Query 030242
Match_columns 180
No_of_seqs 145 out of 851
Neff 7.2
Searched_HMMs 46136
Date Fri Mar 29 10:45:01 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030242.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030242hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2523 Predicted RNA-binding 100.0 3E-47 6.4E-52 290.0 12.2 178 1-178 1-179 (181)
2 PRK14560 putative RNA-binding 100.0 7.8E-43 1.7E-47 271.2 18.9 158 9-178 2-159 (160)
3 COG2016 Predicted RNA-binding 100.0 2E-42 4.4E-47 265.2 16.3 159 9-179 2-160 (161)
4 TIGR03684 arCOG00985 arCOG0415 100.0 9.8E-41 2.1E-45 256.9 19.0 149 14-176 2-150 (150)
5 KOG2522 Filamentous baseplate 100.0 2.9E-37 6.3E-42 266.1 13.7 171 1-178 1-176 (560)
6 TIGR00451 unchar_dom_2 unchara 100.0 1.1E-29 2.3E-34 185.2 12.0 107 61-172 1-107 (107)
7 PRK13534 7-cyano-7-deazaguanin 99.9 1.1E-23 2.4E-28 193.3 15.6 150 15-171 484-638 (639)
8 PRK13795 hypothetical protein; 99.9 1.1E-21 2.4E-26 180.7 15.6 146 14-171 46-201 (636)
9 PRK13794 hypothetical protein; 99.9 1.1E-20 2.4E-25 169.1 15.3 146 14-170 44-199 (479)
10 COG1370 Prefoldin, molecular c 99.9 1.8E-20 3.9E-25 141.6 13.2 146 15-168 2-152 (155)
11 TIGR00432 arcsn_tRNA_tgt tRNA- 99.8 8.3E-19 1.8E-23 158.3 13.9 145 16-167 388-537 (540)
12 PF01472 PUA: PUA domain; Int 99.8 1.5E-19 3.3E-24 123.4 6.5 74 92-170 1-74 (74)
13 COG5270 PUA domain (predicted 99.6 9.8E-15 2.1E-19 114.1 11.7 141 15-167 49-199 (202)
14 smart00359 PUA Putative RNA-bi 99.3 1.7E-11 3.6E-16 83.2 8.0 74 93-171 2-77 (77)
15 TIGR00425 CBF5 rRNA pseudourid 99.2 4.6E-11 9.9E-16 102.3 9.2 78 91-173 237-314 (322)
16 PRK04270 H/ACA RNA-protein com 99.2 2E-10 4.3E-15 97.6 9.6 76 91-171 225-300 (300)
17 PRK05429 gamma-glutamyl kinase 99.0 2.4E-09 5.2E-14 93.5 8.7 64 89-157 278-342 (372)
18 COG1549 Queuine tRNA-ribosyltr 98.9 6.2E-09 1.3E-13 92.5 10.4 70 91-171 450-519 (519)
19 TIGR01027 proB glutamate 5-kin 98.7 6.5E-08 1.4E-12 84.3 8.4 63 90-157 271-334 (363)
20 PF09183 DUF1947: Domain of un 98.4 1.4E-06 2.9E-11 57.6 6.8 63 13-87 2-64 (65)
21 PRK08557 hypothetical protein; 98.3 3.4E-06 7.5E-11 74.8 8.7 127 15-162 8-141 (417)
22 PRK13402 gamma-glutamyl kinase 98.0 2.2E-05 4.8E-10 68.6 7.5 63 90-157 275-338 (368)
23 PF14810 TGT_C2: Patch-forming 97.8 2.5E-05 5.5E-10 53.2 4.3 61 22-84 2-63 (74)
24 COG0263 ProB Glutamate 5-kinas 97.4 0.00033 7.1E-09 60.7 6.0 61 91-157 279-340 (369)
25 KOG2529 Pseudouridine synthase 96.2 0.0028 6.2E-08 55.6 2.0 76 91-171 275-350 (395)
26 PRK14124 tRNA pseudouridine sy 96.1 0.021 4.5E-07 49.0 7.0 74 91-170 228-305 (308)
27 PF03657 UPF0113: Uncharacteri 90.6 0.49 1.1E-05 36.9 4.6 119 15-148 5-141 (162)
28 KOG3492 Ribosome biogenesis pr 90.1 0.62 1.3E-05 36.0 4.6 72 92-169 95-166 (180)
29 PRK00130 truB tRNA pseudouridi 87.0 1.7 3.7E-05 37.0 5.7 50 91-148 229-278 (290)
30 PF09157 TruB-C_2: Pseudouridi 84.3 3.6 7.8E-05 25.9 5.1 47 92-149 1-47 (58)
31 COG0130 TruB Pseudouridine syn 81.4 3 6.4E-05 35.2 4.8 49 90-154 212-260 (271)
32 PRK05033 truB tRNA pseudouridi 80.9 4 8.8E-05 35.1 5.5 47 91-148 249-295 (312)
33 PRK01550 truB tRNA pseudouridi 78.0 5.6 0.00012 34.1 5.5 48 91-148 240-287 (304)
34 PRK15128 23S rRNA m(5)C1962 me 77.9 5.5 0.00012 35.3 5.6 51 93-148 4-55 (396)
35 PRK02755 truB tRNA pseudouridi 74.7 7.9 0.00017 33.1 5.5 46 91-148 234-279 (295)
36 PRK04099 truB tRNA pseudouridi 67.2 12 0.00025 31.7 4.8 45 91-148 214-258 (273)
37 cd02573 PseudoU_synth_EcTruB P 66.9 14 0.00031 31.2 5.4 45 91-147 232-276 (277)
38 PRK01851 truB tRNA pseudouridi 62.1 21 0.00045 30.6 5.5 46 91-148 245-290 (303)
39 PRK03287 truB tRNA pseudouridi 59.5 21 0.00046 30.5 5.1 44 91-148 239-282 (298)
40 PRK04642 truB tRNA pseudouridi 52.2 37 0.0008 29.1 5.4 45 91-148 242-286 (300)
41 PRK05389 truB tRNA pseudouridi 50.9 48 0.001 28.5 5.9 48 91-148 244-291 (305)
42 PF01878 EVE: EVE domain; Int 48.4 31 0.00067 25.6 4.0 25 125-149 39-65 (143)
43 COG4103 Uncharacterized protei 42.1 21 0.00046 27.3 2.1 30 14-43 43-72 (148)
44 PRK04980 hypothetical protein; 40.9 63 0.0014 23.2 4.4 25 124-148 30-54 (102)
45 PRK14122 tRNA pseudouridine sy 39.6 62 0.0013 27.9 4.9 43 91-148 257-299 (312)
46 COG1374 NIP7 Protein involved 39.0 40 0.00086 26.7 3.3 72 77-156 87-158 (176)
47 COG2012 RPB5 DNA-directed RNA 38.4 34 0.00073 23.5 2.5 32 87-138 36-67 (80)
48 PF01191 RNA_pol_Rpb5_C: RNA p 38.1 41 0.00089 22.8 2.9 30 88-137 31-60 (74)
49 PRK09570 rpoH DNA-directed RNA 35.5 46 0.001 22.8 2.8 30 89-138 35-64 (79)
50 PRK12618 flgA flagellar basal 34.6 1E+02 0.0022 23.3 4.9 56 102-168 63-119 (141)
51 TIGR03170 flgA_cterm flagella 33.6 1.2E+02 0.0025 21.7 5.0 39 124-168 64-103 (122)
52 PRK14123 tRNA pseudouridine sy 33.5 1.1E+02 0.0024 26.2 5.5 49 91-148 241-290 (305)
53 PRK12617 flgA flagellar basal 33.5 1E+02 0.0023 25.0 5.1 56 102-168 137-193 (214)
54 PRK06005 flgA flagellar basal 32.0 95 0.0021 23.9 4.5 58 100-168 80-138 (160)
55 PF15477 SMAP: Small acidic pr 31.2 69 0.0015 21.1 3.1 24 10-33 32-55 (69)
56 cd04710 BAH_fungalPHD BAH, or 27.1 60 0.0013 24.4 2.5 25 125-149 11-35 (135)
57 COG1507 Uncharacterized conser 26.8 33 0.00072 26.5 1.0 24 62-85 28-55 (167)
58 PRK08515 flgA flagellar basal 26.2 1.6E+02 0.0034 23.9 5.0 56 102-168 147-203 (222)
59 PF10246 MRP-S35: Mitochondria 26.1 55 0.0012 23.7 2.0 21 159-179 22-45 (104)
60 CHL00141 rpl24 ribosomal prote 25.9 1.1E+02 0.0024 21.0 3.5 12 125-136 8-19 (83)
61 KOG3342 Signal peptidase I [In 25.5 67 0.0014 25.1 2.5 56 81-142 33-94 (180)
62 PF13403 Hint_2: Hint domain 25.2 1.2E+02 0.0025 22.9 3.8 43 124-166 19-61 (147)
63 PRK06804 flgA flagellar basal 24.8 1.6E+02 0.0035 24.6 4.9 39 124-168 201-240 (261)
64 PRK07018 flgA flagellar basal 24.6 1.9E+02 0.0041 23.5 5.2 38 124-167 175-213 (235)
65 smart00841 Elong-fact-P_C Elon 24.5 89 0.0019 19.9 2.6 25 104-138 26-50 (56)
66 PRK02484 truB tRNA pseudouridi 23.6 2.1E+02 0.0046 24.4 5.4 43 91-148 240-282 (294)
67 PF13144 SAF_2: SAF-like 23.0 2.1E+02 0.0046 22.1 5.1 39 124-168 138-177 (196)
68 PRK00809 hypothetical protein; 23.0 1.5E+02 0.0032 22.4 4.0 26 124-149 33-65 (144)
69 PF04014 Antitoxin-MazE: Antid 22.6 1.1E+02 0.0024 18.1 2.7 17 125-141 20-36 (47)
70 PF09285 Elong-fact-P_C: Elong 21.6 91 0.002 19.9 2.2 28 104-142 26-53 (56)
71 KOG3082 Methionyl-tRNA formylt 20.3 51 0.0011 28.5 1.1 56 75-134 91-154 (338)
No 1
>KOG2523 consensus Predicted RNA-binding protein with PUA domain [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=3e-47 Score=290.00 Aligned_cols=178 Identities=66% Similarity=1.091 Sum_probs=172.1
Q ss_pred CCCCCCC-CCcccccccCHHHHHHHHHHHHhHCCCCchhhcccCCCCCceEEEEeeCceEEEEECCEEEEEEecCCCcch
Q 030242 1 MFKKFSA-EEVSAQNQVKASVQRKIRQSIADEYPGLEPVLDDLLPKKSPLIVAKCQNHLNLVLVNNVPLFFNIRDGPYMP 79 (180)
Q Consensus 1 MFkK~~~-~~~k~~~~l~~sd~kkLr~~i~~~f~~~~~~~~~l~p~~~~v~~~k~~~~~~~y~~dg~pl~f~~~~~~~~P 79 (180)
||||+.. +.+++++++|+|-+|-+|+.+.++||.+..-+++++|+|+++.+.||.+++.+|+++|.++||+.+||.|+|
T Consensus 1 mfkkf~~ke~i~~~~~~Kssvq~~i~~kl~~~yp~le~~~~ellpKk~~~~vikC~d~i~L~s~~G~~~fF~~~dg~~~P 80 (181)
T KOG2523|consen 1 MFKKFDLKEDISSSTQLKSSVQRGIKAKLVDQYPGLEQVIDELLPKKEQYKVIKCKDHIELLSVNGEVLFFCHRDGPYIP 80 (181)
T ss_pred CcccccchhhhhcchhhHHHHHHHHHHHHHHhCcchHHHHHHhccCCCceEEEEccCeeEEEEeCCEEEEEEecCCCccc
Confidence 8999965 789999999999999999999999998777789999999999999999999999999999999999999999
Q ss_pred hhHhhhcCCCCCcEEEECcchhhhhhcCCcccCCcccCCCCCCCcCCCCCCeEEEeeCCCCeEEEEEEEecCHHHHhcCC
Q 030242 80 TLRLLHQYPNIMKKLQVDRGAIKFVLSGANIMCPGLTSPGGSLDEEVGAETPVAIMAEGKQHALAIGFTKMSAKDIKAIN 159 (180)
Q Consensus 80 Tl~~l~~~p~~~p~v~v~~~a~~~i~~GAdLm~pGV~~~~~~~~~~~~~Gd~V~V~~~~~~~~vaVG~~~~s~~~i~~~~ 159 (180)
|+++|+++|..+|.+.||.||++|+++|||+|+||++.+.+.+++.+++|+.|+|+++++..++|||.+.||++||.+..
T Consensus 81 TLRllhk~p~~~~~~qvD~GAIkfvlsGAnIMcPGlts~g~~l~~~~ekd~~V~i~aeGK~~alAiG~~~ms~kei~s~n 160 (181)
T KOG2523|consen 81 TLRLLHKYPFIFPHVQVDRGAIKFVLSGANIMCPGLTSPGAKLPPGVEKDTIVAIMAEGKEHALAIGLTKMSAKEIKSVN 160 (181)
T ss_pred hhHHHhhCCCccceEEecCcceeeeecCCceEcccCCCCcccCCCCccCCCEEEEEecCchhhhhhhhhhhcHHHHHhhc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cceEEEEEEEEcccccCcc
Q 030242 160 KGIGVDNMHYLNDGLWKVS 178 (180)
Q Consensus 160 kG~av~v~H~~~D~Lw~~~ 178 (180)
||.++++.|++||.||.+.
T Consensus 161 KGiGIE~~H~l~DgLw~~~ 179 (181)
T KOG2523|consen 161 KGIGIENYHYLNDGLWKMK 179 (181)
T ss_pred cCCceEEEEecCCchhhee
Confidence 9999999999999999875
No 2
>PRK14560 putative RNA-binding protein; Provisional
Probab=100.00 E-value=7.8e-43 Score=271.21 Aligned_cols=158 Identities=27% Similarity=0.484 Sum_probs=143.6
Q ss_pred CcccccccCHHHHHHHHHHHHhHCCCCchhhcccCCCCCceEEEEeeCceEEEEECCEEEEEEecCCCcchhhHhhhcCC
Q 030242 9 EVSAQNQVKASVQRKIRQSIADEYPGLEPVLDDLLPKKSPLIVAKCQNHLNLVLVNNVPLFFNIRDGPYMPTLRLLHQYP 88 (180)
Q Consensus 9 ~~k~~~~l~~sd~kkLr~~i~~~f~~~~~~~~~l~p~~~~v~~~k~~~~~~~y~~dg~pl~f~~~~~~~~PTl~~l~~~p 88 (180)
++|++++||+||+|+||+++.+|||...+ . +......++.+++.+|++||.|+||+. ++.++||++++|++|
T Consensus 2 ~~~~~~~l~~s~~k~L~~~l~~~~~~~~~-~------~~~~~~~~~~~~~~~~~~~~~p~~f~~-d~~~~Ptl~~~~~~~ 73 (160)
T PRK14560 2 EVKSRHHLSKKEVKEIKEELKEKFGVDID-G------KDAVEEVETDKKEEIYLVDGEPLFFKV-DDELFPTLRGALKLK 73 (160)
T ss_pred ccccccccCHHHHHHHHHHHHHHcCCCcc-c------cccEEEEEcCCcEEEEEECCEEEEEEe-CCcccccHHHHHhCC
Confidence 47899999999999999999999985321 1 334556667789999999999999988 678999999999999
Q ss_pred CCCcEEEECcchhhhhhcCCcccCCcccCCCCCCCcCCCCCCeEEEeeCCCCeEEEEEEEecCHHHHhcCCcceEEEEEE
Q 030242 89 NIMKKLQVDRGAIKFVLSGANIMCPGLTSPGGSLDEEVGAETPVAIMAEGKQHALAIGFTKMSAKDIKAINKGIGVDNMH 168 (180)
Q Consensus 89 ~~~p~v~v~~~a~~~i~~GAdLm~pGV~~~~~~~~~~~~~Gd~V~V~~~~~~~~vaVG~~~~s~~~i~~~~kG~av~v~H 168 (180)
...|+|+||++|+++|++|||||+|||++ .+++|++||+|+|++++++.++|||++.+|++||....+|+||+++|
T Consensus 74 ~~~~~v~Vd~~a~~~i~~Ga~lm~pGV~~----~~~~~~~Gd~V~I~~~~~~~~vavG~~~~s~~ei~~~~kG~~v~~~h 149 (160)
T PRK14560 74 PEKRRVVVDAGAVKFVSNGADVMAPGIVE----ADEDIKEGDIVFVVEETHGKPLAVGRALMDGDEMVEEKKGKAVKNIH 149 (160)
T ss_pred ccCCEEEEeccHHHHHHCCCceecCeeee----CCCCCCCCCEEEEEECCCCeEEEEEEEeeCHHHHhhcCCceEEEEEE
Confidence 99999999999999999999999999998 67799999999999977689999999999999999889999999999
Q ss_pred EEcccccCcc
Q 030242 169 YLNDGLWKVS 178 (180)
Q Consensus 169 ~~~D~Lw~~~ 178 (180)
++||+||++.
T Consensus 150 ~~~D~lw~~~ 159 (160)
T PRK14560 150 HVGDEIWEFE 159 (160)
T ss_pred EcCchhhccc
Confidence 9999999985
No 3
>COG2016 Predicted RNA-binding protein (contains PUA domain) [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2e-42 Score=265.16 Aligned_cols=159 Identities=35% Similarity=0.603 Sum_probs=147.7
Q ss_pred CcccccccCHHHHHHHHHHHHhHCCCCchhhcccCCCCCceEEEEeeCceEEEEECCEEEEEEecCCCcchhhHhhhcCC
Q 030242 9 EVSAQNQVKASVQRKIRQSIADEYPGLEPVLDDLLPKKSPLIVAKCQNHLNLVLVNNVPLFFNIRDGPYMPTLRLLHQYP 88 (180)
Q Consensus 9 ~~k~~~~l~~sd~kkLr~~i~~~f~~~~~~~~~l~p~~~~v~~~k~~~~~~~y~~dg~pl~f~~~~~~~~PTl~~l~~~p 88 (180)
+++++..|++.|+|+|.+++...|+ +.+|.+..+++.++.++..+|++||.|++|+..+ .+||||++|.+++
T Consensus 2 ~~~~r~~lskke~k~l~~~~~~~~~-------~~l~~k~~v~v~~~~~~~~ii~vdG~pl~f~~~~-~~iPTl~~l~~~~ 73 (161)
T COG2016 2 KVKQRHFLSKKEVKKLVEKLEEYSG-------EELPGKAEVEVAKCDDKFEIILVDGEPLLFQRDD-RLIPTLRLLLKLP 73 (161)
T ss_pred ccchhcccCHHHHHHHHHHHHHhcc-------cccCCcceEEEEecCCcEEEEEECCEEEEEEeCC-eechhhHHHHhCC
Confidence 4678889999999999999997776 3567788889999899999999999999999864 8999999999999
Q ss_pred CCCcEEEECcchhhhhhcCCcccCCcccCCCCCCCcCCCCCCeEEEeeCCCCeEEEEEEEecCHHHHhcCCcceEEEEEE
Q 030242 89 NIMKKLQVDRGAIKFVLSGANIMCPGLTSPGGSLDEEVGAETPVAIMAEGKQHALAIGFTKMSAKDIKAINKGIGVDNMH 168 (180)
Q Consensus 89 ~~~p~v~v~~~a~~~i~~GAdLm~pGV~~~~~~~~~~~~~Gd~V~V~~~~~~~~vaVG~~~~s~~~i~~~~kG~av~v~H 168 (180)
.-.+.|+||.||+++|+||||+|+|||++ ++++|++||.|.|..+.++.|+|||+|+||+.||....||+||+++|
T Consensus 74 ~~~~~V~VD~GAvk~v~nGADvM~PGIv~----~~~~ik~Gd~VvV~~e~~~~plAVG~alm~~~em~~~~kGkav~~iH 149 (161)
T COG2016 74 PGKYVVVVDEGAVKFVLNGADVMAPGIVS----ADGEIKEGDIVVVVDEKKGRPLAVGIALMSGKEMEEKKKGKAVKNIH 149 (161)
T ss_pred CCccEEEEcCccHhhhcCCCceeccceee----cCCCccCCCEEEEEEcCCCCeeEEEeeccCHHHHhhhcCCeEEEEEe
Confidence 88889999999999999999999999999 88899999999999988899999999999999999999999999999
Q ss_pred EEcccccCccc
Q 030242 169 YLNDGLWKVSW 179 (180)
Q Consensus 169 ~~~D~Lw~~~~ 179 (180)
++||.||++..
T Consensus 150 hvGD~lw~~~~ 160 (161)
T COG2016 150 HVGDKLWEASV 160 (161)
T ss_pred ccChHHHhhhc
Confidence 99999999763
No 4
>TIGR03684 arCOG00985 arCOG04150 universal archaeal PUA-domain protein. This universal archaeal protein contains a domain possibly associated with RNA binding (pfam01472, TIGR00451).
Probab=100.00 E-value=9.8e-41 Score=256.91 Aligned_cols=149 Identities=30% Similarity=0.543 Sum_probs=137.5
Q ss_pred cccCHHHHHHHHHHHHhHCCCCchhhcccCCCCCceEEEEeeCceEEEEECCEEEEEEecCCCcchhhHhhhcCCCCCcE
Q 030242 14 NQVKASVQRKIRQSIADEYPGLEPVLDDLLPKKSPLIVAKCQNHLNLVLVNNVPLFFNIRDGPYMPTLRLLHQYPNIMKK 93 (180)
Q Consensus 14 ~~l~~sd~kkLr~~i~~~f~~~~~~~~~l~p~~~~v~~~k~~~~~~~y~~dg~pl~f~~~~~~~~PTl~~l~~~p~~~p~ 93 (180)
.++++||+|+|++++.++||. +|++..++..++ +...+|++||.|+||+. ++.++||++++|++|..+|+
T Consensus 2 ~~l~~~d~k~l~~~l~~~~g~--------~~~~~~v~~~~~-~~~~~~~~dg~p~~~~~-~~~~~Ptl~~~~~~~~~~~~ 71 (150)
T TIGR03684 2 HFLSKKELKELLEELKEYYGI--------DIEKAKLEVAET-DKFEIYLVDGKPLLFEK-DGRLIPTLYLLLELNPDKNR 71 (150)
T ss_pred ccCcHHHHHHHHHHHHHHcCC--------CCCCCeEEEEEc-CCeEEEEECCEEEEEEe-CCcccccHHHHHhCCccCCE
Confidence 579999999999999999983 367777888885 44689999999999988 57899999999999999999
Q ss_pred EEECcchhhhhhcCCcccCCcccCCCCCCCcCCCCCCeEEEeeCCCCeEEEEEEEecCHHHHhcCCcceEEEEEEEEccc
Q 030242 94 LQVDRGAIKFVLSGANIMCPGLTSPGGSLDEEVGAETPVAIMAEGKQHALAIGFTKMSAKDIKAINKGIGVDNMHYLNDG 173 (180)
Q Consensus 94 v~v~~~a~~~i~~GAdLm~pGV~~~~~~~~~~~~~Gd~V~V~~~~~~~~vaVG~~~~s~~~i~~~~kG~av~v~H~~~D~ 173 (180)
|+||++|+++|++|||||+|||++ ++++|++||+|+|++++++.++|||++.+|+++|....+|+||+++|++||+
T Consensus 72 v~Vd~~a~~~l~~Ga~lm~pGV~~----~~~~~~~Gd~V~I~~~~~~~~vavG~a~~ss~ei~~~~kG~av~~~h~~~D~ 147 (150)
T TIGR03684 72 VVVDEGAVKFIINGADIMAPGIVS----ADPSIKEGDIVFVVDETHRKPLAVGIALMDAEEMEEEKKGKAVKNIHHVGDK 147 (150)
T ss_pred EEECccHHHHHhcCcccccCceec----CCCCCCCCCEEEEEECCCCeEEEEEEEeeCHHHHhhcCCCeEEEEEEEcCcc
Confidence 999999999999999999999998 7789999999999997778999999999999999988999999999999999
Q ss_pred ccC
Q 030242 174 LWK 176 (180)
Q Consensus 174 Lw~ 176 (180)
||+
T Consensus 148 lw~ 150 (150)
T TIGR03684 148 IWE 150 (150)
T ss_pred ccC
Confidence 996
No 5
>KOG2522 consensus Filamentous baseplate protein Ligatin, contains PUA domain [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.9e-37 Score=266.08 Aligned_cols=171 Identities=30% Similarity=0.444 Sum_probs=148.0
Q ss_pred CCCCCCCCCcccccccCHHHHHHHHHHHHhHCCCC-chhhcccCCCCCceEEEEeeCceEEE-EECCEEEEEEecC-CCc
Q 030242 1 MFKKFSAEEVSAQNQVKASVQRKIRQSIADEYPGL-EPVLDDLLPKKSPLIVAKCQNHLNLV-LVNNVPLFFNIRD-GPY 77 (180)
Q Consensus 1 MFkK~~~~~~k~~~~l~~sd~kkLr~~i~~~f~~~-~~~~~~l~p~~~~v~~~k~~~~~~~y-~~dg~pl~f~~~~-~~~ 77 (180)
||||. +++|+++++|||||||||++.. ++.+ +++.+.+.|.+.++.++|+.+...+| ..+|.|++|+++. |.+
T Consensus 1 MFkKa--f~vKsntnlknSDrkKLr~rt~--~p~lg~e~~s~~~p~k~q~nl~kf~~~~~vyy~egg~PilFe~~~ng~l 76 (560)
T KOG2522|consen 1 MFKKA--FHVKSNTNLKNSDRKKLRQRTF--QPQLGNEEYSFRTPTKKQTNLNKFKSVGTVYYDEGGTPILFEEKHNGQL 76 (560)
T ss_pred CCCcc--cchhcccccccchHHHHHHhhc--ccccCchhhhhcCCceeEEEeeeeeeeeEEEEecCCceEEEEEcCCCcc
Confidence 99998 9999999999999999999333 3322 36788889989999999998876555 5677999999864 569
Q ss_pred chhhHhhhcCCCCCcEEEECcchhh-hhhcCCcccCCcccCCCCCCCcCCCCCCeEEEeeCCCCeEEEEEEEecCHHHHh
Q 030242 78 MPTLRLLHQYPNIMKKLQVDRGAIK-FVLSGANIMCPGLTSPGGSLDEEVGAETPVAIMAEGKQHALAIGFTKMSAKDIK 156 (180)
Q Consensus 78 ~PTl~~l~~~p~~~p~v~v~~~a~~-~i~~GAdLm~pGV~~~~~~~~~~~~~Gd~V~V~~~~~~~~vaVG~~~~s~~~i~ 156 (180)
|||||+||.+|.++|.+.+|.-|++ ++.+||+||.-|...+ .+|.++.|++++|...++..|+|||++.||++||.
T Consensus 77 fPTVy~lWeyp~llP~f~t~~~v~e~~~~~~~~l~~~~m~pp---g~p~~~~G~lcai~lpgn~ap~AiGc~~Msseem~ 153 (560)
T KOG2522|consen 77 FPTVYSLWEYPALLPIFLTHGFVIEEHLFNGANLMISGMIPP---GDPRCKIGTLCAIALPGNEAPLAIGCVEMSSEEMK 153 (560)
T ss_pred cchhHhhhcChhhcceeeccchhhhhhhcccccccccccCCC---CCcccccCceeeEecCCCcCceeeeeeecchHHHH
Confidence 9999999999999999999999986 5557777777776654 55789999999999999999999999999999998
Q ss_pred c-CCcceEEEEEEEEcccccCcc
Q 030242 157 A-INKGIGVDNMHYLNDGLWKVS 178 (180)
Q Consensus 157 ~-~~kG~av~v~H~~~D~Lw~~~ 178 (180)
. +.+|+|++|+|++.|.||+.+
T Consensus 154 v~GlkGkav~ilH~frD~Lw~sg 176 (560)
T KOG2522|consen 154 VIGLKGKAVKILHHFRDGLWKSG 176 (560)
T ss_pred HhccccceEEEEeehhhhhhhcC
Confidence 7 689999999999999999875
No 6
>TIGR00451 unchar_dom_2 uncharacterized domain 2. This uncharacterized domain is found a number of enzymes and uncharacterized proteins, often at the C-terminus. It is found in some but not all members of a family of related tRNA-guanine transglycosylases (tgt), which exchange a guanine base for some modified base without breaking the phosphodiester backbone of the tRNA. It is also found in rRNA pseudouridine synthase, another enzyme of RNA base modification not otherwise homologous to tgt. It is found, again at the C-terminus, in two putative glutamate 5-kinases. It is also found in a family of small, uncharacterized archaeal proteins consisting mostly of this domain.
Probab=99.96 E-value=1.1e-29 Score=185.17 Aligned_cols=107 Identities=34% Similarity=0.611 Sum_probs=99.7
Q ss_pred EEECCEEEEEEecCCCcchhhHhhhcCCCCCcEEEECcchhhhhhcCCcccCCcccCCCCCCCcCCCCCCeEEEeeCCCC
Q 030242 61 VLVNNVPLFFNIRDGPYMPTLRLLHQYPNIMKKLQVDRGAIKFVLSGANIMCPGLTSPGGSLDEEVGAETPVAIMAEGKQ 140 (180)
Q Consensus 61 y~~dg~pl~f~~~~~~~~PTl~~l~~~p~~~p~v~v~~~a~~~i~~GAdLm~pGV~~~~~~~~~~~~~Gd~V~V~~~~~~ 140 (180)
|++||.|++|... +.++||++++|++|...|+|+||++|+++|++||+||+|||+. .+++|++||+|+|++++++
T Consensus 1 i~~dg~~~~~~~~-~~~~ptl~~~~~~~~~~~~v~vd~~a~~~l~~Ga~L~~pGV~~----~~~~~~~gd~V~I~~~~~~ 75 (107)
T TIGR00451 1 ILVDGEPLYFIYD-DKVIPSLKGALKLMEDKKIVVVDNGAVKFLKNGADVMRPGIVD----ADEDIKEGDDVVVVDENKD 75 (107)
T ss_pred CeECCEEEEEEEC-CeEcccHHHHHhChhhCCEEEEChhHHHHHHCCccccCCeeEe----CCCCcCCCCEEEEEECCCC
Confidence 3579999999764 5799999999999999999999999999999999999999998 6678999999999996668
Q ss_pred eEEEEEEEecCHHHHhcCCcceEEEEEEEEcc
Q 030242 141 HALAIGFTKMSAKDIKAINKGIGVDNMHYLND 172 (180)
Q Consensus 141 ~~vaVG~~~~s~~~i~~~~kG~av~v~H~~~D 172 (180)
+++|+|++.+|++||....+|+|++++|+++|
T Consensus 76 ~~iavG~a~~~s~e~~~~~~G~~v~~~h~~~D 107 (107)
T TIGR00451 76 RPLAVGIALMSGEEMKEMDKGKAVKNIHHIGD 107 (107)
T ss_pred eEEEEEEEecCHHHHHhcCCCeEEEEEEecCC
Confidence 99999999999999999999999999999998
No 7
>PRK13534 7-cyano-7-deazaguanine tRNA-ribosyltransferase; Provisional
Probab=99.91 E-value=1.1e-23 Score=193.25 Aligned_cols=150 Identities=17% Similarity=0.158 Sum_probs=128.7
Q ss_pred ccCHHHHHHHHHHHHhHCCCCchhhcccCCCCCceEEEEeeCceEEEEECCEEEE-EEecCCCcchhhHhhhcC----CC
Q 030242 15 QVKASVQRKIRQSIADEYPGLEPVLDDLLPKKSPLIVAKCQNHLNLVLVNNVPLF-FNIRDGPYMPTLRLLHQY----PN 89 (180)
Q Consensus 15 ~l~~sd~kkLr~~i~~~f~~~~~~~~~l~p~~~~v~~~k~~~~~~~y~~dg~pl~-f~~~~~~~~PTl~~l~~~----p~ 89 (180)
..++.|.+.|+..+.+|||.. ..+.++|++..++.+|-+++.+.+++||.+++ ++..++.++||+.++.+. +.
T Consensus 484 ~~~~~d~~~l~~il~yqFG~~--~~~~l~~~~~~v~~~k~~dr~~~I~vdg~~l~~l~~~dg~~~pt~~GA~~l~~~~~~ 561 (639)
T PRK13534 484 PKINDDLLRIRAIAEYQFGEG--AGDAEFFDKVKIERSKKTGRIRQVLDKGEILATMRANDGFLILSKEGAKRLHEKLPF 561 (639)
T ss_pred ccCHHHHHHHHHHHHHHhCcc--hhhhcCCCCcEEEeccCCCceEEEEECCEEEEEEEecCCEEEEcHHHHHHHHhccCC
Confidence 578999999999999999852 23567888876766665677888899999997 776678899999765444 33
Q ss_pred CCcEEEECcchhhhhhcCCcccCCcccCCCCCCCcCCCCCCeEEEeeCCCCeEEEEEEEecCHHHHhcCCcceEEEEEEE
Q 030242 90 IMKKLQVDRGAIKFVLSGANIMCPGLTSPGGSLDEEVGAETPVAIMAEGKQHALAIGFTKMSAKDIKAINKGIGVDNMHY 169 (180)
Q Consensus 90 ~~p~v~v~~~a~~~i~~GAdLm~pGV~~~~~~~~~~~~~Gd~V~V~~~~~~~~vaVG~~~~s~~~i~~~~kG~av~v~H~ 169 (180)
..++|+||++|.+++.+|||||+|||++ +++++++||+|.|+. +++.++|||+|+||++||....+|+||+++|.
T Consensus 562 ~~~~V~Vd~~a~~~v~~G~~v~apgVv~----~d~~ir~gDeV~Vv~-e~~~~lavG~A~~~~~em~~~~~G~avkvR~~ 636 (639)
T PRK13534 562 PKYRVVVDKESEPFARKGKSVFAKFVID----CDEEIRPYDEVLVVN-EDDELLAYGKALLNGRELMEFNYGLAVKVRGG 636 (639)
T ss_pred CCcEEEECCcchhhhhCCCcccCCccee----cCCCCCCCCEEEEEe-cCCcEEEEEEEecCHHHHhhcCCceEEEEeec
Confidence 3479999999999999999999999999 889999999999998 45899999999999999999999999999998
Q ss_pred Ec
Q 030242 170 LN 171 (180)
Q Consensus 170 ~~ 171 (180)
..
T Consensus 637 ~~ 638 (639)
T PRK13534 637 VK 638 (639)
T ss_pred CC
Confidence 65
No 8
>PRK13795 hypothetical protein; Provisional
Probab=99.88 E-value=1.1e-21 Score=180.72 Aligned_cols=146 Identities=20% Similarity=0.332 Sum_probs=124.1
Q ss_pred cccCHHHHHHHHHHHHhHCCCCchhhcccCCCCCceEEEEe--eCceEEEEECCEE---EEEEecCCC--cchhhHh---
Q 030242 14 NQVKASVQRKIRQSIADEYPGLEPVLDDLLPKKSPLIVAKC--QNHLNLVLVNNVP---LFFNIRDGP--YMPTLRL--- 83 (180)
Q Consensus 14 ~~l~~sd~kkLr~~i~~~f~~~~~~~~~l~p~~~~v~~~k~--~~~~~~y~~dg~p---l~f~~~~~~--~~PTl~~--- 83 (180)
-+..++|++.|+..+.+|||.. ++|++..+.++|. ++++++|++||.+ ++|+..++. +.||+++
T Consensus 46 r~a~~~d~~~i~~~l~~~fG~~------~~~~~~~vllnK~~~~d~~~~vivdg~~~~~l~fd~~~~~~~~~p~l~ga~~ 119 (636)
T PRK13795 46 RPAFPYDIEFIRRVLEEEFGCD------LIPEDKLVLLNKIPGEDRADEIIVDGRVIGHLRFDLLELRWRFEPRLEGAKR 119 (636)
T ss_pred CcCCHHHHHHHHHHHHHHcCCC------CCCCCcEEEEecCCCCCcceEEEECCEEEEEEEeecccccceEecCHHHHHH
Confidence 3568899999999999999842 1567777888887 5688999999998 466654444 6788864
Q ss_pred hhcCCCCCcEEEECcchhhhhhcCCcccCCcccCCCCCCCcCCCCCCeEEEeeCCCCeEEEEEEEecCHHHHhcCCcceE
Q 030242 84 LHQYPNIMKKLQVDRGAIKFVLSGANIMCPGLTSPGGSLDEEVGAETPVAIMAEGKQHALAIGFTKMSAKDIKAINKGIG 163 (180)
Q Consensus 84 l~~~p~~~p~v~v~~~a~~~i~~GAdLm~pGV~~~~~~~~~~~~~Gd~V~V~~~~~~~~vaVG~~~~s~~~i~~~~kG~a 163 (180)
|++ +...++|+||++|+++|++||+||+|||++ ++++|++||+|+|++ +++.++|||++.+|+++|....+|+|
T Consensus 120 l~~-~~~~~~VvVd~ga~~~v~~Ga~l~~~GI~~----~~~~i~~gd~V~I~~-e~g~~vavG~a~~s~~e~~~~~kG~~ 193 (636)
T PRK13795 120 LLK-KRLKKWVIVDKGALEPIKNGKNVLAPGVVE----ADLDIKKGDEVVVVT-EDGEVVGVGRAKMDGDDMIKRFRGRA 193 (636)
T ss_pred Hhh-ccCCcEEEEcccHHHHHHcCCcccCCceEE----EeCCCCCCCEEEEEe-CCCCEEEEEEeccCHHHHhhccCCeE
Confidence 444 566899999999999999999999999999 778999999999998 45889999999999999999999999
Q ss_pred EEEEEEEc
Q 030242 164 VDNMHYLN 171 (180)
Q Consensus 164 v~v~H~~~ 171 (180)
|+++|...
T Consensus 194 Vkvr~~~~ 201 (636)
T PRK13795 194 VKVRKSGR 201 (636)
T ss_pred EEEEEccc
Confidence 99999863
No 9
>PRK13794 hypothetical protein; Provisional
Probab=99.85 E-value=1.1e-20 Score=169.06 Aligned_cols=146 Identities=16% Similarity=0.277 Sum_probs=120.7
Q ss_pred cccCHHHHHHHHHHHHhHCCCCchhhcccCCCCCceEEEEee--CceEEEEECCEEE---EEEecCCC--cchhhHhhhc
Q 030242 14 NQVKASVQRKIRQSIADEYPGLEPVLDDLLPKKSPLIVAKCQ--NHLNLVLVNNVPL---FFNIRDGP--YMPTLRLLHQ 86 (180)
Q Consensus 14 ~~l~~sd~kkLr~~i~~~f~~~~~~~~~l~p~~~~v~~~k~~--~~~~~y~~dg~pl---~f~~~~~~--~~PTl~~l~~ 86 (180)
-+....|.+.||..+.+|||. +++|++..+.++|+. +++..+++||.++ +|+..++. +.||+.++-.
T Consensus 44 r~a~~~d~~~i~~i~~~qFG~------~l~p~~~~vllnK~~~~~~~~eVi~dg~~l~~l~~~~~~~~w~~~l~~~ga~~ 117 (479)
T PRK13794 44 RPAFKYDIDLINKILEEQFGI------ENIPEGKIVLLNKVPGIERMEEIIVDGAVVGIIRYNEKKHRWKIIPRPEGARR 117 (479)
T ss_pred CcCChHHHHHHHHHHHHHcCC------cccCCCcEEEEecCCCCCcceEEEECCEEEEEEEeccccceeEEecCHHHHHH
Confidence 346789999999999999994 478888888888984 4667778999876 56665665 5667655433
Q ss_pred CCCC--CcEEEECcchhhhhh-cCCcccCCcccCCCCCCCcCCCCCCeEEEeeCCCCeEEEEEEEecCHHHHhcCCcceE
Q 030242 87 YPNI--MKKLQVDRGAIKFVL-SGANIMCPGLTSPGGSLDEEVGAETPVAIMAEGKQHALAIGFTKMSAKDIKAINKGIG 163 (180)
Q Consensus 87 ~p~~--~p~v~v~~~a~~~i~-~GAdLm~pGV~~~~~~~~~~~~~Gd~V~V~~~~~~~~vaVG~~~~s~~~i~~~~kG~a 163 (180)
+... .++|+||++|+++|+ +||+||+|||++ ++++|++||+|+|++ ++++++|+|++.+|+++|....+|+|
T Consensus 118 l~~~~~~~~V~Vd~ga~~~v~~~G~~v~~~GV~~----~~~~i~~gd~V~Iv~-~~g~~iavG~a~~s~~ei~~~~~G~~ 192 (479)
T PRK13794 118 LIPTAKKKFIVVKDDVPKFIRNKGASVLRPGVAE----ASEDIEEGDDVIILD-ENGDVVGVGRARMSYEEIVNMEKGMV 192 (479)
T ss_pred hhhccCCcEEEECccHHHHHHhCCCeecCCceEE----ecCCcCCCCEEEEEc-CCCcEEEEEEeecCHHHHHhccCceE
Confidence 3111 357999999999999 999999999999 778999999999998 45789999999999999999999999
Q ss_pred EEEEEEE
Q 030242 164 VDNMHYL 170 (180)
Q Consensus 164 v~v~H~~ 170 (180)
|+++|.-
T Consensus 193 Vkvr~~~ 199 (479)
T PRK13794 193 VKVRKSE 199 (479)
T ss_pred EEEEecc
Confidence 9999943
No 10
>COG1370 Prefoldin, molecular chaperone implicated in de novo protein folding, alpha subunit [Posttranslational modification, protein turnover, chaperones]
Probab=99.85 E-value=1.8e-20 Score=141.59 Aligned_cols=146 Identities=19% Similarity=0.333 Sum_probs=124.2
Q ss_pred ccCHHHHHHHHHHHHhHCCCCchhhcccCCCCCceEEEEeeCceEEEEECCEEEE-EEecCCCcchhhHh---hhcC-CC
Q 030242 15 QVKASVQRKIRQSIADEYPGLEPVLDDLLPKKSPLIVAKCQNHLNLVLVNNVPLF-FNIRDGPYMPTLRL---LHQY-PN 89 (180)
Q Consensus 15 ~l~~sd~kkLr~~i~~~f~~~~~~~~~l~p~~~~v~~~k~~~~~~~y~~dg~pl~-f~~~~~~~~PTl~~---l~~~-p~ 89 (180)
+..+.+.+++|..+.+|||. +..+++||++..+.++ -+++++.++.+|++++ .+.+||.+.||++. ||+. |.
T Consensus 2 ~~~~~~~~~vr~ia~YQfG~--~a~~~l~~~~v~~~~s-~tGRiRqV~~~G~~~~t~Ra~DG~~tL~~~Ga~~L~~~l~~ 78 (155)
T COG1370 2 EMRSRDLRRVRMIADYQFGR--GAGRALFPDDVKIVLS-KTGRIRQVFVDGERIATVRANDGLFTLTIEGARRLHRALPF 78 (155)
T ss_pred cchHHHHHHHHHHHHHHhch--hHHHHhccCCceEEEc-CCCceEEEEECCEEEEEEEcCCceEEechhhhHHHHhcCCC
Confidence 35688999999999999995 4577899999777633 3788988889998874 56678888999975 4542 22
Q ss_pred CCcEEEECcchhhhhhcCCcccCCcccCCCCCCCcCCCCCCeEEEeeCCCCeEEEEEEEecCHHHHhcCCcceEEEEEE
Q 030242 90 IMKKLQVDRGAIKFVLSGANIMCPGLTSPGGSLDEEVGAETPVAIMAEGKQHALAIGFTKMSAKDIKAINKGIGVDNMH 168 (180)
Q Consensus 90 ~~p~v~v~~~a~~~i~~GAdLm~pGV~~~~~~~~~~~~~Gd~V~V~~~~~~~~vaVG~~~~s~~~i~~~~kG~av~v~H 168 (180)
.--+|+|.+++.+|+.+|.|+|+..|++ .|+++++||+|+|+. ++++++|+|++++|..||...++|.||++..
T Consensus 79 P~~RVvV~~E~e~f~r~Gk~VFaKfVi~----~D~~iR~~dEvlVVn-e~d~LlAvGra~ls~~E~~~~~~G~AVkVr~ 152 (155)
T COG1370 79 PRMRVVVSDEAEEFVRKGKSVFAKFVID----VDEEIRAGDEVLVVN-EDDELLAVGRALLSGAEMREFERGMAVKVRE 152 (155)
T ss_pred CceEEEeccccHHHHHhccchhhhheec----cCcccCCCCeEEEEC-CCCcEEEeeeEeecHHHHhhccccEEEEEec
Confidence 1228999999999999999999999999 899999999999998 6689999999999999999999999999874
No 11
>TIGR00432 arcsn_tRNA_tgt tRNA-guanine transglycosylase, archaeosine-15-forming. This tRNA-guanine transglycosylase (tgt) differs from the tgt of E. coli and other Bacteria in the site of action and the modification that results. It exchanges 7-cyano-7-deazaguanine (preQ0) with guanine at position 15 of archaeal tRNA; this nucleotide is subsequently converted to archaeosine, found exclusively in the Archaea. This enzyme from Haloferax volcanii has been purified, characterized, and partially sequenced and is the basis for identifying this family. In contrast, bacterial tgt catalyzes the exchange of preQ0 or preQ1 for the guanine base at position 34; this nucleotide is subsequently modified to queuosine. Archeoglobus fulgidus has both enzymes, while some other Archaea have just this one.
Probab=99.80 E-value=8.3e-19 Score=158.30 Aligned_cols=145 Identities=12% Similarity=0.139 Sum_probs=122.2
Q ss_pred cCHHHHHHHHHHHHhHCCCCchhhcccCCCCCceEEEEeeCceEEEEECCEEEE-EEecCCCcchhhHhhhcC----CCC
Q 030242 16 VKASVQRKIRQSIADEYPGLEPVLDDLLPKKSPLIVAKCQNHLNLVLVNNVPLF-FNIRDGPYMPTLRLLHQY----PNI 90 (180)
Q Consensus 16 l~~sd~kkLr~~i~~~f~~~~~~~~~l~p~~~~v~~~k~~~~~~~y~~dg~pl~-f~~~~~~~~PTl~~l~~~----p~~ 90 (180)
.++.+..++|..+.+|||. ...+++||++..+..+|.+++...+..+|..++ ++.+||.+.||+++..+. +..
T Consensus 388 ~~~~~~~~ir~ia~YQFG~--g~g~~l~~~~~~v~~s~~tgr~r~v~~~~~~l~t~r~~dg~l~lt~~Ga~~l~~~~~~p 465 (540)
T TIGR00432 388 TTVDDLDRVRWMKHYQNGP--PNGELNVLSDVRIERSRNTGKIRHIYAGDELICTMRASDGLLVLGAEGAVRLHKGTDYP 465 (540)
T ss_pred hhhHHHHHHHHHHHhhcCc--CchHhhCCCCcEEEEeccCCcceEEEECCEEEEEEEcCCCeEEeCHHHHHHHHhcCCCC
Confidence 3668889999999999995 246789999877777766888877777777653 466788899999664332 333
Q ss_pred CcEEEECcchhhhhhcCCcccCCcccCCCCCCCcCCCCCCeEEEeeCCCCeEEEEEEEecCHHHHhcCCcceEEEEE
Q 030242 91 MKKLQVDRGAIKFVLSGANIMCPGLTSPGGSLDEEVGAETPVAIMAEGKQHALAIGFTKMSAKDIKAINKGIGVDNM 167 (180)
Q Consensus 91 ~p~v~v~~~a~~~i~~GAdLm~pGV~~~~~~~~~~~~~Gd~V~V~~~~~~~~vaVG~~~~s~~~i~~~~kG~av~v~ 167 (180)
--+|+|++.+.+++..|.++++|||++ .|+++++||+|+|+. ++++.+|||+|.||+.||....+|.||+|+
T Consensus 466 ~~rV~v~~~~~~f~~~g~~vfak~V~~----ad~~IR~~dEV~vv~-~~~~llavGra~lsg~em~~~~~G~AVkvR 537 (540)
T TIGR00432 466 AWRVAVNEESEPFARKGKSVFAKFIID----CDNNIRANDEVLIVN-ADDELLATGKALLCAEEMMDLNHGQAVKTR 537 (540)
T ss_pred ceEEEECCcchhhccCCCcccCCcccc----CCCCCCCCCeEEEEc-CCCcEEEEEehhcCHHHHHhhcCceEEEEe
Confidence 359999999999999999999999999 899999999999987 557999999999999999999999999997
No 12
>PF01472 PUA: PUA domain; InterPro: IPR002478 The PUA (PseudoUridine synthase and Archaeosine transglycosylase) domain was named after the proteins in which it was first found []. PUA is a highly conserved RNA-binding motif found in a wide range of archaeal, bacterial and eukaryotic proteins, including enzymes that catalyse tRNA and rRNA post-transcriptional modifications, proteins involved in ribosome biogenesis and translation, as well as in enzymes involved in proline biosynthesis [, ]. The structures of several PUA-RNA complexes reveal a common RNA recognition surface, but also some versatility in the way in which the motif binds to RNA []. PUA motifs are involved in dyskeratosis congenita and cancer, pointing to links between RNA metabolism and human diseases [].; GO: 0003723 RNA binding; PDB: 1ZE2_A 1ZE1_A 1R3E_A 2AB4_A 3R90_D 2J5T_A 2J5V_B 1Q7H_A 2APO_A 2RFK_A ....
Probab=99.79 E-value=1.5e-19 Score=123.40 Aligned_cols=74 Identities=32% Similarity=0.573 Sum_probs=67.1
Q ss_pred cEEEECcchhhhhhcCCcccCCcccCCCCCCCcCCCCCCeEEEeeCCCCeEEEEEEEecCHHHHhcCCcceEEEEEEEE
Q 030242 92 KKLQVDRGAIKFVLSGANIMCPGLTSPGGSLDEEVGAETPVAIMAEGKQHALAIGFTKMSAKDIKAINKGIGVDNMHYL 170 (180)
Q Consensus 92 p~v~v~~~a~~~i~~GAdLm~pGV~~~~~~~~~~~~~Gd~V~V~~~~~~~~vaVG~~~~s~~~i~~~~kG~av~v~H~~ 170 (180)
|+|++|++|+++|++||+||+|||+. ++++|++||+|.|++ .++.++|+|++.+|++||....+|+++++.|++
T Consensus 1 g~vvVd~~a~~~i~~Ga~L~~~GV~~----~~~~f~~gd~V~i~~-~~g~~ia~G~a~~ss~ei~~~~~g~~~~~~~~l 74 (74)
T PF01472_consen 1 GRVVVDDGAVEAILNGASLFAPGVVE----VDGDFRKGDEVAIVD-EDGEVIAVGRANMSSEEIKKMKKGKAVKIRHVL 74 (74)
T ss_dssp EEEEE-HHHHHHHHTTSEEEGGGEEE----EETT--TTSEEEEEE-TTSSEEEEEEESSTHHHHHHHSSSEEEEEEEEC
T ss_pred CEEEECccHHHHHHcCCCcchHHhEE----CCCCcCCCCEEEEEc-CCCeEEEEEEEecCHHHHHHHcCCcEehhhhhC
Confidence 68999999999999999999999999 778999999999999 558999999999999999999999999999974
No 13
>COG5270 PUA domain (predicted RNA-binding domain) [Translation, ribosomal structure and biogenesis]
Probab=99.61 E-value=9.8e-15 Score=114.07 Aligned_cols=141 Identities=20% Similarity=0.350 Sum_probs=116.5
Q ss_pred ccCHHHHHHHHHHHHhHCCCCchhhcccCCCCCceEEEEeeC--ceEEEEECCEE---EEEEecCCCcchhh-----Hhh
Q 030242 15 QVKASVQRKIRQSIADEYPGLEPVLDDLLPKKSPLIVAKCQN--HLNLVLVNNVP---LFFNIRDGPYMPTL-----RLL 84 (180)
Q Consensus 15 ~l~~sd~kkLr~~i~~~f~~~~~~~~~l~p~~~~v~~~k~~~--~~~~y~~dg~p---l~f~~~~~~~~PTl-----~~l 84 (180)
+....|+.-+|+.+.+.||. ..++++++.+.++|+++ ...++.+||.. ++|+.+..+|-+-+ ..|
T Consensus 49 ~~fp~die~Irevl~ee~G~-----~~~vl~g~ivLLNKIPG~D~~dEIvvdG~i~g~i~fd~~k~rW~~~lk~eGAk~L 123 (202)
T COG5270 49 PAFPYDIEVIREVLVEEFGV-----EKLVLEGEIVLLNKIPGEDDADEIVVDGFIFGIIRFDLRKLRWRFGLKLEGAKLL 123 (202)
T ss_pred ccCchHHHHHHHHHHHhcCc-----hhcccCCeEEEeecCCCCcccceEEecceEEEEEEecchhcccccccChHHHHHH
Confidence 45678999999999999984 23567778889999964 67888899964 57887665554443 334
Q ss_pred hcCCCCCcEEEECcchhhhhhcCCcccCCcccCCCCCCCcCCCCCCeEEEeeCCCCeEEEEEEEecCHHHHhcCCcceEE
Q 030242 85 HQYPNIMKKLQVDRGAIKFVLSGANIMCPGLTSPGGSLDEEVGAETPVAIMAEGKQHALAIGFTKMSAKDIKAINKGIGV 164 (180)
Q Consensus 85 ~~~p~~~p~v~v~~~a~~~i~~GAdLm~pGV~~~~~~~~~~~~~Gd~V~V~~~~~~~~vaVG~~~~s~~~i~~~~kG~av 164 (180)
|..- ...+.++.++.+++.||+|+.+|||++ ++.++++||.|+|.+ +|+.++|||++.+|++++....+|++|
T Consensus 124 ~e~~--~k~~~i~~~~~E~~~Ng~nV~~~gV~e----~~~~i~~~d~viVv~-~ng~~vGVg~a~~~~~~~in~~rG~~v 196 (202)
T COG5270 124 LEKG--KKGRKIDRGAVEPVKNGKNVLPPGVIE----AEDSIERGDEVIVVS-ENGRVVGVGIAKKSYEELINPERGTGV 196 (202)
T ss_pred HHhc--CccEEEEcccchhhhccCcccCCceee----ccCCcccCCeEEEEe-cCCEEEEEEEEecCHHHhcCcccCccc
Confidence 4431 567889999999999999999999999 777899999999988 789999999999999999998899999
Q ss_pred EEE
Q 030242 165 DNM 167 (180)
Q Consensus 165 ~v~ 167 (180)
++.
T Consensus 197 ~~~ 199 (202)
T COG5270 197 KPR 199 (202)
T ss_pred CCC
Confidence 875
No 14
>smart00359 PUA Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase.
Probab=99.29 E-value=1.7e-11 Score=83.20 Aligned_cols=74 Identities=32% Similarity=0.572 Sum_probs=66.8
Q ss_pred EEEECcchhhhhhcCCcccCCcccCCCCCCCcCCCCCCeEEEeeCCCCeEEEEEEEecCHHHHhcC--CcceEEEEEEEE
Q 030242 93 KLQVDRGAIKFVLSGANIMCPGLTSPGGSLDEEVGAETPVAIMAEGKQHALAIGFTKMSAKDIKAI--NKGIGVDNMHYL 170 (180)
Q Consensus 93 ~v~v~~~a~~~i~~GAdLm~pGV~~~~~~~~~~~~~Gd~V~V~~~~~~~~vaVG~~~~s~~~i~~~--~kG~av~v~H~~ 170 (180)
++++++++.+++++|++||.|||.. .++++++||+|.|++ .+++++|+|.+.+++.++... .+|.++++.|++
T Consensus 2 ~i~v~~~~~~~i~~g~~v~~~~v~~----~~~~~~~g~~V~v~~-~~g~~vg~G~~~~~s~~~~~~~~~~g~~v~~~~~~ 76 (77)
T smart00359 2 KVVVDDGAVKAILNGASLLAPGVVR----VDGGIKEGDVVVIVD-EKGEPLGIGLANMSSEEMARIKGEKGLAVKVRRAV 76 (77)
T ss_pred EEEEchhHHHHHHcCCCcccceeEE----EeCCcCCCCEEEEEc-CCCCEEEEEEEeCCHHHHHHHhccCceEEEEEEec
Confidence 5889999999999999999999988 556799999999998 568999999999999998876 599999999986
Q ss_pred c
Q 030242 171 N 171 (180)
Q Consensus 171 ~ 171 (180)
.
T Consensus 77 ~ 77 (77)
T smart00359 77 M 77 (77)
T ss_pred C
Confidence 3
No 15
>TIGR00425 CBF5 rRNA pseudouridine synthase, putative. This family, found in archaea and eukaryotes, includes the only archaeal proteins markedly similar to bacterial TruB, the tRNA pseudouridine 55 synthase. However, among two related yeast proteins, the archaeal set matches yeast YLR175w far better than YNL292w. The first, termed centromere/microtubule binding protein 5 (CBF5), is an apparent rRNA pseudouridine synthase, while the second is the exclusive tRNA pseudouridine 55 synthase for both cytosolic and mitochondrial compartments. It is unclear whether archaeal proteins found by this model modify tRNA, rRNA, or both.
Probab=99.23 E-value=4.6e-11 Score=102.33 Aligned_cols=78 Identities=28% Similarity=0.479 Sum_probs=70.9
Q ss_pred CcEEEECcchhhhhhcCCcccCCcccCCCCCCCcCCCCCCeEEEeeCCCCeEEEEEEEecCHHHHhcCCcceEEEEEEEE
Q 030242 91 MKKLQVDRGAIKFVLSGANIMCPGLTSPGGSLDEEVGAETPVAIMAEGKQHALAIGFTKMSAKDIKAINKGIGVDNMHYL 170 (180)
Q Consensus 91 ~p~v~v~~~a~~~i~~GAdLm~pGV~~~~~~~~~~~~~Gd~V~V~~~~~~~~vaVG~~~~s~~~i~~~~kG~av~v~H~~ 170 (180)
+|.+.+++.+.+++++|++++.||+.. .+.++..|+.|.|+. .++.++|||++.+|+++|....+|+||++.|++
T Consensus 237 lP~V~Vd~~~a~~I~NG~~I~~pgv~~----~d~~i~~gd~V~V~~-~~G~~LAIGea~~s~~ei~~~~kG~vV~~~~~~ 311 (322)
T TIGR00425 237 LKRVVVKDSAVDAICHGADLMVRGIAR----LEKGIEKGDTVAVIT-LKGEAVAVGIALMSTKDIANADKGVVADVKRVI 311 (322)
T ss_pred CCceEeCHHHHHHHHCCCccccccccc----cccccCCCCEEEEEE-CCCEEEEEEEEecCHHHHhhcCCcEEEEEEEEe
Confidence 689999999999999999999999987 555578899999987 457999999999999999998999999999999
Q ss_pred ccc
Q 030242 171 NDG 173 (180)
Q Consensus 171 ~D~ 173 (180)
+|.
T Consensus 312 ~~~ 314 (322)
T TIGR00425 312 MER 314 (322)
T ss_pred eCC
Confidence 985
No 16
>PRK04270 H/ACA RNA-protein complex component Cbf5p; Reviewed
Probab=99.15 E-value=2e-10 Score=97.64 Aligned_cols=76 Identities=25% Similarity=0.398 Sum_probs=69.2
Q ss_pred CcEEEECcchhhhhhcCCcccCCcccCCCCCCCcCCCCCCeEEEeeCCCCeEEEEEEEecCHHHHhcCCcceEEEEEEEE
Q 030242 91 MKKLQVDRGAIKFVLSGANIMCPGLTSPGGSLDEEVGAETPVAIMAEGKQHALAIGFTKMSAKDIKAINKGIGVDNMHYL 170 (180)
Q Consensus 91 ~p~v~v~~~a~~~i~~GAdLm~pGV~~~~~~~~~~~~~Gd~V~V~~~~~~~~vaVG~~~~s~~~i~~~~kG~av~v~H~~ 170 (180)
+|.+.+++++.+++.+|++++.||+.. .+.++.+||.|.|+. .++.++|+|.+.+|++++....+|+||++.|++
T Consensus 225 LP~V~Lde~aa~~I~nG~~L~~~gi~~----~~~~~~~gd~V~I~~-~~G~~LAIG~~~~ss~el~~~~kG~~vk~~~~~ 299 (300)
T PRK04270 225 LPKIIIKDSAVDAIAHGAPLYAPGIAK----LEKGIKKGDLVAVFT-LKGELVALGKALMDSDEILKAEKGIVVDLERVF 299 (300)
T ss_pred CCceEECHHHHHHHHcCCccccCCcee----cccccCCCCEEEEEe-CCCcEEEEEEEccCHHHHHhcCCceEEEEEEee
Confidence 689999999999999999999999987 555678899999987 467899999999999999999999999999998
Q ss_pred c
Q 030242 171 N 171 (180)
Q Consensus 171 ~ 171 (180)
+
T Consensus 300 ~ 300 (300)
T PRK04270 300 M 300 (300)
T ss_pred C
Confidence 4
No 17
>PRK05429 gamma-glutamyl kinase; Provisional
Probab=98.96 E-value=2.4e-09 Score=93.49 Aligned_cols=64 Identities=20% Similarity=0.385 Sum_probs=58.9
Q ss_pred CCCcEEEECcchhhhh-hcCCcccCCcccCCCCCCCcCCCCCCeEEEeeCCCCeEEEEEEEecCHHHHhc
Q 030242 89 NIMKKLQVDRGAIKFV-LSGANIMCPGLTSPGGSLDEEVGAETPVAIMAEGKQHALAIGFTKMSAKDIKA 157 (180)
Q Consensus 89 ~~~p~v~v~~~a~~~i-~~GAdLm~pGV~~~~~~~~~~~~~Gd~V~V~~~~~~~~vaVG~~~~s~~~i~~ 157 (180)
...+.|+||++|+++| ++||+|++|||++ ++.+|++||.|.|++ .+++++|+|++.+|++|+..
T Consensus 278 ~~~g~i~vd~gA~~al~~~g~sLl~~Gi~~----v~g~f~~gd~V~i~~-~~g~~va~G~~~~~s~e~~~ 342 (372)
T PRK05429 278 QPAGEIVVDAGAVKALLERGKSLLPAGVTA----VEGDFSRGDVVRIVD-PDGREIARGLVNYSSDELRR 342 (372)
T ss_pred CCCCeEEECccHHHHHHhcCCccCccchhh----eECcccCCCEEEEEC-CCCCEEEEEEecCCHHHHHH
Confidence 3567999999999999 8999999999999 777999999999998 66899999999999999976
No 18
>COG1549 Queuine tRNA-ribosyltransferases, contain PUA domain [Translation, ribosomal structure and biogenesis]
Probab=98.94 E-value=6.2e-09 Score=92.49 Aligned_cols=70 Identities=19% Similarity=0.324 Sum_probs=59.7
Q ss_pred CcEEEECcchhhhhhcCCcccCCcccCCCCCCCcCCCCCCeEEEeeCCCCeEEEEEEEecCHHHHhcCCcceEEEEEEEE
Q 030242 91 MKKLQVDRGAIKFVLSGANIMCPGLTSPGGSLDEEVGAETPVAIMAEGKQHALAIGFTKMSAKDIKAINKGIGVDNMHYL 170 (180)
Q Consensus 91 ~p~v~v~~~a~~~i~~GAdLm~pGV~~~~~~~~~~~~~Gd~V~V~~~~~~~~vaVG~~~~s~~~i~~~~kG~av~v~H~~ 170 (180)
.-+|-||+... --++++|||++ ++++|++||+|.|+- ++++.|||+|.||+.||...+||.||+|+|+.
T Consensus 450 ~~~VEId~f~~-----~g~v~a~GV~d----a~edIrpnDeV~vv~--~~~v~gVGrA~msg~eM~~akkGiaV~VR~~~ 518 (519)
T COG1549 450 IYWVEIDDFIP-----RGSVFAPGVVD----ADEDIRPNDEVVVVH--GGEVRGVGRAVMSGREMVEAKKGIAVRVRRRK 518 (519)
T ss_pred eeEEEcCCccc-----ccccccccccc----CCCCCCcCCEEEEEe--CCeEEEEeeeecChHHhcccCCceEEEEEecc
Confidence 34677776633 45899999999 889999999997754 37899999999999999999999999999985
Q ss_pred c
Q 030242 171 N 171 (180)
Q Consensus 171 ~ 171 (180)
+
T Consensus 519 ~ 519 (519)
T COG1549 519 K 519 (519)
T ss_pred C
Confidence 3
No 19
>TIGR01027 proB glutamate 5-kinase. Bacterial ProB proteins hit the full length of this model, but the ProB-like domain of delta 1-pyrroline-5-carboxylate synthetase does not hit the C-terminal 100 residues of this model. The noise cutoff is set low enough to hit delta 1-pyrroline-5-carboxylate synthetase and other partial matches to this family.
Probab=98.69 E-value=6.5e-08 Score=84.27 Aligned_cols=63 Identities=17% Similarity=0.369 Sum_probs=57.1
Q ss_pred CCcEEEECcchhhhhhc-CCcccCCcccCCCCCCCcCCCCCCeEEEeeCCCCeEEEEEEEecCHHHHhc
Q 030242 90 IMKKLQVDRGAIKFVLS-GANIMCPGLTSPGGSLDEEVGAETPVAIMAEGKQHALAIGFTKMSAKDIKA 157 (180)
Q Consensus 90 ~~p~v~v~~~a~~~i~~-GAdLm~pGV~~~~~~~~~~~~~Gd~V~V~~~~~~~~vaVG~~~~s~~~i~~ 157 (180)
..+.|+||++|.++|.+ |++||.+||++ +..+|.+||+|.|+. .++.++|.|.+.+|++|+..
T Consensus 271 ~~G~i~vD~gA~~al~~~g~sLl~~Gi~~----v~g~F~~gd~v~i~~-~~~~~ia~g~~~y~s~~~~~ 334 (363)
T TIGR01027 271 PAGEITVDAGAEEALLERGKSLLPAGIVG----VEGNFSRGEVVEILN-PEGQDIGRGLVNYSSDELEK 334 (363)
T ss_pred cCCeEEEChhHHHHHHhcCCccCCcccee----eECcccCCCEEEEEC-CCCCEEEEEEecCCHHHHHH
Confidence 34699999999999985 99999999999 677899999999998 55899999999999999865
No 20
>PF09183 DUF1947: Domain of unknown function (DUF1947); InterPro: IPR015266 Members of this entry are a set of hypothetical archaeal proteins. Their exact function has not, as yet, been defined. ; PDB: 1Q7H_A.
Probab=98.41 E-value=1.4e-06 Score=57.55 Aligned_cols=63 Identities=22% Similarity=0.472 Sum_probs=41.7
Q ss_pred ccccCHHHHHHHHHHHHhHCCCCchhhcccCCCCCceEEEEeeCceEEEEECCEEEEEEecCCCcchhhHhhhcC
Q 030242 13 QNQVKASVQRKIRQSIADEYPGLEPVLDDLLPKKSPLIVAKCQNHLNLVLVNNVPLFFNIRDGPYMPTLRLLHQY 87 (180)
Q Consensus 13 ~~~l~~sd~kkLr~~i~~~f~~~~~~~~~l~p~~~~v~~~k~~~~~~~y~~dg~pl~f~~~~~~~~PTl~~l~~~ 87 (180)
...|+..|+|++.+.+.+.||.. + ++ +.|++.+ +.+...|++||.|+||+ + .++||||+|.++
T Consensus 2 RH~LSkKe~k~~~~k~~~~ygId---i----~~-~~vEI~~-~kk~~~yyi~~~p~ff~--~-~lIPtL~~l~k~ 64 (65)
T PF09183_consen 2 RHFLSKKEIKEIKEKIKEKYGID---I----SG-EKVEIGK-EKKFSIYYIDGVPAFFN--D-KLIPTLCFLNKH 64 (65)
T ss_dssp -EE--HHHHHHHHHHHHT-TT----------TT----EEEE--SS-EEEEETTEEEEEE--S-SEEE-HHHHHHS
T ss_pred cccccHHHHHHHHHHHHHHhCcC---C----Cc-cceeeee-ccceEEEEECCchhhhc--C-CcchhhhhHhhc
Confidence 35689999999999999999831 2 22 4577776 44456899999999986 3 699999999865
No 21
>PRK08557 hypothetical protein; Provisional
Probab=98.29 E-value=3.4e-06 Score=74.77 Aligned_cols=127 Identities=15% Similarity=0.170 Sum_probs=92.0
Q ss_pred ccCHHHHHHHHHHHHhHCCCCchhhcccCCCCCceEEEEee--CceEEEEECCEE---EEEEecCCC--cchhhHhhhcC
Q 030242 15 QVKASVQRKIRQSIADEYPGLEPVLDDLLPKKSPLIVAKCQ--NHLNLVLVNNVP---LFFNIRDGP--YMPTLRLLHQY 87 (180)
Q Consensus 15 ~l~~sd~kkLr~~i~~~f~~~~~~~~~l~p~~~~v~~~k~~--~~~~~y~~dg~p---l~f~~~~~~--~~PTl~~l~~~ 87 (180)
+....|++.|++.+.++||.. ..+.++|+. +++.++++||.. +.|+..+.. +.|+...+. .
T Consensus 8 ~a~~~d~~~~~~~~~~~f~~~-----------~~vllnk~p~~d~~~ev~~~g~~~g~~~~~~~~~~w~~~p~~~~~~-~ 75 (417)
T PRK08557 8 FASPYEIKILNKLTNKNFQYD-----------DAIILEKLSGLDYRKRVYISEDQIGILEFDLLDLDWKFHPSPSYYL-I 75 (417)
T ss_pred cCCHHHHHHHHHHHHHHcCCC-----------eEEEEeCCCCccchhheeECCeEEEEEEEccccceeEEccchhhhh-c
Confidence 467899999999999999831 247788885 578888999975 456654433 466654322 1
Q ss_pred CCCCcEEEECcchhhhhhcCCcccCCcccCCCCCCCcCCCCCCeEEEeeCCCCeEEEEEEEecCHHHHhcCCcce
Q 030242 88 PNIMKKLQVDRGAIKFVLSGANIMCPGLTSPGGSLDEEVGAETPVAIMAEGKQHALAIGFTKMSAKDIKAINKGI 162 (180)
Q Consensus 88 p~~~p~v~v~~~a~~~i~~GAdLm~pGV~~~~~~~~~~~~~Gd~V~V~~~~~~~~vaVG~~~~s~~~i~~~~kG~ 162 (180)
. .+.+.++. +.++| +|+++..++|.+... + +++++||.|.|.. +..+|||++.++...+....+|.
T Consensus 76 ~--~~~~~~~~-~~~~~-~g~~v~~~~~~~~~~-~-~~~~~~~~v~~~~---~~~~gvg~~~~~~~k~~~~~~~~ 141 (417)
T PRK08557 76 E--EPKIKLKP-TKRRL-KGKYIKEELIENPEE-L-NEILENDYVGVEI---GNFLGVGVKKEDRIKIKDLSLKK 141 (417)
T ss_pred c--Cceeeecc-ccccc-CCccccccccccccc-c-ccCCCCCEEEEec---CCEEEEEEeecceEEEEecccCC
Confidence 1 46788876 66666 999999999987332 2 3799999888865 67999999999876666555554
No 22
>PRK13402 gamma-glutamyl kinase; Provisional
Probab=97.98 E-value=2.2e-05 Score=68.63 Aligned_cols=63 Identities=10% Similarity=0.118 Sum_probs=56.6
Q ss_pred CCcEEEECcchhhhhh-cCCcccCCcccCCCCCCCcCCCCCCeEEEeeCCCCeEEEEEEEecCHHHHhc
Q 030242 90 IMKKLQVDRGAIKFVL-SGANIMCPGLTSPGGSLDEEVGAETPVAIMAEGKQHALAIGFTKMSAKDIKA 157 (180)
Q Consensus 90 ~~p~v~v~~~a~~~i~-~GAdLm~pGV~~~~~~~~~~~~~Gd~V~V~~~~~~~~vaVG~~~~s~~~i~~ 157 (180)
....++||++|.++|. +|+.|+..||+. +..+|.+||.|.|+. .++..+|.|.+.+|++|+..
T Consensus 275 ~~G~i~vd~ga~~al~~~~~sLl~~gi~~----v~g~F~~gd~v~i~~-~~g~~~~rg~~~y~s~~~~~ 338 (368)
T PRK13402 275 PQGEIVVENDFDRALDNHSEQLTSDDVVE----IKGDFSVGDTILVRK-GDGTKLAKGKSNYSSCLLNF 338 (368)
T ss_pred CCeeEEECccHHHHHHhcCCcccccceEE----EeCEecCCCEEEEEC-CCCCEEEEEEccCCHHHHHH
Confidence 3459999999999996 689999999999 667899999999998 56899999999999999865
No 23
>PF14810 TGT_C2: Patch-forming domain C2 of tRNA-guanine transglycosylase; PDB: 1J2B_A 1IT8_A 1IT7_B 1IQ8_A.
Probab=97.85 E-value=2.5e-05 Score=53.21 Aligned_cols=61 Identities=21% Similarity=0.249 Sum_probs=39.6
Q ss_pred HHHHHHHHhHCCCCchhhcccCCCCCceEEEEeeCceEEEEECCEEEE-EEecCCCcchhhHhh
Q 030242 22 RKIRQSIADEYPGLEPVLDDLLPKKSPLIVAKCQNHLNLVLVNNVPLF-FNIRDGPYMPTLRLL 84 (180)
Q Consensus 22 kkLr~~i~~~f~~~~~~~~~l~p~~~~v~~~k~~~~~~~y~~dg~pl~-f~~~~~~~~PTl~~l 84 (180)
+.||..+.+|||. ...++|||++..+..++-+.+.+.+..||+.++ ++.+||.+.||++..
T Consensus 2 ~~lr~iAdYQFG~--gag~~lf~d~~~i~~s~~t~riR~v~~~~~~latlr~~DG~l~Lt~~Ga 63 (74)
T PF14810_consen 2 NRLRAIADYQFGR--GAGDALFPDDIEIQRSKKTGRIRQVLVDGERLATLRAQDGLLTLTLEGA 63 (74)
T ss_dssp HHHHHHHHHHT-T--TGGGGTTT---EEEE--SSS-EEEEEETTEEEEEE-TTTS-EEE-HHHH
T ss_pred hHHHHHHHHHcCc--ChHHHhcccCcEEEEeccCCceEEEEeCCeEEEEEEcCCCeEEeCHHHH
Confidence 5799999999995 357889999976766666788887788888543 444688899999653
No 24
>COG0263 ProB Glutamate 5-kinase [Amino acid transport and metabolism]
Probab=97.42 E-value=0.00033 Score=60.66 Aligned_cols=61 Identities=23% Similarity=0.426 Sum_probs=54.4
Q ss_pred CcEEEECcchhhhhh-cCCcccCCcccCCCCCCCcCCCCCCeEEEeeCCCCeEEEEEEEecCHHHHhc
Q 030242 91 MKKLQVDRGAIKFVL-SGANIMCPGLTSPGGSLDEEVGAETPVAIMAEGKQHALAIGFTKMSAKDIKA 157 (180)
Q Consensus 91 ~p~v~v~~~a~~~i~-~GAdLm~pGV~~~~~~~~~~~~~Gd~V~V~~~~~~~~vaVG~~~~s~~~i~~ 157 (180)
-..+++|.+|.++|. +|..|..-||+. +..+|..||.|.|+ .++..+|=|.+.+|++|+..
T Consensus 279 ~G~i~iD~GA~~Al~~~gkSLLpaGV~~----V~G~F~rGdvV~i~--~~g~~iarG~v~Y~s~el~~ 340 (369)
T COG0263 279 AGEITVDAGAVEALLEQGKSLLPAGVTS----VEGNFSRGDVVRIR--PQGGEIARGLVNYSSDELRK 340 (369)
T ss_pred CceEEECccHHHHHHhcCCccccccceE----eeeeecCCCEEEEe--cCCceeEeeeccCCHHHHHH
Confidence 368999999999999 899999999999 66689999999999 34559999999999999865
No 25
>KOG2529 consensus Pseudouridine synthase [Translation, ribosomal structure and biogenesis]
Probab=96.16 E-value=0.0028 Score=55.55 Aligned_cols=76 Identities=20% Similarity=0.351 Sum_probs=67.9
Q ss_pred CcEEEECcchhhhhhcCCcccCCcccCCCCCCCcCCCCCCeEEEeeCCCCeEEEEEEEecCHHHHhcCCcceEEEEEEEE
Q 030242 91 MKKLQVDRGAIKFVLSGANIMCPGLTSPGGSLDEEVGAETPVAIMAEGKQHALAIGFTKMSAKDIKAINKGIGVDNMHYL 170 (180)
Q Consensus 91 ~p~v~v~~~a~~~i~~GAdLm~pGV~~~~~~~~~~~~~Gd~V~V~~~~~~~~vaVG~~~~s~~~i~~~~kG~av~v~H~~ 170 (180)
..+++..+.+++.+|.||-+|.||+.. +++++..+..+++.+ .+++.++.+.+.++..++...+.|...+...++
T Consensus 275 ~~~vv~kd~~v~~~cyg~k~~v~~~~r----~~~~i~~~~e~v~~t-~k~e~~~~~i~~~~~~~~~s~dh~~~a~~k~~~ 349 (395)
T KOG2529|consen 275 YKRVVVKDSTVNAPCYGAKLLVPGLLR----YSDDIDGPFEVVDMT-TKGEAIASKIAEMSLRQVASCDHGVVAKTKRVI 349 (395)
T ss_pred ceeeecccchhcCccccceeeeccccc----cCccccCceeEEEEe-ecchhhhhhhhhhhhhhhceeeeeeeccccccc
Confidence 468999999999999999999999998 677888889999988 678999999999999999999999888888774
Q ss_pred c
Q 030242 171 N 171 (180)
Q Consensus 171 ~ 171 (180)
+
T Consensus 350 m 350 (395)
T KOG2529|consen 350 M 350 (395)
T ss_pred c
Confidence 3
No 26
>PRK14124 tRNA pseudouridine synthase B; Provisional
Probab=96.11 E-value=0.021 Score=48.96 Aligned_cols=74 Identities=11% Similarity=0.159 Sum_probs=58.7
Q ss_pred CcEEEECcchhhhhhcCCcccCCcccCCCCCCCcCCCCCCeEEEeeCCCCeEEEEEEEecCHHHHhc----CCcceEEEE
Q 030242 91 MKKLQVDRGAIKFVLSGANIMCPGLTSPGGSLDEEVGAETPVAIMAEGKQHALAIGFTKMSAKDIKA----INKGIGVDN 166 (180)
Q Consensus 91 ~p~v~v~~~a~~~i~~GAdLm~pGV~~~~~~~~~~~~~Gd~V~V~~~~~~~~vaVG~~~~s~~~i~~----~~kG~av~v 166 (180)
+|.+.+++...+.|++|+.+-.+++.. . .++..++.|.+.. .++.++|+|.+..++..+.. ..+|.+++.
T Consensus 228 lp~v~l~~~~~~~i~~G~~i~~~~~~~----~-~~~~~~~~v~v~~-~~g~~lai~~~~~~~~~~~~~~~~~~~~~v~~~ 301 (308)
T PRK14124 228 LPKVVIHQESTEKILNGSQIYLEMVKE----W-DNFKKDDVVRVFD-EEGRLLAIARAERNSSFLETLKKHERNERVLKL 301 (308)
T ss_pred CceEEeCHHHHHHHHCCCccccccccc----c-cccCCCCEEEEEc-CCCeEEEEEEEecCCceeeeeecccccceEEee
Confidence 689999999999999999997776544 2 2356688888877 46789999999988876554 245999998
Q ss_pred EEEE
Q 030242 167 MHYL 170 (180)
Q Consensus 167 ~H~~ 170 (180)
.+++
T Consensus 302 ~~v~ 305 (308)
T PRK14124 302 KKVF 305 (308)
T ss_pred eeee
Confidence 8876
No 27
>PF03657 UPF0113: Uncharacterised protein family (UPF0113); InterPro: IPR005155 This entry represents PUA (PseudoUridine synthase and Archaeosine transglycosylase) domain containing proteins such as the ribosomal biogenesis factor NIP7 [, ]. PUA domains are predicted to bind RNA molecules with complex folded structures []. NIP7 is required for efficient 60S ribosome subunit biogenesis and has been shown to interact with another essential nucleolar protein, Nop8p, and the exosome subunit Rrp43p. These three proteins are required for 60S subunit synthesis and may be part of a dynamic complex involved in this process.; PDB: 1T5Y_A 1SQW_A 2P38_A.
Probab=90.64 E-value=0.49 Score=36.90 Aligned_cols=119 Identities=15% Similarity=0.247 Sum_probs=65.8
Q ss_pred ccCHHHHHHHHHHHHhHCCCCchhhcccCCCCCceEEEEeeCceEEEEECC--------E------EEEE-EecC-C-Cc
Q 030242 15 QVKASVQRKIRQSIADEYPGLEPVLDDLLPKKSPLIVAKCQNHLNLVLVNN--------V------PLFF-NIRD-G-PY 77 (180)
Q Consensus 15 ~l~~sd~kkLr~~i~~~f~~~~~~~~~l~p~~~~v~~~k~~~~~~~y~~dg--------~------pl~f-~~~~-~-~~ 77 (180)
+|+..|.+.+.+.+. .|+... .++ . ......+.. +-++|++.. . -+++ ++.. + .+
T Consensus 5 ~Lt~eE~~~v~~kL~-~yg~~~-~l~----~-~~~~~~~~~-~~~Vyyvs~~l~~~~~~~~~~~s~G~~~G~f~k~~~kf 76 (162)
T PF03657_consen 5 PLTEEETKIVFEKLS-KYGGNN-LLD----H-FDFYVFRLH-KDRVYYVSEELMKLASNRPNLYSLGTCLGKFTKKGKKF 76 (162)
T ss_dssp E--HHHHHHHHHHHH-CCCCGH-CCE----E-TEEEEEECC-TCEEEEEEHHHHCCCTTCHHHHCCSEEEEEE-TTTSEE
T ss_pred CCCHHHHHHHHHHHH-Hhcchh-hcc----c-ccceeeeee-cceEEEECHHHHHHHhCCCccceeceEEEEEecCCccc
Confidence 588999999999885 687421 111 1 112222221 234443321 0 0222 2222 2 35
Q ss_pred chhhHhhhc-CCCCCcEEEECcchhhhhhcCCcccCCcccCCCCCCCcCCCCCCeEEEeeCCCCeEEEEEEE
Q 030242 78 MPTLRLLHQ-YPNIMKKLQVDRGAIKFVLSGANIMCPGLTSPGGSLDEEVGAETPVAIMAEGKQHALAIGFT 148 (180)
Q Consensus 78 ~PTl~~l~~-~p~~~p~v~v~~~a~~~i~~GAdLm~pGV~~~~~~~~~~~~~Gd~V~V~~~~~~~~vaVG~~ 148 (180)
..++-++.- .+.....|.+.+.+....+.|.|++..||.. +.++..+. |+|+. .++.|+++|..
T Consensus 77 ~l~i~~l~~la~~~~~kvwvk~~~e~~FLYGndV~ks~i~~----i~e~~~~~--VvV~n-~~d~~LGfG~~ 141 (162)
T PF03657_consen 77 RLHITALDYLAPYAKNKVWVKPKAEMLFLYGNDVLKSSIGR----ITEDTPQN--VVVYN-MNDVPLGFGCR 141 (162)
T ss_dssp EEEGHHHHCCCCC-SSEEEE-HHHHHHHCTT--EEGGGEEE----EETTS-TC--EEEEE-TTS-EEEEEEC
T ss_pred eeeHHHHHHhhhccceeEEECCCceEEeeecCCchHhhcEE----ecCCCCce--EEEEe-CCCCeEEEEEe
Confidence 555544433 3444558999999988888999999999988 55555544 88888 77899999943
No 28
>KOG3492 consensus Ribosome biogenesis protein NIP7 [Translation, ribosomal structure and biogenesis]
Probab=90.09 E-value=0.62 Score=36.05 Aligned_cols=72 Identities=17% Similarity=0.248 Sum_probs=60.2
Q ss_pred cEEEECcchhhhhhcCCcccCCcccCCCCCCCcCCCCCCeEEEeeCCCCeEEEEEEEecCHHHHhcCCcceEEEEEEE
Q 030242 92 KKLQVDRGAIKFVLSGANIMCPGLTSPGGSLDEEVGAETPVAIMAEGKQHALAIGFTKMSAKDIKAINKGIGVDNMHY 169 (180)
Q Consensus 92 p~v~v~~~a~~~i~~GAdLm~pGV~~~~~~~~~~~~~Gd~V~V~~~~~~~~vaVG~~~~s~~~i~~~~kG~av~v~H~ 169 (180)
-.|-+.+++-...+.|.++...||-. +.+++...+-|.|++ -++.|++-|.+..|+.+.. ...+.|+-++|-
T Consensus 95 ~KvWiKp~~Em~flYGNhvlKs~vgR----itd~~p~~~GVvVys-m~DvPLGFGv~Akst~d~r-~~dp~aiv~~hQ 166 (180)
T KOG3492|consen 95 YKVWIKPNAEMQFLYGNHVLKSGVGR----ITDGIPQHQGVVVYS-MNDVPLGFGVTAKSTQDCR-KADPTAIVVLHQ 166 (180)
T ss_pred eeEEeccCcccceeecccchhcccce----ecCCCCCcceEEEEe-ccCCccccceeecCccccc-ccCCcEEEEEEe
Confidence 46778888877777999999999976 777888899999998 7789999999999998865 456777878875
No 29
>PRK00130 truB tRNA pseudouridine synthase B; Provisional
Probab=86.95 E-value=1.7 Score=37.03 Aligned_cols=50 Identities=18% Similarity=0.289 Sum_probs=38.4
Q ss_pred CcEEEECcchhhhhhcCCcccCCcccCCCCCCCcCCCCCCeEEEeeCCCCeEEEEEEE
Q 030242 91 MKKLQVDRGAIKFVLSGANIMCPGLTSPGGSLDEEVGAETPVAIMAEGKQHALAIGFT 148 (180)
Q Consensus 91 ~p~v~v~~~a~~~i~~GAdLm~pGV~~~~~~~~~~~~~Gd~V~V~~~~~~~~vaVG~~ 148 (180)
+|.+.+++...+.+++|+.+-.+++.. .+..++.|.+.. .++.++|+|..
T Consensus 229 lp~v~l~~~~~~~i~~G~~i~~~~~~~-------~~~~~~~v~~~~-~~g~~lai~~~ 278 (290)
T PRK00130 229 YPKVSLDEKFEKLLLNGVKIKDRRLLD-------NIEENKLYRVYD-EENKFIGIGMK 278 (290)
T ss_pred CCEEEECHHHHHHHHCcCccccCcccc-------cCCCCCEEEEEc-CCCeEEEEEEE
Confidence 689999999999999999986555432 234567787776 45789999974
No 30
>PF09157 TruB-C_2: Pseudouridine synthase II TruB, C-terminal; InterPro: IPR015240 Pseudouridine synthases catalyse the isomerisation of uridine to pseudouridine (Psi) in a variety of RNA molecules, and may function as RNA chaperones. Pseudouridine is the most abundant modified nucleotide found in all cellular RNAs. There are four distinct families of pseudouridine synthases that share no global sequence similarity, but which do share the same fold of their catalytic domain(s) and uracil-binding site and are descended from a common molecular ancestor. The catalytic domain consists of two subdomains, each of which has an alpha+beta structure that has some similarity to the ferredoxin-like fold (note: some pseudouridine synthases contain additional domains). The active site is the most conserved structural region of the superfamily and is located between the two homologous domains. These families are []: Pseudouridine synthase I, TruA. Pseudouridine synthase II, TruB, which contains and additional C-terminal PUA domain. Pseudouridine synthase RsuA (ribosomal small subunit) and RluC/RluD (ribosomal large subunits), both of which contain an additional N-terminal alpha-L RNA-binding motif. Pseudouridine synthase TruD, which has a natural circular permutation in the catalytic domain, as well as an insertion of a family-specific alpha+beta subdomain. TruB is responsible for the pseudouridine residue present in the T loops of virtually all tRNAs. TruB recognises the preformed 3-D structure of the T loop primarily through shape complementarity. It accesses its substrate uridyl residue by flipping out the nucleotide and disrupts the tertiary structure of tRNA []. The C-terminal domain adopts a secondary structure consisting of a four-stranded beta sheet and one alpha helix, similar to that found in PUA domains. It is predominantly involved in RNA-binding, being mostly found in tRNA pseudouridine synthase B (TruB) []. ; GO: 0003723 RNA binding, 0009982 pseudouridine synthase activity, 0001522 pseudouridine synthesis, 0009451 RNA modification; PDB: 1ZL3_A 1K8W_A 1R3F_A.
Probab=84.33 E-value=3.6 Score=25.93 Aligned_cols=47 Identities=17% Similarity=0.169 Sum_probs=30.3
Q ss_pred cEEEECcchhhhhhcCCcccCCcccCCCCCCCcCCCCCCeEEEeeCCCCeEEEEEEEe
Q 030242 92 KKLQVDRGAIKFVLSGANIMCPGLTSPGGSLDEEVGAETPVAIMAEGKQHALAIGFTK 149 (180)
Q Consensus 92 p~v~v~~~a~~~i~~GAdLm~pGV~~~~~~~~~~~~~Gd~V~V~~~~~~~~vaVG~~~ 149 (180)
|.|.+++.....+++|-.+-... .....| .|.|++ .++.++|||...
T Consensus 1 P~v~L~~~~~~~~~~Gq~v~~~~---------~~~~~~-~vrvy~-~~~~FlGig~~~ 47 (58)
T PF09157_consen 1 PAVVLDEEQAKRFLHGQRVRLRD---------DAPPDG-LVRVYD-EDGRFLGIGEID 47 (58)
T ss_dssp -EEEE-HHHHHHHTTT--B---S---------S--SSS-EEEEET-TTTEEEEEEEE-
T ss_pred CeEEeCHHHHHHHHCcCcccccC---------CCCCCc-eEEEEC-CCCEEEEEEEEc
Confidence 67889999999999999873311 123445 999995 668999999874
No 31
>COG0130 TruB Pseudouridine synthase [Translation, ribosomal structure and biogenesis]
Probab=81.41 E-value=3 Score=35.23 Aligned_cols=49 Identities=18% Similarity=0.284 Sum_probs=37.2
Q ss_pred CCcEEEECcchhhhhhcCCcccCCcccCCCCCCCcCCCCCCeEEEeeCCCCeEEEEEEEecCHHH
Q 030242 90 IMKKLQVDRGAIKFVLSGANIMCPGLTSPGGSLDEEVGAETPVAIMAEGKQHALAIGFTKMSAKD 154 (180)
Q Consensus 90 ~~p~v~v~~~a~~~i~~GAdLm~pGV~~~~~~~~~~~~~Gd~V~V~~~~~~~~vaVG~~~~s~~~ 154 (180)
.+|++.+++.++..+++|+. ||+.. +.+|+.|+|.+.. + .|.+.++.++
T Consensus 212 ~lpk~~i~~~~~~~i~~G~~---~~~~~--------~~~~~~v~v~~~~-~----~~~al~~~~~ 260 (271)
T COG0130 212 DLPRLVLKDSAANAIKYGAK---PGLLD--------IELGGLVRVYTAK-G----LGIALGEIDE 260 (271)
T ss_pred cCCcEecCHHHHHHHHcCCc---hhccc--------cccCCcEEEEccC-C----eEEEEeehhh
Confidence 36899999999999999999 77643 6789999999844 4 4444444443
No 32
>PRK05033 truB tRNA pseudouridine synthase B; Provisional
Probab=80.91 E-value=4 Score=35.13 Aligned_cols=47 Identities=13% Similarity=0.210 Sum_probs=35.2
Q ss_pred CcEEEECcchhhhhhcCCcccCCcccCCCCCCCcCCCCCCeEEEeeCCCCeEEEEEEE
Q 030242 91 MKKLQVDRGAIKFVLSGANIMCPGLTSPGGSLDEEVGAETPVAIMAEGKQHALAIGFT 148 (180)
Q Consensus 91 ~p~v~v~~~a~~~i~~GAdLm~pGV~~~~~~~~~~~~~Gd~V~V~~~~~~~~vaVG~~ 148 (180)
+|.+.+++..++.|++|+.+..+++ ..++.|.+....++.++|+|..
T Consensus 249 lp~v~l~~~~~~~i~~G~~i~~~~~-----------~~~~~v~~~~~~~g~~lai~~~ 295 (312)
T PRK05033 249 LPEVNLPEESAYYFKQGQPVRVSGA-----------PLEGLVRVTEGENGKFIGIGEI 295 (312)
T ss_pred CCeEEECHHHHHHHHCcCccccCcC-----------CCCCEEEEEECCCCEEEEEEEE
Confidence 6899999999999999999854432 2245677762246789999975
No 33
>PRK01550 truB tRNA pseudouridine synthase B; Provisional
Probab=77.98 E-value=5.6 Score=34.13 Aligned_cols=48 Identities=23% Similarity=0.277 Sum_probs=36.0
Q ss_pred CcEEEECcchhhhhhcCCcccCCcccCCCCCCCcCCCCCCeEEEeeCCCCeEEEEEEE
Q 030242 91 MKKLQVDRGAIKFVLSGANIMCPGLTSPGGSLDEEVGAETPVAIMAEGKQHALAIGFT 148 (180)
Q Consensus 91 ~p~v~v~~~a~~~i~~GAdLm~pGV~~~~~~~~~~~~~Gd~V~V~~~~~~~~vaVG~~ 148 (180)
+|.+.+++...+.+++|+.+..++... ..++.+.++. .++.++|+|..
T Consensus 240 lp~v~l~~~~~~~i~~G~~i~~~~~~~---------~~~~~v~~~~-~~g~~lai~~~ 287 (304)
T PRK01550 240 LPKLVIDEKQAEKVKNGAFLKNPLFIT---------VEAEPIVVLD-YNDRCLAIYEH 287 (304)
T ss_pred CCEEEECHHHHHHHHCcCccccCcccc---------cCCCcEEEEc-CCCeEEEEEEE
Confidence 689999999999999999986554321 2245566766 45789999975
No 34
>PRK15128 23S rRNA m(5)C1962 methyltransferase; Provisional
Probab=77.90 E-value=5.5 Score=35.30 Aligned_cols=51 Identities=16% Similarity=0.243 Sum_probs=39.3
Q ss_pred EEEECcchhhhhhcCCc-ccCCcccCCCCCCCcCCCCCCeEEEeeCCCCeEEEEEEE
Q 030242 93 KLQVDRGAIKFVLSGAN-IMCPGLTSPGGSLDEEVGAETPVAIMAEGKQHALAIGFT 148 (180)
Q Consensus 93 ~v~v~~~a~~~i~~GAd-Lm~pGV~~~~~~~~~~~~~Gd~V~V~~~~~~~~vaVG~~ 148 (180)
++++..++.+.|.+|.. ++..-|.. .++++.+||+|.|++ .++.++|.|..
T Consensus 4 ~v~l~~~~~~~~~~ghpwv~~~~i~~----~~~~~~~G~~v~v~~-~~g~~lg~g~~ 55 (396)
T PRK15128 4 RLVLAKGREKSLLRRHPWVFSGAVAR----MEGKASLGETIDIVD-HQGKWLARGAY 55 (396)
T ss_pred EEEECcchHhHHhcCCCeEEhHHhcc----ccCCCCCCCEEEEEc-CCCCEEEEEEE
Confidence 46788888889998885 55555543 444688999999998 56889888876
No 35
>PRK02755 truB tRNA pseudouridine synthase B; Provisional
Probab=74.65 E-value=7.9 Score=33.06 Aligned_cols=46 Identities=17% Similarity=0.236 Sum_probs=34.8
Q ss_pred CcEEEECcchhhhhhcCCcccCCcccCCCCCCCcCCCCCCeEEEeeCCCCeEEEEEEE
Q 030242 91 MKKLQVDRGAIKFVLSGANIMCPGLTSPGGSLDEEVGAETPVAIMAEGKQHALAIGFT 148 (180)
Q Consensus 91 ~p~v~v~~~a~~~i~~GAdLm~pGV~~~~~~~~~~~~~Gd~V~V~~~~~~~~vaVG~~ 148 (180)
+|.+.+++..++.+++|+.+..+. +..++.+.+.. .++.++|+|..
T Consensus 234 lp~v~l~~~~~~~l~~G~~i~~~~-----------~~~~~~~~~~~-~~g~~lai~~~ 279 (295)
T PRK02755 234 LPRVQLSAEEAQRWCCGQRIPLEN-----------LPAGGAVVVYD-ADGRFLGIGLI 279 (295)
T ss_pred CCEEEECHHHHHHHHCcCccccCc-----------CCCCCeEEEEc-CCCeEEEEEEE
Confidence 689999999999999999984321 23356677766 45789999875
No 36
>PRK04099 truB tRNA pseudouridine synthase B; Provisional
Probab=67.17 E-value=12 Score=31.72 Aligned_cols=45 Identities=9% Similarity=-0.062 Sum_probs=33.9
Q ss_pred CcEEEECcchhhhhhcCCcccCCcccCCCCCCCcCCCCCCeEEEeeCCCCeEEEEEEE
Q 030242 91 MKKLQVDRGAIKFVLSGANIMCPGLTSPGGSLDEEVGAETPVAIMAEGKQHALAIGFT 148 (180)
Q Consensus 91 ~p~v~v~~~a~~~i~~GAdLm~pGV~~~~~~~~~~~~~Gd~V~V~~~~~~~~vaVG~~ 148 (180)
+|++.+.+ .++.|++|+-|+.+|+.. . ++..+.+.. +.++||+..
T Consensus 214 l~~~~~~~-~~~~i~~G~ki~~~~~~~----~-----~~g~~~~~~---~~f~~I~e~ 258 (273)
T PRK04099 214 LPQNFYLG-DKNNLELGKKLFVEDLEN----K-----EDGIYYIEF---EDFFSIIEI 258 (273)
T ss_pred cceEechh-HHHHHhCCCeeccCcccc----C-----CCCEEEEEc---CceEEEEEE
Confidence 57888887 899999999999999855 2 234566652 458888766
No 37
>cd02573 PseudoU_synth_EcTruB PseudoU_synth_EcTruB: Pseudouridine synthase, Escherichia coli TruB like. This group consists of bacterial pseudouridine synthases similar to E. coli TruB and Mycobacterium tuberculosis TruB. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). E. coli TruB and M. tuberculosis TruB make psi55 in the T loop of tRNAs. Psi55 is nearly universally conserved. E. coli TruB is not inhibited by RNA containing 5-fluorouridine.
Probab=66.91 E-value=14 Score=31.20 Aligned_cols=45 Identities=22% Similarity=0.287 Sum_probs=34.2
Q ss_pred CcEEEECcchhhhhhcCCcccCCcccCCCCCCCcCCCCCCeEEEeeCCCCeEEEEEE
Q 030242 91 MKKLQVDRGAIKFVLSGANIMCPGLTSPGGSLDEEVGAETPVAIMAEGKQHALAIGF 147 (180)
Q Consensus 91 ~p~v~v~~~a~~~i~~GAdLm~pGV~~~~~~~~~~~~~Gd~V~V~~~~~~~~vaVG~ 147 (180)
+|.+.+++...+.+++|+.+-.+++ ..++.+.+.. .+++++|+|.
T Consensus 232 ~p~v~l~~~~~~~i~~G~~i~~~~~-----------~~~~~~~~~~-~~~~~l~i~~ 276 (277)
T cd02573 232 LPKVELDEEEAKRLRNGQKISLPEE-----------PEDGLVRVYD-PNGRFLALGE 276 (277)
T ss_pred CCEEEeCHHHHHHHHCcCccccCCC-----------CCCCEEEEEe-CCCeEEEEEE
Confidence 6899999999999999999843332 2356677766 4578999985
No 38
>PRK01851 truB tRNA pseudouridine synthase B; Provisional
Probab=62.08 E-value=21 Score=30.65 Aligned_cols=46 Identities=13% Similarity=0.190 Sum_probs=34.3
Q ss_pred CcEEEECcchhhhhhcCCcccCCcccCCCCCCCcCCCCCCeEEEeeCCCCeEEEEEEE
Q 030242 91 MKKLQVDRGAIKFVLSGANIMCPGLTSPGGSLDEEVGAETPVAIMAEGKQHALAIGFT 148 (180)
Q Consensus 91 ~p~v~v~~~a~~~i~~GAdLm~pGV~~~~~~~~~~~~~Gd~V~V~~~~~~~~vaVG~~ 148 (180)
+|.+.+++..++.+++|+.+-.+ .+..++.|.++. .++.++|||..
T Consensus 245 lp~v~l~~~~~~~i~~G~~i~~~-----------~~~~~~~v~i~~-~~g~~lai~~~ 290 (303)
T PRK01851 245 FPRVTLDADAAGRFLHGQRLRLS-----------DLPDAPRVRVYD-DPGRLLGVARW 290 (303)
T ss_pred CCEEEeCHHHHHHHHCcCccccc-----------cCCCCCEEEEEc-CCCeEEEEEEE
Confidence 68999999999999999988321 122345677766 45789999975
No 39
>PRK03287 truB tRNA pseudouridine synthase B; Provisional
Probab=59.50 E-value=21 Score=30.51 Aligned_cols=44 Identities=9% Similarity=0.090 Sum_probs=33.0
Q ss_pred CcEEEECcchhhhhhcCCcccCCcccCCCCCCCcCCCCCCeEEEeeCCCCeEEEEEEE
Q 030242 91 MKKLQVDRGAIKFVLSGANIMCPGLTSPGGSLDEEVGAETPVAIMAEGKQHALAIGFT 148 (180)
Q Consensus 91 ~p~v~v~~~a~~~i~~GAdLm~pGV~~~~~~~~~~~~~Gd~V~V~~~~~~~~vaVG~~ 148 (180)
+|.+.+++...+.+++|+.+-.++ .+..+.++. .++.++|||..
T Consensus 239 lp~v~l~~~~~~~i~~G~~i~~~~-------------~~~~~~~~~-~~~~~lai~~~ 282 (298)
T PRK03287 239 FPRRDLTAAEAEALSHGRRLEPAG-------------IDGVYAAVD-PDGRVIALLEE 282 (298)
T ss_pred CCeEEeCHHHHHHHHCcCccccCC-------------CCCeEEEEc-CCCeEEEEEEE
Confidence 689999999999999999883222 134466665 45789999975
No 40
>PRK04642 truB tRNA pseudouridine synthase B; Provisional
Probab=52.18 E-value=37 Score=29.13 Aligned_cols=45 Identities=11% Similarity=0.194 Sum_probs=33.0
Q ss_pred CcEEEECcchhhhhhcCCcccCCcccCCCCCCCcCCCCCCeEEEeeCCCCeEEEEEEE
Q 030242 91 MKKLQVDRGAIKFVLSGANIMCPGLTSPGGSLDEEVGAETPVAIMAEGKQHALAIGFT 148 (180)
Q Consensus 91 ~p~v~v~~~a~~~i~~GAdLm~pGV~~~~~~~~~~~~~Gd~V~V~~~~~~~~vaVG~~ 148 (180)
+|++.+++.....+++|+.+-.+. .. .+.+.++. .++.++|+|..
T Consensus 242 lp~v~l~~~~~~~i~~G~~i~~~~-----------~~-~~~v~i~~-~~~~~lai~~~ 286 (300)
T PRK04642 242 FPRIELDATLAARFRMGQRLRDAS-----------FP-TGQVAVFG-PDGSPAGLGLV 286 (300)
T ss_pred CCEEEeCHHHHHHHHCcCccCCCc-----------CC-CCeEEEEc-CCCeEEEEEEE
Confidence 689999999999999999983211 11 24566665 45789999975
No 41
>PRK05389 truB tRNA pseudouridine synthase B; Provisional
Probab=50.87 E-value=48 Score=28.47 Aligned_cols=48 Identities=15% Similarity=0.163 Sum_probs=32.5
Q ss_pred CcEEEECcchhhhhhcCCcccCCcccCCCCCCCcCCCCCCeEEEeeCCCCeEEEEEEE
Q 030242 91 MKKLQVDRGAIKFVLSGANIMCPGLTSPGGSLDEEVGAETPVAIMAEGKQHALAIGFT 148 (180)
Q Consensus 91 ~p~v~v~~~a~~~i~~GAdLm~pGV~~~~~~~~~~~~~Gd~V~V~~~~~~~~vaVG~~ 148 (180)
+|.+.+++...+.+++|+.+-.++. ... ..+..+.+ . .++.++|+|..
T Consensus 244 lp~v~l~~~~~~~l~~G~~i~~~~~-------~~~-~~~~~~~~-~-~~g~~lai~~~ 291 (305)
T PRK05389 244 LPALALTDEQAARLRQGNPVLLRGR-------DAP-LPEAEAYA-T-AGGRLVALGEI 291 (305)
T ss_pred CCEEEeCHHHHHHHHCcCccccCcc-------ccC-CCCcEEEE-e-cCCEEEEEEEE
Confidence 6899999999999999999854331 001 11224444 3 45789999975
No 42
>PF01878 EVE: EVE domain; InterPro: IPR002740 The EVE domain is part of the wider PUA domain superfamily. The function of this domain is not known but, given the structural similarities to PUA, is likely to involve RNA binding []. ; PDB: 2G2X_B 2AR1_A 3EOP_A 2EVE_A 2HD9_A 2ZBN_A 1WMM_A 2P5D_A 2GBS_A 1ZCE_A.
Probab=48.44 E-value=31 Score=25.58 Aligned_cols=25 Identities=20% Similarity=0.254 Sum_probs=16.8
Q ss_pred CCCCCCeEEEeeCC--CCeEEEEEEEe
Q 030242 125 EVGAETPVAIMAEG--KQHALAIGFTK 149 (180)
Q Consensus 125 ~~~~Gd~V~V~~~~--~~~~vaVG~~~ 149 (180)
.+++||.|.++..+ ...++|+|+..
T Consensus 39 ~mk~GD~vifY~s~~~~~~ivai~~V~ 65 (143)
T PF01878_consen 39 RMKPGDKVIFYHSGCKERGIVAIGEVV 65 (143)
T ss_dssp C--TT-EEEEEETSSSS-EEEEEEEEE
T ss_pred cCCCCCEEEEEEcCCCCCEEEEEEEEe
Confidence 68999999999966 34677888774
No 43
>COG4103 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=42.14 E-value=21 Score=27.35 Aligned_cols=30 Identities=20% Similarity=0.251 Sum_probs=24.8
Q ss_pred cccCHHHHHHHHHHHHhHCCCCchhhcccC
Q 030242 14 NQVKASVQRKIRQSIADEYPGLEPVLDDLL 43 (180)
Q Consensus 14 ~~l~~sd~kkLr~~i~~~f~~~~~~~~~l~ 43 (180)
-.++.+|+.++|+.+.+.|+...+.+++|+
T Consensus 43 G~v~~~E~~a~r~il~~~f~i~~~~l~ali 72 (148)
T COG4103 43 GTVSESEREAFRAILKENFGIDGEELDALI 72 (148)
T ss_pred cCcCHHHHHHHHHHHHHHcCCCHHHHHHHH
Confidence 458899999999999999998656666654
No 44
>PRK04980 hypothetical protein; Provisional
Probab=40.92 E-value=63 Score=23.25 Aligned_cols=25 Identities=0% Similarity=-0.166 Sum_probs=19.6
Q ss_pred cCCCCCCeEEEeeCCCCeEEEEEEE
Q 030242 124 EEVGAETPVAIMAEGKQHALAIGFT 148 (180)
Q Consensus 124 ~~~~~Gd~V~V~~~~~~~~vaVG~~ 148 (180)
+.+++||.+.|.+.+.+.++|+-+.
T Consensus 30 ~~~~~G~~~~V~~~e~g~~~c~ieI 54 (102)
T PRK04980 30 SHFKPGDVLRVGTFEDDRYFCTIEV 54 (102)
T ss_pred cCCCCCCEEEEEECCCCcEEEEEEE
Confidence 4689999999987677888765543
No 45
>PRK14122 tRNA pseudouridine synthase B; Provisional
Probab=39.61 E-value=62 Score=27.92 Aligned_cols=43 Identities=19% Similarity=0.270 Sum_probs=32.2
Q ss_pred CcEEEECcchhhhhhcCCcccCCcccCCCCCCCcCCCCCCeEEEeeCCCCeEEEEEEE
Q 030242 91 MKKLQVDRGAIKFVLSGANIMCPGLTSPGGSLDEEVGAETPVAIMAEGKQHALAIGFT 148 (180)
Q Consensus 91 ~p~v~v~~~a~~~i~~GAdLm~pGV~~~~~~~~~~~~~Gd~V~V~~~~~~~~vaVG~~ 148 (180)
+|.+.+++...+.+.+|..+-.+ ..+.+.++. .++.++|+|..
T Consensus 257 lp~v~l~~~~~~~i~~G~~i~~~--------------~~~~~~~~~-~~g~~~ai~~~ 299 (312)
T PRK14122 257 FPRVELSHAEARRVRQGKPPAIP--------------AQGRVALVD-PKGQLVAVAEG 299 (312)
T ss_pred CCeEEcCHHHHHHHHCcCcccCC--------------CCceEEEEc-CCCeEEEEEEe
Confidence 78999999999999999987322 123466665 56789999874
No 46
>COG1374 NIP7 Protein involved in ribosomal biogenesis, contains PUA domain [Translation, ribosomal structure and biogenesis]
Probab=39.03 E-value=40 Score=26.70 Aligned_cols=72 Identities=17% Similarity=0.194 Sum_probs=44.8
Q ss_pred cchhhHhhhcCCCCCcEEEECcchhhhhhcCCcccCCcccCCCCCCCcCCCCCCeEEEeeCCCCeEEEEEEEecCHHHHh
Q 030242 77 YMPTLRLLHQYPNIMKKLQVDRGAIKFVLSGANIMCPGLTSPGGSLDEEVGAETPVAIMAEGKQHALAIGFTKMSAKDIK 156 (180)
Q Consensus 77 ~~PTl~~l~~~p~~~p~v~v~~~a~~~i~~GAdLm~pGV~~~~~~~~~~~~~Gd~V~V~~~~~~~~vaVG~~~~s~~~i~ 156 (180)
.++.+..|-++- .-.+.+...+...-+.|-| ..-++.+ ...++.....|.|+. .|+.|.++|....|+++..
T Consensus 87 ~~~~l~~la~~~--~~k~~v~~~~e~~FLYg~~-lkd~~~e----~~~~~~~~~~v~V~~-~nd~~lgiGvg~~s~~ed~ 158 (176)
T COG1374 87 HVESLEELARIA--IIKNYVKERGEMLFLYGND-LKDHVKE----IIDEIPENGGVFVFN-MNDVPLGIGVGALSPSEDG 158 (176)
T ss_pred ehhhhHHHHHHh--heeeeeccCceeEEEeccc-cchhhhh----hccccCCcceEEEEE-cCCCceEEEecccCchhhc
Confidence 355555444332 3345555444333336666 3444555 345677778888887 7899999999999887654
No 47
>COG2012 RPB5 DNA-directed RNA polymerase, subunit H, RpoH/RPB5 [Transcription]
Probab=38.39 E-value=34 Score=23.53 Aligned_cols=32 Identities=16% Similarity=0.208 Sum_probs=24.7
Q ss_pred CCCCCcEEEECcchhhhhhcCCcccCCcccCCCCCCCcCCCCCCeEEEeeCC
Q 030242 87 YPNIMKKLQVDRGAIKFVLSGANIMCPGLTSPGGSLDEEVGAETPVAIMAEG 138 (180)
Q Consensus 87 ~p~~~p~v~v~~~a~~~i~~GAdLm~pGV~~~~~~~~~~~~~Gd~V~V~~~~ 138 (180)
.|.-+|+|..+++++.++ +.+.||+|-|...+
T Consensus 36 ~~~qLPkI~~~DPva~~l--------------------gak~GdvVkIvRkS 67 (80)
T COG2012 36 EPEQLPKIKASDPVAKAL--------------------GAKPGDVVKIVRKS 67 (80)
T ss_pred CHHHCCcccccChhHHHc--------------------cCCCCcEEEEEecC
Confidence 356789999999998876 34668988887643
No 48
>PF01191 RNA_pol_Rpb5_C: RNA polymerase Rpb5, C-terminal domain; InterPro: IPR000783 Prokaryotes contain a single DNA-dependent RNA polymerase (RNAP; 2.7.7.6 from EC) that is responsible for the transcription of all genes, while eukaryotes have three classes of RNAPs (I-III) that transcribe different sets of genes. Each class of RNA polymerase is an assemblage of ten to twelve different polypeptides. Certain subunits of RNAPs, including RPB5 (POLR2E in mammals), are common to all three eukaryotic polymerases. RPB5 plays a role in the transcription activation process. Eukaryotic RPB5 has a bipartite structure consisting of a unique N-terminal region (IPR005571 from INTERPRO), plus a C-terminal region that is structurally homologous to the prokaryotic RPB5 homologue, subunit H (gene rpoH) [, , , ]. This entry represents prokaryotic subunit H and the C-terminal domain of eukaryotic RPB5, which share a two-layer alpha/beta fold, with a core structure of beta/alpha/beta/alpha/beta(2). ; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 1EIK_A 2Y0S_Z 1DZF_A 3GTG_E 2VUM_E 3GTP_E 3GTO_E 3S17_E 3S1R_E 1I3Q_E ....
Probab=38.15 E-value=41 Score=22.75 Aligned_cols=30 Identities=13% Similarity=0.287 Sum_probs=23.0
Q ss_pred CCCCcEEEECcchhhhhhcCCcccCCcccCCCCCCCcCCCCCCeEEEeeC
Q 030242 88 PNIMKKLQVDRGAIKFVLSGANIMCPGLTSPGGSLDEEVGAETPVAIMAE 137 (180)
Q Consensus 88 p~~~p~v~v~~~a~~~i~~GAdLm~pGV~~~~~~~~~~~~~Gd~V~V~~~ 137 (180)
+.-+|++...|++++++ ++++||+|-|.-.
T Consensus 31 ~~qLP~I~~~DPv~r~~--------------------g~k~GdVvkI~R~ 60 (74)
T PF01191_consen 31 PEQLPKILSSDPVARYL--------------------GAKPGDVVKIIRK 60 (74)
T ss_dssp TTCSSEEETTSHHHHHT--------------------T--TTSEEEEEEE
T ss_pred hhhCCcccccChhhhhc--------------------CCCCCCEEEEEec
Confidence 56689999999999887 4678999988653
No 49
>PRK09570 rpoH DNA-directed RNA polymerase subunit H; Reviewed
Probab=35.52 E-value=46 Score=22.85 Aligned_cols=30 Identities=10% Similarity=0.222 Sum_probs=23.7
Q ss_pred CCCcEEEECcchhhhhhcCCcccCCcccCCCCCCCcCCCCCCeEEEeeCC
Q 030242 89 NIMKKLQVDRGAIKFVLSGANIMCPGLTSPGGSLDEEVGAETPVAIMAEG 138 (180)
Q Consensus 89 ~~~p~v~v~~~a~~~i~~GAdLm~pGV~~~~~~~~~~~~~Gd~V~V~~~~ 138 (180)
.-+|++...|++++++ ++++||+|-|.-.+
T Consensus 35 ~qLP~I~~~DPv~r~~--------------------g~k~GdVvkI~R~S 64 (79)
T PRK09570 35 EQLPKIKASDPVVKAI--------------------GAKPGDVIKIVRKS 64 (79)
T ss_pred HHCCceeccChhhhhc--------------------CCCCCCEEEEEECC
Confidence 4589999999988876 46779999997643
No 50
>PRK12618 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=34.62 E-value=1e+02 Score=23.27 Aligned_cols=56 Identities=14% Similarity=0.027 Sum_probs=36.2
Q ss_pred hhhhcCCcccCCcccCCCCCCCcCCCCCCeEEEeeCCCC-eEEEEEEEecCHHHHhcCCcceEEEEEE
Q 030242 102 KFVLSGANIMCPGLTSPGGSLDEEVGAETPVAIMAEGKQ-HALAIGFTKMSAKDIKAINKGIGVDNMH 168 (180)
Q Consensus 102 ~~i~~GAdLm~pGV~~~~~~~~~~~~~Gd~V~V~~~~~~-~~vaVG~~~~s~~~i~~~~kG~av~v~H 168 (180)
+.|..|.-+..--+.. +.=+++||.|.|...+.+ .+-+.|+|+-| +..|..|+|..
T Consensus 63 R~l~aGq~i~~~~L~~-----p~lV~rG~~V~i~~~~ggl~i~~~G~AL~~------G~~Gd~IrV~N 119 (141)
T PRK12618 63 VTLYAGRPIRAADLGP-----PAIVDRNQLVPLAYRLGGLEIRTEGRALSR------GGVGDEIRVMN 119 (141)
T ss_pred eecCCCCeeCHHHcCC-----ccEEeCCCEEEEEEecCCEEEEEEEEEccc------CCCCCEEEEEE
Confidence 3444555554444332 235788999999986655 56699999755 56777776653
No 51
>TIGR03170 flgA_cterm flagella basal body P-ring formation protein FlgA. This model describes a conserved C-terminal region of the flagellar basal body P-ring formation protein FlgA. This sequence region contains a SAF domain, now described by Pfam model pfam08666.
Probab=33.55 E-value=1.2e+02 Score=21.68 Aligned_cols=39 Identities=15% Similarity=0.028 Sum_probs=28.1
Q ss_pred cCCCCCCeEEEeeCCCC-eEEEEEEEecCHHHHhcCCcceEEEEEE
Q 030242 124 EEVGAETPVAIMAEGKQ-HALAIGFTKMSAKDIKAINKGIGVDNMH 168 (180)
Q Consensus 124 ~~~~~Gd~V~V~~~~~~-~~vaVG~~~~s~~~i~~~~kG~av~v~H 168 (180)
+-+++||.|.|...+.+ .+-+-|+|+-| +..|..|++..
T Consensus 64 ~~V~~G~~V~i~~~~~~~~i~~~g~Al~~------g~~G~~I~V~N 103 (122)
T TIGR03170 64 WLVKRGDTVTVIARGGGLSVTTEGKALED------GAVGDQIRVRN 103 (122)
T ss_pred cEEcCCCEEEEEEecCCEEEEEEEEEccc------cCCCCEEEEEE
Confidence 46889999999886655 45588888655 46677766653
No 52
>PRK14123 tRNA pseudouridine synthase B; Provisional
Probab=33.49 E-value=1.1e+02 Score=26.22 Aligned_cols=49 Identities=18% Similarity=0.228 Sum_probs=31.9
Q ss_pred CcEEEECcch-hhhhhcCCcccCCcccCCCCCCCcCCCCCCeEEEeeCCCCeEEEEEEE
Q 030242 91 MKKLQVDRGA-IKFVLSGANIMCPGLTSPGGSLDEEVGAETPVAIMAEGKQHALAIGFT 148 (180)
Q Consensus 91 ~p~v~v~~~a-~~~i~~GAdLm~pGV~~~~~~~~~~~~~Gd~V~V~~~~~~~~vaVG~~ 148 (180)
+|.+.+++.. .+.+.+|+.+-.... ++. ..+..+.+.. .++.++|||..
T Consensus 241 lp~v~l~~~~~~~~i~~G~~i~~~~~-------~~~-~~~~~~~~~~-~~g~~lai~~~ 290 (305)
T PRK14123 241 LPSIKIKDSHIKKRILNGQKFNKNEF-------DNK-IKDQIVFIDD-DSEKVLAIYMV 290 (305)
T ss_pred CCEEEECHHHHHHHHHCcCccccccc-------ccC-CCCcEEEEEC-CCCeEEEEEEe
Confidence 6899999985 789999998843221 111 1233445543 45789999975
No 53
>PRK12617 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=33.45 E-value=1e+02 Score=24.97 Aligned_cols=56 Identities=13% Similarity=0.115 Sum_probs=37.3
Q ss_pred hhhhcCCcccCCcccCCCCCCCcCCCCCCeEEEeeCCCC-eEEEEEEEecCHHHHhcCCcceEEEEEE
Q 030242 102 KFVLSGANIMCPGLTSPGGSLDEEVGAETPVAIMAEGKQ-HALAIGFTKMSAKDIKAINKGIGVDNMH 168 (180)
Q Consensus 102 ~~i~~GAdLm~pGV~~~~~~~~~~~~~Gd~V~V~~~~~~-~~vaVG~~~~s~~~i~~~~kG~av~v~H 168 (180)
..|..|.-|..--+.. +.-+++||.|.|...+++ .+-+-|+|+-+ +..|..|+|..
T Consensus 137 r~l~aGq~i~~~~L~~-----p~lV~rG~~V~I~a~~~g~~Vs~~G~AL~~------G~~Ge~IrVrN 193 (214)
T PRK12617 137 RILPAGSLLSANDLVS-----QRLVRRGDTVPLVSRNGGLEVRMSGRALSD------AGENERVSVEN 193 (214)
T ss_pred eecCCCCeeCHHHcCC-----cceEcCCCEEEEEEecCCEEEEEEEEEccC------CCCCCEEEEEE
Confidence 3455555554444432 235899999999997766 45588999655 57777777764
No 54
>PRK06005 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=31.98 E-value=95 Score=23.92 Aligned_cols=58 Identities=21% Similarity=0.146 Sum_probs=39.2
Q ss_pred hhhhhhcCCcccCCcccCCCCCCCcCCCCCCeEEEeeCCCC-eEEEEEEEecCHHHHhcCCcceEEEEEE
Q 030242 100 AIKFVLSGANIMCPGLTSPGGSLDEEVGAETPVAIMAEGKQ-HALAIGFTKMSAKDIKAINKGIGVDNMH 168 (180)
Q Consensus 100 a~~~i~~GAdLm~pGV~~~~~~~~~~~~~Gd~V~V~~~~~~-~~vaVG~~~~s~~~i~~~~kG~av~v~H 168 (180)
+.+.|..|.-+...-+.. ++-+++||.|.|...+++ .+-+-|+|+-| +..|..|+|..
T Consensus 80 arR~l~aGqpI~~~~L~~-----p~~V~rG~~V~i~~~~~g~~i~~~G~Al~~------G~~Gd~IrVrN 138 (160)
T PRK06005 80 AKRTLLPGRPIPVSALRE-----PSLVTRGSPVKLVFSAGGLTITAAGTPLQS------GAAGDLIRVRN 138 (160)
T ss_pred EEeecCCCCeeCHHHcCC-----CcEEeCCCEEEEEEecCCEEEEEEEEEccc------CCCCCEEEEEE
Confidence 344566666665554443 246889999999997766 45588998655 57777777663
No 55
>PF15477 SMAP: Small acidic protein family
Probab=31.24 E-value=69 Score=21.08 Aligned_cols=24 Identities=21% Similarity=0.382 Sum_probs=20.9
Q ss_pred cccccccCHHHHHHHHHHHHhHCC
Q 030242 10 VSAQNQVKASVQRKIRQSIADEYP 33 (180)
Q Consensus 10 ~k~~~~l~~sd~kkLr~~i~~~f~ 33 (180)
-.++..+..++.++|.+.|..||-
T Consensus 32 ~~~~~~~~~~~~~~l~~~Le~Qy~ 55 (69)
T PF15477_consen 32 ASPNMALSKEKQEKLQQDLEQQYE 55 (69)
T ss_pred CCccccccHHHHHHHHHHHHHHHH
Confidence 356777999999999999999995
No 56
>cd04710 BAH_fungalPHD BAH, or Bromo Adjacent Homology domain, as present in fungal proteins containing PHD domains. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=27.12 E-value=60 Score=24.37 Aligned_cols=25 Identities=12% Similarity=0.072 Sum_probs=22.1
Q ss_pred CCCCCCeEEEeeCCCCeEEEEEEEe
Q 030242 125 EVGAETPVAIMAEGKQHALAIGFTK 149 (180)
Q Consensus 125 ~~~~Gd~V~V~~~~~~~~vaVG~~~ 149 (180)
.++.||-|.|..+..++|.-||+..
T Consensus 11 ~~~vgD~Vyv~~~~~~ePyyIgrI~ 35 (135)
T cd04710 11 LLKVNDHIYMSSEPPGEPYYIGRIM 35 (135)
T ss_pred EEeCCCEEEEecCCCCCCCEEEEEE
Confidence 4789999999987788999999986
No 57
>COG1507 Uncharacterized conserved protein [Function unknown]
Probab=26.76 E-value=33 Score=26.50 Aligned_cols=24 Identities=29% Similarity=0.314 Sum_probs=17.2
Q ss_pred EECCEEEEE-Ee---cCCCcchhhHhhh
Q 030242 62 LVNNVPLFF-NI---RDGPYMPTLRLLH 85 (180)
Q Consensus 62 ~~dg~pl~f-~~---~~~~~~PTl~~l~ 85 (180)
+.+|+|..+ +. .|+..|||+|.|-
T Consensus 28 cp~g~P~VV~t~p~l~dg~PfPTly~lt 55 (167)
T COG1507 28 CPYGEPGVVKTAPKLDDGTPFPTLYYLT 55 (167)
T ss_pred CCCCCceEEeecCCCCCCCcCCceeeec
Confidence 467888754 33 4778899998765
No 58
>PRK08515 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=26.16 E-value=1.6e+02 Score=23.94 Aligned_cols=56 Identities=9% Similarity=-0.072 Sum_probs=36.7
Q ss_pred hhhhcCCcccCCcccCCCCCCCcCCCCCCeEEEeeCCCC-eEEEEEEEecCHHHHhcCCcceEEEEEE
Q 030242 102 KFVLSGANIMCPGLTSPGGSLDEEVGAETPVAIMAEGKQ-HALAIGFTKMSAKDIKAINKGIGVDNMH 168 (180)
Q Consensus 102 ~~i~~GAdLm~pGV~~~~~~~~~~~~~Gd~V~V~~~~~~-~~vaVG~~~~s~~~i~~~~kG~av~v~H 168 (180)
+.|..|.-|..--+.. ++-+++||.|.|...+.+ .+-+-|+|+-| +..|..|+|.-
T Consensus 147 r~i~~G~~i~~~~l~~-----~~lV~rGd~V~i~~~~gg~~I~~~G~Al~~------G~~Gd~IrVrN 203 (222)
T PRK08515 147 SFIPPGTILTADKFKA-----LILVRKNDIINGVLKEGGVSIEISLKALQD------GNLGDIIQAKN 203 (222)
T ss_pred EEcCCCCeECHHHcCC-----cceEecCCEEEEEEECCCEEEEEEEEEccc------CCCCCEEEEEe
Confidence 3444455444333332 246899999999997655 45588998655 57777777764
No 59
>PF10246 MRP-S35: Mitochondrial ribosomal protein MRP-S35; InterPro: IPR019375 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This is a family of short mitochondrial ribosomal proteins, less than 200 amino acids long. MRP-S35 was proposed as a more appropriate name to this group of proteins [].
Probab=26.13 E-value=55 Score=23.67 Aligned_cols=21 Identities=24% Similarity=0.347 Sum_probs=15.2
Q ss_pred CcceEE--EEEEEEccccc-Cccc
Q 030242 159 NKGIGV--DNMHYLNDGLW-KVSW 179 (180)
Q Consensus 159 ~kG~av--~v~H~~~D~Lw-~~~~ 179 (180)
.+|+-| +|.|+.+|.|| .+||
T Consensus 22 ~~gk~V~G~I~hvv~ddLYIDfG~ 45 (104)
T PF10246_consen 22 PEGKIVIGKIFHVVDDDLYIDFGG 45 (104)
T ss_pred ccCCEEEEEEEEEecCceEEEeCC
Confidence 355544 89999999998 4444
No 60
>CHL00141 rpl24 ribosomal protein L24; Validated
Probab=25.90 E-value=1.1e+02 Score=20.96 Aligned_cols=12 Identities=25% Similarity=0.329 Sum_probs=10.9
Q ss_pred CCCCCCeEEEee
Q 030242 125 EVGAETPVAIMA 136 (180)
Q Consensus 125 ~~~~Gd~V~V~~ 136 (180)
.+++||.|.|.+
T Consensus 8 ~I~~GD~V~Vi~ 19 (83)
T CHL00141 8 HVKIGDTVKIIS 19 (83)
T ss_pred cccCCCEEEEeE
Confidence 689999999988
No 61
>KOG3342 consensus Signal peptidase I [Intracellular trafficking, secretion, and vesicular transport]
Probab=25.51 E-value=67 Score=25.09 Aligned_cols=56 Identities=9% Similarity=0.119 Sum_probs=26.5
Q ss_pred hHhhhcCC-----CCCcEEEECcchhhhhhcCCc-ccCCcccCCCCCCCcCCCCCCeEEEeeCCCCeE
Q 030242 81 LRLLHQYP-----NIMKKLQVDRGAIKFVLSGAN-IMCPGLTSPGGSLDEEVGAETPVAIMAEGKQHA 142 (180)
Q Consensus 81 l~~l~~~p-----~~~p~v~v~~~a~~~i~~GAd-Lm~pGV~~~~~~~~~~~~~Gd~V~V~~~~~~~~ 142 (180)
-|..|+-- +-.|.|+|-++..+.=.+--| |+.--- -++.++.||+|.-..++..-|
T Consensus 33 A~MiwK~l~vvt~seSPiVVVLSgSMePaF~RGDlLfL~N~------~~~p~~vGdivVf~vegR~IP 94 (180)
T KOG3342|consen 33 AYMIWKGLMVVTGSESPIVVVLSGSMEPAFHRGDLLFLTNR------NEDPIRVGDIVVFKVEGREIP 94 (180)
T ss_pred HHHHHhhheeeeCCCCCEEEEEcCCcCcccccccEEEEecC------CCCcceeccEEEEEECCccCc
Confidence 35566631 234677766665543333223 222111 113466677776666544333
No 62
>PF13403 Hint_2: Hint domain
Probab=25.16 E-value=1.2e+02 Score=22.94 Aligned_cols=43 Identities=23% Similarity=0.132 Sum_probs=30.2
Q ss_pred cCCCCCCeEEEeeCCCCeEEEEEEEecCHHHHhcCCcceEEEE
Q 030242 124 EEVGAETPVAIMAEGKQHALAIGFTKMSAKDIKAINKGIGVDN 166 (180)
Q Consensus 124 ~~~~~Gd~V~V~~~~~~~~vaVG~~~~s~~~i~~~~kG~av~v 166 (180)
+++++||.|.=.+.+-..+..||+..+++.++.......-|++
T Consensus 19 e~L~~GD~V~T~dgg~~~V~wig~~~~~~~~~~~~~~~~pvri 61 (147)
T PF13403_consen 19 EDLRPGDRVLTRDGGFQPVRWIGRRTVSPADLPAPPRLAPVRI 61 (147)
T ss_pred eccCCCCEEEecCCCEEEEEEEEEEEecccccCcCCCcceEEE
Confidence 5799999999887444467799999998665544444444433
No 63
>PRK06804 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=24.83 E-value=1.6e+02 Score=24.63 Aligned_cols=39 Identities=18% Similarity=0.147 Sum_probs=29.3
Q ss_pred cCCCCCCeEEEeeCCCC-eEEEEEEEecCHHHHhcCCcceEEEEEE
Q 030242 124 EEVGAETPVAIMAEGKQ-HALAIGFTKMSAKDIKAINKGIGVDNMH 168 (180)
Q Consensus 124 ~~~~~Gd~V~V~~~~~~-~~vaVG~~~~s~~~i~~~~kG~av~v~H 168 (180)
.-+++||.|.|...+.+ .+-+-|+|+-| +..|..|+|..
T Consensus 201 ~lV~rG~~V~Iva~~gg~~i~~~G~AL~~------G~~Gd~IrVrN 240 (261)
T PRK06804 201 VLVERGQHVLMIAAQDGIEAQTLGIAQKN------GRKGELIKVKN 240 (261)
T ss_pred cEEecCCEEEEEEecCCEEEEEEEEEccC------CCCCCEEEEEE
Confidence 45899999999996655 45588998655 57777777763
No 64
>PRK07018 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=24.57 E-value=1.9e+02 Score=23.53 Aligned_cols=38 Identities=18% Similarity=0.049 Sum_probs=28.8
Q ss_pred cCCCCCCeEEEeeCCCC-eEEEEEEEecCHHHHhcCCcceEEEEE
Q 030242 124 EEVGAETPVAIMAEGKQ-HALAIGFTKMSAKDIKAINKGIGVDNM 167 (180)
Q Consensus 124 ~~~~~Gd~V~V~~~~~~-~~vaVG~~~~s~~~i~~~~kG~av~v~ 167 (180)
.-+++||.|.|...+++ .+-+-|+|+-+ +..|..|+|.
T Consensus 175 ~~V~~G~~V~i~~~~g~~~i~~~G~Al~~------G~~Gd~IrVr 213 (235)
T PRK07018 175 WVVCKGQTVSIIARGDGFSVKTEGEALND------GAVGQQIRVR 213 (235)
T ss_pred cEeCCCCEEEEEEecCCEEEEEEEEEcCC------CCCCCeEEEE
Confidence 46899999999986655 45588888655 5677777766
No 65
>smart00841 Elong-fact-P_C Elongation factor P, C-terminal. These nucleic acid binding domains are predominantly found in elongation factor P, where they adopt an OB-fold, with five beta-strands forming a beta-barrel in a Greek-key topology PUBMED:15210970.
Probab=24.50 E-value=89 Score=19.94 Aligned_cols=25 Identities=12% Similarity=0.260 Sum_probs=18.4
Q ss_pred hhcCCcccCCcccCCCCCCCcCCCCCCeEEEeeCC
Q 030242 104 VLSGANIMCPGLTSPGGSLDEEVGAETPVAIMAEG 138 (180)
Q Consensus 104 i~~GAdLm~pGV~~~~~~~~~~~~~Gd~V~V~~~~ 138 (180)
|.+|+-+|.|-- ++.||.+.|.+..
T Consensus 26 letG~~i~VP~F----------I~~Gd~I~V~T~~ 50 (56)
T smart00841 26 LETGAVVQVPLF----------INEGDKIKVDTRT 50 (56)
T ss_pred ECCCCEEEcCCc----------ccCCCEEEEECCC
Confidence 457888888875 4569999888744
No 66
>PRK02484 truB tRNA pseudouridine synthase B; Provisional
Probab=23.55 E-value=2.1e+02 Score=24.43 Aligned_cols=43 Identities=19% Similarity=0.082 Sum_probs=30.7
Q ss_pred CcEEEECcchhhhhhcCCcccCCcccCCCCCCCcCCCCCCeEEEeeCCCCeEEEEEEE
Q 030242 91 MKKLQVDRGAIKFVLSGANIMCPGLTSPGGSLDEEVGAETPVAIMAEGKQHALAIGFT 148 (180)
Q Consensus 91 ~p~v~v~~~a~~~i~~GAdLm~pGV~~~~~~~~~~~~~Gd~V~V~~~~~~~~vaVG~~ 148 (180)
+|.+.+++.....|++|+.+-.++ .++.+.+.. ++.++|||..
T Consensus 240 lp~v~l~~~~~~~i~~G~~i~~~~-------------~~~~~~~~~--~~~~lai~~~ 282 (294)
T PRK02484 240 LPKVDLTPEQFTEVSFGRFISLDS-------------QEPKLAAFY--NDKLKAILEK 282 (294)
T ss_pred CCeEEeCHHHHHHHHCcCccccCC-------------CCCeEEEEe--CCeEEEEEEE
Confidence 689999999999999999883221 124455543 3479999864
No 67
>PF13144 SAF_2: SAF-like
Probab=23.03 E-value=2.1e+02 Score=22.13 Aligned_cols=39 Identities=13% Similarity=-0.031 Sum_probs=28.7
Q ss_pred cCCCCCCeEEEeeCCCC-eEEEEEEEecCHHHHhcCCcceEEEEEE
Q 030242 124 EEVGAETPVAIMAEGKQ-HALAIGFTKMSAKDIKAINKGIGVDNMH 168 (180)
Q Consensus 124 ~~~~~Gd~V~V~~~~~~-~~vaVG~~~~s~~~i~~~~kG~av~v~H 168 (180)
+-+++||.|.|....++ .+-+-|+|+-+ +..|..|++.-
T Consensus 138 ~~V~~G~~V~v~~~~g~i~i~~~g~Al~~------G~~G~~I~V~N 177 (196)
T PF13144_consen 138 PLVKRGDIVTVIARSGGISISTEGKALED------GALGDTIRVKN 177 (196)
T ss_pred eecCCCCEEEEEEEeCCEEEEEEEEEccC------CCCCCEEEEEE
Confidence 57999999999885544 45688988655 56777776654
No 68
>PRK00809 hypothetical protein; Provisional
Probab=22.98 E-value=1.5e+02 Score=22.45 Aligned_cols=26 Identities=15% Similarity=0.066 Sum_probs=18.7
Q ss_pred cCCCCCCeEEEeeCC-------CCeEEEEEEEe
Q 030242 124 EEVGAETPVAIMAEG-------KQHALAIGFTK 149 (180)
Q Consensus 124 ~~~~~Gd~V~V~~~~-------~~~~vaVG~~~ 149 (180)
...++||.|..+..+ ...++|||+..
T Consensus 33 r~Mk~GD~v~fYhs~~~~~~~~~~~ivgi~eV~ 65 (144)
T PRK00809 33 EKVKPGDKLIIYVSQEYGAERLPGKIVGIYEVV 65 (144)
T ss_pred hhCCCCCEEEEEECCccCCCCCCceEEEEEEEe
Confidence 358999999998854 24566666664
No 69
>PF04014 Antitoxin-MazE: Antidote-toxin recognition MazE; InterPro: IPR007159 This domain is found in AbrB from Bacillus subtilis. The product of the abrB gene is an ambiactive repressor and activator of the transcription of genes expressed during the transition state between vegetative growth and the onset of stationary phase and sporulation []. AbrB is thought to interact directly with the transcription initiation regions of genes under its control []. AbrB contains a helix-turn-helix structure, but this domain ends before the helix-turn-helix begins []. The product of the B. subtilis gene spoVT is another member of this family and is also a transcriptional regulator []. DNA-binding activity in this AbrB homologue requires hexamerisation []. Another family member has been isolated from the Sulfolobus solfataricus and has been identified as a homologue of bacterial repressor-like proteins. The Escherichia coli family member SohA or Prl1F appears to be bifunctional and is able to regulate its own expression as well as relieve the export block imposed by high-level synthesis of beta-galactosidase hybrid proteins [].; PDB: 2L66_A 2GLW_A 3TND_D 2W1T_B 2RO5_B 2FY9_A 2RO3_B 1UB4_C 3ZVK_G 1YFB_B ....
Probab=22.63 E-value=1.1e+02 Score=18.11 Aligned_cols=17 Identities=24% Similarity=0.290 Sum_probs=13.4
Q ss_pred CCCCCCeEEEeeCCCCe
Q 030242 125 EVGAETPVAIMAEGKQH 141 (180)
Q Consensus 125 ~~~~Gd~V~V~~~~~~~ 141 (180)
.+++||.|.+...+++.
T Consensus 20 ~l~~Gd~v~i~~~~~g~ 36 (47)
T PF04014_consen 20 GLKPGDEVEIEVEGDGK 36 (47)
T ss_dssp TSSTTTEEEEEEETTSE
T ss_pred CCCCCCEEEEEEeCCCE
Confidence 57889999998866643
No 70
>PF09285 Elong-fact-P_C: Elongation factor P, C-terminal; InterPro: IPR015365 These nucleic acid binding domains are predominantly found in elongation factor P, where they adopt an OB-fold, with five beta-strands forming a beta-barrel in a Greek-key topology []. ; GO: 0043043 peptide biosynthetic process, 0005737 cytoplasm; PDB: 1YBY_A 3OYY_B 1UEB_B 3HUW_V 3HUY_V 3A5Z_H.
Probab=21.61 E-value=91 Score=19.90 Aligned_cols=28 Identities=14% Similarity=0.240 Sum_probs=16.6
Q ss_pred hhcCCcccCCcccCCCCCCCcCCCCCCeEEEeeCCCCeE
Q 030242 104 VLSGANIMCPGLTSPGGSLDEEVGAETPVAIMAEGKQHA 142 (180)
Q Consensus 104 i~~GAdLm~pGV~~~~~~~~~~~~~Gd~V~V~~~~~~~~ 142 (180)
|.+|+-++.|-- ++.||.|.|.+.. +.-
T Consensus 26 letG~~i~VP~F----------I~~Gd~I~VdT~~-g~Y 53 (56)
T PF09285_consen 26 LETGAEIQVPLF----------IEEGDKIKVDTRD-GSY 53 (56)
T ss_dssp ETTS-EEEEETT------------TT-EEEEETTT-TEE
T ss_pred EcCCCEEEccce----------ecCCCEEEEECCC-CeE
Confidence 456888877764 4569999998844 443
No 71
>KOG3082 consensus Methionyl-tRNA formyltransferase [Translation, ribosomal structure and biogenesis]
Probab=20.29 E-value=51 Score=28.52 Aligned_cols=56 Identities=14% Similarity=0.234 Sum_probs=38.9
Q ss_pred CCcchhh-------HhhhcCCCCCcEEEECcchhhhhhcCCcccCCcccCCCCCCCc-CCCCCCeEEE
Q 030242 75 GPYMPTL-------RLLHQYPNIMKKLQVDRGAIKFVLSGANIMCPGLTSPGGSLDE-EVGAETPVAI 134 (180)
Q Consensus 75 ~~~~PTl-------~~l~~~p~~~p~v~v~~~a~~~i~~GAdLm~pGV~~~~~~~~~-~~~~Gd~V~V 134 (180)
|+++|+= .++.-||+++|+-.=.-++...|++|-.+-.--|.. +++ .|.+|++++=
T Consensus 91 Grllp~kll~~~pyg~iNVHPSLLPk~RGaAPV~~all~GD~~TGVTI~~----i~p~rFD~G~ilAQ 154 (338)
T KOG3082|consen 91 GRLLPFKLLNQLPYGGINVHPSLLPKYRGAAPVQRALLNGDTLTGVTIQT----IDPKRFDKGPILAQ 154 (338)
T ss_pred hccCcHHHHhhCCcceeecChhhcccccCcchHHHHHhcCCcccceEEEE----ecccccccccceec
Confidence 4566664 246668899998777777889999998765544444 334 7888887654
Done!