Query gi|254781115|ref|YP_003065528.1| poly(A) polymerase protein [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 416
No_of_seqs 186 out of 2831
Neff 9.2
Searched_HMMs 39220
Date Tue May 31 14:59:06 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254781115.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK13299 tRNA CCA-pyrophosphor 100.0 0 0 677.0 28.6 384 14-412 8-394 (394)
2 TIGR02692 tRNA_CCA_actino tRNA 100.0 0 0 579.6 19.9 399 7-408 8-468 (472)
3 COG0617 PcnB tRNA nucleotidylt 100.0 0 0 533.6 20.4 385 8-410 4-406 (412)
4 PRK10885 cca multifunctional t 100.0 0 0 496.5 20.4 348 28-395 2-402 (410)
5 PRK11623 pcnB poly(A) polymera 100.0 0 0 486.7 19.0 256 11-272 51-331 (471)
6 PRK13298 tRNA CCA-pyrophosphor 100.0 0 0 485.1 19.6 347 28-394 2-402 (413)
7 PRK13297 tRNA CCA-pyrophosphor 100.0 0 0 482.2 20.9 344 23-394 8-362 (364)
8 TIGR01942 pcnB poly(A) polymer 100.0 0 0 463.1 7.9 224 11-240 14-252 (448)
9 PRK13296 tRNA CCA-pyrophosphor 100.0 0 0 427.7 17.5 278 27-319 1-290 (360)
10 KOG2159 consensus 100.0 0 0 417.0 11.6 375 12-405 14-410 (416)
11 cd05398 NT_ClassII-CCAase Nucl 100.0 2E-39 5E-44 283.5 12.8 136 12-147 1-139 (139)
12 pfam01743 PolyA_pol Poly A pol 100.0 1.1E-37 2.8E-42 271.8 8.6 123 29-151 1-126 (126)
13 PRK05092 PII uridylyl-transfer 99.3 2.8E-11 7.2E-16 95.0 11.1 197 158-355 398-646 (934)
14 TIGR01693 UTase_glnD protein-P 99.1 1.2E-10 3.2E-15 90.7 7.1 246 157-410 356-659 (903)
15 PRK01759 glnD PII uridylyl-tra 99.1 1.4E-09 3.5E-14 83.7 12.0 192 158-349 345-587 (862)
16 PRK03381 PII uridylyl-transfer 99.1 1.3E-10 3.4E-15 90.6 6.1 187 159-346 326-547 (781)
17 PRK00275 glnD PII uridylyl-tra 99.1 8.7E-10 2.2E-14 85.1 9.0 191 158-348 360-602 (894)
18 PRK04374 PII uridylyl-transfer 99.0 7.2E-10 1.8E-14 85.6 5.5 192 158-349 350-592 (869)
19 PRK05007 PII uridylyl-transfer 99.0 4E-09 1E-13 80.6 8.8 190 159-348 359-600 (881)
20 PRK00227 glnD PII uridylyl-tra 99.0 2.1E-09 5.4E-14 82.5 6.9 176 160-337 289-499 (692)
21 PRK03059 PII uridylyl-transfer 98.9 2.2E-09 5.6E-14 82.4 6.5 190 159-348 342-583 (857)
22 COG2844 GlnD UTP:GlnB (protein 98.4 2.4E-06 6.2E-11 62.0 8.0 190 160-349 349-589 (867)
23 PHA01806 hypothetical protein 97.0 0.0011 2.8E-08 44.2 4.9 122 28-168 42-194 (205)
24 cd07749 NT_Pol-beta-like_1 Nuc 96.0 0.12 3.2E-06 30.5 9.7 109 14-131 5-123 (156)
25 pfam10706 Aminoglyc_resit Amin 95.6 0.026 6.8E-07 35.0 4.9 76 14-91 8-87 (174)
26 cd05397 NT_Pol-beta-like Nucle 93.0 0.18 4.5E-06 29.5 4.5 37 15-53 4-42 (49)
27 pfam09970 DUF2204 Conserved Ar 92.8 0.55 1.4E-05 26.2 6.7 78 13-93 4-91 (184)
28 PRK02126 ribonuclease Z; Provi 86.3 0.74 1.9E-05 25.3 3.1 11 120-130 151-161 (334)
29 COG3575 Uncharacterized protei 85.0 1.1 2.9E-05 24.1 3.5 126 7-152 9-155 (184)
30 pfam06042 DUF925 Bacterial pro 77.3 2.5 6.3E-05 21.8 3.0 103 28-153 11-134 (163)
31 cd05400 NT_2-5OAS_ClassI-CCAas 77.3 5.4 0.00014 19.5 7.0 81 14-95 8-110 (143)
32 cd03804 GT1_wbaZ_like This fam 76.8 5.6 0.00014 19.4 5.6 26 380-410 315-340 (351)
33 COG2860 Predicted membrane pro 72.3 1.9 4.9E-05 22.5 1.4 15 31-45 44-58 (209)
34 pfam03458 UPF0126 UPF0126 doma 65.9 3.2 8.2E-05 21.0 1.5 15 31-45 39-53 (81)
35 PRK11539 hypothetical protein; 65.9 9.8 0.00025 17.8 4.7 69 126-205 160-232 (754)
36 TIGR01935 NOT-MenG RraA family 65.6 4.2 0.00011 20.3 2.0 23 17-39 78-100 (155)
37 pfam01909 NTP_transf_2 Nucleot 61.1 7.6 0.00019 18.5 2.6 28 26-55 14-41 (90)
38 PRK10578 hypothetical protein; 58.6 4.7 0.00012 20.0 1.2 15 31-45 41-55 (207)
39 pfam08843 DUF1814 Domain of un 58.4 13 0.00034 16.9 3.8 33 23-55 9-44 (232)
40 COG4914 Predicted nucleotidylt 52.2 7.3 0.00019 18.7 1.3 39 14-52 9-49 (190)
41 PRK13300 tRNA CCA-pyrophosphor 49.2 18 0.00047 16.0 7.3 67 26-94 45-123 (446)
42 TIGR01769 GGGP geranylgeranylg 44.3 22 0.00055 15.5 3.3 48 2-49 2-51 (212)
43 pfam11372 DUF3173 Protein of u 43.0 23 0.00058 15.4 3.6 33 365-398 4-36 (59)
44 TIGR02651 RNase_Z ribonuclease 43.0 20 0.0005 15.8 2.4 41 82-128 142-182 (327)
45 KOG1531 consensus 41.0 19 0.00048 15.9 2.0 24 29-52 136-159 (304)
46 TIGR02529 EutJ ethanolamine ut 37.7 26 0.00066 15.0 2.3 12 182-193 153-164 (240)
47 PRK12487 ribonuclease activity 36.1 17 0.00043 16.2 1.1 17 23-39 83-99 (163)
48 pfam03020 LEM LEM domain. The 36.1 22 0.00057 15.4 1.8 18 368-385 13-30 (43)
49 COG1708 Predicted nucleotidylt 34.7 12 0.0003 17.2 0.2 29 24-54 24-52 (128)
50 TIGR02955 TMAO_TorT TMAO reduc 34.1 30 0.00077 14.5 2.2 19 204-224 105-123 (304)
51 TIGR02666 moaA molybdenum cofa 33.9 31 0.0008 14.4 7.1 69 4-72 40-122 (346)
52 TIGR02295 HpaD 3,4-dihydroxyph 33.8 27 0.00068 14.9 1.9 82 39-125 190-301 (312)
53 pfam04743 consensus 31.6 26 0.00067 15.0 1.5 11 201-211 27-37 (160)
54 pfam03737 Methyltransf_6 Demet 30.7 24 0.00061 15.2 1.2 19 34-53 47-65 (154)
55 KOG2040 consensus 30.0 36 0.00092 14.0 2.5 16 197-212 337-352 (1001)
56 TIGR01425 SRP54_euk signal rec 29.6 22 0.00057 15.4 0.9 185 4-220 21-236 (453)
57 TIGR01854 lipid_A_lpxH UDP-2,3 29.6 26 0.00066 15.0 1.2 47 191-241 56-102 (241)
58 KOG2792 consensus 28.7 38 0.00096 13.9 1.9 12 275-286 212-223 (280)
59 PRK09372 ribonuclease activity 28.6 30 0.00076 14.6 1.4 19 34-53 46-64 (160)
60 pfam09821 ABC_transp ABC nitra 28.6 38 0.00098 13.8 2.1 38 198-235 79-116 (120)
61 PRK00924 5-keto-4-deoxyuronate 27.6 40 0.001 13.7 3.2 83 30-127 45-129 (276)
62 PRK00805 putative deoxyhypusin 26.3 42 0.0011 13.6 2.5 31 37-68 3-33 (338)
63 COG1669 Predicted nucleotidylt 26.3 42 0.0011 13.6 2.9 41 15-57 11-53 (97)
64 TIGR02392 rpoH_proteo alternat 25.8 36 0.00091 14.1 1.4 24 271-294 139-162 (279)
65 KOG2423 consensus 25.1 44 0.0011 13.4 4.1 17 201-217 199-215 (572)
66 pfam00770 Peptidase_C5 Adenovi 24.7 36 0.00091 14.0 1.2 15 126-140 38-55 (183)
67 TIGR03671 cca_archaeal CCA-add 24.3 46 0.0012 13.3 7.7 68 26-95 40-119 (408)
68 COG4849 Predicted nucleotidylt 24.3 35 0.0009 14.1 1.1 27 27-53 26-60 (269)
69 COG1140 NarY Nitrate reductase 24.1 18 0.00046 16.1 -0.4 88 30-124 61-154 (513)
70 TIGR00033 aroC chorismate synt 23.0 47 0.0012 13.2 1.6 114 70-232 3-125 (391)
71 TIGR01660 narH nitrate reducta 22.8 17 0.00044 16.1 -0.7 32 365-397 426-457 (495)
72 TIGR01703 hybrid_clust hydroxy 22.1 36 0.00093 14.0 0.8 51 105-156 318-374 (567)
73 cd00209 DHFR Dihydrofolate red 21.2 52 0.0013 12.9 2.4 14 197-210 94-107 (158)
74 TIGR01546 GAPDH-II_archae glyc 20.7 54 0.0014 12.9 2.5 33 20-60 56-88 (335)
75 PTZ00232 variable surface prot 20.5 42 0.0011 13.6 0.9 11 142-152 48-58 (363)
76 PRK11098 transport protein; Re 20.0 29 0.00075 14.6 -0.0 17 149-165 182-198 (408)
No 1
>PRK13299 tRNA CCA-pyrophosphorylase; Provisional
Probab=100.00 E-value=0 Score=677.02 Aligned_cols=384 Identities=25% Similarity=0.369 Sum_probs=323.9
Q ss_pred HHHHHHHHHHHCCCEEEEEHHHHHHHHCCCCCCEEEEEEECCHHHHHHHHHHCCCCEECCCCCCCEEEEEECCEEEEEEC
Q ss_conf 89999999997898599970699888778898608999808989999999876995621343144699998998886421
Q gi|254781115|r 14 DLINILSLLNKGEDKSCIVGGAVRDSLMNLSVQDIDIATTILPDRVMRIFSKTRYKVIPTSISYGTIKIICRKKYFDITT 93 (416)
Q Consensus 14 ~~~~i~~~l~~~g~~~~~VGG~VRD~ll~~~~~DiD~~~~~~~~~~~~~~~~~~~~~~~~~~~~gt~~~~~~~~~~di~~ 93 (416)
++..|++.|+++|++||+|||||||+|||++++||||||++.|++++++|++ .+++|.+|||++|+.+|..+||||
T Consensus 8 ~a~~i~~~l~~~G~~ay~VGG~VRD~LLg~~~~DiDi~t~a~p~~~~~~f~~----~~~~g~~~Gtv~v~~~~~~~evtt 83 (394)
T PRK13299 8 KALPILEKIKEAGFEAYFVGGSVRDYLLGRPIHDVDIATSAYPEEVKAIFPR----TVDVGIEHGTVLVLENGEEYEVTT 83 (394)
T ss_pred HHHHHHHHHHHCCCEEEEECHHHHHHHCCCCCCCEEEECCCCHHHHHHHHHH----HHHHHHCCCEEEEEECCEEEEEEE
T ss_conf 9999999999689839998879999985989999877269989999999886----504424268799988998898888
Q ss_pred CCCC-CCCCCCCC-CCCCCHHHHHHCCCCCCCCCCEEECCCCHHHHHCCCHHHHHHHHHHHCCCCCCHHHCCCCCEEEEE
Q ss_conf 3446-67688743-223320133210447800300200032101320000688878777642764310010421003320
Q gi|254781115|r 94 LRSD-LITDGRYA-KVVFTRDWKADSLRRDFTINALYADQQGKVIDYVGGLNDLRNRTIKFIGDAHHRILEDYLRILRFF 171 (416)
Q Consensus 94 ~R~e-~~~~~~~~-~~~~~~~~~eDl~RRDFTINAla~~~~~~l~Dp~gG~~DL~~~~ir~v~~~~~rf~EDpLRiLRa~ 171 (416)
+|+| .|+|+|+| .|.|++||++||+|||||||||||+++|+|+|||||++||++|+||+||+|++||.|||||||||+
T Consensus 84 ~R~e~~y~d~r~p~~v~f~~~i~eDl~RRDFTINAmA~~~~g~liDpf~G~~DL~~~~IR~vg~~~~rf~EDpLRiLRa~ 163 (394)
T PRK13299 84 FRTESEYVDYRRPSSVTFVRSLEEDLKRRDFTINAIAMDENGEIIDLFDGLEDLENRLIRAVGKAEERFQEDALRMMRAL 163 (394)
T ss_pred EECCCCCCCCCCCCCCCCCCCHHHHHHHCCCCHHHHHHCCCCCEECCCCCHHHHHHCHHHHCCCHHHHHHHCHHHHHHHH
T ss_conf 73366655668864241136799998825987103431169987689899999981723522657664233579999999
Q ss_pred EEEECCCCCCCCCCCHHHHHHHHHHCCCCCHHHHHHHHHHHHCCCCHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHH
Q ss_conf 12201364331111000123333210222057768878864211018999998753002334688701058578987786
Q gi|254781115|r 172 RFFAHYGEKNIDSDGLVASIKAKKGLKILSSERIWSEINKLLEAKNPLNAIVHMYNGGIFKEIFLDVQEISLDQLSQVIE 251 (416)
Q Consensus 172 RFasrlg~f~id~~t~~ai~~~~~~L~~iS~ERI~~El~KiL~~~~~~~~l~~L~~~gll~~ifpel~~~~~~~l~~~~~ 251 (416)
||++||| |.||++|.++|+++++.|..||+||||+||.|||.+++|..++..|.++|++.. +|++... ...+.+...
T Consensus 164 RFaa~l~-F~ie~~T~~ai~~~~~~l~~vS~ERI~~El~kiL~~~~~~~~l~~l~~~gl~~~-lp~l~~~-~~~l~~~~~ 240 (394)
T PRK13299 164 RFASQLG-FDLETETFEAMKTQAPLLEKISVERIFVEFEKLLLGPHWRKGLKALIETKAYNY-LPGLKGK-EENLLKLTQ 240 (394)
T ss_pred HHHHHCC-CCCCHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHCCCCHHHHHHHHHHCCCHHH-CCCCCCC-HHHHHHHHH
T ss_conf 9998737-788838999999988764317899999999999839988999999998788652-9210234-799999998
Q ss_pred HHHHCCCCCCHHHHHHHHCCCCCHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCCCHHHHHHHHH
Q ss_conf 77631788016766652047768578998875303425677778888754114333672466789987080245516989
Q gi|254781115|r 252 AEQVFEWKIDSLLRFIVLISWQDKKSILSMAKKFSLPREIRYFLISFFNCNFNQKTLSIPEIKKLFYLYGDKVMIAKLKI 331 (416)
Q Consensus 252 ~~~~~~~~~~~~lrla~Ll~~~~~~~~~~~~~rlkl~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~ 331 (416)
... ........+|++++|..+...+..+++++++|++.++.+..++..+......... ...+|..+.........+
T Consensus 241 ~~~--~~~~~~~~~~~~ll~~~~~~~~~~~l~~lk~s~~~~~~v~~l~~~~~~~~~~~~~--~~~l~~~~~~~~~~~~~l 316 (394)
T PRK13299 241 LLW--FSFETSEQAWAALLIALGIEDISSFLKAWKLSNKFIKDVVALVQAYRLRSERSWE--KLDLYQYGKEIALLAEDI 316 (394)
T ss_pred HHH--CCCCCHHHHHHHHHHHCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHCCCCCC--HHHHHHHCHHHHHHHHHH
T ss_conf 875--1689748999999997783889999998099999999999999998742248840--999998477989859999
Q ss_pred HHHHHCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCHHHHHH-CCCCCCHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHH
Q ss_conf 99864077760138999999987751288888988789996-58987779999999999999638888898999999999
Q gi|254781115|r 332 FLALHYNNLTHQDTCFILQVLSDIIHWKKPLFPLTGDDVVK-YGIPPGKKVGNILVHCKQEWINSSFQLSQEDLHHLLRK 410 (416)
Q Consensus 332 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~p~~pI~G~dL~~-~Gi~pGp~iG~iL~~l~~~~i~~~~~n~~e~l~~~lk~ 410 (416)
..+. ........+.+.+..+..+..+.++|||+|||+ +|++|||++|++|++++++|++|+++|++|+|++++++
T Consensus 317 ~~~~----~~~~~~~~l~~~~~~l~i~~~~~l~I~G~DLm~~lG~~pGp~iG~iL~~l~~~~l~g~~~n~~eaLl~~l~~ 392 (394)
T PRK13299 317 RQAR----GLSVNLEEIQELYQALPIHSKKELAINGGDLLKHFGKKPGPWLGETLRKIEEAIVTGELENEKEAILEWLDE 392 (394)
T ss_pred HHHC----CCCCCHHHHHHHHHHCCCCCCCCCCCCHHHHHHHCCCCCCHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHH
T ss_conf 9862----364479999999974601458789847899999709992389999999999998169999969999999997
Q ss_pred HH
Q ss_conf 98
Q gi|254781115|r 411 LI 412 (416)
Q Consensus 411 l~ 412 (416)
++
T Consensus 393 ~l 394 (394)
T PRK13299 393 HL 394 (394)
T ss_pred HC
T ss_conf 49
No 2
>TIGR02692 tRNA_CCA_actino tRNA adenylyltransferase; InterPro: IPR014065 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 IPR002646 from INTERPRO (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=0 Score=579.57 Aligned_cols=399 Identities=22% Similarity=0.323 Sum_probs=335.7
Q ss_pred CHHCCCHHHHHHHHHHHHCCCEEEEEHHHHHHHHCCCCC-CEEEEEEECCHHHHHHHHHHCCCCEECCCCCCCEEEEEEC
Q ss_conf 522199889999999997898599970699888778898-6089998089899999998769956213431446999989
Q gi|254781115|r 7 HKWFHDSDLINILSLLNKGEDKSCIVGGAVRDSLMNLSV-QDIDIATTILPDRVMRIFSKTRYKVIPTSISYGTIKIICR 85 (416)
Q Consensus 7 ~~~~~~~~~~~i~~~l~~~g~~~~~VGG~VRD~ll~~~~-~DiD~~~~~~~~~~~~~~~~~~~~~~~~~~~~gt~~~~~~ 85 (416)
+....++-+..+...+.+.|++.|+|||.|||+|||+.. +|+||+|+|.|+++.+++...--.++.+|.+||||....+
T Consensus 8 ~~~~~~~~~~~L~~~F~~~Gh~L~LVGGsVRDAlLgrl~~~DLDFTTdArP~~~~~il~~~a~~vWd~G~~fGTv~a~~~ 87 (472)
T TIGR02692 8 ALLELAPVLAELAAAFAAAGHELYLVGGSVRDALLGRLGSHDLDFTTDARPEEVLAILRPWADAVWDTGIAFGTVGAEKD 87 (472)
T ss_pred HHHHHHHHHHHHHHHHHHCCCEEEEECCCHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCEEEEEC
T ss_conf 88766688999999998649858861661454313656776676578998689999997766677552102121223443
Q ss_pred CEEEEEECCCCCCCC-CCCCCCCCCCHHHHHHCCCCCCCCCCEEECCC--C--HHHHHCCCHHHHHHHHHHHCCCCCCHH
Q ss_conf 988864213446676-88743223320133210447800300200032--1--013200006888787776427643100
Q gi|254781115|r 86 KKYFDITTLRSDLIT-DGRYAKVVFTRDWKADSLRRDFTINALYADQQ--G--KVIDYVGGLNDLRNRTIKFIGDAHHRI 160 (416)
Q Consensus 86 ~~~~di~~~R~e~~~-~~~~~~~~~~~~~~eDl~RRDFTINAla~~~~--~--~l~Dp~gG~~DL~~~~ir~v~~~~~rf 160 (416)
++.+||||||+|.|. ..|+|+|.||.++++||.||||||||||+... | .++||.||+.||.+++|+++..|+.||
T Consensus 88 ~~~~EiTTyRsD~Yd~~sR~P~V~FGd~Le~DL~RRDFtvNAmA~~~~~~G~~~f~Dp~gGl~~l~~~~L~TP~~Pe~SF 167 (472)
T TIGR02692 88 GQQVEITTYRSDSYDGTSRKPEVEFGDTLEGDLIRRDFTVNAMAVRIAADGSLEFVDPLGGLDDLLAKVLDTPATPEQSF 167 (472)
T ss_pred CCEEEEEEEECCCCCCCCCCCEEEECCCCCCCCEECCHHHHHHHHHHCCCCCEEEECHHHHHHHHHHHHCCCCCCCCCCC
T ss_conf 70789886003146777887414448754456231302462566421057955886426779999998405788743567
Q ss_pred HCCCCCEEEEEEEEECCCCCCCCCCCHHHHHHHHHHCCCCCHHHHHHHHHHHHCCCCHHHHHHHHHHCCCCCCCCCCCCC
Q ss_conf 10421003320122013643311110001233332102220577688788642110189999987530023346887010
Q gi|254781115|r 161 LEDYLRILRFFRFFAHYGEKNIDSDGLVASIKAKKGLKILSSERIWSEINKLLEAKNPLNAIVHMYNGGIFKEIFLDVQE 240 (416)
Q Consensus 161 ~EDpLRiLRa~RFasrlg~f~id~~t~~ai~~~~~~L~~iS~ERI~~El~KiL~~~~~~~~l~~L~~~gll~~ifpel~~ 240 (416)
.|||||||||+||+|||| |.+.+++..||.+++..|..||.|||..||.|+|.+++|..++.+|.++|+-+.|+||+..
T Consensus 168 ~DDPLRMLRAARf~sQLg-F~v~~~v~~Am~~mA~~i~~isAERv~~EL~Kll~~~~P~~Gi~llV~TGla~~vlPE~~a 246 (472)
T TIGR02692 168 SDDPLRMLRAARFVSQLG-FEVAPRVRAAMTEMADRIEIISAERVRDELDKLLLGDHPREGIDLLVETGLADRVLPEIPA 246 (472)
T ss_pred CCCHHHHHHHHHHHHHHC-CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHCCHHHCCCCCCH
T ss_conf 888168999999877607-6124789999999887743324788888874201477836678998740401110467620
Q ss_pred CCH----------------HHHHHHHHHHHH--CCCCCCHHHHHHHHCCCCCHHH----------------------HHH
Q ss_conf 585----------------789877867763--1788016766652047768578----------------------998
Q gi|254781115|r 241 ISL----------------DQLSQVIEAEQV--FEWKIDSLLRFIVLISWQDKKS----------------------ILS 280 (416)
Q Consensus 241 ~~~----------------~~l~~~~~~~~~--~~~~~~~~lrla~Ll~~~~~~~----------------------~~~ 280 (416)
+.+ .-+.+.+..++. ....|+-.+|||||+||.||+. +.+
T Consensus 247 lrl~~DEHh~HKDVY~HSL~VL~QAi~~e~~r~~~~~PDLvLRlAALLHDiGKP~TR~~~~~G~VSFhhHevVGAKm~rk 326 (472)
T TIGR02692 247 LRLEIDEHHQHKDVYEHSLTVLRQAIDLEKERFEDDGPDLVLRLAALLHDIGKPATRRFEPDGRVSFHHHEVVGAKMVRK 326 (472)
T ss_pred HHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCEEEEECCCHHHHHHHH
T ss_conf 24132233567547889999999999998861557888257888998503778523451879967656522056789999
Q ss_pred HHHHCCCHHHHHHHHHHHHHHHCCCC-----CCCHHHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHH
Q ss_conf 87530342567777888875411433-----3672466789987080245516989998640777601389999999877
Q gi|254781115|r 281 MAKKFSLPREIRYFLISFFNCNFNQK-----TLSIPEIKKLFYLYGDKVMIAKLKIFLALHYNNLTHQDTCFILQVLSDI 355 (416)
Q Consensus 281 ~~~rlkl~~~~~~~l~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~~ 355 (416)
-...|++|+..+..+..++..|++.. .++.+.++|+..-.|.... .+..+.-...+..+.+....+...|+.+
T Consensus 327 R~~aLky~k~~~~~Vs~Lv~LHLRFhGYg~g~WTDSAVRRYV~DAG~~L~--RLH~L~RaDcTTRNkrkA~rL~~~YD~L 404 (472)
T TIGR02692 327 RLRALKYSKQVVEDVSRLVELHLRFHGYGDGEWTDSAVRRYVRDAGPLLE--RLHKLVRADCTTRNKRKAERLQAAYDDL 404 (472)
T ss_pred HHHHCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHH--HCCEECCCCCCCCHHHHHHHHHHHHHHH
T ss_conf 99851487578999999999751010068994022445641651001001--3010011576600368999987523379
Q ss_pred ----------HHCCCCCCCCCHHHHHH-CCCCCCHHHHHHHHHHHHHHHCCCCCCCHHHHHHHH
Q ss_conf ----------51288888988789996-589877799999999999996388888989999999
Q gi|254781115|r 356 ----------IHWKKPLFPLTGDDVVK-YGIPPGKKVGNILVHCKQEWINSSFQLSQEDLHHLL 408 (416)
Q Consensus 356 ----------~~~~~p~~pI~G~dL~~-~Gi~pGp~iG~iL~~l~~~~i~~~~~n~~e~l~~~l 408 (416)
.......|.++|+.+|+ +|++|||++|++-++|.+..++++--..+|+...++
T Consensus 405 E~RIA~l~~~E~L~~vRPDLDG~~iM~iL~i~pG~~VG~A~~yL~eLRL~~GPl~~~~A~~~L~ 468 (472)
T TIGR02692 405 EERIAELAAKEDLDAVRPDLDGNEIMEILGIKPGPEVGKAWKYLKELRLERGPLEREEAIAELL 468 (472)
T ss_pred HHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCCCHHHHHHHHHHHHHCCCCCCCCHHHHHHHHH
T ss_conf 9999988853316631887784799997089998757899999987212578988789999998
No 3
>COG0617 PcnB tRNA nucleotidyltransferase/poly(A) polymerase [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=0 Score=533.58 Aligned_cols=385 Identities=28% Similarity=0.373 Sum_probs=281.6
Q ss_pred HHCCCHHHHHHHHHHHHCCCEEEEEHHHHHHHHCCCCCCEEEEEEECCHHHHHHHHHHCCCCEECCCCCCCEEEEEECCE
Q ss_conf 22199889999999997898599970699888778898608999808989999999876995621343144699998998
Q gi|254781115|r 8 KWFHDSDLINILSLLNKGEDKSCIVGGAVRDSLMNLSVQDIDIATTILPDRVMRIFSKTRYKVIPTSISYGTIKIICRKK 87 (416)
Q Consensus 8 ~~~~~~~~~~i~~~l~~~g~~~~~VGG~VRD~ll~~~~~DiD~~~~~~~~~~~~~~~~~~~~~~~~~~~~gt~~~~~~~~ 87 (416)
.+..++.++.|+..+.++|+++|+|||||||+|||++++|+||||++.|+++.++|. +.+++|.+|||+++..++.
T Consensus 4 ~~~~~~~~~~v~~~l~~~g~eaylVGGaVRD~LLG~~~~D~Diat~~~p~~~~~~~~----~~~~~G~~f~t~~v~~~~~ 79 (412)
T COG0617 4 LKDLSPNALKVLSKLKEAGYEAYLVGGAVRDLLLGRPPKDVDIATNATPEEVKKLFR----NTRPVGRKFGTVTVPFNGE 79 (412)
T ss_pred HHHHHHHHHHHHHHHHHCCCEEEEECCCHHHHHCCCCCCCEEEEECCCHHHHHHHHH----HHHHCCCCCCEEEECCCCE
T ss_conf 133327899999999966985999732087877699966753771288799999987----4010166766589754985
Q ss_pred EEEEECCCCCCC-CCCCCCCCCCCHHHHHHCCCCCCCCCCEEECC-CCHHHHHCCCHHHHHHHHHHHCCCCCCHHHCCCC
Q ss_conf 886421344667-68874322332013321044780030020003-2101320000688878777642764310010421
Q gi|254781115|r 88 YFDITTLRSDLI-TDGRYAKVVFTRDWKADSLRRDFTINALYADQ-QGKVIDYVGGLNDLRNRTIKFIGDAHHRILEDYL 165 (416)
Q Consensus 88 ~~di~~~R~e~~-~~~~~~~~~~~~~~~eDl~RRDFTINAla~~~-~~~l~Dp~gG~~DL~~~~ir~v~~~~~rf~EDpL 165 (416)
.+|+||+|+|.| .+|++.++++.+||++||.|||||||||||++ +|+|+|||||+.||++|+||+||+|++||.||||
T Consensus 80 ~~ev~T~R~~~~~~~~~~~~~~~~~tleeDl~RRDFTINAla~~~~~~~iiD~~gG~~DL~~~~lR~i~~~~~rf~EDpl 159 (412)
T COG0617 80 IIEVTTFRKEGYGYNGRPLPVVFPGTLEEDLKRRDFTINALAYDPEDGEIIDPFGGLKDLENRVLRHIGDASERFREDPL 159 (412)
T ss_pred EEEEEEEECCCCCCCCCCCCCCCCCCHHHCCCCCCCCHHHHCCCCCCCEECCCCCCHHHHCCCEEECCCCCHHCCCCCHH
T ss_conf 89998730357776788778788999587565658609871468656905079899768717857534682420452648
Q ss_pred CEEEEEEEEECCCCCCCCCCCHHHHHHHHHHCCCCCHHHHHHHHHHHHCCCCHHHHHHHHHHCCCCCCCCCCCCCCCHHH
Q ss_conf 00332012201364331111000123333210222057768878864211018999998753002334688701058578
Q gi|254781115|r 166 RILRFFRFFAHYGEKNIDSDGLVASIKAKKGLKILSSERIWSEINKLLEAKNPLNAIVHMYNGGIFKEIFLDVQEISLDQ 245 (416)
Q Consensus 166 RiLRa~RFasrlg~f~id~~t~~ai~~~~~~L~~iS~ERI~~El~KiL~~~~~~~~l~~L~~~gll~~ifpel~~~~~~~ 245 (416)
|||||+||+|+|| |.++++|..+|+.....+..+|+||||.|+.|||.+++|..+++.|.++|+++.+||++.......
T Consensus 160 RiLRa~RFaa~l~-f~i~~~t~~~i~~~~~~~~~is~ERi~~El~KlL~~~~~~~~l~~l~~~g~l~~l~p~~~~~~~~~ 238 (412)
T COG0617 160 RILRAARFAARLG-FTIEPETEEAIRLMAPLLAKISRERLWDELKKLLLSPNPREALQLLREYGALKILFPELDKLFGVP 238 (412)
T ss_pred HHHHHHHHHHHCC-CCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHCCCCHHHHHHHHHHCCCHHHCCCCHHHHHCCH
T ss_conf 9999999999837-889856999999998764408888999999999779989999999998698654296044433000
Q ss_pred --HHHHHHHHHHCCCCCCHHHHHHHHCCCCCHHHHHHHHH-------------HCCCHHHHHHHHHHHHHHHCCCCCCCH
Q ss_conf --98778677631788016766652047768578998875-------------303425677778888754114333672
Q gi|254781115|r 246 --LSQVIEAEQVFEWKIDSLLRFIVLISWQDKKSILSMAK-------------KFSLPREIRYFLISFFNCNFNQKTLSI 310 (416)
Q Consensus 246 --l~~~~~~~~~~~~~~~~~lrla~Ll~~~~~~~~~~~~~-------------rlkl~~~~~~~l~~~~~~~~~~~~~~~ 310 (416)
....................++++.+... .....+.. .+..+......+..+...+.......
T Consensus 239 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~- 316 (412)
T COG0617 239 KLLLALREIELLLHNTDELLLALAALLPAFL-LAAATLPLLLRKGKTIAKKRRELKHDEAAAKAVNDLLKRLLRPNYLG- 316 (412)
T ss_pred HHHHHHHHHHHHHCCCCHHHHHHHHHCHHHH-HHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH-
T ss_conf 2567789999851341159999987473467-78876315677676578877531415667777999999874113556-
Q ss_pred HHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCHHHHHH-CCCCCCHHHHHHHHHHH
Q ss_conf 46678998708024551698999864077760138999999987751288888988789996-58987779999999999
Q gi|254781115|r 311 PEIKKLFYLYGDKVMIAKLKIFLALHYNNLTHQDTCFILQVLSDIIHWKKPLFPLTGDDVVK-YGIPPGKKVGNILVHCK 389 (416)
Q Consensus 311 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~p~~pI~G~dL~~-~Gi~pGp~iG~iL~~l~ 389 (416)
.... .......++......... ......+..+.......-...+.|.++.+ .+.+|||+++++++.+.
T Consensus 317 -~~~~---------~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~ 385 (412)
T COG0617 317 -YLKR---------LVEEVREIWHEAGELLPR-TGKRARKLLRLLAFRAALELLILGRDLGEAAGYKPGPKLGEILQLLE 385 (412)
T ss_pred -HHHH---------HHHHHHHHHHHHHHHHHC-CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHH
T ss_conf -6789---------999999999999875101-02334558777999976666651242033217765338999999875
Q ss_pred HHHHCCCCCCCHHHHHHHHHH
Q ss_conf 999638888898999999999
Q gi|254781115|r 390 QEWINSSFQLSQEDLHHLLRK 410 (416)
Q Consensus 390 ~~~i~~~~~n~~e~l~~~lk~ 410 (416)
..++.+.+++..+...+-.++
T Consensus 386 ~~~~~~~~~~~~~~~~~~~~~ 406 (412)
T COG0617 386 EKPLKGVIKNLKEALIERLER 406 (412)
T ss_pred HHHHHHHHHHHHHHHHHHHCC
T ss_conf 200122223046777887502
No 4
>PRK10885 cca multifunctional tRNA nucleotidyl transferase/2'3'-cyclic phosphodiesterase/2'nucleotidase/phosphatase; Reviewed
Probab=100.00 E-value=0 Score=496.55 Aligned_cols=348 Identities=22% Similarity=0.336 Sum_probs=260.5
Q ss_pred EEEEEHHHHHHHHCCCCCCEEEE-EEECCHHHHHHHHHHCCCCEECCCCCCCEEEEEECCEEEEEECCCCCCCCC-CCCC
Q ss_conf 59997069988877889860899-980898999999987699562134314469999899888642134466768-8743
Q gi|254781115|r 28 KSCIVGGAVRDSLMNLSVQDIDI-ATTILPDRVMRIFSKTRYKVIPTSISYGTIKIICRKKYFDITTLRSDLITD-GRYA 105 (416)
Q Consensus 28 ~~~~VGG~VRD~ll~~~~~DiD~-~~~~~~~~~~~~~~~~~~~~~~~~~~~gt~~~~~~~~~~di~~~R~e~~~~-~~~~ 105 (416)
++|+|||||||.|||++++|+|+ ||+++|+++... +++ ++|..|++. +......|++.+|+|.++. |.+.
T Consensus 2 ~~ylVGGaVRD~LLg~~~~D~D~vv~ga~pe~~~~~----g~~--~vG~~f~v~--l~~~~~~e~alarterk~~~g~~g 73 (410)
T PRK10885 2 KIYLVGGAVRDALLGLPVKDRDWVVVGATPEEMLAQ----GYQ--PVGKDFPVF--LHPKTHEEYALARTERKSGRGYTG 73 (410)
T ss_pred CEEEEEEHHHHHHCCCCCCCEEEECCCCCHHHHHHC----CCC--EECCCCEEE--EECCCCEEEEEEEEEEECCCCCCC
T ss_conf 789972099899769899886785789999999980----883--107632179--867887189999888604667575
Q ss_pred CCCCCH---HHHHHCCCCCCCCCCEEECCCCHHHHHCCCHHHHHHHHHHHCCCCCCHHHCCCCCEEEEEEEEECC---CC
Q ss_conf 223320---133210447800300200032101320000688878777642764310010421003320122013---64
Q gi|254781115|r 106 KVVFTR---DWKADSLRRDFTINALYADQQGKVIDYVGGLNDLRNRTIKFIGDAHHRILEDYLRILRFFRFFAHY---GE 179 (416)
Q Consensus 106 ~~~~~~---~~~eDl~RRDFTINAla~~~~~~l~Dp~gG~~DL~~~~ir~v~~~~~rf~EDpLRiLRa~RFasrl---g~ 179 (416)
..++.+ |++|||.||||||||||+|.+|+|||||||++||++|+||+||++ |.|||||||||+||+||| |
T Consensus 74 ~~~~~~p~vtleeDl~RRDfTINAmA~d~~g~liDp~~G~~DL~~~ilR~v~~~---F~EDpLRilRa~RFaar~~~lg- 149 (410)
T PRK10885 74 FTCYAAPDVTLEEDLIRRDLTINAMAQDDDGEIIDPYGGQRDLEARLLRHVSPA---FAEDPLRVLRVARFAARFAHLG- 149 (410)
T ss_pred EEEECCCCCCHHHHHHHCCCCEEEEEECCCCCEEECCCCHHHHHCCCCCCCCCC---CCCCHHHHHHHHHHHHHHCCCC-
T ss_conf 377248987778887633776000006799998627998588974951055533---3217699999999998524389-
Q ss_pred CCCCCCCHHHHHHHHH--HCCCCCHHHHHHHHHHHHCCCCHHHHHHHHHHCCCCCCCCCCCCCCCH-----------HHH
Q ss_conf 3311110001233332--102220577688788642110189999987530023346887010585-----------789
Q gi|254781115|r 180 KNIDSDGLVASIKAKK--GLKILSSERIWSEINKLLEAKNPLNAIVHMYNGGIFKEIFLDVQEISL-----------DQL 246 (416)
Q Consensus 180 f~id~~t~~ai~~~~~--~L~~iS~ERI~~El~KiL~~~~~~~~l~~L~~~gll~~ifpel~~~~~-----------~~l 246 (416)
|.|+++|+.+|++.+. .|..+|+||||.|+.|+|.+++|+.+|..|.++|++..+|||+..+.. +..
T Consensus 150 F~i~~eT~~~m~~~~~~g~L~~ls~ERi~~E~~k~l~~~~p~~~~~~L~~~g~l~~~~PEl~~l~gv~q~~~~H~e~d~~ 229 (410)
T PRK10885 150 FRIAPETLALMREMVASGELDALTPERVWKETERALMERNPQVFFQVLRDCGALAVLLPEIDALFGVPQPAKWHPEIDTG 229 (410)
T ss_pred CCCCHHHHHHHHHHHHCCCHHHCCHHHHHHHHHHHHCCCCHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCCCCCCHH
T ss_conf 96784699999997835713226876689999999768888999999998568888624189864998862358764379
Q ss_pred HHHHHH-HHHCCCCCCHHHHHHHHCCCCCHH-------------------HHHHHHHHCCCHHHHHHHHHHHHHHHCCCC
Q ss_conf 877867-763178801676665204776857-------------------899887530342567777888875411433
Q gi|254781115|r 247 SQVIEA-EQVFEWKIDSLLRFIVLISWQDKK-------------------SILSMAKKFSLPREIRYFLISFFNCNFNQK 306 (416)
Q Consensus 247 ~~~~~~-~~~~~~~~~~~lrla~Ll~~~~~~-------------------~~~~~~~rlkl~~~~~~~l~~~~~~~~~~~ 306 (416)
.+.... ........+..+||++|+|+++|. .+..+++||++||+.+.....+..+|....
T Consensus 230 ~Htl~~l~~a~~~~~~~~~r~aaL~HDlgK~~t~~~~~~~~~gh~~~g~~~~~~l~~RLk~Pn~~~~la~l~~~~H~~~~ 309 (410)
T PRK10885 230 IHTLMVLDQAAKLSPSLDVRFAALCHDLGKGLTPPEEWPRHHGHEPRGVKLVEQLCQRLRVPNECRDLALLVAEEHDNIH 309 (410)
T ss_pred HHHHHHHHHHHHCCCCHHHHHHHHHHHHCCCCCCHHHCCCCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
T ss_conf 99999999998549988999999974632668973436531113321059999999995899999999999999999874
Q ss_pred C---CCHHHHHHHHHHCCC---HHHHHHHHHHHHH-HCC--CCCC---CCHHHHHHHHHHHHHCCCCCCCCCHHHHHHCC
Q ss_conf 3---672466789987080---2455169899986-407--7760---13899999998775128888898878999658
Q gi|254781115|r 307 T---LSIPEIKKLFYLYGD---KVMIAKLKIFLAL-HYN--NLTH---QDTCFILQVLSDIIHWKKPLFPLTGDDVVKYG 374 (416)
Q Consensus 307 ~---~~~~~~~~~~~~~~~---~~~~~~l~~~~~~-~~~--~~~~---~~~~~~~~~l~~~~~~~~p~~pI~G~dL~~~G 374 (416)
. +....+.+++....- ......+...+-. ..+ +... +....+...++... .|++++|++.|
T Consensus 310 ~~~~l~~~~ll~ll~~~Da~RrPerf~~~L~~c~ad~~gr~~~e~~~ypq~~~L~~a~~~a~-------~V~~~~ii~~G 382 (410)
T PRK10885 310 RAPELRPKTLVKLLDRIDAWRKPQRFEQFLLACEADARGRLGFEDRPYPQAEYLREALQAAR-------SVDVKAVVEAG 382 (410)
T ss_pred CCCCCCHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHH-------CCCHHHHHHCC
T ss_conf 11537999999999975864587999999998655553136754476639999999999996-------89999998768
Q ss_pred CCCCHHHHHHHHHHHHHHHCC
Q ss_conf 987779999999999999638
Q gi|254781115|r 375 IPPGKKVGNILVHCKQEWINS 395 (416)
Q Consensus 375 i~pGp~iG~iL~~l~~~~i~~ 395 (416)
++ ||+||+.|+..+..+|+.
T Consensus 383 ~~-G~~Ig~aL~~~Ri~ai~~ 402 (410)
T PRK10885 383 FK-GAAIREELTRRRIAAVAA 402 (410)
T ss_pred CC-HHHHHHHHHHHHHHHHHH
T ss_conf 98-589999999999999999
No 5
>PRK11623 pcnB poly(A) polymerase I; Provisional
Probab=100.00 E-value=0 Score=486.74 Aligned_cols=256 Identities=24% Similarity=0.413 Sum_probs=216.7
Q ss_pred CCHHHHHHHHHHHHCCCEEEEEHHHHHHHHCCCCCCEEEEEEECCHHHHHHHHHHCCCCEECCCCCCCEEEEEECCEEEE
Q ss_conf 99889999999997898599970699888778898608999808989999999876995621343144699998998886
Q gi|254781115|r 11 HDSDLINILSLLNKGEDKSCIVGGAVRDSLMNLSVQDIDIATTILPDRVMRIFSKTRYKVIPTSISYGTIKIICRKKYFD 90 (416)
Q Consensus 11 ~~~~~~~i~~~l~~~g~~~~~VGG~VRD~ll~~~~~DiD~~~~~~~~~~~~~~~~~~~~~~~~~~~~gt~~~~~~~~~~d 90 (416)
-++++.+|+..|+++|++||+|||||||+|||++|+|+|++|+|+|+++.++|.++. .+|..||+++|.+++..||
T Consensus 51 is~~alkVl~~L~~aGfeAylVGG~VRDlLLg~~PkDfDvaT~AtPeei~~lF~~~r----~iGrrf~~vhV~~~~~~iE 126 (471)
T PRK11623 51 ISENALKVLYRLNKAGYEAYLVGGGVRDLLLGKKPKDFDVTTNATPEQVRKLFRNCR----LVGRRFRLAHVMFGPEIIE 126 (471)
T ss_pred CCHHHHHHHHHHHHCCCEEEEECHHHHHHHCCCCCCCEEEECCCCHHHHHHHHHHCC----CCCCCCCEEEEEECCEEEE
T ss_conf 797699999999967975999772898997598999864618998899999998530----3053774589998995899
Q ss_pred EECCCCCC-CCCC-----------CCC-CCCCCHHHHHHCCCCCCCCCCEEECC-CCHHHHHCCCHHHHHHHHHHHCCCC
Q ss_conf 42134466-7688-----------743-22332013321044780030020003-2101320000688878777642764
Q gi|254781115|r 91 ITTLRSDL-ITDG-----------RYA-KVVFTRDWKADSLRRDFTINALYADQ-QGKVIDYVGGLNDLRNRTIKFIGDA 156 (416)
Q Consensus 91 i~~~R~e~-~~~~-----------~~~-~~~~~~~~~eDl~RRDFTINAla~~~-~~~l~Dp~gG~~DL~~~~ir~v~~~ 156 (416)
|||||.+. +.++ +.. +.+|+ |++||+.||||||||||||+ ++.|+||+||++||++|+||+||+|
T Consensus 127 VtTFR~~~~~~~~~~~~~~~~~~g~~lrdn~~g-tieeDa~RRDFTINALyyd~~~~~i~D~~gG~~DL~~~~iR~IGdP 205 (471)
T PRK11623 127 VATFRGHHEGNVSDRTTSQRGQNGMLLRDNIFG-SIEEDAQRRDFTINSLYYSVADFTVRDYVGGMKDLKEGVIRLIGNP 205 (471)
T ss_pred EECCCCCCCCCCCCCCCCCCCCCCCEECCCCCC-CHHHHHHHCCCCCHHHEECCCCCEEECCCCCHHHHHCCCEECCCCH
T ss_conf 963357766666666654426776032034558-7888866327520221122799967689898999965955502798
Q ss_pred CCHHHCCCCCEEEEEEEEECCCCCCCCCCCHHHHHHHHHHCCCCCHHHHHHHHHHHHCCCCHHHHHHHHHHCCCCCCCCC
Q ss_conf 31001042100332012201364331111000123333210222057768878864211018999998753002334688
Q gi|254781115|r 157 HHRILEDYLRILRFFRFFAHYGEKNIDSDGLVASIKAKKGLKILSSERIWSEINKLLEAKNPLNAIVHMYNGGIFKEIFL 236 (416)
Q Consensus 157 ~~rf~EDpLRiLRa~RFasrlg~f~id~~t~~ai~~~~~~L~~iS~ERI~~El~KiL~~~~~~~~l~~L~~~gll~~ifp 236 (416)
.+||.|||+|||||+||+|+|| |.||++|..+|.+++++|.+||++|+++|+.|++.+.+...+++.|.+.|+++.+||
T Consensus 206 ~~Rf~EDpvRmLRAvRFaakL~-f~i~~~t~~~I~~~~~lL~~i~~aRLfdE~lKLf~sG~a~~~~~~L~~~gL~~~LfP 284 (471)
T PRK11623 206 ETRYREDPVRMLRAVRFAAKLD-MRISPETAEPIPRLATLLNDIPPARLFEESLKLLQAGYGYETYKLLCEYHLFQPLFP 284 (471)
T ss_pred HHHHHHCHHHHHHHHHHHHHCC-CCCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCHHHHHHHHHHCCCHHHHHH
T ss_conf 9997667899999999999719-976878999999999988548876789999999865858999999998687676515
Q ss_pred CCCCCC-------HHHH-H-HHHHHHHH--CCCCCCHHHHHHHHCCC
Q ss_conf 701058-------5789-8-77867763--17880167666520477
Q gi|254781115|r 237 DVQEIS-------LDQL-S-QVIEAEQV--FEWKIDSLLRFIVLISW 272 (416)
Q Consensus 237 el~~~~-------~~~l-~-~~~~~~~~--~~~~~~~~lrla~Ll~~ 272 (416)
.+...- ..++ . .+..+... ......+-..+|+|++.
T Consensus 285 ~~~~~l~~~~~~~~~~~i~~aL~nTD~RI~~gK~VtPaFLfAalLW~ 331 (471)
T PRK11623 285 TITRYFTENGDSPMERIIEQVLKNTDTRIHNDMRVNPAFLFAAMFWY 331 (471)
T ss_pred HHHHHHHHCCCCHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHH
T ss_conf 27877631267089999999999799998688977829999999718
No 6
>PRK13298 tRNA CCA-pyrophosphorylase; Provisional
Probab=100.00 E-value=0 Score=485.14 Aligned_cols=347 Identities=24% Similarity=0.325 Sum_probs=253.8
Q ss_pred EEEEEHHHHHHHHCCCCCCEEEEEE-ECCHHHHHHHHHHCCCCEECCCCCCCEEEEEECCEEEEEECCCCCCCCCCCCC-
Q ss_conf 5999706998887788986089998-08989999999876995621343144699998998886421344667688743-
Q gi|254781115|r 28 KSCIVGGAVRDSLMNLSVQDIDIAT-TILPDRVMRIFSKTRYKVIPTSISYGTIKIICRKKYFDITTLRSDLITDGRYA- 105 (416)
Q Consensus 28 ~~~~VGG~VRD~ll~~~~~DiD~~~-~~~~~~~~~~~~~~~~~~~~~~~~~gt~~~~~~~~~~di~~~R~e~~~~~~~~- 105 (416)
++|+|||||||.|||++++|+|++| .++|+++.... + ..+|..|++. .......|++++|+|.++..++.
T Consensus 2 k~YlVGGaVRD~LLg~~~~D~D~vv~g~~p~~~~~~~----~--~~vGk~f~v~--l~~~~~~e~~~ar~e~k~~~g~~g 73 (413)
T PRK13298 2 KKYLVGGAVRDSLLNLPVQDRDWVVVGSTPQEMLSIN----Y--QQVGKDFPVF--LHPESHEEYSLARTERKSGVGYTG 73 (413)
T ss_pred CEEEECCHHHHHHCCCCCCCEEEECCCCCHHHHHHHH----H--HHCCCCEEEE--EECCCCEEEEEEEEEECCCCCCCC
T ss_conf 7799630998997699998846754799899999841----5--6428863899--988876699998776336777477
Q ss_pred ---CCCCCHHHHHHCCCCCCCCCCEEECCCCHHHHHCCCHHHHHHHHHHHCCCCCCHHHCCCCCEEEEEEEEECC---CC
Q ss_conf ---223320133210447800300200032101320000688878777642764310010421003320122013---64
Q gi|254781115|r 106 ---KVVFTRDWKADSLRRDFTINALYADQQGKVIDYVGGLNDLRNRTIKFIGDAHHRILEDYLRILRFFRFFAHY---GE 179 (416)
Q Consensus 106 ---~~~~~~~~~eDl~RRDFTINAla~~~~~~l~Dp~gG~~DL~~~~ir~v~~~~~rf~EDpLRiLRa~RFasrl---g~ 179 (416)
......||+|||.||||||||||+|.+|+|||||||++||++|+||+|++ +|.|||||||||+||+|+| |
T Consensus 74 ~~~~~~~~~tleeDl~RRDfTINAmA~d~~G~liDp~~G~~DL~~~ilR~v~~---~F~EDPLRilRa~RFaar~~~Lg- 149 (413)
T PRK13298 74 FIFDTSSSITLEEDLYRRDLTINAIAQDSNGNYIDPFNGQKDIQLRLLRHVSE---SFSEDPLRVLRVARFAALLHHLG- 149 (413)
T ss_pred EEEECCCCCCHHHHHHHCCCCCCEEEECCCCCEEECCCCHHHHHCCCCCCCCC---CCCCCCHHHHHHHHHHHHCCCCC-
T ss_conf 25306888788999886257410159999998761798999996796548987---76668789999999998516799-
Q ss_pred CCCCCCCHHHHHHHH--HHCCCCCHHHHHHHHHHHHCCCCHHHHHHHHHHCCCCCCCCCCCCCCCH------------HH
Q ss_conf 331111000123333--2102220577688788642110189999987530023346887010585------------78
Q gi|254781115|r 180 KNIDSDGLVASIKAK--KGLKILSSERIWSEINKLLEAKNPLNAIVHMYNGGIFKEIFLDVQEISL------------DQ 245 (416)
Q Consensus 180 f~id~~t~~ai~~~~--~~L~~iS~ERI~~El~KiL~~~~~~~~l~~L~~~gll~~ifpel~~~~~------------~~ 245 (416)
|+|+++|+.+|++++ +.|..+|+||||.|+.|+|.+++|+.+|+.|.++|+++.||||+..+.. +.
T Consensus 150 F~I~~eT~~lm~~~~~~~el~~ls~ERv~~E~~K~L~~~~P~~~~~~L~~~g~l~~i~PEl~~l~gv~q~~~~~~~~~d~ 229 (413)
T PRK13298 150 FRIAKETMILMKIMVKKHELLYLTPERIWKETEKALITDNPHVYFQVLKNCNALKFLFPEINFLYEIPYFTNSFFKNFNL 229 (413)
T ss_pred CCCCHHHHHHHHHHHHCCCHHHCCHHHHHHHHHHHHCCCCCHHHHHHHHHCCCHHHHCCCHHHHCCCCCCHHHCCCCCCH
T ss_conf 84587999999998704862116988999999999769990899999998088877571568762998753322766433
Q ss_pred HHHHH-HHHHHCCCCCCHHHHHHHHCCCCCHH-------------------HHHHHHHHCCCHHHHHHHHHHHHHHHCCC
Q ss_conf 98778-67763178801676665204776857-------------------89988753034256777788887541143
Q gi|254781115|r 246 LSQVI-EAEQVFEWKIDSLLRFIVLISWQDKK-------------------SILSMAKKFSLPREIRYFLISFFNCNFNQ 305 (416)
Q Consensus 246 l~~~~-~~~~~~~~~~~~~lrla~Ll~~~~~~-------------------~~~~~~~rlkl~~~~~~~l~~~~~~~~~~ 305 (416)
..+.. ........+.+..+||++|+|+++|. .+..+|+||++||..+........+|...
T Consensus 230 ~~h~l~~l~~a~~~~~~~~~RfaaL~hdlgK~~t~~~~~p~h~~he~~g~~~i~~lc~RLkvPn~~~~LA~lv~~~h~~~ 309 (413)
T PRK13298 230 GNYTMTGLSKISKLTKDIDIRFSYLCQFLGRMLNIINSSTKKVFFDKELASLIKNLCNRFKIPSEIRNLSKINSGFYKFL 309 (413)
T ss_pred HHHHHHHHHHHHHHCCCHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHH
T ss_conf 99999999999871798889999999863445787543420110234147999999998489799999999999999987
Q ss_pred CC---CCHHHHHHHHHHCC---CHHHHHHHHHHHHHH---CCCC---CCCCHHHHHHHHHHHHHCCCCCCCCCHHHHHHC
Q ss_conf 33---67246678998708---024551698999864---0777---601389999999877512888889887899965
Q gi|254781115|r 306 KT---LSIPEIKKLFYLYG---DKVMIAKLKIFLALH---YNNL---THQDTCFILQVLSDIIHWKKPLFPLTGDDVVKY 373 (416)
Q Consensus 306 ~~---~~~~~~~~~~~~~~---~~~~~~~l~~~~~~~---~~~~---~~~~~~~~~~~l~~~~~~~~p~~pI~G~dL~~~ 373 (416)
.. +....+-.++.... .......+...+... .... ..+....+...++... .|++++|++.
T Consensus 310 ~~~~~l~~~~ll~ll~~~Da~RrPer~~~~l~~c~ad~~~~~~~~~~~~~q~~~l~~a~~~a~-------sV~~~~li~~ 382 (413)
T PRK13298 310 YNIHYQSSKMIITFFSIIDAWRKPNRIRKLIFLNQFNLLRYKKNINYSFFQGNLLKYAFNVTK-------KISVKDIIKM 382 (413)
T ss_pred HHHHHCCHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHH-------CCCHHHHHHC
T ss_conf 404208999999999972752588999999999699885423654555608999999999986-------7998999877
Q ss_pred CCCCCHHHHHHHHHHHHHHHC
Q ss_conf 898777999999999999963
Q gi|254781115|r 374 GIPPGKKVGNILVHCKQEWIN 394 (416)
Q Consensus 374 Gi~pGp~iG~iL~~l~~~~i~ 394 (416)
|++ ||+||+.|++.+-..|+
T Consensus 383 G~~-G~~Ig~aL~~~Ri~ai~ 402 (413)
T PRK13298 383 GFK-GINIKNELYRLRIHALK 402 (413)
T ss_pred CCC-HHHHHHHHHHHHHHHHH
T ss_conf 997-39999999999999999
No 7
>PRK13297 tRNA CCA-pyrophosphorylase; Provisional
Probab=100.00 E-value=0 Score=482.18 Aligned_cols=344 Identities=19% Similarity=0.263 Sum_probs=253.9
Q ss_pred HHCCCEEEEEHHHHHHHHCCCCCCEEEE-EEECCHHHHHHHHHHCCCCEECCCCCCCEEEEEECCEEEEEECCCCCCCCC
Q ss_conf 9789859997069988877889860899-980898999999987699562134314469999899888642134466768
Q gi|254781115|r 23 NKGEDKSCIVGGAVRDSLMNLSVQDIDI-ATTILPDRVMRIFSKTRYKVIPTSISYGTIKIICRKKYFDITTLRSDLITD 101 (416)
Q Consensus 23 ~~~g~~~~~VGG~VRD~ll~~~~~DiD~-~~~~~~~~~~~~~~~~~~~~~~~~~~~gt~~~~~~~~~~di~~~R~e~~~~ 101 (416)
.-+|+++|+|||||||.|||++++|+|+ +|+++|+++.+ . +++++|.+||++ +......|++++|+|.++.
T Consensus 8 ~~aGm~~YLVGGaVRD~LLgr~~kD~D~VvtgAtPee~~~----~--g~~~VG~~F~v~--l~~~~~eE~alaRtE~k~g 79 (364)
T PRK13297 8 GVAGLQVYIVGGAVRDALLGLPAGDRDWVVVGATPEDMAR----R--GFIPVGGDFPVF--LHPRTKEEYALARTERKSG 79 (364)
T ss_pred CCCCCEEEEECCHHHHHHCCCCCCCEEEEECCCCHHHHHH----C--CCEEECCCEEEE--EECCCCEEEEEEEEEECCC
T ss_conf 1049869996609889974989988788647998999985----1--878528826999--9787554999998886378
Q ss_pred CCCCCCCC-C---HHHHHHCCCCCCCCCCEEECCCCHHHHHCCCHHHHHHHHHHHCCCCCCHHHCCCCCEEEEEEEEECC
Q ss_conf 87432233-2---0133210447800300200032101320000688878777642764310010421003320122013
Q gi|254781115|r 102 GRYAKVVF-T---RDWKADSLRRDFTINALYADQQGKVIDYVGGLNDLRNRTIKFIGDAHHRILEDYLRILRFFRFFAHY 177 (416)
Q Consensus 102 ~~~~~~~~-~---~~~~eDl~RRDFTINAla~~~~~~l~Dp~gG~~DL~~~~ir~v~~~~~rf~EDpLRiLRa~RFasrl 177 (416)
.++...++ . .|++|||.||||||||||++++|+|||||||++||++|+||+||+ +|.|||||||||+||+|||
T Consensus 80 ~g~~gf~~~~~~~vtLEeDL~RRDFTINAmA~d~~G~LIDpfgG~~DL~~riLR~v~~---aF~EDPLRiLRaaRFAArl 156 (364)
T PRK13297 80 RGYKGFTFYTGADVTLEQDLQRRDLTVNAIARTPQGELVDPLDGVADVRARVLRHVGE---AFAEDPVRILRLGRFAARF 156 (364)
T ss_pred CCCCCCEEECCCCCCHHHHHHHCCCCHHEEEECCCCCEECCCCCHHHHHCCCEECCCC---CCCCCHHHHHHHHHHHHHC
T ss_conf 7889964206999888999874256100469999998851898899995867416888---7565869999999999981
Q ss_pred CCCCCCCCCHHHHHHH--HHHCCCCCHHHHHHHHHHHHCCCCHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHH
Q ss_conf 6433111100012333--32102220577688788642110189999987530023346887010585789877867763
Q gi|254781115|r 178 GEKNIDSDGLVASIKA--KKGLKILSSERIWSEINKLLEAKNPLNAIVHMYNGGIFKEIFLDVQEISLDQLSQVIEAEQV 255 (416)
Q Consensus 178 g~f~id~~t~~ai~~~--~~~L~~iS~ERI~~El~KiL~~~~~~~~l~~L~~~gll~~ifpel~~~~~~~l~~~~~~~~~ 255 (416)
|+|+|+++|+.+|+++ ++.+..+|+||||.|+.|.|.+++|+.+|..|.++|.+..+|||+....... . +....
T Consensus 157 ~~F~I~~eT~~lm~~mv~~gel~~L~~ERvw~E~~k~L~~~~P~~~f~~L~~~gal~~~~Pe~~~~~~~~--~--~~d~~ 232 (364)
T PRK13297 157 GDFSIAPETMQLCRRMVEAGEADALVPERVWKEVSRGLMAQAPSRMLDVLARAGALARVMPELHDDAAVR--A--EIDRA 232 (364)
T ss_pred CCCEECHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCCHHHHCCCCCCCCCCC--H--HHHHH
T ss_conf 6875888899999998827767664456899999999768885999999998587788591628622246--6--69999
Q ss_pred CCCCCCHHHHHHHHCCCCCHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCC-CCHHHHHHHHHHCC---CHHHHHHHHH
Q ss_conf 1788016766652047768578998875303425677778888754114333-67246678998708---0245516989
Q gi|254781115|r 256 FEWKIDSLLRFIVLISWQDKKSILSMAKKFSLPREIRYFLISFFNCNFNQKT-LSIPEIKKLFYLYG---DKVMIAKLKI 331 (416)
Q Consensus 256 ~~~~~~~~lrla~Ll~~~~~~~~~~~~~rlkl~~~~~~~l~~~~~~~~~~~~-~~~~~~~~~~~~~~---~~~~~~~l~~ 331 (416)
.......-.||++|++..+. ...++++++.||..+.......++|.+... ......-+++...- +......+..
T Consensus 233 ~~~~~~l~~r~a~l~~~~~~--~~~l~~rl~vP~~~~~la~~~~~~~~~~~~~~~~~~~~~l~~~~d~~r~per~~~~l~ 310 (364)
T PRK13297 233 AAAGLPLAGRYALLCRHTPE--RDALGRRLRAPVECMDQARLLPLAVDALAASATPAAQLDLIERCDALRKPERFDALLQ 310 (364)
T ss_pred HHCCCCHHHHHHHHHCCCCH--HHHHHHHHCCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHCCCCHHHHHHHHH
T ss_conf 75279818899988167834--8999998289899999999999999864234898999999997440059289999999
Q ss_pred HHHHHCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCHHHHHHCCCCCCHHHHHHHHHHHHHHHC
Q ss_conf 998640777601389999999877512888889887899965898777999999999999963
Q gi|254781115|r 332 FLALHYNNLTHQDTCFILQVLSDIIHWKKPLFPLTGDDVVKYGIPPGKKVGNILVHCKQEWIN 394 (416)
Q Consensus 332 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~p~~pI~G~dL~~~Gi~pGp~iG~iL~~l~~~~i~ 394 (416)
.+.. . .......+.+.++... .|+..++.+.|...|.+||+.+++.+-..+.
T Consensus 311 a~~~---~-~~~~~~~~~~~~~a~~-------~v~a~~i~~~~~~~~a~i~~a~~~aR~~aia 362 (364)
T PRK13297 311 AAAI---V-APVDLSAWRARVQAVR-------AIDAGAIARQCAGDPARIKPALRQARLQALG 362 (364)
T ss_pred HHHH---H-CCCCHHHHHHHHHHHH-------CCCHHHHHHHCCCCHHHHHHHHHHHHHHHHH
T ss_conf 9864---1-4425699999999997-------5799999987279857899999999999974
No 8
>TIGR01942 pcnB poly(A) polymerase; InterPro: IPR010206 This entry 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.; GO: 0003723 RNA binding, 0004652 polynucleotide adenylyltransferase activity, 0006378 mRNA polyadenylation.
Probab=100.00 E-value=0 Score=463.13 Aligned_cols=224 Identities=31% Similarity=0.531 Sum_probs=206.2
Q ss_pred CCHHHHHHHHHHHHCCCEEEEEHHHHHHHHCCCCCCEEEEEEECCHHHHHHHHHHCCCCEECCCCCCCEEEEEECCEEEE
Q ss_conf 99889999999997898599970699888778898608999808989999999876995621343144699998998886
Q gi|254781115|r 11 HDSDLINILSLLNKGEDKSCIVGGAVRDSLMNLSVQDIDIATTILPDRVMRIFSKTRYKVIPTSISYGTIKIICRKKYFD 90 (416)
Q Consensus 11 ~~~~~~~i~~~l~~~g~~~~~VGG~VRD~ll~~~~~DiD~~~~~~~~~~~~~~~~~~~~~~~~~~~~gt~~~~~~~~~~d 90 (416)
-+..+.+|++.|+.+|||||||||||||+|||.+|||+|++|+|.|+++.++|.++. + +|..|.-|+|.++.+.||
T Consensus 14 ~S~~A~~Vv~rL~~AGyqAY~VGG~vRDLlLG~ePKDFDv~T~A~PE~v~~LFRN~R--i--vGRRFrlvHv~fG~~iIE 89 (448)
T TIGR01942 14 FSAHALNVVRRLKKAGYQAYIVGGAVRDLLLGIEPKDFDVATSATPEEVKKLFRNSR--I--VGRRFRLVHVSFGRQIIE 89 (448)
T ss_pred HHHHHHHHHHHHHHCCEEEEEECCHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHCCE--E--ECCCEEEEEEECCCCEEE
T ss_conf 649999999987007823767231587765479886442127896278998552055--6--404306888815880577
Q ss_pred EECCCC---CCC-------C---CCCCC-CCCCCHHHHHHCCCCCCCCCCEEECCC-CHHHHHCCCHHHHHHHHHHHCCC
Q ss_conf 421344---667-------6---88743-223320133210447800300200032-10132000068887877764276
Q gi|254781115|r 91 ITTLRS---DLI-------T---DGRYA-KVVFTRDWKADSLRRDFTINALYADQQ-GKVIDYVGGLNDLRNRTIKFIGD 155 (416)
Q Consensus 91 i~~~R~---e~~-------~---~~~~~-~~~~~~~~~eDl~RRDFTINAla~~~~-~~l~Dp~gG~~DL~~~~ir~v~~ 155 (416)
|||||. |.- + +|+.. +-++|+ +|||+.||||||||||||+. ..|+|+.||+.||++|.||+|||
T Consensus 90 VaTFR~HHgE~~~Gda~~~~~na~Gri~~DN~YG~-~EEDA~RRDFT~NALYYDP~~e~I~Dy~gG~~Dlk~R~LR~IGD 168 (448)
T TIGR01942 90 VATFRSHHGEDDEGDAKKSSANAEGRILKDNVYGS-LEEDALRRDFTVNALYYDPSKEVILDYVGGVEDLKARRLRLIGD 168 (448)
T ss_pred EECCCCCCCCCCCCCCHHCCCCCCCCEECCCCCCC-CCCCCCCCCCEECCEECCCCCCEEECCCCCHHHHHCCCCEECCC
T ss_conf 51225546888654210002288632333775301-01033335520421000753256750357678661781010178
Q ss_pred CCCHHHCCCCCEEEEEEEEECCCCCCCCCCCHHHHHHHHHHCCCCCHHHHHHHHHHHHCCCCHHHHHHHHHHCCCCCCCC
Q ss_conf 43100104210033201220136433111100012333321022205776887886421101899999875300233468
Q gi|254781115|r 156 AHHRILEDYLRILRFFRFFAHYGEKNIDSDGLVASIKAKKGLKILSSERIWSEINKLLEAKNPLNAIVHMYNGGIFKEIF 235 (416)
Q Consensus 156 ~~~rf~EDpLRiLRa~RFasrlg~f~id~~t~~ai~~~~~~L~~iS~ERI~~El~KiL~~~~~~~~l~~L~~~gll~~if 235 (416)
|..||+|||+|||||+||+++|+ |+|++.|...|++.++.|.++|+-|+++|+.|||.+......|+.|.+..++..+|
T Consensus 169 p~~Ry~EDPVRmLRA~r~~~kl~-f~i~~~t~~pI~~s~~~L~~~p~aRlfeE~~KllfSG~~~~~f~~l~~~~l~~~Lf 247 (448)
T TIGR01942 169 PEERYQEDPVRMLRALRFSSKLE-FTIDEKTAEPIRESAPLLKKIPPARLFEEILKLLFSGKSAILFKMLSEYKLLEPLF 247 (448)
T ss_pred HHHHCCCCCHHHHHHHHHHHHHC-CCCCHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHCCCHHHHHHHHHHCCCCHHHHH
T ss_conf 36531568578999999987722-67898999999998786227897714788999860424899999860565214643
Q ss_pred CCCCC
Q ss_conf 87010
Q gi|254781115|r 236 LDVQE 240 (416)
Q Consensus 236 pel~~ 240 (416)
|.+..
T Consensus 248 P~~~~ 252 (448)
T TIGR01942 248 PSVAK 252 (448)
T ss_pred HHHHH
T ss_conf 89999
No 9
>PRK13296 tRNA CCA-pyrophosphorylase; Provisional
Probab=100.00 E-value=0 Score=427.72 Aligned_cols=278 Identities=24% Similarity=0.295 Sum_probs=208.9
Q ss_pred CEEEEEHHHHHHHHCCCCCCEEEEEEE-CCHHHHHHHHHHCCCCEECCCCCCCEEEEEECCEEEEEECCCCCCCC-CCCC
Q ss_conf 859997069988877889860899980-89899999998769956213431446999989988864213446676-8874
Q gi|254781115|r 27 DKSCIVGGAVRDSLMNLSVQDIDIATT-ILPDRVMRIFSKTRYKVIPTSISYGTIKIICRKKYFDITTLRSDLIT-DGRY 104 (416)
Q Consensus 27 ~~~~~VGG~VRD~ll~~~~~DiD~~~~-~~~~~~~~~~~~~~~~~~~~~~~~gt~~~~~~~~~~di~~~R~e~~~-~~~~ 104 (416)
.++|+|||||||+|||++++|+|++|. ++|+++.. .+ ...+|..|++ ++..+...|++++|+|.++ +|++
T Consensus 1 MkiYLVGGaVRD~LLG~~~kDiDiVV~gat~ee~l~----~g--f~~Vgk~FpV--flh~~~~~E~alaRtE~k~~~G~~ 72 (360)
T PRK13296 1 MKFYLVGGAVRDMLLGITPKDKDWVVVGATEDEMLA----NG--FIKIAANFPV--FIHPQTKQEYALARSEKKTASGYH 72 (360)
T ss_pred CCEEEECCHHHHHHCCCCCCCEEEEECCCCHHHHHH----HC--CEEEECCCEE--EEECCCCEEEEEEEEEEECCCCCC
T ss_conf 979997219989975989999578747999899986----13--6677217289--997886669998755542257888
Q ss_pred C-CCCCCH--HHHHHCCCCCCCCCCEEECCCCHHHHHCCCHHHHHHHHHHHCCCCCCHHHCCCCCEEEEEEEEECCC--C
Q ss_conf 3-223320--1332104478003002000321013200006888787776427643100104210033201220136--4
Q gi|254781115|r 105 A-KVVFTR--DWKADSLRRDFTINALYADQQGKVIDYVGGLNDLRNRTIKFIGDAHHRILEDYLRILRFFRFFAHYG--E 179 (416)
Q Consensus 105 ~-~~~~~~--~~~eDl~RRDFTINAla~~~~~~l~Dp~gG~~DL~~~~ir~v~~~~~rf~EDpLRiLRa~RFasrlg--~ 179 (416)
+ .+.+.. +++|||.||||||||||+|.+|+|+|||||++||++|+||+|+ .+|.|||||||||+||+|||+ .
T Consensus 73 gf~V~~~~~vTLEEDL~RRDFTINAMA~D~~G~LIDPfgGl~DLk~kiLR~vs---~aF~EDPLRILRa~RFAARL~~~~ 149 (360)
T PRK13296 73 GFEVNFSKYITLEDDLKRRDLTINSIAIDQNNKVIDPFNGQADLQNRILRHTS---IAFIEDPLRVVRLARFKAQLSNFN 149 (360)
T ss_pred CCEEECCCCCCHHHHHHHCCCCCCEEEECCCCCEEECCCCHHHHHCCCCCCCC---CCCCCCHHHHHHHHHHHHHHCCCC
T ss_conf 85663599998899998546763417987999988689999999579888998---566658599999999999835499
Q ss_pred CCCCCCCHHHHHHH--HHHCCCCCHHHHHHHHHHHHCCCCHHHHHHHHHHCCCCCCCCCCCCCCCHHH-HHHHHHHHHHC
Q ss_conf 33111100012333--3210222057768878864211018999998753002334688701058578-98778677631
Q gi|254781115|r 180 KNIDSDGLVASIKA--KKGLKILSSERIWSEINKLLEAKNPLNAIVHMYNGGIFKEIFLDVQEISLDQ-LSQVIEAEQVF 256 (416)
Q Consensus 180 f~id~~t~~ai~~~--~~~L~~iS~ERI~~El~KiL~~~~~~~~l~~L~~~gll~~ifpel~~~~~~~-l~~~~~~~~~~ 256 (416)
|.|+++|+..|+++ ++.|..+|+||||.|+.|.|. +|+..+..|.+||.+..+|||+..+...- ..+..+.. .
T Consensus 150 F~i~~eT~~lm~~~v~~gel~~l~~eRvw~E~~k~l~--~p~~~~~~l~~~~al~~~~pe~~~~~~~~~~~~~~~~~--~ 225 (360)
T PRK13296 150 FSIAQEMLALIKELVKTGELNHLTRERLHIEFVKALN--NPKIFFTTLKELEALKIIFPNISCILPLIPNKSFFENP--I 225 (360)
T ss_pred CEECHHHHHHHHHHHHCCCHHHCCHHHHHHHHHHHHC--CCHHHHHHHHHCCCHHHHCCCHHHHHCCCCHHHHHHHC--C
T ss_conf 7886899999999985688121581277999999873--90989999998487888670513442125122233301--0
Q ss_pred CCCCCHHHHHHHHCCCCCHHHHHHHHHHCCCHHHHHHHHHHHHHHH--CCCCCCCHHHHHHHHHH
Q ss_conf 7880167666520477685789988753034256777788887541--14333672466789987
Q gi|254781115|r 257 EWKIDSLLRFIVLISWQDKKSILSMAKKFSLPREIRYFLISFFNCN--FNQKTLSIPEIKKLFYL 319 (416)
Q Consensus 257 ~~~~~~~lrla~Ll~~~~~~~~~~~~~rlkl~~~~~~~l~~~~~~~--~~~~~~~~~~~~~~~~~ 319 (416)
....++-.+.++++-..+......+..+++++|+..+.+....... ....+.+..++-.+++.
T Consensus 226 ~~~~~~e~k~~~~~~~~~~~~~~~i~~~~~~~n~~~~~~~~~~~~~k~~~~~~~~~~~il~~i~~ 290 (360)
T PRK13296 226 YKGSNINEKITLCLLKIPQQQLDDIRKELLLTNKHYKLLKASIAISKILEDRSITAEEIFQLIKN 290 (360)
T ss_pred CCCCCHHHHHHHHHHCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHH
T ss_conf 02698778899998504099999999986184889999999999999987603899999999997
No 10
>KOG2159 consensus
Probab=100.00 E-value=0 Score=416.99 Aligned_cols=375 Identities=26% Similarity=0.314 Sum_probs=257.3
Q ss_pred CHHHHHHHHHHHHCCCEEEEEHHHHHHHHCCCCCCEEEEEEECCHHHHHHHHHHCCCCEEC-CCCCC---C--------E
Q ss_conf 9889999999997898599970699888778898608999808989999999876995621-34314---4--------6
Q gi|254781115|r 12 DSDLINILSLLNKGEDKSCIVGGAVRDSLMNLSVQDIDIATTILPDRVMRIFSKTRYKVIP-TSISY---G--------T 79 (416)
Q Consensus 12 ~~~~~~i~~~l~~~g~~~~~VGG~VRD~ll~~~~~DiD~~~~~~~~~~~~~~~~~~~~~~~-~~~~~---g--------t 79 (416)
.+....+...+.+.|+++|+|||||||.|||++|+|+|++|++.+.++.+.|.....++.. .++.| | |
T Consensus 14 ~~~~~~v~~~~~~~~~elRiaGGwVRD~LLg~~p~DiDiatta~~g~~~e~f~~~~~~~~~~~~~~h~~~np~~skhlet 93 (416)
T KOG2159 14 TDSTRLVLSKLKKKGYELRLAGGWVRDLLLGREPKDIDIATTAMSGQMKEMFQSAQIRVGKKFPICHVIMGPIKSKHLET 93 (416)
T ss_pred CHHHHHHHHHHHCCCCEEEEECCCHHHHHCCCCCCCCCEEECCCCHHHHHHHHHHHHHHCCCCCCCEEECCCCCEEEECC
T ss_conf 47999999875138970688432178887289975502320225078999999877763356773023048751113020
Q ss_pred EEEEECCEEEEEECCCCCCCCCCCCCCCCCCHHHHHHCCCCCCCCCCEEECC-CCHHHHHCCCHHHHHHHHHHHCCCCCC
Q ss_conf 9999899888642134466768874322332013321044780030020003-210132000068887877764276431
Q gi|254781115|r 80 IKIICRKKYFDITTLRSDLITDGRYAKVVFTRDWKADSLRRDFTINALYADQ-QGKVIDYVGGLNDLRNRTIKFIGDAHH 158 (416)
Q Consensus 80 ~~~~~~~~~~di~~~R~e~~~~~~~~~~~~~~~~~eDl~RRDFTINAla~~~-~~~l~Dp~gG~~DL~~~~ir~v~~~~~ 158 (416)
+++.+.+..+|++++|.+.|++...|.+.+++ ..+|+.||||||||++|++ +|.++|++||.+||++++||+|++|.+
T Consensus 94 at~~i~~~~iD~v~lr~~~y~e~~~~~~~dgt-~~~nalRRD~TIN~Lffn~~~~~VeDytgG~eDL~~~kvrt~~~A~~ 172 (416)
T KOG2159 94 ATFRITTLRIDFVNLRREAYTETSIPYVTDGT-RDENALRRDFTINSLFFNPFDGTVEDYTGGLEDLKNKKVRTVLHAKQ 172 (416)
T ss_pred EEEEEECCCCCEEECCCCCCCCCCCCCCCCCC-CHHHHHHHCCCHHHHHCCCCCCCEEECCCCHHHHHCCEEEEECCCCC
T ss_conf 00244112022010476322235788777673-40345652122123340677770222214676772272885416521
Q ss_pred HHHCCCCCEEEEEEEEECCCCCCC---CCCCHHHHHHHHHHCCCCCHHHHHHHHHHHHCCCCHHHHHHHHHH-CCCCCCC
Q ss_conf 001042100332012201364331---111000123333210222057768878864211018999998753-0023346
Q gi|254781115|r 159 RILEDYLRILRFFRFFAHYGEKNI---DSDGLVASIKAKKGLKILSSERIWSEINKLLEAKNPLNAIVHMYN-GGIFKEI 234 (416)
Q Consensus 159 rf~EDpLRiLRa~RFasrlg~f~i---d~~t~~ai~~~~~~L~~iS~ERI~~El~KiL~~~~~~~~l~~L~~-~gll~~i 234 (416)
||.||||||||++||++||| |++ +.+|+.+++.++.++++||+||||.|+.|||.++++..++.+|++ .++....
T Consensus 173 tf~eDpLRILR~iRFaaRlg-ftid~~~~e~~~~~k~~~~~~~kIS~ERI~~Ei~kmL~g~~~~~~L~ll~~~~~~~~i~ 251 (416)
T KOG2159 173 TFLEDPLRILRGIRFAARLG-FTIDEESKETLEAIKENVALLAKISRERIGVEINKMLVGNSAEASLRLLWRLFGFEYIF 251 (416)
T ss_pred EECCCHHHHHHHHHHHHHHC-CCCCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCEEEE
T ss_conf 01425599999988887634-76571208777548888887523668889999999972884888999999725804873
Q ss_pred CCCCCCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHCCCCCHHHHHHHHHHCCCHHHHHHHHHHHHHHHCC---CCCCCHH
Q ss_conf 8870105857898778677631788016766652047768578998875303425677778888754114---3336724
Q gi|254781115|r 235 FLDVQEISLDQLSQVIEAEQVFEWKIDSLLRFIVLISWQDKKSILSMAKKFSLPREIRYFLISFFNCNFN---QKTLSIP 311 (416)
Q Consensus 235 fpel~~~~~~~l~~~~~~~~~~~~~~~~~lrla~Ll~~~~~~~~~~~~~rlkl~~~~~~~l~~~~~~~~~---~~~~~~~ 311 (416)
+|-.. +..++..... .-.....++..++.|++..-.... ..+.+++++-. ....+...... ....+..
T Consensus 252 lp~~~--s~~~f~~~~~---~~~~s~~~~sl~~~l~~~~~~~~~--~~~~l~l~~~~--~~~~~~~~~r~~~v~~~~~~~ 322 (416)
T KOG2159 252 LPIEA--SLEEFQGFNR---RDGFSNEPLSLLANLDKSLAPDEP--CHLRLKLSILE--LLKKFIDQPRFPTVPAVSSSA 322 (416)
T ss_pred CCCHH--HHHHCCCCCC---CCCCCHHHHHHHHCCCCCCCCCCH--HHHHHHHHHHH--HHHHHHCCCCCCCEEEEECCC
T ss_conf 36516--6544155442---122103079987060002355404--55667877776--666763265545301110114
Q ss_pred HHHHHHHHCC--CHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCHHHHHHCCCCCCHHHHHHHHHHH
Q ss_conf 6678998708--02455169899986407776013899999998775128888898878999658987779999999999
Q gi|254781115|r 312 EIKKLFYLYG--DKVMIAKLKIFLALHYNNLTHQDTCFILQVLSDIIHWKKPLFPLTGDDVVKYGIPPGKKVGNILVHCK 389 (416)
Q Consensus 312 ~~~~~~~~~~--~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~p~~pI~G~dL~~~Gi~pGp~iG~iL~~l~ 389 (416)
.+.. ..... .........+...+. .+.. -...-+....|..|.+|++++|+...|...|+.+|..++++.
T Consensus 323 ~~~~-~~~~~i~~~i~~~~~~~~~~l~-----~~~~--~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~g~llr~l~ 394 (416)
T KOG2159 323 PLSK-LQDVEIPKKIEKDHDRLRQLLV-----SQEK--NELDNETLLDWSVPDFPISINDLAIEGTSKGSIIGALLRYLQ 394 (416)
T ss_pred CHHH-HHHHHCCCCCCCCHHHHHHHHC-----CHHH--HHHHHHHHHHHCCCCHHHHHHHHHHHHCCCCHHHHHHHHHHH
T ss_conf 2113-5565245223441577888851-----2676--566888776521586177899999864111056778998654
Q ss_pred HHHHCCCCCCCHHHHH
Q ss_conf 9996388888989999
Q gi|254781115|r 390 QEWINSSFQLSQEDLH 405 (416)
Q Consensus 390 ~~~i~~~~~n~~e~l~ 405 (416)
..|-+.-+......+.
T Consensus 395 ~~w~~~~~~~~~~~~l 410 (416)
T KOG2159 395 APWSDSVFTSLKDSLL 410 (416)
T ss_pred HHHHHHHHHHHHHHHH
T ss_conf 5678777689888774
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=2e-39 Score=283.46 Aligned_cols=136 Identities=37% Similarity=0.513 Sum_probs=121.4
Q ss_pred CHHHHHHHHHHHHC-CCEEEEEHHHHHHHHCCCCCCEEEEEEECCHHHHH-HHHHHCCCCEECCCCCCCEEEEEECCEEE
Q ss_conf 98899999999978-98599970699888778898608999808989999-99987699562134314469999899888
Q gi|254781115|r 12 DSDLINILSLLNKG-EDKSCIVGGAVRDSLMNLSVQDIDIATTILPDRVM-RIFSKTRYKVIPTSISYGTIKIICRKKYF 89 (416)
Q Consensus 12 ~~~~~~i~~~l~~~-g~~~~~VGG~VRD~ll~~~~~DiD~~~~~~~~~~~-~~~~~~~~~~~~~~~~~gt~~~~~~~~~~ 89 (416)
.|++.+++..+.++ |+++|+|||||||+|||++++|+||+|++.+.+++ +++.+.+.+.+..+.+|||+++..++..+
T Consensus 1 ~~~~~~~l~~l~~~~g~~~ylVGG~VRD~llg~~~~DiDi~v~~~~~~~~~~l~~~~~~~~v~~~~~~g~~~v~~~~~~~ 80 (139)
T cd05398 1 TPELLKLLRELKKALGYEAYLVGGAVRDLLLGRPPKDIDIATDADGPEFAEALFKKIGGRVVGLGEEFGTATVVINGLTI 80 (139)
T ss_pred CHHHHHHHHHHHHHCCCEEEEECHHHHHHHCCCCCCCCEEEECCCCHHHHHHHHHHCCCCEEECCCCCCEEEEEECCEEE
T ss_conf 90699999999985599899986899999849999875698618879999999987397177426545634898899689
Q ss_pred EEECCCCCCCCCCCCCCCCCCHHHHHHCCCCCCCCCCEEECC-CCHHHHHCCCHHHHHH
Q ss_conf 642134466768874322332013321044780030020003-2101320000688878
Q gi|254781115|r 90 DITTLRSDLITDGRYAKVVFTRDWKADSLRRDFTINALYADQ-QGKVIDYVGGLNDLRN 147 (416)
Q Consensus 90 di~~~R~e~~~~~~~~~~~~~~~~~eDl~RRDFTINAla~~~-~~~l~Dp~gG~~DL~~ 147 (416)
|||++|+|.|+.+++.+.+...++++||.|||||||||||++ +|+|+|||||++||++
T Consensus 81 di~~~R~e~~~~~~~~~~~~~~~i~~Dl~RRDFTINAma~~l~~g~liDp~~G~~DL~n 139 (139)
T cd05398 81 DVATLRTETYTDPGRRPPVVGFTIEEDLLRRDFTINAMAYDLDDGELIDPFGGLKDLEN 139 (139)
T ss_pred EEEECCCCCCCCCCCCCCCCCCCCHHHHCCCCCEEEEEEECCCCCEEEECCCCHHHCCC
T ss_conf 98642344556788676334678167652577601556730799928818899878079
No 12
>pfam01743 PolyA_pol Poly A polymerase head domain. This family includes nucleic acid independent RNA polymerases, such as Poly(A) polymerase, which adds the poly (A) tail to mRNA EC:2.7.7.19. This family also includes the tRNA nucleotidyltransferase that adds the CCA to the 3' of the tRNA EC:2.7.7.25.
Probab=100.00 E-value=1.1e-37 Score=271.79 Aligned_cols=123 Identities=38% Similarity=0.588 Sum_probs=113.7
Q ss_pred EEEEHHHHHHHHCCCCCCEEEEEEECCHHHHHHHHHHCCCCEECCCCCCCEEEEEECCEEEEEECCCCCCCC-CCCCCC-
Q ss_conf 999706998887788986089998089899999998769956213431446999989988864213446676-887432-
Q gi|254781115|r 29 SCIVGGAVRDSLMNLSVQDIDIATTILPDRVMRIFSKTRYKVIPTSISYGTIKIICRKKYFDITTLRSDLIT-DGRYAK- 106 (416)
Q Consensus 29 ~~~VGG~VRD~ll~~~~~DiD~~~~~~~~~~~~~~~~~~~~~~~~~~~~gt~~~~~~~~~~di~~~R~e~~~-~~~~~~- 106 (416)
+|+|||||||+|||++++|+|++|+++|+++++.|.+.....+..+.+|||+++..++..+||+++|+|.|. ++++|.
T Consensus 1 iyiVGG~VRD~llg~~~~DiD~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~ei~~~R~e~~~~~~~~~~~ 80 (126)
T pfam01743 1 LYLVGGAVRDLLLGRPPKDVDIATDAGPEQVATLFRNRIIVHLESGKEFGTIHVLFGNQILEVATFRTESDESDFRNPKS 80 (126)
T ss_pred CEEECHHHHHHHCCCCCCCEEEEECCCHHHHHHHHHHHCCCCCCCCCCCCEEEEEECCCCEEEEEEECCCCCCCCCCCCC
T ss_conf 98945799999859999878999569789999999985174422475231478874586211005530123367757643
Q ss_pred CCCCHHHHHHCCCCCCCCCCEEECC-CCHHHHHCCCHHHHHHHHHH
Q ss_conf 2332013321044780030020003-21013200006888787776
Q gi|254781115|r 107 VVFTRDWKADSLRRDFTINALYADQ-QGKVIDYVGGLNDLRNRTIK 151 (416)
Q Consensus 107 ~~~~~~~~eDl~RRDFTINAla~~~-~~~l~Dp~gG~~DL~~~~ir 151 (416)
+.++.+|++||.|||||||||||++ .|+|+|||||++||++|+||
T Consensus 81 ~~~~~~i~~Dl~rRDFTiNAia~~l~~g~iiDp~~G~~DL~~~~iR 126 (126)
T pfam01743 81 EEFTGTLEEDLKRRDFTINALAYDPNDGEVIDPFGGIKDLKNGVIR 126 (126)
T ss_pred CCCCCCHHHHHCCCCCEEEEEEEECCCCEEEECCCCHHHHHCCCCC
T ss_conf 5258897885433166300255317999598289999999758879
No 13
>PRK05092 PII uridylyl-transferase; Provisional
Probab=99.32 E-value=2.8e-11 Score=95.04 Aligned_cols=197 Identities=13% Similarity=0.119 Sum_probs=138.7
Q ss_pred CHHHCCCCCEEEEEEEEECCCCCCCCCCCHHHHHHHHHHCCC--CCHHHHHHHHHHHHCCC-CHHHHHHHHHHCCCCCCC
Q ss_conf 100104210033201220136433111100012333321022--20577688788642110-189999987530023346
Q gi|254781115|r 158 HRILEDYLRILRFFRFFAHYGEKNIDSDGLVASIKAKKGLKI--LSSERIWSEINKLLEAK-NPLNAIVHMYNGGIFKEI 234 (416)
Q Consensus 158 ~rf~EDpLRiLRa~RFasrlg~f~id~~t~~ai~~~~~~L~~--iS~ERI~~El~KiL~~~-~~~~~l~~L~~~gll~~i 234 (416)
..|..||..+||.|..+++.| ..|+|+|+..+..+.+.+.. -...+.+..|..||.++ ++..+++.|.++|+|..+
T Consensus 398 ~~f~~dP~~llrlF~~a~~~~-l~i~p~t~r~i~~~~~li~~~~r~~~~a~~~Fl~iL~~~~~~~~~Lr~M~e~GvLg~~ 476 (934)
T PRK05092 398 DVFERDPVNLIRLFHLADRHG-LEIHPDAMRLVTRSLRLIDAALREDPEANRLFLDILTSRNNPERILRRMNEAGVLGRF 476 (934)
T ss_pred CHHHHCHHHHHHHHHHHHHCC-CCCCHHHHHHHHHHHHHCCHHHCCCHHHHHHHHHHHCCCCCHHHHHHHHHHCCCHHHH
T ss_conf 046669999999999998739-9879899999999887455642389999999999972898669999999983871320
Q ss_pred CCCCCCCCH------------HH-HHHHHHH----------------HHH-CCCCCCHHHHHHHHCCCCCH---------
Q ss_conf 887010585------------78-9877867----------------763-17880167666520477685---------
Q gi|254781115|r 235 FLDVQEISL------------DQ-LSQVIEA----------------EQV-FEWKIDSLLRFIVLISWQDK--------- 275 (416)
Q Consensus 235 fpel~~~~~------------~~-l~~~~~~----------------~~~-~~~~~~~~lrla~Ll~~~~~--------- 275 (416)
+|+...+-. ++ ..+.+.. ... .......++++|+||||.+|
T Consensus 477 iPeF~~I~g~mQfD~yH~YTVDeHtL~~v~~L~~i~~g~~~~e~P~~s~l~~~i~~~~lLylA~LlHDIGKGrggDHS~~ 556 (934)
T PRK05092 477 IPDFGRIVAMMQFNMYHHYTVDEHLIRAIGVLAEIERGELEDEHPLASRLMRTIKSRRALYVAVLLHDIAKGRPEDHSIA 556 (934)
T ss_pred CCCHHHHEECCCCCCHHCCCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCCCHHHH
T ss_conf 66325311032455201274008999999999998633220132789999871576778999999877515888865788
Q ss_pred --HHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCC-------CCHHHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCCCCHH
Q ss_conf --78998875303425677778888754114333-------672466789987080245516989998640777601389
Q gi|254781115|r 276 --KSILSMAKKFSLPREIRYFLISFFNCNFNQKT-------LSIPEIKKLFYLYGDKVMIAKLKIFLALHYNNLTHQDTC 346 (416)
Q Consensus 276 --~~~~~~~~rlkl~~~~~~~l~~~~~~~~~~~~-------~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~ 346 (416)
..+..+|.|+.++.++...+..++++|..+.. ..+.-+..+....+....++.+.++..+......+..+.
T Consensus 557 GA~~A~~~~~RlGL~~~d~elV~wLV~~HLlMS~tAqrRDi~Dp~tI~~FA~~V~s~erL~~LylLTvADIrAtgP~vWN 636 (934)
T PRK05092 557 GARIARRLCPRLGLSPAETETVAWLVEHHLLMSDTAQKRDLSDPKTIEDFADAVQSPERLKLLLILTVADIRAVGPGVWN 636 (934)
T ss_pred HHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCCCHHH
T ss_conf 89999999998599878999999999999878889874378987999999997299999999999998664056864024
Q ss_pred HHHH-HHHHH
Q ss_conf 9999-99877
Q gi|254781115|r 347 FILQ-VLSDI 355 (416)
Q Consensus 347 ~~~~-~l~~~ 355 (416)
-|.. ++.++
T Consensus 637 ~WKa~LL~~L 646 (934)
T PRK05092 637 GWKAQLLRTL 646 (934)
T ss_pred HHHHHHHHHH
T ss_conf 7899999999
No 14
>TIGR01693 UTase_glnD protein-P-II uridylyltransferase; InterPro: IPR010043 This entry describes GlnD, the uridylyltransferase/uridylyl-removing enzyme for signal-transduction protein PII, and acts as the sensory component of the nitrogen regulation (ntr) system . The ntr system modulates nitrogen metabolism in response to the prevailing nitrogen source and the requirements of the cell. During nitrogen fixation, ammonia and 2-oxoglutarate can be used to produce glutamate. The activity of the PII protein is stimulated by glutamine and inhibited by 2-oxoglutarate. Under glutamate-limiting conditions, PII is uridylylated by GlnD leading to the activation of glutamate synthetase and to the stimulation of NtrC-dependent promoters. Under high concentrations of fixed nitrogen, PII is de-uridylylated leading to the inactivation of the glutamate synthetase pathway and switching off NtrC-dependent promoters . Not all homologues of PII share the property of uridylyltransferase modification on the characteristic Tyr residue (see IPR002332 from INTERPRO), but the modification site is preserved in the PII homologue of all species with a member of this family. ; GO: 0008773 [protein-PII] uridylyltransferase activity, 0006807 nitrogen compound metabolic process.
Probab=99.15 E-value=1.2e-10 Score=90.71 Aligned_cols=246 Identities=13% Similarity=0.119 Sum_probs=159.0
Q ss_pred CCHHHCCCCCEEEEEEEEECCCC-CCCCCCCHHHHHHHHHHCCCCCH--HHHHHHHHHHHCC-CCHHHHHHHHHHCCCCC
Q ss_conf 31001042100332012201364-33111100012333321022205--7768878864211-01899999875300233
Q gi|254781115|r 157 HHRILEDYLRILRFFRFFAHYGE-KNIDSDGLVASIKAKKGLKILSS--ERIWSEINKLLEA-KNPLNAIVHMYNGGIFK 232 (416)
Q Consensus 157 ~~rf~EDpLRiLRa~RFasrlg~-f~id~~t~~ai~~~~~~L~~iS~--ERI~~El~KiL~~-~~~~~~l~~L~~~gll~ 232 (416)
...|++||-+|||.|-.+++.|. ..|+|+|+..+..+...|+.-=+ ++-...|..||.+ +....+|..|.++|++-
T Consensus 356 ~~~Fe~dP~~~l~lF~~~~~~g~i~~~~p~alr~l~~~~~~l~~~~r~~~~A~~~Fl~ll~~~~~~~~~l~~Mn~~GvLg 435 (903)
T TIGR01693 356 TAVFEEDPALLLRLFAIAAQRGEILPIHPDALRQLTASLRLLDTPLREDPEAREKFLELLTSGNAIVRALRAMNRAGVLG 435 (903)
T ss_pred CCCCCCCHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHCCCHH
T ss_conf 76770463479999999616787100127899999998852271236577888999998607862789999864216023
Q ss_pred CCCCCCCCCCH------------H-HHHHHHHHHHH-----------------CCCCCCHHHHHHHHCCCCCH-------
Q ss_conf 46887010585------------7-89877867763-----------------17880167666520477685-------
Q gi|254781115|r 233 EIFLDVQEISL------------D-QLSQVIEAEQV-----------------FEWKIDSLLRFIVLISWQDK------- 275 (416)
Q Consensus 233 ~ifpel~~~~~------------~-~l~~~~~~~~~-----------------~~~~~~~~lrla~Ll~~~~~------- 275 (416)
-.+||...+-. + ...+....... ......-++++|+||||.+|
T Consensus 436 R~lPef~~I~g~mQfdlfH~YTVDeH~l~~~~~l~~~~~~~~~~~hPla~~l~~~i~dp~lL~lAaLlHDIgKGRgGDHs 515 (903)
T TIGR01693 436 RFLPEFGRIVGQMQFDLFHVYTVDEHTLRAVKHLAKIAAGRLAEEHPLASELIPKIEDPELLYLAALLHDIGKGRGGDHS 515 (903)
T ss_pred HHCCCCCCCCCCCCCCCEEEEECHHHHHHHHHHHHHHCCCCHHHHCCHHHHHCCCCCCHHHHHHHHHHHHCCCCCCCCHH
T ss_conf 41343345037887576255410289999999987511610243255166751468866799999998513688996688
Q ss_pred ----HHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCC-------CCHHHHHHHHHHCC-CHHHHHHHHHHHHHHCCCCCCC
Q ss_conf ----78998875303425677778888754114333-------67246678998708-0245516989998640777601
Q gi|254781115|r 276 ----KSILSMAKKFSLPREIRYFLISFFNCNFNQKT-------LSIPEIKKLFYLYG-DKVMIAKLKIFLALHYNNLTHQ 343 (416)
Q Consensus 276 ----~~~~~~~~rlkl~~~~~~~l~~~~~~~~~~~~-------~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~~~~~~~ 343 (416)
..+..+|.|+.+++.....+..++++|..+.. ..+.-+..+...++ ++..++.+..+.-....-..+.
T Consensus 516 ~~GA~~A~~~C~R~GL~~~~~~~vawLVr~HLlmS~tAqRRDl~DP~tv~~FA~~v~G~~~~L~~L~~LTVADI~AtgP~ 595 (903)
T TIGR01693 516 VLGAEDARDVCQRLGLDRPDTELVAWLVRNHLLMSITAQRRDLNDPETVFAFAEAVGGDEERLEYLLVLTVADIRATGPG 595 (903)
T ss_pred HHHHHHHHHHHHHCCCCHHHHHHHHHHHHHCCCCCCCCEECCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHCCCCC
T ss_conf 98599999998753889889999999986003254210001589738999999983688768899999978756215878
Q ss_pred CHH-HHHHHHHHHHHCCCCCCCCCHHHHHHCCCCCCHHHHH---HHHHHHHHHHCCCCC-CCHHHHHHHHHH
Q ss_conf 389-9999998775128888898878999658987779999---999999999638888-898999999999
Q gi|254781115|r 344 DTC-FILQVLSDIIHWKKPLFPLTGDDVVKYGIPPGKKVGN---ILVHCKQEWINSSFQ-LSQEDLHHLLRK 410 (416)
Q Consensus 344 ~~~-~~~~~l~~~~~~~~p~~pI~G~dL~~~Gi~pGp~iG~---iL~~l~~~~i~~~~~-n~~e~l~~~lk~ 410 (416)
.|. +..++++.+.... +.++.-|..+--..-+ --+.+..+.+..++. .+..+...+..+
T Consensus 596 vWnsWK~sLlr~Ly~~T--------~~vl~gG~~~~~~~~~~~~~~~~la~~~l~~~ysg~~~~~~~~l~~~ 659 (903)
T TIGR01693 596 VWNSWKASLLRELYNET--------EQVLRGGLEEPADKEEQIAEQRKLAVALLRKDYSGKTSNEIEVLWLR 659 (903)
T ss_pred CCHHHHHHHHHHHHHHH--------HHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHH
T ss_conf 55446888999999999--------99971477644679999999999999998510688881358999997
No 15
>PRK01759 glnD PII uridylyl-transferase; Provisional
Probab=99.13 E-value=1.4e-09 Score=83.73 Aligned_cols=192 Identities=15% Similarity=0.115 Sum_probs=135.9
Q ss_pred CHHHCCCCCEEEEEEEEECCCCCCCCCCCHHHHHHHHHHCCC-C-CHHHHHHHHHHHHCCCCH-HHHHHHHHHCCCCCCC
Q ss_conf 100104210033201220136433111100012333321022-2-057768878864211018-9999987530023346
Q gi|254781115|r 158 HRILEDYLRILRFFRFFAHYGEKNIDSDGLVASIKAKKGLKI-L-SSERIWSEINKLLEAKNP-LNAIVHMYNGGIFKEI 234 (416)
Q Consensus 158 ~rf~EDpLRiLRa~RFasrlg~f~id~~t~~ai~~~~~~L~~-i-S~ERI~~El~KiL~~~~~-~~~l~~L~~~gll~~i 234 (416)
..|..+|..|||.|.+.++.+.-.+++.|+..++...+.+.. . ...+.+..|..||.+++. ..++..|+++|++..+
T Consensus 345 ~~f~~~P~~il~lF~~~a~~~~~~i~~~tlr~lr~~~~~i~~~~~~~p~~r~~F~~il~~p~~~~~~l~~M~~~GvL~~y 424 (862)
T PRK01759 345 DCFTETPASILDLFFYLTQYPHAEIHSDTLRQLYIALHQLGQPLSELPAARERFLRLFNQPNAIKRALVPMHQYGVLTAY 424 (862)
T ss_pred CHHHHCHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHCCCHHHCCHHHHHHHHHHHCCCCCHHHHHHHHHHHCCHHHH
T ss_conf 05652989999999999857799869779999999998567421008588999999982988579999999982878988
Q ss_pred CCCCCCCC------------HH--------HHHHHHHHHH---------H-CCCCCCHHHHHHHHCCCCCH---------
Q ss_conf 88701058------------57--------8987786776---------3-17880167666520477685---------
Q gi|254781115|r 235 FLDVQEIS------------LD--------QLSQVIEAEQ---------V-FEWKIDSLLRFIVLISWQDK--------- 275 (416)
Q Consensus 235 fpel~~~~------------~~--------~l~~~~~~~~---------~-~~~~~~~~lrla~Ll~~~~~--------- 275 (416)
+|+...+- -+ .+.++...+. . .......++++|+|+||.+|
T Consensus 425 iPef~~I~g~mQfDlfH~YTVDeHtl~~v~~l~~~~~~~~~~~~P~~~~i~~~l~~~~lL~LAaLfHDIgKGrggDHSel 504 (862)
T PRK01759 425 LPQWKHIEGLMQFDLFHIYTVDEHTLRVMLKLESFLDEETAEQHPICHQIFSQLSDRTLLYIAALFHDIAKGRGGDHAEL 504 (862)
T ss_pred HHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCHHCCHHHHHHHCCCCHHHHHHHHHHHHHHCCCCCCHHHH
T ss_conf 47888774364754355784768999999999998613200104359999872465889999999999716788865899
Q ss_pred --HHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCC-------CCHHHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCCCCHH
Q ss_conf --78998875303425677778888754114333-------672466789987080245516989998640777601389
Q gi|254781115|r 276 --KSILSMAKKFSLPREIRYFLISFFNCNFNQKT-------LSIPEIKKLFYLYGDKVMIAKLKIFLALHYNNLTHQDTC 346 (416)
Q Consensus 276 --~~~~~~~~rlkl~~~~~~~l~~~~~~~~~~~~-------~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~ 346 (416)
..+..+|+++.++.++...+..+++.|..+.. ..+.-+..+....+....++.+.++.........+..+.
T Consensus 505 GA~~a~~f~~r~gl~~~d~elv~wLV~~HLlMS~~AqrrDi~Dp~vI~~FA~~V~~~erL~~LylLTvADi~AT~p~~WN 584 (862)
T PRK01759 505 GAVDMAQFAQQHGFDPREIETMAWLVQEHLLMSITAQRRDIHDPEVVMNFAEEVQNQVRLDYLTCLTVADICATNETLWN 584 (862)
T ss_pred HHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCHHHHHHHHHHHHHHHHCCCCCHHH
T ss_conf 99999999998599999999999999989999999986289987999999997599999999999998787403811456
Q ss_pred HHH
Q ss_conf 999
Q gi|254781115|r 347 FIL 349 (416)
Q Consensus 347 ~~~ 349 (416)
.|.
T Consensus 585 ~WK 587 (862)
T PRK01759 585 SWK 587 (862)
T ss_pred HHH
T ss_conf 889
No 16
>PRK03381 PII uridylyl-transferase; Provisional
Probab=99.12 E-value=1.3e-10 Score=90.55 Aligned_cols=187 Identities=13% Similarity=0.044 Sum_probs=129.0
Q ss_pred HHHCCCCCEEEEEEEEECCCCCCCCCCCHHHHHHHHHHCCCCCHHHHHHHHHHHHCC-CCHHHHHHHHHHCCCCCCCCCC
Q ss_conf 001042100332012201364331111000123333210222057768878864211-0189999987530023346887
Q gi|254781115|r 159 RILEDYLRILRFFRFFAHYGEKNIDSDGLVASIKAKKGLKILSSERIWSEINKLLEA-KNPLNAIVHMYNGGIFKEIFLD 237 (416)
Q Consensus 159 rf~EDpLRiLRa~RFasrlg~f~id~~t~~ai~~~~~~L~~iS~ERI~~El~KiL~~-~~~~~~l~~L~~~gll~~ifpe 237 (416)
.|..||..+||.+..+++.| ..+++.|+..+..+.+.++.--+..-+..|..||.+ ++...+++.|+++|++..++|+
T Consensus 326 ~~~~dp~~~Lr~~~~a~~~~-l~i~~~t~~~l~~~~~~l~~~~~~~~~~~f~~il~~~~~~~~~l~~m~~~GvL~~~iPe 404 (781)
T PRK03381 326 RPERDPGLVLRVAAAAATTG-LPLAAATLSRLAATAPPLPTPWPAEARDDLLVLLGAGPAAVAVIEALDRTGLWGRLLPE 404 (781)
T ss_pred CHHHCHHHHHHHHHHHHHCC-CCCCHHHHHHHHHHCHHCCCCCCHHHHHHHHHHHCCCCCHHHHHHHHHHCCCHHHHCCC
T ss_conf 52139799999999963528-87699999999984721256788999999999974899658999998760868775864
Q ss_pred CCCCCH------------HHH--HHHHHHHHH-CCCCCCHHHHHHHHCCCCCH-----------HHHHHHHHHCCCHHHH
Q ss_conf 010585------------789--877867763-17880167666520477685-----------7899887530342567
Q gi|254781115|r 238 VQEISL------------DQL--SQVIEAEQV-FEWKIDSLLRFIVLISWQDK-----------KSILSMAKKFSLPREI 291 (416)
Q Consensus 238 l~~~~~------------~~l--~~~~~~~~~-~~~~~~~~lrla~Ll~~~~~-----------~~~~~~~~rlkl~~~~ 291 (416)
...+-. ++. ......... .......++++|+||||.+| +.+..+|+|+.++.++
T Consensus 405 f~~i~~~~Q~D~yH~YTVD~H~l~~~~~a~~l~~~v~~p~lL~lAaLlHDIGKGrggDHS~~Ga~~a~~~~~rlgl~~~d 484 (781)
T PRK03381 405 WEAVRDLPQRDVVHRWTVDRHLVETAVRAAALTRRVARPDLLLLGALLHDIGKGRGGDHSVAGAELARQIGTRLGLWPSD 484 (781)
T ss_pred HHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHCCCCHHH
T ss_conf 45320676776450155216899999999999862653589999998606621578864667599999999986999899
Q ss_pred HHHHHHHHHHHCCCCC-------CCHHHHHHHHHHCCC-HHHHHHHHHHHHHHCCCCCCCCHH
Q ss_conf 7778888754114333-------672466789987080-245516989998640777601389
Q gi|254781115|r 292 RYFLISFFNCNFNQKT-------LSIPEIKKLFYLYGD-KVMIAKLKIFLALHYNNLTHQDTC 346 (416)
Q Consensus 292 ~~~l~~~~~~~~~~~~-------~~~~~~~~~~~~~~~-~~~~~~l~~~~~~~~~~~~~~~~~ 346 (416)
...+..++++|..+.. ..+.-+..+....|. ...++.+.++.........+..+.
T Consensus 485 ~~~v~~LV~~HLlMs~tAqRrDi~DP~vI~~FA~~Vgs~~~~L~~LylLTvADi~ATgP~~Wn 547 (781)
T PRK03381 485 VDLLSKLVRHHLLLPETATRRDLDDPATIEAVAEALGGDPQLLELLHALTEADSLATGPGVWS 547 (781)
T ss_pred HHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHCCCCCCCCCCCH
T ss_conf 999999999999899999763789879999999996544999999887760521056963006
No 17
>PRK00275 glnD PII uridylyl-transferase; Provisional
Probab=99.08 E-value=8.7e-10 Score=85.05 Aligned_cols=191 Identities=14% Similarity=0.092 Sum_probs=131.0
Q ss_pred CHHHCCCCCEEEEEEEEECCCCC-CCCCCCHHHHHHHHHHCCCC-C-HHHHHHHHHHHHCCCC-HHHHHHHHHHCCCCCC
Q ss_conf 10010421003320122013643-31111000123333210222-0-5776887886421101-8999998753002334
Q gi|254781115|r 158 HRILEDYLRILRFFRFFAHYGEK-NIDSDGLVASIKAKKGLKIL-S-SERIWSEINKLLEAKN-PLNAIVHMYNGGIFKE 233 (416)
Q Consensus 158 ~rf~EDpLRiLRa~RFasrlg~f-~id~~t~~ai~~~~~~L~~i-S-~ERI~~El~KiL~~~~-~~~~l~~L~~~gll~~ 233 (416)
..|.+||..++|.|..+++-... .+.+.|+.+++.+.+.+..- . ..+...-|..||.++. +..+++.|+++|+|..
T Consensus 360 ~~f~~~P~~ll~lF~~~a~~~~i~gi~~~t~r~ir~~~~~id~~~r~~~~~~~~Fl~iL~~~~~~~~~Lr~M~~~GvLg~ 439 (894)
T PRK00275 360 NVFKRTPFALLEIFVLMAQHPEIKGVRADTIRLLREHRHLIDDAFRNDIRNTSLFIELFKCPHGIHRNLRRMNRYGILGR 439 (894)
T ss_pred HHHHCCHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHCCHHHCCCHHHHHHHHHHHHCCCCHHHHHHHHHHCCCHHH
T ss_conf 44430948899999999858675676846899999877527955300988789999997088877999999987597331
Q ss_pred CCCCCCCCCH------------H--------HHHHHHH---------HHHHC-CCCCCHHHHHHHHCCCCCH--------
Q ss_conf 6887010585------------7--------8987786---------77631-7880167666520477685--------
Q gi|254781115|r 234 IFLDVQEISL------------D--------QLSQVIE---------AEQVF-EWKIDSLLRFIVLISWQDK-------- 275 (416)
Q Consensus 234 ifpel~~~~~------------~--------~l~~~~~---------~~~~~-~~~~~~~lrla~Ll~~~~~-------- 275 (416)
++|+...+-. + .+.++.. ....+ ......++++|+|+||.+|
T Consensus 440 ~iPef~~I~g~mQfD~yH~YTVDeHtl~~v~~L~~~~~~~~~~~~p~~~~l~~~l~~~~lLylA~L~HDIGKGrggDHS~ 519 (894)
T PRK00275 440 YLPEFGHIVGQMQHDLFHIYTVDAHTLNLIKHLRKLRYPEVSEKFPLASKLMGRLPKPELLYIAGLYHDIGKGRGGDHSE 519 (894)
T ss_pred CCCCHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHCHHCCCCCHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCCCHHH
T ss_conf 09967765255244410026121779999999999857010102467799885267677999999864640488898056
Q ss_pred ---HHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCC-------CCHHHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCCCCH
Q ss_conf ---78998875303425677778888754114333-------67246678998708024551698999864077760138
Q gi|254781115|r 276 ---KSILSMAKKFSLPREIRYFLISFFNCNFNQKT-------LSIPEIKKLFYLYGDKVMIAKLKIFLALHYNNLTHQDT 345 (416)
Q Consensus 276 ---~~~~~~~~rlkl~~~~~~~l~~~~~~~~~~~~-------~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~ 345 (416)
..+..+|+|+.+|.++...+..++++|..+.. ..+.-+..+....+....++.+.++.........+..+
T Consensus 520 ~GA~~A~~~~~r~gl~~~d~elv~wLV~~HLlMS~tAqRrDi~DP~vI~~FA~~Vgs~erL~~LylLTvADi~Atgp~~W 599 (894)
T PRK00275 520 LGAVDAEAFCQRHQLPAWDTRLVVWLVENHLVMSTTAQRKDLSDPQVIHDFALAVGDETHLDYLYVLTVADINATNPTLW 599 (894)
T ss_pred HHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCCCHH
T ss_conf 67999999999869987898999999998998888986148998799999999809788999987666754416782223
Q ss_pred HHH
Q ss_conf 999
Q gi|254781115|r 346 CFI 348 (416)
Q Consensus 346 ~~~ 348 (416)
..|
T Consensus 600 N~W 602 (894)
T PRK00275 600 NSW 602 (894)
T ss_pred HHH
T ss_conf 478
No 18
>PRK04374 PII uridylyl-transferase; Provisional
Probab=98.99 E-value=7.2e-10 Score=85.60 Aligned_cols=192 Identities=13% Similarity=0.082 Sum_probs=133.2
Q ss_pred CHHHCCCCCEEEEEEEEECCC-CCCCCCCCHHHHHHHHHHCC--CCCHHHHHHHHHHHHCCCCHHHHHHHHHHCCCCCCC
Q ss_conf 100104210033201220136-43311110001233332102--220577688788642110189999987530023346
Q gi|254781115|r 158 HRILEDYLRILRFFRFFAHYG-EKNIDSDGLVASIKAKKGLK--ILSSERIWSEINKLLEAKNPLNAIVHMYNGGIFKEI 234 (416)
Q Consensus 158 ~rf~EDpLRiLRa~RFasrlg-~f~id~~t~~ai~~~~~~L~--~iS~ERI~~El~KiL~~~~~~~~l~~L~~~gll~~i 234 (416)
..|.+||+.+||.+-..++.. -..+.+.|+..+....+.+. .-+....+.-|..||.++++..++..|+++|+|..+
T Consensus 350 ~~~~~~p~~ll~lf~~~~~~~~i~~i~~~t~r~l~~~~~~i~~~~~~~~~~r~~Fl~iL~~p~~~~~L~~M~~~GvL~~y 429 (869)
T PRK04374 350 SWPDGDVLQVFALFAQWAAHREVRGLHSLTARALAEVLRDLPAYDVADATARERFMALLRGPRAVETLNRMARLGVLGQW 429 (869)
T ss_pred CCCCCCHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHCCHHHH
T ss_conf 12101899999999998638653577655899999765537821148989999999980798637999998872869999
Q ss_pred CCCCCCCCH------------HH-HHHHHHHH----------------HHC-CCCCCHHHHHHHHCCCCCH---------
Q ss_conf 887010585------------78-98778677----------------631-7880167666520477685---------
Q gi|254781115|r 235 FLDVQEISL------------DQ-LSQVIEAE----------------QVF-EWKIDSLLRFIVLISWQDK--------- 275 (416)
Q Consensus 235 fpel~~~~~------------~~-l~~~~~~~----------------~~~-~~~~~~~lrla~Ll~~~~~--------- 275 (416)
+|+...+-. ++ ....+... ..+ ......++++|+||||.+|
T Consensus 430 iPef~~I~g~mQfDlfH~YTVDeHTl~~v~~l~~f~~~~~~~~~p~~~~l~~~l~kpelL~LAaLfHDIgKGrggDHS~l 509 (869)
T PRK04374 430 IPAFASVSGRMQFDLFHVYTVDQHTLMVLRNIALFAAGRADERFSIAHEVWPRLRKPELLLLAGLFHDIAKGRGGDHSEL 509 (869)
T ss_pred HHHHHHHHCCCCCCHHHCCCHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHCCCCHHHHHHHHHHHHHHCCCCCCHHHH
T ss_conf 88999873872443023070768999999999998544444226069999871476889999999888625888765899
Q ss_pred --HHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCC-------CCHHHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCCCCHH
Q ss_conf --78998875303425677778888754114333-------672466789987080245516989998640777601389
Q gi|254781115|r 276 --KSILSMAKKFSLPREIRYFLISFFNCNFNQKT-------LSIPEIKKLFYLYGDKVMIAKLKIFLALHYNNLTHQDTC 346 (416)
Q Consensus 276 --~~~~~~~~rlkl~~~~~~~l~~~~~~~~~~~~-------~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~ 346 (416)
..+..+|+++.++.++...+..++++|..+.. ..+.-+..+....|+...++.+.++.........+..+.
T Consensus 510 GA~~A~~f~~r~gl~~~d~~lv~wLV~~HLlMS~tAqRrDi~DP~vI~~FA~~Vg~~~rL~~LylLTvADi~AT~p~~WN 589 (869)
T PRK04374 510 GAVDARAFCLAHRLSEGDTELVTWLVEQHLRMSVTAQKQDISDPEVIHRFATLVGTRERLDYLYLLTCADIAGTSPKLWN 589 (869)
T ss_pred HHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCHHHHHHHHHHHHHHHHCCCCCHHH
T ss_conf 89999999998499988999999999999999999985089988999999998399999999999999998522844114
Q ss_pred HHH
Q ss_conf 999
Q gi|254781115|r 347 FIL 349 (416)
Q Consensus 347 ~~~ 349 (416)
-|.
T Consensus 590 ~WK 592 (869)
T PRK04374 590 AWK 592 (869)
T ss_pred HHH
T ss_conf 899
No 19
>PRK05007 PII uridylyl-transferase; Provisional
Probab=98.97 E-value=4e-09 Score=80.60 Aligned_cols=190 Identities=14% Similarity=0.086 Sum_probs=130.4
Q ss_pred HHHCCCCCEEEEEEEEECCCCC-CCCCCCHHHHHHHHHHCCC--CCHHHHHHHHHHHHCCCCH-HHHHHHHHHCCCCCCC
Q ss_conf 0010421003320122013643-3111100012333321022--2057768878864211018-9999987530023346
Q gi|254781115|r 159 RILEDYLRILRFFRFFAHYGEK-NIDSDGLVASIKAKKGLKI--LSSERIWSEINKLLEAKNP-LNAIVHMYNGGIFKEI 234 (416)
Q Consensus 159 rf~EDpLRiLRa~RFasrlg~f-~id~~t~~ai~~~~~~L~~--iS~ERI~~El~KiL~~~~~-~~~l~~L~~~gll~~i 234 (416)
-|.+||..|||.|..+++-+.. .|.+.|+..++.....+.. -.....+..|..||..++. ..+++.|+++|++..+
T Consensus 359 ~f~~~P~~il~lF~~~a~~~~i~gi~~~tlr~lr~~~~~i~~~~~~~p~~r~~F~~iL~~p~~~~~~L~~M~~~GvL~~y 438 (881)
T PRK05007 359 LFQRQPEAILRMFLLMARNSNITGIYSTTLRQLRHARRHLNQPLCEIPEARKLFMEILRHPGAVSRALSPMHRHSVLSAY 438 (881)
T ss_pred HHHHCHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHCCCHHCCCHHHHHHHHHHHHCCCCHHHHHHHHHHCCCHHHH
T ss_conf 54319899999999998567755679799999999877457031059799999999981888579999999872889886
Q ss_pred CCCCCCCCH------------H--------HHHHHHHHH---------HHC-CCCCCHHHHHHHHCCCCCH---------
Q ss_conf 887010585------------7--------898778677---------631-7880167666520477685---------
Q gi|254781115|r 235 FLDVQEISL------------D--------QLSQVIEAE---------QVF-EWKIDSLLRFIVLISWQDK--------- 275 (416)
Q Consensus 235 fpel~~~~~------------~--------~l~~~~~~~---------~~~-~~~~~~~lrla~Ll~~~~~--------- 275 (416)
+|+...+.. + .+.++...+ ..+ ......++++|+||||.+|
T Consensus 439 lPef~~I~g~mQfDlfH~YTVDeHTl~~i~~l~~~~~~~~~~~~pl~~~l~~~l~~~~lLylA~LfHDIgKGrggDHS~l 518 (881)
T PRK05007 439 LPQWSHIVGQMQFDLFHAYTVDEHTIRVLLKIESFAQEETRQRHPLCVELYPRLPKKELLLLAALFHDIAKGRGGDHSKL 518 (881)
T ss_pred CCHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHCCCHHHHHHHHHHHHHCCCCCCCHHHH
T ss_conf 62477750663557762354008899999999998463223225268999872576778999999876126889984652
Q ss_pred --HHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCC-------CCHHHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCCCCHH
Q ss_conf --78998875303425677778888754114333-------672466789987080245516989998640777601389
Q gi|254781115|r 276 --KSILSMAKKFSLPREIRYFLISFFNCNFNQKT-------LSIPEIKKLFYLYGDKVMIAKLKIFLALHYNNLTHQDTC 346 (416)
Q Consensus 276 --~~~~~~~~rlkl~~~~~~~l~~~~~~~~~~~~-------~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~ 346 (416)
..+..+|+++.++.++...+..+++.|..+.. ..+.-+..+....++...++.+.++.........+..+.
T Consensus 519 GA~~a~~f~~r~gl~~~d~~lv~wLV~~HLlMS~tAqRRDI~DP~vI~~FA~~V~~~erL~~LylLTvADi~AT~p~~WN 598 (881)
T PRK05007 519 GAQDALDFCELHGLNSRETQLVAWLVRNHLLMSVTAQRRDIQDPDVIKQFAEEVRDEVRLRYLVCLTVADICATNETLWN 598 (881)
T ss_pred HHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCHHHHHHHHHHHHHHHHCCCCCCCH
T ss_conf 18999999998599988999999999999988899986489988999999870496888999999999998624911000
Q ss_pred HH
Q ss_conf 99
Q gi|254781115|r 347 FI 348 (416)
Q Consensus 347 ~~ 348 (416)
-|
T Consensus 599 ~W 600 (881)
T PRK05007 599 SW 600 (881)
T ss_pred HH
T ss_conf 77
No 20
>PRK00227 glnD PII uridylyl-transferase; Provisional
Probab=98.95 E-value=2.1e-09 Score=82.47 Aligned_cols=176 Identities=15% Similarity=0.068 Sum_probs=123.0
Q ss_pred HHCCCCCEEEEEEEEECCCCCCCCCCCHHHHHHHHHHCCCCCHHHHHHHHHHHHCCC-CHHHHHHHHHHCCCCCCCCCCC
Q ss_conf 010421003320122013643311110001233332102220577688788642110-1899999875300233468870
Q gi|254781115|r 160 ILEDYLRILRFFRFFAHYGEKNIDSDGLVASIKAKKGLKILSSERIWSEINKLLEAK-NPLNAIVHMYNGGIFKEIFLDV 238 (416)
Q Consensus 160 f~EDpLRiLRa~RFasrlg~f~id~~t~~ai~~~~~~L~~iS~ERI~~El~KiL~~~-~~~~~l~~L~~~gll~~ifpel 238 (416)
..+||..+||.+.-+++.| ..+.+.|...+.+..+....- .......|..||.++ ++..+++.|+++|++..++||.
T Consensus 289 ~~~dP~llLrlf~~aa~~~-l~i~~~t~r~l~~~~~l~~~~-~~~a~~~Fl~IL~sp~~~~~~Lr~M~~~GVLgryIPEF 366 (692)
T PRK00227 289 DLTDPALPLRVAAAAAKTG-LPVSESTWKRLNECPPLPEPW-PAAAAGDFFRILSSPVNSRRVVKQMDRHGLWSRYVPEW 366 (692)
T ss_pred CCCCCHHHHHHHHHHHHCC-CCCCHHHHHHHHHCCCCCCCC-CHHHHHHHHHHHCCCCCHHHHHHHHHHHCCHHHHCCHH
T ss_conf 5448078999999876539-976989999998381036777-79999999999849986689999987735679867007
Q ss_pred CCCCH------------HH-HHHHHH--HHHHCCCCCCHHHHHHHHCCCCCH-----------HHHHHHHHHCCCHHHHH
Q ss_conf 10585------------78-987786--776317880167666520477685-----------78998875303425677
Q gi|254781115|r 239 QEISL------------DQ-LSQVIE--AEQVFEWKIDSLLRFIVLISWQDK-----------KSILSMAKKFSLPREIR 292 (416)
Q Consensus 239 ~~~~~------------~~-l~~~~~--~~~~~~~~~~~~lrla~Ll~~~~~-----------~~~~~~~~rlkl~~~~~ 292 (416)
..+-. ++ ....+. ...........++++|+||||.+| +.+..+|+|+.++..+.
T Consensus 367 g~IvgqMQfDlfH~YTVDeHtL~~v~~~a~~~~~v~rpeLLylAaLlHDIGKGrggDHS~~GA~~A~~~c~RlGl~~~dt 446 (692)
T PRK00227 367 DRIRGLMPREPSHISTIDEHSLNTVAGCALETVTVARPDLLVLGALYHDIGKGTDRPHEQVGAEMVARAASRMGLNLRDR 446 (692)
T ss_pred HHHCCCCCCCCCEECCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHCCCCHHHH
T ss_conf 86517757665501640178999999998753367882799999998940478999867887999999999859999999
Q ss_pred HHHHHHHHHHCCCCC-------CCHHHHHHHHHHCC-CHHHHHHHHHHHHHHC
Q ss_conf 778888754114333-------67246678998708-0245516989998640
Q gi|254781115|r 293 YFLISFFNCNFNQKT-------LSIPEIKKLFYLYG-DKVMIAKLKIFLALHY 337 (416)
Q Consensus 293 ~~l~~~~~~~~~~~~-------~~~~~~~~~~~~~~-~~~~~~~l~~~~~~~~ 337 (416)
..+..++++|..+.. -.+..+..+....+ +..-+..+.++.....
T Consensus 447 elV~wLVr~HLlMS~tAqRRDisDP~tI~~fa~~V~~~~~rL~lL~~LTvADi 499 (692)
T PRK00227 447 ASVQTLVAEHTTIAKIAARLDPSSEEAVDKLLDAVRYDLVTLNLLEVLTEADA 499 (692)
T ss_pred HHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHH
T ss_conf 99999999886210877325899889999999986798899999999999874
No 21
>PRK03059 PII uridylyl-transferase; Provisional
Probab=98.94 E-value=2.2e-09 Score=82.37 Aligned_cols=190 Identities=15% Similarity=0.121 Sum_probs=130.0
Q ss_pred HHHCCCCCEEEEEEEEECCCC-CCCCCCCHHHHHHHHHHCCCC--CHHHHHHHHHHHHCCCC-HHHHHHHHHHCCCCCCC
Q ss_conf 001042100332012201364-331111000123333210222--05776887886421101-89999987530023346
Q gi|254781115|r 159 RILEDYLRILRFFRFFAHYGE-KNIDSDGLVASIKAKKGLKIL--SSERIWSEINKLLEAKN-PLNAIVHMYNGGIFKEI 234 (416)
Q Consensus 159 rf~EDpLRiLRa~RFasrlg~-f~id~~t~~ai~~~~~~L~~i--S~ERI~~El~KiL~~~~-~~~~l~~L~~~gll~~i 234 (416)
-|..||..+||.|..+++-.. ..+++.|+..+..+.+.+..- +.+.-...|..||.+++ ...+++.|+++|++..+
T Consensus 342 ~f~~~P~~ll~~F~~~~~~~~~~gi~~~tlr~i~~~~~~i~~~~r~~~~~~~~F~~iL~~~~~~~~~l~~M~~~GvL~~~ 421 (857)
T PRK03059 342 LFERHPHAILEAFLLYQQTPGLKGLSARTLRALYNARDVMDAAFRRDPVNRALFMQILQQPRGITHALRLMNQTSVLGRY 421 (857)
T ss_pred CHHCCHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHCCHHHHCCHHHHHHHHHHHCCCCCHHHHHHHHHHHCCHHHH
T ss_conf 00019899999999998477745789779999999877379666328788999999973898589999999874862753
Q ss_pred CCCCCCCCH------------HH--------HHHHHHHH---------HHC-CCCCCHHHHHHHHCCCCCH---------
Q ss_conf 887010585------------78--------98778677---------631-7880167666520477685---------
Q gi|254781115|r 235 FLDVQEISL------------DQ--------LSQVIEAE---------QVF-EWKIDSLLRFIVLISWQDK--------- 275 (416)
Q Consensus 235 fpel~~~~~------------~~--------l~~~~~~~---------~~~-~~~~~~~lrla~Ll~~~~~--------- 275 (416)
+|+...+-. ++ +.++...+ ... ......++++|+|+||.+|
T Consensus 422 iPef~~I~g~mQfD~yH~YTVDeHtl~~v~~l~~~~~~~~~~e~p~~~~l~~~~~~p~lL~LA~L~HDIgKGrggDHS~~ 501 (857)
T PRK03059 422 LPNFRRIVGQMQHDLFHVYTVDQHILMVLRNLRRFAMAEHAHEYPFCSQLIAGFDRPWLLYVAALFHDIAKGRGGDHSEL 501 (857)
T ss_pred CCCHHHHHCCCCCCCHHHCCHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHCCCCHHHHHHHHHHHHHHCCCCCCHHHH
T ss_conf 66578671663455024160637899999999997432100004057899854798469999999988517888973777
Q ss_pred --HHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCC-------CCHHHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCCCCHH
Q ss_conf --78998875303425677778888754114333-------672466789987080245516989998640777601389
Q gi|254781115|r 276 --KSILSMAKKFSLPREIRYFLISFFNCNFNQKT-------LSIPEIKKLFYLYGDKVMIAKLKIFLALHYNNLTHQDTC 346 (416)
Q Consensus 276 --~~~~~~~~rlkl~~~~~~~l~~~~~~~~~~~~-------~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~ 346 (416)
..+..+|.|+.++.++...+..++++|..+.. ..+.-+..+....++...+..+.++.........+..+.
T Consensus 502 GA~~a~~~~~r~gl~~~d~~lv~wLV~~HLlMS~tAqrrDi~Dp~vI~~FA~~Vg~~erL~~LylLTvADi~Atgp~~WN 581 (857)
T PRK03059 502 GAADARRFCRQHGIAREDAELVVWLVEHHLTMSQVAQKQDLSDPEVIAAFAELVGDERRLTALYLLTVADIRGTSPKVWN 581 (857)
T ss_pred HHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHCCCHHHHHHHHHHHHHHHHCCCCCHHH
T ss_conf 69999999998599989999999999846288889852799985999999987399999999887889887434800335
Q ss_pred HH
Q ss_conf 99
Q gi|254781115|r 347 FI 348 (416)
Q Consensus 347 ~~ 348 (416)
-|
T Consensus 582 ~W 583 (857)
T PRK03059 582 AW 583 (857)
T ss_pred HH
T ss_conf 78
No 22
>COG2844 GlnD UTP:GlnB (protein PII) uridylyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=98.36 E-value=2.4e-06 Score=62.02 Aligned_cols=190 Identities=14% Similarity=0.056 Sum_probs=123.7
Q ss_pred HHCCCCCEEEEEEEEECCCCCCCCCCCHHHHHHHHHHCCC-CC-HHHHHHHHHHHHC-CCCHHHHHHHHHHCCCCCCCCC
Q ss_conf 0104210033201220136433111100012333321022-20-5776887886421-1018999998753002334688
Q gi|254781115|r 160 ILEDYLRILRFFRFFAHYGEKNIDSDGLVASIKAKKGLKI-LS-SERIWSEINKLLE-AKNPLNAIVHMYNGGIFKEIFL 236 (416)
Q Consensus 160 f~EDpLRiLRa~RFasrlg~f~id~~t~~ai~~~~~~L~~-iS-~ERI~~El~KiL~-~~~~~~~l~~L~~~gll~~ifp 236 (416)
|..||-.|||-|-.+.+.|.-...++|+.+.....+.|+. +. -+.=..=|..||. .+++..++..|.+.|++...+|
T Consensus 349 f~~dP~~ilrlf~~~~~~~~~~~~~~Tlr~L~~a~~~l~~~l~~~peA~~~Fl~il~~~~~~~r~l~~Mn~~GVLgrylP 428 (867)
T COG2844 349 FERDPEAILRLFAIMAQTGLITGHPDTLRQLRRALRLLNQPLREDPEARRLFLSILRSPNAIRRTLRPMNRYGVLGRYLP 428 (867)
T ss_pred HHCCHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHCC
T ss_conf 22086999999999864388555748999999750125861113988999999998389857899997777434887553
Q ss_pred CCCCCC------------HHH-HHHHHH-HHH------H----------CCCCCCHHHHHHHHCCCCCH-----------
Q ss_conf 701058------------578-987786-776------3----------17880167666520477685-----------
Q gi|254781115|r 237 DVQEIS------------LDQ-LSQVIE-AEQ------V----------FEWKIDSLLRFIVLISWQDK----------- 275 (416)
Q Consensus 237 el~~~~------------~~~-l~~~~~-~~~------~----------~~~~~~~~lrla~Ll~~~~~----------- 275 (416)
+...+- .++ ..+.+. ... . .......++++++|+||.+|
T Consensus 429 ew~~Ivg~MQfdlfH~YTVDeH~lr~v~~l~~~a~~~~~~~hPl~~~l~~~~~~~elLylAaLfHDIaKGRggDHs~lGA 508 (867)
T COG2844 429 EWGKIVGLMQFDLFHIYTVDEHTLRVVLKLARFARGEARHEHPLASQLMPRLEKRELLYLAALFHDIAKGRGGDHSILGA 508 (867)
T ss_pred CHHHHHCCCCCCCCEECCHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCHHHHHH
T ss_conf 37765402466743012242999999998887501212334752676503788731999999988862378986677619
Q ss_pred HHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCC-------CCHHHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCCCCHHHH
Q ss_conf 78998875303425677778888754114333-------67246678998708024551698999864077760138999
Q gi|254781115|r 276 KSILSMAKKFSLPREIRYFLISFFNCNFNQKT-------LSIPEIKKLFYLYGDKVMIAKLKIFLALHYNNLTHQDTCFI 348 (416)
Q Consensus 276 ~~~~~~~~rlkl~~~~~~~l~~~~~~~~~~~~-------~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~ 348 (416)
..+..+|.+..++.++...+..+++.|..+.. .++.-+..+....++..-+..+..+.........+..+.-|
T Consensus 509 ~~a~~fc~~hGL~~~e~~lvaWLVe~HLlMS~tAQrrDl~Dp~vI~~Fa~~Vq~~~rL~~L~~LTVaDI~AtgP~vWN~W 588 (867)
T COG2844 509 EDARRFCERHGLNSRETELVAWLVENHLLMSVTAQRRDLNDPKVIDAFAEAVQDEERLRYLLVLTVADIRATGPGVWNSW 588 (867)
T ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCHHHHHHHHHHHHHHHHCCCCCHHHHH
T ss_conf 99999999829987776899999998777678887617898699999999856889988999988776506686503788
Q ss_pred H
Q ss_conf 9
Q gi|254781115|r 349 L 349 (416)
Q Consensus 349 ~ 349 (416)
.
T Consensus 589 K 589 (867)
T COG2844 589 K 589 (867)
T ss_pred H
T ss_conf 9
No 23
>PHA01806 hypothetical protein
Probab=97.04 E-value=0.0011 Score=44.19 Aligned_cols=122 Identities=20% Similarity=0.270 Sum_probs=66.5
Q ss_pred EEEEEHHHHHHHHCCCCCCEEEEEE-ECCHHHHHHHHHHCCCCEEC-------------C----CCCCCEEEEE----EC
Q ss_conf 5999706998887788986089998-08989999999876995621-------------3----4314469999----89
Q gi|254781115|r 28 KSCIVGGAVRDSLMNLSVQDIDIAT-TILPDRVMRIFSKTRYKVIP-------------T----SISYGTIKII----CR 85 (416)
Q Consensus 28 ~~~~VGG~VRD~ll~~~~~DiD~~~-~~~~~~~~~~~~~~~~~~~~-------------~----~~~~gt~~~~----~~ 85 (416)
.+-++|||.||.+-|..|+|||++- +++-..+.++.........| . +.-+|++.++ .+
T Consensus 42 G~alaGG~~RDL~hg~~PkDiDialysms~~rae~l~~~~~p~l~p~~~r~ggws~eyad~gd~~~f~gv~~L~Gcr~l~ 121 (205)
T PHA01806 42 GAALAGGCARDLMHGVEPKDIDIALYSMSQDRAEKLIAGSLPELDPRALRGGGWSSEYADGGDSDIFKGVMSLVGCRGLE 121 (205)
T ss_pred CCHHHCCCHHHHHCCCCCCCCCEEEEECCHHHHHHHHHCCCCCCCCHHCCCCCCEEECCCCCCCCCCCCEEEEEEEECCC
T ss_conf 62110655588765788654313432212678999875026545622104883322205566677412415676320357
Q ss_pred CEEEEEECCCCCCCCCCCCCCCCCCHHHHHHCCCCCCCCCCE--EECCCCHHHHHCCC-------HHHHHHHHHHHCCCC
Q ss_conf 988864213446676887432233201332104478003002--00032101320000-------688878777642764
Q gi|254781115|r 86 KKYFDITTLRSDLITDGRYAKVVFTRDWKADSLRRDFTINAL--YADQQGKVIDYVGG-------LNDLRNRTIKFIGDA 156 (416)
Q Consensus 86 ~~~~di~~~R~e~~~~~~~~~~~~~~~~~eDl~RRDFTINAl--a~~~~~~l~Dp~gG-------~~DL~~~~ir~v~~~ 156 (416)
+..+|+--+-. .++-+-+.-=|||||-. ||+. -||-+| -+|..=|+=|-|+-
T Consensus 122 g~dvDf~~Y~a--------------dslgrvlesFDytlNQvgiay~w----pdpe~gprlgaylhkdvtwGVnrei~~- 182 (205)
T PHA01806 122 GMDVDFNLYNA--------------DSLGRVLESFDYTLNQVGIAYNW----PDPEDGPRLGAYLHKDVTWGVNREIGG- 182 (205)
T ss_pred CCCCCEEEECC--------------HHHHHHHHHHCCCHHHEEEEEEC----CCCCCCCCHHHEEECCCEECCCCCCCC-
T ss_conf 86444577512--------------37888998824104444688606----997888522102312301213400158-
Q ss_pred CCHHHCCCCCEE
Q ss_conf 310010421003
Q gi|254781115|r 157 HHRILEDYLRIL 168 (416)
Q Consensus 157 ~~rf~EDpLRiL 168 (416)
..|..|+.-+|+
T Consensus 183 gsRl~Er~ekmr 194 (205)
T PHA01806 183 GSRLPERAEKMR 194 (205)
T ss_pred CCCCHHHHHHHH
T ss_conf 889778999999
No 24
>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=95.96 E-value=0.12 Score=30.51 Aligned_cols=109 Identities=17% Similarity=0.149 Sum_probs=70.3
Q ss_pred HHHHHHHHHHHCCCEEEEEHHHHHHHHCCCC--CCEEEEEEE-CCHHHHHHHHHHCCCCEECCC------CCCCEEEEEE
Q ss_conf 8999999999789859997069988877889--860899980-898999999987699562134------3144699998
Q gi|254781115|r 14 DLINILSLLNKGEDKSCIVGGAVRDSLMNLS--VQDIDIATT-ILPDRVMRIFSKTRYKVIPTS------ISYGTIKIIC 84 (416)
Q Consensus 14 ~~~~i~~~l~~~g~~~~~VGG~VRD~ll~~~--~~DiD~~~~-~~~~~~~~~~~~~~~~~~~~~------~~~gt~~~~~ 84 (416)
.+..|.+.++..+. .|.|||.+.=++-|.+ |+||||-|+ -+.+++.++|...+.+.+..- ..| -.+.+
T Consensus 5 ~L~~i~~~l~~~nI-~W~v~gS~~l~~~Gl~~~p~DIDi~~d~~~~~~i~~if~~~~~~~~~~~s~~~~~s~F--ge~~I 81 (156)
T cd07749 5 ALRKFYERLKNINV-NWALTGSLSFALQGVPVEPHDIDIQTDNEGAYEIERIFHEFVNTEVRFSESEGIRSHF--GELQI 81 (156)
T ss_pred HHHHHHHHHCCCCC-EEEEHHHHHHHHCCCCCCCCCCEEEECHHHHHHHHHHHHHHCCCCCCCCCCCCHHCEE--EEEEE
T ss_conf 99999997343796-3983135889975999998623478624009999999999605677778765110000--48898
Q ss_pred CCEEEEEECCCCCC-CCCCCCCCCCCCHHHHHHCCCCCCCCCCEEECC
Q ss_conf 99888642134466-768874322332013321044780030020003
Q gi|254781115|r 85 RKKYFDITTLRSDL-ITDGRYAKVVFTRDWKADSLRRDFTINALYADQ 131 (416)
Q Consensus 85 ~~~~~di~~~R~e~-~~~~~~~~~~~~~~~~eDl~RRDFTINAla~~~ 131 (416)
+|..+||.. .-+. ..+|.....+... -.-|=+.||.|....
T Consensus 82 ~g~~VdIM~-d~~~~~~~g~~e~p~d~~-----~~~~~vei~G~~IPv 123 (156)
T cd07749 82 DGIKVEIMG-DVQKRLEDGWWETPVDLN-----RYKRFVEVEGMKIPV 123 (156)
T ss_pred CCEEEEEEC-CEEEECCCCEEECCCCCH-----HHHHHHEECCEECCC
T ss_conf 788889962-516751897671552431-----355440276677356
No 25
>pfam10706 Aminoglyc_resit Aminoglycoside-2''-adenylyltransferase. This family 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.
Probab=95.56 E-value=0.026 Score=34.99 Aligned_cols=76 Identities=18% Similarity=0.133 Sum_probs=53.0
Q ss_pred HHHHHHHHHHHCCCEEEEEHHHHHHHHCCCCC---CEEEEEEECCH-HHHHHHHHHCCCCEECCCCCCCEEEEEECCEEE
Q ss_conf 89999999997898599970699888778898---60899980898-999999987699562134314469999899888
Q gi|254781115|r 14 DLINILSLLNKGEDKSCIVGGAVRDSLMNLSV---QDIDIATTILP-DRVMRIFSKTRYKVIPTSISYGTIKIICRKKYF 89 (416)
Q Consensus 14 ~~~~i~~~l~~~g~~~~~VGG~VRD~ll~~~~---~DiD~~~~~~~-~~~~~~~~~~~~~~~~~~~~~gt~~~~~~~~~~ 89 (416)
-+..|+..+.+.|..+|+-|||-=|++|||.. .|||++.+++- .++..++...++ ++-..-+||.. ...+|..+
T Consensus 8 lI~~il~~ad~~~lp~Wi~GGWaIDA~lGRiTR~H~DIDl~~P~d~~ae~~~ll~~~g~-~i~eq~dYGFL-aq~~g~Ll 85 (174)
T pfam10706 8 LIHQIFAAADKINLPLWIGGGWAIDARLGRITREHDDIDLTFPGDRHAEFECLLHAFGG-VITEQTDYGFL-AQSQGILL 85 (174)
T ss_pred HHHHHHHHHHHCCCCEEECCCEEEEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHCCC-EEEEECCCEEE-EECCCEEE
T ss_conf 99999998885698567637301000001004556671113762447899999997488-88664151211-20187687
Q ss_pred EE
Q ss_conf 64
Q gi|254781115|r 90 DI 91 (416)
Q Consensus 90 di 91 (416)
|-
T Consensus 86 Dc 87 (174)
T pfam10706 86 DC 87 (174)
T ss_pred CC
T ss_conf 05
No 26
>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=93.01 E-value=0.18 Score=29.46 Aligned_cols=37 Identities=32% Similarity=0.271 Sum_probs=31.7
Q ss_pred HHHHHHHHHHC--CCEEEEEHHHHHHHHCCCCCCEEEEEEE
Q ss_conf 99999999978--9859997069988877889860899980
Q gi|254781115|r 15 LINILSLLNKG--EDKSCIVGGAVRDSLMNLSVQDIDIATT 53 (416)
Q Consensus 15 ~~~i~~~l~~~--g~~~~~VGG~VRD~ll~~~~~DiD~~~~ 53 (416)
+..|.+.+.+. +++++.+|+.+|..+ .++.|||+.+.
T Consensus 4 l~~i~~~l~~~~~~~~i~~~Gs~~r~~~--~~~~DID~~~v 42 (49)
T cd05397 4 LDIIKERLKKLVPGYEIVVYGSLVRGLL--KKSSDIDLACV 42 (49)
T ss_pred HHHHHHHHHHHCCCCEEEEEHHHHHHHH--HCCCCCCEEEE
T ss_conf 9999999985289927998788989886--03456643789
No 27
>pfam09970 DUF2204 Conserved Archaeal protein (DUF2204). This domain, found in various hypothetical archaeal proteins, has no known function.
Probab=92.75 E-value=0.55 Score=26.20 Aligned_cols=78 Identities=18% Similarity=0.187 Sum_probs=52.7
Q ss_pred HHHHHHHHHHHHCCCEEEEEHHHHHHHHCCCC--CCEEEEEE-ECCH---HHHH-HHHHHCCCCEECCC-CCCCEEEE--
Q ss_conf 88999999999789859997069988877889--86089998-0898---9999-99987699562134-31446999--
Q gi|254781115|r 13 SDLINILSLLNKGEDKSCIVGGAVRDSLMNLS--VQDIDIAT-TILP---DRVM-RIFSKTRYKVIPTS-ISYGTIKI-- 82 (416)
Q Consensus 13 ~~~~~i~~~l~~~g~~~~~VGG~VRD~ll~~~--~~DiD~~~-~~~~---~~~~-~~~~~~~~~~~~~~-~~~gt~~~-- 82 (416)
.++..++..|++.|.+.-++|++|=++-+|++ +.|+|+-+ +-++ +++. .+..+.+ +..| -.+||...
T Consensus 4 ~~l~~v~~~L~~~Gv~fViIG~tVv~lal~~k~~~~DVDLF~~n~S~llded~~r~iA~e~~---Wd~g~t~~gTp~~i~ 80 (184)
T pfam09970 4 SDLGEVLRKLQERGIDFVIIGSTVVPLALGRKGFESDVDLFILNKSTLVDEDFFREIAEEEG---WDYGTTPLGTPRYIA 80 (184)
T ss_pred HHHHHHHHHHHHCCCEEEEECCEEEEEHHCCCCCCCCCEEEECCCCCCCCHHHHHHHHHHCC---CCCCCCCCCCEEEEE
T ss_conf 89999999999739629998860763201367887762257538863212899999898708---776788899868999
Q ss_pred EECCEEEEEEC
Q ss_conf 98998886421
Q gi|254781115|r 83 ICRKKYFDITT 93 (416)
Q Consensus 83 ~~~~~~~di~~ 93 (416)
..++..+.|-.
T Consensus 81 ~~~ge~v~Vdl 91 (184)
T pfam09970 81 IVGGEEVRVDL 91 (184)
T ss_pred ECCCCEEEEEH
T ss_conf 72885788888
No 28
>PRK02126 ribonuclease Z; Provisional
Probab=86.34 E-value=0.74 Score=25.31 Aligned_cols=11 Identities=27% Similarity=0.422 Sum_probs=5.6
Q ss_pred CCCCCCCEEEC
Q ss_conf 78003002000
Q gi|254781115|r 120 RDFTINALYAD 130 (416)
Q Consensus 120 RDFTINAla~~ 130 (416)
.+|||.|..++
T Consensus 151 ~~~~V~a~~l~ 161 (334)
T PRK02126 151 PWFRVRAAFLD 161 (334)
T ss_pred CCEEEEEEECC
T ss_conf 98799999747
No 29
>COG3575 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=85.01 E-value=1.1 Score=24.09 Aligned_cols=126 Identities=20% Similarity=0.244 Sum_probs=67.0
Q ss_pred CHHCCCHHHHHHHHHHHHCCC-EEEEEHHHHHH----HHCCCC----CCEEEEEEEC----CHHH---HHHHHHHCCCCE
Q ss_conf 522199889999999997898-59997069988----877889----8608999808----9899---999998769956
Q gi|254781115|r 7 HKWFHDSDLINILSLLNKGED-KSCIVGGAVRD----SLMNLS----VQDIDIATTI----LPDR---VMRIFSKTRYKV 70 (416)
Q Consensus 7 ~~~~~~~~~~~i~~~l~~~g~-~~~~VGG~VRD----~ll~~~----~~DiD~~~~~----~~~~---~~~~~~~~~~~~ 70 (416)
+-...+|....+++.+.+-|- ..|+++|+||- .|-|+. .+|||++--- +-+. +.+.+.+.-
T Consensus 9 ~i~r~~p~~~~~L~~v~~L~LP~~~laaGsV~n~VWn~l~gn~~~~~ikDiDv~yFD~~dls~e~e~~~~kkl~~~f--- 85 (184)
T COG3575 9 EIVRKSPLLMAILDTVRQLGLPDWWLAAGSVRNTVWNHLFGNNPMTGIKDIDVIYFDDADLSYEAEAALEKKLAEQF--- 85 (184)
T ss_pred HHHHHCHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEEECCCCCCHHHHHHHHHHHHHHC---
T ss_conf 99982928899999998738851443130888878887338987777542027985476667588999999999866---
Q ss_pred ECCCCCCCEEEEEECCEEEEEE-CCCCCCCCCCCCCCCCCCHHHHHHCCCCCCCCCCEEE--CCCC--HHHHHCCCHHHH
Q ss_conf 2134314469999899888642-1344667688743223320133210447800300200--0321--013200006888
Q gi|254781115|r 71 IPTSISYGTIKIICRKKYFDIT-TLRSDLITDGRYAKVVFTRDWKADSLRRDFTINALYA--DQQG--KVIDYVGGLNDL 145 (416)
Q Consensus 71 ~~~~~~~gt~~~~~~~~~~di~-~~R~e~~~~~~~~~~~~~~~~~eDl~RRDFTINAla~--~~~~--~l~Dp~gG~~DL 145 (416)
+- -. ..+||- .+|----..|.+| +++ -++...+===|.-|... +.+| +++-|| |++||
T Consensus 86 -~~-~~----------~~~evkNQArmHlw~~~~~~---yts-t~~ais~w~~~~taVGvRl~~~g~~E~~aPy-GLedl 148 (184)
T COG3575 86 -PQ-LR----------YPWEVKNQARMHLWSNGKFP---YTS-TEEAISYWLETATAVGVRLNAQGQIELFAPY-GLEDL 148 (184)
T ss_pred -CC-CC----------CCEEEECCEEEEEECCCCCC---CCC-HHHHHHHHHHHHEEEEEEECCCCCEEEEECC-CHHHH
T ss_conf -57-77----------76454020114322278888---653-8999998876633578885278968998055-78889
Q ss_pred HHHHHHH
Q ss_conf 7877764
Q gi|254781115|r 146 RNRTIKF 152 (416)
Q Consensus 146 ~~~~ir~ 152 (416)
=++.||.
T Consensus 149 fa~~irp 155 (184)
T COG3575 149 FAGTIRP 155 (184)
T ss_pred HHCEEEC
T ss_conf 5033016
No 30
>pfam06042 DUF925 Bacterial protein of unknown function (DUF925). This family consists of several hypothetical bacterial proteins of unknown function.
Probab=77.34 E-value=2.5 Score=21.82 Aligned_cols=103 Identities=19% Similarity=0.182 Sum_probs=53.6
Q ss_pred EEEEEHHHHHH----HHCCCC----CCEEEEEEE----CCHHH---HHHHHHHCCCCEECCCCCCCEEEEEECCEEEEEE
Q ss_conf 59997069988----877889----860899980----89899---9999987699562134314469999899888642
Q gi|254781115|r 28 KSCIVGGAVRD----SLMNLS----VQDIDIATT----ILPDR---VMRIFSKTRYKVIPTSISYGTIKIICRKKYFDIT 92 (416)
Q Consensus 28 ~~~~VGG~VRD----~ll~~~----~~DiD~~~~----~~~~~---~~~~~~~~~~~~~~~~~~~gt~~~~~~~~~~di~ 92 (416)
..|+++||||- .|-|++ .+|+|++-- .+.+. +.+.+.+.. .-++ ..|.-
T Consensus 11 d~~l~AG~vrn~VWn~L~g~~~~~~i~DiDviYfD~~d~s~e~e~~~e~~l~~~~-p~~~-------weVkN-------- 74 (163)
T pfam06042 11 DWWLAAGFVRNLVWDVLHGRPPMTGINDIDVIYFDPSDLSYEAEDALEARLKELL-PGYP-------WEVKN-------- 74 (163)
T ss_pred CEEEEHHHHHHHHHHHHCCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHC-CCCC-------EEEEE--------
T ss_conf 5687600688999888519987678775438984787579899999999999878-9998-------47862--------
Q ss_pred CCCCC-CCCCCCCCCCCCCHHHHHHCCCCCC-CCCCEEECC--CC--HHHHHCCCHHHHHHHHHHHC
Q ss_conf 13446-6768874322332013321044780-030020003--21--01320000688878777642
Q gi|254781115|r 93 TLRSD-LITDGRYAKVVFTRDWKADSLRRDF-TINALYADQ--QG--KVIDYVGGLNDLRNRTIKFI 153 (416)
Q Consensus 93 ~~R~e-~~~~~~~~~~~~~~~~~eDl~RRDF-TINAla~~~--~~--~l~Dp~gG~~DL~~~~ir~v 153 (416)
.+|-- -|. ..+| +++ .+ |+..+-- |--|++..+ +| +++=|| |++||-+.+||.-
T Consensus 75 QArmHl~~~--~~~P--y~S-~~-dAis~wpe~~TavGvrl~~~~~le~~AP~-Gl~dlf~~~vrpn 134 (163)
T pfam06042 75 QARMHLWNG--DKPP--YTS-ST-DAISRWPETATAVGVRLNADGQLELYAPF-GLEDLFSLTVRPN 134 (163)
T ss_pred EEEEEECCC--CCCC--CCC-HH-HHHHHCCHHHEEEEEEECCCCCEEEECCC-CHHHHHCCEEECC
T ss_conf 011010169--9898--648-89-99970744340899998789968998756-8788837777338
No 31
>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=77.30 E-value=5.4 Score=19.52 Aligned_cols=81 Identities=11% Similarity=0.119 Sum_probs=49.9
Q ss_pred HHHHHHHHHHHCC-------CEEEEEHHHHHHHHCCCCCCEEEEEEEC---------CHHHHHHH----HHHCCCCEECC
Q ss_conf 8999999999789-------8599970699888778898608999808---------98999999----98769956213
Q gi|254781115|r 14 DLINILSLLNKGE-------DKSCIVGGAVRDSLMNLSVQDIDIATTI---------LPDRVMRI----FSKTRYKVIPT 73 (416)
Q Consensus 14 ~~~~i~~~l~~~g-------~~~~~VGG~VRD~ll~~~~~DiD~~~~~---------~~~~~~~~----~~~~~~~~~~~ 73 (416)
....|.+.|.+.. .+++++|-+-|+-.+. +..|||+++-. .+..+... +.+.....-..
T Consensus 8 ~~~~I~~~L~~~~~~~~~~~~~v~~~GS~~~~T~l~-~~~DiDi~~~~~~~~~~~~~~~~~~l~~i~~~L~~~~~~~~~~ 86 (143)
T cd05400 8 RYREIREALKESLSELAGRVAEVFLQGSYARGTALR-GDSDIDLVVVLPDDTSFAEYGPAELLDELGEALKEYYGANEEV 86 (143)
T ss_pred HHHHHHHHHHHHHCCCCCCCCCEEEECCCCCCCCCC-CCCCEEEEEEECCCCCCCCCCHHHHHHHHHHHHHHHCCCCCEE
T ss_conf 999999999765112357878779846650784048-8765259999366434455389999999999999867986446
Q ss_pred CCCCCEEEEEEC--CEEEEEECCC
Q ss_conf 431446999989--9888642134
Q gi|254781115|r 74 SISYGTIKIICR--KKYFDITTLR 95 (416)
Q Consensus 74 ~~~~gt~~~~~~--~~~~di~~~R 95 (416)
..++-.+++.+. +.++||..+-
T Consensus 87 ~~~~~~v~v~~~~~~~~vDvvPa~ 110 (143)
T cd05400 87 KAQHRSVTVKFKGQGFHVDVVPAF 110 (143)
T ss_pred ECCCCEEEEEECCCCCEEEEEEEE
T ss_conf 448747999987888158988768
No 32
>cd03804 GT1_wbaZ_like This family is most closely related to the GT1 family of glycosyltransferases. wbaZ in Salmonella enterica has been shown to possess the mannosyl transferase activity. The members of this family are found in certain bacteria and Archaea.
Probab=76.78 E-value=5.6 Score=19.42 Aligned_cols=26 Identities=0% Similarity=0.156 Sum_probs=11.0
Q ss_pred HHHHHHHHHHHHHHCCCCCCCHHHHHHHHHH
Q ss_conf 9999999999999638888898999999999
Q gi|254781115|r 380 KVGNILVHCKQEWINSSFQLSQEDLHHLLRK 410 (416)
Q Consensus 380 ~iG~iL~~l~~~~i~~~~~n~~e~l~~~lk~ 410 (416)
.+.+.++++.. .+ .-.++++.+.+++
T Consensus 315 ~la~ai~~~~~----~~-~~~~~~~r~~a~~ 340 (351)
T cd03804 315 SLAAAVERFEK----NE-DFDPQAIRAHAER 340 (351)
T ss_pred HHHHHHHHHHH----CC-CCCHHHHHHHHHH
T ss_conf 99999999985----95-0159999999996
No 33
>COG2860 Predicted membrane protein [Function unknown]
Probab=72.34 E-value=1.9 Score=22.54 Aligned_cols=15 Identities=40% Similarity=0.589 Sum_probs=11.2
Q ss_pred EEHHHHHHHHCCCCC
Q ss_conf 970699888778898
Q gi|254781115|r 31 IVGGAVRDSLMNLSV 45 (416)
Q Consensus 31 ~VGG~VRD~ll~~~~ 45 (416)
+=||.+||+|||+-|
T Consensus 44 iGGGtiRDlLLG~~P 58 (209)
T COG2860 44 IGGGTIRDLLLGHYP 58 (209)
T ss_pred HCCHHHHHHHCCCCC
T ss_conf 256199999816788
No 34
>pfam03458 UPF0126 UPF0126 domain. Domain always found as pair in bacterial membrane proteins of unknown function. This domain contains three transmembrane helices. The conserved glycines are suggestive of an ion channel (C. Yeats unpublished obs.).
Probab=65.88 E-value=3.2 Score=21.03 Aligned_cols=15 Identities=33% Similarity=0.534 Sum_probs=12.8
Q ss_pred EEHHHHHHHHCCCCC
Q ss_conf 970699888778898
Q gi|254781115|r 31 IVGGAVRDSLMNLSV 45 (416)
Q Consensus 31 ~VGG~VRD~ll~~~~ 45 (416)
+-||.+||.|+|+.|
T Consensus 39 ~gGG~iRDil~~~~P 53 (81)
T pfam03458 39 VGGGILRDVLLGEVP 53 (81)
T ss_pred HCCHHHHHHHCCCCC
T ss_conf 113569999917898
No 35
>PRK11539 hypothetical protein; Provisional
Probab=65.88 E-value=9.8 Score=17.82 Aligned_cols=69 Identities=17% Similarity=0.167 Sum_probs=33.3
Q ss_pred CEEECCCCHHHHHCCCHHHHHHHHHHHCCCCCCHHHC-CCCCEEEEEEEEECCCCC-CCCCCCHHHHHHH--HHHCCCCC
Q ss_conf 0200032101320000688878777642764310010-421003320122013643-3111100012333--32102220
Q gi|254781115|r 126 ALYADQQGKVIDYVGGLNDLRNRTIKFIGDAHHRILE-DYLRILRFFRFFAHYGEK-NIDSDGLVASIKA--KKGLKILS 201 (416)
Q Consensus 126 Ala~~~~~~l~Dp~gG~~DL~~~~ir~v~~~~~rf~E-DpLRiLRa~RFasrlg~f-~id~~t~~ai~~~--~~~L~~iS 201 (416)
+-.+-.+.+++++ ..+++++.+..+. +.+.+ .---++.|.=| |+. .+++++.+..++. ++ |--||
T Consensus 160 ~tg~v~~~~~~~~---~~~~R~~~~~~~~---~~~~~~~~~~~l~AL~~----Gdr~~l~~~~~~~~~~tG~~H-LlAIS 228 (754)
T PRK11539 160 LTGRFLQAKLIDP---NCSLRQQYLASLE---QTLQPYPWRAVILALGF----GERLAVSKEIKNLMRDTGTAH-LMAIS 228 (754)
T ss_pred EEEEEEEEEECCC---CCHHHHHHHHHHH---HHCCCCCHHHHHHHHHC----CCCCCCCHHHHHHHHHHCHHH-HHHHH
T ss_conf 6999964142487---6409999999999---86047750479999970----472569999999999858478-99983
Q ss_pred HHHH
Q ss_conf 5776
Q gi|254781115|r 202 SERI 205 (416)
Q Consensus 202 ~ERI 205 (416)
+=-|
T Consensus 229 GLHI 232 (754)
T PRK11539 229 GLHI 232 (754)
T ss_pred HHHH
T ss_conf 6579
No 36
>TIGR01935 NOT-MenG RraA family; InterPro: IPR010203 This entry includes a number of closely related sequences bacteria and plants. The Escherichia coli member of this family has been characterised as a regulator of RNase E (see IPR004659 from INTERPRO), and its crystal structure has been analysed . E. coli RraA acts as a trans-acting modulator of RNA turnover, binding essential endonuclease RNase E and inhibiting RNA processing . RNase E forms the core of a large RNA-catalysis machine termed the degradosomes. RraA (and RraB) causes remodelling of degradosome composition, which is associated with alterations in RNA decay and global transcript abundance and as such is a bacterial mechanism for the regulation of RNA cleavage .; GO: 0008428 ribonuclease inhibitor activity, 0051252 regulation of RNA metabolic process.
Probab=65.59 E-value=4.2 Score=20.28 Aligned_cols=23 Identities=35% Similarity=0.456 Sum_probs=19.0
Q ss_pred HHHHHHHHCCCEEEEEHHHHHHH
Q ss_conf 99999997898599970699888
Q gi|254781115|r 17 NILSLLNKGEDKSCIVGGAVRDS 39 (416)
Q Consensus 17 ~i~~~l~~~g~~~~~VGG~VRD~ 39 (416)
.|.....++|++--||=|||||-
T Consensus 78 ~lA~~A~~NGWeGviv~GcVRDv 100 (155)
T TIGR01935 78 NLAELAEENGWEGVIVHGCVRDV 100 (155)
T ss_pred HHHHHHHHCCCCEEEEECCHHHH
T ss_conf 56788650595149996230168
No 37
>pfam01909 NTP_transf_2 Nucleotidyltransferase domain. Members of this family belong to a large family of nucleotidyltransferases. This family includes kanamycin nucleotidyltransferase (KNTase) which is a plasmid-coded enzyme responsible for some types of bacterial resistance to aminoglycosides. KNTase in-activates antibiotics by catalysing the addition of a nucleotidyl group onto the drug.
Probab=61.10 E-value=7.6 Score=18.53 Aligned_cols=28 Identities=18% Similarity=0.248 Sum_probs=21.9
Q ss_pred CCEEEEEHHHHHHHHCCCCCCEEEEEEECC
Q ss_conf 985999706998887788986089998089
Q gi|254781115|r 26 EDKSCIVGGAVRDSLMNLSVQDIDIATTIL 55 (416)
Q Consensus 26 g~~~~~VGG~VRD~ll~~~~~DiD~~~~~~ 55 (416)
..++|+.|.++|.-...- .|||++|..+
T Consensus 14 ~~~i~lfGS~arg~~~~~--SDIDl~V~~~ 41 (90)
T pfam01909 14 VAEVVLFGSYARGTYLPG--SDIDLLVVSP 41 (90)
T ss_pred CCEEEEEECCCCCCCCCC--CCEEEEEEEC
T ss_conf 868999707745998999--9867999847
No 38
>PRK10578 hypothetical protein; Provisional
Probab=58.57 E-value=4.7 Score=19.96 Aligned_cols=15 Identities=27% Similarity=0.536 Sum_probs=9.5
Q ss_pred EEHHHHHHHHCCCCC
Q ss_conf 970699888778898
Q gi|254781115|r 31 IVGGAVRDSLMNLSV 45 (416)
Q Consensus 31 ~VGG~VRD~ll~~~~ 45 (416)
+=||.+||.|||+.|
T Consensus 41 ~GGGtlRDlLL~~~P 55 (207)
T PRK10578 41 VGGGTIRDMALDNGP 55 (207)
T ss_pred CCCHHHHHHHCCCCC
T ss_conf 243377655237889
No 39
>pfam08843 DUF1814 Domain of unknown function (DUF1814). This large family of proteins are largely uncharacterized. Some are annotated as abortive infective proteins but support for this annotation could not be found.
Probab=58.43 E-value=13 Score=16.95 Aligned_cols=33 Identities=24% Similarity=0.173 Sum_probs=25.5
Q ss_pred HHCCCEEEEEHHHHHHHHCC---CCCCEEEEEEECC
Q ss_conf 97898599970699888778---8986089998089
Q gi|254781115|r 23 NKGEDKSCIVGGAVRDSLMN---LSVQDIDIATTIL 55 (416)
Q Consensus 23 ~~~g~~~~~VGG~VRD~ll~---~~~~DiD~~~~~~ 55 (416)
...+.+..+.||.......+ |.+.|||+++...
T Consensus 9 ~~~~~~~vfkGGT~L~~~~~~~~R~SeDIDf~~~~~ 44 (232)
T pfam08843 9 SPLADKFVFKGGTALSLLYGLIPRFSEDIDFLLSGP 44 (232)
T ss_pred CCCCCCEEEECHHHHHHHHCCCCCCCCCCCCCCCCC
T ss_conf 966686798489999998779998372515688887
No 40
>COG4914 Predicted nucleotidyltransferase [General function prediction only]
Probab=52.19 E-value=7.3 Score=18.67 Aligned_cols=39 Identities=23% Similarity=0.371 Sum_probs=34.2
Q ss_pred HHHHHHHHHHHCCCEEEEEHHHHHHHHCCCC--CCEEEEEE
Q ss_conf 8999999999789859997069988877889--86089998
Q gi|254781115|r 14 DLINILSLLNKGEDKSCIVGGAVRDSLMNLS--VQDIDIAT 52 (416)
Q Consensus 14 ~~~~i~~~l~~~g~~~~~VGG~VRD~ll~~~--~~DiD~~~ 52 (416)
.+-++++.|+..|.+.-+.||.|=++-||+. +.|+|+-.
T Consensus 9 ~v~~vl~~L~d~g~~FviIG~tvv~~~l~~~~~~~DVDLF~ 49 (190)
T COG4914 9 AVRKVLKSLNDKGVEFVIIGSTVVPFVLNIDYDPRDVDLFI 49 (190)
T ss_pred HHHHHHHHHHHCCEEEEEECCEEEEEEECCCCCCCCCCEEE
T ss_conf 89999999985480899987757888851678865561563
No 41
>PRK13300 tRNA CCA-pyrophosphorylase; Provisional
Probab=49.18 E-value=18 Score=15.98 Aligned_cols=67 Identities=13% Similarity=0.072 Sum_probs=42.4
Q ss_pred CCEEEEEHHHHHHHHCCCCCCEEEEEEEC---C-HHHHHH--------HHHHCCCCEECCCCCCCEEEEEECCEEEEEEC
Q ss_conf 98599970699888778898608999808---9-899999--------99876995621343144699998998886421
Q gi|254781115|r 26 EDKSCIVGGAVRDSLMNLSVQDIDIATTI---L-PDRVMR--------IFSKTRYKVIPTSISYGTIKIICRKKYFDITT 93 (416)
Q Consensus 26 g~~~~~VGG~VRD~ll~~~~~DiD~~~~~---~-~~~~~~--------~~~~~~~~~~~~~~~~gt~~~~~~~~~~di~~ 93 (416)
..++.+||-.-||-+|.- -+||||=+-- . -+++.+ .+++. +.....+-+|--++..++|..+||..
T Consensus 45 ~~~~~~vGS~AkgTwL~g-d~DIDiFv~Fp~~~~~e~l~~~gl~~~~~~~~~~-~~~~~~yAeHPYv~~~~~g~~vDiVP 122 (446)
T PRK13300 45 DAEVELVGSYARGTWLKG-DRDIDIFVLFPKDTSREELEEKGLELGKEVLKEL-GSYEERYAEHPYVTGEIEGFEVDIVP 122 (446)
T ss_pred CEEEEEEECCCCCCCCCC-CCCEEEEEECCCCCCHHHHHHHHHHHHHHHHHHC-CCCEEEECCCCEEEEEECCEEEEEEE
T ss_conf 704999703236662699-8650499976888888999999999999998634-76045553686499998788999997
Q ss_pred C
Q ss_conf 3
Q gi|254781115|r 94 L 94 (416)
Q Consensus 94 ~ 94 (416)
+
T Consensus 123 c 123 (446)
T PRK13300 123 C 123 (446)
T ss_pred E
T ss_conf 6
No 42
>TIGR01769 GGGP geranylgeranylglyceryl phosphate synthase; InterPro: IPR010946 This entry represents geranylgeranylglyceryl phosphate synthase which catalyses the first committed step in the synthesis of ether-linked membrane lipids in archaea ..
Probab=44.29 E-value=22 Score=15.49 Aligned_cols=48 Identities=15% Similarity=0.318 Sum_probs=35.9
Q ss_pred CCCCCCHHCCCHHHHHHHHHHHHCCCEEEEEHHH--HHHHHCCCCCCEEE
Q ss_conf 7765752219988999999999789859997069--98887788986089
Q gi|254781115|r 2 VSIVQHKWFHDSDLINILSLLNKGEDKSCIVGGA--VRDSLMNLSVQDID 49 (416)
Q Consensus 2 ~~~~~~~~~~~~~~~~i~~~l~~~g~~~~~VGG~--VRD~ll~~~~~DiD 49 (416)
+|++|=.-....+..+|.+-+.++|.-+.+|||. |+...|...+++||
T Consensus 2 ~tLiDP~~~~~~~~~~IAk~~~~aGtD~ilvGGs~Gi~e~~ld~~v~~ik 51 (212)
T TIGR01769 2 FTLIDPEKKSSDELKKIAKNAKEAGTDAILVGGSLGISEDKLDQVVKKIK 51 (212)
T ss_pred CCCCCCCCCCHHHHHHHHHHHHHCCCCEEEECCCCCCCHHHHHHHHHHHH
T ss_conf 86657432584569999999985289889836633733547889999864
No 43
>pfam11372 DUF3173 Protein of unknown function (DUF3173). This family of proteins with unknown function appears to be restricted to Firmicutes.
Probab=43.00 E-value=23 Score=15.36 Aligned_cols=33 Identities=21% Similarity=0.486 Sum_probs=24.8
Q ss_pred CCHHHHHHCCCCCCHHHHHHHHHHHHHHHCCCCC
Q ss_conf 8878999658987779999999999999638888
Q gi|254781115|r 365 LTGDDVVKYGIPPGKKVGNILVHCKQEWINSSFQ 398 (416)
Q Consensus 365 I~G~dL~~~Gi~pGp~iG~iL~~l~~~~i~~~~~ 398 (416)
++-+|||++|++|+-. ..|+++..+.-++..+.
T Consensus 4 vt~~dLi~lGf~~~~A-~~IIrqAK~~lV~~G~~ 36 (59)
T pfam11372 4 VTKKDLIKLGFKPHTA-RDIIRQAKELLVERGYS 36 (59)
T ss_pred CCHHHHHHHCCCHHHH-HHHHHHHHHHHHHCCCC
T ss_conf 6799999957988799-99999999999981887
No 44
>TIGR02651 RNase_Z ribonuclease Z; InterPro: IPR013471 All tRNA molecules are synthesised as long precursors with extra sequence at both the 5' and 3' ends, which undergo several processing steps to form the mature tRNA molecule. In many bacteria the tRNA precursors do not contain the CCA sequence which forms the 3' end of the mature tRNA and is essential for aminoacylation. In these organisms ribonucleotide Z cleaves the precursor to form a 3' end to which CCA is added. Species where all tRNA sequences already have the CCA tail, such as E. coli, do not generally posses this form of ribonuclease Z. ; GO: 0016891 endoribonuclease activity producing 5'-phosphomonoesters, 0042779 removal of tRNA 3'-trailer sequence.
Probab=42.98 E-value=20 Score=15.78 Aligned_cols=41 Identities=7% Similarity=0.125 Sum_probs=19.1
Q ss_pred EEECCEEEEEECCCCCCCCCCCCCCCCCCHHHHHHCCCCCCCCCCEE
Q ss_conf 99899888642134466768874322332013321044780030020
Q gi|254781115|r 82 IICRKKYFDITTLRSDLITDGRYAKVVFTRDWKADSLRRDFTINALY 128 (416)
Q Consensus 82 ~~~~~~~~di~~~R~e~~~~~~~~~~~~~~~~~eDl~RRDFTINAla 128 (416)
++++...|.|.+++.+.-. | .++=.++|.-.++=|-+....
T Consensus 142 ~~~~~~~f~v~~~~l~H~~----~--~~GY~~~Ekd~~g~~~~eka~ 182 (327)
T TIGR02651 142 LVFEDDGFKVEAFPLDHSI----P--SLGYRFEEKDRPGKFDREKAK 182 (327)
T ss_pred EEEECCCEEEEEEECCCCC----E--EEEEEEEECCCCCCCCHHHHH
T ss_conf 2676584489999505784----1--467899863889987389999
No 45
>KOG1531 consensus
Probab=41.02 E-value=19 Score=15.91 Aligned_cols=24 Identities=25% Similarity=0.441 Sum_probs=11.6
Q ss_pred EEEEHHHHHHHHCCCCCCEEEEEE
Q ss_conf 999706998887788986089998
Q gi|254781115|r 29 SCIVGGAVRDSLMNLSVQDIDIAT 52 (416)
Q Consensus 29 ~~~VGG~VRD~ll~~~~~DiD~~~ 52 (416)
+..||-=+|-.|+-..+.+|+++.
T Consensus 136 vv~iGdK~ra~l~R~~~~~i~ls~ 159 (304)
T KOG1531 136 VVIIGDKIRAILLRLHPNSILLSI 159 (304)
T ss_pred EEEECHHHHHHEEECCCHHHHHHH
T ss_conf 999730122440012742031357
No 46
>TIGR02529 EutJ ethanolamine utilization protein EutJ family protein; InterPro: IPR013366 Salmonella typhimurium is capable of growth on ethanolamine as a sole source of carbon nitrogen and energy . During growth on this compound the cells form a multimolecular structure known as a metabolosome, which is similar to the carboxysome used by some photosynthetic bacteria to fix CO2, and is thought to contain the enzymes needed to metabolise this compound to acetyl-CoA. The metabolosome is not directly involved in the biochemistry of ethanolamine utilization - instead its role is thought to be to concentrate the enzymes involved in this process, while also protecting the cell from the build-up of toxic intermediates . The genes involved in growth on ethanolamine are encoded in a 17-gene operon known as the ethanolamine utilization (eut) operon. EutJ shows similarity to chaperonins and may play a role in assembly of the metabolosme , though it is not necessary for growth on this compound..
Probab=37.66 E-value=26 Score=14.96 Aligned_cols=12 Identities=8% Similarity=-0.025 Sum_probs=4.7
Q ss_pred CCCCCHHHHHHH
Q ss_conf 111100012333
Q gi|254781115|r 182 IDSDGLVASIKA 193 (416)
Q Consensus 182 id~~t~~ai~~~ 193 (416)
|+=|+.+.+|++
T Consensus 153 i~~EEAEe~K~~ 164 (240)
T TIGR02529 153 ISFEEAEEIKRD 164 (240)
T ss_pred CCHHHHHHHHHC
T ss_conf 888898878630
No 47
>PRK12487 ribonuclease activity regulator protein RraA; Reviewed
Probab=36.14 E-value=17 Score=16.22 Aligned_cols=17 Identities=24% Similarity=0.353 Sum_probs=6.2
Q ss_pred HHCCCEEEEEHHHHHHH
Q ss_conf 97898599970699888
Q gi|254781115|r 23 NKGEDKSCIVGGAVRDS 39 (416)
Q Consensus 23 ~~~g~~~~~VGG~VRD~ 39 (416)
.++|+...+|=|||||.
T Consensus 83 ~~nG~aGiVidG~VRDv 99 (163)
T PRK12487 83 LDNGWEGIVINGCVRDV 99 (163)
T ss_pred HHCCCCEEECCEEECCH
T ss_conf 98698889704523589
No 48
>pfam03020 LEM LEM domain. The LEM domain is 50 residues long and is composed of two parallel alpha helices. This domain is found in inner nuclear membrane proteins. It is called the LEM domain after LAP2, Emerin, and Man1.
Probab=36.12 E-value=22 Score=15.40 Aligned_cols=18 Identities=39% Similarity=0.756 Sum_probs=13.7
Q ss_pred HHHHHCCCCCCHHHHHHH
Q ss_conf 899965898777999999
Q gi|254781115|r 368 DDVVKYGIPPGKKVGNIL 385 (416)
Q Consensus 368 ~dL~~~Gi~pGp~iG~iL 385 (416)
..|+++|++|||.+|..-
T Consensus 13 ~~L~~~G~~~GPI~~sTR 30 (43)
T pfam03020 13 SELRKYGISPGPITGTTR 30 (43)
T ss_pred HHHHHCCCCCCCCCCCHH
T ss_conf 999983999999663208
No 49
>COG1708 Predicted nucleotidyltransferases [General function prediction only]
Probab=34.66 E-value=12 Score=17.25 Aligned_cols=29 Identities=21% Similarity=0.333 Sum_probs=21.8
Q ss_pred HCCCEEEEEHHHHHHHHCCCCCCEEEEEEEC
Q ss_conf 7898599970699888778898608999808
Q gi|254781115|r 24 KGEDKSCIVGGAVRDSLMNLSVQDIDIATTI 54 (416)
Q Consensus 24 ~~g~~~~~VGG~VRD~ll~~~~~DiD~~~~~ 54 (416)
..-..+|+.|.++|.-... -.|||+++-.
T Consensus 24 ~~~~~v~LfGS~arG~~~~--~SDiDv~vv~ 52 (128)
T COG1708 24 GGDLLIYLFGSYARGDFVK--ESDIDLLVVS 52 (128)
T ss_pred CCCEEEEEEEEEEECCCCC--CCCCEEEEEE
T ss_conf 8940999984687078877--6642699982
No 50
>TIGR02955 TMAO_TorT TMAO reductase system periplasmic protein TorT; InterPro: IPR014301 Members of this entry are the periplasmic protein TorT that, together with the TorS/TorR histidine kinase/response regulator system, regulates expression of the torCAD operon for trimethylamine N-oxide reductase (TMAO reductase). It appears to bind an inducer for TMAO reductase and shows homology to a periplasmic D-ribose binding protein..
Probab=34.13 E-value=30 Score=14.54 Aligned_cols=19 Identities=5% Similarity=0.069 Sum_probs=8.8
Q ss_pred HHHHHHHHHHCCCCHHHHHHH
Q ss_conf 768878864211018999998
Q gi|254781115|r 204 RIWSEINKLLEAKNPLNAIVH 224 (416)
Q Consensus 204 RI~~El~KiL~~~~~~~~l~~ 224 (416)
||...|..| +-.+..+|..
T Consensus 105 ~vGV~WY~M--Gy~~G~yL~~ 123 (304)
T TIGR02955 105 RVGVDWYQM--GYQAGEYLAK 123 (304)
T ss_pred EECCCHHHH--HHHHHHHHHH
T ss_conf 236863331--3376578986
No 51
>TIGR02666 moaA molybdenum cofactor biosynthesis protein A; InterPro: IPR013483 The majority of molybdenum-containing enzymes utilise a molybdenum cofactor (MoCF or Moco) consisting of a Mo atom coordinated via a cisdithiolene moiety to molybdopterin (MPT). MoCF is ubiquitous in nature, and the pathway for MoCF biosynthesis is conserved in all three domains of life. MoCF-containing enzymes function as oxidoreductases in carbon, nitrogen, and sulphur metabolism , . In Escherichia coli, biosynthesis of MoCF is a three stage process. It begins with the MoaA and MoaC conversion of GTP to the meta-stable pterin intermediate precursor Z. The second stage involves MPT synthase (MoaD and MoaE), which coverts precursor Z to MPT; MoeB is involved in the recycling of MPT synthase. The final step in MoCF synthesis is the attachment of mononuclear Mo to MPT, a process that requires MoeA and which is enhanced by MogA in an Mg2 ATP-dependent manner . MoCF is the active co-factor in eukaryotic and some prokaryotic molybdoenzymes, but the majority of bacterial enzymes requiring MoCF, need a modification of MTP for it to be active; MobA is involved in the attachment of a nucleotide monophosphate to MPT resulting in the MGD co-factor, the active co-factor for most prokaryotic molybdoenzymes. Bacterial two-hybrid studies have revealed the close interactions between MoeA, MogA, and MobA in the synthesis of MoCF . Moreover the close functional association of MoeA and MogA in the synthesis of MoCF is supported by fact that the known eukaryotic homologues to MoeA and MogA exist as fusion proteins: CNX1 () of Arabidopsis thaliana (Mouse-ear cress), mammalian Gephryin (e.g. Q9NQX3 from SWISSPROT) and Drosophila melanogaster (Fruit fly) Cinnamon (P39205 from SWISSPROT) . This entry represents the bacterial form of MoaA (molybdenum cofactor biosynthesis protein A). The MoaA protein is a member of the wider S-adenosylmethionine(SAM)-dependent enzyme family which catalyze the formation of protein and/or substrate radicals by reductive cleavage of SAM via a [4Fe-4S] cluster. Monomeric and homodimeric forms of MoaA have been observed in vivo, and it is not clear what the physiologically relevant form of the enzyme is . The core of each monomer consists of an incomplete TIM barrel, formed by the N-terminal region of the protein, containing a [4Fe-4S] cluster. The C-terminal region of the protein, which also contains a [4Fe-4S] cluster consists of a beta-sheet covering the lateral opening of the barrel, an extended loop and three alpha helices. The N-terminal [4Fe-4S] cluster is coordinated with 3 cysteines and an exchangeable SAM molecule, while the C-terminal [4Fe-4S], also coordinated with 3 cysteines, is the binding and activation site for GTP .; GO: 0046872 metal ion binding, 0006777 Mo-molybdopterin cofactor biosynthetic process.
Probab=33.85 E-value=31 Score=14.42 Aligned_cols=69 Identities=14% Similarity=0.160 Sum_probs=52.9
Q ss_pred CCCCHHCCCHHHHHHHHHHHHCCC-EEEEEHH----------HHHHHHCCCC--CCEEEEEEECCH-HHHHHHHHHCCCC
Q ss_conf 657522199889999999997898-5999706----------9988877889--860899980898-9999999876995
Q gi|254781115|r 4 IVQHKWFHDSDLINILSLLNKGED-KSCIVGG----------AVRDSLMNLS--VQDIDIATTILP-DRVMRIFSKTRYK 69 (416)
Q Consensus 4 ~~~~~~~~~~~~~~i~~~l~~~g~-~~~~VGG----------~VRD~ll~~~--~~DiD~~~~~~~-~~~~~~~~~~~~~ 69 (416)
++...+++-.++.++++++-.-|. ++++-|| -||..=--.. +.||=|+|||.- ...++.|+++|.+
T Consensus 40 ~~~~~~Lt~eEi~rl~~~~v~~Gv~KvRlTGGEPLlR~~l~~lv~~~~~~~g~~~~di~lTTNG~~L~~~a~~L~eAGL~ 119 (346)
T TIGR02666 40 LPKEELLTFEEIERLVRAFVGLGVRKVRLTGGEPLLRKDLVELVARLAALPGIEIEDIALTTNGLLLERHAKDLKEAGLK 119 (346)
T ss_pred CCCCCCCCHHHHHHHHHHHHHCCCEEEEEECCCCCCCCCHHHHHHHHHHCCCCCCCEEEECCCHHHHHHHHHHHHHCCCC
T ss_conf 87556689899999999999749716875277744136758999999842785433554100522358899999971888
Q ss_pred EEC
Q ss_conf 621
Q gi|254781115|r 70 VIP 72 (416)
Q Consensus 70 ~~~ 72 (416)
-+.
T Consensus 120 rvN 122 (346)
T TIGR02666 120 RVN 122 (346)
T ss_pred CEE
T ss_conf 036
No 52
>TIGR02295 HpaD 3,4-dihydroxyphenylacetate 2,3-dioxygenase; InterPro: IPR011981 This enzyme catalyses the second step in the degradation of 4-hydroxyphenylacetate to succinate and pyruvate. 4-hydroxyphenylacetate arises from the degradation of tyrosine. The substrate, 3,4-dihydroxyphenylacetate (homoprotocatechuate) arises from the action of a hydroxylase on 4-hydroxyphenylacetate. The aromatic ring is opened by this dioxygenase exo to the 3,4-diol resulting in 2-hydroxy-5-carboxymethylmuconate semialdehyde..
Probab=33.82 E-value=27 Score=14.88 Aligned_cols=82 Identities=17% Similarity=0.204 Sum_probs=52.4
Q ss_pred HHCCCC--CCEEEEEEE-C-------------CH---HHHHHHHHHCCC-CEECCCC-CCCEEEEE------ECCEEEEE
Q ss_conf 877889--860899980-8-------------98---999999987699-5621343-14469999------89988864
Q gi|254781115|r 39 SLMNLS--VQDIDIATT-I-------------LP---DRVMRIFSKTRY-KVIPTSI-SYGTIKII------CRKKYFDI 91 (416)
Q Consensus 39 ~ll~~~--~~DiD~~~~-~-------------~~---~~~~~~~~~~~~-~~~~~~~-~~gt~~~~------~~~~~~di 91 (416)
++|.|+ +||+=|+-. + +| ++.|.+++..++ ..|.-|. .||.--.. .+|.-||+
T Consensus 190 aWlhRkG~vHD~Al~~g~GnvPrLHH~aY~v~dp~~iI~~cD~LA~~g~~D~IERGPGRHG~SNAffLYlrDPDghRIEl 269 (312)
T TIGR02295 190 AWLHRKGGVHDIALTNGNGNVPRLHHIAYWVHDPLNIIKACDILASAGLSDSIERGPGRHGVSNAFFLYLRDPDGHRIEL 269 (312)
T ss_pred EECCCCCCCCEEEEECCCCCCCCCCEEEEECCCHHHHHHHCCHHHCCCCCCEECCCCCCCCCCCCEEEEEECCCCCEEEE
T ss_conf 97013849630888767379896412665618879997431343304654300207787652220043334689978999
Q ss_pred ECCCCCCCC-CCC-CCCCCCCHHHHHHC-CCCCCCCC
Q ss_conf 213446676-887-43223320133210-44780030
Q gi|254781115|r 92 TTLRSDLIT-DGR-YAKVVFTRDWKADS-LRRDFTIN 125 (416)
Q Consensus 92 ~~~R~e~~~-~~~-~~~~~~~~~~~eDl-~RRDFTIN 125 (416)
-| .|||+ |+= .|||+.+ .+|. +|+||.=+
T Consensus 270 Yt--~DY~t~D~Dk~~Pi~W~---~~d~~~R~~lWG~ 301 (312)
T TIGR02295 270 YT--GDYLTGDPDKLPPIRWT---LDDPRQRQTLWGH 301 (312)
T ss_pred EC--CCCEEECCCCCCCEEEC---CCCCHHCCCCCCC
T ss_conf 82--88225427889874623---4421000002588
No 53
>pfam04743 consensus
Probab=31.59 E-value=26 Score=14.95 Aligned_cols=11 Identities=36% Similarity=0.435 Sum_probs=7.3
Q ss_pred CHHHHHHHHHH
Q ss_conf 05776887886
Q gi|254781115|r 201 SSERIWSEINK 211 (416)
Q Consensus 201 S~ERI~~El~K 211 (416)
-+||...|+..
T Consensus 27 ~peRwr~EI~l 37 (160)
T pfam04743 27 EPERWRAEIDL 37 (160)
T ss_pred CCHHHHHHHHC
T ss_conf 61999999973
No 54
>pfam03737 Methyltransf_6 Demethylmenaquinone methyltransferase. Members of this family are demethylmenaquinone methyltransferases that convert dimethylmenaquinone (DMK) to menaquinone (MK) in the final step of menaquinone biosynthesis. This region is also found at the C-terminus of the DlpA protein.
Probab=30.73 E-value=24 Score=15.23 Aligned_cols=19 Identities=21% Similarity=0.335 Sum_probs=9.2
Q ss_pred HHHHHHHCCCCCCEEEEEEE
Q ss_conf 69988877889860899980
Q gi|254781115|r 34 GAVRDSLMNLSVQDIDIATT 53 (416)
Q Consensus 34 G~VRD~ll~~~~~DiD~~~~ 53 (416)
+.+++++-.-++.|+ ++++
T Consensus 47 ~~~~~ai~~~~~G~V-lVid 65 (154)
T pfam03737 47 GLVREVLDQAGPGRV-LVVD 65 (154)
T ss_pred HHHHHHHHHCCCCEE-EEEE
T ss_conf 999999965698859-9998
No 55
>KOG2040 consensus
Probab=29.97 E-value=36 Score=14.00 Aligned_cols=16 Identities=13% Similarity=0.183 Sum_probs=6.8
Q ss_pred CCCCCHHHHHHHHHHH
Q ss_conf 0222057768878864
Q gi|254781115|r 197 LKILSSERIWSEINKL 212 (416)
Q Consensus 197 L~~iS~ERI~~El~Ki 212 (416)
+-.||..|...|-.++
T Consensus 337 iiGvtkD~~gk~a~RL 352 (1001)
T KOG2040 337 IIGVTKDALGKEAYRL 352 (1001)
T ss_pred EEEEECCCCCCHHHHH
T ss_conf 5755305666688999
No 56
>TIGR01425 SRP54_euk signal recognition particle protein SRP54; InterPro: IPR006325 The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes , . SRP recognises the signal sequence of the nascent polypeptide on the ribosome, retards its elongation, and docks the SRP-ribosome-polypeptide complex to the RER membrane via the SR receptor. SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor . In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane. This entry represents the 54 kDa SRP54 component, a GTP-binding protein that interacts with the signal sequence when it emerges from the ribosome. SRP54 of the signal recognition particle has a three-domain structure: an N-terminal helical bundle domain, a GTPase domain, and the M-domain that binds the 7s RNA and also binds the signal sequence. The extreme C-terminal region is glycine-rich and lower in complexity and poorly conserved between species.; GO: 0005525 GTP binding, 0008312 7S RNA binding, 0006614 SRP-dependent cotranslational protein targeting to membrane, 0048500 signal recognition particle.
Probab=29.60 E-value=22 Score=15.41 Aligned_cols=185 Identities=17% Similarity=0.226 Sum_probs=92.1
Q ss_pred CCC-CHHCCCHHHHHHHHHHHHCCCEEEEEHHHHHHHHCCCCC--CEEEEEEECCHHHHHHHHHHC----CCCEECC---
Q ss_conf 657-522199889999999997898599970699888778898--608999808989999999876----9956213---
Q gi|254781115|r 4 IVQ-HKWFHDSDLINILSLLNKGEDKSCIVGGAVRDSLMNLSV--QDIDIATTILPDRVMRIFSKT----RYKVIPT--- 73 (416)
Q Consensus 4 ~~~-~~~~~~~~~~~i~~~l~~~g~~~~~VGG~VRD~ll~~~~--~DiD~~~~~~~~~~~~~~~~~----~~~~~~~--- 73 (416)
|+| +.-++. -++.|..+|-+...++- .||++-=|... ..+|+...+.+..=.+.+++. .+..++-
T Consensus 21 v~dse~vl~~-~Lkei~~ALL~~dvn~k----lv~~l~~Nik~kid~~n~e~~~~g~nKRk~iq~~vF~EL~~LvDp~~~ 95 (453)
T TIGR01425 21 VIDSEEVLNE-MLKEICTALLESDVNVK----LVRQLRENIKKKIDKINLEELASGLNKRKLIQKAVFEELCNLVDPGVE 95 (453)
T ss_pred CCCCHHHHHH-HHHHHHHHHHHCCCCHH----HHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC
T ss_conf 1044899999-99999887511335267----789888878874050351332103247899999899998976086323
Q ss_pred ---CCCCCEEEEEECCEEEEEECCCCCCCCCCCCCCCCC---------CHHHHHHCCCCCCCCCCEEECCCC---HHH--
Q ss_conf ---431446999989988864213446676887432233---------201332104478003002000321---013--
Q gi|254781115|r 74 ---SISYGTIKIICRKKYFDITTLRSDLITDGRYAKVVF---------TRDWKADSLRRDFTINALYADQQG---KVI-- 136 (416)
Q Consensus 74 ---~~~~gt~~~~~~~~~~di~~~R~e~~~~~~~~~~~~---------~~~~~eDl~RRDFTINAla~~~~~---~l~-- 136 (416)
-.+..|.+-.++|..+- +.++- +-|+- ++|+ |==|+||-..| -|+
T Consensus 96 APkPkklststktinGkk~~---p~Kgk------~~ViMfVGLQGaGKTTtc---------tKLA~YYk~rGfK~~lvCA 157 (453)
T TIGR01425 96 APKPKKLSTSTKTINGKKFT---PKKGK------SSVIMFVGLQGAGKTTTC---------TKLAYYYKRRGFKPALVCA 157 (453)
T ss_pred CCCCCCCCCCCEEECCCEEE---CCCCC------CEEEEEEECCCCCHHHHH---------HHHHHHHHCCCCCEEEECC
T ss_conf 46875333211010350341---15688------215888621488715668---------7877776326643256517
Q ss_pred HHC--CCHHHHHHHHHHHCCCCCCHHHC-CCCCEEEEEEEEECCCCCCCCCCCHHHHH-HHHHHCCCCCHHHHHHHHHHH
Q ss_conf 200--00688878777642764310010-42100332012201364331111000123-333210222057768878864
Q gi|254781115|r 137 DYV--GGLNDLRNRTIKFIGDAHHRILE-DYLRILRFFRFFAHYGEKNIDSDGLVASI-KAKKGLKILSSERIWSEINKL 212 (416)
Q Consensus 137 Dp~--gG~~DL~~~~ir~v~~~~~rf~E-DpLRiLRa~RFasrlg~f~id~~t~~ai~-~~~~~L~~iS~ERI~~El~Ki 212 (416)
|=| |-.+=|+..=.|+=-+-.=+..| ||+.| |+. |--..-.|-...|. ..+. +|=--+.++.|...+
T Consensus 158 DTFRAGAFdQLkqNA~kA~iPFYGsy~E~DPVki------A~E-Gv~~Fk~E~~diIivDTSG--RHkQe~~LF~Em~qv 228 (453)
T TIGR01425 158 DTFRAGAFDQLKQNATKAKIPFYGSYLESDPVKI------ASE-GVEKFKKEKFDIIIVDTSG--RHKQEEELFEEMVQV 228 (453)
T ss_pred CCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCEEE------ECC-CHHHHHCCCCCEEEEECCC--CCHHHHHHHHHHHHH
T ss_conf 7542324899987476448971201048987078------002-0113221278479983798--732258888998768
Q ss_pred HCCCCHHH
Q ss_conf 21101899
Q gi|254781115|r 213 LEAKNPLN 220 (416)
Q Consensus 213 L~~~~~~~ 220 (416)
-..-.|..
T Consensus 229 ~~Ai~Pd~ 236 (453)
T TIGR01425 229 AEAIKPDS 236 (453)
T ss_pred HHCCCCCC
T ss_conf 63349983
No 57
>TIGR01854 lipid_A_lpxH UDP-2,3-diacylglucosamine hydrolase; InterPro: IPR010138 This entry represents LpxH, or UDP-2,3-diacylglucosamine hydrolase (or pyrophosphatase), which is an essential enzyme in Escherichia coli that catalyses the fourth step in lipid A biosynthesis. This reaction involves pyrophosphate bond hydrolysis of the precursor UDP-2,3-diacylglucosamine to yield 2,3-diacylglucosamine 1-phosphate and UMP . Several Gram-negative bacteria have homologues of LpxH and/or LpxH2, while others have only distant orthologues of LpxH or LpxH2, or lack these enzymes altogether .; GO: 0016462 pyrophosphatase activity, 0009245 lipid A biosynthetic process, 0005737 cytoplasm.
Probab=29.55 E-value=26 Score=14.99 Aligned_cols=47 Identities=11% Similarity=0.122 Sum_probs=22.6
Q ss_pred HHHHHHCCCCCHHHHHHHHHHHHCCCCHHHHHHHHHHCCCCCCCCCCCCCC
Q ss_conf 333321022205776887886421101899999875300233468870105
Q gi|254781115|r 191 IKAKKGLKILSSERIWSEINKLLEAKNPLNAIVHMYNGGIFKEIFLDVQEI 241 (416)
Q Consensus 191 ~~~~~~L~~iS~ERI~~El~KiL~~~~~~~~l~~L~~~gll~~ifpel~~~ 241 (416)
.+.+..|+.||-.=+.-=|.+ .+-.+..+=..-+++|. .++|+-+-+
T Consensus 56 ~~va~~~r~vsd~GV~~YF~~--GNRDFLiG~~Far~aG~--~LLPD~~Vi 102 (241)
T TIGR01854 56 RSVAEAIRAVSDQGVPCYFMH--GNRDFLIGKRFAREAGM--TLLPDESVI 102 (241)
T ss_pred HHHHHHHHHHHCCCEEEEEEC--CCCHHHHHHHHHHHHCC--EECCCHHHH
T ss_conf 999999998732890798405--98515666899997088--107862465
No 58
>KOG2792 consensus
Probab=28.71 E-value=38 Score=13.90 Aligned_cols=12 Identities=25% Similarity=0.501 Sum_probs=5.9
Q ss_pred HHHHHHHHHHCC
Q ss_conf 578998875303
Q gi|254781115|r 275 KKSILSMAKKFS 286 (416)
Q Consensus 275 ~~~~~~~~~rlk 286 (416)
.+++.++|+.++
T Consensus 212 ~eqvk~vak~yR 223 (280)
T KOG2792 212 TEQVKQVAKKYR 223 (280)
T ss_pred HHHHHHHHHHHE
T ss_conf 999999998807
No 59
>PRK09372 ribonuclease activity regulator protein RraA; Provisional
Probab=28.63 E-value=30 Score=14.57 Aligned_cols=19 Identities=16% Similarity=0.281 Sum_probs=8.3
Q ss_pred HHHHHHHCCCCCCEEEEEEE
Q ss_conf 69988877889860899980
Q gi|254781115|r 34 GAVRDSLMNLSVQDIDIATT 53 (416)
Q Consensus 34 G~VRD~ll~~~~~DiD~~~~ 53 (416)
-.||.+|-.-.+.|+ ++++
T Consensus 46 ~~v~~al~~~~~G~V-LVVd 64 (160)
T PRK09372 46 GLVKELLEEPGEGRV-LVVD 64 (160)
T ss_pred HHHHHHHHCCCCCCE-EEEE
T ss_conf 999999852599959-9998
No 60
>pfam09821 ABC_transp ABC nitrate/sulfonate/bicarbonate family transporter, ATPase subunit. Members of this family are found in various prokaryotic ABC transporters, predominantly involved in nitrate, sulfonate and bicarbonate translocation.
Probab=28.57 E-value=38 Score=13.85 Aligned_cols=38 Identities=18% Similarity=0.344 Sum_probs=29.5
Q ss_pred CCCCHHHHHHHHHHHHCCCCHHHHHHHHHHCCCCCCCC
Q ss_conf 22205776887886421101899999875300233468
Q gi|254781115|r 198 KILSSERIWSEINKLLEAKNPLNAIVHMYNGGIFKEIF 235 (416)
Q Consensus 198 ~~iS~ERI~~El~KiL~~~~~~~~l~~L~~~gll~~if 235 (416)
..++.||+..|+.--++...+...+..+.+||-...+|
T Consensus 79 ~~~~~~~f~~~L~~~~s~~~ae~~l~~~I~WGRYaeLf 116 (120)
T pfam09821 79 HRAPEERFLDELEDYLSPEEAERTLRTAIDWGRYAELF 116 (120)
T ss_pred CCCCHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHH
T ss_conf 88778999999998679888999999999999878862
No 61
>PRK00924 5-keto-4-deoxyuronate isomerase; Provisional
Probab=27.55 E-value=40 Score=13.73 Aligned_cols=83 Identities=20% Similarity=0.286 Sum_probs=43.6
Q ss_pred EEEHHHHHHHHCCCCCCEEEEEEECCHHHHHHHHHHCCCCEECCCCCCCEEEEEECCEEEEEECCCCC-CCCCCCCCCCC
Q ss_conf 99706998887788986089998089899999998769956213431446999989988864213446-67688743223
Q gi|254781115|r 30 CIVGGAVRDSLMNLSVQDIDIATTILPDRVMRIFSKTRYKVIPTSISYGTIKIICRKKYFDITTLRSD-LITDGRYAKVV 108 (416)
Q Consensus 30 ~~VGG~VRD~ll~~~~~DiD~~~~~~~~~~~~~~~~~~~~~~~~~~~~gt~~~~~~~~~~di~~~R~e-~~~~~~~~~~~ 108 (416)
.+|||+|=- .+.+-+.+ .......-.+.+-..+++.+| |.-+|..+|..+++.. .| .|..-+..+|+
T Consensus 45 ~ivGGa~P~------~~~l~L~~-~~~l~~~~FLeRRElGiiNiG---g~G~V~vdG~~y~l~~--~d~LYvG~G~k~V~ 112 (276)
T PRK00924 45 IIVGGAMPV------SKPLELEV-GKQLGVSYFLERRELGVINIG---GPGTVTVDGQTYELGH--RDALYVGKGAKEVV 112 (276)
T ss_pred EEEECEEEC------CCCEECCC-CHHHCCHHHHHHEEEEEEEEC---CCEEEEECCEEEEECC--CCEEEEECCCCCEE
T ss_conf 588110127------88566567-412154233323045689708---9779998999987447--63799806875048
Q ss_pred CCHHHHHHCCC-CCCCCCCE
Q ss_conf 32013321044-78003002
Q gi|254781115|r 109 FTRDWKADSLR-RDFTINAL 127 (416)
Q Consensus 109 ~~~~~~eDl~R-RDFTINAl 127 (416)
|.+. |... =-|=+|+-
T Consensus 113 F~S~---d~~~PAkFY~~Sa 129 (276)
T PRK00924 113 FASI---DAANPAKFYLNSA 129 (276)
T ss_pred EECC---CCCCCCEEEEECC
T ss_conf 8616---8788815999715
No 62
>PRK00805 putative deoxyhypusine synthase; Provisional
Probab=26.30 E-value=42 Score=13.58 Aligned_cols=31 Identities=6% Similarity=0.184 Sum_probs=24.1
Q ss_pred HHHHCCCCCCEEEEEEECCHHHHHHHHHHCCC
Q ss_conf 88877889860899980898999999987699
Q gi|254781115|r 37 RDSLMNLSVQDIDIATTILPDRVMRIFSKTRY 68 (416)
Q Consensus 37 RD~ll~~~~~DiD~~~~~~~~~~~~~~~~~~~ 68 (416)
||-+|.+|++|||+. +.+..++.+.+.+.++
T Consensus 3 ~~~~l~~pv~~i~i~-~~~v~~Lv~~~~~~gF 33 (338)
T PRK00805 3 HNVFLMKPTVPIKVK-DRSIAELLEAMARTGF 33 (338)
T ss_pred HHHHHCCCCCCCCCC-CCCHHHHHHHHHHCCC
T ss_conf 667732985225666-4849999999987292
No 63
>COG1669 Predicted nucleotidyltransferases [General function prediction only]
Probab=26.26 E-value=42 Score=13.58 Aligned_cols=41 Identities=27% Similarity=0.293 Sum_probs=30.0
Q ss_pred HHHHHHHHH-HCCC-EEEEEHHHHHHHHCCCCCCEEEEEEECCHH
Q ss_conf 999999999-7898-599970699888778898608999808989
Q gi|254781115|r 15 LINILSLLN-KGED-KSCIVGGAVRDSLMNLSVQDIDIATTILPD 57 (416)
Q Consensus 15 ~~~i~~~l~-~~g~-~~~~VGG~VRD~ll~~~~~DiD~~~~~~~~ 57 (416)
+.++...++ ++|. ++.+-|-++|+- .+|-.||||.|+..|.
T Consensus 11 lr~~~~~l~~k~gv~~~~vFGS~aRgE--~~~~SDIDILVef~~~ 53 (97)
T COG1669 11 LRKIKPELKEKYGVKRVAVFGSYARGE--QKPDSDIDILVEFEPG 53 (97)
T ss_pred HHHHHHHHHHHHCCCEEEEEEEEECCC--CCCCCCCEEEEEECCC
T ss_conf 999999999872876588864022488--9998872057762688
No 64
>TIGR02392 rpoH_proteo alternative sigma factor RpoH; InterPro: IPR012759 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , . This entry represents the proteobacterial clade of sigma factors called RpoH. This protein may be called sigma-32, sigma factor H, heat shock sigma factor, and alternative sigma factor RpoH. Note that in some species the single locus rpoH may be replaced by two or more differentially regulated stress response sigma factors.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0008270 zinc ion binding, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent, 0009408 response to heat.
Probab=25.85 E-value=36 Score=14.06 Aligned_cols=24 Identities=13% Similarity=0.344 Sum_probs=11.1
Q ss_pred CCCCHHHHHHHHHHCCCHHHHHHH
Q ss_conf 776857899887530342567777
Q gi|254781115|r 271 SWQDKKSILSMAKKFSLPREIRYF 294 (416)
Q Consensus 271 ~~~~~~~~~~~~~rlkl~~~~~~~ 294 (416)
.+.+..++..+++.|..+.++...
T Consensus 139 gw~~~~e~~~~A~~L~V~~~eV~e 162 (279)
T TIGR02392 139 GWLNPEEVEAIAEELGVSEEEVLE 162 (279)
T ss_pred CCCCHHHHHHHHHHCCCCHHHHHH
T ss_conf 798989999999763898889988
No 65
>KOG2423 consensus
Probab=25.13 E-value=44 Score=13.44 Aligned_cols=17 Identities=35% Similarity=0.898 Sum_probs=12.7
Q ss_pred CHHHHHHHHHHHHCCCC
Q ss_conf 05776887886421101
Q gi|254781115|r 201 SSERIWSEINKLLEAKN 217 (416)
Q Consensus 201 S~ERI~~El~KiL~~~~ 217 (416)
-.-|||.||.|.+.+.+
T Consensus 199 QSkRIW~ELyKViDSSD 215 (572)
T KOG2423 199 QSKRIWGELYKVIDSSD 215 (572)
T ss_pred CHHHHHHHHHHHHCCCC
T ss_conf 30578998887503220
No 66
>pfam00770 Peptidase_C5 Adenovirus endoprotease. This family of adenovirus thiol endoproteases specifically cleave Gly-Ala peptides in viral precursor peptides.
Probab=24.68 E-value=36 Score=14.04 Aligned_cols=15 Identities=27% Similarity=0.297 Sum_probs=10.9
Q ss_pred CEEECCCCH---HHHHCC
Q ss_conf 020003210---132000
Q gi|254781115|r 126 ALYADQQGK---VIDYVG 140 (416)
Q Consensus 126 Ala~~~~~~---l~Dp~g 140 (416)
|||+++... ++||||
T Consensus 38 A~Aw~P~s~t~Y~FDPfG 55 (183)
T pfam00770 38 ALAWNPKSYTFYMFDPFG 55 (183)
T ss_pred EEEECCCCCEEEEECCCC
T ss_conf 857658767588878988
No 67
>TIGR03671 cca_archaeal CCA-adding enzyme.
Probab=24.29 E-value=46 Score=13.34 Aligned_cols=68 Identities=12% Similarity=0.060 Sum_probs=43.3
Q ss_pred CCEEEEEHHHHHHHHCCCCCCEEEEEEEC----CHHHHHHH--------HHHCCCCEECCCCCCCEEEEEECCEEEEEEC
Q ss_conf 98599970699888778898608999808----98999999--------9876995621343144699998998886421
Q gi|254781115|r 26 EDKSCIVGGAVRDSLMNLSVQDIDIATTI----LPDRVMRI--------FSKTRYKVIPTSISYGTIKIICRKKYFDITT 93 (416)
Q Consensus 26 g~~~~~VGG~VRD~ll~~~~~DiD~~~~~----~~~~~~~~--------~~~~~~~~~~~~~~~gt~~~~~~~~~~di~~ 93 (416)
..++.+||-.-|+-+|.- -.||||=+-- +-+++.+. +.+ +......+-+|--++..++|..+||..
T Consensus 40 ~~~~~~vGS~AkgTwL~g-d~DIDiFv~F~~~~~~e~l~~~gl~~~~~~~~~-~~~~~~~yaeHPYv~~~~~g~~vdvVP 117 (408)
T TIGR03671 40 DAEVVLVGSYARGTWLKG-DRDIDIFILFPKDTSREELEEYGLEIGHEVLKR-GGNYEERYAEHPYVSGEIEGFEVDVVP 117 (408)
T ss_pred CEEEEEEECCCCCCCCCC-CCCCEEEEECCCCCCHHHHHHHHHHHHHHHHHH-CCCEEEEECCCCEEEEEECCEEEEEEE
T ss_conf 614999723246663799-876049997588888899999999999999862-798157762687599998788999997
Q ss_pred CC
Q ss_conf 34
Q gi|254781115|r 94 LR 95 (416)
Q Consensus 94 ~R 95 (416)
+-
T Consensus 118 cy 119 (408)
T TIGR03671 118 CY 119 (408)
T ss_pred EE
T ss_conf 56
No 68
>COG4849 Predicted nucleotidyltransferase [General function prediction only]
Probab=24.28 E-value=35 Score=14.10 Aligned_cols=27 Identities=30% Similarity=0.450 Sum_probs=21.5
Q ss_pred CEEEEEHHHHHHHHC--------CCCCCEEEEEEE
Q ss_conf 859997069988877--------889860899980
Q gi|254781115|r 27 DKSCIVGGAVRDSLM--------NLSVQDIDIATT 53 (416)
Q Consensus 27 ~~~~~VGG~VRD~ll--------~~~~~DiD~~~~ 53 (416)
.+.-+||.--||.+. +|..+|+||+..
T Consensus 26 e~~mlVGA~cRDil~~~~~~~~~~Rat~D~DfA~a 60 (269)
T COG4849 26 ERYMLVGAQCRDILHWRFCRGVPPRATNDTDFAGA 60 (269)
T ss_pred HHHEEEHHHHHHHHHHHHHCCCCCCCCCCCCHHHH
T ss_conf 44222005588999999715898878886314443
No 69
>COG1140 NarY Nitrate reductase beta subunit [Energy production and conversion]
Probab=24.13 E-value=18 Score=16.06 Aligned_cols=88 Identities=19% Similarity=0.187 Sum_probs=42.4
Q ss_pred EEEHHHHHHHHCCCCCCEEEEEEECCHHHHHHHHHHCCCCEECCC-----CCCCEEEEEECCEEEEEECCCCCCCCCCCC
Q ss_conf 997069988877889860899980898999999987699562134-----314469999899888642134466768874
Q gi|254781115|r 30 CIVGGAVRDSLMNLSVQDIDIATTILPDRVMRIFSKTRYKVIPTS-----ISYGTIKIICRKKYFDITTLRSDLITDGRY 104 (416)
Q Consensus 30 ~~VGG~VRD~ll~~~~~DiD~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~gt~~~~~~~~~~di~~~R~e~~~~~~~ 104 (416)
-.-||||||.==...++ ..+....++.+|.+.....+.-. .+|...+---.+.+--+|..|+.+ +|..
T Consensus 61 k~~GGWvr~~~Gkl~pr-----~G~r~~~l~~iFaNp~~P~idDYYEP~tydYe~L~sap~~~~qP~ArP~S~i--tG~~ 133 (513)
T COG1140 61 KWKGGWVRDKNGKLRPR-----MGGRIEKLAKIFANPKLPGIDDYYEPFTYDYENLHSAPEGKHQPTARPRSLI--TGER 133 (513)
T ss_pred HCCCCEEECCCCCCCCC-----CCCHHHHHHHHHCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCCCCCHHHC--CCCC
T ss_conf 20684378678854525-----5723888877414899997444358664667765558434789876745430--6870
Q ss_pred -CCCCCCHHHHHHCCCCCCCC
Q ss_conf -32233201332104478003
Q gi|254781115|r 105 -AKVVFTRDWKADSLRRDFTI 124 (416)
Q Consensus 105 -~~~~~~~~~~eDl~RRDFTI 124 (416)
.+|+.+.+|++||.--+-|.
T Consensus 134 m~kiewGpNweddLaG~~~~~ 154 (513)
T COG1140 134 MDKIEWGPNWEDDLAGEFEKR 154 (513)
T ss_pred CHHHCCCCCHHHHCCCCCCCC
T ss_conf 112022788122116774335
No 70
>TIGR00033 aroC chorismate synthase; InterPro: IPR000453 Chorismate synthase (4.2.3.5 from EC) catalyzes the last of the seven steps in the shikimate pathway which is used in prokaryotes, fungi and plants for the biosynthesis of aromatic amino acids. It catalyzes the 1,4-trans elimination of the phosphate group from 5-enolpyruvylshikimate-3-phosphate (EPSP) to form chorismate which can then be used in phenylalanine, tyrosine or tryptophan biosynthesis. Chorismate synthase requires the presence of a reduced flavin mononucleotide (FMNH2 or FADH2) for its activity. Chorismate synthase from various sources shows , a high degree of sequence conservation. It is a protein of about 360 to 400 amino-acid residues.; GO: 0004107 chorismate synthase activity, 0009073 aromatic amino acid family biosynthetic process.
Probab=23.04 E-value=47 Score=13.22 Aligned_cols=114 Identities=22% Similarity=0.160 Sum_probs=57.9
Q ss_pred EECCCCCCCE-EEEEECCEE--EEEECCCCCCCCCCCCCCCCCCHHHHHHCCCCCCCCCCEEECCCCHHHHHCCCHHHHH
Q ss_conf 6213431446-999989988--8642134466768874322332013321044780030020003210132000068887
Q gi|254781115|r 70 VIPTSISYGT-IKIICRKKY--FDITTLRSDLITDGRYAKVVFTRDWKADSLRRDFTINALYADQQGKVIDYVGGLNDLR 146 (416)
Q Consensus 70 ~~~~~~~~gt-~~~~~~~~~--~di~~~R~e~~~~~~~~~~~~~~~~~eDl~RRDFTINAla~~~~~~l~Dp~gG~~DL~ 146 (416)
+...|+.||- +..+++|.. +.+ ...+|+.||.|| ..|.
T Consensus 3 ~TtfGESHG~~~gaiidG~PaGl~l-----------------~~e~i~~~L~RR----------RpG~------------ 43 (391)
T TIGR00033 3 VTTFGESHGKALGAIIDGCPAGLPL-----------------TEEDIQKDLDRR----------RPGQ------------ 43 (391)
T ss_pred EEEEEECCCCEEEEEECCCCCCCCC-----------------CHHHHHHHHHHC----------CCCC------------
T ss_conf 5886302077434798130869711-----------------789999887637----------8988------------
Q ss_pred HHHHHHCCCCCCHHHCCCCCEEEEEEEEECCCCCCCCCCCHHHHHHH-HHHCCCCCHHHHHH----HHHHHHCCCCHHHH
Q ss_conf 87776427643100104210033201220136433111100012333-32102220577688----78864211018999
Q gi|254781115|r 147 NRTIKFIGDAHHRILEDYLRILRFFRFFAHYGEKNIDSDGLVASIKA-KKGLKILSSERIWS----EINKLLEAKNPLNA 221 (416)
Q Consensus 147 ~~~ir~v~~~~~rf~EDpLRiLRa~RFasrlg~f~id~~t~~ai~~~-~~~L~~iS~ERI~~----El~KiL~~~~~~~~ 221 (416)
=| | .+.|..+|-.-|+=++++=--.| .|=|+...-++ -+.++-++++=+-+ .-+++...+.|..+
T Consensus 44 ---s~--~-~~~r~E~D~Vei~SGv~~G~TtG----aPia~~i~N~d~~KW~~~~~s~dy~~ev~~~~~~~~~~pRPGHa 113 (391)
T TIGR00033 44 ---SR--G-TRMRKEEDEVEILSGVFEGKTTG----APIALMIRNKDHQKWLDVVRSKDYSDEVLLKRKAIRTVPRPGHA 113 (391)
T ss_pred ---CC--C-CCCCCCCCEEEEEECEEECCCCC----CCEEEEECCCCCCCHHHCCCCCCCCHHHHHHHHHHHCCCCCCHH
T ss_conf ---98--8-88841053279950337722158----84689962788512664307888866889865212216778626
Q ss_pred -HHHHHHCCCCC
Q ss_conf -99875300233
Q gi|254781115|r 222 -IVHMYNGGIFK 232 (416)
Q Consensus 222 -l~~L~~~gll~ 232 (416)
+...++.|+..
T Consensus 114 Dyty~~KYg~~d 125 (391)
T TIGR00033 114 DYTYFLKYGIDD 125 (391)
T ss_pred HHHHHHHCCCCC
T ss_conf 776345426322
No 71
>TIGR01660 narH nitrate reductase, beta subunit; InterPro: IPR006547 The nitrate reductase enzyme complex allows bacteria to use nitrate as an electron acceptor during anaerobic growth. The enzyme complex consists of a tetramer that has an alpha, beta and 2 gamma subunits. The alpha and beta subunits have catalytic activity and the gamma subunits attach the enzyme to the membrane and are b-type cytochromes that receive electrons from the quinone pool and transfers them to the beta subunit. The sequences in this family are the beta subunit for nitrate reductase I (narH) and nitrate reductase II (narY) for Gram-positive and Gram-negative bacteria. A few thermophiles and archaea also match the model. A number of the sequences in this set are experimentally characterised, these include: E.Coli NarH (P11349 from SWISSPROT) and NarY (P19318 from SWISSPROT) , , P42176 from SWISSPROT from Bacillus subtilis, and related proteins from Psuedomonas fluorescens, Paracoccus denitrificans, and Halomonas halodenitrificans.; GO: 0008940 nitrate reductase activity, 0042126 nitrate metabolic process, 0009325 nitrate reductase complex.
Probab=22.78 E-value=17 Score=16.13 Aligned_cols=32 Identities=6% Similarity=0.107 Sum_probs=15.4
Q ss_pred CCHHHHHHCCCCCCHHHHHHHHHHHHHHHCCCC
Q ss_conf 887899965898777999999999999963888
Q gi|254781115|r 365 LTGDDVVKYGIPPGKKVGNILVHCKQEWINSSF 397 (416)
Q Consensus 365 I~G~dL~~~Gi~pGp~iG~iL~~l~~~~i~~~~ 397 (416)
++-.-|.+.|+.+ .++-+.-+.|-.+-=+..|
T Consensus 426 ~~~~~~~~VGLt~-~Q~~~MYr~LA~A~YeDRF 457 (495)
T TIGR01660 426 VDLEVLEDVGLTE-QQIEEMYRYLAIANYEDRF 457 (495)
T ss_pred CCHHHHHHCCCCH-HHHHHHHHHHHHCCCCCCE
T ss_conf 0469997628888-8999999997411557743
No 72
>TIGR01703 hybrid_clust hydroxylamine reductase; InterPro: IPR010048 Hybrid cluster proteins (HCP, or Prismane) have been identified in bacteria, archaea and eukaryotic protozoa. No specific function has yet been assigned to these proteins, but it may involve oxidoreductase enzymatic activity. These proteins contain one 4Fe-4S cluster, and one hybrid 4Fe-2O-2S cluster, the latter being similar to the Ni-Fe-S cluster found in carbon monoxide dehydrogenase enzymes (IPR010047 from INTERPRO) , . This subfamily is heterogeneous with respect to the presence or absence of a region of about 100 amino acids not far from the N terminus of the protein. Members have been described as monomeric. ; GO: 0016661 oxidoreductase activity acting on other nitrogenous compounds as donors, 0051536 iron-sulfur cluster binding, 0006118 electron transport, 0005737 cytoplasm.
Probab=22.07 E-value=36 Score=13.99 Aligned_cols=51 Identities=16% Similarity=0.097 Sum_probs=37.0
Q ss_pred CCCCCCHH----HHHHCCCCCCCCCCEEECCCCHHHHH--CCCHHHHHHHHHHHCCCC
Q ss_conf 32233201----33210447800300200032101320--000688878777642764
Q gi|254781115|r 105 AKVVFTRD----WKADSLRRDFTINALYADQQGKVIDY--VGGLNDLRNRTIKFIGDA 156 (416)
Q Consensus 105 ~~~~~~~~----~~eDl~RRDFTINAla~~~~~~l~Dp--~gG~~DL~~~~ir~v~~~ 156 (416)
.++..+|+ +. +=.=|=||.+.-+|+--..|-|. .||++|=..=+=++..-|
T Consensus 318 GpIlmTsNCi~~P~-~Y~DRiFT~G~vG~pGv~Hi~~~~~vnGqKDF~pvI~~Al~~p 374 (567)
T TIGR01703 318 GPILMTSNCIIPPR-SYKDRIFTTGVVGWPGVKHIENDKDVNGQKDFSPVIEKALELP 374 (567)
T ss_pred CCCCCCCCCEECCC-CCCCCEEECCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHCCC
T ss_conf 86021315300777-6668406437342777624886966777778289999985388
No 73
>cd00209 DHFR Dihydrofolate reductase (DHFR). Reduces 7,8-dihydrofolate to 5,6,7,8-tetrahydrofolate with NADPH as a cofactor. This is an essential step in the biosynthesis of deoxythymidine phosphate since 5,6,7,8-tetrahydrofolate is required to regenerate 5,10-methylenetetrahydrofolate which is then utilized by thymidylate synthase. Inhibition of DHFR interrupts thymidilate synthesis and DNA replication, inhibitors of DHFR (such as Methotrexate) are used in cancer chemotherapy. 5,6,7,8-tetrahydrofolate also is involved in glycine, serine, and threonine metabolism and aminoacyl-tRNA biosynthesis.
Probab=21.23 E-value=52 Score=12.94 Aligned_cols=14 Identities=7% Similarity=0.304 Sum_probs=6.2
Q ss_pred CCCCCHHHHHHHHH
Q ss_conf 02220577688788
Q gi|254781115|r 197 LKILSSERIWSEIN 210 (416)
Q Consensus 197 L~~iS~ERI~~El~ 210 (416)
+--+-+..|..++.
T Consensus 94 i~IiGG~~iY~~~l 107 (158)
T cd00209 94 IFVIGGAEIYKQAL 107 (158)
T ss_pred EEEECHHHHHHHHH
T ss_conf 99957899999999
No 74
>TIGR01546 GAPDH-II_archae glyceraldehyde-3-phosphate dehydrogenase, type II; InterPro: IPR006436 This family describes the type II glyceraldehyde-3-phosphate dehydrogenases which are limited to archaea. These enzymes catalyze the interconversion of 1,3-diphosphoglycerate and glyceraldehyde-3-phosphate, a central step in glycolysis and gluconeogenesis. In archaea, either NAD or NADP may be utilised as the cofactor.; GO: 0008943 glyceraldehyde-3-phosphate dehydrogenase activity, 0050661 NADP binding, 0051287 NAD binding, 0006096 glycolysis, 0005737 cytoplasm.
Probab=20.69 E-value=54 Score=12.87 Aligned_cols=33 Identities=27% Similarity=0.391 Sum_probs=22.1
Q ss_pred HHHHHCCCEEEEEHHHHHHHHCCCCCCEEEEEEECCHHHHH
Q ss_conf 99997898599970699888778898608999808989999
Q gi|254781115|r 20 SLLNKGEDKSCIVGGAVRDSLMNLSVQDIDIATTILPDRVM 60 (416)
Q Consensus 20 ~~l~~~g~~~~~VGG~VRD~ll~~~~~DiD~~~~~~~~~~~ 60 (416)
..+.++|. =|-|.|-|+| +-.||+|+++|+-+-
T Consensus 56 ~~FEeaGi---~V~GT~edL~-----ek~DIvVD~TP~G~G 88 (335)
T TIGR01546 56 KKFEEAGI---KVAGTVEDLL-----EKVDIVVDATPEGVG 88 (335)
T ss_pred HHHHHCCC---EEECCHHHHH-----HHCCEEEECCCCCCC
T ss_conf 12543687---0442578731-----042888856878744
No 75
>PTZ00232 variable surface protein Vir27; Provisional
Probab=20.49 E-value=42 Score=13.56 Aligned_cols=11 Identities=18% Similarity=0.359 Sum_probs=4.4
Q ss_pred HHHHHHHHHHH
Q ss_conf 68887877764
Q gi|254781115|r 142 LNDLRNRTIKF 152 (416)
Q Consensus 142 ~~DL~~~~ir~ 152 (416)
+.+...+++++
T Consensus 48 ~~~~sekI~ka 58 (363)
T PTZ00232 48 LPGVSEKIVKA 58 (363)
T ss_pred CHHHHHHHHHH
T ss_conf 40579999998
No 76
>PRK11098 transport protein; Reviewed
Probab=20.01 E-value=29 Score=14.60 Aligned_cols=17 Identities=29% Similarity=0.530 Sum_probs=13.6
Q ss_pred HHHHCCCCCCHHHCCCC
Q ss_conf 77642764310010421
Q gi|254781115|r 149 TIKFIGDAHHRILEDYL 165 (416)
Q Consensus 149 ~ir~v~~~~~rf~EDpL 165 (416)
.+|.|-+|+||++||--
T Consensus 182 ~~r~IdnpdQRIqED~~ 198 (408)
T PRK11098 182 KLRHIEGAAQRVQEDTM 198 (408)
T ss_pred HCCCCCCHHHHHHHHHH
T ss_conf 53789990260899999
Done!