Query 005645
Match_columns 686
No_of_seqs 318 out of 1613
Neff 4.3
Searched_HMMs 46136
Date Thu Mar 28 11:34:40 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/005645.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/005645hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK11623 pcnB poly(A) polymera 100.0 1.9E-67 4.1E-72 574.8 33.9 280 51-339 37-324 (472)
2 TIGR01942 pcnB poly(A) polymer 100.0 1.4E-65 3.1E-70 553.3 33.7 282 52-343 1-283 (410)
3 KOG2159 tRNA nucleotidyltransf 100.0 9.3E-60 2E-64 503.7 16.6 380 52-439 2-410 (416)
4 COG0617 PcnB tRNA nucleotidylt 100.0 2.6E-58 5.6E-63 496.2 20.4 233 59-301 1-234 (412)
5 TIGR02692 tRNA_CCA_actino tRNA 100.0 7.7E-55 1.7E-59 477.2 25.9 253 65-327 12-273 (466)
6 PRK13299 tRNA CCA-pyrophosphor 100.0 1.1E-54 2.3E-59 468.3 21.0 223 65-299 5-229 (394)
7 PRK10885 cca multifunctional t 100.0 9E-50 1.9E-54 432.0 27.7 233 81-327 1-242 (409)
8 PRK13297 tRNA CCA-pyrophosphor 100.0 2.4E-49 5.1E-54 421.7 20.5 212 77-302 8-223 (364)
9 PRK13298 tRNA CCA-pyrophosphor 100.0 1.4E-48 2.9E-53 422.7 26.5 230 81-325 1-241 (417)
10 PRK13296 tRNA CCA-pyrophosphor 100.0 4.7E-46 1E-50 394.6 20.4 203 81-302 1-212 (360)
11 cd05398 NT_ClassII-CCAase Nucl 100.0 8.6E-33 1.9E-37 260.0 13.6 132 67-208 2-139 (139)
12 PF01743 PolyA_pol: Poly A pol 100.0 9.9E-33 2.2E-37 255.1 11.4 122 83-212 1-126 (126)
13 PHA01806 hypothetical protein 99.9 8E-22 1.7E-26 194.2 12.4 113 56-192 11-151 (200)
14 PRK03381 PII uridylyl-transfer 99.6 1.1E-14 2.4E-19 169.9 13.1 141 207-351 314-457 (774)
15 PRK00227 glnD PII uridylyl-tra 99.6 1.9E-14 4E-19 165.9 13.4 139 206-350 275-416 (693)
16 TIGR01693 UTase_glnD [Protein- 99.5 2.1E-14 4.5E-19 168.9 13.0 122 206-329 319-445 (850)
17 PRK00275 glnD PII uridylyl-tra 99.5 2.2E-14 4.7E-19 169.7 11.9 133 196-330 339-478 (895)
18 PRK05092 PII uridylyl-transfer 99.5 1.5E-13 3.3E-18 163.1 11.7 120 206-329 384-510 (931)
19 PRK03059 PII uridylyl-transfer 99.5 2.1E-13 4.6E-18 160.7 12.2 123 205-329 328-457 (856)
20 PRK01759 glnD PII uridylyl-tra 99.3 5.9E-12 1.3E-16 148.7 12.9 122 205-330 325-454 (854)
21 PF12627 PolyA_pol_RNAbd: Prob 99.2 1.3E-11 2.8E-16 101.1 6.5 62 239-300 1-62 (64)
22 PRK05007 PII uridylyl-transfer 99.2 5.1E-11 1.1E-15 141.3 12.3 123 206-330 350-479 (884)
23 PRK04374 PII uridylyl-transfer 98.9 5.2E-09 1.1E-13 124.2 12.9 119 209-329 342-466 (869)
24 COG2844 GlnD UTP:GlnB (protein 98.5 1.8E-06 4E-11 100.7 16.2 122 207-330 337-464 (867)
25 cd07749 NT_Pol-beta-like_1 Nuc 90.7 1.3 2.9E-05 43.8 8.7 70 70-142 7-89 (156)
26 PF09970 DUF2204: Nucleotidyl 89.6 0.93 2E-05 45.3 6.8 41 69-109 5-47 (181)
27 PF10706 Aminoglyc_resit: Amin 75.4 2.6 5.6E-05 42.4 3.1 51 68-118 8-62 (174)
28 PF06042 DUF925: Bacterial pro 75.1 3.3 7.1E-05 41.3 3.8 35 73-107 1-44 (163)
29 cd05397 NT_Pol-beta-like Nucle 74.1 3.9 8.4E-05 32.6 3.3 35 71-107 6-42 (49)
30 cd05402 NT_PAP_TUTase Nucleoti 66.1 27 0.00059 31.3 7.4 63 79-143 18-98 (114)
31 PF08843 DUF1814: Nucleotidyl 57.7 12 0.00027 36.7 3.9 38 72-109 2-44 (233)
32 COG3575 Uncharacterized protei 57.4 11 0.00023 38.5 3.4 42 66-107 14-64 (184)
33 PF03458 UPF0126: UPF0126 doma 55.9 6.3 0.00014 34.6 1.4 16 85-100 39-54 (80)
34 COG2860 Predicted membrane pro 48.0 9.3 0.0002 39.7 1.3 15 85-99 44-58 (209)
35 PF01909 NTP_transf_2: Nucleot 46.7 22 0.00048 30.3 3.3 34 71-107 6-39 (93)
36 PF14907 NTP_transf_5: Unchara 42.7 2E+02 0.0043 29.0 9.9 56 64-119 55-115 (249)
37 COG4914 Predicted nucleotidylt 39.0 16 0.00035 36.8 1.4 39 68-106 9-49 (190)
38 TIGR01493 HAD-SF-IA-v2 Haloaci 31.1 2.4E+02 0.0052 26.7 7.9 24 186-210 1-24 (175)
39 PRK10578 hypothetical protein; 29.8 28 0.0006 36.1 1.4 14 86-99 42-55 (207)
40 PRK13973 thymidylate kinase; P 24.7 90 0.0019 31.5 4.0 44 59-102 10-61 (213)
41 TIGR03671 cca_archaeal CCA-add 20.7 1.8E+02 0.0039 33.3 5.7 74 69-143 23-117 (408)
No 1
>PRK11623 pcnB poly(A) polymerase I; Provisional
Probab=100.00 E-value=1.9e-67 Score=574.77 Aligned_cols=280 Identities=30% Similarity=0.475 Sum_probs=256.3
Q ss_pred eeccccccCcCcCCCChhHHHHHHHHHHCCCcEEEEchhHHHHHhCCCCCCeEEEeCCCHHHHHHHhccCcccccccCeE
Q 005645 51 KTVDSRNLGITRAMIPQPSWVVLKILKSQGFQAYLVGGCVRDLLLRRVPKDFDVITTANLKQIRRQFHRSEIIGRRFPIC 130 (686)
Q Consensus 51 ~~~~~~~~gI~~~~ip~~a~~VL~~L~~~G~eAYLVGG~VRDLLLGr~PkD~DIvT~A~peei~k~F~~~~ivGrrF~i~ 130 (686)
..++.++|||++.+||+.+++|++.|+++||++|||||||||+|||++|+||||+|+|+|+++.+.|++|.++|++|+++
T Consensus 37 ~~i~~~~H~i~~~~i~~~a~~Vl~~L~~~G~eaYLVGG~VRDlLLG~~pkD~DIaT~A~peev~~lf~~~r~iGrrF~~~ 116 (472)
T PRK11623 37 TVIPREQHAISRKDISENALKVLYRLNKAGYEAYLVGGGVRDLLLGKKPKDFDVTTNATPEQVRKLFRNCRLVGRRFRLA 116 (472)
T ss_pred eEeeccccCcCcccCCHHHHHHHHHHHHCCCeEEEeChHHHHHHcCCCCCCEEEecCCCHHHHHHHhhhCeeecCCCCEE
Confidence 58999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEECCEEEEEecccccccccCC--------CceeeecCCCCCCchhhhhhhhhhccCccccccccccCCCCeEeeCcCc
Q 005645 131 RVHIKGSVIEVSSFETVAKHGEG--------KETVLLSQIPYGCDEIDLVRWRNSIHRDFTINSLFFDPFLNKIYDYANG 202 (686)
Q Consensus 131 ~V~~~G~~IEVaTfRte~~~~~~--------~~~V~fs~~~~gt~eeDL~~~eDa~RRDFTINALAyd~~~g~LiDyfGG 202 (686)
||.+++..|||+|||++.+...+ .....+.++.+|++++|+ .||||||||||||+.++.|+|||||
T Consensus 117 hV~~~~~~iEVaTfR~~~~~~~~~~~~~~~~~~g~~~rdn~~gtieeDl------~RRDFTINALayd~~~~~IiD~~gG 190 (472)
T PRK11623 117 HVMFGPEIIEVATFRGHHEGNESDRNTSQRGQNGMLLRDNIFGSIEEDA------QRRDFTINSLYYSVADFTVRDYVGG 190 (472)
T ss_pred EEEECCceEEEeccccccccccccccccccCCCCceecccCCCCHHHHH------HhccccHHHheecCCCCeEecCCCC
Confidence 99999999999999987643321 123445566788999986 7999999999999988999999999
Q ss_pred HHHHhcCceeecccCcccccccHHhHHHHHHHHHHhCCCCCHHHHHHHHHhhhhhcCCCHHHHHHHHHHHHhCCCHHHHH
Q 005645 203 ISDLRCLKLRTLIPAYLSFTEDCARILRGLRIAARLGLSFCKDIDTAMHSLSSSIERLDKSRIMMELNYMLSYGAAESSI 282 (686)
Q Consensus 203 leDLk~riIR~Vg~p~~rF~EDPlRILRAiRFAaRLGF~Id~eT~~aIr~~a~lL~~Is~eRI~~EL~KLL~~~~~~~~L 282 (686)
++||++|+||+||+|..+|.|||+|||||+|||++|||+|+++|..+|++++.+|..+|++||++|+.|||.++++..++
T Consensus 191 ~~DLk~riLR~IGdp~~rf~EDPlRmLRAvRFAArLgF~Ie~~T~~aI~~~a~lL~~vs~eRI~~El~KlL~~~~~~~~~ 270 (472)
T PRK11623 191 MKDLKEGVIRLIGNPETRYREDPVRMLRAVRFAAKLDMRISPETAEPIPRLATLLNDIPPARLFEESLKLLQAGYGYETY 270 (472)
T ss_pred HHHHhCCceeecCChHhhcccchHHHHHHHHHHHHhCCCcCHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHcCCCHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHcCCchhhhhhhhhhhhhccCcCCCchhHHHHHHHHhHHhhhhCCCCCchhhH
Q 005645 283 CLLRRYNLLKILLPFHAAYLDQQAGKITAENPMMLMRLFFNLDKLVSCDRPADYTLW 339 (686)
Q Consensus 283 ~lL~e~GLL~~LfPela~~~~qq~~~h~~t~d~~Ll~lL~~ld~ll~~~rp~~~~lW 339 (686)
++|+++|||..+||++..++..... .....++..++.++|.++..+.++++...
T Consensus 271 ~lL~e~GLl~~lfPel~~~~~~~~~---~~~~~~~~~~l~~tD~ri~~~~~v~p~fl 324 (472)
T PRK11623 271 KLLCEYHLFQPLFPTITRYFTENGD---SPMERIIEQVLKNTDTRIHNDMRVNPAFL 324 (472)
T ss_pred HHHHHcCCHHHHhHhHHHHhccccc---cHHHHHHHHHHHHHHHHHhCCCCCCHHHH
Confidence 9999999999999999987654322 12346788999999999999999987433
No 2
>TIGR01942 pcnB poly(A) polymerase. This model describes the pcnB family of poly(A) polymerases (also known as plasmid copy number protein). These enzymes sequentially add adenosine nucleotides to the 3' end of RNAs, targeting them for degradation by the cell. This was originally described for anti-sense RNAs, but was later demonstrated for mRNAs as well. Members of this family are as yet limited to the gamma- and beta-proteobacteria, with putative members in the Chlamydiacae and spirochetes. This family has homology to tRNA nucleotidyltransferase (cca).
Probab=100.00 E-value=1.4e-65 Score=553.28 Aligned_cols=282 Identities=31% Similarity=0.498 Sum_probs=253.1
Q ss_pred eccccccCcCcCCCChhHHHHHHHHHHCCCcEEEEchhHHHHHhCCCCCCeEEEeCCCHHHHHHHhccCcccccccCeEE
Q 005645 52 TVDSRNLGITRAMIPQPSWVVLKILKSQGFQAYLVGGCVRDLLLRRVPKDFDVITTANLKQIRRQFHRSEIIGRRFPICR 131 (686)
Q Consensus 52 ~~~~~~~gI~~~~ip~~a~~VL~~L~~~G~eAYLVGG~VRDLLLGr~PkD~DIvT~A~peei~k~F~~~~ivGrrF~i~~ 131 (686)
++++++|||++++||+.+.+|++.|+++||++|||||||||+|||++|+||||+|+|+|+++++.|+++.++|++|++++
T Consensus 1 ~~~~~~h~i~r~~i~~~a~~Vl~~L~~~G~~aYlVGG~VRDlLLG~~pkD~DIat~a~peei~~lf~~~~~iG~rf~~~~ 80 (410)
T TIGR01942 1 VIPESEHNIPRQSFSAHALNVVERLKGAGYQAYIVGGAVRDLLLGIEPKDFDVVTSATPEEVRKLFRNSRIVGRRFRLVH 80 (410)
T ss_pred CcchHhCCcChHHCCHHHHHHHHHHHHCCCcEEEECHHHHHHHcCCCCCCEEEEcCCCHHHHHHHhhhCeecCCCCCEEE
Confidence 36789999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEECCEEEEEecccccccccCCCceeeecCCCCCCchhhhhhhhhhccCccccccccccCCCCeEeeCcCcHHHHhcCce
Q 005645 132 VHIKGSVIEVSSFETVAKHGEGKETVLLSQIPYGCDEIDLVRWRNSIHRDFTINSLFFDPFLNKIYDYANGISDLRCLKL 211 (686)
Q Consensus 132 V~~~G~~IEVaTfRte~~~~~~~~~V~fs~~~~gt~eeDL~~~eDa~RRDFTINALAyd~~~g~LiDyfGGleDLk~riI 211 (686)
|.+++..|||+|||++.+...........++.+|++++|+ .||||||||||||+.+++|+||+||++||++|+|
T Consensus 81 v~~~~~~iEvatfR~~~~~~~~~~g~~~~d~~~gtieeDl------~RRDFTINALayd~~~~~IiD~~gG~~DL~~~~L 154 (410)
T TIGR01942 81 VSFGRQIIEVATFRSGHKSSVNAEGRILKDNVYGTLEEDA------WRRDFTVNALYYDPSREVIIDYVGGMEDLKNRRL 154 (410)
T ss_pred EEECCEEEEEecccccccCCCCCCCCcccccccCCHHHHh------hcCCchhhheeecCCCCeeeCCCCcHHHHHCCce
Confidence 9999999999999997543222223334456678999996 7999999999999998999999999999999999
Q ss_pred eecccCcccccccHHhHHHHHHHHHHhCCCCCHHHHHHHHHhhhhhcCCCHHHHHHHHHHHHhCCCHHHHHHHHHHcCCc
Q 005645 212 RTLIPAYLSFTEDCARILRGLRIAARLGLSFCKDIDTAMHSLSSSIERLDKSRIMMELNYMLSYGAAESSICLLRRYNLL 291 (686)
Q Consensus 212 R~Vg~p~~rF~EDPlRILRAiRFAaRLGF~Id~eT~~aIr~~a~lL~~Is~eRI~~EL~KLL~~~~~~~~L~lL~e~GLL 291 (686)
|+||+|..+|.|||+|||||+|||++|||.|+++|..+|++++..|..+|++||++|+.|||.++++..++++|.++|++
T Consensus 155 R~igdp~~rf~EDPlRiLRAvRFaa~LgF~Ie~~T~~~I~~~a~~L~~vs~eRI~~El~Kll~~~~~~~~l~~L~~~gll 234 (410)
T TIGR01942 155 RLIGDPRSRYQEDPVRMLRALRFSVKLEFTIDESTARPIRESAPLLKGIPPARLFEEILKLLFSGRSAALFRMLCGYQLL 234 (410)
T ss_pred eecCChhhcccccHHHHHHHHHHHHHhCCCcCHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHcCCCHHHHHHHHHHcCCH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhhhhhhhhhhhccCcCCCchhHHHHHHHHh-HHhhhhCCCCCchhhHHHHH
Q 005645 292 KILLPFHAAYLDQQAGKITAENPMMLMRLFFN-LDKLVSCDRPADYTLWVGLL 343 (686)
Q Consensus 292 ~~LfPela~~~~qq~~~h~~t~d~~Ll~lL~~-ld~ll~~~rp~~~~lWlalL 343 (686)
..+||++...+..... ....++..++.+ +|.++..++++++..+.+++
T Consensus 235 ~~lfPel~~~l~~~~~----~~~~~~~~~l~~~~d~r~~~~~~v~p~fl~a~l 283 (410)
T TIGR01942 235 EPLFPSVAYALRESPK----FESAFTVQALVNDTDFRVKRDKPVTPAFLYAAL 283 (410)
T ss_pred HHHhHhHHHHHhcCCc----hHHHHHHHHHHhhhHHHHhCCCCCCHHHHHHHH
Confidence 9999998865432211 134467777888 99999999999875554433
No 3
>KOG2159 consensus tRNA nucleotidyltransferase/poly(A) polymerase [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=9.3e-60 Score=503.65 Aligned_cols=380 Identities=32% Similarity=0.444 Sum_probs=305.7
Q ss_pred eccccccCcCcCCCChhHHHHHHHHHHCCCcEEEEchhHHHHHhCCCCCCeEEEeCCCHHHHHHHhccCcc-cccccCeE
Q 005645 52 TVDSRNLGITRAMIPQPSWVVLKILKSQGFQAYLVGGCVRDLLLRRVPKDFDVITTANLKQIRRQFHRSEI-IGRRFPIC 130 (686)
Q Consensus 52 ~~~~~~~gI~~~~ip~~a~~VL~~L~~~G~eAYLVGG~VRDLLLGr~PkD~DIvT~A~peei~k~F~~~~i-vGrrF~i~ 130 (686)
+++..++| .+++++....|+..+++.||++|+|||||||+|||++|+||||+|+|.+.|+++.|..+.+ +|.+|+.+
T Consensus 2 k~~~~e~~--~s~~~~~~~~v~~~~~~~~~elRiaGGwVRD~LLg~~p~DiDiatta~~g~~~e~f~~~~~~~~~~~~~~ 79 (416)
T KOG2159|consen 2 KLDSEEFG--TSLLTDSTRLVLSKLKKKGYELRLAGGWVRDLLLGREPKDIDIATTAMSGQMKEMFQSAQIRVGKKFPIC 79 (416)
T ss_pred CccHHHHH--HHhccHHHHHHHHHhhcCCCeeEEecccHHHHHcCCCCcccceeeccccHHHHHHHHHHHHhhcccCCcc
Confidence 45566666 7899999999999999999999999999999999999999999999999999999998877 99999999
Q ss_pred EEEECCEEE---EEeccc-----ccccccCCCceeeecCCCCCCchhhhhhhhhhccCccccccccccCCCCeEeeCcCc
Q 005645 131 RVHIKGSVI---EVSSFE-----TVAKHGEGKETVLLSQIPYGCDEIDLVRWRNSIHRDFTINSLFFDPFLNKIYDYANG 202 (686)
Q Consensus 131 ~V~~~G~~I---EVaTfR-----te~~~~~~~~~V~fs~~~~gt~eeDL~~~eDa~RRDFTINALAyd~~~g~LiDyfGG 202 (686)
|+..+.... |.+++| -+.........++-+ +....|..+|+||.|||||||+++||+++|+|+||+||
T Consensus 80 h~~~np~~skhletat~~i~~~~iD~v~lr~~~y~e~~----~~~~~dgt~~~nalRRD~TIN~Lffn~~~~~VeDytgG 155 (416)
T KOG2159|consen 80 HVIMGPIKSKHLETATFRITTLRIDFVNLRREAYTETS----IPYVTDGTRDENALRRDFTINSLFFNPFDGTVEDYTGG 155 (416)
T ss_pred eeecCCcceeeecceeeeeeccccceeecCcccccccC----CCCCCcCcchhhhhhhccchhhhhccCCCCceeecccc
Confidence 977654322 222332 211111111111100 11234555677899999999999999999999999999
Q ss_pred HHHHhcCceeecccCcccccccHHhHHHHHHHHHHhCCCC---CHHHHHHHHHhhhhhcCCCHHHHHHHHHHHHhCCCHH
Q 005645 203 ISDLRCLKLRTLIPAYLSFTEDCARILRGLRIAARLGLSF---CKDIDTAMHSLSSSIERLDKSRIMMELNYMLSYGAAE 279 (686)
Q Consensus 203 leDLk~riIR~Vg~p~~rF~EDPlRILRAiRFAaRLGF~I---d~eT~~aIr~~a~lL~~Is~eRI~~EL~KLL~~~~~~ 279 (686)
++||++++||||++|.++|.|||+||||+||||+|+||+| +++|..+++.++.++.+||+|||+.|+.|||.++.+.
T Consensus 156 ~eDL~~~kvrt~~~A~~tf~eDpLRILR~iRFaaRlgftid~~~~e~~~~~k~~~~~~~kIS~ERI~~Ei~kmL~g~~~~ 235 (416)
T KOG2159|consen 156 LEDLKNKKVRTVLHAKQTFLEDPLRILRGIRFAARLGFTIDEESKETLEAIKENVALLAKISRERIGVEINKMLVGNSAE 235 (416)
T ss_pred HhHHhcCeEEeeccccceeccchHHHHHHHHHHHhhcCccCcccHHHHhhHHHHHHHhccccHHHHHHHHHHHHcCCcHH
Confidence 9999999999999999999999999999999999999999 8888889999999999999999999999999999999
Q ss_pred HHHHHHHH-cCCchhhhhhhhhhhhhccCcCCCchhHHHHHHHHhHHhhhhCCCCCchhhHHHHHHHHHHhcCCchhHHH
Q 005645 280 SSICLLRR-YNLLKILLPFHAAYLDQQAGKITAENPMMLMRLFFNLDKLVSCDRPADYTLWVGLLSFHQALVSDPQDAFV 358 (686)
Q Consensus 280 ~~L~lL~e-~GLL~~LfPela~~~~qq~~~h~~t~d~~Ll~lL~~ld~ll~~~rp~~~~lWlalLaf~~aL~~~p~~a~v 358 (686)
.+|++|++ .|+...++|..+.+..-+.......-..+.+.++.++++....+.+|+..+|++.+.+|..+..+|..+.+
T Consensus 236 ~~L~ll~~~~~~~~i~lp~~~s~~~f~~~~~~~~~s~~~~sl~~~l~~~~~~~~~~~~~l~l~~~~~~~~~~~~~r~~~v 315 (416)
T KOG2159|consen 236 ASLRLLWRLFGFEYIFLPIEASLEEFQGFNRRDGFSNEPLSLLANLDKSLAPDEPCHLRLKLSILELLKKFIDQPRFPTV 315 (416)
T ss_pred HHHHHHHHhcCceEEeccchhhhhhccccccccccchhHHHHHhcccccccccchhhhhHHHHHHhhhhHhhccccccce
Confidence 99999999 77777888977765442222112223347788899999999999999999999999999999999999999
Q ss_pred HHHHHHhhccCchhhhhHHHHHHhCCCCcchhhhcccccccchHH-H-HHHHHHHHHHHHHHHHHhc-------------
Q 005645 359 VWVFASVLYHGKWKEGVKFARDRAKEPVKFVPEISGFSEIESDEQ-L-AVKVTELALSVQDCVNDLT------------- 423 (686)
Q Consensus 359 ~~a~a~ll~~g~~~~~vk~~r~~~~~~~~~~~el~~~~~~~~~~~-L-~e~v~~la~lv~~~~~~~~------------- 423 (686)
.|+...+.+.. .+.+...+.+.+.+..+...+..+.+-..+.+ + ...+..+.+++.+++..++
T Consensus 316 ~~~~~~~~~~~--~~~~~i~~~i~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~g~llr~l 393 (416)
T KOG2159|consen 316 PAVSSSAPLSK--LQDVEIPKKIEKDHDRLRQLLVSQEKNELDNETLLDWSVPDFPISINDLAIEGTSKGSIIGALLRYL 393 (416)
T ss_pred eeeecccchhh--hhhhhcccccccchHHHHHHhcchHhhhhHHHHHhhhccCchHHHHHHHHHhhcccchhHHHHHHhh
Confidence 98877666533 45677777777788777777777665322222 2 2336778888888888887
Q ss_pred -cCCCCcEEeehHHHHH
Q 005645 424 -KASSGYVFVSKKIERN 439 (686)
Q Consensus 424 -~~~s~~vfv~~~~~~~ 439 (686)
.|+++.||.+..++..
T Consensus 394 ~~~w~~~~~~~~~~~~l 410 (416)
T KOG2159|consen 394 QAPWSDSVFTSLKDSLL 410 (416)
T ss_pred hhhHHHHHhHHHHHHHh
Confidence 3588889888887654
No 4
>COG0617 PcnB tRNA nucleotidyltransferase/poly(A) polymerase [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.6e-58 Score=496.20 Aligned_cols=233 Identities=36% Similarity=0.540 Sum_probs=217.4
Q ss_pred CcCcCCCChhHHHHHHHHHHCCCcEEEEchhHHHHHhCCCCCCeEEEeCCCHHHHHHHhccCcccccccCeEEEEECCEE
Q 005645 59 GITRAMIPQPSWVVLKILKSQGFQAYLVGGCVRDLLLRRVPKDFDVITTANLKQIRRQFHRSEIIGRRFPICRVHIKGSV 138 (686)
Q Consensus 59 gI~~~~ip~~a~~VL~~L~~~G~eAYLVGG~VRDLLLGr~PkD~DIvT~A~peei~k~F~~~~ivGrrF~i~~V~~~G~~ 138 (686)
++....+++.+..|+..|+++||++|+|||||||+|||++|+|+||+|++.|+++...|+++..+|++|+++++.++|..
T Consensus 1 ~~~~~~~~~~~~~v~~~l~~~g~eaylVGGaVRD~LLG~~~~D~Diat~~~p~~~~~~~~~~~~~G~~f~t~~v~~~~~~ 80 (412)
T COG0617 1 GIMLKDLSPNALKVLSKLKEAGYEAYLVGGAVRDLLLGRPPKDVDIATNATPEEVKKLFRNTRPVGRKFGTVTVPFNGEI 80 (412)
T ss_pred CCChhhhhHHHHHHHHHHHhCCCeEEEeCcHHHHHHcCCCCcceeeeCCCCCHHHHHHHhhhhhhhhhcCeEEeccCCEE
Confidence 35567888999999999999999999999999999999999999999999999999999999999999999999998899
Q ss_pred EEEeccccccc-ccCCCceeeecCCCCCCchhhhhhhhhhccCccccccccccCCCCeEeeCcCcHHHHhcCceeecccC
Q 005645 139 IEVSSFETVAK-HGEGKETVLLSQIPYGCDEIDLVRWRNSIHRDFTINSLFFDPFLNKIYDYANGISDLRCLKLRTLIPA 217 (686)
Q Consensus 139 IEVaTfRte~~-~~~~~~~V~fs~~~~gt~eeDL~~~eDa~RRDFTINALAyd~~~g~LiDyfGGleDLk~riIR~Vg~p 217 (686)
+||+|||++.+ ..+....+ ..++++++|+ .||||||||||||+.+|+|+|||||+.||++|+||+||+|
T Consensus 81 ~ev~T~R~~~~~~~~~~~~~----~~~~tleeDl------~RRDFTINAla~~~~~~~iiD~~gG~~DL~~~~lR~i~~~ 150 (412)
T COG0617 81 IEVTTFRKEGYGYNGRPLPV----VFPGTLEEDL------KRRDFTINALAYDPEDGEIIDPFGGLKDLENRVLRHIGDA 150 (412)
T ss_pred EEEEEeecCCCCcCCCcCCc----CCCCCHHHHH------HHhcccHHhhccCCCCCeEEeCCCCHHHHhcCceeccCCH
Confidence 99999999875 33333333 3457888886 7999999999999999999999999999999999999999
Q ss_pred cccccccHHhHHHHHHHHHHhCCCCCHHHHHHHHHhhhhhcCCCHHHHHHHHHHHHhCCCHHHHHHHHHHcCCchhhhhh
Q 005645 218 YLSFTEDCARILRGLRIAARLGLSFCKDIDTAMHSLSSSIERLDKSRIMMELNYMLSYGAAESSICLLRRYNLLKILLPF 297 (686)
Q Consensus 218 ~~rF~EDPlRILRAiRFAaRLGF~Id~eT~~aIr~~a~lL~~Is~eRI~~EL~KLL~~~~~~~~L~lL~e~GLL~~LfPe 297 (686)
++||.|||+|||||+|||++|||.|++.|..+|+.....+..+|+|||+.|+.|||.++++..++++|.++|+++.+||+
T Consensus 151 ~~rf~EDplRiLRa~RFaa~l~f~i~~~t~~~i~~~~~~~~~is~ERi~~El~KlL~~~~~~~~l~~l~~~g~l~~l~p~ 230 (412)
T COG0617 151 SERFREDPLRILRAARFAARLGFTIEPETEEAIRLMAPLLAKISRERLWDELKKLLLSPNPREALQLLREYGALKILFPE 230 (412)
T ss_pred HHhcccchHHHHHHHHHHHHcCCCCChhHHHHHHHHHHHhhcCCHHHHHHHHHHHHcCCCHHHHHHHHHHcCChhhcChh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhh
Q 005645 298 HAAY 301 (686)
Q Consensus 298 la~~ 301 (686)
+..+
T Consensus 231 ~~~~ 234 (412)
T COG0617 231 LDKL 234 (412)
T ss_pred HHHh
Confidence 8763
No 5
>TIGR02692 tRNA_CCA_actino tRNA adenylyltransferase. The enzyme tRNA adenylyltransferase, also called tRNA-nucleotidyltransferase and CCA-adding enzyme, can add or repair the required CCA triplet at the 3'-end of tRNA molecules. Genes encoding tRNA include the CCA tail in some but not all bacteria, and this enzyme may be required for viability. Members of this family represent a distinct clade within the larger family pfam01743 (tRNA nucleotidyltransferase/poly(A) polymerase family protein). The example from Streptomyces coelicolor was shown to act as a CCA-adding enzyme and not as a poly(A) polymerase.
Probab=100.00 E-value=7.7e-55 Score=477.20 Aligned_cols=253 Identities=25% Similarity=0.314 Sum_probs=227.4
Q ss_pred CChhHHHHHHHHHHCCCcEEEEchhHHHHHhCCCCCCeEEEeCCCHHHHHHHhcc----CcccccccCeEEEEECCEEEE
Q 005645 65 IPQPSWVVLKILKSQGFQAYLVGGCVRDLLLRRVPKDFDVITTANLKQIRRQFHR----SEIIGRRFPICRVHIKGSVIE 140 (686)
Q Consensus 65 ip~~a~~VL~~L~~~G~eAYLVGG~VRDLLLGr~PkD~DIvT~A~peei~k~F~~----~~ivGrrF~i~~V~~~G~~IE 140 (686)
.++.+..|++.|.++||++|+|||||||+|||++|+|+||+|+++|+++.+.|+. ...+|..|+++++..+|..||
T Consensus 12 ~~~~~~~i~~~l~~~g~~~y~VGG~VRD~llg~~~~D~Di~~~~~~~~~~~~~~~~~~~~~~~g~~~g~~~v~~~~~~~e 91 (466)
T TIGR02692 12 LSPLLAPLAAAFAAAGHELYLVGGSVRDALLGRLGHDLDFTTDARPEETLAILRPWADAVWDTGIAFGTVGAEKDGQQIE 91 (466)
T ss_pred ccHHHHHHHHHHHhCCCEEEEeCcHHHHHHcCCCCCCEEEEeCCCHHHHHHHHHHhhhhccccCcccceEEEEECCcEEE
Confidence 4678889999999999999999999999999999999999999999999999873 456799999999999999999
Q ss_pred EecccccccccCCC-ceeeecCCCCCCchhhhhhhhhhccCccccccccccCCCC---eEeeCcCcHHHHhcCceeeccc
Q 005645 141 VSSFETVAKHGEGK-ETVLLSQIPYGCDEIDLVRWRNSIHRDFTINSLFFDPFLN---KIYDYANGISDLRCLKLRTLIP 216 (686)
Q Consensus 141 VaTfRte~~~~~~~-~~V~fs~~~~gt~eeDL~~~eDa~RRDFTINALAyd~~~g---~LiDyfGGleDLk~riIR~Vg~ 216 (686)
|++||++.|..++. +.|.+ .+++++|| .||||||||||||+.++ .|+|||||++||++|+||+|++
T Consensus 92 i~~~r~e~~~~~~~~~~v~~----~~~i~~Dl------~rRDFTiNA~a~~~~~~~~g~l~D~~~G~~Dl~~~~ir~v~~ 161 (466)
T TIGR02692 92 ITTFRSDSYDGTSRKPEVTF----GDTLEGDL------IRRDFTVNAMAVRIPADGSLEFHDPVGGLDDLLAKVLDTPAT 161 (466)
T ss_pred EEecccccCcCCCCCCcccC----CCCHHHHH------HhccccHHHhhccccCCCCceeecCCCcHHHHhCCceEecCC
Confidence 99999987765443 33333 23678886 79999999999998754 8999999999999999999999
Q ss_pred CcccccccHHhHHHHHHHHHHhCCCCCHHHHHHHHHhhhhhcCCCHHHHHHHHHHHHhCCCHHHHHHHHHHcCCchhhhh
Q 005645 217 AYLSFTEDCARILRGLRIAARLGLSFCKDIDTAMHSLSSSIERLDKSRIMMELNYMLSYGAAESSICLLRRYNLLKILLP 296 (686)
Q Consensus 217 p~~rF~EDPlRILRAiRFAaRLGF~Id~eT~~aIr~~a~lL~~Is~eRI~~EL~KLL~~~~~~~~L~lL~e~GLL~~LfP 296 (686)
|..+|.|||+|||||+|||+++||.|+++|..+|++.+..+..+++|||+.|+.+||.++++..++++|.++|+|..+||
T Consensus 162 ~~~~f~eDPlRiLRa~Rfaa~lgf~i~~~T~~~i~~~~~~l~~i~~eRi~~E~~kil~~~~~~~~l~~l~~~glL~~~~P 241 (466)
T TIGR02692 162 PEQSFGDDPLRMLRAARFVSQLGFEVAPRVRAAMTEMADQIERISAERVRVELDKLLLGDHPRAGIDLMVETGLADRVLP 241 (466)
T ss_pred hHHhhhhChHHHHHHHHHHHHhCCCcCHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHcCCCcHHHHHHHHhhhhhhhcCc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhhhhh-hccCcCCCchhHHHHHHHHhHHhh
Q 005645 297 FHAAYLD-QQAGKITAENPMMLMRLFFNLDKL 327 (686)
Q Consensus 297 ela~~~~-qq~~~h~~t~d~~Ll~lL~~ld~l 327 (686)
++..... +...+|.+++..|++.++..+..+
T Consensus 242 e~~~~~~~~~~~~h~~~v~~Htl~vl~~~~~l 273 (466)
T TIGR02692 242 EIPALRLEIDEHHQHKDVYEHSLTVLRQAIDL 273 (466)
T ss_pred hHHHHhcccccCCCCCcHHHHHHHHHHHHHhc
Confidence 9886543 445678889999999988877654
No 6
>PRK13299 tRNA CCA-pyrophosphorylase; Provisional
Probab=100.00 E-value=1.1e-54 Score=468.31 Aligned_cols=223 Identities=30% Similarity=0.411 Sum_probs=204.6
Q ss_pred CChhHHHHHHHHHHCCCcEEEEchhHHHHHhCCCCCCeEEEeCCCHHHHHHHhccCcccccccCeEEEEECCEEEEEecc
Q 005645 65 IPQPSWVVLKILKSQGFQAYLVGGCVRDLLLRRVPKDFDVITTANLKQIRRQFHRSEIIGRRFPICRVHIKGSVIEVSSF 144 (686)
Q Consensus 65 ip~~a~~VL~~L~~~G~eAYLVGG~VRDLLLGr~PkD~DIvT~A~peei~k~F~~~~ivGrrF~i~~V~~~G~~IEVaTf 144 (686)
....+..|++.|+++|+++|+|||||||+|||++|+|+||+|++.|+++.+.|+++..+|.+|++++|..+|..|||+||
T Consensus 5 ~~~~~~~i~~~l~~~g~~~ylVGG~VRD~LLg~~~~DiDi~~~~~~~~~~~~~~~~~~~g~~~gt~~v~~~~~~~ei~t~ 84 (394)
T PRK13299 5 EFQKALPILEKIKEAGFEAYFVGGSVRDYLLGRPIHDVDIATSAYPEEVKAIFPRTVDVGIEHGTVLVLENGEEYEVTTF 84 (394)
T ss_pred HHHHHHHHHHHHHHcCCeEeeccchHHHHHcCCCCCCEEEecCCCHHHHHHHhhhhhhccccCCEEEEEECCEEEEEEee
Confidence 34678899999999999999999999999999999999999999999999999987778999999999999999999999
Q ss_pred cccccc--cCCCceeeecCCCCCCchhhhhhhhhhccCccccccccccCCCCeEeeCcCcHHHHhcCceeecccCccccc
Q 005645 145 ETVAKH--GEGKETVLLSQIPYGCDEIDLVRWRNSIHRDFTINSLFFDPFLNKIYDYANGISDLRCLKLRTLIPAYLSFT 222 (686)
Q Consensus 145 Rte~~~--~~~~~~V~fs~~~~gt~eeDL~~~eDa~RRDFTINALAyd~~~g~LiDyfGGleDLk~riIR~Vg~p~~rF~ 222 (686)
|++... .+.+..+.+. +++++|| +||||||||||||+. |.|+|||||++||++|+||++|+|..+|.
T Consensus 85 R~e~~~~d~~~p~~~~~~----~~i~eDl------~RRDFTINAma~~~~-g~liDpf~G~~DL~~~~iR~v~~~~~~f~ 153 (394)
T PRK13299 85 RTESEYVDYRRPSEVTFV----RSLEEDL------KRRDFTINAIAMDEN-GEIIDLFDGLEDLKNRLIRAVGNAEERFQ 153 (394)
T ss_pred ccccCccCCCCCccccCC----CCHHHHH------HhccccHHHhhcCCC-CCEeeCCCCHHHHhCCceeecCCHHHhhc
Confidence 997322 2223344443 4677886 799999999999984 89999999999999999999999999999
Q ss_pred ccHHhHHHHHHHHHHhCCCCCHHHHHHHHHhhhhhcCCCHHHHHHHHHHHHhCCCHHHHHHHHHHcCCchhhhhhhh
Q 005645 223 EDCARILRGLRIAARLGLSFCKDIDTAMHSLSSSIERLDKSRIMMELNYMLSYGAAESSICLLRRYNLLKILLPFHA 299 (686)
Q Consensus 223 EDPlRILRAiRFAaRLGF~Id~eT~~aIr~~a~lL~~Is~eRI~~EL~KLL~~~~~~~~L~lL~e~GLL~~LfPela 299 (686)
|||+|||||+|||++|||+|+++|+.+|++++..+..+|+|||+.|+.+||.++++..++++|.++|++.. +|++.
T Consensus 154 eDplRiLRa~Rfaa~l~f~i~~~t~~~i~~~~~~l~~vs~eRI~~El~kll~~~~~~~~l~~l~~~gll~~-~p~l~ 229 (394)
T PRK13299 154 EDALRMMRAVRFASQLGFDLETETFEAMKTQAPLLEKISVERIFVEFEKLLLGPFWRKGLKLLIETGLYNY-LPGLK 229 (394)
T ss_pred cCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHcCCCHHHHHHHHHHCChHHh-Ccccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999 89865
No 7
>PRK10885 cca multifunctional tRNA nucleotidyl transferase/2'3'-cyclic phosphodiesterase/2'nucleotidase/phosphatase; Reviewed
Probab=100.00 E-value=9e-50 Score=431.95 Aligned_cols=233 Identities=29% Similarity=0.353 Sum_probs=199.6
Q ss_pred CcEEEEchhHHHHHhCCCCCCeEEE-eCCCHHHHHHHhccCcccccccCeEEEEECCEEEEEecccccccccCCCceeee
Q 005645 81 FQAYLVGGCVRDLLLRRVPKDFDVI-TTANLKQIRRQFHRSEIIGRRFPICRVHIKGSVIEVSSFETVAKHGEGKETVLL 159 (686)
Q Consensus 81 ~eAYLVGG~VRDLLLGr~PkD~DIv-T~A~peei~k~F~~~~ivGrrF~i~~V~~~G~~IEVaTfRte~~~~~~~~~V~f 159 (686)
+++|+|||||||+|||++|+|+||+ +.++|+++... ....+|+.|+++.+ .+..+|++++|++.+.+.+...+.+
T Consensus 1 ~~~ylVGG~VRD~Llg~~~~D~D~vv~~~~~~~~~~~--~~~~~g~~f~v~~~--~~~~~e~~~~r~er~~~~g~~~~~~ 76 (409)
T PRK10885 1 MKIYLVGGAVRDALLGLPVKDRDWVVVGATPEEMLAQ--GYQQVGKDFPVFLH--PKTHEEYALARTERKSGRGYTGFTC 76 (409)
T ss_pred CcEEEeccHHHHHHcCCCCCCeeEEeeCChHHHHHhC--CCeecCceeEEEEe--CCceEEEEeeeeccccCCCCCCcee
Confidence 5799999999999999999999986 55788888764 33458999998754 3456799999999877665544443
Q ss_pred cCCCCCCchhhhhhhhhhccCccccccccccCCCCeEeeCcCcHHHHhcCceeecccCcccccccHHhHHHHHHHHHHh-
Q 005645 160 SQIPYGCDEIDLVRWRNSIHRDFTINSLFFDPFLNKIYDYANGISDLRCLKLRTLIPAYLSFTEDCARILRGLRIAARL- 238 (686)
Q Consensus 160 s~~~~gt~eeDL~~~eDa~RRDFTINALAyd~~~g~LiDyfGGleDLk~riIR~Vg~p~~rF~EDPlRILRAiRFAaRL- 238 (686)
...+..++++|| .||||||||||||+ +|.|||||||++||++|+||+|++ +|.|||+|||||+|||++|
T Consensus 77 ~~~~~~~l~eDl------~RRDfTiNA~a~~~-~~~liDp~~G~~Dl~~~~lr~v~~---~f~eDPlRiLRa~RFaarl~ 146 (409)
T PRK10885 77 YAAPDVTLEEDL------IRRDLTINAMAQDD-DGELIDPYGGQRDLEARLLRHVSP---AFAEDPLRVLRVARFAARFA 146 (409)
T ss_pred ccCCCCCHHHHH------HhccchhhhheeCC-CCCEecCCCCHHHHhCCceEeCCc---hhhhCHHHHHHHHHHHHHhc
Confidence 334456888887 79999999999995 589999999999999999999996 5999999999999999999
Q ss_pred --CCCCCHHHHHHHHHhhh--hhcCCCHHHHHHHHHHHHhCCCHHHHHHHHHHcCCchhhhhhhhhhhh--hccCcCC-C
Q 005645 239 --GLSFCKDIDTAMHSLSS--SIERLDKSRIMMELNYMLSYGAAESSICLLRRYNLLKILLPFHAAYLD--QQAGKIT-A 311 (686)
Q Consensus 239 --GF~Id~eT~~aIr~~a~--lL~~Is~eRI~~EL~KLL~~~~~~~~L~lL~e~GLL~~LfPela~~~~--qq~~~h~-~ 311 (686)
||+|+++|+.+|++.+. .|..+++|||+.|+.++|.++++..+++.|.++|+|..+||++..... +...+|. +
T Consensus 147 ~lgf~i~~~T~~~i~~~~~~~~L~~~~~ERi~~El~kiL~~~~p~~~l~~L~~~g~L~~l~PEl~~l~~~~Q~~~~H~e~ 226 (409)
T PRK10885 147 HLGFRIAPETLALMREMVASGELDALTPERVWKETERALMERNPQVFFQVLRDCGALAVLLPEIDALFGVPQPAKWHPEI 226 (409)
T ss_pred cCCCCcCHHHHHHHHHhhhhchhhhCCHHHHHHHHHHHHcCCCHHHHHHHHHHhhHHHHHhhHHHHHhcCCCCcCCCCCC
Confidence 99999999999999887 899999999999999999999999999999999999999999988765 3344554 5
Q ss_pred chhHHHHHHHHhHHhh
Q 005645 312 ENPMMLMRLFFNLDKL 327 (686)
Q Consensus 312 t~d~~Ll~lL~~ld~l 327 (686)
++..|++.++..+..+
T Consensus 227 dv~~Htl~~l~~~~~l 242 (409)
T PRK10885 227 DTGIHTLMVLDQAAKL 242 (409)
T ss_pred cHHHHHHHHHHHHHhc
Confidence 7888998888776653
No 8
>PRK13297 tRNA CCA-pyrophosphorylase; Provisional
Probab=100.00 E-value=2.4e-49 Score=421.73 Aligned_cols=212 Identities=28% Similarity=0.324 Sum_probs=186.4
Q ss_pred HHCCCcEEEEchhHHHHHhCCCCCCeEEEe-CCCHHHHHHHhccCcccccccCeEEEEECCEEEEEecccccccccCCCc
Q 005645 77 KSQGFQAYLVGGCVRDLLLRRVPKDFDVIT-TANLKQIRRQFHRSEIIGRRFPICRVHIKGSVIEVSSFETVAKHGEGKE 155 (686)
Q Consensus 77 ~~~G~eAYLVGG~VRDLLLGr~PkD~DIvT-~A~peei~k~F~~~~ivGrrF~i~~V~~~G~~IEVaTfRte~~~~~~~~ 155 (686)
..+|+++|+|||||||+|||++|+|+|+++ .++|+++.+. ....+|+.|+++.. .+..+|++++|++.+.+.+..
T Consensus 8 ~~~G~~~YlVGGaVRD~LLg~~~~D~D~vv~ga~pe~l~~~--~~~~vG~~f~v~l~--~~~~~e~a~aRterk~g~g~~ 83 (364)
T PRK13297 8 GVAGLQVYIVGGAVRDALLGLPAGDRDWVVVGATPEDMARR--GFIPVGGDFPVFLH--PRTKEEYALARTERKSGRGYK 83 (364)
T ss_pred hhCCCEEEEeCcHHHHHHcCCCCCCeeeeccCChHHHHHhc--CceeeCCEEEEEEe--CCceEEEEEEEEeeccCCCCc
Confidence 357999999999999999999999999764 5779999885 34557989985532 345689999999988877766
Q ss_pred eeeecCCCCCCchhhhhhhhhhccCccccccccccCCCCeEeeCcCcHHHHhcCceeecccCcccccccHHhHHHHHHHH
Q 005645 156 TVLLSQIPYGCDEIDLVRWRNSIHRDFTINSLFFDPFLNKIYDYANGISDLRCLKLRTLIPAYLSFTEDCARILRGLRIA 235 (686)
Q Consensus 156 ~V~fs~~~~gt~eeDL~~~eDa~RRDFTINALAyd~~~g~LiDyfGGleDLk~riIR~Vg~p~~rF~EDPlRILRAiRFA 235 (686)
.+.+...+..++++|| .||||||||||||+. |.|||||||++||++|+||+|++ +|.|||+|||||+|||
T Consensus 84 ~f~~~~~~~~tLeeDL------~RRDFTINAmA~~~~-g~liDpfgG~~DL~~riLR~v~~---~F~EDPLRILRa~RFa 153 (364)
T PRK13297 84 GFTFYTGADVTLEQDL------QRRDLTVNAIARTPQ-GELVDPLDGVADVRARVLRHVGE---AFAEDPVRILRLGRFA 153 (364)
T ss_pred eeEEeCCCCCCHHHHH------HhccceeeeeEECCC-CCEEECCCCHHHHhCCCeeeCcc---ccccCHHHHHHHHHHH
Confidence 6666544456788886 799999999999974 89999999999999999999985 7999999999999999
Q ss_pred HHhC-CCCCHHHHHHHHHhhh--hhcCCCHHHHHHHHHHHHhCCCHHHHHHHHHHcCCchhhhhhhhhhh
Q 005645 236 ARLG-LSFCKDIDTAMHSLSS--SIERLDKSRIMMELNYMLSYGAAESSICLLRRYNLLKILLPFHAAYL 302 (686)
Q Consensus 236 aRLG-F~Id~eT~~aIr~~a~--lL~~Is~eRI~~EL~KLL~~~~~~~~L~lL~e~GLL~~LfPela~~~ 302 (686)
++|| |+|+++|..+|++.+. .|..+++|||+.|+.|+|.++++..++++|.++|+|..+||++....
T Consensus 154 arlg~F~i~~eT~~~~~~~~~~~~l~~l~~ERI~~El~k~L~~~~p~~~l~~L~~~g~L~~l~Pel~~~~ 223 (364)
T PRK13297 154 ARFGDFSIAPETMQLCRRMVEAGEADALVPERVWKEVSRGLMAQAPSRMLDVLARAGALARVMPELHDDA 223 (364)
T ss_pred HHhCCCCCCHHHHHHHHHHhhhcccccCCHHHHHHHHHHHHcCCCHHHHHHHHHHcCCHHHhCccccccc
Confidence 9996 9999999999999875 68999999999999999999999999999999999999999987543
No 9
>PRK13298 tRNA CCA-pyrophosphorylase; Provisional
Probab=100.00 E-value=1.4e-48 Score=422.70 Aligned_cols=230 Identities=27% Similarity=0.277 Sum_probs=190.6
Q ss_pred CcEEEEchhHHHHHhCCCCCCeEEEeCC-CHHHHHHH-hccCcccccccCeEEEEECCEEEEEecccccccccCCCceee
Q 005645 81 FQAYLVGGCVRDLLLRRVPKDFDVITTA-NLKQIRRQ-FHRSEIIGRRFPICRVHIKGSVIEVSSFETVAKHGEGKETVL 158 (686)
Q Consensus 81 ~eAYLVGG~VRDLLLGr~PkD~DIvT~A-~peei~k~-F~~~~ivGrrF~i~~V~~~G~~IEVaTfRte~~~~~~~~~V~ 158 (686)
+++|+|||||||+|||++|+|+|++|.+ +|+++... |. .+|+.|+++.+ .+...|++++|++.+.+.+.....
T Consensus 1 m~~YlVGGaVRD~LLg~~~~D~D~vv~g~~~~~~~~~~~~---~vG~~f~v~l~--~~~~~e~a~aRter~~g~g~~g~~ 75 (417)
T PRK13298 1 MKIYLVGGAVRDSLLNLPVKDKDWVVVGGTPKILLSINFQ---QVGKDFPVFLH--PETHEEYALARTERKSGVGYTGFI 75 (417)
T ss_pred CcEEEEccHHHHHHcCCCCCCeeEEecCCCHHHHHHHHHH---HhCCeeEEEEe--CceeEEEEeecccccccCCCCCcc
Confidence 5799999999999999999999987765 58877553 32 37999998765 345679999999987665544333
Q ss_pred ecCCCCCCchhhhhhhhhhccCccccccccccCCCCeEeeCcCcHHHHhcCceeecccCcccccccHHhHHHHHHHHHHh
Q 005645 159 LSQIPYGCDEIDLVRWRNSIHRDFTINSLFFDPFLNKIYDYANGISDLRCLKLRTLIPAYLSFTEDCARILRGLRIAARL 238 (686)
Q Consensus 159 fs~~~~gt~eeDL~~~eDa~RRDFTINALAyd~~~g~LiDyfGGleDLk~riIR~Vg~p~~rF~EDPlRILRAiRFAaRL 238 (686)
+...+..++++|| .||||||||||||+. |.|||||||++||++|+||+|++ +|.|||+|||||+|||++|
T Consensus 76 ~~~~~~~tleeDL------~RRDFTINAmA~~~~-g~liDp~~G~~DL~~r~lR~v~~---~F~EDPLRiLRa~RFaar~ 145 (417)
T PRK13298 76 TDTSSDVTLEEDL------IRRDLTINAIAQDEN-GNYIDPFQGKKDIQLRLLRHVSE---SFIEDPLRVLRVARFAALL 145 (417)
T ss_pred cccCCCCCHHHHH------HhcccceeeeEECCC-CCEEeCCCcHHHHHCCcEecCCc---ccccCHHHHHHHHHHHHHh
Confidence 3323346888887 799999999999985 78999999999999999999984 7999999999999999995
Q ss_pred ---CCCCCHHHHHHHHHhh--hhhcCCCHHHHHHHHHHHHhCCCHHHHHHHHHHcCCchhhhhhhhhhhh-hcc---CcC
Q 005645 239 ---GLSFCKDIDTAMHSLS--SSIERLDKSRIMMELNYMLSYGAAESSICLLRRYNLLKILLPFHAAYLD-QQA---GKI 309 (686)
Q Consensus 239 ---GF~Id~eT~~aIr~~a--~lL~~Is~eRI~~EL~KLL~~~~~~~~L~lL~e~GLL~~LfPela~~~~-qq~---~~h 309 (686)
||+|+++|..+|++.+ ..|..+|+|||+.|+.|+|.+++|..++++|.++|+|..+||++..... .+. ..|
T Consensus 146 ~~lgF~i~~~T~~~i~~~~~~~~l~~~s~ERI~~El~k~L~~~~p~~~~~~L~~~g~L~~~~PEl~~~~g~~q~~~~~~~ 225 (417)
T PRK13298 146 VHLGFKIAKETMILMCIMVKKHELLYLTPERIWNETEKALKTDNPHVYFQVLYECNALKFLFPEIDFLYEKPYFLNSFFK 225 (417)
T ss_pred ccCCCccCHHHHHHHHHHhhhhhhhcCCHHHHHHHHHHHHcCCCHHHHHHHHHHcCCHHHhCcchHHHcCCCCCccccCC
Confidence 9999999999999998 7899999999999999999999999999999999999999999987654 222 133
Q ss_pred CCchhHHHHHHHHhHH
Q 005645 310 TAENPMMLMRLFFNLD 325 (686)
Q Consensus 310 ~~t~d~~Ll~lL~~ld 325 (686)
......|++..+....
T Consensus 226 ~~d~~~htl~~l~~~~ 241 (417)
T PRK13298 226 KFNLGNYILMGLSKIS 241 (417)
T ss_pred chhHHHHHHHHHHHHH
Confidence 3344556665555443
No 10
>PRK13296 tRNA CCA-pyrophosphorylase; Provisional
Probab=100.00 E-value=4.7e-46 Score=394.60 Aligned_cols=203 Identities=31% Similarity=0.424 Sum_probs=172.3
Q ss_pred CcEEEEchhHHHHHhCCCCCCeEEEeCCCH-HHHHH-HhccCcccccccCeEEEEECCEEEEEecccccccccCCCc--e
Q 005645 81 FQAYLVGGCVRDLLLRRVPKDFDVITTANL-KQIRR-QFHRSEIIGRRFPICRVHIKGSVIEVSSFETVAKHGEGKE--T 156 (686)
Q Consensus 81 ~eAYLVGG~VRDLLLGr~PkD~DIvT~A~p-eei~k-~F~~~~ivGrrF~i~~V~~~G~~IEVaTfRte~~~~~~~~--~ 156 (686)
+++|+|||||||+|||++|+|+||++++.+ +++.. .|. .+|..|+++. ..+..+||+++|++.+..++.. .
T Consensus 1 m~vYLVGGaVRD~LLgr~p~DiDivV~g~~~~~~l~~~~~---~vg~~f~V~~--~~~~~~Eiat~R~E~~~~~g~~~~~ 75 (360)
T PRK13296 1 MKFYLVGGAVRDMLLGITPKDKDWVVVGATEDEMLANGFI---KIAANFPVFI--HPQTKQEYALARSEKKTASGYHGFE 75 (360)
T ss_pred CcEEEeccHHHHHHcCCCCCCeeEEecCCcHHHHHHhhhh---hcCCceEEEE--ECCeeEEEeeccccccccCCCCCCe
Confidence 579999999999999999999999876654 44432 343 3577777653 2567899999999887666543 4
Q ss_pred eeecCCCCCCchhhhhhhhhhccCccccccccccCCCCeEeeCcCcHHHHhcCceeecccCcccccccHHhHHHHHHHHH
Q 005645 157 VLLSQIPYGCDEIDLVRWRNSIHRDFTINSLFFDPFLNKIYDYANGISDLRCLKLRTLIPAYLSFTEDCARILRGLRIAA 236 (686)
Q Consensus 157 V~fs~~~~gt~eeDL~~~eDa~RRDFTINALAyd~~~g~LiDyfGGleDLk~riIR~Vg~p~~rF~EDPlRILRAiRFAa 236 (686)
|+++. .+++++|| .||||||||||||+. |.|+|||||++||++|+||+++ .+|.|||+|||||+|||+
T Consensus 76 v~~~~--~~tieeDL------~RRDFTINAmA~d~~-g~liDpfgG~~DL~~kiLR~v~---~sF~EDPLRILRa~RFaa 143 (360)
T PRK13296 76 VNFSK--YITLEDDL------KRRDLTINSIAIDQN-NKVIDPFNGQADLQNRILRHTS---IAFIEDPLRVVRLARFKA 143 (360)
T ss_pred EeeCC--CCCHHHHH------HhcCcceeeeEECCC-CCEecCCCCHHHHHCCceecCc---cccccCHHHHHHHHHHHH
Confidence 66553 34778886 799999999999985 8899999999999999999985 389999999999999999
Q ss_pred Hh---CCCCCHHHHHHHHHhh--hhhcCCCHHHHHHHHHHHHhCCCHHHHHHHHHHcCCchhhhhhhhhhh
Q 005645 237 RL---GLSFCKDIDTAMHSLS--SSIERLDKSRIMMELNYMLSYGAAESSICLLRRYNLLKILLPFHAAYL 302 (686)
Q Consensus 237 RL---GF~Id~eT~~aIr~~a--~lL~~Is~eRI~~EL~KLL~~~~~~~~L~lL~e~GLL~~LfPela~~~ 302 (686)
+| ||.|+++|..+|++.+ ..|..+|+|||+.|+.|+|.. +..+++.|.++|+|..+||++....
T Consensus 144 rL~~~gF~ie~eT~~~i~~~~~~~~L~~vs~ERI~~El~kiL~~--p~~~l~~L~~~glL~~lfPel~~~~ 212 (360)
T PRK13296 144 QLSNFNFSIAQEMLALIKELVKTGELNHLTRERLHIEFVKALNN--PKIFFTTLKELEALKIIFPNISCIL 212 (360)
T ss_pred HhccCCCCcCHHHHHHHHHhhhhhhhhcCCHHHHHHHHHHHHhC--hHHHHHHHHHcCCHHHhCcchHHHh
Confidence 86 9999999999999985 589999999999999999984 5689999999999999999987643
No 11
>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=100.00 E-value=8.6e-33 Score=259.99 Aligned_cols=132 Identities=36% Similarity=0.540 Sum_probs=110.4
Q ss_pred hhHHHHHHHHHHC-CCcEEEEchhHHHHHhCCCCCCeEEEeCC-CHHHHHHHhcc--Cccc--ccccCeEEEEECCEEEE
Q 005645 67 QPSWVVLKILKSQ-GFQAYLVGGCVRDLLLRRVPKDFDVITTA-NLKQIRRQFHR--SEII--GRRFPICRVHIKGSVIE 140 (686)
Q Consensus 67 ~~a~~VL~~L~~~-G~eAYLVGG~VRDLLLGr~PkD~DIvT~A-~peei~k~F~~--~~iv--GrrF~i~~V~~~G~~IE 140 (686)
+.+..|++.|.++ |+++|+|||||||+|||++|+|+||+|++ .++.+.+.++. ...+ |.+|+++++.+++..+|
T Consensus 2 ~~~~~il~~l~~~~g~~~ylVGG~VRD~Llg~~~~DiDi~v~~~~~~~~~~l~~~~~~~~v~~~~~f~t~~v~~~~~~~d 81 (139)
T cd05398 2 PELLKLLRELKKALGYEAYLVGGAVRDLLLGRPPKDIDIATDADGPEFAEALFKKIGGRVVGLGEEFGTATVVINGLTID 81 (139)
T ss_pred HHHHHHHHHHHhccCceEEEECChHHHHHcCCCCCCceEEEeCCCHHHHHHHHHhcCCcEEecCCcccEEEEEECCEEEE
Confidence 5678999999999 99999999999999999999999999999 66667776652 3334 56999999999999999
Q ss_pred EecccccccccCCCceeeecCCCCCCchhhhhhhhhhccCccccccccccCCCCeEeeCcCcHHHHhc
Q 005645 141 VSSFETVAKHGEGKETVLLSQIPYGCDEIDLVRWRNSIHRDFTINSLFFDPFLNKIYDYANGISDLRC 208 (686)
Q Consensus 141 VaTfRte~~~~~~~~~V~fs~~~~gt~eeDL~~~eDa~RRDFTINALAyd~~~g~LiDyfGGleDLk~ 208 (686)
|+++|++.+..++... .....++++|| .|||||||||||++.++.|+|||||++||++
T Consensus 82 i~~~R~e~~~~~~~~p----~~~~~~~~~Dl------~RRDFTINAmA~~~~~~~liDp~~G~~DL~~ 139 (139)
T cd05398 82 VATLRTETYTDPGRRP----PVVGFTIEEDL------LRRDFTINAMAYDLDDGELIDPFGGLKDLEN 139 (139)
T ss_pred EcccccccccCCCCCC----cccCCCCHHHH------hhcCcchhheEecCCCCEEEeCCCCHHHHhC
Confidence 9999999876654321 11223456675 7999999999999988999999999999985
No 12
>PF01743 PolyA_pol: Poly A polymerase head domain; InterPro: IPR002646 This group includes nucleic acid independent RNA polymerases, such as polynucleotide adenylyltransferase (2.7.7.19 from EC), which adds the poly (A) tail to mRNA. This group also includes the tRNA nucleotidyltransferase that adds the CCA to the 3' of the tRNA 2.7.7.25 from EC.; GO: 0003723 RNA binding, 0016779 nucleotidyltransferase activity, 0006396 RNA processing; PDB: 1VFG_A 3H38_A 3H3A_B 3H39_B 3H37_A 1MIY_A 1MIV_B 1MIW_B 1OU5_B 3AQN_A ....
Probab=99.98 E-value=9.9e-33 Score=255.10 Aligned_cols=122 Identities=39% Similarity=0.598 Sum_probs=97.0
Q ss_pred EEEEchhHHHHHhCCCCCCeEEEeCCCHHHHHHHhccCc----ccccccCeEEEEECCEEEEEecccccccccCCCceee
Q 005645 83 AYLVGGCVRDLLLRRVPKDFDVITTANLKQIRRQFHRSE----IIGRRFPICRVHIKGSVIEVSSFETVAKHGEGKETVL 158 (686)
Q Consensus 83 AYLVGG~VRDLLLGr~PkD~DIvT~A~peei~k~F~~~~----ivGrrF~i~~V~~~G~~IEVaTfRte~~~~~~~~~V~ 158 (686)
+|+|||||||+|||++|+|+||+|+++|+++++.|.... .+|++|+++++..++..+||++||++.+..++.....
T Consensus 1 ~ylVGG~VRD~Llg~~~~DiDi~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~di~~~r~~~~~~~~~~~~~ 80 (126)
T PF01743_consen 1 AYLVGGAVRDLLLGRPPKDIDIVTNADPEEFAKLLAKKLGGVFVVGKRFGTVRVVFGGGSIDIASFRGEFYIGDGRNPDV 80 (126)
T ss_dssp EEEETHHHHHHHHTS--SEEEEEESS-HHHHHHHHCTTCCEEEEEETTTTEEEEEETTCEEEEEE-ECE--SSSSS--CC
T ss_pred CEEecHHHHHHHcCCCCCCeEEEEeCCHHHHHHHHHhhcccccccccccceeeecCCCcccccccccccccccccccccc
Confidence 799999999999999999999999999999999987543 3489999999999998999999999887665432211
Q ss_pred ecCCCCCCchhhhhhhhhhccCccccccccccCCCCeEeeCcCcHHHHhcCcee
Q 005645 159 LSQIPYGCDEIDLVRWRNSIHRDFTINSLFFDPFLNKIYDYANGISDLRCLKLR 212 (686)
Q Consensus 159 fs~~~~gt~eeDL~~~eDa~RRDFTINALAyd~~~g~LiDyfGGleDLk~riIR 212 (686)
.. ...++++|| .|||||||||||++.+|+|+|||||++||++|+||
T Consensus 81 ~~--~~~~i~~Dl------~rRDFTiNAla~~~~~~~liDp~gG~~DL~~~~iR 126 (126)
T PF01743_consen 81 VE--FGPTIEEDL------KRRDFTINALAYDLETGKLIDPFGGLEDLKNKIIR 126 (126)
T ss_dssp CC--CSSTHHHHH------CTSSBGGGSEEEECTTTCEEESSSHHHHHHTTEE-
T ss_pred cc--ccCCHHHHH------HhcCCeehheeEECCCCeEEcCCCCHHHHHcCCCC
Confidence 11 112566665 89999999999999999999999999999999998
No 13
>PHA01806 hypothetical protein
Probab=99.87 E-value=8e-22 Score=194.20 Aligned_cols=113 Identities=18% Similarity=0.116 Sum_probs=86.0
Q ss_pred cccCcCcCCCChhHHHHHHHHHHCCCcEEEEchhHHHHHhCCCCCCeEEEe-CCCHHHHHHHhccC----cccccccCeE
Q 005645 56 RNLGITRAMIPQPSWVVLKILKSQGFQAYLVGGCVRDLLLRRVPKDFDVIT-TANLKQIRRQFHRS----EIIGRRFPIC 130 (686)
Q Consensus 56 ~~~gI~~~~ip~~a~~VL~~L~~~G~eAYLVGG~VRDLLLGr~PkD~DIvT-~A~peei~k~F~~~----~ivGrrF~i~ 130 (686)
....|++..|++.++.|++.|+++|+++|+|||||||+|||++|+|+||+| .+.|+++.++.... .....+.+++
T Consensus 11 ~~~~I~~~~is~~al~v~~~l~~~g~~aYlVGG~VRD~Llgr~~kDiDivt~~~~pe~v~~L~~klG~k~V~~~~~~ggw 90 (200)
T PHA01806 11 GTKEIPEGLIAKALLLRLYSDARHSEGVALAGGAARDLMHGAEPKDIDIALYGMDDRQAELLIGCILPKLVSRFLRDGGW 90 (200)
T ss_pred CccccChhHcCHHHHHHHHHHHHCCcEEEEECchHHHHHcCCCCCceEEEccCCCHHHHHHHHHHhCCccccccccccee
Confidence 345688899999999999999999999999999999999999999999999 57898888774421 1122233444
Q ss_pred E---------------------EEECCEEEEEecccccccccCCCceeeecCCCCCCchhhhhhhhhhccCccccc--cc
Q 005645 131 R---------------------VHIKGSVIEVSSFETVAKHGEGKETVLLSQIPYGCDEIDLVRWRNSIHRDFTIN--SL 187 (686)
Q Consensus 131 ~---------------------V~~~G~~IEVaTfRte~~~~~~~~~V~fs~~~~gt~eeDL~~~eDa~RRDFTIN--AL 187 (686)
+ +.++|.+||++.+ ...++++|| .||||||| ||
T Consensus 91 r~~~~~~gd~~~~~~~~~l~g~~vl~g~tvD~A~~------------------~g~sleeDL------~rRDFTINq~AI 146 (200)
T PHA01806 91 SQEYHDGGDGGIFKGVVSLKGCRGLEGMDVDFNYY------------------DTDSVGEVM------ESFDYTINQVGI 146 (200)
T ss_pred eeeccccccccccccceeeeeeEEeCCeEEEeeec------------------cCCCHHHHH------HHcCCccchhhh
Confidence 4 3344455554444 444668887 79999999 88
Q ss_pred cccCC
Q 005645 188 FFDPF 192 (686)
Q Consensus 188 Ayd~~ 192 (686)
||++.
T Consensus 147 A~~~~ 151 (200)
T PHA01806 147 AYNWP 151 (200)
T ss_pred cccCC
Confidence 88754
No 14
>PRK03381 PII uridylyl-transferase; Provisional
Probab=99.57 E-value=1.1e-14 Score=169.91 Aligned_cols=141 Identities=18% Similarity=0.070 Sum_probs=115.1
Q ss_pred hcCceeecccCcccccccHHhHHHHHHHHHHhCCCCCHHHHHHHHHhhhhhcCCCHHHHHHHHHHHHhCCCH-HHHHHHH
Q 005645 207 RCLKLRTLIPAYLSFTEDCARILRGLRIAARLGLSFCKDIDTAMHSLSSSIERLDKSRIMMELNYMLSYGAA-ESSICLL 285 (686)
Q Consensus 207 k~riIR~Vg~p~~rF~EDPlRILRAiRFAaRLGF~Id~eT~~aIr~~a~lL~~Is~eRI~~EL~KLL~~~~~-~~~L~lL 285 (686)
.++.|-+..+ ..|.+||+||||++|||+++||.|+++|+.+|+..+..+..++.||++.|+.++|.++++ ..+++.|
T Consensus 314 ~~~~l~~~~~--~~~~~DplRiLRa~rfaa~lgf~I~~~T~~~i~~~~~~l~~~~~eri~~ef~kiL~~~~~~~~~l~~m 391 (774)
T PRK03381 314 HAGEVVLARD--ARPARDPGLVLRVAAAAATTGLPIAAATLSRLAASAPPLPTPWPAEARDDLLVLLGAGPAAVAVIEAL 391 (774)
T ss_pred ECCEEEeCCc--cccccCHHHHHHHHHHHHhcCCCcCHHHHHHHHHHHHhcCccccHHHHHHHHHHHcCCCchHHHHHHH
Confidence 4466666554 478999999999999999999999999999999999999999999999999999988755 5799999
Q ss_pred HHcCCchhhhhhhhhhhh--hccCcCCCchhHHHHHHHHhHHhhhhCCCCCchhhHHHHHHHHHHhcC
Q 005645 286 RRYNLLKILLPFHAAYLD--QQAGKITAENPMMLMRLFFNLDKLVSCDRPADYTLWVGLLSFHQALVS 351 (686)
Q Consensus 286 ~e~GLL~~LfPela~~~~--qq~~~h~~t~d~~Ll~lL~~ld~ll~~~rp~~~~lWlalLaf~~aL~~ 351 (686)
+++|+|..+||+++...+ |...+|.|+++.|++.++.++..+...-.+.....|.++ ||+.-..
T Consensus 392 ~~~GvL~~~iPE~~~i~~~~Q~~~~H~ytVd~Htl~~l~~~~~~~~~~~~~~lL~lAaL--lHDiGKg 457 (774)
T PRK03381 392 DRTGLWGRLLPEWEAVRDLPPRDPVHRWTVDRHLVETAVRAAALTRRVARPDLLLLGAL--LHDIGKG 457 (774)
T ss_pred HHhCCHHHhchhHHHhhCCCCCCCCccChHHHHHHHHHHHHHHHHhccCCHHHHHHHHH--HHhhcCC
Confidence 999999999999998765 556789999999999999888766543322222234332 7776543
No 15
>PRK00227 glnD PII uridylyl-transferase; Provisional
Probab=99.56 E-value=1.9e-14 Score=165.91 Aligned_cols=139 Identities=14% Similarity=0.024 Sum_probs=115.2
Q ss_pred HhcCceeecccCcccccccHHhHHHHHHHHHHhCCCCCHHHHHHHHHhhhhhcCCCHHHHHHHHHHHHhCC-CHHHHHHH
Q 005645 206 LRCLKLRTLIPAYLSFTEDCARILRGLRIAARLGLSFCKDIDTAMHSLSSSIERLDKSRIMMELNYMLSYG-AAESSICL 284 (686)
Q Consensus 206 Lk~riIR~Vg~p~~rF~EDPlRILRAiRFAaRLGF~Id~eT~~aIr~~a~lL~~Is~eRI~~EL~KLL~~~-~~~~~L~l 284 (686)
+.+|.|+++++|. + |||+||||++|||+++||.|+++|+++|+.. ..+.....+|+..|+.++|..+ ++..+++.
T Consensus 275 ~~~~~I~~~~~~~--~-eDPlRiLRafrfAa~~gf~I~~~Tl~~i~~~-~~L~~~~~er~~~ef~kiL~s~~~~~~~L~~ 350 (693)
T PRK00227 275 DANGTIALSRTPD--L-DDPALPLRVAAAAARTGLPVSESVWKRLEEC-PELPEPWPASAAGDFFRLLSSPVNSRRVIKQ 350 (693)
T ss_pred EECCEEEeCCCCc--c-cCHHHHHHHHHHHHhcCCCcCHHHHHHHHhh-hhcchhhHHHHHHHHHHHHcCCCChHHHHHH
Confidence 5679999999864 4 8999999999999999999999999999987 6677778899999999999996 78899999
Q ss_pred HHHcCCchhhhhhhhhhhh--hccCcCCCchhHHHHHHHHhHHhhhhCCCCCchhhHHHHHHHHHHhc
Q 005645 285 LRRYNLLKILLPFHAAYLD--QQAGKITAENPMMLMRLFFNLDKLVSCDRPADYTLWVGLLSFHQALV 350 (686)
Q Consensus 285 L~e~GLL~~LfPela~~~~--qq~~~h~~t~d~~Ll~lL~~ld~ll~~~rp~~~~lWlalLaf~~aL~ 350 (686)
|+++|+|..+||++....+ |+..+|.|+++.|++.++.+...+.....+.....|.++ ||+.-.
T Consensus 351 M~~~GvL~~llPE~~~i~g~~Q~d~yH~ytVDeHTL~~l~~~~~~~~~~~~~~lL~LAAL--lHDIGK 416 (693)
T PRK00227 351 MDRHGLWERIVPEWDRIRGLMPREPSHIHTIDEHSLNTVANCALETVTVARPDLLLLGAL--YHDIGK 416 (693)
T ss_pred HHHcCCHHHHhHHHHHHhCCCCCCCCCCCcHHHHHHHHHHHHHHhhhccCccHHHHHHHH--HHhhcC
Confidence 9999999999999998775 566789999999999999987666544333333334332 777654
No 16
>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=99.55 E-value=2.1e-14 Score=168.87 Aligned_cols=122 Identities=16% Similarity=0.075 Sum_probs=110.6
Q ss_pred HhcCceeecccCcccccccHHhHHHHHHHHHHhCCCCCHHHHHHHHHhhhhhcCCCH--HHHHHHHHHHHhCC-CHHHHH
Q 005645 206 LRCLKLRTLIPAYLSFTEDCARILRGLRIAARLGLSFCKDIDTAMHSLSSSIERLDK--SRIMMELNYMLSYG-AAESSI 282 (686)
Q Consensus 206 Lk~riIR~Vg~p~~rF~EDPlRILRAiRFAaRLGF~Id~eT~~aIr~~a~lL~~Is~--eRI~~EL~KLL~~~-~~~~~L 282 (686)
+.+|.|++.++ .+|.+||+||||++||++++||.|+++|..+|++.+..+..++. +|++.||.+||..+ .+..++
T Consensus 319 ~~~~~l~~~~~--~~f~eDPlriLR~~rfaa~~~~~i~~~T~~~i~~~~~~l~~~~~~~er~~~ef~~iL~~~~~~~~~l 396 (850)
T TIGR01693 319 EDGGELVLART--AVFERDPALLLRLFAIAAQRGLPIHPAALRQLTASLPLLPTPLREDPEARELFLELLTSGNGTVRAL 396 (850)
T ss_pred EECCEEEecCc--cchhhCHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCchhhcCHHHHHHHHHHHcCCCchHHHH
Confidence 67899999875 59999999999999999999999999999999999999999988 99999999999976 568899
Q ss_pred HHHHHcCCchhhhhhhhhhhh--hccCcCCCchhHHHHHHHHhHHhhhh
Q 005645 283 CLLRRYNLLKILLPFHAAYLD--QQAGKITAENPMMLMRLFFNLDKLVS 329 (686)
Q Consensus 283 ~lL~e~GLL~~LfPela~~~~--qq~~~h~~t~d~~Ll~lL~~ld~ll~ 329 (686)
+.|.++|+|..+||++....+ +...+|.++++.|++.++.++..+..
T Consensus 397 ~~m~~~gvL~~~iPe~~~i~~~~Q~~~~H~~tVd~Htl~~l~~~~~~~~ 445 (850)
T TIGR01693 397 RAMNRAGVLGRFLPEWGRIVGQMQFDLFHVYTVDEHTLRTVVHLAPFAR 445 (850)
T ss_pred HHHHHhCCHHHhCchHhhheeccccCceeecchhHHHHHHHHHHHHHhc
Confidence 999999999999999987665 55578999999999999999887643
No 17
>PRK00275 glnD PII uridylyl-transferase; Provisional
Probab=99.54 E-value=2.2e-14 Score=169.65 Aligned_cols=133 Identities=16% Similarity=0.069 Sum_probs=119.2
Q ss_pred EeeCcCcHHHHhcCceeecccCcccccccHHhHHHHHHHHHHhC--CCCCHHHHHHHHHhhhhhcCC--CHHHHHHHHHH
Q 005645 196 IYDYANGISDLRCLKLRTLIPAYLSFTEDCARILRGLRIAARLG--LSFCKDIDTAMHSLSSSIERL--DKSRIMMELNY 271 (686)
Q Consensus 196 LiDyfGGleDLk~riIR~Vg~p~~rF~EDPlRILRAiRFAaRLG--F~Id~eT~~aIr~~a~lL~~I--s~eRI~~EL~K 271 (686)
.+||++|..||++|.|++++++ .|.+||+||||+|||+++.+ ..|++.|..+|+..+..+..+ +.+|++.||.+
T Consensus 339 ~~~~~~~~~~l~~~~i~~~~~~--~f~~dP~riLr~f~~~a~~~~i~~i~~~t~~~i~~~~~~i~~~~~~~~~~~~~f~~ 416 (895)
T PRK00275 339 TIQPLNSRFQLRDGYIEATHPN--VFKRTPFALLEIFVLMAQHPEIKGVRADTIRLLREHRHLIDDAFRNDIRNTSLFIE 416 (895)
T ss_pred cccccCCCeEEECCEEEecChh--hhhcCHHHHHHHHHHHHhCCCcCCCCHHHHHHHHHHHHhcCchhccCHHHHHHHHH
Confidence 6799999999999999999975 69999999999999999954 467799999999999999887 67789999999
Q ss_pred HHhCCC-HHHHHHHHHHcCCchhhhhhhhhhhh--hccCcCCCchhHHHHHHHHhHHhhhhC
Q 005645 272 MLSYGA-AESSICLLRRYNLLKILLPFHAAYLD--QQAGKITAENPMMLMRLFFNLDKLVSC 330 (686)
Q Consensus 272 LL~~~~-~~~~L~lL~e~GLL~~LfPela~~~~--qq~~~h~~t~d~~Ll~lL~~ld~ll~~ 330 (686)
||..++ ...+|+.|+++|+|..++|+++...+ |...+|.|+++.|++.++.+++.+...
T Consensus 417 iL~~~~~~~~~l~~M~~~GvL~~~iPe~~~i~~~~Q~d~yH~ytVdeHtl~~v~~l~~l~~~ 478 (895)
T PRK00275 417 LFKCPIGIHRNLRRMNRYGILGRYLPEFGHIVGQMQHDLFHIYTVDAHTLNLIKNLRKLRYP 478 (895)
T ss_pred HHcCCCchHHHHHHHHHcCCHHHhCchHhhEeeeccCcccccCcHHHHHHHHHHHHHHhhcc
Confidence 999987 46789999999999999999998775 556799999999999999999887544
No 18
>PRK05092 PII uridylyl-transferase; Provisional
Probab=99.47 E-value=1.5e-13 Score=163.12 Aligned_cols=120 Identities=15% Similarity=0.149 Sum_probs=105.6
Q ss_pred HhcCceeecccCcccccccHHhHHHHHHHHHHhCCCCCHHHHHHHHHhhhhhcC-----CCHHHHHHHHHHHHhCCCHHH
Q 005645 206 LRCLKLRTLIPAYLSFTEDCARILRGLRIAARLGLSFCKDIDTAMHSLSSSIER-----LDKSRIMMELNYMLSYGAAES 280 (686)
Q Consensus 206 Lk~riIR~Vg~p~~rF~EDPlRILRAiRFAaRLGF~Id~eT~~aIr~~a~lL~~-----Is~eRI~~EL~KLL~~~~~~~ 280 (686)
+.+|.|+++++ .+|.+||+||||++|||+++||.|+++|+.+|++.+..+.. .+.+|+|.|+ ++..+.+..
T Consensus 384 ~~~~~i~~~~~--~~f~edPlriLR~fr~aa~~~~~i~~~T~~~i~~~~~~i~~~~~~~~~~~r~f~ei--l~~~~~~~~ 459 (931)
T PRK05092 384 VDNGRINLADP--DVFERDPVNLIRLFHLADRHGLDIHPDAMRLVTRSLRLIDAALREDPEANRLFLDI--LTSRRNPER 459 (931)
T ss_pred EECCEEEecCh--hhhhhCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHhcChhhccCHHHHHHHHHH--HcCCCchHH
Confidence 57799999986 47999999999999999999999999999999999988776 4679999886 455567789
Q ss_pred HHHHHHHcCCchhhhhhhhhhhh--hccCcCCCchhHHHHHHHHhHHhhhh
Q 005645 281 SICLLRRYNLLKILLPFHAAYLD--QQAGKITAENPMMLMRLFFNLDKLVS 329 (686)
Q Consensus 281 ~L~lL~e~GLL~~LfPela~~~~--qq~~~h~~t~d~~Ll~lL~~ld~ll~ 329 (686)
++++|+++|+|..++|++....+ ++..+|.|+++.|++.++.++..+..
T Consensus 460 ~l~~m~~~GvL~~~iPef~~i~~~~Q~d~~H~ytVd~Htl~~l~~l~~~~~ 510 (931)
T PRK05092 460 VLRRMNEAGVLGRFIPDFGRIVAMMQFNMYHHYTVDEHTIRAIGVLAEIER 510 (931)
T ss_pred HHHHHHHhCChHHhcccHHhcccccccccceeccHhHHHHHHHHHHHHHhc
Confidence 99999999999999999998665 66679999999999999999887754
No 19
>PRK03059 PII uridylyl-transferase; Provisional
Probab=99.46 E-value=2.1e-13 Score=160.71 Aligned_cols=123 Identities=11% Similarity=0.049 Sum_probs=110.9
Q ss_pred HHhcCceeecccCcccccccHHhHHHHHHHHHHh-C-CCCCHHHHHHHHHhhhhhcCC--CHHHHHHHHHHHHhCCCH-H
Q 005645 205 DLRCLKLRTLIPAYLSFTEDCARILRGLRIAARL-G-LSFCKDIDTAMHSLSSSIERL--DKSRIMMELNYMLSYGAA-E 279 (686)
Q Consensus 205 DLk~riIR~Vg~p~~rF~EDPlRILRAiRFAaRL-G-F~Id~eT~~aIr~~a~lL~~I--s~eRI~~EL~KLL~~~~~-~ 279 (686)
.+.+|.||+++++ .|.+||+||||+|||++++ | +.|++.|..+|+..+..+..+ +.+|++.||.+||..+++ .
T Consensus 328 ~~~~~~i~~~~~~--~f~~dP~riLr~fr~aa~~~~~~~i~~~T~~~i~~~~~~i~~~~~~~er~~~ef~~iL~~~~~~~ 405 (856)
T PRK03059 328 VEKQGMLEIASDD--LFERHPHAILEAFLLYQQTPGLKGLSARTLRALYNARDVMNAAFRRDPVNRALFMQILQQPRGIT 405 (856)
T ss_pred EEECCEEEecCch--hhhcCHHHHHHHHHHHHhcCCccCcCHHHHHHHHHHHHhcCcccccCHHHHHHHHHHHcCCCchH
Confidence 4789999999874 6999999999999999999 5 699999999999999999888 679999999999999875 6
Q ss_pred HHHHHHHHcCCchhhhhhhhhhhh--hccCcCCCchhHHHHHHHHhHHhhhh
Q 005645 280 SSICLLRRYNLLKILLPFHAAYLD--QQAGKITAENPMMLMRLFFNLDKLVS 329 (686)
Q Consensus 280 ~~L~lL~e~GLL~~LfPela~~~~--qq~~~h~~t~d~~Ll~lL~~ld~ll~ 329 (686)
.+++.|+++|+|..+||+++...+ |...+|.|++++|++.++.++..+..
T Consensus 406 ~~l~~m~~~GlL~~~lPe~~~i~~~~Q~~~~H~ytVd~Htl~~v~~l~~~~~ 457 (856)
T PRK03059 406 HALRLMNQTSVLGRYLPNFRRIVGQMQHDLFHVYTVDQHILMVLRNLRRFAM 457 (856)
T ss_pred HHHHHHHHhCCHHHhCchHhheeeeecccccccCcHhHHHHHHHHHHHHhhc
Confidence 899999999999999999998765 55668999999999999999877644
No 20
>PRK01759 glnD PII uridylyl-transferase; Provisional
Probab=99.33 E-value=5.9e-12 Score=148.67 Aligned_cols=122 Identities=12% Similarity=0.096 Sum_probs=104.3
Q ss_pred HHhcCceeecccCcccccccHHhHHHHHHHHHHh-CCCCCHHHHHHHHHh----hhhhcCCCHHHHHHHHHHHHhCCCH-
Q 005645 205 DLRCLKLRTLIPAYLSFTEDCARILRGLRIAARL-GLSFCKDIDTAMHSL----SSSIERLDKSRIMMELNYMLSYGAA- 278 (686)
Q Consensus 205 DLk~riIR~Vg~p~~rF~EDPlRILRAiRFAaRL-GF~Id~eT~~aIr~~----a~lL~~Is~eRI~~EL~KLL~~~~~- 278 (686)
.+.++.|.+..+ ..|.+||+||||+|||++++ ||.|+++|..+|+.. ...+..+|.+| .||.+||.++.+
T Consensus 325 ~~~~~~i~~~~~--~~f~~dp~riLr~fr~~a~~~~~~i~~~t~~~i~~~~~~~~~~l~~~~~eR--~ef~kiL~~~~~~ 400 (854)
T PRK01759 325 YLINNAICLRNP--DCFEQQPESILDLFFYLTQYPQAEIHSTTLRQLRLALEQLQQPLCELPAAR--ERFLRLFNQPNAI 400 (854)
T ss_pred EEECCEEEecCh--hhhhhCHHHHHHHHHHHHHCCCCCcCHHHHHHHHHHHHhccchhccCHHHH--HHHHHHHcCCCch
Confidence 356677877664 48999999999999999999 699999999988765 44566788888 899999999775
Q ss_pred HHHHHHHHHcCCchhhhhhhhhhhh--hccCcCCCchhHHHHHHHHhHHhhhhC
Q 005645 279 ESSICLLRRYNLLKILLPFHAAYLD--QQAGKITAENPMMLMRLFFNLDKLVSC 330 (686)
Q Consensus 279 ~~~L~lL~e~GLL~~LfPela~~~~--qq~~~h~~t~d~~Ll~lL~~ld~ll~~ 330 (686)
..+++.|+++|+|..++|+++...+ ++..+|.|+++.|++.++.+++.+...
T Consensus 401 ~~~l~~M~~~GvL~~~iPe~~~i~~~~Q~d~yH~ytVd~Htl~~l~~l~~~~~~ 454 (854)
T PRK01759 401 KRALVPMHQYGVLTAYLPQWKGIVGLMQFDLFHIYTVDEHTLRVMLKLESFLDE 454 (854)
T ss_pred HHHHHHHHHhCCHHHhChHHHheeeccCCcccccCcHHHHHHHHHHHHHHHhcc
Confidence 6889999999999999999998765 566789999999999999999877543
No 21
>PF12627 PolyA_pol_RNAbd: Probable RNA and SrmB- binding site of polymerase A; PDB: 1OU5_B 3H38_A 3H3A_B 3H39_B 3H37_A 3AQN_A 3AQK_A 3AQM_B 3AQL_B 1MIY_A ....
Probab=99.25 E-value=1.3e-11 Score=101.07 Aligned_cols=62 Identities=24% Similarity=0.360 Sum_probs=57.3
Q ss_pred CCCCCHHHHHHHHHhhhhhcCCCHHHHHHHHHHHHhCCCHHHHHHHHHHcCCchhhhhhhhh
Q 005645 239 GLSFCKDIDTAMHSLSSSIERLDKSRIMMELNYMLSYGAAESSICLLRRYNLLKILLPFHAA 300 (686)
Q Consensus 239 GF~Id~eT~~aIr~~a~lL~~Is~eRI~~EL~KLL~~~~~~~~L~lL~e~GLL~~LfPela~ 300 (686)
||+|+++|..+|++.+..|..+|+|||+.|+.|||.++++..+++.|+++|+++.+||+++.
T Consensus 1 gF~ie~~t~~ai~~~~~~L~~is~ERi~~El~kil~~~~~~~~~~~l~~~gll~~ifP~l~~ 62 (64)
T PF12627_consen 1 GFKIEPETEEAIKENAELLSKISKERIREELEKILSSPNPSRAFKLLDELGLLEYIFPELDA 62 (64)
T ss_dssp T-EE-HHHHHHHHHHGGGGGGS-HHHHHHHHHHHHTSTTHHHHHHHHHHTTCHHHHSTTHHT
T ss_pred CCccCHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHcCCCHHHHHHHHHHcCCHHHHCccccc
Confidence 89999999999999999999999999999999999999999999999999999999998864
No 22
>PRK05007 PII uridylyl-transferase; Provisional
Probab=99.22 E-value=5.1e-11 Score=141.26 Aligned_cols=123 Identities=14% Similarity=0.097 Sum_probs=105.2
Q ss_pred HhcCceeecccCcccccccHHhHHHHHHHHHHhC--CCCCHHHHHHHHHhhhhhcCC--CHHHHHHHHHHHHhCCCHHH-
Q 005645 206 LRCLKLRTLIPAYLSFTEDCARILRGLRIAARLG--LSFCKDIDTAMHSLSSSIERL--DKSRIMMELNYMLSYGAAES- 280 (686)
Q Consensus 206 Lk~riIR~Vg~p~~rF~EDPlRILRAiRFAaRLG--F~Id~eT~~aIr~~a~lL~~I--s~eRI~~EL~KLL~~~~~~~- 280 (686)
+.+++|++++++ .|.+||+||||+|||+++.+ ..|+++|..+|+..+..+..- ..++++.||.+||..+++..
T Consensus 350 ~~~~~i~~~~~~--~f~~dp~~iLr~f~~aa~~~~i~~i~~~t~~~i~~~~~~i~~~~~~~~~~~~~f~~iL~~~~~~~~ 427 (884)
T PRK05007 350 LRGTLIDLRDET--LFQRQPEAILRMFYLMARNSNITGIYSTTLRQLRHARRHLNQPLCEIPEARKLFMEILRHPGAVSR 427 (884)
T ss_pred EECCEEeecChh--hhhhCHHHHHHHHHHHHhCCCcCCCCHHHHHHHHHHHHhcCcccccCHHHHHHHHHHHcCCCchHH
Confidence 577889999985 59999999999999999955 356799999999998877632 23569999999999988764
Q ss_pred HHHHHHHcCCchhhhhhhhhhhh--hccCcCCCchhHHHHHHHHhHHhhhhC
Q 005645 281 SICLLRRYNLLKILLPFHAAYLD--QQAGKITAENPMMLMRLFFNLDKLVSC 330 (686)
Q Consensus 281 ~L~lL~e~GLL~~LfPela~~~~--qq~~~h~~t~d~~Ll~lL~~ld~ll~~ 330 (686)
+++.|+++|+|..++|++..+.+ |...+|.|+++.|++.++.++..+...
T Consensus 428 ~l~~m~~~GlL~~~iPe~~~i~~~~Q~d~~H~ytVd~Htl~~l~~l~~~~~~ 479 (884)
T PRK05007 428 ALLPMHRHSVLSAYMPQWSHIVGQMQFDLFHAYTVDEHTIRVLLKLESFADE 479 (884)
T ss_pred HHHHHHHhCCHHHhCchHhheeeccccCccccCcHhHHHHHHHHHHHHHhcc
Confidence 99999999999999999998765 556799999999999999999876543
No 23
>PRK04374 PII uridylyl-transferase; Provisional
Probab=98.93 E-value=5.2e-09 Score=124.21 Aligned_cols=119 Identities=10% Similarity=-0.035 Sum_probs=103.5
Q ss_pred CceeecccCcccccccHHhHHHHHHHHHHhC--CCCCHHHHHHHHHhhhhhcCC--CHHHHHHHHHHHHhCCCHHHHHHH
Q 005645 209 LKLRTLIPAYLSFTEDCARILRGLRIAARLG--LSFCKDIDTAMHSLSSSIERL--DKSRIMMELNYMLSYGAAESSICL 284 (686)
Q Consensus 209 riIR~Vg~p~~rF~EDPlRILRAiRFAaRLG--F~Id~eT~~aIr~~a~lL~~I--s~eRI~~EL~KLL~~~~~~~~L~l 284 (686)
|.|-+.. | ..|..||.+|||+|.++++.+ ..|++.|+..|++....+..- ...|++.||.+||..+++..++++
T Consensus 342 ~~i~~~~-~-~~f~~~P~~il~lf~~~~~~~~~~~i~~~t~r~l~~~~~~l~~~~~~~~ri~~ef~kiL~~~~~~~~l~~ 419 (869)
T PRK04374 342 GYLAADA-D-SWPDGDVLQVFALFAQWAAHREVRGLHSLTARALAEVLRDLPAYDVADATARERFMALLRGPRAVETLNR 419 (869)
T ss_pred CEEeecC-c-ccchhCHHHHHHHHHHHHhCCCcCCCCHHHHHHHHHHHHhcCccccCCHHHHHHHHHHHcCCChhHHHHH
Confidence 3444433 2 579999999999999999999 999999999999988777543 577999999999999999899999
Q ss_pred HHHcCCchhhhhhhhhhhh--hccCcCCCchhHHHHHHHHhHHhhhh
Q 005645 285 LRRYNLLKILLPFHAAYLD--QQAGKITAENPMMLMRLFFNLDKLVS 329 (686)
Q Consensus 285 L~e~GLL~~LfPela~~~~--qq~~~h~~t~d~~Ll~lL~~ld~ll~ 329 (686)
|+++|+|..++|+++...+ |...+|.|+++.|++.++.++..+..
T Consensus 420 m~~~GvL~~~lPE~~~i~~~~Q~d~yH~ytVd~Htl~~l~~l~~~~~ 466 (869)
T PRK04374 420 MARLGVLGQWIPAFASVSGRMQFDLFHVYTVDQHTLMVLRNIALFAA 466 (869)
T ss_pred HHHhCCHHHHhhhHHHHhccccccCccCCcHHHHHHHHHHHHHHHhc
Confidence 9999999999999998775 66679999999999999999886543
No 24
>COG2844 GlnD UTP:GlnB (protein PII) uridylyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=98.51 E-value=1.8e-06 Score=100.72 Aligned_cols=122 Identities=18% Similarity=0.127 Sum_probs=98.3
Q ss_pred hcCceeecccCcccccccHHhHHHHHHHHHHhCCCC-CHHHHHHHHHhhhhhcCCCH--HHHHHHHHHHHhCC-CHHHHH
Q 005645 207 RCLKLRTLIPAYLSFTEDCARILRGLRIAARLGLSF-CKDIDTAMHSLSSSIERLDK--SRIMMELNYMLSYG-AAESSI 282 (686)
Q Consensus 207 k~riIR~Vg~p~~rF~EDPlRILRAiRFAaRLGF~I-d~eT~~aIr~~a~lL~~Is~--eRI~~EL~KLL~~~-~~~~~L 282 (686)
.+|.|-+-++ .-|..||..|||.|-++++.|... .|+|+..+....+.|..-=. +.-..-+..||+.+ +...+|
T Consensus 337 ~~g~I~l~~~--~~f~~dP~~ilrlf~~~~~~~~~~~~~~Tlr~L~~a~~~l~~~l~~~peA~~~Fl~il~~~~~~~r~l 414 (867)
T COG2844 337 RNGRIELRDP--DLFERDPEAILRLFAIMAQTGLITGHPDTLRQLRRALRLLNQPLREDPEARRLFLSILRSPNAIRRTL 414 (867)
T ss_pred eCCEEEecCc--hhhhhChHHHHHHHHHHHhcCCcccchHHHHHHHHhccccCcccccCHHHHHHHHHHHhCCCcHHHHH
Confidence 3455655554 369999999999999999999998 79999999988776654322 33445566677776 567899
Q ss_pred HHHHHcCCchhhhhhhhhhhh--hccCcCCCchhHHHHHHHHhHHhhhhC
Q 005645 283 CLLRRYNLLKILLPFHAAYLD--QQAGKITAENPMMLMRLFFNLDKLVSC 330 (686)
Q Consensus 283 ~lL~e~GLL~~LfPela~~~~--qq~~~h~~t~d~~Ll~lL~~ld~ll~~ 330 (686)
+.|+++|+|..++|++..+.. |..-+|.||+|+|++.++.++..+...
T Consensus 415 ~~Mn~~GVLgrylPew~~Ivg~MQfdlfH~YTVDeH~lr~v~~l~~~a~~ 464 (867)
T COG2844 415 RPMNRYGVLGRYLPEWGKIVGLMQFDLFHIYTVDEHTLRVVLKLARFARG 464 (867)
T ss_pred HHHHHhhhHHHhcccHHhhhcccccCcceecchhHHHHHHHHHHHHhhcc
Confidence 999999999999999998775 677799999999999999888766443
No 25
>cd07749 NT_Pol-beta-like_1 Nucleotidyltransferase (NT) domain of an uncharacterized subgroup of the Pol beta-like NT superfamily. The Pol beta-like NT superfamily includes DNA polymerase beta and other family X DNA Polymerases, as well as 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, Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins. Proteins belonging to this subgroup are uncharacterized. 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 essential for catalysis. These divalent metal ions are involved in a two-metal ion mechanism of nucleotide addition. These carboxylate residues are conserved in this subgroup.
Probab=90.74 E-value=1.3 Score=43.83 Aligned_cols=70 Identities=24% Similarity=0.319 Sum_probs=49.4
Q ss_pred HHHHHHHHHCCCcEEEEchhHHHHHhCCC--CCCeEEEeC-CCHHHHHHHhccCcc----------cccccCeEEEEECC
Q 005645 70 WVVLKILKSQGFQAYLVGGCVRDLLLRRV--PKDFDVITT-ANLKQIRRQFHRSEI----------IGRRFPICRVHIKG 136 (686)
Q Consensus 70 ~~VL~~L~~~G~eAYLVGG~VRDLLLGr~--PkD~DIvT~-A~peei~k~F~~~~i----------vGrrF~i~~V~~~G 136 (686)
..+.+.|+..+ =.+.|||.+.=.+-|.+ |+||||-|+ .+.+++.++|..... +=+.|+ ...++|
T Consensus 7 ~~i~~~ln~~~-i~W~lgGS~~L~l~Gl~~~p~DIDI~~D~~d~e~i~~il~~~~~~~~~~~~~~~~ts~F~--e~~I~g 83 (156)
T cd07749 7 RKFYERLKNIN-VNWALTGSLSFALQGVPVEPHDIDIQTDNEGAYEIERIFHEFVNTEVRFSESEGIRSHFG--ELQIDG 83 (156)
T ss_pred HHHHHHhccCC-ceEEehhhHHHHHcCCCCCCCcceEEEchhhHHHHHHHHHHhccCCCccCCCCceeeeee--EEEECC
Confidence 35666777777 56999999999998876 999999887 567888888764321 112232 334578
Q ss_pred EEEEEe
Q 005645 137 SVIEVS 142 (686)
Q Consensus 137 ~~IEVa 142 (686)
..|||-
T Consensus 84 v~Vdvm 89 (156)
T cd07749 84 IKVEIM 89 (156)
T ss_pred EEEEEe
Confidence 888876
No 26
>PF09970 DUF2204: Nucleotidyl transferase of unknown function (DUF2204); InterPro: IPR018700 This family of hypothetical prokaryotic proteins has no known function.
Probab=89.64 E-value=0.93 Score=45.35 Aligned_cols=41 Identities=27% Similarity=0.399 Sum_probs=35.3
Q ss_pred HHHHHHHHHHCCCcEEEEchhHHHHHhCCC--CCCeEEEeCCC
Q 005645 69 SWVVLKILKSQGFQAYLVGGCVRDLLLRRV--PKDFDVITTAN 109 (686)
Q Consensus 69 a~~VL~~L~~~G~eAYLVGG~VRDLLLGr~--PkD~DIvT~A~ 109 (686)
...+++.|++.|.+.++|||++=.+.+|.+ ++|+|+.+..+
T Consensus 5 l~~~~~~L~~~gv~~~ivGG~av~l~~g~~r~T~DIDlfi~~~ 47 (181)
T PF09970_consen 5 LKEILEELNKRGVEYVIVGGAAVNLAYGRRRTTKDIDLFIENP 47 (181)
T ss_pred HHHHHHHHHHcCCeEEEECHHHHHHHhCCCCCCCCeEEEeCCC
Confidence 456899999999999999999999888865 89999987544
No 27
>PF10706 Aminoglyc_resit: Aminoglycoside-2''-adenylyltransferase; InterPro: IPR019646 Aminoglycoside-2''-adenylyltransferase is conserved in Bacteria. It confers resistance to kanamycin, gentamicin, and tobramycin []. The protein is also produced by plasmids in various bacterial species and confers resistance to essentially all clinically available aminoglycosides except streptomycin, and it eliminates the synergism between aminoglycosides and cell-wall active agents []. ; PDB: 4E8I_A 4E8J_B.
Probab=75.36 E-value=2.6 Score=42.39 Aligned_cols=51 Identities=22% Similarity=0.370 Sum_probs=32.8
Q ss_pred hHHHHHHHHHHCCCcEEEEchhHHHHHhCCC---CCCeEEEeCCC-HHHHHHHhc
Q 005645 68 PSWVVLKILKSQGFQAYLVGGCVRDLLLRRV---PKDFDVITTAN-LKQIRRQFH 118 (686)
Q Consensus 68 ~a~~VL~~L~~~G~eAYLVGG~VRDLLLGr~---PkD~DIvT~A~-peei~k~F~ 118 (686)
.+..|+..+.+.|.+.||-|||-=|+++|+. ..|+||.+.++ -.++.....
T Consensus 8 ~I~~Il~~~~~~~i~~wi~GGWaiD~~lG~qTReH~DiDi~~~~~~~~~l~~~L~ 62 (174)
T PF10706_consen 8 LIHEILDAADELGIPWWIAGGWAIDALLGRQTREHRDIDIFVPREDQAELRALLK 62 (174)
T ss_dssp --------HHHTT--EEEEHHHHHHHHHTS--S--SEEEEEEEGGGHHHHHHHHH
T ss_pred cchhhhhhHhhCCCCEEEECceeeeEeccccccCcCCeEEEEEcchhHHHHHHHH
Confidence 3557888999999999999999999999975 68999988765 456666544
No 28
>PF06042 DUF925: Bacterial protein of unknown function (DUF925); InterPro: IPR009267 This entry consists of several hypothetical bacterial proteins of unknown function.; PDB: 2LA3_A.
Probab=75.08 E-value=3.3 Score=41.34 Aligned_cols=35 Identities=43% Similarity=0.665 Sum_probs=23.1
Q ss_pred HHHHHHCCC-cEEEEchhHHHH----HhCCCC----CCeEEEeC
Q 005645 73 LKILKSQGF-QAYLVGGCVRDL----LLRRVP----KDFDVITT 107 (686)
Q Consensus 73 L~~L~~~G~-eAYLVGG~VRDL----LLGr~P----kD~DIvT~ 107 (686)
|+.+.+.|. +.||++||||.. |-|+++ +||||+--
T Consensus 1 L~~~~~L~Lpd~~l~AG~vrn~VWn~L~g~~~~~~i~DiDviYf 44 (163)
T PF06042_consen 1 LEIVRSLGLPDWWLAAGFVRNTVWNHLHGRPPSTPINDIDVIYF 44 (163)
T ss_dssp HHHHHHT--SS-EEETHHHHHHHHGGGTTS-TT---SEEEEEE-
T ss_pred CchHhhCCCCceEeehhhHHHHHHHHhcCCCCCCCCCceeEEEe
Confidence 345566664 689999999975 457765 99999853
No 29
>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=74.13 E-value=3.9 Score=32.58 Aligned_cols=35 Identities=29% Similarity=0.524 Sum_probs=26.4
Q ss_pred HHHHHHHHC--CCcEEEEchhHHHHHhCCCCCCeEEEeC
Q 005645 71 VVLKILKSQ--GFQAYLVGGCVRDLLLRRVPKDFDVITT 107 (686)
Q Consensus 71 ~VL~~L~~~--G~eAYLVGG~VRDLLLGr~PkD~DIvT~ 107 (686)
.+.+.+++. +..+|+.|..+|... .+..|+||++.
T Consensus 6 ~i~~~l~~~~~~~~v~lfGS~arg~~--~~~SDIDi~v~ 42 (49)
T cd05397 6 IIKERLKKLVPGYEIVVYGSLVRGLL--KKSSDIDLACV 42 (49)
T ss_pred HHHHHHHhhcCCcEEEEECCcCCCCC--CCCCCEEEEEE
Confidence 344555555 789999999999764 56789999875
No 30
>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=66.12 E-value=27 Score=31.33 Aligned_cols=63 Identities=27% Similarity=0.381 Sum_probs=41.1
Q ss_pred CCCcEEEEchhHHHHHhCCCCCCeEEEeCCCH-----HH----HHHHhccCc-------ccccccCeEEEEEC--CEEEE
Q 005645 79 QGFQAYLVGGCVRDLLLRRVPKDFDVITTANL-----KQ----IRRQFHRSE-------IIGRRFPICRVHIK--GSVIE 140 (686)
Q Consensus 79 ~G~eAYLVGG~VRDLLLGr~PkD~DIvT~A~p-----ee----i~k~F~~~~-------ivGrrF~i~~V~~~--G~~IE 140 (686)
-+.++|+.|.++..+.+ +..|+|+++..+. .+ +.+.+++.. +.+.+.|++++... |..+|
T Consensus 18 ~~~~v~~fGS~~~g~~~--~~SDiDl~i~~~~~~~~~~~~l~~l~~~l~~~~~~~~~~~i~~ArVPiik~~~~~~~i~~D 95 (114)
T cd05402 18 PGAKLYPFGSYVTGLGL--PGSDIDLCLLGPNHRVDREDFLRKLAKLLKKSGEVVEVEPIINARVPIIKFVDKPTGIEVD 95 (114)
T ss_pred CCCEEEEecccccCCCC--CCCCeeEEEEeCCCCccHHHHHHHHHHHHHhCCCceeeEEeccCCCCEEEEEEcCCCeEEE
Confidence 36789999999998644 5689998765432 22 333343322 34667788887776 67777
Q ss_pred Eec
Q 005645 141 VSS 143 (686)
Q Consensus 141 VaT 143 (686)
|+-
T Consensus 96 is~ 98 (114)
T cd05402 96 ISF 98 (114)
T ss_pred EEc
Confidence 653
No 31
>PF08843 DUF1814: Nucleotidyl transferase of unknown function (DUF1814); InterPro: IPR014942 This large group of proteins are largely uncharacterised. Some are annotated as abortive infective proteins but support for this annotation could not be found.
Probab=57.71 E-value=12 Score=36.66 Aligned_cols=38 Identities=29% Similarity=0.397 Sum_probs=30.0
Q ss_pred HHHHH--HHCCCcEEEEchhHHHHHhC---CCCCCeEEEeCCC
Q 005645 72 VLKIL--KSQGFQAYLVGGCVRDLLLR---RVPKDFDVITTAN 109 (686)
Q Consensus 72 VL~~L--~~~G~eAYLVGG~VRDLLLG---r~PkD~DIvT~A~ 109 (686)
+|..| ...+...++.||..-.+..+ |...|+|+++...
T Consensus 2 ~L~~l~~~~~~~~~~l~GGtal~l~~~~~~R~S~DiD~~~~~~ 44 (233)
T PF08843_consen 2 LLRRLASSSLGDPFVLKGGTALSLRYGGSHRFSEDIDFVVDRD 44 (233)
T ss_pred hHHHhhccccCCCEEEECHHHHHHhcCCCcEecCcccEEEecc
Confidence 44555 56788999999999999843 6789999988654
No 32
>COG3575 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=57.44 E-value=11 Score=38.47 Aligned_cols=42 Identities=29% Similarity=0.411 Sum_probs=31.5
Q ss_pred ChhHHHHHHHHHHCCCc-EEEEchhHHHH----HhCCC----CCCeEEEeC
Q 005645 66 PQPSWVVLKILKSQGFQ-AYLVGGCVRDL----LLRRV----PKDFDVITT 107 (686)
Q Consensus 66 p~~a~~VL~~L~~~G~e-AYLVGG~VRDL----LLGr~----PkD~DIvT~ 107 (686)
++....+|.++...|.. .||++|+||.. |-|.. .+||||+--
T Consensus 14 ~p~~~~~L~~v~~L~LP~~~laaGsV~n~VWn~l~gn~~~~~ikDiDv~yF 64 (184)
T COG3575 14 SPLLMAILDTVRQLGLPDWWLAAGSVRNTVWNHLFGNNPMTGIKDIDVIYF 64 (184)
T ss_pred ChHHHHHHHHHHHcCCchhhhhhhHHHHHHHHHhcCCCCCCCcccceEEEe
Confidence 34556788888888874 78999999975 45655 489999853
No 33
>PF03458 UPF0126: UPF0126 domain; InterPro: IPR005115 This domain is duplicated in bacterial membrane proteins of unknown function and each domain contains three transmembrane helices. The conserved glycines are suggestive of an ion channel.
Probab=55.94 E-value=6.3 Score=34.62 Aligned_cols=16 Identities=50% Similarity=0.858 Sum_probs=13.4
Q ss_pred EEchhHHHHHhCCCCC
Q 005645 85 LVGGCVRDLLLRRVPK 100 (686)
Q Consensus 85 LVGG~VRDLLLGr~Pk 100 (686)
+-||-+||.|+|+.|.
T Consensus 39 ~GGG~lRDvll~~~P~ 54 (80)
T PF03458_consen 39 VGGGILRDVLLGRTPV 54 (80)
T ss_pred hhcHHHHHHHcCCCCh
Confidence 3499999999999763
No 34
>COG2860 Predicted membrane protein [Function unknown]
Probab=48.02 E-value=9.3 Score=39.68 Aligned_cols=15 Identities=53% Similarity=0.950 Sum_probs=12.9
Q ss_pred EEchhHHHHHhCCCC
Q 005645 85 LVGGCVRDLLLRRVP 99 (686)
Q Consensus 85 LVGG~VRDLLLGr~P 99 (686)
+=||.+||+|||+.|
T Consensus 44 iGGGtiRDlLLG~~P 58 (209)
T COG2860 44 IGGGTIRDLLLGHYP 58 (209)
T ss_pred hcchHHHHHHccCCC
Confidence 349999999999776
No 35
>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=46.68 E-value=22 Score=30.28 Aligned_cols=34 Identities=26% Similarity=0.324 Sum_probs=23.3
Q ss_pred HHHHHHHHCCCcEEEEchhHHHHHhCCCCCCeEEEeC
Q 005645 71 VVLKILKSQGFQAYLVGGCVRDLLLRRVPKDFDVITT 107 (686)
Q Consensus 71 ~VL~~L~~~G~eAYLVGG~VRDLLLGr~PkD~DIvT~ 107 (686)
..++.... ...+|+.|..+|.. ..+..|+||++-
T Consensus 6 ~~l~~~~~-~~~v~lfGS~a~g~--~~~~SDIDl~i~ 39 (93)
T PF01909_consen 6 EILKELFG-VAEVYLFGSYARGD--ATPDSDIDLLII 39 (93)
T ss_dssp HHHHHHHT-TEEEEEEHHHHHTS--SCTTSCEEEEEE
T ss_pred HHHHHHCC-CCEEEEECCcccCc--CCCCCCEEEEEE
Confidence 33443333 77899999999964 334599998653
No 36
>PF14907 NTP_transf_5: Uncharacterised nucleotidyltransferase
Probab=42.65 E-value=2e+02 Score=29.03 Aligned_cols=56 Identities=18% Similarity=0.262 Sum_probs=40.0
Q ss_pred CCChhHHHHHHHHHHCCCcEEEEchhHHHHHhC----CCCCCeEEEeC-CCHHHHHHHhcc
Q 005645 64 MIPQPSWVVLKILKSQGFQAYLVGGCVRDLLLR----RVPKDFDVITT-ANLKQIRRQFHR 119 (686)
Q Consensus 64 ~ip~~a~~VL~~L~~~G~eAYLVGG~VRDLLLG----r~PkD~DIvT~-A~peei~k~F~~ 119 (686)
.+......|++.|+++|.++.+.+|..=-.+-+ |...|+||.+. .+...+.+.+..
T Consensus 55 ~~~~~~~~i~~~l~~~gI~~~~lKG~~l~~~Y~~~~~R~~~DiDlLV~~~d~~~a~~~L~~ 115 (249)
T PF14907_consen 55 RLLAELQEILAALNANGIPVILLKGAALAQLYPDPGLRPMGDIDLLVPPEDLERAVELLEE 115 (249)
T ss_pred HHHHHHHHHHHHHHHcCCCEEEEchHHHHHhCCCCCCCCCCCeEEEEeCCcHHHHHHHHHH
Confidence 334566778999999999999997765333443 55799999875 556666666543
No 37
>COG4914 Predicted nucleotidyltransferase [General function prediction only]
Probab=39.02 E-value=16 Score=36.76 Aligned_cols=39 Identities=28% Similarity=0.467 Sum_probs=34.7
Q ss_pred hHHHHHHHHHHCCCcEEEEchhHHHHHhCCC--CCCeEEEe
Q 005645 68 PSWVVLKILKSQGFQAYLVGGCVRDLLLRRV--PKDFDVIT 106 (686)
Q Consensus 68 ~a~~VL~~L~~~G~eAYLVGG~VRDLLLGr~--PkD~DIvT 106 (686)
.+..+|+.|+..|++..+.||.|=+..||+. |.|+|+-.
T Consensus 9 ~v~~vl~~L~d~g~~FviIG~tvv~~~l~~~~~~~DVDLF~ 49 (190)
T COG4914 9 AVRKVLKSLNDKGVEFVIIGSTVVPFVLNIDYDPRDVDLFI 49 (190)
T ss_pred HHHHHHHHHHhcCeEEEEECCeEEEEEeccCCCccccceee
Confidence 3567999999999999999999999999986 89999743
No 38
>TIGR01493 HAD-SF-IA-v2 Haloacid dehalogenase superfamily, subfamily IA, variant 2 with 3rd motif like haloacid dehalogenase. The Subfamily IA and IB capping domains are predicted by PSI-PRED to consist of an alpha helical bundle. Subfamily I encompasses such a wide region of sequence space (the sequences are highly divergent) that modelling it with a single alignment is impossible, resulting in an overly broad description which allows in many unrelated sequences. Subfamily IA and IB are separated based on an aparrent phylogenetic bifurcation. Subfamily IA is still too broad to model, but cannot be further subdivided into large chunks based on phylogenetic trees. Of the three motifs defining the HAD superfamily, the third has three variant forms : (1) hhhhsDxxx(x)D, (2) hhhhssxxx(x)D and (3) hhhhDDxxx(x)s where _s_ refers to a small amino acid and _h_ to a hydrophobic one. All three of these variants are found in subfamily IA. Individual models were made based on seeds exhibiting only o
Probab=31.06 E-value=2.4e+02 Score=26.68 Aligned_cols=24 Identities=17% Similarity=0.307 Sum_probs=15.5
Q ss_pred cccccCCCCeEeeCcCcHHHHhcCc
Q 005645 186 SLFFDPFLNKIYDYANGISDLRCLK 210 (686)
Q Consensus 186 ALAyd~~~g~LiDyfGGleDLk~ri 210 (686)
|+.+|. +|+|+|+..+....-+..
T Consensus 1 ~viFD~-DGTL~D~~~~~~~~~~~~ 24 (175)
T TIGR01493 1 AMVFDV-YGTLVDVHGGVRACLAAI 24 (175)
T ss_pred CeEEec-CCcCcccHHHHHHHHHHh
Confidence 456775 588888887665554433
No 39
>PRK10578 hypothetical protein; Provisional
Probab=29.82 E-value=28 Score=36.12 Aligned_cols=14 Identities=43% Similarity=0.757 Sum_probs=12.7
Q ss_pred EchhHHHHHhCCCC
Q 005645 86 VGGCVRDLLLRRVP 99 (686)
Q Consensus 86 VGG~VRDLLLGr~P 99 (686)
=||-+||+|+|+.|
T Consensus 42 GGG~iRDill~~~P 55 (207)
T PRK10578 42 GGGTIRDMALDNGP 55 (207)
T ss_pred hcHHHHHHHcCCCC
Confidence 39999999999987
No 40
>PRK13973 thymidylate kinase; Provisional
Probab=24.74 E-value=90 Score=31.48 Aligned_cols=44 Identities=16% Similarity=0.286 Sum_probs=35.0
Q ss_pred CcCcCCCChhHHHHHHHHHHCCCcEEEE--------chhHHHHHhCCCCCCe
Q 005645 59 GITRAMIPQPSWVVLKILKSQGFQAYLV--------GGCVRDLLLRRVPKDF 102 (686)
Q Consensus 59 gI~~~~ip~~a~~VL~~L~~~G~eAYLV--------GG~VRDLLLGr~PkD~ 102 (686)
||+.+-=+..+..+-+.|...|+.++.. |..+|++|++..+..+
T Consensus 10 G~dGsGKtTq~~~l~~~l~~~g~~~~~~~~p~~~~~g~~ir~~l~~~~~~~~ 61 (213)
T PRK13973 10 GGEGAGKSTQIRLLAERLRAAGYDVLVTREPGGSPGAEAIRHVLLSGAAELY 61 (213)
T ss_pred cCCCCCHHHHHHHHHHHHHHCCCeEEEEECCCCCchHHHHHHHHcCCCccCC
Confidence 5666666677778888899999999887 9999999998654443
No 41
>TIGR03671 cca_archaeal CCA-adding enzyme.
Probab=20.67 E-value=1.8e+02 Score=33.33 Aligned_cols=74 Identities=20% Similarity=0.258 Sum_probs=42.5
Q ss_pred HHHHHHHHHH----CC--CcEEEEchhHHHHHhCCCCCCeEEEeCC----CHHHHHHHh----ccC-------ccccccc
Q 005645 69 SWVVLKILKS----QG--FQAYLVGGCVRDLLLRRVPKDFDVITTA----NLKQIRRQF----HRS-------EIIGRRF 127 (686)
Q Consensus 69 a~~VL~~L~~----~G--~eAYLVGG~VRDLLLGr~PkD~DIvT~A----~peei~k~F----~~~-------~ivGrrF 127 (686)
+..++..|++ .+ .++|++|.+.|+-.|-- ..|+||.+-- +-+++.+.. ..+ ...-..+
T Consensus 23 ~~~l~~~l~~~~~e~~~~~~v~~~GS~ArgT~L~G-~sDIDIfi~f~~~~~~e~l~~~gl~i~~~~~~~~~~~~~~yaeH 101 (408)
T TIGR03671 23 ADELIARLEEIIEELGVDAEVVLVGSYARGTWLKG-DRDIDIFILFPKDTSREELEEYGLEIGHEVLKRGGNYEERYAEH 101 (408)
T ss_pred HHHHHHHHHHHHHhcCCcceEEEEeeEecCCccCC-CCceeEEEEeCCCCCHHHHHHHHHHHHHHHHhhCCCHhheeccC
Confidence 3445555543 22 58999999999987752 2499986532 234444331 111 1112244
Q ss_pred CeEEEEECCEEEEEec
Q 005645 128 PICRVHIKGSVIEVSS 143 (686)
Q Consensus 128 ~i~~V~~~G~~IEVaT 143 (686)
+-+++.+.|..+||-.
T Consensus 102 pYv~~~~~G~~VDiVP 117 (408)
T TIGR03671 102 PYVSGEIEGFEVDVVP 117 (408)
T ss_pred ceEEEEEccEEEEEEe
Confidence 6677777787776653
Done!