Query 005149
Match_columns 712
No_of_seqs 248 out of 968
Neff 4.8
Searched_HMMs 46136
Date Thu Mar 28 18:52:15 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/005149.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/005149hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1906 DNA polymerase sigma [ 100.0 1.7E-39 3.7E-44 360.8 34.5 253 40-335 61-343 (514)
2 COG5260 TRF4 DNA polymerase si 100.0 8.7E-38 1.9E-42 341.0 23.3 274 33-335 48-344 (482)
3 PTZ00418 Poly(A) polymerase; P 100.0 2E-29 4.2E-34 283.9 26.8 248 53-336 83-391 (593)
4 KOG2245 Poly(A) polymerase and 99.9 7.2E-26 1.6E-30 247.5 25.8 266 30-337 25-349 (562)
5 KOG2277 S-M checkpoint control 99.8 1E-19 2.2E-24 207.1 20.7 284 41-334 113-431 (596)
6 COG5186 PAP1 Poly(A) polymeras 99.8 3E-19 6.5E-24 189.7 21.7 241 53-336 38-340 (552)
7 cd05402 NT_PAP_TUTase Nucleoti 99.8 3.8E-20 8.3E-25 168.1 11.5 105 62-173 1-111 (114)
8 PRK13300 tRNA CCA-pyrophosphor 99.8 1E-16 2.2E-21 177.8 24.4 231 46-325 3-252 (447)
9 TIGR03671 cca_archaeal CCA-add 99.8 1E-16 2.2E-21 175.7 23.6 232 46-328 2-252 (408)
10 PF04928 PAP_central: Poly(A) 99.7 3.6E-18 7.8E-23 177.5 10.3 204 41-336 21-242 (254)
11 COG1746 CCA1 tRNA nucleotidylt 99.7 4.6E-15 1E-19 161.6 23.2 224 41-323 2-252 (443)
12 PF03828 PAP_assoc: Cid1 famil 98.2 3.4E-07 7.3E-12 74.8 1.0 23 220-242 6-29 (60)
13 PF09249 tRNA_NucTransf2: tRNA 97.9 3.3E-05 7.2E-10 72.0 6.7 90 189-323 3-99 (114)
14 PF01909 NTP_transf_2: Nucleot 97.8 1.8E-05 3.9E-10 68.8 3.5 43 67-109 1-44 (93)
15 cd05397 NT_Pol-beta-like Nucle 97.7 7.3E-05 1.6E-09 59.7 5.1 40 65-104 2-42 (49)
16 cd05400 NT_2-5OAS_ClassI-CCAas 97.6 0.00034 7.3E-09 66.1 9.3 93 61-162 7-112 (143)
17 cd05403 NT_KNTase_like Nucleot 97.4 0.00046 9.9E-09 59.4 6.8 44 66-109 3-48 (93)
18 PF10421 OAS1_C: 2'-5'-oligoad 97.4 0.0013 2.8E-08 66.6 10.7 59 163-222 21-81 (190)
19 smart00572 DZF domain in DSRM 97.3 0.0089 1.9E-07 62.9 15.6 197 81-331 4-229 (246)
20 COG1669 Predicted nucleotidylt 96.4 0.0058 1.3E-07 55.9 5.5 46 63-108 7-53 (97)
21 COG1708 Predicted nucleotidylt 96.0 0.011 2.4E-07 53.5 5.2 28 78-105 25-52 (128)
22 PRK13746 aminoglycoside resist 95.9 0.022 4.8E-07 60.6 7.7 53 67-119 13-68 (262)
23 PF03813 Nrap: Nrap protein; 95.0 0.16 3.4E-06 63.1 11.9 119 174-333 155-299 (972)
24 KOG3793 Transcription factor N 94.2 0.69 1.5E-05 49.5 12.5 149 40-195 39-217 (362)
25 PF07528 DZF: DZF domain; Int 93.6 2 4.3E-05 45.6 14.8 127 85-220 2-160 (248)
26 KOG2054 Nucleolar RNA-associat 93.2 0.41 8.9E-06 58.6 9.9 119 174-333 299-435 (1121)
27 PF14091 DUF4269: Domain of un 92.2 2 4.4E-05 42.5 11.6 104 79-193 15-125 (152)
28 PRK02098 phosphoribosyl-dephos 90.3 0.77 1.7E-05 47.9 7.1 41 67-108 109-155 (221)
29 TIGR03135 malonate_mdcG holo-A 89.5 0.95 2.1E-05 46.6 6.9 41 67-108 97-143 (202)
30 PF03813 Nrap: Nrap protein; 88.7 5 0.00011 50.2 13.5 129 175-332 675-824 (972)
31 PF10620 MdcG: Phosphoribosyl- 81.4 5.5 0.00012 41.3 7.8 54 66-123 104-163 (213)
32 PF14792 DNA_pol_B_palm: DNA p 78.5 3.8 8.1E-05 38.2 5.0 57 66-123 10-72 (112)
33 cd05401 NT_GlnE_GlnD_like Nucl 73.9 28 0.00061 34.0 10.0 30 79-108 55-84 (172)
34 PRK00227 glnD PII uridylyl-tra 71.7 10 0.00022 45.9 7.5 49 60-108 5-56 (693)
35 PRK01293 phosphoribosyl-dephos 68.9 11 0.00024 39.1 6.1 32 78-109 108-145 (207)
36 PF03445 DUF294: Putative nucl 67.3 38 0.00082 32.6 9.1 29 79-107 49-77 (138)
37 PRK05007 PII uridylyl-transfer 61.5 55 0.0012 40.8 11.2 50 60-109 55-110 (884)
38 PRK04374 PII uridylyl-transfer 55.5 63 0.0014 40.3 10.2 83 26-108 6-101 (869)
39 KOG1906 DNA polymerase sigma [ 55.0 6.5 0.00014 45.9 1.7 69 297-368 246-314 (514)
40 KOG2534 DNA polymerase IV (fam 52.6 39 0.00085 37.5 6.9 43 66-109 157-200 (353)
41 COG2844 GlnD UTP:GlnB (protein 51.3 71 0.0015 39.6 9.4 39 79-117 66-104 (867)
42 PRK03059 PII uridylyl-transfer 51.0 71 0.0015 39.8 9.7 49 60-108 38-90 (856)
43 COG2413 Predicted nucleotidylt 47.3 45 0.00096 35.0 6.0 42 63-106 23-64 (228)
44 COG1665 Predicted nucleotidylt 46.3 33 0.00071 37.4 5.1 29 78-106 120-148 (315)
45 PRK00275 glnD PII uridylyl-tra 46.1 1.1E+02 0.0023 38.5 10.2 49 60-108 53-107 (895)
46 TIGR01693 UTase_glnD [Protein- 41.7 1.1E+02 0.0023 38.0 9.3 30 79-108 43-72 (850)
47 PF10127 Nuc-transf: Predicted 41.3 19 0.00042 37.5 2.5 45 63-107 2-48 (247)
48 KOG2054 Nucleolar RNA-associat 40.2 41 0.00089 42.2 5.3 55 176-235 812-885 (1121)
49 PRK01759 glnD PII uridylyl-tra 36.7 1.4E+02 0.003 37.3 9.1 49 60-108 31-85 (854)
50 cd05398 NT_ClassII-CCAase Nucl 34.1 1.4E+02 0.0031 28.7 7.0 68 78-162 15-86 (139)
51 cd00141 NT_POLXc Nucleotidyltr 33.1 97 0.0021 33.8 6.3 41 67-108 147-188 (307)
52 PHA02603 nrdC.11 hypothetical 31.1 26 0.00056 39.0 1.5 24 82-105 6-29 (330)
53 COG3541 Predicted nucleotidylt 24.5 37 0.00081 36.3 1.3 22 85-106 16-37 (248)
54 PF03296 Pox_polyA_pol: Poxvir 22.1 1.4E+02 0.0031 29.6 4.6 63 42-105 5-79 (149)
55 smart00483 POLXc DNA polymeras 21.6 2.4E+02 0.0053 31.2 6.9 43 65-108 149-192 (334)
56 PF09970 DUF2204: Nucleotidyl 21.6 3.7E+02 0.008 27.2 7.7 80 78-168 15-99 (181)
57 PRK05092 PII uridylyl-transfer 21.5 4.7E+02 0.01 33.0 10.1 29 80-108 106-134 (931)
58 PF12633 Adenyl_cycl_N: Adenyl 20.8 1.9E+02 0.004 30.3 5.4 32 81-112 99-130 (204)
No 1
>KOG1906 consensus DNA polymerase sigma [Replication, recombination and repair]
Probab=100.00 E-value=1.7e-39 Score=360.79 Aligned_cols=253 Identities=33% Similarity=0.553 Sum_probs=198.6
Q ss_pred HHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHH-hhcCCceEEeeccccCCCCCCCCceEEeecC-CcchhHHHHHH
Q 005149 40 QRAEEATQGIIAQVQPTVVSEERRKAVIDYVQRLIR-NYLGCEVFPFGSVPLKTYLPDGDIDLTAFGG-LNVEEALANDV 117 (712)
Q Consensus 40 ~~le~ei~e~v~~I~PT~eE~~~R~~VI~~Vq~lI~-~~p~a~V~~FGS~~tGL~LP~SDIDL~V~~~-~~~~e~l~~~V 117 (712)
..++++|.+|+++|.||.+|.+.|..+++.++++|+ +||+|.|++|||+.||||||+|||||+|+.. ...++.....+
T Consensus 61 ~~l~~eI~~fv~~l~pt~~e~~~R~~~~~~i~~~v~~~~~~a~v~~FGS~~tglyLP~sDIDl~v~~~~~~~~e~~~~~~ 140 (514)
T KOG1906|consen 61 ERLRNEILDFVQYLIPTPEEIEVRSELVEKIRDVVKQKWPDASVYVFGSVPTGLYLPDSDIDLVVLSKFLNDKEDRAVKL 140 (514)
T ss_pred HHHHHHHHHHHHHhcCCchHHHHHHHHHHHHHHHHHHhcccceeEEeeeeeccccccccceEEEEecccccCchhhHHHH
Confidence 346789999999999999999999999999999999 7999999999999999999999999999998 45556666555
Q ss_pred HHHHHHHhhccccccceeeeEEE-EeeeeeEEEee--cCeeEEeeeccCCcchhhHHHHHHHHHhCCChhhHHHHHHHHH
Q 005149 118 CSVLEREDQNKAAEFVVKDAQLI-RAEVKLVKCLV--QNIVVDISFNQLGGLSTLCFLEQVDRLIGKDHLFKRSIILIKA 194 (712)
Q Consensus 118 ~~iL~~~~~~~~a~f~V~~V~vI-~ArVPIIK~~~--~gI~VDISfNn~~Gl~~s~fLe~Vd~~v~~~p~fr~LvlLIK~ 194 (712)
..+++..+. ... ..|.+| .||||||||++ .+|.||||||+.+|++++.|+ ..++.++|.+++|++++|+
T Consensus 141 ~l~~~~e~~--~~~---~~v~~v~karvpiik~~d~~s~i~vDISFn~~~G~~aa~~i---~~~~~~~p~~~~lvlvlk~ 212 (514)
T KOG1906|consen 141 ELALELEED--NSA---FHVKVVQKARVPIIKFKDPVSNIHVDISFNQTNGVKAAKFI---KDFLRDHPFLRSLVLVLKQ 212 (514)
T ss_pred HHHHhhhhc--ccc---ceEEEeeeeeeeeEEeecCccceEEEeeecccCchhHHHHH---HHHHhcCccchhHHHHHHH
Confidence 544444321 112 357788 99999999997 499999999999999999885 5668888999999999999
Q ss_pred HHHHhhCccCCCCCCCcHHHHHHHH------------------------HHHHHhhhc-CCCCCCceeeccCCcccCCCC
Q 005149 195 WCYYESRILGAHHGLISTYALETLV------------------------LYKFLDYFS-KFDWDSYCISLNGPVRISSLP 249 (712)
Q Consensus 195 Wa~yesRil~a~~GgLSSYaL~lMV------------------------L~~FL~yYs-kFD~~~~~ISi~GpVplssLp 249 (712)
|++ +++++++++|||+||+|++|| |..||++|+ +|.++..+|++..+..
T Consensus 213 fl~-~r~ln~v~tGgisSyal~~Lv~~fl~l~~~~~s~~~~~~~~~~vll~~f~e~yG~~f~~~k~~i~~~~~g~----- 286 (514)
T KOG1906|consen 213 FLY-ERRLNGVHTGGISSYALELLVLSFLQLHPRSKSGRLAVLKNLGVLLIKFFELYGRNFGYDKLGISLSLGGE----- 286 (514)
T ss_pred HHH-hhcccccccccchHHHHHHHHHHHHhhcccccCCccchhcccchHHHHHHHHhccccCchhhceeccCCcc-----
Confidence 985 788999999999999999999 345666665 4665555554442210
Q ss_pred cccccCCCCCCCcccccHHHHHHHHhhcCCCCCCCCCCCCCCCCCCeEEcCCCCCCCCcCCCCCHHHHHHHHHHHHHHHH
Q 005149 250 EVVVETPENSGGDLLLSSEFLKECVEQFSVPSRGFDTNSRSFPPKHLNIVDPLKENNNLGRSVSKGNFYRIRSAFTYGAR 329 (712)
Q Consensus 250 ~~~~e~pe~~~g~lLL~~efLr~~~~~fs~~~rG~~~~~r~f~~~~L~IeDPfdpsNNLGRSVsk~nf~rIR~AF~~aa~ 329 (712)
.+ .++- .++..+ .......++||||.+|.||+||+.+ ++..|+.+|.+|+.
T Consensus 287 -------------~~-~~~~------------~~~~~~-~~~~~~~LsieDP~~P~ndigr~s~--~~~~v~~~F~~af~ 337 (514)
T KOG1906|consen 287 -------------YV-SKEL------------TGFFNN-SLERPGSLSIEDPVDPTNDIGRSSF--NFSQVKGAFAYAFK 337 (514)
T ss_pred -------------cc-cHHh------------hhhhcc-cccCCCccccCCCCCcccccccccc--cHHHHHHHHHHHHH
Confidence 00 0000 011111 0122456999999999999999987 89999999999999
Q ss_pred HHHhhh
Q 005149 330 KLGHIL 335 (712)
Q Consensus 330 ~L~~il 335 (712)
.|....
T Consensus 338 ~l~~~~ 343 (514)
T KOG1906|consen 338 VLTNAV 343 (514)
T ss_pred HHhhhh
Confidence 987754
No 2
>COG5260 TRF4 DNA polymerase sigma [DNA replication, recombination, and repair]
Probab=100.00 E-value=8.7e-38 Score=341.03 Aligned_cols=274 Identities=22% Similarity=0.363 Sum_probs=202.1
Q ss_pred CCChhhHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHH-hhcCCceEEeeccccCCCCCCCCceEEeecCCcchh
Q 005149 33 AIGAEYWQRAEEATQGIIAQVQPTVVSEERRKAVIDYVQRLIR-NYLGCEVFPFGSVPLKTYLPDGDIDLTAFGGLNVEE 111 (712)
Q Consensus 33 ~i~~~~w~~le~ei~e~v~~I~PT~eE~~~R~~VI~~Vq~lI~-~~p~a~V~~FGS~~tGL~LP~SDIDL~V~~~~~~~e 111 (712)
++..+.-..+..++.+|+.+|.|+.+|.++|..+++.|+++++ .||++.+++|||+.+||++|.|||||||..+.....
T Consensus 48 s~~~~~~~~lt~el~~~y~~I~ps~eEl~~R~~~leklr~~lk~~~pda~l~vFGS~~t~L~l~~SDiDl~I~s~~~~~~ 127 (482)
T COG5260 48 SVFNEESDELTSELLEFYDYIAPSDEELKRRKALLEKLRTLLKKEFPDADLKVFGSTETGLALPKSDIDLCIISDPRGYK 127 (482)
T ss_pred hhhhhhHHHHHHHHHHHHHhhCCCHHHHHHHHHHHHHHHHHHHHhCCccceeEecccccccccCcccccEEEecCCcccc
Confidence 3444555668889999999999999999999999999999999 699999999999999999999999999999654322
Q ss_pred HHHH--HHHHHHHHHhhccccccceeeeEEE-EeeeeeEEEeec--CeeEEeeeccCCcchhhHHHHHHHHHhCCChhhH
Q 005149 112 ALAN--DVCSVLEREDQNKAAEFVVKDAQLI-RAEVKLVKCLVQ--NIVVDISFNQLGGLSTLCFLEQVDRLIGKDHLFK 186 (712)
Q Consensus 112 ~l~~--~V~~iL~~~~~~~~a~f~V~~V~vI-~ArVPIIK~~~~--gI~VDISfNn~~Gl~~s~fLe~Vd~~v~~~p~fr 186 (712)
+-.. .+...+.. .....++.+| +|||||||+++. ++.|||+||+..|+.++.++ ..++..+|++|
T Consensus 128 et~~~~~l~~~l~~-------~~~~~~~~~v~tarVPIIKl~d~~s~l~~Disfn~~~~~~~akl~---~~~~~~~P~lr 197 (482)
T COG5260 128 ETRNAGSLASHLFK-------KNLAKEVVVVSTARVPIIKLVDPQSGLHCDISFNNTNGIVNAKLI---RSYLKEDPRLR 197 (482)
T ss_pred ccccHHHHHHHHHH-------hccCeeeEEEEecccceEEEecCccceEEEeecCchhHHHHHHHH---HHHHhcCcccc
Confidence 1111 12222222 1123577788 999999999985 99999999999999999885 67889999999
Q ss_pred HHHHHHHHHHHHhhCccCCCCCCCcHHHHHHHHHHHHHhhhcCCCCCCceeeccCCcccCCCCcccccCCCCCCCccccc
Q 005149 187 RSIILIKAWCYYESRILGAHHGLISTYALETLVLYKFLDYFSKFDWDSYCISLNGPVRISSLPEVVVETPENSGGDLLLS 266 (712)
Q Consensus 187 ~LvlLIK~Wa~yesRil~a~~GgLSSYaL~lMVL~~FL~yYskFD~~~~~ISi~GpVplssLp~~~~e~pe~~~g~lLL~ 266 (712)
||+++||+|++ +++++++++|||+||++++||+ .||+....|-+....+- . | + ..+.-....|-+|
T Consensus 198 pLvliIKhwl~-~R~ln~~~~GtL~sy~i~cmV~-sfLq~~~~~~~~~~~~~-~-~--l------~~~~~~~~lgvLf-- 263 (482)
T COG5260 198 PLVLIIKHWLK-RRALNDVATGTLSSYTISCMVL-SFLQMHPPFLFFDNGLL-S-P--L------KYNKNIDNLGVLF-- 263 (482)
T ss_pred hHHHHHHHHHH-HHhhcccccCcchhhhhHHHHH-HHHHhCCcccccccccc-c-h--h------hccccccccchHH--
Confidence 99999999997 6677899999999999999994 56666543221111000 0 0 0 0000001122233
Q ss_pred HHHHHHHHhhcCCC----------------CCCCCCCCCCCCCCCeEEcCCC-CCCCCcCCCCCHHHHHHHHHHHHHHHH
Q 005149 267 SEFLKECVEQFSVP----------------SRGFDTNSRSFPPKHLNIVDPL-KENNNLGRSVSKGNFYRIRSAFTYGAR 329 (712)
Q Consensus 267 ~efLr~~~~~fs~~----------------~rG~~~~~r~f~~~~L~IeDPf-dpsNNLGRSVsk~nf~rIR~AF~~aa~ 329 (712)
.+||..|+..|.+. .+||....+ +..||||||+ ++++++++... ++..|+.+|.+|.+
T Consensus 264 ~dFf~~yG~~f~Y~~~~~si~~g~~~~~K~e~g~~~~~~---p~~LsiqdP~td~n~~~~a~s~--~ik~i~~~F~~aF~ 338 (482)
T COG5260 264 DDFFELYGKSFNYSLVVLSINSGDFYLPKYEKGWLKPSK---PNSLSIQDPGTDRNNDISAVSF--NIKDIKAAFIRAFE 338 (482)
T ss_pred HHHHHHhccccChhheEEEecCCceeeehhhcccccccC---CCcEeecCCCCCcccccccccc--hHHHHHHHHHHHHH
Confidence 36666665554431 235544333 3669999999 99999998766 89999999999888
Q ss_pred HHHhhh
Q 005149 330 KLGHIL 335 (712)
Q Consensus 330 ~L~~il 335 (712)
.|..-+
T Consensus 339 lls~~~ 344 (482)
T COG5260 339 LLSNKL 344 (482)
T ss_pred HHhhhc
Confidence 887643
No 3
>PTZ00418 Poly(A) polymerase; Provisional
Probab=99.97 E-value=2e-29 Score=283.86 Aligned_cols=248 Identities=21% Similarity=0.354 Sum_probs=194.3
Q ss_pred cCCCHHHHHHHHHHHHHHHHHHHhhc-----------------CCceEEeeccccCCCCCCCCceEEeecCCcc-hhHHH
Q 005149 53 VQPTVVSEERRKAVIDYVQRLIRNYL-----------------GCEVFPFGSVPLKTYLPDGDIDLTAFGGLNV-EEALA 114 (712)
Q Consensus 53 I~PT~eE~~~R~~VI~~Vq~lI~~~p-----------------~a~V~~FGS~~tGL~LP~SDIDL~V~~~~~~-~e~l~ 114 (712)
+-|++||.++|++|++.|++++++|. +++|++||||.+|++.|+||||++|++|..+ .++|+
T Consensus 83 ~fes~ee~~kR~~vL~~L~~iv~~wv~~vs~~k~~~~~~~~~~~g~I~tfGSYrLGV~~pgSDID~L~V~P~~vtredFF 162 (593)
T PTZ00418 83 LYETEEGKKKRERVLGSLNKLVREFVVEASIEQGINEEEASQISGKLFTFGSYRLGVVAPGSDIDTLCLAPRHITRESFF 162 (593)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCChhHHhcCCeEEEEeccccccCCCCCCcccEEEECCCCCCHHHHH
Confidence 78999999999999999999998862 4789999999999999999999999999765 46777
Q ss_pred HHHHHHHHHHhhccccccceeeeEEE-EeeeeeEEEeecCeeEEeeeccCCc--------------------------ch
Q 005149 115 NDVCSVLEREDQNKAAEFVVKDAQLI-RAEVKLVKCLVQNIVVDISFNQLGG--------------------------LS 167 (712)
Q Consensus 115 ~~V~~iL~~~~~~~~a~f~V~~V~vI-~ArVPIIK~~~~gI~VDISfNn~~G--------------------------l~ 167 (712)
..+..+|++ ...|++++.| .|+||||||...||.||+.|.++.. +.
T Consensus 163 ~~f~~~L~~-------~~~V~eL~~V~~A~VPiIk~~~~GI~iDL~fa~l~~~~vp~~~~~l~d~~lL~nlde~s~rSLN 235 (593)
T PTZ00418 163 SDFYAKLQQ-------DPNITKLQPVPDAYTPVIKFVYDGIDIDLLFANLPLPTIPDCLNSLDDDYILRNVDEKTVRSLN 235 (593)
T ss_pred HHHHHHHhc-------CCCcceeeccCccccCeEEEEECCEEEeeeecccCCCCCCccccccCchhhhhcCCHHHhhhhc
Confidence 778777765 2356888888 9999999999999999999973321 01
Q ss_pred hhHHHHHHHHHhCCChhhHHHHHHHHHHHHHhhCccCCCCCCCcHHHHHHHH---------------HHHHHhhhcCCCC
Q 005149 168 TLCFLEQVDRLIGKDHLFKRSIILIKAWCYYESRILGAHHGLISTYALETLV---------------LYKFLDYFSKFDW 232 (712)
Q Consensus 168 ~s~fLe~Vd~~v~~~p~fr~LvlLIK~Wa~yesRil~a~~GgLSSYaL~lMV---------------L~~FL~yYskFD~ 232 (712)
..+-.++|.+++.....||.++++||.||+ +++|+++..|+|++.+|++|| |.+||.+|++|+|
T Consensus 236 G~Rvtd~Il~lVPn~~~Fr~aLR~IKlWAk-rRGIYsNv~GflGGV~wAILvARVCQLyPna~~s~Lv~~FF~iys~W~W 314 (593)
T PTZ00418 236 GCRVADLILASVPNKDYFRTTLRFIKLWAK-RRGIYSNVLGYLGGVSWAILTARICQLYPNFAPSQLIHKFFRVYSIWNW 314 (593)
T ss_pred cHHHHHHHHHHCCChHHHHHHHHHHHHHHH-HhccccccccccchHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhhcCCC
Confidence 123345677888888899999999999997 556778999999999999999 6799999999999
Q ss_pred CCceeeccCCcccCCCCcccccCCCCCCCcccccHHHHHHHHhhcCCCCCCCCCC-CCCCCCCCeEEcCCCCCCCCcCCC
Q 005149 233 DSYCISLNGPVRISSLPEVVVETPENSGGDLLLSSEFLKECVEQFSVPSRGFDTN-SRSFPPKHLNIVDPLKENNNLGRS 311 (712)
Q Consensus 233 ~~~~ISi~GpVplssLp~~~~e~pe~~~g~lLL~~efLr~~~~~fs~~~rG~~~~-~r~f~~~~L~IeDPfdpsNNLGRS 311 (712)
.+ ||.|..+.+. + +..|.+- + +.|... ........|.|+.|..|..|.+++
T Consensus 315 p~-------PV~L~~i~~~----~-~~~g~~~------------~----~VWdPr~~~~dr~h~MPIITPayP~mNst~n 366 (593)
T PTZ00418 315 KN-------PVLLCKIKEV----P-NIPGLMN------------F----KVWDPRVNPQDRAHLMPIITPAFPSMNSTHN 366 (593)
T ss_pred CC-------CeEccccccc----c-cCCcccC------------C----cccCCCCCcccccccCCeecCCCCCcccccc
Confidence 86 4433322110 0 0001000 0 012211 011224679999999999999999
Q ss_pred CCHHHHHHHHHHHHHHHHHHHhhhc
Q 005149 312 VSKGNFYRIRSAFTYGARKLGHILS 336 (712)
Q Consensus 312 Vsk~nf~rIR~AF~~aa~~L~~il~ 336 (712)
|++.+++.|+++|++|.+.+..+..
T Consensus 367 Vt~sT~~vI~~Ef~Ra~~i~~~i~~ 391 (593)
T PTZ00418 367 VTYTTKRVITEEFKRAHEIIKYIEK 391 (593)
T ss_pred ccHHHHHHHHHHHHHHHHHHHHHHh
Confidence 9999999999999999999987653
No 4
>KOG2245 consensus Poly(A) polymerase and related nucleotidyltransferases [RNA processing and modification]
Probab=99.95 E-value=7.2e-26 Score=247.54 Aligned_cols=266 Identities=22% Similarity=0.338 Sum_probs=201.5
Q ss_pred CCCCCChhhHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHhhc-----------------CCceEEeeccccCC
Q 005149 30 NQTAIGAEYWQRAEEATQGIIAQVQPTVVSEERRKAVIDYVQRLIRNYL-----------------GCEVFPFGSVPLKT 92 (712)
Q Consensus 30 ~p~~i~~~~w~~le~ei~e~v~~I~PT~eE~~~R~~VI~~Vq~lI~~~p-----------------~a~V~~FGS~~tGL 92 (712)
.|+..+-++-..|+..++++ -+-++++|..+|.+|++.|++++++|. |+++++||||.+|+
T Consensus 25 ~p~~~d~~lt~~L~~~L~~~--g~fEs~eEt~~R~~VL~~L~~iVk~wVk~vs~~k~~p~~~~~~aggkIftfGSYRLGV 102 (562)
T KOG2245|consen 25 GPTEADIALTQELIKTLKNE--GLFESKEETQRREEVLGKLNQIVKEWVKKVSEQKGLPDGMIENAGGKIFTFGSYRLGV 102 (562)
T ss_pred CCcHHHHHHHHHHHHHHHhc--CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCChhhhhhcCceEEeccceeecc
Confidence 34444444444443333322 367789999999999999999999882 58999999999999
Q ss_pred CCCCCCceEEeecCCcc-hhHHHHHHHHHHHHHhhccccccceeeeEEE-EeeeeeEEEeecCeeEEeeeccCCc-----
Q 005149 93 YLPDGDIDLTAFGGLNV-EEALANDVCSVLEREDQNKAAEFVVKDAQLI-RAEVKLVKCLVQNIVVDISFNQLGG----- 165 (712)
Q Consensus 93 ~LP~SDIDL~V~~~~~~-~e~l~~~V~~iL~~~~~~~~a~f~V~~V~vI-~ArVPIIK~~~~gI~VDISfNn~~G----- 165 (712)
+.|++|||-.|++|..+ +++|+..+..+|+. ..+|+++..+ .|.||||||..+||+|||-|.++.-
T Consensus 103 hg~GADIDtLcV~Prhv~R~DFF~sf~~mL~~-------~~eVteL~~V~dAfVPiikfKf~GI~IDllfArL~l~~VP~ 175 (562)
T KOG2245|consen 103 HGPGADIDTLCVGPRHVSRSDFFTSFYDMLKE-------RPEVTELHAVEDAFVPIIKFKFDGIEIDLLFARLALPVVPE 175 (562)
T ss_pred cCCCCCcceeeeccccccHHHHHHHHHHHHhc-------CccccccccccccccceEEEEecCeeeeeeehhcccccCCC
Confidence 99999999999999765 56788888888865 2357888888 9999999999999999998876421
Q ss_pred ---chhhH-----------------HHHHHHHHhCCChhhHHHHHHHHHHHHHhhCccCCCCCCCcHHHHHHHH------
Q 005149 166 ---LSTLC-----------------FLEQVDRLIGKDHLFKRSIILIKAWCYYESRILGAHHGLISTYALETLV------ 219 (712)
Q Consensus 166 ---l~~s~-----------------fLe~Vd~~v~~~p~fr~LvlLIK~Wa~yesRil~a~~GgLSSYaL~lMV------ 219 (712)
+.... ..++|-+++.....|+-.++.||.||+ ++++++...|.+++-+|++||
T Consensus 176 dldl~ddslLknlDe~~vrSLNGcRVtdqiL~LVPn~~~F~~tLRaiKlWAK-rrgVYsN~~GF~GGV~wA~LVARiCQL 254 (562)
T KOG2245|consen 176 DLDLSDDSLLKNLDERCVRSLNGCRVTDQILKLVPNQENFRITLRAIKLWAK-RRGVYSNVMGFLGGVAWAMLVARICQL 254 (562)
T ss_pred cccccchHhhhcccHHHHHHhcCcCHHHHHHHhCCCHHHHHHHHHHHHHHHH-hcccccccccccchHHHHHHHHHHHcc
Confidence 11111 223456777778899999999999997 566788899999999999999
Q ss_pred ---------HHHHHhhhcCCCCCCceeeccCCcccCCCCcccccCCCCCCCcccccHHHHHHHHhhcCCCCCCCCCCCCC
Q 005149 220 ---------LYKFLDYFSKFDWDSYCISLNGPVRISSLPEVVVETPENSGGDLLLSSEFLKECVEQFSVPSRGFDTNSRS 290 (712)
Q Consensus 220 ---------L~~FL~yYskFD~~~~~ISi~GpVplssLp~~~~e~pe~~~g~lLL~~efLr~~~~~fs~~~rG~~~~~r~ 290 (712)
+-+||..|++|+|.+ ||-|..+.+ +.+-+ .-..|.++..
T Consensus 255 YPNA~~s~Lv~kfF~ifs~W~WP~-------PVlL~~ie~----------~~L~~----------~VWdPr~n~~----- 302 (562)
T KOG2245|consen 255 YPNASPSTLVAKFFRVFSQWNWPN-------PVLLKPIEE----------GNLNL----------PVWDPRVNPS----- 302 (562)
T ss_pred CCCcchHHHHHHHHHHHhhccCCC-------ceEeccccc----------cccCc----------cccCCCCCCC-----
Confidence 569999999999986 443322211 01100 0011211111
Q ss_pred CCCCCeEEcCCCCCCCCcCCCCCHHHHHHHHHHHHHHHHHHHhhhcC
Q 005149 291 FPPKHLNIVDPLKENNNLGRSVSKGNFYRIRSAFTYGARKLGHILSQ 337 (712)
Q Consensus 291 f~~~~L~IeDPfdpsNNLGRSVsk~nf~rIR~AF~~aa~~L~~il~~ 337 (712)
-.-+.|.|+.|..|+.|...+|++.++..|..+|.+|...+.+|+..
T Consensus 303 DryHlMPIITPAyP~~nsthNVS~ST~~Vi~~Ef~~g~~I~~~i~~~ 349 (562)
T KOG2245|consen 303 DRYHLMPIITPAYPQMNSTHNVSRSTLKVITEEFKRGLEICDDIELN 349 (562)
T ss_pred CcceecccccCCcccccccccccHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 11246999999999999999999999999999999999999998753
No 5
>KOG2277 consensus S-M checkpoint control protein CID1 and related nucleotidyltransferases [Cell cycle control, cell division, chromosome partitioning]
Probab=99.83 E-value=1e-19 Score=207.07 Aligned_cols=284 Identities=21% Similarity=0.256 Sum_probs=195.6
Q ss_pred HHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHH-hhcCCceE--EeeccccCCCCCCCCceEEeecCCc-ch-h-HHH
Q 005149 41 RAEEATQGIIAQVQPTVVSEERRKAVIDYVQRLIR-NYLGCEVF--PFGSVPLKTYLPDGDIDLTAFGGLN-VE-E-ALA 114 (712)
Q Consensus 41 ~le~ei~e~v~~I~PT~eE~~~R~~VI~~Vq~lI~-~~p~a~V~--~FGS~~tGL~LP~SDIDL~V~~~~~-~~-e-~l~ 114 (712)
.++..+.++++..++...+...|....+.++.++. ..|..... .|||..+++....+|+|+++..... .. . .-.
T Consensus 113 ~l~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~p~~~~~~~~~gs~~~~~~~~~~d~d~~~~~~~~~~~~~~~~~ 192 (596)
T KOG2277|consen 113 FLDPQLNELLESFKLPHSDVKTRKLILDKLRALASLLFPDSILSLYLFGSSDLGLGERSSDLDLCVDFTSSFLSFEKIKG 192 (596)
T ss_pred hhchhhhhhhhccCCCccccchHHHHHHHHHHHHHHhcCCCcceeeccCcccccccccccCcceeecccccccccchhhh
Confidence 37788888889999999999999988889998888 46765554 9999999999999999977776654 21 1 111
Q ss_pred HHHHHHHHHHhhccccccceeeeEEE-EeeeeeEEEeec--CeeEEeeeccCCcchhhHHHHHHHHHhCCChhhHHHHHH
Q 005149 115 NDVCSVLEREDQNKAAEFVVKDAQLI-RAEVKLVKCLVQ--NIVVDISFNQLGGLSTLCFLEQVDRLIGKDHLFKRSIIL 191 (712)
Q Consensus 115 ~~V~~iL~~~~~~~~a~f~V~~V~vI-~ArVPIIK~~~~--gI~VDISfNn~~Gl~~s~fLe~Vd~~v~~~p~fr~LvlL 191 (712)
..+..++.+......... +..++.| .|+|||||+.+. +++||+++++..++.|+.+++ .+...++++++|+++
T Consensus 193 ~~~~~l~~~~~~~~~~~~-~~~~~~i~~A~vPiik~~~~~~~~~~d~s~~n~~~~~nS~ll~---~~~~~d~r~~~L~~~ 268 (596)
T KOG2277|consen 193 LEILKLLAKCLASLLEEG-VREVQQILSARVPIIKFNDSGSGLECDLSVNNSDAILNSQLLR---NYSEIDPRVRPLVLL 268 (596)
T ss_pred HHHHHHHHHHHHhccccc-cceeeeeeecCCCEEEecCCCCCCceeeeeccchhhhhhHHHH---HhHhcCCCcchHhHH
Confidence 122223333222111111 4556655 999999999765 899999999999999999974 456678899999999
Q ss_pred HHHHHHHhhCccCCCCCCCc-HHHHHHHHHHHHHhhhcC--C----------CCCCceeeccCCcccCCCCcccccC---
Q 005149 192 IKAWCYYESRILGAHHGLIS-TYALETLVLYKFLDYFSK--F----------DWDSYCISLNGPVRISSLPEVVVET--- 255 (712)
Q Consensus 192 IK~Wa~yesRil~a~~GgLS-SYaL~lMVL~~FL~yYsk--F----------D~~~~~ISi~GpVplssLp~~~~e~--- 255 (712)
||+|++ ++.++++..|+++ +|+|++||+ +||+-++. . +.....+.. ..+..+ +.......
T Consensus 269 vk~wa~-~~~~~d~~~g~~~s~ysl~lmvi-~fLq~~~~~ilp~l~~l~~~~~~~~~~~~~-~~~~~~-~~~~~~~~~~~ 344 (596)
T KOG2277|consen 269 VKHWAK-EKGLNDAKPGGLNSSYSLTLMVI-HFLQTLSPPILPPLSKLLPESDSNDKPVVK-KKVLCS-FLRVFQRNPSN 344 (596)
T ss_pred HHHHHH-hccCCCCCCCceeccccHHHHHH-HHHHhcCCcCCCchhhhchhcccccccchh-hhhhhc-ccccccccccc
Confidence 999996 6667799999999 599999995 67776641 0 100000000 000000 00000000
Q ss_pred -CCC-CCCcccccHHHHHHHHhhcCCCCC------CCCCC--CCCCCCCCeEEcCCCCCCCCcCCCCCHHHHHHHHHHHH
Q 005149 256 -PEN-SGGDLLLSSEFLKECVEQFSVPSR------GFDTN--SRSFPPKHLNIVDPLKENNNLGRSVSKGNFYRIRSAFT 325 (712)
Q Consensus 256 -pe~-~~g~lLL~~efLr~~~~~fs~~~r------G~~~~--~r~f~~~~L~IeDPfdpsNNLGRSVsk~nf~rIR~AF~ 325 (712)
+.. ..+.+++ +|+.+|...|..+.. +.... ...+..+.++|+||++..+|++..++...+.+|+.+|+
T Consensus 345 ~~~~~~l~~l~~--~f~~yy~~~Fdf~~~~I~~r~~~~l~~~~~~~~~~~l~i~dp~~~~~n~~~~~~~~~~~~i~~~~~ 422 (596)
T KOG2277|consen 345 SQNTGSLGELLL--GFFSYYASLFDFRKNAISIRRGRALKRAKKIKSKKFLCIEDPFEVSHNADAGVTLKVLLLIQDEFQ 422 (596)
T ss_pred ccccchHHHHHH--HHHHHHhhhcccccceeeeeecccccccchhhhccceeeccccccccCccccchHHHHHHHHHHHH
Confidence 111 1123443 888888766654332 11111 12334678999999999999999999999999999999
Q ss_pred HHHHHHHhh
Q 005149 326 YGARKLGHI 334 (712)
Q Consensus 326 ~aa~~L~~i 334 (712)
..++.|...
T Consensus 423 ~~~~~~~~~ 431 (596)
T KOG2277|consen 423 ESRRVFKDV 431 (596)
T ss_pred HHHHHhhhh
Confidence 999998776
No 6
>COG5186 PAP1 Poly(A) polymerase [RNA processing and modification]
Probab=99.83 E-value=3e-19 Score=189.68 Aligned_cols=241 Identities=20% Similarity=0.344 Sum_probs=181.0
Q ss_pred cCCCHHHHHHHHHHHHHHHHHHHhhc-----------------CCceEEeeccccCCCCCCCCceEEeecCCcc-hhHHH
Q 005149 53 VQPTVVSEERRKAVIDYVQRLIRNYL-----------------GCEVFPFGSVPLKTYLPDGDIDLTAFGGLNV-EEALA 114 (712)
Q Consensus 53 I~PT~eE~~~R~~VI~~Vq~lI~~~p-----------------~a~V~~FGS~~tGL~LP~SDIDL~V~~~~~~-~e~l~ 114 (712)
.--++.|-+.|.+|++.+|.+++++. |.+++.||||.+|++-|+||||-.|+.|..+ +++|+
T Consensus 38 ~FE~~~E~~~Rv~VL~~Lq~~~~eFV~~vs~~K~m~dgmar~aGGKIFTyGSYRLGVhgpGsDIDtLvvVPkHVsR~dFF 117 (552)
T COG5186 38 FFEDDKEGQTRVRVLGKLQFMVREFVARVSRNKGMGDGMARPAGGKIFTYGSYRLGVHGPGSDIDTLVVVPKHVSRSDFF 117 (552)
T ss_pred CcCCchhhhhHHHHHHHHHHHHHHHHHHHHhhcCCCccccccCCceeeeecceeeeccCCCCCcceEEEecccccHHHHH
Confidence 45578889999999999999988651 4689999999999999999999999988765 57788
Q ss_pred HHHHHHHHHHhhccccccceeeeEEE-EeeeeeEEEeecCeeEEeeeccCC------cch-------------------h
Q 005149 115 NDVCSVLEREDQNKAAEFVVKDAQLI-RAEVKLVKCLVQNIVVDISFNQLG------GLS-------------------T 168 (712)
Q Consensus 115 ~~V~~iL~~~~~~~~a~f~V~~V~vI-~ArVPIIK~~~~gI~VDISfNn~~------Gl~-------------------~ 168 (712)
..+...|+.. ..+.+|.-| .|-|||||+...||.+|+-|..+. |+. .
T Consensus 118 t~f~~~Lrer-------~ei~eva~vpDAfVPIIK~KF~GIsIDLifARLs~P~Vp~~l~Lsd~nLLk~~dEkcilsLNG 190 (552)
T COG5186 118 THFYEELRER-------PEIEEVAKVPDAFVPIIKLKFQGISIDLIFARLSIPVVPDGLNLSDDNLLKSMDEKCILSLNG 190 (552)
T ss_pred HHHHHHhccC-------cchhhhccCCcccceeEEEEecCccceeeeeeccCCcCCCcccccchhhhhcchHHHHHhhcC
Confidence 8888777652 245677777 999999999999999999886542 211 1
Q ss_pred hHHHHHHHHHhCCChhhHHHHHHHHHHHHHhhCccCCCCCCCcHHHHHHHH---------------HHHHHhhhcCCCCC
Q 005149 169 LCFLEQVDRLIGKDHLFKRSIILIKAWCYYESRILGAHHGLISTYALETLV---------------LYKFLDYFSKFDWD 233 (712)
Q Consensus 169 s~fLe~Vd~~v~~~p~fr~LvlLIK~Wa~yesRil~a~~GgLSSYaL~lMV---------------L~~FL~yYskFD~~ 233 (712)
++..++|-.++..-..|+-.++.||+||+ ++-++..-.|..++-||.+|| +-+||+.++.|+|.
T Consensus 191 tRVTDeiL~LVP~~~vF~~ALRaIK~WAq-RRavYaN~~GfpGGVAwam~VARiCQLYPNA~S~vIv~kFF~ils~WnWP 269 (552)
T COG5186 191 TRVTDEILNLVPSVKVFHSALRAIKYWAQ-RRAVYANPYGFPGGVAWAMCVARICQLYPNASSFVIVCKFFEILSSWNWP 269 (552)
T ss_pred ceehHHHHHhCCchHHHHHHHHHHHHHHH-hhhhhccccCCcchHHHHHHHHHHHhhccCcchHhHHHHHHHHHHhcCCC
Confidence 12233455666666788999999999996 344677778999999999999 56999999999998
Q ss_pred CceeeccCCcccCCCCcccccCCCCCCCcccccHHHHHHHHhhcCCCCCCCCCCCCCCC---CCCeEEcCCCCCCCCcCC
Q 005149 234 SYCISLNGPVRISSLPEVVVETPENSGGDLLLSSEFLKECVEQFSVPSRGFDTNSRSFP---PKHLNIVDPLKENNNLGR 310 (712)
Q Consensus 234 ~~~ISi~GpVplssLp~~~~e~pe~~~g~lLL~~efLr~~~~~fs~~~rG~~~~~r~f~---~~~L~IeDPfdpsNNLGR 310 (712)
.-+| +.-+.+ .| +-+ |-| +.+.++ ...|.|+.|..|+.=...
T Consensus 270 qPvi-------LkPieD----gp------lqv----------------rvW--nPKvYpsDk~HRMPvITPAYPSMCATH 314 (552)
T COG5186 270 QPVI-------LKPIED----GP------LQV----------------RVW--NPKVYPSDKYHRMPVITPAYPSMCATH 314 (552)
T ss_pred CCeE-------eeeccC----CC------eeE----------------Eee--CCccCcccccccCccccCCchhhhhhc
Confidence 6333 211111 11 100 112 111222 356999999999976677
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHhhhc
Q 005149 311 SVSKGNFYRIRSAFTYGARKLGHILS 336 (712)
Q Consensus 311 SVsk~nf~rIR~AF~~aa~~L~~il~ 336 (712)
+++..+-..|-.+|-+|.+.+.+++.
T Consensus 315 Nit~STq~vIl~EfvRa~~I~~di~~ 340 (552)
T COG5186 315 NITNSTQHVILMEFVRAHKILSDIER 340 (552)
T ss_pred cccchhhhhHHHHHHHHHHhhhhHhh
Confidence 77777788999999999999999885
No 7
>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=99.82 E-value=3.8e-20 Score=168.08 Aligned_cols=105 Identities=33% Similarity=0.566 Sum_probs=89.2
Q ss_pred HHHHHHHHHHHHHHh-hcCCceEEeeccccCCCCCCCCceEEeecCCc--chhHHHHHHHHHHHHHhhccccccceeeeE
Q 005149 62 RRKAVIDYVQRLIRN-YLGCEVFPFGSVPLKTYLPDGDIDLTAFGGLN--VEEALANDVCSVLEREDQNKAAEFVVKDAQ 138 (712)
Q Consensus 62 ~R~~VI~~Vq~lI~~-~p~a~V~~FGS~~tGL~LP~SDIDL~V~~~~~--~~e~l~~~V~~iL~~~~~~~~a~f~V~~V~ 138 (712)
.|+++++.|+++++. ||+++|++|||+++|+++|+||||++|..+.. ....+...+.+.|++.. .+.++.
T Consensus 1 ~r~~i~~~l~~~i~~~~~~~~v~~fGS~~~g~~~~~SDiDl~i~~~~~~~~~~~~l~~l~~~l~~~~-------~~~~~~ 73 (114)
T cd05402 1 KREEVLDRLQELIKEWFPGAKLYPFGSYVTGLGLPGSDIDLCLLGPNHRVDREDFLRKLAKLLKKSG-------EVVEVE 73 (114)
T ss_pred CHHHHHHHHHHHHHHHCCCCEEEEecccccCCCCCCCCeeEEEEeCCCCccHHHHHHHHHHHHHhCC-------CceeeE
Confidence 489999999999996 79999999999999999999999999999874 33455566666665521 135677
Q ss_pred EE-EeeeeeEEEeec--CeeEEeeeccCCcchhhHHHH
Q 005149 139 LI-RAEVKLVKCLVQ--NIVVDISFNQLGGLSTLCFLE 173 (712)
Q Consensus 139 vI-~ArVPIIK~~~~--gI~VDISfNn~~Gl~~s~fLe 173 (712)
.| +||||||||++. |+.|||||++.+|+.|+.+++
T Consensus 74 ~i~~ArVPiik~~~~~~~i~~Dis~~~~~g~~~s~li~ 111 (114)
T cd05402 74 PIINARVPIIKFVDKPTGIEVDISFNNLNGIRNTKLLR 111 (114)
T ss_pred EeccCCCCEEEEEEcCCCeEEEEEcccchHHHHHHHHH
Confidence 77 999999999998 999999999999999999864
No 8
>PRK13300 tRNA CCA-pyrophosphorylase; Provisional
Probab=99.76 E-value=1e-16 Score=177.75 Aligned_cols=231 Identities=20% Similarity=0.246 Sum_probs=150.9
Q ss_pred HHHHHHHcCCCHHHHHHHHHHHHHHHHHHHhh----c-CCceEEeeccccCCCCC-CCCceEEeecCCcchh-HHHHHHH
Q 005149 46 TQGIIAQVQPTVVSEERRKAVIDYVQRLIRNY----L-GCEVFPFGSVPLKTYLP-DGDIDLTAFGGLNVEE-ALANDVC 118 (712)
Q Consensus 46 i~e~v~~I~PT~eE~~~R~~VI~~Vq~lI~~~----p-~a~V~~FGS~~tGL~LP-~SDIDL~V~~~~~~~e-~l~~~V~ 118 (712)
++++++.|+||++|.+.-..+++.|...|++. + +++|+.+||++.|++|+ ++||||+|+.+..... ++.+...
T Consensus 3 ~~evl~~i~Ps~eE~~~l~~~~~~l~~~L~~~~~~~~~~~~V~l~GS~ArgT~L~GdsDIDIFv~fp~~~~~e~L~~~gl 82 (447)
T PRK13300 3 LEEVLERIKPTEEEREKLKKVAEELIERLEEAIKELGLDAEVELVGSTARGTWLSGDRDIDIFVLFPKDTSREELEEKGL 82 (447)
T ss_pred HHHHHHhcCCCHHHHHHHHHHHHHHHHHHHHHHHhcCCceEEEEEeeecCCcccCCCCceeEEEEeCCCCCHHHHHHHHH
Confidence 57889999999999887777777777766643 2 39999999999999999 7999999999876543 3333333
Q ss_pred HHHHHHhhccccccceeeeEEEEeeeeeEEEeecCeeEEe--eeccCCc--ch-----hhHHHHHHHHHhCCChhhHHHH
Q 005149 119 SVLEREDQNKAAEFVVKDAQLIRAEVKLVKCLVQNIVVDI--SFNQLGG--LS-----TLCFLEQVDRLIGKDHLFKRSI 189 (712)
Q Consensus 119 ~iL~~~~~~~~a~f~V~~V~vI~ArVPIIK~~~~gI~VDI--SfNn~~G--l~-----~s~fLe~Vd~~v~~~p~fr~Lv 189 (712)
.+.+...+.. ..-..++ .|..|-|+...+|++||| +++...| +. +-.-.+.|..++.. .++..+
T Consensus 83 ~i~~~~~~~~---~~~~~~~--yaeHpyv~~~~~G~~VDiVPcy~v~~~~~~~saVDRtp~H~~fv~~rl~~--~~~d~V 155 (447)
T PRK13300 83 EIGKEVAKEL---LGDYEER--YAEHPYVTGEIDGFEVDIVPCYKVESGEEIISAVDRTPFHTKYVKERLKG--KLEDEV 155 (447)
T ss_pred HHHHHHHHhh---CCcceee--eccCceEEEEECCEEEEEEeeEEccCcCcccccccCchHHHHHHHHhhhh--hHHHHH
Confidence 3333321100 1111233 599999999999999998 4443333 22 22224455666543 378899
Q ss_pred HHHHHHHHHhhCccC--CCCCCCcHHHHHHHHHHHHHhhhcCCCCCCceeeccCC-cccCCCCcccccCCCCCCCccccc
Q 005149 190 ILIKAWCYYESRILG--AHHGLISTYALETLVLYKFLDYFSKFDWDSYCISLNGP-VRISSLPEVVVETPENSGGDLLLS 266 (712)
Q Consensus 190 lLIK~Wa~yesRil~--a~~GgLSSYaL~lMVL~~FL~yYskFD~~~~~ISi~Gp-VplssLp~~~~e~pe~~~g~lLL~ 266 (712)
+|+|+|++ ..+++| .+++|||||...+||++ |+.|.=--..++-+.| +. .+ ++.
T Consensus 156 RLlK~f~k-~~gvYGsE~k~~GFSGYl~ELLv~~-----yG~F~~~l~~a~~w~~~~~--------I~-~~~-------- 212 (447)
T PRK13300 156 RLLKQFLK-GIGVYGSELKTRGFSGYLCELLIIH-----YGSFENVLKAASKWKPPVK--------ID-LEK-------- 212 (447)
T ss_pred HHHHHHHH-hCCccchhhccCCccHHHHHHHHHH-----hCCHHHHHHHHHhCCCCce--------Ee-ccc--------
Confidence 99999997 466664 69999999999999974 4444200000000001 00 00 000
Q ss_pred HHHHHHHHhhcCCCCCCCCCCCCCCCCCCeEEcCCCCCCCCcCCCCCHHHHHHHHHHHH
Q 005149 267 SEFLKECVEQFSVPSRGFDTNSRSFPPKHLNIVDPLKENNNLGRSVSKGNFYRIRSAFT 325 (712)
Q Consensus 267 ~efLr~~~~~fs~~~rG~~~~~r~f~~~~L~IeDPfdpsNNLGRSVsk~nf~rIR~AF~ 325 (712)
+ +. ...| ..+|.|.||.||.||+|+++|..++.++..+-+
T Consensus 213 ----------~-----~~---~~~f-~~PlvViDPvDp~RNVAaa~S~~~~~~fv~aar 252 (447)
T PRK13300 213 ----------H-----GK---EYKF-DDPLVVIDPVDPNRNVAAALSLENLATFILAAR 252 (447)
T ss_pred ----------c-----Cc---cccC-CCCEEEeCCCCCcchHHHHcCHHHHHHHHHHHH
Confidence 0 00 0122 567999999999999999999888776655433
No 9
>TIGR03671 cca_archaeal CCA-adding enzyme.
Probab=99.75 E-value=1e-16 Score=175.69 Aligned_cols=232 Identities=19% Similarity=0.219 Sum_probs=153.1
Q ss_pred HHHHHHHcCCCHHHHHHHHHHHHHHHHHHHhh-----cCCceEEeeccccCCCCC-CCCceEEeecCCcchh-HHHHHHH
Q 005149 46 TQGIIAQVQPTVVSEERRKAVIDYVQRLIRNY-----LGCEVFPFGSVPLKTYLP-DGDIDLTAFGGLNVEE-ALANDVC 118 (712)
Q Consensus 46 i~e~v~~I~PT~eE~~~R~~VI~~Vq~lI~~~-----p~a~V~~FGS~~tGL~LP-~SDIDL~V~~~~~~~e-~l~~~V~ 118 (712)
++++++.+.||++|.+..+.+.+.|...|+++ +.++|..|||++-|++|+ +|||||+|+.+..... ++.....
T Consensus 2 ~~~vl~~i~Ps~eE~~~~~~~~~~l~~~l~~~~~e~~~~~~v~~~GS~ArgT~L~G~sDIDIfi~f~~~~~~e~l~~~gl 81 (408)
T TIGR03671 2 LEEVLERIKPTEEEREKLKKVADELIARLEEIIEELGVDAEVVLVGSYARGTWLKGDRDIDIFILFPKDTSREELEEYGL 81 (408)
T ss_pred hHHHhhhcCCCHHHHHHHHHHHHHHHHHHHHHHHhcCCcceEEEEeeEecCCccCCCCceeEEEEeCCCCCHHHHHHHHH
Confidence 46788999999999888777777766666642 469999999999999999 9999999999865533 3332222
Q ss_pred HHHHHHhhccccccceeeeEEEEeeeeeEEEeecCeeEEe--eeccCCc--ch-----hhHHHHHHHHHhCCChhhHHHH
Q 005149 119 SVLEREDQNKAAEFVVKDAQLIRAEVKLVKCLVQNIVVDI--SFNQLGG--LS-----TLCFLEQVDRLIGKDHLFKRSI 189 (712)
Q Consensus 119 ~iL~~~~~~~~a~f~V~~V~vI~ArVPIIK~~~~gI~VDI--SfNn~~G--l~-----~s~fLe~Vd~~v~~~p~fr~Lv 189 (712)
.+.+...+. . .....-.|..|-|+...+|++||| ++....| +. +-.-++.|..++.. .++..+
T Consensus 82 ~i~~~~~~~---~---~~~~~~yaeHpYv~~~~~G~~VDiVPcy~v~~g~~~~taVDRtp~H~~fv~~rl~~--~~~d~V 153 (408)
T TIGR03671 82 EIGHEVLKR---G---GNYEERYAEHPYVSGEIEGFEVDVVPCYKVESGEEIISAVDRTPFHTRYVLERLDG--KLRDDV 153 (408)
T ss_pred HHHHHHHhh---C---CCHhheeccCceEEEEEccEEEEEEeeEEccCcCeeeccccCchHHHHHHHHhhhh--hHHHHH
Confidence 333322110 0 122223899999999999999998 4544433 21 22224455566543 378899
Q ss_pred HHHHHHHHHhhCccC--CCCCCCcHHHHHHHHHHHHHhhhcCCCCCCceeec-cCCcccCCCCcccccCCCCCCCccccc
Q 005149 190 ILIKAWCYYESRILG--AHHGLISTYALETLVLYKFLDYFSKFDWDSYCISL-NGPVRISSLPEVVVETPENSGGDLLLS 266 (712)
Q Consensus 190 lLIK~Wa~yesRil~--a~~GgLSSYaL~lMVL~~FL~yYskFD~~~~~ISi-~GpVplssLp~~~~e~pe~~~g~lLL~ 266 (712)
+|+|+|++ ..+++| .+++|||||...|||++ |+.|.=--..++= ..++-
T Consensus 154 RLlK~f~k-~igvYGsE~~~~GFSGYl~ELLv~~-----yG~F~~~l~~a~~wk~~~~---------------------- 205 (408)
T TIGR03671 154 RLLKQFLK-GIGVYGSELKTRGFSGYLCELLVIH-----YGSFENVLKAASKWKPGVV---------------------- 205 (408)
T ss_pred HHHHHHHH-hCCccchhhccCCccHHHHHHHHHH-----hCCHHHHHHHHHhcCCCeE----------------------
Confidence 99999997 456664 68999999999999974 4433100000000 00000
Q ss_pred HHHHHHHHhhcCCCCCCCCCCCCCCCCCCeEEcCCCCCCCCcCCCCCHHHHHHHHHHHHHHH
Q 005149 267 SEFLKECVEQFSVPSRGFDTNSRSFPPKHLNIVDPLKENNNLGRSVSKGNFYRIRSAFTYGA 328 (712)
Q Consensus 267 ~efLr~~~~~fs~~~rG~~~~~r~f~~~~L~IeDPfdpsNNLGRSVsk~nf~rIR~AF~~aa 328 (712)
+... +. ....| ..+|.|.||.|+.||+|++++..++.+|..+-+.+.
T Consensus 206 ----------id~~--~~--~~~~f-~~PlvViDPvDp~RNVAaalS~~~~~~fv~aar~fl 252 (408)
T TIGR03671 206 ----------IDIE--EH--GTKKF-DDPLVVIDPVDPKRNVAAALSLENLARFILAARMFL 252 (408)
T ss_pred ----------EecC--cc--ccccC-CCCEEEeCCCCCcchHHHHcCHHHHHHHHHHHHHHH
Confidence 0000 00 01233 467999999999999999999988887776655444
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=99.75 E-value=3.6e-18 Score=177.54 Aligned_cols=204 Identities=18% Similarity=0.329 Sum_probs=122.5
Q ss_pred HHHHHHHHHHHH--cCCCHHHHHHHHHHHHHHHHHHHhhcCCceEEeeccccCCCCCCCCceEEeecCCcchhHHHHHHH
Q 005149 41 RAEEATQGIIAQ--VQPTVVSEERRKAVIDYVQRLIRNYLGCEVFPFGSVPLKTYLPDGDIDLTAFGGLNVEEALANDVC 118 (712)
Q Consensus 41 ~le~ei~e~v~~--I~PT~eE~~~R~~VI~~Vq~lI~~~p~a~V~~FGS~~tGL~LP~SDIDL~V~~~~~~~e~l~~~V~ 118 (712)
+...++.++++. +-||+||.++|++|++.|+++|++|... .+..-.-+||
T Consensus 21 ~~s~~L~~~l~~~~~~es~ee~~~R~~vl~~L~~iv~~wv~~----------~~~~~p~~l~------------------ 72 (254)
T PF04928_consen 21 KRSASLEEFLKDYGLFESEEEEQKREEVLRKLQQIVKEWVKQ----------ALPRVPEDLD------------------ 72 (254)
T ss_dssp HHHHHHHHHHHHCT-S--HHHHHHHHHHHHHHHHHHHHHHHH----------SSSSB-TT--------------------
T ss_pred HhHHHHHHHHHHcCCCCChHHHhHHHHHHHHHHHHHHHHHHh----------hhcCCCcccc------------------
Confidence 344556666644 4799999999999999999999988533 0000000111
Q ss_pred HHHHHHhhccccccceeeeEEEEeeeeeEEEeecCeeEEeeeccCCcchhhHHHHHHHHHhCCChhhHHHHHHHHHHHHH
Q 005149 119 SVLEREDQNKAAEFVVKDAQLIRAEVKLVKCLVQNIVVDISFNQLGGLSTLCFLEQVDRLIGKDHLFKRSIILIKAWCYY 198 (712)
Q Consensus 119 ~iL~~~~~~~~a~f~V~~V~vI~ArVPIIK~~~~gI~VDISfNn~~Gl~~s~fLe~Vd~~v~~~p~fr~LvlLIK~Wa~y 198 (712)
+..+.+-.|+.......+...+..++|.+.+.....||.++++||+||+
T Consensus 73 ------------------------------~~~~~~l~~ld~~s~~sLnG~Rv~~~il~~Vp~~~~Fr~~lR~IK~WAk- 121 (254)
T PF04928_consen 73 ------------------------------LLDDDPLRNLDEASVRSLNGVRVTDYILRLVPNQETFRTALRFIKLWAK- 121 (254)
T ss_dssp ------------------------------TT-GGGGTT--HHHHHHHHHHHHHHHHHCTSS-HHHHHHHHHHHHHHHH-
T ss_pred ------------------------------cCCchhhhCCCHhhccCcccccHHHHHHHHCCCHHHHHHHHHHHHHHHH-
Confidence 1111111111111111222233445567888888899999999999997
Q ss_pred hhCccCCCCCCCcHHHHHHHH---------------HHHHHhhhcCCCCCCceeeccCCcccCCCCcccccCCCCCCCcc
Q 005149 199 ESRILGAHHGLISTYALETLV---------------LYKFLDYFSKFDWDSYCISLNGPVRISSLPEVVVETPENSGGDL 263 (712)
Q Consensus 199 esRil~a~~GgLSSYaL~lMV---------------L~~FL~yYskFD~~~~~ISi~GpVplssLp~~~~e~pe~~~g~l 263 (712)
+++|+++..|.|++.+|++|| |.+||.+|++|||.+ ||.+..+.+ . .+
T Consensus 122 ~RGIYsn~~GylGGI~waILvArvcql~Pn~~~~~ll~~FF~~ys~W~W~~-------PV~l~~~~~--------~--~~ 184 (254)
T PF04928_consen 122 RRGIYSNVFGYLGGIHWAILVARVCQLYPNASPSTLLSRFFQIYSQWDWPN-------PVVLDPIED--------G--PL 184 (254)
T ss_dssp HTT-B-CCCTSB-HHHHHHHHHHHHHHSTT--HHHHHHHHHHHHHCS-TTS--------EESS---------------SS
T ss_pred HccccchhhccchHHHHHHHHHHHHHHCccccccchHHHHHHHhcCCCCCC-------ceeeccccc--------C--cc
Confidence 667789999999999999999 679999999999987 332211100 0 00
Q ss_pred cccHHHHHHHHhhcCCCCCCCCCC-CCCCCCCCeEEcCCCCCCCCcCCCCCHHHHHHHHHHHHHHHHHHHhhhc
Q 005149 264 LLSSEFLKECVEQFSVPSRGFDTN-SRSFPPKHLNIVDPLKENNNLGRSVSKGNFYRIRSAFTYGARKLGHILS 336 (712)
Q Consensus 264 LL~~efLr~~~~~fs~~~rG~~~~-~r~f~~~~L~IeDPfdpsNNLGRSVsk~nf~rIR~AF~~aa~~L~~il~ 336 (712)
- .+.|... ........|+|+.|..|..|.+++|++.+++.|+++|++|++.|.+++.
T Consensus 185 ~----------------~~~w~p~~~~~~~~~~MpIiTP~yP~~Nst~nVt~st~~~i~~Ef~ra~~i~~~~~~ 242 (254)
T PF04928_consen 185 G----------------FKVWNPRLYPRDRRHLMPIITPAYPSMNSTYNVTRSTLRIIREEFQRAHEILSEILK 242 (254)
T ss_dssp S----------------CGS--TTT-HHHHC-SS-EE-SSSS--BTTTT--HHHHHHHHHHHHHHHHHHHHHHT
T ss_pred c----------------ccCCCCCCCCCCcccceeEccCCCCccccccccCHHHHHHHHHHHHHHHHHHHHHHc
Confidence 0 0011111 0112356799999999999999999999999999999999999999873
No 11
>COG1746 CCA1 tRNA nucleotidyltransferase (CCA-adding enzyme) [Translation, ribosomal structure and biogenesis]
Probab=99.68 E-value=4.6e-15 Score=161.57 Aligned_cols=224 Identities=22% Similarity=0.297 Sum_probs=151.8
Q ss_pred HHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHh-----hcCCceEEeeccccCCCCC-CCCceEEeecCCcch-hHH
Q 005149 41 RAEEATQGIIAQVQPTVVSEERRKAVIDYVQRLIRN-----YLGCEVFPFGSVPLKTYLP-DGDIDLTAFGGLNVE-EAL 113 (712)
Q Consensus 41 ~le~ei~e~v~~I~PT~eE~~~R~~VI~~Vq~lI~~-----~p~a~V~~FGS~~tGL~LP-~SDIDL~V~~~~~~~-e~l 113 (712)
.+++-++++++.+.||++|.++-+.+.+.|+..+.. ..++.|...||++-|+||+ +.|||+.|..|.... +.+
T Consensus 2 ~~~~~l~evl~~i~P~~eE~~~~~~~~e~l~~~~~~~~~e~~~~aev~lVGS~AkgTwL~gd~DIDvFi~Fp~d~~~eel 81 (443)
T COG1746 2 TLEEVLEEVLKRIKPTEEERKKLKEVAEELRERINEIIEELGIDAEVVLVGSYAKGTWLRGDHDIDVFIAFPKDTSEEEL 81 (443)
T ss_pred chHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHhcCCcceEEEEeecccCcccCCCcceeEEEECCCCCCHHHH
Confidence 356778899999999999988877766666655542 4689999999999999999 899999999997653 333
Q ss_pred HHHHHHHHHHHhhccccccceeeeEEE-EeeeeeEEEeecCeeEEe--eeccCCc------ch-hhHHHHHHHHHhCCCh
Q 005149 114 ANDVCSVLEREDQNKAAEFVVKDAQLI-RAEVKLVKCLVQNIVVDI--SFNQLGG------LS-TLCFLEQVDRLIGKDH 183 (712)
Q Consensus 114 ~~~V~~iL~~~~~~~~a~f~V~~V~vI-~ArVPIIK~~~~gI~VDI--SfNn~~G------l~-~s~fLe~Vd~~v~~~p 183 (712)
-+.-..+.+....+. +- -+ .|..|.|....+|++||| |++-..| +. |..-.++|...+....
T Consensus 82 ~~~GL~ig~~~l~~~-------~~-~~~YAeHPYV~g~v~G~eVDvVPCy~v~~~~~~~sAVDRTplHt~yv~e~L~~~~ 153 (443)
T COG1746 82 EEKGLEIGREVLKRG-------NY-EERYAEHPYVTGEVDGYEVDVVPCYKVEDGEKIISAVDRTPLHTRYVEEHLKGRQ 153 (443)
T ss_pred HHHHHHHHHHHhcCC-------ch-hhhhccCCeeEEEEccEEEEEEecccccCcccccccccCcchhHHHHHHHhcccc
Confidence 222222332222111 11 24 899999999999999998 4443322 21 1112334555554332
Q ss_pred hhHHHHHHHHHHHHHhhCccC--CCCCCCcHHHHHHHHHHHHHhhhcCCC--------CCCceeeccCCcccCCCCcccc
Q 005149 184 LFKRSIILIKAWCYYESRILG--AHHGLISTYALETLVLYKFLDYFSKFD--------WDSYCISLNGPVRISSLPEVVV 253 (712)
Q Consensus 184 ~fr~LvlLIK~Wa~yesRil~--a~~GgLSSYaL~lMVL~~FL~yYskFD--------~~~~~ISi~GpVplssLp~~~~ 253 (712)
+.=++|+|+|+| .-+++| .+++|||+|.-.+||+ +|+.|. |...
T Consensus 154 --~deVrLLK~FlK-~iGvYGaE~rt~GFSGYL~ELLII-----~yGsFe~vl~~a~~wrp~------------------ 207 (443)
T COG1746 154 --KDEVRLLKQFLK-GIGVYGAELRTQGFSGYLCELLII-----HYGSFENVLKAASRWRPG------------------ 207 (443)
T ss_pred --hhHHHHHHHHHh-ccCccceeeeeccchHHHHHHHHh-----hhccHHHHHHHHhccCCC------------------
Confidence 356889999996 555665 6899999999999997 344442 3221
Q ss_pred cCCCCCCCcccccHHHHHHHHhhcCCCCCCCCCCCCCCCCCCeEEcCCCCCCCCcCCCCCHHHHHHHHHH
Q 005149 254 ETPENSGGDLLLSSEFLKECVEQFSVPSRGFDTNSRSFPPKHLNIVDPLKENNNLGRSVSKGNFYRIRSA 323 (712)
Q Consensus 254 e~pe~~~g~lLL~~efLr~~~~~fs~~~rG~~~~~r~f~~~~L~IeDPfdpsNNLGRSVsk~nf~rIR~A 323 (712)
..++.+ ++ +...|...+|.|.||.||++|+|.+||..++.++..|
T Consensus 208 ---------~~ID~~--------------~~--~~e~f~d~PliVvDPVDP~RNVAAalSl~~la~f~~a 252 (443)
T COG1746 208 ---------KIIDLE--------------GH--KRERFEDEPLIVVDPVDPKRNVAAALSLENLARFVHA 252 (443)
T ss_pred ---------eEEecc--------------ch--hhhccCCCCeEecCCCCCccchhhhcCHHHHHHHHHH
Confidence 001000 00 1234555689999999999999999998888765543
No 12
>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=98.23 E-value=3.4e-07 Score=74.83 Aligned_cols=23 Identities=35% Similarity=0.829 Sum_probs=19.6
Q ss_pred HHHHHhhhc-CCCCCCceeeccCC
Q 005149 220 LYKFLDYFS-KFDWDSYCISLNGP 242 (712)
Q Consensus 220 L~~FL~yYs-kFD~~~~~ISi~Gp 242 (712)
|+.||+||+ +|||++++||++.+
T Consensus 6 l~~Ff~~Y~~~Fd~~~~~Isi~~g 29 (60)
T PF03828_consen 6 LLGFFEYYGRKFDYENNVISIRNG 29 (60)
T ss_dssp HHHHHHHHHHTS-TTTEEEESSSS
T ss_pred HHHHHHHhCCcCCCCceEEEecCC
Confidence 469999999 89999999999843
No 13
>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=97.86 E-value=3.3e-05 Score=71.95 Aligned_cols=90 Identities=24% Similarity=0.372 Sum_probs=52.7
Q ss_pred HHHHHHHHHHhhCccC--CCCCCCcHHHHHHHHHH-----HHHhhhcCCCCCCceeeccCCcccCCCCcccccCCCCCCC
Q 005149 189 IILIKAWCYYESRILG--AHHGLISTYALETLVLY-----KFLDYFSKFDWDSYCISLNGPVRISSLPEVVVETPENSGG 261 (712)
Q Consensus 189 vlLIK~Wa~yesRil~--a~~GgLSSYaL~lMVL~-----~FL~yYskFD~~~~~ISi~GpVplssLp~~~~e~pe~~~g 261 (712)
++|+|+|++ ..+++| .+++|+|+|.-++||+. ..++.-++|.- ...|-+. ..
T Consensus 3 VrLLK~FlK-~igvYGse~~~~GFSGYL~ELLii~yGsF~~~l~~a~~W~~-~~~Id~~-----------------~~-- 61 (114)
T PF09249_consen 3 VRLLKQFLK-GIGVYGSELKTRGFSGYLCELLIIHYGSFENVLEAAAKWKP-PVVIDLE-----------------DH-- 61 (114)
T ss_dssp HHHHHHHHH-HTT-B-SSTTT-SB-HHHHHHHHHHHSSHHHHHHHHTT--T-TEEEETT------------------T--
T ss_pred hHHHHHHHh-cCCCcchhhhcCcchHHHHHHHHHHHCCHHHHHHHHHhcCC-CeEEccC-----------------cc--
Confidence 678999997 667774 68999999999999962 33443443321 1111111 00
Q ss_pred cccccHHHHHHHHhhcCCCCCCCCCCCCCCCCCCeEEcCCCCCCCCcCCCCCHHHHHHHHHH
Q 005149 262 DLLLSSEFLKECVEQFSVPSRGFDTNSRSFPPKHLNIVDPLKENNNLGRSVSKGNFYRIRSA 323 (712)
Q Consensus 262 ~lLL~~efLr~~~~~fs~~~rG~~~~~r~f~~~~L~IeDPfdpsNNLGRSVsk~nf~rIR~A 323 (712)
+ ...+.| ...|.|+||.||.+|+|.+||..++.++..+
T Consensus 62 ---------------------~--~~~~~f-~~PlvviDPvDp~RNVAAalS~~~~~~fv~~ 99 (114)
T PF09249_consen 62 ---------------------G--EPSKKF-DDPLVVIDPVDPNRNVAAALSLENLAEFVHA 99 (114)
T ss_dssp ---------------------T--E--EEE--SS-EEEETTEEEEETTTTS-HHHHHHHHHH
T ss_pred ---------------------c--hhhhhc-CCCeEEcCCCCCCchHhHhcCHHHHHHHHHH
Confidence 0 001122 4669999999999999999998887765443
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=97.79 E-value=1.8e-05 Score=68.83 Aligned_cols=43 Identities=28% Similarity=0.383 Sum_probs=36.8
Q ss_pred HHHHHHHHH-hhcCCceEEeeccccCCCCCCCCceEEeecCCcc
Q 005149 67 IDYVQRLIR-NYLGCEVFPFGSVPLKTYLPDGDIDLTAFGGLNV 109 (712)
Q Consensus 67 I~~Vq~lI~-~~p~a~V~~FGS~~tGL~LP~SDIDL~V~~~~~~ 109 (712)
|+.+.+.++ .++.+.|.+|||+++|.+.|+||||++|+.+...
T Consensus 1 i~~i~~~l~~~~~~~~v~lfGS~a~g~~~~~SDIDl~i~~~~~~ 44 (93)
T PF01909_consen 1 IEEIKEILKELFGVAEVYLFGSYARGDATPDSDIDLLIILDEPE 44 (93)
T ss_dssp HHHHHHHHHHHHTTEEEEEEHHHHHTSSCTTSCEEEEEEESSTS
T ss_pred CHHHHHHHHHHCCCCEEEEECCcccCcCCCCCCEEEEEEeCCcc
Confidence 456677777 4568899999999999999999999999998764
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=97.67 E-value=7.3e-05 Score=59.67 Aligned_cols=40 Identities=23% Similarity=0.430 Sum_probs=34.1
Q ss_pred HHHHHHHHHHHh-hcCCceEEeeccccCCCCCCCCceEEee
Q 005149 65 AVIDYVQRLIRN-YLGCEVFPFGSVPLKTYLPDGDIDLTAF 104 (712)
Q Consensus 65 ~VI~~Vq~lI~~-~p~a~V~~FGS~~tGL~LP~SDIDL~V~ 104 (712)
++++.+++.+++ ....++..|||++.|.+.+.||||+++.
T Consensus 2 ~~l~~i~~~l~~~~~~~~v~lfGS~arg~~~~~SDIDi~v~ 42 (49)
T cd05397 2 ELLDIIKERLKKLVPGYEIVVYGSLVRGLLKKSSDIDLACV 42 (49)
T ss_pred HHHHHHHHHHHhhcCCcEEEEECCcCCCCCCCCCCEEEEEE
Confidence 456777777774 4678999999999999999999999987
No 16
>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=97.59 E-value=0.00034 Score=66.10 Aligned_cols=93 Identities=23% Similarity=0.284 Sum_probs=55.8
Q ss_pred HHHHHHHHHHHHHHHhh--cCCceEEeeccccCCCCC-CCCceEEeecCCcch------hHHHHHHHHHHHHHhhccccc
Q 005149 61 ERRKAVIDYVQRLIRNY--LGCEVFPFGSVPLKTYLP-DGDIDLTAFGGLNVE------EALANDVCSVLEREDQNKAAE 131 (712)
Q Consensus 61 ~~R~~VI~~Vq~lI~~~--p~a~V~~FGS~~tGL~LP-~SDIDL~V~~~~~~~------e~l~~~V~~iL~~~~~~~~a~ 131 (712)
.....|.+.|++-.... +...+++|||++.|++++ .||||++|..+.... ..+...|...|++....
T Consensus 7 ~~~~~i~~~L~~~~~~~~~~~~~~~~~GS~a~~T~i~~~sDiD~~v~~~~~~~~~~~~~~~~~~~l~~~L~~~~~~---- 82 (143)
T cd05400 7 ERYREIREALKESLSELAGRVAEVFLQGSYARGTALRGDSDIDLVVVLPDDTSFAEYGPAELLDELGEALKEYYGA---- 82 (143)
T ss_pred HHHHHHHHHHHHhcccccccccEEEEEcceeCCCCCCCCCceeEEEEEcCcccccccCHHHHHHHHHHHHHHhcCc----
Confidence 33444555555544321 357999999999999998 899999999875432 12334444444442210
Q ss_pred cceeeeEEEEeeeeeEEEeec--CeeEEe--eecc
Q 005149 132 FVVKDAQLIRAEVKLVKCLVQ--NIVVDI--SFNQ 162 (712)
Q Consensus 132 f~V~~V~vI~ArVPIIK~~~~--gI~VDI--SfNn 162 (712)
-..+..+-|.|.+... ++.+|| ++..
T Consensus 83 -----~~~~~~~~~~v~v~~~~~~~~vDvvP~~~~ 112 (143)
T cd05400 83 -----NEEVKAQHRSVTVKFKGQGFHVDVVPAFEA 112 (143)
T ss_pred -----ccccccCceEEEEEEcCCCeEEEEEEEeec
Confidence 1123334445555544 899999 5543
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=97.40 E-value=0.00046 Score=59.35 Aligned_cols=44 Identities=27% Similarity=0.403 Sum_probs=35.8
Q ss_pred HHHHHHHHHHhhc--CCceEEeeccccCCCCCCCCceEEeecCCcc
Q 005149 66 VIDYVQRLIRNYL--GCEVFPFGSVPLKTYLPDGDIDLTAFGGLNV 109 (712)
Q Consensus 66 VI~~Vq~lI~~~p--~a~V~~FGS~~tGL~LP~SDIDL~V~~~~~~ 109 (712)
.++.+.++++..+ -..|+.|||++.|-+-++|||||+|+.....
T Consensus 3 ~~~~i~~~l~~~~~~i~~i~LfGS~arg~~~~~SDiDl~vi~~~~~ 48 (93)
T cd05403 3 ILEEILEILRELLGGVEKVYLFGSYARGDARPDSDIDLLVIFDDPL 48 (93)
T ss_pred hHHHHHHHHHHHhCCccEEEEEeeeecCCCCCCCCeeEEEEeCCCC
Confidence 4556666666554 5789999999999999999999999987654
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=97.38 E-value=0.0013 Score=66.64 Aligned_cols=59 Identities=27% Similarity=0.415 Sum_probs=38.5
Q ss_pred CCcchhhHHHHHHHHHhCCCh-hhHHHHHHHHHHHHHhhCcc-CCCCCCCcHHHHHHHHHHH
Q 005149 163 LGGLSTLCFLEQVDRLIGKDH-LFKRSIILIKAWCYYESRIL-GAHHGLISTYALETLVLYK 222 (712)
Q Consensus 163 ~~Gl~~s~fLe~Vd~~v~~~p-~fr~LvlLIK~Wa~yesRil-~a~~GgLSSYaL~lMVL~~ 222 (712)
..|-.++||.+.=..++...| .+|.||+|||+|.+ +..-. ....+..++|+|.||++|.
T Consensus 21 ~~gefS~cftelQ~~Fvk~rP~klK~LIrLVKhWy~-~~~~~~~~~~~lPpsYaLELLtIyA 81 (190)
T PF10421_consen 21 KPGEFSACFTELQRNFVKHRPTKLKNLIRLVKHWYQ-QCKKKKCGGGSLPPSYALELLTIYA 81 (190)
T ss_dssp -TTTTGGGGHHHHHHHHHTS-HHHHHHHHHHHHHHH-HHHCC--HTT-S--HHHHHHHHHHH
T ss_pred CCccchHHHHHHHHHHHHhCCHHHHHHHHHHHHHHH-HHHhhccCCCCCcHHHHHHHHHHHH
Confidence 345667788776566776666 69999999999975 22222 2445567799999999764
No 19
>smart00572 DZF domain in DSRM or ZnF_C2H2 domain containing proteins.
Probab=97.26 E-value=0.0089 Score=62.85 Aligned_cols=197 Identities=15% Similarity=0.167 Sum_probs=105.0
Q ss_pred ceEEeeccccCCCCCC-CCceEEeecCCcchhHHHHHHHHHHHHHhhccccccceeeeEEEEeeeeeEEEeec----Cee
Q 005149 81 EVFPFGSVPLKTYLPD-GDIDLTAFGGLNVEEALANDVCSVLEREDQNKAAEFVVKDAQLIRAEVKLVKCLVQ----NIV 155 (712)
Q Consensus 81 ~V~~FGS~~tGL~LP~-SDIDL~V~~~~~~~e~l~~~V~~iL~~~~~~~~a~f~V~~V~vI~ArVPIIK~~~~----gI~ 155 (712)
.|.-.||++.||.+.+ -+.||++++...-..++.+.|...|....+....+ . ..+.+..+.+|.+++... .+.
T Consensus 4 gV~rVG~~aKG~ll~Gd~~~~lVv~c~~~PT~~ll~~v~~~l~e~l~~~~~~-e-~~~~~~~~~~~~~~~~i~ltSp~~r 81 (246)
T smart00572 4 GVMRVGSFAKGTLLKGDNVAELVLLCKEKPTSELVARLARKLPEQLKAVTED-E-ALIIVTSTKEPTMEVGILITSPLAR 81 (246)
T ss_pred ceEEeeeeccCceecCCCceeEEEEecCCCcHHHHHHHHHHHHHHHhhcCcc-c-ceeeeeccCCCceeEEEEEeccccc
Confidence 5778899999999995 78999999876433444445544333322211100 0 112222666677766642 222
Q ss_pred EEeeec----------------------cCCcchhhHHHHHHHHHhCCChhhHHHHHHHHHHHHHhhCccCCCCCCCcHH
Q 005149 156 VDISFN----------------------QLGGLSTLCFLEQVDRLIGKDHLFKRSIILIKAWCYYESRILGAHHGLISTY 213 (712)
Q Consensus 156 VDISfN----------------------n~~Gl~~s~fLe~Vd~~v~~~p~fr~LvlLIK~Wa~yesRil~a~~GgLSSY 213 (712)
+++... .+..++.++|.+ +...-...++.+++++|-|+. |. +..+-|++|
T Consensus 82 ~~~~~~~~~~~~~~~~p~~~ld~~~cl~aLAalRhakWFq---~~a~~l~s~~iviRilKd~~~---R~--~~~~pL~~w 153 (246)
T smart00572 82 VELLITTVPENLRKLDPEDHLDRKKCLSALASLRHAKWFQ---ARASGLQSCVIVIRVLRDLCN---RV--PTWQPLSGW 153 (246)
T ss_pred ccccccccCcccccCCccccCCHHHHHHHHHHHHHhHHHH---HhccCCcchhhHHHHHHHHHH---hc--ccccccccc
Confidence 222211 111222222322 222222357889999999984 32 222349999
Q ss_pred HHHHHHHHHHHhhhcCCCCCCceeecc-CCcccCCCCcccccCCCCCCCcccccHHHHHHHHhhcCCCCCCCCCCCCCCC
Q 005149 214 ALETLVLYKFLDYFSKFDWDSYCISLN-GPVRISSLPEVVVETPENSGGDLLLSSEFLKECVEQFSVPSRGFDTNSRSFP 292 (712)
Q Consensus 214 aL~lMVL~~FL~yYskFD~~~~~ISi~-GpVplssLp~~~~e~pe~~~g~lLL~~efLr~~~~~fs~~~rG~~~~~r~f~ 292 (712)
.+.+++-+ +|.-. +|.. + ++.| +.||...+.-+ -|
T Consensus 154 ~iELl~~~--------------~i~~~~~~l~---~------------~~a~--RR~fe~lAsG~------------l~- 189 (246)
T smart00572 154 PLELLVEK--------------AIGSARQPLG---L------------GDAF--RRVFECLASGI------------LL- 189 (246)
T ss_pred cHHHHHHH--------------HhccCCCCCC---H------------HHHH--HHHHHHHHhcc------------Cc-
Confidence 99999832 11111 1110 0 0111 23444332211 12
Q ss_pred CCCeEEcCCCCC-CCCcCCCCCHHHHHHHHHHHHHHHHHH
Q 005149 293 PKHLNIVDPLKE-NNNLGRSVSKGNFYRIRSAFTYGARKL 331 (712)
Q Consensus 293 ~~~L~IeDPfdp-sNNLGRSVsk~nf~rIR~AF~~aa~~L 331 (712)
+....|.||.+. .+|+.+..+...-..|-.+-+.+.+.+
T Consensus 190 p~~~gI~DPce~~~~nv~~~lT~qqrd~It~sAQ~alRl~ 229 (246)
T smart00572 190 PGSPGLTDPCEKDNTDALTALTLQQREDVTASAQTALRLL 229 (246)
T ss_pred CCCCCCcCCCCCCcccHHHhcCHHHHHHHHHHHHHHHHHH
Confidence 234789999997 899999988766666666555555544
No 20
>COG1669 Predicted nucleotidyltransferases [General function prediction only]
Probab=96.41 E-value=0.0058 Score=55.90 Aligned_cols=46 Identities=24% Similarity=0.266 Sum_probs=38.8
Q ss_pred HHHHHHHHHHHHHhhcC-CceEEeeccccCCCCCCCCceEEeecCCc
Q 005149 63 RKAVIDYVQRLIRNYLG-CEVFPFGSVPLKTYLPDGDIDLTAFGGLN 108 (712)
Q Consensus 63 R~~VI~~Vq~lI~~~p~-a~V~~FGS~~tGL~LP~SDIDL~V~~~~~ 108 (712)
.+.++..+...+++|.+ +++-.|||++-|-.-|+|||||.|-+...
T Consensus 7 ~~~~lr~~~~~l~~k~gv~~~~vFGS~aRgE~~~~SDIDILVef~~~ 53 (97)
T COG1669 7 LKKILRKIKPELKEKYGVKRVAVFGSYARGEQKPDSDIDILVEFEPG 53 (97)
T ss_pred HHHHHHHHHHHHHHHhCCceEEEeeeeecCCCCCCCCceeEEeecCC
Confidence 44557777888887776 68999999999999999999999998654
No 21
>COG1708 Predicted nucleotidyltransferases [General function prediction only]
Probab=95.99 E-value=0.011 Score=53.48 Aligned_cols=28 Identities=25% Similarity=0.419 Sum_probs=26.5
Q ss_pred cCCceEEeeccccCCCCCCCCceEEeec
Q 005149 78 LGCEVFPFGSVPLKTYLPDGDIDLTAFG 105 (712)
Q Consensus 78 p~a~V~~FGS~~tGL~LP~SDIDL~V~~ 105 (712)
..+.|+.|||++.|-+.+.||||++|+.
T Consensus 25 ~~~~v~LfGS~arG~~~~~SDiDv~vv~ 52 (128)
T COG1708 25 GDLLIYLFGSYARGDFVKESDIDLLVVS 52 (128)
T ss_pred CCeEEEEEccCcccccccCCCeeEEEEc
Confidence 4689999999999999999999999997
No 22
>PRK13746 aminoglycoside resistance protein; Provisional
Probab=95.91 E-value=0.022 Score=60.56 Aligned_cols=53 Identities=19% Similarity=0.227 Sum_probs=38.1
Q ss_pred HHHHHHHHHhhcCC---ceEEeeccccCCCCCCCCceEEeecCCcchhHHHHHHHH
Q 005149 67 IDYVQRLIRNYLGC---EVFPFGSVPLKTYLPDGDIDLTAFGGLNVEEALANDVCS 119 (712)
Q Consensus 67 I~~Vq~lI~~~p~a---~V~~FGS~~tGL~LP~SDIDL~V~~~~~~~e~l~~~V~~ 119 (712)
+..++++++..++- .|+.|||++.|-+-|.||||+.|+...........++..
T Consensus 13 l~~~~~~l~~~l~~~l~~vyLfGS~~~G~~~p~SDIDllvvv~~~l~~~~~~~L~~ 68 (262)
T PRK13746 13 LSEACAVIERHLEPTLLAIHLYGSAVDGGLKPHSDIDLLVTVAVPLDETTRRALMN 68 (262)
T ss_pred HHHHHHHHHHhCcccEEEEEEECCcccCCCCCCCceeEEEEeCCCCCHHHHHHHHH
Confidence 34455666655553 589999999999999999999999887654333333433
No 23
>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=95.04 E-value=0.16 Score=63.08 Aligned_cols=119 Identities=18% Similarity=0.264 Sum_probs=78.1
Q ss_pred HHHHHhCCChhhHHHHHHHHHHHHHhhCccCCCC--CCCcHHHHHHHHHH------------------------HHHhhh
Q 005149 174 QVDRLIGKDHLFKRSIILIKAWCYYESRILGAHH--GLISTYALETLVLY------------------------KFLDYF 227 (712)
Q Consensus 174 ~Vd~~v~~~p~fr~LvlLIK~Wa~yesRil~a~~--GgLSSYaL~lMVL~------------------------~FL~yY 227 (712)
.+.......|.|+..++|+|.|+. +|.++... ||+++|-|.+|+.| .+++|-
T Consensus 155 ~l~~~~~~~p~f~dA~iLlkvWl~--QRg~~~~~~~~Gf~~f~~s~lla~Ll~~g~~~~~~~l~~~mSsyQlFr~~l~fL 232 (972)
T PF03813_consen 155 YLHEASKSSPAFRDACILLKVWLR--QRGFGSGISQGGFGGFEWSMLLAYLLQGGGRNGKKKLSKSMSSYQLFRAVLQFL 232 (972)
T ss_pred HHHHHHhcCHHHHHHHHHHHHHHh--cCCCCcccCCCCcchHHHHHHHHHHHcCCCccCCcccCCCCCHHHHHHHHHHHH
Confidence 455666788999999999999995 78776555 99999988887722 344444
Q ss_pred cCCCCCCceeeccCCcccCCCCcccccCCCCCCCcccccHHHHHHHHhhcCCCCCCCCCCCCCCCCCCeEEcCCCCCCCC
Q 005149 228 SKFDWDSYCISLNGPVRISSLPEVVVETPENSGGDLLLSSEFLKECVEQFSVPSRGFDTNSRSFPPKHLNIVDPLKENNN 307 (712)
Q Consensus 228 skFD~~~~~ISi~GpVplssLp~~~~e~pe~~~g~lLL~~efLr~~~~~fs~~~rG~~~~~r~f~~~~L~IeDPfdpsNN 307 (712)
++-||.+..+.+..... . .+.+..+ .......+.||-.. .|
T Consensus 233 A~~d~~~~~l~~~~~~~---------------~------~~~~~~~-----------------~~~~~~vf~D~sg~-~N 273 (972)
T PF03813_consen 233 ATTDLSKKPLFFKSSSD---------------S------TESLEEF-----------------HSAFDPVFVDPSGG-LN 273 (972)
T ss_pred hccccccCceEEecCCC---------------c------cchhhhh-----------------hccCCeEEEeCCCC-EE
Confidence 55555554444331100 0 0000000 01233677788654 67
Q ss_pred cCCCCCHHHHHHHHHHHHHHHHHHHh
Q 005149 308 LGRSVSKGNFYRIRSAFTYGARKLGH 333 (712)
Q Consensus 308 LGRSVsk~nf~rIR~AF~~aa~~L~~ 333 (712)
+...++..+++.||.+-+.+...|.+
T Consensus 274 l~~~ms~~s~~~L~~eA~~tl~lL~~ 299 (972)
T PF03813_consen 274 LLAKMSPSSYEELQHEAKLTLELLDD 299 (972)
T ss_pred EEEcCCHHHHHHHHHHHHHHHHHhcc
Confidence 88899999999999998877777654
No 24
>KOG3793 consensus Transcription factor NFAT, subunit NF45 [Transcription]
Probab=94.17 E-value=0.69 Score=49.49 Aligned_cols=149 Identities=21% Similarity=0.237 Sum_probs=88.3
Q ss_pred HHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHh--hcC------CceEEeeccccCCCCCCCCc-eEEeecCCc-c
Q 005149 40 QRAEEATQGIIAQVQPTVVSEERRKAVIDYVQRLIRN--YLG------CEVFPFGSVPLKTYLPDGDI-DLTAFGGLN-V 109 (712)
Q Consensus 40 ~~le~ei~e~v~~I~PT~eE~~~R~~VI~~Vq~lI~~--~p~------a~V~~FGS~~tGL~LP~SDI-DL~V~~~~~-~ 109 (712)
..+++++.+=-+.+.|+.+|...-...+.+|+.++.. .|+ .+|.-.|||.+|+.+-++|. |++|+...- .
T Consensus 39 ~~f~~alLkRnqdL~P~~~~q~~I~~~vtKV~~vLdn~~~~~L~~~~ieevrqVGSF~k~T~~tg~~~advVViLkTLPt 118 (362)
T KOG3793|consen 39 TSFSEALLKRNQDLAPNSAEQASILSLVTKVNNVLDNLVAPGLFEVQIEEVRQVGSFKKGTMTTGHNVADLVVILKTLPT 118 (362)
T ss_pred hHHHHHHHhhhccCCCCHHHHHHHHHHHHHHHHHHHhhccCCceEeehhhhhhccceeccccccCCcccceEEEeecCCc
Confidence 3455556555577999999988777788888887773 344 35667899999999988775 777775431 1
Q ss_pred hh---HHHHHHHHHHHHHhhc-------cccccceeeeEEEEeeeeeEEEeec--------CeeEEeeec--cCCcchhh
Q 005149 110 EE---ALANDVCSVLEREDQN-------KAAEFVVKDAQLIRAEVKLVKCLVQ--------NIVVDISFN--QLGGLSTL 169 (712)
Q Consensus 110 ~e---~l~~~V~~iL~~~~~~-------~~a~f~V~~V~vI~ArVPIIK~~~~--------gI~VDISfN--n~~Gl~~s 169 (712)
.+ .+.+++.+-|+..... ....| +|.-.+|+|.|+--... -++.|+-.= +..+++..
T Consensus 119 ~EaV~aLg~Kv~e~lka~d~~Evltvl~~e~G~---~I~s~~~~VRiLIt~iP~n~~KLEP~lHLD~K~M~~~l~a~RH~ 195 (362)
T KOG3793|consen 119 LEAVAALGNKVVESLRAQDPSEVLTVLTNETGF---EISSSDATVRILITTVPPNLRKLEPELHLDIKVMQSALAAIRHA 195 (362)
T ss_pred HHHHHHHHHHHHHHhhhcChHHHHHHHhhccce---eeecccceEEEEEeecCchhcccChhhhhhHHHHHHHHHHHhhh
Confidence 22 2334444333322110 01122 22223788888766542 456666432 33445555
Q ss_pred HHHHHHHHHhCCChhhHHHHHHHHHH
Q 005149 170 CFLEQVDRLIGKDHLFKRSIILIKAW 195 (712)
Q Consensus 170 ~fLe~Vd~~v~~~p~fr~LvlLIK~W 195 (712)
.|.+++.. ....+-|++++|-.
T Consensus 196 ~WFee~A~----~s~~~~lir~LKDl 217 (362)
T KOG3793|consen 196 RWFEENAS----QSTVKVLIRLLKDL 217 (362)
T ss_pred hhhhhhhh----HHHHHHHHHHHHHH
Confidence 56555421 12357778888876
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=93.60 E-value=2 Score=45.62 Aligned_cols=127 Identities=19% Similarity=0.215 Sum_probs=67.9
Q ss_pred eeccccCCCCCC-CCceEEeecCCcchhHHHHHHHHHHHHHhhcccccccee---eeE-EE-EeeeeeEEEee--c--Ce
Q 005149 85 FGSVPLKTYLPD-GDIDLTAFGGLNVEEALANDVCSVLEREDQNKAAEFVVK---DAQ-LI-RAEVKLVKCLV--Q--NI 154 (712)
Q Consensus 85 FGS~~tGL~LP~-SDIDL~V~~~~~~~e~l~~~V~~iL~~~~~~~~a~f~V~---~V~-vI-~ArVPIIK~~~--~--gI 154 (712)
.||++.||.|.+ -++|++|++...-..++.++|...|....+....+ .|. +.- +| ..+.|.+.+.. . .+
T Consensus 2 VG~~aKGllL~Gd~~~eLVVlck~kPT~~lL~~v~~~L~~~L~~~~~~-ev~~~~e~~~~~~~~~~~~~~~~~~lts~~~ 80 (248)
T PF07528_consen 2 VGSFAKGLLLKGDNDVELVVLCKEKPTKELLNRVAEKLPEQLKKVTPE-EVTNSVEAAIIIDSCKEPKLEVGIDLTSPVM 80 (248)
T ss_pred cceecCCceecCCceEeEEEEcCCCCcHHHHHHHHHHHHHHHhhhCcc-ccccchhhhhhhcccccccceeeEEecCCce
Confidence 499999999985 78999999876544555555555444333211111 000 111 11 22233333322 1 22
Q ss_pred eEEeee----------------------ccCCcchhhHHHHHHHHHhCCChhhHHHHHHHHHHHHHhhCccCCCCCCCcH
Q 005149 155 VVDISF----------------------NQLGGLSTLCFLEQVDRLIGKDHLFKRSIILIKAWCYYESRILGAHHGLIST 212 (712)
Q Consensus 155 ~VDISf----------------------Nn~~Gl~~s~fLe~Vd~~v~~~p~fr~LvlLIK~Wa~yesRil~a~~GgLSS 212 (712)
.+.+.+ ..+..++-++|. .+.....+..+.+++++|..+ +|. +..+.|++
T Consensus 81 r~~~~~~~~~~~~~~~dp~~~Ld~~~cl~aLaalRhakWF---q~~a~~l~s~~~viRIlrDl~---~R~--p~w~~L~~ 152 (248)
T PF07528_consen 81 RVRVLITTIPENLSKLDPEDHLDRKKCLSALAALRHAKWF---QARANGLQSCVIVIRILRDLR---QRV--PTWQPLSS 152 (248)
T ss_pred EEEEeccccCccccccChhhcCCHHHHHHHHHHHHHhHHH---HHHhccCCCcceehhhHHHHH---HhC--CCCCCCCh
Confidence 222221 112222223332 233333445678899999997 354 44667999
Q ss_pred HHHHHHHH
Q 005149 213 YALETLVL 220 (712)
Q Consensus 213 YaL~lMVL 220 (712)
|++.+|+-
T Consensus 153 W~leLL~~ 160 (248)
T PF07528_consen 153 WALELLVE 160 (248)
T ss_pred hHHHHHHH
Confidence 99999884
No 26
>KOG2054 consensus Nucleolar RNA-associated protein (NRAP) [Function unknown]
Probab=93.15 E-value=0.41 Score=58.64 Aligned_cols=119 Identities=22% Similarity=0.397 Sum_probs=81.6
Q ss_pred HHHHHhCCChhhHHHHHHHHHHHHHhhCccCCCCCCCcHHHHHHHHH--------------H----HHHhhhcCCCCCCc
Q 005149 174 QVDRLIGKDHLFKRSIILIKAWCYYESRILGAHHGLISTYALETLVL--------------Y----KFLDYFSKFDWDSY 235 (712)
Q Consensus 174 ~Vd~~v~~~p~fr~LvlLIK~Wa~yesRil~a~~GgLSSYaL~lMVL--------------~----~FL~yYskFD~~~~ 235 (712)
++.+.....+.|+..+.|+|.|+ ++|-++-..|||+.+-|.++|. | .-|+|.+.+||+..
T Consensus 299 ~L~K~~s~~~~f~da~~Llk~Wl--rqRs~~~~~~gfg~f~~s~lvv~L~s~~ki~~~~S~yqvfR~vl~flat~dlt~~ 376 (1121)
T KOG2054|consen 299 LLSKTLSSAKGFKDALALLKVWL--RQRSLDIGQGGFGGFLLSALVVYLVSTRKIHTTLSAYQVFRSVLQFLATTDLTVN 376 (1121)
T ss_pred HHHHHHhhhhhHHHHHHHHHHHH--HhhhhhcccCcchHHHHHHHHHHHHhcCchhhcchHHHHHHHHHHHHhhhhhhcc
Confidence 45556667889999999999999 4776666788999999987761 2 45677899999988
Q ss_pred eeeccCCcccCCCCcccccCCCCCCCcccccHHHHHHHHhhcCCCCCCCCCCCCCCCCCCeEEcCCCCCCCCcCCCCCHH
Q 005149 236 CISLNGPVRISSLPEVVVETPENSGGDLLLSSEFLKECVEQFSVPSRGFDTNSRSFPPKHLNIVDPLKENNNLGRSVSKG 315 (712)
Q Consensus 236 ~ISi~GpVplssLp~~~~e~pe~~~g~lLL~~efLr~~~~~fs~~~rG~~~~~r~f~~~~L~IeDPfdpsNNLGRSVsk~ 315 (712)
+|++. |-+ .+++.. .+|-. ....+..| .....|+..+++..
T Consensus 377 ~~~l~-~~~-~s~~~~---------------~~f~e---------------------~~~~~f~D-~s~~~NLc~~mt~s 417 (1121)
T KOG2054|consen 377 GISLV-PSS-PSLPAL---------------ADFHE---------------------GQLVTFID-SSGHLNLCANMTAS 417 (1121)
T ss_pred ceEec-cCC-CCchhh---------------hhhhh---------------------cceeeEec-cCCcchhhhhccHH
Confidence 88765 111 111110 01110 01133344 22346788888888
Q ss_pred HHHHHHHHHHHHHHHHHh
Q 005149 316 NFYRIRSAFTYGARKLGH 333 (712)
Q Consensus 316 nf~rIR~AF~~aa~~L~~ 333 (712)
.|+++|.+.+.++..|.+
T Consensus 418 ~y~~~q~ea~ltl~lL~~ 435 (1121)
T KOG2054|consen 418 TYEQVQEEARLTLMLLDS 435 (1121)
T ss_pred HHHHHHHHHHHHHHHHhh
Confidence 999999999999999874
No 27
>PF14091 DUF4269: Domain of unknown function (DUF4269)
Probab=92.19 E-value=2 Score=42.52 Aligned_cols=104 Identities=16% Similarity=0.213 Sum_probs=62.0
Q ss_pred CCceEEeeccccCCCCCCCCceEEeecCCcchhHHHHHHHHHHHHHhhccccccceeeeEEE-EeeeeeEEEeecCeeEE
Q 005149 79 GCEVFPFGSVPLKTYLPDGDIDLTAFGGLNVEEALANDVCSVLEREDQNKAAEFVVKDAQLI-RAEVKLVKCLVQNIVVD 157 (712)
Q Consensus 79 ~a~V~~FGS~~tGL~LP~SDIDL~V~~~~~~~e~l~~~V~~iL~~~~~~~~a~f~V~~V~vI-~ArVPIIK~~~~gI~VD 157 (712)
...-..-|..+.|+..|+|||||+|..++ .+.|...+. +...+ ...|.++. ..| .-..=++.|...|..+-
T Consensus 15 ~~~PiL~GTiPi~Idi~~SDLDIic~~~d--~~~F~~~l~----~~f~~-~~~f~~~~-~~i~~~~~~~~~F~~~~~~~E 86 (152)
T PF14091_consen 15 AYDPILVGTIPIGIDIPGSDLDIICEVPD--PEAFEQLLQ----SLFGQ-FEGFTIKE-KTIRGEPSIVANFRYEGFPFE 86 (152)
T ss_pred cCCCEEecccccccCCCCCCccEEEEeCC--HHHHHHHHH----HHhcc-CCCceeee-ceeCCceeEEEEEEECCceEE
Confidence 34778899999999999999999999874 233433333 32221 13454443 123 33333456667788888
Q ss_pred eeecc-----CCcchhhHHHHHHHHHhCCC-hhhHHHHHHHH
Q 005149 158 ISFNQ-----LGGLSTLCFLEQVDRLIGKD-HLFKRSIILIK 193 (712)
Q Consensus 158 ISfNn-----~~Gl~~s~fLe~Vd~~v~~~-p~fr~LvlLIK 193 (712)
|--.+ .+|.+-.. + -.+.+... |.||.-++-+|
T Consensus 87 iF~Q~~Pv~~QnayrHm~-i--E~rLL~~~g~~~r~~Ii~LK 125 (152)
T PF14091_consen 87 IFGQPIPVEEQNAYRHML-I--EHRLLELHGPSFREEIIELK 125 (152)
T ss_pred EeecCCChhhHHHHHHHH-H--HHHHHHhcCHHHHHHHHHHH
Confidence 86532 22222211 1 23445544 88888888777
No 28
>PRK02098 phosphoribosyl-dephospho-CoA transferase; Provisional
Probab=90.33 E-value=0.77 Score=47.90 Aligned_cols=41 Identities=20% Similarity=0.148 Sum_probs=31.2
Q ss_pred HHHHHHHHHhhcCCceEEeeccc----cCC--CCCCCCceEEeecCCc
Q 005149 67 IDYVQRLIRNYLGCEVFPFGSVP----LKT--YLPDGDIDLTAFGGLN 108 (712)
Q Consensus 67 I~~Vq~lI~~~p~a~V~~FGS~~----tGL--~LP~SDIDL~V~~~~~ 108 (712)
+..|+.+... .++.+.+|||++ ||+ -.++|||||.|-.+..
T Consensus 109 l~~l~~~~~~-~g~~~gv~GS~a~qlaTG~~~l~~~SDLDLLi~~~~~ 155 (221)
T PRK02098 109 LRALLALAAA-HGVDCRVFGSLAWQALTGLPYLSASSDLDLLWPLPAA 155 (221)
T ss_pred HHHHHHHHHh-CCCcEEEeeehHHHHhhCCcccCCCCCeeEEEecCCh
Confidence 3344444433 567999999999 999 6789999999988743
No 29
>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=89.46 E-value=0.95 Score=46.56 Aligned_cols=41 Identities=20% Similarity=0.187 Sum_probs=30.8
Q ss_pred HHHHHHHHHhhcCCceEEeecc----ccCC--CCCCCCceEEeecCCc
Q 005149 67 IDYVQRLIRNYLGCEVFPFGSV----PLKT--YLPDGDIDLTAFGGLN 108 (712)
Q Consensus 67 I~~Vq~lI~~~p~a~V~~FGS~----~tGL--~LP~SDIDL~V~~~~~ 108 (712)
+..|..+... .++.+-+|||+ +||+ -.++|||||.|-.+..
T Consensus 97 l~~l~~~~~~-~~~~~gv~GS~~~qlaTg~~~~~~~SDLDLLi~~~~~ 143 (202)
T TIGR03135 97 LRALDALLDA-LGVPWGVYGSAGWQLLTGLPYLHASSDLDLLLRAPSP 143 (202)
T ss_pred HHHHHHHHHh-CCCcEEEecchHHHHhcCCcccCCCCCeeEEEcCCCh
Confidence 3334433333 56899999999 8999 6789999999998753
No 30
>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=88.67 E-value=5 Score=50.22 Aligned_cols=129 Identities=24% Similarity=0.330 Sum_probs=80.8
Q ss_pred HHHHhCCChhhHHHHHHHHHHHHHhhCccCCCCCCCcHHHHHHHH-------------------HHHHHhhhcCCCCCCc
Q 005149 175 VDRLIGKDHLFKRSIILIKAWCYYESRILGAHHGLISTYALETLV-------------------LYKFLDYFSKFDWDSY 235 (712)
Q Consensus 175 Vd~~v~~~p~fr~LvlLIK~Wa~yesRil~a~~GgLSSYaL~lMV-------------------L~~FL~yYskFD~~~~ 235 (712)
|.....++|.|-+.++|+|.|+. ++.+ .+.++.=++++|| +++||++-++|||.+.
T Consensus 675 i~~l~~~~p~fs~tvRL~KrW~~--shlL---s~~i~~E~vELlva~vfl~~~p~~~P~S~~~GFlRfL~lLs~~dW~~~ 749 (972)
T PF03813_consen 675 IHGLHTRFPSFSPTVRLAKRWLS--SHLL---SGHISEEAVELLVASVFLSPAPWSPPSSPQTGFLRFLHLLSTWDWREE 749 (972)
T ss_pred HHHHHhhCCchhHHHHHHHHHHH--hccC---cccCCHHHHHHHHHHHhcCCCCCCCCCCHhHHHHHHHHHHHhCCCCcC
Confidence 44556789999999999999994 7777 3468999999999 5688888899999875
Q ss_pred eeeccCCcccCCCCcccccCCCCCCCcccccHHHHHHHHhhcCCCCCCCCCCCCCCCCCCeEEcCCCCCCCCcCC--CCC
Q 005149 236 CISLNGPVRISSLPEVVVETPENSGGDLLLSSEFLKECVEQFSVPSRGFDTNSRSFPPKHLNIVDPLKENNNLGR--SVS 313 (712)
Q Consensus 236 ~ISi~GpVplssLp~~~~e~pe~~~g~lLL~~efLr~~~~~fs~~~rG~~~~~r~f~~~~L~IeDPfdpsNNLGR--SVs 313 (712)
-+-+. +. ++ ++.+-.......|..-.+ ... ......|.|-.|.|+..-+-. +-+
T Consensus 750 PLiVd----~~--------------~~--l~~~~~~~i~~~f~~~R~-~dp---~~~~p~~~IaT~~D~~g~~wT~~~Ps 805 (972)
T PF03813_consen 750 PLIVD----FN--------------NE--LTEEDRAEIETNFDAWRK-IDP---AMNLPAMFIATPYDPEGSLWTRNGPS 805 (972)
T ss_pred CEEEE----CC--------------CC--CCHHHHHHHHHHHHHhhc-cCc---cccCCcEEEEeCCCCCCCEeECCCCC
Confidence 33221 10 00 112222233333321111 000 011345999999998754322 345
Q ss_pred HHHHHHHHHHHHHHHHHHH
Q 005149 314 KGNFYRIRSAFTYGARKLG 332 (712)
Q Consensus 314 k~nf~rIR~AF~~aa~~L~ 332 (712)
+..+.||+..-+.+++.|.
T Consensus 806 ~~v~~Rl~~LAk~sl~~l~ 824 (972)
T PF03813_consen 806 KVVAKRLTALAKASLKLLE 824 (972)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 5577888887777776665
No 31
>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=81.36 E-value=5.5 Score=41.26 Aligned_cols=54 Identities=20% Similarity=0.246 Sum_probs=36.9
Q ss_pred HHHHHHHHHHhhcCCceEEeeccc----cCC--CCCCCCceEEeecCCcchhHHHHHHHHHHHH
Q 005149 66 VIDYVQRLIRNYLGCEVFPFGSVP----LKT--YLPDGDIDLTAFGGLNVEEALANDVCSVLER 123 (712)
Q Consensus 66 VI~~Vq~lI~~~p~a~V~~FGS~~----tGL--~LP~SDIDL~V~~~~~~~e~l~~~V~~iL~~ 123 (712)
.+..++.+. ...++..-+|||+. ||+ -.++|||||.|..+... .+..+...|+.
T Consensus 104 ~l~~l~~~~-~~~~~~~gv~GS~g~qlaTGl~~l~~~SDLDLli~~~~~~---~~~~l~~~L~~ 163 (213)
T PF10620_consen 104 ALQALRALL-DALGLRWGVYGSLGFQLATGLPYLHADSDLDLLIRPPSPS---QADALLALLQA 163 (213)
T ss_pred HHHHHHHHH-HHcCCCEEEehhHHHHHHhCccccCCCCCceEEEeCCChh---HHHHHHHHHHH
Confidence 444555544 45799999999986 777 35689999999988644 23344455544
No 32
>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=78.53 E-value=3.8 Score=38.24 Aligned_cols=57 Identities=25% Similarity=0.214 Sum_probs=38.3
Q ss_pred HHHHHHHHHHh-hcCCceEEeeccccCCCCCCCCceEEeecCCcch-----hHHHHHHHHHHHH
Q 005149 66 VIDYVQRLIRN-YLGCEVFPFGSVPLKTYLPDGDIDLTAFGGLNVE-----EALANDVCSVLER 123 (712)
Q Consensus 66 VI~~Vq~lI~~-~p~a~V~~FGS~~tGL~LP~SDIDL~V~~~~~~~-----e~l~~~V~~iL~~ 123 (712)
+.+.|++.++. .|++++.+-|||.-|--.- +|||+.|..+.... ..+...|.+.|++
T Consensus 10 i~~~V~~~~~~i~p~~~v~i~GSyRRGK~~~-gDiDiLIt~~~~~~~~~~~~~~l~~lv~~L~~ 72 (112)
T PF14792_consen 10 IEEIVKEALEKIDPGLEVEICGSYRRGKETS-GDIDILITHPDPSSVSKKLEGLLEKLVKRLEE 72 (112)
T ss_dssp HHHHHHHHHHCCSTT-EEEEEHHHHTT-SEE-SSEEEEEEETTCSTTTCSTTCHHHHHHHHHHH
T ss_pred HHHHHHHHHHhcCCCcEEEEccccccCCCcC-CCeEEEEeCCCcCcchhhHHHHHHHHHHHHHh
Confidence 34455666664 4899999999999887654 59999999886543 3455555555544
No 33
>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=73.92 E-value=28 Score=33.99 Aligned_cols=30 Identities=20% Similarity=0.193 Sum_probs=27.0
Q ss_pred CCceEEeeccccCCCCCCCCceEEeecCCc
Q 005149 79 GCEVFPFGSVPLKTYLPDGDIDLTAFGGLN 108 (712)
Q Consensus 79 ~a~V~~FGS~~tGL~LP~SDIDL~V~~~~~ 108 (712)
+.-+..+||+.-+=-.+.||+|+.++....
T Consensus 55 ~~~~la~Gs~GR~E~~~~SD~D~~~v~~~~ 84 (172)
T cd05401 55 PFALLALGSYGRGELNPSSDQDLLLLYDDD 84 (172)
T ss_pred cEEEEEeCCcccCCcCCCcCcceEEEeCCC
Confidence 467999999999999999999999998754
No 34
>PRK00227 glnD PII uridylyl-transferase; Provisional
Probab=71.71 E-value=10 Score=45.93 Aligned_cols=49 Identities=18% Similarity=0.225 Sum_probs=41.0
Q ss_pred HHHHHHHHHHHHHHHHh--h-cCCceEEeeccccCCCCCCCCceEEeecCCc
Q 005149 60 EERRKAVIDYVQRLIRN--Y-LGCEVFPFGSVPLKTYLPDGDIDLTAFGGLN 108 (712)
Q Consensus 60 ~~~R~~VI~~Vq~lI~~--~-p~a~V~~FGS~~tGL~LP~SDIDL~V~~~~~ 108 (712)
-+.|+.+......+++. . .++.+...|+|.-|--.|-|||||.++.+..
T Consensus 5 ~~~~~~~~~~~~~~~~~~~~~~~~aLvAvGGYGR~EL~P~SDIDLLiL~~~~ 56 (693)
T PRK00227 5 AQLREDAEASALALLGSLQLPPGTALAATGSLARREMTPYSDLDLILLHPPG 56 (693)
T ss_pred HHHHHHHHHHHHHHHHhcCCCCCeEEEEeccccccCcCCCcCceEEEEeCCc
Confidence 34788888888888884 3 3578999999999999999999999998743
No 35
>PRK01293 phosphoribosyl-dephospho-CoA transferase; Provisional
Probab=68.90 E-value=11 Score=39.11 Aligned_cols=32 Identities=25% Similarity=0.150 Sum_probs=26.0
Q ss_pred cCCceEEeeccc----cCC--CCCCCCceEEeecCCcc
Q 005149 78 LGCEVFPFGSVP----LKT--YLPDGDIDLTAFGGLNV 109 (712)
Q Consensus 78 p~a~V~~FGS~~----tGL--~LP~SDIDL~V~~~~~~ 109 (712)
.+...-+|||.. ||+ ..++|||||+|..+...
T Consensus 108 ~~~~wgv~GS~g~qlaTGl~~l~~~SDLDLlir~~~~l 145 (207)
T PRK01293 108 LGLAWGVTGSAGFELATGIPVLHADSDLDLLIRAPQPL 145 (207)
T ss_pred CCCceeeehhHHHHHhhCCccccCCCCccEeecCCCcc
Confidence 488999999986 676 45689999999987644
No 36
>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=67.32 E-value=38 Score=32.59 Aligned_cols=29 Identities=14% Similarity=-0.088 Sum_probs=27.0
Q ss_pred CCceEEeeccccCCCCCCCCceEEeecCC
Q 005149 79 GCEVFPFGSVPLKTYLPDGDIDLTAFGGL 107 (712)
Q Consensus 79 ~a~V~~FGS~~tGL~LP~SDIDL~V~~~~ 107 (712)
.+.+..+||+.-+=-+|.||+|..|+...
T Consensus 49 ~~a~lalGS~GR~E~~~~sDqD~alv~~d 77 (138)
T PF03445_consen 49 PFAWLALGSYGRREQTLYSDQDNALVFED 77 (138)
T ss_pred CEEEEEECcccccCCCcCccccceeeecC
Confidence 46799999999999999999999999887
No 37
>PRK05007 PII uridylyl-transferase; Provisional
Probab=61.55 E-value=55 Score=40.84 Aligned_cols=50 Identities=26% Similarity=0.265 Sum_probs=35.4
Q ss_pred HHHHHHHHHHH-HHHHHhh-----cCCceEEeeccccCCCCCCCCceEEeecCCcc
Q 005149 60 EERRKAVIDYV-QRLIRNY-----LGCEVFPFGSVPLKTYLPDGDIDLTAFGGLNV 109 (712)
Q Consensus 60 ~~~R~~VI~~V-q~lI~~~-----p~a~V~~FGS~~tGL~LP~SDIDL~V~~~~~~ 109 (712)
.+.|-.+++.+ +.+.... ++..|...|+|.-|--.|.|||||.++.+...
T Consensus 55 ~~~~s~~~D~~l~~l~~~~~~~~~~~~alvAvGgyGR~EL~p~SDiDll~l~~~~~ 110 (884)
T PRK05007 55 VEARTEFIDQLLQRLWIEAGFDQIPDLALVAVGGYGRGELHPLSDIDLLILSRKKL 110 (884)
T ss_pred HHHHHHHHHHHHHHHHHHccCCCcCceEEEecCCCCCcccCCcccceEEEEeCCCC
Confidence 34445555543 3333321 24689999999999999999999999987543
No 38
>PRK04374 PII uridylyl-transferase; Provisional
Probab=55.46 E-value=63 Score=40.30 Aligned_cols=83 Identities=16% Similarity=0.240 Sum_probs=48.5
Q ss_pred CCCCCCCCCChhhHHHH-HHHHHH----HHHHc---CCCHHHHHHHHHHHHH-HHHHHHhh-c---CCceEEeeccccCC
Q 005149 26 SVPSNQTAIGAEYWQRA-EEATQG----IIAQV---QPTVVSEERRKAVIDY-VQRLIRNY-L---GCEVFPFGSVPLKT 92 (712)
Q Consensus 26 ~~~p~p~~i~~~~w~~l-e~ei~e----~v~~I---~PT~eE~~~R~~VI~~-Vq~lI~~~-p---~a~V~~FGS~~tGL 92 (712)
..-|+|--.....|... .+.+.+ +.+.. .+..+=.+.|-.+++. ++++...+ | +..|...|+|.-|-
T Consensus 6 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~~~~~~~~~~~~~~s~~~D~~l~~~~~~~~~~~~~~alvAvGgYGR~E 85 (869)
T PRK04374 6 ADRPDPGVAGDADWAAAARPLLVHADMRLCKRFDQGEPIERLLALRARAVDQLMRNAWTRCIPADSGLSLHAVGGYGRGE 85 (869)
T ss_pred ccCCCCCCCCchhhHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHhCCCcCCEEEEEcCCccccc
Confidence 34567766677777653 111211 11111 1122223334445553 33344332 3 35799999999999
Q ss_pred CCCCCCceEEeecCCc
Q 005149 93 YLPDGDIDLTAFGGLN 108 (712)
Q Consensus 93 ~LP~SDIDL~V~~~~~ 108 (712)
--|.|||||.++.+..
T Consensus 86 L~p~SDIDLliL~~~~ 101 (869)
T PRK04374 86 LFPRSDVDLLVLGETA 101 (869)
T ss_pred cCCcccceEEEEecCC
Confidence 9999999999998743
No 39
>KOG1906 consensus DNA polymerase sigma [Replication, recombination and repair]
Probab=55.01 E-value=6.5 Score=45.89 Aligned_cols=69 Identities=36% Similarity=0.467 Sum_probs=52.1
Q ss_pred EEcCCCCCCCCcCCCCCHHHHHHHHHHHHHHHHHHHhhhcCCCchhHHHHHHHHHHhHhhcCCCCCCCCCCC
Q 005149 297 NIVDPLKENNNLGRSVSKGNFYRIRSAFTYGARKLGHILSQPEESLTDELRKFFSNTLDRHGSGQRPDVQDP 368 (712)
Q Consensus 297 ~IeDPfdpsNNLGRSVsk~nf~rIR~AF~~aa~~L~~il~~p~~~i~~~l~~fF~ntl~r~g~g~rpd~~~~ 368 (712)
....+.....|+| |-...|...-. |.+++.+|+..+.++.+.+..+...||.+++.|+|.+.++|..+|
T Consensus 246 ~~s~~~~~~~~~~--vll~~f~e~yG-~~f~~~k~~i~~~~~g~~~~~~~~~~~~~~~~~~~~LsieDP~~P 314 (514)
T KOG1906|consen 246 SKSGRLAVLKNLG--VLLIKFFELYG-RNFGYDKLGISLSLGGEYVSKELTGFFNNSLERPGSLSIEDPVDP 314 (514)
T ss_pred ccCCccchhcccc--hHHHHHHHHhc-cccCchhhceeccCCcccccHHhhhhhcccccCCCccccCCCCCc
Confidence 3345666666776 33223333332 566788898888899999999999999999999999999998666
No 40
>KOG2534 consensus DNA polymerase IV (family X) [Replication, recombination and repair]
Probab=52.62 E-value=39 Score=37.47 Aligned_cols=43 Identities=19% Similarity=0.026 Sum_probs=33.1
Q ss_pred HHHHHHHHHHh-hcCCceEEeeccccCCCCCCCCceEEeecCCcc
Q 005149 66 VIDYVQRLIRN-YLGCEVFPFGSVPLKTYLPDGDIDLTAFGGLNV 109 (712)
Q Consensus 66 VI~~Vq~lI~~-~p~a~V~~FGS~~tGL~LP~SDIDL~V~~~~~~ 109 (712)
+.+.|++++.. -|++.|.+-|||.-| +.-+.|||+.|.-|...
T Consensus 157 i~~~V~~av~~~~p~~~vt~~GsfRRG-k~~ggDvD~LithP~~~ 200 (353)
T KOG2534|consen 157 IQQTVQEAVWAFDPEAFVTVTGSFRRG-KKMGGDVDFLITHPGST 200 (353)
T ss_pred HHHHHHHHHhhcCCCcEEEEeccccCC-cccCCCeeEEEeCCCCC
Confidence 44455566654 389999999999988 45689999999988643
No 41
>COG2844 GlnD UTP:GlnB (protein PII) uridylyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=51.31 E-value=71 Score=39.56 Aligned_cols=39 Identities=21% Similarity=0.296 Sum_probs=31.7
Q ss_pred CCceEEeeccccCCCCCCCCceEEeecCCcchhHHHHHH
Q 005149 79 GCEVFPFGSVPLKTYLPDGDIDLTAFGGLNVEEALANDV 117 (712)
Q Consensus 79 ~a~V~~FGS~~tGL~LP~SDIDL~V~~~~~~~e~l~~~V 117 (712)
++.+...|.|.-|--.|-||||+.++.+....+...+.|
T Consensus 66 ~~aLvAVGGyGRgEL~P~SDiDlL~L~p~~~~~~~e~~i 104 (867)
T COG2844 66 GLALVAVGGYGRGELHPLSDIDLLLLSPQKLTDWLEQKI 104 (867)
T ss_pred ceEEEEeccccccccCCCccceEEEecCCCCChHHHHHH
Confidence 478999999999999999999999999876554333333
No 42
>PRK03059 PII uridylyl-transferase; Provisional
Probab=50.97 E-value=71 Score=39.78 Aligned_cols=49 Identities=18% Similarity=0.257 Sum_probs=34.3
Q ss_pred HHHHHHHHHH-HHHHHHhh---cCCceEEeeccccCCCCCCCCceEEeecCCc
Q 005149 60 EERRKAVIDY-VQRLIRNY---LGCEVFPFGSVPLKTYLPDGDIDLTAFGGLN 108 (712)
Q Consensus 60 ~~~R~~VI~~-Vq~lI~~~---p~a~V~~FGS~~tGL~LP~SDIDL~V~~~~~ 108 (712)
.+.|-.+++. |+.+.... .+..|...|+|.-|---|.|||||.++.+..
T Consensus 38 ~~~~s~l~d~~l~~~~~~~~~~~~~alvAvGgyGR~EL~p~SDiDll~l~~~~ 90 (856)
T PRK03059 38 LHALSRLVDQALRRLWQECGLPAGAALVAVGGYGRGELFPYSDVDLLVLLPDA 90 (856)
T ss_pred HHHHHHHHHHHHHHHHHhcCCCCCeEEEEcCCCCCcccCCCCCCEEEEEecCC
Confidence 3344455553 33333321 2468999999999999999999999998643
No 43
>COG2413 Predicted nucleotidyltransferase [General function prediction only]
Probab=47.26 E-value=45 Score=34.96 Aligned_cols=42 Identities=24% Similarity=0.348 Sum_probs=30.8
Q ss_pred HHHHHHHHHHHHHhhcCCceEEeeccccCCCCCCCCceEEeecC
Q 005149 63 RKAVIDYVQRLIRNYLGCEVFPFGSVPLKTYLPDGDIDLTAFGG 106 (712)
Q Consensus 63 R~~VI~~Vq~lI~~~p~a~V~~FGS~~tGL~LP~SDIDL~V~~~ 106 (712)
|+++.+.++.+.. ++..-..+||.+.|=--|+||+|++|..+
T Consensus 23 Re~A~~i~e~l~~--f~ie~~v~gSvarGDV~p~SDvDV~I~~~ 64 (228)
T COG2413 23 REKARKIMEGLSD--FGIEAVVYGSVARGDVRPGSDVDVAIPEP 64 (228)
T ss_pred HHHHHHHHHHHHH--hcchhEEEeeeeccCcCCCCCceEEEecC
Confidence 4444444444443 34577889999999888999999999975
No 44
>COG1665 Predicted nucleotidyltransferase [General function prediction only]
Probab=46.30 E-value=33 Score=37.36 Aligned_cols=29 Identities=28% Similarity=0.329 Sum_probs=25.2
Q ss_pred cCCceEEeeccccCCCCCCCCceEEeecC
Q 005149 78 LGCEVFPFGSVPLKTYLPDGDIDLTAFGG 106 (712)
Q Consensus 78 p~a~V~~FGS~~tGL~LP~SDIDL~V~~~ 106 (712)
|--.+=+-||...||+-.+||||++|.+.
T Consensus 120 p~~~mGVTGSiL~gl~~~nSDIDfVVYG~ 148 (315)
T COG1665 120 PVNSMGVTGSILLGLYDENSDIDFVVYGQ 148 (315)
T ss_pred chhhccccccccccccCCCCCceEEEEcH
Confidence 44566678999999999999999999994
No 45
>PRK00275 glnD PII uridylyl-transferase; Provisional
Probab=46.14 E-value=1.1e+02 Score=38.51 Aligned_cols=49 Identities=18% Similarity=0.192 Sum_probs=34.9
Q ss_pred HHHHHHHHHHHHH-HHHhh--c---CCceEEeeccccCCCCCCCCceEEeecCCc
Q 005149 60 EERRKAVIDYVQR-LIRNY--L---GCEVFPFGSVPLKTYLPDGDIDLTAFGGLN 108 (712)
Q Consensus 60 ~~~R~~VI~~Vq~-lI~~~--p---~a~V~~FGS~~tGL~LP~SDIDL~V~~~~~ 108 (712)
.+.|-.+++.+-+ +.+.. + +..|...|.|.-|---|.|||||.++.+..
T Consensus 53 ~~~~s~~~d~~l~~~~~~~~~~~~~~~alvAvGgyGR~EL~p~SDiDll~l~~~~ 107 (895)
T PRK00275 53 IEDRAWFVDQILQQAWHQFDWSDDADIALVAVGGYGRGELHPYSDIDLLILLDSA 107 (895)
T ss_pred HHHHHHHHHHHHHHHHHHhccCCCCCEEEEEcCCccccCcCCCCCceEEEEecCC
Confidence 4445556664433 33322 1 358999999999999999999999998754
No 46
>TIGR01693 UTase_glnD [Protein-PII] uridylyltransferase. This model describes GlnD, the uridylyltransferase/uridylyl-removing enzyme for the nitrogen regulatory protein PII. Not all homologs of PII share the property of uridylyltransferase modification on the characteristic Tyr residue (see Prosite pattern PS00496 and document PDOC00439), but the modification site is preserved in the PII homolog of all species with a member of this family.
Probab=41.67 E-value=1.1e+02 Score=38.01 Aligned_cols=30 Identities=23% Similarity=0.264 Sum_probs=27.1
Q ss_pred CCceEEeeccccCCCCCCCCceEEeecCCc
Q 005149 79 GCEVFPFGSVPLKTYLPDGDIDLTAFGGLN 108 (712)
Q Consensus 79 ~a~V~~FGS~~tGL~LP~SDIDL~V~~~~~ 108 (712)
++.+...|+|.-|--.|.||||++++....
T Consensus 43 ~~aliA~GgyGR~El~p~SDiDll~l~~~~ 72 (850)
T TIGR01693 43 GIALVAVGGYGRGELAPYSDIDLLFLHDGK 72 (850)
T ss_pred CeEEEEeCCccccCcCCCCCCeEEEEeCCC
Confidence 568999999999999999999999998754
No 47
>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=41.27 E-value=19 Score=37.55 Aligned_cols=45 Identities=16% Similarity=0.132 Sum_probs=33.0
Q ss_pred HHHHHHHHHHHHHhh-cC-CceEEeeccccCCCCCCCCceEEeecCC
Q 005149 63 RKAVIDYVQRLIRNY-LG-CEVFPFGSVPLKTYLPDGDIDLTAFGGL 107 (712)
Q Consensus 63 R~~VI~~Vq~lI~~~-p~-a~V~~FGS~~tGL~LP~SDIDL~V~~~~ 107 (712)
|..|.+.++++-++. .. .-+...||.+-||..|+||.|+..+.-.
T Consensus 2 ~~~i~~~l~~ie~~~~~~il~~~~sGS~a~G~~s~dSD~D~r~vy~~ 48 (247)
T PF10127_consen 2 RETIQEKLNEIEKEHNVKILYACESGSRAYGFASPDSDYDVRGVYIP 48 (247)
T ss_pred chHHHHHHHHHHHhcCCcEEEEecccccccCCCCCCcCcccchhccC
Confidence 456667777776643 11 2355789999999999999999877643
No 48
>KOG2054 consensus Nucleolar RNA-associated protein (NRAP) [Function unknown]
Probab=40.22 E-value=41 Score=42.25 Aligned_cols=55 Identities=29% Similarity=0.504 Sum_probs=43.2
Q ss_pred HHHhCCChhhHHHHHHHHHHHHHhhCccCCCCCCCcHHHHHHHH-------------------HHHHHhhhcCCCCCCc
Q 005149 176 DRLIGKDHLFKRSIILIKAWCYYESRILGAHHGLISTYALETLV-------------------LYKFLDYFSKFDWDSY 235 (712)
Q Consensus 176 d~~v~~~p~fr~LvlLIK~Wa~yesRil~a~~GgLSSYaL~lMV-------------------L~~FL~yYskFD~~~~ 235 (712)
....+.++.|-+.++|-|.|+. +++++ |++.=-++.++| ..+||.+-++|||..+
T Consensus 812 ~~l~qsh~~ys~vvrLaKrWl~--shLL~---~h~~De~iELLva~lf~~p~p~~~psS~~~gFlRfL~llS~~dW~~~ 885 (1121)
T KOG2054|consen 812 QSLSQSHPFYSSVVRLAKRWLG--SHLLS---GHHLDEAIELLVAALFLKPGPLVPPSSPENGFLRFLSLLSTWDWKFD 885 (1121)
T ss_pred HHHhhcccchhHHHHHHHHHHH--HHhhc---cchHHHHHHHHHHHHhcCccCCCCCCCcchhHHHHHHHHhcCcccCC
Confidence 3445678888899999999984 77764 455578889998 4588888899999865
No 49
>PRK01759 glnD PII uridylyl-transferase; Provisional
Probab=36.71 E-value=1.4e+02 Score=37.32 Aligned_cols=49 Identities=16% Similarity=0.261 Sum_probs=35.0
Q ss_pred HHHHHHHHHH-HHHHHHhh--c---CCceEEeeccccCCCCCCCCceEEeecCCc
Q 005149 60 EERRKAVIDY-VQRLIRNY--L---GCEVFPFGSVPLKTYLPDGDIDLTAFGGLN 108 (712)
Q Consensus 60 ~~~R~~VI~~-Vq~lI~~~--p---~a~V~~FGS~~tGL~LP~SDIDL~V~~~~~ 108 (712)
.+.|-.+++. |+++.... + ++.+...|+|.-|---|-|||||.|+.+..
T Consensus 31 ~~~~~~~~D~~l~~l~~~~~~~~~~~iaLvAvGGYGR~eL~P~SDIDlliL~~~~ 85 (854)
T PRK01759 31 IENRSDFYDQLLIHLWQQFGLEEQSDLALIAVGGYGRREMFPLSDLDILILTEQP 85 (854)
T ss_pred HHHHHHHHHHHHHHHHHHccCCCCCCeEEEEeCCcccccCCCcccceEEEEeCCC
Confidence 3445555554 34444432 2 357999999999999999999999998754
No 50
>cd05398 NT_ClassII-CCAase Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes. 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 II group is comprised mainly of eubacterial and eukaryotic enzymes and includes Bacillus stearothermophilus CCAase, Escherichia coli poly(A) polymerase I, human mitochondrial CCAase, and Saccharomyces cerevisiae CCAase (CCA1). CCA-adding enzymes have a single catalytic pocket, which recognizes both ATP and CTP substrates. Included in this subgroup are CC- and A-adding enzymes from various ancient species of bacteria such as Aquifex aeolicus; these enzymes collaborate to add CCA to tRNAs. 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 io
Probab=34.11 E-value=1.4e+02 Score=28.70 Aligned_cols=68 Identities=15% Similarity=0.277 Sum_probs=42.7
Q ss_pred cCCceEEeeccccCC--CCCCCCceEEeecCCcchhHHHHHHHHHHHHHhhccccccceeeeEEE--EeeeeeEEEeecC
Q 005149 78 LGCEVFPFGSVPLKT--YLPDGDIDLTAFGGLNVEEALANDVCSVLEREDQNKAAEFVVKDAQLI--RAEVKLVKCLVQN 153 (712)
Q Consensus 78 p~a~V~~FGS~~tGL--~LP~SDIDL~V~~~~~~~e~l~~~V~~iL~~~~~~~~a~f~V~~V~vI--~ArVPIIK~~~~g 153 (712)
.+.+++..|-++-.+ ..+..|||+++.... ..+ +.++.+.. . ...+ ..+-+++++...+
T Consensus 15 ~g~~~ylVGG~VRD~Llg~~~~DiDi~v~~~~---~~~---~~~l~~~~------~-----~~~v~~~~~f~t~~v~~~~ 77 (139)
T cd05398 15 LGYEAYLVGGAVRDLLLGRPPKDIDIATDADG---PEF---AEALFKKI------G-----GRVVGLGEEFGTATVVING 77 (139)
T ss_pred cCceEEEECChHHHHHcCCCCCCceEEEeCCC---HHH---HHHHHHhc------C-----CcEEecCCcccEEEEEECC
Confidence 489999999988443 457899999998741 122 22222221 0 1122 3566677777778
Q ss_pred eeEEeeecc
Q 005149 154 IVVDISFNQ 162 (712)
Q Consensus 154 I~VDISfNn 162 (712)
..+||+.-.
T Consensus 78 ~~~di~~~R 86 (139)
T cd05398 78 LTIDVATLR 86 (139)
T ss_pred EEEEEcccc
Confidence 999998644
No 51
>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=33.10 E-value=97 Score=33.82 Aligned_cols=41 Identities=20% Similarity=0.086 Sum_probs=29.7
Q ss_pred HHHHHHHHHhh-cCCceEEeeccccCCCCCCCCceEEeecCCc
Q 005149 67 IDYVQRLIRNY-LGCEVFPFGSVPLKTYLPDGDIDLTAFGGLN 108 (712)
Q Consensus 67 I~~Vq~lI~~~-p~a~V~~FGS~~tGL~LP~SDIDL~V~~~~~ 108 (712)
.+.|...++.. +.++|.+-||+.-|.-. .+|||++|..+..
T Consensus 147 a~~i~~~l~~~~~~~~v~i~GS~RRg~et-~gDiDilv~~~~~ 188 (307)
T cd00141 147 AEIIKEALREVDPVLQVEIAGSYRRGKET-VGDIDILVTHPDA 188 (307)
T ss_pred HHHHHHHHHhCCCceEEEEcccccCCCCc-cCCEEEEEecCCc
Confidence 33444444433 67999999999877654 5899999988753
No 52
>PHA02603 nrdC.11 hypothetical protein; Provisional
Probab=31.09 E-value=26 Score=38.98 Aligned_cols=24 Identities=29% Similarity=0.281 Sum_probs=20.8
Q ss_pred eEEeeccccCCCCCCCCceEEeec
Q 005149 82 VFPFGSVPLKTYLPDGDIDLTAFG 105 (712)
Q Consensus 82 V~~FGS~~tGL~LP~SDIDL~V~~ 105 (712)
+..+||.+-||..|+||+|+-=+.
T Consensus 6 ~~~~GShaYG~~tp~SD~D~rGV~ 29 (330)
T PHA02603 6 KGLFGSHLYGTSTPESDVDYKGIF 29 (330)
T ss_pred EEecccceeCCCCCCcccccceee
Confidence 457999999999999999986554
No 53
>COG3541 Predicted nucleotidyltransferase [General function prediction only]
Probab=24.53 E-value=37 Score=36.29 Aligned_cols=22 Identities=27% Similarity=0.167 Sum_probs=18.9
Q ss_pred eeccccCCCCCCCCceEEeecC
Q 005149 85 FGSVPLKTYLPDGDIDLTAFGG 106 (712)
Q Consensus 85 FGS~~tGL~LP~SDIDL~V~~~ 106 (712)
=||.+-|+..|+||+|+--+.-
T Consensus 16 sGS~~yGf~spdSDyDvR~V~i 37 (248)
T COG3541 16 SGSHLYGFPSPDSDYDVRGVHI 37 (248)
T ss_pred ccccccCCCCCCCccceeeEEe
Confidence 3999999999999999976643
No 54
>PF03296 Pox_polyA_pol: Poxvirus poly(A) polymerase nucleotidyltransferase domain; InterPro: IPR024231 Poly(A) polymerase (2.7.7.19 from EC) catalyses template-independent extension of the 3'-end of a DNA or RNA strand by one nucleotide at a time. The Poxvirus enzyme creates the 3'(poly)A tail of mRNAs, and is a heterodimer of a catalytic and a regulatory subunit. This entry represents the nucleotidyltransferase domain of the catalytic subunit [].; PDB: 3ERC_C 3ER8_D 3OWG_A 2GA9_D 2GAF_D 3ER9_B.
Probab=22.13 E-value=1.4e+02 Score=29.57 Aligned_cols=63 Identities=22% Similarity=0.415 Sum_probs=34.2
Q ss_pred HHHHHHHHHHH---cCCCHHHHHHHHH---HHHHHHHHHHhh---cCCceEEeeccccCCCCCC---CCceEEeec
Q 005149 42 AEEATQGIIAQ---VQPTVVSEERRKA---VIDYVQRLIRNY---LGCEVFPFGSVPLKTYLPD---GDIDLTAFG 105 (712)
Q Consensus 42 le~ei~e~v~~---I~PT~eE~~~R~~---VI~~Vq~lI~~~---p~a~V~~FGS~~tGL~LP~---SDIDL~V~~ 105 (712)
+++...+.+.. ..|+. +...|.. .++.|.++++++ -.-+...||||.+-+--|+ +|||+.=..
T Consensus 5 ~~~ia~~~l~s~~v~~~~~-~~~grh~vS~lV~~V~klmeEyLrrhNk~CicYGSyslhllN~~I~YgDIDilqTN 79 (149)
T PF03296_consen 5 MEKIASDYLNSYNVANPSG-KVMGRHNVSDLVENVNKLMEEYLRRHNKSCICYGSYSLHLLNPNIKYGDIDILQTN 79 (149)
T ss_dssp GHHHHHHHHHHH--S--------------THHHHHHHHHHHHHHH-TTTEEEESHHHHHTTSTTS--SS-EEEEST
T ss_pred HHHHHHHHHHHhcccccCc-cccccccCcHHHHHHHHHHHHHHHhhCCCeEEeeeeeEEecCCCcccCcchhhhcc
Confidence 34445555533 34444 4444544 466677777754 4678999999998886665 999997553
No 55
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=21.64 E-value=2.4e+02 Score=31.15 Aligned_cols=43 Identities=23% Similarity=0.115 Sum_probs=31.7
Q ss_pred HHHHHHHHHHHh-hcCCceEEeeccccCCCCCCCCceEEeecCCc
Q 005149 65 AVIDYVQRLIRN-YLGCEVFPFGSVPLKTYLPDGDIDLTAFGGLN 108 (712)
Q Consensus 65 ~VI~~Vq~lI~~-~p~a~V~~FGS~~tGL~LP~SDIDL~V~~~~~ 108 (712)
.+.+.|.+.++. .+.++|.+-||+.-|--. .+|||++|..+..
T Consensus 149 ~i~~~i~~~l~~~~~~~~v~i~GSyRRgket-~gDIDili~~~~~ 192 (334)
T smart00483 149 AVEYIVKRAVRKILPDAIVTLTGSFRRGKET-GHDVDFLITSPHP 192 (334)
T ss_pred HHHHHHHHHHHhhCCCcEEEEecccccCCCc-CCCeeEEEecCCc
Confidence 344445555553 478999999999988654 6899999998763
No 56
>PF09970 DUF2204: Nucleotidyl transferase of unknown function (DUF2204); InterPro: IPR018700 This family of hypothetical prokaryotic proteins has no known function.
Probab=21.56 E-value=3.7e+02 Score=27.18 Aligned_cols=80 Identities=19% Similarity=0.191 Sum_probs=45.3
Q ss_pred cCCceEEeecccc----CCCCCCCCceEEeecCCcchhHHHHH-HHHHHHHHhhccccccceeeeEEEEeeeeeEEEeec
Q 005149 78 LGCEVFPFGSVPL----KTYLPDGDIDLTAFGGLNVEEALAND-VCSVLEREDQNKAAEFVVKDAQLIRAEVKLVKCLVQ 152 (712)
Q Consensus 78 p~a~V~~FGS~~t----GL~LP~SDIDL~V~~~~~~~e~l~~~-V~~iL~~~~~~~~a~f~V~~V~vI~ArVPIIK~~~~ 152 (712)
.+.++++.|+++. |.--.+.|||+.+..+... ...+ +..+.+.. .+... -.-..+.-.++++...
T Consensus 15 ~gv~~~ivGG~av~l~~g~~r~T~DIDlfi~~~~~~---~~~~~~~~~a~~~------g~~~~-~~~~~~~~~~~~~~~~ 84 (181)
T PF09970_consen 15 RGVEYVIVGGAAVNLAYGRRRTTKDIDLFIENPSPN---LEADALREVAEEN------GWDLG-WTDFGTPRYVVKVGGE 84 (181)
T ss_pred cCCeEEEECHHHHHHHhCCCCCCCCeEEEeCCCchH---HHHHHHHHHHHHc------CCCcC-ccccCCCceEEEeCCC
Confidence 4778999999974 4455689999999876432 1112 22221111 11100 0112233445666677
Q ss_pred CeeEEeeeccCCcchh
Q 005149 153 NIVVDISFNQLGGLST 168 (712)
Q Consensus 153 gI~VDISfNn~~Gl~~ 168 (712)
++.||+ +.+..|+..
T Consensus 85 ~v~IDl-~~ni~~~~v 99 (181)
T PF09970_consen 85 DVRIDL-LENIGDFYV 99 (181)
T ss_pred CeEEEc-hhccCCccc
Confidence 899999 667777643
No 57
>PRK05092 PII uridylyl-transferase; Provisional
Probab=21.53 E-value=4.7e+02 Score=33.01 Aligned_cols=29 Identities=24% Similarity=0.263 Sum_probs=26.3
Q ss_pred CceEEeeccccCCCCCCCCceEEeecCCc
Q 005149 80 CEVFPFGSVPLKTYLPDGDIDLTAFGGLN 108 (712)
Q Consensus 80 a~V~~FGS~~tGL~LP~SDIDL~V~~~~~ 108 (712)
+.|...|.|.-|=--|.|||||.++.+..
T Consensus 106 ~alvA~GgyGr~EL~p~SDiDLl~l~~~~ 134 (931)
T PRK05092 106 LAVLAVGGYGRGELAPGSDIDLLFLLPYK 134 (931)
T ss_pred eEEEEecCcCCcccCCCCCceEEEEeCCC
Confidence 57999999999999999999999998753
No 58
>PF12633 Adenyl_cycl_N: Adenylate cyclase NT domain; InterPro: IPR024685 Adenylate cyclase is the enzyme responsible for the synthesis of cAMP from ATP. On the basis of sequence similarity, it has been proposed that there are three different classes of adenylate cyclases [, ]. Class I cyclases are found in enterobacteria and related Gram-negative bacteria. This entry represents the N-terminal domain of class-I adenylate cyclases.
Probab=20.78 E-value=1.9e+02 Score=30.34 Aligned_cols=32 Identities=13% Similarity=0.196 Sum_probs=27.0
Q ss_pred ceEEeeccccCCCCCCCCceEEeecCCcchhH
Q 005149 81 EVFPFGSVPLKTYLPDGDIDLTAFGGLNVEEA 112 (712)
Q Consensus 81 ~V~~FGS~~tGL~LP~SDIDL~V~~~~~~~e~ 112 (712)
-|+.-||..+=--.+.||+|+=|+....+..+
T Consensus 99 GlY~MGS~gSi~Qs~~SDlDiWvCh~~~L~~~ 130 (204)
T PF12633_consen 99 GLYSMGSTGSIGQSSSSDLDIWVCHDSDLSPE 130 (204)
T ss_pred EEEecCCCccccCCCCCCCeEEEEcCCCCCHH
Confidence 48899999999999999999999887666443
Done!