KFDDPLVVIDPVDPNR 233 (447)
T ss_pred ccHHHHHHHHHHh-------C-----CHHHHHHHHHh-----CCC-CceEeccccCccc-----cCCCCEEEeCCCCCcc
Confidence 9999999999996 2 22333333332 333 2445555433210 2247999999999999
Q ss_pred ccccCcc
Q 000387 1532 NVGRNCF 1538 (1588)
Q Consensus 1532 NVGRnsf 1538 (1588)
||++.+.
T Consensus 234 NVAaa~S 240 (447)
T PRK13300 234 NVAAALS 240 (447)
T ss_pred hHHHHcC
Confidence 9998854
No 10
>PF04928 PAP_central: Poly(A) polymerase central domain; InterPro: IPR007012 In eukaryotes, polyadenylation of pre-mRNA plays an essential role in the initiation step of protein synthesis, as well as in the export and stability of mRNAs. Poly(A) polymerase, the enzyme at the heart of the polyadenylation machinery, is a template-independent RNA polymerase which specifically incorporates ATP at the 3' end of mRNA. The crystal structure of bovine poly(A) polymerase bound to an ATP analog at 2.5 A resolutio has been determined []. The structure revealed expected and unexpected similarities to other proteins. As expected, the catalytic domain of poly(A) polymerase shares substantial structural homology with other nucleotidyl transferases such as DNA polymerase beta and kanamycin transferase. The central domain of Poly(A) polymerase shares structural similarity with the allosteric activity domain of ribonucleotide reductase R1, which comprises a four-helix bundle and a three-stranded mixed beta-sheet. Even though the two enzymes bind ATP, the ATP-recognition motifs are different.; GO: 0004652 polynucleotide adenylyltransferase activity, 0006351 transcription, DNA-dependent; PDB: 1Q79_A 1Q78_A 1F5A_A 2O1P_A 2HHP_A 3C66_B 1FA0_A 2Q66_A.
Probab=99.20 E-value=5.6e-11 Score=132.21 Aligned_cols=143 Identities=19% Similarity=0.199 Sum_probs=105.7
Q ss_pred CcHHHHHHHHHHHHhhCCChHHHHHHHHHHHHhCCCCCCCCCCcchHHHHHHHHHHHhccCcCCCCCCCcHHHHHHHHHH
Q 000387 1409 HTGLQTTDLVKELTEQFPASTPLALVLKQFLADRSLDQSYSGGLSSYCLMLLITRFLQHEHHLGRPINQNYGRLLMDFLY 1488 (1588)
Q Consensus 1409 h~GLrnSeLIreyieqyPrLRPLVLVLK~WLKqRGLNDpytGGLSSYALVLMVIaFLQ~~p~LGRPiNqnLGeLLLdFF~ 1488 (1588)
.+|++.+++|.+++.....||.+.++||.|+++|||+....|.||+.++.+||.+.+|..+. .+.+.||..||.
T Consensus 90 LnG~Rv~~~il~~Vp~~~~Fr~~lR~IK~WAk~RGIYsn~~GylGGI~waILvArvcql~Pn------~~~~~ll~~FF~ 163 (254)
T PF04928_consen 90 LNGVRVTDYILRLVPNQETFRTALRFIKLWAKRRGIYSNVFGYLGGIHWAILVARVCQLYPN------ASPSTLLSRFFQ 163 (254)
T ss_dssp HHHHHHHHHHHCTSS-HHHHHHHHHHHHHHHHHTT-B-CCCTSB-HHHHHHHHHHHHHHSTT--------HHHHHHHHHH
T ss_pred cccccHHHHHHHHCCCHHHHHHHHHHHHHHHHHccccchhhccchHHHHHHHHHHHHHHCcc------ccccchHHHHHH
Confidence 68999999999999888889999999999999999999999999999999999999999874 567889999999
Q ss_pred HhccCCCCCCceEEeeCC--cccc-----cc-cCCCCCCCeEEeCCCCCCCccccCc--ccHHHHHHHHHHHHHHHHHHh
Q 000387 1489 FFGNVFDPRQMRISVQGS--GVYI-----KR-ERGYSIDPIHIDDPRFPTNNVGRNC--FRIHQCIKAFSDAYSILESEL 1558 (1588)
Q Consensus 1489 FYG~eFDy~ttgISIr~g--Giy~-----kK-ErG~s~spL~IEDPfdpsNNVGRns--frI~qIqkaFarAyeiLs~~L 1558 (1588)
+|+ .|||.+- |.+... +.+. ++ ........|.|..|..|..|.+++. ...+.|+++|++|++++.+.+
T Consensus 164 ~ys-~W~W~~P-V~l~~~~~~~~~~~~w~p~~~~~~~~~~MpIiTP~yP~~Nst~nVt~st~~~i~~Ef~ra~~i~~~~~ 241 (254)
T PF04928_consen 164 IYS-QWDWPNP-VVLDPIEDGPLGFKVWNPRLYPRDRRHLMPIITPAYPSMNSTYNVTRSTLRIIREEFQRAHEILSEIL 241 (254)
T ss_dssp HHH-CS-TTS--EESS-----SSSCGS--TTT-HHHHC-SS-EE-SSSS--BTTTT--HHHHHHHHHHHHHHHHHHHHHH
T ss_pred Hhc-CCCCCCc-eeecccccCcccccCCCCCCCCCCcccceeEccCCCCccccccccCHHHHHHHHHHHHHHHHHHHHHH
Confidence 998 6999873 444321 1110 00 0011247899999999999999885 356779999999999999866
Q ss_pred h
Q 000387 1559 T 1559 (1588)
Q Consensus 1559 ~ 1559 (1588)
.
T Consensus 242 ~ 242 (254)
T PF04928_consen 242 K 242 (254)
T ss_dssp T
T ss_pred c
Confidence 3
No 11
>PF03828 PAP_assoc: Cid1 family poly A polymerase; InterPro: IPR002058 These PAP/25A associated domains are found in uncharacterised eukaryotic proteins, a number of which are described as 'topoisomerase 1-related' though they appear to have little or no homology to topoisomerase 1. The signatures that define this group of sequences often occur towards the C terminus after the PAP/25A core domain IPR001201 from INTERPRO.; PDB: 2B4V_A 2B56_A 2B51_A 4EP7_B 2NOM_B 2Q0G_B 2Q0D_B 2Q0C_A 2Q0F_A 2Q0E_A ....
Probab=99.09 E-value=3.7e-11 Score=105.28 Aligned_cols=54 Identities=33% Similarity=0.651 Sum_probs=44.8
Q ss_pred cHHHHHHHHHHHhccCCCCCCceEEeeCCcccccccCCCC------CCCeEEeCCCCCCC
Q 000387 1478 NYGRLLMDFLYFFGNVFDPRQMRISVQGSGVYIKRERGYS------IDPIHIDDPRFPTN 1531 (1588)
Q Consensus 1478 nLGeLLLdFF~FYG~eFDy~ttgISIr~gGiy~kKErG~s------~spL~IEDPfdpsN 1531 (1588)
+||+||++||+|||++|||.+.+|||+.++.+.+.+..+. ..+|+|+||++++|
T Consensus 1 slg~Ll~~Ff~~Y~~~Fd~~~~~Isi~~g~~~~k~~~~~~~~~~~~~~~l~IeDP~~~~n 60 (60)
T PF03828_consen 1 SLGELLLGFFEYYGRKFDYENNVISIRNGGYFPKEEKNWSKSRNQRKKRLCIEDPFDPSN 60 (60)
T ss_dssp -HHHHHHHHHHHHHHTS-TTTEEEESSSSSEEEHHHHTGCHCCCCECSSSEBBESSSTTE
T ss_pred CHHHHHHHHHHHhCCcCCCCceEEEecCCceEEhhhccccccccCCCCeEEEECCCCCCC
Confidence 5899999999999999999999999999877666554443 58999999999864
No 12
>COG1746 CCA1 tRNA nucleotidyltransferase (CCA-adding enzyme) [Translation, ribosomal structure and biogenesis]
Probab=98.70 E-value=9.5e-07 Score=104.07 Aligned_cols=236 Identities=22% Similarity=0.291 Sum_probs=138.3
Q ss_pred HHHHHHHHHHhhhhHHhhhHH---HHHHHHHHHHHHhccCCCCceEEecccccCCCCC-CCCceEEEEcCCCCCCccccc
Q 000387 1214 HEEIDSFCKQVAAENTARKPY---INWAVKRVTRSLQVLWPRSRTNIFGSNATGLSLP-SSDVDLVVCLPPVRNLEPIKE 1289 (1588)
Q Consensus 1214 heEIldF~k~I~PEeeeRK~~---I~~AVkrVe~vIQsLwPdArVepFGS~ATGLaLP-sSDIDLVVi~PpvrnlEPike 1289 (1588)
.+.|..-.+.+.|++++|+.+ -+.+..++..+++..-.++.+.+.||+|-|.+|+ ..|||+.|.+|.-..
T Consensus 4 ~~~l~evl~~i~P~~eE~~~~~~~~e~l~~~~~~~~~e~~~~aev~lVGS~AkgTwL~gd~DIDvFi~Fp~d~~------ 77 (443)
T COG1746 4 EEVLEEVLKRIKPTEEERKKLKEVAEELRERINEIIEELGIDAEVVLVGSYAKGTWLRGDHDIDVFIAFPKDTS------ 77 (443)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHhcCCcceEEEEeecccCcccCCCcceeEEEECCCCCC------
Confidence 334445566678876665532 1234455566666777899999999999999999 999999999974221
Q ss_pred ccccccccchhHHHHHHHHHHHhhcCCcccCCeEEecCCCccEEEEEEccCchhhhhhccccCCCcccccccccccCCcc
Q 000387 1290 AGILEGRNGIKETCLQHAARYLANQEWVKSDSLKTVENTAIPIIMLVVEVPHDLIASAASSVQSPKEDAAHTTLKHDNHV 1369 (1588)
Q Consensus 1290 AGiLE~RN~IKet~Lq~LAR~Lr~~~~Vks~sVqvIenARVPIIKfv~dVP~DLs~~y~~~i~Sske~pv~i~~~~~spv 1369 (1588)
+..+++.-|.....+|.+..+ .+..|.=|=+....
T Consensus 78 ------~eel~~~GL~ig~~~l~~~~~-------~~~YAeHPYV~g~v-------------------------------- 112 (443)
T COG1746 78 ------EEELEEKGLEIGREVLKRGNY-------EERYAEHPYVTGEV-------------------------------- 112 (443)
T ss_pred ------HHHHHHHHHHHHHHHhcCCch-------hhhhccCCeeEEEE--------------------------------
Confidence 122333334444444543111 12233334433321
Q ss_pred ccccccccCCCCCCCCCCCCCcccCCCccEEEEE--eeC----CCC----cHHHHHHHHHHHHhhCCChHHHHHHHHHHH
Q 000387 1370 HSDMVALDDSASPKCSHTSSDNIKAATSVRLDIS--FKS----PSH----TGLQTTDLVKELTEQFPASTPLALVLKQFL 1439 (1588)
Q Consensus 1370 ~sDi~~sedS~sp~C~~~~~ds~D~~tGIsVDIS--Fnn----pSh----~GLrnSeLIreyieqyPrLRPLVLVLK~WL 1439 (1588)
.|+.|||- ++- ... --+..++++..=+..- .+-=++++|+||
T Consensus 113 --------------------------~G~eVDvVPCy~v~~~~~~~sAVDRTplHt~yv~e~L~~~--~~deVrLLK~Fl 164 (443)
T COG1746 113 --------------------------DGYEVDVVPCYKVEDGEKIISAVDRTPLHTRYVEEHLKGR--QKDEVRLLKQFL 164 (443)
T ss_pred --------------------------ccEEEEEEecccccCcccccccccCcchhHHHHHHHhccc--chhHHHHHHHHH
Confidence 11222220 000 000 1123355555544333 334589999999
Q ss_pred HhCCCC--CCCCCCcchHHHHHHHHHHHhccCcCCCCCCCcHHHHHHHHHHHhccCCCCCCceEEeeCCcccccccCCCC
Q 000387 1440 ADRSLD--QSYSGGLSSYCLMLLITRFLQHEHHLGRPINQNYGRLLMDFLYFFGNVFDPRQMRISVQGSGVYIKRERGYS 1517 (1588)
Q Consensus 1440 KqRGLN--DpytGGLSSYALVLMVIaFLQ~~p~LGRPiNqnLGeLLLdFF~FYG~eFDy~ttgISIr~gGiy~kKErG~s 1517 (1588)
|.-|.. +..++|+|+|.-=||||+| | . +.+-|+.... |... ..|.+... +++ .+.
T Consensus 165 K~iGvYGaE~rt~GFSGYL~ELLII~y-------G--------s-Fe~vl~~a~~-wrp~-~~ID~~~~----~~e-~f~ 221 (443)
T COG1746 165 KGIGVYGAELRTQGFSGYLCELLIIHY-------G--------S-FENVLKAASR-WRPG-KIIDLEGH----KRE-RFE 221 (443)
T ss_pred hccCccceeeeeccchHHHHHHHHhhh-------c--------c-HHHHHHHHhc-cCCC-eEEeccch----hhh-ccC
Confidence 999997 4569999999999999997 2 1 4555555542 4444 44555433 122 122
Q ss_pred CCCeEEeCCCCCCCccccCcccHHHHHHHHHHHHHH
Q 000387 1518 IDPIHIDDPRFPTNNVGRNCFRIHQCIKAFSDAYSI 1553 (1588)
Q Consensus 1518 ~spL~IEDPfdpsNNVGRnsfrI~qIqkaFarAyei 1553 (1588)
..||.|.||.||.+|++.+...- . ...|..|...
T Consensus 222 d~PliVvDPVDP~RNVAAalSl~-~-la~f~~aar~ 255 (443)
T COG1746 222 DEPLIVVDPVDPKRNVAAALSLE-N-LARFVHAARE 255 (443)
T ss_pred CCCeEecCCCCCccchhhhcCHH-H-HHHHHHHHHH
Confidence 34999999999999999886532 2 2345544443
No 13
>KOG1906 consensus DNA polymerase sigma [Replication, recombination and repair]
Probab=98.47 E-value=2.1e-07 Score=112.18 Aligned_cols=76 Identities=21% Similarity=0.203 Sum_probs=68.8
Q ss_pred cccEEEecCCCCCCCCCCCccccccccchhhHhhhhcccchhHHhhhcccccccccccccccCCCccCcceeehHHHHhh
Q 000387 98 HGFFIILPDLPSRDPPYLPGLCYKKSRGLLSRVAESNESGRWVFESTRLFSSREGEKIEEWSCPVNCLDTFTVSVEFVEN 177 (1588)
Q Consensus 98 ~~~f~ilp~~~~~~~~~~p~~~~~~srgll~r~~~~~~~~~~~~~~~~lf~s~~~~~~~~~~~s~~~~d~~~v~~~~~~~ 177 (1588)
.+++++||+.|+++ .+|..|+++++|.. +++.+++|++.++..+.+. .+|+|+...+++.-+.+|++.+
T Consensus 2 ~~~~~~~~~s~ssS--~~~~~~~~~~~~~~--~s~~~e~e~~~~~e~~~~~-------~~~~~~~~~~~s~~l~~eI~~f 70 (514)
T KOG1906|consen 2 AESQDFLPVSPSSS--DSPSFGSLPSEGPT--VSEPIEAEKWMIAEERTKE-------IHCHSSPSNLVSERLRNEILDF 70 (514)
T ss_pred CcccccccCCCCcc--ccccccccCCcccc--ccccccchhheeccccccC-------CceeeccCchhHHHHHHHHHHH
Confidence 46789999988888 88999999999998 9999999999999999887 7899999999999999999999
Q ss_pred HHHHHHH
Q 000387 178 VDRFIDI 184 (1588)
Q Consensus 178 ~d~fv~~ 184 (1588)
||.++..
T Consensus 71 v~~l~pt 77 (514)
T KOG1906|consen 71 VQYLIPT 77 (514)
T ss_pred HHHhcCC
Confidence 9988654
No 14
>PF01909 NTP_transf_2: Nucleotidyltransferase domain A subset of this Pfam family; InterPro: IPR002934 A small region that overlaps with a nuclear localization signal and binds to the RNA primer contains three aspartates that are essential for catalysis. Sequence and secondary structure comparisons of regions surrounding these aspartates with sequences of other polymerases revealed a significant homology to the palm structure of DNA polymerase beta, terminal deoxynucleotidyltransferase and DNA polymerase IV of Saccharomyces cerevisiae, all members of the family X of polymerases. This homology extends as far as cca: tRNA nucleotidyltransferase and streptomycin adenylyltransferase, an antibiotic resistance factor [, ]. Proteins containing this domain include kanamycin nucleotidyltransferase (KNTase) which is a plasmid-coded enzyme responsible for some types of bacterial resistance to aminoglycosides. KNTase inactivates antibiotics by catalysing the addition of a nucleotidyl group onto the drug. In experiments, Mn2+ strongly stimulated this reaction due to a 50-fold lower Ki for 8-azido-ATP in the presence of Mn2+. Mutations of the highly conserved Asp residues 113, 115, and 167, critical for metal binding in the catalytic domain of bovine poly(A) polymerase, led to a strong reduction of cross-linking efficiency, and Mn2+ no longer stimulated the reaction. Mutations in the region of the "helical turn motif" (a domain binding the triphosphate moiety of the nucleotide) and in the suspected nucleotide-binding helix of bovine poly(A) polymerase impaired ATP binding and catalysis. The results indicate that ATP is bound in part by the helical turn motif and in part by a region that may be a structural analogue of the fingers domain found in many polymerases.; GO: 0016779 nucleotidyltransferase activity; PDB: 4EBK_B 4EBJ_A 1KNY_A 2B4V_A 2B56_A 2B51_A 1NO5_B 1Q79_A 1Q78_A 1F5A_A ....
Probab=97.75 E-value=1.8e-05 Score=73.54 Aligned_cols=42 Identities=31% Similarity=0.551 Sum_probs=38.2
Q ss_pred HHHHHHHHhccCCCCceEEecccccCCCCCCCCceEEEEcCC
Q 000387 1239 VKRVTRSLQVLWPRSRTNIFGSNATGLSLPSSDVDLVVCLPP 1280 (1588)
Q Consensus 1239 VkrVe~vIQsLwPdArVepFGS~ATGLaLPsSDIDLVVi~Pp 1280 (1588)
++++.+.+++.++...|.+|||+++|.+.|.|||||+|..+.
T Consensus 1 i~~i~~~l~~~~~~~~v~lfGS~a~g~~~~~SDIDl~i~~~~ 42 (93)
T PF01909_consen 1 IEEIKEILKELFGVAEVYLFGSYARGDATPDSDIDLLIILDE 42 (93)
T ss_dssp HHHHHHHHHHHHTTEEEEEEHHHHHTSSCTTSCEEEEEEESS
T ss_pred CHHHHHHHHHHCCCCEEEEECCcccCcCCCCCCEEEEEEeCC
Confidence 367888889999999999999999999999999999999864
No 15
>cd05397 NT_Pol-beta-like Nucleotidyltransferase (NT) domain of DNA polymerase beta and similar proteins. This superfamily includes the NT domains of DNA polymerase beta and other family X DNA polymerases, as well as the NT domains of Class I and Class II CCA-adding enzymes, RelA- and SpoT-like ppGpp synthetases and hydrolases, 2'5'-oligoadenylate (2-5A)synthetases, Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), poly (A) polymerases, terminal uridylyl transferases, and Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins. The Escherichia coli CCA-adding enzyme belongs to this superfamily but is not included as this enzyme lacks the N-terminal helix conserved in the remainder of the superfamily. In the majority of the Pol beta-like superfamily NTs, two carboxylates, Dx[D/E], together with a third more distal carboxylate coordinate two divalent metal cations that are essential for catalysis. These divalent metal ions are
Probab=97.43 E-value=0.00023 Score=61.90 Aligned_cols=40 Identities=30% Similarity=0.420 Sum_probs=36.4
Q ss_pred HHHHHHHHHhccCCCCceEEecccccCCCCCCCCceEEEE
Q 000387 1238 AVKRVTRSLQVLWPRSRTNIFGSNATGLSLPSSDVDLVVC 1277 (1588)
Q Consensus 1238 AVkrVe~vIQsLwPdArVepFGS~ATGLaLPsSDIDLVVi 1277 (1588)
+++.+.+.+++.++..++.+|||++.|.+.+.|||||.+.
T Consensus 3 ~l~~i~~~l~~~~~~~~v~lfGS~arg~~~~~SDIDi~v~ 42 (49)
T cd05397 3 LLDIIKERLKKLVPGYEIVVYGSLVRGLLKKSSDIDLACV 42 (49)
T ss_pred HHHHHHHHHHhhcCCcEEEEECCcCCCCCCCCCCEEEEEE
Confidence 4577888888888999999999999999999999999987
No 16
>PF09249 tRNA_NucTransf2: tRNA nucleotidyltransferase, second domain; InterPro: IPR015329 This domain adopts a structure consisting of a five helical bundle core. It is predominantly found in Archaeal tRNA nucleotidyltransferases, following the catalytic nucleotidyltransferase domain []. ; GO: 0004810 tRNA adenylyltransferase activity, 0016437 tRNA cytidylyltransferase activity; PDB: 3OUY_B 2ZHB_A 2ZH1_A 2ZH2_A 1UET_A 2ZH7_A 1R8B_A 2DR5_A 1TFW_C 3OVA_A ....
Probab=97.01 E-value=0.0016 Score=66.24 Aligned_cols=85 Identities=28% Similarity=0.389 Sum_probs=55.6
Q ss_pred HHHHHHHHHhCCCC--CCCCCCcchHHHHHHHHHHHhccCcCCCCCCCcHHHHHHHHHHHhccCCCCCCceEEeeCCccc
Q 000387 1432 ALVLKQFLADRSLD--QSYSGGLSSYCLMLLITRFLQHEHHLGRPINQNYGRLLMDFLYFFGNVFDPRQMRISVQGSGVY 1509 (1588)
Q Consensus 1432 VLVLK~WLKqRGLN--DpytGGLSSYALVLMVIaFLQ~~p~LGRPiNqnLGeLLLdFF~FYG~eFDy~ttgISIr~gGiy 1509 (1588)
++++|+|+|..|+. +.+++|+|+|..=|||++| | + +.++++.-. .+.. ...|.+.+.+..
T Consensus 3 VrLLK~FlK~igvYGse~~~~GFSGYL~ELLii~y-------G-----s----F~~~l~~a~-~W~~-~~~Id~~~~~~~ 64 (114)
T PF09249_consen 3 VRLLKQFLKGIGVYGSELKTRGFSGYLCELLIIHY-------G-----S----FENVLEAAA-KWKP-PVVIDLEDHGEP 64 (114)
T ss_dssp HHHHHHHHHHTT-B-SSTTT-SB-HHHHHHHHHHH-------S-----S----HHHHHHHHT-T--T-TEEEETT-TTE-
T ss_pred hHHHHHHHhcCCCcchhhhcCcchHHHHHHHHHHH-------C-----C----HHHHHHHHH-hcCC-CeEEccCccchh
Confidence 68999999999997 5679999999999999998 2 1 466666665 4544 344555433221
Q ss_pred ccccCCCCCCCeEEeCCCCCCCccccCcc
Q 000387 1510 IKRERGYSIDPIHIDDPRFPTNNVGRNCF 1538 (1588)
Q Consensus 1510 ~kKErG~s~spL~IEDPfdpsNNVGRnsf 1538 (1588)
.++ ..+||.|.||.|+.+||+..+.
T Consensus 65 ~~~----f~~PlvviDPvDp~RNVAAalS 89 (114)
T PF09249_consen 65 SKK----FDDPLVVIDPVDPNRNVAAALS 89 (114)
T ss_dssp -EE----E-SS-EEEETTEEEEETTTTS-
T ss_pred hhh----cCCCeEEcCCCCCCchHhHhcC
Confidence 111 1479999999999999998864
No 17
>cd05403 NT_KNTase_like Nucleotidyltransferase (NT) domain of Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins. S. aureus KNTase is a plasmid encoded enzyme which confers resistance to a wide range of aminoglycoside antibiotics which have a 4'- or 4''-hydroxyl group in the equatorial position, such as kanamycin A. This enzyme transfers a nucleoside monophosphate group from a nucleotide (ATP,GTP, or UTP) to the 4'-hydroxyl group of kanamycin A. This enzyme is a homodimer, having two NT active sites. The nucleotide and antibiotic binding sites of each active site include residues from each monomer. Included in this subgroup is Escherichia coli AadA5 which confers resistance to the antibiotic spectinomycin and is a putative aminoglycoside-3'-adenylyltransferase. It is part of the aadA5 cassette of a class 1 integron. This subgroup also includes Haemophilus influenzae HI0073 which forms a 2:2 heterotetramer with an unrelated protein HI0074. Structurally HI0074 is
Probab=96.87 E-value=0.0014 Score=60.29 Aligned_cols=42 Identities=31% Similarity=0.485 Sum_probs=34.9
Q ss_pred HHHHHHHHhccCC-CCceEEecccccCCCCCCCCceEEEEcCC
Q 000387 1239 VKRVTRSLQVLWP-RSRTNIFGSNATGLSLPSSDVDLVVCLPP 1280 (1588)
Q Consensus 1239 VkrVe~vIQsLwP-dArVepFGS~ATGLaLPsSDIDLVVi~Pp 1280 (1588)
++++...++..+. -..+.+|||++.|-+-+.|||||+|....
T Consensus 4 ~~~i~~~l~~~~~~i~~i~LfGS~arg~~~~~SDiDl~vi~~~ 46 (93)
T cd05403 4 LEEILEILRELLGGVEKVYLFGSYARGDARPDSDIDLLVIFDD 46 (93)
T ss_pred HHHHHHHHHHHhCCccEEEEEeeeecCCCCCCCCeeEEEEeCC
Confidence 3556666666666 78899999999999999999999999853
No 18
>PF10421 OAS1_C: 2'-5'-oligoadenylate synthetase 1, domain 2, C-terminus ; InterPro: IPR018952 This is the largely alpha-helical, C-terminal half of 2'-5'-oligoadenylate synthetase 1, being described as domain 2 of the enzyme and homologous to a tandem ubiquitin repeat. It carries the region of enzymic activity between residues 320 and 344 at the extreme C-terminal end []. Oligoadenylate synthetases are antiviral enzymes that counteract viral attack by degrading viral RNA. The enzyme uses ATP in 2'-specific nucleotidyl transfer reactions to synthesise 2'.5'-oligoadenylates, which activate latent ribonuclease, resulting in degradation of viral RNA and inhibition of virus replication []. This domain is often associated with IPR002934 from INTERPRO. ; PDB: 1PX5_B.
Probab=96.81 E-value=0.0025 Score=69.70 Aligned_cols=117 Identities=20% Similarity=0.149 Sum_probs=63.6
Q ss_pred HHHHHHHHHHhhCCC-hHHHHHHHHHHHHhCCCCCCCCCC-cchHHHHHHHHHHHhccCcCCCCCCCcHHHHHHHHHHHh
Q 000387 1413 QTTDLVKELTEQFPA-STPLALVLKQFLADRSLDQSYSGG-LSSYCLMLLITRFLQHEHHLGRPINQNYGRLLMDFLYFF 1490 (1588)
Q Consensus 1413 rnSeLIreyieqyPr-LRPLVLVLK~WLKqRGLNDpytGG-LSSYALVLMVIaFLQ~~p~LGRPiNqnLGeLLLdFF~FY 1490 (1588)
-.+++=+.++...|. ++-|++++|+|-++..-.....++ .+||+|-||+|+.-.+... ..+-++.+=+...|+.-
T Consensus 28 cftelQ~~Fvk~rP~klK~LIrLVKhWy~~~~~~~~~~~~lPpsYaLELLtIyAWE~g~~---~~~F~~a~gfrtVLeLi 104 (190)
T PF10421_consen 28 CFTELQRNFVKHRPTKLKNLIRLVKHWYQQCKKKKCGGGSLPPSYALELLTIYAWEQGCG---AEDFSTAEGFRTVLELI 104 (190)
T ss_dssp GGHHHHHHHHHTS-HHHHHHHHHHHHHHHHHHCC--HTT-S--HHHHHHHHHHHHHHHT----SSS--HHHHHHHHHHHH
T ss_pred HHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHhhccCCCCCcHHHHHHHHHHHHHHhcCC---CcCcchhhhHhHHHHHH
Confidence 347788888888887 999999999999887666444455 5689999999998765422 22345555555555442
Q ss_pred ccCCCCCCceEEeeCCccccccc--------CCCCCCCeEEeCCCCCCCccccCc
Q 000387 1491 GNVFDPRQMRISVQGSGVYIKRE--------RGYSIDPIHIDDPRFPTNNVGRNC 1537 (1588)
Q Consensus 1491 G~eFDy~ttgISIr~gGiy~kKE--------rG~s~spL~IEDPfdpsNNVGRns 1537 (1588)
-+|++.+|.=+. .|.-.+ ..-...+=.|.||.||+||||.+.
T Consensus 105 ---~~y~~LcIyWt~--~Y~f~~~~v~~~l~~qL~~~RPvILDPAdPtnNV~~~~ 154 (190)
T PF10421_consen 105 ---QKYEQLCIYWTV--YYDFEDETVRNYLQSQLKKPRPVILDPADPTNNVAGGN 154 (190)
T ss_dssp ---HCGGG-EE---S--S--SSSHHHHHHHHHHHTSSS-EEB-TT-TT-BTT-S-
T ss_pred ---hCcceeEEEecc--cCCCcCHHHHHHHHHhhccCCCceeCCCCCCCccccCC
Confidence 234443333221 121000 000123457999999999999873
No 19
>PF03813 Nrap: Nrap protein; InterPro: IPR005554 Members of this family are nucleolar RNA-associated proteins (Nrap) which are highly conserved from yeast (Saccharomyces cerevisiae) to human. In the mouse, Nrap is ubiquitously expressed and is specifically localized in the nucleolus []. Nrap is a large nucleolar protein (of more than 1000 amino acids). Nrap appears to be associated with ribosome biogenesis by interacting with pre-rRNA primary transcript [].
Probab=96.28 E-value=0.031 Score=73.39 Aligned_cols=142 Identities=17% Similarity=0.176 Sum_probs=99.5
Q ss_pred HHHHHHHHHHhhCCChHHHHHHHHHHHHhCCCCCCC-CCCcchHHHHHHHHHHHhccCcCCC-CCCC--cHHHHHHHHHH
Q 000387 1413 QTTDLVKELTEQFPASTPLALVLKQFLADRSLDQSY-SGGLSSYCLMLLITRFLQHEHHLGR-PINQ--NYGRLLMDFLY 1488 (1588)
Q Consensus 1413 rnSeLIreyieqyPrLRPLVLVLK~WLKqRGLNDpy-tGGLSSYALVLMVIaFLQ~~p~LGR-PiNq--nLGeLLLdFF~ 1488 (1588)
...+++.+..+..|.++.-++++|.||++||++..+ .||++.|-+.+|+++-||.....|+ ..+. +-=+++-.+++
T Consensus 151 ~~l~~l~~~~~~~p~f~dA~iLlkvWl~QRg~~~~~~~~Gf~~f~~s~lla~Ll~~g~~~~~~~l~~~mSsyQlFr~~l~ 230 (972)
T PF03813_consen 151 EHLKYLHEASKSSPAFRDACILLKVWLRQRGFGSGISQGGFGGFEWSMLLAYLLQGGGRNGKKKLSKSMSSYQLFRAVLQ 230 (972)
T ss_pred HHHHHHHHHHhcCHHHHHHHHHHHHHHhcCCCCcccCCCCcchHHHHHHHHHHHcCCCccCCcccCCCCCHHHHHHHHHH
Confidence 445677777888999999999999999999998765 5899999888888887777433332 2233 33478899999
Q ss_pred HhccCCCCCCceEEeeCCcc-cccccCCCCCCCeEEeCCCCCCCccccCc--ccHHHHHHHHHHHHHHHHH
Q 000387 1489 FFGNVFDPRQMRISVQGSGV-YIKRERGYSIDPIHIDDPRFPTNNVGRNC--FRIHQCIKAFSDAYSILES 1556 (1588)
Q Consensus 1489 FYG~eFDy~ttgISIr~gGi-y~kKErG~s~spL~IEDPfdpsNNVGRns--frI~qIqkaFarAyeiLs~ 1556 (1588)
|-+. -|+.+.+|.+..... -............++.||--. .|+..+. ..+.+++.+=+.++++|.+
T Consensus 231 fLA~-~d~~~~~l~~~~~~~~~~~~~~~~~~~~~vf~D~sg~-~Nl~~~ms~~s~~~L~~eA~~tl~lL~~ 299 (972)
T PF03813_consen 231 FLAT-TDLSKKPLFFKSSSDSTESLEEFHSAFDPVFVDPSGG-LNLLAKMSPSSYEELQHEAKLTLELLDD 299 (972)
T ss_pred HHhc-cccccCceEEecCCCccchhhhhhccCCeEEEeCCCC-EEEEEcCCHHHHHHHHHHHHHHHHHhcc
Confidence 9984 788888888875431 000111122356778898876 4665442 3567787777777777764
No 20
>cd05400 NT_2-5OAS_ClassI-CCAase Nucleotidyltransferase (NT) domain of 2'5'-oligoadenylate (2-5A)synthetase (2-5OAS) and class I CCA-adding enzyme. In vertebrates, 2-5OASs are induced by interferon during the innate immune response to protect against RNA virus infections. In the presence of an RNA activator, 2-5OASs catalyze the oligomerization of ATP into 2-5A. 2-5A activates endoribonuclease L, which leads to degradation of the viral RNA. 2-5OASs are also implicated in cell growth control, differentiation, and apoptosis. This family includes human OAS1, -2, -3, and OASL. CCA-adding enzymes add the sequence [cytidine(C)-cytidine-adenosine (A)], one nucleotide at a time, onto the 3' end of tRNA, in a template-independent reaction. This class I group includes the archaeal Sulfolobus shibatae and Archeoglobus fulgidus CCA-adding enzymes. It belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more dis
Probab=95.94 E-value=0.022 Score=57.70 Aligned_cols=64 Identities=27% Similarity=0.362 Sum_probs=42.2
Q ss_pred HHHHHHHhccC-----CCCceEEecccccCCCCC-CCCceEEEEcCCCCCCcccccccccccccchhHHHHHHHHHHHhh
Q 000387 1240 KRVTRSLQVLW-----PRSRTNIFGSNATGLSLP-SSDVDLVVCLPPVRNLEPIKEAGILEGRNGIKETCLQHAARYLAN 1313 (1588)
Q Consensus 1240 krVe~vIQsLw-----PdArVepFGS~ATGLaLP-sSDIDLVVi~PpvrnlEPikeAGiLE~RN~IKet~Lq~LAR~Lr~ 1313 (1588)
+.|.+.|+..+ +...+.+|||++.|.+++ .|||||+|..+..... .... ...++..+.+.|.+
T Consensus 10 ~~i~~~L~~~~~~~~~~~~~~~~~GS~a~~T~i~~~sDiD~~v~~~~~~~~----------~~~~-~~~~~~~l~~~L~~ 78 (143)
T cd05400 10 REIREALKESLSELAGRVAEVFLQGSYARGTALRGDSDIDLVVVLPDDTSF----------AEYG-PAELLDELGEALKE 78 (143)
T ss_pred HHHHHHHHHhcccccccccEEEEEcceeCCCCCCCCCceeEEEEEcCcccc----------cccC-HHHHHHHHHHHHHH
Confidence 44555555443 347899999999999988 8999999998642110 0000 12466777777775
Q ss_pred c
Q 000387 1314 Q 1314 (1588)
Q Consensus 1314 ~ 1314 (1588)
.
T Consensus 79 ~ 79 (143)
T cd05400 79 Y 79 (143)
T ss_pred h
Confidence 3
No 21
>smart00572 DZF domain in DSRM or ZnF_C2H2 domain containing proteins.
Probab=95.89 E-value=0.15 Score=58.15 Aligned_cols=98 Identities=13% Similarity=0.162 Sum_probs=71.8
Q ss_pred CcHHHHHHHHHHHHhhCCChHHHHHHHHHHHHhCCCCCCCCCCcchHHHHHHHHHHHhccCcCCCCCCCcHHHHHHHHHH
Q 000387 1409 HTGLQTTDLVKELTEQFPASTPLALVLKQFLADRSLDQSYSGGLSSYCLMLLITRFLQHEHHLGRPINQNYGRLLMDFLY 1488 (1588)
Q Consensus 1409 h~GLrnSeLIreyieqyPrLRPLVLVLK~WLKqRGLNDpytGGLSSYALVLMVIaFLQ~~p~LGRPiNqnLGeLLLdFF~ 1488 (1588)
.-.++.++++++-......++.+++++|-|-+....-. -|+||.+=|++-+-+-.. + ...++|+.|..||+
T Consensus 111 LAalRhakWFq~~a~~l~s~~iviRilKd~~~R~~~~~----pL~~w~iELl~~~~i~~~---~--~~l~~~~a~RR~fe 181 (246)
T smart00572 111 LASLRHAKWFQARASGLQSCVIVIRVLRDLCNRVPTWQ----PLSGWPLELLVEKAIGSA---R--QPLGLGDAFRRVFE 181 (246)
T ss_pred HHHHHHhHHHHHhccCCcchhhHHHHHHHHHHhccccc----ccccccHHHHHHHHhccC---C--CCCCHHHHHHHHHH
Confidence 45678888888877777789999999999988764332 388999888875554321 1 23579999999999
Q ss_pred HhccCCCCCCceEEeeCCcccccccCCCCCCCeEEeCCCCC-CCccccC
Q 000387 1489 FFGNVFDPRQMRISVQGSGVYIKRERGYSIDPIHIDDPRFP-TNNVGRN 1536 (1588)
Q Consensus 1489 FYG~eFDy~ttgISIr~gGiy~kKErG~s~spL~IEDPfdp-sNNVGRn 1536 (1588)
|-+. |++++ .-..|.||.+. .+|+...
T Consensus 182 ~lAs--------------G~l~p-------~~~gI~DPce~~~~nv~~~ 209 (246)
T smart00572 182 CLAS--------------GILLP-------GSPGLTDPCEKDNTDALTA 209 (246)
T ss_pred HHHh--------------ccCcC-------CCCCCcCCCCCCcccHHHh
Confidence 9985 33432 12578899997 7787655
No 22
>COG1708 Predicted nucleotidyltransferases [General function prediction only]
Probab=95.50 E-value=0.024 Score=54.81 Aligned_cols=37 Identities=30% Similarity=0.276 Sum_probs=31.3
Q ss_pred HHHHHhccCCCCceEEecccccCCCCCCCCceEEEEc
Q 000387 1242 VTRSLQVLWPRSRTNIFGSNATGLSLPSSDVDLVVCL 1278 (1588)
Q Consensus 1242 Ve~vIQsLwPdArVepFGS~ATGLaLPsSDIDLVVi~ 1278 (1588)
+............|++|||++.|=+.+.||||++|..
T Consensus 16 ~~~~~~~~~~~~~v~LfGS~arG~~~~~SDiDv~vv~ 52 (128)
T COG1708 16 LEAIEKKLGGDLLIYLFGSYARGDFVKESDIDLLVVS 52 (128)
T ss_pred HHHHHHhcCCCeEEEEEccCcccccccCCCeeEEEEc
Confidence 4444455567899999999999999999999999997
No 23
>COG1669 Predicted nucleotidyltransferases [General function prediction only]
Probab=94.84 E-value=0.045 Score=54.80 Aligned_cols=44 Identities=30% Similarity=0.534 Sum_probs=38.6
Q ss_pred HHHHHHHHHHhccCCCCceEEecccccCCCCCCCCceEEEEcCC
Q 000387 1237 WAVKRVTRSLQVLWPRSRTNIFGSNATGLSLPSSDVDLVVCLPP 1280 (1588)
Q Consensus 1237 ~AVkrVe~vIQsLwPdArVepFGS~ATGLaLPsSDIDLVVi~Pp 1280 (1588)
.+++++...+++.+.=+++-+|||++-|=.-|+|||||.|-+.+
T Consensus 9 ~~lr~~~~~l~~k~gv~~~~vFGS~aRgE~~~~SDIDILVef~~ 52 (97)
T COG1669 9 KILRKIKPELKEKYGVKRVAVFGSYARGEQKPDSDIDILVEFEP 52 (97)
T ss_pred HHHHHHHHHHHHHhCCceEEEeeeeecCCCCCCCCceeEEeecC
Confidence 34677888888888889999999999999999999999998753
No 24
>PRK13746 aminoglycoside resistance protein; Provisional
Probab=93.69 E-value=0.099 Score=59.95 Aligned_cols=42 Identities=21% Similarity=0.366 Sum_probs=34.3
Q ss_pred HHHHHHHHhccCCCC--ceEEecccccCCCCCCCCceEEEEcCC
Q 000387 1239 VKRVTRSLQVLWPRS--RTNIFGSNATGLSLPSSDVDLVVCLPP 1280 (1588)
Q Consensus 1239 VkrVe~vIQsLwPdA--rVepFGS~ATGLaLPsSDIDLVVi~Pp 1280 (1588)
++.+.++++...++. -|++|||.+.|-+-|.|||||.|+...
T Consensus 13 l~~~~~~l~~~l~~~l~~vyLfGS~~~G~~~p~SDIDllvvv~~ 56 (262)
T PRK13746 13 LSEACAVIERHLEPTLLAIHLYGSAVDGGLKPHSDIDLLVTVAV 56 (262)
T ss_pred HHHHHHHHHHhCcccEEEEEEECCcccCCCCCCCceeEEEEeCC
Confidence 345667777777764 689999999998999999999999853
No 25
>PF07528 DZF: DZF domain; InterPro: IPR006561 This domain is found in proteins containing the double-stranded RNA-binding motif, DSRM (IPR001159 from INTERPRO), or the zinc finger domain C2H2 (IPR007087 from INTERPRO). This domain is found exclusively in the metazoa.
Probab=89.97 E-value=4.3 Score=46.69 Aligned_cols=82 Identities=12% Similarity=0.171 Sum_probs=62.1
Q ss_pred EEeeCCCCcHHHHHHHHHHHHhhCCChHHHHHHHHHHHHhCCCCCCCCCCcchHHHHHHHHHHHhccCcCCCCCCCcHHH
Q 000387 1402 ISFKSPSHTGLQTTDLVKELTEQFPASTPLALVLKQFLADRSLDQSYSGGLSSYCLMLLITRFLQHEHHLGRPINQNYGR 1481 (1588)
Q Consensus 1402 ISFnnpSh~GLrnSeLIreyieqyPrLRPLVLVLK~WLKqRGLNDpytGGLSSYALVLMVIaFLQ~~p~LGRPiNqnLGe 1481 (1588)
.+..+ .-.++.++++++-....+.++.+++++|-+-... +.-+.|++|.+=+|+-+-+-..+. ++ ..++|.
T Consensus 106 ~cl~a--LaalRhakWFq~~a~~l~s~~~viRIlrDl~~R~----p~w~~L~~W~leLL~~~~i~~~~~-~~--~l~~g~ 176 (248)
T PF07528_consen 106 KCLSA--LAALRHAKWFQARANGLQSCVIVIRILRDLRQRV----PTWQPLSSWALELLVEKAISNNSS-RQ--PLSPGD 176 (248)
T ss_pred HHHHH--HHHHHHhHHHHHHhccCCCcceehhhHHHHHHhC----CCCCCCChhHHHHHHHHHeeeCCC-CC--CCChHH
Confidence 34444 5678899999998888889999999999887654 445679999999987665553322 22 356899
Q ss_pred HHHHHHHHhcc
Q 000387 1482 LLMDFLYFFGN 1492 (1588)
Q Consensus 1482 LLLdFF~FYG~ 1492 (1588)
.|-.||+.-+.
T Consensus 177 a~RRvle~las 187 (248)
T PF07528_consen 177 AFRRVLECLAS 187 (248)
T ss_pred HHHHHHHHHhC
Confidence 99999999984
No 26
>KOG2054 consensus Nucleolar RNA-associated protein (NRAP) [Function unknown]
Probab=87.13 E-value=4 Score=54.21 Aligned_cols=132 Identities=19% Similarity=0.188 Sum_probs=88.4
Q ss_pred HHHHHHHhhCCChHHHHHHHHHHHHhCCCCCCCCCCcchHHHHHHHHHHHhccCcCCCCCCCcHHHHHHHHHHHhccCCC
Q 000387 1416 DLVKELTEQFPASTPLALVLKQFLADRSLDQSYSGGLSSYCLMLLITRFLQHEHHLGRPINQNYGRLLMDFLYFFGNVFD 1495 (1588)
Q Consensus 1416 eLIreyieqyPrLRPLVLVLK~WLKqRGLNDpytGGLSSYALVLMVIaFLQ~~p~LGRPiNqnLGeLLLdFF~FYG~eFD 1495 (1588)
+++..-....+.++--+.++|.||++|.++- ..||++.+-+++++++-+... .+- .+.+.-+++-..|+|.+ ..|
T Consensus 298 q~L~K~~s~~~~f~da~~Llk~WlrqRs~~~-~~~gfg~f~~s~lvv~L~s~~-ki~--~~~S~yqvfR~vl~fla-t~d 372 (1121)
T KOG2054|consen 298 QLLSKTLSSAKGFKDALALLKVWLRQRSLDI-GQGGFGGFLLSALVVYLVSTR-KIH--TTLSAYQVFRSVLQFLA-TTD 372 (1121)
T ss_pred HHHHHHHhhhhhHHHHHHHHHHHHHhhhhhc-ccCcchHHHHHHHHHHHHhcC-chh--hcchHHHHHHHHHHHHh-hhh
Confidence 3444445677889999999999999995543 467899999888887766543 210 12445678888999999 589
Q ss_pred CCCceEEeeCCcc----cccccCCCCCCCeEEeCCCCCCCccccC--cccHHHHHHHHHHHHHHHHH
Q 000387 1496 PRQMRISVQGSGV----YIKRERGYSIDPIHIDDPRFPTNNVGRN--CFRIHQCIKAFSDAYSILES 1556 (1588)
Q Consensus 1496 y~ttgISIr~gGi----y~kKErG~s~spL~IEDPfdpsNNVGRn--sfrI~qIqkaFarAyeiLs~ 1556 (1588)
...++|++..... +.+.+.+ +..+..| .....|+..+ ...++++|++-..++..|.+
T Consensus 373 lt~~~~~l~~~~~s~~~~~~f~e~---~~~~f~D-~s~~~NLc~~mt~s~y~~~q~ea~ltl~lL~~ 435 (1121)
T KOG2054|consen 373 LTVNGISLVPSSPSLPALADFHEG---QLVTFID-SSGHLNLCANMTASTYEQVQEEARLTLMLLDS 435 (1121)
T ss_pred hhccceEeccCCCCchhhhhhhhc---ceeeEec-cCCcchhhhhccHHHHHHHHHHHHHHHHHHhh
Confidence 9998998876421 1111222 3455555 2333455544 23467889999999988885
No 27
>PF14792 DNA_pol_B_palm: DNA polymerase beta palm ; PDB: 1RZT_A 3PML_A 2PFN_A 3HX0_K 3HWT_A 2GWS_E 2BCQ_A 3UPQ_A 2BCS_A 3UQ2_A ....
Probab=86.75 E-value=1.9 Score=43.72 Aligned_cols=69 Identities=20% Similarity=0.311 Sum_probs=49.4
Q ss_pred HHHHHHHHHHhccCCCCceEEecccccCCCCCCCCceEEEEcCCCCCCcccccccccccccchhHHHHHHHHHHHhhcCC
Q 000387 1237 WAVKRVTRSLQVLWPRSRTNIFGSNATGLSLPSSDVDLVVCLPPVRNLEPIKEAGILEGRNGIKETCLQHAARYLANQEW 1316 (1588)
Q Consensus 1237 ~AVkrVe~vIQsLwPdArVepFGS~ATGLaLPsSDIDLVVi~PpvrnlEPikeAGiLE~RN~IKet~Lq~LAR~Lr~~~~ 1316 (1588)
.+.+.|.+.++.+.|++.+.+-|||.=|-. -.+|||++|..++..... +. ...+|..+...|.+.++
T Consensus 9 ~i~~~V~~~~~~i~p~~~v~i~GSyRRGK~-~~gDiDiLIt~~~~~~~~-----------~~-~~~~l~~lv~~L~~~g~ 75 (112)
T PF14792_consen 9 EIEEIVKEALEKIDPGLEVEICGSYRRGKE-TSGDIDILITHPDPSSVS-----------KK-LEGLLEKLVKRLEEKGF 75 (112)
T ss_dssp HHHHHHHHHHHCCSTT-EEEEEHHHHTT-S-EESSEEEEEEETTCSTTT-----------CS-TTCHHHHHHHHHHHTTS
T ss_pred HHHHHHHHHHHhcCCCcEEEEccccccCCC-cCCCeEEEEeCCCcCcch-----------hh-HHHHHHHHHHHHHhCCe
Confidence 445667888899999999999999999988 467999999997543210 00 01356777888888887
Q ss_pred cc
Q 000387 1317 VK 1318 (1588)
Q Consensus 1317 Vk 1318 (1588)
+.
T Consensus 76 i~ 77 (112)
T PF14792_consen 76 IT 77 (112)
T ss_dssp EE
T ss_pred EE
Confidence 64
No 28
>KOG3793 consensus Transcription factor NFAT, subunit NF45 [Transcription]
Probab=86.45 E-value=9.2 Score=44.77 Aligned_cols=70 Identities=24% Similarity=0.282 Sum_probs=54.4
Q ss_pred HHHHHHHHHHHHHhhhhHHhhhHHHHHHHHHHHHHHhccC-CC------CceEEecccccCCCCCCCCc-eEEEEcCCC
Q 000387 1211 SLLHEEIDSFCKQVAAENTARKPYINWAVKRVTRSLQVLW-PR------SRTNIFGSNATGLSLPSSDV-DLVVCLPPV 1281 (1588)
Q Consensus 1211 s~LheEIldF~k~I~PEeeeRK~~I~~AVkrVe~vIQsLw-Pd------ArVepFGS~ATGLaLPsSDI-DLVVi~Ppv 1281 (1588)
..+.+||++=.+.+.|+.++|+. |...+.+|..++..+. |. ..|.-.||+.+|..+-++|+ |+||+..-.
T Consensus 39 ~~f~~alLkRnqdL~P~~~~q~~-I~~~vtKV~~vLdn~~~~~L~~~~ieevrqVGSF~k~T~~tg~~~advVViLkTL 116 (362)
T KOG3793|consen 39 TSFSEALLKRNQDLAPNSAEQAS-ILSLVTKVNNVLDNLVAPGLFEVQIEEVRQVGSFKKGTMTTGHNVADLVVILKTL 116 (362)
T ss_pred hHHHHHHHhhhccCCCCHHHHHH-HHHHHHHHHHHHHhhccCCceEeehhhhhhccceeccccccCCcccceEEEeecC
Confidence 35899999999999998888875 6778888888887764 33 24456899999999888775 888887533
No 29
>PF03813 Nrap: Nrap protein; InterPro: IPR005554 Members of this family are nucleolar RNA-associated proteins (Nrap) which are highly conserved from yeast (Saccharomyces cerevisiae) to human. In the mouse, Nrap is ubiquitously expressed and is specifically localized in the nucleolus []. Nrap is a large nucleolar protein (of more than 1000 amino acids). Nrap appears to be associated with ribosome biogenesis by interacting with pre-rRNA primary transcript [].
Probab=79.68 E-value=16 Score=49.23 Aligned_cols=114 Identities=19% Similarity=0.293 Sum_probs=80.7
Q ss_pred HHHHHHHHHHHHhhCCChHHHHHHHHHHHHhCCCCCCCCCCcchHHHHHHHHHHH-hccCcCCCCCCCcHHHHHHHHHHH
Q 000387 1411 GLQTTDLVKELTEQFPASTPLALVLKQFLADRSLDQSYSGGLSSYCLMLLITRFL-QHEHHLGRPINQNYGRLLMDFLYF 1489 (1588)
Q Consensus 1411 GLrnSeLIreyieqyPrLRPLVLVLK~WLKqRGLNDpytGGLSSYALVLMVIaFL-Q~~p~LGRPiNqnLGeLLLdFF~F 1489 (1588)
..+-+..|+.+..+||.+-+-++++|+|+..+-| .+.++.-++=|||++.+ +..+. . ...+.-.-|+.||++
T Consensus 668 ~p~h~~~i~~l~~~~p~fs~tvRL~KrW~~shlL----s~~i~~E~vELlva~vfl~~~p~-~--~P~S~~~GFlRfL~l 740 (972)
T PF03813_consen 668 LPKHTSAIHGLHTRFPSFSPTVRLAKRWLSSHLL----SGHISEEAVELLVASVFLSPAPW-S--PPSSPQTGFLRFLHL 740 (972)
T ss_pred hHHHHHHHHHHHhhCCchhHHHHHHHHHHHhccC----cccCCHHHHHHHHHHHhcCCCCC-C--CCCCHhHHHHHHHHH
Confidence 4466778899999999999999999999999977 56788999999988855 44332 1 123334448899999
Q ss_pred hccCCCCCCceEEeeCCccccc-------------cc--CCCCCCCeEEeCCCCCCCc
Q 000387 1490 FGNVFDPRQMRISVQGSGVYIK-------------RE--RGYSIDPIHIDDPRFPTNN 1532 (1588)
Q Consensus 1490 YG~eFDy~ttgISIr~gGiy~k-------------KE--rG~s~spL~IEDPfdpsNN 1532 (1588)
-. .|||...-+=|.-.+.+.. +. .......|+|--|.|+..-
T Consensus 741 Ls-~~dW~~~PLiVd~~~~l~~~~~~~i~~~f~~~R~~dp~~~~p~~~IaT~~D~~g~ 797 (972)
T PF03813_consen 741 LS-TWDWREEPLIVDFNNELTEEDRAEIETNFDAWRKIDPAMNLPAMFIATPYDPEGS 797 (972)
T ss_pred HH-hCCCCcCCEEEECCCCCCHHHHHHHHHHHHHhhccCccccCCcEEEEeCCCCCCC
Confidence 98 6999987766654433321 11 1112357899988888543
No 30
>PRK02098 phosphoribosyl-dephospho-CoA transferase; Provisional
Probab=77.50 E-value=3.2 Score=47.04 Aligned_cols=38 Identities=37% Similarity=0.438 Sum_probs=29.0
Q ss_pred HHHHHHHhccCCCCceEEecccc----cCC--CCCCCCceEEEEcC
Q 000387 1240 KRVTRSLQVLWPRSRTNIFGSNA----TGL--SLPSSDVDLVVCLP 1279 (1588)
Q Consensus 1240 krVe~vIQsLwPdArVepFGS~A----TGL--aLPsSDIDLVVi~P 1279 (1588)
+.|..+.+. -...+.+|||.+ ||+ -.++|||||.|-.+
T Consensus 110 ~~l~~~~~~--~g~~~gv~GS~a~qlaTG~~~l~~~SDLDLLi~~~ 153 (221)
T PRK02098 110 RALLALAAA--HGVDCRVFGSLAWQALTGLPYLSASSDLDLLWPLP 153 (221)
T ss_pred HHHHHHHHh--CCCcEEEeeehHHHHhhCCcccCCCCCeeEEEecC
Confidence 344444443 245889999999 999 78999999999765
No 31
>TIGR03135 malonate_mdcG holo-ACP synthase, malonate decarboxylase-specific. Malonate decarboxylase, like citrate lyase, has a unique acyl carrier protein subunit with a prosthetic group derived from, and distinct from, coenzyme A. Members of this protein family are the phosphoribosyl-dephospho-CoA transferase specific to the malonate decarboxylase system. This enzyme can also be designated holo-ACP synthase (2.7.7.61). The corresponding component of the citrate lyase system, CitX, shows little or no sequence similarity to this family.
Probab=76.93 E-value=3.4 Score=46.08 Aligned_cols=39 Identities=31% Similarity=0.459 Sum_probs=29.5
Q ss_pred HHHHHHHHhccCCCCceEEeccc----ccCC--CCCCCCceEEEEcC
Q 000387 1239 VKRVTRSLQVLWPRSRTNIFGSN----ATGL--SLPSSDVDLVVCLP 1279 (1588)
Q Consensus 1239 VkrVe~vIQsLwPdArVepFGS~----ATGL--aLPsSDIDLVVi~P 1279 (1588)
++.|..+... + ...+.+|||. +||+ -.++|||||+|..+
T Consensus 97 l~~l~~~~~~-~-~~~~gv~GS~~~qlaTg~~~~~~~SDLDLLi~~~ 141 (202)
T TIGR03135 97 LRALDALLDA-L-GVPWGVYGSAGWQLLTGLPYLHASSDLDLLLRAP 141 (202)
T ss_pred HHHHHHHHHh-C-CCcEEEecchHHHHhcCCcccCCCCCeeEEEcCC
Confidence 3444444443 2 4588999999 9999 88999999999875
No 32
>KOG2534 consensus DNA polymerase IV (family X) [Replication, recombination and repair]
Probab=68.57 E-value=18 Score=43.39 Aligned_cols=66 Identities=18% Similarity=0.194 Sum_probs=49.1
Q ss_pred HHHHHHHHHHhccCCCCceEEecccccCCCCCCCCceEEEEcCCCCCCcccccccccccccchhHHHHHHHHHHHhhcCC
Q 000387 1237 WAVKRVTRSLQVLWPRSRTNIFGSNATGLSLPSSDVDLVVCLPPVRNLEPIKEAGILEGRNGIKETCLQHAARYLANQEW 1316 (1588)
Q Consensus 1237 ~AVkrVe~vIQsLwPdArVepFGS~ATGLaLPsSDIDLVVi~PpvrnlEPikeAGiLE~RN~IKet~Lq~LAR~Lr~~~~ 1316 (1588)
.+.+-|...++...|.+.|.+-||+.-|-. -..|||++|..|..... ...+++.|...|.+.++
T Consensus 156 ~i~~~V~~av~~~~p~~~vt~~GsfRRGk~-~ggDvD~LithP~~~s~---------------~~~~~~~l~~~le~~g~ 219 (353)
T KOG2534|consen 156 AIQQTVQEAVWAFDPEAFVTVTGSFRRGKK-MGGDVDFLITHPGSTST---------------EAKLLQLLMILLEKKGL 219 (353)
T ss_pred HHHHHHHHHHhhcCCCcEEEEeccccCCcc-cCCCeeEEEeCCCCCch---------------hhhHHHHHHHHHHhcCe
Confidence 344567777888889999999999999976 78999999998753321 12456677777777776
Q ss_pred cc
Q 000387 1317 VK 1318 (1588)
Q Consensus 1317 Vk 1318 (1588)
+.
T Consensus 220 il 221 (353)
T KOG2534|consen 220 LL 221 (353)
T ss_pred EE
Confidence 53
No 33
>KOG2054 consensus Nucleolar RNA-associated protein (NRAP) [Function unknown]
Probab=53.13 E-value=1.4e+02 Score=40.90 Aligned_cols=112 Identities=18% Similarity=0.244 Sum_probs=71.7
Q ss_pred HHHHHHHHHHhhCCChHHHHHHHHHHHHhCCCCCCCCCCcchHHHHHHHHHHHhccCcCCCCCCCcHHHHHHHHHHHhcc
Q 000387 1413 QTTDLVKELTEQFPASTPLALVLKQFLADRSLDQSYSGGLSSYCLMLLITRFLQHEHHLGRPINQNYGRLLMDFLYFFGN 1492 (1588)
Q Consensus 1413 rnSeLIreyieqyPrLRPLVLVLK~WLKqRGLNDpytGGLSSYALVLMVIaFLQ~~p~LGRPiNqnLGeLLLdFF~FYG~ 1492 (1588)
+-+..|+.+.+.||.+-+.+++.|.|+..+=| .||+.=-++=|+|++-+++....+-|...--| ++.||++-+
T Consensus 806 ~ht~aL~~l~qsh~~ys~vvrLaKrWl~shLL----~~h~~De~iELLva~lf~~p~p~~~psS~~~g--FlRfL~llS- 878 (1121)
T KOG2054|consen 806 LHTLALQSLSQSHPFYSSVVRLAKRWLGSHLL----SGHHLDEAIELLVAALFLKPGPLVPPSSPENG--FLRFLSLLS- 878 (1121)
T ss_pred HHHHHHHHHhhcccchhHHHHHHHHHHHHHhh----ccchHHHHHHHHHHHHhcCccCCCCCCCcchh--HHHHHHHHh-
Confidence 55667889999999999999999999999865 45666777778888766554322212111123 688888887
Q ss_pred CCCCCCceEEeeCCccccccc----------CCCCCCCeEEeCCCCCCC
Q 000387 1493 VFDPRQMRISVQGSGVYIKRE----------RGYSIDPIHIDDPRFPTN 1531 (1588)
Q Consensus 1493 eFDy~ttgISIr~gGiy~kKE----------rG~s~spL~IEDPfdpsN 1531 (1588)
.|||...-.=|.-.+.+...+ ......+|.|.-|++-.+
T Consensus 879 ~~dW~~~PLIvd~nn~~~ed~~~e~~e~f~s~R~~lp~m~vit~yD~~~ 927 (1121)
T KOG2054|consen 879 TWDWKFDPLIVDFNNGFPEDERSELEEKFISARKQLPPMVVITPYDHLG 927 (1121)
T ss_pred cCcccCCceEEEcCCCCcHHHHHHHHHHHhhhcccCCceEEeecccccc
Confidence 577766543333222222111 011235788988888744
No 34
>cd05401 NT_GlnE_GlnD_like Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins. Escherichia coli GlnD and -E participate in the Glutamine synthetase (GS)/Glutamate synthase (GOGAT) pathway for the assimilation of ammonium nitrogen. In nitrogen sufficiency, GlnE adenylates GS, reducing GS activity; when nitrogen is limiting, GlnE deadenylates GS-AMP, restoring GS activity. When nitrogen is limiting, GlnD uridylylates the nitrogen regulatory protein PII to PII-UTP, and in nitrogen sufficiency, it removes the modifying groups. The activity of Escherichia coli GlnE is modulated by PII-proteins. PII-UMP promotes GlnE deadenylation activity, and PII promotes GlnE adenylation activity. Escherichia coli GlnE has two separate NT domains. The N-terminal NT domain catalyzes the deadenylylation of GS, and the C-terminal NT domain the adenylylation reaction. The majority of proteins in this family conta
Probab=46.80 E-value=30 Score=36.68 Aligned_cols=29 Identities=31% Similarity=0.273 Sum_probs=25.7
Q ss_pred CCceEEecccccCCCCCCCCceEEEEcCC
Q 000387 1252 RSRTNIFGSNATGLSLPSSDVDLVVCLPP 1280 (1588)
Q Consensus 1252 dArVepFGS~ATGLaLPsSDIDLVVi~Pp 1280 (1588)
..-+..+||+.-+=..+.||+|+.++..+
T Consensus 55 ~~~~la~Gs~GR~E~~~~SD~D~~~v~~~ 83 (172)
T cd05401 55 PFALLALGSYGRGELNPSSDQDLLLLYDD 83 (172)
T ss_pred cEEEEEeCCcccCCcCCCcCcceEEEeCC
Confidence 35778999999999999999999999853
No 35
>PRK05007 PII uridylyl-transferase; Provisional
Probab=36.86 E-value=1.1e+02 Score=41.21 Aligned_cols=29 Identities=24% Similarity=0.260 Sum_probs=25.5
Q ss_pred CCceEEecccccCCCCCCCCceEEEEcCC
Q 000387 1252 RSRTNIFGSNATGLSLPSSDVDLVVCLPP 1280 (1588)
Q Consensus 1252 dArVepFGS~ATGLaLPsSDIDLVVi~Pp 1280 (1588)
+.-|...|+|.-|=.-|.|||||+++.++
T Consensus 80 ~~alvAvGgyGR~EL~p~SDiDll~l~~~ 108 (884)
T PRK05007 80 DLALVAVGGYGRGELHPLSDIDLLILSRK 108 (884)
T ss_pred ceEEEecCCCCCcccCCcccceEEEEeCC
Confidence 35778999999999999999999999863
No 36
>PF03281 Mab-21: Mab-21 protein
Probab=35.16 E-value=1.3e+02 Score=34.61 Aligned_cols=65 Identities=22% Similarity=0.227 Sum_probs=51.2
Q ss_pred CCChHHHHHHHHHHHHhCCCCCCCCCCcchHHHHHHHHHHHhccCcCCCCCCCcHHHHHHHHHHHhcc
Q 000387 1425 FPASTPLALVLKQFLADRSLDQSYSGGLSSYCLMLLITRFLQHEHHLGRPINQNYGRLLMDFLYFFGN 1492 (1588)
Q Consensus 1425 yPrLRPLVLVLK~WLKqRGLNDpytGGLSSYALVLMVIaFLQ~~p~LGRPiNqnLGeLLLdFF~FYG~ 1492 (1588)
....+..+.++|.+.+... ...++|+||.|-.++++-+...+....=...++|..|+++|.+.-.
T Consensus 190 ~~~~~~~l~llk~l~~~~~---~~~~~l~syhLkt~ll~~~~~~p~~~~W~~~~l~~~l~~~l~~L~~ 254 (292)
T PF03281_consen 190 NGCRKKCLRLLKALRDRHL---TNLSGLSSYHLKTVLLWLCEKHPSSSDWSEENLGERLLDLLDFLIK 254 (292)
T ss_pred cccHHHHHHHHHHHHHhcc---ccCCCccHHHHHHHHHHHHHcCCCCCCCChHHHHHHHHHHHHHHHH
Confidence 5667788999999987776 5677899999999999988887653100146899999999998865
No 37
>PF03445 DUF294: Putative nucleotidyltransferase DUF294; InterPro: IPR005105 This domain is found associated with an N-terminal cyclic nucleotide-binding domain (IPR000595 from INTERPRO) and two CBS domains (IPR000644 from INTERPRO). This domain, normally represents the C-terminal region, is uncharacterised; however, it seems to be similar to the nucleotidyltransferase domain (IPR002934 from INTERPRO), conserving the DXD motif, which strongly suggests that proteins containing this domain are also nucleotidyltransferases.; GO: 0008773 [protein-PII] uridylyltransferase activity
Probab=30.78 E-value=1.6e+02 Score=31.02 Aligned_cols=29 Identities=17% Similarity=-0.011 Sum_probs=25.7
Q ss_pred CCceEEecccccCCCCCCCCceEEEEcCC
Q 000387 1252 RSRTNIFGSNATGLSLPSSDVDLVVCLPP 1280 (1588)
Q Consensus 1252 dArVepFGS~ATGLaLPsSDIDLVVi~Pp 1280 (1588)
..-+.++||+.=+=.++.||+|..|+..+
T Consensus 49 ~~a~lalGS~GR~E~~~~sDqD~alv~~d 77 (138)
T PF03445_consen 49 PFAWLALGSYGRREQTLYSDQDNALVFED 77 (138)
T ss_pred CEEEEEECcccccCCCcCccccceeeecC
Confidence 35678999999999999999999999864
No 38
>PF10127 Nuc-transf: Predicted nucleotidyltransferase; InterPro: IPR018775 Proteins in this entry are predicted to catalyse the transfer of nucleotide residues from nucleoside diphosphates or triphosphates into dimer or polymer forms.
Probab=30.76 E-value=41 Score=38.02 Aligned_cols=24 Identities=33% Similarity=0.357 Sum_probs=21.6
Q ss_pred eEEecccccCCCCCCCCceEEEEc
Q 000387 1255 TNIFGSNATGLSLPSSDVDLVVCL 1278 (1588)
Q Consensus 1255 VepFGS~ATGLaLPsSDIDLVVi~ 1278 (1588)
....||.+-||..|+||.|+..+.
T Consensus 23 ~~~sGS~a~G~~s~dSD~D~r~vy 46 (247)
T PF10127_consen 23 ACESGSRAYGFASPDSDYDVRGVY 46 (247)
T ss_pred EecccccccCCCCCCcCcccchhc
Confidence 357999999999999999998876
No 39
>PF14091 DUF4269: Domain of unknown function (DUF4269)
Probab=29.96 E-value=5.1e+02 Score=28.77 Aligned_cols=28 Identities=18% Similarity=0.180 Sum_probs=24.1
Q ss_pred CcHHHHHHHHHHHHhhC-CChHHHHHHHH
Q 000387 1409 HTGLQTTDLVKELTEQF-PASTPLALVLK 1436 (1588)
Q Consensus 1409 h~GLrnSeLIreyieqy-PrLRPLVLVLK 1436 (1588)
.+|.+...+-..+++.. |.+|.=++-||
T Consensus 97 QnayrHm~iE~rLL~~~g~~~r~~Ii~LK 125 (152)
T PF14091_consen 97 QNAYRHMLIEHRLLELHGPSFREEIIELK 125 (152)
T ss_pred HHHHHHHHHHHHHHHhcCHHHHHHHHHHH
Confidence 57888888888888888 99999888887
No 40
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=28.57 E-value=1.4e+02 Score=35.74 Aligned_cols=44 Identities=23% Similarity=0.309 Sum_probs=36.9
Q ss_pred HHHHHHHHHHHhccCCCCceEEecccccCCCCCCCCceEEEEcCC
Q 000387 1236 NWAVKRVTRSLQVLWPRSRTNIFGSNATGLSLPSSDVDLVVCLPP 1280 (1588)
Q Consensus 1236 ~~AVkrVe~vIQsLwPdArVepFGS~ATGLaLPsSDIDLVVi~Pp 1280 (1588)
..+.+.|...++.+.|.++|.+-||+.=|.. -..||||+|..++
T Consensus 148 ~~i~~~i~~~l~~~~~~~~v~i~GSyRRgke-t~gDIDili~~~~ 191 (334)
T smart00483 148 FAVEYIVKRAVRKILPDAIVTLTGSFRRGKE-TGHDVDFLITSPH 191 (334)
T ss_pred HHHHHHHHHHHHhhCCCcEEEEecccccCCC-cCCCeeEEEecCC
Confidence 3445667778888899999999999999987 5889999999864
No 41
>PHA02603 nrdC.11 hypothetical protein; Provisional
Probab=28.25 E-value=30 Score=41.76 Aligned_cols=24 Identities=42% Similarity=0.585 Sum_probs=21.0
Q ss_pred eEEecccccCCCCCCCCceEEEEc
Q 000387 1255 TNIFGSNATGLSLPSSDVDLVVCL 1278 (1588)
Q Consensus 1255 VepFGS~ATGLaLPsSDIDLVVi~ 1278 (1588)
..++||.+.|+..|+||+|+--+.
T Consensus 6 ~~~~GShaYG~~tp~SD~D~rGV~ 29 (330)
T PHA02603 6 KGLFGSHLYGTSTPESDVDYKGIF 29 (330)
T ss_pred EEecccceeCCCCCCcccccceee
Confidence 358999999999999999997654
No 42
>PF10620 MdcG: Phosphoribosyl-dephospho-CoA transferase MdcG; InterPro: IPR017557 Malonate decarboxylase, like citrate lyase, has a unique acyl carrier protein subunit with a prosthetic group derived from, and distinct from, coenzyme A. Members of this protein family are the phosphoribosyl-dephospho-CoA transferase specific to the malonate decarboxylase system. This enzyme can also be designated holo-ACP synthase (2.7.7.61 from EC). The corresponding component of the citrate lyase system, CitX, shows little or no sequence similarity to this family.; GO: 0016779 nucleotidyltransferase activity
Probab=26.53 E-value=48 Score=37.46 Aligned_cols=40 Identities=35% Similarity=0.496 Sum_probs=28.8
Q ss_pred HHHHHHHHHhccCCCCceEEeccc----ccCCC--CCCCCceEEEEcC
Q 000387 1238 AVKRVTRSLQVLWPRSRTNIFGSN----ATGLS--LPSSDVDLVVCLP 1279 (1588)
Q Consensus 1238 AVkrVe~vIQsLwPdArVepFGS~----ATGLa--LPsSDIDLVVi~P 1279 (1588)
++..+...... -+...-+|||. +||+. -++|||||.|..+
T Consensus 104 ~l~~l~~~~~~--~~~~~gv~GS~g~qlaTGl~~l~~~SDLDLli~~~ 149 (213)
T PF10620_consen 104 ALQALRALLDA--LGLRWGVYGSLGFQLATGLPYLHADSDLDLLIRPP 149 (213)
T ss_pred HHHHHHHHHHH--cCCCEEEehhHHHHHHhCccccCCCCCceEEEeCC
Confidence 45555555522 37888999997 57764 4699999999875
No 43
>PF08310 LGFP: LGFP repeat; InterPro: IPR013207 This 54 amino acid repeat is found in many hypothetical proteins. Several hypothetical proteins from Corynebacterium glutamicum (Brevibacterium flavum) and Corynebacterium efficiens along with PS1 protein contain this repeat region. The N-terminal region of PS1 contains an esterase domain which transfers corynomycolic acid. The C-terminal region consists of 4 tandem LGFP repeats. It is hypothesised that the PS1 proteins in Corynebacterium, when associated with the cell wall, may be anchored via the LGFP tandem repeats that may be important for maintaining cell wall integrity. Deletion of Q01377 from SWISSPROT protein results in a 10-fold increase in the cell volume of the organism and infers the corresponding involvement of the protein in the cell shape formation []. The secondary structure of each repeat is predicted to comprise two beta-strands and one alpha-helix.
Probab=26.12 E-value=37 Score=30.49 Aligned_cols=20 Identities=30% Similarity=0.685 Sum_probs=15.8
Q ss_pred cccccccccccceeeecCCC
Q 000387 898 SGIDYNQYFGGGVMYWNTSD 917 (1588)
Q Consensus 898 ~~~d~nq~fgggvmyw~~~~ 917 (1588)
.|.=.-|.|=||++||+|+-
T Consensus 13 ~G~G~~q~F~~G~Iywsp~t 32 (54)
T PF08310_consen 13 DGRGRYQDFQNGTIYWSPAT 32 (54)
T ss_pred CCCEEEEEcCCeEEEEeCCC
Confidence 34456789999999999874
No 44
>COG1665 Predicted nucleotidyltransferase [General function prediction only]
Probab=23.76 E-value=84 Score=37.50 Aligned_cols=37 Identities=30% Similarity=0.278 Sum_probs=29.3
Q ss_pred HHHHHhc-cCCCCceEEecccccCCCCCCCCceEEEEc
Q 000387 1242 VTRSLQV-LWPRSRTNIFGSNATGLSLPSSDVDLVVCL 1278 (1588)
Q Consensus 1242 Ve~vIQs-LwPdArVepFGS~ATGLaLPsSDIDLVVi~ 1278 (1588)
|-.++.. -.|--.+=+-||..-||+-.+||||++|.+
T Consensus 110 i~~~led~gVp~~~mGVTGSiL~gl~~~nSDIDfVVYG 147 (315)
T COG1665 110 IVEFLEDAGVPVNSMGVTGSILLGLYDENSDIDFVVYG 147 (315)
T ss_pred HHHHHHHcCCchhhccccccccccccCCCCCceEEEEc
Confidence 3334443 346677778999999999999999999998
No 45
>cd00141 NT_POLXc Nucleotidyltransferase (NT) domain of family X DNA Polymerases. X family polymerases fill in short gaps during DNA repair. They are relatively inaccurate enzymes and play roles in base excision repair, in non-homologous end joining (NHEJ) which acts mainly to repair damage due to ionizing radiation, and in V(D)J recombination. This family includes eukaryotic Pol beta, Pol lambda, Pol mu, and terminal deoxyribonucleotidyl transferase (TdT). Pol beta and Pol lambda are primarily DNA template-dependent polymerases. TdT is a DNA template-independent polymerase. Pol mu has both template dependent and template independent activities. This subgroup belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. These three carboxylate residues are fairly well conserved in this
Probab=22.77 E-value=1.3e+02 Score=35.56 Aligned_cols=43 Identities=23% Similarity=0.333 Sum_probs=35.8
Q ss_pred HHHHHHHHHHhccCCCCceEEecccccCCCCCCCCceEEEEcCC
Q 000387 1237 WAVKRVTRSLQVLWPRSRTNIFGSNATGLSLPSSDVDLVVCLPP 1280 (1588)
Q Consensus 1237 ~AVkrVe~vIQsLwPdArVepFGS~ATGLaLPsSDIDLVVi~Pp 1280 (1588)
.+.+.|...++.+-|..+|.+-||+.-|.. -.+||||+|..++
T Consensus 145 ~~a~~i~~~l~~~~~~~~v~i~GS~RRg~e-t~gDiDilv~~~~ 187 (307)
T cd00141 145 AIAEIIKEALREVDPVLQVEIAGSYRRGKE-TVGDIDILVTHPD 187 (307)
T ss_pred HHHHHHHHHHHhCCCceEEEEcccccCCCC-ccCCEEEEEecCC
Confidence 345667777888778999999999999887 5889999998764
No 46
>PRK00227 glnD PII uridylyl-transferase; Provisional
Probab=22.15 E-value=1.3e+02 Score=39.62 Aligned_cols=44 Identities=32% Similarity=0.292 Sum_probs=33.8
Q ss_pred HHHHHHHHHHhccC-C-CCceEEecccccCCCCCCCCceEEEEcCC
Q 000387 1237 WAVKRVTRSLQVLW-P-RSRTNIFGSNATGLSLPSSDVDLVVCLPP 1280 (1588)
Q Consensus 1237 ~AVkrVe~vIQsLw-P-dArVepFGS~ATGLaLPsSDIDLVVi~Pp 1280 (1588)
.+.+.-..+++.+. | +.-+..-|+|.-|=..|.|||||.|+.++
T Consensus 10 ~~~~~~~~~~~~~~~~~~~aLvAvGGYGR~EL~P~SDIDLLiL~~~ 55 (693)
T PRK00227 10 DAEASALALLGSLQLPPGTALAATGSLARREMTPYSDLDLILLHPP 55 (693)
T ss_pred HHHHHHHHHHHhcCCCCCeEEEEeccccccCcCCCcCceEEEEeCC
Confidence 34455556666554 3 45888999999999999999999999863
Done!