Query 013307
Match_columns 445
No_of_seqs 216 out of 1381
Neff 7.3
Searched_HMMs 46136
Date Fri Mar 29 02:31:41 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/013307.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/013307hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG5260 TRF4 DNA polymerase si 100.0 9.5E-46 2E-50 373.3 25.4 287 4-335 54-344 (482)
2 KOG1906 DNA polymerase sigma [ 100.0 6.6E-39 1.4E-43 331.2 23.7 280 4-335 60-343 (514)
3 PTZ00418 Poly(A) polymerase; P 100.0 9.7E-36 2.1E-40 311.1 27.1 295 7-368 70-433 (593)
4 KOG2245 Poly(A) polymerase and 100.0 7.1E-30 1.5E-34 257.3 24.2 273 6-344 32-359 (562)
5 KOG2277 S-M checkpoint control 100.0 3E-29 6.6E-34 271.5 27.3 316 6-335 113-432 (596)
6 COG5186 PAP1 Poly(A) polymeras 99.9 3.9E-23 8.4E-28 201.2 21.3 263 16-342 36-349 (552)
7 PF04928 PAP_central: Poly(A) 99.9 4.1E-23 8.8E-28 199.1 12.4 217 6-343 21-252 (254)
8 cd05402 NT_PAP_TUTase Nucleoti 99.9 1.2E-22 2.5E-27 173.6 13.2 114 27-149 1-114 (114)
9 TIGR03671 cca_archaeal CCA-add 99.8 6.7E-17 1.5E-21 164.2 26.0 236 11-328 2-252 (408)
10 PRK13300 tRNA CCA-pyrophosphor 99.8 1E-16 2.3E-21 165.2 27.1 241 11-335 3-259 (447)
11 COG1746 CCA1 tRNA nucleotidylt 99.7 1.9E-15 4.1E-20 151.6 20.7 243 6-334 2-260 (443)
12 PF03828 PAP_assoc: Cid1 famil 99.0 1.1E-10 2.5E-15 87.9 2.6 55 249-306 1-60 (60)
13 PF03813 Nrap: Nrap protein; 98.9 1.5E-07 3.3E-12 107.4 21.4 236 55-336 1-302 (972)
14 PF09249 tRNA_NucTransf2: tRNA 98.5 6E-07 1.3E-11 75.3 7.5 103 159-334 3-107 (114)
15 smart00572 DZF domain in DSRM 98.2 2.4E-05 5.2E-10 74.9 14.2 200 49-335 4-233 (246)
16 cd05397 NT_Pol-beta-like Nucle 98.0 1.1E-05 2.4E-10 58.2 5.4 41 30-72 2-42 (49)
17 cd05400 NT_2-5OAS_ClassI-CCAas 98.0 7E-05 1.5E-09 66.1 11.3 97 28-131 9-106 (143)
18 PF01909 NTP_transf_2: Nucleot 97.9 1.1E-05 2.4E-10 65.6 3.6 43 32-76 1-43 (93)
19 KOG2054 Nucleolar RNA-associat 97.7 0.00059 1.3E-08 75.7 14.4 233 46-335 146-437 (1121)
20 PF10421 OAS1_C: 2'-5'-oligoad 97.5 0.00097 2.1E-08 61.5 10.2 56 140-195 28-85 (190)
21 cd05403 NT_KNTase_like Nucleot 97.4 0.00024 5.2E-09 57.3 5.5 45 31-76 3-47 (93)
22 COG1669 Predicted nucleotidylt 97.0 0.0049 1.1E-07 50.7 8.3 44 31-76 10-53 (97)
23 PF07528 DZF: DZF domain; Int 96.8 0.058 1.3E-06 52.4 15.6 197 53-335 2-235 (248)
24 PF03813 Nrap: Nrap protein; 96.5 1.1 2.3E-05 52.1 25.5 262 21-334 497-826 (972)
25 COG1708 Predicted nucleotidylt 96.3 0.0075 1.6E-07 51.3 5.7 30 45-74 24-53 (128)
26 PF14091 DUF4269: Domain of un 95.9 0.14 3E-06 45.8 11.3 113 47-172 15-142 (152)
27 PRK13746 aminoglycoside resist 95.9 0.033 7.1E-07 54.5 8.1 29 48-76 29-57 (262)
28 KOG2054 Nucleolar RNA-associat 94.3 5.5 0.00012 45.4 20.4 140 145-335 811-958 (1121)
29 PF14792 DNA_pol_B_palm: DNA p 92.9 0.27 5.8E-06 41.8 5.9 71 30-107 9-79 (112)
30 KOG3793 Transcription factor N 92.4 3.7 7.9E-05 40.0 13.2 70 4-74 38-114 (362)
31 PRK02098 phosphoribosyl-dephos 92.4 0.19 4.1E-06 48.0 4.7 40 32-75 109-154 (221)
32 TIGR03135 malonate_mdcG holo-A 91.6 0.27 5.8E-06 46.3 4.7 30 46-75 107-142 (202)
33 cd00141 NT_POLXc Nucleotidyltr 91.4 1.8 3.8E-05 43.5 10.7 124 32-173 147-271 (307)
34 cd05401 NT_GlnE_GlnD_like Nucl 82.9 13 0.00029 33.4 10.2 29 47-75 55-83 (172)
35 PF10620 MdcG: Phosphoribosyl- 80.0 4.7 0.0001 38.2 6.3 41 31-75 104-150 (213)
36 PF03445 DUF294: Putative nucl 79.5 24 0.00052 30.9 10.3 30 46-75 48-77 (138)
37 PF10127 Nuc-transf: Predicted 79.1 1.9 4.1E-05 41.7 3.4 46 28-74 2-47 (247)
38 PRK00227 glnD PII uridylyl-tra 77.6 4.9 0.00011 44.8 6.4 50 25-75 5-55 (693)
39 COG2413 Predicted nucleotidylt 72.9 6.3 0.00014 36.9 4.8 44 26-74 21-64 (228)
40 COG1796 POL4 DNA polymerase IV 72.8 55 0.0012 33.0 11.6 123 30-178 165-287 (326)
41 KOG2534 DNA polymerase IV (fam 72.1 25 0.00053 35.3 8.9 64 31-104 157-220 (353)
42 PF09970 DUF2204: Nucleotidyl 70.3 19 0.00041 33.2 7.5 92 34-141 4-99 (181)
43 PRK01759 glnD PII uridylyl-tra 68.4 26 0.00056 40.3 9.6 29 47-75 56-84 (854)
44 PRK05007 PII uridylyl-transfer 66.9 31 0.00066 39.9 9.8 30 46-75 79-108 (884)
45 PRK01293 phosphoribosyl-dephos 65.4 14 0.0003 34.9 5.6 30 46-75 108-143 (207)
46 COG2844 GlnD UTP:GlnB (protein 65.3 21 0.00045 40.2 7.6 30 47-76 66-95 (867)
47 PHA02603 nrdC.11 hypothetical 64.7 3.9 8.5E-05 41.3 1.9 25 49-73 5-29 (330)
48 PRK08609 hypothetical protein; 59.8 52 0.0011 36.0 9.6 117 32-177 162-281 (570)
49 PRK04374 PII uridylyl-transfer 59.1 57 0.0012 37.6 10.1 51 25-75 48-100 (869)
50 COG3541 Predicted nucleotidylt 59.0 5.1 0.00011 38.6 1.4 21 53-73 16-36 (248)
51 smart00483 POLXc DNA polymeras 56.9 26 0.00056 35.6 6.2 43 30-75 149-191 (334)
52 PF03296 Pox_polyA_pol: Poxvir 55.0 78 0.0017 27.9 7.8 106 7-130 8-123 (149)
53 PRK00275 glnD PII uridylyl-tra 50.4 96 0.0021 35.9 10.1 29 47-75 78-106 (895)
54 COG1665 Predicted nucleotidylt 49.6 19 0.00041 35.4 3.6 29 45-73 119-147 (315)
55 TIGR01693 UTase_glnD [Protein- 48.5 1.2E+02 0.0026 34.9 10.5 30 46-75 42-71 (850)
56 PRK03059 PII uridylyl-transfer 46.9 61 0.0013 37.3 7.8 29 47-75 61-89 (856)
57 PHA02996 poly(A) polymerase la 44.9 99 0.0021 32.0 8.0 112 5-135 123-244 (467)
58 PRK03381 PII uridylyl-transfer 43.1 51 0.0011 37.5 6.3 29 47-75 57-85 (774)
59 PF03710 GlnE: Glutamate-ammon 41.8 75 0.0016 30.7 6.5 52 47-99 127-178 (247)
60 PF04229 GrpB: GrpB protein; 40.5 72 0.0016 28.8 5.9 105 47-167 32-142 (167)
61 PRK03333 coaE dephospho-CoA ki 39.7 3.8E+02 0.0082 27.8 11.8 152 5-169 180-361 (395)
62 PRK05092 PII uridylyl-transfer 27.5 54 0.0012 38.1 3.4 29 47-75 105-133 (931)
63 PF12633 Adenyl_cycl_N: Adenyl 26.9 1.7E+02 0.0036 27.7 5.9 27 49-75 99-125 (204)
64 PF11774 Lsr2: Lsr2 ; InterPr 26.8 54 0.0012 27.7 2.5 64 117-182 21-102 (110)
65 cd05398 NT_ClassII-CCAase Nucl 24.4 4.7E+02 0.01 22.7 8.2 69 47-135 16-86 (139)
66 PRK14109 bifunctional glutamin 23.3 1.5E+02 0.0033 34.8 6.1 29 47-75 723-751 (1007)
67 PF14907 NTP_transf_5: Unchara 20.3 5.4E+02 0.012 24.1 8.4 38 34-72 59-102 (249)
No 1
>COG5260 TRF4 DNA polymerase sigma [DNA replication, recombination, and repair]
Probab=100.00 E-value=9.5e-46 Score=373.29 Aligned_cols=287 Identities=25% Similarity=0.363 Sum_probs=240.5
Q ss_pred ccchHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHhhhcCCCcEEEEecccccCCCCCCCCcceEEeecCCCcccccc
Q 013307 4 YNVLEPILKDILGMLNPLREDWETRMKVISDLREVVESVESLRGATVEPFGSFVSNLFSRWGDLDISIELSNGSCISSAG 83 (445)
Q Consensus 4 ~~~L~~ei~~f~~~~~Pt~ee~~~R~~vi~~l~~il~~~~~~~~~~v~~fGS~~tGl~l~~SDIDl~i~~~~~~~iss~~ 83 (445)
.+.|+.+|.+|+.++.|+.+|.+.|.++++.|+.++++. +|++.+.+|||+.+|++++.|||||||.+++..+
T Consensus 54 ~~~lt~el~~~y~~I~ps~eEl~~R~~~leklr~~lk~~--~pda~l~vFGS~~t~L~l~~SDiDl~I~s~~~~~----- 126 (482)
T COG5260 54 SDELTSELLEFYDYIAPSDEELKRRKALLEKLRTLLKKE--FPDADLKVFGSTETGLALPKSDIDLCIISDPRGY----- 126 (482)
T ss_pred HHHHHHHHHHHHHhhCCCHHHHHHHHHHHHHHHHHHHHh--CCccceeEecccccccccCcccccEEEecCCccc-----
Confidence 357999999999999999999999999999999999998 7999999999999999999999999998865321
Q ss_pred hhhHHHHHHHHHHHHHhcCCceEEEEecccccceEEEEeeccceEEEEeecccccccccHHHhHHhcccchhHHHHHHHH
Q 013307 84 KKVKQSLLGDLLRALRQKGGYRRLQFVAHARVPILKFETIHQNISCDISIDNLCGQIKSKFLFWISQIDGRFRDMVLLVK 163 (445)
Q Consensus 84 k~~~~~~L~~l~~~L~~~~~~~~v~~I~~ArVPIIk~~~~~~gi~~DIs~~n~~g~~~s~ll~~~~~~~~~~r~Lv~~iK 163 (445)
+..+ ... .++..+.....+.+++++.+||||||||.++.+|+.|||+|++..|+.++.+++.|.+.+|++|+|+++||
T Consensus 127 ~et~-~~~-~l~~~l~~~~~~~~~~~v~tarVPIIKl~d~~s~l~~Disfn~~~~~~~akl~~~~~~~~P~lrpLvliIK 204 (482)
T COG5260 127 KETR-NAG-SLASHLFKKNLAKEVVVVSTARVPIIKLVDPQSGLHCDISFNNTNGIVNAKLIRSYLKEDPRLRPLVLIIK 204 (482)
T ss_pred cccc-cHH-HHHHHHHHhccCeeeEEEEecccceEEEecCccceEEEeecCchhHHHHHHHHHHHHhcCcccchHHHHHH
Confidence 2122 222 45555656677889999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHCCCCCCCCCCCcchHHHHHHHHHhhhcCCCCCCCccccCCCCCCCcccccchhhhhHHHHHhhcccccccccccc
Q 013307 164 EWAKAHDINNPKTGTFNSYSLSLLVLFHFQTCVPAILPPLKDIYPGNLVDDLKGVRANAERQIAEICAFNIARFSSDKYR 243 (445)
Q Consensus 164 ~Wak~rgL~~~~~G~Lssy~l~lMvi~fLQ~~~p~ilP~Lq~l~~~~~~~~~~~~~~~~e~~~~e~~~~n~~~~~~~~~~ 243 (445)
+||+.|.|++++.|||+||++++||+.|||++.|. +.+ +...... ...
T Consensus 205 hwl~~R~ln~~~~GtL~sy~i~cmV~sfLq~~~~~--~~~----~~~~~~~--------------------------l~~ 252 (482)
T COG5260 205 HWLKRRALNDVATGTLSSYTISCMVLSFLQMHPPF--LFF----DNGLLSP--------------------------LKY 252 (482)
T ss_pred HHHHHHhhcccccCcchhhhhHHHHHHHHHhCCcc--ccc----cccccch--------------------------hhc
Confidence 99999999999999999999999999999999431 111 1110000 001
Q ss_pred cCCCCCHHHHHHHHHHhhccCCCCcccceeeccCC-ceeeecccCCCCC-C-CCCeEEecCC-CCCCCccccCCHHHHHH
Q 013307 244 KINRSSLAHLFVSFLEKFSGLSLKASELGICPFTG-QWEHIRSNTRWLP-N-NHPLFIEDPF-EQPENSARAVSEKNLAK 319 (445)
Q Consensus 244 ~~n~~sl~~LL~~FF~~Ys~~df~~~~~~Is~~~g-~~~~~~~~~~~~~-~-~~~L~I~DPf-~~~~Nvar~vs~~~~~~ 319 (445)
..|..++|.||.+||+||+ ..|+|..+++++..| .+.++. .++|.. - ...|+||||+ ++++++++. .+++..
T Consensus 253 ~~~~~~lgvLf~dFf~~yG-~~f~Y~~~~~si~~g~~~~~K~-e~g~~~~~~p~~LsiqdP~td~n~~~~a~--s~~ik~ 328 (482)
T COG5260 253 NKNIDNLGVLFDDFFELYG-KSFNYSLVVLSINSGDFYLPKY-EKGWLKPSKPNSLSIQDPGTDRNNDISAV--SFNIKD 328 (482)
T ss_pred cccccccchHHHHHHHHhc-cccChhheEEEecCCceeeehh-hcccccccCCCcEeecCCCCCcccccccc--cchHHH
Confidence 3456789999999999998 799999999999998 344433 366743 2 2689999999 888888875 678999
Q ss_pred HHHHHHHHHHHhhccC
Q 013307 320 ISNAFEMTHFRLTSTN 335 (445)
Q Consensus 320 I~~~f~~A~~~L~~~~ 335 (445)
++.+|.+|.++|.+..
T Consensus 329 i~~~F~~aF~lls~~~ 344 (482)
T COG5260 329 IKAAFIRAFELLSNKL 344 (482)
T ss_pred HHHHHHHHHHHHhhhc
Confidence 9999999999999865
No 2
>KOG1906 consensus DNA polymerase sigma [Replication, recombination and repair]
Probab=100.00 E-value=6.6e-39 Score=331.19 Aligned_cols=280 Identities=26% Similarity=0.349 Sum_probs=229.3
Q ss_pred ccchHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHhhhcCCCcEEEEecccccCCCCCCCCcceEEeecCCCcccccc
Q 013307 4 YNVLEPILKDILGMLNPLREDWETRMKVISDLREVVESVESLRGATVEPFGSFVSNLFSRWGDLDISIELSNGSCISSAG 83 (445)
Q Consensus 4 ~~~L~~ei~~f~~~~~Pt~ee~~~R~~vi~~l~~il~~~~~~~~~~v~~fGS~~tGl~l~~SDIDl~i~~~~~~~iss~~ 83 (445)
...|++||.+|++++.||.+|.+.|..+++.++..|.+. ||++.|.+|||+.||++||+|||||++..+.-. .
T Consensus 60 s~~l~~eI~~fv~~l~pt~~e~~~R~~~~~~i~~~v~~~--~~~a~v~~FGS~~tglyLP~sDIDl~v~~~~~~-----~ 132 (514)
T KOG1906|consen 60 SERLRNEILDFVQYLIPTPEEIEVRSELVEKIRDVVKQK--WPDASVYVFGSVPTGLYLPDSDIDLVVLSKFLN-----D 132 (514)
T ss_pred HHHHHHHHHHHHHHhcCCchHHHHHHHHHHHHHHHHHHh--cccceeEEeeeeeccccccccceEEEEeccccc-----C
Confidence 467999999999999999999999999999999999976 899999999999999999999999999776321 1
Q ss_pred hhhHHHHHHHHHHHHHhcCCceEEEEecccccceEEEEeeccceEEEEeecccccccccHHHhHHhcccchhHHHHHHHH
Q 013307 84 KKVKQSLLGDLLRALRQKGGYRRLQFVAHARVPILKFETIHQNISCDISIDNLCGQIKSKFLFWISQIDGRFRDMVLLVK 163 (445)
Q Consensus 84 k~~~~~~L~~l~~~L~~~~~~~~v~~I~~ArVPIIk~~~~~~gi~~DIs~~n~~g~~~s~ll~~~~~~~~~~r~Lv~~iK 163 (445)
+ +.......++..++....-..+.++..|||||+||++..++|.+|||||+.+|++.+++++++.+.+|.++.|++++|
T Consensus 133 ~-e~~~~~~~l~~~~e~~~~~~~v~~v~karvpiik~~d~~s~i~vDISFn~~~G~~aa~~i~~~~~~~p~~~~lvlvlk 211 (514)
T KOG1906|consen 133 K-EDRAVKLELALELEEDNSAFHVKVVQKARVPIIKFKDPVSNIHVDISFNQTNGVKAAKFIKDFLRDHPFLRSLVLVLK 211 (514)
T ss_pred c-hhhHHHHHHHHhhhhccccceEEEeeeeeeeeEEeecCccceEEEeeecccCchhHHHHHHHHHhcCccchhHHHHHH
Confidence 1 112223333333433444566888999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHCCCCCCCCCCCcchHHHHHHHHHhhhcCCCCCCCccccCCCCCCCcccccchhhhhHHHHHhhcccccccccccc
Q 013307 164 EWAKAHDINNPKTGTFNSYSLSLLVLFHFQTCVPAILPPLKDIYPGNLVDDLKGVRANAERQIAEICAFNIARFSSDKYR 243 (445)
Q Consensus 164 ~Wak~rgL~~~~~G~Lssy~l~lMvi~fLQ~~~p~ilP~Lq~l~~~~~~~~~~~~~~~~e~~~~e~~~~n~~~~~~~~~~ 243 (445)
+|+..|++++++.||++||++++|+++|||++. .+ + .+ .
T Consensus 212 ~fl~~r~ln~v~tGgisSyal~~Lv~~fl~l~~-~~----~---s~----~----------------------------- 250 (514)
T KOG1906|consen 212 QFLYERRLNGVHTGGISSYALELLVLSFLQLHP-RS----K---SG----R----------------------------- 250 (514)
T ss_pred HHHHhhcccccccccchHHHHHHHHHHHHhhcc-cc----c---CC----c-----------------------------
Confidence 999999999999999999999999999999982 10 0 00 0
Q ss_pred cCCCCCHHHHHHHHHHhhccCCCCcccceeeccCCceeeecccCCCC----CCCCCeEEecCCCCCCCccccCCHHHHHH
Q 013307 244 KINRSSLAHLFVSFLEKFSGLSLKASELGICPFTGQWEHIRSNTRWL----PNNHPLFIEDPFEQPENSARAVSEKNLAK 319 (445)
Q Consensus 244 ~~n~~sl~~LL~~FF~~Ys~~df~~~~~~Is~~~g~~~~~~~~~~~~----~~~~~L~I~DPf~~~~Nvar~vs~~~~~~ 319 (445)
......++.||+.||++|| +.|.+.+++|+...+......+...|. .....|+|+||.+|.+|+||+ .+++..
T Consensus 251 ~~~~~~~~vll~~f~e~yG-~~f~~~k~~i~~~~~g~~~~~~~~~~~~~~~~~~~~LsieDP~~P~ndigr~--s~~~~~ 327 (514)
T KOG1906|consen 251 LAVLKNLGVLLIKFFELYG-RNFGYDKLGISLSLGGEYVSKELTGFFNNSLERPGSLSIEDPVDPTNDIGRS--SFNFSQ 327 (514)
T ss_pred cchhcccchHHHHHHHHhc-cccCchhhceeccCCcccccHHhhhhhcccccCCCccccCCCCCcccccccc--cccHHH
Confidence 0012346799999999998 788888899987654432222222222 124569999999999999996 588999
Q ss_pred HHHHHHHHHHHhhccC
Q 013307 320 ISNAFEMTHFRLTSTN 335 (445)
Q Consensus 320 I~~~f~~A~~~L~~~~ 335 (445)
|+.+|..|+..|..+.
T Consensus 328 v~~~F~~af~~l~~~~ 343 (514)
T KOG1906|consen 328 VKGAFAYAFKVLTNAV 343 (514)
T ss_pred HHHHHHHHHHHHhhhh
Confidence 9999999999999875
No 3
>PTZ00418 Poly(A) polymerase; Provisional
Probab=100.00 E-value=9.7e-36 Score=311.11 Aligned_cols=295 Identities=21% Similarity=0.264 Sum_probs=233.5
Q ss_pred hHHHHHHHHHH--cCCCHHHHHHHHHHHHHHHHHHHhhh--------------cCCCcEEEEecccccCCCCCCCCcceE
Q 013307 7 LEPILKDILGM--LNPLREDWETRMKVISDLREVVESVE--------------SLRGATVEPFGSFVSNLFSRWGDLDIS 70 (445)
Q Consensus 7 L~~ei~~f~~~--~~Pt~ee~~~R~~vi~~l~~il~~~~--------------~~~~~~v~~fGS~~tGl~l~~SDIDl~ 70 (445)
+..+|.++++. +.|++||.++|+++++.|++++++.. ...+.+|++||||.+|++.|+||||++
T Consensus 70 ~s~~L~~~L~~~~~fes~ee~~kR~~vL~~L~~iv~~wv~~vs~~k~~~~~~~~~~~g~I~tfGSYrLGV~~pgSDID~L 149 (593)
T PTZ00418 70 LSNELINLLKSYNLYETEEGKKKRERVLGSLNKLVREFVVEASIEQGINEEEASQISGKLFTFGSYRLGVVAPGSDIDTL 149 (593)
T ss_pred hhHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCChhHHhcCCeEEEEeccccccCCCCCCcccEE
Confidence 45566666554 67999999999999999999997631 124689999999999999999999999
Q ss_pred EeecCCCcccccchhhHHHHHHHHHHHHHhcCCceEEEEecccccceEEEEeeccceEEEEeeccc--------------
Q 013307 71 IELSNGSCISSAGKKVKQSLLGDLLRALRQKGGYRRLQFVAHARVPILKFETIHQNISCDISIDNL-------------- 136 (445)
Q Consensus 71 i~~~~~~~iss~~k~~~~~~L~~l~~~L~~~~~~~~v~~I~~ArVPIIk~~~~~~gi~~DIs~~n~-------------- 136 (445)
|+.|.. ++ +..|+..+.+.|++.+.+.+++.|..|+||||||+. .||.|||.|...
T Consensus 150 ~V~P~~--vt------redFF~~f~~~L~~~~~V~eL~~V~~A~VPiIk~~~--~GI~iDL~fa~l~~~~vp~~~~~l~d 219 (593)
T PTZ00418 150 CLAPRH--IT------RESFFSDFYAKLQQDPNITKLQPVPDAYTPVIKFVY--DGIDIDLLFANLPLPTIPDCLNSLDD 219 (593)
T ss_pred EECCCC--CC------HHHHHHHHHHHHhcCCCcceeeccCccccCeEEEEE--CCEEEeeeecccCCCCCCccccccCc
Confidence 988863 21 357999999999999999999999999999999998 799999998621
Q ss_pred ---------------ccccccHHHhHHhcccchhHHHHHHHHHHHHHCCCCCCCCCCCcchHHHHHHHHHhhhcCCCCCC
Q 013307 137 ---------------CGQIKSKFLFWISQIDGRFRDMVLLVKEWAKAHDINNPKTGTFNSYSLSLLVLFHFQTCVPAILP 201 (445)
Q Consensus 137 ---------------~g~~~s~ll~~~~~~~~~~r~Lv~~iK~Wak~rgL~~~~~G~Lssy~l~lMvi~fLQ~~~p~ilP 201 (445)
+|++.+..|....--...||.++++||.|||+||||++..|+|||.+|+|||...||..
T Consensus 220 ~~lL~nlde~s~rSLNG~Rvtd~Il~lVPn~~~Fr~aLR~IKlWAkrRGIYsNv~GflGGV~wAILvARVCQLy------ 293 (593)
T PTZ00418 220 DYILRNVDEKTVRSLNGCRVADLILASVPNKDYFRTTLRFIKLWAKRRGIYSNVLGYLGGVSWAILTARICQLY------ 293 (593)
T ss_pred hhhhhcCCHHHhhhhccHHHHHHHHHHCCChHHHHHHHHHHHHHHHHhccccccccccchHHHHHHHHHHHHhC------
Confidence 34455555544444446899999999999999999999999999999999999999996
Q ss_pred CccccCCCCCCCcccccchhhhhHHHHHhhcccccccccccccCCCCCHHHHHHHHHHhhccCCCCcccceeec-cC---
Q 013307 202 PLKDIYPGNLVDDLKGVRANAERQIAEICAFNIARFSSDKYRKINRSSLAHLFVSFLEKFSGLSLKASELGICP-FT--- 277 (445)
Q Consensus 202 ~Lq~l~~~~~~~~~~~~~~~~e~~~~e~~~~n~~~~~~~~~~~~n~~sl~~LL~~FF~~Ys~~df~~~~~~Is~-~~--- 277 (445)
| ..+.+.|+..||.+|++|+|... +.++. ..
T Consensus 294 ------P--------------------------------------na~~s~Lv~~FF~iys~W~Wp~P-V~L~~i~~~~~ 328 (593)
T PTZ00418 294 ------P--------------------------------------NFAPSQLIHKFFRVYSIWNWKNP-VLLCKIKEVPN 328 (593)
T ss_pred ------C--------------------------------------CCCHHHHHHHHHHHhhcCCCCCC-eEccccccccc
Confidence 1 13579999999999999999853 33332 11
Q ss_pred -CceeeecccCCCCC------CCCCeEEecCCCCCCCccccCCHHHHHHHHHHHHHHHHHhhc----cCCCcchhhhc--
Q 013307 278 -GQWEHIRSNTRWLP------NNHPLFIEDPFEQPENSARAVSEKNLAKISNAFEMTHFRLTS----TNQTRYALLSS-- 344 (445)
Q Consensus 278 -g~~~~~~~~~~~~~------~~~~L~I~DPf~~~~Nvar~vs~~~~~~I~~~f~~A~~~L~~----~~~~~~s~L~~-- 344 (445)
.+.. .-..|.| +.+.|.|..|..|..|.+.+|+..+++.|.+||++|.+++.. ...+|..+|+.
T Consensus 329 ~~g~~---~~~VWdPr~~~~dr~h~MPIITPayP~mNst~nVt~sT~~vI~~Ef~Ra~~i~~~i~~~~~~~W~~Lfep~~ 405 (593)
T PTZ00418 329 IPGLM---NFKVWDPRVNPQDRAHLMPIITPAFPSMNSTHNVTYTTKRVITEEFKRAHEIIKYIEKNSENTWTNVLEPLD 405 (593)
T ss_pred CCccc---CCcccCCCCCcccccccCCeecCCCCCccccccccHHHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHcCCcc
Confidence 1110 0112443 346899999999999999999999999999999999999994 44567777643
Q ss_pred -------ccccccccccccCCCcccccCCCC
Q 013307 345 -------LARPFILQFFGESPVRYANYNNGH 368 (445)
Q Consensus 345 -------~~~~~~~~~~~~~~~~~~~~~~~~ 368 (445)
+++.+ .++.+...+..+.||+
T Consensus 406 Ff~~Yk~yl~V~---v~a~~~~~~~~w~G~V 433 (593)
T PTZ00418 406 FFTSYKHFLVIQ---VYATNEHVHNKWEGWI 433 (593)
T ss_pred hhhhcceEEEEE---EEECCHHHhhhhhhHH
Confidence 24444 4777776677777887
No 4
>KOG2245 consensus Poly(A) polymerase and related nucleotidyltransferases [RNA processing and modification]
Probab=99.97 E-value=7.1e-30 Score=257.31 Aligned_cols=273 Identities=22% Similarity=0.278 Sum_probs=216.2
Q ss_pred chHHHHHHHH--HHcCCCHHHHHHHHHHHHHHHHHHHhhhc--------------CCCcEEEEecccccCCCCCCCCcce
Q 013307 6 VLEPILKDIL--GMLNPLREDWETRMKVISDLREVVESVES--------------LRGATVEPFGSFVSNLFSRWGDLDI 69 (445)
Q Consensus 6 ~L~~ei~~f~--~~~~Pt~ee~~~R~~vi~~l~~il~~~~~--------------~~~~~v~~fGS~~tGl~l~~SDIDl 69 (445)
.|..+|.+.+ ..+.+++||...|..++..|+.++++..+ ..+.++.+||||.+|++.+++|||-
T Consensus 32 ~lt~~L~~~L~~~g~fEs~eEt~~R~~VL~~L~~iVk~wVk~vs~~k~~p~~~~~~aggkIftfGSYRLGVhg~GADIDt 111 (562)
T KOG2245|consen 32 ALTQELIKTLKNEGLFESKEETQRREEVLGKLNQIVKEWVKKVSEQKGLPDGMIENAGGKIFTFGSYRLGVHGPGADIDT 111 (562)
T ss_pred HHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCChhhhhhcCceEEeccceeecccCCCCCcce
Confidence 4555555544 34668999999999999999999986421 2468999999999999999999999
Q ss_pred EEeecCCCcccccchhhHHHHHHHHHHHHHhcCCceEEEEecccccceEEEEeeccceEEEEeeccc-------------
Q 013307 70 SIELSNGSCISSAGKKVKQSLLGDLLRALRQKGGYRRLQFVAHARVPILKFETIHQNISCDISIDNL------------- 136 (445)
Q Consensus 70 ~i~~~~~~~iss~~k~~~~~~L~~l~~~L~~~~~~~~v~~I~~ArVPIIk~~~~~~gi~~DIs~~n~------------- 136 (445)
.|+.|... .+.+|+..+...|+....+.++..+..|.||||||+. .||++||-|...
T Consensus 112 LcV~Prhv--------~R~DFF~sf~~mL~~~~eVteL~~V~dAfVPiikfKf--~GI~IDllfArL~l~~VP~dldl~d 181 (562)
T KOG2245|consen 112 LCVGPRHV--------SRSDFFTSFYDMLKERPEVTELHAVEDAFVPIIKFKF--DGIEIDLLFARLALPVVPEDLDLSD 181 (562)
T ss_pred eeeccccc--------cHHHHHHHHHHHHhcCccccccccccccccceEEEEe--cCeeeeeeehhcccccCCCcccccc
Confidence 99888642 2347999999999999999999999999999999998 899999977531
Q ss_pred ---------------ccccccH-HHhHHhcccchhHHHHHHHHHHHHHCCCCCCCCCCCcchHHHHHHHHHhhhcCCCCC
Q 013307 137 ---------------CGQIKSK-FLFWISQIDGRFRDMVLLVKEWAKAHDINNPKTGTFNSYSLSLLVLFHFQTCVPAIL 200 (445)
Q Consensus 137 ---------------~g~~~s~-ll~~~~~~~~~~r~Lv~~iK~Wak~rgL~~~~~G~Lssy~l~lMvi~fLQ~~~p~il 200 (445)
+|++-++ +|+..-. ...|+..+++||.|||.||+|+...|+|||.+|.|||+..||..
T Consensus 182 dslLknlDe~~vrSLNGcRVtdqiL~LVPn-~~~F~~tLRaiKlWAKrrgVYsN~~GF~GGV~wA~LVARiCQLY----- 255 (562)
T KOG2245|consen 182 DSLLKNLDERCVRSLNGCRVTDQILKLVPN-QENFRITLRAIKLWAKRRGVYSNVMGFLGGVAWAMLVARICQLY----- 255 (562)
T ss_pred hHhhhcccHHHHHHhcCcCHHHHHHHhCCC-HHHHHHHHHHHHHHHHhcccccccccccchHHHHHHHHHHHccC-----
Confidence 2334332 2222222 24699999999999999999999999999999999999999996
Q ss_pred CCccccCCCCCCCcccccchhhhhHHHHHhhcccccccccccccCCCCCHHHHHHHHHHhhccCCCCcccceeec-cCCc
Q 013307 201 PPLKDIYPGNLVDDLKGVRANAERQIAEICAFNIARFSSDKYRKINRSSLAHLFVSFLEKFSGLSLKASELGICP-FTGQ 279 (445)
Q Consensus 201 P~Lq~l~~~~~~~~~~~~~~~~e~~~~e~~~~n~~~~~~~~~~~~n~~sl~~LL~~FF~~Ys~~df~~~~~~Is~-~~g~ 279 (445)
|+ .+...|+..||.-|++|.|... +.+++ ..|.
T Consensus 256 -------PN--------------------------------------A~~s~Lv~kfF~ifs~W~WP~P-VlL~~ie~~~ 289 (562)
T KOG2245|consen 256 -------PN--------------------------------------ASPSTLVAKFFRVFSQWNWPNP-VLLKPIEEGN 289 (562)
T ss_pred -------CC--------------------------------------cchHHHHHHHHHHHhhccCCCc-eEeccccccc
Confidence 21 3568899999999999999854 34443 2332
Q ss_pred eeeecccCCCCC------CCCCeEEecCCCCCCCccccCCHHHHHHHHHHHHHHHHHhhccC---CCcchhhhc
Q 013307 280 WEHIRSNTRWLP------NNHPLFIEDPFEQPENSARAVSEKNLAKISNAFEMTHFRLTSTN---QTRYALLSS 344 (445)
Q Consensus 280 ~~~~~~~~~~~~------~~~~L~I~DPf~~~~Nvar~vs~~~~~~I~~~f~~A~~~L~~~~---~~~~s~L~~ 344 (445)
... .-|.| +.+.|.|+.|..|..|.+.+|+.++...|.+||.+|..++..-. .+|..+|..
T Consensus 290 L~~----~VWdPr~n~~DryHlMPIITPAyP~~nsthNVS~ST~~Vi~~Ef~~g~~I~~~i~~~k~~W~~LFE~ 359 (562)
T KOG2245|consen 290 LNL----PVWDPRVNPSDRYHLMPIITPAYPQMNSTHNVSRSTLKVITEEFKRGLEICDDIELNKLDWSDLFEL 359 (562)
T ss_pred cCc----cccCCCCCCCCcceecccccCCcccccccccccHHHHHHHHHHHHHHHHHHHHHHhccccHHHHhhh
Confidence 110 12433 34579999999999999999999999999999999999988543 468777643
No 5
>KOG2277 consensus S-M checkpoint control protein CID1 and related nucleotidyltransferases [Cell cycle control, cell division, chromosome partitioning]
Probab=99.97 E-value=3e-29 Score=271.46 Aligned_cols=316 Identities=30% Similarity=0.442 Sum_probs=247.3
Q ss_pred chHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHhhhcCCCcEEEEecccccCCCCCCCCcceEEeecCCCcccccchh
Q 013307 6 VLEPILKDILGMLNPLREDWETRMKVISDLREVVESVESLRGATVEPFGSFVSNLFSRWGDLDISIELSNGSCISSAGKK 85 (445)
Q Consensus 6 ~L~~ei~~f~~~~~Pt~ee~~~R~~vi~~l~~il~~~~~~~~~~v~~fGS~~tGl~l~~SDIDl~i~~~~~~~iss~~k~ 85 (445)
.|+..+...++...+...+...|......++.++....+.....+..|||...|+....+|+|+++.+.... . +..+.
T Consensus 113 ~l~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~p~~~~~~~~~gs~~~~~~~~~~d~d~~~~~~~~~-~-~~~~~ 190 (596)
T KOG2277|consen 113 FLDPQLNELLESFKLPHSDVKTRKLILDKLRALASLLFPDSILSLYLFGSSDLGLGERSSDLDLCVDFTSSF-L-SFEKI 190 (596)
T ss_pred hhchhhhhhhhccCCCccccchHHHHHHHHHHHHHHhcCCCcceeeccCcccccccccccCcceeecccccc-c-ccchh
Confidence 477888889999999999999999999999999988743333445699999999999999999776554431 1 11222
Q ss_pred hHHHHHHHHHHHHHhcCC--ceEEEEecccccceEEEEeeccceEEEEeecccccccccHHHhHHhcccchhHHHHHHHH
Q 013307 86 VKQSLLGDLLRALRQKGG--YRRLQFVAHARVPILKFETIHQNISCDISIDNLCGQIKSKFLFWISQIDGRFRDMVLLVK 163 (445)
Q Consensus 86 ~~~~~L~~l~~~L~~~~~--~~~v~~I~~ArVPIIk~~~~~~gi~~DIs~~n~~g~~~s~ll~~~~~~~~~~r~Lv~~iK 163 (445)
....++..+++++..... +..++.+..|+|||||+.+...+++||++++|..++.||.|++.|..+|+++++|++++|
T Consensus 191 ~~~~~~~l~~~~~~~~~~~~~~~~~~i~~A~vPiik~~~~~~~~~~d~s~~n~~~~~nS~ll~~~~~~d~r~~~L~~~vk 270 (596)
T KOG2277|consen 191 KGLEILKLLAKCLASLLEEGVREVQQILSARVPIIKFNDSGSGLECDLSVNNSDAILNSQLLRNYSEIDPRVRPLVLLVK 270 (596)
T ss_pred hhHHHHHHHHHHHHhccccccceeeeeeecCCCEEEecCCCCCCceeeeeccchhhhhhHHHHHhHhcCCCcchHhHHHH
Confidence 344567777777776432 778888899999999999989999999999999999999999999999999999999999
Q ss_pred HHHHHCCCCCCCCCCCc-chHHHHHHHHHhhhcCCCCCCCccccCCCCCCCcccccchhhhhHHHHHhhccccccccccc
Q 013307 164 EWAKAHDINNPKTGTFN-SYSLSLLVLFHFQTCVPAILPPLKDIYPGNLVDDLKGVRANAERQIAEICAFNIARFSSDKY 242 (445)
Q Consensus 164 ~Wak~rgL~~~~~G~Ls-sy~l~lMvi~fLQ~~~p~ilP~Lq~l~~~~~~~~~~~~~~~~e~~~~e~~~~n~~~~~~~~~ 242 (445)
+||+.++++++..|+++ +|++++||++|||+..|+|+|.+..+++.....+...+.. .. .+. ....+.....
T Consensus 271 ~wa~~~~~~d~~~g~~~s~ysl~lmvi~fLq~~~~~ilp~l~~l~~~~~~~~~~~~~~----~~--~~~-~~~~~~~~~~ 343 (596)
T KOG2277|consen 271 HWAKEKGLNDAKPGGLNSSYSLTLMVIHFLQTLSPPILPPLSKLLPESDSNDKPVVKK----KV--LCS-FLRVFQRNPS 343 (596)
T ss_pred HHHHhccCCCCCCCceeccccHHHHHHHHHHhcCCcCCCchhhhchhcccccccchhh----hh--hhc-cccccccccc
Confidence 99999999999999998 6999999999999999999999999876643222111100 00 000 0001111112
Q ss_pred ccCCCCCHHHHHHHHHHhhc-cCCCCcccceeeccCCceeeecccCCCCCCCCCeEEecCCCCCCCccccCCHHHHHHHH
Q 013307 243 RKINRSSLAHLFVSFLEKFS-GLSLKASELGICPFTGQWEHIRSNTRWLPNNHPLFIEDPFEQPENSARAVSEKNLAKIS 321 (445)
Q Consensus 243 ~~~n~~sl~~LL~~FF~~Ys-~~df~~~~~~Is~~~g~~~~~~~~~~~~~~~~~L~I~DPf~~~~Nvar~vs~~~~~~I~ 321 (445)
...+..+++.|+.+||.||+ .|||. +.+|+++.|.....+ ... .....++|+|||+..+|++.+++......|+
T Consensus 344 ~~~~~~~l~~l~~~f~~yy~~~Fdf~--~~~I~~r~~~~l~~~-~~~--~~~~~l~i~dp~~~~~n~~~~~~~~~~~~i~ 418 (596)
T KOG2277|consen 344 NSQNTGSLGELLLGFFSYYASLFDFR--KNAISIRRGRALKRA-KKI--KSKKFLCIEDPFEVSHNADAGVTLKVLLLIQ 418 (596)
T ss_pred cccccchHHHHHHHHHHHHhhhcccc--cceeeeeeccccccc-chh--hhccceeeccccccccCccccchHHHHHHHH
Confidence 35567889999999999999 57775 678888877644321 111 1357899999999999999999999999999
Q ss_pred HHHHHHHHHhhccC
Q 013307 322 NAFEMTHFRLTSTN 335 (445)
Q Consensus 322 ~~f~~A~~~L~~~~ 335 (445)
.+|+.+...+....
T Consensus 419 ~~~~~~~~~~~~~~ 432 (596)
T KOG2277|consen 419 DEFQESRRVFKDVN 432 (596)
T ss_pred HHHHHHHHHhhhhc
Confidence 99999999999764
No 6
>COG5186 PAP1 Poly(A) polymerase [RNA processing and modification]
Probab=99.91 E-value=3.9e-23 Score=201.16 Aligned_cols=263 Identities=19% Similarity=0.250 Sum_probs=204.1
Q ss_pred HHcCCCHHHHHHHHHHHHHHHHHHHhhhc--------------CCCcEEEEecccccCCCCCCCCcceEEeecCCCcccc
Q 013307 16 GMLNPLREDWETRMKVISDLREVVESVES--------------LRGATVEPFGSFVSNLFSRWGDLDISIELSNGSCISS 81 (445)
Q Consensus 16 ~~~~Pt~ee~~~R~~vi~~l~~il~~~~~--------------~~~~~v~~fGS~~tGl~l~~SDIDl~i~~~~~~~iss 81 (445)
+...-++.|-+.|.+++..|+.++++... ..+-++..||||..|++.|+||||-.|+.|...
T Consensus 36 ~g~FE~~~E~~~Rv~VL~~Lq~~~~eFV~~vs~~K~m~dgmar~aGGKIFTyGSYRLGVhgpGsDIDtLvvVPkHV---- 111 (552)
T COG5186 36 RGFFEDDKEGQTRVRVLGKLQFMVREFVARVSRNKGMGDGMARPAGGKIFTYGSYRLGVHGPGSDIDTLVVVPKHV---- 111 (552)
T ss_pred cCCcCCchhhhhHHHHHHHHHHHHHHHHHHHHhhcCCCccccccCCceeeeecceeeeccCCCCCcceEEEecccc----
Confidence 45667899999999999999988876531 135799999999999999999999999888643
Q ss_pred cchhhHHHHHHHHHHHHHhcCCceEEEEecccccceEEEEeeccceEEEEeecccc------c--ccccHHHhH------
Q 013307 82 AGKKVKQSLLGDLLRALRQKGGYRRLQFVAHARVPILKFETIHQNISCDISIDNLC------G--QIKSKFLFW------ 147 (445)
Q Consensus 82 ~~k~~~~~~L~~l~~~L~~~~~~~~v~~I~~ArVPIIk~~~~~~gi~~DIs~~n~~------g--~~~s~ll~~------ 147 (445)
.+.+++..+...|+....+.++..++.|-|||||++. .||.+|+-|.... | +.+-.||+.
T Consensus 112 ----sR~dFFt~f~~~Lrer~ei~eva~vpDAfVPIIK~KF--~GIsIDLifARLs~P~Vp~~l~Lsd~nLLk~~dEkci 185 (552)
T COG5186 112 ----SRSDFFTHFYEELRERPEIEEVAKVPDAFVPIIKLKF--QGISIDLIFARLSIPVVPDGLNLSDDNLLKSMDEKCI 185 (552)
T ss_pred ----cHHHHHHHHHHHhccCcchhhhccCCcccceeEEEEe--cCccceeeeeeccCCcCCCcccccchhhhhcchHHHH
Confidence 2457999999999999999999999999999999998 8999999875421 1 111122221
Q ss_pred -----------Hhcc---cchhHHHHHHHHHHHHHCCCCCCCCCCCcchHHHHHHHHHhhhcCCCCCCCccccCCCCCCC
Q 013307 148 -----------ISQI---DGRFRDMVLLVKEWAKAHDINNPKTGTFNSYSLSLLVLFHFQTCVPAILPPLKDIYPGNLVD 213 (445)
Q Consensus 148 -----------~~~~---~~~~r~Lv~~iK~Wak~rgL~~~~~G~Lssy~l~lMvi~fLQ~~~p~ilP~Lq~l~~~~~~~ 213 (445)
...+ ...|+..++.||+||+.|.++..-.|+.||-+|.|||...||.. |+
T Consensus 186 lsLNGtRVTDeiL~LVP~~~vF~~ALRaIK~WAqRRavYaN~~GfpGGVAwam~VARiCQLY------------PN---- 249 (552)
T COG5186 186 LSLNGTRVTDEILNLVPSVKVFHSALRAIKYWAQRRAVYANPYGFPGGVAWAMCVARICQLY------------PN---- 249 (552)
T ss_pred HhhcCceehHHHHHhCCchHHHHHHHHHHHHHHHhhhhhccccCCcchHHHHHHHHHHHhhc------------cC----
Confidence 1111 24689999999999999999999999999999999999999996 21
Q ss_pred cccccchhhhhHHHHHhhcccccccccccccCCCCCHHHHHHHHHHhhccCCCCcccceeeccCCceeeecccCCCCC--
Q 013307 214 DLKGVRANAERQIAEICAFNIARFSSDKYRKINRSSLAHLFVSFLEKFSGLSLKASELGICPFTGQWEHIRSNTRWLP-- 291 (445)
Q Consensus 214 ~~~~~~~~~e~~~~e~~~~n~~~~~~~~~~~~n~~sl~~LL~~FF~~Ys~~df~~~~~~Is~~~g~~~~~~~~~~~~~-- 291 (445)
.+-..++..||+.++.|+|.. .+.+-|-..+....+ -|.|
T Consensus 250 ----------------------------------A~S~vIv~kFF~ils~WnWPq-PviLkPieDgplqvr---vWnPKv 291 (552)
T COG5186 250 ----------------------------------ASSFVIVCKFFEILSSWNWPQ-PVILKPIEDGPLQVR---VWNPKV 291 (552)
T ss_pred ----------------------------------cchHhHHHHHHHHHHhcCCCC-CeEeeeccCCCeeEE---eeCCcc
Confidence 234678899999999999973 333344322222222 2544
Q ss_pred ----CCCCeEEecCCCCCCCccccCCHHHHHHHHHHHHHHHHHhhccC---CCcchhh
Q 013307 292 ----NNHPLFIEDPFEQPENSARAVSEKNLAKISNAFEMTHFRLTSTN---QTRYALL 342 (445)
Q Consensus 292 ----~~~~L~I~DPf~~~~Nvar~vs~~~~~~I~~~f~~A~~~L~~~~---~~~~s~L 342 (445)
+.++|.|..|..|+.-.+.+++..+-..|..||.+|.+++.... .+|..++
T Consensus 292 YpsDk~HRMPvITPAYPSMCATHNit~STq~vIl~EfvRa~~I~~di~~n~~~w~~lF 349 (552)
T COG5186 292 YPSDKYHRMPVITPAYPSMCATHNITNSTQHVILMEFVRAHKILSDIERNALDWRRLF 349 (552)
T ss_pred CcccccccCccccCCchhhhhhccccchhhhhHHHHHHHHHHhhhhHhhccccHHHHH
Confidence 35689999999999999999999999999999999999998654 2454443
No 7
>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=99.89 E-value=4.1e-23 Score=199.09 Aligned_cols=217 Identities=21% Similarity=0.280 Sum_probs=142.0
Q ss_pred chHHHHHHHHHHc--CCCHHHHHHHHHHHHHHHHHHHhhhcCCCcEEEEecccccCCCCCCCCcceEEeecCCCcccccc
Q 013307 6 VLEPILKDILGML--NPLREDWETRMKVISDLREVVESVESLRGATVEPFGSFVSNLFSRWGDLDISIELSNGSCISSAG 83 (445)
Q Consensus 6 ~L~~ei~~f~~~~--~Pt~ee~~~R~~vi~~l~~il~~~~~~~~~~v~~fGS~~tGl~l~~SDIDl~i~~~~~~~iss~~ 83 (445)
..+.+|.++++.. .||+||.++|+++++.|++++++....
T Consensus 21 ~~s~~L~~~l~~~~~~es~ee~~~R~~vl~~L~~iv~~wv~~-------------------------------------- 62 (254)
T PF04928_consen 21 KRSASLEEFLKDYGLFESEEEEQKREEVLRKLQQIVKEWVKQ-------------------------------------- 62 (254)
T ss_dssp HHHHHHHHHHHHCT-S--HHHHHHHHHHHHHHHHHHHHHHHH--------------------------------------
T ss_pred HhHHHHHHHHHHcCCCCChHHHhHHHHHHHHHHHHHHHHHHh--------------------------------------
Confidence 3567788887776 689999999999999999999986322
Q ss_pred hhhHHHHHHHHHHHHHhcCCceEEEEecccccc-eEEEEeeccceEEEE---eecccccccccHHHhHHhcccchhHHHH
Q 013307 84 KKVKQSLLGDLLRALRQKGGYRRLQFVAHARVP-ILKFETIHQNISCDI---SIDNLCGQIKSKFLFWISQIDGRFRDMV 159 (445)
Q Consensus 84 k~~~~~~L~~l~~~L~~~~~~~~v~~I~~ArVP-IIk~~~~~~gi~~DI---s~~n~~g~~~s~ll~~~~~~~~~~r~Lv 159 (445)
...++| .+.+.+ ..+-.|+ |+...+|++.+..|....--...||.++
T Consensus 63 ---------------------------~~~~~p~~l~~~~--~~~l~~ld~~s~~sLnG~Rv~~~il~~Vp~~~~Fr~~l 113 (254)
T PF04928_consen 63 ---------------------------ALPRVPEDLDLLD--DDPLRNLDEASVRSLNGVRVTDYILRLVPNQETFRTAL 113 (254)
T ss_dssp ---------------------------SSSSB-TT--TT---GGGGTT--HHHHHHHHHHHHHHHHHCTSS-HHHHHHHH
T ss_pred ---------------------------hhcCCCcccccCC--chhhhCCCHhhccCcccccHHHHHHHHCCCHHHHHHHH
Confidence 111121 111111 1111111 2334567777777665554447899999
Q ss_pred HHHHHHHHHCCCCCCCCCCCcchHHHHHHHHHhhhcCCCCCCCccccCCCCCCCcccccchhhhhHHHHHhhcccccccc
Q 013307 160 LLVKEWAKAHDINNPKTGTFNSYSLSLLVLFHFQTCVPAILPPLKDIYPGNLVDDLKGVRANAERQIAEICAFNIARFSS 239 (445)
Q Consensus 160 ~~iK~Wak~rgL~~~~~G~Lssy~l~lMvi~fLQ~~~p~ilP~Lq~l~~~~~~~~~~~~~~~~e~~~~e~~~~n~~~~~~ 239 (445)
++||.||++||||++..|+|||++|++||++.||.. |
T Consensus 114 R~IK~WAk~RGIYsn~~GylGGI~waILvArvcql~------------P------------------------------- 150 (254)
T PF04928_consen 114 RFIKLWAKRRGIYSNVFGYLGGIHWAILVARVCQLY------------P------------------------------- 150 (254)
T ss_dssp HHHHHHHHHTT-B-CCCTSB-HHHHHHHHHHHHHHS------------T-------------------------------
T ss_pred HHHHHHHHHccccchhhccchHHHHHHHHHHHHHHC------------c-------------------------------
Confidence 999999999999999999999999999999999996 1
Q ss_pred cccccCCCCCHHHHHHHHHHhhccCCCCcccceeeccCCceeeecccCCCCCC------CCCeEEecCCCCCCCccccCC
Q 013307 240 DKYRKINRSSLAHLFVSFLEKFSGLSLKASELGICPFTGQWEHIRSNTRWLPN------NHPLFIEDPFEQPENSARAVS 313 (445)
Q Consensus 240 ~~~~~~n~~sl~~LL~~FF~~Ys~~df~~~~~~Is~~~g~~~~~~~~~~~~~~------~~~L~I~DPf~~~~Nvar~vs 313 (445)
..+.+.|+..||.+|++|+|.. .+.+++..... -....|.|. .+.|.|.+|..|..|+|++|+
T Consensus 151 -------n~~~~~ll~~FF~~ys~W~W~~-PV~l~~~~~~~---~~~~~w~p~~~~~~~~~~MpIiTP~yP~~Nst~nVt 219 (254)
T PF04928_consen 151 -------NASPSTLLSRFFQIYSQWDWPN-PVVLDPIEDGP---LGFKVWNPRLYPRDRRHLMPIITPAYPSMNSTYNVT 219 (254)
T ss_dssp -------T--HHHHHHHHHHHHHCS-TTS--EESS-----S---SSCGS--TTT-HHHHC-SS-EE-SSSS--BTTTT--
T ss_pred -------cccccchHHHHHHHhcCCCCCC-ceeecccccCc---ccccCCCCCCCCCCcccceeEccCCCCccccccccC
Confidence 1246789999999999999985 34444432111 111235443 678999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHhhcc---CCCcchhhh
Q 013307 314 EKNLAKISNAFEMTHFRLTST---NQTRYALLS 343 (445)
Q Consensus 314 ~~~~~~I~~~f~~A~~~L~~~---~~~~~s~L~ 343 (445)
..++..|++||++|++++... ..+|..+|.
T Consensus 220 ~st~~~i~~Ef~ra~~i~~~~~~~~~~W~~L~e 252 (254)
T PF04928_consen 220 RSTLRIIREEFQRAHEILSEILKGGASWSDLFE 252 (254)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHTTSS-HHHCT-
T ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCCCHHHHcC
Confidence 999999999999999999984 345666553
No 8
>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=99.89 E-value=1.2e-22 Score=173.59 Aligned_cols=114 Identities=31% Similarity=0.467 Sum_probs=103.7
Q ss_pred HHHHHHHHHHHHHHhhhcCCCcEEEEecccccCCCCCCCCcceEEeecCCCcccccchhhHHHHHHHHHHHHHhcCCceE
Q 013307 27 TRMKVISDLREVVESVESLRGATVEPFGSFVSNLFSRWGDLDISIELSNGSCISSAGKKVKQSLLGDLLRALRQKGGYRR 106 (445)
Q Consensus 27 ~R~~vi~~l~~il~~~~~~~~~~v~~fGS~~tGl~l~~SDIDl~i~~~~~~~iss~~k~~~~~~L~~l~~~L~~~~~~~~ 106 (445)
.|+++++.|++++++. +|++++++|||+++|+++++||||+++..+.. +....+++..+++.|++.+.+.+
T Consensus 1 ~r~~i~~~l~~~i~~~--~~~~~v~~fGS~~~g~~~~~SDiDl~i~~~~~-------~~~~~~~l~~l~~~l~~~~~~~~ 71 (114)
T cd05402 1 KREEVLDRLQELIKEW--FPGAKLYPFGSYVTGLGLPGSDIDLCLLGPNH-------RVDREDFLRKLAKLLKKSGEVVE 71 (114)
T ss_pred CHHHHHHHHHHHHHHH--CCCCEEEEecccccCCCCCCCCeeEEEEeCCC-------CccHHHHHHHHHHHHHhCCCcee
Confidence 3889999999999987 78999999999999999999999999988753 12356799999999999888889
Q ss_pred EEEecccccceEEEEeeccceEEEEeecccccccccHHHhHHh
Q 013307 107 LQFVAHARVPILKFETIHQNISCDISIDNLCGQIKSKFLFWIS 149 (445)
Q Consensus 107 v~~I~~ArVPIIk~~~~~~gi~~DIs~~n~~g~~~s~ll~~~~ 149 (445)
++.|.+|||||||+.+..+|+.|||||+|.+|+.||++++.|.
T Consensus 72 ~~~i~~ArVPiik~~~~~~~i~~Dis~~~~~g~~~s~li~~y~ 114 (114)
T cd05402 72 VEPIINARVPIIKFVDKPTGIEVDISFNNLNGIRNTKLLRAYV 114 (114)
T ss_pred eEEeccCCCCEEEEEEcCCCeEEEEEcccchHHHHHHHHHHhC
Confidence 9999999999999999889999999999999999999999884
No 9
>TIGR03671 cca_archaeal CCA-adding enzyme.
Probab=99.78 E-value=6.7e-17 Score=164.22 Aligned_cols=236 Identities=23% Similarity=0.273 Sum_probs=159.7
Q ss_pred HHHHHHHcCCCHHHHHHHHHHHHHHHHHHHhhhc--CCCcEEEEecccccCCCCC-CCCcceEEeecCCCcccccchhhH
Q 013307 11 LKDILGMLNPLREDWETRMKVISDLREVVESVES--LRGATVEPFGSFVSNLFSR-WGDLDISIELSNGSCISSAGKKVK 87 (445)
Q Consensus 11 i~~f~~~~~Pt~ee~~~R~~vi~~l~~il~~~~~--~~~~~v~~fGS~~tGl~l~-~SDIDl~i~~~~~~~iss~~k~~~ 87 (445)
+...++.+.||++|.+....+.+.|...|++... .+.+++..|||++-|+|++ +|||||++.++... .++..
T Consensus 2 ~~~vl~~i~Ps~eE~~~~~~~~~~l~~~l~~~~~e~~~~~~v~~~GS~ArgT~L~G~sDIDIfi~f~~~~-----~~e~l 76 (408)
T TIGR03671 2 LEEVLERIKPTEEEREKLKKVADELIARLEEIIEELGVDAEVVLVGSYARGTWLKGDRDIDIFILFPKDT-----SREEL 76 (408)
T ss_pred hHHHhhhcCCCHHHHHHHHHHHHHHHHHHHHHHHhcCCcceEEEEeeEecCCccCCCCceeEEEEeCCCC-----CHHHH
Confidence 3567788999999999888777777776665421 3568999999999999999 89999999986532 12233
Q ss_pred HHHHHHHHHHHHhcCCceEEEEecccccceEEEEeeccceEEEE--eecccc------cccccHHHhHHh--cccchhHH
Q 013307 88 QSLLGDLLRALRQKGGYRRLQFVAHARVPILKFETIHQNISCDI--SIDNLC------GQIKSKFLFWIS--QIDGRFRD 157 (445)
Q Consensus 88 ~~~L~~l~~~L~~~~~~~~v~~I~~ArVPIIk~~~~~~gi~~DI--s~~n~~------g~~~s~ll~~~~--~~~~~~r~ 157 (445)
......++..+.+.+.-.. ...|..|-++... .|++||| |+.-.. ++-.|.|...|. +++..++.
T Consensus 77 ~~~gl~i~~~~~~~~~~~~---~~yaeHpYv~~~~--~G~~VDiVPcy~v~~g~~~~taVDRtp~H~~fv~~rl~~~~~d 151 (408)
T TIGR03671 77 EEYGLEIGHEVLKRGGNYE---ERYAEHPYVSGEI--EGFEVDVVPCYKVESGEEIISAVDRTPFHTRYVLERLDGKLRD 151 (408)
T ss_pred HHHHHHHHHHHHhhCCCHh---heeccCceEEEEE--ccEEEEEEeeEEccCcCeeeccccCchHHHHHHHHhhhhhHHH
Confidence 3444445555443322112 2468999999887 5999999 443322 223344544443 23445889
Q ss_pred HHHHHHHHHHHCCCCCC--CCCCCcchHHHHHHHHHhhhcCCCCCCCccccCCCCCCCcccccchhhhhHHHHHhhcccc
Q 013307 158 MVLLVKEWAKAHDINNP--KTGTFNSYSLSLLVLFHFQTCVPAILPPLKDIYPGNLVDDLKGVRANAERQIAEICAFNIA 235 (445)
Q Consensus 158 Lv~~iK~Wak~rgL~~~--~~G~Lssy~l~lMvi~fLQ~~~p~ilP~Lq~l~~~~~~~~~~~~~~~~e~~~~e~~~~n~~ 235 (445)
.|+++|.|+|..|+|++ +.+||+||..-||+++|=
T Consensus 152 ~VRLlK~f~k~igvYGsE~~~~GFSGYl~ELLv~~yG------------------------------------------- 188 (408)
T TIGR03671 152 DVRLLKQFLKGIGVYGSELKTRGFSGYLCELLVIHYG------------------------------------------- 188 (408)
T ss_pred HHHHHHHHHHhCCccchhhccCCccHHHHHHHHHHhC-------------------------------------------
Confidence 99999999999999965 689999999999999730
Q ss_pred cccccccccCCCCCHHHHHHHHHHhhccCCCCcccceeeccCCceeeecccCCCCCCCCCeEEecCCCCCCCccccCCHH
Q 013307 236 RFSSDKYRKINRSSLAHLFVSFLEKFSGLSLKASELGICPFTGQWEHIRSNTRWLPNNHPLFIEDPFEQPENSARAVSEK 315 (445)
Q Consensus 236 ~~~~~~~~~~n~~sl~~LL~~FF~~Ys~~df~~~~~~Is~~~g~~~~~~~~~~~~~~~~~L~I~DPf~~~~Nvar~vs~~ 315 (445)
+...++-.+- +|. ....|++.... . .....+|.|.||-++.+|||+++|..
T Consensus 189 -------------~F~~~l~~a~------~wk-~~~~id~~~~~--~-------~~f~~PlvViDPvDp~RNVAaalS~~ 239 (408)
T TIGR03671 189 -------------SFENVLKAAS------KWK-PGVVIDIEEHG--T-------KKFDDPLVVIDPVDPKRNVAAALSLE 239 (408)
T ss_pred -------------CHHHHHHHHH------hcC-CCeEEecCccc--c-------ccCCCCEEEeCCCCCcchHHHHcCHH
Confidence 0111221111 222 12334332110 0 01257999999999999999999998
Q ss_pred HHHHHHHHHHHHH
Q 013307 316 NLAKISNAFEMTH 328 (445)
Q Consensus 316 ~~~~I~~~f~~A~ 328 (445)
++.+|..+.++++
T Consensus 240 ~~~~fv~aar~fl 252 (408)
T TIGR03671 240 NLARFILAARMFL 252 (408)
T ss_pred HHHHHHHHHHHHH
Confidence 8888887766543
No 10
>PRK13300 tRNA CCA-pyrophosphorylase; Provisional
Probab=99.78 E-value=1e-16 Score=165.17 Aligned_cols=241 Identities=23% Similarity=0.243 Sum_probs=161.9
Q ss_pred HHHHHHHcCCCHHHHHHHHHHHHHHHHHHHhhhc--CCCcEEEEecccccCCCCC-CCCcceEEeecCCCcccccchhhH
Q 013307 11 LKDILGMLNPLREDWETRMKVISDLREVVESVES--LRGATVEPFGSFVSNLFSR-WGDLDISIELSNGSCISSAGKKVK 87 (445)
Q Consensus 11 i~~f~~~~~Pt~ee~~~R~~vi~~l~~il~~~~~--~~~~~v~~fGS~~tGl~l~-~SDIDl~i~~~~~~~iss~~k~~~ 87 (445)
+.+.++.+.||++|.+.-..+.+.|...+++... ..++.+.++||++-|+|++ +|||||++.++... .+..-
T Consensus 3 ~~evl~~i~Ps~eE~~~l~~~~~~l~~~L~~~~~~~~~~~~V~l~GS~ArgT~L~GdsDIDIFv~fp~~~-----~~e~L 77 (447)
T PRK13300 3 LEEVLERIKPTEEEREKLKKVAEELIERLEEAIKELGLDAEVELVGSTARGTWLSGDRDIDIFVLFPKDT-----SREEL 77 (447)
T ss_pred HHHHHHhcCCCHHHHHHHHHHHHHHHHHHHHHHHhcCCceEEEEEeeecCCcccCCCCceeEEEEeCCCC-----CHHHH
Confidence 5577889999999998888877777777765432 1238999999999999999 78999999987532 12222
Q ss_pred HHHHHHHHHHHHhc-CCceEEEEecccccceEEEEeeccceEEEE--eecccc------cccccHHHhHHh--cccchhH
Q 013307 88 QSLLGDLLRALRQK-GGYRRLQFVAHARVPILKFETIHQNISCDI--SIDNLC------GQIKSKFLFWIS--QIDGRFR 156 (445)
Q Consensus 88 ~~~L~~l~~~L~~~-~~~~~v~~I~~ArVPIIk~~~~~~gi~~DI--s~~n~~------g~~~s~ll~~~~--~~~~~~r 156 (445)
.+....+...+.+. ..-..++ -|..|-++... .|++||| |+.-.. ++-.|.|...|. +++..++
T Consensus 78 ~~~gl~i~~~~~~~~~~~~~~~---yaeHpyv~~~~--~G~~VDiVPcy~v~~~~~~~saVDRtp~H~~fv~~rl~~~~~ 152 (447)
T PRK13300 78 EEKGLEIGKEVAKELLGDYEER---YAEHPYVTGEI--DGFEVDIVPCYKVESGEEIISAVDRTPFHTKYVKERLKGKLE 152 (447)
T ss_pred HHHHHHHHHHHHHhhCCcceee---eccCceEEEEE--CCEEEEEEeeEEccCcCcccccccCchHHHHHHHHhhhhhHH
Confidence 23333344443332 3333444 38999999987 5999999 343322 333345544443 2345689
Q ss_pred HHHHHHHHHHHHCCCCCC--CCCCCcchHHHHHHHHHhhhcCCCCCCCccccCCCCCCCcccccchhhhhHHHHHhhccc
Q 013307 157 DMVLLVKEWAKAHDINNP--KTGTFNSYSLSLLVLFHFQTCVPAILPPLKDIYPGNLVDDLKGVRANAERQIAEICAFNI 234 (445)
Q Consensus 157 ~Lv~~iK~Wak~rgL~~~--~~G~Lssy~l~lMvi~fLQ~~~p~ilP~Lq~l~~~~~~~~~~~~~~~~e~~~~e~~~~n~ 234 (445)
..|+++|.|+|..|+|++ +.+|||||..-||+++| .
T Consensus 153 d~VRLlK~f~k~~gvYGsE~k~~GFSGYl~ELLv~~y---G--------------------------------------- 190 (447)
T PRK13300 153 DEVRLLKQFLKGIGVYGSELKTRGFSGYLCELLIIHY---G--------------------------------------- 190 (447)
T ss_pred HHHHHHHHHHHhCCccchhhccCCccHHHHHHHHHHh---C---------------------------------------
Confidence 999999999999999965 68999999999999973 0
Q ss_pred ccccccccccCCCCCHHHHHHHHHHhhccCCCCcccceeeccCCceeeecccCCCCCCCCCeEEecCCCCCCCccccCCH
Q 013307 235 ARFSSDKYRKINRSSLAHLFVSFLEKFSGLSLKASELGICPFTGQWEHIRSNTRWLPNNHPLFIEDPFEQPENSARAVSE 314 (445)
Q Consensus 235 ~~~~~~~~~~~n~~sl~~LL~~FF~~Ys~~df~~~~~~Is~~~g~~~~~~~~~~~~~~~~~L~I~DPf~~~~Nvar~vs~ 314 (445)
+...++-.+ + +|.. ...|++...... ...+.+|.|.||-||.+|+|+++|.
T Consensus 191 --------------~F~~~l~~a----~--~w~~-~~~I~~~~~~~~--------~~f~~PlvViDPvDp~RNVAaa~S~ 241 (447)
T PRK13300 191 --------------SFENVLKAA----S--KWKP-PVKIDLEKHGKE--------YKFDDPLVVIDPVDPNRNVAAALSL 241 (447)
T ss_pred --------------CHHHHHHHH----H--hCCC-CceEeccccCcc--------ccCCCCEEEeCCCCCcchHHHHcCH
Confidence 011122111 1 1221 234544322110 0236799999999999999999998
Q ss_pred HHHHHHHHHHHHHHHHhhccC
Q 013307 315 KNLAKISNAFEMTHFRLTSTN 335 (445)
Q Consensus 315 ~~~~~I~~~f~~A~~~L~~~~ 335 (445)
.++.+|..+.+ ..|.++.
T Consensus 242 ~~~~~fv~aar---~fL~~Ps 259 (447)
T PRK13300 242 ENLATFILAAR---EFLKNPS 259 (447)
T ss_pred HHHHHHHHHHH---HHHhCCC
Confidence 88777776554 5566654
No 11
>COG1746 CCA1 tRNA nucleotidyltransferase (CCA-adding enzyme) [Translation, ribosomal structure and biogenesis]
Probab=99.69 E-value=1.9e-15 Score=151.63 Aligned_cols=243 Identities=23% Similarity=0.295 Sum_probs=168.0
Q ss_pred chHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHhhh--cCCCcEEEEecccccCCCCC-CCCcceEEeecCCCccccc
Q 013307 6 VLEPILKDILGMLNPLREDWETRMKVISDLREVVESVE--SLRGATVEPFGSFVSNLFSR-WGDLDISIELSNGSCISSA 82 (445)
Q Consensus 6 ~L~~ei~~f~~~~~Pt~ee~~~R~~vi~~l~~il~~~~--~~~~~~v~~fGS~~tGl~l~-~SDIDl~i~~~~~~~iss~ 82 (445)
.|...|.+.++.+.||++|.+.-+.+.+.|+..+.++. ...++.+..+||++-|+|++ +.|||+.|.+|...
T Consensus 2 ~~~~~l~evl~~i~P~~eE~~~~~~~~e~l~~~~~~~~~e~~~~aev~lVGS~AkgTwL~gd~DIDvFi~Fp~d~----- 76 (443)
T COG1746 2 TLEEVLEEVLKRIKPTEEERKKLKEVAEELRERINEIIEELGIDAEVVLVGSYAKGTWLRGDHDIDVFIAFPKDT----- 76 (443)
T ss_pred chHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHhcCCcceEEEEeecccCcccCCCcceeEEEECCCCC-----
Confidence 36677889999999999999988888887777776553 24689999999999999999 55999999988632
Q ss_pred chhh-HHHHHHHHHHHHHhcCCceEEEEecccccceEEEEeeccceEEEE--eecc------cccccccHHHhHHh--cc
Q 013307 83 GKKV-KQSLLGDLLRALRQKGGYRRLQFVAHARVPILKFETIHQNISCDI--SIDN------LCGQIKSKFLFWIS--QI 151 (445)
Q Consensus 83 ~k~~-~~~~L~~l~~~L~~~~~~~~v~~I~~ArVPIIk~~~~~~gi~~DI--s~~n------~~g~~~s~ll~~~~--~~ 151 (445)
.+.. ...-|.....+|.. + -.. +.-|..|.+.... .|+++|| |+.- ..++..|-|...|. ++
T Consensus 77 ~~eel~~~GL~ig~~~l~~-~-~~~---~~YAeHPYV~g~v--~G~eVDvVPCy~v~~~~~~~sAVDRTplHt~yv~e~L 149 (443)
T COG1746 77 SEEELEEKGLEIGREVLKR-G-NYE---ERYAEHPYVTGEV--DGYEVDVVPCYKVEDGEKIISAVDRTPLHTRYVEEHL 149 (443)
T ss_pred CHHHHHHHHHHHHHHHhcC-C-chh---hhhccCCeeEEEE--ccEEEEEEecccccCcccccccccCcchhHHHHHHHh
Confidence 1211 12334444444443 1 122 2468999999886 6999999 3332 34555666665554 34
Q ss_pred cchhHHHHHHHHHHHHHCCCCCC--CCCCCcchHHHHHHHHHhhhcCCCCCCCccccCCCCCCCcccccchhhhhHHHHH
Q 013307 152 DGRFRDMVLLVKEWAKAHDINNP--KTGTFNSYSLSLLVLFHFQTCVPAILPPLKDIYPGNLVDDLKGVRANAERQIAEI 229 (445)
Q Consensus 152 ~~~~r~Lv~~iK~Wak~rgL~~~--~~G~Lssy~l~lMvi~fLQ~~~p~ilP~Lq~l~~~~~~~~~~~~~~~~e~~~~e~ 229 (445)
+.+-+.=++++|.|+|.-|+|++ +.+|+|||.--||+|+| ++|
T Consensus 150 ~~~~~deVrLLK~FlK~iGvYGaE~rt~GFSGYL~ELLII~y-----------------GsF------------------ 194 (443)
T COG1746 150 KGRQKDEVRLLKQFLKGIGVYGAELRTQGFSGYLCELLIIHY-----------------GSF------------------ 194 (443)
T ss_pred cccchhHHHHHHHHHhccCccceeeeeccchHHHHHHHHhhh-----------------ccH------------------
Confidence 56667789999999999999987 57999999999999962 111
Q ss_pred hhcccccccccccccCCCCCHHHHHHHHHHhhccCCCCcccceeeccCCceeeecccCCCCCCCCCeEEecCCCCCCCcc
Q 013307 230 CAFNIARFSSDKYRKINRSSLAHLFVSFLEKFSGLSLKASELGICPFTGQWEHIRSNTRWLPNNHPLFIEDPFEQPENSA 309 (445)
Q Consensus 230 ~~~n~~~~~~~~~~~~n~~sl~~LL~~FF~~Ys~~df~~~~~~Is~~~g~~~~~~~~~~~~~~~~~L~I~DPf~~~~Nva 309 (445)
... ++..+ .|... ..|++.... + -...+.+|.+.||-||.+|||
T Consensus 195 ---------------------e~v----l~~a~--~wrp~-~~ID~~~~~----~----e~f~d~PliVvDPVDP~RNVA 238 (443)
T COG1746 195 ---------------------ENV----LKAAS--RWRPG-KIIDLEGHK----R----ERFEDEPLIVVDPVDPKRNVA 238 (443)
T ss_pred ---------------------HHH----HHHHh--ccCCC-eEEeccchh----h----hccCCCCeEecCCCCCccchh
Confidence 111 11111 35432 455553220 0 012356999999999999999
Q ss_pred ccCCHHHHHHHHHHHHHHHHHhhcc
Q 013307 310 RAVSEKNLAKISNAFEMTHFRLTST 334 (445)
Q Consensus 310 r~vs~~~~~~I~~~f~~A~~~L~~~ 334 (445)
+++|..++.++..+.+ ..|.++
T Consensus 239 AalSl~~la~f~~aar---~FL~~P 260 (443)
T COG1746 239 AALSLENLARFVHAAR---EFLKNP 260 (443)
T ss_pred hhcCHHHHHHHHHHHH---HHhcCC
Confidence 9999888777766554 445554
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=99.03 E-value=1.1e-10 Score=87.95 Aligned_cols=55 Identities=25% Similarity=0.468 Sum_probs=41.4
Q ss_pred CHHHHHHHHHHhhc-cCCCCcccceeeccCCceeeecccCCCC----CCCCCeEEecCCCCCC
Q 013307 249 SLAHLFVSFLEKFS-GLSLKASELGICPFTGQWEHIRSNTRWL----PNNHPLFIEDPFEQPE 306 (445)
Q Consensus 249 sl~~LL~~FF~~Ys-~~df~~~~~~Is~~~g~~~~~~~~~~~~----~~~~~L~I~DPf~~~~ 306 (445)
|+|+||++||+||| .||| ...+||++.|+...+ +...|. ....+|||||||+++|
T Consensus 1 slg~Ll~~Ff~~Y~~~Fd~--~~~~Isi~~g~~~~k-~~~~~~~~~~~~~~~l~IeDP~~~~n 60 (60)
T PF03828_consen 1 SLGELLLGFFEYYGRKFDY--ENNVISIRNGGYFPK-EEKNWSKSRNQRKKRLCIEDPFDPSN 60 (60)
T ss_dssp -HHHHHHHHHHHHHHTS-T--TTEEEESSSSSEEEH-HHHTGCHCCCCECSSSEBBESSSTTE
T ss_pred CHHHHHHHHHHHhCCcCCC--CceEEEecCCceEEh-hhccccccccCCCCeEEEECCCCCCC
Confidence 58999999999999 4555 678999999887553 333343 3467999999999853
No 13
>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=98.87 E-value=1.5e-07 Score=107.36 Aligned_cols=236 Identities=16% Similarity=0.195 Sum_probs=154.1
Q ss_pred ccccCCCCC---CCCcceEEeecCCCc-----ccccchhhHHHHHHHHHHHH--HhcCCceEEEE---ecccccceEEEE
Q 013307 55 SFVSNLFSR---WGDLDISIELSNGSC-----ISSAGKKVKQSLLGDLLRAL--RQKGGYRRLQF---VAHARVPILKFE 121 (445)
Q Consensus 55 S~~tGl~l~---~SDIDl~i~~~~~~~-----iss~~k~~~~~~L~~l~~~L--~~~~~~~~v~~---I~~ArVPIIk~~ 121 (445)
||+.++..+ +-.|||.|.+|.... ++-..-..+..+|..|++.| ++.....++.. ..+.+-|||.+.
T Consensus 1 S~~l~t~~k~~~~~~VDl~v~mP~~~fq~KDyln~RY~~KRA~YLa~iA~~L~~~~~~~~~~v~~~~~~gd~~kPil~l~ 80 (972)
T PF03813_consen 1 SYALKTMIKSKPNLTVDLAVEMPKSLFQEKDYLNYRYFHKRALYLAYIAAHLQKKKSKLFVDVSFEYLNGDPLKPILVLR 80 (972)
T ss_pred CcccccccccCCCCeeEEEEeCChhhcCchhhccchHHHHHHHHHHHHHHHHhhhccccceeEEEEeCCCCCCCCeEEEE
Confidence 677777766 349999999997431 11100112345788899999 33344444443 256688999887
Q ss_pred eec---------cceEEEEee----------------cc---------------cccccccHHH------------hHHh
Q 013307 122 TIH---------QNISCDISI----------------DN---------------LCGQIKSKFL------------FWIS 149 (445)
Q Consensus 122 ~~~---------~gi~~DIs~----------------~n---------------~~g~~~s~ll------------~~~~ 149 (445)
-.. .++.+-|-. || .+-..|+.++ ....
T Consensus 81 p~~~~~~~~~~~~~~~iRi~~~~~~~~F~~~rl~P~rnnvR~~~~~~~~~~~~~pTP~YNssIL~D~~~~~~l~~l~~~~ 160 (972)
T PF03813_consen 81 PKGKKDSDDFSKTKFRIRIIPSIPSDTFPLSRLAPSRNNVRPSWFDEEDSSSLPPTPHYNSSILEDMLMEEHLKYLHEAS 160 (972)
T ss_pred ECCccccccccCCcEEEEEEecCCcccCCHHhcCCCCCccCcCcccccccCCCCCCCcchHHHHHHHhHHHHHHHHHHHH
Confidence 311 123333321 11 1122344332 2233
Q ss_pred cccchhHHHHHHHHHHHHHCCCCCCC-CCCCcchHHHHHHHHHhhhcCCCCCCCccccCCCCCCCcccccchhhhhHHHH
Q 013307 150 QIDGRFRDMVLLVKEWAKAHDINNPK-TGTFNSYSLSLLVLFHFQTCVPAILPPLKDIYPGNLVDDLKGVRANAERQIAE 228 (445)
Q Consensus 150 ~~~~~~r~Lv~~iK~Wak~rgL~~~~-~G~Lssy~l~lMvi~fLQ~~~p~ilP~Lq~l~~~~~~~~~~~~~~~~e~~~~e 228 (445)
+..|.|+..++++|.|+++||+.... .||+|++.|++++++.++..... ...
T Consensus 161 ~~~p~f~dA~iLlkvWl~QRg~~~~~~~~Gf~~f~~s~lla~Ll~~g~~~---------~~~------------------ 213 (972)
T PF03813_consen 161 KSSPAFRDACILLKVWLRQRGFGSGISQGGFGGFEWSMLLAYLLQGGGRN---------GKK------------------ 213 (972)
T ss_pred hcCHHHHHHHHHHHHHHhcCCCCcccCCCCcchHHHHHHHHHHHcCCCcc---------CCc------------------
Confidence 44589999999999999999997753 48999999999999988884100 000
Q ss_pred HhhcccccccccccccCCCCCHHHHHHHHHHhhccCCCCcccceeeccCCceeeecccCCCCCCCCCeEEecCCCCCCCc
Q 013307 229 ICAFNIARFSSDKYRKINRSSLAHLFVSFLEKFSGLSLKASELGICPFTGQWEHIRSNTRWLPNNHPLFIEDPFEQPENS 308 (445)
Q Consensus 229 ~~~~n~~~~~~~~~~~~n~~sl~~LL~~FF~~Ys~~df~~~~~~Is~~~g~~~~~~~~~~~~~~~~~L~I~DPf~~~~Nv 308 (445)
.-...+|--++|..++.|-++.||....+.++...+...... . ....+..++.||-.. .|+
T Consensus 214 --------------~l~~~mSsyQlFr~~l~fLA~~d~~~~~l~~~~~~~~~~~~~---~-~~~~~~~vf~D~sg~-~Nl 274 (972)
T PF03813_consen 214 --------------KLSKSMSSYQLFRAVLQFLATTDLSKKPLFFKSSSDSTESLE---E-FHSAFDPVFVDPSGG-LNL 274 (972)
T ss_pred --------------ccCCCCCHHHHHHHHHHHHhccccccCceEEecCCCccchhh---h-hhccCCeEEEeCCCC-EEE
Confidence 011246778999999999999999654444444332111111 1 123567889999986 999
Q ss_pred cccCCHHHHHHHHHHHHHHHHHhhccCC
Q 013307 309 ARAVSEKNLAKISNAFEMTHFRLTSTNQ 336 (445)
Q Consensus 309 ar~vs~~~~~~I~~~f~~A~~~L~~~~~ 336 (445)
+..++...++.++.|-+.+.++|.....
T Consensus 275 ~~~ms~~s~~~L~~eA~~tl~lL~~~~~ 302 (972)
T PF03813_consen 275 LAKMSPSSYEELQHEAKLTLELLDDSSD 302 (972)
T ss_pred EEcCCHHHHHHHHHHHHHHHHHhccccc
Confidence 9999999999999999999999987643
No 14
>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=98.45 E-value=6e-07 Score=75.28 Aligned_cols=103 Identities=28% Similarity=0.300 Sum_probs=63.9
Q ss_pred HHHHHHHHHHCCCCCC--CCCCCcchHHHHHHHHHhhhcCCCCCCCccccCCCCCCCcccccchhhhhHHHHHhhccccc
Q 013307 159 VLLVKEWAKAHDINNP--KTGTFNSYSLSLLVLFHFQTCVPAILPPLKDIYPGNLVDDLKGVRANAERQIAEICAFNIAR 236 (445)
Q Consensus 159 v~~iK~Wak~rgL~~~--~~G~Lssy~l~lMvi~fLQ~~~p~ilP~Lq~l~~~~~~~~~~~~~~~~e~~~~e~~~~n~~~ 236 (445)
|+++|.++|..|+|++ +.+|+|||.-.|||++|=
T Consensus 3 VrLLK~FlK~igvYGse~~~~GFSGYL~ELLii~yG-------------------------------------------- 38 (114)
T PF09249_consen 3 VRLLKQFLKGIGVYGSELKTRGFSGYLCELLIIHYG-------------------------------------------- 38 (114)
T ss_dssp HHHHHHHHHHTT-B-SSTTT-SB-HHHHHHHHHHHS--------------------------------------------
T ss_pred hHHHHHHHhcCCCcchhhhcCcchHHHHHHHHHHHC--------------------------------------------
Confidence 6899999999999987 579999999999999631
Q ss_pred ccccccccCCCCCHHHHHHHHHHhhccCCCCcccceeeccCCceeeecccCCCCCCCCCeEEecCCCCCCCccccCCHHH
Q 013307 237 FSSDKYRKINRSSLAHLFVSFLEKFSGLSLKASELGICPFTGQWEHIRSNTRWLPNNHPLFIEDPFEQPENSARAVSEKN 316 (445)
Q Consensus 237 ~~~~~~~~~n~~sl~~LL~~FF~~Ys~~df~~~~~~Is~~~g~~~~~~~~~~~~~~~~~L~I~DPf~~~~Nvar~vs~~~ 316 (445)
+ |.+.++.-+ +|.. ...|++....-.. + ..+.+|+|.||.||.+|+|+++|..+
T Consensus 39 ------------s----F~~~l~~a~--~W~~-~~~Id~~~~~~~~-~------~f~~PlvviDPvDp~RNVAAalS~~~ 92 (114)
T PF09249_consen 39 ------------S----FENVLEAAA--KWKP-PVVIDLEDHGEPS-K------KFDDPLVVIDPVDPNRNVAAALSLEN 92 (114)
T ss_dssp ------------S----HHHHHHHHT--T--T-TEEEETT-TTE---E------EE-SS-EEEETTEEEEETTTTS-HHH
T ss_pred ------------C----HHHHHHHHH--hcCC-CeEEccCccchhh-h------hcCCCeEEcCCCCCCchHhHhcCHHH
Confidence 0 112333333 5553 4567765321100 0 12578999999999999999999888
Q ss_pred HHHHHHHHHHHHHHhhcc
Q 013307 317 LAKISNAFEMTHFRLTST 334 (445)
Q Consensus 317 ~~~I~~~f~~A~~~L~~~ 334 (445)
+.++..+.+ ..|.++
T Consensus 93 ~~~fv~~ar---~fl~~P 107 (114)
T PF09249_consen 93 LAEFVHAAR---EFLKNP 107 (114)
T ss_dssp HHHHHHHHH---HHHHS-
T ss_pred HHHHHHHHH---HHHHCc
Confidence 777776554 445544
No 15
>smart00572 DZF domain in DSRM or ZnF_C2H2 domain containing proteins.
Probab=98.25 E-value=2.4e-05 Score=74.85 Aligned_cols=200 Identities=14% Similarity=0.155 Sum_probs=129.8
Q ss_pred EEEEecccccCCCCCCC-CcceEEeecCCCcccccchhhHHHHHHHHHHHHHh----cCCceEEEEecccccceEEEEee
Q 013307 49 TVEPFGSFVSNLFSRWG-DLDISIELSNGSCISSAGKKVKQSLLGDLLRALRQ----KGGYRRLQFVAHARVPILKFETI 123 (445)
Q Consensus 49 ~v~~fGS~~tGl~l~~S-DIDl~i~~~~~~~iss~~k~~~~~~L~~l~~~L~~----~~~~~~v~~I~~ArVPIIk~~~~ 123 (445)
.|.-+||++.|+.+.+. ++|+++.+..- +..+.+..+++.|-. ...-.....+..+.+|.+++...
T Consensus 4 gV~rVG~~aKG~ll~Gd~~~~lVv~c~~~---------PT~~ll~~v~~~l~e~l~~~~~~e~~~~~~~~~~~~~~~~i~ 74 (246)
T smart00572 4 GVMRVGSFAKGTLLKGDNVAELVLLCKEK---------PTSELVARLARKLPEQLKAVTEDEALIIVTSTKEPTMEVGIL 74 (246)
T ss_pred ceEEeeeeccCceecCCCceeEEEEecCC---------CcHHHHHHHHHHHHHHHhhcCcccceeeeeccCCCceeEEEE
Confidence 46789999999999987 99999987642 234566666655443 11111112223444565544432
Q ss_pred ccc--eEEEE----------------------eecccccccccHHHhHHhcccchhHHHHHHHHHHHHHCCCCCCCCCCC
Q 013307 124 HQN--ISCDI----------------------SIDNLCGQIKSKFLFWISQIDGRFRDMVLLVKEWAKAHDINNPKTGTF 179 (445)
Q Consensus 124 ~~g--i~~DI----------------------s~~n~~g~~~s~ll~~~~~~~~~~r~Lv~~iK~Wak~rgL~~~~~G~L 179 (445)
-++ ...++ |.....+++.+++.+.-+.--..++.+++++|-|.+.... .+-|
T Consensus 75 ltSp~~r~~~~~~~~~~~~~~~~p~~~ld~~~cl~aLAalRhakWFq~~a~~l~s~~iviRilKd~~~R~~~----~~pL 150 (246)
T smart00572 75 ITSPLARVELLITTVPENLRKLDPEDHLDRKKCLSALASLRHAKWFQARASGLQSCVIVIRVLRDLCNRVPT----WQPL 150 (246)
T ss_pred EecccccccccccccCcccccCCccccCCHHHHHHHHHHHHHhHHHHHhccCCcchhhHHHHHHHHHHhccc----cccc
Confidence 111 11111 1112223445555444444334699999999999888754 3359
Q ss_pred cchHHHHHHHHHhhhcCCCCCCCccccCCCCCCCcccccchhhhhHHHHHhhcccccccccccccCCCCCHHHHHHHHHH
Q 013307 180 NSYSLSLLVLFHFQTCVPAILPPLKDIYPGNLVDDLKGVRANAERQIAEICAFNIARFSSDKYRKINRSSLAHLFVSFLE 259 (445)
Q Consensus 180 ssy~l~lMvi~fLQ~~~p~ilP~Lq~l~~~~~~~~~~~~~~~~e~~~~e~~~~n~~~~~~~~~~~~n~~sl~~LL~~FF~ 259 (445)
++|.+.+++-+.+-.. ....++++.|..||+
T Consensus 151 ~~w~iELl~~~~i~~~-------------------------------------------------~~~l~~~~a~RR~fe 181 (246)
T smart00572 151 SGWPLELLVEKAIGSA-------------------------------------------------RQPLGLGDAFRRVFE 181 (246)
T ss_pred ccccHHHHHHHHhccC-------------------------------------------------CCCCCHHHHHHHHHH
Confidence 9999999997644221 123578999999999
Q ss_pred hhccCCCCcccceeeccCCceeeecccCCCCCCCCCeEEecCCCC-CCCccccCCHHHHHHHHHHHHHHHHHhhccC
Q 013307 260 KFSGLSLKASELGICPFTGQWEHIRSNTRWLPNNHPLFIEDPFEQ-PENSARAVSEKNLAKISNAFEMTHFRLTSTN 335 (445)
Q Consensus 260 ~Ys~~df~~~~~~Is~~~g~~~~~~~~~~~~~~~~~L~I~DPf~~-~~Nvar~vs~~~~~~I~~~f~~A~~~L~~~~ 335 (445)
+-++=.| +.| ...|.||.+. .+|++..++....+.|...-..|.+++.-..
T Consensus 182 ~lAsG~l---------~p~----------------~~gI~DPce~~~~nv~~~lT~qqrd~It~sAQ~alRl~Afgq 233 (246)
T smart00572 182 CLASGIL---------LPG----------------SPGLTDPCEKDNTDALTALTLQQREDVTASAQTALRLLAFGQ 233 (246)
T ss_pred HHHhccC---------cCC----------------CCCCcCCCCCCcccHHHhcCHHHHHHHHHHHHHHHHHHHhcc
Confidence 9986222 011 1478999996 8999999999999999999999999998653
No 16
>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=98.03 E-value=1.1e-05 Score=58.20 Aligned_cols=41 Identities=20% Similarity=0.469 Sum_probs=34.6
Q ss_pred HHHHHHHHHHHhhhcCCCcEEEEecccccCCCCCCCCcceEEe
Q 013307 30 KVISDLREVVESVESLRGATVEPFGSFVSNLFSRWGDLDISIE 72 (445)
Q Consensus 30 ~vi~~l~~il~~~~~~~~~~v~~fGS~~tGl~l~~SDIDl~i~ 72 (445)
++++.+++.+++. .+...+..|||++.|.+.+.||||+++.
T Consensus 2 ~~l~~i~~~l~~~--~~~~~v~lfGS~arg~~~~~SDIDi~v~ 42 (49)
T cd05397 2 ELLDIIKERLKKL--VPGYEIVVYGSLVRGLLKKSSDIDLACV 42 (49)
T ss_pred HHHHHHHHHHHhh--cCCcEEEEECCcCCCCCCCCCCEEEEEE
Confidence 4566777777765 4578999999999999999999999985
No 17
>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=98.00 E-value=7e-05 Score=66.15 Aligned_cols=97 Identities=21% Similarity=0.216 Sum_probs=62.3
Q ss_pred HHHHHHHHHHHHHhhhcCCCcEEEEecccccCCCCC-CCCcceEEeecCCCcccccchhhHHHHHHHHHHHHHhcCCceE
Q 013307 28 RMKVISDLREVVESVESLRGATVEPFGSFVSNLFSR-WGDLDISIELSNGSCISSAGKKVKQSLLGDLLRALRQKGGYRR 106 (445)
Q Consensus 28 R~~vi~~l~~il~~~~~~~~~~v~~fGS~~tGl~l~-~SDIDl~i~~~~~~~iss~~k~~~~~~L~~l~~~L~~~~~~~~ 106 (445)
...+.+.|++-..... .+...+.+|||++.|++++ .||||+++.++..... .......++..|.+.|.....- .
T Consensus 9 ~~~i~~~L~~~~~~~~-~~~~~~~~~GS~a~~T~i~~~sDiD~~v~~~~~~~~---~~~~~~~~~~~l~~~L~~~~~~-~ 83 (143)
T cd05400 9 YREIREALKESLSELA-GRVAEVFLQGSYARGTALRGDSDIDLVVVLPDDTSF---AEYGPAELLDELGEALKEYYGA-N 83 (143)
T ss_pred HHHHHHHHHHhccccc-ccccEEEEEcceeCCCCCCCCCceeEEEEEcCcccc---cccCHHHHHHHHHHHHHHhcCc-c
Confidence 3344444444433210 2457999999999999988 7999999998764211 0123457888899988875431 1
Q ss_pred EEEecccccceEEEEeeccceEEEE
Q 013307 107 LQFVAHARVPILKFETIHQNISCDI 131 (445)
Q Consensus 107 v~~I~~ArVPIIk~~~~~~gi~~DI 131 (445)
... ...-|-|++.....++.+||
T Consensus 84 ~~~--~~~~~~v~v~~~~~~~~vDv 106 (143)
T cd05400 84 EEV--KAQHRSVTVKFKGQGFHVDV 106 (143)
T ss_pred ccc--ccCceEEEEEEcCCCeEEEE
Confidence 121 34446666666435899999
No 18
>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=97.88 E-value=1.1e-05 Score=65.56 Aligned_cols=43 Identities=26% Similarity=0.398 Sum_probs=36.4
Q ss_pred HHHHHHHHHhhhcCCCcEEEEecccccCCCCCCCCcceEEeecCC
Q 013307 32 ISDLREVVESVESLRGATVEPFGSFVSNLFSRWGDLDISIELSNG 76 (445)
Q Consensus 32 i~~l~~il~~~~~~~~~~v~~fGS~~tGl~l~~SDIDl~i~~~~~ 76 (445)
++.+.+.+++. ++...+.+|||++.|.+.++||||++|..+..
T Consensus 1 i~~i~~~l~~~--~~~~~v~lfGS~a~g~~~~~SDIDl~i~~~~~ 43 (93)
T PF01909_consen 1 IEEIKEILKEL--FGVAEVYLFGSYARGDATPDSDIDLLIILDEP 43 (93)
T ss_dssp HHHHHHHHHHH--HTTEEEEEEHHHHHTSSCTTSCEEEEEEESST
T ss_pred CHHHHHHHHHH--CCCCEEEEECCcccCcCCCCCCEEEEEEeCCc
Confidence 45677777776 35789999999999999999999999988763
No 19
>KOG2054 consensus Nucleolar RNA-associated protein (NRAP) [Function unknown]
Probab=97.71 E-value=0.00059 Score=75.74 Aligned_cols=233 Identities=16% Similarity=0.176 Sum_probs=143.3
Q ss_pred CCcEEE-EecccccCCCC-CCCCcceEEeecCCC-----cccccchh--hHHHHHHHHHHHHHhcCCceEEEEec---cc
Q 013307 46 RGATVE-PFGSFVSNLFS-RWGDLDISIELSNGS-----CISSAGKK--VKQSLLGDLLRALRQKGGYRRLQFVA---HA 113 (445)
Q Consensus 46 ~~~~v~-~fGS~~tGl~l-~~SDIDl~i~~~~~~-----~iss~~k~--~~~~~L~~l~~~L~~~~~~~~v~~I~---~A 113 (445)
+..++. +.||+..|..+ |++-+|+.+.+|.+. +.+ .|. .+.-.|..++..|-....+..++... .-
T Consensus 146 ~p~~v~~vv~sal~~~~~~P~i~vDvll~mP~e~~~~kd~ln--~Ryf~kra~yla~~~~hl~e~l~~~~~~f~~~n~d~ 223 (1121)
T KOG2054|consen 146 PPAQVTKVVGSALLGTCLRPDISVDVLLTMPREILQQKDGLN--QRYFRKRALYLAYLAHHLLEDLLFGSLEFSYTNGDH 223 (1121)
T ss_pred CccccceeeeecccCcccCCcchhhhhhhhhHHhhcCccccc--ccccchHHHHHHHHHHHHHhccccceeeecccCCcc
Confidence 345555 66788777665 458999999888542 111 111 12346667777777666555555432 23
Q ss_pred ccceEEEEeeccceEEEEe---------------ec------ccc--------------cccccHH-----HhHHh----
Q 013307 114 RVPILKFETIHQNISCDIS---------------ID------NLC--------------GQIKSKF-----LFWIS---- 149 (445)
Q Consensus 114 rVPIIk~~~~~~gi~~DIs---------------~~------n~~--------------g~~~s~l-----l~~~~---- 149 (445)
+-||+.+.. .|-..|.. |. +.+ -..|+.. +..|.
T Consensus 224 ~~pil~i~~--~~~~~~~~~~~~~~~li~~~~~~f~~~kllp~~~~ir~~~e~~e~ppTP~yN~svL~~~~le~~~q~L~ 301 (1121)
T KOG2054|consen 224 LKPILLIRP--RGKDERLVTVRPPDFLIPCRLLPFKNNKLLPWYNGIRPAGEGSEEPPTPRYNTSVLEDQVLEEYLQLLS 301 (1121)
T ss_pred ccchhhccc--cCCccccccccCccccccccccccccccccchhcccCccccCCCCCCCCccchhHHHHHHHHHHHHHHH
Confidence 568887764 22222221 00 011 1233322 12222
Q ss_pred ---cccchhHHHHHHHHHHHHHCCCCCCCCCCCcchHHHHHHHHHhhhcCCCCCCCccccCCCCCCCcccccchhhhhHH
Q 013307 150 ---QIDGRFRDMVLLVKEWAKAHDINNPKTGTFNSYSLSLLVLFHFQTCVPAILPPLKDIYPGNLVDDLKGVRANAERQI 226 (445)
Q Consensus 150 ---~~~~~~r~Lv~~iK~Wak~rgL~~~~~G~Lssy~l~lMvi~fLQ~~~p~ilP~Lq~l~~~~~~~~~~~~~~~~e~~~ 226 (445)
+..+.|+..+.++|.|+++|.+.. ..||+|++-+++++++.+... ++
T Consensus 302 K~~s~~~~f~da~~Llk~WlrqRs~~~-~~~gfg~f~~s~lvv~L~s~~---ki-------------------------- 351 (1121)
T KOG2054|consen 302 KTLSSAKGFKDALALLKVWLRQRSLDI-GQGGFGGFLLSALVVYLVSTR---KI-------------------------- 351 (1121)
T ss_pred HHHhhhhhHHHHHHHHHHHHHhhhhhc-ccCcchHHHHHHHHHHHHhcC---ch--------------------------
Confidence 234679999999999999995432 468999999999999766553 11
Q ss_pred HHHhhcccccccccccccCCCCCHHHHHHHHHHhhccCCCCcccceeeccCCceeeecccCCCCCCCCCeEEecCCCCCC
Q 013307 227 AEICAFNIARFSSDKYRKINRSSLAHLFVSFLEKFSGLSLKASELGICPFTGQWEHIRSNTRWLPNNHPLFIEDPFEQPE 306 (445)
Q Consensus 227 ~e~~~~n~~~~~~~~~~~~n~~sl~~LL~~FF~~Ys~~df~~~~~~Is~~~g~~~~~~~~~~~~~~~~~L~I~DPf~~~~ 306 (445)
....|..++|..-++|.++.|+.. .+|+..... .......... ..+..+..|=-. ..
T Consensus 352 ------------------~~~~S~yqvfR~vl~flat~dlt~--~~~~l~~~~-~s~~~~~~f~-e~~~~~f~D~s~-~~ 408 (1121)
T KOG2054|consen 352 ------------------HTTLSAYQVFRSVLQFLATTDLTV--NGISLVPSS-PSLPALADFH-EGQLVTFIDSSG-HL 408 (1121)
T ss_pred ------------------hhcchHHHHHHHHHHHHhhhhhhc--cceEeccCC-CCchhhhhhh-hcceeeEeccCC-cc
Confidence 013567899999999999888863 355432211 0001111011 124566666554 58
Q ss_pred CccccCCHHHHHHHHHHHHHHHHHhhccC
Q 013307 307 NSARAVSEKNLAKISNAFEMTHFRLTSTN 335 (445)
Q Consensus 307 Nvar~vs~~~~~~I~~~f~~A~~~L~~~~ 335 (445)
|++.+++...+++++++.+.++.+|.+..
T Consensus 409 NLc~~mt~s~y~~~q~ea~ltl~lL~~~~ 437 (1121)
T KOG2054|consen 409 NLCANMTASTYEQVQEEARLTLMLLDSRA 437 (1121)
T ss_pred hhhhhccHHHHHHHHHHHHHHHHHHhhhh
Confidence 99999999999999999999999999654
No 20
>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=97.47 E-value=0.00097 Score=61.54 Aligned_cols=56 Identities=18% Similarity=0.377 Sum_probs=40.3
Q ss_pred cccHHHhHHhcccc-hhHHHHHHHHHHHHHCCCCCCCCCCC-cchHHHHHHHHHhhhc
Q 013307 140 IKSKFLFWISQIDG-RFRDMVLLVKEWAKAHDINNPKTGTF-NSYSLSLLVLFHFQTC 195 (445)
Q Consensus 140 ~~s~ll~~~~~~~~-~~r~Lv~~iK~Wak~rgL~~~~~G~L-ssy~l~lMvi~fLQ~~ 195 (445)
..+++-+.|++..| .++.|+++||+|.++..-.....+.+ ++|+|.||+||.-.+.
T Consensus 28 cftelQ~~Fvk~rP~klK~LIrLVKhWy~~~~~~~~~~~~lPpsYaLELLtIyAWE~g 85 (190)
T PF10421_consen 28 CFTELQRNFVKHRPTKLKNLIRLVKHWYQQCKKKKCGGGSLPPSYALELLTIYAWEQG 85 (190)
T ss_dssp GGHHHHHHHHHTS-HHHHHHHHHHHHHHHHHHCC--HTT-S--HHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHhhccCCCCCcHHHHHHHHHHHHHHhc
Confidence 44566667766555 89999999999999876654444555 6899999999987664
No 21
>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=97.45 E-value=0.00024 Score=57.25 Aligned_cols=45 Identities=16% Similarity=0.279 Sum_probs=34.4
Q ss_pred HHHHHHHHHHhhhcCCCcEEEEecccccCCCCCCCCcceEEeecCC
Q 013307 31 VISDLREVVESVESLRGATVEPFGSFVSNLFSRWGDLDISIELSNG 76 (445)
Q Consensus 31 vi~~l~~il~~~~~~~~~~v~~fGS~~tGl~l~~SDIDl~i~~~~~ 76 (445)
.++.+.+.+++... .-..+..|||++.|-+.++||||+++.....
T Consensus 3 ~~~~i~~~l~~~~~-~i~~i~LfGS~arg~~~~~SDiDl~vi~~~~ 47 (93)
T cd05403 3 ILEEILEILRELLG-GVEKVYLFGSYARGDARPDSDIDLLVIFDDP 47 (93)
T ss_pred hHHHHHHHHHHHhC-CccEEEEEeeeecCCCCCCCCeeEEEEeCCC
Confidence 34555556655421 2579999999999999999999999987653
No 22
>COG1669 Predicted nucleotidyltransferases [General function prediction only]
Probab=96.97 E-value=0.0049 Score=50.68 Aligned_cols=44 Identities=20% Similarity=0.353 Sum_probs=34.2
Q ss_pred HHHHHHHHHHhhhcCCCcEEEEecccccCCCCCCCCcceEEeecCC
Q 013307 31 VISDLREVVESVESLRGATVEPFGSFVSNLFSRWGDLDISIELSNG 76 (445)
Q Consensus 31 vi~~l~~il~~~~~~~~~~v~~fGS~~tGl~l~~SDIDl~i~~~~~ 76 (445)
++..+...+++. +.-.++..|||++-|-..|+||||+.|.+..+
T Consensus 10 ~lr~~~~~l~~k--~gv~~~~vFGS~aRgE~~~~SDIDILVef~~~ 53 (97)
T COG1669 10 ILRKIKPELKEK--YGVKRVAVFGSYARGEQKPDSDIDILVEFEPG 53 (97)
T ss_pred HHHHHHHHHHHH--hCCceEEEeeeeecCCCCCCCCceeEEeecCC
Confidence 355555556543 33469999999999999999999999987654
No 23
>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=96.79 E-value=0.058 Score=52.35 Aligned_cols=197 Identities=16% Similarity=0.189 Sum_probs=118.2
Q ss_pred ecccccCCCCCCC-CcceEEeecCCCcccccchhhHHHHHHHHHHHHHhc----CCceEEE-------EecccccceEEE
Q 013307 53 FGSFVSNLFSRWG-DLDISIELSNGSCISSAGKKVKQSLLGDLLRALRQK----GGYRRLQ-------FVAHARVPILKF 120 (445)
Q Consensus 53 fGS~~tGl~l~~S-DIDl~i~~~~~~~iss~~k~~~~~~L~~l~~~L~~~----~~~~~v~-------~I~~ArVPIIk~ 120 (445)
+||++-|+.+.+. ++|+++.+..- ...++|.++++.|.+. .. .++. .+.....|.+..
T Consensus 2 VG~~aKGllL~Gd~~~eLVVlck~k---------PT~~lL~~v~~~L~~~L~~~~~-~ev~~~~e~~~~~~~~~~~~~~~ 71 (248)
T PF07528_consen 2 VGSFAKGLLLKGDNDVELVVLCKEK---------PTKELLNRVAEKLPEQLKKVTP-EEVTNSVEAAIIIDSCKEPKLEV 71 (248)
T ss_pred cceecCCceecCCceEeEEEEcCCC---------CcHHHHHHHHHHHHHHHhhhCc-cccccchhhhhhhccccccccee
Confidence 6999999999988 99999987652 2345666666655432 11 1111 011122233332
Q ss_pred Eeecc--ceEEEEee----------------------cccccccccHHHhHHhcccchhHHHHHHHHHHHHHCCCCCCCC
Q 013307 121 ETIHQ--NISCDISI----------------------DNLCGQIKSKFLFWISQIDGRFRDMVLLVKEWAKAHDINNPKT 176 (445)
Q Consensus 121 ~~~~~--gi~~DIs~----------------------~n~~g~~~s~ll~~~~~~~~~~r~Lv~~iK~Wak~rgL~~~~~ 176 (445)
...-+ .+.+.+.. .+..+++.+++.+.-+..-+..+.+++++|-...+.. ..
T Consensus 72 ~~~lts~~~r~~~~~~~~~~~~~~~dp~~~Ld~~~cl~aLaalRhakWFq~~a~~l~s~~~viRIlrDl~~R~p----~w 147 (248)
T PF07528_consen 72 GIDLTSPVMRVRVLITTIPENLSKLDPEDHLDRKKCLSALAALRHAKWFQARANGLQSCVIVIRILRDLRQRVP----TW 147 (248)
T ss_pred eEEecCCceEEEEeccccCccccccChhhcCCHHHHHHHHHHHHHhHHHHHHhccCCCcceehhhHHHHHHhCC----CC
Confidence 21111 12222211 1122334444444434333456778888888765542 35
Q ss_pred CCCcchHHHHHHHHHhhhcCCCCCCCccccCCCCCCCcccccchhhhhHHHHHhhcccccccccccccCCCCCHHHHHHH
Q 013307 177 GTFNSYSLSLLVLFHFQTCVPAILPPLKDIYPGNLVDDLKGVRANAERQIAEICAFNIARFSSDKYRKINRSSLAHLFVS 256 (445)
Q Consensus 177 G~Lssy~l~lMvi~fLQ~~~p~ilP~Lq~l~~~~~~~~~~~~~~~~e~~~~e~~~~n~~~~~~~~~~~~n~~sl~~LL~~ 256 (445)
+.|+++.+-+|+-+-+-... .....++++.|..
T Consensus 148 ~~L~~W~leLL~~~~i~~~~-----------------------------------------------~~~~l~~g~a~RR 180 (248)
T PF07528_consen 148 QPLSSWALELLVEKAISNNS-----------------------------------------------SRQPLSPGDAFRR 180 (248)
T ss_pred CCCChhHHHHHHHHHeeeCC-----------------------------------------------CCCCCChHHHHHH
Confidence 67888888887775333210 1124678999999
Q ss_pred HHHhhccCCCCcccceeeccCCceeeecccCCCCCCCCCeEEecCCC-CCCCccccCCHHHHHHHHHHHHHHHHHhhccC
Q 013307 257 FLEKFSGLSLKASELGICPFTGQWEHIRSNTRWLPNNHPLFIEDPFE-QPENSARAVSEKNLAKISNAFEMTHFRLTSTN 335 (445)
Q Consensus 257 FF~~Ys~~df~~~~~~Is~~~g~~~~~~~~~~~~~~~~~L~I~DPf~-~~~Nvar~vs~~~~~~I~~~f~~A~~~L~~~~ 335 (445)
||+.-|. ||=. .| .--|.||.+ .+.|+...++....+.|...-+.+.+++.-..
T Consensus 181 vle~las--------Gill-p~----------------~~gl~DPcE~~~~~~~~~lt~qq~e~it~sAQ~~LRllafgq 235 (248)
T PF07528_consen 181 VLECLAS--------GILL-PG----------------SPGLRDPCEKDPVDVLDTLTLQQREDITSSAQTALRLLAFGQ 235 (248)
T ss_pred HHHHHhC--------ceec-CC----------------CCCCcCCCCCCCceeeccCCHHHHHHHHHHHHHHHHHHHhcC
Confidence 9999874 2210 01 124678998 67889999999999999999999999998653
No 24
>PF03813 Nrap: Nrap protein; InterPro: IPR005554 Members of this family are nucleolar RNA-associated proteins (Nrap) which are highly conserved from yeast (Saccharomyces cerevisiae) to human. In the mouse, Nrap is ubiquitously expressed and is specifically localized in the nucleolus []. Nrap is a large nucleolar protein (of more than 1000 amino acids). Nrap appears to be associated with ribosome biogenesis by interacting with pre-rRNA primary transcript [].
Probab=96.46 E-value=1.1 Score=52.13 Aligned_cols=262 Identities=17% Similarity=0.202 Sum_probs=153.6
Q ss_pred CHHHHHHHHHHHHHHHHHHHhhhcCCC--cEEEEeccc--ccCCCCCC--------CCcceEEeecCCC-ccccc--chh
Q 013307 21 LREDWETRMKVISDLREVVESVESLRG--ATVEPFGSF--VSNLFSRW--------GDLDISIELSNGS-CISSA--GKK 85 (445)
Q Consensus 21 t~ee~~~R~~vi~~l~~il~~~~~~~~--~~v~~fGS~--~tGl~l~~--------SDIDl~i~~~~~~-~iss~--~k~ 85 (445)
..+....-.++++.|.+.|+++...|= ..|.|.++. .|.+..|. --+|++|.+.... |.... -++
T Consensus 497 ~~~~~~~~~~af~~L~k~lr~L~~LPL~I~~v~p~sp~lRyts~~pp~p~~~~~~~~p~~vvl~fE~S~kWPddl~AI~~ 576 (972)
T PF03813_consen 497 DEESFQSVMRAFDELEKDLRSLEDLPLSITSVQPASPALRYTSVFPPVPHAVPRYIPPIEVVLQFESSGKWPDDLEAIQK 576 (972)
T ss_pred chHHHHHHHHHHHHHHHHHhcCccCCcceeeeccCCHhhhcCCCCCCCCccccCCCCCEEEEEEEecCCCCCCCHHHHHH
Confidence 344555666888888888888743331 244555444 22333322 2578888776432 21110 012
Q ss_pred hHHHHHHHHHHHHHh-cCCceEEEEe-ccc-----ccceEEEEeeccceEEEEeecc-------------cccc------
Q 013307 86 VKQSLLGDLLRALRQ-KGGYRRLQFV-AHA-----RVPILKFETIHQNISCDISIDN-------------LCGQ------ 139 (445)
Q Consensus 86 ~~~~~L~~l~~~L~~-~~~~~~v~~I-~~A-----rVPIIk~~~~~~gi~~DIs~~n-------------~~g~------ 139 (445)
-+..++-+|++.|++ .+......+. .+. ..--+-+.. ..|+.+.+.+.. ..+.
T Consensus 577 ~K~Af~lkiae~L~~~~~~~~~~~v~~~~~~~~~~~~~~ldV~~-~~G~~FRl~I~~~rE~~Ll~~~~~~~~~~~k~~~~ 655 (972)
T PF03813_consen 577 TKTAFLLKIAEELEKQYGDGIKARVGLDNSLSPIANQAFLDVLY-PEGYVFRLRIYHDREETLLKRQLKTEDGQLKQEAT 655 (972)
T ss_pred HHHHHHHHHHHHHHHhhCCcceeeecccccccceeccceEEEEe-cCccEEEEEEecchhHHHHHHhhcccCcccchhhh
Confidence 345788899999984 3311111111 111 111222222 256666654421 1111
Q ss_pred --------------cccHHHhHHhcccchhHHHHHHHHHHHHHCCCCCCCCCCCcchHHHHHHHHHhhhcCCCCCCCccc
Q 013307 140 --------------IKSKFLFWISQIDGRFRDMVLLVKEWAKAHDINNPKTGTFNSYSLSLLVLFHFQTCVPAILPPLKD 205 (445)
Q Consensus 140 --------------~~s~ll~~~~~~~~~~r~Lv~~iK~Wak~rgL~~~~~G~Lssy~l~lMvi~fLQ~~~p~ilP~Lq~ 205 (445)
..+..|..+...+|.|-+.++++|+|+..+-| .+.++.-++.|||++.+-... |.
T Consensus 656 ~~~~~~~~~~~~~p~h~~~i~~l~~~~p~fs~tvRL~KrW~~shlL----s~~i~~E~vELlva~vfl~~~-p~------ 724 (972)
T PF03813_consen 656 EALASLERRFIHLPKHTSAIHGLHTRFPSFSPTVRLAKRWLSSHLL----SGHISEEAVELLVASVFLSPA-PW------ 724 (972)
T ss_pred HHHHHHHHHHHhhHHHHHHHHHHHhhCCchhHHHHHHHHHHHhccC----cccCCHHHHHHHHHHHhcCCC-CC------
Confidence 12233555566779999999999999999977 468899999999998775531 10
Q ss_pred cCCCCCCCcccccchhhhhHHHHHhhcccccccccccccCCCCCHHHHHHHHHHhhccCCCCcccceeeccCCceee---
Q 013307 206 IYPGNLVDDLKGVRANAERQIAEICAFNIARFSSDKYRKINRSSLAHLFVSFLEKFSGLSLKASELGICPFTGQWEH--- 282 (445)
Q Consensus 206 l~~~~~~~~~~~~~~~~e~~~~e~~~~n~~~~~~~~~~~~n~~sl~~LL~~FF~~Ys~~df~~~~~~Is~~~g~~~~--- 282 (445)
....|...-|+.|+++-++|||..+-.+|+... ....
T Consensus 725 ---------------------------------------~~P~S~~~GFlRfL~lLs~~dW~~~PLiVd~~~-~l~~~~~ 764 (972)
T PF03813_consen 725 ---------------------------------------SPPSSPQTGFLRFLHLLSTWDWREEPLIVDFNN-ELTEEDR 764 (972)
T ss_pred ---------------------------------------CCCCCHhHHHHHHHHHHHhCCCCcCCEEEECCC-CCCHHHH
Confidence 012355667889999999999987666666542 1110
Q ss_pred --ecc----cCCCCC--CCCCeEEecCCCCCCCccc--cCCHHHHHHHHHHHHHHHHHhhcc
Q 013307 283 --IRS----NTRWLP--NNHPLFIEDPFEQPENSAR--AVSEKNLAKISNAFEMTHFRLTST 334 (445)
Q Consensus 283 --~~~----~~~~~~--~~~~L~I~DPf~~~~Nvar--~vs~~~~~~I~~~f~~A~~~L~~~ 334 (445)
+.. .+...| ....|+|-.|+|+.--... .-+...+.+|+..-+.|+++|...
T Consensus 765 ~~i~~~f~~~R~~dp~~~~p~~~IaT~~D~~g~~wT~~~Ps~~v~~Rl~~LAk~sl~~l~~~ 826 (972)
T PF03813_consen 765 AEIETNFDAWRKIDPAMNLPAMFIATPYDPEGSLWTRNGPSKVVAKRLTALAKASLKLLEEQ 826 (972)
T ss_pred HHHHHHHHHhhccCccccCCcEEEEeCCCCCCCEeECCCCCHHHHHHHHHHHHHHHHHHHhc
Confidence 000 000011 2457999999998544333 344557899999999999999943
No 25
>COG1708 Predicted nucleotidyltransferases [General function prediction only]
Probab=96.35 E-value=0.0075 Score=51.32 Aligned_cols=30 Identities=20% Similarity=0.277 Sum_probs=27.1
Q ss_pred CCCcEEEEecccccCCCCCCCCcceEEeec
Q 013307 45 LRGATVEPFGSFVSNLFSRWGDLDISIELS 74 (445)
Q Consensus 45 ~~~~~v~~fGS~~tGl~l~~SDIDl~i~~~ 74 (445)
.....++.|||++.|-+.+.||||+++...
T Consensus 24 ~~~~~v~LfGS~arG~~~~~SDiDv~vv~~ 53 (128)
T COG1708 24 GGDLLIYLFGSYARGDFVKESDIDLLVVSD 53 (128)
T ss_pred CCCeEEEEEccCcccccccCCCeeEEEEcC
Confidence 456899999999999999999999999863
No 26
>PF14091 DUF4269: Domain of unknown function (DUF4269)
Probab=95.87 E-value=0.14 Score=45.78 Aligned_cols=113 Identities=14% Similarity=0.110 Sum_probs=66.6
Q ss_pred CcEEEEecccccCCCCCCCCcceEEeecCCCcccccchhhHHHHHHHHHHHHHhcCCceEE-EEecccccceEEEEeecc
Q 013307 47 GATVEPFGSFVSNLFSRWGDLDISIELSNGSCISSAGKKVKQSLLGDLLRALRQKGGYRRL-QFVAHARVPILKFETIHQ 125 (445)
Q Consensus 47 ~~~v~~fGS~~tGl~l~~SDIDl~i~~~~~~~iss~~k~~~~~~L~~l~~~L~~~~~~~~v-~~I~~ArVPIIk~~~~~~ 125 (445)
.......|....|+..++|||||+|..++ ...+...+.+...+...+.-- ..| ...|.+.......
T Consensus 15 ~~~PiL~GTiPi~Idi~~SDLDIic~~~d-----------~~~F~~~l~~~f~~~~~f~~~~~~i--~~~~~~~~~F~~~ 81 (152)
T PF14091_consen 15 AYDPILVGTIPIGIDIPGSDLDIICEVPD-----------PEAFEQLLQSLFGQFEGFTIKEKTI--RGEPSIVANFRYE 81 (152)
T ss_pred cCCCEEecccccccCCCCCCccEEEEeCC-----------HHHHHHHHHHHhccCCCceeeecee--CCceeEEEEEEEC
Confidence 45778899999999999999999998764 223444444443333333211 112 2334333333348
Q ss_pred ceEEEEeecc-----cccccccHHHhHHhccc-chhHHHHHHHH--------HHHHHCCCC
Q 013307 126 NISCDISIDN-----LCGQIKSKFLFWISQID-GRFRDMVLLVK--------EWAKAHDIN 172 (445)
Q Consensus 126 gi~~DIs~~n-----~~g~~~s~ll~~~~~~~-~~~r~Lv~~iK--------~Wak~rgL~ 172 (445)
|..+.|-..+ .+|.+.-.+-....+.. |.+|.=++-+| +||+.-||.
T Consensus 82 ~~~~EiF~Q~~Pv~~QnayrHm~iE~rLL~~~g~~~r~~Ii~LK~~GlKTEPAFa~lLgL~ 142 (152)
T PF14091_consen 82 GFPFEIFGQPIPVEEQNAYRHMLIEHRLLELHGPSFREEIIELKESGLKTEPAFAKLLGLE 142 (152)
T ss_pred CceEEEeecCCChhhHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHcCCcchHHHHHHhCCC
Confidence 9999986643 23333333323333333 78888888887 466666654
No 27
>PRK13746 aminoglycoside resistance protein; Provisional
Probab=95.87 E-value=0.033 Score=54.51 Aligned_cols=29 Identities=17% Similarity=0.322 Sum_probs=26.0
Q ss_pred cEEEEecccccCCCCCCCCcceEEeecCC
Q 013307 48 ATVEPFGSFVSNLFSRWGDLDISIELSNG 76 (445)
Q Consensus 48 ~~v~~fGS~~tGl~l~~SDIDl~i~~~~~ 76 (445)
.-|+.|||.+.|-+.+.||||+.++....
T Consensus 29 ~~vyLfGS~~~G~~~p~SDIDllvvv~~~ 57 (262)
T PRK13746 29 LAIHLYGSAVDGGLKPHSDIDLLVTVAVP 57 (262)
T ss_pred EEEEEECCcccCCCCCCCceeEEEEeCCC
Confidence 37899999999999999999999988753
No 28
>KOG2054 consensus Nucleolar RNA-associated protein (NRAP) [Function unknown]
Probab=94.35 E-value=5.5 Score=45.43 Aligned_cols=140 Identities=19% Similarity=0.203 Sum_probs=88.6
Q ss_pred HhHHhcccchhHHHHHHHHHHHHHCCCCCCCCCCCcchHHHHHHHHHhhhcCCCCCCCccccCCCCCCCcccccchhhhh
Q 013307 145 LFWISQIDGRFRDMVLLVKEWAKAHDINNPKTGTFNSYSLSLLVLFHFQTCVPAILPPLKDIYPGNLVDDLKGVRANAER 224 (445)
Q Consensus 145 l~~~~~~~~~~r~Lv~~iK~Wak~rgL~~~~~G~Lssy~l~lMvi~fLQ~~~p~ilP~Lq~l~~~~~~~~~~~~~~~~e~ 224 (445)
|+.+.+.++.+-+.+++.|.|+...=|. |++---++.|+|++.++...|...
T Consensus 811 L~~l~qsh~~ys~vvrLaKrWl~shLL~----~h~~De~iELLva~lf~~p~p~~~------------------------ 862 (1121)
T KOG2054|consen 811 LQSLSQSHPFYSSVVRLAKRWLGSHLLS----GHHLDEAIELLVAALFLKPGPLVP------------------------ 862 (1121)
T ss_pred HHHHhhcccchhHHHHHHHHHHHHHhhc----cchHHHHHHHHHHHHhcCccCCCC------------------------
Confidence 4555667789999999999999888664 466689999999998887532211
Q ss_pred HHHHHhhcccccccccccccCCCCCHHHHHHHHHHhhccCCCCcccceeeccCCceee-----ecccC-CCCCCCCCeEE
Q 013307 225 QIAEICAFNIARFSSDKYRKINRSSLAHLFVSFLEKFSGLSLKASELGICPFTGQWEH-----IRSNT-RWLPNNHPLFI 298 (445)
Q Consensus 225 ~~~e~~~~n~~~~~~~~~~~~n~~sl~~LL~~FF~~Ys~~df~~~~~~Is~~~g~~~~-----~~~~~-~~~~~~~~L~I 298 (445)
..|...=|+.|+++-++|||...-..++. ++++.. +.++- .--+.-.+|+|
T Consensus 863 ----------------------psS~~~gFlRfL~llS~~dW~~~PLIvd~-nn~~~ed~~~e~~e~f~s~R~~lp~m~v 919 (1121)
T KOG2054|consen 863 ----------------------PSSPENGFLRFLSLLSTWDWKFDPLIVDF-NNGFPEDERSELEEKFISARKQLPPMVV 919 (1121)
T ss_pred ----------------------CCCcchhHHHHHHHHhcCcccCCceEEEc-CCCCcHHHHHHHHHHHhhhcccCCceEE
Confidence 12333447889999999999877666665 443321 01100 00012238999
Q ss_pred ecCCCCCCCccccCCHH--HHHHHHHHHHHHHHHhhccC
Q 013307 299 EDPFEQPENSARAVSEK--NLAKISNAFEMTHFRLTSTN 335 (445)
Q Consensus 299 ~DPf~~~~Nvar~vs~~--~~~~I~~~f~~A~~~L~~~~ 335 (445)
..|+|-..+.--.-+.. -..++...-+.+..++....
T Consensus 920 it~yD~~~~~~t~~~P~~~v~~r~~alar~sl~ll~k~~ 958 (1121)
T KOG2054|consen 920 ITPYDHLGSKFTRTSPNQIVLNRLVALARESLKLLEKQA 958 (1121)
T ss_pred eeccccccccccccCchHHHHHHHHHhhhhhHHhhcccc
Confidence 99999755443333332 24555555566666666543
No 29
>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=92.93 E-value=0.27 Score=41.79 Aligned_cols=71 Identities=30% Similarity=0.363 Sum_probs=48.9
Q ss_pred HHHHHHHHHHHhhhcCCCcEEEEecccccCCCCCCCCcceEEeecCCCcccccchhhHHHHHHHHHHHHHhcCCceEE
Q 013307 30 KVISDLREVVESVESLRGATVEPFGSFVSNLFSRWGDLDISIELSNGSCISSAGKKVKQSLLGDLLRALRQKGGYRRL 107 (445)
Q Consensus 30 ~vi~~l~~il~~~~~~~~~~v~~fGS~~tGl~l~~SDIDl~i~~~~~~~iss~~k~~~~~~L~~l~~~L~~~~~~~~v 107 (445)
++.+.|++.+..+ .|++.+.+-|||.-|-.+ .+|||+++..++..... .....+|..+...|.+.+.+...
T Consensus 9 ~i~~~V~~~~~~i--~p~~~v~i~GSyRRGK~~-~gDiDiLIt~~~~~~~~----~~~~~~l~~lv~~L~~~g~i~~~ 79 (112)
T PF14792_consen 9 EIEEIVKEALEKI--DPGLEVEICGSYRRGKET-SGDIDILITHPDPSSVS----KKLEGLLEKLVKRLEEKGFITDD 79 (112)
T ss_dssp HHHHHHHHHHHCC--STT-EEEEEHHHHTT-SE-ESSEEEEEEETTCSTTT----CSTTCHHHHHHHHHHHTTSEEEE
T ss_pred HHHHHHHHHHHhc--CCCcEEEEccccccCCCc-CCCeEEEEeCCCcCcch----hhHHHHHHHHHHHHHhCCeEEEe
Confidence 3445566677776 689999999999988766 45999999887643210 11235888899999887766543
No 30
>KOG3793 consensus Transcription factor NFAT, subunit NF45 [Transcription]
Probab=92.38 E-value=3.7 Score=39.95 Aligned_cols=70 Identities=16% Similarity=0.241 Sum_probs=54.2
Q ss_pred ccchHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHhhhcCCC------cEEEEecccccCCCCCCCC-cceEEeec
Q 013307 4 YNVLEPILKDILGMLNPLREDWETRMKVISDLREVVESVESLRG------ATVEPFGSFVSNLFSRWGD-LDISIELS 74 (445)
Q Consensus 4 ~~~L~~ei~~f~~~~~Pt~ee~~~R~~vi~~l~~il~~~~~~~~------~~v~~fGS~~tGl~l~~SD-IDl~i~~~ 74 (445)
-+.++.+|.+=-..+.|+.+|...-...+..+..++.... -|+ ..|.-+||+.+|+-+-++| -|+++...
T Consensus 38 D~~f~~alLkRnqdL~P~~~~q~~I~~~vtKV~~vLdn~~-~~~L~~~~ieevrqVGSF~k~T~~tg~~~advVViLk 114 (362)
T KOG3793|consen 38 DTSFSEALLKRNQDLAPNSAEQASILSLVTKVNNVLDNLV-APGLFEVQIEEVRQVGSFKKGTMTTGHNVADLVVILK 114 (362)
T ss_pred chHHHHHHHhhhccCCCCHHHHHHHHHHHHHHHHHHHhhc-cCCceEeehhhhhhccceeccccccCCcccceEEEee
Confidence 3568888998889999999998887788888887777652 333 3567789999999988875 47777654
No 31
>PRK02098 phosphoribosyl-dephospho-CoA transferase; Provisional
Probab=92.37 E-value=0.19 Score=47.97 Aligned_cols=40 Identities=28% Similarity=0.446 Sum_probs=30.5
Q ss_pred HHHHHHHHHhhhcCCCcEEEEecccc----cCC--CCCCCCcceEEeecC
Q 013307 32 ISDLREVVESVESLRGATVEPFGSFV----SNL--FSRWGDLDISIELSN 75 (445)
Q Consensus 32 i~~l~~il~~~~~~~~~~v~~fGS~~----tGl--~l~~SDIDl~i~~~~ 75 (445)
+..|..+... .+..+.+|||.+ ||+ ..++||||+++..+.
T Consensus 109 l~~l~~~~~~----~g~~~gv~GS~a~qlaTG~~~l~~~SDLDLLi~~~~ 154 (221)
T PRK02098 109 LRALLALAAA----HGVDCRVFGSLAWQALTGLPYLSASSDLDLLWPLPA 154 (221)
T ss_pred HHHHHHHHHh----CCCcEEEeeehHHHHhhCCcccCCCCCeeEEEecCC
Confidence 3444444443 367999999999 999 788999999996653
No 32
>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=91.59 E-value=0.27 Score=46.33 Aligned_cols=30 Identities=23% Similarity=0.383 Sum_probs=26.0
Q ss_pred CCcEEEEeccc----ccCC--CCCCCCcceEEeecC
Q 013307 46 RGATVEPFGSF----VSNL--FSRWGDLDISIELSN 75 (445)
Q Consensus 46 ~~~~v~~fGS~----~tGl--~l~~SDIDl~i~~~~ 75 (445)
.+....+|||. +||+ ..++||||+++..+.
T Consensus 107 ~~~~~gv~GS~~~qlaTg~~~~~~~SDLDLLi~~~~ 142 (202)
T TIGR03135 107 LGVPWGVYGSAGWQLLTGLPYLHASSDLDLLLRAPS 142 (202)
T ss_pred CCCcEEEecchHHHHhcCCcccCCCCCeeEEEcCCC
Confidence 46799999999 8999 788999999997653
No 33
>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=91.39 E-value=1.8 Score=43.48 Aligned_cols=124 Identities=18% Similarity=0.195 Sum_probs=68.9
Q ss_pred HHHHHHHHHhhhcCCCcEEEEecccccCCCCCCCCcceEEeecCCCcccccchhhHHHHHHHHHHHHHhcCCceEEEEec
Q 013307 32 ISDLREVVESVESLRGATVEPFGSFVSNLFSRWGDLDISIELSNGSCISSAGKKVKQSLLGDLLRALRQKGGYRRLQFVA 111 (445)
Q Consensus 32 i~~l~~il~~~~~~~~~~v~~fGS~~tGl~l~~SDIDl~i~~~~~~~iss~~k~~~~~~L~~l~~~L~~~~~~~~v~~I~ 111 (445)
.+.|...++.+ .+..++.+.||+.-|..+ .+|||+++..+.... ..++..+...|.+.+.+..+..-.
T Consensus 147 a~~i~~~l~~~--~~~~~v~i~GS~RRg~et-~gDiDilv~~~~~~~---------~~~~~~v~~~l~~~~~~~~~~~~g 214 (307)
T cd00141 147 AEIIKEALREV--DPVLQVEIAGSYRRGKET-VGDIDILVTHPDATS---------RGLLEKVVDALVELGFVTEVLSKG 214 (307)
T ss_pred HHHHHHHHHhC--CCceEEEEcccccCCCCc-cCCEEEEEecCCccc---------cccHHHHHHHHHhCCCeehhhhCC
Confidence 44455555554 467899999999877665 469999996554210 235566667776655543321111
Q ss_pred ccccc-eEEEEeeccceEEEEeecccccccccHHHhHHhcccchhHHHHHHHHHHHHHCCCCC
Q 013307 112 HARVP-ILKFETIHQNISCDISIDNLCGQIKSKFLFWISQIDGRFRDMVLLVKEWAKAHDINN 173 (445)
Q Consensus 112 ~ArVP-IIk~~~~~~gi~~DIs~~n~~g~~~s~ll~~~~~~~~~~r~Lv~~iK~Wak~rgL~~ 173 (445)
..++= +++..+...++.|||-+......-.+ ++ ++.. =....+-++.||+.+|..=
T Consensus 215 ~~k~~~~~~~~~~~~~~rVDl~~~p~~~~~~a-ll-~fTG----s~~~nr~lR~~A~~~G~~L 271 (307)
T cd00141 215 DTKASGILKLPGGWKGRRVDLRVVPPEEFGAA-LL-YFTG----SKQFNRALRRLAKEKGLKL 271 (307)
T ss_pred CceEEEEEecCCCCCceEEEEEEeCHHHHHHH-HH-HhhC----CHHHHHHHHHHHHHcCCee
Confidence 11110 22221123489999988664332221 11 1222 2344555699999998753
No 34
>cd05401 NT_GlnE_GlnD_like Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins. Escherichia coli GlnD and -E participate in the Glutamine synthetase (GS)/Glutamate synthase (GOGAT) pathway for the assimilation of ammonium nitrogen. In nitrogen sufficiency, GlnE adenylates GS, reducing GS activity; when nitrogen is limiting, GlnE deadenylates GS-AMP, restoring GS activity. When nitrogen is limiting, GlnD uridylylates the nitrogen regulatory protein PII to PII-UTP, and in nitrogen sufficiency, it removes the modifying groups. The activity of Escherichia coli GlnE is modulated by PII-proteins. PII-UMP promotes GlnE deadenylation activity, and PII promotes GlnE adenylation activity. Escherichia coli GlnE has two separate NT domains. The N-terminal NT domain catalyzes the deadenylylation of GS, and the C-terminal NT domain the adenylylation reaction. The majority of proteins in this family conta
Probab=82.86 E-value=13 Score=33.43 Aligned_cols=29 Identities=14% Similarity=0.189 Sum_probs=26.8
Q ss_pred CcEEEEecccccCCCCCCCCcceEEeecC
Q 013307 47 GATVEPFGSFVSNLFSRWGDLDISIELSN 75 (445)
Q Consensus 47 ~~~v~~fGS~~tGl~l~~SDIDl~i~~~~ 75 (445)
+..+..+||++-+=.++.||+|+.++.++
T Consensus 55 ~~~~la~Gs~GR~E~~~~SD~D~~~v~~~ 83 (172)
T cd05401 55 PFALLALGSYGRGELNPSSDQDLLLLYDD 83 (172)
T ss_pred cEEEEEeCCcccCCcCCCcCcceEEEeCC
Confidence 57999999999999999999999998865
No 35
>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=80.04 E-value=4.7 Score=38.22 Aligned_cols=41 Identities=24% Similarity=0.335 Sum_probs=27.9
Q ss_pred HHHHHHHHHHhhhcCCCcEEEEecccc----cCCC--CCCCCcceEEeecC
Q 013307 31 VISDLREVVESVESLRGATVEPFGSFV----SNLF--SRWGDLDISIELSN 75 (445)
Q Consensus 31 vi~~l~~il~~~~~~~~~~v~~fGS~~----tGl~--l~~SDIDl~i~~~~ 75 (445)
.+..|+.... ..+....+|||.+ ||+- .++||||+++..+.
T Consensus 104 ~l~~l~~~~~----~~~~~~gv~GS~g~qlaTGl~~l~~~SDLDLli~~~~ 150 (213)
T PF10620_consen 104 ALQALRALLD----ALGLRWGVYGSLGFQLATGLPYLHADSDLDLLIRPPS 150 (213)
T ss_pred HHHHHHHHHH----HcCCCEEEehhHHHHHHhCccccCCCCCceEEEeCCC
Confidence 4444544442 3479999999985 4443 45899999986554
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=79.54 E-value=24 Score=30.89 Aligned_cols=30 Identities=13% Similarity=0.137 Sum_probs=27.4
Q ss_pred CCcEEEEecccccCCCCCCCCcceEEeecC
Q 013307 46 RGATVEPFGSFVSNLFSRWGDLDISIELSN 75 (445)
Q Consensus 46 ~~~~v~~fGS~~tGl~l~~SDIDl~i~~~~ 75 (445)
..+.+..+||++-+=.++.||+|..++..+
T Consensus 48 ~~~a~lalGS~GR~E~~~~sDqD~alv~~d 77 (138)
T PF03445_consen 48 VPFAWLALGSYGRREQTLYSDQDNALVFED 77 (138)
T ss_pred CCEEEEEECcccccCCCcCccccceeeecC
Confidence 357999999999999999999999998876
No 37
>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=79.13 E-value=1.9 Score=41.68 Aligned_cols=46 Identities=17% Similarity=0.070 Sum_probs=32.8
Q ss_pred HHHHHHHHHHHHHhhhcCCCcEEEEecccccCCCCCCCCcceEEeec
Q 013307 28 RMKVISDLREVVESVESLRGATVEPFGSFVSNLFSRWGDLDISIELS 74 (445)
Q Consensus 28 R~~vi~~l~~il~~~~~~~~~~v~~fGS~~tGl~l~~SDIDl~i~~~ 74 (445)
++.+.+.|+++-++. ...=.-....||.+.|+.+++||.|+..+.-
T Consensus 2 ~~~i~~~l~~ie~~~-~~~il~~~~sGS~a~G~~s~dSD~D~r~vy~ 47 (247)
T PF10127_consen 2 RETIQEKLNEIEKEH-NVKILYACESGSRAYGFASPDSDYDVRGVYI 47 (247)
T ss_pred chHHHHHHHHHHHhc-CCcEEEEecccccccCCCCCCcCcccchhcc
Confidence 345666777776653 1122456778999999999999999987543
No 38
>PRK00227 glnD PII uridylyl-transferase; Provisional
Probab=77.56 E-value=4.9 Score=44.85 Aligned_cols=50 Identities=18% Similarity=0.280 Sum_probs=41.9
Q ss_pred HHHHHHHHHHHHHHHHhhhcC-CCcEEEEecccccCCCCCCCCcceEEeecC
Q 013307 25 WETRMKVISDLREVVESVESL-RGATVEPFGSFVSNLFSRWGDLDISIELSN 75 (445)
Q Consensus 25 ~~~R~~vi~~l~~il~~~~~~-~~~~v~~fGS~~tGl~l~~SDIDl~i~~~~ 75 (445)
.+.|+.+.+.-..+++.+. . .++.+...|+|+-|--.|.||||++++.++
T Consensus 5 ~~~~~~~~~~~~~~~~~~~-~~~~~aLvAvGGYGR~EL~P~SDIDLLiL~~~ 55 (693)
T PRK00227 5 AQLREDAEASALALLGSLQ-LPPGTALAATGSLARREMTPYSDLDLILLHPP 55 (693)
T ss_pred HHHHHHHHHHHHHHHHhcC-CCCCeEEEEeccccccCcCCCcCceEEEEeCC
Confidence 4567888888788888763 4 468999999999999999999999998874
No 39
>COG2413 Predicted nucleotidyltransferase [General function prediction only]
Probab=72.86 E-value=6.3 Score=36.89 Aligned_cols=44 Identities=20% Similarity=0.237 Sum_probs=33.4
Q ss_pred HHHHHHHHHHHHHHHhhhcCCCcEEEEecccccCCCCCCCCcceEEeec
Q 013307 26 ETRMKVISDLREVVESVESLRGATVEPFGSFVSNLFSRWGDLDISIELS 74 (445)
Q Consensus 26 ~~R~~vi~~l~~il~~~~~~~~~~v~~fGS~~tGl~l~~SDIDl~i~~~ 74 (445)
.+|+++...++.+.+. +..-..+||.+.|=..|.||+|++|..+
T Consensus 21 ekRe~A~~i~e~l~~f-----~ie~~v~gSvarGDV~p~SDvDV~I~~~ 64 (228)
T COG2413 21 EKREKARKIMEGLSDF-----GIEAVVYGSVARGDVRPGSDVDVAIPEP 64 (228)
T ss_pred HHHHHHHHHHHHHHHh-----cchhEEEeeeeccCcCCCCCceEEEecC
Confidence 4566666666655543 3567889999999889999999999664
No 40
>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair]
Probab=72.76 E-value=55 Score=32.97 Aligned_cols=123 Identities=16% Similarity=0.152 Sum_probs=72.0
Q ss_pred HHHHHHHHHHHhhhcCCCcEEEEecccccCCCCCCCCcceEEeecCCCcccccchhhHHHHHHHHHHHHHhcCCceEEEE
Q 013307 30 KVISDLREVVESVESLRGATVEPFGSFVSNLFSRWGDLDISIELSNGSCISSAGKKVKQSLLGDLLRALRQKGGYRRLQF 109 (445)
Q Consensus 30 ~vi~~l~~il~~~~~~~~~~v~~fGS~~tGl~l~~SDIDl~i~~~~~~~iss~~k~~~~~~L~~l~~~L~~~~~~~~v~~ 109 (445)
.+...|+..+.++ .+-.++...||..-|-++ .+|||+++..... .. +.+.+.+.+.+.++..
T Consensus 165 ~ia~ei~~yl~~~--~~~~~~~~aGs~RR~ret-v~DiD~~~s~~~~-----------~~----v~~~~~~~~~~~~vi~ 226 (326)
T COG1796 165 PIAQEIEGYLEEL--TPIIQASIAGSLRRGRET-VGDIDILISTSHP-----------ES----VLEELLEMPNVQEVIA 226 (326)
T ss_pred HHHHHHHHHHHhc--cchheeeeccchhhcccc-ccceeeEeccCCc-----------HH----HHHHHhcCCCcceeee
Confidence 3444555555555 334688888999877766 4799999965431 11 3333434444555555
Q ss_pred ecccccceEEEEeeccceEEEEeecccccccccHHHhHHhcccchhHHHHHHHHHHHHHCCCCCCCCCC
Q 013307 110 VAHARVPILKFETIHQNISCDISIDNLCGQIKSKFLFWISQIDGRFRDMVLLVKEWAKAHDINNPKTGT 178 (445)
Q Consensus 110 I~~ArVPIIk~~~~~~gi~~DIs~~n~~g~~~s~ll~~~~~~~~~~r~Lv~~iK~Wak~rgL~~~~~G~ 178 (445)
-...++-++...+ .|+.||+-+......-++. ..|.. -+.--.-|+..|+.+|..-+..|-
T Consensus 227 ~G~~k~s~~~~~~--~~~svD~r~v~~e~fGaal--~~fTG----SkehNi~iR~lA~~kg~klseyGl 287 (326)
T COG1796 227 KGETKVSMLLILD--EGTSVDFRVVPPEAFGAAL--QHFTG----SKEHNIKIRQLAKAKGEKLSEYGL 287 (326)
T ss_pred cCCceeeEEEEec--CCCeeEEEEcCHHHhhhhh--hhccc----chhhhHHHHHHHHHhCcchhhcce
Confidence 4555665555444 7999999776544333222 22222 223345577788999876655543
No 41
>KOG2534 consensus DNA polymerase IV (family X) [Replication, recombination and repair]
Probab=72.13 E-value=25 Score=35.32 Aligned_cols=64 Identities=27% Similarity=0.239 Sum_probs=42.5
Q ss_pred HHHHHHHHHHhhhcCCCcEEEEecccccCCCCCCCCcceEEeecCCCcccccchhhHHHHHHHHHHHHHhcCCc
Q 013307 31 VISDLREVVESVESLRGATVEPFGSFVSNLFSRWGDLDISIELSNGSCISSAGKKVKQSLLGDLLRALRQKGGY 104 (445)
Q Consensus 31 vi~~l~~il~~~~~~~~~~v~~fGS~~tGl~l~~SDIDl~i~~~~~~~iss~~k~~~~~~L~~l~~~L~~~~~~ 104 (445)
+...+++.+... .|++.|.+-||+.-|-. .+.|||+++.-|... .....++..|...+.+.+.+
T Consensus 157 i~~~V~~av~~~--~p~~~vt~~GsfRRGk~-~ggDvD~LithP~~~-------s~~~~~~~~l~~~le~~g~i 220 (353)
T KOG2534|consen 157 IQQTVQEAVWAF--DPEAFVTVTGSFRRGKK-MGGDVDFLITHPGST-------STEAKLLQLLMILLEKKGLL 220 (353)
T ss_pred HHHHHHHHHhhc--CCCcEEEEeccccCCcc-cCCCeeEEEeCCCCC-------chhhhHHHHHHHHHHhcCeE
Confidence 334455555555 68999999999987754 467999999766531 11335667777777665543
No 42
>PF09970 DUF2204: Nucleotidyl transferase of unknown function (DUF2204); InterPro: IPR018700 This family of hypothetical prokaryotic proteins has no known function.
Probab=70.30 E-value=19 Score=33.17 Aligned_cols=92 Identities=16% Similarity=0.207 Sum_probs=50.0
Q ss_pred HHHHHHHhhhcCCCcEEEEeccccc----CCCCCCCCcceEEeecCCCcccccchhhHHHHHHHHHHHHHhcCCceEEEE
Q 013307 34 DLREVVESVESLRGATVEPFGSFVS----NLFSRWGDLDISIELSNGSCISSAGKKVKQSLLGDLLRALRQKGGYRRLQF 109 (445)
Q Consensus 34 ~l~~il~~~~~~~~~~v~~fGS~~t----Gl~l~~SDIDl~i~~~~~~~iss~~k~~~~~~L~~l~~~L~~~~~~~~v~~ 109 (445)
.++.+++.+. ..++++.+.|+++. |.--.+.|||+.+..++. ....+.++.++. ..+.-..-..
T Consensus 4 ~l~~~~~~L~-~~gv~~~ivGG~av~l~~g~~r~T~DIDlfi~~~~~--------~~~~~~~~~~a~---~~g~~~~~~~ 71 (181)
T PF09970_consen 4 ALKEILEELN-KRGVEYVIVGGAAVNLAYGRRRTTKDIDLFIENPSP--------NLEADALREVAE---ENGWDLGWTD 71 (181)
T ss_pred HHHHHHHHHH-HcCCeEEEECHHHHHHHhCCCCCCCCeEEEeCCCch--------HHHHHHHHHHHH---HcCCCcCccc
Confidence 3444454442 35789999999964 555567899999854431 112234555544 2222011111
Q ss_pred ecccccceEEEEeeccceEEEEeecccccccc
Q 013307 110 VAHARVPILKFETIHQNISCDISIDNLCGQIK 141 (445)
Q Consensus 110 I~~ArVPIIk~~~~~~gi~~DIs~~n~~g~~~ 141 (445)
. ...-.++++. ..++.+|+ +.|..|+.-
T Consensus 72 ~-~~~~~~~~~~--~~~v~IDl-~~ni~~~~v 99 (181)
T PF09970_consen 72 F-GTPRYVVKVG--GEDVRIDL-LENIGDFYV 99 (181)
T ss_pred c-CCCceEEEeC--CCCeEEEc-hhccCCccc
Confidence 1 1122245554 47899999 666666643
No 43
>PRK01759 glnD PII uridylyl-transferase; Provisional
Probab=68.43 E-value=26 Score=40.31 Aligned_cols=29 Identities=21% Similarity=0.218 Sum_probs=26.6
Q ss_pred CcEEEEecccccCCCCCCCCcceEEeecC
Q 013307 47 GATVEPFGSFVSNLFSRWGDLDISIELSN 75 (445)
Q Consensus 47 ~~~v~~fGS~~tGl~l~~SDIDl~i~~~~ 75 (445)
++.+..+|+|+-|---|.||||++++.++
T Consensus 56 ~iaLvAvGGYGR~eL~P~SDIDlliL~~~ 84 (854)
T PRK01759 56 DLALIAVGGYGRREMFPLSDLDILILTEQ 84 (854)
T ss_pred CeEEEEeCCcccccCCCcccceEEEEeCC
Confidence 46999999999999999999999998864
No 44
>PRK05007 PII uridylyl-transferase; Provisional
Probab=66.89 E-value=31 Score=39.87 Aligned_cols=30 Identities=13% Similarity=0.205 Sum_probs=27.3
Q ss_pred CCcEEEEecccccCCCCCCCCcceEEeecC
Q 013307 46 RGATVEPFGSFVSNLFSRWGDLDISIELSN 75 (445)
Q Consensus 46 ~~~~v~~fGS~~tGl~l~~SDIDl~i~~~~ 75 (445)
+++.|...|+|+-|--.|.||||++++.++
T Consensus 79 ~~~alvAvGgyGR~EL~p~SDiDll~l~~~ 108 (884)
T PRK05007 79 PDLALVAVGGYGRGELHPLSDIDLLILSRK 108 (884)
T ss_pred CceEEEecCCCCCcccCCcccceEEEEeCC
Confidence 457999999999999999999999998874
No 45
>PRK01293 phosphoribosyl-dephospho-CoA transferase; Provisional
Probab=65.41 E-value=14 Score=34.92 Aligned_cols=30 Identities=23% Similarity=0.102 Sum_probs=22.5
Q ss_pred CCcEEEEeccccc----CCC--CCCCCcceEEeecC
Q 013307 46 RGATVEPFGSFVS----NLF--SRWGDLDISIELSN 75 (445)
Q Consensus 46 ~~~~v~~fGS~~t----Gl~--l~~SDIDl~i~~~~ 75 (445)
.+...-+|||.+. |+- .++||||+++..+.
T Consensus 108 ~~~~wgv~GS~g~qlaTGl~~l~~~SDLDLlir~~~ 143 (207)
T PRK01293 108 LGLAWGVTGSAGFELATGIPVLHADSDLDLLIRAPQ 143 (207)
T ss_pred CCCceeeehhHHHHHhhCCccccCCCCccEeecCCC
Confidence 3789999999864 433 45799999996653
No 46
>COG2844 GlnD UTP:GlnB (protein PII) uridylyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=65.30 E-value=21 Score=40.25 Aligned_cols=30 Identities=13% Similarity=0.267 Sum_probs=27.3
Q ss_pred CcEEEEecccccCCCCCCCCcceEEeecCC
Q 013307 47 GATVEPFGSFVSNLFSRWGDLDISIELSNG 76 (445)
Q Consensus 47 ~~~v~~fGS~~tGl~l~~SDIDl~i~~~~~ 76 (445)
++.++.+|.|+-|--.|.||||+.++.|..
T Consensus 66 ~~aLvAVGGyGRgEL~P~SDiDlL~L~p~~ 95 (867)
T COG2844 66 GLALVAVGGYGRGELHPLSDIDLLLLSPQK 95 (867)
T ss_pred ceEEEEeccccccccCCCccceEEEecCCC
Confidence 489999999999999999999999988753
No 47
>PHA02603 nrdC.11 hypothetical protein; Provisional
Probab=64.70 E-value=3.9 Score=41.27 Aligned_cols=25 Identities=20% Similarity=0.117 Sum_probs=21.4
Q ss_pred EEEEecccccCCCCCCCCcceEEee
Q 013307 49 TVEPFGSFVSNLFSRWGDLDISIEL 73 (445)
Q Consensus 49 ~v~~fGS~~tGl~l~~SDIDl~i~~ 73 (445)
-...+||.+.|+.+|+||+|+--+.
T Consensus 5 ~~~~~GShaYG~~tp~SD~D~rGV~ 29 (330)
T PHA02603 5 MKGLFGSHLYGTSTPESDVDYKGIF 29 (330)
T ss_pred EEEecccceeCCCCCCcccccceee
Confidence 4678999999999999999996543
No 48
>PRK08609 hypothetical protein; Provisional
Probab=59.84 E-value=52 Score=35.97 Aligned_cols=117 Identities=16% Similarity=0.184 Sum_probs=60.1
Q ss_pred HHHHHHHHHhhhcCCCcEEEEecccccCCCCCCCCcceEEeecCCCcccccchhhHHHHHH---HHHHHHHhcCCceEEE
Q 013307 32 ISDLREVVESVESLRGATVEPFGSFVSNLFSRWGDLDISIELSNGSCISSAGKKVKQSLLG---DLLRALRQKGGYRRLQ 108 (445)
Q Consensus 32 i~~l~~il~~~~~~~~~~v~~fGS~~tGl~l~~SDIDl~i~~~~~~~iss~~k~~~~~~L~---~l~~~L~~~~~~~~v~ 108 (445)
.+.|...++.+ .+..+|.+-||+.-|..+ ..|||+++..++.. .....|. .+.+.+.. + ..
T Consensus 162 a~~i~~~l~~~--~~~~~v~~~GS~RR~~et-~gDiDili~~~~~~--------~~~~~l~~~~~v~~~~~~-g-~~--- 225 (570)
T PRK08609 162 AQEIEEYLATI--DEIIRFSRAGSLRRARET-VKDLDFIIATDEPE--------AVREQLLQLPNIVEVIAA-G-DT--- 225 (570)
T ss_pred HHHHHHHHHhC--CCccEEEeccchhccccc-cCCeeEEEecCCHH--------HHHHHHHcCccHHHHHhc-C-Cc---
Confidence 33444444443 356799999999987766 46999999654310 1111221 12222221 1 11
Q ss_pred EecccccceEEEEeeccceEEEEeecccccccccHHHhHHhcccchhHHHHHHHHHHHHHCCCCCCCCC
Q 013307 109 FVAHARVPILKFETIHQNISCDISIDNLCGQIKSKFLFWISQIDGRFRDMVLLVKEWAKAHDINNPKTG 177 (445)
Q Consensus 109 ~I~~ArVPIIk~~~~~~gi~~DIs~~n~~g~~~s~ll~~~~~~~~~~r~Lv~~iK~Wak~rgL~~~~~G 177 (445)
++- +.+.. ..|+.|||-+......-. . +.++.. -+...+-++.||+.+|+.=+..|
T Consensus 226 -----~~~-~~~~~-~~~~~vDl~~v~~~~~~~-a-L~yfTG----S~~hn~~lr~~A~~~g~~l~e~g 281 (570)
T PRK08609 226 -----KVS-VELEY-EYTISVDFRLVEPEAFAT-T-LHHFTG----SKDHNVRMRQLAKERGEKISEYG 281 (570)
T ss_pred -----eEE-EEEec-CCCeEEEEEEeCHHHHHH-H-HHHHhc----cHHHHHHHHHHHHHcCCcccccc
Confidence 111 11221 258999998765332221 1 222222 23444555999999987544333
No 49
>PRK04374 PII uridylyl-transferase; Provisional
Probab=59.08 E-value=57 Score=37.61 Aligned_cols=51 Identities=12% Similarity=0.196 Sum_probs=34.8
Q ss_pred HHHHHHHHHH-HHHHHHhhhc-CCCcEEEEecccccCCCCCCCCcceEEeecC
Q 013307 25 WETRMKVISD-LREVVESVES-LRGATVEPFGSFVSNLFSRWGDLDISIELSN 75 (445)
Q Consensus 25 ~~~R~~vi~~-l~~il~~~~~-~~~~~v~~fGS~~tGl~l~~SDIDl~i~~~~ 75 (445)
...|..+++. |+++.+...+ ..++.|...|+|+-|--.|.||||++++.+.
T Consensus 48 ~~~~s~~~D~~l~~~~~~~~~~~~~~alvAvGgYGR~EL~p~SDIDLliL~~~ 100 (869)
T PRK04374 48 LALRARAVDQLMRNAWTRCIPADSGLSLHAVGGYGRGELFPRSDVDLLVLGET 100 (869)
T ss_pred HHHHHHHHHHHHHHHHHHhCCCcCCEEEEEcCCccccccCCcccceEEEEecC
Confidence 4444455553 3333333211 1247999999999999999999999998874
No 50
>COG3541 Predicted nucleotidyltransferase [General function prediction only]
Probab=58.98 E-value=5.1 Score=38.61 Aligned_cols=21 Identities=24% Similarity=0.080 Sum_probs=18.3
Q ss_pred ecccccCCCCCCCCcceEEee
Q 013307 53 FGSFVSNLFSRWGDLDISIEL 73 (445)
Q Consensus 53 fGS~~tGl~l~~SDIDl~i~~ 73 (445)
=||.+-|+..|+||+||--+.
T Consensus 16 sGS~~yGf~spdSDyDvR~V~ 36 (248)
T COG3541 16 SGSHLYGFPSPDSDYDVRGVH 36 (248)
T ss_pred ccccccCCCCCCCccceeeEE
Confidence 499999999999999997643
No 51
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=56.90 E-value=26 Score=35.61 Aligned_cols=43 Identities=26% Similarity=0.219 Sum_probs=31.4
Q ss_pred HHHHHHHHHHHhhhcCCCcEEEEecccccCCCCCCCCcceEEeecC
Q 013307 30 KVISDLREVVESVESLRGATVEPFGSFVSNLFSRWGDLDISIELSN 75 (445)
Q Consensus 30 ~vi~~l~~il~~~~~~~~~~v~~fGS~~tGl~l~~SDIDl~i~~~~ 75 (445)
.+.+.|...++.+ .+...+.+-||+.-|..+ .+|||+++..+.
T Consensus 149 ~i~~~i~~~l~~~--~~~~~v~i~GSyRRgket-~gDIDili~~~~ 191 (334)
T smart00483 149 AVEYIVKRAVRKI--LPDAIVTLTGSFRRGKET-GHDVDFLITSPH 191 (334)
T ss_pred HHHHHHHHHHHhh--CCCcEEEEecccccCCCc-CCCeeEEEecCC
Confidence 3444455555555 477899999999987766 469999997654
No 52
>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=55.05 E-value=78 Score=27.91 Aligned_cols=106 Identities=19% Similarity=0.299 Sum_probs=44.9
Q ss_pred hHHHHHHHHHHcCCCHHHHHHHHHH---HHHHHHHHHhhhcCCCcEEEEecccccCCCCC---CCCcceEEeecCCCccc
Q 013307 7 LEPILKDILGMLNPLREDWETRMKV---ISDLREVVESVESLRGATVEPFGSFVSNLFSR---WGDLDISIELSNGSCIS 80 (445)
Q Consensus 7 L~~ei~~f~~~~~Pt~ee~~~R~~v---i~~l~~il~~~~~~~~~~v~~fGS~~tGl~l~---~SDIDl~i~~~~~~~is 80 (445)
|-.++..-+.-..|+. +...|..+ +..+.+++++.....+-...+|||+..-+-.| -.|||+.=.
T Consensus 8 ia~~~l~s~~v~~~~~-~~~grh~vS~lV~~V~klmeEyLrrhNk~CicYGSyslhllN~~I~YgDIDilqT-------- 78 (149)
T PF03296_consen 8 IASDYLNSYNVANPSG-KVMGRHNVSDLVENVNKLMEEYLRRHNKSCICYGSYSLHLLNPNIKYGDIDILQT-------- 78 (149)
T ss_dssp HHHHHHHHH--S--------------THHHHHHHHHHHHHHH-TTTEEEESHHHHHTTSTTS--SS-EEEES--------
T ss_pred HHHHHHHHhcccccCc-cccccccCcHHHHHHHHHHHHHHHhhCCCeEEeeeeeEEecCCCcccCcchhhhc--------
Confidence 3334444444444544 44555443 22233333332222456788999998766655 479999742
Q ss_pred ccchhhHHHHHHHHHHHHHhcCCceEEEEecccccce----EEEEeeccceEEE
Q 013307 81 SAGKKVKQSLLGDLLRALRQKGGYRRLQFVAHARVPI----LKFETIHQNISCD 130 (445)
Q Consensus 81 s~~k~~~~~~L~~l~~~L~~~~~~~~v~~I~~ArVPI----Ik~~~~~~gi~~D 130 (445)
..+.+|-.++..+.=--+ .++.. -+||. +.+++...+.-+|
T Consensus 79 -----Nar~flI~laflI~fitG-~~~~L---~kvPyLknyivlkd~~~~hIiD 123 (149)
T PF03296_consen 79 -----NARTFLINLAFLIKFITG-RDVVL---LKVPYLKNYIVLKDEEDNHIID 123 (149)
T ss_dssp -----THHHHHHHHHHHHHHHCS-S-EEE---EEETTSTTEEEEEETTS-EEEE
T ss_pred -----ccHHHHHHHHHHHhhhcC-cceEE---EEchhhhceEEEEecCCCEEEE
Confidence 123566666666553222 23332 26673 3455544444444
No 53
>PRK00275 glnD PII uridylyl-transferase; Provisional
Probab=50.43 E-value=96 Score=35.92 Aligned_cols=29 Identities=17% Similarity=0.361 Sum_probs=26.7
Q ss_pred CcEEEEecccccCCCCCCCCcceEEeecC
Q 013307 47 GATVEPFGSFVSNLFSRWGDLDISIELSN 75 (445)
Q Consensus 47 ~~~v~~fGS~~tGl~l~~SDIDl~i~~~~ 75 (445)
++.|...|+|+-|--.|.||||++++.++
T Consensus 78 ~~alvAvGgyGR~EL~p~SDiDll~l~~~ 106 (895)
T PRK00275 78 DIALVAVGGYGRGELHPYSDIDLLILLDS 106 (895)
T ss_pred CEEEEEcCCccccCcCCCCCceEEEEecC
Confidence 47999999999999999999999998864
No 54
>COG1665 Predicted nucleotidyltransferase [General function prediction only]
Probab=49.59 E-value=19 Score=35.38 Aligned_cols=29 Identities=17% Similarity=0.237 Sum_probs=24.5
Q ss_pred CCCcEEEEecccccCCCCCCCCcceEEee
Q 013307 45 LRGATVEPFGSFVSNLFSRWGDLDISIEL 73 (445)
Q Consensus 45 ~~~~~v~~fGS~~tGl~l~~SDIDl~i~~ 73 (445)
.|--.+-+-||...|+.-.+||||++|-.
T Consensus 119 Vp~~~mGVTGSiL~gl~~~nSDIDfVVYG 147 (315)
T COG1665 119 VPVNSMGVTGSILLGLYDENSDIDFVVYG 147 (315)
T ss_pred CchhhccccccccccccCCCCCceEEEEc
Confidence 35557778899999999999999999954
No 55
>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=48.53 E-value=1.2e+02 Score=34.92 Aligned_cols=30 Identities=13% Similarity=0.329 Sum_probs=27.0
Q ss_pred CCcEEEEecccccCCCCCCCCcceEEeecC
Q 013307 46 RGATVEPFGSFVSNLFSRWGDLDISIELSN 75 (445)
Q Consensus 46 ~~~~v~~fGS~~tGl~l~~SDIDl~i~~~~ 75 (445)
.++.+...|||+-|--.|.||||++++.++
T Consensus 42 ~~~aliA~GgyGR~El~p~SDiDll~l~~~ 71 (850)
T TIGR01693 42 SGIALVAVGGYGRGELAPYSDIDLLFLHDG 71 (850)
T ss_pred CCeEEEEeCCccccCcCCCCCCeEEEEeCC
Confidence 367899999999999999999999998764
No 56
>PRK03059 PII uridylyl-transferase; Provisional
Probab=46.91 E-value=61 Score=37.32 Aligned_cols=29 Identities=21% Similarity=0.434 Sum_probs=26.6
Q ss_pred CcEEEEecccccCCCCCCCCcceEEeecC
Q 013307 47 GATVEPFGSFVSNLFSRWGDLDISIELSN 75 (445)
Q Consensus 47 ~~~v~~fGS~~tGl~l~~SDIDl~i~~~~ 75 (445)
++.|...|+|+-|--.|.||||++++.++
T Consensus 61 ~~alvAvGgyGR~EL~p~SDiDll~l~~~ 89 (856)
T PRK03059 61 GAALVAVGGYGRGELFPYSDVDLLVLLPD 89 (856)
T ss_pred CeEEEEcCCCCCcccCCCCCCEEEEEecC
Confidence 57999999999999999999999998864
No 57
>PHA02996 poly(A) polymerase large subunit; Provisional
Probab=44.90 E-value=99 Score=32.04 Aligned_cols=112 Identities=17% Similarity=0.184 Sum_probs=59.1
Q ss_pred cchHHHHHHHHHHcCCCHHHHHHHH---HHHHHHHHHHHhhhcCCCcEEEEecccccCCCCCC---CCcceEEeecCCCc
Q 013307 5 NVLEPILKDILGMLNPLREDWETRM---KVISDLREVVESVESLRGATVEPFGSFVSNLFSRW---GDLDISIELSNGSC 78 (445)
Q Consensus 5 ~~L~~ei~~f~~~~~Pt~ee~~~R~---~vi~~l~~il~~~~~~~~~~v~~fGS~~tGl~l~~---SDIDl~i~~~~~~~ 78 (445)
+.|-.++.+-+.-..|++ +..-|. .++..+.+++++.....+-...+||||..-+-.|. .|||++=..
T Consensus 123 ~~la~~~L~synv~~~~~-kvmgrh~VSdLV~~V~klmeEyLrrhNk~CicYGSySlhllNp~I~YgDIDilqTN----- 196 (467)
T PHA02996 123 EKLARDALNSYNVAVISE-KVMGRHNVSDLVGNVNKLMEEYLRRHNKSCICYGSYSLHLLNPEIEYGDIDILQTN----- 196 (467)
T ss_pred HHHHHHHHHhccccCCCc-cccccccccHHHHHHHHHHHHHHHhcCCceEEeeceeeeecCCccccCCcceeeec-----
Confidence 344556666565556664 322232 23444444443333234668899999988776654 799997521
Q ss_pred ccccchhhHHHHHHHHHHHHHhcCCceEEEEecccccceE----EEEeeccceEEEEeecc
Q 013307 79 ISSAGKKVKQSLLGDLLRALRQKGGYRRLQFVAHARVPIL----KFETIHQNISCDISIDN 135 (445)
Q Consensus 79 iss~~k~~~~~~L~~l~~~L~~~~~~~~v~~I~~ArVPII----k~~~~~~gi~~DIs~~n 135 (445)
.+.+|-.++-.++=- .-.++-. -+||-+ .+++...+.-+| ||+-
T Consensus 197 --------ar~fLInlaflI~fi-tG~~v~L---lkVPyLknyivlkdee~~hIiD-sfni 244 (467)
T PHA02996 197 --------SRTFLINLAFLIKFI-TGRNVVL---LKVPYLKNYMVLKDEEDNHIID-SFNI 244 (467)
T ss_pred --------cHHHHHHHHHHHhhh-cCceEEE---EEcccccceEEEEecCCCEEEE-eccc
Confidence 225666666655421 1233333 378844 344543444444 3443
No 58
>PRK03381 PII uridylyl-transferase; Provisional
Probab=43.07 E-value=51 Score=37.52 Aligned_cols=29 Identities=17% Similarity=0.327 Sum_probs=26.6
Q ss_pred CcEEEEecccccCCCCCCCCcceEEeecC
Q 013307 47 GATVEPFGSFVSNLFSRWGDLDISIELSN 75 (445)
Q Consensus 47 ~~~v~~fGS~~tGl~l~~SDIDl~i~~~~ 75 (445)
++.|...|+|+-|--.|.||||++++.++
T Consensus 57 ~~alvAvg~~gr~el~p~SD~Dll~l~~~ 85 (774)
T PRK03381 57 GVALVAVGGLGRRELLPYSDLDLVLLHDG 85 (774)
T ss_pred CeEEEEeCCcCCcCcCCCCCCeEEEEeCC
Confidence 47999999999999999999999998873
No 59
>PF03710 GlnE: Glutamate-ammonia ligase adenylyltransferase; InterPro: IPR005190 This is a conserved repeated domain found in GlnE proteins. These proteins adenylate and deadenylate glutamine synthases: ATP + {L-Glutamate:ammonia ligase (ADP-forming)} = Diphosphate + Adenylyl-{L-Glutamate:Ammonia ligase (ADP-forming)}. The domain is related to the nucleotidyltransferase domain IPR002934 from INTERPRO.; GO: 0008882 [glutamate-ammonia-ligase] adenylyltransferase activity; PDB: 1V4A_A 3K7D_A.
Probab=41.76 E-value=75 Score=30.71 Aligned_cols=52 Identities=15% Similarity=0.163 Sum_probs=26.3
Q ss_pred CcEEEEecccccCCCCCCCCcceEEeecCCCcccccchhhHHHHHHHHHHHHH
Q 013307 47 GATVEPFGSFVSNLFSRWGDLDISIELSNGSCISSAGKKVKQSLLGDLLRALR 99 (445)
Q Consensus 47 ~~~v~~fGS~~tGl~l~~SDIDl~i~~~~~~~iss~~k~~~~~~L~~l~~~L~ 99 (445)
++.|...|-.+.+=-...||||++++.+..... .........++.++++.+.
T Consensus 127 ~~~ViamGKlGg~ELny~SDiDLifvy~~~~~~-~~~~~~~~~~~~rl~~~~~ 178 (247)
T PF03710_consen 127 GFAVIAMGKLGGRELNYSSDIDLIFVYDPDGET-GRRSISNQEFFTRLAQRLI 178 (247)
T ss_dssp SEEEEE-HHHHTT---TT--EEEEEEE---TT--SSS-SBHHHHHHHHHHHHH
T ss_pred CeEEEEeccccccccCCccCCceEEEecccccc-ccChhhHHHHHHHHHHHHH
Confidence 468888888887777889999999988764322 1111123455666665544
No 60
>PF04229 GrpB: GrpB protein; InterPro: IPR007344 This family of uncharacterised proteins is also known as GrpB.; PDB: 2NRK_A.
Probab=40.54 E-value=72 Score=28.85 Aligned_cols=105 Identities=14% Similarity=0.066 Sum_probs=52.0
Q ss_pred CcEEEEeccccc-CCCCCCCCcceEEeecCCCcccccchhhHHHHHHHHHHHHHhcCCceEEEEecccccceEEEE---e
Q 013307 47 GATVEPFGSFVS-NLFSRWGDLDISIELSNGSCISSAGKKVKQSLLGDLLRALRQKGGYRRLQFVAHARVPILKFE---T 122 (445)
Q Consensus 47 ~~~v~~fGS~~t-Gl~l~~SDIDl~i~~~~~~~iss~~k~~~~~~L~~l~~~L~~~~~~~~v~~I~~ArVPIIk~~---~ 122 (445)
-+.|.-+||++. |+.-+. .|||.+..++... +..+...|...| +.. ......+|--.+. .
T Consensus 32 ~~~IeHIGSTsVpgl~AKp-iIDI~v~V~~~~~------------~~~~~~~L~~~G-y~~--~~~~~~~~~~~~f~k~~ 95 (167)
T PF04229_consen 32 ALRIEHIGSTSVPGLAAKP-IIDILVGVEDLED------------LDAYIEALEALG-YVY--NRGEPGIPGRRFFRKGD 95 (167)
T ss_dssp EEEEEEESGGGSTT--B-S--EEEEEEES-SGG------------GGGGHHHHHHTT--EE----TTTTSTTEEEEEE--
T ss_pred hhEEEEeccceeCCcccCC-eeeEEeccCChHH------------HHHHHHHHHHcC-CEe--cCCCCCCccceeeEccC
Confidence 469999999976 776665 7888887765321 111233343332 211 1123444421111 1
Q ss_pred eccceEEEE--eecccccccccHHHhHHhcccchhHHHHHHHHHHHH
Q 013307 123 IHQNISCDI--SIDNLCGQIKSKFLFWISQIDGRFRDMVLLVKEWAK 167 (445)
Q Consensus 123 ~~~gi~~DI--s~~n~~g~~~s~ll~~~~~~~~~~r~Lv~~iK~Wak 167 (445)
....-.+-| +..+......--.++.|...+|..+.-.--+|.=+.
T Consensus 96 ~~~~~~~hlhv~~~~~~~~~~~l~FRDyLr~~p~~~~~Y~~lK~~la 142 (167)
T PF04229_consen 96 EDGERTHHLHVCPAGSPEWRRHLLFRDYLRAHPELRREYEALKRELA 142 (167)
T ss_dssp -SSS--EEEEEEETT-HHHHHHHHHHHHHHH-HHHHHHHHHHHHHHH
T ss_pred CCCCccEEEEEEeCCCHHHHHHHHHHHHHhhCHHHHHHHHHHHHHHH
Confidence 123333334 333333344555678888889999999999998544
No 61
>PRK03333 coaE dephospho-CoA kinase/protein folding accessory domain-containing protein; Provisional
Probab=39.70 E-value=3.8e+02 Score=27.80 Aligned_cols=152 Identities=16% Similarity=0.136 Sum_probs=80.6
Q ss_pred cchHHHHHHHH-HHcCCCHHHHHHHH-----------------HHHHHHHHHHHhhhcCCCcEEEEeccccc-CCCCCCC
Q 013307 5 NVLEPILKDIL-GMLNPLREDWETRM-----------------KVISDLREVVESVESLRGATVEPFGSFVS-NLFSRWG 65 (445)
Q Consensus 5 ~~L~~ei~~f~-~~~~Pt~ee~~~R~-----------------~vi~~l~~il~~~~~~~~~~v~~fGS~~t-Gl~l~~S 65 (445)
+.|..++..++ .++.|-..++..|. ..++..+..|..+.......|.-+||++- |+.-+.
T Consensus 180 e~l~~~v~~~l~~~~~~~~~~~~~~~~~~~~~v~v~~ydp~W~~~f~~e~~~l~~~l~~~~~~IeHIGSTsVpGl~AKP- 258 (395)
T PRK03333 180 DELVEAVRALWADRLLPFAHNLRARRRAARAPPRLVPADPSWPAQAQRIVARLKTAAGHKALRVDHIGSTAVPGLDAKD- 258 (395)
T ss_pred HHHHHHHHHHHHHHHhhHHHHHhcCCCCCCCCceEeCCCCCcHHHHHHHHHHHHHhcCccceEEEEeccCCCCCCccCC-
Confidence 44555565543 55567666665543 23555666666554334468999999954 777766
Q ss_pred CcceEEeecCCCcccccchhhHHHHHHHHHHHHHhcCCceEEEE-----ecccccceE--EEEee-cc-ceEEEEeecc-
Q 013307 66 DLDISIELSNGSCISSAGKKVKQSLLGDLLRALRQKGGYRRLQF-----VAHARVPIL--KFETI-HQ-NISCDISIDN- 135 (445)
Q Consensus 66 DIDl~i~~~~~~~iss~~k~~~~~~L~~l~~~L~~~~~~~~v~~-----I~~ArVPII--k~~~~-~~-gi~~DIs~~n- 135 (445)
.|||.+...+.. .+..+...|...+....-+. .+...+|-. ++... .. +-.+.|.+..
T Consensus 259 iIDI~v~V~~~~------------~~~~~~~~l~~~Gy~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~lHv~~~ 326 (395)
T PRK03333 259 VIDIQVTVESLA------------VADELAEPLAAAGFPRLPGITQDTPKPDDPDPALWGKRLHASADPGRPVNLHVRVD 326 (395)
T ss_pred eeeEEEeeCChH------------HHHHHHHHHHHCCCcccccccccCCCcCCCCCcccceeeeccCCCCCcEEEEEecC
Confidence 677777665421 12233444444332111110 011123321 21111 11 2234444433
Q ss_pred -cccccccHHHhHHhcccchhHHHHHHHHHHHHHC
Q 013307 136 -LCGQIKSKFLFWISQIDGRFRDMVLLVKEWAKAH 169 (445)
Q Consensus 136 -~~g~~~s~ll~~~~~~~~~~r~Lv~~iK~Wak~r 169 (445)
...+.+.-+++.|...+|..+.-+--+|.=+...
T Consensus 327 ~~~~~~~~l~FRDyLr~~p~~~~~Y~~lK~~la~~ 361 (395)
T PRK03333 327 GWPGQRFALLFRDWLRADPAARAEYLAVKRRAARR 361 (395)
T ss_pred CCHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHh
Confidence 2334445567889889999999988888776655
No 62
>PRK05092 PII uridylyl-transferase; Provisional
Probab=27.51 E-value=54 Score=38.13 Aligned_cols=29 Identities=17% Similarity=0.212 Sum_probs=26.5
Q ss_pred CcEEEEecccccCCCCCCCCcceEEeecC
Q 013307 47 GATVEPFGSFVSNLFSRWGDLDISIELSN 75 (445)
Q Consensus 47 ~~~v~~fGS~~tGl~l~~SDIDl~i~~~~ 75 (445)
++.|...|+|+-|=-.+.|||||+++.++
T Consensus 105 ~~alvA~GgyGr~EL~p~SDiDLl~l~~~ 133 (931)
T PRK05092 105 RLAVLAVGGYGRGELAPGSDIDLLFLLPY 133 (931)
T ss_pred ceEEEEecCcCCcccCCCCCceEEEEeCC
Confidence 46899999999999999999999998874
No 63
>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=26.94 E-value=1.7e+02 Score=27.70 Aligned_cols=27 Identities=30% Similarity=0.107 Sum_probs=23.5
Q ss_pred EEEEecccccCCCCCCCCcceEEeecC
Q 013307 49 TVEPFGSFVSNLFSRWGDLDISIELSN 75 (445)
Q Consensus 49 ~v~~fGS~~tGl~l~~SDIDl~i~~~~ 75 (445)
-|+.-||.++=.-++.||+|+=|+...
T Consensus 99 GlY~MGS~gSi~Qs~~SDlDiWvCh~~ 125 (204)
T PF12633_consen 99 GLYSMGSTGSIGQSSSSDLDIWVCHDS 125 (204)
T ss_pred EEEecCCCccccCCCCCCCeEEEEcCC
Confidence 677889999988899999999997764
No 64
>PF11774 Lsr2: Lsr2 ; InterPro: IPR024412 This entry represents Lsr2, which is a small, basic DNA-bridging protein present in Mycobacterium and related actinomycetes. It is a functional homologue of the H-NS-like proteins []. H-NS proteins play a role in nucleoid organisation and also function as a pleiotropic regulator of gene expression [, ].; PDB: 4E1R_B 4E1P_B 2KNG_A.
Probab=26.84 E-value=54 Score=27.72 Aligned_cols=64 Identities=16% Similarity=0.187 Sum_probs=36.4
Q ss_pred eEEEEeeccceEEEEeecccccccccHHHhHHhcc----c--------------chhHHHHHHHHHHHHHCCCCCCCCCC
Q 013307 117 ILKFETIHQNISCDISIDNLCGQIKSKFLFWISQI----D--------------GRFRDMVLLVKEWAKAHDINNPKTGT 178 (445)
Q Consensus 117 IIk~~~~~~gi~~DIs~~n~~g~~~s~ll~~~~~~----~--------------~~~r~Lv~~iK~Wak~rgL~~~~~G~ 178 (445)
.+.|-......++|||-.|...++. .|..|... . ..-++-..-|+.||+..|+.-+..|-
T Consensus 21 tv~F~ldG~~YeIDLs~~na~~lr~--~l~~yi~~arr~~g~~~~~~~~~~~~~~~~~~~~~~IR~WA~~nG~~Vs~RGR 98 (110)
T PF11774_consen 21 TVRFGLDGVDYEIDLSAENAAKLRD--ALAPYIAAARRVGGRARRRRRRARSAAAAPREDTAAIREWARENGYEVSDRGR 98 (110)
T ss_dssp EEEEEETTEEEEEEE-HHHHHHHHH--HHHHHHHHSEEE---------SSGGG---SSTHHHHHHHHHHHTT----SSS-
T ss_pred EEEEEECCeEEEEECCHHHHHHHHH--HHHHHHHHheEccccccccccCccccCCCCccchHHHHHHHHHcCCcCCCCCc
Confidence 5666655567888888887655554 34444321 1 23456688999999999998888887
Q ss_pred Ccch
Q 013307 179 FNSY 182 (445)
Q Consensus 179 Lssy 182 (445)
++.=
T Consensus 99 Ip~~ 102 (110)
T PF11774_consen 99 IPAE 102 (110)
T ss_dssp --HH
T ss_pred CCHH
Confidence 7643
No 65
>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=24.42 E-value=4.7e+02 Score=22.70 Aligned_cols=69 Identities=16% Similarity=0.186 Sum_probs=39.3
Q ss_pred CcEEEEecccccCCC--CCCCCcceEEeecCCCcccccchhhHHHHHHHHHHHHHhcCCceEEEEecccccceEEEEeec
Q 013307 47 GATVEPFGSFVSNLF--SRWGDLDISIELSNGSCISSAGKKVKQSLLGDLLRALRQKGGYRRLQFVAHARVPILKFETIH 124 (445)
Q Consensus 47 ~~~v~~fGS~~tGl~--l~~SDIDl~i~~~~~~~iss~~k~~~~~~L~~l~~~L~~~~~~~~v~~I~~ArVPIIk~~~~~ 124 (445)
+.+++.+|-++-.+. .+..|||+++.... ...+..+.+. ....-+. ...+.+.+++..
T Consensus 16 g~~~ylVGG~VRD~Llg~~~~DiDi~v~~~~------------~~~~~~l~~~----~~~~~v~--~~~~f~t~~v~~-- 75 (139)
T cd05398 16 GYEAYLVGGAVRDLLLGRPPKDIDIATDADG------------PEFAEALFKK----IGGRVVG--LGEEFGTATVVI-- 75 (139)
T ss_pred CceEEEECChHHHHHcCCCCCCceEEEeCCC------------HHHHHHHHHh----cCCcEEe--cCCcccEEEEEE--
Confidence 789999998875443 35579999885421 1233333322 1111121 124556666655
Q ss_pred cceEEEEeecc
Q 013307 125 QNISCDISIDN 135 (445)
Q Consensus 125 ~gi~~DIs~~n 135 (445)
.+..+||+...
T Consensus 76 ~~~~~di~~~R 86 (139)
T cd05398 76 NGLTIDVATLR 86 (139)
T ss_pred CCEEEEEcccc
Confidence 47888886543
No 66
>PRK14109 bifunctional glutamine-synthetase adenylyltransferase/deadenyltransferase; Provisional
Probab=23.31 E-value=1.5e+02 Score=34.78 Aligned_cols=29 Identities=14% Similarity=0.070 Sum_probs=26.3
Q ss_pred CcEEEEecccccCCCCCCCCcceEEeecC
Q 013307 47 GATVEPFGSFVSNLFSRWGDLDISIELSN 75 (445)
Q Consensus 47 ~~~v~~fGS~~tGl~l~~SDIDl~i~~~~ 75 (445)
++.|..+|+++-+=-.+.||+|++++...
T Consensus 723 ~~avia~Gk~Gr~EL~~~SDlDl~fl~~~ 751 (1007)
T PRK14109 723 RIAVIGMGRLGGRELGYGSDADVMFVHEP 751 (1007)
T ss_pred CEEEEEeccccccccCCCCCCcEEEEeCC
Confidence 37999999999999999999999998864
No 67
>PF14907 NTP_transf_5: Uncharacterised nucleotidyltransferase
Probab=20.27 E-value=5.4e+02 Score=24.07 Aligned_cols=38 Identities=26% Similarity=0.504 Sum_probs=20.9
Q ss_pred HHHHHHHhhhcCCCcEEEEe-cccccCC----CCC-CCCcceEEe
Q 013307 34 DLREVVESVESLRGATVEPF-GSFVSNL----FSR-WGDLDISIE 72 (445)
Q Consensus 34 ~l~~il~~~~~~~~~~v~~f-GS~~tGl----~l~-~SDIDl~i~ 72 (445)
.+.++++.+ ...++.+.++ |.....+ +++ .+|||+.|.
T Consensus 59 ~~~~i~~~l-~~~gI~~~~lKG~~l~~~Y~~~~~R~~~DiDlLV~ 102 (249)
T PF14907_consen 59 ELQEILAAL-NANGIPVILLKGAALAQLYPDPGLRPMGDIDLLVP 102 (249)
T ss_pred HHHHHHHHH-HHcCCCEEEEchHHHHHhCCCCCCCCCCCeEEEEe
Confidence 344444443 2357788887 4432222 222 379999984
Done!